Multiple sequence alignment - TraesCS3D01G026300

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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 TraesCS3D01G026300 chr3D 100.000 3696 0 0 1 3696 8970606 8966911 0.000000e+00 6826.0
1 TraesCS3D01G026300 chr3D 95.898 2779 85 15 870 3648 4875301 4878050 0.000000e+00 4473.0
2 TraesCS3D01G026300 chr3D 98.684 380 4 1 345 723 29699870 29699491 0.000000e+00 673.0
3 TraesCS3D01G026300 chr3D 91.549 142 3 2 1 134 4874855 4874995 1.750000e-43 187.0
4 TraesCS3D01G026300 chr3D 100.000 50 0 0 3647 3696 10748118 10748167 3.930000e-15 93.5
5 TraesCS3D01G026300 chr3D 100.000 50 0 0 3647 3696 256068357 256068406 3.930000e-15 93.5
6 TraesCS3D01G026300 chr3D 100.000 37 0 0 287 323 29700067 29700031 6.620000e-08 69.4
7 TraesCS3D01G026300 chr3D 100.000 29 0 0 450 478 29699876 29699848 2.000000e-03 54.7
8 TraesCS3D01G026300 chr6A 95.456 2685 103 9 966 3648 16548698 16546031 0.000000e+00 4265.0
9 TraesCS3D01G026300 chr6A 95.177 2322 101 7 1332 3648 25223511 25225826 0.000000e+00 3657.0
10 TraesCS3D01G026300 chr6A 95.113 2292 100 7 1359 3648 396388863 396391144 0.000000e+00 3602.0
11 TraesCS3D01G026300 chr6A 93.234 1005 39 12 870 1873 18055857 18054881 0.000000e+00 1452.0
12 TraesCS3D01G026300 chr6A 90.435 115 3 1 28 134 11506567 11506681 1.070000e-30 145.0
13 TraesCS3D01G026300 chr6A 84.553 123 3 3 28 134 18056295 18056173 1.400000e-19 108.0
14 TraesCS3D01G026300 chr5A 95.257 2319 104 4 1332 3648 320486360 320488674 0.000000e+00 3668.0
15 TraesCS3D01G026300 chr5A 94.891 548 27 1 870 1417 311633697 311633151 0.000000e+00 856.0
16 TraesCS3D01G026300 chr6B 95.321 2308 104 3 1344 3648 331030358 331032664 0.000000e+00 3661.0
17 TraesCS3D01G026300 chr6B 93.782 193 12 0 679 871 494094345 494094153 1.300000e-74 291.0
18 TraesCS3D01G026300 chr6B 91.279 172 15 0 413 584 494094703 494094532 6.170000e-58 235.0
19 TraesCS3D01G026300 chr7B 95.232 2307 107 2 1344 3648 231204044 231206349 0.000000e+00 3648.0
20 TraesCS3D01G026300 chr7B 95.479 553 23 2 870 1421 158736606 158737157 0.000000e+00 881.0
21 TraesCS3D01G026300 chr7B 94.466 253 14 0 626 878 591564564 591564816 1.240000e-104 390.0
22 TraesCS3D01G026300 chr7B 95.031 161 8 0 163 323 591564254 591564414 1.700000e-63 254.0
23 TraesCS3D01G026300 chr7B 93.684 95 5 1 582 675 84214273 84214179 1.380000e-29 141.0
24 TraesCS3D01G026300 chr7B 86.957 115 4 2 28 134 158736082 158736193 6.480000e-23 119.0
25 TraesCS3D01G026300 chr7A 95.127 2319 102 7 1332 3648 309552614 309554923 0.000000e+00 3646.0
26 TraesCS3D01G026300 chr7A 95.046 545 26 1 870 1414 572342743 572343286 0.000000e+00 856.0
27 TraesCS3D01G026300 chr7A 91.549 142 4 1 1 134 572342296 572342437 4.870000e-44 189.0
28 TraesCS3D01G026300 chr3B 95.147 2308 103 6 1344 3649 769136269 769138569 0.000000e+00 3633.0
29 TraesCS3D01G026300 chr3B 96.642 536 14 4 345 879 27052580 27052048 0.000000e+00 887.0
30 TraesCS3D01G026300 chr3B 94.969 159 8 0 163 321 27052897 27052739 2.200000e-62 250.0
31 TraesCS3D01G026300 chr3B 100.000 29 0 0 450 478 27052586 27052558 2.000000e-03 54.7
32 TraesCS3D01G026300 chr5D 97.482 953 10 2 1 945 366008494 366007548 0.000000e+00 1615.0
33 TraesCS3D01G026300 chr5D 94.521 146 0 1 1 138 331841405 331841550 6.210000e-53 219.0
34 TraesCS3D01G026300 chr5D 100.000 50 0 0 3647 3696 6199930 6199979 3.930000e-15 93.5
35 TraesCS3D01G026300 chr5D 100.000 50 0 0 3647 3696 329163529 329163480 3.930000e-15 93.5
36 TraesCS3D01G026300 chr5D 100.000 50 0 0 3647 3696 560873820 560873771 3.930000e-15 93.5
37 TraesCS3D01G026300 chr1B 92.243 709 36 13 870 1562 485191588 485192293 0.000000e+00 987.0
38 TraesCS3D01G026300 chr1B 97.976 247 3 1 626 870 295102906 295103152 9.490000e-116 427.0
39 TraesCS3D01G026300 chr1B 96.273 161 6 0 163 323 295102596 295102756 7.870000e-67 265.0
40 TraesCS3D01G026300 chr4A 95.803 548 20 3 870 1417 595357648 595357104 0.000000e+00 881.0
41 TraesCS3D01G026300 chr4A 95.126 554 24 3 870 1423 313708301 313707751 0.000000e+00 870.0
42 TraesCS3D01G026300 chr4A 89.565 115 4 2 28 134 313708731 313708617 4.980000e-29 139.0
43 TraesCS3D01G026300 chr4A 88.696 115 5 2 28 134 308661901 308662015 2.320000e-27 134.0
44 TraesCS3D01G026300 chr4A 84.553 123 3 3 28 134 595358086 595357964 1.400000e-19 108.0
45 TraesCS3D01G026300 chr7D 95.580 543 22 2 870 1411 453001576 453002117 0.000000e+00 869.0
46 TraesCS3D01G026300 chr2A 92.609 460 21 10 374 833 645956625 645957071 0.000000e+00 649.0
47 TraesCS3D01G026300 chr4B 98.785 247 3 0 626 872 40065859 40066105 1.220000e-119 440.0
48 TraesCS3D01G026300 chr4B 97.516 161 4 0 163 323 40065549 40065709 3.640000e-70 276.0
49 TraesCS3D01G026300 chrUn 98.374 246 4 0 626 871 40598968 40598723 2.040000e-117 433.0
50 TraesCS3D01G026300 chrUn 97.516 161 4 0 163 323 40599278 40599118 3.640000e-70 276.0
51 TraesCS3D01G026300 chrUn 100.000 50 0 0 3647 3696 30305999 30306048 3.930000e-15 93.5
52 TraesCS3D01G026300 chr3A 94.915 236 5 1 374 609 383712587 383712359 2.710000e-96 363.0
53 TraesCS3D01G026300 chr3A 97.516 161 4 0 163 323 383712923 383712763 3.640000e-70 276.0
54 TraesCS3D01G026300 chr4D 96.569 204 7 0 667 870 477012505 477012708 4.570000e-89 339.0
55 TraesCS3D01G026300 chr4D 92.991 214 6 2 374 585 477012298 477012504 1.670000e-78 303.0
56 TraesCS3D01G026300 chr4D 94.805 154 8 0 170 323 477011966 477012119 1.330000e-59 241.0
57 TraesCS3D01G026300 chr4D 100.000 50 0 0 3647 3696 348382289 348382240 3.930000e-15 93.5
58 TraesCS3D01G026300 chr1D 95.349 172 0 1 1 164 408852618 408852789 2.190000e-67 267.0
59 TraesCS3D01G026300 chr1D 100.000 50 0 0 3647 3696 68406612 68406563 3.930000e-15 93.5
60 TraesCS3D01G026300 chr6D 100.000 50 0 0 3647 3696 82029558 82029509 3.930000e-15 93.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G026300 chr3D 8966911 8970606 3695 True 6826.000000 6826 100.000000 1 3696 1 chr3D.!!$R1 3695
1 TraesCS3D01G026300 chr3D 4874855 4878050 3195 False 2330.000000 4473 93.723500 1 3648 2 chr3D.!!$F3 3647
2 TraesCS3D01G026300 chr3D 29699491 29700067 576 True 265.700000 673 99.561333 287 723 3 chr3D.!!$R2 436
3 TraesCS3D01G026300 chr6A 16546031 16548698 2667 True 4265.000000 4265 95.456000 966 3648 1 chr6A.!!$R1 2682
4 TraesCS3D01G026300 chr6A 25223511 25225826 2315 False 3657.000000 3657 95.177000 1332 3648 1 chr6A.!!$F2 2316
5 TraesCS3D01G026300 chr6A 396388863 396391144 2281 False 3602.000000 3602 95.113000 1359 3648 1 chr6A.!!$F3 2289
6 TraesCS3D01G026300 chr6A 18054881 18056295 1414 True 780.000000 1452 88.893500 28 1873 2 chr6A.!!$R2 1845
7 TraesCS3D01G026300 chr5A 320486360 320488674 2314 False 3668.000000 3668 95.257000 1332 3648 1 chr5A.!!$F1 2316
8 TraesCS3D01G026300 chr5A 311633151 311633697 546 True 856.000000 856 94.891000 870 1417 1 chr5A.!!$R1 547
9 TraesCS3D01G026300 chr6B 331030358 331032664 2306 False 3661.000000 3661 95.321000 1344 3648 1 chr6B.!!$F1 2304
10 TraesCS3D01G026300 chr6B 494094153 494094703 550 True 263.000000 291 92.530500 413 871 2 chr6B.!!$R1 458
11 TraesCS3D01G026300 chr7B 231204044 231206349 2305 False 3648.000000 3648 95.232000 1344 3648 1 chr7B.!!$F1 2304
12 TraesCS3D01G026300 chr7B 158736082 158737157 1075 False 500.000000 881 91.218000 28 1421 2 chr7B.!!$F2 1393
13 TraesCS3D01G026300 chr7B 591564254 591564816 562 False 322.000000 390 94.748500 163 878 2 chr7B.!!$F3 715
14 TraesCS3D01G026300 chr7A 309552614 309554923 2309 False 3646.000000 3646 95.127000 1332 3648 1 chr7A.!!$F1 2316
15 TraesCS3D01G026300 chr7A 572342296 572343286 990 False 522.500000 856 93.297500 1 1414 2 chr7A.!!$F2 1413
16 TraesCS3D01G026300 chr3B 769136269 769138569 2300 False 3633.000000 3633 95.147000 1344 3649 1 chr3B.!!$F1 2305
17 TraesCS3D01G026300 chr3B 27052048 27052897 849 True 397.233333 887 97.203667 163 879 3 chr3B.!!$R1 716
18 TraesCS3D01G026300 chr5D 366007548 366008494 946 True 1615.000000 1615 97.482000 1 945 1 chr5D.!!$R2 944
19 TraesCS3D01G026300 chr1B 485191588 485192293 705 False 987.000000 987 92.243000 870 1562 1 chr1B.!!$F1 692
20 TraesCS3D01G026300 chr1B 295102596 295103152 556 False 346.000000 427 97.124500 163 870 2 chr1B.!!$F2 707
21 TraesCS3D01G026300 chr4A 313707751 313708731 980 True 504.500000 870 92.345500 28 1423 2 chr4A.!!$R1 1395
22 TraesCS3D01G026300 chr4A 595357104 595358086 982 True 494.500000 881 90.178000 28 1417 2 chr4A.!!$R2 1389
23 TraesCS3D01G026300 chr7D 453001576 453002117 541 False 869.000000 869 95.580000 870 1411 1 chr7D.!!$F1 541
24 TraesCS3D01G026300 chr4B 40065549 40066105 556 False 358.000000 440 98.150500 163 872 2 chr4B.!!$F1 709
25 TraesCS3D01G026300 chrUn 40598723 40599278 555 True 354.500000 433 97.945000 163 871 2 chrUn.!!$R1 708
26 TraesCS3D01G026300 chr3A 383712359 383712923 564 True 319.500000 363 96.215500 163 609 2 chr3A.!!$R1 446
27 TraesCS3D01G026300 chr4D 477011966 477012708 742 False 294.333333 339 94.788333 170 870 3 chr4D.!!$F1 700

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
609 893 8.979534 ACTTCCTCCGTAAAGAAATATAAGAGT 58.02 33.333 0.00 0.00 0.00 3.24 F
2293 2958 1.169577 TGTTTCACCAACGTTGTGCT 58.83 45.000 25.63 6.07 38.36 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2509 3174 0.739561 ACACTCCGCGATACTCCTTC 59.260 55.0 8.23 0.0 0.00 3.46 R
3651 4319 1.165270 CCTAGGCCAAAACGAACTGG 58.835 55.0 5.01 0.0 35.67 4.00 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
609 893 8.979534 ACTTCCTCCGTAAAGAAATATAAGAGT 58.020 33.333 0.00 0.00 0.00 3.24
1176 1647 5.862845 AGAGCTTATCATGGTGAGTATTGG 58.137 41.667 0.00 0.00 0.00 3.16
1295 1766 2.661675 CGTTCACAAGACACTCGTATGG 59.338 50.000 0.00 0.00 0.00 2.74
1296 1767 3.650139 GTTCACAAGACACTCGTATGGT 58.350 45.455 0.00 0.00 0.00 3.55
1297 1768 4.056050 GTTCACAAGACACTCGTATGGTT 58.944 43.478 0.00 0.00 0.00 3.67
1298 1769 3.649073 TCACAAGACACTCGTATGGTTG 58.351 45.455 0.00 0.00 0.00 3.77
1299 1770 3.319689 TCACAAGACACTCGTATGGTTGA 59.680 43.478 10.64 0.00 0.00 3.18
1300 1771 4.021456 TCACAAGACACTCGTATGGTTGAT 60.021 41.667 10.64 0.00 0.00 2.57
1301 1772 4.690748 CACAAGACACTCGTATGGTTGATT 59.309 41.667 10.64 0.00 0.00 2.57
1302 1773 4.690748 ACAAGACACTCGTATGGTTGATTG 59.309 41.667 10.64 0.00 0.00 2.67
1303 1774 4.537135 AGACACTCGTATGGTTGATTGT 57.463 40.909 0.00 0.00 31.62 2.71
1304 1775 4.245660 AGACACTCGTATGGTTGATTGTG 58.754 43.478 0.00 0.00 29.45 3.33
1305 1776 4.021456 AGACACTCGTATGGTTGATTGTGA 60.021 41.667 0.00 0.00 29.45 3.58
1306 1777 4.637276 ACACTCGTATGGTTGATTGTGAA 58.363 39.130 0.00 0.00 0.00 3.18
1307 1778 4.690748 ACACTCGTATGGTTGATTGTGAAG 59.309 41.667 0.00 0.00 0.00 3.02
1308 1779 4.929211 CACTCGTATGGTTGATTGTGAAGA 59.071 41.667 0.00 0.00 0.00 2.87
1309 1780 5.408299 CACTCGTATGGTTGATTGTGAAGAA 59.592 40.000 0.00 0.00 0.00 2.52
1310 1781 5.639506 ACTCGTATGGTTGATTGTGAAGAAG 59.360 40.000 0.00 0.00 0.00 2.85
1311 1782 5.789521 TCGTATGGTTGATTGTGAAGAAGA 58.210 37.500 0.00 0.00 0.00 2.87
1312 1783 6.406370 TCGTATGGTTGATTGTGAAGAAGAT 58.594 36.000 0.00 0.00 0.00 2.40
1313 1784 6.313658 TCGTATGGTTGATTGTGAAGAAGATG 59.686 38.462 0.00 0.00 0.00 2.90
1314 1785 6.313658 CGTATGGTTGATTGTGAAGAAGATGA 59.686 38.462 0.00 0.00 0.00 2.92
1315 1786 6.754702 ATGGTTGATTGTGAAGAAGATGAG 57.245 37.500 0.00 0.00 0.00 2.90
1316 1787 5.005740 TGGTTGATTGTGAAGAAGATGAGG 58.994 41.667 0.00 0.00 0.00 3.86
1317 1788 4.142513 GGTTGATTGTGAAGAAGATGAGGC 60.143 45.833 0.00 0.00 0.00 4.70
1318 1789 4.564782 TGATTGTGAAGAAGATGAGGCT 57.435 40.909 0.00 0.00 0.00 4.58
1319 1790 4.259356 TGATTGTGAAGAAGATGAGGCTG 58.741 43.478 0.00 0.00 0.00 4.85
1320 1791 4.019950 TGATTGTGAAGAAGATGAGGCTGA 60.020 41.667 0.00 0.00 0.00 4.26
1321 1792 4.564782 TTGTGAAGAAGATGAGGCTGAT 57.435 40.909 0.00 0.00 0.00 2.90
1322 1793 3.870274 TGTGAAGAAGATGAGGCTGATG 58.130 45.455 0.00 0.00 0.00 3.07
1323 1794 3.516700 TGTGAAGAAGATGAGGCTGATGA 59.483 43.478 0.00 0.00 0.00 2.92
1324 1795 4.019950 TGTGAAGAAGATGAGGCTGATGAA 60.020 41.667 0.00 0.00 0.00 2.57
1325 1796 4.571580 GTGAAGAAGATGAGGCTGATGAAG 59.428 45.833 0.00 0.00 0.00 3.02
1326 1797 4.468868 TGAAGAAGATGAGGCTGATGAAGA 59.531 41.667 0.00 0.00 0.00 2.87
1327 1798 5.046087 TGAAGAAGATGAGGCTGATGAAGAA 60.046 40.000 0.00 0.00 0.00 2.52
1328 1799 5.026038 AGAAGATGAGGCTGATGAAGAAG 57.974 43.478 0.00 0.00 0.00 2.85
1329 1800 4.715792 AGAAGATGAGGCTGATGAAGAAGA 59.284 41.667 0.00 0.00 0.00 2.87
1330 1801 5.367352 AGAAGATGAGGCTGATGAAGAAGAT 59.633 40.000 0.00 0.00 0.00 2.40
1338 1809 5.188555 AGGCTGATGAAGAAGATGTTGACTA 59.811 40.000 0.00 0.00 0.00 2.59
1348 1819 9.429359 GAAGAAGATGTTGACTATGAAGAAGAA 57.571 33.333 0.00 0.00 0.00 2.52
1349 1820 9.434420 AAGAAGATGTTGACTATGAAGAAGAAG 57.566 33.333 0.00 0.00 0.00 2.85
1350 1821 8.811017 AGAAGATGTTGACTATGAAGAAGAAGA 58.189 33.333 0.00 0.00 0.00 2.87
1351 1822 9.086336 GAAGATGTTGACTATGAAGAAGAAGAG 57.914 37.037 0.00 0.00 0.00 2.85
1352 1823 7.555087 AGATGTTGACTATGAAGAAGAAGAGG 58.445 38.462 0.00 0.00 0.00 3.69
1353 1824 6.918067 TGTTGACTATGAAGAAGAAGAGGA 57.082 37.500 0.00 0.00 0.00 3.71
1354 1825 7.303182 TGTTGACTATGAAGAAGAAGAGGAA 57.697 36.000 0.00 0.00 0.00 3.36
1355 1826 7.382110 TGTTGACTATGAAGAAGAAGAGGAAG 58.618 38.462 0.00 0.00 0.00 3.46
1356 1827 6.537453 TGACTATGAAGAAGAAGAGGAAGG 57.463 41.667 0.00 0.00 0.00 3.46
1357 1828 6.256819 TGACTATGAAGAAGAAGAGGAAGGA 58.743 40.000 0.00 0.00 0.00 3.36
1371 1842 4.016666 AGAGGAAGGAGAAGAAGATGAGGA 60.017 45.833 0.00 0.00 0.00 3.71
1385 1922 8.036585 AGAAGATGAGGATGATGAAGAAGAAT 57.963 34.615 0.00 0.00 0.00 2.40
1416 2022 8.591940 TGATGATGAAGAAGAAGAAGAAGAAGA 58.408 33.333 0.00 0.00 0.00 2.87
1417 2023 9.434420 GATGATGAAGAAGAAGAAGAAGAAGAA 57.566 33.333 0.00 0.00 0.00 2.52
1418 2024 8.830201 TGATGAAGAAGAAGAAGAAGAAGAAG 57.170 34.615 0.00 0.00 0.00 2.85
1419 2025 8.646004 TGATGAAGAAGAAGAAGAAGAAGAAGA 58.354 33.333 0.00 0.00 0.00 2.87
1420 2026 9.487790 GATGAAGAAGAAGAAGAAGAAGAAGAA 57.512 33.333 0.00 0.00 0.00 2.52
1421 2027 8.885494 TGAAGAAGAAGAAGAAGAAGAAGAAG 57.115 34.615 0.00 0.00 0.00 2.85
1422 2028 8.700051 TGAAGAAGAAGAAGAAGAAGAAGAAGA 58.300 33.333 0.00 0.00 0.00 2.87
1423 2029 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
1424 2030 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
1425 2031 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
1426 2032 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
1427 2033 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
1428 2034 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
1429 2035 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
1430 2036 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
1431 2037 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
1432 2038 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
1433 2039 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
1434 2040 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
1435 2041 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
1436 2042 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
1437 2043 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
1438 2044 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
1439 2045 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
1501 2113 3.624777 GGTTGAGATCATTGACATGGGT 58.375 45.455 0.00 0.00 0.00 4.51
1756 2368 2.079088 TTGCAATGGGGCTCTGGACA 62.079 55.000 0.00 0.00 34.04 4.02
2293 2958 1.169577 TGTTTCACCAACGTTGTGCT 58.830 45.000 25.63 6.07 38.36 4.40
2509 3174 7.761249 TCAACCTACATGATGATTGATATAGCG 59.239 37.037 0.00 0.00 0.00 4.26
2548 3213 3.068024 TGTTTGACTCTTTGGCCATTCAC 59.932 43.478 6.09 0.00 0.00 3.18
2650 3315 7.889589 TTATGAAGCCACTAATGTGATATCG 57.110 36.000 0.00 0.00 46.55 2.92
2695 3360 9.585099 GCTAATTTGTATTTCCATGAAATGTGA 57.415 29.630 11.33 0.00 44.81 3.58
2755 3420 4.104086 AGGATTCTGAGATGGGTACAACA 58.896 43.478 0.00 0.00 0.00 3.33
2889 3554 0.323957 GGCCTAGAGTTTGGGAACGT 59.676 55.000 0.00 0.00 40.75 3.99
3199 3864 2.435586 GCTGAGTCGCATGGCAGT 60.436 61.111 0.00 0.00 0.00 4.40
3502 4168 8.954950 AGGTATGAGAAACTTTCTGATGTATG 57.045 34.615 8.83 0.00 40.87 2.39
3651 4319 4.349663 TGTTTTACACACAGAACTGCAC 57.650 40.909 1.46 0.00 0.00 4.57
3652 4320 3.127895 TGTTTTACACACAGAACTGCACC 59.872 43.478 1.46 0.00 0.00 5.01
3653 4321 2.700722 TTACACACAGAACTGCACCA 57.299 45.000 1.46 0.00 0.00 4.17
3654 4322 2.238942 TACACACAGAACTGCACCAG 57.761 50.000 1.46 0.00 37.52 4.00
3664 4332 0.738389 ACTGCACCAGTTCGTTTTGG 59.262 50.000 0.00 1.31 42.59 3.28
3665 4333 0.594796 CTGCACCAGTTCGTTTTGGC 60.595 55.000 0.00 0.00 38.03 4.52
3667 4335 1.734388 GCACCAGTTCGTTTTGGCCT 61.734 55.000 3.32 0.00 38.03 5.19
3669 4337 1.535462 CACCAGTTCGTTTTGGCCTAG 59.465 52.381 3.32 0.00 38.03 3.02
3670 4338 1.165270 CCAGTTCGTTTTGGCCTAGG 58.835 55.000 3.67 3.67 0.00 3.02
3671 4339 1.544759 CCAGTTCGTTTTGGCCTAGGT 60.545 52.381 11.31 0.00 0.00 3.08
3672 4340 2.227194 CAGTTCGTTTTGGCCTAGGTT 58.773 47.619 11.31 0.00 0.00 3.50
3674 4342 3.816523 CAGTTCGTTTTGGCCTAGGTTTA 59.183 43.478 11.31 0.00 0.00 2.01
3675 4343 4.070009 AGTTCGTTTTGGCCTAGGTTTAG 58.930 43.478 11.31 0.00 0.00 1.85
3678 4346 4.067192 TCGTTTTGGCCTAGGTTTAGAAC 58.933 43.478 11.31 8.54 0.00 3.01
3679 4347 4.070009 CGTTTTGGCCTAGGTTTAGAACT 58.930 43.478 11.31 0.00 0.00 3.01
3681 4349 5.878669 CGTTTTGGCCTAGGTTTAGAACTAT 59.121 40.000 11.31 0.00 0.00 2.12
3682 4350 6.036844 CGTTTTGGCCTAGGTTTAGAACTATC 59.963 42.308 11.31 0.00 0.00 2.08
3685 4353 6.481434 TGGCCTAGGTTTAGAACTATCTTC 57.519 41.667 11.31 0.00 37.10 2.87
3688 4356 6.762187 GGCCTAGGTTTAGAACTATCTTCAAC 59.238 42.308 11.31 0.00 37.10 3.18
3689 4357 6.476053 GCCTAGGTTTAGAACTATCTTCAACG 59.524 42.308 11.31 0.00 37.10 4.10
3694 4362 7.172703 AGGTTTAGAACTATCTTCAACGGTTTG 59.827 37.037 0.00 0.00 37.10 2.93
3695 4363 7.041576 GGTTTAGAACTATCTTCAACGGTTTGT 60.042 37.037 0.00 0.00 37.10 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1176 1647 8.281212 TGCATCCCTAGAAAAAGAAAGATTAC 57.719 34.615 0.00 0.00 0.00 1.89
1227 1698 8.263940 AGTGTTAACATTGCAATTACGAGTAT 57.736 30.769 12.26 0.00 0.00 2.12
1295 1766 4.699257 AGCCTCATCTTCTTCACAATCAAC 59.301 41.667 0.00 0.00 0.00 3.18
1296 1767 4.698780 CAGCCTCATCTTCTTCACAATCAA 59.301 41.667 0.00 0.00 0.00 2.57
1297 1768 4.019950 TCAGCCTCATCTTCTTCACAATCA 60.020 41.667 0.00 0.00 0.00 2.57
1298 1769 4.511527 TCAGCCTCATCTTCTTCACAATC 58.488 43.478 0.00 0.00 0.00 2.67
1299 1770 4.564782 TCAGCCTCATCTTCTTCACAAT 57.435 40.909 0.00 0.00 0.00 2.71
1300 1771 4.019950 TCATCAGCCTCATCTTCTTCACAA 60.020 41.667 0.00 0.00 0.00 3.33
1301 1772 3.516700 TCATCAGCCTCATCTTCTTCACA 59.483 43.478 0.00 0.00 0.00 3.58
1302 1773 4.134379 TCATCAGCCTCATCTTCTTCAC 57.866 45.455 0.00 0.00 0.00 3.18
1303 1774 4.468868 TCTTCATCAGCCTCATCTTCTTCA 59.531 41.667 0.00 0.00 0.00 3.02
1304 1775 5.021033 TCTTCATCAGCCTCATCTTCTTC 57.979 43.478 0.00 0.00 0.00 2.87
1305 1776 5.189342 TCTTCTTCATCAGCCTCATCTTCTT 59.811 40.000 0.00 0.00 0.00 2.52
1306 1777 4.715792 TCTTCTTCATCAGCCTCATCTTCT 59.284 41.667 0.00 0.00 0.00 2.85
1307 1778 5.021033 TCTTCTTCATCAGCCTCATCTTC 57.979 43.478 0.00 0.00 0.00 2.87
1308 1779 5.104444 ACATCTTCTTCATCAGCCTCATCTT 60.104 40.000 0.00 0.00 0.00 2.40
1309 1780 4.409574 ACATCTTCTTCATCAGCCTCATCT 59.590 41.667 0.00 0.00 0.00 2.90
1310 1781 4.706035 ACATCTTCTTCATCAGCCTCATC 58.294 43.478 0.00 0.00 0.00 2.92
1311 1782 4.774660 ACATCTTCTTCATCAGCCTCAT 57.225 40.909 0.00 0.00 0.00 2.90
1312 1783 4.019950 TCAACATCTTCTTCATCAGCCTCA 60.020 41.667 0.00 0.00 0.00 3.86
1313 1784 4.332268 GTCAACATCTTCTTCATCAGCCTC 59.668 45.833 0.00 0.00 0.00 4.70
1314 1785 4.019501 AGTCAACATCTTCTTCATCAGCCT 60.020 41.667 0.00 0.00 0.00 4.58
1315 1786 4.260170 AGTCAACATCTTCTTCATCAGCC 58.740 43.478 0.00 0.00 0.00 4.85
1316 1787 6.760298 TCATAGTCAACATCTTCTTCATCAGC 59.240 38.462 0.00 0.00 0.00 4.26
1317 1788 8.713737 TTCATAGTCAACATCTTCTTCATCAG 57.286 34.615 0.00 0.00 0.00 2.90
1318 1789 8.534496 TCTTCATAGTCAACATCTTCTTCATCA 58.466 33.333 0.00 0.00 0.00 3.07
1319 1790 8.939201 TCTTCATAGTCAACATCTTCTTCATC 57.061 34.615 0.00 0.00 0.00 2.92
1320 1791 9.381033 CTTCTTCATAGTCAACATCTTCTTCAT 57.619 33.333 0.00 0.00 0.00 2.57
1321 1792 8.588472 TCTTCTTCATAGTCAACATCTTCTTCA 58.412 33.333 0.00 0.00 0.00 3.02
1322 1793 8.994429 TCTTCTTCATAGTCAACATCTTCTTC 57.006 34.615 0.00 0.00 0.00 2.87
1323 1794 9.434420 CTTCTTCTTCATAGTCAACATCTTCTT 57.566 33.333 0.00 0.00 0.00 2.52
1324 1795 8.811017 TCTTCTTCTTCATAGTCAACATCTTCT 58.189 33.333 0.00 0.00 0.00 2.85
1325 1796 8.994429 TCTTCTTCTTCATAGTCAACATCTTC 57.006 34.615 0.00 0.00 0.00 2.87
1326 1797 8.040132 CCTCTTCTTCTTCATAGTCAACATCTT 58.960 37.037 0.00 0.00 0.00 2.40
1327 1798 7.398618 TCCTCTTCTTCTTCATAGTCAACATCT 59.601 37.037 0.00 0.00 0.00 2.90
1328 1799 7.551585 TCCTCTTCTTCTTCATAGTCAACATC 58.448 38.462 0.00 0.00 0.00 3.06
1329 1800 7.487822 TCCTCTTCTTCTTCATAGTCAACAT 57.512 36.000 0.00 0.00 0.00 2.71
1330 1801 6.918067 TCCTCTTCTTCTTCATAGTCAACA 57.082 37.500 0.00 0.00 0.00 3.33
1338 1809 6.022315 TCTTCTCCTTCCTCTTCTTCTTCAT 58.978 40.000 0.00 0.00 0.00 2.57
1348 1819 4.016666 TCCTCATCTTCTTCTCCTTCCTCT 60.017 45.833 0.00 0.00 0.00 3.69
1349 1820 4.285863 TCCTCATCTTCTTCTCCTTCCTC 58.714 47.826 0.00 0.00 0.00 3.71
1350 1821 4.344938 TCCTCATCTTCTTCTCCTTCCT 57.655 45.455 0.00 0.00 0.00 3.36
1351 1822 4.653341 TCATCCTCATCTTCTTCTCCTTCC 59.347 45.833 0.00 0.00 0.00 3.46
1352 1823 5.867903 TCATCCTCATCTTCTTCTCCTTC 57.132 43.478 0.00 0.00 0.00 3.46
1353 1824 5.904169 TCATCATCCTCATCTTCTTCTCCTT 59.096 40.000 0.00 0.00 0.00 3.36
1354 1825 5.465901 TCATCATCCTCATCTTCTTCTCCT 58.534 41.667 0.00 0.00 0.00 3.69
1355 1826 5.804944 TCATCATCCTCATCTTCTTCTCC 57.195 43.478 0.00 0.00 0.00 3.71
1356 1827 7.053316 TCTTCATCATCCTCATCTTCTTCTC 57.947 40.000 0.00 0.00 0.00 2.87
1357 1828 7.345132 TCTTCTTCATCATCCTCATCTTCTTCT 59.655 37.037 0.00 0.00 0.00 2.85
1416 2022 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
1417 2023 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
1418 2024 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
1419 2025 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
1420 2026 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
1421 2027 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
1422 2028 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
1423 2029 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
1424 2030 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
1425 2031 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
1426 2032 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
1427 2033 9.196552 CTCTTCTTCTTCTTCTTCTTCTTCTTC 57.803 37.037 0.00 0.00 0.00 2.87
1428 2034 8.150296 CCTCTTCTTCTTCTTCTTCTTCTTCTT 58.850 37.037 0.00 0.00 0.00 2.52
1429 2035 7.256296 CCCTCTTCTTCTTCTTCTTCTTCTTCT 60.256 40.741 0.00 0.00 0.00 2.85
1430 2036 6.873605 CCCTCTTCTTCTTCTTCTTCTTCTTC 59.126 42.308 0.00 0.00 0.00 2.87
1431 2037 6.556874 TCCCTCTTCTTCTTCTTCTTCTTCTT 59.443 38.462 0.00 0.00 0.00 2.52
1432 2038 6.081356 TCCCTCTTCTTCTTCTTCTTCTTCT 58.919 40.000 0.00 0.00 0.00 2.85
1433 2039 6.210584 TCTCCCTCTTCTTCTTCTTCTTCTTC 59.789 42.308 0.00 0.00 0.00 2.87
1434 2040 6.081356 TCTCCCTCTTCTTCTTCTTCTTCTT 58.919 40.000 0.00 0.00 0.00 2.52
1435 2041 5.650283 TCTCCCTCTTCTTCTTCTTCTTCT 58.350 41.667 0.00 0.00 0.00 2.85
1436 2042 5.993748 TCTCCCTCTTCTTCTTCTTCTTC 57.006 43.478 0.00 0.00 0.00 2.87
1437 2043 8.485392 CATTATCTCCCTCTTCTTCTTCTTCTT 58.515 37.037 0.00 0.00 0.00 2.52
1438 2044 7.623278 ACATTATCTCCCTCTTCTTCTTCTTCT 59.377 37.037 0.00 0.00 0.00 2.85
1439 2045 7.710475 CACATTATCTCCCTCTTCTTCTTCTTC 59.290 40.741 0.00 0.00 0.00 2.87
1501 2113 4.093472 TCTTCCCGGTTCAGAAAATGAA 57.907 40.909 0.00 0.00 45.79 2.57
1756 2368 4.228912 GCGTGCTAATGCCTGATTAAAT 57.771 40.909 0.00 0.00 38.71 1.40
2293 2958 6.545567 ACATATCAGATTTATGACATGGGCA 58.454 36.000 0.00 0.00 38.22 5.36
2509 3174 0.739561 ACACTCCGCGATACTCCTTC 59.260 55.000 8.23 0.00 0.00 3.46
2548 3213 7.490962 TGGCTTGAAGGTATATTGTTTATCG 57.509 36.000 0.00 0.00 0.00 2.92
2650 3315 2.497273 AGCAGTTGGATATTTTGTGCCC 59.503 45.455 0.00 0.00 0.00 5.36
2695 3360 4.068599 GCTCTAAGGTCAGCTTCACTTTT 58.931 43.478 0.00 0.00 32.48 2.27
2788 3453 2.681848 GCTCAACCATGTCATCTTCCAG 59.318 50.000 0.00 0.00 0.00 3.86
3199 3864 1.895798 CAGGAGCCGCCAAGATATCTA 59.104 52.381 5.46 0.00 40.02 1.98
3258 3923 6.627395 TCGAAAATCTGATAGGACTCTCTC 57.373 41.667 0.00 0.00 0.00 3.20
3502 4168 7.926555 AGTGTACTTTCATATACATGGCACTAC 59.073 37.037 0.00 0.00 34.00 2.73
3539 4205 6.549364 TGAAATCCCTCTTTAAAAAGCAGACA 59.451 34.615 0.00 0.00 35.99 3.41
3648 4316 1.299850 GGCCAAAACGAACTGGTGC 60.300 57.895 0.00 0.00 34.97 5.01
3649 4317 1.535462 CTAGGCCAAAACGAACTGGTG 59.465 52.381 5.01 0.00 34.97 4.17
3650 4318 1.544759 CCTAGGCCAAAACGAACTGGT 60.545 52.381 5.01 0.00 34.97 4.00
3651 4319 1.165270 CCTAGGCCAAAACGAACTGG 58.835 55.000 5.01 0.00 35.67 4.00
3652 4320 1.892209 ACCTAGGCCAAAACGAACTG 58.108 50.000 9.30 0.00 0.00 3.16
3653 4321 2.651382 AACCTAGGCCAAAACGAACT 57.349 45.000 9.30 0.00 0.00 3.01
3654 4322 4.067192 TCTAAACCTAGGCCAAAACGAAC 58.933 43.478 9.30 0.00 0.00 3.95
3655 4323 4.354893 TCTAAACCTAGGCCAAAACGAA 57.645 40.909 9.30 0.00 0.00 3.85
3656 4324 4.067192 GTTCTAAACCTAGGCCAAAACGA 58.933 43.478 9.30 0.00 0.00 3.85
3658 4326 7.110810 AGATAGTTCTAAACCTAGGCCAAAAC 58.889 38.462 9.30 7.54 0.00 2.43
3661 4329 6.442564 TGAAGATAGTTCTAAACCTAGGCCAA 59.557 38.462 9.30 0.00 0.00 4.52
3663 4331 6.481434 TGAAGATAGTTCTAAACCTAGGCC 57.519 41.667 9.30 0.00 0.00 5.19
3664 4332 6.476053 CGTTGAAGATAGTTCTAAACCTAGGC 59.524 42.308 9.30 0.00 30.38 3.93
3665 4333 6.979238 CCGTTGAAGATAGTTCTAAACCTAGG 59.021 42.308 7.41 7.41 30.38 3.02
3667 4335 7.472334 ACCGTTGAAGATAGTTCTAAACCTA 57.528 36.000 0.00 0.00 30.38 3.08
3669 4337 7.041576 ACAAACCGTTGAAGATAGTTCTAAACC 60.042 37.037 0.00 0.00 38.20 3.27
3670 4338 7.858583 ACAAACCGTTGAAGATAGTTCTAAAC 58.141 34.615 0.00 0.00 38.20 2.01


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

AutoCloner maintained by Alex Coulton.