Multiple sequence alignment - TraesCS1A01G414300

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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 TraesCS1A01G414300 chr1A 100.000 3342 0 0 1 3342 573816331 573819672 0.000000e+00 6172.0
1 TraesCS1A01G414300 chr1A 83.121 1179 125 44 1714 2853 573921447 573922590 0.000000e+00 1007.0
2 TraesCS1A01G414300 chr1A 87.938 257 21 9 1069 1320 573817438 573817689 9.070000e-76 294.0
3 TraesCS1A01G414300 chr1A 83.598 189 12 7 403 586 573920245 573920419 3.450000e-35 159.0
4 TraesCS1A01G414300 chr1D 92.252 2349 136 30 787 3100 477434636 477436973 0.000000e+00 3288.0
5 TraesCS1A01G414300 chr1D 92.265 2340 132 19 1030 3342 477434926 477437243 0.000000e+00 3273.0
6 TraesCS1A01G414300 chr1D 84.314 1173 117 35 1718 2853 477480184 477481326 0.000000e+00 1085.0
7 TraesCS1A01G414300 chr1D 82.609 437 49 13 1329 1754 477479707 477480127 8.810000e-96 361.0
8 TraesCS1A01G414300 chr1D 89.623 212 19 2 1143 1351 477434961 477435172 1.980000e-67 267.0
9 TraesCS1A01G414300 chr1D 95.276 127 6 0 1489 1615 1836282 1836408 5.650000e-48 202.0
10 TraesCS1A01G414300 chr1D 78.151 357 50 13 2687 3017 477481447 477481801 5.650000e-48 202.0
11 TraesCS1A01G414300 chr1D 85.965 171 18 4 130 297 477433984 477434151 9.530000e-41 178.0
12 TraesCS1A01G414300 chr1D 82.927 205 26 8 1182 1380 477434961 477435162 3.430000e-40 176.0
13 TraesCS1A01G414300 chr1B 91.456 1545 86 17 1030 2566 665048806 665050312 0.000000e+00 2080.0
14 TraesCS1A01G414300 chr1B 83.061 980 82 53 1718 2669 665061335 665062258 0.000000e+00 813.0
15 TraesCS1A01G414300 chr1B 84.532 556 49 17 823 1362 665048568 665049102 1.780000e-142 516.0
16 TraesCS1A01G414300 chr1B 76.816 647 56 45 198 777 665047833 665048452 9.130000e-71 278.0
17 TraesCS1A01G414300 chr1B 85.081 248 24 12 1143 1382 665048841 665049083 1.200000e-59 241.0
18 TraesCS1A01G414300 chr1B 89.024 164 11 3 143 302 665044295 665044455 2.630000e-46 196.0
19 TraesCS1A01G414300 chr1B 89.394 66 7 0 297 362 665060093 665060158 2.140000e-12 84.2
20 TraesCS1A01G414300 chr1B 97.727 44 1 0 134 177 665047796 665047839 3.580000e-10 76.8
21 TraesCS1A01G414300 chr7A 87.461 319 26 3 1396 1714 705667554 705667250 4.100000e-94 355.0
22 TraesCS1A01G414300 chr5A 89.655 232 18 1 1489 1714 41973612 41973843 1.170000e-74 291.0
23 TraesCS1A01G414300 chr5A 86.047 215 26 4 1489 1700 76127540 76127753 9.330000e-56 228.0
24 TraesCS1A01G414300 chr3A 87.838 222 27 0 2096 2317 434069272 434069051 9.200000e-66 261.0
25 TraesCS1A01G414300 chr5D 89.071 183 20 0 1497 1679 80205191 80205009 9.330000e-56 228.0
26 TraesCS1A01G414300 chr4A 80.631 222 36 6 2083 2302 143252301 143252517 7.420000e-37 165.0
27 TraesCS1A01G414300 chr4B 80.645 217 29 7 2091 2302 407056966 407056758 4.460000e-34 156.0
28 TraesCS1A01G414300 chr3B 81.022 137 16 10 1923 2056 13365300 13365429 2.120000e-17 100.0
29 TraesCS1A01G414300 chr3D 75.248 202 40 7 1479 1680 5512899 5513090 1.650000e-13 87.9
30 TraesCS1A01G414300 chr3D 100.000 31 0 0 1754 1784 5493897 5493867 1.300000e-04 58.4
31 TraesCS1A01G414300 chr2B 81.818 99 15 2 2091 2189 188855826 188855731 2.760000e-11 80.5


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 TraesCS1A01G414300 chr1A 573816331 573819672 3341 False 3233.000000 6172 93.969000 1 3342 2 chr1A.!!$F1 3341
1 TraesCS1A01G414300 chr1A 573920245 573922590 2345 False 583.000000 1007 83.359500 403 2853 2 chr1A.!!$F2 2450
2 TraesCS1A01G414300 chr1D 477433984 477437243 3259 False 1436.400000 3288 88.606400 130 3342 5 chr1D.!!$F2 3212
3 TraesCS1A01G414300 chr1D 477479707 477481801 2094 False 549.333333 1085 81.691333 1329 3017 3 chr1D.!!$F3 1688
4 TraesCS1A01G414300 chr1B 665044295 665050312 6017 False 564.633333 2080 87.439333 134 2566 6 chr1B.!!$F1 2432
5 TraesCS1A01G414300 chr1B 665060093 665062258 2165 False 448.600000 813 86.227500 297 2669 2 chr1B.!!$F2 2372

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
777 4266 0.098728 GCTGTGTTTGTTGCTGTCGT 59.901 50.0 0.0 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2393 6222 0.252467 AGGAAGGAGTGAGGGAGTGG 60.252 60.0 0.0 0.0 0.0 4.0 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
17 18 3.948719 TCAACCGGGGTCACCTGC 61.949 66.667 6.32 0.00 42.17 4.85
19 20 3.637273 AACCGGGGTCACCTGCTC 61.637 66.667 6.32 0.00 42.17 4.26
22 23 4.742201 CGGGGTCACCTGCTCGTG 62.742 72.222 0.00 0.00 36.06 4.35
27 28 4.357947 TCACCTGCTCGTGACGCC 62.358 66.667 0.00 0.00 37.85 5.68
28 29 4.662961 CACCTGCTCGTGACGCCA 62.663 66.667 0.00 0.00 35.68 5.69
29 30 3.923864 ACCTGCTCGTGACGCCAA 61.924 61.111 0.00 0.00 0.00 4.52
30 31 2.664851 CCTGCTCGTGACGCCAAA 60.665 61.111 0.00 0.00 0.00 3.28
32 33 2.202946 TGCTCGTGACGCCAAACA 60.203 55.556 0.00 0.00 0.00 2.83
33 34 2.248431 GCTCGTGACGCCAAACAC 59.752 61.111 0.00 0.00 0.00 3.32
46 47 1.537776 CCAAACACGGCATTTTCAGCA 60.538 47.619 0.00 0.00 0.00 4.41
47 48 2.200067 CAAACACGGCATTTTCAGCAA 58.800 42.857 0.00 0.00 0.00 3.91
48 49 2.593346 AACACGGCATTTTCAGCAAA 57.407 40.000 0.00 0.00 0.00 3.68
49 50 2.138596 ACACGGCATTTTCAGCAAAG 57.861 45.000 0.00 0.00 0.00 2.77
50 51 0.785979 CACGGCATTTTCAGCAAAGC 59.214 50.000 0.00 0.00 0.00 3.51
51 52 0.664166 ACGGCATTTTCAGCAAAGCG 60.664 50.000 0.00 0.00 0.00 4.68
52 53 0.664166 CGGCATTTTCAGCAAAGCGT 60.664 50.000 0.00 0.00 0.00 5.07
53 54 0.785979 GGCATTTTCAGCAAAGCGTG 59.214 50.000 0.00 0.00 0.00 5.34
54 55 0.785979 GCATTTTCAGCAAAGCGTGG 59.214 50.000 0.00 0.00 0.00 4.94
55 56 0.785979 CATTTTCAGCAAAGCGTGGC 59.214 50.000 0.00 0.00 0.00 5.01
56 57 0.388659 ATTTTCAGCAAAGCGTGGCA 59.611 45.000 0.72 0.00 0.00 4.92
57 58 0.248990 TTTTCAGCAAAGCGTGGCAG 60.249 50.000 0.72 0.00 0.00 4.85
58 59 1.383456 TTTCAGCAAAGCGTGGCAGT 61.383 50.000 0.72 0.00 0.00 4.40
59 60 1.383456 TTCAGCAAAGCGTGGCAGTT 61.383 50.000 0.72 0.00 0.00 3.16
60 61 1.066257 CAGCAAAGCGTGGCAGTTT 59.934 52.632 0.72 0.00 0.00 2.66
62 63 2.588585 GCAAAGCGTGGCAGTTTGC 61.589 57.895 19.93 19.93 46.57 3.68
74 75 3.337301 GCAGTTTGCCCAAATTTTGTG 57.663 42.857 8.26 0.00 37.42 3.33
75 76 2.541383 GCAGTTTGCCCAAATTTTGTGC 60.541 45.455 9.33 9.33 37.42 4.57
77 78 1.936547 GTTTGCCCAAATTTTGTGCGA 59.063 42.857 11.17 7.18 36.80 5.10
78 79 2.315925 TTGCCCAAATTTTGTGCGAA 57.684 40.000 11.17 5.19 36.80 4.70
81 82 2.209273 GCCCAAATTTTGTGCGAAAGT 58.791 42.857 8.26 0.00 0.00 2.66
82 83 2.032979 GCCCAAATTTTGTGCGAAAGTG 60.033 45.455 8.26 0.00 0.00 3.16
85 86 3.616379 CCAAATTTTGTGCGAAAGTGTGT 59.384 39.130 8.26 0.00 0.00 3.72
86 87 4.492247 CCAAATTTTGTGCGAAAGTGTGTG 60.492 41.667 8.26 0.00 0.00 3.82
87 88 2.999507 TTTTGTGCGAAAGTGTGTGT 57.000 40.000 0.00 0.00 0.00 3.72
88 89 2.999507 TTTGTGCGAAAGTGTGTGTT 57.000 40.000 0.00 0.00 0.00 3.32
98 99 4.515432 GAAAGTGTGTGTTCGAACTTAGC 58.485 43.478 27.32 15.45 32.69 3.09
99 100 2.480845 AGTGTGTGTTCGAACTTAGCC 58.519 47.619 27.32 13.33 0.00 3.93
100 101 2.159014 AGTGTGTGTTCGAACTTAGCCA 60.159 45.455 27.32 14.30 0.00 4.75
102 103 1.798813 GTGTGTTCGAACTTAGCCAGG 59.201 52.381 27.32 0.00 0.00 4.45
103 104 1.270625 TGTGTTCGAACTTAGCCAGGG 60.271 52.381 27.32 0.00 0.00 4.45
104 105 1.001633 GTGTTCGAACTTAGCCAGGGA 59.998 52.381 27.32 1.71 0.00 4.20
105 106 1.906574 TGTTCGAACTTAGCCAGGGAT 59.093 47.619 27.32 0.00 0.00 3.85
106 107 2.304761 TGTTCGAACTTAGCCAGGGATT 59.695 45.455 27.32 0.00 0.00 3.01
107 108 2.937149 GTTCGAACTTAGCCAGGGATTC 59.063 50.000 20.97 0.00 0.00 2.52
108 109 1.136305 TCGAACTTAGCCAGGGATTCG 59.864 52.381 0.00 0.00 40.10 3.34
110 111 2.224066 CGAACTTAGCCAGGGATTCGAT 60.224 50.000 0.00 0.00 40.96 3.59
111 112 2.918712 ACTTAGCCAGGGATTCGATG 57.081 50.000 0.00 0.00 0.00 3.84
112 113 1.202698 ACTTAGCCAGGGATTCGATGC 60.203 52.381 0.00 0.00 0.00 3.91
114 115 0.836606 TAGCCAGGGATTCGATGCAA 59.163 50.000 0.00 0.00 0.00 4.08
117 118 1.204467 GCCAGGGATTCGATGCAAAAA 59.796 47.619 0.00 0.00 0.00 1.94
314 3716 1.609501 CCCTGGTTCCGGAGACTGA 60.610 63.158 3.34 0.00 0.00 3.41
316 3718 1.213013 CTGGTTCCGGAGACTGACG 59.787 63.158 3.34 0.00 0.00 4.35
377 3798 0.911856 CGCGACGGTTATACACAGTG 59.088 55.000 0.00 0.00 33.37 3.66
378 3799 1.274596 GCGACGGTTATACACAGTGG 58.725 55.000 5.31 0.00 33.37 4.00
380 3801 1.648504 GACGGTTATACACAGTGGCC 58.351 55.000 5.31 0.00 33.37 5.36
381 3802 0.978151 ACGGTTATACACAGTGGCCA 59.022 50.000 0.00 0.00 31.78 5.36
382 3803 1.066430 ACGGTTATACACAGTGGCCAG 60.066 52.381 5.11 0.00 31.78 4.85
383 3804 1.742411 CGGTTATACACAGTGGCCAGG 60.742 57.143 5.11 3.68 0.00 4.45
384 3805 1.557832 GGTTATACACAGTGGCCAGGA 59.442 52.381 5.11 0.00 0.00 3.86
385 3806 2.629051 GTTATACACAGTGGCCAGGAC 58.371 52.381 5.11 0.00 0.00 3.85
386 3807 0.821517 TATACACAGTGGCCAGGACG 59.178 55.000 5.11 0.00 0.00 4.79
387 3808 1.899437 ATACACAGTGGCCAGGACGG 61.899 60.000 5.11 0.00 38.11 4.79
400 3821 3.936203 GACGGCACCCACTCCACA 61.936 66.667 0.00 0.00 0.00 4.17
424 3845 3.827898 GACGTCCTCCTCCGCCTG 61.828 72.222 3.51 0.00 0.00 4.85
451 3877 1.000771 TCTCTCTCCACCCTCCACG 60.001 63.158 0.00 0.00 0.00 4.94
452 3878 2.680352 TCTCTCCACCCTCCACGC 60.680 66.667 0.00 0.00 0.00 5.34
453 3879 4.135153 CTCTCCACCCTCCACGCG 62.135 72.222 3.53 3.53 0.00 6.01
552 3979 4.357947 GACCGACTCGCAGGTGCA 62.358 66.667 2.33 0.00 41.51 4.57
594 4029 2.214216 ACCGCTGCTTGGACCACTA 61.214 57.895 0.00 0.00 0.00 2.74
602 4048 1.537135 GCTTGGACCACTATCTCGCTC 60.537 57.143 0.00 0.00 0.00 5.03
656 4127 1.877443 AGGTTTCCATCCGTCGTTTTG 59.123 47.619 0.00 0.00 0.00 2.44
712 4191 1.007734 GTCGCCGTGTCTCTGTTGA 60.008 57.895 0.00 0.00 0.00 3.18
744 4223 0.651551 TTTTTGGTTCGTCGTCACCG 59.348 50.000 10.50 0.00 35.60 4.94
745 4224 0.459934 TTTTGGTTCGTCGTCACCGT 60.460 50.000 10.50 0.00 35.60 4.83
747 4226 2.002509 TTGGTTCGTCGTCACCGTGA 62.003 55.000 0.00 0.00 35.60 4.35
748 4227 1.299316 GGTTCGTCGTCACCGTGAA 60.299 57.895 1.88 0.00 35.01 3.18
749 4228 0.665369 GGTTCGTCGTCACCGTGAAT 60.665 55.000 1.88 0.00 34.16 2.57
752 4241 2.092291 CGTCGTCACCGTGAATGGG 61.092 63.158 1.88 0.00 35.01 4.00
755 4244 3.124921 GTCACCGTGAATGGGGCG 61.125 66.667 1.88 0.00 30.15 6.13
777 4266 0.098728 GCTGTGTTTGTTGCTGTCGT 59.901 50.000 0.00 0.00 0.00 4.34
781 4270 1.368850 GTTTGTTGCTGTCGTCGCC 60.369 57.895 0.00 0.00 0.00 5.54
783 4272 1.163420 TTTGTTGCTGTCGTCGCCAT 61.163 50.000 0.00 0.00 0.00 4.40
803 4399 2.972625 TGATTGCGATCGAGTTCCTTT 58.027 42.857 21.57 0.00 34.91 3.11
845 4445 3.072184 TGCAATGCTGGGTGGTTTAATTT 59.928 39.130 6.82 0.00 0.00 1.82
864 4464 3.822192 TCCCGTGCTCGATCGTGG 61.822 66.667 15.94 10.45 39.71 4.94
872 4472 3.825833 CTCGATCGTGGGCGCCTAC 62.826 68.421 31.24 31.24 38.14 3.18
882 4482 2.355956 GCGCCTACTACGGATGCC 60.356 66.667 0.00 0.00 0.00 4.40
1064 4724 1.434622 CTCTTCGTCTACGGCGGCTA 61.435 60.000 13.24 0.00 40.29 3.93
1065 4725 1.298190 CTTCGTCTACGGCGGCTAC 60.298 63.158 13.24 4.69 40.29 3.58
1066 4726 1.712977 CTTCGTCTACGGCGGCTACT 61.713 60.000 13.24 0.00 40.29 2.57
1067 4727 1.709147 TTCGTCTACGGCGGCTACTC 61.709 60.000 13.24 0.00 40.29 2.59
1068 4728 2.720605 GTCTACGGCGGCTACTCC 59.279 66.667 13.24 0.00 0.00 3.85
1069 4729 2.517875 TCTACGGCGGCTACTCCC 60.518 66.667 13.24 0.00 0.00 4.30
1070 4730 3.603671 CTACGGCGGCTACTCCCC 61.604 72.222 13.24 0.00 0.00 4.81
1074 4734 3.862991 GGCGGCTACTCCCCCTTC 61.863 72.222 0.00 0.00 0.00 3.46
1075 4735 4.222847 GCGGCTACTCCCCCTTCG 62.223 72.222 0.00 0.00 0.00 3.79
1076 4736 2.758737 CGGCTACTCCCCCTTCGT 60.759 66.667 0.00 0.00 0.00 3.85
1077 4737 2.783288 CGGCTACTCCCCCTTCGTC 61.783 68.421 0.00 0.00 0.00 4.20
1078 4738 2.433146 GGCTACTCCCCCTTCGTCC 61.433 68.421 0.00 0.00 0.00 4.79
1079 4739 2.433146 GCTACTCCCCCTTCGTCCC 61.433 68.421 0.00 0.00 0.00 4.46
1080 4740 2.043652 TACTCCCCCTTCGTCCCG 60.044 66.667 0.00 0.00 0.00 5.14
1081 4741 2.850828 CTACTCCCCCTTCGTCCCGT 62.851 65.000 0.00 0.00 0.00 5.28
1082 4742 3.771160 CTCCCCCTTCGTCCCGTG 61.771 72.222 0.00 0.00 0.00 4.94
1083 4743 4.626402 TCCCCCTTCGTCCCGTGT 62.626 66.667 0.00 0.00 0.00 4.49
1084 4744 4.078516 CCCCCTTCGTCCCGTGTC 62.079 72.222 0.00 0.00 0.00 3.67
1085 4745 4.078516 CCCCTTCGTCCCGTGTCC 62.079 72.222 0.00 0.00 0.00 4.02
1086 4746 4.078516 CCCTTCGTCCCGTGTCCC 62.079 72.222 0.00 0.00 0.00 4.46
1087 4747 3.307906 CCTTCGTCCCGTGTCCCA 61.308 66.667 0.00 0.00 0.00 4.37
1088 4748 2.261671 CTTCGTCCCGTGTCCCAG 59.738 66.667 0.00 0.00 0.00 4.45
1089 4749 3.934391 CTTCGTCCCGTGTCCCAGC 62.934 68.421 0.00 0.00 0.00 4.85
1240 4900 4.796231 CTCCCTTCGTCCCGTGCG 62.796 72.222 0.00 0.00 0.00 5.34
1501 5224 2.415426 GCTACGAGCTCTGCCTCC 59.585 66.667 12.85 0.00 38.45 4.30
1842 5655 2.750888 GGGAAAGCATCGCGTCACC 61.751 63.158 5.77 1.47 0.00 4.02
1856 5669 3.499737 CACCAAGCCGATGGACGC 61.500 66.667 7.71 0.00 43.54 5.19
1907 5720 2.352814 CCTCCACTCGTTCGACTGAATT 60.353 50.000 0.00 0.00 36.29 2.17
2238 6067 2.820037 GCGCTACAAGACCCAGGC 60.820 66.667 0.00 0.00 0.00 4.85
2329 6158 1.229400 TGCCGACTACTTCCCCCTT 60.229 57.895 0.00 0.00 0.00 3.95
2393 6222 1.153862 CCACTCACTCTGCTCGCTC 60.154 63.158 0.00 0.00 0.00 5.03
2416 6245 2.726351 CCCTCACTCCTTCCTCGGC 61.726 68.421 0.00 0.00 0.00 5.54
2469 6303 4.364415 TGGAAAACAAACCAAGAACTCG 57.636 40.909 0.00 0.00 32.93 4.18
2609 6458 3.785325 TGTTACATGGGGATTGATCTGGA 59.215 43.478 0.00 0.00 0.00 3.86
2615 6464 4.886755 TGGGGATTGATCTGGAATTCTT 57.113 40.909 5.23 0.00 0.00 2.52
2632 6481 4.750021 TTCTTGATCATCAGAGAGGTGG 57.250 45.455 0.00 0.00 0.00 4.61
2651 6500 4.202315 GGTGGATTTTTATATGTTGGGGGC 60.202 45.833 0.00 0.00 0.00 5.80
2715 6565 8.918202 ACAGTTACATGATCTTTGTTCCTTAA 57.082 30.769 0.00 0.00 0.00 1.85
3006 7184 6.011981 ACTGGTTGGGTTTATAAGGAAGATGA 60.012 38.462 0.00 0.00 0.00 2.92
3068 7246 2.019984 GCAAGATCATCTTCCACACCC 58.980 52.381 0.00 0.00 33.78 4.61
3140 7345 7.458397 TCCGAACCTATATGGATGCTATTTTT 58.542 34.615 0.00 0.00 39.71 1.94
3202 7407 4.961438 ACCAATCCAAATGAACAAAGCT 57.039 36.364 0.00 0.00 0.00 3.74
3215 7420 8.560355 AATGAACAAAGCTTAAAACCAAAGTT 57.440 26.923 0.00 0.00 38.03 2.66
3234 7439 1.741770 GCGGTCGTGAGAAGCCAAT 60.742 57.895 0.00 0.00 45.01 3.16
3246 7451 3.939564 GCCAATTGCTACCCCCTG 58.060 61.111 0.00 0.00 36.87 4.45
3260 7465 0.889186 CCCCTGAACTTTCACCACCG 60.889 60.000 0.00 0.00 32.90 4.94
3284 7489 4.203076 CCGCCTAACCCGTCTCCG 62.203 72.222 0.00 0.00 0.00 4.63
3303 7508 0.105039 GTCCCAGCCTATTCAGGTCG 59.895 60.000 0.00 0.00 44.68 4.79
3306 7511 0.824109 CCAGCCTATTCAGGTCGTCA 59.176 55.000 0.00 0.00 44.68 4.35
3327 7532 1.146041 GCCACCATCCTCGTGCATA 59.854 57.895 0.00 0.00 0.00 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.948719 GCAGGTGACCCCGGTTGA 61.949 66.667 0.00 0.00 38.74 3.18
1 2 3.901797 GAGCAGGTGACCCCGGTTG 62.902 68.421 0.00 0.00 38.74 3.77
2 3 3.637273 GAGCAGGTGACCCCGGTT 61.637 66.667 0.00 0.00 38.74 4.44
5 6 4.742201 CACGAGCAGGTGACCCCG 62.742 72.222 0.00 0.00 40.38 5.73
6 7 3.311110 TCACGAGCAGGTGACCCC 61.311 66.667 0.00 0.00 41.76 4.95
11 12 4.662961 TGGCGTCACGAGCAGGTG 62.663 66.667 0.00 1.07 39.29 4.00
12 13 3.454587 TTTGGCGTCACGAGCAGGT 62.455 57.895 0.00 0.00 36.08 4.00
13 14 2.664851 TTTGGCGTCACGAGCAGG 60.665 61.111 0.00 0.00 36.08 4.85
14 15 2.243957 TGTTTGGCGTCACGAGCAG 61.244 57.895 0.00 0.00 36.08 4.24
16 17 2.248431 GTGTTTGGCGTCACGAGC 59.752 61.111 0.00 0.00 0.00 5.03
27 28 1.850377 TGCTGAAAATGCCGTGTTTG 58.150 45.000 0.00 0.00 0.00 2.93
28 29 2.593346 TTGCTGAAAATGCCGTGTTT 57.407 40.000 0.00 0.00 0.00 2.83
29 30 2.472816 CTTTGCTGAAAATGCCGTGTT 58.527 42.857 0.00 0.00 0.00 3.32
30 31 1.869342 GCTTTGCTGAAAATGCCGTGT 60.869 47.619 0.00 0.00 0.00 4.49
32 33 0.664166 CGCTTTGCTGAAAATGCCGT 60.664 50.000 0.00 0.00 0.00 5.68
33 34 0.664166 ACGCTTTGCTGAAAATGCCG 60.664 50.000 0.00 0.00 0.00 5.69
36 37 0.785979 GCCACGCTTTGCTGAAAATG 59.214 50.000 0.00 0.00 0.00 2.32
37 38 0.388659 TGCCACGCTTTGCTGAAAAT 59.611 45.000 0.00 0.00 0.00 1.82
38 39 0.248990 CTGCCACGCTTTGCTGAAAA 60.249 50.000 0.00 0.00 0.00 2.29
39 40 1.359833 CTGCCACGCTTTGCTGAAA 59.640 52.632 0.00 0.00 0.00 2.69
40 41 1.383456 AACTGCCACGCTTTGCTGAA 61.383 50.000 0.41 0.00 0.00 3.02
41 42 1.383456 AAACTGCCACGCTTTGCTGA 61.383 50.000 0.41 0.00 0.00 4.26
42 43 1.066257 AAACTGCCACGCTTTGCTG 59.934 52.632 0.00 0.00 0.00 4.41
43 44 1.066257 CAAACTGCCACGCTTTGCT 59.934 52.632 0.00 0.00 0.00 3.91
54 55 3.337301 CACAAAATTTGGGCAAACTGC 57.663 42.857 10.71 0.00 44.08 4.40
62 63 3.001127 CACACTTTCGCACAAAATTTGGG 59.999 43.478 10.71 7.18 37.05 4.12
63 64 3.616379 ACACACTTTCGCACAAAATTTGG 59.384 39.130 10.71 0.00 34.12 3.28
64 65 4.091220 ACACACACTTTCGCACAAAATTTG 59.909 37.500 3.89 3.89 0.00 2.32
65 66 4.241681 ACACACACTTTCGCACAAAATTT 58.758 34.783 0.00 0.00 0.00 1.82
66 67 3.843999 ACACACACTTTCGCACAAAATT 58.156 36.364 0.00 0.00 0.00 1.82
67 68 3.502191 ACACACACTTTCGCACAAAAT 57.498 38.095 0.00 0.00 0.00 1.82
69 70 2.726373 CGAACACACACTTTCGCACAAA 60.726 45.455 0.00 0.00 38.31 2.83
70 71 1.201976 CGAACACACACTTTCGCACAA 60.202 47.619 0.00 0.00 38.31 3.33
71 72 0.371989 CGAACACACACTTTCGCACA 59.628 50.000 0.00 0.00 38.31 4.57
72 73 0.648441 TCGAACACACACTTTCGCAC 59.352 50.000 0.00 0.00 43.44 5.34
73 74 1.061421 GTTCGAACACACACTTTCGCA 59.939 47.619 23.12 0.00 43.44 5.10
74 75 1.326548 AGTTCGAACACACACTTTCGC 59.673 47.619 28.78 0.00 43.44 4.70
75 76 3.651562 AAGTTCGAACACACACTTTCG 57.348 42.857 28.78 0.00 44.79 3.46
77 78 3.311596 GGCTAAGTTCGAACACACACTTT 59.688 43.478 28.78 15.08 31.83 2.66
78 79 2.870411 GGCTAAGTTCGAACACACACTT 59.130 45.455 28.78 15.90 33.95 3.16
81 82 2.479837 CTGGCTAAGTTCGAACACACA 58.520 47.619 28.78 17.83 0.00 3.72
82 83 1.798813 CCTGGCTAAGTTCGAACACAC 59.201 52.381 28.78 15.04 0.00 3.82
85 86 1.344065 TCCCTGGCTAAGTTCGAACA 58.656 50.000 28.78 9.52 0.00 3.18
86 87 2.693267 ATCCCTGGCTAAGTTCGAAC 57.307 50.000 20.71 20.71 0.00 3.95
87 88 2.418197 CGAATCCCTGGCTAAGTTCGAA 60.418 50.000 0.00 0.00 40.39 3.71
88 89 1.136305 CGAATCCCTGGCTAAGTTCGA 59.864 52.381 9.81 0.00 40.39 3.71
90 91 2.981859 TCGAATCCCTGGCTAAGTTC 57.018 50.000 0.00 0.00 0.00 3.01
93 94 1.202687 TGCATCGAATCCCTGGCTAAG 60.203 52.381 0.00 0.00 0.00 2.18
95 96 0.836606 TTGCATCGAATCCCTGGCTA 59.163 50.000 0.00 0.00 0.00 3.93
96 97 0.034186 TTTGCATCGAATCCCTGGCT 60.034 50.000 0.00 0.00 0.00 4.75
97 98 0.817013 TTTTGCATCGAATCCCTGGC 59.183 50.000 0.00 0.00 0.00 4.85
126 127 3.510459 AGCAATCCCTGGCTAAGTTTTT 58.490 40.909 0.00 0.00 38.90 1.94
127 128 3.175438 AGCAATCCCTGGCTAAGTTTT 57.825 42.857 0.00 0.00 38.90 2.43
131 132 5.506317 CGAAAAATAGCAATCCCTGGCTAAG 60.506 44.000 0.00 0.00 44.93 2.18
141 3510 8.226543 TCATCAACAAACGAAAAATAGCAATC 57.773 30.769 0.00 0.00 0.00 2.67
193 3563 1.508088 GCCTTTTCGGGATGCACTG 59.492 57.895 0.00 0.00 0.00 3.66
204 3574 2.391389 CCCTCAGCGACGCCTTTTC 61.391 63.158 17.79 0.00 0.00 2.29
256 3630 3.947132 CTGCCCTGGACAGCTGTCG 62.947 68.421 34.28 23.67 45.65 4.35
323 3725 1.000019 TCGAGAAGATCCGGTGGGT 60.000 57.895 0.00 0.00 33.83 4.51
380 3801 4.394712 GGAGTGGGTGCCGTCCTG 62.395 72.222 0.00 0.00 0.00 3.86
381 3802 4.954118 TGGAGTGGGTGCCGTCCT 62.954 66.667 0.00 0.00 32.35 3.85
382 3803 4.699522 GTGGAGTGGGTGCCGTCC 62.700 72.222 0.00 0.00 31.91 4.79
383 3804 3.936203 TGTGGAGTGGGTGCCGTC 61.936 66.667 0.00 0.00 0.00 4.79
384 3805 4.250305 GTGTGGAGTGGGTGCCGT 62.250 66.667 0.00 0.00 0.00 5.68
386 3807 4.660938 GGGTGTGGAGTGGGTGCC 62.661 72.222 0.00 0.00 0.00 5.01
388 3809 4.329545 CCGGGTGTGGAGTGGGTG 62.330 72.222 0.00 0.00 0.00 4.61
389 3810 4.892291 ACCGGGTGTGGAGTGGGT 62.892 66.667 6.32 0.00 0.00 4.51
390 3811 4.329545 CACCGGGTGTGGAGTGGG 62.330 72.222 19.15 0.00 41.52 4.61
391 3812 3.238497 TCACCGGGTGTGGAGTGG 61.238 66.667 25.53 0.00 45.48 4.00
400 3821 4.296729 AGGAGGACGTCACCGGGT 62.297 66.667 18.91 0.00 38.78 5.28
404 3825 4.131088 GCGGAGGAGGACGTCACC 62.131 72.222 18.91 18.96 33.25 4.02
426 3847 1.075600 GGTGGAGAGAGAGAGGGGG 60.076 68.421 0.00 0.00 0.00 5.40
428 3849 0.106217 GAGGGTGGAGAGAGAGAGGG 60.106 65.000 0.00 0.00 0.00 4.30
552 3979 1.889829 GGAGGATCGATCGATGGAACT 59.110 52.381 33.86 23.68 34.60 3.01
589 4020 5.223382 ACAATTAATCGAGCGAGATAGTGG 58.777 41.667 0.00 0.00 0.00 4.00
594 4029 5.812642 ACTGAAACAATTAATCGAGCGAGAT 59.187 36.000 0.00 0.00 0.00 2.75
602 4048 2.770865 GCGCGACTGAAACAATTAATCG 59.229 45.455 12.10 0.00 0.00 3.34
671 4146 4.643387 GGGAACACCGGCACTGCT 62.643 66.667 0.00 0.00 0.00 4.24
695 4174 0.388520 CATCAACAGAGACACGGCGA 60.389 55.000 16.62 0.00 0.00 5.54
739 4218 3.599285 GACGCCCCATTCACGGTGA 62.599 63.158 6.76 6.76 33.69 4.02
740 4219 3.124921 GACGCCCCATTCACGGTG 61.125 66.667 0.56 0.56 35.68 4.94
741 4220 4.752879 CGACGCCCCATTCACGGT 62.753 66.667 0.00 0.00 0.00 4.83
744 4223 3.499737 CAGCGACGCCCCATTCAC 61.500 66.667 17.79 0.00 0.00 3.18
745 4224 4.015406 ACAGCGACGCCCCATTCA 62.015 61.111 17.79 0.00 0.00 2.57
747 4226 3.842925 AACACAGCGACGCCCCATT 62.843 57.895 17.79 3.59 0.00 3.16
748 4227 3.842925 AAACACAGCGACGCCCCAT 62.843 57.895 17.79 0.00 0.00 4.00
749 4228 4.555709 AAACACAGCGACGCCCCA 62.556 61.111 17.79 0.00 0.00 4.96
752 4241 1.654137 CAACAAACACAGCGACGCC 60.654 57.895 17.79 0.00 0.00 5.68
755 4244 0.098728 ACAGCAACAAACACAGCGAC 59.901 50.000 0.00 0.00 0.00 5.19
781 4270 2.477825 AGGAACTCGATCGCAATCATG 58.522 47.619 11.09 0.00 31.76 3.07
783 4272 2.672961 AAGGAACTCGATCGCAATCA 57.327 45.000 11.09 0.00 38.49 2.57
803 4399 2.293122 CACCCGCTGTTTCAGAAATCAA 59.707 45.455 0.00 0.00 32.44 2.57
845 4445 3.060000 ACGATCGAGCACGGGACA 61.060 61.111 24.34 0.00 40.21 4.02
864 4464 2.355956 GCATCCGTAGTAGGCGCC 60.356 66.667 21.89 21.89 0.00 6.53
866 4466 1.007271 CTGGCATCCGTAGTAGGCG 60.007 63.158 0.00 0.00 0.00 5.52
867 4467 1.301009 GCTGGCATCCGTAGTAGGC 60.301 63.158 0.00 0.00 0.00 3.93
868 4468 1.007271 CGCTGGCATCCGTAGTAGG 60.007 63.158 0.00 0.00 0.00 3.18
869 4469 1.007271 CCGCTGGCATCCGTAGTAG 60.007 63.158 6.89 0.00 0.00 2.57
934 4538 6.755206 ACGGATCGGAATGTCAGAAATATTA 58.245 36.000 7.35 0.00 0.00 0.98
1051 4711 2.720605 GGAGTAGCCGCCGTAGAC 59.279 66.667 0.00 0.00 0.00 2.59
1097 4757 2.356818 GACGAAGGGGATGCCGAGAG 62.357 65.000 0.00 0.00 0.00 3.20
1098 4758 2.363795 ACGAAGGGGATGCCGAGA 60.364 61.111 0.00 0.00 0.00 4.04
1099 4759 2.107141 GACGAAGGGGATGCCGAG 59.893 66.667 0.00 0.00 0.00 4.63
1100 4760 3.467226 GGACGAAGGGGATGCCGA 61.467 66.667 0.00 0.00 0.00 5.54
1101 4761 4.547367 GGGACGAAGGGGATGCCG 62.547 72.222 0.00 0.00 0.00 5.69
1341 5064 4.410400 CTGGGGCTCGGGGTGAAC 62.410 72.222 0.00 0.00 0.00 3.18
2238 6067 3.274586 CGATGACCATGCGGCAGG 61.275 66.667 9.25 8.52 34.57 4.85
2329 6158 0.755698 GTAGCGATCAGGGGTGGAGA 60.756 60.000 0.00 0.00 0.00 3.71
2393 6222 0.252467 AGGAAGGAGTGAGGGAGTGG 60.252 60.000 0.00 0.00 0.00 4.00
2416 6245 7.760340 GCATATATAGTTTACGAAAGGGAGGAG 59.240 40.741 0.00 0.00 0.00 3.69
2469 6303 5.891551 TGCCTTATTTAGGTCTCCCATTTTC 59.108 40.000 0.00 0.00 46.61 2.29
2523 6359 3.411446 TGTGCCAACTCTAATGAAGTGG 58.589 45.455 0.00 0.00 32.33 4.00
2609 6458 5.427806 TCCACCTCTCTGATGATCAAGAATT 59.572 40.000 0.00 0.00 0.00 2.17
2615 6464 5.705397 AAAATCCACCTCTCTGATGATCA 57.295 39.130 0.00 0.00 0.00 2.92
2632 6481 4.929819 ACGCCCCCAACATATAAAAATC 57.070 40.909 0.00 0.00 0.00 2.17
2678 6527 5.073428 TCATGTAACTGTAACCAATGGCAA 58.927 37.500 0.00 0.00 0.00 4.52
2679 6528 4.657013 TCATGTAACTGTAACCAATGGCA 58.343 39.130 0.00 0.00 0.00 4.92
2715 6565 8.411683 GCTGATAATTTCCTCTCAAAACATGAT 58.588 33.333 0.00 0.00 37.44 2.45
2782 6942 2.106338 TGATCTTCCTGCCACAAGACAA 59.894 45.455 0.00 0.00 31.42 3.18
2856 7034 7.789202 ACATCTATACTTGACATGCTCCTAT 57.211 36.000 0.00 0.00 0.00 2.57
3006 7184 3.935203 CACTCTCAAGCATAATTGTCCGT 59.065 43.478 0.00 0.00 0.00 4.69
3110 7315 4.811557 GCATCCATATAGGTTCGGATTAGC 59.188 45.833 0.00 0.00 36.07 3.09
3115 7320 6.620877 AAATAGCATCCATATAGGTTCGGA 57.379 37.500 0.00 0.00 39.02 4.55
3202 7407 2.422832 ACGACCGCAACTTTGGTTTTAA 59.577 40.909 0.00 0.00 38.99 1.52
3215 7420 2.449031 ATTGGCTTCTCACGACCGCA 62.449 55.000 0.00 0.00 0.00 5.69
3234 7439 1.777878 TGAAAGTTCAGGGGGTAGCAA 59.222 47.619 0.00 0.00 32.50 3.91
3243 7448 0.817634 TGCGGTGGTGAAAGTTCAGG 60.818 55.000 0.00 0.00 37.98 3.86
3246 7451 0.586802 GACTGCGGTGGTGAAAGTTC 59.413 55.000 0.80 0.00 0.00 3.01
3279 7484 0.032515 TGAATAGGCTGGGACGGAGA 60.033 55.000 0.00 0.00 36.31 3.71
3292 7497 1.772182 GGCGATGACGACCTGAATAG 58.228 55.000 0.00 0.00 42.35 1.73
3293 7498 3.959478 GGCGATGACGACCTGAATA 57.041 52.632 0.00 0.00 42.35 1.75
3303 7508 1.592669 CGAGGATGGTGGCGATGAC 60.593 63.158 0.00 0.00 0.00 3.06
3306 7511 2.501128 CACGAGGATGGTGGCGAT 59.499 61.111 0.00 0.00 41.46 4.58


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

AutoCloner maintained by Alex Coulton.