Multiple sequence alignment - TraesCS1B01G400700

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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 TraesCS1B01G400700 chr1B 100.000 3113 0 0 1 3113 631220195 631217083 0.000000e+00 5749.0
1 TraesCS1B01G400700 chr1B 86.670 2228 262 26 1 2222 631201998 631199800 0.000000e+00 2436.0
2 TraesCS1B01G400700 chr1B 82.979 94 11 5 2635 2723 631198794 631198701 2.570000e-11 80.5
3 TraesCS1B01G400700 chr1D 87.393 2229 244 25 4 2222 459040494 459038293 0.000000e+00 2525.0
4 TraesCS1B01G400700 chr1D 83.576 2332 343 35 1 2316 459029722 459027415 0.000000e+00 2148.0
5 TraesCS1B01G400700 chr1D 89.333 150 8 2 2964 3113 459025701 459025560 6.860000e-42 182.0
6 TraesCS1B01G400700 chr1D 91.358 81 6 1 2689 2769 459027006 459026927 3.280000e-20 110.0
7 TraesCS1B01G400700 chr1A 84.324 1952 220 36 942 2871 551443258 551441371 0.000000e+00 1831.0
8 TraesCS1B01G400700 chr1A 86.427 1444 168 17 2 1435 551461906 551460481 0.000000e+00 1555.0
9 TraesCS1B01G400700 chr1A 83.310 713 115 4 1419 2129 551458803 551458093 0.000000e+00 654.0
10 TraesCS1B01G400700 chr1A 89.262 149 13 3 2967 3113 551441353 551441206 1.910000e-42 183.0
11 TraesCS1B01G400700 chr3D 76.679 2174 446 56 21 2166 428253172 428255312 0.000000e+00 1149.0
12 TraesCS1B01G400700 chr3D 75.613 2120 453 56 21 2108 428247218 428249305 0.000000e+00 992.0
13 TraesCS1B01G400700 chr3B 76.960 1888 385 47 303 2166 559890712 559892573 0.000000e+00 1031.0
14 TraesCS1B01G400700 chr3B 75.613 2120 448 57 21 2108 559882700 559884782 0.000000e+00 987.0
15 TraesCS1B01G400700 chr6D 74.704 2194 474 62 21 2180 469801927 469804073 0.000000e+00 902.0
16 TraesCS1B01G400700 chr4A 74.724 2176 465 74 21 2158 735560911 735558783 0.000000e+00 893.0
17 TraesCS1B01G400700 chr4A 73.465 1726 408 44 453 2158 734482989 734484684 3.430000e-169 604.0
18 TraesCS1B01G400700 chr4A 72.270 1172 272 46 1019 2158 736122459 736123609 6.480000e-82 315.0
19 TraesCS1B01G400700 chr3A 74.694 2122 459 61 21 2106 557417323 557415244 0.000000e+00 872.0
20 TraesCS1B01G400700 chrUn 74.342 2202 490 61 21 2191 62078054 62075897 0.000000e+00 867.0
21 TraesCS1B01G400700 chr7D 75.908 523 110 14 1643 2156 5456796 5456281 1.430000e-63 254.0


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 TraesCS1B01G400700 chr1B 631217083 631220195 3112 True 5749.000000 5749 100.0000 1 3113 1 chr1B.!!$R1 3112
1 TraesCS1B01G400700 chr1B 631198701 631201998 3297 True 1258.250000 2436 84.8245 1 2723 2 chr1B.!!$R2 2722
2 TraesCS1B01G400700 chr1D 459038293 459040494 2201 True 2525.000000 2525 87.3930 4 2222 1 chr1D.!!$R1 2218
3 TraesCS1B01G400700 chr1D 459025560 459029722 4162 True 813.333333 2148 88.0890 1 3113 3 chr1D.!!$R2 3112
4 TraesCS1B01G400700 chr1A 551458093 551461906 3813 True 1104.500000 1555 84.8685 2 2129 2 chr1A.!!$R2 2127
5 TraesCS1B01G400700 chr1A 551441206 551443258 2052 True 1007.000000 1831 86.7930 942 3113 2 chr1A.!!$R1 2171
6 TraesCS1B01G400700 chr3D 428247218 428255312 8094 False 1070.500000 1149 76.1460 21 2166 2 chr3D.!!$F1 2145
7 TraesCS1B01G400700 chr3B 559890712 559892573 1861 False 1031.000000 1031 76.9600 303 2166 1 chr3B.!!$F2 1863
8 TraesCS1B01G400700 chr3B 559882700 559884782 2082 False 987.000000 987 75.6130 21 2108 1 chr3B.!!$F1 2087
9 TraesCS1B01G400700 chr6D 469801927 469804073 2146 False 902.000000 902 74.7040 21 2180 1 chr6D.!!$F1 2159
10 TraesCS1B01G400700 chr4A 735558783 735560911 2128 True 893.000000 893 74.7240 21 2158 1 chr4A.!!$R1 2137
11 TraesCS1B01G400700 chr4A 734482989 734484684 1695 False 604.000000 604 73.4650 453 2158 1 chr4A.!!$F1 1705
12 TraesCS1B01G400700 chr4A 736122459 736123609 1150 False 315.000000 315 72.2700 1019 2158 1 chr4A.!!$F2 1139
13 TraesCS1B01G400700 chr3A 557415244 557417323 2079 True 872.000000 872 74.6940 21 2106 1 chr3A.!!$R1 2085
14 TraesCS1B01G400700 chrUn 62075897 62078054 2157 True 867.000000 867 74.3420 21 2191 1 chrUn.!!$R1 2170
15 TraesCS1B01G400700 chr7D 5456281 5456796 515 True 254.000000 254 75.9080 1643 2156 1 chr7D.!!$R1 513

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
298 305 2.034999 GGTCCGCCACAAATCCCA 59.965 61.111 0.0 0.0 34.09 4.37 F
1545 9229 1.205655 CCGCACCTGAGAGATCTTGAA 59.794 52.381 0.0 0.0 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1681 9368 0.390472 CTGAGCTTCGGGACACCTTC 60.390 60.0 0.00 0.00 33.28 3.46 R
2513 10304 0.175760 AACACACGTGTCTCAGCAGT 59.824 50.0 20.49 9.11 44.13 4.40 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
193 194 6.882140 TCCTTAAGTTCAGTGACAAAGTTGAA 59.118 34.615 0.97 0.00 0.00 2.69
260 267 6.599244 TCTTGAAGGGCACAATGTTAATCTAG 59.401 38.462 0.00 0.00 0.00 2.43
261 268 4.640201 TGAAGGGCACAATGTTAATCTAGC 59.360 41.667 0.00 0.00 0.00 3.42
271 278 6.203530 ACAATGTTAATCTAGCACATGATCCG 59.796 38.462 0.00 0.00 31.37 4.18
276 283 3.990318 TCTAGCACATGATCCGTACAG 57.010 47.619 0.00 0.00 0.00 2.74
277 284 2.623416 TCTAGCACATGATCCGTACAGG 59.377 50.000 0.00 0.00 42.97 4.00
298 305 2.034999 GGTCCGCCACAAATCCCA 59.965 61.111 0.00 0.00 34.09 4.37
331 338 5.043737 ACCTAACTTTGCTCCAACAACTA 57.956 39.130 0.00 0.00 0.00 2.24
459 6420 5.072741 TGCAAAGGATGAAGCTTTAGAGTT 58.927 37.500 0.00 0.00 0.00 3.01
472 6433 4.798593 GCTTTAGAGTTGAACCTACACCGT 60.799 45.833 0.00 0.00 0.00 4.83
493 6455 8.500773 CACCGTAAAACTCATCTTAAAAGCTTA 58.499 33.333 0.00 0.00 0.00 3.09
500 6462 8.807948 AACTCATCTTAAAAGCTTATGCCTTA 57.192 30.769 0.00 0.00 40.80 2.69
538 6500 7.217200 TGGATAACATAAATGTAGAGGACAGC 58.783 38.462 0.00 0.00 42.79 4.40
540 6502 7.600752 GGATAACATAAATGTAGAGGACAGCTC 59.399 40.741 0.00 0.00 42.79 4.09
547 6509 3.763057 TGTAGAGGACAGCTCACACTTA 58.237 45.455 0.00 0.00 32.86 2.24
567 6529 5.420739 ACTTAGAGATTCTGGAAGGTCTGAC 59.579 44.000 0.00 0.00 31.18 3.51
607 6569 3.161866 GGGCCTCACAATCAAAGGTTAA 58.838 45.455 0.84 0.00 32.49 2.01
677 6639 4.339530 AGAACTTGGAAACCTTTGAGCTTC 59.660 41.667 0.00 0.00 0.00 3.86
769 6731 4.415596 TCTGGAATGTGCCAAACCTAAAT 58.584 39.130 0.00 0.00 37.52 1.40
771 6733 6.194235 TCTGGAATGTGCCAAACCTAAATAT 58.806 36.000 0.00 0.00 37.52 1.28
802 6764 6.248569 TGTCTTCCAGAAGGTCTTAAAAGT 57.751 37.500 7.53 0.00 38.88 2.66
890 6852 7.445121 TCAGTGGGAGAACATCATGAATATAC 58.555 38.462 0.00 0.00 0.00 1.47
897 6859 8.725148 GGAGAACATCATGAATATACACCAATC 58.275 37.037 0.00 0.00 0.00 2.67
912 6874 4.261801 CACCAATCGGTATCAAACCTTCT 58.738 43.478 0.00 0.00 46.94 2.85
926 6888 5.466058 TCAAACCTTCTTTTGATAACGCGTA 59.534 36.000 14.46 0.72 39.94 4.42
927 6889 5.927954 AACCTTCTTTTGATAACGCGTAA 57.072 34.783 14.46 0.00 0.00 3.18
995 6958 2.275318 GGAACTTTCATCTCTGGAGCG 58.725 52.381 0.00 0.00 0.00 5.03
1088 7078 7.333921 GGAATTTGTGATAGAGGATAGCATCAG 59.666 40.741 0.00 0.00 0.00 2.90
1184 7174 6.183360 CCACCATCACAACTTAACAGACTTTT 60.183 38.462 0.00 0.00 0.00 2.27
1288 7278 8.994429 AACTAAGATCATGACTTTGACTACAG 57.006 34.615 18.51 10.65 0.00 2.74
1324 7314 4.351111 AGGTCCTCCTACATTTGACAAAGT 59.649 41.667 6.77 7.36 43.12 2.66
1336 7326 5.906113 TTTGACAAAGTTAAGTTGGCTGA 57.094 34.783 0.00 0.00 34.88 4.26
1411 7401 4.880696 CCTCCCTTTCAGATGTCAGATTTC 59.119 45.833 0.00 0.00 0.00 2.17
1545 9229 1.205655 CCGCACCTGAGAGATCTTGAA 59.794 52.381 0.00 0.00 0.00 2.69
1582 9266 1.820519 GCCTTGCATCCTTGTCAATCA 59.179 47.619 0.00 0.00 0.00 2.57
1592 9276 6.405508 GCATCCTTGTCAATCAGTCATTTGAT 60.406 38.462 0.00 0.00 39.42 2.57
1615 9299 7.290014 TGATCTCCCTTGCATCATTAGTACTAA 59.710 37.037 17.41 17.41 0.00 2.24
1676 9363 1.732259 CCTGCAACTTCACCGTGTATC 59.268 52.381 0.00 0.00 0.00 2.24
1681 9368 4.688879 TGCAACTTCACCGTGTATCTTTAG 59.311 41.667 0.00 0.00 0.00 1.85
1685 9372 5.721232 ACTTCACCGTGTATCTTTAGAAGG 58.279 41.667 0.00 0.00 36.47 3.46
1779 9466 3.771479 TGATACTCAACCACATGCTCTCT 59.229 43.478 0.00 0.00 0.00 3.10
1796 9483 6.164176 TGCTCTCTACTAAAGGTTTTACAGC 58.836 40.000 0.00 0.00 0.00 4.40
1891 9578 4.985409 CCCTGAGAAAGCTGATATTACGTC 59.015 45.833 0.00 0.00 0.00 4.34
1905 9592 6.699642 TGATATTACGTCAATGCGAAATGAGA 59.300 34.615 0.00 0.00 35.59 3.27
1929 9622 2.089980 CTGCCAGGAAATCTCAAGTGG 58.910 52.381 0.00 0.00 0.00 4.00
1935 9628 2.373169 AGGAAATCTCAAGTGGCTGACA 59.627 45.455 0.00 0.00 0.00 3.58
1996 9689 3.995199 TCATCTTTATCCGATCTGCCAC 58.005 45.455 0.00 0.00 0.00 5.01
2014 9710 3.053077 CCACCCTCCCTCCAACATATAA 58.947 50.000 0.00 0.00 0.00 0.98
2040 9739 0.465460 AGGGTTGTGAGCGCTTGAAA 60.465 50.000 13.26 3.08 0.00 2.69
2086 9785 0.318120 AAGTTGGCCAAAGATTGCGG 59.682 50.000 22.47 0.00 0.00 5.69
2096 9795 2.614057 CAAAGATTGCGGGTATCCACTC 59.386 50.000 0.00 0.00 0.00 3.51
2171 9874 1.068125 GGTAAATGTTCCACCAACGCC 60.068 52.381 0.00 0.00 37.90 5.68
2191 9894 4.513442 GCCCTCAAAGAAAACCTTTTGTT 58.487 39.130 0.00 0.00 42.13 2.83
2206 9909 8.986477 AACCTTTTGTTGACATTATCTTATGC 57.014 30.769 0.00 0.00 35.31 3.14
2207 9910 8.121305 ACCTTTTGTTGACATTATCTTATGCA 57.879 30.769 0.00 0.00 0.00 3.96
2304 10020 4.522722 ACGAAGTTTTGTTTTCCCAACA 57.477 36.364 0.00 0.00 37.78 3.33
2307 10023 5.164954 CGAAGTTTTGTTTTCCCAACAGAA 58.835 37.500 0.00 0.00 0.00 3.02
2309 10025 5.993748 AGTTTTGTTTTCCCAACAGAAGA 57.006 34.783 0.00 0.00 0.00 2.87
2310 10026 6.353404 AGTTTTGTTTTCCCAACAGAAGAA 57.647 33.333 0.00 0.00 0.00 2.52
2311 10027 6.764379 AGTTTTGTTTTCCCAACAGAAGAAA 58.236 32.000 0.00 0.00 0.00 2.52
2312 10028 7.220740 AGTTTTGTTTTCCCAACAGAAGAAAA 58.779 30.769 0.00 0.00 37.20 2.29
2313 10029 7.717436 AGTTTTGTTTTCCCAACAGAAGAAAAA 59.283 29.630 0.00 0.00 40.20 1.94
2337 10053 2.430332 CAGTCTCAAGATCTGTCCCCTC 59.570 54.545 0.00 0.00 0.00 4.30
2364 10080 3.699894 CGTCTCCACTGCCTGCCT 61.700 66.667 0.00 0.00 0.00 4.75
2375 10091 1.372683 GCCTGCCTGTCAGAAGTCA 59.627 57.895 0.00 0.00 45.72 3.41
2385 10101 4.384056 CTGTCAGAAGTCAAGTGTTGGAT 58.616 43.478 0.00 0.00 0.00 3.41
2386 10102 4.129380 TGTCAGAAGTCAAGTGTTGGATG 58.871 43.478 0.00 0.00 0.00 3.51
2387 10103 4.130118 GTCAGAAGTCAAGTGTTGGATGT 58.870 43.478 0.00 0.00 0.00 3.06
2388 10104 4.024556 GTCAGAAGTCAAGTGTTGGATGTG 60.025 45.833 0.00 0.00 0.00 3.21
2389 10105 3.879295 CAGAAGTCAAGTGTTGGATGTGT 59.121 43.478 0.00 0.00 0.00 3.72
2390 10106 4.024556 CAGAAGTCAAGTGTTGGATGTGTC 60.025 45.833 0.00 0.00 0.00 3.67
2406 10125 5.163814 GGATGTGTCAGCTCACTTACAATTC 60.164 44.000 7.05 0.00 38.90 2.17
2412 10131 4.997395 TCAGCTCACTTACAATTCAACTCC 59.003 41.667 0.00 0.00 0.00 3.85
2419 10138 0.400213 ACAATTCAACTCCCTCCGCA 59.600 50.000 0.00 0.00 0.00 5.69
2440 10159 4.002506 TGTGTCGCTGGTGCCGAT 62.003 61.111 0.00 0.00 35.36 4.18
2443 10162 4.451150 GTCGCTGGTGCCGATCCA 62.451 66.667 0.00 0.00 35.36 3.41
2451 10170 0.394352 GGTGCCGATCCATTGGTTCT 60.394 55.000 11.14 0.00 33.62 3.01
2494 10213 3.875727 CGCATCATTCTTCCACTCTTGAT 59.124 43.478 0.00 0.00 0.00 2.57
2512 10303 2.125512 GGCTCCACTACTGTGCGG 60.126 66.667 0.00 0.00 42.54 5.69
2513 10304 2.646175 GGCTCCACTACTGTGCGGA 61.646 63.158 0.00 0.00 42.54 5.54
2532 10323 0.175760 ACTGCTGAGACACGTGTGTT 59.824 50.000 28.82 14.32 45.05 3.32
2570 10585 7.573916 TGTTCTATGTTGTTGTGTTTTGTTG 57.426 32.000 0.00 0.00 0.00 3.33
2580 10595 4.592485 TGTGTTTTGTTGTCCTGTGTTT 57.408 36.364 0.00 0.00 0.00 2.83
2595 10612 4.798387 CCTGTGTTTGAGTGTTACTTTTGC 59.202 41.667 0.00 0.00 0.00 3.68
2601 10618 7.115663 GTGTTTGAGTGTTACTTTTGCTTTTGA 59.884 33.333 0.00 0.00 0.00 2.69
2611 10628 1.868469 TTGCTTTTGATTGGTGCTGC 58.132 45.000 0.00 0.00 0.00 5.25
2612 10629 0.033781 TGCTTTTGATTGGTGCTGCC 59.966 50.000 0.00 0.00 37.90 4.85
2614 10631 0.388907 CTTTTGATTGGTGCTGCCCG 60.389 55.000 0.00 0.00 36.04 6.13
2616 10633 0.250945 TTTGATTGGTGCTGCCCGTA 60.251 50.000 0.00 0.00 36.04 4.02
2617 10634 0.250945 TTGATTGGTGCTGCCCGTAA 60.251 50.000 0.00 0.00 36.04 3.18
2619 10636 0.676782 GATTGGTGCTGCCCGTAAGT 60.677 55.000 0.00 0.00 36.04 2.24
2620 10637 0.616371 ATTGGTGCTGCCCGTAAGTA 59.384 50.000 0.00 0.00 36.04 2.24
2641 11107 8.621532 AAGTATTATTTCTTGTGTGCTGAGAA 57.378 30.769 0.00 0.00 0.00 2.87
2658 11124 6.488344 TGCTGAGAAGTACTTCGATATCTCAT 59.512 38.462 25.92 8.68 41.53 2.90
2682 11148 0.030705 TCTGGAGGGCTAAGCTCCAT 60.031 55.000 10.14 0.00 45.04 3.41
2684 11150 2.158097 TCTGGAGGGCTAAGCTCCATAT 60.158 50.000 10.14 0.00 45.04 1.78
2694 11244 5.698545 GGCTAAGCTCCATATTTCAGTACAG 59.301 44.000 0.00 0.00 0.00 2.74
2731 11281 5.009010 ACTTCTGCAGTTTATGTTTGGAGTG 59.991 40.000 14.67 0.00 32.82 3.51
2739 11289 2.592102 ATGTTTGGAGTGTGCTGGAT 57.408 45.000 0.00 0.00 0.00 3.41
2771 11412 6.371548 TGTGAAGCAAATCTGAATACACTACC 59.628 38.462 0.00 0.00 0.00 3.18
2811 11452 3.519510 ACAGCAGGCCTTAACTTCTCATA 59.480 43.478 0.00 0.00 0.00 2.15
2843 11484 4.321452 GCAGTCACCATGTGAATCATTTGT 60.321 41.667 0.00 0.00 44.49 2.83
2845 11486 6.218019 CAGTCACCATGTGAATCATTTGTTT 58.782 36.000 0.00 0.00 44.49 2.83
2846 11487 6.702723 CAGTCACCATGTGAATCATTTGTTTT 59.297 34.615 0.00 0.00 44.49 2.43
2849 11490 7.011295 GTCACCATGTGAATCATTTGTTTTTGT 59.989 33.333 0.00 0.00 44.49 2.83
2852 11493 5.731599 TGTGAATCATTTGTTTTTGTGGC 57.268 34.783 0.00 0.00 0.00 5.01
2866 11507 0.036732 TGTGGCCATTCTGGAGACAC 59.963 55.000 9.72 3.69 40.96 3.67
2871 11512 0.898320 CCATTCTGGAGACACGGAGT 59.102 55.000 0.00 0.00 41.16 3.85
2885 11526 3.110178 GAGTGTACGCCGTGTGCC 61.110 66.667 0.00 0.00 36.24 5.01
2891 11980 1.598407 TACGCCGTGTGCCATTGTT 60.598 52.632 0.00 0.00 36.24 2.83
2901 11990 2.642311 TGTGCCATTGTTTCCCTCTAGA 59.358 45.455 0.00 0.00 0.00 2.43
2902 11991 3.274288 GTGCCATTGTTTCCCTCTAGAG 58.726 50.000 13.18 13.18 0.00 2.43
2903 11992 2.912956 TGCCATTGTTTCCCTCTAGAGT 59.087 45.455 18.42 0.00 0.00 3.24
2904 11993 3.330701 TGCCATTGTTTCCCTCTAGAGTT 59.669 43.478 18.42 0.00 0.00 3.01
2905 11994 3.942115 GCCATTGTTTCCCTCTAGAGTTC 59.058 47.826 18.42 4.82 0.00 3.01
2906 11995 4.323868 GCCATTGTTTCCCTCTAGAGTTCT 60.324 45.833 18.42 0.00 0.00 3.01
2910 12491 4.011023 TGTTTCCCTCTAGAGTTCTCTCG 58.989 47.826 18.42 1.22 44.65 4.04
2915 12496 2.356330 CCTCTAGAGTTCTCTCGGGTGT 60.356 54.545 18.42 0.00 44.65 4.16
2931 12512 1.886542 GGTGTGATCTTGTTTGGGGAC 59.113 52.381 0.00 0.00 0.00 4.46
2932 12513 2.489073 GGTGTGATCTTGTTTGGGGACT 60.489 50.000 0.00 0.00 0.00 3.85
2937 12518 2.507407 TCTTGTTTGGGGACTATGGC 57.493 50.000 0.00 0.00 0.00 4.40
2943 12524 2.109181 GGGGACTATGGCGACTGC 59.891 66.667 0.00 0.00 41.71 4.40
2948 12529 2.419574 GGGACTATGGCGACTGCTAAAA 60.420 50.000 0.00 0.00 42.25 1.52
2950 12531 3.877508 GGACTATGGCGACTGCTAAAATT 59.122 43.478 0.00 0.00 42.25 1.82
2951 12532 4.024809 GGACTATGGCGACTGCTAAAATTC 60.025 45.833 0.00 0.00 42.25 2.17
2953 12534 1.083489 TGGCGACTGCTAAAATTCCG 58.917 50.000 0.00 0.00 42.25 4.30
2954 12535 1.084289 GGCGACTGCTAAAATTCCGT 58.916 50.000 0.00 0.00 42.25 4.69
2972 12559 9.715121 AAATTCCGTAGAACTAAGTGTAAATGA 57.285 29.630 0.00 0.00 33.97 2.57
3007 12615 1.278985 TGATGGTCAGGGTGCACTAAG 59.721 52.381 17.98 6.71 0.00 2.18
3079 12688 1.286880 GCGCACAAGCAAATCCAGT 59.713 52.632 0.30 0.00 42.27 4.00
3081 12690 1.466360 GCGCACAAGCAAATCCAGTAG 60.466 52.381 0.30 0.00 42.27 2.57
3103 12712 4.162698 AGTGTAGAAAACCACACCACAGTA 59.837 41.667 1.46 0.00 44.94 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 2.642139 ATTGATTCTGGCAACTTGCG 57.358 45.000 7.67 0.00 46.21 4.85
202 203 8.244113 AGCTTACTTAAATTGCATAGTTTGTCC 58.756 33.333 0.00 0.00 0.00 4.02
271 278 1.600107 TGGCGGACCAATCCTGTAC 59.400 57.895 0.00 0.00 45.37 2.90
282 289 0.038618 GTTTGGGATTTGTGGCGGAC 60.039 55.000 0.00 0.00 0.00 4.79
285 292 2.159254 CCTATGTTTGGGATTTGTGGCG 60.159 50.000 0.00 0.00 0.00 5.69
289 296 3.260632 GGTTGCCTATGTTTGGGATTTGT 59.739 43.478 0.00 0.00 0.00 2.83
298 305 5.134202 GCAAAGTTAGGTTGCCTATGTTT 57.866 39.130 0.00 0.00 44.53 2.83
459 6420 4.669206 TGAGTTTTACGGTGTAGGTTCA 57.331 40.909 0.00 0.00 0.00 3.18
472 6433 9.243105 AGGCATAAGCTTTTAAGATGAGTTTTA 57.757 29.630 3.20 0.00 41.70 1.52
493 6455 6.763715 TCCATATAACTCCAGTTAAGGCAT 57.236 37.500 3.31 0.00 42.93 4.40
538 6500 5.186797 ACCTTCCAGAATCTCTAAGTGTGAG 59.813 44.000 1.83 0.00 0.00 3.51
540 6502 5.186797 AGACCTTCCAGAATCTCTAAGTGTG 59.813 44.000 1.83 0.00 0.00 3.82
547 6509 2.757868 CGTCAGACCTTCCAGAATCTCT 59.242 50.000 0.00 0.00 0.00 3.10
567 6529 1.635663 CTTAAGTTGAGGCGGTGGCG 61.636 60.000 0.00 0.00 41.24 5.69
607 6569 5.361857 CCAACCTGGATATTTTGCAGATCTT 59.638 40.000 0.00 0.00 46.09 2.40
658 6620 4.926140 AAGAAGCTCAAAGGTTTCCAAG 57.074 40.909 0.00 0.00 35.86 3.61
677 6639 5.393962 GCCTTCTAACACAGTGCAATTAAG 58.606 41.667 0.00 0.00 0.00 1.85
769 6731 7.989947 ACCTTCTGGAAGACAAGGTAATATA 57.010 36.000 11.44 0.00 46.03 0.86
789 6751 8.646900 TGGCAATTGATAAACTTTTAAGACCTT 58.353 29.630 10.34 0.00 0.00 3.50
802 6764 4.832266 AGTGGACACTTGGCAATTGATAAA 59.168 37.500 22.40 4.24 38.83 1.40
912 6874 4.063689 TGAACCCTTACGCGTTATCAAAA 58.936 39.130 20.78 2.78 0.00 2.44
926 6888 3.394606 ACTGAACCATGTACTGAACCCTT 59.605 43.478 0.00 0.00 0.00 3.95
927 6889 2.979678 ACTGAACCATGTACTGAACCCT 59.020 45.455 0.00 0.00 0.00 4.34
930 6892 7.667043 TTTGATACTGAACCATGTACTGAAC 57.333 36.000 0.00 0.00 0.00 3.18
1184 7174 6.946340 TCTGTAATACTGCATGAAGAAAGGA 58.054 36.000 8.02 0.00 0.00 3.36
1288 7278 1.737008 GGACCTCTTGCGACGGAAC 60.737 63.158 0.00 0.00 0.00 3.62
1310 7300 7.067615 TCAGCCAACTTAACTTTGTCAAATGTA 59.932 33.333 0.00 0.00 0.00 2.29
1336 7326 5.171339 AGACACCAGCAAGAACTGATATT 57.829 39.130 0.00 0.00 40.25 1.28
1411 7401 3.037549 AGTCTAGAGAAGGGCAGGAATG 58.962 50.000 0.00 0.00 0.00 2.67
1545 9229 2.639327 GCTTCCGCAGCCAACCATT 61.639 57.895 0.00 0.00 43.65 3.16
1582 9266 3.726557 TGCAAGGGAGATCAAATGACT 57.273 42.857 0.00 0.00 0.00 3.41
1592 9276 7.432148 TTTAGTACTAATGATGCAAGGGAGA 57.568 36.000 15.92 0.00 0.00 3.71
1676 9363 2.028020 AGCTTCGGGACACCTTCTAAAG 60.028 50.000 0.00 0.00 33.28 1.85
1681 9368 0.390472 CTGAGCTTCGGGACACCTTC 60.390 60.000 0.00 0.00 33.28 3.46
1685 9372 2.811317 CGCTGAGCTTCGGGACAC 60.811 66.667 1.78 0.00 0.00 3.67
1779 9466 6.675413 TCTGGAGCTGTAAAACCTTTAGTA 57.325 37.500 0.00 0.00 0.00 1.82
1878 9565 4.708868 TTCGCATTGACGTAATATCAGC 57.291 40.909 0.00 0.00 0.00 4.26
1891 9578 2.287427 GCAGGGATCTCATTTCGCATTG 60.287 50.000 0.00 0.00 0.00 2.82
1905 9592 1.600058 TGAGATTTCCTGGCAGGGAT 58.400 50.000 32.23 24.89 35.59 3.85
1929 9622 1.132588 GTCGTGTCAGACTTGTCAGC 58.867 55.000 1.31 0.00 38.09 4.26
1996 9689 5.324832 ACAATTATATGTTGGAGGGAGGG 57.675 43.478 7.36 0.00 0.00 4.30
2014 9710 1.238439 CGCTCACAACCCTCAACAAT 58.762 50.000 0.00 0.00 0.00 2.71
2021 9717 0.465460 TTTCAAGCGCTCACAACCCT 60.465 50.000 12.06 0.00 0.00 4.34
2086 9785 4.099573 TCTGATTTCCTTCGAGTGGATACC 59.900 45.833 9.56 0.00 33.09 2.73
2096 9795 6.051717 ACCATAGTTCATCTGATTTCCTTCG 58.948 40.000 0.00 0.00 0.00 3.79
2171 9874 6.162777 TGTCAACAAAAGGTTTTCTTTGAGG 58.837 36.000 8.20 0.00 44.30 3.86
2225 9928 8.328758 TGAGGGATACAGTGAAATGAATAAACT 58.671 33.333 0.00 0.00 39.74 2.66
2227 9930 9.699410 AATGAGGGATACAGTGAAATGAATAAA 57.301 29.630 0.00 0.00 39.74 1.40
2248 9964 7.115378 GCCTGCATCCGAATTAAAATAAATGAG 59.885 37.037 0.00 0.00 0.00 2.90
2311 10027 5.066593 GGGACAGATCTTGAGACTGTTTTT 58.933 41.667 13.55 0.00 43.49 1.94
2312 10028 4.505742 GGGGACAGATCTTGAGACTGTTTT 60.506 45.833 13.55 0.00 43.49 2.43
2313 10029 3.008485 GGGGACAGATCTTGAGACTGTTT 59.992 47.826 13.55 0.00 43.49 2.83
2331 10047 2.037367 CGAGGTCACTGGAGGGGA 59.963 66.667 0.00 0.00 0.00 4.81
2332 10048 2.283966 ACGAGGTCACTGGAGGGG 60.284 66.667 0.00 0.00 0.00 4.79
2333 10049 1.304547 AGACGAGGTCACTGGAGGG 60.305 63.158 0.00 0.00 34.60 4.30
2337 10053 0.896019 AGTGGAGACGAGGTCACTGG 60.896 60.000 0.00 0.00 38.80 4.00
2364 10080 3.904800 TCCAACACTTGACTTCTGACA 57.095 42.857 0.00 0.00 0.00 3.58
2375 10091 2.158769 TGAGCTGACACATCCAACACTT 60.159 45.455 0.00 0.00 0.00 3.16
2385 10101 4.702831 TGAATTGTAAGTGAGCTGACACA 58.297 39.130 5.98 0.00 42.45 3.72
2386 10102 5.237344 AGTTGAATTGTAAGTGAGCTGACAC 59.763 40.000 5.98 1.24 35.87 3.67
2387 10103 5.368145 AGTTGAATTGTAAGTGAGCTGACA 58.632 37.500 5.98 0.00 34.34 3.58
2388 10104 5.106908 GGAGTTGAATTGTAAGTGAGCTGAC 60.107 44.000 0.00 0.00 0.00 3.51
2389 10105 4.997395 GGAGTTGAATTGTAAGTGAGCTGA 59.003 41.667 0.00 0.00 0.00 4.26
2390 10106 4.154918 GGGAGTTGAATTGTAAGTGAGCTG 59.845 45.833 0.00 0.00 0.00 4.24
2406 10125 1.669115 CACAGTGCGGAGGGAGTTG 60.669 63.158 0.00 0.00 0.00 3.16
2412 10131 2.734723 CGACACACAGTGCGGAGG 60.735 66.667 0.00 0.00 36.98 4.30
2419 10138 2.588877 GCACCAGCGACACACAGT 60.589 61.111 0.00 0.00 0.00 3.55
2440 10159 4.072131 CGAGGAAGAAAAGAACCAATGGA 58.928 43.478 6.16 0.00 0.00 3.41
2443 10162 5.335976 GCAATCGAGGAAGAAAAGAACCAAT 60.336 40.000 0.00 0.00 0.00 3.16
2451 10170 1.464608 CGCAGCAATCGAGGAAGAAAA 59.535 47.619 0.00 0.00 0.00 2.29
2478 10197 3.371380 GGAGCCATCAAGAGTGGAAGAAT 60.371 47.826 0.00 0.00 39.12 2.40
2494 10213 2.656646 CGCACAGTAGTGGAGCCA 59.343 61.111 1.92 0.00 45.98 4.75
2512 10303 0.249073 ACACACGTGTCTCAGCAGTC 60.249 55.000 20.49 0.00 40.24 3.51
2513 10304 0.175760 AACACACGTGTCTCAGCAGT 59.824 50.000 20.49 9.11 44.13 4.40
2570 10585 5.813080 AAAGTAACACTCAAACACAGGAC 57.187 39.130 0.00 0.00 0.00 3.85
2580 10595 6.756074 CCAATCAAAAGCAAAAGTAACACTCA 59.244 34.615 0.00 0.00 0.00 3.41
2595 10612 0.388907 CGGGCAGCACCAATCAAAAG 60.389 55.000 0.00 0.00 42.05 2.27
2601 10618 0.616371 TACTTACGGGCAGCACCAAT 59.384 50.000 0.00 0.00 42.05 3.16
2611 10628 6.315393 AGCACACAAGAAATAATACTTACGGG 59.685 38.462 0.00 0.00 0.00 5.28
2612 10629 7.064134 TCAGCACACAAGAAATAATACTTACGG 59.936 37.037 0.00 0.00 0.00 4.02
2614 10631 9.151471 TCTCAGCACACAAGAAATAATACTTAC 57.849 33.333 0.00 0.00 0.00 2.34
2616 10633 8.621532 TTCTCAGCACACAAGAAATAATACTT 57.378 30.769 0.00 0.00 0.00 2.24
2617 10634 7.880195 ACTTCTCAGCACACAAGAAATAATACT 59.120 33.333 0.00 0.00 0.00 2.12
2619 10636 9.151471 GTACTTCTCAGCACACAAGAAATAATA 57.849 33.333 0.00 0.00 0.00 0.98
2620 10637 7.880195 AGTACTTCTCAGCACACAAGAAATAAT 59.120 33.333 0.00 0.00 0.00 1.28
2641 11107 7.040755 CCAGAAGTCATGAGATATCGAAGTACT 60.041 40.741 0.00 0.00 0.00 2.73
2658 11124 0.905357 GCTTAGCCCTCCAGAAGTCA 59.095 55.000 0.00 0.00 0.00 3.41
2682 11148 9.582431 GTTCAGCTACAATACTGTACTGAAATA 57.418 33.333 20.55 6.74 45.28 1.40
2684 11150 7.667557 AGTTCAGCTACAATACTGTACTGAAA 58.332 34.615 20.55 10.10 45.28 2.69
2694 11244 4.932200 ACTGCAGAAGTTCAGCTACAATAC 59.068 41.667 23.35 0.00 34.57 1.89
2731 11281 2.391616 TCACATCAGACATCCAGCAC 57.608 50.000 0.00 0.00 0.00 4.40
2739 11289 4.644498 TCAGATTTGCTTCACATCAGACA 58.356 39.130 0.00 0.00 0.00 3.41
2771 11412 1.160137 GTGAGGGCTTGTAACTGCTG 58.840 55.000 0.00 0.00 0.00 4.41
2811 11452 5.804639 TCACATGGTGACTGCTATAACTTT 58.195 37.500 0.00 0.00 37.67 2.66
2881 11522 3.274288 CTCTAGAGGGAAACAATGGCAC 58.726 50.000 12.27 0.00 0.00 5.01
2883 11524 3.636153 ACTCTAGAGGGAAACAATGGC 57.364 47.619 23.50 0.00 0.00 4.40
2885 11526 6.293004 AGAGAACTCTAGAGGGAAACAATG 57.707 41.667 23.50 0.00 38.35 2.82
2891 11980 2.092321 CCCGAGAGAACTCTAGAGGGAA 60.092 54.545 23.50 0.00 44.67 3.97
2901 11990 2.223803 AGATCACACCCGAGAGAACT 57.776 50.000 0.00 0.00 0.00 3.01
2902 11991 2.028930 ACAAGATCACACCCGAGAGAAC 60.029 50.000 0.00 0.00 0.00 3.01
2903 11992 2.248248 ACAAGATCACACCCGAGAGAA 58.752 47.619 0.00 0.00 0.00 2.87
2904 11993 1.924731 ACAAGATCACACCCGAGAGA 58.075 50.000 0.00 0.00 0.00 3.10
2905 11994 2.738846 CAAACAAGATCACACCCGAGAG 59.261 50.000 0.00 0.00 0.00 3.20
2906 11995 2.549992 CCAAACAAGATCACACCCGAGA 60.550 50.000 0.00 0.00 0.00 4.04
2910 12491 1.203001 TCCCCAAACAAGATCACACCC 60.203 52.381 0.00 0.00 0.00 4.61
2915 12496 3.624707 GCCATAGTCCCCAAACAAGATCA 60.625 47.826 0.00 0.00 0.00 2.92
2931 12512 3.059597 CGGAATTTTAGCAGTCGCCATAG 60.060 47.826 0.00 0.00 39.83 2.23
2932 12513 2.869801 CGGAATTTTAGCAGTCGCCATA 59.130 45.455 0.00 0.00 39.83 2.74
2937 12518 4.863131 AGTTCTACGGAATTTTAGCAGTCG 59.137 41.667 0.00 0.00 33.71 4.18
2948 12529 9.886132 ATTCATTTACACTTAGTTCTACGGAAT 57.114 29.630 0.00 0.00 33.71 3.01
2950 12531 9.715121 AAATTCATTTACACTTAGTTCTACGGA 57.285 29.630 0.00 0.00 0.00 4.69
2951 12532 9.968743 GAAATTCATTTACACTTAGTTCTACGG 57.031 33.333 0.00 0.00 0.00 4.02
2972 12559 7.559170 CCCTGACCATCATCTCTAAAAGAAATT 59.441 37.037 0.00 0.00 37.61 1.82
3007 12615 7.907045 CAGAACACATGCTGTCAAGATTAATAC 59.093 37.037 0.00 0.00 30.29 1.89
3062 12671 1.806542 ACTACTGGATTTGCTTGTGCG 59.193 47.619 0.00 0.00 43.34 5.34


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

AutoCloner maintained by Alex Coulton.