Multiple sequence alignment - TraesCS7D01G045200

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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 TraesCS7D01G045200 chr7D 100.000 3862 0 0 1 3862 22860250 22864111 0.000000e+00 7132.0
1 TraesCS7D01G045200 chr7D 84.702 2301 295 32 1065 3348 22943997 22946257 0.000000e+00 2246.0
2 TraesCS7D01G045200 chr7D 84.555 2279 301 31 1087 3348 22974796 22972552 0.000000e+00 2211.0
3 TraesCS7D01G045200 chr7D 84.772 394 41 10 295 685 47847423 47847800 1.010000e-100 377.0
4 TraesCS7D01G045200 chr7D 85.870 92 7 6 511 598 47847598 47847687 4.110000e-15 93.5
5 TraesCS7D01G045200 chr7A 92.633 3054 170 18 817 3862 23354481 23357487 0.000000e+00 4342.0
6 TraesCS7D01G045200 chr7A 84.303 2287 298 35 1087 3348 23386283 23388533 0.000000e+00 2178.0
7 TraesCS7D01G045200 chr7A 84.305 2281 303 32 1087 3348 23523334 23521090 0.000000e+00 2178.0
8 TraesCS7D01G045200 chr7A 91.089 202 17 1 80 281 23354246 23354446 4.920000e-69 272.0
9 TraesCS7D01G045200 chr7A 75.964 337 46 12 3525 3859 23357619 23357922 1.450000e-29 141.0
10 TraesCS7D01G045200 chr7A 95.890 73 3 0 1 73 23353674 23353746 6.780000e-23 119.0
11 TraesCS7D01G045200 chr5A 91.544 3063 182 29 817 3862 41953559 41956561 0.000000e+00 4150.0
12 TraesCS7D01G045200 chr5A 83.922 2295 311 30 1028 3314 41966772 41969016 0.000000e+00 2141.0
13 TraesCS7D01G045200 chr5A 87.081 209 24 2 1 207 41952858 41953065 2.320000e-57 233.0
14 TraesCS7D01G045200 chr5A 76.331 338 43 15 3525 3859 41956693 41956996 3.110000e-31 147.0
15 TraesCS7D01G045200 chr4A 92.397 1802 95 21 2064 3862 706643524 706641762 0.000000e+00 2531.0
16 TraesCS7D01G045200 chr4A 84.160 2279 306 34 1087 3348 706838685 706836445 0.000000e+00 2158.0
17 TraesCS7D01G045200 chr4A 84.717 2048 260 33 1087 3113 706706820 706708835 0.000000e+00 1999.0
18 TraesCS7D01G045200 chr4A 83.526 1730 247 22 1028 2752 706970210 706971906 0.000000e+00 1581.0
19 TraesCS7D01G045200 chr4A 83.410 1730 249 22 1028 2752 706945974 706947670 0.000000e+00 1570.0
20 TraesCS7D01G045200 chr4A 94.405 840 40 1 916 1755 706658159 706657327 0.000000e+00 1284.0
21 TraesCS7D01G045200 chr4A 90.252 318 25 6 281 596 706659866 706659553 9.990000e-111 411.0
22 TraesCS7D01G045200 chr4A 92.883 281 18 1 1 281 706660459 706660181 1.290000e-109 407.0
23 TraesCS7D01G045200 chr4A 93.583 187 11 1 700 885 706659330 706659144 1.060000e-70 278.0
24 TraesCS7D01G045200 chr4A 76.627 338 42 15 3525 3859 706641630 706641327 6.680000e-33 152.0
25 TraesCS7D01G045200 chr4A 95.745 47 2 0 868 914 706658231 706658185 4.140000e-10 76.8
26 TraesCS7D01G045200 chrUn 83.837 2283 302 42 1087 3348 89917548 89915312 0.000000e+00 2109.0
27 TraesCS7D01G045200 chrUn 83.837 2283 302 41 1087 3348 89979760 89981996 0.000000e+00 2109.0
28 TraesCS7D01G045200 chr5D 85.083 1562 197 23 1068 2620 361184009 361182475 0.000000e+00 1561.0
29 TraesCS7D01G045200 chr5D 90.000 490 27 4 3374 3862 361173059 361172591 7.090000e-172 614.0
30 TraesCS7D01G045200 chr5D 81.618 408 53 15 294 686 463240671 463240271 6.230000e-83 318.0
31 TraesCS7D01G045200 chr2D 82.850 414 45 18 295 704 469720351 469719960 7.940000e-92 348.0
32 TraesCS7D01G045200 chr2D 82.486 354 43 11 298 649 469504935 469504599 3.770000e-75 292.0
33 TraesCS7D01G045200 chr3A 82.447 376 49 10 294 667 662791211 662791571 2.900000e-81 313.0
34 TraesCS7D01G045200 chr6A 79.821 446 59 21 294 726 98599017 98598590 2.920000e-76 296.0
35 TraesCS7D01G045200 chr3D 80.556 396 57 16 293 673 348150511 348150121 1.760000e-73 287.0
36 TraesCS7D01G045200 chr1B 79.418 447 58 19 296 716 571430878 571431316 6.320000e-73 285.0
37 TraesCS7D01G045200 chr6D 88.372 215 25 0 294 508 266954100 266954314 3.830000e-65 259.0


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 TraesCS7D01G045200 chr7D 22860250 22864111 3861 False 7132.00 7132 100.000000 1 3862 1 chr7D.!!$F1 3861
1 TraesCS7D01G045200 chr7D 22943997 22946257 2260 False 2246.00 2246 84.702000 1065 3348 1 chr7D.!!$F2 2283
2 TraesCS7D01G045200 chr7D 22972552 22974796 2244 True 2211.00 2211 84.555000 1087 3348 1 chr7D.!!$R1 2261
3 TraesCS7D01G045200 chr7A 23386283 23388533 2250 False 2178.00 2178 84.303000 1087 3348 1 chr7A.!!$F1 2261
4 TraesCS7D01G045200 chr7A 23521090 23523334 2244 True 2178.00 2178 84.305000 1087 3348 1 chr7A.!!$R1 2261
5 TraesCS7D01G045200 chr7A 23353674 23357922 4248 False 1218.50 4342 88.894000 1 3862 4 chr7A.!!$F2 3861
6 TraesCS7D01G045200 chr5A 41966772 41969016 2244 False 2141.00 2141 83.922000 1028 3314 1 chr5A.!!$F1 2286
7 TraesCS7D01G045200 chr5A 41952858 41956996 4138 False 1510.00 4150 84.985333 1 3862 3 chr5A.!!$F2 3861
8 TraesCS7D01G045200 chr4A 706836445 706838685 2240 True 2158.00 2158 84.160000 1087 3348 1 chr4A.!!$R1 2261
9 TraesCS7D01G045200 chr4A 706706820 706708835 2015 False 1999.00 1999 84.717000 1087 3113 1 chr4A.!!$F1 2026
10 TraesCS7D01G045200 chr4A 706970210 706971906 1696 False 1581.00 1581 83.526000 1028 2752 1 chr4A.!!$F3 1724
11 TraesCS7D01G045200 chr4A 706945974 706947670 1696 False 1570.00 1570 83.410000 1028 2752 1 chr4A.!!$F2 1724
12 TraesCS7D01G045200 chr4A 706641327 706643524 2197 True 1341.50 2531 84.512000 2064 3862 2 chr4A.!!$R2 1798
13 TraesCS7D01G045200 chr4A 706657327 706660459 3132 True 491.36 1284 93.373600 1 1755 5 chr4A.!!$R3 1754
14 TraesCS7D01G045200 chrUn 89915312 89917548 2236 True 2109.00 2109 83.837000 1087 3348 1 chrUn.!!$R1 2261
15 TraesCS7D01G045200 chrUn 89979760 89981996 2236 False 2109.00 2109 83.837000 1087 3348 1 chrUn.!!$F1 2261
16 TraesCS7D01G045200 chr5D 361182475 361184009 1534 True 1561.00 1561 85.083000 1068 2620 1 chr5D.!!$R2 1552

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
45 46 0.179018 GGTGTTGTGAAGGGAGCACT 60.179 55.000 0.00 0.0 37.18 4.40 F
664 2041 0.317020 GATGCGGCAAATCTAACGGC 60.317 55.000 6.82 0.0 0.00 5.68 F
682 2059 0.462759 GCTCGCTACCTGGCTGATTT 60.463 55.000 0.00 0.0 0.00 2.17 F
831 2209 1.000019 CCGGGTAGGACCAGTCTCA 60.000 63.158 0.00 0.0 45.00 3.27 F
2424 4808 1.067212 GTGGTTCTGTGTCACGTCTCT 59.933 52.381 0.00 0.0 0.00 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1956 4328 0.984230 TCTCCTCCGGTGCATTTCTT 59.016 50.000 0.00 0.00 0.00 2.52 R
2330 4714 0.947244 ACTTCTCGGCAAGTGCTTTG 59.053 50.000 2.85 0.00 41.70 2.77 R
2354 4738 3.557595 GGACTAATGCCTTCTCATTGTCG 59.442 47.826 0.00 0.00 37.27 4.35 R
2601 4994 4.739793 ACCTTGAAAATTGAGGGATGTGA 58.260 39.130 0.00 0.00 34.81 3.58 R
3807 6225 0.178967 TTGATTGGGCACAAGCTCCA 60.179 50.000 19.12 5.18 43.19 3.86 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
45 46 0.179018 GGTGTTGTGAAGGGAGCACT 60.179 55.000 0.00 0.00 37.18 4.40
69 70 4.717313 AAAAGGCCGCCGAGGGTC 62.717 66.667 3.05 0.00 41.48 4.46
91 585 3.624410 CCTTCGAGTTGCAATGATGATCA 59.376 43.478 0.59 0.00 0.00 2.92
112 606 1.604593 AGTGTTGTGATGGCAGCCC 60.605 57.895 9.64 0.00 0.00 5.19
128 622 3.135457 CCACGATGCTGCATGGCA 61.135 61.111 21.53 2.80 46.63 4.92
140 636 1.226542 CATGGCACTGGAGATGGCT 59.773 57.895 0.00 0.00 42.86 4.75
213 1097 1.169661 TTTCATCAAACGGCTGGCGT 61.170 50.000 24.13 24.13 0.00 5.68
269 1153 5.475909 CGACTCCCAGTACTAGCCATATTTA 59.524 44.000 0.00 0.00 0.00 1.40
368 1567 1.300388 GCGTTACACGTGTCCCAGT 60.300 57.895 27.16 1.11 44.73 4.00
376 1575 2.665603 GTGTCCCAGTGAGAGCCC 59.334 66.667 0.00 0.00 0.00 5.19
404 1603 1.154654 CCTTTGTCGAACGCGCTTC 60.155 57.895 5.73 8.71 37.46 3.86
424 1623 3.338249 TCTGCAACAGGAGCTATGTTTC 58.662 45.455 12.83 9.72 38.80 2.78
426 1625 3.076621 TGCAACAGGAGCTATGTTTCTG 58.923 45.455 12.83 5.89 38.80 3.02
531 1730 1.003972 TGCAACGAAACTTCTCTTGCG 60.004 47.619 13.02 0.00 39.46 4.85
536 1735 4.813296 ACGAAACTTCTCTTGCGAAAAT 57.187 36.364 0.00 0.00 0.00 1.82
537 1736 5.169836 ACGAAACTTCTCTTGCGAAAATT 57.830 34.783 0.00 0.00 0.00 1.82
546 1745 4.739716 TCTCTTGCGAAAATTTTCTGCAAC 59.260 37.500 33.76 19.46 43.93 4.17
547 1746 4.428209 TCTTGCGAAAATTTTCTGCAACA 58.572 34.783 33.76 27.89 43.93 3.33
551 1750 5.049167 TGCGAAAATTTTCTGCAACAAGAT 58.951 33.333 30.27 0.12 40.69 2.40
555 1754 6.638063 CGAAAATTTTCTGCAACAAGATCTCA 59.362 34.615 24.53 0.00 35.07 3.27
558 1757 5.428496 TTTTCTGCAACAAGATCTCAGTG 57.572 39.130 0.00 0.00 0.00 3.66
594 1816 5.964887 GCAACAAACAACTATTGCAAGAA 57.035 34.783 4.94 0.00 45.38 2.52
596 1818 6.770076 GCAACAAACAACTATTGCAAGAAAA 58.230 32.000 4.94 0.00 45.38 2.29
598 1820 7.909641 GCAACAAACAACTATTGCAAGAAAATT 59.090 29.630 4.94 0.00 45.38 1.82
600 1822 8.947055 ACAAACAACTATTGCAAGAAAATTCT 57.053 26.923 4.94 0.00 39.74 2.40
601 1823 8.819974 ACAAACAACTATTGCAAGAAAATTCTG 58.180 29.630 4.94 0.00 37.65 3.02
602 1824 8.819974 CAAACAACTATTGCAAGAAAATTCTGT 58.180 29.630 4.94 0.00 37.65 3.41
611 1988 6.503524 TGCAAGAAAATTCTGTAACAAGACC 58.496 36.000 0.00 0.00 37.65 3.85
623 2000 5.373222 TGTAACAAGACCTGTGTTGCTATT 58.627 37.500 7.04 0.00 40.82 1.73
638 2015 2.486636 CTATTATGGGGCGCGCTCGA 62.487 60.000 32.29 26.82 38.10 4.04
639 2016 1.884075 TATTATGGGGCGCGCTCGAT 61.884 55.000 30.98 30.98 38.10 3.59
640 2017 3.740818 TATTATGGGGCGCGCTCGATC 62.741 57.143 32.12 15.66 38.10 3.69
649 2026 2.543383 CGCTCGATCGCTTGATGC 59.457 61.111 11.09 6.61 38.57 3.91
660 2037 2.849880 GCTTGATGCGGCAAATCTAA 57.150 45.000 6.82 0.00 0.00 2.10
661 2038 2.454055 GCTTGATGCGGCAAATCTAAC 58.546 47.619 6.82 0.00 0.00 2.34
662 2039 2.708514 CTTGATGCGGCAAATCTAACG 58.291 47.619 6.82 0.00 0.00 3.18
663 2040 1.013596 TGATGCGGCAAATCTAACGG 58.986 50.000 6.82 0.00 0.00 4.44
664 2041 0.317020 GATGCGGCAAATCTAACGGC 60.317 55.000 6.82 0.00 0.00 5.68
665 2042 0.748005 ATGCGGCAAATCTAACGGCT 60.748 50.000 6.82 0.00 0.00 5.52
666 2043 1.352056 GCGGCAAATCTAACGGCTC 59.648 57.895 0.00 0.00 0.00 4.70
667 2044 1.636340 CGGCAAATCTAACGGCTCG 59.364 57.895 0.00 0.00 0.00 5.03
668 2045 1.352056 GGCAAATCTAACGGCTCGC 59.648 57.895 0.00 0.00 0.00 5.03
669 2046 1.090052 GGCAAATCTAACGGCTCGCT 61.090 55.000 0.00 0.00 0.00 4.93
670 2047 1.567504 GCAAATCTAACGGCTCGCTA 58.432 50.000 0.00 0.00 0.00 4.26
671 2048 1.258197 GCAAATCTAACGGCTCGCTAC 59.742 52.381 0.00 0.00 0.00 3.58
672 2049 1.859080 CAAATCTAACGGCTCGCTACC 59.141 52.381 0.00 0.00 0.00 3.18
673 2050 1.400737 AATCTAACGGCTCGCTACCT 58.599 50.000 0.00 0.00 0.00 3.08
674 2051 0.669077 ATCTAACGGCTCGCTACCTG 59.331 55.000 0.00 0.00 0.00 4.00
675 2052 1.065928 CTAACGGCTCGCTACCTGG 59.934 63.158 0.00 0.00 0.00 4.45
676 2053 2.955751 CTAACGGCTCGCTACCTGGC 62.956 65.000 0.00 0.00 0.00 4.85
678 2055 4.880537 CGGCTCGCTACCTGGCTG 62.881 72.222 0.00 0.00 0.00 4.85
679 2056 3.461773 GGCTCGCTACCTGGCTGA 61.462 66.667 0.00 0.00 0.00 4.26
680 2057 2.801631 GGCTCGCTACCTGGCTGAT 61.802 63.158 0.00 0.00 0.00 2.90
681 2058 1.144936 GCTCGCTACCTGGCTGATT 59.855 57.895 0.00 0.00 0.00 2.57
682 2059 0.462759 GCTCGCTACCTGGCTGATTT 60.463 55.000 0.00 0.00 0.00 2.17
683 2060 2.014068 GCTCGCTACCTGGCTGATTTT 61.014 52.381 0.00 0.00 0.00 1.82
684 2061 2.359900 CTCGCTACCTGGCTGATTTTT 58.640 47.619 0.00 0.00 0.00 1.94
726 2103 4.036734 CGTAGCACTGCCCATATCATTTTT 59.963 41.667 0.00 0.00 0.00 1.94
733 2110 6.096705 CACTGCCCATATCATTTTTACTGGAA 59.903 38.462 0.00 0.00 0.00 3.53
749 2126 2.019948 GGAATTAGTTTCCGAGCGGT 57.980 50.000 8.96 0.00 44.46 5.68
759 2136 1.153823 CCGAGCGGTCCAGTGTTAG 60.154 63.158 9.39 0.00 0.00 2.34
829 2207 3.516780 TCCGGGTAGGACCAGTCT 58.483 61.111 0.00 0.00 45.98 3.24
831 2209 1.000019 CCGGGTAGGACCAGTCTCA 60.000 63.158 0.00 0.00 45.00 3.27
879 3187 4.843728 AGAAATCGATCAAACCCAGCTTA 58.156 39.130 0.00 0.00 0.00 3.09
976 3311 3.314553 TCGTCTTCGATCACTTCCAAAC 58.685 45.455 0.00 0.00 41.35 2.93
1400 3748 1.301244 CGATCAATCAGGCGGAGGG 60.301 63.158 0.00 0.00 0.00 4.30
1670 4021 3.564345 CTGCAGGGGCTGAAGCAGT 62.564 63.158 5.57 0.00 46.92 4.40
1757 4119 3.691118 CGCCCGCTATATTACAGGTAGTA 59.309 47.826 0.00 0.00 0.00 1.82
1760 4122 5.126707 GCCCGCTATATTACAGGTAGTATGT 59.873 44.000 5.13 0.00 31.53 2.29
1763 4125 7.122353 CCCGCTATATTACAGGTAGTATGTTCT 59.878 40.741 5.13 0.00 31.53 3.01
1764 4126 7.968956 CCGCTATATTACAGGTAGTATGTTCTG 59.031 40.741 5.13 0.00 31.53 3.02
1765 4127 8.512956 CGCTATATTACAGGTAGTATGTTCTGT 58.487 37.037 5.13 0.00 42.32 3.41
1766 4128 9.627395 GCTATATTACAGGTAGTATGTTCTGTG 57.373 37.037 0.00 0.00 40.24 3.66
1818 4185 4.077300 TCATATTGGGTCTGTGCATCTC 57.923 45.455 0.00 0.00 0.00 2.75
1841 4213 9.354673 TCTCAAAGAAATTGTGGATTTTACTCT 57.645 29.630 0.00 0.00 38.06 3.24
1842 4214 9.971922 CTCAAAGAAATTGTGGATTTTACTCTT 57.028 29.630 0.00 0.00 38.06 2.85
1843 4215 9.748708 TCAAAGAAATTGTGGATTTTACTCTTG 57.251 29.630 0.00 0.00 38.06 3.02
1844 4216 9.533253 CAAAGAAATTGTGGATTTTACTCTTGT 57.467 29.630 0.00 0.00 38.06 3.16
1845 4217 9.533253 AAAGAAATTGTGGATTTTACTCTTGTG 57.467 29.630 0.00 0.00 38.06 3.33
1846 4218 8.463930 AGAAATTGTGGATTTTACTCTTGTGA 57.536 30.769 0.00 0.00 38.06 3.58
1847 4219 9.082313 AGAAATTGTGGATTTTACTCTTGTGAT 57.918 29.630 0.00 0.00 38.06 3.06
1848 4220 9.346725 GAAATTGTGGATTTTACTCTTGTGATC 57.653 33.333 0.00 0.00 38.06 2.92
1985 4357 2.973420 CGGAGGAGATAACCGTTGC 58.027 57.895 0.00 0.00 41.47 4.17
2013 4385 7.862372 CCATGTCATATTGCACAGGTAAATTAC 59.138 37.037 0.00 0.00 0.00 1.89
2014 4386 8.623903 CATGTCATATTGCACAGGTAAATTACT 58.376 33.333 2.96 0.00 0.00 2.24
2015 4387 9.845740 ATGTCATATTGCACAGGTAAATTACTA 57.154 29.630 2.96 0.00 0.00 1.82
2034 4410 7.766219 TTACTAACATTCCTTGCTAATCGTC 57.234 36.000 0.00 0.00 0.00 4.20
2045 4424 2.166459 TGCTAATCGTCTCCTTGTGAGG 59.834 50.000 0.00 0.00 45.02 3.86
2247 4631 2.069273 CCCAAGAAGTGCTACGTTCTG 58.931 52.381 0.00 0.00 33.21 3.02
2330 4714 1.268079 GTTGGAAAGACAGAGCTTGCC 59.732 52.381 0.00 0.00 42.95 4.52
2354 4738 1.334149 GCACTTGCCGAGAAGTTGTTC 60.334 52.381 0.00 0.00 33.75 3.18
2424 4808 1.067212 GTGGTTCTGTGTCACGTCTCT 59.933 52.381 0.00 0.00 0.00 3.10
2464 4853 5.066764 GGTTTAGCTTGTACACACTTTGGAA 59.933 40.000 0.00 0.00 0.00 3.53
2476 4865 9.394477 GTACACACTTTGGAATTGTATTTCTTC 57.606 33.333 0.00 0.00 0.00 2.87
2601 4994 4.894784 TCTTTTTGACGAGGCAGATAAGT 58.105 39.130 0.00 0.00 0.00 2.24
2986 5394 1.186200 TCCAGATGAAGAGGGTCGTG 58.814 55.000 0.00 0.00 0.00 4.35
3004 5412 3.585862 CGTGGATACGGCAGCTTATAAT 58.414 45.455 0.00 0.00 46.23 1.28
3016 5424 5.337894 GGCAGCTTATAATGGCATCTCTCTA 60.338 44.000 0.00 0.00 41.35 2.43
3032 5440 5.016831 TCTCTCTACTTGTAACAGATGCCA 58.983 41.667 0.00 0.00 0.00 4.92
3144 5560 5.808540 TGTTTGTACATATCCTGCTTACGAC 59.191 40.000 0.00 0.00 0.00 4.34
3155 5573 2.603110 CTGCTTACGACGCATACATGTT 59.397 45.455 2.30 0.00 36.70 2.71
3166 5584 6.143919 CGACGCATACATGTTCTATGTATTGT 59.856 38.462 2.30 10.49 41.69 2.71
3178 5596 7.070696 TGTTCTATGTATTGTAGGTGTATGGCT 59.929 37.037 0.00 0.00 0.00 4.75
3276 5694 1.134280 CAAGGCTCGACCATCTCCATT 60.134 52.381 6.78 0.00 43.14 3.16
3289 5707 1.442526 CTCCATTGATGCCGCTGACC 61.443 60.000 0.00 0.00 0.00 4.02
3356 5774 1.517832 GCAGATCTACGTGGCCAGT 59.482 57.895 5.11 9.57 0.00 4.00
3357 5775 0.807667 GCAGATCTACGTGGCCAGTG 60.808 60.000 5.11 4.02 0.00 3.66
3365 5783 0.973632 ACGTGGCCAGTGATGAGTTA 59.026 50.000 5.11 0.00 0.00 2.24
3414 5832 1.758280 ACGGTCAGTACAAGTTCCACA 59.242 47.619 0.00 0.00 0.00 4.17
3448 5866 3.806949 AATCTTGCTTGGTGGGACTTA 57.193 42.857 0.00 0.00 0.00 2.24
3461 5879 3.802685 GTGGGACTTATACTTCACGATGC 59.197 47.826 0.00 0.00 0.00 3.91
3484 5902 0.608308 CACCGAGGGAAGGGAAAACC 60.608 60.000 0.00 0.00 40.67 3.27
3564 5982 5.816777 GCTTGAGCTGACTCTGATTTTCTAT 59.183 40.000 0.00 0.00 43.85 1.98
3586 6004 1.544691 TCGAAACCTTTCTCCCTCTCG 59.455 52.381 0.00 0.00 35.07 4.04
3666 6084 3.869272 GAAGGTGCGCATCGGCAG 61.869 66.667 15.91 0.00 44.93 4.85
3672 6090 4.183686 GCGCATCGGCAGCACATT 62.184 61.111 0.30 0.00 41.24 2.71
3673 6091 2.277692 CGCATCGGCAGCACATTG 60.278 61.111 0.00 0.00 41.24 2.82
3674 6092 2.879907 GCATCGGCAGCACATTGT 59.120 55.556 0.00 0.00 40.72 2.71
3675 6093 1.704387 CGCATCGGCAGCACATTGTA 61.704 55.000 0.00 0.00 41.24 2.41
3676 6094 0.451383 GCATCGGCAGCACATTGTAA 59.549 50.000 0.00 0.00 40.72 2.41
3677 6095 1.066002 GCATCGGCAGCACATTGTAAT 59.934 47.619 0.00 0.00 40.72 1.89
3678 6096 2.480073 GCATCGGCAGCACATTGTAATT 60.480 45.455 0.00 0.00 40.72 1.40
3679 6097 2.917701 TCGGCAGCACATTGTAATTG 57.082 45.000 0.00 0.00 0.00 2.32
3680 6098 2.158559 TCGGCAGCACATTGTAATTGT 58.841 42.857 0.00 0.00 0.00 2.71
3681 6099 2.095314 TCGGCAGCACATTGTAATTGTG 60.095 45.455 0.00 0.00 36.70 3.33
3694 6112 5.363562 TGTAATTGTGCCATCTCTCTGAT 57.636 39.130 0.00 0.00 35.40 2.90
3761 6179 4.279145 AGCCAATCTGAATTTGAGATGCT 58.721 39.130 0.00 2.58 30.30 3.79
3762 6180 4.098044 AGCCAATCTGAATTTGAGATGCTG 59.902 41.667 9.02 1.70 31.41 4.41
3763 6181 4.736759 GCCAATCTGAATTTGAGATGCTGG 60.737 45.833 10.54 10.54 33.53 4.85
3769 6187 5.412594 TCTGAATTTGAGATGCTGGTGTAAC 59.587 40.000 0.00 0.00 0.00 2.50
3781 6199 4.278170 TGCTGGTGTAACATTTGAAGAAGG 59.722 41.667 0.00 0.00 39.98 3.46
3786 6204 5.946377 GGTGTAACATTTGAAGAAGGAGGAT 59.054 40.000 0.00 0.00 39.98 3.24
3798 6216 2.176247 AGGAGGATGGTCGGTACATT 57.824 50.000 0.00 0.00 0.00 2.71
3807 6225 2.303600 TGGTCGGTACATTGCTTACCTT 59.696 45.455 0.00 0.00 37.45 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 3.294493 GGCGGCCTTTTCAGCACA 61.294 61.111 12.87 0.00 0.00 4.57
69 70 3.624410 TGATCATCATTGCAACTCGAAGG 59.376 43.478 0.00 0.00 0.00 3.46
91 585 0.670162 GCTGCCATCACAACACTGTT 59.330 50.000 0.00 0.00 31.64 3.16
112 606 2.101575 GTGCCATGCAGCATCGTG 59.898 61.111 4.38 0.00 46.24 4.35
128 622 1.378250 GCAAGCAGCCATCTCCAGT 60.378 57.895 0.00 0.00 37.23 4.00
213 1097 1.657751 CGCTCCCAGATCTGTCGACA 61.658 60.000 21.11 18.88 0.00 4.35
274 1158 8.370182 GTTTCCCAAATGATATGGCTATTTCAT 58.630 33.333 9.65 9.65 36.80 2.57
339 1538 2.436115 GTAACGCAGGGGAGGTGC 60.436 66.667 0.00 0.00 37.58 5.01
368 1567 1.748403 GATGGTATGCGGGCTCTCA 59.252 57.895 0.00 0.00 0.00 3.27
376 1575 1.934589 TCGACAAAGGATGGTATGCG 58.065 50.000 0.00 0.00 0.00 4.73
404 1603 3.126514 CAGAAACATAGCTCCTGTTGCAG 59.873 47.826 17.89 9.43 36.95 4.41
494 1693 7.763172 TCGTTGCAATTTTGTTGTAGAATTT 57.237 28.000 0.59 0.00 0.00 1.82
495 1694 7.763172 TTCGTTGCAATTTTGTTGTAGAATT 57.237 28.000 0.59 0.00 0.00 2.17
496 1695 7.491048 AGTTTCGTTGCAATTTTGTTGTAGAAT 59.509 29.630 0.59 0.00 0.00 2.40
512 1711 1.260561 TCGCAAGAGAAGTTTCGTTGC 59.739 47.619 17.73 17.73 45.01 4.17
531 1730 7.650903 ACTGAGATCTTGTTGCAGAAAATTTTC 59.349 33.333 21.00 21.00 37.45 2.29
536 1735 4.276678 CCACTGAGATCTTGTTGCAGAAAA 59.723 41.667 13.67 0.00 0.00 2.29
537 1736 3.817084 CCACTGAGATCTTGTTGCAGAAA 59.183 43.478 13.67 0.00 0.00 2.52
585 1807 7.653311 GGTCTTGTTACAGAATTTTCTTGCAAT 59.347 33.333 0.00 0.00 34.74 3.56
592 1814 7.027778 ACACAGGTCTTGTTACAGAATTTTC 57.972 36.000 0.00 0.00 38.16 2.29
594 1816 6.680378 GCAACACAGGTCTTGTTACAGAATTT 60.680 38.462 0.00 0.00 38.16 1.82
596 1818 4.275936 GCAACACAGGTCTTGTTACAGAAT 59.724 41.667 0.00 0.00 38.16 2.40
598 1820 3.118408 AGCAACACAGGTCTTGTTACAGA 60.118 43.478 0.00 0.00 38.16 3.41
600 1822 3.275617 AGCAACACAGGTCTTGTTACA 57.724 42.857 0.00 0.00 38.16 2.41
601 1823 5.941948 AATAGCAACACAGGTCTTGTTAC 57.058 39.130 0.00 0.00 38.16 2.50
602 1824 6.597672 CCATAATAGCAACACAGGTCTTGTTA 59.402 38.462 0.00 0.00 38.16 2.41
611 1988 1.603802 CGCCCCATAATAGCAACACAG 59.396 52.381 0.00 0.00 0.00 3.66
623 2000 4.357947 GATCGAGCGCGCCCCATA 62.358 66.667 30.33 9.77 37.46 2.74
641 2018 2.454055 GTTAGATTTGCCGCATCAAGC 58.546 47.619 0.00 0.00 40.87 4.01
642 2019 2.539547 CCGTTAGATTTGCCGCATCAAG 60.540 50.000 0.00 0.00 0.00 3.02
643 2020 1.400142 CCGTTAGATTTGCCGCATCAA 59.600 47.619 0.00 0.00 0.00 2.57
644 2021 1.013596 CCGTTAGATTTGCCGCATCA 58.986 50.000 0.00 0.00 0.00 3.07
645 2022 0.317020 GCCGTTAGATTTGCCGCATC 60.317 55.000 0.00 0.00 0.00 3.91
646 2023 0.748005 AGCCGTTAGATTTGCCGCAT 60.748 50.000 0.00 0.00 0.00 4.73
647 2024 1.366111 GAGCCGTTAGATTTGCCGCA 61.366 55.000 0.00 0.00 0.00 5.69
648 2025 1.352056 GAGCCGTTAGATTTGCCGC 59.648 57.895 0.00 0.00 0.00 6.53
649 2026 1.636340 CGAGCCGTTAGATTTGCCG 59.364 57.895 0.00 0.00 0.00 5.69
650 2027 1.090052 AGCGAGCCGTTAGATTTGCC 61.090 55.000 0.00 0.00 0.00 4.52
651 2028 1.258197 GTAGCGAGCCGTTAGATTTGC 59.742 52.381 0.00 0.00 0.00 3.68
652 2029 1.859080 GGTAGCGAGCCGTTAGATTTG 59.141 52.381 0.00 0.00 0.00 2.32
653 2030 1.755380 AGGTAGCGAGCCGTTAGATTT 59.245 47.619 0.00 0.00 0.00 2.17
654 2031 1.067212 CAGGTAGCGAGCCGTTAGATT 59.933 52.381 0.00 0.00 0.00 2.40
655 2032 0.669077 CAGGTAGCGAGCCGTTAGAT 59.331 55.000 0.00 0.00 0.00 1.98
656 2033 1.381928 CCAGGTAGCGAGCCGTTAGA 61.382 60.000 0.00 0.00 0.00 2.10
657 2034 1.065928 CCAGGTAGCGAGCCGTTAG 59.934 63.158 0.00 0.00 0.00 2.34
658 2035 3.072486 GCCAGGTAGCGAGCCGTTA 62.072 63.158 0.00 0.00 0.00 3.18
659 2036 4.452733 GCCAGGTAGCGAGCCGTT 62.453 66.667 0.00 0.00 0.00 4.44
661 2038 4.880537 CAGCCAGGTAGCGAGCCG 62.881 72.222 5.72 0.00 38.01 5.52
662 2039 2.317149 AATCAGCCAGGTAGCGAGCC 62.317 60.000 5.72 0.00 38.01 4.70
663 2040 0.462759 AAATCAGCCAGGTAGCGAGC 60.463 55.000 1.49 1.49 38.01 5.03
664 2041 2.029838 AAAATCAGCCAGGTAGCGAG 57.970 50.000 0.00 0.00 38.01 5.03
665 2042 2.489938 AAAAATCAGCCAGGTAGCGA 57.510 45.000 0.00 0.00 38.01 4.93
681 2058 2.356135 GTCGGCTGGCTGATCTAAAAA 58.644 47.619 7.39 0.00 33.49 1.94
682 2059 1.739035 CGTCGGCTGGCTGATCTAAAA 60.739 52.381 7.39 0.00 33.49 1.52
683 2060 0.179111 CGTCGGCTGGCTGATCTAAA 60.179 55.000 7.39 0.00 33.49 1.85
684 2061 1.437573 CGTCGGCTGGCTGATCTAA 59.562 57.895 7.39 0.00 33.49 2.10
685 2062 3.120105 CGTCGGCTGGCTGATCTA 58.880 61.111 7.39 0.00 33.49 1.98
686 2063 4.521062 GCGTCGGCTGGCTGATCT 62.521 66.667 7.39 0.00 35.83 2.75
694 2071 4.778415 AGTGCTACGCGTCGGCTG 62.778 66.667 28.21 13.05 36.88 4.85
695 2072 4.778415 CAGTGCTACGCGTCGGCT 62.778 66.667 28.21 16.10 36.88 5.52
733 2110 0.899720 TGGACCGCTCGGAAACTAAT 59.100 50.000 15.95 0.00 38.96 1.73
829 2207 2.268920 GCCACGCTGAATCCCTGA 59.731 61.111 0.00 0.00 0.00 3.86
831 2209 3.706373 ACGCCACGCTGAATCCCT 61.706 61.111 0.00 0.00 0.00 4.20
879 3187 1.003851 CGACGACGGCAACCAATAAT 58.996 50.000 0.00 0.00 35.72 1.28
976 3311 2.449322 CTCCCCCTCCCCCATCTG 60.449 72.222 0.00 0.00 0.00 2.90
1757 4119 7.765695 AATTCTTAACCACATCACAGAACAT 57.234 32.000 0.00 0.00 0.00 2.71
1818 4185 9.533253 ACAAGAGTAAAATCCACAATTTCTTTG 57.467 29.630 0.00 0.00 36.54 2.77
1841 4213 2.364002 TGACGACCTGACAAGATCACAA 59.636 45.455 0.00 0.00 32.37 3.33
1842 4214 1.960689 TGACGACCTGACAAGATCACA 59.039 47.619 0.00 0.00 32.37 3.58
1843 4215 2.029828 ACTGACGACCTGACAAGATCAC 60.030 50.000 0.00 0.00 32.37 3.06
1844 4216 2.239400 ACTGACGACCTGACAAGATCA 58.761 47.619 0.00 0.00 35.45 2.92
1845 4217 3.305398 AACTGACGACCTGACAAGATC 57.695 47.619 0.00 0.00 0.00 2.75
1846 4218 3.555168 GGAAACTGACGACCTGACAAGAT 60.555 47.826 0.00 0.00 0.00 2.40
1847 4219 2.223971 GGAAACTGACGACCTGACAAGA 60.224 50.000 0.00 0.00 0.00 3.02
1848 4220 2.135933 GGAAACTGACGACCTGACAAG 58.864 52.381 0.00 0.00 0.00 3.16
1956 4328 0.984230 TCTCCTCCGGTGCATTTCTT 59.016 50.000 0.00 0.00 0.00 2.52
1958 4330 2.872858 GTTATCTCCTCCGGTGCATTTC 59.127 50.000 0.00 0.00 0.00 2.17
1985 4357 3.548770 ACCTGTGCAATATGACATGGAG 58.451 45.455 0.00 0.00 0.00 3.86
2013 4385 5.463724 GGAGACGATTAGCAAGGAATGTTAG 59.536 44.000 0.00 0.00 0.00 2.34
2014 4386 5.128827 AGGAGACGATTAGCAAGGAATGTTA 59.871 40.000 0.00 0.00 0.00 2.41
2015 4387 4.080863 AGGAGACGATTAGCAAGGAATGTT 60.081 41.667 0.00 0.00 0.00 2.71
2045 4424 4.041723 CACACCGAAACAAATGGAAACTC 58.958 43.478 0.00 0.00 0.00 3.01
2247 4631 1.025041 GATTGATCAAAGCCGACCCC 58.975 55.000 13.09 0.00 0.00 4.95
2330 4714 0.947244 ACTTCTCGGCAAGTGCTTTG 59.053 50.000 2.85 0.00 41.70 2.77
2354 4738 3.557595 GGACTAATGCCTTCTCATTGTCG 59.442 47.826 0.00 0.00 37.27 4.35
2464 4853 9.620259 GAGTAGGAATTCAGGAAGAAATACAAT 57.380 33.333 7.93 0.00 40.22 2.71
2476 4865 5.128499 AGTGAGACATGAGTAGGAATTCAGG 59.872 44.000 7.93 0.00 0.00 3.86
2601 4994 4.739793 ACCTTGAAAATTGAGGGATGTGA 58.260 39.130 0.00 0.00 34.81 3.58
2986 5394 2.678336 GCCATTATAAGCTGCCGTATCC 59.322 50.000 0.00 0.00 0.00 2.59
3004 5412 5.016831 TCTGTTACAAGTAGAGAGATGCCA 58.983 41.667 0.00 0.00 0.00 4.92
3016 5424 3.507233 CCAATGTGGCATCTGTTACAAGT 59.493 43.478 0.00 0.00 0.00 3.16
3111 5525 6.091577 CAGGATATGTACAAACAACTACGCAA 59.908 38.462 0.00 0.00 39.58 4.85
3121 5535 5.051907 CGTCGTAAGCAGGATATGTACAAAC 60.052 44.000 0.00 0.00 37.18 2.93
3144 5560 7.598869 ACCTACAATACATAGAACATGTATGCG 59.401 37.037 0.00 7.67 42.48 4.73
3155 5573 6.780522 TGAGCCATACACCTACAATACATAGA 59.219 38.462 0.00 0.00 0.00 1.98
3178 5596 4.938575 TCCACCTTTTAATAGGCCTTGA 57.061 40.909 12.58 0.00 38.99 3.02
3276 5694 3.402110 CTTATTATGGTCAGCGGCATCA 58.598 45.455 1.45 0.00 0.00 3.07
3289 5707 5.711976 CCTGGTATTTCAGCCCCTTATTATG 59.288 44.000 0.00 0.00 33.64 1.90
3356 5774 6.095377 CAGATATAGCACGCATAACTCATCA 58.905 40.000 0.00 0.00 0.00 3.07
3357 5775 6.096036 ACAGATATAGCACGCATAACTCATC 58.904 40.000 0.00 0.00 0.00 2.92
3365 5783 5.651387 ACAGATACAGATATAGCACGCAT 57.349 39.130 0.00 0.00 0.00 4.73
3414 5832 5.852282 AGCAAGATTAATTACCCGCAAAT 57.148 34.783 0.00 0.00 0.00 2.32
3448 5866 0.810031 GTGGGCGCATCGTGAAGTAT 60.810 55.000 10.83 0.00 0.00 2.12
3473 5891 5.187967 TCAGTCATAGAGAGGTTTTCCCTTC 59.812 44.000 0.00 0.00 46.51 3.46
3484 5902 5.122519 TCAGTAGCAGTCAGTCATAGAGAG 58.877 45.833 0.00 0.00 0.00 3.20
3485 5903 5.104259 TCAGTAGCAGTCAGTCATAGAGA 57.896 43.478 0.00 0.00 0.00 3.10
3564 5982 2.299297 GAGAGGGAGAAAGGTTTCGACA 59.701 50.000 0.00 0.00 41.92 4.35
3644 6062 2.778679 GATGCGCACCTTCGACAC 59.221 61.111 14.90 0.00 0.00 3.67
3649 6067 3.869272 CTGCCGATGCGCACCTTC 61.869 66.667 14.90 5.66 41.78 3.46
3743 6161 5.014858 ACACCAGCATCTCAAATTCAGATT 58.985 37.500 0.00 0.00 0.00 2.40
3761 6179 5.070001 CCTCCTTCTTCAAATGTTACACCA 58.930 41.667 0.00 0.00 0.00 4.17
3762 6180 5.313712 TCCTCCTTCTTCAAATGTTACACC 58.686 41.667 0.00 0.00 0.00 4.16
3763 6181 6.127897 CCATCCTCCTTCTTCAAATGTTACAC 60.128 42.308 0.00 0.00 0.00 2.90
3769 6187 3.624861 CGACCATCCTCCTTCTTCAAATG 59.375 47.826 0.00 0.00 0.00 2.32
3781 6199 1.139058 AGCAATGTACCGACCATCCTC 59.861 52.381 0.00 0.00 0.00 3.71
3786 6204 1.903860 AGGTAAGCAATGTACCGACCA 59.096 47.619 0.00 0.00 44.91 4.02
3798 6216 1.896220 CACAAGCTCCAAGGTAAGCA 58.104 50.000 3.07 0.00 41.06 3.91
3807 6225 0.178967 TTGATTGGGCACAAGCTCCA 60.179 50.000 19.12 5.18 43.19 3.86


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

AutoCloner maintained by Alex Coulton.