Multiple sequence alignment - TraesCS6A01G242500

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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 TraesCS6A01G242500 chr6A 100.000 2806 0 0 1 2806 454350655 454347850 0.000000e+00 5182.0
1 TraesCS6A01G242500 chr6B 91.187 1736 91 24 154 1867 508184027 508185722 0.000000e+00 2302.0
2 TraesCS6A01G242500 chr6B 89.538 411 38 4 2090 2497 508189605 508190013 1.490000e-142 516.0
3 TraesCS6A01G242500 chr6B 88.502 287 28 5 2497 2779 508190055 508190340 2.680000e-90 342.0
4 TraesCS6A01G242500 chr6B 85.492 193 23 5 1858 2047 508185748 508185938 2.210000e-46 196.0
5 TraesCS6A01G242500 chr6B 90.196 51 2 1 2032 2079 508185959 508186009 2.330000e-06 63.9
6 TraesCS6A01G242500 chr6D 92.543 751 31 8 526 1276 316412511 316411786 0.000000e+00 1053.0
7 TraesCS6A01G242500 chr6D 92.412 738 29 7 1363 2079 316411748 316411017 0.000000e+00 1027.0
8 TraesCS6A01G242500 chr6D 91.822 538 20 9 1 519 316413137 316412605 0.000000e+00 728.0
9 TraesCS6A01G242500 chr6D 89.051 411 39 5 2091 2497 316399619 316399211 3.230000e-139 505.0
10 TraesCS6A01G242500 chr6D 88.780 410 42 3 2091 2497 316401757 316401349 1.500000e-137 499.0
11 TraesCS6A01G242500 chr6D 88.753 409 40 5 2091 2495 316406029 316405623 1.940000e-136 496.0
12 TraesCS6A01G242500 chr6D 88.564 411 41 5 2091 2497 316403894 316403486 6.980000e-136 494.0
13 TraesCS6A01G242500 chr6D 88.293 410 44 3 2091 2497 316408167 316407759 3.250000e-134 488.0
14 TraesCS6A01G242500 chr6D 89.007 282 30 1 2497 2777 316403444 316403163 5.750000e-92 348.0
15 TraesCS6A01G242500 chr6D 89.007 282 30 1 2497 2777 316407717 316407436 5.750000e-92 348.0
16 TraesCS6A01G242500 chr6D 88.298 282 32 1 2497 2777 316399169 316398888 1.250000e-88 337.0
17 TraesCS6A01G242500 chr6D 88.448 277 31 1 2497 2772 316405579 316405303 1.610000e-87 333.0
18 TraesCS6A01G242500 chr6D 88.087 277 32 1 2497 2772 316401307 316401031 7.490000e-86 327.0
19 TraesCS6A01G242500 chrUn 88.564 411 41 5 2091 2497 409720876 409721284 6.980000e-136 494.0
20 TraesCS6A01G242500 chrUn 89.007 282 30 1 2497 2777 409721326 409721607 5.750000e-92 348.0


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 TraesCS6A01G242500 chr6A 454347850 454350655 2805 True 5182.000000 5182 100.000000 1 2806 1 chr6A.!!$R1 2805
1 TraesCS6A01G242500 chr6B 508184027 508190340 6313 False 683.980000 2302 88.983000 154 2779 5 chr6B.!!$F1 2625
2 TraesCS6A01G242500 chr6D 316398888 316413137 14249 True 537.153846 1053 89.466538 1 2777 13 chr6D.!!$R1 2776
3 TraesCS6A01G242500 chrUn 409720876 409721607 731 False 421.000000 494 88.785500 2091 2777 2 chrUn.!!$F1 686

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
176 195 0.451783 GCCCAGTTGTAATTCGGCAG 59.548 55.0 0.00 0.0 36.38 4.85 F
1038 1144 0.324943 TAGCTGCAGGTTTGGTCCTC 59.675 55.0 25.47 0.0 35.37 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1252 1358 0.033366 ACGAACCATTTTGCCAAGCC 59.967 50.0 0.0 0.0 0.00 4.35 R
2678 11553 0.034863 GTTGGGACCTAAATGGCGGA 60.035 55.0 0.0 0.0 40.22 5.54 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
110 112 7.221452 CGTTGTACACAGTACTTTTAGTTCAGT 59.779 37.037 0.00 0.00 0.00 3.41
111 113 7.997107 TGTACACAGTACTTTTAGTTCAGTG 57.003 36.000 8.57 0.00 38.38 3.66
112 114 5.986004 ACACAGTACTTTTAGTTCAGTGC 57.014 39.130 0.00 0.00 36.81 4.40
131 134 5.178623 CAGTGCGGTTATTAAGACAAACTGA 59.821 40.000 0.00 0.00 34.62 3.41
139 142 7.824779 GGTTATTAAGACAAACTGAGTGATCCT 59.175 37.037 0.00 0.00 0.00 3.24
176 195 0.451783 GCCCAGTTGTAATTCGGCAG 59.548 55.000 0.00 0.00 36.38 4.85
200 219 0.928229 GCTAACAACGATGCCTACCG 59.072 55.000 0.00 0.00 0.00 4.02
307 326 9.188588 CACATGCATGAATTAGAATAATTGGTC 57.811 33.333 32.75 0.00 0.00 4.02
414 433 8.934825 GCTTTCTTTCCAAATTATGCACATTTA 58.065 29.630 5.56 0.00 0.00 1.40
433 452 7.480542 CACATTTACTACAAACGGTCTATTTGC 59.519 37.037 0.00 0.00 40.10 3.68
533 639 9.965824 CTATTAAAAATGGTACCATAGCAAAGG 57.034 33.333 27.58 10.93 39.89 3.11
567 673 5.584442 TGCTAATTTGCAGTTGCTGATATG 58.416 37.500 10.62 0.00 42.66 1.78
570 676 3.853831 TTTGCAGTTGCTGATATGTGG 57.146 42.857 5.62 0.00 42.66 4.17
617 723 6.599244 CCAACCTCTAACATGAAATTAGCTGA 59.401 38.462 0.00 0.00 30.95 4.26
638 744 9.033711 AGCTGATCAATATGACTATATGAGTGT 57.966 33.333 0.00 0.00 39.06 3.55
639 745 9.650539 GCTGATCAATATGACTATATGAGTGTT 57.349 33.333 0.00 0.00 39.06 3.32
644 750 9.481340 TCAATATGACTATATGAGTGTTGAAGC 57.519 33.333 0.00 0.00 39.06 3.86
645 751 8.715998 CAATATGACTATATGAGTGTTGAAGCC 58.284 37.037 0.00 0.00 39.06 4.35
646 752 5.675684 TGACTATATGAGTGTTGAAGCCA 57.324 39.130 0.00 0.00 39.06 4.75
647 753 6.048732 TGACTATATGAGTGTTGAAGCCAA 57.951 37.500 0.00 0.00 39.06 4.52
674 780 2.094494 AGTGGCTGTAACGACTGATGAG 60.094 50.000 0.00 0.00 0.00 2.90
848 954 1.107945 ACCCGAACAAACCAAACCAG 58.892 50.000 0.00 0.00 0.00 4.00
864 970 1.135373 ACCAGATCGCGTTAGTCAGTG 60.135 52.381 5.77 0.00 0.00 3.66
937 1043 1.278985 CACCTGCCATCCTTGTACTCA 59.721 52.381 0.00 0.00 0.00 3.41
945 1051 4.194640 CCATCCTTGTACTCACATTCCAG 58.805 47.826 0.00 0.00 33.76 3.86
946 1052 3.334583 TCCTTGTACTCACATTCCAGC 57.665 47.619 0.00 0.00 33.76 4.85
947 1053 2.906389 TCCTTGTACTCACATTCCAGCT 59.094 45.455 0.00 0.00 33.76 4.24
948 1054 3.055819 TCCTTGTACTCACATTCCAGCTC 60.056 47.826 0.00 0.00 33.76 4.09
949 1055 3.265791 CTTGTACTCACATTCCAGCTCC 58.734 50.000 0.00 0.00 33.76 4.70
950 1056 2.256306 TGTACTCACATTCCAGCTCCA 58.744 47.619 0.00 0.00 0.00 3.86
976 1082 5.595952 AGCAAAGTCTCCAAGAATTCAAAGT 59.404 36.000 8.44 0.00 30.49 2.66
1036 1142 1.616159 TTTAGCTGCAGGTTTGGTCC 58.384 50.000 25.47 0.00 0.00 4.46
1037 1143 0.771127 TTAGCTGCAGGTTTGGTCCT 59.229 50.000 25.47 7.60 38.51 3.85
1038 1144 0.324943 TAGCTGCAGGTTTGGTCCTC 59.675 55.000 25.47 0.00 35.37 3.71
1140 1246 2.281761 ACCTGGGCAAGCGACAAG 60.282 61.111 0.00 0.00 0.00 3.16
1206 1312 3.121944 CGATCATTGCTAGTATCAACGGC 59.878 47.826 0.00 0.00 0.00 5.68
1220 1326 2.120232 CAACGGCGCTCTTAGTGATAG 58.880 52.381 6.90 0.00 0.00 2.08
1222 1328 2.569059 ACGGCGCTCTTAGTGATAGTA 58.431 47.619 6.90 0.00 0.00 1.82
1223 1329 2.290093 ACGGCGCTCTTAGTGATAGTAC 59.710 50.000 6.90 0.00 0.00 2.73
1224 1330 2.548904 CGGCGCTCTTAGTGATAGTACT 59.451 50.000 7.64 0.00 34.71 2.73
1225 1331 3.607310 CGGCGCTCTTAGTGATAGTACTG 60.607 52.174 7.64 0.00 32.19 2.74
1226 1332 3.304794 GGCGCTCTTAGTGATAGTACTGG 60.305 52.174 7.64 0.00 32.19 4.00
1227 1333 3.854045 GCGCTCTTAGTGATAGTACTGGC 60.854 52.174 5.39 0.00 32.19 4.85
1270 1376 1.008361 CGGCTTGGCAAAATGGTTCG 61.008 55.000 0.00 0.00 0.00 3.95
1276 1382 1.264557 TGGCAAAATGGTTCGTGTACG 59.735 47.619 0.00 0.00 41.45 3.67
1277 1383 1.264826 GGCAAAATGGTTCGTGTACGT 59.735 47.619 4.20 0.00 40.80 3.57
1311 1417 4.368808 CTTGTTCGCCGGTGCACG 62.369 66.667 11.05 6.23 43.80 5.34
1313 1419 3.786901 TTGTTCGCCGGTGCACGTA 62.787 57.895 11.05 0.00 42.24 3.57
1314 1420 2.812178 GTTCGCCGGTGCACGTAT 60.812 61.111 11.05 0.00 42.24 3.06
1315 1421 2.048033 TTCGCCGGTGCACGTATT 60.048 55.556 11.05 0.00 42.24 1.89
1316 1422 2.384309 TTCGCCGGTGCACGTATTG 61.384 57.895 11.05 0.00 42.24 1.90
1317 1423 3.115892 CGCCGGTGCACGTATTGT 61.116 61.111 11.45 0.00 42.24 2.71
1326 1432 2.673074 CACGTATTGTGTAGGCCGG 58.327 57.895 0.00 0.00 43.88 6.13
1327 1433 1.153509 ACGTATTGTGTAGGCCGGC 60.154 57.895 21.18 21.18 0.00 6.13
1328 1434 1.143183 CGTATTGTGTAGGCCGGCT 59.857 57.895 28.56 15.07 0.00 5.52
1329 1435 0.461339 CGTATTGTGTAGGCCGGCTT 60.461 55.000 28.56 23.35 0.00 4.35
1330 1436 1.746470 GTATTGTGTAGGCCGGCTTT 58.254 50.000 28.56 17.66 0.00 3.51
1332 1438 1.024579 ATTGTGTAGGCCGGCTTTCG 61.025 55.000 28.56 0.00 38.88 3.46
1337 1461 1.669760 TAGGCCGGCTTTCGTTGTG 60.670 57.895 28.56 0.00 37.11 3.33
1391 1515 3.116531 GTGTTCCAGTACGGCGCC 61.117 66.667 19.07 19.07 33.14 6.53
1763 1908 1.739049 CTCCGTGATGGGCTCTCTC 59.261 63.158 0.00 0.00 38.76 3.20
1848 1993 2.500098 CCCTTCTCCGAATTGTCCAGTA 59.500 50.000 0.00 0.00 0.00 2.74
1964 2146 3.082548 GGTAGATCCTCCGATTCGATCA 58.917 50.000 7.83 0.00 35.82 2.92
1983 2165 0.385223 ACGACTCGTGCTTGTACGAC 60.385 55.000 9.66 1.61 46.94 4.34
2000 2182 9.314321 CTTGTACGACCACTTTGAAATATAGAT 57.686 33.333 0.00 0.00 0.00 1.98
2008 2190 9.566432 ACCACTTTGAAATATAGATTCTCCATC 57.434 33.333 0.00 0.00 0.00 3.51
2015 2197 9.152327 TGAAATATAGATTCTCCATCTGTCTGT 57.848 33.333 0.00 0.00 42.76 3.41
2016 2198 9.638239 GAAATATAGATTCTCCATCTGTCTGTC 57.362 37.037 0.00 0.00 42.76 3.51
2080 2301 4.864334 GCTGGCGTGGGGATCCTG 62.864 72.222 12.58 0.53 0.00 3.86
2083 2304 3.161450 GGCGTGGGGATCCTGCTA 61.161 66.667 12.58 0.00 36.08 3.49
2084 2305 2.742116 GGCGTGGGGATCCTGCTAA 61.742 63.158 12.58 0.00 36.08 3.09
2085 2306 1.223487 GCGTGGGGATCCTGCTAAA 59.777 57.895 12.58 0.00 34.04 1.85
2086 2307 0.179018 GCGTGGGGATCCTGCTAAAT 60.179 55.000 12.58 0.00 34.04 1.40
2089 2310 2.368875 CGTGGGGATCCTGCTAAATACT 59.631 50.000 12.58 0.00 0.00 2.12
2133 8829 2.159268 TGTCTTGTCCGTCAACGTGTAA 60.159 45.455 1.48 0.00 37.74 2.41
2163 8861 3.450457 ACTTCAGGGAGCTCAGTCTATTG 59.550 47.826 17.19 2.85 0.00 1.90
2179 8877 6.260936 CAGTCTATTGTACAATGGAACCCATC 59.739 42.308 29.45 18.60 44.40 3.51
2180 8878 6.069673 AGTCTATTGTACAATGGAACCCATCA 60.070 38.462 29.45 8.52 44.40 3.07
2200 8898 4.689062 TCAGGAACAGGGTCTATCTTTCT 58.311 43.478 0.00 0.00 0.00 2.52
2204 8902 4.383226 GGAACAGGGTCTATCTTTCTGACC 60.383 50.000 0.00 0.00 46.83 4.02
2212 8910 1.196012 ATCTTTCTGACCGAGGTCCC 58.804 55.000 18.57 0.00 43.97 4.46
2213 8911 0.903454 TCTTTCTGACCGAGGTCCCC 60.903 60.000 18.57 0.00 43.97 4.81
2264 8962 7.147724 TGGTAGATAGTCAGGTACAATTTGAGG 60.148 40.741 2.79 0.00 0.00 3.86
2276 8974 7.284034 AGGTACAATTTGAGGACATGATCAATC 59.716 37.037 0.00 0.04 35.47 2.67
2284 8982 7.429374 TGAGGACATGATCAATCTCTAAGTT 57.571 36.000 0.00 0.00 0.00 2.66
2285 8983 7.495901 TGAGGACATGATCAATCTCTAAGTTC 58.504 38.462 0.00 0.00 0.00 3.01
2287 8985 8.032045 AGGACATGATCAATCTCTAAGTTCAT 57.968 34.615 0.00 0.00 0.00 2.57
2289 8987 9.770097 GGACATGATCAATCTCTAAGTTCATTA 57.230 33.333 0.00 0.00 0.00 1.90
2318 9016 7.481798 CGCCTTCTGAAATTTAAGACAATACAC 59.518 37.037 4.60 0.00 0.00 2.90
2331 9029 2.027469 ACAATACACGTTCCCCCTCTTC 60.027 50.000 0.00 0.00 0.00 2.87
2338 9036 1.755380 CGTTCCCCCTCTTCGATTAGT 59.245 52.381 0.00 0.00 0.00 2.24
2342 9040 3.721021 TCCCCCTCTTCGATTAGTTTCT 58.279 45.455 0.00 0.00 0.00 2.52
2358 9056 4.636249 AGTTTCTGAGTCTTGGCTAACAG 58.364 43.478 0.00 0.00 0.00 3.16
2380 11213 3.285484 CCTCTTTGGAATGACATCCTGG 58.715 50.000 0.00 0.00 40.35 4.45
2398 11231 3.899981 GACGCCATCACCCTGCACA 62.900 63.158 0.00 0.00 0.00 4.57
2399 11232 3.129502 CGCCATCACCCTGCACAG 61.130 66.667 0.00 0.00 0.00 3.66
2410 11243 1.250328 CCTGCACAGAAAGCATGGAA 58.750 50.000 0.00 0.00 41.82 3.53
2412 11245 0.961019 TGCACAGAAAGCATGGAACC 59.039 50.000 0.00 0.00 37.02 3.62
2413 11246 1.251251 GCACAGAAAGCATGGAACCT 58.749 50.000 0.00 0.00 0.00 3.50
2414 11247 2.224744 TGCACAGAAAGCATGGAACCTA 60.225 45.455 0.00 0.00 37.02 3.08
2415 11248 2.819608 GCACAGAAAGCATGGAACCTAA 59.180 45.455 0.00 0.00 0.00 2.69
2418 11251 5.125417 GCACAGAAAGCATGGAACCTAATTA 59.875 40.000 0.00 0.00 0.00 1.40
2433 11266 5.812286 ACCTAATTACCGGACAAAAGACAT 58.188 37.500 9.46 0.00 0.00 3.06
2437 11270 7.334921 CCTAATTACCGGACAAAAGACATAACA 59.665 37.037 9.46 0.00 0.00 2.41
2443 11276 5.912955 CCGGACAAAAGACATAACAAAAGAC 59.087 40.000 0.00 0.00 0.00 3.01
2455 11288 6.882140 ACATAACAAAAGACCGAACATCCATA 59.118 34.615 0.00 0.00 0.00 2.74
2459 11292 1.794714 AGACCGAACATCCATAGGCT 58.205 50.000 0.00 0.00 0.00 4.58
2468 11301 3.270877 ACATCCATAGGCTTCAAACGTC 58.729 45.455 0.00 0.00 0.00 4.34
2472 11305 3.751175 TCCATAGGCTTCAAACGTCAAAG 59.249 43.478 0.00 0.00 0.00 2.77
2489 11322 9.673454 AACGTCAAAGAAAGTAATAAATTCACC 57.327 29.630 0.00 0.00 0.00 4.02
2528 11403 1.865248 GCATGCACGAATTGGCCATAC 60.865 52.381 14.21 0.00 0.00 2.39
2529 11404 1.404748 CATGCACGAATTGGCCATACA 59.595 47.619 6.09 0.00 0.00 2.29
2556 11431 8.165239 AGTAACAATAAAGACATGAGCACAAA 57.835 30.769 0.00 0.00 0.00 2.83
2557 11432 8.796475 AGTAACAATAAAGACATGAGCACAAAT 58.204 29.630 0.00 0.00 0.00 2.32
2582 11457 3.230134 CCCACCTTCTCATTGACCAAAA 58.770 45.455 0.00 0.00 0.00 2.44
2608 11483 2.435805 GTGCACCCATAAGAGATCTCCA 59.564 50.000 19.30 8.08 0.00 3.86
2613 11488 4.596643 CACCCATAAGAGATCTCCATTCCT 59.403 45.833 19.30 0.00 0.00 3.36
2614 11489 4.596643 ACCCATAAGAGATCTCCATTCCTG 59.403 45.833 19.30 9.00 0.00 3.86
2615 11490 4.019501 CCCATAAGAGATCTCCATTCCTGG 60.020 50.000 19.30 15.82 44.64 4.45
2616 11491 4.565236 CCATAAGAGATCTCCATTCCTGGC 60.565 50.000 19.30 0.00 42.80 4.85
2622 11497 0.911769 TCTCCATTCCTGGCATCGTT 59.088 50.000 0.00 0.00 42.80 3.85
2624 11499 2.158957 TCTCCATTCCTGGCATCGTTAC 60.159 50.000 0.00 0.00 42.80 2.50
2625 11500 1.837439 TCCATTCCTGGCATCGTTACT 59.163 47.619 0.00 0.00 42.80 2.24
2628 11503 3.997021 CCATTCCTGGCATCGTTACTATC 59.003 47.826 0.00 0.00 35.23 2.08
2635 11510 2.028930 GGCATCGTTACTATCCTCCCAG 60.029 54.545 0.00 0.00 0.00 4.45
2639 11514 4.726035 TCGTTACTATCCTCCCAGAGAT 57.274 45.455 0.00 0.00 0.00 2.75
2640 11515 4.399219 TCGTTACTATCCTCCCAGAGATG 58.601 47.826 0.00 0.00 0.00 2.90
2644 11519 3.843422 ACTATCCTCCCAGAGATGACAG 58.157 50.000 0.00 0.00 0.00 3.51
2645 11520 2.864885 ATCCTCCCAGAGATGACAGT 57.135 50.000 0.00 0.00 0.00 3.55
2655 11530 0.605083 AGATGACAGTCTCTTGCGCA 59.395 50.000 5.66 5.66 0.00 6.09
2678 11553 2.739943 TGGATTCGTCAGTCCTGAGAT 58.260 47.619 0.00 0.00 40.75 2.75
2679 11554 2.690497 TGGATTCGTCAGTCCTGAGATC 59.310 50.000 0.00 2.72 40.75 2.75
2682 11557 1.064946 CGTCAGTCCTGAGATCCGC 59.935 63.158 0.00 0.00 40.75 5.54
2711 11586 3.386402 GGTCCCAACAACAAATTCTCCAA 59.614 43.478 0.00 0.00 0.00 3.53
2766 11641 6.947733 ACATAGAGATTCCCATGTGTGAAAAA 59.052 34.615 0.00 0.00 30.64 1.94
2767 11642 5.972107 AGAGATTCCCATGTGTGAAAAAG 57.028 39.130 0.00 0.00 0.00 2.27
2768 11643 4.768968 AGAGATTCCCATGTGTGAAAAAGG 59.231 41.667 0.00 0.00 0.00 3.11
2769 11644 4.739793 AGATTCCCATGTGTGAAAAAGGA 58.260 39.130 0.00 0.00 0.00 3.36
2770 11645 4.768968 AGATTCCCATGTGTGAAAAAGGAG 59.231 41.667 0.00 0.00 0.00 3.69
2771 11646 2.238521 TCCCATGTGTGAAAAAGGAGC 58.761 47.619 0.00 0.00 0.00 4.70
2772 11647 2.158475 TCCCATGTGTGAAAAAGGAGCT 60.158 45.455 0.00 0.00 0.00 4.09
2774 11649 2.095567 CCATGTGTGAAAAAGGAGCTCG 60.096 50.000 7.83 0.00 0.00 5.03
2775 11650 2.325583 TGTGTGAAAAAGGAGCTCGT 57.674 45.000 7.83 5.12 0.00 4.18
2776 11651 3.462483 TGTGTGAAAAAGGAGCTCGTA 57.538 42.857 9.76 0.00 0.00 3.43
2778 11653 3.807622 TGTGTGAAAAAGGAGCTCGTAAG 59.192 43.478 9.76 0.00 0.00 2.34
2780 11655 4.056050 TGTGAAAAAGGAGCTCGTAAGAC 58.944 43.478 9.76 3.62 45.01 3.01
2781 11656 4.202223 TGTGAAAAAGGAGCTCGTAAGACT 60.202 41.667 9.76 0.00 45.01 3.24
2783 11658 6.100668 GTGAAAAAGGAGCTCGTAAGACTAT 58.899 40.000 9.76 0.00 45.01 2.12
2784 11659 6.253942 GTGAAAAAGGAGCTCGTAAGACTATC 59.746 42.308 9.76 2.97 45.01 2.08
2785 11660 4.922471 AAAGGAGCTCGTAAGACTATCC 57.078 45.455 9.76 0.00 45.01 2.59
2788 11663 2.950309 GGAGCTCGTAAGACTATCCACA 59.050 50.000 7.83 0.00 45.01 4.17
2789 11664 3.003897 GGAGCTCGTAAGACTATCCACAG 59.996 52.174 7.83 0.00 45.01 3.66
2790 11665 3.622630 AGCTCGTAAGACTATCCACAGT 58.377 45.455 0.00 0.00 45.01 3.55
2791 11666 3.378742 AGCTCGTAAGACTATCCACAGTG 59.621 47.826 0.00 0.00 45.01 3.66
2792 11667 3.489398 GCTCGTAAGACTATCCACAGTGG 60.489 52.174 14.19 14.19 45.01 4.00
2793 11668 3.021695 TCGTAAGACTATCCACAGTGGG 58.978 50.000 20.14 6.26 45.01 4.61
2794 11669 2.100916 CGTAAGACTATCCACAGTGGGG 59.899 54.545 20.14 4.49 37.66 4.96
2795 11670 2.344093 AAGACTATCCACAGTGGGGT 57.656 50.000 20.14 15.24 38.32 4.95
2796 11671 3.484953 AAGACTATCCACAGTGGGGTA 57.515 47.619 20.14 11.80 38.32 3.69
2798 11673 4.008916 AGACTATCCACAGTGGGGTAAT 57.991 45.455 20.14 8.18 38.32 1.89
2799 11674 5.152306 AGACTATCCACAGTGGGGTAATA 57.848 43.478 20.14 8.91 38.32 0.98
2800 11675 5.727630 AGACTATCCACAGTGGGGTAATAT 58.272 41.667 20.14 7.07 38.32 1.28
2803 11678 6.871035 ACTATCCACAGTGGGGTAATATAGA 58.129 40.000 22.15 2.56 38.32 1.98
2804 11679 7.488205 ACTATCCACAGTGGGGTAATATAGAT 58.512 38.462 22.15 8.78 38.32 1.98
2805 11680 6.627087 ATCCACAGTGGGGTAATATAGATG 57.373 41.667 20.14 0.00 38.32 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 77 5.709164 AGTACTGTGTACAACGGAAGACTAT 59.291 40.000 0.00 0.00 38.65 2.12
76 78 5.065914 AGTACTGTGTACAACGGAAGACTA 58.934 41.667 0.00 0.00 38.65 2.59
77 79 3.887716 AGTACTGTGTACAACGGAAGACT 59.112 43.478 0.00 2.27 38.65 3.24
78 80 4.234530 AGTACTGTGTACAACGGAAGAC 57.765 45.455 0.00 0.20 38.65 3.01
110 112 5.178623 CACTCAGTTTGTCTTAATAACCGCA 59.821 40.000 0.00 0.00 0.00 5.69
111 113 5.407387 TCACTCAGTTTGTCTTAATAACCGC 59.593 40.000 0.00 0.00 0.00 5.68
112 114 7.201530 GGATCACTCAGTTTGTCTTAATAACCG 60.202 40.741 0.00 0.00 0.00 4.44
131 134 0.325484 AGGAGCTCTGCAGGATCACT 60.325 55.000 15.13 9.19 0.00 3.41
139 142 1.969200 GCTGGATCAGGAGCTCTGCA 61.969 60.000 14.64 4.12 43.06 4.41
176 195 1.429423 GCATCGTTGTTAGCAGCCC 59.571 57.895 0.00 0.00 0.00 5.19
200 219 0.984995 AAGGTAAGGTGAGGTGAGGC 59.015 55.000 0.00 0.00 0.00 4.70
307 326 2.162608 TGTTGGTTGAACCGTTGAACAG 59.837 45.455 14.40 0.00 42.58 3.16
414 433 6.403878 ACATAGCAAATAGACCGTTTGTAGT 58.596 36.000 0.00 0.00 38.49 2.73
433 452 4.393062 AGGAACGCAAAACAGATGACATAG 59.607 41.667 0.00 0.00 0.00 2.23
519 538 6.605995 AGGGTAAATTTCCTTTGCTATGGTAC 59.394 38.462 0.00 0.00 30.90 3.34
521 540 5.422012 CAGGGTAAATTTCCTTTGCTATGGT 59.578 40.000 0.00 0.00 30.90 3.55
522 541 5.682212 GCAGGGTAAATTTCCTTTGCTATGG 60.682 44.000 18.02 0.00 34.92 2.74
523 542 5.127682 AGCAGGGTAAATTTCCTTTGCTATG 59.872 40.000 21.97 6.27 40.76 2.23
567 673 9.524106 GGTACAAGTTAAATAATTAATGCCCAC 57.476 33.333 0.00 0.00 33.76 4.61
674 780 2.268730 AGCGCTAAAGAAAGCAATGC 57.731 45.000 8.99 0.00 42.91 3.56
848 954 3.402058 AGTACACTGACTAACGCGATC 57.598 47.619 15.93 5.22 0.00 3.69
864 970 0.989890 CGAAGCGGTGCAGTTAGTAC 59.010 55.000 0.00 0.00 0.00 2.73
937 1043 0.111061 TTGCTGTGGAGCTGGAATGT 59.889 50.000 0.00 0.00 46.39 2.71
945 1051 0.250467 TGGAGACTTTGCTGTGGAGC 60.250 55.000 0.00 0.00 46.44 4.70
946 1052 2.149578 CTTGGAGACTTTGCTGTGGAG 58.850 52.381 0.00 0.00 0.00 3.86
947 1053 1.768275 TCTTGGAGACTTTGCTGTGGA 59.232 47.619 0.00 0.00 0.00 4.02
948 1054 2.260844 TCTTGGAGACTTTGCTGTGG 57.739 50.000 0.00 0.00 0.00 4.17
949 1055 4.276678 TGAATTCTTGGAGACTTTGCTGTG 59.723 41.667 7.05 0.00 0.00 3.66
950 1056 4.464008 TGAATTCTTGGAGACTTTGCTGT 58.536 39.130 7.05 0.00 0.00 4.40
976 1082 5.483937 TGATAGCAAGTTAAGGTCTTGGAGA 59.516 40.000 6.47 0.00 41.50 3.71
1174 1280 2.732366 AGCAATGATCGTAGTACTGCG 58.268 47.619 25.14 25.14 40.03 5.18
1206 1312 3.304794 GGCCAGTACTATCACTAAGAGCG 60.305 52.174 0.00 0.00 0.00 5.03
1227 1333 1.674221 GCACTGTGCTCTACTTGAGGG 60.674 57.143 24.68 0.00 42.87 4.30
1252 1358 0.033366 ACGAACCATTTTGCCAAGCC 59.967 50.000 0.00 0.00 0.00 4.35
1270 1376 3.777925 CTGCGCTGGCACGTACAC 61.778 66.667 9.73 0.00 46.21 2.90
1287 1393 2.480555 CGGCGAACAAGTCATGCC 59.519 61.111 0.00 0.00 42.29 4.40
1311 1417 1.669265 GAAAGCCGGCCTACACAATAC 59.331 52.381 26.15 0.00 0.00 1.89
1313 1419 1.024579 CGAAAGCCGGCCTACACAAT 61.025 55.000 26.15 0.00 33.91 2.71
1314 1420 1.669760 CGAAAGCCGGCCTACACAA 60.670 57.895 26.15 0.00 33.91 3.33
1315 1421 2.047655 CGAAAGCCGGCCTACACA 60.048 61.111 26.15 0.00 33.91 3.72
1316 1422 1.670083 AACGAAAGCCGGCCTACAC 60.670 57.895 26.15 9.72 43.93 2.90
1317 1423 1.669760 CAACGAAAGCCGGCCTACA 60.670 57.895 26.15 0.00 43.93 2.74
1322 1428 1.495951 CTACACAACGAAAGCCGGC 59.504 57.895 21.89 21.89 43.93 6.13
1323 1429 1.908066 GCCTACACAACGAAAGCCGG 61.908 60.000 0.00 0.00 43.93 6.13
1324 1430 1.495951 GCCTACACAACGAAAGCCG 59.504 57.895 0.00 0.00 45.44 5.52
1325 1431 1.873863 GGCCTACACAACGAAAGCC 59.126 57.895 0.00 0.00 0.00 4.35
1326 1432 0.947180 TCGGCCTACACAACGAAAGC 60.947 55.000 0.00 0.00 31.79 3.51
1327 1433 0.788391 GTCGGCCTACACAACGAAAG 59.212 55.000 1.78 0.00 37.08 2.62
1328 1434 0.600782 GGTCGGCCTACACAACGAAA 60.601 55.000 9.95 0.00 37.08 3.46
1329 1435 1.005867 GGTCGGCCTACACAACGAA 60.006 57.895 9.95 0.00 37.08 3.85
1330 1436 1.904865 AGGTCGGCCTACACAACGA 60.905 57.895 6.89 0.00 44.90 3.85
1332 1438 0.669625 GTCAGGTCGGCCTACACAAC 60.670 60.000 9.07 0.00 44.97 3.32
1337 1461 2.893398 CCAGTCAGGTCGGCCTAC 59.107 66.667 9.07 7.96 44.97 3.18
1354 1478 1.371635 GCACGCACACATGGGAAAC 60.372 57.895 0.00 0.00 41.24 2.78
1358 1482 2.979676 ACTGCACGCACACATGGG 60.980 61.111 0.00 0.00 44.23 4.00
1439 1563 1.379044 CTGGATGGAGTTGGTGGCC 60.379 63.158 0.00 0.00 0.00 5.36
1891 2070 3.251484 CCCCAGATAAAGAGGAGCCATA 58.749 50.000 0.00 0.00 0.00 2.74
1892 2071 2.061061 CCCCAGATAAAGAGGAGCCAT 58.939 52.381 0.00 0.00 0.00 4.40
1964 2146 1.944035 TCGTACAAGCACGAGTCGT 59.056 52.632 13.56 13.56 45.45 4.34
1983 2165 9.790344 AGATGGAGAATCTATATTTCAAAGTGG 57.210 33.333 0.00 0.00 44.22 4.00
2000 2182 3.897505 TCACAAGACAGACAGATGGAGAA 59.102 43.478 0.00 0.00 0.00 2.87
2008 2190 2.120232 GACACGTCACAAGACAGACAG 58.880 52.381 0.00 0.00 45.23 3.51
2010 2192 2.493713 AGACACGTCACAAGACAGAC 57.506 50.000 0.00 0.00 45.23 3.51
2012 2194 1.258982 GCAAGACACGTCACAAGACAG 59.741 52.381 0.00 0.00 45.23 3.51
2015 2197 0.101579 TCGCAAGACACGTCACAAGA 59.898 50.000 0.00 0.00 45.01 3.02
2016 2198 2.588731 TCGCAAGACACGTCACAAG 58.411 52.632 0.00 0.00 45.01 3.16
2108 6642 3.303495 CACGTTGACGGACAAGACATATC 59.697 47.826 8.52 0.00 44.95 1.63
2120 8080 5.156355 AGTACATAACTTACACGTTGACGG 58.844 41.667 8.52 0.00 38.45 4.79
2121 8081 6.680055 AAGTACATAACTTACACGTTGACG 57.320 37.500 1.41 1.41 46.85 4.35
2133 8829 4.353777 TGAGCTCCCTGAAGTACATAACT 58.646 43.478 12.15 0.00 41.49 2.24
2163 8861 3.644966 TCCTGATGGGTTCCATTGTAC 57.355 47.619 0.59 0.00 45.26 2.90
2179 8877 4.467795 TCAGAAAGATAGACCCTGTTCCTG 59.532 45.833 0.00 0.00 0.00 3.86
2180 8878 4.468153 GTCAGAAAGATAGACCCTGTTCCT 59.532 45.833 0.00 0.00 0.00 3.36
2212 8910 4.868450 TTTGAATTATAGTTCACGCCGG 57.132 40.909 9.96 0.00 37.80 6.13
2213 8911 6.287107 AGATTTGAATTATAGTTCACGCCG 57.713 37.500 9.96 0.00 37.80 6.46
2215 8913 8.774586 ACCATAGATTTGAATTATAGTTCACGC 58.225 33.333 9.96 3.69 37.80 5.34
2244 8942 6.620877 TGTCCTCAAATTGTACCTGACTAT 57.379 37.500 0.00 0.00 0.00 2.12
2248 8946 5.497464 TCATGTCCTCAAATTGTACCTGA 57.503 39.130 0.00 0.00 0.00 3.86
2251 8949 6.757897 TTGATCATGTCCTCAAATTGTACC 57.242 37.500 0.00 0.00 0.00 3.34
2276 8974 5.050499 CAGAAGGCGCATAATGAACTTAGAG 60.050 44.000 10.83 0.00 0.00 2.43
2284 8982 5.581126 AAATTTCAGAAGGCGCATAATGA 57.419 34.783 10.83 7.45 0.00 2.57
2285 8983 7.166473 GTCTTAAATTTCAGAAGGCGCATAATG 59.834 37.037 10.83 4.71 0.00 1.90
2287 8985 6.150307 TGTCTTAAATTTCAGAAGGCGCATAA 59.850 34.615 10.83 0.00 0.00 1.90
2289 8987 4.458989 TGTCTTAAATTTCAGAAGGCGCAT 59.541 37.500 10.83 0.00 0.00 4.73
2318 9016 1.755380 ACTAATCGAAGAGGGGGAACG 59.245 52.381 0.00 0.00 43.63 3.95
2331 9029 4.499183 AGCCAAGACTCAGAAACTAATCG 58.501 43.478 0.00 0.00 0.00 3.34
2338 9036 3.403038 GCTGTTAGCCAAGACTCAGAAA 58.597 45.455 0.00 0.00 34.48 2.52
2358 9056 2.686915 CAGGATGTCATTCCAAAGAGGC 59.313 50.000 4.70 0.00 38.32 4.70
2380 11213 3.127533 GTGCAGGGTGATGGCGTC 61.128 66.667 0.00 0.00 0.00 5.19
2398 11231 4.881850 CGGTAATTAGGTTCCATGCTTTCT 59.118 41.667 0.00 0.00 0.00 2.52
2399 11232 4.036380 CCGGTAATTAGGTTCCATGCTTTC 59.964 45.833 0.00 0.00 0.00 2.62
2410 11243 5.231702 TGTCTTTTGTCCGGTAATTAGGT 57.768 39.130 0.00 0.00 0.00 3.08
2412 11245 8.259049 TGTTATGTCTTTTGTCCGGTAATTAG 57.741 34.615 0.00 0.00 0.00 1.73
2413 11246 8.618702 TTGTTATGTCTTTTGTCCGGTAATTA 57.381 30.769 0.00 0.00 0.00 1.40
2414 11247 7.513371 TTGTTATGTCTTTTGTCCGGTAATT 57.487 32.000 0.00 0.00 0.00 1.40
2415 11248 7.513371 TTTGTTATGTCTTTTGTCCGGTAAT 57.487 32.000 0.00 0.00 0.00 1.89
2418 11251 5.591067 TCTTTTGTTATGTCTTTTGTCCGGT 59.409 36.000 0.00 0.00 0.00 5.28
2433 11266 5.878116 CCTATGGATGTTCGGTCTTTTGTTA 59.122 40.000 0.00 0.00 0.00 2.41
2437 11270 3.054361 AGCCTATGGATGTTCGGTCTTTT 60.054 43.478 0.00 0.00 0.00 2.27
2443 11276 2.620251 TGAAGCCTATGGATGTTCGG 57.380 50.000 0.00 0.00 0.00 4.30
2455 11288 3.694566 ACTTTCTTTGACGTTTGAAGCCT 59.305 39.130 0.00 0.00 0.00 4.58
2486 11319 6.680810 TGCATCTTTTTGTATCTCTTTGGTG 58.319 36.000 0.00 0.00 0.00 4.17
2488 11321 6.255020 GCATGCATCTTTTTGTATCTCTTTGG 59.745 38.462 14.21 0.00 0.00 3.28
2489 11322 6.809689 TGCATGCATCTTTTTGTATCTCTTTG 59.190 34.615 18.46 0.00 0.00 2.77
2501 11376 3.255725 CCAATTCGTGCATGCATCTTTT 58.744 40.909 25.64 12.82 0.00 2.27
2528 11403 8.882736 TGTGCTCATGTCTTTATTGTTACTATG 58.117 33.333 0.00 0.00 0.00 2.23
2529 11404 9.448438 TTGTGCTCATGTCTTTATTGTTACTAT 57.552 29.630 0.00 0.00 0.00 2.12
2543 11418 2.557924 TGGGTTGATTTGTGCTCATGTC 59.442 45.455 0.00 0.00 0.00 3.06
2556 11431 3.562176 GGTCAATGAGAAGGTGGGTTGAT 60.562 47.826 0.00 0.00 0.00 2.57
2557 11432 2.224769 GGTCAATGAGAAGGTGGGTTGA 60.225 50.000 0.00 0.00 0.00 3.18
2582 11457 1.985159 TCTCTTATGGGTGCACTTGGT 59.015 47.619 17.98 3.40 0.00 3.67
2608 11483 3.904339 AGGATAGTAACGATGCCAGGAAT 59.096 43.478 0.00 0.00 0.00 3.01
2613 11488 1.968493 GGGAGGATAGTAACGATGCCA 59.032 52.381 0.00 0.00 0.00 4.92
2614 11489 1.968493 TGGGAGGATAGTAACGATGCC 59.032 52.381 0.00 0.00 0.00 4.40
2615 11490 2.891580 TCTGGGAGGATAGTAACGATGC 59.108 50.000 0.00 0.00 0.00 3.91
2616 11491 4.399219 TCTCTGGGAGGATAGTAACGATG 58.601 47.826 0.00 0.00 0.00 3.84
2622 11497 4.991776 CTGTCATCTCTGGGAGGATAGTA 58.008 47.826 7.67 0.00 38.53 1.82
2624 11499 3.826157 GACTGTCATCTCTGGGAGGATAG 59.174 52.174 13.39 13.39 45.20 2.08
2625 11500 3.465210 AGACTGTCATCTCTGGGAGGATA 59.535 47.826 10.88 0.00 37.10 2.59
2628 11503 2.031120 GAGACTGTCATCTCTGGGAGG 58.969 57.143 10.88 0.00 41.72 4.30
2635 11510 1.276415 GCGCAAGAGACTGTCATCTC 58.724 55.000 10.88 0.00 44.76 2.75
2639 11514 0.605083 ATCTGCGCAAGAGACTGTCA 59.395 50.000 13.05 0.00 38.67 3.58
2640 11515 0.997932 CATCTGCGCAAGAGACTGTC 59.002 55.000 13.05 0.00 38.67 3.51
2644 11519 1.596727 GAATCCATCTGCGCAAGAGAC 59.403 52.381 13.05 1.32 38.67 3.36
2645 11520 1.803998 CGAATCCATCTGCGCAAGAGA 60.804 52.381 13.05 5.80 38.67 3.10
2653 11528 1.137872 AGGACTGACGAATCCATCTGC 59.862 52.381 0.00 0.00 37.47 4.26
2655 11530 2.692557 CTCAGGACTGACGAATCCATCT 59.307 50.000 0.00 0.00 37.47 2.90
2678 11553 0.034863 GTTGGGACCTAAATGGCGGA 60.035 55.000 0.00 0.00 40.22 5.54
2679 11554 0.322997 TGTTGGGACCTAAATGGCGG 60.323 55.000 0.00 0.00 40.22 6.13
2682 11557 4.946478 TTTGTTGTTGGGACCTAAATGG 57.054 40.909 0.00 0.00 42.93 3.16
2735 11610 8.204160 CACACATGGGAATCTCTATGTAGTTTA 58.796 37.037 0.00 0.00 32.86 2.01
2766 11641 3.215975 GTGGATAGTCTTACGAGCTCCT 58.784 50.000 8.47 0.00 0.00 3.69
2767 11642 2.950309 TGTGGATAGTCTTACGAGCTCC 59.050 50.000 8.47 0.00 0.00 4.70
2768 11643 3.628487 ACTGTGGATAGTCTTACGAGCTC 59.372 47.826 2.73 2.73 0.00 4.09
2769 11644 3.378742 CACTGTGGATAGTCTTACGAGCT 59.621 47.826 0.00 0.00 0.00 4.09
2770 11645 3.489398 CCACTGTGGATAGTCTTACGAGC 60.489 52.174 22.33 0.00 40.96 5.03
2771 11646 3.066900 CCCACTGTGGATAGTCTTACGAG 59.933 52.174 27.94 2.51 40.96 4.18
2772 11647 3.021695 CCCACTGTGGATAGTCTTACGA 58.978 50.000 27.94 0.00 40.96 3.43
2774 11649 3.105283 ACCCCACTGTGGATAGTCTTAC 58.895 50.000 27.94 0.00 40.96 2.34
2775 11650 3.484953 ACCCCACTGTGGATAGTCTTA 57.515 47.619 27.94 0.00 40.96 2.10
2776 11651 2.344093 ACCCCACTGTGGATAGTCTT 57.656 50.000 27.94 1.10 40.96 3.01
2778 11653 6.952358 TCTATATTACCCCACTGTGGATAGTC 59.048 42.308 27.94 0.00 40.96 2.59
2780 11655 7.786030 CATCTATATTACCCCACTGTGGATAG 58.214 42.308 27.94 22.00 40.96 2.08
2781 11656 7.733773 CATCTATATTACCCCACTGTGGATA 57.266 40.000 27.94 16.83 40.96 2.59


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

AutoCloner maintained by Alex Coulton.