Multiple sequence alignment - TraesCS6A01G121900

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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 TraesCS6A01G121900 chr6A 100.000 3310 0 0 1 3310 94066455 94069764 0.000000e+00 6113.0
1 TraesCS6A01G121900 chr6D 92.949 1475 82 6 752 2225 78352825 78354278 0.000000e+00 2128.0
2 TraesCS6A01G121900 chr6D 94.159 719 39 3 1 717 78352111 78352828 0.000000e+00 1092.0
3 TraesCS6A01G121900 chr6D 93.382 544 31 4 2772 3310 78355648 78356191 0.000000e+00 800.0
4 TraesCS6A01G121900 chr6D 91.867 541 34 5 2242 2774 78354448 78354986 0.000000e+00 747.0
5 TraesCS6A01G121900 chr6D 88.350 103 11 1 568 669 78352784 78352682 4.490000e-24 122.0
6 TraesCS6A01G121900 chr5D 85.547 1370 179 12 870 2225 367415129 367413765 0.000000e+00 1415.0
7 TraesCS6A01G121900 chr5D 84.436 1375 186 20 870 2227 367251729 367250366 0.000000e+00 1328.0
8 TraesCS6A01G121900 chr5D 83.037 1126 157 25 870 1978 367382226 367381118 0.000000e+00 990.0
9 TraesCS6A01G121900 chr5B 85.350 1372 179 15 870 2225 434700192 434698827 0.000000e+00 1400.0
10 TraesCS6A01G121900 chr5B 84.643 1374 181 22 870 2225 434425254 434423893 0.000000e+00 1341.0
11 TraesCS6A01G121900 chr5B 87.059 85 10 1 579 662 582391975 582392059 9.780000e-16 95.3
12 TraesCS6A01G121900 chr5A 84.985 1372 184 15 870 2225 469063918 469062553 0.000000e+00 1373.0
13 TraesCS6A01G121900 chr5A 92.754 69 5 0 594 662 706470810 706470878 2.100000e-17 100.0
14 TraesCS6A01G121900 chr5A 87.059 85 10 1 579 662 382114942 382114858 9.780000e-16 95.3
15 TraesCS6A01G121900 chr3B 90.244 82 7 1 578 658 74812180 74812099 4.520000e-19 106.0
16 TraesCS6A01G121900 chr4A 91.781 73 5 1 590 662 662286431 662286502 2.100000e-17 100.0
17 TraesCS6A01G121900 chr4A 86.517 89 8 4 579 665 699895944 699896030 9.780000e-16 95.3
18 TraesCS6A01G121900 chr1D 87.805 82 10 0 581 662 17195723 17195804 2.720000e-16 97.1


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 TraesCS6A01G121900 chr6A 94066455 94069764 3309 False 6113.00 6113 100.00000 1 3310 1 chr6A.!!$F1 3309
1 TraesCS6A01G121900 chr6D 78352111 78356191 4080 False 1191.75 2128 93.08925 1 3310 4 chr6D.!!$F1 3309
2 TraesCS6A01G121900 chr5D 367413765 367415129 1364 True 1415.00 1415 85.54700 870 2225 1 chr5D.!!$R3 1355
3 TraesCS6A01G121900 chr5D 367250366 367251729 1363 True 1328.00 1328 84.43600 870 2227 1 chr5D.!!$R1 1357
4 TraesCS6A01G121900 chr5D 367381118 367382226 1108 True 990.00 990 83.03700 870 1978 1 chr5D.!!$R2 1108
5 TraesCS6A01G121900 chr5B 434698827 434700192 1365 True 1400.00 1400 85.35000 870 2225 1 chr5B.!!$R2 1355
6 TraesCS6A01G121900 chr5B 434423893 434425254 1361 True 1341.00 1341 84.64300 870 2225 1 chr5B.!!$R1 1355
7 TraesCS6A01G121900 chr5A 469062553 469063918 1365 True 1373.00 1373 84.98500 870 2225 1 chr5A.!!$R2 1355

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
248 249 1.339438 GCATGTGAGAAGAGGCCTCAA 60.339 52.381 33.9 11.45 41.72 3.02 F
1090 1094 1.880027 ACGAAGAAATGGGTCACAAGC 59.120 47.619 0.0 0.00 0.00 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1336 1352 0.178992 CTTTGGTGAACCTCCTGCCA 60.179 55.0 0.37 0.00 36.82 4.92 R
2312 2486 0.750546 CACTGATGCCTCATGTGGGG 60.751 60.0 15.39 6.82 31.98 4.96 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
60 61 5.181811 CAGTCAATTGTGCAGGTAGATTTCA 59.818 40.000 5.13 0.00 0.00 2.69
62 63 7.066163 CAGTCAATTGTGCAGGTAGATTTCATA 59.934 37.037 5.13 0.00 0.00 2.15
121 122 7.580007 AGTAAATAACTTACAGGTATTGGGGG 58.420 38.462 0.00 0.00 37.12 5.40
138 139 3.232720 GGGGGTGTTTGAGGTTCTAAA 57.767 47.619 0.00 0.00 0.00 1.85
156 157 9.106070 GGTTCTAAAGTTGTTTCTCTTGTTAGA 57.894 33.333 0.00 0.00 0.00 2.10
184 185 1.620323 AGATGGCAAAGACCAAAAGGC 59.380 47.619 0.00 0.00 44.65 4.35
197 198 4.666512 ACCAAAAGGCAGTTGATAGTGAT 58.333 39.130 2.09 0.00 0.00 3.06
231 232 2.566724 CCAACCCTTGTTTACATGGCAT 59.433 45.455 8.81 0.00 39.19 4.40
248 249 1.339438 GCATGTGAGAAGAGGCCTCAA 60.339 52.381 33.90 11.45 41.72 3.02
259 260 2.171448 AGAGGCCTCAACATCACCATAC 59.829 50.000 33.90 2.59 0.00 2.39
294 296 4.871993 CAATGAATGCTCTGGTACACTC 57.128 45.455 0.00 0.00 0.00 3.51
297 299 2.632512 TGAATGCTCTGGTACACTCACA 59.367 45.455 0.00 0.00 0.00 3.58
305 307 5.541845 CTCTGGTACACTCACAAATCTTGA 58.458 41.667 0.00 0.00 0.00 3.02
311 313 3.070446 ACACTCACAAATCTTGACCCGTA 59.930 43.478 0.00 0.00 0.00 4.02
321 323 4.247267 TCTTGACCCGTAACACTAAGTG 57.753 45.455 0.00 0.00 39.75 3.16
324 326 2.297033 TGACCCGTAACACTAAGTGACC 59.703 50.000 0.00 0.00 36.96 4.02
334 336 5.917541 ACACTAAGTGACCGTTTATTGTG 57.082 39.130 0.00 0.00 36.96 3.33
387 389 8.607459 CATTATCTTGTACTGACCATTCTTGAC 58.393 37.037 0.00 0.00 0.00 3.18
431 433 9.994432 CATATTCTAATTCACAACCTTGAAGTC 57.006 33.333 0.00 0.00 38.87 3.01
471 473 4.278419 GCTGGACAAGAGTAACCAAAATGT 59.722 41.667 0.00 0.00 31.85 2.71
473 475 6.016610 GCTGGACAAGAGTAACCAAAATGTTA 60.017 38.462 0.00 0.00 31.85 2.41
476 478 7.040062 TGGACAAGAGTAACCAAAATGTTATGG 60.040 37.037 0.00 0.00 42.60 2.74
529 531 6.426587 AGCATAAAGTTGACACCCTGATAAT 58.573 36.000 0.00 0.00 0.00 1.28
604 607 8.912614 ACTACCCCCTACCTAAATATAAGATG 57.087 38.462 0.00 0.00 0.00 2.90
652 655 9.743937 TGCAAAAACGTCTTATATTTAGTTACG 57.256 29.630 0.00 0.00 35.17 3.18
670 673 3.111741 ACGGAGGTAGTATTTGGGAGT 57.888 47.619 0.00 0.00 0.00 3.85
697 700 6.043243 TGAGAGTTGAGGAAATGTAAGAACCT 59.957 38.462 0.00 0.00 0.00 3.50
707 710 8.170730 AGGAAATGTAAGAACCTCCACTTTTAT 58.829 33.333 0.00 0.00 0.00 1.40
708 711 8.244113 GGAAATGTAAGAACCTCCACTTTTATG 58.756 37.037 0.00 0.00 0.00 1.90
710 713 6.442541 TGTAAGAACCTCCACTTTTATGGA 57.557 37.500 0.00 0.00 46.92 3.41
713 716 5.584551 AGAACCTCCACTTTTATGGACTT 57.415 39.130 0.00 0.00 44.14 3.01
714 717 5.953571 AGAACCTCCACTTTTATGGACTTT 58.046 37.500 0.00 0.00 44.14 2.66
715 718 6.373759 AGAACCTCCACTTTTATGGACTTTT 58.626 36.000 0.00 0.00 44.14 2.27
716 719 6.839134 AGAACCTCCACTTTTATGGACTTTTT 59.161 34.615 0.00 0.00 44.14 1.94
717 720 6.405278 ACCTCCACTTTTATGGACTTTTTG 57.595 37.500 0.00 0.00 44.14 2.44
718 721 5.897250 ACCTCCACTTTTATGGACTTTTTGT 59.103 36.000 0.00 0.00 44.14 2.83
719 722 6.183360 ACCTCCACTTTTATGGACTTTTTGTG 60.183 38.462 0.00 0.00 44.14 3.33
720 723 6.040391 CCTCCACTTTTATGGACTTTTTGTGA 59.960 38.462 0.00 0.00 44.14 3.58
721 724 7.411486 TCCACTTTTATGGACTTTTTGTGAA 57.589 32.000 0.00 0.00 44.14 3.18
722 725 7.841956 TCCACTTTTATGGACTTTTTGTGAAA 58.158 30.769 0.00 0.00 44.14 2.69
723 726 8.314751 TCCACTTTTATGGACTTTTTGTGAAAA 58.685 29.630 0.00 0.00 44.14 2.29
724 727 8.940952 CCACTTTTATGGACTTTTTGTGAAAAA 58.059 29.630 0.00 0.00 43.02 1.94
740 743 9.689976 TTTGTGAAAAAGTGTGGTGAATATATG 57.310 29.630 0.00 0.00 0.00 1.78
741 744 8.628630 TGTGAAAAAGTGTGGTGAATATATGA 57.371 30.769 0.00 0.00 0.00 2.15
742 745 8.729756 TGTGAAAAAGTGTGGTGAATATATGAG 58.270 33.333 0.00 0.00 0.00 2.90
743 746 8.730680 GTGAAAAAGTGTGGTGAATATATGAGT 58.269 33.333 0.00 0.00 0.00 3.41
744 747 9.952030 TGAAAAAGTGTGGTGAATATATGAGTA 57.048 29.630 0.00 0.00 0.00 2.59
749 752 9.770097 AAGTGTGGTGAATATATGAGTATCTTG 57.230 33.333 0.00 0.00 34.92 3.02
750 753 8.370940 AGTGTGGTGAATATATGAGTATCTTGG 58.629 37.037 0.00 0.00 34.92 3.61
788 791 8.114331 ACAAAAACTCATTCATGAATGCTAGA 57.886 30.769 34.12 20.80 45.77 2.43
820 823 6.788218 ACTACCAAGTACTAACTACCAGTCT 58.212 40.000 0.00 0.00 33.75 3.24
831 834 5.407407 AACTACCAGTCTTGTCTGTATGG 57.593 43.478 0.00 0.00 34.02 2.74
832 835 4.417437 ACTACCAGTCTTGTCTGTATGGT 58.583 43.478 0.00 0.00 43.26 3.55
833 836 5.577100 ACTACCAGTCTTGTCTGTATGGTA 58.423 41.667 0.00 0.00 41.20 3.25
834 837 6.195700 ACTACCAGTCTTGTCTGTATGGTAT 58.804 40.000 2.60 0.00 41.21 2.73
835 838 5.599999 ACCAGTCTTGTCTGTATGGTATC 57.400 43.478 0.00 0.00 39.21 2.24
836 839 4.406003 ACCAGTCTTGTCTGTATGGTATCC 59.594 45.833 0.00 0.00 39.21 2.59
837 840 4.405680 CCAGTCTTGTCTGTATGGTATCCA 59.594 45.833 0.00 0.00 34.20 3.41
838 841 5.452496 CCAGTCTTGTCTGTATGGTATCCAG 60.452 48.000 0.00 0.00 33.62 3.86
839 842 5.127845 CAGTCTTGTCTGTATGGTATCCAGT 59.872 44.000 0.00 0.00 36.75 4.00
840 843 5.361285 AGTCTTGTCTGTATGGTATCCAGTC 59.639 44.000 0.00 0.00 36.75 3.51
841 844 5.361285 GTCTTGTCTGTATGGTATCCAGTCT 59.639 44.000 0.00 0.00 36.75 3.24
842 845 5.958380 TCTTGTCTGTATGGTATCCAGTCTT 59.042 40.000 0.00 0.00 36.75 3.01
843 846 5.598416 TGTCTGTATGGTATCCAGTCTTG 57.402 43.478 0.00 0.00 36.75 3.02
844 847 5.023452 TGTCTGTATGGTATCCAGTCTTGT 58.977 41.667 0.00 0.00 36.75 3.16
845 848 5.127194 TGTCTGTATGGTATCCAGTCTTGTC 59.873 44.000 0.00 0.00 36.75 3.18
846 849 4.649674 TCTGTATGGTATCCAGTCTTGTCC 59.350 45.833 0.00 0.00 36.75 4.02
847 850 3.383505 TGTATGGTATCCAGTCTTGTCCG 59.616 47.826 0.00 0.00 36.75 4.79
848 851 1.933021 TGGTATCCAGTCTTGTCCGT 58.067 50.000 0.00 0.00 0.00 4.69
849 852 3.090210 TGGTATCCAGTCTTGTCCGTA 57.910 47.619 0.00 0.00 0.00 4.02
850 853 3.638860 TGGTATCCAGTCTTGTCCGTAT 58.361 45.455 0.00 0.00 0.00 3.06
851 854 3.383505 TGGTATCCAGTCTTGTCCGTATG 59.616 47.826 0.00 0.00 0.00 2.39
852 855 3.243771 GGTATCCAGTCTTGTCCGTATGG 60.244 52.174 0.00 0.00 0.00 2.74
989 993 5.822519 GGGTATCATCAGTGATAAGCAACAA 59.177 40.000 5.03 0.00 46.09 2.83
1008 1012 5.178096 ACAACCCTGTCATCATGAATGTA 57.822 39.130 0.00 0.00 36.68 2.29
1015 1019 6.183360 CCCTGTCATCATGAATGTAGACTGTA 60.183 42.308 0.00 0.00 36.68 2.74
1019 1023 9.750125 TGTCATCATGAATGTAGACTGTAATAC 57.250 33.333 0.00 0.00 36.68 1.89
1028 1032 9.395707 GAATGTAGACTGTAATACGTATTCCAG 57.604 37.037 29.01 29.01 36.20 3.86
1034 1038 5.810587 ACTGTAATACGTATTCCAGCAACAG 59.189 40.000 30.00 29.20 34.23 3.16
1036 1040 2.753055 TACGTATTCCAGCAACAGCA 57.247 45.000 0.00 0.00 0.00 4.41
1090 1094 1.880027 ACGAAGAAATGGGTCACAAGC 59.120 47.619 0.00 0.00 0.00 4.01
1120 1124 5.268118 TGTGCAGTATCCTCAGAACTATG 57.732 43.478 0.00 0.00 0.00 2.23
1173 1177 5.688814 ACTCTCTCCATGTCATCAATGAA 57.311 39.130 0.00 0.00 38.75 2.57
1182 1186 5.505819 CCATGTCATCAATGAAGTCAGCATC 60.506 44.000 0.00 0.00 38.75 3.91
1183 1187 4.581868 TGTCATCAATGAAGTCAGCATCA 58.418 39.130 0.00 0.00 38.75 3.07
1185 1189 5.650703 TGTCATCAATGAAGTCAGCATCATT 59.349 36.000 0.00 0.00 44.81 2.57
1191 1195 8.791327 TCAATGAAGTCAGCATCATTAAACTA 57.209 30.769 1.11 0.00 42.72 2.24
1202 1206 9.764363 CAGCATCATTAAACTATAACCTGAGTA 57.236 33.333 0.00 0.00 0.00 2.59
1203 1207 9.765795 AGCATCATTAAACTATAACCTGAGTAC 57.234 33.333 0.00 0.00 0.00 2.73
1229 1243 9.903682 CCATTGTCATGTTCTCCATAATATTTC 57.096 33.333 0.00 0.00 30.71 2.17
1233 1247 8.052141 TGTCATGTTCTCCATAATATTTCCACA 58.948 33.333 0.00 0.00 30.71 4.17
1247 1261 7.715265 ATATTTCCACAAACATAGCTACTCG 57.285 36.000 0.00 0.00 0.00 4.18
1357 1373 1.478654 GGCAGGAGGTTCACCAAAGAA 60.479 52.381 0.00 0.00 38.89 2.52
1376 1392 7.391554 CCAAAGAATATCAAGAAGACTGGAACA 59.608 37.037 0.00 0.00 29.08 3.18
1499 1515 7.461749 GGGAGATGAGATTGGGTTGAAATATA 58.538 38.462 0.00 0.00 0.00 0.86
1500 1516 7.944554 GGGAGATGAGATTGGGTTGAAATATAA 59.055 37.037 0.00 0.00 0.00 0.98
1508 1524 4.624913 TGGGTTGAAATATAATTGCCCCA 58.375 39.130 0.00 0.00 37.27 4.96
1590 1606 3.308438 TCCTACAAGACCAGCGTTTAC 57.692 47.619 0.00 0.00 0.00 2.01
1645 1661 2.936919 TGCAACACAAGAGATGGAGT 57.063 45.000 0.00 0.00 0.00 3.85
1669 1685 7.455008 AGTGAGGGTAGTTTCTCAATCTTTCTA 59.545 37.037 0.00 0.00 41.07 2.10
1727 1743 9.528018 GAAAAACCAAGTTAAGACATCAAATGA 57.472 29.630 0.00 0.00 0.00 2.57
1735 1751 6.314896 AGTTAAGACATCAAATGAGCTACTGC 59.685 38.462 0.00 0.00 40.05 4.40
1852 1869 8.680903 CCCAAGGTAATGATTCATAATATGAGC 58.319 37.037 2.98 1.40 40.94 4.26
1870 1887 0.594796 GCAAAGCGTCACCTTGGTTG 60.595 55.000 0.00 0.00 0.00 3.77
2002 2023 3.497103 TGAGGCATTATCATGTGGAGG 57.503 47.619 0.00 0.00 32.28 4.30
2006 2027 2.300433 GCATTATCATGTGGAGGCACA 58.700 47.619 0.00 0.00 39.62 4.57
2083 2104 3.726557 TCTCTTTGGAGCCATTGACAT 57.273 42.857 0.00 0.00 39.31 3.06
2122 2143 4.340381 AGGGCTATCAAAGATGACATTTGC 59.660 41.667 0.00 0.00 38.69 3.68
2143 2164 2.482721 CGGTTACACCAAAGGTAAGCAG 59.517 50.000 12.95 4.51 44.99 4.24
2227 2248 6.732531 ATATGTGATCATCGCAACTATTGG 57.267 37.500 4.67 0.00 40.59 3.16
2228 2249 2.613595 TGTGATCATCGCAACTATTGGC 59.386 45.455 0.00 0.00 33.43 4.52
2229 2250 2.031682 GTGATCATCGCAACTATTGGCC 60.032 50.000 0.00 0.00 0.00 5.36
2231 2252 1.953559 TCATCGCAACTATTGGCCTC 58.046 50.000 3.32 0.00 0.00 4.70
2232 2253 1.486310 TCATCGCAACTATTGGCCTCT 59.514 47.619 3.32 0.00 0.00 3.69
2234 2255 2.489938 TCGCAACTATTGGCCTCTTT 57.510 45.000 3.32 0.00 0.00 2.52
2235 2256 2.790433 TCGCAACTATTGGCCTCTTTT 58.210 42.857 3.32 0.00 0.00 2.27
2236 2257 2.487762 TCGCAACTATTGGCCTCTTTTG 59.512 45.455 3.32 2.25 0.00 2.44
2237 2258 2.415893 CGCAACTATTGGCCTCTTTTGG 60.416 50.000 3.32 0.00 0.00 3.28
2312 2486 6.206829 ACTTTCTGGTGCCAATAGTTTAAGTC 59.793 38.462 0.00 0.00 0.00 3.01
2319 2493 4.264172 TGCCAATAGTTTAAGTCCCCACAT 60.264 41.667 0.00 0.00 0.00 3.21
2323 2497 3.721087 AGTTTAAGTCCCCACATGAGG 57.279 47.619 0.00 0.00 0.00 3.86
2462 2636 1.669795 CGCAATTTGTCCAAGCCCTTC 60.670 52.381 0.00 0.00 0.00 3.46
2487 2667 5.915175 ACTCGAGATTAGACCAAATTACCC 58.085 41.667 21.68 0.00 0.00 3.69
2492 2672 5.826643 AGATTAGACCAAATTACCCTTGCA 58.173 37.500 0.00 0.00 0.00 4.08
2496 2676 5.622346 AGACCAAATTACCCTTGCAAAAA 57.378 34.783 0.00 0.00 0.00 1.94
2529 2710 7.911651 TGCCCAAATGGAAAATGTTAAGAATA 58.088 30.769 0.00 0.00 37.39 1.75
2531 2712 8.040727 GCCCAAATGGAAAATGTTAAGAATACT 58.959 33.333 0.00 0.00 37.39 2.12
2609 2790 9.504708 GTCAATACTACTCCTCTAGCAATAGTA 57.495 37.037 0.00 0.00 31.59 1.82
2634 2815 7.648177 AAATCCTGGTATGGGACTTGTATAT 57.352 36.000 0.00 0.00 35.51 0.86
2641 2822 9.658799 CTGGTATGGGACTTGTATATAATCAAG 57.341 37.037 14.56 14.56 44.29 3.02
2679 2860 7.006509 CCTATGAATACAAAGGATCCAACCAT 58.993 38.462 15.82 7.84 0.00 3.55
2681 2862 6.773976 TGAATACAAAGGATCCAACCATTC 57.226 37.500 15.82 14.91 0.00 2.67
2682 2863 5.356751 TGAATACAAAGGATCCAACCATTCG 59.643 40.000 15.82 0.00 0.00 3.34
2731 2913 2.173569 AGATTTAGCAAGGTGGCTAGGG 59.826 50.000 0.00 0.00 46.25 3.53
2738 2920 1.926426 AAGGTGGCTAGGGCATGGAC 61.926 60.000 0.00 0.00 40.92 4.02
2755 2937 4.529716 TGGACTTTTTGTAAACCCCTCT 57.470 40.909 0.00 0.00 0.00 3.69
2808 3654 3.071602 ACACTCTAAGATGCCACAACACT 59.928 43.478 0.00 0.00 0.00 3.55
2825 3673 5.600484 ACAACACTCCCTCTCTTATATCCTG 59.400 44.000 0.00 0.00 0.00 3.86
2863 3711 9.597681 ATCTTGCTAATGAGGGAATTCATTAAT 57.402 29.630 7.93 0.00 44.85 1.40
2864 3712 9.425248 TCTTGCTAATGAGGGAATTCATTAATT 57.575 29.630 7.93 4.63 44.85 1.40
2866 3714 9.820725 TTGCTAATGAGGGAATTCATTAATTTG 57.179 29.630 7.93 4.49 44.85 2.32
2882 3730 9.734620 TCATTAATTTGAAACTCTTCACAACAG 57.265 29.630 0.00 0.00 41.34 3.16
2898 3746 7.189693 TCACAACAGCTGAGTAAAATTGTAG 57.810 36.000 23.35 12.39 0.00 2.74
2960 3811 7.390440 TCCATATTTTCCTAACCAGCATATTCG 59.610 37.037 0.00 0.00 0.00 3.34
3012 3863 6.917477 TGTTGAAGAGTATGCAATGTCAAAAC 59.083 34.615 0.00 0.00 0.00 2.43
3021 3872 4.148079 TGCAATGTCAAAACCACCATCTA 58.852 39.130 0.00 0.00 0.00 1.98
3051 3902 9.130312 TGGTACGAATTAATTTTTAACATGTGC 57.870 29.630 0.00 0.00 0.00 4.57
3072 3923 4.202315 TGCCCATGTGAGCGTAATATTAGT 60.202 41.667 0.00 0.00 0.00 2.24
3076 3927 5.333339 CCATGTGAGCGTAATATTAGTGCAC 60.333 44.000 9.40 9.40 0.00 4.57
3118 3969 3.956199 TGGGAGTAACTTGTATAGGACCG 59.044 47.826 0.00 0.00 0.00 4.79
3126 3977 6.610075 AACTTGTATAGGACCGGACTTTTA 57.390 37.500 9.46 0.00 0.00 1.52
3127 3978 6.218108 ACTTGTATAGGACCGGACTTTTAG 57.782 41.667 9.46 3.12 0.00 1.85
3183 4034 1.986882 AAGGTGGAGACAAAGCAAGG 58.013 50.000 0.00 0.00 46.06 3.61
3184 4035 1.140312 AGGTGGAGACAAAGCAAGGA 58.860 50.000 0.00 0.00 46.06 3.36
3250 4101 4.090354 TCGCAATAACGTTTAGGTCTTTCG 59.910 41.667 5.91 0.00 0.00 3.46
3295 4146 4.271696 TGAATGACTGTAAGGTGTCTGG 57.728 45.455 0.00 0.00 39.30 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 6.318648 GGTATGAAATCTACCTGCACAATTGA 59.681 38.462 13.59 0.00 36.50 2.57
121 122 5.830000 ACAACTTTAGAACCTCAAACACC 57.170 39.130 0.00 0.00 0.00 4.16
122 123 7.535997 AGAAACAACTTTAGAACCTCAAACAC 58.464 34.615 0.00 0.00 0.00 3.32
127 128 7.110155 ACAAGAGAAACAACTTTAGAACCTCA 58.890 34.615 0.00 0.00 0.00 3.86
156 157 5.378230 TGGTCTTTGCCATCTATCAGAAT 57.622 39.130 0.00 0.00 32.81 2.40
184 185 5.356190 AGCACATTTCCATCACTATCAACTG 59.644 40.000 0.00 0.00 0.00 3.16
231 232 1.423584 TGTTGAGGCCTCTTCTCACA 58.576 50.000 32.28 21.95 40.51 3.58
248 249 4.012374 CAGCTTTGAAGGTATGGTGATGT 58.988 43.478 0.00 0.00 34.49 3.06
259 260 1.259609 TCATTGCCCAGCTTTGAAGG 58.740 50.000 0.00 0.00 0.00 3.46
294 296 3.813166 AGTGTTACGGGTCAAGATTTGTG 59.187 43.478 0.00 0.00 0.00 3.33
297 299 5.699458 CACTTAGTGTTACGGGTCAAGATTT 59.301 40.000 3.88 0.00 0.00 2.17
305 307 1.270550 CGGTCACTTAGTGTTACGGGT 59.729 52.381 12.41 0.00 34.79 5.28
311 313 6.050432 TCACAATAAACGGTCACTTAGTGTT 58.950 36.000 12.41 1.54 34.95 3.32
321 323 7.360575 ACTATGAAGTTCACAATAAACGGTC 57.639 36.000 7.96 0.00 29.00 4.79
365 367 5.047306 TCGTCAAGAATGGTCAGTACAAGAT 60.047 40.000 0.00 0.00 0.00 2.40
431 433 7.144722 TGTCCAGCAATACTGTTTATCAAAG 57.855 36.000 0.00 0.00 45.68 2.77
471 473 8.215050 TCTCAAAGGAAAGAAAGTACACCATAA 58.785 33.333 0.00 0.00 0.00 1.90
473 475 6.601332 TCTCAAAGGAAAGAAAGTACACCAT 58.399 36.000 0.00 0.00 0.00 3.55
476 478 9.803315 AATTTTCTCAAAGGAAAGAAAGTACAC 57.197 29.630 0.00 0.00 41.22 2.90
529 531 7.440198 TGTTGATACAATGCTGGAAAATTGAA 58.560 30.769 2.60 0.00 37.26 2.69
652 655 6.075984 TCTCATACTCCCAAATACTACCTCC 58.924 44.000 0.00 0.00 0.00 4.30
670 673 8.041323 GGTTCTTACATTTCCTCAACTCTCATA 58.959 37.037 0.00 0.00 0.00 2.15
697 700 7.411486 TTCACAAAAAGTCCATAAAAGTGGA 57.589 32.000 0.00 0.00 45.78 4.02
714 717 9.689976 CATATATTCACCACACTTTTTCACAAA 57.310 29.630 0.00 0.00 0.00 2.83
715 718 9.072375 TCATATATTCACCACACTTTTTCACAA 57.928 29.630 0.00 0.00 0.00 3.33
716 719 8.628630 TCATATATTCACCACACTTTTTCACA 57.371 30.769 0.00 0.00 0.00 3.58
717 720 8.730680 ACTCATATATTCACCACACTTTTTCAC 58.269 33.333 0.00 0.00 0.00 3.18
718 721 8.862325 ACTCATATATTCACCACACTTTTTCA 57.138 30.769 0.00 0.00 0.00 2.69
723 726 9.770097 CAAGATACTCATATATTCACCACACTT 57.230 33.333 0.00 0.00 0.00 3.16
724 727 8.370940 CCAAGATACTCATATATTCACCACACT 58.629 37.037 0.00 0.00 0.00 3.55
725 728 8.150945 ACCAAGATACTCATATATTCACCACAC 58.849 37.037 0.00 0.00 0.00 3.82
726 729 8.262601 ACCAAGATACTCATATATTCACCACA 57.737 34.615 0.00 0.00 0.00 4.17
727 730 9.561069 AAACCAAGATACTCATATATTCACCAC 57.439 33.333 0.00 0.00 0.00 4.16
776 779 7.013369 TGGTAGTACTAGTGTCTAGCATTCATG 59.987 40.741 24.40 0.00 37.29 3.07
808 811 6.014647 ACCATACAGACAAGACTGGTAGTTA 58.985 40.000 4.71 0.00 41.59 2.24
820 823 5.483937 ACAAGACTGGATACCATACAGACAA 59.516 40.000 5.39 0.00 44.28 3.18
831 834 3.383825 ACCATACGGACAAGACTGGATAC 59.616 47.826 0.00 0.00 35.59 2.24
832 835 3.638860 ACCATACGGACAAGACTGGATA 58.361 45.455 0.00 0.00 35.59 2.59
833 836 2.467880 ACCATACGGACAAGACTGGAT 58.532 47.619 0.00 0.00 35.59 3.41
834 837 1.933021 ACCATACGGACAAGACTGGA 58.067 50.000 0.00 0.00 35.59 3.86
835 838 2.494471 TGTACCATACGGACAAGACTGG 59.506 50.000 0.00 0.00 35.59 4.00
836 839 3.861276 TGTACCATACGGACAAGACTG 57.139 47.619 0.00 0.00 35.59 3.51
837 840 4.222145 ACATTGTACCATACGGACAAGACT 59.778 41.667 0.00 0.00 36.44 3.24
838 841 4.501071 ACATTGTACCATACGGACAAGAC 58.499 43.478 0.00 0.00 36.44 3.01
839 842 4.811969 ACATTGTACCATACGGACAAGA 57.188 40.909 0.00 0.00 36.44 3.02
840 843 6.759356 TGATAACATTGTACCATACGGACAAG 59.241 38.462 0.00 0.00 36.44 3.16
841 844 6.641474 TGATAACATTGTACCATACGGACAA 58.359 36.000 0.00 0.00 37.00 3.18
842 845 6.223351 TGATAACATTGTACCATACGGACA 57.777 37.500 0.00 0.00 35.59 4.02
843 846 6.367969 GGATGATAACATTGTACCATACGGAC 59.632 42.308 0.00 0.00 36.82 4.79
844 847 6.042208 TGGATGATAACATTGTACCATACGGA 59.958 38.462 0.00 0.00 36.82 4.69
845 848 6.227522 TGGATGATAACATTGTACCATACGG 58.772 40.000 0.00 0.00 36.82 4.02
846 849 7.722795 TTGGATGATAACATTGTACCATACG 57.277 36.000 0.00 0.00 36.82 3.06
939 942 5.614923 TCTGCGTTTCGATGGAAAAATTA 57.385 34.783 4.31 0.00 43.39 1.40
951 955 3.713288 TGATACCCTTATCTGCGTTTCG 58.287 45.455 0.00 0.00 35.90 3.46
989 993 4.718774 AGTCTACATTCATGATGACAGGGT 59.281 41.667 0.00 0.00 39.15 4.34
1015 1019 3.605634 TGCTGTTGCTGGAATACGTATT 58.394 40.909 20.46 20.46 40.48 1.89
1019 1023 3.940303 GTATTGCTGTTGCTGGAATACG 58.060 45.455 11.93 0.00 37.08 3.06
1028 1032 1.394917 CTCTGACCGTATTGCTGTTGC 59.605 52.381 0.00 0.00 40.20 4.17
1034 1038 1.939974 TGCATCTCTGACCGTATTGC 58.060 50.000 0.00 0.00 0.00 3.56
1036 1040 3.873361 CACAATGCATCTCTGACCGTATT 59.127 43.478 0.00 0.00 0.00 1.89
1149 1153 6.796785 TCATTGATGACATGGAGAGAGTTA 57.203 37.500 0.00 0.00 0.00 2.24
1155 1159 5.425196 TGACTTCATTGATGACATGGAGA 57.575 39.130 6.56 0.00 36.36 3.71
1173 1177 8.486210 TCAGGTTATAGTTTAATGATGCTGACT 58.514 33.333 0.00 0.00 0.00 3.41
1185 1189 9.038072 TGACAATGGTACTCAGGTTATAGTTTA 57.962 33.333 0.00 0.00 0.00 2.01
1191 1195 6.313519 ACATGACAATGGTACTCAGGTTAT 57.686 37.500 0.00 0.00 38.19 1.89
1202 1206 9.425248 AAATATTATGGAGAACATGACAATGGT 57.575 29.630 0.00 0.00 40.82 3.55
1203 1207 9.903682 GAAATATTATGGAGAACATGACAATGG 57.096 33.333 0.00 0.00 40.82 3.16
1208 1213 8.450578 TGTGGAAATATTATGGAGAACATGAC 57.549 34.615 0.00 0.00 40.82 3.06
1229 1243 7.534085 TTAAATCGAGTAGCTATGTTTGTGG 57.466 36.000 0.00 0.00 0.00 4.17
1233 1247 7.280205 CCACCTTTAAATCGAGTAGCTATGTTT 59.720 37.037 0.00 0.00 0.00 2.83
1247 1261 3.954258 CCACCCATCTCCACCTTTAAATC 59.046 47.826 0.00 0.00 0.00 2.17
1336 1352 0.178992 CTTTGGTGAACCTCCTGCCA 60.179 55.000 0.37 0.00 36.82 4.92
1357 1373 5.130145 CCCTCTGTTCCAGTCTTCTTGATAT 59.870 44.000 0.00 0.00 32.61 1.63
1376 1392 1.904440 ATTCTGCCCTTGATCCCTCT 58.096 50.000 0.00 0.00 0.00 3.69
1455 1471 1.135603 CCCATTGCGTGTCATGTTCAG 60.136 52.381 0.00 0.00 0.00 3.02
1499 1515 0.638292 ACATCCTCCATGGGGCAATT 59.362 50.000 13.02 0.00 36.72 2.32
1500 1516 1.533187 TACATCCTCCATGGGGCAAT 58.467 50.000 13.02 1.44 36.72 3.56
1508 1524 5.457197 CCAATCCAGTGATTACATCCTCCAT 60.457 44.000 0.00 0.00 39.20 3.41
1525 1541 1.948834 CTGCAATGTATCGCCAATCCA 59.051 47.619 0.00 0.00 0.00 3.41
1590 1606 1.246056 TGTCGTTGGACCTAGACCCG 61.246 60.000 10.52 0.00 42.73 5.28
1645 1661 6.688073 AGAAAGATTGAGAAACTACCCTCA 57.312 37.500 0.00 0.00 37.61 3.86
1669 1685 4.677182 ACAAGAAGGGGCAGTATTTTGAT 58.323 39.130 0.00 0.00 0.00 2.57
1715 1731 4.212143 TGCAGTAGCTCATTTGATGTCT 57.788 40.909 0.00 0.00 42.74 3.41
1727 1743 1.727062 AGCCCATAGATGCAGTAGCT 58.273 50.000 0.00 0.00 42.74 3.32
1735 1751 1.340405 GGTGCCCATAGCCCATAGATG 60.340 57.143 0.00 0.00 42.71 2.90
1852 1869 0.594796 GCAACCAAGGTGACGCTTTG 60.595 55.000 3.98 3.98 34.39 2.77
1896 1917 7.044249 CGTAATCTGAAGGACACGTAAATACTG 60.044 40.741 0.00 0.00 33.64 2.74
1903 1924 4.005650 ACTCGTAATCTGAAGGACACGTA 58.994 43.478 0.00 0.00 37.17 3.57
2002 2023 2.170166 TCCACCATCCTTTCAATGTGC 58.830 47.619 0.00 0.00 0.00 4.57
2006 2027 2.041081 TCCGTTCCACCATCCTTTCAAT 59.959 45.455 0.00 0.00 0.00 2.57
2083 2104 1.206371 GCCCTAGTAGCTTCCGAACAA 59.794 52.381 0.00 0.00 0.00 2.83
2143 2164 6.586344 TCATACCTCTTGGATTCATCTTCAC 58.414 40.000 0.00 0.00 37.04 3.18
2228 2249 5.652014 TGTGAATGGTATAAGCCAAAAGAGG 59.348 40.000 0.00 0.00 42.48 3.69
2229 2250 6.375455 ACTGTGAATGGTATAAGCCAAAAGAG 59.625 38.462 0.00 0.00 42.48 2.85
2231 2252 6.515272 ACTGTGAATGGTATAAGCCAAAAG 57.485 37.500 0.00 0.00 42.48 2.27
2232 2253 7.448777 TGTTACTGTGAATGGTATAAGCCAAAA 59.551 33.333 0.00 0.00 42.48 2.44
2234 2255 6.477253 TGTTACTGTGAATGGTATAAGCCAA 58.523 36.000 0.00 0.00 42.48 4.52
2235 2256 6.056090 TGTTACTGTGAATGGTATAAGCCA 57.944 37.500 0.00 0.00 43.48 4.75
2236 2257 7.568199 AATGTTACTGTGAATGGTATAAGCC 57.432 36.000 0.00 0.00 0.00 4.35
2237 2258 8.283291 GCTAATGTTACTGTGAATGGTATAAGC 58.717 37.037 0.00 0.00 0.00 3.09
2312 2486 0.750546 CACTGATGCCTCATGTGGGG 60.751 60.000 15.39 6.82 31.98 4.96
2319 2493 6.299805 ACTTTATTAGACACTGATGCCTCA 57.700 37.500 0.00 0.00 0.00 3.86
2323 2497 8.703604 TTGAGTACTTTATTAGACACTGATGC 57.296 34.615 0.00 0.00 0.00 3.91
2404 2578 4.632251 CGGTGCCACATATAAACACAAGTA 59.368 41.667 0.00 0.00 32.89 2.24
2405 2579 3.438781 CGGTGCCACATATAAACACAAGT 59.561 43.478 0.00 0.00 32.89 3.16
2406 2580 3.730662 GCGGTGCCACATATAAACACAAG 60.731 47.826 0.00 0.00 32.89 3.16
2443 2617 1.669795 CGAAGGGCTTGGACAAATTGC 60.670 52.381 0.00 0.00 0.00 3.56
2444 2618 1.885887 TCGAAGGGCTTGGACAAATTG 59.114 47.619 0.00 0.00 0.00 2.32
2454 2628 1.187087 AATCTCGAGTCGAAGGGCTT 58.813 50.000 17.27 0.14 34.74 4.35
2462 2636 5.686397 GGTAATTTGGTCTAATCTCGAGTCG 59.314 44.000 13.13 6.09 0.00 4.18
2487 2667 7.998753 TTTGGGCATTTTTAATTTTTGCAAG 57.001 28.000 0.00 0.00 35.04 4.01
2496 2676 8.419922 ACATTTTCCATTTGGGCATTTTTAAT 57.580 26.923 0.00 0.00 36.21 1.40
2504 2684 5.815233 TCTTAACATTTTCCATTTGGGCA 57.185 34.783 0.00 0.00 36.21 5.36
2505 2685 8.040727 AGTATTCTTAACATTTTCCATTTGGGC 58.959 33.333 0.00 0.00 36.21 5.36
2546 2727 9.638239 CCTGCAATAAATAGAGAGTTAGATCTC 57.362 37.037 0.00 0.00 45.10 2.75
2567 2748 9.982651 GTAGTATTGACTTAGATATTTCCTGCA 57.017 33.333 0.00 0.00 37.10 4.41
2576 2757 9.947433 GCTAGAGGAGTAGTATTGACTTAGATA 57.053 37.037 0.00 0.00 37.10 1.98
2609 2790 4.675063 ACAAGTCCCATACCAGGATTTT 57.325 40.909 0.00 0.00 35.38 1.82
2634 2815 5.975988 AGGTCCATCTAAAGCCTTGATTA 57.024 39.130 0.00 0.00 0.00 1.75
2641 2822 6.769512 TGTATTCATAGGTCCATCTAAAGCC 58.230 40.000 0.00 0.00 0.00 4.35
2679 2860 9.653287 AACTCATTCTTCATTCAGTTATACGAA 57.347 29.630 0.00 0.00 0.00 3.85
2731 2913 3.323691 AGGGGTTTACAAAAAGTCCATGC 59.676 43.478 0.00 0.00 0.00 4.06
2762 2944 6.594788 AGTTGTTGATTAAGCATTGTGGAT 57.405 33.333 0.00 0.00 0.00 3.41
2808 3654 7.309091 AGAAATGACAGGATATAAGAGAGGGA 58.691 38.462 0.00 0.00 0.00 4.20
2825 3673 8.772705 CCTCATTAGCAAGATCTAAGAAATGAC 58.227 37.037 14.63 0.35 32.66 3.06
2863 3711 4.699735 TCAGCTGTTGTGAAGAGTTTCAAA 59.300 37.500 14.67 0.00 44.49 2.69
2864 3712 4.260985 TCAGCTGTTGTGAAGAGTTTCAA 58.739 39.130 14.67 0.00 44.49 2.69
2865 3713 3.872696 TCAGCTGTTGTGAAGAGTTTCA 58.127 40.909 14.67 0.00 40.92 2.69
2866 3714 3.873952 ACTCAGCTGTTGTGAAGAGTTTC 59.126 43.478 14.67 0.00 32.88 2.78
3051 3902 4.152402 GCACTAATATTACGCTCACATGGG 59.848 45.833 0.00 0.00 0.00 4.00
3057 3908 6.978343 AAAAGTGCACTAATATTACGCTCA 57.022 33.333 22.01 0.00 0.00 4.26
3072 3923 9.469807 CCAAGTAAAATGTATTGTAAAAGTGCA 57.530 29.630 0.00 0.00 0.00 4.57
3101 3952 5.588958 AAGTCCGGTCCTATACAAGTTAC 57.411 43.478 0.00 0.00 0.00 2.50
3103 3954 5.494390 AAAAGTCCGGTCCTATACAAGTT 57.506 39.130 0.00 0.00 0.00 2.66
3118 3969 8.779354 ATCTTGTGTATTCACTCTAAAAGTCC 57.221 34.615 4.01 0.00 44.14 3.85
3126 3977 5.658634 TGGCTAGATCTTGTGTATTCACTCT 59.341 40.000 0.00 1.32 44.14 3.24
3127 3978 5.907207 TGGCTAGATCTTGTGTATTCACTC 58.093 41.667 0.00 0.00 44.14 3.51
3163 4014 2.091885 TCCTTGCTTTGTCTCCACCTTT 60.092 45.455 0.00 0.00 0.00 3.11
3183 4034 6.573434 TGTGATATGTACATTCTGGTCACTC 58.427 40.000 14.77 2.30 36.57 3.51
3184 4035 6.544928 TGTGATATGTACATTCTGGTCACT 57.455 37.500 14.77 0.00 36.57 3.41
3283 4134 9.042008 CATTACAATATACACCAGACACCTTAC 57.958 37.037 0.00 0.00 0.00 2.34


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

AutoCloner maintained by Alex Coulton.