Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009175.1 Hibiscus syriacus cultivar Beakdansim tig00112738_pilon, whole genome shotgun sequence
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: 10629029
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 23 of 51
Found at i:4555890 original size:4 final size:4
Alignment explanation
Indices: 4555881--4555906 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
4555871 TCTTTATTTG
4555881 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
4555907 TTCTTTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:4555922 original size:23 final size:23
Alignment explanation
Indices: 4555896--4555941 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
4555886 TATTTATTTA
**
4555896 TTTATTTATTTTTCTTTCTTTTC
1 TTTATTTAACTTTCTTTCTTTTC
*
4555919 TTTATTTAACTTTCTTTGTTTTC
1 TTTATTTAACTTTCTTTCTTTTC
4555942 AATTTATCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.11, C:0.13, G:0.02, T:0.74
Consensus pattern (23 bp):
TTTATTTAACTTTCTTTCTTTTC
Found at i:4556339 original size:36 final size:36
Alignment explanation
Indices: 4556287--4556355 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
4556277 GGATCCACCC
*
4556287 GAAAGAAGGTTCTGACACTATACAAAAAAAAAACAG
1 GAAAAAAGGTTCTGACACTATACAAAAAAAAAACAG
4556323 GAAAAAAGGTTCTGACACTATACAAAAAAAAAA
1 GAAAAAAGGTTCTGACACTATACAAAAAAAAAA
4556356 AAAAAACAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.58, C:0.13, G:0.14, T:0.14
Consensus pattern (36 bp):
GAAAAAAGGTTCTGACACTATACAAAAAAAAAACAG
Found at i:4556371 original size:13 final size:14
Alignment explanation
Indices: 4556353--4556382 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
4556343 TACAAAAAAA
4556353 AAAAAAAAACA-AG
1 AAAAAAAAACACAG
4556366 AAAAAAAAACACAG
1 AAAAAAAAACACAG
4556380 AAA
1 AAA
4556383 TACAAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.83, C:0.10, G:0.07, T:0.00
Consensus pattern (14 bp):
AAAAAAAAACACAG
Found at i:4557488 original size:30 final size:30
Alignment explanation
Indices: 4557454--4557548 Score: 74
Period size: 27 Copynumber: 3.2 Consensus size: 30
4557444 TTTATCCAAT
4557454 AATAAAATATTTTGTATAATTATTAAATGA
1 AATAAAATATTTTGTATAATTATTAAATGA
*** *
4557484 AAT-AAAT-TTTAAAAT-ATTATTCAAT--
1 AATAAAATATTTTGTATAATTATTAAATGA
*
4557509 AATAAAATATTATTTTTGTGTAATTATTAAATGA
1 AAT-AAA-A-TA-TTTTGTATAATTATTAAATGA
4557543 AATAAA
1 AATAAA
4557549 TTAAAAATAT
Statistics
Matches: 47, Mismatches: 9, Indels: 15
0.66 0.13 0.21
Matches are distributed among these distances:
25 3 0.06
27 11 0.23
28 6 0.13
29 5 0.11
30 3 0.06
31 4 0.09
32 9 0.19
33 3 0.06
34 3 0.06
ACGTcount: A:0.51, C:0.01, G:0.05, T:0.43
Consensus pattern (30 bp):
AATAAAATATTTTGTATAATTATTAAATGA
Found at i:4557511 original size:55 final size:54
Alignment explanation
Indices: 4557445--4557576 Score: 192
Period size: 59 Copynumber: 2.4 Consensus size: 54
4557435 GTTCGTACAT
* *
4557445 TTATCCAATAATAAAATATTTTGTATAATTATTAAATGAAATAAATTTTAAAATA
1 TTATTCAATAATAAAATATTTTGTATAATTATTAAATGAAATAAA-TTAAAAATA
*
4557500 TTATTCAATAATAAAATATTATTTTTGTGTAATTATTAAATGAAATAAATTAAAAATA
1 TTATTCAATAAT-AAA-A-TA-TTTTGTATAATTATTAAATGAAATAAATTAAAAATA
4557558 TTATTCAATAATAAAATAT
1 TTATTCAATAATAAAATAT
4557577 GAAAATAATA
Statistics
Matches: 70, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
54 1 0.01
55 13 0.19
56 4 0.06
57 4 0.06
58 22 0.31
59 26 0.37
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (54 bp):
TTATTCAATAATAAAATATTTTGTATAATTATTAAATGAAATAAATTAAAAATA
Found at i:4557558 original size:58 final size:59
Alignment explanation
Indices: 4557463--4557576 Score: 203
Period size: 58 Copynumber: 1.9 Consensus size: 59
4557453 TAATAAAATA
*
4557463 TTTTGTATAATTATTAAATGAAATAAATTTTAAAATATTATTCAATAATAAAATATTAT
1 TTTTGTATAATTATTAAATGAAATAAATTTAAAAATATTATTCAATAATAAAATATTAT
*
4557522 TTTTGTGTAATTATTAAATGAAATAAA-TTAAAAATATTATTCAATAATAAAATAT
1 TTTTGTATAATTATTAAATGAAATAAATTTAAAAATATTATTCAATAATAAAATAT
4557577 GAAAATAATA
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
58 27 0.51
59 26 0.49
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (59 bp):
TTTTGTATAATTATTAAATGAAATAAATTTAAAAATATTATTCAATAATAAAATATTAT
Found at i:4564836 original size:15 final size:15
Alignment explanation
Indices: 4564816--4564847 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
4564806 TAAGTTGCAT
4564816 CAGGCTGTATTTTAC
1 CAGGCTGTATTTTAC
4564831 CAGGCTGTATTTTAC
1 CAGGCTGTATTTTAC
4564846 CA
1 CA
4564848 CGAGAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.38
Consensus pattern (15 bp):
CAGGCTGTATTTTAC
Found at i:4565912 original size:26 final size:26
Alignment explanation
Indices: 4565876--4565932 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
4565866 ACTAGTATTT
4565876 CCAACTCTATGTGGGACTGAGCATTA
1 CCAACTCTATGTGGGACTGAGCATTA
*
4565902 CCAACTCTATGTGGGATTGAGCATTA
1 CCAACTCTATGTGGGACTGAGCATTA
*
4565928 TCAAC
1 CCAAC
4565933 AACGGAGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (26 bp):
CCAACTCTATGTGGGACTGAGCATTA
Found at i:4576086 original size:14 final size:14
Alignment explanation
Indices: 4576044--4576091 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
4576034 CATTTTCACA
4576044 TATTTTTTAAAAAT
1 TATTTTTTAAAAAT
*
4576058 ATAATTTTTTTAAAAT
1 -T-ATTTTTTAAAAAT
* *
4576074 TATTTCTTAAAAAA
1 TATTTTTTAAAAAT
4576088 TATT
1 TATT
4576092 AAAATGAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 14 0.50
15 2 0.07
16 12 0.43
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (14 bp):
TATTTTTTAAAAAT
Found at i:4576887 original size:36 final size:36
Alignment explanation
Indices: 4576831--4577010 Score: 155
Period size: 36 Copynumber: 5.0 Consensus size: 36
4576821 CGTTCTGGGA
* *
4576831 AAAGCTAAACAAGCTACACCACCGCCGGCTCAGAAC
1 AAAGCTAAACAATCTGCACCACCGCCGGCTCAGAAC
* * * *** * *
4576867 AATGCTAAACAATCTGCACCACTGTCGGAAAAGCAG
1 AAAGCTAAACAATCTGCACCACCGCCGGCTCAGAAC
* * *** *
4576903 AAAGGTAAACAATCTGCAACACCGCCGGAAAAGAAG
1 AAAGCTAAACAATCTGCACCACCGCCGGCTCAGAAC
* * * *
4576939 AAAGATAAACAATCTGCAACATCGCCGGCTCAGAAT
1 AAAGCTAAACAATCTGCACCACCGCCGGCTCAGAAC
*
4576975 AAAGCTAAACAATCTG-AGCCACTGCCGGCTCAGAAC
1 AAAGCTAAACAATCTGCA-CCACCGCCGGCTCAGAAC
4577011 CGTACACTTC
Statistics
Matches: 116, Mismatches: 27, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
35 1 0.01
36 115 0.99
ACGTcount: A:0.41, C:0.28, G:0.19, T:0.13
Consensus pattern (36 bp):
AAAGCTAAACAATCTGCACCACCGCCGGCTCAGAAC
Found at i:4577571 original size:15 final size:15
Alignment explanation
Indices: 4577551--4577604 Score: 63
Period size: 15 Copynumber: 3.4 Consensus size: 15
4577541 CGACGAGTAC
*
4577551 GAAGAAGATGATGAA
1 GAAGAAGAGGATGAA
*
4577566 GAAGAAGAGGAGGAA
1 GAAGAAGAGGATGAA
4577581 GAAGAGCAAGAGGATGAA
1 G-A-AG-AAGAGGATGAA
4577599 GAAGAA
1 GAAGAA
4577605 ATCGTGCAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 16 0.48
16 3 0.09
17 3 0.09
18 11 0.33
ACGTcount: A:0.54, C:0.02, G:0.39, T:0.06
Consensus pattern (15 bp):
GAAGAAGAGGATGAA
Found at i:4577584 original size:18 final size:19
Alignment explanation
Indices: 4577563--4577604 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
4577553 AGAAGATGAT
4577563 GAAGAAG-AAGAGGAGGAA
1 GAAGAAGCAAGAGGAGGAA
*
4577581 GAAG-AGCAAGAGGATGAA
1 GAAGAAGCAAGAGGAGGAA
4577599 GAAGAA
1 GAAGAA
4577605 ATCGTGCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 2 0.10
18 18 0.86
19 1 0.05
ACGTcount: A:0.55, C:0.02, G:0.40, T:0.02
Consensus pattern (19 bp):
GAAGAAGCAAGAGGAGGAA
Found at i:4578440 original size:11 final size:11
Alignment explanation
Indices: 4578424--4578486 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
4578414 AAAATTACAT
4578424 TATTAAAAATA
1 TATTAAAAATA
4578435 TATTAAAAATA
1 TATTAAAAATA
* ***
4578446 CATTATTGATA
1 TATTAAAAATA
4578457 -ATTATAAAAT-
1 TATTA-AAAATA
4578467 T-TTAAAAATA
1 TATTAAAAATA
4578477 TATTAAAAAT
1 TATTAAAAAT
4578487 TCTATAATAC
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
9 5 0.12
10 8 0.20
11 28 0.68
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:4578817 original size:25 final size:26
Alignment explanation
Indices: 4578781--4578835 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
4578771 ATTAATAAAA
4578781 AATATTTATCTAATGACAAT-TATTT
1 AATATTTATCTAATGACAATATATTT
* *
4578806 AATATATT-TCTAATGATAATATTTTT
1 AATAT-TTATCTAATGACAATATATTT
4578832 AATA
1 AATA
4578836 ACTAATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 16 0.62
26 10 0.38
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (26 bp):
AATATTTATCTAATGACAATATATTT
Found at i:4578843 original size:16 final size:15
Alignment explanation
Indices: 4578805--4578846 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
4578795 GACAATTATT
*
4578805 TAAT-ATATTTCTAA
1 TAATAATATTTTTAA
*
4578819 TGATAATATTTTTAA
1 TAATAATATTTTTAA
4578834 TAACTAATATTTT
1 TAA-TAATATTTT
4578847 AAATTGTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 3 0.13
15 11 0.48
16 9 0.39
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.52
Consensus pattern (15 bp):
TAATAATATTTTTAA
Found at i:4579006 original size:14 final size:13
Alignment explanation
Indices: 4578985--4579026 Score: 57
Period size: 14 Copynumber: 3.1 Consensus size: 13
4578975 TGTAATGAAT
4578985 CTTAAACCCTAAA
1 CTTAAACCCTAAA
4578998 CTATAAACCCTAAA
1 CT-TAAACCCTAAA
*
4579012 CCTTAAACACTAAA
1 -CTTAAACCCTAAA
4579026 C
1 C
4579027 ACTTAATCTG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 3 0.12
14 21 0.81
15 2 0.08
ACGTcount: A:0.48, C:0.31, G:0.00, T:0.21
Consensus pattern (13 bp):
CTTAAACCCTAAA
Found at i:4581090 original size:20 final size:20
Alignment explanation
Indices: 4581065--4581117 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
4581055 ATATAATAAA
4581065 GGTACCGATACCCTAAAGAG
1 GGTACCGATACCCTAAAGAG
*
4581085 GGTACCGATACCCTAAGGAG
1 GGTACCGATACCCTAAAGAG
*
4581105 GGTATCGATACCC
1 GGTACCGATACCC
4581118 CCTAAAGGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.17
Consensus pattern (20 bp):
GGTACCGATACCCTAAAGAG
Found at i:4581501 original size:31 final size:30
Alignment explanation
Indices: 4581466--4581525 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
4581456 ATATGAGCTA
*
4581466 TGTGAT-AAAGATATGGAAAATGATATGTCTG
1 TGTGATAAAAG-TATGG-AAATAATATGTCTG
4581497 TGTGATAAAAGTATGGAAATAATATGTCT
1 TGTGATAAAAGTATGGAAATAATATGTCT
4581526 ACGCGATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 12 0.44
31 11 0.41
32 4 0.15
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.33
Consensus pattern (30 bp):
TGTGATAAAAGTATGGAAATAATATGTCTG
Found at i:4581524 original size:30 final size:31
Alignment explanation
Indices: 4581466--4581525 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
4581456 ATATGAGCTA
*
4581466 TGTGATAAAGATATGGAAAATGATATGTCTG
1 TGTGATAAAGATATGGAAAATAATATGTCTG
4581497 TGTGATAAA-AGTATGG-AAATAATATGTCT
1 TGTGATAAAGA-TATGGAAAATAATATGTCT
4581526 ACGCGATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 13 0.48
31 14 0.52
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.33
Consensus pattern (31 bp):
TGTGATAAAGATATGGAAAATAATATGTCTG
Found at i:4581804 original size:23 final size:23
Alignment explanation
Indices: 4581778--4581875 Score: 83
Period size: 23 Copynumber: 4.2 Consensus size: 23
4581768 GGTACTACGA
*
4581778 TGCAATTCTATGTGGCACTTCGG
1 TGCAATTCTACGTGGCACTTCGG
** *
4581801 TGCAATTCTATATGGAACTTCGG
1 TGCAATTCTACGTGGCACTTCGG
* * *
4581824 TGTATTTCTACGCGGTC-CTTCGG
1 TGCAATTCTACGTGG-CACTTCGG
*
4581847 -GACAAATTCTACGTGGCACTTCGA
1 TG-C-AATTCTACGTGGCACTTCGG
4581871 TGCAA
1 TGCAA
4581876 ATTTATACGA
Statistics
Matches: 58, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
22 1 0.02
23 40 0.69
24 16 0.28
25 1 0.02
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.33
Consensus pattern (23 bp):
TGCAATTCTACGTGGCACTTCGG
Found at i:4583545 original size:11 final size:11
Alignment explanation
Indices: 4583529--4583561 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
4583519 CGAGTTTGAG
4583529 ATCGAGCTCGA
1 ATCGAGCTCGA
4583540 ATCGAGCTTC-A
1 ATCGAGC-TCGA
4583551 ATCGAGCTCGA
1 ATCGAGCTCGA
4583562 GTCTCGAGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 2 0.10
11 16 0.80
12 2 0.10
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.21
Consensus pattern (11 bp):
ATCGAGCTCGA
Found at i:4583587 original size:17 final size:17
Alignment explanation
Indices: 4583541--4583589 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
4583531 CGAGCTCGAA
4583541 TCGAGCTTCAATCGAGC
1 TCGAGCTTCAATCGAGC
4583558 TCGAG--TC--TCGAGC
1 TCGAGCTTCAATCGAGC
4583571 TCGAGCTTCAATCGAGC
1 TCGAGCTTCAATCGAGC
4583588 TC
1 TC
4583590 TTGAAATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.39
15 4 0.14
17 13 0.46
ACGTcount: A:0.20, C:0.31, G:0.24, T:0.24
Consensus pattern (17 bp):
TCGAGCTTCAATCGAGC
Found at i:4585561 original size:20 final size:20
Alignment explanation
Indices: 4585536--4585573 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4585526 CACATGTTAA
4585536 AGAATGCATCGATGCACTAT
1 AGAATGCATCGATGCACTAT
*
4585556 AGAATGTATCGATGCACT
1 AGAATGCATCGATGCACT
4585574 TCAAGGGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (20 bp):
AGAATGCATCGATGCACTAT
Found at i:4586494 original size:14 final size:14
Alignment explanation
Indices: 4586449--4586496 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
4586439 TGTATGTGAT
4586449 ATATATAT-ATATG
1 ATATATATGATATG
*
4586462 -T-TTTATGATATG
1 ATATATATGATATG
4586474 A-ATTATATGATATG
1 ATA-TATATGATATG
4586488 ATATATATG
1 ATATATATG
4586497 TGTGTGTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
11 4 0.14
12 6 0.21
14 17 0.61
15 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (14 bp):
ATATATATGATATG
Found at i:4589491 original size:20 final size:22
Alignment explanation
Indices: 4589450--4589492 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
4589440 TCATGATGAG
4589450 ATATGGAATATAAAGATGGTTT
1 ATATGGAATATAAAGATGGTTT
*
4589472 ATATGG-ATAT-AAGTTGGTTT
1 ATATGGAATATAAAGATGGTTT
4589492 A
1 A
4589493 AATAATGGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 4 0.20
22 6 0.30
ACGTcount: A:0.37, C:0.00, G:0.23, T:0.40
Consensus pattern (22 bp):
ATATGGAATATAAAGATGGTTT
Found at i:4589788 original size:20 final size:20
Alignment explanation
Indices: 4589763--4589800 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4589753 CACATGTTAA
4589763 AGAATGCATCGATGCACTAT
1 AGAATGCATCGATGCACTAT
*
4589783 AGAATGTATCGATGCACT
1 AGAATGCATCGATGCACT
4589801 TCAAGGGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (20 bp):
AGAATGCATCGATGCACTAT
Found at i:4590769 original size:32 final size:34
Alignment explanation
Indices: 4590700--4590774 Score: 88
Period size: 32 Copynumber: 2.3 Consensus size: 34
4590690 ATGTATGTGA
4590700 TATAT-ATATATGTTTTGTGATATGAATTATATG
1 TATATGATATATGTTTTGTGATATGAATTATATG
*
4590733 -ATATGATATATGTGTTTGTTA-ATG-ATTAT-TG
1 TATATGATATATGT-TTTGTGATATGAATTATATG
*
4590764 TATATGTTATA
1 TATATGATATA
4590775 ATATATATGA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
31 2 0.05
32 18 0.49
33 11 0.30
34 6 0.16
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (34 bp):
TATATGATATATGTTTTGTGATATGAATTATATG
Found at i:4593953 original size:16 final size:16
Alignment explanation
Indices: 4593922--4593971 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 16
4593912 ATTACACTTG
4593922 AAGAAGAAGAAAAAGAAA
1 AAGAA-AAG-AAAAGAAA
4593940 AAGAAAAGAAAAGAAA
1 AAGAAAAGAAAAGAAA
*
4593956 AA-AAAACAAAAAGAAA
1 AAGAAAA-GAAAAGAAA
4593972 TACACATATG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 4 0.13
16 18 0.60
17 3 0.10
18 5 0.17
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (16 bp):
AAGAAAAGAAAAGAAA
Found at i:4595642 original size:86 final size:86
Alignment explanation
Indices: 4595386--4595642 Score: 354
Period size: 86 Copynumber: 3.0 Consensus size: 86
4595376 ATATCTGACT
* *
4595386 GAGGAATATACCACATGGCTTTCCTGTGAAGGGTAGTCATCTAAAGA-CTATCTCACTTGGTTCA
1 GAGGAATATACCACATGGCTTTCCTGTGAAGGGGAGTCATCCAAAGATC-ATCTCACTTGGTTCA
* *
4595450 GACCCGCTAAGGGGAACCACTC
65 GACCCGCTAAGGGGAATCACCC
* * * * * *
4595472 GAGGAATATACCGCATAGCTTTCCTATGAATGGGAGTCATCCAAAAATCATCTCACTTGGTTCAT
1 GAGGAATATACCACATGGCTTTCCTGTGAAGGGGAGTCATCCAAAGATCATCTCACTTGGTTCAG
4595537 ACCCGCTAAGGGGAATCACCC
66 ACCCGCTAAGGGGAATCACCC
* * *
4595558 GAGGAATATACCACATGGTTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTAACTTGGTTCAG
1 GAGGAATATACCACATGGCTTTCCTGTGAAGGGGAGTCATCCAAAGATCATCTCACTTGGTTCAG
** *
4595623 ACCCATTAAGGGGATTCACC
66 ACCCGCTAAGGGGAATCACC
4595643 TGAAGAATTA
Statistics
Matches: 148, Mismatches: 22, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
86 147 0.99
87 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (86 bp):
GAGGAATATACCACATGGCTTTCCTGTGAAGGGGAGTCATCCAAAGATCATCTCACTTGGTTCAG
ACCCGCTAAGGGGAATCACCC
Found at i:4595673 original size:86 final size:85
Alignment explanation
Indices: 4595407--4595683 Score: 262
Period size: 86 Copynumber: 3.2 Consensus size: 85
4595397 CACATGGCTT
* * *
4595407 TCCTGTGAAGGGTAGTCATCTAAAGA-CTATCTCACTTGGTTCAGACCCGCTAAGGGGAACCA-C
1 TCCTGTGAAGGGGAGTCATCCAAAGATC-ATCTCACTTGGTTCAGACCCGCTAAGGGGAATCACC
*
4595470 TCGAGGAA-TATACC-GCATAG
65 T-GAGGAATTATACCGGCTTAG
* * * *
4595490 CTTTCCTATGAATGGGAGTCATCCAAAAATCATCTCACTTGGTTCATACCCGCTAAGGGGAATCA
1 ---TCCTGTGAAGGGGAGTCATCCAAAGATCATCTCACTTGGTTCAGACCCGCTAAGGGGAATCA
* *
4595555 CCCGAGGAA-TATACCACATGG-TT-T
63 CCTGAGGAATTATA-C-C--GGCTTAG
* * ** *
4595579 TCCCGTGAAGGGGAGTCATCCAAAGATCATCTAACTTGGTTCAGACCCATTAAGGGGATTCACCT
1 TCCTGTGAAGGGGAGTCATCCAAAGATCATCTCACTTGGTTCAGACCCGCTAAGGGGAATCACCT
*
4595644 GAAGAATTATGACCGGCTTAG
66 GAGGAATTAT-ACCGGCTTAG
*
4595665 ACCTGTGAAGGGGAGTCAT
1 TCCTGTGAAGGGGAGTCAT
4595684 TTTTTACTTA
Statistics
Matches: 156, Mismatches: 24, Indels: 22
0.77 0.12 0.11
Matches are distributed among these distances:
84 2 0.01
85 2 0.01
86 141 0.90
87 7 0.04
88 2 0.01
90 1 0.01
91 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (85 bp):
TCCTGTGAAGGGGAGTCATCCAAAGATCATCTCACTTGGTTCAGACCCGCTAAGGGGAATCACCT
GAGGAATTATACCGGCTTAG
Found at i:4595858 original size:85 final size:85
Alignment explanation
Indices: 4595710--4596193 Score: 573
Period size: 85 Copynumber: 5.7 Consensus size: 85
4595700 CTATTGACAA
* * * * *
4595710 CATAACTCAAGGCGAAAAGGGTTATCTGTCAACCAAGACCTTTGAGTTTGATTATACTCAGCTCA
1 CATAACTCAAGGCGAAAAGGGTTATCTGTCAACCAAAACCTTCGAGTTCGATTACATTCAGCTCA
* *
4595775 AAGGCACATCAAATTTATAG
66 AAGGCATATCAAATTTACAG
* * * * * *
4595795 CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAGACCTTCAAGTTCGATTACACTCAGCTCA
1 CATAACTCAAGGCGAAAAGGGTTATCTGTCAACCAAAACCTTCGAGTTCGATTACATTCAGCTCA
4595860 AAGGCATATCAAATTTACAG
66 AAGGCATATCAAATTTACAG
* * *
4595880 AATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAAACCTTCGAGTTCGATTCCATTCAGCTC-
1 CATAACTCAAGGCGAAAAGGGTTATCTGTCAACCAAAACCTTCGAGTTCGATTACATTCAGCTCA
* * *
4595944 AA-GTATAGCCAAATTCACAG
66 AAGGCATA-TCAAATTTACAG
* * *
4595964 CATATCTCAAGGCGAAAAGGGTTATCTGTCAA-CACAAACCTTCGATTTCGATTACATTAAGCTC
1 CATAACTCAAGGCGAAAAGGGTTATCTGTCAACCA-AAACCTTCGAGTTCGATTACATTCAGCTC
* * *
4596028 TAAGACATATCAAATTCACAG
65 AAAGGCATATCAAATTTACAG
* * * * *
4596049 AATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGATTTCGATTACATTCAGCT-A
1 CATAACTCAAGGCGAAAAGGGTTATCTGTCAACCAAAACCTTCGAGTTCGATTACATTCAGCTCA
* *
4596113 TAAGACATGTCAAATTTACAG
66 -AAGGCATATCAAATTTACAG
* * * *
4596134 CATAACTCAAGACGAAAAGGGTTATCTGTCAA-CAAACACCTCCGAGTTTGATTTCATTCA
1 CATAACTCAAGGCGAAAAGGGTTATCTGTCAACCAAA-ACCTTCGAGTTCGATTACATTCA
4596194 ACTCGATGAC
Statistics
Matches: 347, Mismatches: 45, Indels: 14
0.85 0.11 0.03
Matches are distributed among these distances:
83 6 0.02
84 70 0.20
85 267 0.77
86 4 0.01
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (85 bp):
CATAACTCAAGGCGAAAAGGGTTATCTGTCAACCAAAACCTTCGAGTTCGATTACATTCAGCTCA
AAGGCATATCAAATTTACAG
Found at i:4596051 original size:169 final size:169
Alignment explanation
Indices: 4595711--4596167 Score: 596
Period size: 169 Copynumber: 2.7 Consensus size: 169
4595701 TATTGACAAC
* * * * * *
4595711 ATAACTCAAGGCGAAAAGGGTTATCTGTCAACCAAGACCTTTGAGTTTGATTATACTCAGCTCAA
1 ATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAAACCTTCGAGTTCGATTACATTCAGCTC-A
* * * *
4595776 AGGCACA-TCAAATTTATAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAAC-CAAGACCTTCA
65 A-G-ACAGTCAAATTTACAGCATAACTCAAGGCGAAAAGGGTTATCTGTCAACACAAGACCTTCA
* * *
4595839 AGTTCGATTACACTCAGCTCAAAGGCATATCAAATTTACAGA
128 AGTTCGATTACACTAAGCTCAAAGACATATCAAATTCACAGA
*
4595881 ATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAAACCTTCGAGTTCGATTCCATTCAGCTCAA
1 ATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAAACCTTCGAGTTCGATTACATTCAGCTCAA
* * * * * *
4595946 GTATAGCCAAATTCACAGCATATCTCAAGGCGAAAAGGGTTATCTGTCAACACAA-ACCTTCGAT
66 G-ACAGTCAAATTTACAGCATAACTCAAGGCGAAAAGGGTTATCTGTCAACACAAGACCTTCAAG
* *
4596010 TTCGATTACATTAAGCTCTAAGACATATCAAATTCACAGA
130 TTCGATTACACTAAGCTCAAAGACATATCAAATTCACAGA
* * * *
4596050 ATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGATTTCGATTACATTCAGCTATA
1 ATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAAACCTTCGAGTTCGATTACATTCAGCT-CA
*
4596115 AGACATGTCAAATTTACAGCATAACTCAAGACGAAAAGGGTTATCTGTCAACA
65 AGACA-GTCAAATTTACAGCATAACTCAAGGCGAAAAGGGTTATCTGTCAACA
4596168 AACACCTCCG
Statistics
Matches: 251, Mismatches: 32, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
168 3 0.01
169 143 0.57
170 105 0.42
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (169 bp):
ATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAAACCTTCGAGTTCGATTACATTCAGCTCAA
GACAGTCAAATTTACAGCATAACTCAAGGCGAAAAGGGTTATCTGTCAACACAAGACCTTCAAGT
TCGATTACACTAAGCTCAAAGACATATCAAATTCACAGA
Found at i:4596164 original size:254 final size:254
Alignment explanation
Indices: 4595710--4596193 Score: 679
Period size: 254 Copynumber: 1.9 Consensus size: 254
4595700 CTATTGACAA
* * *
4595710 CATAACTCAAGGCGAAAAGGGTTATCTGTCAACCAAGACCTTTGAGTTTGATTATACTCAGCTCA
1 CATAACTCAAGGCGAAAAGGGTTATCTGTCAACCAAGACCTTCGAGTTTGATTACACTAAGCTCA
* * * * * *
4595775 AAGGCACATCAAATTTATAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAGACCTTCAA
66 AAGACACATCAAATTCACAGAATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCAA
* * *
4595840 GTTCGATTACACTCAGCTCAAAGGCATATCAAATTTACAGAATAACTCAAGGCGAGAAGGGTTAT
131 GTTCGATTACACTCAGCTCAAAGACATATCAAATTTACAGAATAACTCAAGACGAAAAGGGTTAT
*
4595905 CTGTCAACCAAA-ACCTTCGAGTTCGATTCCATTCAGCTCAAGTATAGCCAAATTCACAG
196 CTGTCAA-CAAACACCTCCGAGTTCGATTCCATTCAGCTCAAGTATAGCCAAATTCACAG
* *
4595964 CATATCTCAAGGCGAAAAGGGTTATCTGTCAACACAA-ACCTTCGA-TTTCGATTACATTAAGCT
1 CATAACTCAAGGCGAAAAGGGTTATCTGTCAAC-CAAGACCTTCGAGTTT-GATTACACTAAGCT
* * *
4596027 CTAAGACATATCAAATTCACAGAATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTC
64 CAAAGACACATCAAATTCACAGAATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTC
* * * * *
4596092 GATTTCGATTACATTCAGCT-ATAAGACATGTCAAATTTACAGCATAACTCAAGACGAAAAGGGT
129 AAGTTCGATTACACTCAGCTCA-AAGACATATCAAATTTACAGAATAACTCAAGACGAAAAGGGT
* *
4596156 TATCTGTCAACAAACACCTCCGAGTTTGATTTCATTCA
193 TATCTGTCAACAAACACCTCCGAGTTCGATTCCATTCA
4596194 ACTCGATGAC
Statistics
Matches: 201, Mismatches: 25, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
253 8 0.04
254 190 0.95
255 3 0.01
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (254 bp):
CATAACTCAAGGCGAAAAGGGTTATCTGTCAACCAAGACCTTCGAGTTTGATTACACTAAGCTCA
AAGACACATCAAATTCACAGAATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCAA
GTTCGATTACACTCAGCTCAAAGACATATCAAATTTACAGAATAACTCAAGACGAAAAGGGTTAT
CTGTCAACAAACACCTCCGAGTTCGATTCCATTCAGCTCAAGTATAGCCAAATTCACAG
Found at i:4596659 original size:46 final size:44
Alignment explanation
Indices: 4596516--4596890 Score: 188
Period size: 43 Copynumber: 8.7 Consensus size: 44
4596506 CGACCTGATC
* * * * * *
4596516 TCCTCATCACGTAGGAGCCGTGTCAAC-CCCAGATAATCAGTCG
1 TCCTCATCACGTAGGAACCGTGTTATCACCTAGATAACCAGACG
* *
4596559 TCCTCATCATGTAGGAACCGTGTTATCACCTAGATAACCAGCCG
1 TCCTCATCACGTAGGAACCGTGTTATCACCTAGATAACCAGACG
**
4596603 TCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAAC-
1 TCCTCATCACGTAGGAACCGTGTTATCACC--TAGATAACCAG-ACG
* * * * *
4596649 TCTTCATCACGTATGAGA-CGTGTCATCACC-CG---ACCTGATC-
1 TCCTCATCACGTAGGA-ACCGTGTTATCACCTAGATAACCAGA-CG
* * * * * * *
4596689 TCCTCATCACATAGGAGCCGTGTCAAC-CCCAGATAACCAGTCA
1 TCCTCATCACGTAGGAACCGTGTTATCACCTAGATAACCAGACG
* ** * * *
4596732 TCCTCATCACGTAAGAAATGTGTTATCACCCTTAGATGGACTA-ACA
1 TCCTCATCACGTAGGAACCGTGTTATCA-CC-TAGAT-AACCAGACG
* * *
4596778 TCCTCATCACGTAGGAACCGTGTCATCACC-CG---ACCTGATC-
1 TCCTCATCACGTAGGAACCGTGTTATCACCTAGATAACCAGA-CG
* * * * * * * * *
4596818 TCCTTATAACATAGGAGCCGTGTCAAC-CCCAGATAACCAGCCA
1 TCCTCATCACGTAGGAACCGTGTTATCACCTAGATAACCAGACG
*
4596861 TCCTCATCACGTAGGAATCGTGTTATCACC
1 TCCTCATCACGTAGGAACCGTGTTATCACC
4596891 CTTAGATGGC
Statistics
Matches: 250, Mismatches: 58, Indels: 47
0.70 0.16 0.13
Matches are distributed among these distances:
39 7 0.03
40 50 0.20
41 1 0.00
42 2 0.01
43 73 0.29
44 44 0.18
45 4 0.02
46 64 0.26
47 5 0.02
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (44 bp):
TCCTCATCACGTAGGAACCGTGTTATCACCTAGATAACCAGACG
Found at i:4596985 original size:129 final size:129
Alignment explanation
Indices: 4596590--4596974 Score: 569
Period size: 129 Copynumber: 3.0 Consensus size: 129
4596580 GTTATCACCT
* * *
4596590 AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
1 AGATAACCAGCCATCCTCATCACGTAGGAATCGTGTTATCACCCTTAGATGGCCAGAACTCTTCA
4596655 TCACGTATGAGACGTGTCATCACCCGACCTGATCTCCTCATCACATAGGAGCCGTGTCAACCCC
66 TCACGTATGAGACGTGTCATCACCCGACCTGATCTCCTCATCACATAGGAGCCGTGTCAACCCC
* * * * *
4596719 AGATAACCAGTCATCCTCATCACGTAAGAAAT-GTGTTATCACCCTTAGATGGAC-TAACATCCT
1 AGATAACCAGCCATCCTCATCACGT-AGGAATCGTGTTATCACCCTTAGATGGCCAGAAC-TCTT
* * *
4596782 CATCACGTAGGA-ACCGTGTCATCACCCGACCTGATCTCCTTATAACATAGGAGCCGTGTCAACC
64 CATCACGTATGAGA-CGTGTCATCACCCGACCTGATCTCCTCATCACATAGGAGCCGTGTCAACC
4596846 CC
128 CC
4596848 AGATAACCAGCCATCCTCATCACGTAGGAATCGTGTTATCACCCTTAGATGGCCAGAACTCTTCA
1 AGATAACCAGCCATCCTCATCACGTAGGAATCGTGTTATCACCCTTAGATGGCCAGAACTCTTCA
* * * * **
4596913 TCACATATGAGTCGTGTCATCACCCGACATGATCTCCTCATCACGTAGGAGATGTGTCAACC
66 TCACGTATGAGACGTGTCATCACCCGACCTGATCTCCTCATCACATAGGAGCCGTGTCAACC
4596975 TTTGATAACC
Statistics
Matches: 225, Mismatches: 25, Indels: 12
0.86 0.10 0.05
Matches are distributed among these distances:
128 9 0.04
129 209 0.93
130 7 0.03
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.24
Consensus pattern (129 bp):
AGATAACCAGCCATCCTCATCACGTAGGAATCGTGTTATCACCCTTAGATGGCCAGAACTCTTCA
TCACGTATGAGACGTGTCATCACCCGACCTGATCTCCTCATCACATAGGAGCCGTGTCAACCCC
Found at i:4598667 original size:23 final size:23
Alignment explanation
Indices: 4598641--4598717 Score: 102
Period size: 23 Copynumber: 3.3 Consensus size: 23
4598631 AAATACACCA
4598641 AAGTGCCACGTAGAAATGCAACG
1 AAGTGCCACGTAGAAATGCAACG
*
4598664 AAGTGCCGCGTAGAAATGC-ACTG
1 AAGTGCCACGTAGAAATGCAAC-G
* *
4598687 AAGTGCCACGTAGAACTGCACCG
1 AAGTGCCACGTAGAAATGCAACG
*
4598710 TAGTGCCA
1 AAGTGCCA
4598718 TATAATGTCC
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
22 2 0.04
23 44 0.94
24 1 0.02
ACGTcount: A:0.32, C:0.25, G:0.27, T:0.16
Consensus pattern (23 bp):
AAGTGCCACGTAGAAATGCAACG
Found at i:4600295 original size:20 final size:20
Alignment explanation
Indices: 4600270--4600307 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4600260 TCCCCTTTGA
4600270 AGTGCATCGATACATTCTAT
1 AGTGCATCGATACATTCTAT
*
4600290 AGTGCATCGATGCATTCT
1 AGTGCATCGATACATTCT
4600308 TTAACATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.34
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAT
Found at i:4600438 original size:64 final size:63
Alignment explanation
Indices: 4600315--4600451 Score: 143
Period size: 64 Copynumber: 2.2 Consensus size: 63
4600305 TCTTTAACAT
* * * *
4600315 GTGCATCGATGCATTACCCATGCATCGATACACTAATCACCTTCAATGTTTTCATTTTAAGGGG
1 GTGCATCGATGCACTACCCATGCATCGATACACTAATCACATTCAATGTTTTCATTTTAA-AGA
* * ** * *
4600379 GTGCATCGATGCACT-CCTTATGCATCGATGCACTAATTGCATTCGATG-TTTCTTCTTTAAAGA
1 GTGCATCGATGCACTACC-CATGCATCGATACACTAATCACATTCAATGTTTTCAT-TTTAAAGA
4600442 GTGCATCGAT
1 GTGCATCGAT
4600452 ACACATTGAA
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
63 18 0.30
64 43 0.70
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (63 bp):
GTGCATCGATGCACTACCCATGCATCGATACACTAATCACATTCAATGTTTTCATTTTAAAGA
Found at i:4602239 original size:30 final size:30
Alignment explanation
Indices: 4602165--4602298 Score: 94
Period size: 30 Copynumber: 4.3 Consensus size: 30
4602155 TAATTACTGG
4602165 TTTAGTCATTTT-AGTTGT-TATTTTTTTTACT
1 TTTAGTC-TTTTAAGTT-TCTATTTTTTTTA-T
*
4602196 ATTTA-ACTCTTTAAGTTTCTATTTTTTTTAT
1 -TTTAGTCT-TTTAAGTTTCTATTTTTTTTAT
* * * *
4602227 TTTAGTCTTTTAAATGTCTGTTTTTGTTAT
1 TTTAGTCTTTTAAGTTTCTATTTTTTTTAT
* ** * *
4602257 TTTAATAATTTAACTTTCTGTTTTTTTTTAT
1 TTTAGTCTTTTAAGTTTCT-ATTTTTTTTAT
4602288 TTTAGTACTTT
1 TTTAGT-CTTT
4602299 AAATGTTTAT
Statistics
Matches: 80, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
30 37 0.46
31 22 0.28
32 21 0.26
ACGTcount: A:0.19, C:0.07, G:0.07, T:0.66
Consensus pattern (30 bp):
TTTAGTCTTTTAAGTTTCTATTTTTTTTAT
Found at i:4602288 original size:31 final size:30
Alignment explanation
Indices: 4602217--4602304 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 30
4602207 TAAGTTTCTA
**
4602217 TTTTTTTTATTTTAGTCTTTTAAATGTCTG
1 TTTTTTTTATTTTAGTAATTTAAATGTCTG
* * * *
4602247 TTTTTGTTATTTTAATAATTTAACTTTCTG
1 TTTTTTTTATTTTAGTAATTTAAATGTCTG
*
4602277 TTTTTTTTTATTTTAGTACTTTAAATGT
1 -TTTTTTTTATTTTAGTAATTTAAATGT
4602305 TTATTAATAT
Statistics
Matches: 46, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
30 24 0.52
31 22 0.48
ACGTcount: A:0.20, C:0.06, G:0.08, T:0.66
Consensus pattern (30 bp):
TTTTTTTTATTTTAGTAATTTAAATGTCTG
Found at i:4602453 original size:30 final size:29
Alignment explanation
Indices: 4602384--4602491 Score: 78
Period size: 30 Copynumber: 3.7 Consensus size: 29
4602374 GCCATTTTAA
* *
4602384 TCTTTTAAATTTC-ATTTTGTGATATT-TGG
1 TCTTTTAAATTTCTATTTT-T-CTATTCTAG
**
4602413 TCTTCAAAATTTCTATTTTTACTATTCTAG
1 TCTTTTAAATTTCTATTTTT-CTATTCTAG
* * *
4602443 -CTTTTTAAATTTTTGTTTGTTCTATTTTAG
1 TC-TTTTAAATTTCTATTT-TTCTATTCTAG
*
4602473 TCTTTTAATTTTCTATTTT
1 TCTTTTAAATTTCTATTTT
4602492 AAAACTTAAA
Statistics
Matches: 61, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
29 18 0.30
30 40 0.66
31 3 0.05
ACGTcount: A:0.20, C:0.10, G:0.07, T:0.62
Consensus pattern (29 bp):
TCTTTTAAATTTCTATTTTTCTATTCTAG
Found at i:4603311 original size:2 final size:2
Alignment explanation
Indices: 4603304--4603381 Score: 156
Period size: 2 Copynumber: 39.0 Consensus size: 2
4603294 AATCACCAAC
4603304 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4603346 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4603382 TTTGCATCAA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4614070 original size:23 final size:24
Alignment explanation
Indices: 4614042--4614090 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
4614032 TATTATATTA
4614042 AAGG-AATGAA-TTAATAAAATTTT
1 AAGGAAATGAAGTT-ATAAAATTTT
4614065 AAGGAAAATGAAGTTATAAAATTTT
1 AAGG-AAATGAAGTTATAAAATTTT
4614090 A
1 A
4614091 GAGTTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 4 0.17
25 17 0.74
26 2 0.09
ACGTcount: A:0.53, C:0.00, G:0.14, T:0.33
Consensus pattern (24 bp):
AAGGAAATGAAGTTATAAAATTTT
Found at i:4614390 original size:83 final size:82
Alignment explanation
Indices: 4614239--4614507 Score: 324
Period size: 83 Copynumber: 3.3 Consensus size: 82
4614229 GTCGCGACAA
* * * * ** * *
4614239 TAGTAGTTTAGCTGTGTTTTTATACAAACGCTGCAATA-GGTTCATCCTTAGTGGCATTTTTTCA
1 TAGTACTTTAGCGGCGTTTTTACACAAATACTGCAATAGGGTTCAT-CTTAGTGGCGTTTATTCA
*** ** *
4614303 ACAAATGTCGTGACAGAG
65 ACAAACACCGCAACAAAG
* * *
4614321 TAGAACTTTAGCGGCGTTTTTACACAAATTCTGTAATAGGGTTCATCTATAGTGGCGTTTATTCA
1 TAGTACTTTAGCGGCGTTTTTACACAAATACTGCAATAGGGTTCATCT-TAGTGGCGTTTATTCA
*
4614386 ACAAACACCGCAACAAAA
65 ACAAACACCGCAACAAAG
*
4614404 TAGTACTTTAGCGGCGTTTTTACACAAATACTGCAATAGGGTTCATCTGTAGTGGCGTTTATTTA
1 TAGTACTTTAGCGGCGTTTTTACACAAATACTGCAATAGGGTTCATCT-TAGTGGCGTTTATTCA
*
4614469 ATAAACACCGCAACAAAG
65 ACAAACACCGCAACAAAG
4614487 TAGTACTTTAGCGGCGTTTTT
1 TAGTACTTTAGCGGCGTTTTT
4614508 TTGTCATCCA
Statistics
Matches: 161, Mismatches: 24, Indels: 3
0.86 0.13 0.02
Matches are distributed among these distances:
82 32 0.20
83 129 0.80
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.34
Consensus pattern (82 bp):
TAGTACTTTAGCGGCGTTTTTACACAAATACTGCAATAGGGTTCATCTTAGTGGCGTTTATTCAA
CAAACACCGCAACAAAG
Found at i:4614420 original size:42 final size:41
Alignment explanation
Indices: 4614374--4614505 Score: 117
Period size: 42 Copynumber: 3.2 Consensus size: 41
4614364 CATCTATAGT
*
4614374 GGCGTTTATTCAACAAACACCGCAACAAAATAGTACTTTAGC
1 GGCGTTTATT-AACAAACACCGCAACAAAGTAGTACTTTAGC
* * * ** * *
4614416 GGCGTTT-TTACACAAATACTGCAATAGGGT--TCATCTGTAGT
1 GGCGTTTATTA-ACAAACACCGCAACAAAGTAGT-A-CTTTAGC
*
4614457 GGCGTTTATTTAATAAACACCGCAACAAAGTAGTACTTTAGC
1 GGCGTTTA-TTAACAAACACCGCAACAAAGTAGTACTTTAGC
4614499 GGCGTTT
1 GGCGTTT
4614506 TTTTGTCATC
Statistics
Matches: 67, Mismatches: 16, Indels: 14
0.69 0.16 0.14
Matches are distributed among these distances:
39 1 0.01
40 2 0.03
41 27 0.40
42 32 0.48
43 4 0.06
44 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.30
Consensus pattern (41 bp):
GGCGTTTATTAACAAACACCGCAACAAAGTAGTACTTTAGC
Found at i:4614461 original size:41 final size:41
Alignment explanation
Indices: 4614333--4614463 Score: 106
Period size: 41 Copynumber: 3.2 Consensus size: 41
4614323 GAACTTTAGC
* *
4614333 GGCGTTTTTACACAAATTCTGTAATAGGGTTCATCTATAGT
1 GGCGTTTTTACACAAATACTGCAATAGGGTTCATCTATAGT
* * * *** * *
4614374 GGCGTTTATT-CAACAAACACCGCAACA-AAAT-AGTACTTTAGC
1 GGCGTTT-TTAC-ACAAATACTGCAATAGGGTTCA-T-CTATAGT
*
4614416 GGCGTTTTTACACAAATACTGCAATAGGGTTCATCTGTAGT
1 GGCGTTTTTACACAAATACTGCAATAGGGTTCATCTATAGT
4614457 GGCGTTT
1 GGCGTTT
4614464 ATTTAATAAA
Statistics
Matches: 65, Mismatches: 18, Indels: 14
0.67 0.19 0.14
Matches are distributed among these distances:
40 1 0.02
41 36 0.55
42 27 0.42
43 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (41 bp):
GGCGTTTTTACACAAATACTGCAATAGGGTTCATCTATAGT
Found at i:4618920 original size:21 final size:21
Alignment explanation
Indices: 4618896--4618937 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
4618886 CCTACTATAG
*
4618896 TGCTACAGTGCATCGATGCAT
1 TGCTACAGTGCACCGATGCAT
*
4618917 TGCTACAGTGCACCGTTGCAT
1 TGCTACAGTGCACCGATGCAT
4618938 AAAACTTCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (21 bp):
TGCTACAGTGCACCGATGCAT
Found at i:4619670 original size:31 final size:31
Alignment explanation
Indices: 4619632--4619898 Score: 453
Period size: 31 Copynumber: 8.6 Consensus size: 31
4619622 TTCATAGATT
* *
4619632 CCGAAGAACCTAGGTAATCAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
4619663 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
*
4619694 CCGAAGAACATAGGTAAATAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
4619725 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
*
4619756 CTGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
*
4619787 CCGAAGAACATAGGTAAATAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
4619818 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
* *
4619849 CTGAATAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
* *
4619880 CAGAAGAACATACGTAAAC
1 CCGAAGAACATAGGTAAAC
4619899 CCTCGACCCT
Statistics
Matches: 223, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 223 1.00
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAGTCCATATGTC
Found at i:4620655 original size:20 final size:20
Alignment explanation
Indices: 4620630--4620684 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
4620620 CAAAATATCC
4620630 ATGCATCGATGCACCCCTTA
1 ATGCATCGATGCACCCCTTA
* *
4620650 ATGCATCGATGCAGCTCTTA
1 ATGCATCGATGCACCCCTTA
4620670 ATGCATCGATGCACC
1 ATGCATCGATGCACC
4620685 ACCCAGAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.25
Consensus pattern (20 bp):
ATGCATCGATGCACCCCTTA
Found at i:4623725 original size:21 final size:21
Alignment explanation
Indices: 4623701--4623742 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
4623691 CATATTATAG
*
4623701 TGCTACAGTGCATCGATGCAT
1 TGCTACAGTGCACCGATGCAT
*
4623722 TGCTACAGTGCACCGTTGCAT
1 TGCTACAGTGCACCGATGCAT
4623743 AAAACTTCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (21 bp):
TGCTACAGTGCACCGATGCAT
Found at i:4624454 original size:31 final size:31
Alignment explanation
Indices: 4624418--4624558 Score: 228
Period size: 31 Copynumber: 4.5 Consensus size: 31
4624408 TATAGATTCT
* * *
4624418 GAAGAACCTAGGTGATCAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
* *
4624449 AAAGAACATAGGTAAACATTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
4624480 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
*
4624511 GAAGAACATAGGTAAACAGTCCATATGTCCT
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
4624542 GAAGAACATAGGTAAAC
1 GAAGAACATAGGTAAAC
4624559 CCTCGACCCT
Statistics
Matches: 102, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 102 1.00
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (31 bp):
GAAGAACATAGGTAAACAGTCCATATGTCCC
Found at i:4624781 original size:30 final size:29
Alignment explanation
Indices: 4624735--4624795 Score: 104
Period size: 30 Copynumber: 2.1 Consensus size: 29
4624725 TACGTACTAC
4624735 ATGTATGTGTAACATTTATTTCATACCAT
1 ATGTATGTGTAACATTTATTTCATACCAT
*
4624764 ATGTATGTGTAAACATTTATTTCATATCAT
1 ATGTATGTGT-AACATTTATTTCATACCAT
4624794 AT
1 AT
4624796 AACATATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.33, C:0.11, G:0.10, T:0.46
Consensus pattern (29 bp):
ATGTATGTGTAACATTTATTTCATACCAT
Found at i:4627395 original size:29 final size:29
Alignment explanation
Indices: 4627328--4627395 Score: 68
Period size: 29 Copynumber: 2.3 Consensus size: 29
4627318 TAATTGAATT
4627328 TTTAAGGATTAAAATGTAAGAGAGCTAAAA
1 TTTAAGGA-TAAAATGTAAGAGAGCTAAAA
** *
4627358 TCCATGGATACAAATGTAA-A-AGTCTAAAA
1 TTTAAGGATA-AAATGTAAGAGAG-CTAAAA
4627387 TTTAAGGAT
1 TTTAAGGAT
4627396 CTAAATTTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
28 2 0.07
29 15 0.50
30 13 0.43
ACGTcount: A:0.47, C:0.07, G:0.18, T:0.28
Consensus pattern (29 bp):
TTTAAGGATAAAATGTAAGAGAGCTAAAA
Found at i:4627740 original size:21 final size:21
Alignment explanation
Indices: 4627715--4627761 Score: 78
Period size: 20 Copynumber: 2.3 Consensus size: 21
4627705 AAACCCAATT
4627715 AAAATAAAAAAAAAACAAGAA
1 AAAATAAAAAAAAAACAAGAA
*
4627736 AAAAT-AAAAAAAAACAAGTA
1 AAAATAAAAAAAAAACAAGAA
4627756 AAAATA
1 AAAATA
4627762 TGCAAGGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.83, C:0.04, G:0.04, T:0.09
Consensus pattern (21 bp):
AAAATAAAAAAAAAACAAGAA
Found at i:4628145 original size:100 final size:106
Alignment explanation
Indices: 4628041--4628266 Score: 266
Period size: 110 Copynumber: 2.2 Consensus size: 106
4628031 GTCATTATAT
*
4628041 GTGACCAAAATGCAAAAACAAGCTAAAATAAGGGGGACTAAACAAC-AAT-A-AA-C-ATATAAC
1 GTGACCAAAATGCAAAAACAAGCTAAAATAAGAGGGACTAAACAACAAATAACAATCAATATAAC
*
4628101 ATATA-AAAAAAAGGGTAAATAACAATTTTGGTCCTTGCAG
66 ATATATAAAAAAAGGGTAAATAACAATTTTGGTCCTCGCAG
** *** * *
4628141 GTGACCAATGTGCAAAAATGCGCTAAACTTAGAGGGACTAAACAACAAATAACCCAATCAATATA
1 GTGACCAAAATGCAAAAACAAGCTAAAATAAGAGGGACTAAACAACAAATAA--CAATC-A-ATA
* * *
4628206 TAACATATATGAAAAAAGGGTAAATACCAATTTTGGTTCTCGCAG
62 TAACATATATAAAAAAAGGGTAAATAACAATTTTGGTCCTCGCAG
4628251 GTGACCAAAATGCAAA
1 GTGACCAAAATGCAAA
4628267 TACTTTCAAA
Statistics
Matches: 102, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
100 38 0.37
101 3 0.03
102 1 0.01
105 2 0.02
106 1 0.01
109 12 0.12
110 45 0.44
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.20
Consensus pattern (106 bp):
GTGACCAAAATGCAAAAACAAGCTAAAATAAGAGGGACTAAACAACAAATAACAATCAATATAAC
ATATATAAAAAAAGGGTAAATAACAATTTTGGTCCTCGCAG
Found at i:4629045 original size:3 final size:3
Alignment explanation
Indices: 4629039--4629110 Score: 58
Period size: 3 Copynumber: 24.7 Consensus size: 3
4629029 GGTTTTTTTG
* * * * * *
4629039 TAA TAA TAA TAA TGA TAT TTA TAA TAA TAT TAA TAA TAA AAA TAA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
4629087 T-G TAT TAA TAA T-A TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
4629111 TAAGATATTA
Statistics
Matches: 52, Mismatches: 15, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
2 3 0.06
3 49 0.94
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:4630636 original size:7 final size:6
Alignment explanation
Indices: 4630614--4630653 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
4630604 ATTTTCATCA
4630614 TTTTTC -TTTTC TTTTTCC TTTTTC TTTTTC TTTTT- TTTTT
1 TTTTTC TTTTTC TTTTT-C TTTTTC TTTTTC TTTTTC TTTTT
4630654 GCTTAGGCGT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
5 10 0.31
6 16 0.50
7 6 0.19
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTC
Found at i:4630638 original size:13 final size:12
Alignment explanation
Indices: 4630614--4630653 Score: 57
Period size: 11 Copynumber: 3.4 Consensus size: 12
4630604 ATTTTCATCA
4630614 TTTTTC-TTTTC
1 TTTTTCTTTTTC
4630625 TTTTTCCTTTTTC
1 TTTTT-CTTTTTC
4630638 TTTTTCTTTTT-
1 TTTTTCTTTTTC
4630649 TTTTT
1 TTTTT
4630654 GCTTAGGCGT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 10 0.37
12 7 0.26
13 10 0.37
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTCTTTTTC
Found at i:4643579 original size:29 final size:30
Alignment explanation
Indices: 4643510--4643583 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
4643500 TAATTGAATT
* * *
4643510 TTTAAGG-TCTAAAATGTAAGAGATCTAACA
1 TTTAAGGATCT-AAATGTAAAAGATATAAAA
*
4643540 TTCAAGGATCTAAATGTAAAAG-TATAAAA
1 TTTAAGGATCTAAATGTAAAAGATATAAAA
4643569 TTTAAGGATCTAAAT
1 TTTAAGGATCTAAAT
4643584 TTATAATATT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
29 19 0.50
30 16 0.42
31 3 0.08
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (30 bp):
TTTAAGGATCTAAATGTAAAAGATATAAAA
Found at i:4643582 original size:15 final size:15
Alignment explanation
Indices: 4643510--4643586 Score: 54
Period size: 14 Copynumber: 5.3 Consensus size: 15
4643500 TAATTGAATT
4643510 TTTAAGG-TCTAAAA
1 TTTAAGGATCTAAAA
* *
4643524 TGTAAGAGATCTAACA
1 TTTAAG-GATCTAAAA
*
4643540 TTCAAGGATCT-AAA
1 TTTAAGGATCTAAAA
* * *
4643554 TGTAA-AAGTATAAAA
1 TTTAAGGA-TCTAAAA
4643569 TTTAAGGATCT-AAA
1 TTTAAGGATCTAAAA
4643583 TTTA
1 TTTA
4643587 TAATATTTAA
Statistics
Matches: 46, Mismatches: 12, Indels: 10
0.68 0.18 0.15
Matches are distributed among these distances:
13 1 0.02
14 19 0.41
15 15 0.33
16 11 0.24
ACGTcount: A:0.45, C:0.08, G:0.14, T:0.32
Consensus pattern (15 bp):
TTTAAGGATCTAAAA
Found at i:4645201 original size:3 final size:3
Alignment explanation
Indices: 4645195--4645239 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
4645185 TGTTTTTTTT
* * * *
4645195 TAA TAA TAA TAA TGA TAT TTA TAA TAA TAT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4645240 GATAAGGTAT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:4648665 original size:34 final size:33
Alignment explanation
Indices: 4648627--4648706 Score: 81
Period size: 34 Copynumber: 2.4 Consensus size: 33
4648617 CCCTAGCCGT
*
4648627 TCTTCTGCTCTT-GCCGTTCTATCGTGTTCTCCTA
1 TCTTCTGCT-TTAGCCATTCTATC-TGTTCTCCTA
* * *
4648661 TCTTCTTCTTTAATCTATTCTATCTGTTCTCCTA
1 TCTTCTGCTTT-AGCCATTCTATCTGTTCTCCTA
*
4648695 TCTTCTTCTTTA
1 TCTTCTGCTTTA
4648707 ATCTATTCTA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
33 3 0.08
34 29 0.73
35 8 0.20
ACGTcount: A:0.10, C:0.29, G:0.07, T:0.54
Consensus pattern (33 bp):
TCTTCTGCTTTAGCCATTCTATCTGTTCTCCTA
Found at i:4648707 original size:34 final size:35
Alignment explanation
Indices: 4648643--4648716 Score: 141
Period size: 34 Copynumber: 2.1 Consensus size: 35
4648633 GCTCTTGCCG
4648643 TTCTATCGTGTTCTCCTATCTTCTTCTTTAATCTA
1 TTCTATCGTGTTCTCCTATCTTCTTCTTTAATCTA
4648678 TTCTATC-TGTTCTCCTATCTTCTTCTTTAATCTA
1 TTCTATCGTGTTCTCCTATCTTCTTCTTTAATCTA
4648712 TTCTA
1 TTCTA
4648717 ACCAAGTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
34 32 0.82
35 7 0.18
ACGTcount: A:0.15, C:0.26, G:0.04, T:0.55
Consensus pattern (35 bp):
TTCTATCGTGTTCTCCTATCTTCTTCTTTAATCTA
Found at i:4648712 original size:17 final size:17
Alignment explanation
Indices: 4648658--4648712 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
4648648 TCGTGTTCTC
4648658 CTATCTTCTTCTTTAAT
1 CTATCTTCTTCTTTAAT
*
4648675 CTA--TTCTATCTGTT-CT
1 CTATCTTCT-TCT-TTAAT
4648691 CCTATCTTCTTCTTTAAT
1 -CTATCTTCTTCTTTAAT
4648709 CTAT
1 CTAT
4648713 TCTAACCAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
15 4 0.13
16 4 0.13
17 14 0.47
18 4 0.13
19 4 0.13
ACGTcount: A:0.16, C:0.25, G:0.02, T:0.56
Consensus pattern (17 bp):
CTATCTTCTTCTTTAAT
Found at i:4655073 original size:30 final size:30
Alignment explanation
Indices: 4655037--4655110 Score: 103
Period size: 30 Copynumber: 2.5 Consensus size: 30
4655027 GGTTAACTTG
** *
4655037 TTGACTTTGACCGAGTCAACTTGTTGATCA
1 TTGACTTTGACCGAGTCAACCCGTTGACCA
* *
4655067 TTGACTTTGACCAAGTCAACCCGTTGACCG
1 TTGACTTTGACCGAGTCAACCCGTTGACCA
4655097 TTGACTTTGACCGA
1 TTGACTTTGACCGA
4655111 AAAAGTCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.32
Consensus pattern (30 bp):
TTGACTTTGACCGAGTCAACCCGTTGACCA
Found at i:4658832 original size:15 final size:17
Alignment explanation
Indices: 4658812--4658851 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
4658802 AAACCTCGAG
4658812 AAGAAG-GATG-AGAAA
1 AAGAAGAGATGAAGAAA
4658827 AAGAAGGAGATGAAGAAA
1 AAGAA-GAGATGAAGAAA
4658845 AAGAAGA
1 AAGAAGA
4658852 ACGTTAGAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 5 0.23
16 1 0.05
17 6 0.27
18 10 0.45
ACGTcount: A:0.62, C:0.00, G:0.33, T:0.05
Consensus pattern (17 bp):
AAGAAGAGATGAAGAAA
Found at i:4661589 original size:17 final size:17
Alignment explanation
Indices: 4661567--4661609 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
4661557 CTTGTTGCTC
4661567 GAGGGTATACTCAAGAA
1 GAGGGTATACTCAAGAA
4661584 GAGGGTATACTCAAGAA
1 GAGGGTATACTCAAGAA
4661601 GAGGGTATA
1 GAGGGTATA
4661610 AATTATGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.40, C:0.09, G:0.33, T:0.19
Consensus pattern (17 bp):
GAGGGTATACTCAAGAA
Found at i:4664352 original size:15 final size:15
Alignment explanation
Indices: 4664332--4664361 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
4664322 CCTAGGAAAT
4664332 TTGGTTTAGATAACG
1 TTGGTTTAGATAACG
4664347 TTGGTTTAGATAACG
1 TTGGTTTAGATAACG
4664362 AGAGAGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.27, T:0.40
Consensus pattern (15 bp):
TTGGTTTAGATAACG
Found at i:4674094 original size:182 final size:182
Alignment explanation
Indices: 4673783--4674258 Score: 731
Period size: 182 Copynumber: 2.6 Consensus size: 182
4673773 CGATCCAAAT
* * * *
4673783 TAAAAATGTATCGATCCATATCAATATAACAGGTAAAAATATCGATAAAACCGGTCA-CGAAAAG
1 TAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATAT-GATAAAACCGGT-ATCGAAATG
* * * ** *
4673847 ACAATACCGGTAAA-TCCTTACCGGATATATTGAACGTGTCGATACTTTAATATAAGAATCGACA
64 ATAAAACCAGTAAAGAGC-TACCGGATATATTGAAAGTGTCGATACTTTAATATAAGAATCGACA
*
4673911 CTTTGTGAATTTAAAAGAGAAGCAGTTTTAACGCCTATAAAGTGTCGATACTTTA
128 CTTTGTGAATTTAAAAGAAAAGCAGTTTTAACGCCTATAAAGTGTCGATACTTTA
*
4673966 TAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCGGTATCGAAATGAT
1 TAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCGAAATGAT
* * * *
4674031 AAAACCAGAAAAGAGCTACCGGATATATTTAAAGTGTCGGTACTTTAATATAAGTATCGACACTT
66 AAAACCAGTAAAGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGAATCGACACTT
*
4674096 TGTGAATTTAAAAGAAAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTA
131 TGTGAATTTAAAAGAAAAGCAGTTTTAACGCCTATAAAGTGTCGATACTTTA
* *
4674148 TAAAAATGTATCGATCCACAACGATATAAGAGGTAAAAATATGATAAAACCGGTATCAAAATGAT
1 TAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCGAAATGAT
*
4674213 AAAACCAGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTT
66 AAAACCAGTAAAGAGCTACCGGATATATTGAAAGTGTCGATACTTT
4674259 CATAATTACT
Statistics
Matches: 267, Mismatches: 24, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
181 1 0.00
182 226 0.85
183 40 0.15
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.27
Consensus pattern (182 bp):
TAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCGAAATGAT
AAAACCAGTAAAGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGAATCGACACTT
TGTGAATTTAAAAGAAAAGCAGTTTTAACGCCTATAAAGTGTCGATACTTTA
Found at i:4674202 original size:20 final size:19
Alignment explanation
Indices: 4674179--4674224 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
4674169 CGATATAAGA
4674179 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
4674199 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
*
4674219 AGTAAA
1 GGTAAA
4674225 GCGCTACCGG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.05
20 18 0.82
21 3 0.14
ACGTcount: A:0.54, C:0.11, G:0.15, T:0.20
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:4676483 original size:21 final size:21
Alignment explanation
Indices: 4676459--4676523 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
4676449 AAGACAATCA
*
4676459 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAAAAACTTGAG
*
4676480 AGAGTTGAAGAAAAACTTGAG
1 AGAGTCGAAGAAAAACTTGAG
* *
4676501 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAAAAACTTGAG
4676522 AG
1 AG
4676524 GCATAAGGGG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.43, C:0.09, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAAAAACTTGAG
Found at i:4676619 original size:33 final size:33
Alignment explanation
Indices: 4676557--4676622 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
4676547 AAATAGATGG
* *
4676557 AGTGGTGAATAAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAATAAAGTAGAGATGTTAAGGGGTGA
*
4676590 AGTGGTGAA-AGAAGTTGAGATGTTAAGGGGTGA
1 AGTGGTGAATA-AAGTAGAGATGTTAAGGGGTGA
4676623 TCTTAAGATG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 1 0.03
33 28 0.97
ACGTcount: A:0.32, C:0.00, G:0.44, T:0.24
Consensus pattern (33 bp):
AGTGGTGAATAAAGTAGAGATGTTAAGGGGTGA
Found at i:4679309 original size:201 final size:201
Alignment explanation
Indices: 4678711--4679421 Score: 1176
Period size: 201 Copynumber: 3.5 Consensus size: 201
4678701 CATCCACAAG
* *
4678711 TATAATGTAATAGGTAAATTTTCAATGTAACCGGTATAAATATACCGATTTTATGAGAGAATAGG
1 TATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGG
** *
4678776 TCTACAACATGTATCGACACTTTGTGGAATTTTGTGTCAATACTTTTGGTCTAGAATGGATGCAC
66 TCTACAACATGTATCGACACTTT-TTTAATTTTGTGTCGATACTTTTGGTCTAGAATGGATGC-C
*
4678841 AAAAAGGGTGAACACATAAAGTGTCGATATATTTTCAAAAAGTGTCGATCCC-AAAACATCGAAA
129 AAAAAGGGTGAACACATAAAGTGTCGATACATTTTCAAAAAGTGTCGATCCCAAAAACATCGAAA
4678905 CCCATAAT
194 CCCATAAT
* * *
4678913 TATAATGTAATAGGTAAATTTACAATGTAATCGGTATACATATACCGGTTTTATGAGAGAATAAG
1 TATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGG
* * ** * * * *
4678978 TCTATAATATGTATTAACAC-TTCTTAATATTGTGTCGATAATTTTTGTCTAGAATGGATGCCAA
66 TCTACAACATGTATCGACACTTTTTTAATTTTGTGTCGATACTTTTGGTCTAGAATGGATGCCAA
* *
4679042 AAAGGGTGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGTCGATCCGAAAAACATCGAAACC
131 AAAGGGTGAACACATAAAGTGTCGATACATTTTCAAAAAGTGTCGATCCCAAAAACATCGAAACC
4679107 CATAAT
196 CATAAT
4679113 TATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGG
1 TATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGG
* *
4679178 TCTACAACATGTATCGACACTTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATAGATGCCAA
66 TCTACAACATGTATCGACACTTTTTTAATTTTGTGTCGATACTTTTGGTCTAGAATGGATGCCAA
4679243 AAAGGGTGCAAC-CATAAAGTGTCGATACATTTTCAAAAAGTGTCGATCCCAAAAACATCGAAAC
131 AAAGGGTG-AACACATAAAGTGTCGATACATTTTCAAAAAGTGTCGATCCCAAAAACATCGAAAC
4679307 CCATAAT
195 CCATAAT
*
4679314 TATAATGTAATAGGTAAATTTACAATGTAACTGGTATAAATATACCGGTTTTATGAGAGAATAGG
1 TATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGG
4679379 TCTACAACATGTATCGACACTTTTTTAATTTTGTGTCGATACT
66 TCTACAACATGTATCGACACTTTTTTAATTTTGTGTCGATACT
4679422 AATTTAAATA
Statistics
Matches: 472, Mismatches: 34, Indels: 7
0.92 0.07 0.01
Matches are distributed among these distances:
199 50 0.11
200 130 0.28
201 213 0.45
202 79 0.17
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (201 bp):
TATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGG
TCTACAACATGTATCGACACTTTTTTAATTTTGTGTCGATACTTTTGGTCTAGAATGGATGCCAA
AAAGGGTGAACACATAAAGTGTCGATACATTTTCAAAAAGTGTCGATCCCAAAAACATCGAAACC
CATAAT
Found at i:4680658 original size:20 final size:20
Alignment explanation
Indices: 4680635--4680687 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
4680625 ATTCGCGTTG
4680635 CATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
4680655 CATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
4680675 CATTTCGCGTTGC
1 CATTTCGCGTTGC
4680688 AATAGTCTAC
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:0.09, C:0.26, G:0.21, T:0.43
Consensus pattern (20 bp):
CATTTCGCGTTGCGATTTTC
Found at i:4680714 original size:22 final size:22
Alignment explanation
Indices: 4680689--4680734 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
4680679 TCGCGTTGCA
*
4680689 ATAGTCTACAGTTGTTGTTACG
1 ATAGTCTACAGTTGTCGTTACG
*
4680711 ATAGTCTACAGTTGTCGTTGCG
1 ATAGTCTACAGTTGTCGTTACG
4680733 AT
1 AT
4680735 TTTCCAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (22 bp):
ATAGTCTACAGTTGTCGTTACG
Found at i:4681399 original size:6 final size:6
Alignment explanation
Indices: 4681349--4681402 Score: 78
Period size: 6 Copynumber: 9.5 Consensus size: 6
4681339 GTCCATCTCG
*
4681349 GGTCG- GGTCG- GGTCG- GGTCGG GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
4681394 GGTCGT GGT
1 GGTCGT GGT
4681403 AATACGTGTC
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
5 15 0.32
6 32 0.68
ACGTcount: A:0.00, C:0.17, G:0.56, T:0.28
Consensus pattern (6 bp):
GGTCGT
Found at i:4681569 original size:19 final size:19
Alignment explanation
Indices: 4681547--4681641 Score: 100
Period size: 19 Copynumber: 4.7 Consensus size: 19
4681537 ACTGTAGACT
4681547 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
4681566 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
** *
4681585 ATCGCAACGACAACTGTAAA
1 ATCGCAACGA-ATTTGGAAA
**
4681605 CTATCGCAACGCAAAATGGAAA
1 --ATCGCAACG-AATTTGGAAA
4681627 ATCGCAACGCAATTT
1 ATCGCAACG-AATTT
4681642 TCAACTATCG
Statistics
Matches: 65, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
19 29 0.45
20 19 0.29
22 16 0.25
23 1 0.02
ACGTcount: A:0.42, C:0.21, G:0.18, T:0.19
Consensus pattern (19 bp):
ATCGCAACGAATTTGGAAA
Found at i:4681613 original size:22 final size:22
Alignment explanation
Indices: 4681503--4681615 Score: 103
Period size: 22 Copynumber: 5.4 Consensus size: 22
4681493 AATTTGGAAA
*
4681503 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAAACT
* *
4681525 ATCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAAACT
** *
4681547 ATCGCAACGA-ATTTGGAAA--
1 ATCGCAACGACAACTGTAAACT
** *
4681566 ATCGCAACGA-ATTTGGAAA--
1 ATCGCAACGACAACTGTAAACT
4681585 ATCGCAACGACAACTGTAAACT
1 ATCGCAACGACAACTGTAAACT
4681607 ATCGCAACG
1 ATCGCAACG
4681616 CAAAATGGAA
Statistics
Matches: 79, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 29 0.37
20 6 0.08
21 5 0.06
22 39 0.49
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.19
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAAACT
Found at i:4681651 original size:41 final size:41
Alignment explanation
Indices: 4681485--4681635 Score: 139
Period size: 41 Copynumber: 3.7 Consensus size: 41
4681475 CAACGAATTT
** *
4681485 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
1 TCGCAACGAAAATGGAAAATCGCAACGACAACTGTAAACTA
** ** *
4681526 TCGCAAC-AACAACTGTAGACTATCGCAACGA-ATTTGGAAA--A
1 TCGCAACGAA-AA-TG--GAAAATCGCAACGACAACTGTAAACTA
**
4681567 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAAACTA
1 TCGCAACGAAAATGGAAAATCGCAACGACAACTGTAAACTA
4681608 TCGCAACGCAAAATGGAAAATCGCAACG
1 TCGCAACG-AAAATGGAAAATCGCAACG
4681636 CAATTTTCAA
Statistics
Matches: 84, Mismatches: 17, Indels: 17
0.71 0.14 0.14
Matches are distributed among these distances:
38 12 0.14
39 6 0.07
40 4 0.05
41 24 0.29
42 21 0.25
43 5 0.06
44 12 0.14
ACGTcount: A:0.41, C:0.23, G:0.19, T:0.18
Consensus pattern (41 bp):
TCGCAACGAAAATGGAAAATCGCAACGACAACTGTAAACTA
Found at i:4681656 original size:21 final size:21
Alignment explanation
Indices: 4681627--4681678 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
4681617 AAAATGGAAA
4681627 ATCGCAACGCAATTTTCAACT
1 ATCGCAACGCAATTTTCAACT
* **
4681648 ATCGTAACGTGATTTTCAACT
1 ATCGCAACGCAATTTTCAACT
4681669 ATCGCAACGC
1 ATCGCAACGC
4681679 GAACTGGAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (21 bp):
ATCGCAACGCAATTTTCAACT
Found at i:4686094 original size:23 final size:23
Alignment explanation
Indices: 4686042--4686105 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
4686032 CAGCTTGTAT
*
4686042 AATTGCACCGAAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
* * *
4686065 AAATGCACTGTAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
4686088 GATTGCACCGAAGTGCCA
1 AATTGCACCGAAGTGCCA
4686106 TATAACATGT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.28, C:0.25, G:0.28, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:4686359 original size:23 final size:21
Alignment explanation
Indices: 4686310--4686361 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
4686300 TCATTTTGTT
*
4686310 TGTCACATATTCACATATTCA
1 TGTCACATATGCACATATTCA
* *
4686331 TTTCACATATGCATATAATCTCA
1 TGTCACATATGCACAT-AT-TCA
4686354 TGTCACAT
1 TGTCACAT
4686362 TCTCATATGG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 13 0.52
22 2 0.08
23 10 0.40
ACGTcount: A:0.33, C:0.23, G:0.06, T:0.38
Consensus pattern (21 bp):
TGTCACATATGCACATATTCA
Found at i:4686376 original size:16 final size:16
Alignment explanation
Indices: 4686355--4686437 Score: 79
Period size: 16 Copynumber: 5.4 Consensus size: 16
4686345 ATAATCTCAT
4686355 GTCACATTCTCATATG
1 GTCACATTCTCATATG
*
4686371 GTCACATAGCTC--AT-
1 GTCACAT-TCTCATATG
4686385 GTCACATTCTCATATG
1 GTCACATTCTCATATG
*
4686401 GTCACATAGCTC--AT-
1 GTCACAT-TCTCATATG
*
4686415 GTCACATTCCCATATG
1 GTCACATTCTCATATG
4686431 GTCACAT
1 GTCACAT
4686438 AGATCATATC
Statistics
Matches: 54, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
13 5 0.09
14 14 0.26
15 8 0.15
16 21 0.39
17 6 0.11
ACGTcount: A:0.27, C:0.28, G:0.13, T:0.33
Consensus pattern (16 bp):
GTCACATTCTCATATG
Found at i:4686385 original size:30 final size:30
Alignment explanation
Indices: 4686350--4686449 Score: 173
Period size: 30 Copynumber: 3.3 Consensus size: 30
4686340 TGCATATAAT
4686350 CTCATGTCACATTCTCATATGGTCACATAG
1 CTCATGTCACATTCTCATATGGTCACATAG
4686380 CTCATGTCACATTCTCATATGGTCACATAG
1 CTCATGTCACATTCTCATATGGTCACATAG
*
4686410 CTCATGTCACATTCCCATATGGTCACATAG
1 CTCATGTCACATTCTCATATGGTCACATAG
* *
4686440 ATCATATCAC
1 CTCATGTCAC
4686450 GTGGTTGCTA
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 67 1.00
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.32
Consensus pattern (30 bp):
CTCATGTCACATTCTCATATGGTCACATAG
Found at i:4686390 original size:14 final size:14
Alignment explanation
Indices: 4686371--4686421 Score: 59
Period size: 14 Copynumber: 3.5 Consensus size: 14
4686361 TTCTCATATG
4686371 GTCACATAGCTCAT
1 GTCACATAGCTCAT
*
4686385 GTCACAT-TCTCATAT
1 GTCACATAGCTC--AT
4686400 GGTCACATAGCTCAT
1 -GTCACATAGCTCAT
4686415 GTCACAT
1 GTCACAT
4686422 TCCCATATGG
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
13 3 0.10
14 14 0.45
15 4 0.13
16 7 0.23
17 3 0.10
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.31
Consensus pattern (14 bp):
GTCACATAGCTCAT
Found at i:4688974 original size:251 final size:251
Alignment explanation
Indices: 4688502--4688993 Score: 693
Period size: 251 Copynumber: 2.0 Consensus size: 251
4688492 TAAAGTTTCC
* * *
4688502 CATAAAGTGTCGATCCATATATAAAAAGTAACGACCCAAAAAATATCGAAACTCATAATTATAAT
1 CATAAAGTGTCGATACATATATAAAAAGTAACGACCCAAAAAACATCGAAACCCATAATTATAAT
* * *
4688567 GTAATGGGTAATTTTTCAATATAACCGGTATAAATATACCGGTTTTATGAAAAATATGTCTACAA
66 GTAATAGGTAATTTTTCAATATAACCGGTATAAATATACCAGTTTTATGAAAAATAGGTCTACAA
* * * * *
4688632 CATTTATCGACACTTATTAGTATTGTTTCGATACTTTTTGTCCAGAATGGATGCCAAAAAGGGTG
131 CATGTATCGACACTTATTAATATTATGTCGATAATTTTTGTCCAGAATGGATGCCAAAAAGGGTG
* *
4688697 AACCTACAAAGTGTCGATACATTTTCATAAAGTGTCGAT-CCAAAAGGGTTGCACG
196 AACCAACAAAGTGTCGATACATTTTCAAAAAGTGTCGATCCCAAAAGGGTTGCACG
* * ** *
4688752 CATAAAGTGTCGATACATTTATTAAAAGTTTCTATCCC-AAAAACATCGAAACCCATAATTATAA
1 CATAAAGTGTCGATACATATATAAAAAGTAACGA-CCCAAAAAACATCGAAACCCATAATTATAA
* *
4688816 TGTAATAGGTAATTTTGT-AATATAACCGGTATACATATACCAGTTTTATGAGAGAATAGGTCTA
65 TGTAATAGGTAATTTT-TCAATATAACCGGTATAAATATACCAGTTTTATGA-AAAATAGGTCTA
* * *
4688880 TAATATGTATCGACACTTCTTAATATTATGTCGATAATTTTTGTCCAGAATGGATGCCAAAAAGG
128 CAACATGTATCGACACTTATTAATATTATGTCGATAATTTTTGTCCAGAATGGATGCCAAAAAGG
** * *
4688945 GTGAATGAATAAAGTGTCGATATATTTTCAAAAAGTGTCGATCCCAAAA
193 GTGAACCAACAAAGTGTCGATACATTTTCAAAAAGTGTCGATCCCAAAA
4688994 ACATCGAAAC
Statistics
Matches: 211, Mismatches: 27, Indels: 6
0.86 0.11 0.02
Matches are distributed among these distances:
250 98 0.46
251 107 0.51
252 6 0.03
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.32
Consensus pattern (251 bp):
CATAAAGTGTCGATACATATATAAAAAGTAACGACCCAAAAAACATCGAAACCCATAATTATAAT
GTAATAGGTAATTTTTCAATATAACCGGTATAAATATACCAGTTTTATGAAAAATAGGTCTACAA
CATGTATCGACACTTATTAATATTATGTCGATAATTTTTGTCCAGAATGGATGCCAAAAAGGGTG
AACCAACAAAGTGTCGATACATTTTCAAAAAGTGTCGATCCCAAAAGGGTTGCACG
Found at i:4692030 original size:200 final size:195
Alignment explanation
Indices: 4691630--4692338 Score: 712
Period size: 200 Copynumber: 3.5 Consensus size: 195
4691620 ACCTAAATAT
* * *
4691630 GTGTCGATACATTT-TATACAAGTATCGA-CCCAAAAAACATCAAAACTAATAATTATAATGTAA
1 GTGTCGATACATTTAT-TAAAAGTATCGATCCC-AAAAACATCGAAAC-CATAATTATAATGTAA
* * * *
4691693 TAGGTAAATTAACAATGTAACCGGTATAAATATACCGG-TTAATTAGAAAACAGGTCAACATAAT
63 TAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTC-ACATAAT
* * * *
4691757 GTATCGACACTTGTGTAATTTGTGTTGATACTTATTGTCCAGGATGAATGCACAAACGAGGTGC-
127 GTATCGACACTTGT-TAATTTGTGTCGATACTT-TTGTCCAGAATGAATAC-CAAA-AAGGTGCA
4691821 ACGCATAAA
188 AC-CATAAA
* * *
4691830 GTGTCGATACATTTATTAAAAGTATCGATCTCAAAAACATTGAAACCGATAATTATAATGTATTA
1 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACC-ATAATTATAATGTAATA
** *
4691895 GGTAAATTTACAATGTAACCTATATAAATATACCGGTTTTATGATAAAATAGGTCAGCATCAA-G
65 GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCA-CAT-AATG
*
4691959 TATCGACACTTGCTAAATTTGTGTCGATACTTTTGCTCCAGAATGAATACCAAAAAGGATGCAAC
128 TATCGACACTTG-TTAATTTGTGTCGATACTTTTG-TCCAGAATGAATACCAAAAAGG-TGCAAC
4692024 CATAAA
190 CATAAA
* * * ** *
4692030 GTTTCGATATATTTATAAAAAGTATCGATCCCGGAAACATCGAAACTCATAAGTATAATGTAATA
1 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAAC-CATAATTATAATGTAATA
** * * * *
4692095 GGTAAATTTTTAATGTAACTGGTATAAATATACCGGTTTTATGAGAGAATAGGTGTAAATAATGT
65 GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGT-CACATAATGT
* * **
4692160 ATCGACACGTTGTTAGTTTGTGTCGATACTTTTTTCCAGAATGAAATATGAATGCCCAACCAGGT
129 ATCGACAC-TTGTTAATTTGTGTCGATACTTTTGTCCAGAATG--A-AT--A---CCAAAAAGGT
*
4692225 GCAAGCATAAA
185 GCAACCATAAA
* * * ** * *
4692236 GTTTCGATACATTTA--AAATTGTATTGATCTAAAAAACATCGTAACCTATAATAATAATGTAAT
1 GTGTCGATACATTTATTAAA-AGTATCGATCCCAAAAACATCGAAACC-ATAATTATAATGTAAT
* * *
4692299 AGGTAAATTTGCAATGTTACCGGTATAAATATATCGGTTT
64 AGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTT
4692339 ACTTCGAAAA
Statistics
Matches: 428, Mismatches: 57, Indels: 43
0.81 0.11 0.08
Matches are distributed among these distances:
199 14 0.03
200 235 0.55
201 69 0.16
202 5 0.01
204 5 0.01
205 68 0.16
206 25 0.06
207 7 0.02
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (195 bp):
GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCATAATTATAATGTAATAG
GTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCACATAATGTAT
CGACACTTGTTAATTTGTGTCGATACTTTTGTCCAGAATGAATACCAAAAAGGTGCAACCATAAA
Found at i:4692461 original size:87 final size:87
Alignment explanation
Indices: 4692356--4692517 Score: 270
Period size: 87 Copynumber: 1.9 Consensus size: 87
4692346 AAATAGATCA
*
4692356 ATATAAGCGCTACTTATTACATTAAATAAGAGATACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTAAATAAGAGATACCTAATATGTTATTGTACTTGATAATATTT
4692421 CCGGTTAAATTCTTATTTCATT
66 CCGGTTAAATTCTTATTTCATT
* * * *
4692443 ATATAAGCGCTACCTATTACATTATATAAGCGTTACCTAATATGTTATTGTATTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTAAATAAGAGATACCTAATATGTTATTGTACTTGATAATATTT
*
4692508 TCGGTTAAAT
66 CCGGTTAAAT
4692518 GATATAACAT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 69 1.00
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTAAATAAGAGATACCTAATATGTTATTGTACTTGATAATATTT
CCGGTTAAATTCTTATTTCATT
Found at i:4692465 original size:23 final size:23
Alignment explanation
Indices: 4692434--4692481 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
4692424 GTTAAATTCT
*
4692434 TATTTCATTATATAAGCGCTACC
1 TATTACATTATATAAGCGCTACC
*
4692457 TATTACATTATATAAGCGTTACC
1 TATTACATTATATAAGCGCTACC
4692480 TA
1 TA
4692482 ATATGTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.33, C:0.19, G:0.08, T:0.40
Consensus pattern (23 bp):
TATTACATTATATAAGCGCTACC
Found at i:4694852 original size:31 final size:33
Alignment explanation
Indices: 4694795--4694857 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 33
4694785 CTTTTTTATA
*
4694795 TTTTTAATTTTGTAAAAAAAAAATATA-AATAC
1 TTTTTAATCTTGTAAAAAAAAAATATATAATAC
* *
4694827 TTTTTAA-CTTGTTAAAAAAATATATATAATA
1 TTTTTAATCTTGTAAAAAAAAAATATATAATA
4694858 AGGACAATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 16 0.59
32 11 0.41
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (33 bp):
TTTTTAATCTTGTAAAAAAAAAATATATAATAC
Found at i:4700317 original size:16 final size:16
Alignment explanation
Indices: 4700292--4700348 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
4700282 GTCTACAAAA
4700292 ATAT-TTTATTATATT
1 ATATATTTATTATATT
4700307 ATATATTTATT-TATT
1 ATATATTTATTATATT
4700322 AT-TA-TTATTAT-TT
1 ATATATTTATTATATT
*
4700335 ATTTAATTTATTAT
1 ATAT-ATTTATTAT
4700349 TTTTACAAGC
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
13 9 0.24
14 4 0.11
15 11 0.30
16 13 0.35
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
ATATATTTATTATATT
Found at i:4700321 original size:20 final size:19
Alignment explanation
Indices: 4700296--4700353 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 19
4700286 ACAAAAATAT
4700296 TTTATTATATTATATATTTA
1 TTTATTATATTAT-TATTTA
4700316 TTTATTATTATTATTATTTA
1 TTTATTA-TATTATTATTTA
4700336 TTTAATT-TATTATT-TTTA
1 TTT-ATTATATTATTATTTA
4700354 CAAGCCCCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.11
19 7 0.19
20 16 0.44
21 9 0.25
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTATTATATTATTATTTA
Found at i:4701294 original size:21 final size:22
Alignment explanation
Indices: 4701260--4701316 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 22
4701250 ATTATATATA
4701260 TATATATATATATT-TATAAAATT
1 TATAT-TATATATTCTA-AAAATT
*
4701283 TATATTAT-TATTCTAAAAGTT
1 TATATTATATATTCTAAAAATT
4701304 TAT-TTATAATATT
1 TATATTAT-ATATT
4701317 ATGAATTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 4 0.13
21 12 0.40
22 9 0.30
23 5 0.17
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (22 bp):
TATATTATATATTCTAAAAATT
Found at i:4701395 original size:27 final size:27
Alignment explanation
Indices: 4701358--4701409 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
4701348 TAAAATCATG
*
4701358 TTATTTGTTT-ATTTGAAATAATATTAA
1 TTATTTATTTAATTT-AAATAATATTAA
4701385 TTATTTATTTAATTTAAATAATATT
1 TTATTTATTTAATTTAAATAATATT
4701410 GTTCGGAACC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (27 bp):
TTATTTATTTAATTTAAATAATATTAA
Found at i:4702522 original size:32 final size:32
Alignment explanation
Indices: 4702480--4702561 Score: 94
Period size: 32 Copynumber: 2.6 Consensus size: 32
4702470 AAAGGACATT
* * * *
4702480 TTTCTTAAATGAATTTATTTATCATTGAAAAG
1 TTTCTGAAATGAATTAATATATCAATGAAAAG
4702512 TTTCTGAAATGAATTAATATATCAATGAAAAG
1 TTTCTGAAATGAATTAATATATCAATGAAAAG
* *
4702544 TGTCT-AAAGTGAAGTAAT
1 TTTCTGAAA-TGAATTAAT
4702562 TGGCCAATGA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 3 0.07
32 40 0.93
ACGTcount: A:0.41, C:0.06, G:0.13, T:0.39
Consensus pattern (32 bp):
TTTCTGAAATGAATTAATATATCAATGAAAAG
Found at i:4708482 original size:21 final size:21
Alignment explanation
Indices: 4708458--4708510 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
4708448 AATTTGTGTT
*
4708458 TAGTTAAAAATTATT-TATGAG
1 TAGTTAAAAATT-TTGTATGAA
* *
4708479 TAGTTTACAATTTTGTATGAA
1 TAGTTAAAAATTTTGTATGAA
*
4708500 AAGTTAAAAAT
1 TAGTTAAAAAT
4708511 CTAAACGGTT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.43, C:0.02, G:0.13, T:0.42
Consensus pattern (21 bp):
TAGTTAAAAATTTTGTATGAA
Found at i:4715887 original size:12 final size:12
Alignment explanation
Indices: 4715870--4715904 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
4715860 AAAAATAATT
4715870 AAATAATAAACA
1 AAATAATAAACA
*
4715882 AAATAAGAAACA
1 AAATAATAAACA
4715894 AAATAAATAAA
1 AAAT-AATAAA
4715905 AATTCCATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.77, C:0.06, G:0.03, T:0.14
Consensus pattern (12 bp):
AAATAATAAACA
Found at i:4715887 original size:20 final size:17
Alignment explanation
Indices: 4715840--4715879 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
4715830 CAACTAAAAA
4715840 AATAAAAATAACTAAAT
1 AATAAAAATAACTAAAT
*
4715857 AATAAAAATAATTAAAT
1 AATAAAAATAACTAAAT
4715874 AATAAA
1 AATAAA
4715880 CAAAATAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (17 bp):
AATAAAAATAACTAAAT
Found at i:4716456 original size:21 final size:21
Alignment explanation
Indices: 4716415--4716456 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
4716405 AAATGGTTGT
* *
4716415 GGTGCCATCTGATACGGCTAC
1 GGTGCCATCTGAAACGACTAC
*
4716436 GGTGCCATCTGAAACTACTAC
1 GGTGCCATCTGAAACGACTAC
4716457 AAAATGTACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.24
Consensus pattern (21 bp):
GGTGCCATCTGAAACGACTAC
Found at i:4719644 original size:43 final size:42
Alignment explanation
Indices: 4719508--4719633 Score: 155
Period size: 43 Copynumber: 3.0 Consensus size: 42
4719498 CTAATAAAGG
* * *
4719508 TGTTTGGGTGGAAAACACATCTATATATTATGACTATTAGTGA
1 TGTTTGGGTGGAAAACGCA-CTATATATCATGACTATTAGCGA
* * *
4719551 TGTTTGGGT-AAAAATGCCACTATATATCATGACTATTAGCGG
1 TGTTTGGGTGGAAAACG-CACTATATATCATGACTATTAGCGA
*
4719593 TGTTTGTGTGGAAAACGCTACTATATATCATGACTATTAGC
1 TGTTTGGGTGGAAAACGC-ACTATATATCATGACTATTAGC
4719634 AACGTTTGTG
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
42 33 0.46
43 38 0.54
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.36
Consensus pattern (42 bp):
TGTTTGGGTGGAAAACGCACTATATATCATGACTATTAGCGA
Found at i:4719660 original size:43 final size:42
Alignment explanation
Indices: 4719528--4719649 Score: 154
Period size: 43 Copynumber: 2.9 Consensus size: 42
4719518 GAAAACACAT
* * *
4719528 CTATATATTATGACTATTAGTGATGTTTGGGTAAAAATGCCA
1 CTATATATCATGACTATTAGCGATGTTTGTGTAAAAATGCCA
* * * *
4719570 CTATATATCATGACTATTAGCGGTGTTTGTGTGGAAAACGCTA
1 CTATATATCATGACTATTAGCGATGTTTGTGT-AAAAATGCCA
* *
4719613 CTATATATCATGACTATTAGCAACGTTTGTGTAAAAA
1 CTATATATCATGACTATTAGCGATGTTTGTGTAAAAA
4719650 ATACCGCTAT
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
42 32 0.47
43 36 0.53
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (42 bp):
CTATATATCATGACTATTAGCGATGTTTGTGTAAAAATGCCA
Found at i:4719947 original size:31 final size:32
Alignment explanation
Indices: 4719884--4719954 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
4719874 ATTACATCAC
* *
4719884 TTCAGTAACTTTTCAGTGATATATAACTTTAT
1 TTCAGAAACTTTGCAGTGATATATAACTTTAT
*
4719916 TTCAGAAACTTTGCATTGATATAT-ACTTTAT
1 TTCAGAAACTTTGCAGTGATATATAACTTTAT
4719947 TTCAGAAA
1 TTCAGAAA
4719955 AATGTCGTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
31 15 0.42
32 21 0.58
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.44
Consensus pattern (32 bp):
TTCAGAAACTTTGCAGTGATATATAACTTTAT
Found at i:4720126 original size:102 final size:100
Alignment explanation
Indices: 4719916--4720143 Score: 239
Period size: 102 Copynumber: 2.2 Consensus size: 100
4719906 ATAACTTTAT
** ** * *
4719916 TTCAGAAA-CTTTGCATTGATATATACTTTATTTCAGAAAAATGTCGTTTTCTCGTACACCATTT
1 TTCAGAAACCTTT-CAGAGATATATACTTTATTTCAGAAAAACATCCTTTTCTCATACACCATTT
* *
4719980 AATGCACAATGACAAAAACTTTTCAATGCCCTATTAC
65 AATACACAATGACAAAAACTTTTCAAT-CCATATTAC
* * *
4720017 TTCAGAAACTTTTTAGAGATATAT-CATTTCATTTCAGAAAAACATCCTTTTCTCATTCACCATT
1 TTCAGAAACCTTTCAGAGATATATAC-TTT-ATTTCAGAAAAACATCCTTTTCTCATACACCATT
*
4720081 TAATACACAATGACAAAAACTTTGTCCAAT-CAT-TTCAT
64 TAATACACAATGACAAAAACTTT-T-CAATCCATATT-AC
* *
4720119 TTTAGAAACCTTTCAGTGATATATA
1 TTCAGAAACCTTTCAGAGATATATA
4720144 GAGTTCGTTG
Statistics
Matches: 104, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
100 1 0.01
101 21 0.20
102 77 0.74
103 1 0.01
104 4 0.04
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.37
Consensus pattern (100 bp):
TTCAGAAACCTTTCAGAGATATATACTTTATTTCAGAAAAACATCCTTTTCTCATACACCATTTA
ATACACAATGACAAAAACTTTTCAATCCATATTAC
Found at i:4720470 original size:32 final size:32
Alignment explanation
Indices: 4720424--4720522 Score: 146
Period size: 32 Copynumber: 3.1 Consensus size: 32
4720414 TTCACTTAAA
*
4720424 AAACGTTTCAGTGATATAT-ACCTTTATTTTAG
1 AAACTTTTCAGTGATATATCA-CTTTATTTTAG
* *
4720456 AAACTTTTCAGTGATATATCACTTTATTTCAT
1 AAACTTTTCAGTGATATATCACTTTATTTTAG
*
4720488 AAACTTTTCAGTGATATATCACTTCATTTTAG
1 AAACTTTTCAGTGATATATCACTTTATTTTAG
4720520 AAA
1 AAA
4720523 AATGTCCTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
32 59 0.98
33 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.43
Consensus pattern (32 bp):
AAACTTTTCAGTGATATATCACTTTATTTTAG
Found at i:4720629 original size:32 final size:32
Alignment explanation
Indices: 4720585--4720661 Score: 109
Period size: 32 Copynumber: 2.4 Consensus size: 32
4720575 GTCCAACCAT
* *
4720585 TTCAGTTCAGAAACTTTTCAGTTATATATAAC
1 TTCATTTCAGAAACTTTTCAGTGATATATAAC
* * *
4720617 TTCATTTTAGAAACTTTTTAGTGATATATCAC
1 TTCATTTCAGAAACTTTTCAGTGATATATAAC
4720649 TTCATTTCAGAAA
1 TTCATTTCAGAAA
4720662 AAGGTCTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (32 bp):
TTCATTTCAGAAACTTTTCAGTGATATATAAC
Found at i:4720736 original size:139 final size:139
Alignment explanation
Indices: 4720445--4720761 Score: 388
Period size: 139 Copynumber: 2.3 Consensus size: 139
4720435 TGATATATAC
* * * *
4720445 CTTTATTTTAGAAACTTTTCAGTGATATATCACTTTATTTCATAAACTTTTCAGTGATATATCAC
1 CTTTACTTTAGAAACTTTTCAGTAATATATCACTTCATTTCAGAAACTTTTCAGTGATATATCAC
* * * *
4720510 TTCATTTTAGAAAAATGTCCTTTTCTCATTCATACTTTAATACACAACGACAAAAACTTCTTAGT
66 TTCATTTCAGAAAAAGGTCCTTTTCTCATACACACTTTAATACACAACGACAAAAACTTCTTAGT
4720575 GTCCAACCA
131 GTCCAACCA
* * * * * *
4720584 -TTTCAGTTCAGAAACTTTTCAGTTATATATAACTTCATTTTAGAAACTTTTTAGTGATATATCA
1 CTTT-ACTTTAGAAACTTTTCAGTAATATATCACTTCATTTCAGAAACTTTTCAGTGATATATCA
* * *
4720648 CTTCATTTCAGAAAAAGGTCTTTTTCTTATACAC-CATTTAATACACAATGACAAAAACTT-TTC
65 CTTCATTTCAGAAAAAGGTCCTTTTCTCATACACAC-TTTAATACACAACGACAAAAACTTCTT-
* * *
4720711 ATTGTTCAATCA
128 AGTGTCCAACCA
* *
4720723 CTTTACTTTAGAAACTTTTTAGTAATATATCACTCCATT
1 CTTTACTTTAGAAACTTTTCAGTAATATATCACTTCATT
4720762 CTAGTGTTAT
Statistics
Matches: 150, Mismatches: 24, Indels: 8
0.82 0.13 0.04
Matches are distributed among these distances:
138 6 0.04
139 141 0.94
140 3 0.02
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.41
Consensus pattern (139 bp):
CTTTACTTTAGAAACTTTTCAGTAATATATCACTTCATTTCAGAAACTTTTCAGTGATATATCAC
TTCATTTCAGAAAAAGGTCCTTTTCTCATACACACTTTAATACACAACGACAAAAACTTCTTAGT
GTCCAACCA
Found at i:4721443 original size:32 final size:32
Alignment explanation
Indices: 4721402--4721499 Score: 101
Period size: 32 Copynumber: 3.1 Consensus size: 32
4721392 GTAATGACAA
* * *
4721402 AAACTTTTCAATGCCCTATTACTTCACTTT-AG
1 AAACTTTTCAATGACATATAACTTCA-TTTCAG
* *
4721434 AAACTTTTCAGTGATATATAACTTCATTTCAG
1 AAACTTTTCAATGACATATAACTTCATTTCAG
* * *
4721466 AAACTTTTCAGTGATATATCACTTCA-TTCAG
1 AAACTTTTCAATGACATATAACTTCATTTCAG
4721497 AAA
1 AAA
4721500 AACGTCATTT
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
31 11 0.19
32 48 0.81
ACGTcount: A:0.34, C:0.19, G:0.08, T:0.39
Consensus pattern (32 bp):
AAACTTTTCAATGACATATAACTTCATTTCAG
Found at i:4721499 original size:31 final size:32
Alignment explanation
Indices: 4721422--4721499 Score: 122
Period size: 32 Copynumber: 2.5 Consensus size: 32
4721412 ATGCCCTATT
*
4721422 ACTTCACTTTAGAAACTTTTCAGTGATATATA
1 ACTTCACTTCAGAAACTTTTCAGTGATATATA
* *
4721454 ACTTCATTTCAGAAACTTTTCAGTGATATATC
1 ACTTCACTTCAGAAACTTTTCAGTGATATATA
4721486 ACTTCA-TTCAGAAA
1 ACTTCACTTCAGAAA
4721500 AACGTCATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
31 8 0.19
32 35 0.81
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.38
Consensus pattern (32 bp):
ACTTCACTTCAGAAACTTTTCAGTGATATATA
Found at i:4721608 original size:138 final size:140
Alignment explanation
Indices: 4721360--4721744 Score: 497
Period size: 138 Copynumber: 2.8 Consensus size: 140
4721350 TATGAGGATT
* * ** * * * *
4721360 AAAACGTCATTTCCTCATACACCATTTAATGCGTAATGACAAAAACTTTTCAATGCCCTATTACT
1 AAAACGTCATTTTCTCATACACCATTTAATACACAATAACAAAAACTTTTCAATGTCCAATCACT
* * *
4721425 TCACTTTAGAAACTTTTCAGTGATATATAACTTCATTTCAGAAACTTT-TCAGTGATATATCACT
66 TCACTTCAGAAACTTTTCAGTGATATATAACTTCATTTTAGAAACTTTGT-ACTGATATATCACT
4721489 TCA-TTCAG-A
130 TCATTTCAGAA
* * * * *
4721498 AAAACGTCATTTTCTCATTCACCATTTAATACACAATAACAAAAACTTTTTAGTGTTCAATCATT
1 AAAACGTCATTTTCTCATACACCATTTAATACACAATAACAAAAACTTTTCAATGTCCAATCACT
* *
4721563 TCACTTCAGAAACTTTTTAGTGATATATAACTTCATTTTAGAAACTTTGTACTGATATATCATTT
66 TCACTTCAGAAACTTTTCAGTGATATATAACTTCATTTTAGAAACTTTGTACTGATATATCACTT
*
4721628 TATTTCAGAA
131 CATTTCAGAA
* * * *
4721638 AAAACATCTTTTTTCTTATACACCATTTAATACACAATTACAAAAACTTTTCAATGTCCAATCAC
1 AAAACGTC-ATTTTCTCATACACCATTTAATACACAATAACAAAAACTTTTCAATGTCCAATCAC
* * *
4721703 TTCACTTCAAAAACTTTTCAGTGATATATCATTTCATTTTAG
65 TTCACTTCAGAAACTTTTCAGTGATATATAACTTCATTTTAG
4721745 TGTTATACTA
Statistics
Matches: 211, Mismatches: 32, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
138 111 0.53
139 6 0.03
140 8 0.04
141 86 0.41
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.39
Consensus pattern (140 bp):
AAAACGTCATTTTCTCATACACCATTTAATACACAATAACAAAAACTTTTCAATGTCCAATCACT
TCACTTCAGAAACTTTTCAGTGATATATAACTTCATTTTAGAAACTTTGTACTGATATATCACTT
CATTTCAGAA
Found at i:4721638 original size:32 final size:32
Alignment explanation
Indices: 4721557--4721638 Score: 101
Period size: 32 Copynumber: 2.6 Consensus size: 32
4721547 TTAGTGTTCA
* * *
4721557 ATCATTTCACTTCAGAAACTTTTTAGTGATAT
1 ATCATTTCATTTCAGAAACTTTGTACTGATAT
* * *
4721589 ATAACTTCATTTTAGAAACTTTGTACTGATAT
1 ATCATTTCATTTCAGAAACTTTGTACTGATAT
*
4721621 ATCATTTTATTTCAGAAA
1 ATCATTTCATTTCAGAAA
4721639 AAACATCTTT
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.44
Consensus pattern (32 bp):
ATCATTTCATTTCAGAAACTTTGTACTGATAT
Found at i:4726558 original size:22 final size:22
Alignment explanation
Indices: 4726530--4727092 Score: 751
Period size: 22 Copynumber: 25.5 Consensus size: 22
4726520 ATTTTAAAAT
*
4726530 TTTATTTTAAAATATGAATTGA
1 TTTATTTTAAAATATGGATTGA
4726552 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
**
4726574 TTTATTTTAAAATATTAATTGA
1 TTTATTTTAAAATATGGATTGA
* ***
4726596 TTTATTTTAAAATATGAAAAAA
1 TTTATTTTAAAATATGGATTGA
*
4726618 ATTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
4726640 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
**
4726662 TTTATTTTAAAATATGGA-AAA
1 TTTATTTTAAAATATGGATTGA
*
4726683 TTTTATTTTAAAAAATGGATTGA
1 -TTTATTTTAAAATATGGATTGA
***
4726706 TTTATTTTAAAATATGGAAAAA
1 TTTATTTTAAAATATGGATTGA
* *
4726728 ATTATTTTAAAATATTGATTGA
1 TTTATTTTAAAATATGGATTGA
**
4726750 TTTATTTTAAAATATGGA-AAA
1 TTTATTTTAAAATATGGATTGA
*
4726771 TTTTATTTTAAAATATGAATTGA
1 -TTTATTTTAAAATATGGATTGA
*
4726794 TTTATTTTAAATTATGGATTGA
1 TTTATTTTAAAATATGGATTGA
**
4726816 TTTATTTTAAAATATGGA-AAA
1 TTTATTTTAAAATATGGATTGA
4726837 TTTTATTTTAAAATATGGATTGA
1 -TTTATTTTAAAATATGGATTGA
4726860 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
**
4726882 TTTATTTTAAAATATGGA-AAA
1 TTTATTTTAAAATATGGATTGA
4726903 TTTTATTTTAAAATATGGATTGA
1 -TTTATTTTAAAATATGGATTGA
4726926 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
4726948 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
***
4726970 TTTATTTTAAAATAT-GAAAAA
1 TTTATTTTAAAATATGGATTGA
4726991 TTTTATTTTAAAATATGGATTGA
1 -TTTATTTTAAAATATGGATTGA
* **
4727014 TTTATATTAAAATATGGA-AAA
1 TTTATTTTAAAATATGGATTGA
4727035 TTTTATTTTAAAATATGGATTGA
1 -TTTATTTTAAAATATGGATTGA
4727058 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
4727080 TTTATTTTTAAAA
1 TTTA-TTTTAAAA
4727093 ATTTATTATT
Statistics
Matches: 471, Mismatches: 57, Indels: 25
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.02
22 447 0.95
23 16 0.03
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (22 bp):
TTTATTTTAAAATATGGATTGA
Found at i:4727172 original size:31 final size:31
Alignment explanation
Indices: 4727115--4727173 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
4727105 AGTTGTATGG
*
4727115 ATTATTTAAATTTCAGTATTATAAAACTAAA
1 ATTATTTAAATTTCAGTATTACAAAACTAAA
*
4727146 ATTATTTAAATTTCAGTATTGCAAAACT
1 ATTATTTAAATTTCAGTATTACAAAACT
4727174 CTTTTAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTACAAAACTAAA
Found at i:4733226 original size:19 final size:19
Alignment explanation
Indices: 4733202--4733240 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
4733192 ATGGATATTT
4733202 TTTCTGAT-TTATGTTCTGA
1 TTTCTGATCTTAT-TTCTGA
*
4733221 TTTCTGCTCTTATTTCTGA
1 TTTCTGATCTTATTTCTGA
4733240 T
1 T
4733241 ATCTCTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.13, C:0.15, G:0.13, T:0.59
Consensus pattern (19 bp):
TTTCTGATCTTATTTCTGA
Found at i:4733252 original size:19 final size:18
Alignment explanation
Indices: 4733202--4733253 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 18
4733192 ATGGATATTT
4733202 TTTCTGATTTATGTTCTGA
1 TTTCTGATTTAT-TTCTGA
*
4733221 TTTCTGCTCTTATTTCTGA
1 TTTCTGAT-TTATTTCTGA
4733240 TATCTCTG-TTTATT
1 T-T-TCTGATTTATT
4733254 GACTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 19 0.66
20 6 0.21
21 4 0.14
ACGTcount: A:0.13, C:0.15, G:0.12, T:0.60
Consensus pattern (18 bp):
TTTCTGATTTATTTCTGA
Found at i:4733416 original size:66 final size:66
Alignment explanation
Indices: 4733300--4733429 Score: 172
Period size: 66 Copynumber: 2.0 Consensus size: 66
4733290 TGTATGAAGA
* * *
4733300 CTCTGGAAGGTTCAGTCGTTGTGGGTAATTACTTGTATAAGTTCTGCACCGACTGGTAATTCCTA
1 CTCTGGAAGGTTCAATCGCTGTGGGTAATTACTTGTATAAGTTCTACACCGACTGGTAATTCCTA
4733365 T
66 T
* * * * *
4733366 CTCTGGCAGGTTCAATCGCTGTTGGTAATTCCTTTTATAGGTT-TAACACCGACTGGTAATTCCT
1 CTCTGGAAGGTTCAATCGCTGTGGGTAATTACTTGTATAAGTTCT-ACACCGACTGGTAATTCCT
4733430 TATGGACCTA
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
65 1 0.02
66 54 0.98
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (66 bp):
CTCTGGAAGGTTCAATCGCTGTGGGTAATTACTTGTATAAGTTCTACACCGACTGGTAATTCCTA
T
Found at i:4738202 original size:30 final size:32
Alignment explanation
Indices: 4738166--4738232 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 32
4738156 TTAAAAGTAT
4738166 TTTTTATATTAACTT-A-TT-AAATATATTTTA
1 TTTTTATATTAACTTAATTTAAAAT-TATTTTA
4738196 -TTTT-TATTAACTTAATTTAAAATTATTTTA
1 TTTTTATATTAACTTAATTTAAAATTATTTTA
4738226 TTTTTAT
1 TTTTTAT
4738233 TTTCATTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
28 9 0.28
29 5 0.16
30 9 0.28
31 8 0.25
32 1 0.03
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (32 bp):
TTTTTATATTAACTTAATTTAAAATTATTTTA
Found at i:4738233 original size:30 final size:30
Alignment explanation
Indices: 4738151--4738233 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 30
4738141 TTTATATATA
* *
4738151 TTAATTTAAAAGTA-TTT-TTTATATTAAC
1 TTAATTTAAAATTATTTTATTTTTATTAAC
4738179 TT-A-TT-AAATATATTTTATTTTTATTAAC
1 TTAATTTAAAAT-TATTTTATTTTTATTAAC
4738207 TTAATTTAAAATTATTTTATTTTTATT
1 TTAATTTAAAATTATTTTATTTTTATT
4738234 TTCATTTAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
25 3 0.06
26 4 0.09
27 4 0.09
28 14 0.30
29 1 0.02
30 17 0.36
31 4 0.09
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.60
Consensus pattern (30 bp):
TTAATTTAAAATTATTTTATTTTTATTAAC
Found at i:4738254 original size:30 final size:29
Alignment explanation
Indices: 4738166--4738249 Score: 93
Period size: 30 Copynumber: 2.9 Consensus size: 29
4738156 TTAAAAGTAT
*
4738166 TTTTTA-TATTAACTTATTAAATATATTTTA
1 TTTTTATTATTAA-TT-TAAAATATATTTTA
4738196 TTTTTATTAACTTAATTTAAAAT-TATTTTA
1 TTTTTATT-A-TTAATTTAAAATATATTTTA
*
4738226 TTTTTATT-TTCATTTAAAATATAT
1 TTTTTATTATTAATTTAAAATATAT
4738250 ATTTTCTATT
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
27 11 0.23
28 3 0.06
30 21 0.44
31 6 0.12
32 3 0.06
33 4 0.08
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.61
Consensus pattern (29 bp):
TTTTTATTATTAATTTAAAATATATTTTA
Found at i:4741134 original size:52 final size:52
Alignment explanation
Indices: 4741056--4741158 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
4741046 TTATAATATT
4741056 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
*
4741108 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTTTCCTATTTCTATG
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATG
4741159 TGTCCAATTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (52 bp):
CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
Done.