Multiple sequence alignment - TraesCS4D01G065200

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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 TraesCS4D01G065200 chr4D 100.000 2486 0 0 1 2486 40410466 40407981 0.000000e+00 4591.0
1 TraesCS4D01G065200 chr4D 94.227 918 42 6 1 910 351567333 351566419 0.000000e+00 1391.0
2 TraesCS4D01G065200 chr4D 86.846 631 69 8 1251 1869 40456895 40456267 0.000000e+00 693.0
3 TraesCS4D01G065200 chr4D 84.483 232 33 1 950 1178 40397820 40398051 2.490000e-55 226.0
4 TraesCS4D01G065200 chr7D 94.908 923 36 5 1 915 493539812 493540731 0.000000e+00 1434.0
5 TraesCS4D01G065200 chr3D 94.553 918 40 5 1 911 555528105 555529019 0.000000e+00 1410.0
6 TraesCS4D01G065200 chr3D 93.023 43 2 1 910 951 171131475 171131517 7.420000e-06 62.1
7 TraesCS4D01G065200 chr6D 94.541 916 43 3 1 910 114220530 114219616 0.000000e+00 1408.0
8 TraesCS4D01G065200 chr1D 94.553 918 38 5 1 910 45260572 45259659 0.000000e+00 1408.0
9 TraesCS4D01G065200 chr1D 94.227 918 43 6 1 910 453051155 453052070 0.000000e+00 1393.0
10 TraesCS4D01G065200 chr1D 94.227 918 41 5 1 911 45282885 45281973 0.000000e+00 1391.0
11 TraesCS4D01G065200 chr1D 94.015 919 45 5 1 910 146737025 146736108 0.000000e+00 1384.0
12 TraesCS4D01G065200 chr2D 94.227 918 44 4 1 910 556164793 556163877 0.000000e+00 1393.0
13 TraesCS4D01G065200 chr4A 92.349 928 52 11 1438 2352 559454794 559455715 0.000000e+00 1303.0
14 TraesCS4D01G065200 chr4A 92.443 397 29 1 1049 1445 559453495 559453890 1.290000e-157 566.0
15 TraesCS4D01G065200 chr4A 83.060 183 31 0 950 1132 559494822 559494640 1.530000e-37 167.0
16 TraesCS4D01G065200 chr4B 93.734 766 43 5 1255 2018 58974417 58973655 0.000000e+00 1144.0
17 TraesCS4D01G065200 chr4B 87.479 607 61 7 1278 1873 58976174 58975572 0.000000e+00 686.0
18 TraesCS4D01G065200 chr4B 95.415 349 16 0 910 1258 58975027 58974679 7.770000e-155 556.0
19 TraesCS4D01G065200 chr4B 92.708 288 18 3 2201 2486 58962716 58962430 1.780000e-111 412.0
20 TraesCS4D01G065200 chr4B 78.268 589 104 17 950 1522 58927262 58927842 8.460000e-95 357.0
21 TraesCS4D01G065200 chr4B 85.714 329 46 1 1251 1578 58979034 58978706 1.830000e-91 346.0
22 TraesCS4D01G065200 chr4B 84.592 331 50 1 1251 1580 58943999 58944329 6.630000e-86 327.0
23 TraesCS4D01G065200 chr4B 88.780 205 7 4 2012 2203 58973619 58973418 1.150000e-58 237.0
24 TraesCS4D01G065200 chr4B 81.600 250 30 7 1070 1319 59418281 59418514 2.520000e-45 193.0
25 TraesCS4D01G065200 chr4B 94.286 35 1 1 918 951 656897698 656897732 4.000000e-03 52.8
26 TraesCS4D01G065200 chr5B 93.023 43 2 1 910 951 696724903 696724861 7.420000e-06 62.1
27 TraesCS4D01G065200 chr3A 93.023 43 2 1 910 951 208644421 208644463 7.420000e-06 62.1
28 TraesCS4D01G065200 chr3B 97.143 35 0 1 918 951 132643606 132643572 9.600000e-05 58.4
29 TraesCS4D01G065200 chr2A 90.698 43 3 1 910 951 762723081 762723039 3.450000e-04 56.5
30 TraesCS4D01G065200 chr7B 94.286 35 1 1 918 951 577202952 577202918 4.000000e-03 52.8
31 TraesCS4D01G065200 chr5D 94.286 35 1 1 918 951 67346513 67346479 4.000000e-03 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G065200 chr4D 40407981 40410466 2485 True 4591.0 4591 100.0000 1 2486 1 chr4D.!!$R1 2485
1 TraesCS4D01G065200 chr4D 351566419 351567333 914 True 1391.0 1391 94.2270 1 910 1 chr4D.!!$R3 909
2 TraesCS4D01G065200 chr4D 40456267 40456895 628 True 693.0 693 86.8460 1251 1869 1 chr4D.!!$R2 618
3 TraesCS4D01G065200 chr7D 493539812 493540731 919 False 1434.0 1434 94.9080 1 915 1 chr7D.!!$F1 914
4 TraesCS4D01G065200 chr3D 555528105 555529019 914 False 1410.0 1410 94.5530 1 911 1 chr3D.!!$F2 910
5 TraesCS4D01G065200 chr6D 114219616 114220530 914 True 1408.0 1408 94.5410 1 910 1 chr6D.!!$R1 909
6 TraesCS4D01G065200 chr1D 45259659 45260572 913 True 1408.0 1408 94.5530 1 910 1 chr1D.!!$R1 909
7 TraesCS4D01G065200 chr1D 453051155 453052070 915 False 1393.0 1393 94.2270 1 910 1 chr1D.!!$F1 909
8 TraesCS4D01G065200 chr1D 45281973 45282885 912 True 1391.0 1391 94.2270 1 911 1 chr1D.!!$R2 910
9 TraesCS4D01G065200 chr1D 146736108 146737025 917 True 1384.0 1384 94.0150 1 910 1 chr1D.!!$R3 909
10 TraesCS4D01G065200 chr2D 556163877 556164793 916 True 1393.0 1393 94.2270 1 910 1 chr2D.!!$R1 909
11 TraesCS4D01G065200 chr4A 559453495 559455715 2220 False 934.5 1303 92.3960 1049 2352 2 chr4A.!!$F1 1303
12 TraesCS4D01G065200 chr4B 58973418 58979034 5616 True 593.8 1144 90.2244 910 2203 5 chr4B.!!$R2 1293
13 TraesCS4D01G065200 chr4B 58927262 58927842 580 False 357.0 357 78.2680 950 1522 1 chr4B.!!$F1 572

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
235 244 1.999002 CCCGGGGAGTGTAATGGGT 60.999 63.158 14.71 0.0 31.82 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1684 5972 0.957395 CAACCTCCAACATGCGCTCT 60.957 55.0 9.73 0.0 0.0 4.09 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
235 244 1.999002 CCCGGGGAGTGTAATGGGT 60.999 63.158 14.71 0.00 31.82 4.51
375 387 2.181196 CTCCTCCTTCCTTCCCTCCTAT 59.819 54.545 0.00 0.00 0.00 2.57
683 697 2.423892 GCTCTACTGGATCGTGAGTTCA 59.576 50.000 0.00 0.00 0.00 3.18
911 926 4.628963 AATTACTACGTTCCCCAACACT 57.371 40.909 0.00 0.00 32.14 3.55
1008 4107 1.131693 CACATCGTGCTCATGTGCAAT 59.868 47.619 22.97 11.93 43.48 3.56
1026 4125 4.033932 TGCAATGACGTATCCAAATCTTCG 59.966 41.667 0.00 0.00 0.00 3.79
1267 4643 5.992217 CCCTGCACTAACTAACAATAGATCC 59.008 44.000 0.00 0.00 33.15 3.36
1280 4656 6.989155 ACAATAGATCCCAATGATGCATTT 57.011 33.333 0.00 0.00 31.05 2.32
1388 4764 2.588877 CGATAAGGCACGCCCCTG 60.589 66.667 3.95 0.00 34.80 4.45
1412 4788 0.321564 TTCAACCATGGCGAGTCAGG 60.322 55.000 13.04 0.00 0.00 3.86
1517 5804 6.961359 TCAACACGGAAGATAATTGTACAG 57.039 37.500 0.00 0.00 0.00 2.74
1584 5871 0.466124 GAGAGGCTAGACGGGCATTT 59.534 55.000 0.00 0.00 0.00 2.32
1675 5963 2.571212 GATGGGGCATACACGAATCAA 58.429 47.619 0.00 0.00 0.00 2.57
1684 5972 0.107081 ACACGAATCAACGTCCCCAA 59.893 50.000 0.00 0.00 44.76 4.12
1857 6154 4.742201 AGAGCGGCGTTGCGATGT 62.742 61.111 9.37 0.00 40.67 3.06
1878 6175 4.113354 GTTTCCAGATACTCCATCGTGTC 58.887 47.826 0.00 0.00 38.81 3.67
1945 6242 4.507710 TGGATTTTAGAGCTAGCACACAG 58.492 43.478 18.83 0.00 0.00 3.66
1949 6246 6.986817 GGATTTTAGAGCTAGCACACAGATTA 59.013 38.462 18.83 0.00 0.00 1.75
2037 6376 4.673968 ACACCAGAGAGTAGTACCAATGA 58.326 43.478 0.00 0.00 0.00 2.57
2059 6398 6.726230 TGACGAATACGAAATTTTTGTTGGA 58.274 32.000 7.32 0.00 42.66 3.53
2149 6500 6.654161 GCTTCTTATATGTGATTCCATGAGCT 59.346 38.462 0.00 0.00 0.00 4.09
2187 6538 5.689961 GCAATAATGAACGACAACAACCTTT 59.310 36.000 0.00 0.00 0.00 3.11
2238 6591 2.996621 GCACACCAGCTTTGTAGTCTAG 59.003 50.000 0.00 0.00 0.00 2.43
2239 6592 3.555168 GCACACCAGCTTTGTAGTCTAGT 60.555 47.826 0.00 0.00 0.00 2.57
2240 6593 4.321750 GCACACCAGCTTTGTAGTCTAGTA 60.322 45.833 0.00 0.00 0.00 1.82
2264 6617 6.794534 ACTAATCCTCCCAAGAAAAACATCT 58.205 36.000 0.00 0.00 0.00 2.90
2266 6619 4.722526 TCCTCCCAAGAAAAACATCTGA 57.277 40.909 0.00 0.00 0.00 3.27
2274 6627 7.015487 TCCCAAGAAAAACATCTGACATGAAAT 59.985 33.333 0.00 0.00 0.00 2.17
2302 6655 2.009774 CTCGCAACCAAGTCCCTAATG 58.990 52.381 0.00 0.00 0.00 1.90
2352 6705 5.794894 TGTTTCTTTACAAACAAGGCCAAA 58.205 33.333 5.01 0.00 42.11 3.28
2353 6706 6.231211 TGTTTCTTTACAAACAAGGCCAAAA 58.769 32.000 5.01 0.00 42.11 2.44
2354 6707 6.881602 TGTTTCTTTACAAACAAGGCCAAAAT 59.118 30.769 5.01 0.00 42.11 1.82
2355 6708 7.391833 TGTTTCTTTACAAACAAGGCCAAAATT 59.608 29.630 5.01 0.00 42.11 1.82
2356 6709 7.929941 TTCTTTACAAACAAGGCCAAAATTT 57.070 28.000 5.01 0.00 0.00 1.82
2357 6710 9.449719 TTTCTTTACAAACAAGGCCAAAATTTA 57.550 25.926 5.01 0.00 0.00 1.40
2358 6711 9.449719 TTCTTTACAAACAAGGCCAAAATTTAA 57.550 25.926 5.01 0.00 0.00 1.52
2359 6712 8.884726 TCTTTACAAACAAGGCCAAAATTTAAC 58.115 29.630 5.01 0.00 0.00 2.01
2360 6713 8.561738 TTTACAAACAAGGCCAAAATTTAACA 57.438 26.923 5.01 0.00 0.00 2.41
2361 6714 8.561738 TTACAAACAAGGCCAAAATTTAACAA 57.438 26.923 5.01 0.00 0.00 2.83
2362 6715 7.082700 ACAAACAAGGCCAAAATTTAACAAG 57.917 32.000 5.01 0.00 0.00 3.16
2363 6716 6.657117 ACAAACAAGGCCAAAATTTAACAAGT 59.343 30.769 5.01 0.00 0.00 3.16
2364 6717 6.918892 AACAAGGCCAAAATTTAACAAGTC 57.081 33.333 5.01 0.00 0.00 3.01
2365 6718 5.047188 ACAAGGCCAAAATTTAACAAGTCG 58.953 37.500 5.01 0.00 0.00 4.18
2366 6719 3.649073 AGGCCAAAATTTAACAAGTCGC 58.351 40.909 5.01 0.00 0.00 5.19
2367 6720 3.068873 AGGCCAAAATTTAACAAGTCGCA 59.931 39.130 5.01 0.00 0.00 5.10
2368 6721 3.428534 GGCCAAAATTTAACAAGTCGCAG 59.571 43.478 0.00 0.00 0.00 5.18
2369 6722 3.428534 GCCAAAATTTAACAAGTCGCAGG 59.571 43.478 0.00 0.00 0.00 4.85
2370 6723 4.794655 GCCAAAATTTAACAAGTCGCAGGA 60.795 41.667 0.00 0.00 0.00 3.86
2371 6724 5.285651 CCAAAATTTAACAAGTCGCAGGAA 58.714 37.500 0.00 0.00 0.00 3.36
2372 6725 5.751028 CCAAAATTTAACAAGTCGCAGGAAA 59.249 36.000 0.00 0.00 0.00 3.13
2373 6726 6.423604 CCAAAATTTAACAAGTCGCAGGAAAT 59.576 34.615 0.00 0.00 0.00 2.17
2374 6727 7.042119 CCAAAATTTAACAAGTCGCAGGAAATT 60.042 33.333 0.00 0.00 0.00 1.82
2375 6728 7.637709 AAATTTAACAAGTCGCAGGAAATTC 57.362 32.000 0.00 0.00 0.00 2.17
2376 6729 4.759516 TTAACAAGTCGCAGGAAATTCC 57.240 40.909 3.29 3.29 36.58 3.01
2377 6730 2.270352 ACAAGTCGCAGGAAATTCCA 57.730 45.000 15.21 0.00 39.61 3.53
2378 6731 1.880027 ACAAGTCGCAGGAAATTCCAC 59.120 47.619 15.21 3.44 39.61 4.02
2379 6732 1.200020 CAAGTCGCAGGAAATTCCACC 59.800 52.381 15.21 3.43 39.61 4.61
2380 6733 0.673644 AGTCGCAGGAAATTCCACCG 60.674 55.000 15.21 15.15 39.61 4.94
2381 6734 0.672401 GTCGCAGGAAATTCCACCGA 60.672 55.000 18.41 18.41 39.61 4.69
2382 6735 0.035598 TCGCAGGAAATTCCACCGAA 59.964 50.000 19.50 7.90 39.61 4.30
2383 6736 0.878416 CGCAGGAAATTCCACCGAAA 59.122 50.000 15.21 0.00 39.61 3.46
2384 6737 1.268352 CGCAGGAAATTCCACCGAAAA 59.732 47.619 15.21 0.00 39.61 2.29
2385 6738 2.094752 CGCAGGAAATTCCACCGAAAAT 60.095 45.455 15.21 0.00 39.61 1.82
2386 6739 3.613910 CGCAGGAAATTCCACCGAAAATT 60.614 43.478 15.21 0.00 39.61 1.82
2387 6740 4.314961 GCAGGAAATTCCACCGAAAATTT 58.685 39.130 15.21 0.00 39.61 1.82
2388 6741 4.388773 GCAGGAAATTCCACCGAAAATTTC 59.611 41.667 15.21 10.58 45.04 2.17
2389 6742 4.621034 CAGGAAATTCCACCGAAAATTTCG 59.379 41.667 19.95 19.95 45.98 3.46
2401 6754 3.753842 GAAAATTTCGGCAGCATAACGA 58.246 40.909 0.00 0.00 34.47 3.85
2402 6755 3.405170 AAATTTCGGCAGCATAACGAG 57.595 42.857 0.00 0.00 37.95 4.18
2403 6756 2.024176 ATTTCGGCAGCATAACGAGT 57.976 45.000 0.00 0.00 37.95 4.18
2404 6757 1.803334 TTTCGGCAGCATAACGAGTT 58.197 45.000 0.00 0.00 37.95 3.01
2405 6758 1.075542 TTCGGCAGCATAACGAGTTG 58.924 50.000 0.00 0.00 37.95 3.16
2406 6759 0.739462 TCGGCAGCATAACGAGTTGG 60.739 55.000 0.00 0.00 32.29 3.77
2407 6760 1.705337 CGGCAGCATAACGAGTTGGG 61.705 60.000 0.00 0.00 0.00 4.12
2408 6761 0.392461 GGCAGCATAACGAGTTGGGA 60.392 55.000 0.00 0.00 0.00 4.37
2409 6762 1.448985 GCAGCATAACGAGTTGGGAA 58.551 50.000 0.00 0.00 0.00 3.97
2410 6763 1.810151 GCAGCATAACGAGTTGGGAAA 59.190 47.619 0.00 0.00 0.00 3.13
2411 6764 2.159517 GCAGCATAACGAGTTGGGAAAG 60.160 50.000 0.00 0.00 0.00 2.62
2412 6765 2.420022 CAGCATAACGAGTTGGGAAAGG 59.580 50.000 0.00 0.00 0.00 3.11
2413 6766 1.132453 GCATAACGAGTTGGGAAAGGC 59.868 52.381 0.00 0.00 0.00 4.35
2414 6767 1.743394 CATAACGAGTTGGGAAAGGCC 59.257 52.381 0.00 0.00 0.00 5.19
2415 6768 0.766131 TAACGAGTTGGGAAAGGCCA 59.234 50.000 5.01 0.00 38.95 5.36
2416 6769 0.106419 AACGAGTTGGGAAAGGCCAA 60.106 50.000 5.01 0.00 38.95 4.52
2417 6770 0.112412 ACGAGTTGGGAAAGGCCAAT 59.888 50.000 5.01 0.00 38.95 3.16
2418 6771 0.811281 CGAGTTGGGAAAGGCCAATC 59.189 55.000 5.01 1.60 38.95 2.67
2419 6772 0.811281 GAGTTGGGAAAGGCCAATCG 59.189 55.000 5.01 0.00 38.95 3.34
2420 6773 1.215382 GTTGGGAAAGGCCAATCGC 59.785 57.895 5.01 11.76 38.95 4.58
2421 6774 1.228706 TTGGGAAAGGCCAATCGCA 60.229 52.632 19.36 19.36 40.31 5.10
2422 6775 0.614415 TTGGGAAAGGCCAATCGCAT 60.614 50.000 22.43 0.00 38.16 4.73
2423 6776 0.257328 TGGGAAAGGCCAATCGCATA 59.743 50.000 19.36 2.98 40.31 3.14
2424 6777 1.133513 TGGGAAAGGCCAATCGCATAT 60.134 47.619 19.36 0.00 40.31 1.78
2425 6778 1.270550 GGGAAAGGCCAATCGCATATG 59.729 52.381 16.73 0.00 40.31 1.78
2426 6779 1.336240 GGAAAGGCCAATCGCATATGC 60.336 52.381 18.08 18.08 40.31 3.14
2427 6780 1.337703 GAAAGGCCAATCGCATATGCA 59.662 47.619 26.52 14.35 42.21 3.96
2428 6781 0.956633 AAGGCCAATCGCATATGCAG 59.043 50.000 26.52 18.50 42.21 4.41
2429 6782 1.080974 GGCCAATCGCATATGCAGC 60.081 57.895 26.52 18.65 42.21 5.25
2430 6783 1.655885 GCCAATCGCATATGCAGCA 59.344 52.632 26.52 10.68 42.21 4.41
2431 6784 0.386858 GCCAATCGCATATGCAGCAG 60.387 55.000 26.52 13.23 42.21 4.24
2432 6785 0.949397 CCAATCGCATATGCAGCAGT 59.051 50.000 26.52 6.94 42.21 4.40
2433 6786 2.145536 CCAATCGCATATGCAGCAGTA 58.854 47.619 26.52 5.54 42.21 2.74
2434 6787 2.159037 CCAATCGCATATGCAGCAGTAG 59.841 50.000 26.52 9.13 42.21 2.57
2435 6788 2.804527 CAATCGCATATGCAGCAGTAGT 59.195 45.455 26.52 1.92 42.21 2.73
2436 6789 3.942130 ATCGCATATGCAGCAGTAGTA 57.058 42.857 26.52 3.47 42.21 1.82
2437 6790 3.942130 TCGCATATGCAGCAGTAGTAT 57.058 42.857 26.52 0.00 42.21 2.12
2438 6791 5.582689 ATCGCATATGCAGCAGTAGTATA 57.417 39.130 26.52 2.19 42.21 1.47
2439 6792 5.385509 TCGCATATGCAGCAGTAGTATAA 57.614 39.130 26.52 0.00 42.21 0.98
2440 6793 5.965922 TCGCATATGCAGCAGTAGTATAAT 58.034 37.500 26.52 0.00 42.21 1.28
2441 6794 7.095695 TCGCATATGCAGCAGTAGTATAATA 57.904 36.000 26.52 0.00 42.21 0.98
2442 6795 6.972901 TCGCATATGCAGCAGTAGTATAATAC 59.027 38.462 26.52 2.07 42.21 1.89
2443 6796 6.751888 CGCATATGCAGCAGTAGTATAATACA 59.248 38.462 26.52 0.00 42.21 2.29
2444 6797 7.275560 CGCATATGCAGCAGTAGTATAATACAA 59.724 37.037 26.52 0.00 42.21 2.41
2445 6798 8.383619 GCATATGCAGCAGTAGTATAATACAAC 58.616 37.037 22.84 4.20 41.59 3.32
2446 6799 9.423061 CATATGCAGCAGTAGTATAATACAACA 57.577 33.333 12.51 3.86 0.00 3.33
2447 6800 7.715265 ATGCAGCAGTAGTATAATACAACAC 57.285 36.000 12.51 0.00 0.00 3.32
2448 6801 6.873997 TGCAGCAGTAGTATAATACAACACT 58.126 36.000 12.51 1.82 0.00 3.55
2449 6802 8.002984 TGCAGCAGTAGTATAATACAACACTA 57.997 34.615 12.51 0.00 0.00 2.74
2450 6803 8.638873 TGCAGCAGTAGTATAATACAACACTAT 58.361 33.333 12.51 0.00 0.00 2.12
2465 6818 7.907214 ACAACACTATAAATCACTCCTCAAC 57.093 36.000 0.00 0.00 0.00 3.18
2466 6819 6.879458 ACAACACTATAAATCACTCCTCAACC 59.121 38.462 0.00 0.00 0.00 3.77
2467 6820 6.620877 ACACTATAAATCACTCCTCAACCA 57.379 37.500 0.00 0.00 0.00 3.67
2468 6821 7.200434 ACACTATAAATCACTCCTCAACCAT 57.800 36.000 0.00 0.00 0.00 3.55
2469 6822 7.050377 ACACTATAAATCACTCCTCAACCATG 58.950 38.462 0.00 0.00 0.00 3.66
2470 6823 6.017605 CACTATAAATCACTCCTCAACCATGC 60.018 42.308 0.00 0.00 0.00 4.06
2471 6824 2.134789 AATCACTCCTCAACCATGCC 57.865 50.000 0.00 0.00 0.00 4.40
2472 6825 1.293062 ATCACTCCTCAACCATGCCT 58.707 50.000 0.00 0.00 0.00 4.75
2473 6826 1.067295 TCACTCCTCAACCATGCCTT 58.933 50.000 0.00 0.00 0.00 4.35
2474 6827 1.003580 TCACTCCTCAACCATGCCTTC 59.996 52.381 0.00 0.00 0.00 3.46
2475 6828 1.004044 CACTCCTCAACCATGCCTTCT 59.996 52.381 0.00 0.00 0.00 2.85
2476 6829 1.280421 ACTCCTCAACCATGCCTTCTC 59.720 52.381 0.00 0.00 0.00 2.87
2477 6830 1.558756 CTCCTCAACCATGCCTTCTCT 59.441 52.381 0.00 0.00 0.00 3.10
2478 6831 1.988107 TCCTCAACCATGCCTTCTCTT 59.012 47.619 0.00 0.00 0.00 2.85
2479 6832 2.376518 TCCTCAACCATGCCTTCTCTTT 59.623 45.455 0.00 0.00 0.00 2.52
2480 6833 3.160269 CCTCAACCATGCCTTCTCTTTT 58.840 45.455 0.00 0.00 0.00 2.27
2481 6834 3.057033 CCTCAACCATGCCTTCTCTTTTG 60.057 47.826 0.00 0.00 0.00 2.44
2482 6835 3.565307 TCAACCATGCCTTCTCTTTTGT 58.435 40.909 0.00 0.00 0.00 2.83
2483 6836 3.318839 TCAACCATGCCTTCTCTTTTGTG 59.681 43.478 0.00 0.00 0.00 3.33
2484 6837 1.615392 ACCATGCCTTCTCTTTTGTGC 59.385 47.619 0.00 0.00 0.00 4.57
2485 6838 1.614903 CCATGCCTTCTCTTTTGTGCA 59.385 47.619 0.00 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
235 244 3.414759 TCTCCACTAAGGCCCAATAGA 57.585 47.619 13.22 0.00 37.29 1.98
332 344 1.080354 GGGGGAAGGAAAAAGGGGG 59.920 63.158 0.00 0.00 0.00 5.40
375 387 2.642807 CCAACCCTTCCAAGAGTAGGAA 59.357 50.000 0.00 0.00 42.62 3.36
1008 4107 4.345288 CGTACGAAGATTTGGATACGTCA 58.655 43.478 10.44 0.00 42.51 4.35
1026 4125 1.171308 TGTAGAGGTGGTCAGCGTAC 58.829 55.000 8.03 8.03 0.00 3.67
1210 4314 3.100671 AGAGCTACTTGTAGTTCCAGGG 58.899 50.000 17.05 0.00 0.00 4.45
1267 4643 1.326245 CTGCGCAAAATGCATCATTGG 59.674 47.619 13.05 13.98 45.36 3.16
1280 4656 1.446099 GAGTGGTCGATCTGCGCAA 60.446 57.895 13.05 2.72 40.61 4.85
1385 4761 1.580942 CCATGGTTGAACACGCAGG 59.419 57.895 2.57 0.00 0.00 4.85
1388 4764 2.126888 CGCCATGGTTGAACACGC 60.127 61.111 14.67 0.00 0.00 5.34
1543 5830 4.962362 TCATATCAAGGCACCTCAAGTCTA 59.038 41.667 0.00 0.00 0.00 2.59
1556 5843 3.192422 CCGTCTAGCCTCTCATATCAAGG 59.808 52.174 0.00 0.00 0.00 3.61
1675 5963 3.706373 ATGCGCTCTTGGGGACGT 61.706 61.111 9.73 0.00 0.00 4.34
1684 5972 0.957395 CAACCTCCAACATGCGCTCT 60.957 55.000 9.73 0.00 0.00 4.09
1816 6113 1.475280 CGACAACCTCCGACCATCTAA 59.525 52.381 0.00 0.00 0.00 2.10
1857 6154 4.023980 AGACACGATGGAGTATCTGGAAA 58.976 43.478 0.00 0.00 33.44 3.13
2037 6376 8.582433 AATTCCAACAAAAATTTCGTATTCGT 57.418 26.923 0.00 0.00 38.33 3.85
2149 6500 5.504853 TCATTATTGCTTGGGATGTGTGTA 58.495 37.500 0.00 0.00 0.00 2.90
2194 6546 5.106475 GCGTACCCACATCAAATAAGAAACA 60.106 40.000 0.00 0.00 0.00 2.83
2238 6591 7.829706 AGATGTTTTTCTTGGGAGGATTAGTAC 59.170 37.037 0.00 0.00 0.00 2.73
2239 6592 7.829211 CAGATGTTTTTCTTGGGAGGATTAGTA 59.171 37.037 0.00 0.00 0.00 1.82
2240 6593 6.660949 CAGATGTTTTTCTTGGGAGGATTAGT 59.339 38.462 0.00 0.00 0.00 2.24
2264 6617 8.935844 GGTTGCGAGATTATATATTTCATGTCA 58.064 33.333 0.00 0.00 0.00 3.58
2266 6619 8.846943 TGGTTGCGAGATTATATATTTCATGT 57.153 30.769 0.00 0.00 0.00 3.21
2274 6627 5.542635 AGGGACTTGGTTGCGAGATTATATA 59.457 40.000 0.00 0.00 27.25 0.86
2352 6705 6.156519 GGAATTTCCTGCGACTTGTTAAATT 58.843 36.000 8.25 0.00 32.53 1.82
2353 6706 5.242838 TGGAATTTCCTGCGACTTGTTAAAT 59.757 36.000 16.25 0.00 37.46 1.40
2354 6707 4.580995 TGGAATTTCCTGCGACTTGTTAAA 59.419 37.500 16.25 0.00 37.46 1.52
2355 6708 4.023536 GTGGAATTTCCTGCGACTTGTTAA 60.024 41.667 16.25 0.00 37.46 2.01
2356 6709 3.500680 GTGGAATTTCCTGCGACTTGTTA 59.499 43.478 16.25 0.00 37.46 2.41
2357 6710 2.293399 GTGGAATTTCCTGCGACTTGTT 59.707 45.455 16.25 0.00 37.46 2.83
2358 6711 1.880027 GTGGAATTTCCTGCGACTTGT 59.120 47.619 16.25 0.00 37.46 3.16
2359 6712 1.200020 GGTGGAATTTCCTGCGACTTG 59.800 52.381 16.25 0.00 37.46 3.16
2360 6713 1.534729 GGTGGAATTTCCTGCGACTT 58.465 50.000 16.25 0.00 37.46 3.01
2361 6714 0.673644 CGGTGGAATTTCCTGCGACT 60.674 55.000 16.25 0.00 37.46 4.18
2362 6715 0.672401 TCGGTGGAATTTCCTGCGAC 60.672 55.000 16.25 6.10 37.46 5.19
2363 6716 0.035598 TTCGGTGGAATTTCCTGCGA 59.964 50.000 16.25 8.34 37.46 5.10
2364 6717 0.878416 TTTCGGTGGAATTTCCTGCG 59.122 50.000 16.25 6.56 37.46 5.18
2365 6718 3.592898 ATTTTCGGTGGAATTTCCTGC 57.407 42.857 16.25 9.05 37.46 4.85
2380 6733 3.753842 TCGTTATGCTGCCGAAATTTTC 58.246 40.909 0.00 0.00 0.00 2.29
2381 6734 3.190535 ACTCGTTATGCTGCCGAAATTTT 59.809 39.130 0.00 0.00 0.00 1.82
2382 6735 2.747446 ACTCGTTATGCTGCCGAAATTT 59.253 40.909 0.00 0.00 0.00 1.82
2383 6736 2.356135 ACTCGTTATGCTGCCGAAATT 58.644 42.857 0.00 0.00 0.00 1.82
2384 6737 2.024176 ACTCGTTATGCTGCCGAAAT 57.976 45.000 0.00 0.00 0.00 2.17
2385 6738 1.463056 CAACTCGTTATGCTGCCGAAA 59.537 47.619 0.00 0.00 0.00 3.46
2386 6739 1.075542 CAACTCGTTATGCTGCCGAA 58.924 50.000 0.00 0.00 0.00 4.30
2387 6740 0.739462 CCAACTCGTTATGCTGCCGA 60.739 55.000 0.00 0.00 0.00 5.54
2388 6741 1.705337 CCCAACTCGTTATGCTGCCG 61.705 60.000 0.00 0.00 0.00 5.69
2389 6742 0.392461 TCCCAACTCGTTATGCTGCC 60.392 55.000 0.00 0.00 0.00 4.85
2390 6743 1.448985 TTCCCAACTCGTTATGCTGC 58.551 50.000 0.00 0.00 0.00 5.25
2391 6744 2.420022 CCTTTCCCAACTCGTTATGCTG 59.580 50.000 0.00 0.00 0.00 4.41
2392 6745 2.711542 CCTTTCCCAACTCGTTATGCT 58.288 47.619 0.00 0.00 0.00 3.79
2393 6746 1.132453 GCCTTTCCCAACTCGTTATGC 59.868 52.381 0.00 0.00 0.00 3.14
2394 6747 1.743394 GGCCTTTCCCAACTCGTTATG 59.257 52.381 0.00 0.00 0.00 1.90
2395 6748 1.353022 TGGCCTTTCCCAACTCGTTAT 59.647 47.619 3.32 0.00 30.32 1.89
2396 6749 0.766131 TGGCCTTTCCCAACTCGTTA 59.234 50.000 3.32 0.00 30.32 3.18
2397 6750 0.106419 TTGGCCTTTCCCAACTCGTT 60.106 50.000 3.32 0.00 39.85 3.85
2398 6751 0.112412 ATTGGCCTTTCCCAACTCGT 59.888 50.000 3.32 0.00 46.85 4.18
2399 6752 0.811281 GATTGGCCTTTCCCAACTCG 59.189 55.000 3.32 0.00 46.85 4.18
2400 6753 0.811281 CGATTGGCCTTTCCCAACTC 59.189 55.000 3.32 0.00 46.85 3.01
2401 6754 1.250840 GCGATTGGCCTTTCCCAACT 61.251 55.000 3.32 0.00 46.85 3.16
2402 6755 1.215382 GCGATTGGCCTTTCCCAAC 59.785 57.895 3.32 0.00 46.85 3.77
2404 6757 0.257328 TATGCGATTGGCCTTTCCCA 59.743 50.000 3.32 0.00 42.61 4.37
2405 6758 1.270550 CATATGCGATTGGCCTTTCCC 59.729 52.381 3.32 0.00 42.61 3.97
2406 6759 1.336240 GCATATGCGATTGGCCTTTCC 60.336 52.381 12.82 0.00 42.61 3.13
2407 6760 1.337703 TGCATATGCGATTGGCCTTTC 59.662 47.619 22.21 0.00 45.83 2.62
2408 6761 1.338973 CTGCATATGCGATTGGCCTTT 59.661 47.619 22.21 0.00 45.83 3.11
2409 6762 0.956633 CTGCATATGCGATTGGCCTT 59.043 50.000 22.21 0.00 45.83 4.35
2410 6763 1.521450 GCTGCATATGCGATTGGCCT 61.521 55.000 22.21 0.00 45.83 5.19
2411 6764 1.080974 GCTGCATATGCGATTGGCC 60.081 57.895 22.21 0.00 45.83 5.36
2412 6765 0.386858 CTGCTGCATATGCGATTGGC 60.387 55.000 22.21 18.87 45.83 4.52
2413 6766 0.949397 ACTGCTGCATATGCGATTGG 59.051 50.000 22.21 13.11 45.83 3.16
2414 6767 2.804527 ACTACTGCTGCATATGCGATTG 59.195 45.455 22.21 14.45 45.83 2.67
2415 6768 3.117491 ACTACTGCTGCATATGCGATT 57.883 42.857 22.21 7.63 45.83 3.34
2416 6769 2.827800 ACTACTGCTGCATATGCGAT 57.172 45.000 22.21 8.44 45.83 4.58
2417 6770 3.942130 ATACTACTGCTGCATATGCGA 57.058 42.857 22.21 10.84 45.83 5.10
2418 6771 6.751888 TGTATTATACTACTGCTGCATATGCG 59.248 38.462 22.21 17.15 45.83 4.73
2419 6772 8.383619 GTTGTATTATACTACTGCTGCATATGC 58.616 37.037 21.09 21.09 35.34 3.14
2420 6773 9.423061 TGTTGTATTATACTACTGCTGCATATG 57.577 33.333 15.46 0.00 35.82 1.78
2421 6774 9.424319 GTGTTGTATTATACTACTGCTGCATAT 57.576 33.333 15.46 0.43 35.82 1.78
2422 6775 8.638873 AGTGTTGTATTATACTACTGCTGCATA 58.361 33.333 15.46 0.00 35.82 3.14
2423 6776 7.500992 AGTGTTGTATTATACTACTGCTGCAT 58.499 34.615 15.46 0.00 35.82 3.96
2424 6777 6.873997 AGTGTTGTATTATACTACTGCTGCA 58.126 36.000 15.46 0.88 35.82 4.41
2439 6792 9.601217 GTTGAGGAGTGATTTATAGTGTTGTAT 57.399 33.333 0.00 0.00 0.00 2.29
2440 6793 8.038944 GGTTGAGGAGTGATTTATAGTGTTGTA 58.961 37.037 0.00 0.00 0.00 2.41
2441 6794 6.879458 GGTTGAGGAGTGATTTATAGTGTTGT 59.121 38.462 0.00 0.00 0.00 3.32
2442 6795 6.878923 TGGTTGAGGAGTGATTTATAGTGTTG 59.121 38.462 0.00 0.00 0.00 3.33
2443 6796 7.016153 TGGTTGAGGAGTGATTTATAGTGTT 57.984 36.000 0.00 0.00 0.00 3.32
2444 6797 6.620877 TGGTTGAGGAGTGATTTATAGTGT 57.379 37.500 0.00 0.00 0.00 3.55
2445 6798 6.017605 GCATGGTTGAGGAGTGATTTATAGTG 60.018 42.308 0.00 0.00 0.00 2.74
2446 6799 6.058183 GCATGGTTGAGGAGTGATTTATAGT 58.942 40.000 0.00 0.00 0.00 2.12
2447 6800 5.471456 GGCATGGTTGAGGAGTGATTTATAG 59.529 44.000 0.00 0.00 0.00 1.31
2448 6801 5.132648 AGGCATGGTTGAGGAGTGATTTATA 59.867 40.000 0.00 0.00 0.00 0.98
2449 6802 4.079558 AGGCATGGTTGAGGAGTGATTTAT 60.080 41.667 0.00 0.00 0.00 1.40
2450 6803 3.266772 AGGCATGGTTGAGGAGTGATTTA 59.733 43.478 0.00 0.00 0.00 1.40
2451 6804 2.042162 AGGCATGGTTGAGGAGTGATTT 59.958 45.455 0.00 0.00 0.00 2.17
2452 6805 1.637553 AGGCATGGTTGAGGAGTGATT 59.362 47.619 0.00 0.00 0.00 2.57
2453 6806 1.293062 AGGCATGGTTGAGGAGTGAT 58.707 50.000 0.00 0.00 0.00 3.06
2454 6807 1.003580 GAAGGCATGGTTGAGGAGTGA 59.996 52.381 0.00 0.00 0.00 3.41
2455 6808 1.004044 AGAAGGCATGGTTGAGGAGTG 59.996 52.381 0.00 0.00 0.00 3.51
2456 6809 1.280421 GAGAAGGCATGGTTGAGGAGT 59.720 52.381 0.00 0.00 0.00 3.85
2457 6810 1.558756 AGAGAAGGCATGGTTGAGGAG 59.441 52.381 0.00 0.00 0.00 3.69
2458 6811 1.661463 AGAGAAGGCATGGTTGAGGA 58.339 50.000 0.00 0.00 0.00 3.71
2459 6812 2.503895 AAGAGAAGGCATGGTTGAGG 57.496 50.000 0.00 0.00 0.00 3.86
2460 6813 3.571401 ACAAAAGAGAAGGCATGGTTGAG 59.429 43.478 0.00 0.00 0.00 3.02
2461 6814 3.318839 CACAAAAGAGAAGGCATGGTTGA 59.681 43.478 0.00 0.00 0.00 3.18
2462 6815 3.645884 CACAAAAGAGAAGGCATGGTTG 58.354 45.455 0.00 0.00 0.00 3.77
2463 6816 2.036346 GCACAAAAGAGAAGGCATGGTT 59.964 45.455 0.00 0.00 0.00 3.67
2464 6817 1.615392 GCACAAAAGAGAAGGCATGGT 59.385 47.619 0.00 0.00 0.00 3.55
2465 6818 1.614903 TGCACAAAAGAGAAGGCATGG 59.385 47.619 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.