Multiple sequence alignment - TraesCS3B01G519300

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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 TraesCS3B01G519300 chr3B 100.000 2375 0 0 1 2375 762517831 762515457 0.000000e+00 4386.0
1 TraesCS3B01G519300 chr3B 91.667 48 3 1 2231 2277 196650244 196650291 5.480000e-07 65.8
2 TraesCS3B01G519300 chr3B 91.667 48 3 1 2231 2277 197106410 197106457 5.480000e-07 65.8
3 TraesCS3B01G519300 chr5B 93.197 2249 119 8 1 2245 345115936 345118154 0.000000e+00 3275.0
4 TraesCS3B01G519300 chr5B 92.578 2250 124 17 1 2245 291681300 291679089 0.000000e+00 3190.0
5 TraesCS3B01G519300 chr6B 92.661 2262 125 19 1 2245 159276830 159274593 0.000000e+00 3219.0
6 TraesCS3B01G519300 chr6B 92.635 2254 138 15 1 2245 70651234 70653468 0.000000e+00 3217.0
7 TraesCS3B01G519300 chr6B 92.081 745 51 7 1507 2245 152341745 152342487 0.000000e+00 1042.0
8 TraesCS3B01G519300 chr7B 91.847 2269 141 16 1 2245 669515786 669518034 0.000000e+00 3125.0
9 TraesCS3B01G519300 chr7B 89.410 1728 138 28 1 1715 731577170 731575475 0.000000e+00 2135.0
10 TraesCS3B01G519300 chr7B 85.415 1241 136 30 1035 2256 3664988 3666202 0.000000e+00 1247.0
11 TraesCS3B01G519300 chr7B 93.182 44 3 0 2234 2277 693465415 693465372 5.480000e-07 65.8
12 TraesCS3B01G519300 chr2B 91.456 2259 138 28 1 2245 32828797 32831014 0.000000e+00 3051.0
13 TraesCS3B01G519300 chr2B 94.000 50 2 1 2231 2279 295699672 295699721 9.100000e-10 75.0
14 TraesCS3B01G519300 chr4B 90.382 2277 143 30 1 2243 343834221 343836455 0.000000e+00 2922.0
15 TraesCS3B01G519300 chr4B 88.413 2287 167 40 1 2245 288454855 288452625 0.000000e+00 2665.0
16 TraesCS3B01G519300 chr4B 92.979 1410 84 6 1 1399 200942536 200943941 0.000000e+00 2041.0
17 TraesCS3B01G519300 chr4B 94.700 868 33 6 561 1423 505003032 505002173 0.000000e+00 1336.0
18 TraesCS3B01G519300 chr4B 87.086 906 73 22 1369 2245 368730352 368731242 0.000000e+00 985.0
19 TraesCS3B01G519300 chr4B 88.682 804 56 13 1447 2245 15054778 15054005 0.000000e+00 948.0
20 TraesCS3B01G519300 chr2A 90.451 1686 107 25 572 2245 605786894 605788537 0.000000e+00 2172.0
21 TraesCS3B01G519300 chr2A 88.421 1710 112 39 572 2245 655901693 655900034 0.000000e+00 1982.0
22 TraesCS3B01G519300 chr2A 91.667 48 2 1 2234 2281 689213635 689213590 5.480000e-07 65.8
23 TraesCS3B01G519300 chr3A 90.283 1698 98 26 572 2245 733879240 733877586 0.000000e+00 2159.0
24 TraesCS3B01G519300 chr4A 90.124 1448 101 25 809 2245 29673360 29671944 0.000000e+00 1844.0
25 TraesCS3B01G519300 chr4A 92.339 744 52 4 1506 2245 549635619 549636361 0.000000e+00 1053.0
26 TraesCS3B01G519300 chr4A 97.561 41 1 0 2231 2271 660551618 660551658 1.180000e-08 71.3
27 TraesCS3B01G519300 chr6A 89.675 1046 77 18 1210 2245 136675188 136676212 0.000000e+00 1304.0
28 TraesCS3B01G519300 chr5D 92.899 845 49 3 1 842 16459549 16458713 0.000000e+00 1218.0
29 TraesCS3B01G519300 chr4D 92.162 842 54 6 4 842 222623667 222622835 0.000000e+00 1179.0
30 TraesCS3B01G519300 chr1B 95.349 43 2 0 2231 2273 105096586 105096628 4.240000e-08 69.4
31 TraesCS3B01G519300 chr5A 91.667 48 2 1 2231 2278 681610144 681610189 5.480000e-07 65.8
32 TraesCS3B01G519300 chr1A 93.182 44 3 0 2234 2277 181968026 181967983 5.480000e-07 65.8


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 TraesCS3B01G519300 chr3B 762515457 762517831 2374 True 4386 4386 100.000 1 2375 1 chr3B.!!$R1 2374
1 TraesCS3B01G519300 chr5B 345115936 345118154 2218 False 3275 3275 93.197 1 2245 1 chr5B.!!$F1 2244
2 TraesCS3B01G519300 chr5B 291679089 291681300 2211 True 3190 3190 92.578 1 2245 1 chr5B.!!$R1 2244
3 TraesCS3B01G519300 chr6B 159274593 159276830 2237 True 3219 3219 92.661 1 2245 1 chr6B.!!$R1 2244
4 TraesCS3B01G519300 chr6B 70651234 70653468 2234 False 3217 3217 92.635 1 2245 1 chr6B.!!$F1 2244
5 TraesCS3B01G519300 chr6B 152341745 152342487 742 False 1042 1042 92.081 1507 2245 1 chr6B.!!$F2 738
6 TraesCS3B01G519300 chr7B 669515786 669518034 2248 False 3125 3125 91.847 1 2245 1 chr7B.!!$F2 2244
7 TraesCS3B01G519300 chr7B 731575475 731577170 1695 True 2135 2135 89.410 1 1715 1 chr7B.!!$R2 1714
8 TraesCS3B01G519300 chr7B 3664988 3666202 1214 False 1247 1247 85.415 1035 2256 1 chr7B.!!$F1 1221
9 TraesCS3B01G519300 chr2B 32828797 32831014 2217 False 3051 3051 91.456 1 2245 1 chr2B.!!$F1 2244
10 TraesCS3B01G519300 chr4B 343834221 343836455 2234 False 2922 2922 90.382 1 2243 1 chr4B.!!$F2 2242
11 TraesCS3B01G519300 chr4B 288452625 288454855 2230 True 2665 2665 88.413 1 2245 1 chr4B.!!$R2 2244
12 TraesCS3B01G519300 chr4B 200942536 200943941 1405 False 2041 2041 92.979 1 1399 1 chr4B.!!$F1 1398
13 TraesCS3B01G519300 chr4B 505002173 505003032 859 True 1336 1336 94.700 561 1423 1 chr4B.!!$R3 862
14 TraesCS3B01G519300 chr4B 368730352 368731242 890 False 985 985 87.086 1369 2245 1 chr4B.!!$F3 876
15 TraesCS3B01G519300 chr4B 15054005 15054778 773 True 948 948 88.682 1447 2245 1 chr4B.!!$R1 798
16 TraesCS3B01G519300 chr2A 605786894 605788537 1643 False 2172 2172 90.451 572 2245 1 chr2A.!!$F1 1673
17 TraesCS3B01G519300 chr2A 655900034 655901693 1659 True 1982 1982 88.421 572 2245 1 chr2A.!!$R1 1673
18 TraesCS3B01G519300 chr3A 733877586 733879240 1654 True 2159 2159 90.283 572 2245 1 chr3A.!!$R1 1673
19 TraesCS3B01G519300 chr4A 29671944 29673360 1416 True 1844 1844 90.124 809 2245 1 chr4A.!!$R1 1436
20 TraesCS3B01G519300 chr4A 549635619 549636361 742 False 1053 1053 92.339 1506 2245 1 chr4A.!!$F1 739
21 TraesCS3B01G519300 chr6A 136675188 136676212 1024 False 1304 1304 89.675 1210 2245 1 chr6A.!!$F1 1035
22 TraesCS3B01G519300 chr5D 16458713 16459549 836 True 1218 1218 92.899 1 842 1 chr5D.!!$R1 841
23 TraesCS3B01G519300 chr4D 222622835 222623667 832 True 1179 1179 92.162 4 842 1 chr4D.!!$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
80 81 0.392193 GCTCTGGTGGAGATGTGGTG 60.392 60.0 0.0 0.0 44.45 4.17 F
1157 1265 0.465460 AACTCCGGCAAAGCAACTGA 60.465 50.0 0.0 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1301 1411 0.712775 CTCTTGAGACTTCTTGCGCG 59.287 55.0 0.0 0.0 0.00 6.86 R
2312 2690 0.035915 GCAGGAAGGACCCAGTTCTC 60.036 60.0 0.0 0.0 40.05 2.87 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
55 56 1.254026 AGATCTGACGGACGGTGAAA 58.746 50.000 0.00 0.00 0.00 2.69
80 81 0.392193 GCTCTGGTGGAGATGTGGTG 60.392 60.000 0.00 0.00 44.45 4.17
148 149 6.160576 TGTTCTGCACATGATATGCTAGTA 57.839 37.500 0.00 0.00 43.77 1.82
149 150 6.218746 TGTTCTGCACATGATATGCTAGTAG 58.781 40.000 0.00 0.00 43.77 2.57
229 233 7.722795 TCGAGAAAAAGTCATGTACAATCAA 57.277 32.000 0.00 0.00 0.00 2.57
243 247 5.888724 TGTACAATCAAAGAACTGGTTCCAA 59.111 36.000 9.51 0.00 40.33 3.53
396 400 1.757699 GAAGAGCGTAAGGGTGAGGAT 59.242 52.381 0.00 0.00 38.28 3.24
521 526 4.036852 AGCCAGTTCAAACTTTTGTCTAGC 59.963 41.667 1.75 6.74 37.08 3.42
642 666 3.373748 CACACGCTATGTTCCATGCTTTA 59.626 43.478 0.00 0.00 40.64 1.85
778 828 3.964688 TCACTCGGGAAGCCATCTTATAA 59.035 43.478 0.00 0.00 31.48 0.98
853 903 5.472137 GTCTCTAGGTCACTAGTCATCATCC 59.528 48.000 0.00 0.00 45.60 3.51
915 965 4.420522 AATCCATTTGTGTGCTGGTTTT 57.579 36.364 0.00 0.00 0.00 2.43
916 966 3.176552 TCCATTTGTGTGCTGGTTTTG 57.823 42.857 0.00 0.00 0.00 2.44
917 967 2.499289 TCCATTTGTGTGCTGGTTTTGT 59.501 40.909 0.00 0.00 0.00 2.83
918 968 3.055530 TCCATTTGTGTGCTGGTTTTGTT 60.056 39.130 0.00 0.00 0.00 2.83
919 969 3.688673 CCATTTGTGTGCTGGTTTTGTTT 59.311 39.130 0.00 0.00 0.00 2.83
920 970 4.201802 CCATTTGTGTGCTGGTTTTGTTTC 60.202 41.667 0.00 0.00 0.00 2.78
921 971 3.951775 TTGTGTGCTGGTTTTGTTTCT 57.048 38.095 0.00 0.00 0.00 2.52
922 972 3.502191 TGTGTGCTGGTTTTGTTTCTC 57.498 42.857 0.00 0.00 0.00 2.87
923 973 3.088532 TGTGTGCTGGTTTTGTTTCTCT 58.911 40.909 0.00 0.00 0.00 3.10
924 974 3.509575 TGTGTGCTGGTTTTGTTTCTCTT 59.490 39.130 0.00 0.00 0.00 2.85
925 975 3.859386 GTGTGCTGGTTTTGTTTCTCTTG 59.141 43.478 0.00 0.00 0.00 3.02
926 976 2.860136 GTGCTGGTTTTGTTTCTCTTGC 59.140 45.455 0.00 0.00 0.00 4.01
927 977 2.760092 TGCTGGTTTTGTTTCTCTTGCT 59.240 40.909 0.00 0.00 0.00 3.91
928 978 3.195396 TGCTGGTTTTGTTTCTCTTGCTT 59.805 39.130 0.00 0.00 0.00 3.91
929 979 3.553105 GCTGGTTTTGTTTCTCTTGCTTG 59.447 43.478 0.00 0.00 0.00 4.01
930 980 4.114794 CTGGTTTTGTTTCTCTTGCTTGG 58.885 43.478 0.00 0.00 0.00 3.61
931 981 3.513515 TGGTTTTGTTTCTCTTGCTTGGT 59.486 39.130 0.00 0.00 0.00 3.67
932 982 4.020662 TGGTTTTGTTTCTCTTGCTTGGTT 60.021 37.500 0.00 0.00 0.00 3.67
933 983 4.935205 GGTTTTGTTTCTCTTGCTTGGTTT 59.065 37.500 0.00 0.00 0.00 3.27
1087 1156 2.286365 AGAAATGCCCAAGACCGAAA 57.714 45.000 0.00 0.00 0.00 3.46
1157 1265 0.465460 AACTCCGGCAAAGCAACTGA 60.465 50.000 0.00 0.00 0.00 3.41
1380 1527 4.123506 GAGCTAAGGTAGTTTGATGGCTC 58.876 47.826 0.00 0.00 37.19 4.70
1558 1869 6.260050 TGAAGTTATGTGAACCTGTGAAGTTC 59.740 38.462 0.00 0.00 43.20 3.01
1568 1882 5.808366 ACCTGTGAAGTTCTGTGATCTTA 57.192 39.130 4.17 0.00 0.00 2.10
1616 1950 3.796764 TGTGGATCACTTGTGCACA 57.203 47.368 17.42 17.42 44.08 4.57
1669 2014 2.674380 CTTGTGCACCTGGGCCTC 60.674 66.667 15.69 0.00 0.00 4.70
1684 2029 3.129109 GGGCCTCGCTGTTTATAGTTAC 58.871 50.000 0.84 0.00 0.00 2.50
1914 2282 4.176120 AGGCTCCATTCCCAGAAAATAG 57.824 45.455 0.00 0.00 0.00 1.73
2041 2413 4.383335 GGACCGGGTTGATTCTATGTTACA 60.383 45.833 6.32 0.00 0.00 2.41
2067 2439 6.264518 ACCTTTTCATTTGGTCGTAATTCTGT 59.735 34.615 0.00 0.00 0.00 3.41
2075 2447 3.243468 TGGTCGTAATTCTGTCACGTCAA 60.243 43.478 0.00 0.00 37.02 3.18
2234 2612 3.119352 GGCCAGCTTTTGACCTTCTATTG 60.119 47.826 0.00 0.00 0.00 1.90
2235 2613 3.119352 GCCAGCTTTTGACCTTCTATTGG 60.119 47.826 0.00 0.00 0.00 3.16
2246 2624 3.394606 ACCTTCTATTGGTGGTCACAAGT 59.605 43.478 3.40 0.00 36.30 3.16
2248 2626 4.216257 CCTTCTATTGGTGGTCACAAGTTG 59.784 45.833 0.00 0.00 0.00 3.16
2264 2642 8.902540 TCACAAGTTGACATATTTCTTGTAGT 57.097 30.769 10.54 0.00 44.11 2.73
2265 2643 8.773645 TCACAAGTTGACATATTTCTTGTAGTG 58.226 33.333 10.54 0.00 44.11 2.74
2266 2644 8.773645 CACAAGTTGACATATTTCTTGTAGTGA 58.226 33.333 10.54 0.00 44.11 3.41
2267 2645 9.337396 ACAAGTTGACATATTTCTTGTAGTGAA 57.663 29.630 10.54 0.00 44.11 3.18
2270 2648 8.507249 AGTTGACATATTTCTTGTAGTGAAAGC 58.493 33.333 0.00 0.00 36.94 3.51
2271 2649 7.377766 TGACATATTTCTTGTAGTGAAAGCC 57.622 36.000 0.00 0.00 36.94 4.35
2272 2650 6.092122 TGACATATTTCTTGTAGTGAAAGCCG 59.908 38.462 0.00 0.00 36.94 5.52
2273 2651 3.831715 ATTTCTTGTAGTGAAAGCCGC 57.168 42.857 0.00 0.00 36.94 6.53
2274 2652 1.519408 TTCTTGTAGTGAAAGCCGCC 58.481 50.000 0.00 0.00 0.00 6.13
2275 2653 0.321298 TCTTGTAGTGAAAGCCGCCC 60.321 55.000 0.00 0.00 0.00 6.13
2276 2654 1.302993 TTGTAGTGAAAGCCGCCCC 60.303 57.895 0.00 0.00 0.00 5.80
2277 2655 2.058125 TTGTAGTGAAAGCCGCCCCA 62.058 55.000 0.00 0.00 0.00 4.96
2278 2656 1.302993 GTAGTGAAAGCCGCCCCAA 60.303 57.895 0.00 0.00 0.00 4.12
2279 2657 1.302993 TAGTGAAAGCCGCCCCAAC 60.303 57.895 0.00 0.00 0.00 3.77
2280 2658 2.757980 TAGTGAAAGCCGCCCCAACC 62.758 60.000 0.00 0.00 0.00 3.77
2281 2659 4.211330 TGAAAGCCGCCCCAACCA 62.211 61.111 0.00 0.00 0.00 3.67
2282 2660 2.679996 GAAAGCCGCCCCAACCAT 60.680 61.111 0.00 0.00 0.00 3.55
2283 2661 2.996734 AAAGCCGCCCCAACCATG 60.997 61.111 0.00 0.00 0.00 3.66
2287 2665 4.067913 CCGCCCCAACCATGCAAC 62.068 66.667 0.00 0.00 0.00 4.17
2288 2666 3.301554 CGCCCCAACCATGCAACA 61.302 61.111 0.00 0.00 0.00 3.33
2289 2667 2.343387 GCCCCAACCATGCAACAC 59.657 61.111 0.00 0.00 0.00 3.32
2290 2668 2.650196 CCCCAACCATGCAACACG 59.350 61.111 0.00 0.00 0.00 4.49
2291 2669 2.199652 CCCCAACCATGCAACACGT 61.200 57.895 0.00 0.00 0.00 4.49
2292 2670 1.739049 CCCAACCATGCAACACGTT 59.261 52.632 0.00 0.00 0.00 3.99
2293 2671 0.597118 CCCAACCATGCAACACGTTG 60.597 55.000 5.53 5.53 43.14 4.10
2294 2672 0.383590 CCAACCATGCAACACGTTGA 59.616 50.000 13.97 0.00 42.93 3.18
2295 2673 1.202348 CCAACCATGCAACACGTTGAA 60.202 47.619 13.97 3.31 42.93 2.69
2296 2674 1.851666 CAACCATGCAACACGTTGAAC 59.148 47.619 13.97 0.00 42.93 3.18
2297 2675 0.383949 ACCATGCAACACGTTGAACC 59.616 50.000 13.97 0.00 42.93 3.62
2298 2676 0.667993 CCATGCAACACGTTGAACCT 59.332 50.000 13.97 0.00 42.93 3.50
2299 2677 1.876799 CCATGCAACACGTTGAACCTA 59.123 47.619 13.97 0.00 42.93 3.08
2300 2678 2.292016 CCATGCAACACGTTGAACCTAA 59.708 45.455 13.97 0.00 42.93 2.69
2301 2679 3.057596 CCATGCAACACGTTGAACCTAAT 60.058 43.478 13.97 0.00 42.93 1.73
2302 2680 4.545610 CATGCAACACGTTGAACCTAATT 58.454 39.130 13.97 0.00 42.93 1.40
2303 2681 5.335269 CCATGCAACACGTTGAACCTAATTA 60.335 40.000 13.97 0.00 42.93 1.40
2304 2682 5.752892 TGCAACACGTTGAACCTAATTAA 57.247 34.783 13.97 0.00 42.93 1.40
2305 2683 5.512473 TGCAACACGTTGAACCTAATTAAC 58.488 37.500 13.97 0.00 42.93 2.01
2306 2684 5.066117 TGCAACACGTTGAACCTAATTAACA 59.934 36.000 13.97 0.00 42.93 2.41
2307 2685 5.972382 GCAACACGTTGAACCTAATTAACAA 59.028 36.000 13.97 0.00 42.93 2.83
2308 2686 6.141685 GCAACACGTTGAACCTAATTAACAAG 59.858 38.462 13.97 0.00 42.93 3.16
2309 2687 7.411274 CAACACGTTGAACCTAATTAACAAGA 58.589 34.615 3.79 0.00 42.93 3.02
2310 2688 7.556733 ACACGTTGAACCTAATTAACAAGAA 57.443 32.000 0.00 0.00 0.00 2.52
2311 2689 7.987649 ACACGTTGAACCTAATTAACAAGAAA 58.012 30.769 0.00 0.00 0.00 2.52
2312 2690 8.126700 ACACGTTGAACCTAATTAACAAGAAAG 58.873 33.333 0.00 0.00 0.00 2.62
2313 2691 8.339714 CACGTTGAACCTAATTAACAAGAAAGA 58.660 33.333 0.00 0.00 0.00 2.52
2314 2692 8.557029 ACGTTGAACCTAATTAACAAGAAAGAG 58.443 33.333 0.00 0.00 0.00 2.85
2315 2693 8.770828 CGTTGAACCTAATTAACAAGAAAGAGA 58.229 33.333 0.00 0.00 0.00 3.10
2318 2696 9.847224 TGAACCTAATTAACAAGAAAGAGAACT 57.153 29.630 0.00 0.00 0.00 3.01
2320 2698 8.622948 ACCTAATTAACAAGAAAGAGAACTGG 57.377 34.615 0.00 0.00 0.00 4.00
2321 2699 7.665974 ACCTAATTAACAAGAAAGAGAACTGGG 59.334 37.037 0.00 0.00 0.00 4.45
2322 2700 7.665974 CCTAATTAACAAGAAAGAGAACTGGGT 59.334 37.037 0.00 0.00 0.00 4.51
2323 2701 7.511959 AATTAACAAGAAAGAGAACTGGGTC 57.488 36.000 0.00 0.00 0.00 4.46
2324 2702 3.493767 ACAAGAAAGAGAACTGGGTCC 57.506 47.619 0.00 0.00 0.00 4.46
2325 2703 3.049344 ACAAGAAAGAGAACTGGGTCCT 58.951 45.455 0.00 0.00 0.00 3.85
2326 2704 3.459969 ACAAGAAAGAGAACTGGGTCCTT 59.540 43.478 0.00 0.00 0.00 3.36
2327 2705 4.068599 CAAGAAAGAGAACTGGGTCCTTC 58.931 47.826 0.00 0.00 0.00 3.46
2328 2706 2.640332 AGAAAGAGAACTGGGTCCTTCC 59.360 50.000 0.00 0.00 0.00 3.46
2329 2707 2.424684 AAGAGAACTGGGTCCTTCCT 57.575 50.000 0.00 0.00 36.25 3.36
2330 2708 1.650528 AGAGAACTGGGTCCTTCCTG 58.349 55.000 0.00 0.00 36.25 3.86
2331 2709 0.035915 GAGAACTGGGTCCTTCCTGC 60.036 60.000 0.00 0.00 36.25 4.85
2332 2710 1.002011 GAACTGGGTCCTTCCTGCC 60.002 63.158 0.00 0.00 36.25 4.85
2333 2711 1.774217 AACTGGGTCCTTCCTGCCA 60.774 57.895 0.00 0.00 36.25 4.92
2334 2712 1.783250 AACTGGGTCCTTCCTGCCAG 61.783 60.000 0.00 0.00 36.25 4.85
2335 2713 2.121963 TGGGTCCTTCCTGCCAGT 60.122 61.111 0.00 0.00 36.25 4.00
2336 2714 2.352805 GGGTCCTTCCTGCCAGTG 59.647 66.667 0.00 0.00 36.25 3.66
2337 2715 2.352805 GGTCCTTCCTGCCAGTGG 59.647 66.667 4.20 4.20 0.00 4.00
2338 2716 2.352805 GTCCTTCCTGCCAGTGGG 59.647 66.667 12.15 0.00 37.18 4.61
2339 2717 2.935481 TCCTTCCTGCCAGTGGGG 60.935 66.667 12.15 4.54 40.85 4.96
2340 2718 4.052518 CCTTCCTGCCAGTGGGGG 62.053 72.222 12.15 0.00 37.04 5.40
2355 2733 3.412408 GGGCCCAAGGTCCTCCTC 61.412 72.222 19.95 0.00 45.53 3.71
2356 2734 3.787001 GGCCCAAGGTCCTCCTCG 61.787 72.222 0.00 0.00 44.35 4.63
2357 2735 4.475135 GCCCAAGGTCCTCCTCGC 62.475 72.222 0.00 0.00 44.35 5.03
2358 2736 3.787001 CCCAAGGTCCTCCTCGCC 61.787 72.222 0.00 0.00 44.35 5.54
2359 2737 2.685380 CCAAGGTCCTCCTCGCCT 60.685 66.667 0.00 0.00 44.35 5.52
2360 2738 2.726351 CCAAGGTCCTCCTCGCCTC 61.726 68.421 0.00 0.00 44.35 4.70
2361 2739 2.364448 AAGGTCCTCCTCGCCTCC 60.364 66.667 0.00 0.00 44.35 4.30
2362 2740 3.239627 AAGGTCCTCCTCGCCTCCA 62.240 63.158 0.00 0.00 44.35 3.86
2363 2741 2.444895 GGTCCTCCTCGCCTCCAT 60.445 66.667 0.00 0.00 0.00 3.41
2364 2742 2.801631 GGTCCTCCTCGCCTCCATG 61.802 68.421 0.00 0.00 0.00 3.66
2365 2743 2.444706 TCCTCCTCGCCTCCATGG 60.445 66.667 4.97 4.97 39.35 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 0.913451 ATCTCCACCAGAGCTTGCCT 60.913 55.000 0.00 0.00 42.90 4.75
80 81 2.651382 AACCTTGTGTCTTGGGGTAC 57.349 50.000 0.00 0.00 0.00 3.34
229 233 2.736670 AGTGCTTGGAACCAGTTCTT 57.263 45.000 10.19 0.00 39.45 2.52
243 247 5.522456 CAAAAATGTGTGATGTGTAGTGCT 58.478 37.500 0.00 0.00 0.00 4.40
321 325 8.452989 AATGTTATTCAGCGAAAATCAGAAAC 57.547 30.769 0.00 0.00 0.00 2.78
331 335 9.039870 ACAAAAATCAAAATGTTATTCAGCGAA 57.960 25.926 0.00 0.00 0.00 4.70
333 337 9.094459 CAACAAAAATCAAAATGTTATTCAGCG 57.906 29.630 0.00 0.00 34.45 5.18
396 400 2.820059 ACAAGTCAATCGCAGACAGA 57.180 45.000 0.00 0.00 42.51 3.41
521 526 1.915141 ATCAAACAGGGCTGAGGTTG 58.085 50.000 0.00 0.00 0.00 3.77
778 828 5.514500 TTAAGCCTAGAATGGTGGTTCTT 57.486 39.130 0.00 0.00 39.15 2.52
853 903 6.372659 ACCAGCACACAAAATCTATACAAGAG 59.627 38.462 0.00 0.00 37.74 2.85
915 965 3.096092 ACCAAACCAAGCAAGAGAAACA 58.904 40.909 0.00 0.00 0.00 2.83
916 966 3.801114 ACCAAACCAAGCAAGAGAAAC 57.199 42.857 0.00 0.00 0.00 2.78
917 967 4.502962 CAAACCAAACCAAGCAAGAGAAA 58.497 39.130 0.00 0.00 0.00 2.52
918 968 3.678529 GCAAACCAAACCAAGCAAGAGAA 60.679 43.478 0.00 0.00 0.00 2.87
919 969 2.159114 GCAAACCAAACCAAGCAAGAGA 60.159 45.455 0.00 0.00 0.00 3.10
920 970 2.204237 GCAAACCAAACCAAGCAAGAG 58.796 47.619 0.00 0.00 0.00 2.85
921 971 1.552337 TGCAAACCAAACCAAGCAAGA 59.448 42.857 0.00 0.00 0.00 3.02
922 972 2.021355 TGCAAACCAAACCAAGCAAG 57.979 45.000 0.00 0.00 0.00 4.01
923 973 2.479566 TTGCAAACCAAACCAAGCAA 57.520 40.000 0.00 0.00 39.38 3.91
924 974 2.479566 TTTGCAAACCAAACCAAGCA 57.520 40.000 8.05 0.00 38.46 3.91
925 975 3.128415 ACATTTTGCAAACCAAACCAAGC 59.872 39.130 12.39 0.00 42.81 4.01
926 976 4.394300 TCACATTTTGCAAACCAAACCAAG 59.606 37.500 12.39 0.00 42.81 3.61
927 977 4.326826 TCACATTTTGCAAACCAAACCAA 58.673 34.783 12.39 0.00 42.81 3.67
928 978 3.942829 TCACATTTTGCAAACCAAACCA 58.057 36.364 12.39 0.00 42.81 3.67
929 979 4.954092 TTCACATTTTGCAAACCAAACC 57.046 36.364 12.39 0.00 42.81 3.27
930 980 7.914465 TCTATTTCACATTTTGCAAACCAAAC 58.086 30.769 12.39 0.00 42.81 2.93
931 981 8.674263 ATCTATTTCACATTTTGCAAACCAAA 57.326 26.923 12.39 6.96 41.48 3.28
932 982 8.149647 AGATCTATTTCACATTTTGCAAACCAA 58.850 29.630 12.39 0.00 0.00 3.67
933 983 7.669427 AGATCTATTTCACATTTTGCAAACCA 58.331 30.769 12.39 0.00 0.00 3.67
1021 1090 1.893801 CTCTTCACCTTCTGGTACCGT 59.106 52.381 7.57 0.00 46.60 4.83
1042 1111 7.374272 TCAACAATTTGAACAACAGACTTTGA 58.626 30.769 2.79 0.00 38.87 2.69
1072 1141 2.094675 CTTGATTTCGGTCTTGGGCAT 58.905 47.619 0.00 0.00 0.00 4.40
1076 1145 3.568538 CTTTGCTTGATTTCGGTCTTGG 58.431 45.455 0.00 0.00 0.00 3.61
1087 1156 3.159472 TGAGGAATGTGCTTTGCTTGAT 58.841 40.909 0.00 0.00 0.00 2.57
1157 1265 2.089980 GAACATGAGCAGCCACTTCAT 58.910 47.619 0.00 0.00 0.00 2.57
1301 1411 0.712775 CTCTTGAGACTTCTTGCGCG 59.287 55.000 0.00 0.00 0.00 6.86
1380 1527 3.629398 AGAGGTTCAAAGACAAACTGCAG 59.371 43.478 13.48 13.48 0.00 4.41
1453 1672 1.412079 TGCAACAAAATGCTCCCAGT 58.588 45.000 0.67 0.00 46.54 4.00
1558 1869 6.808008 AAACACAGGTTCATAAGATCACAG 57.192 37.500 0.00 0.00 35.82 3.66
1568 1882 7.581213 TCACAGAAAATAAACACAGGTTCAT 57.419 32.000 0.00 0.00 35.82 2.57
1616 1950 1.070601 GGTTCAAACAGCAAAGCCCAT 59.929 47.619 0.00 0.00 0.00 4.00
1669 2014 8.111836 TCTTATTTTGCGTAACTATAAACAGCG 58.888 33.333 0.00 0.00 0.00 5.18
1684 2029 1.818674 AGCCCAGGTTCTTATTTTGCG 59.181 47.619 0.00 0.00 0.00 4.85
1727 2087 6.602009 GCCCAAGCCTTTTTAGTCTAATTCTA 59.398 38.462 0.00 0.00 0.00 2.10
1802 2165 4.224147 GGGCCTTGGCCTTTTTATTTTCTA 59.776 41.667 27.45 0.00 45.39 2.10
1914 2282 1.836802 TGGCCCAATAATTTGCCCTTC 59.163 47.619 0.00 0.00 43.35 3.46
1977 2349 2.391678 CCAAGCCCAATAATTCAGCCT 58.608 47.619 0.00 0.00 0.00 4.58
2041 2413 7.145323 CAGAATTACGACCAAATGAAAAGGTT 58.855 34.615 0.00 0.00 35.36 3.50
2067 2439 1.885388 CCGTGGCAAGTTGACGTGA 60.885 57.895 7.16 0.00 0.00 4.35
2075 2447 1.003355 CAGATCCACCGTGGCAAGT 60.003 57.895 13.19 0.00 37.47 3.16
2246 2624 7.360861 CGGCTTTCACTACAAGAAATATGTCAA 60.361 37.037 0.00 0.00 34.75 3.18
2248 2626 6.478588 CGGCTTTCACTACAAGAAATATGTC 58.521 40.000 0.00 0.00 34.75 3.06
2252 2630 3.687698 GGCGGCTTTCACTACAAGAAATA 59.312 43.478 0.00 0.00 34.75 1.40
2256 2634 0.321298 GGGCGGCTTTCACTACAAGA 60.321 55.000 9.56 0.00 0.00 3.02
2257 2635 1.305930 GGGGCGGCTTTCACTACAAG 61.306 60.000 9.56 0.00 0.00 3.16
2258 2636 1.302993 GGGGCGGCTTTCACTACAA 60.303 57.895 9.56 0.00 0.00 2.41
2259 2637 2.058125 TTGGGGCGGCTTTCACTACA 62.058 55.000 9.56 0.00 0.00 2.74
2260 2638 1.302993 TTGGGGCGGCTTTCACTAC 60.303 57.895 9.56 0.00 0.00 2.73
2261 2639 1.302993 GTTGGGGCGGCTTTCACTA 60.303 57.895 9.56 0.00 0.00 2.74
2262 2640 2.597510 GTTGGGGCGGCTTTCACT 60.598 61.111 9.56 0.00 0.00 3.41
2263 2641 3.680786 GGTTGGGGCGGCTTTCAC 61.681 66.667 9.56 0.62 0.00 3.18
2264 2642 3.521765 ATGGTTGGGGCGGCTTTCA 62.522 57.895 9.56 2.33 0.00 2.69
2265 2643 2.679996 ATGGTTGGGGCGGCTTTC 60.680 61.111 9.56 0.00 0.00 2.62
2266 2644 2.996734 CATGGTTGGGGCGGCTTT 60.997 61.111 9.56 0.00 0.00 3.51
2270 2648 4.067913 GTTGCATGGTTGGGGCGG 62.068 66.667 0.00 0.00 0.00 6.13
2271 2649 3.301554 TGTTGCATGGTTGGGGCG 61.302 61.111 0.00 0.00 0.00 6.13
2272 2650 2.343387 GTGTTGCATGGTTGGGGC 59.657 61.111 0.00 0.00 0.00 5.80
2273 2651 1.743321 AACGTGTTGCATGGTTGGGG 61.743 55.000 0.00 0.00 0.00 4.96
2274 2652 0.597118 CAACGTGTTGCATGGTTGGG 60.597 55.000 0.00 0.00 33.45 4.12
2275 2653 0.383590 TCAACGTGTTGCATGGTTGG 59.616 50.000 7.85 3.17 40.24 3.77
2276 2654 1.851666 GTTCAACGTGTTGCATGGTTG 59.148 47.619 7.85 11.29 40.24 3.77
2277 2655 1.202359 GGTTCAACGTGTTGCATGGTT 60.202 47.619 7.85 0.00 40.24 3.67
2278 2656 0.383949 GGTTCAACGTGTTGCATGGT 59.616 50.000 7.85 0.00 40.24 3.55
2279 2657 0.667993 AGGTTCAACGTGTTGCATGG 59.332 50.000 7.85 0.00 40.24 3.66
2280 2658 3.617540 TTAGGTTCAACGTGTTGCATG 57.382 42.857 7.85 0.00 40.24 4.06
2281 2659 4.846779 AATTAGGTTCAACGTGTTGCAT 57.153 36.364 7.85 0.00 40.24 3.96
2282 2660 5.066117 TGTTAATTAGGTTCAACGTGTTGCA 59.934 36.000 7.85 0.00 40.24 4.08
2283 2661 5.512473 TGTTAATTAGGTTCAACGTGTTGC 58.488 37.500 7.85 0.00 40.24 4.17
2284 2662 7.411274 TCTTGTTAATTAGGTTCAACGTGTTG 58.589 34.615 6.39 6.39 41.71 3.33
2285 2663 7.556733 TCTTGTTAATTAGGTTCAACGTGTT 57.443 32.000 0.00 0.00 0.00 3.32
2286 2664 7.556733 TTCTTGTTAATTAGGTTCAACGTGT 57.443 32.000 0.00 0.00 0.00 4.49
2287 2665 8.339714 TCTTTCTTGTTAATTAGGTTCAACGTG 58.660 33.333 0.00 0.00 0.00 4.49
2288 2666 8.441312 TCTTTCTTGTTAATTAGGTTCAACGT 57.559 30.769 0.00 0.00 0.00 3.99
2289 2667 8.770828 TCTCTTTCTTGTTAATTAGGTTCAACG 58.229 33.333 0.00 0.00 0.00 4.10
2292 2670 9.847224 AGTTCTCTTTCTTGTTAATTAGGTTCA 57.153 29.630 0.00 0.00 0.00 3.18
2294 2672 9.067986 CCAGTTCTCTTTCTTGTTAATTAGGTT 57.932 33.333 0.00 0.00 0.00 3.50
2295 2673 7.665974 CCCAGTTCTCTTTCTTGTTAATTAGGT 59.334 37.037 0.00 0.00 0.00 3.08
2296 2674 7.665974 ACCCAGTTCTCTTTCTTGTTAATTAGG 59.334 37.037 0.00 0.00 0.00 2.69
2297 2675 8.622948 ACCCAGTTCTCTTTCTTGTTAATTAG 57.377 34.615 0.00 0.00 0.00 1.73
2298 2676 7.664318 GGACCCAGTTCTCTTTCTTGTTAATTA 59.336 37.037 0.00 0.00 0.00 1.40
2299 2677 6.490381 GGACCCAGTTCTCTTTCTTGTTAATT 59.510 38.462 0.00 0.00 0.00 1.40
2300 2678 6.004574 GGACCCAGTTCTCTTTCTTGTTAAT 58.995 40.000 0.00 0.00 0.00 1.40
2301 2679 5.132144 AGGACCCAGTTCTCTTTCTTGTTAA 59.868 40.000 0.00 0.00 0.00 2.01
2302 2680 4.658901 AGGACCCAGTTCTCTTTCTTGTTA 59.341 41.667 0.00 0.00 0.00 2.41
2303 2681 3.459969 AGGACCCAGTTCTCTTTCTTGTT 59.540 43.478 0.00 0.00 0.00 2.83
2304 2682 3.049344 AGGACCCAGTTCTCTTTCTTGT 58.951 45.455 0.00 0.00 0.00 3.16
2305 2683 3.778954 AGGACCCAGTTCTCTTTCTTG 57.221 47.619 0.00 0.00 0.00 3.02
2306 2684 3.073209 GGAAGGACCCAGTTCTCTTTCTT 59.927 47.826 0.00 0.00 0.00 2.52
2307 2685 2.640332 GGAAGGACCCAGTTCTCTTTCT 59.360 50.000 0.00 0.00 0.00 2.52
2308 2686 2.640332 AGGAAGGACCCAGTTCTCTTTC 59.360 50.000 0.00 0.00 40.05 2.62
2309 2687 2.373502 CAGGAAGGACCCAGTTCTCTTT 59.626 50.000 0.00 0.00 40.05 2.52
2310 2688 1.981495 CAGGAAGGACCCAGTTCTCTT 59.019 52.381 0.00 0.00 40.05 2.85
2311 2689 1.650528 CAGGAAGGACCCAGTTCTCT 58.349 55.000 0.00 0.00 40.05 3.10
2312 2690 0.035915 GCAGGAAGGACCCAGTTCTC 60.036 60.000 0.00 0.00 40.05 2.87
2313 2691 1.492993 GGCAGGAAGGACCCAGTTCT 61.493 60.000 0.00 0.00 40.05 3.01
2314 2692 1.002011 GGCAGGAAGGACCCAGTTC 60.002 63.158 0.00 0.00 40.05 3.01
2315 2693 1.774217 TGGCAGGAAGGACCCAGTT 60.774 57.895 0.00 0.00 40.05 3.16
2316 2694 2.121963 TGGCAGGAAGGACCCAGT 60.122 61.111 0.00 0.00 40.05 4.00
2317 2695 2.673523 CTGGCAGGAAGGACCCAG 59.326 66.667 6.61 0.00 38.93 4.45
2318 2696 2.121963 ACTGGCAGGAAGGACCCA 60.122 61.111 20.34 0.00 40.05 4.51
2319 2697 2.352805 CACTGGCAGGAAGGACCC 59.647 66.667 20.34 0.00 40.05 4.46
2320 2698 2.352805 CCACTGGCAGGAAGGACC 59.647 66.667 20.34 0.00 39.35 4.46
2321 2699 2.352805 CCCACTGGCAGGAAGGAC 59.647 66.667 20.34 0.00 0.00 3.85
2322 2700 2.935481 CCCCACTGGCAGGAAGGA 60.935 66.667 20.34 0.00 0.00 3.36
2323 2701 4.052518 CCCCCACTGGCAGGAAGG 62.053 72.222 20.34 16.59 0.00 3.46
2346 2724 2.444895 ATGGAGGCGAGGAGGACC 60.445 66.667 0.00 0.00 0.00 4.46
2347 2725 2.801631 CCATGGAGGCGAGGAGGAC 61.802 68.421 5.56 0.00 0.00 3.85
2348 2726 2.444706 CCATGGAGGCGAGGAGGA 60.445 66.667 5.56 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.