Multiple sequence alignment - TraesCS6D01G015500

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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 TraesCS6D01G015500 chr6D 100.000 4371 0 0 1 4371 6350248 6354618 0.000000e+00 8072.0
1 TraesCS6D01G015500 chr6D 89.406 1699 177 2 2667 4365 6371318 6373013 0.000000e+00 2137.0
2 TraesCS6D01G015500 chr6D 85.831 1715 220 15 2667 4365 6497433 6499140 0.000000e+00 1799.0
3 TraesCS6D01G015500 chr6D 91.509 1213 61 16 1 1207 6369041 6370217 0.000000e+00 1631.0
4 TraesCS6D01G015500 chr6D 86.069 1450 186 11 2925 4371 6426508 6427944 0.000000e+00 1544.0
5 TraesCS6D01G015500 chr6D 93.827 810 32 9 1889 2697 6496742 6497534 0.000000e+00 1203.0
6 TraesCS6D01G015500 chr6D 88.829 931 104 0 2369 3299 6442714 6443644 0.000000e+00 1144.0
7 TraesCS6D01G015500 chr6D 80.530 1433 265 14 2946 4371 7033393 7034818 0.000000e+00 1088.0
8 TraesCS6D01G015500 chr6D 89.239 539 45 9 1325 1854 6496245 6496779 0.000000e+00 662.0
9 TraesCS6D01G015500 chr6D 84.370 659 77 12 1202 1851 6441657 6442298 1.330000e-174 623.0
10 TraesCS6D01G015500 chr6D 86.052 466 64 1 1844 2308 6425590 6426055 2.350000e-137 499.0
11 TraesCS6D01G015500 chr6D 84.418 507 59 7 1355 1858 6370241 6370730 8.500000e-132 481.0
12 TraesCS6D01G015500 chr6D 87.724 391 48 0 1873 2263 6370673 6371063 1.430000e-124 457.0
13 TraesCS6D01G015500 chr6D 85.816 423 54 4 1889 2308 6442264 6442683 1.120000e-120 444.0
14 TraesCS6D01G015500 chr6D 85.714 399 57 0 2362 2760 6426079 6426477 5.230000e-114 422.0
15 TraesCS6D01G015500 chr6D 81.746 504 79 7 1371 1863 7032265 7032766 4.070000e-110 409.0
16 TraesCS6D01G015500 chr6D 84.384 333 50 2 2579 2910 6426368 6426699 4.220000e-85 326.0
17 TraesCS6D01G015500 chr6D 96.117 103 3 1 2667 2768 6352842 6352944 2.700000e-37 167.0
18 TraesCS6D01G015500 chr6D 96.117 103 3 1 2595 2697 6352914 6353015 2.700000e-37 167.0
19 TraesCS6D01G015500 chr6D 90.909 88 8 0 2595 2682 6443012 6443099 7.680000e-23 119.0
20 TraesCS6D01G015500 chr6D 80.808 99 19 0 1851 1949 6352026 6352124 1.300000e-10 78.7
21 TraesCS6D01G015500 chr6D 80.808 99 19 0 1779 1877 6352098 6352196 1.300000e-10 78.7
22 TraesCS6D01G015500 chr6A 88.473 2004 224 3 2369 4371 5917349 5919346 0.000000e+00 2414.0
23 TraesCS6D01G015500 chr6A 88.089 1444 170 2 2929 4371 5901924 5903366 0.000000e+00 1712.0
24 TraesCS6D01G015500 chr6A 86.345 1450 182 11 2925 4371 5940875 5942311 0.000000e+00 1567.0
25 TraesCS6D01G015500 chr6A 80.251 1433 269 14 2946 4371 6699821 6701246 0.000000e+00 1066.0
26 TraesCS6D01G015500 chr6A 88.394 853 72 6 1025 1858 5900366 5901210 0.000000e+00 1002.0
27 TraesCS6D01G015500 chr6A 89.552 603 34 12 169 765 5881908 5882487 0.000000e+00 737.0
28 TraesCS6D01G015500 chr6A 81.021 764 86 28 1112 1857 5939321 5940043 1.780000e-153 553.0
29 TraesCS6D01G015500 chr6A 86.902 481 57 3 1374 1851 5916509 5916986 6.430000e-148 534.0
30 TraesCS6D01G015500 chr6A 85.622 466 66 1 1844 2308 5939957 5940422 5.080000e-134 488.0
31 TraesCS6D01G015500 chr6A 89.714 350 36 0 1959 2308 5901263 5901612 8.620000e-122 448.0
32 TraesCS6D01G015500 chr6A 85.464 399 58 0 2362 2760 5940446 5940844 2.430000e-112 416.0
33 TraesCS6D01G015500 chr6A 92.797 236 14 2 803 1037 5882485 5882718 5.410000e-89 339.0
34 TraesCS6D01G015500 chr6A 82.493 377 62 4 2579 2953 5940735 5941109 1.170000e-85 327.0
35 TraesCS6D01G015500 chr6A 92.982 171 12 0 1 171 5881648 5881818 2.610000e-62 250.0
36 TraesCS6D01G015500 chr6A 82.927 246 33 3 2063 2308 5917082 5917318 3.420000e-51 213.0
37 TraesCS6D01G015500 chr6A 87.407 135 14 2 1889 2023 5916952 5917083 7.570000e-33 152.0
38 TraesCS6D01G015500 chr6B 88.731 1553 140 26 314 1858 11591813 11593338 0.000000e+00 1866.0
39 TraesCS6D01G015500 chr6B 85.435 1689 222 15 2696 4371 11793442 11795119 0.000000e+00 1735.0
40 TraesCS6D01G015500 chr6B 93.700 1000 61 2 3373 4371 11599598 11600596 0.000000e+00 1496.0
41 TraesCS6D01G015500 chr6B 93.052 734 41 3 1966 2698 11792792 11793516 0.000000e+00 1064.0
42 TraesCS6D01G015500 chr6B 85.411 706 76 14 1101 1792 11792085 11792777 0.000000e+00 708.0
43 TraesCS6D01G015500 chr6B 91.608 286 24 0 1885 2170 11593293 11593578 3.170000e-106 396.0
44 TraesCS6D01G015500 chr6B 94.372 231 11 2 54 284 11591588 11591816 1.930000e-93 353.0
45 TraesCS6D01G015500 chr6B 88.931 262 24 3 2667 2928 11593696 11593952 7.050000e-83 318.0
46 TraesCS6D01G015500 chr6B 81.065 169 28 2 745 910 11761888 11762055 9.860000e-27 132.0
47 TraesCS6D01G015500 chr5D 76.773 719 158 8 21 735 73793775 73794488 1.140000e-105 394.0
48 TraesCS6D01G015500 chr5D 76.761 710 156 8 21 725 553903157 553903862 5.300000e-104 388.0
49 TraesCS6D01G015500 chr1D 76.836 708 157 6 21 725 70334757 70334054 4.100000e-105 392.0
50 TraesCS6D01G015500 chr1B 75.284 704 167 6 21 720 207376146 207376846 3.260000e-86 329.0
51 TraesCS6D01G015500 chr2B 75.588 680 155 8 63 738 488046959 488046287 4.220000e-85 326.0
52 TraesCS6D01G015500 chr4B 77.406 478 100 7 267 737 665325608 665325132 1.200000e-70 278.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G015500 chr6D 6350248 6354618 4370 False 1712.680000 8072 90.770000 1 4371 5 chr6D.!!$F1 4370
1 TraesCS6D01G015500 chr6D 6496245 6499140 2895 False 1221.333333 1799 89.632333 1325 4365 3 chr6D.!!$F5 3040
2 TraesCS6D01G015500 chr6D 6369041 6373013 3972 False 1176.500000 2137 88.264250 1 4365 4 chr6D.!!$F2 4364
3 TraesCS6D01G015500 chr6D 7032265 7034818 2553 False 748.500000 1088 81.138000 1371 4371 2 chr6D.!!$F6 3000
4 TraesCS6D01G015500 chr6D 6425590 6427944 2354 False 697.750000 1544 85.554750 1844 4371 4 chr6D.!!$F3 2527
5 TraesCS6D01G015500 chr6D 6441657 6443644 1987 False 582.500000 1144 87.481000 1202 3299 4 chr6D.!!$F4 2097
6 TraesCS6D01G015500 chr6A 6699821 6701246 1425 False 1066.000000 1066 80.251000 2946 4371 1 chr6A.!!$F1 1425
7 TraesCS6D01G015500 chr6A 5900366 5903366 3000 False 1054.000000 1712 88.732333 1025 4371 3 chr6A.!!$F3 3346
8 TraesCS6D01G015500 chr6A 5916509 5919346 2837 False 828.250000 2414 86.427250 1374 4371 4 chr6A.!!$F4 2997
9 TraesCS6D01G015500 chr6A 5939321 5942311 2990 False 670.200000 1567 84.189000 1112 4371 5 chr6A.!!$F5 3259
10 TraesCS6D01G015500 chr6A 5881648 5882718 1070 False 442.000000 737 91.777000 1 1037 3 chr6A.!!$F2 1036
11 TraesCS6D01G015500 chr6B 11599598 11600596 998 False 1496.000000 1496 93.700000 3373 4371 1 chr6B.!!$F1 998
12 TraesCS6D01G015500 chr6B 11792085 11795119 3034 False 1169.000000 1735 87.966000 1101 4371 3 chr6B.!!$F4 3270
13 TraesCS6D01G015500 chr6B 11591588 11593952 2364 False 733.250000 1866 90.910500 54 2928 4 chr6B.!!$F3 2874
14 TraesCS6D01G015500 chr5D 73793775 73794488 713 False 394.000000 394 76.773000 21 735 1 chr5D.!!$F1 714
15 TraesCS6D01G015500 chr5D 553903157 553903862 705 False 388.000000 388 76.761000 21 725 1 chr5D.!!$F2 704
16 TraesCS6D01G015500 chr1D 70334054 70334757 703 True 392.000000 392 76.836000 21 725 1 chr1D.!!$R1 704
17 TraesCS6D01G015500 chr1B 207376146 207376846 700 False 329.000000 329 75.284000 21 720 1 chr1B.!!$F1 699
18 TraesCS6D01G015500 chr2B 488046287 488046959 672 True 326.000000 326 75.588000 63 738 1 chr2B.!!$R1 675

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
973 1081 0.392461 TACTTGGCCGAATGCAGTCC 60.392 55.0 8.83 0.0 43.89 3.85 F
1810 2001 0.107703 CGGCATGCCTTTCTCTGGTA 60.108 55.0 33.07 0.0 0.00 3.25 F
2617 2835 0.030092 TGGAGCTATACCCCTTGGCT 60.030 55.0 0.00 0.0 35.86 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1824 2015 0.598419 GCTTTGACAGGTTGCCAAGC 60.598 55.000 0.00 0.0 0.00 4.01 R
2682 2972 2.025510 AGAGAGATTCCCAAAGCCAAGG 60.026 50.000 0.00 0.0 0.00 3.61 R
4307 4678 2.026822 ACAGGCTCGGAAACATTCTGAT 60.027 45.455 2.32 0.0 43.68 2.90 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
39 40 6.125029 AGCTTGCTATACATCCAAAGTTGAT 58.875 36.000 0.00 0.00 0.00 2.57
47 48 5.972107 ACATCCAAAGTTGATCTTCAAGG 57.028 39.130 0.00 0.00 37.00 3.61
75 76 0.820226 GTAGTCGGAGGTTGGTACCC 59.180 60.000 10.07 0.00 46.28 3.69
106 107 7.121168 TGGATCCAAAGACAAATCACTCATAAC 59.879 37.037 13.46 0.00 0.00 1.89
479 577 9.091220 AGGTTATTAACTACTAGGATAGGCAAG 57.909 37.037 6.52 0.00 44.97 4.01
599 702 1.091771 CAAGCGGGTCATGTGCTAGG 61.092 60.000 0.00 0.00 38.17 3.02
673 777 3.901222 TGGTTCTGTGGTCAGTAATCTCA 59.099 43.478 0.00 0.00 41.91 3.27
728 832 2.223665 GCTAGCCATGATGACCTTTTGC 60.224 50.000 2.29 0.00 0.00 3.68
794 901 3.440522 GGAAAAACCTTAGTAGCAGCCAG 59.559 47.826 0.00 0.00 35.41 4.85
796 903 1.657804 AACCTTAGTAGCAGCCAGGT 58.342 50.000 0.00 0.00 39.69 4.00
816 923 1.621317 TCACAGGGCAGACGATAAACA 59.379 47.619 0.00 0.00 0.00 2.83
826 933 4.436050 GCAGACGATAAACAACATCCACAG 60.436 45.833 0.00 0.00 0.00 3.66
949 1057 0.678048 GCCAGTTCCTGCCCAGTTAG 60.678 60.000 0.00 0.00 0.00 2.34
957 1065 2.024273 TCCTGCCCAGTTAGTAGCTACT 60.024 50.000 28.50 28.50 40.24 2.57
958 1066 2.766828 CCTGCCCAGTTAGTAGCTACTT 59.233 50.000 30.40 11.22 37.73 2.24
959 1067 3.430929 CCTGCCCAGTTAGTAGCTACTTG 60.431 52.174 30.40 21.65 37.73 3.16
960 1068 2.500098 TGCCCAGTTAGTAGCTACTTGG 59.500 50.000 30.40 28.11 37.73 3.61
961 1069 2.742204 GCCCAGTTAGTAGCTACTTGGC 60.742 54.545 30.40 26.00 37.73 4.52
962 1070 2.158943 CCCAGTTAGTAGCTACTTGGCC 60.159 54.545 30.40 15.64 37.73 5.36
963 1071 2.481449 CCAGTTAGTAGCTACTTGGCCG 60.481 54.545 30.40 15.34 37.73 6.13
964 1072 2.426024 CAGTTAGTAGCTACTTGGCCGA 59.574 50.000 30.40 9.68 37.73 5.54
965 1073 3.094572 AGTTAGTAGCTACTTGGCCGAA 58.905 45.455 30.40 15.18 37.73 4.30
966 1074 3.705072 AGTTAGTAGCTACTTGGCCGAAT 59.295 43.478 30.40 6.71 37.73 3.34
967 1075 2.604046 AGTAGCTACTTGGCCGAATG 57.396 50.000 20.95 0.00 31.13 2.67
968 1076 0.938008 GTAGCTACTTGGCCGAATGC 59.062 55.000 16.88 0.43 40.16 3.56
969 1077 0.539518 TAGCTACTTGGCCGAATGCA 59.460 50.000 12.32 0.00 43.89 3.96
970 1078 0.745845 AGCTACTTGGCCGAATGCAG 60.746 55.000 12.32 0.58 43.89 4.41
971 1079 1.026718 GCTACTTGGCCGAATGCAGT 61.027 55.000 0.00 0.00 43.89 4.40
972 1080 1.009829 CTACTTGGCCGAATGCAGTC 58.990 55.000 3.54 3.54 43.89 3.51
973 1081 0.392461 TACTTGGCCGAATGCAGTCC 60.392 55.000 8.83 0.00 43.89 3.85
974 1082 1.675310 CTTGGCCGAATGCAGTCCA 60.675 57.895 8.83 0.00 43.89 4.02
975 1083 1.926511 CTTGGCCGAATGCAGTCCAC 61.927 60.000 8.83 0.24 43.89 4.02
976 1084 2.359850 GGCCGAATGCAGTCCACA 60.360 61.111 8.83 0.00 43.89 4.17
977 1085 1.750399 GGCCGAATGCAGTCCACAT 60.750 57.895 8.83 0.00 43.89 3.21
978 1086 0.463654 GGCCGAATGCAGTCCACATA 60.464 55.000 8.83 0.00 43.89 2.29
979 1087 0.657840 GCCGAATGCAGTCCACATAC 59.342 55.000 8.83 0.00 40.77 2.39
1090 1223 2.550606 TGTTTAATTGTGGACGTCCTGC 59.449 45.455 33.39 25.20 36.82 4.85
1113 1262 1.001020 GACCACCATGGCATCCACA 60.001 57.895 13.04 0.00 42.67 4.17
1276 1446 3.926616 ACGTGCCTATGCCTTCATATAC 58.073 45.455 0.00 0.00 34.88 1.47
1319 1490 4.004314 CCGGGAAAATATACACACACACA 58.996 43.478 0.00 0.00 0.00 3.72
1321 1492 4.452795 CGGGAAAATATACACACACACACA 59.547 41.667 0.00 0.00 0.00 3.72
1342 1513 2.218934 CGTAGCACGAAACAACCGT 58.781 52.632 3.04 0.00 46.05 4.83
1394 1573 2.418777 CATGGATCGCTCGCCTGA 59.581 61.111 0.00 0.00 0.00 3.86
1402 1581 1.373497 CGCTCGCCTGACAAGTTCT 60.373 57.895 0.00 0.00 0.00 3.01
1453 1635 2.214181 GAGCTTCTTCCTCGTCGCCA 62.214 60.000 0.00 0.00 0.00 5.69
1632 1820 1.364626 GCCATGTCGTCAAGCTGGAG 61.365 60.000 5.16 0.00 0.00 3.86
1717 1908 1.095600 CCTCGATCTCAACTGGACGA 58.904 55.000 0.00 0.00 0.00 4.20
1724 1915 3.136009 TCTCAACTGGACGAGACTGTA 57.864 47.619 0.00 0.00 33.37 2.74
1728 1919 2.492088 CAACTGGACGAGACTGTATGGA 59.508 50.000 0.00 0.00 0.00 3.41
1746 1937 1.292223 ACCTGATGGTCGTGTTCCG 59.708 57.895 0.00 0.00 44.78 4.30
1748 1939 1.292223 CTGATGGTCGTGTTCCGGT 59.708 57.895 0.00 0.00 37.11 5.28
1807 1998 1.078214 TCCGGCATGCCTTTCTCTG 60.078 57.895 33.07 16.17 0.00 3.35
1808 1999 2.117156 CCGGCATGCCTTTCTCTGG 61.117 63.158 33.07 21.13 0.00 3.86
1809 2000 1.377725 CGGCATGCCTTTCTCTGGT 60.378 57.895 33.07 0.00 0.00 4.00
1810 2001 0.107703 CGGCATGCCTTTCTCTGGTA 60.108 55.000 33.07 0.00 0.00 3.25
1811 2002 1.673168 GGCATGCCTTTCTCTGGTAG 58.327 55.000 29.98 0.00 0.00 3.18
1812 2003 1.673168 GCATGCCTTTCTCTGGTAGG 58.327 55.000 6.36 0.00 0.00 3.18
1813 2004 1.748591 GCATGCCTTTCTCTGGTAGGG 60.749 57.143 6.36 0.00 0.00 3.53
1814 2005 1.561542 CATGCCTTTCTCTGGTAGGGT 59.438 52.381 0.00 0.00 0.00 4.34
1815 2006 0.984230 TGCCTTTCTCTGGTAGGGTG 59.016 55.000 0.00 0.00 0.00 4.61
1816 2007 0.393132 GCCTTTCTCTGGTAGGGTGC 60.393 60.000 0.00 0.00 0.00 5.01
1817 2008 0.253327 CCTTTCTCTGGTAGGGTGCC 59.747 60.000 0.00 0.00 0.00 5.01
1818 2009 1.280457 CTTTCTCTGGTAGGGTGCCT 58.720 55.000 0.00 0.00 37.71 4.75
1819 2010 1.208293 CTTTCTCTGGTAGGGTGCCTC 59.792 57.143 0.00 0.00 34.61 4.70
1820 2011 0.617820 TTCTCTGGTAGGGTGCCTCC 60.618 60.000 0.00 0.00 34.61 4.30
1821 2012 1.002274 CTCTGGTAGGGTGCCTCCT 59.998 63.158 0.54 0.54 40.79 3.69
1822 2013 1.001760 TCTGGTAGGGTGCCTCCTC 59.998 63.158 0.00 0.00 38.30 3.71
1823 2014 1.306141 CTGGTAGGGTGCCTCCTCA 60.306 63.158 0.00 0.00 38.30 3.86
1824 2015 1.306141 TGGTAGGGTGCCTCCTCAG 60.306 63.158 0.00 0.00 38.30 3.35
1825 2016 2.736826 GGTAGGGTGCCTCCTCAGC 61.737 68.421 0.00 0.00 38.30 4.26
1826 2017 1.687493 GTAGGGTGCCTCCTCAGCT 60.687 63.158 0.00 0.00 38.30 4.24
1827 2018 1.081092 TAGGGTGCCTCCTCAGCTT 59.919 57.895 0.00 0.00 38.30 3.74
1828 2019 1.267574 TAGGGTGCCTCCTCAGCTTG 61.268 60.000 0.00 0.00 38.30 4.01
1829 2020 2.045536 GGTGCCTCCTCAGCTTGG 60.046 66.667 0.00 0.00 0.00 3.61
1830 2021 2.749441 GTGCCTCCTCAGCTTGGC 60.749 66.667 0.00 0.00 45.10 4.52
1832 2023 2.034687 GCCTCCTCAGCTTGGCAA 59.965 61.111 0.00 0.00 44.34 4.52
1833 2024 2.338785 GCCTCCTCAGCTTGGCAAC 61.339 63.158 0.00 0.00 44.34 4.17
1834 2025 1.676967 CCTCCTCAGCTTGGCAACC 60.677 63.158 0.00 0.00 0.00 3.77
1835 2026 1.377994 CTCCTCAGCTTGGCAACCT 59.622 57.895 0.00 0.00 0.00 3.50
1836 2027 0.959372 CTCCTCAGCTTGGCAACCTG 60.959 60.000 14.98 14.98 0.00 4.00
1837 2028 1.228367 CCTCAGCTTGGCAACCTGT 60.228 57.895 19.19 0.00 0.00 4.00
1838 2029 1.239968 CCTCAGCTTGGCAACCTGTC 61.240 60.000 19.19 0.00 0.00 3.51
1839 2030 0.535780 CTCAGCTTGGCAACCTGTCA 60.536 55.000 19.19 3.67 0.00 3.58
1840 2031 0.106769 TCAGCTTGGCAACCTGTCAA 60.107 50.000 19.19 1.16 40.00 3.18
1841 2032 0.746063 CAGCTTGGCAACCTGTCAAA 59.254 50.000 13.28 0.00 41.88 2.69
1842 2033 1.035139 AGCTTGGCAACCTGTCAAAG 58.965 50.000 0.00 0.00 41.88 2.77
1843 2034 0.598419 GCTTGGCAACCTGTCAAAGC 60.598 55.000 0.00 0.00 41.88 3.51
1844 2035 1.035139 CTTGGCAACCTGTCAAAGCT 58.965 50.000 0.00 0.00 41.88 3.74
1845 2036 0.746063 TTGGCAACCTGTCAAAGCTG 59.254 50.000 0.00 0.00 39.25 4.24
1846 2037 1.108727 TGGCAACCTGTCAAAGCTGG 61.109 55.000 0.00 0.00 0.00 4.85
1847 2038 0.823356 GGCAACCTGTCAAAGCTGGA 60.823 55.000 0.00 0.00 0.00 3.86
1848 2039 1.032014 GCAACCTGTCAAAGCTGGAA 58.968 50.000 0.00 0.00 0.00 3.53
1854 2045 4.775236 ACCTGTCAAAGCTGGAATATCTC 58.225 43.478 0.00 0.00 0.00 2.75
1860 2051 5.633182 GTCAAAGCTGGAATATCTCGATCTC 59.367 44.000 0.00 0.00 0.00 2.75
1863 2054 4.922206 AGCTGGAATATCTCGATCTCTCT 58.078 43.478 0.00 0.00 0.00 3.10
1868 2059 4.219507 GGAATATCTCGATCTCTCTGGCAA 59.780 45.833 0.00 0.00 0.00 4.52
1869 2060 5.105392 GGAATATCTCGATCTCTCTGGCAAT 60.105 44.000 0.00 0.00 0.00 3.56
1871 2062 7.363355 GGAATATCTCGATCTCTCTGGCAATTA 60.363 40.741 0.00 0.00 0.00 1.40
1876 2067 5.917462 TCGATCTCTCTGGCAATTATTTCA 58.083 37.500 0.00 0.00 0.00 2.69
1882 2073 4.701651 TCTCTGGCAATTATTTCACTGGTG 59.298 41.667 0.00 0.00 0.00 4.17
1936 2127 3.555168 GCTGGAATACCTTGACCTATCCG 60.555 52.174 0.00 0.00 37.04 4.18
1937 2128 2.367567 TGGAATACCTTGACCTATCCGC 59.632 50.000 0.00 0.00 37.04 5.54
1980 2198 3.450457 GGATGGTCTCAACTGACATCTCT 59.550 47.826 0.00 0.00 38.61 3.10
2009 2227 1.592223 GTCTACCTCTGTTGGCGCT 59.408 57.895 7.64 0.00 0.00 5.92
2570 2788 4.458295 GGGGAACTTAACCAACTTAGCTTC 59.542 45.833 0.00 0.00 0.00 3.86
2584 2802 2.171341 AGCTTCGTTGGACCTTTCTC 57.829 50.000 0.00 0.00 0.00 2.87
2610 2828 7.387948 CACAATAACATTACTGGAGCTATACCC 59.612 40.741 0.00 0.00 0.00 3.69
2613 2831 4.567857 ACATTACTGGAGCTATACCCCTT 58.432 43.478 0.00 0.00 0.00 3.95
2617 2835 0.030092 TGGAGCTATACCCCTTGGCT 60.030 55.000 0.00 0.00 35.86 4.75
2641 2859 7.121907 GCTTTGGGAATCTCTCTTGTTTAGAAT 59.878 37.037 0.00 0.00 30.91 2.40
2682 2972 4.224762 ACCTTCTTACTGGAGCTATACCC 58.775 47.826 0.00 0.00 0.00 3.69
2685 2975 4.554553 TCTTACTGGAGCTATACCCCTT 57.445 45.455 0.00 0.00 0.00 3.95
2689 2979 0.030092 TGGAGCTATACCCCTTGGCT 60.030 55.000 0.00 0.00 35.86 4.75
2691 2981 1.495148 GGAGCTATACCCCTTGGCTTT 59.505 52.381 0.00 0.00 33.13 3.51
2713 3003 7.121907 GCTTTGGGAATCTCTCTTGTTTAGAAT 59.878 37.037 0.00 0.00 30.91 2.40
2911 3282 0.607620 AATGTTGGGGAATTGCACCG 59.392 50.000 0.00 0.00 46.01 4.94
2914 3285 0.038618 GTTGGGGAATTGCACCGAAC 60.039 55.000 0.00 3.74 46.01 3.95
2934 3305 9.193806 ACCGAACTATATTACCTTACTCTTTCA 57.806 33.333 0.00 0.00 0.00 2.69
2993 3364 4.395231 GGGGAATTACACTAGTTTGCAGTC 59.605 45.833 0.00 0.00 0.00 3.51
3021 3392 3.596214 TCTTTCGAGCAACCATCTTACC 58.404 45.455 0.00 0.00 0.00 2.85
3045 3416 3.990369 ACCTATACTGCTAGGGACAACA 58.010 45.455 8.31 0.00 42.29 3.33
3160 3531 6.879458 GCACCTTTCTCTTTCTAAGAACCATA 59.121 38.462 0.00 0.00 37.02 2.74
3172 3543 5.958380 TCTAAGAACCATATCACTGGACACT 59.042 40.000 0.00 0.00 39.73 3.55
3223 3594 1.534235 ACTGGACTCGACCTTGGCT 60.534 57.895 0.00 0.00 0.00 4.75
3261 3632 2.289072 CGTGATCACAGAGGAACACCTT 60.289 50.000 24.93 0.00 37.30 3.50
3277 3648 6.764560 GGAACACCTTGTTACTCTAAAGAACA 59.235 38.462 0.00 0.00 41.28 3.18
3291 3662 7.824779 ACTCTAAAGAACATAAACCATCTGGAC 59.175 37.037 2.55 0.00 38.94 4.02
3385 3756 4.946160 TCCTCCAATAAATTCACTGGGT 57.054 40.909 1.12 0.00 0.00 4.51
3387 3758 5.751586 TCCTCCAATAAATTCACTGGGTAC 58.248 41.667 1.12 0.00 0.00 3.34
3397 3768 4.715534 TTCACTGGGTACATTCCTGAAA 57.284 40.909 0.00 0.00 0.00 2.69
3580 3951 7.893124 AGTTTAGCATTCATGGATCTTTCAT 57.107 32.000 0.00 0.00 0.00 2.57
3630 4001 7.415765 CCATCATGGATCGGAGACTTAGTATAC 60.416 44.444 0.00 0.00 42.51 1.47
3691 4062 7.238486 GGAGATATTCCAGTGACTATCACAT 57.762 40.000 11.33 0.00 44.87 3.21
4021 4392 2.821378 TCATGCAACCAATTGAGTGGAG 59.179 45.455 7.12 0.00 41.65 3.86
4197 4568 0.818040 GACGCCAACTTGACACCCTT 60.818 55.000 0.00 0.00 0.00 3.95
4239 4610 6.239373 CCATATACACGGGTAACATTGGTCTA 60.239 42.308 0.00 0.00 39.74 2.59
4307 4678 4.335315 AGAGCACGACAATCAACAGAAAAA 59.665 37.500 0.00 0.00 0.00 1.94
4365 4736 0.887836 GACTTGGGTCCGGGTTTGTC 60.888 60.000 0.00 0.00 36.53 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 5.163509 CCGACTACAATGATCTCCTTGAAGA 60.164 44.000 0.00 0.00 0.00 2.87
47 48 4.363999 CAACCTCCGACTACAATGATCTC 58.636 47.826 0.00 0.00 0.00 2.75
106 107 2.032550 CCAAGCTGGCAGAACATATTCG 59.967 50.000 20.86 0.00 40.04 3.34
290 385 2.152016 CTATCGTCTCGGAGTATGGCA 58.848 52.381 4.69 0.00 0.00 4.92
412 509 4.065088 CCTCCACTCGATTGACTCAAAAA 58.935 43.478 4.04 0.00 0.00 1.94
469 567 1.952296 CACCATCTTGCTTGCCTATCC 59.048 52.381 0.00 0.00 0.00 2.59
479 577 1.434696 CCGAATGCCACCATCTTGC 59.565 57.895 0.00 0.00 0.00 4.01
741 848 5.765677 AGCCTAGTTTCAAGAGAGAAAAACC 59.234 40.000 0.00 0.00 39.05 3.27
743 850 5.998363 GGAGCCTAGTTTCAAGAGAGAAAAA 59.002 40.000 0.00 0.00 39.05 1.94
756 863 4.724279 TTTTCCTCAAGGAGCCTAGTTT 57.276 40.909 0.00 0.00 46.36 2.66
794 901 0.535335 TTATCGTCTGCCCTGTGACC 59.465 55.000 0.00 0.00 0.00 4.02
796 903 1.621317 TGTTTATCGTCTGCCCTGTGA 59.379 47.619 0.00 0.00 0.00 3.58
826 933 3.982701 CGAGACTTGATGAGAGATGCATC 59.017 47.826 19.37 19.37 41.87 3.91
949 1057 0.938008 GCATTCGGCCAAGTAGCTAC 59.062 55.000 16.43 16.43 36.11 3.58
957 1065 1.971167 GTGGACTGCATTCGGCCAA 60.971 57.895 2.24 0.00 43.89 4.52
958 1066 2.359850 GTGGACTGCATTCGGCCA 60.360 61.111 2.24 0.00 43.89 5.36
959 1067 0.463654 TATGTGGACTGCATTCGGCC 60.464 55.000 0.00 0.00 43.89 6.13
960 1068 0.657840 GTATGTGGACTGCATTCGGC 59.342 55.000 0.00 0.00 45.13 5.54
961 1069 2.315925 AGTATGTGGACTGCATTCGG 57.684 50.000 0.00 0.00 0.00 4.30
962 1070 4.046938 ACTAGTATGTGGACTGCATTCG 57.953 45.455 0.00 0.00 0.00 3.34
963 1071 9.712305 AATAATACTAGTATGTGGACTGCATTC 57.288 33.333 16.11 0.00 0.00 2.67
1090 1223 1.647545 GATGCCATGGTGGTCACGTG 61.648 60.000 14.67 9.94 40.46 4.49
1113 1262 0.110486 ACTCATTCGTGGGGTGCTTT 59.890 50.000 0.00 0.00 0.00 3.51
1276 1446 4.657824 AACGTCGGGTGGTGCTCG 62.658 66.667 0.00 0.00 43.78 5.03
1342 1513 0.470766 GTGGTGGTGGTAGTGGTGAA 59.529 55.000 0.00 0.00 0.00 3.18
1394 1573 5.006386 CCATAAGGAGCAAGAAGAACTTGT 58.994 41.667 10.51 0.00 46.49 3.16
1402 1581 1.004628 TGCTGCCATAAGGAGCAAGAA 59.995 47.619 6.40 0.00 41.72 2.52
1428 1607 0.174617 CGAGGAAGAAGCTCCAGGTC 59.825 60.000 0.00 0.00 38.02 3.85
1453 1635 4.711949 CTGGAGCCTGCCTGCGTT 62.712 66.667 0.00 0.00 34.08 4.84
1559 1747 4.751431 AGCAATCTTGGTGCCCTC 57.249 55.556 0.00 0.00 43.27 4.30
1565 1753 0.899720 CCATTGGCAGCAATCTTGGT 59.100 50.000 0.00 0.00 39.91 3.67
1608 1796 2.358125 TTGACGACATGGCCGGTG 60.358 61.111 1.90 5.47 0.00 4.94
1632 1820 3.695816 GACCAAATATCTTTCGCCAAGC 58.304 45.455 0.00 0.00 31.70 4.01
1746 1937 4.466827 TCTTTAAGGAACCCAAGAACACC 58.533 43.478 0.00 0.00 0.00 4.16
1807 1998 2.736826 GCTGAGGAGGCACCCTACC 61.737 68.421 0.00 0.00 34.26 3.18
1808 1999 1.268283 AAGCTGAGGAGGCACCCTAC 61.268 60.000 0.00 0.00 40.05 3.18
1809 2000 1.081092 AAGCTGAGGAGGCACCCTA 59.919 57.895 0.00 0.00 40.05 3.53
1810 2001 2.204059 AAGCTGAGGAGGCACCCT 60.204 61.111 0.00 0.00 40.05 4.34
1811 2002 2.045536 CAAGCTGAGGAGGCACCC 60.046 66.667 0.00 0.00 40.05 4.61
1812 2003 2.045536 CCAAGCTGAGGAGGCACC 60.046 66.667 0.00 0.00 39.35 5.01
1813 2004 2.749441 GCCAAGCTGAGGAGGCAC 60.749 66.667 9.55 0.00 46.26 5.01
1816 2007 1.676967 GGTTGCCAAGCTGAGGAGG 60.677 63.158 9.55 0.00 0.00 4.30
1817 2008 1.377994 AGGTTGCCAAGCTGAGGAG 59.622 57.895 8.60 0.00 37.93 3.69
1818 2009 3.580084 AGGTTGCCAAGCTGAGGA 58.420 55.556 8.60 0.00 37.93 3.71
1823 2014 1.035139 CTTTGACAGGTTGCCAAGCT 58.965 50.000 2.71 2.71 40.45 3.74
1824 2015 0.598419 GCTTTGACAGGTTGCCAAGC 60.598 55.000 0.00 0.00 0.00 4.01
1825 2016 1.035139 AGCTTTGACAGGTTGCCAAG 58.965 50.000 0.00 0.00 0.00 3.61
1826 2017 0.746063 CAGCTTTGACAGGTTGCCAA 59.254 50.000 0.00 0.00 0.00 4.52
1827 2018 1.108727 CCAGCTTTGACAGGTTGCCA 61.109 55.000 0.00 0.00 0.00 4.92
1828 2019 0.823356 TCCAGCTTTGACAGGTTGCC 60.823 55.000 0.00 0.00 0.00 4.52
1829 2020 1.032014 TTCCAGCTTTGACAGGTTGC 58.968 50.000 0.00 0.00 0.00 4.17
1830 2021 4.946157 AGATATTCCAGCTTTGACAGGTTG 59.054 41.667 0.00 0.00 0.00 3.77
1831 2022 5.184892 AGATATTCCAGCTTTGACAGGTT 57.815 39.130 0.00 0.00 0.00 3.50
1832 2023 4.681781 CGAGATATTCCAGCTTTGACAGGT 60.682 45.833 0.00 0.00 0.00 4.00
1833 2024 3.806521 CGAGATATTCCAGCTTTGACAGG 59.193 47.826 0.00 0.00 0.00 4.00
1834 2025 4.686972 TCGAGATATTCCAGCTTTGACAG 58.313 43.478 0.00 0.00 0.00 3.51
1835 2026 4.736126 TCGAGATATTCCAGCTTTGACA 57.264 40.909 0.00 0.00 0.00 3.58
1836 2027 5.537188 AGATCGAGATATTCCAGCTTTGAC 58.463 41.667 0.00 0.00 0.00 3.18
1837 2028 5.538053 AGAGATCGAGATATTCCAGCTTTGA 59.462 40.000 0.00 0.00 0.00 2.69
1838 2029 5.782047 AGAGATCGAGATATTCCAGCTTTG 58.218 41.667 0.00 0.00 0.00 2.77
1839 2030 5.774690 AGAGAGATCGAGATATTCCAGCTTT 59.225 40.000 0.00 0.00 0.00 3.51
1840 2031 5.183713 CAGAGAGATCGAGATATTCCAGCTT 59.816 44.000 0.00 0.00 0.00 3.74
1841 2032 4.701651 CAGAGAGATCGAGATATTCCAGCT 59.298 45.833 0.00 0.00 0.00 4.24
1842 2033 4.142403 CCAGAGAGATCGAGATATTCCAGC 60.142 50.000 0.00 0.00 0.00 4.85
1843 2034 4.142403 GCCAGAGAGATCGAGATATTCCAG 60.142 50.000 0.00 0.00 0.00 3.86
1844 2035 3.761218 GCCAGAGAGATCGAGATATTCCA 59.239 47.826 0.00 0.00 0.00 3.53
1845 2036 3.761218 TGCCAGAGAGATCGAGATATTCC 59.239 47.826 0.00 0.00 0.00 3.01
1846 2037 5.384063 TTGCCAGAGAGATCGAGATATTC 57.616 43.478 0.00 0.00 0.00 1.75
1847 2038 5.999205 ATTGCCAGAGAGATCGAGATATT 57.001 39.130 0.00 0.00 0.00 1.28
1848 2039 5.999205 AATTGCCAGAGAGATCGAGATAT 57.001 39.130 0.00 0.00 0.00 1.63
1854 2045 5.757320 AGTGAAATAATTGCCAGAGAGATCG 59.243 40.000 0.00 0.00 0.00 3.69
1860 2051 4.676196 GCACCAGTGAAATAATTGCCAGAG 60.676 45.833 0.99 0.00 0.00 3.35
1863 2054 2.094803 CGCACCAGTGAAATAATTGCCA 60.095 45.455 0.99 0.00 0.00 4.92
1882 2073 1.153549 CAAGCTGAGGAGGTACCGC 60.154 63.158 7.18 7.18 44.74 5.68
1936 2127 7.667043 TCCTCGTATTGTTGAAATATATGGC 57.333 36.000 0.00 0.00 0.00 4.40
1937 2128 8.668353 CCATCCTCGTATTGTTGAAATATATGG 58.332 37.037 0.00 0.00 0.00 2.74
1980 2198 4.147321 ACAGAGGTAGACGAGTTAACCAA 58.853 43.478 0.88 0.00 34.29 3.67
2570 2788 4.513692 TGTTATTGTGAGAAAGGTCCAACG 59.486 41.667 0.00 0.00 0.00 4.10
2584 2802 7.387948 GGGTATAGCTCCAGTAATGTTATTGTG 59.612 40.741 1.32 0.00 0.00 3.33
2610 2828 2.025510 AGAGAGATTCCCAAAGCCAAGG 60.026 50.000 0.00 0.00 0.00 3.61
2613 2831 2.376518 ACAAGAGAGATTCCCAAAGCCA 59.623 45.455 0.00 0.00 0.00 4.75
2617 2835 9.449719 GTATTCTAAACAAGAGAGATTCCCAAA 57.550 33.333 0.00 0.00 35.05 3.28
2641 2859 7.974504 AGAAGGTTGTTAGAAAGATGAAGGTA 58.025 34.615 0.00 0.00 0.00 3.08
2682 2972 2.025510 AGAGAGATTCCCAAAGCCAAGG 60.026 50.000 0.00 0.00 0.00 3.61
2685 2975 2.376518 ACAAGAGAGATTCCCAAAGCCA 59.623 45.455 0.00 0.00 0.00 4.75
2689 2979 9.449719 GTATTCTAAACAAGAGAGATTCCCAAA 57.550 33.333 0.00 0.00 35.05 3.28
2691 2981 7.403231 AGGTATTCTAAACAAGAGAGATTCCCA 59.597 37.037 0.00 0.00 35.05 4.37
2713 3003 7.974504 AGAAGGTTGTTAGAAAGATGAAGGTA 58.025 34.615 0.00 0.00 0.00 3.08
2904 3275 7.069085 AGAGTAAGGTAATATAGTTCGGTGCAA 59.931 37.037 0.00 0.00 0.00 4.08
2934 3305 4.635699 ATCTCCGGTAAGAAGGTTGTTT 57.364 40.909 0.00 0.00 0.00 2.83
3021 3392 3.220110 TGTCCCTAGCAGTATAGGTTCG 58.780 50.000 0.00 0.00 40.77 3.95
3117 3488 3.568538 GTGCCTCAAACTAGTGCAATTG 58.431 45.455 6.42 0.00 33.11 2.32
3172 3543 4.293494 AGCAGACTGATCTTAGATGGGAA 58.707 43.478 6.65 0.00 30.42 3.97
3223 3594 5.303333 TGATCACGCCATCTAGGTTATTGTA 59.697 40.000 0.00 0.00 40.61 2.41
3277 3648 6.957631 TGTGTGATAAGTCCAGATGGTTTAT 58.042 36.000 0.00 5.19 36.34 1.40
3282 3653 4.836825 AGTTGTGTGATAAGTCCAGATGG 58.163 43.478 0.00 0.00 0.00 3.51
3291 3662 5.641209 CCCTGAGAAAGAGTTGTGTGATAAG 59.359 44.000 0.00 0.00 0.00 1.73
3331 3702 6.732896 TTCTACTAATCCCTTAGCTCCAAG 57.267 41.667 0.00 0.00 38.33 3.61
3342 3713 9.713713 GAGGATAAAGTCAATTCTACTAATCCC 57.286 37.037 17.90 11.53 38.86 3.85
3375 3746 4.927267 TTCAGGAATGTACCCAGTGAAT 57.073 40.909 0.00 0.00 0.00 2.57
3385 3756 7.499321 ACGTACAAATTGTTTCAGGAATGTA 57.501 32.000 3.17 0.00 0.00 2.29
3387 3758 6.915300 TCAACGTACAAATTGTTTCAGGAATG 59.085 34.615 3.17 0.00 0.00 2.67
3397 3768 4.457466 AGGTTCCTCAACGTACAAATTGT 58.543 39.130 3.43 3.43 32.68 2.71
3691 4062 3.451178 AGTTGGCGAAGGAGCTTAAGATA 59.549 43.478 6.67 0.00 37.29 1.98
3701 4072 2.870435 GCTAAACTCAGTTGGCGAAGGA 60.870 50.000 0.00 0.00 0.00 3.36
3832 4203 5.966742 ACTTCTCTAAATTTGCCCACTTC 57.033 39.130 0.00 0.00 0.00 3.01
3957 4328 3.845781 TTGAGAGAGGTTATGCCATCC 57.154 47.619 0.00 0.00 40.61 3.51
4021 4392 5.689835 AGCTCCAATCTTCCTAGGAATTTC 58.310 41.667 24.48 9.39 33.28 2.17
4197 4568 6.670464 TGTATATGGACTGGTTCTCCAAGTAA 59.330 38.462 0.00 0.00 43.81 2.24
4239 4610 4.168101 TCCTTTCAAGAGGAGTACCACAT 58.832 43.478 0.00 0.00 40.87 3.21
4307 4678 2.026822 ACAGGCTCGGAAACATTCTGAT 60.027 45.455 2.32 0.00 43.68 2.90


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

AutoCloner maintained by Alex Coulton.