Multiple sequence alignment - TraesCS2A01G121300

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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 TraesCS2A01G121300 chr2A 100.000 2190 0 0 428 2617 71112250 71114439 0.000000e+00 4045.0
1 TraesCS2A01G121300 chr2A 88.786 651 63 8 1360 2006 71078583 71079227 0.000000e+00 789.0
2 TraesCS2A01G121300 chr2A 91.042 480 38 2 695 1173 71073592 71074067 0.000000e+00 643.0
3 TraesCS2A01G121300 chr2A 97.241 145 4 0 444 588 71073466 71073610 2.010000e-61 246.0
4 TraesCS2A01G121300 chr2A 94.964 139 7 0 2479 2617 71158034 71158172 4.390000e-53 219.0
5 TraesCS2A01G121300 chr2A 94.964 139 7 0 2479 2617 71210794 71210932 4.390000e-53 219.0
6 TraesCS2A01G121300 chr2A 94.964 139 7 0 2479 2617 71263423 71263561 4.390000e-53 219.0
7 TraesCS2A01G121300 chr2A 94.964 139 7 0 2479 2617 71312351 71312489 4.390000e-53 219.0
8 TraesCS2A01G121300 chr2A 84.091 176 5 7 1199 1362 71074543 71074707 5.840000e-32 148.0
9 TraesCS2A01G121300 chr2A 100.000 51 0 0 1 51 71111823 71111873 7.710000e-16 95.3
10 TraesCS2A01G121300 chr2D 97.911 1580 27 3 428 2006 72651505 72653079 0.000000e+00 2730.0
11 TraesCS2A01G121300 chr2D 97.658 1580 26 4 428 2006 72371050 72372619 0.000000e+00 2702.0
12 TraesCS2A01G121300 chr2D 96.479 568 15 2 428 994 72627855 72628418 0.000000e+00 933.0
13 TraesCS2A01G121300 chr2D 97.512 201 5 0 2417 2617 72653079 72653279 6.930000e-91 344.0
14 TraesCS2A01G121300 chr2D 86.207 203 4 3 2417 2617 72372619 72372799 5.710000e-47 198.0
15 TraesCS2A01G121300 chr2B 95.745 1551 50 8 428 1970 109082351 109083893 0.000000e+00 2484.0
16 TraesCS2A01G121300 chr2B 96.894 1288 29 4 428 1713 109161609 109162887 0.000000e+00 2146.0
17 TraesCS2A01G121300 chr2B 96.587 1289 32 8 428 1713 109789182 109790461 0.000000e+00 2126.0
18 TraesCS2A01G121300 chr2B 88.520 662 66 9 1260 1919 109357666 109358319 0.000000e+00 793.0
19 TraesCS2A01G121300 chr2B 90.503 358 30 4 433 788 109356852 109357207 1.100000e-128 470.0
20 TraesCS2A01G121300 chr2B 88.487 304 13 5 1704 2006 109180351 109180633 5.360000e-92 348.0
21 TraesCS2A01G121300 chr2B 97.512 201 5 0 2417 2617 109180633 109180833 6.930000e-91 344.0
22 TraesCS2A01G121300 chr2B 97.512 201 5 0 2417 2617 109869024 109869224 6.930000e-91 344.0
23 TraesCS2A01G121300 chr2B 97.015 201 6 0 2417 2617 109084123 109084323 3.230000e-89 339.0
24 TraesCS2A01G121300 chr2B 96.111 180 5 2 1828 2006 109868846 109869024 2.550000e-75 292.0
25 TraesCS2A01G121300 chr2B 94.483 145 8 0 984 1128 109357463 109357607 9.430000e-55 224.0
26 TraesCS2A01G121300 chr2B 98.039 51 1 0 1 51 109161520 109161570 3.590000e-14 89.8
27 TraesCS2A01G121300 chr2B 96.078 51 2 0 1 51 109076608 109076658 1.670000e-12 84.2
28 TraesCS2A01G121300 chr2B 96.000 50 2 0 2 51 109356753 109356802 6.000000e-12 82.4
29 TraesCS2A01G121300 chr2B 97.917 48 0 1 1 47 109789088 109789135 6.000000e-12 82.4
30 TraesCS2A01G121300 chr7A 94.390 410 19 3 1996 2403 91381506 91381099 6.150000e-176 627.0
31 TraesCS2A01G121300 chr7A 94.195 379 22 0 2025 2403 84489620 84489998 1.750000e-161 579.0
32 TraesCS2A01G121300 chr6B 80.116 865 130 32 782 1620 176969891 176969043 8.010000e-170 606.0
33 TraesCS2A01G121300 chr6D 93.797 403 24 1 1997 2399 81701495 81701896 2.880000e-169 604.0
34 TraesCS2A01G121300 chr6D 93.995 383 22 1 2015 2397 466598693 466599074 1.750000e-161 579.0
35 TraesCS2A01G121300 chr6D 83.845 489 69 8 772 1258 95787880 95788360 8.540000e-125 457.0
36 TraesCS2A01G121300 chr6D 97.674 43 1 0 1 43 112914612 112914570 1.000000e-09 75.0
37 TraesCS2A01G121300 chr1A 96.919 357 10 1 2047 2403 422493926 422493571 4.820000e-167 597.0
38 TraesCS2A01G121300 chr1A 95.068 365 16 2 2039 2403 202323245 202322883 8.120000e-160 573.0
39 TraesCS2A01G121300 chr3A 92.289 402 28 3 2002 2403 711691930 711691532 3.780000e-158 568.0
40 TraesCS2A01G121300 chr3A 92.658 395 25 4 2009 2403 497108440 497108830 1.360000e-157 566.0
41 TraesCS2A01G121300 chr3A 95.652 46 1 1 3 47 121652275 121652230 3.610000e-09 73.1
42 TraesCS2A01G121300 chr4D 92.857 392 23 4 2010 2399 329894768 329894380 4.890000e-157 564.0
43 TraesCS2A01G121300 chrUn 94.964 139 7 0 2479 2617 289659160 289659298 4.390000e-53 219.0
44 TraesCS2A01G121300 chr6A 96.000 50 0 2 3 51 140568963 140568915 2.160000e-11 80.5
45 TraesCS2A01G121300 chr5D 100.000 38 0 0 7 44 254834339 254834376 1.300000e-08 71.3
46 TraesCS2A01G121300 chr7B 97.436 39 1 0 6 44 184497032 184496994 1.680000e-07 67.6


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 TraesCS2A01G121300 chr2A 71111823 71114439 2616 False 2070.15 4045 100.0000 1 2617 2 chr2A.!!$F6 2616
1 TraesCS2A01G121300 chr2A 71073466 71079227 5761 False 456.50 789 90.2900 444 2006 4 chr2A.!!$F5 1562
2 TraesCS2A01G121300 chr2D 72651505 72653279 1774 False 1537.00 2730 97.7115 428 2617 2 chr2D.!!$F3 2189
3 TraesCS2A01G121300 chr2D 72371050 72372799 1749 False 1450.00 2702 91.9325 428 2617 2 chr2D.!!$F2 2189
4 TraesCS2A01G121300 chr2D 72627855 72628418 563 False 933.00 933 96.4790 428 994 1 chr2D.!!$F1 566
5 TraesCS2A01G121300 chr2B 109082351 109084323 1972 False 1411.50 2484 96.3800 428 2617 2 chr2B.!!$F2 2189
6 TraesCS2A01G121300 chr2B 109161520 109162887 1367 False 1117.90 2146 97.4665 1 1713 2 chr2B.!!$F3 1712
7 TraesCS2A01G121300 chr2B 109789088 109790461 1373 False 1104.20 2126 97.2520 1 1713 2 chr2B.!!$F6 1712
8 TraesCS2A01G121300 chr2B 109356753 109358319 1566 False 392.35 793 92.3765 2 1919 4 chr2B.!!$F5 1917
9 TraesCS2A01G121300 chr6B 176969043 176969891 848 True 606.00 606 80.1160 782 1620 1 chr6B.!!$R1 838


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
840 884 4.557205 GTGTGCTTATCTTATCCTACGGG 58.443 47.826 0.0 0.0 0.0 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2414 7051 0.034186 TAGGATTGCTTGCCACCAGG 60.034 55.0 0.0 0.0 38.23 4.45 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
840 884 4.557205 GTGTGCTTATCTTATCCTACGGG 58.443 47.826 0.00 0.00 0.00 5.28
1153 1229 7.927629 TCAACGTACACTACAAAAGTTAGGATT 59.072 33.333 0.00 0.00 35.76 3.01
1367 5794 7.410407 GCCTGTTTTTCGCTTGTTATATTGTTC 60.410 37.037 0.00 0.00 0.00 3.18
1653 6086 5.872617 TGATTAATCAACGTAGTGGACCAAG 59.127 40.000 15.82 0.00 46.92 3.61
1821 6256 9.851686 AACTTATCTACAATTCCAGCATTATGA 57.148 29.630 0.00 0.00 0.00 2.15
2081 6718 2.846039 ATATAGGGTCGCGCTATTCG 57.154 50.000 17.00 0.00 39.65 3.34
2082 6719 1.527034 TATAGGGTCGCGCTATTCGT 58.473 50.000 17.00 0.00 39.65 3.85
2083 6720 0.240411 ATAGGGTCGCGCTATTCGTC 59.760 55.000 5.56 0.00 36.44 4.20
2084 6721 1.096967 TAGGGTCGCGCTATTCGTCA 61.097 55.000 5.56 0.00 41.07 4.35
2085 6722 2.228914 GGGTCGCGCTATTCGTCAC 61.229 63.158 5.56 0.00 41.07 3.67
2086 6723 2.228914 GGTCGCGCTATTCGTCACC 61.229 63.158 5.56 0.00 41.07 4.02
2087 6724 2.103538 TCGCGCTATTCGTCACCC 59.896 61.111 5.56 0.00 41.07 4.61
2088 6725 2.104331 CGCGCTATTCGTCACCCT 59.896 61.111 5.56 0.00 41.07 4.34
2089 6726 2.230940 CGCGCTATTCGTCACCCTG 61.231 63.158 5.56 0.00 41.07 4.45
2090 6727 1.883084 GCGCTATTCGTCACCCTGG 60.883 63.158 0.00 0.00 41.07 4.45
2091 6728 1.227263 CGCTATTCGTCACCCTGGG 60.227 63.158 12.28 12.28 0.00 4.45
2092 6729 1.905512 GCTATTCGTCACCCTGGGT 59.094 57.895 14.05 14.05 35.62 4.51
2103 6740 2.361085 ACCCTGGGTGAGGAATAGTT 57.639 50.000 19.82 0.00 46.33 2.24
2104 6741 3.502051 ACCCTGGGTGAGGAATAGTTA 57.498 47.619 19.82 0.00 46.33 2.24
2105 6742 4.022359 ACCCTGGGTGAGGAATAGTTAT 57.978 45.455 19.82 0.00 46.33 1.89
2106 6743 4.380791 ACCCTGGGTGAGGAATAGTTATT 58.619 43.478 19.82 0.00 46.33 1.40
2107 6744 4.412528 ACCCTGGGTGAGGAATAGTTATTC 59.587 45.833 19.82 3.75 46.33 1.75
2108 6745 4.660771 CCCTGGGTGAGGAATAGTTATTCT 59.339 45.833 3.97 0.00 46.33 2.40
2109 6746 5.132816 CCCTGGGTGAGGAATAGTTATTCTT 59.867 44.000 3.97 4.41 46.33 2.52
2110 6747 6.292150 CCTGGGTGAGGAATAGTTATTCTTC 58.708 44.000 13.90 13.90 46.33 2.87
2115 6752 6.248569 TGAGGAATAGTTATTCTTCACCCC 57.751 41.667 17.60 0.81 46.85 4.95
2116 6753 5.132144 TGAGGAATAGTTATTCTTCACCCCC 59.868 44.000 17.60 0.23 46.85 5.40
2117 6754 5.297799 AGGAATAGTTATTCTTCACCCCCT 58.702 41.667 10.71 0.00 41.33 4.79
2118 6755 5.369993 AGGAATAGTTATTCTTCACCCCCTC 59.630 44.000 10.71 0.00 41.33 4.30
2119 6756 5.369993 GGAATAGTTATTCTTCACCCCCTCT 59.630 44.000 10.71 0.00 41.33 3.69
2120 6757 6.464607 GGAATAGTTATTCTTCACCCCCTCTC 60.465 46.154 10.71 0.00 41.33 3.20
2121 6758 4.081695 AGTTATTCTTCACCCCCTCTCT 57.918 45.455 0.00 0.00 0.00 3.10
2122 6759 5.222278 AGTTATTCTTCACCCCCTCTCTA 57.778 43.478 0.00 0.00 0.00 2.43
2123 6760 5.600749 AGTTATTCTTCACCCCCTCTCTAA 58.399 41.667 0.00 0.00 0.00 2.10
2124 6761 6.213525 AGTTATTCTTCACCCCCTCTCTAAT 58.786 40.000 0.00 0.00 0.00 1.73
2125 6762 6.678857 AGTTATTCTTCACCCCCTCTCTAATT 59.321 38.462 0.00 0.00 0.00 1.40
2126 6763 7.184753 AGTTATTCTTCACCCCCTCTCTAATTT 59.815 37.037 0.00 0.00 0.00 1.82
2127 6764 4.844349 TCTTCACCCCCTCTCTAATTTG 57.156 45.455 0.00 0.00 0.00 2.32
2128 6765 4.435137 TCTTCACCCCCTCTCTAATTTGA 58.565 43.478 0.00 0.00 0.00 2.69
2129 6766 4.225267 TCTTCACCCCCTCTCTAATTTGAC 59.775 45.833 0.00 0.00 0.00 3.18
2130 6767 2.500098 TCACCCCCTCTCTAATTTGACG 59.500 50.000 0.00 0.00 0.00 4.35
2131 6768 2.236395 CACCCCCTCTCTAATTTGACGT 59.764 50.000 0.00 0.00 0.00 4.34
2132 6769 2.500504 ACCCCCTCTCTAATTTGACGTC 59.499 50.000 9.11 9.11 0.00 4.34
2133 6770 2.500098 CCCCCTCTCTAATTTGACGTCA 59.500 50.000 15.76 15.76 0.00 4.35
2134 6771 3.055385 CCCCCTCTCTAATTTGACGTCAA 60.055 47.826 26.53 26.53 0.00 3.18
2135 6772 4.384208 CCCCCTCTCTAATTTGACGTCAAT 60.384 45.833 30.10 19.28 35.55 2.57
2136 6773 4.572389 CCCCTCTCTAATTTGACGTCAATG 59.428 45.833 30.10 19.55 35.55 2.82
2137 6774 4.034510 CCCTCTCTAATTTGACGTCAATGC 59.965 45.833 30.10 0.00 35.55 3.56
2138 6775 4.631377 CCTCTCTAATTTGACGTCAATGCA 59.369 41.667 30.10 17.05 35.55 3.96
2139 6776 5.446473 CCTCTCTAATTTGACGTCAATGCAC 60.446 44.000 30.10 0.00 35.55 4.57
2140 6777 4.391830 TCTCTAATTTGACGTCAATGCACC 59.608 41.667 30.10 0.00 35.55 5.01
2141 6778 2.330231 AATTTGACGTCAATGCACCG 57.670 45.000 30.10 0.00 35.55 4.94
2142 6779 1.234821 ATTTGACGTCAATGCACCGT 58.765 45.000 30.10 9.01 35.55 4.83
2143 6780 1.867166 TTTGACGTCAATGCACCGTA 58.133 45.000 30.10 11.18 35.55 4.02
2144 6781 2.087501 TTGACGTCAATGCACCGTAT 57.912 45.000 26.53 0.00 34.51 3.06
2145 6782 2.087501 TGACGTCAATGCACCGTATT 57.912 45.000 17.62 0.00 34.51 1.89
2146 6783 2.418692 TGACGTCAATGCACCGTATTT 58.581 42.857 17.62 0.00 34.51 1.40
2147 6784 2.809119 TGACGTCAATGCACCGTATTTT 59.191 40.909 17.62 0.00 34.51 1.82
2148 6785 3.251245 TGACGTCAATGCACCGTATTTTT 59.749 39.130 17.62 0.00 34.51 1.94
2149 6786 4.451435 TGACGTCAATGCACCGTATTTTTA 59.549 37.500 17.62 0.00 34.51 1.52
2150 6787 4.965062 ACGTCAATGCACCGTATTTTTAG 58.035 39.130 0.00 0.00 32.22 1.85
2151 6788 4.142773 ACGTCAATGCACCGTATTTTTAGG 60.143 41.667 0.00 0.00 32.22 2.69
2152 6789 4.142773 CGTCAATGCACCGTATTTTTAGGT 60.143 41.667 0.00 0.00 39.12 3.08
2153 6790 5.618195 CGTCAATGCACCGTATTTTTAGGTT 60.618 40.000 0.00 0.00 35.85 3.50
2154 6791 6.153756 GTCAATGCACCGTATTTTTAGGTTT 58.846 36.000 0.00 0.00 35.85 3.27
2155 6792 6.307077 GTCAATGCACCGTATTTTTAGGTTTC 59.693 38.462 0.00 0.00 35.85 2.78
2156 6793 4.407496 TGCACCGTATTTTTAGGTTTCG 57.593 40.909 0.00 0.00 35.85 3.46
2157 6794 3.814283 TGCACCGTATTTTTAGGTTTCGT 59.186 39.130 0.00 0.00 35.85 3.85
2158 6795 4.993584 TGCACCGTATTTTTAGGTTTCGTA 59.006 37.500 0.00 0.00 35.85 3.43
2159 6796 5.468072 TGCACCGTATTTTTAGGTTTCGTAA 59.532 36.000 0.00 0.00 35.85 3.18
2160 6797 6.017605 TGCACCGTATTTTTAGGTTTCGTAAA 60.018 34.615 0.00 0.00 35.85 2.01
2161 6798 7.022979 GCACCGTATTTTTAGGTTTCGTAAAT 58.977 34.615 0.00 0.00 35.85 1.40
2162 6799 7.538334 GCACCGTATTTTTAGGTTTCGTAAATT 59.462 33.333 0.00 0.00 35.85 1.82
2163 6800 9.396938 CACCGTATTTTTAGGTTTCGTAAATTT 57.603 29.630 0.00 0.00 35.85 1.82
2164 6801 9.611284 ACCGTATTTTTAGGTTTCGTAAATTTC 57.389 29.630 0.00 0.00 33.96 2.17
2165 6802 9.609950 CCGTATTTTTAGGTTTCGTAAATTTCA 57.390 29.630 0.00 0.00 0.00 2.69
2175 6812 9.238368 AGGTTTCGTAAATTTCATCCTATTTCA 57.762 29.630 0.00 0.00 0.00 2.69
2180 6817 9.537192 TCGTAAATTTCATCCTATTTCATACGT 57.463 29.630 0.00 0.00 30.87 3.57
2192 6829 9.079833 TCCTATTTCATACGTAAAAAGAGAACG 57.920 33.333 20.94 10.73 42.17 3.95
2211 6848 9.609950 AGAGAACGTAAGAAAATATATACTCGC 57.390 33.333 0.00 0.00 43.62 5.03
2212 6849 8.739649 AGAACGTAAGAAAATATATACTCGCC 57.260 34.615 0.00 0.00 43.62 5.54
2213 6850 7.536622 AGAACGTAAGAAAATATATACTCGCCG 59.463 37.037 0.00 0.00 43.62 6.46
2214 6851 6.672147 ACGTAAGAAAATATATACTCGCCGT 58.328 36.000 0.00 0.00 43.62 5.68
2215 6852 7.806690 ACGTAAGAAAATATATACTCGCCGTA 58.193 34.615 0.00 0.00 43.62 4.02
2216 6853 8.289618 ACGTAAGAAAATATATACTCGCCGTAA 58.710 33.333 0.00 0.00 43.62 3.18
2217 6854 9.117145 CGTAAGAAAATATATACTCGCCGTAAA 57.883 33.333 0.00 0.00 43.02 2.01
2259 6896 9.842444 TGTAAAGTTACGAACGTAAAAACATAC 57.158 29.630 18.81 16.31 41.51 2.39
2260 6897 9.842444 GTAAAGTTACGAACGTAAAAACATACA 57.158 29.630 18.81 0.00 41.51 2.29
2361 6998 8.755696 TGAATGTTACTATTTGCATTCCAAAC 57.244 30.769 11.87 0.00 45.52 2.93
2362 6999 7.540400 TGAATGTTACTATTTGCATTCCAAACG 59.460 33.333 11.87 0.00 45.52 3.60
2363 7000 6.320494 TGTTACTATTTGCATTCCAAACGT 57.680 33.333 0.00 0.00 45.52 3.99
2364 7001 7.436430 TGTTACTATTTGCATTCCAAACGTA 57.564 32.000 0.00 0.00 45.52 3.57
2365 7002 7.872881 TGTTACTATTTGCATTCCAAACGTAA 58.127 30.769 0.00 0.00 45.52 3.18
2366 7003 8.516234 TGTTACTATTTGCATTCCAAACGTAAT 58.484 29.630 0.00 0.00 45.52 1.89
2367 7004 9.349145 GTTACTATTTGCATTCCAAACGTAATT 57.651 29.630 0.00 0.00 45.52 1.40
2368 7005 9.915629 TTACTATTTGCATTCCAAACGTAATTT 57.084 25.926 0.00 0.00 45.52 1.82
2369 7006 8.238481 ACTATTTGCATTCCAAACGTAATTTG 57.762 30.769 0.00 0.00 45.52 2.32
2370 7007 7.870445 ACTATTTGCATTCCAAACGTAATTTGT 59.130 29.630 0.00 0.00 45.52 2.83
2371 7008 6.910536 TTTGCATTCCAAACGTAATTTGTT 57.089 29.167 0.00 0.00 45.45 2.83
2372 7009 6.910536 TTGCATTCCAAACGTAATTTGTTT 57.089 29.167 0.00 3.43 45.45 2.83
2373 7010 8.420374 TTTGCATTCCAAACGTAATTTGTTTA 57.580 26.923 7.83 0.00 45.45 2.01
2374 7011 8.594881 TTGCATTCCAAACGTAATTTGTTTAT 57.405 26.923 7.83 0.00 45.45 1.40
2375 7012 8.012151 TGCATTCCAAACGTAATTTGTTTATG 57.988 30.769 7.83 9.17 45.45 1.90
2376 7013 7.867909 TGCATTCCAAACGTAATTTGTTTATGA 59.132 29.630 14.85 9.94 45.45 2.15
2377 7014 8.704234 GCATTCCAAACGTAATTTGTTTATGAA 58.296 29.630 14.85 14.92 45.45 2.57
2379 7016 7.861176 TCCAAACGTAATTTGTTTATGAAGC 57.139 32.000 7.83 0.00 45.45 3.86
2380 7017 6.579292 TCCAAACGTAATTTGTTTATGAAGCG 59.421 34.615 7.83 0.00 45.45 4.68
2381 7018 6.579292 CCAAACGTAATTTGTTTATGAAGCGA 59.421 34.615 7.83 0.00 45.45 4.93
2382 7019 7.272515 CCAAACGTAATTTGTTTATGAAGCGAT 59.727 33.333 7.83 0.00 45.45 4.58
2383 7020 7.948513 AACGTAATTTGTTTATGAAGCGATC 57.051 32.000 0.00 0.00 32.17 3.69
2384 7021 6.182634 ACGTAATTTGTTTATGAAGCGATCG 58.817 36.000 11.69 11.69 32.17 3.69
2385 7022 6.182634 CGTAATTTGTTTATGAAGCGATCGT 58.817 36.000 17.81 0.00 0.00 3.73
2386 7023 7.009448 ACGTAATTTGTTTATGAAGCGATCGTA 59.991 33.333 17.81 0.00 32.17 3.43
2387 7024 7.842239 CGTAATTTGTTTATGAAGCGATCGTAA 59.158 33.333 17.81 3.98 37.67 3.18
2388 7025 9.144085 GTAATTTGTTTATGAAGCGATCGTAAG 57.856 33.333 17.81 0.00 39.92 2.34
2402 7039 3.003394 TCGTAAGATTACCTCGGGTGA 57.997 47.619 5.90 0.00 45.01 4.02
2403 7040 3.559069 TCGTAAGATTACCTCGGGTGAT 58.441 45.455 5.90 3.33 45.01 3.06
2404 7041 3.956199 TCGTAAGATTACCTCGGGTGATT 59.044 43.478 5.90 0.00 45.01 2.57
2405 7042 5.132502 TCGTAAGATTACCTCGGGTGATTA 58.867 41.667 5.90 0.00 45.01 1.75
2406 7043 5.771666 TCGTAAGATTACCTCGGGTGATTAT 59.228 40.000 5.90 0.63 45.01 1.28
2407 7044 6.266103 TCGTAAGATTACCTCGGGTGATTATT 59.734 38.462 5.90 5.58 45.01 1.40
2408 7045 6.585322 CGTAAGATTACCTCGGGTGATTATTC 59.415 42.308 5.90 0.00 36.23 1.75
2409 7046 6.749036 AAGATTACCTCGGGTGATTATTCT 57.251 37.500 5.90 0.00 36.19 2.40
2410 7047 6.102897 AGATTACCTCGGGTGATTATTCTG 57.897 41.667 5.90 0.00 36.19 3.02
2411 7048 2.622064 ACCTCGGGTGATTATTCTGC 57.378 50.000 0.00 0.00 32.98 4.26
2412 7049 1.837439 ACCTCGGGTGATTATTCTGCA 59.163 47.619 0.00 0.00 32.98 4.41
2413 7050 2.213499 CCTCGGGTGATTATTCTGCAC 58.787 52.381 0.00 0.00 0.00 4.57
2503 7142 5.051641 GCACCGAAATCTGAATAGTTAGACG 60.052 44.000 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1318 1861 4.984161 CACATACATACGACATGCATGAGA 59.016 41.667 32.75 14.32 0.00 3.27
1648 6081 3.319122 GGACAGAAACATCAAAGCTTGGT 59.681 43.478 0.00 0.00 0.00 3.67
1653 6086 3.426695 CCGATGGACAGAAACATCAAAGC 60.427 47.826 0.00 0.00 42.72 3.51
1819 6254 1.810151 GCCCTGTGCGAATAAAAGTCA 59.190 47.619 0.00 0.00 0.00 3.41
1821 6256 1.904287 TGCCCTGTGCGAATAAAAGT 58.096 45.000 0.00 0.00 45.60 2.66
2055 6692 9.038803 CGAATAGCGCGACCCTATATATATATA 57.961 37.037 12.10 11.21 0.00 0.86
2056 6693 7.551974 ACGAATAGCGCGACCCTATATATATAT 59.448 37.037 12.10 10.10 46.04 0.86
2057 6694 6.875726 ACGAATAGCGCGACCCTATATATATA 59.124 38.462 12.10 2.49 46.04 0.86
2058 6695 5.704515 ACGAATAGCGCGACCCTATATATAT 59.295 40.000 12.10 0.00 46.04 0.86
2059 6696 5.059161 ACGAATAGCGCGACCCTATATATA 58.941 41.667 12.10 0.00 46.04 0.86
2060 6697 3.881688 ACGAATAGCGCGACCCTATATAT 59.118 43.478 12.10 0.00 46.04 0.86
2061 6698 3.273434 ACGAATAGCGCGACCCTATATA 58.727 45.455 12.10 0.00 46.04 0.86
2062 6699 2.089980 ACGAATAGCGCGACCCTATAT 58.910 47.619 12.10 0.00 46.04 0.86
2063 6700 1.466167 GACGAATAGCGCGACCCTATA 59.534 52.381 12.10 0.00 46.04 1.31
2064 6701 0.240411 GACGAATAGCGCGACCCTAT 59.760 55.000 12.10 4.35 46.04 2.57
2065 6702 1.096967 TGACGAATAGCGCGACCCTA 61.097 55.000 12.10 1.47 46.04 3.53
2066 6703 2.412112 GACGAATAGCGCGACCCT 59.588 61.111 12.10 0.00 46.04 4.34
2067 6704 2.103538 TGACGAATAGCGCGACCC 59.896 61.111 12.10 0.00 46.04 4.46
2068 6705 2.228914 GGTGACGAATAGCGCGACC 61.229 63.158 12.10 0.00 46.04 4.79
2069 6706 2.228914 GGGTGACGAATAGCGCGAC 61.229 63.158 12.10 0.04 46.04 5.19
2070 6707 2.103538 GGGTGACGAATAGCGCGA 59.896 61.111 12.10 0.00 46.04 5.87
2071 6708 2.104331 AGGGTGACGAATAGCGCG 59.896 61.111 0.00 0.00 46.04 6.86
2072 6709 1.883084 CCAGGGTGACGAATAGCGC 60.883 63.158 0.00 0.00 46.04 5.92
2073 6710 1.956629 ACCCAGGGTGACGAATAGCG 61.957 60.000 11.70 0.00 39.57 4.26
2074 6711 1.905512 ACCCAGGGTGACGAATAGC 59.094 57.895 11.70 0.00 32.98 2.97
2081 6718 9.736671 GAATAACTATTCCTCACCCAGGGTGAC 62.737 48.148 34.62 17.53 44.45 3.67
2082 6719 7.827072 GAATAACTATTCCTCACCCAGGGTGA 61.827 46.154 35.32 35.32 45.54 4.02
2083 6720 5.687706 GAATAACTATTCCTCACCCAGGGTG 60.688 48.000 31.06 31.06 43.50 4.61
2084 6721 2.361085 AACTATTCCTCACCCAGGGT 57.639 50.000 4.76 4.76 43.67 4.34
2085 6722 4.660771 AGAATAACTATTCCTCACCCAGGG 59.339 45.833 2.85 2.85 43.67 4.45
2086 6723 5.896073 AGAATAACTATTCCTCACCCAGG 57.104 43.478 5.95 0.00 42.29 4.45
2087 6724 6.889198 TGAAGAATAACTATTCCTCACCCAG 58.111 40.000 6.65 0.00 42.29 4.45
2088 6725 6.884472 TGAAGAATAACTATTCCTCACCCA 57.116 37.500 6.65 0.00 42.29 4.51
2092 6729 5.132144 GGGGGTGAAGAATAACTATTCCTCA 59.868 44.000 6.65 6.65 42.29 3.86
2093 6730 5.369993 AGGGGGTGAAGAATAACTATTCCTC 59.630 44.000 5.95 4.07 42.29 3.71
2094 6731 5.297799 AGGGGGTGAAGAATAACTATTCCT 58.702 41.667 5.95 0.00 42.29 3.36
2095 6732 5.369993 AGAGGGGGTGAAGAATAACTATTCC 59.630 44.000 5.95 0.00 42.29 3.01
2096 6733 6.327887 AGAGAGGGGGTGAAGAATAACTATTC 59.672 42.308 1.83 1.83 41.78 1.75
2097 6734 6.213525 AGAGAGGGGGTGAAGAATAACTATT 58.786 40.000 0.00 0.00 0.00 1.73
2098 6735 5.793967 AGAGAGGGGGTGAAGAATAACTAT 58.206 41.667 0.00 0.00 0.00 2.12
2099 6736 5.222278 AGAGAGGGGGTGAAGAATAACTA 57.778 43.478 0.00 0.00 0.00 2.24
2100 6737 4.081695 AGAGAGGGGGTGAAGAATAACT 57.918 45.455 0.00 0.00 0.00 2.24
2101 6738 5.952347 TTAGAGAGGGGGTGAAGAATAAC 57.048 43.478 0.00 0.00 0.00 1.89
2102 6739 7.183839 TCAAATTAGAGAGGGGGTGAAGAATAA 59.816 37.037 0.00 0.00 0.00 1.40
2103 6740 6.676632 TCAAATTAGAGAGGGGGTGAAGAATA 59.323 38.462 0.00 0.00 0.00 1.75
2104 6741 5.492524 TCAAATTAGAGAGGGGGTGAAGAAT 59.507 40.000 0.00 0.00 0.00 2.40
2105 6742 4.849810 TCAAATTAGAGAGGGGGTGAAGAA 59.150 41.667 0.00 0.00 0.00 2.52
2106 6743 4.225267 GTCAAATTAGAGAGGGGGTGAAGA 59.775 45.833 0.00 0.00 0.00 2.87
2107 6744 4.518249 GTCAAATTAGAGAGGGGGTGAAG 58.482 47.826 0.00 0.00 0.00 3.02
2108 6745 3.055385 CGTCAAATTAGAGAGGGGGTGAA 60.055 47.826 0.00 0.00 0.00 3.18
2109 6746 2.500098 CGTCAAATTAGAGAGGGGGTGA 59.500 50.000 0.00 0.00 0.00 4.02
2110 6747 2.236395 ACGTCAAATTAGAGAGGGGGTG 59.764 50.000 0.00 0.00 0.00 4.61
2111 6748 2.500504 GACGTCAAATTAGAGAGGGGGT 59.499 50.000 11.55 0.00 0.00 4.95
2112 6749 2.500098 TGACGTCAAATTAGAGAGGGGG 59.500 50.000 17.62 0.00 0.00 5.40
2113 6750 3.887621 TGACGTCAAATTAGAGAGGGG 57.112 47.619 17.62 0.00 0.00 4.79
2114 6751 4.034510 GCATTGACGTCAAATTAGAGAGGG 59.965 45.833 32.69 13.54 39.55 4.30
2115 6752 4.631377 TGCATTGACGTCAAATTAGAGAGG 59.369 41.667 32.69 12.12 39.55 3.69
2116 6753 5.446473 GGTGCATTGACGTCAAATTAGAGAG 60.446 44.000 32.69 16.02 39.55 3.20
2117 6754 4.391830 GGTGCATTGACGTCAAATTAGAGA 59.608 41.667 32.69 9.96 39.55 3.10
2118 6755 4.651994 GGTGCATTGACGTCAAATTAGAG 58.348 43.478 32.69 18.73 39.55 2.43
2119 6756 3.124466 CGGTGCATTGACGTCAAATTAGA 59.876 43.478 32.69 11.54 39.55 2.10
2120 6757 3.120338 ACGGTGCATTGACGTCAAATTAG 60.120 43.478 32.69 22.44 39.55 1.73
2121 6758 2.809119 ACGGTGCATTGACGTCAAATTA 59.191 40.909 32.69 18.95 39.55 1.40
2122 6759 1.606668 ACGGTGCATTGACGTCAAATT 59.393 42.857 32.69 16.45 39.55 1.82
2123 6760 1.234821 ACGGTGCATTGACGTCAAAT 58.765 45.000 32.69 18.82 39.55 2.32
2124 6761 1.867166 TACGGTGCATTGACGTCAAA 58.133 45.000 32.69 15.69 41.53 2.69
2125 6762 2.087501 ATACGGTGCATTGACGTCAA 57.912 45.000 31.41 31.41 41.53 3.18
2126 6763 2.087501 AATACGGTGCATTGACGTCA 57.912 45.000 15.76 15.76 41.53 4.35
2127 6764 3.465122 AAAATACGGTGCATTGACGTC 57.535 42.857 9.11 9.11 41.53 4.34
2128 6765 3.907894 AAAAATACGGTGCATTGACGT 57.092 38.095 12.08 12.08 43.88 4.34
2129 6766 4.142773 ACCTAAAAATACGGTGCATTGACG 60.143 41.667 0.00 0.00 0.00 4.35
2130 6767 5.305139 ACCTAAAAATACGGTGCATTGAC 57.695 39.130 0.00 0.00 0.00 3.18
2131 6768 5.968528 AACCTAAAAATACGGTGCATTGA 57.031 34.783 0.00 0.00 0.00 2.57
2132 6769 5.285134 CGAAACCTAAAAATACGGTGCATTG 59.715 40.000 0.00 0.00 0.00 2.82
2133 6770 5.048573 ACGAAACCTAAAAATACGGTGCATT 60.049 36.000 0.00 0.00 0.00 3.56
2134 6771 4.456566 ACGAAACCTAAAAATACGGTGCAT 59.543 37.500 0.00 0.00 0.00 3.96
2135 6772 3.814283 ACGAAACCTAAAAATACGGTGCA 59.186 39.130 0.00 0.00 0.00 4.57
2136 6773 4.408993 ACGAAACCTAAAAATACGGTGC 57.591 40.909 0.00 0.00 0.00 5.01
2137 6774 8.953507 AATTTACGAAACCTAAAAATACGGTG 57.046 30.769 0.00 0.00 0.00 4.94
2138 6775 9.611284 GAAATTTACGAAACCTAAAAATACGGT 57.389 29.630 0.00 0.00 0.00 4.83
2139 6776 9.609950 TGAAATTTACGAAACCTAAAAATACGG 57.390 29.630 0.00 0.00 0.00 4.02
2149 6786 9.238368 TGAAATAGGATGAAATTTACGAAACCT 57.762 29.630 0.00 0.00 0.00 3.50
2154 6791 9.537192 ACGTATGAAATAGGATGAAATTTACGA 57.463 29.630 7.20 0.00 36.84 3.43
2166 6803 9.079833 CGTTCTCTTTTTACGTATGAAATAGGA 57.920 33.333 0.00 0.00 36.84 2.94
2167 6804 8.866956 ACGTTCTCTTTTTACGTATGAAATAGG 58.133 33.333 0.00 0.00 45.59 2.57
2171 6808 9.462174 TCTTACGTTCTCTTTTTACGTATGAAA 57.538 29.630 15.49 0.38 46.28 2.69
2173 6810 9.462174 TTTCTTACGTTCTCTTTTTACGTATGA 57.538 29.630 14.47 14.47 46.28 2.15
2185 6822 9.609950 GCGAGTATATATTTTCTTACGTTCTCT 57.390 33.333 0.00 0.00 0.00 3.10
2186 6823 8.848528 GGCGAGTATATATTTTCTTACGTTCTC 58.151 37.037 0.00 0.00 0.00 2.87
2187 6824 7.536622 CGGCGAGTATATATTTTCTTACGTTCT 59.463 37.037 0.00 0.00 0.00 3.01
2188 6825 7.324616 ACGGCGAGTATATATTTTCTTACGTTC 59.675 37.037 16.62 0.00 0.00 3.95
2189 6826 7.141363 ACGGCGAGTATATATTTTCTTACGTT 58.859 34.615 16.62 0.00 0.00 3.99
2190 6827 6.672147 ACGGCGAGTATATATTTTCTTACGT 58.328 36.000 16.62 0.00 0.00 3.57
2191 6828 8.659569 TTACGGCGAGTATATATTTTCTTACG 57.340 34.615 16.62 0.00 34.88 3.18
2233 6870 9.842444 GTATGTTTTTACGTTCGTAACTTTACA 57.158 29.630 15.70 15.63 33.28 2.41
2234 6871 9.842444 TGTATGTTTTTACGTTCGTAACTTTAC 57.158 29.630 15.70 13.00 31.32 2.01
2335 6972 9.369904 GTTTGGAATGCAAATAGTAACATTCAT 57.630 29.630 15.64 0.00 46.51 2.57
2336 6973 7.540400 CGTTTGGAATGCAAATAGTAACATTCA 59.460 33.333 15.64 4.44 46.51 2.57
2337 6974 7.540745 ACGTTTGGAATGCAAATAGTAACATTC 59.459 33.333 2.74 8.72 44.85 2.67
2338 6975 7.375053 ACGTTTGGAATGCAAATAGTAACATT 58.625 30.769 2.74 0.00 35.52 2.71
2339 6976 6.919721 ACGTTTGGAATGCAAATAGTAACAT 58.080 32.000 2.74 0.00 0.00 2.71
2340 6977 6.320494 ACGTTTGGAATGCAAATAGTAACA 57.680 33.333 2.74 0.00 0.00 2.41
2341 6978 8.905103 ATTACGTTTGGAATGCAAATAGTAAC 57.095 30.769 22.17 4.68 34.18 2.50
2342 6979 9.915629 AAATTACGTTTGGAATGCAAATAGTAA 57.084 25.926 22.07 22.07 34.93 2.24
2343 6980 9.347934 CAAATTACGTTTGGAATGCAAATAGTA 57.652 29.630 2.74 8.46 42.79 1.82
2344 6981 8.238481 CAAATTACGTTTGGAATGCAAATAGT 57.762 30.769 2.74 9.37 42.79 2.12
2358 6995 7.215568 CGATCGCTTCATAAACAAATTACGTTT 59.784 33.333 0.26 9.95 39.75 3.60
2359 6996 6.681178 CGATCGCTTCATAAACAAATTACGTT 59.319 34.615 0.26 0.00 0.00 3.99
2360 6997 6.182634 CGATCGCTTCATAAACAAATTACGT 58.817 36.000 0.26 0.00 0.00 3.57
2361 6998 6.182634 ACGATCGCTTCATAAACAAATTACG 58.817 36.000 16.60 0.00 0.00 3.18
2362 6999 9.144085 CTTACGATCGCTTCATAAACAAATTAC 57.856 33.333 16.60 0.00 0.00 1.89
2363 7000 9.089601 TCTTACGATCGCTTCATAAACAAATTA 57.910 29.630 16.60 0.00 0.00 1.40
2364 7001 7.970384 TCTTACGATCGCTTCATAAACAAATT 58.030 30.769 16.60 0.00 0.00 1.82
2365 7002 7.534085 TCTTACGATCGCTTCATAAACAAAT 57.466 32.000 16.60 0.00 0.00 2.32
2366 7003 6.954616 TCTTACGATCGCTTCATAAACAAA 57.045 33.333 16.60 0.00 0.00 2.83
2367 7004 7.534085 AATCTTACGATCGCTTCATAAACAA 57.466 32.000 16.60 0.00 0.00 2.83
2368 7005 7.168637 GGTAATCTTACGATCGCTTCATAAACA 59.831 37.037 16.60 0.00 34.50 2.83
2369 7006 7.381678 AGGTAATCTTACGATCGCTTCATAAAC 59.618 37.037 16.60 5.11 34.50 2.01
2370 7007 7.431249 AGGTAATCTTACGATCGCTTCATAAA 58.569 34.615 16.60 0.00 34.50 1.40
2371 7008 6.978338 AGGTAATCTTACGATCGCTTCATAA 58.022 36.000 16.60 4.99 34.50 1.90
2372 7009 6.570672 AGGTAATCTTACGATCGCTTCATA 57.429 37.500 16.60 0.00 34.50 2.15
2373 7010 5.455056 AGGTAATCTTACGATCGCTTCAT 57.545 39.130 16.60 0.00 34.50 2.57
2374 7011 4.554134 CGAGGTAATCTTACGATCGCTTCA 60.554 45.833 16.60 0.00 37.02 3.02
2375 7012 3.907194 CGAGGTAATCTTACGATCGCTTC 59.093 47.826 16.60 1.12 37.02 3.86
2376 7013 3.304525 CCGAGGTAATCTTACGATCGCTT 60.305 47.826 16.60 0.00 39.81 4.68
2377 7014 2.225963 CCGAGGTAATCTTACGATCGCT 59.774 50.000 16.60 5.20 39.81 4.93
2378 7015 2.582687 CCGAGGTAATCTTACGATCGC 58.417 52.381 16.60 0.00 39.81 4.58
2379 7016 2.551459 ACCCGAGGTAATCTTACGATCG 59.449 50.000 14.88 14.88 40.33 3.69
2380 7017 3.567164 TCACCCGAGGTAATCTTACGATC 59.433 47.826 0.00 0.00 32.11 3.69
2381 7018 3.559069 TCACCCGAGGTAATCTTACGAT 58.441 45.455 0.00 0.00 32.11 3.73
2382 7019 3.003394 TCACCCGAGGTAATCTTACGA 57.997 47.619 0.00 0.00 32.11 3.43
2383 7020 4.317671 AATCACCCGAGGTAATCTTACG 57.682 45.455 0.00 0.00 32.11 3.18
2384 7021 7.599245 CAGAATAATCACCCGAGGTAATCTTAC 59.401 40.741 0.00 0.00 32.11 2.34
2385 7022 7.667557 CAGAATAATCACCCGAGGTAATCTTA 58.332 38.462 0.00 0.00 32.11 2.10
2386 7023 6.525629 CAGAATAATCACCCGAGGTAATCTT 58.474 40.000 0.00 0.00 32.11 2.40
2387 7024 5.511545 GCAGAATAATCACCCGAGGTAATCT 60.512 44.000 0.00 0.00 32.11 2.40
2388 7025 4.691216 GCAGAATAATCACCCGAGGTAATC 59.309 45.833 0.00 0.00 32.11 1.75
2389 7026 4.102524 TGCAGAATAATCACCCGAGGTAAT 59.897 41.667 0.00 0.00 32.11 1.89
2390 7027 3.452990 TGCAGAATAATCACCCGAGGTAA 59.547 43.478 0.00 0.00 32.11 2.85
2391 7028 3.035363 TGCAGAATAATCACCCGAGGTA 58.965 45.455 0.00 0.00 32.11 3.08
2392 7029 1.837439 TGCAGAATAATCACCCGAGGT 59.163 47.619 0.00 0.00 35.62 3.85
2393 7030 2.213499 GTGCAGAATAATCACCCGAGG 58.787 52.381 0.00 0.00 0.00 4.63
2394 7031 2.213499 GGTGCAGAATAATCACCCGAG 58.787 52.381 0.00 0.00 43.27 4.63
2395 7032 2.325583 GGTGCAGAATAATCACCCGA 57.674 50.000 0.00 0.00 43.27 5.14
2399 7036 2.684881 CACCAGGGTGCAGAATAATCAC 59.315 50.000 5.38 0.00 39.39 3.06
2400 7037 2.357050 CCACCAGGGTGCAGAATAATCA 60.357 50.000 13.03 0.00 44.16 2.57
2401 7038 2.301346 CCACCAGGGTGCAGAATAATC 58.699 52.381 13.03 0.00 44.16 1.75
2402 7039 1.686115 GCCACCAGGGTGCAGAATAAT 60.686 52.381 13.03 0.00 44.16 1.28
2403 7040 0.323360 GCCACCAGGGTGCAGAATAA 60.323 55.000 13.03 0.00 44.16 1.40
2404 7041 1.302949 GCCACCAGGGTGCAGAATA 59.697 57.895 13.03 0.00 44.16 1.75
2405 7042 2.036256 GCCACCAGGGTGCAGAAT 59.964 61.111 13.03 0.00 44.16 2.40
2406 7043 2.981914 CTTGCCACCAGGGTGCAGAA 62.982 60.000 13.03 4.30 44.16 3.02
2407 7044 3.496309 CTTGCCACCAGGGTGCAGA 62.496 63.158 13.03 0.03 44.16 4.26
2408 7045 2.987547 CTTGCCACCAGGGTGCAG 60.988 66.667 13.03 4.79 44.16 4.41
2411 7048 1.880819 GATTGCTTGCCACCAGGGTG 61.881 60.000 11.55 11.55 45.02 4.61
2412 7049 1.607467 GATTGCTTGCCACCAGGGT 60.607 57.895 0.00 0.00 39.65 4.34
2413 7050 2.353610 GGATTGCTTGCCACCAGGG 61.354 63.158 0.00 0.00 40.85 4.45
2414 7051 0.034186 TAGGATTGCTTGCCACCAGG 60.034 55.000 0.00 0.00 38.23 4.45
2415 7052 1.838112 TTAGGATTGCTTGCCACCAG 58.162 50.000 0.00 0.00 0.00 4.00
2503 7142 3.485216 CGGCGATGAAGGTTTACATTGTC 60.485 47.826 0.00 0.00 32.37 3.18



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

AutoCloner maintained by Alex Coulton.