Multiple sequence alignment - TraesCS2B01G430300

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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 TraesCS2B01G430300 chr2B 100.000 2839 0 0 1 2839 619046083 619043245 0.000000e+00 5243.0
1 TraesCS2B01G430300 chr2B 93.215 1017 44 5 883 1897 618968797 618967804 0.000000e+00 1472.0
2 TraesCS2B01G430300 chr2B 96.252 667 22 3 2174 2839 50113022 50113686 0.000000e+00 1090.0
3 TraesCS2B01G430300 chr2B 95.522 670 26 1 2174 2839 73768614 73767945 0.000000e+00 1068.0
4 TraesCS2B01G430300 chr2B 95.502 667 29 1 2174 2839 748303056 748302390 0.000000e+00 1064.0
5 TraesCS2B01G430300 chr2B 80.871 1056 105 55 883 1899 618873848 618872851 0.000000e+00 741.0
6 TraesCS2B01G430300 chr2B 96.330 109 1 1 2038 2143 35254940 35255048 2.910000e-40 176.0
7 TraesCS2B01G430300 chr2B 96.330 109 1 1 2038 2143 635671234 635671126 2.910000e-40 176.0
8 TraesCS2B01G430300 chr2A 89.611 1338 64 20 631 1949 669620417 669619136 0.000000e+00 1631.0
9 TraesCS2B01G430300 chr2A 80.058 1038 103 54 883 1871 669568157 669567175 0.000000e+00 675.0
10 TraesCS2B01G430300 chr2A 82.401 608 47 27 42 599 669621418 669620821 2.560000e-130 475.0
11 TraesCS2B01G430300 chr2A 86.979 192 23 2 1751 1941 669618646 669618456 6.160000e-52 215.0
12 TraesCS2B01G430300 chr2A 82.653 98 12 1 1945 2037 669618251 669618154 6.520000e-12 82.4
13 TraesCS2B01G430300 chr2D 90.406 1282 46 22 800 2038 524003515 524002268 0.000000e+00 1615.0
14 TraesCS2B01G430300 chr2D 91.328 738 50 12 2108 2839 23145045 23145774 0.000000e+00 996.0
15 TraesCS2B01G430300 chr2D 92.040 201 16 0 602 802 524003796 524003596 1.660000e-72 283.0
16 TraesCS2B01G430300 chr6B 94.687 734 30 2 2107 2839 720682226 720682951 0.000000e+00 1131.0
17 TraesCS2B01G430300 chr6B 95.646 666 28 1 2174 2839 115385428 115384764 0.000000e+00 1068.0
18 TraesCS2B01G430300 chr6B 90.120 749 52 13 2111 2839 5361938 5361192 0.000000e+00 953.0
19 TraesCS2B01G430300 chr5B 95.946 666 26 1 2174 2839 535280492 535281156 0.000000e+00 1079.0
20 TraesCS2B01G430300 chr5B 96.396 111 1 1 2036 2143 536880538 536880428 2.250000e-41 180.0
21 TraesCS2B01G430300 chr5B 96.364 110 1 1 2038 2144 660760699 660760590 8.080000e-41 178.0
22 TraesCS2B01G430300 chr1B 94.813 694 33 3 2149 2839 561791684 561792377 0.000000e+00 1079.0
23 TraesCS2B01G430300 chr1B 98.131 107 1 1 2038 2143 21607356 21607250 4.830000e-43 185.0
24 TraesCS2B01G430300 chr4B 93.443 732 36 5 2109 2839 533967181 533967901 0.000000e+00 1075.0
25 TraesCS2B01G430300 chr4B 80.952 147 25 3 314 460 665268348 665268205 2.310000e-21 113.0
26 TraesCS2B01G430300 chr3B 95.659 668 27 2 2174 2839 171158955 171158288 0.000000e+00 1072.0
27 TraesCS2B01G430300 chr3B 88.828 734 45 14 2109 2839 710938167 710938866 0.000000e+00 867.0
28 TraesCS2B01G430300 chr3B 97.248 109 0 1 2038 2143 14794457 14794565 6.250000e-42 182.0
29 TraesCS2B01G430300 chr3B 94.690 113 3 1 2034 2143 710938045 710938157 3.760000e-39 172.0
30 TraesCS2B01G430300 chr7B 91.734 738 48 8 2109 2839 610663571 610662840 0.000000e+00 1013.0
31 TraesCS2B01G430300 chr4D 91.576 736 50 10 2111 2839 411908885 411908155 0.000000e+00 1005.0
32 TraesCS2B01G430300 chr3D 91.293 735 50 13 2111 2839 530739330 530738604 0.000000e+00 990.0
33 TraesCS2B01G430300 chr3D 89.768 733 40 12 2109 2839 79054694 79053995 0.000000e+00 905.0
34 TraesCS2B01G430300 chr3D 81.720 93 10 6 431 520 584162406 584162318 1.410000e-08 71.3
35 TraesCS2B01G430300 chr5D 90.418 741 56 15 2108 2839 70696346 70697080 0.000000e+00 961.0
36 TraesCS2B01G430300 chr5D 87.261 157 11 2 2037 2184 448796974 448796818 1.350000e-38 171.0
37 TraesCS2B01G430300 chr5D 80.102 196 30 9 314 507 14129204 14129016 1.370000e-28 137.0
38 TraesCS2B01G430300 chr5A 88.347 738 54 16 2108 2839 131411555 131412266 0.000000e+00 857.0
39 TraesCS2B01G430300 chr5A 89.062 64 4 3 437 499 704831560 704831499 3.030000e-10 76.8
40 TraesCS2B01G430300 chr5A 75.926 162 25 10 324 478 528279130 528279284 1.410000e-08 71.3
41 TraesCS2B01G430300 chr4A 93.333 120 4 2 2027 2143 677670783 677670665 1.050000e-39 174.0
42 TraesCS2B01G430300 chr7A 81.739 115 18 3 374 488 550304289 550304178 3.010000e-15 93.5
43 TraesCS2B01G430300 chrUn 89.333 75 3 5 448 520 108958578 108958649 3.900000e-14 89.8
44 TraesCS2B01G430300 chrUn 87.059 85 4 7 448 530 335717773 335717694 3.900000e-14 89.8
45 TraesCS2B01G430300 chr3A 75.238 210 35 15 325 523 621985815 621986018 1.810000e-12 84.2
46 TraesCS2B01G430300 chr3A 79.412 102 10 9 420 518 656975623 656975716 8.490000e-06 62.1
47 TraesCS2B01G430300 chr1A 84.884 86 7 4 431 513 546795327 546795409 6.520000e-12 82.4
48 TraesCS2B01G430300 chr6D 100.000 28 0 0 335 362 97785994 97785967 5.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G430300 chr2B 619043245 619046083 2838 True 5243.00 5243 100.000 1 2839 1 chr2B.!!$R4 2838
1 TraesCS2B01G430300 chr2B 618967804 618968797 993 True 1472.00 1472 93.215 883 1897 1 chr2B.!!$R3 1014
2 TraesCS2B01G430300 chr2B 50113022 50113686 664 False 1090.00 1090 96.252 2174 2839 1 chr2B.!!$F2 665
3 TraesCS2B01G430300 chr2B 73767945 73768614 669 True 1068.00 1068 95.522 2174 2839 1 chr2B.!!$R1 665
4 TraesCS2B01G430300 chr2B 748302390 748303056 666 True 1064.00 1064 95.502 2174 2839 1 chr2B.!!$R6 665
5 TraesCS2B01G430300 chr2B 618872851 618873848 997 True 741.00 741 80.871 883 1899 1 chr2B.!!$R2 1016
6 TraesCS2B01G430300 chr2A 669567175 669568157 982 True 675.00 675 80.058 883 1871 1 chr2A.!!$R1 988
7 TraesCS2B01G430300 chr2A 669618154 669621418 3264 True 600.85 1631 85.411 42 2037 4 chr2A.!!$R2 1995
8 TraesCS2B01G430300 chr2D 23145045 23145774 729 False 996.00 996 91.328 2108 2839 1 chr2D.!!$F1 731
9 TraesCS2B01G430300 chr2D 524002268 524003796 1528 True 949.00 1615 91.223 602 2038 2 chr2D.!!$R1 1436
10 TraesCS2B01G430300 chr6B 720682226 720682951 725 False 1131.00 1131 94.687 2107 2839 1 chr6B.!!$F1 732
11 TraesCS2B01G430300 chr6B 115384764 115385428 664 True 1068.00 1068 95.646 2174 2839 1 chr6B.!!$R2 665
12 TraesCS2B01G430300 chr6B 5361192 5361938 746 True 953.00 953 90.120 2111 2839 1 chr6B.!!$R1 728
13 TraesCS2B01G430300 chr5B 535280492 535281156 664 False 1079.00 1079 95.946 2174 2839 1 chr5B.!!$F1 665
14 TraesCS2B01G430300 chr1B 561791684 561792377 693 False 1079.00 1079 94.813 2149 2839 1 chr1B.!!$F1 690
15 TraesCS2B01G430300 chr4B 533967181 533967901 720 False 1075.00 1075 93.443 2109 2839 1 chr4B.!!$F1 730
16 TraesCS2B01G430300 chr3B 171158288 171158955 667 True 1072.00 1072 95.659 2174 2839 1 chr3B.!!$R1 665
17 TraesCS2B01G430300 chr3B 710938045 710938866 821 False 519.50 867 91.759 2034 2839 2 chr3B.!!$F2 805
18 TraesCS2B01G430300 chr7B 610662840 610663571 731 True 1013.00 1013 91.734 2109 2839 1 chr7B.!!$R1 730
19 TraesCS2B01G430300 chr4D 411908155 411908885 730 True 1005.00 1005 91.576 2111 2839 1 chr4D.!!$R1 728
20 TraesCS2B01G430300 chr3D 530738604 530739330 726 True 990.00 990 91.293 2111 2839 1 chr3D.!!$R2 728
21 TraesCS2B01G430300 chr3D 79053995 79054694 699 True 905.00 905 89.768 2109 2839 1 chr3D.!!$R1 730
22 TraesCS2B01G430300 chr5D 70696346 70697080 734 False 961.00 961 90.418 2108 2839 1 chr5D.!!$F1 731
23 TraesCS2B01G430300 chr5A 131411555 131412266 711 False 857.00 857 88.347 2108 2839 1 chr5A.!!$F1 731

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
924 1431 0.107459 GATCAGACTCCCAACTGCCC 60.107 60.0 0.0 0.0 34.57 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2188 3767 0.392461 ATTCTAATGGCGCACCGTGT 60.392 50.0 10.83 0.0 39.7 4.49 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
25 26 6.606768 TGTTTCCTTCATTGTTTTTGTTTGC 58.393 32.000 0.00 0.00 0.00 3.68
26 27 6.429385 TGTTTCCTTCATTGTTTTTGTTTGCT 59.571 30.769 0.00 0.00 0.00 3.91
27 28 7.040823 TGTTTCCTTCATTGTTTTTGTTTGCTT 60.041 29.630 0.00 0.00 0.00 3.91
28 29 7.446001 TTCCTTCATTGTTTTTGTTTGCTTT 57.554 28.000 0.00 0.00 0.00 3.51
29 30 7.446001 TCCTTCATTGTTTTTGTTTGCTTTT 57.554 28.000 0.00 0.00 0.00 2.27
30 31 8.553459 TCCTTCATTGTTTTTGTTTGCTTTTA 57.447 26.923 0.00 0.00 0.00 1.52
31 32 9.171877 TCCTTCATTGTTTTTGTTTGCTTTTAT 57.828 25.926 0.00 0.00 0.00 1.40
32 33 9.786105 CCTTCATTGTTTTTGTTTGCTTTTATT 57.214 25.926 0.00 0.00 0.00 1.40
39 40 9.950680 TGTTTTTGTTTGCTTTTATTTGTTTCA 57.049 22.222 0.00 0.00 0.00 2.69
50 51 8.925700 GCTTTTATTTGTTTCACTTTATCCTGG 58.074 33.333 0.00 0.00 0.00 4.45
66 67 7.604657 TTATCCTGGTTTCTTTGCCTTTTTA 57.395 32.000 0.00 0.00 0.00 1.52
111 112 9.107367 GTTTTCTTTACTGTTTTCATCGATCAG 57.893 33.333 8.96 8.96 0.00 2.90
120 121 7.604164 ACTGTTTTCATCGATCAGTAGAACATT 59.396 33.333 13.36 3.81 37.55 2.71
129 130 7.742151 TCGATCAGTAGAACATTTGTTGATTG 58.258 34.615 0.00 2.60 38.56 2.67
136 137 9.520204 AGTAGAACATTTGTTGATTGTTTCTTG 57.480 29.630 0.00 0.00 38.56 3.02
148 149 6.279882 TGATTGTTTCTTGTTCATTGGGTTC 58.720 36.000 0.00 0.00 0.00 3.62
160 161 8.430801 TGTTCATTGGGTTCTTTTATGTTTTG 57.569 30.769 0.00 0.00 0.00 2.44
161 162 8.260818 TGTTCATTGGGTTCTTTTATGTTTTGA 58.739 29.630 0.00 0.00 0.00 2.69
168 169 8.887717 TGGGTTCTTTTATGTTTTGAATTGTTG 58.112 29.630 0.00 0.00 0.00 3.33
177 178 9.831737 TTATGTTTTGAATTGTTGTTTTGTTGG 57.168 25.926 0.00 0.00 0.00 3.77
180 188 7.857885 TGTTTTGAATTGTTGTTTTGTTGGTTC 59.142 29.630 0.00 0.00 0.00 3.62
189 197 6.811170 TGTTGTTTTGTTGGTTCTCATCTTTC 59.189 34.615 0.00 0.00 0.00 2.62
192 200 7.257722 TGTTTTGTTGGTTCTCATCTTTCTTC 58.742 34.615 0.00 0.00 0.00 2.87
193 201 5.673337 TTGTTGGTTCTCATCTTTCTTCG 57.327 39.130 0.00 0.00 0.00 3.79
194 202 4.703897 TGTTGGTTCTCATCTTTCTTCGT 58.296 39.130 0.00 0.00 0.00 3.85
195 203 4.511454 TGTTGGTTCTCATCTTTCTTCGTG 59.489 41.667 0.00 0.00 0.00 4.35
196 204 4.336889 TGGTTCTCATCTTTCTTCGTGT 57.663 40.909 0.00 0.00 0.00 4.49
197 205 5.462530 TGGTTCTCATCTTTCTTCGTGTA 57.537 39.130 0.00 0.00 0.00 2.90
198 206 5.470368 TGGTTCTCATCTTTCTTCGTGTAG 58.530 41.667 0.00 0.00 0.00 2.74
199 207 5.243060 TGGTTCTCATCTTTCTTCGTGTAGA 59.757 40.000 0.00 0.00 0.00 2.59
200 208 5.573669 GGTTCTCATCTTTCTTCGTGTAGAC 59.426 44.000 0.00 0.00 0.00 2.59
202 210 6.516739 TCTCATCTTTCTTCGTGTAGACAT 57.483 37.500 0.00 0.00 0.00 3.06
203 211 6.925211 TCTCATCTTTCTTCGTGTAGACATT 58.075 36.000 0.00 0.00 0.00 2.71
204 212 8.051901 TCTCATCTTTCTTCGTGTAGACATTA 57.948 34.615 0.00 0.00 0.00 1.90
205 213 8.520351 TCTCATCTTTCTTCGTGTAGACATTAA 58.480 33.333 0.00 0.00 0.00 1.40
206 214 8.462143 TCATCTTTCTTCGTGTAGACATTAAC 57.538 34.615 0.00 0.00 0.00 2.01
208 216 8.873830 CATCTTTCTTCGTGTAGACATTAACAT 58.126 33.333 0.00 0.00 0.00 2.71
402 411 6.968131 TTGATGTCTACTTTGCTCATACAC 57.032 37.500 0.00 0.00 0.00 2.90
413 445 7.978982 ACTTTGCTCATACACATTCTACATTC 58.021 34.615 0.00 0.00 0.00 2.67
415 447 8.565896 TTTGCTCATACACATTCTACATTCTT 57.434 30.769 0.00 0.00 0.00 2.52
417 449 7.977904 TGCTCATACACATTCTACATTCTTTG 58.022 34.615 0.00 0.00 0.00 2.77
540 590 6.220881 ACATCAGGTATACCTAGATCTGGT 57.779 41.667 24.15 17.44 46.65 4.00
542 592 4.907809 TCAGGTATACCTAGATCTGGTCG 58.092 47.826 24.15 8.05 46.65 4.79
547 597 4.832590 ATACCTAGATCTGGTCGTTTCG 57.167 45.455 16.95 0.00 38.88 3.46
563 613 5.940595 TCGTTTCGACAAAAAGAAAAAGGA 58.059 33.333 0.00 0.00 37.98 3.36
564 614 6.380190 TCGTTTCGACAAAAAGAAAAAGGAA 58.620 32.000 0.00 0.00 37.98 3.36
614 696 2.421424 GCTAACCATCTGAAGCAACAGG 59.579 50.000 9.61 0.00 38.31 4.00
626 708 2.972505 AACAGGCCGTTCTGTGCG 60.973 61.111 8.36 0.00 46.17 5.34
716 1138 7.099764 TCTGGTTTGATTTTTGTGCAAAGTTA 58.900 30.769 0.00 0.00 32.76 2.24
722 1144 9.809096 TTTGATTTTTGTGCAAAGTTATACTCA 57.191 25.926 0.00 0.00 0.00 3.41
919 1426 2.223923 CGATCCAGATCAGACTCCCAAC 60.224 54.545 8.31 0.00 37.69 3.77
924 1431 0.107459 GATCAGACTCCCAACTGCCC 60.107 60.000 0.00 0.00 34.57 5.36
1077 1603 4.431809 CAGAACTCCAGATCAGCTACTTG 58.568 47.826 0.00 0.00 0.00 3.16
1078 1604 4.159321 CAGAACTCCAGATCAGCTACTTGA 59.841 45.833 0.00 0.00 0.00 3.02
1079 1605 4.961730 AGAACTCCAGATCAGCTACTTGAT 59.038 41.667 0.00 0.00 40.40 2.57
1122 1669 3.982316 CTCGGCAGCAATGGCAGGA 62.982 63.158 0.00 0.00 44.61 3.86
1126 1673 1.252904 GGCAGCAATGGCAGGAAAGA 61.253 55.000 0.00 0.00 44.61 2.52
1143 1690 0.391661 AGACATCCATCGCGCTGTTT 60.392 50.000 9.34 0.00 0.00 2.83
1513 2060 1.570813 CGGATTCATGTGCTAAGCGA 58.429 50.000 0.00 0.00 0.00 4.93
1514 2061 2.138320 CGGATTCATGTGCTAAGCGAT 58.862 47.619 0.00 0.00 0.00 4.58
1515 2062 2.156504 CGGATTCATGTGCTAAGCGATC 59.843 50.000 0.00 0.00 0.00 3.69
1516 2063 3.397482 GGATTCATGTGCTAAGCGATCT 58.603 45.455 0.00 0.00 0.00 2.75
1517 2064 4.560128 GGATTCATGTGCTAAGCGATCTA 58.440 43.478 0.00 0.00 0.00 1.98
1518 2065 4.624882 GGATTCATGTGCTAAGCGATCTAG 59.375 45.833 0.00 0.00 0.00 2.43
1519 2066 3.018598 TCATGTGCTAAGCGATCTAGC 57.981 47.619 5.69 5.69 37.35 3.42
1520 2067 2.362077 TCATGTGCTAAGCGATCTAGCA 59.638 45.455 10.27 10.27 43.63 3.49
1521 2068 2.959507 TGTGCTAAGCGATCTAGCAA 57.040 45.000 14.70 5.43 46.69 3.91
1522 2069 2.814269 TGTGCTAAGCGATCTAGCAAG 58.186 47.619 14.70 4.31 46.69 4.01
1523 2070 2.131183 GTGCTAAGCGATCTAGCAAGG 58.869 52.381 14.70 0.00 46.69 3.61
1524 2071 1.757118 TGCTAAGCGATCTAGCAAGGT 59.243 47.619 11.58 0.00 42.99 3.50
1525 2072 2.131183 GCTAAGCGATCTAGCAAGGTG 58.869 52.381 7.42 0.00 40.15 4.00
1526 2073 2.482142 GCTAAGCGATCTAGCAAGGTGT 60.482 50.000 7.42 0.00 40.15 4.16
1527 2074 2.015736 AAGCGATCTAGCAAGGTGTG 57.984 50.000 0.00 0.00 40.15 3.82
1656 2254 5.570589 CGGTTACGTTGTTTGTTTGGTTTTA 59.429 36.000 0.00 0.00 34.81 1.52
1717 2329 1.860399 GCATGCTACGGAGAGTACGTG 60.860 57.143 11.37 0.00 45.20 4.49
1739 2351 6.735063 CGTGTGTAGACGGTTTAATCATTTTC 59.265 38.462 0.00 0.00 35.65 2.29
1747 2359 7.812669 AGACGGTTTAATCATTTTCATTGTTCC 59.187 33.333 0.00 0.00 0.00 3.62
1769 2384 8.894731 GTTCCTGTTATTAATCTCTTTCTTCCC 58.105 37.037 0.00 0.00 0.00 3.97
1899 2514 6.641169 TGTAATACTGTTTGGTGATTTGCA 57.359 33.333 0.00 0.00 0.00 4.08
1910 2525 4.819769 TGGTGATTTGCAAAATAGGCTTC 58.180 39.130 17.19 7.82 0.00 3.86
1938 2553 0.389948 CTGGACGAAGGTTTCCCTCG 60.390 60.000 5.42 5.42 41.56 4.63
1990 3492 6.501781 ACCAGAAGTATACGAAAATCCTACG 58.498 40.000 0.00 0.00 0.00 3.51
1991 3493 5.919141 CCAGAAGTATACGAAAATCCTACGG 59.081 44.000 0.00 0.00 0.00 4.02
1992 3494 6.238842 CCAGAAGTATACGAAAATCCTACGGA 60.239 42.308 0.00 0.00 35.55 4.69
1993 3495 7.198390 CAGAAGTATACGAAAATCCTACGGAA 58.802 38.462 0.00 0.00 34.34 4.30
1995 3497 7.919621 AGAAGTATACGAAAATCCTACGGAAAG 59.080 37.037 0.00 0.00 34.34 2.62
2002 3522 4.635699 AAATCCTACGGAAAGTTGACCT 57.364 40.909 0.00 0.00 34.34 3.85
2090 3610 0.391661 ACTAATGGCGCACCTGTCAG 60.392 55.000 10.83 0.00 36.63 3.51
2188 3767 0.541392 ATCCTAATGGCGCACTGTGA 59.459 50.000 12.86 0.00 0.00 3.58
2326 3909 1.166531 GCGCCATTAGTAAGCTGGGG 61.167 60.000 12.90 12.90 43.70 4.96
2448 4032 4.403432 CCACCTCATTTGCACCATAGATTT 59.597 41.667 0.00 0.00 0.00 2.17
2521 4122 6.603599 GGGGAAGCTATCTTTATGTTGTTCTT 59.396 38.462 0.00 0.00 31.48 2.52
2522 4123 7.201741 GGGGAAGCTATCTTTATGTTGTTCTTC 60.202 40.741 0.00 0.00 31.48 2.87
2597 4202 4.202060 TGTTCGTGGTGTTGCATATGTTTT 60.202 37.500 4.29 0.00 0.00 2.43
2671 4276 3.007398 AGTTGCCAATATTTTGCCGGAAA 59.993 39.130 5.05 0.00 0.00 3.13
2692 4297 5.682943 AAGTTGATTCATTTCCGTTTCGA 57.317 34.783 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.040823 AGCAAACAAAAACAATGAAGGAAACAA 60.041 29.630 0.00 0.00 0.00 2.83
1 2 6.429385 AGCAAACAAAAACAATGAAGGAAACA 59.571 30.769 0.00 0.00 0.00 2.83
2 3 6.841119 AGCAAACAAAAACAATGAAGGAAAC 58.159 32.000 0.00 0.00 0.00 2.78
4 5 7.446001 AAAGCAAACAAAAACAATGAAGGAA 57.554 28.000 0.00 0.00 0.00 3.36
6 7 9.786105 AATAAAAGCAAACAAAAACAATGAAGG 57.214 25.926 0.00 0.00 0.00 3.46
13 14 9.950680 TGAAACAAATAAAAGCAAACAAAAACA 57.049 22.222 0.00 0.00 0.00 2.83
23 24 9.474920 CAGGATAAAGTGAAACAAATAAAAGCA 57.525 29.630 0.00 0.00 41.43 3.91
24 25 8.925700 CCAGGATAAAGTGAAACAAATAAAAGC 58.074 33.333 0.00 0.00 41.43 3.51
25 26 9.981114 ACCAGGATAAAGTGAAACAAATAAAAG 57.019 29.630 0.00 0.00 41.43 2.27
28 29 9.974980 GAAACCAGGATAAAGTGAAACAAATAA 57.025 29.630 0.00 0.00 41.43 1.40
29 30 9.362151 AGAAACCAGGATAAAGTGAAACAAATA 57.638 29.630 0.00 0.00 41.43 1.40
30 31 8.250143 AGAAACCAGGATAAAGTGAAACAAAT 57.750 30.769 0.00 0.00 41.43 2.32
31 32 7.654022 AGAAACCAGGATAAAGTGAAACAAA 57.346 32.000 0.00 0.00 41.43 2.83
32 33 7.654022 AAGAAACCAGGATAAAGTGAAACAA 57.346 32.000 0.00 0.00 41.43 2.83
33 34 7.488322 CAAAGAAACCAGGATAAAGTGAAACA 58.512 34.615 0.00 0.00 41.43 2.83
34 35 6.420903 GCAAAGAAACCAGGATAAAGTGAAAC 59.579 38.462 0.00 0.00 0.00 2.78
35 36 6.462347 GGCAAAGAAACCAGGATAAAGTGAAA 60.462 38.462 0.00 0.00 0.00 2.69
36 37 5.010617 GGCAAAGAAACCAGGATAAAGTGAA 59.989 40.000 0.00 0.00 0.00 3.18
37 38 4.522789 GGCAAAGAAACCAGGATAAAGTGA 59.477 41.667 0.00 0.00 0.00 3.41
38 39 4.524328 AGGCAAAGAAACCAGGATAAAGTG 59.476 41.667 0.00 0.00 0.00 3.16
39 40 4.740902 AGGCAAAGAAACCAGGATAAAGT 58.259 39.130 0.00 0.00 0.00 2.66
40 41 5.728637 AAGGCAAAGAAACCAGGATAAAG 57.271 39.130 0.00 0.00 0.00 1.85
85 86 9.107367 CTGATCGATGAAAACAGTAAAGAAAAC 57.893 33.333 0.54 0.00 0.00 2.43
111 112 9.301153 ACAAGAAACAATCAACAAATGTTCTAC 57.699 29.630 0.00 0.00 36.33 2.59
120 121 6.538021 CCCAATGAACAAGAAACAATCAACAA 59.462 34.615 0.00 0.00 0.00 2.83
129 130 8.764287 CATAAAAGAACCCAATGAACAAGAAAC 58.236 33.333 0.00 0.00 0.00 2.78
136 137 8.655651 TCAAAACATAAAAGAACCCAATGAAC 57.344 30.769 0.00 0.00 0.00 3.18
160 161 6.959671 TGAGAACCAACAAAACAACAATTC 57.040 33.333 0.00 0.00 0.00 2.17
161 162 7.330262 AGATGAGAACCAACAAAACAACAATT 58.670 30.769 0.00 0.00 0.00 2.32
168 169 6.414987 CGAAGAAAGATGAGAACCAACAAAAC 59.585 38.462 0.00 0.00 0.00 2.43
170 171 5.588648 ACGAAGAAAGATGAGAACCAACAAA 59.411 36.000 0.00 0.00 0.00 2.83
173 174 4.511826 ACACGAAGAAAGATGAGAACCAAC 59.488 41.667 0.00 0.00 0.00 3.77
174 175 4.703897 ACACGAAGAAAGATGAGAACCAA 58.296 39.130 0.00 0.00 0.00 3.67
176 177 5.573669 GTCTACACGAAGAAAGATGAGAACC 59.426 44.000 0.00 0.00 0.00 3.62
177 178 6.150318 TGTCTACACGAAGAAAGATGAGAAC 58.850 40.000 0.00 0.00 0.00 3.01
180 188 8.587950 GTTAATGTCTACACGAAGAAAGATGAG 58.412 37.037 0.00 0.00 0.00 2.90
189 197 9.658475 TTGAAAAATGTTAATGTCTACACGAAG 57.342 29.630 0.00 0.00 0.00 3.79
381 390 7.493971 AGAATGTGTATGAGCAAAGTAGACATC 59.506 37.037 0.00 0.00 33.00 3.06
499 531 8.038944 ACCTGATGTATACAAAAATGTAGACGT 58.961 33.333 10.14 7.88 38.79 4.34
500 532 8.420374 ACCTGATGTATACAAAAATGTAGACG 57.580 34.615 10.14 0.00 38.79 4.18
540 590 5.940595 TCCTTTTTCTTTTTGTCGAAACGA 58.059 33.333 0.00 0.00 0.00 3.85
626 708 4.917906 AGGACCAGCCATATTCTAATCC 57.082 45.455 0.00 0.00 40.02 3.01
722 1144 1.970114 ATCTGTCGGTCACGGACGT 60.970 57.895 10.63 0.00 43.60 4.34
919 1426 0.745486 TTGCATGTGATCGAGGGCAG 60.745 55.000 0.00 0.00 32.31 4.85
924 1431 2.222663 CGTGAACTTGCATGTGATCGAG 60.223 50.000 5.94 0.00 0.00 4.04
1059 1570 4.935352 GATCAAGTAGCTGATCTGGAGT 57.065 45.455 0.00 0.00 45.56 3.85
1078 1604 7.012138 GTGATCACTAAGCACAGATCAAATGAT 59.988 37.037 18.83 0.00 45.78 2.45
1079 1605 6.314648 GTGATCACTAAGCACAGATCAAATGA 59.685 38.462 18.83 0.00 45.78 2.57
1080 1606 6.315642 AGTGATCACTAAGCACAGATCAAATG 59.684 38.462 26.87 0.00 45.78 2.32
1081 1607 6.413052 AGTGATCACTAAGCACAGATCAAAT 58.587 36.000 26.87 0.00 45.78 2.32
1082 1608 5.798132 AGTGATCACTAAGCACAGATCAAA 58.202 37.500 26.87 0.00 45.78 2.69
1083 1609 5.411831 AGTGATCACTAAGCACAGATCAA 57.588 39.130 26.87 0.00 45.78 2.57
1084 1610 4.439289 CGAGTGATCACTAAGCACAGATCA 60.439 45.833 27.95 0.00 43.14 2.92
1122 1669 0.391661 ACAGCGCGATGGATGTCTTT 60.392 50.000 29.52 0.92 0.00 2.52
1126 1673 0.391661 AGAAACAGCGCGATGGATGT 60.392 50.000 29.52 12.38 0.00 3.06
1143 1690 2.915659 ACCAGGTTCACGGCGAGA 60.916 61.111 16.62 8.96 0.00 4.04
1287 1834 1.569493 GTTCAGCGCGTTGACACAT 59.431 52.632 25.73 0.00 0.00 3.21
1519 2066 0.957395 AGATCGCTTGGCACACCTTG 60.957 55.000 0.00 0.00 39.29 3.61
1520 2067 0.613260 TAGATCGCTTGGCACACCTT 59.387 50.000 0.00 0.00 39.29 3.50
1521 2068 0.176680 CTAGATCGCTTGGCACACCT 59.823 55.000 0.00 0.00 39.29 4.00
1522 2069 1.432270 GCTAGATCGCTTGGCACACC 61.432 60.000 0.00 0.00 39.29 4.16
1523 2070 0.740868 TGCTAGATCGCTTGGCACAC 60.741 55.000 0.00 0.00 39.29 3.82
1524 2071 0.036483 TTGCTAGATCGCTTGGCACA 60.036 50.000 0.00 0.00 33.58 4.57
1525 2072 0.654683 CTTGCTAGATCGCTTGGCAC 59.345 55.000 0.00 0.00 33.58 5.01
1526 2073 0.462581 CCTTGCTAGATCGCTTGGCA 60.463 55.000 0.00 0.00 32.56 4.92
1527 2074 0.462759 ACCTTGCTAGATCGCTTGGC 60.463 55.000 0.00 0.00 0.00 4.52
1528 2075 1.293924 CACCTTGCTAGATCGCTTGG 58.706 55.000 0.00 0.00 0.00 3.61
1529 2076 1.662629 CACACCTTGCTAGATCGCTTG 59.337 52.381 0.00 0.00 0.00 4.01
1530 2077 2.015736 CACACCTTGCTAGATCGCTT 57.984 50.000 0.00 0.00 0.00 4.68
1531 2078 3.748863 CACACCTTGCTAGATCGCT 57.251 52.632 0.00 0.00 0.00 4.93
1656 2254 2.159599 GCTAGCACGTACGTCAACTAGT 60.160 50.000 30.60 13.46 31.34 2.57
1717 2329 9.061610 CAATGAAAATGATTAAACCGTCTACAC 57.938 33.333 0.00 0.00 0.00 2.90
1747 2359 9.898152 AGAAGGGAAGAAAGAGATTAATAACAG 57.102 33.333 0.00 0.00 0.00 3.16
1767 2382 2.485814 CTCGCCAAGAAAGAAAGAAGGG 59.514 50.000 0.00 0.00 0.00 3.95
1769 2384 4.513318 AGAACTCGCCAAGAAAGAAAGAAG 59.487 41.667 0.00 0.00 0.00 2.85
1899 2514 3.129287 CAGCATTGACCGAAGCCTATTTT 59.871 43.478 0.00 0.00 0.00 1.82
1910 2525 1.361668 CCTTCGTCCAGCATTGACCG 61.362 60.000 0.00 0.00 0.00 4.79
1990 3492 5.882557 ACATGATCACATAGGTCAACTTTCC 59.117 40.000 0.00 0.00 35.09 3.13
1991 3493 6.372659 ACACATGATCACATAGGTCAACTTTC 59.627 38.462 0.00 0.00 35.09 2.62
1992 3494 6.240894 ACACATGATCACATAGGTCAACTTT 58.759 36.000 0.00 0.00 35.09 2.66
1993 3495 5.809001 ACACATGATCACATAGGTCAACTT 58.191 37.500 0.00 0.00 35.09 2.66
1995 3497 4.572389 GGACACATGATCACATAGGTCAAC 59.428 45.833 0.00 0.00 38.91 3.18
2002 3522 5.187576 TGAGAGTTGGACACATGATCACATA 59.812 40.000 0.00 0.00 35.09 2.29
2171 3750 0.673333 TGTCACAGTGCGCCATTAGG 60.673 55.000 4.18 0.00 38.23 2.69
2188 3767 0.392461 ATTCTAATGGCGCACCGTGT 60.392 50.000 10.83 0.00 39.70 4.49
2230 3813 2.595386 GTGCGCCATTAGAAGTTTTGG 58.405 47.619 4.18 0.00 0.00 3.28
2326 3909 4.176271 GCTGTCCAAAATATCTTGTTGGC 58.824 43.478 0.00 0.00 41.38 4.52
2425 4009 3.003394 TCTATGGTGCAAATGAGGTGG 57.997 47.619 0.00 0.00 0.00 4.61
2521 4122 0.531974 GTGCACGTTGTTGGAGAGGA 60.532 55.000 0.00 0.00 0.00 3.71
2522 4123 0.813610 TGTGCACGTTGTTGGAGAGG 60.814 55.000 13.13 0.00 0.00 3.69
2597 4202 6.338214 ACACAAACATATATGCAACACCAA 57.662 33.333 12.79 0.00 0.00 3.67
2671 4276 4.377022 CGTCGAAACGGAAATGAATCAACT 60.377 41.667 0.00 0.00 45.21 3.16
2692 4297 3.081061 TGCATAGTGCCAAAATTCTCGT 58.919 40.909 0.00 0.00 44.23 4.18
2762 4368 8.837389 GGGTAGAGCAAAACGATATTTTAGAAT 58.163 33.333 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.