Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 213 of 214
Found at i:63013605 original size:14 final size:14
Alignment explanation
Indices: 63013586--63013612 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
63013576 TAATGACATA
63013586 ACATAATTATAATC
1 ACATAATTATAATC
63013600 ACATAATTATAAT
1 ACATAATTATAAT
63013613 TTTTTTCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (14 bp):
ACATAATTATAATC
Found at i:63028870 original size:10 final size:9
Alignment explanation
Indices: 63028850--63028874 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
63028840 ACTGATATAC
63028850 AAAAAATAA
1 AAAAAATAA
63028859 AAAAAATAA
1 AAAAAATAA
63028868 AAAAAAT
1 AAAAAAT
63028875 TGGGTGTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAAATAA
Found at i:63029061 original size:54 final size:55
Alignment explanation
Indices: 63028970--63029106 Score: 150
Period size: 54 Copynumber: 2.5 Consensus size: 55
63028960 TACGAAAACG
* * * ** * * *
63028970 AAAAAAAAATTCATTTTCGTACTGATGGTGTCGGCCATTGACAGGTCAGCA-CAA
1 AAAAAAAAATTCGTTTTCGTACTGGTGATCCCAGCCATAGACAGGCCAGCACCAA
* *
63029024 AAAAAAAAATCCGTTTTCGTACTGGTGATCCCAGCCATAGATAGGCCAGCACCCAA
1 AAAAAAAAATTCGTTTTCGTACTGGTGATCCCAGCCATAGACAGGCCAGCA-CCAA
**
63029080 AAAAAAATTTTCGTTTTCGTACTGGTG
1 AAAAAAAAATTCGTTTTCGTACTGGTG
63029107 CTTGCTATTG
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
54 41 0.60
56 27 0.40
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.26
Consensus pattern (55 bp):
AAAAAAAAATTCGTTTTCGTACTGGTGATCCCAGCCATAGACAGGCCAGCACCAA
Found at i:63029212 original size:53 final size:51
Alignment explanation
Indices: 63029087--63029697 Score: 383
Period size: 52 Copynumber: 11.4 Consensus size: 51
63029077 CAAAAAAAAA
** * *
63029087 TTTTCGTTTTCGTACTGGTGCTTGCTATTGACAGGCCAGTACCTAAAAAATATATTT
1 TTTTCGTTTTCGTACTGGTGC-CACCATTGACAGGCCAGCACC---AAAAT-T-TTT
63029144 TTTTCGTTTTCGTACTGGTGCCACCATTGACAGGCCAGCACCTAAAATTATTT
1 TTTTCGTTTTCGTACTGGTGCCACCATTGACAGGCCAGCACC-AAAATT-TTT
* **
63029197 TTTTCGTTTTCGTACTAGTGGTGCCAGCCATTGATAGGCCAGCACCCAATTTTTTT
1 TTTTCGTTTTCGTAC---TGGTGCCA-CCATTGACAGGCCAGCA-CCAAAATTTTT
* ** * *
63029253 TTTTCGTTTTCATACTAATGCCAGCAATTGACAAGCCAGCACCACAAATTTTT
1 TTTTCGTTTTCGTACTGGTGCCA-CCATTGACAGGCCAGCACCA-AAATTTTT
* * * * * * **
63029306 TTTTTGTTTTCGTAGTGGTGGTGCCGGCCATTTACAGGCCAACACAAAAAAAAAATTTAG
1 TTTTCGTTTTCGTA---CTGGTGCC-ACCATTGACAGGCCAGCAC-----CAAAATTTTT
* * *
63029366 TTTTCGTTCT-G-A-TGGTGCCGACCATTGACAGGCTAGCACCTAAATTTTTT
1 TTTTCGTTTTCGTACTGGTGCC-ACCATTGACAGGCCAGCACC-AAAATTTTT
* ** * * * ** * **
63029416 TTTTCATTTTTATGCT-GTTCTCGGCCATTGACAAACCAGCGCCAATTTTTTT
1 TTTTCGTTTTCGTACTGGTGC-C-ACCATTGACAGGCCAGCACCAAAATTTTT
* *
63029468 TTTTCGTTTTTGTACTGGTGTCGACCATTGACAGGCCAGCACC--AATTTTT
1 TTTTCGTTTTCGTACTGGTG-CCACCATTGACAGGCCAGCACCAAAATTTTT
* * *
63029518 TTTT-GTTTTCGTACTGGTGGTGCCGACCATTAACAGGCTAGCACCCAAATTTTT
1 TTTTCGTTTTCGTAC---TGGTGCC-ACCATTGACAGGCCAGCACCAAAATTTTT
* * * * * *
63029572 TTTT-GTTTTCATACTAGTGCCGGCCATTAACAGGTCAGCACCCAAATTTTT
1 TTTTCGTTTTCGTACTGGTGCC-ACCATTGACAGGCCAGCACCAAAATTTTT
* * *
63029623 TTTTCGTTTTCGTACTAGTGCCCGCCATTGACAGGCCAGCACAAAAAATTATTTT
1 TTTTCGTTTTCGTACTGGTG-CCACCATTGACAGGCCAGCAC-CAAAA-T-TTTT
*
63029678 TTTTTGTTTTCGTACTGGTG
1 TTTTCGTTTTCGTACTGGTG
63029698 GTATTGGGCA
Statistics
Matches: 444, Mismatches: 77, Indels: 68
0.75 0.13 0.12
Matches are distributed among these distances:
49 9 0.02
50 23 0.05
51 38 0.09
52 97 0.22
53 84 0.19
54 50 0.11
55 22 0.05
56 61 0.14
57 41 0.09
58 3 0.01
59 1 0.00
60 14 0.03
61 1 0.00
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (51 bp):
TTTTCGTTTTCGTACTGGTGCCACCATTGACAGGCCAGCACCAAAATTTTT
Found at i:63029327 original size:109 final size:109
Alignment explanation
Indices: 63029141--63029664 Score: 308
Period size: 109 Copynumber: 4.9 Consensus size: 109
63029131 AAAAAATATA
* ** * *
63029141 TTTTTTTCGTTTTCGTACTGGTGCCACCATTGACAGGCCAGCACCTAAAATTATTTTTTTCGTTT
1 TTTTTTTCGTTTTCATACTAATGCCACAATTGACAAGCCAGCACCTAAAATTATTTTTTTCGTTT
*
63029206 TCGTACTAGTGGTGCCAGCCATTGATAGGCCAGCACCCAATTTT
66 TCGTACTAGTGGTGCCAGCCATTGACAGGCCAGCACCCAATTTT
*
63029250 TTTTTTTCGTTTTCATACTAATGCCAGCAATTGACAAGCCAGCACC-ACAAATT-TTTTTTTTGT
1 TTTTTTTCGTTTTCATACTAATGCCA-CAATTGACAAGCCAGCACCTA-AAATTATTTTTTTCGT
* * * * * ** **
63029313 TTTCGTAGTGGTGGTGCCGGCCATTTACAGGCCAACACAAAAAAAAAATT
64 TTTCGTACTAGTGGTGCCAGCCATTGACAGGCCAGCAC----CCAATTTT
** ** * * * * *
63029363 TAGTTTTCG--TTC-TGA-TGGTGCCGACCATTGACAGGCTAGCACCT-AAATTTTTTTTTTCAT
1 TTTTTTTCGTTTTCAT-ACTAATGCC-ACAATTGACAAGCCAGCACCTAAAATTATTTTTTTCGT
* * ** *
63029423 TTT--TA-T-GCT-GTTCTCGGCCATTGACAAACCAGC-GCCAATTTT
64 TTTCGTACTAG-TGGTGC-CAGCCATTGACAGGCCAGCACCCAATTTT
** ** * * *
63029465 TTTTTTTCGTTTTTGTACTGGTGTCGACCATTGACAGGCCAGCACC---AATT-TTTTTTT-GTT
1 TTTTTTTCGTTTTCATACTAATG-CCACAATTGACAAGCCAGCACCTAAAATTATTTTTTTCGTT
* * * *
63029525 TTCGTACTGGTGGTGCC-GACCATTAACAGGCTAGCACCCAA-ATT
65 TTCGTACTAGTGGTGCCAG-CCATTGACAGGCCAGCACCCAATTTT
* * * * * * *
63029569 TTTTTTT-GTTTTCATACTAGTGCCGGCCATTAACAGGTCAGCACC-CAAATT-TTTTTTTCGTT
1 TTTTTTTCGTTTTCATACTAATGCC-ACAATTGACAAGCCAGCACCTAAAATTATTTTTTTCGTT
*
63029631 TTCGTACTA---GTGCCCGCCATTGACAGGCCAGCAC
65 TTCGTACTAGTGGTGCCAGCCATTGACAGGCCAGCAC
63029665 AAAAAATTAT
Statistics
Matches: 328, Mismatches: 58, Indels: 64
0.73 0.13 0.14
Matches are distributed among these distances:
101 4 0.01
102 19 0.06
103 57 0.17
104 28 0.09
105 44 0.13
106 16 0.05
107 17 0.05
108 2 0.01
109 70 0.21
110 55 0.17
111 5 0.02
113 11 0.03
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (109 bp):
TTTTTTTCGTTTTCATACTAATGCCACAATTGACAAGCCAGCACCTAAAATTATTTTTTTCGTTT
TCGTACTAGTGGTGCCAGCCATTGACAGGCCAGCACCCAATTTT
Found at i:63029644 original size:103 final size:102
Alignment explanation
Indices: 63029141--63029664 Score: 267
Period size: 103 Copynumber: 4.9 Consensus size: 102
63029131 AAAAAATATA
* * *
63029141 TTTTTTTCGTTTTCGTACTGGTGCC-ACCATTGACAGGCCAGCACCTAAAATTATTTTTTTCGTT
1 TTTTTTTCGTTTTCATACTAGTGCCGACCATTAACAGGCCAGCACC---AATT-TTTTTTT-GTT
* * * * *
63029205 TTCGTACTAGTGGTGCCAGCCATTGATAGGCCAGCACCCAATTTT
61 TTCGTAC--GTAGTGCCCGCCATTAACAGGCCAGCACCCAA-ATT
* * * *
63029250 TTTTTTTCGTTTTCATACTAATGCC-AGCAATTGACAAGCCAGCACCACAAATTTTTTTTTTGTT
1 TTTTTTTCGTTTTCATACTAGTGCCGA-CCATTAACAGGCCAGCA-C-C-AA-TTTTTTTTTGTT
* * * * * * **
63029314 TTCGTAGTGGTGGTGCCGGCCATTTACAGGCCAACA-CAAAAAA
61 TTCGTA--CGTAGTGCCCGCCATTAACAGGCCAGCACCCAAATT
**** * * * * *
63029357 AAAATTTAGTTTTCGTTCTGATGGTGCCGACCATTGACAGGCTAGCACCTAAATTTTTTTTT-TC
1 TTTTTTTCGTTTTCATACT-A--GTGCCGACCATTAACAGGCCAGCACC--AATTTTTTTTTGT-
* * * * * ** * *
63029421 ATTT-TTATGCT-GTTCTCGGCCATTGACAAACCAGC-GCCAATTTT
60 -TTTCGTACG-TAGTGC-CCGCCATTAACAGGCCAGCACCCAA-ATT
** * * *
63029465 TTTTTTTCGTTTTTGTACTGGTGTCGACCATTGACAGGCCAGCACCAATTTTTTTTTGTTTTCGT
1 TTTTTTTCGTTTTCATACTAGTGCCGACCATTAACAGGCCAGCACCAATTTTTTTTTGTTTTCGT
* *
63029530 ACTGGTGGTG-CCGACCATTAACAGGCTAGCACCCAAATT
66 AC--GTAGTGCCCG-CCATTAACAGGCCAGCACCCAAATT
* *
63029569 TTTTTTT-GTTTTCATACTAGTGCCGGCCATTAACAGGTCAGCACCCAAATTTTTTTTTCGTTTT
1 TTTTTTTCGTTTTCATACTAGTGCCGACCATTAACAGGCCAGCA-CC-AATTTTTTTTT-GTTTT
*
63029633 CGTAC-TAGTGCCCGCCATTGACAGGCCAGCAC
63 CGTACGTAGTGCCCGCCATTAACAGGCCAGCAC
63029665 AAAAAATTAT
Statistics
Matches: 321, Mismatches: 66, Indels: 62
0.71 0.15 0.14
Matches are distributed among these distances:
102 3 0.01
103 64 0.20
104 28 0.09
105 42 0.13
106 14 0.04
107 32 0.10
108 28 0.09
109 62 0.19
110 43 0.13
111 4 0.01
112 1 0.00
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (102 bp):
TTTTTTTCGTTTTCATACTAGTGCCGACCATTAACAGGCCAGCACCAATTTTTTTTTGTTTTCGT
ACGTAGTGCCCGCCATTAACAGGCCAGCACCCAAATT
Found at i:63029716 original size:58 final size:61
Alignment explanation
Indices: 63029616--63029784 Score: 181
Period size: 62 Copynumber: 2.9 Consensus size: 61
63029606 TCAGCACCCA
* * * *
63029616 AATTTT-TTTTTCGTTTTCGTACTAGT-G--CCCGCCATTGACAGGCCAGCAC-AAAAAAT
1 AATTTTATTTTTAGTTTTCGTACTAGTGGTACCGGGCATTGACAGGCCAGCACGAAAAAAG
* * **
63029672 TATTTT-TTTTT-GTTTTCGTACTGGTGGTATTGGGCATTGACAGGCCAGCACCGAAAAAAG
1 AATTTTATTTTTAGTTTTCGTACTAGTGGTACCGGGCATTGACAGGCCAGCA-CGAAAAAAG
* * *
63029732 AATTTTATTTTTAGTTTTCGTACTAGTGGTGCCGGTCATTGACAGGCTAGCAC
1 AATTTTATTTTTAGTTTTCGTACTAGTGGTACCGGGCATTGACAGGCCAGCAC
63029785 CTAATTTTTT
Statistics
Matches: 92, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
55 13 0.14
56 11 0.12
58 17 0.18
59 1 0.01
60 11 0.12
61 6 0.07
62 33 0.36
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (61 bp):
AATTTTATTTTTAGTTTTCGTACTAGTGGTACCGGGCATTGACAGGCCAGCACGAAAAAAG
Found at i:63030146 original size:175 final size:170
Alignment explanation
Indices: 63029706--63030163 Score: 506
Period size: 175 Copynumber: 2.7 Consensus size: 170
63029696 TGGTATTGGG
* * *
63029706 CATTGACAGGCCAGCACCGAAAAAAGAATTTTATTTTTAGTTTTCGTACTAGTGGTGCCGGTCAT
1 CATTGACAGGCCAGCACC-CAAAAATAATTTT-TTTTTAGTTTTCGTACTAGTGGTGTCGGTCAT
* * * *
63029771 TGACAGGC-TAGCA-CC--TAAT-TTTTTTTTCATTTTCGTATTAGTGGTGCCGGCCATTAATAG
64 TGACAGGCAT-GCACCCAAAAATATTTTTTTTCGTTTTCGTACTGGTGGTGCCGGCCATTAATAG
* *
63029831 GCTAGCACCAAAAAAAAAATTTTGTTTTCGTGTTGGTGCAGGC
128 GCTAGCACCAAAAAAAAAATTTTGTTTTCATGTTGGAGCAGGC
* ** * *
63029874 CATTGACAGGCAAGCA-CC-AAAATTTTTTTTTTTTGAGTTTTCTTACT-GATGGTGTCGGTTAT
1 CATTGACAGGCCAGCACCCAAAAATAATTTTTTTTT-AGTTTTCGTACTAG-TGGTGTCGGTCAT
* *
63029936 TAACAGGCCA-GCACCCTAAAAA-ATTTTATTTTTCGTTTTCGTACTGGTGGTGCCGGCCATTGA
64 TGACAGG-CATGCACCC-AAAAATA-TTT-TTTTTCGTTTTCGTACTGGTGGTGCCGGCCATTAA
*
63029999 TAGG-TCAGCACCCAAAGAATAAAAATTTTCGTTTTCATGTTGGAGCCGGC
125 TAGGCT-AGCA-CCAAA-AA-AAAAATTTT-GTTTTCATGTTGGAGCAGGC
* *
63030049 CATTGACAGGCCAGCACCCAAAAATAATTTTTTTTTCGTTTTCGTACTAGTGGTGTCGGCCATTG
1 CATTGACAGGCCAGCACCCAAAAATAATTTTTTTTTAGTTTTCGTACTAGTGGTGTCGGTCATTG
* * *
63030114 ACAAGCATGCACCCAAAAATAATTTCTTTTCGTTTTTGTACTGGTGGTGC
66 ACAGGCATGCACCCAAAAAT-ATTTTTTTTCGTTTTCGTACTGGTGGTGC
63030164 TGACTATTGA
Statistics
Matches: 240, Mismatches: 28, Indels: 37
0.79 0.09 0.12
Matches are distributed among these distances:
164 6 0.03
165 39 0.16
166 3 0.01
167 1 0.00
168 15 0.06
169 2 0.01
170 4 0.02
171 39 0.16
172 5 0.02
173 2 0.01
174 9 0.04
175 62 0.26
176 37 0.15
177 16 0.07
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (170 bp):
CATTGACAGGCCAGCACCCAAAAATAATTTTTTTTTAGTTTTCGTACTAGTGGTGTCGGTCATTG
ACAGGCATGCACCCAAAAATATTTTTTTTCGTTTTCGTACTGGTGGTGCCGGCCATTAATAGGCT
AGCACCAAAAAAAAAATTTTGTTTTCATGTTGGAGCAGGC
Found at i:63030155 original size:59 final size:60
Alignment explanation
Indices: 63029511--63030162 Score: 264
Period size: 60 Copynumber: 11.5 Consensus size: 60
63029501 GGCCAGCACC
* * * * * * *
63029511 AATTTT-TTTTTGTTTTCGTACTGGTGGTGCCGACCATTAACAGGCTAGCACCC--AAAT
1 AATTTTCTTTTCGTTTTCGTACTAGTGGTGTCGGCCATTGACAAGCCAGCACCCAAAAAT
* * * * *
63029568 --TTTT-TTTT-GTTTTCATACTA---GTGCCGGCCATTAACAGGTCAGCACCC--AAAT
1 AATTTTCTTTTCGTTTTCGTACTAGTGGTGTCGGCCATTGACAAGCCAGCACCCAAAAAT
* * * *
63029619 --TTTT-TTTTCGTTTTCGTACTA---GTGCCCGCCATTGACAGGCCAGCA-CAAAAAAT
1 AATTTTCTTTTCGTTTTCGTACTAGTGGTGTCGGCCATTGACAAGCCAGCACCCAAAAAT
* * * * * * * * *
63029672 TATTTT-TTTTTGTTTTCGTACTGGTGGTATTGGGCATTGACAGGCCAGCACCGAAAAAAG
1 AATTTTCTTTTCGTTTTCGTACTAGTGGTGTCGGCCATTGACAAGCCAGCACC-CAAAAAT
* * * * * *
63029732 AATTTTATTTTTAGTTTTCGTACTAGTGGTGCCGGTCATTGACAGGCTAGCA-CC-----T
1 AATTTT-CTTTTCGTTTTCGTACTAGTGGTGTCGGCCATTGACAAGCCAGCACCCAAAAAT
* * * * * * * *
63029787 AATTTTTTTTTCATTTTCGTATTAGTGGTGCCGGCCATTAATAGGCTAGCA-CCAAAAA-
1 AATTTTCTTTTCGTTTTCGTACTAGTGGTGTCGGCCATTGACAAGCCAGCACCCAAAAAT
*** * * *
63029845 AA--AAATTTT-GTTTTCGT-GT--TGGTG-CAGGCCATTGACAGGCAAGCA-CC-AAAAT
1 AATTTTCTTTTCGTTTTCGTACTAGTGGTGTC-GGCCATTGACAAGCCAGCACCCAAAAAT
** * * * ** * * *
63029897 TTTTTTTTTTTGAGTTTTCTTACT-GATGGTGTCGGTTATTAACAGGCCAGCACCCTAAAA-
1 AATTTTCTTTT-CGTTTTCGTACTAG-TGGTGTCGGCCATTGACAAGCCAGCACCCAAAAAT
* * * * * *
63029957 AATTTTATTTTTCGTTTTCGTACTGGTGGTGCCGGCCATTGATAGGTCAGCACCCAAAGAAT
1 AATTTT-CTTTTCGTTTTCGTACTAGTGGTGTCGGCCATTGACAAGCCAGCACCCAAA-AAT
*** * * *
63030019 AA--AAATTTTCGTTTTC--A-T-GTTGGAGCCGGCCATTGACAGGCCAGCACCCAAAAAT
1 AATTTTCTTTTCGTTTTCGTACTAG-TGGTGTCGGCCATTGACAAGCCAGCACCCAAAAAT
*
63030074 AATTTTTTTTTCGTTTTCGTACTAGTGGTGTCGGCCATTGACAAG-CATGCACCCAAAAAT
1 AATTTTCTTTTCGTTTTCGTACTAGTGGTGTCGGCCATTGACAAGCCA-GCACCCAAAAAT
* *
63030134 AA-TTTCTTTTCGTTTTTGTACTGGTGGTG
1 AATTTTCTTTTCGTTTTCGTACTAGTGGTG
63030163 CTGACTATTG
Statistics
Matches: 475, Mismatches: 79, Indels: 80
0.75 0.12 0.13
Matches are distributed among these distances:
51 42 0.09
52 55 0.12
53 4 0.01
54 56 0.12
55 46 0.10
56 41 0.09
57 13 0.03
58 21 0.04
59 59 0.12
60 85 0.18
61 14 0.03
62 39 0.08
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (60 bp):
AATTTTCTTTTCGTTTTCGTACTAGTGGTGTCGGCCATTGACAAGCCAGCACCCAAAAAT
Found at i:63030173 original size:59 final size:60
Alignment explanation
Indices: 63030048--63030175 Score: 163
Period size: 59 Copynumber: 2.1 Consensus size: 60
63030038 TTGGAGCCGG
* * *
63030048 CCATTGACAGGCCA-GCACCCAAAAATAATTTTTTTTTCGTTTTCGTACTAGTGGTGTCGG
1 CCATTGACAAG-CATGCACCCAAAAATAATTTTCTTTTCGTTTTCGTACTAGTGGTGTCGA
* *
63030108 CCATTGACAAGCATGCACCCAAAAATAA-TTTCTTTTCGTTTTTGTACTGGTGGTG-CTGA
1 CCATTGACAAGCATGCACCCAAAAATAATTTTCTTTTCGTTTTCGTACTAGTGGTGTC-GA
*
63030167 CTATTGACA
1 CCATTGACA
63030176 GTCCCACACC
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
58 1 0.02
59 35 0.58
60 24 0.40
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (60 bp):
CCATTGACAAGCATGCACCCAAAAATAATTTTCTTTTCGTTTTCGTACTAGTGGTGTCGA
Found at i:63030301 original size:57 final size:56
Alignment explanation
Indices: 63029035--63030311 Score: 638
Period size: 56 Copynumber: 23.0 Consensus size: 56
63029025 AAAAAAAATC
* * ** * * *****
63029035 CGTTTTCGTACTGGTGATCCCAGCCATAGATAGGCCAGCACCCAAAAAAAAATTTT
1 CGTTTTCGTACTGGTGGTGCTGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTT
* * * *
63029091 CGTTTTCGTAC---TGGTGCTTGCTATTGACAGGCCAGTACCTAAAAAATATATTTTTTT
1 CGTTTTCGTACTGGTGGTGCTGGCCATTGACAGGCCAGCACC--CAAAAT-T-TTTTTTT
** *
63029148 CGTTTTCGTAC---TGGTGC-CACCATTGACAGGCCAGCACCTAAAATTATTTTTTT
1 CGTTTTCGTACTGGTGGTGCTGGCCATTGACAGGCCAGCACCCAAAATT-TTTTTTT
* ** * **
63029201 CGTTTTCGTACTAGTGGTGCCAGCCATTGATAGGCCAGCACCCAATTTTTTTTTTT
1 CGTTTTCGTACTGGTGGTGCTGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTT
* ** ** * *
63029257 CGTTTTCATAC---TAATGCCAGCAATTGACAAGCCAGCA-CCACAAATTTTTTTTT
1 CGTTTTCGTACTGGTGGTGCTGGCCATTGACAGGCCAGCACCCA-AAATTTTTTTTT
* * * * * ******
63029310 TGTTTTCGTAGTGGTGGTGCCGGCCATTTACAGGCCA--ACACAAAAAAAAAATTT
1 CGTTTTCGTACTGGTGGTGCTGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTT
* * * * * * * *
63029364 AGTTTTCGTTCTGATGGTGCCGACCATTGACAGGCTAGCACCTAAATTTTTTTTTT
1 CGTTTTCGTACTGGTGGTGCTGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTT
* * * ** * **
63029420 CATTTT--TA-TGCT-GTTCTCGGCCATTGACAAACCAGC-GCCAATTTTTTTTTTT
1 CGTTTTCGTACTGGTGGTGCT-GGCCATTGACAGGCCAGCACCCAAAATTTTTTTTT
* *
63029472 CGTTTTTGTACTGGT-GT-C-GACCATTGACAGGCCAGCA-CC--AATTTTTTTTT
1 CGTTTTCGTACTGGTGGTGCTGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTT
* * * *
63029522 -GTTTTCGTACTGGTGGTGCCGACCATTAACAGGCTAGCACCC-AAATTTTTTTTT
1 CGTTTTCGTACTGGTGGTGCTGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTT
* * * * *
63029576 -GTTTTCATAC---TAGTGCCGGCCATTAACAGGTCAGCACCC-AAATTTTTTTTT
1 CGTTTTCGTACTGGTGGTGCTGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTT
* ** **
63029627 CGTTTTCGTAC---TAGTGCCCGCCATTGACAGGCCAGCACAAAAAATTATTTTTTTT
1 CGTTTTCGTACTGGTGGTGCTGGCCATTGACAGGCCAGCACCCAAAA-T-TTTTTTTT
* ** * *
63029682 TGTTTTCGTACTGGTGGTATTGGGCATTGACAGGCCAGCACCGAAAAAAGAATTTTATTTTT
1 CGTTTTCGTACTGGTGGTGCTGGCCATTGACAGGCCAGCACC----CAA-AATTTT-TTTTT
* * * * * *
63029744 AGTTTTCGTACTAGTGGTGCCGGTCATTGACAGGCTAGCA-CC-TAATTTTTTTTT
1 CGTTTTCGTACTGGTGGTGCTGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTT
* * * * * * * * *****
63029798 CATTTTCGTATTAGTGGTGCCGGCCATTAATAGGCTAGCACCAAAAAAAAAATTTT
1 CGTTTTCGTACTGGTGGTGCTGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTT
* * *
63029854 -GTTTTCG---TGTTGGTGCAGGCCATTGACAGGCAAGCA-CCAAAATTTTTTTTTTTT
1 CGTTTTCGTACTGGTGGTGCTGGCCATTGACAGGCCAGCACCCAAAA---TTTTTTTTT
* * * ** *
63029908 GAGTTTTCTTACTGATGGTG-TCGGTTATTAACAGGCCAGCACCCTAAAAAATTTTATTTTT
1 -CGTTTTCGTACTGGTGGTGCT-GGCCATTGACAGGCCAGCACCC---AAAATTTT-TTTTT
* * * ****
63029969 CGTTTTCGTACTGGTGGTGCCGGCCATTGATAGGTCAGCACCCAAAGAATAAAAATTTT
1 CGTTTTCGTACTGGTGGTGCTGGCCATTGACAGGCCAGCACCC-AA-AAT-TTTTTTTT
* * *
63030028 CGTTTTC--A-TGTTGGAGCCGGCCATTGACAGGCCAGCACCCAAAAATAATTTTTTTTT
1 CGTTTTCGTACTGGTGGTGCTGGCCATTGACAGGCCAGCACCC---AA-AATTTTTTTTT
* * *
63030085 CGTTTTCGTACTAGTGGTG-TCGGCCATTGACAAG-CATGCACCCAAAAATAATTTCTTTT
1 CGTTTTCGTACTGGTGGTGCT-GGCCATTGACAGGCCA-GCACCC-AAAAT--TTTTTTTT
* * * *
63030144 CGTTTTTGTACTGGTGGTGCTGACTATTGACAGTCC--CACACCAAAATTTTTTTTT
1 CGTTTTCGTACTGGTGGTGCTGGCCATTGACAGGCCAGCAC-CCAAAATTTTTTTTT
* * * ** * *
63030199 CGTTTTCATATTGGTGCTGCCAGCCATTGACTA-GCCTGCAACCAAAATTTTGTTTTT
1 CGTTTTCGTACTGGTGGTGCTGGCCATTGAC-AGGCCAGCACCCAAAATTTT-TTTTT
* * * *
63030256 CTTTTTTGTACTGGTGGTGCTGGCCATTGACCGGCCAGCACCCAAATTTTTTTTTT
1 CGTTTTCGTACTGGTGGTGCTGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTT
63030312 GTGCCGGTGA
Statistics
Matches: 942, Mismatches: 205, Indels: 148
0.73 0.16 0.11
Matches are distributed among these distances:
49 13 0.01
50 11 0.01
51 43 0.05
52 114 0.12
53 101 0.11
54 110 0.12
55 74 0.08
56 136 0.14
57 112 0.12
58 35 0.04
59 72 0.08
60 64 0.07
61 9 0.01
62 42 0.04
63 6 0.01
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (56 bp):
CGTTTTCGTACTGGTGGTGCTGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTT
Found at i:63032410 original size:107 final size:105
Alignment explanation
Indices: 63032274--63032590 Score: 311
Period size: 107 Copynumber: 3.0 Consensus size: 105
63032264 AAAATAAATA
* * * *
63032274 AAAACAAAAAAAAAATTGGGTGTTGGCCTGTAAATGGCCGACACAACCAGTACGAGAACGAAAAA
1 AAAACAAAAAAAAAATTTGGTGCTAGCCTGTAAATGGCCG-CAC-ACCAGTACGAAAACGAAAAA
* *
63032339 AAATTTTTTAGGTGCTGGCCTGTCAAT-GACCTG-CACCAGTACG
64 AAA--TTTTAGGTGCTGGCCTGTCAATAG-CCAGACACCAATACG
* * * *
63032382 AAAA-AGAAAAAAAATTTGGTGCTAGCCTGTCAATAGCCGGCACCACCAGTATGAAAACGAAAAA
1 AAAACAAAAAAAAAATTTGGTGCTAGCCTGTAAATGGCC-GCA-CACCAGTACGAAAACGAAAAA
* * *
63032446 AAATTTTGGGTGTTGGTCTGTCAATAGCCAGCATCACCAATACG
64 AAATTTTAGGTGCTGGCCTGTCAATAGCCAG-A-CACCAATACG
* * *
63032490 AAAACAAAAAAAAAATTTGAGTGCTAGCCTGTTAATGGCCG-GCACCAGTACGAAAACTAAAAAA
1 AAAACAAAAAAAAAATTTG-GTGCTAGCCTGTAAATGGCCGCACACCAGTACGAAAAC-GAAAAA
* * * * *
63032554 AAAATTTGGGTGTTGGCCTATCAATGGCCAG-CACCAA
64 AAATTTTAGGTGCTGGCCTGTCAATAGCCAGACACCAA
63032591 AAAAAAGTTT
Statistics
Matches: 177, Mismatches: 23, Indels: 21
0.80 0.10 0.10
Matches are distributed among these distances:
105 28 0.16
106 1 0.01
107 65 0.37
108 51 0.29
109 14 0.08
110 18 0.10
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.21
Consensus pattern (105 bp):
AAAACAAAAAAAAAATTTGGTGCTAGCCTGTAAATGGCCGCACACCAGTACGAAAACGAAAAAAA
ATTTTAGGTGCTGGCCTGTCAATAGCCAGACACCAATACG
Found at i:63032473 original size:55 final size:55
Alignment explanation
Indices: 63032274--63032589 Score: 281
Period size: 55 Copynumber: 5.9 Consensus size: 55
63032264 AAAATAAATA
* * * * *
63032274 AAAAC-AAAAAAAAAATTGGGTGTTGGCCTGTAAATGGCCGACACAACCAGTACG
1 AAAACGAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACG
* * * * *
63032328 AGAACGAAAAAAAATTTTTTAGGTGCTGGCCTGTCAATGACCTG---CACCAGTACG
1 AAAACGAAAAAAAA--ATTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACG
* * * *
63032382 AAAAAG-AAAAAAAATTT-GGTGCTAGCCTGTCAATAGCCGGCACCACCAGTATG
1 AAAACGAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACG
* * * * * * *
63032435 AAAACGAAAAAAAATTTTGGGTGTTGGTCTGTCAATAGCCAGCATCACCAATACG
1 AAAACGAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACG
* * * *
63032490 AAAACAAAAAAAAAATTTGAGTGCTAGCCTGTTAATGGCCGG---CACCAGTACG
1 AAAACGAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACG
* * * *
63032542 AAAACTAAAAAAAAAATTTGGGTGTTGGCCTATCAATGGCCAGCACCA
1 AAAAC-GAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCA
63032590 AAAAAAAGTT
Statistics
Matches: 207, Mismatches: 43, Indels: 22
0.76 0.16 0.08
Matches are distributed among these distances:
50 19 0.09
51 3 0.01
52 14 0.07
53 52 0.25
54 27 0.13
55 70 0.34
56 2 0.01
57 20 0.10
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.21
Consensus pattern (55 bp):
AAAACGAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACG
Found at i:63032564 original size:108 final size:106
Alignment explanation
Indices: 63032372--63032586 Score: 288
Period size: 108 Copynumber: 2.0 Consensus size: 106
63032362 CAATGACCTG
* * *
63032372 CACCAGTACGAAAAAGAAAAAAAATTTGGTGCTAGCCTGTCAATAGCCGGCACCACCAGTATGAA
1 CACCAATACGAAAAAAAAAAAAAATTTGGTGCTAGCCTGTCAATAGCCGG--CCACCAGTACGAA
* * * *
63032437 AACGAAAAAAAATTTTGGGTGTTGGTCTGTCAATAGCCAGCAT
64 AACAAAAAAAAAATTTGGGTGTTGGCCTATCAATAGCCAGCAT
* *
63032480 CACCAATACGAAAACAAAAAAAAAATTTGAGTGCTAGCCTGTTAATGGCCGG-CACCAGTACGAA
1 CACCAATACGAAAA-AAAAAAAAAATTTG-GTGCTAGCCTGTCAATAGCCGGCCACCAGTACGAA
*
63032544 AACTAAAAAAAAAATTTGGGTGTTGGCCTATCAATGGCCAGCA
64 AAC-AAAAAAAAAATTTGGGTGTTGGCCTATCAATAGCCAGCA
63032587 CCAAAAAAAA
Statistics
Matches: 94, Mismatches: 10, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
107 14 0.15
108 47 0.50
109 13 0.14
110 20 0.21
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (106 bp):
CACCAATACGAAAAAAAAAAAAAATTTGGTGCTAGCCTGTCAATAGCCGGCCACCAGTACGAAAA
CAAAAAAAAAATTTGGGTGTTGGCCTATCAATAGCCAGCAT
Found at i:63034305 original size:17 final size:17
Alignment explanation
Indices: 63034280--63034316 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
63034270 TAACTTTGTT
*
63034280 AATCGCTTTAATTATGA
1 AATCCCTTTAATTATGA
*
63034297 AATCCCTTTAATTATTA
1 AATCCCTTTAATTATGA
63034314 AAT
1 AAT
63034317 TAGTTGTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.43
Consensus pattern (17 bp):
AATCCCTTTAATTATGA
Found at i:63034915 original size:36 final size:36
Alignment explanation
Indices: 63034868--63034940 Score: 105
Period size: 36 Copynumber: 2.0 Consensus size: 36
63034858 TCCGAAAAAG
*
63034868 TTATTTTTACATAT-AT-TAATAAATTTATATTTTAAA
1 TTATTTTTACATATAATGTAAT-AATTTAT-TTATAAA
63034904 TTATTTTTACATATAATGTAATAATTTATTTATAAA
1 TTATTTTTACATATAATGTAATAATTTATTTATAAA
63034940 T
1 T
63034941 AAATAAATCA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
36 21 0.62
37 9 0.26
38 4 0.12
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (36 bp):
TTATTTTTACATATAATGTAATAATTTATTTATAAA
Found at i:63037400 original size:25 final size:25
Alignment explanation
Indices: 63037372--63037421 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
63037362 GGAAGAGAAG
*
63037372 ATGAAGAACGGAAGAAGGAAAAGGA
1 ATGAAGAACAGAAGAAGGAAAAGGA
*
63037397 ATGAAGAACAGAAGAAGGAGAAGGA
1 ATGAAGAACAGAAGAAGGAAAAGGA
63037422 GCCTTACCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.56, C:0.04, G:0.36, T:0.04
Consensus pattern (25 bp):
ATGAAGAACAGAAGAAGGAAAAGGA
Found at i:63041064 original size:14 final size:14
Alignment explanation
Indices: 63041045--63041075 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
63041035 TTAATTAATT
63041045 TTTAATTAAATAAA
1 TTTAATTAAATAAA
*
63041059 TTTAATTAATTAAA
1 TTTAATTAAATAAA
63041073 TTT
1 TTT
63041076 TATAAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTAATTAAATAAA
Found at i:63057093 original size:23 final size:24
Alignment explanation
Indices: 63057058--63057102 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
63057048 GACTTGTAGG
*
63057058 TATTATTTGATAAA-ATTTCTAGA
1 TATTATTTCATAAACATTTCTAGA
*
63057081 TATTTTTTCATAAACATTTCTA
1 TATTATTTCATAAACATTTCTA
63057103 AAAAATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.51
Consensus pattern (24 bp):
TATTATTTCATAAACATTTCTAGA
Found at i:63063244 original size:72 final size:72
Alignment explanation
Indices: 63063110--63063246 Score: 168
Period size: 72 Copynumber: 1.9 Consensus size: 72
63063100 AGGTGGTTGT
* * * ** ** *
63063110 TTTCTTTTCTTTTGAATGGAAACATGTTGTGCTGGTTTGGTATGATTATTATTTCCTGAAGGTGG
1 TTTCTTTTCTTTTGAAAGGAAACATCTTCTGCTGGTTCAGTACAATTATTATTTCCTAAAGGTGG
63063175 TTCTCTC
66 TTCTCTC
* *
63063182 TTTCTTTTCTTTTGAAAGGTAACATCTTCTGCTGGTTCAGTACAATTGTTATTCTCC-AAAGGTG
1 TTTCTTTTCTTTTGAAAGGAAACATCTTCTGCTGGTTCAGTACAATTATTATT-TCCTAAAGGTG
63063246 G
65 G
63063247 GTTTCGTCCA
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
72 51 0.94
73 3 0.06
ACGTcount: A:0.19, C:0.15, G:0.20, T:0.46
Consensus pattern (72 bp):
TTTCTTTTCTTTTGAAAGGAAACATCTTCTGCTGGTTCAGTACAATTATTATTTCCTAAAGGTGG
TTCTCTC
Found at i:63063473 original size:12 final size:12
Alignment explanation
Indices: 63063456--63063480 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
63063446 TGAATAAGGA
63063456 GCTACGAAATTG
1 GCTACGAAATTG
63063468 GCTACGAAATTG
1 GCTACGAAATTG
63063480 G
1 G
63063481 ATGTAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.24
Consensus pattern (12 bp):
GCTACGAAATTG
Found at i:63084388 original size:40 final size:42
Alignment explanation
Indices: 63084301--63084388 Score: 110
Period size: 40 Copynumber: 2.1 Consensus size: 42
63084291 AGGTCCCCAA
* *
63084301 AATAAATAAAAATCAAATTGACTCATTTATATTTTATAAAAT
1 AATAAATAAAAATCAAATTGACACATTTATATTCTATAAAAT
* *
63084343 TATAAATAAATAATCAAATT-ACAC-TTTA-CTTCTATAAAAT
1 AATAAATAAA-AATCAAATTGACACATTTATATTCTATAAAAT
63084383 AATAAA
1 AATAAA
63084389 ATTTTAATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
40 15 0.38
41 4 0.10
42 12 0.30
43 9 0.22
ACGTcount: A:0.53, C:0.09, G:0.01, T:0.36
Consensus pattern (42 bp):
AATAAATAAAAATCAAATTGACACATTTATATTCTATAAAAT
Found at i:63087555 original size:17 final size:17
Alignment explanation
Indices: 63087517--63087558 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
63087507 ATAGTTTATA
63087517 TATATTTTATATACATT
1 TATATTTTATATACATT
* *
63087534 CATATTTT-TATGATATT
1 TATATTTTATAT-ACATT
63087551 TATATTTT
1 TATATTTT
63087559 CATGTTTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (17 bp):
TATATTTTATATACATT
Found at i:63089323 original size:15 final size:15
Alignment explanation
Indices: 63089305--63089333 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
63089295 GATTATAAAG
63089305 AAAAATAAATTTATA
1 AAAAATAAATTTATA
63089320 AAAAATAAATTTAT
1 AAAAATAAATTTAT
63089334 TTAATGTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAAAATAAATTTATA
Found at i:63090410 original size:22 final size:22
Alignment explanation
Indices: 63090382--63090425 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
63090372 TTTAATTTTT
63090382 TTAAAATAAAAAATAT-AAATAA
1 TTAAAATAAAAAA-ATCAAATAA
63090404 TTAAAATAAAAAAATCAAATAA
1 TTAAAATAAAAAAATCAAATAA
63090426 CATAAAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 2 0.10
22 19 0.90
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (22 bp):
TTAAAATAAAAAAATCAAATAA
Found at i:63098392 original size:262 final size:262
Alignment explanation
Indices: 63097927--63098454 Score: 1056
Period size: 262 Copynumber: 2.0 Consensus size: 262
63097917 TTTTAATTTT
63097927 ATTTTTGCTTTTCTGTAATTTATTTAATAGAGTTTATGTTAGTTGACTCATGATATCAAACTTAG
1 ATTTTTGCTTTTCTGTAATTTATTTAATAGAGTTTATGTTAGTTGACTCATGATATCAAACTTAG
63097992 TATGCCCTTTTATAATTACCATAGTATGGCACATGAATATACTCTTAAATAATAATTATATGCTA
66 TATGCCCTTTTATAATTACCATAGTATGGCACATGAATATACTCTTAAATAATAATTATATGCTA
63098057 AATCCACATAGAGTTTATTGCTTTTGACAGTAATGAAAAATTAAAACCTCCATTTTCATCAATCA
131 AATCCACATAGAGTTTATTGCTTTTGACAGTAATGAAAAATTAAAACCTCCATTTTCATCAATCA
63098122 TAAGTTTTACCAACATTTGTGCCTTTATATGTTGTAGAATATTATTGTTTGACATTGGAGATGGG
196 TAAGTTTTACCAACATTTGTGCCTTTATATGTTGTAGAATATTATTGTTTGACATTGGAGATGGG
63098187 GG
261 GG
63098189 ATTTTTGCTTTTCTGTAATTTATTTAATAGAGTTTATGTTAGTTGACTCATGATATCAAACTTAG
1 ATTTTTGCTTTTCTGTAATTTATTTAATAGAGTTTATGTTAGTTGACTCATGATATCAAACTTAG
63098254 TATGCCCTTTTATAATTACCATAGTATGGCACATGAATATACTCTTAAATAATAATTATATGCTA
66 TATGCCCTTTTATAATTACCATAGTATGGCACATGAATATACTCTTAAATAATAATTATATGCTA
63098319 AATCCACATAGAGTTTATTGCTTTTGACAGTAATGAAAAATTAAAACCTCCATTTTCATCAATCA
131 AATCCACATAGAGTTTATTGCTTTTGACAGTAATGAAAAATTAAAACCTCCATTTTCATCAATCA
63098384 TAAGTTTTACCAACATTTGTGCCTTTATATGTTGTAGAATATTATTGTTTGACATTGGAGATGGG
196 TAAGTTTTACCAACATTTGTGCCTTTATATGTTGTAGAATATTATTGTTTGACATTGGAGATGGG
63098449 GG
261 GG
63098451 ATTT
1 ATTT
63098455 GAACCCAGCT
Statistics
Matches: 266, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
262 266 1.00
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (262 bp):
ATTTTTGCTTTTCTGTAATTTATTTAATAGAGTTTATGTTAGTTGACTCATGATATCAAACTTAG
TATGCCCTTTTATAATTACCATAGTATGGCACATGAATATACTCTTAAATAATAATTATATGCTA
AATCCACATAGAGTTTATTGCTTTTGACAGTAATGAAAAATTAAAACCTCCATTTTCATCAATCA
TAAGTTTTACCAACATTTGTGCCTTTATATGTTGTAGAATATTATTGTTTGACATTGGAGATGGG
GG
Found at i:63109308 original size:38 final size:38
Alignment explanation
Indices: 63109221--63109299 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
63109211 AACACACATC
63109221 AAATATAAATTACTTATACAATACAAACAAAGGTGTTT
1 AAATATAAATTACTTATACAATACAAACAAAGGTGTTT
*
63109259 AAATATAAATTACTTATACAATAGAAACAAAGGTGTTT
1 AAATATAAATTACTTATACAATACAAACAAAGGTGTTT
63109297 AAA
1 AAA
63109300 ATTTAATTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.30
Consensus pattern (38 bp):
AAATATAAATTACTTATACAATACAAACAAAGGTGTTT
Found at i:63115473 original size:18 final size:18
Alignment explanation
Indices: 63115450--63115492 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
63115440 ACCCAATCAA
**
63115450 AACCCAAGTATTCAACCC
1 AACCCAAGTACCCAACCC
*
63115468 AACCCAATTACCCAACCC
1 AACCCAAGTACCCAACCC
63115486 AACCCAA
1 AACCCAA
63115493 TCATAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.44, G:0.02, T:0.12
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:63119931 original size:22 final size:22
Alignment explanation
Indices: 63119898--63119953 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
63119888 GTATCTCACA
*
63119898 AAAATATT-TATTATTTGTTATT
1 AAAAT-TTATATTATTTATTATT
*
63119920 -AAATTATATATTATTTATTTTT
1 AAAATT-TATATTATTTATTATT
63119942 AAAATTTATATT
1 AAAATTTATATT
63119954 TATCAAATGG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 1 0.03
21 5 0.17
22 18 0.62
23 5 0.17
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
AAAATTTATATTATTTATTATT
Found at i:63120437 original size:25 final size:24
Alignment explanation
Indices: 63120409--63120457 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
63120399 AAAGTATTCT
63120409 AATTTAATAAATTTTATTTATTTGA
1 AATTTAAT-AATTTTATTTATTTGA
**
63120434 AATTTAATTTTTTTATTTATTTGA
1 AATTTAATAATTTTATTTATTTGA
63120458 TATGTAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (24 bp):
AATTTAATAATTTTATTTATTTGA
Found at i:63120467 original size:30 final size:28
Alignment explanation
Indices: 63120421--63120478 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 28
63120411 TTTAATAAAT
*
63120421 TTTATTTATTTGAAATTTAATTTTTTTA
1 TTTATTTATATGAAATTTAATTTTTTTA
*
63120449 TTTATTTGATATGTAAATTTGATTTTTTTA
1 TTTATTT-ATATG-AAATTTAATTTTTTTA
63120479 GGTACTAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 7 0.27
29 4 0.15
30 15 0.58
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.66
Consensus pattern (28 bp):
TTTATTTATATGAAATTTAATTTTTTTA
Found at i:63123852 original size:9 final size:9
Alignment explanation
Indices: 63123838--63123881 Score: 61
Period size: 9 Copynumber: 4.9 Consensus size: 9
63123828 ATAGTAAGGG
63123838 TAATAGTAA
1 TAATAGTAA
63123847 TAATAGTAA
1 TAATAGTAA
*
63123856 TAATAATAA
1 TAATAGTAA
*
63123865 TAATAATAA
1 TAATAGTAA
*
63123874 TAGTAGTA
1 TAATAGTA
63123882 GTAAATACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (9 bp):
TAATAGTAA
Found at i:63123859 original size:3 final size:3
Alignment explanation
Indices: 63123838--63123875 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
63123828 ATAGTAAGGG
* *
63123838 TAA TAG TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
63123876 GTAGTAGTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:63125445 original size:44 final size:45
Alignment explanation
Indices: 63125356--63125453 Score: 135
Period size: 44 Copynumber: 2.2 Consensus size: 45
63125346 AAGACTTGTA
* ** *
63125356 TCTTCGATCTACTTCACCACCAGTATGGGAAGACAATATCTGCTT
1 TCTTCGATCTACTTCACCACCAATACAGGAAGACAAGATCTGCTT
* *
63125401 TCTTCGATCTACTTCA-CGCCAATACATGAAGACAAGATCTGCTT
1 TCTTCGATCTACTTCACCACCAATACAGGAAGACAAGATCTGCTT
63125445 TCTTCGATC
1 TCTTCGATC
63125454 GATTCTACTG
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 31 0.66
45 16 0.34
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.32
Consensus pattern (45 bp):
TCTTCGATCTACTTCACCACCAATACAGGAAGACAAGATCTGCTT
Found at i:63125716 original size:44 final size:44
Alignment explanation
Indices: 63125649--63125937 Score: 175
Period size: 45 Copynumber: 6.5 Consensus size: 44
63125639 ACCGATATAG
* * * * *
63125649 GAAGACAAGACCTACTATCTTTGATCTGTTTCACGCCGGTACAT
1 GAAGACAAGATCTGCTTTCTTTGATCTGCTTCACGCCAGTACAT
* * * * ***
63125693 GAAAACAAGATCTGCTTTCTTTGATTTGCTTCGCCACCAGTATGG
1 GAAGACAAGATCTGCTTTCTTTGATCTGCTTC-ACGCCAGTACAT
* * * * * * *
63125738 GTAGGCAAGATCTGGTATCTCTGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTTTCTTTGATCTGCTTCACGCCAGTACAT
* * * ***
63125782 GAAGACAAGATCTGCTTTCTTTGATCTGCTCCGCCACCAGTATGG
1 GAAGACAAGATCTGCTTTCTTTGATCTGCTTC-ACGCCAGTACAT
* * * * * * **
63125827 GAAGGCAAGATCTGCTTTCTTCGATCTACTCCACCACCTGTACGG
1 GAAGACAAGATCTGCTTTCTTTGATCTGCTTCA-CGCCAGTACAT
* * * * * *
63125872 GGAGACAAGATCTGGTATCTATGATCTACTTTACGCCAGTACAT
1 GAAGACAAGATCTGCTTTCTTTGATCTGCTTCACGCCAGTACAT
*
63125916 GAAGACAGGATCTG-TTATCTTT
1 GAAGACAAGATCTGCTT-TCTTT
63125938 CAACCTGCTC
Statistics
Matches: 180, Mismatches: 61, Indels: 8
0.72 0.24 0.03
Matches are distributed among these distances:
43 1 0.01
44 80 0.44
45 99 0.55
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (44 bp):
GAAGACAAGATCTGCTTTCTTTGATCTGCTTCACGCCAGTACAT
Found at i:63125853 original size:89 final size:89
Alignment explanation
Indices: 63125648--63125856 Score: 276
Period size: 89 Copynumber: 2.3 Consensus size: 89
63125638 TACCGATATA
* * * * ** **
63125648 GGAAGACAAGACCTACTATCTTTGATCTGTTTCACGCCGGTACATGAAAACAAGATCTGCTTTCT
1 GGAAGGCAAGATCTGCTATCTCTGATCTACTTCACGCCAATACATGAAAACAAGATCTGCTTTCT
* *
63125713 TTGATTTGCTTCGCCACCAGTATG
66 TTGATCTGCTCCGCCACCAGTATG
* * *
63125737 GGTAGGCAAGATCTGGTATCTCTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCT
1 GGAAGGCAAGATCTGCTATCTCTGATCTACTTCACGCCAATACATGAAAACAAGATCTGCTTTCT
63125802 TTGATCTGCTCCGCCACCAGTATG
66 TTGATCTGCTCCGCCACCAGTATG
*
63125826 GGAAGGCAAGATCTGCTTTCT-TCGATCTACT
1 GGAAGGCAAGATCTGCTATCTCT-GATCTACT
63125857 CCACCACCTG
Statistics
Matches: 103, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
88 1 0.01
89 102 0.99
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (89 bp):
GGAAGGCAAGATCTGCTATCTCTGATCTACTTCACGCCAATACATGAAAACAAGATCTGCTTTCT
TTGATCTGCTCCGCCACCAGTATG
Found at i:63138074 original size:3 final size:3
Alignment explanation
Indices: 63138066--63138108 Score: 50
Period size: 3 Copynumber: 13.3 Consensus size: 3
63138056 AGTAATTCCT
*
63138066 ATA ATA ATA ATA ATA ATA ATA ATA GTAA ATA CATA ATTA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA -ATA A-TA ATA A
63138109 CATATAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
3 27 0.77
4 8 0.23
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:63156971 original size:13 final size:13
Alignment explanation
Indices: 63156953--63156977 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
63156943 TTGACCTCAG
63156953 TTTAATTGATTAA
1 TTTAATTGATTAA
63156966 TTTAATTGATTA
1 TTTAATTGATTA
63156978 TTGATTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (13 bp):
TTTAATTGATTAA
Found at i:63162206 original size:5 final size:5
Alignment explanation
Indices: 63162198--63162222 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
63162188 GCAAATTGAA
63162198 TTGTG TTGTG TTGTG TTGTG TTGTG
1 TTGTG TTGTG TTGTG TTGTG TTGTG
63162223 GAAGTTTAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.40, T:0.60
Consensus pattern (5 bp):
TTGTG
Found at i:63167437 original size:41 final size:42
Alignment explanation
Indices: 63167359--63167486 Score: 192
Period size: 41 Copynumber: 3.1 Consensus size: 42
63167349 AAATATATTT
* * *
63167359 ATTTTTTTT-AATGTTAAAATATATTTTACATAC--TTTTTA
1 ATTTTTTTTAAATTTTAAAATATATTTAAAATACTTTTTTTA
63167398 ATTTTTTTTAAATTTTAAAATATATTTAAAATACTTTTTTTA
1 ATTTTTTTTAAATTTTAAAATATATTTAAAATACTTTTTTTA
*
63167440 A-TTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTTTTAAATTTTAAAATATATTTAAAATACTTTTTTTA
63167481 ATTTTT
1 ATTTTT
63167487 AAAATTTTTT
Statistics
Matches: 81, Mismatches: 4, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
39 9 0.11
40 21 0.26
41 40 0.49
42 11 0.14
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (42 bp):
ATTTTTTTTAAATTTTAAAATATATTTAAAATACTTTTTTTA
Found at i:63167485 original size:31 final size:32
Alignment explanation
Indices: 63167400--63167465 Score: 68
Period size: 30 Copynumber: 2.2 Consensus size: 32
63167390 ACTTTTTAAT
*
63167400 TTTTTTTAAA-TTTTAAAATATATTTAAAATAC
1 TTTTTTTAAATTTTTAAAAT-TTTTTAAAATAC
* *
63167432 TTTTTTTAATTTTTTTAAA--TTTTAAAATA-
1 TTTTTTTAAATTTTTAAAATTTTTTAAAATAC
63167461 TTTTT
1 TTTTT
63167466 AAAATACTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
29 5 0.17
30 9 0.30
32 9 0.30
33 7 0.23
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (32 bp):
TTTTTTTAAATTTTTAAAATTTTTTAAAATAC
Found at i:63167496 original size:31 final size:32
Alignment explanation
Indices: 63167441--63167502 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
63167431 CTTTTTTTAA
63167441 TTTTTTTAAATTTTAAAATATTTTTAAAATAC
1 TTTTTTTAAATTTTAAAATATTTTTAAAATAC
*
63167473 TTTTTTTAATTTTTAAAAT-TTTTTAAAATA
1 TTTTTTTAAATTTTAAAATATTTTTAAAATA
63167503 AAAATGGGCC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 11 0.38
32 18 0.62
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (32 bp):
TTTTTTTAAATTTTAAAATATTTTTAAAATAC
Found at i:63169533 original size:18 final size:20
Alignment explanation
Indices: 63169510--63169549 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
63169500 CTGAATTGCT
*
63169510 AAAATA-TT-AAACATATAA
1 AAAATATTTAAAAAATATAA
63169528 AAAATATTTAAAAAATATAA
1 AAAATATTTAAAAAATATAA
63169548 AA
1 AA
63169550 TGTTTTAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 2 0.11
20 11 0.58
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAATATTTAAAAAATATAA
Found at i:63169550 original size:18 final size:18
Alignment explanation
Indices: 63169509--63169550 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
63169499 ACTGAATTGC
*
63169509 TAAAATATTAAACATATA
1 TAAAATATTAAACAAATA
*
63169527 AAAAATATTTAAA-AAATA
1 TAAAATA-TTAAACAAATA
63169545 TAAAAT
1 TAAAAT
63169551 GTTTTAACTT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAATATTAAACAAATA
Found at i:63173960 original size:11 final size:11
Alignment explanation
Indices: 63173938--63173969 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
63173928 AACTTATAGG
63173938 AAAAAAAG--A
1 AAAAAAAGAAA
63173947 AAAAAAAGAAA
1 AAAAAAAGAAA
63173958 AAAAAAAGAAA
1 AAAAAAAGAAA
63173969 A
1 A
63173970 GAGAGGCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 8 0.38
11 13 0.62
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:63173960 original size:16 final size:16
Alignment explanation
Indices: 63173937--63173971 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
63173927 AAACTTATAG
*
63173937 GAAAAAAAGAAAAAAAA
1 GAAAAAAA-AAAGAAAA
63173954 GAAAAAAAAAAGAAAA
1 GAAAAAAAAAAGAAAA
63173970 GA
1 GA
63173972 GAGGCAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (16 bp):
GAAAAAAAAAAGAAAA
Found at i:63173969 original size:9 final size:9
Alignment explanation
Indices: 63173938--63173962 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
63173928 AACTTATAGG
63173938 AAAAAAAGA
1 AAAAAAAGA
63173947 AAAAAAAGA
1 AAAAAAAGA
63173956 AAAAAAA
1 AAAAAAA
63173963 AAGAAAAGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:63174172 original size:5 final size:6
Alignment explanation
Indices: 63174145--63174169 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
63174135 TTTTATTTTA
63174145 TTAATT TTAATT TTAATT TTAATT T
1 TTAATT TTAATT TTAATT TTAATT T
63174170 AATATTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTAATT
Found at i:63189723 original size:13 final size:13
Alignment explanation
Indices: 63189707--63189770 Score: 52
Period size: 13 Copynumber: 5.3 Consensus size: 13
63189697 CAAATAGAAG
63189707 AACATAATATAAT
1 AACATAATATAAT
63189720 AACA-AAT-TAACAT
1 AACATAATAT-A-AT
*
63189733 AACATCATATAAT
1 AACATAATATAAT
63189746 AAC--AA-AT--T
1 AACATAATATAAT
63189754 AACATAATATAAT
1 AACATAATATAAT
63189767 AACA
1 AACA
63189771 AATTATATTA
Statistics
Matches: 40, Mismatches: 2, Indels: 18
0.67 0.03 0.30
Matches are distributed among these distances:
8 4 0.10
10 4 0.10
11 4 0.10
12 4 0.10
13 20 0.50
14 3 0.08
15 1 0.03
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.27
Consensus pattern (13 bp):
AACATAATATAAT
Found at i:63189731 original size:21 final size:21
Alignment explanation
Indices: 63189707--63189775 Score: 93
Period size: 21 Copynumber: 3.0 Consensus size: 21
63189697 CAAATAGAAG
63189707 AACATAATATAATAACAAATT
1 AACATAATATAATAACAAATT
63189728 AACATAACATCATATAATAACAAATT
1 AACAT---A--ATATAATAACAAATT
63189754 AACATAATATAATAACAAATT
1 AACATAATATAATAACAAATT
63189775 A
1 A
63189776 TATTATGGCA
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
21 21 0.49
23 1 0.02
24 1 0.02
26 20 0.47
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.28
Consensus pattern (21 bp):
AACATAATATAATAACAAATT
Found at i:63189737 original size:26 final size:26
Alignment explanation
Indices: 63189707--63189767 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 26
63189697 CAAATAGAAG
63189707 AACATAATATAATAACAAATTAACAT
1 AACATAATATAATAACAAATTAACAT
*
63189733 AACATCATATAATAACAAATTAACAT
1 AACATAATATAATAACAAATTAACAT
*
63189759 AATATAATA
1 AACATAATA
63189768 ACAAATTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (26 bp):
AACATAATATAATAACAAATTAACAT
Found at i:63189780 original size:26 final size:25
Alignment explanation
Indices: 63189707--63189780 Score: 84
Period size: 26 Copynumber: 3.0 Consensus size: 25
63189697 CAAATAGAAG
*
63189707 AACATAATATAATAACAAATTAACAT
1 AACATAATATAATAACAAATTAA-TT
*
63189733 AACATCATATAATAAC--A--AATT
1 AACATAATATAATAACAAATTAATT
63189754 AACATAATATAATAACAAATTATATT
1 AACATAATATAATAACAAATTA-ATT
63189780 A
1 A
63189781 TGGCATAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
21 16 0.40
22 2 0.05
23 1 0.03
24 1 0.03
25 1 0.03
26 19 0.47
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (25 bp):
AACATAATATAATAACAAATTAATT
Found at i:63195870 original size:242 final size:242
Alignment explanation
Indices: 63195445--63195934 Score: 980
Period size: 242 Copynumber: 2.0 Consensus size: 242
63195435 TAAAGATCAA
63195445 GGTTTAACATATCTAATAGTGGAAAATGAAATACATATACACGCATTGTGCAAATTCCTAATTAC
1 GGTTTAACATATCTAATAGTGGAAAATGAAATACATATACACGCATTGTGCAAATTCCTAATTAC
63195510 TAGTTGAAACCATAAATGTTTTGCTAATATATATAGGTAACAAGCATCGTTCTGCATCGGTAAAA
66 TAGTTGAAACCATAAATGTTTTGCTAATATATATAGGTAACAAGCATCGTTCTGCATCGGTAAAA
63195575 AATTGGTTCCAATGAAAATCTAGAAGCTATAGAACATTGGGAATGGTTATCTAGGAAAAGATGCA
131 AATTGGTTCCAATGAAAATCTAGAAGCTATAGAACATTGGGAATGGTTATCTAGGAAAAGATGCA
63195640 GCTTCAGAATCTAAGCACAGAATGTTCTCCTATATGATCCGAGTGTT
196 GCTTCAGAATCTAAGCACAGAATGTTCTCCTATATGATCCGAGTGTT
63195687 GGTTTAACATATCTAATAGTGGAAAATGAAATACATATACACGCATTGTGCAAATTCCTAATTAC
1 GGTTTAACATATCTAATAGTGGAAAATGAAATACATATACACGCATTGTGCAAATTCCTAATTAC
63195752 TAGTTGAAACCATAAATGTTTTGCTAATATATATAGGTAACAAGCATCGTTCTGCATCGGTAAAA
66 TAGTTGAAACCATAAATGTTTTGCTAATATATATAGGTAACAAGCATCGTTCTGCATCGGTAAAA
63195817 AATTGGTTCCAATGAAAATCTAGAAGCTATAGAACATTGGGAATGGTTATCTAGGAAAAGATGCA
131 AATTGGTTCCAATGAAAATCTAGAAGCTATAGAACATTGGGAATGGTTATCTAGGAAAAGATGCA
63195882 GCTTCAGAATCTAAGCACAGAATGTTCTCCTATATGATCCGAGTGTT
196 GCTTCAGAATCTAAGCACAGAATGTTCTCCTATATGATCCGAGTGTT
63195929 GGTTTA
1 GGTTTA
63195935 TCAAACCAGA
Statistics
Matches: 248, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
242 248 1.00
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (242 bp):
GGTTTAACATATCTAATAGTGGAAAATGAAATACATATACACGCATTGTGCAAATTCCTAATTAC
TAGTTGAAACCATAAATGTTTTGCTAATATATATAGGTAACAAGCATCGTTCTGCATCGGTAAAA
AATTGGTTCCAATGAAAATCTAGAAGCTATAGAACATTGGGAATGGTTATCTAGGAAAAGATGCA
GCTTCAGAATCTAAGCACAGAATGTTCTCCTATATGATCCGAGTGTT
Found at i:63204896 original size:31 final size:29
Alignment explanation
Indices: 63204819--63204899 Score: 92
Period size: 29 Copynumber: 2.7 Consensus size: 29
63204809 GAATTAGATC
*
63204819 AAATCAAAATTTAATGTATAAAATTACACA
1 AAATC-AAAGTTAATGTATAAAATTACACA
*
63204849 AAATCAAAGTTAATGTATACAATTACACA
1 AAATCAAAGTTAATGTATAAAATTACACA
*
63204878 TTAAATCATAA-TTCATGTATAA
1 --AAATCA-AAGTTAATGTATAA
63204900 TTTTAGGATG
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
29 22 0.50
30 5 0.11
31 15 0.34
32 2 0.05
ACGTcount: A:0.52, C:0.11, G:0.05, T:0.32
Consensus pattern (29 bp):
AAATCAAAGTTAATGTATAAAATTACACA
Found at i:63218707 original size:31 final size:31
Alignment explanation
Indices: 63218672--63218745 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
63218662 GTTACAAAAT
*
63218672 AGTCATTGAACT-ATTCAAAAGTTTTCATTTA
1 AGTCACTGAACTAATTCAAAA-TTTTCATTTA
* * * *
63218703 AGTCACTAAACTAATTGAATATTTTTATTTA
1 AGTCACTGAACTAATTCAAAATTTTCATTTA
63218734 AGTCACTGAACT
1 AGTCACTGAACT
63218746 GTTAAGTTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
31 30 0.83
32 6 0.17
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (31 bp):
AGTCACTGAACTAATTCAAAATTTTCATTTA
Found at i:63232137 original size:7 final size:7
Alignment explanation
Indices: 63232125--63232157 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
63232115 AGTTTCGAAT
63232125 TTTTTTA
1 TTTTTTA
63232132 TTTTTTA
1 TTTTTTA
63232139 TTTTTTA
1 TTTTTTA
63232146 TTTTTTA
1 TTTTTTA
63232153 TTTTT
1 TTTTT
63232158 AAATTCATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:63234874 original size:13 final size:13
Alignment explanation
Indices: 63234858--63234882 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
63234848 AAAATAAAAA
63234858 ATAATCATTTAAT
1 ATAATCATTTAAT
63234871 ATAATCATTTAA
1 ATAATCATTTAA
63234883 AAGTAATTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAATCATTTAAT
Found at i:63235965 original size:24 final size:24
Alignment explanation
Indices: 63235933--63235978 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
63235923 CACACTCCTT
63235933 AAAGGTATCCCTAAGGAGCCCCTC
1 AAAGGTATCCCTAAGGAGCCCCTC
63235957 AAAGGTATCCCTAAGGAGCCCC
1 AAAGGTATCCCTAAGGAGCCCC
63235979 CTTGCCTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.33, G:0.22, T:0.15
Consensus pattern (24 bp):
AAAGGTATCCCTAAGGAGCCCCTC
Found at i:63239502 original size:3 final size:3
Alignment explanation
Indices: 63239496--63239542 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
63239486 TTTAGCCACT
*
63239496 TTA TTA TT- TTG TTTA TT- TTA TTA TTA TTA TTA TTA TTA TTA CTTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
63239541 TT
1 TT
63239543 TGTTTATGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
2 4 0.10
3 30 0.77
4 5 0.13
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:63245414 original size:21 final size:22
Alignment explanation
Indices: 63245390--63245434 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
63245380 AGAAAAAGAG
63245390 AAATACAAAAAAG-AATAG-ATC
1 AAAT-CAAAAAAGAAATAGAATC
*
63245411 AAATCAAAAAGGAAATAGAATC
1 AAATCAAAAAAGAAATAGAATC
63245433 AA
1 AA
63245435 CAATTTGCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 7 0.33
21 9 0.43
22 5 0.24
ACGTcount: A:0.67, C:0.09, G:0.11, T:0.13
Consensus pattern (22 bp):
AAATCAAAAAAGAAATAGAATC
Found at i:63248280 original size:32 final size:32
Alignment explanation
Indices: 63248242--63248548 Score: 436
Period size: 32 Copynumber: 9.3 Consensus size: 32
63248232 AAATAATACA
63248242 TGAACAGGAGAGATTCCCTGCAAGAAATGATG
1 TGAACAGGAGAGATTCCCTGCAAGAAATGATG
63248274 TGAACAGGAGAGATTCCCTGCAAGAAATGATG
1 TGAACAGGAGAGATTCCCTGCAAGAAATGATG
* * *
63248306 TGAACAGGAGAGATTCCCTGTAACAAAATAATCCG
1 TGAACAGGAGAGATTCCCTGCAA-GAAATGAT--G
63248341 TGAACAGGAGAGATTCCCTGCAAGAAATGATG
1 TGAACAGGAGAGATTCCCTGCAAGAAATGATG
* * *
63248373 TGAACAGGAAAGATTCCCTGCAACAAAATAATGTG
1 TGAACAGGAGAGATTCCCTGCAA-GAAATGA--TG
* *
63248408 TGAACAGGAGAGATTCCCTGCAACAAAATAATGCG
1 TGAACAGGAGAGATTCCCTGCAA-GAAATGAT--G
63248443 TGAACAGGAGAGATTCCCTGCAAGAAATGATG
1 TGAACAGGAGAGATTCCCTGCAAGAAATGATG
* *
63248475 TGAACAGGAAATATTCCCTGCAAGAAATGATG
1 TGAACAGGAGAGATTCCCTGCAAGAAATGATG
63248507 TGAACAGGAGAGATTCCCTGCAAG-AATGATG
1 TGAACAGGAGAGATTCCCTGCAAGAAATGATG
63248538 TGAACAGGAGA
1 TGAACAGGAGA
63248549 TACGATTTCA
Statistics
Matches: 251, Mismatches: 16, Indels: 17
0.88 0.06 0.06
Matches are distributed among these distances:
31 18 0.07
32 130 0.52
33 12 0.05
34 12 0.05
35 79 0.31
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.19
Consensus pattern (32 bp):
TGAACAGGAGAGATTCCCTGCAAGAAATGATG
Found at i:63248359 original size:67 final size:64
Alignment explanation
Indices: 63248242--63248548 Score: 418
Period size: 67 Copynumber: 4.7 Consensus size: 64
63248232 AAATAATACA
* *
63248242 TGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAGAGATTCCCTGCAAGAAATGATG
1 TGAACAGGAGAGATTCCCTGCAAAAAATAATGTGAACAGGAGAGATTCCCTGCAAGAAATGATG
*
63248306 TGAACAGGAGAGATTCCCTGTAACAAAATAATCCGTGAACAGGAGAGATTCCCTGCAAGAAATGA
1 TGAACAGGAGAGATTCCCTGCAA-AAAATAAT--GTGAACAGGAGAGATTCCCTGCAAGAAATGA
63248371 TG
63 TG
* * *
63248373 TGAACAGGAAAGATTCCCTGCAACAAAATAATGTGTGAACAGGAGAGATTCCCTGCAACAAAATA
1 TGAACAGGAGAGATTCCCTGCAA-AAAATAA--TGTGAACAGGAGAGATTCCCTGCAA-GAAATG
63248438 ATGCG
62 AT--G
* * * *
63248443 TGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAATATTCCCTGCAAGAAATGATG
1 TGAACAGGAGAGATTCCCTGCAAAAAATAATGTGAACAGGAGAGATTCCCTGCAAGAAATGATG
* *
63248507 TGAACAGGAGAGATTCCCTGC-AAGAATGATGTGAACAGGAGA
1 TGAACAGGAGAGATTCCCTGCAAAAAATAATGTGAACAGGAGA
63248549 TACGATTTCA
Statistics
Matches: 218, Mismatches: 17, Indels: 17
0.87 0.07 0.07
Matches are distributed among these distances:
63 18 0.08
64 44 0.20
65 6 0.03
66 6 0.03
67 109 0.50
68 6 0.03
69 6 0.03
70 23 0.11
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.19
Consensus pattern (64 bp):
TGAACAGGAGAGATTCCCTGCAAAAAATAATGTGAACAGGAGAGATTCCCTGCAAGAAATGATG
Found at i:63248461 original size:102 final size:99
Alignment explanation
Indices: 63248232--63248529 Score: 497
Period size: 102 Copynumber: 3.0 Consensus size: 99
63248222 GTCCAAAAAG
* *
63248232 AAATAATACATGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAGAGATTCCCTGCAA
1 AAATAATACGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGCAA
*
63248297 GAAATGATGTGAACAGGAGAGATTCCCTGTAACA
66 GAAATGATGTGAACAGGAGAGATTCCCTGCAACA
*
63248331 AAATAATCCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGCAA
1 AAATAATACGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGCAA
* *
63248396 CAAAATAATGTGTGAACAGGAGAGATTCCCTGCAACA
66 -GAAATGA--TGTGAACAGGAGAGATTCCCTGCAACA
* *
63248433 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAATATTCCCTGCAA
1 AAATAATACGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGCAA
63248498 GAAATGATGTGAACAGGAGAGATTCCCTGCAA
66 GAAATGATGTGAACAGGAGAGATTCCCTGCAA
63248530 GAATGATGTG
Statistics
Matches: 186, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
99 87 0.47
100 5 0.03
101 5 0.03
102 89 0.48
ACGTcount: A:0.40, C:0.17, G:0.24, T:0.19
Consensus pattern (99 bp):
AAATAATACGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGCAA
GAAATGATGTGAACAGGAGAGATTCCCTGCAACA
Found at i:63249169 original size:9 final size:9
Alignment explanation
Indices: 63249155--63249180 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
63249145 ACCGGTTCCA
63249155 AAAACACCT
1 AAAACACCT
63249164 AAAACACCT
1 AAAACACCT
63249173 AAAACACC
1 AAAACACC
63249181 AAAGAACATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.35, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAACACCT
Found at i:63249500 original size:24 final size:24
Alignment explanation
Indices: 63249464--63249512 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
63249454 ACCGTCGTGG
63249464 ACACCAGCGACAACTCCTAGTGTA
1 ACACCAGCGACAACTCCTAGTGTA
* * *
63249488 ACACCGGCTACAACTCTTAGTGTA
1 ACACCAGCGACAACTCCTAGTGTA
63249512 A
1 A
63249513 GAAGCTATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.33, C:0.31, G:0.16, T:0.20
Consensus pattern (24 bp):
ACACCAGCGACAACTCCTAGTGTA
Found at i:63252350 original size:45 final size:45
Alignment explanation
Indices: 63252286--63252491 Score: 337
Period size: 45 Copynumber: 4.6 Consensus size: 45
63252276 TTTGAGTACT
63252286 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
63252331 TCTGATCAAGTGACAAAGTGATAAGTGGTAG-TCTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCT-TAGCTACACTTA
*
63252376 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACATTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
*
63252422 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
63252467 TCTGATC-AGGGAC-AAGTGGTAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
63252492 ATCATACGTA
Statistics
Matches: 153, Mismatches: 5, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
43 11 0.07
44 6 0.04
45 92 0.60
46 43 0.28
47 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.29
Consensus pattern (45 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:63252443 original size:91 final size:90
Alignment explanation
Indices: 63252286--63252491 Score: 353
Period size: 91 Copynumber: 2.3 Consensus size: 90
63252276 TTTGAGTACT
63252286 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGTGACAAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGTGACAAAGTG
*
63252351 ATAAGTGGTAGTCTAGCTACACTTA
66 ATAAGTGGTAGCCTAGCTACACTTA
*
63252376 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACATTTATCTGATCAAGTGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAAGTGACAAAGT
63252441 GATAAGTGGTAGCCTAGCTACACTTA
65 GATAAGTGGTAGCCTAGCTACACTTA
* *
63252467 TCTGATC-AGGGAC-AAGTGGTAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
63252492 ATCATACGTA
Statistics
Matches: 111, Mismatches: 4, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
89 11 0.10
90 37 0.33
91 63 0.57
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.29
Consensus pattern (90 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGTGACAAAGTG
ATAAGTGGTAGCCTAGCTACACTTA
Found at i:63253848 original size:3 final size:3
Alignment explanation
Indices: 63253840--63253878 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
63253830 GTTAATTTGC
63253840 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
63253879 TTACGATACC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:63255096 original size:24 final size:25
Alignment explanation
Indices: 63255050--63255099 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
63255040 ATTTATATAG
***
63255050 TGCTTCCTCTTCTCTTTTGTTCCTT
1 TGCTTCCTCTTCTCTTCCATTCCTT
63255075 TGCTTCC-CTTCTCTTCCATTCCTT
1 TGCTTCCTCTTCTCTTCCATTCCTT
63255099 T
1 T
63255100 TTTTTTCCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.02, C:0.36, G:0.06, T:0.56
Consensus pattern (25 bp):
TGCTTCCTCTTCTCTTCCATTCCTT
Found at i:63263586 original size:22 final size:22
Alignment explanation
Indices: 63263561--63263604 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
63263551 CATAGTTGTC
63263561 TTGTCCAATTAGACCAGTTGAA
1 TTGTCCAATTAGACCAGTTGAA
63263583 TTGTCCAATTAGACCAGTTGAA
1 TTGTCCAATTAGACCAGTTGAA
63263605 CCATTTGGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (22 bp):
TTGTCCAATTAGACCAGTTGAA
Found at i:63270518 original size:17 final size:17
Alignment explanation
Indices: 63270483--63270530 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
63270473 TAAATATTTG
* *
63270483 TTAAATTTA-AATTTAA
1 TTAAATATATAATATAA
63270499 TTAAATATATAATATAA
1 TTAAATATATAATATAA
*
63270516 TTAAAAATATAATAT
1 TTAAATATATAATAT
63270531 TTAATACTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 8 0.29
17 20 0.71
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAATATATAATATAA
Found at i:63270717 original size:35 final size:35
Alignment explanation
Indices: 63270661--63270729 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
63270651 ACCATTAACC
63270661 TTTTTGTTAACTTCACATTCGCCAAGTGGCATGCT
1 TTTTTGTTAACTTCACATTCGCCAAGTGGCATGCT
* * * *
63270696 TTTTTGTTAATTTTACCTTCGCCACGTGGCATGC
1 TTTTTGTTAACTTCACATTCGCCAAGTGGCATGC
63270730 CAAAGTTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.42
Consensus pattern (35 bp):
TTTTTGTTAACTTCACATTCGCCAAGTGGCATGCT
Found at i:63278344 original size:26 final size:26
Alignment explanation
Indices: 63278277--63278344 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 26
63278267 TTTAAATACC
** *
63278277 TTTTTAGAATTTTACAAAATAAATTTA
1 TTTTTA-AATTTTTTAAAAAAAATTTA
* *
63278304 TTTTTAAACTCTTTAAAAAAAATTT-
1 TTTTTAAATTTTTTAAAAAAAATTTA
63278329 TTTTTACAATTTTTTA
1 TTTTTA-AATTTTTTA
63278345 TAATTTCTAC
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
25 6 0.18
26 21 0.64
27 6 0.18
ACGTcount: A:0.40, C:0.06, G:0.01, T:0.53
Consensus pattern (26 bp):
TTTTTAAATTTTTTAAAAAAAATTTA
Found at i:63288707 original size:18 final size:18
Alignment explanation
Indices: 63288684--63288776 Score: 141
Period size: 18 Copynumber: 5.2 Consensus size: 18
63288674 CCCAACTACT
* *
63288684 GTATACGTGAACAGTCCC
1 GTATACGTGAATAGTACC
*
63288702 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
*
63288720 GTATACGTGAATAGTACT
1 GTATACGTGAATAGTACC
*
63288738 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
63288756 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
63288774 GTA
1 GTA
63288777 AACGGTCGTA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:63288742 original size:36 final size:36
Alignment explanation
Indices: 63288684--63288776 Score: 159
Period size: 36 Copynumber: 2.6 Consensus size: 36
63288674 CCCAACTACT
* *
63288684 GTATACGTGAACAGTCCCGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
*
63288720 GTATACGTGAATAGTACTGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
63288756 GTATACGTGAATAGTACCGTA
1 GTATACGTGAATAGTACCGTA
63288777 AACGGTCGTA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 53 1.00
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (36 bp):
GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
Found at i:63293591 original size:21 final size:22
Alignment explanation
Indices: 63293555--63293595 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
63293545 AGTGTATTAA
*
63293555 AATCAAATTTTCATGTATACCG
1 AATCAAAATTTCATGTATACCG
63293577 AATCAAAATTT-ATGTATAC
1 AATCAAAATTTCATGTATAC
63293596 AGATCATCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (22 bp):
AATCAAAATTTCATGTATACCG
Found at i:63298017 original size:11 final size:11
Alignment explanation
Indices: 63298001--63298025 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
63297991 CATCCTTATA
63298001 AGAAAAATGTT
1 AGAAAAATGTT
63298012 AGAAAAATGTT
1 AGAAAAATGTT
63298023 AGA
1 AGA
63298026 GTTAAGTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.20, T:0.24
Consensus pattern (11 bp):
AGAAAAATGTT
Found at i:63300524 original size:16 final size:16
Alignment explanation
Indices: 63300503--63300533 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
63300493 AACATTCTCA
63300503 TTAAATCTTTTAATTT
1 TTAAATCTTTTAATTT
*
63300519 TTAAATTTTTTAATT
1 TTAAATCTTTTAATT
63300534 AAATCCCTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TTAAATCTTTTAATTT
Found at i:63302360 original size:10 final size:9
Alignment explanation
Indices: 63302347--63302429 Score: 50
Period size: 9 Copynumber: 9.1 Consensus size: 9
63302337 CTATAAAGAG
63302347 ATATATACAT
1 ATATATA-AT
63302357 ATATATAAT
1 ATATATAAT
*
63302366 AAGATATAA-
1 -ATATATAAT
63302375 ATATATAAT
1 ATATATAAT
* *
63302384 A-AGATGAT
1 ATATATAAT
63302392 ATATATAA-
1 ATATATAAT
63302400 ATAGTTATAAT
1 ATA--TATAAT
63302411 A-ATAATAAT
1 ATAT-ATAAT
63302420 A-ATAATAAT
1 ATAT-ATAAT
63302429 A
1 A
63302430 GGACAAATAT
Statistics
Matches: 60, Mismatches: 6, Indels: 15
0.74 0.07 0.19
Matches are distributed among these distances:
8 17 0.28
9 22 0.37
10 20 0.33
11 1 0.02
ACGTcount: A:0.58, C:0.01, G:0.05, T:0.36
Consensus pattern (9 bp):
ATATATAAT
Found at i:63302378 original size:18 final size:18
Alignment explanation
Indices: 63302357--63302418 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 18
63302347 ATATATACAT
63302357 ATATATAATAAGATATAA
1 ATATATAATAAGATATAA
*
63302375 ATATATAATAAGATGATAT
1 ATATATAATAAGAT-ATAA
*
63302394 ATATA-AAT-AGTTAT-A
1 ATATATAATAAGATATAA
63302409 ATA-ATAATAA
1 ATATATAATAA
63302419 TAATAATAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
14 1 0.03
15 6 0.16
16 3 0.08
17 3 0.08
18 17 0.45
19 8 0.21
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (18 bp):
ATATATAATAAGATATAA
Found at i:63304915 original size:52 final size:52
Alignment explanation
Indices: 63304844--63305145 Score: 427
Period size: 52 Copynumber: 5.9 Consensus size: 52
63304834 ATCAAGTGAC
** *
63304844 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTAATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGG
* *
63304896 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTAATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGG
* *
63304948 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC------
1 AAAGTGATAAGTAATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGG
** *
63304994 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTAATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGG
* *
63305046 AAAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTAATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGG
* * *
63305098 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAA
1 AAAGTGATAAGTAATAGCTTCAGCTACACTTATCTGATCAAGTGACAA
63305146 AGTGATAAGT
Statistics
Matches: 225, Mismatches: 19, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
46 41 0.18
52 184 0.82
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (52 bp):
AAAGTGATAAGTAATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGG
Found at i:63305050 original size:150 final size:150
Alignment explanation
Indices: 63304830--63305157 Score: 593
Period size: 150 Copynumber: 2.2 Consensus size: 150
63304820 TTTGAGTACT
63304830 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
* *
63304895 GAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGT
66 GAAAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGT
* *
63304960 AATAGCTTCGGCTATACTTA
131 AATAGCTTCAGCTACACTTA
63304980 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
63305045 GAAAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGT
66 GAAAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGT
* *
63305110 GATAGCTTTAGCTACACTTA
131 AATAGCTTCAGCTACACTTA
*
63305130 TCTGATCAAGAGACAAAGTGATAAGTGG
1 TCTGATCAAGTGACAAAGTGATAAGTGG
63305158 CTACACTTAT
Statistics
Matches: 171, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
150 171 1.00
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (150 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
GAAAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGT
AATAGCTTCAGCTACACTTA
Found at i:63305148 original size:98 final size:98
Alignment explanation
Indices: 63304830--63305155 Score: 396
Period size: 98 Copynumber: 3.3 Consensus size: 98
63304820 TTTGAGTACT
** **
63304830 TCTGATCAAGTGAC-AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGT
1 TCTGATCAAGTGACGAAAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGT
* ** *
63304894 GGAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 -GAAAGTGATAAGTGATAGCTTTAGCTACACTTA
*
63304928 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGA
1 TCTGATCAAGTGAC-----GAAAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGTGA
*
63304993 C-----AAAGTGATAAGTGGTAGCTTTAGCTACACTTA
61 CAAGTGAAAGTGATAAGTGATAGCTTTAGCTACACTTA
63305026 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGTGA
1 TCTGATCAAGTGAC-----GAAAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGTGA
63305091 CAAGTGAAAAGTGATAAGTGATAGCTTTAGCTACACTTA
61 CAAGTG-AAAGTGATAAGTGATAGCTTTAGCTACACTTA
*
63305130 TCTGATCAAGAGAC-AAAGTGATAAGT
1 TCTGATCAAGTGACGAAAGTGATAAGT
63305156 GGCTACACTT
Statistics
Matches: 203, Mismatches: 13, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
98 118 0.58
104 85 0.42
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (98 bp):
TCTGATCAAGTGACGAAAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGT
GAAAGTGATAAGTGATAGCTTTAGCTACACTTA
Found at i:63305164 original size:37 final size:37
Alignment explanation
Indices: 63305120--63305302 Score: 307
Period size: 37 Copynumber: 5.0 Consensus size: 37
63305110 GATAGCTTTA
*
63305120 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
63305157 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
63305194 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
63305231 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
63305268 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
63305303 ATCATACGTA
Statistics
Matches: 141, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
35 11 0.08
36 4 0.03
37 126 0.89
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:63313568 original size:16 final size:16
Alignment explanation
Indices: 63313547--63313585 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
63313537 TTTTTAGTTG
* *
63313547 TATTTAACTATTATTA
1 TATTTAAATATTATCA
*
63313563 TATTTAAATTTTATCA
1 TATTTAAATATTATCA
63313579 TATTTAA
1 TATTTAA
63313586 TGTCGATTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (16 bp):
TATTTAAATATTATCA
Found at i:63319044 original size:29 final size:28
Alignment explanation
Indices: 63319000--63319058 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
63318990 TTTAATTTGA
* *
63319000 TACTTGAATTTATTTTTGGTCTCAATTAAG
1 TACTTGAAGTTATTTTT--TCCCAATTAAG
63319030 TACTTG-AGTTATTTTTTCCCAATTAAG
1 TACTTGAAGTTATTTTTTCCCAATTAAG
63319057 TA
1 TA
63319059 TCTTTATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 12 0.44
29 9 0.33
30 6 0.22
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.49
Consensus pattern (28 bp):
TACTTGAAGTTATTTTTTCCCAATTAAG
Found at i:63347872 original size:68 final size:68
Alignment explanation
Indices: 63347763--63347899 Score: 265
Period size: 68 Copynumber: 2.0 Consensus size: 68
63347753 AAGATATAGG
*
63347763 TATAAAAAAGAACCTAATTACAAAATTCATTTACCAATTTCTACTATATATTAAACTGTTAAGTA
1 TATAAAAAAGAACCTAATTACAAAATTCATTTACCAATTTCTACTATATATTAAACTCTTAAGTA
63347828 AGT
66 AGT
63347831 TATAAAAAAGAACCTAATTACAAAATTCATTTACCAATTTCTACTATATATTAAACTCTTAAGTA
1 TATAAAAAAGAACCTAATTACAAAATTCATTTACCAATTTCTACTATATATTAAACTCTTAAGTA
63347896 AGT
66 AGT
63347899 T
1 T
63347900 GATATTACGA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (68 bp):
TATAAAAAAGAACCTAATTACAAAATTCATTTACCAATTTCTACTATATATTAAACTCTTAAGTA
AGT
Found at i:63354593 original size:16 final size:17
Alignment explanation
Indices: 63354572--63354604 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
63354562 ACTTACATAT
*
63354572 TTAAA-TCATTAAAATA
1 TTAAATTCATAAAAATA
63354588 TTAAATTCATAAAAATA
1 TTAAATTCATAAAAATA
63354605 AAAGTAGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (17 bp):
TTAAATTCATAAAAATA
Found at i:63360028 original size:21 final size:23
Alignment explanation
Indices: 63359976--63360031 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 23
63359966 GGATGATCCT
*
63359976 AATTATATTTTTGAATTTTTTTAC
1 AATTA-ATTTTTGAATTTTTATAC
* *
63360000 TATCAATTTTT-AATTTTTATA-
1 AATTAATTTTTGAATTTTTATAC
63360021 AATTAATTTTT
1 AATTAATTTTT
63360032 TCTAACATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
21 9 0.33
22 9 0.33
23 6 0.22
24 3 0.11
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (23 bp):
AATTAATTTTTGAATTTTTATAC
Found at i:63366452 original size:18 final size:20
Alignment explanation
Indices: 63366421--63366460 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
63366411 TTAATTTTAA
*
63366421 TTTTTCAATATTATTTAATT
1 TTTTTCAATATTATGTAATT
63366441 TTTTTC-AT-TTATGTAATT
1 TTTTTCAATATTATGTAATT
63366459 TT
1 TT
63366461 AATTAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
19 2 0.11
20 6 0.32
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (20 bp):
TTTTTCAATATTATGTAATT
Found at i:63367997 original size:18 final size:18
Alignment explanation
Indices: 63367970--63368012 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
63367960 TGCCAGGTAC
*
63367970 GTATCATAACCCTTATAT
1 GTATCCTAACCCTTATAT
63367988 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
63368006 GTTTCCT
1 GTATCCT
63368013 TTTCCCAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.07, T:0.42
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:63368270 original size:21 final size:22
Alignment explanation
Indices: 63368228--63368271 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
63368218 CCAAACATCC
* * *
63368228 ACAACTATAAACCCTCGTTGGA
1 ACAACCATAAACCCCCGCTGGA
63368250 ACAACCAT-AACCCCCGCTGGA
1 ACAACCATAAACCCCCGCTGGA
63368271 A
1 A
63368272 GTTAAACCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.36, C:0.34, G:0.14, T:0.16
Consensus pattern (22 bp):
ACAACCATAAACCCCCGCTGGA
Found at i:63368495 original size:46 final size:46
Alignment explanation
Indices: 63368391--63368497 Score: 142
Period size: 46 Copynumber: 2.3 Consensus size: 46
63368381 TATTATTTCG
* * * ***
63368391 TTTAATAAAATAAAAGTTGTTTTTAATATTTTAATAGTATTATATT
1 TTTAATAAAATAGAAGTTCTTTTGAATAAGGTAATAGTATTATATT
* *
63368437 TTTAATAAAATAGAAGTTCTTTTGAATAAGGTAATATTTTTATATT
1 TTTAATAAAATAGAAGTTCTTTTGAATAAGGTAATAGTATTATATT
63368483 TTTAATAAAATAGAA
1 TTTAATAAAATAGAA
63368498 ATAATGCAAC
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 53 1.00
ACGTcount: A:0.43, C:0.01, G:0.08, T:0.48
Consensus pattern (46 bp):
TTTAATAAAATAGAAGTTCTTTTGAATAAGGTAATAGTATTATATT
Found at i:63371764 original size:34 final size:34
Alignment explanation
Indices: 63371716--63371803 Score: 92
Period size: 34 Copynumber: 2.6 Consensus size: 34
63371706 TAAAAAAATT
* *
63371716 AAACATAATTTAATTAATTT-TCTTAAAAACCC-T
1 AAACCTAATTTAATTAATTTAT-TTAAAAACCCAA
* * *
63371749 AAACCTTAATTTAATTTATTTATTTGAAACCCCAA
1 AAACC-TAATTTAATTAATTTATTTAAAAACCCAA
63371784 AAACCTAATTTAATT-ATTTA
1 AAACCTAATTTAATTAATTTA
63371804 AAAAACCCTA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
33 9 0.19
34 32 0.68
35 6 0.13
ACGTcount: A:0.43, C:0.15, G:0.01, T:0.41
Consensus pattern (34 bp):
AAACCTAATTTAATTAATTTATTTAAAAACCCAA
Found at i:63371816 original size:29 final size:32
Alignment explanation
Indices: 63371721--63371817 Score: 83
Period size: 34 Copynumber: 3.0 Consensus size: 32
63371711 AAATTAAACA
* *
63371721 TAATTTAATTAATTTTCTTAAAAACCCTAAACCT
1 TAATTTAATTTA-TTT-ATAAAAACCCTAAACCT
* * *
63371755 TAATTTAATTTATTTATTTGAAACCCCAAAAACC-
1 TAATTTAATTTATTTA--TAAAAACCC-TAAACCT
63371789 TAATTTAA-TTATTTA-AAAAACCCTAAACC
1 TAATTTAATTTATTTATAAAAACCCTAAACC
63371818 CTAAACCTAC
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
29 5 0.10
30 6 0.12
33 10 0.19
34 26 0.50
35 5 0.10
ACGTcount: A:0.43, C:0.18, G:0.01, T:0.38
Consensus pattern (32 bp):
TAATTTAATTTATTTATAAAAACCCTAAACCT
Found at i:63372989 original size:11 final size:11
Alignment explanation
Indices: 63372969--63373031 Score: 64
Period size: 11 Copynumber: 6.0 Consensus size: 11
63372959 TAAAAATTAA
63372969 AAAAAGTATTTT
1 AAAAA-TATTTT
63372981 AAAAATATTTT
1 AAAAATATTTT
63372992 --AAA-A--TT
1 AAAAATATTTT
*
63372998 AAAAAAATTTT
1 AAAAATATTTT
63373009 AAAAAATATTTT
1 -AAAAATATTTT
63373021 AAAAATATTTT
1 AAAAATATTTT
63373032 TAAATTGAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
6 2 0.05
8 4 0.09
9 4 0.09
11 19 0.43
12 15 0.34
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:63373001 original size:17 final size:17
Alignment explanation
Indices: 63372979--63373012 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
63372969 AAAAAGTATT
*
63372979 TTAAAAATATTTTAAAA
1 TTAAAAAAATTTTAAAA
63372996 TTAAAAAAATTTTAAAA
1 TTAAAAAAATTTTAAAA
63373013 AATATTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TTAAAAAAATTTTAAAA
Found at i:63373013 original size:40 final size:41
Alignment explanation
Indices: 63372960--63373076 Score: 157
Period size: 40 Copynumber: 2.9 Consensus size: 41
63372950 AATTTATTTT
63372960 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATT-AA
1 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTGAA
* *
63373000 AAAAATTTTAAAAAA-TATTTTAAAAATATTTTTAAATTGAA
1 AAAAA-TTAAAAAAAGTATTTTAAAAATATTTTAAAATTGAA
* * *
63373041 AAATAATAAAAAAAAGCATTTTAAAAATATTCTAAA
1 AAA-AATTAAAAAAAGTATTTTAAAAATATTTTAAA
63373077 CGGGCCTCGT
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
40 27 0.41
41 20 0.30
42 19 0.29
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.35
Consensus pattern (41 bp):
AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTGAA
Found at i:63373032 original size:12 final size:12
Alignment explanation
Indices: 63372996--63373035 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
63372986 TATTTTAAAA
*
63372996 TTAAAAAAATTT
1 TTAAAAATATTT
*
63373008 TAAAAAATA-TT
1 TTAAAAATATTT
63373019 TTAAAAATATTT
1 TTAAAAATATTT
63373031 TTAAA
1 TTAAA
63373036 TTGAAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TTAAAAATATTT
Found at i:63374721 original size:55 final size:55
Alignment explanation
Indices: 63374621--63374724 Score: 131
Period size: 55 Copynumber: 1.9 Consensus size: 55
63374611 TATGTAACAG
* ** * *
63374621 TCGATTTAAACATAAAAACAATTGATTCAAAAGAAGTAGTGTTCCAACATGACAA
1 TCGATTTAAAAATAAAAACAATTGATTCAAAAGAAACAATATTCCAACATGACAA
63374676 TCGATTTAAAAATATAAAA-AATAT-ATTCAAAAGAAACAATATTCCAACA
1 TCGATTTAAAAATA-AAAACAAT-TGATTCAAAAGAAACAATATTCCAACA
63374725 ATTAAGACAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
55 37 0.88
56 5 0.12
ACGTcount: A:0.52, C:0.13, G:0.09, T:0.26
Consensus pattern (55 bp):
TCGATTTAAAAATAAAAACAATTGATTCAAAAGAAACAATATTCCAACATGACAA
Found at i:63376842 original size:19 final size:21
Alignment explanation
Indices: 63376814--63376858 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
63376804 TTTAAGCATT
*
63376814 TAAA-AAGTAAA-AGA-ATAA
1 TAAATAAGTAAATAGATAAAA
63376832 TAAATAAGTAAATAGATAAAA
1 TAAATAAGTAAATAGATAAAA
63376853 TAAATA
1 TAAATA
63376859 TACATAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 7 0.30
20 3 0.13
21 9 0.39
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.22
Consensus pattern (21 bp):
TAAATAAGTAAATAGATAAAA
Found at i:63376866 original size:69 final size:68
Alignment explanation
Indices: 63376726--63377109 Score: 342
Period size: 69 Copynumber: 5.6 Consensus size: 68
63376716 AACAAATGAC
* * * * *
63376726 ATTAAATTGAAGTATTTAAAAAAAGTAAAATAATAAATAAGTGAATAAATAGATAAAACAAACAT
1 ATTAAATTTAAGTATTT--AAAAAGTAAAAGAAT-AATAAAT-AATAAATAGATAAAATAAATAT
63376791 AAATAAT
62 AAATAAT
* *
63376798 ATTAAATTTAAGCATTTAAAAAGTAAAAGAATAATAAATAAGTAAATAGATAAAATAAATATACA
1 ATTAAATTTAAGTATTTAAAAAGTAAAAGAATAATAAATAA-TAAATAGATAAAATAAATATAAA
63376863 TAAT
65 TAAT
* * * *
63376867 ATTAAATTTAAATATTTTAAAAGTAAAAGAATAATAAATAAATGAATAAATTGATAAAATATATA
1 ATTAAATTTAAGTATTTAAAAAGTAAAAG---AAT-AATAAAT-AATAAATAGATAAAATAAATA
63376932 TAAA-AAT
61 TAAATAAT
* * * *
63376939 ATTAAATTTAA--ACTTTTAAAAGATAAAAGAATAATAAACAAATAAATA-ATTATAATAGATAT
1 ATTAAATTTAAGTA-TTTAAAAAG-TAAAAGAATAATAAA-TAATAAATAGA-TAAAATAAATAT
63377001 AAATAAT
62 AAATAAT
* * * **
63377008 ATTAAATTTAGGTATTT----A--AAAA-AATAATGAATAATAAATATATAAAACGAATATAAAT
1 ATTAAATTTAAGTATTTAAAAAGTAAAAGAATAATAAATAATAAATAGATAAAATAAATATAAAT
63377066 AAT
66 AAT
* * *
63377069 ATTAACTTTTAGGTATTTAAAAAGT-GAAGAATAATAAATAA
1 ATTAA-ATTTAAGTATTTAAAAAGTAAAAGAATAATAAATAA
63377110 ATTAATATAT
Statistics
Matches: 263, Mismatches: 27, Indels: 48
0.78 0.08 0.14
Matches are distributed among these distances:
61 28 0.11
62 20 0.08
63 4 0.02
66 2 0.01
67 3 0.01
68 39 0.15
69 72 0.27
70 18 0.07
71 10 0.04
72 38 0.14
73 27 0.10
74 2 0.01
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.31
Consensus pattern (68 bp):
ATTAAATTTAAGTATTTAAAAAGTAAAAGAATAATAAATAATAAATAGATAAAATAAATATAAAT
AAT
Found at i:63376967 original size:141 final size:142
Alignment explanation
Indices: 63376726--63377047 Score: 397
Period size: 141 Copynumber: 2.3 Consensus size: 142
63376716 AACAAATGAC
* * *
63376726 ATTAAATTGAAGTATTTAAAAAAAGTAA--AATAATAAATAAGTGAATAAATAGATAAAACAAAC
1 ATTAAATTTAAATATTTAAAAAAA-TAATGAATAATAAATAAATGAATAAATAGATAAAACAAAC
* * *
63376789 ATAAATAATATTAAATTTAAGCATTTAAAAAGTAAAAGAATAATAAATAAGTAAATAGA-TAAAA
65 ATAAATAATATTAAATTTAAACATTTAAAAAGTAAAAGAATAATAAACAAATAAATA-ATTAAAA
*
63376853 TAAATATACATAAT
129 TAAATATAAATAAT
* * * *
63376867 ATTAAATTTAAATATTTTAAAAGTAA-AA-GAATAATAAATAAATGAATAAATTGATAAAATATA
1 ATTAAATTTAAATA-TTTAAAA-AAATAATGAATAATAAATAAATGAATAAATAGATAAAACAAA
* * *
63376930 TATAAA-AATATTAAATTTAAAC-TTTTAAAAGATAAAAGAATAATAAACAAATAAATAATTATA
64 CATAAATAATATTAAATTTAAACATTTAAAAAG-TAAAAGAATAATAAACAAATAAATAATTAAA
*
63376993 ATAGATATAAATAAT
128 ATAAATATAAATAAT
**
63377008 ATTAAATTTAGGTATTTAAAAAAATAATGAATAATAAATA
1 ATTAAATTTAAATATTTAAAAAAATAATGAATAATAAATA
63377048 TATAAAACGA
Statistics
Matches: 156, Mismatches: 18, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
139 2 0.01
140 18 0.12
141 92 0.59
142 42 0.27
143 2 0.01
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.31
Consensus pattern (142 bp):
ATTAAATTTAAATATTTAAAAAAATAATGAATAATAAATAAATGAATAAATAGATAAAACAAACA
TAAATAATATTAAATTTAAACATTTAAAAAGTAAAAGAATAATAAACAAATAAATAATTAAAATA
AATATAAATAAT
Found at i:63377134 original size:61 final size:61
Alignment explanation
Indices: 63376979--63377111 Score: 164
Period size: 61 Copynumber: 2.2 Consensus size: 61
63376969 ATAATAAACA
* * * *
63376979 AATAAATAATTATAATAGATATAAATAATATTAA-ATTTAGGTATTTAAAAAAATAATGAAT
1 AATAAATAAATAAAACA-ATATAAATAATATTAACTTTTAGGTATTTAAAAAAATAATGAAT
* *
63377040 AATAAATATATAAAACGAATATAAATAATATTAACTTTTAGGTATTT-AAAAAGTGAA-GAAT
1 AATAAATAAATAAAAC-AATATAAATAATATTAACTTTTAGGTATTTAAAAAAAT-AATGAAT
63377101 AATAAATAAAT
1 AATAAATAAAT
63377112 TAATATATAA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
61 48 0.77
62 14 0.23
ACGTcount: A:0.57, C:0.02, G:0.08, T:0.34
Consensus pattern (61 bp):
AATAAATAAATAAAACAATATAAATAATATTAACTTTTAGGTATTTAAAAAAATAATGAAT
Found at i:63379688 original size:37 final size:37
Alignment explanation
Indices: 63379643--63379719 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 37
63379633 TTCATATGAC
63379643 ATAATTCATTCGCATATCCATTATATTTAAACACATA
1 ATAATTCATTCGCATATCCATTATATTTAAACACATA
*
63379680 ATAATTCATTCGCATATCCATTATATTTAAACACGTA
1 ATAATTCATTCGCATATCCATTATATTTAAACACATA
63379717 ATA
1 ATA
63379720 TAAACAGATT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.38
Consensus pattern (37 bp):
ATAATTCATTCGCATATCCATTATATTTAAACACATA
Found at i:63379884 original size:82 final size:82
Alignment explanation
Indices: 63379783--63379942 Score: 221
Period size: 82 Copynumber: 2.0 Consensus size: 82
63379773 CCGGCTTTTG
* *
63379783 GCCTGCTAGACTTAAAGTCTGAAATATTTCACCGGCATCAAGACTGCTAGACATAAAGTCTAAAT
1 GCCTGCTAGACATAAAGTCTGAAATATTTCACCGGCATCAAGACTGCTAGAAATAAAGTCTAAAT
* *
63379848 TGTTTCACTGGCATCCA
66 TATCTCACTGGCATCCA
* * * * * * *
63379865 GCCTGCTAGACATAGAGTCTGAATTGTTTCACCGGCATCCAGTCTGCTAGAAATAGAGTCTGAAT
1 GCCTGCTAGACATAAAGTCTGAAATATTTCACCGGCATCAAGACTGCTAGAAATAAAGTCTAAAT
63379930 TATCTCACTGGCA
66 TATCTCACTGGCA
63379943 ATAAGCCTTC
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
82 67 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.28
Consensus pattern (82 bp):
GCCTGCTAGACATAAAGTCTGAAATATTTCACCGGCATCAAGACTGCTAGAAATAAAGTCTAAAT
TATCTCACTGGCATCCA
Found at i:63379929 original size:41 final size:41
Alignment explanation
Indices: 63379785--63379930 Score: 193
Period size: 41 Copynumber: 3.6 Consensus size: 41
63379775 GGCTTTTGGC
* * * * *
63379785 CTGCTAGACTTAAAGTCTGAAATATTTCACCGGCATCAAGA
1 CTGCTAGACATAGAGTCTGAATTGTTTCACCGGCATCCAGA
* * * *
63379826 CTGCTAGACATAAAGTCTAAATTGTTTCACTGGCATCCAGC
1 CTGCTAGACATAGAGTCTGAATTGTTTCACCGGCATCCAGA
*
63379867 CTGCTAGACATAGAGTCTGAATTGTTTCACCGGCATCCAGT
1 CTGCTAGACATAGAGTCTGAATTGTTTCACCGGCATCCAGA
*
63379908 CTGCTAGAAATAGAGTCTGAATT
1 CTGCTAGACATAGAGTCTGAATT
63379931 ATCTCACTGG
Statistics
Matches: 93, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 93 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (41 bp):
CTGCTAGACATAGAGTCTGAATTGTTTCACCGGCATCCAGA
Found at i:63388133 original size:31 final size:31
Alignment explanation
Indices: 63388046--63388142 Score: 96
Period size: 31 Copynumber: 3.2 Consensus size: 31
63388036 TTGGTACCTG
63388046 AACTTGACACTTTTTTCTTAATTTAGTATCTA
1 AACTTGACA-TTTTTTCTTAATTTAGTATCTA
* * *
63388078 AATCTT----TTTTTAACTCAACTTAGTA-CATA
1 AA-CTTGACATTTTT-TCTTAATTTAGTATC-TA
63388107 AACTTGACATTTTTTCTTAATTTAGTATCTA
1 AACTTGACATTTTTTCTTAATTTAGTATCTA
63388138 AACTT
1 AACTT
63388143 TTTTGGACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 17
0.69 0.08 0.23
Matches are distributed among these distances:
28 9 0.18
29 14 0.27
31 17 0.33
32 8 0.16
33 3 0.06
ACGTcount: A:0.31, C:0.15, G:0.05, T:0.48
Consensus pattern (31 bp):
AACTTGACATTTTTTCTTAATTTAGTATCTA
Found at i:63388162 original size:59 final size:61
Alignment explanation
Indices: 63388046--63388167 Score: 185
Period size: 60 Copynumber: 2.0 Consensus size: 61
63388036 TTGGTACCTG
* *
63388046 AACTTGACACTTTTTTCTTAATTTAGTATCTAAATCTTTTTTTAACTCAACTTAGTACATA
1 AACTTGACACTTTTTTCTTAATTTAGTATCTAAATCTTTTTTGAACCCAACTTAGTACATA
* * *
63388107 AACTTGACA-TTTTTTCTTAATTTAGTATCTAAA-CTTTTTTGGACCCAATTTAGTACCTA
1 AACTTGACACTTTTTTCTTAATTTAGTATCTAAATCTTTTTTGAACCCAACTTAGTACATA
63388166 AA
1 AA
63388168 TTTATTAAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
59 23 0.41
60 24 0.43
61 9 0.16
ACGTcount: A:0.31, C:0.16, G:0.07, T:0.46
Consensus pattern (61 bp):
AACTTGACACTTTTTTCTTAATTTAGTATCTAAATCTTTTTTGAACCCAACTTAGTACATA
Found at i:63391846 original size:27 final size:28
Alignment explanation
Indices: 63391797--63391850 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
63391787 TGGATGGTGC
* *
63391797 AAATAACTTTTATATATTATTATTTTCG
1 AAATAACTATAATATATTATTATTTTCG
63391825 AAATAACTATAATA-ATTATTATTTTC
1 AAATAACTATAATATATTATTATTTTC
63391851 ATTTACATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 12 0.50
28 12 0.50
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (28 bp):
AAATAACTATAATATATTATTATTTTCG
Found at i:63399623 original size:4 final size:4
Alignment explanation
Indices: 63399614--63399642 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
63399604 ATTTAAGGGA
63399614 TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG T
63399643 CGATGTTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:63403893 original size:18 final size:19
Alignment explanation
Indices: 63403852--63403898 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
63403842 CATTACAACC
63403852 CAAAAAGAAAAAGGAGATA
1 CAAAAAGAAAAAGGAGATA
* * *
63403871 GAAAAAGAAAAGGGGGAT-
1 CAAAAAGAAAAAGGAGATA
63403889 CAAAAAGAAA
1 CAAAAAGAAA
63403899 GAACATATCC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.66, C:0.04, G:0.26, T:0.04
Consensus pattern (19 bp):
CAAAAAGAAAAAGGAGATA
Found at i:63416970 original size:21 final size:22
Alignment explanation
Indices: 63416930--63416970 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
63416920 ATAATTTAAA
*
63416930 ATTTTCAAAAAATATGAAAACT
1 ATTTTCAAAAAATATAAAAACT
*
63416952 ATTTT-AAAAATTATAAAAA
1 ATTTTCAAAAAATATAAAAA
63416971 AAATATTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (22 bp):
ATTTTCAAAAAATATAAAAACT
Found at i:63420340 original size:14 final size:14
Alignment explanation
Indices: 63420323--63420357 Score: 61
Period size: 14 Copynumber: 2.4 Consensus size: 14
63420313 CTCACATTTC
63420323 TTTTCTTTTCTCCA
1 TTTTCTTTTCTCCA
63420337 TTTTCTTTTCTCCA
1 TTTTCTTTTCTCCA
63420351 TATTTCT
1 T-TTTCT
63420358 GCTTCTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.09, C:0.26, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTTCTTTTCTCCA
Found at i:63420341 original size:19 final size:18
Alignment explanation
Indices: 63420303--63420347 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
63420293 TACGGTACGC
63420303 TTCTTTTC-TTCTCACAT
1 TTCTTTTCTTTCTCACAT
63420320 TTCTTTTCTTTTCTC-CATT
1 TTCTTTTC-TTTCTCACA-T
63420339 TTCTTTTCT
1 TTCTTTTCT
63420348 CCATATTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.32
18 3 0.12
19 14 0.56
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.67
Consensus pattern (18 bp):
TTCTTTTCTTTCTCACAT
Found at i:63421035 original size:41 final size:41
Alignment explanation
Indices: 63420990--63421082 Score: 177
Period size: 41 Copynumber: 2.2 Consensus size: 41
63420980 TACATTGTGA
63420990 ATTTGTGTAGTTGAAATGCTAAGTTGTAGGAGGTGTTGAGT
1 ATTTGTGTAGTTGAAATGCTAAGTTGTAGGAGGTGTTGAGT
63421031 ATTTGTGTAGTTGAAATGCTAAGTTGTAGGAGGTGTTGAGT
1 ATTTGTGTAGTTGAAATGCTAAGTTGTAGGAGGTGTTGAGT
63421072 ATTTGTAGTAG
1 ATTTGT-GTAG
63421083 GTCGAAGTTG
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 47 0.92
42 4 0.08
ACGTcount: A:0.25, C:0.02, G:0.33, T:0.40
Consensus pattern (41 bp):
ATTTGTGTAGTTGAAATGCTAAGTTGTAGGAGGTGTTGAGT
Found at i:63421100 original size:20 final size:19
Alignment explanation
Indices: 63421077--63421136 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
63421067 TGAGTATTTG
63421077 TAGTAGGTCGA-AGTTGTAAT
1 TAGTAGGT-GACA-TTGTAAT
*
63421097 TAGTAGGTTACATTGTAAT
1 TAGTAGGTGACATTGTAAT
*
63421116 TAGTAGGTTACATTGTGAAT
1 TAGTAGGTGACATTGT-AAT
63421136 T
1 T
63421137 TGTGTAGTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
19 24 0.65
20 13 0.35
ACGTcount: A:0.30, C:0.05, G:0.25, T:0.40
Consensus pattern (19 bp):
TAGTAGGTGACATTGTAAT
Found at i:63421114 original size:19 final size:19
Alignment explanation
Indices: 63421090--63421136 Score: 85
Period size: 19 Copynumber: 2.4 Consensus size: 19
63421080 TAGGTCGAAG
63421090 TTGTAATTAGTAGGTTACA
1 TTGTAATTAGTAGGTTACA
63421109 TTGTAATTAGTAGGTTACA
1 TTGTAATTAGTAGGTTACA
63421128 TTGTGAATT
1 TTGT-AATT
63421137 TGTGTAGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 23 0.85
20 4 0.15
ACGTcount: A:0.30, C:0.04, G:0.21, T:0.45
Consensus pattern (19 bp):
TTGTAATTAGTAGGTTACA
Found at i:63422926 original size:16 final size:17
Alignment explanation
Indices: 63422907--63422938 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
63422897 TTATTAAATC
63422907 ATATATTTAA-ATTAAA
1 ATATATTTAATATTAAA
63422923 ATATATTTAATATTAA
1 ATATATTTAATATTAA
63422939 TTATTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATATTTAATATTAAA
Found at i:63423002 original size:66 final size:63
Alignment explanation
Indices: 63422931--63423143 Score: 194
Period size: 61 Copynumber: 3.4 Consensus size: 63
63422921 AAATATATTT
63422931 AATATTAATTATTTAA-AATTTTATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATA
1 AATATTAATTA-TTAAGAATTTTA--TTA-AGTATCATATATTATGATTTGAGTAAATTCATATA
63422995 AG
62 AG
* * * * * * *
63422997 AATATTAATTATTAAGAATTTTATTAA--ATTATATATTTTAATTAT-ATTATATTTA-ATAAT
1 AATATTAATTATTAAGAATTTTATTAAGTATCATATATTATGATT-TGAGTAAATTCATATAAG
* * * *
63423057 AATTATGTTATT-TT-A-TATTTTA--CAGTATCATATATTATGGTTTGAGTAAATTCATATAAG
1 AA-TAT-TAATTATTAAGAATTTTATTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
63423117 AATATTAATTATTAAGAATTTTATTAA
1 AATATTAATTATTAAGAATTTTATTAA
63423144 ATTATATATT
Statistics
Matches: 113, Mismatches: 21, Indels: 29
0.69 0.13 0.18
Matches are distributed among these distances:
57 1 0.01
58 5 0.04
59 30 0.27
60 14 0.12
61 31 0.27
62 5 0.04
63 2 0.02
64 3 0.03
65 4 0.04
66 18 0.16
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (63 bp):
AATATTAATTATTAAGAATTTTATTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
Done.