Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 180 of 213
Found at i:54280874 original size:7 final size:7
Alignment explanation
Indices: 54280862--54280904 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
54280852 TACCTATCCA
54280862 TAACCCC
1 TAACCCC
*
54280869 TAACCCT
1 TAACCCC
* *
54280876 TAATCCT
1 TAACCCC
*
54280883 TAACCTC
1 TAACCCC
54280890 TAACCCC
1 TAACCCC
54280897 TAACCCC
1 TAACCCC
54280904 T
1 T
54280905 CTTTTACAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.28, C:0.47, G:0.00, T:0.26
Consensus pattern (7 bp):
TAACCCC
Found at i:54281144 original size:60 final size:62
Alignment explanation
Indices: 54281042--54281156 Score: 173
Period size: 60 Copynumber: 1.9 Consensus size: 62
54281032 AACTATTAAC
*
54281042 CCCTAAACCTTATTTAATATATAAATTTAAAAACACTAATTAATCTAAACCCTAACCCAAAT
1 CCCTAAACCTTATTTAATATATAAATTTAAAAACACTAATTAATATAAACCCTAACCCAAAT
* *
54281104 CCCTAAATCTTATTT-A-ATATAAA-TTAAATCACACTAATTAATATAAACCCTAA
1 CCCTAAACCTTATTTAATATATAAATTTAAA-AACACTAATTAATATAAACCCTAA
54281157 AGCCTAACCT
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
59 5 0.10
60 29 0.59
61 1 0.02
62 14 0.29
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (62 bp):
CCCTAAACCTTATTTAATATATAAATTTAAAAACACTAATTAATATAAACCCTAACCCAAAT
Found at i:54281762 original size:41 final size:41
Alignment explanation
Indices: 54281645--54281774 Score: 142
Period size: 40 Copynumber: 3.2 Consensus size: 41
54281635 ATAAAATGTT
* *
54281645 TTAGCGGCGCTTTTTCAAAAATGCAGCTAAAAGC-C-GAGTA
1 TTAGCGACGCTTTTTCAAAAATGCAGCTAAAA-CTCTGAGCA
* * *
54281685 TTAGCGGCGATTTTT-AAAAATGCCGCTAAAGA-TCTGAGCA
1 TTAGCGACGCTTTTTCAAAAATGCAGCTAAA-ACTCTGAGCA
* *
54281725 TTAGCGACGCTTTTTCAAAAACGCTGCTAAAACTCTGAGCA
1 TTAGCGACGCTTTTTCAAAAATGCAGCTAAAACTCTGAGCA
*
54281766 TTAGTGACG
1 TTAGCGACG
54281775 AAAACGTCGC
Statistics
Matches: 77, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
39 15 0.19
40 33 0.43
41 29 0.38
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27
Consensus pattern (41 bp):
TTAGCGACGCTTTTTCAAAAATGCAGCTAAAACTCTGAGCA
Found at i:54283411 original size:5 final size:5
Alignment explanation
Indices: 54283392--54283451 Score: 61
Period size: 5 Copynumber: 12.0 Consensus size: 5
54283382 AACATGTAAG
* * *
54283392 AAAAT -AAAG AAAAT AAAAT AGAAAAT AAAAA AAAAT AAAAT -ATAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT --AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
54283442 AAAAT AAAAT
1 AAAAT AAAAT
54283452 TGGGTTGCCT
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
4 6 0.13
5 34 0.76
7 5 0.11
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:54283430 original size:31 final size:29
Alignment explanation
Indices: 54283392--54283450 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 29
54283382 AACATGTAAG
54283392 AAAATAAAGA-AAATAAAATAGAAAATAAAAA
1 AAAATAAA-ATAAATAAAAT--AAAATAAAAA
*
54283423 AAAATAAAATATATAAAATAAAATAAAA
1 AAAATAAAATAAATAAAATAAAATAAAA
54283451 TTGGGTTGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 9 0.35
30 1 0.04
31 16 0.62
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (29 bp):
AAAATAAAATAAATAAAATAAAATAAAAA
Found at i:54283445 original size:24 final size:22
Alignment explanation
Indices: 54283390--54283451 Score: 72
Period size: 24 Copynumber: 2.8 Consensus size: 22
54283380 TTAACATGTA
*
54283390 AGAAAAT-AAAGAAAATAAAAT
1 AGAAAATAAAAAAAAATAAAAT
54283411 AGAAAATAAAAAAAAATAAAATAT
1 AGAAAATAAAAAAAAAT-AAA-AT
* *
54283435 ATAAAATAAAATAAAAT
1 AGAAAATAAAAAAAAAT
54283452 TGGGTTGCCT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 7 0.20
22 8 0.23
23 3 0.09
24 17 0.49
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (22 bp):
AGAAAATAAAAAAAAATAAAAT
Found at i:54293791 original size:73 final size:73
Alignment explanation
Indices: 54293704--54293889 Score: 345
Period size: 73 Copynumber: 2.5 Consensus size: 73
54293694 ACAACTTGAC
*
54293704 AACTTAGTTCGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
54293769 CACTAACA
66 CACTAACA
*
54293777 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCTACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
54293842 CACTAACA
66 CACTAACA
*
54293850 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCA
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCA
54293890 AATAATAATA
Statistics
Matches: 109, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 109 1.00
ACGTcount: A:0.41, C:0.25, G:0.06, T:0.28
Consensus pattern (73 bp):
AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
CACTAACA
Found at i:54293898 original size:3 final size:3
Alignment explanation
Indices: 54293890--54293918 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
54293880 ATTACATCCA
54293890 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
54293919 AACATGTGAT
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:54298256 original size:3 final size:3
Alignment explanation
Indices: 54298248--54298300 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
54298238 ATTCCATCCA
*
54298248 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
54298296 AAT AA
1 AAT AA
54298301 AACATGTGAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:54300605 original size:18 final size:16
Alignment explanation
Indices: 54300582--54300628 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
54300572 TATAATGATG
54300582 ATTATAATCTCATATGTT
1 ATTATAATCTCATA--TT
*
54300600 ATTATAATATC-TATT
1 ATTATAATCTCATATT
*
54300615 AATATAATCTCATA
1 ATTATAATCTCATA
54300629 AATATTTGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
15 11 0.44
16 2 0.08
17 2 0.08
18 10 0.40
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (16 bp):
ATTATAATCTCATATT
Found at i:54300818 original size:24 final size:24
Alignment explanation
Indices: 54300783--54300861 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 24
54300773 CATTTATATA
54300783 TTATTACTTTATATATTACCTATTT
1 TTATTA-TTTATATATTACCTATTT
* **
54300808 TTATTTTTTATATATTATTTATTT
1 TTATTATTTATATATTACCTATTT
* **
54300832 TAAACTTATACATATATTACCTATTT
1 T-TA-TTATTTATATATTACCTATTT
54300858 TTAT
1 TTAT
54300862 ATATATAATT
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
24 18 0.43
25 7 0.17
26 17 0.40
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (24 bp):
TTATTATTTATATATTACCTATTT
Found at i:54301580 original size:21 final size:22
Alignment explanation
Indices: 54301538--54301580 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
54301528 TCGAATTTTG
54301538 TAAACCAAAATCATTATTTTAA
1 TAAACCAAAATCATTATTTTAA
* *
54301560 TAAATCAAAAT-ATTTTTTTAA
1 TAAACCAAAATCATTATTTTAA
54301581 AATGATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAACCAAAATCATTATTTTAA
Found at i:54305029 original size:100 final size:99
Alignment explanation
Indices: 54304864--54305441 Score: 693
Period size: 100 Copynumber: 5.8 Consensus size: 99
54304854 AATGTCGGGA
* * * ** *
54304864 AAGTAAGATTCACTGTTGTAGCTTCAATC-TATTAACCGCAATGTCAGGGAAGCGAGATTCGCCG
1 AAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTC-GGGAAGCAAGATTCGCCG
54304928 TTGTAGCTTCAATCTGTTCCACTACACTG-CTGGGG
65 TTGTAGCTTCAATCTGTTCCACTACACTGCCT-GGG
* * * *
54304963 AAATAAGATTCACCGTTGTGGCCTCAATCTTTTTGATTGCAATGTCAGGGAAAG-AAGATTCACC
1 AAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTC-GGG-AAGCAAGATTCGCC
* * * *
54305027 GTTCTAGCTTCAATCTATTCTACGACACCT-CCTGGG
64 GTTGTAGCTTCAATCTGTTCCACTACA-CTGCCTGGG
* * * *
54305063 AAGTAAGATT-AGCCGTTGTGGTTTCGATCTTTTAAATTCCAATGTCGAGGAGAG-AAGATTCGC
1 AAGTAAGATTCA-CCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCG-GGA-AGCAAGATTCGC
* * * *
54305126 CGTTGTAGCTTCATTCTATTCCACTGCACCGCCTGGG
63 CGTTGTAGCTTCAATCTGTTCCACTACACTGCCTGGG
* * * *
54305163 AAGTAAGATTCATCGTTGTGGCTTCAATCTTTTTAATTACAATGTCGGGGAAGTAGGATTCGCCG
1 AAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTC-GGGAAGCAAGATTCGCCG
* * *
54305228 TTGTAGCTTCAATCTGTTCCACTGCACCGTCTGGG
65 TTGTAGCTTCAATCTGTTCCACTACACTGCCTGGG
* *
54305263 AAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGCATGATTCTCCG
1 AAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTC-GGGAAGCAAGATTCGCCG
**
54305328 TTGTAGCTTCAA-CTGTTCCACTTTACTGCCTGGG
65 TTGTAGCTTCAATCTGTTCCACTACACTGCCTGGG
* *
54305362 AAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAGGATTCGCCG
1 AAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTC-GGGAAGCAAGATTCGCCG
54305427 TTGTAGCTTCAATCT
65 TTGTAGCTTCAATCT
54305442 TTTTAAAAAT
Statistics
Matches: 416, Mismatches: 51, Indels: 23
0.85 0.10 0.05
Matches are distributed among these distances:
99 122 0.29
100 285 0.69
101 9 0.02
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.33
Consensus pattern (99 bp):
AAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGAAGCAAGATTCGCCGT
TGTAGCTTCAATCTGTTCCACTACACTGCCTGGG
Found at i:54305445 original size:50 final size:50
Alignment explanation
Indices: 54304851--54305447 Score: 420
Period size: 50 Copynumber: 12.0 Consensus size: 50
54304841 CCTGTTCAAC
* * * * *
54304851 TGCAATGTCGGGAAAGTAAGATTCACTGTTGTAGCTTCAATC-TATTAAC
1 TGCAATGTCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAAT
* * ** * ** *
54304900 CGCAATGTCAGGGAAGCGAGATTCGCCGTTGTAGCTTCAATCTGTTCCAC
1 TGCAATGTCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAAT
* * * * * * *
54304950 TACACTG-CTGGGGAAATAAGATTCACCGTTGTGGCCTCAATCTTTTTGAT
1 TGCAATGTC-GGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAAT
* * * *
54305000 TGCAATGTCAGGGAAAG-AAGATTCACCGTTCTAGCTTCAATCTATTCT-A-
1 TGCAATGTC-GGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCT-TTTTAAT
* * * * * * * * *
54305049 CGACACCT-CCTGGGAAGTAAGATTAGCCGTTGTGGTTTCGATCTTTTAAAT
1 TG-CA-ATGTCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAAT
* * * * ** *
54305100 TCCAATGTCGAGGAGAG-AAGATTCGCCGTTGTAGCTTCATTCTATTCCAC
1 TGCAATGTCGGGGA-AGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAAT
** * * ** *
54305150 TGCACCGCCTGGGAAGTAAGATTCATCGTTGTGGCTTCAATCTTTTTAAT
1 TGCAATGTCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAAT
* * * ** *
54305200 TACAATGTCGGGGAAGTAGGATTCGCCGTTGTAGCTTCAATCTGTTCCAC
1 TGCAATGTCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAAT
** * * *
54305250 TGCACCGTCTGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAAT
1 TGCAATGTCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAAT
* * * * ** *
54305300 TGCAATGTCAGGGAAGCATGATTCTCCGTTGTAGCTTCAA-CTGTTCCACT
1 TGCAATGTCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCT-TTTTAAT
* * * * *
54305350 T-TACTGCCTGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAAT
1 TGCAATGTCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAAT
* *
54305399 TGCAATGTCGGGGAAGCAGGATTCGCCGTTGTAGCTTCAATCTTTTTAA
1 TGCAATGTCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAA
54305448 AAATTCATTA
Statistics
Matches: 405, Mismatches: 128, Indels: 29
0.72 0.23 0.05
Matches are distributed among these distances:
49 84 0.21
50 309 0.76
51 12 0.03
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.33
Consensus pattern (50 bp):
TGCAATGTCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAAT
Found at i:54307836 original size:13 final size:13
Alignment explanation
Indices: 54307818--54307842 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54307808 TATTTTAATA
54307818 TTATTTTGTGTGT
1 TTATTTTGTGTGT
54307831 TTATTTTGTGTG
1 TTATTTTGTGTG
54307843 CATTTGATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:54309712 original size:41 final size:41
Alignment explanation
Indices: 54309655--54309756 Score: 168
Period size: 41 Copynumber: 2.5 Consensus size: 41
54309645 AGATAATTCG
* * *
54309655 GACTTTACATCTAGCAGGCTTGATGCCGGTGAAATGTTTCA
1 GACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATATTTCA
*
54309696 GACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATATTTCG
1 GACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATATTTCA
54309737 GACTTTACGTCTAGCAGGCT
1 GACTTTACGTCTAGCAGGCT
54309757 AATTGCCAGT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (41 bp):
GACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATATTTCA
Found at i:54315717 original size:13 final size:13
Alignment explanation
Indices: 54315699--54315723 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54315689 TATTTTAATA
54315699 TTATTTTGTGTGT
1 TTATTTTGTGTGT
54315712 TTATTTTGTGTG
1 TTATTTTGTGTG
54315724 CATTTGATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:54317589 original size:41 final size:41
Alignment explanation
Indices: 54317532--54317637 Score: 176
Period size: 41 Copynumber: 2.6 Consensus size: 41
54317522 AATGAGATAA
* * *
54317532 TTCAGACTTTACGTCTAGCAGGCTTGATGCTGGTGAAATGT
1 TTCAGACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATAT
54317573 TTCAGACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATAT
1 TTCAGACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATAT
*
54317614 TTCGGACTTTACGTCTAGCAGGCT
1 TTCAGACTTTACGTCTAGCAGGCT
54317638 AATTGCCAGT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 61 1.00
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (41 bp):
TTCAGACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATAT
Found at i:54323690 original size:18 final size:16
Alignment explanation
Indices: 54323667--54323713 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
54323657 TATAATGATG
54323667 ATTATAATCTCATATGTT
1 ATTATAATCTCATA--TT
*
54323685 ATTATAATATC-TATT
1 ATTATAATCTCATATT
*
54323700 AATATAATCTCATA
1 ATTATAATCTCATA
54323714 AATATTTGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
15 11 0.44
16 2 0.08
17 2 0.08
18 10 0.40
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (16 bp):
ATTATAATCTCATATT
Found at i:54323903 original size:23 final size:24
Alignment explanation
Indices: 54323868--54323945 Score: 77
Period size: 23 Copynumber: 3.2 Consensus size: 24
54323858 CATTTATATA
54323868 TTATTACTTTATATATTACCTATTT
1 TTATTA-TTTATATATTACCTATTT
**
54323893 TTATT-TTTATATATTATTTATTT
1 TTATTATTTATATATTACCTATTT
* **
54323916 TAAACTTATACATATATTACCTATTT
1 T-TA-TTATTTATATATTACCTATTT
54323942 TTAT
1 TTAT
54323946 ATATATAATT
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
23 17 0.40
24 2 0.05
25 8 0.19
26 15 0.36
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (24 bp):
TTATTATTTATATATTACCTATTT
Found at i:54327411 original size:18 final size:16
Alignment explanation
Indices: 54327388--54327434 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
54327378 TATAATGATG
54327388 ATTATAATCTCATATGTT
1 ATTATAATCTCATA--TT
*
54327406 ATTATAATATC-TATT
1 ATTATAATCTCATATT
*
54327421 AATATAATCTCATA
1 ATTATAATCTCATA
54327435 AATATTTGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
15 11 0.44
16 2 0.08
17 2 0.08
18 10 0.40
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (16 bp):
ATTATAATCTCATATT
Found at i:54327624 original size:24 final size:24
Alignment explanation
Indices: 54327589--54327667 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 24
54327579 CATTTATATA
54327589 TTATTACTTTATATATTACCTATTT
1 TTATTA-TTTATATATTACCTATTT
* **
54327614 TTATTTTTTATATATTATTTATTT
1 TTATTATTTATATATTACCTATTT
* **
54327638 TAAACTTATACATATATTACCTATTT
1 T-TA-TTATTTATATATTACCTATTT
54327664 TTAT
1 TTAT
54327668 ATATATAATT
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
24 18 0.43
25 7 0.17
26 17 0.40
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (24 bp):
TTATTATTTATATATTACCTATTT
Found at i:54328386 original size:21 final size:22
Alignment explanation
Indices: 54328344--54328386 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
54328334 TCGAATTTTG
54328344 TAAACCAAAATCATTATTTTAA
1 TAAACCAAAATCATTATTTTAA
* *
54328366 TAAATCAAAAT-ATTTTTTTAA
1 TAAACCAAAATCATTATTTTAA
54328387 AATGATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAACCAAAATCATTATTTTAA
Found at i:54331871 original size:100 final size:100
Alignment explanation
Indices: 54331668--54332249 Score: 672
Period size: 100 Copynumber: 5.8 Consensus size: 100
54331658 TGCAATGTTG
* * * ** * * *
54331668 GGGAAGTAAGATTCGCTGTTGTAGCTTCAATC-TATTAACCGCAGTGTCAGGGAAGCAAGATTCG
1 GGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGTAAGATTCG
* *
54331732 CTGTTGTAGCTTCAATCTGTTCCACTGCACC-GCT
66 CCGTTGTAGCTTCAATCTGTTCCACTGCACCTCCT
* * * * * *
54331766 GGGGAAATAAGATTCACCGTTGTGGCCTCAATCTTTTTGATTGCAAGTTTC-GGGAAATAAGATT
1 -GGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAA-TGTCGGGGAAGTAAGATT
* * * * * * *
54331830 CACCGTTCTAGCTTCAATCTATTCTACGGTACCTCTT
64 CGCCGTTGTAGCTTCAATCTGTTCCACTGCACCTCCT
* * * * *
54331867 GGGAAGTAAGATTTGCCATTGTGGCTTCGATCTTTTAAATTGGAATGTCGGGGAGAG-AAGATTC
1 GGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGA-AGTAAGATTC
* * * * * *
54331931 GCCATTGTGGCTTCATTCTATTCCAGTGCACCGCCT
65 GCCGTTGTAGCTTCAATCTGTTCCACTGCACCTCCT
* * * *
54331967 GGGAAGTAAGATTCGTCGTTGTGGCTTCAATCTTTTTAATTACAATGTCGGGGAAGTAGGATTTG
1 GGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGTAAGATTCG
54332032 CCGTTGTAGCTTCAATCTGTTCCACTGCACCGT-CT
66 CCGTTGTAGCTTCAATCTGTTCCACTGCACC-TCCT
* * * *
54332067 GGGAAGTAAGATTCGCCGTTGTGACTTCAATCTTTTTAATTGCAATGTCGGGGAAGCATGATTCA
1 GGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGTAAGATTCG
* *
54332132 CCGTTGTAGCTTCAATATGTTCCACTGTA-CTGCCT
66 CCGTTGTAGCTTCAATCTGTTCCACTGCACCT-CCT
*
54332167 GGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGTAGGATTCG
1 GGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGTAAGATTCG
54332232 CCGTTGTAGCTTCAATCT
66 CCGTTGTAGCTTCAATCT
54332250 TTTTAAAAAT
Statistics
Matches: 401, Mismatches: 73, Indels: 17
0.82 0.15 0.03
Matches are distributed among these distances:
98 1 0.00
99 33 0.08
100 362 0.90
101 5 0.01
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (100 bp):
GGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGTAAGATTCG
CCGTTGTAGCTTCAATCTGTTCCACTGCACCTCCT
Found at i:54332253 original size:50 final size:50
Alignment explanation
Indices: 54331658--54332255 Score: 427
Period size: 50 Copynumber: 12.0 Consensus size: 50
54331648 TCTGTTCAAC
* * * *
54331658 TGCAATGTTGGGGAAGTAAGATTCGCTGTTGTAGCTTCAATC-TATTAAC
1 TGCAATGTCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAAT
* * * * * * ** *
54331707 CGCAGTGTCAGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCAC
1 TGCAATGTCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAAT
** * * * * *
54331757 TGCACCG-CTGGGGAAATAAGATTCACCGTTGTGGCCTCAATCTTTTTGAT
1 TGCAATGTC-GGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAAT
* * * * *
54331807 TGCAAGTTTC-GGGAAATAAGATTCACCGTTCTAGCTTCAATCTATTCT-A-
1 TGCAA-TGTCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCT-TTTTAAT
* ** ** * * * * * *
54331856 CGGTACCTCTTGGGAAGTAAGATTTGCCATTGTGGCTTCGATCTTTTAAAT
1 TGCAATGTC-GGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAAT
* * * * * ** *
54331907 TGGAATGTCGGGGAGAG-AAGATTCGCCATTGTGGCTTCATTCTATTCCAG
1 TGCAATGTCGGGGA-AGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAAT
** * * * *
54331957 TGCACCGCCTGGGAAGTAAGATTCGTCGTTGTGGCTTCAATCTTTTTAAT
1 TGCAATGTCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAAT
* * * * ** *
54332007 TACAATGTCGGGGAAGTAGGATTTGCCGTTGTAGCTTCAATCTGTTCCAC
1 TGCAATGTCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAAT
** *
54332057 TGCACCGTCTGGGAAGTAAGATTCGCCGTTGT-GACTTCAATCTTTTTAAT
1 TGCAATGTCGGGGAAGTAAGATTCGCCGTTGTAG-CTTCAATCTTTTTAAT
* * * * * ** *
54332107 TGCAATGTCGGGGAAGCATGATTCACCGTTGTAGCTTCAATATGTTCCAC
1 TGCAATGTCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAAT
* * * * *
54332157 TGTACTGCCTGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAAT
1 TGCAATGTCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAAT
*
54332207 TGCAATGTCGGGGAAGTAGGATTCGCCGTTGTAGCTTCAATCTTTTTAA
1 TGCAATGTCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAA
54332256 AAATTCATTA
Statistics
Matches: 415, Mismatches: 121, Indels: 25
0.74 0.22 0.04
Matches are distributed among these distances:
48 2 0.00
49 45 0.11
50 356 0.86
51 11 0.03
52 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (50 bp):
TGCAATGTCGGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTTAAT
Found at i:54343448 original size:181 final size:181
Alignment explanation
Indices: 54343137--54343498 Score: 636
Period size: 181 Copynumber: 2.0 Consensus size: 181
54343127 ACCCAATCGA
* * *
54343137 GCTTCCGATAATCTGAAAAGTAGAAGAAAACAAATACATAAGCAATGAATGCTTAGTAAGCTCAT
1 GCTTCCAATAATCTAAAAAGTAGAAGAAAACAAATACATAAGCAATGAATGCTTAATAAGCTCAT
*
54343202 ATAAACTTTAATCATAATACTTCCTTTTCAAATATGAAATTTATACTTATCAAGAATAATCTAAT
66 ATAAAATTTAATCATAATACTTCCTTTTCAAATATGAAATTTATACTTATCAAGAATAATCTAAT
*
54343267 GTTGTTGCCACAATATTCATGAAGTTATATTTAACAACTCACTAAGTGAAT
131 GTTGCTGCCACAATATTCATGAAGTTATATTTAACAACTCACTAAGTGAAT
* *
54343318 GCTTCCAATAATCTAAAAAGTAGAAGAAAAACAAATACATAAGTAATGAATGCTTAATAAGCTCG
1 GCTTCCAATAATCTAAAAAGTAGAAG-AAAACAAATACATAAGCAATGAATGCTTAATAAGCTCA
54343383 TATAAAATTTAATCATAATACTTCC-TTTCAAATATGAAATTTATACTTATCAAGAATAATCTAA
65 TATAAAATTTAATCATAATACTTCCTTTTCAAATATGAAATTTATACTTATCAAGAATAATCTAA
*
54343447 TGTTGCTGCCACAATATTCATGAAGTTATATTTAGCAACTCACTAAGTGAAT
130 TGTTGCTGCCACAATATTCATGAAGTTATATTTAACAACTCACTAAGTGAAT
54343499 AAATCTACAG
Statistics
Matches: 172, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
181 113 0.66
182 59 0.34
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (181 bp):
GCTTCCAATAATCTAAAAAGTAGAAGAAAACAAATACATAAGCAATGAATGCTTAATAAGCTCAT
ATAAAATTTAATCATAATACTTCCTTTTCAAATATGAAATTTATACTTATCAAGAATAATCTAAT
GTTGCTGCCACAATATTCATGAAGTTATATTTAACAACTCACTAAGTGAAT
Found at i:54351309 original size:21 final size:22
Alignment explanation
Indices: 54351285--54351327 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
54351275 ATTAATCATT
54351285 TTAAAAAAAT-ATTTTGATTTA
1 TTAAAAAAATGATTTTGATTTA
* *
54351306 TTAAAATAATGATTTTGGTTTA
1 TTAAAAAAATGATTTTGATTTA
54351328 CAAAATTCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (22 bp):
TTAAAAAAATGATTTTGATTTA
Found at i:54352026 original size:23 final size:23
Alignment explanation
Indices: 54351996--54352071 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
54351986 ATAAATAAAT
54351996 TATATATATAAAAATAGGTAATA
1 TATATATATAAAAATAGGTAATA
* * **
54352019 TATGTATAAGTTTAAAATAAATAATA
1 TATATAT-A--TAAAAATAGGTAATA
* *
54352045 TATAAAAATAAAAATAGGTAATA
1 TATATATATAAAAATAGGTAATA
54352068 TATA
1 TATA
54352072 AAGTAATAAT
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
23 22 0.55
24 1 0.03
25 1 0.03
26 16 0.40
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (23 bp):
TATATATATAAAAATAGGTAATA
Found at i:54352088 original size:49 final size:48
Alignment explanation
Indices: 54351985--54352104 Score: 122
Period size: 49 Copynumber: 2.5 Consensus size: 48
54351975 TATACAAATC
* * *
54351985 AATAAATAAATTATATATATAAAAATAGGTAATATATGTATAAGTTTAA
1 AATAAATAAATTATAAAAATAAAAATAGGTAATATA-GTATAAGTATAA
54352034 AATAAAT-AATATATAAAAATAAAAATAGGTAATATA-TA-AAGTAATAA
1 AATAAATAAAT-TATAAAAATAAAAATAGGTAATATAGTATAAGT-ATAA
* *
54352081 TATATAAATGAGTT-TAAAAATAAA
1 -A-ATAAATAAATTATAAAAATAAA
54352105 TATTGTGTAA
Statistics
Matches: 62, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
46 4 0.06
47 5 0.08
48 14 0.23
49 37 0.60
50 2 0.03
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (48 bp):
AATAAATAAATTATAAAAATAAAAATAGGTAATATAGTATAAGTATAA
Found at i:54352280 original size:18 final size:17
Alignment explanation
Indices: 54352236--54352282 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
54352226 TACAAATATT
*
54352236 TATGAGATTAT-ATTAA
1 TATGAGATTATAATAAA
*
54352252 TA-GATATTATAATAACA
1 TATGAGATTATAATAA-A
54352269 TATGAGATTATAAT
1 TATGAGATTATAAT
54352283 CATCATTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
15 7 0.28
16 5 0.20
17 3 0.12
18 10 0.40
ACGTcount: A:0.47, C:0.02, G:0.11, T:0.40
Consensus pattern (17 bp):
TATGAGATTATAATAAA
Found at i:54353870 original size:19 final size:19
Alignment explanation
Indices: 54353828--54353870 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
54353818 TATGAATATC
*
54353828 TAATGCATATGATGCAATG
1 TAATGCAGATGATGCAATG
*
54353847 TAATGCAGATGCATGGAATG
1 TAATGCAGATG-ATGCAATG
54353867 -AATG
1 TAATG
54353871 TAAAAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.37, C:0.09, G:0.26, T:0.28
Consensus pattern (19 bp):
TAATGCAGATGATGCAATG
Found at i:54355792 original size:26 final size:24
Alignment explanation
Indices: 54355724--54355795 Score: 72
Period size: 24 Copynumber: 2.9 Consensus size: 24
54355714 AATTATATAT
* *
54355724 ATAAAAATAGGTAATATATGTATAAG
1 ATAAAAATAGGTAATATA--TAAAAA
* * **
54355750 TTTAAAATAAATAATATATAAAAA
1 ATAAAAATAGGTAATATATAAAAA
54355774 ATAAAAATAGGTAATATATAAA
1 ATAAAAATAGGTAATATATAAA
54355796 GTAATAATAT
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
24 22 0.61
26 14 0.39
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.31
Consensus pattern (24 bp):
ATAAAAATAGGTAATATATAAAAA
Found at i:54356002 original size:18 final size:17
Alignment explanation
Indices: 54355958--54356004 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
54355948 TACAAATATT
*
54355958 TATGAGATTAT-ATTAA
1 TATGAGATTATAATAAA
*
54355974 TA-GATATTATAATAACA
1 TATGAGATTATAATAA-A
54355991 TATGAGATTATAAT
1 TATGAGATTATAAT
54356005 CATCATTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
15 7 0.28
16 5 0.20
17 3 0.12
18 10 0.40
ACGTcount: A:0.47, C:0.02, G:0.11, T:0.40
Consensus pattern (17 bp):
TATGAGATTATAATAAA
Found at i:54365995 original size:21 final size:21
Alignment explanation
Indices: 54365969--54366011 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
54365959 ACAAACTATT
54365969 GATTTTCAAAAGAAAATAGAG
1 GATTTTCAAAAGAAAATAGAG
*
54365990 GATTTTCAATAGAAAATAGAG
1 GATTTTCAAAAGAAAATAGAG
54366011 G
1 G
54366012 CATCTATAAA
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:0.49, C:0.05, G:0.21, T:0.26
Consensus pattern (21 bp):
GATTTTCAAAAGAAAATAGAG
Found at i:54367412 original size:15 final size:15
Alignment explanation
Indices: 54367387--54367419 Score: 50
Period size: 14 Copynumber: 2.2 Consensus size: 15
54367377 CCCAATTTGA
54367387 TTTTTATTTTTAT-T
1 TTTTTATTTTTATAT
54367401 TTTTTATATTTTATAT
1 TTTTTAT-TTTTATAT
54367417 TTT
1 TTT
54367420 ATTTTCTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 6 0.35
16 4 0.24
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTATTTTTATAT
Found at i:54367429 original size:23 final size:21
Alignment explanation
Indices: 54367388--54367430 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
54367378 CCAATTTGAT
54367388 TTTTATTTTTATTTTTTTATA
1 TTTTATTTTTATTTTTTTATA
54367409 TTTTATATTTTATTTTCTTTAT
1 TTTTAT-TTTTATTTT-TTTAT
54367431 TTTCTTACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 6 0.30
22 9 0.45
23 5 0.25
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTTATTTTTATTTTTTTATA
Found at i:54367431 original size:21 final size:21
Alignment explanation
Indices: 54367388--54367433 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
54367378 CCAATTTGAT
*
54367388 TTTTATTTTTATTTTTTTATA
1 TTTTATTTTTATTTTCTTATA
54367409 TTTTATATTTTATTTTCTT-TA
1 TTTTAT-TTTTATTTTCTTATA
54367430 TTTT
1 TTTT
54367434 CTTACATGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTATTTTTATTTTCTTATA
Found at i:54369474 original size:12 final size:12
Alignment explanation
Indices: 54369459--54369489 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
54369449 AATTTGAATT
*
54369459 TTATTTTTAGGA
1 TTATTATTAGGA
54369471 TTATTATTAGGA
1 TTATTATTAGGA
54369483 TTATTAT
1 TTATTAT
54369490 GATATTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (12 bp):
TTATTATTAGGA
Found at i:54371501 original size:18 final size:19
Alignment explanation
Indices: 54371465--54371506 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
54371455 TTATTTTGTC
* *
54371465 AATATGTTACAAATTACAT
1 AATATGTTAAAAATAACAT
54371484 AATAT-TTAAAAATAACAT
1 AATATGTTAAAAATAACAT
54371502 AATAT
1 AATAT
54371507 AAATTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (19 bp):
AATATGTTAAAAATAACAT
Found at i:54374199 original size:25 final size:25
Alignment explanation
Indices: 54374171--54374224 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
54374161 TGTAGTGGCA
*
54374171 AGGTGGCGACACAAGTGTGGCAAGG
1 AGGTGGCGACACAAGTGTGGCAAAG
* * *
54374196 AGGTGGCGTCACAGGTGTGGTAAAG
1 AGGTGGCGACACAAGTGTGGCAAAG
54374221 AGGT
1 AGGT
54374225 CAGAGATTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.26, C:0.13, G:0.44, T:0.17
Consensus pattern (25 bp):
AGGTGGCGACACAAGTGTGGCAAAG
Found at i:54374810 original size:14 final size:13
Alignment explanation
Indices: 54374791--54374837 Score: 51
Period size: 12 Copynumber: 3.6 Consensus size: 13
54374781 GTGGATCATG
54374791 GAGGATTTCTAGGA
1 GAGGATTT-TAGGA
*
54374805 GAGGATTTGAGGA
1 GAGGATTTTAGGA
*
54374818 G-TGATTTTAGGA
1 GAGGATTTTAGGA
*
54374830 GAGAATTT
1 GAGGATTT
54374838 GGGAATTTGA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
12 10 0.37
13 9 0.33
14 8 0.30
ACGTcount: A:0.30, C:0.02, G:0.36, T:0.32
Consensus pattern (13 bp):
GAGGATTTTAGGA
Found at i:54374828 original size:25 final size:25
Alignment explanation
Indices: 54374790--54374838 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
54374780 AGTGGATCAT
*
54374790 GGAGGATTTCTAGGAGAGGATTTGA
1 GGAGGATTTCTAGGAGAGAATTTGA
54374815 GGAGTGATTT-TAGGAGAGAATTTG
1 GGAG-GATTTCTAGGAGAGAATTTG
54374839 GGAATTTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.29, C:0.02, G:0.39, T:0.31
Consensus pattern (25 bp):
GGAGGATTTCTAGGAGAGAATTTGA
Found at i:54375781 original size:27 final size:27
Alignment explanation
Indices: 54375751--54375918 Score: 162
Period size: 27 Copynumber: 6.3 Consensus size: 27
54375741 CTCGTGCAGG
* *
54375751 AAAACTACCAAAATACCCTCGATGGAT
1 AAAATTACCAAAATACCCTCGATGGGT
* * *
54375778 AAAATAACTAAAATACTCC-CGAT-AGT
1 AAAATTACCAAAATAC-CCTCGATGGGT
54375804 AAAATTACCAAAATACCCTCGATGGGT
1 AAAATTACCAAAATACCCTCGATGGGT
* *
54375831 AAAATTATCGAAATACCCTCGATGGGT
1 AAAATTACCAAAATACCCTCGATGGGT
** * *
54375858 AAAATTA-CAGAAATACCCTTAATAGAT
1 AAAATTACCA-AAATACCCTCGATGGGT
** * *
54375885 AAAATTACTGAAATACCCCCGATAGGT
1 AAAATTACCAAAATACCCTCGATGGGT
54375912 AAAATTA
1 AAAATTA
54375919 TCGAATTACC
Statistics
Matches: 115, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
25 2 0.02
26 20 0.17
27 91 0.79
28 2 0.02
ACGTcount: A:0.45, C:0.20, G:0.12, T:0.23
Consensus pattern (27 bp):
AAAATTACCAAAATACCCTCGATGGGT
Found at i:54375888 original size:54 final size:54
Alignment explanation
Indices: 54375751--54375918 Score: 189
Period size: 54 Copynumber: 3.1 Consensus size: 54
54375741 CTCGTGCAGG
* * * * * *
54375751 AAAACTACCAAAATACCCTCGATGGATAAAATAACTAAAATACTCCCGATA-GT
1 AAAATTACCAAAATACCCTCAATAGATAAAATTACTGAAATACCCCCGATAGGT
* * * * *
54375804 AAAATTACCAAAATACCCTCGATGGGTAAAATTA-TCGAAATACCCTCGATGGGT
1 AAAATTACCAAAATACCCTCAATAGATAAAATTACT-GAAATACCCCCGATAGGT
*
54375858 AAAATTA-CAGAAATACCCTTAATAGATAAAATTACTGAAATACCCCCGATAGGT
1 AAAATTACCA-AAATACCCTCAATAGATAAAATTACTGAAATACCCCCGATAGGT
54375912 AAAATTA
1 AAAATTA
54375919 TCGAATTACC
Statistics
Matches: 98, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
52 1 0.01
53 44 0.45
54 52 0.53
55 1 0.01
ACGTcount: A:0.45, C:0.20, G:0.12, T:0.23
Consensus pattern (54 bp):
AAAATTACCAAAATACCCTCAATAGATAAAATTACTGAAATACCCCCGATAGGT
Found at i:54375918 original size:81 final size:80
Alignment explanation
Indices: 54375761--54375928 Score: 214
Period size: 81 Copynumber: 2.1 Consensus size: 80
54375751 AAAACTACCA
* *
54375761 AAATACCCTCGATGGATAAAATAACTAAAATACTCCCGATAGTAAAATTACCAAAATACCCTCGA
1 AAATACCCTCGATGGATAAAATAACTAAAATACTCCCAATAGTAAAATTACCAAAATACCCCCGA
*
54375826 TGGGTAAAATTATCG
66 TAGGTAAAATTATCG
* * * **
54375841 AAATACCCTCGATGGGTAAAATTAC-AGAAATAC-CCTTAATAGATAAAATTACTGAAATACCCC
1 AAATACCCTCGATGGATAAAATAACTA-AAATACTCC-CAATAG-TAAAATTACCAAAATACCCC
54375904 CGATAGGTAAAATTATCG
63 CGATAGGTAAAATTATCG
*
54375922 AATTACC
1 AAATACC
54375929 ACTATAGGGT
Statistics
Matches: 76, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
79 3 0.04
80 33 0.43
81 40 0.53
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.24
Consensus pattern (80 bp):
AAATACCCTCGATGGATAAAATAACTAAAATACTCCCAATAGTAAAATTACCAAAATACCCCCGA
TAGGTAAAATTATCG
Found at i:54382482 original size:20 final size:21
Alignment explanation
Indices: 54382444--54382482 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
54382434 TAAAGTCTGA
*
54382444 TGTCGCGACATCGAAGGGCCG
1 TGTCGAGACATCGAAGGGCCG
54382465 TGTCGAGACATC-AAGGGC
1 TGTCGAGACATCGAAGGGC
54382483 AGTTTTGCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.23, C:0.26, G:0.36, T:0.15
Consensus pattern (21 bp):
TGTCGAGACATCGAAGGGCCG
Found at i:54387243 original size:27 final size:27
Alignment explanation
Indices: 54386974--54387236 Score: 285
Period size: 27 Copynumber: 9.7 Consensus size: 27
54386964 CTGCACCGAG
54386974 ACCCCCATAGGGTAAAATGACCGAAAT
1 ACCCCCATAGGGTAAAATGACCGAAAT
*
54387001 ACCCTCATAGGGTAAAATGACCGAAAT
1 ACCCCCATAGGGTAAAATGACCGAAAT
* * *
54387028 A-CCCTATTAAGGTAAAATGATCGAAAT
1 ACCCCCA-TAGGGTAAAATGACCGAAAT
* *
54387055 ACCCCCTTAGGGTAAAAAGACCGAAAT
1 ACCCCCATAGGGTAAAATGACCGAAAT
* * * *
54387082 ACCCCTATTGGGTAAAATAACCAAAAT
1 ACCCCCATAGGGTAAAATGACCGAAAT
* * *
54387109 ACCTCCATAGGGTAAAATGGCCAAAAT
1 ACCCCCATAGGGTAAAATGACCGAAAT
* * **
54387136 ACCCCTATAGAGTAAAATGGTCGAAAT
1 ACCCCCATAGGGTAAAATGACCGAAAT
** * *
54387163 ACCCTAATATGTTAAAATGACCGAAAT
1 ACCCCCATAGGGTAAAATGACCGAAAT
* * **
54387190 ACCCCTATAGGGTAAAATAACAAAAAT
1 ACCCCCATAGGGTAAAATGACCGAAAT
54387217 ACCCCCATAGGGTAAAATGA
1 ACCCCCATAGGGTAAAATGA
54387237 TTGAAATGAA
Statistics
Matches: 192, Mismatches: 42, Indels: 4
0.81 0.18 0.02
Matches are distributed among these distances:
26 3 0.02
27 186 0.97
28 3 0.02
ACGTcount: A:0.43, C:0.21, G:0.16, T:0.20
Consensus pattern (27 bp):
ACCCCCATAGGGTAAAATGACCGAAAT
Found at i:54395069 original size:65 final size:65
Alignment explanation
Indices: 54394960--54395086 Score: 245
Period size: 65 Copynumber: 2.0 Consensus size: 65
54394950 CATTTAAACC
*
54394960 AAGAAATTAGAGATTTTCTCAAAGATTTATGATTGACCGGGTCTCAGTCCTGAGTTGTGTGGTTG
1 AAGAAATTAGAGATTTTCTCAAAGATTTATGATTGACCGAGTCTCAGTCCTGAGTTGTGTGGTTG
54395025 AAGAAATTAGAGATTTTCTCAAAGATTTATGATTGACCGAGTCTCAGTCCTGAGTTGTGTGG
1 AAGAAATTAGAGATTTTCTCAAAGATTTATGATTGACCGAGTCTCAGTCCTGAGTTGTGTGG
54395087 CATCTAAAAT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 61 1.00
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.35
Consensus pattern (65 bp):
AAGAAATTAGAGATTTTCTCAAAGATTTATGATTGACCGAGTCTCAGTCCTGAGTTGTGTGGTTG
Found at i:54405599 original size:13 final size:14
Alignment explanation
Indices: 54405581--54405609 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
54405571 AAAATTGCTT
54405581 AAAAATCAAG-CAA
1 AAAAATCAAGTCAA
54405594 AAAAATCAAGTCAA
1 AAAAATCAAGTCAA
54405608 AA
1 AA
54405610 GCCACTCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.69, C:0.14, G:0.07, T:0.10
Consensus pattern (14 bp):
AAAAATCAAGTCAA
Found at i:54427709 original size:20 final size:19
Alignment explanation
Indices: 54427645--54427711 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 19
54427635 GAACTACTCT
54427645 ATTT-CTTACTTATCATTCC
1 ATTTACTTACTT-TCATTCC
* *
54427664 ATTTTCTTACTTTTCATTTC
1 ATTTACTTAC-TTTCATTCC
54427684 ATTTACTTACTTTCCATTCC
1 ATTTACTTACTTT-CATTCC
*
54427704 ACTTACTT
1 ATTTACTT
54427712 GGCATAAGCC
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
19 7 0.17
20 32 0.78
21 2 0.05
ACGTcount: A:0.19, C:0.25, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTTACTTACTTTCATTCC
Found at i:54429031 original size:22 final size:23
Alignment explanation
Indices: 54429006--54429059 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 23
54428996 GTCTTACCAC
*
54429006 TTAAACC-TAATTAATCTTCTAT
1 TTAAACCACAATTAATCTTCTAT
54429028 TT-AACCACAATTAATCTTCTAT
1 TTAAACCACAATTAATCTTCTAT
54429050 TT-AACCACAA
1 TTAAACCACAA
54429060 ATCATTAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 4 0.13
22 26 0.87
ACGTcount: A:0.39, C:0.22, G:0.00, T:0.39
Consensus pattern (23 bp):
TTAAACCACAATTAATCTTCTAT
Found at i:54429067 original size:26 final size:22
Alignment explanation
Indices: 54429014--54429059 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
54429004 ACTTAAACCT
54429014 AATTAATCTTCTATTTAACCAC
1 AATTAATCTTCTATTTAACCAC
54429036 AATTAATCTTCTATTTAACCAC
1 AATTAATCTTCTATTTAACCAC
54429058 AA
1 AA
54429060 ATCATTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.39, C:0.22, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTAATCTTCTATTTAACCAC
Found at i:54442325 original size:6 final size:7
Alignment explanation
Indices: 54442308--54442342 Score: 61
Period size: 7 Copynumber: 4.9 Consensus size: 7
54442298 TAATCATTAT
54442308 TTTTTTC
1 TTTTTTC
54442315 TTTTTTC
1 TTTTTTC
54442322 TTTTTTC
1 TTTTTTC
54442329 TTTTTTCC
1 TTTTTT-C
54442337 TTTTTT
1 TTTTTT
54442343 ACAAGAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 20 0.74
8 7 0.26
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTTC
Found at i:54448984 original size:16 final size:17
Alignment explanation
Indices: 54448952--54448984 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
54448942 GAATACAAGC
54448952 ATTTTCGTTATGTTTTA
1 ATTTTCGTTATGTTTTA
*
54448969 ATTTTCTTTA-GTTTTA
1 ATTTTCGTTATGTTTTA
54448985 CTTACATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.18, C:0.06, G:0.09, T:0.67
Consensus pattern (17 bp):
ATTTTCGTTATGTTTTA
Found at i:54456118 original size:20 final size:21
Alignment explanation
Indices: 54456095--54456133 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
54456085 AGTGAAACTG
54456095 CCCT-CGATGTCGTGACATGA
1 CCCTCCGATGTCGTGACATGA
*
54456115 CCCTCCTATGTCGTGACAT
1 CCCTCCGATGTCGTGACAT
54456134 ACCACCTGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.18, C:0.33, G:0.21, T:0.28
Consensus pattern (21 bp):
CCCTCCGATGTCGTGACATGA
Found at i:54463568 original size:41 final size:41
Alignment explanation
Indices: 54463444--54463595 Score: 173
Period size: 41 Copynumber: 3.7 Consensus size: 41
54463434 ATTAATTATA
* * *
54463444 CCCTGAATTGCACACACGTGCCCCTATTTGTACTTCGATAA
1 CCCTGAATTACACATACGTGCCCCTATTTGTACTTCGATAC
* ** *
54463485 CCCTAAATGCCACATATGTGCCCCTATTTGTACTTCGATAC
1 CCCTGAATTACACATACGTGCCCCTATTTGTACTTCGATAC
* *
54463526 CCCTGAATTACACATACGTGCCCCTTTTTGTACTT-TAGTAC
1 CCCTGAATTACACATACGTGCCCCTATTTGTACTTCGA-TAC
* *
54463567 CCTTGAA-TAGCACATGCGTGCCCCTATTT
1 CCCTGAATTA-CACATACGTGCCCCTATTT
54463596 ACACTCTAGT
Statistics
Matches: 94, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
40 3 0.03
41 91 0.97
ACGTcount: A:0.23, C:0.31, G:0.14, T:0.32
Consensus pattern (41 bp):
CCCTGAATTACACATACGTGCCCCTATTTGTACTTCGATAC
Found at i:54463581 original size:82 final size:82
Alignment explanation
Indices: 54463444--54463595 Score: 193
Period size: 82 Copynumber: 1.9 Consensus size: 82
54463434 ATTAATTATA
* * *
54463444 CCCTGAATTGCACACACGTGCCCCTATTTGTACTTCGATAACCCTAAATGCCACATATGTGCCCC
1 CCCTGAATTACACACACGTGCCCCTATTTGTACTTAGATAACCCTAAATGCCACATACGTGCCCC
54463509 TATTTGTACTTCGATAC
66 TATTTGTACTTCGATAC
* * * *
54463526 CCCTGAATTACACATACGTGCCCCTTTTTGTACTTTAG-T-ACCCTTGAATAG-CACATGCGTGC
1 CCCTGAATTACACACACGTGCCCCTATTTGTAC-TTAGATAACCC-TAAAT-GCCACATACGTGC
54463588 CCCTATTT
63 CCCTATTT
54463596 ACACTCTAGT
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
81 4 0.07
82 52 0.87
83 4 0.07
ACGTcount: A:0.23, C:0.31, G:0.14, T:0.32
Consensus pattern (82 bp):
CCCTGAATTACACACACGTGCCCCTATTTGTACTTAGATAACCCTAAATGCCACATACGTGCCCC
TATTTGTACTTCGATAC
Found at i:54470820 original size:41 final size:39
Alignment explanation
Indices: 54470762--54470915 Score: 191
Period size: 41 Copynumber: 3.8 Consensus size: 39
54470752 TAATTAATTA
* * *
54470762 TACCCTAAATTGCACATACGTGCCTCTGTTTGTACTTCGG
1 TACCCTGAA-TGCACATACGTGCCTCTATTTGTACTTTGG
*
54470802 TACCCTTGAATGCCACATACGTGCCCCTATTTGTACTTTGG
1 TACCC-TGAATG-CACATACGTGCCTCTATTTGTACTTTGG
*
54470843 TACCACTGAATTGCACATACATGCCTCTATTTGTACTTTGG
1 TACC-CTGAA-TGCACATACGTGCCTCTATTTGTACTTTGG
*
54470884 TACCCCTGAATAGCACATGCGTGCCTCTATTT
1 TA-CCCTGAAT-GCACATACGTGCCTCTATTT
54470916 ACACTCTATT
Statistics
Matches: 100, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
40 8 0.08
41 87 0.87
42 5 0.05
ACGTcount: A:0.21, C:0.28, G:0.16, T:0.34
Consensus pattern (39 bp):
TACCCTGAATGCACATACGTGCCTCTATTTGTACTTTGG
Found at i:54473927 original size:102 final size:102
Alignment explanation
Indices: 54473751--54473949 Score: 398
Period size: 102 Copynumber: 2.0 Consensus size: 102
54473741 GTTCGAAAAC
54473751 TGTGACAACCCAAATTAGACCCTGGTCGGAATGTGGTTTCGAGACCACATTACCGAGCCAAAAAT
1 TGTGACAACCCAAATTAGACCCTGGTCGGAATGTGGTTTCGAGACCACATTACCGAGCCAAAAAT
54473816 TTATTTTCGTGTTTTAATTGCATAAATTGTTGAGAGT
66 TTATTTTCGTGTTTTAATTGCATAAATTGTTGAGAGT
54473853 TGTGACAACCCAAATTAGACCCTGGTCGGAATGTGGTTTCGAGACCACATTACCGAGCCAAAAAT
1 TGTGACAACCCAAATTAGACCCTGGTCGGAATGTGGTTTCGAGACCACATTACCGAGCCAAAAAT
54473918 TTATTTTCGTGTTTTAATTGCATAAATTGTTG
66 TTATTTTCGTGTTTTAATTGCATAAATTGTTG
54473950 CGTGTCAGTG
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
102 97 1.00
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (102 bp):
TGTGACAACCCAAATTAGACCCTGGTCGGAATGTGGTTTCGAGACCACATTACCGAGCCAAAAAT
TTATTTTCGTGTTTTAATTGCATAAATTGTTGAGAGT
Found at i:54475657 original size:55 final size:54
Alignment explanation
Indices: 54475542--54475693 Score: 166
Period size: 54 Copynumber: 2.8 Consensus size: 54
54475532 TTAAATTGTA
* *
54475542 CAGCACTAAGTGTGCGAAATGGATATGATGCACTAAGTGTGCGAATTGACCATG
1 CAGCACTAAGTGTGCGAGATGGATATGATGCACTAAGTGTGCGAATTGACCACG
* * **
54475596 CGGCACTAAGTGTGCGAGATGGACTATG-TGGCACTAAGTGTGCGATTTGATTACG
1 CAGCACTAAGTGTGCGAGATGGA-TATGAT-GCACTAAGTGTGCGAATTGACCACG
* * *
54475651 TAGCACTAAGTGTGCGAG-TTGATTAT-ATAGCACTGAGTGTGCG
1 CAGCACTAAGTGTGCGAGATGGA-TATGAT-GCACTAAGTGTGCG
54475694 GGCTCAATAA
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
54 42 0.51
55 41 0.49
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.27
Consensus pattern (54 bp):
CAGCACTAAGTGTGCGAGATGGATATGATGCACTAAGTGTGCGAATTGACCACG
Found at i:54475672 original size:27 final size:27
Alignment explanation
Indices: 54475543--54475693 Score: 135
Period size: 27 Copynumber: 5.6 Consensus size: 27
54475533 TAAATTGTAC
* *
54475543 AGCACTAAGTGTGCGAAATGGA-TATG-
1 AGCACTAAGTGTGCG-AGTTGACTATGT
* * *
54475569 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAGTTGACTATGT
* *
54475597 GGCACTAAGTGTGCGAGATGGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
* * * *
54475625 GGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
* *
54475652 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
54475679 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
54475694 GGCTCAATAA
Statistics
Matches: 105, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
26 6 0.06
27 76 0.72
28 23 0.22
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.27
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:54483657 original size:55 final size:54
Alignment explanation
Indices: 54483542--54483693 Score: 166
Period size: 54 Copynumber: 2.8 Consensus size: 54
54483532 TTAAATTGTA
* *
54483542 CAGCACTAAGTGTGCGAAATGGATATGATGCACTAAGTGTGCGAATTGACCATG
1 CAGCACTAAGTGTGCGAGATGGATATGATGCACTAAGTGTGCGAATTGACCACG
* * **
54483596 CGGCACTAAGTGTGCGAGATGGACTATG-TGGCACTAAGTGTGCGATTTGATTACG
1 CAGCACTAAGTGTGCGAGATGGA-TATGAT-GCACTAAGTGTGCGAATTGACCACG
* * *
54483651 TAGCACTAAGTGTGCGAG-TTGATTAT-ATAGCACTGAGTGTGCG
1 CAGCACTAAGTGTGCGAGATGGA-TATGAT-GCACTAAGTGTGCG
54483694 GGCTCAATAA
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
54 42 0.51
55 41 0.49
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.27
Consensus pattern (54 bp):
CAGCACTAAGTGTGCGAGATGGATATGATGCACTAAGTGTGCGAATTGACCACG
Found at i:54483672 original size:27 final size:27
Alignment explanation
Indices: 54483543--54483693 Score: 135
Period size: 27 Copynumber: 5.6 Consensus size: 27
54483533 TAAATTGTAC
* *
54483543 AGCACTAAGTGTGCGAAATGGA-TATG-
1 AGCACTAAGTGTGCG-AGTTGACTATGT
* * *
54483569 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAGTTGACTATGT
* *
54483597 GGCACTAAGTGTGCGAGATGGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
* * * *
54483625 GGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
* *
54483652 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
54483679 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
54483694 GGCTCAATAA
Statistics
Matches: 105, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
26 6 0.06
27 76 0.72
28 23 0.22
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.27
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:54485726 original size:17 final size:17
Alignment explanation
Indices: 54485706--54485741 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
54485696 TAATTTAAAT
*
54485706 AATTAATTAATTTTCTC
1 AATTAAATAATTTTCTC
54485723 AATTAAATAATTTTCTC
1 AATTAAATAATTTTCTC
54485740 AA
1 AA
54485742 CTGAATTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTAAATAATTTTCTC
Found at i:54493471 original size:24 final size:22
Alignment explanation
Indices: 54493424--54493472 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 22
54493414 AAAATATTAG
54493424 TAGGTAATAGAGTAATATATAAA
1 TAGGTAATAGAG-AATATATAAA
54493447 TAGGTAAATAGA-AATATTATCAAA
1 TAGGT-AATAGAGAATA-TAT-AAA
54493471 TA
1 TA
54493473 TAATAGTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
22 4 0.17
23 8 0.35
24 11 0.48
ACGTcount: A:0.53, C:0.02, G:0.14, T:0.31
Consensus pattern (22 bp):
TAGGTAATAGAGAATATATAAA
Found at i:54493495 original size:24 final size:23
Alignment explanation
Indices: 54493468--54493523 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
54493458 AAATATTATC
*
54493468 AAATATAATAGTAATAACAAGAAT
1 AAATATAATA-TAAAAACAAGAAT
* *
54493492 AAATAGTAATATAAAAATAATAAT
1 AAATA-TAATATAAAAACAAGAAT
54493516 AAAT-TAAT
1 AAATATAAT
54493524 TAATAGCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 4 0.14
24 19 0.68
25 5 0.18
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (23 bp):
AAATATAATATAAAAACAAGAAT
Found at i:54495305 original size:44 final size:43
Alignment explanation
Indices: 54495256--54495395 Score: 104
Period size: 44 Copynumber: 3.2 Consensus size: 43
54495246 CAACCCATGG
54495256 AGGCAAGGCTGGTATCTTCGATCTGCTTCGCTATCAGTACAGGA
1 AGGCAAGGCTGGTATCTTCGATCTGCTTCGCT-TCAGTACAGGA
* ** * * * * **
54495300 AGGCAAGATCTACTTTCTTC-AGTCTGCTCCACTGCAAGCCCAAGG-
1 AGGCAAG-GCTGGTATCTTCGA-TCTGCTTCGCTTC-AGTAC-AGGA
* * *
54495345 AGGCAAGGCTGGTGTCTTCGATCTGTTTCGCTGTCAGTATAGGA
1 AGGCAAGGCTGGTATCTTCGATCTGCTTCGCT-TCAGTACAGGA
54495389 AGGCAAG
1 AGGCAAG
54495396 ATCTGCTTTC
Statistics
Matches: 69, Mismatches: 20, Indels: 14
0.67 0.19 0.14
Matches are distributed among these distances:
43 3 0.04
44 34 0.49
45 29 0.42
46 3 0.04
ACGTcount: A:0.23, C:0.24, G:0.27, T:0.26
Consensus pattern (43 bp):
AGGCAAGGCTGGTATCTTCGATCTGCTTCGCTTCAGTACAGGA
Found at i:54495321 original size:89 final size:88
Alignment explanation
Indices: 54495186--54495435 Score: 322
Period size: 89 Copynumber: 2.8 Consensus size: 88
54495176 TGGTGTTTTT
* * * **
54495186 GATCTGTTTCGCTGTCAGTACAGGAAGGCAAAATCTGTTATATTCAGTCTACTCTGCTGGCAA-C
1 GATCTGTTTCGCTGTCAGTACAGGAAGGCAAGATCTCTT-TCTTCAGTCTACTCCACT-GCAAGC
*
54495250 CCATGGAGGCAAGGCTGGTATCTTC
64 CCAAGGAGGCAAGGCTGGTATCTTC
* * *
54495275 GATCTGCTTCGCTATCAGTACAGGAAGGCAAGATCTACTTTCTTCAGTCTGCTCCACTGCAAGCC
1 GATCTGTTTCGCTGTCAGTACAGGAAGGCAAGATCT-CTTTCTTCAGTCTACTCCACTGCAAGCC
*
54495340 CAAGGAGGCAAGGCTGGTGTCTTC
65 CAAGGAGGCAAGGCTGGTATCTTC
* * * *
54495364 GATCTGTTTCGCTGTCAGTATAGGAAGGCAAGATCTGCTTTCTTTAGTCTGCTCCACTGCAAACC
1 GATCTGTTTCGCTGTCAGTACAGGAAGGCAAGATCT-CTTTCTTCAGTCTACTCCACTGCAAGCC
*
54495429 CAGGGAG
65 CAAGGAG
54495436 ATAAGACTTG
Statistics
Matches: 142, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
88 4 0.03
89 136 0.96
90 2 0.01
ACGTcount: A:0.23, C:0.24, G:0.25, T:0.28
Consensus pattern (88 bp):
GATCTGTTTCGCTGTCAGTACAGGAAGGCAAGATCTCTTTCTTCAGTCTACTCCACTGCAAGCCC
AAGGAGGCAAGGCTGGTATCTTC
Found at i:54495474 original size:41 final size:44
Alignment explanation
Indices: 54495411--54495523 Score: 135
Period size: 44 Copynumber: 2.6 Consensus size: 44
54495401 CTTTCTTTAG
* *
54495411 TCTGCTCCACTGCAAAC-CCAGGGAGATAAGA-CT-TGATGTGA-
1 TCTGCTCTACTGC-AACTTCAGGGAGATAAGATCTATGATGTGAT
* *
54495452 TCTGCTCTACTGCAACTTCAGGGAGATAAGATCTATTATTTGAT
1 TCTGCTCTACTGCAACTTCAGGGAGATAAGATCTATGATGTGAT
* *
54495496 TCCGCTCTACTGCCACTTCAGGGAGATA
1 TCTGCTCTACTGCAACTTCAGGGAGATA
54495524 GGATTACTGG
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
40 3 0.05
41 25 0.40
42 2 0.03
43 6 0.10
44 26 0.42
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (44 bp):
TCTGCTCTACTGCAACTTCAGGGAGATAAGATCTATGATGTGAT
Found at i:54495734 original size:44 final size:44
Alignment explanation
Indices: 54495560--54496409 Score: 344
Period size: 44 Copynumber: 19.6 Consensus size: 44
54495550 TCAGTCTTCC
* * * * * *
54495560 CCACTGCAACTTCAGGGGGATAAGACTTGCT-TCCTCAGTCAGCT
1 CCACTGCAACTTCAGGGAGATAAGA-TTACTGACTTCAATCTGCT
* * * * *
54495604 TCGCTGCAACCTCAGGGAGATAAGA--CCTGA-TGT-GATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTACTGACT-TCAATCTGCT
* * * * * * *
54495645 CTACTGCAACTTCAGAGAGACAAGATCTA-TTATTTGAATCCGCT
1 CCACTGCAACTTCAGGGAGATAAGAT-TACTGACTTCAATCTGCT
* *
54495689 CCACTGCCACTTCAGGGAGATAGGATTACTGACTTCAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTACTGACTTCAATCTGCT
* * *
54495733 CCACTGCAAAC-TCAGGGAGATAAGATTCAC-CATCTTCAGTCTGCC
1 CCACTGC-AACTTCAGGGAGATAAGATT-ACTGA-CTTCAATCTGCT
* * * * ** * *
54495778 CCACTACAACTTTAGGGGGATAAGACTTGCTTTC-TCAGTCTACT
1 CCACTGCAACTTCAGGGAGATAAGA-TTACTGACTTCAATCTGCT
** * * * *
54495822 CCGTTGCAACCTCAGGGAGATAAGACT--TGA-TGT-GATCTGCA
1 CCACTGCAACTTCAGGGAGATAAGATTACTGACT-TCAATCTGCT
* * * * * * *
54495863 CTACTACAAATTCAGAGAGATAAGATCTA-TTATTTGAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGAT-TACTGACTTCAATCTGCT
* * * * *
54495907 CCACTGCCACTTCAGTGAGATAGGATTACTGGCTTCAATATGCT
1 CCACTGCAACTTCAGGGAGATAAGATTACTGACTTCAATCTGCT
* * * *
54495951 CCCCTACAAAC-TCAGAGAGATAAGATTCAC-CATCTTCAATCTGCT
1 CCACTGC-AACTTCAGGGAGATAAGATT-ACTGA-CTTCAATCTGCT
* * * * * *
54495996 CCACTACAGCTT-AGGGAGATAAGA--CCTGA-TGCGATCTACT
1 CCACTGCAACTTCAGGGAGATAAGATTACTGACTTCAATCTGCT
* * * * * *
54496036 CTACTGCAACTTTAGAGAGATAAGATCTATTG-TTTTAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGAT-TACTGACTTCAATCTGCT
* * *
54496080 CCACTGTAACTTCAGGGAGATAGGATTA-TCGTCTTCAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTACT-GACTTCAATCTGCT
* * *
54496124 CCACTGCAACCTCAGCGAGATAAGATT--TGCCATCTTCGATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTACTG--A-CTTCAATCTGCT
* * * * **
54496169 CCACTACTACTT-AGGGAGATAAGATTTGCT-TCTTCGGTCTGCT
1 CCACTGCAACTTCAGGGAGATAAGA-TTACTGACTTCAATCTGCT
** * * * * * *
54496212 CTGCTGCAACCTCAGGGAGATAAGA--CCT-AATACGATCTACT
1 CCACTGCAACTTCAGGGAGATAAGATTACTGACTTCAATCTGCT
* * * * * * *
54496253 CTACAGCAACTTCAGAGAGATAAGATCTATTG-TTTTAATC-CCT
1 CCACTGCAACTTCAGGGAGATAAGAT-TACTGACTTCAATCTGCT
* * * * *
54496296 CCACTACAACTTCAAGGAGATAGGATTACTGGCTTTAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTACTGACTTCAATCTGCT
* * * * *
54496340 CCACTACAAAC-TCAGGGAGATAAGATTCAC-CATCTTTAGTCTGCC
1 CCACTGC-AACTTCAGGGAGATAAGATT-ACTGA-CTTCAATCTGCT
*
54496385 CCACTGCAACTTCAGGGGGATAAGA
1 CCACTGCAACTTCAGGGAGATAAGA
54496410 CTAGCGATTT
Statistics
Matches: 595, Mismatches: 161, Indels: 99
0.70 0.19 0.12
Matches are distributed among these distances:
40 17 0.03
41 92 0.15
42 10 0.02
43 62 0.10
44 299 0.50
45 112 0.19
46 2 0.00
47 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (44 bp):
CCACTGCAACTTCAGGGAGATAAGATTACTGACTTCAATCTGCT
Found at i:54495917 original size:218 final size:218
Alignment explanation
Indices: 54495539--54496020 Score: 743
Period size: 218 Copynumber: 2.2 Consensus size: 218
54495529 ACTGGCTTCA
* * *
54495539 ATTCACCATCTTCAGTCTTCCCCACTGCAACTTCAGGGGGATAAGACTTGCTTCCTCAGTCAGCT
1 ATTCACCATCTTCAGTCTGCCCCACTACAACTTTAGGGGGATAAGACTTGCTTCCTCAGTCAGCT
* * * *
54495604 TCGCTGCAACCTCAGGGAGATAAGACCTGATGTGATCTGCTCTACTGCAACTTCAGAGAGACAAG
66 CCGCTGCAACCTCAGGGAGATAAGACCTGATGTGATCTGCACTACTACAAATTCAGAGAGACAAG
*
54495669 ATCTATTATTTGAATCCGCTCCACTGCCACTTCAGGGAGATAGGATTACTGACTTCAATCTGCTC
131 ATCTATTATTTGAATCCGCTCCACTGCCACTTCAGGGAGATAGGATTACTGACTTCAATATGCTC
* *
54495734 CACTGCAAACTCAGGGAGATAAG
196 CACTACAAACTCAGAGAGATAAG
*
54495757 ATTCACCATCTTCAGTCTGCCCCACTACAACTTTAGGGGGATAAGACTTGCTTTCTCAGTCTA-C
1 ATTCACCATCTTCAGTCTGCCCCACTACAACTTTAGGGGGATAAGACTTGCTTCCTCAGTC-AGC
* * *
54495821 TCCGTTGCAACCTCAGGGAGATAAGACTTGATGTGATCTGCACTACTACAAATTCAGAGAGATAA
65 TCCGCTGCAACCTCAGGGAGATAAGACCTGATGTGATCTGCACTACTACAAATTCAGAGAGACAA
* * *
54495886 GATCTATTATTTGAATCTGCTCCACTGCCACTTCAGTGAGATAGGATTACTGGCTTCAATATGCT
130 GATCTATTATTTGAATCCGCTCCACTGCCACTTCAGGGAGATAGGATTACTGACTTCAATATGCT
*
54495951 CCCCTACAAACTCAGAGAGATAAG
195 CCACTACAAACTCAGAGAGATAAG
* * * *
54495975 ATTCACCATCTTCAATCTGCTCCACTACAGC-TTAGGGAGATAAGAC
1 ATTCACCATCTTCAGTCTGCCCCACTACAACTTTAGGGGGATAAGAC
54496021 CTGATGCGAT
Statistics
Matches: 241, Mismatches: 22, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
217 14 0.06
218 226 0.94
219 1 0.00
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (218 bp):
ATTCACCATCTTCAGTCTGCCCCACTACAACTTTAGGGGGATAAGACTTGCTTCCTCAGTCAGCT
CCGCTGCAACCTCAGGGAGATAAGACCTGATGTGATCTGCACTACTACAAATTCAGAGAGACAAG
ATCTATTATTTGAATCCGCTCCACTGCCACTTCAGGGAGATAGGATTACTGACTTCAATATGCTC
CACTACAAACTCAGAGAGATAAG
Found at i:54496060 original size:173 final size:173
Alignment explanation
Indices: 54495835--54496192 Score: 495
Period size: 173 Copynumber: 2.1 Consensus size: 173
54495825 TTGCAACCTC
* * *
54495835 AGGGAGATAAGACTTGATGTGATCTGCACTACTACAAATTCAGAGAGATAAGATCTATTATTTGA
1 AGGGAGATAAGACCTGATGCGATCTACACTACTACAAATTCAGAGAGATAAGATCTATTATTTGA
* * *
54495900 ATCTGCTCCACTGCCACTTCAGTGAGATAGGATTA-CTGGCTTCAATATGCTCCCCTACAAACTC
66 ATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATC-GGCTTCAATATGCTCCACTACAAACTC
54495964 AGAGAGATAAGATTCACCATCTTCAATCTGCTCCACTAC-AGCTT
130 AGAGAGATAAGATTCACCATCTTCAATCTGCTCCACTACTA-CTT
* * * * * *
54496008 AGGGAGATAAGACCTGATGCGATCTACTCTACTGCAACTTTAGAGAGATAAGATCTATTGTTTTA
1 AGGGAGATAAGACCTGATGCGATCTACACTACTACAAATTCAGAGAGATAAGATCTATTATTTGA
* * * * *
54496073 ATCTGCTCCACTGTAACTTCAGGGAGATAGGATTATCGTCTTCAATCTGCTCCACTGCAACCTCA
66 ATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTCAATATGCTCCACTACAAACTCA
* ** *
54496138 GCGAGATAAGATTTGCCATCTTCGATCTGCTCCACTACTACTT
131 GAGAGATAAGATTCACCATCTTCAATCTGCTCCACTACTACTT
54496181 AGGGAGATAAGA
1 AGGGAGATAAGA
54496193 TTTGCTTCTT
Statistics
Matches: 162, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
173 160 0.99
174 2 0.01
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.29
Consensus pattern (173 bp):
AGGGAGATAAGACCTGATGCGATCTACACTACTACAAATTCAGAGAGATAAGATCTATTATTTGA
ATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTCAATATGCTCCACTACAAACTCA
GAGAGATAAGATTCACCATCTTCAATCTGCTCCACTACTACTT
Found at i:54496190 original size:217 final size:216
Alignment explanation
Indices: 54495967--54496375 Score: 552
Period size: 216 Copynumber: 1.9 Consensus size: 216
54495957 CAAACTCAGA
* * * *
54495967 GAGATAAGATTCACCATCTTCAATCTGCTCCACTAC-AGCTTAGGGAGATAAGACCTGATGCGAT
1 GAGATAAGATT-ACCATCTTCAATCTGCTCCACTACAACCTCAGGGAGATAAGACCTAATACGAT
* * * ** *
54496031 CTACTCTACTGCAACTTTAGAGAGATAAGATCTATTGTTTTAATCTGCTCCACTGTAACTTCAGG
65 CTACTCTACAGCAACTTCAGAGAGATAAGATCTATTGTTTTAATC-CCTCCACTACAACTTCAAG
* * * **
54496096 GAGATAGGATTA-TCGTCTTCAATCTGCTCCACTGCAACCTCAGCGAGATAAGATTTGCCATCTT
129 GAGATAGGATTACT-GGCTTCAATCTGCTCCACTACAAACTCAGCGAGATAAGATTCACCATCTT
54496160 CGATCTGCTCCACTACTACTTAGG
193 CGATCTGCTCCACTACTACTTAGG
** * ** ** *
54496184 GAGATAAGATTTGCTTCTTCGGTCTGCTCTGCTGCAACCTCAGGGAGATAAGACCTAATACGATC
1 GAGATAAGATTACCATCTTCAATCTGCTCCACTACAACCTCAGGGAGATAAGACCTAATACGATC
54496249 TACTCTACAGCAACTTCAGAGAGATAAGATCTATTGTTTTAATCCCTCCACTACAACTTCAAGGA
66 TACTCTACAGCAACTTCAGAGAGATAAGATCTATTGTTTTAATCCCTCCACTACAACTTCAAGGA
* *
54496314 GATAGGATTACTGGCTTTAATCTGCTCCACTACAAACTCAGGGAGATAAGATTCACCATCTT
131 GATAGGATTACTGGCTTCAATCTGCTCCACTACAAACTCAGCGAGATAAGATTCACCATCTT
54496376 TAGTCTGCCC
Statistics
Matches: 165, Mismatches: 25, Indels: 5
0.85 0.13 0.03
Matches are distributed among these distances:
216 86 0.52
217 79 0.48
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (216 bp):
GAGATAAGATTACCATCTTCAATCTGCTCCACTACAACCTCAGGGAGATAAGACCTAATACGATC
TACTCTACAGCAACTTCAGAGAGATAAGATCTATTGTTTTAATCCCTCCACTACAACTTCAAGGA
GATAGGATTACTGGCTTCAATCTGCTCCACTACAAACTCAGCGAGATAAGATTCACCATCTTCGA
TCTGCTCCACTACTACTTAGG
Found at i:54496266 original size:173 final size:171
Alignment explanation
Indices: 54495835--54496274 Score: 391
Period size: 173 Copynumber: 2.5 Consensus size: 171
54495825 TTGCAACCTC
* * * * * ** * **
54495835 AGGGAGATAAGACTTGATGTGATCTGCACTACTACAAATTCAGAGAGATAAGATCTATTATTTGA
1 AGGGAGATAAGACCTGATGCGATCTACTCTACTGCAACCTCAGAGAGATAAGACCTA-TA-TACA
* * * * *
54495900 ATCTGCTCCACTGCCACTTCAGTGAGATAGGATTACTGGCTTCAATATGCTCCCCTACAAACTCA
64 ATCTACTCCACAGCAACTTCAGAGAGATAGGATTACTGGCTTCAATATGCTCCACTACAAACTCA
54495965 GAGAGATAAGATTCACCATCTTCAATCTGCTCCACTACAGCTT
129 GAGAGATAAGATTCACCATCTTCAATCTGCTCCACTACAGCTT
* * * * **
54496008 AGGGAGATAAGACCTGATGCGATCTACTCTACTGCAACTTTAGAGAGATAAGATCTATTGTTTTA
1 AGGGAGATAAGACCTGATGCGATCTACTCTACTGCAACCTCAGAGAGATAAGACCTA-T-ATACA
* * * * * * * *
54496073 ATCTGCTCCACTGTAACTTCAGGGAGATAGGATTA-TCGTCTTCAATCTGCTCCACTGCAACCTC
64 ATCTACTCCACAGCAACTTCAGAGAGATAGGATTACT-GGCTTCAATATGCTCCACTACAAACTC
* ** *
54496137 AGCGAGATAAGATTTGCCATCTTCGATCTGCTCCACTACTA-CTT
128 AGAGAGATAAGATTCACCATCTTCAATCTGCTCCACTAC-AGCTT
* ** * * * * *
54496181 AGGGAGATAAGATTTGCTTCTTCGGTCTGCTCTGCTGCAACCTCAGGGAGATAAGACCTA-ATAC
1 AGGGAGATAAGA---CCTGATGCGATCTACTCTACTGCAACCTCAGAGAGATAAGACCTATATAC
* *
54496245 GATCTACTCTACAGCAACTTCAGAGAGATA
63 AATCTACTCCACAGCAACTTCAGAGAGATA
54496275 AGATCTATTG
Statistics
Matches: 220, Mismatches: 41, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
172 1 0.00
173 184 0.84
174 1 0.00
176 34 0.15
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (171 bp):
AGGGAGATAAGACCTGATGCGATCTACTCTACTGCAACCTCAGAGAGATAAGACCTATATACAAT
CTACTCCACAGCAACTTCAGAGAGATAGGATTACTGGCTTCAATATGCTCCACTACAAACTCAGA
GAGATAAGATTCACCATCTTCAATCTGCTCCACTACAGCTT
Found at i:54496316 original size:43 final size:44
Alignment explanation
Indices: 54496259--54496366 Score: 116
Period size: 43 Copynumber: 2.5 Consensus size: 44
54496249 TACTCTACAG
* *
54496259 CAACTTC-AGAGAGATAAGATCTA-TTGTTTTAATC-CCTCCACTA
1 CAACTTCAAG-GAGATAAGAT-TACTGGCTTTAATCTCCTCCACTA
* *
54496302 CAACTTCAAGGAGATAGGATTACTGGCTTTAATCTGCTCCACTA
1 CAACTTCAAGGAGATAAGATTACTGGCTTTAATCTCCTCCACTA
*
54496346 CAAAC-TCAGGGAGATAAGATT
1 C-AACTTCAAGGAGATAAGATT
54496367 CACCATCTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
42 2 0.04
43 25 0.45
44 25 0.45
45 3 0.05
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (44 bp):
CAACTTCAAGGAGATAAGATTACTGGCTTTAATCTCCTCCACTA
Found at i:54496400 original size:45 final size:44
Alignment explanation
Indices: 54496296--54496409 Score: 122
Period size: 45 Copynumber: 2.6 Consensus size: 44
54496286 TTTAATCCCT
* * ** *
54496296 CCACTACAACTTCAAGGAGATAGGATTACTGGCTTTAATCTGCT
1 CCACTACAACTTCAGGGAGATAAGATTACCAGCTTTAATCTGCC
* *
54496340 CCACTACAAAC-TCAGGGAGATAAGATTCACCATCTTTAGTCTGCC
1 CCACTAC-AACTTCAGGGAGATAAGATT-ACCAGCTTTAATCTGCC
* *
54496385 CCACTGCAACTTCAGGGGGATAAGA
1 CCACTACAACTTCAGGGAGATAAGA
54496410 CTAGCGATTT
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
44 24 0.41
45 34 0.59
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (44 bp):
CCACTACAACTTCAGGGAGATAAGATTACCAGCTTTAATCTGCC
Found at i:54496409 original size:217 final size:217
Alignment explanation
Indices: 54496008--54496409 Score: 576
Period size: 216 Copynumber: 1.9 Consensus size: 217
54495998 ACTACAGCTT
* * * *
54496008 AGGGAGATAAGACCTGATGCGATCTACTCTACTGCAACTTTAGAGAGATAAGATCTATTGTTTTA
1 AGGGAGATAAGACCTAATACGATCTACTCTACAGCAACTTCAGAGAGATAAGATCTATTGTTTTA
* ** * * * *
54496073 ATCTGCTCCACTGTAACTTCAGGGAGATAGGATTATCGTCTTCAATCTGCTCCACTGCAACCTCA
66 ATCTCCTCCACTACAACTTCAAGGAGATAGGATTATCGGCTTCAATCTGCTCCACTACAAACTCA
** * * *
54496138 GCGAGATAAGATTTGCCATCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATTTGCTTCTT
131 GCGAGATAAGATTCACCATCTTAGATCTGCCCCACTACAACTTAGGGAGATAAGATTTGCTTCTT
54496203 CGGTCTGCTCTGCTGCAACCTC
196 CGGTCTGCTCTGCTGCAACCTC
54496225 AGGGAGATAAGACCTAATACGATCTACTCTACAGCAACTTCAGAGAGATAAGATCTATTGTTTTA
1 AGGGAGATAAGACCTAATACGATCTACTCTACAGCAACTTCAGAGAGATAAGATCTATTGTTTTA
*
54496290 ATC-CCTCCACTACAACTTCAAGGAGATAGGATTA-CTGGCTTTAATCTGCTCCACTACAAACTC
66 ATCTCCTCCACTACAACTTCAAGGAGATAGGATTATC-GGCTTCAATCTGCTCCACTACAAACTC
* * *
54496353 AGGGAGATAAGATTCACCATCTTTAG-TCTGCCCCACTGCAACTTCAGGGGGATAAGA
130 AGCGAGATAAGATTCACCATC-TTAGATCTGCCCCACTACAACTT-AGGGAGATAAGA
54496410 CTAGCGATTT
Statistics
Matches: 162, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
215 1 0.01
216 83 0.51
217 78 0.48
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (217 bp):
AGGGAGATAAGACCTAATACGATCTACTCTACAGCAACTTCAGAGAGATAAGATCTATTGTTTTA
ATCTCCTCCACTACAACTTCAAGGAGATAGGATTATCGGCTTCAATCTGCTCCACTACAAACTCA
GCGAGATAAGATTCACCATCTTAGATCTGCCCCACTACAACTTAGGGAGATAAGATTTGCTTCTT
CGGTCTGCTCTGCTGCAACCTC
Found at i:54498578 original size:17 final size:17
Alignment explanation
Indices: 54498556--54498592 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
54498546 TTAACCTCTC
**
54498556 TTTTTTCTTTTTCTTTT
1 TTTTTTCTTCCTCTTTT
54498573 TTTTTTCTTCCTCTTTT
1 TTTTTTCTTCCTCTTTT
54498590 TTT
1 TTT
54498593 CATTTTTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTTTTCTTCCTCTTTT
Found at i:54503027 original size:17 final size:18
Alignment explanation
Indices: 54503005--54503038 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
54502995 ACAATGAAGT
54503005 TATATAT-GTATAAAATA
1 TATATATAGTATAAAATA
*
54503022 TATATATAGTTTAAAAT
1 TATATATAGTATAAAAT
54503039 TAAATAACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (18 bp):
TATATATAGTATAAAATA
Found at i:54503170 original size:24 final size:22
Alignment explanation
Indices: 54503143--54503198 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 22
54503133 AAATATTATC
*
54503143 AAATATAATAGTAATAACAATAAT
1 AAAT-TAATA-TAAAAACAATAAT
*
54503167 AAATTGTAATATAAAAATAATAAT
1 AAA-T-TAATATAAAAACAATAAT
54503191 AAATTAAT
1 AAATTAAT
54503199 TAATAGCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 4 0.14
23 1 0.04
24 17 0.61
25 6 0.21
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (22 bp):
AAATTAATATAAAAACAATAAT
Found at i:54510812 original size:89 final size:89
Alignment explanation
Indices: 54510661--54510840 Score: 333
Period size: 89 Copynumber: 2.0 Consensus size: 89
54510651 GCTTCTTTGC
* *
54510661 AAATGATCGAATACTTCAGAGGAAATCAGGTTCTCTATTCTCTCCATTTTTGTTGAATTTCTTTT
1 AAATGATCGAATACTTCAGAGGAAATCAGGTTCTCCATTCTCTCCATTTTTGTTAAATTTCTTTT
54510726 TATAAATTTCAATATAATGATTAT
66 TATAAATTTCAATATAATGATTAT
*
54510750 AAATGATCGAATATTTCAGAGGAAATCAGGTTCTCCATTCTCTCCATTTTTGTTAAATTTCTTTT
1 AAATGATCGAATACTTCAGAGGAAATCAGGTTCTCCATTCTCTCCATTTTTGTTAAATTTCTTTT
54510815 TATAAATTTCAATATAATGATTAT
66 TATAAATTTCAATATAATGATTAT
54510839 AA
1 AA
54510841 TATATGTATT
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
89 88 1.00
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (89 bp):
AAATGATCGAATACTTCAGAGGAAATCAGGTTCTCCATTCTCTCCATTTTTGTTAAATTTCTTTT
TATAAATTTCAATATAATGATTAT
Found at i:54525023 original size:16 final size:17
Alignment explanation
Indices: 54524994--54525027 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
54524984 TTACATCGAC
*
54524994 AAAATAAATTAATTTAA
1 AAAATAAATAAATTTAA
54525011 AAAATAAA-AAATTTAA
1 AAAATAAATAAATTTAA
54525027 A
1 A
54525028 TTTAACGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAATAAATAAATTTAA
Found at i:54527217 original size:11 final size:11
Alignment explanation
Indices: 54527201--54527231 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
54527191 TTTCATGCAT
54527201 TTGGAGGGTCC
1 TTGGAGGGTCC
54527212 TTGGAGGGTCC
1 TTGGAGGGTCC
54527223 TTGGAGGGT
1 TTGGAGGGT
54527232 TACTTCTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.10, C:0.13, G:0.48, T:0.29
Consensus pattern (11 bp):
TTGGAGGGTCC
Found at i:54532561 original size:20 final size:19
Alignment explanation
Indices: 54532533--54532571 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
54532523 TTTAGAAAAA
54532533 TTTTAATTTCTTTA-AATTT
1 TTTTAATTT-TTTAGAATTT
54532552 TTTTATATTTTTTAGAATTT
1 TTTTA-ATTTTTTAGAATTT
54532572 GTTGTGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (19 bp):
TTTTAATTTTTTAGAATTT
Found at i:54532630 original size:19 final size:20
Alignment explanation
Indices: 54532608--54532671 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
54532598 ATTTGGAAAT
*
54532608 TTTTTTTAAA-TATTTTGAA
1 TTTTTTAAAATTATTTTGAA
* *
54532627 -TTTTAAAAATTGTTTTGAA
1 TTTTTTAAAATTATTTTGAA
* *
54532646 TTTTTGAAAATTATATTGAA
1 TTTTTTAAAATTATTTTGAA
54532666 TTTTTT
1 TTTTTT
54532672 TTTGTAATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
18 7 0.19
19 8 0.22
20 21 0.58
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (20 bp):
TTTTTTAAAATTATTTTGAA
Found at i:54532655 original size:20 final size:20
Alignment explanation
Indices: 54532618--54532670 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
54532608 TTTTTTTAAA
54532618 TATTTTGAA-TTTTAAAAAT
1 TATTTTGAATTTTTAAAAAT
* *
54532637 TGTTTTGAATTTTTGAAAAT
1 TATTTTGAATTTTTAAAAAT
*
54532657 TATATTGAATTTTT
1 TATTTTGAATTTTT
54532671 TTTTGTAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 8 0.28
20 21 0.72
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (20 bp):
TATTTTGAATTTTTAAAAAT
Found at i:54533213 original size:31 final size:29
Alignment explanation
Indices: 54533177--54533243 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 29
54533167 ATATGCCCTC
*
54533177 AGTCCCTGTACTTTTCACTATTTTGAAATT-T
1 AGTCCCTGTACTTTT-A-T-TTTTAAAATTAT
* *
54533208 AGTCCCTTTGCTTTTATTTTTAAAATTAT
1 AGTCCCTGTACTTTTATTTTTAAAATTAT
54533237 AGTCCCT
1 AGTCCCT
54533244 TTGATTTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 9 0.28
29 9 0.28
30 1 0.03
31 13 0.41
ACGTcount: A:0.22, C:0.19, G:0.09, T:0.49
Consensus pattern (29 bp):
AGTCCCTGTACTTTTATTTTTAAAATTAT
Found at i:54536561 original size:25 final size:25
Alignment explanation
Indices: 54536533--54536596 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 25
54536523 GTATATTGAT
*
54536533 ATATATATTTCTTTTAT-TCACATAC
1 ATATATATTTCTTATATGT-ACATAC
*
54536558 ATATAAATTTCTTATATGTACAT--
1 ATATATATTTCTTATATGTACATAC
54536581 ATATATATTT-TTATAT
1 ATATATATTTCTTATAT
54536597 TTTATATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 6 0.17
23 9 0.26
25 19 0.54
26 1 0.03
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (25 bp):
ATATATATTTCTTATATGTACATAC
Found at i:54541251 original size:16 final size:16
Alignment explanation
Indices: 54541230--54541263 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
54541220 CTTCACTTGA
54541230 AAAAAGA-AATGAAAAG
1 AAAAAGAGAA-GAAAAG
54541246 AAAAAGAGAAGAAAAG
1 AAAAAGAGAAGAAAAG
54541262 AA
1 AA
54541264 GAACGAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (16 bp):
AAAAAGAGAAGAAAAG
Found at i:54542735 original size:87 final size:88
Alignment explanation
Indices: 54542342--54542845 Score: 681
Period size: 88 Copynumber: 5.8 Consensus size: 88
54542332 TTTTCTTGGA
* *
54542342 GTTGTAGCGGGGCAAATTAAAGCTGAAGGCAGCGAATCTTATCTCCCTAGCGTTAAGACCGAAGA
1 GTTGTAGCGGAGCAGATTAAAGCTGAAGGCAGCGAATCTTATCTCCCTAGCGTTAAGACCGAAGA
* * *
54542407 TAACGAGTATTCTTTTCCCTAGT
66 CAACGAGTCTTCTTTTCCCTAGC
* * *
54542430 GTTGTAGCGGAGCAGATTAAAGTTGAAGGCAGCGAATCTTATCTCCCTAGCATTAAGATCGAAGA
1 GTTGTAGCGGAGCAGATTAAAGCTGAAGGCAGCGAATCTTATCTCCCTAGCGTTAAGACCGAAGA
* *
54542495 GAACGAGTATTCTTTTCCCTAGC
66 CAACGAGTCTTCTTTTCCCTAGC
* * * *
54542518 GTTGTAGCGGAGCAGATTAAAGCTGAAGACAGCGAATCTTATCTCCCTGGCATTAAGATCGAAGA
1 GTTGTAGCGGAGCAGATTAAAGCTGAAGGCAGCGAATCTTATCTCCCTAGCGTTAAGACCGAAGA
* *
54542583 TAACGAGTCTTCTTTTCCCT-GAT
66 CAACGAGTCTTCTTTTCCCTAG-C
* * * * * *
54542606 GTTTTAACGGAGTAGATTAAAACTGAAGGCAGTGAATCTTATCTCCTTAGCGTTAAGACCGAAGA
1 GTTGTAGCGGAGCAGATTAAAGCTGAAGGCAGCGAATCTTATCTCCCTAGCGTTAAGACCGAAGA
* *
54542671 CAATGAGTCTTC-TTTCCCTGGC
66 CAACGAGTCTTCTTTTCCCTAGC
* * * * *
54542693 GTTGTAGTGGAGCAGATTAAAGCTGAAGGCAGTGAATTTTATCTCCCTGGCGTTAAGACTGAAGA
1 GTTGTAGCGGAGCAGATTAAAGCTGAAGGCAGCGAATCTTATCTCCCTAGCGTTAAGACCGAAGA
*
54542758 CAGCGAGTCTT-TTTTCCCTAGC
66 CAACGAGTCTTCTTTTCCCTAGC
* * *
54542780 GTTGTAGCGGAGCAGATTAAAGCTGAAAGTAGCGAATCTTATCTCCCTAGCGTTAAGACAGAAGA
1 GTTGTAGCGGAGCAGATTAAAGCTGAAGGCAGCGAATCTTATCTCCCTAGCGTTAAGACCGAAGA
54542845 C
66 C
54542846 GTGAAATAAG
Statistics
Matches: 368, Mismatches: 45, Indels: 7
0.88 0.11 0.02
Matches are distributed among these distances:
87 141 0.38
88 227 0.62
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (88 bp):
GTTGTAGCGGAGCAGATTAAAGCTGAAGGCAGCGAATCTTATCTCCCTAGCGTTAAGACCGAAGA
CAACGAGTCTTCTTTTCCCTAGC
Found at i:54542979 original size:50 final size:50
Alignment explanation
Indices: 54542917--54543486 Score: 413
Period size: 50 Copynumber: 11.4 Consensus size: 50
54542907 TTAGTGTTAT
* * * * *
54542917 AGTGGAATAGATTAAAACTACAACGGCGAATCTTACTTCCCTGGCGGTGT
1 AGTGGAACAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGACGGTGC
* * * **
54542967 AGTGGAACAGATTGAAGCTACAACAGTGAATCTTACTTCCCTAACATTGC
1 AGTGGAACAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGACGGTGC
* * * * * * *
54543017 AAT-TAATTAGATTAAAGCTACAACGGCGAATCTTCCTTCCTTGGCGGTGC
1 AGTGGAA-CAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGACGGTGC
* * * * *
54543067 AGTAGAGCAGATTGAAGCCACAACGGCAAATCTTACTTCCCTGGCGGTGC
1 AGTGGAACAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGACGGTGC
* ** * ** **
54543117 AGTGGAACAGCTTGAAGCTACAACGATGAATCTTGCTTCCCCAACATTGC
1 AGTGGAACAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGACGGTGC
* ** * * * *
54543167 AATTAAAAAGATTGAAGCCACAACGACGAATCTTACTTCCCTGGCGGTGC
1 AGTGGAACAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGACGGTGC
* * * ** ** *
54543217 AGTGGAACAAATTGAAGCTACAACGGTGAATCTTGCTTCCCCAACATTGT
1 AGTGGAACAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGACGGTGC
* ** * * * * ** *
54543267 AATTAAAAAGATTGAAGCCACAACGGTGAATCTTACTTCTCTGGTGGTAC
1 AGTGGAACAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGACGGTGC
* * * * ** *
54543317 AGTGGAACAGATTGAAGCTACAACAGTGAATCTTGCTTCCCCGACATTGT
1 AGTGGAACAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGACGGTGC
** * * * ** *
54543367 AGTTAAAAAGGTTGAACCTACAACAACGAATCTTACTTCCCTGACGGTGT
1 AGTGGAACAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGACGGTGC
* * *** * * *
54543417 AATGGAACAAATTGAAGCTACAATAACGAATCTTACTTTCCTGAAGTTGC
1 AGTGGAACAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGACGGTGC
*
54543467 AGTGGAGCAGATTGAAGCTA
1 AGTGGAACAGATTGAAGCTA
54543487 TAAATTACTG
Statistics
Matches: 389, Mismatches: 129, Indels: 4
0.75 0.25 0.01
Matches are distributed among these distances:
49 2 0.01
50 386 0.99
51 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (50 bp):
AGTGGAACAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGACGGTGC
Found at i:54543135 original size:100 final size:99
Alignment explanation
Indices: 54543025--54543439 Score: 463
Period size: 100 Copynumber: 4.2 Consensus size: 99
54543015 GCAATTAATT
* * * **** * **
54543025 AGATTAAAGCTACAACGGCGAATCTTCCTTCCTTGGCGGTGCAGTAGAGCAGATTGAAGCCACAA
1 AGATTGAAGCTACAACGGTGAATCTTGCTTCCCCAACAGTGCAGTA-AAAAGATTGAAGCCACAA
*
54543090 CGGCAAATCTTACTTCCCTGGCGGTGCAGTGGAAC
65 CGGCGAATCTTACTTCCCTGGCGGTGCAGTGGAAC
* * * *
54543125 AGCTTGAAGCTACAACGATGAATCTTGCTTCCCCAACATTGCAATTAAAAAGATTGAAGCCACAA
1 AGATTGAAGCTACAACGGTGAATCTTGCTTCCCCAACAGTGC-AGTAAAAAGATTGAAGCCACAA
*
54543190 CGACGAATCTTACTTCCCTGGCGGTGCAGTGGAAC
65 CGGCGAATCTTACTTCCCTGGCGGTGCAGTGGAAC
* * * *
54543225 AAATTGAAGCTACAACGGTGAATCTTGCTTCCCCAACATTGTAATTAAAAAGATTGAAGCCACAA
1 AGATTGAAGCTACAACGGTGAATCTTGCTTCCCCAACAGTG-CAGTAAAAAGATTGAAGCCACAA
* * * *
54543290 CGGTGAATCTTACTTCTCTGGTGGTACAGTGGAAC
65 CGGCGAATCTTACTTCCCTGGCGGTGCAGTGGAAC
* * * * *
54543325 AGATTGAAGCTACAACAGTGAATCTTGCTTCCCCGACATTGTAGTTAAAAAGGTTGAA-CCTACA
1 AGATTGAAGCTACAACGGTGAATCTTGCTTCCCCAACAGTGCAG-TAAAAAGATTGAAGCC-ACA
** * * *
54543389 ACAACGAATCTTACTTCCCTGACGGTGTAATGGAAC
64 ACGGCGAATCTTACTTCCCTGGCGGTGCAGTGGAAC
*
54543425 AAATTGAAGCTACAA
1 AGATTGAAGCTACAA
54543440 TAACGAATCT
Statistics
Matches: 270, Mismatches: 41, Indels: 8
0.85 0.13 0.03
Matches are distributed among these distances:
99 3 0.01
100 264 0.98
101 3 0.01
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (99 bp):
AGATTGAAGCTACAACGGTGAATCTTGCTTCCCCAACAGTGCAGTAAAAAGATTGAAGCCACAAC
GGCGAATCTTACTTCCCTGGCGGTGCAGTGGAAC
Found at i:54543197 original size:150 final size:150
Alignment explanation
Indices: 54542936--54543257 Score: 466
Period size: 150 Copynumber: 2.1 Consensus size: 150
54542926 GATTAAAACT
*
54542936 ACAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACAACAGTGAATCTT
1 ACAACGGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAACAGTGAATCTT
* ** * * * *
54543001 ACTTCCCTAACATTGCAATTAATTAGATTAAAGCTACAACGGCGAATCTTCCTTCCTTGGCGGTG
66 ACTTCCCCAACATTGCAATTAAAAAGATTAAAGCCACAACGACGAATCTTACTTCCCTGGCGGTG
* *
54543066 CAGTAGAGCAGATTGAAGCC
131 CAGTAGAACAAATTGAAGCC
* *
54543086 ACAACGGCAAATCTTACTTCCCTGGCGGTGCAGTGGAACAGCTTGAAGCTACAAC-GATGAATCT
1 ACAACGGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAACAG-TGAATCT
* *
54543150 TGCTTCCCCAACATTGCAATTAAAAAGATTGAAGCCACAACGACGAATCTTACTTCCCTGGCGGT
65 TACTTCCCCAACATTGCAATTAAAAAGATTAAAGCCACAACGACGAATCTTACTTCCCTGGCGGT
* *
54543215 GCAGTGGAACAAATTGAAGCT
130 GCAGTAGAACAAATTGAAGCC
* *
54543236 ACAACGGTGAATCTTGCTTCCC
1 ACAACGGCGAATCTTACTTCCC
54543258 CAACATTGTA
Statistics
Matches: 152, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
149 1 0.01
150 151 0.99
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (150 bp):
ACAACGGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAACAGTGAATCTT
ACTTCCCCAACATTGCAATTAAAAAGATTAAAGCCACAACGACGAATCTTACTTCCCTGGCGGTG
CAGTAGAACAAATTGAAGCC
Found at i:54543237 original size:200 final size:199
Alignment explanation
Indices: 54542975--54543484 Score: 560
Period size: 200 Copynumber: 2.5 Consensus size: 199
54542965 GTAGTGGAAC
* ** * ** * * * *
54542975 AGATTGAAGCTACAACAGTGAATCTTACTTCCCTAACATTGCAAT-TAATTAGATTAAAGCTACA
1 AGATTGAACCTACAACAACGAATCTTACTTCCCTGACGGTGCAATGGAA-CAAATTGAAGCTACA
* *
54543039 ACGGCGAATCTTCCTTCCTTGGCGGTGCAGTAGAGCAGATTGAAGCCACAACGGCAAATCTTACT
65 ACGGCGAATCTTCCTTCC-TGACGTTGCAGTAGAGCAGATTGAAGCCACAACGGCAAATCTTACT
* *
54543104 TCCCTGGCGGTGCAGTGGAACAGCTTGAAGCTACAAC-GATGAATCTTGCTTCCCCAACATTGCA
129 TCCCTGGCGGTACAGTGGAACAGATTGAAGCTACAACAG-TGAATCTTGCTTCCCCAACATTGCA
54543168 ATTAAAA
193 ATTAAAA
* * *
54543175 AGATTGAAGCC-ACAACGACGAATCTTACTTCCCTGGCGGTGCAGTGGAACAAATTGAAGCTACA
1 AGATTGAA-CCTACAACAACGAATCTTACTTCCCTGACGGTGCAATGGAACAAATTGAAGCTACA
* * ** * * * ** **
54543239 ACGGTGAATCTTGCTTCCCCAACATTGTAATTA-AAAAGATTGAAGCCACAACGGTGAATCTTAC
65 ACGGCGAATCTTCCTT-CCTGACGTTG-CAGTAGAGCAGATTGAAGCCACAACGGCAAATCTTAC
* * * *
54543303 TTCTCTGGTGGTACAGTGGAACAGATTGAAGCTACAACAGTGAATCTTGCTTCCCCGACATTGTA
128 TTCCCTGGCGGTACAGTGGAACAGATTGAAGCTACAACAGTGAATCTTGCTTCCCCAACATTGCA
*
54543368 GTTAAAA
193 ATTAAAA
* *
54543375 AGGTTGAACCTACAACAACGAATCTTACTTCCCTGACGGTGTAATGGAACAAATTGAAGCTACAA
1 AGATTGAACCTACAACAACGAATCTTACTTCCCTGACGGTGCAATGGAACAAATTGAAGCTACAA
*** * * *
54543440 TAACGAATCTTACTTTCCTGAAGTTGCAGTGGAGCAGATTGAAGC
66 CGGCGAATCTT-CCTTCCTGACGTTGCAGTAGAGCAGATTGAAGC
54543485 TATAAATTAC
Statistics
Matches: 249, Mismatches: 53, Indels: 16
0.78 0.17 0.05
Matches are distributed among these distances:
199 4 0.02
200 234 0.94
201 11 0.04
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.25
Consensus pattern (199 bp):
AGATTGAACCTACAACAACGAATCTTACTTCCCTGACGGTGCAATGGAACAAATTGAAGCTACAA
CGGCGAATCTTCCTTCCTGACGTTGCAGTAGAGCAGATTGAAGCCACAACGGCAAATCTTACTTC
CCTGGCGGTACAGTGGAACAGATTGAAGCTACAACAGTGAATCTTGCTTCCCCAACATTGCAATT
AAAA
Found at i:54543448 original size:100 final size:100
Alignment explanation
Indices: 54543075--54543450 Score: 520
Period size: 100 Copynumber: 3.8 Consensus size: 100
54543065 GCAGTAGAGC
* * **
54543075 AGATTGAAGCCACAACGGCAAATCTTACTTCCCTGGCGGTGCAGTGGAACAGCTTGAAGCTACAA
1 AGATTGAAGCCACAACGACGAATCTTACTTCCCTGGCGGTGCAGTGGAACAAATTGAAGCTACAA
* *
54543140 CGATGAATCTTGCTTCCCCAACATTGCAATTAAAA
66 CAATGAATCTTGCTTCCCCAACATTGTAATTAAAA
54543175 AGATTGAAGCCACAACGACGAATCTTACTTCCCTGGCGGTGCAGTGGAACAAATTGAAGCTACAA
1 AGATTGAAGCCACAACGACGAATCTTACTTCCCTGGCGGTGCAGTGGAACAAATTGAAGCTACAA
**
54543240 CGGTGAATCTTGCTTCCCCAACATTGTAATTAAAA
66 CAATGAATCTTGCTTCCCCAACATTGTAATTAAAA
** * * * *
54543275 AGATTGAAGCCACAACGGTGAATCTTACTTCTCTGGTGGTACAGTGGAACAGATTGAAGCTACAA
1 AGATTGAAGCCACAACGACGAATCTTACTTCCCTGGCGGTGCAGTGGAACAAATTGAAGCTACAA
* * *
54543340 CAGTGAATCTTGCTTCCCCGACATTGTAGTTAAAA
66 CAATGAATCTTGCTTCCCCAACATTGTAATTAAAA
* * * * *
54543375 AGGTTGAA-CCTACAACAACGAATCTTACTTCCCTGACGGTGTAATGGAACAAATTGAAGCTACA
1 AGATTGAAGCC-ACAACGACGAATCTTACTTCCCTGGCGGTGCAGTGGAACAAATTGAAGCTACA
* *
54543439 ATAACGAATCTT
65 ACAATGAATCTT
54543451 ACTTTCCTGA
Statistics
Matches: 246, Mismatches: 29, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
99 2 0.01
100 244 0.99
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (100 bp):
AGATTGAAGCCACAACGACGAATCTTACTTCCCTGGCGGTGCAGTGGAACAAATTGAAGCTACAA
CAATGAATCTTGCTTCCCCAACATTGTAATTAAAA
Found at i:54543617 original size:44 final size:45
Alignment explanation
Indices: 54543537--54543745 Score: 196
Period size: 44 Copynumber: 4.7 Consensus size: 45
54543527 GATCTTATCA
* * * * *
54543537 AACCTTATCTCTCTGAAGTTGTAGTAGAGCAGGTTGAA-ATCA-CT
1 AACCTTATCTCCCTGAAGTTGCAGTGGAGCAAGTTGAAGAT-AGCG
* *
54543581 AACCTTATCCCCCTGAAGTTGCAGTGGGGCAAGTTGAAGATAGCG
1 AACCTTATCTCCCTGAAGTTGCAGTGGAGCAAGTTGAAGATAGCG
** * * *
54543626 AGTCTTATCTCCCTGAAGTTGCAGTGGAGC-AGACTGAAGCTA-CT
1 AACCTTATCTCCCTGAAGTTGCAGTGGAGCAAG-TTGAAGATAGCG
* * *
54543670 AATCC-TATCTCCCTGAAGTTACAGTGGAGC-AGACTGAAGATAGCA
1 AA-CCTTATCTCCCTGAAGTTGCAGTGGAGCAAG-TTGAAGATAGCG
*
54543715 AACCTTATCTCTCTGAAGTTGCAGTGGAGCA
1 AACCTTATCTCCCTGAAGTTGCAGTGGAGCA
54543746 GATTGAGGAT
Statistics
Matches: 137, Mismatches: 21, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
44 74 0.54
45 63 0.46
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (45 bp):
AACCTTATCTCCCTGAAGTTGCAGTGGAGCAAGTTGAAGATAGCG
Found at i:54543644 original size:45 final size:45
Alignment explanation
Indices: 54543535--54543756 Score: 209
Period size: 45 Copynumber: 5.0 Consensus size: 45
54543525 TAGATCTTAT
* * * * **
54543535 CAAACCTTATCTCTCTGAAGTTGTAGTAGAGCAGGTTGAA-ATCA-
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAT-AG
* * * * *
54543579 CTAACCTTATCCCCCTGAAGTTGCAGTGGGGCA-AGTTGAAGATAG
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CTGAAGATAG
* * *
54543624 CGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGCTA-
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAG
* * *
54543668 CTAATCCTATCTCCCTGAAGTTACAGTGGAGCAGACTGAAGATAG
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAG
* * * *
54543713 CAAACCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAGGATA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATA
54543757 CAAGTCATAT
Statistics
Matches: 147, Mismatches: 26, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
44 72 0.49
45 74 0.50
46 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (45 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAG
Found at i:54543656 original size:89 final size:90
Alignment explanation
Indices: 54543535--54543751 Score: 271
Period size: 89 Copynumber: 2.4 Consensus size: 90
54543525 TAGATCTTAT
* * * *
54543535 CAAACCTTATCTCTCTGAAGTTGTAGTAGAGCAGGTTGAAATC-ACTAA-CCTTATCCCCCTGAA
1 CAAACCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAAGCTACTAATCC-TATCCCCCTGAA
* * *
54543598 GTTGCAGTGGGGCA-AGTTGAAGATAG
65 GTTACAGTGGAGCAGA-CTGAAGATAG
* ** * * *
54543624 CGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTG-AAGCTACTAATCCTATCTCCCTGAAG
1 CAAACCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAAGCTACTAATCCTATCCCCCTGAAG
54543688 TTACAGTGGAGCAGACTGAAGATAG
66 TTACAGTGGAGCAGACTGAAGATAG
54543713 CAAACCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGA
1 CAAACCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGA
54543752 GGATACAAGT
Statistics
Matches: 106, Mismatches: 18, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
88 3 0.03
89 100 0.94
90 3 0.03
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (90 bp):
CAAACCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAAGCTACTAATCCTATCCCCCTGAAG
TTACAGTGGAGCAGACTGAAGATAG
Found at i:54544968 original size:46 final size:46
Alignment explanation
Indices: 54544874--54545025 Score: 220
Period size: 46 Copynumber: 3.4 Consensus size: 46
54544864 TACGTATGAT
* * * *
54544874 CACTTATCAC-TTGTC-CCTGATTAGATAAGTGTAACT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
54544917 CACTTATCATTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
54544963 CACTTATCACTTTGTCACTTGATCAGATAAGGGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
54545009 CACTTATCACTTTGTCA
1 CACTTATCACTTTGTCA
54545026 TTTGTCACTG
Statistics
Matches: 98, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
43 9 0.09
44 5 0.05
45 18 0.18
46 66 0.67
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:54548655 original size:23 final size:24
Alignment explanation
Indices: 54548621--54548674 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
54548611 TATATATATT
54548621 TATTTCTTTTAT-T-CACATACATA
1 TATTT-TTTTATATGCACATACATA
* *
54548644 TATTTTTCTTATATGTACATATATA
1 TATTTTT-TTATATGCACATACATA
54548669 TATTTT
1 TATTTT
54548675 ATATTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 2 0.08
23 9 0.35
24 1 0.04
25 14 0.54
ACGTcount: A:0.30, C:0.11, G:0.02, T:0.57
Consensus pattern (24 bp):
TATTTTTTTATATGCACATACATA
Found at i:54548676 original size:21 final size:21
Alignment explanation
Indices: 54548638--54548678 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
54548628 TTTATTCACA
*
54548638 TACATATATTTTTCTTATATG
1 TACATATATTATTCTTATATG
54548659 TACATATATATATT-TTATAT
1 TACATATAT-TATTCTTATAT
54548679 TTTTTTATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.56
Consensus pattern (21 bp):
TACATATATTATTCTTATATG
Found at i:54555074 original size:16 final size:15
Alignment explanation
Indices: 54555032--54555078 Score: 55
Period size: 13 Copynumber: 3.3 Consensus size: 15
54555022 AGCTCAATTC
54555032 CAAA-ATATTTTTT-
1 CAAACATATTTTTTA
*
54555045 C-AGCATATTTTTTA
1 CAAACATATTTTTTA
54555059 CAAACATATGTTTTTA
1 CAAACATAT-TTTTTA
54555075 CAAA
1 CAAA
54555079 TGATTTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
12 1 0.04
13 10 0.36
14 1 0.04
15 6 0.21
16 10 0.36
ACGTcount: A:0.38, C:0.13, G:0.04, T:0.45
Consensus pattern (15 bp):
CAAACATATTTTTTA
Found at i:54559415 original size:3 final size:3
Alignment explanation
Indices: 54559407--54559434 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
54559397 TTTGCATATC
54559407 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
54559435 CAATATCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:54560852 original size:36 final size:38
Alignment explanation
Indices: 54560806--54560884 Score: 103
Period size: 36 Copynumber: 2.2 Consensus size: 38
54560796 TTTTAAATCC
*
54560806 AATAAAAGTAAAAAT-ACTAG-AA-ATAACTTAAATTGA
1 AATAAAAGTAAAAATAAATAGAAACATAAC-TAAATTGA
*
54560842 AATAACAGTAAAAATAAATAGAAACATAACTAAATTG-
1 AATAAAAGTAAAAATAAATAGAAACATAACTAAATTGA
54560879 AATAAA
1 AATAAA
54560885 CTAATGGGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
36 14 0.38
37 9 0.24
38 9 0.24
39 5 0.14
ACGTcount: A:0.63, C:0.06, G:0.08, T:0.23
Consensus pattern (38 bp):
AATAAAAGTAAAAATAAATAGAAACATAACTAAATTGA
Found at i:54566608 original size:4 final size:4
Alignment explanation
Indices: 54566599--54566623 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
54566589 AGATTCTCTT
54566599 TTTG TTTG TTTG TTTG TTTG TTTG T
1 TTTG TTTG TTTG TTTG TTTG TTTG T
54566624 ATGGTTGGCA
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:0.00, C:0.00, G:0.24, T:0.76
Consensus pattern (4 bp):
TTTG
Found at i:54568558 original size:12 final size:12
Alignment explanation
Indices: 54568543--54568567 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54568533 GATTTTTTCA
54568543 CATAATTTTTGT
1 CATAATTTTTGT
54568555 CATAATTTTTGT
1 CATAATTTTTGT
54568567 C
1 C
54568568 GATATTGGAA
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:0.24, C:0.12, G:0.08, T:0.56
Consensus pattern (12 bp):
CATAATTTTTGT
Found at i:54570855 original size:6 final size:7
Alignment explanation
Indices: 54570840--54570867 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
54570830 TTTTAATAAA
54570840 TTTTATT
1 TTTTATT
54570847 TTTTATT
1 TTTTATT
54570854 TTTTATT
1 TTTTATT
54570861 TTTTATT
1 TTTTATT
54570868 AAAATAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTATT
Found at i:54571146 original size:14 final size:14
Alignment explanation
Indices: 54571121--54571155 Score: 61
Period size: 14 Copynumber: 2.4 Consensus size: 14
54571111 AGAAGGAAAG
54571121 AGAAAGGGAGAAGAA
1 AGAAA-GGAGAAGAA
54571136 AGAAAGGAGAAGAA
1 AGAAAGGAGAAGAA
54571150 AGAAAG
1 AGAAAG
54571156 AAAAAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (14 bp):
AGAAAGGAGAAGAA
Found at i:54571162 original size:14 final size:14
Alignment explanation
Indices: 54571131--54571164 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
54571121 AGAAAGGGAG
* *
54571131 AAGAAAGAAAGGAG
1 AAGAAAGAAAGAAA
54571145 AAGAAAGAAAGAAA
1 AAGAAAGAAAGAAA
54571159 AAGAAA
1 AAGAAA
54571165 AAAAATGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (14 bp):
AAGAAAGAAAGAAA
Found at i:54571328 original size:25 final size:26
Alignment explanation
Indices: 54571282--54571330 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
54571272 GTTTTTAATT
*
54571282 TATTTTAAAGTTATTTTGTTAGTTAC
1 TATTATAAAGTTATTTTGTTAGTTAC
54571308 TATTATAAA-TTA-TTTGTTTAGTT
1 TATTATAAAGTTATTTTG-TTAGTT
54571331 TAATGTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
25 9 0.43
26 8 0.38
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.59
Consensus pattern (26 bp):
TATTATAAAGTTATTTTGTTAGTTAC
Found at i:54575301 original size:33 final size:34
Alignment explanation
Indices: 54575258--54575336 Score: 83
Period size: 33 Copynumber: 2.4 Consensus size: 34
54575248 GAGCTCGAAT
* * * *
54575258 GAGTGAAGTACTGCA-GTGGATATGGGTCAG-GAG
1 GAGTGGAGTACTGAAGGTGGATACGAG-CAGAGAG
*
54575291 GAGTGGAGTACT-AAGGTGGATACGAGCTGAGAG
1 GAGTGGAGTACTGAAGGTGGATACGAGCAGAGAG
54575324 GAGTGGAGTACTG
1 GAGTGGAGTACTG
54575337 TGATGGTAGT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
32 3 0.08
33 35 0.92
ACGTcount: A:0.28, C:0.09, G:0.43, T:0.20
Consensus pattern (34 bp):
GAGTGGAGTACTGAAGGTGGATACGAGCAGAGAG
Found at i:54577302 original size:108 final size:108
Alignment explanation
Indices: 54577151--54577946 Score: 872
Period size: 108 Copynumber: 7.3 Consensus size: 108
54577141 CATTATAACG
* * * *
54577151 AATCACAATACACATTAAACT-GA-ACAAATAATTTATAACCTAATCATAAATTACTAACAAAAT
1 AATCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAATCATAAATTACTAACAAAAT
54577214 AACTTTAAAATAATTTAAAAAAACAAAAAAAATATTCATAAAA
66 AACTTTAAAATAATTTAAAAAAACAAAAAAAATATTCATAAAA
* * *
54577257 AATCACAATAAATACTAAACTAAACACAAGCAATTTATAATCTAATCATAAATTACTAACAAAAT
1 AATCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAATCATAAATTACTAACAAAAT
* * *** * *
54577322 AAATTTAAAATCATTTAAAAAACACAAAAATTTTCATTTATAACA
66 AACTTTAAAATAATTTAAAAAA-ACAAAAAAAAT-ATTCATAAAA
* * * * * * *
54577367 AGTCACAATAAACAATAAACTAAATACAAAAAAATTATAATCTAATCATAAATTGCTAACAAAAT
1 AATCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAATCATAAATTACTAACAAAAT
* *
54577432 AACTTTAAAATAATTTTAAAAAACAAAAAAAAATACATTCGTAAAA
66 AACTTTAAAATAATTTAAAAAAAC-AAAAAAAAT--ATTCATAAAA
* * *
54577478 GATCACAATAAACACTAAACTAAATACAAACAATTTATAACCTAATCATAAATTACTAACAAAAC
1 AATCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAATCATAAATTACTAACAAAAT
* * *
54577543 AACATTCAAATAA-TTAAAAAAACAAAAAAAAAAATTACATTAATAAAA
66 AACTTTAAAATAATTTAAAAAAAC---AAAAAAAA-T--ATTCATAAAA
* * *
54577591 AATCACAATAAACATTAAACTAAAGACAAACAATTTATAACCTAACCATAAATTACTAACAAAAT
1 AATCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAATCATAAATTACTAACAAAAT
* * * *
54577656 GACTATAAAATAATTTAAAAAATATAAAAAAATTACATTCATAAAA
66 AACTTTAAAATAATTTAAAAAA-ACAAAAAAA--ATATTCATAAAA
* * *
54577702 AATCAC-A-GAGCACTAAACTAAACACAAACAATTTATAACCTAACCATAAATTACTAACAAAAT
1 AATCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAATCATAAATTACTAACAAAAT
* * * *
54577765 AACTATAAAATAATTAAAAAAAACAAAAAAATTACATTAATAAAA
66 AACTTTAAAATAATTTAAAAAAACAAAAAAA--ATATTCATAAAA
* * * *
54577810 ATTCAC-A-AAACGCTAAACTAAACACAAACAATTTAGAATCTAATCATAAATTACTAACAAAAT
1 AATCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAATCATAAATTACTAACAAAAT
* * * * *
54577873 AACTTTAAAATAATTTTAAAATATAAAAAAATTTACATTCATAACA
66 AACTTTAAAATAATTTAAAAAAACAAAAAAA---ATATTCATAAAA
* *
54577919 AATCAC-A-AATCACTAAACTAAATACAAA
1 AATCACAATAAACACTAAACTAAACACAAA
54577947 AAAAAAAAAA
Statistics
Matches: 594, Mismatches: 82, Indels: 25
0.85 0.12 0.04
Matches are distributed among these distances:
106 18 0.03
107 1 0.00
108 160 0.27
109 118 0.20
110 100 0.17
111 91 0.15
112 16 0.03
113 80 0.13
114 9 0.02
115 1 0.00
ACGTcount: A:0.59, C:0.14, G:0.02, T:0.25
Consensus pattern (108 bp):
AATCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAATCATAAATTACTAACAAAAT
AACTTTAAAATAATTTAAAAAAACAAAAAAAATATTCATAAAA
Found at i:54577935 original size:217 final size:219
Alignment explanation
Indices: 54577133--54577946 Score: 977
Period size: 224 Copynumber: 3.7 Consensus size: 219
54577123 AATCATAAAT
* ** * * * *
54577133 AAAATTTACATT-ATAACGAATCACAATACACATTAAACT-GA-ACAAATAATTTATAACCTAAT
1 AAAAATTACATTAATAAAAAATCACAATAAACAATAAACTAAACACAAACAATTTATAACCTAAT
*
54577195 CATAAATTACTAACAAAATAACTTTAAAATAATTTAAAAAAACAAAAAAA--ATATTCATAAAAA
66 CATAAATTACTAACAAAATAACTTTAAAATAATTTAAAAAAACAAAAAAATTACATTCATAAAAA
* *
54577258 ATCACAATAAAT-ACTAAACTAAACACAAGCAATTTATAATCTAATCATAAATTACTAACAAAAT
131 ATCAC-A-AAATCACTAAACTAAACACAAACAATTTATAACCTAATCATAAATTACTAACAAAAT
* * * *
54577322 AAATTTAAAATCATT-TAAAAAACACA
194 AACTATAAAATAATTAAAAAAAACA-A
* * * * * * * * *
54577348 AAAATTTTCATTTATAACAAGTCACAATAAACAATAAACTAAATACAAAAAAATTATAATCTAAT
1 AAAAATTACATTAATAAAAAATCACAATAAACAATAAACTAAACACAAACAATTTATAACCTAAT
* * * *
54577413 CATAAATTGCTAACAAAATAACTTTAAAATAATTTTAAAAAACAAAAAAAAATACATTCGTAAAA
66 CATAAATTACTAACAAAATAACTTTAAAATAATTTAAAAAAAC-AAAAAAATTACATTCATAAAA
* * * *
54577478 GATCACAATAAACACTAAACTAAATACAAACAATTTATAACCTAATCATAAATTACTAACAAAAC
130 AATCACAA-AATCACTAAACTAAACACAAACAATTTATAACCTAATCATAAATTACTAACAAAAT
* *
54577543 AAC-ATTCAAATAATTAAAAAAACAAAAAA
194 AACTA-TAAAATAATT--AAAAA-AAACAA
* * *
54577572 AAAAATTACATTAATAAAAAATCACAATAAACATTAAACTAAAGACAAACAATTTATAACCTAAC
1 AAAAATTACATTAATAAAAAATCACAATAAACAATAAACTAAACACAAACAATTTATAACCTAAT
* * *
54577637 CATAAATTACTAACAAAATGACTATAAAATAATTTAAAAAATATAAAAAAATTACATTCATAAAA
66 CATAAATTACTAACAAAATAACTTTAAAATAATTTAAAAAA-ACAAAAAAATTACATTCATAAAA
* * *
54577702 AATCAC-AGAGCACTAAACTAAACACAAACAATTTATAACCTAACCATAAATTACTAACAAAATA
130 AATCACAAAATCACTAAACTAAACACAAACAATTTATAACCTAATCATAAATTACTAACAAAATA
54577766 ACTATAAAATAATTAAAAAAAACAA
195 ACTATAAAATAATTAAAAAAAACAA
* ** * *
54577791 AAAAATTACATTAATAAAAATTCAC-A-AAACGCTAAACTAAACACAAACAATTTAGAATCTAAT
1 AAAAATTACATTAATAAAAAATCACAATAAACAATAAACTAAACACAAACAATTTATAACCTAAT
* * * *
54577854 CATAAATTACTAACAAAATAACTTTAAAATAATTTTAAAATATAAAAAAATTTACATTCATAACA
66 CATAAATTACTAACAAAATAACTTTAAAATAATTTAAAAAAACAAAAAAA-TTACATTCATAAAA
*
54577919 AATCAC-AAATCACTAAACTAAATACAAA
130 AATCACAAAATCACTAAACTAAACACAAA
54577947 AAAAAAAAAA
Statistics
Matches: 517, Mismatches: 66, Indels: 30
0.84 0.11 0.05
Matches are distributed among these distances:
215 11 0.02
216 32 0.06
217 107 0.21
218 60 0.12
219 37 0.07
220 8 0.02
221 73 0.14
222 63 0.12
223 2 0.00
224 119 0.23
225 5 0.01
ACGTcount: A:0.59, C:0.14, G:0.02, T:0.25
Consensus pattern (219 bp):
AAAAATTACATTAATAAAAAATCACAATAAACAATAAACTAAACACAAACAATTTATAACCTAAT
CATAAATTACTAACAAAATAACTTTAAAATAATTTAAAAAAACAAAAAAATTACATTCATAAAAA
ATCACAAAATCACTAAACTAAACACAAACAATTTATAACCTAATCATAAATTACTAACAAAATAA
CTATAAAATAATTAAAAAAAACAA
Found at i:54578059 original size:4 final size:4
Alignment explanation
Indices: 54578014--54578038 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
54578004 CATACATACA
54578014 TTCT TTCT TTCT TTCT TTCT TTCT T
1 TTCT TTCT TTCT TTCT TTCT TTCT T
54578039 CTCCTTCCTC
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:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTCT
Found at i:54581583 original size:16 final size:17
Alignment explanation
Indices: 54581547--54581585 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
54581537 TATGTTATAT
* *
54581547 AAGTGTCATAGGTATTA
1 AAGTGTCATAGGAAATA
54581564 AAGTGTCAT-GGAAATA
1 AAGTGTCATAGGAAATA
54581580 AAGTGT
1 AAGTGT
54581586 AGATACCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.38, C:0.05, G:0.26, T:0.31
Consensus pattern (17 bp):
AAGTGTCATAGGAAATA
Found at i:54585692 original size:17 final size:17
Alignment explanation
Indices: 54585672--54585730 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 17
54585662 TTAATAGATA
54585672 ATTGAAGTGAATATGAT
1 ATTGAAGTGAATATGAT
*
54585689 ATTG-AGTTGATTAATAGAT
1 ATTGAAG-TGAAT-AT-GAT
*
54585708 AATTGAAGTGAATGTGAT
1 -ATTGAAGTGAATATGAT
54585726 ATTGA
1 ATTGA
54585731 GTTATGAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
16 2 0.06
17 13 0.38
18 5 0.15
19 4 0.12
20 8 0.24
21 2 0.06
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.37
Consensus pattern (17 bp):
ATTGAAGTGAATATGAT
Found at i:54585700 original size:37 final size:37
Alignment explanation
Indices: 54585659--54585733 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
54585649 AATTAATGAA
54585659 TGATTAATAGATAATTGAAGTGAATATGATATTGAGT
1 TGATTAATAGATAATTGAAGTGAATATGATATTGAGT
*
54585696 TGATTAATAGATAATTGAAGTGAATGTGATATTGAGT
1 TGATTAATAGATAATTGAAGTGAATATGATATTGAGT
54585733 T
1 T
54585734 ATGAAATGCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.39, C:0.00, G:0.23, T:0.39
Consensus pattern (37 bp):
TGATTAATAGATAATTGAAGTGAATATGATATTGAGT
Found at i:54585712 original size:20 final size:19
Alignment explanation
Indices: 54585659--54585718 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
54585649 AATTAATGAA
54585659 TGATTAATAGATAATTGAAG
1 TGATTAATAGATAATTG-AG
*
54585679 TGAAT-AT-GAT-ATTGAG
1 TGATTAATAGATAATTGAG
54585695 TTGATTAATAGATAATTGAAG
1 -TGATTAATAGATAATTG-AG
54585716 TGA
1 TGA
54585719 ATGTGATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
16 2 0.06
17 8 0.24
18 5 0.15
19 5 0.15
20 11 0.33
21 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.37
Consensus pattern (19 bp):
TGATTAATAGATAATTGAG
Found at i:54585747 original size:20 final size:21
Alignment explanation
Indices: 54585724--54585762 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
54585714 AGTGAATGTG
*
54585724 ATATTGAG-TTATGAAATGCA
1 ATATTAAGATTATGAAATGCA
54585744 ATATTAAGATTATGAAATG
1 ATATTAAGATTATGAAATG
54585763 TGATTTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.44, C:0.03, G:0.18, T:0.36
Consensus pattern (21 bp):
ATATTAAGATTATGAAATGCA
Found at i:54585931 original size:75 final size:75
Alignment explanation
Indices: 54585793--54586122 Score: 372
Period size: 75 Copynumber: 4.4 Consensus size: 75
54585783 TGAGTAATTG
* *
54585793 ATATTGTCGGT-TCATCCGACTAGCGCTGGGCGC-AATCATCGTT-GTTCATCCAACTAGAGCTG
1 ATATCGTCGGTAT-ATCCGACTAGCGCTGGGCGCAAAT-ATCGTTGGTTTATCCAACTAGAGCTG
54585855 GGCTCACAATTAT
64 GGCTCAC-ATTAT
* * * * *
54585868 A-ATCGTTGGTATA-CTCGACTAGCACTAGGTGCAAATATCGGTGGTTTATCCAACTAGAGCTGG
1 ATATCGTCGGTATATC-CGACTAGCGCTGGGCGCAAATATCGTTGGTTTATCCAACTAGAGCTGG
* *
54585931 GCTCACTTTTT
65 GCTCACATTAT
*
54585942 ATATCGTCGGTTTATCCGACTAGCGCTGGGCGCAAATATCGTTGGTTTATCCAACTAGAGCTGGG
1 ATATCGTCGGTATATCCGACTAGCGCTGGGCGCAAATATCGTTGGTTTATCCAACTAGAGCTGGG
54586007 CTCACTATT-T
66 CTCAC-ATTAT
* * * * * *
54586017 ATATTGTCGGTTTATCCAACTAGCGCTGGGCGCAAATATCATTGGTTTATCCAACCAGAGTTGGG
1 ATATCGTCGGTATATCCGACTAGCGCTGGGCGCAAATATCGTTGGTTTATCCAACTAGAGCTGGG
*
54586082 CTCAC-TGAT
66 CTCACATTAT
*
54586091 -TATTCGTTGGTATATCTC-ACTAGCGCTGGGCG
1 ATA-TCGTCGGTATATC-CGACTAGCGCTGGGCG
54586123 TAACTTCCGT
Statistics
Matches: 220, Mismatches: 25, Indels: 21
0.83 0.09 0.08
Matches are distributed among these distances:
73 4 0.02
74 56 0.25
75 157 0.71
76 3 0.01
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (75 bp):
ATATCGTCGGTATATCCGACTAGCGCTGGGCGCAAATATCGTTGGTTTATCCAACTAGAGCTGGG
CTCACATTAT
Done.