Multiple sequence alignment - TraesCS6A01G055700

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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 TraesCS6A01G055700 chr6A 100.000 3348 0 0 1 3348 29363895 29367242 0.000000e+00 6183.0
1 TraesCS6A01G055700 chr6A 75.909 220 51 2 1001 1219 16439022 16438804 9.820000e-21 111.0
2 TraesCS6A01G055700 chr6A 88.158 76 8 1 611 686 29344543 29344617 4.600000e-14 89.8
3 TraesCS6A01G055700 chr4D 92.437 714 54 0 2635 3348 425281811 425281098 0.000000e+00 1020.0
4 TraesCS6A01G055700 chr4D 90.756 714 63 1 2635 3348 36552525 36553235 0.000000e+00 950.0
5 TraesCS6A01G055700 chr1D 92.050 717 57 0 2632 3348 22188275 22188991 0.000000e+00 1009.0
6 TraesCS6A01G055700 chr1D 91.760 716 59 0 2633 3348 88381298 88382013 0.000000e+00 996.0
7 TraesCS6A01G055700 chr3A 91.643 718 59 1 2632 3348 46874582 46873865 0.000000e+00 992.0
8 TraesCS6A01G055700 chr1B 91.365 718 61 1 2632 3348 608840573 608841290 0.000000e+00 981.0
9 TraesCS6A01G055700 chr1A 91.064 705 61 2 2645 3348 589651636 589652339 0.000000e+00 952.0
10 TraesCS6A01G055700 chr2D 90.503 716 67 1 2633 3348 629843479 629842765 0.000000e+00 944.0
11 TraesCS6A01G055700 chr3D 90.503 716 65 3 2633 3348 536918590 536917878 0.000000e+00 942.0
12 TraesCS6A01G055700 chrUn 93.056 576 40 0 2054 2629 103347674 103347099 0.000000e+00 843.0
13 TraesCS6A01G055700 chrUn 98.233 283 5 0 979 1261 103347954 103347672 2.320000e-136 496.0
14 TraesCS6A01G055700 chrUn 92.097 329 15 4 653 980 103348318 103348000 1.420000e-123 453.0
15 TraesCS6A01G055700 chrUn 86.098 410 26 6 1 382 103349173 103348767 2.400000e-111 412.0
16 TraesCS6A01G055700 chr6D 80.774 827 151 8 1522 2344 14523216 14522394 1.010000e-179 640.0
17 TraesCS6A01G055700 chr6D 77.232 224 41 9 1001 1219 16139491 16139273 4.540000e-24 122.0
18 TraesCS6A01G055700 chr6D 100.000 28 0 0 1182 1209 14489043 14489016 6.000000e-03 52.8
19 TraesCS6A01G055700 chr6B 80.732 820 154 4 1522 2339 26650040 26650857 1.310000e-178 636.0
20 TraesCS6A01G055700 chr6B 85.206 534 59 10 997 1519 52466059 52465535 6.360000e-147 531.0
21 TraesCS6A01G055700 chr6B 87.273 330 20 11 653 980 52466457 52466148 1.140000e-94 357.0
22 TraesCS6A01G055700 chr6B 84.307 274 22 10 389 642 52466835 52466563 7.170000e-62 248.0
23 TraesCS6A01G055700 chr6B 75.566 221 50 4 1001 1219 27896849 27896631 4.570000e-19 106.0
24 TraesCS6A01G055700 chr6B 76.695 236 27 13 173 382 52467818 52467585 4.570000e-19 106.0
25 TraesCS6A01G055700 chr6B 97.619 42 0 1 1182 1222 26515644 26515603 1.670000e-08 71.3


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 TraesCS6A01G055700 chr6A 29363895 29367242 3347 False 6183.0 6183 100.00000 1 3348 1 chr6A.!!$F2 3347
1 TraesCS6A01G055700 chr4D 425281098 425281811 713 True 1020.0 1020 92.43700 2635 3348 1 chr4D.!!$R1 713
2 TraesCS6A01G055700 chr4D 36552525 36553235 710 False 950.0 950 90.75600 2635 3348 1 chr4D.!!$F1 713
3 TraesCS6A01G055700 chr1D 22188275 22188991 716 False 1009.0 1009 92.05000 2632 3348 1 chr1D.!!$F1 716
4 TraesCS6A01G055700 chr1D 88381298 88382013 715 False 996.0 996 91.76000 2633 3348 1 chr1D.!!$F2 715
5 TraesCS6A01G055700 chr3A 46873865 46874582 717 True 992.0 992 91.64300 2632 3348 1 chr3A.!!$R1 716
6 TraesCS6A01G055700 chr1B 608840573 608841290 717 False 981.0 981 91.36500 2632 3348 1 chr1B.!!$F1 716
7 TraesCS6A01G055700 chr1A 589651636 589652339 703 False 952.0 952 91.06400 2645 3348 1 chr1A.!!$F1 703
8 TraesCS6A01G055700 chr2D 629842765 629843479 714 True 944.0 944 90.50300 2633 3348 1 chr2D.!!$R1 715
9 TraesCS6A01G055700 chr3D 536917878 536918590 712 True 942.0 942 90.50300 2633 3348 1 chr3D.!!$R1 715
10 TraesCS6A01G055700 chrUn 103347099 103349173 2074 True 551.0 843 92.37100 1 2629 4 chrUn.!!$R1 2628
11 TraesCS6A01G055700 chr6D 14522394 14523216 822 True 640.0 640 80.77400 1522 2344 1 chr6D.!!$R2 822
12 TraesCS6A01G055700 chr6B 26650040 26650857 817 False 636.0 636 80.73200 1522 2339 1 chr6B.!!$F1 817
13 TraesCS6A01G055700 chr6B 52465535 52467818 2283 True 310.5 531 83.37025 173 1519 4 chr6B.!!$R3 1346

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
646 1454 0.107848 ACGCGCAAATTACTAGGCCT 60.108 50.0 11.78 11.78 0.0 5.19 F
1323 2307 0.393808 CAAATCCCAGTACCCCACGG 60.394 60.0 0.00 0.00 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1481 2475 0.179124 GATCGAGTGAGCTGGTGGTC 60.179 60.0 0.0 0.0 40.79 4.02 R
2763 3757 0.605319 TCCACAAACGATGCTCCCAC 60.605 55.0 0.0 0.0 0.00 4.61 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
30 31 2.811431 CACTTGGCCACGTTTGAGATTA 59.189 45.455 13.05 0.00 0.00 1.75
31 32 3.440173 CACTTGGCCACGTTTGAGATTAT 59.560 43.478 13.05 0.00 0.00 1.28
35 36 4.839121 TGGCCACGTTTGAGATTATAAGT 58.161 39.130 0.00 0.00 0.00 2.24
122 123 1.211969 CAGTCAACCGATCGACCGT 59.788 57.895 18.66 2.71 32.33 4.83
130 131 1.080366 CGATCGACCGTGGTTCCAA 60.080 57.895 10.26 0.00 0.00 3.53
147 148 5.072329 GGTTCCAAATCTGAGATCCCTGATA 59.928 44.000 0.00 0.00 0.00 2.15
150 151 5.667172 TCCAAATCTGAGATCCCTGATACAA 59.333 40.000 0.00 0.00 0.00 2.41
160 161 7.510343 TGAGATCCCTGATACAACATCTCATAA 59.490 37.037 5.51 0.00 38.52 1.90
162 163 7.732140 AGATCCCTGATACAACATCTCATAAGA 59.268 37.037 0.00 0.00 35.54 2.10
208 212 7.066043 TCCCGTTGTTTATTTACGCTAATCAAT 59.934 33.333 0.00 0.00 34.16 2.57
219 223 8.774890 TTTACGCTAATCAATTTGGTAGTACA 57.225 30.769 2.06 0.00 0.00 2.90
339 379 7.437713 ACATCTCACATTATAGGACAAAGGA 57.562 36.000 0.00 0.00 0.00 3.36
374 414 1.483827 TCCACTCCATGAGCTTAGCTG 59.516 52.381 13.01 0.00 39.88 4.24
382 422 0.252239 TGAGCTTAGCTGGGAGTCCA 60.252 55.000 13.01 0.00 39.88 4.02
383 423 0.176910 GAGCTTAGCTGGGAGTCCAC 59.823 60.000 13.01 0.78 39.88 4.02
384 424 0.545309 AGCTTAGCTGGGAGTCCACA 60.545 55.000 12.30 5.85 37.57 4.17
385 425 0.324943 GCTTAGCTGGGAGTCCACAA 59.675 55.000 12.30 0.00 38.32 3.33
387 427 0.320374 TTAGCTGGGAGTCCACAACG 59.680 55.000 12.30 0.00 38.32 4.10
388 428 2.167398 TAGCTGGGAGTCCACAACGC 62.167 60.000 12.30 7.51 38.32 4.84
389 429 2.425592 CTGGGAGTCCACAACGCA 59.574 61.111 12.30 0.00 38.32 5.24
390 430 1.227823 CTGGGAGTCCACAACGCAA 60.228 57.895 12.30 0.00 38.32 4.85
391 431 1.227823 TGGGAGTCCACAACGCAAG 60.228 57.895 12.30 0.00 38.32 4.01
435 1219 1.308998 AAAGCCTTCAACGACTGGTG 58.691 50.000 0.00 0.00 0.00 4.17
436 1220 0.468226 AAGCCTTCAACGACTGGTGA 59.532 50.000 0.00 0.00 0.00 4.02
437 1221 0.687354 AGCCTTCAACGACTGGTGAT 59.313 50.000 0.00 0.00 0.00 3.06
438 1222 1.079503 GCCTTCAACGACTGGTGATC 58.920 55.000 0.00 0.00 0.00 2.92
440 1224 2.936993 GCCTTCAACGACTGGTGATCAT 60.937 50.000 0.00 0.00 0.00 2.45
441 1225 3.338249 CCTTCAACGACTGGTGATCATT 58.662 45.455 0.00 0.00 0.00 2.57
442 1226 4.503910 CCTTCAACGACTGGTGATCATTA 58.496 43.478 0.00 0.00 0.00 1.90
444 1228 5.235186 CCTTCAACGACTGGTGATCATTATC 59.765 44.000 0.00 0.00 0.00 1.75
485 1288 7.714813 TGATGACACATAGTTTCAGACTTTCAA 59.285 33.333 0.00 0.00 39.86 2.69
488 1291 7.095649 TGACACATAGTTTCAGACTTTCAATCG 60.096 37.037 0.00 0.00 39.86 3.34
513 1316 1.871126 GCCAGCCACCTTTGCTTCTC 61.871 60.000 0.00 0.00 36.81 2.87
547 1350 2.017049 GCCCAGTATTTTCATGAGCGT 58.983 47.619 0.00 0.00 0.00 5.07
576 1383 2.684374 TCACATGCATGCCATTACAGAC 59.316 45.455 26.53 0.00 29.71 3.51
597 1404 4.222124 CCAGAAGTGGTGCTACCTAAAT 57.778 45.455 6.83 0.00 39.58 1.40
607 1414 6.640907 GTGGTGCTACCTAAATTTTTGTCTTG 59.359 38.462 0.00 0.00 39.58 3.02
608 1415 5.633601 GGTGCTACCTAAATTTTTGTCTTGC 59.366 40.000 0.00 1.72 34.73 4.01
609 1416 6.212955 GTGCTACCTAAATTTTTGTCTTGCA 58.787 36.000 0.00 4.04 0.00 4.08
642 1450 3.703420 AGACCTACGCGCAAATTACTAG 58.297 45.455 5.73 0.00 0.00 2.57
643 1451 2.793232 GACCTACGCGCAAATTACTAGG 59.207 50.000 5.73 9.94 0.00 3.02
646 1454 0.107848 ACGCGCAAATTACTAGGCCT 60.108 50.000 11.78 11.78 0.00 5.19
648 1456 1.400494 CGCGCAAATTACTAGGCCTTT 59.600 47.619 12.58 0.00 0.00 3.11
649 1457 2.791158 CGCGCAAATTACTAGGCCTTTG 60.791 50.000 12.58 9.72 0.00 2.77
650 1458 2.163613 GCGCAAATTACTAGGCCTTTGT 59.836 45.455 12.58 13.69 32.51 2.83
651 1459 3.758300 CGCAAATTACTAGGCCTTTGTG 58.242 45.455 12.58 11.43 34.13 3.33
654 1462 4.459337 GCAAATTACTAGGCCTTTGTGTCT 59.541 41.667 12.58 0.00 32.51 3.41
655 1463 5.619981 GCAAATTACTAGGCCTTTGTGTCTG 60.620 44.000 12.58 2.89 32.51 3.51
666 1573 3.561725 CCTTTGTGTCTGAAGTCTGAACC 59.438 47.826 0.00 0.00 0.00 3.62
696 1603 1.223187 GGTCACTTTGTGTGGTACCG 58.777 55.000 7.57 0.00 46.20 4.02
712 1619 4.162698 TGGTACCGTAGACTAATTTGGCAT 59.837 41.667 7.57 0.00 0.00 4.40
737 1644 4.024133 CACGAGGATGAGATCTAGTCACAG 60.024 50.000 0.00 0.00 30.84 3.66
739 1646 4.452114 CGAGGATGAGATCTAGTCACAGAG 59.548 50.000 0.00 0.00 30.84 3.35
810 1719 6.539103 GGGAGGTTCAATAGATTACACAACTC 59.461 42.308 0.00 0.00 0.00 3.01
1064 2048 4.503314 GTACGTCTTCCCGCCGGG 62.503 72.222 18.41 18.41 46.11 5.73
1323 2307 0.393808 CAAATCCCAGTACCCCACGG 60.394 60.000 0.00 0.00 0.00 4.94
1324 2308 0.548197 AAATCCCAGTACCCCACGGA 60.548 55.000 0.00 0.00 0.00 4.69
1325 2309 0.981277 AATCCCAGTACCCCACGGAG 60.981 60.000 0.00 0.00 0.00 4.63
1328 2312 1.196104 CCCAGTACCCCACGGAGAAA 61.196 60.000 0.00 0.00 0.00 2.52
1329 2313 0.909623 CCAGTACCCCACGGAGAAAT 59.090 55.000 0.00 0.00 0.00 2.17
1330 2314 1.134491 CCAGTACCCCACGGAGAAATC 60.134 57.143 0.00 0.00 0.00 2.17
1332 2316 1.201424 GTACCCCACGGAGAAATCCT 58.799 55.000 0.00 0.00 0.00 3.24
1333 2317 1.134491 GTACCCCACGGAGAAATCCTG 60.134 57.143 0.00 0.00 0.00 3.86
1334 2318 0.546747 ACCCCACGGAGAAATCCTGA 60.547 55.000 0.00 0.00 0.00 3.86
1336 2320 1.212935 CCCCACGGAGAAATCCTGAAT 59.787 52.381 0.00 0.00 0.00 2.57
1338 2322 3.356290 CCCACGGAGAAATCCTGAATTT 58.644 45.455 0.00 0.00 40.34 1.82
1339 2323 3.763897 CCCACGGAGAAATCCTGAATTTT 59.236 43.478 0.00 0.00 37.70 1.82
1340 2324 4.947388 CCCACGGAGAAATCCTGAATTTTA 59.053 41.667 0.00 0.00 37.70 1.52
1341 2325 5.594317 CCCACGGAGAAATCCTGAATTTTAT 59.406 40.000 0.00 0.00 37.70 1.40
1342 2326 6.238759 CCCACGGAGAAATCCTGAATTTTATC 60.239 42.308 0.00 0.00 37.70 1.75
1343 2327 6.543831 CCACGGAGAAATCCTGAATTTTATCT 59.456 38.462 0.00 0.00 37.70 1.98
1344 2328 7.412853 CACGGAGAAATCCTGAATTTTATCTG 58.587 38.462 0.00 0.00 37.70 2.90
1428 2422 2.319136 TCGTTCGGTATTTCCCCATG 57.681 50.000 0.00 0.00 0.00 3.66
1430 2424 2.159014 TCGTTCGGTATTTCCCCATGAG 60.159 50.000 0.00 0.00 0.00 2.90
1436 2430 4.656575 TCGGTATTTCCCCATGAGATGTTA 59.343 41.667 0.00 0.00 0.00 2.41
1443 2437 7.976414 TTTCCCCATGAGATGTTATTTCATT 57.024 32.000 0.00 0.00 29.48 2.57
1481 2475 3.685139 ACATATACCCTTCCATGAGCG 57.315 47.619 0.00 0.00 0.00 5.03
1513 2507 8.983724 CAGCTCACTCGATCGATCTTATATATA 58.016 37.037 19.78 1.00 0.00 0.86
1557 2551 2.159490 TTGGGGAGGATGTGGTGCA 61.159 57.895 0.00 0.00 0.00 4.57
1558 2552 1.724148 TTGGGGAGGATGTGGTGCAA 61.724 55.000 0.00 0.00 0.00 4.08
1567 2561 2.203294 GTGGTGCAAGGGTTCCGT 60.203 61.111 0.00 0.00 0.00 4.69
1612 2606 3.775654 CCGGCGGAGGAGAAGCTT 61.776 66.667 24.41 0.00 0.00 3.74
1641 2635 0.894835 TCCTACGACATGAGCAAGCA 59.105 50.000 0.00 0.00 0.00 3.91
1646 2640 1.150827 CGACATGAGCAAGCACTTCA 58.849 50.000 0.00 0.00 0.00 3.02
1685 2679 2.397413 CTTCCACCGCAACCAGACCT 62.397 60.000 0.00 0.00 0.00 3.85
1696 2690 2.185350 CAGACCTGCTACTGGCGG 59.815 66.667 0.00 0.00 45.43 6.13
1703 2697 1.000019 TGCTACTGGCGGGACTACT 60.000 57.895 0.00 0.00 45.43 2.57
1707 2701 1.405821 CTACTGGCGGGACTACTTCAG 59.594 57.143 0.00 0.00 0.00 3.02
1709 2703 0.970937 CTGGCGGGACTACTTCAGGA 60.971 60.000 0.00 0.00 0.00 3.86
1723 2717 2.844839 AGGATCCGCTGCTACCCC 60.845 66.667 5.98 0.00 0.00 4.95
1725 2719 3.537874 GATCCGCTGCTACCCCGT 61.538 66.667 0.00 0.00 0.00 5.28
1729 2723 3.760035 CGCTGCTACCCCGTCACT 61.760 66.667 0.00 0.00 0.00 3.41
1801 2795 1.011019 CGCAGAGTACTCTACGGCG 60.011 63.158 29.89 29.89 41.44 6.46
1822 2816 2.487428 CACGAGCTCTCCCAGACG 59.513 66.667 12.85 0.00 0.00 4.18
1823 2817 3.444805 ACGAGCTCTCCCAGACGC 61.445 66.667 12.85 0.00 0.00 5.19
1825 2819 2.493973 GAGCTCTCCCAGACGCTG 59.506 66.667 6.43 0.52 31.90 5.18
1829 2823 3.071206 TCTCCCAGACGCTGCTCC 61.071 66.667 0.00 0.00 0.00 4.70
1834 2828 2.202544 CAGACGCTGCTCCGACTC 60.203 66.667 0.00 0.00 31.35 3.36
1837 2831 1.153745 GACGCTGCTCCGACTCATT 60.154 57.895 0.00 0.00 0.00 2.57
1840 2834 1.742880 GCTGCTCCGACTCATTGCA 60.743 57.895 0.00 0.00 0.00 4.08
1841 2835 1.975363 GCTGCTCCGACTCATTGCAC 61.975 60.000 0.00 0.00 0.00 4.57
1849 2843 0.610232 GACTCATTGCACAGGGGCTT 60.610 55.000 0.00 0.00 34.04 4.35
1870 2864 0.741221 GCCTCGACGATGGCTTCTTT 60.741 55.000 22.92 0.00 45.26 2.52
1893 2887 3.753434 CGACCTCAGCAGCGGAGT 61.753 66.667 19.71 9.12 0.00 3.85
1894 2888 2.125753 GACCTCAGCAGCGGAGTG 60.126 66.667 19.71 13.75 0.00 3.51
1897 2891 2.125753 CTCAGCAGCGGAGTGACC 60.126 66.667 14.00 0.00 0.00 4.02
1900 2894 3.699894 AGCAGCGGAGTGACCCAG 61.700 66.667 0.00 0.00 34.64 4.45
1905 2899 0.904865 AGCGGAGTGACCCAGATGAA 60.905 55.000 0.00 0.00 34.64 2.57
1906 2900 0.179000 GCGGAGTGACCCAGATGAAT 59.821 55.000 0.00 0.00 34.64 2.57
1909 2903 2.636830 GGAGTGACCCAGATGAATGTG 58.363 52.381 0.00 0.00 0.00 3.21
1921 2915 5.129485 CCAGATGAATGTGAACTACTACCCT 59.871 44.000 0.00 0.00 0.00 4.34
1924 2918 4.422057 TGAATGTGAACTACTACCCTCCA 58.578 43.478 0.00 0.00 0.00 3.86
1946 2940 4.436998 CGGACCCCTCTGTCACGC 62.437 72.222 0.00 0.00 36.97 5.34
1948 2942 2.574399 GACCCCTCTGTCACGCTC 59.426 66.667 0.00 0.00 35.29 5.03
1951 2945 4.135153 CCCTCTGTCACGCTCGGG 62.135 72.222 0.00 0.00 0.00 5.14
1954 2948 3.691744 CTCTGTCACGCTCGGGCTC 62.692 68.421 5.36 0.00 36.09 4.70
1955 2949 3.753434 CTGTCACGCTCGGGCTCT 61.753 66.667 5.36 0.00 36.09 4.09
1958 2952 3.760035 TCACGCTCGGGCTCTTCC 61.760 66.667 5.36 0.00 36.09 3.46
1984 2978 2.997897 GACCGCCACCTCCTCACT 60.998 66.667 0.00 0.00 0.00 3.41
1990 2984 1.004080 CCACCTCCTCACTGTGCTG 60.004 63.158 2.12 0.00 0.00 4.41
1998 2992 2.033141 CACTGTGCTGTCCCAGGG 59.967 66.667 0.00 0.00 32.90 4.45
1999 2993 3.958860 ACTGTGCTGTCCCAGGGC 61.959 66.667 0.00 0.00 32.90 5.19
2017 3011 4.373116 GACGTCGCTGGGCTCCAA 62.373 66.667 0.00 0.00 30.80 3.53
2111 3105 0.815615 GGAGATCGTCACCAATGGGC 60.816 60.000 3.55 0.00 37.90 5.36
2152 3146 2.953821 GTGGTCACCAATGCCACG 59.046 61.111 0.00 0.00 40.66 4.94
2231 3225 3.770040 CGCCGGAGATGGTGGACA 61.770 66.667 5.05 0.00 35.83 4.02
2234 3228 1.899437 GCCGGAGATGGTGGACAAGA 61.899 60.000 5.05 0.00 0.00 3.02
2239 3233 2.237143 GGAGATGGTGGACAAGATGACA 59.763 50.000 0.00 0.00 0.00 3.58
2285 3279 1.618343 TGTTCAGCGAGTTCATGGAGA 59.382 47.619 0.00 0.00 0.00 3.71
2418 3412 2.271800 CTCTCCTTCGGTTTTGATCGG 58.728 52.381 0.00 0.00 0.00 4.18
2484 3478 4.382685 CCAGATTTGTAAGCCCGACTAAGA 60.383 45.833 0.00 0.00 0.00 2.10
2488 3482 1.202371 TGTAAGCCCGACTAAGATGCG 60.202 52.381 0.00 0.00 0.00 4.73
2502 3496 1.956477 AGATGCGCCCCATATGTTTTC 59.044 47.619 4.18 0.00 33.29 2.29
2516 3510 3.755112 TGTTTTCTCCGTGTCATGGTA 57.245 42.857 10.97 0.00 0.00 3.25
2517 3511 4.280436 TGTTTTCTCCGTGTCATGGTAT 57.720 40.909 10.97 0.00 0.00 2.73
2520 3514 1.190643 TCTCCGTGTCATGGTATGCA 58.809 50.000 10.97 0.00 0.00 3.96
2542 3536 7.889589 GCAATAGTGCCAATTCTTTTAGTTT 57.110 32.000 3.16 0.00 45.68 2.66
2543 3537 7.953393 GCAATAGTGCCAATTCTTTTAGTTTC 58.047 34.615 3.16 0.00 45.68 2.78
2608 3602 5.515626 GCCGCTACAATTTATCGGATAGTAG 59.484 44.000 13.66 13.66 42.43 2.57
2609 3603 6.618811 CCGCTACAATTTATCGGATAGTAGT 58.381 40.000 16.87 9.92 42.43 2.73
2643 3637 1.863446 GAAATTCGTTCTGCGCCGC 60.863 57.895 4.18 0.00 41.07 6.53
2763 3757 0.878523 TTGCGGTGTCGTTTCTCTGG 60.879 55.000 0.00 0.00 38.89 3.86
2788 3782 1.001974 AGCATCGTTTGTGGAGCAGTA 59.998 47.619 0.00 0.00 0.00 2.74
2820 3814 1.455217 GTAGGAGGTGGAGCGGCTA 60.455 63.158 0.60 0.00 0.00 3.93
2821 3815 1.041447 GTAGGAGGTGGAGCGGCTAA 61.041 60.000 0.60 0.00 0.00 3.09
2877 3871 2.903357 CTGGCCGACAGGTGCTAT 59.097 61.111 0.00 0.00 43.70 2.97
2943 3937 2.224137 CCAGAGACTTCAAGCTGTGTCA 60.224 50.000 10.01 0.00 32.41 3.58
3035 4030 1.079336 GGGAGGTGGTGACGTTAGC 60.079 63.158 2.09 2.09 0.00 3.09
3038 4033 2.433664 GGTGGTGACGTTAGCCGG 60.434 66.667 7.09 0.00 42.24 6.13
3055 4050 4.634133 GCGTGGTGGTGTCGACGA 62.634 66.667 11.62 0.00 40.81 4.20
3173 4168 2.192175 CCCCATACCCGGCAAGTC 59.808 66.667 0.00 0.00 0.00 3.01
3191 4186 2.037847 GCTTGGTTGGGGCCTCAT 59.962 61.111 5.88 0.00 0.00 2.90
3243 4239 1.342496 GTGGTATTAGGCCCGGACTAC 59.658 57.143 0.73 0.00 0.00 2.73
3304 4300 2.577059 CCTAGACGGCGGCTTCAA 59.423 61.111 25.39 0.49 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 9.392259 CGTAGTCCAGTCCATATATGATACTTA 57.608 37.037 14.54 5.42 0.00 2.24
35 36 5.296035 CGCGTAGTCCAGTCCATATATGATA 59.704 44.000 14.54 0.00 0.00 2.15
108 109 1.349259 GAACCACGGTCGATCGGTTG 61.349 60.000 23.84 12.38 41.76 3.77
122 123 3.054139 CAGGGATCTCAGATTTGGAACCA 60.054 47.826 0.00 0.00 0.00 3.67
130 131 6.558014 AGATGTTGTATCAGGGATCTCAGATT 59.442 38.462 5.73 0.00 0.00 2.40
147 148 4.245660 CGGTGTGTCTTATGAGATGTTGT 58.754 43.478 0.00 0.00 33.70 3.32
150 151 2.497675 AGCGGTGTGTCTTATGAGATGT 59.502 45.455 0.00 0.00 33.70 3.06
208 212 3.731089 CTCCCGTGTTTGTACTACCAAA 58.269 45.455 0.00 0.00 32.12 3.28
219 223 0.608856 TGCATGATGCTCCCGTGTTT 60.609 50.000 19.19 0.00 45.31 2.83
312 352 9.784531 CCTTTGTCCTATAATGTGAGATGTTAT 57.215 33.333 0.00 0.00 0.00 1.89
313 353 8.988060 TCCTTTGTCCTATAATGTGAGATGTTA 58.012 33.333 0.00 0.00 0.00 2.41
321 361 7.225538 CAGCTACTTCCTTTGTCCTATAATGTG 59.774 40.741 0.00 0.00 0.00 3.21
323 363 6.203723 GCAGCTACTTCCTTTGTCCTATAATG 59.796 42.308 0.00 0.00 0.00 1.90
334 374 1.981495 AGTGAGGCAGCTACTTCCTTT 59.019 47.619 0.00 0.00 0.00 3.11
339 379 0.610687 GTGGAGTGAGGCAGCTACTT 59.389 55.000 0.00 0.00 0.00 2.24
374 414 0.534203 TTCTTGCGTTGTGGACTCCC 60.534 55.000 0.00 0.00 0.00 4.30
382 422 1.947456 GAGGGAGTTTTCTTGCGTTGT 59.053 47.619 0.00 0.00 0.00 3.32
383 423 1.266989 GGAGGGAGTTTTCTTGCGTTG 59.733 52.381 0.00 0.00 0.00 4.10
384 424 1.133915 TGGAGGGAGTTTTCTTGCGTT 60.134 47.619 0.00 0.00 0.00 4.84
385 425 0.472471 TGGAGGGAGTTTTCTTGCGT 59.528 50.000 0.00 0.00 0.00 5.24
387 427 2.294512 CACTTGGAGGGAGTTTTCTTGC 59.705 50.000 0.00 0.00 0.00 4.01
388 428 2.887152 CCACTTGGAGGGAGTTTTCTTG 59.113 50.000 0.00 0.00 37.39 3.02
389 429 2.753168 GCCACTTGGAGGGAGTTTTCTT 60.753 50.000 0.00 0.00 37.39 2.52
390 430 1.202940 GCCACTTGGAGGGAGTTTTCT 60.203 52.381 0.00 0.00 37.39 2.52
391 431 1.248486 GCCACTTGGAGGGAGTTTTC 58.752 55.000 0.00 0.00 37.39 2.29
435 1219 6.510746 TGAAATGTGACGACGATAATGATC 57.489 37.500 0.00 0.00 0.00 2.92
436 1220 6.701400 TCATGAAATGTGACGACGATAATGAT 59.299 34.615 0.00 0.00 46.80 2.45
437 1221 6.039616 TCATGAAATGTGACGACGATAATGA 58.960 36.000 0.00 0.00 46.80 2.57
438 1222 6.272698 TCATGAAATGTGACGACGATAATG 57.727 37.500 0.00 0.00 46.80 1.90
440 1224 6.019881 GTCATCATGAAATGTGACGACGATAA 60.020 38.462 10.55 0.00 46.80 1.75
441 1225 5.458779 GTCATCATGAAATGTGACGACGATA 59.541 40.000 10.55 0.00 46.80 2.92
442 1226 4.268644 GTCATCATGAAATGTGACGACGAT 59.731 41.667 10.55 0.00 46.80 3.73
444 1228 3.916255 GTCATCATGAAATGTGACGACG 58.084 45.455 10.55 0.00 46.80 5.12
465 1264 6.017933 GCGATTGAAAGTCTGAAACTATGTG 58.982 40.000 0.00 0.00 37.17 3.21
466 1265 5.934625 AGCGATTGAAAGTCTGAAACTATGT 59.065 36.000 0.00 0.00 37.17 2.29
513 1316 0.030638 CTGGGCAGGTTTTGTTCGTG 59.969 55.000 0.00 0.00 0.00 4.35
563 1370 3.614092 CACTTCTGGTCTGTAATGGCAT 58.386 45.455 0.00 0.00 0.00 4.40
564 1371 2.290260 CCACTTCTGGTCTGTAATGGCA 60.290 50.000 0.00 0.00 32.03 4.92
565 1372 2.359900 CCACTTCTGGTCTGTAATGGC 58.640 52.381 0.00 0.00 32.03 4.40
576 1383 3.695830 TTTAGGTAGCACCACTTCTGG 57.304 47.619 7.86 0.00 41.95 3.86
587 1394 7.707774 TTTGCAAGACAAAAATTTAGGTAGC 57.292 32.000 0.00 0.00 45.22 3.58
607 1414 6.290904 GCGCGTAGGTCTTTTAAATATTTTGC 60.291 38.462 8.43 0.00 0.00 3.68
608 1415 6.743627 TGCGCGTAGGTCTTTTAAATATTTTG 59.256 34.615 8.43 0.00 0.00 2.44
609 1416 6.844254 TGCGCGTAGGTCTTTTAAATATTTT 58.156 32.000 8.43 0.00 0.00 1.82
619 1427 3.332034 AGTAATTTGCGCGTAGGTCTTT 58.668 40.909 8.43 0.00 0.00 2.52
642 1450 1.876156 CAGACTTCAGACACAAAGGCC 59.124 52.381 0.00 0.00 30.33 5.19
643 1451 2.838736 TCAGACTTCAGACACAAAGGC 58.161 47.619 0.00 0.00 0.00 4.35
646 1454 3.199946 AGGGTTCAGACTTCAGACACAAA 59.800 43.478 0.00 0.00 0.00 2.83
648 1456 2.398588 AGGGTTCAGACTTCAGACACA 58.601 47.619 0.00 0.00 0.00 3.72
649 1457 3.056465 CCTAGGGTTCAGACTTCAGACAC 60.056 52.174 0.00 0.00 0.00 3.67
650 1458 3.165875 CCTAGGGTTCAGACTTCAGACA 58.834 50.000 0.00 0.00 0.00 3.41
651 1459 2.093921 GCCTAGGGTTCAGACTTCAGAC 60.094 54.545 11.72 0.00 0.00 3.51
654 1462 1.276622 GGCCTAGGGTTCAGACTTCA 58.723 55.000 11.72 0.00 0.00 3.02
655 1463 1.276622 TGGCCTAGGGTTCAGACTTC 58.723 55.000 11.72 0.00 0.00 3.01
666 1573 0.698818 AAAGTGACCCTTGGCCTAGG 59.301 55.000 24.89 24.89 32.32 3.02
696 1603 4.439057 TCGTGGATGCCAAATTAGTCTAC 58.561 43.478 0.00 0.00 34.18 2.59
810 1719 4.803426 GGTCGGTCGGCTGCTGAG 62.803 72.222 12.25 1.02 0.00 3.35
832 1741 1.773856 TTGGATCTGGAACCACGCCA 61.774 55.000 0.00 0.00 35.81 5.69
833 1742 0.394352 ATTGGATCTGGAACCACGCC 60.394 55.000 0.00 0.00 35.81 5.68
834 1743 0.734889 CATTGGATCTGGAACCACGC 59.265 55.000 0.00 0.00 35.81 5.34
835 1744 1.739466 CACATTGGATCTGGAACCACG 59.261 52.381 0.00 0.00 35.81 4.94
836 1745 2.094675 CCACATTGGATCTGGAACCAC 58.905 52.381 0.00 0.00 40.96 4.16
837 1746 1.991813 TCCACATTGGATCTGGAACCA 59.008 47.619 0.00 0.00 42.67 3.67
838 1747 2.806945 TCCACATTGGATCTGGAACC 57.193 50.000 0.00 0.00 42.67 3.62
1064 2048 1.578206 GAACAGGTCAAGGCGCTTCC 61.578 60.000 7.64 0.00 0.00 3.46
1073 2057 0.323629 GTCATCGGGGAACAGGTCAA 59.676 55.000 0.00 0.00 0.00 3.18
1247 2231 6.041979 TCGGTACCCAAAACCTTACTATATCC 59.958 42.308 6.25 0.00 34.66 2.59
1295 2279 0.402504 ACTGGGATTTGCGGTAACCA 59.597 50.000 0.00 0.00 0.00 3.67
1351 2345 9.669887 TCCCAGATAAAAATTCATTCAAATTGG 57.330 29.630 0.00 0.00 0.00 3.16
1398 2392 1.574134 ACCGAACGATCAACAAACGT 58.426 45.000 0.00 0.00 41.97 3.99
1402 2396 3.685756 GGGAAATACCGAACGATCAACAA 59.314 43.478 0.00 0.00 40.11 2.83
1405 2399 2.236644 TGGGGAAATACCGAACGATCAA 59.763 45.455 0.00 0.00 40.11 2.57
1407 2401 2.607631 TGGGGAAATACCGAACGATC 57.392 50.000 0.00 0.00 40.11 3.69
1411 2405 3.553828 TCTCATGGGGAAATACCGAAC 57.446 47.619 0.00 0.00 40.11 3.95
1428 2422 7.587037 TGGATCCCAAATGAAATAACATCTC 57.413 36.000 9.90 0.00 0.00 2.75
1443 2437 7.562088 GGTATATGTTAAGGTTTTGGATCCCAA 59.438 37.037 9.90 0.59 42.29 4.12
1460 2454 3.646162 TCGCTCATGGAAGGGTATATGTT 59.354 43.478 0.00 0.00 0.00 2.71
1481 2475 0.179124 GATCGAGTGAGCTGGTGGTC 60.179 60.000 0.00 0.00 40.79 4.02
1540 2534 2.141011 CTTGCACCACATCCTCCCCA 62.141 60.000 0.00 0.00 0.00 4.96
1548 2542 1.603455 CGGAACCCTTGCACCACAT 60.603 57.895 0.00 0.00 0.00 3.21
1592 2586 4.521062 CTTCTCCTCCGCCGGCAG 62.521 72.222 28.98 16.96 0.00 4.85
1606 2600 1.199615 AGGAGCAGTAGGGAAGCTTC 58.800 55.000 18.54 18.54 39.02 3.86
1612 2606 0.622136 TGTCGTAGGAGCAGTAGGGA 59.378 55.000 0.00 0.00 0.00 4.20
1641 2635 1.228367 CTGGTGGCAAGCCTGAAGT 60.228 57.895 12.96 0.00 36.94 3.01
1663 2657 4.966787 TGGTTGCGGTGGAAGGCC 62.967 66.667 0.00 0.00 0.00 5.19
1664 2658 3.365265 CTGGTTGCGGTGGAAGGC 61.365 66.667 0.00 0.00 0.00 4.35
1668 2662 2.847234 AGGTCTGGTTGCGGTGGA 60.847 61.111 0.00 0.00 0.00 4.02
1670 2664 2.449031 TAGCAGGTCTGGTTGCGGTG 62.449 60.000 8.01 0.00 44.80 4.94
1679 2673 2.185350 CCGCCAGTAGCAGGTCTG 59.815 66.667 0.00 0.00 44.04 3.51
1685 2679 0.613853 AAGTAGTCCCGCCAGTAGCA 60.614 55.000 0.00 0.00 44.04 3.49
1696 2690 1.067821 CAGCGGATCCTGAAGTAGTCC 59.932 57.143 10.75 0.00 34.77 3.85
1703 2697 1.686325 GGGTAGCAGCGGATCCTGAA 61.686 60.000 10.75 0.00 34.77 3.02
1707 2701 4.301027 CGGGGTAGCAGCGGATCC 62.301 72.222 0.00 0.00 0.00 3.36
1709 2703 3.537874 GACGGGGTAGCAGCGGAT 61.538 66.667 0.00 0.00 0.00 4.18
1725 2719 0.594028 GCGTGTGACTTCGTCAGTGA 60.594 55.000 0.00 0.00 43.57 3.41
1727 2721 1.299926 GGCGTGTGACTTCGTCAGT 60.300 57.895 0.00 0.00 43.57 3.41
1729 2723 1.590525 GTGGCGTGTGACTTCGTCA 60.591 57.895 4.33 4.33 40.50 4.35
1773 2767 1.076923 TACTCTGCGAGGGAGGTCC 60.077 63.158 9.75 0.00 35.34 4.46
1775 2769 0.394625 GAGTACTCTGCGAGGGAGGT 60.395 60.000 15.91 0.00 35.34 3.85
1778 2772 2.328819 GTAGAGTACTCTGCGAGGGA 57.671 55.000 31.47 10.19 40.71 4.20
1785 2779 0.377554 CACCGCCGTAGAGTACTCTG 59.622 60.000 31.47 18.03 40.71 3.35
1786 2780 1.375098 GCACCGCCGTAGAGTACTCT 61.375 60.000 27.72 27.72 43.40 3.24
1801 2795 3.655810 CTGGGAGAGCTCGTGCACC 62.656 68.421 12.15 11.26 42.74 5.01
1813 2807 4.504916 CGGAGCAGCGTCTGGGAG 62.505 72.222 8.57 0.00 31.21 4.30
1822 2816 1.742880 TGCAATGAGTCGGAGCAGC 60.743 57.895 0.00 0.00 0.00 5.25
1823 2817 0.671472 TGTGCAATGAGTCGGAGCAG 60.671 55.000 3.77 0.00 35.66 4.24
1825 2819 1.364626 CCTGTGCAATGAGTCGGAGC 61.365 60.000 0.00 0.00 0.00 4.70
1829 2823 2.401766 GCCCCTGTGCAATGAGTCG 61.402 63.158 0.00 0.00 0.00 4.18
1831 2825 0.896940 CAAGCCCCTGTGCAATGAGT 60.897 55.000 0.00 0.00 0.00 3.41
1834 2828 2.975536 CCAAGCCCCTGTGCAATG 59.024 61.111 0.00 0.00 0.00 2.82
1886 2880 0.904865 TTCATCTGGGTCACTCCGCT 60.905 55.000 0.00 0.00 37.00 5.52
1891 2885 3.328931 AGTTCACATTCATCTGGGTCACT 59.671 43.478 0.00 0.00 0.00 3.41
1893 2887 4.532126 AGTAGTTCACATTCATCTGGGTCA 59.468 41.667 0.00 0.00 0.00 4.02
1894 2888 5.091261 AGTAGTTCACATTCATCTGGGTC 57.909 43.478 0.00 0.00 0.00 4.46
1897 2891 5.129485 AGGGTAGTAGTTCACATTCATCTGG 59.871 44.000 0.00 0.00 0.00 3.86
1900 2894 5.128827 TGGAGGGTAGTAGTTCACATTCATC 59.871 44.000 0.00 0.00 0.00 2.92
1905 2899 3.134804 GCATGGAGGGTAGTAGTTCACAT 59.865 47.826 0.00 0.00 0.00 3.21
1906 2900 2.500098 GCATGGAGGGTAGTAGTTCACA 59.500 50.000 0.00 0.00 0.00 3.58
1909 2903 1.416772 GGGCATGGAGGGTAGTAGTTC 59.583 57.143 0.00 0.00 0.00 3.01
1924 2918 4.741239 ACAGAGGGGTCCGGGCAT 62.741 66.667 9.07 0.00 0.00 4.40
1936 2930 3.691744 GAGCCCGAGCGTGACAGAG 62.692 68.421 0.00 0.00 46.67 3.35
1937 2931 3.749064 GAGCCCGAGCGTGACAGA 61.749 66.667 0.00 0.00 46.67 3.41
1939 2933 3.282745 GAAGAGCCCGAGCGTGACA 62.283 63.158 0.00 0.00 46.67 3.58
1951 2945 2.029844 GTCACAGTGCGGGAAGAGC 61.030 63.158 0.00 0.00 0.00 4.09
1954 2948 2.738521 CGGTCACAGTGCGGGAAG 60.739 66.667 0.00 0.00 0.00 3.46
1955 2949 4.980805 GCGGTCACAGTGCGGGAA 62.981 66.667 0.00 0.00 0.00 3.97
1966 2960 3.311110 GTGAGGAGGTGGCGGTCA 61.311 66.667 0.00 0.00 0.00 4.02
2020 3014 4.803426 CACCTCTCGCGGTGCCTC 62.803 72.222 6.13 0.00 46.98 4.70
2066 3060 0.389817 TGGCCGAAGTTGATGACGAG 60.390 55.000 0.00 0.00 0.00 4.18
2173 3167 2.022129 CTTGGGCGTGACGAGTGTC 61.022 63.158 10.10 0.00 45.71 3.67
2176 3170 1.079819 CATCTTGGGCGTGACGAGT 60.080 57.895 10.10 0.00 0.00 4.18
2185 3179 2.825836 CGGCACTCCATCTTGGGC 60.826 66.667 0.00 0.00 38.32 5.36
2231 3225 3.771216 ACTTGGCTGGATTTGTCATCTT 58.229 40.909 0.00 0.00 0.00 2.40
2234 3228 4.012374 CTGTACTTGGCTGGATTTGTCAT 58.988 43.478 0.00 0.00 0.00 3.06
2239 3233 1.992557 TCCCTGTACTTGGCTGGATTT 59.007 47.619 0.00 0.00 0.00 2.17
2456 3450 1.745653 GGGCTTACAAATCTGGTGAGC 59.254 52.381 0.00 0.00 44.43 4.26
2484 3478 1.956477 GAGAAAACATATGGGGCGCAT 59.044 47.619 21.24 21.24 0.00 4.73
2488 3482 1.676006 CACGGAGAAAACATATGGGGC 59.324 52.381 7.80 0.00 0.00 5.80
2502 3496 2.022764 TTGCATACCATGACACGGAG 57.977 50.000 0.00 0.00 0.00 4.63
2520 3514 7.312899 CGGAAACTAAAAGAATTGGCACTATT 58.687 34.615 0.00 0.00 0.00 1.73
2608 3602 8.950403 ACGAATTTCTTTTGCTGTAAGATAAC 57.050 30.769 0.00 0.00 34.07 1.89
2609 3603 9.607285 GAACGAATTTCTTTTGCTGTAAGATAA 57.393 29.630 0.00 0.00 34.07 1.75
2744 3738 0.878523 CCAGAGAAACGACACCGCAA 60.879 55.000 0.00 0.00 39.95 4.85
2763 3757 0.605319 TCCACAAACGATGCTCCCAC 60.605 55.000 0.00 0.00 0.00 4.61
2788 3782 2.291930 CCTCCTACCTCTGACTTCCAGT 60.292 54.545 0.00 0.00 43.38 4.00
2820 3814 0.946221 CGAAGCTCCGTGCAAGACTT 60.946 55.000 0.00 1.74 45.94 3.01
2821 3815 1.373497 CGAAGCTCCGTGCAAGACT 60.373 57.895 0.00 0.00 45.94 3.24
2877 3871 1.236616 CGACCAGGCATGACAAAGCA 61.237 55.000 0.00 0.00 0.00 3.91
2943 3937 1.376466 CTGCCAAGTACCACCAGCT 59.624 57.895 0.00 0.00 0.00 4.24
3038 4033 4.634133 TCGTCGACACCACCACGC 62.634 66.667 17.16 0.00 32.21 5.34
3055 4050 2.660064 CCTTGCCCGGTCTAGCTGT 61.660 63.158 0.00 0.00 0.00 4.40
3097 4092 1.003355 AACTGCCACCACTCCATCG 60.003 57.895 0.00 0.00 0.00 3.84
3173 4168 3.944250 ATGAGGCCCCAACCAAGCG 62.944 63.158 0.00 0.00 0.00 4.68
3191 4186 5.724328 CAGTCAAGCCTAACATCTAAGACA 58.276 41.667 0.00 0.00 0.00 3.41
3243 4239 4.599041 TCCAGTTAATGAAGGGATGTTGG 58.401 43.478 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.