Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 86 of 172
Found at i:28665765 original size:16 final size:16
Alignment explanation
Indices: 28665734--28665770 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
28665724 ATGTGAATAA
28665734 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
28665750 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
28665766 TATTA
1 TATTA
28665771 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:28665822 original size:22 final size:22
Alignment explanation
Indices: 28665782--28665837 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
28665772 AATAAAATTG
*
28665782 AAATATTAAA-TA-ATTTATTA
1 AAATAATAAATTATATTTATTA
28665802 AAATAATAAATTATATTTATTA
1 AAATAATAAATTATATTTATTA
* * *
28665824 TATTAATAATTTAT
1 AAATAATAAATTAT
28665838 TATATGACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 9 0.30
21 2 0.07
22 19 0.63
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAATAATAAATTATATTTATTA
Found at i:28668912 original size:48 final size:48
Alignment explanation
Indices: 28668816--28669092 Score: 284
Period size: 48 Copynumber: 5.8 Consensus size: 48
28668806 TCTCATATCG
* * **** * * *
28668816 ATGCCATGTCCCAGACATGGTCTTAGACAAAATAACTTATTGATGCCA
1 ATGCCATATCCCAGACATGGTCTTACATGGGATCACATATAGATGCCA
* * * * *
28668864 ATGTCATATCCCAAATATGGTCTTACAAGGGATCACATATAGACGCCA
1 ATGCCATATCCCAGACATGGTCTTACATGGGATCACATATAGATGCCA
* * *
28668912 ATTCCATATCCCAGATATGGTCTTACATGGGATCACATATCGATGCCA
1 ATGCCATATCCCAGACATGGTCTTACATGGGATCACATATAGATGCCA
* * * * * * *
28668960 ATGCCATGTCTCAGACATGGTATTACACGAGATCACATGTCGATGCCA
1 ATGCCATATCCCAGACATGGTCTTACATGGGATCACATATAGATGCCA
* * * * *
28669008 ATGCCATGTCCTAAACATGGTCTCACATGGGATCACATATTGATGCCA
1 ATGCCATATCCCAGACATGGTCTTACATGGGATCACATATAGATGCCA
*
28669056 ATGCCATATCCCAGACATGTTCTTACATGGGATCACA
1 ATGCCATATCCCAGACATGGTCTTACATGGGATCACA
28669093 CATAACCCTA
Statistics
Matches: 188, Mismatches: 41, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 188 1.00
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.27
Consensus pattern (48 bp):
ATGCCATATCCCAGACATGGTCTTACATGGGATCACATATAGATGCCA
Found at i:28669006 original size:144 final size:144
Alignment explanation
Indices: 28668816--28669092 Score: 374
Period size: 144 Copynumber: 1.9 Consensus size: 144
28668806 TCTCATATCG
* * * * * *
28668816 ATGCCATGTCCCAGACATGGTCTTAGACAAAATAACTTATTGATGCCAATGTCATATCCCAAATA
1 ATGCCATGTCCCAGACATGGTATTACACAAAATAACATATCGATGCCAATGCCATATCCCAAACA
* * *
28668881 TGGTCTTACAAGGGATCACATATAGACGCCAATTCCATATCCCAGATATGGTCTTACATGGGATC
66 TGGTCTCACAAGGGATCACATATAGACGCCAATGCCATATCCCAGACATGGTCTTACATGGGATC
28668946 ACATATCGATGCCA
131 ACATATCGATGCCA
* * * * * * *
28668960 ATGCCATGTCTCAGACATGGTATTACACGAGATCACATGTCGATGCCAATGCCATGTCCTAAACA
1 ATGCCATGTCCCAGACATGGTATTACACAAAATAACATATCGATGCCAATGCCATATCCCAAACA
* * * *
28669025 TGGTCTCACATGGGATCACATATTGATGCCAATGCCATATCCCAGACATGTTCTTACATGGGATC
66 TGGTCTCACAAGGGATCACATATAGACGCCAATGCCATATCCCAGACATGGTCTTACATGGGATC
28669090 ACA
131 ACA
28669093 CATAACCCTA
Statistics
Matches: 113, Mismatches: 20, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
144 113 1.00
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.27
Consensus pattern (144 bp):
ATGCCATGTCCCAGACATGGTATTACACAAAATAACATATCGATGCCAATGCCATATCCCAAACA
TGGTCTCACAAGGGATCACATATAGACGCCAATGCCATATCCCAGACATGGTCTTACATGGGATC
ACATATCGATGCCA
Found at i:28673334 original size:27 final size:27
Alignment explanation
Indices: 28673302--28673480 Score: 207
Period size: 27 Copynumber: 6.6 Consensus size: 27
28673292 TTAAATTGTA
28673302 TAGCACTAAGTGTGCGATTTGACTATG
1 TAGCACTAAGTGTGCGATTTGACTATG
* ** *
28673329 TTGCACTAAGTGTGCGAAATGAATATG
1 TAGCACTAAGTGTGCGATTTGACTATG
* *
28673356 -ATGCACTAAGTGTGCGAATTGACCATG
1 TA-GCACTAAGTGTGCGATTTGACTATG
**
28673383 CGGCACTAAGTGTGCGAGTTTGACTATG
1 TAGCACTAAGTGTGCGA-TTTGACTATG
* *
28673411 TAGCACTAAGTGTGCGATTTGATTACG
1 TAGCACTAAGTGTGCGATTTGACTATG
* * *
28673438 TAGCACTAAGTGTGCGAGTTGATTATA
1 TAGCACTAAGTGTGCGATTTGACTATG
*
28673465 TAGCACTGAGTGTGCG
1 TAGCACTAAGTGTGCG
28673481 GACTCAATAT
Statistics
Matches: 130, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 107 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
TAGCACTAAGTGTGCGATTTGACTATG
Found at i:28673417 original size:82 final size:81
Alignment explanation
Indices: 28673304--28673459 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
28673294 AAATTGTATA
* *
28673304 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
28673368 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
28673385 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
28673450 TGCGAGTTGA
65 TGCGAATTGA
28673460 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:28673471 original size:82 final size:81
Alignment explanation
Indices: 28673300--28673480 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
28673290 GATTAAATTG
* *
28673300 TATAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TATAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
28673365 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
*** ** *
28673381 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TATAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
28673445 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
*
28673463 TATAGCACTGAGTGTGCG
1 TATAGCACTAAGTGTGCG
28673481 GACTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 17 0.20
82 66 0.80
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TATAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:28678744 original size:40 final size:40
Alignment explanation
Indices: 28678700--28678783 Score: 168
Period size: 40 Copynumber: 2.1 Consensus size: 40
28678690 AATCTCATAC
28678700 ACATAGTAAGATGCCAATGTAATATCCCAGATATGGTCTT
1 ACATAGTAAGATGCCAATGTAATATCCCAGATATGGTCTT
28678740 ACATAGTAAGATGCCAATGTAATATCCCAGATATGGTCTT
1 ACATAGTAAGATGCCAATGTAATATCCCAGATATGGTCTT
28678780 ACAT
1 ACAT
28678784 GGGATCACAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.30
Consensus pattern (40 bp):
ACATAGTAAGATGCCAATGTAATATCCCAGATATGGTCTT
Found at i:28678927 original size:48 final size:48
Alignment explanation
Indices: 28678749--28679072 Score: 303
Period size: 48 Copynumber: 7.0 Consensus size: 48
28678739 TACATAGTAA
** *
28678749 GATGCCAATGTAATATCCCAGATATGGTCTTACATGGGATCACAGATC
1 GATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATCACATATC
* * * * *
28678797 GAAGCC---G--ATAGCCCAGCTATGGTCTTACATGATG-TCTCATATC
1 GATGCCAATGCCATATCCCAGATATGGTCTTACATG-GGATCACATATC
* * * * ** *
28678840 GATGCC-ATGCC-T-T---AAACATGGTGTTAGATGAAATAACATATC
1 GATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATCACATATC
* * * *
28678882 AATGCCAATGCCATATCCCAGATATGATCTTATATGTGATCACATATC
1 GATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATCACATATC
* *
28678930 GATGCCAATGTCATATCCCAGATATGGTCTTACGTGGGATCACATATC
1 GATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATCACATATC
* * ** *
28678978 GATGCCAATGCCATGTCCCAGACATGGTCTTATGTGGGATCACATATT
1 GATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATCACATATC
* *
28679026 GATGCCAACGCCATATCCCAGAAATGGTCTTACATGGGATCACATAT
1 GATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATCACATAT
28679073 AACCCTAATA
Statistics
Matches: 222, Mismatches: 42, Indels: 24
0.77 0.15 0.08
Matches are distributed among these distances:
42 24 0.11
43 39 0.18
44 2 0.01
45 3 0.01
46 1 0.00
48 153 0.69
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (48 bp):
GATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATCACATATC
Found at i:28684788 original size:20 final size:20
Alignment explanation
Indices: 28684760--28684797 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28684750 ATATAATTTA
*
28684760 TATTTTAAAAAAATATTATT
1 TATTATAAAAAAATATTATT
*
28684780 TATTATAAAAAATTATTA
1 TATTATAAAAAAATATTA
28684798 GCACTAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TATTATAAAAAAATATTATT
Found at i:28687805 original size:2 final size:2
Alignment explanation
Indices: 28687798--28687827 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
28687788 ATTAGGTTAG
28687798 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
28687828 TTTATTTGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:28711164 original size:27 final size:27
Alignment explanation
Indices: 28711124--28711264 Score: 155
Period size: 27 Copynumber: 5.2 Consensus size: 27
28711114 AGGAAGCGTC
* *
28711124 CTGGTGCCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
28711151 CTGGTGGCTCTGCCAC-ATATATTTG-T
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
* *
28711177 CCTGGTGGCTATGCCACAATTATCAGAT
1 -CTGGTGGCTCTGCCACAATTATCTGAT
* *
28711205 TTGGTGGCTCTGCCAC-ATATATCTGTT
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
28711232 CTGGTGGCTCTGCCACAA-TATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
28711259 CTGGTG
1 CTGGTG
28711265 ACTTCGTCAC
Statistics
Matches: 95, Mismatches: 12, Indels: 14
0.79 0.10 0.12
Matches are distributed among these distances:
26 11 0.12
27 80 0.84
28 4 0.04
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:28711210 original size:54 final size:54
Alignment explanation
Indices: 28711121--28711264 Score: 209
Period size: 54 Copynumber: 2.7 Consensus size: 54
28711111 TGGAGGAAGC
* * *
28711121 GTCCTGGTGCCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATTT
1 GTCCTGGTGGCTATGCCACAATTATCAGATCTGGTGGCTCTGCCACATATATCT
*
28711175 GTCCTGGTGGCTATGCCACAATTATCAGATTTGGTGGCTCTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCAGATCTGGTGGCTCTGCCACATATATCT
* * *
28711229 GTTCTGGTGGCTCTGCCACAA-TATCTGTATCTGGTG
1 GTCCTGGTGGCTATGCCACAATTATCAG-ATCTGGTG
28711265 ACTTCGTCAC
Statistics
Matches: 81, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
53 5 0.06
54 76 0.94
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (54 bp):
GTCCTGGTGGCTATGCCACAATTATCAGATCTGGTGGCTCTGCCACATATATCT
Found at i:28711275 original size:27 final size:26
Alignment explanation
Indices: 28711124--28711282 Score: 133
Period size: 27 Copynumber: 5.9 Consensus size: 26
28711114 AGGAAGCGTC
* * *
28711124 CTGGTGCCTATGCCACAATTATCTGAT
1 CTGGTGACTCTGCCACAA-TATCTGTT
* * *
28711151 CTGGTGGCTCTGCCACATATATTTGTC
1 CTGGTGACTCTGCCACA-ATATCTGTT
* * *
28711178 CTGGTGGCTATGCCACAATTATCAGATT
1 CTGGTGACTCTGCCACAA-TATCTG-TT
*
28711206 -TGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGACTCTGCCACA-ATATCTGTT
*
28711232 CTGGTGGCTCTGCCACAATATCTGTAT
1 CTGGTGACTCTGCCACAATATCTGT-T
*
28711259 CTGGTGACT-TCGTCACAATATCTG
1 CTGGTGACTCT-GCCACAATATCTG
28711283 GCAGCCTCGC
Statistics
Matches: 112, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
26 12 0.11
27 97 0.87
28 3 0.03
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.35
Consensus pattern (26 bp):
CTGGTGACTCTGCCACAATATCTGTT
Found at i:28714603 original size:11 final size:12
Alignment explanation
Indices: 28714582--28714610 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
28714572 TTAACGTTAG
28714582 TTTTCTCTAGGT
1 TTTTCTCTAGGT
28714594 TTTTCT-TAGGT
1 TTTTCTCTAGGT
28714605 TTTTCT
1 TTTTCT
28714611 GCAACTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.07, C:0.14, G:0.14, T:0.66
Consensus pattern (12 bp):
TTTTCTCTAGGT
Found at i:28717750 original size:74 final size:74
Alignment explanation
Indices: 28717594--28717742 Score: 289
Period size: 74 Copynumber: 2.0 Consensus size: 74
28717584 TCGTTGATGC
*
28717594 AAAGATGTTCTTTCAAGAATAAAGTATTCGTTAATGCATTTTAGTAATAAAGCTCATTAAGTACT
1 AAAGATGTTCTTTCAAGAATAAAGAATTCGTTAATGCATTTTAGTAATAAAGCTCATTAAGTACT
28717659 CTTATATTT
66 CTTATATTT
28717668 AAAGATGTTCTTTCAAGAATAAAGAATTCGTTAATGCATTTTAGTAATAAAGCTCATTAAGTACT
1 AAAGATGTTCTTTCAAGAATAAAGAATTCGTTAATGCATTTTAGTAATAAAGCTCATTAAGTACT
28717733 CTTATATTT
66 CTTATATTT
28717742 A
1 A
28717743 CTTATGTTAT
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.40
Consensus pattern (74 bp):
AAAGATGTTCTTTCAAGAATAAAGAATTCGTTAATGCATTTTAGTAATAAAGCTCATTAAGTACT
CTTATATTT
Found at i:28719233 original size:70 final size:71
Alignment explanation
Indices: 28719119--28719259 Score: 275
Period size: 70 Copynumber: 2.0 Consensus size: 71
28719109 TTGATAACAG
28719119 ATAAGTTTTTTTTTGGCTTACGAAATTATGCACACTTTAAGGAAAAATTGAACAGAGAGTAAAGG
1 ATAAGTTTTTTTTTGGCTTACGAAATTATGCACACTTTAAGGAAAAATTGAACAGAGAGTAAAGG
28719184 TTTTAT
66 TTTTAT
28719190 ATAAG-TTTTTTTTGGCTTACGAAATTATGCACACTTTAAGGAAAAATTGAACAGAGAGTAAAGG
1 ATAAGTTTTTTTTTGGCTTACGAAATTATGCACACTTTAAGGAAAAATTGAACAGAGAGTAAAGG
28719254 TTTTAT
66 TTTTAT
28719260 GGCGTTGAAA
Statistics
Matches: 70, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
70 65 0.93
71 5 0.07
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.36
Consensus pattern (71 bp):
ATAAGTTTTTTTTTGGCTTACGAAATTATGCACACTTTAAGGAAAAATTGAACAGAGAGTAAAGG
TTTTAT
Found at i:28719718 original size:72 final size:72
Alignment explanation
Indices: 28719601--28719744 Score: 279
Period size: 72 Copynumber: 2.0 Consensus size: 72
28719591 ATTGATGACT
28719601 GCATTTTATTTGGAGAGGCTACTGATAAGAGGCCCACATTCTGAAAGATATACTTACGGAGTATG
1 GCATTTTATTTGGAGAGGCTACTGATAAGAGGCCCACATTCTGAAAGATATACTTACGGAGTATG
28719666 AAGTATG
66 AAGTATG
*
28719673 GCATTTTATTTGGAGAGGCTACTGATAAGAGGCCCACATTCTGAAAGATATACTTAGGGAGTATG
1 GCATTTTATTTGGAGAGGCTACTGATAAGAGGCCCACATTCTGAAAGATATACTTACGGAGTATG
28719738 AAGTATG
66 AAGTATG
28719745 TTCTGGGCAG
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (72 bp):
GCATTTTATTTGGAGAGGCTACTGATAAGAGGCCCACATTCTGAAAGATATACTTACGGAGTATG
AAGTATG
Found at i:28724704 original size:14 final size:14
Alignment explanation
Indices: 28724685--28724713 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
28724675 GGTATAAGGG
28724685 ACAATATGTATGTC
1 ACAATATGTATGTC
28724699 ACAATATGTATGTC
1 ACAATATGTATGTC
28724713 A
1 A
28724714 TTGATTGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (14 bp):
ACAATATGTATGTC
Found at i:28726886 original size:24 final size:24
Alignment explanation
Indices: 28726840--28726886 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
28726830 ATTTAAGAAA
* *
28726840 TTAATAATTATAATAATATAATAG
1 TTAATAATTATAATAAAAAAATAG
28726864 TTAATAA-TATAATAAAAGAAATA
1 TTAATAATTATAATAAAA-AAATA
28726887 ATAAAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (24 bp):
TTAATAATTATAATAAAAAAATAG
Found at i:28726888 original size:20 final size:19
Alignment explanation
Indices: 28726865--28726910 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
28726855 ATATAATAGT
28726865 TAATAATATAATAAAAGAAA
1 TAATAATATAAT-AAAGAAA
*
28726885 TAATAAAATAATAAAGAAA
1 TAATAATATAATAAAGAAA
28726904 TAA-AATA
1 TAATAATA
28726911 AAGAAAAAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 3 0.12
19 10 0.42
20 11 0.46
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (19 bp):
TAATAATATAATAAAGAAA
Found at i:28726919 original size:19 final size:18
Alignment explanation
Indices: 28726877--28726919 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
28726867 ATAATATAAT
* *
28726877 AAAAGAAATAATAAAATA
1 AAAAGAAATAAAAAAAGA
28726895 ATAAAGAAATAAAATAAAGA
1 A-AAAGAAATAAAA-AAAGA
28726915 AAAAG
1 AAAAG
28726920 GAAAGAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 15 0.71
20 5 0.24
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (18 bp):
AAAAGAAATAAAAAAAGA
Found at i:28726972 original size:12 final size:12
Alignment explanation
Indices: 28726948--28726988 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
28726938 ATAGAACAGG
28726948 GAAAGAAAG-AAA
1 GAAA-AAAGAAAA
28726960 GAAAAAAGAAAA
1 GAAAAAAGAAAA
*
28726972 G-AAAAAGAAAG
1 GAAAAAAGAAAA
28726983 GAAAAA
1 GAAAAA
28726989 TAGGGTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 14 0.54
12 12 0.46
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (12 bp):
GAAAAAAGAAAA
Found at i:28740283 original size:26 final size:29
Alignment explanation
Indices: 28740219--28740288 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
28740209 GTCGTTTCTC
*
28740219 TTTTCTCCTCTACTGGCGTTCATCTCTTA
1 TTTTCTCCTCCACTGGCGTTCATCTCTTA
* * *
28740248 TTTTCCCCTCCATTGTCGTTCA-C-C-TA
1 TTTTCTCCTCCACTGGCGTTCATCTCTTA
28740274 TTTTCTCCTCCACTG
1 TTTTCTCCTCCACTG
28740289 CTATTTGCCT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
26 15 0.43
27 1 0.03
28 1 0.03
29 18 0.51
ACGTcount: A:0.10, C:0.36, G:0.09, T:0.46
Consensus pattern (29 bp):
TTTTCTCCTCCACTGGCGTTCATCTCTTA
Found at i:28742517 original size:4 final size:4
Alignment explanation
Indices: 28742510--28742551 Score: 50
Period size: 4 Copynumber: 10.0 Consensus size: 4
28742500 TTTTTGCTTG
28742510 TAAA TAAA TAAA -AAA TAAAA TGAAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA T-AAA T--AAA TAAA TAAA TAAA TAAA
28742552 GGCTCATGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
3 3 0.09
4 23 0.66
5 4 0.11
6 5 0.14
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.21
Consensus pattern (4 bp):
TAAA
Found at i:28748109 original size:14 final size:14
Alignment explanation
Indices: 28748090--28748123 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
28748080 ACCCGAAGTG
*
28748090 GATGATATGATTAT
1 GATGATATGACTAT
*
28748104 GATGATATTACTAT
1 GATGATATGACTAT
28748118 GATGAT
1 GATGAT
28748124 GAAAGTCGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.35, C:0.03, G:0.21, T:0.41
Consensus pattern (14 bp):
GATGATATGACTAT
Found at i:28749882 original size:48 final size:47
Alignment explanation
Indices: 28749808--28750132 Score: 262
Period size: 48 Copynumber: 6.8 Consensus size: 47
28749798 ATATGTGTGT
* * * *
28749808 GCCAGCGTAAGACCATGTTTGAAACATGGCATCGACGATGTAATAAGA
1 GCCAGTGTAAGACCATGTTTGGAACATGGCATCGGC-ATGTAATGAGA
** * *
28749856 GCCAGCATAAGACCATGTTTGGAACATGGAATC-TCTAATGTAATGAGA
1 GCCAGTGTAAGACCATGTTTGGAACATGGCATCGGC--ATGTAATGAGA
* * * * * * * *
28749904 GCTAGTGTAGGACCATGTCTGGGACATGGCGTCGTCAT-TGATATGTGC
1 GCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATGT-A-ATGAGA
* * ** *
28749952 GCTAGTGTAAGACCATGTCTGGAACATGGCATCGGCCACATTATGAGA
1 GCCAGTGTAAGACCATGTTTGGAACATGGCATCGG-CATGTAATGAGA
** * *
28750000 GCCAACGTAAGACCAAGTTTGGGACATGGCATCGGCAT-TGAGATGAGA
1 GCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATGT-A-ATGAGA
* * * * *
28750048 GCTAGTGTAAGACCATGTTTGGGAGATGGCATCGGCCT-TGACATGTGA
1 GCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATGT-A-ATGAGA
28750096 GCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCA
1 GCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCA
28750133 ATGGTTTCAG
Statistics
Matches: 225, Mismatches: 44, Indels: 16
0.79 0.15 0.06
Matches are distributed among these distances:
46 2 0.01
47 6 0.03
48 212 0.94
49 4 0.02
50 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.24
Consensus pattern (47 bp):
GCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATGTAATGAGA
Found at i:28750077 original size:144 final size:144
Alignment explanation
Indices: 28749803--28750131 Score: 392
Period size: 144 Copynumber: 2.3 Consensus size: 144
28749793 GGGTGATATG
* * * * * ** *
28749803 TGTGTGCCAGCGTAAGACCATGTTTGAAACATGGCATCGACGATGTAATAAGAGCCAGCATAAGA
1 TGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCCACATAATAAGAGCCAACATAAGA
* * *
28749868 CCATGTTTGGAACATGGAATCTCTAATGTAATGAGAGCTAGTGTAGGACCATGTCTGGGACATGG
66 CCAAGTTTGGAACATGGAATCGCTAATGTAATGAGAGCTAGTGTAAGACCATGTCTGGGACATGG
* * *
28749933 CGTCGTCATTGATA
131 CATCGGCATTGACA
* * * * * *
28749947 TGTGCGCTAGTGTAAGACCATGTCTGGAACATGGCATCGGCCACATTATGAGAGCCAACGTAAGA
1 TGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCCACATAATAAGAGCCAACATAAGA
* * * * *
28750012 CCAAGTTTGGGACATGGCATCGGC-ATTG-AGATGAGAGCTAGTGTAAGACCATGTTTGGGAGAT
66 CCAAGTTTGGAACATGGAATC-GCTAATGTA-ATGAGAGCTAGTGTAAGACCATGTCTGGGACAT
*
28750075 GGCATCGGCCTTGACA
129 GGCATCGGCATTGACA
28750091 TGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGC
1 TGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGC
28750132 AATGGTTTCA
Statistics
Matches: 155, Mismatches: 28, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
143 1 0.01
144 153 0.99
145 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (144 bp):
TGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCCACATAATAAGAGCCAACATAAGA
CCAAGTTTGGAACATGGAATCGCTAATGTAATGAGAGCTAGTGTAAGACCATGTCTGGGACATGG
CATCGGCATTGACA
Found at i:28751279 original size:21 final size:21
Alignment explanation
Indices: 28751246--28751285 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
28751236 TTAAGAAGCC
*
28751246 ACACGGGCATGTTGCCCTGCT
1 ACACGGGCATGTTCCCCTGCT
**
28751267 ACACGGGTGTGTTCCCCTG
1 ACACGGGCATGTTCCCCTG
28751286 TCTGCTTGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.12, C:0.33, G:0.30, T:0.25
Consensus pattern (21 bp):
ACACGGGCATGTTCCCCTGCT
Found at i:28751745 original size:15 final size:15
Alignment explanation
Indices: 28751725--28751768 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
28751715 TATGATATTG
28751725 TATTTTGGATTTCTC
1 TATTTTGGATTTCTC
*
28751740 TATTTTGGATTCCTC
1 TATTTTGGATTTCTC
*
28751755 TATTTTGGTTTTCT
1 TATTTTGGATTTCT
28751769 TGTCATCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.11, C:0.14, G:0.14, T:0.61
Consensus pattern (15 bp):
TATTTTGGATTTCTC
Found at i:28754930 original size:45 final size:44
Alignment explanation
Indices: 28754856--28754941 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 44
28754846 GAACTATGTG
28754856 ATCTGAACTCATGAGTTGTGGTCTGAGTTCATGACATATGTGAC
1 ATCTGAACTCATGAGTTGTGGTCTGAGTTCATGACATATGTGAC
*
28754900 ATCTGAACTCATTGAGGTT-TGGTCTGAGTTCATGATATATGT
1 ATCTGAACTCA-TGA-GTTGTGGTCTGAGTTCATGACATATGT
28754942 TACACATGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
44 11 0.28
45 25 0.64
46 3 0.08
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.37
Consensus pattern (44 bp):
ATCTGAACTCATGAGTTGTGGTCTGAGTTCATGACATATGTGAC
Found at i:28761355 original size:6 final size:6
Alignment explanation
Indices: 28761346--28761413 Score: 63
Period size: 6 Copynumber: 12.0 Consensus size: 6
28761336 CTAAGAAAAT
* * * * *
28761346 AATAAA AAT--A ACTAAA AATAAC AATAAA CATAAA CAT-TA AATAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
28761391 AATAAA AATAAA AAT-AA AATAAA
1 AATAAA AATAAA AATAAA AATAAA
28761414 TAAACTTAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
4 3 0.06
5 8 0.16
6 39 0.78
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (6 bp):
AATAAA
Found at i:28761394 original size:23 final size:23
Alignment explanation
Indices: 28761346--28761413 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
28761336 CTAAGAAAAT
** *
28761346 AATAAAAATAACTA-AAAATAAC
1 AATAAAAATAAAAATAAAATAAA
* * *
28761368 AATAAACATAAACATTAAATAAA
1 AATAAAAATAAAAATAAAATAAA
28761391 AATAAAAATAAAAATAAAATAAA
1 AATAAAAATAAAAATAAAATAAA
28761414 TAAACTTAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
22 11 0.30
23 26 0.70
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (23 bp):
AATAAAAATAAAAATAAAATAAA
Found at i:28762869 original size:18 final size:17
Alignment explanation
Indices: 28762846--28762879 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
28762836 ACTAGCTAAG
28762846 AAATAATAATGAAGAAAA
1 AAATAATAA-GAAGAAAA
28762864 AAATAATAAGAAGAAA
1 AAATAATAAGAAGAAA
28762880 CGAAGTGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.15
Consensus pattern (17 bp):
AAATAATAAGAAGAAAA
Found at i:28762958 original size:17 final size:18
Alignment explanation
Indices: 28762926--28762960 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
28762916 ACTACTAGTA
28762926 AAAATAAATTAAAATAAT
1 AAAATAAATTAAAATAAT
*
28762944 AAAAT-AATTATAATAAT
1 AAAATAAATTAAAATAAT
28762961 TATAATGGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAATAAATTAAAATAAT
Found at i:28767020 original size:46 final size:46
Alignment explanation
Indices: 28766953--28767180 Score: 332
Period size: 46 Copynumber: 5.0 Consensus size: 46
28766943 AGTGTGCTCT
28766953 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
28766999 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
28767045 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * **
28767091 GTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
28767137 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
28767181 TCATGTCAAA
Statistics
Matches: 170, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
45 1 0.01
46 169 0.99
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:28767511 original size:17 final size:17
Alignment explanation
Indices: 28767459--28767512 Score: 51
Period size: 15 Copynumber: 3.4 Consensus size: 17
28767449 ATATACATAA
*
28767459 GATATAAGGAAATG-AT
1 GATATAACGAAATGAAT
* * *
28767475 GATA-CATGAAAT-ATT
1 GATATAACGAAATGAAT
28767490 GATATAACGAAATGAAT
1 GATATAACGAAATGAAT
28767507 GATATA
1 GATATA
28767513 TGCTTATGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
15 11 0.38
16 10 0.34
17 8 0.28
ACGTcount: A:0.50, C:0.04, G:0.19, T:0.28
Consensus pattern (17 bp):
GATATAACGAAATGAAT
Found at i:28770994 original size:85 final size:85
Alignment explanation
Indices: 28770844--28771017 Score: 206
Period size: 85 Copynumber: 2.0 Consensus size: 85
28770834 ACCACCGTTG
* *** **
28770844 ATTTGCAATTATTGCCACTTGTTTTGGGTCCACAACATATTTGTAAATTAAATGAACTGCCACTT
1 ATTTGCAATTAGTGCCACTTGTTGAAGGTCCACAACATATTTGTAAATTAAACAAACTGCCACTT
*
28770909 GGCTCGTGATCGAACCACAT
66 GGCTCATGATCGAACCACAT
* * * *
28770929 ATTTGCAATTAGTGCCACTTGTTGAAGGTGCACAACA-AGTTTGTAGATTAAACAAATTGCTACT
1 ATTTGCAATTAGTGCCACTTGTTGAAGGTCCACAACATA-TTTGTAAATTAAACAAACTGCCACT
* **
28770993 TGGTTCATGATCGAACTGCAT
65 TGGCTCATGATCGAACCACAT
28771014 ATTT
1 ATTT
28771018 ACTATTACTA
Statistics
Matches: 74, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
84 1 0.01
85 73 0.99
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Consensus pattern (85 bp):
ATTTGCAATTAGTGCCACTTGTTGAAGGTCCACAACATATTTGTAAATTAAACAAACTGCCACTT
GGCTCATGATCGAACCACAT
Found at i:28775120 original size:20 final size:20
Alignment explanation
Indices: 28775092--28775141 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
28775082 ATTATATAAA
*
28775092 TCAATAAACGGATCAACCGG
1 TCAATAAACGGATCAACCAG
*
28775112 TCAAGAAACGGATCAACCAG
1 TCAATAAACGGATCAACCAG
28775132 TCAATAAACG
1 TCAATAAACG
28775142 CGAAAAAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.44, C:0.24, G:0.18, T:0.14
Consensus pattern (20 bp):
TCAATAAACGGATCAACCAG
Found at i:28775350 original size:13 final size:13
Alignment explanation
Indices: 28775332--28775358 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28775322 TTATAAATTG
28775332 AGGTTTAATTGAT
1 AGGTTTAATTGAT
28775345 AGGTTTAATTGAT
1 AGGTTTAATTGAT
28775358 A
1 A
28775359 AATACAAGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (13 bp):
AGGTTTAATTGAT
Found at i:28782525 original size:4 final size:4
Alignment explanation
Indices: 28782518--28782577 Score: 77
Period size: 4 Copynumber: 15.0 Consensus size: 4
28782508 ATGGTTTATT
* * *
28782518 TATG TATG TATG TTTG TATG TATG TACG TATG TAAG TATAG -ATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT-G TATG TATG
28782566 TATG TATG TATG
1 TATG TATG TATG
28782578 AATAAACTTG
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
3 1 0.02
4 46 0.96
5 1 0.02
ACGTcount: A:0.27, C:0.02, G:0.25, T:0.47
Consensus pattern (4 bp):
TATG
Found at i:28784149 original size:22 final size:22
Alignment explanation
Indices: 28784118--28784161 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
28784108 AATAACTTAA
*
28784118 GTGGACGAAATGCAATCAACCT
1 GTGGACGAAATGCAACCAACCT
*
28784140 GTGGATGAAATGCAACCAACCT
1 GTGGACGAAATGCAACCAACCT
28784162 AACACGAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (22 bp):
GTGGACGAAATGCAACCAACCT
Found at i:28800891 original size:43 final size:42
Alignment explanation
Indices: 28800826--28800953 Score: 132
Period size: 43 Copynumber: 3.0 Consensus size: 42
28800816 AACTCGTACA
* * * *
28800826 ATGCCATATCCCAAAGATGGTCTTACATGTTATCACATATCG
1 ATGCCATATCCCAGACATGGTCTTACAAGTAATCACATATCG
* * * *
28800868 ATGCCACTATCCCAGACAGGGTCTTACACGAAATCA-ATTAACG
1 ATGCCA-TATCCCAGACATGGTCTTACAAGTAATCACA-TATCG
* *
28800911 ATGCCAATGTTCCAGACATGGTCTTACAAGTAATCACATATCG
1 ATGCC-ATATCCCAGACATGGTCTTACAAGTAATCACATATCG
28800954 GTAACCTAAT
Statistics
Matches: 69, Mismatches: 13, Indels: 7
0.78 0.15 0.08
Matches are distributed among these distances:
42 7 0.10
43 60 0.87
44 2 0.03
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.27
Consensus pattern (42 bp):
ATGCCATATCCCAGACATGGTCTTACAAGTAATCACATATCG
Found at i:28808688 original size:10 final size:10
Alignment explanation
Indices: 28808673--28808700 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
28808663 CTTACTGGAG
28808673 ATATTCAAAA
1 ATATTCAAAA
28808683 ATATTCAAAA
1 ATATTCAAAA
28808693 ATATTCAA
1 ATATTCAA
28808701 CGAACCATTT
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:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (10 bp):
ATATTCAAAA
Found at i:28810033 original size:35 final size:35
Alignment explanation
Indices: 28809987--28810055 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
28809977 TTGCTACGTC
*
28809987 CAACATATGAAGGCATAATTTAAACTTAATGATTT
1 CAACATATGAAGGCATAAGTTAAACTTAATGATTT
28810022 CAACATATGAAGGCATAAGTTAAACTTAATGATT
1 CAACATATGAAGGCATAAGTTAAACTTAATGATT
28810056 GTAGCTTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (35 bp):
CAACATATGAAGGCATAAGTTAAACTTAATGATTT
Found at i:28817189 original size:20 final size:22
Alignment explanation
Indices: 28817166--28817213 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 22
28817156 AATATTTCTA
*
28817166 ATTTTTTAATT-TCTTAAA-AT
1 ATTTTATAATTATCTTAAATAT
*
28817186 ATTTTATAATTATTTTAAATAT
1 ATTTTATAATTATCTTAAATAT
28817208 ATTTTA
1 ATTTTA
28817214 ATATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.42
21 6 0.25
22 8 0.33
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTTTATAATTATCTTAAATAT
Found at i:28817215 original size:20 final size:20
Alignment explanation
Indices: 28817168--28817225 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
28817158 TATTTCTAAT
*
28817168 TTTTTAATT-TCTTAAAATA
1 TTTTTAATTATTTTAAAATA
28817187 TTTTATAATTATTTT-AAATA
1 TTTT-TAATTATTTTAAAATA
*
28817207 TATTTTAA-TATTTAAAAAT
1 T-TTTTAATTATTTTAAAAT
28817226 TTAAAAGTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
19 9 0.27
20 18 0.55
21 6 0.18
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTTTAATTATTTTAAAATA
Found at i:28817823 original size:17 final size:16
Alignment explanation
Indices: 28817790--28817836 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
28817780 ATTTTATTTG
*
28817790 AAATTTAATATACTTAT
1 AAATTTAATA-ATTTAT
28817807 AAATTATAATAATTTAT
1 AAATT-TAATAATTTAT
28817824 AAATTTTAATAAT
1 AAA-TTTAATAAT
28817837 ATTTTAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 20 0.74
18 7 0.26
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATTTAATAATTTAT
Found at i:28817855 original size:20 final size:20
Alignment explanation
Indices: 28817810--28817855 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
28817800 TACTTATAAA
28817810 TTATAATAATTTATAAATTT
1 TTATAATAATTTATAAATTT
* *
28817830 TAATAATATTTTA-AAATTGT
1 TTATAATAATTTATAAATT-T
28817850 TTATAA
1 TTATAA
28817856 ATTACGATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TTATAATAATTTATAAATTT
Found at i:28818995 original size:29 final size:28
Alignment explanation
Indices: 28818953--28819008 Score: 85
Period size: 30 Copynumber: 1.9 Consensus size: 28
28818943 AAACCTATCT
*
28818953 ACTTTCCCCAAAAATTTTTACTTCCTCCC
1 ACTTTCCCCAAAAACTTTTA-TTCCTCCC
28818982 ACTTTCTCCCAAAAACTTTTATTCCTC
1 ACTTTC-CCCAAAAACTTTTATTCCTC
28819009 TCCCATCCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.25, C:0.36, G:0.00, T:0.39
Consensus pattern (28 bp):
ACTTTCCCCAAAAACTTTTATTCCTCCC
Found at i:28819097 original size:30 final size:31
Alignment explanation
Indices: 28819063--28819121 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
28819053 TTTTTTTGAA
*
28819063 TATTTGT-CCCCAAAATTTTACTCTCTCATT
1 TATTTGTCCCCCAAAATTTTACTCCCTCATT
*
28819093 TATTTTTCCCCCAAAATTTTACTCCCTCA
1 TATTTGTCCCCCAAAATTTTACTCCCTCA
28819122 ACTACTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 6 0.23
31 20 0.77
ACGTcount: A:0.24, C:0.31, G:0.02, T:0.44
Consensus pattern (31 bp):
TATTTGTCCCCCAAAATTTTACTCCCTCATT
Found at i:28824051 original size:19 final size:21
Alignment explanation
Indices: 28823998--28824055 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 21
28823988 TAACTTCATT
*
28823998 TATTTTAATAAAATAATATTAA
1 TATTTTAATAAAAT-ATATGAA
28824020 TATTTTTATATAAAAT-T-TGAA
1 TA-TTTTA-ATAAAATATATGAA
28824041 TATTTTAATAAAATA
1 TATTTTAATAAAATA
28824056 ATATCTTAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
19 7 0.22
20 5 0.16
21 5 0.16
22 3 0.09
23 5 0.16
24 7 0.22
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
TATTTTAATAAAATATATGAA
Found at i:28824064 original size:16 final size:17
Alignment explanation
Indices: 28824039--28824071 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
28824029 ATAAAATTTG
*
28824039 AATATTTTAA-TAAAAT
1 AATATCTTAACTAAAAT
28824055 AATATCTTAACTAAAAT
1 AATATCTTAACTAAAAT
28824072 TTATTATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (17 bp):
AATATCTTAACTAAAAT
Found at i:28824672 original size:34 final size:34
Alignment explanation
Indices: 28824599--28824682 Score: 82
Period size: 34 Copynumber: 2.5 Consensus size: 34
28824589 ATTTAGTGTT
**
28824599 ATTTTATAA-AAATTATTTAAATTAGGATTTATGG
1 ATTTTA-AATAAATTAAGTAAATTAGGATTTATGG
* * *
28824633 TTTTTAAATAGATTAAGTAAATTAGGGTTCTA-GG
1 ATTTTAAATAAATTAAGTAAATTAGGATT-TATGG
*
28824667 ATTTTAGATAAATTAA
1 ATTTTAAATAAATTAA
28824683 ATTAGGGTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
33 2 0.05
34 36 0.90
35 2 0.05
ACGTcount: A:0.40, C:0.01, G:0.14, T:0.44
Consensus pattern (34 bp):
ATTTTAAATAAATTAAGTAAATTAGGATTTATGG
Found at i:28824699 original size:22 final size:22
Alignment explanation
Indices: 28824674--28824715 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
28824664 AGGATTTTAG
28824674 ATAAATTAAATTAGGGTTTAAA
1 ATAAATTAAATTAGGGTTTAAA
28824696 ATAAATTAAATTAGGGTTTA
1 ATAAATTAAATTAGGGTTTA
28824716 TGGTTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (22 bp):
ATAAATTAAATTAGGGTTTAAA
Found at i:28824705 original size:86 final size:86
Alignment explanation
Indices: 28824615--28824772 Score: 273
Period size: 86 Copynumber: 1.8 Consensus size: 86
28824605 TAAAAATTAT
*
28824615 TTAAATTAGGATTTATGGTTTTTAAATAGATTAAGTAAATTAGGGTTCTAG-GATTTTAGATAAA
1 TTAAATTAGGATTTATGGTTTTTAAATAGATTAAGTAAATTAGGGCTCTAGAG-TTTTAGATAAA
28824679 TTAAATTAGGGTTTAAAATAAA
65 TTAAATTAGGGTTTAAAATAAA
*
28824701 TTAAATTAGGGTTTATGGTTTTTAAATAGATTAAGTAAATTAGGGCTCTAGAGTTTTAGATAAAT
1 TTAAATTAGGATTTATGGTTTTTAAATAGATTAAGTAAATTAGGGCTCTAGAGTTTTAGATAAAT
*
28824766 TAGATTA
66 TAAATTA
28824773 AGATTTTGGG
Statistics
Matches: 68, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
86 67 0.99
87 1 0.01
ACGTcount: A:0.39, C:0.02, G:0.18, T:0.41
Consensus pattern (86 bp):
TTAAATTAGGATTTATGGTTTTTAAATAGATTAAGTAAATTAGGGCTCTAGAGTTTTAGATAAAT
TAAATTAGGGTTTAAAATAAA
Found at i:28828095 original size:49 final size:49
Alignment explanation
Indices: 28828034--28828164 Score: 174
Period size: 49 Copynumber: 2.7 Consensus size: 49
28828024 ACATCAAAGT
*
28828034 CGATGCCATGTCCCAGACAGGTCTTACACTGACTTTCATATATTG-AGGC
1 CGATGCCATGTCCCAGACAGGTCTTACACTGACTCTCATATA-TGAAGGC
* * * * * *
28828083 CGATGCCGTGTCCCAGATAGGTCTTACACTGGCTCTCATCTATGAATGT
1 CGATGCCATGTCCCAGACAGGTCTTACACTGACTCTCATATATGAAGGC
*
28828132 CGATGCCATGTCCCAGACAGGTCTTACGCTGAC
1 CGATGCCATGTCCCAGACAGGTCTTACACTGAC
28828165 ACACATCAAG
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
48 2 0.03
49 68 0.97
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.27
Consensus pattern (49 bp):
CGATGCCATGTCCCAGACAGGTCTTACACTGACTCTCATATATGAAGGC
Found at i:28829621 original size:37 final size:37
Alignment explanation
Indices: 28829580--28829654 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
28829570 GATAGGTGAG
28829580 AATGAAAATGAATAAATACAAGAAGATTCAGGTATGT
1 AATGAAAATGAATAAATACAAGAAGATTCAGGTATGT
*
28829617 AATGAAAATGAATAAATACAGGAAGATTCAGGTATGT
1 AATGAAAATGAATAAATACAAGAAGATTCAGGTATGT
28829654 A
1 A
28829655 TGATACCTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.51, C:0.05, G:0.20, T:0.24
Consensus pattern (37 bp):
AATGAAAATGAATAAATACAAGAAGATTCAGGTATGT
Found at i:28836117 original size:68 final size:67
Alignment explanation
Indices: 28836045--28836194 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
28836035 CATCATGTGT
* * * *
28836045 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
28836107 ATGTAG
62 ATGTAG
** * *
28836113 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
28836178 AG
66 AG
28836180 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
28836195 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:28836150 original size:64 final size:64
Alignment explanation
Indices: 28836069--28836252 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
28836059 AGACATTATG
* *
28836069 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
28836133 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
28836198 AA
63 AA
* * * *
28836200 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
28836253 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:28838798 original size:19 final size:20
Alignment explanation
Indices: 28838774--28838825 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
28838764 ACTATAGCAA
28838774 CACACAATTT-CAA-TTATTT
1 CACAC-ATTTACAACTTATTT
28838793 CACACATTTACAACTTATTT
1 CACACATTTACAACTTATTT
*
28838813 TACA-ACTTTACAA
1 CACACA-TTTACAA
28838826 AATAGCACTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 4 0.14
19 9 0.31
20 16 0.55
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.38
Consensus pattern (20 bp):
CACACATTTACAACTTATTT
Found at i:28841953 original size:10 final size:10
Alignment explanation
Indices: 28841940--28841965 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
28841930 TATATAAATA
28841940 AAAAATATTC
1 AAAAATATTC
28841950 AAAAATATTC
1 AAAAATATTC
28841960 AAAAAT
1 AAAAAT
28841966 TAAAATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (10 bp):
AAAAATATTC
Found at i:28841965 original size:52 final size:52
Alignment explanation
Indices: 28841863--28842020 Score: 257
Period size: 52 Copynumber: 3.0 Consensus size: 52
28841853 TATAAAATAC
28841863 AAATTAATTAAAATTACATAAATGAAAAAATATTAAACAATATTCAAAAATTA
1 AAATTAATTAAAATTACATAAAT-AAAAAATATTAAACAATATTCAAAAATTA
*
28841916 AAATTAATTAAAATTATATAAATAAAAAATATTCAAA-AATATTCAAAAATTA
1 AAATTAATTAAAATTACATAAATAAAAAATATT-AAACAATATTCAAAAATTA
* *
28841968 AAATTAATTAAAATTACATAAAT-AAAAATATTAAATAATATTCAAAATTTA
1 AAATTAATTAAAATTACATAAATAAAAAATATTAAACAATATTCAAAAATTA
28842019 AA
1 AA
28842021 GTAAACCGTT
Statistics
Matches: 100, Mismatches: 3, Indels: 6
0.92 0.03 0.06
Matches are distributed among these distances:
50 3 0.03
51 25 0.25
52 47 0.47
53 25 0.25
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.32
Consensus pattern (52 bp):
AAATTAATTAAAATTACATAAATAAAAAATATTAAACAATATTCAAAAATTA
Found at i:28842548 original size:17 final size:18
Alignment explanation
Indices: 28842528--28842562 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
28842518 ATTTCTTGTA
28842528 AACTTTTA-AAATTTTAT
1 AACTTTTATAAATTTTAT
*
28842545 AACTTTTATATATTTTAT
1 AACTTTTATAAATTTTAT
28842563 TTTTAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (18 bp):
AACTTTTATAAATTTTAT
Found at i:28845655 original size:13 final size:13
Alignment explanation
Indices: 28845637--28845667 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
28845627 GAGAAAAAAA
28845637 TAAATTAATTAAT
1 TAAATTAATTAAT
28845650 TAAATTAATTAAT
1 TAAATTAATTAAT
28845663 TAAAT
1 TAAAT
28845668 GTCTAGGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TAAATTAATTAAT
Found at i:28849187 original size:23 final size:23
Alignment explanation
Indices: 28849144--28849187 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
28849134 AACAATAAAA
* *
28849144 TTTTAGTATTAATAATTATATTG
1 TTTTAGTATTAAAAATAATATTG
28849167 TTTTA-TATTCAAAAATAATAT
1 TTTTAGTATT-AAAAATAATAT
28849188 ATACATGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (23 bp):
TTTTAGTATTAAAAATAATATTG
Found at i:28859392 original size:93 final size:93
Alignment explanation
Indices: 28859280--28859451 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
28859270 CGCCCATAAG
* *
28859280 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
28859345 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
28859373 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
28859438 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
28859452 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:28859448 original size:46 final size:46
Alignment explanation
Indices: 28859273--28859448 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
28859263 TGTAACCCGC
* * *
28859273 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
28859319 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
28859369 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
28859412 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
28859449 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:28866968 original size:93 final size:93
Alignment explanation
Indices: 28866856--28867027 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
28866846 CGCCCATAAG
* *
28866856 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
28866921 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
28866949 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
28867014 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
28867028 TCAATCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:28867024 original size:46 final size:46
Alignment explanation
Indices: 28866849--28867024 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
28866839 TGTAACCCGC
* * *
28866849 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
28866895 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
28866945 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
28866988 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
28867025 TGCTCAATCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:28869025 original size:48 final size:48
Alignment explanation
Indices: 28868934--28869059 Score: 184
Period size: 48 Copynumber: 2.7 Consensus size: 48
28868924 TATTTGTGCA
* *
28868934 CTAGTGTAAGA-CATATTTGGGACAT-ACATCGACCACATTATGAGAG
1 CTAGTGTAAGACCATGTTTGGGACATGACATTGACCACATTATGAGAG
* * *
28868980 CTAGTGTAAGACCATGTCTCGGACATGACATTGGCCACATTATGAGAG
1 CTAGTGTAAGACCATGTTTGGGACATGACATTGACCACATTATGAGAG
*
28869028 CCAGTGTAAGACCATGTTTGGGACATGACATT
1 CTAGTGTAAGACCATGTTTGGGACATGACATT
28869060 AGGATTGAGA
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
46 11 0.16
47 11 0.16
48 48 0.69
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (48 bp):
CTAGTGTAAGACCATGTTTGGGACATGACATTGACCACATTATGAGAG
Found at i:28869163 original size:46 final size:44
Alignment explanation
Indices: 28869081--28869197 Score: 123
Period size: 46 Copynumber: 2.6 Consensus size: 44
28869071 GAGAGCTAGT
28869081 GTAAGACAT-TCTGGGACATGCATCGGCCTCTAGATGTAAGCCAAA
1 GTAAGACATGTCTGGGACATGCATCGGCCTCTAGATGT--GCCAAA
* **
28869126 GTAAGACATGTCTGGGACATGCATTGG-CTAC-ATGATGTGCCAGT
1 GTAAGACATGTCTGGGACATGCATCGGCCT-CTA-GATGTGCCAAA
*
28869170 GTAAGACCATGTCTAGGACATGGCATCG
1 GTAAGA-CATGTCTGGGACAT-GCATCG
28869198 CCTTAACGTG
Statistics
Matches: 62, Mismatches: 5, Indels: 9
0.82 0.07 0.12
Matches are distributed among these distances:
44 10 0.16
45 25 0.40
46 27 0.44
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (44 bp):
GTAAGACATGTCTGGGACATGCATCGGCCTCTAGATGTGCCAAA
Found at i:28870435 original size:20 final size:21
Alignment explanation
Indices: 28870397--28870435 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
28870387 TTATAATGAA
28870397 CACACGGGCGTGTTGCCCTTC
1 CACACGGGCGTGTTGCCCTTC
28870418 CACACGGGCGTG-TGCCCT
1 CACACGGGCGTGTTGCCCT
28870436 GTTTCAAGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.10, C:0.38, G:0.31, T:0.21
Consensus pattern (21 bp):
CACACGGGCGTGTTGCCCTTC
Found at i:28878686 original size:38 final size:38
Alignment explanation
Indices: 28878641--28878800 Score: 214
Period size: 38 Copynumber: 4.2 Consensus size: 38
28878631 ACTTTAAGCT
*
28878641 CGGATATAATACCAGCACTAAGCCTGCGGGATTTAACC
1 CGGATATAATACCAGCACGAAGCCTGCGGGATTTAACC
* *
28878679 CGGATATAATACCAGCACGAAGCCTGTGGGATTTAACT
1 CGGATATAATACCAGCACGAAGCCTGCGGGATTTAACC
*
28878717 CGGATATATTACCAGCACGAAGCCTGCGGGATTTAACC
1 CGGATATAATACCAGCACGAAGCCTGCGGGATTTAACC
* * * *
28878755 CAGATATAATTCCAGCA-TATAGCCTGCGGGTCTTTAAGCC
1 CGGATATAATACCAGCACGA-AGCCTGCGGG-ATTTAA-CC
28878795 CGGATA
1 CGGATA
28878801 CACATCAAAT
Statistics
Matches: 107, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
37 1 0.01
38 94 0.88
39 5 0.05
40 7 0.07
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (38 bp):
CGGATATAATACCAGCACGAAGCCTGCGGGATTTAACC
Found at i:28878780 original size:76 final size:78
Alignment explanation
Indices: 28878611--28878771 Score: 245
Period size: 76 Copynumber: 2.1 Consensus size: 78
28878601 GAATCTAGTC
* * *
28878611 ACCAGCACAAAACCTGTGGAACTTTAAGCTCGGATATAATACCAGCACTAAGCCTGCGGGATTTA
1 ACCAGCACGAAGCCTGTGGAACTTTAAGCTCGGATATAATACCAGCACGAAGCCTGCGGGATTTA
*
28878676 ACCCGGATATAAT
66 ACCCAGATATAAT
* *
28878689 ACCAGCACGAAGCCTGTGGGA-TTTAA-CTCGGATATATTACCAGCACGAAGCCTGCGGGATTTA
1 ACCAGCACGAAGCCTGTGGAACTTTAAGCTCGGATATAATACCAGCACGAAGCCTGCGGGATTTA
28878752 ACCCAGATATAAT
66 ACCCAGATATAAT
*
28878765 TCCAGCA
1 ACCAGCA
28878772 TATAGCCTGC
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
76 53 0.70
77 5 0.07
78 18 0.24
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (78 bp):
ACCAGCACGAAGCCTGTGGAACTTTAAGCTCGGATATAATACCAGCACGAAGCCTGCGGGATTTA
ACCCAGATATAAT
Found at i:28883675 original size:38 final size:38
Alignment explanation
Indices: 28883630--28883789 Score: 214
Period size: 38 Copynumber: 4.2 Consensus size: 38
28883620 ACTTTAAGCT
*
28883630 CGGATATAATACCAGCACTAAGCCTGCGGGATTTAACC
1 CGGATATAATACCAGCACGAAGCCTGCGGGATTTAACC
* *
28883668 CGGATATAATACCAGCACGAAGCCTGTGGGATTTAACT
1 CGGATATAATACCAGCACGAAGCCTGCGGGATTTAACC
*
28883706 CGGATATATTACCAGCACGAAGCCTGCGGGATTTAACC
1 CGGATATAATACCAGCACGAAGCCTGCGGGATTTAACC
* * * *
28883744 CAGATATAATTCCAGCA-TATAGCCTGCGGGTCTTTAAGCC
1 CGGATATAATACCAGCACGA-AGCCTGCGGG-ATTTAA-CC
28883784 CGGATA
1 CGGATA
28883790 CACATCAAAT
Statistics
Matches: 107, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
37 1 0.01
38 94 0.88
39 5 0.05
40 7 0.07
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (38 bp):
CGGATATAATACCAGCACGAAGCCTGCGGGATTTAACC
Found at i:28883769 original size:76 final size:78
Alignment explanation
Indices: 28883600--28883760 Score: 245
Period size: 76 Copynumber: 2.1 Consensus size: 78
28883590 GAATCTAGTC
* * *
28883600 ACCAGCACAAAACCTGTGGAACTTTAAGCTCGGATATAATACCAGCACTAAGCCTGCGGGATTTA
1 ACCAGCACGAAGCCTGTGGAACTTTAAGCTCGGATATAATACCAGCACGAAGCCTGCGGGATTTA
*
28883665 ACCCGGATATAAT
66 ACCCAGATATAAT
* *
28883678 ACCAGCACGAAGCCTGTGGGA-TTTAA-CTCGGATATATTACCAGCACGAAGCCTGCGGGATTTA
1 ACCAGCACGAAGCCTGTGGAACTTTAAGCTCGGATATAATACCAGCACGAAGCCTGCGGGATTTA
28883741 ACCCAGATATAAT
66 ACCCAGATATAAT
*
28883754 TCCAGCA
1 ACCAGCA
28883761 TATAGCCTGC
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
76 53 0.70
77 5 0.07
78 18 0.24
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (78 bp):
ACCAGCACGAAGCCTGTGGAACTTTAAGCTCGGATATAATACCAGCACGAAGCCTGCGGGATTTA
ACCCAGATATAAT
Found at i:28888007 original size:45 final size:46
Alignment explanation
Indices: 28887899--28888065 Score: 169
Period size: 47 Copynumber: 3.5 Consensus size: 46
28887889 TTTGTGTGCT
*
28887899 AGTGTAAGACCATGTCTGGGACATGCATCGGCCACATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGCATCGGCCACATGAT-AGAGCC
* * * * * *
28887946 AGTGTAAGATCATGTCTAGGATATGCATCGGCTACATGAT-GTGTC
1 AGTGTAAGACCATGTCTGGGACATGCATCGGCCACATGATAGAGCC
* *
28887991 AGTGTAAGACCATGTCTGGGACATGGCATC-GACACGGAT-ACGTGAGAGTC
1 AGTGTAAGACCATGTCTGGGACAT-GCATCGGCCAC--ATGA--T-AGAGCC
28888041 AGTGTAAGACCATGTCTGGGACATG
1 AGTGTAAGACCATGTCTGGGACATG
28888066 GCATTGACAT
Statistics
Matches: 100, Mismatches: 13, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
45 27 0.27
46 6 0.06
47 37 0.37
48 1 0.01
49 1 0.01
50 28 0.28
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACCATGTCTGGGACATGCATCGGCCACATGATAGAGCC
Found at i:28888044 original size:50 final size:48
Alignment explanation
Indices: 28887899--28888074 Score: 161
Period size: 50 Copynumber: 3.7 Consensus size: 48
28887889 TTTGTGTGCT
* *
28887899 AGTGTAAGACCATGTCTGGGACATGCATCGGCCAC--ATTA-TGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGCATC-GACACGGA-TACTGAGAGTC
* * * * *
28887946 AGTGTAAGATCATGTCTAGGATATGCAT-----CGGCTACATGATGTGTC
1 AGTGTAAGACCATGTCTGGGACATGCATCGACACGGATAC-TGA-GAGTC
28887991 AGTGTAAGACCATGTCTGGGACATGGCATCGACACGGATACGTGAGAGTC
1 AGTGTAAGACCATGTCTGGGACAT-GCATCGACACGGATAC-TGAGAGTC
*
28888041 AGTGTAAGACCATGTCTGGGACATGGCATTGACA
1 AGTGTAAGACCATGTCTGGGACAT-GCATCGACA
28888075 TTATACCCTA
Statistics
Matches: 105, Mismatches: 13, Indels: 19
0.77 0.09 0.14
Matches are distributed among these distances:
41 1 0.01
42 2 0.02
44 3 0.03
45 24 0.23
46 4 0.04
47 25 0.24
50 37 0.35
51 9 0.09
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGCATCGACACGGATACTGAGAGTC
Found at i:28892164 original size:34 final size:35
Alignment explanation
Indices: 28892126--28892192 Score: 93
Period size: 34 Copynumber: 1.9 Consensus size: 35
28892116 ATTCTGTAGT
*
28892126 TAGGGTAATACTG-AAACTATAGAA-ACTGAGACAG
1 TAGGG-AAAACTGAAAACTATAGAAGACTGAGACAG
*
28892160 TAGGGAAAACTGAAAACTTTAGAAGACTGAGAC
1 TAGGGAAAACTGAAAACTATAGAAGACTGAGAC
28892193 TATAGCTAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 6 0.21
34 15 0.52
35 8 0.28
ACGTcount: A:0.45, C:0.12, G:0.24, T:0.19
Consensus pattern (35 bp):
TAGGGAAAACTGAAAACTATAGAAGACTGAGACAG
Found at i:28896836 original size:33 final size:36
Alignment explanation
Indices: 28896789--28896855 Score: 95
Period size: 34 Copynumber: 1.9 Consensus size: 36
28896779 ATTCTGTAGT
*
28896789 TAGGGTAATACTG-AAACTGTAGAA-ACTGAGACAG
1 TAGGGTAAAACTGAAAACTGTAGAAGACTGAGACAG
*
28896823 TAGGG-AAAACTGAAAACTTTAGAAGACTGAGAC
1 TAGGGTAAAACTGAAAACTGTAGAAGACTGAGAC
28896856 TATAGCTAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 6 0.21
34 15 0.52
35 8 0.28
ACGTcount: A:0.43, C:0.12, G:0.25, T:0.19
Consensus pattern (36 bp):
TAGGGTAAAACTGAAAACTGTAGAAGACTGAGACAG
Found at i:28899596 original size:64 final size:65
Alignment explanation
Indices: 28899495--28899624 Score: 235
Period size: 64 Copynumber: 2.0 Consensus size: 65
28899485 CCCCTAGGGT
28899495 TAAGGTTGACCTAAATGCATGTTTGACTGTTACTATTTACTACATGCCATG-TATTATTATCTGA
1 TAAGGTTGACCTAAATGCATGTTTGACTGTTACTATTTACTACATGCCATGTTATTATTATCTGA
* *
28899559 TAAGGTTGACCTGAATGCATGTTTGACTGTTACTATTTACTGCATGCCATGTTATTATTATCTGA
1 TAAGGTTGACCTAAATGCATGTTTGACTGTTACTATTTACTACATGCCATGTTATTATTATCTGA
28899624 T
1 T
28899625 GTATGGGACT
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
64 49 0.78
65 14 0.22
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (65 bp):
TAAGGTTGACCTAAATGCATGTTTGACTGTTACTATTTACTACATGCCATGTTATTATTATCTGA
Found at i:28899610 original size:30 final size:30
Alignment explanation
Indices: 28899512--28899611 Score: 76
Period size: 30 Copynumber: 3.2 Consensus size: 30
28899502 GACCTAAATG
*
28899512 CATGTTTGACTGTTACTATTTACTACATGC
1 CATGTTTGACTGTTACTATTTACTGCATGC
* * *** * *
28899542 CATGTATTATTATCTGATAAGGTTGACCTGAATG-
1 CATG--TT-TGA-CTGTTACTATTTA-CTGCATGC
28899576 CATGTTTGACTGTTACTATTTACTGCATGC
1 CATGTTTGACTGTTACTATTTACTGCATGC
28899606 CATGTT
1 CATGTT
28899612 ATTATTATCT
Statistics
Matches: 49, Mismatches: 15, Indels: 12
0.64 0.20 0.16
Matches are distributed among these distances:
29 6 0.12
30 18 0.37
31 2 0.04
32 4 0.08
33 2 0.04
34 12 0.24
35 5 0.10
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.42
Consensus pattern (30 bp):
CATGTTTGACTGTTACTATTTACTGCATGC
Found at i:28905580 original size:56 final size:56
Alignment explanation
Indices: 28905520--28905693 Score: 180
Period size: 56 Copynumber: 3.1 Consensus size: 56
28905510 TTATTAATAG
28905520 AATATTAAAGTGATTATCTTAATATTAAATTAAATTTAATGTTTATCTTGTAGATA
1 AATATTAAAGTGATTATCTTAATATTAAATTAAATTTAATGTTTATCTTGTAGATA
** * * * * * *
28905576 AATATTCTACT-A--AT-TTAATA--AGATTTAATATAATATTTATCTTGTTATATTAA
1 AATATTAAAGTGATTATCTTAATATTAAATTAAATTTAATGTTTATCTTG-TAGA-T-A
28905629 TTTAATATTAAAGTGATTATCTTAATATTAAATTAAATTTAATGTTTATCTTGTAGATA
1 ---AATATTAAAGTGATTATCTTAATATTAAATTAAATTTAATGTTTATCTTGTAGATA
28905688 AATATT
1 AATATT
28905694 CTACTAATTT
Statistics
Matches: 90, Mismatches: 16, Indels: 24
0.69 0.12 0.18
Matches are distributed among these distances:
50 20 0.22
51 3 0.03
52 7 0.08
53 3 0.03
55 1 0.01
56 22 0.24
57 1 0.01
59 3 0.03
60 7 0.08
61 3 0.03
62 20 0.22
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (56 bp):
AATATTAAAGTGATTATCTTAATATTAAATTAAATTTAATGTTTATCTTGTAGATA
Found at i:28905619 original size:50 final size:50
Alignment explanation
Indices: 28905556--28905732 Score: 165
Period size: 50 Copynumber: 3.3 Consensus size: 50
28905546 AAATTAAATT
*
28905556 TAATGTTTATCTTGTAGATAAATATTCTACTAATTTAATAAGATTTAATA
1 TAATATTTATCTTGTAGATAAATATTCTACTAATTTAATAAGATTTAATA
* ** * * * *
28905606 TAATATTTATCTTGTTATATTAATTTAATATTAAAGTGATTATCTTAATATTAAATTAAATT
1 TAATATTTATCTTG-TAGA-T-A---AATATTCTACT-A--AT-TTAATA--AGATTTAATA
*
28905668 TAATGTTTATCTTGTAGATAAATATTCTACTAATTTAATAAGATTTAATA
1 TAATATTTATCTTGTAGATAAATATTCTACTAATTTAATAAGATTTAATA
28905718 TAATATTTATCTTGT
1 TAATATTTATCTTGT
28905733 TATATTAATT
Statistics
Matches: 98, Mismatches: 17, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
50 34 0.35
51 3 0.03
52 7 0.07
53 3 0.03
55 1 0.01
56 16 0.16
57 1 0.01
59 3 0.03
60 7 0.07
61 3 0.03
62 20 0.20
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (50 bp):
TAATATTTATCTTGTAGATAAATATTCTACTAATTTAATAAGATTTAATA
Found at i:28905639 original size:112 final size:112
Alignment explanation
Indices: 28905511--28905759 Score: 480
Period size: 112 Copynumber: 2.2 Consensus size: 112
28905501 AATAGTAATT
**
28905511 TATTAATAGAATATTAAAGTGATTATCTTAATATTAAATTAAATTTAATGTTTATCTTGTAGATA
1 TATTAATTTAATATTAAAGTGATTATCTTAATATTAAATTAAATTTAATGTTTATCTTGTAGATA
28905576 AATATTCTACTAATTTAATAAGATTTAATATAATATTTATCTTGTTA
66 AATATTCTACTAATTTAATAAGATTTAATATAATATTTATCTTGTTA
28905623 TATTAATTTAATATTAAAGTGATTATCTTAATATTAAATTAAATTTAATGTTTATCTTGTAGATA
1 TATTAATTTAATATTAAAGTGATTATCTTAATATTAAATTAAATTTAATGTTTATCTTGTAGATA
28905688 AATATTCTACTAATTTAATAAGATTTAATATAATATTTATCTTGTTA
66 AATATTCTACTAATTTAATAAGATTTAATATAATATTTATCTTGTTA
28905735 TATTAATTTAATATTAAAGTGATTA
1 TATTAATTTAATATTAAAGTGATTA
28905760 AGTTTAATCA
Statistics
Matches: 135, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
112 135 1.00
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (112 bp):
TATTAATTTAATATTAAAGTGATTATCTTAATATTAAATTAAATTTAATGTTTATCTTGTAGATA
AATATTCTACTAATTTAATAAGATTTAATATAATATTTATCTTGTTA
Found at i:28905884 original size:26 final size:22
Alignment explanation
Indices: 28905855--28905902 Score: 60
Period size: 26 Copynumber: 2.0 Consensus size: 22
28905845 AGTTGTAAAG
28905855 AGAAAATTCTCTGAAAAGATTATTTT
1 AGAAAATT-TCT--AAAGA-TATTTT
28905881 AGAAAATTTCTAAAGATATTTT
1 AGAAAATTTCTAAAGATATTTT
28905903 TTATTTACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 6 0.27
23 5 0.23
25 3 0.14
26 8 0.36
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (22 bp):
AGAAAATTTCTAAAGATATTTT
Found at i:28907207 original size:20 final size:21
Alignment explanation
Indices: 28907169--28907207 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
28907159 AAAGTTGAAG
* *
28907169 TAGTATTTTATGTTTTTTTTA
1 TAGTATTTTATGATATTTTTA
28907190 TAGT-TTTTATGATATTTT
1 TAGTATTTTATGATATTTT
28907208 CAAACTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (21 bp):
TAGTATTTTATGATATTTTTA
Found at i:28911717 original size:27 final size:27
Alignment explanation
Indices: 28911687--28911745 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
28911677 AAGAGCCTTC
* * *
28911687 CTTTTATATTTCGCGACAAAGGATTTT
1 CTTTCATATTTCACCACAAAGGATTTT
*
28911714 CTTTCATATTTCACCACAAAGGCTTTT
1 CTTTCATATTTCACCACAAAGGATTTT
28911741 CTTTC
1 CTTTC
28911746 TCGCCGTGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.44
Consensus pattern (27 bp):
CTTTCATATTTCACCACAAAGGATTTT
Found at i:28914830 original size:50 final size:49
Alignment explanation
Indices: 28914720--28914895 Score: 190
Period size: 50 Copynumber: 3.5 Consensus size: 49
28914710 CTGGTACGCA
* * * ** *
28914720 TAGTAGCCTGCACATAGTACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAACCATCCGATACACG
*
28914769 TAGTAGCCTGCACTTAGTACTACACACGTGACCAAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AACCATCCGATACACG
**** * * * *
28914819 TAGTAGCCTGCACTTAGTACTACACACGTGATCGCAGTTTTCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-C-CAACCATCCGATACACG
28914870 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
28914896 TGCGACCTCA
Statistics
Matches: 109, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
49 30 0.28
50 43 0.39
51 35 0.32
52 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAACCATCCGATACACG
Found at i:28916872 original size:16 final size:16
Alignment explanation
Indices: 28916853--28916884 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28916843 AATTGTTTTA
28916853 TTACAAAATTTCACTT
1 TTACAAAATTTCACTT
*
28916869 TTACATAATTTCACTT
1 TTACAAAATTTCACTT
28916885 ACTCCATTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.19, G:0.00, T:0.47
Consensus pattern (16 bp):
TTACAAAATTTCACTT
Found at i:28917174 original size:50 final size:50
Alignment explanation
Indices: 28917098--28917460 Score: 322
Period size: 50 Copynumber: 7.2 Consensus size: 50
28917088 GTACGCATAC
* * * *
28917098 CACATGCGACCTATCAATTTGGTACACGTAGTAGCCTGCACTTAGTACTA
1 CACATGTGACTTAACAATCTGGTACACGTAGTAGCCTGCACTTAGTACTA
* *
28917148 CACATGTGACTTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACTA
1 CACATGTGACTTAACAATCTGGTACACGTAGTAGCCTGCACTTAGTACTA
** * * * * * *
28917198 CACACATTA-TCGAAGTTAA-CGGGTACGCATAGTAGCCTGCACTTAGTA-TGA
1 CACATGTGACT-TAA--CAATCTGGTACACGTAGTAGCCTGCACTTAGTACT-A
* * * *
28917249 CACATGCGACCTATCAATCTGGTACACGTAGTAGCCTACACTTAGTACTA
1 CACATGTGACTTAACAATCTGGTACACGTAGTAGCCTGCACTTAGTACTA
* * * * * *
28917299 CATACGTGACTTAACCATCTGATACACGTAGTAGTCTACACTTAGTACTA
1 CACATGTGACTTAACAATCTGGTACACGTAGTAGCCTGCACTTAGTACTA
* * * * * *
28917349 CATATGTGA-TCGAAGTTAA-CGGGTACGCATAGTAGCCTGCACTTAGTACTA
1 CACATGTGACT-TAA--CAATCTGGTACACGTAGTAGCCTGCACTTAGTACTA
* * *
28917400 CACATGCGACCTATCAATCTGGTACACGTAGTAGCCTGCACTTAGTACTA
1 CACATGTGACTTAACAATCTGGTACACGTAGTAGCCTGCACTTAGTACTA
*
28917450 CACACGTGACT
1 CACATGTGACT
28917461 CACAATGAAT
Statistics
Matches: 243, Mismatches: 58, Indels: 24
0.75 0.18 0.07
Matches are distributed among these distances:
49 6 0.02
50 168 0.69
51 67 0.28
52 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (50 bp):
CACATGTGACTTAACAATCTGGTACACGTAGTAGCCTGCACTTAGTACTA
Found at i:28917372 original size:151 final size:151
Alignment explanation
Indices: 28917098--28917460 Score: 620
Period size: 151 Copynumber: 2.4 Consensus size: 151
28917088 GTACGCATAC
* *
28917098 CACATGCGACCTATCAATTTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACTTAAC
1 CACATGCGACCTATCAATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACTTAAC
* *
28917163 CATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACATTATCGAAGTTAACGGGTACGCAT
66 CATCTGATACACGTAGTAGCCTACACTTAGTACTACACACATGATCGAAGTTAACGGGTACGCAT
28917228 AGTAGCCTGCACTTAGTA-TGA
131 AGTAGCCTGCACTTAGTACT-A
* *
28917249 CACATGCGACCTATCAATCTGGTACACGTAGTAGCCTACACTTAGTACTACATACGTGACTTAAC
1 CACATGCGACCTATCAATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACTTAAC
* * **
28917314 CATCTGATACACGTAGTAGTCTACACTTAGTACTACATATGTGATCGAAGTTAACGGGTACGCAT
66 CATCTGATACACGTAGTAGCCTACACTTAGTACTACACACATGATCGAAGTTAACGGGTACGCAT
28917379 AGTAGCCTGCACTTAGTACTA
131 AGTAGCCTGCACTTAGTACTA
28917400 CACATGCGACCTATCAATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACT
1 CACATGCGACCTATCAATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACT
28917461 CACAATGAAT
Statistics
Matches: 199, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
151 198 0.99
152 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (151 bp):
CACATGCGACCTATCAATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACTTAAC
CATCTGATACACGTAGTAGCCTACACTTAGTACTACACACATGATCGAAGTTAACGGGTACGCAT
AGTAGCCTGCACTTAGTACTA
Found at i:28917374 original size:101 final size:101
Alignment explanation
Indices: 28917269--28917451 Score: 258
Period size: 101 Copynumber: 1.8 Consensus size: 101
28917259 CTATCAATCT
* * * * * *
28917269 GGTACACGTAGTAGCCTACACTTAGTACTACATACGTGACTTAACCATCTGATACACGTAGTAGT
1 GGTACACATAGTAGCCTACACTTAGTACTACACACGCGACCTAACAATCTGATACACGTAGTAGC
28917334 CTACACTTAGTACTACATATGTGATCGAAGTTAACG
66 CTACACTTAGTACTACATATGTGATCGAAGTTAACG
* * * * *
28917370 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGTAGC
1 GGTACACATAGTAGCCTACACTTAGTACTACACACGCGACCTAACAATCTGATACACGTAGTAGC
*
28917435 CTGCACTTAGTACTACA
66 CTACACTTAGTACTACA
28917452 CACGTGACTC
Statistics
Matches: 70, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
101 70 1.00
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (101 bp):
GGTACACATAGTAGCCTACACTTAGTACTACACACGCGACCTAACAATCTGATACACGTAGTAGC
CTACACTTAGTACTACATATGTGATCGAAGTTAACG
Found at i:28917836 original size:19 final size:20
Alignment explanation
Indices: 28917808--28917854 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
28917798 AAGAACATGT
28917808 TATATCATCAAAATAATCACA
1 TATAT-ATCAAAATAATCACA
* *
28917829 TA-ATATCAAATTATTCACA
1 TATATATCAAAATAATCACA
28917848 TATATAT
1 TATATAT
28917855 AGTTATAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 15 0.65
20 6 0.26
21 2 0.09
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (20 bp):
TATATATCAAAATAATCACA
Found at i:28927946 original size:48 final size:51
Alignment explanation
Indices: 28927824--28928094 Score: 197
Period size: 48 Copynumber: 5.6 Consensus size: 51
28927814 CAAAATGGAG
* *
28927824 GCCGATGCCATGTCCCAGACATGGTCTTACACT-AGCTCTAACATATCCGT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGAGCACTAACATATACGT
* * * *
28927874 GCTGATGCCATGTCCCAGATATGGTCTCACACTGA-CACT-TC-TATACGT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGAGCACTAACATATACGT
* * *
28927922 GCCGATGCCATGTCCTAGACATGGTCTTACACTG-GCTCT--CATA-ATGT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGAGCACTAACATATACGT
* * * **
28927969 AGCCAATG-CATGTCCCAGACAT-GTCTTGCACT-AGCTCTTGTC-TCA-A-G-
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTGAGCAC-TAACAT-ATACGT
* * * *
28928016 GCCGATGCCATGTACTAGACATGGTCTTACACT-AGCTCT--CATA-ATGT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGAGCACTAACATATACGT
28928063 GGCCGATG-CATGTCCCAGACAT-GTCTTACACT
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACT
28928095 AGAACACAAA
Statistics
Matches: 185, Mismatches: 21, Indels: 34
0.77 0.09 0.14
Matches are distributed among these distances:
45 3 0.02
46 31 0.17
47 43 0.23
48 70 0.38
49 4 0.02
50 33 0.18
51 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (51 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGAGCACTAACATATACGT
Found at i:28928038 original size:94 final size:94
Alignment explanation
Indices: 28927822--28928096 Score: 315
Period size: 94 Copynumber: 2.9 Consensus size: 94
28927812 ATCAAAATGG
* * **
28927822 AGGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTAACAT-ATCCGT-GCTGATGCCAT
1 AGGCCGATGCCATGTACTAGACATGGTCTTACACTAGCTCT--CATAAT--GTAGCCAATG-CAT
* * * * *
28927885 GTCCCAGATATGGTCTCACACT-GACACTTCTAT-A
61 GTCCCAGACAT-GTCTTACACTAG-CTCTTGTCTCA
* * *
28927919 CGTGCCGATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATAATGTAGCCAATGCATGTCC
1 AG-GCCGATGCCATGTACTAGACATGGTCTTACACTAGCTCTCATAATGTAGCCAATGCATGTCC
*
28927984 CAGACATGTCTTGCACTAGCTCTTGTCTCA
65 CAGACATGTCTTACACTAGCTCTTGTCTCA
* *
28928014 AGGCCGATGCCATGTACTAGACATGGTCTTACACTAGCTCTCATAATGTGGCCGATGCATGTCCC
1 AGGCCGATGCCATGTACTAGACATGGTCTTACACTAGCTCTCATAATGTAGCCAATGCATGTCCC
28928079 AGACATGTCTTACACTAG
66 AGACATGTCTTACACTAG
28928097 AACACAAATA
Statistics
Matches: 156, Mismatches: 17, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
94 90 0.58
95 18 0.12
96 8 0.05
97 3 0.02
98 37 0.24
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.28
Consensus pattern (94 bp):
AGGCCGATGCCATGTACTAGACATGGTCTTACACTAGCTCTCATAATGTAGCCAATGCATGTCCC
AGACATGTCTTACACTAGCTCTTGTCTCA
Found at i:28928068 original size:142 final size:146
Alignment explanation
Indices: 28927777--28928094 Score: 332
Period size: 147 Copynumber: 2.2 Consensus size: 146
28927767 TCTATCAAGT
* * * *
28927777 CGATGCCATGTTCTAGACATGGTATTACATTGACTATCAAAATGGAGGCCGATGCCATGTCCCAG
1 CGATGCCATGTCCTAGACATGGTCTTACACTGACTATCAAAATGGAGGCCAATGCCATGTCCCAG
* * * *
28927842 ACATGGTCTTACACTAGCTCTAACATATCCGTGCTGATGCCATGTCCCAGATATGGTCTCACACT
66 ACATGGTCTTACACTAGCTCT-ACATATCAGTGCCGATGCCATGTACCAGACATGGTCTCACACT
28927907 GACACTTCTATACGTGC
130 GACACTTCTATACGTGC
* * * *
28927924 CGATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATAATGTA-GCCAATG-CATGTCCCAG
1 CGATGCCATGTCCTAGACATGGTCTTACACTGACTATCAAAATGGAGGCCAATGCCATGTCCCAG
* ** * * *
28927987 ACAT-GTCTTGCACTAGCTCT-TGTCTCAAG-GCCGATGCCATGTACTAGACATGGTCTTACACT
66 ACATGGTCTTACACTAGCTCTACATATC-AGTGCCGATGCCATGTACCAGACATGGTCTCACACT
* *
28928049 -A-GC-TCTCATAATGTGGC
130 GACACTTCT-AT-ACGT-GC
*
28928066 CGATG-CATGTCCCAGACAT-GTCTTACACT
1 CGATGCCATGTCCTAGACATGGTCTTACACT
28928095 AGAACACAAA
Statistics
Matches: 146, Mismatches: 21, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
139 3 0.02
140 13 0.09
141 17 0.12
142 38 0.26
143 1 0.01
144 15 0.10
145 14 0.10
146 6 0.04
147 39 0.27
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (146 bp):
CGATGCCATGTCCTAGACATGGTCTTACACTGACTATCAAAATGGAGGCCAATGCCATGTCCCAG
ACATGGTCTTACACTAGCTCTACATATCAGTGCCGATGCCATGTACCAGACATGGTCTCACACTG
ACACTTCTATACGTGC
Found at i:28930414 original size:43 final size:43
Alignment explanation
Indices: 28930353--28930435 Score: 157
Period size: 43 Copynumber: 1.9 Consensus size: 43
28930343 CTTGGTGTTC
*
28930353 GGCCTTCACTTGTTGACAAACTAGACACTTAGAAACAAACATA
1 GGCCTTCACTTGTTGACAAACTAGACACTTAAAAACAAACATA
28930396 GGCCTTCACTTGTTGACAAACTAGACACTTAAAAACAAAC
1 GGCCTTCACTTGTTGACAAACTAGACACTTAAAAACAAAC
28930436 TCGGAAATGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.40, C:0.24, G:0.13, T:0.23
Consensus pattern (43 bp):
GGCCTTCACTTGTTGACAAACTAGACACTTAAAAACAAACATA
Found at i:28934306 original size:20 final size:21
Alignment explanation
Indices: 28934281--28934320 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
28934271 CCCTTGAAAT
28934281 AGGGC-ACACGCCCATGTGGA
1 AGGGCAACACGCCCATGTGGA
* *
28934301 AGGGCAACATGCCCGTGTGG
1 AGGGCAACACGCCCATGTGG
28934321 TTTACTATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.23, C:0.28, G:0.38, T:0.12
Consensus pattern (21 bp):
AGGGCAACACGCCCATGTGGA
Found at i:28935677 original size:48 final size:48
Alignment explanation
Indices: 28935431--28935800 Score: 255
Period size: 47 Copynumber: 7.8 Consensus size: 48
28935421 AGGGTATAAT
* *
28935431 GCCGATGCCATGTCCCAGACATGGTCTTACACAGGCTCATCCATCAA-GT-
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTC-T-TAT-AATGTG
* * * * *
28935480 --CGATGCCATGTTCTAGACATGGTCTTACACTGACTATCTA-AATCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-TATAAT-GTG
* * * * *
28935527 GCCGACGCCATGTCCCAGACATGGTGTTACACTAGCTCTAACATAT-TCG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTTATA-ATGT-G
* * * * *
28935576 TGCCGATGTCATGTCCCAGACATGGCCTTACACTGACACCTT-TATACGT-
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTGGC-TCTTATA-ATGTG
* * *
28935625 GTCGATGCCATGTCCTAGACAGGGTCTTACACTGGCTCTTATAATGTG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTTATAATGTG
* * * * ** *
28935673 GTCGATG-CATCTCACAGACAT-GTCTTACACTAGCTCTCGT-CTCGAT-
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTTATAAT-G-TG
* * *
28935719 GCCGATGCCATGTCCCAAACATGTTCTTACACTGGCTCTCATAATGTG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTTATAATGTG
*
28935767 GCTGATG-CATGTCCCAGACAT-GTCTTACACTGGC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGC
28935801 ACACAAATAA
Statistics
Matches: 249, Mismatches: 53, Indels: 41
0.73 0.15 0.12
Matches are distributed among these distances:
44 2 0.01
45 1 0.00
46 39 0.16
47 73 0.29
48 63 0.25
49 33 0.13
50 35 0.14
51 3 0.01
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (48 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTTATAATGTG
Found at i:28939052 original size:16 final size:16
Alignment explanation
Indices: 28939031--28939061 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
28939021 AAACACATAG
28939031 AGTAAGCTACAAAGAA
1 AGTAAGCTACAAAGAA
28939047 AGTAAGCTACAAAGA
1 AGTAAGCTACAAAGA
28939062 GCTTAGTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.55, C:0.13, G:0.19, T:0.13
Consensus pattern (16 bp):
AGTAAGCTACAAAGAA
Found at i:28942187 original size:27 final size:27
Alignment explanation
Indices: 28942157--28942485 Score: 192
Period size: 27 Copynumber: 12.2 Consensus size: 27
28942147 ATTACCGTTT
*
28942157 TACCCTCGATTAGCAAAATTACCAAAA
1 TACCCTCGATTAGTAAAATTACCAAAA
* *
28942184 TACCC-CTGGTTTGTAAAATTACCAAAA
1 TACCCTC-GATTAGTAAAATTACCAAAA
* * *
28942211 TACCCTTGGCTTA-CAAAATTACCAAAA
1 TACCC-TCGATTAGTAAAATTACCAAAA
* * * **
28942238 TTCCCTCGATTTGTGAAATTACTGAAA
1 TACCCTCGATTAGTAAAATTACCAAAA
28942265 TACCCTCGACTT-GTAAAATTACCAAAA
1 TACCCTCGA-TTAGTAAAATTACCAAAA
* * *
28942292 TACCCTTGGCTTA-CAAAATTACCAAAA
1 TACCC-TCGATTAGTAAAATTACCAAAA
* * **
28942319 TACCCTCGATTTGTGAAATTACTGAAA
1 TACCCTCGATTAGTAAAATTACCAAAA
* * *
28942346 TACCCT-TA-TAGGATAGAATTACCGAAA
1 TACCCTCGATTA-G-TAAAATTACCAAAA
* * * * *
28942373 TACCATTGTAGT-GTGAAATTACTAAAA
1 TACCCTCG-ATTAGTAAAATTACCAAAA
28942400 TACCCTCGACTT-GTAAAATTACCAAAA
1 TACCCTCGA-TTAGTAAAATTACCAAAA
* * * *
28942427 TACCCTTAGTTTA-CAAAATTATCAAAA
1 TACCC-TCGATTAGTAAAATTACCAAAA
* * **
28942454 TACACC-CAATTAGTGAAATTACTGAAA
1 TAC-CCTCGATTAGTAAAATTACCAAAA
28942481 TACCC
1 TACCC
28942486 CTGTAAGGTA
Statistics
Matches: 227, Mismatches: 57, Indels: 37
0.71 0.18 0.12
Matches are distributed among these distances:
25 1 0.00
26 17 0.07
27 195 0.86
28 12 0.05
29 1 0.00
30 1 0.00
ACGTcount: A:0.40, C:0.22, G:0.10, T:0.29
Consensus pattern (27 bp):
TACCCTCGATTAGTAAAATTACCAAAA
Found at i:28942244 original size:81 final size:81
Alignment explanation
Indices: 28942157--28942329 Score: 258
Period size: 81 Copynumber: 2.1 Consensus size: 81
28942147 ATTACCGTTT
**
28942157 TACCCTCGATTAGCAAAATTACCAAAATACCC-CTGGTTTGTAAAATTACCAAAATACCCTTGGC
1 TACCCTCGATTAGCAAAATTACCAAAATACCCTC-GACTTGTAAAATTACCAAAATACCCTTGGC
28942221 TTACAAAATTACCAAAA
65 TTACAAAATTACCAAAA
* * ** **
28942238 TTCCCTCGATTTGTGAAATTACTGAAATACCCTCGACTTGTAAAATTACCAAAATACCCTTGGCT
1 TACCCTCGATTAGCAAAATTACCAAAATACCCTCGACTTGTAAAATTACCAAAATACCCTTGGCT
28942303 TACAAAATTACCAAAA
66 TACAAAATTACCAAAA
28942319 TACCCTCGATT
1 TACCCTCGATT
28942330 TGTGAAATTA
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
81 81 0.99
82 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.09, T:0.28
Consensus pattern (81 bp):
TACCCTCGATTAGCAAAATTACCAAAATACCCTCGACTTGTAAAATTACCAAAATACCCTTGGCT
TACAAAATTACCAAAA
Found at i:28942330 original size:81 final size:81
Alignment explanation
Indices: 28942194--28942351 Score: 307
Period size: 81 Copynumber: 2.0 Consensus size: 81
28942184 TACCCCTGGT
*
28942194 TTGTAAAATTACCAAAATACCCTTGGCTTACAAAATTACCAAAATTCCCTCGATTTGTGAAATTA
1 TTGTAAAATTACCAAAATACCCTTGGCTTACAAAATTACCAAAATACCCTCGATTTGTGAAATTA
28942259 CTGAAATACCCTCGAC
66 CTGAAATACCCTCGAC
28942275 TTGTAAAATTACCAAAATACCCTTGGCTTACAAAATTACCAAAATACCCTCGATTTGTGAAATTA
1 TTGTAAAATTACCAAAATACCCTTGGCTTACAAAATTACCAAAATACCCTCGATTTGTGAAATTA
28942340 CTGAAATACCCT
66 CTGAAATACCCT
28942352 TATAGGATAG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 76 1.00
ACGTcount: A:0.38, C:0.23, G:0.09, T:0.30
Consensus pattern (81 bp):
TTGTAAAATTACCAAAATACCCTTGGCTTACAAAATTACCAAAATACCCTCGATTTGTGAAATTA
CTGAAATACCCTCGAC
Found at i:28942338 original size:54 final size:54
Alignment explanation
Indices: 28942157--28942432 Score: 216
Period size: 54 Copynumber: 5.1 Consensus size: 54
28942147 ATTACCGTTT
* * * **
28942157 TACCCTCGATTAGCAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAA
1 TACCCTCGATTTGTAAAATTACCAAAATACCCTTGACTTGTAAAATTACCAAAA
* ** ** * * * * **
28942211 TACCCTTGGCTTACAAAATTACCAAAATTCCCTCGATTTGTGAAATTACTGAAA
1 TACCCTCGATTTGTAAAATTACCAAAATACCCTTGACTTGTAAAATTACCAAAA
* * **
28942265 TACCCTCGACTTGTAAAATTACCAAAATACCCTTGGCTTACAAAATTACCAAAA
1 TACCCTCGATTTGTAAAATTACCAAAATACCCTTGACTTGTAAAATTACCAAAA
* ** * * *
28942319 TACCCTCGATTTGTGAAATTACTGAAATACCCTT-A-TAGGATAGAATTACCGAAA
1 TACCCTCGATTTGTAAAATTACCAAAATACCCTTGACT-TG-TAAAATTACCAAAA
* * * * * *
28942373 TACCATTG-TAGTGTGAAATTACTAAAATACCCTCGACTTGTAAAATTACCAAAA
1 TACCCTCGAT-TTGTAAAATTACCAAAATACCCTTGACTTGTAAAATTACCAAAA
28942427 TACCCT
1 TACCCT
28942433 TAGTTTACAA
Statistics
Matches: 173, Mismatches: 44, Indels: 10
0.76 0.19 0.04
Matches are distributed among these distances:
52 1 0.01
53 1 0.01
54 168 0.97
55 2 0.01
56 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.29
Consensus pattern (54 bp):
TACCCTCGATTTGTAAAATTACCAAAATACCCTTGACTTGTAAAATTACCAAAA
Found at i:28942366 original size:81 final size:80
Alignment explanation
Indices: 28942196--28942434 Score: 291
Period size: 81 Copynumber: 3.0 Consensus size: 80
28942186 CCCCTGGTTT
*
28942196 GTAAAATTACCAAAATACCCTTGGCTTACAAAATTACCAAAATTCCCTCGATTTGTGAAATTACT
1 GTAAAATTACCAAAATACCCTTGGCTTACAAAATTACCAAAATACCCTCGATTTGTGAAATTACT
* *
28942261 GAAATACCCTCGACTT
66 GAAATACCCT-TACTG
28942277 GTAAAATTACCAAAATACCCTTGGCTTACAAAATTACCAAAATACCCTCGATTTGTGAAATTACT
1 GTAAAATTACCAAAATACCCTTGGCTTACAAAATTACCAAAATACCCTCGATTTGTGAAATTACT
28942342 GAAATACCCTTA-TAG
66 GAAATACCCTTACT-G
* * * *** *** * * *
28942357 GATAGAATTACCGAAATACCATTGTAGTGTGAAATTACTAAAATACCCTCGACTTGTAAAATTAC
1 G-TAAAATTACCAAAATACCCTTGGCTTACAAAATTACCAAAATACCCTCGATTTGTGAAATTAC
**
28942422 CAAAATACCCTTA
65 TGAAATACCCTTA
28942435 GTTTACAAAA
Statistics
Matches: 139, Mismatches: 17, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
79 1 0.01
80 2 0.01
81 136 0.98
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.29
Consensus pattern (80 bp):
GTAAAATTACCAAAATACCCTTGGCTTACAAAATTACCAAAATACCCTCGATTTGTGAAATTACT
GAAATACCCTTACTG
Found at i:28942500 original size:27 final size:27
Alignment explanation
Indices: 28942470--28942664 Score: 259
Period size: 27 Copynumber: 7.2 Consensus size: 27
28942460 CAATTAGTGA
*
28942470 AATTACTGAAATACCCCTGTAAGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * *
28942497 AATTACCGGAATACCCCTATAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
28942524 AATTA-TCGAAATACCCTTGTAGGGTAG
1 AATTACT-GAAATACCCCTGTAGGGTAG
* *
28942551 AATTACTAAAATACCCCCGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
28942578 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
28942605 AATTATTGAAATACCCCTGTAAGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
28942632 AATTAC-CAAGATACCCCTGTAGGGTAG
1 AATTACTGAA-ATACCCCTGTAGGGTAG
28942659 AATTAC
1 AATTAC
28942665 CATTTTGCCC
Statistics
Matches: 145, Mismatches: 20, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
26 2 0.01
27 142 0.98
28 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.25
Consensus pattern (27 bp):
AATTACTGAAATACCCCTGTAGGGTAG
Found at i:28942501 original size:54 final size:53
Alignment explanation
Indices: 28942443--28942663 Score: 209
Period size: 54 Copynumber: 4.1 Consensus size: 53
28942433 TAGTTTACAA
* *
28942443 AATTATCAAAATACACCCAATTAGTG-A-AATTACTGAAATACCCCTGTAAGGTAG
1 AATTATCAAAATAC-CCC-A-TAGGGTAGAATTACTGAAATACCCCTGTAGGGTAG
* ** *
28942497 AATTACCGGAATACCCCTATAGGGTAGAATTA-TCGAAATACCCTTGTAGGGTAG
1 AATTATCAAAATACCCC-ATAGGGTAGAATTACT-GAAATACCCCTGTAGGGTAG
* *
28942551 AATTA-CTAAAATACCCCCGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAG
1 AATTATC-AAAATA-CCCCATAGGGTAGAATTACTGAAATACCCCTGTAGGGTAG
** * * *
28942605 AATTATTGAAATACCCCTGTAAGGTAGAATTAC-CAAGATACCCCTGTAGGGTAG
1 AATTATCAAAATACCCC-ATAGGGTAGAATTACTGAA-ATACCCCTGTAGGGTAG
28942659 AATTA
1 AATTA
28942664 CCATTTTGCC
Statistics
Matches: 142, Mismatches: 16, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
52 4 0.03
53 13 0.09
54 121 0.85
55 4 0.03
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (53 bp):
AATTATCAAAATACCCCATAGGGTAGAATTACTGAAATACCCCTGTAGGGTAG
Found at i:28942528 original size:81 final size:81
Alignment explanation
Indices: 28942335--28942665 Score: 264
Period size: 81 Copynumber: 4.1 Consensus size: 81
28942325 CGATTTGTGA
* * * * * *
28942335 AATTACTGAAATACCCTTATAGGATAGAATTACCGAAATA-CCATTGTAGTGT-GAAATTACTAA
1 AATTACCGAAATACCCCTATAGGGTAGAATTATCAAAATACCCA-TGTAGGGTAG-AATTACTAA
* ** *
28942398 AATACCCTCG-ACTTGTAA
64 AATACCCCCGTA-AGGTAG
* ** * *
28942416 AATTACCAAAATA-CCCT-TAGTTTACAAAATTATCAAAATACACCCAAT-TAGTG-A-AATTAC
1 AATTACCGAAATACCCCTATAGGGT--AGAATTATCAAAAT--ACCC-ATGTAGGGTAGAATTAC
* *
28942476 TGAAATACCCCTGTAAGGTAG
61 TAAAATACCCCCGTAAGGTAG
* * *
28942497 AATTACCGGAATACCCCTATAGGGTAGAATTATCGAAATACCCTTGTAGGGTAGAATTACTAAAA
1 AATTACCGAAATACCCCTATAGGGTAGAATTATCAAAATACCCATGTAGGGTAGAATTACTAAAA
*
28942562 TACCCCCGTAGGGTAG
66 TACCCCCGTAAGGTAG
* ** * * * *
28942578 AATTACCGAAATACCCCTGTAGGGTAGAATTATTGAAATACCCCTGTAAGGTAGAATTACCAAGA
1 AATTACCGAAATACCCCTATAGGGTAGAATTATCAAAATACCCATGTAGGGTAGAATTACTAAAA
* *
28942643 TACCCCTGTAGGGTAG
66 TACCCCCGTAAGGTAG
28942659 AATTACC
1 AATTACC
28942666 ATTTTGCCCC
Statistics
Matches: 204, Mismatches: 33, Indels: 26
0.78 0.13 0.10
Matches are distributed among these distances:
78 1 0.00
79 12 0.06
80 4 0.02
81 168 0.82
82 5 0.02
83 10 0.05
84 3 0.01
85 1 0.00
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (81 bp):
AATTACCGAAATACCCCTATAGGGTAGAATTATCAAAATACCCATGTAGGGTAGAATTACTAAAA
TACCCCCGTAAGGTAG
Found at i:28944950 original size:27 final size:26
Alignment explanation
Indices: 28944920--28945236 Score: 166
Period size: 27 Copynumber: 11.8 Consensus size: 26
28944910 CTCGATTAAC
28944920 AAAATTACCAAAATACCCCTATTTTGT
1 AAAATTACCAAAATACCCCTA-TTTGT
*
28944947 AAAACTACCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTA-TTTGT
* *
28944974 GAAATTACCAAAATGCCCCTGATTTGT
1 AAAATTACCAAAATACCCCT-ATTTGT
* ** * * *
28945001 GAAATTACTGAAATACCATCGACTTGT
1 AAAATTACCAAAATACC-CCTATTTGT
*
28945028 AAAATTACCAAAATACCCCCGATTTGT
1 AAAATTACCAAAATA-CCCCTATTTGT
* * ** * **
28945055 GAAACTACTGAAATACCCTTATAGGGT
1 AAAATTACCAAAATACCCCTAT-TTGT
* ** * * * *
28945082 AGAATTACTGAAATATCCTTGTAGTGT
1 AAAATTACCAAAATACCCCTAT-TTGT
* ** * *
28945109 GAAATTACTGAAATACCCTCGACTTGT
1 AAAATTACCAAAATACCC-CTATTTGT
* * **
28945136 AAAATTACCAAAATACCCTTGGTTTAC
1 AAAATTACCAAAATACCCCT-ATTTGT
*
28945163 AAAATTACCAAAATACCCCTGATTAGT
1 AAAATTACCAAAATACCCCT-ATTTGT
* ** * **
28945190 GAAATTACTGAAATACCCCTGTAGGGT
1 AAAATTACCAAAATACCCCTAT-TTGT
*
28945217 AGAATTACCAAAATACCCCT
1 AAAATTACCAAAATACCCCT
28945237 GTAGGGTAGA
Statistics
Matches: 221, Mismatches: 62, Indels: 14
0.74 0.21 0.05
Matches are distributed among these distances:
26 6 0.03
27 211 0.95
28 4 0.02
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.28
Consensus pattern (26 bp):
AAAATTACCAAAATACCCCTATTTGT
Found at i:28945054 original size:108 final size:108
Alignment explanation
Indices: 28944920--28945213 Score: 310
Period size: 108 Copynumber: 2.7 Consensus size: 108
28944910 CTCGATTAAC
* *
28944920 AAAATTACCAAAATA-CCCCTATTTTGTAAAACTACCAAAATACCCCTAGTTTGTGAAATTACCA
1 AAAATTACCAAAATACCCCCGA-TTTGTAAAACTACCAAAATACCCCTAGTTAGTGAAATTACCA
* *
28944984 AAATGCCCCTG-ATTTGTGAAATTACTGAAATACCATCGACTTGT
65 AAATACCCCTGTA-GTGTGAAATTACTGAAATACCATCGACTTGT
* ** * * *
28945028 AAAATTACCAAAATACCCCCGATTTGTGAAACTACTGAAATACCCTTA--TAGGGTAGAATTACT
1 AAAATTACCAAAATACCCCCGATTTGTAAAACTACCAAAATACCCCTAGTTAGTG-A-AATTACC
* * * *
28945091 GAAATATCCTTGTAGTGTGAAATTACTGAAATACCCTCGACTTGT
64 AAAATACCCCTGTAGTGTGAAATTACTGAAATACCATCGACTTGT
** * ** * **
28945136 AAAATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATACCCCT-GATTAGTGAAATTACTG
1 AAAATTACCAAAATACCCCCGATTTGTAAAACTACCAAAATACCCCTAG-TTAGTGAAATTACCA
28945200 AAATACCCCTGTAG
65 AAATACCCCTGTAG
28945214 GGTAGAATTA
Statistics
Matches: 152, Mismatches: 27, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
106 3 0.02
107 1 0.01
108 137 0.90
109 7 0.05
110 4 0.03
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (108 bp):
AAAATTACCAAAATACCCCCGATTTGTAAAACTACCAAAATACCCCTAGTTAGTGAAATTACCAA
AATACCCCTGTAGTGTGAAATTACTGAAATACCATCGACTTGT
Found at i:28945170 original size:54 final size:54
Alignment explanation
Indices: 28944920--28945153 Score: 217
Period size: 54 Copynumber: 4.3 Consensus size: 54
28944910 CTCGATTAAC
* * ** * *
28944920 AAAATTACCAAAATACCCCT-ATTTTGTAAAACTACCAAAATACCC-CTAGTTTGT
1 AAAATTACCAAAATACCCCTGA-TTTGTGAAATTACTGAAATACCCTCGA-CTTGT
* * *
28944974 GAAATTACCAAAATGCCCCTGATTTGTGAAATTACTGAAATACCATCGACTTGT
1 AAAATTACCAAAATACCCCTGATTTGTGAAATTACTGAAATACCCTCGACTTGT
* * * *
28945028 AAAATTACCAAAATACCCCCGATTTGTGAAACTACTGAAATACCCT-TA-TAGGGT
1 AAAATTACCAAAATACCCCTGATTTGTGAAATTACTGAAATACCCTCGACT--TGT
* ** * * *
28945082 AGAATTACTGAAATATCCTTG-TAGTGTGAAATTACTGAAATACCCTCGACTTGT
1 AAAATTACCAAAATACCCCTGAT-TTGTGAAATTACTGAAATACCCTCGACTTGT
28945136 AAAATTACCAAAATACCC
1 AAAATTACCAAAATACCC
28945154 TTGGTTTACA
Statistics
Matches: 143, Mismatches: 30, Indels: 14
0.76 0.16 0.07
Matches are distributed among these distances:
52 1 0.01
53 2 0.01
54 135 0.94
55 4 0.03
56 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (54 bp):
AAAATTACCAAAATACCCCTGATTTGTGAAATTACTGAAATACCCTCGACTTGT
Found at i:28945223 original size:81 final size:78
Alignment explanation
Indices: 28945065--28945388 Score: 242
Period size: 81 Copynumber: 4.0 Consensus size: 78
28945055 GAAACTACTG
* * ** * *
28945065 AAATACCCTTATAGGGTAGAATTACTGAAATATCCTTGTAGTGTGAAATTACTGAAATA-CCCTC
1 AAATACCC-TGTAGGGTAAAATTACCAAAATACCCCTGTA--GTGAAATTACTGAAATACCCCT-
** *
28945129 G-ACTTGTAAAATTACCA
62 GTA-GGGTAGAATTACCA
*
28945146 AAATACCCT-T-GGTTTACAAAATTACCAAAATACCCCTGATTAGTGAAATTACTGAAATACCCC
1 AAATACCCTGTAGG-GT--AAAATTACCAAAATACCCCTG--TAGTGAAATTACTGAAATACCCC
28945209 TGTAGGGTAGAATTACCA
61 TGTAGGGTAGAATTACCA
* * * * *
28945227 AAATACCCCTGTAGGGTAGAATTATCGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTG
1 AAATA-CCCTGTAGGGTAAAATTACCAAAATACCCCTGTAGTG-A-AATTACTGAAATACCCCTG
*
28945292 TAGGGTAGAATTACCG
63 TAGGGTAGAATTACCA
* * ** * * * *
28945308 AAATACCCCTATAGGGTAGAATTACTGAAATACCCCTGTAGGGTAGAATTACCGAGATACCCTTG
1 AAATA-CCCTGTAGGGTAAAATTACCAAAATACCCCTGTAGTG-A-AATTACTGAAATACCCCTG
* *
28945373 TGGGGTAAAATTACCA
63 TAGGGTAGAATTACCA
28945389 TTTTTCCCCT
Statistics
Matches: 207, Mismatches: 24, Indels: 24
0.81 0.09 0.09
Matches are distributed among these distances:
78 2 0.01
79 6 0.03
80 2 0.01
81 182 0.88
82 9 0.04
83 4 0.02
84 2 0.01
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.27
Consensus pattern (78 bp):
AAATACCCTGTAGGGTAAAATTACCAAAATACCCCTGTAGTGAAATTACTGAAATACCCCTGTAG
GGTAGAATTACCA
Found at i:28945237 original size:27 final size:27
Alignment explanation
Indices: 28945165--28945387 Score: 315
Period size: 27 Copynumber: 8.3 Consensus size: 27
28945155 TGGTTTACAA
* *
28945165 AATTACCAAAATACCCCTGATTAGTG-A-
1 AATTACCGAAATACCCCTG--TAGGGTAG
*
28945192 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
28945219 AATTACCAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
28945246 AATTATCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
28945273 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
28945300 AATTACCGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
28945327 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
28945354 AATTACCGAGATACCCTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
28945381 AATTACC
1 AATTACC
28945388 ATTTTTCCCC
Statistics
Matches: 178, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
25 4 0.02
26 1 0.01
27 173 0.97
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.25
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:28945623 original size:25 final size:25
Alignment explanation
Indices: 28945590--28945659 Score: 122
Period size: 25 Copynumber: 2.8 Consensus size: 25
28945580 AGGAAGTGCT
*
28945590 AAAAGGGCTATGCCCCAGTTTACCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
*
28945615 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
28945640 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
28945660 ATTAAAAGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Found at i:28945672 original size:24 final size:25
Alignment explanation
Indices: 28945590--28945684 Score: 113
Period size: 25 Copynumber: 3.8 Consensus size: 25
28945580 AGGAAGTGCT
*
28945590 AAAAGGGCTATGCCCCAGTTTACCA
1 AAAAGGGCTATGCCCCAGTTTATCA
*
28945615 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTATGCCCCAGTTTATCA
* *
28945640 AAAAGGGCTTTGCCCCAG-TTAT-T
1 AAAAGGGCTATGCCCCAGTTTATCA
*
28945663 AAAAGAGGCTAGGCCTCCAGTT
1 AAAAG-GGCTATGCC-CCAGTT
28945685 ATATGATAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
23 5 0.08
24 11 0.18
25 45 0.73
26 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (25 bp):
AAAAGGGCTATGCCCCAGTTTATCA
Found at i:28952418 original size:13 final size:13
Alignment explanation
Indices: 28952398--28952443 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
28952388 CTAGGGACGG
28952398 GCGTGTGCCCTGA
1 GCGTGTGCCCTGA
* *
28952411 GTGTGTGCCCTGG
1 GCGTGTGCCCTGA
* *
28952424 GCGTGTGCCTTGG
1 GCGTGTGCCCTGA
28952437 GCGTGTG
1 GCGTGTG
28952444 AAGTCTGCAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.02, C:0.24, G:0.46, T:0.28
Consensus pattern (13 bp):
GCGTGTGCCCTGA
Found at i:28975607 original size:15 final size:16
Alignment explanation
Indices: 28975587--28975625 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
28975577 AATTAGAAAG
28975587 ATGAAAAGTT-ATTAA
1 ATGAAAAGTTAATTAA
*
28975602 ATGAAAAATTAATTAA
1 ATGAAAAGTTAATTAA
28975618 ATGAAAAG
1 ATGAAAAG
28975626 GAAAACAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.59, C:0.00, G:0.13, T:0.28
Consensus pattern (16 bp):
ATGAAAAGTTAATTAA
Found at i:28977981 original size:42 final size:42
Alignment explanation
Indices: 28977903--28978065 Score: 147
Period size: 42 Copynumber: 3.8 Consensus size: 42
28977893 CAATTCCAAC
* * * *
28977903 GTCCCAGAC-GTGTCTTACATGTAATCAAATATCGATGCCACT
1 GTCCCAGACAGGGTCTTACACGAAATCATATATCGATGCCA-T
28977945 GTCCCAGACAGGGTCTTACACGAAATCATATA-CGATGCCGAT
1 GTCCCAGACAGGGTCTTACACGAAATCATATATCGATGCC-AT
* * *
28977987 GTCCCAGACATGATCTTACACGTAAATC-TCAAATCGATGCCAAT
1 GTCCCAGACAGGGTCTTACACG-AAATCAT-ATATCGATGCC-AT
* *
28978031 GTCCCAGA-TGTGGTCTTACACAAAATC-TCATATCG
1 GTCCCAGACAG-GGTCTTACACGAAATCAT-ATATCG
28978066 GAATCCTATG
Statistics
Matches: 102, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
42 38 0.37
43 38 0.37
44 26 0.25
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (42 bp):
GTCCCAGACAGGGTCTTACACGAAATCATATATCGATGCCAT
Done.