Multiple sequence alignment - TraesCS1A01G410700

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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 TraesCS1A01G410700 chr1A 100.000 2744 0 0 1 2744 571786041 571788784 0.000000e+00 5068
1 TraesCS1A01G410700 chr1A 82.594 879 96 30 996 1833 571737472 571738334 0.000000e+00 723
2 TraesCS1A01G410700 chr1A 81.586 744 85 30 991 1714 571724737 571725448 3.970000e-158 568
3 TraesCS1A01G410700 chr1D 87.794 2851 185 68 2 2744 475922092 475924887 0.000000e+00 3186
4 TraesCS1A01G410700 chr1D 82.051 858 101 26 996 1830 475913212 475914039 0.000000e+00 682
5 TraesCS1A01G410700 chr1D 86.680 518 47 21 981 1484 475863786 475864295 3.090000e-154 555
6 TraesCS1A01G410700 chr1D 85.133 565 59 16 990 1544 475918703 475919252 3.090000e-154 555
7 TraesCS1A01G410700 chr1B 91.049 972 52 15 992 1951 662020295 662021243 0.000000e+00 1280
8 TraesCS1A01G410700 chr1B 91.134 688 40 9 1996 2677 662021254 662021926 0.000000e+00 913
9 TraesCS1A01G410700 chr1B 85.089 731 75 21 996 1699 662005167 662005890 0.000000e+00 715
10 TraesCS1A01G410700 chr1B 87.478 567 45 12 990 1544 662016387 662016939 4.990000e-177 630
11 TraesCS1A01G410700 chr1B 81.342 477 49 19 50 520 662019416 662019858 4.350000e-93 351
12 TraesCS1A01G410700 chr1B 88.652 282 12 12 538 800 662019849 662020129 2.640000e-85 326
13 TraesCS1A01G410700 chr2B 84.256 921 106 17 971 1888 99520600 99521484 0.000000e+00 861
14 TraesCS1A01G410700 chr2B 87.286 409 40 9 2049 2447 99555393 99555799 8.960000e-125 457
15 TraesCS1A01G410700 chr4B 82.278 711 90 11 1021 1730 357955667 357954992 1.420000e-162 582
16 TraesCS1A01G410700 chr4B 88.742 302 22 4 2446 2744 357911383 357911091 2.600000e-95 359
17 TraesCS1A01G410700 chr3B 87.679 349 24 9 484 813 12624532 12624184 3.310000e-104 388
18 TraesCS1A01G410700 chr3B 83.704 270 38 5 905 1169 12598329 12598061 1.630000e-62 250
19 TraesCS1A01G410700 chr4D 88.235 204 17 7 2172 2372 240937309 240937508 1.270000e-58 237
20 TraesCS1A01G410700 chr4A 92.308 91 4 3 2655 2742 261877039 261876949 2.870000e-25 126


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 TraesCS1A01G410700 chr1A 571786041 571788784 2743 False 5068.0 5068 100.0000 1 2744 1 chr1A.!!$F3 2743
1 TraesCS1A01G410700 chr1A 571737472 571738334 862 False 723.0 723 82.5940 996 1833 1 chr1A.!!$F2 837
2 TraesCS1A01G410700 chr1A 571724737 571725448 711 False 568.0 568 81.5860 991 1714 1 chr1A.!!$F1 723
3 TraesCS1A01G410700 chr1D 475918703 475924887 6184 False 1870.5 3186 86.4635 2 2744 2 chr1D.!!$F3 2742
4 TraesCS1A01G410700 chr1D 475913212 475914039 827 False 682.0 682 82.0510 996 1830 1 chr1D.!!$F2 834
5 TraesCS1A01G410700 chr1D 475863786 475864295 509 False 555.0 555 86.6800 981 1484 1 chr1D.!!$F1 503
6 TraesCS1A01G410700 chr1B 662005167 662005890 723 False 715.0 715 85.0890 996 1699 1 chr1B.!!$F1 703
7 TraesCS1A01G410700 chr1B 662016387 662021926 5539 False 700.0 1280 87.9310 50 2677 5 chr1B.!!$F2 2627
8 TraesCS1A01G410700 chr2B 99520600 99521484 884 False 861.0 861 84.2560 971 1888 1 chr2B.!!$F1 917
9 TraesCS1A01G410700 chr4B 357954992 357955667 675 True 582.0 582 82.2780 1021 1730 1 chr4B.!!$R2 709

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
515 4670 0.028902 AAAAGCGCGGTGAACTTCAC 59.971 50.0 13.41 12.81 46.23 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2286 6643 0.108138 CGGAATCGCTTCTCACCCTT 60.108 55.0 0.0 0.0 0.0 3.95 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
17 18 3.372730 TGATGCAGCAAACGGGGC 61.373 61.111 0.00 0.00 0.00 5.80
18 19 3.372730 GATGCAGCAAACGGGGCA 61.373 61.111 0.00 0.00 41.00 5.36
19 20 3.631487 GATGCAGCAAACGGGGCAC 62.631 63.158 0.00 0.00 39.34 5.01
21 22 3.910490 GCAGCAAACGGGGCACAA 61.910 61.111 0.00 0.00 0.00 3.33
23 24 1.142748 CAGCAAACGGGGCACAAAA 59.857 52.632 0.00 0.00 0.00 2.44
24 25 1.142965 AGCAAACGGGGCACAAAAC 59.857 52.632 0.00 0.00 0.00 2.43
25 26 1.885388 GCAAACGGGGCACAAAACC 60.885 57.895 0.00 0.00 0.00 3.27
26 27 1.517832 CAAACGGGGCACAAAACCA 59.482 52.632 0.00 0.00 0.00 3.67
27 28 0.808060 CAAACGGGGCACAAAACCAC 60.808 55.000 0.00 0.00 0.00 4.16
30 31 2.835895 GGGGCACAAAACCACGGT 60.836 61.111 0.00 0.00 0.00 4.83
31 32 2.415426 GGGCACAAAACCACGGTG 59.585 61.111 0.00 0.00 35.68 4.94
32 33 2.122167 GGGCACAAAACCACGGTGA 61.122 57.895 10.28 0.00 34.52 4.02
33 34 1.668101 GGGCACAAAACCACGGTGAA 61.668 55.000 10.28 0.00 34.52 3.18
34 35 0.173708 GGCACAAAACCACGGTGAAA 59.826 50.000 10.28 0.00 34.52 2.69
35 36 1.555477 GCACAAAACCACGGTGAAAG 58.445 50.000 10.28 0.00 34.52 2.62
36 37 1.133407 GCACAAAACCACGGTGAAAGA 59.867 47.619 10.28 0.00 34.52 2.52
37 38 2.223711 GCACAAAACCACGGTGAAAGAT 60.224 45.455 10.28 0.00 34.52 2.40
41 42 2.536761 AACCACGGTGAAAGATCGAA 57.463 45.000 10.28 0.00 0.00 3.71
42 43 1.792006 ACCACGGTGAAAGATCGAAC 58.208 50.000 10.28 0.00 0.00 3.95
43 44 1.069513 ACCACGGTGAAAGATCGAACA 59.930 47.619 10.28 0.00 0.00 3.18
44 45 1.459592 CCACGGTGAAAGATCGAACAC 59.540 52.381 10.28 9.51 0.00 3.32
46 47 0.713883 CGGTGAAAGATCGAACACGG 59.286 55.000 0.00 10.64 34.59 4.94
49 50 1.725164 GTGAAAGATCGAACACGGTCC 59.275 52.381 0.00 0.00 37.82 4.46
50 51 1.337447 TGAAAGATCGAACACGGTCCC 60.337 52.381 0.00 0.00 37.82 4.46
51 52 0.389426 AAAGATCGAACACGGTCCCG 60.389 55.000 3.76 3.76 46.03 5.14
161 4313 1.133407 CCTCTCAGCTTGTACGTCCTC 59.867 57.143 0.00 0.00 0.00 3.71
168 4320 1.983972 CTTGTACGTCCTCTCACTGC 58.016 55.000 0.00 0.00 0.00 4.40
207 4359 1.317613 TGTCCACATGGTGCAAACTC 58.682 50.000 0.00 0.00 36.34 3.01
208 4360 0.598065 GTCCACATGGTGCAAACTCC 59.402 55.000 0.00 0.00 36.34 3.85
211 4363 0.540365 CACATGGTGCAAACTCCCCT 60.540 55.000 0.00 0.00 0.00 4.79
221 4373 0.540597 AAACTCCCCTTTGCTCTGCC 60.541 55.000 0.00 0.00 0.00 4.85
227 4379 2.253452 CTTTGCTCTGCCACACGC 59.747 61.111 0.00 0.00 38.31 5.34
234 4386 4.794439 CTGCCACACGCCGATCGA 62.794 66.667 18.66 0.00 41.67 3.59
235 4387 4.141965 TGCCACACGCCGATCGAT 62.142 61.111 18.66 0.00 41.67 3.59
313 4468 1.672356 CTCACTTCCCGGCAACCAG 60.672 63.158 0.00 0.00 0.00 4.00
346 4501 2.330924 CTTCCGGGCATCTTCCTCCC 62.331 65.000 0.00 0.00 36.68 4.30
445 4600 2.823154 CCAGGCGGAAATTTTACTTCCA 59.177 45.455 0.00 0.00 42.22 3.53
446 4601 3.447229 CCAGGCGGAAATTTTACTTCCAT 59.553 43.478 0.00 0.00 42.22 3.41
454 4609 7.027161 CGGAAATTTTACTTCCATGGTTACTG 58.973 38.462 12.58 1.42 42.22 2.74
455 4610 7.308951 CGGAAATTTTACTTCCATGGTTACTGT 60.309 37.037 12.58 7.27 42.22 3.55
456 4611 8.027189 GGAAATTTTACTTCCATGGTTACTGTC 58.973 37.037 12.58 0.00 41.79 3.51
457 4612 8.472007 AAATTTTACTTCCATGGTTACTGTCA 57.528 30.769 12.58 0.00 0.00 3.58
515 4670 0.028902 AAAAGCGCGGTGAACTTCAC 59.971 50.000 13.41 12.81 46.23 3.18
526 4686 2.031682 GTGAACTTCACATGCCACTCAC 60.032 50.000 15.77 0.00 46.22 3.51
533 4693 0.679002 ACATGCCACTCACTGCCATC 60.679 55.000 0.00 0.00 0.00 3.51
586 4746 2.835431 AGGCGATCCGGTGAGAGG 60.835 66.667 0.00 0.00 37.47 3.69
634 4794 1.002990 TCACTCGTCAGCTACCGGA 60.003 57.895 9.46 0.00 0.00 5.14
635 4795 0.393944 TCACTCGTCAGCTACCGGAT 60.394 55.000 9.46 0.00 0.00 4.18
637 4797 1.674441 CACTCGTCAGCTACCGGATTA 59.326 52.381 9.46 0.00 0.00 1.75
661 4821 3.321968 ACAGAGAGCGTATATTCATGGCA 59.678 43.478 0.00 0.00 0.00 4.92
734 4906 0.661187 GTCCGAGCGTGACGTGTTTA 60.661 55.000 6.91 0.00 0.00 2.01
787 4964 1.860078 CGGTCTTCAGTCAAACCGC 59.140 57.895 0.00 0.00 46.89 5.68
792 4969 2.215478 CTTCAGTCAAACCGCGCTCG 62.215 60.000 5.56 0.00 0.00 5.03
794 4971 2.094659 CAGTCAAACCGCGCTCGAT 61.095 57.895 5.56 0.00 38.10 3.59
795 4972 1.374252 AGTCAAACCGCGCTCGATT 60.374 52.632 5.56 0.00 38.10 3.34
823 5012 1.125093 TCCCCGTCCATCAACAGTGT 61.125 55.000 0.00 0.00 0.00 3.55
825 5014 0.874390 CCCGTCCATCAACAGTGTTG 59.126 55.000 26.87 26.87 0.00 3.33
834 5023 5.598005 TCCATCAACAGTGTTGGATTCTTTT 59.402 36.000 30.57 7.66 45.01 2.27
835 5024 6.775142 TCCATCAACAGTGTTGGATTCTTTTA 59.225 34.615 30.57 12.43 45.01 1.52
836 5025 6.863126 CCATCAACAGTGTTGGATTCTTTTAC 59.137 38.462 30.57 0.00 44.44 2.01
872 5067 1.063174 GCTTGATCAGCGCTTACTTGG 59.937 52.381 7.50 0.00 39.29 3.61
891 5086 0.536687 GCCCGGGCCTATAAAAGACC 60.537 60.000 36.64 1.37 34.56 3.85
892 5087 1.137697 CCCGGGCCTATAAAAGACCT 58.862 55.000 8.08 0.00 0.00 3.85
912 5139 3.748568 CCTGCTCATCATCATCATCACAG 59.251 47.826 0.00 0.00 0.00 3.66
913 5140 3.740115 TGCTCATCATCATCATCACAGG 58.260 45.455 0.00 0.00 0.00 4.00
921 5148 3.694043 TCATCATCACAGGGAACGAAA 57.306 42.857 0.00 0.00 0.00 3.46
925 5152 1.539827 CATCACAGGGAACGAAAACCC 59.460 52.381 0.00 0.00 45.88 4.11
930 5157 2.194889 GGGAACGAAAACCCGCCAA 61.195 57.895 0.00 0.00 36.56 4.52
959 5186 4.200851 CACGCGCACGCTCATGAG 62.201 66.667 18.84 18.84 45.53 2.90
960 5187 4.419939 ACGCGCACGCTCATGAGA 62.420 61.111 27.04 0.00 45.53 3.27
961 5188 3.181290 CGCGCACGCTCATGAGAA 61.181 61.111 27.04 0.00 39.32 2.87
964 5197 1.808799 CGCACGCTCATGAGAAGCT 60.809 57.895 27.04 7.27 0.00 3.74
965 5198 1.357258 CGCACGCTCATGAGAAGCTT 61.357 55.000 27.04 0.00 0.00 3.74
969 5202 1.720301 GCTCATGAGAAGCTTGCCG 59.280 57.895 27.04 0.00 0.00 5.69
987 5220 1.463056 CCGCTGATCGACTAGCTAGAG 59.537 57.143 27.45 18.94 41.67 2.43
988 5221 1.136085 CGCTGATCGACTAGCTAGAGC 60.136 57.143 27.45 20.97 41.67 4.09
1072 5307 2.277072 CGAGGGAGCTGGAGGAGA 59.723 66.667 0.00 0.00 0.00 3.71
1079 5314 3.086600 GCTGGAGGAGAGGGTGGG 61.087 72.222 0.00 0.00 0.00 4.61
1285 5580 3.402681 CGATGCAGGACCTGGGGT 61.403 66.667 23.09 0.00 39.44 4.95
1534 5835 1.979155 GCTTCCTTGGGCCAGGAAC 60.979 63.158 24.65 19.15 46.34 3.62
1536 5837 0.610232 CTTCCTTGGGCCAGGAACAG 60.610 60.000 24.65 16.49 46.34 3.16
1537 5838 2.677875 CCTTGGGCCAGGAACAGC 60.678 66.667 18.51 0.00 35.71 4.40
1538 5839 2.115910 CTTGGGCCAGGAACAGCA 59.884 61.111 10.68 0.00 0.00 4.41
1539 5840 1.975407 CTTGGGCCAGGAACAGCAG 60.975 63.158 10.68 0.00 0.00 4.24
1540 5841 4.666253 TGGGCCAGGAACAGCAGC 62.666 66.667 0.00 0.00 0.00 5.25
1541 5842 4.666253 GGGCCAGGAACAGCAGCA 62.666 66.667 4.39 0.00 0.00 4.41
1542 5843 3.060615 GGCCAGGAACAGCAGCAG 61.061 66.667 0.00 0.00 0.00 4.24
1686 6005 2.889018 GGCAACTACGGCTACGCC 60.889 66.667 0.00 0.00 46.75 5.68
1716 6035 2.187946 CTCGGGGCTGACATGGAC 59.812 66.667 0.00 0.00 0.00 4.02
1792 6129 2.585247 GCGCCGTGTCCACTATCC 60.585 66.667 0.00 0.00 0.00 2.59
1860 6200 8.877808 TTATCGCAATGGAAGCTATATATCTG 57.122 34.615 0.00 0.00 0.00 2.90
1861 6201 5.111989 TCGCAATGGAAGCTATATATCTGC 58.888 41.667 0.00 0.00 0.00 4.26
1900 6240 6.183360 CCATCACTAGTAGAACTGTAGTGGTC 60.183 46.154 17.81 0.00 36.15 4.02
1960 6306 1.202698 AGACTCTGAACAACACTGGCC 60.203 52.381 0.00 0.00 0.00 5.36
1961 6307 0.546122 ACTCTGAACAACACTGGCCA 59.454 50.000 4.71 4.71 0.00 5.36
1963 6309 0.546122 TCTGAACAACACTGGCCACT 59.454 50.000 0.00 0.00 0.00 4.00
1964 6310 0.664761 CTGAACAACACTGGCCACTG 59.335 55.000 0.00 5.99 0.00 3.66
1965 6311 1.360192 GAACAACACTGGCCACTGC 59.640 57.895 0.00 0.00 0.00 4.40
1967 6313 0.969917 AACAACACTGGCCACTGCAA 60.970 50.000 0.00 0.00 40.13 4.08
1969 6315 1.246649 CAACACTGGCCACTGCAATA 58.753 50.000 0.00 0.00 40.13 1.90
1970 6316 1.820519 CAACACTGGCCACTGCAATAT 59.179 47.619 0.00 0.00 40.13 1.28
1972 6318 2.643551 ACACTGGCCACTGCAATATAC 58.356 47.619 0.00 0.00 40.13 1.47
1974 6320 2.874701 CACTGGCCACTGCAATATACTC 59.125 50.000 0.00 0.00 40.13 2.59
1975 6321 2.158755 ACTGGCCACTGCAATATACTCC 60.159 50.000 0.00 0.00 40.13 3.85
1976 6322 1.142870 TGGCCACTGCAATATACTCCC 59.857 52.381 0.00 0.00 40.13 4.30
1977 6323 1.421646 GGCCACTGCAATATACTCCCT 59.578 52.381 0.00 0.00 40.13 4.20
1978 6324 2.551071 GGCCACTGCAATATACTCCCTC 60.551 54.545 0.00 0.00 40.13 4.30
1979 6325 2.551071 GCCACTGCAATATACTCCCTCC 60.551 54.545 0.00 0.00 37.47 4.30
1980 6326 2.975489 CCACTGCAATATACTCCCTCCT 59.025 50.000 0.00 0.00 0.00 3.69
1981 6327 3.392616 CCACTGCAATATACTCCCTCCTT 59.607 47.826 0.00 0.00 0.00 3.36
1982 6328 4.593206 CCACTGCAATATACTCCCTCCTTA 59.407 45.833 0.00 0.00 0.00 2.69
1983 6329 5.511545 CCACTGCAATATACTCCCTCCTTAC 60.512 48.000 0.00 0.00 0.00 2.34
1984 6330 5.070446 CACTGCAATATACTCCCTCCTTACA 59.930 44.000 0.00 0.00 0.00 2.41
1985 6331 5.305644 ACTGCAATATACTCCCTCCTTACAG 59.694 44.000 0.00 0.00 0.00 2.74
1986 6332 5.464069 TGCAATATACTCCCTCCTTACAGA 58.536 41.667 0.00 0.00 0.00 3.41
1987 6333 5.540337 TGCAATATACTCCCTCCTTACAGAG 59.460 44.000 0.00 0.00 0.00 3.35
1988 6334 5.775701 GCAATATACTCCCTCCTTACAGAGA 59.224 44.000 0.00 0.00 35.82 3.10
1989 6335 6.071616 GCAATATACTCCCTCCTTACAGAGAG 60.072 46.154 0.00 0.00 35.82 3.20
1990 6336 7.235079 CAATATACTCCCTCCTTACAGAGAGA 58.765 42.308 0.00 0.00 35.82 3.10
1991 6337 3.662759 ACTCCCTCCTTACAGAGAGAG 57.337 52.381 0.00 0.00 42.68 3.20
1992 6338 2.923629 ACTCCCTCCTTACAGAGAGAGT 59.076 50.000 0.42 0.42 44.44 3.24
1993 6339 4.113085 ACTCCCTCCTTACAGAGAGAGTA 58.887 47.826 4.16 0.00 46.54 2.59
1994 6340 4.165372 ACTCCCTCCTTACAGAGAGAGTAG 59.835 50.000 4.16 0.00 46.54 2.57
2112 6465 7.762382 TCACTACAGTACAATGTCATCACTAG 58.238 38.462 0.00 0.00 34.56 2.57
2114 6467 8.409371 CACTACAGTACAATGTCATCACTAGAT 58.591 37.037 0.00 0.00 34.56 1.98
2277 6634 1.822990 CTCAGCCCAAGCACAATGAAT 59.177 47.619 0.00 0.00 43.56 2.57
2286 6643 5.593909 CCCAAGCACAATGAATAGATTGGTA 59.406 40.000 7.41 0.00 37.60 3.25
2322 6679 3.372730 GCCGTCCCATGCAGCAAA 61.373 61.111 0.00 0.00 0.00 3.68
2331 6688 2.355310 CCCATGCAGCAAATCCACATTT 60.355 45.455 0.00 0.00 31.91 2.32
2380 6737 3.118261 GGCTGAAAGAGGATGGTGATGTA 60.118 47.826 0.00 0.00 34.07 2.29
2385 6742 1.620819 AGAGGATGGTGATGTATCGGC 59.379 52.381 0.00 0.00 0.00 5.54
2399 6756 7.798516 GTGATGTATCGGCAAATACTTATTGTG 59.201 37.037 8.61 0.00 33.98 3.33
2401 6758 7.241663 TGTATCGGCAAATACTTATTGTGTC 57.758 36.000 8.61 0.00 33.98 3.67
2405 6762 5.233476 TCGGCAAATACTTATTGTGTCGATC 59.767 40.000 12.59 0.00 36.69 3.69
2411 6773 7.539712 AATACTTATTGTGTCGATCAAGGTG 57.460 36.000 10.69 6.48 0.00 4.00
2486 6849 2.105993 GGTACTGCTCCGGGGATAAAAT 59.894 50.000 4.80 0.00 0.00 1.82
2523 6886 7.387397 TGTGCATGAAACAAAAGGGAAATAATC 59.613 33.333 0.00 0.00 0.00 1.75
2536 6899 6.051717 AGGGAAATAATCAATGACGTGAGAG 58.948 40.000 0.00 0.00 0.00 3.20
2550 6915 5.011738 TGACGTGAGAGGAGGTAATTTTCTT 59.988 40.000 0.00 0.00 0.00 2.52
2558 6923 8.611051 AGAGGAGGTAATTTTCTTCTAGCTAA 57.389 34.615 0.00 0.00 29.18 3.09
2609 6975 8.451908 AAAATAGAAGAGGCCAATGTATACAC 57.548 34.615 7.96 0.00 0.00 2.90
2610 6976 7.380423 AATAGAAGAGGCCAATGTATACACT 57.620 36.000 7.96 0.00 0.00 3.55
2611 6977 8.492415 AATAGAAGAGGCCAATGTATACACTA 57.508 34.615 7.96 1.61 0.00 2.74
2645 7014 7.994425 TGGACACATACACATATTTTGTTCT 57.006 32.000 0.00 0.00 36.00 3.01
2650 7019 8.289618 ACACATACACATATTTTGTTCTGACAC 58.710 33.333 0.00 0.00 36.00 3.67
2699 7068 7.254137 GCTTTTTGCCAAAAGGATAACAAAAA 58.746 30.769 20.87 10.07 46.36 1.94
2700 7069 7.920151 GCTTTTTGCCAAAAGGATAACAAAAAT 59.080 29.630 20.87 0.00 46.36 1.82
2705 7074 7.504403 TGCCAAAAGGATAACAAAAATCAAGA 58.496 30.769 0.00 0.00 0.00 3.02
2706 7075 8.156165 TGCCAAAAGGATAACAAAAATCAAGAT 58.844 29.630 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.372730 GCCCCGTTTGCTGCATCA 61.373 61.111 1.84 0.00 0.00 3.07
2 3 3.683937 GTGCCCCGTTTGCTGCAT 61.684 61.111 1.84 0.00 35.96 3.96
6 7 1.142965 GTTTTGTGCCCCGTTTGCT 59.857 52.632 0.00 0.00 0.00 3.91
9 10 1.518302 GTGGTTTTGTGCCCCGTTT 59.482 52.632 0.00 0.00 0.00 3.60
11 12 3.213402 CGTGGTTTTGTGCCCCGT 61.213 61.111 0.00 0.00 0.00 5.28
12 13 3.972276 CCGTGGTTTTGTGCCCCG 61.972 66.667 0.00 0.00 0.00 5.73
14 15 1.668101 TTCACCGTGGTTTTGTGCCC 61.668 55.000 0.00 0.00 0.00 5.36
17 18 3.628017 GATCTTTCACCGTGGTTTTGTG 58.372 45.455 0.00 0.00 0.00 3.33
18 19 2.289547 CGATCTTTCACCGTGGTTTTGT 59.710 45.455 0.00 0.00 0.00 2.83
19 20 2.546368 TCGATCTTTCACCGTGGTTTTG 59.454 45.455 0.00 0.00 0.00 2.44
20 21 2.841215 TCGATCTTTCACCGTGGTTTT 58.159 42.857 0.00 0.00 0.00 2.43
21 22 2.536761 TCGATCTTTCACCGTGGTTT 57.463 45.000 0.00 0.00 0.00 3.27
23 24 1.069513 TGTTCGATCTTTCACCGTGGT 59.930 47.619 0.00 0.00 0.00 4.16
24 25 1.459592 GTGTTCGATCTTTCACCGTGG 59.540 52.381 0.00 0.00 0.00 4.94
25 26 1.124297 CGTGTTCGATCTTTCACCGTG 59.876 52.381 0.00 0.00 39.71 4.94
26 27 1.415374 CGTGTTCGATCTTTCACCGT 58.585 50.000 0.00 0.00 39.71 4.83
27 28 0.713883 CCGTGTTCGATCTTTCACCG 59.286 55.000 0.00 0.00 39.71 4.94
28 29 1.725164 GACCGTGTTCGATCTTTCACC 59.275 52.381 0.00 0.00 39.71 4.02
29 30 1.725164 GGACCGTGTTCGATCTTTCAC 59.275 52.381 0.00 0.00 39.71 3.18
30 31 1.337447 GGGACCGTGTTCGATCTTTCA 60.337 52.381 0.00 0.00 39.71 2.69
31 32 1.356938 GGGACCGTGTTCGATCTTTC 58.643 55.000 0.00 0.00 39.71 2.62
32 33 0.389426 CGGGACCGTGTTCGATCTTT 60.389 55.000 1.86 0.00 39.71 2.52
33 34 1.214589 CGGGACCGTGTTCGATCTT 59.785 57.895 1.86 0.00 39.71 2.40
34 35 2.882876 CGGGACCGTGTTCGATCT 59.117 61.111 1.86 0.00 39.71 2.75
143 4285 2.085320 GAGAGGACGTACAAGCTGAGA 58.915 52.381 0.00 0.00 0.00 3.27
147 4289 1.542030 CAGTGAGAGGACGTACAAGCT 59.458 52.381 0.00 0.00 0.00 3.74
161 4313 2.577112 CCGCGTACGAGCAGTGAG 60.577 66.667 21.65 0.00 43.93 3.51
188 4340 1.317613 GAGTTTGCACCATGTGGACA 58.682 50.000 5.96 0.83 32.77 4.02
207 4359 2.115910 TGTGGCAGAGCAAAGGGG 59.884 61.111 0.00 0.00 0.00 4.79
208 4360 2.620112 CGTGTGGCAGAGCAAAGGG 61.620 63.158 0.00 0.00 0.00 3.95
211 4363 3.286751 GGCGTGTGGCAGAGCAAA 61.287 61.111 10.26 0.00 46.16 3.68
433 4588 7.724061 ACTGACAGTAACCATGGAAGTAAAATT 59.276 33.333 21.47 1.50 0.00 1.82
434 4589 7.231467 ACTGACAGTAACCATGGAAGTAAAAT 58.769 34.615 21.47 0.00 0.00 1.82
439 4594 3.904339 AGACTGACAGTAACCATGGAAGT 59.096 43.478 21.47 8.83 0.00 3.01
441 4596 3.646162 ACAGACTGACAGTAACCATGGAA 59.354 43.478 21.47 2.58 0.00 3.53
445 4600 3.239449 TGGACAGACTGACAGTAACCAT 58.761 45.455 8.41 0.00 0.00 3.55
446 4601 2.673258 TGGACAGACTGACAGTAACCA 58.327 47.619 8.41 12.27 0.00 3.67
454 4609 0.108615 CCGTCCATGGACAGACTGAC 60.109 60.000 37.42 14.74 44.77 3.51
455 4610 1.888436 GCCGTCCATGGACAGACTGA 61.888 60.000 37.42 3.39 44.77 3.41
456 4611 1.448540 GCCGTCCATGGACAGACTG 60.449 63.158 37.42 23.50 44.77 3.51
457 4612 1.892819 CTGCCGTCCATGGACAGACT 61.893 60.000 37.42 0.00 44.77 3.24
526 4686 2.438434 GGTGAACGGGGATGGCAG 60.438 66.667 0.00 0.00 0.00 4.85
586 4746 3.098555 CAATAACCAGCGGCGTCC 58.901 61.111 9.37 0.00 0.00 4.79
620 4780 1.945394 GTCTAATCCGGTAGCTGACGA 59.055 52.381 12.65 1.15 0.00 4.20
634 4794 7.542890 CCATGAATATACGCTCTCTGTCTAAT 58.457 38.462 0.00 0.00 0.00 1.73
635 4795 6.570571 GCCATGAATATACGCTCTCTGTCTAA 60.571 42.308 0.00 0.00 0.00 2.10
637 4797 4.321601 GCCATGAATATACGCTCTCTGTCT 60.322 45.833 0.00 0.00 0.00 3.41
692 4855 3.648739 GGTCCTAGTCTCCTCTCCATTT 58.351 50.000 0.00 0.00 0.00 2.32
695 4858 0.547075 CGGTCCTAGTCTCCTCTCCA 59.453 60.000 0.00 0.00 0.00 3.86
734 4906 4.974399 AGACTTTGAACCGAGAAGGAAAT 58.026 39.130 0.00 0.00 45.00 2.17
795 4972 5.187687 GTTGATGGACGGGGACTATAAAAA 58.812 41.667 0.00 0.00 0.00 1.94
800 4977 1.762957 CTGTTGATGGACGGGGACTAT 59.237 52.381 0.00 0.00 0.00 2.12
802 4979 0.836400 ACTGTTGATGGACGGGGACT 60.836 55.000 0.00 0.00 0.00 3.85
803 4980 0.673644 CACTGTTGATGGACGGGGAC 60.674 60.000 0.00 0.00 30.63 4.46
815 5004 8.472683 TTTTGTAAAAGAATCCAACACTGTTG 57.527 30.769 14.11 14.11 0.00 3.33
872 5067 0.536687 GGTCTTTTATAGGCCCGGGC 60.537 60.000 38.57 38.57 43.28 6.13
888 5083 3.747010 GTGATGATGATGATGAGCAGGTC 59.253 47.826 0.00 0.00 0.00 3.85
889 5084 3.135895 TGTGATGATGATGATGAGCAGGT 59.864 43.478 0.00 0.00 0.00 4.00
891 5086 3.748568 CCTGTGATGATGATGATGAGCAG 59.251 47.826 0.00 0.00 0.00 4.24
892 5087 3.496160 CCCTGTGATGATGATGATGAGCA 60.496 47.826 0.00 0.00 0.00 4.26
912 5139 2.137425 CTTGGCGGGTTTTCGTTCCC 62.137 60.000 0.00 0.00 40.26 3.97
913 5140 1.284715 CTTGGCGGGTTTTCGTTCC 59.715 57.895 0.00 0.00 0.00 3.62
969 5202 1.876799 TGCTCTAGCTAGTCGATCAGC 59.123 52.381 20.10 19.08 42.66 4.26
1203 5489 2.281070 CTGTGCTGGCCGTTCACT 60.281 61.111 18.52 0.00 0.00 3.41
1493 5794 2.125391 GCTGCTGATCTGTGCCGA 60.125 61.111 1.27 0.00 0.00 5.54
1524 5825 4.666253 TGCTGCTGTTCCTGGCCC 62.666 66.667 0.00 0.00 0.00 5.80
1534 5835 1.913451 GAGCTCTGTTGCTGCTGCTG 61.913 60.000 17.00 0.77 44.17 4.41
1536 5837 2.868920 GAGCTCTGTTGCTGCTGC 59.131 61.111 6.43 8.89 44.17 5.25
1537 5838 3.024782 GCGAGCTCTGTTGCTGCTG 62.025 63.158 12.85 0.00 44.17 4.41
1538 5839 2.741598 GCGAGCTCTGTTGCTGCT 60.742 61.111 12.85 0.00 44.17 4.24
1539 5840 3.797546 GGCGAGCTCTGTTGCTGC 61.798 66.667 12.85 5.54 44.17 5.25
1540 5841 3.485431 CGGCGAGCTCTGTTGCTG 61.485 66.667 12.85 8.93 44.17 4.41
1562 5872 4.162690 GCATCCCTTCCGACGCCT 62.163 66.667 0.00 0.00 0.00 5.52
1716 6035 0.241213 TCCAGAACAGCTCGTCGAAG 59.759 55.000 0.00 0.00 0.00 3.79
1792 6129 9.796180 ATCTAAGTACTAGTGGGAATACAGTAG 57.204 37.037 5.39 6.53 45.56 2.57
1860 6200 5.398603 AGTGATGGTGCTATATCTACTGC 57.601 43.478 0.00 0.00 0.00 4.40
1861 6201 7.695480 ACTAGTGATGGTGCTATATCTACTG 57.305 40.000 0.00 0.00 0.00 2.74
1900 6240 4.184629 GTTCTTCCAGTGGCTAGTGTATG 58.815 47.826 3.51 0.00 0.00 2.39
1908 6254 0.550914 TTGGTGTTCTTCCAGTGGCT 59.449 50.000 3.51 0.00 36.28 4.75
1952 6298 2.239654 AGTATATTGCAGTGGCCAGTGT 59.760 45.455 35.27 21.78 40.13 3.55
1955 6301 2.498167 GGAGTATATTGCAGTGGCCAG 58.502 52.381 5.11 0.00 40.13 4.85
1956 6302 1.142870 GGGAGTATATTGCAGTGGCCA 59.857 52.381 0.00 0.00 40.13 5.36
1960 6306 4.696479 AAGGAGGGAGTATATTGCAGTG 57.304 45.455 0.00 0.00 0.00 3.66
1961 6307 5.216622 TGTAAGGAGGGAGTATATTGCAGT 58.783 41.667 0.00 0.00 0.00 4.40
1963 6309 5.464069 TCTGTAAGGAGGGAGTATATTGCA 58.536 41.667 0.00 0.00 0.00 4.08
1964 6310 5.775701 TCTCTGTAAGGAGGGAGTATATTGC 59.224 44.000 0.00 0.00 34.39 3.56
1965 6311 7.235079 TCTCTCTGTAAGGAGGGAGTATATTG 58.765 42.308 0.00 0.00 37.85 1.90
1974 6320 4.513406 ACTACTCTCTCTGTAAGGAGGG 57.487 50.000 0.00 0.00 37.63 4.30
1975 6321 9.226606 CATAATACTACTCTCTCTGTAAGGAGG 57.773 40.741 0.00 0.00 33.69 4.30
1976 6322 9.226606 CCATAATACTACTCTCTCTGTAAGGAG 57.773 40.741 0.00 0.00 34.03 3.69
1977 6323 8.946248 TCCATAATACTACTCTCTCTGTAAGGA 58.054 37.037 0.00 0.00 0.00 3.36
1978 6324 9.747898 ATCCATAATACTACTCTCTCTGTAAGG 57.252 37.037 0.00 0.00 0.00 2.69
1981 6327 9.952030 CTGATCCATAATACTACTCTCTCTGTA 57.048 37.037 0.00 0.00 0.00 2.74
1982 6328 7.393234 GCTGATCCATAATACTACTCTCTCTGT 59.607 40.741 0.00 0.00 0.00 3.41
1983 6329 7.392953 TGCTGATCCATAATACTACTCTCTCTG 59.607 40.741 0.00 0.00 0.00 3.35
1984 6330 7.393234 GTGCTGATCCATAATACTACTCTCTCT 59.607 40.741 0.00 0.00 0.00 3.10
1985 6331 7.175816 TGTGCTGATCCATAATACTACTCTCTC 59.824 40.741 0.00 0.00 0.00 3.20
1986 6332 7.007116 TGTGCTGATCCATAATACTACTCTCT 58.993 38.462 0.00 0.00 0.00 3.10
1987 6333 7.220741 TGTGCTGATCCATAATACTACTCTC 57.779 40.000 0.00 0.00 0.00 3.20
1988 6334 7.609960 CATGTGCTGATCCATAATACTACTCT 58.390 38.462 0.00 0.00 0.00 3.24
1989 6335 6.312426 GCATGTGCTGATCCATAATACTACTC 59.688 42.308 0.00 0.00 38.21 2.59
1990 6336 6.169094 GCATGTGCTGATCCATAATACTACT 58.831 40.000 0.00 0.00 38.21 2.57
1991 6337 5.934043 TGCATGTGCTGATCCATAATACTAC 59.066 40.000 6.55 0.00 42.66 2.73
1992 6338 5.934043 GTGCATGTGCTGATCCATAATACTA 59.066 40.000 6.55 0.00 42.66 1.82
1993 6339 4.758674 GTGCATGTGCTGATCCATAATACT 59.241 41.667 6.55 0.00 42.66 2.12
1994 6340 4.516321 TGTGCATGTGCTGATCCATAATAC 59.484 41.667 6.55 0.00 42.66 1.89
2112 6465 2.489722 GAGAACCTTTTCCTGGTGCATC 59.510 50.000 0.00 0.00 37.93 3.91
2114 6467 1.214175 TGAGAACCTTTTCCTGGTGCA 59.786 47.619 0.00 0.00 37.93 4.57
2277 6634 3.132289 CGCTTCTCACCCTTACCAATCTA 59.868 47.826 0.00 0.00 0.00 1.98
2286 6643 0.108138 CGGAATCGCTTCTCACCCTT 60.108 55.000 0.00 0.00 0.00 3.95
2313 6670 3.965379 TCAAATGTGGATTTGCTGCAT 57.035 38.095 1.84 0.00 45.61 3.96
2322 6679 2.749621 GACCTCGCTTTCAAATGTGGAT 59.250 45.455 0.00 0.00 0.00 3.41
2331 6688 0.899720 ATTACGGGACCTCGCTTTCA 59.100 50.000 2.68 0.00 0.00 2.69
2334 6691 0.899720 TTCATTACGGGACCTCGCTT 59.100 50.000 2.68 0.00 0.00 4.68
2380 6737 5.113383 TCGACACAATAAGTATTTGCCGAT 58.887 37.500 0.00 0.00 0.00 4.18
2385 6742 7.904977 CACCTTGATCGACACAATAAGTATTTG 59.095 37.037 7.21 0.00 0.00 2.32
2399 6756 5.062308 GTGAATCTTACACACCTTGATCGAC 59.938 44.000 0.00 0.00 38.05 4.20
2401 6758 5.062683 CAGTGAATCTTACACACCTTGATCG 59.937 44.000 0.00 0.00 40.25 3.69
2405 6762 6.618287 TTTCAGTGAATCTTACACACCTTG 57.382 37.500 6.36 0.00 40.25 3.61
2440 6803 5.887598 TGCTGGGATATATGGTAATTGCATC 59.112 40.000 0.00 0.00 0.00 3.91
2523 6886 3.868757 TTACCTCCTCTCACGTCATTG 57.131 47.619 0.00 0.00 0.00 2.82
2550 6915 7.344095 AGTTTCCGCTATTTAGTTAGCTAGA 57.656 36.000 0.00 0.00 41.99 2.43
2596 6962 6.455647 TCTGCTGTATAGTGTATACATTGGC 58.544 40.000 9.18 7.67 46.98 4.52
2599 6965 8.307483 GTCCATCTGCTGTATAGTGTATACATT 58.693 37.037 9.18 7.53 46.98 2.71
2604 6970 5.598417 TGTGTCCATCTGCTGTATAGTGTAT 59.402 40.000 0.00 0.00 0.00 2.29
2605 6971 4.953579 TGTGTCCATCTGCTGTATAGTGTA 59.046 41.667 0.00 0.00 0.00 2.90
2606 6972 3.769300 TGTGTCCATCTGCTGTATAGTGT 59.231 43.478 0.00 0.00 0.00 3.55
2607 6973 4.391405 TGTGTCCATCTGCTGTATAGTG 57.609 45.455 0.00 0.00 0.00 2.74
2608 6974 5.598417 TGTATGTGTCCATCTGCTGTATAGT 59.402 40.000 0.00 0.00 32.29 2.12
2609 6975 5.923114 GTGTATGTGTCCATCTGCTGTATAG 59.077 44.000 0.00 0.00 32.29 1.31
2610 6976 5.362430 TGTGTATGTGTCCATCTGCTGTATA 59.638 40.000 0.00 0.00 32.29 1.47
2611 6977 4.162131 TGTGTATGTGTCCATCTGCTGTAT 59.838 41.667 0.00 0.00 32.29 2.29
2645 7014 5.476599 CCATTTGATTGGGACTTAAGTGTCA 59.523 40.000 14.14 8.06 38.61 3.58
2650 7019 5.404466 TTGCCATTTGATTGGGACTTAAG 57.596 39.130 0.00 0.00 36.77 1.85
2699 7068 9.246670 TGTTCCTCAATTAATGTGAATCTTGAT 57.753 29.630 0.00 0.00 0.00 2.57
2700 7069 8.634335 TGTTCCTCAATTAATGTGAATCTTGA 57.366 30.769 0.00 0.00 0.00 3.02
2705 7074 9.439500 CCAATTTGTTCCTCAATTAATGTGAAT 57.561 29.630 0.00 0.00 35.84 2.57
2706 7075 8.428063 ACCAATTTGTTCCTCAATTAATGTGAA 58.572 29.630 0.00 0.00 35.84 3.18
2712 7081 7.045126 ACGAACCAATTTGTTCCTCAATTAA 57.955 32.000 14.82 0.00 41.24 1.40
2713 7082 6.642707 ACGAACCAATTTGTTCCTCAATTA 57.357 33.333 14.82 0.00 41.24 1.40
2721 7090 3.000825 GGCACAAACGAACCAATTTGTTC 59.999 43.478 11.45 11.45 44.61 3.18


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

AutoCloner maintained by Alex Coulton.