Multiple sequence alignment - TraesCS1B01G097200

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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 TraesCS1B01G097200 chr1B 100.000 2935 0 0 1 2935 101518246 101521180 0.000000e+00 5421
1 TraesCS1B01G097200 chr1B 97.826 644 14 0 1 644 551885679 551886322 0.000000e+00 1112
2 TraesCS1B01G097200 chr1B 97.372 647 17 0 1 647 675678716 675679362 0.000000e+00 1101
3 TraesCS1B01G097200 chr1B 92.935 736 49 3 2202 2935 649377146 649376412 0.000000e+00 1068
4 TraesCS1B01G097200 chr1B 92.537 737 51 4 2202 2935 586065044 586064309 0.000000e+00 1053
5 TraesCS1B01G097200 chr1B 93.030 703 42 2 1408 2103 101591293 101590591 0.000000e+00 1020
6 TraesCS1B01G097200 chr1B 90.018 571 22 11 656 1199 101592160 101591598 0.000000e+00 706
7 TraesCS1B01G097200 chr1B 88.636 132 12 2 1192 1320 101591513 101591382 1.090000e-34 158
8 TraesCS1B01G097200 chr7B 96.933 652 20 0 1 652 493502750 493502099 0.000000e+00 1094
9 TraesCS1B01G097200 chr7B 93.324 734 48 1 2202 2935 678804797 678805529 0.000000e+00 1083
10 TraesCS1B01G097200 chr7B 92.673 737 47 7 2202 2935 555781921 555782653 0.000000e+00 1055
11 TraesCS1B01G097200 chr2B 93.443 732 47 1 2202 2933 213548250 213547520 0.000000e+00 1085
12 TraesCS1B01G097200 chr2B 92.925 735 49 3 2202 2935 382413140 382413872 0.000000e+00 1066
13 TraesCS1B01G097200 chr6B 96.899 645 20 0 1 645 592447470 592448114 0.000000e+00 1081
14 TraesCS1B01G097200 chr6B 96.600 647 22 0 1 647 567497561 567498207 0.000000e+00 1074
15 TraesCS1B01G097200 chr6B 92.643 734 52 2 2202 2935 435743004 435743735 0.000000e+00 1055
16 TraesCS1B01G097200 chr5B 96.899 645 20 0 1 645 464625504 464626148 0.000000e+00 1081
17 TraesCS1B01G097200 chr5B 96.899 645 20 0 1 645 556174779 556175423 0.000000e+00 1081
18 TraesCS1B01G097200 chr5B 92.507 734 54 1 2202 2935 466663224 466663956 0.000000e+00 1050
19 TraesCS1B01G097200 chr5B 80.000 385 58 16 1527 1900 588156355 588155979 1.730000e-67 267
20 TraesCS1B01G097200 chr5B 77.934 426 85 8 1472 1891 441811578 441811156 1.040000e-64 257
21 TraesCS1B01G097200 chr3B 96.764 649 20 1 1 649 21963848 21963201 0.000000e+00 1081
22 TraesCS1B01G097200 chr3B 96.904 646 19 1 1 645 38043971 38044616 0.000000e+00 1081
23 TraesCS1B01G097200 chr1D 92.713 741 36 7 1410 2136 63544003 63544739 0.000000e+00 1053
24 TraesCS1B01G097200 chr1D 90.030 672 32 21 646 1286 63543203 63543870 0.000000e+00 837
25 TraesCS1B01G097200 chr4B 92.527 736 47 6 2202 2935 548205082 548204353 0.000000e+00 1048
26 TraesCS1B01G097200 chr1A 89.750 800 74 3 1341 2139 61714071 61714863 0.000000e+00 1016
27 TraesCS1B01G097200 chr1A 89.723 759 52 12 1400 2143 61576277 61577024 0.000000e+00 946
28 TraesCS1B01G097200 chr1A 88.796 714 36 20 645 1325 61575470 61576172 0.000000e+00 835
29 TraesCS1B01G097200 chr1A 83.163 588 46 28 775 1327 61713442 61714011 3.400000e-134 488
30 TraesCS1B01G097200 chr5A 82.235 349 50 12 1558 1900 598637650 598637308 1.030000e-74 291
31 TraesCS1B01G097200 chr5A 88.387 155 18 0 1001 1155 616878691 616878845 1.390000e-43 187
32 TraesCS1B01G097200 chr5D 80.779 385 55 16 1527 1900 480154929 480154553 1.720000e-72 283
33 TraesCS1B01G097200 chr5D 77.704 453 90 10 1472 1917 371872591 371872143 1.730000e-67 267
34 TraesCS1B01G097200 chr5D 87.179 156 20 0 1001 1156 493833640 493833795 8.360000e-41 178
35 TraesCS1B01G097200 chr6D 82.143 308 37 9 999 1288 6982172 6982479 6.280000e-62 248
36 TraesCS1B01G097200 chr2D 86.512 215 26 2 964 1178 597939498 597939709 1.760000e-57 233
37 TraesCS1B01G097200 chr2D 86.512 215 26 2 964 1178 641960763 641960974 1.760000e-57 233


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 TraesCS1B01G097200 chr1B 101518246 101521180 2934 False 5421.0 5421 100.000000 1 2935 1 chr1B.!!$F1 2934
1 TraesCS1B01G097200 chr1B 551885679 551886322 643 False 1112.0 1112 97.826000 1 644 1 chr1B.!!$F2 643
2 TraesCS1B01G097200 chr1B 675678716 675679362 646 False 1101.0 1101 97.372000 1 647 1 chr1B.!!$F3 646
3 TraesCS1B01G097200 chr1B 649376412 649377146 734 True 1068.0 1068 92.935000 2202 2935 1 chr1B.!!$R2 733
4 TraesCS1B01G097200 chr1B 586064309 586065044 735 True 1053.0 1053 92.537000 2202 2935 1 chr1B.!!$R1 733
5 TraesCS1B01G097200 chr1B 101590591 101592160 1569 True 628.0 1020 90.561333 656 2103 3 chr1B.!!$R3 1447
6 TraesCS1B01G097200 chr7B 493502099 493502750 651 True 1094.0 1094 96.933000 1 652 1 chr7B.!!$R1 651
7 TraesCS1B01G097200 chr7B 678804797 678805529 732 False 1083.0 1083 93.324000 2202 2935 1 chr7B.!!$F2 733
8 TraesCS1B01G097200 chr7B 555781921 555782653 732 False 1055.0 1055 92.673000 2202 2935 1 chr7B.!!$F1 733
9 TraesCS1B01G097200 chr2B 213547520 213548250 730 True 1085.0 1085 93.443000 2202 2933 1 chr2B.!!$R1 731
10 TraesCS1B01G097200 chr2B 382413140 382413872 732 False 1066.0 1066 92.925000 2202 2935 1 chr2B.!!$F1 733
11 TraesCS1B01G097200 chr6B 592447470 592448114 644 False 1081.0 1081 96.899000 1 645 1 chr6B.!!$F3 644
12 TraesCS1B01G097200 chr6B 567497561 567498207 646 False 1074.0 1074 96.600000 1 647 1 chr6B.!!$F2 646
13 TraesCS1B01G097200 chr6B 435743004 435743735 731 False 1055.0 1055 92.643000 2202 2935 1 chr6B.!!$F1 733
14 TraesCS1B01G097200 chr5B 464625504 464626148 644 False 1081.0 1081 96.899000 1 645 1 chr5B.!!$F1 644
15 TraesCS1B01G097200 chr5B 556174779 556175423 644 False 1081.0 1081 96.899000 1 645 1 chr5B.!!$F3 644
16 TraesCS1B01G097200 chr5B 466663224 466663956 732 False 1050.0 1050 92.507000 2202 2935 1 chr5B.!!$F2 733
17 TraesCS1B01G097200 chr3B 21963201 21963848 647 True 1081.0 1081 96.764000 1 649 1 chr3B.!!$R1 648
18 TraesCS1B01G097200 chr3B 38043971 38044616 645 False 1081.0 1081 96.904000 1 645 1 chr3B.!!$F1 644
19 TraesCS1B01G097200 chr1D 63543203 63544739 1536 False 945.0 1053 91.371500 646 2136 2 chr1D.!!$F1 1490
20 TraesCS1B01G097200 chr4B 548204353 548205082 729 True 1048.0 1048 92.527000 2202 2935 1 chr4B.!!$R1 733
21 TraesCS1B01G097200 chr1A 61575470 61577024 1554 False 890.5 946 89.259500 645 2143 2 chr1A.!!$F1 1498
22 TraesCS1B01G097200 chr1A 61713442 61714863 1421 False 752.0 1016 86.456500 775 2139 2 chr1A.!!$F2 1364

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
827 853 0.772124 TCCCCTGCTCTTTCACCCTT 60.772 55.0 0.0 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2028 2271 0.318955 GCAATTCCAGCCACACACAC 60.319 55.0 0.0 0.0 0.0 3.82 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
218 219 3.953775 CCTGCACCAAGACCCGGT 61.954 66.667 0.00 0.00 37.16 5.28
229 230 2.819608 CAAGACCCGGTCACATTTGAAT 59.180 45.455 19.95 0.00 34.60 2.57
374 375 7.479980 TGTTCAGTCAAGACAATTTCGATTTT 58.520 30.769 2.72 0.00 0.00 1.82
453 454 5.667539 TTTCAGACAAACATTTGGGTTGA 57.332 34.783 9.09 6.49 42.34 3.18
630 633 2.968697 GTTCGTTTGGGGTCGCGT 60.969 61.111 5.77 0.00 0.00 6.01
640 643 2.652530 GGTCGCGTGGTGGAGTTA 59.347 61.111 5.77 0.00 0.00 2.24
748 759 4.184629 GCTGTTCTAGAAACATCACGGAT 58.815 43.478 6.78 0.00 0.00 4.18
770 781 2.297895 AATGGCACCCACCTCGCTA 61.298 57.895 0.00 0.00 35.80 4.26
773 784 2.345991 GCACCCACCTCGCTAACA 59.654 61.111 0.00 0.00 0.00 2.41
813 839 2.923035 CACACCTCACGGTCCCCT 60.923 66.667 0.00 0.00 43.24 4.79
814 840 2.923035 ACACCTCACGGTCCCCTG 60.923 66.667 0.00 0.00 43.24 4.45
820 846 1.831652 CTCACGGTCCCCTGCTCTTT 61.832 60.000 0.00 0.00 0.00 2.52
821 847 1.376037 CACGGTCCCCTGCTCTTTC 60.376 63.158 0.00 0.00 0.00 2.62
825 851 1.002011 GTCCCCTGCTCTTTCACCC 60.002 63.158 0.00 0.00 0.00 4.61
827 853 0.772124 TCCCCTGCTCTTTCACCCTT 60.772 55.000 0.00 0.00 0.00 3.95
924 960 2.177531 GTTGGCGTCATGCTGCAG 59.822 61.111 10.11 10.11 45.43 4.41
997 1065 1.298859 CGTGTAGCAACCAAGGGAGC 61.299 60.000 0.00 0.00 0.00 4.70
1165 1233 1.203287 GAAACGTAAGCTACCCGACCT 59.797 52.381 6.60 0.00 45.62 3.85
1187 1255 3.832490 TCTCAAATCCTCTGGTTTCTCGA 59.168 43.478 0.00 0.00 0.00 4.04
1203 1363 4.829064 TCTCGAATCAACTTGTTTTGGG 57.171 40.909 0.00 0.00 0.00 4.12
1223 1383 3.256631 GGGTCTGATGCAAGATGTTTTGT 59.743 43.478 0.00 0.00 0.00 2.83
1236 1396 2.626840 TGTTTTGTTTTCTTGCAGCCC 58.373 42.857 0.00 0.00 0.00 5.19
1288 1451 3.553922 GGATCTGCTTCTCTTCGGTATGG 60.554 52.174 0.00 0.00 0.00 2.74
1289 1452 1.137086 TCTGCTTCTCTTCGGTATGGC 59.863 52.381 0.00 0.00 0.00 4.40
1291 1454 0.466124 GCTTCTCTTCGGTATGGCCT 59.534 55.000 3.32 0.00 34.25 5.19
1292 1455 1.134371 GCTTCTCTTCGGTATGGCCTT 60.134 52.381 3.32 0.00 34.25 4.35
1293 1456 2.555199 CTTCTCTTCGGTATGGCCTTG 58.445 52.381 3.32 0.00 34.25 3.61
1294 1457 0.830648 TCTCTTCGGTATGGCCTTGG 59.169 55.000 3.32 0.00 34.25 3.61
1295 1458 0.815615 CTCTTCGGTATGGCCTTGGC 60.816 60.000 3.32 2.49 34.25 4.52
1296 1459 1.224592 CTTCGGTATGGCCTTGGCT 59.775 57.895 11.71 0.00 34.25 4.75
1320 1498 7.628580 GCTCTTTTCAGTTACTTTGTCCTTGTT 60.629 37.037 0.00 0.00 0.00 2.83
1330 1508 9.888878 GTTACTTTGTCCTTGTTAAAATACTCC 57.111 33.333 0.00 0.00 0.00 3.85
1331 1509 7.520451 ACTTTGTCCTTGTTAAAATACTCCC 57.480 36.000 0.00 0.00 0.00 4.30
1333 1511 7.447545 ACTTTGTCCTTGTTAAAATACTCCCTC 59.552 37.037 0.00 0.00 0.00 4.30
1335 1513 4.874396 GTCCTTGTTAAAATACTCCCTCCG 59.126 45.833 0.00 0.00 0.00 4.63
1337 1515 4.874396 CCTTGTTAAAATACTCCCTCCGTC 59.126 45.833 0.00 0.00 0.00 4.79
1338 1516 4.476628 TGTTAAAATACTCCCTCCGTCC 57.523 45.455 0.00 0.00 0.00 4.79
1339 1517 3.119029 TGTTAAAATACTCCCTCCGTCCG 60.119 47.826 0.00 0.00 0.00 4.79
1343 1567 1.856629 ATACTCCCTCCGTCCGAAAA 58.143 50.000 0.00 0.00 0.00 2.29
1385 1616 9.442047 AAGGAAAGTAGAGTATTGAAGTGAATG 57.558 33.333 0.00 0.00 0.00 2.67
1392 1623 7.372260 AGAGTATTGAAGTGAATGATAGCCT 57.628 36.000 0.00 0.00 0.00 4.58
1438 1669 5.406780 GCTCGGTGTCCAAATATCTTATCAG 59.593 44.000 0.00 0.00 0.00 2.90
1556 1788 0.112412 GGGAAGGCAACCTGAAGGAA 59.888 55.000 2.62 0.00 38.94 3.36
1718 1950 0.990374 AGCTCAAGAAGGTGCTGGAT 59.010 50.000 0.00 0.00 33.44 3.41
1729 1961 0.818296 GTGCTGGATGTCTACGAGGT 59.182 55.000 0.00 0.00 0.00 3.85
1733 1965 1.065928 GGATGTCTACGAGGTGCGG 59.934 63.158 0.00 0.00 46.49 5.69
1767 1999 0.971447 GTACCTCGCTGGGGACTTCT 60.971 60.000 1.29 0.00 41.11 2.85
1799 2031 2.197465 GACCTCAACCACTTCCCCTAT 58.803 52.381 0.00 0.00 0.00 2.57
1889 2121 3.543536 GAGGATCATGGCGAGGCCC 62.544 68.421 0.00 0.00 41.51 5.80
1940 2172 0.597568 CCAAGAAGCCGTGATTTGCA 59.402 50.000 0.00 0.00 0.00 4.08
2027 2270 2.472695 TAAGGCAAATGAGCTCGTGT 57.527 45.000 9.75 0.00 34.17 4.49
2028 2271 0.877071 AAGGCAAATGAGCTCGTGTG 59.123 50.000 20.18 20.18 34.17 3.82
2066 2317 2.949106 CCAGCGTGCAGTTTCTGG 59.051 61.111 8.49 8.49 39.95 3.86
2139 2394 6.514947 TCATAATGCTTCCATATTTGTTGCC 58.485 36.000 0.00 0.00 0.00 4.52
2140 2395 4.822685 AATGCTTCCATATTTGTTGCCA 57.177 36.364 0.00 0.00 0.00 4.92
2141 2396 4.822685 ATGCTTCCATATTTGTTGCCAA 57.177 36.364 0.00 0.00 0.00 4.52
2142 2397 4.191033 TGCTTCCATATTTGTTGCCAAG 57.809 40.909 0.00 0.00 0.00 3.61
2143 2398 3.577848 TGCTTCCATATTTGTTGCCAAGT 59.422 39.130 0.00 0.00 0.00 3.16
2144 2399 4.040217 TGCTTCCATATTTGTTGCCAAGTT 59.960 37.500 0.00 0.00 0.00 2.66
2145 2400 5.244851 TGCTTCCATATTTGTTGCCAAGTTA 59.755 36.000 0.00 0.00 0.00 2.24
2146 2401 6.070881 TGCTTCCATATTTGTTGCCAAGTTAT 60.071 34.615 0.00 0.00 0.00 1.89
2147 2402 6.818142 GCTTCCATATTTGTTGCCAAGTTATT 59.182 34.615 0.00 0.00 0.00 1.40
2148 2403 7.334171 GCTTCCATATTTGTTGCCAAGTTATTT 59.666 33.333 0.00 0.00 0.00 1.40
2149 2404 9.218440 CTTCCATATTTGTTGCCAAGTTATTTT 57.782 29.630 0.00 0.00 0.00 1.82
2150 2405 9.566432 TTCCATATTTGTTGCCAAGTTATTTTT 57.434 25.926 0.00 0.00 0.00 1.94
2151 2406 8.997323 TCCATATTTGTTGCCAAGTTATTTTTG 58.003 29.630 0.00 0.00 0.00 2.44
2152 2407 8.782144 CCATATTTGTTGCCAAGTTATTTTTGT 58.218 29.630 0.00 0.00 0.00 2.83
2155 2410 7.778470 TTTGTTGCCAAGTTATTTTTGTAGG 57.222 32.000 0.00 0.00 0.00 3.18
2156 2411 5.848406 TGTTGCCAAGTTATTTTTGTAGGG 58.152 37.500 0.00 0.00 0.00 3.53
2157 2412 5.598830 TGTTGCCAAGTTATTTTTGTAGGGA 59.401 36.000 0.00 0.00 0.00 4.20
2158 2413 6.268847 TGTTGCCAAGTTATTTTTGTAGGGAT 59.731 34.615 0.00 0.00 0.00 3.85
2159 2414 6.279513 TGCCAAGTTATTTTTGTAGGGATG 57.720 37.500 0.00 0.00 0.00 3.51
2160 2415 6.013379 TGCCAAGTTATTTTTGTAGGGATGA 58.987 36.000 0.00 0.00 0.00 2.92
2161 2416 6.495181 TGCCAAGTTATTTTTGTAGGGATGAA 59.505 34.615 0.00 0.00 0.00 2.57
2162 2417 6.811665 GCCAAGTTATTTTTGTAGGGATGAAC 59.188 38.462 0.00 0.00 0.00 3.18
2163 2418 7.524698 GCCAAGTTATTTTTGTAGGGATGAACA 60.525 37.037 0.00 0.00 0.00 3.18
2164 2419 8.364142 CCAAGTTATTTTTGTAGGGATGAACAA 58.636 33.333 0.00 0.00 0.00 2.83
2165 2420 9.757227 CAAGTTATTTTTGTAGGGATGAACAAA 57.243 29.630 0.00 0.00 0.00 2.83
2172 2427 8.885494 TTTTGTAGGGATGAACAAAAATTCTG 57.115 30.769 10.08 0.00 38.57 3.02
2173 2428 7.595819 TTGTAGGGATGAACAAAAATTCTGT 57.404 32.000 0.00 0.00 0.00 3.41
2174 2429 7.595819 TGTAGGGATGAACAAAAATTCTGTT 57.404 32.000 5.75 5.75 39.69 3.16
2175 2430 8.017418 TGTAGGGATGAACAAAAATTCTGTTT 57.983 30.769 7.17 0.00 37.14 2.83
2176 2431 7.925483 TGTAGGGATGAACAAAAATTCTGTTTG 59.075 33.333 7.17 4.00 40.95 2.93
2177 2432 5.759763 AGGGATGAACAAAAATTCTGTTTGC 59.240 36.000 7.17 0.00 39.16 3.68
2178 2433 5.049474 GGGATGAACAAAAATTCTGTTTGCC 60.049 40.000 7.17 8.45 39.16 4.52
2179 2434 5.526846 GGATGAACAAAAATTCTGTTTGCCA 59.473 36.000 7.17 4.20 39.16 4.92
2180 2435 6.205270 GGATGAACAAAAATTCTGTTTGCCAT 59.795 34.615 7.17 7.78 39.16 4.40
2181 2436 6.360844 TGAACAAAAATTCTGTTTGCCATG 57.639 33.333 7.17 0.00 39.16 3.66
2182 2437 6.111382 TGAACAAAAATTCTGTTTGCCATGA 58.889 32.000 0.00 0.00 39.16 3.07
2183 2438 6.766944 TGAACAAAAATTCTGTTTGCCATGAT 59.233 30.769 0.00 0.00 39.16 2.45
2184 2439 7.282675 TGAACAAAAATTCTGTTTGCCATGATT 59.717 29.630 0.00 0.00 39.16 2.57
2185 2440 7.571080 ACAAAAATTCTGTTTGCCATGATTT 57.429 28.000 0.00 0.00 39.16 2.17
2186 2441 7.998580 ACAAAAATTCTGTTTGCCATGATTTT 58.001 26.923 0.00 0.00 39.16 1.82
2187 2442 7.916450 ACAAAAATTCTGTTTGCCATGATTTTG 59.084 29.630 0.00 0.00 39.16 2.44
2188 2443 7.571080 AAAATTCTGTTTGCCATGATTTTGT 57.429 28.000 0.00 0.00 31.58 2.83
2189 2444 8.674263 AAAATTCTGTTTGCCATGATTTTGTA 57.326 26.923 0.00 0.00 31.58 2.41
2190 2445 7.894376 AATTCTGTTTGCCATGATTTTGTAG 57.106 32.000 0.00 0.00 0.00 2.74
2191 2446 5.389859 TCTGTTTGCCATGATTTTGTAGG 57.610 39.130 0.00 0.00 0.00 3.18
2192 2447 4.220382 TCTGTTTGCCATGATTTTGTAGGG 59.780 41.667 0.00 0.00 0.00 3.53
2193 2448 4.155709 TGTTTGCCATGATTTTGTAGGGA 58.844 39.130 0.00 0.00 0.00 4.20
2194 2449 4.776837 TGTTTGCCATGATTTTGTAGGGAT 59.223 37.500 0.00 0.00 0.00 3.85
2195 2450 5.954752 TGTTTGCCATGATTTTGTAGGGATA 59.045 36.000 0.00 0.00 0.00 2.59
2196 2451 6.438741 TGTTTGCCATGATTTTGTAGGGATAA 59.561 34.615 0.00 0.00 0.00 1.75
2197 2452 7.125507 TGTTTGCCATGATTTTGTAGGGATAAT 59.874 33.333 0.00 0.00 0.00 1.28
2198 2453 6.899393 TGCCATGATTTTGTAGGGATAATC 57.101 37.500 0.00 0.00 0.00 1.75
2199 2454 6.613699 TGCCATGATTTTGTAGGGATAATCT 58.386 36.000 0.00 0.00 0.00 2.40
2200 2455 7.068702 TGCCATGATTTTGTAGGGATAATCTT 58.931 34.615 0.00 0.00 0.00 2.40
2352 2608 2.291365 TGGATCTGAACATTCATGCCG 58.709 47.619 0.00 0.00 36.46 5.69
2620 2877 7.119553 CCATATTGCTGTTTTATTGCCTGTTTT 59.880 33.333 0.00 0.00 0.00 2.43
2760 3017 2.290745 GCCCAGGAGATAGGGGGT 59.709 66.667 0.00 0.00 45.58 4.95
2861 3120 6.138967 ACCCTACGTACCCTAAAACTATCAT 58.861 40.000 0.00 0.00 0.00 2.45
2890 3149 4.411927 AGATAGATCGGTAGTTCTGCCAT 58.588 43.478 7.62 0.98 0.00 4.40
2906 3165 1.001406 GCCATCGCAAGCCTCTATAGT 59.999 52.381 0.00 0.00 34.03 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
218 219 8.087750 GGAATTGGACAAACTATTCAAATGTGA 58.912 33.333 0.00 0.00 0.00 3.58
229 230 4.900684 TCACGATGGAATTGGACAAACTA 58.099 39.130 0.00 0.00 29.54 2.24
453 454 7.441017 TGCCTAAATTTGCATCAAACTACTTT 58.559 30.769 0.00 0.00 36.13 2.66
630 633 2.289819 CGGTTTTAGGCTAACTCCACCA 60.290 50.000 19.88 0.00 0.00 4.17
640 643 3.773119 TCATCTTCCTACGGTTTTAGGCT 59.227 43.478 0.00 0.00 38.92 4.58
748 759 1.302949 GAGGTGGGTGCCATTGCTA 59.697 57.895 0.00 0.00 35.28 3.49
770 781 2.747446 GACGGGTGCAGTCAATTATGTT 59.253 45.455 0.00 0.00 38.42 2.71
773 784 2.779755 TGACGGGTGCAGTCAATTAT 57.220 45.000 4.89 0.00 44.56 1.28
813 839 1.774254 TCTCCAAAGGGTGAAAGAGCA 59.226 47.619 0.00 0.00 33.89 4.26
814 840 2.431454 CTCTCCAAAGGGTGAAAGAGC 58.569 52.381 0.00 0.00 36.32 4.09
820 846 0.687354 GTGAGCTCTCCAAAGGGTGA 59.313 55.000 16.19 0.00 35.48 4.02
821 847 0.671781 CGTGAGCTCTCCAAAGGGTG 60.672 60.000 16.19 0.00 34.93 4.61
825 851 0.318441 TGGACGTGAGCTCTCCAAAG 59.682 55.000 18.27 2.34 30.81 2.77
827 853 0.033504 GTTGGACGTGAGCTCTCCAA 59.966 55.000 24.70 24.70 40.97 3.53
924 960 1.661112 GCTATCTGTGTTTGAGCGGTC 59.339 52.381 7.89 7.89 0.00 4.79
945 984 0.040425 GATCGGGTGTGTGTTTGTGC 60.040 55.000 0.00 0.00 0.00 4.57
997 1065 2.179018 CTTCACCGGCGCCATTTG 59.821 61.111 28.98 19.39 0.00 2.32
1157 1225 1.196012 GAGGATTTGAGAGGTCGGGT 58.804 55.000 0.00 0.00 0.00 5.28
1165 1233 3.832490 TCGAGAAACCAGAGGATTTGAGA 59.168 43.478 0.00 0.00 0.00 3.27
1187 1255 5.739935 GCATCAGACCCAAAACAAGTTGATT 60.740 40.000 10.54 0.23 0.00 2.57
1203 1363 6.698766 AGAAAACAAAACATCTTGCATCAGAC 59.301 34.615 0.00 0.00 0.00 3.51
1236 1396 2.418083 GGCAGGGATTTGGCCGAAG 61.418 63.158 12.01 0.00 38.04 3.79
1288 1451 3.149981 AGTAACTGAAAAGAGCCAAGGC 58.850 45.455 2.02 2.02 42.33 4.35
1289 1452 5.067805 ACAAAGTAACTGAAAAGAGCCAAGG 59.932 40.000 0.00 0.00 0.00 3.61
1291 1454 5.067283 GGACAAAGTAACTGAAAAGAGCCAA 59.933 40.000 0.00 0.00 0.00 4.52
1292 1455 4.578928 GGACAAAGTAACTGAAAAGAGCCA 59.421 41.667 0.00 0.00 0.00 4.75
1293 1456 4.822350 AGGACAAAGTAACTGAAAAGAGCC 59.178 41.667 0.00 0.00 0.00 4.70
1294 1457 6.183360 ACAAGGACAAAGTAACTGAAAAGAGC 60.183 38.462 0.00 0.00 0.00 4.09
1295 1458 7.321745 ACAAGGACAAAGTAACTGAAAAGAG 57.678 36.000 0.00 0.00 0.00 2.85
1296 1459 7.696992 AACAAGGACAAAGTAACTGAAAAGA 57.303 32.000 0.00 0.00 0.00 2.52
1320 1498 3.017048 TCGGACGGAGGGAGTATTTTA 57.983 47.619 0.00 0.00 0.00 1.52
1327 1505 0.535335 TCATTTTCGGACGGAGGGAG 59.465 55.000 0.00 0.00 0.00 4.30
1329 1507 1.670811 CATTCATTTTCGGACGGAGGG 59.329 52.381 0.00 0.00 0.00 4.30
1330 1508 1.064060 GCATTCATTTTCGGACGGAGG 59.936 52.381 0.00 0.00 0.00 4.30
1331 1509 2.009774 AGCATTCATTTTCGGACGGAG 58.990 47.619 0.00 0.00 0.00 4.63
1333 1511 2.785679 GAAGCATTCATTTTCGGACGG 58.214 47.619 0.00 0.00 46.62 4.79
1385 1616 5.949735 TCGGAAACAAATTTGAAGGCTATC 58.050 37.500 24.64 10.45 0.00 2.08
1392 1623 4.541779 CGTCCATCGGAAACAAATTTGAA 58.458 39.130 24.64 3.39 31.38 2.69
1454 1685 7.412563 CGTGACTCTGAAAACACAAGAAAACTA 60.413 37.037 0.00 0.00 33.56 2.24
1455 1686 6.612306 GTGACTCTGAAAACACAAGAAAACT 58.388 36.000 0.00 0.00 34.05 2.66
1556 1788 2.252072 ATACGTCCACCATTGCCGCT 62.252 55.000 0.00 0.00 0.00 5.52
1718 1950 2.675423 AGCCGCACCTCGTAGACA 60.675 61.111 0.00 0.00 36.19 3.41
1757 1989 0.321671 CGAAGCTGAAGAAGTCCCCA 59.678 55.000 0.00 0.00 0.00 4.96
1799 2031 2.167693 CGTGGCCATGAAGTAGAAGGTA 59.832 50.000 21.08 0.00 0.00 3.08
1889 2121 3.843240 GCGAGCTTCTTGACGGCG 61.843 66.667 4.80 4.80 0.00 6.46
1965 2197 2.543445 CGCCACACAGATCAGAGATCTC 60.543 54.545 15.29 15.29 0.00 2.75
2027 2270 1.031235 CAATTCCAGCCACACACACA 58.969 50.000 0.00 0.00 0.00 3.72
2028 2271 0.318955 GCAATTCCAGCCACACACAC 60.319 55.000 0.00 0.00 0.00 3.82
2063 2314 2.332514 CACACACGCAAAGCCCAG 59.667 61.111 0.00 0.00 0.00 4.45
2066 2317 2.026014 CCACACACACGCAAAGCC 59.974 61.111 0.00 0.00 0.00 4.35
2139 2394 9.757227 TTTGTTCATCCCTACAAAAATAACTTG 57.243 29.630 0.00 0.00 40.26 3.16
2147 2402 8.482128 ACAGAATTTTTGTTCATCCCTACAAAA 58.518 29.630 8.56 8.56 46.61 2.44
2148 2403 8.017418 ACAGAATTTTTGTTCATCCCTACAAA 57.983 30.769 0.00 0.00 41.16 2.83
2149 2404 7.595819 ACAGAATTTTTGTTCATCCCTACAA 57.404 32.000 0.00 0.00 32.76 2.41
2150 2405 7.595819 AACAGAATTTTTGTTCATCCCTACA 57.404 32.000 0.00 0.00 33.72 2.74
2151 2406 7.095649 GCAAACAGAATTTTTGTTCATCCCTAC 60.096 37.037 5.85 0.00 37.77 3.18
2152 2407 6.928492 GCAAACAGAATTTTTGTTCATCCCTA 59.072 34.615 5.85 0.00 37.77 3.53
2153 2408 5.759763 GCAAACAGAATTTTTGTTCATCCCT 59.240 36.000 5.85 0.00 37.77 4.20
2154 2409 5.049474 GGCAAACAGAATTTTTGTTCATCCC 60.049 40.000 5.85 2.01 37.77 3.85
2155 2410 5.526846 TGGCAAACAGAATTTTTGTTCATCC 59.473 36.000 5.85 7.89 37.77 3.51
2156 2411 6.601741 TGGCAAACAGAATTTTTGTTCATC 57.398 33.333 5.85 0.84 37.77 2.92
2157 2412 6.766944 TCATGGCAAACAGAATTTTTGTTCAT 59.233 30.769 5.85 3.54 37.77 2.57
2158 2413 6.111382 TCATGGCAAACAGAATTTTTGTTCA 58.889 32.000 5.85 1.54 37.77 3.18
2159 2414 6.601741 TCATGGCAAACAGAATTTTTGTTC 57.398 33.333 5.85 0.00 37.77 3.18
2160 2415 7.571080 AATCATGGCAAACAGAATTTTTGTT 57.429 28.000 0.00 0.00 40.30 2.83
2161 2416 7.571080 AAATCATGGCAAACAGAATTTTTGT 57.429 28.000 0.00 0.00 36.50 2.83
2162 2417 7.916450 ACAAAATCATGGCAAACAGAATTTTTG 59.084 29.630 0.00 5.75 36.11 2.44
2163 2418 7.998580 ACAAAATCATGGCAAACAGAATTTTT 58.001 26.923 0.00 0.00 36.11 1.94
2164 2419 7.571080 ACAAAATCATGGCAAACAGAATTTT 57.429 28.000 0.00 0.00 37.49 1.82
2165 2420 7.388500 CCTACAAAATCATGGCAAACAGAATTT 59.612 33.333 0.00 0.00 31.94 1.82
2166 2421 6.875195 CCTACAAAATCATGGCAAACAGAATT 59.125 34.615 0.00 0.00 0.00 2.17
2167 2422 6.400568 CCTACAAAATCATGGCAAACAGAAT 58.599 36.000 0.00 0.00 0.00 2.40
2168 2423 5.279406 CCCTACAAAATCATGGCAAACAGAA 60.279 40.000 0.00 0.00 0.00 3.02
2169 2424 4.220382 CCCTACAAAATCATGGCAAACAGA 59.780 41.667 0.00 0.00 0.00 3.41
2170 2425 4.220382 TCCCTACAAAATCATGGCAAACAG 59.780 41.667 0.00 0.00 0.00 3.16
2171 2426 4.155709 TCCCTACAAAATCATGGCAAACA 58.844 39.130 0.00 0.00 0.00 2.83
2172 2427 4.799564 TCCCTACAAAATCATGGCAAAC 57.200 40.909 0.00 0.00 0.00 2.93
2173 2428 7.564660 AGATTATCCCTACAAAATCATGGCAAA 59.435 33.333 0.00 0.00 32.04 3.68
2174 2429 7.068702 AGATTATCCCTACAAAATCATGGCAA 58.931 34.615 0.00 0.00 32.04 4.52
2175 2430 6.613699 AGATTATCCCTACAAAATCATGGCA 58.386 36.000 0.00 0.00 32.04 4.92
2176 2431 7.309438 GGAAGATTATCCCTACAAAATCATGGC 60.309 40.741 0.00 0.00 33.05 4.40
2177 2432 7.946776 AGGAAGATTATCCCTACAAAATCATGG 59.053 37.037 0.00 0.00 40.59 3.66
2178 2433 8.930846 AGGAAGATTATCCCTACAAAATCATG 57.069 34.615 0.00 0.00 40.59 3.07
2180 2435 9.847224 GTTAGGAAGATTATCCCTACAAAATCA 57.153 33.333 0.00 0.00 40.59 2.57
2197 2452 9.976511 CCGTACAAAATCATATAGTTAGGAAGA 57.023 33.333 0.00 0.00 0.00 2.87
2198 2453 9.976511 TCCGTACAAAATCATATAGTTAGGAAG 57.023 33.333 0.00 0.00 0.00 3.46
2200 2455 9.923143 CATCCGTACAAAATCATATAGTTAGGA 57.077 33.333 0.00 0.00 0.00 2.94
2221 2476 3.641437 TGGCAAAAGAAAGTTCATCCG 57.359 42.857 0.00 0.00 0.00 4.18
2573 2830 1.420430 CTGGGCCTCCGGTTAATAGA 58.580 55.000 4.53 0.00 34.69 1.98
2727 2984 0.391228 GGGCTCCTCGAGGATCTTTC 59.609 60.000 33.66 19.55 44.46 2.62
2728 2985 0.325671 TGGGCTCCTCGAGGATCTTT 60.326 55.000 33.66 0.00 44.46 2.52
2787 3046 2.681591 TCGAGGGGTCCACGAGAT 59.318 61.111 2.56 0.00 41.21 2.75
2824 3083 5.163713 GGTACGTAGGGTTATATAGGCGAAG 60.164 48.000 0.00 0.00 0.00 3.79
2861 3120 8.894731 GCAGAACTACCGATCTATCTTGATATA 58.105 37.037 0.00 0.00 0.00 0.86
2890 3149 1.681793 GGTGACTATAGAGGCTTGCGA 59.318 52.381 6.78 0.00 0.00 5.10


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

AutoCloner maintained by Alex Coulton.