Multiple sequence alignment - TraesCS6A01G137900

Loading Multiple Alignment...

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 TraesCS6A01G137900 chr6A 100.000 3425 0 0 3996 7420 109122224 109125648 0.000000e+00 6325.0
1 TraesCS6A01G137900 chr6A 100.000 1772 0 0 1 1772 109118229 109120000 0.000000e+00 3273.0
2 TraesCS6A01G137900 chr6A 100.000 1695 0 0 2050 3744 109120278 109121972 0.000000e+00 3131.0
3 TraesCS6A01G137900 chr6A 86.765 68 6 3 121 187 581025572 581025637 1.030000e-08 73.1
4 TraesCS6A01G137900 chr6D 95.997 1299 47 3 2132 3425 90882336 90883634 0.000000e+00 2106.0
5 TraesCS6A01G137900 chr6D 94.428 1382 49 8 5147 6510 90890557 90891928 0.000000e+00 2100.0
6 TraesCS6A01G137900 chr6D 92.809 1182 39 6 3996 5149 90888909 90890072 0.000000e+00 1670.0
7 TraesCS6A01G137900 chr6D 90.827 883 47 14 812 1670 90881323 90882195 0.000000e+00 1151.0
8 TraesCS6A01G137900 chr6D 90.665 782 56 7 1 771 90880549 90881324 0.000000e+00 1024.0
9 TraesCS6A01G137900 chr6D 88.953 697 57 9 6734 7416 90892229 90892919 0.000000e+00 843.0
10 TraesCS6A01G137900 chr6D 96.049 329 12 1 3416 3744 90888538 90888865 1.100000e-147 534.0
11 TraesCS6A01G137900 chr6D 92.090 177 12 1 6508 6684 90891957 90892131 1.600000e-61 248.0
12 TraesCS6A01G137900 chr6B 91.587 1367 61 27 5147 6510 173024422 173025737 0.000000e+00 1838.0
13 TraesCS6A01G137900 chr6B 96.449 1070 27 4 2683 3744 173021851 173022917 0.000000e+00 1755.0
14 TraesCS6A01G137900 chr6B 93.492 1137 29 8 3996 5105 173022961 173024079 0.000000e+00 1648.0
15 TraesCS6A01G137900 chr6B 91.885 764 40 10 904 1651 173019844 173020601 0.000000e+00 1048.0
16 TraesCS6A01G137900 chr6B 92.516 628 37 5 2054 2678 173020770 173021390 0.000000e+00 891.0
17 TraesCS6A01G137900 chr6B 87.815 714 64 17 6716 7420 173025937 173026636 0.000000e+00 815.0
18 TraesCS6A01G137900 chr6B 86.412 655 69 14 121 767 173018048 173018690 0.000000e+00 699.0
19 TraesCS6A01G137900 chr6B 89.848 197 11 5 756 944 173019663 173019858 2.070000e-60 244.0
20 TraesCS6A01G137900 chr6B 89.266 177 17 1 6508 6684 173025766 173025940 3.490000e-53 220.0
21 TraesCS6A01G137900 chr4D 86.207 87 7 5 121 206 4377126 4377044 1.030000e-13 89.8
22 TraesCS6A01G137900 chr2D 78.322 143 21 10 86 223 97229535 97229672 4.770000e-12 84.2
23 TraesCS6A01G137900 chr2B 100.000 28 0 0 623 650 10793874 10793901 1.300000e-02 52.8


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 TraesCS6A01G137900 chr6A 109118229 109125648 7419 False 4243.000000 6325 100.000000 1 7420 3 chr6A.!!$F2 7419
1 TraesCS6A01G137900 chr6D 90880549 90883634 3085 False 1427.000000 2106 92.496333 1 3425 3 chr6D.!!$F1 3424
2 TraesCS6A01G137900 chr6D 90888538 90892919 4381 False 1079.000000 2100 92.865800 3416 7416 5 chr6D.!!$F2 4000
3 TraesCS6A01G137900 chr6B 173018048 173026636 8588 False 1017.555556 1838 91.030000 121 7420 9 chr6B.!!$F1 7299


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
951 1987 0.296642 CTAATTTTCGCCGTCGACCG 59.703 55.000 10.58 8.99 45.43 4.79 F
1404 2454 0.532573 CTCCGCTCTAGCAGTTTCCA 59.467 55.000 2.44 0.00 42.21 3.53 F
1405 2455 0.532573 TCCGCTCTAGCAGTTTCCAG 59.467 55.000 2.44 0.00 42.21 3.86 F
1443 2493 1.531365 CTGTTTCCCTGCCTGGCAA 60.531 57.895 23.51 4.95 38.41 4.52 F
2501 3606 1.303236 CGACCATCACCCCAAAGCA 60.303 57.895 0.00 0.00 0.00 3.91 F
2653 3758 1.549037 GGTTATGGGTGTGGGCTCAAA 60.549 52.381 0.00 0.00 0.00 2.69 F
4499 6070 0.671781 AGAAGTGCGTGCATGGACTC 60.672 55.000 30.12 22.38 39.85 3.36 F
5724 7813 0.601558 CTTGCAATGCTGGCTCTTGT 59.398 50.000 6.82 0.00 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2406 3510 0.323629 TTAACCAGGCAAGGACCTCG 59.676 55.000 0.00 0.00 38.26 4.63 R
2488 3593 0.698238 TGTAGCTGCTTTGGGGTGAT 59.302 50.000 7.79 0.00 0.00 3.06 R
2501 3606 0.916358 ATCCAGCCCCTTGTGTAGCT 60.916 55.000 0.00 0.00 35.52 3.32 R
2653 3758 1.201429 ATCACCCGAAGCCCAAGAGT 61.201 55.000 0.00 0.00 0.00 3.24 R
4265 5836 1.138859 CAAGTGAGATATCGGGGCACA 59.861 52.381 17.21 3.95 32.16 4.57 R
4620 6191 1.003928 TGCTGCAGTGATGTTGATCCT 59.996 47.619 16.64 0.00 0.00 3.24 R
5922 8024 0.828762 TTGCCACAGGAAGCAATGCT 60.829 50.000 0.00 0.00 43.74 3.79 R
6777 8995 0.178990 ATGAGCCGGGCTAAATTCCC 60.179 55.000 23.92 8.17 39.88 3.97 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
191 193 9.364989 TGTTCTTCATTTCGAAACAAATTTTCT 57.635 25.926 13.81 0.00 31.71 2.52
255 258 9.180678 CTTATGAATTTGTAAAAACTGCTCGTT 57.819 29.630 0.00 0.00 37.47 3.85
350 354 5.859648 TCACCAGTTCGAAAAGTTCAAAAAC 59.140 36.000 0.00 0.00 35.50 2.43
353 357 5.288472 CCAGTTCGAAAAGTTCAAAAACTGG 59.712 40.000 20.71 20.71 45.07 4.00
442 446 9.942850 AAGATAGAAAGGAAAGAAAGAGAAGAG 57.057 33.333 0.00 0.00 0.00 2.85
449 453 6.303054 AGGAAAGAAAGAGAAGAGGGAAAAG 58.697 40.000 0.00 0.00 0.00 2.27
451 455 3.669536 AGAAAGAGAAGAGGGAAAAGCG 58.330 45.455 0.00 0.00 0.00 4.68
462 466 3.756963 GAGGGAAAAGCGGAACAGTAAAT 59.243 43.478 0.00 0.00 0.00 1.40
605 614 1.003355 ATCTGACGCTGTTGGGGTG 60.003 57.895 0.00 0.00 41.29 4.61
610 619 0.321298 GACGCTGTTGGGGTGTGTAT 60.321 55.000 0.00 0.00 41.29 2.29
611 620 0.605319 ACGCTGTTGGGGTGTGTATG 60.605 55.000 0.00 0.00 39.69 2.39
612 621 0.605319 CGCTGTTGGGGTGTGTATGT 60.605 55.000 0.00 0.00 0.00 2.29
613 622 1.338294 CGCTGTTGGGGTGTGTATGTA 60.338 52.381 0.00 0.00 0.00 2.29
614 623 2.081462 GCTGTTGGGGTGTGTATGTAC 58.919 52.381 0.00 0.00 0.00 2.90
615 624 2.343101 CTGTTGGGGTGTGTATGTACG 58.657 52.381 0.00 0.00 0.00 3.67
784 1785 2.750350 CCGTTTCCTGGCAGACCT 59.250 61.111 17.94 0.00 36.63 3.85
812 1813 0.678684 CCCGGCCCTTTTATTCGTGT 60.679 55.000 0.00 0.00 0.00 4.49
863 1864 2.329614 CCGGCCTTACAAACACGGG 61.330 63.158 0.00 0.00 37.80 5.28
893 1894 3.506398 CCAGGGTTGGGTAACAAAATCT 58.494 45.455 0.00 0.00 41.58 2.40
925 1957 2.170817 GACTAATTTTCGCCTCCCCTCT 59.829 50.000 0.00 0.00 0.00 3.69
928 1964 3.283259 AATTTTCGCCTCCCCTCTAAG 57.717 47.619 0.00 0.00 0.00 2.18
951 1987 0.296642 CTAATTTTCGCCGTCGACCG 59.703 55.000 10.58 8.99 45.43 4.79
1023 2059 2.124403 GACCTCCGCCTCCGACTA 60.124 66.667 0.00 0.00 36.29 2.59
1044 2080 1.908793 CCAGACACAGAGGGTCCGT 60.909 63.158 0.00 0.00 35.89 4.69
1073 2109 1.954362 GCACTCCACGAGCTCCAGAT 61.954 60.000 8.47 0.00 32.04 2.90
1081 2117 3.206211 GAGCTCCAGATCCTCGCCG 62.206 68.421 0.87 0.00 0.00 6.46
1186 2228 1.509548 ATCCCCCTTCCCACCTGTTG 61.510 60.000 0.00 0.00 0.00 3.33
1188 2230 2.845345 CCCCTTCCCACCTGTTGCT 61.845 63.158 0.00 0.00 0.00 3.91
1209 2251 1.787847 GCTCGTGTTTCGTGATGGG 59.212 57.895 0.00 0.00 40.80 4.00
1213 2255 1.069513 TCGTGTTTCGTGATGGGACTT 59.930 47.619 0.00 0.00 40.80 3.01
1222 2264 3.640029 TCGTGATGGGACTTATAGGGTTC 59.360 47.826 0.00 0.00 0.00 3.62
1280 2330 1.126488 ATGGCACGTCTGATCAGGAT 58.874 50.000 22.42 5.72 0.00 3.24
1378 2428 2.741055 GCTCTCTCCCTGCCTTCCC 61.741 68.421 0.00 0.00 0.00 3.97
1395 2445 1.395826 CCCCCTGTTCTCCGCTCTAG 61.396 65.000 0.00 0.00 0.00 2.43
1403 2453 0.818296 TCTCCGCTCTAGCAGTTTCC 59.182 55.000 2.44 0.00 42.21 3.13
1404 2454 0.532573 CTCCGCTCTAGCAGTTTCCA 59.467 55.000 2.44 0.00 42.21 3.53
1405 2455 0.532573 TCCGCTCTAGCAGTTTCCAG 59.467 55.000 2.44 0.00 42.21 3.86
1430 2480 4.984161 CAGCGATTTGATTGGTTTCTGTTT 59.016 37.500 0.00 0.00 0.00 2.83
1443 2493 1.531365 CTGTTTCCCTGCCTGGCAA 60.531 57.895 23.51 4.95 38.41 4.52
1449 2504 3.458163 CCTGCCTGGCAATGCTGG 61.458 66.667 23.51 15.85 38.41 4.85
1513 2568 6.324512 AGCATGAATTGATTGGTTGGCTTATA 59.675 34.615 0.00 0.00 0.00 0.98
1517 2572 8.815565 TGAATTGATTGGTTGGCTTATACTTA 57.184 30.769 0.00 0.00 0.00 2.24
1518 2573 9.420118 TGAATTGATTGGTTGGCTTATACTTAT 57.580 29.630 0.00 0.00 0.00 1.73
1572 2634 9.104965 TGAAGTTTCATACTGAAATATTACGGG 57.895 33.333 5.67 0.00 46.55 5.28
1608 2670 3.685550 GCAGGGTGGTTATTATCTGTGCT 60.686 47.826 0.00 0.00 0.00 4.40
1636 2698 6.570692 TCGAACTCTAGATATTTGGGTTCAC 58.429 40.000 15.15 0.00 33.50 3.18
1670 2738 9.337396 TGTTATACTAATTGATTTACAGGGCAG 57.663 33.333 0.00 0.00 0.00 4.85
1671 2739 8.784043 GTTATACTAATTGATTTACAGGGCAGG 58.216 37.037 0.00 0.00 0.00 4.85
1673 2741 3.756082 AATTGATTTACAGGGCAGGGA 57.244 42.857 0.00 0.00 0.00 4.20
1693 2780 4.058817 GGAGTGCATTCTACCCTAATTCG 58.941 47.826 9.27 0.00 0.00 3.34
1694 2781 4.443034 GGAGTGCATTCTACCCTAATTCGT 60.443 45.833 9.27 0.00 0.00 3.85
1702 2789 1.734163 ACCCTAATTCGTTGAAGGCG 58.266 50.000 0.00 0.00 0.00 5.52
1724 2812 7.027161 GGCGTAGTTGTTTGTTTGATTATCAT 58.973 34.615 0.00 0.00 0.00 2.45
1726 2814 8.365210 GCGTAGTTGTTTGTTTGATTATCATTG 58.635 33.333 0.00 0.00 0.00 2.82
1728 2816 9.691362 GTAGTTGTTTGTTTGATTATCATTGGT 57.309 29.630 0.00 0.00 0.00 3.67
1729 2817 8.816640 AGTTGTTTGTTTGATTATCATTGGTC 57.183 30.769 0.00 0.00 0.00 4.02
1731 2819 8.702438 GTTGTTTGTTTGATTATCATTGGTCTG 58.298 33.333 0.00 0.00 0.00 3.51
1732 2820 7.950512 TGTTTGTTTGATTATCATTGGTCTGT 58.049 30.769 0.00 0.00 0.00 3.41
1733 2821 8.081633 TGTTTGTTTGATTATCATTGGTCTGTC 58.918 33.333 0.00 0.00 0.00 3.51
1734 2822 7.757941 TTGTTTGATTATCATTGGTCTGTCA 57.242 32.000 0.00 0.00 0.00 3.58
1736 2824 8.352137 TGTTTGATTATCATTGGTCTGTCAAT 57.648 30.769 0.00 0.00 37.81 2.57
1765 2867 8.548877 ACAGATGGTAAAAATAAGCCTTCTCTA 58.451 33.333 0.00 0.00 34.56 2.43
1766 2868 9.050601 CAGATGGTAAAAATAAGCCTTCTCTAG 57.949 37.037 0.00 0.00 34.56 2.43
1767 2869 8.773216 AGATGGTAAAAATAAGCCTTCTCTAGT 58.227 33.333 0.00 0.00 32.29 2.57
1769 2871 9.833917 ATGGTAAAAATAAGCCTTCTCTAGTAC 57.166 33.333 0.00 0.00 0.00 2.73
1770 2872 8.262933 TGGTAAAAATAAGCCTTCTCTAGTACC 58.737 37.037 0.00 0.00 0.00 3.34
1771 2873 7.714377 GGTAAAAATAAGCCTTCTCTAGTACCC 59.286 40.741 0.00 0.00 0.00 3.69
2082 3184 7.591821 AGGGGCCATTTGATTCTACTTTAATA 58.408 34.615 4.39 0.00 0.00 0.98
2160 3264 5.414144 GCTTAGCTCATTTTTCTCTTGGACT 59.586 40.000 0.00 0.00 0.00 3.85
2193 3297 2.158755 AAGCCACAGAAAGGGGATATCG 60.159 50.000 0.00 0.00 39.72 2.92
2219 3323 1.859427 GCCGTGTCAGTGAGGTACGA 61.859 60.000 20.03 0.00 36.94 3.43
2241 3345 3.118629 AGCACTTTGTGTCACTCTCTCAA 60.119 43.478 4.27 0.00 35.75 3.02
2252 3356 5.167845 GTCACTCTCTCAATGTTCTTCTCC 58.832 45.833 0.00 0.00 0.00 3.71
2273 3377 7.695055 TCTCCTTTTTATAACATGGTTCCTGA 58.305 34.615 0.00 0.00 0.00 3.86
2501 3606 1.303236 CGACCATCACCCCAAAGCA 60.303 57.895 0.00 0.00 0.00 3.91
2525 3630 1.561542 ACACAAGGGGCTGGATTCTAG 59.438 52.381 0.00 0.00 0.00 2.43
2653 3758 1.549037 GGTTATGGGTGTGGGCTCAAA 60.549 52.381 0.00 0.00 0.00 2.69
2773 4342 3.654414 AGGCTTGTACTTCGAACTCTTG 58.346 45.455 0.00 0.00 0.00 3.02
2907 4476 7.331791 AGTCTCAACTATTTTGTATGGGTCTC 58.668 38.462 0.00 0.00 32.59 3.36
2913 4482 7.865706 ACTATTTTGTATGGGTCTCATTGTC 57.134 36.000 0.00 0.00 37.30 3.18
3066 4635 6.997655 TGTATTCTATTCTGGCCAGTATCAG 58.002 40.000 31.58 22.02 0.00 2.90
3119 4688 1.557269 AAGCGCTGGAGGTTGGAGAT 61.557 55.000 12.58 0.00 0.00 2.75
3296 4865 7.627293 TGCATAATGGATATGGAGGGTAAGATA 59.373 37.037 0.00 0.00 41.51 1.98
3425 4996 4.130118 CAAACCACACTTTCTAGCTGACT 58.870 43.478 0.00 0.00 0.00 3.41
3443 5014 5.779922 CTGACTTAACAGTAGCTTGTACCA 58.220 41.667 0.00 0.00 31.22 3.25
3729 5300 6.769341 ACTGATGTTGATGAGCTTAATATGCA 59.231 34.615 0.00 0.00 0.00 3.96
4216 5787 4.636206 GGTTGAACCATCATTCTCACTACC 59.364 45.833 9.98 0.00 38.42 3.18
4293 5864 4.442893 CCCGATATCTCACTTGCTTGGTAA 60.443 45.833 0.34 0.00 0.00 2.85
4320 5891 5.302823 GGGTTCGGCTAGTAATAGAAGGTAA 59.697 44.000 0.38 0.00 0.00 2.85
4414 5985 4.394920 GTGACCAATATGTGTAGTTGTGGG 59.605 45.833 0.00 0.00 0.00 4.61
4499 6070 0.671781 AGAAGTGCGTGCATGGACTC 60.672 55.000 30.12 22.38 39.85 3.36
4512 6083 1.808411 TGGACTCGAAGTTGGCAATC 58.192 50.000 1.92 0.00 0.00 2.67
4547 6118 4.246458 GGGATGCAAATATAGGAGACGAC 58.754 47.826 0.00 0.00 0.00 4.34
4620 6191 3.790416 AAGCCAACTTGCGCCCTGA 62.790 57.895 4.18 0.00 33.84 3.86
4665 6236 9.298774 CACTTGGTAAAAACAAACCGTAATAAA 57.701 29.630 0.00 0.00 38.70 1.40
4675 6246 3.975168 ACCGTAATAAAGGAGCACAGT 57.025 42.857 0.00 0.00 0.00 3.55
4684 6255 3.560636 AAGGAGCACAGTACACAAAGT 57.439 42.857 0.00 0.00 0.00 2.66
4810 6383 3.997021 GACTGTAGAACCAACCTGTGATG 59.003 47.826 0.00 0.00 0.00 3.07
4828 6401 7.297936 TGTGATGAGGTCTTAACAGAAGTTA 57.702 36.000 0.00 0.00 39.15 2.24
4935 6534 7.596749 AACTGACAATAATAAAGACACGAGG 57.403 36.000 0.00 0.00 0.00 4.63
5026 6625 9.766277 TTGTGTTTTCTTCAAATTTTTGCATAC 57.234 25.926 0.00 0.00 38.05 2.39
5028 6627 8.394121 GTGTTTTCTTCAAATTTTTGCATACCA 58.606 29.630 0.00 0.00 38.05 3.25
5032 6631 6.454795 TCTTCAAATTTTTGCATACCAGGTC 58.545 36.000 0.00 0.00 38.05 3.85
5192 7278 6.814146 GCTCTGATGGCATAGTATTTAGTACC 59.186 42.308 0.00 0.00 33.58 3.34
5219 7305 9.995003 GGATCTCATGATGTAGAGAATTTAGTT 57.005 33.333 0.00 0.00 43.47 2.24
5272 7358 0.898789 TTCAGAGACGGGTCCCACTC 60.899 60.000 19.00 19.00 0.00 3.51
5300 7386 4.766891 ACCAGGATGTTTGTTCATTGGTAG 59.233 41.667 0.00 0.00 37.24 3.18
5372 7458 5.888982 TTCCTTAGGGGAGTTCATGATAC 57.111 43.478 0.00 0.00 46.01 2.24
5376 7462 2.412591 AGGGGAGTTCATGATACTGGG 58.587 52.381 13.14 0.00 0.00 4.45
5378 7464 2.370189 GGGGAGTTCATGATACTGGGAG 59.630 54.545 13.14 0.00 0.00 4.30
5386 7472 7.118723 AGTTCATGATACTGGGAGCATTTTTA 58.881 34.615 0.00 0.00 0.00 1.52
5392 7478 3.092301 ACTGGGAGCATTTTTAGGCTTC 58.908 45.455 0.00 0.00 41.22 3.86
5399 7485 2.223044 GCATTTTTAGGCTTCTCGTCCG 60.223 50.000 0.00 0.00 0.00 4.79
5411 7497 4.031426 GCTTCTCGTCCGTTACTATGTTTG 59.969 45.833 0.00 0.00 0.00 2.93
5414 7500 5.957798 TCTCGTCCGTTACTATGTTTGATT 58.042 37.500 0.00 0.00 0.00 2.57
5415 7501 7.087409 TCTCGTCCGTTACTATGTTTGATTA 57.913 36.000 0.00 0.00 0.00 1.75
5416 7502 7.709947 TCTCGTCCGTTACTATGTTTGATTAT 58.290 34.615 0.00 0.00 0.00 1.28
5417 7503 8.192774 TCTCGTCCGTTACTATGTTTGATTATT 58.807 33.333 0.00 0.00 0.00 1.40
5418 7504 8.706492 TCGTCCGTTACTATGTTTGATTATTT 57.294 30.769 0.00 0.00 0.00 1.40
5419 7505 9.800433 TCGTCCGTTACTATGTTTGATTATTTA 57.200 29.630 0.00 0.00 0.00 1.40
5455 7544 5.626142 TGTCACCCTTTGCTTATTTACTGA 58.374 37.500 0.00 0.00 0.00 3.41
5464 7553 8.946085 CCTTTGCTTATTTACTGAATGAGTACA 58.054 33.333 0.00 0.00 36.86 2.90
5531 7620 4.572389 GCTGAAGTTCGTCATATCCAACAT 59.428 41.667 0.00 0.00 0.00 2.71
5564 7653 1.623811 GACCTACAGCCAAGGAGTCAA 59.376 52.381 3.73 0.00 37.57 3.18
5596 7685 6.407187 GGAAAGGTAGATAAGAGACCAACTCC 60.407 46.154 0.00 0.00 45.96 3.85
5598 7687 6.593759 AGGTAGATAAGAGACCAACTCCTA 57.406 41.667 0.00 0.00 45.96 2.94
5724 7813 0.601558 CTTGCAATGCTGGCTCTTGT 59.398 50.000 6.82 0.00 0.00 3.16
5733 7822 5.927281 ATGCTGGCTCTTGTCATTATTTT 57.073 34.783 0.00 0.00 0.00 1.82
5854 7949 8.642432 CCTGATATCTCATGTTGTTAAGTCCTA 58.358 37.037 3.98 0.00 0.00 2.94
5922 8024 3.070159 CAGTCTCACCTCTTTCAGAACCA 59.930 47.826 0.00 0.00 0.00 3.67
5978 8081 7.918562 GCTAACCTGTTGAATTGTTTTGAGTTA 59.081 33.333 0.00 0.00 0.00 2.24
6041 8144 4.796369 CCTATTTGGTAAAACGGCGAAAA 58.204 39.130 16.62 2.78 0.00 2.29
6136 8239 1.153369 ATGTCGCGGTGGATGAAGG 60.153 57.895 6.13 0.00 0.00 3.46
6145 8248 3.886123 CGGTGGATGAAGGGACTAATTT 58.114 45.455 0.00 0.00 38.49 1.82
6149 8252 5.893824 GGTGGATGAAGGGACTAATTTGAAT 59.106 40.000 0.00 0.00 38.49 2.57
6263 8366 2.800250 CTTTCAGCCCTTGGATTCACT 58.200 47.619 0.00 0.00 0.00 3.41
6266 8369 1.280133 TCAGCCCTTGGATTCACTCTG 59.720 52.381 0.00 0.00 0.00 3.35
6269 8372 1.680249 GCCCTTGGATTCACTCTGACC 60.680 57.143 0.00 0.00 0.00 4.02
6325 8428 6.073494 AGTCTATCATCACACGTCGAGATAAG 60.073 42.308 0.00 0.00 0.00 1.73
6529 8664 7.522073 GCCAATCAAGAACTGTTTTGAGATGTA 60.522 37.037 16.96 2.11 36.81 2.29
6533 8668 6.420903 TCAAGAACTGTTTTGAGATGTAGACG 59.579 38.462 11.46 0.00 0.00 4.18
6582 8717 7.898918 TGTAGTTAGTGGTAGCAGTATCAAAA 58.101 34.615 16.38 0.45 0.00 2.44
6583 8718 8.537016 TGTAGTTAGTGGTAGCAGTATCAAAAT 58.463 33.333 16.38 4.92 0.00 1.82
6640 8775 3.508845 ATGTAGGCCACTGTTCACTTT 57.491 42.857 5.01 0.00 0.00 2.66
6644 8779 2.233271 AGGCCACTGTTCACTTTCATG 58.767 47.619 5.01 0.00 0.00 3.07
6676 8811 1.566703 TGTGTTCTTTTGGGGTCTGGA 59.433 47.619 0.00 0.00 0.00 3.86
6680 8815 0.771127 TCTTTTGGGGTCTGGACAGG 59.229 55.000 3.10 0.00 0.00 4.00
6681 8816 0.771127 CTTTTGGGGTCTGGACAGGA 59.229 55.000 3.10 0.00 0.00 3.86
6682 8817 0.771127 TTTTGGGGTCTGGACAGGAG 59.229 55.000 3.10 0.00 0.00 3.69
6683 8818 0.401395 TTTGGGGTCTGGACAGGAGT 60.401 55.000 3.10 0.00 0.00 3.85
6684 8819 1.127567 TTGGGGTCTGGACAGGAGTG 61.128 60.000 3.10 0.00 0.00 3.51
6685 8820 2.665603 GGGTCTGGACAGGAGTGC 59.334 66.667 3.10 0.00 36.51 4.40
6686 8821 1.915769 GGGTCTGGACAGGAGTGCT 60.916 63.158 3.10 0.00 36.96 4.40
6687 8822 1.294780 GGTCTGGACAGGAGTGCTG 59.705 63.158 10.51 10.51 36.96 4.41
6688 8823 1.375268 GTCTGGACAGGAGTGCTGC 60.375 63.158 12.13 4.61 36.96 5.25
6689 8824 2.046507 CTGGACAGGAGTGCTGCC 60.047 66.667 12.13 13.91 36.96 4.85
6690 8825 2.848679 TGGACAGGAGTGCTGCCA 60.849 61.111 18.94 18.94 36.96 4.92
6691 8826 2.046507 GGACAGGAGTGCTGCCAG 60.047 66.667 12.13 0.00 32.70 4.85
6692 8827 2.746359 GACAGGAGTGCTGCCAGT 59.254 61.111 12.13 0.00 0.00 4.00
6693 8828 1.072159 GACAGGAGTGCTGCCAGTT 59.928 57.895 12.13 0.00 0.00 3.16
6694 8829 0.952984 GACAGGAGTGCTGCCAGTTC 60.953 60.000 12.13 0.00 0.00 3.01
6695 8830 1.071987 CAGGAGTGCTGCCAGTTCA 59.928 57.895 0.00 0.00 0.00 3.18
6696 8831 0.322277 CAGGAGTGCTGCCAGTTCAT 60.322 55.000 0.00 0.00 0.00 2.57
6697 8832 1.065926 CAGGAGTGCTGCCAGTTCATA 60.066 52.381 0.00 0.00 0.00 2.15
6698 8833 1.065854 AGGAGTGCTGCCAGTTCATAC 60.066 52.381 0.00 0.00 0.00 2.39
6699 8834 1.339055 GGAGTGCTGCCAGTTCATACA 60.339 52.381 0.00 0.00 0.00 2.29
6700 8835 1.734465 GAGTGCTGCCAGTTCATACAC 59.266 52.381 0.00 0.00 0.00 2.90
6701 8836 0.443869 GTGCTGCCAGTTCATACACG 59.556 55.000 0.00 0.00 0.00 4.49
6702 8837 0.320050 TGCTGCCAGTTCATACACGA 59.680 50.000 0.00 0.00 0.00 4.35
6703 8838 1.002366 GCTGCCAGTTCATACACGAG 58.998 55.000 0.00 0.00 0.00 4.18
6704 8839 1.404181 GCTGCCAGTTCATACACGAGA 60.404 52.381 0.00 0.00 0.00 4.04
6705 8840 2.534298 CTGCCAGTTCATACACGAGAG 58.466 52.381 0.00 0.00 0.00 3.20
6706 8841 2.164422 CTGCCAGTTCATACACGAGAGA 59.836 50.000 0.00 0.00 0.00 3.10
6707 8842 2.164422 TGCCAGTTCATACACGAGAGAG 59.836 50.000 0.00 0.00 0.00 3.20
6708 8843 2.480416 GCCAGTTCATACACGAGAGAGG 60.480 54.545 0.00 0.00 0.00 3.69
6709 8844 3.017442 CCAGTTCATACACGAGAGAGGA 58.983 50.000 0.00 0.00 0.00 3.71
6710 8845 3.444034 CCAGTTCATACACGAGAGAGGAA 59.556 47.826 0.00 0.00 0.00 3.36
6711 8846 4.082190 CCAGTTCATACACGAGAGAGGAAA 60.082 45.833 0.00 0.00 0.00 3.13
6712 8847 5.470368 CAGTTCATACACGAGAGAGGAAAA 58.530 41.667 0.00 0.00 0.00 2.29
6713 8848 5.574830 CAGTTCATACACGAGAGAGGAAAAG 59.425 44.000 0.00 0.00 0.00 2.27
6714 8849 5.477291 AGTTCATACACGAGAGAGGAAAAGA 59.523 40.000 0.00 0.00 0.00 2.52
6726 8861 8.244802 CGAGAGAGGAAAAGAGAGTATTTACAA 58.755 37.037 0.00 0.00 0.00 2.41
6767 8985 3.408288 TGTCTGGTTACAAAAACGCAC 57.592 42.857 0.00 0.00 0.00 5.34
6776 8994 2.869897 ACAAAAACGCACGAACACAAT 58.130 38.095 0.00 0.00 0.00 2.71
6777 8995 2.596419 ACAAAAACGCACGAACACAATG 59.404 40.909 0.00 0.00 0.00 2.82
6780 8998 0.816018 AACGCACGAACACAATGGGA 60.816 50.000 0.00 0.00 0.00 4.37
6795 9013 1.226262 GGGAATTTAGCCCGGCTCA 59.774 57.895 17.40 0.89 40.44 4.26
6798 9016 0.868406 GAATTTAGCCCGGCTCATCG 59.132 55.000 17.40 0.00 40.44 3.84
6829 9047 1.136057 CGTTCAGAAGGCCGTTAAAGC 60.136 52.381 0.00 0.00 0.00 3.51
6904 9122 1.516386 GAGTCGAAGATGCGCCGAA 60.516 57.895 4.18 0.00 40.67 4.30
6919 9137 1.208293 GCCGAAATCTCTCCTTCCACT 59.792 52.381 0.00 0.00 0.00 4.00
6920 9138 2.431057 GCCGAAATCTCTCCTTCCACTA 59.569 50.000 0.00 0.00 0.00 2.74
6922 9140 4.797933 GCCGAAATCTCTCCTTCCACTATC 60.798 50.000 0.00 0.00 0.00 2.08
6928 9146 8.800370 AAATCTCTCCTTCCACTATCTTTTTC 57.200 34.615 0.00 0.00 0.00 2.29
6930 9148 6.940739 TCTCTCCTTCCACTATCTTTTTCTG 58.059 40.000 0.00 0.00 0.00 3.02
6943 9161 3.828451 TCTTTTTCTGGAGGAAATGGCAG 59.172 43.478 0.00 0.00 42.63 4.85
6944 9162 2.978156 TTTCTGGAGGAAATGGCAGT 57.022 45.000 0.00 0.00 38.81 4.40
6964 9182 5.163519 GCAGTGTGCCTATTCATTAATTGGT 60.164 40.000 2.70 0.00 39.40 3.67
6972 9190 7.014230 TGCCTATTCATTAATTGGTTAGAAGCC 59.986 37.037 2.70 0.00 39.40 4.35
7016 9239 0.250640 CAGGACAAGGTGCAGAAGCT 60.251 55.000 0.00 0.00 42.74 3.74
7028 9259 1.615384 GCAGAAGCTCCCAAAGGACAT 60.615 52.381 0.00 0.00 37.19 3.06
7109 9340 3.708220 CTCGGTGGAGAGCTTCGGC 62.708 68.421 0.00 0.00 43.27 5.54
7119 9350 1.078848 AGCTTCGGCGCTGAAGATT 60.079 52.632 46.91 34.72 46.64 2.40
7128 9359 2.031437 GGCGCTGAAGATTCATCTTGAC 59.969 50.000 7.64 0.00 46.47 3.18
7134 9365 5.523188 GCTGAAGATTCATCTTGACGAGATT 59.477 40.000 6.79 0.00 46.47 2.40
7142 9373 7.631717 TTCATCTTGACGAGATTAGAGAGAA 57.368 36.000 2.11 0.43 42.55 2.87
7172 9403 4.210120 CGGAGATGGAATGAGATCGAAAAC 59.790 45.833 0.00 0.00 0.00 2.43
7180 9411 0.108945 GAGATCGAAAACCCCGACGT 60.109 55.000 0.00 0.00 38.97 4.34
7193 9425 0.672711 CCGACGTTTCCCTCTTTCCC 60.673 60.000 0.00 0.00 0.00 3.97
7221 9453 2.160205 CGCCCCGTATGAGAGAGATTA 58.840 52.381 0.00 0.00 0.00 1.75
7222 9454 2.557056 CGCCCCGTATGAGAGAGATTAA 59.443 50.000 0.00 0.00 0.00 1.40
7223 9455 3.366476 CGCCCCGTATGAGAGAGATTAAG 60.366 52.174 0.00 0.00 0.00 1.85
7227 9459 4.827835 CCCGTATGAGAGAGATTAAGTCCA 59.172 45.833 0.00 0.00 0.00 4.02
7228 9460 5.478679 CCCGTATGAGAGAGATTAAGTCCAT 59.521 44.000 0.00 0.00 0.00 3.41
7250 9483 4.343231 TCCAAATGGCAGCTGAAAGAATA 58.657 39.130 20.43 0.00 32.10 1.75
7251 9484 4.957954 TCCAAATGGCAGCTGAAAGAATAT 59.042 37.500 20.43 0.00 32.10 1.28
7321 9554 2.277591 GCCCATGCAGCAGGTCAAA 61.278 57.895 6.27 0.00 37.47 2.69
7322 9555 1.888018 CCCATGCAGCAGGTCAAAG 59.112 57.895 6.27 0.00 0.00 2.77
7323 9556 0.896940 CCCATGCAGCAGGTCAAAGT 60.897 55.000 6.27 0.00 0.00 2.66
7324 9557 0.524862 CCATGCAGCAGGTCAAAGTC 59.475 55.000 6.27 0.00 0.00 3.01
7325 9558 1.531423 CATGCAGCAGGTCAAAGTCT 58.469 50.000 0.00 0.00 0.00 3.24
7326 9559 2.616256 CCATGCAGCAGGTCAAAGTCTA 60.616 50.000 6.27 0.00 0.00 2.59
7328 9561 1.694150 TGCAGCAGGTCAAAGTCTAGT 59.306 47.619 0.00 0.00 0.00 2.57
7329 9562 2.104792 TGCAGCAGGTCAAAGTCTAGTT 59.895 45.455 0.00 0.00 0.00 2.24
7366 9599 1.214175 TCAGCAGTTTCCAAACTCCCA 59.786 47.619 1.52 0.00 45.65 4.37
7400 9633 3.510388 TTGGTGAGAGCAACTCTATCG 57.490 47.619 11.18 0.00 41.35 2.92
7401 9634 2.447443 TGGTGAGAGCAACTCTATCGT 58.553 47.619 11.18 0.00 41.35 3.73
7403 9636 3.377485 TGGTGAGAGCAACTCTATCGTAC 59.623 47.826 11.18 0.00 41.35 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 9.824534 GAACATTTTTGAATTGTGTGAACTTTT 57.175 25.926 0.00 0.00 0.00 2.27
50 51 8.605746 CATGAACATTTTTGAATTGTGTGAACT 58.394 29.630 0.00 0.00 0.00 3.01
227 229 9.559958 CGAGCAGTTTTTACAAATTCATAAGAT 57.440 29.630 0.00 0.00 0.00 2.40
330 334 5.861787 ACCAGTTTTTGAACTTTTCGAACTG 59.138 36.000 0.00 15.53 41.77 3.16
350 354 7.161773 ACATACTTTCCAAAATCATGACCAG 57.838 36.000 0.00 0.00 0.00 4.00
353 357 8.081633 TGTGAACATACTTTCCAAAATCATGAC 58.918 33.333 0.00 0.00 0.00 3.06
418 422 7.768582 CCCTCTTCTCTTTCTTTCCTTTCTATC 59.231 40.741 0.00 0.00 0.00 2.08
426 430 5.048364 GCTTTTCCCTCTTCTCTTTCTTTCC 60.048 44.000 0.00 0.00 0.00 3.13
442 446 5.632244 TTATTTACTGTTCCGCTTTTCCC 57.368 39.130 0.00 0.00 0.00 3.97
449 453 6.973006 TTTCGTTTTTATTTACTGTTCCGC 57.027 33.333 0.00 0.00 0.00 5.54
537 546 5.333566 TCCTTCCCCACACTTCTTTTAAT 57.666 39.130 0.00 0.00 0.00 1.40
542 551 2.041755 GGATTCCTTCCCCACACTTCTT 59.958 50.000 0.00 0.00 38.75 2.52
544 553 2.130272 GGATTCCTTCCCCACACTTC 57.870 55.000 0.00 0.00 38.75 3.01
592 601 0.605319 CATACACACCCCAACAGCGT 60.605 55.000 0.00 0.00 0.00 5.07
605 614 3.539431 ATAGCGAGCTCGTACATACAC 57.461 47.619 34.46 16.86 42.22 2.90
610 619 1.801395 GCCAAATAGCGAGCTCGTACA 60.801 52.381 34.46 21.01 42.22 2.90
611 620 0.853419 GCCAAATAGCGAGCTCGTAC 59.147 55.000 34.46 20.47 42.22 3.67
612 621 3.267900 GCCAAATAGCGAGCTCGTA 57.732 52.632 34.46 24.72 42.22 3.43
613 622 4.110493 GCCAAATAGCGAGCTCGT 57.890 55.556 34.46 23.50 42.22 4.18
863 1864 0.468029 CCCAACCCTGGTCATATGGC 60.468 60.000 2.13 0.00 41.72 4.40
882 1883 7.045416 AGTCAAAACCCCAAAGATTTTGTTAC 58.955 34.615 8.14 1.99 41.77 2.50
893 1894 5.051153 GCGAAAATTAGTCAAAACCCCAAA 58.949 37.500 0.00 0.00 0.00 3.28
925 1957 4.100529 CGACGGCGAAAATTAGTCTCTTA 58.899 43.478 16.62 0.00 40.82 2.10
928 1964 2.523015 TCGACGGCGAAAATTAGTCTC 58.477 47.619 13.07 0.00 44.78 3.36
1013 2049 0.606604 TGTCTGGTTTAGTCGGAGGC 59.393 55.000 0.00 0.00 0.00 4.70
1017 2053 2.352814 CCTCTGTGTCTGGTTTAGTCGG 60.353 54.545 0.00 0.00 0.00 4.79
1023 2059 0.765510 GGACCCTCTGTGTCTGGTTT 59.234 55.000 0.00 0.00 33.22 3.27
1152 2194 3.785859 GATGTGAGGGCGGGCTGA 61.786 66.667 0.00 0.00 0.00 4.26
1188 2230 1.006825 CATCACGAAACACGAGCGGA 61.007 55.000 0.00 0.00 45.77 5.54
1209 2251 1.000496 CGCCCGAGAACCCTATAAGTC 60.000 57.143 0.00 0.00 0.00 3.01
1213 2255 1.741327 GCACGCCCGAGAACCCTATA 61.741 60.000 0.00 0.00 0.00 1.31
1236 2284 0.801451 CTGCACGCAAAGCAAACACA 60.801 50.000 0.00 0.00 42.17 3.72
1238 2286 1.226916 CCTGCACGCAAAGCAAACA 60.227 52.632 0.00 0.00 42.17 2.83
1280 2330 3.948719 GTCGCCACAACCTCCCCA 61.949 66.667 0.00 0.00 0.00 4.96
1378 2428 1.323271 TGCTAGAGCGGAGAACAGGG 61.323 60.000 0.00 0.00 45.83 4.45
1403 2453 0.813184 ACCAATCAAATCGCTGGCTG 59.187 50.000 0.00 0.00 31.74 4.85
1404 2454 1.549203 AACCAATCAAATCGCTGGCT 58.451 45.000 0.00 0.00 31.74 4.75
1405 2455 2.094545 AGAAACCAATCAAATCGCTGGC 60.095 45.455 0.00 0.00 31.74 4.85
1430 2480 3.664888 AGCATTGCCAGGCAGGGA 61.665 61.111 15.50 0.00 40.61 4.20
1443 2493 2.662535 TGCCATAGTAATGCCAGCAT 57.337 45.000 0.00 0.00 38.46 3.79
1449 2504 1.466167 CTCGGCATGCCATAGTAATGC 59.534 52.381 34.93 5.36 44.75 3.56
1464 2519 3.547613 CGTAGACCATTGTACTACTCGGC 60.548 52.174 0.00 0.00 35.69 5.54
1517 2572 7.195646 CGCACTACAATAATCCATTCACAAAT 58.804 34.615 0.00 0.00 0.00 2.32
1518 2573 6.550843 CGCACTACAATAATCCATTCACAAA 58.449 36.000 0.00 0.00 0.00 2.83
1570 2632 1.002624 TGCTCGAATCCAACACCCC 60.003 57.895 0.00 0.00 0.00 4.95
1571 2633 1.026718 CCTGCTCGAATCCAACACCC 61.027 60.000 0.00 0.00 0.00 4.61
1572 2634 1.026718 CCCTGCTCGAATCCAACACC 61.027 60.000 0.00 0.00 0.00 4.16
1608 2670 7.361457 ACCCAAATATCTAGAGTTCGATTCA 57.639 36.000 0.00 0.00 0.00 2.57
1645 2713 8.784043 CCTGCCCTGTAAATCAATTAGTATAAC 58.216 37.037 0.00 0.00 0.00 1.89
1651 2719 4.792068 TCCCTGCCCTGTAAATCAATTAG 58.208 43.478 0.00 0.00 0.00 1.73
1663 2731 1.751927 GAATGCACTCCCTGCCCTG 60.752 63.158 0.00 0.00 46.51 4.45
1670 2738 4.390264 GAATTAGGGTAGAATGCACTCCC 58.610 47.826 0.00 0.00 34.82 4.30
1671 2739 4.058817 CGAATTAGGGTAGAATGCACTCC 58.941 47.826 0.00 0.00 34.82 3.85
1673 2741 4.755266 ACGAATTAGGGTAGAATGCACT 57.245 40.909 0.00 0.00 38.69 4.40
1693 2780 3.685836 ACAAACAACTACGCCTTCAAC 57.314 42.857 0.00 0.00 0.00 3.18
1694 2781 4.156190 TCAAACAAACAACTACGCCTTCAA 59.844 37.500 0.00 0.00 0.00 2.69
1702 2789 9.691362 ACCAATGATAATCAAACAAACAACTAC 57.309 29.630 0.00 0.00 0.00 2.73
1731 2819 9.076596 GCTTATTTTTACCATCTGTCAATTGAC 57.923 33.333 28.10 28.10 44.97 3.18
1732 2820 8.250332 GGCTTATTTTTACCATCTGTCAATTGA 58.750 33.333 3.38 3.38 0.00 2.57
1733 2821 8.253113 AGGCTTATTTTTACCATCTGTCAATTG 58.747 33.333 0.00 0.00 0.00 2.32
1734 2822 8.366359 AGGCTTATTTTTACCATCTGTCAATT 57.634 30.769 0.00 0.00 0.00 2.32
1736 2824 7.669722 AGAAGGCTTATTTTTACCATCTGTCAA 59.330 33.333 0.00 0.00 29.52 3.18
2050 3152 1.156095 CAAATGGCCCCTATCCCCC 59.844 63.158 0.00 0.00 0.00 5.40
2051 3153 0.786435 ATCAAATGGCCCCTATCCCC 59.214 55.000 0.00 0.00 0.00 4.81
2052 3154 2.110721 AGAATCAAATGGCCCCTATCCC 59.889 50.000 0.00 0.00 0.00 3.85
2057 3159 4.337264 AAAGTAGAATCAAATGGCCCCT 57.663 40.909 0.00 0.00 0.00 4.79
2112 3214 7.017056 AGCCTAGCTAGAAGTCATCCATAATTT 59.983 37.037 22.70 0.00 36.99 1.82
2113 3215 6.500049 AGCCTAGCTAGAAGTCATCCATAATT 59.500 38.462 22.70 0.00 36.99 1.40
2114 3216 6.022315 AGCCTAGCTAGAAGTCATCCATAAT 58.978 40.000 22.70 0.00 36.99 1.28
2115 3217 5.398236 AGCCTAGCTAGAAGTCATCCATAA 58.602 41.667 22.70 0.00 36.99 1.90
2116 3218 5.004361 AGCCTAGCTAGAAGTCATCCATA 57.996 43.478 22.70 0.00 36.99 2.74
2117 3219 3.855668 AGCCTAGCTAGAAGTCATCCAT 58.144 45.455 22.70 0.00 36.99 3.41
2118 3220 3.320610 AGCCTAGCTAGAAGTCATCCA 57.679 47.619 22.70 0.00 36.99 3.41
2119 3221 4.321675 GCTAAGCCTAGCTAGAAGTCATCC 60.322 50.000 22.70 0.04 46.12 3.51
2120 3222 4.805219 GCTAAGCCTAGCTAGAAGTCATC 58.195 47.826 22.70 2.12 46.12 2.92
2121 3223 4.864704 GCTAAGCCTAGCTAGAAGTCAT 57.135 45.455 22.70 4.75 46.12 3.06
2160 3264 6.208599 CCTTTCTGTGGCTTATACCTGAAAAA 59.791 38.462 0.00 0.00 0.00 1.94
2193 3297 1.732259 CTCACTGACACGGCCAATAAC 59.268 52.381 2.24 0.00 0.00 1.89
2219 3323 2.432146 TGAGAGAGTGACACAAAGTGCT 59.568 45.455 8.59 0.00 36.98 4.40
2241 3345 9.533831 ACCATGTTATAAAAAGGAGAAGAACAT 57.466 29.630 3.88 0.00 36.88 2.71
2252 3356 9.627123 TCCTATCAGGAACCATGTTATAAAAAG 57.373 33.333 0.00 0.00 42.51 2.27
2273 3377 4.290093 TCAGGTGTGTAGCTCATTCCTAT 58.710 43.478 0.00 0.00 33.38 2.57
2282 3386 7.663905 TGTTTTATTACATTCAGGTGTGTAGCT 59.336 33.333 0.00 0.00 32.87 3.32
2406 3510 0.323629 TTAACCAGGCAAGGACCTCG 59.676 55.000 0.00 0.00 38.26 4.63
2462 3567 3.490759 GCATGCCACCAGTCGACG 61.491 66.667 6.36 5.16 0.00 5.12
2484 3589 1.598701 GCTGCTTTGGGGTGATGGTC 61.599 60.000 0.00 0.00 0.00 4.02
2488 3593 0.698238 TGTAGCTGCTTTGGGGTGAT 59.302 50.000 7.79 0.00 0.00 3.06
2501 3606 0.916358 ATCCAGCCCCTTGTGTAGCT 60.916 55.000 0.00 0.00 35.52 3.32
2525 3630 4.219288 GCATCCAGGATATCAAAATGGTCC 59.781 45.833 0.00 0.00 32.68 4.46
2653 3758 1.201429 ATCACCCGAAGCCCAAGAGT 61.201 55.000 0.00 0.00 0.00 3.24
2840 4409 5.654497 GGAAAACTGATTGTCCAATCCATC 58.346 41.667 15.44 7.79 44.93 3.51
3066 4635 4.698575 TGCAGGGGAAAAACACATTTAAC 58.301 39.130 0.00 0.00 0.00 2.01
3119 4688 3.827722 ACAGCACCTTGGCTAAAGTTTA 58.172 40.909 0.00 0.00 43.68 2.01
3296 4865 2.045561 TGTCCCACACACGTTTTCAT 57.954 45.000 0.00 0.00 0.00 2.57
3425 4996 5.303589 AGACACTGGTACAAGCTACTGTTAA 59.696 40.000 0.00 0.00 38.70 2.01
4216 5787 3.624861 GTGCAAGATTGACTGGTGGATAG 59.375 47.826 0.00 0.00 0.00 2.08
4265 5836 1.138859 CAAGTGAGATATCGGGGCACA 59.861 52.381 17.21 3.95 32.16 4.57
4293 5864 5.221661 CCTTCTATTACTAGCCGAACCCATT 60.222 44.000 0.00 0.00 0.00 3.16
4320 5891 4.889409 TCCACTCTGTTGCAAGATTTCTTT 59.111 37.500 0.00 0.00 33.11 2.52
4520 6091 5.012239 TCTCCTATATTTGCATCCCATTGC 58.988 41.667 0.00 0.00 43.07 3.56
4529 6100 6.345298 TGATTTGTCGTCTCCTATATTTGCA 58.655 36.000 0.00 0.00 0.00 4.08
4547 6118 6.154445 CACCCTCTTTCATTGTTCTGATTTG 58.846 40.000 0.00 0.00 0.00 2.32
4620 6191 1.003928 TGCTGCAGTGATGTTGATCCT 59.996 47.619 16.64 0.00 0.00 3.24
4665 6236 2.170607 ACACTTTGTGTACTGTGCTCCT 59.829 45.455 1.12 0.00 45.56 3.69
4675 6246 5.620206 AGATGACATGGAACACTTTGTGTA 58.380 37.500 3.68 0.00 46.79 2.90
4828 6401 9.797556 GTACACTTTCTGGTCTTATTTGTTTTT 57.202 29.630 0.00 0.00 0.00 1.94
5026 6625 4.220693 TGATGGTAGTTCATTGACCTGG 57.779 45.455 0.00 0.00 34.13 4.45
5192 7278 8.303156 ACTAAATTCTCTACATCATGAGATCCG 58.697 37.037 0.09 0.00 38.85 4.18
5219 7305 7.936847 ACACAGAAGTCATACTCCAAAAATACA 59.063 33.333 0.00 0.00 0.00 2.29
5272 7358 5.964958 ATGAACAAACATCCTGGTTACAG 57.035 39.130 0.00 0.00 44.51 2.74
5346 7432 6.152638 TCATGAACTCCCCTAAGGAAAAAT 57.847 37.500 0.00 0.00 46.94 1.82
5372 7458 3.359950 AGAAGCCTAAAAATGCTCCCAG 58.640 45.455 0.00 0.00 36.66 4.45
5376 7462 3.064134 GGACGAGAAGCCTAAAAATGCTC 59.936 47.826 0.00 0.00 36.66 4.26
5378 7464 2.223044 CGGACGAGAAGCCTAAAAATGC 60.223 50.000 0.00 0.00 0.00 3.56
5386 7472 2.119801 TAGTAACGGACGAGAAGCCT 57.880 50.000 0.00 0.00 0.00 4.58
5392 7478 7.925703 ATAATCAAACATAGTAACGGACGAG 57.074 36.000 0.00 0.00 0.00 4.18
5419 7505 9.255029 AGCAAAGGGTGACAAACTATAATAAAT 57.745 29.630 0.00 0.00 0.00 1.40
5420 7506 8.644374 AGCAAAGGGTGACAAACTATAATAAA 57.356 30.769 0.00 0.00 0.00 1.40
5421 7507 8.644374 AAGCAAAGGGTGACAAACTATAATAA 57.356 30.769 0.00 0.00 0.00 1.40
5422 7508 9.914834 ATAAGCAAAGGGTGACAAACTATAATA 57.085 29.630 0.00 0.00 0.00 0.98
5423 7509 8.823220 ATAAGCAAAGGGTGACAAACTATAAT 57.177 30.769 0.00 0.00 0.00 1.28
5455 7544 8.671921 CAGCATCAGATTTAAACTGTACTCATT 58.328 33.333 13.77 0.00 36.81 2.57
5464 7553 7.391554 TCAAAGTAGCAGCATCAGATTTAAACT 59.608 33.333 0.00 0.00 0.00 2.66
5531 7620 3.386078 GCTGTAGGTCAAGAGATCCATCA 59.614 47.826 0.00 0.00 0.00 3.07
5596 7685 9.862371 CACTACCCAATAATAATAGCTGACTAG 57.138 37.037 0.00 0.00 0.00 2.57
5598 7687 7.016661 AGCACTACCCAATAATAATAGCTGACT 59.983 37.037 0.00 0.00 0.00 3.41
5755 7844 3.606687 GGGTAATCAACATCGACCAACT 58.393 45.455 0.00 0.00 31.41 3.16
5807 7896 9.770097 ATCAGGACTTAACATGTATATGAACTG 57.230 33.333 6.45 3.50 37.73 3.16
5922 8024 0.828762 TTGCCACAGGAAGCAATGCT 60.829 50.000 0.00 0.00 43.74 3.79
5978 8081 1.340795 CCCCTCTGAAGCTGCAAAGAT 60.341 52.381 0.00 0.00 0.00 2.40
6041 8144 3.380637 GCTCAAGATGATGGAAATGCTGT 59.619 43.478 0.00 0.00 0.00 4.40
6124 8227 3.560636 AATTAGTCCCTTCATCCACCG 57.439 47.619 0.00 0.00 0.00 4.94
6263 8366 3.066342 GGATTATCAGTTCGACGGTCAGA 59.934 47.826 9.10 3.93 0.00 3.27
6266 8369 3.066342 TCTGGATTATCAGTTCGACGGTC 59.934 47.826 0.00 0.00 36.25 4.79
6269 8372 3.372954 GGTCTGGATTATCAGTTCGACG 58.627 50.000 0.00 0.00 36.25 5.12
6529 8664 1.302033 CAGGGTTGAGCAAGCGTCT 60.302 57.895 4.83 0.00 39.53 4.18
6533 8668 2.970974 GCGACAGGGTTGAGCAAGC 61.971 63.158 3.94 3.94 38.03 4.01
6582 8717 3.875125 TCTCCGTCGATAGCAGCTATAT 58.125 45.455 15.28 0.00 0.00 0.86
6583 8718 3.329929 TCTCCGTCGATAGCAGCTATA 57.670 47.619 15.28 0.00 0.00 1.31
6668 8803 1.915769 AGCACTCCTGTCCAGACCC 60.916 63.158 0.00 0.00 0.00 4.46
6671 8806 2.587247 GGCAGCACTCCTGTCCAGA 61.587 63.158 0.00 0.00 43.71 3.86
6676 8811 1.072159 GAACTGGCAGCACTCCTGT 59.928 57.895 15.89 0.00 43.71 4.00
6680 8815 1.734465 GTGTATGAACTGGCAGCACTC 59.266 52.381 15.89 9.56 0.00 3.51
6681 8816 1.813513 GTGTATGAACTGGCAGCACT 58.186 50.000 15.89 0.00 0.00 4.40
6682 8817 0.443869 CGTGTATGAACTGGCAGCAC 59.556 55.000 15.89 12.15 0.00 4.40
6683 8818 0.320050 TCGTGTATGAACTGGCAGCA 59.680 50.000 15.89 5.77 0.00 4.41
6684 8819 1.002366 CTCGTGTATGAACTGGCAGC 58.998 55.000 15.89 0.00 0.00 5.25
6685 8820 2.164422 TCTCTCGTGTATGAACTGGCAG 59.836 50.000 14.16 14.16 0.00 4.85
6686 8821 2.164422 CTCTCTCGTGTATGAACTGGCA 59.836 50.000 0.00 0.00 0.00 4.92
6687 8822 2.480416 CCTCTCTCGTGTATGAACTGGC 60.480 54.545 0.00 0.00 0.00 4.85
6688 8823 3.017442 TCCTCTCTCGTGTATGAACTGG 58.983 50.000 0.00 0.00 0.00 4.00
6689 8824 4.703645 TTCCTCTCTCGTGTATGAACTG 57.296 45.455 0.00 0.00 0.00 3.16
6690 8825 5.477291 TCTTTTCCTCTCTCGTGTATGAACT 59.523 40.000 0.00 0.00 0.00 3.01
6691 8826 5.710984 TCTTTTCCTCTCTCGTGTATGAAC 58.289 41.667 0.00 0.00 0.00 3.18
6692 8827 5.710567 TCTCTTTTCCTCTCTCGTGTATGAA 59.289 40.000 0.00 0.00 0.00 2.57
6693 8828 5.254115 TCTCTTTTCCTCTCTCGTGTATGA 58.746 41.667 0.00 0.00 0.00 2.15
6694 8829 5.124776 ACTCTCTTTTCCTCTCTCGTGTATG 59.875 44.000 0.00 0.00 0.00 2.39
6695 8830 5.258051 ACTCTCTTTTCCTCTCTCGTGTAT 58.742 41.667 0.00 0.00 0.00 2.29
6696 8831 4.653868 ACTCTCTTTTCCTCTCTCGTGTA 58.346 43.478 0.00 0.00 0.00 2.90
6697 8832 3.492337 ACTCTCTTTTCCTCTCTCGTGT 58.508 45.455 0.00 0.00 0.00 4.49
6698 8833 5.828299 ATACTCTCTTTTCCTCTCTCGTG 57.172 43.478 0.00 0.00 0.00 4.35
6699 8834 6.844097 AAATACTCTCTTTTCCTCTCTCGT 57.156 37.500 0.00 0.00 0.00 4.18
6700 8835 7.763356 TGTAAATACTCTCTTTTCCTCTCTCG 58.237 38.462 0.00 0.00 0.00 4.04
6701 8836 9.581099 CTTGTAAATACTCTCTTTTCCTCTCTC 57.419 37.037 0.00 0.00 0.00 3.20
6702 8837 9.315363 TCTTGTAAATACTCTCTTTTCCTCTCT 57.685 33.333 0.00 0.00 0.00 3.10
6726 8861 8.504005 CAGACATTTCGTGGTTACTTTTTATCT 58.496 33.333 0.00 0.00 0.00 1.98
6742 8960 4.145756 GCGTTTTTGTAACCAGACATTTCG 59.854 41.667 0.00 0.00 0.00 3.46
6747 8965 2.223066 CGTGCGTTTTTGTAACCAGACA 60.223 45.455 0.00 0.00 0.00 3.41
6767 8985 3.428862 GGGCTAAATTCCCATTGTGTTCG 60.429 47.826 0.00 0.00 43.37 3.95
6776 8994 1.226262 GAGCCGGGCTAAATTCCCA 59.774 57.895 23.92 0.00 44.11 4.37
6777 8995 0.178990 ATGAGCCGGGCTAAATTCCC 60.179 55.000 23.92 8.17 39.88 3.97
6780 8998 0.180406 ACGATGAGCCGGGCTAAATT 59.820 50.000 23.92 6.87 39.88 1.82
6795 9013 2.031420 TCTGAACGACGAAACTGACGAT 60.031 45.455 0.00 0.00 34.70 3.73
6798 9016 2.471743 CCTTCTGAACGACGAAACTGAC 59.528 50.000 0.00 0.00 0.00 3.51
6829 9047 2.047560 GAACGACCGGTCCAAGGG 60.048 66.667 28.52 16.36 0.00 3.95
6904 9122 8.046107 CAGAAAAAGATAGTGGAAGGAGAGATT 58.954 37.037 0.00 0.00 0.00 2.40
6928 9146 1.171308 CACACTGCCATTTCCTCCAG 58.829 55.000 0.00 0.00 0.00 3.86
6930 9148 1.885871 GCACACTGCCATTTCCTCC 59.114 57.895 0.00 0.00 37.42 4.30
6943 9161 8.220755 TCTAACCAATTAATGAATAGGCACAC 57.779 34.615 0.00 0.00 0.00 3.82
6944 9162 8.815565 TTCTAACCAATTAATGAATAGGCACA 57.184 30.769 0.00 0.00 0.00 4.57
6984 9202 6.100004 CACCTTGTCCTGTACATAACTGTAG 58.900 44.000 0.00 0.00 38.51 2.74
6999 9222 0.957888 GGAGCTTCTGCACCTTGTCC 60.958 60.000 0.00 0.00 44.80 4.02
7016 9239 2.661176 AGGTCCTATGTCCTTTGGGA 57.339 50.000 0.00 0.00 39.70 4.37
7072 9303 1.714899 GCGGTTGTTCGATGATGGGG 61.715 60.000 0.00 0.00 0.00 4.96
7119 9350 7.284261 ACATTCTCTCTAATCTCGTCAAGATGA 59.716 37.037 0.00 0.00 44.26 2.92
7142 9373 3.963374 TCTCATTCCATCTCCGAGAACAT 59.037 43.478 1.27 0.00 30.04 2.71
7153 9384 3.565902 GGGGTTTTCGATCTCATTCCATC 59.434 47.826 0.00 0.00 0.00 3.51
7154 9385 3.555966 GGGGTTTTCGATCTCATTCCAT 58.444 45.455 0.00 0.00 0.00 3.41
7155 9386 2.679639 CGGGGTTTTCGATCTCATTCCA 60.680 50.000 0.00 0.00 0.00 3.53
7156 9387 1.940613 CGGGGTTTTCGATCTCATTCC 59.059 52.381 0.00 0.00 0.00 3.01
7157 9388 2.608090 GTCGGGGTTTTCGATCTCATTC 59.392 50.000 0.00 0.00 38.93 2.67
7180 9411 2.247358 GCACATTGGGAAAGAGGGAAA 58.753 47.619 0.00 0.00 0.00 3.13
7193 9425 2.515991 ATACGGGGCGGCACATTG 60.516 61.111 13.33 0.00 0.00 2.82
7206 9438 6.207614 TGGATGGACTTAATCTCTCTCATACG 59.792 42.308 0.00 0.00 0.00 3.06
7227 9459 2.811410 TCTTTCAGCTGCCATTTGGAT 58.189 42.857 9.47 0.00 37.39 3.41
7228 9460 2.291209 TCTTTCAGCTGCCATTTGGA 57.709 45.000 9.47 0.00 37.39 3.53
7321 9554 4.027437 GACTGGGATGAGGAAACTAGACT 58.973 47.826 0.00 0.00 44.43 3.24
7322 9555 3.769844 TGACTGGGATGAGGAAACTAGAC 59.230 47.826 0.00 0.00 44.43 2.59
7323 9556 4.026744 CTGACTGGGATGAGGAAACTAGA 58.973 47.826 0.00 0.00 44.43 2.43
7324 9557 3.772025 ACTGACTGGGATGAGGAAACTAG 59.228 47.826 0.00 0.00 44.43 2.57
7325 9558 3.769844 GACTGACTGGGATGAGGAAACTA 59.230 47.826 0.00 0.00 44.43 2.24
7328 9561 2.568956 CTGACTGACTGGGATGAGGAAA 59.431 50.000 0.00 0.00 0.00 3.13
7329 9562 2.182827 CTGACTGACTGGGATGAGGAA 58.817 52.381 0.00 0.00 0.00 3.36
7366 9599 3.070018 CTCACCAAAACTGCTTCTCGAT 58.930 45.455 0.00 0.00 0.00 3.59



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

AutoCloner maintained by Alex Coulton.