Multiple sequence alignment - TraesCS2A01G325600

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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 TraesCS2A01G325600 chr2A 100.000 4802 0 0 1 4802 555820288 555825089 0.000000e+00 8868.0
1 TraesCS2A01G325600 chr2B 88.702 1788 112 34 700 2399 508251437 508249652 0.000000e+00 2100.0
2 TraesCS2A01G325600 chr2B 95.798 952 31 9 3292 4240 508248411 508247466 0.000000e+00 1528.0
3 TraesCS2A01G325600 chr2B 95.448 703 27 2 2502 3204 508249559 508248862 0.000000e+00 1116.0
4 TraesCS2A01G325600 chr2B 87.708 480 37 10 1 474 508365580 508365117 1.520000e-149 540.0
5 TraesCS2A01G325600 chr2B 92.237 219 13 4 4261 4476 508247400 508247183 1.680000e-79 307.0
6 TraesCS2A01G325600 chr2B 94.366 71 3 1 2394 2464 508249627 508249558 1.830000e-19 108.0
7 TraesCS2A01G325600 chr2D 95.330 1242 30 10 3290 4529 430462403 430461188 0.000000e+00 1947.0
8 TraesCS2A01G325600 chr2D 90.565 1505 85 17 930 2401 430464833 430463353 0.000000e+00 1940.0
9 TraesCS2A01G325600 chr2D 95.402 870 35 2 2398 3266 430463327 430462462 0.000000e+00 1380.0
10 TraesCS2A01G325600 chr2D 92.642 965 38 13 1 942 430465811 430464857 0.000000e+00 1358.0
11 TraesCS2A01G325600 chr2D 89.338 272 12 7 4534 4802 430461154 430460897 4.630000e-85 326.0
12 TraesCS2A01G325600 chr6D 86.654 532 61 8 1019 1545 266959524 266958998 8.960000e-162 580.0
13 TraesCS2A01G325600 chr6D 84.694 294 42 3 3376 3669 266955821 266955531 1.690000e-74 291.0
14 TraesCS2A01G325600 chr6D 85.200 250 37 0 2679 2928 266956722 266956473 1.710000e-64 257.0
15 TraesCS2A01G325600 chr6A 86.654 532 61 8 1019 1545 379662663 379662137 8.960000e-162 580.0
16 TraesCS2A01G325600 chr6A 84.932 292 41 3 3378 3669 379658381 379658093 4.700000e-75 292.0
17 TraesCS2A01G325600 chr6B 86.441 531 64 7 1019 1545 415040796 415040270 4.170000e-160 575.0
18 TraesCS2A01G325600 chr6B 84.589 292 42 3 3378 3669 415036962 415036674 2.190000e-73 287.0
19 TraesCS2A01G325600 chr6B 85.600 250 36 0 2679 2928 415037864 415037615 3.690000e-66 263.0
20 TraesCS2A01G325600 chr5D 92.115 279 12 4 1 276 481667863 481667592 7.540000e-103 385.0
21 TraesCS2A01G325600 chr1B 85.511 352 46 2 1057 1407 634782719 634783066 3.530000e-96 363.0
22 TraesCS2A01G325600 chr1B 82.494 417 46 14 1 408 634782177 634782575 1.660000e-89 340.0
23 TraesCS2A01G325600 chr1B 86.266 233 32 0 1175 1407 634998319 634998551 2.220000e-63 254.0
24 TraesCS2A01G325600 chr1D 80.622 418 34 21 2 408 461765452 461765833 3.660000e-71 279.0
25 TraesCS2A01G325600 chr1D 87.665 227 27 1 1181 1407 461785071 461785296 3.690000e-66 263.0
26 TraesCS2A01G325600 chr1A 87.166 187 17 3 1 185 553053227 553053408 6.300000e-49 206.0
27 TraesCS2A01G325600 chr1A 80.695 259 27 13 229 476 553061042 553061288 3.820000e-41 180.0
28 TraesCS2A01G325600 chr1A 79.231 260 30 14 229 476 552982532 552982779 4.970000e-35 159.0
29 TraesCS2A01G325600 chr1A 91.304 69 6 0 1336 1404 553066383 553066451 1.420000e-15 95.3


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 TraesCS2A01G325600 chr2A 555820288 555825089 4801 False 8868.0 8868 100.000000 1 4802 1 chr2A.!!$F1 4801
1 TraesCS2A01G325600 chr2B 508247183 508251437 4254 True 1031.8 2100 93.310200 700 4476 5 chr2B.!!$R2 3776
2 TraesCS2A01G325600 chr2D 430460897 430465811 4914 True 1390.2 1947 92.655400 1 4802 5 chr2D.!!$R1 4801
3 TraesCS2A01G325600 chr6D 266955531 266959524 3993 True 376.0 580 85.516000 1019 3669 3 chr6D.!!$R1 2650
4 TraesCS2A01G325600 chr6A 379658093 379662663 4570 True 436.0 580 85.793000 1019 3669 2 chr6A.!!$R1 2650
5 TraesCS2A01G325600 chr6B 415036674 415040796 4122 True 375.0 575 85.543333 1019 3669 3 chr6B.!!$R1 2650
6 TraesCS2A01G325600 chr1B 634782177 634783066 889 False 351.5 363 84.002500 1 1407 2 chr1B.!!$F2 1406

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
415 436 0.674895 GGAGCTGTACTTGGTGCCTG 60.675 60.000 0.00 0.0 0.00 4.85 F
780 814 1.208052 CCGTGTCTCCTTGATGGTGAT 59.792 52.381 0.00 0.0 40.06 3.06 F
1631 1738 0.179156 GGCGAATGATGTGCCTTGTG 60.179 55.000 1.32 0.0 45.40 3.33 F
2002 2171 0.454600 CCAGTGATTGGCATGTGCTC 59.545 55.000 4.84 0.0 40.87 4.26 F
3294 6364 1.196581 TCGCACATGATTTTGACACCG 59.803 47.619 0.00 0.0 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1613 1720 0.804364 TCACAAGGCACATCATTCGC 59.196 50.000 0.00 0.0 0.00 4.70 R
2002 2171 1.750778 ACCACAAGTTTGGACAAGCAG 59.249 47.619 10.03 0.0 39.24 4.24 R
3234 5976 0.532573 AGGCATGTCACACTAGTCGG 59.467 55.000 0.00 0.0 0.00 4.79 R
3587 7087 1.073284 TCCTTTGTCCTGTACTTGCCC 59.927 52.381 0.00 0.0 0.00 5.36 R
4713 8304 0.515127 CAACTTGATGGCGTGCGTAA 59.485 50.000 0.00 0.0 0.00 3.18 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
146 147 1.475682 CTCCTCTTTTTGGCTGGATGC 59.524 52.381 0.00 0.00 41.94 3.91
160 161 1.704628 TGGATGCTTTCTGGACTTCCA 59.295 47.619 0.00 0.00 45.30 3.53
161 162 2.108075 TGGATGCTTTCTGGACTTCCAA 59.892 45.455 0.00 0.00 46.97 3.53
162 163 3.157087 GGATGCTTTCTGGACTTCCAAA 58.843 45.455 0.00 0.00 46.97 3.28
163 164 3.057245 GGATGCTTTCTGGACTTCCAAAC 60.057 47.826 0.00 0.00 46.97 2.93
358 369 4.393371 GGTTAAGCAGATTCAAGTCCAGTC 59.607 45.833 0.00 0.00 0.00 3.51
362 373 2.027745 GCAGATTCAAGTCCAGTCTGGA 60.028 50.000 18.15 18.15 45.98 3.86
415 436 0.674895 GGAGCTGTACTTGGTGCCTG 60.675 60.000 0.00 0.00 0.00 4.85
487 508 8.989980 GGCCCTCTTTAATATAATATCGTATGC 58.010 37.037 0.00 0.00 0.00 3.14
508 529 4.082841 TGCGAAATGCTCTGCTTGAATTAA 60.083 37.500 0.00 0.00 46.63 1.40
510 531 5.393124 CGAAATGCTCTGCTTGAATTAACA 58.607 37.500 0.00 0.00 0.00 2.41
527 548 9.800433 TGAATTAACAATATACATGTGCCAAAG 57.200 29.630 9.11 0.00 0.00 2.77
528 549 9.801873 GAATTAACAATATACATGTGCCAAAGT 57.198 29.630 9.11 0.00 0.00 2.66
533 555 8.574251 ACAATATACATGTGCCAAAGTAAGAA 57.426 30.769 9.11 0.00 0.00 2.52
568 590 6.259550 ACTTGGCTGATGTGATAGTTTTTC 57.740 37.500 0.00 0.00 0.00 2.29
616 642 1.829349 GATCGCTCGCTTGCATGAGG 61.829 60.000 3.33 0.00 32.78 3.86
672 698 8.564574 ACGTTTCACTATCAGCAATTCTAAAAA 58.435 29.630 0.00 0.00 0.00 1.94
706 732 3.565516 TCTATCAGCACGATACGATTGC 58.434 45.455 0.00 0.00 35.39 3.56
765 794 4.066490 TCAACCGAAAACAATATCCGTGT 58.934 39.130 0.00 0.00 0.00 4.49
780 814 1.208052 CCGTGTCTCCTTGATGGTGAT 59.792 52.381 0.00 0.00 40.06 3.06
789 823 4.504596 GATGGTGATGGGCCCGCA 62.505 66.667 19.37 15.72 0.00 5.69
820 854 1.996191 GTGTCTCTCATTCTTGCGGAC 59.004 52.381 0.00 0.00 0.00 4.79
860 895 4.262851 GCAAATACCCAACAATTCCAAGGT 60.263 41.667 0.00 0.00 0.00 3.50
1575 1682 2.875933 TCGCTCCCTGTTGTTTGTTTAG 59.124 45.455 0.00 0.00 0.00 1.85
1577 1684 3.058914 CGCTCCCTGTTGTTTGTTTAGAG 60.059 47.826 0.00 0.00 0.00 2.43
1584 1691 6.209391 CCCTGTTGTTTGTTTAGAGGATTCAT 59.791 38.462 0.00 0.00 0.00 2.57
1588 1695 8.352201 TGTTGTTTGTTTAGAGGATTCATCTTG 58.648 33.333 6.11 0.00 0.00 3.02
1590 1697 8.868522 TGTTTGTTTAGAGGATTCATCTTGAT 57.131 30.769 6.11 0.00 0.00 2.57
1591 1698 9.300681 TGTTTGTTTAGAGGATTCATCTTGATT 57.699 29.630 6.11 0.00 0.00 2.57
1613 1720 3.573538 TCCTTCACATGTTCATTGGTTGG 59.426 43.478 0.00 0.00 0.00 3.77
1616 1723 1.269174 CACATGTTCATTGGTTGGCGA 59.731 47.619 0.00 0.00 0.00 5.54
1617 1724 1.959985 ACATGTTCATTGGTTGGCGAA 59.040 42.857 0.00 0.00 0.00 4.70
1630 1737 2.183409 GGCGAATGATGTGCCTTGT 58.817 52.632 1.32 0.00 45.40 3.16
1631 1738 0.179156 GGCGAATGATGTGCCTTGTG 60.179 55.000 1.32 0.00 45.40 3.33
1632 1739 0.804364 GCGAATGATGTGCCTTGTGA 59.196 50.000 0.00 0.00 0.00 3.58
1634 1741 1.399440 CGAATGATGTGCCTTGTGAGG 59.601 52.381 0.00 0.00 46.50 3.86
1636 1749 3.609853 GAATGATGTGCCTTGTGAGGTA 58.390 45.455 0.00 0.00 45.44 3.08
1638 1751 1.339055 TGATGTGCCTTGTGAGGTAGC 60.339 52.381 0.00 0.00 45.44 3.58
1643 1756 3.709141 TGTGCCTTGTGAGGTAGCATATA 59.291 43.478 0.00 0.00 45.44 0.86
1645 1758 4.511826 GTGCCTTGTGAGGTAGCATATAAC 59.488 45.833 0.00 0.00 45.44 1.89
1648 1761 5.685075 GCCTTGTGAGGTAGCATATAACTGT 60.685 44.000 0.00 0.00 45.44 3.55
1650 1763 7.497595 CCTTGTGAGGTAGCATATAACTGTTA 58.502 38.462 2.26 2.26 38.32 2.41
1657 1770 8.608844 AGGTAGCATATAACTGTTAGATTTGC 57.391 34.615 11.02 11.02 0.00 3.68
1658 1771 8.210946 AGGTAGCATATAACTGTTAGATTTGCA 58.789 33.333 17.81 6.33 0.00 4.08
1659 1772 9.003658 GGTAGCATATAACTGTTAGATTTGCAT 57.996 33.333 17.81 9.20 0.00 3.96
1663 1776 9.694520 GCATATAACTGTTAGATTTGCATATCG 57.305 33.333 13.12 0.51 0.00 2.92
1667 1785 6.771188 ACTGTTAGATTTGCATATCGTAGC 57.229 37.500 10.91 7.25 0.00 3.58
1691 1809 7.618512 AGCTAGTTAGTACATGGTTAAGAGGAA 59.381 37.037 0.00 0.00 0.00 3.36
1755 1877 6.490566 TGATTTGTCTGTGATGAACTGATG 57.509 37.500 0.00 0.00 38.78 3.07
1761 1883 2.340337 TGTGATGAACTGATGCTGTCG 58.660 47.619 0.00 0.00 0.00 4.35
1829 1951 5.027293 TGTGACCAGGATGATGTAGATTG 57.973 43.478 0.00 0.00 39.69 2.67
1833 1955 5.011431 TGACCAGGATGATGTAGATTGCTAG 59.989 44.000 0.00 0.00 39.69 3.42
1934 2078 4.789095 CGGGTAGATCCGTGTAAAATTG 57.211 45.455 0.00 0.00 44.60 2.32
1935 2079 3.001939 CGGGTAGATCCGTGTAAAATTGC 59.998 47.826 0.00 0.00 44.60 3.56
1936 2080 3.314357 GGGTAGATCCGTGTAAAATTGCC 59.686 47.826 0.00 0.00 37.00 4.52
1937 2081 3.942748 GGTAGATCCGTGTAAAATTGCCA 59.057 43.478 0.00 0.00 0.00 4.92
1938 2082 4.396790 GGTAGATCCGTGTAAAATTGCCAA 59.603 41.667 0.00 0.00 0.00 4.52
1939 2083 5.106078 GGTAGATCCGTGTAAAATTGCCAAA 60.106 40.000 0.00 0.00 0.00 3.28
1940 2084 5.659440 AGATCCGTGTAAAATTGCCAAAT 57.341 34.783 0.00 0.00 0.00 2.32
1941 2085 5.410067 AGATCCGTGTAAAATTGCCAAATG 58.590 37.500 0.00 0.00 0.00 2.32
1942 2086 4.592485 TCCGTGTAAAATTGCCAAATGT 57.408 36.364 0.00 0.00 0.00 2.71
1943 2087 4.302455 TCCGTGTAAAATTGCCAAATGTG 58.698 39.130 0.00 0.00 0.00 3.21
2002 2171 0.454600 CCAGTGATTGGCATGTGCTC 59.545 55.000 4.84 0.00 40.87 4.26
2034 2203 2.767505 ACTTGTGGTGTAGCTTAGCAC 58.232 47.619 19.90 19.90 44.45 4.40
2099 2596 2.159254 CCAGGTAAATGATTTGGCGGTG 60.159 50.000 0.00 0.00 0.00 4.94
2146 2650 9.509956 TCCTTATTTTCCTCGTTTATTGAGAAA 57.490 29.630 0.00 0.00 35.43 2.52
2150 2654 7.867445 TTTTCCTCGTTTATTGAGAAATTGC 57.133 32.000 0.00 0.00 35.43 3.56
2151 2655 5.216566 TCCTCGTTTATTGAGAAATTGCG 57.783 39.130 0.00 0.00 35.43 4.85
2268 2789 8.924303 AGCCTTATGTAGAATAATACACTGTCA 58.076 33.333 0.00 0.00 38.43 3.58
2289 2810 8.984891 TGTCATTATTTTGATCAAACCATGAC 57.015 30.769 32.14 32.14 41.93 3.06
2295 2816 3.118905 TGATCAAACCATGACGTGACA 57.881 42.857 0.00 0.00 41.93 3.58
2299 2820 1.536766 CAAACCATGACGTGACATGCT 59.463 47.619 10.86 0.00 44.11 3.79
2346 2867 8.605947 TCTGGATGTATTTATCCCAGGAAATAG 58.394 37.037 0.00 0.00 44.93 1.73
2357 2878 5.224441 TCCCAGGAAATAGTAGCCAATAGT 58.776 41.667 0.00 0.00 0.00 2.12
2475 3233 8.458843 CAAATAGACCAAGATACACCGAAAATT 58.541 33.333 0.00 0.00 0.00 1.82
2560 4335 6.099701 TCCTTGCAAGCCTATTATCAGTTCTA 59.900 38.462 21.43 0.00 0.00 2.10
2606 4382 7.253552 GCTTGCTCAAAACATTATCGATGAAAG 60.254 37.037 8.54 0.00 39.15 2.62
2970 5452 6.513180 TCAGATGCTCCTATTAAGTAAACCG 58.487 40.000 0.00 0.00 0.00 4.44
3131 5873 6.385033 AGATTTCAGCATACTTTGTTTCTGC 58.615 36.000 0.00 0.00 0.00 4.26
3137 5879 3.810373 CATACTTTGTTTCTGCGGTCAC 58.190 45.455 0.00 0.00 0.00 3.67
3150 5892 2.488937 TGCGGTCACTTCATACTACGAA 59.511 45.455 0.00 0.00 0.00 3.85
3180 5922 5.798125 TTGGATTAACTTGGTCAATTGCA 57.202 34.783 0.00 0.00 0.00 4.08
3214 5956 5.280317 GGTCAACACTTCCTTCCTGGTATTA 60.280 44.000 0.00 0.00 37.07 0.98
3220 5962 7.643123 ACACTTCCTTCCTGGTATTATTGAAT 58.357 34.615 0.00 0.00 37.07 2.57
3234 5976 6.731292 ATTATTGAATACTTTTCTGGGGGC 57.269 37.500 0.00 0.00 0.00 5.80
3244 5986 2.683933 CTGGGGGCCGACTAGTGT 60.684 66.667 0.00 0.00 0.00 3.55
3260 6330 1.694150 AGTGTGACATGCCTAGTGTGT 59.306 47.619 0.00 0.00 0.00 3.72
3261 6331 2.104792 AGTGTGACATGCCTAGTGTGTT 59.895 45.455 0.00 0.00 0.00 3.32
3262 6332 2.224079 GTGTGACATGCCTAGTGTGTTG 59.776 50.000 0.00 0.00 0.00 3.33
3263 6333 2.158827 TGTGACATGCCTAGTGTGTTGT 60.159 45.455 0.00 0.00 0.00 3.32
3264 6334 3.070302 TGTGACATGCCTAGTGTGTTGTA 59.930 43.478 0.00 0.00 0.00 2.41
3265 6335 3.679980 GTGACATGCCTAGTGTGTTGTAG 59.320 47.826 0.00 0.00 0.00 2.74
3266 6336 3.576550 TGACATGCCTAGTGTGTTGTAGA 59.423 43.478 0.00 0.00 0.00 2.59
3267 6337 3.926616 ACATGCCTAGTGTGTTGTAGAC 58.073 45.455 0.00 0.00 0.00 2.59
3291 6361 4.061596 TGTAGTCGCACATGATTTTGACA 58.938 39.130 0.00 0.00 0.00 3.58
3293 6363 2.226437 AGTCGCACATGATTTTGACACC 59.774 45.455 0.00 0.00 0.00 4.16
3294 6364 1.196581 TCGCACATGATTTTGACACCG 59.803 47.619 0.00 0.00 0.00 4.94
3297 6411 1.541147 CACATGATTTTGACACCGCCT 59.459 47.619 0.00 0.00 0.00 5.52
3359 6473 5.453567 AAGCCAACATAAGTTTGAGGTTC 57.546 39.130 0.00 0.00 35.28 3.62
3587 7087 0.674581 TGAAGCGGGTCATTGCAGAG 60.675 55.000 0.00 0.00 0.00 3.35
3817 7317 3.073062 CCCACGAGGATTATTCTTCCCAT 59.927 47.826 0.00 0.00 38.24 4.00
3860 7360 1.604593 CCTTGTGTTGCAGAGGGGG 60.605 63.158 0.00 0.00 0.00 5.40
3949 7450 1.489230 ACTCCCATGTAACCGGAATCC 59.511 52.381 9.46 0.00 0.00 3.01
4065 7566 1.003233 CCTGTCCCCCTGTTACTTCAC 59.997 57.143 0.00 0.00 0.00 3.18
4071 7572 2.296190 CCCCCTGTTACTTCACTTTTGC 59.704 50.000 0.00 0.00 0.00 3.68
4415 7977 3.937814 TGAGCGGTCTTTTCACATGTAT 58.062 40.909 16.64 0.00 0.00 2.29
4495 8057 8.773645 TGTCACACTATTCAATTTTGTCACTAG 58.226 33.333 0.00 0.00 0.00 2.57
4529 8091 2.253392 ACTCGACACCGTTATCGTTC 57.747 50.000 2.68 0.00 39.38 3.95
4530 8092 1.536766 ACTCGACACCGTTATCGTTCA 59.463 47.619 2.68 0.00 39.38 3.18
4532 8094 1.536766 TCGACACCGTTATCGTTCAGT 59.463 47.619 2.68 0.00 39.38 3.41
4549 8140 0.610232 AGTGTTCAGGGGCAAGCATC 60.610 55.000 0.00 0.00 0.00 3.91
4567 8158 2.270434 TCCCCAGCTCTTTATCCTGT 57.730 50.000 0.00 0.00 0.00 4.00
4574 8165 5.282510 CCAGCTCTTTATCCTGTAACGTAG 58.717 45.833 0.00 0.00 0.00 3.51
4576 8167 6.039047 CCAGCTCTTTATCCTGTAACGTAGTA 59.961 42.308 0.00 0.00 45.00 1.82
4577 8168 7.255520 CCAGCTCTTTATCCTGTAACGTAGTAT 60.256 40.741 0.00 0.00 45.00 2.12
4578 8169 7.591795 CAGCTCTTTATCCTGTAACGTAGTATG 59.408 40.741 0.00 0.00 45.00 2.39
4579 8170 7.501559 AGCTCTTTATCCTGTAACGTAGTATGA 59.498 37.037 0.00 0.00 45.00 2.15
4580 8171 7.804129 GCTCTTTATCCTGTAACGTAGTATGAG 59.196 40.741 0.00 0.00 45.00 2.90
4581 8172 7.646314 TCTTTATCCTGTAACGTAGTATGAGC 58.354 38.462 0.00 0.00 45.00 4.26
4582 8173 7.501559 TCTTTATCCTGTAACGTAGTATGAGCT 59.498 37.037 0.00 0.00 45.00 4.09
4588 8179 6.017357 CCTGTAACGTAGTATGAGCTGTATGA 60.017 42.308 0.00 0.00 45.00 2.15
4617 8208 0.606401 ACCAGCACAGGTGAAATCCG 60.606 55.000 3.10 0.00 41.30 4.18
4618 8209 1.308069 CCAGCACAGGTGAAATCCGG 61.308 60.000 3.10 0.00 32.22 5.14
4712 8303 3.441101 TGTACATTCACTCCCTGTAGCT 58.559 45.455 0.00 0.00 0.00 3.32
4713 8304 3.838317 TGTACATTCACTCCCTGTAGCTT 59.162 43.478 0.00 0.00 0.00 3.74
4734 8325 2.126346 GCACGCCATCAAGTTGCC 60.126 61.111 0.00 0.00 0.00 4.52
4735 8326 2.918345 GCACGCCATCAAGTTGCCA 61.918 57.895 0.00 0.00 0.00 4.92
4742 8333 1.466167 CCATCAAGTTGCCAAGAGTCG 59.534 52.381 0.00 0.00 0.00 4.18
4765 8359 5.615544 CGCAGTTTATGGTCTGAGTCTTTTG 60.616 44.000 0.00 0.00 34.02 2.44
4767 8361 6.150140 GCAGTTTATGGTCTGAGTCTTTTGAT 59.850 38.462 0.00 0.00 34.02 2.57
4779 8373 8.037758 TCTGAGTCTTTTGATTTGTATCTCTCC 58.962 37.037 0.00 0.00 0.00 3.71
4782 8376 9.877178 GAGTCTTTTGATTTGTATCTCTCCTTA 57.123 33.333 0.00 0.00 0.00 2.69
4793 8387 7.865706 TGTATCTCTCCTTATTTTCTTTGGC 57.134 36.000 0.00 0.00 0.00 4.52
4796 8390 5.256474 TCTCTCCTTATTTTCTTTGGCTGG 58.744 41.667 0.00 0.00 0.00 4.85
4797 8391 5.014123 TCTCTCCTTATTTTCTTTGGCTGGA 59.986 40.000 0.00 0.00 0.00 3.86
4798 8392 5.831103 TCTCCTTATTTTCTTTGGCTGGAT 58.169 37.500 0.00 0.00 0.00 3.41
4799 8393 5.653769 TCTCCTTATTTTCTTTGGCTGGATG 59.346 40.000 0.00 0.00 0.00 3.51
4800 8394 4.160252 TCCTTATTTTCTTTGGCTGGATGC 59.840 41.667 0.00 0.00 41.94 3.91
4801 8395 4.161001 CCTTATTTTCTTTGGCTGGATGCT 59.839 41.667 0.00 0.00 42.39 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
160 161 4.518970 AGAACAAACATGCGATACTGGTTT 59.481 37.500 0.00 0.00 32.33 3.27
161 162 4.072131 AGAACAAACATGCGATACTGGTT 58.928 39.130 0.00 0.00 0.00 3.67
162 163 3.674997 AGAACAAACATGCGATACTGGT 58.325 40.909 0.00 0.00 0.00 4.00
163 164 4.685169 AAGAACAAACATGCGATACTGG 57.315 40.909 0.00 0.00 0.00 4.00
294 304 0.604780 CATTCAGCTATCCAGGGGCG 60.605 60.000 0.00 0.00 0.00 6.13
415 436 1.739196 GAACGCTGACCCGGTAACC 60.739 63.158 0.00 0.00 0.00 2.85
424 445 3.173240 GGCTCGACGAACGCTGAC 61.173 66.667 8.72 0.00 42.26 3.51
463 484 9.961265 TCGCATACGATATTATATTAAAGAGGG 57.039 33.333 0.00 0.00 45.12 4.30
487 508 5.393124 TGTTAATTCAAGCAGAGCATTTCG 58.607 37.500 0.00 0.00 0.00 3.46
508 529 8.574251 TTCTTACTTTGGCACATGTATATTGT 57.426 30.769 0.00 0.00 39.30 2.71
510 531 9.461312 TCTTTCTTACTTTGGCACATGTATATT 57.539 29.630 0.00 0.00 39.30 1.28
550 572 8.292448 TCTCAAAAGAAAAACTATCACATCAGC 58.708 33.333 0.00 0.00 0.00 4.26
568 590 5.924475 ACGTACATCAGGTTTCTCAAAAG 57.076 39.130 0.00 0.00 0.00 2.27
616 642 1.235281 GGAACTTGGAACCCAGCGAC 61.235 60.000 0.00 0.00 33.81 5.19
674 700 4.748102 TCGTGCTGATAGAGAAACGTTTTT 59.252 37.500 15.89 9.72 35.72 1.94
675 701 4.304110 TCGTGCTGATAGAGAAACGTTTT 58.696 39.130 15.89 5.23 35.72 2.43
706 732 1.126113 GTCGGTGCACAGAAATACGTG 59.874 52.381 21.46 0.00 36.18 4.49
765 794 0.548031 GCCCATCACCATCAAGGAGA 59.452 55.000 0.00 0.00 41.43 3.71
820 854 1.153353 TGCGAACCTTTAAAGCCTCG 58.847 50.000 22.80 22.80 34.03 4.63
886 921 2.584608 GGACGGTGGAGATGGGTG 59.415 66.667 0.00 0.00 0.00 4.61
1143 1250 3.458163 GGGATGAGCGTGACGGGA 61.458 66.667 7.25 0.00 0.00 5.14
1577 1684 6.320672 ACATGTGAAGGAATCAAGATGAATCC 59.679 38.462 0.00 6.38 44.81 3.01
1584 1691 6.071784 CCAATGAACATGTGAAGGAATCAAGA 60.072 38.462 0.00 0.00 40.50 3.02
1588 1695 5.649782 ACCAATGAACATGTGAAGGAATC 57.350 39.130 0.00 0.00 0.00 2.52
1590 1697 4.039004 CCAACCAATGAACATGTGAAGGAA 59.961 41.667 0.00 0.00 0.00 3.36
1591 1698 3.573538 CCAACCAATGAACATGTGAAGGA 59.426 43.478 0.00 0.00 0.00 3.36
1599 1706 2.824936 TCATTCGCCAACCAATGAACAT 59.175 40.909 0.00 0.00 36.33 2.71
1613 1720 0.804364 TCACAAGGCACATCATTCGC 59.196 50.000 0.00 0.00 0.00 4.70
1626 1733 8.414003 TCTAACAGTTATATGCTACCTCACAAG 58.586 37.037 0.00 0.00 0.00 3.16
1629 1736 9.765795 AAATCTAACAGTTATATGCTACCTCAC 57.234 33.333 0.00 0.00 0.00 3.51
1630 1737 9.764363 CAAATCTAACAGTTATATGCTACCTCA 57.236 33.333 0.00 0.00 0.00 3.86
1631 1738 8.713271 GCAAATCTAACAGTTATATGCTACCTC 58.287 37.037 0.00 0.00 0.00 3.85
1632 1739 8.210946 TGCAAATCTAACAGTTATATGCTACCT 58.789 33.333 15.23 0.00 32.74 3.08
1643 1756 6.986817 AGCTACGATATGCAAATCTAACAGTT 59.013 34.615 0.00 0.00 0.00 3.16
1645 1758 7.810282 ACTAGCTACGATATGCAAATCTAACAG 59.190 37.037 0.00 0.00 0.00 3.16
1648 1761 9.841880 CTAACTAGCTACGATATGCAAATCTAA 57.158 33.333 0.00 0.00 0.00 2.10
1650 1763 7.887381 ACTAACTAGCTACGATATGCAAATCT 58.113 34.615 0.00 0.00 0.00 2.40
1657 1770 8.041829 ACCATGTACTAACTAGCTACGATATG 57.958 38.462 0.00 0.00 0.00 1.78
1658 1771 8.632906 AACCATGTACTAACTAGCTACGATAT 57.367 34.615 0.00 0.00 0.00 1.63
1659 1772 9.559732 TTAACCATGTACTAACTAGCTACGATA 57.440 33.333 0.00 0.00 0.00 2.92
1660 1773 6.956202 AACCATGTACTAACTAGCTACGAT 57.044 37.500 0.00 0.00 0.00 3.73
1661 1774 7.770433 TCTTAACCATGTACTAACTAGCTACGA 59.230 37.037 0.00 0.00 0.00 3.43
1662 1775 7.923888 TCTTAACCATGTACTAACTAGCTACG 58.076 38.462 0.00 0.00 0.00 3.51
1663 1776 8.351461 CCTCTTAACCATGTACTAACTAGCTAC 58.649 40.741 0.00 0.00 0.00 3.58
1667 1785 9.804758 CTTTCCTCTTAACCATGTACTAACTAG 57.195 37.037 0.00 0.00 0.00 2.57
1691 1809 2.874086 GCAGCTTTGCAATGGAAAACTT 59.126 40.909 13.62 0.00 34.41 2.66
1709 1827 7.880105 TCATATATCTACTCTGACAGTTGCAG 58.120 38.462 1.59 0.00 36.43 4.41
1755 1877 4.868171 TGTGATTGATAACTAACCGACAGC 59.132 41.667 0.00 0.00 0.00 4.40
1829 1951 9.057089 ACAGTACATTTATAAAAGCATCCTAGC 57.943 33.333 1.21 0.00 0.00 3.42
1924 2068 5.296748 ACTCCACATTTGGCAATTTTACAC 58.703 37.500 0.00 0.00 43.56 2.90
1928 2072 4.686191 TGACTCCACATTTGGCAATTTT 57.314 36.364 0.00 0.00 43.56 1.82
1929 2073 4.686191 TTGACTCCACATTTGGCAATTT 57.314 36.364 0.00 0.00 43.56 1.82
1930 2074 4.686191 TTTGACTCCACATTTGGCAATT 57.314 36.364 0.00 0.00 43.56 2.32
1931 2075 4.322953 GGATTTGACTCCACATTTGGCAAT 60.323 41.667 0.00 0.00 43.56 3.56
1932 2076 3.006752 GGATTTGACTCCACATTTGGCAA 59.993 43.478 0.00 0.00 43.56 4.52
1933 2077 2.562298 GGATTTGACTCCACATTTGGCA 59.438 45.455 0.00 0.00 43.56 4.92
1934 2078 2.827921 AGGATTTGACTCCACATTTGGC 59.172 45.455 0.00 0.00 43.56 4.52
1935 2079 4.081406 TGAGGATTTGACTCCACATTTGG 58.919 43.478 0.00 0.00 45.56 3.28
1936 2080 4.763793 ACTGAGGATTTGACTCCACATTTG 59.236 41.667 0.00 0.00 35.69 2.32
1937 2081 4.990526 ACTGAGGATTTGACTCCACATTT 58.009 39.130 0.00 0.00 35.69 2.32
1938 2082 4.288105 AGACTGAGGATTTGACTCCACATT 59.712 41.667 0.00 0.00 35.69 2.71
1939 2083 3.843027 AGACTGAGGATTTGACTCCACAT 59.157 43.478 0.00 0.00 35.69 3.21
1940 2084 3.007290 CAGACTGAGGATTTGACTCCACA 59.993 47.826 0.00 0.00 37.81 4.17
1941 2085 3.259374 TCAGACTGAGGATTTGACTCCAC 59.741 47.826 0.00 0.00 37.81 4.02
1942 2086 3.510459 TCAGACTGAGGATTTGACTCCA 58.490 45.455 0.00 0.00 37.81 3.86
1943 2087 4.751767 ATCAGACTGAGGATTTGACTCC 57.248 45.455 11.52 0.00 34.06 3.85
1944 2088 5.811613 CAGAATCAGACTGAGGATTTGACTC 59.188 44.000 11.52 0.00 37.54 3.36
1945 2089 5.338219 CCAGAATCAGACTGAGGATTTGACT 60.338 44.000 11.52 0.00 37.54 3.41
1946 2090 4.874966 CCAGAATCAGACTGAGGATTTGAC 59.125 45.833 11.52 0.00 37.54 3.18
1947 2091 4.624843 GCCAGAATCAGACTGAGGATTTGA 60.625 45.833 11.52 0.00 37.54 2.69
1948 2092 3.626670 GCCAGAATCAGACTGAGGATTTG 59.373 47.826 11.52 5.49 37.54 2.32
2002 2171 1.750778 ACCACAAGTTTGGACAAGCAG 59.249 47.619 10.03 0.00 39.24 4.24
2055 2552 5.183522 GGTAAACACCGACCCAATAATTCAA 59.816 40.000 0.00 0.00 0.00 2.69
2125 2622 7.273381 CGCAATTTCTCAATAAACGAGGAAAAT 59.727 33.333 0.00 0.00 31.76 1.82
2146 2650 9.911138 TGCATAATGTTAAATGAATATCGCAAT 57.089 25.926 0.00 0.00 0.00 3.56
2268 2789 7.754924 GTCACGTCATGGTTTGATCAAAATAAT 59.245 33.333 22.07 12.82 36.54 1.28
2277 2798 2.162208 GCATGTCACGTCATGGTTTGAT 59.838 45.455 16.38 0.00 43.54 2.57
2295 2816 3.548770 CATGATACCAACCTCACAGCAT 58.451 45.455 0.00 0.00 0.00 3.79
2299 2820 4.474651 AGAATCCATGATACCAACCTCACA 59.525 41.667 0.00 0.00 0.00 3.58
2346 2867 3.121544 GACGGCAGTAACTATTGGCTAC 58.878 50.000 0.00 0.00 36.54 3.58
2357 2878 3.752665 TGTTTATTTGGGACGGCAGTAA 58.247 40.909 0.00 0.00 0.00 2.24
2425 2975 7.018826 TGAAAATAATGGAAACGAAGCTAACG 58.981 34.615 10.86 10.86 0.00 3.18
2475 3233 7.777440 TGAATATTGTGAACATATACAGGGCAA 59.223 33.333 0.00 0.00 0.00 4.52
2538 4313 7.739825 AGATAGAACTGATAATAGGCTTGCAA 58.260 34.615 0.00 0.00 0.00 4.08
2560 4335 6.373779 CAAGCAAACTCACGTCATTTAAGAT 58.626 36.000 0.00 0.00 0.00 2.40
2571 4346 2.473530 TTTGAGCAAGCAAACTCACG 57.526 45.000 2.46 0.00 42.42 4.35
2583 4358 6.029607 GCTTTCATCGATAATGTTTTGAGCA 58.970 36.000 0.00 0.00 36.68 4.26
2584 4359 6.029607 TGCTTTCATCGATAATGTTTTGAGC 58.970 36.000 0.00 0.00 36.68 4.26
2585 4360 8.624701 ATTGCTTTCATCGATAATGTTTTGAG 57.375 30.769 0.00 0.00 36.68 3.02
2586 4361 8.862074 CAATTGCTTTCATCGATAATGTTTTGA 58.138 29.630 0.00 0.00 36.68 2.69
2606 4382 3.411415 AAGCATAAGTCGAGCAATTGC 57.589 42.857 23.05 23.05 42.49 3.56
2621 4397 7.555965 ACAAAACAGACTTAAAAGGAAAGCAT 58.444 30.769 0.00 0.00 0.00 3.79
2856 5338 5.164158 GCAGCAGTTGTCAACAATAATTTCG 60.164 40.000 17.78 0.00 38.24 3.46
2862 5344 3.612241 GCATGCAGCAGTTGTCAACAATA 60.612 43.478 14.21 0.00 44.79 1.90
2942 5424 9.771534 GTTTACTTAATAGGAGCATCTGAGAAT 57.228 33.333 0.00 0.00 33.73 2.40
2970 5452 1.073284 TCTGCAGTAACCCCAAGGAAC 59.927 52.381 14.67 0.00 36.73 3.62
3131 5873 4.042398 CCATTCGTAGTATGAAGTGACCG 58.958 47.826 10.47 0.00 0.00 4.79
3137 5879 8.657074 TCCAATTAACCATTCGTAGTATGAAG 57.343 34.615 10.47 1.21 0.00 3.02
3180 5922 3.319122 GGAAGTGTTGACCAGCATTTCTT 59.681 43.478 16.77 5.42 37.99 2.52
3193 5935 6.884295 TCAATAATACCAGGAAGGAAGTGTTG 59.116 38.462 0.00 0.00 41.22 3.33
3214 5956 3.374764 GGCCCCCAGAAAAGTATTCAAT 58.625 45.455 0.00 0.00 0.00 2.57
3220 5962 0.838987 AGTCGGCCCCCAGAAAAGTA 60.839 55.000 0.00 0.00 0.00 2.24
3226 5968 2.363795 CACTAGTCGGCCCCCAGA 60.364 66.667 0.00 0.00 0.00 3.86
3234 5976 0.532573 AGGCATGTCACACTAGTCGG 59.467 55.000 0.00 0.00 0.00 4.79
3244 5986 2.928801 ACAACACACTAGGCATGTCA 57.071 45.000 0.00 0.00 0.00 3.58
3260 6330 3.994204 TGTGCGACTACAAGTCTACAA 57.006 42.857 5.59 0.00 42.92 2.41
3261 6331 3.504520 TCATGTGCGACTACAAGTCTACA 59.495 43.478 12.99 12.99 42.92 2.74
3262 6332 4.092771 TCATGTGCGACTACAAGTCTAC 57.907 45.455 5.59 5.30 42.92 2.59
3263 6333 4.983671 ATCATGTGCGACTACAAGTCTA 57.016 40.909 5.59 0.00 42.92 2.59
3264 6334 3.876274 ATCATGTGCGACTACAAGTCT 57.124 42.857 5.59 0.00 42.92 3.24
3265 6335 4.928661 AAATCATGTGCGACTACAAGTC 57.071 40.909 0.00 0.00 41.71 3.01
3266 6336 4.754618 TCAAAATCATGTGCGACTACAAGT 59.245 37.500 0.00 0.00 33.69 3.16
3267 6337 5.082059 GTCAAAATCATGTGCGACTACAAG 58.918 41.667 0.00 0.00 33.69 3.16
3359 6473 3.761752 TGCAGCATCCATGGATCAATATG 59.238 43.478 24.93 14.93 31.62 1.78
3587 7087 1.073284 TCCTTTGTCCTGTACTTGCCC 59.927 52.381 0.00 0.00 0.00 5.36
3817 7317 5.300539 TGTTTTGCCTTGCTACAAAGTATCA 59.699 36.000 0.00 0.00 37.11 2.15
3860 7360 6.552629 GTTTAAATTGAAGGTAGCCAGCTAC 58.447 40.000 19.35 19.35 45.89 3.58
3875 7375 5.527511 TTCAATGCATGCCGTTTAAATTG 57.472 34.783 16.68 15.67 0.00 2.32
3949 7450 3.253432 CCTTTCCAAAGAAAAGAGGACCG 59.747 47.826 0.32 0.00 41.40 4.79
4146 7647 9.932207 TGCTTTTGATTTTGAATTATGACTGAT 57.068 25.926 0.00 0.00 0.00 2.90
4147 7648 9.932207 ATGCTTTTGATTTTGAATTATGACTGA 57.068 25.926 0.00 0.00 0.00 3.41
4148 7649 9.967245 CATGCTTTTGATTTTGAATTATGACTG 57.033 29.630 0.00 0.00 0.00 3.51
4149 7650 9.158233 CCATGCTTTTGATTTTGAATTATGACT 57.842 29.630 0.00 0.00 0.00 3.41
4150 7651 8.938906 ACCATGCTTTTGATTTTGAATTATGAC 58.061 29.630 0.00 0.00 0.00 3.06
4154 7655 9.638239 GACTACCATGCTTTTGATTTTGAATTA 57.362 29.630 0.00 0.00 0.00 1.40
4155 7656 8.149647 TGACTACCATGCTTTTGATTTTGAATT 58.850 29.630 0.00 0.00 0.00 2.17
4393 7955 2.571212 ACATGTGAAAAGACCGCTCAA 58.429 42.857 0.00 0.00 0.00 3.02
4395 7957 5.581085 AGTTATACATGTGAAAAGACCGCTC 59.419 40.000 9.11 0.00 0.00 5.03
4415 7977 8.034215 TGTTTCGATTTAGTTATTCCCGAGTTA 58.966 33.333 0.00 0.00 0.00 2.24
4495 8057 6.028987 GGTGTCGAGTAGTAGATCAAACTTC 58.971 44.000 6.11 2.21 0.00 3.01
4502 8064 5.388268 CGATAACGGTGTCGAGTAGTAGATC 60.388 48.000 15.06 0.00 40.52 2.75
4504 8066 3.798878 CGATAACGGTGTCGAGTAGTAGA 59.201 47.826 15.06 0.00 40.52 2.59
4509 8071 2.741517 TGAACGATAACGGTGTCGAGTA 59.258 45.455 26.78 8.35 40.52 2.59
4529 8091 0.896940 ATGCTTGCCCCTGAACACTG 60.897 55.000 0.00 0.00 0.00 3.66
4530 8092 0.610232 GATGCTTGCCCCTGAACACT 60.610 55.000 0.00 0.00 0.00 3.55
4532 8094 1.304381 GGATGCTTGCCCCTGAACA 60.304 57.895 0.00 0.00 0.00 3.18
4549 8140 3.741388 CGTTACAGGATAAAGAGCTGGGG 60.741 52.174 0.00 0.00 0.00 4.96
4567 8158 5.240183 GGGTCATACAGCTCATACTACGTTA 59.760 44.000 0.00 0.00 0.00 3.18
4574 8165 3.118408 TGGTTGGGTCATACAGCTCATAC 60.118 47.826 0.00 0.00 0.00 2.39
4575 8166 3.111484 TGGTTGGGTCATACAGCTCATA 58.889 45.455 0.00 0.00 0.00 2.15
4576 8167 1.915489 TGGTTGGGTCATACAGCTCAT 59.085 47.619 0.00 0.00 0.00 2.90
4577 8168 1.278985 CTGGTTGGGTCATACAGCTCA 59.721 52.381 0.00 0.00 0.00 4.26
4578 8169 1.555075 TCTGGTTGGGTCATACAGCTC 59.445 52.381 0.00 0.00 0.00 4.09
4579 8170 1.279271 GTCTGGTTGGGTCATACAGCT 59.721 52.381 0.00 0.00 0.00 4.24
4580 8171 1.679032 GGTCTGGTTGGGTCATACAGC 60.679 57.143 0.00 0.00 0.00 4.40
4581 8172 1.628340 TGGTCTGGTTGGGTCATACAG 59.372 52.381 0.00 0.00 0.00 2.74
4582 8173 1.628340 CTGGTCTGGTTGGGTCATACA 59.372 52.381 0.00 0.00 0.00 2.29
4588 8179 2.343475 CTGTGCTGGTCTGGTTGGGT 62.343 60.000 0.00 0.00 0.00 4.51
4675 8266 9.167311 GTGAATGTACATGAAGGAAATAAGAGT 57.833 33.333 9.63 0.00 0.00 3.24
4712 8303 1.069568 CAACTTGATGGCGTGCGTAAA 60.070 47.619 0.00 0.00 0.00 2.01
4713 8304 0.515127 CAACTTGATGGCGTGCGTAA 59.485 50.000 0.00 0.00 0.00 3.18
4734 8325 3.369147 CAGACCATAAACTGCGACTCTTG 59.631 47.826 0.00 0.00 0.00 3.02
4735 8326 3.258372 TCAGACCATAAACTGCGACTCTT 59.742 43.478 0.00 0.00 34.57 2.85
4742 8333 5.470098 TCAAAAGACTCAGACCATAAACTGC 59.530 40.000 0.00 0.00 34.57 4.40
4767 8361 8.739972 GCCAAAGAAAATAAGGAGAGATACAAA 58.260 33.333 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.