Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A10
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: 110302803
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1825971 characters in sequence are not A, C, G, or T
File 139 of 343
Found at i:46402761 original size:16 final size:16
Alignment explanation
Indices: 46402740--46402772 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
46402730 AACCAAATTC
46402740 TCTGCTCATCTCTTCT
1 TCTGCTCATCTCTTCT
*
46402756 TCTGCTCATCTTTTCT
1 TCTGCTCATCTCTTCT
46402772 T
1 T
46402773 TTTCTTTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.33, G:0.06, T:0.55
Consensus pattern (16 bp):
TCTGCTCATCTCTTCT
Found at i:46404209 original size:27 final size:27
Alignment explanation
Indices: 46404179--46404356 Score: 180
Period size: 27 Copynumber: 6.6 Consensus size: 27
46404169 ATATTGAGTC
* *
46404179 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
46404206 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
46404233 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
46404261 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
**
46404288 CGCACACTTAGTGCATCACAT--TCATTT
1 CGCACACTTAGTGC-T-ACATAATCAACT
* * *
46404315 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
46404342 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
46404357 GTACAATTTA
Statistics
Matches: 128, Mismatches: 18, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
25 4 0.03
27 98 0.77
28 23 0.18
29 3 0.02
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:46407356 original size:27 final size:26
Alignment explanation
Indices: 46407315--46407425 Score: 116
Period size: 27 Copynumber: 4.2 Consensus size: 26
46407305 AGGAAGCGTC
*
46407315 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
* *
46407342 CTGGTGGCTCCGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
*
46407369 CTGGTGGCTCTACCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTG-AT
* * *
46407397 CTGGTGACTCTG-TACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGAT
46407422 CTGG
1 CTGG
46407426 CAGCCATGCA
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
25 5 0.07
26 10 0.14
27 43 0.61
28 13 0.18
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:46412673 original size:20 final size:20
Alignment explanation
Indices: 46412648--46412702 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
46412638 TGTGGTTCAA
*
46412648 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
46412668 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
46412688 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
46412703 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:46413086 original size:45 final size:45
Alignment explanation
Indices: 46413036--46413229 Score: 280
Period size: 45 Copynumber: 4.3 Consensus size: 45
46413026 GAACGGCATG
*
46413036 AAATTAAGGAAGCATTTGACCAACATCATGCATAATTTATGGAAC
1 AAATTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAC
* * *
46413081 AAATTAAGGAAGCACTGGACCAACATCATGCATAATTCATGGAAG
1 AAATTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAC
* * *
46413126 AATTTGAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAG
1 AAATTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAC
* * * *
46413171 AATTTAAGGAAGCATTTGGCCAACATCATGCATAATTTAAGGAAC
1 AAATTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAC
*
46413216 AAATTGAGGAAGCA
1 AAATTAAGGAAGCA
46413230 CCATGGCCGA
Statistics
Matches: 134, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 134 1.00
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.24
Consensus pattern (45 bp):
AAATTAAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAC
Found at i:46415747 original size:21 final size:22
Alignment explanation
Indices: 46415708--46415751 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
46415698 ATGCATACTC
46415708 CTTCAAGCTCAAATCAGCTCAA
1 CTTCAAGCTCAAATCAGCTCAA
* *
46415730 CTTCAA-CTCAACTTAGCTCAA
1 CTTCAAGCTCAAATCAGCTCAA
46415751 C
1 C
46415752 GGGCTCGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.34, C:0.34, G:0.07, T:0.25
Consensus pattern (22 bp):
CTTCAAGCTCAAATCAGCTCAA
Found at i:46428353 original size:22 final size:22
Alignment explanation
Indices: 46428325--46428368 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
46428315 TTTTGAACCA
46428325 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
46428347 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
46428369 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:46430454 original size:16 final size:15
Alignment explanation
Indices: 46430435--46430485 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
46430425 AAAAAAAGTG
46430435 AAAAAAATCAAGCAAA
1 AAAAAAAT-AAGCAAA
*
46430451 AAAAAAAGAAAG-AAA
1 AAAAAAA-TAAGCAAA
* *
46430466 AAAAAAGTGAGCAAA
1 AAAAAAATAAGCAAA
46430481 AAAAA
1 AAAAA
46430486 TCAAGTTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
14 2 0.07
15 17 0.59
16 10 0.34
ACGTcount: A:0.78, C:0.06, G:0.12, T:0.04
Consensus pattern (15 bp):
AAAAAAATAAGCAAA
Found at i:46430456 original size:30 final size:30
Alignment explanation
Indices: 46430422--46430485 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
46430412 ATTGAAATTC
**
46430422 AAAAAAAAAAGTGAAAAAAA-TCAAGCAAAA
1 AAAAAAAAAAGAAAAAAAAAGT-AAGCAAAA
* *
46430452 AAAAAAGAAAGAAAAAAAAAGTGAGCAAAA
1 AAAAAAAAAAGAAAAAAAAAGTAAGCAAAA
46430482 AAAA
1 AAAA
46430486 TCAAGTTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.78, C:0.05, G:0.12, T:0.05
Consensus pattern (30 bp):
AAAAAAAAAAGAAAAAAAAAGTAAGCAAAA
Found at i:46431515 original size:18 final size:18
Alignment explanation
Indices: 46431488--46431581 Score: 95
Period size: 18 Copynumber: 5.4 Consensus size: 18
46431478 CATTGAGCGA
* *
46431488 GAAAAGGAAAAAGAGATT
1 GAAAAAGAAAAAGAAATT
**
46431506 GAAAAAGAAATTGAAA--
1 GAAAAAGAAAAAGAAATT
* *
46431522 G-AAAACAAAAAGAAAAT
1 GAAAAAGAAAAAGAAATT
46431539 GAAAAAGAAAAAGAAATT
1 GAAAAAGAAAAAGAAATT
* *
46431557 GCAAAAGAAAAAGAAATC
1 GAAAAAGAAAAAGAAATT
46431575 GAAAAAG
1 GAAAAAG
46431582 TGAGAAAAAA
Statistics
Matches: 61, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
15 11 0.18
16 1 0.02
17 1 0.02
18 48 0.79
ACGTcount: A:0.69, C:0.03, G:0.19, T:0.09
Consensus pattern (18 bp):
GAAAAAGAAAAAGAAATT
Found at i:46431549 original size:12 final size:12
Alignment explanation
Indices: 46431487--46431622 Score: 72
Period size: 12 Copynumber: 11.5 Consensus size: 12
46431477 CCATTGAGCG
*
46431487 AGAAAAGGAAAA
1 AGAAAATGAAAA
* *
46431499 AGAGATTGAAAA
1 AGAAAATGAAAA
*
46431511 AGAAATTG--AA
1 AGAAAATGAAAA
*
46431521 AGAAAA-CAAAA
1 AGAAAATGAAAA
46431532 AGAAAATGAAAA
1 AGAAAATGAAAA
* *
46431544 AGAAAAAGAAAT
1 AGAAAATGAAAA
*
46431556 TGCAAAA-GAAAA
1 AG-AAAATGAAAA
46431568 AG-AAATCGAAAA
1 AGAAAAT-GAAAA
**
46431580 AG-TGA-GAAAAA
1 AGAAAATG-AAAA
46431591 AGAAAATGAAGAAA
1 AGAAAATG-A-AAA
46431605 AGAAAATTG-AAA
1 AGAAAA-TGAAAA
46431617 AGAAAA
1 AGAAAA
46431623 AGCGAAAAAA
Statistics
Matches: 97, Mismatches: 16, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
10 11 0.11
11 14 0.14
12 54 0.56
13 7 0.07
14 9 0.09
15 2 0.02
ACGTcount: A:0.70, C:0.02, G:0.19, T:0.09
Consensus pattern (12 bp):
AGAAAATGAAAA
Found at i:46431642 original size:13 final size:13
Alignment explanation
Indices: 46431585--46431642 Score: 55
Period size: 13 Copynumber: 4.3 Consensus size: 13
46431575 GAAAAAGTGA
*
46431585 GAAAAAAGAAAAT
1 GAAAAAAGAAATT
46431598 GAAGAAAAGAAAATT
1 GAA-AAAAG-AAATT
**
46431613 GAAAAGAA-AAAGC
1 GAAAA-AAGAAATT
46431626 GAAAAAAGAAATT
1 GAAAAAAGAAATT
46431639 GAAA
1 GAAA
46431643 GAGAGCTTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
12 2 0.06
13 18 0.50
14 7 0.19
15 9 0.25
ACGTcount: A:0.71, C:0.02, G:0.19, T:0.09
Consensus pattern (13 bp):
GAAAAAAGAAATT
Found at i:46431676 original size:33 final size:33
Alignment explanation
Indices: 46431639--46431701 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
46431629 AAAAGAAATT
46431639 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
46431672 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
46431702 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:46440525 original size:20 final size:20
Alignment explanation
Indices: 46440479--46440525 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
46440469 AGCTCGTTTC
*
46440479 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
46440499 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
46440519 CAGCTCA
1 CAGCTCA
46440526 ATTTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:46442293 original size:20 final size:20
Alignment explanation
Indices: 46442268--46442312 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
46442258 AGTAAGTTTC
46442268 AAAAAAAAGAAAAAAAAT-TG
1 AAAAAAAA-AAAAAAAATCTG
*
46442288 AAAAAAAAAAACAAAATCTG
1 AAAAAAAAAAAAAAAATCTG
46442308 AAAAA
1 AAAAA
46442313 TTTGAACATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.80, C:0.04, G:0.07, T:0.09
Consensus pattern (20 bp):
AAAAAAAAAAAAAAAATCTG
Found at i:46445535 original size:20 final size:20
Alignment explanation
Indices: 46445489--46445535 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
46445479 AGCTCGTTTC
*
46445489 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
46445509 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
46445529 CAGCTCA
1 CAGCTCA
46445536 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:46448174 original size:48 final size:47
Alignment explanation
Indices: 46448095--46448200 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
46448085 GAGTGTCATG
*
46448095 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
46448143 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
46448191 GAAAAAGAAA
1 GAAAAAGAAA
46448201 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:46449914 original size:20 final size:20
Alignment explanation
Indices: 46449868--46449914 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
46449858 AGCTCGTTTC
*
46449868 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
46449888 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
46449908 CAGCTCA
1 CAGCTCA
46449915 ATTTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:46454459 original size:11 final size:10
Alignment explanation
Indices: 46454445--46454483 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
46454435 CTTTTCACTT
46454445 TTTTTTTGTTC
1 TTTTTTT-TTC
46454456 TTTTTTTTTAC
1 TTTTTTTTT-C
*
46454467 TTTTTTTTAC
1 TTTTTTTTTC
46454477 TTTTTTT
1 TTTTTTT
46454484 GCTCACTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 10 0.38
11 16 0.62
ACGTcount: A:0.05, C:0.08, G:0.03, T:0.85
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:46454470 original size:9 final size:10
Alignment explanation
Indices: 46454457--46454483 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
46454447 TTTTTGTTCT
46454457 TTTTTTTTAC
1 TTTTTTTTAC
46454467 TTTTTTTTAC
1 TTTTTTTTAC
46454477 TTTTTTT
1 TTTTTTT
46454484 GCTCACTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTTTAC
Found at i:46454483 original size:24 final size:24
Alignment explanation
Indices: 46454436--46454498 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
46454426 CTCACAAGAC
**
46454436 TTTTCACTTTTTTTTTGTTCTTTT
1 TTTTCACTTTTTTTTACTTCTTTT
*
46454460 TTTTTACTTTTTTTTACTT-TTTT
1 TTTTCACTTTTTTTTACTTCTTTT
**
46454483 TGCTCACTTCTTTTTT
1 TTTTCACTT-TTTTTT
46454499 TTTTGAATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 10 0.31
24 22 0.69
ACGTcount: A:0.06, C:0.14, G:0.03, T:0.76
Consensus pattern (24 bp):
TTTTCACTTTTTTTTACTTCTTTT
Found at i:46456056 original size:20 final size:20
Alignment explanation
Indices: 46456033--46456079 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
46456023 GGGTTAAGAT
*
46456033 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
46456053 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
46456073 TGAGCTG
1 TGAGCTG
46456080 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:46461836 original size:158 final size:158
Alignment explanation
Indices: 46461638--46461925 Score: 576
Period size: 158 Copynumber: 1.8 Consensus size: 158
46461628 TAGCCTAATT
46461638 TATATATTAAGCTTACTAAATGAGCTATTTATAAATCATTCACTTTGTAACCAACCACTTCAAAC
1 TATATATTAAGCTTACTAAATGAGCTATTTATAAATCATTCACTTTGTAACCAACCACTTCAAAC
46461703 CATATTCACCTACAAATTTGTTTCATAGCCGAATATGTCAACCACAATCAATATATCAACCACAT
66 CATATTCACCTACAAATTTGTTTCATAGCCGAATATGTCAACCACAATCAATATATCAACCACAT
46461768 TACAACTCATCACACTTGCAAATCAATC
131 TACAACTCATCACACTTGCAAATCAATC
46461796 TATATATTAAGCTTACTAAATGAGCTATTTATAAATCATTCACTTTGTAACCAACCACTTCAAAC
1 TATATATTAAGCTTACTAAATGAGCTATTTATAAATCATTCACTTTGTAACCAACCACTTCAAAC
46461861 CATATTCACCTACAAATTTGTTTCATAGCCGAATATGTCAACCACAATCAATATATCAACCACAT
66 CATATTCACCTACAAATTTGTTTCATAGCCGAATATGTCAACCACAATCAATATATCAACCACAT
46461926 CATTTACTCA
Statistics
Matches: 130, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
158 130 1.00
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.32
Consensus pattern (158 bp):
TATATATTAAGCTTACTAAATGAGCTATTTATAAATCATTCACTTTGTAACCAACCACTTCAAAC
CATATTCACCTACAAATTTGTTTCATAGCCGAATATGTCAACCACAATCAATATATCAACCACAT
TACAACTCATCACACTTGCAAATCAATC
Found at i:46467706 original size:24 final size:24
Alignment explanation
Indices: 46467674--46467729 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
46467664 CTAGTTTCAA
* *
46467674 TTTTTTTTGAATTTTTTTTGAAAC
1 TTTTTTTTGAACTTTTTTCGAAAC
46467698 TTTTTTTTGAACTTTTTTCGAAAC
1 TTTTTTTTGAACTTTTTTCGAAAC
46467722 TTTTTTTT
1 TTTTTTTT
46467730 CACTTACTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.18, C:0.07, G:0.07, T:0.68
Consensus pattern (24 bp):
TTTTTTTTGAACTTTTTTCGAAAC
Found at i:46467726 original size:13 final size:13
Alignment explanation
Indices: 46467674--46467729 Score: 75
Period size: 11 Copynumber: 4.6 Consensus size: 13
46467664 CTAGTTTCAA
46467674 TTTTTTTTG-AA-
1 TTTTTTTTGAAAC
46467685 TTTTTTTTGAAAC
1 TTTTTTTTGAAAC
46467698 TTTTTTTTG-AAC
1 TTTTTTTTGAAAC
*
46467710 -TTTTTTCGAAAC
1 TTTTTTTTGAAAC
46467722 TTTTTTTT
1 TTTTTTTT
46467730 CACTTACTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
11 16 0.41
12 8 0.21
13 15 0.38
ACGTcount: A:0.18, C:0.07, G:0.07, T:0.68
Consensus pattern (13 bp):
TTTTTTTTGAAAC
Found at i:46472268 original size:16 final size:16
Alignment explanation
Indices: 46472247--46472278 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
46472237 TAATGTGTTT
46472247 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
46472263 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
46472279 ATGCAGAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.25, T:0.50
Consensus pattern (16 bp):
TGCTGCTGTTGTTTAA
Found at i:46472566 original size:72 final size:73
Alignment explanation
Indices: 46472431--46472578 Score: 192
Period size: 72 Copynumber: 2.0 Consensus size: 73
46472421 GCAGGTACAT
* * *
46472431 GGACGACATTTAAAGAAAAGGTGGCTGCTGCATTTTTCCAAAGCTGCCGAATTTATTGAGTGCAT
1 GGACGACATTTAAAGAAAAGGTGGCTGCTGCATTTTTCCAAACCAGCCGAATTTAGTGAGTGCAT
46472496 GGGACTTG
66 GGGACTTG
* * * * * *
46472504 GGACGACATTTAAAGTGAAA-GTTGCTGTTGTA-TTTTCCCAACCAGCCGAATTTAGTGTGTGCA
1 GGACGACATTTAAAG-AAAAGGTGGCTGCTGCATTTTTCCAAACCAGCCGAATTTAGTGAGTGCA
46472567 TGGGACTTG
65 TGGGACTTG
46472576 GGA
1 GGA
46472579 TAGCATTAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
72 38 0.58
73 24 0.37
74 3 0.05
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (73 bp):
GGACGACATTTAAAGAAAAGGTGGCTGCTGCATTTTTCCAAACCAGCCGAATTTAGTGAGTGCAT
GGGACTTG
Found at i:46473751 original size:11 final size:11
Alignment explanation
Indices: 46473735--46473760 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
46473725 GGAAATTTGA
46473735 AAAAAAAATTC
1 AAAAAAAATTC
46473746 AAAAAAAATTC
1 AAAAAAAATTC
46473757 AAAA
1 AAAA
46473761 TTTTTTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:46476278 original size:18 final size:18
Alignment explanation
Indices: 46476222--46476281 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
46476212 AGTGCGAGCG
46476222 AGAAAAAGAAATCAAAAGAAA
1 AGAAAAAGAAATC--AA-AAA
* **
46476243 AGAAAAAGAGATTGAAAA
1 AGAAAAAGAAATCAAAAA
46476261 AGAAAAAGAAATCAAAAA
1 AGAAAAAGAAATCAAAAA
46476279 AGA
1 AGA
46476282 GAGTGAGGTC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
18 21 0.64
19 1 0.03
21 11 0.33
ACGTcount: A:0.73, C:0.03, G:0.17, T:0.07
Consensus pattern (18 bp):
AGAAAAAGAAATCAAAAA
Found at i:46478322 original size:16 final size:16
Alignment explanation
Indices: 46478301--46478332 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
46478291 TAATGTGTTT
46478301 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
46478317 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
46478333 ATGCAGAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.25, T:0.50
Consensus pattern (16 bp):
TGCTGCTGTTGTTTAA
Found at i:46478654 original size:72 final size:73
Alignment explanation
Indices: 46478519--46478691 Score: 192
Period size: 72 Copynumber: 2.4 Consensus size: 73
46478509 GCAGGTACAT
* * *
46478519 GGACGGCATTTAAAGAAAAGGTGGCTGCTGCATTTTTCCAAAGCTGCCGAATTTATTGAGTGCAT
1 GGACGGCATTTAAAGAAAAGGTGGCTGCTGCATTTTTCCAAACCAGCCGAATTTAGTGAGTGCAT
46478584 GGGACTTG
66 GGGACTTG
* * * * * *
46478592 GGACGGCATTTAAAGCGAAA-GTTGCTGTTGTA-TTTTCCCAACCAGCCGAATTTAGTGTGTGCA
1 GGACGGCATTTAAAG-AAAAGGTGGCTGCTGCATTTTTCCAAACCAGCCGAATTTAGTGAGTGCA
46478655 TGGGACTTG
65 TGGGACTTG
** * *
46478664 GGATAGCA-TTAAA-AAGAGGAGGCTGCTG
1 GGACGGCATTTAAAGAAAAGGTGGCTGCTG
46478692 TTGCAATTTT
Statistics
Matches: 82, Mismatches: 16, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
69 2 0.02
70 7 0.09
71 5 0.06
72 41 0.50
73 24 0.29
74 3 0.04
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (73 bp):
GGACGGCATTTAAAGAAAAGGTGGCTGCTGCATTTTTCCAAACCAGCCGAATTTAGTGAGTGCAT
GGGACTTG
Found at i:46482477 original size:15 final size:17
Alignment explanation
Indices: 46482452--46482485 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
46482442 TTATATCATA
46482452 TATATTATTT-ACCTTT
1 TATATTATTTAACCTTT
46482468 TATA-TATTTAACCTTT
1 TATATTATTTAACCTTT
46482484 TA
1 TA
46482486 AAATTAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.59
Consensus pattern (17 bp):
TATATTATTTAACCTTT
Found at i:46487792 original size:34 final size:34
Alignment explanation
Indices: 46487749--46487815 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
46487739 TGCATTTCTA
46487749 ATACTGTTACTATAATGGGCTAAGGCCCACACTG
1 ATACTGTTACTATAATGGGCTAAGGCCCACACTG
46487783 ATACTGTTACTATAATGGGCTAAGGCCCACACT
1 ATACTGTTACTATAATGGGCTAAGGCCCACACT
46487816 AATATTAGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (34 bp):
ATACTGTTACTATAATGGGCTAAGGCCCACACTG
Found at i:46494040 original size:13 final size:13
Alignment explanation
Indices: 46493976--46494059 Score: 64
Period size: 13 Copynumber: 6.1 Consensus size: 13
46493966 TGAGAGAGAA
46493976 AGAAAAGAAAAATG
1 AGAAAAGAAAAA-G
46493990 AGAAAAAGAGAGGAAAG
1 AG-AAAAGA-A--AAAG
*
46494007 ACAACAA-AAGAAAG
1 AGAA-AAGAA-AAAG
* *
46494021 TGAAAAGAAAATG
1 AGAAAAGAAAAAG
46494034 AGAAAAGAAAAAG
1 AGAAAAGAAAAAG
46494047 A-AAAAGAAAAAG
1 AGAAAAGAAAAAG
46494059 A
1 A
46494060 ATGTGAGAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
12 12 0.21
13 17 0.29
14 11 0.19
15 7 0.12
16 4 0.07
17 4 0.07
18 3 0.05
ACGTcount: A:0.71, C:0.02, G:0.23, T:0.04
Consensus pattern (13 bp):
AGAAAAGAAAAAG
Found at i:46494047 original size:6 final size:6
Alignment explanation
Indices: 46494023--46494060 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
46494013 AAAGAAAGTG
*
46494023 AAAAGA AAATGA GAAAAGA AAAAGA AAAAGA AAAAGA A
1 AAAAGA AAAAGA -AAAAGA AAAAGA AAAAGA AAAAGA A
46494061 TGTGAGAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 24 0.83
7 5 0.17
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (6 bp):
AAAAGA
Found at i:46494048 original size:11 final size:11
Alignment explanation
Indices: 46494012--46494060 Score: 53
Period size: 11 Copynumber: 4.2 Consensus size: 11
46494002 GAAAGACAAC
**
46494012 AAAAGAAAGTG
1 AAAAGAAAAAG
46494023 AAAAGAAAATGAG
1 AAAAGAAAA--AG
46494036 AAAAGAAAAAG
1 AAAAGAAAAAG
46494047 AAAAAGAAAAAG
1 -AAAAGAAAAAG
46494059 AA
1 AA
46494061 TGTGAGAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
11 12 0.36
12 11 0.33
13 10 0.30
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:46496760 original size:30 final size:30
Alignment explanation
Indices: 46496726--46496822 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
46496716 AGCTCACTCC
46496726 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
46496756 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
46496786 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
46496816 TAGCTCA
1 TAGCTCA
46496823 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:46498556 original size:12 final size:13
Alignment explanation
Indices: 46498520--46498554 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
46498510 AGGAAATTTG
*
46498520 AAAATAAAAATTC
1 AAAAAAAAAATTC
46498533 AAAAAAAAAATTC
1 AAAAAAAAAATTC
46498546 AAAAAAAAA
1 AAAAAAAAA
46498555 TTTGAAGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.80, C:0.06, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAAAAAAAATTC
Found at i:46499507 original size:37 final size:37
Alignment explanation
Indices: 46499456--46499526 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
46499446 CATTCTTGTA
46499456 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
46499493 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
46499527 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:46499526 original size:6 final size:6
Alignment explanation
Indices: 46499466--46499515 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
46499456 AAGAGAAAAC
*
46499466 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
46499515 A
1 A
46499516 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:46499608 original size:11 final size:12
Alignment explanation
Indices: 46499576--46499606 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
46499566 TTGAGAGAAC
46499576 TTGAAAAAGCCT
1 TTGAAAAAGCCT
46499588 TTGAAAAAGCCT
1 TTGAAAAAGCCT
46499600 TTGAAAA
1 TTGAAAA
46499607 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:46501820 original size:30 final size:30
Alignment explanation
Indices: 46501786--46501882 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
46501776 AGCTCACTCC
46501786 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
46501816 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
46501846 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
46501876 TAGCTCA
1 TAGCTCA
46501883 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:46504515 original size:24 final size:23
Alignment explanation
Indices: 46504461--46504516 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 23
46504451 GATTAATTAA
**
46504461 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
46504484 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
46504508 GAAATGGTA
1 GAAATGGTA
46504517 ATGGTTCAAA
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.23, C:0.04, G:0.32, T:0.41
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:46507858 original size:20 final size:20
Alignment explanation
Indices: 46507835--46507881 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
46507825 GGGTTAAGAT
*
46507835 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
46507855 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
46507875 TGAGCTG
1 TGAGCTG
46507882 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:46509603 original size:48 final size:48
Alignment explanation
Indices: 46509548--46509653 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
46509538 TTGTCTTTTC
*
46509548 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
46509596 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
46509644 TTTCTTTTTC
1 TTTCTTTTTC
46509654 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:46509696 original size:18 final size:18
Alignment explanation
Indices: 46509629--46509696 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 18
46509619 TTTTCACATC
* *
46509629 CTTTTTCAATCTCAATTT
1 CTTTTTCAATCTCACTCT
* **
46509647 CTTTTTCCATGACACTCGTTT
1 CTTTTTCAATCTCACTC---T
46509668 CTTTCTTCAATCTCACTCT
1 CTTT-TTCAATCTCACTCT
46509687 CTTTTTCAAT
1 CTTTTTCAAT
46509697 TTCTTGTTCC
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
18 18 0.47
19 5 0.13
21 5 0.13
22 10 0.26
ACGTcount: A:0.18, C:0.28, G:0.03, T:0.51
Consensus pattern (18 bp):
CTTTTTCAATCTCACTCT
Found at i:46510807 original size:11 final size:11
Alignment explanation
Indices: 46510792--46510826 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
46510782 TTTTTGCTCG
46510792 ATTTTTTTTCA
1 ATTTTTTTTCA
* *
46510803 CTTTTTTTTGA
1 ATTTTTTTTCA
46510814 ATTTTTTTTCA
1 ATTTTTTTTCA
46510825 AT
1 AT
46510827 CAAATTTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.17, C:0.09, G:0.03, T:0.71
Consensus pattern (11 bp):
ATTTTTTTTCA
Found at i:46510807 original size:32 final size:30
Alignment explanation
Indices: 46510747--46510811 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 30
46510737 TTAAACTTGA
*
46510747 TTTTTTTTGCTCACCTTTTTTTTTCTTTTCTT
1 TTTTTTTTGCTCA-CTTTTTTTTACTTTT-TT
46510779 TTTTTTTTGCTCGA-TTTTTTTTCACTTTTTT
1 TTTTTTTTGCTC-ACTTTTTTTT-ACTTTTTT
46510810 TT
1 TT
46510812 GAATTTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
31 12 0.40
32 17 0.57
33 1 0.03
ACGTcount: A:0.05, C:0.15, G:0.05, T:0.75
Consensus pattern (30 bp):
TTTTTTTTGCTCACTTTTTTTTACTTTTTT
Found at i:46510848 original size:11 final size:12
Alignment explanation
Indices: 46510804--46510860 Score: 69
Period size: 12 Copynumber: 4.4 Consensus size: 12
46510794 TTTTTTTCAC
46510804 TTTTTTTTGAAT
1 TTTTTTTTGAAT
*
46510816 TTTTTTTCAATCAAAT
1 TTTTTTT---T-GAAT
46510832 TTTTTTTTGAAT
1 TTTTTTTTGAAT
46510844 TTTTTTTTGAAT
1 TTTTTTTTGAAT
46510856 TTTTT
1 TTTTT
46510861 GTTACTCCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
12 27 0.69
13 1 0.03
15 1 0.03
16 10 0.26
ACGTcount: A:0.19, C:0.04, G:0.05, T:0.72
Consensus pattern (12 bp):
TTTTTTTTGAAT
Found at i:46512371 original size:20 final size:20
Alignment explanation
Indices: 46512348--46512394 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
46512338 GGGTTAAGAT
*
46512348 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
46512368 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
46512388 TGAGCTG
1 TGAGCTG
46512395 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:46518635 original size:10 final size:10
Alignment explanation
Indices: 46518620--46518681 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
46518610 TTTGAACCAT
*
46518620 TACCAATTCG
1 TACCAATTCA
*
46518630 TACCAAATACCA
1 TACC-AAT-TCA
*
46518642 TACCATTTCA
1 TACCAATTCA
46518652 TACCAATTCCA
1 TACCAATT-CA
* *
46518663 TACCATTTCG
1 TACCAATTCA
46518673 TACCAATTC
1 TACCAATTC
46518682 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:46518665 original size:21 final size:21
Alignment explanation
Indices: 46518620--46518682 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
46518610 TTTGAACCAT
* *
46518620 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
46518642 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
46518663 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
46518683 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:46519390 original size:17 final size:18
Alignment explanation
Indices: 46519368--46519407 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
46519358 CATTTCTTTT
46519368 TCTTTTGAATCACTC-TC
1 TCTTTTGAATCACTCATC
*
46519385 TCTTTT-TATCACTCATC
1 TCTTTTGAATCACTCATC
46519402 T-TTTTG
1 TCTTTTG
46519408 TTTTTCTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.15, C:0.25, G:0.05, T:0.55
Consensus pattern (18 bp):
TCTTTTGAATCACTCATC
Found at i:46520174 original size:20 final size:20
Alignment explanation
Indices: 46520128--46520174 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
46520118 AGCTCGTTTC
*
46520128 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
46520148 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
46520168 CAGCTCA
1 CAGCTCA
46520175 ATTTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:46522362 original size:24 final size:23
Alignment explanation
Indices: 46522308--46522363 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 23
46522298 GATTAATTAA
*
46522308 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGATTTGGTAC
***
46522331 GTTTTGGTATTTGGGATTTGGTAC
1 GAAATGGTATTT-GGATTTGGTAC
46522355 GAAATGGTA
1 GAAATGGTA
46522364 ATGGTTCAAA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.21, C:0.04, G:0.32, T:0.43
Consensus pattern (23 bp):
GAAATGGTATTTGGATTTGGTAC
Found at i:46524780 original size:14 final size:13
Alignment explanation
Indices: 46524761--46524805 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
46524751 CCGTATGCAA
46524761 TTTTTTTTCAAATT
1 TTTTTTTTC-AATT
46524775 TTTTTTTTCAA-T
1 TTTTTTTTCAATT
* *
46524787 TATTTTTTCGATT
1 TTTTTTTTCAATT
46524800 TTTTTT
1 TTTTTT
46524806 GAATCTACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 10 0.37
13 8 0.30
14 9 0.33
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.76
Consensus pattern (13 bp):
TTTTTTTTCAATT
Found at i:46524786 original size:25 final size:25
Alignment explanation
Indices: 46524758--46524805 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
46524748 AGACCGTATG
46524758 CAATT-TTTTTTCAAATTTTTTTTTT
1 CAATTATTTTTTC-AATTTTTTTTTT
*
46524783 CAATTATTTTTTCGATTTTTTTT
1 CAATTATTTTTTCAATTTTTTTT
46524806 GAATCTACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.19, C:0.08, G:0.02, T:0.71
Consensus pattern (25 bp):
CAATTATTTTTTCAATTTTTTTTTT
Found at i:46538615 original size:12 final size:12
Alignment explanation
Indices: 46538598--46538654 Score: 71
Period size: 12 Copynumber: 4.8 Consensus size: 12
46538588 GACCGTATGC
46538598 AATTTTTTTTCA
1 AATTTTTTTTCA
46538610 AATTTTTTTTCA
1 AATTTTTTTTCA
* *
46538622 ATTTTTTTTTCG
1 AATTTTTTTTCA
*
46538634 ATTTTTTTTTC-
1 AATTTTTTTTCA
*
46538645 GATTTTTTTT
1 AATTTTTTTT
46538655 GAATCTACAA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
11 8 0.20
12 33 0.80
ACGTcount: A:0.16, C:0.07, G:0.04, T:0.74
Consensus pattern (12 bp):
AATTTTTTTTCA
Found at i:46538632 original size:24 final size:24
Alignment explanation
Indices: 46538600--46538654 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
46538590 CCGTATGCAA
46538600 TTTTTTTTCAAATTTTTTTTCAAT
1 TTTTTTTTCAAATTTTTTTTCAAT
* * *
46538624 TTTTTTTTCGATTTTTTTTTCGAT
1 TTTTTTTTCAAATTTTTTTTCAAT
46538648 TTTTTTT
1 TTTTTTT
46538655 GAATCTACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.13, C:0.07, G:0.04, T:0.76
Consensus pattern (24 bp):
TTTTTTTTCAAATTTTTTTTCAAT
Found at i:46548041 original size:20 final size:19
Alignment explanation
Indices: 46548018--46548082 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
46548008 AAGCTCAAAC
46548018 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
46548038 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
46548058 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
46548078 GAGCT
1 GAGCT
46548083 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:46548896 original size:9 final size:10
Alignment explanation
Indices: 46548889--46548945 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
46548879 AAGAGAAAAC
46548889 AAAGAAAAGA
1 AAAGAAAAGA
46548899 AAAGAAAAAGTA
1 AAAG-AAAAG-A
*
46548911 AAAGAAGA-A
1 AAAGAAAAGA
46548920 AAAGAAAACGA
1 AAAGAAAA-GA
46548931 AATA-AAAAGA
1 AA-AGAAAAGA
46548941 AAAGA
1 AAAGA
46548946 GAGGCAAGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:46548913 original size:6 final size:5
Alignment explanation
Indices: 46548889--46548945 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
46548879 AAGAGAAAAC
*
46548889 AAAGA AAAGA AAAGAA AAAGTA AAAGA AGA-A AAAGA AAACGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
46548936 AAAGA AAAGA
1 AAAGA AAAGA
46548946 GAGGCAAGTA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:46548920 original size:15 final size:14
Alignment explanation
Indices: 46548889--46548945 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
46548879 AAGAGAAAAC
46548889 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
46548905 AAAGTAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
46548920 AAAGAAAACGAAATAA
1 AAAGAAAA-G-AAGAA
46548936 AAAGAAAAGA
1 AAAGAAAAGA
46548946 GAGGCAAGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:46549041 original size:30 final size:31
Alignment explanation
Indices: 46549007--46549088 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 31
46548997 TTTGAAAAGC
*
46549007 AAAAAGAAAAAGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAAAGAAAAAGAAATATGAGAGTG
* * *
46549037 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAAAGAAAAAGAAATATGAGAGTG
* *
46549067 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAAAGAAAAAGAAAT
46549089 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.66, C:0.01, G:0.22, T:0.11
Consensus pattern (31 bp):
AAAAAGAAAAAGAAAAAGAAATATGAGAGTG
Found at i:46549061 original size:24 final size:24
Alignment explanation
Indices: 46549012--46549081 Score: 61
Period size: 24 Copynumber: 2.9 Consensus size: 24
46549002 AAAGCAAAAA
*
46549012 GAAAAAGAAAAAGAAAATGAGATT
1 GAAAAAGAAAAAGAAAATGAAATT
* *
46549036 GAAAAAGAGAACGAAAA-GAAATTT
1 GAAAAAGAAAAAGAAAATGAAA-TT
* ** *
46549060 GAGAGTGAAAAAGAAGATGAAA
1 GAAAAAGAAAAAGAAAATGAAA
46549082 AAGAAATTGA
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
23 3 0.09
24 28 0.80
25 4 0.11
ACGTcount: A:0.63, C:0.01, G:0.24, T:0.11
Consensus pattern (24 bp):
GAAAAAGAAAAAGAAAATGAAATT
Found at i:46552359 original size:14 final size:14
Alignment explanation
Indices: 46552338--46552368 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
46552328 ATCGTAGCTT
46552338 CAAAAAAAAAATTTG
1 CAAAAAAAAAA-TTG
46552353 CAAAAAAAAAATTG
1 CAAAAAAAAAATTG
46552367 CA
1 CA
46552369 TACGGTCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.68, C:0.10, G:0.06, T:0.16
Consensus pattern (14 bp):
CAAAAAAAAAATTG
Found at i:46554646 original size:24 final size:25
Alignment explanation
Indices: 46554619--46554672 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
46554609 ATGAGTGATA
*
46554619 AAAAAAGAGA-GAGTGATTCAAAA-G
1 AAAAAAGAAACGAGTGA-TCAAAATG
*
46554643 -AAAAAGAAACGAGTGATGAAAATG
1 AAAAAAGAAACGAGTGATCAAAATG
46554667 AAAAAA
1 AAAAAA
46554673 AGAATTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 13 0.52
24 7 0.28
25 5 0.20
ACGTcount: A:0.63, C:0.04, G:0.22, T:0.11
Consensus pattern (25 bp):
AAAAAAGAAACGAGTGATCAAAATG
Found at i:46562054 original size:30 final size:30
Alignment explanation
Indices: 46561959--46562055 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
46561949 AGCTCACTCC
* *
46561959 TAGCTC-ACTTTCAACTCACGAGCTAAATCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAAGCT
* * * **
46561989 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAG-CT
*
46562019 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
46562049 TAGCTCA
1 TAGCTCA
46562056 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 41 0.82
31 7 0.14
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAAGCT
Found at i:46562451 original size:14 final size:14
Alignment explanation
Indices: 46562432--46562476 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
46562422 AACTCATCTT
*
46562432 AGTTTAATTAAATG
1 AGTTTAATTTAATG
46562446 AGTTT-ATTTAATG
1 AGTTTAATTTAATG
*
46562459 AATTTAATTTAATG
1 AGTTTAATTTAATG
46562473 AGTT
1 AGTT
46562477 GCTTCTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:46563009 original size:14 final size:14
Alignment explanation
Indices: 46562990--46563034 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
46562980 AACTCATCTT
*
46562990 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
46563004 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
46563017 AATTTAATTTAATG
1 AGTTTAATTTAATG
46563031 AGTT
1 AGTT
46563035 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:46563127 original size:558 final size:558
Alignment explanation
Indices: 46562073--46563179 Score: 2108
Period size: 558 Copynumber: 2.0 Consensus size: 558
46562063 TTAAACTAGG
46562073 TGATACGATCGCGACCTGGAGTGCATCAAGTTCGAGCAAGGACTCAATGGTGCTGCCTCAAGGAC
1 TGATACGATCGCGACCTGGAGTGCATCAAGTTCGAGCAAGGACTCAATGGTGCTGCCTCAAGGAC
* *
46562138 CAATTACGTGAGCTCGAGCTAAGCAATTCAAGGAGGCCGTTTCGACCTTAGTTAATCAAGTGTGG
66 CAATTACGCGAGCTCGAGCTAAGCAATTCAAGGAGGCCATTTCGACCTTAGTTAATCAAGTGTGG
46562203 GGCGAGGCTTTGGTTGGAGAAATAGATCGAGTTGGGACCAGCTTAATAAAGTGTCCTTGCAACAT
131 GGCGAGGCTTTGGTTGGAGAAATAGATCGAGTTGGGACCAGCTTAATAAAGTGTCCTTGCAACAT
46562268 ATTGCAAACTAATTTCAGCTCAATTTCCGCTCCTTGAACCCGTTCCAACTAAATTGAACTTTTAT
196 ATTGCAAACTAATTTCAGCTCAATTTCCGCTCCTTGAACCCGTTCCAACTAAATTGAACTTTTAT
46562333 TTATTTCTTTTAGCTTTGCATTTAGTTTGCATTTTAATACTTGCATTTAAGCCTCTTAGTTTAAT
261 TTATTTCTTTTAGCTTTGCATTTAGTTTGCATTTTAATACTTGCATTTAAGCCTCTTAGTTTAAT
46562398 AAATGAGTTGCTGATCATTAATACAACTCATCTTAGTTTAATTAAATGAGTTTATTTAATGAATT
326 AAATGAGTTGCTGATCATTAATACAACTCATCTTAGTTTAATTAAATGAGTTTATTTAATGAATT
*
46562463 TAATTTAATGAGTTGCTTCTTTAATTAATCTAGTTACTAGGTTAATTTATTAGTGCATGAGTTAA
391 TAATTTAATGAGTTGCTTCTTTAATTAATCTAGTTACTAGGTTAATTTATCAGTGCATGAGTTAA
*
46562528 AGTTCATTAAATACTTCTTTTAATTAACTAGTTGTTGGAATAATTGATGCATAAGTGTGTGTTCA
456 AGTTCATTAAATACTTCTTTTAATTAACTAGTTGTTGGAATAAATGATGCATAAGTGTGTGTTCA
46562593 TTTATTTACGTAGTTGTTAATTTGTTTAATTGAATAAA
521 TTTATTTACGTAGTTGTTAATTTGTTTAATTGAATAAA
46562631 TGATACGATCGCGACCTGGAGTGCATCAAGTTCGAGCAAGGACTCAATGGTGCTGCCTCAAGGAC
1 TGATACGATCGCGACCTGGAGTGCATCAAGTTCGAGCAAGGACTCAATGGTGCTGCCTCAAGGAC
* *
46562696 CAATTACGCGAGCTCGAGCTAAGCAATTGAAGGAGGCCATTTCGGCCTTAGTTAATCAAGTGTGG
66 CAATTACGCGAGCTCGAGCTAAGCAATTCAAGGAGGCCATTTCGACCTTAGTTAATCAAGTGTGG
46562761 GGCGAGGCTTTGGTTGGAGAAATAGATCGAGTTGGGACCAGCTTAATAAAGTGTCCTTGCAACAT
131 GGCGAGGCTTTGGTTGGAGAAATAGATCGAGTTGGGACCAGCTTAATAAAGTGTCCTTGCAACAT
*
46562826 TTTGCAAACTAATTTCAGCTCAATTTCCGCTCCTTGAACCCGTTCCAACTAAATTGAACTTTTAT
196 ATTGCAAACTAATTTCAGCTCAATTTCCGCTCCTTGAACCCGTTCCAACTAAATTGAACTTTTAT
46562891 TTATTTCTTTTAGCTTTGCATTTAGTTTGCATTTTAATACTTGCATTTAAGCCTCTTAGTTTAAT
261 TTATTTCTTTTAGCTTTGCATTTAGTTTGCATTTTAATACTTGCATTTAAGCCTCTTAGTTTAAT
*
46562956 AAATGAGTTGCT-AGTCATTAATACAACTCATCTTAGTTTAATTAAATGAGTTTATTTGATGAAT
326 AAATGAGTTGCTGA-TCATTAATACAACTCATCTTAGTTTAATTAAATGAGTTTATTTAATGAAT
* *
46563020 TTAATTTAATGAGTTGCTTCTTTAATTTATCTAGTTACTAGGTTAATTTATCGGTGCATGAGTTA
390 TTAATTTAATGAGTTGCTTCTTTAATTAATCTAGTTACTAGGTTAATTTATCAGTGCATGAGTTA
46563085 AAGTTCATTAAATACTTCTTTTAATTAACTAGTTGTTGGAATAAATGATGCATAAGTGTGTGTTC
455 AAGTTCATTAAATACTTCTTTTAATTAACTAGTTGTTGGAATAAATGATGCATAAGTGTGTGTTC
46563150 ATTTATTTACGTAGTTGTTAATTTGTTTAA
520 ATTTATTTACGTAGTTGTTAATTTGTTTAA
46563180 AGCTTAATAA
Statistics
Matches: 538, Mismatches: 10, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
557 1 0.00
558 537 1.00
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.38
Consensus pattern (558 bp):
TGATACGATCGCGACCTGGAGTGCATCAAGTTCGAGCAAGGACTCAATGGTGCTGCCTCAAGGAC
CAATTACGCGAGCTCGAGCTAAGCAATTCAAGGAGGCCATTTCGACCTTAGTTAATCAAGTGTGG
GGCGAGGCTTTGGTTGGAGAAATAGATCGAGTTGGGACCAGCTTAATAAAGTGTCCTTGCAACAT
ATTGCAAACTAATTTCAGCTCAATTTCCGCTCCTTGAACCCGTTCCAACTAAATTGAACTTTTAT
TTATTTCTTTTAGCTTTGCATTTAGTTTGCATTTTAATACTTGCATTTAAGCCTCTTAGTTTAAT
AAATGAGTTGCTGATCATTAATACAACTCATCTTAGTTTAATTAAATGAGTTTATTTAATGAATT
TAATTTAATGAGTTGCTTCTTTAATTAATCTAGTTACTAGGTTAATTTATCAGTGCATGAGTTAA
AGTTCATTAAATACTTCTTTTAATTAACTAGTTGTTGGAATAAATGATGCATAAGTGTGTGTTCA
TTTATTTACGTAGTTGTTAATTTGTTTAATTGAATAAA
Found at i:46564034 original size:15 final size:15
Alignment explanation
Indices: 46564016--46564063 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
46564006 AAACCTACAA
*
46564016 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
46564031 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
46564045 AAACTTCATATCCAT
1 AAACTTCATATCCAT
46564060 AAAC
1 AAAC
46564064 CTATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:46564048 original size:29 final size:29
Alignment explanation
Indices: 46564010--46564069 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
46564000 AAAACCAAAC
*
46564010 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
* *
46564039 CTACATAAACTTCATATCCATAAACCTAT
1 CTACAAAAACTTCATATCCATAAACCCAT
46564068 CT
1 CT
46564070 TTGAATCCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:46565243 original size:18 final size:18
Alignment explanation
Indices: 46565220--46565269 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
46565210 GAAAGAAAAA
*
46565220 GAAAAAGAGATTGAGAGT
1 GAAAAAGAGAATGAGAGT
* *
46565238 GAAAAAGAAAATGAGATT
1 GAAAAAGAGAATGAGAGT
46565256 GAAAAAGAGAATGA
1 GAAAAAGAGAATGA
46565270 AAAAGAGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.58, C:0.00, G:0.28, T:0.14
Consensus pattern (18 bp):
GAAAAAGAGAATGAGAGT
Found at i:46565246 original size:24 final size:24
Alignment explanation
Indices: 46565213--46565294 Score: 92
Period size: 24 Copynumber: 3.4 Consensus size: 24
46565203 AAGAAATGAA
46565213 AGAAAAAGAAAAAGAGATTGAGAG
1 AGAAAAAGAAAAAGAGATTGAGAG
* * * *
46565237 TGAAAAAGAAAATGAGATTGAAAA
1 AGAAAAAGAAAAAGAGATTGAGAG
* * *
46565261 AGAGAATGAAAAAGAGTTTGAGAG
1 AGAAAAAGAAAAAGAGATTGAGAG
*
46565285 AGAGAAAGAA
1 AGAAAAAGAA
46565295 TGTGAACAAG
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.60, C:0.00, G:0.28, T:0.12
Consensus pattern (24 bp):
AGAAAAAGAAAAAGAGATTGAGAG
Found at i:46568021 original size:30 final size:30
Alignment explanation
Indices: 46567987--46568083 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
46567977 AGCTCACTCC
*
46567987 TAGCTCATA-TTCAACTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
46568017 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
46568047 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
46568077 TAGCTCA
1 TAGCTCA
46568084 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:46570665 original size:21 final size:21
Alignment explanation
Indices: 46570639--46570701 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
46570629 TTGGTATTTG
46570639 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
46570660 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
46570681 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
46570702 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:46573808 original size:11 final size:9
Alignment explanation
Indices: 46573787--46573835 Score: 64
Period size: 9 Copynumber: 5.2 Consensus size: 9
46573777 CATAAATCAC
46573787 TTTTTTTAT
1 TTTTTTTAT
46573796 TTTTTTTCGAT
1 TTTTTTT--AT
46573807 TTTTTTTA-
1 TTTTTTTAT
46573815 TTTTTTTAT
1 TTTTTTTAT
46573824 TTTTTTTGAT
1 TTTTTTT-AT
46573834 TT
1 TT
46573836 GCATAAATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
8 8 0.22
9 15 0.42
10 4 0.11
11 9 0.25
ACGTcount: A:0.10, C:0.02, G:0.04, T:0.84
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:46573818 original size:7 final size:8
Alignment explanation
Indices: 46573787--46573829 Score: 50
Period size: 8 Copynumber: 4.9 Consensus size: 8
46573777 CATAAATCAC
46573787 TTTTTTTA
1 TTTTTTTA
46573795 TTTTTTTTCGA
1 -TTTTTTT--A
46573806 TTTTTTTTA
1 -TTTTTTTA
46573815 TTTTTTTA
1 TTTTTTTA
46573823 TTTTTTT
1 TTTTTTT
46573830 TGATTTGCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
8 15 0.47
9 8 0.25
11 9 0.28
ACGTcount: A:0.09, C:0.02, G:0.02, T:0.86
Consensus pattern (8 bp):
TTTTTTTA
Found at i:46575160 original size:9 final size:9
Alignment explanation
Indices: 46575146--46575198 Score: 72
Period size: 9 Copynumber: 5.7 Consensus size: 9
46575136 CATAAATCAC
46575146 TTTTTTTAT
1 TTTTTTTAT
46575155 TTTTTTTCGAT
1 TTTTTTT--AT
46575166 TTTTTTTA-
1 TTTTTTTAT
46575174 TTTTTTTAT
1 TTTTTTTAT
46575183 TTTTTTTGAT
1 TTTTTTT-AT
46575193 TTTTTT
1 TTTTTT
46575199 AACTTGTATA
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
8 8 0.20
9 15 0.38
10 8 0.20
11 9 0.22
ACGTcount: A:0.09, C:0.02, G:0.04, T:0.85
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:46575186 original size:28 final size:27
Alignment explanation
Indices: 46575146--46575198 Score: 97
Period size: 28 Copynumber: 1.9 Consensus size: 27
46575136 CATAAATCAC
46575146 TTTTTTTATTTTTTTTCGATTTTTTTTA
1 TTTTTTTATTTTTTTT-GATTTTTTTTA
46575174 TTTTTTTATTTTTTTTGATTTTTTT
1 TTTTTTTATTTTTTTTGATTTTTTT
46575199 AACTTGTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 9 0.36
28 16 0.64
ACGTcount: A:0.09, C:0.02, G:0.04, T:0.85
Consensus pattern (27 bp):
TTTTTTTATTTTTTTTGATTTTTTTTA
Found at i:46575197 original size:17 final size:17
Alignment explanation
Indices: 46575146--46575199 Score: 72
Period size: 17 Copynumber: 2.9 Consensus size: 17
46575136 CATAAATCAC
46575146 TTTTTTTATTTTTTTTCGAT
1 TTTTTTTA-TTTTTTT--AT
46575166 TTTTTTTATTTTTTTAT
1 TTTTTTTATTTTTTTAT
46575183 TTTTTTTGATTTTTTTA
1 TTTTTTT-ATTTTTTTA
46575200 ACTTGTATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.27
18 9 0.27
19 7 0.21
20 8 0.24
ACGTcount: A:0.11, C:0.02, G:0.04, T:0.83
Consensus pattern (17 bp):
TTTTTTTATTTTTTTAT
Found at i:46575597 original size:14 final size:14
Alignment explanation
Indices: 46575550--46575597 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
46575540 GTACGAATGG
*
46575550 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
46575564 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
46575578 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
46575592 ATTGGT
1 AATGGT
46575598 CAGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:46578418 original size:10 final size:10
Alignment explanation
Indices: 46578403--46578464 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
46578393 TTTGAACCAT
*
46578403 TACCAATTCG
1 TACCAATTCA
*
46578413 TACCAAATACCA
1 TACC-AAT-TCA
*
46578425 TACCATTTCA
1 TACCAATTCA
46578435 TACCAATTCCA
1 TACCAATT-CA
* *
46578446 TACCATTTCG
1 TACCAATTCA
46578456 TACCAATTC
1 TACCAATTC
46578465 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:46578448 original size:21 final size:21
Alignment explanation
Indices: 46578403--46578465 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
46578393 TTTGAACCAT
* *
46578403 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
46578425 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
46578446 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
46578466 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:46579445 original size:33 final size:33
Alignment explanation
Indices: 46579390--46579455 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
46579380 TTTTATGCAA
* *
46579390 AGGTACATGCATGGACGGCTTCAATGCATGGTG
1 AGGTACATGCATGAACGACTTCAATGCATGGTG
* * *
46579423 AGGTACATGCATGAATGACTTCACTGTATGGTG
1 AGGTACATGCATGAACGACTTCAATGCATGGTG
46579456 TGCTGATGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.27
Consensus pattern (33 bp):
AGGTACATGCATGAACGACTTCAATGCATGGTG
Found at i:46587260 original size:10 final size:10
Alignment explanation
Indices: 46587254--46587281 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
46587244 CTTTTTTTTT
46587254 ATTTTTTTGA
1 ATTTTTTTGA
46587264 ATTTTTTTGA
1 ATTTTTTTGA
46587274 ATTTTTTT
1 ATTTTTTT
46587282 TCAAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.18, C:0.00, G:0.07, T:0.75
Consensus pattern (10 bp):
ATTTTTTTGA
Found at i:46587684 original size:14 final size:14
Alignment explanation
Indices: 46587667--46587706 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
46587657 CGAAAGGAAT
46587667 GGTAGGAACAAAAG
1 GGTAGGAACAAAAG
46587681 GGTAGGAACAAAAG
1 GGTAGGAACAAAAG
* *
46587695 GATATGAACAAA
1 GGTAGGAACAAA
46587707 TTGGTCGGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.53, C:0.07, G:0.30, T:0.10
Consensus pattern (14 bp):
GGTAGGAACAAAAG
Found at i:46589434 original size:30 final size:30
Alignment explanation
Indices: 46589339--46589435 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
46589329 AGCTCACTCC
*
46589339 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAACCT
* * * * * *
46589369 TAGCTCAACTTCAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* * *
46589399 CAGCTCAACTTTAGCTCACAAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
46589429 TAGCTCA
1 TAGCTCA
46589436 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
30 46 0.92
31 4 0.08
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:46592471 original size:20 final size:19
Alignment explanation
Indices: 46592448--46592512 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
46592438 AAGCTCAAAC
46592448 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
46592468 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
46592488 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
46592508 GAGCT
1 GAGCT
46592513 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:46594323 original size:33 final size:33
Alignment explanation
Indices: 46594285--46594347 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
46594275 GATTACTCAC
46594285 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
46594318 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
46594348 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:46594374 original size:21 final size:21
Alignment explanation
Indices: 46594345--46594400 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
46594335 CAAGCTCTCT
*
46594345 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
46594366 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
46594387 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
46594401 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:46594393 original size:14 final size:14
Alignment explanation
Indices: 46594344--46594400 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
46594334 TCAAGCTCTC
46594344 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
46594357 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
46594371 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
46594385 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
46594399 TT
1 TT
46594401 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:46594428 original size:18 final size:18
Alignment explanation
Indices: 46594407--46594458 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
46594397 TTTTCTCTCA
46594407 CTTTTTCGATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
46594425 CTTTTGCAATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
46594443 CTTCTTCGTTTTCTTT
1 CTTTTTCGATTTCTTT
46594459 CAATTTCTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.06, C:0.19, G:0.06, T:0.69
Consensus pattern (18 bp):
CTTTTTCGATTTCTTTTT
Found at i:46594471 original size:6 final size:6
Alignment explanation
Indices: 46594362--46594458 Score: 59
Period size: 6 Copynumber: 15.7 Consensus size: 6
46594352 TCTTTTTTCG
* * * **
46594362 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** * *
46594413 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTCTT CGTTTT CTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTT
46594459 CAATTTCTTT
Statistics
Matches: 64, Mismatches: 25, Indels: 4
0.69 0.27 0.04
Matches are distributed among these distances:
6 52 0.81
7 9 0.14
8 3 0.05
ACGTcount: A:0.07, C:0.21, G:0.03, T:0.69
Consensus pattern (6 bp):
CTTTTT
Found at i:46597105 original size:6 final size:5
Alignment explanation
Indices: 46597081--46597137 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
46597071 AAGAGCAAAC
*
46597081 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAACGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
46597128 AAAGA AAAGA
1 AAAGA AAAGA
46597138 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:46597110 original size:25 final size:27
Alignment explanation
Indices: 46597074--46597124 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
46597064 TCTTGTAAAG
46597074 AGCAAACAAAG-AAAAGAAAA-GAAAA
1 AGCAAACAAAGAAAAAGAAAACGAAAA
46597099 AGCAAA-AGAAGAAAAAGAAAACGAAA
1 AGCAAACA-AAGAAAAAGAAAACGAAA
46597125 TAAAAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 1 0.04
25 9 0.39
26 9 0.39
27 4 0.17
ACGTcount: A:0.75, C:0.08, G:0.18, T:0.00
Consensus pattern (27 bp):
AGCAAACAAAGAAAAAGAAAACGAAAA
Found at i:46597112 original size:15 final size:14
Alignment explanation
Indices: 46597081--46597137 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
46597071 AAGAGCAAAC
46597081 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
46597097 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
46597112 AAAGAAAACGAAATAA
1 AAAGAAAA-G-AAGAA
46597128 AAAGAAAAGA
1 AAAGAAAAGA
46597138 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:46597240 original size:30 final size:31
Alignment explanation
Indices: 46597206--46597287 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 31
46597196 TTTGAAAAGC
* *
46597206 AAAAATAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
46597236 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
46597266 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
46597288 TGAAACAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 8 0.19
30 25 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.21, T:0.13
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:46599495 original size:30 final size:30
Alignment explanation
Indices: 46599400--46599496 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
46599390 AGCTCACTCC
*
46599400 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAACCT
* * * * *
46599430 TAGCTCAACTTTAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* * *
46599460 CAGCTCAACTTTAGCTCACAAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
46599490 TAGCTCA
1 TAGCTCA
46599497 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
30 47 0.90
31 5 0.10
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.30
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:46601328 original size:20 final size:20
Alignment explanation
Indices: 46601305--46601350 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
46601295 CCAGCTCGAA
*
46601305 TTAGCTCACATGAGCTTAAT
1 TTAGCTCACATGAGCTCAAT
***
46601325 TTAGCTCGTTTGAGCTCAAT
1 TTAGCTCACATGAGCTCAAT
46601345 TTAGCT
1 TTAGCT
46601351 TACTTTAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
TTAGCTCACATGAGCTCAAT
Found at i:46601332 original size:30 final size:30
Alignment explanation
Indices: 46601297--46601370 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
46601287 CATTTTTCCC
46601297 AGCTCGAATT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-ATTGAGCTCA-ATTGAGCTTAATTT
* * *
46601327 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGATTGAGCTCAATTGAGCTTAATTT
*
46601357 AGCTCGTTTGAGCT
1 AGCTCGATTGAGCT
46601371 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 3 0.08
30 36 0.92
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGATTGAGCTCAATTGAGCTTAATTT
Found at i:46605740 original size:10 final size:11
Alignment explanation
Indices: 46605711--46605773 Score: 66
Period size: 10 Copynumber: 6.2 Consensus size: 11
46605701 AAATGAGATG
46605711 AAAT-GAGCT-
1 AAATCGAGCTC
46605720 AAATTCGAGCTC
1 AAA-TCGAGCTC
46605732 AAA-CGAGCT-
1 AAATCGAGCTC
46605741 AAATCGAGCTC
1 AAATCGAGCTC
46605752 AAA-CGAGCT-
1 AAATCGAGCTC
*
46605761 AAATCAAGCTC
1 AAATCGAGCTC
46605772 AA
1 AA
46605774 GTGAGCTGAT
Statistics
Matches: 46, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
9 9 0.20
10 24 0.52
11 10 0.22
12 3 0.07
ACGTcount: A:0.43, C:0.22, G:0.17, T:0.17
Consensus pattern (11 bp):
AAATCGAGCTC
Found at i:46605780 original size:20 final size:20
Alignment explanation
Indices: 46605715--46605773 Score: 100
Period size: 20 Copynumber: 2.9 Consensus size: 20
46605705 GAGATGAAAT
46605715 GAGCTAAATTCGAGCTCAAAC
1 GAGCTAAA-TCGAGCTCAAAC
46605736 GAGCTAAATCGAGCTCAAAC
1 GAGCTAAATCGAGCTCAAAC
*
46605756 GAGCTAAATCAAGCTCAA
1 GAGCTAAATCGAGCTCAA
46605774 GTGAGCTGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 29 0.78
21 8 0.22
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.17
Consensus pattern (20 bp):
GAGCTAAATCGAGCTCAAAC
Found at i:46608525 original size:20 final size:20
Alignment explanation
Indices: 46608502--46608548 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
46608492 GGGTTAAGAT
*
46608502 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
46608522 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
46608542 TGAGCTG
1 TGAGCTG
46608549 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:46610442 original size:30 final size:30
Alignment explanation
Indices: 46610406--46610490 Score: 100
Period size: 30 Copynumber: 2.8 Consensus size: 30
46610396 TTCTTTTGTT
* *
46610406 TCAATTTCTTTTTCATCTTCTTTTTCACTC
1 TCAATTTCTTTTTCTTCTTCTTTTTCAATC
**
46610436 TCAATTTTCTTTTAGTTC-TCTTTTTCAATC
1 TCAA-TTTCTTTTTCTTCTTCTTTTTCAATC
* *
46610466 TCATTTTCTTTTTCTTTTTCTTTTT
1 TCAATTTCTTTTTCTTCTTCTTTTT
46610491 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
29 10 0.22
30 25 0.56
31 10 0.22
ACGTcount: A:0.12, C:0.21, G:0.01, T:0.66
Consensus pattern (30 bp):
TCAATTTCTTTTTCTTCTTCTTTTTCAATC
Found at i:46610508 original size:12 final size:12
Alignment explanation
Indices: 46610493--46610523 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
46610483 TTCTTTTTGC
*
46610493 TTTTCAAAGTCT
1 TTTTCAAAGGCT
46610505 TTTTCAAAGGCT
1 TTTTCAAAGGCT
46610517 TTTTCAA
1 TTTTCAA
46610524 GTTCTCTCAA
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:0.26, C:0.16, G:0.10, T:0.48
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:46610581 original size:5 final size:5
Alignment explanation
Indices: 46610571--46610639 Score: 61
Period size: 5 Copynumber: 13.0 Consensus size: 5
46610561 CTCTTGCCTC
*
46610571 TCTTT TCTTT T-TATT TCGTTT TCTTTT TCTTT T-TCT TCTTT TGCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TC-TTT TCTTT TCTTT TCTTT T-CTTT
46610618 TGCTTTT TCTTT TCTTT TCTTT
1 T-C-TTT TCTTT TCTTT TCTTT
46610640 ATTTTCTCTT
Statistics
Matches: 55, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
4 4 0.07
5 29 0.53
6 17 0.31
7 5 0.09
ACGTcount: A:0.01, C:0.17, G:0.04, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:46610593 original size:6 final size:6
Alignment explanation
Indices: 46610584--46610639 Score: 53
Period size: 6 Copynumber: 9.2 Consensus size: 6
46610574 TTTCTTTTTA
* *
46610584 TTTCGT TTTCTT TTTCTT TTTCTTCT TTTGCTT TTGCTT TTTC-T TTTC-T
1 TTTCTT TTTCTT TTTCTT TTTC-T-T TTT-CTT TTTCTT TTTCTT TTTCTT
46610633 TTTCTT T
1 TTTCTT T
46610640 ATTTTCTCTT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
5 10 0.23
6 23 0.53
7 4 0.09
8 5 0.12
9 1 0.02
ACGTcount: A:0.00, C:0.18, G:0.05, T:0.77
Consensus pattern (6 bp):
TTTCTT
Found at i:46610597 original size:21 final size:19
Alignment explanation
Indices: 46610571--46610646 Score: 68
Period size: 22 Copynumber: 3.9 Consensus size: 19
46610561 CTCTTGCCTC
46610571 TCTTTTCTTTTTATTTCGTTT
1 TCTTTTCTTTTT-TTTC-TTT
*
46610592 TCTTTTTCTTTTTCTTCTTT
1 TC-TTTTCTTTTTTTTCTTT
46610612 TGCTTTTGC---TTTTTCTTT
1 T-CTTTT-CTTTTTTTTCTTT
*
46610630 TCTTTTCTTTATTTTCT
1 TCTTTTCTTTTTTTTCT
46610647 CTTTACAAGA
Statistics
Matches: 46, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
16 1 0.02
17 5 0.11
18 9 0.20
19 6 0.13
20 8 0.17
21 7 0.15
22 10 0.22
ACGTcount: A:0.03, C:0.17, G:0.04, T:0.76
Consensus pattern (19 bp):
TCTTTTCTTTTTTTTCTTT
Found at i:46611887 original size:20 final size:20
Alignment explanation
Indices: 46611862--46611928 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 20
46611852 TTGCTGGTCA
46611862 TTAATACAACTCATCTTAGT
1 TTAATACAACTCATCTTAGT
*
46611882 TTAATA-AA-TGAGT-TGCTAGT
1 TTAATACAACTCA-TCT--TAGT
46611902 CATTAATACAACTCATCTTAGT
1 --TTAATACAACTCATCTTAGT
46611924 TTAAT
1 TTAAT
46611929 TAAATGAGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 16
0.67 0.04 0.29
Matches are distributed among these distances:
18 3 0.08
19 3 0.08
20 15 0.41
22 10 0.27
23 3 0.08
24 3 0.08
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (20 bp):
TTAATACAACTCATCTTAGT
Found at i:46611892 original size:42 final size:42
Alignment explanation
Indices: 46611833--46611938 Score: 194
Period size: 42 Copynumber: 2.5 Consensus size: 42
46611823 CATTTAAGCC
*
46611833 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
1 TCTTAGTTTAATAAATGAGTTGCTAGTCATTAATACAACTCA
46611875 TCTTAGTTTAATAAATGAGTTGCTAGTCATTAATACAACTCA
1 TCTTAGTTTAATAAATGAGTTGCTAGTCATTAATACAACTCA
46611917 TCTTAGTTTAATTAAATGAGTT
1 TCTTAGTTTAA-TAAATGAGTT
46611939 TATTTAATGA
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
42 52 0.84
43 10 0.16
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.41
Consensus pattern (42 bp):
TCTTAGTTTAATAAATGAGTTGCTAGTCATTAATACAACTCA
Found at i:46611907 original size:22 final size:22
Alignment explanation
Indices: 46611840--46611909 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
46611830 GCCTCTTAGT
*
46611840 TTAATAAATGAGTTGCTGGTCA
1 TTAATAAATGAGTTGCTAGTCA
*
46611862 TTAATACAACTCA--T-CTTAGT--
1 TTAATA-AA-TGAGTTGC-TAGTCA
46611882 TTAATAAATGAGTTGCTAGTCA
1 TTAATAAATGAGTTGCTAGTCA
46611904 TTAATA
1 TTAATA
46611910 CAACTCATCT
Statistics
Matches: 37, Mismatches: 3, Indels: 16
0.66 0.05 0.29
Matches are distributed among these distances:
18 2 0.05
19 2 0.05
20 11 0.30
21 2 0.05
22 16 0.43
23 2 0.05
24 2 0.05
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (22 bp):
TTAATAAATGAGTTGCTAGTCA
Found at i:46611923 original size:22 final size:22
Alignment explanation
Indices: 46611858--46611923 Score: 61
Period size: 22 Copynumber: 3.1 Consensus size: 22
46611848 TGAGTTGCTG
46611858 GTCATTAATACAACTCATCTTA
1 GTCATTAATACAACTCATCTTA
*
46611880 GT--TTAATA-AA-TGAGT-TGCTA
1 GTCATTAATACAACTCA-TCT--TA
46611900 GTCATTAATACAACTCATCTTA
1 GTCATTAATACAACTCATCTTA
46611922 GT
1 GT
46611924 TTAATTAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 16
0.65 0.04 0.31
Matches are distributed among these distances:
18 3 0.09
19 3 0.09
20 10 0.29
22 12 0.35
23 3 0.09
24 3 0.09
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.38
Consensus pattern (22 bp):
GTCATTAATACAACTCATCTTA
Found at i:46611940 original size:14 final size:14
Alignment explanation
Indices: 46611921--46611965 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
46611911 AACTCATCTT
*
46611921 AGTTTAATTAAATG
1 AGTTTAATTTAATG
46611935 AGTTT-ATTTAATG
1 AGTTTAATTTAATG
*
46611948 AATTTAATTTAATG
1 AGTTTAATTTAATG
46611962 AGTT
1 AGTT
46611966 GCTTCTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:46614799 original size:30 final size:30
Alignment explanation
Indices: 46614765--46614861 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
46614755 TAAACTAAAA
46614765 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
46614795 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
46614825 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
46614855 TGAGCTA
1 TGAGCTA
46614862 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:46617395 original size:14 final size:14
Alignment explanation
Indices: 46617376--46617420 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
46617366 AACTCATCTT
*
46617376 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
46617390 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
46617403 AATTTAATTTAATG
1 AGTTTAATTTAATG
46617417 AGTT
1 AGTT
46617421 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:46617628 original size:20 final size:20
Alignment explanation
Indices: 46617603--46617657 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
46617593 TGTGGTTCAA
*
46617603 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
46617623 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
46617643 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
46617658 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:46620305 original size:30 final size:30
Alignment explanation
Indices: 46620271--46620367 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
46620261 TAAACTAAAA
46620271 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
46620301 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
46620331 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
46620360 ATGAGCTA
1 -TGAGCTA
46620368 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:46622514 original size:12 final size:12
Alignment explanation
Indices: 46622499--46622529 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
46622489 TTCTTTTTTC
46622499 TTTTCAAAGGCT
1 TTTTCAAAGGCT
46622511 TTTTCAAAGGCT
1 TTTTCAAAGGCT
46622523 TTTTCAA
1 TTTTCAA
46622530 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Done.