Multiple sequence alignment - TraesCS4A01G105900

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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 TraesCS4A01G105900 chr4A 100.000 4213 0 0 1 4213 120139143 120143355 0.000000e+00 7781
1 TraesCS4A01G105900 chr4D 94.017 2390 84 22 1844 4196 345431072 345428705 0.000000e+00 3567
2 TraesCS4A01G105900 chr4D 91.419 1142 62 13 652 1788 345432198 345431088 0.000000e+00 1533
3 TraesCS4A01G105900 chr4D 94.118 578 34 0 1 578 345434684 345435261 0.000000e+00 880
4 TraesCS4A01G105900 chr4D 92.908 423 28 2 238 660 345433714 345433294 7.740000e-172 614
5 TraesCS4A01G105900 chr4B 94.826 1836 71 14 2267 4087 427070406 427068580 0.000000e+00 2843
6 TraesCS4A01G105900 chr4B 88.454 996 65 26 634 1596 427073108 427072130 0.000000e+00 1157
7 TraesCS4A01G105900 chr4B 94.896 431 20 2 1844 2272 427070921 427070491 0.000000e+00 673
8 TraesCS4A01G105900 chr4B 92.000 100 8 0 1589 1688 427071965 427071866 1.580000e-29 141
9 TraesCS4A01G105900 chr7B 91.339 635 46 7 2887 3513 486675988 486675355 0.000000e+00 859
10 TraesCS4A01G105900 chr2B 91.574 629 44 7 2893 3513 51991109 51990482 0.000000e+00 859
11 TraesCS4A01G105900 chr1A 91.574 629 42 8 2893 3513 453782631 453783256 0.000000e+00 857
12 TraesCS4A01G105900 chr5B 91.388 627 48 5 2893 3513 237114367 237113741 0.000000e+00 854
13 TraesCS4A01G105900 chr5A 91.097 629 47 7 2893 3513 603010077 603009450 0.000000e+00 843
14 TraesCS4A01G105900 chr3B 90.709 635 41 8 2893 3510 188239526 188240159 0.000000e+00 830
15 TraesCS4A01G105900 chr1B 88.571 630 43 8 2893 3513 216531527 216530918 0.000000e+00 737
16 TraesCS4A01G105900 chr7D 87.302 630 45 13 2893 3513 70124354 70124957 0.000000e+00 688


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 TraesCS4A01G105900 chr4A 120139143 120143355 4212 False 7781.000000 7781 100.000000 1 4213 1 chr4A.!!$F1 4212
1 TraesCS4A01G105900 chr4D 345428705 345433714 5009 True 1904.666667 3567 92.781333 238 4196 3 chr4D.!!$R1 3958
2 TraesCS4A01G105900 chr4D 345434684 345435261 577 False 880.000000 880 94.118000 1 578 1 chr4D.!!$F1 577
3 TraesCS4A01G105900 chr4B 427068580 427073108 4528 True 1203.500000 2843 92.544000 634 4087 4 chr4B.!!$R1 3453
4 TraesCS4A01G105900 chr7B 486675355 486675988 633 True 859.000000 859 91.339000 2887 3513 1 chr7B.!!$R1 626
5 TraesCS4A01G105900 chr2B 51990482 51991109 627 True 859.000000 859 91.574000 2893 3513 1 chr2B.!!$R1 620
6 TraesCS4A01G105900 chr1A 453782631 453783256 625 False 857.000000 857 91.574000 2893 3513 1 chr1A.!!$F1 620
7 TraesCS4A01G105900 chr5B 237113741 237114367 626 True 854.000000 854 91.388000 2893 3513 1 chr5B.!!$R1 620
8 TraesCS4A01G105900 chr5A 603009450 603010077 627 True 843.000000 843 91.097000 2893 3513 1 chr5A.!!$R1 620
9 TraesCS4A01G105900 chr3B 188239526 188240159 633 False 830.000000 830 90.709000 2893 3510 1 chr3B.!!$F1 617
10 TraesCS4A01G105900 chr1B 216530918 216531527 609 True 737.000000 737 88.571000 2893 3513 1 chr1B.!!$R1 620
11 TraesCS4A01G105900 chr7D 70124354 70124957 603 False 688.000000 688 87.302000 2893 3513 1 chr7D.!!$F1 620

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
426 427 0.395862 GATCAGGAGGTGGGAGACGA 60.396 60.0 0.00 0.0 0.0 4.20 F
1123 2243 0.036010 AGGTATGAGCAGCACACCAC 60.036 55.0 9.33 0.0 0.0 4.16 F
1541 2686 0.250597 GGCCGGTGTTAAGGTTGTCT 60.251 55.0 1.90 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1521 2666 0.250597 GACAACCTTAACACCGGCCT 60.251 55.000 0.00 0.00 0.00 5.19 R
2844 5112 1.135228 GTTTTCACCGGCAAACAGTGT 60.135 47.619 16.02 0.00 33.75 3.55 R
3499 5801 4.773149 ACCTGAAGTTACTAGGAAGTGAGG 59.227 45.833 15.29 15.29 36.36 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
99 100 4.214383 CGATGTTCAGCGCTGGCG 62.214 66.667 35.36 24.95 46.35 5.69
100 101 3.869272 GATGTTCAGCGCTGGCGG 61.869 66.667 35.36 12.14 46.35 6.13
130 131 1.377202 GGCTCCATCTCCGCACAAA 60.377 57.895 0.00 0.00 0.00 2.83
180 181 2.886859 CGTCCCATCGCAGTATCAC 58.113 57.895 0.00 0.00 0.00 3.06
234 235 1.087501 CGGGGTAGCAAAAGAGAAGC 58.912 55.000 0.00 0.00 0.00 3.86
412 413 4.043750 GCGAAGAAGAGACATGAGATCAG 58.956 47.826 0.00 0.00 0.00 2.90
424 425 1.342474 TGAGATCAGGAGGTGGGAGAC 60.342 57.143 0.00 0.00 0.00 3.36
425 426 0.396417 AGATCAGGAGGTGGGAGACG 60.396 60.000 0.00 0.00 0.00 4.18
426 427 0.395862 GATCAGGAGGTGGGAGACGA 60.396 60.000 0.00 0.00 0.00 4.20
427 428 0.684805 ATCAGGAGGTGGGAGACGAC 60.685 60.000 0.00 0.00 38.50 4.34
440 441 2.159490 GGAGACGACGGAGAGAAAAGAG 60.159 54.545 0.00 0.00 0.00 2.85
446 447 2.164827 GACGGAGAGAAAAGAGGAGACC 59.835 54.545 0.00 0.00 0.00 3.85
468 469 1.275291 TCCGTTTGTAGCTGAGGAAGG 59.725 52.381 0.00 0.00 0.00 3.46
485 486 3.117851 GGAAGGGATAAGGTCAGGGAAAG 60.118 52.174 0.00 0.00 0.00 2.62
495 496 0.889186 TCAGGGAAAGAAAGCGGTGC 60.889 55.000 0.00 0.00 0.00 5.01
496 497 1.966451 AGGGAAAGAAAGCGGTGCG 60.966 57.895 0.00 0.00 0.00 5.34
499 500 1.503818 GGAAAGAAAGCGGTGCGTGA 61.504 55.000 0.00 0.00 0.00 4.35
506 507 2.803155 AAGCGGTGCGTGATCCACAT 62.803 55.000 0.00 0.00 34.94 3.21
508 509 1.087202 GCGGTGCGTGATCCACATAA 61.087 55.000 3.47 0.00 34.94 1.90
546 547 2.534939 CGAAGCGGTTTATTTCAGAGCG 60.535 50.000 0.00 0.00 37.35 5.03
555 556 2.543067 ATTTCAGAGCGGGGTCAGCC 62.543 60.000 0.32 0.00 34.64 4.85
607 608 2.708325 AGTCAGGAGCAGAAGAAAACCT 59.292 45.455 0.00 0.00 0.00 3.50
610 611 1.002544 AGGAGCAGAAGAAAACCTCCG 59.997 52.381 0.00 0.00 45.20 4.63
745 1850 8.720562 GGAAAACAACAAATTAGCATAGCAAAT 58.279 29.630 0.00 0.00 0.00 2.32
746 1851 9.745323 GAAAACAACAAATTAGCATAGCAAATC 57.255 29.630 0.00 0.00 0.00 2.17
747 1852 9.492973 AAAACAACAAATTAGCATAGCAAATCT 57.507 25.926 0.00 0.00 0.00 2.40
748 1853 9.492973 AAACAACAAATTAGCATAGCAAATCTT 57.507 25.926 0.00 0.00 0.00 2.40
749 1854 8.693542 ACAACAAATTAGCATAGCAAATCTTC 57.306 30.769 0.00 0.00 0.00 2.87
909 2023 3.223589 GCCTCCTCCTCTCCTCGC 61.224 72.222 0.00 0.00 0.00 5.03
910 2024 2.520741 CCTCCTCCTCTCCTCGCC 60.521 72.222 0.00 0.00 0.00 5.54
911 2025 2.520741 CTCCTCCTCTCCTCGCCC 60.521 72.222 0.00 0.00 0.00 6.13
912 2026 4.144727 TCCTCCTCTCCTCGCCCC 62.145 72.222 0.00 0.00 0.00 5.80
976 2096 3.118223 GGAAAGAATCCTTCCTGATCGGT 60.118 47.826 3.45 0.00 45.56 4.69
986 2106 2.505405 TCCTGATCGGTAGAATCTCGG 58.495 52.381 0.00 0.00 0.00 4.63
1123 2243 0.036010 AGGTATGAGCAGCACACCAC 60.036 55.000 9.33 0.00 0.00 4.16
1124 2244 0.321564 GGTATGAGCAGCACACCACA 60.322 55.000 0.00 0.00 0.00 4.17
1125 2245 0.798776 GTATGAGCAGCACACCACAC 59.201 55.000 0.00 0.00 0.00 3.82
1127 2247 2.203195 GAGCAGCACACCACACCA 60.203 61.111 0.00 0.00 0.00 4.17
1136 2256 2.680805 GCACACCACACCATACTAGCAT 60.681 50.000 0.00 0.00 0.00 3.79
1143 2263 3.873361 CACACCATACTAGCATCTGTTGG 59.127 47.826 0.00 0.00 0.00 3.77
1166 2286 1.517257 CTCGTTGCTCCCTGTAGCG 60.517 63.158 0.00 0.00 45.85 4.26
1207 2327 6.935741 ATGCCGCTGTTGATTACTTAATTA 57.064 33.333 0.00 0.00 0.00 1.40
1211 2331 5.195379 CGCTGTTGATTACTTAATTACCGC 58.805 41.667 0.00 0.00 0.00 5.68
1217 2344 7.767198 TGTTGATTACTTAATTACCGCTTAGCT 59.233 33.333 1.76 0.00 0.00 3.32
1274 2405 6.069331 TGATAGTGTCACCCCTCTAGAATAC 58.931 44.000 0.00 0.00 0.00 1.89
1301 2432 0.829990 TTAGCCCGATCACTGCATCA 59.170 50.000 0.00 0.00 0.00 3.07
1312 2443 4.430137 TCACTGCATCAGAAATTCAAGC 57.570 40.909 0.29 0.00 35.18 4.01
1330 2461 3.278668 AGCTGCTGATGCTCACTTTAT 57.721 42.857 0.00 0.00 40.48 1.40
1379 2517 4.256920 ACCATACAGATTGCAGAACAGTC 58.743 43.478 0.00 0.00 35.31 3.51
1413 2558 9.317936 CTCATTTCATGTGCTAACATAGTAAGA 57.682 33.333 0.00 0.00 45.50 2.10
1480 2625 0.441533 GTGCTCTCTTCATGTGTGCG 59.558 55.000 0.00 0.00 33.13 5.34
1510 2655 0.308684 ACTGCATGTTCACAACTGCG 59.691 50.000 0.00 0.59 37.93 5.18
1521 2666 5.524281 TGTTCACAACTGCGTCTACAATAAA 59.476 36.000 0.00 0.00 0.00 1.40
1523 2668 4.688879 TCACAACTGCGTCTACAATAAAGG 59.311 41.667 0.00 0.00 0.00 3.11
1534 2679 5.064325 GTCTACAATAAAGGCCGGTGTTAAG 59.936 44.000 1.90 0.00 0.00 1.85
1535 2680 3.086282 ACAATAAAGGCCGGTGTTAAGG 58.914 45.455 1.90 0.00 0.00 2.69
1541 2686 0.250597 GGCCGGTGTTAAGGTTGTCT 60.251 55.000 1.90 0.00 0.00 3.41
1542 2687 1.154197 GCCGGTGTTAAGGTTGTCTC 58.846 55.000 1.90 0.00 0.00 3.36
1556 2702 6.426646 AGGTTGTCTCTCATTAGTGTTCTT 57.573 37.500 0.00 0.00 0.00 2.52
1576 2722 7.876068 TGTTCTTTACAGGTCGTTTATTGATCT 59.124 33.333 0.00 0.00 31.68 2.75
1599 2917 1.846782 CAATAGGTTCTCGCTTCGTCG 59.153 52.381 0.00 0.00 0.00 5.12
1617 2936 3.243771 CGTCGGCATCTATTTACCTCCTT 60.244 47.826 0.00 0.00 0.00 3.36
1626 2945 8.303876 GCATCTATTTACCTCCTTTTTCAAACA 58.696 33.333 0.00 0.00 0.00 2.83
1705 3852 4.019950 TGCCTGATTTCTCTGATCAAGTCA 60.020 41.667 0.00 0.00 33.45 3.41
1721 3868 8.565416 TGATCAAGTCATTTATGCTTCATCATC 58.435 33.333 0.00 4.93 31.89 2.92
1722 3869 7.868906 TCAAGTCATTTATGCTTCATCATCA 57.131 32.000 0.00 0.00 0.00 3.07
1733 3880 3.427233 GCTTCATCATCAGTCTTTGCCAC 60.427 47.826 0.00 0.00 0.00 5.01
1757 3904 1.692519 ACAGCTTTCCTTCACCGTACT 59.307 47.619 0.00 0.00 0.00 2.73
1788 3936 6.109320 TCTTTTACCAAGTACAAACGTGTG 57.891 37.500 3.56 3.56 38.82 3.82
1789 3937 3.948196 TTACCAAGTACAAACGTGTGC 57.052 42.857 5.39 0.00 40.40 4.57
1790 3938 1.018910 ACCAAGTACAAACGTGTGCC 58.981 50.000 5.39 0.00 40.95 5.01
1791 3939 0.309612 CCAAGTACAAACGTGTGCCC 59.690 55.000 5.39 0.00 40.95 5.36
1793 3941 1.002900 CAAGTACAAACGTGTGCCCTG 60.003 52.381 5.39 0.00 40.95 4.45
1794 3942 0.466543 AGTACAAACGTGTGCCCTGA 59.533 50.000 5.39 0.00 40.95 3.86
1798 3946 1.336755 ACAAACGTGTGCCCTGATTTC 59.663 47.619 5.39 0.00 36.31 2.17
1799 3947 1.336440 CAAACGTGTGCCCTGATTTCA 59.664 47.619 0.00 0.00 0.00 2.69
1801 3949 1.238439 ACGTGTGCCCTGATTTCAAG 58.762 50.000 0.00 0.00 0.00 3.02
1803 3951 1.197721 CGTGTGCCCTGATTTCAAGAC 59.802 52.381 0.00 0.00 0.00 3.01
1804 3952 1.541588 GTGTGCCCTGATTTCAAGACC 59.458 52.381 0.00 0.00 0.00 3.85
1805 3953 1.144708 TGTGCCCTGATTTCAAGACCA 59.855 47.619 0.00 0.00 0.00 4.02
1806 3954 2.238521 GTGCCCTGATTTCAAGACCAA 58.761 47.619 0.00 0.00 0.00 3.67
1807 3955 2.627699 GTGCCCTGATTTCAAGACCAAA 59.372 45.455 0.00 0.00 0.00 3.28
1808 3956 2.892852 TGCCCTGATTTCAAGACCAAAG 59.107 45.455 0.00 0.00 0.00 2.77
1809 3957 2.893489 GCCCTGATTTCAAGACCAAAGT 59.107 45.455 0.00 0.00 0.00 2.66
1810 3958 3.305608 GCCCTGATTTCAAGACCAAAGTG 60.306 47.826 0.00 0.00 0.00 3.16
1811 3959 3.256631 CCCTGATTTCAAGACCAAAGTGG 59.743 47.826 0.00 0.00 45.02 4.00
1812 3960 4.144297 CCTGATTTCAAGACCAAAGTGGA 58.856 43.478 0.18 0.00 40.96 4.02
1813 3961 4.217118 CCTGATTTCAAGACCAAAGTGGAG 59.783 45.833 0.18 0.00 40.96 3.86
1814 3962 5.047566 TGATTTCAAGACCAAAGTGGAGA 57.952 39.130 0.18 0.00 40.96 3.71
1815 3963 5.634118 TGATTTCAAGACCAAAGTGGAGAT 58.366 37.500 0.18 0.00 40.96 2.75
1816 3964 5.707298 TGATTTCAAGACCAAAGTGGAGATC 59.293 40.000 0.18 0.00 40.96 2.75
1817 3965 4.705110 TTCAAGACCAAAGTGGAGATCA 57.295 40.909 0.18 0.00 40.96 2.92
1818 3966 4.008074 TCAAGACCAAAGTGGAGATCAC 57.992 45.455 0.18 0.00 40.96 3.06
1828 3976 3.409026 GTGGAGATCACAGTGGTTCTT 57.591 47.619 0.00 0.00 45.39 2.52
1829 3977 3.330267 GTGGAGATCACAGTGGTTCTTC 58.670 50.000 0.00 3.48 45.39 2.87
1830 3978 3.007398 GTGGAGATCACAGTGGTTCTTCT 59.993 47.826 0.00 0.00 45.39 2.85
1831 3979 3.648067 TGGAGATCACAGTGGTTCTTCTT 59.352 43.478 0.00 0.00 0.00 2.52
1832 3980 4.103153 TGGAGATCACAGTGGTTCTTCTTT 59.897 41.667 0.00 0.00 0.00 2.52
1833 3981 4.693095 GGAGATCACAGTGGTTCTTCTTTC 59.307 45.833 0.00 0.00 0.00 2.62
1834 3982 5.296151 AGATCACAGTGGTTCTTCTTTCA 57.704 39.130 0.00 0.00 0.00 2.69
1835 3983 5.874093 AGATCACAGTGGTTCTTCTTTCAT 58.126 37.500 0.00 0.00 0.00 2.57
1836 3984 7.009179 AGATCACAGTGGTTCTTCTTTCATA 57.991 36.000 0.00 0.00 0.00 2.15
1837 3985 7.453393 AGATCACAGTGGTTCTTCTTTCATAA 58.547 34.615 0.00 0.00 0.00 1.90
1838 3986 7.939039 AGATCACAGTGGTTCTTCTTTCATAAA 59.061 33.333 0.00 0.00 0.00 1.40
1839 3987 8.641498 ATCACAGTGGTTCTTCTTTCATAAAT 57.359 30.769 0.00 0.00 0.00 1.40
1840 3988 8.463930 TCACAGTGGTTCTTCTTTCATAAATT 57.536 30.769 0.00 0.00 0.00 1.82
1841 3989 8.912988 TCACAGTGGTTCTTCTTTCATAAATTT 58.087 29.630 0.00 0.00 0.00 1.82
1842 3990 9.533253 CACAGTGGTTCTTCTTTCATAAATTTT 57.467 29.630 0.00 0.00 0.00 1.82
1884 4032 9.875691 TTTCTATCCATAATCCATATGAACGAG 57.124 33.333 3.65 0.00 43.52 4.18
1887 4035 9.689976 CTATCCATAATCCATATGAACGAGATC 57.310 37.037 3.65 0.00 43.52 2.75
2155 4305 2.109834 TGGACCACCACTTCCATTCAAT 59.890 45.455 0.00 0.00 41.77 2.57
2457 4701 2.937591 TCGACGAAACATCCAGTACAC 58.062 47.619 0.00 0.00 0.00 2.90
2518 4786 2.092699 AGCTCCCTTATTGAACTCCAGC 60.093 50.000 0.00 0.00 0.00 4.85
2519 4787 2.356125 GCTCCCTTATTGAACTCCAGCA 60.356 50.000 0.00 0.00 0.00 4.41
2536 4804 3.323115 CCAGCACTATTATCCAGCAGAGA 59.677 47.826 0.00 0.00 0.00 3.10
2537 4805 4.558178 CAGCACTATTATCCAGCAGAGAG 58.442 47.826 0.00 0.00 0.00 3.20
2627 4895 5.692928 AGTATGACCCTAGTATTCAGTCGT 58.307 41.667 0.00 0.00 0.00 4.34
2753 5021 6.983906 AACAACTTGATTGGAGGATTTTCT 57.016 33.333 0.00 0.00 43.20 2.52
2792 5060 7.910441 ATTTGATATGCGATGATGTATGACA 57.090 32.000 0.00 0.00 0.00 3.58
2811 5079 7.865706 ATGACATAACTGGAAATTGTAGGTC 57.134 36.000 0.00 0.00 0.00 3.85
2815 5083 1.349688 ACTGGAAATTGTAGGTCGGCA 59.650 47.619 0.00 0.00 0.00 5.69
2876 5144 3.316283 CGGTGAAAACATCCACATTTGG 58.684 45.455 0.00 0.00 45.56 3.28
2928 5196 5.916318 TGTTTGCAGGTTGAATCATTTCTT 58.084 33.333 0.00 0.00 32.78 2.52
2949 5218 6.650120 TCTTTGTCTTACTTTTCAGGTGACT 58.350 36.000 0.00 0.00 46.44 3.41
3158 5439 0.997363 GGTTTACCTTGGTAGGGGCT 59.003 55.000 0.00 0.00 46.58 5.19
3168 5449 4.536090 CCTTGGTAGGGGCTATTATCATCA 59.464 45.833 0.00 0.00 37.94 3.07
3382 5675 7.069826 TCCTTCATTTTGGTGATTTTCTTCACT 59.930 33.333 4.75 0.00 44.39 3.41
3406 5699 7.671398 ACTTGTACATCAATTGGATCCTCTTTT 59.329 33.333 14.23 0.00 35.35 2.27
3499 5801 6.677781 TCCCGATGTGAATTTTTCATAGTC 57.322 37.500 0.00 0.00 42.47 2.59
3552 5854 4.271049 GTGTGACCAACGGATCATCTAATG 59.729 45.833 0.00 0.00 0.00 1.90
3619 5935 0.953727 GAGCAAGTGGACATGTGCAA 59.046 50.000 22.48 3.45 39.50 4.08
3637 5953 6.351711 TGTGCAAAGCATCTAGTAATCTGAT 58.648 36.000 0.00 0.00 41.91 2.90
3774 6090 9.528489 AAGCAATTCAACTTACCTTATTTCCTA 57.472 29.630 0.00 0.00 0.00 2.94
3775 6091 9.700831 AGCAATTCAACTTACCTTATTTCCTAT 57.299 29.630 0.00 0.00 0.00 2.57
3831 6147 2.507484 TGGAGGCATCAAAACAGAGTG 58.493 47.619 0.00 0.00 0.00 3.51
3869 6185 7.983307 TGTAGTTAGACTCTTAGACGGAATTC 58.017 38.462 0.00 0.00 0.00 2.17
3871 6187 5.066246 AGTTAGACTCTTAGACGGAATTCGG 59.934 44.000 11.17 11.17 44.45 4.30
3911 6227 2.428530 TGAGGACCATCTCATCTTGTCG 59.571 50.000 0.00 0.00 38.70 4.35
3921 6237 4.817517 TCTCATCTTGTCGTTTAAGACCC 58.182 43.478 0.00 0.00 40.26 4.46
3926 6242 0.039256 TGTCGTTTAAGACCCGGTCG 60.039 55.000 12.04 0.00 40.26 4.79
4021 6337 8.103948 ACTTCTCATCCTTTAAACATTGAGTG 57.896 34.615 12.66 10.47 33.88 3.51
4079 6396 6.972901 CGATGCTAGTCTACAATTAACACTGA 59.027 38.462 0.00 0.00 0.00 3.41
4080 6397 7.166638 CGATGCTAGTCTACAATTAACACTGAG 59.833 40.741 0.00 0.00 0.00 3.35
4094 6411 5.904362 AACACTGAGAAATTAGCATTCCC 57.096 39.130 0.00 0.00 0.00 3.97
4102 6419 4.952335 AGAAATTAGCATTCCCCAAGACAG 59.048 41.667 0.00 0.00 0.00 3.51
4104 6421 3.350219 TTAGCATTCCCCAAGACAGTC 57.650 47.619 0.00 0.00 0.00 3.51
4108 6425 2.827921 GCATTCCCCAAGACAGTCAATT 59.172 45.455 2.66 0.00 0.00 2.32
4113 6430 7.614494 CATTCCCCAAGACAGTCAATTAAATT 58.386 34.615 2.66 0.00 0.00 1.82
4121 6438 7.150783 AGACAGTCAATTAAATTTCCAGAGC 57.849 36.000 2.66 0.00 0.00 4.09
4129 6446 8.950210 TCAATTAAATTTCCAGAGCTTCTACAG 58.050 33.333 0.00 0.00 0.00 2.74
4130 6447 8.734386 CAATTAAATTTCCAGAGCTTCTACAGT 58.266 33.333 0.00 0.00 0.00 3.55
4197 6514 7.812690 ATTCAGATATGCTGCTTACATTTCA 57.187 32.000 0.00 0.00 44.52 2.69
4198 6515 7.628769 TTCAGATATGCTGCTTACATTTCAA 57.371 32.000 0.00 0.00 44.52 2.69
4199 6516 7.628769 TCAGATATGCTGCTTACATTTCAAA 57.371 32.000 0.00 0.00 44.52 2.69
4200 6517 8.054152 TCAGATATGCTGCTTACATTTCAAAA 57.946 30.769 0.00 0.00 44.52 2.44
4201 6518 8.522003 TCAGATATGCTGCTTACATTTCAAAAA 58.478 29.630 0.00 0.00 44.52 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 83 4.214383 CGCCAGCGCTGAACATCG 62.214 66.667 38.06 25.22 0.00 3.84
172 173 2.987593 GCGTGACGCGTGATACTG 59.012 61.111 20.70 10.35 44.55 2.74
330 331 1.924731 ACCTGATTCTCGTCACTCCA 58.075 50.000 0.00 0.00 0.00 3.86
412 413 3.450115 CCGTCGTCTCCCACCTCC 61.450 72.222 0.00 0.00 0.00 4.30
424 425 2.085320 TCTCCTCTTTTCTCTCCGTCG 58.915 52.381 0.00 0.00 0.00 5.12
425 426 2.164827 GGTCTCCTCTTTTCTCTCCGTC 59.835 54.545 0.00 0.00 0.00 4.79
426 427 2.172679 GGTCTCCTCTTTTCTCTCCGT 58.827 52.381 0.00 0.00 0.00 4.69
427 428 1.133407 CGGTCTCCTCTTTTCTCTCCG 59.867 57.143 0.00 0.00 0.00 4.63
440 441 0.735287 GCTACAAACGGACGGTCTCC 60.735 60.000 8.23 0.00 35.33 3.71
446 447 0.242825 TCCTCAGCTACAAACGGACG 59.757 55.000 0.00 0.00 0.00 4.79
450 451 1.275291 TCCCTTCCTCAGCTACAAACG 59.725 52.381 0.00 0.00 0.00 3.60
468 469 3.948473 GCTTTCTTTCCCTGACCTTATCC 59.052 47.826 0.00 0.00 0.00 2.59
485 486 2.032634 TGGATCACGCACCGCTTTC 61.033 57.895 0.00 0.00 0.00 2.62
517 518 0.601576 TAAACCGCTTCGCTTGCTCA 60.602 50.000 0.00 0.00 0.00 4.26
546 547 1.146263 CTATCAACCGGCTGACCCC 59.854 63.158 10.31 0.00 0.00 4.95
555 556 6.803154 AAGGAAAAGTCTTTCTATCAACCG 57.197 37.500 0.00 0.00 40.76 4.44
617 618 2.158813 TGCTCCTTTTTCTCTTGTCCGT 60.159 45.455 0.00 0.00 0.00 4.69
618 619 2.481952 CTGCTCCTTTTTCTCTTGTCCG 59.518 50.000 0.00 0.00 0.00 4.79
619 620 3.744660 TCTGCTCCTTTTTCTCTTGTCC 58.255 45.455 0.00 0.00 0.00 4.02
620 621 5.059833 TCTTCTGCTCCTTTTTCTCTTGTC 58.940 41.667 0.00 0.00 0.00 3.18
624 625 5.411053 CGATTTCTTCTGCTCCTTTTTCTCT 59.589 40.000 0.00 0.00 0.00 3.10
745 1850 3.253188 CGGGTGATGCAAAGAAAAGAAGA 59.747 43.478 0.00 0.00 0.00 2.87
746 1851 3.004734 ACGGGTGATGCAAAGAAAAGAAG 59.995 43.478 0.00 0.00 0.00 2.85
747 1852 2.955660 ACGGGTGATGCAAAGAAAAGAA 59.044 40.909 0.00 0.00 0.00 2.52
748 1853 2.293122 CACGGGTGATGCAAAGAAAAGA 59.707 45.455 0.00 0.00 0.00 2.52
749 1854 2.664916 CACGGGTGATGCAAAGAAAAG 58.335 47.619 0.00 0.00 0.00 2.27
788 1902 2.050269 CACCAGAGAACCCTCACGT 58.950 57.895 0.00 0.00 41.87 4.49
976 2096 0.178998 CCTCCCCGTCCGAGATTCTA 60.179 60.000 0.00 0.00 0.00 2.10
1123 2243 3.118261 ACCCAACAGATGCTAGTATGGTG 60.118 47.826 0.00 0.00 0.00 4.17
1124 2244 3.115390 ACCCAACAGATGCTAGTATGGT 58.885 45.455 0.00 0.00 0.00 3.55
1125 2245 3.389329 AGACCCAACAGATGCTAGTATGG 59.611 47.826 0.00 0.00 0.00 2.74
1127 2247 4.551671 AGAGACCCAACAGATGCTAGTAT 58.448 43.478 0.00 0.00 0.00 2.12
1136 2256 0.033504 GCAACGAGAGACCCAACAGA 59.966 55.000 0.00 0.00 0.00 3.41
1143 2263 1.216710 CAGGGAGCAACGAGAGACC 59.783 63.158 0.00 0.00 0.00 3.85
1166 2286 4.485163 GGCATTTCATCAAACACCTACAC 58.515 43.478 0.00 0.00 0.00 2.90
1207 2327 0.970937 TAGTGGCAGAGCTAAGCGGT 60.971 55.000 4.02 0.00 0.00 5.68
1211 2331 3.020274 TGAGACTAGTGGCAGAGCTAAG 58.980 50.000 0.00 0.00 0.00 2.18
1217 2344 0.251209 ACCGTGAGACTAGTGGCAGA 60.251 55.000 0.00 0.00 0.00 4.26
1274 2405 4.748892 CAGTGATCGGGCTAATACTATGG 58.251 47.826 0.00 0.00 0.00 2.74
1301 2432 3.090037 AGCATCAGCAGCTTGAATTTCT 58.910 40.909 0.00 0.00 45.49 2.52
1464 2609 0.997932 GAGCGCACACATGAAGAGAG 59.002 55.000 11.47 0.00 0.00 3.20
1468 2613 2.097160 GCGAGCGCACACATGAAG 59.903 61.111 11.47 0.00 41.49 3.02
1510 2655 2.981898 ACACCGGCCTTTATTGTAGAC 58.018 47.619 0.00 0.00 0.00 2.59
1521 2666 0.250597 GACAACCTTAACACCGGCCT 60.251 55.000 0.00 0.00 0.00 5.19
1523 2668 1.154197 GAGACAACCTTAACACCGGC 58.846 55.000 0.00 0.00 0.00 6.13
1534 2679 7.656137 TGTAAAGAACACTAATGAGAGACAACC 59.344 37.037 0.00 0.00 31.43 3.77
1535 2680 8.589335 TGTAAAGAACACTAATGAGAGACAAC 57.411 34.615 0.00 0.00 31.43 3.32
1541 2686 6.015688 ACGACCTGTAAAGAACACTAATGAGA 60.016 38.462 0.00 0.00 33.45 3.27
1542 2687 6.157211 ACGACCTGTAAAGAACACTAATGAG 58.843 40.000 0.00 0.00 33.45 2.90
1556 2702 6.869695 TGCTAGATCAATAAACGACCTGTAA 58.130 36.000 0.00 0.00 0.00 2.41
1576 2722 2.426024 ACGAAGCGAGAACCTATTGCTA 59.574 45.455 0.00 0.00 34.19 3.49
1599 2917 7.404671 TTGAAAAAGGAGGTAAATAGATGCC 57.595 36.000 0.00 0.00 0.00 4.40
1617 2936 4.162812 GTTCGCTGTCACTTGTTTGAAAA 58.837 39.130 0.00 0.00 0.00 2.29
1626 2945 3.728845 ACAGTATTGTTCGCTGTCACTT 58.271 40.909 0.00 0.00 38.96 3.16
1705 3852 7.201145 GCAAAGACTGATGATGAAGCATAAAT 58.799 34.615 0.00 0.00 0.00 1.40
1733 3880 1.576421 GTGAAGGAAAGCTGTGCCG 59.424 57.895 0.00 0.00 0.00 5.69
1738 3885 2.457366 AGTACGGTGAAGGAAAGCTG 57.543 50.000 0.00 0.00 0.00 4.24
1739 3886 2.496470 CCTAGTACGGTGAAGGAAAGCT 59.504 50.000 0.00 0.00 0.00 3.74
1761 3908 9.709495 ACACGTTTGTACTTGGTAAAAGATATA 57.291 29.630 0.00 0.00 32.60 0.86
1788 3936 2.893489 ACTTTGGTCTTGAAATCAGGGC 59.107 45.455 0.00 0.00 0.00 5.19
1789 3937 3.256631 CCACTTTGGTCTTGAAATCAGGG 59.743 47.826 0.00 0.00 31.35 4.45
1790 3938 4.144297 TCCACTTTGGTCTTGAAATCAGG 58.856 43.478 0.00 0.00 39.03 3.86
1791 3939 5.065914 TCTCCACTTTGGTCTTGAAATCAG 58.934 41.667 0.00 0.00 39.03 2.90
1793 3941 5.707298 TGATCTCCACTTTGGTCTTGAAATC 59.293 40.000 0.00 0.00 39.03 2.17
1794 3942 5.474876 GTGATCTCCACTTTGGTCTTGAAAT 59.525 40.000 0.00 0.00 42.44 2.17
1798 3946 3.743521 TGTGATCTCCACTTTGGTCTTG 58.256 45.455 0.00 0.00 45.86 3.02
1799 3947 3.392616 ACTGTGATCTCCACTTTGGTCTT 59.607 43.478 0.00 0.00 45.86 3.01
1801 3949 3.070018 CACTGTGATCTCCACTTTGGTC 58.930 50.000 0.32 0.00 45.86 4.02
1803 3951 2.224621 ACCACTGTGATCTCCACTTTGG 60.225 50.000 9.86 0.00 45.78 3.28
1804 3952 3.131709 ACCACTGTGATCTCCACTTTG 57.868 47.619 9.86 0.00 45.86 2.77
1805 3953 3.392616 AGAACCACTGTGATCTCCACTTT 59.607 43.478 9.86 0.00 45.86 2.66
1806 3954 2.975489 AGAACCACTGTGATCTCCACTT 59.025 45.455 9.86 0.00 45.86 3.16
1807 3955 2.614259 AGAACCACTGTGATCTCCACT 58.386 47.619 9.86 0.00 45.86 4.00
1808 3956 3.007398 AGAAGAACCACTGTGATCTCCAC 59.993 47.826 9.86 7.88 45.88 4.02
1809 3957 3.242867 AGAAGAACCACTGTGATCTCCA 58.757 45.455 9.86 0.00 0.00 3.86
1810 3958 3.971245 AGAAGAACCACTGTGATCTCC 57.029 47.619 9.86 0.57 0.00 3.71
1811 3959 5.300752 TGAAAGAAGAACCACTGTGATCTC 58.699 41.667 9.86 2.71 0.00 2.75
1812 3960 5.296151 TGAAAGAAGAACCACTGTGATCT 57.704 39.130 9.86 9.57 0.00 2.75
1813 3961 7.672983 TTATGAAAGAAGAACCACTGTGATC 57.327 36.000 9.86 7.36 0.00 2.92
1814 3962 8.641498 ATTTATGAAAGAAGAACCACTGTGAT 57.359 30.769 9.86 0.00 0.00 3.06
1815 3963 8.463930 AATTTATGAAAGAAGAACCACTGTGA 57.536 30.769 9.86 0.00 0.00 3.58
1816 3964 9.533253 AAAATTTATGAAAGAAGAACCACTGTG 57.467 29.630 0.00 0.00 0.00 3.66
1864 4012 7.724490 AGATCTCGTTCATATGGATTATGGA 57.276 36.000 2.13 0.00 38.61 3.41
1929 4078 7.148086 GCAAATATCCAGTATTGACCAGTGAAA 60.148 37.037 0.00 0.00 33.32 2.69
2029 4179 5.410355 ACTATGCGTAACAGGACCTTTTA 57.590 39.130 0.00 0.00 0.00 1.52
2155 4305 9.802039 AGGTTACTGTTCCACTTCAAAATAATA 57.198 29.630 4.93 0.00 0.00 0.98
2236 4389 7.708998 TGAAACCTTTTACATACTGTTTCACC 58.291 34.615 10.54 0.00 43.68 4.02
2433 4677 5.747197 GTGTACTGGATGTTTCGTCGATATT 59.253 40.000 0.00 0.00 0.00 1.28
2434 4678 5.279384 GTGTACTGGATGTTTCGTCGATAT 58.721 41.667 0.00 0.00 0.00 1.63
2435 4679 4.439153 GGTGTACTGGATGTTTCGTCGATA 60.439 45.833 0.00 0.00 0.00 2.92
2518 4786 6.587206 TCATCTCTCTGCTGGATAATAGTG 57.413 41.667 0.00 0.00 0.00 2.74
2519 4787 7.508636 TCTTTCATCTCTCTGCTGGATAATAGT 59.491 37.037 0.00 0.00 0.00 2.12
2536 4804 9.129532 GGAATCACATATCCTTTTCTTTCATCT 57.870 33.333 0.00 0.00 32.75 2.90
2537 4805 9.129532 AGGAATCACATATCCTTTTCTTTCATC 57.870 33.333 0.00 0.00 43.59 2.92
2611 4879 4.882427 TCTGAGAACGACTGAATACTAGGG 59.118 45.833 0.00 0.00 0.00 3.53
2627 4895 9.031360 GTTACGAAATATAACATGCTCTGAGAA 57.969 33.333 9.28 0.00 33.52 2.87
2733 5001 6.294955 GCTCAAGAAAATCCTCCAATCAAGTT 60.295 38.462 0.00 0.00 0.00 2.66
2753 5021 8.445493 CGCATATCAAATTCATATGTAGCTCAA 58.555 33.333 14.48 0.00 36.81 3.02
2792 5060 4.196971 GCCGACCTACAATTTCCAGTTAT 58.803 43.478 0.00 0.00 0.00 1.89
2844 5112 1.135228 GTTTTCACCGGCAAACAGTGT 60.135 47.619 16.02 0.00 33.75 3.55
2876 5144 5.802064 TCATCGTATACAAAATTCGGCAAC 58.198 37.500 3.32 0.00 0.00 4.17
2928 5196 5.984725 TGAGTCACCTGAAAAGTAAGACAA 58.015 37.500 0.00 0.00 0.00 3.18
3158 5439 6.822667 AGCAATGCCGAAATGATGATAATA 57.177 33.333 0.00 0.00 0.00 0.98
3168 5449 7.928307 ATGTATAGATTAGCAATGCCGAAAT 57.072 32.000 0.00 0.00 0.00 2.17
3382 5675 9.699410 ATAAAAGAGGATCCAATTGATGTACAA 57.301 29.630 15.82 0.00 38.37 2.41
3479 5777 7.065085 AGTGAGGACTATGAAAAATTCACATCG 59.935 37.037 4.40 0.00 43.48 3.84
3499 5801 4.773149 ACCTGAAGTTACTAGGAAGTGAGG 59.227 45.833 15.29 15.29 36.36 3.86
3564 5873 5.109903 CACTACAAGCTACCCATCACTAAC 58.890 45.833 0.00 0.00 0.00 2.34
3619 5935 6.465035 GGGTTCCATCAGATTACTAGATGCTT 60.465 42.308 0.00 0.00 38.21 3.91
3637 5953 0.250295 CGTGCTTCTCTTGGGTTCCA 60.250 55.000 0.00 0.00 0.00 3.53
3891 6207 2.428890 ACGACAAGATGAGATGGTCCTC 59.571 50.000 0.00 0.00 0.00 3.71
3911 6227 1.270550 TCTGACGACCGGGTCTTAAAC 59.729 52.381 23.86 11.11 37.81 2.01
3921 6237 1.947456 TGGATACAGATCTGACGACCG 59.053 52.381 29.27 0.65 46.17 4.79
3955 6271 2.238521 TGGAAATGCCTTTGTCTGACC 58.761 47.619 5.17 0.00 37.63 4.02
4021 6337 0.392327 GAGAGCAAGACCTTGGCCTC 60.392 60.000 3.32 9.66 40.74 4.70
4079 6396 4.934356 TGTCTTGGGGAATGCTAATTTCT 58.066 39.130 0.00 0.00 0.00 2.52
4080 6397 4.706962 ACTGTCTTGGGGAATGCTAATTTC 59.293 41.667 0.00 0.00 0.00 2.17
4087 6404 1.909700 TTGACTGTCTTGGGGAATGC 58.090 50.000 9.51 0.00 0.00 3.56
4094 6411 7.885297 TCTGGAAATTTAATTGACTGTCTTGG 58.115 34.615 9.51 0.00 0.00 3.61
4102 6419 8.730680 TGTAGAAGCTCTGGAAATTTAATTGAC 58.269 33.333 0.00 0.00 0.00 3.18
4104 6421 8.734386 ACTGTAGAAGCTCTGGAAATTTAATTG 58.266 33.333 0.00 0.00 0.00 2.32
4108 6425 7.174946 CCAAACTGTAGAAGCTCTGGAAATTTA 59.825 37.037 0.00 0.00 0.00 1.40
4113 6430 3.391296 ACCAAACTGTAGAAGCTCTGGAA 59.609 43.478 0.00 0.00 0.00 3.53
4121 6438 7.548196 TCTACACAAAACCAAACTGTAGAAG 57.452 36.000 3.84 0.00 40.07 2.85


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

AutoCloner maintained by Alex Coulton.