Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 130 of 187
Found at i:39490635 original size:59 final size:59
Alignment explanation
Indices: 39490564--39490682 Score: 229
Period size: 59 Copynumber: 2.0 Consensus size: 59
39490554 TGTAATTAAG
39490564 TAAATTAGAAAATTAATCAAAAGATGATAAAATAATCATCTTCATCTTCTTCCTTTTCT
1 TAAATTAGAAAATTAATCAAAAGATGATAAAATAATCATCTTCATCTTCTTCCTTTTCT
*
39490623 TAAATTAGAAAATTCATCAAAAGATGATAAAATAATCATCTTCATCTTCTTCCTTTTCT
1 TAAATTAGAAAATTAATCAAAAGATGATAAAATAATCATCTTCATCTTCTTCCTTTTCT
39490682 T
1 T
39490683 TTATTGAAAA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.39
Consensus pattern (59 bp):
TAAATTAGAAAATTAATCAAAAGATGATAAAATAATCATCTTCATCTTCTTCCTTTTCT
Found at i:39492883 original size:39 final size:42
Alignment explanation
Indices: 39492838--39492918 Score: 114
Period size: 44 Copynumber: 2.0 Consensus size: 42
39492828 TATTTAAGTA
*
39492838 TTGATACCTTTTG-TT-AAA-ACAATAGTATAGTATTTTGTT
1 TTGATACCTTTTGTTTGAAAGAAAATAGTATAGTATTTTGTT
39492877 TTGATACCTTTTGTTTTGAAATGAAAATAGTATAGTATTTTG
1 TTGATACCTTTTG-TTTGAAA-GAAAATAGTATAGTATTTTG
39492919 GTATTGATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
39 13 0.36
41 2 0.06
42 3 0.08
44 18 0.50
ACGTcount: A:0.31, C:0.06, G:0.15, T:0.48
Consensus pattern (42 bp):
TTGATACCTTTTGTTTGAAAGAAAATAGTATAGTATTTTGTT
Found at i:39495143 original size:41 final size:41
Alignment explanation
Indices: 39495086--39495166 Score: 162
Period size: 41 Copynumber: 2.0 Consensus size: 41
39495076 TTGCGGCTAG
39495086 GATAGGAATATACATAATGCCCTAATCAACCCGATAGGTTT
1 GATAGGAATATACATAATGCCCTAATCAACCCGATAGGTTT
39495127 GATAGGAATATACATAATGCCCTAATCAACCCGATAGGTT
1 GATAGGAATATACATAATGCCCTAATCAACCCGATAGGTT
39495167 GAACAAATGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (41 bp):
GATAGGAATATACATAATGCCCTAATCAACCCGATAGGTTT
Found at i:39497758 original size:74 final size:73
Alignment explanation
Indices: 39497579--39497770 Score: 188
Period size: 74 Copynumber: 2.6 Consensus size: 73
39497569 CAGGTGAAAA
* * * *
39497579 AATAGTGTTTAGTTGCCCTTTTTAGGTTAAACCTACACGATAAACATCAATTGCTCATCCAAGCT
1 AATAGTGTTT-GTTG-CCTGTTTGGGTTAAACCTACACAACAAACATCAATTGCTCATCCAAGCT
*
39497644 AATCATGAAC
64 AATCATAAAC
* * * ** * **
39497654 AATAGTGTTTGGTTACCCAG-TCGGGTTAAACCTACACAACAAGTATCAATTGCTTATCTGAGCT
1 AATAGTGTTT-GTT-GCCTGTTTGGGTTAAACCTACACAACAAACATCAATTGCTCATCCAAGCT
*
39497718 TATCATAAAC
64 AATCATAAAC
* *
39497728 AATAGTGTTTGCTTGCCTGTTTGGGATAAACCTACACAGCAAA
1 AATAGTGTTTG-TTGCCTGTTTGGGTTAAACCTACACAACAAA
39497771 TGTAACAACT
Statistics
Matches: 93, Mismatches: 21, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
73 4 0.04
74 74 0.80
75 15 0.16
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.31
Consensus pattern (73 bp):
AATAGTGTTTGTTGCCTGTTTGGGTTAAACCTACACAACAAACATCAATTGCTCATCCAAGCTAA
TCATAAAC
Found at i:39499303 original size:16 final size:16
Alignment explanation
Indices: 39499265--39499304 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
39499255 TTTTTTGTGT
*
39499265 TTAAATCGGTTAATTC
1 TTAAATTGGTTAATTC
39499281 TTAAATTGGTTAATTC
1 TTAAATTGGTTAATTC
39499297 TTAAATTG
1 TTAAATTG
39499305 ATCCCTGCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.47
Consensus pattern (16 bp):
TTAAATTGGTTAATTC
Found at i:39508175 original size:18 final size:19
Alignment explanation
Indices: 39508131--39508179 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
39508121 CCAAAATGAA
39508131 ATTGAGAAAAGAAAAAAATG
1 ATTGA-AAAAGAAAAAAATG
** *
39508151 AGAGAAAAAGAAAAAGA-G
1 ATTGAAAAAGAAAAAAATG
39508169 ATTGAAAAAGA
1 ATTGAAAAAGA
39508180 GCAAAAAGCG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
18 10 0.42
19 11 0.46
20 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.22, T:0.10
Consensus pattern (19 bp):
ATTGAAAAAGAAAAAAATG
Found at i:39530918 original size:13 final size:13
Alignment explanation
Indices: 39530897--39530934 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
39530887 TTTATAAATT
*
39530897 ATAAGATATTTAA
1 ATAAAATATTTAA
39530910 ATAAAATATTTAA
1 ATAAAATATTTAA
39530923 A-AAAATTATTTA
1 ATAAAA-TATTTA
39530935 GGTGGACTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 4 0.17
13 19 0.83
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (13 bp):
ATAAAATATTTAA
Found at i:39533270 original size:22 final size:23
Alignment explanation
Indices: 39533242--39533294 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
39533232 ACACATTAGC
39533242 AAACAAATATATAAATAT-AAAT
1 AAACAAATATATAAATATAAAAT
* *
39533264 AAACAAATATTTATATATAAAAT
1 AAACAAATATATAAATATAAAAT
*
39533287 AAATAAAT
1 AAACAAAT
39533295 TGAATAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 16 0.59
23 11 0.41
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (23 bp):
AAACAAATATATAAATATAAAAT
Found at i:39533300 original size:28 final size:29
Alignment explanation
Indices: 39533248--39533313 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
39533238 TAGCAAACAA
39533248 ATATATAAATATAAATAAACAAAT-ATTT
1 ATATATAAATATAAATAAACAAATAATTT
**
39533276 ATATATAAA-ATAAATAAATTGAATAATTT
1 ATATATAAATATAAATAAA-CAAATAATTT
*
39533305 ATATTTAAA
1 ATATATAAA
39533314 CTATCAAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 9 0.27
28 12 0.36
29 12 0.36
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (29 bp):
ATATATAAATATAAATAAACAAATAATTT
Found at i:39538517 original size:87 final size:88
Alignment explanation
Indices: 39538411--39538622 Score: 306
Period size: 87 Copynumber: 2.4 Consensus size: 88
39538401 TATTAAACAC
*
39538411 CAGGAATAAATCCCAAAACAGATTTTATTTAATTTTAAAT-TCTCGTTTGGAAACAAAAT-AAAA
1 CAGGAATAAATCCCTAAACAGATTTTATTTAATTTTAAATAT-TCGTTTGGAAACAAAATCAAAA
* *
39538474 AATGGAATAAAATATGTTGAATGA
65 AATGAAATAAAATATGTTGAACGA
* * *
39538498 CGGGAATAAATCCCTAAACAGATTTTATTTAATTTT-AATATTCGTTTTGAAACAAAGTCAAAAA
1 CAGGAATAAATCCCTAAACAGATTTTATTTAATTTTAAATATTCGTTTGGAAACAAAATCAAAAA
39538562 ATGAAATAAAATATGTTGAACGA
66 ATGAAATAAAATATGTTGAACGA
*
39538585 CAGGAATAAAT-CCTAAAACAGATTTTATTCAATATTTA
1 CAGGAATAAATCCCT-AAACAGATTTTATTTAAT-TTTA
39538623 TTTTTATTTT
Statistics
Matches: 112, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
86 21 0.19
87 88 0.79
88 3 0.03
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (88 bp):
CAGGAATAAATCCCTAAACAGATTTTATTTAATTTTAAATATTCGTTTGGAAACAAAATCAAAAA
ATGAAATAAAATATGTTGAACGA
Found at i:39539016 original size:14 final size:14
Alignment explanation
Indices: 39538997--39539028 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
39538987 GATGATCAAA
39538997 GCAGTAACACCTCT
1 GCAGTAACACCTCT
39539011 GCAGTAACACCTCT
1 GCAGTAACACCTCT
39539025 GCAG
1 GCAG
39539029 CAATCAACGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.28, C:0.34, G:0.19, T:0.19
Consensus pattern (14 bp):
GCAGTAACACCTCT
Found at i:39540069 original size:20 final size:20
Alignment explanation
Indices: 39540044--39540082 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
39540034 GTTAATGTGA
39540044 AAATTTGTCACTATATTTTG
1 AAATTTGTCACTATATTTTG
39540064 AAATTTGTCACTATATTTT
1 AAATTTGTCACTATATTTT
39540083 ACTTTAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (20 bp):
AAATTTGTCACTATATTTTG
Found at i:39540127 original size:29 final size:29
Alignment explanation
Indices: 39540061--39540127 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
39540051 TCACTATATT
* *
39540061 TTGAAATTTGTCACTATATTTTACTTTAA
1 TTGAAATTTGCCACTATATTTTACTCTAA
* *
39540090 TTGATATTTGCCATTATATTTTACTCTATA
1 TTGAAATTTGCCACTATATTTTACTCTA-A
39540120 TT-AAATTT
1 TTGAAATTT
39540128 TACATTTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 29 0.91
30 3 0.09
ACGTcount: A:0.30, C:0.10, G:0.06, T:0.54
Consensus pattern (29 bp):
TTGAAATTTGCCACTATATTTTACTCTAA
Found at i:39542620 original size:19 final size:18
Alignment explanation
Indices: 39542593--39542644 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
39542583 GTAAGGGTTA
*
39542593 ATTTCATTTTTTTAATATT
1 ATTTAATTTTTTTAAT-TT
*
39542612 ATTTAATTTTTATAATTT
1 ATTTAATTTTTTTAATTT
*
39542630 AATTAATATTTTTTA
1 ATTTAAT-TTTTTTA
39542645 TAATTTTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 8 0.29
19 20 0.71
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTTAATTTTTTTAATTT
Found at i:39544691 original size:59 final size:59
Alignment explanation
Indices: 39544585--39544778 Score: 298
Period size: 59 Copynumber: 3.3 Consensus size: 59
39544575 ATTGATTTAT
* * *
39544585 TTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTCATTAAATAAAATGGAAGTTC
1 TTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTA
* * *
39544644 TTTTGAATATTTTTGTACAAATTATTTTTATATGGTTTTATTTAATAAAATAAAAGTTA
1 TTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTA
* * * *
39544703 TTTTGAATATTTTTATACAACTTATTTTTATATTATTTCATTTAATAAAATAGAAGTTT
1 TTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTA
39544762 TTTTGAATATTTTTGTA
1 TTTTGAATATTTTTGTA
39544779 AATATATTAT
Statistics
Matches: 121, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 121 1.00
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.54
Consensus pattern (59 bp):
TTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTA
Found at i:39544867 original size:29 final size:29
Alignment explanation
Indices: 39544830--39544908 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 29
39544820 AAAAAAAATT
* * *
39544830 CATCTTGTCAAAATAATTTTTTCAGAACA
1 CATCATGTCAAAATTATTTTTTCAAAACA
* *
39544859 CATCATGTCAAATTTATTTTTTCAAAATA
1 CATCATGTCAAAATTATTTTTTCAAAACA
39544888 CAT-ATTGTCAAAATTATTTTT
1 CATCA-TGTCAAAATTATTTTT
39544909 CCCATAACAA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
28 1 0.02
29 42 0.98
ACGTcount: A:0.37, C:0.14, G:0.05, T:0.44
Consensus pattern (29 bp):
CATCATGTCAAAATTATTTTTTCAAAACA
Found at i:39544978 original size:24 final size:23
Alignment explanation
Indices: 39544937--39544981 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
39544927 AATTAAAAAA
*
39544937 AATTAAACCCTAAAACCCTAAAC
1 AATTAAAACCTAAAACCCTAAAC
*
39544960 AATTAAAAACCTAATACCCTAA
1 AATT-AAAACCTAAAACCCTAA
39544982 TTTAATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.53, C:0.27, G:0.00, T:0.20
Consensus pattern (23 bp):
AATTAAAACCTAAAACCCTAAAC
Found at i:39545634 original size:22 final size:20
Alignment explanation
Indices: 39545603--39545643 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
39545593 AAATTTAAAA
39545603 ATTTTAAAAATATATAAAAATT
1 ATTTTAAAAA-A-ATAAAAATT
*
39545625 ATTTTTAAAAAATAAAAAT
1 ATTTTAAAAAAATAAAAAT
39545644 CATTAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 1 0.06
22 9 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATTTTAAAAAAATAAAAATT
Found at i:39546450 original size:31 final size:31
Alignment explanation
Indices: 39546393--39546454 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
39546383 ATTATTATTT
** *
39546393 TAGTTAAATTTGATGATCAATTTTTTAAAAA
1 TAGTTAAATTTGACAATCAATCTTTTAAAAA
39546424 TAGTTAAATTTGACAA-CTAATCTTTTAAAAA
1 TAGTTAAATTTGACAATC-AATCTTTTAAAAA
39546455 AAATTGAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 1 0.04
31 26 0.96
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (31 bp):
TAGTTAAATTTGACAATCAATCTTTTAAAAA
Found at i:39554716 original size:9 final size:9
Alignment explanation
Indices: 39554702--39554732 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
39554692 GTTAAACGAA
39554702 TCGAGTTAT
1 TCGAGTTAT
*
39554711 TCGAGTTAA
1 TCGAGTTAT
39554720 TCGAGTTAT
1 TCGAGTTAT
39554729 TCGA
1 TCGA
39554733 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:39562759 original size:68 final size:70
Alignment explanation
Indices: 39562667--39562815 Score: 191
Period size: 69 Copynumber: 2.2 Consensus size: 70
39562657 GTCATAGCTG
* *
39562667 AGCCATGG-CTTATACCTCGAAATCCCTGT-TTTACTATC-CTGATGAACTAACCTAGTTGCCAT
1 AGCCATGGTCTTATACCTCAAAATCCCTATGTTTACTATCTC-GATGAACTAACCTAGTTGCCAT
39562729 AG-CCA
65 AGTCCA
* * **
39562734 AGCCATGGTCTTATACCTCAAAATCCCTATGTTTACTATCTCGGTGGACTAACCTAGTTTTCATA
1 AGCCATGGTCTTATACCTCAAAATCCCTATGTTTACTATCTCGATGAACTAACCTAGTTGCCATA
39562799 GTCCA
66 GTCCA
*
39562804 A-CCATGTTCTTA
1 AGCCATGGTCTTA
39562816 CATAGTATAT
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
67 8 0.11
68 19 0.27
69 39 0.55
70 5 0.07
ACGTcount: A:0.26, C:0.27, G:0.14, T:0.33
Consensus pattern (70 bp):
AGCCATGGTCTTATACCTCAAAATCCCTATGTTTACTATCTCGATGAACTAACCTAGTTGCCATA
GTCCA
Found at i:39562836 original size:69 final size:69
Alignment explanation
Indices: 39562696--39563114 Score: 180
Period size: 69 Copynumber: 6.1 Consensus size: 69
39562686 AAATCCCTGT
* * * * *
39562696 TTTACTATCCT-G-ATGAACTAACCTAGTTGCCATAG-CCAAGCCATGGTCTTATACCT-CAAAA
1 TTTACTATCCTGGCA-G-ACTAACCTAGTTGTCATAGTCCAA-CCATGGTCTTACA-CTGTATAT
39562757 T-CCCTATG
62 TCCCCT-TG
** * *
39562765 TTTACTAT-CTCGGTGGACTAACCTAGTTTTCATAGTCCAACCATGTTCTTACA-TAGTATATTC
1 TTTACTATCCT-GGCAGACTAACCTAGTTGTCATAGTCCAACCATGGTCTTACACT-GTATATTC
39562828 CCCTTG
64 CCCTTG
** * * * * *
39562834 TTTGTTGTCCTGGCAGACTATCCTGGTTGTCATAGTCTAACCATGGTCTTACACTGTATATTCCT
1 TTTACTATCCTGGCAGACTAACCTAGTTGTCATAGTCCAACCATGGTCTTACACTGTATATTCCC
*
39562899 CGTG
66 CTTG
* * * * * **
39562903 TTTACTGTCCTGG-TGAACTATCC-AGGTTG-CTATAATCCAACCATAGTCTTACACCATATATT
1 TTTACTATCCTGGCAG-ACTAACCTA-GTTGTC-ATAGTCCAACCATGGTCTTACACTGTATATT
**
39562965 -CATTATG
63 CCCCT-TG
* * * * * * * * * * **
39562972 TTTACTGTCCCGG-TGAACTATCCTGGTTGCCATTGTCCAACAATGGTATTATACTGTATATTTA
1 TTTACTATCCTGGCAG-ACTAACCTAGTTGTCATAGTCCAACCATGGTCTTACACTGTATATTCC
* **
39563036 TCGGG
65 CCTTG
* ** * * * * * *
39563041 TTTACTGTTATGGCAGACTATCTTGGTTGCCATAGTCCAACCATGGTCTTA-ACCGTATATTCCT
1 TTTACTATCCTGGCAGACTAACCTAGTTGTCATAGTCCAACCATGGTCTTACACTGTATATTCCC
*
39563105 CATG
66 CTTG
39563109 TTTACT
1 TTTACT
39563115 CAGAGCTTCG
Statistics
Matches: 273, Mismatches: 60, Indels: 35
0.74 0.16 0.10
Matches are distributed among these distances:
67 1 0.00
68 23 0.08
69 234 0.86
70 15 0.05
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.37
Consensus pattern (69 bp):
TTTACTATCCTGGCAGACTAACCTAGTTGTCATAGTCCAACCATGGTCTTACACTGTATATTCCC
CTTG
Found at i:39562974 original size:138 final size:137
Alignment explanation
Indices: 39562850--39563114 Score: 316
Period size: 138 Copynumber: 1.9 Consensus size: 137
39562840 GTCCTGGCAG
* * * * * * *
39562850 ACTATCCTGGTTGTCATAGTCTAACCATGGTCTTACACTGTATATTCCTCGTGTTTACTGTCCTG
1 ACTATCCTGGTTGCCATAGTCCAACAATGGTATTACACTGTATATTCATCGGGTTTACTGTCATG
* * *
39562915 G-TGAACTATCCAGGTTGCTATAATCCAACCATAGTCTTACACCATATATTCATTATGTTTACTG
66 GCAG-ACTATCCAGGTTGCCATAATCCAACCATAGTCTTA-ACCATATATTCATCATGTTTACTG
*
39562979 TCCCGGTGA
129 TCCCGGAGA
* * * *
39562988 ACTATCCTGGTTGCCATTGTCCAACAATGGTATTATACTGTATATTTATCGGGTTTACTGTTATG
1 ACTATCCTGGTTGCCATAGTCCAACAATGGTATTACACTGTATATTCATCGGGTTTACTGTCATG
** * * * *
39563053 GCAGACTATCTTGGTTGCCATAGTCCAACCATGGTCTTAACCGTATATTCCTCATGTTTACT
66 GCAGACTATCCAGGTTGCCATAATCCAACCATAGTCTTAACCATATATTCATCATGTTTACT
39563115 CAGAGCTTCG
Statistics
Matches: 106, Mismatches: 20, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
137 20 0.19
138 85 0.80
139 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.38
Consensus pattern (137 bp):
ACTATCCTGGTTGCCATAGTCCAACAATGGTATTACACTGTATATTCATCGGGTTTACTGTCATG
GCAGACTATCCAGGTTGCCATAATCCAACCATAGTCTTAACCATATATTCATCATGTTTACTGTC
CCGGAGA
Found at i:39565569 original size:41 final size:39
Alignment explanation
Indices: 39565500--39565583 Score: 123
Period size: 41 Copynumber: 2.1 Consensus size: 39
39565490 ATAAACAGTA
* *
39565500 ATAAACATAACATATATAATATCCTACTAATATACATAC
1 ATAAACATAACATACAAAATATCCTACTAATATACATAC
*
39565539 ATAAACATTAATATACAAAATATCCATACTAATATACATAC
1 ATAAACA-TAACATACAAAATATCC-TACTAATATACATAC
39565580 ATAA
1 ATAA
39565584 TAGACATAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
39 7 0.17
40 14 0.35
41 19 0.47
ACGTcount: A:0.54, C:0.17, G:0.00, T:0.30
Consensus pattern (39 bp):
ATAAACATAACATACAAAATATCCTACTAATATACATAC
Found at i:39565573 original size:21 final size:22
Alignment explanation
Indices: 39565517--39565578 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 22
39565507 TAACATATAT
39565517 AATATCC-TACTAATATACATA
1 AATATCCATACTAATATACATA
* **
39565538 CATAAACAT--TAATATACA-A
1 AATATCCATACTAATATACATA
39565557 AATATCCATACTAATATACATA
1 AATATCCATACTAATATACATA
39565579 CATAATAGAC
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
19 7 0.23
20 9 0.29
21 13 0.42
22 2 0.06
ACGTcount: A:0.52, C:0.18, G:0.00, T:0.31
Consensus pattern (22 bp):
AATATCCATACTAATATACATA
Found at i:39565578 original size:12 final size:12
Alignment explanation
Indices: 39565524--39565601 Score: 62
Period size: 12 Copynumber: 7.0 Consensus size: 12
39565514 TATAATATCC
39565524 TACTAATATACA
1 TACTAATATACA
*
39565536 TAC--ATAAACA
1 TACTAATATACA
39565546 T--TAATATACA
1 TACTAATATACA
*
39565556 -A--AATATCCA
1 TACTAATATACA
39565565 TACTAATATACA
1 TACTAATATACA
*
39565577 TACATAATAGACA
1 TAC-TAATATACA
*
39565590 TAATAATATACA
1 TACTAATATACA
39565602 ATTGACTGAC
Statistics
Matches: 52, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
9 7 0.13
10 14 0.27
12 21 0.40
13 10 0.19
ACGTcount: A:0.54, C:0.15, G:0.01, T:0.29
Consensus pattern (12 bp):
TACTAATATACA
Found at i:39565579 original size:25 final size:25
Alignment explanation
Indices: 39565551--39565601 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
39565541 AAACATTAAT
** *
39565551 ATACAAAATATCCATACTAATATAC
1 ATACAAAATAGACATAATAATATAC
*
39565576 ATACATAATAGACATAATAATATAC
1 ATACAAAATAGACATAATAATATAC
39565601 A
1 A
39565602 ATTGACTGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.55, C:0.16, G:0.02, T:0.27
Consensus pattern (25 bp):
ATACAAAATAGACATAATAATATAC
Found at i:39568126 original size:19 final size:20
Alignment explanation
Indices: 39568089--39568126 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
39568079 GGAGTGAGTT
* *
39568089 AATATTTTTTTTAAGAAATA
1 AATAATTTTTATAAGAAATA
39568109 AATAATTTTTATAA-AAAT
1 AATAATTTTTATAAGAAAT
39568127 TCCAAGATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
AATAATTTTTATAAGAAATA
Found at i:39570542 original size:19 final size:19
Alignment explanation
Indices: 39570510--39570553 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
39570500 ATGTTCTTAC
* * *
39570510 TAAAAATTAGAAAAGATTA
1 TAAAAATAAAAAAAAATTA
*
39570529 TAAAAATAAAAAAAAATTT
1 TAAAAATAAAAAAAAATTA
39570548 TAAAAA
1 TAAAAA
39570554 ATTTAAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (19 bp):
TAAAAATAAAAAAAAATTA
Found at i:39570582 original size:17 final size:17
Alignment explanation
Indices: 39570546--39570598 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
39570536 AAAAAAAAAT
* *
39570546 TTTAAAAAATTTA-AAT
1 TTTAAAAAAATTAGAAA
39570562 TTTAAAAAAATTAGAAA
1 TTTAAAAAAATTAGAAA
**
39570579 TTTATTAAAATTAGAAA
1 TTTAAAAAAATTAGAAA
39570596 TTT
1 TTT
39570599 TTTTATAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
16 12 0.38
17 20 0.62
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (17 bp):
TTTAAAAAAATTAGAAA
Found at i:39570886 original size:20 final size:18
Alignment explanation
Indices: 39570868--39570957 Score: 78
Period size: 17 Copynumber: 4.9 Consensus size: 18
39570858 GACTTTATAA
*
39570868 AATTTTATATTTTTTTAT
1 AATTTTATATATTTTTAT
39570886 -ATTTCTATATA-TTTTAT
1 AATTT-TATATATTTTTAT
*
39570903 AATTTTCTATGATTTTTAT
1 AATTTTATAT-ATTTTTAT
* *
39570922 AAAATTTTAAATATTTTTAC
1 --AATTTTATATATTTTTAT
*
39570942 GATTTT-TATATTTTTA
1 AATTTTATATATTTTTA
39570958 ATAACTTTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
17 23 0.39
18 15 0.25
19 6 0.10
20 7 0.12
21 8 0.14
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.63
Consensus pattern (18 bp):
AATTTTATATATTTTTAT
Found at i:39570909 original size:19 final size:20
Alignment explanation
Indices: 39570861--39570938 Score: 69
Period size: 19 Copynumber: 4.2 Consensus size: 20
39570851 TTCTTACGAC
*
39570861 TTTATAAAATTT-TATAT-T
1 TTTATAATATTTCTATATAT
*
39570879 TTT-TTATATTTCTATATAT
1 TTTATAATATTTCTATATAT
39570898 TTTATAAT-TTTCTATGAT-T
1 TTTATAATATTTCTAT-ATAT
* *
39570917 TTTATAAAATTT-TAAATAT
1 TTTATAATATTTCTATATAT
39570936 TTT
1 TTT
39570939 TACGATTTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
17 6 0.12
18 10 0.20
19 25 0.51
20 8 0.16
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (20 bp):
TTTATAATATTTCTATATAT
Found at i:39570921 original size:56 final size:56
Alignment explanation
Indices: 39570823--39570966 Score: 148
Period size: 56 Copynumber: 2.5 Consensus size: 56
39570813 TTTTACGAAA
* * * *
39570823 TTTATATTTCTTTACATTTTGTATAATTTTCTTACGACTTTATAAAATTTTATATTTT
1 TTTATATTTCTATATA-TTT-TATAATTTTCTTACGACTTTATAAAATTTTAAATATT
* *
39570881 TTTATATTTCTATATATTTTATAATTTTC-TATGATTTTTATAAAATTTTAAATATT
1 TTTATATTTCTATATATTTTATAATTTTCTTACGA-CTTTATAAAATTTTAAATATT
* *
39570937 TTTACGATTTTTATAT-TTTTAATAACTTTT
1 TTTA-TATTTCTATATATTTT-ATAA-TTTT
39570967 TAATATTTGA
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
55 4 0.05
56 36 0.49
57 16 0.22
58 18 0.24
ACGTcount: A:0.30, C:0.06, G:0.03, T:0.61
Consensus pattern (56 bp):
TTTATATTTCTATATATTTTATAATTTTCTTACGACTTTATAAAATTTTAAATATT
Found at i:39570954 original size:8 final size:8
Alignment explanation
Indices: 39570869--39570957 Score: 52
Period size: 9 Copynumber: 9.9 Consensus size: 8
39570859 ACTTTATAAA
39570869 ATTTTATAT
1 ATTTT-TAT
*
39570878 TTTTTTAT
1 ATTTTTAT
*
39570886 ATTTCTAT
1 ATTTTTAT
39570894 ATATTTTAT
1 AT-TTTTAT
39570903 AATTTTCTAT
1 -ATTTT-TAT
39570913 GATTTTTAT
1 -ATTTTTAT
*
39570922 AAAATTTTAAAT
1 ---ATTTT-TAT
*
39570934 ATTTTTACG
1 ATTTTTA-T
39570943 ATTTTTAT
1 ATTTTTAT
39570951 ATTTTTA
1 ATTTTTA
39570958 ATAACTTTTT
Statistics
Matches: 63, Mismatches: 10, Indels: 15
0.72 0.11 0.17
Matches are distributed among these distances:
8 19 0.30
9 27 0.43
10 10 0.16
11 5 0.08
12 2 0.03
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.64
Consensus pattern (8 bp):
ATTTTTAT
Found at i:39571276 original size:90 final size:89
Alignment explanation
Indices: 39571054--39571276 Score: 338
Period size: 91 Copynumber: 2.5 Consensus size: 89
39571044 AATAAAAGAA
*
39571054 AGGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGTCTTTTGACACATTTTGAAAGTTCAAGTA
1 AGGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGTCTTTTGACACATTTTGAAAGTTCAAATA
* * * *
39571119 CCCAATTGAGTGATAAAAAAAGGT
66 CCCAATTGAGTCAAAAAAAAAAGC
* * * **
39571143 AGGGGCTTAATTGCTTTTTTTTAAAAGGTTTGAGGGCTTTTTTGATGCATTTTGAAAGTTCAAAT
1 AGGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGG-TCTTTTGACACATTTTGAAAGTTCAAAT
39571208 ACCCAATTGAGTACAAAAAAAAAAGC
65 ACCCAATTGAGT-CAAAAAAAAAAGC
39571234 AGGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGTCTTTTG
1 AGGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGTCTTTTG
39571277 CACCCTTAAG
Statistics
Matches: 119, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
89 34 0.29
90 42 0.35
91 43 0.36
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (89 bp):
AGGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGTCTTTTGACACATTTTGAAAGTTCAAATA
CCCAATTGAGTCAAAAAAAAAAGC
Found at i:39572808 original size:43 final size:42
Alignment explanation
Indices: 39572714--39572843 Score: 215
Period size: 42 Copynumber: 3.1 Consensus size: 42
39572704 TACAAAACAA
39572714 AAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTAC
1 AAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTAC
*
39572756 AAATGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTTAC
1 AAACGCCGCTAAAGAACATGTTCTTTAGCGGCG-TTTTTTTAC
* * *
39572799 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTTTATAC
1 AAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTAC
39572841 AAA
1 AAA
39572844 AACGCCACTA
Statistics
Matches: 81, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
42 41 0.51
43 40 0.49
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (42 bp):
AAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTAC
Found at i:39573207 original size:21 final size:21
Alignment explanation
Indices: 39573143--39573209 Score: 89
Period size: 21 Copynumber: 3.2 Consensus size: 21
39573133 GCTCTGCTCC
* *
39573143 GCTTCTCTCGCTGCAGCCTCC
1 GCTTCCCTCGCTGCAGCCTCT
*
39573164 GCTTCCCTCGCTGCAGCCGCT
1 GCTTCCCTCGCTGCAGCCTCT
* *
39573185 GCTTCCCTCGCTTCCGCCTCT
1 GCTTCCCTCGCTGCAGCCTCT
39573206 GCTT
1 GCTT
39573210 TAAGTTGTAG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.03, C:0.48, G:0.19, T:0.30
Consensus pattern (21 bp):
GCTTCCCTCGCTGCAGCCTCT
Found at i:39573562 original size:25 final size:25
Alignment explanation
Indices: 39573532--39573910 Score: 168
Period size: 25 Copynumber: 15.3 Consensus size: 25
39573522 TGATATATGT
*
39573532 TTATGTATTAAGTAAATTATGTAAG
1 TTATGTATTAAGTAAGTTATGTAAG
*
39573557 TTATGTACGTGT-A-TAAGTTAAGTAAG
1 TTATGTA--T-TAAGTAAGTTATGTAAG
39573583 TTATGTATTAAGTAAGTTATGTAAG
1 TTATGTATTAAGTAAGTTATGTAAG
39573608 TTATG-A--AAGTAA-TGTATGTAA-
1 TTATGTATTAAGTAAGT-TATGTAAG
* *
39573629 TGTAAGT-TGTAAGTTA-TTATGT-A-
1 T-TATGTAT-TAAGTAAGTTATGTAAG
*
39573652 TTATGTAAGTTATGTAAGTTATGTAAG
1 TTATGT-A-TTAAGTAAGTTATGTAAG
*
39573679 TTAAATGTATTATGTAAG-T-TGTAAG
1 TT--ATGTATTAAGTAAGTTATGTAAG
*
39573704 TTAAATGTATTATGTAAG---T-T-A-
1 TT--ATGTATTAAGTAAGTTATGTAAG
*
39573725 TTATGTATTATGTAAG-T-TGTAAG
1 TTATGTATTAAGTAAGTTATGTAAG
*
39573748 TTAAATGTATTATGTAAG-T-TGTAAG
1 TT--ATGTATTAAGTAAGTTATGTAAG
*
39573773 TTAAGTGTATTATGTAAG-T-TGTAAG
1 TT-A-TGTATTAAGTAAGTTATGTAAG
*
39573798 TTATTATGTATTATGTAAG-T-TGTAAG
1 ---TTATGTATTAAGTAAGTTATGTAAG
**
39573824 TTAAATGTATTGTGTAAG-T-TGTAAG
1 TT--ATGTATTAAGTAAGTTATGTAAG
*
39573849 TTATTATGTATTATGTAAGTTATGTAAG
1 ---TTATGTATTAAGTAAGTTATGTAAG
* *
39573877 TTAAATGTATTATGTAGGTTATGTAAG
1 TT--ATGTATTAAGTAAGTTATGTAAG
*
39573904 TTGTGTA
1 TTATGTA
39573911 AGAGATTTAA
Statistics
Matches: 304, Mismatches: 12, Indels: 76
0.78 0.03 0.19
Matches are distributed among these distances:
19 14 0.05
20 1 0.00
21 5 0.02
22 22 0.07
23 8 0.03
24 16 0.05
25 130 0.43
26 53 0.17
27 39 0.13
28 12 0.04
29 4 0.01
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (25 bp):
TTATGTATTAAGTAAGTTATGTAAG
Found at i:39573763 original size:51 final size:52
Alignment explanation
Indices: 39573650--39573892 Score: 310
Period size: 51 Copynumber: 4.8 Consensus size: 52
39573640 AGTTATTATG
39573650 TATTATGTAAGTTATGTAAGTTATGTAAGTTAAATGTATTATGTAAGTTGTAAGT
1 TATTATGT-A-TTATGTAA-TTATGTAAGTTAAATGTATTATGTAAGTTGTAAGT
* *
39573705 TA-AATGTATTATGT-A--A-GTTA-TT--ATGTATTATGTAAGTTGTAAGT
1 TATTATGTATTATGTAATTATGTAAGTTAAATGTATTATGTAAGTTGTAAGT
* * *
39573749 TA-AATGTATTATGTAAGT-TGTAAGTTAAGTGTATTATGTAAGTTGTAAGT
1 TATTATGTATTATGTAATTATGTAAGTTAAATGTATTATGTAAGTTGTAAGT
* *
39573799 TATTATGTATTATGTAAGT-TGTAAGTTAAATGTATTGTGTAAGTTGTAAGT
1 TATTATGTATTATGTAATTATGTAAGTTAAATGTATTATGTAAGTTGTAAGT
39573850 TATTATGTATTATGTAAGTTATGTAAGTTAAATGTATTATGTA
1 TATTATGTATTATGTAA-TTATGTAAGTTAAATGTATTATGTA
39573893 GGTTATGTAA
Statistics
Matches: 169, Mismatches: 9, Indels: 22
0.85 0.05 0.11
Matches are distributed among these distances:
44 36 0.21
45 1 0.01
46 2 0.01
47 6 0.04
48 3 0.02
50 23 0.14
51 63 0.37
52 7 0.04
53 22 0.13
54 4 0.02
55 2 0.01
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.47
Consensus pattern (52 bp):
TATTATGTATTATGTAATTATGTAAGTTAAATGTATTATGTAAGTTGTAAGT
Found at i:39573873 original size:9 final size:9
Alignment explanation
Indices: 39573543--39574001 Score: 230
Period size: 9 Copynumber: 52.4 Consensus size: 9
39573533 TATGTATTAA
*
39573543 GTAAATTAT
1 GTAAGTTAT
39573552 GTAAGTTAT
1 GTAAGTTAT
*
39573561 GTACGTGTA-
1 GTAAGT-TAT
*
39573570 -TAAGTTAA
1 GTAAGTTAT
39573578 GTAAGTTAT
1 GTAAGTTAT
*
39573587 GT-A-TTAA
1 GTAAGTTAT
39573594 GTAAGTTAT
1 GTAAGTTAT
39573603 GTAAGTTAT
1 GTAAGTTAT
* *
39573612 GAAAGTAAT
1 GTAAGTTAT
* *
39573621 GTATGTAAT
1 GTAAGTTAT
39573630 GTAAG-T-T
1 GTAAGTTAT
39573637 GTAAGTTAT
1 GTAAGTTAT
*
39573646 -TATGTATTAT
1 GTAAG--TTAT
39573656 GTAAGTTAT
1 GTAAGTTAT
39573665 GTAAGTTAT
1 GTAAGTTAT
39573674 GTAAGTTAAAT
1 GTAAGTT--AT
39573685 GT-A-TTAT
1 GTAAGTTAT
39573692 GTAAG-T-T
1 GTAAGTTAT
39573699 GTAAGTTAAAT
1 GTAAGTT--AT
39573710 GT-A-TTAT
1 GTAAGTTAT
39573717 GTAAGTTAT
1 GTAAGTTAT
*
39573726 -TATGTATTAT
1 GTAAG--TTAT
39573736 GTAAG-T-T
1 GTAAGTTAT
39573743 GTAAGTTAAAT
1 GTAAGTT--AT
39573754 GT-A-TTAT
1 GTAAGTTAT
39573761 GTAAG-T-T
1 GTAAGTTAT
39573768 GTAAGTTAAGT
1 GTAAGTT-A-T
39573779 GT-A-TTAT
1 GTAAGTTAT
39573786 GTAAG-T-T
1 GTAAGTTAT
39573793 GTAAGTTAT
1 GTAAGTTAT
*
39573802 -TATGTATTAT
1 GTAAG--TTAT
39573812 GTAAG-T-T
1 GTAAGTTAT
39573819 GTAAGTTAAAT
1 GTAAGTT--AT
*
39573830 GT-A-TTGT
1 GTAAGTTAT
39573837 GTAAG-T-T
1 GTAAGTTAT
39573844 GTAAGTTAT
1 GTAAGTTAT
*
39573853 -TATGTATTAT
1 GTAAG--TTAT
39573863 GTAAGTTAT
1 GTAAGTTAT
39573872 GTAAGTTAAAT
1 GTAAGTT--AT
39573883 GT-A-TTAT
1 GTAAGTTAT
*
39573890 GTAGGTTAT
1 GTAAGTTAT
*
39573899 GTAAGTTGT
1 GTAAGTTAT
**
39573908 GTAAGAGAT
1 GTAAGTTAT
*
39573917 TTAAGTTAT
1 GTAAGTTAT
*
39573926 GTAGGTTAT
1 GTAAGTTAT
* *
39573935 TTAGGTTAT
1 GTAAGTTAT
*
39573944 GTAAGTTGT
1 GTAAGTTAT
**
39573953 GTAAGAGAT
1 GTAAGTTAT
*
39573962 TTAAGTTAT
1 GTAAGTTAT
*
39573971 GTAGGTTAT
1 GTAAGTTAT
* *
39573980 TTAGGTTAT
1 GTAAGTTAT
*
39573989 GTAAGTTTT
1 GTAAGTTAT
39573998 GTAA
1 GTAA
39574002 TGTGCAAGTG
Statistics
Matches: 347, Mismatches: 48, Indels: 110
0.69 0.10 0.22
Matches are distributed among these distances:
7 71 0.20
8 37 0.11
9 183 0.53
10 24 0.07
11 32 0.09
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.45
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:39576580 original size:83 final size:83
Alignment explanation
Indices: 39576436--39576597 Score: 279
Period size: 83 Copynumber: 2.0 Consensus size: 83
39576426 NNNNNNNNNN
* * *
39576436 CATTTCATGAAACGGCTCCGTTTTATTCAATTTTCCAAATATTGTTTGCGGCGTTTTTTACAAAA
1 CATTTCACGAAACGGCTCCGTTTTATTCAATTTTCCAAATATTATTTGCGGCGTTTGTTACAAAA
39576501 ACGCCACTAAATTAATTT
66 ACGCCACTAAATTAATTT
* *
39576519 CATTTCACGAAACGGCTCTGTTTTATTCAATTTTTCAAATATTATTTGCGGCGTTTGTTACAAAA
1 CATTTCACGAAACGGCTCCGTTTTATTCAATTTTCCAAATATTATTTGCGGCGTTTGTTACAAAA
39576584 ACGCCACTAAATTA
66 ACGCCACTAAATTA
39576598 TTTATATTTA
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 74 1.00
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (83 bp):
CATTTCACGAAACGGCTCCGTTTTATTCAATTTTCCAAATATTATTTGCGGCGTTTGTTACAAAA
ACGCCACTAAATTAATTT
Found at i:39577005 original size:39 final size:40
Alignment explanation
Indices: 39576936--39577016 Score: 119
Period size: 39 Copynumber: 2.0 Consensus size: 40
39576926 TAACCCCCAT
**
39576936 AACCCCTAAATCCCCCTTAACCTTTAAAGCATAAACCCTA
1 AACCCCTAAATCCCCCTTAACCCCTAAAGCATAAACCCTA
* *
39576976 AACCCCTAAATCTCCC-TAACCCCTAAAGCATAACCCCTA
1 AACCCCTAAATCCCCCTTAACCCCTAAAGCATAAACCCTA
39577015 AA
1 AA
39577017 TAATTTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 22 0.59
40 15 0.41
ACGTcount: A:0.38, C:0.40, G:0.02, T:0.20
Consensus pattern (40 bp):
AACCCCTAAATCCCCCTTAACCCCTAAAGCATAAACCCTA
Found at i:39577764 original size:39 final size:40
Alignment explanation
Indices: 39577699--39577775 Score: 113
Period size: 39 Copynumber: 1.9 Consensus size: 40
39577689 ACCCATAACC
*
39577699 CCTAAATCCCCCTTAACCCTTAAAGCATAAA-CCCTAAACT
1 CCTAAATCCCCCTTAACCCCTAAAGCA-AAACCCCTAAACT
*
39577739 CCTAAATCTCCC-TAACCCCTAAAGCAAAACCCCTAAA
1 CCTAAATCCCCCTTAACCCCTAAAGCAAAACCCCTAAA
39577776 AAAATTTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
38 3 0.09
39 20 0.59
40 11 0.32
ACGTcount: A:0.39, C:0.39, G:0.03, T:0.19
Consensus pattern (40 bp):
CCTAAATCCCCCTTAACCCCTAAAGCAAAACCCCTAAACT
Found at i:39577952 original size:15 final size:16
Alignment explanation
Indices: 39577927--39577958 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
39577917 TTAAATAATA
39577927 TAAACTATATTAAATT
1 TAAACTATATTAAATT
39577943 TAAA-TATATTAAATT
1 TAAACTATATTAAATT
39577958 T
1 T
39577959 CTTATTAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
TAAACTATATTAAATT
Found at i:39578075 original size:8 final size:8
Alignment explanation
Indices: 39578045--39578087 Score: 63
Period size: 8 Copynumber: 5.6 Consensus size: 8
39578035 CGTTCAAACT
39578045 CTAAACCC
1 CTAAACCC
*
39578053 C-AAATCC
1 CTAAACCC
39578060 CT-AACCC
1 CTAAACCC
39578067 CTAAACCC
1 CTAAACCC
39578075 CTAAACCC
1 CTAAACCC
39578083 CTAAA
1 CTAAA
39578088 TCCTAACTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 12 0.39
8 19 0.61
ACGTcount: A:0.40, C:0.47, G:0.00, T:0.14
Consensus pattern (8 bp):
CTAAACCC
Found at i:39578132 original size:7 final size:7
Alignment explanation
Indices: 39578122--39578146 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
39578112 CCCAAAAGCA
39578122 TAAACCC
1 TAAACCC
39578129 TAAACCC
1 TAAACCC
39578136 TAAACCC
1 TAAACCC
39578143 TAAA
1 TAAA
39578147 TCTCAAACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.16
Consensus pattern (7 bp):
TAAACCC
Found at i:39578141 original size:14 final size:14
Alignment explanation
Indices: 39578040--39578146 Score: 63
Period size: 14 Copynumber: 7.2 Consensus size: 14
39578030 TTTACCGTTC
* *
39578040 AAACTCTAAACCCC
1 AAACCCTAAACCCT
*
39578054 AAATCCCTAACCCCT
1 AAA-CCCTAAACCCT
39578069 AAACCCCTAAACCCCT
1 AAA-CCCTAAA-CCCT
* *
39578085 AAATCCT-AACTCTT
1 AAACCCTAAAC-CCT
* *
39578099 AAATCCCCCTAACCCCA
1 AAA---CCCTAAACCCT
* *
39578116 AAAGCATAAACCCT
1 AAACCCTAAACCCT
39578130 AAACCCTAAACCCT
1 AAACCCTAAACCCT
39578144 AAA
1 AAA
39578147 TCTCAAACCA
Statistics
Matches: 69, Mismatches: 17, Indels: 14
0.69 0.17 0.14
Matches are distributed among these distances:
13 1 0.01
14 32 0.46
15 20 0.29
16 7 0.10
17 7 0.10
18 2 0.03
ACGTcount: A:0.41, C:0.41, G:0.01, T:0.17
Consensus pattern (14 bp):
AAACCCTAAACCCT
Found at i:39578788 original size:113 final size:113
Alignment explanation
Indices: 39578368--39578797 Score: 423
Period size: 114 Copynumber: 3.8 Consensus size: 113
39578358 TTTAAATCCT
* * * *
39578368 TGAGCATTAGCGGCGCTTTTTTAAAAACGCCGCTAAAACCCCTAAAGCTAAGAAAACGATGTCGT
1 TGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAAACCCCGAAAGCTTAGAAAACGACGTCGT
* *
39578433 TGGGCTTAGGTTTTTAGCGGCACTT--TTACAAAAAACGCCGCTAAAAACC
66 TGCGCTTAGGTTTTTAGCGGCGCTTCCTT---AAAAACGCCGCTAAAAACC
* * * * * * *
39578482 TGAGCATTAGCGGCGCTTT-ATATAAAGCGCCACTAAAACCCTGAAAGC-TGGCGAGACGACGTC
1 TGAGCATTAGCGGCGCTTTCTTA-AAAACGCCGCTAAAACCCCGAAAGCTTAG-AAAACGACGTC
* * * * *
39578545 GTTGCGC-TAGATTTTTTTGCGGCGCTTTCC-CATAAACGCCGCTAAAAGACA
64 GTTGCGCTTAG-GTTTTTAGCGGCGC-TTCCTTAAAAACGCCGCTAAAA-ACC
* * *
39578596 TGAGCATTAGCGGCGCTTTCATAAAAACGCCGCTAAATCCCCGAAAGCTTAGAAAAC-AGCGTGG
1 TGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAAACCCCGAAAGCTTAGAAAACGA-CGTCG
39578660 TTG-GCCTTAGGTTTTTAGCGGCGCTTCCTTAAAAACGCCGCTAAAAACC
65 TTGCG-CTTAGGTTTTTAGCGGCGCTTCCTTAAAAACGCCGCTAAAAACC
* * * * *
39578709 TGAGCATTAGCGGCGCTTACTTAAAAACGCCGCTAAATCACC-AAATGCTCTTG-AAACGGCGTC
1 TGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAAACCCCGAAA-GCT-TAGAAAACGACGTC
* *
39578772 GTTGCGC-TAGATTTTTTGCGGCGCTT
64 GTTGCGCTTAGGTTTTTAGCGGCGCTT
39578798 TCCCGAAAAC
Statistics
Matches: 261, Mismatches: 38, Indels: 36
0.78 0.11 0.11
Matches are distributed among these distances:
112 20 0.08
113 83 0.32
114 148 0.57
115 10 0.04
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (113 bp):
TGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAAACCCCGAAAGCTTAGAAAACGACGTCGT
TGCGCTTAGGTTTTTAGCGGCGCTTCCTTAAAAACGCCGCTAAAAACC
Found at i:39580282 original size:21 final size:20
Alignment explanation
Indices: 39580253--39580294 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
39580243 CTTAATTCGT
* *
39580253 TGTTTTATTTTTTATTAATTA
1 TGTTATATTTATTATT-ATTA
39580274 TGTTATATTTATTATTATTA
1 TGTTATATTTATTATTATTA
39580294 T
1 T
39580295 TATTATTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (20 bp):
TGTTATATTTATTATTATTA
Found at i:39580587 original size:21 final size:21
Alignment explanation
Indices: 39580527--39580591 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
39580517 TGTACACACA
*
39580527 TTTATA-TATATATTTACA-T
1 TTTATATTATATATATACATT
* *
39580546 TTTATAATTCA-AAATACACATT
1 TTTAT-ATT-ATATATATACATT
39580568 TTTATATTATATATATACATT
1 TTTATATTATATATATACATT
39580589 TTT
1 TTT
39580592 TTATATTGCC
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
19 5 0.14
20 2 0.06
21 22 0.61
22 7 0.19
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTATATTATATATATACATT
Found at i:39582524 original size:19 final size:20
Alignment explanation
Indices: 39582484--39582527 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
39582474 ATCTCTTTAG
* *
39582484 GCATT-CATTTCATGCATTT
1 GCATTACATTGCATGCATAT
39582503 GCATTACATTGCAT-CATAT
1 GCATTACATTGCATGCATAT
39582522 GCATTA
1 GCATTA
39582528 AACACCTCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.41
Consensus pattern (20 bp):
GCATTACATTGCATGCATAT
Found at i:39584453 original size:18 final size:18
Alignment explanation
Indices: 39584417--39584456 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
39584407 GCAAATGTTC
*
39584417 TTTCATTCTTTACGTTTT
1 TTTCATTCTTTACGATTT
39584435 TTTCATTCTTTTA-GATTT
1 TTTCATTC-TTTACGATTT
39584453 TTTC
1 TTTC
39584457 TGCCAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.12, C:0.15, G:0.05, T:0.68
Consensus pattern (18 bp):
TTTCATTCTTTACGATTT
Found at i:39587383 original size:132 final size:132
Alignment explanation
Indices: 39586609--39587370 Score: 925
Period size: 133 Copynumber: 5.8 Consensus size: 132
39586599 CAGATCAGTG
* *
39586609 AAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCT
1 AAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCC
* *
39586674 CTGAAGTTGCAGTGGAGTACATTGACGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATAGAT
66 CTGAAGTTGCAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGAT
*
39586739 TG
131 TA
* * *
39586741 AAGATTTTAGATCTTGCCTCCCTAAGCAGTAGTGGGGCAGGTCGAAGATGGCAGATTTTACCTCC
1 AAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCC
*
39586806 CTGAAGTTGCAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATAAAT
66 CTGAAGTTGCAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGAT
39586871 TA
131 TA
* * ** ** * * *
39586873 AAGATTTCAGATCTTGCCTTCCTGCATAAACAGCGGAGCAGATCAAAGATGG-TGAATTTTACCT
1 AAGATTTCAGATCTTGCCTCCCT-AAGCAGTAGTGGAGCAGATCGAAGATGGCAG-ATTTTACCT
* * *
39586937 CCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGAAATTCTACTTCCCTGGTCAGCAGTGGAATAG
64 CCCTGAAGTTGCAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATAG
39587002 ATTA
129 ATTA
* * * * *
39587006 AAGATTTCAGATCTTGCCTTCCT--GCATAGACAGCGGAGCAGATCAAAGATGG-TGAATTTTAC
1 AAGATTTCAGATCTTGCCTCCCTAAGC--AG-TAGTGGAGCAGATCGAAGATGGCAG-ATTTTAC
* * *
39587068 CTCCTCGTG--GTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGACAACAGTGGA
62 CTCC-C-TGAAGTTGCAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGA
39587131 ATAGATTA
125 ATAGATTA
* * * * *
39587139 TAGATTGCAGATCTTGCCTTCCT--GCA-TAGACAGCGAAGCAGATCGAAGATGGCAAATTTTAC
1 AAGATTTCAGATCTTGCCTCCCTAAGCAGTAG--TG-G-AGCAGATCGAAGATGGCAGATTTTAC
* * * *
39587201 CTCCCTGAGGTTGCAGTGGAGTATATTGAAGCCAATAATTCTA-TCTCCCTGGGCAACAGTGGAA
62 CTCCCTGAAGTTGCAGTGGAGTACATTGAAGCCAGTAATTCTACT-TCCCTGGGCAGCAGTGGAA
*
39587265 TAGATTG
126 TAGATTA
* * * **
39587272 AAGATTACAAATTTTATCTCCCTAAGCAGTAGTGGAGCAGATC-AAGGATGGCAGATTTTACCTC
1 AAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCGAA-GATGGCAGATTTTACCTC
39587336 CCTGAAGTTGCAGTGGAGTACATTGAAGCCAGTAA
65 CCTGAAGTTGCAGTGGAGTACATTGAAGCCAGTAA
39587371 GCCTATCTCC
Statistics
Matches: 555, Mismatches: 56, Indels: 38
0.86 0.09 0.06
Matches are distributed among these distances:
129 2 0.00
131 6 0.01
132 206 0.37
133 331 0.60
134 2 0.00
135 5 0.01
136 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (132 bp):
AAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCC
CTGAAGTTGCAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGAT
TA
Found at i:39589949 original size:24 final size:24
Alignment explanation
Indices: 39589921--39589972 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
39589911 TTTTGAGAAG
* **
39589921 ATTTAGTATTTATTAGTATAATTT
1 ATTTAGAATTTATTAACATAATTT
39589945 ATTTAGAATTTATTAACATAATTT
1 ATTTAGAATTTATTAACATAATTT
39589969 ATTT
1 ATTT
39589973 GACCTACGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.56
Consensus pattern (24 bp):
ATTTAGAATTTATTAACATAATTT
Found at i:39593070 original size:20 final size:21
Alignment explanation
Indices: 39593031--39593071 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
39593021 TGTTTTGACA
39593031 TGTTTTAAGCATGCTTAAATG
1 TGTTTTAAGCATGCTTAAATG
* *
39593052 TGTTTTGAGTATG-TTAAATG
1 TGTTTTAAGCATGCTTAAATG
39593072 GTTGGTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.27, C:0.05, G:0.22, T:0.46
Consensus pattern (21 bp):
TGTTTTAAGCATGCTTAAATG
Found at i:39602400 original size:32 final size:31
Alignment explanation
Indices: 39602363--39602438 Score: 100
Period size: 32 Copynumber: 2.4 Consensus size: 31
39602353 TTTAATCACT
39602363 TTTATATTAAATTAATATAATATT-TATTAAA
1 TTTATATTAAATTAATATAATATTATATT-AA
* *
39602394 TATTATATTAATTTAATTTAATATTATATTAA
1 T-TTATATTAAATTAATATAATATTATATTAA
39602426 TTTAATATTAAAT
1 TTT-ATATTAAAT
39602439 CTTCTTAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
31 3 0.08
32 32 0.82
33 4 0.10
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (31 bp):
TTTATATTAAATTAATATAATATTATATTAA
Found at i:39602430 original size:5 final size:6
Alignment explanation
Indices: 39602366--39602436 Score: 70
Period size: 5 Copynumber: 13.2 Consensus size: 6
39602356 AATCACTTTT
39602366 ATATTA A-ATTA ATA-TA ATATT- -TATTAA ATATT- ATATTA AT-TTA
1 ATATTA ATATTA ATATTA ATATTA ATATT-A ATATTA ATATTA ATATTA
39602409 AT-TTA ATATT- ATATTA AT-TTA ATATTA A
1 ATATTA ATATTA ATATTA ATATTA ATATTA A
39602437 ATCTTCTTAA
Statistics
Matches: 56, Mismatches: 0, Indels: 18
0.76 0.00 0.24
Matches are distributed among these distances:
4 4 0.07
5 35 0.62
6 13 0.23
7 4 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
ATATTA
Found at i:39602435 original size:16 final size:16
Alignment explanation
Indices: 39602366--39602435 Score: 74
Period size: 16 Copynumber: 4.4 Consensus size: 16
39602356 AATCACTTTT
* *
39602366 ATATTAAATTAATATA
1 ATATTATATTAATTTA
39602382 ATATT-TATTAAATATT-
1 ATATTATATT-AAT-TTA
39602398 ATATTA-ATTTAATTTA
1 ATATTATA-TTAATTTA
39602414 ATATTATATTAATTTA
1 ATATTATATTAATTTA
39602430 ATATTA
1 ATATTA
39602436 AATCTTCTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
15 5 0.11
16 37 0.80
17 4 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATTATATTAATTTA
Found at i:39602446 original size:21 final size:21
Alignment explanation
Indices: 39602384--39602436 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 21
39602374 TTAATATAAT
*
39602384 ATTT-ATTAAATATTATATTA
1 ATTTAATTTAATATTATATTA
39602404 ATTTAATTTAATATTATATTA
1 ATTTAATTTAATATTATATTA
39602425 ATTTAATATTAA
1 ATTTAAT-TTAA
39602437 ATCTTCTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 4 0.13
21 22 0.73
22 4 0.13
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTTAATTTAATATTATATTA
Found at i:39602524 original size:20 final size:18
Alignment explanation
Indices: 39602477--39602525 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
39602467 TATGATAAAC
39602477 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
39602494 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
39602514 ATTAAATTAATA
1 ATTAAATTAATA
39602526 AAATACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:39609743 original size:18 final size:17
Alignment explanation
Indices: 39609710--39609748 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
39609700 TTGTATAAAT
39609710 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
39609728 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
39609745 TGTG
1 TGTG
39609749 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:39609880 original size:8 final size:8
Alignment explanation
Indices: 39609867--39609895 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
39609857 CACTAGAGAC
39609867 CAGTGTTA
1 CAGTGTTA
39609875 CAGTGTTA
1 CAGTGTTA
39609883 CAGTGTTA
1 CAGTGTTA
39609891 CAGTG
1 CAGTG
39609896 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:39610008 original size:23 final size:23
Alignment explanation
Indices: 39609982--39610057 Score: 152
Period size: 23 Copynumber: 3.3 Consensus size: 23
39609972 AGTGTTATTG
39609982 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
39610005 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
39610028 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
39610051 ATCAGTG
1 ATCAGTG
39610058 TGGCACTTAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:39621575 original size:42 final size:42
Alignment explanation
Indices: 39621468--39621624 Score: 151
Period size: 42 Copynumber: 3.8 Consensus size: 42
39621458 GCACATAAGT
* * * *
39621468 GCTAAA-TGAAAACCCGTAAGGGTTGAA-TGGAAGCTCATAGGA
1 GCTAAACTG-AAACCCATAAGGGTTAAACT-GAAGCTCAAAAGA
* * * *
39621510 -CTGAACGGAAACCCATAAGGGTTAATCTGAAGCTCAGAAGA
1 GCTAAACTGAAACCCATAAGGGTTAAACTGAAGCTCAAAAGA
39621551 GCTAAACTGAAACCCATTAA-GGTTAAACTGAAGCTCAAAAGA
1 GCTAAACTGAAACCCA-TAAGGGTTAAACTGAAGCTCAAAAGA
** * *
39621593 GCTAAACTGAAACTTAGAAGGGTTAATCTGAA
1 GCTAAACTGAAACCCATAAGGGTTAAACTGAA
39621625 ACCCATATGA
Statistics
Matches: 95, Mismatches: 15, Indels: 10
0.79 0.12 0.08
Matches are distributed among these distances:
41 32 0.34
42 60 0.63
43 3 0.03
ACGTcount: A:0.41, C:0.17, G:0.23, T:0.20
Consensus pattern (42 bp):
GCTAAACTGAAACCCATAAGGGTTAAACTGAAGCTCAAAAGA
Found at i:39621598 original size:21 final size:21
Alignment explanation
Indices: 39621536--39621603 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
39621526 AAGGGTTAAT
*
39621536 CTGAAGCTCAGAAGAGCTAAA
1 CTGAAGCTCAAAAGAGCTAAA
* * * *
39621557 CTGAAACCCATTAAG-GTTAAA
1 CTGAAGCTCA-AAAGAGCTAAA
39621578 CTGAAGCTCAAAAGAGCTAAA
1 CTGAAGCTCAAAAGAGCTAAA
39621599 CTGAA
1 CTGAA
39621604 ACTTAGAAGG
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
20 3 0.08
21 31 0.84
22 3 0.08
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.18
Consensus pattern (21 bp):
CTGAAGCTCAAAAGAGCTAAA
Found at i:39634542 original size:83 final size:80
Alignment explanation
Indices: 39634387--39634547 Score: 223
Period size: 83 Copynumber: 2.0 Consensus size: 80
39634377 TGCAAGGTGC
** * * * *
39634387 TGGATCTTGACTCTGCTTTTTTTTCTTTCAGTAGAATGATTGTTTTCTGATAATGGACGAATAAT
1 TGGATCTTGACTCTGCTTTGGTTTCTATCAGTACAATCATAGTTTTCTGATAATGGACGAATAAT
39634452 AAAATGAACGGTTGT
66 AAAATGAACGGTTGT
* *
39634467 TGGATCTTGACTCTCTGCTTTGGTTTCTATCAGTACAATCATAGTTTTTGTGATAATTGACGAAT
1 TGGATCTTGA--CTCTGCTTTGGTTTCTATCAGTACAATCATAG-TTTTCTGATAATGGACGAAT
39634532 AATAAAATGAACGGTT
63 AATAAAATGAACGGTT
39634548 CCATTTGGCT
Statistics
Matches: 70, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
80 10 0.14
82 26 0.37
83 34 0.49
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.41
Consensus pattern (80 bp):
TGGATCTTGACTCTGCTTTGGTTTCTATCAGTACAATCATAGTTTTCTGATAATGGACGAATAAT
AAAATGAACGGTTGT
Found at i:39643446 original size:24 final size:24
Alignment explanation
Indices: 39643414--39643481 Score: 109
Period size: 24 Copynumber: 2.8 Consensus size: 24
39643404 ACTGCAATAA
*
39643414 TGAGTGGCTTGACCATAACGTTAT
1 TGAGTGGCTTGACCACAACGTTAT
* *
39643438 TGAGTGGCTTGATCACAACCTTAT
1 TGAGTGGCTTGACCACAACGTTAT
39643462 TGAGTGGCTTGACCACAACG
1 TGAGTGGCTTGACCACAACG
39643482 ATGCAGCTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (24 bp):
TGAGTGGCTTGACCACAACGTTAT
Found at i:39643621 original size:21 final size:24
Alignment explanation
Indices: 39643597--39643640 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
39643587 AATGTTTTTG
*
39643597 AAAAAC-CTGCATTGAT-TTCTGA
1 AAAAACTCTACATTGATATTCTGA
39643619 AAAAACTCTACATTGATATTCT
1 AAAAACTCTACATTGATATTCT
39643641 CGTGCACCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 9 0.47
24 4 0.21
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (24 bp):
AAAAACTCTACATTGATATTCTGA
Found at i:39646557 original size:16 final size:16
Alignment explanation
Indices: 39646513--39646559 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
39646503 ATAGATTTAA
39646513 TATTAAATTTAATATTT
1 TATT-AATTTAATATTT
*
39646530 T-TCTTA-TTAATATTT
1 TAT-TAATTTAATATTT
39646545 TATTAATTTAATATT
1 TATTAATTTAATATT
39646560 AAAGTGATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
15 12 0.48
16 11 0.44
17 2 0.08
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTAATTTAATATTT
Found at i:39646592 original size:10 final size:10
Alignment explanation
Indices: 39646577--39646603 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
39646567 TGATATTAAT
39646577 ATTTAATTTA
1 ATTTAATTTA
39646587 ATTTAATTTA
1 ATTTAATTTA
39646597 ATTTAAT
1 ATTTAAT
39646604 ATTTATCTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
ATTTAATTTA
Found at i:39647684 original size:19 final size:20
Alignment explanation
Indices: 39647648--39647689 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
39647638 TAAAATACCA
* *
39647648 AAAAAACCAAAGATCAAAGC
1 AAAAAACCAAAGAACAAACC
*
39647668 AAAAACCCAAA-AACAAACC
1 AAAAAACCAAAGAACAAACC
39647687 AAA
1 AAA
39647690 TCTGAAAACT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.69, C:0.24, G:0.05, T:0.02
Consensus pattern (20 bp):
AAAAAACCAAAGAACAAACC
Found at i:39649521 original size:45 final size:45
Alignment explanation
Indices: 39649471--39649561 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
39649461 TTGAAATAAA
39649471 TTATTTTCTCATTTTATTAAAAATTTAAATATTCAAATTTTATTT
1 TTATTTTCTCATTTTATTAAAAATTTAAATATTCAAATTTTATTT
39649516 TTATTTTCTCATTTTATTAAAAATTTAAATATTCAAATTTTATTT
1 TTATTTTCTCATTTTATTAAAAATTTAAATATTCAAATTTTATTT
39649561 T
1 T
39649562 AACTTTTATC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (45 bp):
TTATTTTCTCATTTTATTAAAAATTTAAATATTCAAATTTTATTT
Found at i:39649577 original size:38 final size:41
Alignment explanation
Indices: 39649480--39649577 Score: 103
Period size: 45 Copynumber: 2.4 Consensus size: 41
39649470 ATTATTTTCT
* *
39649480 CATTTTATTAAAAATTTAAATATTCAAATTTTATTTTTATTTTCT
1 CATTTTATCAAAAATTTAAATATTCAAATTTTATTTTTA---T-A
*
39649525 CATTTTATTAAAAATTTAAATATTCAAATTTTA-TTTTA-A
1 CATTTTATCAAAAATTTAAATATTCAAATTTTATTTTTATA
*
39649564 C-TTTTATCCAAAAT
1 CATTTTATCAAAAAT
39649578 AAAATAAAAG
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
38 11 0.22
39 1 0.02
44 5 0.10
45 33 0.66
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (41 bp):
CATTTTATCAAAAATTTAAATATTCAAATTTTATTTTTATA
Found at i:39650232 original size:2 final size:2
Alignment explanation
Indices: 39650221--39650253 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
39650211 ATTTTATAAG
*
39650221 TA TA TA -A TA TA TA TA TA TA TA TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39650254 AAAGATGAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39651309 original size:20 final size:21
Alignment explanation
Indices: 39651286--39651324 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39651276 TATTTTATAT
*
39651286 ATAAAAA-TTGTATTTATTCA
1 ATAAAAACTTGAATTTATTCA
39651306 ATAAAAACTTGAATTTATT
1 ATAAAAACTTGAATTTATT
39651325 GATGATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (21 bp):
ATAAAAACTTGAATTTATTCA
Found at i:39651735 original size:51 final size:51
Alignment explanation
Indices: 39651656--39651759 Score: 154
Period size: 51 Copynumber: 2.0 Consensus size: 51
39651646 GTATATAGCT
* *
39651656 CATTATCATATAGTTCACCTGCACGGTTCGCCTACGCACTTCGCCGCCATG
1 CATTAACATATAGTTCACCTGCACGGTTCGCCTACGCACTTCGCCACCATG
* * * *
39651707 CATTAACATATTGTTCGCCTGCATGGTTCGCCTATGCACTTCGCCACCATG
1 CATTAACATATAGTTCACCTGCACGGTTCGCCTACGCACTTCGCCACCATG
39651758 CA
1 CA
39651760 GGTGAACTCA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.20, C:0.34, G:0.17, T:0.29
Consensus pattern (51 bp):
CATTAACATATAGTTCACCTGCACGGTTCGCCTACGCACTTCGCCACCATG
Found at i:39656265 original size:14 final size:14
Alignment explanation
Indices: 39656246--39656277 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
39656236 AAAAAGAAAG
39656246 TTGATAGGATCTAA
1 TTGATAGGATCTAA
39656260 TTGATAGGATCTAA
1 TTGATAGGATCTAA
39656274 TTGA
1 TTGA
39656278 CTTTTATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.38
Consensus pattern (14 bp):
TTGATAGGATCTAA
Found at i:39659485 original size:27 final size:27
Alignment explanation
Indices: 39659445--39659505 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
39659435 TAAAAACGGG
* *
39659445 AATGATCCTGGTCTCAACGATAATCTA
1 AATGGTCCTAGTCTCAACGATAATCTA
*
39659472 AATGGTCCTAGTCTCAATGATAATCTA
1 AATGGTCCTAGTCTCAACGATAATCTA
39659499 AATGGTC
1 AATGGTC
39659506 AGGATGTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (27 bp):
AATGGTCCTAGTCTCAACGATAATCTA
Found at i:39664433 original size:18 final size:18
Alignment explanation
Indices: 39664410--39664451 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
39664400 AAAGGTTGCT
39664410 AGAGTTGAATGAAATGGA
1 AGAGTTGAATGAAATGGA
39664428 AGAGTTGAATGAAATGGA
1 AGAGTTGAATGAAATGGA
39664446 AGAGTT
1 AGAGTT
39664452 TCGGGCACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.43, C:0.00, G:0.33, T:0.24
Consensus pattern (18 bp):
AGAGTTGAATGAAATGGA
Found at i:39677688 original size:15 final size:17
Alignment explanation
Indices: 39677670--39677701 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
39677660 CAATGACAAT
39677670 ACCAG-CAA-TTGCTCC
1 ACCAGACAACTTGCTCC
39677685 ACCAGACAACTTGCTCC
1 ACCAGACAACTTGCTCC
39677702 CACTACTCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 3 0.20
17 7 0.47
ACGTcount: A:0.28, C:0.41, G:0.12, T:0.19
Consensus pattern (17 bp):
ACCAGACAACTTGCTCC
Found at i:39679142 original size:21 final size:22
Alignment explanation
Indices: 39679103--39679143 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
39679093 AATTTAAAAA
39679103 TTCAAAATATTATAAAATTATT
1 TTCAAAATATTATAAAATTATT
*
39679125 TTCAAACTATTA-AAAATTA
1 TTCAAAATATTATAAAATTA
39679144 CTAAAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (22 bp):
TTCAAAATATTATAAAATTATT
Found at i:39679170 original size:30 final size:29
Alignment explanation
Indices: 39679106--39679178 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
39679096 TTAAAAATTC
* *
39679106 AAAATATTATAAAATTATTTTCAAACTAT
1 AAAAAATTATAAAATTATTTTAAAACTAT
* *
39679135 TAAAAATTACTAAAATTA-TTTAAAAGTAT
1 AAAAAATTA-TAAAATTATTTTAAAACTAT
*
39679164 AAAAAAACTATAAAA
1 -AAAAAATTATAAAA
39679179 AATATTTTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
29 21 0.58
30 15 0.42
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.34
Consensus pattern (29 bp):
AAAAAATTATAAAATTATTTTAAAACTAT
Found at i:39680689 original size:18 final size:17
Alignment explanation
Indices: 39680668--39680707 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 17
39680658 TAAGTTTTGG
39680668 ATTTAATATTTGTTTTTA
1 ATTTAATATTT-TTTTTA
*
39680686 ATTTTTATATTTTTTTTA
1 A-TTTAATATTTTTTTTA
39680704 ATTT
1 ATTT
39680708 TAGTTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 3 0.15
18 8 0.40
19 9 0.45
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (17 bp):
ATTTAATATTTTTTTTA
Found at i:39680708 original size:18 final size:19
Alignment explanation
Indices: 39680673--39680708 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
39680663 TTTGGATTTA
39680673 ATATTTGTTTTTAATTTTT
1 ATATTTGTTTTTAATTTTT
39680692 ATATTT-TTTTTAATTTT
1 ATATTTGTTTTTAATTTT
39680709 AGTTTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (19 bp):
ATATTTGTTTTTAATTTTT
Found at i:39680730 original size:24 final size:24
Alignment explanation
Indices: 39680681--39680731 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
39680671 TAATATTTGT
**
39680681 TTTTAATTTTTATATTTTTTTTAA
1 TTTTAATTTTTATATTTTTTAAAA
*
39680705 TTTTAGTTTTTATATTTTTTAAAA
1 TTTTAATTTTTATATTTTTTAAAA
39680729 TTT
1 TTT
39680732 AAAATTTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (24 bp):
TTTTAATTTTTATATTTTTTAAAA
Found at i:39681793 original size:20 final size:20
Alignment explanation
Indices: 39681765--39681809 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
39681755 TTATATGTAC
*
39681765 ATTAAT-AAATAATTTAAAAA
1 ATTAATAAAAT-ATTCAAAAA
*
39681785 ATTATTAAAATATTCAAAAA
1 ATTAATAAAATATTCAAAAA
39681805 ATTAA
1 ATTAA
39681810 AAATTTTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
ATTAATAAAATATTCAAAAA
Found at i:39681826 original size:27 final size:27
Alignment explanation
Indices: 39681781--39681832 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
39681771 AAATAATTTA
39681781 AAAAATTATTAAAATATTCAAAAAATT
1 AAAAATTATTAAAATATTCAAAAAATT
*
39681808 AAAAATT-TTATAATAATTCAAAAAA
1 AAAAATTATTAAAAT-ATTCAAAAAA
39681833 GTTAGCATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (27 bp):
AAAAATTATTAAAATATTCAAAAAATT
Found at i:39682588 original size:31 final size:31
Alignment explanation
Indices: 39682549--39682623 Score: 132
Period size: 31 Copynumber: 2.4 Consensus size: 31
39682539 CTTAACAGCA
*
39682549 CAGTGACTTAAATAATTTTTTTTGAATAGTT
1 CAGTGACTTAAATAATTTTTTTTGAATAGCT
*
39682580 TAGTGACTTAAATAATTTTTTTTGAATAGCT
1 CAGTGACTTAAATAATTTTTTTTGAATAGCT
39682611 CAGTGACTTAAAT
1 CAGTGACTTAAAT
39682624 GAAAACTTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.45
Consensus pattern (31 bp):
CAGTGACTTAAATAATTTTTTTTGAATAGCT
Found at i:39682647 original size:31 final size:31
Alignment explanation
Indices: 39682550--39682647 Score: 90
Period size: 31 Copynumber: 3.2 Consensus size: 31
39682540 TTAACAGCAC
*** *
39682550 AGTGACTTAAATAATTTTTTTTGAATAGTTT
1 AGTGACTTAAATAATAACTTTCGAATAGTTT
*** * * *
39682581 AGTGACTTAAATAATTTTTTTTGAATAGCTC
1 AGTGACTTAAATAATAACTTTCGAATAGTTT
39682612 AGTGACTTAAATGAA-AACTTTCGAATAGTTT
1 AGTGACTTAAAT-AATAACTTTCGAATAGTTT
39682643 AGTGA
1 AGTGA
39682648 TCAAATTGTA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
31 56 0.97
32 2 0.03
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (31 bp):
AGTGACTTAAATAATAACTTTCGAATAGTTT
Found at i:39682838 original size:29 final size:30
Alignment explanation
Indices: 39682776--39682845 Score: 97
Period size: 29 Copynumber: 2.3 Consensus size: 30
39682766 ATCTCAAAAC
*
39682776 TATACATGAACTATGGTTTAATGTGCAATTT
1 TATACATGAACTATGATTT-ATGTGCAATTT
* *
39682807 TATACATGAACTTTGATTT-TGTGTAATTT
1 TATACATGAACTATGATTTATGTGCAATTT
39682836 TATACATGAA
1 TATACATGAA
39682846 ATTTTTATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 19 0.53
31 17 0.47
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (30 bp):
TATACATGAACTATGATTTATGTGCAATTT
Found at i:39686386 original size:21 final size:22
Alignment explanation
Indices: 39686362--39686402 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
39686352 GGCAACTGAT
39686362 CGGTCTTGAAG-TGTGAACATG
1 CGGTCTTGAAGATGTGAACATG
* *
39686383 CGGTTTTGTAGATGTGAACA
1 CGGTCTTGAAGATGTGAACA
39686403 ACAACAAACG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.24, C:0.12, G:0.32, T:0.32
Consensus pattern (22 bp):
CGGTCTTGAAGATGTGAACATG
Found at i:39688781 original size:68 final size:69
Alignment explanation
Indices: 39688632--39688791 Score: 209
Period size: 68 Copynumber: 2.3 Consensus size: 69
39688622 TTTTTCCAAC
* * **
39688632 ATATAACTTTTTGTATGCCATAGAGGCTTGTCACTTTGTGTATGTGTTAATGGATGTGGTGGTGA
1 ATATAACTTTTTGTATGCAATTGAGGCTTGTCACTTTGTGTATGTGTTAAACGATGTGGTGGTGA
39688697 ACTA
66 ACTA
*
39688701 ATATAACCTTTTGTATGCAATTGTAGG-TTGTCACTTT-TGTATGT-TTAAACGAGTGTGGTGGT
1 ATATAACTTTTTGTATGCAATTG-AGGCTTGTCACTTTGTGTATGTGTTAAACGA-TGTGGTGGT
* *
39688763 GGAGTA
64 GAACTA
*
39688769 ATATAACTTTTTGTATGTAATTG
1 ATATAACTTTTTGTATGCAATTG
39688792 CAGGATGATA
Statistics
Matches: 80, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
67 6 0.08
68 41 0.51
69 30 0.38
70 3 0.04
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.42
Consensus pattern (69 bp):
ATATAACTTTTTGTATGCAATTGAGGCTTGTCACTTTGTGTATGTGTTAAACGATGTGGTGGTGA
ACTA
Found at i:39689276 original size:20 final size:20
Alignment explanation
Indices: 39689248--39689487 Score: 115
Period size: 20 Copynumber: 11.8 Consensus size: 20
39689238 TCTTCAACAA
*
39689248 TTTTGAATCAAGTGAAATTT
1 TTTTAAATCAAGTGAAATTT
* * ***
39689268 TTTTAAATCGAGTAAAACCG
1 TTTTAAATCAAGTGAAATTT
** *
39689288 TTTTAAATTGAGTGAATTTT
1 TTTTAAATCAAGTGAAATTT
* * ***
39689308 TTTTGACTCAAGTGAAAAACA
1 TTTTAAATCAAGTG-AAATTT
* ***
39689329 ATTTAAATCAAGTGAAACGA
1 TTTTAAATCAAGTGAAATTT
*
39689349 TTTTAAATCAAGTGAAAATT
1 TTTTAAATCAAGTGAAATTT
***
39689369 TTTTAAATCGAA-TGAAACAA
1 TTTTAAATC-AAGTGAAATTT
*
39689389 TTTTAAATCAGGTGAAATTT
1 TTTTAAATCAAGTGAAATTT
* ** * *
39689409 TTTTTACCCAAGTGAAAAATA
1 TTTTAAATCAAGTG-AAATTT
* **
39689430 TTTTAAATCGAGTGAAATAG
1 TTTTAAATCAAGTGAAATTT
*
39689450 TTTTAAATCCAA-TGAATTTTT
1 TTTTAAAT-CAAGTGAA-ATTT
* *
39689471 TTTTGACTCAAGTGAAA
1 TTTTAAATCAAGTGAAA
39689488 AACTGCTCCC
Statistics
Matches: 157, Mismatches: 56, Indels: 14
0.69 0.25 0.06
Matches are distributed among these distances:
19 1 0.01
20 114 0.73
21 42 0.27
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (20 bp):
TTTTAAATCAAGTGAAATTT
Found at i:39689343 original size:41 final size:40
Alignment explanation
Indices: 39689243--39689366 Score: 104
Period size: 41 Copynumber: 3.0 Consensus size: 40
39689233 AAAATTCTTC
* *
39689243 AACAATTTTGAATCAAGTGAAATTTTTTTAAATCGAGTAAA
1 AACAA-TTTAAATCAAGTGAAATTTTTTTAAATCAAGTAAA
* ** ** * * *
39689284 ACCGTTTTAAATTGAGTGAATTTTTTTTGACTCAAGTGAAA
1 AACAATTTAAATCAAGTGAAATTTTTTTAAATCAAGT-AAA
*** *
39689325 AACAATTTAAATCAAGTGAAACGATTTTAAATCAAGTGAA
1 AACAATTTAAATCAAGTGAAATTTTTTTAAATCAAGTAAA
39689365 AA
1 AA
39689367 TTTTTTAAAT
Statistics
Matches: 60, Mismatches: 22, Indels: 3
0.71 0.26 0.04
Matches are distributed among these distances:
40 29 0.48
41 31 0.52
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.35
Consensus pattern (40 bp):
AACAATTTAAATCAAGTGAAATTTTTTTAAATCAAGTAAA
Found at i:39689371 original size:61 final size:60
Alignment explanation
Indices: 39689268--39689458 Score: 145
Period size: 61 Copynumber: 3.1 Consensus size: 60
39689258 AGTGAAATTT
* * ** ** * *
39689268 TTTTAAATCGAGTAAAACCGTTTTAAATTGAGTGAATTTTTTTTGACTC-AAGTGAAAAACAA
1 TTTTAAATCAAGTGAAACCGTTTTAAATCAAGTGAAAATTTTTTAAATCGAA-TG--AAACAA
39689330 -TTTAAATCAAGTGAAA-CGATTTTAAATCAAGTGAAAATTTTTTAAATCGAATGAAACAA
1 TTTTAAATCAAGTGAAACCG-TTTTAAATCAAGTGAAAATTTTTTAAATCGAATGAAACAA
* *** * ** * * * *
39689389 TTTTAAATCAGGTGAAATTTTTTTTACCCAAGTGAAAAATATTTTAAATCGAGTGAAATAG
1 TTTTAAATCAAGTGAAACCGTTTTAAATCAAGTG-AAAATTTTTTAAATCGAATGAAACAA
39689450 TTTTAAATC
1 TTTTAAATC
39689459 CAATGAATTT
Statistics
Matches: 106, Mismatches: 18, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
59 6 0.06
60 28 0.26
61 70 0.66
62 2 0.02
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (60 bp):
TTTTAAATCAAGTGAAACCGTTTTAAATCAAGTGAAAATTTTTTAAATCGAATGAAACAA
Found at i:39689385 original size:40 final size:40
Alignment explanation
Indices: 39689330--39689446 Score: 137
Period size: 40 Copynumber: 2.9 Consensus size: 40
39689320 TGAAAAACAA
*
39689330 TTTAAATCAAGTGAAACGATTTTAAATCAAGTGAAAATTT
1 TTTAAATCAAGTGAAACAATTTTAAATCAAGTGAAAATTT
* *
39689370 TTTAAATCGAA-TGAAACAATTTTAAATCAGGTGAAATTTT
1 TTTAAATC-AAGTGAAACAATTTTAAATCAAGTGAAAATTT
* ** * *
39689410 TTTTACCCAAGTGAAAAATATTTTAAATCGAGTGAAA
1 TTTAAATCAAGTGAAACA-ATTTTAAATCAAGTGAAA
39689447 TAGTTTTAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
39 2 0.03
40 45 0.69
41 18 0.28
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.35
Consensus pattern (40 bp):
TTTAAATCAAGTGAAACAATTTTAAATCAAGTGAAAATTT
Found at i:39689471 original size:61 final size:62
Alignment explanation
Indices: 39689357--39689489 Score: 173
Period size: 61 Copynumber: 2.2 Consensus size: 62
39689347 GATTTTAAAT
* *
39689357 CAAGTG-AAAATTTTTTAAATCGAATGAAACAATTTTAAATCAGGTGAAATTTTTTTT-ACC
1 CAAGTGAAAAATATTTTAAATCGAATGAAACAATTTTAAATCAGATGAAATTTTTTTTGACC
* * * * *
39689417 CAAGTGAAAAATATTTTAAATCGAGTGAAATAGTTTTAAATCCA-ATGAATTTTTTTTTGACT
1 CAAGTGAAAAATATTTTAAATCGAATGAAACAATTTTAAAT-CAGATGAAATTTTTTTTGACC
39689479 CAAGTGAAAAA
1 CAAGTGAAAAA
39689490 CTGCTCCCTA
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
60 6 0.10
61 42 0.67
62 15 0.24
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (62 bp):
CAAGTGAAAAATATTTTAAATCGAATGAAACAATTTTAAATCAGATGAAATTTTTTTTGACC
Found at i:39689472 original size:101 final size:101
Alignment explanation
Indices: 39689247--39689473 Score: 273
Period size: 101 Copynumber: 2.2 Consensus size: 101
39689237 TTCTTCAACA
* * ** *
39689247 ATTTTGAATCAAGTGAAATTTTTTTAAATCGAGTAAAACCGTTTTAAATTGAGTGAATTTTTTTT
1 ATTTTAAATCAAGTGAAATTTTTTTAAATCGAATAAAACAATTTTAAATAGAGTGAATTTTTTTT
* *
39689312 GACTCAAGTGAAAAACAATTTAAATCAAGTGAAACG
66 GACCCAAGTGAAAAACAATTTAAATCAAGTGAAAAG
* *
39689348 ATTTTAAATCAAGTGAAAATTTTTTAAATCGAATGAAACAATTTTAAATCAG-GTGAAATTTTTT
1 ATTTTAAATCAAGTGAAATTTTTTTAAATCGAATAAAACAATTTTAAAT-AGAGTG-AATTTTTT
* * *
39689412 TT-ACCCAAGTGAAAAATATTTTAAATCGAGTGAAATAG
64 TTGACCCAAGTGAAAAACAATTTAAATCAAGTGAAA-AG
*
39689450 -TTTTAAATCCAA-TGAATTTTTTTT
1 ATTTTAAAT-CAAGTGAAATTTTTTT
39689474 TGACTCAAGT
Statistics
Matches: 108, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
101 93 0.86
102 15 0.14
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (101 bp):
ATTTTAAATCAAGTGAAATTTTTTTAAATCGAATAAAACAATTTTAAATAGAGTGAATTTTTTTT
GACCCAAGTGAAAAACAATTTAAATCAAGTGAAAAG
Found at i:39689644 original size:113 final size:113
Alignment explanation
Indices: 39689527--39689765 Score: 281
Period size: 112 Copynumber: 2.1 Consensus size: 113
39689517 TTATAAAAGC
* * * *
39689527 ATCGATACCAAAATGTGA-TTCTGACTTCAAAGGAATTTGATCAAACACATTTTTATTGATAGTT
1 ATCGATACCAAAATGTAACTTCTGACTTCAAAGGAATTTGAGCAAACACATTTTTATCGATACTT
* *
39689591 TGCAAAAAGTATCGATACTT-CAAGAAAAATCATCGATA-CCTTTTTCAGT
66 TGCAAAAAGTATCAATACTTAC-A-AAAAATCATCGATATAC-TTTTCAGT
* * * **
39689640 ATCGATACCAAAA--TAACTTGTGACTTCGAAGGAATTTGAGCAAGCATGTTTTTATCGATACTT
1 ATCGATACCAAAATGTAACTTCTGACTTCAAAGGAATTTGAGCAAACACATTTTTATCGATACTT
* * *
39689703 TGCAAAAAGTATCAATACTTACAAAATATTATCGATATACTTTTCGGT
66 TGCAAAAAGTATCAATACTTACAAAAAATCATCGATATACTTTTCAGT
*
39689751 ATCGATACGAAAATG
1 ATCGATACCAAAATG
39689766 ACATTCAACG
Statistics
Matches: 106, Mismatches: 15, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
111 33 0.31
112 59 0.56
113 14 0.13
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.33
Consensus pattern (113 bp):
ATCGATACCAAAATGTAACTTCTGACTTCAAAGGAATTTGAGCAAACACATTTTTATCGATACTT
TGCAAAAAGTATCAATACTTACAAAAAATCATCGATATACTTTTCAGT
Found at i:39691799 original size:16 final size:16
Alignment explanation
Indices: 39691762--39691801 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
39691752 TGACTCAAAT
* *
39691762 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
39691778 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
39691794 TAAAATTA
1 TAAAATTA
39691802 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:39691866 original size:66 final size:67
Alignment explanation
Indices: 39691790--39691928 Score: 262
Period size: 68 Copynumber: 2.1 Consensus size: 67
39691780 AAATTAATTG
39691790 TTAGTAAAATTATCAAATTATTAATTG-TTAATTGTATTAATTGTTGTAACAAAATCTAACATTT
1 TTAGTAAAATTATCAAATTATTAATTGATTAATTGTATTAATTGTTGTAACAAAATCTAACATTT
39691854 GA
66 GA
39691856 TTAGTAAAATTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
1 TTAGTAAAATTATCAAATTATTAATTG-ATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
39691921 TGA
65 TGA
39691924 TTAGT
1 TTAGT
39691929 TTACATTTTT
Statistics
Matches: 71, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
66 27 0.38
68 44 0.62
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.45
Consensus pattern (67 bp):
TTAGTAAAATTATCAAATTATTAATTGATTAATTGTATTAATTGTTGTAACAAAATCTAACATTT
GA
Found at i:39691886 original size:9 final size:9
Alignment explanation
Indices: 39691874--39691901 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
39691864 ATTATCAAAT
39691874 TATTAATTG
1 TATTAATTG
39691883 TATTAATTG
1 TATTAATTG
39691892 TATTAATTG
1 TATTAATTG
39691901 T
1 T
39691902 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:39693143 original size:16 final size:16
Alignment explanation
Indices: 39693122--39693154 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
39693112 TATATTTTTT
39693122 AAACATAAAAAACTTA
1 AAACATAAAAAACTTA
39693138 AAACATAAAAAACTTA
1 AAACATAAAAAACTTA
39693154 A
1 A
39693155 TATATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.70, C:0.12, G:0.00, T:0.18
Consensus pattern (16 bp):
AAACATAAAAAACTTA
Found at i:39694903 original size:2 final size:2
Alignment explanation
Indices: 39694896--39694930 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
39694886 ACATACCTTA
39694896 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
39694931 TATATATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:39695295 original size:43 final size:43
Alignment explanation
Indices: 39695200--39695315 Score: 139
Period size: 43 Copynumber: 2.7 Consensus size: 43
39695190 CGTACAACGC
* *
39695200 CAACGTCCCAAACGTGGTCTTACATG-TAATCACAAATCGATA
1 CAACGTCCCAAACGTGGTCTTACACGAAAATCACAAATCGATA
* *
39695242 CCACTATCCCAAACAG-GGTCTTACACGAAAAT-ACAAATCGATAA
1 CAAC-GTCCCAAAC-GTGGTCTTACACGAAAATCACAAATCGAT-A
*
39695286 CAACGTCCCAGACGTGGTCTTACACGAAAA
1 CAACGTCCCAAACGTGGTCTTACACGAAAA
39695316 CACTTATCAA
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
42 4 0.06
43 50 0.81
44 8 0.13
ACGTcount: A:0.38, C:0.28, G:0.15, T:0.20
Consensus pattern (43 bp):
CAACGTCCCAAACGTGGTCTTACACGAAAATCACAAATCGATA
Found at i:39698203 original size:6 final size:6
Alignment explanation
Indices: 39698182--39698216 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
39698172 TATTTTTTTG
*
39698182 TTTTCT TTCTTTT TTTTCT TTTTCT TTTTCT TTTT
1 TTTTCT TT-TTCT TTTTCT TTTTCT TTTTCT TTTT
39698217 GTTAATTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTCT
Found at i:39698215 original size:19 final size:20
Alignment explanation
Indices: 39698167--39698216 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
39698157 CTTCCCCATC
*
39698167 TTTTCTATTTTTTTGTTTTCT
1 TTTTCT-TTTTTCTGTTTTCT
39698188 TTCTT-TTTTTTCT-TTTTCT
1 TT-TTCTTTTTTCTGTTTTCT
39698207 TTTTCTTTTT
1 TTTTCTTTTT
39698217 GTTAATTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 2 0.08
19 13 0.50
20 6 0.23
21 3 0.12
22 2 0.08
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.84
Consensus pattern (20 bp):
TTTTCTTTTTTCTGTTTTCT
Found at i:39699408 original size:34 final size:33
Alignment explanation
Indices: 39699370--39699467 Score: 108
Period size: 33 Copynumber: 2.9 Consensus size: 33
39699360 TTCTGGTCTG
*
39699370 ATATGACATTCTGTTCTAATATATGTTTCTGAAA
1 ATATGACATT-TGATCTAATATATGTTTCTGAAA
* * *
39699404 ATATGATATTTCGATCCAAAATATG-TTCTGAAA
1 ATATGACATTT-GATCTAATATATGTTTCTGAAA
* *
39699437 ATATGACATTATGATCTGATGTATGTTTCTG
1 ATATGACATT-TGATCTAATATATGTTTCTG
39699468 GTAATACAAT
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
33 27 0.52
34 25 0.48
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (33 bp):
ATATGACATTTGATCTAATATATGTTTCTGAAA
Found at i:39702417 original size:19 final size:19
Alignment explanation
Indices: 39702382--39702436 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 19
39702372 CTTTACTTTA
* *
39702382 TATT-ATAATAATATAATT
1 TATTAATAATCATTTAATT
39702400 TATTAATAATCATTTAATT
1 TATTAATAATCATTTAATT
* * *
39702419 AATAAAT-ATCTTTTAATT
1 TATTAATAATCATTTAATT
39702437 ATAACACAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 14 0.45
19 17 0.55
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTAATAATCATTTAATT
Found at i:39704913 original size:20 final size:19
Alignment explanation
Indices: 39704888--39704929 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
39704878 TACGGTGGCT
39704888 AAAAAAGAAAGAAAAGAGAG
1 AAAAAAGAAAGAAAAGA-AG
* *
39704908 AAAAAAGAGAGAAGAGAAG
1 AAAAAAGAAAGAAAAGAAG
39704927 AAA
1 AAA
39704930 CAACTCAAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (19 bp):
AAAAAAGAAAGAAAAGAAG
Found at i:39705913 original size:21 final size:21
Alignment explanation
Indices: 39705887--39705927 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
39705877 TAACGGGACC
39705887 GCTGATGTGG-CAAGTTAACTA
1 GCTGATGTGGCCAA-TTAACTA
39705908 GCTGATGTGGCCAATTAACT
1 GCTGATGTGGCCAATTAACT
39705928 TGCCACGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (21 bp):
GCTGATGTGGCCAATTAACTA
Found at i:39707448 original size:17 final size:17
Alignment explanation
Indices: 39707426--39707503 Score: 83
Period size: 17 Copynumber: 4.8 Consensus size: 17
39707416 GCATCTCCAT
39707426 TTTTTC-TCTTCTCCTCC
1 TTTTTCTTCTTCTCCT-C
39707443 TTTTTCTTCTTCTCCTC
1 TTTTTCTTCTTCTCCTC
*
39707460 TTCTTCTTCTTCT--TC
1 TTTTTCTTCTTCTCCTC
* **
39707475 TTCTTCTTCTTCTTTTC
1 TTTTTCTTCTTCTCCTC
39707492 TTTTTC-TCTTCT
1 TTTTTCTTCTTCT
39707504 TAAACCTTAA
Statistics
Matches: 56, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
15 15 0.27
16 6 0.11
17 26 0.46
18 9 0.16
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTTCTTCTTCTCCTC
Found at i:39707452 original size:3 final size:3
Alignment explanation
Indices: 39707432--39707504 Score: 80
Period size: 3 Copynumber: 25.3 Consensus size: 3
39707422 CCATTTTTTC
* * * *
39707432 TCT TCT CCT CCT TTT TCT TCT TC- TCC TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
39707479 TCT TCT TCT T-T TCT TTT TC- TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
39707505 AAACCTTAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
2 6 0.10
3 54 0.90
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:39707462 original size:26 final size:26
Alignment explanation
Indices: 39707431--39707481 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
39707421 TCCATTTTTT
*
39707431 CTCTTCTCCTCCTTTTTCTTCTTCTC
1 CTCTTCTCCTCCTTCTTCTTCTTCTC
* *
39707457 CTCTTCTTCTTCTTCTTCTTCTTCT
1 CTCTTCTCCTCCTTCTTCTTCTTCT
39707482 TCTTCTTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (26 bp):
CTCTTCTCCTCCTTCTTCTTCTTCTC
Found at i:39707478 original size:29 final size:29
Alignment explanation
Indices: 39707432--39707504 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 29
39707422 CCATTTTTTC
* * *
39707432 TCTTCTCCTCCTTTTTCTTCTTCTCCTCT
1 TCTTCTTCTTCTTCTTCTTCTTCTCCTCT
* *
39707461 TCTTCTTCTTCTTCTTCTTCTTCTTCTTT
1 TCTTCTTCTTCTTCTTCTTCTTCTCCTCT
*
39707490 TCTTTTTC-TCTTCTT
1 TCTTCTTCTTCTTCTT
39707505 AAACCTTAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
28 7 0.18
29 31 0.82
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (29 bp):
TCTTCTTCTTCTTCTTCTTCTTCTCCTCT
Found at i:39711009 original size:27 final size:27
Alignment explanation
Indices: 39710979--39711045 Score: 134
Period size: 27 Copynumber: 2.5 Consensus size: 27
39710969 ACTGATAGAA
39710979 TTTGATGGAGTTTGAATGGCTCACAGG
1 TTTGATGGAGTTTGAATGGCTCACAGG
39711006 TTTGATGGAGTTTGAATGGCTCACAGG
1 TTTGATGGAGTTTGAATGGCTCACAGG
39711033 TTTGATGGAGTTT
1 TTTGATGGAGTTT
39711046 ATTTTTTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.21, C:0.09, G:0.33, T:0.37
Consensus pattern (27 bp):
TTTGATGGAGTTTGAATGGCTCACAGG
Found at i:39711013 original size:16 final size:17
Alignment explanation
Indices: 39710988--39711037 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
39710978 ATTTGATGGA
39710988 GTTTGAATGGCTCACAG
1 GTTTGAATGGCTCACAG
39711005 GTTTG-ATGG-----A-
1 GTTTGAATGGCTCACAG
39711015 GTTTGAATGGCTCACAG
1 GTTTGAATGGCTCACAG
39711032 GTTTGA
1 GTTTGA
39711038 TGGAGTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 14
0.65 0.00 0.35
Matches are distributed among these distances:
10 5 0.19
11 5 0.19
16 5 0.19
17 11 0.42
ACGTcount: A:0.22, C:0.12, G:0.32, T:0.34
Consensus pattern (17 bp):
GTTTGAATGGCTCACAG
Found at i:39711377 original size:21 final size:21
Alignment explanation
Indices: 39711309--39711378 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
39711299 TTTCAACTTT
*
39711309 TTTATAGTATTATACATTATA
1 TTTATAGTATTATATATTATA
* *
39711330 --AAGTAG-ATTATATATTATT
1 TTTA-TAGTATTATATATTATA
39711349 TTTATAGTATTATATATTATGA
1 TTTATAGTATTATATATTAT-A
39711371 TTT-TAGTA
1 TTTATAGTA
39711379 AATTCATATA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
19 12 0.31
20 6 0.15
21 18 0.46
22 3 0.08
ACGTcount: A:0.37, C:0.01, G:0.09, T:0.53
Consensus pattern (21 bp):
TTTATAGTATTATATATTATA
Found at i:39711420 original size:17 final size:18
Alignment explanation
Indices: 39711395--39711440 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
39711385 TATAAGAATA
*
39711395 ATTATATTA-AGAATTTT
1 ATTAAATTATAGAATTTT
* *
39711412 ATTAAATTATATATTTTT
1 ATTAAATTATAGAATTTT
39711430 ATTAAATTATA
1 ATTAAATTATA
39711441 TTTAATAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
ATTAAATTATAGAATTTT
Found at i:39711516 original size:59 final size:59
Alignment explanation
Indices: 39711343--39711516 Score: 167
Period size: 59 Copynumber: 2.9 Consensus size: 59
39711333 TAGATTATAT
* *
39711343 ATTAT-TTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATA-ATTAT
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTTAG
* * * * ** * * * *
39711400 ATTAAGAATTTTATTA-AATTATATATTTTTATTAAATTATATTTA-ATAATAATTATTTTAG
1 ATT-A-TATTTTA-TAGTATTATATATTATGATTTTAGTAAATTCATATAAGAA-TATTTTAG
*
39711461 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATTTAAGAATATTT
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTT
39711517 AATATTAAGA
Statistics
Matches: 86, Mismatches: 23, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
57 3 0.03
58 3 0.03
59 38 0.44
60 34 0.40
61 8 0.09
ACGTcount: A:0.40, C:0.01, G:0.06, T:0.53
Consensus pattern (59 bp):
ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTTAG
Done.