Multiple sequence alignment - TraesCS6A01G160500

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 TraesCS6A01G160500 chr6A 100.000 5611 0 0 1 5611 154042828 154037218 0.000000e+00 10362.0
1 TraesCS6A01G160500 chr6A 88.571 105 9 2 1963 2067 222678955 222678854 2.120000e-24 124.0
2 TraesCS6A01G160500 chr6B 93.149 3620 163 28 2063 5611 224254593 224258198 0.000000e+00 5232.0
3 TraesCS6A01G160500 chr6B 96.673 1052 33 2 929 1979 224253544 224254594 0.000000e+00 1748.0
4 TraesCS6A01G160500 chr6B 93.371 890 40 10 1 877 224252669 224253552 0.000000e+00 1299.0
5 TraesCS6A01G160500 chr6B 92.222 90 5 1 1978 2067 646750059 646750146 5.900000e-25 126.0
6 TraesCS6A01G160500 chr6D 94.250 2939 125 17 2063 4973 125987647 125990569 0.000000e+00 4451.0
7 TraesCS6A01G160500 chr6D 96.673 1052 33 2 929 1979 125986598 125987648 0.000000e+00 1748.0
8 TraesCS6A01G160500 chr6D 93.214 840 39 9 51 877 125985772 125986606 0.000000e+00 1219.0
9 TraesCS6A01G160500 chr6D 93.126 611 36 5 5006 5611 125990569 125991178 0.000000e+00 891.0
10 TraesCS6A01G160500 chr6D 86.404 228 25 1 2844 3071 291716154 291715933 1.560000e-60 244.0
11 TraesCS6A01G160500 chr6D 97.273 110 3 0 1 110 125985665 125985774 2.670000e-43 187.0
12 TraesCS6A01G160500 chr6D 87.619 105 10 2 1963 2067 162954552 162954451 9.870000e-23 119.0
13 TraesCS6A01G160500 chr1D 89.837 492 42 2 3571 4058 249618523 249619010 4.770000e-175 625.0
14 TraesCS6A01G160500 chr3A 86.815 493 53 6 3571 4058 434451098 434450613 1.780000e-149 540.0
15 TraesCS6A01G160500 chr7D 89.520 229 24 0 2843 3071 451621763 451621535 1.980000e-74 291.0
16 TraesCS6A01G160500 chr7D 85.088 228 28 1 2844 3071 23078052 23077831 1.570000e-55 228.0
17 TraesCS6A01G160500 chr1A 90.521 211 16 1 3851 4057 548308448 548308238 5.540000e-70 276.0
18 TraesCS6A01G160500 chr1A 87.879 231 28 0 2841 3071 466042077 466042307 7.160000e-69 272.0
19 TraesCS6A01G160500 chrUn 85.714 231 27 1 2841 3071 96527184 96527408 7.260000e-59 239.0
20 TraesCS6A01G160500 chr5D 85.714 231 27 1 2841 3071 178477709 178477933 7.260000e-59 239.0
21 TraesCS6A01G160500 chr5D 90.323 93 6 2 1976 2067 128577674 128577584 9.870000e-23 119.0
22 TraesCS6A01G160500 chr4D 84.681 235 26 2 2841 3071 215190198 215190426 5.660000e-55 226.0
23 TraesCS6A01G160500 chr4B 91.753 97 4 3 1974 2069 673204563 673204470 1.270000e-26 132.0
24 TraesCS6A01G160500 chr4A 94.253 87 3 1 1978 2064 712603262 712603178 1.270000e-26 132.0
25 TraesCS6A01G160500 chr4A 97.143 35 1 0 4947 4981 429242589 429242555 6.070000e-05 60.2
26 TraesCS6A01G160500 chr2B 94.048 84 3 1 1981 2064 665189800 665189719 5.900000e-25 126.0
27 TraesCS6A01G160500 chr5A 89.691 97 6 3 1969 2064 442712364 442712457 2.750000e-23 121.0
28 TraesCS6A01G160500 chr5B 90.323 93 6 2 1976 2067 140966016 140965926 9.870000e-23 119.0
29 TraesCS6A01G160500 chr2D 97.826 46 1 0 4930 4975 318561215 318561170 4.660000e-11 80.5
30 TraesCS6A01G160500 chr2A 94.737 38 2 0 4939 4976 7528438 7528401 6.070000e-05 60.2


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 TraesCS6A01G160500 chr6A 154037218 154042828 5610 True 10362.000000 10362 100.000000 1 5611 1 chr6A.!!$R1 5610
1 TraesCS6A01G160500 chr6B 224252669 224258198 5529 False 2759.666667 5232 94.397667 1 5611 3 chr6B.!!$F2 5610
2 TraesCS6A01G160500 chr6D 125985665 125991178 5513 False 1699.200000 4451 94.907200 1 5611 5 chr6D.!!$F1 5610

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
859 930 0.034089 GACCTCCCAACCCTTCATGG 60.034 60.000 0.00 0.0 36.42 3.66 F
1056 1127 1.891933 TCTGGGATGGGCTTCACATA 58.108 50.000 0.00 0.0 0.00 2.29 F
1768 1840 1.066303 CGCTGTTTGCCAGGTTAACAA 59.934 47.619 8.10 0.0 41.81 2.83 F
3323 3414 1.226746 AGCTTGTGCAAGTTCGTACC 58.773 50.000 12.75 0.0 42.74 3.34 F
3426 3517 3.095332 TCAGCTACAATGCAGAGACTCT 58.905 45.455 0.00 0.0 34.99 3.24 F
4192 4283 2.347490 CGGGTTCTCCACACAGGG 59.653 66.667 0.00 0.0 38.24 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1738 1810 1.202568 CAAACAGCGTGCTGACTCG 59.797 57.895 27.26 9.40 46.30 4.18 R
2667 2758 1.493022 AGAACTTGGTACCTTGTGCCA 59.507 47.619 14.36 0.00 45.91 4.92 R
3556 3647 1.135402 GTGCGGAAAGTAAATGGCTGG 60.135 52.381 0.00 0.00 0.00 4.85 R
4135 4226 0.383231 GTTTGCTGACTGCTTGCTGT 59.617 50.000 4.86 4.86 43.37 4.40 R
4508 4613 0.464036 TCGTCGGATGGAAATCTGGG 59.536 55.000 0.00 0.00 0.00 4.45 R
5460 5614 0.820226 GAGGCCAAGGAAATCAAGGC 59.180 55.000 5.01 0.00 44.48 4.35 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
212 270 1.230635 GCGCAGTCCAATCAGTGTGT 61.231 55.000 0.30 0.00 30.97 3.72
214 272 1.873486 CGCAGTCCAATCAGTGTGTGA 60.873 52.381 0.00 0.00 40.38 3.58
215 273 2.221169 GCAGTCCAATCAGTGTGTGAA 58.779 47.619 0.00 0.00 39.19 3.18
219 277 0.874390 CCAATCAGTGTGTGAACCGG 59.126 55.000 0.00 0.00 39.19 5.28
229 287 2.027653 TGTGTGAACCGGCAATATCTCA 60.028 45.455 0.00 0.00 0.00 3.27
245 303 2.364632 TCTCAATGGCGGTAAATGGTG 58.635 47.619 0.00 0.00 0.00 4.17
272 330 0.109597 GAACACGCAGGCTTGGATTG 60.110 55.000 0.00 0.00 0.00 2.67
279 337 1.959282 GCAGGCTTGGATTGGATTAGG 59.041 52.381 0.00 0.00 0.00 2.69
287 345 3.889815 TGGATTGGATTAGGCTTGACAG 58.110 45.455 0.00 0.00 0.00 3.51
292 350 4.689612 TGGATTAGGCTTGACAGGATAC 57.310 45.455 0.00 0.00 0.00 2.24
333 391 3.889538 CCATTCATCTGCACCAATGAGAT 59.110 43.478 4.48 0.00 33.66 2.75
340 398 4.910195 TCTGCACCAATGAGATGTAAACT 58.090 39.130 0.00 0.00 0.00 2.66
395 457 6.986817 ACCGAAAGATGATAAGTATGTGAAGG 59.013 38.462 0.00 0.00 0.00 3.46
398 460 7.169982 CGAAAGATGATAAGTATGTGAAGGGTC 59.830 40.741 0.00 0.00 0.00 4.46
399 461 7.437713 AAGATGATAAGTATGTGAAGGGTCA 57.562 36.000 0.00 0.00 0.00 4.02
420 482 4.163268 TCACTTCCGGAAATGACATCCATA 59.837 41.667 23.67 0.00 36.74 2.74
478 540 3.067742 GCGGAAGGCACTGTATAACTAGA 59.932 47.826 0.00 0.00 40.86 2.43
543 605 6.378564 ACAGATTCAAGAAGACGAGAGGATAA 59.621 38.462 0.00 0.00 0.00 1.75
576 639 2.157474 TGAATTCATGTTGCGAGTCACG 59.843 45.455 3.38 0.00 45.66 4.35
627 692 4.771590 AATAATGCACACCAGACAGTTG 57.228 40.909 0.00 0.00 0.00 3.16
644 709 2.501723 AGTTGACGGCTGAAGTGGATAT 59.498 45.455 0.00 0.00 0.00 1.63
658 723 5.864418 AGTGGATATTAGCACTCGGTTTA 57.136 39.130 0.00 0.00 0.00 2.01
659 724 5.598769 AGTGGATATTAGCACTCGGTTTAC 58.401 41.667 0.00 0.00 0.00 2.01
660 725 4.748600 GTGGATATTAGCACTCGGTTTACC 59.251 45.833 0.00 0.00 0.00 2.85
665 730 1.125711 AGCACTCGGTTTACCCACCT 61.126 55.000 0.00 0.00 34.22 4.00
686 751 3.738982 TGAAGAATCGAACAAGGCTTCA 58.261 40.909 0.00 0.00 39.30 3.02
766 831 3.085010 CACAGAAAACACGCGCGC 61.085 61.111 32.58 23.91 0.00 6.86
767 832 3.568743 ACAGAAAACACGCGCGCA 61.569 55.556 32.58 0.00 0.00 6.09
812 877 2.789409 ATAAAACAGGAGCGGCTTCT 57.211 45.000 4.55 4.55 0.00 2.85
844 909 3.245052 CCAAGATTCTCCCACTTTGACCT 60.245 47.826 0.00 0.00 0.00 3.85
852 917 0.539669 CCACTTTGACCTCCCAACCC 60.540 60.000 0.00 0.00 0.00 4.11
854 919 1.133482 CACTTTGACCTCCCAACCCTT 60.133 52.381 0.00 0.00 0.00 3.95
859 930 0.034089 GACCTCCCAACCCTTCATGG 60.034 60.000 0.00 0.00 36.42 3.66
877 948 6.443995 TCATGGGCTGCAGCATATATATAT 57.556 37.500 37.63 16.84 44.36 0.86
878 949 7.557875 TCATGGGCTGCAGCATATATATATA 57.442 36.000 37.63 12.43 44.36 0.86
879 950 8.154420 TCATGGGCTGCAGCATATATATATAT 57.846 34.615 37.63 13.97 44.36 0.86
880 951 9.270707 TCATGGGCTGCAGCATATATATATATA 57.729 33.333 37.63 13.60 44.36 0.86
1056 1127 1.891933 TCTGGGATGGGCTTCACATA 58.108 50.000 0.00 0.00 0.00 2.29
1144 1215 6.475504 TCCAATAAGCTGAAGAAGTTCATCA 58.524 36.000 10.20 10.20 41.96 3.07
1474 1546 3.588955 CACATCTTCTTGTGGACGATCA 58.411 45.455 0.00 0.00 42.63 2.92
1475 1547 3.996363 CACATCTTCTTGTGGACGATCAA 59.004 43.478 0.00 0.00 42.63 2.57
1484 1556 5.639506 TCTTGTGGACGATCAAAAGAGAATC 59.360 40.000 9.95 0.00 36.41 2.52
1521 1593 5.405269 GCACCTGGTTCATAATTTGTTTCAC 59.595 40.000 0.00 0.00 0.00 3.18
1528 1600 9.703892 TGGTTCATAATTTGTTTCACCTTAATG 57.296 29.630 0.00 0.00 0.00 1.90
1540 1612 5.522315 TCACCTTAATGACCCCACATTTA 57.478 39.130 0.00 0.00 40.36 1.40
1547 1619 2.265367 TGACCCCACATTTAGAGCTGA 58.735 47.619 0.00 0.00 0.00 4.26
1580 1652 6.126863 AGGTGATTCTGTCCTGACATTAAA 57.873 37.500 0.00 0.00 41.01 1.52
1614 1686 5.821995 TCTGATCCTCTGCAGATATCTATCG 59.178 44.000 26.90 17.64 36.31 2.92
1638 1710 7.768582 TCGACTTGGTTCATATTTGATGTATGT 59.231 33.333 0.00 0.00 32.63 2.29
1647 1719 8.278729 TCATATTTGATGTATGTTCAACAGCA 57.721 30.769 0.00 0.00 41.17 4.41
1674 1746 4.387026 TCAACCCATCATCCTTCTGTTT 57.613 40.909 0.00 0.00 0.00 2.83
1738 1810 2.460757 TAGGTTGTGGCGTCTTAACC 57.539 50.000 15.28 15.28 42.19 2.85
1768 1840 1.066303 CGCTGTTTGCCAGGTTAACAA 59.934 47.619 8.10 0.00 41.81 2.83
1770 1842 2.159170 GCTGTTTGCCAGGTTAACAACA 60.159 45.455 8.10 7.27 41.81 3.33
1774 1846 4.404073 TGTTTGCCAGGTTAACAACATCTT 59.596 37.500 8.10 0.00 0.00 2.40
1777 1849 4.406456 TGCCAGGTTAACAACATCTTCAT 58.594 39.130 8.10 0.00 0.00 2.57
1974 2046 9.807649 AAGTTTCAACCATGCAGAATATTAATC 57.192 29.630 0.00 0.00 0.00 1.75
1982 2054 9.236006 ACCATGCAGAATATTAATCATTACTCC 57.764 33.333 0.00 0.00 0.00 3.85
1983 2055 8.680903 CCATGCAGAATATTAATCATTACTCCC 58.319 37.037 0.00 0.00 0.00 4.30
1984 2056 9.458727 CATGCAGAATATTAATCATTACTCCCT 57.541 33.333 0.00 0.00 0.00 4.20
1985 2057 9.678260 ATGCAGAATATTAATCATTACTCCCTC 57.322 33.333 0.00 0.00 0.00 4.30
1986 2058 8.884323 TGCAGAATATTAATCATTACTCCCTCT 58.116 33.333 0.00 0.00 0.00 3.69
1987 2059 9.160496 GCAGAATATTAATCATTACTCCCTCTG 57.840 37.037 0.00 0.00 0.00 3.35
2004 2076 9.495382 ACTCCCTCTGTAAAGAAATATAAGAGT 57.505 33.333 0.00 0.00 0.00 3.24
2005 2077 9.757227 CTCCCTCTGTAAAGAAATATAAGAGTG 57.243 37.037 0.00 0.00 0.00 3.51
2006 2078 9.268282 TCCCTCTGTAAAGAAATATAAGAGTGT 57.732 33.333 0.00 0.00 0.00 3.55
2007 2079 9.892130 CCCTCTGTAAAGAAATATAAGAGTGTT 57.108 33.333 0.00 0.00 0.00 3.32
2023 2095 7.736447 AAGAGTGTTTAGATCACCAAAGAAG 57.264 36.000 0.00 0.00 36.58 2.85
2024 2096 6.831976 AGAGTGTTTAGATCACCAAAGAAGT 58.168 36.000 0.00 0.00 36.58 3.01
2025 2097 7.283329 AGAGTGTTTAGATCACCAAAGAAGTT 58.717 34.615 0.00 0.00 36.58 2.66
2026 2098 8.429641 AGAGTGTTTAGATCACCAAAGAAGTTA 58.570 33.333 0.00 0.00 36.58 2.24
2027 2099 9.220767 GAGTGTTTAGATCACCAAAGAAGTTAT 57.779 33.333 0.00 0.00 36.58 1.89
2028 2100 9.574516 AGTGTTTAGATCACCAAAGAAGTTATT 57.425 29.630 0.00 0.00 36.58 1.40
2038 2110 9.403583 TCACCAAAGAAGTTATTTAAACACTCT 57.596 29.630 0.00 1.10 0.00 3.24
2059 2131 9.640963 CACTCTTATATATTTCTTTACGGAGGG 57.359 37.037 0.00 0.00 0.00 4.30
2060 2132 9.597681 ACTCTTATATATTTCTTTACGGAGGGA 57.402 33.333 0.00 0.00 0.00 4.20
2062 2134 9.597681 TCTTATATATTTCTTTACGGAGGGAGT 57.402 33.333 0.00 0.00 0.00 3.85
2083 2155 7.290813 GGAGTATATTCCCAGGAGAACAAAAT 58.709 38.462 2.83 0.00 0.00 1.82
2219 2291 1.996786 GATTGGTGCCGTGATGCCTG 61.997 60.000 0.00 0.00 0.00 4.85
2231 2303 2.033049 GTGATGCCTGCATTCAGATCAC 59.967 50.000 6.02 10.07 42.30 3.06
2237 2309 2.420269 CCTGCATTCAGATCACAGAGCT 60.420 50.000 0.00 0.00 42.95 4.09
2477 2563 3.937079 CTCACAGAGCATTCAATGTAGCA 59.063 43.478 0.00 0.00 0.00 3.49
2478 2564 3.686241 TCACAGAGCATTCAATGTAGCAC 59.314 43.478 0.00 0.00 0.00 4.40
2481 2567 4.763793 ACAGAGCATTCAATGTAGCACTTT 59.236 37.500 0.00 0.00 0.00 2.66
2482 2568 5.242393 ACAGAGCATTCAATGTAGCACTTTT 59.758 36.000 0.00 0.00 0.00 2.27
2483 2569 6.430925 ACAGAGCATTCAATGTAGCACTTTTA 59.569 34.615 0.00 0.00 0.00 1.52
2484 2570 7.121759 ACAGAGCATTCAATGTAGCACTTTTAT 59.878 33.333 0.00 0.00 0.00 1.40
2486 2572 9.177608 AGAGCATTCAATGTAGCACTTTTATTA 57.822 29.630 0.00 0.00 0.00 0.98
2487 2573 9.956720 GAGCATTCAATGTAGCACTTTTATTAT 57.043 29.630 0.00 0.00 0.00 1.28
2493 2579 9.589111 TCAATGTAGCACTTTTATTATACGACA 57.411 29.630 0.00 0.00 0.00 4.35
2497 2583 7.709182 TGTAGCACTTTTATTATACGACATGCT 59.291 33.333 0.00 0.00 42.10 3.79
2498 2584 7.553881 AGCACTTTTATTATACGACATGCTT 57.446 32.000 0.00 0.00 36.31 3.91
2499 2585 7.409697 AGCACTTTTATTATACGACATGCTTG 58.590 34.615 0.00 0.00 36.31 4.01
2500 2586 6.632834 GCACTTTTATTATACGACATGCTTGG 59.367 38.462 4.44 0.00 0.00 3.61
2501 2587 7.466725 GCACTTTTATTATACGACATGCTTGGA 60.467 37.037 4.44 0.00 0.00 3.53
2502 2588 8.394877 CACTTTTATTATACGACATGCTTGGAA 58.605 33.333 4.44 0.00 0.00 3.53
2503 2589 8.952278 ACTTTTATTATACGACATGCTTGGAAA 58.048 29.630 4.44 0.00 0.00 3.13
2504 2590 9.781834 CTTTTATTATACGACATGCTTGGAAAA 57.218 29.630 4.44 0.00 0.00 2.29
2506 2592 9.729023 TTTATTATACGACATGCTTGGAAAATG 57.271 29.630 4.44 0.00 0.00 2.32
2510 2600 5.138125 ACGACATGCTTGGAAAATGAAAT 57.862 34.783 4.44 0.00 0.00 2.17
2512 2602 6.324819 ACGACATGCTTGGAAAATGAAATAG 58.675 36.000 4.44 0.00 0.00 1.73
2540 2630 6.064060 CAGAAATAGGCTGTATTTGGATCCA 58.936 40.000 11.44 11.44 0.00 3.41
2541 2631 6.718454 CAGAAATAGGCTGTATTTGGATCCAT 59.282 38.462 17.06 3.82 0.00 3.41
2542 2632 7.884877 CAGAAATAGGCTGTATTTGGATCCATA 59.115 37.037 17.06 11.90 0.00 2.74
2543 2633 7.885399 AGAAATAGGCTGTATTTGGATCCATAC 59.115 37.037 17.06 16.30 0.00 2.39
2544 2634 6.702449 ATAGGCTGTATTTGGATCCATACA 57.298 37.500 21.57 21.57 0.00 2.29
2546 2636 5.957132 AGGCTGTATTTGGATCCATACAAT 58.043 37.500 22.60 18.26 29.18 2.71
2572 2663 6.874288 AAGTTGTGAAGATCTTGAGAAAGG 57.126 37.500 14.00 0.00 0.00 3.11
2598 2689 9.953825 GTAGCACTTTTATTATATACGACATGC 57.046 33.333 0.00 0.00 0.00 4.06
2667 2758 7.122353 GCATTAGAATCCTATTCTTGCATGGAT 59.878 37.037 16.11 0.00 38.99 3.41
2669 2760 5.322754 AGAATCCTATTCTTGCATGGATGG 58.677 41.667 3.62 0.57 37.56 3.51
2804 2895 5.422214 AGTTACCGTCATTCTTCTTCCAT 57.578 39.130 0.00 0.00 0.00 3.41
3095 3186 9.461312 TTTCATTGCAGAACTGGTAATATAGTT 57.539 29.630 3.99 0.00 39.67 2.24
3323 3414 1.226746 AGCTTGTGCAAGTTCGTACC 58.773 50.000 12.75 0.00 42.74 3.34
3336 3427 6.905609 GCAAGTTCGTACCATTAAGCTAATTC 59.094 38.462 0.00 0.00 0.00 2.17
3341 3432 4.213482 CGTACCATTAAGCTAATTCCCAGC 59.787 45.833 0.00 0.00 39.41 4.85
3412 3503 6.144724 CGAGCAGGTATAATTTCTTCAGCTAC 59.855 42.308 0.00 0.00 0.00 3.58
3426 3517 3.095332 TCAGCTACAATGCAGAGACTCT 58.905 45.455 0.00 0.00 34.99 3.24
3438 3529 3.120199 GCAGAGACTCTCAGATATCGCTC 60.120 52.174 0.69 0.00 32.06 5.03
3445 3536 6.939730 AGACTCTCAGATATCGCTCAGATTTA 59.060 38.462 0.00 0.00 40.66 1.40
3450 3541 7.611855 TCTCAGATATCGCTCAGATTTACCATA 59.388 37.037 0.00 0.00 40.66 2.74
3556 3647 4.682778 TGGTGCTCTATGTAACATACCC 57.317 45.455 0.00 0.00 0.00 3.69
3643 3734 4.012374 GAGAGGCCATTCAAAATCACAGA 58.988 43.478 5.01 0.00 0.00 3.41
3658 3749 6.981762 AATCACAGAGAAGACAATGACATC 57.018 37.500 0.00 0.00 0.00 3.06
3667 3758 7.768120 AGAGAAGACAATGACATCCTAATGAAC 59.232 37.037 0.00 0.00 36.67 3.18
3713 3804 6.931281 TCAATTTTGGAACACAGTCAAACAAA 59.069 30.769 0.00 0.00 39.29 2.83
3720 3811 7.254852 TGGAACACAGTCAAACAAATTAAGAC 58.745 34.615 0.00 0.00 0.00 3.01
3752 3843 7.208080 TCGTCTAAAGAGAAGCTAACAACTTT 58.792 34.615 14.42 14.42 31.96 2.66
3863 3954 8.577296 CCTATTTCATATACCTCGAGAAGAACA 58.423 37.037 15.71 0.00 0.00 3.18
3956 4047 4.042884 TCTGGAGATGGTCCTGATTCAAT 58.957 43.478 0.00 0.00 45.81 2.57
3964 4055 6.825721 AGATGGTCCTGATTCAATGAAGTTAC 59.174 38.462 1.10 0.00 0.00 2.50
4043 4134 8.850007 AGATTATCAGATGGAATGATGAACAG 57.150 34.615 0.00 0.00 37.91 3.16
4192 4283 2.347490 CGGGTTCTCCACACAGGG 59.653 66.667 0.00 0.00 38.24 4.45
4375 4466 7.437862 TCAAAATTGGCAGTAAGTGAAAATGTC 59.562 33.333 0.00 0.00 0.00 3.06
4390 4481 7.661437 AGTGAAAATGTCTTTAGCATGTGACTA 59.339 33.333 0.00 0.00 0.00 2.59
4404 4495 7.833786 AGCATGTGACTAATTTTGATTCATGT 58.166 30.769 0.00 0.00 34.56 3.21
4406 4497 9.571810 GCATGTGACTAATTTTGATTCATGTTA 57.428 29.630 0.00 0.00 34.56 2.41
4421 4526 5.521906 TCATGTTATAGCAGAGACCAGAC 57.478 43.478 0.00 0.00 0.00 3.51
4442 4547 4.995124 ACATACACCGCACTTTCTAGTAG 58.005 43.478 0.00 0.00 31.96 2.57
4443 4548 4.461781 ACATACACCGCACTTTCTAGTAGT 59.538 41.667 0.00 0.00 31.96 2.73
4444 4549 5.649395 ACATACACCGCACTTTCTAGTAGTA 59.351 40.000 0.00 0.00 31.96 1.82
4508 4613 1.929836 CGCTATGCAGGACAGAAGTTC 59.070 52.381 0.00 0.00 0.00 3.01
4526 4631 0.464036 TCCCAGATTTCCATCCGACG 59.536 55.000 0.00 0.00 0.00 5.12
4545 4650 4.705337 ACGAAAGTGGTCAGTAGAGATC 57.295 45.455 0.00 0.00 46.97 2.75
4583 4688 1.275666 TTGGTGTCATCCGAGATGGT 58.724 50.000 12.17 0.00 39.52 3.55
4805 4935 2.765699 TGCACAGAGTCATGTATGCCTA 59.234 45.455 0.00 0.00 0.00 3.93
4875 5005 8.234136 TCGAGTCATGTGGTAATCTTATTACT 57.766 34.615 9.09 0.00 0.00 2.24
4919 5049 8.770438 TCTTTATTGTTTGTTTTGACTGCTTT 57.230 26.923 0.00 0.00 0.00 3.51
4932 5062 9.143631 GTTTTGACTGCTTTGAATATTTGCTAT 57.856 29.630 0.00 0.00 0.00 2.97
4985 5115 0.034089 ATGCAGAGGCCAGGGTTAAC 60.034 55.000 5.01 0.00 40.13 2.01
5036 5166 1.597937 CCGCTTCAACTGCAAACTCAC 60.598 52.381 0.00 0.00 0.00 3.51
5066 5196 2.239400 GGCCTTACAAAGCTGGAGTTT 58.761 47.619 0.00 0.00 0.00 2.66
5078 5209 2.880890 GCTGGAGTTTGAAGAGCTTTGA 59.119 45.455 0.00 0.00 0.00 2.69
5134 5265 6.582636 ACAATTATTAGCCTGTTCGATCAGA 58.417 36.000 22.26 5.24 37.61 3.27
5185 5327 1.142097 GAGCTGGCTTAGACGGGAC 59.858 63.158 0.00 0.00 0.00 4.46
5209 5357 6.204882 ACATTAAGAAGAAACTTCTTGACCCG 59.795 38.462 26.60 16.93 46.84 5.28
5210 5358 2.495084 AGAAGAAACTTCTTGACCCGC 58.505 47.619 9.40 0.00 46.84 6.13
5235 5386 3.912496 AAAGCTTCTTGGGTTTTGCTT 57.088 38.095 0.00 0.00 41.67 3.91
5264 5415 0.748005 ATGTATGGCCAGACAACGCC 60.748 55.000 34.92 6.89 45.92 5.68
5296 5447 2.507471 CTGGCTTAATCTTGGGGAGACT 59.493 50.000 0.00 0.00 37.17 3.24
5318 5469 8.478877 AGACTAACACCTCCTATTTTCACATAG 58.521 37.037 0.00 0.00 0.00 2.23
5327 5478 1.075542 TTTTCACATAGACGCCAGCG 58.924 50.000 11.05 11.05 46.03 5.18
5353 5507 5.709164 CAGGAGGAAAAACTTCATCAGTCAT 59.291 40.000 2.43 0.00 32.94 3.06
5365 5519 8.088463 ACTTCATCAGTCATCTTAAGGAGAAT 57.912 34.615 1.85 0.00 38.06 2.40
5370 5524 7.911130 TCAGTCATCTTAAGGAGAATGATCT 57.089 36.000 17.92 10.34 38.06 2.75
5374 5528 9.599056 AGTCATCTTAAGGAGAATGATCTGATA 57.401 33.333 1.85 0.00 38.06 2.15
5436 5590 1.299926 CGGTAAGAGAATCGGCCGG 60.300 63.158 27.83 6.80 41.89 6.13
5442 5596 4.569180 AGAATCGGCCGGCCCATG 62.569 66.667 39.24 25.64 0.00 3.66
5460 5614 2.959507 TGTACAGATCACATGACGGG 57.040 50.000 0.00 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 144 7.190871 TGTTATTTGAAGTTCCGTCTTGTTTC 58.809 34.615 0.00 0.00 0.00 2.78
156 214 1.783250 AAGGGCTGAACAGACTGGGG 61.783 60.000 7.51 0.00 36.46 4.96
212 270 3.213506 CCATTGAGATATTGCCGGTTCA 58.786 45.455 1.90 0.00 0.00 3.18
214 272 1.956477 GCCATTGAGATATTGCCGGTT 59.044 47.619 1.90 0.00 0.00 4.44
215 273 1.609208 GCCATTGAGATATTGCCGGT 58.391 50.000 1.90 0.00 0.00 5.28
219 277 4.829064 TTTACCGCCATTGAGATATTGC 57.171 40.909 0.00 0.00 0.00 3.56
229 287 1.326951 GCCCACCATTTACCGCCATT 61.327 55.000 0.00 0.00 0.00 3.16
235 293 2.427095 GTTCTGATGCCCACCATTTACC 59.573 50.000 0.00 0.00 33.29 2.85
245 303 2.401766 CCTGCGTGTTCTGATGCCC 61.402 63.158 0.00 0.00 0.00 5.36
272 330 3.648545 AGGTATCCTGTCAAGCCTAATCC 59.351 47.826 0.00 0.00 29.57 3.01
279 337 2.501723 TCTCCAAGGTATCCTGTCAAGC 59.498 50.000 0.00 0.00 32.13 4.01
287 345 8.050930 TGGTTAATAAGTTTCTCCAAGGTATCC 58.949 37.037 0.00 0.00 0.00 2.59
292 350 8.348285 TGAATGGTTAATAAGTTTCTCCAAGG 57.652 34.615 0.00 0.00 0.00 3.61
333 391 5.991861 TGGTGGTTCAAGACTTAGTTTACA 58.008 37.500 0.00 0.00 0.00 2.41
340 398 4.764050 TTGTCTGGTGGTTCAAGACTTA 57.236 40.909 3.94 0.00 0.00 2.24
398 460 2.710377 TGGATGTCATTTCCGGAAGTG 58.290 47.619 28.61 28.61 35.94 3.16
399 461 3.652057 ATGGATGTCATTTCCGGAAGT 57.348 42.857 17.97 12.31 35.94 3.01
420 482 0.675633 GAACAAGCATGGCCACAACT 59.324 50.000 8.16 2.02 0.00 3.16
457 519 4.338682 AGTCTAGTTATACAGTGCCTTCCG 59.661 45.833 0.00 0.00 0.00 4.30
491 553 0.389037 GTGAGCGTCATCAGTGAGCA 60.389 55.000 0.00 0.00 34.36 4.26
496 558 1.633561 CAATCGTGAGCGTCATCAGT 58.366 50.000 0.00 0.00 39.49 3.41
564 627 3.712881 GTGGCCGTGACTCGCAAC 61.713 66.667 0.00 0.00 38.35 4.17
568 631 0.670546 ATTGAAGTGGCCGTGACTCG 60.671 55.000 0.00 0.00 39.52 4.18
576 639 2.749621 CAGTCCTTACATTGAAGTGGCC 59.250 50.000 0.00 0.00 0.00 5.36
627 692 3.060602 GCTAATATCCACTTCAGCCGTC 58.939 50.000 0.00 0.00 0.00 4.79
644 709 1.002315 GGTGGGTAAACCGAGTGCTAA 59.998 52.381 0.00 0.00 44.64 3.09
658 723 1.697432 TGTTCGATTCTTCAGGTGGGT 59.303 47.619 0.00 0.00 0.00 4.51
659 724 2.472695 TGTTCGATTCTTCAGGTGGG 57.527 50.000 0.00 0.00 0.00 4.61
660 725 2.744202 CCTTGTTCGATTCTTCAGGTGG 59.256 50.000 0.00 0.00 0.00 4.61
665 730 3.738982 TGAAGCCTTGTTCGATTCTTCA 58.261 40.909 0.00 0.00 37.97 3.02
686 751 2.957402 TGCATCACACCTTCTCCTTT 57.043 45.000 0.00 0.00 0.00 3.11
766 831 0.310854 GAGGAAAACAACAGGGCGTG 59.689 55.000 5.50 5.50 0.00 5.34
767 832 0.106918 TGAGGAAAACAACAGGGCGT 60.107 50.000 0.00 0.00 0.00 5.68
852 917 1.617322 ATATGCTGCAGCCCATGAAG 58.383 50.000 34.64 0.00 41.18 3.02
854 919 4.783560 ATATATATGCTGCAGCCCATGA 57.216 40.909 34.64 17.30 41.18 3.07
927 998 9.769677 GTGGAGGATGGCACCTATATATATATA 57.230 37.037 11.21 11.21 40.73 0.86
928 999 8.241612 TGTGGAGGATGGCACCTATATATATAT 58.758 37.037 10.10 10.10 40.73 0.86
929 1000 7.509318 GTGTGGAGGATGGCACCTATATATATA 59.491 40.741 8.34 2.49 40.73 0.86
930 1001 6.327626 GTGTGGAGGATGGCACCTATATATAT 59.672 42.308 8.34 0.00 40.73 0.86
931 1002 5.661312 GTGTGGAGGATGGCACCTATATATA 59.339 44.000 8.34 0.00 40.73 0.86
932 1003 4.471386 GTGTGGAGGATGGCACCTATATAT 59.529 45.833 8.34 0.00 40.73 0.86
933 1004 3.838317 GTGTGGAGGATGGCACCTATATA 59.162 47.826 8.34 0.00 40.73 0.86
934 1005 2.639839 GTGTGGAGGATGGCACCTATAT 59.360 50.000 8.34 0.00 40.73 0.86
935 1006 2.047061 GTGTGGAGGATGGCACCTATA 58.953 52.381 8.34 0.00 40.73 1.31
936 1007 0.839946 GTGTGGAGGATGGCACCTAT 59.160 55.000 8.34 0.00 40.73 2.57
937 1008 1.271840 GGTGTGGAGGATGGCACCTA 61.272 60.000 8.34 0.00 45.64 3.08
951 1022 4.036852 TCGACTCTATATGCAGAAGGTGTG 59.963 45.833 0.00 0.00 0.00 3.82
1056 1127 2.357517 CTGTCGCTGCTCCCGTTT 60.358 61.111 0.00 0.00 0.00 3.60
1474 1546 4.389077 CGAACCTTACTGCGATTCTCTTTT 59.611 41.667 0.00 0.00 0.00 2.27
1475 1547 3.927142 CGAACCTTACTGCGATTCTCTTT 59.073 43.478 0.00 0.00 0.00 2.52
1484 1556 1.374252 AGGTGCGAACCTTACTGCG 60.374 57.895 10.19 0.00 36.56 5.18
1521 1593 4.580580 GCTCTAAATGTGGGGTCATTAAGG 59.419 45.833 0.00 0.00 37.09 2.69
1528 1600 3.350219 TTCAGCTCTAAATGTGGGGTC 57.650 47.619 0.00 0.00 0.00 4.46
1540 1612 0.251519 CCTGGGCCTTTTTCAGCTCT 60.252 55.000 4.53 0.00 0.00 4.09
1547 1619 2.250924 CAGAATCACCTGGGCCTTTTT 58.749 47.619 4.53 0.00 0.00 1.94
1580 1652 7.515586 TCTGCAGAGGATCAGATCATATTTTT 58.484 34.615 13.74 0.00 37.82 1.94
1614 1686 9.722056 GAACATACATCAAATATGAACCAAGTC 57.278 33.333 0.00 0.00 39.49 3.01
1638 1710 2.102252 GGGTTGAAATGGTGCTGTTGAA 59.898 45.455 0.00 0.00 0.00 2.69
1647 1719 3.763557 AGGATGATGGGTTGAAATGGT 57.236 42.857 0.00 0.00 0.00 3.55
1674 1746 4.447138 AAGGTCATTTCCCTTGTGTGTA 57.553 40.909 0.00 0.00 40.79 2.90
1707 1779 3.679389 CCACAACCTAAGCAGATTGAGT 58.321 45.455 0.00 0.00 0.00 3.41
1738 1810 1.202568 CAAACAGCGTGCTGACTCG 59.797 57.895 27.26 9.40 46.30 4.18
1791 1863 6.729391 TGTGCCATTTTTCATTCATCATTG 57.271 33.333 0.00 0.00 0.00 2.82
1804 1876 8.316214 AGTAGATGATCAAATTTGTGCCATTTT 58.684 29.630 17.47 12.55 0.00 1.82
1927 1999 8.861033 AACTTTTGAAGGTAACGGTAAAAATC 57.139 30.769 0.00 0.00 46.39 2.17
1939 2011 5.127845 TGCATGGTTGAAACTTTTGAAGGTA 59.872 36.000 0.00 0.00 0.00 3.08
1978 2050 9.495382 ACTCTTATATTTCTTTACAGAGGGAGT 57.505 33.333 0.00 0.00 32.21 3.85
1979 2051 9.757227 CACTCTTATATTTCTTTACAGAGGGAG 57.243 37.037 0.00 0.00 32.92 4.30
1980 2052 9.268282 ACACTCTTATATTTCTTTACAGAGGGA 57.732 33.333 2.59 0.00 34.50 4.20
1981 2053 9.892130 AACACTCTTATATTTCTTTACAGAGGG 57.108 33.333 0.00 0.00 36.55 4.30
1997 2069 9.442047 CTTCTTTGGTGATCTAAACACTCTTAT 57.558 33.333 0.00 0.00 38.20 1.73
1998 2070 8.429641 ACTTCTTTGGTGATCTAAACACTCTTA 58.570 33.333 0.00 0.00 38.20 2.10
1999 2071 7.283329 ACTTCTTTGGTGATCTAAACACTCTT 58.717 34.615 0.00 0.00 38.20 2.85
2000 2072 6.831976 ACTTCTTTGGTGATCTAAACACTCT 58.168 36.000 0.00 0.00 38.20 3.24
2001 2073 7.497925 AACTTCTTTGGTGATCTAAACACTC 57.502 36.000 0.00 0.00 38.20 3.51
2002 2074 9.574516 AATAACTTCTTTGGTGATCTAAACACT 57.425 29.630 0.00 0.00 38.20 3.55
2012 2084 9.403583 AGAGTGTTTAAATAACTTCTTTGGTGA 57.596 29.630 7.65 0.00 0.00 4.02
2033 2105 9.640963 CCCTCCGTAAAGAAATATATAAGAGTG 57.359 37.037 0.00 0.00 0.00 3.51
2034 2106 9.597681 TCCCTCCGTAAAGAAATATATAAGAGT 57.402 33.333 0.00 0.00 0.00 3.24
2036 2108 9.597681 ACTCCCTCCGTAAAGAAATATATAAGA 57.402 33.333 0.00 0.00 0.00 2.10
2043 2115 8.810041 GGAATATACTCCCTCCGTAAAGAAATA 58.190 37.037 0.00 0.00 0.00 1.40
2044 2116 7.677892 GGAATATACTCCCTCCGTAAAGAAAT 58.322 38.462 0.00 0.00 0.00 2.17
2045 2117 7.059202 GGAATATACTCCCTCCGTAAAGAAA 57.941 40.000 0.00 0.00 0.00 2.52
2046 2118 6.661304 GGAATATACTCCCTCCGTAAAGAA 57.339 41.667 0.00 0.00 0.00 2.52
2058 2130 5.888982 TTGTTCTCCTGGGAATATACTCC 57.111 43.478 0.00 0.00 34.41 3.85
2061 2133 8.936864 CGATATTTTGTTCTCCTGGGAATATAC 58.063 37.037 0.00 0.00 0.00 1.47
2062 2134 7.606456 GCGATATTTTGTTCTCCTGGGAATATA 59.394 37.037 0.00 0.00 0.00 0.86
2083 2155 8.495148 TCGTTACGTATTTTATAGTCAGCGATA 58.505 33.333 4.24 0.00 0.00 2.92
2219 2291 4.213694 CCATAAGCTCTGTGATCTGAATGC 59.786 45.833 0.00 0.00 0.00 3.56
2231 2303 9.019656 AGTAACATATCTAGTCCATAAGCTCTG 57.980 37.037 0.00 0.00 0.00 3.35
2237 2309 8.797438 CAGAGCAGTAACATATCTAGTCCATAA 58.203 37.037 0.00 0.00 0.00 1.90
2477 2563 8.500753 TTCCAAGCATGTCGTATAATAAAAGT 57.499 30.769 0.00 0.00 0.00 2.66
2478 2564 9.781834 TTTTCCAAGCATGTCGTATAATAAAAG 57.218 29.630 0.00 0.00 0.00 2.27
2481 2567 9.114952 TCATTTTCCAAGCATGTCGTATAATAA 57.885 29.630 0.00 0.00 0.00 1.40
2482 2568 8.669946 TCATTTTCCAAGCATGTCGTATAATA 57.330 30.769 0.00 0.00 0.00 0.98
2483 2569 7.566760 TCATTTTCCAAGCATGTCGTATAAT 57.433 32.000 0.00 0.00 0.00 1.28
2484 2570 6.993786 TCATTTTCCAAGCATGTCGTATAA 57.006 33.333 0.00 0.00 0.00 0.98
2486 2572 5.895636 TTCATTTTCCAAGCATGTCGTAT 57.104 34.783 0.00 0.00 0.00 3.06
2487 2573 5.697473 TTTCATTTTCCAAGCATGTCGTA 57.303 34.783 0.00 0.00 0.00 3.43
2488 2574 4.582701 TTTCATTTTCCAAGCATGTCGT 57.417 36.364 0.00 0.00 0.00 4.34
2489 2575 5.745294 CCTATTTCATTTTCCAAGCATGTCG 59.255 40.000 0.00 0.00 0.00 4.35
2490 2576 6.866480 TCCTATTTCATTTTCCAAGCATGTC 58.134 36.000 0.00 0.00 0.00 3.06
2491 2577 6.855763 TCCTATTTCATTTTCCAAGCATGT 57.144 33.333 0.00 0.00 0.00 3.21
2492 2578 7.098477 TGTTCCTATTTCATTTTCCAAGCATG 58.902 34.615 0.00 0.00 0.00 4.06
2493 2579 7.178983 TCTGTTCCTATTTCATTTTCCAAGCAT 59.821 33.333 0.00 0.00 0.00 3.79
2494 2580 6.493115 TCTGTTCCTATTTCATTTTCCAAGCA 59.507 34.615 0.00 0.00 0.00 3.91
2500 2586 9.521503 GCCTATTTCTGTTCCTATTTCATTTTC 57.478 33.333 0.00 0.00 0.00 2.29
2501 2587 9.259832 AGCCTATTTCTGTTCCTATTTCATTTT 57.740 29.630 0.00 0.00 0.00 1.82
2502 2588 8.689972 CAGCCTATTTCTGTTCCTATTTCATTT 58.310 33.333 0.00 0.00 0.00 2.32
2503 2589 7.836183 ACAGCCTATTTCTGTTCCTATTTCATT 59.164 33.333 0.00 0.00 41.61 2.57
2504 2590 7.349598 ACAGCCTATTTCTGTTCCTATTTCAT 58.650 34.615 0.00 0.00 41.61 2.57
2505 2591 6.721318 ACAGCCTATTTCTGTTCCTATTTCA 58.279 36.000 0.00 0.00 41.61 2.69
2506 2592 8.910351 ATACAGCCTATTTCTGTTCCTATTTC 57.090 34.615 0.77 0.00 41.61 2.17
2510 2600 7.054124 CCAAATACAGCCTATTTCTGTTCCTA 58.946 38.462 0.77 0.00 41.61 2.94
2512 2602 5.885912 TCCAAATACAGCCTATTTCTGTTCC 59.114 40.000 0.77 0.00 41.61 3.62
2542 2632 9.342308 TCTCAAGATCTTCACAACTTTAATTGT 57.658 29.630 4.57 0.00 43.67 2.71
2546 2636 8.840321 CCTTTCTCAAGATCTTCACAACTTTAA 58.160 33.333 4.57 0.00 30.57 1.52
2572 2663 9.953825 GCATGTCGTATATAATAAAAGTGCTAC 57.046 33.333 0.00 0.00 0.00 3.58
2598 2689 6.796785 AGGGGATACATTTCATTTTCCAAG 57.203 37.500 0.00 0.00 39.74 3.61
2667 2758 1.493022 AGAACTTGGTACCTTGTGCCA 59.507 47.619 14.36 0.00 45.91 4.92
2669 2760 2.949644 ACAAGAACTTGGTACCTTGTGC 59.050 45.455 14.36 10.32 45.01 4.57
2798 2889 6.611613 TCAATAGGACTATAGGCATGGAAG 57.388 41.667 8.15 0.00 0.00 3.46
2919 3010 3.256879 TGAACTGTAGGCAGAAGTGAGAG 59.743 47.826 1.30 0.00 45.28 3.20
3113 3204 7.676683 TTAGCAGTTCTCCCAAGATAGTTAT 57.323 36.000 0.00 0.00 0.00 1.89
3161 3252 7.559335 TGCACTTCCATGACCTATATTATCT 57.441 36.000 0.00 0.00 0.00 1.98
3323 3414 6.939163 AGATAGTGCTGGGAATTAGCTTAATG 59.061 38.462 0.00 0.00 41.66 1.90
3387 3478 5.053145 AGCTGAAGAAATTATACCTGCTCG 58.947 41.667 0.00 0.00 0.00 5.03
3412 3503 5.155643 CGATATCTGAGAGTCTCTGCATTG 58.844 45.833 20.64 14.82 31.05 2.82
3426 3517 6.596309 ATGGTAAATCTGAGCGATATCTGA 57.404 37.500 0.34 0.00 0.00 3.27
3502 3593 8.026607 CCAAACATATCACCATTCGTAACTTTT 58.973 33.333 0.00 0.00 0.00 2.27
3556 3647 1.135402 GTGCGGAAAGTAAATGGCTGG 60.135 52.381 0.00 0.00 0.00 4.85
3595 3686 2.902486 TCTTGTCCTGCTGATTCTCAGT 59.098 45.455 6.06 0.00 45.94 3.41
3643 3734 7.397221 TGTTCATTAGGATGTCATTGTCTTCT 58.603 34.615 0.00 0.00 34.77 2.85
3658 3749 6.949352 ACCTGCAATAGATTGTTCATTAGG 57.051 37.500 4.27 0.00 39.88 2.69
3667 3758 7.734924 TTGAAGCTATACCTGCAATAGATTG 57.265 36.000 11.14 0.00 36.08 2.67
3676 3767 5.835113 TCCAAAATTGAAGCTATACCTGC 57.165 39.130 0.00 0.00 0.00 4.85
3736 3827 4.740205 GGCACAAAAAGTTGTTAGCTTCTC 59.260 41.667 0.00 0.00 46.01 2.87
3741 3832 4.570369 ACATTGGCACAAAAAGTTGTTAGC 59.430 37.500 0.00 0.00 46.01 3.09
3752 3843 4.642437 TCAGTTTCTGTACATTGGCACAAA 59.358 37.500 0.00 0.00 36.67 2.83
3863 3954 1.683011 GGTGTGGCCATTGTAGCATCT 60.683 52.381 9.72 0.00 37.17 2.90
3956 4047 3.133901 TGGCACTTGTCTGAGTAACTTCA 59.866 43.478 0.00 0.00 0.00 3.02
3964 4055 0.533531 TGCTGTGGCACTTGTCTGAG 60.534 55.000 19.83 6.85 44.28 3.35
4039 4130 4.082845 TCGTTGAGATCCTCTTCTCTGTT 58.917 43.478 3.41 0.00 42.22 3.16
4043 4134 3.020984 ACCTCGTTGAGATCCTCTTCTC 58.979 50.000 0.00 0.00 42.10 2.87
4122 4213 2.564771 CTTGCTGTGGTCTTGTCTTCA 58.435 47.619 0.00 0.00 0.00 3.02
4135 4226 0.383231 GTTTGCTGACTGCTTGCTGT 59.617 50.000 4.86 4.86 43.37 4.40
4192 4283 4.555511 GCTCCTTGATATGTTTTCGGATGC 60.556 45.833 0.00 0.00 0.00 3.91
4375 4466 9.844790 TGAATCAAAATTAGTCACATGCTAAAG 57.155 29.630 0.00 0.00 32.92 1.85
4404 4495 5.302059 GGTGTATGTCTGGTCTCTGCTATAA 59.698 44.000 0.00 0.00 0.00 0.98
4406 4497 3.639094 GGTGTATGTCTGGTCTCTGCTAT 59.361 47.826 0.00 0.00 0.00 2.97
4421 4526 4.995124 ACTACTAGAAAGTGCGGTGTATG 58.005 43.478 0.00 0.00 36.36 2.39
4444 4549 9.672673 AGAAGTGCATGTTACAGTATCTAATTT 57.327 29.630 0.00 0.00 0.00 1.82
4457 4562 8.969260 ATATTTGATGAGAGAAGTGCATGTTA 57.031 30.769 0.00 0.00 0.00 2.41
4508 4613 0.464036 TCGTCGGATGGAAATCTGGG 59.536 55.000 0.00 0.00 0.00 4.45
4526 4631 4.416620 CGTGATCTCTACTGACCACTTTC 58.583 47.826 0.00 0.00 0.00 2.62
4545 4650 4.333649 ACCAATGTCATCTATTTCAGCGTG 59.666 41.667 0.00 0.00 0.00 5.34
4583 4688 8.868522 AAATCTGAAGAAAGAATATGTGGTCA 57.131 30.769 0.00 0.00 0.00 4.02
4762 4892 5.760253 GCACCTGCTATATTGTACAGTGAAT 59.240 40.000 9.51 0.00 38.21 2.57
4805 4935 5.482006 GAACTAAGAAATGCTTTTGCCCAT 58.518 37.500 1.76 0.00 46.87 4.00
5036 5166 3.716601 CTTTGTAAGGCCCTTGTGTTTG 58.283 45.455 6.16 0.00 0.00 2.93
5066 5196 6.542821 TCTTTTATCCCTTCAAAGCTCTTCA 58.457 36.000 0.00 0.00 0.00 3.02
5078 5209 6.183360 CCAAACAGGTTGTTCTTTTATCCCTT 60.183 38.462 0.00 0.00 40.14 3.95
5185 5327 6.603095 CGGGTCAAGAAGTTTCTTCTTAATG 58.397 40.000 19.72 11.81 45.23 1.90
5218 5369 2.888834 TCAAGCAAAACCCAAGAAGC 57.111 45.000 0.00 0.00 0.00 3.86
5228 5379 6.405065 GCCATACATCTCTCAATCAAGCAAAA 60.405 38.462 0.00 0.00 0.00 2.44
5235 5386 3.969312 TCTGGCCATACATCTCTCAATCA 59.031 43.478 5.51 0.00 0.00 2.57
5264 5415 1.917336 TTAAGCCAGGTAAGCCCCGG 61.917 60.000 0.00 0.00 34.57 5.73
5296 5447 7.262772 CGTCTATGTGAAAATAGGAGGTGTTA 58.737 38.462 0.00 0.00 32.03 2.41
5318 5469 4.803426 CCTCCTGTCGCTGGCGTC 62.803 72.222 14.55 9.84 40.74 5.19
5327 5478 5.066593 ACTGATGAAGTTTTTCCTCCTGTC 58.933 41.667 0.00 0.00 34.57 3.51
5353 5507 8.855110 GTCACTATCAGATCATTCTCCTTAAGA 58.145 37.037 3.36 0.00 0.00 2.10
5365 5519 8.096414 TCTTTGTGATTTGTCACTATCAGATCA 58.904 33.333 9.64 0.00 40.97 2.92
5442 5596 1.571919 GCCCGTCATGTGATCTGTAC 58.428 55.000 0.00 0.00 0.00 2.90
5460 5614 0.820226 GAGGCCAAGGAAATCAAGGC 59.180 55.000 5.01 0.00 44.48 4.35


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

AutoCloner maintained by Alex Coulton.