Multiple sequence alignment - TraesCS2A01G180700

Loading Multiple Alignment...

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 TraesCS2A01G180700 chr2A 100.000 2588 0 0 1 2588 139887168 139889755 0.000000e+00 4780.0
1 TraesCS2A01G180700 chr3A 94.208 1623 58 12 760 2377 535798189 535796598 0.000000e+00 2444.0
2 TraesCS2A01G180700 chr3A 97.541 732 16 2 1 731 535800615 535799885 0.000000e+00 1251.0
3 TraesCS2A01G180700 chr3A 88.235 187 20 2 2399 2584 575483223 575483038 3.350000e-54 222.0
4 TraesCS2A01G180700 chr3A 94.737 57 3 0 708 764 535799883 535799827 3.550000e-14 89.8
5 TraesCS2A01G180700 chr4B 84.286 630 66 23 1760 2381 240213202 240212598 3.710000e-163 584.0
6 TraesCS2A01G180700 chr4B 91.515 330 13 2 455 769 240214250 240213921 8.500000e-120 440.0
7 TraesCS2A01G180700 chr4B 97.030 101 3 0 1658 1758 240213920 240213820 1.230000e-38 171.0
8 TraesCS2A01G180700 chr6B 82.576 396 53 11 1763 2153 615281081 615281465 4.130000e-88 335.0
9 TraesCS2A01G180700 chr7B 91.053 190 14 2 2400 2587 453303549 453303737 1.190000e-63 254.0
10 TraesCS2A01G180700 chr7B 86.294 197 25 2 2392 2587 436090834 436090639 2.020000e-51 213.0
11 TraesCS2A01G180700 chr5D 88.889 189 20 1 2400 2587 399294801 399294613 5.570000e-57 231.0
12 TraesCS2A01G180700 chr5D 88.542 192 21 1 2397 2587 435220607 435220798 5.570000e-57 231.0
13 TraesCS2A01G180700 chr1B 88.421 190 21 1 2399 2587 652284081 652283892 7.200000e-56 228.0
14 TraesCS2A01G180700 chr1B 86.979 192 23 2 2398 2587 41444743 41444934 5.610000e-52 215.0
15 TraesCS2A01G180700 chr1B 87.234 188 22 2 2401 2587 289286671 289286485 2.020000e-51 213.0
16 TraesCS2A01G180700 chr4D 87.958 191 21 2 2398 2587 378304144 378303955 9.320000e-55 224.0
17 TraesCS2A01G180700 chr1D 100.000 28 0 0 1266 1293 124524666 124524639 5.000000e-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 TraesCS2A01G180700 chr2A 139887168 139889755 2587 False 4780.000000 4780 100.000000 1 2588 1 chr2A.!!$F1 2587
1 TraesCS2A01G180700 chr3A 535796598 535800615 4017 True 1261.600000 2444 95.495333 1 2377 3 chr3A.!!$R2 2376
2 TraesCS2A01G180700 chr4B 240212598 240214250 1652 True 398.333333 584 90.943667 455 2381 3 chr4B.!!$R1 1926

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
731 773 2.920076 AAAGCGGTGTTGGCTGGGAA 62.92 55.0 0.0 0.0 41.39 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2219 4580 0.035317 TACAACACTGGCTGGCAGAG 59.965 55.0 34.18 28.46 0.0 3.35 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
84 85 7.786988 TGCAATGCAAATGTGGAATGATTTCC 61.787 38.462 5.01 0.00 43.08 3.13
102 103 8.044060 TGATTTCCAGCATAACTAACTCTTTG 57.956 34.615 0.00 0.00 0.00 2.77
124 125 6.951062 TGTAAGTTTGTGGATGTGATTGAA 57.049 33.333 0.00 0.00 0.00 2.69
222 224 3.118992 GGATCTCCCAAATTCAACTTGGC 60.119 47.826 0.00 0.00 41.80 4.52
308 310 6.399743 GTTACCAAAAGGAGTTCACCAAAAA 58.600 36.000 0.00 0.00 0.00 1.94
347 349 7.872993 TCTCATCTTCGACTTGTTTTTCACTAT 59.127 33.333 0.00 0.00 0.00 2.12
483 485 5.789643 ATTGGCTTGTGTAGTTGTGAAAT 57.210 34.783 0.00 0.00 0.00 2.17
671 688 9.406113 CTTCAAATTCAAGATAAGGAGAAGGAT 57.594 33.333 0.00 0.00 0.00 3.24
731 773 2.920076 AAAGCGGTGTTGGCTGGGAA 62.920 55.000 0.00 0.00 41.39 3.97
936 2621 3.190744 TGACTTGCTAGGAGAACTGTACG 59.809 47.826 0.00 0.00 0.00 3.67
938 2623 3.190953 ACTTGCTAGGAGAACTGTACGAC 59.809 47.826 0.00 0.00 0.00 4.34
974 2659 3.643792 ACTTCTGTTGCTACCTCTCACTT 59.356 43.478 0.00 0.00 0.00 3.16
1021 2706 2.607631 GCATTTTGCAGGGCATACAT 57.392 45.000 0.00 0.00 44.26 2.29
1054 2739 7.823745 ACCTATAATTTCACATCCATTGGAC 57.176 36.000 7.76 0.00 32.98 4.02
1061 2746 3.355378 TCACATCCATTGGACAACCATC 58.645 45.455 7.76 0.00 46.34 3.51
1148 2833 6.569780 TGGAGATGATGAATCAATTGCAAAG 58.430 36.000 1.71 0.00 40.69 2.77
1161 2846 3.811722 TTGCAAAGTGATGATGACGAC 57.188 42.857 0.00 0.00 0.00 4.34
1173 2858 4.408993 TGATGACGACTTGCAAATTCTG 57.591 40.909 0.00 0.10 0.00 3.02
1279 2964 2.597455 CCCAAAAGAAGCCCAAGAAGA 58.403 47.619 0.00 0.00 0.00 2.87
1311 2996 3.008813 AGAACAGTGGAGATGTGATTGCT 59.991 43.478 0.00 0.00 0.00 3.91
1366 3051 5.620738 AAGGCAAGTAGATGATGAAGCTA 57.379 39.130 0.00 0.00 0.00 3.32
1376 3061 6.737720 AGATGATGAAGCTACATACTTGGA 57.262 37.500 0.00 0.00 0.00 3.53
1407 3092 3.448660 GGGCAGAGGCAACAAAATTAGAT 59.551 43.478 0.00 0.00 43.71 1.98
1413 3098 6.805271 CAGAGGCAACAAAATTAGATGACTTG 59.195 38.462 0.00 0.00 41.41 3.16
1425 3110 9.739276 AAATTAGATGACTTGTCTATCACCAAA 57.261 29.630 2.35 0.42 0.00 3.28
1454 3139 2.942804 TGTGCTCAAAACAATGGAGGA 58.057 42.857 0.00 0.00 0.00 3.71
1465 3150 2.593468 AATGGAGGATGTCACCCGCG 62.593 60.000 0.00 0.00 0.00 6.46
1473 3158 2.811317 GTCACCCGCGCAGAGAAG 60.811 66.667 8.75 0.00 0.00 2.85
1481 3166 0.459237 CGCGCAGAGAAGATCAAGGT 60.459 55.000 8.75 0.00 0.00 3.50
1550 3235 3.431572 GCCGCTGATGATGATAAAGAGAC 59.568 47.826 0.00 0.00 0.00 3.36
1552 3237 4.502087 CCGCTGATGATGATAAAGAGACCA 60.502 45.833 0.00 0.00 0.00 4.02
1555 3240 5.466058 GCTGATGATGATAAAGAGACCACTG 59.534 44.000 0.00 0.00 0.00 3.66
1650 3335 5.541101 TGGTTGAGTTAGTTGGTAAGCTAGA 59.459 40.000 0.00 0.00 0.00 2.43
1749 3434 8.572185 TCAGAAACTTCTCTGGAATATATCTCG 58.428 37.037 1.03 0.00 42.68 4.04
1760 3621 7.339721 TCTGGAATATATCTCGGATAGTTGACC 59.660 40.741 0.00 0.00 0.00 4.02
1928 4229 1.719063 AAGGAAAGAGCTGCCACCCA 61.719 55.000 0.00 0.00 0.00 4.51
1944 4246 1.768870 ACCCACAGAAGCTAGTTGTGT 59.231 47.619 18.27 3.24 43.30 3.72
1994 4296 5.069318 TGTTCATGAAGTGTGCAATTCCTA 58.931 37.500 8.80 0.00 34.80 2.94
2174 4476 1.338011 CCAGCCAACGGATGCAAAAAT 60.338 47.619 0.00 0.00 37.84 1.82
2219 4580 8.213518 TCATCTTATCAGGATGTTTTTACTGC 57.786 34.615 0.00 0.00 40.76 4.40
2220 4581 8.049117 TCATCTTATCAGGATGTTTTTACTGCT 58.951 33.333 0.00 0.00 40.76 4.24
2221 4582 7.849804 TCTTATCAGGATGTTTTTACTGCTC 57.150 36.000 0.00 0.00 37.40 4.26
2222 4583 7.624549 TCTTATCAGGATGTTTTTACTGCTCT 58.375 34.615 0.00 0.00 37.40 4.09
2223 4584 7.550551 TCTTATCAGGATGTTTTTACTGCTCTG 59.449 37.037 0.00 0.00 37.40 3.35
2224 4585 3.753272 TCAGGATGTTTTTACTGCTCTGC 59.247 43.478 0.00 0.00 37.40 4.26
2225 4586 3.084786 AGGATGTTTTTACTGCTCTGCC 58.915 45.455 0.00 0.00 0.00 4.85
2226 4587 2.819608 GGATGTTTTTACTGCTCTGCCA 59.180 45.455 0.00 0.00 0.00 4.92
2227 4588 3.119708 GGATGTTTTTACTGCTCTGCCAG 60.120 47.826 0.00 0.00 38.78 4.85
2235 4596 2.282040 GCTCTGCCAGCCAGTGTT 60.282 61.111 0.00 0.00 43.17 3.32
2266 4627 0.048749 AGGGAATTATGGGGGTGGGA 59.951 55.000 0.00 0.00 0.00 4.37
2336 4697 0.193574 CCCTCTAATCCCCTAGCCCA 59.806 60.000 0.00 0.00 0.00 5.36
2380 4744 3.053831 CCGAACAAGGCCTAAGAGAAA 57.946 47.619 5.16 0.00 0.00 2.52
2381 4745 3.610911 CCGAACAAGGCCTAAGAGAAAT 58.389 45.455 5.16 0.00 0.00 2.17
2382 4746 3.375299 CCGAACAAGGCCTAAGAGAAATG 59.625 47.826 5.16 0.00 0.00 2.32
2383 4747 4.253685 CGAACAAGGCCTAAGAGAAATGA 58.746 43.478 5.16 0.00 0.00 2.57
2384 4748 4.878397 CGAACAAGGCCTAAGAGAAATGAT 59.122 41.667 5.16 0.00 0.00 2.45
2385 4749 5.220739 CGAACAAGGCCTAAGAGAAATGATG 60.221 44.000 5.16 0.00 0.00 3.07
2386 4750 4.530875 ACAAGGCCTAAGAGAAATGATGG 58.469 43.478 5.16 0.00 0.00 3.51
2387 4751 4.228210 ACAAGGCCTAAGAGAAATGATGGA 59.772 41.667 5.16 0.00 0.00 3.41
2388 4752 4.429854 AGGCCTAAGAGAAATGATGGAC 57.570 45.455 1.29 0.00 0.00 4.02
2389 4753 3.782523 AGGCCTAAGAGAAATGATGGACA 59.217 43.478 1.29 0.00 0.00 4.02
2390 4754 4.133078 GGCCTAAGAGAAATGATGGACAG 58.867 47.826 0.00 0.00 0.00 3.51
2391 4755 4.141620 GGCCTAAGAGAAATGATGGACAGA 60.142 45.833 0.00 0.00 0.00 3.41
2392 4756 5.431765 GCCTAAGAGAAATGATGGACAGAA 58.568 41.667 0.00 0.00 0.00 3.02
2393 4757 5.882557 GCCTAAGAGAAATGATGGACAGAAA 59.117 40.000 0.00 0.00 0.00 2.52
2394 4758 6.038050 GCCTAAGAGAAATGATGGACAGAAAG 59.962 42.308 0.00 0.00 0.00 2.62
2395 4759 7.334090 CCTAAGAGAAATGATGGACAGAAAGA 58.666 38.462 0.00 0.00 0.00 2.52
2396 4760 7.992033 CCTAAGAGAAATGATGGACAGAAAGAT 59.008 37.037 0.00 0.00 0.00 2.40
2397 4761 9.393512 CTAAGAGAAATGATGGACAGAAAGATT 57.606 33.333 0.00 0.00 0.00 2.40
2399 4763 9.745018 AAGAGAAATGATGGACAGAAAGATTAA 57.255 29.630 0.00 0.00 0.00 1.40
2400 4764 9.393512 AGAGAAATGATGGACAGAAAGATTAAG 57.606 33.333 0.00 0.00 0.00 1.85
2401 4765 8.517062 AGAAATGATGGACAGAAAGATTAAGG 57.483 34.615 0.00 0.00 0.00 2.69
2402 4766 8.331740 AGAAATGATGGACAGAAAGATTAAGGA 58.668 33.333 0.00 0.00 0.00 3.36
2403 4767 7.872113 AATGATGGACAGAAAGATTAAGGAC 57.128 36.000 0.00 0.00 0.00 3.85
2404 4768 5.419542 TGATGGACAGAAAGATTAAGGACG 58.580 41.667 0.00 0.00 0.00 4.79
2405 4769 3.596214 TGGACAGAAAGATTAAGGACGC 58.404 45.455 0.00 0.00 0.00 5.19
2406 4770 3.260884 TGGACAGAAAGATTAAGGACGCT 59.739 43.478 0.00 0.00 0.00 5.07
2407 4771 3.619038 GGACAGAAAGATTAAGGACGCTG 59.381 47.826 0.00 0.00 0.00 5.18
2408 4772 4.495422 GACAGAAAGATTAAGGACGCTGA 58.505 43.478 0.00 0.00 0.00 4.26
2409 4773 5.091261 ACAGAAAGATTAAGGACGCTGAT 57.909 39.130 0.00 0.00 0.00 2.90
2410 4774 6.222038 ACAGAAAGATTAAGGACGCTGATA 57.778 37.500 0.00 0.00 0.00 2.15
2411 4775 6.640518 ACAGAAAGATTAAGGACGCTGATAA 58.359 36.000 0.00 0.00 0.00 1.75
2412 4776 6.535508 ACAGAAAGATTAAGGACGCTGATAAC 59.464 38.462 0.00 0.00 0.00 1.89
2413 4777 5.749109 AGAAAGATTAAGGACGCTGATAACG 59.251 40.000 0.00 0.00 0.00 3.18
2414 4778 3.381949 AGATTAAGGACGCTGATAACGC 58.618 45.455 0.00 0.00 0.00 4.84
2415 4779 1.930567 TTAAGGACGCTGATAACGCC 58.069 50.000 0.00 0.00 0.00 5.68
2416 4780 0.103572 TAAGGACGCTGATAACGCCC 59.896 55.000 0.00 0.00 32.65 6.13
2417 4781 1.895020 AAGGACGCTGATAACGCCCA 61.895 55.000 0.00 0.00 35.26 5.36
2418 4782 2.171725 GGACGCTGATAACGCCCAC 61.172 63.158 0.00 0.00 32.77 4.61
2419 4783 1.447140 GACGCTGATAACGCCCACA 60.447 57.895 0.00 0.00 0.00 4.17
2420 4784 1.693083 GACGCTGATAACGCCCACAC 61.693 60.000 0.00 0.00 0.00 3.82
2421 4785 2.798501 CGCTGATAACGCCCACACG 61.799 63.158 0.00 0.00 39.50 4.49
2435 4799 3.986970 ACACGTGTGATGAGAGCAA 57.013 47.368 22.71 0.00 0.00 3.91
2436 4800 1.502231 ACACGTGTGATGAGAGCAAC 58.498 50.000 22.71 0.00 0.00 4.17
2437 4801 1.202521 ACACGTGTGATGAGAGCAACA 60.203 47.619 22.71 0.00 0.00 3.33
2438 4802 2.071540 CACGTGTGATGAGAGCAACAT 58.928 47.619 7.58 0.00 0.00 2.71
2439 4803 2.093310 CACGTGTGATGAGAGCAACATC 59.907 50.000 7.58 9.69 42.81 3.06
2440 4804 1.662629 CGTGTGATGAGAGCAACATCC 59.337 52.381 12.68 7.07 42.11 3.51
2441 4805 1.662629 GTGTGATGAGAGCAACATCCG 59.337 52.381 12.68 0.00 42.11 4.18
2442 4806 1.276138 TGTGATGAGAGCAACATCCGT 59.724 47.619 12.68 0.00 42.11 4.69
2443 4807 1.929836 GTGATGAGAGCAACATCCGTC 59.070 52.381 12.68 0.00 42.11 4.79
2444 4808 1.134699 TGATGAGAGCAACATCCGTCC 60.135 52.381 12.68 0.00 42.11 4.79
2445 4809 0.904649 ATGAGAGCAACATCCGTCCA 59.095 50.000 0.00 0.00 0.00 4.02
2446 4810 0.037326 TGAGAGCAACATCCGTCCAC 60.037 55.000 0.00 0.00 0.00 4.02
2447 4811 0.037326 GAGAGCAACATCCGTCCACA 60.037 55.000 0.00 0.00 0.00 4.17
2448 4812 0.320771 AGAGCAACATCCGTCCACAC 60.321 55.000 0.00 0.00 0.00 3.82
2449 4813 1.626654 GAGCAACATCCGTCCACACG 61.627 60.000 0.00 0.00 46.29 4.49
2450 4814 1.959226 GCAACATCCGTCCACACGT 60.959 57.895 0.00 0.00 45.17 4.49
2451 4815 1.897398 GCAACATCCGTCCACACGTC 61.897 60.000 0.00 0.00 45.17 4.34
2452 4816 1.005394 AACATCCGTCCACACGTCC 60.005 57.895 0.00 0.00 45.17 4.79
2453 4817 1.469335 AACATCCGTCCACACGTCCT 61.469 55.000 0.00 0.00 45.17 3.85
2454 4818 0.609957 ACATCCGTCCACACGTCCTA 60.610 55.000 0.00 0.00 45.17 2.94
2455 4819 0.744874 CATCCGTCCACACGTCCTAT 59.255 55.000 0.00 0.00 45.17 2.57
2456 4820 1.951602 CATCCGTCCACACGTCCTATA 59.048 52.381 0.00 0.00 45.17 1.31
2457 4821 1.382522 TCCGTCCACACGTCCTATAC 58.617 55.000 0.00 0.00 45.17 1.47
2458 4822 1.097232 CCGTCCACACGTCCTATACA 58.903 55.000 0.00 0.00 45.17 2.29
2459 4823 1.202222 CCGTCCACACGTCCTATACAC 60.202 57.143 0.00 0.00 45.17 2.90
2460 4824 1.469703 CGTCCACACGTCCTATACACA 59.530 52.381 0.00 0.00 41.42 3.72
2461 4825 2.730090 CGTCCACACGTCCTATACACAC 60.730 54.545 0.00 0.00 41.42 3.82
2462 4826 2.229543 GTCCACACGTCCTATACACACA 59.770 50.000 0.00 0.00 0.00 3.72
2463 4827 3.093814 TCCACACGTCCTATACACACAT 58.906 45.455 0.00 0.00 0.00 3.21
2464 4828 4.096833 GTCCACACGTCCTATACACACATA 59.903 45.833 0.00 0.00 0.00 2.29
2465 4829 4.891168 TCCACACGTCCTATACACACATAT 59.109 41.667 0.00 0.00 0.00 1.78
2466 4830 5.361571 TCCACACGTCCTATACACACATATT 59.638 40.000 0.00 0.00 0.00 1.28
2467 4831 5.462068 CCACACGTCCTATACACACATATTG 59.538 44.000 0.00 0.00 0.00 1.90
2468 4832 6.040247 CACACGTCCTATACACACATATTGT 58.960 40.000 0.00 0.00 39.97 2.71
2479 4843 3.425577 CACATATTGTGCCATGTCACC 57.574 47.619 4.13 0.00 41.89 4.02
2480 4844 2.016318 ACATATTGTGCCATGTCACCG 58.984 47.619 4.13 0.00 36.17 4.94
2481 4845 1.024271 ATATTGTGCCATGTCACCGC 58.976 50.000 4.13 0.00 36.17 5.68
2482 4846 0.322008 TATTGTGCCATGTCACCGCA 60.322 50.000 4.13 0.00 36.17 5.69
2483 4847 0.966875 ATTGTGCCATGTCACCGCAT 60.967 50.000 4.13 0.00 36.17 4.73
2484 4848 1.864725 TTGTGCCATGTCACCGCATG 61.865 55.000 4.13 0.00 44.18 4.06
2485 4849 3.442167 TGCCATGTCACCGCATGC 61.442 61.111 7.91 7.91 43.46 4.06
2486 4850 3.442167 GCCATGTCACCGCATGCA 61.442 61.111 19.57 0.00 43.46 3.96
2487 4851 2.777972 GCCATGTCACCGCATGCAT 61.778 57.895 19.57 1.32 43.46 3.96
2488 4852 1.065109 CCATGTCACCGCATGCATG 59.935 57.895 22.70 22.70 43.46 4.06
2497 4861 3.180423 GCATGCATGCGTGTGAGA 58.820 55.556 33.99 7.92 44.67 3.27
2498 4862 1.503091 GCATGCATGCGTGTGAGAA 59.497 52.632 33.99 7.15 44.67 2.87
2499 4863 0.099968 GCATGCATGCGTGTGAGAAT 59.900 50.000 33.99 9.24 44.67 2.40
2500 4864 1.858798 GCATGCATGCGTGTGAGAATC 60.859 52.381 33.99 16.55 44.67 2.52
2501 4865 1.669265 CATGCATGCGTGTGAGAATCT 59.331 47.619 28.25 0.00 34.92 2.40
2502 4866 1.812235 TGCATGCGTGTGAGAATCTT 58.188 45.000 14.09 0.00 34.92 2.40
2503 4867 2.153645 TGCATGCGTGTGAGAATCTTT 58.846 42.857 14.09 0.00 34.92 2.52
2504 4868 2.553602 TGCATGCGTGTGAGAATCTTTT 59.446 40.909 14.09 0.00 34.92 2.27
2505 4869 3.004629 TGCATGCGTGTGAGAATCTTTTT 59.995 39.130 14.09 0.00 34.92 1.94
2506 4870 3.362831 GCATGCGTGTGAGAATCTTTTTG 59.637 43.478 0.00 0.00 34.92 2.44
2507 4871 3.624326 TGCGTGTGAGAATCTTTTTGG 57.376 42.857 0.00 0.00 34.92 3.28
2508 4872 3.210227 TGCGTGTGAGAATCTTTTTGGA 58.790 40.909 0.00 0.00 34.92 3.53
2509 4873 3.820467 TGCGTGTGAGAATCTTTTTGGAT 59.180 39.130 0.00 0.00 34.92 3.41
2510 4874 4.278170 TGCGTGTGAGAATCTTTTTGGATT 59.722 37.500 0.00 0.00 38.47 3.01
2511 4875 5.221224 TGCGTGTGAGAATCTTTTTGGATTT 60.221 36.000 0.00 0.00 36.24 2.17
2512 4876 5.343325 GCGTGTGAGAATCTTTTTGGATTTC 59.657 40.000 0.00 0.00 36.24 2.17
2513 4877 5.858581 CGTGTGAGAATCTTTTTGGATTTCC 59.141 40.000 0.00 0.00 36.24 3.13
2514 4878 6.514870 CGTGTGAGAATCTTTTTGGATTTCCA 60.515 38.462 0.00 0.00 39.53 3.53
2515 4879 6.865205 GTGTGAGAATCTTTTTGGATTTCCAG 59.135 38.462 0.00 0.00 41.46 3.86
2516 4880 6.550854 TGTGAGAATCTTTTTGGATTTCCAGT 59.449 34.615 0.00 0.00 41.46 4.00
2517 4881 7.069826 TGTGAGAATCTTTTTGGATTTCCAGTT 59.930 33.333 0.00 0.00 41.46 3.16
2518 4882 7.928167 GTGAGAATCTTTTTGGATTTCCAGTTT 59.072 33.333 0.00 0.00 41.46 2.66
2519 4883 8.485392 TGAGAATCTTTTTGGATTTCCAGTTTT 58.515 29.630 0.00 0.00 41.46 2.43
2536 4900 9.535878 TTCCAGTTTTTAAAATGTTTTATCGCT 57.464 25.926 0.55 0.00 32.52 4.93
2537 4901 9.535878 TCCAGTTTTTAAAATGTTTTATCGCTT 57.464 25.926 0.55 0.00 32.52 4.68
2557 4921 9.859427 ATCGCTTAAATGAAAAATCTGATTGAA 57.141 25.926 3.22 0.00 0.00 2.69
2558 4922 9.859427 TCGCTTAAATGAAAAATCTGATTGAAT 57.141 25.926 3.22 0.00 0.00 2.57
2585 4949 7.254852 TCTGTTTTTACCATTAAATCCATCGC 58.745 34.615 0.00 0.00 0.00 4.58
2586 4950 6.030849 TGTTTTTACCATTAAATCCATCGCG 58.969 36.000 0.00 0.00 0.00 5.87
2587 4951 4.822036 TTTACCATTAAATCCATCGCGG 57.178 40.909 6.13 0.00 0.00 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 6.093633 GTGTTGTTCCCTTGGTAGTTATCATC 59.906 42.308 0.00 0.00 0.00 2.92
78 79 8.045176 ACAAAGAGTTAGTTATGCTGGAAATC 57.955 34.615 0.00 0.00 0.00 2.17
84 85 9.599322 CAAACTTACAAAGAGTTAGTTATGCTG 57.401 33.333 0.83 0.00 46.19 4.41
102 103 7.820648 AGATTCAATCACATCCACAAACTTAC 58.179 34.615 0.00 0.00 0.00 2.34
308 310 6.814146 GTCGAAGATGAGAAACAAGAATACCT 59.186 38.462 0.00 0.00 40.67 3.08
347 349 7.544566 GCTAGTACAACAATGCTACTGTTCTTA 59.455 37.037 0.00 0.00 34.80 2.10
483 485 5.938125 GTCCTAAACTCCATTGTGCTCTTTA 59.062 40.000 0.00 0.00 0.00 1.85
671 688 4.228210 AGCATCCTGTATTCCCTTTTGAGA 59.772 41.667 0.00 0.00 0.00 3.27
731 773 5.298777 GGCTTCTATCATGCATCTTTTGTCT 59.701 40.000 0.00 0.00 0.00 3.41
891 2575 9.057089 GTCAAAGTGAGGAAAAGATTTCTTCTA 57.943 33.333 13.73 1.69 34.61 2.10
892 2576 7.777440 AGTCAAAGTGAGGAAAAGATTTCTTCT 59.223 33.333 13.73 0.46 34.61 2.85
893 2577 7.935520 AGTCAAAGTGAGGAAAAGATTTCTTC 58.064 34.615 7.71 7.71 34.61 2.87
1021 2706 5.210430 TGTGAAATTATAGGTACCCTCGGA 58.790 41.667 8.74 0.00 34.61 4.55
1061 2746 4.057406 TCAAAGCCTTCACCAATTTGTG 57.943 40.909 3.27 3.27 37.59 3.33
1148 2833 3.811722 TTTGCAAGTCGTCATCATCAC 57.188 42.857 0.00 0.00 0.00 3.06
1161 2846 5.726397 TCCATTTGATCCAGAATTTGCAAG 58.274 37.500 0.00 0.00 0.00 4.01
1173 2858 2.304092 TGAGCAGCATCCATTTGATCC 58.696 47.619 0.00 0.00 0.00 3.36
1279 2964 1.494721 TCCACTGTTCTTGGGCTTCTT 59.505 47.619 0.00 0.00 34.56 2.52
1311 2996 6.015856 GCTCTATGTACTTCTCTAATGCTCCA 60.016 42.308 0.00 0.00 0.00 3.86
1320 3005 7.710676 TTTCTTCAGCTCTATGTACTTCTCT 57.289 36.000 0.00 0.00 0.00 3.10
1366 3051 3.763897 GCCCTTTCATTGTCCAAGTATGT 59.236 43.478 0.00 0.00 0.00 2.29
1376 3061 0.112995 TGCCTCTGCCCTTTCATTGT 59.887 50.000 0.00 0.00 36.33 2.71
1407 3092 4.650734 TGCATTTGGTGATAGACAAGTCA 58.349 39.130 2.72 0.00 0.00 3.41
1413 3098 4.581824 ACATCCATGCATTTGGTGATAGAC 59.418 41.667 12.12 0.00 38.01 2.59
1454 3139 2.842394 CTTCTCTGCGCGGGTGACAT 62.842 60.000 17.88 0.00 0.00 3.06
1465 3150 3.668447 TGAACACCTTGATCTTCTCTGC 58.332 45.455 0.00 0.00 0.00 4.26
1473 3158 5.947228 TGAAGACATTGAACACCTTGATC 57.053 39.130 0.00 0.00 0.00 2.92
1481 3166 4.216902 CAGCATCCTTGAAGACATTGAACA 59.783 41.667 0.00 0.00 0.00 3.18
1552 3237 0.537188 CTCCGGAGCCACATAACAGT 59.463 55.000 20.67 0.00 0.00 3.55
1555 3240 0.535335 TGACTCCGGAGCCACATAAC 59.465 55.000 31.56 12.31 0.00 1.89
1650 3335 6.741992 TGCAACGAGATATCAAATTGAACT 57.258 33.333 5.32 0.20 0.00 3.01
1749 3434 2.223735 TGCGAAGATCGGTCAACTATCC 60.224 50.000 0.00 0.00 40.84 2.59
1760 3621 2.797491 TCAGTGTACATGCGAAGATCG 58.203 47.619 0.00 0.00 43.89 3.69
1767 3628 2.688507 AGGAACTTCAGTGTACATGCG 58.311 47.619 0.00 0.00 27.25 4.73
1859 4160 5.643777 GCAGCCAAGACTCAAAATAACTCTA 59.356 40.000 0.00 0.00 0.00 2.43
1928 4229 3.838244 TCCAACACAACTAGCTTCTGT 57.162 42.857 0.00 0.00 0.00 3.41
1944 4246 7.639378 AGTAGCAGGTCCTTAAATAATTCCAA 58.361 34.615 0.00 0.00 0.00 3.53
2130 4432 6.654582 GGGATAAGATGGTGCAAAACAAAATT 59.345 34.615 0.00 0.00 0.00 1.82
2136 4438 3.429410 GCTGGGATAAGATGGTGCAAAAC 60.429 47.826 0.00 0.00 0.00 2.43
2219 4580 0.035317 TACAACACTGGCTGGCAGAG 59.965 55.000 34.18 28.46 0.00 3.35
2220 4581 0.250295 GTACAACACTGGCTGGCAGA 60.250 55.000 34.18 10.87 0.00 4.26
2221 4582 1.237285 GGTACAACACTGGCTGGCAG 61.237 60.000 27.32 27.32 0.00 4.85
2222 4583 1.228124 GGTACAACACTGGCTGGCA 60.228 57.895 3.18 3.18 0.00 4.92
2223 4584 1.228124 TGGTACAACACTGGCTGGC 60.228 57.895 0.00 0.00 31.92 4.85
2235 4596 6.369629 CCCATAATTCCCTATGTTTGGTACA 58.630 40.000 0.00 0.00 41.97 2.90
2266 4627 4.916963 TCCCCTCAATTCCCCAATAATT 57.083 40.909 0.00 0.00 0.00 1.40
2373 4737 9.745018 TTAATCTTTCTGTCCATCATTTCTCTT 57.255 29.630 0.00 0.00 0.00 2.85
2376 4740 8.331740 TCCTTAATCTTTCTGTCCATCATTTCT 58.668 33.333 0.00 0.00 0.00 2.52
2377 4741 8.401709 GTCCTTAATCTTTCTGTCCATCATTTC 58.598 37.037 0.00 0.00 0.00 2.17
2380 4744 6.051717 CGTCCTTAATCTTTCTGTCCATCAT 58.948 40.000 0.00 0.00 0.00 2.45
2381 4745 5.419542 CGTCCTTAATCTTTCTGTCCATCA 58.580 41.667 0.00 0.00 0.00 3.07
2382 4746 4.271291 GCGTCCTTAATCTTTCTGTCCATC 59.729 45.833 0.00 0.00 0.00 3.51
2383 4747 4.080863 AGCGTCCTTAATCTTTCTGTCCAT 60.081 41.667 0.00 0.00 0.00 3.41
2384 4748 3.260884 AGCGTCCTTAATCTTTCTGTCCA 59.739 43.478 0.00 0.00 0.00 4.02
2385 4749 3.619038 CAGCGTCCTTAATCTTTCTGTCC 59.381 47.826 0.00 0.00 0.00 4.02
2386 4750 4.495422 TCAGCGTCCTTAATCTTTCTGTC 58.505 43.478 0.00 0.00 0.00 3.51
2387 4751 4.537135 TCAGCGTCCTTAATCTTTCTGT 57.463 40.909 0.00 0.00 0.00 3.41
2388 4752 6.291849 CGTTATCAGCGTCCTTAATCTTTCTG 60.292 42.308 0.00 0.00 0.00 3.02
2389 4753 5.749109 CGTTATCAGCGTCCTTAATCTTTCT 59.251 40.000 0.00 0.00 0.00 2.52
2390 4754 5.556570 GCGTTATCAGCGTCCTTAATCTTTC 60.557 44.000 0.00 0.00 0.00 2.62
2391 4755 4.270325 GCGTTATCAGCGTCCTTAATCTTT 59.730 41.667 0.00 0.00 0.00 2.52
2392 4756 3.802685 GCGTTATCAGCGTCCTTAATCTT 59.197 43.478 0.00 0.00 0.00 2.40
2393 4757 3.381949 GCGTTATCAGCGTCCTTAATCT 58.618 45.455 0.00 0.00 0.00 2.40
2394 4758 2.475487 GGCGTTATCAGCGTCCTTAATC 59.525 50.000 0.00 0.00 35.00 1.75
2395 4759 2.480845 GGCGTTATCAGCGTCCTTAAT 58.519 47.619 0.00 0.00 35.00 1.40
2396 4760 1.930567 GGCGTTATCAGCGTCCTTAA 58.069 50.000 0.00 0.00 35.00 1.85
2397 4761 3.654178 GGCGTTATCAGCGTCCTTA 57.346 52.632 0.00 0.00 35.00 2.69
2398 4762 4.515404 GGCGTTATCAGCGTCCTT 57.485 55.556 0.00 0.00 35.00 3.36
2401 4765 1.447140 TGTGGGCGTTATCAGCGTC 60.447 57.895 0.00 0.00 35.00 5.19
2402 4766 1.740296 GTGTGGGCGTTATCAGCGT 60.740 57.895 0.00 0.00 35.00 5.07
2403 4767 2.798501 CGTGTGGGCGTTATCAGCG 61.799 63.158 0.00 0.00 35.00 5.18
2404 4768 1.740296 ACGTGTGGGCGTTATCAGC 60.740 57.895 0.00 0.00 43.04 4.26
2405 4769 0.669318 ACACGTGTGGGCGTTATCAG 60.669 55.000 22.71 0.00 43.83 2.90
2406 4770 0.946700 CACACGTGTGGGCGTTATCA 60.947 55.000 35.65 0.00 43.83 2.15
2407 4771 0.668096 TCACACGTGTGGGCGTTATC 60.668 55.000 39.88 0.00 45.65 1.75
2408 4772 0.036765 ATCACACGTGTGGGCGTTAT 60.037 50.000 39.88 25.74 45.65 1.89
2409 4773 0.946700 CATCACACGTGTGGGCGTTA 60.947 55.000 39.88 24.77 45.65 3.18
2410 4774 2.110213 ATCACACGTGTGGGCGTT 59.890 55.556 39.88 21.30 45.65 4.84
2411 4775 2.664851 CATCACACGTGTGGGCGT 60.665 61.111 39.88 24.22 45.65 5.68
2412 4776 2.356913 TCATCACACGTGTGGGCG 60.357 61.111 39.88 29.21 45.65 6.13
2413 4777 1.005037 TCTCATCACACGTGTGGGC 60.005 57.895 39.88 0.00 45.65 5.36
2414 4778 1.016130 GCTCTCATCACACGTGTGGG 61.016 60.000 39.88 32.16 45.65 4.61
2415 4779 0.319813 TGCTCTCATCACACGTGTGG 60.320 55.000 39.88 28.05 45.65 4.17
2416 4780 1.193203 GTTGCTCTCATCACACGTGTG 59.807 52.381 37.04 37.04 46.91 3.82
2417 4781 1.202521 TGTTGCTCTCATCACACGTGT 60.203 47.619 17.22 17.22 0.00 4.49
2418 4782 1.501169 TGTTGCTCTCATCACACGTG 58.499 50.000 15.48 15.48 0.00 4.49
2419 4783 2.341257 GATGTTGCTCTCATCACACGT 58.659 47.619 9.98 0.00 40.68 4.49
2420 4784 1.662629 GGATGTTGCTCTCATCACACG 59.337 52.381 14.49 0.00 42.16 4.49
2421 4785 1.662629 CGGATGTTGCTCTCATCACAC 59.337 52.381 14.49 2.13 42.16 3.82
2422 4786 1.276138 ACGGATGTTGCTCTCATCACA 59.724 47.619 14.49 0.00 42.16 3.58
2423 4787 1.929836 GACGGATGTTGCTCTCATCAC 59.070 52.381 14.49 6.67 42.16 3.06
2424 4788 1.134699 GGACGGATGTTGCTCTCATCA 60.135 52.381 14.49 0.00 42.16 3.07
2425 4789 1.134699 TGGACGGATGTTGCTCTCATC 60.135 52.381 7.46 7.46 40.38 2.92
2426 4790 0.904649 TGGACGGATGTTGCTCTCAT 59.095 50.000 0.00 0.00 0.00 2.90
2427 4791 0.037326 GTGGACGGATGTTGCTCTCA 60.037 55.000 0.00 0.00 0.00 3.27
2428 4792 0.037326 TGTGGACGGATGTTGCTCTC 60.037 55.000 0.00 0.00 0.00 3.20
2429 4793 0.320771 GTGTGGACGGATGTTGCTCT 60.321 55.000 0.00 0.00 0.00 4.09
2430 4794 1.626654 CGTGTGGACGGATGTTGCTC 61.627 60.000 0.00 0.00 42.18 4.26
2431 4795 1.667830 CGTGTGGACGGATGTTGCT 60.668 57.895 0.00 0.00 42.18 3.91
2432 4796 2.860293 CGTGTGGACGGATGTTGC 59.140 61.111 0.00 0.00 42.18 4.17
2441 4805 2.229543 TGTGTGTATAGGACGTGTGGAC 59.770 50.000 0.00 0.00 0.00 4.02
2442 4806 2.516906 TGTGTGTATAGGACGTGTGGA 58.483 47.619 0.00 0.00 0.00 4.02
2443 4807 3.520290 ATGTGTGTATAGGACGTGTGG 57.480 47.619 0.00 0.00 0.00 4.17
2444 4808 6.040247 ACAATATGTGTGTATAGGACGTGTG 58.960 40.000 0.00 0.00 39.72 3.82
2445 4809 6.216801 ACAATATGTGTGTATAGGACGTGT 57.783 37.500 0.00 0.00 39.72 4.49
2467 4831 2.486504 CATGCGGTGACATGGCAC 59.513 61.111 24.25 24.25 43.05 5.01
2468 4832 3.442167 GCATGCGGTGACATGGCA 61.442 61.111 0.00 0.00 46.14 4.92
2469 4833 2.777972 ATGCATGCGGTGACATGGC 61.778 57.895 14.09 0.00 46.14 4.40
2470 4834 1.065109 CATGCATGCGGTGACATGG 59.935 57.895 14.93 0.00 46.14 3.66
2472 4836 2.802792 GCATGCATGCGGTGACAT 59.197 55.556 33.99 3.77 44.67 3.06
2481 4845 1.669265 AGATTCTCACACGCATGCATG 59.331 47.619 22.70 22.70 0.00 4.06
2482 4846 2.034104 AGATTCTCACACGCATGCAT 57.966 45.000 19.57 0.00 0.00 3.96
2483 4847 1.812235 AAGATTCTCACACGCATGCA 58.188 45.000 19.57 0.00 0.00 3.96
2484 4848 2.907910 AAAGATTCTCACACGCATGC 57.092 45.000 7.91 7.91 0.00 4.06
2485 4849 3.916172 CCAAAAAGATTCTCACACGCATG 59.084 43.478 0.00 0.00 0.00 4.06
2486 4850 3.820467 TCCAAAAAGATTCTCACACGCAT 59.180 39.130 0.00 0.00 0.00 4.73
2487 4851 3.210227 TCCAAAAAGATTCTCACACGCA 58.790 40.909 0.00 0.00 0.00 5.24
2488 4852 3.896648 TCCAAAAAGATTCTCACACGC 57.103 42.857 0.00 0.00 0.00 5.34
2489 4853 5.858581 GGAAATCCAAAAAGATTCTCACACG 59.141 40.000 0.00 0.00 35.40 4.49
2490 4854 6.748132 TGGAAATCCAAAAAGATTCTCACAC 58.252 36.000 0.00 0.00 44.35 3.82
2491 4855 6.550854 ACTGGAAATCCAAAAAGATTCTCACA 59.449 34.615 3.35 0.00 46.97 3.58
2492 4856 6.986250 ACTGGAAATCCAAAAAGATTCTCAC 58.014 36.000 3.35 0.00 46.97 3.51
2493 4857 7.601705 AACTGGAAATCCAAAAAGATTCTCA 57.398 32.000 3.35 0.00 46.97 3.27
2494 4858 8.893219 AAAACTGGAAATCCAAAAAGATTCTC 57.107 30.769 3.35 0.00 46.97 2.87
2510 4874 9.535878 AGCGATAAAACATTTTAAAAACTGGAA 57.464 25.926 4.44 0.00 36.35 3.53
2511 4875 9.535878 AAGCGATAAAACATTTTAAAAACTGGA 57.464 25.926 4.44 0.00 36.35 3.86
2531 4895 9.859427 TTCAATCAGATTTTTCATTTAAGCGAT 57.141 25.926 0.00 0.00 0.00 4.58
2532 4896 9.859427 ATTCAATCAGATTTTTCATTTAAGCGA 57.141 25.926 0.00 0.00 0.00 4.93
2559 4923 7.920682 GCGATGGATTTAATGGTAAAAACAGAT 59.079 33.333 0.00 0.00 32.98 2.90
2560 4924 7.254852 GCGATGGATTTAATGGTAAAAACAGA 58.745 34.615 0.00 0.00 32.98 3.41
2561 4925 6.196353 CGCGATGGATTTAATGGTAAAAACAG 59.804 38.462 0.00 0.00 32.98 3.16
2562 4926 6.030849 CGCGATGGATTTAATGGTAAAAACA 58.969 36.000 0.00 0.00 32.98 2.83
2563 4927 5.457473 CCGCGATGGATTTAATGGTAAAAAC 59.543 40.000 8.23 0.00 42.00 2.43
2564 4928 5.583495 CCGCGATGGATTTAATGGTAAAAA 58.417 37.500 8.23 0.00 42.00 1.94
2565 4929 5.176407 CCGCGATGGATTTAATGGTAAAA 57.824 39.130 8.23 0.00 42.00 1.52
2566 4930 4.822036 CCGCGATGGATTTAATGGTAAA 57.178 40.909 8.23 0.00 42.00 2.01


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

AutoCloner maintained by Alex Coulton.