Multiple sequence alignment - TraesCS3A01G094100

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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 TraesCS3A01G094100 chr3A 100.000 2701 0 0 1 2701 60241539 60244239 0.000000e+00 4988.0
1 TraesCS3A01G094100 chr3A 92.148 433 22 3 1905 2329 60252228 60252656 3.850000e-168 601.0
2 TraesCS3A01G094100 chr3A 80.742 566 75 18 1001 1553 60250904 60251448 6.960000e-111 411.0
3 TraesCS3A01G094100 chr3A 91.266 229 18 2 234 461 60241674 60241901 7.260000e-81 311.0
4 TraesCS3A01G094100 chr3A 91.266 229 18 2 136 363 60241772 60241999 7.260000e-81 311.0
5 TraesCS3A01G094100 chr3A 91.339 127 9 2 141 266 60241874 60241999 3.580000e-39 172.0
6 TraesCS3A01G094100 chr3A 100.000 32 0 0 22 53 686797912 686797881 2.900000e-05 60.2
7 TraesCS3A01G094100 chr1B 95.046 969 44 3 1 969 501417188 501416224 0.000000e+00 1520.0
8 TraesCS3A01G094100 chr1B 91.266 229 17 3 136 363 501416957 501416731 2.610000e-80 309.0
9 TraesCS3A01G094100 chr1B 89.520 229 22 2 234 461 501417055 501416828 3.400000e-74 289.0
10 TraesCS3A01G094100 chr1B 90.551 127 9 3 141 266 501416855 501416731 5.980000e-37 165.0
11 TraesCS3A01G094100 chr1B 90.476 126 10 2 336 460 501417050 501416926 5.980000e-37 165.0
12 TraesCS3A01G094100 chr3B 89.708 787 51 13 1905 2678 75711339 75712108 0.000000e+00 977.0
13 TraesCS3A01G094100 chr3B 88.650 652 50 11 336 968 29344176 29344822 0.000000e+00 773.0
14 TraesCS3A01G094100 chr3B 86.463 687 63 11 967 1647 75710534 75711196 0.000000e+00 726.0
15 TraesCS3A01G094100 chr3B 91.760 267 19 3 1 266 29344036 29344300 4.250000e-98 368.0
16 TraesCS3A01G094100 chr3B 84.503 342 41 11 969 1307 519477197 519476865 7.210000e-86 327.0
17 TraesCS3A01G094100 chr3B 77.196 592 78 39 969 1553 519451148 519450607 2.630000e-75 292.0
18 TraesCS3A01G094100 chr3B 93.077 130 9 0 234 363 29344171 29344300 9.870000e-45 191.0
19 TraesCS3A01G094100 chr3D 89.724 652 45 4 336 968 18588499 18589147 0.000000e+00 813.0
20 TraesCS3A01G094100 chr3D 87.120 691 59 15 967 1647 48012818 48013488 0.000000e+00 756.0
21 TraesCS3A01G094100 chr3D 80.833 600 81 25 969 1553 48015740 48016320 8.880000e-120 440.0
22 TraesCS3A01G094100 chr3D 94.030 268 11 3 1905 2170 48013633 48013897 4.190000e-108 401.0
23 TraesCS3A01G094100 chr3D 93.916 263 13 3 1 263 18588361 18588620 7.010000e-106 394.0
24 TraesCS3A01G094100 chr3D 78.407 565 76 29 998 1553 395052755 395052228 2.590000e-85 326.0
25 TraesCS3A01G094100 chr3D 95.276 127 6 0 234 360 18588494 18588620 4.560000e-48 202.0
26 TraesCS3A01G094100 chr3D 100.000 32 0 0 22 53 549523171 549523140 2.900000e-05 60.2
27 TraesCS3A01G094100 chr4D 87.994 658 40 17 338 975 330960802 330960164 0.000000e+00 741.0
28 TraesCS3A01G094100 chr4D 92.262 336 25 1 640 974 71410686 71410351 2.430000e-130 475.0
29 TraesCS3A01G094100 chr4D 93.077 260 15 3 8 266 71411177 71410920 7.060000e-101 377.0
30 TraesCS3A01G094100 chr4D 92.520 254 16 3 336 589 71411044 71410794 7.110000e-96 361.0
31 TraesCS3A01G094100 chr4D 93.846 130 8 0 234 363 71411049 71410920 2.120000e-46 196.0
32 TraesCS3A01G094100 chr4D 94.309 123 7 0 241 363 330960802 330960680 3.550000e-44 189.0
33 TraesCS3A01G094100 chr4D 92.742 124 8 1 143 266 330960802 330960680 7.680000e-41 178.0
34 TraesCS3A01G094100 chr4D 96.970 66 2 0 1 66 71411239 71411174 7.910000e-21 111.0
35 TraesCS3A01G094100 chr1D 87.047 579 55 12 976 1553 475825869 475825310 1.050000e-178 636.0
36 TraesCS3A01G094100 chr1A 86.598 582 63 11 976 1553 571680383 571679813 1.770000e-176 628.0
37 TraesCS3A01G094100 chr2A 93.909 197 10 2 1 197 183727227 183727421 2.030000e-76 296.0


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 TraesCS3A01G094100 chr3A 60241539 60244239 2700 False 1445.500000 4988 93.467750 1 2701 4 chr3A.!!$F1 2700
1 TraesCS3A01G094100 chr3A 60250904 60252656 1752 False 506.000000 601 86.445000 1001 2329 2 chr3A.!!$F2 1328
2 TraesCS3A01G094100 chr1B 501416224 501417188 964 True 489.600000 1520 91.371800 1 969 5 chr1B.!!$R1 968
3 TraesCS3A01G094100 chr3B 75710534 75712108 1574 False 851.500000 977 88.085500 967 2678 2 chr3B.!!$F2 1711
4 TraesCS3A01G094100 chr3B 29344036 29344822 786 False 444.000000 773 91.162333 1 968 3 chr3B.!!$F1 967
5 TraesCS3A01G094100 chr3B 519450607 519451148 541 True 292.000000 292 77.196000 969 1553 1 chr3B.!!$R1 584
6 TraesCS3A01G094100 chr3D 48012818 48016320 3502 False 532.333333 756 87.327667 967 2170 3 chr3D.!!$F2 1203
7 TraesCS3A01G094100 chr3D 18588361 18589147 786 False 469.666667 813 92.972000 1 968 3 chr3D.!!$F1 967
8 TraesCS3A01G094100 chr3D 395052228 395052755 527 True 326.000000 326 78.407000 998 1553 1 chr3D.!!$R1 555
9 TraesCS3A01G094100 chr4D 330960164 330960802 638 True 369.333333 741 91.681667 143 975 3 chr4D.!!$R2 832
10 TraesCS3A01G094100 chr4D 71410351 71411239 888 True 304.000000 475 93.735000 1 974 5 chr4D.!!$R1 973
11 TraesCS3A01G094100 chr1D 475825310 475825869 559 True 636.000000 636 87.047000 976 1553 1 chr1D.!!$R1 577
12 TraesCS3A01G094100 chr1A 571679813 571680383 570 True 628.000000 628 86.598000 976 1553 1 chr1A.!!$R1 577

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
792 912 0.175073 CGGTGGGTTAGCTGGAGTAC 59.825 60.0 0.0 0.0 0.0 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2186 2920 0.252197 AATTGTGGTACGGAGGGAGC 59.748 55.0 0.0 0.0 0.0 4.7 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
74 132 1.453155 ATGAAGACACCGGTTGCATC 58.547 50.000 2.97 2.71 0.00 3.91
97 157 0.949105 AAAAAGTCATCGCGGTCGCT 60.949 50.000 6.13 0.00 39.32 4.93
129 189 4.870123 AAGTTGTAAAAGCATCATGGCA 57.130 36.364 0.00 0.00 35.83 4.92
206 266 3.476552 TGAAGCAAAAATGTCGTCCTCT 58.523 40.909 0.00 0.00 0.00 3.69
212 272 2.586258 AAATGTCGTCCTCTCCATCG 57.414 50.000 0.00 0.00 0.00 3.84
230 290 1.202973 CGCTGGTCGCATCTAAGTCG 61.203 60.000 0.00 0.00 39.08 4.18
303 363 2.223144 TGAAGCAAAAATGTCGTCCTCG 59.777 45.455 0.00 0.00 38.55 4.63
440 500 6.278363 TCTAAGTCGTAAAATGGATGTAGCC 58.722 40.000 0.00 0.00 0.00 3.93
444 504 5.885912 AGTCGTAAAATGGATGTAGCCAAAT 59.114 36.000 0.00 0.00 42.16 2.32
515 575 1.415289 TGCGGCTCAGATTCATCATCT 59.585 47.619 0.00 0.00 43.80 2.90
530 590 0.924090 CATCTTCGTTGCTCCTACGC 59.076 55.000 0.00 0.00 38.81 4.42
792 912 0.175073 CGGTGGGTTAGCTGGAGTAC 59.825 60.000 0.00 0.00 0.00 2.73
845 966 4.284490 AGGAAGAAAGTCTGTAGCATGTGA 59.716 41.667 0.00 0.00 0.00 3.58
851 972 3.169099 AGTCTGTAGCATGTGAGTCCTT 58.831 45.455 0.00 0.00 0.00 3.36
863 984 1.132977 TGAGTCCTTGTGTGGGTCCTA 60.133 52.381 0.00 0.00 0.00 2.94
969 1090 4.470664 ACCGGACACAAACATTACCCTATA 59.529 41.667 9.46 0.00 0.00 1.31
974 1095 9.280174 CGGACACAAACATTACCCTATATAAAT 57.720 33.333 0.00 0.00 0.00 1.40
1016 1141 1.021390 CCTCACGCACAGAATCCACC 61.021 60.000 0.00 0.00 0.00 4.61
1036 1163 1.332375 CGAGCAAACCAAGGAAACGAA 59.668 47.619 0.00 0.00 0.00 3.85
1092 1219 4.388080 CGCGTGTACGACCGGTCA 62.388 66.667 32.80 13.21 43.02 4.02
1269 1402 2.125350 GAGGAGGAGCCGCAACTG 60.125 66.667 0.00 0.00 43.43 3.16
1314 1447 1.621814 TCTGGGTACTACTGCACAACC 59.378 52.381 0.00 0.00 0.00 3.77
1401 1549 1.743252 GGAAGTGCAAGCTCCTCGG 60.743 63.158 0.00 0.00 0.00 4.63
1521 1672 1.809619 CGATGTCGTTGATGGGCGT 60.810 57.895 0.00 0.00 34.11 5.68
1536 1687 3.687125 TGGGCGTCTCGATTATCTCTAT 58.313 45.455 0.00 0.00 0.00 1.98
1557 1708 9.689976 CTCTATTGACTTCGATTCATGATTACT 57.310 33.333 0.00 0.00 0.00 2.24
1562 2263 8.777865 TGACTTCGATTCATGATTACTTTTCT 57.222 30.769 0.00 0.00 0.00 2.52
1576 2277 7.563556 TGATTACTTTTCTCCCTTTGTTTTCCT 59.436 33.333 0.00 0.00 0.00 3.36
1577 2278 9.074576 GATTACTTTTCTCCCTTTGTTTTCCTA 57.925 33.333 0.00 0.00 0.00 2.94
1578 2279 8.826293 TTACTTTTCTCCCTTTGTTTTCCTAA 57.174 30.769 0.00 0.00 0.00 2.69
1579 2280 7.348080 ACTTTTCTCCCTTTGTTTTCCTAAG 57.652 36.000 0.00 0.00 0.00 2.18
1580 2281 6.895756 ACTTTTCTCCCTTTGTTTTCCTAAGT 59.104 34.615 0.00 0.00 0.00 2.24
1581 2282 6.709018 TTTCTCCCTTTGTTTTCCTAAGTG 57.291 37.500 0.00 0.00 0.00 3.16
1640 2349 4.695455 CGATGTGTGTATCTTTGTCCCTTT 59.305 41.667 0.00 0.00 0.00 3.11
1647 2356 9.005777 GTGTGTATCTTTGTCCCTTTTGTTATA 57.994 33.333 0.00 0.00 0.00 0.98
1648 2357 9.575868 TGTGTATCTTTGTCCCTTTTGTTATAA 57.424 29.630 0.00 0.00 0.00 0.98
1650 2359 9.802039 TGTATCTTTGTCCCTTTTGTTATAAGT 57.198 29.630 0.00 0.00 0.00 2.24
1652 2361 8.706322 ATCTTTGTCCCTTTTGTTATAAGTGT 57.294 30.769 0.00 0.00 0.00 3.55
1653 2362 9.802039 ATCTTTGTCCCTTTTGTTATAAGTGTA 57.198 29.630 0.00 0.00 0.00 2.90
1654 2363 9.802039 TCTTTGTCCCTTTTGTTATAAGTGTAT 57.198 29.630 0.00 0.00 0.00 2.29
1670 2379 2.493278 GTGTATCCAATGCAGGTGCTTT 59.507 45.455 3.18 0.15 42.66 3.51
1676 2385 3.054139 TCCAATGCAGGTGCTTTCTCTAT 60.054 43.478 3.18 0.00 42.66 1.98
1681 2390 4.397420 TGCAGGTGCTTTCTCTATTGAAA 58.603 39.130 3.18 0.00 42.66 2.69
1684 2393 6.658816 TGCAGGTGCTTTCTCTATTGAAAATA 59.341 34.615 3.18 0.00 42.66 1.40
1686 2395 8.028938 GCAGGTGCTTTCTCTATTGAAAATAAA 58.971 33.333 0.00 0.00 35.79 1.40
1688 2397 9.520515 AGGTGCTTTCTCTATTGAAAATAAAGA 57.479 29.630 0.00 0.00 35.79 2.52
1689 2398 9.561270 GGTGCTTTCTCTATTGAAAATAAAGAC 57.439 33.333 0.00 0.00 35.79 3.01
1702 2411 9.985318 TTGAAAATAAAGACTTCGTTACGAAAA 57.015 25.926 20.63 5.15 45.23 2.29
1708 2417 6.941218 AAGACTTCGTTACGAAAATACTCC 57.059 37.500 20.63 5.70 45.23 3.85
1709 2418 6.017400 AGACTTCGTTACGAAAATACTCCA 57.983 37.500 20.63 0.00 45.23 3.86
1712 2421 6.392354 ACTTCGTTACGAAAATACTCCATGA 58.608 36.000 20.63 0.00 45.23 3.07
1713 2422 6.309737 ACTTCGTTACGAAAATACTCCATGAC 59.690 38.462 20.63 0.00 45.23 3.06
1717 2426 6.899771 CGTTACGAAAATACTCCATGACATTG 59.100 38.462 0.00 0.00 0.00 2.82
1724 2433 6.560003 AATACTCCATGACATTGTACTCCA 57.440 37.500 0.00 0.00 0.00 3.86
1725 2434 4.908601 ACTCCATGACATTGTACTCCAA 57.091 40.909 0.00 0.00 37.49 3.53
1726 2435 4.579869 ACTCCATGACATTGTACTCCAAC 58.420 43.478 0.00 0.00 35.44 3.77
1732 2443 6.348498 CATGACATTGTACTCCAACTCCATA 58.652 40.000 0.00 0.00 35.44 2.74
1741 2452 7.918076 TGTACTCCAACTCCATAGAATCTTTT 58.082 34.615 0.00 0.00 0.00 2.27
1759 2470 9.612620 GAATCTTTTAACGTGTTGATCTCAAAT 57.387 29.630 0.00 0.00 37.63 2.32
1788 2503 4.846779 TGAAATTTTGGTAGTGACAGCC 57.153 40.909 0.00 0.00 0.00 4.85
1865 2582 9.965824 TTTTCATACTTTTTGTGAGGAATCTTC 57.034 29.630 0.00 0.00 0.00 2.87
1866 2583 8.924511 TTCATACTTTTTGTGAGGAATCTTCT 57.075 30.769 0.00 0.00 0.00 2.85
1867 2584 8.327941 TCATACTTTTTGTGAGGAATCTTCTG 57.672 34.615 0.00 0.00 0.00 3.02
1868 2585 7.939039 TCATACTTTTTGTGAGGAATCTTCTGT 59.061 33.333 0.00 0.00 0.00 3.41
1869 2586 9.219603 CATACTTTTTGTGAGGAATCTTCTGTA 57.780 33.333 0.00 0.00 0.00 2.74
1870 2587 9.793259 ATACTTTTTGTGAGGAATCTTCTGTAA 57.207 29.630 0.00 0.00 0.00 2.41
1871 2588 8.697507 ACTTTTTGTGAGGAATCTTCTGTAAT 57.302 30.769 0.00 0.00 0.00 1.89
1872 2589 9.136323 ACTTTTTGTGAGGAATCTTCTGTAATT 57.864 29.630 0.00 0.00 0.00 1.40
1876 2593 9.658799 TTTGTGAGGAATCTTCTGTAATTAGAG 57.341 33.333 3.22 3.22 0.00 2.43
1877 2594 7.786030 TGTGAGGAATCTTCTGTAATTAGAGG 58.214 38.462 9.57 0.00 0.00 3.69
1878 2595 6.704050 GTGAGGAATCTTCTGTAATTAGAGGC 59.296 42.308 9.57 0.00 0.00 4.70
1879 2596 6.384015 TGAGGAATCTTCTGTAATTAGAGGCA 59.616 38.462 9.57 0.00 0.00 4.75
1880 2597 6.587273 AGGAATCTTCTGTAATTAGAGGCAC 58.413 40.000 9.57 0.00 0.00 5.01
1882 2599 6.481644 GGAATCTTCTGTAATTAGAGGCACTG 59.518 42.308 9.57 0.00 41.55 3.66
1883 2600 5.344743 TCTTCTGTAATTAGAGGCACTGG 57.655 43.478 9.57 0.00 41.55 4.00
1884 2601 5.023452 TCTTCTGTAATTAGAGGCACTGGA 58.977 41.667 9.57 0.00 41.55 3.86
1885 2602 4.737855 TCTGTAATTAGAGGCACTGGAC 57.262 45.455 9.57 0.00 41.55 4.02
1886 2603 4.353777 TCTGTAATTAGAGGCACTGGACT 58.646 43.478 9.57 0.00 41.55 3.85
1887 2604 4.777896 TCTGTAATTAGAGGCACTGGACTT 59.222 41.667 9.57 0.00 41.55 3.01
1888 2605 5.248477 TCTGTAATTAGAGGCACTGGACTTT 59.752 40.000 9.57 0.00 41.55 2.66
1889 2606 5.876357 TGTAATTAGAGGCACTGGACTTTT 58.124 37.500 0.00 0.00 41.55 2.27
1890 2607 5.938125 TGTAATTAGAGGCACTGGACTTTTC 59.062 40.000 0.00 0.00 41.55 2.29
1891 2608 2.743636 TAGAGGCACTGGACTTTTCG 57.256 50.000 0.00 0.00 41.55 3.46
1892 2609 0.759346 AGAGGCACTGGACTTTTCGT 59.241 50.000 0.00 0.00 41.55 3.85
1893 2610 0.868406 GAGGCACTGGACTTTTCGTG 59.132 55.000 0.00 0.00 41.55 4.35
1894 2611 0.468226 AGGCACTGGACTTTTCGTGA 59.532 50.000 0.00 0.00 37.18 4.35
1895 2612 0.868406 GGCACTGGACTTTTCGTGAG 59.132 55.000 0.00 0.00 0.00 3.51
1896 2613 0.868406 GCACTGGACTTTTCGTGAGG 59.132 55.000 0.00 0.00 0.00 3.86
1897 2614 1.540363 GCACTGGACTTTTCGTGAGGA 60.540 52.381 0.00 0.00 0.00 3.71
1898 2615 2.833794 CACTGGACTTTTCGTGAGGAA 58.166 47.619 0.00 0.00 0.00 3.36
1899 2616 3.403038 CACTGGACTTTTCGTGAGGAAT 58.597 45.455 0.00 0.00 33.85 3.01
1900 2617 3.187227 CACTGGACTTTTCGTGAGGAATG 59.813 47.826 0.00 0.00 33.85 2.67
1901 2618 3.071023 ACTGGACTTTTCGTGAGGAATGA 59.929 43.478 0.00 0.00 33.85 2.57
1902 2619 3.399330 TGGACTTTTCGTGAGGAATGAC 58.601 45.455 0.00 0.00 33.85 3.06
1903 2620 3.181459 TGGACTTTTCGTGAGGAATGACA 60.181 43.478 0.00 0.00 33.85 3.58
1927 2644 6.563222 AAATTTTGAACAATTGGCATGAGG 57.437 33.333 10.83 0.00 0.00 3.86
1971 2688 8.023128 CGTCAAATTATTCATGGGGTATGATTC 58.977 37.037 0.00 0.00 44.90 2.52
2130 2864 5.100344 TCGGTCTCTACACTACATTCTCT 57.900 43.478 0.00 0.00 0.00 3.10
2174 2908 5.069914 TCTCACTGTTAGTGGTTTTAGCTCA 59.930 40.000 8.91 0.00 45.94 4.26
2186 2920 7.599998 AGTGGTTTTAGCTCAGCAAAAATTATG 59.400 33.333 0.00 0.00 0.00 1.90
2197 2931 3.630312 GCAAAAATTATGCTCCCTCCGTA 59.370 43.478 8.48 0.00 40.64 4.02
2257 2991 7.412346 CGTCAAGAATTATGAAACAGAGGAGTG 60.412 40.741 0.00 0.00 0.00 3.51
2268 3002 3.878778 ACAGAGGAGTGGCATAAACATC 58.121 45.455 0.00 0.00 0.00 3.06
2362 3096 1.134220 ACCACACAAGCGGAAGAAGAA 60.134 47.619 0.00 0.00 0.00 2.52
2369 3103 4.690748 CACAAGCGGAAGAAGAATTGACTA 59.309 41.667 0.00 0.00 0.00 2.59
2405 3139 3.119708 CCTGCCAAAACTAGCACATCTTC 60.120 47.826 0.00 0.00 34.68 2.87
2414 3148 3.928992 ACTAGCACATCTTCAACATGACG 59.071 43.478 0.00 0.00 0.00 4.35
2432 3166 3.314913 TGACGCACATCAACAAAACTGAT 59.685 39.130 0.00 0.00 33.73 2.90
2450 3184 5.153675 ACTGATGACTATCACATCCCAGAT 58.846 41.667 0.00 0.00 42.11 2.90
2458 3192 3.824001 TCACATCCCAGATTTTTCCCA 57.176 42.857 0.00 0.00 0.00 4.37
2459 3193 4.125124 TCACATCCCAGATTTTTCCCAA 57.875 40.909 0.00 0.00 0.00 4.12
2460 3194 4.686891 TCACATCCCAGATTTTTCCCAAT 58.313 39.130 0.00 0.00 0.00 3.16
2461 3195 5.836705 TCACATCCCAGATTTTTCCCAATA 58.163 37.500 0.00 0.00 0.00 1.90
2462 3196 6.442961 TCACATCCCAGATTTTTCCCAATAT 58.557 36.000 0.00 0.00 0.00 1.28
2463 3197 6.324512 TCACATCCCAGATTTTTCCCAATATG 59.675 38.462 0.00 0.00 0.00 1.78
2464 3198 5.603813 ACATCCCAGATTTTTCCCAATATGG 59.396 40.000 0.86 0.86 42.81 2.74
2465 3199 5.480058 TCCCAGATTTTTCCCAATATGGA 57.520 39.130 8.36 0.00 45.02 3.41
2466 3200 5.848004 TCCCAGATTTTTCCCAATATGGAA 58.152 37.500 8.36 0.00 45.02 3.53
2467 3201 6.451714 TCCCAGATTTTTCCCAATATGGAAT 58.548 36.000 8.36 0.00 45.02 3.01
2468 3202 6.327104 TCCCAGATTTTTCCCAATATGGAATG 59.673 38.462 8.36 0.00 45.02 2.67
2469 3203 6.327104 CCCAGATTTTTCCCAATATGGAATGA 59.673 38.462 8.36 0.00 45.02 2.57
2470 3204 7.016858 CCCAGATTTTTCCCAATATGGAATGAT 59.983 37.037 8.36 0.00 45.02 2.45
2471 3205 8.434392 CCAGATTTTTCCCAATATGGAATGATT 58.566 33.333 1.53 0.00 45.02 2.57
2581 3319 8.594881 ATTTGACTAAGAGACTACTGTTTGTG 57.405 34.615 0.00 0.00 36.12 3.33
2672 3410 2.661537 CGTCGTGCAAGGCAGTGA 60.662 61.111 4.84 0.00 40.08 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 157 4.153475 GCTTTTACAACTTAGATGCGACCA 59.847 41.667 0.00 0.00 0.00 4.02
160 220 5.638234 ACCGTCTCAAATCTTTGCTACTAAC 59.362 40.000 0.00 0.00 38.05 2.34
172 232 3.896648 TTGCTTCAACCGTCTCAAATC 57.103 42.857 0.00 0.00 0.00 2.17
271 331 4.647424 TTTTTGCTTCAACCGTCTCAAT 57.353 36.364 0.00 0.00 0.00 2.57
515 575 2.263540 GGGCGTAGGAGCAACGAA 59.736 61.111 0.00 0.00 42.90 3.85
755 875 1.997874 GCTCACACCCCCAGATCCT 60.998 63.158 0.00 0.00 0.00 3.24
792 912 1.964373 CACCCAAACCGTCCTTCCG 60.964 63.158 0.00 0.00 0.00 4.30
804 924 0.909610 CTCCTCTGGCTACCACCCAA 60.910 60.000 0.00 0.00 30.66 4.12
845 966 1.909302 CATAGGACCCACACAAGGACT 59.091 52.381 0.00 0.00 0.00 3.85
851 972 1.065491 GCACATCATAGGACCCACACA 60.065 52.381 0.00 0.00 0.00 3.72
863 984 2.219847 CGATCGCTTCGCACATCAT 58.780 52.632 0.26 0.00 41.69 2.45
998 1123 1.354337 CGGTGGATTCTGTGCGTGAG 61.354 60.000 0.00 0.00 0.00 3.51
999 1124 1.374125 CGGTGGATTCTGTGCGTGA 60.374 57.895 0.00 0.00 0.00 4.35
1016 1141 0.941542 TCGTTTCCTTGGTTTGCTCG 59.058 50.000 0.00 0.00 0.00 5.03
1036 1163 2.577112 CTCGCGACGCATCTTCGT 60.577 61.111 21.35 0.00 46.38 3.85
1089 1216 2.920912 TCCGGGTCCACCAGTGAC 60.921 66.667 0.00 0.00 40.22 3.67
1181 1308 3.485346 TTGGACTGGTTGGTCGGCC 62.485 63.158 0.00 0.00 37.12 6.13
1290 1423 2.903784 TGTGCAGTAGTACCCAGAATGT 59.096 45.455 0.00 0.00 0.00 2.71
1444 1595 3.058160 CTTGCGGCTCCCCTTGTG 61.058 66.667 0.00 0.00 0.00 3.33
1445 1596 3.133365 AACTTGCGGCTCCCCTTGT 62.133 57.895 0.00 0.00 0.00 3.16
1512 1663 2.229062 GAGATAATCGAGACGCCCATCA 59.771 50.000 0.00 0.00 0.00 3.07
1521 1672 7.964604 TCGAAGTCAATAGAGATAATCGAGA 57.035 36.000 0.00 0.00 33.46 4.04
1536 1687 9.219603 AGAAAAGTAATCATGAATCGAAGTCAA 57.780 29.630 0.00 0.00 0.00 3.18
1555 1706 6.895756 ACTTAGGAAAACAAAGGGAGAAAAGT 59.104 34.615 0.00 0.00 0.00 2.66
1557 1708 6.893005 TCACTTAGGAAAACAAAGGGAGAAAA 59.107 34.615 0.00 0.00 29.52 2.29
1562 2263 5.762279 ACTTCACTTAGGAAAACAAAGGGA 58.238 37.500 0.00 0.00 30.94 4.20
1576 2277 4.345257 ACTCCTCTTGCTGAACTTCACTTA 59.655 41.667 0.00 0.00 0.00 2.24
1577 2278 3.135530 ACTCCTCTTGCTGAACTTCACTT 59.864 43.478 0.00 0.00 0.00 3.16
1578 2279 2.703007 ACTCCTCTTGCTGAACTTCACT 59.297 45.455 0.00 0.00 0.00 3.41
1579 2280 3.118905 ACTCCTCTTGCTGAACTTCAC 57.881 47.619 0.00 0.00 0.00 3.18
1580 2281 3.118261 ACAACTCCTCTTGCTGAACTTCA 60.118 43.478 0.00 0.00 0.00 3.02
1581 2282 3.471680 ACAACTCCTCTTGCTGAACTTC 58.528 45.455 0.00 0.00 0.00 3.01
1615 2324 3.617263 GGGACAAAGATACACACATCGAC 59.383 47.826 0.00 0.00 0.00 4.20
1617 2326 3.861840 AGGGACAAAGATACACACATCG 58.138 45.455 0.00 0.00 0.00 3.84
1647 2356 2.094675 GCACCTGCATTGGATACACTT 58.905 47.619 0.00 0.00 44.62 3.16
1648 2357 1.283029 AGCACCTGCATTGGATACACT 59.717 47.619 0.00 0.00 46.94 3.55
1649 2358 1.755179 AGCACCTGCATTGGATACAC 58.245 50.000 0.00 0.00 46.94 2.90
1650 2359 2.512692 AAGCACCTGCATTGGATACA 57.487 45.000 0.00 0.00 45.94 2.29
1651 2360 3.019564 AGAAAGCACCTGCATTGGATAC 58.980 45.455 0.00 0.00 45.16 2.24
1652 2361 3.054139 AGAGAAAGCACCTGCATTGGATA 60.054 43.478 0.00 0.00 45.16 2.59
1653 2362 2.097825 GAGAAAGCACCTGCATTGGAT 58.902 47.619 0.00 0.00 45.16 3.41
1654 2363 1.074405 AGAGAAAGCACCTGCATTGGA 59.926 47.619 0.00 0.00 45.16 3.53
1655 2364 1.542492 AGAGAAAGCACCTGCATTGG 58.458 50.000 0.00 0.00 45.16 3.16
1676 2385 9.985318 TTTTCGTAACGAAGTCTTTATTTTCAA 57.015 25.926 0.00 0.00 46.43 2.69
1684 2393 6.925165 TGGAGTATTTTCGTAACGAAGTCTTT 59.075 34.615 0.00 0.00 46.43 2.52
1686 2395 6.017400 TGGAGTATTTTCGTAACGAAGTCT 57.983 37.500 0.00 0.00 46.43 3.24
1688 2397 6.309737 GTCATGGAGTATTTTCGTAACGAAGT 59.690 38.462 0.00 0.00 46.43 3.01
1689 2398 6.309494 TGTCATGGAGTATTTTCGTAACGAAG 59.691 38.462 0.00 0.00 46.43 3.79
1690 2399 6.157904 TGTCATGGAGTATTTTCGTAACGAA 58.842 36.000 0.00 0.00 44.28 3.85
1691 2400 5.712004 TGTCATGGAGTATTTTCGTAACGA 58.288 37.500 0.00 0.00 0.00 3.85
1692 2401 6.583912 ATGTCATGGAGTATTTTCGTAACG 57.416 37.500 0.00 0.00 0.00 3.18
1693 2402 7.748847 ACAATGTCATGGAGTATTTTCGTAAC 58.251 34.615 0.00 0.00 0.00 2.50
1694 2403 7.915293 ACAATGTCATGGAGTATTTTCGTAA 57.085 32.000 0.00 0.00 0.00 3.18
1695 2404 8.255206 AGTACAATGTCATGGAGTATTTTCGTA 58.745 33.333 0.00 0.00 0.00 3.43
1696 2405 7.103641 AGTACAATGTCATGGAGTATTTTCGT 58.896 34.615 0.00 0.00 0.00 3.85
1697 2406 7.254455 GGAGTACAATGTCATGGAGTATTTTCG 60.254 40.741 0.00 0.00 0.00 3.46
1698 2407 7.552687 TGGAGTACAATGTCATGGAGTATTTTC 59.447 37.037 0.00 0.00 0.00 2.29
1699 2408 7.402054 TGGAGTACAATGTCATGGAGTATTTT 58.598 34.615 0.00 0.00 0.00 1.82
1700 2409 6.957631 TGGAGTACAATGTCATGGAGTATTT 58.042 36.000 0.00 0.00 0.00 1.40
1701 2410 6.560003 TGGAGTACAATGTCATGGAGTATT 57.440 37.500 0.00 0.00 0.00 1.89
1702 2411 6.156949 AGTTGGAGTACAATGTCATGGAGTAT 59.843 38.462 0.00 0.00 41.95 2.12
1703 2412 5.483937 AGTTGGAGTACAATGTCATGGAGTA 59.516 40.000 0.00 0.00 41.95 2.59
1704 2413 4.287067 AGTTGGAGTACAATGTCATGGAGT 59.713 41.667 0.00 0.00 41.95 3.85
1705 2414 4.836825 AGTTGGAGTACAATGTCATGGAG 58.163 43.478 0.00 0.00 41.95 3.86
1706 2415 4.323485 GGAGTTGGAGTACAATGTCATGGA 60.323 45.833 0.00 0.00 41.95 3.41
1707 2416 3.941483 GGAGTTGGAGTACAATGTCATGG 59.059 47.826 0.00 0.00 41.95 3.66
1708 2417 4.578871 TGGAGTTGGAGTACAATGTCATG 58.421 43.478 0.00 0.00 41.95 3.07
1709 2418 4.908601 TGGAGTTGGAGTACAATGTCAT 57.091 40.909 0.00 0.00 41.95 3.06
1712 2421 6.620877 TTCTATGGAGTTGGAGTACAATGT 57.379 37.500 0.00 0.00 41.95 2.71
1713 2422 7.504403 AGATTCTATGGAGTTGGAGTACAATG 58.496 38.462 0.00 0.00 41.95 2.82
1717 2426 9.886132 TTAAAAGATTCTATGGAGTTGGAGTAC 57.114 33.333 0.00 0.00 0.00 2.73
1724 2433 8.504005 CAACACGTTAAAAGATTCTATGGAGTT 58.496 33.333 0.00 0.00 0.00 3.01
1725 2434 7.876068 TCAACACGTTAAAAGATTCTATGGAGT 59.124 33.333 0.00 0.00 0.00 3.85
1726 2435 8.251750 TCAACACGTTAAAAGATTCTATGGAG 57.748 34.615 0.00 0.00 0.00 3.86
1732 2443 7.962964 TGAGATCAACACGTTAAAAGATTCT 57.037 32.000 0.00 0.00 0.00 2.40
1774 2485 1.270839 GCTTCAGGCTGTCACTACCAA 60.271 52.381 15.27 0.00 38.06 3.67
1778 2490 4.760530 ATAATGCTTCAGGCTGTCACTA 57.239 40.909 15.27 6.15 42.39 2.74
1808 2525 4.873259 CGAAAAGCCTTTTTCCAGGAAAAA 59.127 37.500 30.23 30.23 46.05 1.94
1812 2529 2.661718 ACGAAAAGCCTTTTTCCAGGA 58.338 42.857 3.56 0.00 46.05 3.86
1813 2530 3.452755 AACGAAAAGCCTTTTTCCAGG 57.547 42.857 3.56 0.00 46.05 4.45
1814 2531 5.794687 AAAAACGAAAAGCCTTTTTCCAG 57.205 34.783 3.56 0.00 46.05 3.86
1839 2556 9.965824 GAAGATTCCTCACAAAAAGTATGAAAA 57.034 29.630 0.00 0.00 0.00 2.29
1840 2557 9.354673 AGAAGATTCCTCACAAAAAGTATGAAA 57.645 29.630 0.00 0.00 0.00 2.69
1841 2558 8.786898 CAGAAGATTCCTCACAAAAAGTATGAA 58.213 33.333 0.00 0.00 0.00 2.57
1842 2559 7.939039 ACAGAAGATTCCTCACAAAAAGTATGA 59.061 33.333 0.00 0.00 0.00 2.15
1843 2560 8.103948 ACAGAAGATTCCTCACAAAAAGTATG 57.896 34.615 0.00 0.00 0.00 2.39
1844 2561 9.793259 TTACAGAAGATTCCTCACAAAAAGTAT 57.207 29.630 0.00 0.00 0.00 2.12
1845 2562 9.793259 ATTACAGAAGATTCCTCACAAAAAGTA 57.207 29.630 0.00 0.00 0.00 2.24
1846 2563 8.697507 ATTACAGAAGATTCCTCACAAAAAGT 57.302 30.769 0.00 0.00 0.00 2.66
1850 2567 9.658799 CTCTAATTACAGAAGATTCCTCACAAA 57.341 33.333 0.00 0.00 0.00 2.83
1851 2568 8.260818 CCTCTAATTACAGAAGATTCCTCACAA 58.739 37.037 0.00 0.00 0.00 3.33
1852 2569 7.633772 GCCTCTAATTACAGAAGATTCCTCACA 60.634 40.741 0.00 0.00 0.00 3.58
1853 2570 6.704050 GCCTCTAATTACAGAAGATTCCTCAC 59.296 42.308 0.00 0.00 0.00 3.51
1854 2571 6.384015 TGCCTCTAATTACAGAAGATTCCTCA 59.616 38.462 0.00 0.00 0.00 3.86
1855 2572 6.704050 GTGCCTCTAATTACAGAAGATTCCTC 59.296 42.308 0.00 0.00 0.00 3.71
1856 2573 6.385467 AGTGCCTCTAATTACAGAAGATTCCT 59.615 38.462 0.00 0.00 0.00 3.36
1857 2574 6.481644 CAGTGCCTCTAATTACAGAAGATTCC 59.518 42.308 0.00 0.00 0.00 3.01
1858 2575 6.481644 CCAGTGCCTCTAATTACAGAAGATTC 59.518 42.308 0.00 0.00 0.00 2.52
1859 2576 6.156949 TCCAGTGCCTCTAATTACAGAAGATT 59.843 38.462 0.00 0.00 0.00 2.40
1860 2577 5.663106 TCCAGTGCCTCTAATTACAGAAGAT 59.337 40.000 0.00 0.00 0.00 2.40
1861 2578 5.023452 TCCAGTGCCTCTAATTACAGAAGA 58.977 41.667 0.00 0.00 0.00 2.87
1862 2579 5.105146 AGTCCAGTGCCTCTAATTACAGAAG 60.105 44.000 0.00 0.00 0.00 2.85
1863 2580 4.777896 AGTCCAGTGCCTCTAATTACAGAA 59.222 41.667 0.00 0.00 0.00 3.02
1864 2581 4.353777 AGTCCAGTGCCTCTAATTACAGA 58.646 43.478 0.00 0.00 0.00 3.41
1865 2582 4.744795 AGTCCAGTGCCTCTAATTACAG 57.255 45.455 0.00 0.00 0.00 2.74
1866 2583 5.499004 AAAGTCCAGTGCCTCTAATTACA 57.501 39.130 0.00 0.00 0.00 2.41
1867 2584 5.063564 CGAAAAGTCCAGTGCCTCTAATTAC 59.936 44.000 0.00 0.00 0.00 1.89
1868 2585 5.175859 CGAAAAGTCCAGTGCCTCTAATTA 58.824 41.667 0.00 0.00 0.00 1.40
1869 2586 4.003648 CGAAAAGTCCAGTGCCTCTAATT 58.996 43.478 0.00 0.00 0.00 1.40
1870 2587 3.008049 ACGAAAAGTCCAGTGCCTCTAAT 59.992 43.478 0.00 0.00 0.00 1.73
1871 2588 2.367567 ACGAAAAGTCCAGTGCCTCTAA 59.632 45.455 0.00 0.00 0.00 2.10
1872 2589 1.968493 ACGAAAAGTCCAGTGCCTCTA 59.032 47.619 0.00 0.00 0.00 2.43
1873 2590 0.759346 ACGAAAAGTCCAGTGCCTCT 59.241 50.000 0.00 0.00 0.00 3.69
1874 2591 0.868406 CACGAAAAGTCCAGTGCCTC 59.132 55.000 0.00 0.00 0.00 4.70
1875 2592 0.468226 TCACGAAAAGTCCAGTGCCT 59.532 50.000 0.00 0.00 34.84 4.75
1876 2593 0.868406 CTCACGAAAAGTCCAGTGCC 59.132 55.000 0.00 0.00 34.84 5.01
1877 2594 0.868406 CCTCACGAAAAGTCCAGTGC 59.132 55.000 0.00 0.00 34.84 4.40
1878 2595 2.526304 TCCTCACGAAAAGTCCAGTG 57.474 50.000 0.00 0.00 36.06 3.66
1879 2596 3.071023 TCATTCCTCACGAAAAGTCCAGT 59.929 43.478 0.00 0.00 33.08 4.00
1880 2597 3.433615 GTCATTCCTCACGAAAAGTCCAG 59.566 47.826 0.00 0.00 33.08 3.86
1881 2598 3.181459 TGTCATTCCTCACGAAAAGTCCA 60.181 43.478 0.00 0.00 33.08 4.02
1882 2599 3.399330 TGTCATTCCTCACGAAAAGTCC 58.601 45.455 0.00 0.00 33.08 3.85
1883 2600 5.418310 TTTGTCATTCCTCACGAAAAGTC 57.582 39.130 0.00 0.00 33.08 3.01
1884 2601 5.828299 TTTTGTCATTCCTCACGAAAAGT 57.172 34.783 0.00 0.00 33.08 2.66
1885 2602 7.698836 AAATTTTGTCATTCCTCACGAAAAG 57.301 32.000 0.00 0.00 33.08 2.27
1886 2603 7.761704 TCAAAATTTTGTCATTCCTCACGAAAA 59.238 29.630 25.98 2.51 39.18 2.29
1887 2604 7.261325 TCAAAATTTTGTCATTCCTCACGAAA 58.739 30.769 25.98 2.85 39.18 3.46
1888 2605 6.800543 TCAAAATTTTGTCATTCCTCACGAA 58.199 32.000 25.98 3.44 39.18 3.85
1889 2606 6.384258 TCAAAATTTTGTCATTCCTCACGA 57.616 33.333 25.98 3.83 39.18 4.35
1890 2607 6.475076 TGTTCAAAATTTTGTCATTCCTCACG 59.525 34.615 25.98 0.99 39.18 4.35
1891 2608 7.769272 TGTTCAAAATTTTGTCATTCCTCAC 57.231 32.000 25.98 12.47 39.18 3.51
1892 2609 8.961294 ATTGTTCAAAATTTTGTCATTCCTCA 57.039 26.923 25.98 12.97 39.18 3.86
1893 2610 9.654417 CAATTGTTCAAAATTTTGTCATTCCTC 57.346 29.630 25.98 11.70 39.18 3.71
1894 2611 8.623030 CCAATTGTTCAAAATTTTGTCATTCCT 58.377 29.630 25.98 8.08 39.18 3.36
1895 2612 7.379262 GCCAATTGTTCAAAATTTTGTCATTCC 59.621 33.333 25.98 11.87 39.18 3.01
1896 2613 7.914346 TGCCAATTGTTCAAAATTTTGTCATTC 59.086 29.630 25.98 14.88 39.18 2.67
1897 2614 7.769220 TGCCAATTGTTCAAAATTTTGTCATT 58.231 26.923 25.98 18.94 39.18 2.57
1898 2615 7.330900 TGCCAATTGTTCAAAATTTTGTCAT 57.669 28.000 25.98 13.40 39.18 3.06
1899 2616 6.748333 TGCCAATTGTTCAAAATTTTGTCA 57.252 29.167 25.98 22.17 39.18 3.58
1900 2617 7.416022 TCATGCCAATTGTTCAAAATTTTGTC 58.584 30.769 25.98 20.36 39.18 3.18
1901 2618 7.330900 TCATGCCAATTGTTCAAAATTTTGT 57.669 28.000 25.98 7.82 39.18 2.83
1902 2619 6.858993 CCTCATGCCAATTGTTCAAAATTTTG 59.141 34.615 22.40 22.40 39.48 2.44
1903 2620 6.016108 CCCTCATGCCAATTGTTCAAAATTTT 60.016 34.615 4.43 0.00 0.00 1.82
1927 2644 4.196193 TGACGGTGGACATTTGATATTCC 58.804 43.478 0.00 0.00 0.00 3.01
1971 2688 7.277539 TGTCCTTTTAAGCAAAACAATCAGTTG 59.722 33.333 0.00 0.00 41.19 3.16
2130 2864 5.221762 TGAGAGAAAAACTATTCGGGGAACA 60.222 40.000 0.00 0.00 34.46 3.18
2186 2920 0.252197 AATTGTGGTACGGAGGGAGC 59.748 55.000 0.00 0.00 0.00 4.70
2257 2991 5.922544 GGAAGTGCAATATGATGTTTATGCC 59.077 40.000 0.00 0.00 0.00 4.40
2268 3002 5.587443 TGAGTTGATCTGGAAGTGCAATATG 59.413 40.000 0.00 0.00 32.69 1.78
2362 3096 9.343539 GGCAGGTTTTCTTATTATCTAGTCAAT 57.656 33.333 0.00 0.00 0.00 2.57
2369 3103 8.422577 AGTTTTGGCAGGTTTTCTTATTATCT 57.577 30.769 0.00 0.00 0.00 1.98
2405 3139 2.684754 TGTTGATGTGCGTCATGTTG 57.315 45.000 0.00 0.00 36.83 3.33
2432 3166 6.122277 GGAAAAATCTGGGATGTGATAGTCA 58.878 40.000 0.00 0.00 0.00 3.41
2435 3169 5.448654 TGGGAAAAATCTGGGATGTGATAG 58.551 41.667 0.00 0.00 0.00 2.08
2514 3248 7.906199 TCCCTCAAAAATCACTAAAGGAAAA 57.094 32.000 0.00 0.00 0.00 2.29
2581 3319 2.790433 TCAGTTGGGCCATACTTTCAC 58.210 47.619 7.26 0.00 0.00 3.18
2639 3377 3.702048 CGCTCTTCCCCGGGAACA 61.702 66.667 26.32 4.22 36.71 3.18
2659 3397 2.280797 TCCGTCACTGCCTTGCAC 60.281 61.111 0.00 0.00 33.79 4.57


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

AutoCloner maintained by Alex Coulton.