Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold60
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: 3815296
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 18690 characters in sequence are not A, C, G, or T
File 4 of 21
Found at i:472637 original size:84 final size:84
Alignment explanation
Indices: 472482--472646 Score: 201
Period size: 84 Copynumber: 2.0 Consensus size: 84
472472 CATTTTCCAC
* * * *
472482 TTGCAACTCATTTCTTTTCTCCTCTAATTCATTTATTTTCTTTTTAAAAGAATTATTTTCTAAAC
1 TTGCAACTCATTTCTATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAATTATTCTCTAAAC
472547 TCATTGATTTACTTTCATT
66 TCATTGATTTACTTTCATT
* *
472566 TTGCAACTC-TTTCATATTCTTCTCTAATTCACTTAATTTC-TTTT-CAAGAATATCATTCTCTA
1 TTGCAACTCATTTC-TATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAAT-T-ATTCTCTA
* * *
472628 CACTTATTGATTTATTTTC
63 AACTCATTGATTTACTTTC
472647 TTCTTTGAGT
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
82 6 0.09
83 9 0.13
84 54 0.78
ACGTcount: A:0.25, C:0.19, G:0.04, T:0.52
Consensus pattern (84 bp):
TTGCAACTCATTTCTATTCTCCTCTAATTCACTTAATTTCTTTTTAAAAGAATTATTCTCTAAAC
TCATTGATTTACTTTCATT
Found at i:474717 original size:13 final size:13
Alignment explanation
Indices: 474699--474724 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
474689 CAATTTTTGG
474699 TGTATCGATACAT
1 TGTATCGATACAT
474712 TGTATCGATACAT
1 TGTATCGATACAT
474725 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:474736 original size:32 final size:33
Alignment explanation
Indices: 474679--474742 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
474669 TACAAGCCAA
**
474679 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
474712 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
474743 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:474749 original size:19 final size:18
Alignment explanation
Indices: 474679--474749 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
474669 TACAAGCCAA
474679 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
474699 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
474712 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
474731 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
474750 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:474808 original size:20 final size:20
Alignment explanation
Indices: 474783--474835 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
474773 ACATCTTTTT
474783 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
474803 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
474823 CATGTATCGATAC
1 CATGTATCGATAC
474836 TTTGAATTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACATTGCAA
Found at i:475477 original size:23 final size:24
Alignment explanation
Indices: 475440--475489 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
475430 AAATAAATTT
475440 TTTTATCTAGAGGGAGAAAATCTC
1 TTTTATCTAGAGGGAGAAAATCTC
*
475464 TTTTATCTAG-GGGAGAAAATTTC
1 TTTTATCTAGAGGGAGAAAATCTC
475487 TTT
1 TTT
475490 AACTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 15 0.60
24 10 0.40
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (24 bp):
TTTTATCTAGAGGGAGAAAATCTC
Found at i:475524 original size:13 final size:13
Alignment explanation
Indices: 475506--475530 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
475496 TTATCAAGGG
475506 GGAGAAATTTTTC
1 GGAGAAATTTTTC
475519 GGAGAAATTTTT
1 GGAGAAATTTTT
475531 TAACGAAAGC
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:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GGAGAAATTTTTC
Found at i:476132 original size:13 final size:13
Alignment explanation
Indices: 476114--476140 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
476104 ACATTATGCT
476114 TTGTATCGATACA
1 TTGTATCGATACA
476127 TTGTATCGATACA
1 TTGTATCGATACA
476140 T
1 T
476141 GATCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:476137 original size:33 final size:32
Alignment explanation
Indices: 476095--476159 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
476085 CACACCCAGA
* *
476095 TGTATCGATACATTATGCTTTGTATCGATACAT
1 TGTATCGATACATGAT-CATTGTATCGATACAT
476128 TGTATCGATACATGATCATTGTATCGATACAT
1 TGTATCGATACATGATCATTGTATCGATACAT
476160 GGACAATTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATGATCATTGTATCGATACAT
Found at i:476174 original size:20 final size:20
Alignment explanation
Indices: 476125--476180 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 20
476115 TGTATCGATA
476125 CATTGTATCGATACAT-GAT
1 CATTGTATCGATACATGGAT
476144 CATTGTATCGATACATGGA-
1 CATTGTATCGATACATGGAT
*
476163 CAATTGTGTCGATACATG
1 C-ATTGTATCGATACATG
476181 AAACTGGCAG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 17 0.50
20 17 0.50
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (20 bp):
CATTGTATCGATACATGGAT
Found at i:484726 original size:154 final size:154
Alignment explanation
Indices: 484437--484797 Score: 397
Period size: 154 Copynumber: 2.3 Consensus size: 154
484427 TCGAAGATCT
* *
484437 TAAAGGACTTAAAAAGATTATAGAAGGGATGAACCTATCCTAATTACCCACCTTGGGCATAAAAG
1 TAAAGGACTTAAAAAGATTATAGAAGAGATGAACCTATCCTAAATACCCACCTTGGGCATAAAAG
*
484502 CAAACCCGATGACAACCTAGAACTCGGTTTTAAAAAAATACTAAAATACCCATAAGGGACACCTT
66 CAAACCCGATGACAACCTAGAACTCGGTTCTAAAAAAATACTAAAATACCCATAAGGGACACCTT
484567 CGACGTAAAAATACTTGGTACCAC
131 CGACGTAAAAATACTTGGTACCAC
* ** *
484591 TAAAGGGCTTAAAAAGGA-TATAGCTGAGATGAACCTATCCTAAATACCCACCTTTGGCATAAAA
1 TAAAGGACTTAAAAA-GATTATAGAAGAGATGAACCTATCCTAAATACCCACCTTGGGCATAAAA
* * * * * * * * **
484655 GTAGACCTGGTGACAACCTAGGATTCGGTTCTAAAAAATTAC-AAAA-ACGTTCC-TAGGGGATG
65 GCAAACCCGATGACAACCTAGAACTCGGTTCTAAAAAAATACTAAAATAC---CCATAAGGGACA
* * * * ** *
484717 CCTTTGACGTAGAAGTGCCCGGTACCCC
127 CCTTCGACGTAAAAATACTTGGTACCAC
* * * *
484745 TAAACTGACTTAAATAGATTATAGAAGGGATGAACCTATCTTAAATACCCACC
1 TAAA-GGACTTAAAAAGATTATAGAAGAGATGAACCTATCCTAAATACCCACC
484798 ATTTAAAAAA
Statistics
Matches: 170, Mismatches: 31, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
152 2 0.01
153 4 0.02
154 122 0.72
155 42 0.25
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Consensus pattern (154 bp):
TAAAGGACTTAAAAAGATTATAGAAGAGATGAACCTATCCTAAATACCCACCTTGGGCATAAAAG
CAAACCCGATGACAACCTAGAACTCGGTTCTAAAAAAATACTAAAATACCCATAAGGGACACCTT
CGACGTAAAAATACTTGGTACCAC
Found at i:484968 original size:201 final size:200
Alignment explanation
Indices: 484599--484999 Score: 506
Period size: 201 Copynumber: 2.0 Consensus size: 200
484589 ACTAAAGGGC
* * * * * *
484599 TTAAAAAGGATATAGCTGAGATGAACCTATCCTAAATACCCACCTTTGGCATAAAAGTAGACCTG
1 TTAAAAAAGATATAGCTAAGATGAACCCACCCTAAATACCCACCTTTGGCATAAAAGCAAACCTG
* * * * *
484664 GTGACAACCTAGGATTCGGTTCTAAAAAATTACAAAAACGTTCCTAGGGGATGCCTTTGACGTAG
66 GTGACAACCTAGGACTCGGTTCTAAAAAATTACAAAAACGTTCCTAGAGGATGACTTTAACATAG
* * * * *
484729 AAGTGCCCGGTACCCCTAAACTGACTTAAATAGATTATAGAAGGGATGAACCTATCTTAAATACC
131 AAGTGCCCGATACCCATAAACTGACATAAATAGATTATA-AAGCGATGAACCTATCCTAAATACC
484794 CACCAT
195 CACCAT
*
484800 TTAAAAAAGATATAGTTAAGATGAACCCACCCTAAATACCCACCTTTGGCATAAAAGCAAA-CTC
1 TTAAAAAAGATATAGCTAAGATGAACCCACCCTAAATACCCACCTTTGGCATAAAAGCAAACCT-
* * *
484864 GGTGACAACCTAGGACTCGGTTCTAAAAAATTACGAAGAA-GTTTCTATAGGAT-ACTTTCAACA
65 GGTGACAACCTAGGACTCGGTTCTAAAAAATTAC-AAAAACGTTCCTAGAGGATGACTTT-AACA
** *
484927 TAGAAGTGCTTGATACCCATAAAC-GAACATAAA-ACGATTATAAAGCGATGAACGTATCCTAAA
128 TAGAAGTGCCCGATACCCATAAACTG-ACATAAATA-GATTATAAAGCGATGAACCTATCCTAAA
484990 TACCCACCAT
191 TACCCACCAT
485000 CGGCATAAAA
Statistics
Matches: 172, Mismatches: 23, Indels: 11
0.83 0.11 0.05
Matches are distributed among these distances:
200 36 0.21
201 132 0.77
202 4 0.02
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.24
Consensus pattern (200 bp):
TTAAAAAAGATATAGCTAAGATGAACCCACCCTAAATACCCACCTTTGGCATAAAAGCAAACCTG
GTGACAACCTAGGACTCGGTTCTAAAAAATTACAAAAACGTTCCTAGAGGATGACTTTAACATAG
AAGTGCCCGATACCCATAAACTGACATAAATAGATTATAAAGCGATGAACCTATCCTAAATACCC
ACCAT
Found at i:485303 original size:155 final size:152
Alignment explanation
Indices: 484819--485824 Score: 769
Period size: 156 Copynumber: 6.5 Consensus size: 152
484809 ATATAGTTAA
* * * *
484819 GATGAACCCACCCTAAATACCCACCTTTGGCATAAAAGCAAACTCGGTGACAACCTAGGACTCGG
1 GATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCAGACTCGGTGACAACCTAGGACTCGG
* * ** * * * * * *
484884 TTCTAAAAAATTACGAAGAAGTTTCTATAGGATA-CTTTCAACATAGAAGTGCTTGATACCCATA
66 TTCTAAAAAATTATGAA-AAATCCCTAAAGGATACCTTT-AACGTAAAAGTACCTGATACCCTTA
* * *
484948 AACGAACATAAAACGATTAT-AAAGC
129 AA-G-ACTTAAAAAGATTATAAAAGG
* * * * * *
484973 GATGAACGTATCCTAAATACCCACCATCGGCATAAAAGCAAACCCGATGATAACCTAGGACTCGG
1 GATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCAGACTCGGTGACAACCTAGGACTCGG
** * * * *
485038 TTCTAAAAAA-TACT--AAAATGCCCTTAGGGGATACCTTTGATGTAAAAGTACTTGGTACCAC-
66 TTCTAAAAAATTA-TGAAAAAT-CCC-TAAAGGATACCTTTAACGTAAAAGTACCTGATACC-CT
* *
485099 TAAAGGGCTTAAAAAGGA-TATAGCTAA--
127 TAAA-GACTTAAAAA-GATTATA--AAAGG
* *** * *
485126 GATGAACCTATCCTAAATACCCACCTTTGGCATAAAAGCAGACTTAATGACAACCTAAGACTTGG
1 GATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCAGACTCGGTGACAACCTAGGACTCGG
** * * * *
485191 TTCTAAAAAATTATGAAAACATCCCTAGGGGATACCTTTAACGTAGAAGT-GCTCGGTACCCCTA
66 TTCTAAAAAATTATGAAAA-ATCCCTAAAGGATACCTTTAACGTAAAAGTACCT-GATACCCTTA
485255 AATGAACTTAAAAAGATTATAAAAGG
129 AA-G-ACTTAAAAAGATTATAAAAGG
* * * ** **
485281 GATGAACCTAACCTAAATACCCAACATCGGCATAAAAGCAGACTCGGTGATGACCTAGGACTCAA
1 GATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCAGACTCGGTGACAACCTAGGACTCGG
* * * * * *
485346 TTATAAAAAAATTACGAAAAAGCTCGTAAAAGATACCTTTGACGTAAAAGTACCTGATACCCTTA
66 TTCT-AAAAAATTATGAAAAATC-CCTAAAGGATACCTTTAACGTAAAAGTACCTGATACCCTT-
*
485411 AAAGACTTAAAAAAGATTTTAAAATGG
128 AAAGACTT-AAAAAGATTATAAAA-GG
* * * * * *
485438 G-TGAACCTATCCTAAATGCCCACCTTCGACATAAAAACGGAC-CTGGTGACAACTTAGGACTTG
1 GATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCAGACTC-GGTGACAACCTAGGACTCG
* * * * *
485501 ATTCTAAAAAATTTATG-AAAATGCCCCTAAGGGATACCATCAACGTAAAAGTACCTGAAACCCT
65 GTTCTAAAAAA-TTATGAAAAAT--CCCTAAAGGATACCTTTAACGTAAAAGTACCTGATACCCT
*
485565 TAAAGGACTTAAAAAAGATTTTAAAAAGG
127 TAAA-GACTT-AAAAAGATTAT-AAAAGG
* * * * * *
485594 G-TGAACATATCCTAAATGCCCACCTTCGGCATAAAAGTAGAC-CTTGTGAAAACCTAGTACTCG
1 GATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCAGACTC-GGTGACAACCTAGGACTCG
* * * * *
485657 ATTCT-AAAAATTAT-AAAAATACCCATACAGGATACCTTCAACGTAAAAGCACCTGATAACCTT
65 GTTCTAAAAAATTATGAAAAAT-CCC-TAAAGGATACCTTTAACGTAAAAGTACCTGATACCCTT
485720 AAAAGACTTAAAAAGGATT-T---AGG
128 -AAAGACTTAAAAA-GATTATAAAAGG
* * * * * *
485743 G-TGAACCTATCCTAAATGCCCACCTTCGACATGAAAGCAGACTCAGTGACAACCTAGGAGTTGG
1 GATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCAGACTCGGTGACAACCTAGGACTCGG
**
485807 TTCTCGAAAATTATGAAA
66 TTCTAAAAAATTATGAAA
485825 GTGCCTTTAG
Statistics
Matches: 695, Mismatches: 119, Indels: 79
0.78 0.13 0.09
Matches are distributed among these distances:
149 59 0.08
150 9 0.01
151 6 0.01
152 11 0.02
153 110 0.16
154 159 0.23
155 103 0.15
156 225 0.32
157 13 0.02
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.23
Consensus pattern (152 bp):
GATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCAGACTCGGTGACAACCTAGGACTCGG
TTCTAAAAAATTATGAAAAATCCCTAAAGGATACCTTTAACGTAAAAGTACCTGATACCCTTAAA
GACTTAAAAAGATTATAAAAGG
Found at i:486861 original size:20 final size:20
Alignment explanation
Indices: 486816--486867 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
486806 GTAGCCAAAC
* **
486816 TTGTATCGATACACCAAGTA
1 TTGTATCGATACACAAAAAA
486836 -TGTATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
486855 TTGTATCGATACA
1 TTGTATCGATACA
486868 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:489096 original size:21 final size:21
Alignment explanation
Indices: 489063--489107 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
489053 TTGCAAGTTG
*
489063 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
489085 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
489105 AAA
1 AAA
489108 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:490931 original size:15 final size:15
Alignment explanation
Indices: 490911--490941 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
490901 TAAAAATGTC
*
490911 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
490926 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
490941 C
1 C
490942 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:493038 original size:13 final size:13
Alignment explanation
Indices: 493020--493045 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
493010 ACATTTTTCT
493020 TTGTATCGATACA
1 TTGTATCGATACA
493033 TTGTATCGATACA
1 TTGTATCGATACA
493046 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:493209 original size:20 final size:20
Alignment explanation
Indices: 493166--493211 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
493156 AAATCTTTTG
493166 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
493187 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
493207 CAAAA
1 CAAAA
493212 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:494845 original size:38 final size:40
Alignment explanation
Indices: 494789--494869 Score: 96
Period size: 38 Copynumber: 2.1 Consensus size: 40
494779 TTAATAAACG
**
494789 GGGGGAGAATGCGTAAA-TTGCTACAA-TTATTTT-ATTAA
1 GGGGGAGAATGCACAAATTTGCTA-AATTTATTTTGATTAA
* *
494827 GGGGGAGAATGTACAAATTTGTTAAATTTATTTTGATTAA
1 GGGGGAGAATGCACAAATTTGCTAAATTTATTTTGATTAA
494867 GGG
1 GGG
494870 AGAAATAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
38 16 0.44
39 12 0.33
40 8 0.22
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.36
Consensus pattern (40 bp):
GGGGGAGAATGCACAAATTTGCTAAATTTATTTTGATTAA
Found at i:495512 original size:13 final size:13
Alignment explanation
Indices: 495494--495519 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
495484 TACACCAAGT
495494 ATGTATCGATACA
1 ATGTATCGATACA
495507 ATGTATCGATACA
1 ATGTATCGATACA
495520 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:495517 original size:32 final size:33
Alignment explanation
Indices: 495476--495539 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
495466 TAGCCAAACT
* **
495476 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
495508 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
495540 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:497111 original size:12 final size:12
Alignment explanation
Indices: 497095--497125 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
497085 AAATTTTCCC
497095 CTTTTTTT-TCT
1 CTTTTTTTCTCT
497106 CTTTTTTTCTCT
1 CTTTTTTTCTCT
497118 CTTTTTTT
1 CTTTTTTT
497126 GCTAAGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (12 bp):
CTTTTTTTCTCT
Found at i:497744 original size:156 final size:160
Alignment explanation
Indices: 497565--497864 Score: 360
Period size: 161 Copynumber: 1.9 Consensus size: 160
497555 AAATCCTCTC
* * * *
497565 GAAAATATTTACAGAGTAGAAAACT-CAGT-TTTCGAAAA-AGGGGCATTTCAA-AAAAAATCCA
1 GAAAATATTTACAGAGTACAAAACTCCA-TATTTCAAAAATAAGGGAATTTCAAGAAAAAATCCA
* **
497626 AA-ACTTATGGAAATAAATTAATTTTCTA-AAACTGATTTAATAAGAACCAAATAAAAATATTTG
65 AACACTTATGAAAATAAAAGAATTTT-TACAAACTGATTTAATAAGAACCAAATAAAAATATTTG
*
497689 ATGAGTTTTAAAAATCACAAACCAAGCCCCCT
129 ATGAATTTTAAAAATCACAAACCAAGCCCCCT
** **
497721 GAAAATATTTATGGAGTACAAAACTCCATATTTCAAAAATAAGGGAATTTCAAGGAAAAAATTGA
1 GAAAATATTTACAGAGTACAAAACTCCATATTTCAAAAATAAGGGAATTTCAA-GAAAAAATCCA
* * * ** * *
497786 AACATTTATGAAAATAAAAGAGTTTTTACAAACTGCTTTAATGTGAATCAAATAATAATATTTGA
65 AACACTTATGAAAATAAAAGAATTTTTACAAACTGATTTAATAAGAACCAAATAAAAATATTTGA
497851 TGAATTTTAAAAAT
130 TGAATTTTAAAAAT
497865 TAAAAACTAA
Statistics
Matches: 118, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
156 23 0.19
157 10 0.08
158 11 0.09
160 12 0.10
161 62 0.53
ACGTcount: A:0.48, C:0.11, G:0.12, T:0.29
Consensus pattern (160 bp):
GAAAATATTTACAGAGTACAAAACTCCATATTTCAAAAATAAGGGAATTTCAAGAAAAAATCCAA
ACACTTATGAAAATAAAAGAATTTTTACAAACTGATTTAATAAGAACCAAATAAAAATATTTGAT
GAATTTTAAAAATCACAAACCAAGCCCCCT
Found at i:511872 original size:13 final size:13
Alignment explanation
Indices: 511854--511962 Score: 85
Period size: 14 Copynumber: 8.2 Consensus size: 13
511844 CTATTGGTTG
511854 TAGAATTACTTGA
1 TAGAATTACTTGA
511867 TAGAATTACTTGA
1 TAGAATTACTTGA
*
511880 CTAAAATTACTTGA
1 -TAGAATTACTTGA
** ** *
511894 TACTATTGGTAGAA
1 TAGAATTACTTG-A
** **
511908 TACTATTGGTTG-
1 TAGAATTACTTGA
511920 TAGAATTACTTGA
1 TAGAATTACTTGA
511933 TAGAATTACTTGA
1 TAGAATTACTTGA
*
511946 CTAAAATTACTTGA
1 -TAGAATTACTTGA
511960 TAG
1 TAG
511963 TAGAATACTA
Statistics
Matches: 79, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
12 8 0.10
13 35 0.44
14 36 0.46
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.39
Consensus pattern (13 bp):
TAGAATTACTTGA
Found at i:511940 original size:66 final size:62
Alignment explanation
Indices: 511833--511995 Score: 267
Period size: 66 Copynumber: 2.6 Consensus size: 62
511823 AGCTTGGATC
511833 ATGGTAGAATACTATTGGTTGTAGAATTACTTGATAGAATTACTTGACTAAAATTACTTGATACT
1 ATGGTAGAATACTATTGGTTGTAGAATTACTTGATAGAATTACTTGACTAAAATTACTTG--A-T
511898 ATTGGTAGAATACTATTGGTTGTAGAATTACTTGATAGAATTACTTGACTAAAATTACTTGAT
1 A-TGGTAGAATACTATTGGTTGTAGAATTACTTGATAGAATTACTTGACTAAAATTACTTGAT
*
511961 A--GTAGAATACTATTGGTCGTAGAATTACTTGATAG
1 ATGGTAGAATACTATTGGTTGTAGAATTACTTGATAG
511996 GTAACACTAT
Statistics
Matches: 96, Mismatches: 1, Indels: 7
0.92 0.01 0.07
Matches are distributed among these distances:
60 33 0.34
63 2 0.02
64 1 0.01
65 1 0.01
66 59 0.61
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (62 bp):
ATGGTAGAATACTATTGGTTGTAGAATTACTTGATAGAATTACTTGACTAAAATTACTTGAT
Found at i:515970 original size:22 final size:21
Alignment explanation
Indices: 515922--515987 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 21
515912 TTCACACTAT
515922 TATATT-TTATATATATATATA
1 TATATTCTT-TATATATATATA
*
515943 TATATTCTTTTTATATGATATA
1 TATATTCTTTATATAT-ATATA
* *
515965 TTTATTCTTTATATA-ATAAA
1 TATATTCTTTATATATATATA
515985 TAT
1 TAT
515988 CATATAATGT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
20 6 0.16
21 12 0.32
22 20 0.53
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.58
Consensus pattern (21 bp):
TATATTCTTTATATATATATA
Found at i:517012 original size:17 final size:17
Alignment explanation
Indices: 516987--517029 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
516977 ATGTACTAAG
516987 TTTTTCTTTTT-CTTTT
1 TTTTTCTTTTTGCTTTT
*
517003 TTTTTCCTTTTTGCTTTC
1 TTTTT-CTTTTTGCTTTT
*
517021 TCTTTCTTT
1 TTTTTCTTT
517030 GGGGGTTACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 5 0.22
17 10 0.43
18 8 0.35
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (17 bp):
TTTTTCTTTTTGCTTTT
Found at i:522724 original size:25 final size:22
Alignment explanation
Indices: 522674--522729 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 22
522664 TTAAAAATTC
**
522674 AAGGAAAAAAAAAAAGGGAGTT
1 AAGGAAAAAAAAAAAGGGAGAG
522696 AAGGAAAGAAAAAGAAAGGGAAGAG
1 AAGGAAA-AAAAA-AAAGGG-AGAG
*
522721 AAGGGAAAA
1 AAGGAAAAA
522730 GAGAGCACCG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 7 0.25
23 5 0.18
24 8 0.29
25 8 0.29
ACGTcount: A:0.64, C:0.00, G:0.32, T:0.04
Consensus pattern (22 bp):
AAGGAAAAAAAAAAAGGGAGAG
Found at i:525026 original size:35 final size:35
Alignment explanation
Indices: 524980--525046 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
524970 ATCGATAATC
524980 TAATCTTAAAGTGTTAAGTGCCCTAACAATTTTAA
1 TAATCTTAAAGTGTTAAGTGCCCTAACAATTTTAA
*
525015 TAATCTTAAAGTGTTAAGTTCCCTAACAATTT
1 TAATCTTAAAGTGTTAAGTGCCCTAACAATTT
525047 CATCAATTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (35 bp):
TAATCTTAAAGTGTTAAGTGCCCTAACAATTTTAA
Found at i:525973 original size:153 final size:153
Alignment explanation
Indices: 525693--525985 Score: 428
Period size: 153 Copynumber: 1.9 Consensus size: 153
525683 ATTTTTTTAA
* *
525693 TATGATATATGTATCTATGTGATTGTGGGGAAGTATGGCCATCATGAAATGATTATGCTTAAGAG
1 TATGATATATGTATCTATGTGAATGTGGAGAAGTATGGCCATCATGAAATGATTATGCTTAAGAG
* * *
525758 TCACCATCAATCTTTTTAACTAGATGTGATCAGCAATTATTAAAATCGATCTTTTATGAAAAAAT
66 TCACCATCAATCTTTTTAACTAAATGTGATCAACAATTATTAAAATCGATCTTTTATGAAAAAAA
525823 TTTAAAATTATGAATATGGGAAG
131 TTTAAAATTATGAATATGGGAAG
* *
525846 TATGATATGTGTATCTATGTGAATGTGGAGAAGTATGGCCAT-TTAGAAATGATTATGCTTAAGA
1 TATGATATATGTATCTATGTGAATGTGGAGAAGTATGGCCATCAT-GAAATGATTATGCTTAAGA
* * * * * * *
525910 GTCGCCATTAATTTTTTTTGACTAAATGTGATTAACACTTATTAAAATTGATCTTTTAT-AAAAA
65 GTCACCATCAA-TCTTTTTAACTAAATGTGATCAACAATTATTAAAATCGATCTTTTATGAAAAA
525974 AATTTAAAATTA
129 AATTTAAAATTA
525986 ATTAAAGTTC
Statistics
Matches: 124, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
152 1 0.01
153 83 0.67
154 40 0.32
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (153 bp):
TATGATATATGTATCTATGTGAATGTGGAGAAGTATGGCCATCATGAAATGATTATGCTTAAGAG
TCACCATCAATCTTTTTAACTAAATGTGATCAACAATTATTAAAATCGATCTTTTATGAAAAAAA
TTTAAAATTATGAATATGGGAAG
Found at i:527048 original size:20 final size:20
Alignment explanation
Indices: 527021--527076 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
527011 GTAAACCTAG
*
527021 AATGTATCGATACATTGCTC
1 AATGTATCGATACATTGCAC
* *
527041 ATTGTATCGATACATTTCAC
1 AATGTATCGATACATTGCAC
527061 AATGTATCGATACATT
1 AATGTATCGATACATT
527077 CAGGCATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (20 bp):
AATGTATCGATACATTGCAC
Found at i:527404 original size:20 final size:20
Alignment explanation
Indices: 527360--527417 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
527350 ATTTCAACGA
***
527360 TTTGTATCGATACATAAAAT
1 TTTGTATCGATACATATTTT
*
527380 GTTGTATCGATACATATTTT
1 TTTGTATCGATACATATTTT
527400 TTTGTATCGATACA-ATTT
1 TTTGTATCGATACATATTT
527418 AAGCTACTGC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTGTATCGATACATATTTT
Found at i:527474 original size:13 final size:13
Alignment explanation
Indices: 527456--527480 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
527446 ATTACTCAAA
527456 TGTATCGATACAT
1 TGTATCGATACAT
527469 TGTATCGATACA
1 TGTATCGATACA
527481 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:533504 original size:18 final size:18
Alignment explanation
Indices: 533481--533545 Score: 51
Period size: 18 Copynumber: 3.3 Consensus size: 18
533471 ATCTTCTTCT
533481 CTCCTCCTCCTATCATCC
1 CTCCTCCTCCTATCATCC
*
533499 CTCCT-CTCTCTATTATCTCTC
1 CTCCTCCTC-CTATCA--TC-C
533520 CTGTCTCTCCTCCTATCATCC
1 C--TC-CTCCTCCTATCATCC
533541 CTCCT
1 CTCCT
533546 ATCTCTACTA
Statistics
Matches: 37, Mismatches: 2, Indels: 16
0.67 0.04 0.29
Matches are distributed among these distances:
17 3 0.08
18 12 0.32
19 2 0.05
20 2 0.05
21 4 0.11
22 2 0.05
23 2 0.05
24 7 0.19
25 3 0.08
ACGTcount: A:0.09, C:0.49, G:0.02, T:0.40
Consensus pattern (18 bp):
CTCCTCCTCCTATCATCC
Found at i:533536 original size:42 final size:42
Alignment explanation
Indices: 533484--533602 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
533474 TTCTTCTCTC
*
533484 CTCCTCCTATCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
533526 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* * *
533568 CTCTTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
533603 TTGAGAGCTA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.09, C:0.45, G:0.02, T:0.44
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:533568 original size:18 final size:18
Alignment explanation
Indices: 533499--533569 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
533489 CCTATCATCC
* *
533499 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
533517 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
533539 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
533559 CTCCTGTCTCT
1 CTCCTGTCTCT
533570 CTTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 4 0.10
21 13 0.32
22 4 0.10
24 5 0.12
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:537366 original size:28 final size:28
Alignment explanation
Indices: 537306--537376 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
537296 CACAATTGGA
**
537306 GATACTCAAACCCCGTTATTTCATCGGG
1 GATACTCAAACCCCGTTATTTCAGAGGG
* * * *
537334 AATACTCCAACCCTGTTATTTCCGAGGG
1 GATACTCAAACCCCGTTATTTCAGAGGG
*
537362 GATACTCTAACCCCG
1 GATACTCAAACCCCG
537377 GCTTTATATC
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.27
Consensus pattern (28 bp):
GATACTCAAACCCCGTTATTTCAGAGGG
Found at i:537446 original size:28 final size:27
Alignment explanation
Indices: 537405--537482 Score: 86
Period size: 28 Copynumber: 2.9 Consensus size: 27
537395 TGATTTTTCA
*
537405 TAATC-GGGGTACTCCAACCCCGTTAT
1 TAATCAGGGATACTCCAACCCCGTTAT
*
537431 GTAATCAGGGATACTCCAATCCCGTTAT
1 -TAATCAGGGATACTCCAACCCCGTTAT
** *
537459 TTCTGAAGGGATACTCCAACCCCG
1 TAAT-CAGGGATACTCCAACCCCG
537483 ATTTTATTTC
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
27 7 0.16
28 36 0.84
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (27 bp):
TAATCAGGGATACTCCAACCCCGTTAT
Found at i:537447 original size:106 final size:107
Alignment explanation
Indices: 537253--537525 Score: 277
Period size: 106 Copynumber: 2.6 Consensus size: 107
537243 ACCTCAATCG
* * * * ** *
537253 GGGATACTCCAACTCCGATTTTAT-TTTCAAAACATCAATTTTTCACAATTGGAGATACTCAAAC
1 GGGATACTCCAACCCCGACTTTATATCT-AAAATATTGATTTTTCACAATCGGAGATACTCAAAC
* * *
537317 CCCGTTATTTCATCGGGAATACTCCAA-CCCTGTTATTTCCGAG
65 CCCGTTATGTAATCGGGAATACTCCAATCCC-GTTATTTCCGAA
* * * * *
537360 GGGATACTCTAACCCCGGCTTTATATCTAAAATATTGATTTTTCATAATCGG-GGTACTCCAACC
1 GGGATACTCCAACCCCGACTTTATATCTAAAATATTGATTTTTCACAATCGGAGATACTCAAACC
*
537424 CCGTTATGTAATCAGGG-ATACTCCAATCCCGTTATTTCTGAA
66 CCGTTATGTAATC-GGGAATACTCCAATCCCGTTATTTCCGAA
* * *** *
537466 GGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCACAGTC-GAGGATACTC
1 GGGATACTCCAACCCCGACTTTATATCTAAAATATTGATTTTTCACAATCGGA-GATACTC
537526 CAACTCCGAT
Statistics
Matches: 135, Mismatches: 26, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
105 1 0.01
106 81 0.60
107 51 0.38
108 2 0.01
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.33
Consensus pattern (107 bp):
GGGATACTCCAACCCCGACTTTATATCTAAAATATTGATTTTTCACAATCGGAGATACTCAAACC
CCGTTATGTAATCGGGAATACTCCAATCCCGTTATTTCCGAA
Found at i:537573 original size:51 final size:51
Alignment explanation
Indices: 537465--537582 Score: 134
Period size: 51 Copynumber: 2.3 Consensus size: 51
537455 TTATTTCTGA
* **
537465 AGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCACAGTC
1 AGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCACAACC
* * *
537516 -GAGGATACTCCAACTCCGATTTTATTT-TCAAAACACTAA-TTTTCTATAACC
1 AG-GGATACTCCAACCCCGATTTTATTTCT-AAAACACCAATTTTTC-ACAACC
537567 AGGGATACTCCAACCC
1 AGGGATACTCCAACCC
537583 TGTTATTTCC
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
50 7 0.12
51 48 0.86
52 1 0.02
ACGTcount: A:0.32, C:0.26, G:0.10, T:0.31
Consensus pattern (51 bp):
AGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCACAACC
Found at i:537602 original size:79 final size:79
Alignment explanation
Indices: 537518--537668 Score: 221
Period size: 79 Copynumber: 1.9 Consensus size: 79
537508 TCACAGTCGA
* * * * *
537518 GGATACTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAACCAGGGATACTCCAACCC
1 GGATACTCCAACCCCGATTTTACTTCCAAAACACCAATTTTCCATAACCAGGGATACTCCAACCC
*
537583 TGTTATTTCCGAGG
66 CGTTATTTCCGAGG
* * *
537597 GGATACTCCAACCCCGATTTTACTTCCAAAACACCGATTTTCCATAATCGGGGATACTCCAACCC
1 GGATACTCCAACCCCGATTTTACTTCCAAAACACCAATTTTCCATAACCAGGGATACTCCAACCC
537662 CGTTATT
66 CGTTATT
537669 ATCTCCAAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
79 63 1.00
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.30
Consensus pattern (79 bp):
GGATACTCCAACCCCGATTTTACTTCCAAAACACCAATTTTCCATAACCAGGGATACTCCAACCC
CGTTATTTCCGAGG
Found at i:537678 original size:130 final size:130
Alignment explanation
Indices: 537436--537678 Score: 337
Period size: 130 Copynumber: 1.9 Consensus size: 130
537426 GTTATGTAAT
* * * *
537436 CAGGGATACTCCAATCCCGTTATTTCTGAAGGGATACTCCAACCCCGATTTTATTTCTAAAATAC
1 CAGGGATACTCCAATCCCGTTATTTCCGAAGGGATACTCCAACCCCGATTTTACTTCCAAAACAC
* * * * *
537501 CAATTTTTCACAGTCGAGGATACTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAAC
66 CAATTTTCCACAATCGAGGATACTCCAACCCCGATTTTATCTCCAAAACACTAATTTTCTATAAC
*
537566 CAGGGATACTCCAA-CCCTGTTATTTCCGAGGGGATACTCCAACCCCGATTTTACTTCCAAAACA
1 CAGGGATACTCCAATCCC-GTTATTTCCGAAGGGATACTCCAACCCCGATTTTACTTCCAAAACA
* * *
537630 CCGATTTTCCATAATCGGGGATACTCCAACCCCG-TTATTATCTCCAAAA
65 CCAATTTTCCACAATCGAGGATACTCCAACCCCGATT-TTATCTCCAAAA
537679 TATTAAATTT
Statistics
Matches: 98, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
129 5 0.05
130 93 0.95
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.30
Consensus pattern (130 bp):
CAGGGATACTCCAATCCCGTTATTTCCGAAGGGATACTCCAACCCCGATTTTACTTCCAAAACAC
CAATTTTCCACAATCGAGGATACTCCAACCCCGATTTTATCTCCAAAACACTAATTTTCTATAAC
Found at i:540455 original size:13 final size:13
Alignment explanation
Indices: 540436--540466 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
540426 ACAATTCATC
540436 ATGTATCGATACA
1 ATGTATCGATACA
*
540449 TTGTATCGATACA
1 ATGTATCGATACA
540462 ATGTA
1 ATGTA
540467 CCATGTATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:540461 original size:33 final size:33
Alignment explanation
Indices: 540419--540481 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
540409 AGAAGCAATT
*
540419 TATCGATACAAT-TCATCATGTATCGATACATTG
1 TATCGATACAATGT-ACCATGTATCGATACATTG
540452 TATCGATACAATGTACCATGTATCGATACA
1 TATCGATACAATGTACCATGTATCGATACA
540482 AACAGTGGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (33 bp):
TATCGATACAATGTACCATGTATCGATACATTG
Found at i:540536 original size:20 final size:20
Alignment explanation
Indices: 540511--540565 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
540501 CAGCCAGTTT
**
540511 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
*
540531 CATGTATTGATACAA-TGAA
1 CATGTATCGATACAATTGAA
540550 CATGTATCGATACAAT
1 CATGTATCGATACAAT
540566 ATATCGATAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:541064 original size:12 final size:12
Alignment explanation
Indices: 541049--541088 Score: 62
Period size: 13 Copynumber: 3.2 Consensus size: 12
541039 CTTTTTTGAA
541049 TTTCTTTTATTT
1 TTTCTTTTATTT
541061 TTTCTTTTATTTT
1 TTTCTTTTA-TTT
541074 TTCTCTTTTATTT
1 TT-TCTTTTATTT
541087 TT
1 TT
541089 CTGAATGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.35
13 10 0.38
14 7 0.27
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTCTTTTATTT
Found at i:541080 original size:14 final size:13
Alignment explanation
Indices: 541049--541088 Score: 64
Period size: 14 Copynumber: 3.1 Consensus size: 13
541039 CTTTTTTGAA
541049 TTTCTTTTA-TTT
1 TTTCTTTTATTTT
541061 TTTCTTTTATTTT
1 TTTCTTTTATTTT
541074 TTCTCTTTTATTTT
1 TT-TCTTTTATTTT
541088 T
1 T
541089 CTGAATGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 9 0.35
13 5 0.19
14 12 0.46
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTCTTTTATTTT
Found at i:543261 original size:18 final size:19
Alignment explanation
Indices: 543228--543264 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
543218 AGTAAAATCC
*
543228 ATATTTATCTTAATAAATA
1 ATATTCATCTTAATAAATA
543247 ATATTCATC-TAATAAATA
1 ATATTCATCTTAATAAATA
543265 TAATTATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (19 bp):
ATATTCATCTTAATAAATA
Found at i:548879 original size:17 final size:18
Alignment explanation
Indices: 548852--548885 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
548842 TCGAAAGGGT
*
548852 ATTTCATTTTTTTTAAAA
1 ATTTCATTTTTTGTAAAA
548870 ATTT-ATTTTTTGTAAA
1 ATTTCATTTTTTGTAAA
548886 TACTAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (18 bp):
ATTTCATTTTTTGTAAAA
Found at i:548924 original size:2 final size:2
Alignment explanation
Indices: 548917--548949 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
548907 AGATACATAC
548917 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
548950 AACTTAATTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:549728 original size:19 final size:19
Alignment explanation
Indices: 549693--549730 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
549683 AGTCTAGCAA
*
549693 ATAATAATTTAATATTAAT
1 ATAATAATTTAACATTAAT
*
549712 ATAATAATTTTACATTAAT
1 ATAATAATTTAACATTAAT
549731 TCTAAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (19 bp):
ATAATAATTTAACATTAAT
Found at i:549869 original size:14 final size:14
Alignment explanation
Indices: 549850--549906 Score: 78
Period size: 14 Copynumber: 4.0 Consensus size: 14
549840 AAATTGGAAA
549850 AAATTTAACAAAAT
1 AAATTTAACAAAAT
**
549864 AAATTTTGCAATAAT
1 AAATTTAACAA-AAT
*
549879 AAATTTAATAAAAT
1 AAATTTAACAAAAT
549893 AAATTTAACAAAAT
1 AAATTTAACAAAAT
549907 TAAAAAAACT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
14 25 0.69
15 11 0.31
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (14 bp):
AAATTTAACAAAAT
Found at i:551757 original size:2 final size:2
Alignment explanation
Indices: 551750--551774 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
551740 GAAGCCAAAT
551750 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
551775 TCAAATGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:555433 original size:6 final size:7
Alignment explanation
Indices: 555415--555441 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
555405 ACCCTTCTCA
555415 CTTTTTT
1 CTTTTTT
555422 CTTTTTT
1 CTTTTTT
555429 CTTTTTT
1 CTTTTTT
555436 CTTTTT
1 CTTTTT
555442 ACAAACTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
CTTTTTT
Found at i:559300 original size:21 final size:21
Alignment explanation
Indices: 559275--559361 Score: 68
Period size: 23 Copynumber: 4.0 Consensus size: 21
559265 TATTTAATCA
559275 TTATTTATTTAATAAAAAAAT
1 TTATTTATTTAATAAAAAAAT
* *
559296 TTATTTAAATTTAATTATAAAAT
1 TTATTT--ATTTAATAAAAAAAT
** *
559319 TTATAAATATTAATATAAAAAT
1 TTATTTAT-TTAATAAAAAAAT
* *
559341 AATATTT-TTTAATAATAAAAT
1 -TTATTTATTTAATAAAAAAAT
559362 AAATTTATGA
Statistics
Matches: 50, Mismatches: 12, Indels: 8
0.71 0.17 0.11
Matches are distributed among these distances:
21 19 0.38
22 11 0.22
23 20 0.40
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTATTTATTTAATAAAAAAAT
Found at i:559362 original size:21 final size:20
Alignment explanation
Indices: 559328--559367 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
559318 TTTATAAATA
559328 TTAATATAAAAATAATATTTT
1 TTAATATAAAAATAA-ATTTT
559349 TTAATA-ATAAAATAAATTT
1 TTAATATA-AAAATAAATTT
559368 ATGATAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAATATAAAAATAAATTTT
Found at i:559379 original size:22 final size:20
Alignment explanation
Indices: 559354--559421 Score: 68
Period size: 20 Copynumber: 3.3 Consensus size: 20
559344 ATTTTTTAAT
559354 AATAAAATAAATTTATGATAAA
1 AATAAAATAAATTTA--ATAAA
559376 AAT-AAATCAAATTTAATAAA
1 AATAAAAT-AAATTTAATAAA
* *
559396 AATATAATAAAAATTAA-AAA
1 AATAAAAT-AAATTTAATAAA
559416 AATAAA
1 AATAAA
559422 TTATAATACA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 16 0.40
21 14 0.35
22 10 0.25
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.28
Consensus pattern (20 bp):
AATAAAATAAATTTAATAAA
Found at i:559403 original size:11 final size:11
Alignment explanation
Indices: 559371--559419 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 11
559361 TAAATTTATG
559371 ATAAAAATA-A
1 ATAAAAATATA
* *
559381 AT-CAAATTTA
1 ATAAAAATATA
559391 ATAAAAATATA
1 ATAAAAATATA
559402 ATAAAAAT-TA
1 ATAAAAATATA
559412 A-AAAAATA
1 ATAAAAATA
559420 AATTATAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
9 10 0.31
10 8 0.25
11 14 0.44
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (11 bp):
ATAAAAATATA
Found at i:559417 original size:10 final size:10
Alignment explanation
Indices: 559371--559418 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
559361 TAAATTTATG
*
559371 ATAAAAATAA
1 ATAAAAATTA
* *
559381 ATCAAATTTA
1 ATAAAAATTA
559391 ATAAAAATATA
1 ATAAAAAT-TA
559402 ATAAAAATTA
1 ATAAAAATTA
559412 A-AAAAAT
1 ATAAAAAT
559419 AAATTATAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
9 6 0.19
10 16 0.50
11 10 0.31
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (10 bp):
ATAAAAATTA
Found at i:560434 original size:2 final size:2
Alignment explanation
Indices: 560380--560415 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
560370 ATCCAAAGCC
560380 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
560416 AGGTTAGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:560810 original size:17 final size:17
Alignment explanation
Indices: 560772--560811 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
560762 ATTTAAAAGA
*
560772 AATTA-AATATTAAATT
1 AATTATAATATTAAATC
560788 AATTATAATATTAAATC
1 AATTATAATATTAAATC
*
560805 ATTTATA
1 AATTATA
560812 TGATAGTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
AATTATAATATTAAATC
Found at i:561736 original size:17 final size:17
Alignment explanation
Indices: 561714--561751 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
561704 ATTTAAATGC
*
561714 ATAAAATTAAAT-TATAA
1 ATAAAAATAAATAT-TAA
561731 ATAAAAATAAATATTAA
1 ATAAAAATAAATATTAA
561748 ATAA
1 ATAA
561752 TATAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 18 0.95
18 1 0.05
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAAAAATAAATATTAA
Found at i:562264 original size:106 final size:105
Alignment explanation
Indices: 562070--562265 Score: 284
Period size: 106 Copynumber: 1.9 Consensus size: 105
562060 TTTCACATTC
* *
562070 TTTTTTGCTACGTGTCACTTTACTTTCGATGTAATTAAATATGATTAAATTTATTTATAAAAATA
1 TTTTTTGCTACGTGTCACTTTACTTTCAATGCAATTAAATATGATTAAATTTATTTATAAAAATA
* * * *
562135 ATTATTTGATATATAGATGATGAATCACATTTTATATATT
66 ATTATTTAATATACAAATCATGAATCACATTTTATATATT
* * * *
562175 TTTTTTGTTATGTGTCATTTTTATTTTCAATGCAATTAAATATGATTAAATTTATTTATAAAAAT
1 TTTTTTGCTACGTGTCA-CTTTACTTTCAATGCAATTAAATATGATTAAATTTATTTATAAAAAT
*
562240 AATTGTTTAATATACAAATCATGAAT
65 AATTATTTAATATACAAATCATGAAT
562266 TTTTAAATTT
Statistics
Matches: 79, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
105 15 0.19
106 64 0.81
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.48
Consensus pattern (105 bp):
TTTTTTGCTACGTGTCACTTTACTTTCAATGCAATTAAATATGATTAAATTTATTTATAAAAATA
ATTATTTAATATACAAATCATGAATCACATTTTATATATT
Found at i:562942 original size:32 final size:33
Alignment explanation
Indices: 562878--562946 Score: 97
Period size: 32 Copynumber: 2.1 Consensus size: 33
562868 ATATAAAAAA
* *
562878 ATAATATAAATATATAAATATTTTAAATTTTAT
1 ATAATATAAATATATAAATATATTAAAATTTAT
562911 ATAATATAAAT-TATTAAA-ATATTAAAATTTAT
1 ATAATATAAATATA-TAAATATATTAAAATTTAT
562943 ATAA
1 ATAA
562947 ATTAAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
32 18 0.55
33 15 0.45
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (33 bp):
ATAATATAAATATATAAATATATTAAAATTTAT
Found at i:563007 original size:17 final size:17
Alignment explanation
Indices: 562961--563007 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
562951 AAAATATTTT
* *
562961 AAATATAATTATAATTC
1 AAATAAAATTATAAATC
*
562978 -AATAATAAATATAAATC
1 AAATAA-AATTATAAATC
562995 AAATAAAATTATA
1 AAATAAAATTATA
563008 CAAGTTTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
16 4 0.17
17 15 0.62
18 5 0.21
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATAAAATTATAAATC
Found at i:564330 original size:46 final size:47
Alignment explanation
Indices: 564255--564416 Score: 154
Period size: 46 Copynumber: 3.5 Consensus size: 47
564245 GGATAATTTA
* * * * *
564255 TAATTTTATTCATGTAAAAGTTACGAGTTATTTGTTTGAGAG-TCTG
1 TAATTTTATCCATGCAAAAGTTACTAGTTATTTGTTAGAAAGATCTG
* * ** *
564301 TAGTTTTATCTATGCAAAAGTTACTAGTTATTCATTAGAAAGATTTG
1 TAATTTTATCCATGCAAAAGTTACTAGTTATTTGTTAGAAAGATCTG
* *
564348 TAATTTTATCCATGCAAAAGTTACTAATTATTTGTGA-AAAGAGT-TCG
1 TAATTTTATCCATGCAAAAGTTACTAGTTATTTGTTAGAAAGA-TCT-G
*
564395 T-AGTTTA-CCATGCAAAAGTTAC
1 TAATTTTATCCATGCAAAAGTTAC
564417 ACATTGCAAT
Statistics
Matches: 96, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
45 15 0.16
46 44 0.46
47 37 0.39
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (47 bp):
TAATTTTATCCATGCAAAAGTTACTAGTTATTTGTTAGAAAGATCTG
Found at i:568145 original size:20 final size:20
Alignment explanation
Indices: 568122--568194 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
568112 ATTTGCCTGC
*
568122 ATGTATTGATACATTGAAGA
1 ATGTATCGATACATTGAAGA
* *
568142 ATGTATTGATA-ACCT--AGA
1 ATGTATCGATACA-TTGAAGA
*
568160 ATGTATCGATACAGTGAAGA
1 ATGTATCGATACATTGAAGA
568180 ATGTATCGATACATT
1 ATGTATCGATACATT
568195 TTCATCCAGA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
18 14 0.31
19 2 0.04
20 29 0.64
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACATTGAAGA
Found at i:570229 original size:35 final size:35
Alignment explanation
Indices: 570187--570256 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
570177 TGAAAAACAC
570187 ATAGGTTTTTGCAACGAATACCATAGTGGATACAT
1 ATAGGTTTTTGCAACGAATACCATAGTGGATACAT
* *
570222 ATAGGTTTTTGCAATGAATTCCATAGTGGATACAT
1 ATAGGTTTTTGCAACGAATACCATAGTGGATACAT
570257 GTGTGAACCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (35 bp):
ATAGGTTTTTGCAACGAATACCATAGTGGATACAT
Found at i:573981 original size:114 final size:113
Alignment explanation
Indices: 573833--574165 Score: 358
Period size: 114 Copynumber: 2.9 Consensus size: 113
573823 TGACCTAATC
* * * **
573833 TAATCAAATAAAATAAGCTCCAAATAAATTAATTAAA-ATTGCACATGAGCTCTATTTTATCTAA
1 TAATTAAATAAAATAATCT-CAAATAAATTAATTAAATA-AGCATGTGAGCT-TATTTTATCTAA
573897 TGTATATTTTTTATAAAATTTGACTTTAAATTAAATAATTTATGATCCAATA
63 T-TATATTTTTTATAAAATTTGACTTTAAATTAAATAATTTATGATCCAATA
*
573949 TAATTAAAT-AAATAGA-CAT-AAATAAATTAATTAAATAAGCATGTGAGACTTATTTTATTTAA
1 TAATTAAATAAAATA-ATC-TCAAATAAATTAATTAAATAAGCATGTGAG-CTTATTTTATCTAA
*** * * * *
574011 -TATATTTTTTTATAAGGCTTG-GTCATAAATTAAAAAATTAATGATCCAATA
63 TTATA-TTTTTTATAAAATTTGACT-TTAAATTAAATAATTTATGATCCAATA
**
574062 TAATTAAATAAAATAATCTCAAATAAATTAATTAAATAAGCATGTGAAATATATTTTATCT-ATT
1 TAATTAAATAAAATAATCTCAAATAAATTAATTAAATAAGCATGTGAGCT-TATTTTATCTAATT
*
574126 ATATATTTTTATAAGACTTT-ACTTTAAATTAAATAATTTA
65 ATAT-TTTTTATAA-AATTTGACTTTAAATTAAATAATTTA
574166 CGACTTTACT
Statistics
Matches: 181, Mismatches: 22, Indels: 30
0.78 0.09 0.13
Matches are distributed among these distances:
112 5 0.03
113 51 0.28
114 103 0.57
115 12 0.07
116 10 0.06
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.41
Consensus pattern (113 bp):
TAATTAAATAAAATAATCTCAAATAAATTAATTAAATAAGCATGTGAGCTTATTTTATCTAATTA
TATTTTTTATAAAATTTGACTTTAAATTAAATAATTTATGATCCAATA
Found at i:577695 original size:27 final size:27
Alignment explanation
Indices: 577653--577707 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
577643 ATTAAAGGAT
*
577653 AATCTTATCCTCTATCTTTTTATTTAA
1 AATCTTATCCTCTATCTTTGTATTTAA
* *
577680 AATCTTATTCTTTATCTTTGTATTTAA
1 AATCTTATCCTCTATCTTTGTATTTAA
577707 A
1 A
577708 TTTTGTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.27, C:0.15, G:0.02, T:0.56
Consensus pattern (27 bp):
AATCTTATCCTCTATCTTTGTATTTAA
Found at i:578334 original size:106 final size:105
Alignment explanation
Indices: 578134--578344 Score: 386
Period size: 106 Copynumber: 2.0 Consensus size: 105
578124 TTTTTTTTCA
* * *
578134 CTTATCTATGCACTAAGCTTCAATTTAAAGCATATGTAGAAAAGCAGGATGCAAATCTATTTACC
1 CTTATCTATGCAATAAACTTCAATTTAAAGCATACGTAGAAAAGCAGGATGCAAATCTATTTACC
578199 TATGAGAAGAGGTGAAGGCAAAATCAGTCCAACCCAGAGC
66 TATGAGAAGAGGTGAAGGCAAAATCAGTCCAACCCAGAGC
578239 CTTATCTATGCAATAAACTTCAATTTAAAGCATACGTAGAAAAGCAGGATGGCAAATCTATTTAC
1 CTTATCTATGCAATAAACTTCAATTTAAAGCATACGTAGAAAAGCAGGAT-GCAAATCTATTTAC
578304 CTATGAGAAGAGGTGAAGGCAAAATCAGTCCAACCCAGAGC
65 CTATGAGAAGAGGTGAAGGCAAAATCAGTCCAACCCAGAGC
578345 ATCTCCTTGC
Statistics
Matches: 102, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
105 47 0.46
106 55 0.54
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (105 bp):
CTTATCTATGCAATAAACTTCAATTTAAAGCATACGTAGAAAAGCAGGATGCAAATCTATTTACC
TATGAGAAGAGGTGAAGGCAAAATCAGTCCAACCCAGAGC
Found at i:581861 original size:27 final size:28
Alignment explanation
Indices: 581829--581970 Score: 97
Period size: 29 Copynumber: 5.3 Consensus size: 28
581819 ATTTAAATAA
* *
581829 ATTTAATTTGAT-ATAATAAATATTTTT
1 ATTTAATTTAATAATAAAAAATATTTTT
581856 ATTTAAGTTTAATAATAAAAAATATTTTT
1 ATTTAA-TTTAATAATAAAAAATATTTTT
* * ** **
581885 -TTTAATTT-TTAAT-TAATTTATAAATT
1 ATTTAATTTAATAATAAAAAATAT-TTTT
581911 A-TT-ATTTAATAAT---AAATATTTTT
1 ATTTAATTTAATAATAAAAAATATTTTT
* *
581934 ACTTAAATTTAATAATAAAAAATAATTTT
1 A-TTTAATTTAATAATAAAAAATATTTTT
581963 -TTTAATTT
1 ATTTAATTT
581971 TCAATTTTTA
Statistics
Matches: 88, Mismatches: 16, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
23 3 0.03
24 4 0.05
25 10 0.11
26 22 0.25
27 16 0.18
28 10 0.11
29 23 0.26
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (28 bp):
ATTTAATTTAATAATAAAAAATATTTTT
Found at i:581943 original size:26 final size:25
Alignment explanation
Indices: 581841--581952 Score: 77
Period size: 26 Copynumber: 4.3 Consensus size: 25
581831 TTAATTTGAT
*
581841 ATAATAAATATTTTTATTTAAGTTTA
1 ATAATAAATATTTTTA-TTAAATTTA
*
581867 ATAATAAAAAATATTTTT-TTTAATTT-
1 ATAAT---AAATATTTTTATTAAATTTA
* * ** *
581893 TTAATTAAT-TTATAAATTATTATTTA
1 ATAATAAATATT-TTTATTA-AATTTA
581919 ATAATAAATATTTTTACTTAAATTTA
1 ATAATAAATATTTTTA-TTAAATTTA
581945 ATAATAAA
1 ATAATAAA
581953 AAATAATTTT
Statistics
Matches: 64, Mismatches: 13, Indels: 18
0.67 0.14 0.19
Matches are distributed among these distances:
22 2 0.03
23 4 0.06
24 2 0.03
25 4 0.06
26 31 0.48
27 11 0.17
29 10 0.16
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (25 bp):
ATAATAAATATTTTTATTAAATTTA
Found at i:581945 original size:78 final size:80
Alignment explanation
Indices: 581811--581976 Score: 241
Period size: 78 Copynumber: 2.1 Consensus size: 80
581801 TTAGACGTAA
* *
581811 TTTT-ATTAATTTAAATAAATTTAATTTGATATAATAAATATTTTTATTTAAGTTTAATAATAAA
1 TTTTAATTAATTT-AATAAATTTAATTTGATATAATAAATATTTTTACTTAAATTTAATAATAAA
*
581875 AAATATTTTTTTTAAT
65 AAATAATTTTTTTAAT
*
581891 TTTTAATTAATTT-ATAAATTATTATTT-A-ATAATAAATATTTTTACTTAAATTTAATAATAAA
1 TTTTAATTAATTTAATAAATT-TAATTTGATATAATAAATATTTTTACTTAAATTTAATAATAAA
581953 AAATAATTTTTTTAAT
65 AAATAATTTTTTTAAT
*
581969 TTTCAATT
1 TTTTAATT
581977 TTTAATTTAA
Statistics
Matches: 79, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
78 54 0.68
79 8 0.10
80 9 0.11
81 8 0.10
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (80 bp):
TTTTAATTAATTTAATAAATTTAATTTGATATAATAAATATTTTTACTTAAATTTAATAATAAAA
AATAATTTTTTTAAT
Found at i:584604 original size:19 final size:20
Alignment explanation
Indices: 584560--584604 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
584550 TTAATTAGTT
* **
584560 TATTTTAAATATAGTTAATT
1 TATTTTAAATATAGATAACA
584580 TATTTTAAATA-AGATAACA
1 TATTTTAAATATAGATAACA
584599 TATTTT
1 TATTTT
584605 GTATTTACCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.51
Consensus pattern (20 bp):
TATTTTAAATATAGATAACA
Found at i:586782 original size:13 final size:13
Alignment explanation
Indices: 586733--586790 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
586723 AAAGGTTTTC
*
586733 ATATAATATATCAA
1 ATATAATAT-TTAA
586747 AT-TAA-ATTTAA
1 ATATAATATTTAA
*
586758 ATATAATTTTTATA
1 ATATAATATTTA-A
586772 ATAT-ATATTTAA
1 ATATAATATTTAA
*
586784 ATTTAAT
1 ATATAAT
586791 TCAATTCCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
11 5 0.14
12 9 0.25
13 15 0.42
14 7 0.19
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATAATATTTAA
Found at i:588576 original size:17 final size:17
Alignment explanation
Indices: 588554--588591 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
588544 TACAAATATA
588554 ATTACAT-ATTTATAAAT
1 ATTACATAATTTAT-AAT
588571 ATTACATAAATTTATAAT
1 ATTACAT-AATTTATAAT
588589 ATT
1 ATT
588592 TTAAATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 6 0.32
19 6 0.32
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTACATAATTTATAAT
Found at i:588734 original size:24 final size:24
Alignment explanation
Indices: 588666--588735 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 24
588656 AAATATACAT
588666 AAAATAAAATAAATTATTAATATGTCA
1 AAAATAAAA-AAA-TA-TAATATGTCA
* *
588693 AAAATATACAAAAATATAATATTTTA
1 AAAATA-A-AAAAATATAATATGTCA
588719 AAAATAAAAAAATATAA
1 AAAATAAAAAAATATAA
588736 ATACAAACAT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
24 10 0.26
25 1 0.03
26 14 0.36
27 8 0.21
28 4 0.10
29 2 0.05
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (24 bp):
AAAATAAAAAAATATAATATGTCA
Found at i:588782 original size:16 final size:16
Alignment explanation
Indices: 588763--588797 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
588753 TTTTAATAAT
588763 TTTTTTTTCTTCTTTC
1 TTTTTTTTCTTCTTTC
*
588779 TTTTTTTTTTTCTTTC
1 TTTTTTTTCTTCTTTC
588795 TTT
1 TTT
588798 CTTTCCCACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (16 bp):
TTTTTTTTCTTCTTTC
Found at i:588787 original size:20 final size:20
Alignment explanation
Indices: 588762--588801 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
588752 TTTTTAATAA
588762 TTTTTTTTTC-TTCTTTCTT
1 TTTTTTTTTCTTTCTTTCTT
588781 TTTTTTTTTCTTTCTTTCTT
1 TTTTTTTTTCTTTCTTTCTT
588801 T
1 T
588802 CCCACTACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (20 bp):
TTTTTTTTTCTTTCTTTCTT
Found at i:588944 original size:11 final size:11
Alignment explanation
Indices: 588900--588933 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
588890 ATATTATCAT
588900 TATAATAAAAA
1 TATAATAAAAA
*
588911 -ATAATTAAAA
1 TATAATAAAAA
588921 TATAATAAAAA
1 TATAATAAAAA
588932 TA
1 TA
588934 AAAATATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
TATAATAAAAA
Found at i:588994 original size:29 final size:28
Alignment explanation
Indices: 588910--589038 Score: 74
Period size: 29 Copynumber: 4.6 Consensus size: 28
588900 TATAATAAAA
*
588910 AATA-ATTA-AAATATAATAAAAATA-AA
1 AATATATTATAAATAT-ATAAAAATATAT
* * *
588936 AATATAATATTAAATACTTTAAAATTTATAT
1 AATATATTA-TAAATA-TATAAAA-ATATAT
588967 AATATTATTATAAATATATAAAAATATAT
1 AATA-TATTATAAATATATAAAAATATAT
* * **
588996 ATAAATATAAT-AATAT-TTTAAATATTAT
1 A-ATATATTATAAATATATAAAAATA-TAT
589024 AATAT-TT-TAAATATA
1 AATATATTATAAATATA
589039 ATTATAATTT
Statistics
Matches: 79, Mismatches: 13, Indels: 21
0.70 0.12 0.19
Matches are distributed among these distances:
25 1 0.01
26 10 0.13
27 12 0.15
28 9 0.11
29 21 0.27
30 11 0.14
31 11 0.14
32 4 0.05
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (28 bp):
AATATATTATAAATATATAAAAATATAT
Found at i:589016 original size:59 final size:57
Alignment explanation
Indices: 588914--589040 Score: 136
Period size: 59 Copynumber: 2.2 Consensus size: 57
588904 ATAAAAAATA
* * *
588914 ATTAAAATATAATAAAAATAAAAATATAATATTAAATACTTTAAAATTTATATAATATT
1 ATTAAAATATAATAAAAATAAAAATAAAATAATAAATACTTT-AAATAT-TATAATATT
* * *
588973 ATTATAAATAT-ATAAAAATATATATAAATATAAT-AATATTTTAAATATTATAATATT
1 ATTA-AAATATAATAAAAATAAAAATAAA-ATAATAAATACTTTAAATATTATAATATT
589030 -TT-AAATATAAT
1 ATTAAAATATAAT
589041 TATAATTTGA
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
54 6 0.10
55 2 0.03
56 2 0.03
57 9 0.15
58 5 0.08
59 25 0.42
60 10 0.17
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (57 bp):
ATTAAAATATAATAAAAATAAAAATAAAATAATAAATACTTTAAATATTATAATATT
Found at i:589056 original size:20 final size:17
Alignment explanation
Indices: 588963--589040 Score: 84
Period size: 17 Copynumber: 4.4 Consensus size: 17
588953 TTTAAAATTT
* *
588963 ATATAATATTATTATAAA
1 ATATAATAATATT-TTAA
* *
588981 TATATAAAAATATATATAA
1 -ATATAATAATAT-TTTAA
589000 ATATAATAATATTTTAA
1 ATATAATAATATTTTAA
*
589017 ATATTATAATATTTTAA
1 ATATAATAATATTTTAA
589034 ATATAAT
1 ATATAAT
589041 TATAATTTGA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
17 26 0.52
18 11 0.22
19 12 0.24
20 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATAATAATATTTTAA
Found at i:590527 original size:21 final size:21
Alignment explanation
Indices: 590481--590528 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
590471 ATATTTAAAA
590481 ATATAATATAAAAATAAATAC
1 ATATAATATAAAAATAAATAC
* * **
590502 GTATAATATAAATATACGTAC
1 ATATAATATAAAAATAAATAC
590523 ATATAA
1 ATATAA
590529 AAATATATAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.58, C:0.06, G:0.04, T:0.31
Consensus pattern (21 bp):
ATATAATATAAAAATAAATAC
Found at i:590581 original size:32 final size:30
Alignment explanation
Indices: 590544--590614 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 30
590534 TATATTAAAT
*
590544 AAAATA-AATTATTAATATATAAAAAATATATA
1 AAAATATAA-TATT-ATAAATAAAAAATA-ATA
*
590576 AAAATATAATATTTTAAATAAAAAATAATA
1 AAAATATAATATTATAAATAAAAAATAATA
*
590606 CAAATATAA
1 AAAATATAA
590615 ACAAATAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 11 0.31
31 12 0.34
32 10 0.29
33 2 0.06
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.32
Consensus pattern (30 bp):
AAAATATAATATTATAAATAAAAAATAATA
Found at i:590612 original size:51 final size:47
Alignment explanation
Indices: 590523--590621 Score: 110
Period size: 51 Copynumber: 2.0 Consensus size: 47
590513 ATATACGTAC
* **
590523 ATATAAAAATATATATTAAATAAAATAAATTATTAATATATAAAAAAT
1 ATATAAAAATATATATTAAATAAAATAAAATACAAATATA-AAAAAAT
*
590571 ATATAAAAATATAATATTTTAAATAAAA-AATAATACAAATATAAACAAAT
1 ATATAAAAATAT-ATA--TTAAATAAAATAA-AATACAAATATAAAAAAAT
590621 A
1 A
590622 AATTTTTCTC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
48 12 0.28
49 3 0.07
50 9 0.21
51 19 0.44
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (47 bp):
ATATAAAAATATATATTAAATAAAATAAAATACAAATATAAAAAAAT
Found at i:590957 original size:22 final size:23
Alignment explanation
Indices: 590929--590971 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
590919 TATAAATATA
*
590929 AAAATATGATA-TAAAAATAATT
1 AAAATATAATATTAAAAATAATT
590951 AAAATATAATATTAAAAATAA
1 AAAATATAATATTAAAAATAA
590972 ATGATACGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (23 bp):
AAAATATAATATTAAAAATAATT
Found at i:591134 original size:11 final size:12
Alignment explanation
Indices: 591112--591137 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
591102 TTTCTTTTCC
591112 TTTTTCATTTTT
1 TTTTTCATTTTT
591124 TTTTTCATTTTT
1 TTTTTCATTTTT
591136 TT
1 TT
591138 CTCCCATGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTCATTTTT
Found at i:591748 original size:25 final size:25
Alignment explanation
Indices: 591720--591813 Score: 61
Period size: 25 Copynumber: 3.7 Consensus size: 25
591710 AAATTATTAT
591720 TTAATAATAATAATTTTATTTAAAA
1 TTAATAATAATAATTTTATTTAAAA
* * *
591745 TTAATTATAAAATATTTTAATATTAATA
1 TTAATAATAATA-ATTTT-AT-TTAAAA
* *
591773 -TAAAAATAAT-ATTTTA-ATAATAA
1 TTAATAATAATAATTTTATTTAA-AA
*
591796 ATAATAA-AATAAATTTTA
1 TTAATAATAAT-AATTTTA
591814 AATCAATAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
22 3 0.06
23 4 0.08
24 6 0.11
25 21 0.40
26 5 0.09
27 9 0.17
28 5 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
TTAATAATAATAATTTTATTTAAAA
Found at i:591763 original size:22 final size:22
Alignment explanation
Indices: 591738--591815 Score: 66
Period size: 25 Copynumber: 3.3 Consensus size: 22
591728 AATAATTTTA
591738 TTTAAAATTAATTATAAAATAT
1 TTTAAAATTAATTATAAAATAT
* *
591760 TTTAATATTAATATAAAAATAATAT
1 TTTAAAATTAAT-T-ATAA-AATAT
* *
591785 TTTAATAATAAATAATAAAATAAAT
1 TTTAA-AATTAATTATAAAAT--AT
591810 TTTAAA
1 TTTAAA
591816 TCAATAAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
22 11 0.25
23 4 0.09
24 7 0.16
25 17 0.39
26 5 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TTTAAAATTAATTATAAAATAT
Found at i:591771 original size:47 final size:47
Alignment explanation
Indices: 591683--591782 Score: 110
Period size: 47 Copynumber: 2.1 Consensus size: 47
591673 TAAATTTTAT
* * *
591683 TAATTTTATTTAAATTTAACTTAAATTAAATTATTATTTAATAATAA
1 TAATTTTATTTAAAATTAACTTAAAATAAATTAATATTTAATAATAA
* ** * *
591730 TAATTTTATTTAAAATTAATTATAAAATATTTTAATATTAATATAAAAA
1 TAATTTTATTTAAAATTAACT-TAAAATAAATTAATATTTA-ATAATAA
591779 TAAT
1 TAAT
591783 ATTTTAATAA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
47 19 0.44
48 14 0.33
49 10 0.23
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (47 bp):
TAATTTTATTTAAAATTAACTTAAAATAAATTAATATTTAATAATAA
Found at i:592184 original size:14 final size:14
Alignment explanation
Indices: 592161--592202 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
592151 ATAAAACGGG
*
592161 CTAATGAATTTAAT
1 CTAATTAATTTAAT
592175 CTAATTAATTTAAAT
1 CTAATTAATTT-AAT
*
592190 -TGATTAATTTAAT
1 CTAATTAATTTAAT
592203 TATAAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 3 0.12
14 19 0.76
15 3 0.12
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (14 bp):
CTAATTAATTTAAT
Found at i:593192 original size:19 final size:20
Alignment explanation
Indices: 593170--593211 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
593160 TATTTTTAAA
593170 TTATTATT-AT-AAATATTAT
1 TTATTATTAATAAAAT-TTAT
593189 TTATTATTAATAAAATTTAT
1 TTATTATTAATAAAATTTAT
593209 TTA
1 TTA
593212 ATTTATGAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.38
20 9 0.43
21 4 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTATTATTAATAAAATTTAT
Found at i:597258 original size:2 final size:2
Alignment explanation
Indices: 597251--597327 Score: 55
Period size: 2 Copynumber: 38.5 Consensus size: 2
597241 CATTTGCTTT
* * * ** *
597251 TG TG TG TG TG TG TG TG TG TG TG TG TG CG CG CG CC CG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* * * * *
597293 TG TG CG TG TG TG TG TG CG CG CG CG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
597328 CTGGAACATG
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.00, C:0.14, G:0.48, T:0.38
Consensus pattern (2 bp):
TG
Found at i:597290 original size:32 final size:30
Alignment explanation
Indices: 597254--597327 Score: 121
Period size: 32 Copynumber: 2.4 Consensus size: 30
597244 TTGCTTTTGT
597254 GTGTGTGTGTGTGTGTGTGTGTGCGCGCGCCC
1 GTGTGTGTGTGTGTGTGTGTGTGCGCGCG--C
*
597286 GTGTGTGTGTGCGTGTGTGTGTGCGCGCGC
1 GTGTGTGTGTGTGTGTGTGTGTGCGCGCGC
597316 GTGTGTGTGTGT
1 GTGTGTGTGTGT
597328 CTGGAACATG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
30 12 0.30
32 28 0.70
ACGTcount: A:0.00, C:0.15, G:0.49, T:0.36
Consensus pattern (30 bp):
GTGTGTGTGTGTGTGTGTGTGTGCGCGCGC
Found at i:602876 original size:13 final size:13
Alignment explanation
Indices: 602860--602886 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
602850 TTTTAACGTA
602860 ATTTATTAATATG
1 ATTTATTAATATG
602873 ATTTATTAATATG
1 ATTTATTAATATG
602886 A
1 A
602887 CATAAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (13 bp):
ATTTATTAATATG
Found at i:606104 original size:16 final size:17
Alignment explanation
Indices: 606060--606105 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
606050 TTATTAAAAT
*
606060 TATATTATTTTATTTTTA
1 TATATAATTTTA-TTTTA
606078 TATATAA--TTATTTTA
1 TATATAATTTTATTTTA
606093 T-TATAATTTTATT
1 TATATAATTTTATT
606106 AAATTTGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
14 5 0.20
15 6 0.24
16 8 0.32
18 6 0.24
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TATATAATTTTATTTTA
Found at i:606792 original size:14 final size:15
Alignment explanation
Indices: 606766--606813 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
606756 AGAAGATAAT
*
606766 AAAAATTTTGACTAA
1 AAAAATTGTGACTAA
**
606781 AAAAATTG-GACTGT
1 AAAAATTGTGACTAA
*
606795 AAAAATTGTGATTAA
1 AAAAATTGTGACTAA
606810 AAAA
1 AAAA
606814 TATAATTTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.54, C:0.04, G:0.12, T:0.29
Consensus pattern (15 bp):
AAAAATTGTGACTAA
Found at i:606966 original size:21 final size:21
Alignment explanation
Indices: 606909--606973 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
606899 AAAAATTTAA
*
606909 AAATAATAATAAAATAA-TTTT
1 AAATTATAA-AAAATAATTTTT
*
606930 --ATT-TAAAATATAATTTTT
1 AAATTATAAAAAATAATTTTT
*
606948 AAATTATAAAAAATTATTTTT
1 AAATTATAAAAAATAATTTTT
606969 AAATT
1 AAATT
606974 TTATACTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
17 6 0.17
18 7 0.19
19 2 0.06
20 3 0.08
21 18 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AAATTATAAAAAATAATTTTT
Found at i:607417 original size:25 final size:25
Alignment explanation
Indices: 607362--607447 Score: 68
Period size: 27 Copynumber: 3.2 Consensus size: 25
607352 ATTTAAGTAT
*
607362 TTATATTTGTATTATTTTTTATATAAAATA
1 TTATATTTTTA-TATTTTTT-TAT---ATA
607392 TTATATTTTTATATTTTTTTATATA
1 TTATATTTTTATATTTTTTTATATA
*
607417 TTAATAATTTATT-TATTTTATTATAT-
1 TT-AT-ATTT-TTATATTTTTTTATATA
607443 TTATA
1 TTATA
607448 ATTAAGAATT
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
24 1 0.02
25 7 0.14
26 4 0.08
27 16 0.31
28 5 0.10
29 8 0.16
30 10 0.20
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (25 bp):
TTATATTTTTATATTTTTTTATATA
Found at i:607438 original size:9 final size:10
Alignment explanation
Indices: 607362--607444 Score: 52
Period size: 10 Copynumber: 8.8 Consensus size: 10
607352 ATTTAAGTAT
607362 TTATATTTGTA
1 TTATATTT-TA
*
607373 TTATTTTTTA
1 TTATATTTTA
***
607383 -TATAAAATA
1 TTATATTTTA
607392 TTATA-TTT-
1 TTATATTTTA
*
607400 TTATATTTTT
1 TTATATTTTA
*
607410 TTATATATTA
1 TTATATTTTA
*
607420 --ATAATTTA
1 TTATATTTTA
607428 TT-TATTTTA
1 TTATATTTTA
607437 TTATATTT
1 TTATATTT
607445 ATAATTAAGA
Statistics
Matches: 54, Mismatches: 12, Indels: 13
0.68 0.15 0.16
Matches are distributed among these distances:
8 11 0.20
9 17 0.31
10 19 0.35
11 7 0.13
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (10 bp):
TTATATTTTA
Found at i:607448 original size:25 final size:23
Alignment explanation
Indices: 607403--607450 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 23
607393 TATATTTTTA
607403 TATTTTTTTATATATTAATAATT
1 TATTTTTTTATATATTAATAATT
*
607426 TATTTATTTTATTATATTTATAATT
1 TATTT-TTTTA-TATATTAATAATT
607451 AAGAATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.23
24 5 0.23
25 12 0.55
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
TATTTTTTTATATATTAATAATT
Found at i:607520 original size:5 final size:5
Alignment explanation
Indices: 607488--607529 Score: 57
Period size: 5 Copynumber: 7.8 Consensus size: 5
607478 CTCCATGTGA
607488 CCCTG CCCTAG CCCTAG CCCTAG CCCTG CCCTG CCCTG CCCT
1 CCCTG CCCT-G CCCT-G CCCT-G CCCTG CCCTG CCCTG CCCT
607530 AACCTACCTC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 19 0.53
6 17 0.47
ACGTcount: A:0.07, C:0.57, G:0.17, T:0.19
Consensus pattern (5 bp):
CCCTG
Found at i:607542 original size:27 final size:28
Alignment explanation
Indices: 607488--607546 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 28
607478 CTCCATGTGA
* *
607488 CCCTGCCCTAGCCCTAGCCCTAGCCCTG
1 CCCTGCCCTAGCCCTAGACCTACCCCTG
607516 CCCTGCCCT-GCCCTA-ACCTACCTCCTG
1 CCCTGCCCTAGCCCTAGACCTACC-CCTG
607543 CCCT
1 CCCT
607547 CCACATTACC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 5 0.18
27 14 0.50
28 9 0.32
ACGTcount: A:0.10, C:0.56, G:0.14, T:0.20
Consensus pattern (28 bp):
CCCTGCCCTAGCCCTAGACCTACCCCTG
Found at i:608173 original size:26 final size:24
Alignment explanation
Indices: 608131--608182 Score: 59
Period size: 26 Copynumber: 2.1 Consensus size: 24
608121 TTTTATTTAT
* *
608131 TTTTTAAATTTAAATAATATATAA
1 TTTTTAAATTTAAATAAAATAAAA
*
608155 TTTTTAAATTTTGATATAAAATAAAA
1 TTTTTAAA-TTT-AAATAAAATAAAA
608181 TT
1 TT
608183 ATAATTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 8 0.35
25 3 0.13
26 12 0.52
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
TTTTTAAATTTAAATAAAATAAAA
Found at i:609307 original size:17 final size:17
Alignment explanation
Indices: 609282--609333 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 17
609272 ATTTAAAATT
609282 TAAATTAATTAATTTATA
1 TAAA-TAATTAATTTATA
609300 TAAATAATT--TTT-TA
1 TAAATAATTAATTTATA
*
609314 AAAATAA-TAATTTA-A
1 TAAATAATTAATTTATA
609329 TAAAT
1 TAAAT
609334 TTTATATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
13 1 0.03
14 8 0.28
15 11 0.38
17 5 0.17
18 4 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAATAATTAATTTATA
Found at i:609327 original size:14 final size:15
Alignment explanation
Indices: 609291--609333 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
609281 TTAAATTAAT
609291 TAATTTATATAAATAA
1 TAATTTA-ATAAATAA
**
609307 TTTTTTAA-AAATAA
1 TAATTTAATAAATAA
609321 TAATTTAATAAAT
1 TAATTTAATAAAT
609334 TTTATATTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
14 12 0.55
15 5 0.23
16 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TAATTTAATAAATAA
Found at i:609399 original size:2 final size:2
Alignment explanation
Indices: 609392--609422 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
609382 TTGCAACCTC
609392 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
609423 ATAAAATCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:613828 original size:16 final size:17
Alignment explanation
Indices: 613809--613847 Score: 62
Period size: 16 Copynumber: 2.3 Consensus size: 17
613799 TTTTAAATAA
613809 AATTTATTTTTT-ATTT
1 AATTTATTTTTTAATTT
613825 AATTTATTTTTTAAATTT
1 AATTTATTTTTT-AATTT
613843 AATTT
1 AATTT
613848 TTATTATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 12 0.57
18 9 0.43
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
AATTTATTTTTTAATTT
Found at i:613843 original size:13 final size:13
Alignment explanation
Indices: 613808--613850 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 13
613798 ATTTTAAATA
613808 AAATTTATTTTTT
1 AAATTTATTTTTT
613821 ATTTAATTTATTTTTT
1 A---AATTTATTTTTT
*
613837 AAATTTAATTTTT
1 AAATTTATTTTTT
613850 A
1 A
613851 TTATTTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 13 0.50
16 13 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
AAATTTATTTTTT
Found at i:614623 original size:21 final size:20
Alignment explanation
Indices: 614590--614642 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
614580 TTAAGATATA
614590 ATTT-TTTATAATT-TTAATT
1 ATTTATTTA-AATTATTAATT
614609 GATTTGATTTAAATTATTAATT
1 -ATTT-ATTTAAATTATTAATT
*
614631 ATTTAATTAAAT
1 ATTTATTTAAAT
614643 AATATTTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 11 0.38
21 8 0.28
22 10 0.34
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (20 bp):
ATTTATTTAAATTATTAATT
Found at i:614648 original size:22 final size:22
Alignment explanation
Indices: 614597--614668 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
614587 ATAATTTTTT
* *
614597 ATAATTTTAATTGATTTGATTTAA
1 ATAATATTAATT-ATTT-AATTAA
614621 AT--TATTAATTATTTAATTAA
1 ATAATATTAATTATTTAATTAA
* *
614641 ATAATATT-TTTATTTAATTTTA
1 ATAATATTAATTATTTAA-TTAA
614663 ATAATA
1 ATAATA
614669 AAAATATATA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
20 7 0.17
21 12 0.29
22 20 0.49
24 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (22 bp):
ATAATATTAATTATTTAATTAA
Found at i:614782 original size:7 final size:7
Alignment explanation
Indices: 614770--614800 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
614760 TAGATTTAGA
614770 TTTAAAT
1 TTTAAAT
614777 TTTAAAT
1 TTTAAAT
614784 TTTAAAT
1 TTTAAAT
614791 TTTAAAT
1 TTTAAAT
614798 TTT
1 TTT
614801 TTTAAGATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (7 bp):
TTTAAAT
Found at i:619704 original size:2 final size:2
Alignment explanation
Indices: 619697--619729 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
619687 GACCGACAAT
*
619697 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
619730 GTATTACACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:620102 original size:14 final size:14
Alignment explanation
Indices: 620076--620121 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
620066 AAGGTAAAAA
620076 AAAATTATAAATATT
1 AAAATT-TAAATATT
620091 AAAATTTAAATATT
1 AAAATTTAAATATT
*
620105 AAACTTATTAAATATT
1 AAA-AT-TTAAATATT
620121 A
1 A
620122 TTTTTTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 11 0.39
15 7 0.25
16 10 0.36
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
AAAATTTAAATATT
Found at i:620817 original size:3 final size:3
Alignment explanation
Indices: 620811--620855 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
620801 TTTATTATTG
620811 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
620856 TATTACATGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:621401 original size:21 final size:21
Alignment explanation
Indices: 621377--621416 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
621367 TAAATTGTTA
621377 TTTAAA-TTTAATTATAAAAAT
1 TTTAAATTTTAA-TATAAAAAT
621398 TTTAAATTTTAATATAAAA
1 TTTAAATTTTAATATAAAA
621417 TAAATTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTTAAATTTTAATATAAAAAT
Found at i:621560 original size:6 final size:6
Alignment explanation
Indices: 621549--621619 Score: 60
Period size: 6 Copynumber: 12.3 Consensus size: 6
621539 GTATTTTAAA
* *
621549 TATAAT TATAA- T-TAAT TATAA- TAAATAT TATAA- AATAAT TATAAT
1 TATAAT TATAAT TATAAT TATAAT TATA-AT TATAAT TATAAT TATAAT
* * *
621594 TATAAT AATAAA TATGAT TATAAT TA
1 TATAAT TATAAT TATAAT TATAAT TA
621620 ATTTTGATAA
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
4 3 0.06
5 9 0.18
6 35 0.70
7 3 0.06
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (6 bp):
TATAAT
Found at i:621598 original size:12 final size:11
Alignment explanation
Indices: 621547--621622 Score: 75
Period size: 12 Copynumber: 6.8 Consensus size: 11
621537 ACGTATTTTA
621547 AATATAATTAT
1 AATATAATTAT
621558 AAT-TAATTAT
1 AATATAATTAT
*
621568 AATAAATATTAT
1 AATATA-ATTAT
*
621580 AAAATAATTAT
1 AATATAATTAT
*
621591 AATTATAATAAT
1 AA-TATAATTAT
*
621603 AAATATGATTAT
1 -AATATAATTAT
621615 AAT-TAATT
1 AATATAATT
621623 TTGATAAATA
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
10 14 0.26
11 14 0.26
12 23 0.43
13 2 0.04
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (11 bp):
AATATAATTAT
Done.