Multiple sequence alignment - TraesCS5D01G564800

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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 TraesCS5D01G564800 chr5D 100.000 3466 0 0 1 3466 563641014 563637549 0.000000e+00 6401
1 TraesCS5D01G564800 chr5D 86.169 1446 101 44 1282 2673 563727030 563725630 0.000000e+00 1471
2 TraesCS5D01G564800 chr5D 97.687 562 12 1 2906 3466 563631734 563631173 0.000000e+00 965
3 TraesCS5D01G564800 chr5D 97.331 562 14 1 2906 3466 72935763 72935202 0.000000e+00 953
4 TraesCS5D01G564800 chr5D 91.463 246 21 0 1016 1261 563727266 563727021 4.280000e-89 339
5 TraesCS5D01G564800 chr5D 95.652 46 2 0 2228 2273 563638752 563638707 1.330000e-09 75
6 TraesCS5D01G564800 chr5D 95.652 46 2 0 2263 2308 563638787 563638742 1.330000e-09 75
7 TraesCS5D01G564800 chr7D 94.036 939 54 2 1 937 421421198 421420260 0.000000e+00 1423
8 TraesCS5D01G564800 chr3D 93.943 941 52 5 1 937 454997403 454998342 0.000000e+00 1417
9 TraesCS5D01G564800 chr3D 93.830 940 55 3 1 937 529888754 529889693 0.000000e+00 1411
10 TraesCS5D01G564800 chr3D 93.624 941 56 4 2 939 287088334 287089273 0.000000e+00 1402
11 TraesCS5D01G564800 chr3D 93.617 940 57 3 1 937 95975408 95974469 0.000000e+00 1400
12 TraesCS5D01G564800 chr3D 97.326 561 14 1 2906 3465 501025367 501024807 0.000000e+00 952
13 TraesCS5D01G564800 chr4D 93.843 942 54 4 1 939 432453685 432452745 0.000000e+00 1415
14 TraesCS5D01G564800 chr4D 93.637 943 56 4 1 939 327677285 327676343 0.000000e+00 1406
15 TraesCS5D01G564800 chr4D 97.153 562 14 2 2906 3466 242431807 242432367 0.000000e+00 948
16 TraesCS5D01G564800 chr4D 97.153 562 14 2 2906 3466 437594272 437594832 0.000000e+00 948
17 TraesCS5D01G564800 chr1D 93.559 947 55 5 1 943 257651387 257650443 0.000000e+00 1406
18 TraesCS5D01G564800 chr1D 97.153 562 15 1 2906 3466 345111857 345112418 0.000000e+00 948
19 TraesCS5D01G564800 chr1D 97.153 562 15 1 2906 3466 386735922 386736483 0.000000e+00 948
20 TraesCS5D01G564800 chr1D 96.991 565 15 2 2903 3466 406487214 406487777 0.000000e+00 948
21 TraesCS5D01G564800 chr2D 93.538 944 55 6 1 939 58324886 58323944 0.000000e+00 1400
22 TraesCS5D01G564800 chr2D 96.980 563 15 2 2906 3466 303340875 303340313 0.000000e+00 944
23 TraesCS5D01G564800 chr5B 83.293 1658 117 69 945 2547 706156903 706155351 0.000000e+00 1380
24 TraesCS5D01G564800 chr5B 78.761 678 61 40 2090 2737 705947065 705946441 9.080000e-101 377
25 TraesCS5D01G564800 chr5B 83.565 359 23 11 2341 2664 705978419 705978062 1.560000e-78 303
26 TraesCS5D01G564800 chr5B 82.229 332 41 15 1713 2039 705964628 705964310 1.590000e-68 270
27 TraesCS5D01G564800 chr5B 91.111 90 3 4 2817 2906 705946304 705946220 2.190000e-22 117
28 TraesCS5D01G564800 chr4A 84.441 1414 102 52 1279 2656 608867038 608868369 0.000000e+00 1284
29 TraesCS5D01G564800 chr4A 84.639 319 27 5 948 1260 608866747 608867049 7.270000e-77 298
30 TraesCS5D01G564800 chr7B 94.382 89 5 0 2817 2905 106510918 106510830 1.680000e-28 137


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 TraesCS5D01G564800 chr5D 563637549 563641014 3465 True 2183.666667 6401 97.101333 1 3466 3 chr5D.!!$R3 3465
1 TraesCS5D01G564800 chr5D 563631173 563631734 561 True 965.000000 965 97.687000 2906 3466 1 chr5D.!!$R2 560
2 TraesCS5D01G564800 chr5D 72935202 72935763 561 True 953.000000 953 97.331000 2906 3466 1 chr5D.!!$R1 560
3 TraesCS5D01G564800 chr5D 563725630 563727266 1636 True 905.000000 1471 88.816000 1016 2673 2 chr5D.!!$R4 1657
4 TraesCS5D01G564800 chr7D 421420260 421421198 938 True 1423.000000 1423 94.036000 1 937 1 chr7D.!!$R1 936
5 TraesCS5D01G564800 chr3D 454997403 454998342 939 False 1417.000000 1417 93.943000 1 937 1 chr3D.!!$F2 936
6 TraesCS5D01G564800 chr3D 529888754 529889693 939 False 1411.000000 1411 93.830000 1 937 1 chr3D.!!$F3 936
7 TraesCS5D01G564800 chr3D 287088334 287089273 939 False 1402.000000 1402 93.624000 2 939 1 chr3D.!!$F1 937
8 TraesCS5D01G564800 chr3D 95974469 95975408 939 True 1400.000000 1400 93.617000 1 937 1 chr3D.!!$R1 936
9 TraesCS5D01G564800 chr3D 501024807 501025367 560 True 952.000000 952 97.326000 2906 3465 1 chr3D.!!$R2 559
10 TraesCS5D01G564800 chr4D 432452745 432453685 940 True 1415.000000 1415 93.843000 1 939 1 chr4D.!!$R2 938
11 TraesCS5D01G564800 chr4D 327676343 327677285 942 True 1406.000000 1406 93.637000 1 939 1 chr4D.!!$R1 938
12 TraesCS5D01G564800 chr4D 242431807 242432367 560 False 948.000000 948 97.153000 2906 3466 1 chr4D.!!$F1 560
13 TraesCS5D01G564800 chr4D 437594272 437594832 560 False 948.000000 948 97.153000 2906 3466 1 chr4D.!!$F2 560
14 TraesCS5D01G564800 chr1D 257650443 257651387 944 True 1406.000000 1406 93.559000 1 943 1 chr1D.!!$R1 942
15 TraesCS5D01G564800 chr1D 345111857 345112418 561 False 948.000000 948 97.153000 2906 3466 1 chr1D.!!$F1 560
16 TraesCS5D01G564800 chr1D 386735922 386736483 561 False 948.000000 948 97.153000 2906 3466 1 chr1D.!!$F2 560
17 TraesCS5D01G564800 chr1D 406487214 406487777 563 False 948.000000 948 96.991000 2903 3466 1 chr1D.!!$F3 563
18 TraesCS5D01G564800 chr2D 58323944 58324886 942 True 1400.000000 1400 93.538000 1 939 1 chr2D.!!$R1 938
19 TraesCS5D01G564800 chr2D 303340313 303340875 562 True 944.000000 944 96.980000 2906 3466 1 chr2D.!!$R2 560
20 TraesCS5D01G564800 chr5B 706155351 706156903 1552 True 1380.000000 1380 83.293000 945 2547 1 chr5B.!!$R3 1602
21 TraesCS5D01G564800 chr5B 705946220 705947065 845 True 247.000000 377 84.936000 2090 2906 2 chr5B.!!$R4 816
22 TraesCS5D01G564800 chr4A 608866747 608868369 1622 False 791.000000 1284 84.540000 948 2656 2 chr4A.!!$F1 1708

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
964 973 0.386985 GAGCTGCTGCAAAAGTCTGC 60.387 55.0 18.42 1.35 42.74 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2473 2586 0.032117 TGTCATGGAGGGGAGACGAT 60.032 55.0 0.0 0.0 33.83 3.73 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
128 129 2.789409 AAAACTTGGAGATCCGGGAG 57.211 50.000 0.00 0.00 39.43 4.30
135 136 1.062428 TGGAGATCCGGGAGTACCAAT 60.062 52.381 13.76 0.00 40.22 3.16
297 298 3.668447 CTGACAAGTCAACTGCCATACT 58.332 45.455 4.29 0.00 39.39 2.12
354 355 7.549134 TGTTGCTAATGTTACTATCTTGACTGG 59.451 37.037 0.00 0.00 0.00 4.00
430 431 2.019984 CCCTTCTTGAATACTGCAGGC 58.980 52.381 19.93 4.95 0.00 4.85
587 589 8.832735 TGGAAGTTTTCAAATACCTCTACCTAT 58.167 33.333 0.00 0.00 0.00 2.57
602 604 9.014297 ACCTCTACCTATTGTCAAAAAGAAATG 57.986 33.333 0.00 0.00 0.00 2.32
673 675 9.151471 CTTAGTGATCTACGAAAATTCTTTGGA 57.849 33.333 0.00 0.00 0.00 3.53
787 790 9.478768 GTAAGCACTAATTTCTATCCCTACTTC 57.521 37.037 0.00 0.00 0.00 3.01
845 848 5.917541 TGTCATGTTTAGTCCGTTTTCTC 57.082 39.130 0.00 0.00 0.00 2.87
857 860 2.292292 CCGTTTTCTCAATTTCCCGTGT 59.708 45.455 0.00 0.00 0.00 4.49
955 964 1.100463 TTTTCGTTGGAGCTGCTGCA 61.100 50.000 20.33 20.33 42.74 4.41
964 973 0.386985 GAGCTGCTGCAAAAGTCTGC 60.387 55.000 18.42 1.35 42.74 4.26
975 984 5.118642 GCAAAAGTCTGCATCTTTCTCTT 57.881 39.130 14.45 1.00 42.17 2.85
984 993 3.244215 TGCATCTTTCTCTTTGTCCGTCT 60.244 43.478 0.00 0.00 0.00 4.18
985 994 3.748568 GCATCTTTCTCTTTGTCCGTCTT 59.251 43.478 0.00 0.00 0.00 3.01
986 995 4.377841 GCATCTTTCTCTTTGTCCGTCTTG 60.378 45.833 0.00 0.00 0.00 3.02
987 996 4.402056 TCTTTCTCTTTGTCCGTCTTGT 57.598 40.909 0.00 0.00 0.00 3.16
988 997 5.524971 TCTTTCTCTTTGTCCGTCTTGTA 57.475 39.130 0.00 0.00 0.00 2.41
993 1002 6.395426 TCTCTTTGTCCGTCTTGTAAGTAA 57.605 37.500 0.00 0.00 0.00 2.24
1003 1018 5.220662 CCGTCTTGTAAGTAAATGAGCATGG 60.221 44.000 0.00 0.00 0.00 3.66
1004 1019 5.580691 CGTCTTGTAAGTAAATGAGCATGGA 59.419 40.000 0.00 0.00 0.00 3.41
1009 1024 1.486310 AGTAAATGAGCATGGAGGCGA 59.514 47.619 0.00 0.00 39.27 5.54
1012 1027 0.463295 AATGAGCATGGAGGCGACTG 60.463 55.000 0.00 0.00 44.43 3.51
1051 1066 0.323542 GACTTCCTCCTCCGTCCTCA 60.324 60.000 0.00 0.00 0.00 3.86
1084 1099 2.937689 ACCATGCCACTCCCAGCT 60.938 61.111 0.00 0.00 0.00 4.24
1260 1287 6.725246 CAACGTCAAGGTAACATCTTTCTTT 58.275 36.000 0.00 0.00 41.41 2.52
1261 1288 6.937436 ACGTCAAGGTAACATCTTTCTTTT 57.063 33.333 0.00 0.00 41.41 2.27
1262 1289 7.329588 ACGTCAAGGTAACATCTTTCTTTTT 57.670 32.000 0.00 0.00 41.41 1.94
1310 1342 2.828095 CCAATCCCGCAATCCGCA 60.828 61.111 0.00 0.00 42.60 5.69
1341 1375 0.107456 CCATCGATTCCCCACCTGAG 59.893 60.000 0.00 0.00 0.00 3.35
1342 1376 0.533755 CATCGATTCCCCACCTGAGC 60.534 60.000 0.00 0.00 0.00 4.26
1343 1377 2.032860 ATCGATTCCCCACCTGAGCG 62.033 60.000 0.00 0.00 0.00 5.03
1344 1378 2.190578 GATTCCCCACCTGAGCGG 59.809 66.667 0.00 0.00 39.35 5.52
1353 1387 4.767255 CCTGAGCGGCTGACCCAC 62.767 72.222 7.50 0.00 0.00 4.61
1354 1388 4.767255 CTGAGCGGCTGACCCACC 62.767 72.222 7.50 0.00 0.00 4.61
1359 1393 4.087892 CGGCTGACCCACCTCCTG 62.088 72.222 0.00 0.00 0.00 3.86
1406 1444 0.836400 ACATCGAGGACAAGGTGGGT 60.836 55.000 3.06 0.00 0.00 4.51
1409 1447 2.571216 CGAGGACAAGGTGGGTCGT 61.571 63.158 0.00 0.00 36.12 4.34
1562 1600 2.835895 GCCGAGGAGGAGGAGGAC 60.836 72.222 0.00 0.00 45.00 3.85
1580 1618 0.032017 ACTCCTCCTACGCCTCCATT 60.032 55.000 0.00 0.00 0.00 3.16
1622 1660 3.181367 CGCAAGCTCCGCAAGATT 58.819 55.556 8.63 0.00 43.02 2.40
1646 1684 2.974489 GAAGGAGACCGACGTGCGA 61.974 63.158 0.00 0.00 44.57 5.10
1647 1685 2.267681 GAAGGAGACCGACGTGCGAT 62.268 60.000 0.00 0.00 44.57 4.58
1727 1784 2.691771 GCAGAGGACGACGAGCTCA 61.692 63.158 15.40 0.00 0.00 4.26
1790 1847 1.146041 GTGACCACTGCACTGACCA 59.854 57.895 0.00 0.00 33.57 4.02
1795 1852 0.813610 CCACTGCACTGACCAACGAA 60.814 55.000 0.00 0.00 0.00 3.85
1817 1874 5.831702 ACCATCAATCAATCTCTCTTTGC 57.168 39.130 0.00 0.00 0.00 3.68
1854 1914 3.855689 ATGCCACTCATTTACAACTGC 57.144 42.857 0.00 0.00 29.16 4.40
1957 2025 4.194640 AGAATTCATCTATGTTGCTGCGT 58.805 39.130 8.44 0.00 36.32 5.24
1958 2026 4.637534 AGAATTCATCTATGTTGCTGCGTT 59.362 37.500 8.44 0.00 36.32 4.84
1959 2027 5.817296 AGAATTCATCTATGTTGCTGCGTTA 59.183 36.000 8.44 0.00 36.32 3.18
1960 2028 6.316140 AGAATTCATCTATGTTGCTGCGTTAA 59.684 34.615 8.44 0.00 36.32 2.01
2023 2094 5.737860 TGATGTGTGAGCTCATCAACTATT 58.262 37.500 21.47 7.10 46.31 1.73
2231 2311 5.294306 ACTGTTCATGTGTACAACTCAACTG 59.706 40.000 0.00 5.85 0.00 3.16
2290 2375 7.963532 TGAACTTATCTGAACCAGACTAAACT 58.036 34.615 0.00 0.00 43.63 2.66
2298 2383 7.434492 TCTGAACCAGACTAAACTGAAGTTAG 58.566 38.462 0.00 0.00 39.94 2.34
2305 2390 6.701841 CAGACTAAACTGAAGTTAGCTGAACA 59.298 38.462 0.00 0.00 39.03 3.18
2306 2391 7.386299 CAGACTAAACTGAAGTTAGCTGAACAT 59.614 37.037 0.00 0.00 39.03 2.71
2308 2393 8.535690 ACTAAACTGAAGTTAGCTGAACATAC 57.464 34.615 0.00 0.00 40.86 2.39
2310 2395 4.495422 ACTGAAGTTAGCTGAACATACCG 58.505 43.478 0.00 0.00 40.86 4.02
2311 2396 4.219944 ACTGAAGTTAGCTGAACATACCGA 59.780 41.667 0.00 0.00 40.86 4.69
2312 2397 4.491676 TGAAGTTAGCTGAACATACCGAC 58.508 43.478 0.00 0.00 40.86 4.79
2313 2398 4.219944 TGAAGTTAGCTGAACATACCGACT 59.780 41.667 0.00 0.00 40.86 4.18
2314 2399 5.416639 TGAAGTTAGCTGAACATACCGACTA 59.583 40.000 0.00 0.00 40.86 2.59
2315 2400 5.909621 AGTTAGCTGAACATACCGACTAA 57.090 39.130 0.00 0.00 40.86 2.24
2318 2403 4.530710 AGCTGAACATACCGACTAAACA 57.469 40.909 0.00 0.00 0.00 2.83
2319 2404 5.086104 AGCTGAACATACCGACTAAACAT 57.914 39.130 0.00 0.00 0.00 2.71
2320 2405 6.216801 AGCTGAACATACCGACTAAACATA 57.783 37.500 0.00 0.00 0.00 2.29
2321 2406 6.636705 AGCTGAACATACCGACTAAACATAA 58.363 36.000 0.00 0.00 0.00 1.90
2322 2407 6.534079 AGCTGAACATACCGACTAAACATAAC 59.466 38.462 0.00 0.00 0.00 1.89
2323 2408 6.534079 GCTGAACATACCGACTAAACATAACT 59.466 38.462 0.00 0.00 0.00 2.24
2324 2409 7.464178 GCTGAACATACCGACTAAACATAACTG 60.464 40.741 0.00 0.00 0.00 3.16
2325 2410 7.604549 TGAACATACCGACTAAACATAACTGA 58.395 34.615 0.00 0.00 0.00 3.41
2326 2411 8.089597 TGAACATACCGACTAAACATAACTGAA 58.910 33.333 0.00 0.00 0.00 3.02
2327 2412 7.823149 ACATACCGACTAAACATAACTGAAC 57.177 36.000 0.00 0.00 0.00 3.18
2328 2413 7.609056 ACATACCGACTAAACATAACTGAACT 58.391 34.615 0.00 0.00 0.00 3.01
2329 2414 7.544566 ACATACCGACTAAACATAACTGAACTG 59.455 37.037 0.00 0.00 0.00 3.16
2330 2415 6.092955 ACCGACTAAACATAACTGAACTGA 57.907 37.500 0.00 0.00 0.00 3.41
2331 2416 6.157211 ACCGACTAAACATAACTGAACTGAG 58.843 40.000 0.00 0.00 0.00 3.35
2332 2417 5.062308 CCGACTAAACATAACTGAACTGAGC 59.938 44.000 0.00 0.00 0.00 4.26
2333 2418 5.062308 CGACTAAACATAACTGAACTGAGCC 59.938 44.000 0.00 0.00 0.00 4.70
2334 2419 4.929808 ACTAAACATAACTGAACTGAGCCG 59.070 41.667 0.00 0.00 0.00 5.52
2335 2420 3.402628 AACATAACTGAACTGAGCCGT 57.597 42.857 0.00 0.00 0.00 5.68
2336 2421 2.960819 ACATAACTGAACTGAGCCGTC 58.039 47.619 0.00 0.00 0.00 4.79
2337 2422 2.563179 ACATAACTGAACTGAGCCGTCT 59.437 45.455 0.00 0.00 0.00 4.18
2361 2446 1.450312 GCAGGGGAGGTGAACATCG 60.450 63.158 0.00 0.00 0.00 3.84
2380 2465 2.168496 CGTGTACAAGAGGAAGGAGGA 58.832 52.381 2.23 0.00 0.00 3.71
2411 2496 1.424302 CTCATCATCCCCAAGCAGGAT 59.576 52.381 0.00 0.00 45.28 3.24
2441 2526 1.973281 CAAGGCCACCGTCAATGCT 60.973 57.895 5.01 0.00 0.00 3.79
2474 2587 4.760047 GCCGGCTGACCACGTCAT 62.760 66.667 22.15 0.00 41.94 3.06
2475 2588 2.509336 CCGGCTGACCACGTCATC 60.509 66.667 0.00 0.00 41.94 2.92
2583 2721 2.775890 ACTGCTGGTGTTTCATCAGAG 58.224 47.619 13.27 9.84 44.59 3.35
2591 2729 3.397482 GTGTTTCATCAGAGCAGACAGT 58.603 45.455 0.00 0.00 0.00 3.55
2592 2730 3.812053 GTGTTTCATCAGAGCAGACAGTT 59.188 43.478 0.00 0.00 0.00 3.16
2658 2812 2.510800 TCATGATGATCCCACACACCAT 59.489 45.455 0.00 0.00 0.00 3.55
2659 2813 2.715749 TGATGATCCCACACACCATC 57.284 50.000 0.00 0.00 35.47 3.51
2680 2838 6.318900 CCATCTGGTAAGTTGTTTCTATTCCC 59.681 42.308 0.00 0.00 0.00 3.97
2682 2840 6.708285 TCTGGTAAGTTGTTTCTATTCCCTC 58.292 40.000 0.00 0.00 0.00 4.30
2689 2848 5.048713 AGTTGTTTCTATTCCCTCTTTTGCG 60.049 40.000 0.00 0.00 0.00 4.85
2714 2873 7.548075 CGGGAAAAGGGATACATACATACATAC 59.452 40.741 0.00 0.00 39.74 2.39
2722 2881 7.708322 GGGATACATACATACATACATCTGCAG 59.292 40.741 7.63 7.63 39.74 4.41
2742 2929 9.013229 TCTGCAGTCATGTTAACTAATTGAAAT 57.987 29.630 14.67 0.00 0.00 2.17
2744 2931 9.409312 TGCAGTCATGTTAACTAATTGAAATTG 57.591 29.630 7.22 6.05 0.00 2.32
2756 2943 7.460910 ACTAATTGAAATTGGAAATTTGCCCT 58.539 30.769 7.27 0.00 32.04 5.19
2758 2945 6.822667 ATTGAAATTGGAAATTTGCCCTTC 57.177 33.333 7.27 7.67 0.00 3.46
2760 2947 5.550290 TGAAATTGGAAATTTGCCCTTCTC 58.450 37.500 7.27 0.00 0.00 2.87
2773 2960 2.742530 GCCCTTCTCAAGCTCTGATCTG 60.743 54.545 0.00 0.00 32.14 2.90
2782 2969 5.358090 TCAAGCTCTGATCTGCATAAGAAG 58.642 41.667 0.00 0.00 38.79 2.85
2783 2970 5.105023 TCAAGCTCTGATCTGCATAAGAAGT 60.105 40.000 0.00 0.00 38.79 3.01
2791 2978 7.068716 TCTGATCTGCATAAGAAGTTGCTACTA 59.931 37.037 0.00 0.00 38.79 1.82
2808 2995 7.811117 TGCTACTAGTGGTAAAACATGTTTT 57.189 32.000 32.63 32.63 44.16 2.43
2834 3050 5.006455 GCTGACACTCACTGATGAACATATG 59.994 44.000 0.00 0.00 33.30 1.78
2840 3056 6.648310 CACTCACTGATGAACATATGTATCCC 59.352 42.308 9.21 0.36 33.30 3.85
2863 3079 8.271458 TCCCAATATTTCATACATACACACACT 58.729 33.333 0.00 0.00 0.00 3.55
2871 3087 9.990360 TTTCATACATACACACACTAAGAAAGA 57.010 29.630 0.00 0.00 0.00 2.52
3052 3268 1.356624 GATGCAGCCCGTACATTGC 59.643 57.895 0.00 0.00 37.09 3.56
3370 3588 7.770801 GAAAATGGTTTCAAAAGTAAGCAGT 57.229 32.000 0.00 0.00 42.40 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
128 129 6.296026 TGATGGAGCAAGGTATAATTGGTAC 58.704 40.000 6.46 6.46 38.42 3.34
169 170 7.097192 CAGCTCCTAAATCACACAAAGTAGTA 58.903 38.462 0.00 0.00 0.00 1.82
173 174 4.074970 CCAGCTCCTAAATCACACAAAGT 58.925 43.478 0.00 0.00 0.00 2.66
297 298 4.262036 GCACATCCTCACAGATACCGATAA 60.262 45.833 0.00 0.00 0.00 1.75
354 355 4.260784 CGGGCATCTCAAGTATAACAAAGC 60.261 45.833 0.00 0.00 0.00 3.51
587 589 7.846644 AGCATTTCACATTTCTTTTTGACAA 57.153 28.000 0.00 0.00 0.00 3.18
619 621 8.525729 ACCTTAATGGAGATATAAATGTCCCT 57.474 34.615 0.00 0.00 43.48 4.20
634 636 8.627403 CGTAGATCACTAAGTTACCTTAATGGA 58.373 37.037 0.00 0.00 39.71 3.41
640 642 9.939802 AATTTTCGTAGATCACTAAGTTACCTT 57.060 29.630 0.00 0.00 35.04 3.50
656 658 7.253422 AGCATGAATCCAAAGAATTTTCGTAG 58.747 34.615 0.00 0.00 35.03 3.51
673 675 6.996509 ACAACCACTTTTGATTAGCATGAAT 58.003 32.000 0.00 0.00 0.00 2.57
771 773 9.454859 CAGAAAACAAGAAGTAGGGATAGAAAT 57.545 33.333 0.00 0.00 0.00 2.17
825 828 7.504924 AATTGAGAAAACGGACTAAACATGA 57.495 32.000 0.00 0.00 0.00 3.07
837 840 3.619233 ACACGGGAAATTGAGAAAACG 57.381 42.857 0.00 0.00 0.00 3.60
867 873 6.478512 TCTGAGCACTTTTATTTTTGGGTT 57.521 33.333 0.00 0.00 0.00 4.11
939 948 1.100463 TTTTGCAGCAGCTCCAACGA 61.100 50.000 0.00 0.00 42.74 3.85
940 949 0.662374 CTTTTGCAGCAGCTCCAACG 60.662 55.000 0.00 0.00 42.74 4.10
941 950 0.386838 ACTTTTGCAGCAGCTCCAAC 59.613 50.000 0.00 0.00 42.74 3.77
942 951 0.670162 GACTTTTGCAGCAGCTCCAA 59.330 50.000 1.76 0.00 42.74 3.53
943 952 0.179009 AGACTTTTGCAGCAGCTCCA 60.179 50.000 1.76 0.00 42.74 3.86
955 964 6.238869 GGACAAAGAGAAAGATGCAGACTTTT 60.239 38.462 18.25 10.99 37.64 2.27
964 973 4.752101 ACAAGACGGACAAAGAGAAAGATG 59.248 41.667 0.00 0.00 0.00 2.90
965 974 4.962155 ACAAGACGGACAAAGAGAAAGAT 58.038 39.130 0.00 0.00 0.00 2.40
975 984 5.407387 GCTCATTTACTTACAAGACGGACAA 59.593 40.000 0.00 0.00 0.00 3.18
984 993 4.640201 GCCTCCATGCTCATTTACTTACAA 59.360 41.667 0.00 0.00 0.00 2.41
985 994 4.199310 GCCTCCATGCTCATTTACTTACA 58.801 43.478 0.00 0.00 0.00 2.41
986 995 3.248602 CGCCTCCATGCTCATTTACTTAC 59.751 47.826 0.00 0.00 0.00 2.34
987 996 3.133901 TCGCCTCCATGCTCATTTACTTA 59.866 43.478 0.00 0.00 0.00 2.24
988 997 2.092968 TCGCCTCCATGCTCATTTACTT 60.093 45.455 0.00 0.00 0.00 2.24
993 1002 0.463295 CAGTCGCCTCCATGCTCATT 60.463 55.000 0.00 0.00 0.00 2.57
1022 1037 2.915659 AGGAAGTCGACGGCCACA 60.916 61.111 24.94 0.00 0.00 4.17
1029 1044 1.655885 GGACGGAGGAGGAAGTCGAC 61.656 65.000 7.70 7.70 34.68 4.20
1032 1047 0.323542 TGAGGACGGAGGAGGAAGTC 60.324 60.000 0.00 0.00 0.00 3.01
1035 1050 1.305046 GGTGAGGACGGAGGAGGAA 60.305 63.158 0.00 0.00 0.00 3.36
1161 1176 4.933064 GAGATGGAGACGGCGGCG 62.933 72.222 31.06 31.06 0.00 6.46
1162 1177 4.593864 GGAGATGGAGACGGCGGC 62.594 72.222 13.24 8.92 0.00 6.53
1163 1178 4.271816 CGGAGATGGAGACGGCGG 62.272 72.222 13.24 0.00 0.00 6.13
1164 1179 3.518998 ACGGAGATGGAGACGGCG 61.519 66.667 4.80 4.80 0.00 6.46
1165 1180 2.105128 CACGGAGATGGAGACGGC 59.895 66.667 0.00 0.00 0.00 5.68
1277 1304 4.536090 GGGATTGGGGGAAGAAAGATTTTT 59.464 41.667 0.00 0.00 0.00 1.94
1278 1305 4.104086 GGGATTGGGGGAAGAAAGATTTT 58.896 43.478 0.00 0.00 0.00 1.82
1279 1306 3.724478 GGGATTGGGGGAAGAAAGATTT 58.276 45.455 0.00 0.00 0.00 2.17
1280 1307 2.358195 CGGGATTGGGGGAAGAAAGATT 60.358 50.000 0.00 0.00 0.00 2.40
1281 1308 1.215423 CGGGATTGGGGGAAGAAAGAT 59.785 52.381 0.00 0.00 0.00 2.40
1282 1309 0.623723 CGGGATTGGGGGAAGAAAGA 59.376 55.000 0.00 0.00 0.00 2.52
1283 1310 1.037579 GCGGGATTGGGGGAAGAAAG 61.038 60.000 0.00 0.00 0.00 2.62
1284 1311 1.000145 GCGGGATTGGGGGAAGAAA 60.000 57.895 0.00 0.00 0.00 2.52
1285 1312 1.794885 TTGCGGGATTGGGGGAAGAA 61.795 55.000 0.00 0.00 0.00 2.52
1286 1313 1.580066 ATTGCGGGATTGGGGGAAGA 61.580 55.000 0.00 0.00 0.00 2.87
1287 1314 1.076044 ATTGCGGGATTGGGGGAAG 60.076 57.895 0.00 0.00 0.00 3.46
1288 1315 1.076339 GATTGCGGGATTGGGGGAA 60.076 57.895 0.00 0.00 0.00 3.97
1310 1342 3.304659 GGAATCGATGGCGCATTATTTGT 60.305 43.478 10.83 0.00 37.46 2.83
1342 1376 4.087892 CAGGAGGTGGGTCAGCCG 62.088 72.222 0.00 0.00 34.97 5.52
1343 1377 4.416738 GCAGGAGGTGGGTCAGCC 62.417 72.222 0.00 0.00 31.60 4.85
1344 1378 4.767255 CGCAGGAGGTGGGTCAGC 62.767 72.222 0.00 0.00 34.37 4.26
1347 1381 4.459089 GAGCGCAGGAGGTGGGTC 62.459 72.222 11.47 0.00 41.24 4.46
1562 1600 0.390860 CAATGGAGGCGTAGGAGGAG 59.609 60.000 0.00 0.00 0.00 3.69
1565 1603 0.249073 CGTCAATGGAGGCGTAGGAG 60.249 60.000 0.00 0.00 0.00 3.69
1613 1651 3.133003 TCTCCTTCTCCTTAATCTTGCGG 59.867 47.826 0.00 0.00 0.00 5.69
1622 1660 1.004044 ACGTCGGTCTCCTTCTCCTTA 59.996 52.381 0.00 0.00 0.00 2.69
1646 1684 0.625849 CCTTGGTGCCCTTGAGGTAT 59.374 55.000 0.00 0.00 38.26 2.73
1647 1685 0.474854 TCCTTGGTGCCCTTGAGGTA 60.475 55.000 0.00 0.00 38.26 3.08
1693 1732 2.364970 CTCTGCCTCCGATTCATCTTCT 59.635 50.000 0.00 0.00 0.00 2.85
1790 1847 5.738909 AGAGAGATTGATTGATGGTTCGTT 58.261 37.500 0.00 0.00 0.00 3.85
1795 1852 5.357314 CAGCAAAGAGAGATTGATTGATGGT 59.643 40.000 0.00 0.00 34.68 3.55
1854 1914 4.685924 AGGTGCAAAATTGTCAGTCAAAG 58.314 39.130 0.00 0.00 39.62 2.77
1934 1998 5.359756 ACGCAGCAACATAGATGAATTCTA 58.640 37.500 7.05 0.00 41.18 2.10
1980 2051 2.958355 CAGACCCTGACACCAATTGTTT 59.042 45.455 4.43 0.00 39.17 2.83
1992 2063 0.610174 GCTCACACATCAGACCCTGA 59.390 55.000 0.00 0.00 44.99 3.86
2023 2094 1.476085 CACAACCTGCAAACCAACAGA 59.524 47.619 0.00 0.00 35.90 3.41
2049 2123 0.598065 GCGCCATCTCAAACACCTTT 59.402 50.000 0.00 0.00 0.00 3.11
2124 2198 1.004560 CTGCTCGTTCCTGAAGGCA 60.005 57.895 0.00 0.00 34.44 4.75
2219 2299 7.656137 GGTTCAGATAAGTTCAGTTGAGTTGTA 59.344 37.037 0.00 0.00 0.00 2.41
2231 2311 8.088981 TCAGTTTAGTCTGGTTCAGATAAGTTC 58.911 37.037 0.72 0.00 42.73 3.01
2273 2354 5.871396 ACTTCAGTTTAGTCTGGTTCAGA 57.129 39.130 0.00 0.00 38.25 3.27
2280 2361 6.701841 TGTTCAGCTAACTTCAGTTTAGTCTG 59.298 38.462 0.00 1.78 38.99 3.51
2290 2375 4.219944 AGTCGGTATGTTCAGCTAACTTCA 59.780 41.667 0.00 0.00 38.99 3.02
2298 2383 6.534079 AGTTATGTTTAGTCGGTATGTTCAGC 59.466 38.462 0.00 0.00 0.00 4.26
2305 2390 7.833786 TCAGTTCAGTTATGTTTAGTCGGTAT 58.166 34.615 0.00 0.00 0.00 2.73
2306 2391 7.218228 TCAGTTCAGTTATGTTTAGTCGGTA 57.782 36.000 0.00 0.00 0.00 4.02
2308 2393 5.062308 GCTCAGTTCAGTTATGTTTAGTCGG 59.938 44.000 0.00 0.00 0.00 4.79
2310 2395 5.062308 CGGCTCAGTTCAGTTATGTTTAGTC 59.938 44.000 0.00 0.00 0.00 2.59
2311 2396 4.929808 CGGCTCAGTTCAGTTATGTTTAGT 59.070 41.667 0.00 0.00 0.00 2.24
2312 2397 4.929808 ACGGCTCAGTTCAGTTATGTTTAG 59.070 41.667 0.00 0.00 0.00 1.85
2313 2398 4.890088 ACGGCTCAGTTCAGTTATGTTTA 58.110 39.130 0.00 0.00 0.00 2.01
2314 2399 3.740115 ACGGCTCAGTTCAGTTATGTTT 58.260 40.909 0.00 0.00 0.00 2.83
2315 2400 3.006967 AGACGGCTCAGTTCAGTTATGTT 59.993 43.478 0.00 0.00 0.00 2.71
2318 2403 2.826128 TCAGACGGCTCAGTTCAGTTAT 59.174 45.455 0.00 0.00 0.00 1.89
2319 2404 2.235891 TCAGACGGCTCAGTTCAGTTA 58.764 47.619 0.00 0.00 0.00 2.24
2320 2405 1.040646 TCAGACGGCTCAGTTCAGTT 58.959 50.000 0.00 0.00 0.00 3.16
2321 2406 1.040646 TTCAGACGGCTCAGTTCAGT 58.959 50.000 0.00 0.00 0.00 3.41
2322 2407 2.154854 TTTCAGACGGCTCAGTTCAG 57.845 50.000 0.00 0.00 0.00 3.02
2323 2408 2.416747 CATTTCAGACGGCTCAGTTCA 58.583 47.619 0.00 0.00 0.00 3.18
2324 2409 1.129437 GCATTTCAGACGGCTCAGTTC 59.871 52.381 0.00 0.00 0.00 3.01
2325 2410 1.160137 GCATTTCAGACGGCTCAGTT 58.840 50.000 0.00 0.00 0.00 3.16
2326 2411 0.035317 TGCATTTCAGACGGCTCAGT 59.965 50.000 0.00 0.00 0.00 3.41
2327 2412 0.725686 CTGCATTTCAGACGGCTCAG 59.274 55.000 0.00 0.00 45.72 3.35
2328 2413 0.674581 CCTGCATTTCAGACGGCTCA 60.675 55.000 0.00 0.00 45.72 4.26
2329 2414 1.372087 CCCTGCATTTCAGACGGCTC 61.372 60.000 0.00 0.00 45.72 4.70
2330 2415 1.377725 CCCTGCATTTCAGACGGCT 60.378 57.895 0.00 0.00 45.72 5.52
2331 2416 2.409870 CCCCTGCATTTCAGACGGC 61.410 63.158 0.00 0.00 45.72 5.68
2332 2417 0.745845 CTCCCCTGCATTTCAGACGG 60.746 60.000 0.00 0.00 45.72 4.79
2333 2418 0.745845 CCTCCCCTGCATTTCAGACG 60.746 60.000 0.00 0.00 45.72 4.18
2334 2419 0.329596 ACCTCCCCTGCATTTCAGAC 59.670 55.000 0.00 0.00 45.72 3.51
2335 2420 0.329261 CACCTCCCCTGCATTTCAGA 59.671 55.000 0.00 0.00 45.72 3.27
2336 2421 0.329261 TCACCTCCCCTGCATTTCAG 59.671 55.000 0.00 0.00 42.49 3.02
2337 2422 0.776810 TTCACCTCCCCTGCATTTCA 59.223 50.000 0.00 0.00 0.00 2.69
2361 2446 3.055747 CCTTCCTCCTTCCTCTTGTACAC 60.056 52.174 0.00 0.00 0.00 2.90
2380 2465 0.181350 GATGATGAGCCCGAACCCTT 59.819 55.000 0.00 0.00 0.00 3.95
2411 2496 4.980805 GCCTTGTCGACGTGGCCA 62.981 66.667 29.77 0.00 39.49 5.36
2441 2526 3.766691 GCGACGGGGTGCTCCTTA 61.767 66.667 4.53 0.00 35.33 2.69
2469 2582 1.109920 ATGGAGGGGAGACGATGACG 61.110 60.000 0.00 0.00 45.75 4.35
2470 2583 0.390860 CATGGAGGGGAGACGATGAC 59.609 60.000 0.00 0.00 0.00 3.06
2471 2584 0.261696 TCATGGAGGGGAGACGATGA 59.738 55.000 0.00 0.00 0.00 2.92
2472 2585 0.390860 GTCATGGAGGGGAGACGATG 59.609 60.000 0.00 0.00 0.00 3.84
2473 2586 0.032117 TGTCATGGAGGGGAGACGAT 60.032 55.000 0.00 0.00 33.83 3.73
2474 2587 0.970937 GTGTCATGGAGGGGAGACGA 60.971 60.000 0.00 0.00 33.83 4.20
2475 2588 1.517832 GTGTCATGGAGGGGAGACG 59.482 63.158 0.00 0.00 33.83 4.18
2541 2654 0.110295 TTGACACCCACCACCATCAG 59.890 55.000 0.00 0.00 0.00 2.90
2583 2721 0.398318 ACAAGGGAGGAACTGTCTGC 59.602 55.000 0.00 0.00 41.55 4.26
2591 2729 4.219115 TGTTAATTTGCACAAGGGAGGAA 58.781 39.130 0.00 0.00 0.00 3.36
2592 2730 3.826157 CTGTTAATTTGCACAAGGGAGGA 59.174 43.478 0.00 0.00 0.00 3.71
2658 2812 6.500751 AGAGGGAATAGAAACAACTTACCAGA 59.499 38.462 0.00 0.00 0.00 3.86
2659 2813 6.712276 AGAGGGAATAGAAACAACTTACCAG 58.288 40.000 0.00 0.00 0.00 4.00
2689 2848 8.380099 TGTATGTATGTATGTATCCCTTTTCCC 58.620 37.037 0.00 0.00 0.00 3.97
2714 2873 7.977904 TCAATTAGTTAACATGACTGCAGATG 58.022 34.615 23.35 16.99 0.00 2.90
2742 2929 3.244181 GCTTGAGAAGGGCAAATTTCCAA 60.244 43.478 8.36 0.00 0.00 3.53
2744 2931 2.564504 AGCTTGAGAAGGGCAAATTTCC 59.435 45.455 0.00 0.00 0.00 3.13
2746 2933 3.257624 CAGAGCTTGAGAAGGGCAAATTT 59.742 43.478 0.00 0.00 0.00 1.82
2749 2936 1.421268 TCAGAGCTTGAGAAGGGCAAA 59.579 47.619 0.00 0.00 0.00 3.68
2756 2943 3.908643 ATGCAGATCAGAGCTTGAGAA 57.091 42.857 0.00 0.00 39.68 2.87
2758 2945 4.946445 TCTTATGCAGATCAGAGCTTGAG 58.054 43.478 0.00 1.42 39.68 3.02
2760 2947 5.117584 ACTTCTTATGCAGATCAGAGCTTG 58.882 41.667 0.00 0.00 0.00 4.01
2773 2960 5.420409 ACCACTAGTAGCAACTTCTTATGC 58.580 41.667 0.00 0.00 42.87 3.14
2782 2969 6.796705 ACATGTTTTACCACTAGTAGCAAC 57.203 37.500 0.00 0.00 30.92 4.17
2783 2970 7.811117 AAACATGTTTTACCACTAGTAGCAA 57.189 32.000 18.13 0.00 30.92 3.91
2791 2978 6.320164 TGTCAGCTAAAACATGTTTTACCACT 59.680 34.615 30.77 25.01 42.22 4.00
2808 2995 3.573967 TGTTCATCAGTGAGTGTCAGCTA 59.426 43.478 0.00 0.00 35.39 3.32
2814 3001 7.212976 GGATACATATGTTCATCAGTGAGTGT 58.787 38.462 14.77 0.00 35.39 3.55
2847 3063 9.586435 CATCTTTCTTAGTGTGTGTATGTATGA 57.414 33.333 0.00 0.00 0.00 2.15
2863 3079 6.940298 ACCGTGAATTTCCTTCATCTTTCTTA 59.060 34.615 0.00 0.00 45.36 2.10
2867 3083 7.703058 AATACCGTGAATTTCCTTCATCTTT 57.297 32.000 0.00 0.00 45.36 2.52
2868 3084 8.674607 GTTAATACCGTGAATTTCCTTCATCTT 58.325 33.333 0.00 0.00 45.36 2.40
2869 3085 7.282450 GGTTAATACCGTGAATTTCCTTCATCT 59.718 37.037 0.00 0.00 39.24 2.90
2870 3086 7.415229 GGTTAATACCGTGAATTTCCTTCATC 58.585 38.462 0.00 0.00 39.24 2.92
2871 3087 7.329588 GGTTAATACCGTGAATTTCCTTCAT 57.670 36.000 0.00 0.00 39.24 2.57
3052 3268 2.016393 TAGCTTCGGTCAGCCATCCG 62.016 60.000 0.00 4.96 46.93 4.18
3265 3481 5.422012 AGAACCTTTTGTCAAACCATTCAGT 59.578 36.000 0.00 0.00 0.00 3.41
3370 3588 0.686224 CCCAAGGAAGCCATGCAAAA 59.314 50.000 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.