Multiple sequence alignment - TraesCS1D01G273100

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1D01G273100 chr1D 100.000 4495 0 0 1 4495 367399566 367404060 0.000000e+00 8301.0
1 TraesCS1D01G273100 chr1A 91.908 2076 90 34 1 2038 466895833 466897868 0.000000e+00 2832.0
2 TraesCS1D01G273100 chr1A 98.410 1006 11 4 2120 3123 466897867 466898869 0.000000e+00 1764.0
3 TraesCS1D01G273100 chr1A 90.625 960 31 11 3171 4075 466898866 466899821 0.000000e+00 1219.0
4 TraesCS1D01G273100 chr1A 92.920 226 14 2 4271 4495 466899933 466900157 1.210000e-85 327.0
5 TraesCS1D01G273100 chr1A 85.217 115 14 3 2032 2145 486046073 486046185 1.020000e-21 115.0
6 TraesCS1D01G273100 chr1B 92.000 1650 65 35 419 2038 491530897 491532509 0.000000e+00 2254.0
7 TraesCS1D01G273100 chr1B 91.243 1336 41 20 2797 4073 491533274 491534592 0.000000e+00 1749.0
8 TraesCS1D01G273100 chr1B 97.661 684 11 5 2120 2798 491532508 491533191 0.000000e+00 1170.0
9 TraesCS1D01G273100 chr1B 87.615 436 38 5 1 425 491527737 491528167 4.040000e-135 492.0
10 TraesCS1D01G273100 chr1B 87.188 320 19 6 4174 4492 491534616 491534914 1.200000e-90 344.0
11 TraesCS1D01G273100 chr1B 97.059 34 1 0 4146 4179 44932858 44932825 1.750000e-04 58.4
12 TraesCS1D01G273100 chr7D 94.186 86 5 0 2036 2121 279217 279302 1.010000e-26 132.0
13 TraesCS1D01G273100 chr7D 92.500 40 3 0 4037 4076 212881157 212881196 1.750000e-04 58.4
14 TraesCS1D01G273100 chr7B 91.304 92 7 1 2035 2125 115386719 115386628 1.700000e-24 124.0
15 TraesCS1D01G273100 chr7B 88.776 98 9 1 2024 2121 632954424 632954519 7.900000e-23 119.0
16 TraesCS1D01G273100 chr7B 95.122 41 2 0 4139 4179 436210093 436210133 1.040000e-06 65.8
17 TraesCS1D01G273100 chr7B 97.297 37 1 0 4146 4182 685778905 685778941 3.750000e-06 63.9
18 TraesCS1D01G273100 chr5B 89.796 98 9 1 2037 2133 694322862 694322765 1.700000e-24 124.0
19 TraesCS1D01G273100 chr5B 88.350 103 11 1 2019 2121 490419342 490419443 6.110000e-24 122.0
20 TraesCS1D01G273100 chr4A 88.235 102 11 1 2033 2133 663581722 663581823 2.200000e-23 121.0
21 TraesCS1D01G273100 chr2B 88.889 99 10 1 2036 2133 458967056 458966958 2.200000e-23 121.0
22 TraesCS1D01G273100 chr4B 87.129 101 13 0 2031 2131 117191095 117191195 1.020000e-21 115.0
23 TraesCS1D01G273100 chr4B 97.059 34 1 0 4146 4179 167355516 167355549 1.750000e-04 58.4
24 TraesCS1D01G273100 chr7A 95.652 46 1 1 4134 4179 433736465 433736509 6.240000e-09 73.1
25 TraesCS1D01G273100 chr7A 94.737 38 2 0 4038 4075 517579117 517579154 4.860000e-05 60.2
26 TraesCS1D01G273100 chr2D 95.455 44 2 0 4032 4075 628571443 628571486 2.240000e-08 71.3
27 TraesCS1D01G273100 chr3A 97.368 38 1 0 4038 4075 698563523 698563486 1.040000e-06 65.8
28 TraesCS1D01G273100 chr3A 97.297 37 1 0 4146 4182 7309159 7309123 3.750000e-06 63.9
29 TraesCS1D01G273100 chr2A 93.182 44 3 0 4032 4075 758599188 758599145 1.040000e-06 65.8
30 TraesCS1D01G273100 chr6D 97.222 36 1 0 4146 4181 60481490 60481455 1.350000e-05 62.1
31 TraesCS1D01G273100 chr6B 97.222 36 1 0 4146 4181 390626349 390626384 1.350000e-05 62.1
32 TraesCS1D01G273100 chr6B 92.308 39 3 0 4037 4075 471675499 471675461 6.280000e-04 56.5
33 TraesCS1D01G273100 chrUn 100.000 29 0 0 4047 4075 44270766 44270738 2.000000e-03 54.7
34 TraesCS1D01G273100 chrUn 100.000 29 0 0 4047 4075 44296600 44296572 2.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G273100 chr1D 367399566 367404060 4494 False 8301.0 8301 100.00000 1 4495 1 chr1D.!!$F1 4494
1 TraesCS1D01G273100 chr1A 466895833 466900157 4324 False 1535.5 2832 93.46575 1 4495 4 chr1A.!!$F2 4494
2 TraesCS1D01G273100 chr1B 491527737 491534914 7177 False 1201.8 2254 91.14140 1 4492 5 chr1B.!!$F1 4491

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
693 3468 0.031449 GCTAGACTCACCCATCGAGC 59.969 60.0 0.00 0.00 36.60 5.03 F
906 3706 0.389556 GAAACCTTCGACCCCGAGAC 60.390 60.0 0.00 0.00 46.39 3.36 F
1605 4414 0.541863 ATGTCTCACCGGGGACAATC 59.458 55.0 23.64 8.09 44.10 2.67 F
2476 5300 0.837272 ACCAGGATTACCCACCGATG 59.163 55.0 0.00 0.00 37.41 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2104 4925 0.325016 AAATACTCCCTCCGTCCCGT 60.325 55.000 0.00 0.0 0.0 5.28 R
2105 4926 0.828677 AAAATACTCCCTCCGTCCCG 59.171 55.000 0.00 0.0 0.0 5.14 R
3425 6348 1.659098 CTTACGACGACTTGGAATGCC 59.341 52.381 0.00 0.0 0.0 4.40 R
4115 7084 0.034337 ATGCCAAGCTTTGCCACAAG 59.966 50.000 18.94 0.0 0.0 3.16 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 1.142531 TGCGATCTTCTGCGATGCT 59.857 52.632 0.00 0.00 0.00 3.79
19 20 1.149964 TGCGATCTTCTGCGATGCTG 61.150 55.000 0.00 0.00 0.00 4.41
58 59 6.041296 ACAAGATTCAAGGAAAAGTCAAGCAT 59.959 34.615 0.00 0.00 0.00 3.79
67 68 4.158394 GGAAAAGTCAAGCATGATTAGGCA 59.842 41.667 0.00 0.00 38.01 4.75
79 80 5.474532 GCATGATTAGGCATAGTCATCCAAA 59.525 40.000 12.77 0.00 36.51 3.28
106 107 4.446371 AGGGAATCGACATCTTCAACATC 58.554 43.478 0.00 0.00 0.00 3.06
119 120 5.773575 TCTTCAACATCTGTATATCTCGGC 58.226 41.667 0.00 0.00 0.00 5.54
127 128 1.535896 TGTATATCTCGGCGCTCTCAC 59.464 52.381 7.64 0.00 0.00 3.51
154 155 1.067295 ATCTTCACCACTCCAGGCAA 58.933 50.000 0.00 0.00 0.00 4.52
163 164 3.274288 CCACTCCAGGCAAAGACTTATC 58.726 50.000 0.00 0.00 0.00 1.75
197 199 4.789802 GCAACCAAGCTAGCCGATATTTTC 60.790 45.833 12.13 0.00 0.00 2.29
244 246 2.041701 AGATTGCTTGGTGTTGGCTTT 58.958 42.857 0.00 0.00 0.00 3.51
250 262 0.749818 TTGGTGTTGGCTTTGCGAGA 60.750 50.000 0.00 0.00 0.00 4.04
267 279 2.484889 GAGAACGGTGTTTCAAGCTCT 58.515 47.619 0.00 0.00 0.00 4.09
268 280 2.476997 GAGAACGGTGTTTCAAGCTCTC 59.523 50.000 0.00 0.00 0.00 3.20
277 289 3.817084 TGTTTCAAGCTCTCAGACATTGG 59.183 43.478 0.00 0.00 0.00 3.16
338 350 5.544176 TCCTCCTTCCATCATAGTAACATCC 59.456 44.000 0.00 0.00 0.00 3.51
340 352 4.283467 TCCTTCCATCATAGTAACATCCGG 59.717 45.833 0.00 0.00 0.00 5.14
342 354 2.029380 TCCATCATAGTAACATCCGGCG 60.029 50.000 0.00 0.00 0.00 6.46
350 362 3.454375 AGTAACATCCGGCGTAGAAATG 58.546 45.455 6.01 4.18 0.00 2.32
397 409 7.445900 TTTAGCGTTGAGAATACAATCTACG 57.554 36.000 5.11 5.11 44.01 3.51
398 410 4.995124 AGCGTTGAGAATACAATCTACGT 58.005 39.130 9.98 0.00 43.41 3.57
399 411 6.127810 AGCGTTGAGAATACAATCTACGTA 57.872 37.500 9.98 0.00 43.41 3.57
400 412 6.736123 AGCGTTGAGAATACAATCTACGTAT 58.264 36.000 0.00 0.00 43.41 3.06
401 413 6.637254 AGCGTTGAGAATACAATCTACGTATG 59.363 38.462 0.00 0.00 43.41 2.39
467 3216 4.202101 CCAGCAAGGACATACTCTCTGTAG 60.202 50.000 0.00 0.00 41.22 2.74
479 3247 2.608546 CTCTCTGTAGCAAGCTTGATGC 59.391 50.000 30.39 26.79 44.15 3.91
480 3248 1.669779 CTCTGTAGCAAGCTTGATGCC 59.330 52.381 30.39 18.33 44.91 4.40
481 3249 1.280133 TCTGTAGCAAGCTTGATGCCT 59.720 47.619 30.39 18.56 44.91 4.75
482 3250 2.089980 CTGTAGCAAGCTTGATGCCTT 58.910 47.619 30.39 9.48 44.91 4.35
483 3251 2.490903 CTGTAGCAAGCTTGATGCCTTT 59.509 45.455 30.39 2.50 44.91 3.11
484 3252 2.489329 TGTAGCAAGCTTGATGCCTTTC 59.511 45.455 30.39 9.39 44.91 2.62
485 3253 1.624336 AGCAAGCTTGATGCCTTTCA 58.376 45.000 30.39 0.00 44.91 2.69
486 3254 1.271656 AGCAAGCTTGATGCCTTTCAC 59.728 47.619 30.39 7.91 44.91 3.18
487 3255 1.973138 CAAGCTTGATGCCTTTCACG 58.027 50.000 22.31 0.00 44.23 4.35
488 3256 0.242017 AAGCTTGATGCCTTTCACGC 59.758 50.000 0.00 2.80 44.23 5.34
489 3257 0.607489 AGCTTGATGCCTTTCACGCT 60.607 50.000 6.58 6.58 43.86 5.07
490 3258 0.179179 GCTTGATGCCTTTCACGCTC 60.179 55.000 3.58 0.00 37.76 5.03
491 3259 0.095935 CTTGATGCCTTTCACGCTCG 59.904 55.000 0.00 0.00 0.00 5.03
492 3260 0.602638 TTGATGCCTTTCACGCTCGT 60.603 50.000 0.00 0.00 0.00 4.18
493 3261 1.014044 TGATGCCTTTCACGCTCGTC 61.014 55.000 0.00 0.00 0.00 4.20
494 3262 0.737715 GATGCCTTTCACGCTCGTCT 60.738 55.000 0.00 0.00 0.00 4.18
495 3263 0.530744 ATGCCTTTCACGCTCGTCTA 59.469 50.000 0.00 0.00 0.00 2.59
496 3264 0.530744 TGCCTTTCACGCTCGTCTAT 59.469 50.000 0.00 0.00 0.00 1.98
497 3265 0.924090 GCCTTTCACGCTCGTCTATG 59.076 55.000 0.00 0.00 0.00 2.23
560 3330 4.708726 AAAGAGCTTATGCCAATGTGAC 57.291 40.909 0.00 0.00 40.80 3.67
636 3409 2.605030 TGGTTGCTTCAATTATTGCGC 58.395 42.857 0.00 0.00 0.00 6.09
637 3410 1.583404 GGTTGCTTCAATTATTGCGCG 59.417 47.619 0.00 0.00 32.09 6.86
638 3411 1.583404 GTTGCTTCAATTATTGCGCGG 59.417 47.619 8.83 0.00 32.09 6.46
639 3412 0.525242 TGCTTCAATTATTGCGCGGC 60.525 50.000 8.83 0.00 32.09 6.53
684 3459 6.227522 AGAGGAAAGAAAAAGCTAGACTCAC 58.772 40.000 0.00 0.00 0.00 3.51
693 3468 0.031449 GCTAGACTCACCCATCGAGC 59.969 60.000 0.00 0.00 36.60 5.03
720 3495 1.671054 GGAAAGCAGCGCTGTGGTA 60.671 57.895 35.80 0.00 39.62 3.25
796 3591 1.268285 CCATAGACAGTCGCAGTCTCG 60.268 57.143 7.86 2.97 44.70 4.04
801 3596 2.049985 AGTCGCAGTCTCGCACAC 60.050 61.111 0.00 0.00 0.00 3.82
802 3597 2.354656 GTCGCAGTCTCGCACACA 60.355 61.111 0.00 0.00 0.00 3.72
803 3598 2.050077 TCGCAGTCTCGCACACAG 60.050 61.111 0.00 0.00 0.00 3.66
804 3599 2.050077 CGCAGTCTCGCACACAGA 60.050 61.111 0.00 0.00 0.00 3.41
805 3600 2.085262 CGCAGTCTCGCACACAGAG 61.085 63.158 0.00 0.00 37.09 3.35
806 3601 1.287191 GCAGTCTCGCACACAGAGA 59.713 57.895 0.00 0.00 41.91 3.10
807 3602 0.732196 GCAGTCTCGCACACAGAGAG 60.732 60.000 0.00 0.00 44.41 3.20
906 3706 0.389556 GAAACCTTCGACCCCGAGAC 60.390 60.000 0.00 0.00 46.39 3.36
1594 4403 2.159627 CAGGTTACGCCAAATGTCTCAC 59.840 50.000 0.00 0.00 40.61 3.51
1596 4405 1.127951 GTTACGCCAAATGTCTCACCG 59.872 52.381 0.00 0.00 0.00 4.94
1604 4413 0.991920 AATGTCTCACCGGGGACAAT 59.008 50.000 23.64 16.35 44.10 2.71
1605 4414 0.541863 ATGTCTCACCGGGGACAATC 59.458 55.000 23.64 8.09 44.10 2.67
1616 4427 2.033801 CGGGGACAATCTTGATGCATTC 59.966 50.000 0.00 0.00 0.00 2.67
1648 4459 3.054287 TGACCTTTGTCCCAGTTGTACAA 60.054 43.478 3.59 3.59 41.01 2.41
1683 4494 1.000717 ACGCTTTCATTTGGTTTCGGG 60.001 47.619 0.00 0.00 0.00 5.14
2038 4859 9.291664 CTCTTTCACATAACTACAGTAAGCTAC 57.708 37.037 0.00 0.00 0.00 3.58
2041 4862 9.635520 TTTCACATAACTACAGTAAGCTACTTC 57.364 33.333 0.00 0.00 36.76 3.01
2042 4863 7.769220 TCACATAACTACAGTAAGCTACTTCC 58.231 38.462 0.00 0.00 36.76 3.46
2044 4865 7.916450 CACATAACTACAGTAAGCTACTTCCTC 59.084 40.741 0.00 0.00 36.76 3.71
2045 4866 5.918426 AACTACAGTAAGCTACTTCCTCC 57.082 43.478 0.00 0.00 36.76 4.30
2046 4867 3.946558 ACTACAGTAAGCTACTTCCTCCG 59.053 47.826 0.00 0.00 36.76 4.63
2047 4868 2.805194 ACAGTAAGCTACTTCCTCCGT 58.195 47.619 0.00 0.00 36.76 4.69
2048 4869 2.754002 ACAGTAAGCTACTTCCTCCGTC 59.246 50.000 0.00 0.00 36.76 4.79
2049 4870 3.018149 CAGTAAGCTACTTCCTCCGTCT 58.982 50.000 0.00 0.00 36.76 4.18
2050 4871 3.065648 CAGTAAGCTACTTCCTCCGTCTC 59.934 52.174 0.00 0.00 36.76 3.36
2051 4872 2.217510 AAGCTACTTCCTCCGTCTCA 57.782 50.000 0.00 0.00 0.00 3.27
2052 4873 2.445682 AGCTACTTCCTCCGTCTCAT 57.554 50.000 0.00 0.00 0.00 2.90
2053 4874 3.579534 AGCTACTTCCTCCGTCTCATA 57.420 47.619 0.00 0.00 0.00 2.15
2054 4875 3.899726 AGCTACTTCCTCCGTCTCATAA 58.100 45.455 0.00 0.00 0.00 1.90
2055 4876 4.475345 AGCTACTTCCTCCGTCTCATAAT 58.525 43.478 0.00 0.00 0.00 1.28
2056 4877 5.632118 AGCTACTTCCTCCGTCTCATAATA 58.368 41.667 0.00 0.00 0.00 0.98
2057 4878 6.249951 AGCTACTTCCTCCGTCTCATAATAT 58.750 40.000 0.00 0.00 0.00 1.28
2058 4879 7.403671 AGCTACTTCCTCCGTCTCATAATATA 58.596 38.462 0.00 0.00 0.00 0.86
2059 4880 7.889073 AGCTACTTCCTCCGTCTCATAATATAA 59.111 37.037 0.00 0.00 0.00 0.98
2060 4881 8.185505 GCTACTTCCTCCGTCTCATAATATAAG 58.814 40.741 0.00 0.00 0.00 1.73
2061 4882 9.451002 CTACTTCCTCCGTCTCATAATATAAGA 57.549 37.037 0.00 0.00 0.00 2.10
2062 4883 8.707796 ACTTCCTCCGTCTCATAATATAAGAA 57.292 34.615 0.00 0.00 0.00 2.52
2063 4884 8.578151 ACTTCCTCCGTCTCATAATATAAGAAC 58.422 37.037 0.00 0.00 0.00 3.01
2064 4885 7.142306 TCCTCCGTCTCATAATATAAGAACG 57.858 40.000 0.00 0.00 0.00 3.95
2065 4886 6.713903 TCCTCCGTCTCATAATATAAGAACGT 59.286 38.462 0.00 0.00 0.00 3.99
2066 4887 7.230108 TCCTCCGTCTCATAATATAAGAACGTT 59.770 37.037 0.00 0.00 0.00 3.99
2067 4888 7.866393 CCTCCGTCTCATAATATAAGAACGTTT 59.134 37.037 0.46 0.00 0.00 3.60
2068 4889 9.245962 CTCCGTCTCATAATATAAGAACGTTTT 57.754 33.333 0.46 0.00 0.00 2.43
2069 4890 9.590451 TCCGTCTCATAATATAAGAACGTTTTT 57.410 29.630 9.22 9.22 0.00 1.94
2083 4904 8.707938 AAGAACGTTTTTAACACTACACTAGT 57.292 30.769 0.46 0.00 40.28 2.57
2084 4905 9.801873 AAGAACGTTTTTAACACTACACTAGTA 57.198 29.630 0.46 0.00 37.23 1.82
2085 4906 9.971922 AGAACGTTTTTAACACTACACTAGTAT 57.028 29.630 0.46 0.00 37.23 2.12
2476 5300 0.837272 ACCAGGATTACCCACCGATG 59.163 55.000 0.00 0.00 37.41 3.84
2806 5632 9.896645 CCATATGCCAAATAGATATGTAGAAGT 57.103 33.333 0.00 0.00 30.95 3.01
3295 6218 6.917533 ACACTCTAATCTTGCATTTTCCTTG 58.082 36.000 0.00 0.00 0.00 3.61
3425 6348 3.503363 TGTTTATGCAGCTCAAGGAACAG 59.497 43.478 0.00 0.00 0.00 3.16
3505 6428 2.035449 TGGAATGGTAGAAGTATCCGCG 59.965 50.000 0.00 0.00 0.00 6.46
3597 6520 1.519455 GCGGCGATGTAGAAGCAGT 60.519 57.895 12.98 0.00 0.00 4.40
3598 6521 0.248907 GCGGCGATGTAGAAGCAGTA 60.249 55.000 12.98 0.00 0.00 2.74
3629 6553 1.357334 GCGAAGGACTCTAGCTCGG 59.643 63.158 0.00 0.00 0.00 4.63
3670 6594 0.036952 AGATGAGGTTCTGTGCGTGG 60.037 55.000 0.00 0.00 0.00 4.94
3672 6596 0.108585 ATGAGGTTCTGTGCGTGGTT 59.891 50.000 0.00 0.00 0.00 3.67
3861 6785 6.092944 TCGTACAGTTTCAGTTTGACACATTT 59.907 34.615 0.00 0.00 29.91 2.32
3889 6839 5.880332 TGTTGGTTCATAGCCAGAAATACTC 59.120 40.000 0.00 0.00 37.31 2.59
3890 6840 4.693283 TGGTTCATAGCCAGAAATACTCG 58.307 43.478 0.00 0.00 0.00 4.18
3933 6884 6.593268 TGTGATGATCAATTTGTTCACCAT 57.407 33.333 17.82 0.00 34.11 3.55
3946 6897 3.081061 GTTCACCATACTTGTGATGGCA 58.919 45.455 1.52 0.00 46.76 4.92
3947 6898 3.650281 TCACCATACTTGTGATGGCAT 57.350 42.857 0.00 0.00 46.76 4.40
3971 6922 2.437413 CCCCAACTTACTGAGGAAAGC 58.563 52.381 0.00 0.00 0.00 3.51
4046 7015 5.157770 TGTGGATAGAATCTACTTCCCCT 57.842 43.478 7.30 0.00 40.90 4.79
4053 7022 1.880941 ATCTACTTCCCCTGTCCCAC 58.119 55.000 0.00 0.00 0.00 4.61
4069 7038 6.202954 CCTGTCCCACAATATAAGATCGTTTC 59.797 42.308 0.00 0.00 0.00 2.78
4075 7044 7.495934 CCCACAATATAAGATCGTTTCTCAAGT 59.504 37.037 0.00 0.00 31.78 3.16
4076 7045 8.543774 CCACAATATAAGATCGTTTCTCAAGTC 58.456 37.037 0.00 0.00 31.78 3.01
4081 7050 7.763172 ATAAGATCGTTTCTCAAGTCATCAC 57.237 36.000 0.00 0.00 31.78 3.06
4083 7052 5.541845 AGATCGTTTCTCAAGTCATCACAA 58.458 37.500 0.00 0.00 0.00 3.33
4084 7053 5.636965 AGATCGTTTCTCAAGTCATCACAAG 59.363 40.000 0.00 0.00 0.00 3.16
4086 7055 4.507756 TCGTTTCTCAAGTCATCACAAGTG 59.492 41.667 0.00 0.00 0.00 3.16
4087 7056 4.271049 CGTTTCTCAAGTCATCACAAGTGT 59.729 41.667 0.00 0.00 0.00 3.55
4088 7057 5.505286 GTTTCTCAAGTCATCACAAGTGTG 58.495 41.667 5.02 5.02 46.91 3.82
4089 7058 3.732212 TCTCAAGTCATCACAAGTGTGG 58.268 45.455 11.38 0.00 45.65 4.17
4090 7059 2.221169 TCAAGTCATCACAAGTGTGGC 58.779 47.619 11.38 3.70 45.65 5.01
4091 7060 1.948834 CAAGTCATCACAAGTGTGGCA 59.051 47.619 11.38 0.00 45.65 4.92
4092 7061 2.555325 CAAGTCATCACAAGTGTGGCAT 59.445 45.455 11.38 0.00 45.65 4.40
4093 7062 2.156917 AGTCATCACAAGTGTGGCATG 58.843 47.619 11.38 8.76 45.65 4.06
4094 7063 2.153645 GTCATCACAAGTGTGGCATGA 58.846 47.619 11.38 10.75 45.65 3.07
4095 7064 2.751259 GTCATCACAAGTGTGGCATGAT 59.249 45.455 15.07 0.00 45.65 2.45
4096 7065 3.192001 GTCATCACAAGTGTGGCATGATT 59.808 43.478 15.07 0.00 45.65 2.57
4097 7066 3.827876 TCATCACAAGTGTGGCATGATTT 59.172 39.130 11.38 0.00 45.65 2.17
4098 7067 3.646611 TCACAAGTGTGGCATGATTTG 57.353 42.857 11.38 0.00 45.65 2.32
4099 7068 3.220940 TCACAAGTGTGGCATGATTTGA 58.779 40.909 11.38 0.00 45.65 2.69
4100 7069 3.004629 TCACAAGTGTGGCATGATTTGAC 59.995 43.478 11.38 0.00 45.65 3.18
4101 7070 2.957680 ACAAGTGTGGCATGATTTGACA 59.042 40.909 0.00 0.00 42.71 3.58
4109 7078 5.981088 TGGCATGATTTGACACAAGTATT 57.019 34.783 0.00 0.00 38.92 1.89
4110 7079 6.343716 TGGCATGATTTGACACAAGTATTT 57.656 33.333 0.00 0.00 38.92 1.40
4111 7080 6.389091 TGGCATGATTTGACACAAGTATTTC 58.611 36.000 0.00 0.00 38.92 2.17
4112 7081 6.015603 TGGCATGATTTGACACAAGTATTTCA 60.016 34.615 0.00 0.00 38.92 2.69
4113 7082 6.308766 GGCATGATTTGACACAAGTATTTCAC 59.691 38.462 0.00 0.00 31.51 3.18
4114 7083 6.862608 GCATGATTTGACACAAGTATTTCACA 59.137 34.615 0.00 0.00 0.00 3.58
4115 7084 7.148918 GCATGATTTGACACAAGTATTTCACAC 60.149 37.037 0.00 0.00 0.00 3.82
4116 7085 7.566760 TGATTTGACACAAGTATTTCACACT 57.433 32.000 0.00 0.00 0.00 3.55
4117 7086 7.995289 TGATTTGACACAAGTATTTCACACTT 58.005 30.769 0.00 0.00 36.68 3.16
4123 7092 4.566545 CAAGTATTTCACACTTGTGGCA 57.433 40.909 9.46 0.00 45.06 4.92
4124 7093 4.930963 CAAGTATTTCACACTTGTGGCAA 58.069 39.130 9.46 3.86 45.06 4.52
4125 7094 5.347342 CAAGTATTTCACACTTGTGGCAAA 58.653 37.500 9.46 4.41 45.06 3.68
4126 7095 5.186996 AGTATTTCACACTTGTGGCAAAG 57.813 39.130 9.46 0.00 45.65 2.77
4127 7096 2.292103 TTTCACACTTGTGGCAAAGC 57.708 45.000 9.46 0.00 45.65 3.51
4128 7097 1.473258 TTCACACTTGTGGCAAAGCT 58.527 45.000 9.46 0.00 45.65 3.74
4129 7098 1.473258 TCACACTTGTGGCAAAGCTT 58.527 45.000 9.46 0.00 45.65 3.74
4130 7099 1.134753 TCACACTTGTGGCAAAGCTTG 59.865 47.619 9.46 0.00 45.65 4.01
4131 7100 0.461135 ACACTTGTGGCAAAGCTTGG 59.539 50.000 0.00 0.00 0.00 3.61
4140 7109 1.986698 GCAAAGCTTGGCATGTGTAG 58.013 50.000 21.31 0.00 0.00 2.74
4141 7110 1.986698 CAAAGCTTGGCATGTGTAGC 58.013 50.000 0.00 0.00 0.00 3.58
4180 7149 3.732048 TTTTGGGATGGAGGGAGTAAC 57.268 47.619 0.00 0.00 0.00 2.50
4184 7153 0.470341 GGATGGAGGGAGTAACTGCC 59.530 60.000 0.00 0.00 42.52 4.85
4187 7156 1.440618 TGGAGGGAGTAACTGCCAAA 58.559 50.000 0.00 0.00 44.71 3.28
4189 7158 1.613520 GGAGGGAGTAACTGCCAAACC 60.614 57.143 0.00 0.00 44.71 3.27
4190 7159 0.036306 AGGGAGTAACTGCCAAACCG 59.964 55.000 0.00 0.00 44.71 4.44
4191 7160 0.250597 GGGAGTAACTGCCAAACCGT 60.251 55.000 0.00 0.00 41.77 4.83
4192 7161 1.002315 GGGAGTAACTGCCAAACCGTA 59.998 52.381 0.00 0.00 41.77 4.02
4193 7162 2.344025 GGAGTAACTGCCAAACCGTAG 58.656 52.381 0.00 0.00 0.00 3.51
4210 7179 6.045072 ACCGTAGTACTCAAAATTCCATGA 57.955 37.500 0.00 0.00 0.00 3.07
4253 7222 7.374228 GCAATATTATTTCTGTGACATGACACG 59.626 37.037 20.55 15.65 42.86 4.49
4254 7223 8.603181 CAATATTATTTCTGTGACATGACACGA 58.397 33.333 20.55 17.31 42.86 4.35
4255 7224 5.839262 TTATTTCTGTGACATGACACGAC 57.161 39.130 20.55 1.16 42.86 4.34
4256 7225 2.880963 TTCTGTGACATGACACGACA 57.119 45.000 20.55 6.68 42.86 4.35
4257 7226 2.880963 TCTGTGACATGACACGACAA 57.119 45.000 20.55 5.12 42.86 3.18
4258 7227 2.742774 TCTGTGACATGACACGACAAG 58.257 47.619 20.55 13.46 42.86 3.16
4259 7228 1.193203 CTGTGACATGACACGACAAGC 59.807 52.381 20.55 0.00 42.86 4.01
4260 7229 1.202521 TGTGACATGACACGACAAGCT 60.203 47.619 20.55 0.00 42.86 3.74
4261 7230 1.867233 GTGACATGACACGACAAGCTT 59.133 47.619 12.38 0.00 0.00 3.74
4262 7231 1.866601 TGACATGACACGACAAGCTTG 59.133 47.619 24.84 24.84 0.00 4.01
4263 7232 0.588252 ACATGACACGACAAGCTTGC 59.412 50.000 26.27 17.09 0.00 4.01
4264 7233 0.870393 CATGACACGACAAGCTTGCT 59.130 50.000 26.27 13.39 0.00 3.91
4265 7234 0.870393 ATGACACGACAAGCTTGCTG 59.130 50.000 26.27 20.01 0.00 4.41
4266 7235 1.082496 GACACGACAAGCTTGCTGC 60.082 57.895 26.27 14.49 43.29 5.25
4287 7256 3.744426 GCGACTGGACTTTAAGCTGTAAA 59.256 43.478 0.00 0.00 0.00 2.01
4333 7303 2.896685 GGGGAACAATGTTTGGATCACA 59.103 45.455 0.00 0.00 34.12 3.58
4391 7361 6.127758 CCAGTTATCCATTCCATTTGAAACGA 60.128 38.462 0.00 0.00 36.33 3.85
4402 7372 5.064962 TCCATTTGAAACGACTACAAAACGT 59.935 36.000 0.00 0.00 41.97 3.99
4405 7375 3.260740 TGAAACGACTACAAAACGTGGT 58.739 40.909 0.00 0.00 42.93 4.16
4427 7397 1.882623 GGCTTTGTGAGAAGGGTTGAG 59.117 52.381 0.00 0.00 0.00 3.02
4431 7401 1.801242 TGTGAGAAGGGTTGAGGTCA 58.199 50.000 0.00 0.00 0.00 4.02
4461 7431 6.628856 CCTCGCAAATAAAATGAGATGTTACG 59.371 38.462 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.783031 GCTTCTCCCATGCAGCATCG 61.783 60.000 4.38 0.00 32.17 3.84
13 14 0.750546 TGCTTCTCCCATGCAGCATC 60.751 55.000 4.38 0.00 37.35 3.91
18 19 1.202915 TCTTGTTGCTTCTCCCATGCA 60.203 47.619 0.00 0.00 33.41 3.96
19 20 1.538047 TCTTGTTGCTTCTCCCATGC 58.462 50.000 0.00 0.00 0.00 4.06
58 59 7.289310 TGAATTTGGATGACTATGCCTAATCA 58.711 34.615 0.00 0.00 0.00 2.57
67 68 6.488006 CGATTCCCTTGAATTTGGATGACTAT 59.512 38.462 0.00 0.00 41.30 2.12
79 80 5.102953 TGAAGATGTCGATTCCCTTGAAT 57.897 39.130 0.00 0.00 43.91 2.57
106 107 1.807142 TGAGAGCGCCGAGATATACAG 59.193 52.381 2.29 0.00 0.00 2.74
119 120 1.227205 GATGCTGGAGGTGAGAGCG 60.227 63.158 0.00 0.00 35.36 5.03
127 128 0.617413 AGTGGTGAAGATGCTGGAGG 59.383 55.000 0.00 0.00 0.00 4.30
154 155 6.128254 GGTTGCTAGAAAAAGCGATAAGTCTT 60.128 38.462 0.00 0.00 45.85 3.01
163 164 2.030805 AGCTTGGTTGCTAGAAAAAGCG 60.031 45.455 12.34 0.00 45.85 4.68
186 188 3.442273 TGTTGAACCTGGAAAATATCGGC 59.558 43.478 0.00 0.00 0.00 5.54
223 225 2.584835 AGCCAACACCAAGCAATCTA 57.415 45.000 0.00 0.00 0.00 1.98
224 226 1.708341 AAGCCAACACCAAGCAATCT 58.292 45.000 0.00 0.00 0.00 2.40
244 246 0.934496 CTTGAAACACCGTTCTCGCA 59.066 50.000 0.00 0.00 35.54 5.10
250 262 2.158957 TCTGAGAGCTTGAAACACCGTT 60.159 45.455 0.00 0.00 0.00 4.44
267 279 4.262207 GCGATCTATTCTCCCAATGTCTGA 60.262 45.833 0.00 0.00 0.00 3.27
268 280 3.993081 GCGATCTATTCTCCCAATGTCTG 59.007 47.826 0.00 0.00 0.00 3.51
277 289 3.141398 TGCCAATTGCGATCTATTCTCC 58.859 45.455 0.00 0.00 45.60 3.71
283 295 4.637977 TGTATTGTTGCCAATTGCGATCTA 59.362 37.500 0.00 0.00 45.60 1.98
293 305 4.321899 GGAAGAAGCATGTATTGTTGCCAA 60.322 41.667 0.00 0.00 39.72 4.52
338 350 1.732259 AGCTTTGACATTTCTACGCCG 59.268 47.619 0.00 0.00 0.00 6.46
340 352 4.093408 TGATGAGCTTTGACATTTCTACGC 59.907 41.667 0.00 0.00 0.00 4.42
342 354 5.412594 TGGTGATGAGCTTTGACATTTCTAC 59.587 40.000 0.00 0.00 0.00 2.59
350 362 2.157738 AGCTTGGTGATGAGCTTTGAC 58.842 47.619 0.00 0.00 46.55 3.18
372 384 7.705325 ACGTAGATTGTATTCTCAACGCTAAAT 59.295 33.333 0.00 0.00 33.19 1.40
379 391 9.517609 AAGACATACGTAGATTGTATTCTCAAC 57.482 33.333 0.08 0.00 30.28 3.18
397 409 7.778470 AAGCACTGAATAGCTAAAGACATAC 57.222 36.000 0.00 0.00 40.90 2.39
398 410 9.534565 CTTAAGCACTGAATAGCTAAAGACATA 57.465 33.333 0.00 0.00 40.90 2.29
399 411 8.043710 ACTTAAGCACTGAATAGCTAAAGACAT 58.956 33.333 1.29 0.00 40.90 3.06
400 412 7.386851 ACTTAAGCACTGAATAGCTAAAGACA 58.613 34.615 1.29 0.00 40.90 3.41
401 413 7.835634 ACTTAAGCACTGAATAGCTAAAGAC 57.164 36.000 1.29 0.00 40.90 3.01
467 3216 1.706443 GTGAAAGGCATCAAGCTTGC 58.294 50.000 21.99 11.14 44.79 4.01
479 3247 2.279582 ACATAGACGAGCGTGAAAGG 57.720 50.000 0.00 0.00 0.00 3.11
480 3248 5.756950 TTTTACATAGACGAGCGTGAAAG 57.243 39.130 0.00 0.00 0.00 2.62
481 3249 5.445407 GCATTTTACATAGACGAGCGTGAAA 60.445 40.000 0.00 0.00 0.00 2.69
482 3250 4.032445 GCATTTTACATAGACGAGCGTGAA 59.968 41.667 0.00 0.00 0.00 3.18
483 3251 3.550275 GCATTTTACATAGACGAGCGTGA 59.450 43.478 0.00 0.00 0.00 4.35
484 3252 3.551890 AGCATTTTACATAGACGAGCGTG 59.448 43.478 0.00 0.00 0.00 5.34
485 3253 3.782046 AGCATTTTACATAGACGAGCGT 58.218 40.909 0.00 0.00 0.00 5.07
486 3254 3.182572 GGAGCATTTTACATAGACGAGCG 59.817 47.826 0.00 0.00 0.00 5.03
487 3255 4.372656 AGGAGCATTTTACATAGACGAGC 58.627 43.478 0.00 0.00 0.00 5.03
488 3256 7.867909 TCAATAGGAGCATTTTACATAGACGAG 59.132 37.037 0.00 0.00 0.00 4.18
489 3257 7.722363 TCAATAGGAGCATTTTACATAGACGA 58.278 34.615 0.00 0.00 0.00 4.20
490 3258 7.946655 TCAATAGGAGCATTTTACATAGACG 57.053 36.000 0.00 0.00 0.00 4.18
636 3409 5.351233 TTGTCACTAATTAAACACAGCCG 57.649 39.130 0.00 0.00 0.00 5.52
637 3410 7.422399 TCTTTTGTCACTAATTAAACACAGCC 58.578 34.615 0.00 0.00 0.00 4.85
638 3411 7.591426 CCTCTTTTGTCACTAATTAAACACAGC 59.409 37.037 0.00 0.00 0.00 4.40
639 3412 8.836413 TCCTCTTTTGTCACTAATTAAACACAG 58.164 33.333 0.00 0.00 0.00 3.66
712 3487 2.745884 TGCGCACCATACCACAGC 60.746 61.111 5.66 0.00 0.00 4.40
796 3591 2.267324 GGAGGGCTCTCTGTGTGC 59.733 66.667 14.63 0.00 39.86 4.57
801 3596 3.080121 AAGCGGGAGGGCTCTCTG 61.080 66.667 14.63 7.81 43.93 3.35
802 3597 2.762043 GAAGCGGGAGGGCTCTCT 60.762 66.667 14.63 0.00 43.93 3.10
803 3598 3.855853 GGAAGCGGGAGGGCTCTC 61.856 72.222 4.50 4.50 43.93 3.20
804 3599 4.722535 TGGAAGCGGGAGGGCTCT 62.723 66.667 0.00 0.00 43.93 4.09
805 3600 3.468326 GATGGAAGCGGGAGGGCTC 62.468 68.421 0.00 0.00 43.93 4.70
807 3602 4.918201 CGATGGAAGCGGGAGGGC 62.918 72.222 0.00 0.00 45.34 5.19
860 3660 1.004862 GGTGGAAAGGGAAAGAGGGAG 59.995 57.143 0.00 0.00 0.00 4.30
861 3661 1.073098 GGTGGAAAGGGAAAGAGGGA 58.927 55.000 0.00 0.00 0.00 4.20
862 3662 1.004862 GAGGTGGAAAGGGAAAGAGGG 59.995 57.143 0.00 0.00 0.00 4.30
1594 4403 0.394216 TGCATCAAGATTGTCCCCGG 60.394 55.000 0.00 0.00 0.00 5.73
1596 4405 3.067742 CAGAATGCATCAAGATTGTCCCC 59.932 47.826 0.00 0.00 0.00 4.81
1616 4427 0.738389 ACAAAGGTCAAACCGTGCAG 59.262 50.000 0.00 0.00 44.90 4.41
1648 4459 4.213270 TGAAAGCGTCAAATTTCACTCGAT 59.787 37.500 0.00 0.00 39.76 3.59
1683 4494 2.579207 TCTGCGATGTAAGCCTACAC 57.421 50.000 0.00 0.00 40.84 2.90
2038 4859 7.751348 CGTTCTTATATTATGAGACGGAGGAAG 59.249 40.741 0.00 0.00 0.00 3.46
2041 4862 6.910995 ACGTTCTTATATTATGAGACGGAGG 58.089 40.000 16.71 6.29 0.00 4.30
2042 4863 8.798748 AAACGTTCTTATATTATGAGACGGAG 57.201 34.615 0.00 6.40 0.00 4.63
2057 4878 9.801873 ACTAGTGTAGTGTTAAAAACGTTCTTA 57.198 29.630 0.00 0.00 37.69 2.10
2058 4879 8.707938 ACTAGTGTAGTGTTAAAAACGTTCTT 57.292 30.769 0.00 0.00 37.69 2.52
2059 4880 9.971922 ATACTAGTGTAGTGTTAAAAACGTTCT 57.028 29.630 5.39 0.00 39.81 3.01
2086 4907 9.044150 CCGTCCCGTAATATAAGATTGTTTTTA 57.956 33.333 0.00 0.00 0.00 1.52
2087 4908 7.769970 TCCGTCCCGTAATATAAGATTGTTTTT 59.230 33.333 0.00 0.00 0.00 1.94
2088 4909 7.274447 TCCGTCCCGTAATATAAGATTGTTTT 58.726 34.615 0.00 0.00 0.00 2.43
2089 4910 6.819284 TCCGTCCCGTAATATAAGATTGTTT 58.181 36.000 0.00 0.00 0.00 2.83
2090 4911 6.409524 TCCGTCCCGTAATATAAGATTGTT 57.590 37.500 0.00 0.00 0.00 2.83
2091 4912 5.047519 CCTCCGTCCCGTAATATAAGATTGT 60.048 44.000 0.00 0.00 0.00 2.71
2092 4913 5.408356 CCTCCGTCCCGTAATATAAGATTG 58.592 45.833 0.00 0.00 0.00 2.67
2093 4914 4.465305 CCCTCCGTCCCGTAATATAAGATT 59.535 45.833 0.00 0.00 0.00 2.40
2094 4915 4.021916 CCCTCCGTCCCGTAATATAAGAT 58.978 47.826 0.00 0.00 0.00 2.40
2095 4916 3.074390 TCCCTCCGTCCCGTAATATAAGA 59.926 47.826 0.00 0.00 0.00 2.10
2096 4917 3.424703 TCCCTCCGTCCCGTAATATAAG 58.575 50.000 0.00 0.00 0.00 1.73
2097 4918 3.181429 ACTCCCTCCGTCCCGTAATATAA 60.181 47.826 0.00 0.00 0.00 0.98
2098 4919 2.376518 ACTCCCTCCGTCCCGTAATATA 59.623 50.000 0.00 0.00 0.00 0.86
2099 4920 1.146566 ACTCCCTCCGTCCCGTAATAT 59.853 52.381 0.00 0.00 0.00 1.28
2100 4921 0.552848 ACTCCCTCCGTCCCGTAATA 59.447 55.000 0.00 0.00 0.00 0.98
2101 4922 0.552848 TACTCCCTCCGTCCCGTAAT 59.447 55.000 0.00 0.00 0.00 1.89
2102 4923 0.552848 ATACTCCCTCCGTCCCGTAA 59.447 55.000 0.00 0.00 0.00 3.18
2103 4924 0.552848 AATACTCCCTCCGTCCCGTA 59.447 55.000 0.00 0.00 0.00 4.02
2104 4925 0.325016 AAATACTCCCTCCGTCCCGT 60.325 55.000 0.00 0.00 0.00 5.28
2105 4926 0.828677 AAAATACTCCCTCCGTCCCG 59.171 55.000 0.00 0.00 0.00 5.14
2106 4927 5.720520 AGATATAAAATACTCCCTCCGTCCC 59.279 44.000 0.00 0.00 0.00 4.46
2107 4928 6.854091 AGATATAAAATACTCCCTCCGTCC 57.146 41.667 0.00 0.00 0.00 4.79
2476 5300 4.631813 CAGGAAGATACTTTGGCACACTAC 59.368 45.833 0.00 0.00 39.29 2.73
2744 5569 6.727824 AGTGAGTAATGAAATCCACGAAAG 57.272 37.500 0.00 0.00 0.00 2.62
3148 6059 1.959985 TGCGAATGAAACAACCCACAT 59.040 42.857 0.00 0.00 0.00 3.21
3176 6087 8.712228 AATCCTATGGAAAAATCCTATGGTTC 57.288 34.615 0.00 0.00 34.34 3.62
3295 6218 2.760650 CAGGATTTCCAAAACTAGGGGC 59.239 50.000 0.00 0.00 38.89 5.80
3425 6348 1.659098 CTTACGACGACTTGGAATGCC 59.341 52.381 0.00 0.00 0.00 4.40
3505 6428 7.093992 ACTGTAAGAGAATAACAACAGAGCTC 58.906 38.462 5.27 5.27 38.14 4.09
3597 6520 4.282703 AGTCCTTCGCCTAACAAGTCTTTA 59.717 41.667 0.00 0.00 0.00 1.85
3598 6521 3.071167 AGTCCTTCGCCTAACAAGTCTTT 59.929 43.478 0.00 0.00 0.00 2.52
3654 6578 0.813610 CAACCACGCACAGAACCTCA 60.814 55.000 0.00 0.00 0.00 3.86
3670 6594 0.958822 AATGGCGTGACCTTTCCAAC 59.041 50.000 0.00 0.00 40.22 3.77
3672 6596 2.941210 GAATGGCGTGACCTTTCCA 58.059 52.632 0.00 0.00 43.61 3.53
3861 6785 0.250510 TGGCTATGAACCAACACGCA 60.251 50.000 0.00 0.00 33.12 5.24
3946 6897 3.393687 TCCTCAGTAAGTTGGGGCATAT 58.606 45.455 0.00 0.00 38.67 1.78
3947 6898 2.840511 TCCTCAGTAAGTTGGGGCATA 58.159 47.619 0.00 0.00 38.67 3.14
3971 6922 4.822036 TTTAGGTCATGTTTTCACCACG 57.178 40.909 3.58 0.00 0.00 4.94
3997 6965 8.800370 TTAATGGTCTCAAAATATGCACACTA 57.200 30.769 0.00 0.00 0.00 2.74
4041 7009 4.015617 TCTTATATTGTGGGACAGGGGA 57.984 45.455 0.00 0.00 41.80 4.81
4046 7015 6.884832 AGAAACGATCTTATATTGTGGGACA 58.115 36.000 0.00 0.00 33.39 4.02
4079 7048 3.243468 TGTCAAATCATGCCACACTTGTG 60.243 43.478 2.13 2.13 45.23 3.33
4080 7049 2.957680 TGTCAAATCATGCCACACTTGT 59.042 40.909 0.00 0.00 0.00 3.16
4081 7050 3.243468 TGTGTCAAATCATGCCACACTTG 60.243 43.478 11.30 0.00 42.57 3.16
4083 7052 2.585330 TGTGTCAAATCATGCCACACT 58.415 42.857 11.30 0.00 42.57 3.55
4084 7053 3.243501 ACTTGTGTCAAATCATGCCACAC 60.244 43.478 0.00 0.00 46.69 3.82
4086 7055 3.648339 ACTTGTGTCAAATCATGCCAC 57.352 42.857 0.00 0.00 38.38 5.01
4087 7056 5.981088 AATACTTGTGTCAAATCATGCCA 57.019 34.783 0.00 0.00 0.00 4.92
4088 7057 6.308766 GTGAAATACTTGTGTCAAATCATGCC 59.691 38.462 0.00 0.00 0.00 4.40
4089 7058 6.862608 TGTGAAATACTTGTGTCAAATCATGC 59.137 34.615 0.00 0.00 0.00 4.06
4090 7059 8.077991 AGTGTGAAATACTTGTGTCAAATCATG 58.922 33.333 0.00 0.00 32.90 3.07
4091 7060 8.169977 AGTGTGAAATACTTGTGTCAAATCAT 57.830 30.769 0.00 0.00 32.90 2.45
4092 7061 7.566760 AGTGTGAAATACTTGTGTCAAATCA 57.433 32.000 0.00 0.00 32.90 2.57
4111 7080 1.563111 CAAGCTTTGCCACAAGTGTG 58.437 50.000 0.00 4.38 45.23 3.82
4112 7081 0.461135 CCAAGCTTTGCCACAAGTGT 59.539 50.000 0.00 0.00 0.00 3.55
4113 7082 0.877213 GCCAAGCTTTGCCACAAGTG 60.877 55.000 11.38 0.00 0.00 3.16
4114 7083 1.329171 TGCCAAGCTTTGCCACAAGT 61.329 50.000 18.94 0.00 0.00 3.16
4115 7084 0.034337 ATGCCAAGCTTTGCCACAAG 59.966 50.000 18.94 0.00 0.00 3.16
4116 7085 0.249953 CATGCCAAGCTTTGCCACAA 60.250 50.000 18.94 1.51 0.00 3.33
4117 7086 1.368209 CATGCCAAGCTTTGCCACA 59.632 52.632 18.94 1.87 0.00 4.17
4118 7087 0.947180 CACATGCCAAGCTTTGCCAC 60.947 55.000 18.94 0.00 0.00 5.01
4119 7088 1.368209 CACATGCCAAGCTTTGCCA 59.632 52.632 18.94 8.32 0.00 4.92
4120 7089 0.602562 TACACATGCCAAGCTTTGCC 59.397 50.000 18.94 2.96 0.00 4.52
4121 7090 1.986698 CTACACATGCCAAGCTTTGC 58.013 50.000 15.33 15.33 0.00 3.68
4122 7091 1.542915 AGCTACACATGCCAAGCTTTG 59.457 47.619 9.75 0.00 42.52 2.77
4123 7092 1.915141 AGCTACACATGCCAAGCTTT 58.085 45.000 9.75 0.00 42.52 3.51
4124 7093 3.658398 AGCTACACATGCCAAGCTT 57.342 47.368 9.75 0.00 42.52 3.74
4125 7094 1.171308 CAAGCTACACATGCCAAGCT 58.829 50.000 9.75 9.75 46.96 3.74
4126 7095 1.167851 TCAAGCTACACATGCCAAGC 58.832 50.000 5.81 5.81 35.16 4.01
4127 7096 3.921119 TTTCAAGCTACACATGCCAAG 57.079 42.857 0.00 0.00 0.00 3.61
4128 7097 4.367450 GTTTTTCAAGCTACACATGCCAA 58.633 39.130 0.00 0.00 0.00 4.52
4129 7098 3.549827 CGTTTTTCAAGCTACACATGCCA 60.550 43.478 0.00 0.00 0.00 4.92
4130 7099 2.979813 CGTTTTTCAAGCTACACATGCC 59.020 45.455 0.00 0.00 0.00 4.40
4131 7100 3.884169 TCGTTTTTCAAGCTACACATGC 58.116 40.909 0.00 0.00 0.00 4.06
4132 7101 5.931532 AGATCGTTTTTCAAGCTACACATG 58.068 37.500 0.00 0.00 0.00 3.21
4133 7102 6.560253 AAGATCGTTTTTCAAGCTACACAT 57.440 33.333 0.00 0.00 0.00 3.21
4134 7103 7.667043 ATAAGATCGTTTTTCAAGCTACACA 57.333 32.000 0.00 0.00 0.00 3.72
4139 7108 9.573133 CCAAAATATAAGATCGTTTTTCAAGCT 57.427 29.630 0.00 0.00 0.00 3.74
4140 7109 8.807581 CCCAAAATATAAGATCGTTTTTCAAGC 58.192 33.333 0.00 0.00 0.00 4.01
4163 7132 1.879575 CAGTTACTCCCTCCATCCCA 58.120 55.000 0.00 0.00 0.00 4.37
4168 7137 1.073284 GTTTGGCAGTTACTCCCTCCA 59.927 52.381 0.00 0.00 0.00 3.86
4169 7138 1.613520 GGTTTGGCAGTTACTCCCTCC 60.614 57.143 0.00 0.00 0.00 4.30
4180 7149 2.736144 TGAGTACTACGGTTTGGCAG 57.264 50.000 0.00 0.00 0.00 4.85
4184 7153 6.548441 TGGAATTTTGAGTACTACGGTTTG 57.452 37.500 0.00 0.00 0.00 2.93
4187 7156 6.045072 TCATGGAATTTTGAGTACTACGGT 57.955 37.500 0.00 0.00 0.00 4.83
4189 7158 7.957484 CACTTTCATGGAATTTTGAGTACTACG 59.043 37.037 0.00 0.00 0.00 3.51
4190 7159 8.999431 TCACTTTCATGGAATTTTGAGTACTAC 58.001 33.333 0.00 0.00 0.00 2.73
4191 7160 9.739276 ATCACTTTCATGGAATTTTGAGTACTA 57.261 29.630 0.00 0.00 0.00 1.82
4192 7161 8.641498 ATCACTTTCATGGAATTTTGAGTACT 57.359 30.769 0.00 0.00 0.00 2.73
4193 7162 9.346725 GAATCACTTTCATGGAATTTTGAGTAC 57.653 33.333 0.00 0.00 34.27 2.73
4210 7179 3.988379 TTGCGCTTTCTGAATCACTTT 57.012 38.095 9.73 0.00 0.00 2.66
4253 7222 1.206072 CAGTCGCAGCAAGCTTGTC 59.794 57.895 26.55 18.45 42.61 3.18
4254 7223 2.256591 CCAGTCGCAGCAAGCTTGT 61.257 57.895 26.55 11.54 42.61 3.16
4255 7224 1.962822 TCCAGTCGCAGCAAGCTTG 60.963 57.895 22.44 22.44 42.61 4.01
4256 7225 1.963338 GTCCAGTCGCAGCAAGCTT 60.963 57.895 0.00 0.00 42.61 3.74
4257 7226 2.358003 GTCCAGTCGCAGCAAGCT 60.358 61.111 0.00 0.00 42.61 3.74
4258 7227 1.510480 AAAGTCCAGTCGCAGCAAGC 61.510 55.000 0.00 0.00 40.87 4.01
4259 7228 1.795768 TAAAGTCCAGTCGCAGCAAG 58.204 50.000 0.00 0.00 0.00 4.01
4260 7229 2.143122 CTTAAAGTCCAGTCGCAGCAA 58.857 47.619 0.00 0.00 0.00 3.91
4261 7230 1.795768 CTTAAAGTCCAGTCGCAGCA 58.204 50.000 0.00 0.00 0.00 4.41
4262 7231 0.444260 GCTTAAAGTCCAGTCGCAGC 59.556 55.000 0.00 0.00 0.00 5.25
4263 7232 1.728971 CAGCTTAAAGTCCAGTCGCAG 59.271 52.381 0.00 0.00 0.00 5.18
4264 7233 1.070134 ACAGCTTAAAGTCCAGTCGCA 59.930 47.619 0.00 0.00 0.00 5.10
4265 7234 1.797025 ACAGCTTAAAGTCCAGTCGC 58.203 50.000 0.00 0.00 0.00 5.19
4266 7235 4.748102 TGTTTACAGCTTAAAGTCCAGTCG 59.252 41.667 0.00 0.00 0.00 4.18
4267 7236 6.260271 AGTTGTTTACAGCTTAAAGTCCAGTC 59.740 38.462 0.00 0.00 33.50 3.51
4268 7237 6.120220 AGTTGTTTACAGCTTAAAGTCCAGT 58.880 36.000 0.00 0.00 33.50 4.00
4269 7238 6.619801 AGTTGTTTACAGCTTAAAGTCCAG 57.380 37.500 0.00 0.00 33.50 3.86
4270 7239 7.399245 AAAGTTGTTTACAGCTTAAAGTCCA 57.601 32.000 11.55 0.00 44.75 4.02
4287 7256 9.541143 CCTTTGTTTTGTGGAATATAAAGTTGT 57.459 29.630 0.00 0.00 0.00 3.32
4361 7331 1.557371 TGGAATGGATAACTGGTGCGA 59.443 47.619 0.00 0.00 0.00 5.10
4391 7361 2.047002 AGCCAACCACGTTTTGTAGT 57.953 45.000 6.04 0.00 0.00 2.73
4402 7372 1.691196 CCTTCTCACAAAGCCAACCA 58.309 50.000 0.00 0.00 0.00 3.67
4405 7375 2.031120 CAACCCTTCTCACAAAGCCAA 58.969 47.619 0.00 0.00 0.00 4.52
4427 7397 0.178068 TATTTGCGAGGGAGCTGACC 59.822 55.000 0.00 0.00 38.13 4.02
4431 7401 3.620488 TCATTTTATTTGCGAGGGAGCT 58.380 40.909 0.00 0.00 38.13 4.09
4461 7431 7.308782 ACTGATTTGATGGAACGTTTCTATC 57.691 36.000 8.32 11.52 44.93 2.08


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.