Multiple sequence alignment - TraesCS6A01G113000

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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 TraesCS6A01G113000 chr6A 100.000 8876 0 0 1 8876 83250488 83259363 0.000000e+00 16391.0
1 TraesCS6A01G113000 chr6D 93.801 8776 334 107 191 8876 65506169 65497514 0.000000e+00 12999.0
2 TraesCS6A01G113000 chr6D 80.919 283 41 8 7124 7396 63762171 63761892 2.510000e-50 211.0
3 TraesCS6A01G113000 chr6B 95.524 6435 183 34 2495 8876 140603194 140596812 0.000000e+00 10190.0
4 TraesCS6A01G113000 chr6B 89.607 2444 154 56 1 2382 140605711 140603306 0.000000e+00 3014.0
5 TraesCS6A01G113000 chr7B 84.444 135 21 0 4199 4333 565913116 565912982 5.590000e-27 134.0
6 TraesCS6A01G113000 chr7A 84.444 135 21 0 4199 4333 608402519 608402385 5.590000e-27 134.0
7 TraesCS6A01G113000 chr7D 87.736 106 13 0 1206 1311 112046617 112046722 3.360000e-24 124.0
8 TraesCS6A01G113000 chr2A 85.047 107 14 2 1206 1311 724297748 724297853 3.390000e-19 108.0
9 TraesCS6A01G113000 chr2A 92.500 40 2 1 265 303 35527947 35527986 1.000000e-03 56.5
10 TraesCS6A01G113000 chr5D 100.000 39 0 0 265 303 68233081 68233043 1.240000e-08 73.1
11 TraesCS6A01G113000 chr5D 95.000 40 1 1 265 303 68091469 68091508 2.680000e-05 62.1
12 TraesCS6A01G113000 chr5B 95.000 40 1 1 265 303 301544471 301544510 2.680000e-05 62.1
13 TraesCS6A01G113000 chr4A 97.222 36 1 0 268 303 41917323 41917288 2.680000e-05 62.1
14 TraesCS6A01G113000 chr1D 95.000 40 1 1 265 303 452260460 452260421 2.680000e-05 62.1


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 TraesCS6A01G113000 chr6A 83250488 83259363 8875 False 16391 16391 100.0000 1 8876 1 chr6A.!!$F1 8875
1 TraesCS6A01G113000 chr6D 65497514 65506169 8655 True 12999 12999 93.8010 191 8876 1 chr6D.!!$R2 8685
2 TraesCS6A01G113000 chr6B 140596812 140605711 8899 True 6602 10190 92.5655 1 8876 2 chr6B.!!$R1 8875

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
109 118 0.305313 TTTCAGTTTACACGCGCACC 59.695 50.000 5.73 0.0 0.00 5.01 F
1704 1787 0.256177 CCTCCCTTTGGGCCTACTTC 59.744 60.000 4.53 0.0 43.94 3.01 F
1876 1959 0.102844 TTCTGCACTGCCAAAACAGC 59.897 50.000 0.00 0.0 41.60 4.40 F
2571 2705 0.516877 TGCAAAAGGATGTCGAAGCG 59.483 50.000 0.00 0.0 0.00 4.68 F
2840 2983 0.877071 CTCTGCGTGTTTCCAATGCT 59.123 50.000 0.00 0.0 0.00 3.79 F
3434 3577 1.407299 CCATGCTTCCGTCCATCTTCA 60.407 52.381 0.00 0.0 0.00 3.02 F
4910 5073 1.075374 ACAATGCCTGGCCTGAGTTTA 59.925 47.619 20.88 0.0 0.00 2.01 F
5768 5931 0.885879 CCATTCAGCAAGAGCAGCAA 59.114 50.000 0.00 0.0 45.49 3.91 F
5771 5934 0.949397 TTCAGCAAGAGCAGCAACAG 59.051 50.000 0.00 0.0 45.49 3.16 F
7095 7269 1.546029 GAAGGGTCAGTTGGAAATGCC 59.454 52.381 0.00 0.0 37.10 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1868 1951 0.105408 AAAGCAGGCAGGCTGTTTTG 59.895 50.000 30.17 12.69 45.07 2.44 R
2743 2886 0.249031 TCATCTGCGCATACACCTCG 60.249 55.000 12.24 0.00 0.00 4.63 R
2755 2898 1.066286 ACTGGCTGAAGAGTCATCTGC 60.066 52.381 16.25 16.25 39.99 4.26 R
4116 4261 1.336125 GAGCTGCAATTAGGATGGTGC 59.664 52.381 1.02 0.00 37.51 5.01 R
4319 4478 4.222124 ACCAGACTTACCTAATTGCCTG 57.778 45.455 0.00 0.00 0.00 4.85 R
5177 5340 4.190001 GCTGATCTTGCTTCTGATCTTGA 58.810 43.478 0.00 0.00 39.63 3.02 R
5881 6044 0.108186 TGCAGCACCAGGAACTATCG 60.108 55.000 0.00 0.00 36.02 2.92 R
7336 7535 1.062206 GCCGAGAAGTAGGACGTCG 59.938 63.158 9.92 0.00 31.81 5.12 R
7692 7891 3.264193 ACAGGATCCTAATGCACTTCACA 59.736 43.478 15.67 0.00 0.00 3.58 R
8367 8566 1.586154 GGCCGACAGGTCCATTTGTG 61.586 60.000 0.00 0.00 40.50 3.33 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
54 63 7.203218 TGTCATAGTGAAAGATGAATAGGTCG 58.797 38.462 0.00 0.00 33.96 4.79
65 74 6.712276 AGATGAATAGGTCGGAAGTTTTCTT 58.288 36.000 0.00 0.00 43.55 2.52
67 76 5.860611 TGAATAGGTCGGAAGTTTTCTTGA 58.139 37.500 0.00 0.00 40.61 3.02
72 81 5.891451 AGGTCGGAAGTTTTCTTGAAAAAG 58.109 37.500 9.71 0.00 40.61 2.27
74 83 5.971792 GGTCGGAAGTTTTCTTGAAAAAGAG 59.028 40.000 9.71 2.37 40.61 2.85
87 96 4.067896 TGAAAAAGAGCTAGCAAGACTGG 58.932 43.478 18.83 0.00 0.00 4.00
91 100 3.778954 AGAGCTAGCAAGACTGGTTTT 57.221 42.857 18.83 0.00 34.40 2.43
108 117 2.093972 TTTTCAGTTTACACGCGCAC 57.906 45.000 5.73 0.00 0.00 5.34
109 118 0.305313 TTTCAGTTTACACGCGCACC 59.695 50.000 5.73 0.00 0.00 5.01
129 138 8.233868 GCGCACCAAAAATATTTATTCCTTTTT 58.766 29.630 0.30 0.00 32.57 1.94
130 139 9.753669 CGCACCAAAAATATTTATTCCTTTTTC 57.246 29.630 0.01 0.00 30.58 2.29
140 149 7.770366 ATTTATTCCTTTTTCACTAACCGGT 57.230 32.000 0.00 0.00 0.00 5.28
146 155 4.502604 CCTTTTTCACTAACCGGTCTCTCA 60.503 45.833 8.04 0.00 0.00 3.27
147 156 4.884668 TTTTCACTAACCGGTCTCTCAT 57.115 40.909 8.04 0.00 0.00 2.90
158 167 2.101415 CGGTCTCTCATAATGCCAGTCA 59.899 50.000 0.00 0.00 0.00 3.41
163 172 3.473625 TCTCATAATGCCAGTCATGCAG 58.526 45.455 0.00 0.00 42.92 4.41
164 173 3.135167 TCTCATAATGCCAGTCATGCAGA 59.865 43.478 0.00 0.00 42.92 4.26
165 174 3.881089 CTCATAATGCCAGTCATGCAGAA 59.119 43.478 0.00 0.00 42.92 3.02
166 175 4.466827 TCATAATGCCAGTCATGCAGAAT 58.533 39.130 0.00 0.00 42.92 2.40
167 176 4.891168 TCATAATGCCAGTCATGCAGAATT 59.109 37.500 0.00 0.00 42.92 2.17
168 177 5.361571 TCATAATGCCAGTCATGCAGAATTT 59.638 36.000 0.00 0.00 42.92 1.82
263 273 3.004106 GGCATGTCATCTTCAATGCTACC 59.996 47.826 6.46 0.00 35.57 3.18
312 322 5.965334 CGTGGTTTTAGTTCACATGATATGC 59.035 40.000 0.00 0.00 0.00 3.14
355 370 5.048013 AGGTTCGAGTGGATGAAAATTTTCC 60.048 40.000 24.51 13.33 36.36 3.13
356 371 4.678509 TCGAGTGGATGAAAATTTTCCG 57.321 40.909 24.51 18.62 36.36 4.30
362 377 7.467267 CGAGTGGATGAAAATTTTCCGATACAT 60.467 37.037 24.51 12.95 36.36 2.29
561 591 3.650139 TCGAGCCTCACTTCACTAAAAC 58.350 45.455 0.00 0.00 0.00 2.43
562 592 2.408704 CGAGCCTCACTTCACTAAAACG 59.591 50.000 0.00 0.00 0.00 3.60
563 593 2.737252 GAGCCTCACTTCACTAAAACGG 59.263 50.000 0.00 0.00 0.00 4.44
564 594 2.367567 AGCCTCACTTCACTAAAACGGA 59.632 45.455 0.00 0.00 0.00 4.69
565 595 2.737252 GCCTCACTTCACTAAAACGGAG 59.263 50.000 0.00 0.00 0.00 4.63
567 597 4.560108 GCCTCACTTCACTAAAACGGAGTA 60.560 45.833 0.00 0.00 45.00 2.59
738 802 1.073923 CCTCTCTCTCTAGCTCCCTCC 59.926 61.905 0.00 0.00 0.00 4.30
906 970 1.991167 GGTGTCCGGGACCCATACA 60.991 63.158 23.81 11.07 0.00 2.29
914 978 1.828979 GGGACCCATACAGCGAAAAA 58.171 50.000 5.33 0.00 0.00 1.94
990 1066 2.892334 GCAAGCTTCCGCGTGTGAA 61.892 57.895 4.92 0.04 45.63 3.18
1059 1135 4.886351 GGCTCCATGCGAAGGTACTTGT 62.886 54.545 0.00 0.00 46.07 3.16
1329 1405 3.119316 GGTGTGTGAGTGAGACCTATCTG 60.119 52.174 0.00 0.00 34.34 2.90
1330 1406 3.508012 GTGTGTGAGTGAGACCTATCTGT 59.492 47.826 0.00 0.00 34.34 3.41
1332 1408 4.218635 TGTGTGAGTGAGACCTATCTGTTC 59.781 45.833 0.00 0.00 34.34 3.18
1335 1411 1.751924 AGTGAGACCTATCTGTTCGCC 59.248 52.381 0.00 0.00 34.34 5.54
1385 1464 2.716217 CTCCCCATGGTTCTGTTCTTC 58.284 52.381 11.73 0.00 0.00 2.87
1463 1544 8.129840 TGCTCTATACTTCTTTTAGAGTAAGCG 58.870 37.037 7.73 0.00 40.59 4.68
1468 1549 6.541111 ACTTCTTTTAGAGTAAGCGTTTGG 57.459 37.500 0.00 0.00 0.00 3.28
1473 1554 7.412063 TCTTTTAGAGTAAGCGTTTGGTTTTC 58.588 34.615 0.00 0.00 37.03 2.29
1475 1556 4.547406 AGAGTAAGCGTTTGGTTTTCAC 57.453 40.909 0.00 0.00 37.03 3.18
1478 1559 5.124936 AGAGTAAGCGTTTGGTTTTCACTTT 59.875 36.000 0.00 0.00 37.03 2.66
1481 1562 6.748658 AGTAAGCGTTTGGTTTTCACTTTTAC 59.251 34.615 0.00 0.00 37.03 2.01
1539 1622 7.177392 CCTTTGAAGTTCAAGAGGGTTCATAAT 59.823 37.037 24.61 0.00 37.70 1.28
1589 1672 6.916440 TGCTATCATGGATATGTTGCATTTC 58.084 36.000 0.00 0.00 33.53 2.17
1613 1696 4.040755 AGTAGTTGTGATTGGAGGGCTAT 58.959 43.478 0.00 0.00 0.00 2.97
1614 1697 5.070446 CAGTAGTTGTGATTGGAGGGCTATA 59.930 44.000 0.00 0.00 0.00 1.31
1615 1698 4.423625 AGTTGTGATTGGAGGGCTATAC 57.576 45.455 0.00 0.00 0.00 1.47
1686 1769 2.671682 GAGGAGTGGTTGGGAGCC 59.328 66.667 0.00 0.00 0.00 4.70
1687 1770 1.920835 GAGGAGTGGTTGGGAGCCT 60.921 63.158 0.00 0.00 0.00 4.58
1688 1771 1.904990 GAGGAGTGGTTGGGAGCCTC 61.905 65.000 0.00 0.00 35.63 4.70
1689 1772 2.671682 GAGTGGTTGGGAGCCTCC 59.328 66.667 0.73 0.73 35.23 4.30
1704 1787 0.256177 CCTCCCTTTGGGCCTACTTC 59.744 60.000 4.53 0.00 43.94 3.01
1733 1816 1.756538 CCTTCTGTTGGCTTTTGGTGT 59.243 47.619 0.00 0.00 0.00 4.16
1739 1822 2.094286 TGTTGGCTTTTGGTGTCTTGTG 60.094 45.455 0.00 0.00 0.00 3.33
1751 1834 3.181474 GGTGTCTTGTGGAGTATAGGAGC 60.181 52.174 0.00 0.00 0.00 4.70
1764 1847 4.938226 AGTATAGGAGCACTGTTTTCTTGC 59.062 41.667 0.00 0.00 36.45 4.01
1815 1898 6.930731 TGCATCCATGTATAGCTTCGTATTA 58.069 36.000 0.00 0.00 0.00 0.98
1816 1899 7.555965 TGCATCCATGTATAGCTTCGTATTAT 58.444 34.615 0.00 0.00 0.00 1.28
1867 1950 1.467734 CTTCCACTGATTCTGCACTGC 59.532 52.381 0.00 0.00 0.00 4.40
1868 1951 0.321919 TCCACTGATTCTGCACTGCC 60.322 55.000 0.00 0.00 0.00 4.85
1875 1958 2.034939 TGATTCTGCACTGCCAAAACAG 59.965 45.455 0.00 0.00 43.59 3.16
1876 1959 0.102844 TTCTGCACTGCCAAAACAGC 59.897 50.000 0.00 0.00 41.60 4.40
1877 1960 1.300388 CTGCACTGCCAAAACAGCC 60.300 57.895 0.00 0.00 41.60 4.85
1878 1961 1.741327 CTGCACTGCCAAAACAGCCT 61.741 55.000 0.00 0.00 41.60 4.58
1906 1989 4.385146 GCTTTCAGAAAGATTTTCAGCTGC 59.615 41.667 24.70 3.65 41.02 5.25
1914 1997 6.771749 AGAAAGATTTTCAGCTGCTATGCTAT 59.228 34.615 9.47 0.00 41.98 2.97
1915 1998 6.956202 AAGATTTTCAGCTGCTATGCTATT 57.044 33.333 9.47 0.00 41.98 1.73
1916 1999 6.315091 AGATTTTCAGCTGCTATGCTATTG 57.685 37.500 9.47 0.00 41.98 1.90
1917 2000 3.976793 TTTCAGCTGCTATGCTATTGC 57.023 42.857 9.47 0.00 41.98 3.56
1918 2001 2.924757 TCAGCTGCTATGCTATTGCT 57.075 45.000 9.47 0.00 41.98 3.91
1919 2002 4.341366 TTCAGCTGCTATGCTATTGCTA 57.659 40.909 9.47 0.00 41.98 3.49
1920 2003 4.548451 TCAGCTGCTATGCTATTGCTAT 57.452 40.909 9.47 0.00 41.98 2.97
1932 2015 4.635765 TGCTATTGCTATGGTGTTCTTGAC 59.364 41.667 0.00 0.00 40.48 3.18
2039 2123 1.003839 TGGGACATTCGGCTGTGTC 60.004 57.895 7.58 7.58 43.02 3.67
2287 2372 7.492344 GGAAAGTTTTAGCAATGTATGATTGGG 59.508 37.037 0.00 0.00 0.00 4.12
2301 2386 2.846206 TGATTGGGAGGATAACAGTGCT 59.154 45.455 0.00 0.00 0.00 4.40
2382 2467 1.133025 CTTGGTTTAGCCGCCTGAATG 59.867 52.381 0.00 0.00 41.21 2.67
2383 2468 1.312371 TGGTTTAGCCGCCTGAATGC 61.312 55.000 0.00 0.00 41.21 3.56
2397 2487 5.163723 CGCCTGAATGCTTTTCTTTCTATCA 60.164 40.000 2.42 0.00 32.01 2.15
2400 2490 7.434602 GCCTGAATGCTTTTCTTTCTATCAATC 59.565 37.037 2.42 0.00 32.01 2.67
2472 2564 6.529829 GCCGTGTTGCATCTTTATTCAATAAA 59.470 34.615 2.56 2.56 33.92 1.40
2571 2705 0.516877 TGCAAAAGGATGTCGAAGCG 59.483 50.000 0.00 0.00 0.00 4.68
2574 2708 1.131126 CAAAAGGATGTCGAAGCGCAT 59.869 47.619 11.47 0.00 0.00 4.73
2652 2786 5.182001 CACTTTGCAAGTAATCTAACAGCCT 59.818 40.000 0.00 0.00 40.46 4.58
2653 2787 5.770162 ACTTTGCAAGTAATCTAACAGCCTT 59.230 36.000 0.00 0.00 40.69 4.35
2654 2788 5.627499 TTGCAAGTAATCTAACAGCCTTG 57.373 39.130 0.00 0.00 34.03 3.61
2670 2804 3.153919 GCCTTGTTTCCCATACTGTTCA 58.846 45.455 0.00 0.00 0.00 3.18
2676 2810 3.755112 TTCCCATACTGTTCAACACGA 57.245 42.857 0.00 0.00 0.00 4.35
2734 2877 2.673775 TGATTTTTCAGGCAGACCCA 57.326 45.000 0.00 0.00 36.11 4.51
2743 2886 1.137872 CAGGCAGACCCAGATACTGAC 59.862 57.143 0.00 0.00 39.66 3.51
2755 2898 2.290916 AGATACTGACGAGGTGTATGCG 59.709 50.000 0.00 0.00 0.00 4.73
2827 2970 2.113860 TCCCCAAGAATTTCTCTGCG 57.886 50.000 0.00 0.00 33.37 5.18
2840 2983 0.877071 CTCTGCGTGTTTCCAATGCT 59.123 50.000 0.00 0.00 0.00 3.79
2850 2993 5.124776 CGTGTTTCCAATGCTTTAATCCCTA 59.875 40.000 0.00 0.00 0.00 3.53
3119 3262 5.708230 TGGTGCCATCTTAATTTCGTTACTT 59.292 36.000 0.00 0.00 0.00 2.24
3231 3374 4.460948 TCGGGGTACAGAAAATGTAGTC 57.539 45.455 0.00 0.00 45.06 2.59
3232 3375 3.833650 TCGGGGTACAGAAAATGTAGTCA 59.166 43.478 0.00 0.00 45.06 3.41
3233 3376 4.283978 TCGGGGTACAGAAAATGTAGTCAA 59.716 41.667 0.00 0.00 45.06 3.18
3272 3415 5.104776 TCCTTCTGCTGCAATAACTGAGTAT 60.105 40.000 3.02 0.00 0.00 2.12
3434 3577 1.407299 CCATGCTTCCGTCCATCTTCA 60.407 52.381 0.00 0.00 0.00 3.02
3445 3588 3.243877 CGTCCATCTTCAGAAAGCATACG 59.756 47.826 0.00 0.00 32.18 3.06
3496 3639 7.507733 AGCAGCAGATTATTTGAAATAGAGG 57.492 36.000 0.00 0.00 0.00 3.69
3502 3645 8.772705 GCAGATTATTTGAAATAGAGGACAGAG 58.227 37.037 0.00 0.00 0.00 3.35
3610 3755 1.470805 CGACAGCCCACGAACATATCA 60.471 52.381 0.00 0.00 0.00 2.15
3733 3878 3.430374 GGTGAGCTTCTAAATCTGCGGTA 60.430 47.826 0.00 0.00 0.00 4.02
3779 3924 7.746526 ATTACCTAAAAGTTTCTACGTAGCG 57.253 36.000 18.00 0.00 0.00 4.26
3798 3943 5.776173 AGCGTCAGTAGCTATCATTAGTT 57.224 39.130 0.00 0.00 44.05 2.24
3799 3944 5.764131 AGCGTCAGTAGCTATCATTAGTTC 58.236 41.667 0.00 0.00 44.05 3.01
3800 3945 5.299531 AGCGTCAGTAGCTATCATTAGTTCA 59.700 40.000 0.00 0.00 44.05 3.18
3801 3946 5.977725 GCGTCAGTAGCTATCATTAGTTCAA 59.022 40.000 0.00 0.00 0.00 2.69
3802 3947 6.642950 GCGTCAGTAGCTATCATTAGTTCAAT 59.357 38.462 0.00 0.00 0.00 2.57
3803 3948 7.808381 GCGTCAGTAGCTATCATTAGTTCAATA 59.192 37.037 0.00 0.00 0.00 1.90
3945 4090 1.726533 GCGAGACGGAGGAACTAGGG 61.727 65.000 0.00 0.00 41.55 3.53
4116 4261 5.619981 GCAGCTTACAGGTTGGATTTACAAG 60.620 44.000 0.00 0.00 0.00 3.16
4139 4284 3.698040 CACCATCCTAATTGCAGCTCTTT 59.302 43.478 0.00 0.00 0.00 2.52
4156 4301 7.074502 CAGCTCTTTCACTGTGTTATTCTTTC 58.925 38.462 7.79 0.00 0.00 2.62
4157 4302 6.995091 AGCTCTTTCACTGTGTTATTCTTTCT 59.005 34.615 7.79 0.00 0.00 2.52
4158 4303 7.172361 AGCTCTTTCACTGTGTTATTCTTTCTC 59.828 37.037 7.79 0.00 0.00 2.87
4159 4304 7.572168 GCTCTTTCACTGTGTTATTCTTTCTCC 60.572 40.741 7.79 0.00 0.00 3.71
4160 4305 7.279615 TCTTTCACTGTGTTATTCTTTCTCCA 58.720 34.615 7.79 0.00 0.00 3.86
4161 4306 7.939039 TCTTTCACTGTGTTATTCTTTCTCCAT 59.061 33.333 7.79 0.00 0.00 3.41
4162 4307 8.463930 TTTCACTGTGTTATTCTTTCTCCATT 57.536 30.769 7.79 0.00 0.00 3.16
4163 4308 8.463930 TTCACTGTGTTATTCTTTCTCCATTT 57.536 30.769 7.79 0.00 0.00 2.32
4164 4309 7.874940 TCACTGTGTTATTCTTTCTCCATTTG 58.125 34.615 7.79 0.00 0.00 2.32
4165 4310 7.502226 TCACTGTGTTATTCTTTCTCCATTTGT 59.498 33.333 7.79 0.00 0.00 2.83
4166 4311 7.805071 CACTGTGTTATTCTTTCTCCATTTGTC 59.195 37.037 0.00 0.00 0.00 3.18
4167 4312 7.721399 ACTGTGTTATTCTTTCTCCATTTGTCT 59.279 33.333 0.00 0.00 0.00 3.41
4168 4313 8.463930 TGTGTTATTCTTTCTCCATTTGTCTT 57.536 30.769 0.00 0.00 0.00 3.01
4169 4314 8.912988 TGTGTTATTCTTTCTCCATTTGTCTTT 58.087 29.630 0.00 0.00 0.00 2.52
4319 4478 2.909965 TTTGGTGTGAAGCGCCCC 60.910 61.111 2.29 0.00 46.96 5.80
4403 4564 6.824305 AGACGGTGAATTTCTTCAAATCAT 57.176 33.333 0.00 0.00 42.85 2.45
4475 4637 4.724279 AAGACTACTTGGTGGAATGGTT 57.276 40.909 0.00 0.00 34.80 3.67
4574 4737 3.918591 GTGCATCAAAAGAAGCATGTGAG 59.081 43.478 0.00 0.00 39.43 3.51
4910 5073 1.075374 ACAATGCCTGGCCTGAGTTTA 59.925 47.619 20.88 0.00 0.00 2.01
5160 5323 4.213270 CAGCACTTCCGTTGAATCAACTAA 59.787 41.667 21.89 15.01 41.62 2.24
5177 5340 6.182627 TCAACTAAGTGCCATCAGAAATCAT 58.817 36.000 0.00 0.00 0.00 2.45
5445 5608 6.183360 ACAGCTTTTACTTCACCAACAGTTAC 60.183 38.462 0.00 0.00 0.00 2.50
5446 5609 5.883673 AGCTTTTACTTCACCAACAGTTACA 59.116 36.000 0.00 0.00 0.00 2.41
5447 5610 6.038271 AGCTTTTACTTCACCAACAGTTACAG 59.962 38.462 0.00 0.00 0.00 2.74
5621 5784 6.422100 CACTCTCACGATTACCAATAATCCAG 59.578 42.308 0.00 0.00 42.61 3.86
5642 5805 4.210537 CAGGAGCAGCAAAATTTTCTTGTG 59.789 41.667 0.00 0.00 0.00 3.33
5763 5926 2.768492 CCGCCCATTCAGCAAGAGC 61.768 63.158 0.00 0.00 42.56 4.09
5764 5927 2.042259 CGCCCATTCAGCAAGAGCA 61.042 57.895 0.00 0.00 45.49 4.26
5765 5928 1.807886 GCCCATTCAGCAAGAGCAG 59.192 57.895 0.00 0.00 45.49 4.24
5766 5929 1.807886 CCCATTCAGCAAGAGCAGC 59.192 57.895 0.00 0.00 45.49 5.25
5767 5930 0.963856 CCCATTCAGCAAGAGCAGCA 60.964 55.000 0.00 0.00 45.49 4.41
5768 5931 0.885879 CCATTCAGCAAGAGCAGCAA 59.114 50.000 0.00 0.00 45.49 3.91
5769 5932 1.402456 CCATTCAGCAAGAGCAGCAAC 60.402 52.381 0.00 0.00 45.49 4.17
5770 5933 1.268625 CATTCAGCAAGAGCAGCAACA 59.731 47.619 0.00 0.00 45.49 3.33
5771 5934 0.949397 TTCAGCAAGAGCAGCAACAG 59.051 50.000 0.00 0.00 45.49 3.16
5864 6027 3.099905 CTCTTCTACCAGTGTGATCCCA 58.900 50.000 0.00 0.00 0.00 4.37
5877 6040 3.566322 TGTGATCCCAAAAACTGGTAACG 59.434 43.478 0.00 0.00 44.76 3.18
5881 6044 3.140623 TCCCAAAAACTGGTAACGCTAC 58.859 45.455 0.00 0.00 44.76 3.58
6007 6170 3.619929 GGCAGGAATGATCATTGCAAAAC 59.380 43.478 33.08 21.31 40.94 2.43
6055 6218 7.506971 TCTATTGCTCAGATGTCAATTCTGAT 58.493 34.615 6.60 0.00 46.26 2.90
6077 6240 4.037222 TCCCCATTGAAGCTGTATCAGTA 58.963 43.478 0.00 0.00 33.43 2.74
6350 6513 4.664688 AGAAATTCAAGGTGTGGATCCT 57.335 40.909 14.23 0.00 36.81 3.24
6563 6726 6.455360 TTTGGTCAATCAGATATGGCTTTC 57.545 37.500 0.00 0.00 0.00 2.62
6572 6735 7.850935 ATCAGATATGGCTTTCAATTCCATT 57.149 32.000 1.31 0.00 40.71 3.16
6717 6881 8.780846 TGAAAGTCGATTTTTAAGGCAGTATA 57.219 30.769 7.38 0.00 0.00 1.47
6845 7017 7.690952 AAAATAATGTCATTGCAATTGCCTT 57.309 28.000 26.94 11.94 41.18 4.35
7033 7206 6.456795 CACTTCTATGTGTAGTGGATGAGA 57.543 41.667 0.00 0.00 39.45 3.27
7034 7207 6.867550 CACTTCTATGTGTAGTGGATGAGAA 58.132 40.000 0.00 0.00 39.45 2.87
7093 7267 3.636300 TGTTGAAGGGTCAGTTGGAAATG 59.364 43.478 0.00 0.00 34.49 2.32
7094 7268 2.238521 TGAAGGGTCAGTTGGAAATGC 58.761 47.619 0.00 0.00 0.00 3.56
7095 7269 1.546029 GAAGGGTCAGTTGGAAATGCC 59.454 52.381 0.00 0.00 37.10 4.40
7131 7326 4.320788 GCCATGCTCATTAGTATGCTTTCC 60.321 45.833 0.00 0.00 42.61 3.13
7246 7445 5.860941 TCTCTGGATATGGAGAACTGAAC 57.139 43.478 0.00 0.00 35.91 3.18
7336 7535 5.278266 GCTAGTCTACACAGATCATGAGGAC 60.278 48.000 0.09 10.01 32.09 3.85
7496 7695 4.018141 TGTGAAACAGGATCAATCCAGGAT 60.018 41.667 11.51 0.00 45.67 3.24
7555 7754 5.818678 ACTGGAATAGACTGTGTTTGGTA 57.181 39.130 0.00 0.00 0.00 3.25
7692 7891 2.665165 TGCAGGGAGTTTGTGAATTGT 58.335 42.857 0.00 0.00 0.00 2.71
7767 7966 3.620488 TGGTGATTTAGGGAGCAATGTC 58.380 45.455 0.00 0.00 0.00 3.06
7901 8100 3.458189 ACTTAGAGGCGCATTCACATAC 58.542 45.455 10.83 0.00 0.00 2.39
8238 8437 1.235724 GGTTGTGTGTAGCCCTTGTC 58.764 55.000 0.00 0.00 0.00 3.18
8253 8452 1.352352 CTTGTCAAGGTCACCATCCCT 59.648 52.381 4.52 0.00 0.00 4.20
8306 8505 5.376854 AATTGAAACTGCGATAACAAGCT 57.623 34.783 0.00 0.00 0.00 3.74
8308 8507 5.933187 TTGAAACTGCGATAACAAGCTTA 57.067 34.783 0.00 0.00 0.00 3.09
8367 8566 8.150296 CCCATATGAAATTTGGTTCTAAATCCC 58.850 37.037 3.65 0.00 43.02 3.85
8423 8622 5.599732 TGGAAATGTGATGAGTTTTGTTGG 58.400 37.500 0.00 0.00 0.00 3.77
8457 8656 6.935208 AGGACTACCTCTTACACATGTTTTTC 59.065 38.462 0.00 0.00 44.13 2.29
8459 8658 6.285990 ACTACCTCTTACACATGTTTTTCGT 58.714 36.000 0.00 0.00 0.00 3.85
8461 8660 6.780706 ACCTCTTACACATGTTTTTCGTAG 57.219 37.500 0.00 0.00 0.00 3.51
8511 8710 6.680810 TGGCTGAATTTTATGACAGAACTTG 58.319 36.000 0.00 0.00 32.90 3.16
8678 8877 1.878088 CATGCAAGTGTCTCAAGCAGT 59.122 47.619 0.00 0.00 38.75 4.40
8791 8994 2.223572 GGTTGATGGCAATCCGATGAAC 60.224 50.000 0.00 0.00 36.22 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 44 5.187967 ACTTCCGACCTATTCATCTTTCACT 59.812 40.000 0.00 0.00 0.00 3.41
36 45 5.420409 ACTTCCGACCTATTCATCTTTCAC 58.580 41.667 0.00 0.00 0.00 3.18
51 60 5.455849 GCTCTTTTTCAAGAAAACTTCCGAC 59.544 40.000 7.44 0.00 38.63 4.79
54 63 6.638873 GCTAGCTCTTTTTCAAGAAAACTTCC 59.361 38.462 7.70 0.00 38.63 3.46
65 74 4.067896 CCAGTCTTGCTAGCTCTTTTTCA 58.932 43.478 17.23 0.00 0.00 2.69
67 76 4.092116 ACCAGTCTTGCTAGCTCTTTTT 57.908 40.909 17.23 0.00 0.00 1.94
72 81 3.815401 TGAAAAACCAGTCTTGCTAGCTC 59.185 43.478 17.23 4.13 0.00 4.09
74 83 3.565902 ACTGAAAAACCAGTCTTGCTAGC 59.434 43.478 8.10 8.10 43.34 3.42
87 96 2.212466 GTGCGCGTGTAAACTGAAAAAC 59.788 45.455 8.43 0.00 0.00 2.43
91 100 0.810426 TGGTGCGCGTGTAAACTGAA 60.810 50.000 8.43 0.00 0.00 3.02
129 138 4.202121 GCATTATGAGAGACCGGTTAGTGA 60.202 45.833 9.42 0.00 0.00 3.41
130 139 4.051922 GCATTATGAGAGACCGGTTAGTG 58.948 47.826 9.42 4.09 0.00 2.74
140 149 3.135167 TGCATGACTGGCATTATGAGAGA 59.865 43.478 0.00 0.00 36.11 3.10
146 155 5.864418 AAATTCTGCATGACTGGCATTAT 57.136 34.783 0.00 0.00 41.06 1.28
147 156 5.664294 AAAATTCTGCATGACTGGCATTA 57.336 34.783 0.00 0.00 41.06 1.90
167 176 7.164803 TCAAAGAAGCCAAAAAGAAGGAAAAA 58.835 30.769 0.00 0.00 0.00 1.94
168 177 6.706295 TCAAAGAAGCCAAAAAGAAGGAAAA 58.294 32.000 0.00 0.00 0.00 2.29
177 186 9.921637 AATTATACGAATCAAAGAAGCCAAAAA 57.078 25.926 0.00 0.00 0.00 1.94
263 273 5.183140 ACAATAATTTTGGAACGGAGGAGTG 59.817 40.000 0.00 0.00 0.00 3.51
312 322 2.797156 CCTCATGCGAAGAATTCTACGG 59.203 50.000 8.75 2.28 44.75 4.02
362 377 9.649316 TTCAAAGGGTTTCTAAAGGAATCTTAA 57.351 29.630 0.00 0.00 33.53 1.85
413 429 8.113462 TCTTTTCAGTAAAGGGGCAATAATACT 58.887 33.333 0.10 0.00 42.88 2.12
545 575 3.991367 ACTCCGTTTTAGTGAAGTGAGG 58.009 45.455 0.00 0.00 0.00 3.86
584 614 1.979809 TCTGTCTCTCTCTCCCCTCT 58.020 55.000 0.00 0.00 0.00 3.69
585 615 2.241176 TCTTCTGTCTCTCTCTCCCCTC 59.759 54.545 0.00 0.00 0.00 4.30
586 616 2.283834 TCTTCTGTCTCTCTCTCCCCT 58.716 52.381 0.00 0.00 0.00 4.79
588 618 2.427095 GCTTCTTCTGTCTCTCTCTCCC 59.573 54.545 0.00 0.00 0.00 4.30
589 619 2.097466 CGCTTCTTCTGTCTCTCTCTCC 59.903 54.545 0.00 0.00 0.00 3.71
702 762 1.904990 GAGGGAGGGGTGAGAGTTGC 61.905 65.000 0.00 0.00 0.00 4.17
738 802 7.008941 AGTCCTACTACTACTAGAGAGAGAGG 58.991 46.154 0.00 0.00 0.00 3.69
892 956 3.151710 CGCTGTATGGGTCCCGGA 61.152 66.667 0.73 0.00 0.00 5.14
906 970 0.234884 CGCCGAGTTTCTTTTTCGCT 59.765 50.000 0.00 0.00 33.25 4.93
933 1009 0.610174 GCATGAGTCACAGAGGACCA 59.390 55.000 0.00 0.00 38.59 4.02
935 1011 1.080995 GCGCATGAGTCACAGAGGAC 61.081 60.000 0.30 0.00 38.08 3.85
1036 1112 2.055633 TACCTTCGCATGGAGCCGA 61.056 57.895 0.00 0.00 41.38 5.54
1311 1387 3.440522 CGAACAGATAGGTCTCACTCACA 59.559 47.826 0.00 0.00 30.42 3.58
1329 1405 1.734117 GCAAATGGCACTGGCGAAC 60.734 57.895 0.00 0.00 43.97 3.95
1330 1406 2.650196 GCAAATGGCACTGGCGAA 59.350 55.556 0.00 0.00 43.97 4.70
1335 1411 1.731613 CACTGCGCAAATGGCACTG 60.732 57.895 13.05 0.00 45.17 3.66
1385 1464 6.982724 GCAAAAAGGAGGGAAGATTATCATTG 59.017 38.462 0.00 0.00 0.00 2.82
1506 1589 6.237154 CCTCTTGAACTTCAAAGGATTCTCT 58.763 40.000 18.61 0.00 35.73 3.10
1539 1622 8.472007 TCTGTTTTTCTTTTAAGAAGGCCATA 57.528 30.769 5.01 0.00 45.01 2.74
1561 1644 5.646360 TGCAACATATCCATGATAGCATCTG 59.354 40.000 0.00 0.00 34.41 2.90
1589 1672 2.941415 GCCCTCCAATCACAACTACTGG 60.941 54.545 0.00 0.00 0.00 4.00
1613 1696 6.640518 AGCAATTAGTAGCAAGCAAGTAGTA 58.359 36.000 0.00 0.00 0.00 1.82
1614 1697 5.491982 AGCAATTAGTAGCAAGCAAGTAGT 58.508 37.500 0.00 0.00 0.00 2.73
1615 1698 6.428385 AAGCAATTAGTAGCAAGCAAGTAG 57.572 37.500 0.00 0.00 0.00 2.57
1651 1734 5.731678 ACTCCTCCAATAACCCAAGAATACT 59.268 40.000 0.00 0.00 0.00 2.12
1689 1772 1.341089 GGAAGGAAGTAGGCCCAAAGG 60.341 57.143 0.00 0.00 0.00 3.11
1690 1773 1.636003 AGGAAGGAAGTAGGCCCAAAG 59.364 52.381 0.00 0.00 0.00 2.77
1704 1787 1.889170 GCCAACAGAAGGAAAGGAAGG 59.111 52.381 0.00 0.00 0.00 3.46
1733 1816 3.701542 CAGTGCTCCTATACTCCACAAGA 59.298 47.826 0.00 0.00 0.00 3.02
1739 1822 5.346181 AGAAAACAGTGCTCCTATACTCC 57.654 43.478 0.00 0.00 0.00 3.85
1764 1847 7.119116 TGTTGCATGTACTACCAAACTTGATAG 59.881 37.037 0.00 0.00 0.00 2.08
1809 1892 7.870826 TCAGGACCATAAATGCAAATAATACG 58.129 34.615 0.00 0.00 0.00 3.06
1815 1898 7.270047 CAGAAATCAGGACCATAAATGCAAAT 58.730 34.615 0.00 0.00 0.00 2.32
1816 1899 6.632909 CAGAAATCAGGACCATAAATGCAAA 58.367 36.000 0.00 0.00 0.00 3.68
1867 1950 1.751349 AAGCAGGCAGGCTGTTTTGG 61.751 55.000 24.09 3.09 45.07 3.28
1868 1951 0.105408 AAAGCAGGCAGGCTGTTTTG 59.895 50.000 30.17 12.69 45.07 2.44
1875 1958 0.243095 CTTTCTGAAAGCAGGCAGGC 59.757 55.000 16.43 0.00 42.53 4.85
1876 1959 1.901591 TCTTTCTGAAAGCAGGCAGG 58.098 50.000 22.25 1.00 42.53 4.85
1877 1960 4.516365 AAATCTTTCTGAAAGCAGGCAG 57.484 40.909 22.25 1.39 42.53 4.85
1878 1961 4.341806 TGAAAATCTTTCTGAAAGCAGGCA 59.658 37.500 22.25 14.01 42.53 4.75
1906 1989 6.707608 TCAAGAACACCATAGCAATAGCATAG 59.292 38.462 0.00 0.00 45.49 2.23
1914 1997 4.350368 TCTGTCAAGAACACCATAGCAA 57.650 40.909 0.00 0.00 33.24 3.91
1915 1998 4.558226 ATCTGTCAAGAACACCATAGCA 57.442 40.909 0.00 0.00 35.59 3.49
1916 1999 5.064452 CAGAATCTGTCAAGAACACCATAGC 59.936 44.000 1.31 0.00 35.59 2.97
1917 2000 6.169094 ACAGAATCTGTCAAGAACACCATAG 58.831 40.000 10.56 0.00 41.21 2.23
1918 2001 6.114187 ACAGAATCTGTCAAGAACACCATA 57.886 37.500 10.56 0.00 41.21 2.74
1919 2002 4.978099 ACAGAATCTGTCAAGAACACCAT 58.022 39.130 10.56 0.00 41.21 3.55
1920 2003 4.422073 ACAGAATCTGTCAAGAACACCA 57.578 40.909 10.56 0.00 41.21 4.17
1932 2015 9.618890 TTAGGGATTGATCTTTTACAGAATCTG 57.381 33.333 8.98 8.98 34.16 2.90
2039 2123 1.456296 CCCACATATCATCATGGGCG 58.544 55.000 0.00 0.00 45.26 6.13
2084 2168 4.201990 CCTTTTAGATGAACTCTGCATGCC 60.202 45.833 16.68 0.00 35.28 4.40
2287 2372 3.846360 ACACGTAAGCACTGTTATCCTC 58.154 45.455 0.00 0.00 45.62 3.71
2301 2386 3.805422 CCAGCTGTTTTCTGTACACGTAA 59.195 43.478 13.81 0.00 0.00 3.18
2382 2467 6.546395 TGAAGCGATTGATAGAAAGAAAAGC 58.454 36.000 0.00 0.00 0.00 3.51
2437 2529 0.317436 GCAACACGGCGTTTTCATCA 60.317 50.000 11.19 0.00 34.86 3.07
2571 2705 2.897350 GGGTAGCTCGGCACATGC 60.897 66.667 0.00 0.00 41.14 4.06
2574 2708 2.925706 TTGGGGTAGCTCGGCACA 60.926 61.111 0.00 0.00 0.00 4.57
2652 2786 4.035792 CGTGTTGAACAGTATGGGAAACAA 59.964 41.667 0.00 0.00 43.62 2.83
2653 2787 3.562141 CGTGTTGAACAGTATGGGAAACA 59.438 43.478 0.00 0.00 43.62 2.83
2654 2788 3.810941 TCGTGTTGAACAGTATGGGAAAC 59.189 43.478 0.00 0.00 43.62 2.78
2656 2790 3.395639 GTCGTGTTGAACAGTATGGGAA 58.604 45.455 0.00 0.00 43.62 3.97
2734 2877 2.290916 CGCATACACCTCGTCAGTATCT 59.709 50.000 0.00 0.00 0.00 1.98
2743 2886 0.249031 TCATCTGCGCATACACCTCG 60.249 55.000 12.24 0.00 0.00 4.63
2755 2898 1.066286 ACTGGCTGAAGAGTCATCTGC 60.066 52.381 16.25 16.25 39.99 4.26
2827 2970 5.405935 AGGGATTAAAGCATTGGAAACAC 57.594 39.130 0.00 0.00 42.67 3.32
2840 2983 5.708736 TCAGGAGCAACATAGGGATTAAA 57.291 39.130 0.00 0.00 0.00 1.52
2850 2993 3.361281 ACACATGATCAGGAGCAACAT 57.639 42.857 15.42 0.00 0.00 2.71
3119 3262 4.451096 GCAACGAGAAATCCTACAGAACAA 59.549 41.667 0.00 0.00 0.00 2.83
3231 3374 6.622462 GCAGAAGGAAGCTCTACTCAATTTTG 60.622 42.308 0.00 0.00 0.00 2.44
3232 3375 5.414144 GCAGAAGGAAGCTCTACTCAATTTT 59.586 40.000 0.00 0.00 0.00 1.82
3233 3376 4.940654 GCAGAAGGAAGCTCTACTCAATTT 59.059 41.667 0.00 0.00 0.00 1.82
3434 3577 2.736144 TGAACCGACGTATGCTTTCT 57.264 45.000 0.00 0.00 0.00 2.52
3445 3588 2.758979 TGGAACTCTAGGATGAACCGAC 59.241 50.000 0.00 0.00 44.74 4.79
3496 3639 3.065925 GGCATTACATTTCCAGCTCTGTC 59.934 47.826 0.00 0.00 0.00 3.51
3502 3645 3.806625 ATGTGGCATTACATTTCCAGC 57.193 42.857 0.00 0.00 38.05 4.85
3525 3670 6.530120 TCTCTGGAGTGTAGCAAATAAAACA 58.470 36.000 0.00 0.00 0.00 2.83
3610 3755 3.251571 GTCGCTTGAAAGTACCGAAGAT 58.748 45.455 0.00 0.00 0.00 2.40
3778 3923 9.678941 TTATTGAACTAATGATAGCTACTGACG 57.321 33.333 0.00 0.00 31.96 4.35
3797 3942 9.126151 TCCACAGTTCAAAACATAGTTATTGAA 57.874 29.630 12.07 12.07 38.92 2.69
3798 3943 8.564574 GTCCACAGTTCAAAACATAGTTATTGA 58.435 33.333 0.00 0.00 0.00 2.57
3799 3944 8.567948 AGTCCACAGTTCAAAACATAGTTATTG 58.432 33.333 0.00 0.00 0.00 1.90
3800 3945 8.691661 AGTCCACAGTTCAAAACATAGTTATT 57.308 30.769 0.00 0.00 0.00 1.40
3801 3946 8.691661 AAGTCCACAGTTCAAAACATAGTTAT 57.308 30.769 0.00 0.00 0.00 1.89
3802 3947 8.514330 AAAGTCCACAGTTCAAAACATAGTTA 57.486 30.769 0.00 0.00 0.00 2.24
3803 3948 7.122055 TGAAAGTCCACAGTTCAAAACATAGTT 59.878 33.333 0.00 0.00 0.00 2.24
3945 4090 4.624452 GGTAACTTGACATACCGTCTTGTC 59.376 45.833 7.33 7.33 45.60 3.18
4116 4261 1.336125 GAGCTGCAATTAGGATGGTGC 59.664 52.381 1.02 0.00 37.51 5.01
4139 4284 7.502226 ACAAATGGAGAAAGAATAACACAGTGA 59.498 33.333 7.81 0.00 0.00 3.41
4156 4301 6.429078 TCAGTGAATCAGAAAGACAAATGGAG 59.571 38.462 0.00 0.00 0.00 3.86
4157 4302 6.298361 TCAGTGAATCAGAAAGACAAATGGA 58.702 36.000 0.00 0.00 0.00 3.41
4158 4303 6.564709 TCAGTGAATCAGAAAGACAAATGG 57.435 37.500 0.00 0.00 0.00 3.16
4159 4304 8.912658 CAAATCAGTGAATCAGAAAGACAAATG 58.087 33.333 0.00 0.00 0.00 2.32
4160 4305 8.853126 TCAAATCAGTGAATCAGAAAGACAAAT 58.147 29.630 0.00 0.00 0.00 2.32
4161 4306 8.224389 TCAAATCAGTGAATCAGAAAGACAAA 57.776 30.769 0.00 0.00 0.00 2.83
4162 4307 7.806409 TCAAATCAGTGAATCAGAAAGACAA 57.194 32.000 0.00 0.00 0.00 3.18
4163 4308 7.991084 ATCAAATCAGTGAATCAGAAAGACA 57.009 32.000 0.00 0.00 0.00 3.41
4164 4309 9.688592 AAAATCAAATCAGTGAATCAGAAAGAC 57.311 29.630 0.00 0.00 0.00 3.01
4165 4310 9.903682 GAAAATCAAATCAGTGAATCAGAAAGA 57.096 29.630 0.00 0.00 0.00 2.52
4166 4311 9.909644 AGAAAATCAAATCAGTGAATCAGAAAG 57.090 29.630 0.00 0.00 0.00 2.62
4167 4312 9.903682 GAGAAAATCAAATCAGTGAATCAGAAA 57.096 29.630 0.00 0.00 0.00 2.52
4168 4313 9.293404 AGAGAAAATCAAATCAGTGAATCAGAA 57.707 29.630 0.00 0.00 0.00 3.02
4169 4314 8.727910 CAGAGAAAATCAAATCAGTGAATCAGA 58.272 33.333 0.00 0.00 0.00 3.27
4319 4478 4.222124 ACCAGACTTACCTAATTGCCTG 57.778 45.455 0.00 0.00 0.00 4.85
4349 4508 5.126061 ACTGCAAGAATTCACTGTCTTTGTT 59.874 36.000 8.44 0.00 37.43 2.83
4381 4540 9.013490 CATAATGATTTGAAGAAATTCACCGTC 57.987 33.333 0.00 0.00 31.58 4.79
4383 4542 8.915871 ACATAATGATTTGAAGAAATTCACCG 57.084 30.769 0.00 0.00 31.58 4.94
4418 4579 7.210174 TGCAGTTAAGATCTTTACGCTCATAT 58.790 34.615 26.11 8.05 0.00 1.78
4423 4584 5.932303 TCTTTGCAGTTAAGATCTTTACGCT 59.068 36.000 26.11 14.37 0.00 5.07
4425 4587 8.869897 TGTATCTTTGCAGTTAAGATCTTTACG 58.130 33.333 14.36 11.69 40.53 3.18
4475 4637 9.162764 GATAAAAAGTACCAGAAGCAGTCAATA 57.837 33.333 0.00 0.00 0.00 1.90
4649 4812 5.297547 TCTACTGTTTGCAAGACAACCTAG 58.702 41.667 13.10 11.61 38.23 3.02
4696 4859 4.701956 ATTTTAAGAACAGTGGCATCCG 57.298 40.909 0.00 0.00 0.00 4.18
5160 5323 4.851843 TCTTGATGATTTCTGATGGCACT 58.148 39.130 0.00 0.00 0.00 4.40
5177 5340 4.190001 GCTGATCTTGCTTCTGATCTTGA 58.810 43.478 0.00 0.00 39.63 3.02
5489 5652 3.431486 GCTGACTTGCCAGATTAGCTAGT 60.431 47.826 0.00 0.00 46.58 2.57
5621 5784 3.495753 CCACAAGAAAATTTTGCTGCTCC 59.504 43.478 8.47 0.00 0.00 4.70
5711 5874 6.017934 GTGTTGTCTGCAATGAAGAAGTTCTA 60.018 38.462 5.65 0.00 36.92 2.10
5763 5926 1.660575 GCTGTTGCTGCTGTTGCTG 60.661 57.895 0.00 0.00 40.48 4.41
5764 5927 2.071844 CTGCTGTTGCTGCTGTTGCT 62.072 55.000 0.00 0.00 40.48 3.91
5765 5928 1.660575 CTGCTGTTGCTGCTGTTGC 60.661 57.895 0.00 1.39 40.48 4.17
5766 5929 0.382873 TTCTGCTGTTGCTGCTGTTG 59.617 50.000 0.00 0.00 40.48 3.33
5767 5930 0.666913 CTTCTGCTGTTGCTGCTGTT 59.333 50.000 0.00 0.00 40.48 3.16
5768 5931 1.793134 GCTTCTGCTGTTGCTGCTGT 61.793 55.000 0.00 0.00 40.48 4.40
5769 5932 1.081376 GCTTCTGCTGTTGCTGCTG 60.081 57.895 0.00 0.00 40.48 4.41
5770 5933 2.266627 GGCTTCTGCTGTTGCTGCT 61.267 57.895 0.00 0.00 40.48 4.24
5771 5934 1.803366 AAGGCTTCTGCTGTTGCTGC 61.803 55.000 0.00 0.00 40.48 5.25
5864 6027 5.473039 ACTATCGTAGCGTTACCAGTTTTT 58.527 37.500 3.68 0.00 0.00 1.94
5877 6040 1.409427 AGCACCAGGAACTATCGTAGC 59.591 52.381 0.00 0.00 36.02 3.58
5881 6044 0.108186 TGCAGCACCAGGAACTATCG 60.108 55.000 0.00 0.00 36.02 2.92
5918 6081 5.064834 GGATGTCGAACAAGAAGGTATTTCC 59.935 44.000 0.00 0.00 36.40 3.13
6055 6218 2.846206 ACTGATACAGCTTCAATGGGGA 59.154 45.455 0.00 0.00 34.37 4.81
6077 6240 2.322658 TCCTTGGTCGTTACTGGAGTT 58.677 47.619 0.00 0.00 0.00 3.01
6350 6513 3.695830 CCAAAGAGGGCACTGTTACTA 57.304 47.619 0.00 0.00 28.86 1.82
6572 6735 5.452216 GGCACCATCATTAATTGCAGAATCA 60.452 40.000 10.40 0.00 34.76 2.57
6717 6881 5.592688 GGTAATATAGGCACCACACAACATT 59.407 40.000 0.00 0.00 32.32 2.71
6860 7032 3.451141 TGTTGTTGGTGCATTCCTTTC 57.549 42.857 0.00 0.00 0.00 2.62
6941 7114 5.365403 TCAACCACCATTTCGAACATTAC 57.635 39.130 0.00 0.00 0.00 1.89
7032 7205 2.939103 GTGCCTATGTGTGACCATCTTC 59.061 50.000 0.00 0.00 0.00 2.87
7033 7206 2.305635 TGTGCCTATGTGTGACCATCTT 59.694 45.455 0.00 0.00 0.00 2.40
7034 7207 1.908619 TGTGCCTATGTGTGACCATCT 59.091 47.619 0.00 0.00 0.00 2.90
7075 7249 1.546029 GGCATTTCCAACTGACCCTTC 59.454 52.381 0.00 0.00 34.01 3.46
7131 7326 2.795329 ACAGGGGAAGCATACAACAAG 58.205 47.619 0.00 0.00 0.00 3.16
7336 7535 1.062206 GCCGAGAAGTAGGACGTCG 59.938 63.158 9.92 0.00 31.81 5.12
7382 7581 4.776349 TCACTTAAACACAGGCAGAAAGA 58.224 39.130 0.00 0.00 0.00 2.52
7440 7639 7.875971 AGATTTCTACATGTGTCTTTTTGACC 58.124 34.615 9.11 0.00 44.75 4.02
7464 7663 9.565213 GATTGATCCTGTTTCACATTTCTAAAG 57.435 33.333 0.00 0.00 0.00 1.85
7496 7695 8.387354 CGTATTTATGTTTCAGTTATGTCAGCA 58.613 33.333 0.00 0.00 0.00 4.41
7555 7754 7.682787 AGATGTATGAAAAGAGGATAGTGGT 57.317 36.000 0.00 0.00 0.00 4.16
7692 7891 3.264193 ACAGGATCCTAATGCACTTCACA 59.736 43.478 15.67 0.00 0.00 3.58
7901 8100 8.099364 ACTAACCAAGATGTTAACATGACAAG 57.901 34.615 25.42 14.18 36.57 3.16
8090 8289 6.832384 TCCCTACTACTCGTTTCAACTGATAT 59.168 38.462 0.00 0.00 0.00 1.63
8238 8437 5.630415 TCTATTTAGGGATGGTGACCTTG 57.370 43.478 2.11 0.00 38.30 3.61
8285 8484 5.376854 AAGCTTGTTATCGCAGTTTCAAT 57.623 34.783 0.00 0.00 0.00 2.57
8286 8485 4.829064 AAGCTTGTTATCGCAGTTTCAA 57.171 36.364 0.00 0.00 0.00 2.69
8295 8494 7.757097 AGAACTACATGTAAGCTTGTTATCG 57.243 36.000 9.86 0.00 35.14 2.92
8306 8505 7.959175 AGACCAAACAGTAGAACTACATGTAA 58.041 34.615 7.06 0.00 38.48 2.41
8308 8507 6.420913 AGACCAAACAGTAGAACTACATGT 57.579 37.500 2.69 2.69 38.48 3.21
8367 8566 1.586154 GGCCGACAGGTCCATTTGTG 61.586 60.000 0.00 0.00 40.50 3.33
8423 8622 4.489306 AAGAGGTAGTCCTGGCAATAAC 57.511 45.455 0.00 0.00 45.24 1.89
8459 8658 3.525199 AGGGGTAGAGAAAGTCGTACCTA 59.475 47.826 8.75 0.00 36.06 3.08
8461 8660 2.732763 AGGGGTAGAGAAAGTCGTACC 58.267 52.381 0.00 0.00 35.17 3.34
8511 8710 6.655003 TCCCTCTTGATCAATGAACAGTTAAC 59.345 38.462 8.96 0.00 0.00 2.01
8573 8772 5.184671 TGCCATGTGCTGTCATGTTAAAATA 59.815 36.000 13.02 0.00 42.29 1.40
8678 8877 4.075682 TGTGCTTTTTGGATCCGTCAATA 58.924 39.130 7.39 0.00 0.00 1.90
8709 8909 4.337145 AGACTCGAGGTGTTCAAGTCTAT 58.663 43.478 18.41 0.00 33.98 1.98


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

AutoCloner maintained by Alex Coulton.