Multiple sequence alignment - TraesCS4D01G159000

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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 TraesCS4D01G159000 chr4D 100.000 2375 0 0 1 2375 225306336 225303962 0.000000e+00 4386.0
1 TraesCS4D01G159000 chr4D 90.899 879 79 1 488 1365 239785104 239784226 0.000000e+00 1179.0
2 TraesCS4D01G159000 chr4D 93.872 718 43 1 652 1369 196954663 196955379 0.000000e+00 1081.0
3 TraesCS4D01G159000 chr4D 94.529 658 32 1 1 658 196912037 196912690 0.000000e+00 1013.0
4 TraesCS4D01G159000 chr4D 89.524 105 11 0 2270 2374 234884365 234884261 1.480000e-27 134.0
5 TraesCS4D01G159000 chr3B 88.413 1985 137 32 2 1927 715973800 715975750 0.000000e+00 2305.0
6 TraesCS4D01G159000 chr3B 90.265 339 32 1 1928 2266 715975782 715976119 2.170000e-120 442.0
7 TraesCS4D01G159000 chr3B 93.750 96 5 1 1457 1551 715975332 715975427 2.460000e-30 143.0
8 TraesCS4D01G159000 chr1A 90.920 1674 118 15 270 1924 168324159 168325817 0.000000e+00 2218.0
9 TraesCS4D01G159000 chr1A 90.566 106 10 0 2270 2375 433781068 433781173 8.850000e-30 141.0
10 TraesCS4D01G159000 chr1A 82.474 97 7 4 1504 1590 168325356 168325452 2.530000e-10 76.8
11 TraesCS4D01G159000 chr6B 86.534 1953 202 33 1 1926 443372656 443374574 0.000000e+00 2093.0
12 TraesCS4D01G159000 chr6B 90.455 880 81 2 487 1365 429916380 429915503 0.000000e+00 1157.0
13 TraesCS4D01G159000 chr5B 91.447 1403 109 4 1 1401 189833210 189834603 0.000000e+00 1916.0
14 TraesCS4D01G159000 chr5B 89.461 1224 104 18 730 1933 399765253 399766471 0.000000e+00 1522.0
15 TraesCS4D01G159000 chr5B 90.688 698 61 2 3 696 399764555 399765252 0.000000e+00 926.0
16 TraesCS4D01G159000 chr5B 84.543 427 38 16 1503 1927 189834639 189835039 4.760000e-107 398.0
17 TraesCS4D01G159000 chr5B 90.141 71 7 0 1589 1659 101828834 101828764 2.510000e-15 93.5
18 TraesCS4D01G159000 chr5A 92.529 870 61 3 497 1365 545036518 545037384 0.000000e+00 1243.0
19 TraesCS4D01G159000 chr1D 87.368 950 75 17 709 1622 348139119 348138179 0.000000e+00 1048.0
20 TraesCS4D01G159000 chr1D 89.766 342 35 0 1928 2269 336728182 336727841 2.800000e-119 438.0
21 TraesCS4D01G159000 chr1D 91.509 106 6 1 2270 2375 94370049 94370151 2.460000e-30 143.0
22 TraesCS4D01G159000 chr1D 84.173 139 8 7 1445 1582 348138318 348138193 3.210000e-24 122.0
23 TraesCS4D01G159000 chr3D 94.746 571 29 1 795 1365 420359219 420359788 0.000000e+00 887.0
24 TraesCS4D01G159000 chr3D 93.881 572 33 2 795 1365 416552719 416553289 0.000000e+00 861.0
25 TraesCS4D01G159000 chr3D 96.032 504 18 2 1 503 420358435 420358937 0.000000e+00 819.0
26 TraesCS4D01G159000 chr3D 95.626 503 22 0 1 503 330464911 330464409 0.000000e+00 808.0
27 TraesCS4D01G159000 chr3D 90.323 341 33 0 1928 2268 484483349 484483689 4.660000e-122 448.0
28 TraesCS4D01G159000 chr5D 93.870 571 31 2 795 1365 140952424 140951858 0.000000e+00 857.0
29 TraesCS4D01G159000 chr5D 86.349 630 56 10 1666 2267 16457824 16457197 0.000000e+00 660.0
30 TraesCS4D01G159000 chr5D 90.029 341 32 2 1928 2267 29765623 29765284 7.790000e-120 440.0
31 TraesCS4D01G159000 chr5D 82.039 412 34 12 1559 1933 94348015 94347607 4.930000e-82 315.0
32 TraesCS4D01G159000 chr5D 100.000 30 0 0 1524 1553 94348017 94347988 3.300000e-04 56.5
33 TraesCS4D01G159000 chr7D 84.423 918 83 31 845 1729 66535336 66536226 0.000000e+00 848.0
34 TraesCS4D01G159000 chr7D 95.229 503 24 0 1 503 501764204 501764706 0.000000e+00 797.0
35 TraesCS4D01G159000 chr7D 89.766 342 33 2 1929 2270 103543359 103543698 1.010000e-118 436.0
36 TraesCS4D01G159000 chr7D 89.623 106 11 0 2270 2375 406551314 406551419 4.120000e-28 135.0
37 TraesCS4D01G159000 chr7D 88.679 106 12 0 2270 2375 317634064 317633959 1.920000e-26 130.0
38 TraesCS4D01G159000 chr2D 95.992 499 20 0 1 499 397130531 397131029 0.000000e+00 811.0
39 TraesCS4D01G159000 chr2D 90.323 341 30 3 1928 2267 648927222 648927560 6.020000e-121 444.0
40 TraesCS4D01G159000 chr2D 90.265 339 32 1 1929 2267 397132519 397132856 2.170000e-120 442.0
41 TraesCS4D01G159000 chr2D 90.196 102 10 0 2270 2371 490950672 490950773 1.480000e-27 134.0
42 TraesCS4D01G159000 chr6D 95.626 503 22 0 1 503 46520555 46520053 0.000000e+00 808.0
43 TraesCS4D01G159000 chr6D 90.643 342 30 2 1928 2269 297169461 297169122 1.000000e-123 453.0
44 TraesCS4D01G159000 chr2B 87.869 643 46 13 1656 2267 149804838 149805479 0.000000e+00 726.0
45 TraesCS4D01G159000 chr2B 96.970 66 2 0 1487 1552 5921512 5921447 6.940000e-21 111.0
46 TraesCS4D01G159000 chr2B 82.394 142 9 14 1354 1484 5921584 5921448 2.500000e-20 110.0
47 TraesCS4D01G159000 chr7B 87.003 654 51 12 1647 2271 725311891 725312539 0.000000e+00 706.0
48 TraesCS4D01G159000 chr7B 90.476 105 10 0 2270 2374 272341988 272341884 3.180000e-29 139.0
49 TraesCS4D01G159000 chr1B 92.606 284 15 5 1647 1927 516783231 516783511 1.020000e-108 403.0
50 TraesCS4D01G159000 chr1B 89.474 323 26 6 1647 1963 681900746 681901066 3.680000e-108 401.0
51 TraesCS4D01G159000 chr7A 89.623 106 11 0 2270 2375 302603318 302603213 4.120000e-28 135.0
52 TraesCS4D01G159000 chr4B 90.196 102 10 0 2270 2371 363807581 363807682 1.480000e-27 134.0


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 TraesCS4D01G159000 chr4D 225303962 225306336 2374 True 4386.000000 4386 100.000000 1 2375 1 chr4D.!!$R1 2374
1 TraesCS4D01G159000 chr4D 239784226 239785104 878 True 1179.000000 1179 90.899000 488 1365 1 chr4D.!!$R3 877
2 TraesCS4D01G159000 chr4D 196954663 196955379 716 False 1081.000000 1081 93.872000 652 1369 1 chr4D.!!$F2 717
3 TraesCS4D01G159000 chr4D 196912037 196912690 653 False 1013.000000 1013 94.529000 1 658 1 chr4D.!!$F1 657
4 TraesCS4D01G159000 chr3B 715973800 715976119 2319 False 963.333333 2305 90.809333 2 2266 3 chr3B.!!$F1 2264
5 TraesCS4D01G159000 chr1A 168324159 168325817 1658 False 1147.400000 2218 86.697000 270 1924 2 chr1A.!!$F2 1654
6 TraesCS4D01G159000 chr6B 443372656 443374574 1918 False 2093.000000 2093 86.534000 1 1926 1 chr6B.!!$F1 1925
7 TraesCS4D01G159000 chr6B 429915503 429916380 877 True 1157.000000 1157 90.455000 487 1365 1 chr6B.!!$R1 878
8 TraesCS4D01G159000 chr5B 399764555 399766471 1916 False 1224.000000 1522 90.074500 3 1933 2 chr5B.!!$F2 1930
9 TraesCS4D01G159000 chr5B 189833210 189835039 1829 False 1157.000000 1916 87.995000 1 1927 2 chr5B.!!$F1 1926
10 TraesCS4D01G159000 chr5A 545036518 545037384 866 False 1243.000000 1243 92.529000 497 1365 1 chr5A.!!$F1 868
11 TraesCS4D01G159000 chr1D 348138179 348139119 940 True 585.000000 1048 85.770500 709 1622 2 chr1D.!!$R2 913
12 TraesCS4D01G159000 chr3D 416552719 416553289 570 False 861.000000 861 93.881000 795 1365 1 chr3D.!!$F1 570
13 TraesCS4D01G159000 chr3D 420358435 420359788 1353 False 853.000000 887 95.389000 1 1365 2 chr3D.!!$F3 1364
14 TraesCS4D01G159000 chr3D 330464409 330464911 502 True 808.000000 808 95.626000 1 503 1 chr3D.!!$R1 502
15 TraesCS4D01G159000 chr5D 140951858 140952424 566 True 857.000000 857 93.870000 795 1365 1 chr5D.!!$R3 570
16 TraesCS4D01G159000 chr5D 16457197 16457824 627 True 660.000000 660 86.349000 1666 2267 1 chr5D.!!$R1 601
17 TraesCS4D01G159000 chr7D 66535336 66536226 890 False 848.000000 848 84.423000 845 1729 1 chr7D.!!$F1 884
18 TraesCS4D01G159000 chr7D 501764204 501764706 502 False 797.000000 797 95.229000 1 503 1 chr7D.!!$F4 502
19 TraesCS4D01G159000 chr2D 397130531 397132856 2325 False 626.500000 811 93.128500 1 2267 2 chr2D.!!$F3 2266
20 TraesCS4D01G159000 chr6D 46520053 46520555 502 True 808.000000 808 95.626000 1 503 1 chr6D.!!$R1 502
21 TraesCS4D01G159000 chr2B 149804838 149805479 641 False 726.000000 726 87.869000 1656 2267 1 chr2B.!!$F1 611
22 TraesCS4D01G159000 chr7B 725311891 725312539 648 False 706.000000 706 87.003000 1647 2271 1 chr7B.!!$F1 624

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
459 465 0.963962 ATGCTTTGTCCAGCCAGTTG 59.036 50.0 0.0 0.0 39.25 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1495 1672 1.790623 GCACAGCTTCACAAAATGCAG 59.209 47.619 0.0 0.0 0.0 4.41 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
63 64 4.523083 ACACAAGGTTTGTCTCTGCTTTA 58.477 39.130 0.00 0.00 43.23 1.85
273 277 4.998672 ACCGTTTGATCCTCGTTGAATAAA 59.001 37.500 0.00 0.00 0.00 1.40
337 343 4.756084 AACATTTCAGAAAGAAGAGCGG 57.244 40.909 1.28 0.00 37.57 5.52
392 398 2.127232 GCCACCCACAACAGCAAGT 61.127 57.895 0.00 0.00 0.00 3.16
459 465 0.963962 ATGCTTTGTCCAGCCAGTTG 59.036 50.000 0.00 0.00 39.25 3.16
485 491 4.141482 ACTTTTGTCTAGAAACCTCAGCCA 60.141 41.667 0.00 0.00 0.00 4.75
665 729 1.378514 GGCTCATTCGGGAAGCCAA 60.379 57.895 7.71 0.00 44.42 4.52
686 750 6.770785 GCCAACTTATATAGAACCACCATTCA 59.229 38.462 0.00 0.00 0.00 2.57
828 892 6.096987 TGTCAGGTTACTAGTCATCATCTTCC 59.903 42.308 0.00 0.00 0.00 3.46
1061 1159 1.601412 GCCAAAGTCTGCTGCTGAAAC 60.601 52.381 10.92 0.76 0.00 2.78
1125 1223 2.821378 CCTCATGAATGTTGTGCTCCAA 59.179 45.455 0.00 0.00 0.00 3.53
1217 1315 0.174617 GAGAGGTCGGAGCTTCAAGG 59.825 60.000 11.50 0.00 0.00 3.61
1221 1319 0.250513 GGTCGGAGCTTCAAGGTGAT 59.749 55.000 0.00 0.00 0.00 3.06
1248 1346 3.244284 TGCAAGAAGAATTGGCAGCAATT 60.244 39.130 0.00 1.12 37.47 2.32
1339 1437 2.169352 GAGCAGGATGAGAAGTTAGCCA 59.831 50.000 0.00 0.00 39.69 4.75
1340 1438 2.093235 AGCAGGATGAGAAGTTAGCCAC 60.093 50.000 0.00 0.00 39.69 5.01
1455 1599 3.141398 ACTTGTCGTAGAACCTGTCGTA 58.859 45.455 0.00 0.00 39.69 3.43
1478 1637 7.478667 CGTAGAACTGTGAAGTTATGCATTTTC 59.521 37.037 3.54 7.85 31.35 2.29
1495 1672 5.052370 GCATTTTCGTGAAACTGTGAAGTTC 60.052 40.000 12.40 0.00 34.63 3.01
1567 1962 1.242076 GAAGCTGTGCACCTGTGAAT 58.758 50.000 15.69 0.00 0.00 2.57
1617 2020 8.655651 TTATTTGAGTTTTGTTTGGACCATTC 57.344 30.769 0.00 0.00 0.00 2.67
1713 2116 3.756434 CGAGGCCCAAACAAGAATTAGAA 59.244 43.478 0.00 0.00 0.00 2.10
1829 2234 6.896883 AGAACTAGACTAAAAAGGTTGTGGT 58.103 36.000 0.00 0.00 0.00 4.16
1897 2304 4.141869 CCATCCCAGAAAATAAAAGGCCAG 60.142 45.833 5.01 0.00 0.00 4.85
1944 2382 2.301346 AGAGAATTATTGGGCTTGGCG 58.699 47.619 0.00 0.00 0.00 5.69
1963 2401 1.937223 CGCATGTAGACGGCCAAAATA 59.063 47.619 2.24 0.00 0.00 1.40
2016 2454 2.552599 TTGGTCGTAATTCTGCCACA 57.447 45.000 0.00 0.00 0.00 4.17
2046 2484 0.984230 ACGGTGGATCTGACATGGTT 59.016 50.000 0.00 0.00 0.00 3.67
2060 2498 1.606885 ATGGTTTGGGCGGATTGCTG 61.607 55.000 0.00 0.00 45.43 4.41
2101 2539 6.371825 GGTCGTTGAATCTATGACCTCTTTTT 59.628 38.462 22.74 0.00 44.66 1.94
2116 2555 5.826208 ACCTCTTTTTGGTCGTAAATGTCTT 59.174 36.000 0.00 0.00 31.03 3.01
2142 2581 3.437049 CCATTCCAGAAGAAAGGTCGTTC 59.563 47.826 0.00 0.00 38.33 3.95
2209 2648 5.067674 TCACAAGAAGGTCACAAATGGAAAG 59.932 40.000 0.00 0.00 0.00 2.62
2216 2655 4.021719 AGGTCACAAATGGAAAGCAATGAG 60.022 41.667 0.00 0.00 0.00 2.90
2261 2700 4.386652 GGTCGCAACTTGACGTATTTCTTA 59.613 41.667 0.00 0.00 37.22 2.10
2267 2706 7.399523 GCAACTTGACGTATTTCTTATAGTGG 58.600 38.462 0.00 0.00 0.00 4.00
2270 2709 9.715121 AACTTGACGTATTTCTTATAGTGGAAA 57.285 29.630 0.00 0.00 36.17 3.13
2271 2710 9.148104 ACTTGACGTATTTCTTATAGTGGAAAC 57.852 33.333 0.00 0.00 34.83 2.78
2272 2711 7.745022 TGACGTATTTCTTATAGTGGAAACG 57.255 36.000 0.00 0.00 34.83 3.60
2273 2712 7.537715 TGACGTATTTCTTATAGTGGAAACGA 58.462 34.615 0.00 0.00 34.83 3.85
2274 2713 7.699391 TGACGTATTTCTTATAGTGGAAACGAG 59.301 37.037 0.00 5.77 34.83 4.18
2275 2714 6.976925 ACGTATTTCTTATAGTGGAAACGAGG 59.023 38.462 0.00 7.42 34.83 4.63
2276 2715 6.976925 CGTATTTCTTATAGTGGAAACGAGGT 59.023 38.462 0.00 0.00 34.83 3.85
2277 2716 7.043590 CGTATTTCTTATAGTGGAAACGAGGTG 60.044 40.741 0.00 0.00 34.83 4.00
2278 2717 5.988310 TTCTTATAGTGGAAACGAGGTGA 57.012 39.130 0.00 0.00 0.00 4.02
2279 2718 5.988310 TCTTATAGTGGAAACGAGGTGAA 57.012 39.130 0.00 0.00 0.00 3.18
2280 2719 6.349243 TCTTATAGTGGAAACGAGGTGAAA 57.651 37.500 0.00 0.00 0.00 2.69
2281 2720 6.942976 TCTTATAGTGGAAACGAGGTGAAAT 58.057 36.000 0.00 0.00 0.00 2.17
2282 2721 6.816640 TCTTATAGTGGAAACGAGGTGAAATG 59.183 38.462 0.00 0.00 0.00 2.32
2283 2722 2.504367 AGTGGAAACGAGGTGAAATGG 58.496 47.619 0.00 0.00 0.00 3.16
2284 2723 2.105821 AGTGGAAACGAGGTGAAATGGA 59.894 45.455 0.00 0.00 0.00 3.41
2285 2724 3.081804 GTGGAAACGAGGTGAAATGGAT 58.918 45.455 0.00 0.00 0.00 3.41
2286 2725 4.019681 AGTGGAAACGAGGTGAAATGGATA 60.020 41.667 0.00 0.00 0.00 2.59
2287 2726 4.881850 GTGGAAACGAGGTGAAATGGATAT 59.118 41.667 0.00 0.00 0.00 1.63
2288 2727 5.007724 GTGGAAACGAGGTGAAATGGATATC 59.992 44.000 0.00 0.00 0.00 1.63
2289 2728 4.515567 GGAAACGAGGTGAAATGGATATCC 59.484 45.833 15.39 15.39 0.00 2.59
2290 2729 3.771577 ACGAGGTGAAATGGATATCCC 57.228 47.619 19.34 4.07 34.29 3.85
2291 2730 3.318313 ACGAGGTGAAATGGATATCCCT 58.682 45.455 19.34 6.50 35.38 4.20
2292 2731 4.489737 ACGAGGTGAAATGGATATCCCTA 58.510 43.478 19.34 1.37 35.38 3.53
2293 2732 5.094387 ACGAGGTGAAATGGATATCCCTAT 58.906 41.667 19.34 3.98 35.38 2.57
2294 2733 5.187967 ACGAGGTGAAATGGATATCCCTATC 59.812 44.000 19.34 13.70 35.38 2.08
2302 2741 3.695830 GGATATCCCTATCCGCACAAA 57.304 47.619 11.02 0.00 43.07 2.83
2303 2742 4.015872 GGATATCCCTATCCGCACAAAA 57.984 45.455 11.02 0.00 43.07 2.44
2304 2743 4.394729 GGATATCCCTATCCGCACAAAAA 58.605 43.478 11.02 0.00 43.07 1.94
2305 2744 4.455877 GGATATCCCTATCCGCACAAAAAG 59.544 45.833 11.02 0.00 43.07 2.27
2306 2745 3.644966 ATCCCTATCCGCACAAAAAGA 57.355 42.857 0.00 0.00 0.00 2.52
2307 2746 3.644966 TCCCTATCCGCACAAAAAGAT 57.355 42.857 0.00 0.00 0.00 2.40
2308 2747 4.764050 TCCCTATCCGCACAAAAAGATA 57.236 40.909 0.00 0.00 0.00 1.98
2309 2748 5.105567 TCCCTATCCGCACAAAAAGATAA 57.894 39.130 0.00 0.00 0.00 1.75
2310 2749 5.502079 TCCCTATCCGCACAAAAAGATAAA 58.498 37.500 0.00 0.00 0.00 1.40
2311 2750 5.946972 TCCCTATCCGCACAAAAAGATAAAA 59.053 36.000 0.00 0.00 0.00 1.52
2312 2751 6.434652 TCCCTATCCGCACAAAAAGATAAAAA 59.565 34.615 0.00 0.00 0.00 1.94
2313 2752 6.751888 CCCTATCCGCACAAAAAGATAAAAAG 59.248 38.462 0.00 0.00 0.00 2.27
2314 2753 7.362574 CCCTATCCGCACAAAAAGATAAAAAGA 60.363 37.037 0.00 0.00 0.00 2.52
2315 2754 8.026607 CCTATCCGCACAAAAAGATAAAAAGAA 58.973 33.333 0.00 0.00 0.00 2.52
2316 2755 9.405587 CTATCCGCACAAAAAGATAAAAAGAAA 57.594 29.630 0.00 0.00 0.00 2.52
2317 2756 8.655651 ATCCGCACAAAAAGATAAAAAGAAAA 57.344 26.923 0.00 0.00 0.00 2.29
2318 2757 7.901002 TCCGCACAAAAAGATAAAAAGAAAAC 58.099 30.769 0.00 0.00 0.00 2.43
2319 2758 7.545965 TCCGCACAAAAAGATAAAAAGAAAACA 59.454 29.630 0.00 0.00 0.00 2.83
2320 2759 7.845622 CCGCACAAAAAGATAAAAAGAAAACAG 59.154 33.333 0.00 0.00 0.00 3.16
2321 2760 8.379902 CGCACAAAAAGATAAAAAGAAAACAGT 58.620 29.630 0.00 0.00 0.00 3.55
2328 2767 9.529325 AAAGATAAAAAGAAAACAGTTACTGGC 57.471 29.630 17.21 3.32 35.51 4.85
2329 2768 7.658261 AGATAAAAAGAAAACAGTTACTGGCC 58.342 34.615 17.21 0.00 35.51 5.36
2330 2769 5.669164 AAAAAGAAAACAGTTACTGGCCA 57.331 34.783 17.21 4.71 35.51 5.36
2331 2770 5.669164 AAAAGAAAACAGTTACTGGCCAA 57.331 34.783 17.21 0.00 35.51 4.52
2332 2771 5.869649 AAAGAAAACAGTTACTGGCCAAT 57.130 34.783 17.21 0.00 35.51 3.16
2333 2772 5.869649 AAGAAAACAGTTACTGGCCAATT 57.130 34.783 17.21 0.00 35.51 2.32
2334 2773 6.969993 AAGAAAACAGTTACTGGCCAATTA 57.030 33.333 17.21 0.00 35.51 1.40
2335 2774 6.327279 AGAAAACAGTTACTGGCCAATTAC 57.673 37.500 17.21 0.00 35.51 1.89
2336 2775 5.830991 AGAAAACAGTTACTGGCCAATTACA 59.169 36.000 17.21 0.00 35.51 2.41
2337 2776 6.322712 AGAAAACAGTTACTGGCCAATTACAA 59.677 34.615 17.21 0.00 35.51 2.41
2338 2777 5.705609 AACAGTTACTGGCCAATTACAAG 57.294 39.130 17.21 0.16 35.51 3.16
2339 2778 4.980573 ACAGTTACTGGCCAATTACAAGA 58.019 39.130 17.21 0.00 35.51 3.02
2340 2779 5.570320 ACAGTTACTGGCCAATTACAAGAT 58.430 37.500 17.21 0.00 35.51 2.40
2341 2780 6.717289 ACAGTTACTGGCCAATTACAAGATA 58.283 36.000 17.21 0.00 35.51 1.98
2342 2781 6.598064 ACAGTTACTGGCCAATTACAAGATAC 59.402 38.462 17.21 0.00 35.51 2.24
2343 2782 6.597672 CAGTTACTGGCCAATTACAAGATACA 59.402 38.462 7.01 0.00 0.00 2.29
2344 2783 7.120579 CAGTTACTGGCCAATTACAAGATACAA 59.879 37.037 7.01 0.00 0.00 2.41
2345 2784 7.668052 AGTTACTGGCCAATTACAAGATACAAA 59.332 33.333 7.01 0.00 0.00 2.83
2346 2785 6.909550 ACTGGCCAATTACAAGATACAAAA 57.090 33.333 7.01 0.00 0.00 2.44
2347 2786 6.687604 ACTGGCCAATTACAAGATACAAAAC 58.312 36.000 7.01 0.00 0.00 2.43
2348 2787 6.266558 ACTGGCCAATTACAAGATACAAAACA 59.733 34.615 7.01 0.00 0.00 2.83
2349 2788 7.039082 ACTGGCCAATTACAAGATACAAAACAT 60.039 33.333 7.01 0.00 0.00 2.71
2350 2789 8.354711 TGGCCAATTACAAGATACAAAACATA 57.645 30.769 0.61 0.00 0.00 2.29
2351 2790 8.247562 TGGCCAATTACAAGATACAAAACATAC 58.752 33.333 0.61 0.00 0.00 2.39
2352 2791 7.431084 GGCCAATTACAAGATACAAAACATACG 59.569 37.037 0.00 0.00 0.00 3.06
2353 2792 7.044314 GCCAATTACAAGATACAAAACATACGC 60.044 37.037 0.00 0.00 0.00 4.42
2354 2793 7.965655 CCAATTACAAGATACAAAACATACGCA 59.034 33.333 0.00 0.00 0.00 5.24
2355 2794 9.335891 CAATTACAAGATACAAAACATACGCAA 57.664 29.630 0.00 0.00 0.00 4.85
2356 2795 9.900710 AATTACAAGATACAAAACATACGCAAA 57.099 25.926 0.00 0.00 0.00 3.68
2357 2796 9.900710 ATTACAAGATACAAAACATACGCAAAA 57.099 25.926 0.00 0.00 0.00 2.44
2358 2797 7.617533 ACAAGATACAAAACATACGCAAAAC 57.382 32.000 0.00 0.00 0.00 2.43
2359 2798 6.639279 ACAAGATACAAAACATACGCAAAACC 59.361 34.615 0.00 0.00 0.00 3.27
2360 2799 6.320494 AGATACAAAACATACGCAAAACCA 57.680 33.333 0.00 0.00 0.00 3.67
2361 2800 6.740110 AGATACAAAACATACGCAAAACCAA 58.260 32.000 0.00 0.00 0.00 3.67
2362 2801 7.203910 AGATACAAAACATACGCAAAACCAAA 58.796 30.769 0.00 0.00 0.00 3.28
2363 2802 7.707035 AGATACAAAACATACGCAAAACCAAAA 59.293 29.630 0.00 0.00 0.00 2.44
2364 2803 6.100792 ACAAAACATACGCAAAACCAAAAG 57.899 33.333 0.00 0.00 0.00 2.27
2365 2804 5.869888 ACAAAACATACGCAAAACCAAAAGA 59.130 32.000 0.00 0.00 0.00 2.52
2366 2805 6.369065 ACAAAACATACGCAAAACCAAAAGAA 59.631 30.769 0.00 0.00 0.00 2.52
2367 2806 6.582437 AAACATACGCAAAACCAAAAGAAG 57.418 33.333 0.00 0.00 0.00 2.85
2368 2807 4.048504 ACATACGCAAAACCAAAAGAAGC 58.951 39.130 0.00 0.00 0.00 3.86
2369 2808 2.663826 ACGCAAAACCAAAAGAAGCA 57.336 40.000 0.00 0.00 0.00 3.91
2370 2809 3.177997 ACGCAAAACCAAAAGAAGCAT 57.822 38.095 0.00 0.00 0.00 3.79
2371 2810 2.865551 ACGCAAAACCAAAAGAAGCATG 59.134 40.909 0.00 0.00 0.00 4.06
2372 2811 2.865551 CGCAAAACCAAAAGAAGCATGT 59.134 40.909 0.00 0.00 0.00 3.21
2373 2812 3.309410 CGCAAAACCAAAAGAAGCATGTT 59.691 39.130 0.00 0.00 0.00 2.71
2374 2813 4.550639 CGCAAAACCAAAAGAAGCATGTTC 60.551 41.667 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 4.240096 GTGCAGAACATAAAGCAGCAAAT 58.760 39.130 0.00 0.00 37.72 2.32
136 137 3.726291 TCATCTTGTTCGACACACAGA 57.274 42.857 0.00 0.77 33.98 3.41
241 245 2.500504 AGGATCAAACGGTAAGGTCTCC 59.499 50.000 0.00 0.00 0.00 3.71
337 343 0.248843 CAGACAGCTCCTCACCCTTC 59.751 60.000 0.00 0.00 0.00 3.46
392 398 1.375013 GCTCCGAAAACCCGTGCTA 60.375 57.895 0.00 0.00 0.00 3.49
459 465 6.431278 GCTGAGGTTTCTAGACAAAAGTTTC 58.569 40.000 0.00 0.00 0.00 2.78
485 491 7.039574 TGTTCTTGATGGATGTGAATCAAACAT 60.040 33.333 0.00 0.00 41.10 2.71
653 717 6.285990 GTTCTATATAAGTTGGCTTCCCGAA 58.714 40.000 0.00 0.00 36.22 4.30
665 729 6.998673 GCCTTGAATGGTGGTTCTATATAAGT 59.001 38.462 0.00 0.00 0.00 2.24
686 750 7.362920 AACAATATGTTCGCTTCATTAAGCCTT 60.363 33.333 6.05 0.00 43.60 4.35
703 767 7.396907 TGGAGACATGAAATTGGAACAATATGT 59.603 33.333 0.00 8.00 38.98 2.29
719 783 5.423290 ACACTTATGTGATCTGGAGACATGA 59.577 40.000 15.13 0.00 46.55 3.07
1061 1159 2.219674 GTCTTGAGCACTTCGTCAACAG 59.780 50.000 0.00 0.00 0.00 3.16
1118 1216 2.265367 TGTTCCTAGATGGTTGGAGCA 58.735 47.619 0.00 0.00 38.45 4.26
1125 1223 2.237392 GCCAGAGTTGTTCCTAGATGGT 59.763 50.000 0.00 0.00 37.07 3.55
1159 1257 0.671472 CGAACATGAGCAGCCACAGA 60.671 55.000 0.00 0.00 0.00 3.41
1217 1315 5.100259 CCAATTCTTCTTGCATCACATCAC 58.900 41.667 0.00 0.00 0.00 3.06
1221 1319 2.892215 TGCCAATTCTTCTTGCATCACA 59.108 40.909 0.00 0.00 0.00 3.58
1248 1346 2.501723 AGCTTCTTCCGCCTTCATCTTA 59.498 45.455 0.00 0.00 0.00 2.10
1339 1437 1.988107 TCCAAAGAGAGCCATCAAGGT 59.012 47.619 0.00 0.00 40.61 3.50
1340 1438 2.641305 CTCCAAAGAGAGCCATCAAGG 58.359 52.381 0.00 0.00 43.39 3.61
1455 1599 6.017109 ACGAAAATGCATAACTTCACAGTTCT 60.017 34.615 0.00 0.00 42.66 3.01
1478 1637 2.351418 TGCAGAACTTCACAGTTTCACG 59.649 45.455 0.00 0.00 43.79 4.35
1495 1672 1.790623 GCACAGCTTCACAAAATGCAG 59.209 47.619 0.00 0.00 0.00 4.41
1567 1962 8.659925 ATTCACAACTTCACAAAATGCATAAA 57.340 26.923 0.00 0.00 0.00 1.40
1617 2020 1.970114 CAGGTGCCCAGCTTCACAG 60.970 63.158 11.28 1.99 36.98 3.66
1800 2205 9.761504 ACAACCTTTTTAGTCTAGTTCTAGTTC 57.238 33.333 6.73 2.95 0.00 3.01
1829 2234 7.411486 TTTTATTGTCCACTCTTGTTTTGGA 57.589 32.000 0.00 0.00 37.07 3.53
1920 2327 5.563475 CGCCAAGCCCAATAATTCTCTTATG 60.563 44.000 0.00 0.00 0.00 1.90
1944 2382 3.002348 GTCTATTTTGGCCGTCTACATGC 59.998 47.826 0.00 0.00 0.00 4.06
1963 2401 3.933861 AAAATAGAATCAGCCCGGTCT 57.066 42.857 0.00 0.00 0.00 3.85
2016 2454 2.202236 ATCCACCGTGGCAAGCTGAT 62.202 55.000 13.19 0.00 37.47 2.90
2046 2484 2.676121 CACCAGCAATCCGCCCAA 60.676 61.111 0.00 0.00 44.04 4.12
2060 2498 6.210078 TCAACGACCAATTATTTTTGTCACC 58.790 36.000 0.00 0.00 0.00 4.02
2096 2534 5.981174 TCGAAGACATTTACGACCAAAAAG 58.019 37.500 0.00 0.00 0.00 2.27
2116 2555 3.334583 CCTTTCTTCTGGAATGGTCGA 57.665 47.619 0.00 0.00 41.55 4.20
2142 2581 4.452455 AGCTGACCGTCTTAAACTGAAATG 59.548 41.667 0.00 0.00 0.00 2.32
2209 2648 1.814394 TGGTCACTGAATGCTCATTGC 59.186 47.619 0.00 0.00 43.25 3.56
2216 2655 4.036027 CCATCACTATTGGTCACTGAATGC 59.964 45.833 0.00 0.00 0.00 3.56
2246 2685 8.318876 CGTTTCCACTATAAGAAATACGTCAAG 58.681 37.037 0.00 0.00 34.69 3.02
2261 2700 4.019681 TCCATTTCACCTCGTTTCCACTAT 60.020 41.667 0.00 0.00 0.00 2.12
2267 2706 4.515567 GGGATATCCATTTCACCTCGTTTC 59.484 45.833 23.27 0.00 37.91 2.78
2270 2709 3.318313 AGGGATATCCATTTCACCTCGT 58.682 45.455 23.27 0.00 38.24 4.18
2271 2710 5.395768 GGATAGGGATATCCATTTCACCTCG 60.396 48.000 23.27 0.00 44.19 4.63
2272 2711 5.395768 CGGATAGGGATATCCATTTCACCTC 60.396 48.000 23.27 7.29 44.84 3.85
2273 2712 4.471386 CGGATAGGGATATCCATTTCACCT 59.529 45.833 23.27 11.26 44.84 4.00
2274 2713 4.770795 CGGATAGGGATATCCATTTCACC 58.229 47.826 23.27 15.46 44.84 4.02
2275 2714 4.192317 GCGGATAGGGATATCCATTTCAC 58.808 47.826 23.27 12.40 44.84 3.18
2276 2715 3.843619 TGCGGATAGGGATATCCATTTCA 59.156 43.478 23.27 1.68 44.84 2.69
2277 2716 4.192317 GTGCGGATAGGGATATCCATTTC 58.808 47.826 23.27 19.26 44.84 2.17
2278 2717 3.587061 TGTGCGGATAGGGATATCCATTT 59.413 43.478 23.27 11.64 44.84 2.32
2279 2718 3.181329 TGTGCGGATAGGGATATCCATT 58.819 45.455 23.27 12.93 44.84 3.16
2280 2719 2.832838 TGTGCGGATAGGGATATCCAT 58.167 47.619 23.27 18.99 44.84 3.41
2281 2720 2.319025 TGTGCGGATAGGGATATCCA 57.681 50.000 23.27 4.04 44.84 3.41
2282 2721 3.695830 TTTGTGCGGATAGGGATATCC 57.304 47.619 13.87 13.87 41.96 2.59
2283 2722 5.305585 TCTTTTTGTGCGGATAGGGATATC 58.694 41.667 0.00 0.00 0.00 1.63
2284 2723 5.304686 TCTTTTTGTGCGGATAGGGATAT 57.695 39.130 0.00 0.00 0.00 1.63
2285 2724 4.764050 TCTTTTTGTGCGGATAGGGATA 57.236 40.909 0.00 0.00 0.00 2.59
2286 2725 3.644966 TCTTTTTGTGCGGATAGGGAT 57.355 42.857 0.00 0.00 0.00 3.85
2287 2726 3.644966 ATCTTTTTGTGCGGATAGGGA 57.355 42.857 0.00 0.00 0.00 4.20
2288 2727 5.828299 TTTATCTTTTTGTGCGGATAGGG 57.172 39.130 0.00 0.00 0.00 3.53
2289 2728 7.535139 TCTTTTTATCTTTTTGTGCGGATAGG 58.465 34.615 0.00 0.00 0.00 2.57
2290 2729 8.964420 TTCTTTTTATCTTTTTGTGCGGATAG 57.036 30.769 0.00 0.00 0.00 2.08
2291 2730 9.751542 TTTTCTTTTTATCTTTTTGTGCGGATA 57.248 25.926 0.00 0.00 0.00 2.59
2292 2731 8.547894 GTTTTCTTTTTATCTTTTTGTGCGGAT 58.452 29.630 0.00 0.00 0.00 4.18
2293 2732 7.545965 TGTTTTCTTTTTATCTTTTTGTGCGGA 59.454 29.630 0.00 0.00 0.00 5.54
2294 2733 7.680062 TGTTTTCTTTTTATCTTTTTGTGCGG 58.320 30.769 0.00 0.00 0.00 5.69
2295 2734 8.379902 ACTGTTTTCTTTTTATCTTTTTGTGCG 58.620 29.630 0.00 0.00 0.00 5.34
2302 2741 9.529325 GCCAGTAACTGTTTTCTTTTTATCTTT 57.471 29.630 0.00 0.00 0.00 2.52
2303 2742 8.141909 GGCCAGTAACTGTTTTCTTTTTATCTT 58.858 33.333 0.00 0.00 0.00 2.40
2304 2743 7.286775 TGGCCAGTAACTGTTTTCTTTTTATCT 59.713 33.333 0.00 0.00 0.00 1.98
2305 2744 7.430441 TGGCCAGTAACTGTTTTCTTTTTATC 58.570 34.615 0.00 0.00 0.00 1.75
2306 2745 7.354751 TGGCCAGTAACTGTTTTCTTTTTAT 57.645 32.000 0.00 0.00 0.00 1.40
2307 2746 6.777213 TGGCCAGTAACTGTTTTCTTTTTA 57.223 33.333 0.00 0.00 0.00 1.52
2308 2747 5.669164 TGGCCAGTAACTGTTTTCTTTTT 57.331 34.783 0.00 0.00 0.00 1.94
2309 2748 5.669164 TTGGCCAGTAACTGTTTTCTTTT 57.331 34.783 5.11 0.00 0.00 2.27
2310 2749 5.869649 ATTGGCCAGTAACTGTTTTCTTT 57.130 34.783 5.11 0.00 0.00 2.52
2311 2750 5.869649 AATTGGCCAGTAACTGTTTTCTT 57.130 34.783 5.11 0.00 0.00 2.52
2312 2751 5.830991 TGTAATTGGCCAGTAACTGTTTTCT 59.169 36.000 5.11 0.00 0.00 2.52
2313 2752 6.079424 TGTAATTGGCCAGTAACTGTTTTC 57.921 37.500 5.11 0.00 0.00 2.29
2314 2753 6.322712 TCTTGTAATTGGCCAGTAACTGTTTT 59.677 34.615 5.11 0.00 0.00 2.43
2315 2754 5.830991 TCTTGTAATTGGCCAGTAACTGTTT 59.169 36.000 5.11 0.00 0.00 2.83
2316 2755 5.381757 TCTTGTAATTGGCCAGTAACTGTT 58.618 37.500 5.11 0.00 0.00 3.16
2317 2756 4.980573 TCTTGTAATTGGCCAGTAACTGT 58.019 39.130 5.11 0.00 0.00 3.55
2318 2757 6.597672 TGTATCTTGTAATTGGCCAGTAACTG 59.402 38.462 5.11 3.56 0.00 3.16
2319 2758 6.717289 TGTATCTTGTAATTGGCCAGTAACT 58.283 36.000 5.11 0.00 0.00 2.24
2320 2759 6.995511 TGTATCTTGTAATTGGCCAGTAAC 57.004 37.500 5.11 5.99 0.00 2.50
2321 2760 8.301002 GTTTTGTATCTTGTAATTGGCCAGTAA 58.699 33.333 5.11 0.00 0.00 2.24
2322 2761 7.448777 TGTTTTGTATCTTGTAATTGGCCAGTA 59.551 33.333 5.11 0.00 0.00 2.74
2323 2762 6.266558 TGTTTTGTATCTTGTAATTGGCCAGT 59.733 34.615 5.11 0.00 0.00 4.00
2324 2763 6.686630 TGTTTTGTATCTTGTAATTGGCCAG 58.313 36.000 5.11 0.00 0.00 4.85
2325 2764 6.656632 TGTTTTGTATCTTGTAATTGGCCA 57.343 33.333 0.00 0.00 0.00 5.36
2326 2765 7.431084 CGTATGTTTTGTATCTTGTAATTGGCC 59.569 37.037 0.00 0.00 0.00 5.36
2327 2766 7.044314 GCGTATGTTTTGTATCTTGTAATTGGC 60.044 37.037 0.00 0.00 0.00 4.52
2328 2767 7.965655 TGCGTATGTTTTGTATCTTGTAATTGG 59.034 33.333 0.00 0.00 0.00 3.16
2329 2768 8.888332 TGCGTATGTTTTGTATCTTGTAATTG 57.112 30.769 0.00 0.00 0.00 2.32
2330 2769 9.900710 TTTGCGTATGTTTTGTATCTTGTAATT 57.099 25.926 0.00 0.00 0.00 1.40
2331 2770 9.900710 TTTTGCGTATGTTTTGTATCTTGTAAT 57.099 25.926 0.00 0.00 0.00 1.89
2332 2771 9.171701 GTTTTGCGTATGTTTTGTATCTTGTAA 57.828 29.630 0.00 0.00 0.00 2.41
2333 2772 7.804129 GGTTTTGCGTATGTTTTGTATCTTGTA 59.196 33.333 0.00 0.00 0.00 2.41
2334 2773 6.639279 GGTTTTGCGTATGTTTTGTATCTTGT 59.361 34.615 0.00 0.00 0.00 3.16
2335 2774 6.638873 TGGTTTTGCGTATGTTTTGTATCTTG 59.361 34.615 0.00 0.00 0.00 3.02
2336 2775 6.740110 TGGTTTTGCGTATGTTTTGTATCTT 58.260 32.000 0.00 0.00 0.00 2.40
2337 2776 6.320494 TGGTTTTGCGTATGTTTTGTATCT 57.680 33.333 0.00 0.00 0.00 1.98
2338 2777 6.994868 TTGGTTTTGCGTATGTTTTGTATC 57.005 33.333 0.00 0.00 0.00 2.24
2339 2778 7.707035 TCTTTTGGTTTTGCGTATGTTTTGTAT 59.293 29.630 0.00 0.00 0.00 2.29
2340 2779 7.033791 TCTTTTGGTTTTGCGTATGTTTTGTA 58.966 30.769 0.00 0.00 0.00 2.41
2341 2780 5.869888 TCTTTTGGTTTTGCGTATGTTTTGT 59.130 32.000 0.00 0.00 0.00 2.83
2342 2781 6.337853 TCTTTTGGTTTTGCGTATGTTTTG 57.662 33.333 0.00 0.00 0.00 2.44
2343 2782 6.456315 GCTTCTTTTGGTTTTGCGTATGTTTT 60.456 34.615 0.00 0.00 0.00 2.43
2344 2783 5.006261 GCTTCTTTTGGTTTTGCGTATGTTT 59.994 36.000 0.00 0.00 0.00 2.83
2345 2784 4.506288 GCTTCTTTTGGTTTTGCGTATGTT 59.494 37.500 0.00 0.00 0.00 2.71
2346 2785 4.048504 GCTTCTTTTGGTTTTGCGTATGT 58.951 39.130 0.00 0.00 0.00 2.29
2347 2786 4.047822 TGCTTCTTTTGGTTTTGCGTATG 58.952 39.130 0.00 0.00 0.00 2.39
2348 2787 4.314740 TGCTTCTTTTGGTTTTGCGTAT 57.685 36.364 0.00 0.00 0.00 3.06
2349 2788 3.784701 TGCTTCTTTTGGTTTTGCGTA 57.215 38.095 0.00 0.00 0.00 4.42
2350 2789 2.663826 TGCTTCTTTTGGTTTTGCGT 57.336 40.000 0.00 0.00 0.00 5.24
2351 2790 2.865551 ACATGCTTCTTTTGGTTTTGCG 59.134 40.909 0.00 0.00 0.00 4.85
2352 2791 4.836455 GAACATGCTTCTTTTGGTTTTGC 58.164 39.130 0.00 0.00 0.00 3.68


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

AutoCloner maintained by Alex Coulton.