Multiple sequence alignment - TraesCS7D01G271200

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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 TraesCS7D01G271200 chr7D 100.000 6672 0 0 1 6672 259296149 259289478 0.000000e+00 12321.0
1 TraesCS7D01G271200 chr7D 86.595 373 27 6 2764 3127 601277177 601277535 2.260000e-104 390.0
2 TraesCS7D01G271200 chr7D 86.595 373 27 6 2764 3127 601321012 601320654 2.260000e-104 390.0
3 TraesCS7D01G271200 chr7D 91.078 269 22 2 2446 2714 601276900 601277166 4.920000e-96 363.0
4 TraesCS7D01G271200 chr7D 91.078 269 22 2 2446 2714 601321289 601321023 4.920000e-96 363.0
5 TraesCS7D01G271200 chr7A 95.098 2958 94 12 2818 5765 281376301 281373385 0.000000e+00 4612.0
6 TraesCS7D01G271200 chr7A 95.464 2844 93 12 1 2832 281380508 281377689 0.000000e+00 4505.0
7 TraesCS7D01G271200 chr7A 87.281 684 60 12 2446 3129 693012004 693011348 0.000000e+00 756.0
8 TraesCS7D01G271200 chr7A 84.503 684 57 29 2446 3129 692980884 692980250 1.220000e-176 630.0
9 TraesCS7D01G271200 chr7A 90.426 376 22 6 2764 3129 693106929 693106558 3.620000e-132 483.0
10 TraesCS7D01G271200 chr7A 91.481 270 19 4 2446 2714 693107206 693106940 1.060000e-97 368.0
11 TraesCS7D01G271200 chr7A 88.462 52 4 2 2133 2184 47923281 47923330 2.010000e-05 62.1
12 TraesCS7D01G271200 chr7B 95.765 2007 54 2 2723 4699 238530212 238528207 0.000000e+00 3206.0
13 TraesCS7D01G271200 chr7B 94.789 1900 47 14 849 2724 238532145 238530274 0.000000e+00 2913.0
14 TraesCS7D01G271200 chr7B 91.978 1072 39 19 4696 5765 238528129 238527103 0.000000e+00 1459.0
15 TraesCS7D01G271200 chr7B 89.572 374 25 6 2765 3129 680339072 680338704 4.710000e-126 462.0
16 TraesCS7D01G271200 chr7B 98.086 209 4 0 2 210 238533662 238533454 1.370000e-96 364.0
17 TraesCS7D01G271200 chr7B 88.176 296 21 2 202 497 238533055 238532774 2.300000e-89 340.0
18 TraesCS7D01G271200 chr7B 90.347 259 24 1 2456 2714 680339341 680339084 8.290000e-89 339.0
19 TraesCS7D01G271200 chr7B 97.778 180 3 1 529 707 238532774 238532595 6.500000e-80 309.0
20 TraesCS7D01G271200 chr1D 98.821 848 9 1 5826 6672 485646194 485647041 0.000000e+00 1509.0
21 TraesCS7D01G271200 chr1D 98.585 848 11 1 5826 6672 432742820 432741973 0.000000e+00 1498.0
22 TraesCS7D01G271200 chr1D 97.754 846 19 0 5827 6672 453428128 453428973 0.000000e+00 1458.0
23 TraesCS7D01G271200 chr3D 98.704 849 10 1 5824 6672 511247299 511248146 0.000000e+00 1506.0
24 TraesCS7D01G271200 chr3D 88.710 62 6 1 4814 4874 441260946 441261007 2.580000e-09 75.0
25 TraesCS7D01G271200 chr6D 98.467 848 13 0 5825 6672 462236209 462237056 0.000000e+00 1495.0
26 TraesCS7D01G271200 chr6D 98.239 852 13 2 5823 6672 41949415 41950266 0.000000e+00 1489.0
27 TraesCS7D01G271200 chr6D 92.593 54 2 2 4816 4869 290322025 290321974 7.170000e-10 76.8
28 TraesCS7D01G271200 chr5B 98.118 850 15 1 5824 6672 371305690 371304841 0.000000e+00 1480.0
29 TraesCS7D01G271200 chr5B 97.875 847 17 1 5827 6672 670734387 670735233 0.000000e+00 1463.0
30 TraesCS7D01G271200 chr2B 97.421 853 20 2 5822 6672 43261061 43261913 0.000000e+00 1452.0
31 TraesCS7D01G271200 chr5A 94.340 53 2 1 4818 4870 138089552 138089501 5.550000e-11 80.5
32 TraesCS7D01G271200 chr6B 94.231 52 2 1 4818 4869 701243817 701243767 1.990000e-10 78.7
33 TraesCS7D01G271200 chr3B 91.228 57 5 0 4818 4874 94493052 94493108 1.990000e-10 78.7
34 TraesCS7D01G271200 chr3B 90.164 61 4 2 4815 4874 578810897 578810956 1.990000e-10 78.7
35 TraesCS7D01G271200 chr3A 90.000 60 2 4 4818 4874 581848881 581848939 2.580000e-09 75.0


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 TraesCS7D01G271200 chr7D 259289478 259296149 6671 True 12321.000000 12321 100.000000 1 6672 1 chr7D.!!$R1 6671
1 TraesCS7D01G271200 chr7D 601276900 601277535 635 False 376.500000 390 88.836500 2446 3127 2 chr7D.!!$F1 681
2 TraesCS7D01G271200 chr7D 601320654 601321289 635 True 376.500000 390 88.836500 2446 3127 2 chr7D.!!$R2 681
3 TraesCS7D01G271200 chr7A 281373385 281380508 7123 True 4558.500000 4612 95.281000 1 5765 2 chr7A.!!$R3 5764
4 TraesCS7D01G271200 chr7A 693011348 693012004 656 True 756.000000 756 87.281000 2446 3129 1 chr7A.!!$R2 683
5 TraesCS7D01G271200 chr7A 692980250 692980884 634 True 630.000000 630 84.503000 2446 3129 1 chr7A.!!$R1 683
6 TraesCS7D01G271200 chr7A 693106558 693107206 648 True 425.500000 483 90.953500 2446 3129 2 chr7A.!!$R4 683
7 TraesCS7D01G271200 chr7B 238527103 238533662 6559 True 1431.833333 3206 94.428667 2 5765 6 chr7B.!!$R1 5763
8 TraesCS7D01G271200 chr7B 680338704 680339341 637 True 400.500000 462 89.959500 2456 3129 2 chr7B.!!$R2 673
9 TraesCS7D01G271200 chr1D 485646194 485647041 847 False 1509.000000 1509 98.821000 5826 6672 1 chr1D.!!$F2 846
10 TraesCS7D01G271200 chr1D 432741973 432742820 847 True 1498.000000 1498 98.585000 5826 6672 1 chr1D.!!$R1 846
11 TraesCS7D01G271200 chr1D 453428128 453428973 845 False 1458.000000 1458 97.754000 5827 6672 1 chr1D.!!$F1 845
12 TraesCS7D01G271200 chr3D 511247299 511248146 847 False 1506.000000 1506 98.704000 5824 6672 1 chr3D.!!$F2 848
13 TraesCS7D01G271200 chr6D 462236209 462237056 847 False 1495.000000 1495 98.467000 5825 6672 1 chr6D.!!$F2 847
14 TraesCS7D01G271200 chr6D 41949415 41950266 851 False 1489.000000 1489 98.239000 5823 6672 1 chr6D.!!$F1 849
15 TraesCS7D01G271200 chr5B 371304841 371305690 849 True 1480.000000 1480 98.118000 5824 6672 1 chr5B.!!$R1 848
16 TraesCS7D01G271200 chr5B 670734387 670735233 846 False 1463.000000 1463 97.875000 5827 6672 1 chr5B.!!$F1 845
17 TraesCS7D01G271200 chr2B 43261061 43261913 852 False 1452.000000 1452 97.421000 5822 6672 1 chr2B.!!$F1 850

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
498 906 0.318445 GGCTGGTACTACATACGCGG 60.318 60.000 12.47 0.00 34.22 6.46 F
1231 1955 0.171903 CCGGCAGAGCTCAATTTTGG 59.828 55.000 17.77 5.93 0.00 3.28 F
1803 2549 1.065551 TCTGAGCCATGATACGACACG 59.934 52.381 0.00 0.00 0.00 4.49 F
3156 5399 1.202855 AGCCTCTTGCACAAGTCATGT 60.203 47.619 10.05 0.00 45.34 3.21 F
3536 5779 0.922560 CTCTTGCGCGAAATGCATCG 60.923 55.000 12.10 1.66 46.97 3.84 F
4151 6394 1.310904 TGGACGTTGGCAAACCTTAC 58.689 50.000 0.00 0.00 36.63 2.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2260 3008 0.962356 CAGGGTGCTCGATTTGCCTT 60.962 55.000 0.0 0.0 0.00 4.35 R
3217 5460 0.106719 ACACTGTCACAAGGGTTGGG 60.107 55.000 0.0 0.0 25.41 4.12 R
3536 5779 1.535896 GAAACCGAAAGTGCTTCCTCC 59.464 52.381 0.0 0.0 0.00 4.30 R
4493 6766 0.036732 TGGTGCTCATGTCCTTGACC 59.963 55.000 0.0 0.0 0.00 4.02 R
5060 7449 1.662629 GTGCCACAACTCGATGATCTG 59.337 52.381 0.0 0.0 0.00 2.90 R
5794 8188 0.026285 GGAATATCGCACACGCACAC 59.974 55.000 0.0 0.0 39.84 3.82 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
305 713 0.321671 CGGAGCAACAAGGAGGAGAA 59.678 55.000 0.00 0.00 0.00 2.87
309 717 1.353694 AGCAACAAGGAGGAGAAGCAT 59.646 47.619 0.00 0.00 0.00 3.79
310 718 2.165998 GCAACAAGGAGGAGAAGCATT 58.834 47.619 0.00 0.00 0.00 3.56
314 722 2.579860 ACAAGGAGGAGAAGCATTGGAT 59.420 45.455 0.00 0.00 0.00 3.41
315 723 3.782523 ACAAGGAGGAGAAGCATTGGATA 59.217 43.478 0.00 0.00 0.00 2.59
321 729 2.646798 GGAGAAGCATTGGATAGGGGAT 59.353 50.000 0.00 0.00 0.00 3.85
345 753 1.485838 CGATCTTGCCACTAGCTGCG 61.486 60.000 0.00 0.00 44.23 5.18
386 794 1.538950 GTCGTCTTCTAGTTCCACCGT 59.461 52.381 0.00 0.00 0.00 4.83
391 799 0.971386 TTCTAGTTCCACCGTCCACC 59.029 55.000 0.00 0.00 0.00 4.61
395 803 4.308458 TTCCACCGTCCACCAGCG 62.308 66.667 0.00 0.00 0.00 5.18
491 899 4.471747 TGTTGGATAATGGCTGGTACTACA 59.528 41.667 0.00 0.00 0.00 2.74
495 903 5.047590 TGGATAATGGCTGGTACTACATACG 60.048 44.000 0.00 0.00 34.22 3.06
498 906 0.318445 GGCTGGTACTACATACGCGG 60.318 60.000 12.47 0.00 34.22 6.46
525 933 4.892934 TGCATAGAAAAACAAGTCTTGGGT 59.107 37.500 16.85 1.55 34.12 4.51
755 1164 1.076533 CGCCGGCAGTGTAGTAGTTG 61.077 60.000 28.98 0.12 0.00 3.16
761 1170 2.480419 GGCAGTGTAGTAGTTGCTGTTG 59.520 50.000 0.00 0.00 36.79 3.33
764 1173 4.035208 GCAGTGTAGTAGTTGCTGTTGTTT 59.965 41.667 0.00 0.00 33.88 2.83
765 1174 5.235616 GCAGTGTAGTAGTTGCTGTTGTTTA 59.764 40.000 0.00 0.00 33.88 2.01
767 1176 5.756833 AGTGTAGTAGTTGCTGTTGTTTACC 59.243 40.000 0.00 0.00 0.00 2.85
769 1178 6.259387 GTGTAGTAGTTGCTGTTGTTTACCTT 59.741 38.462 0.00 0.00 0.00 3.50
773 1182 3.380320 AGTTGCTGTTGTTTACCTTGGTC 59.620 43.478 0.00 0.00 0.00 4.02
787 1196 4.416738 GGTCTGGGCAGGCTGGTC 62.417 72.222 17.64 0.00 32.63 4.02
950 1667 0.906756 CAGGTGCAGAGGAAGAGGGA 60.907 60.000 0.00 0.00 0.00 4.20
1081 1799 2.572095 GATCATGGTGTCCGTGCGGA 62.572 60.000 9.48 9.48 40.13 5.54
1231 1955 0.171903 CCGGCAGAGCTCAATTTTGG 59.828 55.000 17.77 5.93 0.00 3.28
1236 1960 3.582780 GCAGAGCTCAATTTTGGAAAGG 58.417 45.455 17.77 0.00 0.00 3.11
1411 2135 5.858381 AGAAGTTGCTCTATCAGTTGTCAA 58.142 37.500 0.00 0.00 0.00 3.18
1461 2185 2.177394 TGCAACTCCTTTACATCGCA 57.823 45.000 0.00 0.00 0.00 5.10
1803 2549 1.065551 TCTGAGCCATGATACGACACG 59.934 52.381 0.00 0.00 0.00 4.49
1908 2655 4.122046 TGATCTCGCGTCATCATTTGAAT 58.878 39.130 15.68 0.00 35.70 2.57
2024 2771 4.876679 GCGGGCTAAAATTTCTAGAGAACT 59.123 41.667 9.97 0.00 33.13 3.01
2089 2836 3.619038 GGTATGTGCTACAGCTCAAAGAC 59.381 47.826 9.75 8.33 45.82 3.01
2103 2850 4.516698 GCTCAAAGACAGATTGGAGAAACA 59.483 41.667 0.00 0.00 0.00 2.83
2173 2920 7.397476 TGGTTGGTGGCTCTCTTATATATCTAG 59.603 40.741 0.00 0.00 0.00 2.43
2208 2956 7.707893 ACCTTTTGAAGATGATTTTGTTGACAG 59.292 33.333 0.00 0.00 0.00 3.51
2210 2958 5.710513 TGAAGATGATTTTGTTGACAGGG 57.289 39.130 0.00 0.00 0.00 4.45
2354 3102 5.032327 TCATGTTTCCATCATCTCTGAGG 57.968 43.478 4.59 0.00 34.12 3.86
2362 3110 3.433314 CCATCATCTCTGAGGGTTCTTGG 60.433 52.174 4.59 2.02 46.09 3.61
2875 5109 1.866853 GCAGCAAGGGAAGAAACGGG 61.867 60.000 0.00 0.00 0.00 5.28
3077 5320 5.157940 AGTGATGTCTGACAAAGCACTAT 57.842 39.130 27.66 14.94 37.32 2.12
3156 5399 1.202855 AGCCTCTTGCACAAGTCATGT 60.203 47.619 10.05 0.00 45.34 3.21
3198 5441 5.652452 AGGATGCACAGATTAAAAAGGTACC 59.348 40.000 2.73 2.73 0.00 3.34
3217 5460 5.183331 GGTACCTTTCCTCACCTGAAATTTC 59.817 44.000 11.41 11.41 31.75 2.17
3536 5779 0.922560 CTCTTGCGCGAAATGCATCG 60.923 55.000 12.10 1.66 46.97 3.84
3662 5905 6.496565 ACTTGTCAATCCCCAATCAAACAATA 59.503 34.615 0.00 0.00 0.00 1.90
3825 6068 4.696479 AGGGAAGTACAATGCATAGAGG 57.304 45.455 0.00 0.00 0.00 3.69
3927 6170 3.146066 GAGGACATCTCTAGAGACGCAT 58.854 50.000 24.62 13.90 40.75 4.73
3985 6228 6.259608 AGCATAACAGAGAAAATGGAAGATCG 59.740 38.462 0.00 0.00 0.00 3.69
4115 6358 3.317993 ACTTTGTCAAACTGTACCCATGC 59.682 43.478 0.00 0.00 0.00 4.06
4130 6373 4.526970 ACCCATGCGATTCTAACATTTCT 58.473 39.130 0.00 0.00 0.00 2.52
4151 6394 1.310904 TGGACGTTGGCAAACCTTAC 58.689 50.000 0.00 0.00 36.63 2.34
4423 6666 3.181516 GCTGATTCTGGCGAAGTAGTTTG 60.182 47.826 0.00 0.00 31.60 2.93
4424 6667 3.997021 CTGATTCTGGCGAAGTAGTTTGT 59.003 43.478 0.00 0.00 31.60 2.83
4425 6668 3.745975 TGATTCTGGCGAAGTAGTTTGTG 59.254 43.478 0.00 0.00 31.60 3.33
4426 6669 3.462483 TTCTGGCGAAGTAGTTTGTGA 57.538 42.857 0.00 0.00 0.00 3.58
4427 6670 3.678056 TCTGGCGAAGTAGTTTGTGAT 57.322 42.857 0.00 0.00 0.00 3.06
4428 6671 3.325870 TCTGGCGAAGTAGTTTGTGATG 58.674 45.455 0.00 0.00 0.00 3.07
4429 6672 3.006430 TCTGGCGAAGTAGTTTGTGATGA 59.994 43.478 0.00 0.00 0.00 2.92
4430 6673 3.734463 TGGCGAAGTAGTTTGTGATGAA 58.266 40.909 0.00 0.00 0.00 2.57
4431 6674 3.745975 TGGCGAAGTAGTTTGTGATGAAG 59.254 43.478 0.00 0.00 0.00 3.02
4432 6675 3.746492 GGCGAAGTAGTTTGTGATGAAGT 59.254 43.478 0.00 0.00 0.00 3.01
4433 6676 4.927425 GGCGAAGTAGTTTGTGATGAAGTA 59.073 41.667 0.00 0.00 0.00 2.24
4434 6677 5.062308 GGCGAAGTAGTTTGTGATGAAGTAG 59.938 44.000 0.00 0.00 0.00 2.57
4435 6678 5.634020 GCGAAGTAGTTTGTGATGAAGTAGT 59.366 40.000 0.00 0.00 0.00 2.73
4436 6679 6.145696 GCGAAGTAGTTTGTGATGAAGTAGTT 59.854 38.462 0.00 0.00 31.51 2.24
4437 6680 7.327761 GCGAAGTAGTTTGTGATGAAGTAGTTA 59.672 37.037 0.00 0.00 29.88 2.24
4438 6681 9.188588 CGAAGTAGTTTGTGATGAAGTAGTTAA 57.811 33.333 0.00 0.00 29.88 2.01
4440 6683 9.490379 AAGTAGTTTGTGATGAAGTAGTTAAGG 57.510 33.333 0.00 0.00 0.00 2.69
4441 6684 8.867097 AGTAGTTTGTGATGAAGTAGTTAAGGA 58.133 33.333 0.00 0.00 0.00 3.36
4442 6685 7.964604 AGTTTGTGATGAAGTAGTTAAGGAC 57.035 36.000 0.00 0.00 0.00 3.85
4443 6686 7.506114 AGTTTGTGATGAAGTAGTTAAGGACA 58.494 34.615 0.00 0.00 0.00 4.02
4444 6687 7.441458 AGTTTGTGATGAAGTAGTTAAGGACAC 59.559 37.037 0.00 0.00 0.00 3.67
4445 6688 5.466819 TGTGATGAAGTAGTTAAGGACACG 58.533 41.667 0.00 0.00 0.00 4.49
4446 6689 5.242171 TGTGATGAAGTAGTTAAGGACACGA 59.758 40.000 0.00 0.00 0.00 4.35
4447 6690 5.800941 GTGATGAAGTAGTTAAGGACACGAG 59.199 44.000 0.00 0.00 0.00 4.18
4448 6691 5.475909 TGATGAAGTAGTTAAGGACACGAGT 59.524 40.000 0.00 0.00 0.00 4.18
4449 6692 6.656270 TGATGAAGTAGTTAAGGACACGAGTA 59.344 38.462 0.00 0.00 0.00 2.59
4450 6693 6.246420 TGAAGTAGTTAAGGACACGAGTAC 57.754 41.667 0.00 0.00 0.00 2.73
4451 6694 5.182001 TGAAGTAGTTAAGGACACGAGTACC 59.818 44.000 0.00 0.00 0.00 3.34
4452 6695 4.655963 AGTAGTTAAGGACACGAGTACCA 58.344 43.478 0.00 0.00 0.00 3.25
4490 6763 2.616256 GGACATGAGCACCAGTGATGAA 60.616 50.000 0.00 0.00 0.00 2.57
4493 6766 2.174363 TGAGCACCAGTGATGAAGTG 57.826 50.000 0.99 0.00 0.00 3.16
4749 7135 5.643664 ACGGGAAACTTAACAAAACAGAAC 58.356 37.500 0.00 0.00 0.00 3.01
4764 7150 7.599245 ACAAAACAGAACTGACTAGTATACTGC 59.401 37.037 15.90 5.58 36.79 4.40
4812 7198 6.422701 CGCCTAAATCACCAGTCGATATTTAA 59.577 38.462 0.00 0.00 0.00 1.52
4813 7199 7.117812 CGCCTAAATCACCAGTCGATATTTAAT 59.882 37.037 0.00 0.00 0.00 1.40
4814 7200 9.431887 GCCTAAATCACCAGTCGATATTTAATA 57.568 33.333 0.00 0.00 0.00 0.98
4928 7317 9.139174 GAATTAAACCAATGTCTTTGTGTATGG 57.861 33.333 0.00 0.00 33.15 2.74
5060 7449 2.346099 TTTTGCAAATAGGCAGCGAC 57.654 45.000 13.65 0.00 45.88 5.19
5140 7529 2.260639 TCCTCTTCAAGGGAGATGCT 57.739 50.000 0.00 0.00 46.23 3.79
5230 7619 2.785868 CGCAGGAGGCAAGCTTAAT 58.214 52.632 0.00 0.00 45.17 1.40
5231 7620 1.953559 CGCAGGAGGCAAGCTTAATA 58.046 50.000 0.00 0.00 45.17 0.98
5298 7687 2.676342 CAGGGTAACAGTATGGTTTCGC 59.324 50.000 0.00 0.00 43.62 4.70
5303 7692 1.156736 ACAGTATGGTTTCGCACTGC 58.843 50.000 0.00 0.00 43.62 4.40
5313 7702 1.255882 TTCGCACTGCCCATGAATTT 58.744 45.000 0.00 0.00 0.00 1.82
5316 7705 2.423185 TCGCACTGCCCATGAATTTAAG 59.577 45.455 0.00 0.00 0.00 1.85
5330 7724 9.736023 CCATGAATTTAAGCCTAAGTATGTTTC 57.264 33.333 0.00 0.00 0.00 2.78
5342 7736 8.230486 GCCTAAGTATGTTTCGATGGAATAATG 58.770 37.037 0.00 0.00 30.88 1.90
5343 7737 8.721478 CCTAAGTATGTTTCGATGGAATAATGG 58.279 37.037 0.00 0.00 30.88 3.16
5443 7837 2.206036 AACGGGGACAAGGAGGGA 59.794 61.111 0.00 0.00 0.00 4.20
5584 7978 1.519455 GATCGACCTGGTTGAGCCG 60.519 63.158 19.48 9.55 41.21 5.52
5662 8056 1.302832 CCGGTCTTTCAGCCTGCTT 60.303 57.895 0.00 0.00 0.00 3.91
5721 8115 3.996363 GGTTTGGTTTACGTAGTACAGGG 59.004 47.826 10.77 0.00 45.76 4.45
5750 8144 6.159928 TCACTTAACAGGAGGAGAGGACTATA 59.840 42.308 0.00 0.00 0.00 1.31
5751 8145 7.007723 CACTTAACAGGAGGAGAGGACTATAT 58.992 42.308 0.00 0.00 0.00 0.86
5770 8164 4.845580 CTCCGCCGCATCTGCCTT 62.846 66.667 0.00 0.00 37.91 4.35
5773 8167 3.434319 CGCCGCATCTGCCTTGTT 61.434 61.111 0.00 0.00 37.91 2.83
5774 8168 2.964978 GCCGCATCTGCCTTGTTT 59.035 55.556 0.00 0.00 37.91 2.83
5775 8169 1.290009 GCCGCATCTGCCTTGTTTT 59.710 52.632 0.00 0.00 37.91 2.43
5776 8170 0.319813 GCCGCATCTGCCTTGTTTTT 60.320 50.000 0.00 0.00 37.91 1.94
5777 8171 1.421382 CCGCATCTGCCTTGTTTTTG 58.579 50.000 0.00 0.00 37.91 2.44
5778 8172 0.785979 CGCATCTGCCTTGTTTTTGC 59.214 50.000 0.00 0.00 37.91 3.68
5779 8173 1.603678 CGCATCTGCCTTGTTTTTGCT 60.604 47.619 0.00 0.00 37.91 3.91
5780 8174 2.486918 GCATCTGCCTTGTTTTTGCTT 58.513 42.857 0.00 0.00 34.31 3.91
5781 8175 2.222445 GCATCTGCCTTGTTTTTGCTTG 59.778 45.455 0.00 0.00 34.31 4.01
5782 8176 3.460103 CATCTGCCTTGTTTTTGCTTGT 58.540 40.909 0.00 0.00 0.00 3.16
5783 8177 2.891112 TCTGCCTTGTTTTTGCTTGTG 58.109 42.857 0.00 0.00 0.00 3.33
5784 8178 2.495270 TCTGCCTTGTTTTTGCTTGTGA 59.505 40.909 0.00 0.00 0.00 3.58
5785 8179 3.056250 TCTGCCTTGTTTTTGCTTGTGAA 60.056 39.130 0.00 0.00 0.00 3.18
5786 8180 3.871485 TGCCTTGTTTTTGCTTGTGAAT 58.129 36.364 0.00 0.00 0.00 2.57
5787 8181 4.260170 TGCCTTGTTTTTGCTTGTGAATT 58.740 34.783 0.00 0.00 0.00 2.17
5788 8182 4.094590 TGCCTTGTTTTTGCTTGTGAATTG 59.905 37.500 0.00 0.00 0.00 2.32
5789 8183 4.094739 GCCTTGTTTTTGCTTGTGAATTGT 59.905 37.500 0.00 0.00 0.00 2.71
5790 8184 5.561993 CCTTGTTTTTGCTTGTGAATTGTG 58.438 37.500 0.00 0.00 0.00 3.33
5791 8185 5.122082 CCTTGTTTTTGCTTGTGAATTGTGT 59.878 36.000 0.00 0.00 0.00 3.72
5792 8186 5.527511 TGTTTTTGCTTGTGAATTGTGTG 57.472 34.783 0.00 0.00 0.00 3.82
5793 8187 4.142945 TGTTTTTGCTTGTGAATTGTGTGC 60.143 37.500 0.00 0.00 0.00 4.57
5794 8188 1.837648 TTGCTTGTGAATTGTGTGCG 58.162 45.000 0.00 0.00 0.00 5.34
5795 8189 0.737804 TGCTTGTGAATTGTGTGCGT 59.262 45.000 0.00 0.00 0.00 5.24
5796 8190 1.122849 GCTTGTGAATTGTGTGCGTG 58.877 50.000 0.00 0.00 0.00 5.34
5797 8191 1.533756 GCTTGTGAATTGTGTGCGTGT 60.534 47.619 0.00 0.00 0.00 4.49
5798 8192 2.110990 CTTGTGAATTGTGTGCGTGTG 58.889 47.619 0.00 0.00 0.00 3.82
5799 8193 0.248417 TGTGAATTGTGTGCGTGTGC 60.248 50.000 0.00 0.00 43.20 4.57
5816 8210 2.677971 GCGTGTGCGATATTCCTGT 58.322 52.632 0.00 0.00 41.33 4.00
5817 8211 0.301687 GCGTGTGCGATATTCCTGTG 59.698 55.000 0.00 0.00 41.33 3.66
5818 8212 1.640428 CGTGTGCGATATTCCTGTGT 58.360 50.000 0.00 0.00 41.33 3.72
5819 8213 1.324435 CGTGTGCGATATTCCTGTGTG 59.676 52.381 0.00 0.00 41.33 3.82
5820 8214 1.062587 GTGTGCGATATTCCTGTGTGC 59.937 52.381 0.00 0.00 0.00 4.57
5821 8215 1.338579 TGTGCGATATTCCTGTGTGCA 60.339 47.619 0.00 0.00 0.00 4.57
5892 8288 4.603094 TTCATCCCTACACAGACTAGGA 57.397 45.455 0.00 0.00 33.65 2.94
6265 8661 3.566853 CGCGCAAGATCATGCCGT 61.567 61.111 16.72 0.00 43.47 5.68
6367 8763 1.634702 CTGAGACTTCCAGCTTACGC 58.365 55.000 0.00 0.00 0.00 4.42
6436 8832 2.221299 CCTTTGTCCCAGTCCCCGA 61.221 63.158 0.00 0.00 0.00 5.14
6527 8923 1.659794 GCGGTGCCTTGTCATGTTT 59.340 52.632 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
305 713 2.107204 GTGTCATCCCCTATCCAATGCT 59.893 50.000 0.00 0.00 0.00 3.79
309 717 2.168458 TCGTGTCATCCCCTATCCAA 57.832 50.000 0.00 0.00 0.00 3.53
310 718 2.158310 AGATCGTGTCATCCCCTATCCA 60.158 50.000 0.00 0.00 0.00 3.41
314 722 1.412710 GCAAGATCGTGTCATCCCCTA 59.587 52.381 10.41 0.00 0.00 3.53
315 723 0.179000 GCAAGATCGTGTCATCCCCT 59.821 55.000 10.41 0.00 0.00 4.79
321 729 1.404181 GCTAGTGGCAAGATCGTGTCA 60.404 52.381 12.08 12.08 41.35 3.58
345 753 2.275318 CAATGCGAGAGGAGGAGAAAC 58.725 52.381 0.00 0.00 32.19 2.78
391 799 4.156622 CATCACCTGCGCACGCTG 62.157 66.667 16.77 15.32 42.51 5.18
395 803 1.021390 AAGCTACATCACCTGCGCAC 61.021 55.000 5.66 0.00 0.00 5.34
405 813 3.131400 AGAAGGGAAGACGAAGCTACATC 59.869 47.826 0.00 0.00 0.00 3.06
491 899 3.671008 TTTCTATGCATACCCGCGTAT 57.329 42.857 4.92 0.00 35.46 3.06
495 903 4.142469 ACTTGTTTTTCTATGCATACCCGC 60.142 41.667 1.16 0.00 0.00 6.13
498 906 7.029563 CCAAGACTTGTTTTTCTATGCATACC 58.970 38.462 14.03 0.00 0.00 2.73
525 933 2.540910 AGGGGGAGAGGGTGGAGA 60.541 66.667 0.00 0.00 0.00 3.71
673 1082 1.798813 GGCTACGGATTATCTTTGGCG 59.201 52.381 0.00 0.00 0.00 5.69
755 1164 2.293399 CCAGACCAAGGTAAACAACAGC 59.707 50.000 0.00 0.00 0.00 4.40
761 1170 1.534729 CTGCCCAGACCAAGGTAAAC 58.465 55.000 0.00 0.00 0.00 2.01
764 1173 2.602676 GCCTGCCCAGACCAAGGTA 61.603 63.158 0.00 0.00 0.00 3.08
765 1174 3.971702 GCCTGCCCAGACCAAGGT 61.972 66.667 0.00 0.00 0.00 3.50
767 1176 2.360852 CAGCCTGCCCAGACCAAG 60.361 66.667 0.00 0.00 0.00 3.61
773 1182 4.463879 CGAGACCAGCCTGCCCAG 62.464 72.222 0.00 0.00 0.00 4.45
950 1667 5.181245 CACCCAAGAACAGTATCAAAATCGT 59.819 40.000 0.00 0.00 0.00 3.73
1231 1955 3.003689 CCAACATCGCCATACATCCTTTC 59.996 47.826 0.00 0.00 0.00 2.62
1236 1960 0.235665 CGCCAACATCGCCATACATC 59.764 55.000 0.00 0.00 0.00 3.06
1461 2185 6.729690 TCAGTTCATCCAAAGACCAAATTT 57.270 33.333 0.00 0.00 0.00 1.82
1803 2549 5.016051 TGGATCATCAAGCAGTCTAAGAC 57.984 43.478 0.00 0.00 0.00 3.01
1897 2644 7.874016 TCCCTTTCTGTTTGAATTCAAATGATG 59.126 33.333 30.63 23.28 46.12 3.07
1908 2655 5.367945 ACAGTAGTCCCTTTCTGTTTGAA 57.632 39.130 0.00 0.00 37.81 2.69
2089 2836 5.218139 GTTCAAAGCTGTTTCTCCAATCTG 58.782 41.667 0.00 0.00 0.00 2.90
2187 2934 5.598005 ACCCTGTCAACAAAATCATCTTCAA 59.402 36.000 0.00 0.00 0.00 2.69
2208 2956 5.856455 CGATTGTCTGAATGTAACAAAACCC 59.144 40.000 0.00 0.00 36.57 4.11
2210 2958 8.555166 TTTCGATTGTCTGAATGTAACAAAAC 57.445 30.769 0.00 0.00 36.57 2.43
2260 3008 0.962356 CAGGGTGCTCGATTTGCCTT 60.962 55.000 0.00 0.00 0.00 4.35
2354 3102 3.142174 CTGTCCAGAAGAACCAAGAACC 58.858 50.000 0.00 0.00 0.00 3.62
2355 3103 4.073293 TCTGTCCAGAAGAACCAAGAAC 57.927 45.455 0.00 0.00 33.91 3.01
2357 3105 4.073293 GTTCTGTCCAGAAGAACCAAGA 57.927 45.455 9.90 0.00 46.93 3.02
2875 5109 6.128063 GCTTTGAATCTCTGTATGGGATATGC 60.128 42.308 0.00 0.00 0.00 3.14
3077 5320 5.157940 AGCTCTCTTTGTAGATGCTTCAA 57.842 39.130 2.07 0.00 37.02 2.69
3156 5399 5.645497 GCATCCTTCTCTCTTAAAGCTTCAA 59.355 40.000 0.00 0.00 0.00 2.69
3198 5441 4.151883 TGGGAAATTTCAGGTGAGGAAAG 58.848 43.478 19.49 0.00 37.64 2.62
3217 5460 0.106719 ACACTGTCACAAGGGTTGGG 60.107 55.000 0.00 0.00 25.41 4.12
3499 5742 2.093341 AGAGACTCTGAGGACCGACTAC 60.093 54.545 3.56 0.00 0.00 2.73
3536 5779 1.535896 GAAACCGAAAGTGCTTCCTCC 59.464 52.381 0.00 0.00 0.00 4.30
3662 5905 3.560882 CCCTTGTTTGCTGAGGAAGATCT 60.561 47.826 0.00 0.00 32.11 2.75
3818 6061 7.459795 TCTTCTATGCTCATGTACCTCTATG 57.540 40.000 0.00 0.00 0.00 2.23
3825 6068 5.111989 TGTGCTTCTTCTATGCTCATGTAC 58.888 41.667 0.00 0.00 29.74 2.90
3927 6170 0.400213 ACTTCATCAGGTTGCGGGAA 59.600 50.000 0.00 0.00 0.00 3.97
3985 6228 8.254508 CCTCTTTGCTAGGGTATATCTTGATAC 58.745 40.741 0.00 0.00 0.00 2.24
4115 6358 6.165659 ACGTCCAAAGAAATGTTAGAATCG 57.834 37.500 0.00 0.00 0.00 3.34
4130 6373 1.187087 AAGGTTTGCCAACGTCCAAA 58.813 45.000 0.00 0.00 37.19 3.28
4151 6394 3.623906 ACAGTCAGACATTCATGAGGG 57.376 47.619 2.66 0.00 0.00 4.30
4423 6666 5.706916 TCGTGTCCTTAACTACTTCATCAC 58.293 41.667 0.00 0.00 0.00 3.06
4424 6667 5.475909 ACTCGTGTCCTTAACTACTTCATCA 59.524 40.000 0.00 0.00 0.00 3.07
4425 6668 5.952033 ACTCGTGTCCTTAACTACTTCATC 58.048 41.667 0.00 0.00 0.00 2.92
4426 6669 5.979288 ACTCGTGTCCTTAACTACTTCAT 57.021 39.130 0.00 0.00 0.00 2.57
4427 6670 5.182001 GGTACTCGTGTCCTTAACTACTTCA 59.818 44.000 0.00 0.00 0.00 3.02
4428 6671 5.182001 TGGTACTCGTGTCCTTAACTACTTC 59.818 44.000 0.00 0.00 0.00 3.01
4429 6672 5.072741 TGGTACTCGTGTCCTTAACTACTT 58.927 41.667 0.00 0.00 0.00 2.24
4430 6673 4.655963 TGGTACTCGTGTCCTTAACTACT 58.344 43.478 0.00 0.00 0.00 2.57
4431 6674 4.457257 ACTGGTACTCGTGTCCTTAACTAC 59.543 45.833 0.00 0.00 0.00 2.73
4432 6675 4.456911 CACTGGTACTCGTGTCCTTAACTA 59.543 45.833 0.00 0.00 0.00 2.24
4433 6676 3.255149 CACTGGTACTCGTGTCCTTAACT 59.745 47.826 0.00 0.00 0.00 2.24
4434 6677 3.254166 TCACTGGTACTCGTGTCCTTAAC 59.746 47.826 12.52 0.00 33.07 2.01
4435 6678 3.489355 TCACTGGTACTCGTGTCCTTAA 58.511 45.455 12.52 0.00 33.07 1.85
4436 6679 3.144657 TCACTGGTACTCGTGTCCTTA 57.855 47.619 12.52 0.00 33.07 2.69
4437 6680 1.991121 TCACTGGTACTCGTGTCCTT 58.009 50.000 12.52 0.00 33.07 3.36
4438 6681 1.819288 CATCACTGGTACTCGTGTCCT 59.181 52.381 12.52 0.96 33.07 3.85
4439 6682 1.816835 TCATCACTGGTACTCGTGTCC 59.183 52.381 12.52 0.00 33.07 4.02
4440 6683 3.057456 ACTTCATCACTGGTACTCGTGTC 60.057 47.826 12.52 0.00 33.07 3.67
4441 6684 2.891580 ACTTCATCACTGGTACTCGTGT 59.108 45.455 12.52 0.00 33.07 4.49
4442 6685 3.577649 ACTTCATCACTGGTACTCGTG 57.422 47.619 8.24 8.24 0.00 4.35
4443 6686 4.333690 ACTACTTCATCACTGGTACTCGT 58.666 43.478 0.00 0.00 0.00 4.18
4444 6687 4.395231 TGACTACTTCATCACTGGTACTCG 59.605 45.833 0.00 0.00 0.00 4.18
4445 6688 5.899120 TGACTACTTCATCACTGGTACTC 57.101 43.478 0.00 0.00 0.00 2.59
4446 6689 5.186021 CCTTGACTACTTCATCACTGGTACT 59.814 44.000 0.00 0.00 32.84 2.73
4447 6690 5.185249 TCCTTGACTACTTCATCACTGGTAC 59.815 44.000 0.00 0.00 32.84 3.34
4448 6691 5.185249 GTCCTTGACTACTTCATCACTGGTA 59.815 44.000 0.00 0.00 32.84 3.25
4449 6692 4.021016 GTCCTTGACTACTTCATCACTGGT 60.021 45.833 0.00 0.00 32.84 4.00
4450 6693 4.021104 TGTCCTTGACTACTTCATCACTGG 60.021 45.833 0.00 0.00 32.84 4.00
4451 6694 5.139435 TGTCCTTGACTACTTCATCACTG 57.861 43.478 0.00 0.00 32.84 3.66
4452 6695 5.481824 TCATGTCCTTGACTACTTCATCACT 59.518 40.000 0.00 0.00 32.84 3.41
4490 6763 1.059098 TGCTCATGTCCTTGACCACT 58.941 50.000 0.00 0.00 0.00 4.00
4493 6766 0.036732 TGGTGCTCATGTCCTTGACC 59.963 55.000 0.00 0.00 0.00 4.02
4635 6938 1.956477 GTCCTCATGGTGTTTTGCTGT 59.044 47.619 0.00 0.00 34.23 4.40
4749 7135 2.879026 TCGGCAGCAGTATACTAGTCAG 59.121 50.000 4.74 0.00 0.00 3.51
4764 7150 5.400782 CGCTATCAGCTATAATATTCGGCAG 59.599 44.000 0.00 0.00 39.60 4.85
4821 7207 4.509122 CCAGGGAAGATCCTCCTTTTCAAA 60.509 45.833 10.25 0.00 36.57 2.69
4928 7317 2.649331 ACAATCTGCTGCTGAAATGC 57.351 45.000 13.26 0.00 0.00 3.56
5060 7449 1.662629 GTGCCACAACTCGATGATCTG 59.337 52.381 0.00 0.00 0.00 2.90
5298 7687 2.762327 AGGCTTAAATTCATGGGCAGTG 59.238 45.455 0.00 0.00 0.00 3.66
5303 7692 7.823745 ACATACTTAGGCTTAAATTCATGGG 57.176 36.000 0.00 0.00 0.00 4.00
5313 7702 6.474140 TCCATCGAAACATACTTAGGCTTA 57.526 37.500 0.00 0.00 0.00 3.09
5316 7705 7.724305 TTATTCCATCGAAACATACTTAGGC 57.276 36.000 0.00 0.00 0.00 3.93
5330 7724 2.221749 CAGCGTCACCATTATTCCATCG 59.778 50.000 0.00 0.00 0.00 3.84
5342 7736 2.335011 GGCAAAACCAGCGTCACC 59.665 61.111 0.00 0.00 38.86 4.02
5343 7737 2.335011 GGGCAAAACCAGCGTCAC 59.665 61.111 0.00 0.00 42.05 3.67
5423 7817 2.359975 CTCCTTGTCCCCGTTGGC 60.360 66.667 0.00 0.00 0.00 4.52
5443 7837 2.587060 TCCCCCATCTGGTGTAGATT 57.413 50.000 0.00 0.00 43.68 2.40
5584 7978 3.011517 TCCTTGAGAGCCTGCCCC 61.012 66.667 0.00 0.00 0.00 5.80
5662 8056 0.602638 ACGTCAAAGATCAAGCGCCA 60.603 50.000 2.29 0.00 0.00 5.69
5721 8115 2.904434 TCTCCTCCTGTTAAGTGAACCC 59.096 50.000 0.00 0.00 37.22 4.11
5765 8159 3.325293 TTCACAAGCAAAAACAAGGCA 57.675 38.095 0.00 0.00 0.00 4.75
5766 8160 4.094739 ACAATTCACAAGCAAAAACAAGGC 59.905 37.500 0.00 0.00 0.00 4.35
5767 8161 5.122082 ACACAATTCACAAGCAAAAACAAGG 59.878 36.000 0.00 0.00 0.00 3.61
5768 8162 6.016718 CACACAATTCACAAGCAAAAACAAG 58.983 36.000 0.00 0.00 0.00 3.16
5769 8163 5.616424 GCACACAATTCACAAGCAAAAACAA 60.616 36.000 0.00 0.00 0.00 2.83
5770 8164 4.142945 GCACACAATTCACAAGCAAAAACA 60.143 37.500 0.00 0.00 0.00 2.83
5771 8165 4.333615 GCACACAATTCACAAGCAAAAAC 58.666 39.130 0.00 0.00 0.00 2.43
5772 8166 3.061831 CGCACACAATTCACAAGCAAAAA 59.938 39.130 0.00 0.00 0.00 1.94
5773 8167 2.602211 CGCACACAATTCACAAGCAAAA 59.398 40.909 0.00 0.00 0.00 2.44
5774 8168 2.191802 CGCACACAATTCACAAGCAAA 58.808 42.857 0.00 0.00 0.00 3.68
5775 8169 1.133982 ACGCACACAATTCACAAGCAA 59.866 42.857 0.00 0.00 0.00 3.91
5776 8170 0.737804 ACGCACACAATTCACAAGCA 59.262 45.000 0.00 0.00 0.00 3.91
5777 8171 1.122849 CACGCACACAATTCACAAGC 58.877 50.000 0.00 0.00 0.00 4.01
5778 8172 2.110990 CACACGCACACAATTCACAAG 58.889 47.619 0.00 0.00 0.00 3.16
5779 8173 1.796982 GCACACGCACACAATTCACAA 60.797 47.619 0.00 0.00 38.36 3.33
5780 8174 0.248417 GCACACGCACACAATTCACA 60.248 50.000 0.00 0.00 38.36 3.58
5781 8175 1.261510 CGCACACGCACACAATTCAC 61.262 55.000 0.00 0.00 38.40 3.18
5782 8176 1.010238 CGCACACGCACACAATTCA 60.010 52.632 0.00 0.00 38.40 2.57
5783 8177 1.010125 ACGCACACGCACACAATTC 60.010 52.632 0.00 0.00 45.53 2.17
5784 8178 1.298264 CACGCACACGCACACAATT 60.298 52.632 0.00 0.00 45.53 2.32
5785 8179 2.327592 CACGCACACGCACACAAT 59.672 55.556 0.00 0.00 45.53 2.71
5786 8180 3.121676 ACACGCACACGCACACAA 61.122 55.556 0.00 0.00 45.53 3.33
5787 8181 3.858989 CACACGCACACGCACACA 61.859 61.111 0.00 0.00 45.53 3.72
5792 8186 2.291508 AATATCGCACACGCACACGC 62.292 55.000 0.00 0.00 45.53 5.34
5794 8188 0.026285 GGAATATCGCACACGCACAC 59.974 55.000 0.00 0.00 39.84 3.82
5795 8189 0.108377 AGGAATATCGCACACGCACA 60.108 50.000 0.00 0.00 39.84 4.57
5796 8190 0.301687 CAGGAATATCGCACACGCAC 59.698 55.000 0.00 0.00 39.84 5.34
5797 8191 0.108377 ACAGGAATATCGCACACGCA 60.108 50.000 0.00 0.00 39.84 5.24
5798 8192 0.301687 CACAGGAATATCGCACACGC 59.698 55.000 0.00 0.00 39.84 5.34
5799 8193 1.324435 CACACAGGAATATCGCACACG 59.676 52.381 0.00 0.00 42.01 4.49
5800 8194 1.062587 GCACACAGGAATATCGCACAC 59.937 52.381 0.00 0.00 0.00 3.82
5801 8195 1.338579 TGCACACAGGAATATCGCACA 60.339 47.619 0.00 0.00 0.00 4.57
5802 8196 1.368641 TGCACACAGGAATATCGCAC 58.631 50.000 0.00 0.00 0.00 5.34
5803 8197 2.106477 TTGCACACAGGAATATCGCA 57.894 45.000 0.00 0.00 0.00 5.10
5804 8198 3.698029 AATTGCACACAGGAATATCGC 57.302 42.857 0.00 0.00 37.28 4.58
5892 8288 1.406069 CGCTCTGGACCTGCTAATGTT 60.406 52.381 0.00 0.00 0.00 2.71
6265 8661 4.467084 GGATGGAAGCGCCGGTGA 62.467 66.667 21.76 0.00 40.66 4.02
6367 8763 0.594602 CAGCCAATATCGCATGTGGG 59.405 55.000 6.39 0.02 0.00 4.61
6436 8832 0.549469 GGGATCCAACAATACCCGGT 59.451 55.000 15.23 0.00 0.00 5.28


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

AutoCloner maintained by Alex Coulton.