Multiple sequence alignment - TraesCS4A01G339200

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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 TraesCS4A01G339200 chr4A 100.000 1856 0 0 1606 3461 621009890 621008035 0.000000e+00 3428.0
1 TraesCS4A01G339200 chr4A 100.000 1260 0 0 1 1260 621011495 621010236 0.000000e+00 2327.0
2 TraesCS4A01G339200 chr4A 84.713 314 44 4 1754 2065 26413808 26413497 9.330000e-81 311.0
3 TraesCS4A01G339200 chr5D 92.203 1398 75 17 2069 3461 549330489 549329121 0.000000e+00 1947.0
4 TraesCS4A01G339200 chr5D 93.279 1235 65 10 1 1224 549332314 549331087 0.000000e+00 1805.0
5 TraesCS4A01G339200 chr5D 97.527 364 8 1 1708 2071 549330938 549330576 3.790000e-174 621.0
6 TraesCS4A01G339200 chr5D 79.200 500 96 8 1747 2242 544799360 544799855 1.190000e-89 340.0
7 TraesCS4A01G339200 chr5B 91.076 1255 72 21 1 1248 700996172 700997393 0.000000e+00 1661.0
8 TraesCS4A01G339200 chr5B 92.689 807 27 20 1708 2497 700997533 700998324 0.000000e+00 1134.0
9 TraesCS4A01G339200 chr5B 80.444 900 109 33 2597 3458 700998436 700999306 2.930000e-175 625.0
10 TraesCS4A01G339200 chr5B 78.270 497 99 9 1747 2239 687212999 687213490 9.330000e-81 311.0
11 TraesCS4A01G339200 chr3A 80.892 628 110 9 1749 2369 170811690 170812314 1.440000e-133 486.0
12 TraesCS4A01G339200 chr3D 80.630 635 113 10 1749 2378 157443377 157442748 1.870000e-132 483.0
13 TraesCS4A01G339200 chr3B 80.671 626 112 9 1749 2369 228690784 228690163 8.690000e-131 477.0
14 TraesCS4A01G339200 chr4B 85.113 309 46 0 1751 2059 547205034 547205342 2.000000e-82 316.0
15 TraesCS4A01G339200 chr4D 74.618 524 123 9 1748 2266 441105777 441106295 4.500000e-54 222.0
16 TraesCS4A01G339200 chr4D 75.401 187 34 9 2845 3021 87413719 87413903 2.860000e-11 80.5
17 TraesCS4A01G339200 chr1D 79.070 129 18 6 2845 2965 135394092 135394219 2.860000e-11 80.5
18 TraesCS4A01G339200 chr7A 76.336 131 22 6 2844 2965 398939326 398939196 1.040000e-05 62.1
19 TraesCS4A01G339200 chr7D 100.000 30 0 0 2841 2870 4582954 4582983 4.830000e-04 56.5
20 TraesCS4A01G339200 chr7B 96.970 33 1 0 2841 2873 85306559 85306591 4.830000e-04 56.5
21 TraesCS4A01G339200 chr6D 100.000 29 0 0 2845 2873 430268481 430268453 2.000000e-03 54.7
22 TraesCS4A01G339200 chr1A 100.000 28 0 0 2845 2872 161678039 161678012 6.000000e-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 TraesCS4A01G339200 chr4A 621008035 621011495 3460 True 2877.500000 3428 100.000000 1 3461 2 chr4A.!!$R2 3460
1 TraesCS4A01G339200 chr5D 549329121 549332314 3193 True 1457.666667 1947 94.336333 1 3461 3 chr5D.!!$R1 3460
2 TraesCS4A01G339200 chr5B 700996172 700999306 3134 False 1140.000000 1661 88.069667 1 3458 3 chr5B.!!$F2 3457
3 TraesCS4A01G339200 chr3A 170811690 170812314 624 False 486.000000 486 80.892000 1749 2369 1 chr3A.!!$F1 620
4 TraesCS4A01G339200 chr3D 157442748 157443377 629 True 483.000000 483 80.630000 1749 2378 1 chr3D.!!$R1 629
5 TraesCS4A01G339200 chr3B 228690163 228690784 621 True 477.000000 477 80.671000 1749 2369 1 chr3B.!!$R1 620
6 TraesCS4A01G339200 chr4D 441105777 441106295 518 False 222.000000 222 74.618000 1748 2266 1 chr4D.!!$F2 518

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
260 263 0.390492 CATAGGCTCATGTGGCGAGA 59.610 55.0 14.7 6.0 37.59 4.04 F
1047 1064 0.750850 TCGGCCCAAGCAGTACTATC 59.249 55.0 0.0 0.0 42.56 2.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1117 1134 0.176680 AGGCTATTCCACAGAGCACG 59.823 55.0 0.0 0.0 37.98 5.34 R
2545 2688 0.475906 AGGTGCAAGAAAGAGTGCCT 59.524 50.0 0.0 0.0 40.14 4.75 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
29 31 8.739108 ATGGATCCAGTACTACTAGTCTACTA 57.261 38.462 21.33 0.00 0.00 1.82
81 83 8.738106 GGTTAGACTTAGTGTACATACAAGTCT 58.262 37.037 31.05 31.05 45.98 3.24
191 194 5.482878 AGCCTACTGTTAGTTTAGCCAAGTA 59.517 40.000 0.00 0.00 0.00 2.24
216 219 4.492494 TCACATATCAGAACATGGCACT 57.508 40.909 0.00 0.00 0.00 4.40
217 220 5.612725 TCACATATCAGAACATGGCACTA 57.387 39.130 0.00 0.00 0.00 2.74
236 239 5.679127 GCACTATACCCTGACAACAGTAGAC 60.679 48.000 0.00 0.00 42.05 2.59
260 263 0.390492 CATAGGCTCATGTGGCGAGA 59.610 55.000 14.70 6.00 37.59 4.04
287 290 4.216042 TGCCTTGTGTGATGTTAATGTGAG 59.784 41.667 0.00 0.00 0.00 3.51
288 291 4.726416 CCTTGTGTGATGTTAATGTGAGC 58.274 43.478 0.00 0.00 0.00 4.26
292 295 3.438087 GTGTGATGTTAATGTGAGCAGCT 59.562 43.478 0.00 0.00 0.00 4.24
296 299 4.633126 TGATGTTAATGTGAGCAGCTTCTC 59.367 41.667 6.41 6.41 0.00 2.87
352 355 7.789273 AATTTTGAGATGTGCAAATTTCACA 57.211 28.000 9.56 19.03 46.86 3.58
418 421 9.872721 AACATGTTAATTTTGATATGTGCATGA 57.127 25.926 9.97 0.00 35.41 3.07
600 607 5.295950 AGATTAGGACATTCAAGCATCTCG 58.704 41.667 0.00 0.00 0.00 4.04
675 682 3.924114 TGGTCAGACTCTTTGTTTCCA 57.076 42.857 0.00 0.00 0.00 3.53
709 716 3.555139 TGGTTGAATTTTTCAGCGCAAAG 59.445 39.130 11.47 0.00 41.20 2.77
783 790 2.146342 ACAGTGCAGGAATTTGTCGAG 58.854 47.619 0.00 0.00 0.00 4.04
784 791 2.224281 ACAGTGCAGGAATTTGTCGAGA 60.224 45.455 0.00 0.00 0.00 4.04
786 793 1.126846 GTGCAGGAATTTGTCGAGACG 59.873 52.381 0.00 0.00 0.00 4.18
913 920 3.391355 CGGCTAAGTTAACCCGCG 58.609 61.111 0.00 0.00 33.77 6.46
925 932 2.125673 CCCGCGAGTACCCAACTG 60.126 66.667 8.23 0.00 39.07 3.16
934 941 3.064931 GAGTACCCAACTGCAACTGTAC 58.935 50.000 0.00 0.00 39.07 2.90
989 1003 2.142292 AAAGCCCAGGGTGCAGTAGG 62.142 60.000 7.55 0.00 0.00 3.18
1003 1017 3.637694 TGCAGTAGGTACACAGTACACAA 59.362 43.478 9.27 0.00 0.00 3.33
1004 1018 4.235360 GCAGTAGGTACACAGTACACAAG 58.765 47.826 9.27 0.00 0.00 3.16
1018 1035 4.876107 AGTACACAAGGCACAGCATATTAC 59.124 41.667 0.00 0.00 0.00 1.89
1038 1055 3.435186 GACTTGCTCGGCCCAAGC 61.435 66.667 17.27 16.74 42.57 4.01
1044 1061 2.982130 CTCGGCCCAAGCAGTACT 59.018 61.111 0.00 0.00 42.56 2.73
1045 1062 1.956629 GCTCGGCCCAAGCAGTACTA 61.957 60.000 17.71 0.00 42.56 1.82
1046 1063 0.753262 CTCGGCCCAAGCAGTACTAT 59.247 55.000 0.00 0.00 42.56 2.12
1047 1064 0.750850 TCGGCCCAAGCAGTACTATC 59.249 55.000 0.00 0.00 42.56 2.08
1048 1065 0.753262 CGGCCCAAGCAGTACTATCT 59.247 55.000 0.00 0.00 42.56 1.98
1049 1066 1.269831 CGGCCCAAGCAGTACTATCTC 60.270 57.143 0.00 0.00 42.56 2.75
1050 1067 1.070914 GGCCCAAGCAGTACTATCTCC 59.929 57.143 0.00 0.00 42.56 3.71
1051 1068 1.070914 GCCCAAGCAGTACTATCTCCC 59.929 57.143 0.00 0.00 39.53 4.30
1052 1069 2.683768 CCCAAGCAGTACTATCTCCCT 58.316 52.381 0.00 0.00 0.00 4.20
1053 1070 2.630580 CCCAAGCAGTACTATCTCCCTC 59.369 54.545 0.00 0.00 0.00 4.30
1054 1071 3.571590 CCAAGCAGTACTATCTCCCTCT 58.428 50.000 0.00 0.00 0.00 3.69
1055 1072 3.572255 CCAAGCAGTACTATCTCCCTCTC 59.428 52.174 0.00 0.00 0.00 3.20
1056 1073 4.469657 CAAGCAGTACTATCTCCCTCTCT 58.530 47.826 0.00 0.00 0.00 3.10
1057 1074 4.098914 AGCAGTACTATCTCCCTCTCTG 57.901 50.000 0.00 0.00 0.00 3.35
1058 1075 3.461831 AGCAGTACTATCTCCCTCTCTGT 59.538 47.826 0.00 0.00 0.00 3.41
1059 1076 3.818773 GCAGTACTATCTCCCTCTCTGTC 59.181 52.174 0.00 0.00 0.00 3.51
1060 1077 4.445735 GCAGTACTATCTCCCTCTCTGTCT 60.446 50.000 0.00 0.00 0.00 3.41
1083 1100 5.323581 TGTCATCTTCAACAATCCAATGGA 58.676 37.500 3.67 3.67 35.55 3.41
1087 1104 6.720748 TCATCTTCAACAATCCAATGGAGAAA 59.279 34.615 8.40 0.00 34.05 2.52
1135 1152 1.432270 GCGTGCTCTGTGGAATAGCC 61.432 60.000 0.00 0.00 35.33 3.93
1223 1244 4.033776 CCGGCACCATGGGTCAGT 62.034 66.667 18.09 0.00 31.02 3.41
1224 1245 2.436646 CGGCACCATGGGTCAGTC 60.437 66.667 18.09 3.44 31.02 3.51
1225 1246 2.756400 GGCACCATGGGTCAGTCA 59.244 61.111 18.09 0.00 31.02 3.41
1226 1247 1.377725 GGCACCATGGGTCAGTCAG 60.378 63.158 18.09 0.00 31.02 3.51
1233 1254 2.938301 TGGGTCAGTCAGTTTCCCA 58.062 52.632 0.00 0.00 44.76 4.37
1234 1255 0.472471 TGGGTCAGTCAGTTTCCCAC 59.528 55.000 0.00 0.00 42.52 4.61
1235 1256 0.765510 GGGTCAGTCAGTTTCCCACT 59.234 55.000 0.00 0.00 38.15 4.00
1237 1258 1.416401 GGTCAGTCAGTTTCCCACTCA 59.584 52.381 0.00 0.00 30.92 3.41
1248 1269 5.467063 CAGTTTCCCACTCACTTCTTTACTC 59.533 44.000 0.00 0.00 30.92 2.59
1251 1272 4.742012 TCCCACTCACTTCTTTACTCTCT 58.258 43.478 0.00 0.00 0.00 3.10
1252 1273 4.767928 TCCCACTCACTTCTTTACTCTCTC 59.232 45.833 0.00 0.00 0.00 3.20
1253 1274 4.770010 CCCACTCACTTCTTTACTCTCTCT 59.230 45.833 0.00 0.00 0.00 3.10
1254 1275 5.105917 CCCACTCACTTCTTTACTCTCTCTC 60.106 48.000 0.00 0.00 0.00 3.20
1255 1276 5.710099 CCACTCACTTCTTTACTCTCTCTCT 59.290 44.000 0.00 0.00 0.00 3.10
1256 1277 6.128007 CCACTCACTTCTTTACTCTCTCTCTC 60.128 46.154 0.00 0.00 0.00 3.20
1257 1278 6.655003 CACTCACTTCTTTACTCTCTCTCTCT 59.345 42.308 0.00 0.00 0.00 3.10
1258 1279 6.879458 ACTCACTTCTTTACTCTCTCTCTCTC 59.121 42.308 0.00 0.00 0.00 3.20
1642 1666 9.182214 TGTAAATAGAGGAGTAGATTTGTACGT 57.818 33.333 0.00 0.00 0.00 3.57
1646 1670 6.680874 AGAGGAGTAGATTTGTACGTAGTG 57.319 41.667 0.00 0.00 45.73 2.74
1647 1671 6.179040 AGAGGAGTAGATTTGTACGTAGTGT 58.821 40.000 0.00 0.00 45.73 3.55
1648 1672 7.334090 AGAGGAGTAGATTTGTACGTAGTGTA 58.666 38.462 0.00 0.00 45.73 2.90
1664 1688 2.095567 AGTGTACCGTGTACGTGTGATC 60.096 50.000 0.00 0.00 37.74 2.92
1667 1691 3.940852 TGTACCGTGTACGTGTGATCTAT 59.059 43.478 0.00 0.00 37.74 1.98
1672 1696 5.007430 ACCGTGTACGTGTGATCTATTCTAG 59.993 44.000 0.00 0.00 37.74 2.43
1685 1713 8.424918 GTGATCTATTCTAGTCATCCAAAGGAA 58.575 37.037 0.00 0.00 34.34 3.36
1689 1717 8.826765 TCTATTCTAGTCATCCAAAGGAAAAGT 58.173 33.333 0.00 0.00 34.34 2.66
1690 1718 7.693969 ATTCTAGTCATCCAAAGGAAAAGTG 57.306 36.000 0.00 0.00 34.34 3.16
1691 1719 6.187727 TCTAGTCATCCAAAGGAAAAGTGT 57.812 37.500 0.00 0.00 34.34 3.55
1692 1720 6.231211 TCTAGTCATCCAAAGGAAAAGTGTC 58.769 40.000 0.00 0.00 34.34 3.67
1693 1721 4.792068 AGTCATCCAAAGGAAAAGTGTCA 58.208 39.130 0.00 0.00 34.34 3.58
1694 1722 4.823989 AGTCATCCAAAGGAAAAGTGTCAG 59.176 41.667 0.00 0.00 34.34 3.51
1695 1723 3.569701 TCATCCAAAGGAAAAGTGTCAGC 59.430 43.478 0.00 0.00 34.34 4.26
1696 1724 3.297134 TCCAAAGGAAAAGTGTCAGCT 57.703 42.857 0.00 0.00 0.00 4.24
1697 1725 4.431416 TCCAAAGGAAAAGTGTCAGCTA 57.569 40.909 0.00 0.00 0.00 3.32
1698 1726 4.389374 TCCAAAGGAAAAGTGTCAGCTAG 58.611 43.478 0.00 0.00 0.00 3.42
1699 1727 3.057946 CCAAAGGAAAAGTGTCAGCTAGC 60.058 47.826 6.62 6.62 0.00 3.42
1700 1728 3.778954 AAGGAAAAGTGTCAGCTAGCT 57.221 42.857 12.68 12.68 0.00 3.32
1701 1729 3.326836 AGGAAAAGTGTCAGCTAGCTC 57.673 47.619 16.15 5.23 0.00 4.09
1702 1730 2.903135 AGGAAAAGTGTCAGCTAGCTCT 59.097 45.455 16.15 6.00 0.00 4.09
1703 1731 3.326297 AGGAAAAGTGTCAGCTAGCTCTT 59.674 43.478 16.15 12.41 0.00 2.85
1704 1732 3.434984 GGAAAAGTGTCAGCTAGCTCTTG 59.565 47.826 16.15 5.03 0.00 3.02
1705 1733 2.758736 AAGTGTCAGCTAGCTCTTGG 57.241 50.000 16.15 3.52 0.00 3.61
1706 1734 1.638529 AGTGTCAGCTAGCTCTTGGT 58.361 50.000 16.15 0.00 0.00 3.67
1713 1741 2.676839 CAGCTAGCTCTTGGTTGATGTG 59.323 50.000 16.15 0.00 30.73 3.21
1729 1757 6.459298 GGTTGATGTGGATCTGATGATGTTTC 60.459 42.308 0.00 0.00 32.19 2.78
1742 1770 9.678941 TCTGATGATGTTTCTATCGTATGTAAC 57.321 33.333 0.00 0.00 0.00 2.50
1785 1823 1.741770 CGGCAACCTGTACAGCTCC 60.742 63.158 17.86 12.80 0.00 4.70
2396 2527 4.138722 GCGTCTAGCGGATCATCG 57.861 61.111 8.31 0.00 41.69 3.84
2398 2529 0.726452 GCGTCTAGCGGATCATCGTC 60.726 60.000 8.31 0.00 41.69 4.20
2399 2530 0.586802 CGTCTAGCGGATCATCGTCA 59.413 55.000 0.00 0.00 36.85 4.35
2400 2531 1.002792 CGTCTAGCGGATCATCGTCAA 60.003 52.381 0.00 0.00 36.85 3.18
2402 2533 2.789893 GTCTAGCGGATCATCGTCAAAC 59.210 50.000 0.00 0.00 0.00 2.93
2403 2534 2.128035 CTAGCGGATCATCGTCAAACC 58.872 52.381 0.00 0.00 0.00 3.27
2404 2535 0.806102 AGCGGATCATCGTCAAACCG 60.806 55.000 0.00 0.00 42.63 4.44
2405 2536 0.804544 GCGGATCATCGTCAAACCGA 60.805 55.000 0.00 0.00 42.40 4.69
2407 2538 1.787155 CGGATCATCGTCAAACCGATC 59.213 52.381 0.00 0.00 45.25 3.69
2425 2556 1.153647 CCATCGACGCCACTGCTTA 60.154 57.895 0.00 0.00 34.43 3.09
2426 2557 0.739462 CCATCGACGCCACTGCTTAA 60.739 55.000 0.00 0.00 34.43 1.85
2428 2559 1.258982 CATCGACGCCACTGCTTAATC 59.741 52.381 0.00 0.00 34.43 1.75
2429 2560 0.800683 TCGACGCCACTGCTTAATCG 60.801 55.000 0.00 0.00 34.43 3.34
2497 2637 2.120232 CCTCTGTTGCGTTCGCTATAG 58.880 52.381 17.63 16.53 0.00 1.31
2525 2668 3.853330 CAGCCGCACATTCGTCCG 61.853 66.667 0.00 0.00 0.00 4.79
2534 2677 2.222445 GCACATTCGTCCGTGTTTTACT 59.778 45.455 0.00 0.00 35.51 2.24
2536 2679 4.787245 GCACATTCGTCCGTGTTTTACTTT 60.787 41.667 0.00 0.00 35.51 2.66
2537 2680 5.267776 CACATTCGTCCGTGTTTTACTTTT 58.732 37.500 0.00 0.00 0.00 2.27
2539 2682 6.572254 CACATTCGTCCGTGTTTTACTTTTAG 59.428 38.462 0.00 0.00 0.00 1.85
2540 2683 6.479660 ACATTCGTCCGTGTTTTACTTTTAGA 59.520 34.615 0.00 0.00 0.00 2.10
2541 2684 7.172019 ACATTCGTCCGTGTTTTACTTTTAGAT 59.828 33.333 0.00 0.00 0.00 1.98
2542 2685 7.481275 TTCGTCCGTGTTTTACTTTTAGATT 57.519 32.000 0.00 0.00 0.00 2.40
2543 2686 8.586570 TTCGTCCGTGTTTTACTTTTAGATTA 57.413 30.769 0.00 0.00 0.00 1.75
2545 2688 8.081633 TCGTCCGTGTTTTACTTTTAGATTAGA 58.918 33.333 0.00 0.00 0.00 2.10
2546 2689 8.371053 CGTCCGTGTTTTACTTTTAGATTAGAG 58.629 37.037 0.00 0.00 0.00 2.43
2547 2690 8.654215 GTCCGTGTTTTACTTTTAGATTAGAGG 58.346 37.037 0.00 0.00 0.00 3.69
2585 2746 7.497595 CACCTACACATAATAACCTGAAGCTA 58.502 38.462 0.00 0.00 0.00 3.32
2586 2747 7.985184 CACCTACACATAATAACCTGAAGCTAA 59.015 37.037 0.00 0.00 0.00 3.09
2587 2748 8.714906 ACCTACACATAATAACCTGAAGCTAAT 58.285 33.333 0.00 0.00 0.00 1.73
2588 2749 9.561069 CCTACACATAATAACCTGAAGCTAATT 57.439 33.333 0.00 0.00 0.00 1.40
2591 2752 8.893727 ACACATAATAACCTGAAGCTAATTCAC 58.106 33.333 0.00 0.00 43.09 3.18
2592 2753 8.892723 CACATAATAACCTGAAGCTAATTCACA 58.107 33.333 0.00 0.00 43.09 3.58
2593 2754 9.461312 ACATAATAACCTGAAGCTAATTCACAA 57.539 29.630 0.00 0.00 43.09 3.33
2625 2786 0.171007 GCACACAATGCGCACCTAAT 59.829 50.000 14.90 0.00 46.55 1.73
2652 2813 9.511144 AAGAATTGTAAAAGAAAAACTGTACGG 57.489 29.630 0.00 0.00 0.00 4.02
2831 2999 4.581309 TGAGGGCTTTTGAATGAGATCT 57.419 40.909 0.00 0.00 0.00 2.75
2836 3004 7.284034 TGAGGGCTTTTGAATGAGATCTATTTC 59.716 37.037 0.00 2.64 0.00 2.17
2886 3079 8.871686 AACTTGGTATGACAAAAATCAAAGTC 57.128 30.769 0.00 0.00 28.98 3.01
2890 3083 7.874940 TGGTATGACAAAAATCAAAGTCTCAG 58.125 34.615 0.00 0.00 30.82 3.35
2986 3179 2.494445 CGCGGATAGACAGGTGCA 59.506 61.111 0.00 0.00 0.00 4.57
2999 3192 2.048603 GGTGCATGCTCCTTCACCC 61.049 63.158 27.58 7.75 42.25 4.61
3000 3193 1.303561 GTGCATGCTCCTTCACCCA 60.304 57.895 20.33 0.00 0.00 4.51
3041 3234 4.021894 CCGAGCATACTTCCAACTATAGCT 60.022 45.833 0.00 0.00 0.00 3.32
3042 3235 5.183331 CCGAGCATACTTCCAACTATAGCTA 59.817 44.000 0.00 0.00 0.00 3.32
3043 3236 6.318628 CGAGCATACTTCCAACTATAGCTAG 58.681 44.000 0.00 0.00 0.00 3.42
3044 3237 6.597832 AGCATACTTCCAACTATAGCTAGG 57.402 41.667 0.00 0.00 0.00 3.02
3045 3238 5.482175 AGCATACTTCCAACTATAGCTAGGG 59.518 44.000 0.00 0.00 0.00 3.53
3046 3239 5.725362 CATACTTCCAACTATAGCTAGGGC 58.275 45.833 0.00 0.00 39.06 5.19
3081 3275 7.609056 AGTTATCTCAAACCGAGCTAAACTAA 58.391 34.615 0.00 0.00 41.98 2.24
3085 3279 6.698380 TCTCAAACCGAGCTAAACTAATCTT 58.302 36.000 0.00 0.00 41.98 2.40
3086 3280 6.590292 TCTCAAACCGAGCTAAACTAATCTTG 59.410 38.462 0.00 0.00 41.98 3.02
3094 3288 5.169295 AGCTAAACTAATCTTGTCGTCACC 58.831 41.667 0.00 0.00 0.00 4.02
3095 3289 4.329256 GCTAAACTAATCTTGTCGTCACCC 59.671 45.833 0.00 0.00 0.00 4.61
3122 3316 0.108138 CAACTCGAGGCAACCCTAGG 60.108 60.000 18.41 0.06 43.12 3.02
3418 3613 2.609610 GGGTAGGGGGTGAGTGCA 60.610 66.667 0.00 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 31 5.130975 TCCTGCAGGTCAATCATGTATTAGT 59.869 40.000 31.58 0.00 36.34 2.24
81 83 8.786826 ACGGACAATTATTTCAGTTAGATTGA 57.213 30.769 0.00 0.00 0.00 2.57
113 116 3.065786 GGTATGCTACGCACTAGTGTACA 59.934 47.826 23.44 14.43 43.04 2.90
172 175 8.565416 GTGATTTTACTTGGCTAAACTAACAGT 58.435 33.333 0.00 0.00 0.00 3.55
191 194 6.379133 AGTGCCATGTTCTGATATGTGATTTT 59.621 34.615 0.00 0.00 0.00 1.82
216 219 4.401519 GCAGTCTACTGTTGTCAGGGTATA 59.598 45.833 11.54 0.00 45.45 1.47
217 220 3.195825 GCAGTCTACTGTTGTCAGGGTAT 59.804 47.826 11.54 0.00 45.45 2.73
255 258 0.445436 CACACAAGGCAAGATCTCGC 59.555 55.000 0.00 0.00 0.00 5.03
256 259 2.084610 TCACACAAGGCAAGATCTCG 57.915 50.000 0.00 0.00 0.00 4.04
260 263 5.477984 ACATTAACATCACACAAGGCAAGAT 59.522 36.000 0.00 0.00 0.00 2.40
287 290 0.391661 TTGACATCCCGAGAAGCTGC 60.392 55.000 0.00 0.00 0.00 5.25
288 291 1.649664 CTTGACATCCCGAGAAGCTG 58.350 55.000 0.00 0.00 0.00 4.24
292 295 1.218047 CCGCTTGACATCCCGAGAA 59.782 57.895 0.00 0.00 0.00 2.87
296 299 2.819595 CCACCGCTTGACATCCCG 60.820 66.667 0.00 0.00 0.00 5.14
350 353 5.048921 CGTATCACTTATACCTCACCGATGT 60.049 44.000 0.00 0.00 37.73 3.06
352 355 5.068636 ACGTATCACTTATACCTCACCGAT 58.931 41.667 0.00 0.00 37.73 4.18
520 527 4.274459 CGAATGGATCTCAACCTGGATTTC 59.726 45.833 0.00 0.00 0.00 2.17
578 585 5.053145 ACGAGATGCTTGAATGTCCTAATC 58.947 41.667 0.00 0.00 0.00 1.75
600 607 9.137459 TCTATTGCAGCTATAGGAGGATATAAC 57.863 37.037 19.85 0.00 0.00 1.89
709 716 1.293924 CCGTGCATGTGAGAGAATCC 58.706 55.000 4.96 0.00 33.66 3.01
759 766 1.610522 ACAAATTCCTGCACTGTCAGC 59.389 47.619 0.00 0.00 32.87 4.26
783 790 4.986659 TGCTCCAAGAAGTTTAACTACGTC 59.013 41.667 0.00 0.00 0.00 4.34
784 791 4.952460 TGCTCCAAGAAGTTTAACTACGT 58.048 39.130 0.00 0.00 0.00 3.57
786 793 7.387948 TCTTGATGCTCCAAGAAGTTTAACTAC 59.612 37.037 15.59 0.00 46.59 2.73
912 919 1.148310 CAGTTGCAGTTGGGTACTCG 58.852 55.000 0.00 0.00 33.85 4.18
913 920 2.256117 ACAGTTGCAGTTGGGTACTC 57.744 50.000 4.79 0.00 33.85 2.59
934 941 4.252073 GAGCATGCATATCCTCTAACTGG 58.748 47.826 21.98 0.00 0.00 4.00
989 1003 2.800544 CTGTGCCTTGTGTACTGTGTAC 59.199 50.000 0.00 1.33 0.00 2.90
1003 1017 4.494091 AGTCTTGTAATATGCTGTGCCT 57.506 40.909 0.00 0.00 0.00 4.75
1004 1018 4.731773 GCAAGTCTTGTAATATGCTGTGCC 60.732 45.833 14.03 0.00 0.00 5.01
1018 1035 1.580845 CTTGGGCCGAGCAAGTCTTG 61.581 60.000 8.12 8.31 0.00 3.02
1038 1055 5.063204 CAGACAGAGAGGGAGATAGTACTG 58.937 50.000 5.39 0.00 0.00 2.74
1040 1057 5.043737 ACAGACAGAGAGGGAGATAGTAC 57.956 47.826 0.00 0.00 0.00 2.73
1044 1061 4.415179 AGATGACAGACAGAGAGGGAGATA 59.585 45.833 0.00 0.00 0.00 1.98
1045 1062 3.205056 AGATGACAGACAGAGAGGGAGAT 59.795 47.826 0.00 0.00 0.00 2.75
1046 1063 2.580322 AGATGACAGACAGAGAGGGAGA 59.420 50.000 0.00 0.00 0.00 3.71
1047 1064 3.017048 AGATGACAGACAGAGAGGGAG 57.983 52.381 0.00 0.00 0.00 4.30
1048 1065 3.245407 TGAAGATGACAGACAGAGAGGGA 60.245 47.826 0.00 0.00 0.00 4.20
1049 1066 3.095332 TGAAGATGACAGACAGAGAGGG 58.905 50.000 0.00 0.00 0.00 4.30
1050 1067 4.021632 TGTTGAAGATGACAGACAGAGAGG 60.022 45.833 0.00 0.00 0.00 3.69
1051 1068 5.131594 TGTTGAAGATGACAGACAGAGAG 57.868 43.478 0.00 0.00 0.00 3.20
1052 1069 5.535753 TTGTTGAAGATGACAGACAGAGA 57.464 39.130 0.00 0.00 0.00 3.10
1053 1070 5.350914 GGATTGTTGAAGATGACAGACAGAG 59.649 44.000 0.00 0.00 0.00 3.35
1054 1071 5.221702 TGGATTGTTGAAGATGACAGACAGA 60.222 40.000 0.00 0.00 0.00 3.41
1055 1072 4.999311 TGGATTGTTGAAGATGACAGACAG 59.001 41.667 0.00 0.00 0.00 3.51
1056 1073 4.971939 TGGATTGTTGAAGATGACAGACA 58.028 39.130 0.00 0.00 0.00 3.41
1057 1074 5.947228 TTGGATTGTTGAAGATGACAGAC 57.053 39.130 0.00 0.00 0.00 3.51
1058 1075 5.416639 CCATTGGATTGTTGAAGATGACAGA 59.583 40.000 0.00 0.00 0.00 3.41
1059 1076 5.416639 TCCATTGGATTGTTGAAGATGACAG 59.583 40.000 0.00 0.00 0.00 3.51
1060 1077 5.323581 TCCATTGGATTGTTGAAGATGACA 58.676 37.500 0.00 0.00 0.00 3.58
1083 1100 2.366916 AGTGCTACTGCTGTCTGTTTCT 59.633 45.455 0.00 0.00 40.48 2.52
1087 1104 2.230025 CACTAGTGCTACTGCTGTCTGT 59.770 50.000 10.54 0.00 40.48 3.41
1111 1128 3.117171 CCACAGAGCACGCTGAGC 61.117 66.667 8.44 0.00 39.20 4.26
1115 1132 0.460987 GCTATTCCACAGAGCACGCT 60.461 55.000 0.00 0.00 36.20 5.07
1117 1134 0.176680 AGGCTATTCCACAGAGCACG 59.823 55.000 0.00 0.00 37.98 5.34
1135 1152 2.105128 GCGTCGACCCCATGAGAG 59.895 66.667 10.58 0.00 0.00 3.20
1213 1230 1.073763 TGGGAAACTGACTGACCCATG 59.926 52.381 0.00 0.00 44.50 3.66
1223 1244 4.503714 AAAGAAGTGAGTGGGAAACTGA 57.496 40.909 0.00 0.00 40.07 3.41
1224 1245 5.368989 AGTAAAGAAGTGAGTGGGAAACTG 58.631 41.667 0.00 0.00 40.07 3.16
1225 1246 5.367060 AGAGTAAAGAAGTGAGTGGGAAACT 59.633 40.000 0.00 0.00 43.85 2.66
1226 1247 5.612351 AGAGTAAAGAAGTGAGTGGGAAAC 58.388 41.667 0.00 0.00 0.00 2.78
1233 1254 6.779860 AGAGAGAGAGAGTAAAGAAGTGAGT 58.220 40.000 0.00 0.00 0.00 3.41
1234 1255 7.106239 AGAGAGAGAGAGAGTAAAGAAGTGAG 58.894 42.308 0.00 0.00 0.00 3.51
1235 1256 7.016153 AGAGAGAGAGAGAGTAAAGAAGTGA 57.984 40.000 0.00 0.00 0.00 3.41
1605 1626 7.271511 ACTCCTCTATTTACAATTGCAGAGAG 58.728 38.462 5.05 10.75 32.98 3.20
1606 1627 7.187824 ACTCCTCTATTTACAATTGCAGAGA 57.812 36.000 5.05 1.46 32.98 3.10
1607 1628 8.417106 TCTACTCCTCTATTTACAATTGCAGAG 58.583 37.037 5.05 9.43 0.00 3.35
1608 1629 8.306313 TCTACTCCTCTATTTACAATTGCAGA 57.694 34.615 5.05 0.25 0.00 4.26
1609 1630 9.553064 AATCTACTCCTCTATTTACAATTGCAG 57.447 33.333 5.05 0.00 0.00 4.41
1610 1631 9.905713 AAATCTACTCCTCTATTTACAATTGCA 57.094 29.630 5.05 0.00 0.00 4.08
1622 1644 7.334090 ACACTACGTACAAATCTACTCCTCTA 58.666 38.462 0.00 0.00 0.00 2.43
1623 1645 6.179040 ACACTACGTACAAATCTACTCCTCT 58.821 40.000 0.00 0.00 0.00 3.69
1640 1664 1.194547 ACACGTACACGGTACACTACG 59.805 52.381 6.72 2.58 44.95 3.51
1641 1665 2.223144 TCACACGTACACGGTACACTAC 59.777 50.000 6.72 0.00 44.95 2.73
1642 1666 2.488952 TCACACGTACACGGTACACTA 58.511 47.619 6.72 0.00 44.95 2.74
1643 1667 1.308047 TCACACGTACACGGTACACT 58.692 50.000 6.72 0.00 44.95 3.55
1644 1668 2.095567 AGATCACACGTACACGGTACAC 60.096 50.000 6.72 0.00 44.95 2.90
1645 1669 2.153645 AGATCACACGTACACGGTACA 58.846 47.619 6.72 0.00 44.95 2.90
1646 1670 2.907910 AGATCACACGTACACGGTAC 57.092 50.000 6.72 0.00 44.95 3.34
1647 1671 4.877823 AGAATAGATCACACGTACACGGTA 59.122 41.667 6.72 0.00 44.95 4.02
1648 1672 3.693085 AGAATAGATCACACGTACACGGT 59.307 43.478 6.72 0.00 44.95 4.83
1649 1673 4.288670 AGAATAGATCACACGTACACGG 57.711 45.455 6.72 0.00 44.95 4.94
1650 1674 6.045698 ACTAGAATAGATCACACGTACACG 57.954 41.667 0.00 0.00 42.77 4.49
1652 1676 7.041303 GGATGACTAGAATAGATCACACGTACA 60.041 40.741 0.00 0.00 42.77 2.90
1653 1677 7.041303 TGGATGACTAGAATAGATCACACGTAC 60.041 40.741 0.00 0.00 42.77 3.67
1654 1678 6.996282 TGGATGACTAGAATAGATCACACGTA 59.004 38.462 0.00 0.00 42.77 3.57
1655 1679 5.828328 TGGATGACTAGAATAGATCACACGT 59.172 40.000 0.00 0.00 42.77 4.49
1656 1680 6.319141 TGGATGACTAGAATAGATCACACG 57.681 41.667 0.00 0.00 42.77 4.49
1664 1688 8.887717 CACTTTTCCTTTGGATGACTAGAATAG 58.112 37.037 0.00 0.00 46.50 1.73
1667 1691 6.601332 ACACTTTTCCTTTGGATGACTAGAA 58.399 36.000 0.00 0.00 0.00 2.10
1672 1696 4.557496 GCTGACACTTTTCCTTTGGATGAC 60.557 45.833 0.00 0.00 0.00 3.06
1685 1713 2.370189 ACCAAGAGCTAGCTGACACTTT 59.630 45.455 24.99 2.14 0.00 2.66
1689 1717 1.970640 TCAACCAAGAGCTAGCTGACA 59.029 47.619 24.99 0.00 0.00 3.58
1690 1718 2.751166 TCAACCAAGAGCTAGCTGAC 57.249 50.000 24.99 8.88 0.00 3.51
1691 1719 2.568956 ACATCAACCAAGAGCTAGCTGA 59.431 45.455 24.99 12.66 0.00 4.26
1692 1720 2.676839 CACATCAACCAAGAGCTAGCTG 59.323 50.000 24.99 10.36 0.00 4.24
1693 1721 2.355513 CCACATCAACCAAGAGCTAGCT 60.356 50.000 19.45 19.45 0.00 3.32
1694 1722 2.012673 CCACATCAACCAAGAGCTAGC 58.987 52.381 6.62 6.62 0.00 3.42
1695 1723 3.616956 TCCACATCAACCAAGAGCTAG 57.383 47.619 0.00 0.00 0.00 3.42
1696 1724 3.776969 AGATCCACATCAACCAAGAGCTA 59.223 43.478 0.00 0.00 0.00 3.32
1697 1725 2.575279 AGATCCACATCAACCAAGAGCT 59.425 45.455 0.00 0.00 0.00 4.09
1698 1726 2.681848 CAGATCCACATCAACCAAGAGC 59.318 50.000 0.00 0.00 0.00 4.09
1699 1727 4.212143 TCAGATCCACATCAACCAAGAG 57.788 45.455 0.00 0.00 0.00 2.85
1700 1728 4.225717 TCATCAGATCCACATCAACCAAGA 59.774 41.667 0.00 0.00 0.00 3.02
1701 1729 4.520179 TCATCAGATCCACATCAACCAAG 58.480 43.478 0.00 0.00 0.00 3.61
1702 1730 4.573021 TCATCAGATCCACATCAACCAA 57.427 40.909 0.00 0.00 0.00 3.67
1703 1731 4.080186 ACATCATCAGATCCACATCAACCA 60.080 41.667 0.00 0.00 30.20 3.67
1704 1732 4.458397 ACATCATCAGATCCACATCAACC 58.542 43.478 0.00 0.00 30.20 3.77
1705 1733 6.318144 AGAAACATCATCAGATCCACATCAAC 59.682 38.462 0.00 0.00 30.20 3.18
1706 1734 6.420638 AGAAACATCATCAGATCCACATCAA 58.579 36.000 0.00 0.00 30.20 2.57
1713 1741 8.031864 ACATACGATAGAAACATCATCAGATCC 58.968 37.037 0.00 0.00 41.38 3.36
1741 1769 4.873129 CGCGCCTCCTGCATACGT 62.873 66.667 0.00 0.00 41.33 3.57
1742 1770 4.873129 ACGCGCCTCCTGCATACG 62.873 66.667 5.73 0.00 41.33 3.06
1785 1823 1.079875 CGTTGTTGATCCCGTACCCG 61.080 60.000 0.00 0.00 0.00 5.28
2387 2518 3.339061 TCGGTTTGACGATGATCCG 57.661 52.632 0.00 0.00 38.06 4.18
2404 2535 2.240500 GCAGTGGCGTCGATGGATC 61.241 63.158 6.79 0.00 0.00 3.36
2405 2536 2.202932 GCAGTGGCGTCGATGGAT 60.203 61.111 6.79 0.00 0.00 3.41
2416 2547 7.148641 ACTAATGATAGACGATTAAGCAGTGG 58.851 38.462 0.00 0.00 33.15 4.00
2447 2581 7.996644 CCCTACCCTTTGATTTAATACTTGCTA 59.003 37.037 0.00 0.00 0.00 3.49
2448 2582 6.833933 CCCTACCCTTTGATTTAATACTTGCT 59.166 38.462 0.00 0.00 0.00 3.91
2449 2583 6.461092 GCCCTACCCTTTGATTTAATACTTGC 60.461 42.308 0.00 0.00 0.00 4.01
2450 2584 6.238648 CGCCCTACCCTTTGATTTAATACTTG 60.239 42.308 0.00 0.00 0.00 3.16
2461 2595 3.723922 GGGCGCCCTACCCTTTGA 61.724 66.667 38.76 0.00 44.68 2.69
2497 2637 2.658268 GCGGCTGCCAAACACAAC 60.658 61.111 20.29 0.00 33.98 3.32
2525 2668 9.000486 AGTGCCTCTAATCTAAAAGTAAAACAC 58.000 33.333 0.00 0.00 0.00 3.32
2534 2677 7.119846 GCAAGAAAGAGTGCCTCTAATCTAAAA 59.880 37.037 14.90 0.00 40.28 1.52
2536 2679 6.109359 GCAAGAAAGAGTGCCTCTAATCTAA 58.891 40.000 14.90 0.00 40.28 2.10
2537 2680 5.187772 TGCAAGAAAGAGTGCCTCTAATCTA 59.812 40.000 14.90 4.36 40.28 1.98
2539 2682 4.094146 GTGCAAGAAAGAGTGCCTCTAATC 59.906 45.833 5.31 7.25 40.28 1.75
2540 2683 4.006319 GTGCAAGAAAGAGTGCCTCTAAT 58.994 43.478 5.31 0.00 40.28 1.73
2541 2684 3.403038 GTGCAAGAAAGAGTGCCTCTAA 58.597 45.455 5.31 0.00 40.28 2.10
2542 2685 2.289694 GGTGCAAGAAAGAGTGCCTCTA 60.290 50.000 5.31 0.00 40.28 2.43
2543 2686 1.544314 GGTGCAAGAAAGAGTGCCTCT 60.544 52.381 0.00 0.00 43.37 3.69
2545 2688 0.475906 AGGTGCAAGAAAGAGTGCCT 59.524 50.000 0.00 0.00 40.14 4.75
2546 2689 1.807142 GTAGGTGCAAGAAAGAGTGCC 59.193 52.381 0.00 0.00 40.14 5.01
2547 2690 2.224314 GTGTAGGTGCAAGAAAGAGTGC 59.776 50.000 0.00 0.00 41.29 4.40
2585 2746 5.870978 GTGCTTGCCTGATTATTTGTGAATT 59.129 36.000 0.00 0.00 0.00 2.17
2586 2747 5.047164 TGTGCTTGCCTGATTATTTGTGAAT 60.047 36.000 0.00 0.00 0.00 2.57
2587 2748 4.280425 TGTGCTTGCCTGATTATTTGTGAA 59.720 37.500 0.00 0.00 0.00 3.18
2588 2749 3.825585 TGTGCTTGCCTGATTATTTGTGA 59.174 39.130 0.00 0.00 0.00 3.58
2589 2750 3.922240 GTGTGCTTGCCTGATTATTTGTG 59.078 43.478 0.00 0.00 0.00 3.33
2590 2751 3.573538 TGTGTGCTTGCCTGATTATTTGT 59.426 39.130 0.00 0.00 0.00 2.83
2591 2752 4.177165 TGTGTGCTTGCCTGATTATTTG 57.823 40.909 0.00 0.00 0.00 2.32
2592 2753 4.870123 TTGTGTGCTTGCCTGATTATTT 57.130 36.364 0.00 0.00 0.00 1.40
2593 2754 4.751060 CATTGTGTGCTTGCCTGATTATT 58.249 39.130 0.00 0.00 0.00 1.40
2594 2755 4.380841 CATTGTGTGCTTGCCTGATTAT 57.619 40.909 0.00 0.00 0.00 1.28
2595 2756 3.853831 CATTGTGTGCTTGCCTGATTA 57.146 42.857 0.00 0.00 0.00 1.75
2645 2806 1.278238 GCCGTCTTCATTCCGTACAG 58.722 55.000 0.00 0.00 0.00 2.74
2652 2813 0.861837 CCGCTATGCCGTCTTCATTC 59.138 55.000 0.00 0.00 0.00 2.67
2724 2889 3.420839 AAGACTGAAAACAGCAAACCG 57.579 42.857 0.00 0.00 0.00 4.44
2831 2999 7.742963 GCAGTTGAAACTTAACGATTCGAAATA 59.257 33.333 13.95 0.25 37.08 1.40
2836 3004 4.840772 CAGCAGTTGAAACTTAACGATTCG 59.159 41.667 4.14 4.14 37.08 3.34
2886 3079 6.127730 ACAAGTTTTAAGTGTTGGTTCCTGAG 60.128 38.462 0.00 0.00 0.00 3.35
2890 3083 6.641176 CAACAAGTTTTAAGTGTTGGTTCC 57.359 37.500 7.67 0.00 45.35 3.62
2966 3159 2.758327 ACCTGTCTATCCGCGCCA 60.758 61.111 0.00 0.00 0.00 5.69
2974 3167 1.504912 AGGAGCATGCACCTGTCTAT 58.495 50.000 32.49 10.52 35.72 1.98
2986 3179 3.483587 ACGTGGGTGAAGGAGCAT 58.516 55.556 0.00 0.00 0.00 3.79
2999 3192 4.988598 AACTCGCAGGGGCACGTG 62.989 66.667 12.28 12.28 41.24 4.49
3000 3193 4.250305 AAACTCGCAGGGGCACGT 62.250 61.111 0.00 0.00 41.24 4.49
3041 3234 5.903010 TGAGATAACTAGTGAAATGGCCCTA 59.097 40.000 0.00 0.00 0.00 3.53
3042 3235 4.721776 TGAGATAACTAGTGAAATGGCCCT 59.278 41.667 0.00 0.00 0.00 5.19
3043 3236 5.036117 TGAGATAACTAGTGAAATGGCCC 57.964 43.478 0.00 0.00 0.00 5.80
3044 3237 6.183360 GGTTTGAGATAACTAGTGAAATGGCC 60.183 42.308 0.00 0.00 0.00 5.36
3045 3238 6.456988 CGGTTTGAGATAACTAGTGAAATGGC 60.457 42.308 0.00 0.00 0.00 4.40
3046 3239 6.816640 TCGGTTTGAGATAACTAGTGAAATGG 59.183 38.462 0.00 0.00 0.00 3.16
3094 3288 1.741770 CCTCGAGTTGCTTTCCCGG 60.742 63.158 12.31 0.00 0.00 5.73
3095 3289 2.391389 GCCTCGAGTTGCTTTCCCG 61.391 63.158 12.31 0.00 0.00 5.14
3141 3335 1.228398 TCCAATGGCAGCGGTTCAA 60.228 52.632 0.00 0.00 0.00 2.69
3418 3613 5.221263 ACACATAGTTGAGAAGTTCGTCACT 60.221 40.000 0.00 3.52 37.30 3.41


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

AutoCloner maintained by Alex Coulton.