Multiple sequence alignment - TraesCS1B01G382000

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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 TraesCS1B01G382000 chr1B 100.000 3452 0 0 3083 6534 614453404 614456855 0.000000e+00 6375.0
1 TraesCS1B01G382000 chr1B 100.000 1926 0 0 993 2918 614451314 614453239 0.000000e+00 3557.0
2 TraesCS1B01G382000 chr1B 100.000 685 0 0 1 685 614450322 614451006 0.000000e+00 1266.0
3 TraesCS1B01G382000 chr1B 92.593 54 3 1 5815 5867 614456082 614456135 7.030000e-10 76.8
4 TraesCS1B01G382000 chr1B 92.593 54 3 1 5761 5814 614456136 614456188 7.030000e-10 76.8
5 TraesCS1B01G382000 chr1D 95.061 2956 114 13 3108 6047 448653767 448656706 0.000000e+00 4621.0
6 TraesCS1B01G382000 chr1D 92.980 1225 57 9 1696 2918 448652203 448653400 0.000000e+00 1759.0
7 TraesCS1B01G382000 chr1D 94.190 568 20 7 993 1548 448651637 448652203 0.000000e+00 854.0
8 TraesCS1B01G382000 chr1D 90.449 356 17 9 332 685 448651169 448651509 2.780000e-123 453.0
9 TraesCS1B01G382000 chr1D 94.792 192 9 1 6072 6262 448656689 448656880 1.380000e-76 298.0
10 TraesCS1B01G382000 chr1D 86.643 277 21 3 6267 6531 448657162 448657434 6.410000e-75 292.0
11 TraesCS1B01G382000 chr1D 87.170 265 13 7 96 342 448649558 448649819 1.390000e-71 281.0
12 TraesCS1B01G382000 chr1D 79.083 349 31 23 28 343 448647607 448647946 1.110000e-47 202.0
13 TraesCS1B01G382000 chr1D 96.226 53 2 0 5815 5867 448656423 448656475 3.250000e-13 87.9
14 TraesCS1B01G382000 chr1D 96.296 54 1 1 5761 5814 448656476 448656528 3.250000e-13 87.9
15 TraesCS1B01G382000 chr1A 92.328 1929 117 17 993 2899 544371406 544373325 0.000000e+00 2713.0
16 TraesCS1B01G382000 chr1A 95.125 1395 62 4 4655 6047 544375675 544377065 0.000000e+00 2194.0
17 TraesCS1B01G382000 chr1A 93.249 1422 78 9 3108 4524 544373429 544374837 0.000000e+00 2078.0
18 TraesCS1B01G382000 chr1A 84.648 697 45 30 28 685 544370283 544370956 7.150000e-179 638.0
19 TraesCS1B01G382000 chr1A 90.299 268 23 1 4271 4538 19275856 19275592 1.350000e-91 348.0
20 TraesCS1B01G382000 chr1A 92.424 198 13 2 6072 6267 544377048 544377245 1.390000e-71 281.0
21 TraesCS1B01G382000 chr1A 85.401 274 23 9 6267 6524 544377522 544377794 1.080000e-67 268.0
22 TraesCS1B01G382000 chr1A 84.259 216 20 7 6267 6474 590096312 590096521 1.440000e-46 198.0
23 TraesCS1B01G382000 chr1A 95.455 66 3 0 4597 4662 544375589 544375654 8.960000e-19 106.0
24 TraesCS1B01G382000 chr1A 96.296 54 1 1 5761 5814 544376834 544376886 3.250000e-13 87.9
25 TraesCS1B01G382000 chr1A 92.593 54 3 1 5815 5867 544376780 544376833 7.030000e-10 76.8
26 TraesCS1B01G382000 chr3D 92.683 656 43 2 3482 4132 112210829 112210174 0.000000e+00 941.0
27 TraesCS1B01G382000 chr3D 92.256 297 23 0 3479 3775 96784082 96784378 7.830000e-114 422.0
28 TraesCS1B01G382000 chr3D 91.324 219 18 1 4134 4352 112210090 112209873 1.380000e-76 298.0
29 TraesCS1B01G382000 chr7B 92.164 268 18 1 4271 4538 126041004 126040740 6.190000e-100 375.0
30 TraesCS1B01G382000 chr5A 91.418 268 20 1 4271 4538 603032351 603032615 1.340000e-96 364.0
31 TraesCS1B01G382000 chr5A 91.418 268 20 1 4271 4538 677628683 677628419 1.340000e-96 364.0
32 TraesCS1B01G382000 chr4B 91.418 268 20 1 4271 4538 232729863 232730127 1.340000e-96 364.0
33 TraesCS1B01G382000 chr3B 91.418 268 20 1 4271 4538 413315003 413315267 1.340000e-96 364.0
34 TraesCS1B01G382000 chr3B 91.698 265 19 1 4271 4535 725606858 725607119 1.340000e-96 364.0
35 TraesCS1B01G382000 chr2B 96.575 146 5 0 3630 3775 75660219 75660364 6.550000e-60 243.0
36 TraesCS1B01G382000 chr2B 95.205 146 7 0 3630 3775 56588208 56588063 1.420000e-56 231.0
37 TraesCS1B01G382000 chrUn 95.890 146 6 0 3630 3775 199439045 199439190 3.050000e-58 237.0
38 TraesCS1B01G382000 chrUn 95.890 146 6 0 3630 3775 237714460 237714605 3.050000e-58 237.0
39 TraesCS1B01G382000 chrUn 95.890 146 6 0 3630 3775 368390987 368391132 3.050000e-58 237.0


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 TraesCS1B01G382000 chr1B 614450322 614456855 6533 False 2270.320000 6375 97.037200 1 6534 5 chr1B.!!$F1 6533
1 TraesCS1B01G382000 chr1D 448647607 448657434 9827 False 893.580000 4621 91.289000 28 6531 10 chr1D.!!$F1 6503
2 TraesCS1B01G382000 chr1A 544370283 544377794 7511 False 938.077778 2713 91.946556 28 6524 9 chr1A.!!$F2 6496
3 TraesCS1B01G382000 chr3D 112209873 112210829 956 True 619.500000 941 92.003500 3482 4352 2 chr3D.!!$R1 870

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
558 3834 1.009675 GAGGCGCAACACAACACAG 60.010 57.895 10.83 0.0 0.00 3.66 F
1198 4619 0.981943 CGACCTCCCCCAGTTAGTTT 59.018 55.000 0.00 0.0 0.00 2.66 F
1755 5188 0.755686 AGAGCACCAGCCTATACTGC 59.244 55.000 0.00 0.0 43.56 4.40 F
2067 5500 0.096454 GGACGCTTATGCACGGTTTC 59.904 55.000 0.00 0.0 39.64 2.78 F
3359 6975 0.037326 TGTAGCTGGTCTTGGAAGCG 60.037 55.000 0.00 0.0 41.88 4.68 F
3775 7391 2.629617 AGTTGCTTGGTTTATGCTGCTT 59.370 40.909 0.00 0.0 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1737 5169 0.250081 GGCAGTATAGGCTGGTGCTC 60.250 60.000 0.00 0.0 39.59 4.26 R
2052 5485 1.060698 GAGACGAAACCGTGCATAAGC 59.939 52.381 0.00 0.0 40.80 3.09 R
3231 6847 1.095130 TACTGGTTCCCCTCCACCTA 58.905 55.000 0.00 0.0 33.76 3.08 R
4017 7638 1.003580 GATCAACAGAGGGTCCAGCAA 59.996 52.381 0.00 0.0 0.00 3.91 R
5287 9709 0.106708 ATGACCGAACAGCGCCATAT 59.893 50.000 2.29 0.0 39.11 1.78 R
5731 10153 0.314935 ATTTGGCGCAAGGACAACAG 59.685 50.000 10.83 0.0 45.44 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
157 2052 7.496591 AGACTTTTTGACGTGTGGAAATAGTAA 59.503 33.333 0.00 0.00 0.00 2.24
158 2053 7.987649 ACTTTTTGACGTGTGGAAATAGTAAA 58.012 30.769 0.00 0.00 0.00 2.01
159 2054 8.460428 ACTTTTTGACGTGTGGAAATAGTAAAA 58.540 29.630 0.00 0.00 0.00 1.52
160 2055 9.291664 CTTTTTGACGTGTGGAAATAGTAAAAA 57.708 29.630 0.00 0.00 0.00 1.94
202 2097 1.754621 CTCCGTGGAGCTCAGCCTA 60.755 63.158 17.19 0.00 35.31 3.93
203 2098 2.010582 CTCCGTGGAGCTCAGCCTAC 62.011 65.000 17.19 5.26 35.31 3.18
235 2147 7.201644 GCACATTTTTCTCGAGAGAATCCAATA 60.202 37.037 18.08 3.87 45.78 1.90
236 2148 8.333908 CACATTTTTCTCGAGAGAATCCAATAG 58.666 37.037 18.08 10.50 45.78 1.73
302 2214 2.283809 CCAACCCAACCCAACCCA 59.716 61.111 0.00 0.00 0.00 4.51
481 3753 2.042831 ACGCATCAGAAGCCAAGCC 61.043 57.895 0.00 0.00 0.00 4.35
482 3754 2.042259 CGCATCAGAAGCCAAGCCA 61.042 57.895 0.00 0.00 0.00 4.75
483 3755 1.807886 GCATCAGAAGCCAAGCCAG 59.192 57.895 0.00 0.00 0.00 4.85
484 3756 1.807886 CATCAGAAGCCAAGCCAGC 59.192 57.895 0.00 0.00 0.00 4.85
485 3757 1.748122 ATCAGAAGCCAAGCCAGCG 60.748 57.895 0.00 0.00 34.64 5.18
486 3758 2.189191 ATCAGAAGCCAAGCCAGCGA 62.189 55.000 0.00 0.00 34.64 4.93
487 3759 2.359230 AGAAGCCAAGCCAGCGAC 60.359 61.111 0.00 0.00 34.64 5.19
488 3760 3.793144 GAAGCCAAGCCAGCGACG 61.793 66.667 0.00 0.00 34.64 5.12
558 3834 1.009675 GAGGCGCAACACAACACAG 60.010 57.895 10.83 0.00 0.00 3.66
1029 4447 2.110006 GCGCTGATTCCCCTCTCC 59.890 66.667 0.00 0.00 0.00 3.71
1178 4596 2.147150 GCAGGCCGAGATATCCTTTTC 58.853 52.381 0.00 0.00 0.00 2.29
1198 4619 0.981943 CGACCTCCCCCAGTTAGTTT 59.018 55.000 0.00 0.00 0.00 2.66
1208 4629 4.141688 CCCCCAGTTAGTTTCCTCAGTATC 60.142 50.000 0.00 0.00 0.00 2.24
1212 4633 5.187967 CCAGTTAGTTTCCTCAGTATCTGGT 59.812 44.000 0.00 0.00 36.02 4.00
1237 4658 1.239296 TGCTGCTGTGTGGATTGAGC 61.239 55.000 0.00 0.00 0.00 4.26
1420 4842 2.173669 CGGTCTATTGCGTGCCCAG 61.174 63.158 0.00 0.00 0.00 4.45
1421 4843 1.819632 GGTCTATTGCGTGCCCAGG 60.820 63.158 0.00 0.00 0.00 4.45
1423 4845 2.272146 CTATTGCGTGCCCAGGGT 59.728 61.111 7.55 0.00 0.00 4.34
1539 4971 8.032952 TGTCTATGCAGTTTGAGAATTTACTG 57.967 34.615 0.00 0.00 40.65 2.74
1564 4996 5.600696 CAAGTTTGTTTTGTCCTAGCCATT 58.399 37.500 0.00 0.00 0.00 3.16
1628 5060 2.038295 TCGCTTGCCCATTTTGGAAAAT 59.962 40.909 0.00 0.00 40.96 1.82
1647 5079 6.369615 GGAAAATGGATGCCAATATATTGTGC 59.630 38.462 21.20 21.72 36.95 4.57
1682 5114 6.914757 GCTAATCACCAATGCTTTTGTCTATC 59.085 38.462 0.00 0.00 0.00 2.08
1687 5119 4.019174 CCAATGCTTTTGTCTATCTGGGT 58.981 43.478 0.00 0.00 0.00 4.51
1755 5188 0.755686 AGAGCACCAGCCTATACTGC 59.244 55.000 0.00 0.00 43.56 4.40
1763 5196 2.551721 CCAGCCTATACTGCCCTGAATG 60.552 54.545 0.00 0.00 36.29 2.67
1767 5200 3.554934 CCTATACTGCCCTGAATGCAAA 58.445 45.455 0.00 0.00 38.46 3.68
1779 5212 5.192927 CCTGAATGCAAAGGTCCATTACTA 58.807 41.667 0.00 0.00 32.20 1.82
1791 5224 4.593634 GGTCCATTACTAGCTCCTAACCAT 59.406 45.833 0.00 0.00 0.00 3.55
1848 5281 4.554330 GCTAGTGCATCTGCTTTTATGCTC 60.554 45.833 8.57 5.27 46.87 4.26
2007 5440 5.123027 GTGAAGATGCTCAAAAGGTAGGAAG 59.877 44.000 0.00 0.00 0.00 3.46
2017 5450 7.266905 TCAAAAGGTAGGAAGGCTTATACTT 57.733 36.000 17.02 10.14 0.00 2.24
2052 5485 1.473434 GGTTGCTTCCTATCTGGGACG 60.473 57.143 0.00 0.00 34.78 4.79
2061 5494 2.408050 CTATCTGGGACGCTTATGCAC 58.592 52.381 0.00 0.00 39.64 4.57
2067 5500 0.096454 GGACGCTTATGCACGGTTTC 59.904 55.000 0.00 0.00 39.64 2.78
2080 5513 1.068474 CGGTTTCGTCTCGCTGAATT 58.932 50.000 0.00 0.00 0.00 2.17
2088 5521 5.450376 TCGTCTCGCTGAATTGTATTTTC 57.550 39.130 0.00 0.00 0.00 2.29
2188 5621 9.184523 CTATTGTTCCTGTTATTACCAATCCAA 57.815 33.333 0.00 0.00 0.00 3.53
2191 5624 6.317642 TGTTCCTGTTATTACCAATCCAATCG 59.682 38.462 0.00 0.00 0.00 3.34
2203 5636 5.714806 ACCAATCCAATCGTTAACCTTGAAT 59.285 36.000 14.19 0.70 0.00 2.57
2320 5753 7.447374 TTTTTCTATACTGGATGTTGTGGTG 57.553 36.000 0.00 0.00 0.00 4.17
2348 5781 8.523915 ACAGCATTTAATTCCATGATGTCTTA 57.476 30.769 12.61 0.00 44.71 2.10
2375 5808 1.122019 GTCTGTGAGGGTGTGAGGGT 61.122 60.000 0.00 0.00 0.00 4.34
2398 5831 9.125026 GGGTTGTTGATTATCACTCTATCATTT 57.875 33.333 0.00 0.00 0.00 2.32
2507 5940 5.545658 TGCTATCGTTTTTGGATCAAGAC 57.454 39.130 0.00 0.00 0.00 3.01
2512 5945 5.418310 TCGTTTTTGGATCAAGACAACTC 57.582 39.130 0.00 0.00 0.00 3.01
2514 5947 5.007626 TCGTTTTTGGATCAAGACAACTCAG 59.992 40.000 0.00 0.00 0.00 3.35
2647 6085 8.275758 TGTTATTTATGTTAATGGCCTAGGTGA 58.724 33.333 11.31 0.00 0.00 4.02
2706 6144 7.013846 CACTAAATGTTAACCCTCAAAAGTGGA 59.986 37.037 2.48 0.00 0.00 4.02
2709 6147 4.601084 TGTTAACCCTCAAAAGTGGACAA 58.399 39.130 2.48 0.00 0.00 3.18
2728 6167 6.868339 TGGACAAGTATATATGTGAAGCATCG 59.132 38.462 0.00 0.00 38.94 3.84
2779 6218 7.452880 TGATGGACATAAAAAGAAGTCAAGG 57.547 36.000 0.00 0.00 32.79 3.61
2857 6296 7.013369 GGAGTATTCCAGAAATGTGGGATAAAC 59.987 40.741 0.00 0.00 39.42 2.01
2868 6307 4.269183 TGTGGGATAAACTGATCGCAATT 58.731 39.130 4.91 0.00 46.60 2.32
3100 6539 3.553109 GTAGACTTTGGGCCCAGTC 57.447 57.895 28.75 28.75 0.00 3.51
3123 6739 1.199789 TGGCAGCACTTTTTATGAGCG 59.800 47.619 0.00 0.00 0.00 5.03
3157 6773 7.923344 TGGGTCAACTATTTAACAATGTGTTTG 59.077 33.333 0.00 0.00 41.45 2.93
3177 6793 4.553330 TGGGCGAGAAAAGATAGAAAGT 57.447 40.909 0.00 0.00 0.00 2.66
3178 6794 4.906618 TGGGCGAGAAAAGATAGAAAGTT 58.093 39.130 0.00 0.00 0.00 2.66
3359 6975 0.037326 TGTAGCTGGTCTTGGAAGCG 60.037 55.000 0.00 0.00 41.88 4.68
3469 7085 8.740123 TTAGGTTCTGATGTTAAAACTGACAA 57.260 30.769 0.00 0.00 0.00 3.18
3472 7088 7.012421 AGGTTCTGATGTTAAAACTGACAACTC 59.988 37.037 0.00 0.00 0.00 3.01
3473 7089 7.012421 GGTTCTGATGTTAAAACTGACAACTCT 59.988 37.037 0.00 0.00 0.00 3.24
3560 7176 3.929610 GACTTGAATGTGCAGGTCTAGAC 59.070 47.826 14.87 14.87 40.50 2.59
3664 7280 5.581126 TTCAGAACAATGAAGCACACTTT 57.419 34.783 0.00 0.00 35.82 2.66
3692 7308 6.316640 TGTTTCTACATTTTGTTTGGACGAGA 59.683 34.615 0.00 0.00 0.00 4.04
3775 7391 2.629617 AGTTGCTTGGTTTATGCTGCTT 59.370 40.909 0.00 0.00 0.00 3.91
3795 7411 7.213216 TGCTTCATTGAATTTGTGTAGCTTA 57.787 32.000 0.00 0.00 0.00 3.09
3844 7462 3.778954 AGGAGCCATAGATAAAGTGCC 57.221 47.619 0.00 0.00 0.00 5.01
3845 7463 3.048600 AGGAGCCATAGATAAAGTGCCA 58.951 45.455 0.00 0.00 0.00 4.92
3955 7573 6.776887 ATGGATCTGTATTCTCCTTTGGAT 57.223 37.500 0.00 0.00 0.00 3.41
3957 7575 7.878621 TGGATCTGTATTCTCCTTTGGATAT 57.121 36.000 0.00 0.00 0.00 1.63
4198 7902 5.520649 GCACTGTATGTTAGCCTTTACTCTC 59.479 44.000 0.00 0.00 0.00 3.20
4209 7913 3.191581 GCCTTTACTCTCTTTTTGCCCTC 59.808 47.826 0.00 0.00 0.00 4.30
4328 8032 9.006839 TGATGGCATATTAACATCTTTCTCATC 57.993 33.333 0.00 0.00 41.12 2.92
4363 8067 4.142004 ACATACTCTCGGGTTCCATGTTAC 60.142 45.833 0.00 0.00 0.00 2.50
4465 8169 8.203485 TCTAATCACTTTGGCAATGTTCTTTTT 58.797 29.630 15.30 8.05 0.00 1.94
4587 8329 6.707608 TGGACTTGGATCGAATTCTCATATTG 59.292 38.462 3.52 0.00 0.00 1.90
4620 9014 6.431234 CCCTTAGTGTTGTTCTAAGCATCTTT 59.569 38.462 7.06 0.00 41.45 2.52
4706 9127 5.106038 TGTCTTTCATCATTCTTCATGCCAC 60.106 40.000 0.00 0.00 32.13 5.01
4752 9173 5.200454 GCTGTGCTTTAACATGACGATATG 58.800 41.667 0.00 0.00 0.00 1.78
5065 9487 3.206150 CCCACTTACATCTATGCACCAC 58.794 50.000 0.00 0.00 0.00 4.16
5104 9526 4.272991 GCTTCTCTATGCAAACTGATGGAG 59.727 45.833 0.00 0.00 0.00 3.86
5151 9573 8.352942 TCTTTTTCTTCTTCTGCTTATCCAAAC 58.647 33.333 0.00 0.00 0.00 2.93
5172 9594 3.249091 CACAGTGACTGCTCATAGTGTC 58.751 50.000 13.37 0.00 34.37 3.67
5179 9601 4.640647 TGACTGCTCATAGTGTCTAATCGT 59.359 41.667 0.00 0.00 0.00 3.73
5190 9612 5.344066 AGTGTCTAATCGTCTGCTAACATG 58.656 41.667 0.00 0.00 0.00 3.21
5287 9709 5.163447 CGGGTGAGTGGACTAGATTTCATTA 60.163 44.000 0.00 0.00 0.00 1.90
5305 9727 0.747852 TATATGGCGCTGTTCGGTCA 59.252 50.000 7.64 0.00 38.94 4.02
5313 9735 1.026718 GCTGTTCGGTCATTCCAGGG 61.027 60.000 0.00 0.00 35.57 4.45
5335 9757 4.038402 GGCTAATGGCTATTTGCTCATTGT 59.962 41.667 23.61 0.00 42.29 2.71
5344 9766 6.308766 GGCTATTTGCTCATTGTAAACAGTTG 59.691 38.462 0.00 0.00 42.39 3.16
5363 9785 0.320050 GGCTATGCTAGTGGAGGAGC 59.680 60.000 0.00 0.00 39.25 4.70
5401 9823 0.179045 AGCAGAGCACGAAAACTGGT 60.179 50.000 0.00 0.00 36.49 4.00
5414 9836 2.156051 AACTGGTTCTCCTCGCCGTC 62.156 60.000 0.00 0.00 34.23 4.79
5513 9935 1.345741 CTATAAGCCCTAGCAGCAGCA 59.654 52.381 3.17 0.00 45.49 4.41
5541 9963 0.543174 AAGGCTCCTTGACTCGGACT 60.543 55.000 0.00 0.00 34.60 3.85
5562 9984 0.745486 TGCTCGCCATTCTGTCATGG 60.745 55.000 0.00 4.77 46.04 3.66
5579 10001 3.967326 TCATGGTGGATAGTCCGATTCTT 59.033 43.478 0.00 0.00 40.17 2.52
5605 10027 0.449388 GCCTGATGCTTTCTGGAACG 59.551 55.000 14.40 0.00 44.21 3.95
5618 10040 1.228154 GGAACGCCAAACCTGTCCT 60.228 57.895 0.00 0.00 0.00 3.85
5620 10042 0.591659 GAACGCCAAACCTGTCCTTC 59.408 55.000 0.00 0.00 0.00 3.46
5621 10043 0.106918 AACGCCAAACCTGTCCTTCA 60.107 50.000 0.00 0.00 0.00 3.02
5625 10047 0.535102 CCAAACCTGTCCTTCAGCGT 60.535 55.000 0.00 0.00 42.38 5.07
5669 10091 6.096846 GCAAATGTACATACCCATCTCCTTTT 59.903 38.462 9.21 0.00 0.00 2.27
5678 10100 1.407437 CCATCTCCTTTTAGCGCCTGT 60.407 52.381 2.29 0.00 0.00 4.00
5707 10129 4.652822 GTCCTTCTGTGGAAGTAACCAAT 58.347 43.478 5.27 0.00 45.36 3.16
5731 10153 2.430694 ACAGTGGTTCCCTTTTGCTTTC 59.569 45.455 0.00 0.00 0.00 2.62
5799 10221 1.153823 GTGTACTCACTGGCGCGAT 60.154 57.895 12.10 0.00 40.98 4.58
5808 10231 4.193334 TGGCGCGATGAGTCTCGG 62.193 66.667 12.10 5.60 39.05 4.63
5849 10272 4.569943 CTTGTAATGTGTACTCACTGGCT 58.430 43.478 0.00 0.00 44.14 4.75
5850 10273 4.617253 TGTAATGTGTACTCACTGGCTT 57.383 40.909 0.00 0.00 44.14 4.35
5903 10326 5.453567 AAAAACTCTTGTACCAATCCTGC 57.546 39.130 0.00 0.00 0.00 4.85
5946 10370 1.599047 GCTTGCCTAGGTGCTCTCA 59.401 57.895 11.31 0.00 0.00 3.27
5967 10392 0.935898 CCTGCGCTGATCTCAATGTC 59.064 55.000 16.65 0.00 0.00 3.06
6034 10459 3.050275 GGCAGCTCCGGTGACAAC 61.050 66.667 7.92 0.00 39.11 3.32
6035 10460 2.031163 GCAGCTCCGGTGACAACT 59.969 61.111 7.92 0.00 32.22 3.16
6036 10461 1.598130 GCAGCTCCGGTGACAACTT 60.598 57.895 7.92 0.00 32.22 2.66
6037 10462 1.845809 GCAGCTCCGGTGACAACTTG 61.846 60.000 7.92 0.00 32.22 3.16
6038 10463 0.532862 CAGCTCCGGTGACAACTTGT 60.533 55.000 7.92 0.00 32.22 3.16
6040 10465 1.228657 GCTCCGGTGACAACTTGTCC 61.229 60.000 17.51 9.78 46.40 4.02
6041 10466 0.602905 CTCCGGTGACAACTTGTCCC 60.603 60.000 17.51 15.97 46.40 4.46
6042 10467 3.637714 CGGTGACAACTTGTCCCG 58.362 61.111 24.83 24.83 46.40 5.14
6043 10468 2.604174 CGGTGACAACTTGTCCCGC 61.604 63.158 25.68 14.77 46.13 6.13
6044 10469 1.227853 GGTGACAACTTGTCCCGCT 60.228 57.895 17.51 0.00 46.40 5.52
6045 10470 1.228657 GGTGACAACTTGTCCCGCTC 61.229 60.000 17.51 5.05 46.40 5.03
6046 10471 0.249911 GTGACAACTTGTCCCGCTCT 60.250 55.000 17.51 0.00 46.40 4.09
6047 10472 0.468226 TGACAACTTGTCCCGCTCTT 59.532 50.000 17.51 0.00 46.40 2.85
6048 10473 1.689813 TGACAACTTGTCCCGCTCTTA 59.310 47.619 17.51 0.00 46.40 2.10
6049 10474 2.067013 GACAACTTGTCCCGCTCTTAC 58.933 52.381 10.42 0.00 41.37 2.34
6050 10475 1.068474 CAACTTGTCCCGCTCTTACG 58.932 55.000 0.00 0.00 0.00 3.18
6051 10476 0.677842 AACTTGTCCCGCTCTTACGT 59.322 50.000 0.00 0.00 0.00 3.57
6052 10477 0.677842 ACTTGTCCCGCTCTTACGTT 59.322 50.000 0.00 0.00 0.00 3.99
6053 10478 1.336609 ACTTGTCCCGCTCTTACGTTC 60.337 52.381 0.00 0.00 0.00 3.95
6054 10479 0.675083 TTGTCCCGCTCTTACGTTCA 59.325 50.000 0.00 0.00 0.00 3.18
6055 10480 0.675083 TGTCCCGCTCTTACGTTCAA 59.325 50.000 0.00 0.00 0.00 2.69
6056 10481 1.068895 TGTCCCGCTCTTACGTTCAAA 59.931 47.619 0.00 0.00 0.00 2.69
6057 10482 2.137523 GTCCCGCTCTTACGTTCAAAA 58.862 47.619 0.00 0.00 0.00 2.44
6058 10483 2.545106 GTCCCGCTCTTACGTTCAAAAA 59.455 45.455 0.00 0.00 0.00 1.94
6059 10484 2.803956 TCCCGCTCTTACGTTCAAAAAG 59.196 45.455 0.00 0.00 0.00 2.27
6060 10485 2.803956 CCCGCTCTTACGTTCAAAAAGA 59.196 45.455 0.00 0.00 0.00 2.52
6061 10486 3.249080 CCCGCTCTTACGTTCAAAAAGAA 59.751 43.478 0.00 0.00 0.00 2.52
6062 10487 4.260866 CCCGCTCTTACGTTCAAAAAGAAA 60.261 41.667 0.00 0.00 38.13 2.52
6063 10488 5.267776 CCGCTCTTACGTTCAAAAAGAAAA 58.732 37.500 0.00 0.00 38.13 2.29
6064 10489 5.740099 CCGCTCTTACGTTCAAAAAGAAAAA 59.260 36.000 0.00 0.00 38.13 1.94
6065 10490 6.075572 CCGCTCTTACGTTCAAAAAGAAAAAG 60.076 38.462 0.00 0.00 38.13 2.27
6066 10491 6.685403 CGCTCTTACGTTCAAAAAGAAAAAGA 59.315 34.615 0.00 0.00 38.13 2.52
6067 10492 7.217447 CGCTCTTACGTTCAAAAAGAAAAAGAA 59.783 33.333 0.00 0.00 38.13 2.52
6068 10493 8.856247 GCTCTTACGTTCAAAAAGAAAAAGAAA 58.144 29.630 0.00 0.00 38.13 2.52
6114 10541 3.169355 CTGCACTGTTTTGGAGCTTTT 57.831 42.857 0.00 0.00 0.00 2.27
6285 11010 2.620115 CGGTTGCTGCTTGGATATGAAT 59.380 45.455 0.00 0.00 0.00 2.57
6371 11096 1.226746 CGGCCATATCCGTTTTCCTC 58.773 55.000 2.24 0.00 44.18 3.71
6372 11097 1.605753 GGCCATATCCGTTTTCCTCC 58.394 55.000 0.00 0.00 0.00 4.30
6373 11098 1.605753 GCCATATCCGTTTTCCTCCC 58.394 55.000 0.00 0.00 0.00 4.30
6375 11100 1.226746 CATATCCGTTTTCCTCCCGC 58.773 55.000 0.00 0.00 0.00 6.13
6377 11102 0.462789 TATCCGTTTTCCTCCCGCTC 59.537 55.000 0.00 0.00 0.00 5.03
6381 11106 0.737715 CGTTTTCCTCCCGCTCTCAG 60.738 60.000 0.00 0.00 0.00 3.35
6385 11122 3.847602 CCTCCCGCTCTCAGCAGG 61.848 72.222 0.00 0.00 42.58 4.85
6420 11157 1.073098 ACATCCCTTTCGGTTTCCCT 58.927 50.000 0.00 0.00 0.00 4.20
6421 11158 1.004394 ACATCCCTTTCGGTTTCCCTC 59.996 52.381 0.00 0.00 0.00 4.30
6425 11162 1.498176 CCTTTCGGTTTCCCTCCCCT 61.498 60.000 0.00 0.00 0.00 4.79
6427 11164 1.494716 TTTCGGTTTCCCTCCCCTCC 61.495 60.000 0.00 0.00 0.00 4.30
6428 11165 2.285442 CGGTTTCCCTCCCCTCCT 60.285 66.667 0.00 0.00 0.00 3.69
6429 11166 1.002533 CGGTTTCCCTCCCCTCCTA 59.997 63.158 0.00 0.00 0.00 2.94
6430 11167 1.335882 CGGTTTCCCTCCCCTCCTAC 61.336 65.000 0.00 0.00 0.00 3.18
6432 11169 1.498264 GTTTCCCTCCCCTCCTACTC 58.502 60.000 0.00 0.00 0.00 2.59
6433 11170 0.342313 TTTCCCTCCCCTCCTACTCC 59.658 60.000 0.00 0.00 0.00 3.85
6481 11221 3.773630 CGTTGATTGCGTCGGCGT 61.774 61.111 12.58 0.00 44.10 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 61 9.926158 ACAAAATTTCATGAAAGCACATATGTA 57.074 25.926 24.17 0.00 33.32 2.29
60 62 8.836268 ACAAAATTTCATGAAAGCACATATGT 57.164 26.923 24.17 17.39 33.32 2.29
64 66 8.714179 CATGTACAAAATTTCATGAAAGCACAT 58.286 29.630 24.17 18.34 39.68 3.21
123 2017 5.060446 CACACGTCAAAAAGTCTGGAAAAAC 59.940 40.000 0.00 0.00 0.00 2.43
129 2024 2.285083 TCCACACGTCAAAAAGTCTGG 58.715 47.619 0.00 0.00 0.00 3.86
134 2029 8.844441 TTTTACTATTTCCACACGTCAAAAAG 57.156 30.769 0.00 0.00 0.00 2.27
199 2094 4.669197 CGAGAAAAATGTGCGAAAGGTAGG 60.669 45.833 0.00 0.00 0.00 3.18
202 2097 2.875933 TCGAGAAAAATGTGCGAAAGGT 59.124 40.909 0.00 0.00 0.00 3.50
203 2098 3.186409 TCTCGAGAAAAATGTGCGAAAGG 59.814 43.478 14.01 0.00 0.00 3.11
235 2147 0.393537 CGGCAGAAGAGAAATGGGCT 60.394 55.000 0.00 0.00 0.00 5.19
236 2148 0.678048 ACGGCAGAAGAGAAATGGGC 60.678 55.000 0.00 0.00 0.00 5.36
379 3651 4.771356 TCGCTGCTCGTGTACGGC 62.771 66.667 4.44 7.60 40.29 5.68
380 3652 2.874780 GTCGCTGCTCGTGTACGG 60.875 66.667 4.44 0.00 40.29 4.02
381 3653 2.874780 GGTCGCTGCTCGTGTACG 60.875 66.667 0.00 0.00 39.67 3.67
382 3654 2.506438 GGGTCGCTGCTCGTGTAC 60.506 66.667 0.00 0.00 39.67 2.90
383 3655 4.111016 CGGGTCGCTGCTCGTGTA 62.111 66.667 0.00 0.00 39.67 2.90
414 3686 1.033574 GCTGTCCGGCACTAGACTAT 58.966 55.000 0.00 0.00 34.02 2.12
459 3731 4.527157 GGCTTCTGATGCGTGCGC 62.527 66.667 9.85 9.85 42.35 6.09
460 3732 2.573341 CTTGGCTTCTGATGCGTGCG 62.573 60.000 9.12 0.00 0.00 5.34
465 3737 1.807886 CTGGCTTGGCTTCTGATGC 59.192 57.895 6.97 6.97 0.00 3.91
471 3743 3.793144 CGTCGCTGGCTTGGCTTC 61.793 66.667 0.00 0.00 0.00 3.86
484 3756 4.829518 TCGATGACGGCTGCGTCG 62.830 66.667 19.24 19.24 43.96 5.12
485 3757 3.248171 GTCGATGACGGCTGCGTC 61.248 66.667 14.64 14.64 41.20 5.19
486 3758 4.796231 GGTCGATGACGGCTGCGT 62.796 66.667 3.43 0.00 44.06 5.24
522 3798 4.704833 TTCTGGGCTCGCTGTGGC 62.705 66.667 0.00 0.00 0.00 5.01
640 3916 1.226802 CCTCCGTCAGCGACATCTG 60.227 63.158 8.91 0.00 41.33 2.90
1069 4487 2.279851 CGACGCGCCCCATATGAA 60.280 61.111 5.73 0.00 0.00 2.57
1178 4596 0.908180 AACTAACTGGGGGAGGTCGG 60.908 60.000 0.00 0.00 0.00 4.79
1198 4619 3.557054 GCAAACACACCAGATACTGAGGA 60.557 47.826 0.00 0.00 32.44 3.71
1208 4629 0.248743 CACAGCAGCAAACACACCAG 60.249 55.000 0.00 0.00 0.00 4.00
1212 4633 0.679321 TCCACACAGCAGCAAACACA 60.679 50.000 0.00 0.00 0.00 3.72
1237 4658 1.702957 TCCCCAAAACCCTACTGTCAG 59.297 52.381 0.00 0.00 0.00 3.51
1412 4834 2.070654 GAAACACAACCCTGGGCACG 62.071 60.000 14.08 3.64 0.00 5.34
1420 4842 3.146066 TGAGCATAGTGAAACACAACCC 58.854 45.455 4.75 0.00 41.43 4.11
1421 4843 4.275936 ACTTGAGCATAGTGAAACACAACC 59.724 41.667 4.75 0.00 41.43 3.77
1423 4845 4.261155 GCACTTGAGCATAGTGAAACACAA 60.261 41.667 14.64 0.00 44.52 3.33
1467 4896 3.894920 TGTGACAAAACAATGCATACGG 58.105 40.909 0.00 0.00 0.00 4.02
1468 4897 5.332205 GGTTTGTGACAAAACAATGCATACG 60.332 40.000 20.29 0.00 41.00 3.06
1499 4928 9.618890 ACTGCATAGACAAAAACTATGTATCAT 57.381 29.630 13.79 0.00 44.96 2.45
1539 4971 3.381045 GCTAGGACAAAACAAACTTGCC 58.619 45.455 0.00 0.00 0.00 4.52
1580 5012 7.091720 ACACTAATGGGGATAATTGAAGGGTTA 60.092 37.037 0.00 0.00 0.00 2.85
1628 5060 2.228582 GCGCACAATATATTGGCATCCA 59.771 45.455 25.45 0.00 41.96 3.41
1641 5073 3.578456 GCTACCACAGCGCACAAT 58.422 55.556 11.47 0.00 41.37 2.71
1667 5099 5.888161 CCTAACCCAGATAGACAAAAGCATT 59.112 40.000 0.00 0.00 0.00 3.56
1682 5114 5.388599 AAATATGGAACTCCCTAACCCAG 57.611 43.478 0.00 0.00 35.38 4.45
1687 5119 8.506196 ACATAGCTAAATATGGAACTCCCTAA 57.494 34.615 0.00 0.00 37.45 2.69
1737 5169 0.250081 GGCAGTATAGGCTGGTGCTC 60.250 60.000 0.00 0.00 39.59 4.26
1745 5177 1.202806 TGCATTCAGGGCAGTATAGGC 60.203 52.381 0.00 0.00 36.11 3.93
1755 5188 1.856629 ATGGACCTTTGCATTCAGGG 58.143 50.000 10.92 0.00 34.02 4.45
1763 5196 3.118223 AGGAGCTAGTAATGGACCTTTGC 60.118 47.826 2.89 1.67 0.00 3.68
1767 5200 4.224762 GGTTAGGAGCTAGTAATGGACCT 58.775 47.826 0.00 0.00 0.00 3.85
1779 5212 2.301870 TGTCGTCAAATGGTTAGGAGCT 59.698 45.455 0.00 0.00 0.00 4.09
2007 5440 8.395633 CCTTAATGTGTACACAAAGTATAAGCC 58.604 37.037 31.01 0.00 45.41 4.35
2017 5450 5.009210 GGAAGCAACCTTAATGTGTACACAA 59.991 40.000 31.01 14.38 45.41 3.33
2052 5485 1.060698 GAGACGAAACCGTGCATAAGC 59.939 52.381 0.00 0.00 40.80 3.09
2061 5494 1.068474 AATTCAGCGAGACGAAACCG 58.932 50.000 0.00 0.00 0.00 4.44
2067 5500 5.203358 TGAAAATACAATTCAGCGAGACG 57.797 39.130 0.00 0.00 33.15 4.18
2188 5621 6.414732 TCCAAGATGATTCAAGGTTAACGAT 58.585 36.000 0.00 0.00 0.00 3.73
2191 5624 7.174946 TGAACTCCAAGATGATTCAAGGTTAAC 59.825 37.037 0.00 0.00 0.00 2.01
2203 5636 4.551702 TTTCGGATGAACTCCAAGATGA 57.448 40.909 0.00 0.00 45.24 2.92
2223 5656 5.163478 GCCCTCAATCAATGCTAATGAGTTT 60.163 40.000 0.00 0.00 36.61 2.66
2320 5753 8.408601 AGACATCATGGAATTAAATGCTGTAAC 58.591 33.333 8.51 1.04 34.29 2.50
2348 5781 2.091885 ACACCCTCACAGACAAAATGGT 60.092 45.455 0.00 0.00 0.00 3.55
2512 5945 9.649167 AAAGGCTCAATTTATTCATTCTTTCTG 57.351 29.630 0.00 0.00 0.00 3.02
2647 6085 4.345257 TCAAGCTTTCCAGTCTAAGACAGT 59.655 41.667 0.00 0.00 34.60 3.55
2706 6144 8.551205 CAAACGATGCTTCACATATATACTTGT 58.449 33.333 0.08 0.00 39.84 3.16
2709 6147 9.494271 AATCAAACGATGCTTCACATATATACT 57.506 29.630 0.08 0.00 39.84 2.12
2728 6167 5.531634 TGGACTCTTGATGCAAAATCAAAC 58.468 37.500 3.04 0.00 37.55 2.93
2737 6176 3.918294 TCATCATGGACTCTTGATGCA 57.082 42.857 13.82 0.00 46.51 3.96
2779 6218 1.102978 GGTTGGATGGTGGTGCATAC 58.897 55.000 0.00 0.00 0.00 2.39
2857 6296 6.789262 AGGAAAAATAGACAATTGCGATCAG 58.211 36.000 5.05 0.00 0.00 2.90
3100 6539 3.676646 GCTCATAAAAAGTGCTGCCAAAG 59.323 43.478 0.00 0.00 0.00 2.77
3157 6773 5.411669 TCAAACTTTCTATCTTTTCTCGCCC 59.588 40.000 0.00 0.00 0.00 6.13
3178 6794 8.739039 CCCAATGAAATAGTTGTCATAGTTCAA 58.261 33.333 1.66 0.00 39.70 2.69
3231 6847 1.095130 TACTGGTTCCCCTCCACCTA 58.905 55.000 0.00 0.00 33.76 3.08
3298 6914 9.128107 GCGACTTCAATGAAAAATTCTGAAATA 57.872 29.630 0.00 0.00 0.00 1.40
3359 6975 7.201145 TCTACTAGGTTGTTTCATATTCGCTC 58.799 38.462 0.00 0.00 0.00 5.03
3469 7085 2.158475 TGGGGTTTTGCTGATCAAGAGT 60.158 45.455 0.00 0.00 35.84 3.24
3472 7088 5.603170 ATTATGGGGTTTTGCTGATCAAG 57.397 39.130 0.00 0.00 35.84 3.02
3473 7089 6.371595 AAATTATGGGGTTTTGCTGATCAA 57.628 33.333 0.00 0.00 0.00 2.57
3560 7176 9.276590 TCTACTCTATCATTTGGTTGCAATATG 57.723 33.333 0.59 5.05 0.00 1.78
3602 7218 6.968335 GTCAGTTTGTTACCACGTTTACAAAT 59.032 34.615 13.80 5.08 41.06 2.32
3664 7280 7.280428 TCGTCCAAACAAAATGTAGAAACAGTA 59.720 33.333 0.00 0.00 39.49 2.74
3795 7411 4.301205 AGTTACCCCGGATTGGTACTTAT 58.699 43.478 0.73 0.00 38.06 1.73
3844 7462 6.882140 TGGTAAGTACAAACCCACAGAATATG 59.118 38.462 12.61 0.00 34.69 1.78
3845 7463 7.023171 TGGTAAGTACAAACCCACAGAATAT 57.977 36.000 12.61 0.00 34.69 1.28
3903 7521 5.492524 TGAGATCTTCCCCAGACCTAAAAAT 59.507 40.000 0.00 0.00 32.83 1.82
3955 7573 6.822442 TGGTAGTCTTGCCGAATGATTTATA 58.178 36.000 0.00 0.00 0.00 0.98
3957 7575 5.092554 TGGTAGTCTTGCCGAATGATTTA 57.907 39.130 0.00 0.00 0.00 1.40
4017 7638 1.003580 GATCAACAGAGGGTCCAGCAA 59.996 52.381 0.00 0.00 0.00 3.91
4161 7865 7.744087 AACATACAGTGCTTAACATTTCTGA 57.256 32.000 0.00 0.00 0.00 3.27
4198 7902 2.772287 AGAGTTCTCGAGGGCAAAAAG 58.228 47.619 13.56 0.00 0.00 2.27
4209 7913 3.384668 TGAACTGCTGAAAGAGTTCTCG 58.615 45.455 12.07 0.00 44.29 4.04
4328 8032 3.686128 GAGAGTATGTGACTGTAGCACG 58.314 50.000 0.00 0.00 39.06 5.34
4422 8126 7.124599 AGTGATTAGATGGCATTGGAAAATTCA 59.875 33.333 0.00 0.00 0.00 2.57
4425 8129 7.427989 AAGTGATTAGATGGCATTGGAAAAT 57.572 32.000 0.00 0.00 0.00 1.82
4510 8214 8.868522 ATCTCATCATCCTAAAGACAACAAAA 57.131 30.769 0.00 0.00 0.00 2.44
4548 8290 4.222145 TCCAAGTCCATTACGCTTAGTTCT 59.778 41.667 0.00 0.00 0.00 3.01
4587 8329 5.612351 AGAACAACACTAAGGGACTCTTTC 58.388 41.667 0.00 0.00 38.49 2.62
4706 9127 3.414700 GCACTTGACAGGTCCGCG 61.415 66.667 0.00 0.00 0.00 6.46
4727 9148 2.223144 TCGTCATGTTAAAGCACAGCAC 59.777 45.455 0.00 0.00 0.00 4.40
5006 9428 4.139183 TGCACAAACAAACAAAACAAGC 57.861 36.364 0.00 0.00 0.00 4.01
5065 9487 3.614092 AGAAGCATTGTATGTGGAGGTG 58.386 45.455 0.00 0.00 0.00 4.00
5104 9526 5.241662 AGAAGATTTTGCTCTCACCAGTAC 58.758 41.667 0.00 0.00 0.00 2.73
5151 9573 3.056962 AGACACTATGAGCAGTCACTGTG 60.057 47.826 6.68 0.17 41.44 3.66
5172 9594 4.205181 CACGACATGTTAGCAGACGATTAG 59.795 45.833 0.00 0.00 0.00 1.73
5179 9601 2.068519 CAAGCACGACATGTTAGCAGA 58.931 47.619 16.85 0.00 0.00 4.26
5190 9612 1.457303 CTAAGACAGCACAAGCACGAC 59.543 52.381 0.00 0.00 45.49 4.34
5287 9709 0.106708 ATGACCGAACAGCGCCATAT 59.893 50.000 2.29 0.00 39.11 1.78
5305 9727 4.154942 CAAATAGCCATTAGCCCTGGAAT 58.845 43.478 0.00 0.00 45.47 3.01
5335 9757 4.224147 TCCACTAGCATAGCCAACTGTTTA 59.776 41.667 0.00 0.00 44.39 2.01
5344 9766 0.320050 GCTCCTCCACTAGCATAGCC 59.680 60.000 0.00 0.00 44.39 3.93
5363 9785 2.009774 CTCGGCCTCCAGTTGTTTATG 58.990 52.381 0.00 0.00 0.00 1.90
5364 9786 1.679032 GCTCGGCCTCCAGTTGTTTAT 60.679 52.381 0.00 0.00 0.00 1.40
5401 9823 2.439701 ATCGGACGGCGAGGAGAA 60.440 61.111 16.62 0.00 0.00 2.87
5562 9984 2.484889 GCCAAGAATCGGACTATCCAC 58.515 52.381 0.00 0.00 35.91 4.02
5605 10027 1.856265 CGCTGAAGGACAGGTTTGGC 61.856 60.000 0.00 0.00 45.82 4.52
5618 10040 1.371183 CTTCACCCCTCACGCTGAA 59.629 57.895 0.00 0.00 0.00 3.02
5620 10042 1.374758 GACTTCACCCCTCACGCTG 60.375 63.158 0.00 0.00 0.00 5.18
5621 10043 2.932234 CGACTTCACCCCTCACGCT 61.932 63.158 0.00 0.00 0.00 5.07
5625 10047 0.321564 CATTGCGACTTCACCCCTCA 60.322 55.000 0.00 0.00 0.00 3.86
5678 10100 3.691342 CACAGAAGGACGGCGGGA 61.691 66.667 13.24 0.00 0.00 5.14
5731 10153 0.314935 ATTTGGCGCAAGGACAACAG 59.685 50.000 10.83 0.00 45.44 3.16
5799 10221 2.997315 CCACTGCCCCGAGACTCA 60.997 66.667 2.82 0.00 0.00 3.41
5849 10272 2.636412 CCTGCCCGAGACTCGTCAA 61.636 63.158 22.61 7.20 38.40 3.18
5850 10273 3.062466 CCTGCCCGAGACTCGTCA 61.062 66.667 22.61 17.71 38.40 4.35
5903 10326 2.160417 GCTTCCCTGAACATTTCGACAG 59.840 50.000 0.00 0.00 0.00 3.51
5946 10370 0.463295 CATTGAGATCAGCGCAGGGT 60.463 55.000 11.47 0.00 0.00 4.34
5954 10378 2.350804 CGGCTGTTGACATTGAGATCAG 59.649 50.000 0.00 0.00 0.00 2.90
5967 10392 0.319211 TCGTCCTTGTACGGCTGTTG 60.319 55.000 1.99 0.00 43.05 3.33
6028 10453 5.942396 CGTAAGAGCGGGACAAGTTGTCA 62.942 52.174 31.52 10.69 45.29 3.58
6029 10454 2.067013 GTAAGAGCGGGACAAGTTGTC 58.933 52.381 25.00 25.00 46.23 3.18
6030 10455 1.604693 CGTAAGAGCGGGACAAGTTGT 60.605 52.381 8.61 8.61 43.02 3.32
6031 10456 1.068474 CGTAAGAGCGGGACAAGTTG 58.932 55.000 0.00 0.00 43.02 3.16
6032 10457 0.677842 ACGTAAGAGCGGGACAAGTT 59.322 50.000 0.00 0.00 43.62 2.66
6033 10458 0.677842 AACGTAAGAGCGGGACAAGT 59.322 50.000 0.00 0.00 43.62 3.16
6034 10459 1.336517 TGAACGTAAGAGCGGGACAAG 60.337 52.381 0.00 0.00 43.62 3.16
6035 10460 0.675083 TGAACGTAAGAGCGGGACAA 59.325 50.000 0.00 0.00 43.62 3.18
6036 10461 0.675083 TTGAACGTAAGAGCGGGACA 59.325 50.000 0.00 0.00 43.62 4.02
6037 10462 1.787012 TTTGAACGTAAGAGCGGGAC 58.213 50.000 0.00 0.00 43.62 4.46
6038 10463 2.529780 TTTTGAACGTAAGAGCGGGA 57.470 45.000 0.00 0.00 43.62 5.14
6039 10464 2.803956 TCTTTTTGAACGTAAGAGCGGG 59.196 45.455 0.00 0.00 43.62 6.13
6040 10465 4.461992 TTCTTTTTGAACGTAAGAGCGG 57.538 40.909 0.00 0.00 43.62 5.52
6041 10466 6.685403 TCTTTTTCTTTTTGAACGTAAGAGCG 59.315 34.615 0.00 0.00 43.62 5.03
6042 10467 7.964545 TCTTTTTCTTTTTGAACGTAAGAGC 57.035 32.000 0.00 0.00 43.62 4.09
6048 10473 9.036671 TGTCTTTTTCTTTTTCTTTTTGAACGT 57.963 25.926 0.00 0.00 33.88 3.99
6049 10474 9.856803 TTGTCTTTTTCTTTTTCTTTTTGAACG 57.143 25.926 0.00 0.00 33.88 3.95
6056 10481 8.988934 GGACAAGTTGTCTTTTTCTTTTTCTTT 58.011 29.630 29.89 0.00 46.19 2.52
6057 10482 8.367911 AGGACAAGTTGTCTTTTTCTTTTTCTT 58.632 29.630 29.89 0.00 46.19 2.52
6058 10483 7.814587 CAGGACAAGTTGTCTTTTTCTTTTTCT 59.185 33.333 29.89 14.41 46.19 2.52
6059 10484 7.411912 GCAGGACAAGTTGTCTTTTTCTTTTTC 60.412 37.037 29.89 12.62 46.19 2.29
6060 10485 6.368791 GCAGGACAAGTTGTCTTTTTCTTTTT 59.631 34.615 29.89 5.88 46.19 1.94
6061 10486 5.869344 GCAGGACAAGTTGTCTTTTTCTTTT 59.131 36.000 29.89 7.15 46.19 2.27
6062 10487 5.185828 AGCAGGACAAGTTGTCTTTTTCTTT 59.814 36.000 29.89 10.27 46.19 2.52
6063 10488 4.706962 AGCAGGACAAGTTGTCTTTTTCTT 59.293 37.500 29.89 11.07 46.19 2.52
6064 10489 4.273318 AGCAGGACAAGTTGTCTTTTTCT 58.727 39.130 29.89 17.96 46.19 2.52
6065 10490 4.336713 AGAGCAGGACAAGTTGTCTTTTTC 59.663 41.667 29.89 21.87 46.19 2.29
6066 10491 4.273318 AGAGCAGGACAAGTTGTCTTTTT 58.727 39.130 29.89 16.00 46.19 1.94
6067 10492 3.891049 AGAGCAGGACAAGTTGTCTTTT 58.109 40.909 29.89 16.32 46.19 2.27
6068 10493 3.567478 AGAGCAGGACAAGTTGTCTTT 57.433 42.857 29.89 18.44 46.19 2.52
6069 10494 4.101741 AGTTAGAGCAGGACAAGTTGTCTT 59.898 41.667 29.89 22.87 46.19 3.01
6070 10495 3.643792 AGTTAGAGCAGGACAAGTTGTCT 59.356 43.478 29.89 14.43 46.19 3.41
6083 10508 0.394192 ACAGTGCAGCAGTTAGAGCA 59.606 50.000 0.00 0.00 34.10 4.26
6084 10509 1.517242 AACAGTGCAGCAGTTAGAGC 58.483 50.000 0.00 0.00 0.00 4.09
6114 10541 7.148474 GCTTCCAAATATCTCACTTTCGTTACA 60.148 37.037 0.00 0.00 0.00 2.41
6231 10658 2.174969 GCGTGGTTTGGTCGTGTGA 61.175 57.895 0.00 0.00 0.00 3.58
6262 10689 1.103398 ATATCCAAGCAGCAACCGGC 61.103 55.000 0.00 0.00 45.30 6.13
6277 11002 3.370366 GCCTGCGATCACTCATTCATATC 59.630 47.826 0.00 0.00 0.00 1.63
6285 11010 1.216444 GTCAGCCTGCGATCACTCA 59.784 57.895 0.00 0.00 0.00 3.41
6363 11088 1.021920 GCTGAGAGCGGGAGGAAAAC 61.022 60.000 0.00 0.00 0.00 2.43
6364 11089 1.296715 GCTGAGAGCGGGAGGAAAA 59.703 57.895 0.00 0.00 0.00 2.29
6366 11091 2.283894 TGCTGAGAGCGGGAGGAA 60.284 61.111 0.00 0.00 46.26 3.36
6367 11092 2.757508 CTGCTGAGAGCGGGAGGA 60.758 66.667 0.00 0.00 46.26 3.71
6372 11097 3.368190 CTGACCCTGCTGAGAGCGG 62.368 68.421 0.00 0.00 46.26 5.52
6373 11098 2.183811 CTGACCCTGCTGAGAGCG 59.816 66.667 0.00 0.00 46.26 5.03
6375 11100 1.896694 GGTCTGACCCTGCTGAGAG 59.103 63.158 16.14 0.00 30.04 3.20
6385 11122 1.827399 ATGTGGACGTGGGTCTGACC 61.827 60.000 18.65 18.65 42.97 4.02
6394 11131 2.456000 CGAAAGGGATGTGGACGTG 58.544 57.895 0.00 0.00 0.00 4.49
6420 11157 3.438131 AATTGATGGAGTAGGAGGGGA 57.562 47.619 0.00 0.00 0.00 4.81
6421 11158 3.181439 GGAAATTGATGGAGTAGGAGGGG 60.181 52.174 0.00 0.00 0.00 4.79
6425 11162 3.716872 GGGAGGAAATTGATGGAGTAGGA 59.283 47.826 0.00 0.00 0.00 2.94
6427 11164 3.388024 TCGGGAGGAAATTGATGGAGTAG 59.612 47.826 0.00 0.00 0.00 2.57
6428 11165 3.380393 TCGGGAGGAAATTGATGGAGTA 58.620 45.455 0.00 0.00 0.00 2.59
6429 11166 2.196595 TCGGGAGGAAATTGATGGAGT 58.803 47.619 0.00 0.00 0.00 3.85
6430 11167 3.406764 GATCGGGAGGAAATTGATGGAG 58.593 50.000 0.00 0.00 0.00 3.86
6432 11169 2.146342 CGATCGGGAGGAAATTGATGG 58.854 52.381 7.38 0.00 0.00 3.51
6433 11170 2.838736 ACGATCGGGAGGAAATTGATG 58.161 47.619 20.98 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.