Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 104 of 186
Found at i:34142089 original size:11 final size:10
Alignment explanation
Indices: 34142045--34142091 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
34142035 AGCTCACTCG
*
34142045 AGCTCAAGTC
1 AGCTCAATTC
34142055 AGCTCAA-TC
1 AGCTCAATTC
*
34142064 GAGCTCAATTT
1 -AGCTCAATTC
34142075 AGCTACAATTC
1 AGCT-CAATTC
34142086 AGCTCA
1 AGCTCA
34142092 TTTATTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 2 0.06
10 20 0.62
11 10 0.31
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:34150036 original size:30 final size:30
Alignment explanation
Indices: 34150002--34150098 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
34149992 AGCTCACTCC
34150002 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
34150032 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
34150062 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
34150092 TAGCTCA
1 TAGCTCA
34150099 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:34154607 original size:24 final size:23
Alignment explanation
Indices: 34154580--34154629 Score: 77
Period size: 22 Copynumber: 2.2 Consensus size: 23
34154570 TTTATTTAGG
34154580 TTATATATAAATA-T-TATATAA
1 TTATATATAAATATTATATATAA
34154601 TTATTATATAAATATTATATATAA
1 TTA-TATATAAATATTATATATAA
34154625 TTATA
1 TTATA
34154630 AACCATCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 3 0.12
22 10 0.38
23 3 0.12
24 10 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TTATATATAAATATTATATATAA
Found at i:34154624 original size:13 final size:11
Alignment explanation
Indices: 34154583--34154621 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
34154573 ATTTAGGTTA
34154583 TATATAAATAT
1 TATATAAATAT
*
34154594 TATATAATTAT
1 TATATAAATAT
34154605 TATATAAATAT
1 TATATAAATAT
34154616 TATATA
1 TATATA
34154622 TAATTATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
TATATAAATAT
Found at i:34154657 original size:3 final size:3
Alignment explanation
Indices: 34154649--34154689 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
34154639 TATGTTTTTA
* *
34154649 TAT TAT TAT TAT TAT TAT TAT TAG TAT TGT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
34154690 AATGAAGTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:34156250 original size:23 final size:23
Alignment explanation
Indices: 34156224--34156311 Score: 85
Period size: 21 Copynumber: 4.0 Consensus size: 23
34156214 GCTTTACTGA
* *
34156224 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
34156247 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
34156268 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
* * *
34156290 T-AGGCACTTTATGTGTCATATT
1 TCAGGCACCTCATGTGTCGTATT
34156312 GTGATCAGGT
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
21 34 0.62
22 3 0.05
23 18 0.33
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.39
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:34156271 original size:21 final size:21
Alignment explanation
Indices: 34156236--34156296 Score: 86
Period size: 21 Copynumber: 2.8 Consensus size: 21
34156226 AGGCACTTTA
34156236 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTA--TCAGGCACCTCG
34156259 TGTGTCGTATCAGGCACCTCG
1 TGTGTCGTATCAGGCACCTCG
* *
34156280 TGTGTCGTTTTAGGCAC
1 TGTGTCGTATCAGGCAC
34156297 TTTATGTGTC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 27 0.75
23 9 0.25
ACGTcount: A:0.13, C:0.25, G:0.28, T:0.34
Consensus pattern (21 bp):
TGTGTCGTATCAGGCACCTCG
Found at i:34159592 original size:17 final size:17
Alignment explanation
Indices: 34159570--34159603 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
34159560 TTGATTATCG
34159570 ACAGTTAAATAAAGTGA
1 ACAGTTAAATAAAGTGA
*
34159587 ACAGTTGAATAAAGTGA
1 ACAGTTAAATAAAGTGA
34159604 CGATCAAGAA
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:0.50, C:0.06, G:0.21, T:0.24
Consensus pattern (17 bp):
ACAGTTAAATAAAGTGA
Found at i:34162519 original size:24 final size:23
Alignment explanation
Indices: 34162492--34162541 Score: 77
Period size: 22 Copynumber: 2.2 Consensus size: 23
34162482 TTTATTTAGG
34162492 TTATATATAAATA-T-TATATAA
1 TTATATATAAATATTATATATAA
34162513 TTATTATATAAATATTATATATAA
1 TTA-TATATAAATATTATATATAA
34162537 TTATA
1 TTATA
34162542 AACCATCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 3 0.12
22 10 0.38
23 3 0.12
24 10 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TTATATATAAATATTATATATAA
Found at i:34162536 original size:13 final size:11
Alignment explanation
Indices: 34162495--34162533 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
34162485 ATTTAGGTTA
34162495 TATATAAATAT
1 TATATAAATAT
*
34162506 TATATAATTAT
1 TATATAAATAT
34162517 TATATAAATAT
1 TATATAAATAT
34162528 TATATA
1 TATATA
34162534 TAATTATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
TATATAAATAT
Found at i:34162569 original size:3 final size:3
Alignment explanation
Indices: 34162561--34162601 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
34162551 TATGTTTTTA
* *
34162561 TAT TAT TAT TAT TAT TAT TAT TAG TAT TGT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
34162602 AATGAAGTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:34164484 original size:23 final size:23
Alignment explanation
Indices: 34164454--34164525 Score: 80
Period size: 21 Copynumber: 3.3 Consensus size: 23
34164444 GCTTTACTGA
* *
34164454 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
34164477 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
34164498 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
34164520 T-AGGCA
1 TCAGGCA
34164526 TTTTATGTGT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
21 25 0.57
22 1 0.02
23 18 0.41
ACGTcount: A:0.15, C:0.24, G:0.26, T:0.35
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:34164501 original size:21 final size:22
Alignment explanation
Indices: 34164466--34164525 Score: 88
Period size: 21 Copynumber: 2.8 Consensus size: 22
34164456 AGGCACTTTA
34164466 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTA-TTCAGGCACCTCG
34164489 TGTGTCGTA-TCAGGCACCTCG
1 TGTGTCGTATTCAGGCACCTCG
*
34164510 TGTGTCGT-TTTAGGCA
1 TGTGTCGTATTCAGGCA
34164526 TTTTATGTGT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
21 26 0.74
23 9 0.26
ACGTcount: A:0.13, C:0.23, G:0.28, T:0.35
Consensus pattern (22 bp):
TGTGTCGTATTCAGGCACCTCG
Found at i:34171020 original size:46 final size:47
Alignment explanation
Indices: 34170907--34171038 Score: 117
Period size: 46 Copynumber: 2.8 Consensus size: 47
34170897 TCCACATTAT
* * *
34170907 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACATTGAGAC
1 GAGAGCTAATGTAAGA-CATGTCTGGGACATGGCATCGACATCGAGAC
* * * * * *
34170955 GAGTGCTAGTGTCAGACATGTCTGGGACAT-GCTTCGGCCTCGAGAC
1 GAGAGCTAATGTAAGACATGTCTGGGACATGGCATCGACATCGAGAC
* * *
34171001 GTA-AGCTAATGTAAGACATGTTTAGGACGT-GCATCGAC
1 G-AGAGCTAATGTAAGACATGTCTGGGACATGGCATCGAC
34171039 TACGAGATGT
Statistics
Matches: 68, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
46 40 0.59
47 15 0.22
48 13 0.19
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (47 bp):
GAGAGCTAATGTAAGACATGTCTGGGACATGGCATCGACATCGAGAC
Found at i:34179428 original size:67 final size:66
Alignment explanation
Indices: 34179316--34179485 Score: 166
Period size: 67 Copynumber: 2.5 Consensus size: 66
34179306 ATTCCATTGG
* * * *
34179316 GACAATAAACATGGGGTGTGTTGTATAAGACCATAGCCTATCTATGGCAGCATAA-AGAG-TC-C
1 GACAGTAAACA-GGGGTATGTTGTGTAAGACCATAGCCTAGCTATGGCAGCA-AAGAGAGTTCAC
34179378 GTCGA
64 -T-GA
* * * *
34179383 GACAGTAAATACGGGGTATGTTGTGTAAGACCATAGCTTGGCTATGGTAGCAAAGAGAGTTCACT
1 GACAGTAAACA-GGGGTATGTTGTGTAAGACCATAGCCTAGCTATGGCAGCAAAGAGAGTTCACT
*
34179448 GG
65 GA
* *
34179450 GATAGTAAACAGGAGGTATGTTGTGTAAGACTATAG
1 GACAGTAAACAGG-GGTATGTTGTGTAAGACCATAG
34179486 TCGACTATGA
Statistics
Matches: 86, Mismatches: 13, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
66 4 0.05
67 78 0.91
68 3 0.03
69 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.29, T:0.25
Consensus pattern (66 bp):
GACAGTAAACAGGGGTATGTTGTGTAAGACCATAGCCTAGCTATGGCAGCAAAGAGAGTTCACTG
A
Found at i:34183162 original size:27 final size:27
Alignment explanation
Indices: 34183106--34183175 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
34183096 GTGTTTCCAA
* *
34183106 ACACTAAACATGGGGTAGTTAGCTAGG
1 ACACTAAACAAGGGGTAGTTAGCGAGG
*
34183133 ACACTAAACAAGGGGTAGTTTGTCGA-G
1 ACACTAAACAAGGGGTAGTTAG-CGAGG
* *
34183160 ACATTAAACACGGGGT
1 ACACTAAACAAGGGGT
34183176 CTGTCAGGAC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 35 0.95
28 2 0.05
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.21
Consensus pattern (27 bp):
ACACTAAACAAGGGGTAGTTAGCGAGG
Found at i:34187992 original size:19 final size:19
Alignment explanation
Indices: 34187952--34187992 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
34187942 TAGCTGTATA
*
34187952 ATTATTATTTTAATAAATT
1 ATTATTATTTTAATAAAGT
34187971 ATTATTACTTTTAAT-AAGT
1 ATTATTA-TTTTAATAAAGT
34187990 ATT
1 ATT
34187993 GATAAGGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (19 bp):
ATTATTATTTTAATAAAGT
Found at i:34189144 original size:20 final size:20
Alignment explanation
Indices: 34189119--34189168 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
34189109 ATGTTAGTCC
* *
34189119 CATGAATAGTGGGGTCAACT
1 CATGAATAGTGGAGTCAAAT
*
34189139 CATGAACAGTGGAGTCAAAT
1 CATGAATAGTGGAGTCAAAT
34189159 CATGAATAGT
1 CATGAATAGT
34189169 TATAACATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.24
Consensus pattern (20 bp):
CATGAATAGTGGAGTCAAAT
Found at i:34196828 original size:70 final size:68
Alignment explanation
Indices: 34196754--34197110 Score: 222
Period size: 70 Copynumber: 5.1 Consensus size: 68
34196744 AGGCTCCCAA
* * *
34196754 GTTCAATTCCACAGCCTCCAAAAAAATTAACAAATGCTCAAGCTGCCATCTATGATCTTAAGGCT
1 GTTCAATACCACAGCCTCCAAAAAAATTAACAAA-GCCCAAGCT-CCAACTATGATCTTAAGGCT
34196819 CATAG
64 CATAG
* * * * * * * * *
34196824 GTTCAATATCGCAGCATCTAAAACAATTAGCGAGAGCCCAAGCTCCCAACTGT-AGCTTTAAGGC
1 GTTCAATACCACAGCCTCCAAAAAAATTAAC-AAAGCCCAAGCT-CCAACTATGATC-TTAAGGC
34196888 TTGCAT--
63 -T-CATAG
* ** * * * * *
34196894 GTTTAATACTGCAGCCTCCAAAATAGTTAACAAGAGCCCAAGCTCTTAGCTACGATCTTAAGGCT
1 GTTCAATACCACAGCCTCCAAAAAAATTAACAA-AGCCCAAGCTC-CAACTATGATCTTAAGGCT
34196959 CATAG
64 CATAG
* * * * * *
34196964 GTTCAATACCACAGCCTCCAAAATAGTTAGTAC-GATCCCAAGCTCCCAACTAT-AGCTTGAAAG
1 GTTCAATACCACAGCCTCCAAAAAAATTA--ACAAAGCCCAAGCT-CCAACTATGATCTT-AAGG
*
34197027 CTCACAG
62 CTCATAG
* * * * * * *
34197034 GTTCAATACTACA-ACTCCAAAACAATTAGCGAGAGCCTAAGCTCCCAACTATAATCTTAAGGCT
1 GTTCAATACCACAGCCTCCAAAAAAATTAAC-AAAGCCCAAGCT-CCAACTATGATCTTAAGGCT
*
34197098 CACAG
64 CATAG
34197103 GTTCAATA
1 GTTCAATA
34197111 TCATAGCTTC
Statistics
Matches: 224, Mismatches: 47, Indels: 33
0.74 0.15 0.11
Matches are distributed among these distances:
67 1 0.00
68 3 0.01
69 57 0.25
70 152 0.68
71 6 0.03
72 5 0.02
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.24
Consensus pattern (68 bp):
GTTCAATACCACAGCCTCCAAAAAAATTAACAAAGCCCAAGCTCCAACTATGATCTTAAGGCTCA
TAG
Found at i:34197173 original size:139 final size:140
Alignment explanation
Indices: 34196722--34197178 Score: 427
Period size: 140 Copynumber: 3.3 Consensus size: 140
34196712 AGCGATAGCT
** * ** * * * * *
34196722 CAAGCTCCCAACTGTAGTTTTGAGGCTCCCAAGTTCAATTCCACAGCCTCCAAAAAAATTAACAA
1 CAAGCTCCCAACTGTAGCCTTAAGGCTTACAGGTTCAATACTACAGACTCCAAAACAATTAACAA
* * * * * *
34196787 -ATGCTCAAGCTGCCATCTATGATCTTAAGGCTCATAGGTTCAATATCGCAGCATCTAAAACAAT
66 GA-GCCCAAGCTCCCAACTATGATCTTAAGGCTCATAGGTTCAATATCACAGCATCTAAAATAGT
*
34196851 TAGCGAGAGCC
130 TAGTGAGAGCC
* * * * * * * *
34196862 CAAGCTCCCAACTGTAGCTTTAAGGCTTGCATGTTTAATACTGCAGCCTCCAAAATAGTTAACAA
1 CAAGCTCCCAACTGTAGCCTTAAGGCTTACAGGTTCAATACTACAGACTCCAAAACAATTAACAA
** * * * * *
34196927 GAGCCCAAGCTCTTAGCTACGATCTTAAGGCTCATAGGTTCAATACCACAGCCTCCAAAATAGTT
66 GAGCCCAAGCTCCCAACTATGATCTTAAGGCTCATAGGTTCAATATCACAGCATCTAAAATAGTT
*
34196992 AGT-ACGATCC
131 AGTGA-GAGCC
* * * * *
34197002 CAAGCTCCCAACTATAG-CTTGAAAGCTCACAGGTTCAATACTACA-ACTCCAAAACAATTAGCG
1 CAAGCTCCCAACTGTAGCCTT-AAGGCTTACAGGTTCAATACTACAGACTCCAAAACAATTAACA
* * * * *
34197065 AGAGCCTAAGCTCCCAACTATAATCTTAAGGCTCACAGGTTCAATATCATAGCTTCTAAAATAGT
65 AGAGCCCAAGCTCCCAACTATGATCTTAAGGCTCATAGGTTCAATATCACAGCATCTAAAATAGT
* *
34197130 TAGTGTGAGCT
130 TAGTGAGAGCC
* * *
34197141 GAAGCTCCCAACTGTTGCCTTAGGGCTTACAGGTTCAA
1 CAAGCTCCCAACTGTAGCCTTAAGGCTTACAGGTTCAA
34197179 CACCGCAACC
Statistics
Matches: 254, Mismatches: 58, Indels: 11
0.79 0.18 0.03
Matches are distributed among these distances:
139 105 0.41
140 148 0.58
141 1 0.00
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (140 bp):
CAAGCTCCCAACTGTAGCCTTAAGGCTTACAGGTTCAATACTACAGACTCCAAAACAATTAACAA
GAGCCCAAGCTCCCAACTATGATCTTAAGGCTCATAGGTTCAATATCACAGCATCTAAAATAGTT
AGTGAGAGCC
Found at i:34200276 original size:23 final size:23
Alignment explanation
Indices: 34200249--34200362 Score: 115
Period size: 23 Copynumber: 4.9 Consensus size: 23
34200239 TCAAATCCTA
34200249 AGAGCTTACTGTTTCAGCTCATT
1 AGAGCTTACTGTTTCAGCTCATT
* *
34200272 GGAGCTTACTGTTTCAGCTCGTT
1 AGAGCTTACTGTTTCAGCTCATT
*
34200295 TGAGCTTACTGTTT-AGCTCGA-T
1 AGAGCTTACTGTTTCAGCTC-ATT
** * *
34200317 AGAGCTTACCATTTCAGCTTAAT
1 AGAGCTTACTGTTTCAGCTCATT
*
34200340 AGAGCTTATTGTTCATCAGCTCA
1 AGAGCTTACTGTT--TCAGCTCA
34200363 GGAGGAGCTT
Statistics
Matches: 74, Mismatches: 12, Indels: 8
0.79 0.13 0.09
Matches are distributed among these distances:
22 18 0.24
23 49 0.66
25 7 0.09
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (23 bp):
AGAGCTTACTGTTTCAGCTCATT
Found at i:34200345 original size:45 final size:46
Alignment explanation
Indices: 34200249--34200362 Score: 115
Period size: 45 Copynumber: 2.5 Consensus size: 46
34200239 TCAAATCCTA
* ** **
34200249 AGAGCTTACTGTTTCAGCTCATTGGAGCTTACTGTTTCAGCTCGTT
1 AGAGCTTACTGTTTCAGCTCATTAGAGCTTACCATTTCAGCTCAAT
* *
34200295 TGAGCTTACTGTTT-AGCTCGA-TAGAGCTTACCATTTCAGCTTAAT
1 AGAGCTTACTGTTTCAGCTC-ATTAGAGCTTACCATTTCAGCTCAAT
*
34200340 AGAGCTTATTGTTCATCAGCTCA
1 AGAGCTTACTGTT--TCAGCTCA
34200363 GGAGGAGCTT
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
45 34 0.62
46 14 0.25
47 2 0.04
48 5 0.09
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (46 bp):
AGAGCTTACTGTTTCAGCTCATTAGAGCTTACCATTTCAGCTCAAT
Found at i:34208086 original size:141 final size:141
Alignment explanation
Indices: 34207832--34208113 Score: 555
Period size: 141 Copynumber: 2.0 Consensus size: 141
34207822 CTACTAGATA
*
34207832 CAGCTCGTTGTACGGAAGCTGGAGCATGGCTCTCGGCTCCCTCGGACTCATCTTGTGCTTGATTG
1 CAGCTCATTGTACGGAAGCTGGAGCATGGCTCTCGGCTCCCTCGGACTCATCTTGTGCTTGATTG
34207897 GAAGACATTCACTATATTCAAAATAGTTTAAACAATTAGCAGACGTCACACTATCAACATTCGAA
66 GAAGACATTCACTATATTCAAAATAGTTTAAACAATTAGCAGACGTCACACTATCAACATTCGAA
34207962 TAATGACATGT
131 TAATGACATGT
34207973 CAGCTCATTGTACGGAAGCTGGAGCATGGCTCTCGGCTCCCTCGGACTCATCTTGTGCTTGATTG
1 CAGCTCATTGTACGGAAGCTGGAGCATGGCTCTCGGCTCCCTCGGACTCATCTTGTGCTTGATTG
34208038 GAAGACATTCACTATATTCAAAATAGTTTAAACAATTAGCAGACGTCACACTATCAACATTCGAA
66 GAAGACATTCACTATATTCAAAATAGTTTAAACAATTAGCAGACGTCACACTATCAACATTCGAA
34208103 TAATGACATGT
131 TAATGACATGT
34208114 ATAGTAACTT
Statistics
Matches: 140, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
141 140 1.00
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (141 bp):
CAGCTCATTGTACGGAAGCTGGAGCATGGCTCTCGGCTCCCTCGGACTCATCTTGTGCTTGATTG
GAAGACATTCACTATATTCAAAATAGTTTAAACAATTAGCAGACGTCACACTATCAACATTCGAA
TAATGACATGT
Found at i:34209618 original size:75 final size:75
Alignment explanation
Indices: 34209531--34209679 Score: 280
Period size: 75 Copynumber: 2.0 Consensus size: 75
34209521 TCCGTCAATG
* *
34209531 CTTACGATTGATCATTTCATATATATGCACTCCCGCGAACCTCACATCTCATGGCAGGATTACCA
1 CTTACGAATGATCATTTCACATATATGCACTCCCGCGAACCTCACATCTCATGGCAGGATTACCA
34209596 GTCCAGGCTT
66 GTCCAGGCTT
34209606 CTTACGAATGATCATTTCACATATATGCACTCCCGCGAACCTCACATCTCATGGCAGGATTACCA
1 CTTACGAATGATCATTTCACATATATGCACTCCCGCGAACCTCACATCTCATGGCAGGATTACCA
34209671 GTCCAGGCT
66 GTCCAGGCT
34209680 AAATCCCTCA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 72 1.00
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.28
Consensus pattern (75 bp):
CTTACGAATGATCATTTCACATATATGCACTCCCGCGAACCTCACATCTCATGGCAGGATTACCA
GTCCAGGCTT
Found at i:34212779 original size:13 final size:13
Alignment explanation
Indices: 34212761--34212788 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
34212751 ATAATCCTTA
34212761 ATTAATTCTAACC
1 ATTAATTCTAACC
34212774 ATTAATTCTAACC
1 ATTAATTCTAACC
34212787 AT
1 AT
34212789 CTCCTTTGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (13 bp):
ATTAATTCTAACC
Found at i:34222473 original size:62 final size:62
Alignment explanation
Indices: 34222397--34222521 Score: 241
Period size: 62 Copynumber: 2.0 Consensus size: 62
34222387 AAATGTTGAT
*
34222397 TAGATGACTATGTTTCCTGGTGTTTCTATTCGACATCTACCATATTCTTTTTTAGATAATTG
1 TAGATGACTATGTTTCCTGGTGTTTCTATTCGACATCTACCATATTCATTTTTAGATAATTG
34222459 TAGATGACTATGTTTCCTGGTGTTTCTATTCGACATCTACCATATTCATTTTTAGATAATTG
1 TAGATGACTATGTTTCCTGGTGTTTCTATTCGACATCTACCATATTCATTTTTAGATAATTG
34222521 T
1 T
34222522 CTTTTCCTTA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.23, C:0.16, G:0.14, T:0.46
Consensus pattern (62 bp):
TAGATGACTATGTTTCCTGGTGTTTCTATTCGACATCTACCATATTCATTTTTAGATAATTG
Found at i:34228138 original size:18 final size:18
Alignment explanation
Indices: 34228104--34228138 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
34228094 AGAAAGTTTC
*
34228104 AAGAGACTCAAGTACAAA
1 AAGAGACTCAAGAACAAA
*
34228122 AAGAGACTCTAGAACAA
1 AAGAGACTCAAGAACAA
34228139 CAGATGTTAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.17, G:0.17, T:0.11
Consensus pattern (18 bp):
AAGAGACTCAAGAACAAA
Found at i:34237345 original size:43 final size:43
Alignment explanation
Indices: 34237298--34237488 Score: 113
Period size: 43 Copynumber: 4.4 Consensus size: 43
34237288 CCTGGTCAGC
*
34237298 AGTGGAATAGGTCGAAGAAACAGATCTTATCTCCCTAAGCAGT
1 AGTGGAATAGATCGAAGAAACAGATCTTATCTCCCTAAGCAGT
* * ** *
34237341 AGTGGAGTTGATCGAAGACGGC-GAATCTTATCTTCCC-AAGGAGT
1 AGTGGAATAGATCGAAGA-AACAG-ATCTTATC-TCCCTAAGCAGT
* * ** ** * * **
34237385 AG-GGAAGCATATTTAAGCCACTA-ATCCTATCTCCCT-GGTCAAC
1 AGTGGAA-TAGATCGAAGAAAC-AGATCTTATCTCCCTAAG-CAGT
* *
34237428 AGTGGAATAGGTCAAAGAAACAGATCTTATCTCCCTAAGCAGT
1 AGTGGAATAGATCGAAGAAACAGATCTTATCTCCCTAAGCAGT
**
34237471 AGTGGAGCAGATCGAAGA
1 AGTGGAATAGATCGAAGA
34237489 CGGCGAATCT
Statistics
Matches: 102, Mismatches: 35, Indels: 22
0.64 0.22 0.14
Matches are distributed among these distances:
42 6 0.06
43 65 0.64
44 27 0.26
45 4 0.04
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (43 bp):
AGTGGAATAGATCGAAGAAACAGATCTTATCTCCCTAAGCAGT
Found at i:34237422 original size:130 final size:130
Alignment explanation
Indices: 34237216--34237551 Score: 582
Period size: 130 Copynumber: 2.6 Consensus size: 130
34237206 ACCACAGCGA
* * *
34237216 AGCAGATCGAAAACGGTGAATCTTATCTTCCCCAGGAGTAGGGAAGAAGATTTAAGCCACTAATC
1 AGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCACTAATC
* *
34237281 CTATCTCCCTGGTCAGCAGTGGAATAGGTCGAAGAAACAGATCTTATCTCCCTAAGCAGTAGTGG
66 CTATCTCCCTGGTCAACAGTGGAATAGGTCAAAGAAACAGATCTTATCTCCCTAAGCAGTAGTGG
** * *
34237346 AGTTGATCGAAGACGGCGAATCTTATCTTCCCAAGGAGTAGGGAAGCATATTTAAGCCACTAATC
1 AGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCACTAATC
34237411 CTATCTCCCTGGTCAACAGTGGAATAGGTCAAAGAAACAGATCTTATCTCCCTAAGCAGTAGTGG
66 CTATCTCCCTGGTCAACAGTGGAATAGGTCAAAGAAACAGATCTTATCTCCCTAAGCAGTAGTGG
34237476 AGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCACTAATC
1 AGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCACTAATC
*
34237541 ATATCTCCCTG
66 CTATCTCCCTG
34237552 AAGTTGCAGT
Statistics
Matches: 192, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 192 1.00
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (130 bp):
AGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCACTAATC
CTATCTCCCTGGTCAACAGTGGAATAGGTCAAAGAAACAGATCTTATCTCCCTAAGCAGTAGTGG
Found at i:34237792 original size:217 final size:216
Alignment explanation
Indices: 34237442--34237852 Score: 578
Period size: 217 Copynumber: 1.9 Consensus size: 216
34237432 GAATAGGTCA
* * *
34237442 AAGAAACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCC
1 AAGAAACAGATCTTATCTCCCTAAGCAGTAGTGAAGCAAATCGAAGACGGCGAATCTTATCCTCC
* *
34237507 CCAGGAGTAGGGAAGCAGATTTAAGCCACTAATCATATCTCCCTGAAGTTGCAGTGGAGCGGATT
66 CCAGGAGTAGGGAAGCACATTGAAGCCACTAATCATATCTCCCTGAAGTTGCAGTGGAGCGGATT
** * * * *
34237572 AAAATAAAAGGTCTTATCTCTTTGAAGTTGCAGCAGAGTAGATCGCATTAGGTCTTATCTCCCTG
131 AAAATAAAAAATCTTATCTATCTGAAGTTGCAACAGAGTAGATCGCATCAGGTCTTATCTCCCTG
34237637 AGGTTACAGCGGAGCATACTG
196 AGGTTACAGCGGAGCATACTG
* *
34237658 AAGAAACAGATCTTATCTCCCTAAGCAGTAGTGAAGCAAATCGAAGATGGC-AGATTTTA-CCTC
1 AAGAAACAGATCTTATCTCCCTAAGCAGTAGTGAAGCAAATCGAAGACGGCGA-ATCTTATCCTC
* * * * *
34237721 CCTGAGGA-TACAGTGG-AGTACATTGAAGCCAGTAATCCTATCTCCCTGAAGTTGCAGTGGAGT
65 CC-CAGGAGT--AG-GGAAGCACATTGAAGCCACTAATCATATCTCCCTGAAGTTGCAGTGGAGC
*
34237784 GGATTAAAATAAAAAATCTTATCTATCTGAAGTTGCAATAGAGTAGATCGCATCAGGTCTTATCT
126 GGATTAAAATAAAAAATCTTATCTATCTGAAGTTGCAACAGAGTAGATCGCATCAGGTCTTATCT
34237849 CCCT
191 CCCT
34237853 AAAGTTGCAG
Statistics
Matches: 171, Mismatches: 19, Indels: 9
0.86 0.10 0.05
Matches are distributed among these distances:
215 7 0.04
216 57 0.33
217 105 0.61
218 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.26
Consensus pattern (216 bp):
AAGAAACAGATCTTATCTCCCTAAGCAGTAGTGAAGCAAATCGAAGACGGCGAATCTTATCCTCC
CCAGGAGTAGGGAAGCACATTGAAGCCACTAATCATATCTCCCTGAAGTTGCAGTGGAGCGGATT
AAAATAAAAAATCTTATCTATCTGAAGTTGCAACAGAGTAGATCGCATCAGGTCTTATCTCCCTG
AGGTTACAGCGGAGCATACTG
Found at i:34237807 original size:44 final size:44
Alignment explanation
Indices: 34237754--34237912 Score: 128
Period size: 44 Copynumber: 3.7 Consensus size: 44
34237744 TGAAGCCAGT
* *
34237754 AATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAATAAAA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGTGGATTAAAATAAAA
** * * *** *
34237798 AATCTTATCTATCTGAAGTTGCAATAGAGTAGA-TCGCAT--CA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGTGGATTAAAATAAAA
** * * * *
34237839 GGTCTTATCTCCCTAAAGTTGCAGTGGAGTGGATTGAAATAATA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGTGGATTAAAATAAAA
*
34237883 GATCTTATC-CCTCTGAAGTTGCAGTAGAGT
1 AATCTTATCTCC-CTGAAGTTGCAGTAGAGT
34237913 ATATCACATC
Statistics
Matches: 86, Mismatches: 25, Indels: 8
0.72 0.21 0.07
Matches are distributed among these distances:
41 26 0.30
42 3 0.03
43 5 0.06
44 52 0.60
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.31
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTAGAGTGGATTAAAATAAAA
Found at i:34237858 original size:41 final size:41
Alignment explanation
Indices: 34237800--34237990 Score: 132
Period size: 41 Copynumber: 4.5 Consensus size: 41
34237790 AAATAAAAAA
**
34237800 TCTTATCTATCTGAAGTTGCAATAGAGTAGATCGCATCAGG
1 TCTTATCTCCCTGAAGTTGCAATAGAGTAGATCGCATCAGG
* * * * * * * *
34237841 TCTTATCTCCCTAAAGTTGCAGTGGAGTGGATTGAAATAATAGA
1 TCTTATCTCCCTGAAGTTGCAATAGAGTAGATCG-CAT--CAGG
* * *
34237885 TCTTATC-CCTCTGAAGTTGCAGTAGAGTATATCACATCAGG
1 TCTTATCTCC-CTGAAGTTGCAATAGAGTAGATCGCATCAGG
* * * * * *
34237926 TCTTATCTCCCTGAGGTTGCAACAGAGCAGATTGAGAAAGCAGG
1 TCTTATCTCCCTGAAGTTGCAATAGAGTAGA-T-CG-CATCAGG
*
34237970 TCTTATCCCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCA
34237991 GTGGGGCAGA
Statistics
Matches: 112, Mismatches: 30, Indels: 13
0.72 0.19 0.08
Matches are distributed among these distances:
41 52 0.46
42 5 0.04
43 4 0.04
44 51 0.46
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (41 bp):
TCTTATCTCCCTGAAGTTGCAATAGAGTAGATCGCATCAGG
Found at i:34237902 original size:85 final size:85
Alignment explanation
Indices: 34237759--34237946 Score: 286
Period size: 85 Copynumber: 2.2 Consensus size: 85
34237749 CCAGTAATCC
*
34237759 TATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAATAAAAAATCTTATCTATCTGAAGTTGCAATA
1 TATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAATAAAAAATCTTATCCATCTGAAGTTGCAATA
*
34237824 GAGTAGATCGCATCAGGTCT
66 GAGTAGATCACATCAGGTCT
* * * * * *
34237844 TATCTCCCTAAAGTTGCAGTGGAGTGGATTGAAATAATAGATCTTATCCCTCTGAAGTTGCAGTA
1 TATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAATAAAAAATCTTATCCATCTGAAGTTGCAATA
*
34237909 GAGTATATCACATCAGGTCT
66 GAGTAGATCACATCAGGTCT
*
34237929 TATCTCCCTGAGGTTGCA
1 TATCTCCCTGAAGTTGCA
34237947 ACAGAGCAGA
Statistics
Matches: 92, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
85 92 1.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (85 bp):
TATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAATAAAAAATCTTATCCATCTGAAGTTGCAATA
GAGTAGATCACATCAGGTCT
Found at i:34237959 original size:85 final size:85
Alignment explanation
Indices: 34237785--34237992 Score: 229
Period size: 85 Copynumber: 2.4 Consensus size: 85
34237775 CAGTGGAGTG
* * ** * *
34237785 GATTAAAATAAAAAATCTTATCTATCTGAAGTTGCAATAGAGTAGATCGCATCAGGTCTTATCTC
1 GATTGAAATAAAAGATCTTATCCCTCTGAAGTTGCAGTAGAGTAGATCACATCAGGTCTTATCTC
*** **
34237850 CCTAAAGTTGCAGTGGAGTG
66 CCTAAAGTTGCAACAGAGCA
* *
34237870 GATTGAAATAATAGATCTTATCCCTCTGAAGTTGCAGTAGAGTATATCACATCAGGTCTTATCTC
1 GATTGAAATAAAAGATCTTATCCCTCTGAAGTTGCAGTAGAGTAGATCACATCAGGTCTTATCTC
* *
34237935 CCTGAGGTTGCAACAGAGCA
66 CCTAAAGTTGCAACAGAGCA
** * *
34237955 GATTGAGAA-AGCAGGTCTTATCCCCCTGAAGTTGCAGT
1 GATTGA-AATAAAAGATCTTATCCCTCTGAAGTTGCAGT
34237993 GGGGCAGACT
Statistics
Matches: 103, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
85 101 0.98
86 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.29
Consensus pattern (85 bp):
GATTGAAATAAAAGATCTTATCCCTCTGAAGTTGCAGTAGAGTAGATCACATCAGGTCTTATCTC
CCTAAAGTTGCAACAGAGCA
Found at i:34238097 original size:50 final size:50
Alignment explanation
Indices: 34238043--34238218 Score: 199
Period size: 50 Copynumber: 3.5 Consensus size: 50
34238033 ACAGTGGAAT
** *
34238043 AGATTAAAGCCACAGTGGCCAATCTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * * * * ** ** *
34238093 AGATTAAAGCTACAACGACGAATCTTACTTCCCAGGCGGTGCAGTGGAAC
1 AGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAA
*
34238143 AGATTAAAGCCACAACGGCAAATCTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * *
34238193 AGATTGAAGCTACAATGGCGAATCTT
1 AGATTAAAGCCACAACGGCGAATCTT
34238219 ACTTTCCAAA
Statistics
Matches: 98, Mismatches: 28, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
50 98 1.00
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.23
Consensus pattern (50 bp):
AGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAA
Found at i:34238184 original size:100 final size:100
Alignment explanation
Indices: 34238011--34238222 Score: 325
Period size: 100 Copynumber: 2.1 Consensus size: 100
34238001 CTGAGAATAG
* * * ** *
34238011 CGAATCTTACTTTCCTGGCAGTACAGTGGAATAGATTAAAGCCACAGTGGCCAATCTTGCTTCCC
1 CGAATCTTACTTCCCAGGCAGTACAGTGGAACAGATTAAAGCCACAACGGCAAATCTTGCTTCCC
34238076 CGACATTGCAGTTAAAAAGATTAAAGCTACAACGA
66 CGACATTGCAGTTAAAAAGATTAAAGCTACAACGA
* *
34238111 CGAATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACAACGGCAAATCTTGCTTCCC
1 CGAATCTTACTTCCCAGGCAGTACAGTGGAACAGATTAAAGCCACAACGGCAAATCTTGCTTCCC
* * *
34238176 CGACATTGCAGTTAAAAAGATTGAAGCTACAATGG
66 CGACATTGCAGTTAAAAAGATTAAAGCTACAACGA
34238211 CGAATCTTACTT
1 CGAATCTTACTT
34238223 TCCAAAAGTT
Statistics
Matches: 101, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
100 101 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.25
Consensus pattern (100 bp):
CGAATCTTACTTCCCAGGCAGTACAGTGGAACAGATTAAAGCCACAACGGCAAATCTTGCTTCCC
CGACATTGCAGTTAAAAAGATTAAAGCTACAACGA
Found at i:34240082 original size:32 final size:32
Alignment explanation
Indices: 34240046--34240110 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
34240036 CAATGTGTTT
34240046 TAATTT-TATCAATATTACTTTAAATATATATA
1 TAATTTATATCAA-ATTACTTTAAATATATATA
* * * *
34240078 TAATTTATATGAAATTATTTTTAGTATATATA
1 TAATTTATATCAAATTACTTTAAATATATATA
34240110 T
1 T
34240111 GTATATAGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 23 0.82
33 5 0.18
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (32 bp):
TAATTTATATCAAATTACTTTAAATATATATA
Found at i:34242853 original size:9 final size:9
Alignment explanation
Indices: 34242839--34242872 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
34242829 CCCAAATTAT
34242839 TTTTTTTTC
1 TTTTTTTTC
34242848 TTTTTTTTC
1 TTTTTTTTC
*
34242857 -TTTTTTCC
1 TTTTTTTTC
34242865 TTTTTTTT
1 TTTTTTTT
34242873 ATGCTTTAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:34242862 original size:17 final size:17
Alignment explanation
Indices: 34242840--34242872 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
34242830 CCAAATTATT
*
34242840 TTTTTTTCTTTTTTTTC
1 TTTTTTCCTTTTTTTTC
34242857 TTTTTTCCTTTTTTTT
1 TTTTTTCCTTTTTTTT
34242873 ATGCTTTAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (17 bp):
TTTTTTCCTTTTTTTTC
Found at i:34243895 original size:9 final size:10
Alignment explanation
Indices: 34243881--34243923 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
34243871 ATTAATATTC
34243881 AAAT-AAGTA
1 AAATAAAGTA
*
34243890 AAATAAAATA
1 AAATAAAGTA
34243900 AAATAAAGTAA
1 AAATAAAGT-A
34243911 TAAATAAAGTA
1 -AAATAAAGTA
34243922 AA
1 AA
34243924 GAAAAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
9 4 0.14
10 14 0.48
11 2 0.07
12 9 0.31
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (10 bp):
AAATAAAGTA
Found at i:34243917 original size:17 final size:16
Alignment explanation
Indices: 34243894--34243952 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 16
34243884 TAAGTAAAAT
34243894 AAAATAAAATAAAGTA
1 AAAATAAAATAAAGTA
*
34243910 ATAAATAAAGTAAAG-A
1 A-AAATAAAATAAAGTA
* *
34243926 AAAAAATAAATAATAATA
1 AAAATA-AAATAA-AGTA
34243944 AAAATAAAA
1 AAAATAAAA
34243953 ATTGGGTTGC
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
15 4 0.12
16 8 0.24
17 16 0.47
18 6 0.18
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (16 bp):
AAAATAAAATAAAGTA
Found at i:34243952 original size:21 final size:21
Alignment explanation
Indices: 34243890--34243954 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 21
34243880 CAAATAAGTA
*
34243890 AAATAAAATAAA-ATAAAGTAAT
1 AAATAAAATAAAGA-AAA-AAAT
*
34243912 AAATAAAGTAAAGAAAAAAAT
1 AAATAAAATAAAGAAAAAAAT
34243933 AAATAATAATAAA-AATAAAAAT
1 AAATAA-AATAAAGAA-AAAAAT
34243955 TGGGTTGCCT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
21 11 0.30
22 25 0.68
23 1 0.03
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (21 bp):
AAATAAAATAAAGAAAAAAAT
Found at i:34258331 original size:147 final size:145
Alignment explanation
Indices: 34258007--34258357 Score: 389
Period size: 146 Copynumber: 2.4 Consensus size: 145
34257997 TACCATCTTG
* * * * * ** * *
34258007 TTAGAAATTTTAGTATATACCAAAATATCTAAGGATGTGCTATTAGAAATAGTGATATTTTATTA
1 TTAGAAATTATGGTATATACCAAAATATCTAAGGATATCCTCTTAGAAATTTTGGTATTTCATTA
* * * *
34258072 GAAATCTTGGTATAGGCTCATAAATTTAGATTTTGGTATATCAAAATTCTAACGAGGTTCCATAG
66 GAAATCTTGGTATAAGCTCATAAA-TCAGATTTTGGTATACCAAAATTCTAACGAGGTTCCATAA
* *
34258137 AAATATTAATATTTCT
130 AAATATTAATATTCCC
* * * * * *
34258153 TTAGAAATTAAGGTATATACCAGAATTTCTAAAGATAACCTCTTAGAAATTTTGGTATTTCGTTA
1 TTAGAAATTATGGTATATACCAAAATATCTAAGGATATCCTCTTAGAAATTTTGGTATTTCATTA
* * * *
34258218 GAAATCTTGTTATAAGTTTATACAA-CACGATTTTGGTATACCAAAATTTCTTACGAGGTTCCAT
66 GAAATCTTGGTATAAGCTCATA-AATCA-GATTTTGGTATACCAAAA-TTCTAACGAGGTTCCAT
**
34258282 AAAAATATTGGTATTCCC
128 AAAAATATTAATATTCCC
* * *
34258300 TTAGAAATTATGGTATATACCAAAATATCTAAGGATATTCACTTATAAATTTTGGTAT
1 TTAGAAATTATGGTATATACCAAAATATCTAAGGATATCCTCTTAGAAATTTTGGTAT
34258358 ACCACAATTT
Statistics
Matches: 167, Mismatches: 35, Indels: 5
0.81 0.17 0.02
Matches are distributed among these distances:
145 1 0.01
146 85 0.51
147 81 0.49
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.38
Consensus pattern (145 bp):
TTAGAAATTATGGTATATACCAAAATATCTAAGGATATCCTCTTAGAAATTTTGGTATTTCATTA
GAAATCTTGGTATAAGCTCATAAATCAGATTTTGGTATACCAAAATTCTAACGAGGTTCCATAAA
AATATTAATATTCCC
Found at i:34267455 original size:88 final size:93
Alignment explanation
Indices: 34267351--34268066 Score: 340
Period size: 106 Copynumber: 7.0 Consensus size: 93
34267341 AAATTATTTT
*
34267351 TTGGGTGCTGGCCTGTCAATGGCCGGCACCCA-AC-A-GTAAAAAAAATTC-TTTTTT-TGTCAA
1 TTGGGTGCTAGCCTGTCAATGGCCGGCACCCAGACAATGTAAAAAAAATTCTTTTTTTCTGTCAA
34267411 AATAAGATATAAATATACGAAAAAAAAA
66 AATAAGATATAAATATACGAAAAAAAAA
*
34267439 TTGGGTGCTAGCCTGTCAATGGCCGGCACCCAGTACAATTTAAAAAAAATTCTTTTTTTTCGTGT
1 TTGGGTGCTAGCCTGTCAATGGCCGGCACCCAG-ACAATGTAAAAAAAATTC-TTTTTTTC-TGT
* * *
34267504 CAGAGTCAGATATAAATATACGAAAAAAATAAATAAAAAAA
63 CAAAATAAGATATAAATATACG---------AA-AAAAAAA
* *
34267545 TTTTGGGTGCT-GGCTGTCAATGGCCGGCACCCAGTACAATTTTAAAAAAAATTTACTTTTTTTT
1 --TTGGGTGCTAGCCTGTCAATGGCCGGCACCCAG-ACAA-TGTAAAAAAAA-TT-C-TTTTTTT
* **
34267609 GTGTCAGAGTTAA-ATATAAATATACGAAAAAAATAAAAAAAAAA
59 CTGTCA-AAATAAGATATAAATATACG---------AAAAAAAAA
* * *
34267653 TTTGGGTGATGGCCTGTCAATGGCCGGCACTCAGTACAAAT-T-AAAAAAATTCTTTTTTTTTCG
1 -TTGGGTGCTAGCCTGTCAATGGCCGGCACCCAG-AC-AATGTAAAAAAAATTC--TTTTTTTC-
* * *
34267716 TGTCAGAATCAA-ATTTAAATATACAAAAAAAATTAAAAAAAAA
60 TGTCAAAAT-AAGATATAAATATAC---------GAAAAAAAAA
** * *
34267759 TTTAAGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAAT-TTAAAAAAATTCTTTTTTTCGTG
1 -TTGGGTGCTAGCCTGTCAATGGCCGGCACCCAG-AC-AATGTAAAAAAAATTCTTTTTTTC-TG
* * *
34267823 TCAGAGTCAGATATAAATATACGAAAAAAATAAAAAAAA
62 TCAAAATAAGATATAAATATACG------A-AAAAAAAA
* * *
34267862 TTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTAAAAAAAAATTAATTTTTTTCG
1 --TTGGGTGCTAGCCTGTCAATGGCCGGCACCCAG-ACAATGT-AAAAAAAATT-CTTTTTTTC-
* * *
34267927 TGTCAGAGTCAGATATAAATATACGAAAAAAAATAAAATAAAAA
60 TGTCAAAATAAGATATAAATATACG---------AAAA-AAAAA
*
34267971 TTTTTGGGTGCTAGCCTGTCAATGGCCGGCATCCAGTACAAAT-TAAAAAAAATTTCTTTTTTTC
1 ---TTGGGTGCTAGCCTGTCAATGGCCGGCACCCAG-AC-AATGTAAAAAAAA-TTCTTTTTTTC
* *
34268035 GTGTCAGAATCAGATATAAATATACGAAAAAA
60 -TGTCAAAATAAGATATAAATATACGAAAAAA
34268067 TTTTAAAAAA
Statistics
Matches: 533, Mismatches: 37, Indels: 105
0.79 0.05 0.16
Matches are distributed among these distances:
88 31 0.06
90 2 0.00
91 1 0.00
92 12 0.02
94 6 0.01
96 22 0.04
99 2 0.00
100 4 0.01
102 1 0.00
103 11 0.02
104 38 0.07
105 50 0.09
106 113 0.21
107 47 0.09
108 55 0.10
109 85 0.16
110 50 0.09
111 3 0.01
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.29
Consensus pattern (93 bp):
TTGGGTGCTAGCCTGTCAATGGCCGGCACCCAGACAATGTAAAAAAAATTCTTTTTTTCTGTCAA
AATAAGATATAAATATACGAAAAAAAAA
Found at i:34267745 original size:106 final size:106
Alignment explanation
Indices: 34267430--34268199 Score: 1063
Period size: 106 Copynumber: 7.2 Consensus size: 106
34267420 TAAATATACG
* *
34267430 AAAAAAAAA-TTGGGTGCTAGCCTGTCAATGGCCGGCACCCAGTACAATTTAAAAAAAATTCTTT
1 AAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATTAAAAAAAATTCTTT
34267494 TTTTTCGTGTCAGAGTCAGATATAAATATACGAAAAAAATA
66 TTTTTCGTGTCAGAGTCAGATATAAATATACGAAAAAAATA
*
34267535 AATAAAAAAATTTTGGGTGCTGG-CTGTCAATGGCCGGCACCCAGTACAATTTTAAAAAAAATTT
1 AA-AAAAAAA-TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAA-ATTAAAAAAAA-TT
* *
34267599 ACTTTTTTTT-GTGTCAGAGTTAAATATAAATATACGAAAAAAATA
62 -CTTTTTTTTCGTGTCAGAGTCAGATATAAATATACGAAAAAAATA
* *
34267644 AAAAAAAAATTTGGGTGATGGCCTGTCAATGGCCGGCACTCAGTACAAATT-AAAAAAATTCTTT
1 AAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATTAAAAAAAATTC-TT
* * * * *
34267708 TTTTTTCGTGTCAGAATCAAATTTAAATATACAAAAAAAATT
65 TTTTTTCGTGTCAGAGTCAGATATAAATATACGAAAAAAATA
** *
34267750 AAAAAAAAATTTAAGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATTTAAAAAAATTC-TT
1 AAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATTAAAAAAAATTCTTT
34267814 TTTTTCGTGTCAGAGTCAGATATAAATATACGAAAAAAAT-
66 TTTTTCGTGTCAGAGTCAGATATAAATATACGAAAAAAATA
* * **
34267854 AAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTAAAAAAAAATTAAT
1 AAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATT-AAAAAAAATTCTT
34267919 TTTTTTCGTGTCAGAGTCAGATATAAATATACGAAAAAAAATA
65 TTTTTTCGTGTCAGAGTCAGATATAAATATACG-AAAAAAATA
* * *
34267962 AAATAAAAATTTTTGGGTGCTAGCCTGTCAATGGCCGGCATCCAGTACAAATTAAAAAAAATT-T
1 AAA-AAAAA-ATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATTAAAAAAAATTCT
* *
34268026 CTTTTTTTCGTGTCAGAATCAGATATAAATATACGAAAAAATTTTA
64 -TTTTTTTCGTGTCAGAGTCAGATATAAATATACGAAAAAA--ATA
* * *
34268072 AAAAAAAAATTTTTGGGTGCTGCCCTGTCAATGGCCGGCACGCAGTACAAATTTTTAAAAAAATT
1 AAAAAAAAA--TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAA--TTAAAAAAAATT
*
34268137 CTTTTTTTT-GTGTCGGAGTCAGATATAAATATACGAAAAAAAT-
62 CTTTTTTTTCGTGTCAGAGTCAGATATAAATATACGAAAAAAATA
*
34268180 AAAAAAAATTTTGGGTGCTG
1 AAAAAAAAATTTGGGTGCTG
34268200 ACCAAACATC
Statistics
Matches: 600, Mismatches: 41, Indels: 47
0.87 0.06 0.07
Matches are distributed among these distances:
104 48 0.08
105 59 0.10
106 136 0.23
107 57 0.09
108 70 0.12
109 91 0.15
110 90 0.15
111 30 0.05
112 18 0.03
113 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (106 bp):
AAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAATTAAAAAAAATTCTTT
TTTTTCGTGTCAGAGTCAGATATAAATATACGAAAAAAATA
Found at i:34270644 original size:108 final size:109
Alignment explanation
Indices: 34270447--34270760 Score: 426
Period size: 108 Copynumber: 2.9 Consensus size: 109
34270437 ATAGCGCATA
* *
34270447 TTTTTCGTATATTTATATCTGACTCTAACACGAAAAAAAAGAAAAAAAGTTTTTTTTTAAATTGT
1 TTTTTCGTATATTTATATCTGATTCTGACACGAAAAAAAAG----AAA-TTTTTTTTT-AATTGT
34270512 ACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAA-TTTT-TTTTTAAT
60 ACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTATTTTTAAT
34270560 TTTTTCGTATATTTATATCTGATTCTGACACGAAAAAAAAGAAATTTTTTTTTAATTTGTACTGG
1 TTTTTCGTATATTTATATCTGATTCTGACACGAAAAAAAAGAAATTTTTTTTTAA-TTGTACTGG
* *
34270625 GTGCCAGCCATTGACAGGCCAGCACCCAAAATTTTTTATTTTTATT
65 GTGCCGGCCATTGACAGGCCAGCACCCAAAA-TTTTTATTTTTAAT
* * * *
34270671 TTTTTCGTATATTTATATCTTATTCTG--AC-AAAAAAAGGAAATTTTTTTTTTACTGT--TGGG
1 TTTTTCGTATATTTATATCTGATTCTGACACGAAAAAAAAGAAATTTTTTTTTAATTGTACTGGG
*
34270731 TGTCGGCCATTGACAGGCCAGCACCCAAAA
66 TGCCGGCCATTGACAGGCCAGCACCCAAAA
34270761 AATAATTTTT
Statistics
Matches: 187, Mismatches: 10, Indels: 16
0.88 0.05 0.08
Matches are distributed among these distances:
105 32 0.17
107 5 0.03
108 69 0.37
109 5 0.03
110 4 0.02
111 33 0.18
113 39 0.21
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.39
Consensus pattern (109 bp):
TTTTTCGTATATTTATATCTGATTCTGACACGAAAAAAAAGAAATTTTTTTTTAATTGTACTGGG
TGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTATTTTTAAT
Found at i:34271808 original size:19 final size:20
Alignment explanation
Indices: 34271784--34271822 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
34271774 AAAATAAAGC
*
34271784 TAATAAATATATA-ATTTTA
1 TAATAAAAATATATATTTTA
34271803 TAATAAAAATATATATTTTA
1 TAATAAAAATATATATTTTA
34271823 CATATATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TAATAAAAATATATATTTTA
Found at i:34274698 original size:185 final size:185
Alignment explanation
Indices: 34274386--34274755 Score: 740
Period size: 185 Copynumber: 2.0 Consensus size: 185
34274376 AAAATAAAGC
34274386 ATCAAAAAGAGGAAATTTTAGAGTTATGTCGACATTGGGTCGTATATTATGACATATTAGTTCAA
1 ATCAAAAAGAGGAAATTTTAGAGTTATGTCGACATTGGGTCGTATATTATGACATATTAGTTCAA
34274451 GAAAGGATTAAATCGTAAAAGTGAGAAAAGTTTTGTTCCCCAAGAGTAAATACTCAAAAATTAAG
66 GAAAGGATTAAATCGTAAAAGTGAGAAAAGTTTTGTTCCCCAAGAGTAAATACTCAAAAATTAAG
34274516 GGGGTTAAAGTGTAAATATGAAAAGTTGAAGGACCAATGGTGTAAATATTTTAAG
131 GGGGTTAAAGTGTAAATATGAAAAGTTGAAGGACCAATGGTGTAAATATTTTAAG
34274571 ATCAAAAAGAGGAAATTTTAGAGTTATGTCGACATTGGGTCGTATATTATGACATATTAGTTCAA
1 ATCAAAAAGAGGAAATTTTAGAGTTATGTCGACATTGGGTCGTATATTATGACATATTAGTTCAA
34274636 GAAAGGATTAAATCGTAAAAGTGAGAAAAGTTTTGTTCCCCAAGAGTAAATACTCAAAAATTAAG
66 GAAAGGATTAAATCGTAAAAGTGAGAAAAGTTTTGTTCCCCAAGAGTAAATACTCAAAAATTAAG
34274701 GGGGTTAAAGTGTAAATATGAAAAGTTGAAGGACCAATGGTGTAAATATTTTAAG
131 GGGGTTAAAGTGTAAATATGAAAAGTTGAAGGACCAATGGTGTAAATATTTTAAG
34274756 GGTGGAATGA
Statistics
Matches: 185, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
185 185 1.00
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.29
Consensus pattern (185 bp):
ATCAAAAAGAGGAAATTTTAGAGTTATGTCGACATTGGGTCGTATATTATGACATATTAGTTCAA
GAAAGGATTAAATCGTAAAAGTGAGAAAAGTTTTGTTCCCCAAGAGTAAATACTCAAAAATTAAG
GGGGTTAAAGTGTAAATATGAAAAGTTGAAGGACCAATGGTGTAAATATTTTAAG
Found at i:34276849 original size:54 final size:54
Alignment explanation
Indices: 34276766--34276912 Score: 204
Period size: 54 Copynumber: 2.7 Consensus size: 54
34276756 ATTAGAGTAA
* * *
34276766 TTATCATTGCAGGGGATTTAGCCTAGACTGGTAATCTCGACAATACTCTATGAGT
1 TTAT-ATTACAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGT
* *
34276821 TTATATTACAGGGGATTTAGCCTGGACTGGCAATCCCGATAATACTCTATGAGT
1 TTATATTACAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGT
* * * *
34276875 TTATATTACATGGGATTTAGCATGAACTAGTAATCCCG
1 TTATATTACAGGGGATTTAGCCTGGACTGGTAATCCCG
34276913 CTGTAAAGAT
Statistics
Matches: 82, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
54 78 0.95
55 4 0.05
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.33
Consensus pattern (54 bp):
TTATATTACAGGGGATTTAGCCTGGACTGGTAATCCCGACAATACTCTATGAGT
Found at i:34284171 original size:25 final size:25
Alignment explanation
Indices: 34284129--34284222 Score: 59
Period size: 25 Copynumber: 3.7 Consensus size: 25
34284119 TTCTCTTCAC
* * *
34284129 TTTTTTTCCAACTAATAAGAATGCA
1 TTTTTTTTCAATTAATAAGAATGAA
* *
34284154 TTTTTTTTCAATTTATAACG-ATTAA
1 TTTTTTTTCAATTAATAA-GAATGAA
* *
34284179 TATTGTAGTTT-AA-TAATAAGAATGTA
1 T-TT-T-TTTTCAATTAATAAGAATGAA
*
34284205 TTTTTTTTCAATTTATAA
1 TTTTTTTTCAATTAATAA
34284223 CGATTAATAT
Statistics
Matches: 51, Mismatches: 11, Indels: 14
0.67 0.14 0.18
Matches are distributed among these distances:
23 3 0.06
24 3 0.06
25 27 0.53
26 12 0.24
27 3 0.06
28 3 0.06
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.50
Consensus pattern (25 bp):
TTTTTTTTCAATTAATAAGAATGAA
Found at i:34284254 original size:48 final size:51
Alignment explanation
Indices: 34284141--34284246 Score: 203
Period size: 51 Copynumber: 2.1 Consensus size: 51
34284131 TTTTTCCAAC
*
34284141 TAATAAGAATGCATTTTTTTTCAATTTATAACGATTAATATTGTAGTTTAA
1 TAATAAGAATGTATTTTTTTTCAATTTATAACGATTAATATTGTAGTTTAA
34284192 TAATAAGAATGTATTTTTTTTCAATTTATAACGATTAATATTGTAGTTTAA
1 TAATAAGAATGTATTTTTTTTCAATTTATAACGATTAATATTGTAGTTTAA
34284243 TAAT
1 TAAT
34284247 TGAGTATTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.38, C:0.05, G:0.09, T:0.48
Consensus pattern (51 bp):
TAATAAGAATGTATTTTTTTTCAATTTATAACGATTAATATTGTAGTTTAA
Found at i:34284282 original size:65 final size:64
Alignment explanation
Indices: 34284206--34284336 Score: 235
Period size: 65 Copynumber: 2.0 Consensus size: 64
34284196 AAGAATGTAT
* *
34284206 TTTTTTTCAATTTATAACGATTAATATTGTAGTTTAATAATTGAGTATTATTATAAATAAATACA
1 TTTTTTTCAATTTATAACGATTAATATTATAGCTTAATAATTGAGTATTATTATAAATAAAT-CA
34284271 TTTTTTTCAATTTATAACGATTAATATTATAGCTTAATAATTGAGTATTATTATAAATAAATCA
1 TTTTTTTCAATTTATAACGATTAATATTATAGCTTAATAATTGAGTATTATTATAAATAAATCA
34284335 TT
1 TT
34284337 GCAATATATG
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
64 4 0.06
65 60 0.94
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (64 bp):
TTTTTTTCAATTTATAACGATTAATATTATAGCTTAATAATTGAGTATTATTATAAATAAATCA
Found at i:34284538 original size:14 final size:14
Alignment explanation
Indices: 34284515--34284553 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
34284505 ACAGAAAAGT
34284515 AAAACATTTT-TGAG
1 AAAACATTTTATG-G
*
34284529 AAATCATTTTATGG
1 AAAACATTTTATGG
34284543 AAAACATTTTA
1 AAAACATTTTA
34284554 CTGGCAATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 20 0.91
15 2 0.09
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (14 bp):
AAAACATTTTATGG
Found at i:34286584 original size:25 final size:24
Alignment explanation
Indices: 34286550--34286610 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
34286540 GTTCACGAAC
* *
34286550 AAGCTTGTTTATTGGCTCATTTTAT
1 AAGCTCGTTTATTGACTCA-TTTAT
*
34286575 AAGCTCGTTTATTGATTCATTTAT
1 AAGCTCGTTTATTGACTCATTTAT
*
34286599 GA-CTCGTTTATT
1 AAGCTCGTTTATT
34286611 TATTAATGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 10 0.31
24 6 0.19
25 16 0.50
ACGTcount: A:0.21, C:0.13, G:0.15, T:0.51
Consensus pattern (24 bp):
AAGCTCGTTTATTGACTCATTTAT
Found at i:34293456 original size:52 final size:52
Alignment explanation
Indices: 34293399--34293521 Score: 246
Period size: 52 Copynumber: 2.4 Consensus size: 52
34293389 TTTAAATGCA
34293399 TATTTGTTACTTTATAACATAAAGTCTAAAATGATATTACAAATGTCTAAAG
1 TATTTGTTACTTTATAACATAAAGTCTAAAATGATATTACAAATGTCTAAAG
34293451 TATTTGTTACTTTATAACATAAAGTCTAAAATGATATTACAAATGTCTAAAG
1 TATTTGTTACTTTATAACATAAAGTCTAAAATGATATTACAAATGTCTAAAG
34293503 TATTTGTTACTTTATAACA
1 TATTTGTTACTTTATAACA
34293522 CTTTTTGACA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.41
Consensus pattern (52 bp):
TATTTGTTACTTTATAACATAAAGTCTAAAATGATATTACAAATGTCTAAAG
Found at i:34294483 original size:42 final size:41
Alignment explanation
Indices: 34294434--34294539 Score: 131
Period size: 42 Copynumber: 2.5 Consensus size: 41
34294424 AGTATTATTA
34294434 CTTCGGTATGTTCGATGATACAAGTACATGCCAGTATGTTTT
1 CTTCGGTAT-TTCGATGATACAAGTACATGCCAGTATGTTTT
* * **
34294476 CTTCGGTATATCAGATGATGCACTTACATGCCAGTATGTTTT
1 CTTCGGTATTTC-GATGATACAAGTACATGCCAGTATGTTTT
* *
34294518 CTTCGGCATATCCGATGATACA
1 CTTCGGTAT-TTCGATGATACA
34294540 TTTAAATGTC
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
41 2 0.04
42 51 0.94
43 1 0.02
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.36
Consensus pattern (41 bp):
CTTCGGTATTTCGATGATACAAGTACATGCCAGTATGTTTT
Found at i:34294555 original size:42 final size:42
Alignment explanation
Indices: 34294447--34294559 Score: 136
Period size: 42 Copynumber: 2.7 Consensus size: 42
34294437 CGGTATGTTC
** * *
34294447 GATGATACAAGTACATGCCAGTATGTTTTCTTCGGTATATCA
1 GATGATACACTTAAATGCCAGTATGTTTTCTTCGGCATATCA
* * *
34294489 GATGATGCACTTACATGCCAGTATGTTTTCTTCGGCATATCC
1 GATGATACACTTAAATGCCAGTATGTTTTCTTCGGCATATCA
* * *
34294531 GATGATACATTTAAATGTCGGTATGTTTT
1 GATGATACACTTAAATGCCAGTATGTTTT
34294560 TTTTTGTACA
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 61 1.00
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (42 bp):
GATGATACACTTAAATGCCAGTATGTTTTCTTCGGCATATCA
Found at i:34296224 original size:20 final size:20
Alignment explanation
Indices: 34296199--34296237 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
34296189 CAACCACATA
34296199 CGTTATATCAATTCACTACT
1 CGTTATATCAATTCACTACT
34296219 CGTTATATCAATTCACTAC
1 CGTTATATCAATTCACTAC
34296238 CATTCATATC
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:0.26, G:0.05, T:0.38
Consensus pattern (20 bp):
CGTTATATCAATTCACTACT
Found at i:34296246 original size:20 final size:20
Alignment explanation
Indices: 34296201--34296248 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
34296191 ACCACATACG
*
34296201 TTATATCAATTCACTACTCG
1 TTATATCAATTCACTACTCA
34296221 TTATATCAATTCACTAC-CA
1 TTATATCAATTCACTACTCA
34296240 TTCATATCA
1 TT-ATATCA
34296249 TTTTATTATC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 3 0.12
20 23 0.88
ACGTcount: A:0.33, C:0.25, G:0.02, T:0.40
Consensus pattern (20 bp):
TTATATCAATTCACTACTCA
Found at i:34298243 original size:24 final size:25
Alignment explanation
Indices: 34298216--34298343 Score: 108
Period size: 25 Copynumber: 5.0 Consensus size: 25
34298206 ATTTTAAAAA
34298216 TTAAAA-TAAAAATTAAAAAATATT
1 TTAAAATTAAAAATTAAAAAATATT
34298240 TTAAAATTAAAAAAATTAAAAAA-A-T
1 TTAAAATT--AAAAATTAAAAAATATT
*
34298265 TTAAAA--AAAGTATTTTAAAAAA-ATT
1 TTAAAATTAAA--A-ATTAAAAAATATT
34298290 TTAAAATTAAAAAATTAAAAAAAAGTATT
1 TTAAAATT-AAAAATT--AAAAAA-TATT
*
34298319 TTAAAATTAAAAAAT-AAAAATATT
1 TTAAAATTAAAAATTAAAAAATATT
34298343 T
1 T
34298344 ATTATTCGGG
Statistics
Matches: 87, Mismatches: 3, Indels: 28
0.74 0.03 0.24
Matches are distributed among these distances:
21 3 0.03
23 1 0.01
24 20 0.23
25 22 0.25
26 2 0.02
27 19 0.22
28 9 0.10
29 11 0.13
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (25 bp):
TTAAAATTAAAAATTAAAAAATATT
Found at i:34298244 original size:19 final size:19
Alignment explanation
Indices: 34298222--34298285 Score: 69
Period size: 18 Copynumber: 3.3 Consensus size: 19
34298212 AAAATTAAAA
34298222 TAAAAATTAAAAAATATTT
1 TAAAAATTAAAAAATATTT
*
34298241 T-AAAATTAAAAAA-ATTA
1 TAAAAATTAAAAAATATTT
*
34298258 AAAAAATTTAAAAAAAGTATTT
1 TAAAAA-TT-AAAAAA-TATTT
34298280 TAAAAA
1 TAAAAA
34298286 AATTTTAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
17 3 0.08
18 16 0.44
19 3 0.08
20 6 0.17
22 8 0.22
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (19 bp):
TAAAAATTAAAAAATATTT
Found at i:34298260 original size:39 final size:41
Alignment explanation
Indices: 34298211--34298340 Score: 134
Period size: 39 Copynumber: 3.3 Consensus size: 41
34298201 AATTTATTTT
34298211 AAAAATTAAAATAAAAATT-AAAAAA-TATTTTAAAATTAA
1 AAAAATTAAAATAAAAATTAAAAAAAGTATTTTAAAATTAA
*
34298250 AAAAATT-AAA-AAAATTTAAAAAAAGTATTTT--AA--AA
1 AAAAATTAAAATAAAAATTAAAAAAAGTATTTTAAAATTAA
**
34298285 AAATTTTAAAATTAAAAAATTAAAAAAAAGTATTTTAAAATT-A
1 AAAAATTAAAA-T-AAAAATT-AAAAAAAGTATTTTAAAATTAA
*
34298328 AAAAATAAAAATA
1 AAAAATTAAAATA
34298341 TTTATTATTC
Statistics
Matches: 73, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
35 7 0.10
36 3 0.04
37 8 0.11
38 9 0.12
39 19 0.26
40 14 0.19
41 1 0.01
42 3 0.04
43 9 0.12
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (41 bp):
AAAAATTAAAATAAAAATTAAAAAAAGTATTTTAAAATTAA
Found at i:34298284 original size:11 final size:11
Alignment explanation
Indices: 34298246--34298295 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 11
34298236 TATTTTAAAA
34298246 TTAAAAAAA--
1 TTAAAAAAATT
34298255 TTAAAAAAATT
1 TTAAAAAAATT
*
34298266 TAAAAAAAGTATT
1 TTAAAAAA--ATT
34298279 TTAAAAAAATT
1 TTAAAAAAATT
34298290 TTAAAA
1 TTAAAA
34298296 TTAAAAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 9 0.26
11 16 0.46
13 10 0.29
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (11 bp):
TTAAAAAAATT
Found at i:34298313 original size:29 final size:28
Alignment explanation
Indices: 34298281--34298338 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 28
34298271 AAAGTATTTT
34298281 AAAAAAATTTTAAAATTAAAAAATTAAAA
1 AAAAAAATTTTAAAATTAAAAAA-TAAAA
**
34298310 AAAAGTATTTTAAAATTAAAAAATAAAA
1 AAAAAAATTTTAAAATTAAAAAATAAAA
34298338 A
1 A
34298339 TATTTATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 6 0.22
29 21 0.78
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.28
Consensus pattern (28 bp):
AAAAAAATTTTAAAATTAAAAAATAAAA
Found at i:34298692 original size:27 final size:27
Alignment explanation
Indices: 34298661--34298824 Score: 220
Period size: 27 Copynumber: 6.1 Consensus size: 27
34298651 TCAATAAACA
*
34298661 ACCGAATTACCCCCGTAGGGTAAAATG
1 ACCGAATTACCCCCATAGGGTAAAATG
* *
34298688 ACCGAATTATCTCCATAGGGTAAAATG
1 ACCGAATTACCCCCATAGGGTAAAATG
* * *
34298715 ACTGAATTACCTCAATAGGGTAAAATG
1 ACCGAATTACCCCCATAGGGTAAAATG
* * *
34298742 ACCGAATTACCTCTACAGGGTAAAATG
1 ACCGAATTACCCCCATAGGGTAAAATG
*
34298769 AACGAATTACCCCCATAGGGTAAAATG
1 ACCGAATTACCCCCATAGGGTAAAATG
* *
34298796 ACCGAAATACCCCTATAGGGTAAAATG
1 ACCGAATTACCCCCATAGGGTAAAATG
34298823 AC
1 AC
34298825 TGTTATACCC
Statistics
Matches: 121, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 121 1.00
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.21
Consensus pattern (27 bp):
ACCGAATTACCCCCATAGGGTAAAATG
Found at i:34299878 original size:42 final size:42
Alignment explanation
Indices: 34299800--34299949 Score: 117
Period size: 42 Copynumber: 3.6 Consensus size: 42
34299790 GATGTAGCCG
* * * * *
34299800 ATGATGCATTTACGTGCCAGTAT-TATTACTTTGGTATGTCCA
1 ATGATGCACTCACGTGCCAGTATGT-TTTCTTCGGTATATCCA
* * **
34299842 ATTATGCACTCATGTGCCAGTATGTTTTCTTCGGTATATCTG
1 ATGATGCACTCACGTGCCAGTATGTTTTCTTCGGTATATCCA
* * * * *
34299884 ATGATGCACTTACGGGCCAATATGTTTTCTTCAGTACAT-CA
1 ATGATGCACTCACGTGCCAGTATGTTTTCTTCGGTATATCCA
*
34299925 GATGATGCAC-CTACGTGTCAGTATG
1 -ATGATGCACTC-ACGTGCCAGTATG
34299950 ATGCTTCAAT
Statistics
Matches: 83, Mismatches: 22, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
42 82 0.99
43 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.37
Consensus pattern (42 bp):
ATGATGCACTCACGTGCCAGTATGTTTTCTTCGGTATATCCA
Found at i:34302695 original size:31 final size:29
Alignment explanation
Indices: 34302630--34302695 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
34302620 GTTAGTGATT
34302630 TAATATAAATATATAATACTTATTTAACA
1 TAATATAAATATATAATACTTATTTAACA
* * *
34302659 T-ATATAATTAATATAATATTTTTTATAACA
1 TAATATAAAT-ATATAATACTTATT-TAACA
34302689 TAATATA
1 TAATATA
34302696 TTCACGTTGG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
28 7 0.23
29 13 0.42
30 6 0.19
31 5 0.16
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (29 bp):
TAATATAAATATATAATACTTATTTAACA
Found at i:34306846 original size:37 final size:37
Alignment explanation
Indices: 34306787--34306867 Score: 117
Period size: 37 Copynumber: 2.2 Consensus size: 37
34306777 CTTTGATCAA
*
34306787 CAAGACATGACCGTCAGCAGTCAATCCGAGATCTCGC
1 CAAGACATGACCATCAGCAGTCAATCCGAGATCTCGC
* * *
34306824 CAAGACATGACCATCAGTAGTCAATCTGGGATCTCGC
1 CAAGACATGACCATCAGCAGTCAATCCGAGATCTCGC
34306861 CACAGAC
1 CA-AGAC
34306868 TCTATAGAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
37 35 0.90
38 4 0.10
ACGTcount: A:0.31, C:0.31, G:0.21, T:0.17
Consensus pattern (37 bp):
CAAGACATGACCATCAGCAGTCAATCCGAGATCTCGC
Found at i:34307290 original size:16 final size:17
Alignment explanation
Indices: 34307264--34307295 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
34307254 AAAATACCTA
34307264 AAATGTTTCAAAAAATT
1 AAATGTTTCAAAAAATT
34307281 AAAT-TTTCAAAAAAT
1 AAATGTTTCAAAAAAT
34307296 GTAATAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.34
Consensus pattern (17 bp):
AAATGTTTCAAAAAATT
Found at i:34308853 original size:21 final size:21
Alignment explanation
Indices: 34308829--34308883 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
34308819 AAATAGAAAA
34308829 AAAAATATTACAAAAAATATT
1 AAAAATATTACAAAAAATATT
*
34308850 AAAAATA-TA-AAAGAATTATT
1 AAAAATATTACAAA-AAATATT
*
34308870 TAAAA-ATTACAAAA
1 AAAAATATTACAAAA
34308884 GTTAATAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
19 4 0.14
20 15 0.52
21 10 0.34
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (21 bp):
AAAAATATTACAAAAAATATT
Found at i:34309997 original size:19 final size:19
Alignment explanation
Indices: 34309973--34310019 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
34309963 TATTTAAATT
**
34309973 TTATAAAAATATGAAAAAA
1 TTATAAAAATAAAAAAAAA
34309992 TTATAAAAATAAAAAAAAA
1 TTATAAAAATAAAAAAAAA
*
34310011 TTGTAAAAA
1 TTATAAAAA
34310020 ATTTATTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (19 bp):
TTATAAAAATAAAAAAAAA
Found at i:34319295 original size:27 final size:27
Alignment explanation
Indices: 34319265--34319326 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
34319255 TAACGTCTTA
34319265 TCGGACTATCCCT-TGTTTAATGTCCCG
1 TCGGACTAT-CCTATGTTTAATGTCCCG
* *
34319292 TCGGACGATCTTATGTTTAATGTCCCG
1 TCGGACTATCCTATGTTTAATGTCCCG
*
34319319 TTGGACTA
1 TCGGACTA
34319327 ACTATGATGC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 2 0.07
27 28 0.93
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.37
Consensus pattern (27 bp):
TCGGACTATCCTATGTTTAATGTCCCG
Found at i:34319549 original size:45 final size:44
Alignment explanation
Indices: 34319494--34319644 Score: 169
Period size: 45 Copynumber: 3.4 Consensus size: 44
34319484 AGTCTTTCAA
* * * *
34319494 CTATGGTCTTAGTCCTGTTTACCATGATGCCATAACGTCTTTTAG
1 CTATGGTCTTACTCAT-TTTATCATGATGCCATAACATCTTTTAG
* * **
34319539 CCATGGTCTTACTCATTTATGTTTTGATGCCATAACAT-TTTTCAG
1 CTATGGTCTTACTCATTT-TATCATGATGCCATAACATCTTTT-AG
* *
34319584 CTAGGGTCTTATTCATTTTTATCATGATGCCATAACATCTTTTAG
1 CTATGGTCTTACTCA-TTTTATCATGATGCCATAACATCTTTTAG
34319629 CTATGGTCTTACTCAT
1 CTATGGTCTTACTCAT
34319645 ATTGACATAT
Statistics
Matches: 86, Mismatches: 16, Indels: 9
0.77 0.14 0.08
Matches are distributed among these distances:
44 7 0.08
45 72 0.84
46 7 0.08
ACGTcount: A:0.22, C:0.21, G:0.15, T:0.43
Consensus pattern (44 bp):
CTATGGTCTTACTCATTTTATCATGATGCCATAACATCTTTTAG
Found at i:34323754 original size:4 final size:4
Alignment explanation
Indices: 34323702--34323765 Score: 51
Period size: 4 Copynumber: 15.8 Consensus size: 4
34323692 TTATCGTTCT
* * * *
34323702 TTTA TTT- TTCA TTTA TATA TATA TTTTA TTTT TTTA TTT- TCTCTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA T-T-TA TTTA
34323751 TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTT
34323766 TTGCCTAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
3 3 0.06
4 40 0.82
5 5 0.10
6 1 0.02
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:34324389 original size:15 final size:15
Alignment explanation
Indices: 34324369--34324405 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
34324359 GTTTAATATA
34324369 ATTATTAGTATTGTT
1 ATTATTAGTATTGTT
*
34324384 ATTATTATTATTGTT
1 ATTATTAGTATTGTT
*
34324399 AATATTA
1 ATTATTA
34324406 TCACTGTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.59
Consensus pattern (15 bp):
ATTATTAGTATTGTT
Found at i:34324847 original size:22 final size:22
Alignment explanation
Indices: 34324821--34324864 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
34324811 TATATATATA
*
34324821 TTTAACGAATATTTTCCTATTT
1 TTTAACGAATATTTTCATATTT
*
34324843 TTTAATGAATATTTTCATATTT
1 TTTAACGAATATTTTCATATTT
34324865 ATATGTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.09, G:0.05, T:0.57
Consensus pattern (22 bp):
TTTAACGAATATTTTCATATTT
Found at i:34325243 original size:15 final size:15
Alignment explanation
Indices: 34325220--34325252 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
34325210 TTTTTATGTC
34325220 ATTGATGTATTTATT
1 ATTGATGTATTTATT
*
34325235 ATTGTTGTATTTATT
1 ATTGATGTATTTATT
34325250 ATT
1 ATT
34325253 ATAGCATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (15 bp):
ATTGATGTATTTATT
Found at i:34335791 original size:7 final size:7
Alignment explanation
Indices: 34335779--34335803 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
34335769 GACCAATCCT
34335779 TTTTAAA
1 TTTTAAA
34335786 TTTTAAA
1 TTTTAAA
34335793 TTTTAAA
1 TTTTAAA
34335800 TTTT
1 TTTT
34335804 TTATATTATG
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
TTTTAAA
Found at i:34342626 original size:48 final size:48
Alignment explanation
Indices: 34342554--34342828 Score: 415
Period size: 48 Copynumber: 5.7 Consensus size: 48
34342544 TAAAGTACCA
* *
34342554 ATGCCATGTCCCAGACATGGTCTTACACGGGCACACATATCATCATCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCATCGTCG
* *
34342602 ATGCCATGTCCCAGACATGATCTTACACTGGCACACATATCATTGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCATCGTCG
* *
34342650 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCATCGCCA
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCATCGTCG
* * * *
34342698 ATGTCATGTCTCAGACATGGTTTTACACTGGCACATATATCATCGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCATCGTCG
* *
34342746 ATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCATCGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCATCGTCG
* * *
34342794 ATTCCATGTCCCAAACATGGTCTTACACAGGCACA
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACA
34342829 TTTAGCACGG
Statistics
Matches: 203, Mismatches: 24, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 203 1.00
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.25
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCATCGTCG
Found at i:34349348 original size:48 final size:48
Alignment explanation
Indices: 34349257--34349627 Score: 406
Period size: 48 Copynumber: 7.7 Consensus size: 48
34349247 TAAAGTACCA
* * * *
34349257 ATGCCATGTCCCCGACATGGTCTTACA-T-GAATCTACATCTCATCGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCA-C-ACATATCATCACCG
* * * *
34349305 ATGCCATCTTCTAGACATGGTCTTACACTGGCACACATATCATCATCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCATCACCG
* * *
34349353 ATGCCATGTCCCAAACATGGTCTTACACCGGCATACATATCATCACCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCATCACCG
* ** * * * * *
34349401 ATACCATGTCCCAGACATATTCTTACACCGGCTCACAGATCATCCCCA
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCATCACCG
* * * ** * *
34349449 ATGCCATGTCCCAGAAATGATCTTACATTGGCACTTATATCATCGCCA
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCATCACCG
* **
34349497 ATGCCATGTCCCAGACATGGTCTTACACTGGCACATATATCATTGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCATCACCG
* * *
34349545 ATGCCATGTCCCAAACATGGTCTTACACTAGCACACATATCATCACTG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCATCACCG
34349593 ATGCCATGTCCCAGACATGGTCTTACA-TAGGCACA
1 ATGCCATGTCCCAGACATGGTCTTACACT-GGCACA
34349628 TTTAGCATGG
Statistics
Matches: 271, Mismatches: 49, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
47 1 0.00
48 266 0.98
49 2 0.01
50 2 0.01
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.26
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCATCACCG
Found at i:34351065 original size:29 final size:29
Alignment explanation
Indices: 34351019--34351101 Score: 96
Period size: 29 Copynumber: 2.9 Consensus size: 29
34351009 TATGATATGC
* *
34351019 GAACCCTAGGAACATGCGAGCCTATGTGCA
1 GAACCCTAGAAACGTGCGAGCCTATGTG-A
* *
34351049 -AACCTTAGTAACGTGCGAGCCTATGTGA
1 GAACCCTAGAAACGTGCGAGCCTATGTGA
* *
34351077 GAACCCTAGAAACTTGCAAGCCTAT
1 GAACCCTAGAAACGTGCGAGCCTAT
34351102 ATACAATCCC
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
28 1 0.02
29 44 0.98
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.20
Consensus pattern (29 bp):
GAACCCTAGAAACGTGCGAGCCTATGTGA
Found at i:34355828 original size:27 final size:27
Alignment explanation
Indices: 34355787--34355838 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
34355777 ATTGGTACCA
* *
34355787 TTAAAATTAAGATGCATAATGGGACCG
1 TTAAAATTAAAATGCACAATGGGACCG
34355814 TTAAAATTAAAATGCACAATGGGAC
1 TTAAAATTAAAATGCACAATGGGAC
34355839 GATTATGACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (27 bp):
TTAAAATTAAAATGCACAATGGGACCG
Found at i:34360405 original size:25 final size:24
Alignment explanation
Indices: 34360376--34360424 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 24
34360366 AGCTAAAGTC
*
34360376 GGTTTTGGCTGAAGCACTTATATTG
1 GGTTTTGGCTGAAGAACTTA-ATTG
34360401 GGTTTTGGCTGAAGAACTTAATTG
1 GGTTTTGGCTGAAGAACTTAATTG
34360425 ACACAGCCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.22, C:0.10, G:0.29, T:0.39
Consensus pattern (24 bp):
GGTTTTGGCTGAAGAACTTAATTG
Found at i:34362930 original size:40 final size:40
Alignment explanation
Indices: 34362886--34363030 Score: 186
Period size: 40 Copynumber: 3.6 Consensus size: 40
34362876 CTTGCTCAAA
*
34362886 TGCCTTCGGGACTTAGCCCAGTTATAGTAACTCGCACAAT
1 TGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAT
* *
34362926 TGCCTTCGAGACTTAGCCCGGTTATAGTAACCTCTCACAAT
1 TGCCTTCGGGACTTAGCCCGGTTATAGTAA-CTCGCACAAT
* ** * *
34362967 TGCCTTCGGG-CTTAGCCCGG-AATTAGTCGCTAGCACAAA
1 TGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCACAAT
34363006 TGCCTTCGGGACTTAGCCCGGTTAT
1 TGCCTTCGGGACTTAGCCCGGTTAT
34363031 CATCCGAATA
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
39 18 0.20
40 53 0.59
41 19 0.21
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (40 bp):
TGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAT
Found at i:34366184 original size:35 final size:35
Alignment explanation
Indices: 34366138--34366227 Score: 162
Period size: 35 Copynumber: 2.6 Consensus size: 35
34366128 TCAGATTTGA
*
34366138 ATTACCAGTCCAGGCTAAATTTAGACCCTAATCAG
1 ATTACCTGTCCAGGCTAAATTTAGACCCTAATCAG
*
34366173 ATTACCTGTCCAGGCTAAATTTAGACCCTAATCGG
1 ATTACCTGTCCAGGCTAAATTTAGACCCTAATCAG
34366208 ATTACCTGTCCAGGCTAAAT
1 ATTACCTGTCCAGGCTAAAT
34366228 CCTCAATGCA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 53 1.00
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.28
Consensus pattern (35 bp):
ATTACCTGTCCAGGCTAAATTTAGACCCTAATCAG
Found at i:34370274 original size:42 final size:42
Alignment explanation
Indices: 34370212--34370304 Score: 168
Period size: 42 Copynumber: 2.2 Consensus size: 42
34370202 GGATTAGGAT
* *
34370212 CACACGGGCAGGTGATATCGGCATGTGTCAAGCTGTATGGGA
1 CACACGGGCAGGTGACATCGGCATGTGTCAAGCTGTATGGAA
34370254 CACACGGGCAGGTGACATCGGCATGTGTCAAGCTGTATGGAA
1 CACACGGGCAGGTGACATCGGCATGTGTCAAGCTGTATGGAA
34370296 CACACGGGC
1 CACACGGGC
34370305 GTGTGCTAGA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.25, C:0.23, G:0.34, T:0.18
Consensus pattern (42 bp):
CACACGGGCAGGTGACATCGGCATGTGTCAAGCTGTATGGAA
Found at i:34379302 original size:57 final size:57
Alignment explanation
Indices: 34379214--34379328 Score: 221
Period size: 57 Copynumber: 2.0 Consensus size: 57
34379204 CTTATGGCTC
*
34379214 TTTCATTCTACAAGTTTGATGTAATTTTGGGCATAGATTGGTTATCCAAATATGAGT
1 TTTCATTCCACAAGTTTGATGTAATTTTGGGCATAGATTGGTTATCCAAATATGAGT
34379271 TTTCATTCCACAAGTTTGATGTAATTTTGGGCATAGATTGGTTATCCAAATATGAGT
1 TTTCATTCCACAAGTTTGATGTAATTTTGGGCATAGATTGGTTATCCAAATATGAGT
34379328 T
1 T
34379329 ATAGTGGATT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (57 bp):
TTTCATTCCACAAGTTTGATGTAATTTTGGGCATAGATTGGTTATCCAAATATGAGT
Found at i:34383286 original size:40 final size:40
Alignment explanation
Indices: 34383231--34383379 Score: 262
Period size: 40 Copynumber: 3.7 Consensus size: 40
34383221 TGAGCATTGG
34383231 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
34383271 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
*
34383311 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
* * *
34383351 GATATGTCCGGGTTAAGACCCGAAGGCAA
1 AATATATCCGGGCTAAGACCCGAAGGCAA
34383380 ATGTGTTTGC
Statistics
Matches: 105, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 105 1.00
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.21
Consensus pattern (40 bp):
AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
Found at i:34385620 original size:15 final size:15
Alignment explanation
Indices: 34385600--34385629 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
34385590 TATGGGGGAA
34385600 ATGTAGAACTTTGGT
1 ATGTAGAACTTTGGT
34385615 ATGTAGAACTTTGGT
1 ATGTAGAACTTTGGT
34385630 GTGTTGGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.27, T:0.40
Consensus pattern (15 bp):
ATGTAGAACTTTGGT
Found at i:34387736 original size:28 final size:27
Alignment explanation
Indices: 34387669--34387729 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
34387659 AAATTAGCTC
* *
34387669 GCTTATCGTATTATGTTGCACTTTGTT
1 GCTTATCGTATTATGTTACACTTTGGT
* *
34387696 GCTTATCAATATTATTTTACACTTTGGT
1 GCTTATC-GTATTATGTTACACTTTGGT
34387724 GCTTAT
1 GCTTAT
34387730 TGTTATTTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 7 0.24
28 22 0.76
ACGTcount: A:0.20, C:0.15, G:0.15, T:0.51
Consensus pattern (27 bp):
GCTTATCGTATTATGTTACACTTTGGT
Found at i:34396503 original size:24 final size:24
Alignment explanation
Indices: 34396469--34396561 Score: 114
Period size: 24 Copynumber: 3.9 Consensus size: 24
34396459 GGACCATAGT
* *
34396469 CGAATGTGGCTCAAAATTATCTGC
1 CGAATGTGGCCCAGAATTATCTGC
* * * **
34396493 CAAATGTGGCTCAGAATTATATAT
1 CGAATGTGGCCCAGAATTATCTGC
*
34396517 CGAATGTGGCCCAGAATTATCAGC
1 CGAATGTGGCCCAGAATTATCTGC
34396541 CGAATGTGGCCCAGAATTATC
1 CGAATGTGGCCCAGAATTATC
34396562 AAAATTCACT
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 58 1.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (24 bp):
CGAATGTGGCCCAGAATTATCTGC
Found at i:34396547 original size:48 final size:48
Alignment explanation
Indices: 34396468--34396560 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
34396458 AGGACCATAG
* * *
34396468 TCGAATGTGGCTCAAAATTATCTGCCAAATGTGGCTCAGAATTATATA
1 TCGAATGTGGCCCAAAATTATCAGCCAAATGTGGCCCAGAATTATATA
* *
34396516 TCGAATGTGGCCCAGAATTATCAGCCGAATGTGGCCCAGAATTAT
1 TCGAATGTGGCCCAAAATTATCAGCCAAATGTGGCCCAGAATTAT
34396561 CAAAATTCAC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (48 bp):
TCGAATGTGGCCCAAAATTATCAGCCAAATGTGGCCCAGAATTATATA
Found at i:34400191 original size:21 final size:20
Alignment explanation
Indices: 34400167--34400205 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
34400157 TGAATTGATT
34400167 AAATGTGTGATTAAATTAGTG
1 AAATGTGT-ATTAAATTAGTG
* *
34400188 AAATTTGTATTAATTTAG
1 AAATGTGTATTAAATTAG
34400206 ATCAAGAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (20 bp):
AAATGTGTATTAAATTAGTG
Found at i:34403574 original size:49 final size:48
Alignment explanation
Indices: 34403465--34403637 Score: 197
Period size: 49 Copynumber: 3.6 Consensus size: 48
34403455 AGGATAAGAT
* * * *
34403465 TCGATGCCATGTCCTAGACATGGTCTTACATTGGCTATC--ACATCAAAG
1 TCGATGCCATGTCCCAGACA-GGTCTTACACTGGCTATCATATATC-AGG
* *
34403513 TCGATGCCATGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAGG
1 TCGATGCCATGTCCCAGACAGGTCTTACACTGGCTATCATATATC-AGG
* * * *
34403562 TTGATGCCATGTCCTAGACAGGTCTTACACTGGCTCTCATCTATCAGTG
1 TCGATGCCATGTCCCAGACAGGTCTTACACTGGCTATCATATATCAG-G
*
34403611 TCGATGTCATGTCCCAGACAGGTCTTA
1 TCGATGCCATGTCCCAGACAGGTCTTA
34403638 TACTAACACA
Statistics
Matches: 107, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
47 15 0.14
48 21 0.20
49 71 0.66
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (48 bp):
TCGATGCCATGTCCCAGACAGGTCTTACACTGGCTATCATATATCAGG
Found at i:34412546 original size:18 final size:18
Alignment explanation
Indices: 34412512--34412546 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
34412502 TTTTCAGAAA
*
34412512 TATGGGCCAACATGCCCG
1 TATGGGCCAACACGCCCG
*
34412530 TATGGGCCCACACGCCC
1 TATGGGCCAACACGCCC
34412547 AGATTGGCCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.40, G:0.26, T:0.14
Consensus pattern (18 bp):
TATGGGCCAACACGCCCG
Found at i:34413934 original size:17 final size:17
Alignment explanation
Indices: 34413912--34413946 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
34413902 TAGGTGGTGT
34413912 TAGAAGCATAGAATGCA
1 TAGAAGCATAGAATGCA
34413929 TAGAAGCATAGAATGCA
1 TAGAAGCATAGAATGCA
34413946 T
1 T
34413947 GAAAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.11, G:0.23, T:0.20
Consensus pattern (17 bp):
TAGAAGCATAGAATGCA
Found at i:34413937 original size:8 final size:9
Alignment explanation
Indices: 34413912--34413946 Score: 56
Period size: 8 Copynumber: 4.1 Consensus size: 9
34413902 TAGGTGGTGT
34413912 TAGAA-GCA
1 TAGAATGCA
34413920 TAGAATGCA
1 TAGAATGCA
34413929 TAGAA-GCA
1 TAGAATGCA
34413937 TAGAATGCA
1 TAGAATGCA
34413946 T
1 T
34413947 GAAAATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 13 0.52
9 12 0.48
ACGTcount: A:0.46, C:0.11, G:0.23, T:0.20
Consensus pattern (9 bp):
TAGAATGCA
Found at i:34414840 original size:13 final size:13
Alignment explanation
Indices: 34414822--34414855 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
34414812 ATATAATTAT
34414822 TAATAATATTTAA
1 TAATAATATTTAA
34414835 TAATAAT-TTTAA
1 TAATAATATTTAA
34414847 T-ATAATATT
1 TAATAATATT
34414856 ATTATTAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 5 0.25
12 8 0.40
13 7 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TAATAATATTTAA
Found at i:34417899 original size:4 final size:4
Alignment explanation
Indices: 34417890--34417914 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
34417880 ATATAATTTA
34417890 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
34417915 TATATATGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:34419524 original size:27 final size:27
Alignment explanation
Indices: 34419486--34419544 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
34419476 GTTTAGTAAT
34419486 TATGTAACATATGTTTACACTTCACAG
1 TATGTAACATATGTTTACACTTCACAG
34419513 TATGTAACATATGTTTACACTTCACAG
1 TATGTAACATATGTTTACACTTCACAG
34419540 TATGT
1 TATGT
34419545 TTCTTTGGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (27 bp):
TATGTAACATATGTTTACACTTCACAG
Found at i:34421170 original size:3 final size:3
Alignment explanation
Indices: 34421164--34421191 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
34421154 AAAAAAAAAA
34421164 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
34421192 GCAAAATAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:34426938 original size:23 final size:23
Alignment explanation
Indices: 34426900--34427011 Score: 93
Period size: 23 Copynumber: 4.8 Consensus size: 23
34426890 AGGTCTTCCC
34426900 GAGCTGATGAACAGTAAGCTCTATT
1 GAGCTGA--AACAGTAAGCTCTATT
*
34426925 GAGCTGAAACAGTAAGCTCTATA
1 GAGCTGAAACAGTAAGCTCTATT
* *
34426948 GAGTTG-AACAGTAAGCTC-ATAC
1 GAGCTGAAACAGTAAGCTCTAT-T
** * *
34426970 GAGCTGAAATGGTAAGCTCCAAT
1 GAGCTGAAACAGTAAGCTCTATT
* *
34426993 GAGCTAAAAATAGTAAGCT
1 GAGCT-GAAACAGTAAGCT
34427012 TTTACGAGCT
Statistics
Matches: 73, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
21 2 0.03
22 17 0.23
23 35 0.48
24 12 0.16
25 7 0.10
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (23 bp):
GAGCTGAAACAGTAAGCTCTATT
Found at i:34426960 original size:22 final size:22
Alignment explanation
Indices: 34426907--34426977 Score: 99
Period size: 22 Copynumber: 3.2 Consensus size: 22
34426897 CCCGAGCTGA
*
34426907 TGAACAGTAAGCTCTATTGAGC
1 TGAACAGTAAGCTCTATAGAGC
*
34426929 TGAAACAGTAAGCTCTATAGAGT
1 TG-AACAGTAAGCTCTATAGAGC
34426952 TGAACAGTAAGCTC-ATACGAGC
1 TGAACAGTAAGCTCTATA-GAGC
34426974 TGAA
1 TGAA
34426978 ATGGTAAGCT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
21 3 0.07
22 21 0.48
23 20 0.45
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.24
Consensus pattern (22 bp):
TGAACAGTAAGCTCTATAGAGC
Found at i:34428240 original size:59 final size:59
Alignment explanation
Indices: 34428154--34428274 Score: 224
Period size: 59 Copynumber: 2.1 Consensus size: 59
34428144 TCAAATAGTA
* *
34428154 AAATTTCTTTACAAAACTTTCATATAATAATTCTATCATGCTGTAAACCTTCTTAAAAT
1 AAATTTCTTTACAAAAATTTCACATAATAATTCTATCATGCTGTAAACCTTCTTAAAAT
34428213 AAATTTCTTTACAAAAATTTCACATAATAATTCTATCATGCTGTAAACCTTCTTAAAAT
1 AAATTTCTTTACAAAAATTTCACATAATAATTCTATCATGCTGTAAACCTTCTTAAAAT
34428272 AAA
1 AAA
34428275 ATGATAGTTT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.39
Consensus pattern (59 bp):
AAATTTCTTTACAAAAATTTCACATAATAATTCTATCATGCTGTAAACCTTCTTAAAAT
Found at i:34432608 original size:43 final size:43
Alignment explanation
Indices: 34432516--34432608 Score: 123
Period size: 43 Copynumber: 2.2 Consensus size: 43
34432506 GCATGAAACT
* * ** *
34432516 CGGTGATGTGTATTCGGGCCTTTGTGCCTAGTAGGCTTCGTGC
1 CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTAATGA
* *
34432559 CAGTGATGTGTATTCGGGTCTTCGTGCCTAGCAGGCTTAATGA
1 CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTAATGA
34432602 CGGTGAT
1 CGGTGAT
34432609 TCGAGCAAGG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.14, C:0.19, G:0.33, T:0.33
Consensus pattern (43 bp):
CGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTAATGA
Found at i:34432855 original size:29 final size:29
Alignment explanation
Indices: 34432779--34432866 Score: 99
Period size: 29 Copynumber: 3.0 Consensus size: 29
34432769 TGTGTTTGCA
34432779 AATTCCTTTAACCGAGCACTATGTGTGCG
1 AATTCCTTTAACCGAGCACTATGTGTGCG
** ** *
34432808 AGA-T-CAGTAATTGAGGCACTGTGTGTGCG
1 A-ATTCCTTTAACCGA-GCACTATGTGTGCG
34432837 AATTCCTTTAACCGAGCACTATGTGTGCG
1 AATTCCTTTAACCGAGCACTATGTGTGCG
34432866 A
1 A
34432867 GATCNNNNNN
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
28 7 0.16
29 31 0.69
30 7 0.16
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (29 bp):
AATTCCTTTAACCGAGCACTATGTGTGCG
Found at i:34441438 original size:46 final size:46
Alignment explanation
Indices: 34441385--34441514 Score: 131
Period size: 46 Copynumber: 2.8 Consensus size: 46
34441375 TATATATACA
* * *
34441385 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACACATCTCACATTAGCCATTCGGCCTTACCACATATC
* * *
34441431 CATCTCATACACGTTTCGCATTAGCCATTCGGCCTTACCACATAT-
1 CATCTCATACACATCTCACATTAGCCATTCGGCCTTACCACATATC
* *
34441476 -AT-TCATGTTCACATTCATCACATTGGCCATTCGGCCTTA
1 CATCTCA--TACACA-TC-TCACATTAGCCATTCGGCCTTA
34441515 TCTCANNNNN
Statistics
Matches: 69, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
43 3 0.04
44 2 0.03
45 4 0.06
46 40 0.58
47 20 0.29
ACGTcount: A:0.25, C:0.31, G:0.10, T:0.34
Consensus pattern (46 bp):
CATCTCATACACATCTCACATTAGCCATTCGGCCTTACCACATATC
Found at i:34449740 original size:16 final size:16
Alignment explanation
Indices: 34449712--34449744 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
34449702 TTCCTTCCAC
34449712 TATATGTTTTTTTTAT
1 TATATGTTTTTTTTAT
34449728 TATAT-TTTATTTTTAT
1 TATATGTTT-TTTTTAT
34449744 T
1 T
34449745 TTCTTTATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.19
16 13 0.81
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (16 bp):
TATATGTTTTTTTTAT
Found at i:34467392 original size:30 final size:30
Alignment explanation
Indices: 34467356--34467414 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
34467346 AAGAATGTCT
34467356 TGAAAATAATATTTAAAAATCTTTTTATCA
1 TGAAAATAATATTTAAAAATCTTTTTATCA
34467386 TGAAAATAATATTTAAAAATCTTTTTATC
1 TGAAAATAATATTTAAAAATCTTTTTATC
34467415 TCTATGTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (30 bp):
TGAAAATAATATTTAAAAATCTTTTTATCA
Found at i:34473511 original size:13 final size:13
Alignment explanation
Indices: 34473493--34473517 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34473483 CCGAACACAC
34473493 GCTCGTGTCCCTG
1 GCTCGTGTCCCTG
34473506 GCTCGTGTCCCT
1 GCTCGTGTCCCT
34473518 CACATGGCCT
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:0.00, C:0.40, G:0.28, T:0.32
Consensus pattern (13 bp):
GCTCGTGTCCCTG
Found at i:34476707 original size:20 final size:20
Alignment explanation
Indices: 34476684--34476727 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
34476674 GGACATGGGC
34476684 GTGTCCCGAGCCACATGAGA
1 GTGTCCCGAGCCACATGAGA
* *
34476704 GTGTCCTGAGCCACATGAGC
1 GTGTCCCGAGCCACATGAGA
34476724 GTGT
1 GTGT
34476728 TTGACCACAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.20, C:0.27, G:0.32, T:0.20
Consensus pattern (20 bp):
GTGTCCCGAGCCACATGAGA
Found at i:34477732 original size:37 final size:36
Alignment explanation
Indices: 34477691--34477774 Score: 96
Period size: 37 Copynumber: 2.3 Consensus size: 36
34477681 TGTGAGTACG
* *
34477691 TGTAAAACCATAACTAGGCTATGACATTGTAATAGCC
1 TGTAAGACCATAACTAGGCTATGACATTGTAATA-CA
** * * *
34477728 TGTAAGACCATATTTGGGCTATGGCATTGTGATACA
1 TGTAAGACCATAACTAGGCTATGACATTGTAATACA
34477764 TGTAAGACCAT
1 TGTAAGACCAT
34477775 GTCTGGGACA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
36 12 0.30
37 28 0.70
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (36 bp):
TGTAAGACCATAACTAGGCTATGACATTGTAATACA
Found at i:34477811 original size:42 final size:41
Alignment explanation
Indices: 34477764--34477958 Score: 142
Period size: 42 Copynumber: 4.7 Consensus size: 41
34477754 TTGTGATACA
34477764 TGTAAGACCATGTCTGGGACATGGCATCGATATGAAATTATG
1 TGTAAGACCATGTCTGGGACATGGCATCGATATGAAATT-TG
* * * * * * *
34477806 TGTAAGACTATATCTGAGATATGGCTTCGGTATGAGATTTCG
1 TGTAAGACCATGTCTGGGACATGGCATCGATATGAAATTT-G
* * ** * *
34477848 TGTAAGACCGTGTCTAGGATGTGGCATCGATATGTGATTTTG
1 TGTAAGACCATGTCTGGGACATGGCATCGATATG-AAATTTG
* * * * * * *
34477890 TATAAGACCATGTTTGGGACATAGCATTGATGTGAGACTTCG
1 TGTAAGACCATGTCTGGGACATGGCATCGATATGA-AATTTG
34477932 TGTAAGACCATAGT-T-GGACTATGGCAT
1 TGTAAGACCAT-GTCTGGGAC-ATGGCAT
34477959 TAAGTAAACG
Statistics
Matches: 116, Mismatches: 32, Indels: 10
0.73 0.20 0.06
Matches are distributed among these distances:
41 5 0.04
42 106 0.91
43 5 0.04
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.32
Consensus pattern (41 bp):
TGTAAGACCATGTCTGGGACATGGCATCGATATGAAATTTG
Found at i:34481948 original size:40 final size:40
Alignment explanation
Indices: 34481904--34481979 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 40
34481894 TGGCTAAGAA
** *
34481904 TGGCACTTAGTGTGCGGTTTGAGATAGCTTTGGCTAAATG
1 TGGCACTTAGTGTGCAATTTGAGATAGCTTCGGCTAAATG
* * *
34481944 TGGCATTTGGTGTGCAATTTGTGATAGCTTCGGCTA
1 TGGCACTTAGTGTGCAATTTGAGATAGCTTCGGCTA
34481980 TATATATATA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.18, C:0.13, G:0.32, T:0.37
Consensus pattern (40 bp):
TGGCACTTAGTGTGCAATTTGAGATAGCTTCGGCTAAATG
Found at i:34482070 original size:28 final size:28
Alignment explanation
Indices: 34481996--34482070 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 28
34481986 TATATGTGTG
* *
34481996 TGGCACTTAGTGTGCGAAATATTGAGAA
1 TGGCACTTAGTGTGCGAGATATTAAGAA
* * *
34482024 TGGCACTTGGTATGTGAGATATTAAGTAA
1 TGGCACTTAGTGTGCGAGATATTAAG-AA
34482053 -GGCACTTAGTGTGCGAGA
1 TGGCACTTAGTGTGCGAGA
34482071 CATCGAAGAT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
28 36 0.95
29 2 0.05
ACGTcount: A:0.29, C:0.11, G:0.31, T:0.29
Consensus pattern (28 bp):
TGGCACTTAGTGTGCGAGATATTAAGAA
Found at i:34489604 original size:28 final size:28
Alignment explanation
Indices: 34489564--34489627 Score: 119
Period size: 28 Copynumber: 2.3 Consensus size: 28
34489554 GTGTCCTTAT
34489564 CCCGTGTCCCTCACATGGCCTAGACACA
1 CCCGTGTCCCTCACATGGCCTAGACACA
34489592 CCCGTGTCCCTCACATGGCCTAGACACA
1 CCCGTGTCCCTCACATGGCCTAGACACA
*
34489620 CCCTTGTC
1 CCCGTGTC
34489628 ATAGTCTATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.19, C:0.44, G:0.17, T:0.20
Consensus pattern (28 bp):
CCCGTGTCCCTCACATGGCCTAGACACA
Found at i:34495625 original size:46 final size:46
Alignment explanation
Indices: 34495558--34495650 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
34495548 TTTAATCAAG
*
34495558 ATTATTTACAAGTGTATAATTGTGTTTTACTTTGAATTTGGTAACC
1 ATTATTTACAAGTCTATAATTGTGTTTTACTTTGAATTTGGTAACC
34495604 ATTATTTACAAGTCTATAATTGTGTTTTACTTTGAATTTGGTAACC
1 ATTATTTACAAGTCTATAATTGTGTTTTACTTTGAATTTGGTAACC
34495650 A
1 A
34495651 CTAAGCACAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (46 bp):
ATTATTTACAAGTCTATAATTGTGTTTTACTTTGAATTTGGTAACC
Found at i:34495661 original size:46 final size:46
Alignment explanation
Indices: 34495565--34495662 Score: 151
Period size: 46 Copynumber: 2.1 Consensus size: 46
34495555 AAGATTATTT
* * ***
34495565 ACAAGTGTATAATTGTGTTTTACTTTGAATTTGGTAACCATTATTT
1 ACAAGTCTATAATTGTGTTTTACTTTGAATTTGGTAACCACTAAGC
34495611 ACAAGTCTATAATTGTGTTTTACTTTGAATTTGGTAACCACTAAGC
1 ACAAGTCTATAATTGTGTTTTACTTTGAATTTGGTAACCACTAAGC
34495657 ACAAGT
1 ACAAGT
34495663 AGTAGAAAGG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (46 bp):
ACAAGTCTATAATTGTGTTTTACTTTGAATTTGGTAACCACTAAGC
Found at i:34501716 original size:110 final size:110
Alignment explanation
Indices: 34501523--34501730 Score: 364
Period size: 110 Copynumber: 1.9 Consensus size: 110
34501513 ATATTCCTTA
34501523 TTGATTTCTTTGTGCTTGACATGGATGAGGATGTTGAAGTGCCTTTAATCTTAGGTCGTCCATTT
1 TTGATTTCTTTGTGCTTGACATGGATGAGGATGTTGAAGTGCCTTTAATCTTAGGTCGTCCATTT
* **
34501588 TTAGTCGTTGCTAGGGCTGTTATTGATATGGGTAATGTTAAGCTG
66 TTAGCCACTGCTAGGGCTGTTATTGATATGGGTAATGTTAAGCTG
34501633 TTGATTT-TGTTGTGCTTGACATGGATGAGGATGTTGAAGTGCCTTTAATCTTAGGTCGTCCATT
1 TTGATTTCT-TTGTGCTTGACATGGATGAGGATGTTGAAGTGCCTTTAATCTTAGGTCGTCCATT
*
34501697 TTTAGCCACTGCTAGGGCTGTTATTGATGTGGGT
65 TTTAGCCACTGCTAGGGCTGTTATTGATATGGGT
34501731 GATGGTAAAT
Statistics
Matches: 93, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
109 1 0.01
110 92 0.99
ACGTcount: A:0.18, C:0.12, G:0.28, T:0.41
Consensus pattern (110 bp):
TTGATTTCTTTGTGCTTGACATGGATGAGGATGTTGAAGTGCCTTTAATCTTAGGTCGTCCATTT
TTAGCCACTGCTAGGGCTGTTATTGATATGGGTAATGTTAAGCTG
Found at i:34505585 original size:7 final size:6
Alignment explanation
Indices: 34505557--34505595 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
34505547 TTTAAACTCA
* *
34505557 TTTTAT TTTTATT TTTTAT TTTTAC TTTTAT TTCTAT TT
1 TTTTAT TTTTA-T TTTTAT TTTTAT TTTTAT TTTTAT TT
34505596 ATTTTTGAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTAT
Done.