Multiple sequence alignment - TraesCS7D01G062900

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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 TraesCS7D01G062900 chr7D 100.000 2975 0 0 1 2975 34304197 34301223 0.000000e+00 5494.0
1 TraesCS7D01G062900 chr7A 91.601 2155 128 34 8 2148 34709328 34707213 0.000000e+00 2928.0
2 TraesCS7D01G062900 chr7A 91.379 754 38 9 2146 2893 34707164 34706432 0.000000e+00 1007.0
3 TraesCS7D01G062900 chr4A 90.295 2071 98 36 878 2892 691123887 691125910 0.000000e+00 2615.0
4 TraesCS7D01G062900 chr4A 93.617 94 6 0 466 559 455925452 455925545 1.110000e-29 141.0
5 TraesCS7D01G062900 chr1B 93.269 104 6 1 467 570 518802184 518802082 5.140000e-33 152.0
6 TraesCS7D01G062900 chr1B 90.385 104 10 0 466 569 670162593 670162696 1.440000e-28 137.0
7 TraesCS7D01G062900 chr1B 89.524 105 11 0 462 566 209132373 209132477 1.860000e-27 134.0
8 TraesCS7D01G062900 chr1B 75.862 145 21 12 568 700 643180823 643180965 8.900000e-06 62.1
9 TraesCS7D01G062900 chr4D 92.000 100 7 1 463 562 93339457 93339359 4.000000e-29 139.0
10 TraesCS7D01G062900 chr5B 90.476 105 9 1 465 569 693583799 693583902 1.440000e-28 137.0
11 TraesCS7D01G062900 chr4B 91.176 102 8 1 460 560 21198755 21198654 1.440000e-28 137.0
12 TraesCS7D01G062900 chr4B 91.089 101 9 0 465 565 31518072 31517972 1.440000e-28 137.0
13 TraesCS7D01G062900 chr3D 80.435 92 15 3 275 366 537798014 537797926 1.910000e-07 67.6
14 TraesCS7D01G062900 chr3A 82.500 80 9 5 275 352 673281662 673281586 6.880000e-07 65.8
15 TraesCS7D01G062900 chr2D 87.931 58 3 4 569 625 370129642 370129696 6.880000e-07 65.8
16 TraesCS7D01G062900 chr7B 82.192 73 13 0 295 367 125548727 125548655 2.480000e-06 63.9
17 TraesCS7D01G062900 chr7B 92.105 38 2 1 560 597 122668689 122668653 5.000000e-03 52.8
18 TraesCS7D01G062900 chr2A 88.462 52 3 3 569 619 501060482 501060531 3.200000e-05 60.2
19 TraesCS7D01G062900 chrUn 94.286 35 1 1 333 366 43285311 43285345 5.000000e-03 52.8
20 TraesCS7D01G062900 chr3B 100.000 28 0 0 333 360 1601795 1601822 5.000000e-03 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G062900 chr7D 34301223 34304197 2974 True 5494.0 5494 100.000 1 2975 1 chr7D.!!$R1 2974
1 TraesCS7D01G062900 chr7A 34706432 34709328 2896 True 1967.5 2928 91.490 8 2893 2 chr7A.!!$R1 2885
2 TraesCS7D01G062900 chr4A 691123887 691125910 2023 False 2615.0 2615 90.295 878 2892 1 chr4A.!!$F2 2014

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
481 484 0.040646 ACATGTACTCCCTCCGTCCA 59.959 55.0 0.0 0.0 0.00 4.02 F
867 872 0.387202 GCAAGAGGCGAGATGAGCTA 59.613 55.0 0.0 0.0 34.52 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1848 1881 0.665835 CCTCCTCGATGTCCTTCTCG 59.334 60.000 0.00 0.0 36.25 4.04 R
2253 2351 2.290789 GCGCGCGCTCGACTATAAA 61.291 57.895 44.38 0.0 38.10 1.40 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
123 124 9.341899 CTTAAAACTGCTAAATACATTCCACAC 57.658 33.333 0.00 0.00 0.00 3.82
124 125 6.892658 AAACTGCTAAATACATTCCACACA 57.107 33.333 0.00 0.00 0.00 3.72
187 188 9.678247 CGTGTAATTTTGGAAAAACTTTTGTAC 57.322 29.630 0.00 0.00 0.00 2.90
188 189 9.976255 GTGTAATTTTGGAAAAACTTTTGTACC 57.024 29.630 0.00 0.00 0.00 3.34
193 194 8.848474 TTTTGGAAAAACTTTTGTACCATTCA 57.152 26.923 0.00 0.00 0.00 2.57
194 195 8.848474 TTTGGAAAAACTTTTGTACCATTCAA 57.152 26.923 0.00 0.00 0.00 2.69
196 197 8.848474 TGGAAAAACTTTTGTACCATTCAAAA 57.152 26.923 0.00 0.00 40.77 2.44
197 198 9.284968 TGGAAAAACTTTTGTACCATTCAAAAA 57.715 25.926 0.00 0.00 41.87 1.94
221 222 5.950758 TGGTTGTGACATATAAGCGTTTT 57.049 34.783 0.00 0.00 31.41 2.43
352 354 7.603404 TCAAGCCTTTCAAAAATATGTTCATGG 59.397 33.333 0.00 0.00 0.00 3.66
361 363 9.381033 TCAAAAATATGTTCATGGCATTTTAGG 57.619 29.630 0.00 0.00 30.70 2.69
479 482 4.081807 ACTTAAACATGTACTCCCTCCGTC 60.082 45.833 0.00 0.00 0.00 4.79
481 484 0.040646 ACATGTACTCCCTCCGTCCA 59.959 55.000 0.00 0.00 0.00 4.02
546 549 5.548836 TGGTACTAAGGTTGGGACACTTATT 59.451 40.000 0.00 0.00 39.29 1.40
551 554 3.506398 AGGTTGGGACACTTATTTTGGG 58.494 45.455 0.00 0.00 39.29 4.12
562 565 3.585732 ACTTATTTTGGGACGGAGGAAGA 59.414 43.478 0.00 0.00 0.00 2.87
568 571 2.667470 TGGGACGGAGGAAGAATCTAG 58.333 52.381 0.00 0.00 0.00 2.43
634 638 8.795786 TCACAAAAATGCTTCTGTGTATAAAC 57.204 30.769 0.00 0.00 40.07 2.01
737 741 6.730960 ACACGTAGAAACAAACAAGAGAAA 57.269 33.333 0.00 0.00 0.00 2.52
753 758 4.344978 AGAGAAAAACCCTAATGGAAGCC 58.655 43.478 0.00 0.00 38.00 4.35
772 777 4.542697 AGCCTCCAAAACCTTTCTAAACA 58.457 39.130 0.00 0.00 0.00 2.83
775 780 5.163447 GCCTCCAAAACCTTTCTAAACAAGT 60.163 40.000 0.00 0.00 0.00 3.16
813 818 0.409092 ACCCAATCCAGAATGCCACA 59.591 50.000 0.00 0.00 31.97 4.17
814 819 1.108776 CCCAATCCAGAATGCCACAG 58.891 55.000 0.00 0.00 31.97 3.66
815 820 1.617804 CCCAATCCAGAATGCCACAGT 60.618 52.381 0.00 0.00 31.97 3.55
816 821 2.357050 CCCAATCCAGAATGCCACAGTA 60.357 50.000 0.00 0.00 31.97 2.74
817 822 2.684881 CCAATCCAGAATGCCACAGTAC 59.315 50.000 0.00 0.00 31.97 2.73
818 823 3.614092 CAATCCAGAATGCCACAGTACT 58.386 45.455 0.00 0.00 31.97 2.73
819 824 2.768253 TCCAGAATGCCACAGTACTG 57.232 50.000 21.44 21.44 31.97 2.74
820 825 2.256306 TCCAGAATGCCACAGTACTGA 58.744 47.619 29.30 7.19 31.97 3.41
821 826 2.234661 TCCAGAATGCCACAGTACTGAG 59.765 50.000 29.30 20.86 31.97 3.35
822 827 2.005451 CAGAATGCCACAGTACTGAGC 58.995 52.381 29.30 27.19 35.22 4.26
823 828 1.065854 AGAATGCCACAGTACTGAGCC 60.066 52.381 29.30 12.19 34.28 4.70
824 829 0.391661 AATGCCACAGTACTGAGCCG 60.392 55.000 29.30 13.41 34.28 5.52
825 830 2.815647 GCCACAGTACTGAGCCGC 60.816 66.667 29.30 16.40 0.00 6.53
826 831 2.125512 CCACAGTACTGAGCCGCC 60.126 66.667 29.30 0.00 0.00 6.13
827 832 2.125512 CACAGTACTGAGCCGCCC 60.126 66.667 29.30 0.00 0.00 6.13
828 833 3.391382 ACAGTACTGAGCCGCCCC 61.391 66.667 29.30 0.00 0.00 5.80
829 834 4.162690 CAGTACTGAGCCGCCCCC 62.163 72.222 18.45 0.00 0.00 5.40
843 848 4.708386 CCCCCTAACGTGGCGCAA 62.708 66.667 10.83 0.00 0.00 4.85
844 849 3.124921 CCCCTAACGTGGCGCAAG 61.125 66.667 10.83 1.38 43.44 4.01
845 850 2.047655 CCCTAACGTGGCGCAAGA 60.048 61.111 10.83 0.00 43.02 3.02
855 860 3.793144 GCGCAAGACGGCAAGAGG 61.793 66.667 0.30 0.00 43.93 3.69
856 861 3.793144 CGCAAGACGGCAAGAGGC 61.793 66.667 0.00 0.00 41.06 4.70
865 870 1.886777 GGCAAGAGGCGAGATGAGC 60.887 63.158 0.00 0.00 46.16 4.26
866 871 1.143620 GCAAGAGGCGAGATGAGCT 59.856 57.895 0.00 0.00 34.52 4.09
867 872 0.387202 GCAAGAGGCGAGATGAGCTA 59.613 55.000 0.00 0.00 34.52 3.32
869 874 1.406898 CAAGAGGCGAGATGAGCTACA 59.593 52.381 0.00 0.00 34.52 2.74
871 876 1.133945 AGAGGCGAGATGAGCTACAGA 60.134 52.381 0.00 0.00 34.52 3.41
873 890 1.133945 AGGCGAGATGAGCTACAGAGA 60.134 52.381 0.00 0.00 34.52 3.10
875 892 2.542824 GGCGAGATGAGCTACAGAGAAC 60.543 54.545 0.00 0.00 34.52 3.01
892 909 8.024145 ACAGAGAACCCAATCCTAATTAGTAG 57.976 38.462 11.50 0.00 0.00 2.57
1075 1093 0.742281 CTCCATTCCGTGCCACTCTG 60.742 60.000 0.00 0.00 0.00 3.35
1109 1136 2.956194 CATTCACCAGCAGCGCAA 59.044 55.556 11.47 0.00 0.00 4.85
1374 1401 2.821366 GTGCAGCTGGACATCCGG 60.821 66.667 30.84 0.00 45.30 5.14
1848 1881 4.208686 CGCGCCTACCTCCACTCC 62.209 72.222 0.00 0.00 0.00 3.85
1994 2030 3.937814 AGCAAATGTGTTCATAGACCGA 58.062 40.909 0.00 0.00 33.49 4.69
1995 2031 3.684788 AGCAAATGTGTTCATAGACCGAC 59.315 43.478 0.00 0.00 33.49 4.79
1996 2032 3.684788 GCAAATGTGTTCATAGACCGACT 59.315 43.478 0.00 0.00 33.49 4.18
1997 2033 4.436050 GCAAATGTGTTCATAGACCGACTG 60.436 45.833 0.00 0.00 33.49 3.51
1999 2035 3.297830 TGTGTTCATAGACCGACTGTG 57.702 47.619 0.00 0.00 38.75 3.66
2002 2038 2.631062 TGTTCATAGACCGACTGTGGTT 59.369 45.455 3.93 0.00 44.01 3.67
2003 2039 2.993899 GTTCATAGACCGACTGTGGTTG 59.006 50.000 3.93 0.37 44.01 3.77
2004 2040 2.244695 TCATAGACCGACTGTGGTTGT 58.755 47.619 3.93 0.00 44.01 3.32
2005 2041 3.423749 TCATAGACCGACTGTGGTTGTA 58.576 45.455 3.93 1.25 44.01 2.41
2011 2047 1.732259 CCGACTGTGGTTGTATCTTGC 59.268 52.381 0.00 0.00 0.00 4.01
2028 2064 4.921547 TCTTGCAGAGTGTAGCTAATACG 58.078 43.478 0.00 0.00 37.17 3.06
2029 2065 4.398358 TCTTGCAGAGTGTAGCTAATACGT 59.602 41.667 0.00 0.00 37.17 3.57
2030 2066 5.587443 TCTTGCAGAGTGTAGCTAATACGTA 59.413 40.000 0.00 0.00 37.17 3.57
2031 2067 5.165911 TGCAGAGTGTAGCTAATACGTAC 57.834 43.478 0.00 0.00 37.17 3.67
2032 2068 4.209870 GCAGAGTGTAGCTAATACGTACG 58.790 47.826 15.01 15.01 37.17 3.67
2040 2076 7.006537 GTGTAGCTAATACGTACGTGTATCTC 58.993 42.308 30.25 14.28 37.17 2.75
2044 2080 8.545229 AGCTAATACGTACGTGTATCTCTAAT 57.455 34.615 30.25 9.84 34.01 1.73
2049 2085 6.768029 ACGTACGTGTATCTCTAATCTCTC 57.232 41.667 22.14 0.00 0.00 3.20
2050 2086 5.401972 ACGTACGTGTATCTCTAATCTCTCG 59.598 44.000 22.14 0.00 0.00 4.04
2051 2087 5.164070 CGTACGTGTATCTCTAATCTCTCGG 60.164 48.000 7.22 0.00 0.00 4.63
2052 2088 4.706035 ACGTGTATCTCTAATCTCTCGGT 58.294 43.478 0.00 0.00 0.00 4.69
2053 2089 4.512198 ACGTGTATCTCTAATCTCTCGGTG 59.488 45.833 0.00 0.00 0.00 4.94
2054 2090 4.083749 CGTGTATCTCTAATCTCTCGGTGG 60.084 50.000 0.00 0.00 0.00 4.61
2055 2091 4.822896 GTGTATCTCTAATCTCTCGGTGGT 59.177 45.833 0.00 0.00 0.00 4.16
2056 2092 5.996513 GTGTATCTCTAATCTCTCGGTGGTA 59.003 44.000 0.00 0.00 0.00 3.25
2057 2093 6.655848 GTGTATCTCTAATCTCTCGGTGGTAT 59.344 42.308 0.00 0.00 0.00 2.73
2058 2094 6.879993 TGTATCTCTAATCTCTCGGTGGTATC 59.120 42.308 0.00 0.00 0.00 2.24
2059 2095 5.570205 TCTCTAATCTCTCGGTGGTATCT 57.430 43.478 0.00 0.00 0.00 1.98
2060 2096 5.553123 TCTCTAATCTCTCGGTGGTATCTC 58.447 45.833 0.00 0.00 0.00 2.75
2061 2097 5.308497 TCTCTAATCTCTCGGTGGTATCTCT 59.692 44.000 0.00 0.00 0.00 3.10
2092 2131 3.492313 GTGGTTCAAGCATGATTCGTTC 58.508 45.455 0.00 0.00 34.96 3.95
2143 2182 1.806542 TGCGCCATGAGTTTCTTCTTC 59.193 47.619 4.18 0.00 0.00 2.87
2210 2307 2.747446 GACTCAGAGTCAGTGAGGAGAC 59.253 54.545 23.62 7.50 44.96 3.36
2213 2310 1.466950 CAGAGTCAGTGAGGAGACGTC 59.533 57.143 7.70 7.70 39.67 4.34
2486 2592 4.986645 TCGTGGGACGACGACGGA 62.987 66.667 12.58 0.00 46.73 4.69
2487 2593 4.029186 CGTGGGACGACGACGGAA 62.029 66.667 12.58 0.00 46.05 4.30
2581 2687 1.152839 CGGAGGAGGAGGAGGAGTC 60.153 68.421 0.00 0.00 0.00 3.36
2582 2688 1.152839 GGAGGAGGAGGAGGAGTCG 60.153 68.421 0.00 0.00 0.00 4.18
2583 2689 1.826487 GAGGAGGAGGAGGAGTCGC 60.826 68.421 0.00 0.00 0.00 5.19
2584 2690 2.835895 GGAGGAGGAGGAGTCGCC 60.836 72.222 0.00 0.00 0.00 5.54
2585 2691 3.213402 GAGGAGGAGGAGTCGCCG 61.213 72.222 0.00 0.00 43.43 6.46
2707 2813 0.321653 GCGAAGGAGGCCAAGAAGAA 60.322 55.000 5.01 0.00 0.00 2.52
2714 2820 2.083002 GAGGCCAAGAAGAAGAGCAAG 58.917 52.381 5.01 0.00 0.00 4.01
2720 2826 0.972883 AGAAGAAGAGCAAGCGGAGT 59.027 50.000 0.00 0.00 0.00 3.85
2882 2988 1.601759 GCAGCAGCTCCTCCACAAA 60.602 57.895 0.00 0.00 37.91 2.83
2893 2999 1.697432 CCTCCACAAACACCAGTAGGA 59.303 52.381 0.00 0.00 38.69 2.94
2894 3000 2.305927 CCTCCACAAACACCAGTAGGAT 59.694 50.000 0.00 0.00 38.69 3.24
2895 3001 3.244911 CCTCCACAAACACCAGTAGGATT 60.245 47.826 0.00 0.00 38.69 3.01
2896 3002 4.019681 CCTCCACAAACACCAGTAGGATTA 60.020 45.833 0.00 0.00 38.69 1.75
2897 3003 5.514136 CCTCCACAAACACCAGTAGGATTAA 60.514 44.000 0.00 0.00 38.69 1.40
2898 3004 5.942961 TCCACAAACACCAGTAGGATTAAA 58.057 37.500 0.00 0.00 38.69 1.52
2899 3005 6.001460 TCCACAAACACCAGTAGGATTAAAG 58.999 40.000 0.00 0.00 38.69 1.85
2900 3006 6.001460 CCACAAACACCAGTAGGATTAAAGA 58.999 40.000 0.00 0.00 38.69 2.52
2901 3007 6.149474 CCACAAACACCAGTAGGATTAAAGAG 59.851 42.308 0.00 0.00 38.69 2.85
2902 3008 5.705905 ACAAACACCAGTAGGATTAAAGAGC 59.294 40.000 0.00 0.00 38.69 4.09
2903 3009 5.763876 AACACCAGTAGGATTAAAGAGCT 57.236 39.130 0.00 0.00 38.69 4.09
2904 3010 5.763876 ACACCAGTAGGATTAAAGAGCTT 57.236 39.130 0.00 0.00 38.69 3.74
2905 3011 6.128138 ACACCAGTAGGATTAAAGAGCTTT 57.872 37.500 0.74 0.74 38.69 3.51
2906 3012 5.940470 ACACCAGTAGGATTAAAGAGCTTTG 59.060 40.000 5.76 0.00 38.69 2.77
2907 3013 5.940470 CACCAGTAGGATTAAAGAGCTTTGT 59.060 40.000 5.76 0.00 38.69 2.83
2908 3014 6.431234 CACCAGTAGGATTAAAGAGCTTTGTT 59.569 38.462 5.76 0.00 38.69 2.83
2909 3015 6.431234 ACCAGTAGGATTAAAGAGCTTTGTTG 59.569 38.462 5.76 0.00 38.69 3.33
2910 3016 6.127897 CCAGTAGGATTAAAGAGCTTTGTTGG 60.128 42.308 5.76 0.00 36.89 3.77
2911 3017 6.431234 CAGTAGGATTAAAGAGCTTTGTTGGT 59.569 38.462 5.76 0.00 34.23 3.67
2912 3018 7.004691 AGTAGGATTAAAGAGCTTTGTTGGTT 58.995 34.615 5.76 0.00 34.23 3.67
2913 3019 8.161425 AGTAGGATTAAAGAGCTTTGTTGGTTA 58.839 33.333 5.76 0.00 34.23 2.85
2914 3020 8.957466 GTAGGATTAAAGAGCTTTGTTGGTTAT 58.043 33.333 5.76 0.00 34.23 1.89
2915 3021 8.056407 AGGATTAAAGAGCTTTGTTGGTTATC 57.944 34.615 5.76 0.00 34.23 1.75
2916 3022 7.669722 AGGATTAAAGAGCTTTGTTGGTTATCA 59.330 33.333 5.76 0.00 34.23 2.15
2917 3023 8.470002 GGATTAAAGAGCTTTGTTGGTTATCAT 58.530 33.333 5.76 0.00 34.23 2.45
2918 3024 9.294030 GATTAAAGAGCTTTGTTGGTTATCATG 57.706 33.333 5.76 0.00 34.23 3.07
2919 3025 5.649782 AAGAGCTTTGTTGGTTATCATGG 57.350 39.130 0.00 0.00 0.00 3.66
2920 3026 3.445096 AGAGCTTTGTTGGTTATCATGGC 59.555 43.478 0.00 0.00 0.00 4.40
2921 3027 3.434309 AGCTTTGTTGGTTATCATGGCT 58.566 40.909 0.00 0.00 0.00 4.75
2922 3028 3.445096 AGCTTTGTTGGTTATCATGGCTC 59.555 43.478 0.00 0.00 0.00 4.70
2923 3029 3.731867 GCTTTGTTGGTTATCATGGCTCG 60.732 47.826 0.00 0.00 0.00 5.03
2924 3030 2.779755 TGTTGGTTATCATGGCTCGT 57.220 45.000 0.00 0.00 0.00 4.18
2925 3031 3.897141 TGTTGGTTATCATGGCTCGTA 57.103 42.857 0.00 0.00 0.00 3.43
2926 3032 3.792401 TGTTGGTTATCATGGCTCGTAG 58.208 45.455 0.00 0.00 0.00 3.51
2927 3033 3.196901 TGTTGGTTATCATGGCTCGTAGT 59.803 43.478 0.00 0.00 0.00 2.73
2928 3034 4.189231 GTTGGTTATCATGGCTCGTAGTT 58.811 43.478 0.00 0.00 0.00 2.24
2929 3035 4.481368 TGGTTATCATGGCTCGTAGTTT 57.519 40.909 0.00 0.00 0.00 2.66
2930 3036 4.188462 TGGTTATCATGGCTCGTAGTTTG 58.812 43.478 0.00 0.00 0.00 2.93
2931 3037 4.189231 GGTTATCATGGCTCGTAGTTTGT 58.811 43.478 0.00 0.00 0.00 2.83
2932 3038 4.270325 GGTTATCATGGCTCGTAGTTTGTC 59.730 45.833 0.00 0.00 0.00 3.18
2933 3039 1.990799 TCATGGCTCGTAGTTTGTCG 58.009 50.000 0.00 0.00 0.00 4.35
2934 3040 1.542472 TCATGGCTCGTAGTTTGTCGA 59.458 47.619 0.00 0.00 34.88 4.20
2938 3044 3.670500 CTCGTAGTTTGTCGAGCGA 57.330 52.632 1.88 0.00 44.82 4.93
2939 3045 1.248721 CTCGTAGTTTGTCGAGCGAC 58.751 55.000 15.49 15.49 44.82 5.19
2940 3046 0.870393 TCGTAGTTTGTCGAGCGACT 59.130 50.000 21.68 6.22 44.80 4.18
2941 3047 2.068519 TCGTAGTTTGTCGAGCGACTA 58.931 47.619 21.68 13.07 44.80 2.59
2942 3048 2.480037 TCGTAGTTTGTCGAGCGACTAA 59.520 45.455 21.68 17.79 44.80 2.24
2943 3049 3.125829 TCGTAGTTTGTCGAGCGACTAAT 59.874 43.478 21.68 12.44 44.80 1.73
2944 3050 3.477802 CGTAGTTTGTCGAGCGACTAATC 59.522 47.826 21.68 14.62 44.80 1.75
2945 3051 2.877335 AGTTTGTCGAGCGACTAATCC 58.123 47.619 21.68 10.87 44.80 3.01
2946 3052 2.230508 AGTTTGTCGAGCGACTAATCCA 59.769 45.455 21.68 0.00 44.80 3.41
2947 3053 3.119101 AGTTTGTCGAGCGACTAATCCAT 60.119 43.478 21.68 7.62 44.80 3.41
2948 3054 2.492019 TGTCGAGCGACTAATCCATG 57.508 50.000 21.68 0.00 44.80 3.66
2949 3055 2.021457 TGTCGAGCGACTAATCCATGA 58.979 47.619 21.68 0.00 44.80 3.07
2950 3056 2.623416 TGTCGAGCGACTAATCCATGAT 59.377 45.455 21.68 0.00 44.80 2.45
2951 3057 3.068165 TGTCGAGCGACTAATCCATGATT 59.932 43.478 21.68 0.00 44.80 2.57
2952 3058 3.426859 GTCGAGCGACTAATCCATGATTG 59.573 47.826 15.13 0.00 41.57 2.67
2953 3059 2.156504 CGAGCGACTAATCCATGATTGC 59.843 50.000 0.00 0.00 33.95 3.56
2954 3060 2.138320 AGCGACTAATCCATGATTGCG 58.862 47.619 0.00 2.90 33.95 4.85
2955 3061 1.398960 GCGACTAATCCATGATTGCGC 60.399 52.381 0.00 0.00 39.23 6.09
2956 3062 1.195448 CGACTAATCCATGATTGCGCC 59.805 52.381 4.18 0.00 33.95 6.53
2957 3063 1.195448 GACTAATCCATGATTGCGCCG 59.805 52.381 4.18 0.00 33.95 6.46
2958 3064 0.518636 CTAATCCATGATTGCGCCGG 59.481 55.000 4.18 0.00 33.95 6.13
2959 3065 1.514678 TAATCCATGATTGCGCCGGC 61.515 55.000 19.07 19.07 33.95 6.13
2973 3079 3.414700 CGGCGAAGAAGCGTGCTT 61.415 61.111 6.84 6.84 39.23 3.91
2974 3080 2.946762 GGCGAAGAAGCGTGCTTT 59.053 55.556 8.72 0.00 36.26 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
148 149 5.178438 CAAAATTACACGGACCCAATTTTGG 59.822 40.000 20.42 2.17 45.64 3.28
194 195 6.919721 ACGCTTATATGTCACAACCATTTTT 58.080 32.000 0.00 0.00 0.00 1.94
196 197 6.509418 AACGCTTATATGTCACAACCATTT 57.491 33.333 0.00 0.00 0.00 2.32
197 198 6.509418 AAACGCTTATATGTCACAACCATT 57.491 33.333 0.00 0.00 0.00 3.16
198 199 6.150307 TGAAAACGCTTATATGTCACAACCAT 59.850 34.615 0.00 0.00 0.00 3.55
249 250 8.557869 ACATCGTATAGTCATCGTTAAGAAAC 57.442 34.615 0.00 0.00 0.00 2.78
310 312 6.259550 AGGCTTGAACATTCTGTAAATGTC 57.740 37.500 4.05 0.39 39.73 3.06
318 320 6.907206 TTTTTGAAAGGCTTGAACATTCTG 57.093 33.333 0.00 0.00 0.00 3.02
456 459 3.836562 ACGGAGGGAGTACATGTTTAAGT 59.163 43.478 2.30 0.00 0.00 2.24
457 460 4.430908 GACGGAGGGAGTACATGTTTAAG 58.569 47.826 2.30 0.00 0.00 1.85
458 461 3.196254 GGACGGAGGGAGTACATGTTTAA 59.804 47.826 2.30 0.00 0.00 1.52
459 462 2.762327 GGACGGAGGGAGTACATGTTTA 59.238 50.000 2.30 0.00 0.00 2.01
460 463 1.553704 GGACGGAGGGAGTACATGTTT 59.446 52.381 2.30 0.00 0.00 2.83
468 471 3.329814 ACTTATTTTTGGACGGAGGGAGT 59.670 43.478 0.00 0.00 0.00 3.85
472 475 4.324267 AGACACTTATTTTTGGACGGAGG 58.676 43.478 0.00 0.00 0.00 4.30
475 478 7.198306 AGTTAAGACACTTATTTTTGGACGG 57.802 36.000 0.00 0.00 0.00 4.79
517 520 5.048294 GTGTCCCAACCTTAGTACCAATTTG 60.048 44.000 0.00 0.00 0.00 2.32
521 524 3.320129 AGTGTCCCAACCTTAGTACCAA 58.680 45.455 0.00 0.00 0.00 3.67
523 526 5.688814 ATAAGTGTCCCAACCTTAGTACC 57.311 43.478 0.00 0.00 0.00 3.34
536 539 3.007635 CTCCGTCCCAAAATAAGTGTCC 58.992 50.000 0.00 0.00 0.00 4.02
546 549 2.266279 AGATTCTTCCTCCGTCCCAAA 58.734 47.619 0.00 0.00 0.00 3.28
551 554 5.326200 TGTTTCTAGATTCTTCCTCCGTC 57.674 43.478 0.00 0.00 0.00 4.79
718 722 7.544622 AGGGTTTTTCTCTTGTTTGTTTCTAC 58.455 34.615 0.00 0.00 0.00 2.59
737 741 2.828661 GGAGGCTTCCATTAGGGTTT 57.171 50.000 10.56 0.00 43.45 3.27
753 758 7.543756 TGAACTTGTTTAGAAAGGTTTTGGAG 58.456 34.615 0.00 0.00 0.00 3.86
826 831 4.708386 TTGCGCCACGTTAGGGGG 62.708 66.667 4.18 7.05 42.67 5.40
827 832 3.124921 CTTGCGCCACGTTAGGGG 61.125 66.667 4.18 4.77 46.15 4.79
828 833 2.047655 TCTTGCGCCACGTTAGGG 60.048 61.111 4.18 0.00 0.00 3.53
829 834 2.726691 CGTCTTGCGCCACGTTAGG 61.727 63.158 4.18 0.00 0.00 2.69
842 847 1.608717 ATCTCGCCTCTTGCCGTCTT 61.609 55.000 0.00 0.00 36.24 3.01
843 848 2.055042 ATCTCGCCTCTTGCCGTCT 61.055 57.895 0.00 0.00 36.24 4.18
844 849 1.880340 CATCTCGCCTCTTGCCGTC 60.880 63.158 0.00 0.00 36.24 4.79
845 850 2.185350 CATCTCGCCTCTTGCCGT 59.815 61.111 0.00 0.00 36.24 5.68
846 851 1.591059 CTCATCTCGCCTCTTGCCG 60.591 63.158 0.00 0.00 36.24 5.69
847 852 1.886777 GCTCATCTCGCCTCTTGCC 60.887 63.158 0.00 0.00 36.24 4.52
848 853 0.387202 TAGCTCATCTCGCCTCTTGC 59.613 55.000 0.00 0.00 0.00 4.01
849 854 1.406898 TGTAGCTCATCTCGCCTCTTG 59.593 52.381 0.00 0.00 0.00 3.02
851 856 1.133945 TCTGTAGCTCATCTCGCCTCT 60.134 52.381 0.00 0.00 0.00 3.69
852 857 1.266718 CTCTGTAGCTCATCTCGCCTC 59.733 57.143 0.00 0.00 0.00 4.70
854 859 1.313772 TCTCTGTAGCTCATCTCGCC 58.686 55.000 0.00 0.00 0.00 5.54
855 860 2.542824 GGTTCTCTGTAGCTCATCTCGC 60.543 54.545 0.00 0.00 0.00 5.03
856 861 2.034053 GGGTTCTCTGTAGCTCATCTCG 59.966 54.545 0.00 0.00 0.00 4.04
857 862 3.027412 TGGGTTCTCTGTAGCTCATCTC 58.973 50.000 0.00 0.00 0.00 2.75
858 863 3.107402 TGGGTTCTCTGTAGCTCATCT 57.893 47.619 0.00 0.00 0.00 2.90
860 865 3.135530 GGATTGGGTTCTCTGTAGCTCAT 59.864 47.826 0.00 0.00 0.00 2.90
861 866 2.501723 GGATTGGGTTCTCTGTAGCTCA 59.498 50.000 0.00 0.00 0.00 4.26
862 867 2.769095 AGGATTGGGTTCTCTGTAGCTC 59.231 50.000 0.00 0.00 0.00 4.09
863 868 2.839228 AGGATTGGGTTCTCTGTAGCT 58.161 47.619 0.00 0.00 0.00 3.32
865 870 8.024145 ACTAATTAGGATTGGGTTCTCTGTAG 57.976 38.462 16.73 0.00 0.00 2.74
866 871 7.989947 ACTAATTAGGATTGGGTTCTCTGTA 57.010 36.000 16.73 0.00 0.00 2.74
867 872 6.893020 ACTAATTAGGATTGGGTTCTCTGT 57.107 37.500 16.73 0.00 0.00 3.41
892 909 1.218196 TGGATAGACCCTCAGAGGACC 59.782 57.143 19.21 8.88 37.67 4.46
893 910 2.312390 GTGGATAGACCCTCAGAGGAC 58.688 57.143 19.21 11.38 37.67 3.85
1050 1068 2.819595 CACGGAATGGAGGGCGTG 60.820 66.667 0.00 0.00 0.00 5.34
1056 1074 0.742281 CAGAGTGGCACGGAATGGAG 60.742 60.000 12.71 0.00 0.00 3.86
1060 1078 0.320771 GACACAGAGTGGCACGGAAT 60.321 55.000 12.71 0.00 41.94 3.01
1062 1080 2.734591 GACACAGAGTGGCACGGA 59.265 61.111 12.71 0.00 41.94 4.69
1485 1512 4.247380 GAGGCCAGCGGGATGGAG 62.247 72.222 7.23 0.00 43.57 3.86
1848 1881 0.665835 CCTCCTCGATGTCCTTCTCG 59.334 60.000 0.00 0.00 36.25 4.04
1994 2030 3.071602 ACTCTGCAAGATACAACCACAGT 59.928 43.478 3.37 0.00 45.62 3.55
1995 2031 3.434641 CACTCTGCAAGATACAACCACAG 59.565 47.826 3.37 0.00 45.62 3.66
1996 2032 3.181455 ACACTCTGCAAGATACAACCACA 60.181 43.478 3.37 0.00 45.62 4.17
1997 2033 3.403038 ACACTCTGCAAGATACAACCAC 58.597 45.455 3.37 0.00 45.62 4.16
1999 2035 3.619038 GCTACACTCTGCAAGATACAACC 59.381 47.826 3.37 0.00 45.62 3.77
2002 2038 5.914898 TTAGCTACACTCTGCAAGATACA 57.085 39.130 0.00 0.00 45.62 2.29
2003 2039 6.579292 CGTATTAGCTACACTCTGCAAGATAC 59.421 42.308 0.00 0.00 45.62 2.24
2004 2040 6.262496 ACGTATTAGCTACACTCTGCAAGATA 59.738 38.462 0.00 0.00 45.62 1.98
2005 2041 5.067936 ACGTATTAGCTACACTCTGCAAGAT 59.932 40.000 0.00 0.00 45.62 2.40
2011 2047 5.196102 CACGTACGTATTAGCTACACTCTG 58.804 45.833 22.34 0.00 0.00 3.35
2028 2064 5.695816 ACCGAGAGATTAGAGATACACGTAC 59.304 44.000 0.00 0.00 0.00 3.67
2029 2065 5.695363 CACCGAGAGATTAGAGATACACGTA 59.305 44.000 0.00 0.00 0.00 3.57
2030 2066 4.512198 CACCGAGAGATTAGAGATACACGT 59.488 45.833 0.00 0.00 0.00 4.49
2031 2067 4.083749 CCACCGAGAGATTAGAGATACACG 60.084 50.000 0.00 0.00 0.00 4.49
2032 2068 4.822896 ACCACCGAGAGATTAGAGATACAC 59.177 45.833 0.00 0.00 0.00 2.90
2040 2076 7.827236 AGATTAGAGATACCACCGAGAGATTAG 59.173 40.741 0.00 0.00 0.00 1.73
2044 2080 5.308497 AGAGATTAGAGATACCACCGAGAGA 59.692 44.000 0.00 0.00 0.00 3.10
2049 2085 3.437395 CCGAGAGATTAGAGATACCACCG 59.563 52.174 0.00 0.00 0.00 4.94
2050 2086 4.216687 CACCGAGAGATTAGAGATACCACC 59.783 50.000 0.00 0.00 0.00 4.61
2051 2087 4.216687 CCACCGAGAGATTAGAGATACCAC 59.783 50.000 0.00 0.00 0.00 4.16
2052 2088 4.141228 ACCACCGAGAGATTAGAGATACCA 60.141 45.833 0.00 0.00 0.00 3.25
2053 2089 4.400120 ACCACCGAGAGATTAGAGATACC 58.600 47.826 0.00 0.00 0.00 2.73
2054 2090 5.531659 TGAACCACCGAGAGATTAGAGATAC 59.468 44.000 0.00 0.00 0.00 2.24
2055 2091 5.691896 TGAACCACCGAGAGATTAGAGATA 58.308 41.667 0.00 0.00 0.00 1.98
2056 2092 4.537751 TGAACCACCGAGAGATTAGAGAT 58.462 43.478 0.00 0.00 0.00 2.75
2057 2093 3.964411 TGAACCACCGAGAGATTAGAGA 58.036 45.455 0.00 0.00 0.00 3.10
2058 2094 4.677584 CTTGAACCACCGAGAGATTAGAG 58.322 47.826 0.00 0.00 0.00 2.43
2059 2095 3.119101 GCTTGAACCACCGAGAGATTAGA 60.119 47.826 0.00 0.00 0.00 2.10
2060 2096 3.190874 GCTTGAACCACCGAGAGATTAG 58.809 50.000 0.00 0.00 0.00 1.73
2061 2097 2.565391 TGCTTGAACCACCGAGAGATTA 59.435 45.455 0.00 0.00 0.00 1.75
2210 2307 2.879933 CAGCTGCTCTGCTCGACG 60.880 66.667 0.00 0.00 41.98 5.12
2229 2327 5.157940 AGAGCTCTCTGTTTTTATCTGCA 57.842 39.130 11.45 0.00 38.75 4.41
2253 2351 2.290789 GCGCGCGCTCGACTATAAA 61.291 57.895 44.38 0.00 38.10 1.40
2707 2813 4.749310 CCGCACTCCGCTTGCTCT 62.749 66.667 0.00 0.00 37.87 4.09
2882 2988 5.763876 AAGCTCTTTAATCCTACTGGTGT 57.236 39.130 0.00 0.00 34.23 4.16
2893 2999 8.253113 CCATGATAACCAACAAAGCTCTTTAAT 58.747 33.333 0.00 0.00 0.00 1.40
2894 3000 7.601856 CCATGATAACCAACAAAGCTCTTTAA 58.398 34.615 0.00 0.00 0.00 1.52
2895 3001 6.350110 GCCATGATAACCAACAAAGCTCTTTA 60.350 38.462 0.00 0.00 0.00 1.85
2896 3002 5.567423 GCCATGATAACCAACAAAGCTCTTT 60.567 40.000 0.00 0.00 0.00 2.52
2897 3003 4.082026 GCCATGATAACCAACAAAGCTCTT 60.082 41.667 0.00 0.00 0.00 2.85
2898 3004 3.445096 GCCATGATAACCAACAAAGCTCT 59.555 43.478 0.00 0.00 0.00 4.09
2899 3005 3.445096 AGCCATGATAACCAACAAAGCTC 59.555 43.478 0.00 0.00 0.00 4.09
2900 3006 3.434309 AGCCATGATAACCAACAAAGCT 58.566 40.909 0.00 0.00 0.00 3.74
2901 3007 3.731867 CGAGCCATGATAACCAACAAAGC 60.732 47.826 0.00 0.00 0.00 3.51
2902 3008 3.440173 ACGAGCCATGATAACCAACAAAG 59.560 43.478 0.00 0.00 0.00 2.77
2903 3009 3.417101 ACGAGCCATGATAACCAACAAA 58.583 40.909 0.00 0.00 0.00 2.83
2904 3010 3.066291 ACGAGCCATGATAACCAACAA 57.934 42.857 0.00 0.00 0.00 2.83
2905 3011 2.779755 ACGAGCCATGATAACCAACA 57.220 45.000 0.00 0.00 0.00 3.33
2906 3012 3.793559 ACTACGAGCCATGATAACCAAC 58.206 45.455 0.00 0.00 0.00 3.77
2907 3013 4.481368 AACTACGAGCCATGATAACCAA 57.519 40.909 0.00 0.00 0.00 3.67
2908 3014 4.188462 CAAACTACGAGCCATGATAACCA 58.812 43.478 0.00 0.00 0.00 3.67
2909 3015 4.189231 ACAAACTACGAGCCATGATAACC 58.811 43.478 0.00 0.00 0.00 2.85
2910 3016 4.026804 CGACAAACTACGAGCCATGATAAC 60.027 45.833 0.00 0.00 0.00 1.89
2911 3017 4.109766 CGACAAACTACGAGCCATGATAA 58.890 43.478 0.00 0.00 0.00 1.75
2912 3018 3.379057 TCGACAAACTACGAGCCATGATA 59.621 43.478 0.00 0.00 34.49 2.15
2913 3019 2.165641 TCGACAAACTACGAGCCATGAT 59.834 45.455 0.00 0.00 34.49 2.45
2914 3020 1.542472 TCGACAAACTACGAGCCATGA 59.458 47.619 0.00 0.00 34.49 3.07
2915 3021 1.920574 CTCGACAAACTACGAGCCATG 59.079 52.381 0.00 0.00 46.54 3.66
2916 3022 2.279582 CTCGACAAACTACGAGCCAT 57.720 50.000 0.00 0.00 46.54 4.40
2917 3023 3.786809 CTCGACAAACTACGAGCCA 57.213 52.632 0.00 0.00 46.54 4.75
2921 3027 0.870393 AGTCGCTCGACAAACTACGA 59.130 50.000 22.18 0.00 46.76 3.43
2922 3028 2.515641 TAGTCGCTCGACAAACTACG 57.484 50.000 22.18 0.00 46.76 3.51
2923 3029 3.790288 GGATTAGTCGCTCGACAAACTAC 59.210 47.826 22.18 9.50 46.76 2.73
2924 3030 3.441222 TGGATTAGTCGCTCGACAAACTA 59.559 43.478 22.18 9.79 46.76 2.24
2925 3031 2.230508 TGGATTAGTCGCTCGACAAACT 59.769 45.455 22.18 6.22 46.76 2.66
2926 3032 2.602878 TGGATTAGTCGCTCGACAAAC 58.397 47.619 22.18 13.07 46.76 2.93
2927 3033 3.119280 TCATGGATTAGTCGCTCGACAAA 60.119 43.478 22.18 8.89 46.76 2.83
2928 3034 2.425668 TCATGGATTAGTCGCTCGACAA 59.574 45.455 22.18 14.75 46.76 3.18
2929 3035 2.021457 TCATGGATTAGTCGCTCGACA 58.979 47.619 22.18 5.19 46.76 4.35
2930 3036 2.776312 TCATGGATTAGTCGCTCGAC 57.224 50.000 13.92 13.92 44.86 4.20
2931 3037 3.642705 CAATCATGGATTAGTCGCTCGA 58.357 45.455 0.00 0.00 30.44 4.04
2932 3038 2.156504 GCAATCATGGATTAGTCGCTCG 59.843 50.000 0.00 0.00 30.44 5.03
2933 3039 2.156504 CGCAATCATGGATTAGTCGCTC 59.843 50.000 0.00 0.00 30.44 5.03
2934 3040 2.138320 CGCAATCATGGATTAGTCGCT 58.862 47.619 0.00 0.00 30.44 4.93
2935 3041 1.398960 GCGCAATCATGGATTAGTCGC 60.399 52.381 0.30 12.81 37.32 5.19
2936 3042 1.195448 GGCGCAATCATGGATTAGTCG 59.805 52.381 10.83 0.00 30.44 4.18
2937 3043 1.195448 CGGCGCAATCATGGATTAGTC 59.805 52.381 10.83 0.00 30.44 2.59
2938 3044 1.229428 CGGCGCAATCATGGATTAGT 58.771 50.000 10.83 0.00 30.44 2.24
2939 3045 0.518636 CCGGCGCAATCATGGATTAG 59.481 55.000 10.83 0.00 30.44 1.73
2940 3046 1.514678 GCCGGCGCAATCATGGATTA 61.515 55.000 12.58 0.00 30.44 1.75
2941 3047 2.848858 GCCGGCGCAATCATGGATT 61.849 57.895 12.58 0.00 31.86 3.01
2942 3048 3.289834 GCCGGCGCAATCATGGAT 61.290 61.111 12.58 0.00 34.03 3.41
2945 3051 3.795280 CTTCGCCGGCGCAATCATG 62.795 63.158 42.78 23.15 39.59 3.07
2946 3052 3.576356 CTTCGCCGGCGCAATCAT 61.576 61.111 42.78 0.00 39.59 2.45
2947 3053 4.751093 TCTTCGCCGGCGCAATCA 62.751 61.111 42.78 24.14 39.59 2.57
2948 3054 3.440356 CTTCTTCGCCGGCGCAATC 62.440 63.158 42.78 3.78 39.59 2.67
2949 3055 3.499737 CTTCTTCGCCGGCGCAAT 61.500 61.111 42.78 0.00 39.59 3.56
2956 3062 2.954753 AAAGCACGCTTCTTCGCCG 61.955 57.895 4.46 0.00 34.84 6.46
2957 3063 2.946762 AAAGCACGCTTCTTCGCC 59.053 55.556 4.46 0.00 34.84 5.54


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

AutoCloner maintained by Alex Coulton.