Multiple sequence alignment - TraesCS7D01G019100

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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 TraesCS7D01G019100 chr7D 100.000 2907 0 0 1 2907 8374937 8377843 0.000000e+00 5369.0
1 TraesCS7D01G019100 chr7D 92.565 1587 97 9 1194 2778 8436055 8437622 0.000000e+00 2257.0
2 TraesCS7D01G019100 chr7D 88.000 850 59 19 1077 1907 8250451 8251276 0.000000e+00 965.0
3 TraesCS7D01G019100 chr7D 93.023 387 25 2 153 539 8433881 8434265 5.440000e-157 564.0
4 TraesCS7D01G019100 chr7D 86.056 251 27 5 1670 1915 7662962 7662715 2.220000e-66 263.0
5 TraesCS7D01G019100 chr7D 86.056 251 27 5 1670 1915 7681434 7681187 2.220000e-66 263.0
6 TraesCS7D01G019100 chr7D 80.124 161 21 8 1861 2010 7933543 7933383 3.060000e-20 110.0
7 TraesCS7D01G019100 chr7D 90.000 70 7 0 1932 2001 8084521 8084452 1.110000e-14 91.6
8 TraesCS7D01G019100 chr7D 94.643 56 3 0 2852 2907 65771592 65771647 1.440000e-13 87.9
9 TraesCS7D01G019100 chr7D 90.909 55 5 0 2853 2907 127694689 127694743 1.120000e-09 75.0
10 TraesCS7D01G019100 chr7A 91.677 1550 93 21 666 2193 8884324 8885859 0.000000e+00 2115.0
11 TraesCS7D01G019100 chr7A 92.636 1290 71 10 900 2184 8822992 8824262 0.000000e+00 1834.0
12 TraesCS7D01G019100 chr7A 85.478 1026 75 32 954 1910 8688624 8689644 0.000000e+00 1002.0
13 TraesCS7D01G019100 chr7A 95.327 214 6 2 666 875 8822131 8822344 1.290000e-88 337.0
14 TraesCS7D01G019100 chr7A 94.631 149 8 0 391 539 8804491 8804639 6.260000e-57 231.0
15 TraesCS7D01G019100 chr7A 95.726 117 2 1 536 652 8821964 8822077 4.950000e-43 185.0
16 TraesCS7D01G019100 chr7A 88.710 124 4 3 536 653 8884149 8884268 3.020000e-30 143.0
17 TraesCS7D01G019100 chr4A 87.394 1539 143 26 664 2191 731389077 731387579 0.000000e+00 1720.0
18 TraesCS7D01G019100 chr4A 92.427 1030 74 4 981 2007 731385374 731384346 0.000000e+00 1467.0
19 TraesCS7D01G019100 chr4A 92.897 535 38 0 1077 1611 731490504 731489970 0.000000e+00 778.0
20 TraesCS7D01G019100 chr4A 90.299 268 16 2 682 939 731385642 731385375 2.770000e-90 342.0
21 TraesCS7D01G019100 chr4A 80.889 225 29 6 268 485 731318082 731318299 6.440000e-37 165.0
22 TraesCS7D01G019100 chr4A 88.889 72 8 0 1930 2001 731740327 731740398 3.990000e-14 89.8
23 TraesCS7D01G019100 chr4A 85.714 63 8 1 2839 2901 546074800 546074861 6.720000e-07 65.8
24 TraesCS7D01G019100 chr5B 83.353 835 106 17 1084 1904 707173710 707174525 0.000000e+00 741.0
25 TraesCS7D01G019100 chr5B 93.902 164 9 1 1 163 15931743 15931580 2.240000e-61 246.0
26 TraesCS7D01G019100 chr6A 84.127 126 19 1 2217 2341 73659094 73659219 1.410000e-23 121.0
27 TraesCS7D01G019100 chr5D 96.364 55 2 0 2853 2907 65740681 65740735 1.110000e-14 91.6
28 TraesCS7D01G019100 chr2A 92.727 55 4 0 2853 2907 605797746 605797692 2.400000e-11 80.5
29 TraesCS7D01G019100 chr3D 92.157 51 3 1 2472 2521 385420452 385420502 1.450000e-08 71.3
30 TraesCS7D01G019100 chr1A 89.091 55 6 0 2853 2907 562136912 562136966 5.200000e-08 69.4
31 TraesCS7D01G019100 chr1B 93.023 43 3 0 113 155 668804109 668804151 2.420000e-06 63.9
32 TraesCS7D01G019100 chr2B 100.000 29 0 0 129 157 465758294 465758322 1.000000e-03 54.7


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 TraesCS7D01G019100 chr7D 8374937 8377843 2906 False 5369.000000 5369 100.0000 1 2907 1 chr7D.!!$F2 2906
1 TraesCS7D01G019100 chr7D 8433881 8437622 3741 False 1410.500000 2257 92.7940 153 2778 2 chr7D.!!$F5 2625
2 TraesCS7D01G019100 chr7D 8250451 8251276 825 False 965.000000 965 88.0000 1077 1907 1 chr7D.!!$F1 830
3 TraesCS7D01G019100 chr7A 8884149 8885859 1710 False 1129.000000 2115 90.1935 536 2193 2 chr7A.!!$F4 1657
4 TraesCS7D01G019100 chr7A 8688624 8689644 1020 False 1002.000000 1002 85.4780 954 1910 1 chr7A.!!$F1 956
5 TraesCS7D01G019100 chr7A 8821964 8824262 2298 False 785.333333 1834 94.5630 536 2184 3 chr7A.!!$F3 1648
6 TraesCS7D01G019100 chr4A 731384346 731389077 4731 True 1176.333333 1720 90.0400 664 2191 3 chr4A.!!$R2 1527
7 TraesCS7D01G019100 chr4A 731489970 731490504 534 True 778.000000 778 92.8970 1077 1611 1 chr4A.!!$R1 534
8 TraesCS7D01G019100 chr5B 707173710 707174525 815 False 741.000000 741 83.3530 1084 1904 1 chr5B.!!$F1 820

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
445 446 0.328258 AACAGGTGACATACTGGGGC 59.672 55.000 12.82 0.0 39.0 5.80 F
1630 6966 1.872234 CGTCGCTACACCACATCCG 60.872 63.158 0.00 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1640 6979 0.032515 TAATGGAGTCGGAGCAGGGA 60.033 55.0 0.0 0.0 0.0 4.20 R
2789 8157 0.109597 GCTGCCGTTTGATGGAGTTG 60.110 55.0 0.0 0.0 0.0 3.16 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
26 27 8.561738 TTGTATCAGTGAACCTTAAGATTTCC 57.438 34.615 3.36 1.66 0.00 3.13
27 28 7.110155 TGTATCAGTGAACCTTAAGATTTCCC 58.890 38.462 3.36 0.00 0.00 3.97
28 29 5.843019 TCAGTGAACCTTAAGATTTCCCT 57.157 39.130 3.36 0.35 0.00 4.20
29 30 5.560724 TCAGTGAACCTTAAGATTTCCCTG 58.439 41.667 16.38 16.38 0.00 4.45
30 31 5.309543 TCAGTGAACCTTAAGATTTCCCTGA 59.690 40.000 19.02 19.02 33.18 3.86
31 32 6.003950 CAGTGAACCTTAAGATTTCCCTGAA 58.996 40.000 17.05 0.00 29.21 3.02
32 33 6.660949 CAGTGAACCTTAAGATTTCCCTGAAT 59.339 38.462 17.05 0.00 29.21 2.57
33 34 7.829211 CAGTGAACCTTAAGATTTCCCTGAATA 59.171 37.037 17.05 0.00 29.21 1.75
34 35 8.390921 AGTGAACCTTAAGATTTCCCTGAATAA 58.609 33.333 3.36 0.00 0.00 1.40
35 36 9.190317 GTGAACCTTAAGATTTCCCTGAATAAT 57.810 33.333 3.36 0.00 0.00 1.28
65 66 9.926751 TGTTTGTGTTTATGCAAATTTATTGTG 57.073 25.926 0.00 0.00 37.02 3.33
66 67 9.928236 GTTTGTGTTTATGCAAATTTATTGTGT 57.072 25.926 0.00 0.00 37.02 3.72
77 78 9.317936 TGCAAATTTATTGTGTTTTATGTGACA 57.682 25.926 0.00 0.00 0.00 3.58
125 126 6.411630 TTTATCGTATAAATACATGGGCGC 57.588 37.500 0.00 0.00 32.87 6.53
126 127 2.330286 TCGTATAAATACATGGGCGCG 58.670 47.619 0.00 0.00 32.87 6.86
127 128 2.030096 TCGTATAAATACATGGGCGCGA 60.030 45.455 12.10 0.00 32.87 5.87
128 129 2.091588 CGTATAAATACATGGGCGCGAC 59.908 50.000 12.10 6.99 32.87 5.19
129 130 2.248280 ATAAATACATGGGCGCGACA 57.752 45.000 17.00 10.86 0.00 4.35
130 131 2.025589 TAAATACATGGGCGCGACAA 57.974 45.000 17.00 0.49 0.00 3.18
131 132 0.450184 AAATACATGGGCGCGACAAC 59.550 50.000 17.00 0.00 0.00 3.32
132 133 1.701545 AATACATGGGCGCGACAACG 61.702 55.000 17.00 0.00 42.93 4.10
148 149 4.633596 CGCGCGCCGTCAATGATC 62.634 66.667 27.72 0.00 0.00 2.92
149 150 3.264897 GCGCGCCGTCAATGATCT 61.265 61.111 23.24 0.00 0.00 2.75
150 151 1.949133 GCGCGCCGTCAATGATCTA 60.949 57.895 23.24 0.00 0.00 1.98
151 152 1.880601 GCGCGCCGTCAATGATCTAG 61.881 60.000 23.24 0.00 0.00 2.43
180 181 3.434940 AAAACTAGACCCAATCGGCTT 57.565 42.857 0.00 0.00 33.26 4.35
188 189 1.147473 CCCAATCGGCTTTTTGTTGC 58.853 50.000 0.00 0.00 0.00 4.17
232 233 5.450453 TGATCTTACCAACCCAAAAGAACA 58.550 37.500 0.00 0.00 32.13 3.18
249 250 6.949352 AAGAACATGAACAACAGACTCAAT 57.051 33.333 0.00 0.00 0.00 2.57
275 276 1.568025 GTTCACGTTGAAGACCGGC 59.432 57.895 0.00 0.00 37.00 6.13
309 310 1.538204 GCTGAAATCCGTATCGAGCCA 60.538 52.381 0.00 0.00 0.00 4.75
322 323 1.067060 TCGAGCCAGACGGTATTGATG 59.933 52.381 0.00 0.00 33.28 3.07
323 324 1.202417 CGAGCCAGACGGTATTGATGT 60.202 52.381 0.00 0.00 33.28 3.06
324 325 2.034179 CGAGCCAGACGGTATTGATGTA 59.966 50.000 0.00 0.00 33.28 2.29
367 368 7.173218 TCACACCAAAGACAAGATATTTCACTC 59.827 37.037 0.00 0.00 0.00 3.51
370 371 7.330946 CACCAAAGACAAGATATTTCACTCGTA 59.669 37.037 0.00 0.00 0.00 3.43
373 374 8.708742 CAAAGACAAGATATTTCACTCGTACAA 58.291 33.333 0.00 0.00 0.00 2.41
435 436 1.523758 GGGATGTGTGAACAGGTGAC 58.476 55.000 0.00 0.00 0.00 3.67
438 439 3.307410 GGGATGTGTGAACAGGTGACATA 60.307 47.826 0.00 0.00 0.00 2.29
445 446 0.328258 AACAGGTGACATACTGGGGC 59.672 55.000 12.82 0.00 39.00 5.80
451 452 4.041567 CAGGTGACATACTGGGGCATATTA 59.958 45.833 2.99 0.00 0.00 0.98
478 479 9.208022 CAATAGTGACTTTGTTTGACATCTCTA 57.792 33.333 0.00 0.00 0.00 2.43
1047 2759 2.307768 CCTCGAGCACTACCCATTCTA 58.692 52.381 6.99 0.00 0.00 2.10
1623 6959 2.181021 CAGGTCCGTCGCTACACC 59.819 66.667 0.00 0.00 0.00 4.16
1630 6966 1.872234 CGTCGCTACACCACATCCG 60.872 63.158 0.00 0.00 0.00 4.18
1640 6979 1.678635 CCACATCCGTGCATGGGTT 60.679 57.895 24.78 10.16 42.17 4.11
1668 7009 2.698797 TCCGACTCCATTATTCTCCACC 59.301 50.000 0.00 0.00 0.00 4.61
1709 7055 8.408043 AAAAACATCCATGATCTTGTTGTAGA 57.592 30.769 12.10 2.36 32.90 2.59
1943 7305 6.638096 TCGTGGGAATACTATCGTTGATTA 57.362 37.500 0.00 0.00 0.00 1.75
2054 7420 2.286184 CGCATTATGACCGCCTTGTTAC 60.286 50.000 0.00 0.00 0.00 2.50
2056 7422 2.747396 TTATGACCGCCTTGTTACGT 57.253 45.000 0.00 0.00 0.00 3.57
2082 7448 6.470235 GCATTGTAGGAAATGAAACAATCTCG 59.530 38.462 1.22 0.00 39.80 4.04
2090 7456 0.095417 GAAACAATCTCGTCGCCAGC 59.905 55.000 0.00 0.00 0.00 4.85
2124 7491 5.001232 CGTTATGGGGAAGAAAACTCTTCA 58.999 41.667 14.91 0.00 45.76 3.02
2251 7618 1.693103 GGGCCCAGTACCCTTAGCT 60.693 63.158 19.95 0.00 44.68 3.32
2257 7624 2.168728 CCCAGTACCCTTAGCTGAGAAC 59.831 54.545 7.16 2.58 32.39 3.01
2271 7638 3.390135 CTGAGAACTACACTCGGCAAAA 58.610 45.455 0.00 0.00 37.22 2.44
2273 7640 5.142061 TGAGAACTACACTCGGCAAAATA 57.858 39.130 0.00 0.00 37.22 1.40
2277 7644 5.812642 AGAACTACACTCGGCAAAATATCTG 59.187 40.000 0.00 0.00 0.00 2.90
2298 7665 1.533625 CGAGTGGGAAATGGCTTTCA 58.466 50.000 10.23 0.00 42.17 2.69
2300 7667 1.546029 GAGTGGGAAATGGCTTTCACC 59.454 52.381 8.52 8.52 43.00 4.02
2301 7668 1.133199 AGTGGGAAATGGCTTTCACCA 60.133 47.619 8.52 10.27 43.00 4.17
2341 7708 4.530946 AGGAAACTCCGAAATTCCAGTAGA 59.469 41.667 12.24 0.00 44.08 2.59
2354 7721 3.472652 TCCAGTAGAACGTGTTGCAAAT 58.527 40.909 0.00 0.00 0.00 2.32
2355 7722 3.880490 TCCAGTAGAACGTGTTGCAAATT 59.120 39.130 0.00 0.00 0.00 1.82
2369 7736 4.235939 TGCAAATTACTGAACGCAACAT 57.764 36.364 0.00 0.00 0.00 2.71
2370 7737 5.363979 TGCAAATTACTGAACGCAACATA 57.636 34.783 0.00 0.00 0.00 2.29
2435 7802 2.436646 GCAAAGGCCTAGCGAGCA 60.437 61.111 5.16 0.00 0.00 4.26
2452 7819 1.873591 AGCAGATCGGACACACAAAAC 59.126 47.619 0.00 0.00 0.00 2.43
2531 7898 0.698238 ACTTGTTGCCAGGGCTCATA 59.302 50.000 12.19 0.00 42.51 2.15
2547 7914 2.557056 CTCATAATGCAGATTGGGCAGG 59.443 50.000 0.00 0.00 45.68 4.85
2552 7919 1.303561 GCAGATTGGGCAGGTGTCA 60.304 57.895 0.00 0.00 0.00 3.58
2627 7995 1.523934 GCAAAACACTGAGCACAATGC 59.476 47.619 0.00 0.00 45.46 3.56
2674 8042 1.140852 CAAATCGGATGGCTGTAGGGA 59.859 52.381 0.00 0.00 0.00 4.20
2677 8045 1.048724 TCGGATGGCTGTAGGGAAGG 61.049 60.000 0.00 0.00 0.00 3.46
2680 8048 1.564348 GGATGGCTGTAGGGAAGGAAA 59.436 52.381 0.00 0.00 0.00 3.13
2736 8104 2.565841 AGACTTGTCTTTCAAAGCGCT 58.434 42.857 2.64 2.64 35.48 5.92
2739 8107 2.682856 ACTTGTCTTTCAAAGCGCTGAA 59.317 40.909 12.58 9.73 35.48 3.02
2747 8115 3.135414 TCAAAGCGCTGAATGCAATAC 57.865 42.857 12.58 0.00 43.06 1.89
2751 8119 1.528586 AGCGCTGAATGCAATACGATC 59.471 47.619 10.39 0.00 43.06 3.69
2767 8135 0.455005 GATCCTTGCTGCAAAGGCTC 59.545 55.000 16.74 15.27 45.49 4.70
2780 8148 2.125753 GGCTCAGAGGCTCACGTG 60.126 66.667 18.26 9.94 37.85 4.49
2781 8149 2.125753 GCTCAGAGGCTCACGTGG 60.126 66.667 18.26 7.71 0.00 4.94
2782 8150 2.936912 GCTCAGAGGCTCACGTGGT 61.937 63.158 18.26 0.00 0.00 4.16
2783 8151 1.668294 CTCAGAGGCTCACGTGGTT 59.332 57.895 18.26 0.00 0.00 3.67
2784 8152 0.668706 CTCAGAGGCTCACGTGGTTG 60.669 60.000 18.26 7.69 0.00 3.77
2785 8153 1.069765 CAGAGGCTCACGTGGTTGT 59.930 57.895 18.26 0.00 0.00 3.32
2786 8154 1.069765 AGAGGCTCACGTGGTTGTG 59.930 57.895 18.26 2.62 41.28 3.33
2787 8155 2.591715 AGGCTCACGTGGTTGTGC 60.592 61.111 17.00 11.97 39.73 4.57
2788 8156 2.899838 GGCTCACGTGGTTGTGCA 60.900 61.111 17.00 0.00 39.73 4.57
2789 8157 2.327940 GCTCACGTGGTTGTGCAC 59.672 61.111 17.00 10.75 39.73 4.57
2790 8158 2.468670 GCTCACGTGGTTGTGCACA 61.469 57.895 17.42 17.42 39.73 4.57
2791 8159 1.987704 GCTCACGTGGTTGTGCACAA 61.988 55.000 27.96 27.96 39.73 3.33
2802 8170 3.435105 TTGTGCACAACTCCATCAAAC 57.565 42.857 27.96 0.00 0.00 2.93
2803 8171 1.333308 TGTGCACAACTCCATCAAACG 59.667 47.619 19.28 0.00 0.00 3.60
2804 8172 0.950836 TGCACAACTCCATCAAACGG 59.049 50.000 0.00 0.00 0.00 4.44
2805 8173 0.387239 GCACAACTCCATCAAACGGC 60.387 55.000 0.00 0.00 0.00 5.68
2806 8174 0.950836 CACAACTCCATCAAACGGCA 59.049 50.000 0.00 0.00 0.00 5.69
2807 8175 1.069022 CACAACTCCATCAAACGGCAG 60.069 52.381 0.00 0.00 0.00 4.85
2808 8176 0.109597 CAACTCCATCAAACGGCAGC 60.110 55.000 0.00 0.00 0.00 5.25
2809 8177 1.244019 AACTCCATCAAACGGCAGCC 61.244 55.000 0.00 0.00 0.00 4.85
2810 8178 2.361104 TCCATCAAACGGCAGCCC 60.361 61.111 5.63 0.00 0.00 5.19
2811 8179 2.676121 CCATCAAACGGCAGCCCA 60.676 61.111 5.63 0.00 0.00 5.36
2812 8180 2.703798 CCATCAAACGGCAGCCCAG 61.704 63.158 5.63 0.00 0.00 4.45
2813 8181 2.361610 ATCAAACGGCAGCCCAGG 60.362 61.111 5.63 0.00 0.00 4.45
2824 8192 4.162690 GCCCAGGCGGTCGATCTT 62.163 66.667 0.00 0.00 0.00 2.40
2825 8193 2.584608 CCCAGGCGGTCGATCTTT 59.415 61.111 0.00 0.00 0.00 2.52
2826 8194 1.078426 CCCAGGCGGTCGATCTTTT 60.078 57.895 0.00 0.00 0.00 2.27
2827 8195 1.090052 CCCAGGCGGTCGATCTTTTC 61.090 60.000 0.00 0.00 0.00 2.29
2828 8196 0.391130 CCAGGCGGTCGATCTTTTCA 60.391 55.000 0.00 0.00 0.00 2.69
2829 8197 1.656652 CAGGCGGTCGATCTTTTCAT 58.343 50.000 0.00 0.00 0.00 2.57
2830 8198 2.483013 CCAGGCGGTCGATCTTTTCATA 60.483 50.000 0.00 0.00 0.00 2.15
2831 8199 2.797156 CAGGCGGTCGATCTTTTCATAG 59.203 50.000 0.00 0.00 0.00 2.23
2832 8200 1.527311 GGCGGTCGATCTTTTCATAGC 59.473 52.381 0.00 0.00 0.00 2.97
2833 8201 2.201732 GCGGTCGATCTTTTCATAGCA 58.798 47.619 0.00 0.00 0.00 3.49
2834 8202 2.802816 GCGGTCGATCTTTTCATAGCAT 59.197 45.455 0.00 0.00 0.00 3.79
2835 8203 3.363378 GCGGTCGATCTTTTCATAGCATG 60.363 47.826 0.00 0.00 0.00 4.06
2836 8204 3.185188 CGGTCGATCTTTTCATAGCATGG 59.815 47.826 0.00 0.00 0.00 3.66
2837 8205 4.380531 GGTCGATCTTTTCATAGCATGGA 58.619 43.478 0.00 0.00 0.00 3.41
2838 8206 4.212214 GGTCGATCTTTTCATAGCATGGAC 59.788 45.833 0.00 0.00 0.00 4.02
2839 8207 4.811024 GTCGATCTTTTCATAGCATGGACA 59.189 41.667 0.00 0.00 0.00 4.02
2840 8208 5.468072 GTCGATCTTTTCATAGCATGGACAT 59.532 40.000 0.00 0.00 0.00 3.06
2841 8209 6.646653 GTCGATCTTTTCATAGCATGGACATA 59.353 38.462 0.00 0.00 0.00 2.29
2842 8210 7.332926 GTCGATCTTTTCATAGCATGGACATAT 59.667 37.037 0.00 0.00 0.00 1.78
2843 8211 7.879677 TCGATCTTTTCATAGCATGGACATATT 59.120 33.333 0.00 0.00 0.00 1.28
2844 8212 9.154847 CGATCTTTTCATAGCATGGACATATTA 57.845 33.333 0.00 0.00 0.00 0.98
2875 8243 3.460857 GAGCATCTCCAATAGACGGTT 57.539 47.619 0.00 0.00 36.93 4.44
2876 8244 3.385577 GAGCATCTCCAATAGACGGTTC 58.614 50.000 0.00 0.00 36.93 3.62
2877 8245 2.766263 AGCATCTCCAATAGACGGTTCA 59.234 45.455 0.00 0.00 36.93 3.18
2878 8246 3.389329 AGCATCTCCAATAGACGGTTCAT 59.611 43.478 0.00 0.00 36.93 2.57
2879 8247 4.588951 AGCATCTCCAATAGACGGTTCATA 59.411 41.667 0.00 0.00 36.93 2.15
2880 8248 4.686554 GCATCTCCAATAGACGGTTCATAC 59.313 45.833 0.00 0.00 36.93 2.39
2881 8249 4.563337 TCTCCAATAGACGGTTCATACG 57.437 45.455 0.00 0.00 37.36 3.06
2883 8251 5.125356 TCTCCAATAGACGGTTCATACGTA 58.875 41.667 0.00 0.00 45.68 3.57
2884 8252 5.589855 TCTCCAATAGACGGTTCATACGTAA 59.410 40.000 0.00 0.00 45.68 3.18
2885 8253 6.095300 TCTCCAATAGACGGTTCATACGTAAA 59.905 38.462 0.00 0.00 45.68 2.01
2886 8254 6.629128 TCCAATAGACGGTTCATACGTAAAA 58.371 36.000 0.00 0.00 45.68 1.52
2887 8255 7.095910 TCCAATAGACGGTTCATACGTAAAAA 58.904 34.615 0.00 0.00 45.68 1.94
2888 8256 7.765360 TCCAATAGACGGTTCATACGTAAAAAT 59.235 33.333 0.00 0.00 45.68 1.82
2889 8257 9.033481 CCAATAGACGGTTCATACGTAAAAATA 57.967 33.333 0.00 0.00 45.68 1.40
2892 8260 7.294676 AGACGGTTCATACGTAAAAATAACC 57.705 36.000 0.00 8.33 45.68 2.85
2893 8261 6.873076 AGACGGTTCATACGTAAAAATAACCA 59.127 34.615 19.19 0.00 45.68 3.67
2894 8262 7.387397 AGACGGTTCATACGTAAAAATAACCAA 59.613 33.333 19.19 0.00 45.68 3.67
2895 8263 8.042944 ACGGTTCATACGTAAAAATAACCAAT 57.957 30.769 19.19 9.95 43.60 3.16
2896 8264 8.513774 ACGGTTCATACGTAAAAATAACCAATT 58.486 29.630 19.19 7.59 43.60 2.32
2897 8265 9.344309 CGGTTCATACGTAAAAATAACCAATTT 57.656 29.630 19.19 0.00 39.56 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.010029 GGAAATCTTAAGGTTCACTGATACAAA 57.990 33.333 16.70 0.00 0.00 2.83
2 3 7.037586 AGGGAAATCTTAAGGTTCACTGATACA 60.038 37.037 18.36 0.00 33.75 2.29
3 4 7.339482 AGGGAAATCTTAAGGTTCACTGATAC 58.661 38.462 18.36 0.00 33.75 2.24
4 5 7.510675 AGGGAAATCTTAAGGTTCACTGATA 57.489 36.000 18.36 0.00 33.75 2.15
6 7 5.843019 AGGGAAATCTTAAGGTTCACTGA 57.157 39.130 18.36 0.00 33.75 3.41
7 8 5.886960 CAGGGAAATCTTAAGGTTCACTG 57.113 43.478 25.02 25.02 44.05 3.66
8 9 5.843019 TCAGGGAAATCTTAAGGTTCACT 57.157 39.130 15.10 15.10 35.37 3.41
9 10 8.575649 TTATTCAGGGAAATCTTAAGGTTCAC 57.424 34.615 16.70 14.42 0.00 3.18
39 40 9.926751 CACAATAAATTTGCATAAACACAAACA 57.073 25.926 0.00 0.00 0.00 2.83
40 41 9.928236 ACACAATAAATTTGCATAAACACAAAC 57.072 25.926 0.00 0.00 0.00 2.93
51 52 9.317936 TGTCACATAAAACACAATAAATTTGCA 57.682 25.926 0.00 0.00 0.00 4.08
99 100 7.966204 GCGCCCATGTATTTATACGATAAAATT 59.034 33.333 0.00 0.00 36.06 1.82
100 101 7.469260 GCGCCCATGTATTTATACGATAAAAT 58.531 34.615 0.00 0.00 36.06 1.82
101 102 6.401260 CGCGCCCATGTATTTATACGATAAAA 60.401 38.462 0.00 0.00 36.06 1.52
102 103 5.062433 CGCGCCCATGTATTTATACGATAAA 59.938 40.000 0.00 0.00 36.06 1.40
103 104 4.563580 CGCGCCCATGTATTTATACGATAA 59.436 41.667 0.00 0.00 36.06 1.75
104 105 4.106909 CGCGCCCATGTATTTATACGATA 58.893 43.478 0.00 0.00 36.06 2.92
105 106 2.927477 CGCGCCCATGTATTTATACGAT 59.073 45.455 0.00 0.00 36.06 3.73
106 107 2.030096 TCGCGCCCATGTATTTATACGA 60.030 45.455 0.00 0.00 36.06 3.43
107 108 2.091588 GTCGCGCCCATGTATTTATACG 59.908 50.000 0.00 0.00 36.06 3.06
108 109 3.061322 TGTCGCGCCCATGTATTTATAC 58.939 45.455 0.00 0.00 0.00 1.47
109 110 3.388345 TGTCGCGCCCATGTATTTATA 57.612 42.857 0.00 0.00 0.00 0.98
110 111 2.248280 TGTCGCGCCCATGTATTTAT 57.752 45.000 0.00 0.00 0.00 1.40
111 112 1.666700 GTTGTCGCGCCCATGTATTTA 59.333 47.619 0.00 0.00 0.00 1.40
112 113 0.450184 GTTGTCGCGCCCATGTATTT 59.550 50.000 0.00 0.00 0.00 1.40
113 114 1.701545 CGTTGTCGCGCCCATGTATT 61.702 55.000 0.00 0.00 0.00 1.89
114 115 2.171079 CGTTGTCGCGCCCATGTAT 61.171 57.895 0.00 0.00 0.00 2.29
115 116 2.811747 CGTTGTCGCGCCCATGTA 60.812 61.111 0.00 0.00 0.00 2.29
131 132 4.633596 GATCATTGACGGCGCGCG 62.634 66.667 28.44 28.44 0.00 6.86
132 133 1.880601 CTAGATCATTGACGGCGCGC 61.881 60.000 25.94 25.94 0.00 6.86
133 134 0.595053 ACTAGATCATTGACGGCGCG 60.595 55.000 6.90 0.00 0.00 6.86
134 135 2.287668 ACTACTAGATCATTGACGGCGC 60.288 50.000 6.90 0.00 0.00 6.53
135 136 3.627732 ACTACTAGATCATTGACGGCG 57.372 47.619 4.80 4.80 0.00 6.46
136 137 9.472361 TTTAATAACTACTAGATCATTGACGGC 57.528 33.333 0.00 0.00 0.00 5.68
150 151 9.813446 CGATTGGGTCTAGTTTTAATAACTACT 57.187 33.333 0.00 0.00 0.00 2.57
151 152 9.038803 CCGATTGGGTCTAGTTTTAATAACTAC 57.961 37.037 0.00 0.00 0.00 2.73
180 181 1.149101 AGGAGGAGGAGGCAACAAAA 58.851 50.000 0.00 0.00 41.41 2.44
188 189 3.577848 CAGATCACAATAGGAGGAGGAGG 59.422 52.174 0.00 0.00 0.00 4.30
232 233 6.348786 CCAAATCGATTGAGTCTGTTGTTCAT 60.349 38.462 12.25 0.00 41.85 2.57
249 250 3.246699 GTCTTCAACGTGAACCAAATCGA 59.753 43.478 0.00 0.00 32.21 3.59
290 291 2.034685 TCTGGCTCGATACGGATTTCAG 59.965 50.000 0.00 0.00 0.00 3.02
292 293 2.395654 GTCTGGCTCGATACGGATTTC 58.604 52.381 1.91 0.00 0.00 2.17
309 310 5.416271 ACCAGTTTACATCAATACCGTCT 57.584 39.130 0.00 0.00 0.00 4.18
322 323 6.293244 GGTGTGAGTGTTGATTACCAGTTTAC 60.293 42.308 0.00 0.00 0.00 2.01
323 324 5.761234 GGTGTGAGTGTTGATTACCAGTTTA 59.239 40.000 0.00 0.00 0.00 2.01
324 325 4.578928 GGTGTGAGTGTTGATTACCAGTTT 59.421 41.667 0.00 0.00 0.00 2.66
398 399 1.212935 CCCCAGTTCCATTCCTAGTGG 59.787 57.143 0.00 0.00 38.11 4.00
402 403 2.509548 CACATCCCCAGTTCCATTCCTA 59.490 50.000 0.00 0.00 0.00 2.94
435 436 7.334421 GTCACTATTGTAATATGCCCCAGTATG 59.666 40.741 0.00 0.00 0.00 2.39
438 439 5.369699 AGTCACTATTGTAATATGCCCCAGT 59.630 40.000 0.00 0.00 0.00 4.00
451 452 7.716998 AGAGATGTCAAACAAAGTCACTATTGT 59.283 33.333 0.00 0.97 41.31 2.71
494 495 8.657074 ACGTTTACATTGCTAGCTGATAATAA 57.343 30.769 17.23 9.13 0.00 1.40
612 691 6.377780 CATGATACGACCATGTTTTGAACAA 58.622 36.000 0.00 0.00 45.86 2.83
613 692 5.618863 GCATGATACGACCATGTTTTGAACA 60.619 40.000 0.00 0.00 46.94 3.18
614 693 4.793216 GCATGATACGACCATGTTTTGAAC 59.207 41.667 0.00 0.00 42.39 3.18
1640 6979 0.032515 TAATGGAGTCGGAGCAGGGA 60.033 55.000 0.00 0.00 0.00 4.20
1668 7009 3.623960 TGTTTTTACTCACAGGGTTCACG 59.376 43.478 0.00 0.00 0.00 4.35
1943 7305 6.947733 TCATCACCAAATTAACTCTTCCATGT 59.052 34.615 0.00 0.00 0.00 3.21
2041 7407 1.296056 ATGCACGTAACAAGGCGGTC 61.296 55.000 0.00 0.00 0.00 4.79
2054 7420 4.793071 TGTTTCATTTCCTACAATGCACG 58.207 39.130 0.00 0.00 34.58 5.34
2056 7422 7.230849 AGATTGTTTCATTTCCTACAATGCA 57.769 32.000 0.00 0.00 40.29 3.96
2082 7448 1.276844 GCAATATCGTGCTGGCGAC 59.723 57.895 0.00 0.00 43.99 5.19
2090 7456 1.804151 CCCCATAACGGCAATATCGTG 59.196 52.381 0.00 0.00 40.96 4.35
2124 7491 9.127277 TCCAAGCAGTTATAAACTTAACAAAGT 57.873 29.630 0.00 0.00 40.46 2.66
2168 7535 1.871676 GGTTGACGGGAAGTGTTTCTC 59.128 52.381 0.00 0.00 33.68 2.87
2251 7618 3.462483 TTTTGCCGAGTGTAGTTCTCA 57.538 42.857 0.00 0.00 32.79 3.27
2257 7624 4.458951 GCAGATATTTTGCCGAGTGTAG 57.541 45.455 2.61 0.00 35.54 2.74
2271 7638 2.224621 CCATTTCCCACTCGGCAGATAT 60.225 50.000 0.00 0.00 0.00 1.63
2273 7640 0.107017 CCATTTCCCACTCGGCAGAT 60.107 55.000 0.00 0.00 0.00 2.90
2277 7644 1.250840 AAAGCCATTTCCCACTCGGC 61.251 55.000 0.00 0.00 43.31 5.54
2298 7665 4.165372 TCCTGAGTACCAGAAAAACTTGGT 59.835 41.667 11.58 1.44 45.78 3.67
2300 7667 6.318900 AGTTTCCTGAGTACCAGAAAAACTTG 59.681 38.462 21.92 6.45 45.59 3.16
2301 7668 6.424032 AGTTTCCTGAGTACCAGAAAAACTT 58.576 36.000 21.92 14.50 45.59 2.66
2341 7708 4.032355 CGTTCAGTAATTTGCAACACGTT 58.968 39.130 0.00 0.00 0.00 3.99
2354 7721 3.670625 AGCCTTATGTTGCGTTCAGTAA 58.329 40.909 0.00 0.00 0.00 2.24
2355 7722 3.328382 AGCCTTATGTTGCGTTCAGTA 57.672 42.857 0.00 0.00 0.00 2.74
2385 7752 4.032960 TGTTGCTTCTCTCTCTCTCTCT 57.967 45.455 0.00 0.00 0.00 3.10
2386 7753 4.398988 TCATGTTGCTTCTCTCTCTCTCTC 59.601 45.833 0.00 0.00 0.00 3.20
2387 7754 4.343231 TCATGTTGCTTCTCTCTCTCTCT 58.657 43.478 0.00 0.00 0.00 3.10
2388 7755 4.440525 CCTCATGTTGCTTCTCTCTCTCTC 60.441 50.000 0.00 0.00 0.00 3.20
2435 7802 4.974368 TTTTGTTTTGTGTGTCCGATCT 57.026 36.364 0.00 0.00 0.00 2.75
2452 7819 2.219216 CGCAATGCCTGAACTGTTTTTG 59.781 45.455 0.00 0.00 0.00 2.44
2531 7898 0.251922 ACACCTGCCCAATCTGCATT 60.252 50.000 0.00 0.00 38.22 3.56
2627 7995 3.181530 CCAAGTATTCGCAACAAGTCTCG 60.182 47.826 0.00 0.00 0.00 4.04
2692 8060 5.916318 TGTTGCAATCTCTGGACAATTTTT 58.084 33.333 0.59 0.00 0.00 1.94
2693 8061 5.534207 TGTTGCAATCTCTGGACAATTTT 57.466 34.783 0.59 0.00 0.00 1.82
2694 8062 5.302568 TCTTGTTGCAATCTCTGGACAATTT 59.697 36.000 0.59 0.00 0.00 1.82
2695 8063 4.828939 TCTTGTTGCAATCTCTGGACAATT 59.171 37.500 0.59 0.00 0.00 2.32
2696 8064 4.217118 GTCTTGTTGCAATCTCTGGACAAT 59.783 41.667 0.59 0.00 0.00 2.71
2697 8065 3.565482 GTCTTGTTGCAATCTCTGGACAA 59.435 43.478 0.59 0.00 0.00 3.18
2701 8069 3.567164 ACAAGTCTTGTTGCAATCTCTGG 59.433 43.478 12.62 0.00 42.22 3.86
2747 8115 1.138247 GCCTTTGCAGCAAGGATCG 59.862 57.895 19.41 3.42 37.47 3.69
2751 8119 0.892358 TCTGAGCCTTTGCAGCAAGG 60.892 55.000 12.15 12.15 41.13 3.61
2767 8135 1.069765 ACAACCACGTGAGCCTCTG 59.930 57.895 19.30 7.00 0.00 3.35
2774 8142 4.303257 TTGTGCACAACCACGTGA 57.697 50.000 27.96 3.56 39.34 4.35
2782 8150 2.223456 CGTTTGATGGAGTTGTGCACAA 60.223 45.455 27.96 27.96 0.00 3.33
2783 8151 1.333308 CGTTTGATGGAGTTGTGCACA 59.667 47.619 17.42 17.42 0.00 4.57
2784 8152 1.334960 CCGTTTGATGGAGTTGTGCAC 60.335 52.381 10.75 10.75 0.00 4.57
2785 8153 0.950836 CCGTTTGATGGAGTTGTGCA 59.049 50.000 0.00 0.00 0.00 4.57
2786 8154 0.387239 GCCGTTTGATGGAGTTGTGC 60.387 55.000 0.00 0.00 0.00 4.57
2787 8155 0.950836 TGCCGTTTGATGGAGTTGTG 59.049 50.000 0.00 0.00 0.00 3.33
2788 8156 1.238439 CTGCCGTTTGATGGAGTTGT 58.762 50.000 0.00 0.00 0.00 3.32
2789 8157 0.109597 GCTGCCGTTTGATGGAGTTG 60.110 55.000 0.00 0.00 0.00 3.16
2790 8158 1.244019 GGCTGCCGTTTGATGGAGTT 61.244 55.000 1.35 0.00 0.00 3.01
2791 8159 1.675641 GGCTGCCGTTTGATGGAGT 60.676 57.895 1.35 0.00 0.00 3.85
2792 8160 2.409870 GGGCTGCCGTTTGATGGAG 61.410 63.158 13.40 0.00 0.00 3.86
2793 8161 2.361104 GGGCTGCCGTTTGATGGA 60.361 61.111 13.40 0.00 0.00 3.41
2794 8162 2.676121 TGGGCTGCCGTTTGATGG 60.676 61.111 13.40 0.00 0.00 3.51
2795 8163 2.703798 CCTGGGCTGCCGTTTGATG 61.704 63.158 13.40 0.00 0.00 3.07
2796 8164 2.361610 CCTGGGCTGCCGTTTGAT 60.362 61.111 13.40 0.00 0.00 2.57
2805 8173 4.899239 GATCGACCGCCTGGGCTG 62.899 72.222 10.04 5.78 43.41 4.85
2807 8175 3.682292 AAAGATCGACCGCCTGGGC 62.682 63.158 0.82 0.82 41.42 5.36
2808 8176 1.078426 AAAAGATCGACCGCCTGGG 60.078 57.895 0.00 0.00 40.75 4.45
2809 8177 0.391130 TGAAAAGATCGACCGCCTGG 60.391 55.000 0.00 0.00 42.84 4.45
2810 8178 1.656652 ATGAAAAGATCGACCGCCTG 58.343 50.000 0.00 0.00 0.00 4.85
2811 8179 2.803492 GCTATGAAAAGATCGACCGCCT 60.803 50.000 0.00 0.00 0.00 5.52
2812 8180 1.527311 GCTATGAAAAGATCGACCGCC 59.473 52.381 0.00 0.00 0.00 6.13
2813 8181 2.201732 TGCTATGAAAAGATCGACCGC 58.798 47.619 0.00 0.00 0.00 5.68
2814 8182 3.185188 CCATGCTATGAAAAGATCGACCG 59.815 47.826 0.00 0.00 0.00 4.79
2815 8183 4.212214 GTCCATGCTATGAAAAGATCGACC 59.788 45.833 0.00 0.00 0.00 4.79
2816 8184 4.811024 TGTCCATGCTATGAAAAGATCGAC 59.189 41.667 0.00 0.00 0.00 4.20
2817 8185 5.022282 TGTCCATGCTATGAAAAGATCGA 57.978 39.130 0.00 0.00 0.00 3.59
2818 8186 5.936686 ATGTCCATGCTATGAAAAGATCG 57.063 39.130 0.00 0.00 0.00 3.69
2845 8213 9.988815 GTCTATTGGAGATGCTCTTATTTTAGA 57.011 33.333 0.00 0.00 36.29 2.10
2846 8214 8.920665 CGTCTATTGGAGATGCTCTTATTTTAG 58.079 37.037 0.00 0.00 36.29 1.85
2847 8215 7.872993 CCGTCTATTGGAGATGCTCTTATTTTA 59.127 37.037 0.00 0.00 39.57 1.52
2848 8216 6.708054 CCGTCTATTGGAGATGCTCTTATTTT 59.292 38.462 0.00 0.00 39.57 1.82
2849 8217 6.183361 ACCGTCTATTGGAGATGCTCTTATTT 60.183 38.462 0.00 0.00 39.57 1.40
2850 8218 5.305644 ACCGTCTATTGGAGATGCTCTTATT 59.694 40.000 0.00 0.00 39.57 1.40
2851 8219 4.835615 ACCGTCTATTGGAGATGCTCTTAT 59.164 41.667 0.00 0.00 39.57 1.73
2852 8220 4.215908 ACCGTCTATTGGAGATGCTCTTA 58.784 43.478 0.00 0.00 39.57 2.10
2853 8221 3.034635 ACCGTCTATTGGAGATGCTCTT 58.965 45.455 0.00 0.00 39.57 2.85
2854 8222 2.672098 ACCGTCTATTGGAGATGCTCT 58.328 47.619 0.00 0.00 39.57 4.09
2855 8223 3.181475 TGAACCGTCTATTGGAGATGCTC 60.181 47.826 0.00 0.00 39.57 4.26
2856 8224 2.766263 TGAACCGTCTATTGGAGATGCT 59.234 45.455 0.00 0.00 39.57 3.79
2857 8225 3.179443 TGAACCGTCTATTGGAGATGC 57.821 47.619 0.00 0.00 39.57 3.91
2858 8226 4.917998 CGTATGAACCGTCTATTGGAGATG 59.082 45.833 0.00 0.00 40.46 2.90
2859 8227 4.583489 ACGTATGAACCGTCTATTGGAGAT 59.417 41.667 0.00 0.00 36.29 2.75
2860 8228 3.949754 ACGTATGAACCGTCTATTGGAGA 59.050 43.478 0.00 0.00 31.97 3.71
2861 8229 4.303086 ACGTATGAACCGTCTATTGGAG 57.697 45.455 0.00 0.00 31.97 3.86
2862 8230 5.833406 TTACGTATGAACCGTCTATTGGA 57.167 39.130 0.00 0.00 39.60 3.53
2863 8231 6.890663 TTTTACGTATGAACCGTCTATTGG 57.109 37.500 0.00 0.00 39.60 3.16
2866 8234 9.034544 GGTTATTTTTACGTATGAACCGTCTAT 57.965 33.333 0.00 0.00 39.60 1.98
2867 8235 8.031864 TGGTTATTTTTACGTATGAACCGTCTA 58.968 33.333 0.00 0.00 38.13 2.59
2868 8236 6.873076 TGGTTATTTTTACGTATGAACCGTCT 59.127 34.615 0.00 0.00 38.13 4.18
2869 8237 7.059448 TGGTTATTTTTACGTATGAACCGTC 57.941 36.000 0.00 0.00 38.13 4.79
2870 8238 7.432350 TTGGTTATTTTTACGTATGAACCGT 57.568 32.000 0.00 0.00 38.13 4.83
2871 8239 8.898983 AATTGGTTATTTTTACGTATGAACCG 57.101 30.769 0.00 0.00 38.13 4.44


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

AutoCloner maintained by Alex Coulton.