Multiple sequence alignment - TraesCS1B01G380000

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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 TraesCS1B01G380000 chr1B 100.000 3444 0 0 1 3444 613019679 613023122 0.000000e+00 6360
1 TraesCS1B01G380000 chr1D 89.607 2569 165 38 15 2509 447549157 447551697 0.000000e+00 3171
2 TraesCS1B01G380000 chr1D 87.500 120 12 2 2440 2556 447551701 447551820 6.000000e-28 135
3 TraesCS1B01G380000 chr1A 91.600 2238 115 28 373 2569 543633659 543635864 0.000000e+00 3024
4 TraesCS1B01G380000 chr1A 80.890 921 101 29 2564 3444 323262871 323261986 0.000000e+00 656
5 TraesCS1B01G380000 chr6A 92.195 205 16 0 3010 3214 591182012 591182216 1.210000e-74 291
6 TraesCS1B01G380000 chr6A 91.220 205 18 0 3010 3214 591103677 591103881 2.620000e-71 279
7 TraesCS1B01G380000 chr6A 90.732 205 19 0 3010 3214 591127411 591127615 1.220000e-69 274
8 TraesCS1B01G380000 chr6A 90.732 205 19 0 3010 3214 591128738 591128942 1.220000e-69 274
9 TraesCS1B01G380000 chr6A 76.781 379 56 18 2570 2939 162908915 162908560 2.110000e-42 183
10 TraesCS1B01G380000 chr4A 92.778 180 10 1 3268 3444 483383045 483383224 1.230000e-64 257
11 TraesCS1B01G380000 chr4A 91.908 173 14 0 3272 3444 455302937 455302765 3.430000e-60 243
12 TraesCS1B01G380000 chr4A 92.308 169 12 1 3079 3247 483382810 483382977 4.440000e-59 239
13 TraesCS1B01G380000 chr4D 93.491 169 10 1 3079 3247 95877270 95877103 2.050000e-62 250
14 TraesCS1B01G380000 chr4D 90.960 177 16 0 3268 3444 95877035 95876859 4.440000e-59 239
15 TraesCS1B01G380000 chr4D 75.569 483 74 26 2668 3129 459258334 459258793 7.540000e-47 198
16 TraesCS1B01G380000 chr4B 92.090 177 14 0 3268 3444 135812666 135812490 2.050000e-62 250
17 TraesCS1B01G380000 chr4B 91.908 173 14 0 3272 3444 142710149 142710321 3.430000e-60 243
18 TraesCS1B01G380000 chr4B 91.716 169 13 1 3079 3247 135812901 135812734 2.070000e-57 233
19 TraesCS1B01G380000 chr4B 84.431 167 12 7 919 1085 121937121 121937273 5.950000e-33 152
20 TraesCS1B01G380000 chr3A 79.052 401 47 24 1727 2114 472791773 472792149 1.240000e-59 241
21 TraesCS1B01G380000 chr3B 78.141 398 56 19 1727 2114 452462913 452463289 1.240000e-54 224
22 TraesCS1B01G380000 chr3B 78.056 319 40 19 1779 2094 362054314 362054023 1.270000e-39 174
23 TraesCS1B01G380000 chr5D 75.960 495 52 31 2668 3129 527100637 527101097 3.510000e-45 193
24 TraesCS1B01G380000 chr2B 79.775 178 35 1 2626 2803 555378915 555379091 1.000000e-25 128
25 TraesCS1B01G380000 chr7D 76.190 252 39 10 2569 2814 199420342 199420106 2.810000e-21 113


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 TraesCS1B01G380000 chr1B 613019679 613023122 3443 False 6360 6360 100.0000 1 3444 1 chr1B.!!$F1 3443
1 TraesCS1B01G380000 chr1D 447549157 447551820 2663 False 1653 3171 88.5535 15 2556 2 chr1D.!!$F1 2541
2 TraesCS1B01G380000 chr1A 543633659 543635864 2205 False 3024 3024 91.6000 373 2569 1 chr1A.!!$F1 2196
3 TraesCS1B01G380000 chr1A 323261986 323262871 885 True 656 656 80.8900 2564 3444 1 chr1A.!!$R1 880
4 TraesCS1B01G380000 chr6A 591127411 591128942 1531 False 274 274 90.7320 3010 3214 2 chr6A.!!$F3 204

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
536 571 0.040646 CCATATGCCCAGCCATCCAT 59.959 55.000 0.0 0.0 0.0 3.41 F
701 737 1.476891 CTCTAGCCGTGTGTGTACCAT 59.523 52.381 0.0 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1347 1409 0.034896 AGAAAGACGTTGGATGGCGT 59.965 50.0 0.0 0.0 44.50 5.68 R
2586 2755 0.038744 CAACCAGACAAGATGGGGCT 59.961 55.0 0.0 0.0 42.48 5.19 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
23 24 1.466950 TCATCCCTAAAAACGCAAGCG 59.533 47.619 13.50 13.50 46.03 4.68
28 29 0.109319 CTAAAAACGCAAGCGCCCAT 60.109 50.000 15.09 1.65 44.19 4.00
52 53 3.376103 CCCTACCCCTATAAACACCTCCT 60.376 52.174 0.00 0.00 0.00 3.69
56 57 5.230746 ACCCCTATAAACACCTCCTAGAA 57.769 43.478 0.00 0.00 0.00 2.10
65 66 4.479786 ACACCTCCTAGAAATTGAGCTC 57.520 45.455 6.82 6.82 0.00 4.09
71 72 5.426504 CTCCTAGAAATTGAGCTCACACAT 58.573 41.667 18.03 4.49 0.00 3.21
75 76 5.814764 AGAAATTGAGCTCACACATCATC 57.185 39.130 18.03 9.71 0.00 2.92
80 81 7.876936 AATTGAGCTCACACATCATCTTAAT 57.123 32.000 18.03 0.00 0.00 1.40
86 87 9.217278 GAGCTCACACATCATCTTAATATTGAT 57.783 33.333 9.40 0.00 0.00 2.57
116 117 1.897137 AGACGCCTCACAGTCGACA 60.897 57.895 19.50 0.00 41.86 4.35
117 118 1.442857 GACGCCTCACAGTCGACAG 60.443 63.158 19.50 12.96 0.00 3.51
127 128 2.468040 CACAGTCGACAGAAACGTCTTC 59.532 50.000 19.50 0.00 33.54 2.87
130 131 2.617308 AGTCGACAGAAACGTCTTCTCA 59.383 45.455 19.50 0.00 33.54 3.27
131 132 3.253677 AGTCGACAGAAACGTCTTCTCAT 59.746 43.478 19.50 3.12 33.54 2.90
132 133 4.454847 AGTCGACAGAAACGTCTTCTCATA 59.545 41.667 19.50 0.00 33.54 2.15
142 143 8.358148 AGAAACGTCTTCTCATACTGAACTAAA 58.642 33.333 7.04 0.00 0.00 1.85
147 148 8.926710 CGTCTTCTCATACTGAACTAAAATTGT 58.073 33.333 0.00 0.00 0.00 2.71
149 150 9.996554 TCTTCTCATACTGAACTAAAATTGTCA 57.003 29.630 0.00 0.00 0.00 3.58
202 203 0.542232 ACCGGTGCAAGTCTAGGACT 60.542 55.000 6.12 0.00 45.64 3.85
232 233 4.385825 TGGTGAACTGATTCTACCACAAC 58.614 43.478 0.00 0.00 39.26 3.32
234 235 4.213482 GGTGAACTGATTCTACCACAACAC 59.787 45.833 0.00 0.00 36.65 3.32
237 238 5.527214 TGAACTGATTCTACCACAACACAAG 59.473 40.000 0.00 0.00 35.69 3.16
238 239 5.290493 ACTGATTCTACCACAACACAAGA 57.710 39.130 0.00 0.00 0.00 3.02
240 241 5.527582 ACTGATTCTACCACAACACAAGAAC 59.472 40.000 0.00 0.00 0.00 3.01
242 243 3.202829 TCTACCACAACACAAGAACCC 57.797 47.619 0.00 0.00 0.00 4.11
243 244 2.775384 TCTACCACAACACAAGAACCCT 59.225 45.455 0.00 0.00 0.00 4.34
244 245 3.968649 TCTACCACAACACAAGAACCCTA 59.031 43.478 0.00 0.00 0.00 3.53
245 246 3.655615 ACCACAACACAAGAACCCTAA 57.344 42.857 0.00 0.00 0.00 2.69
249 250 4.023193 CCACAACACAAGAACCCTAACATC 60.023 45.833 0.00 0.00 0.00 3.06
250 251 4.023193 CACAACACAAGAACCCTAACATCC 60.023 45.833 0.00 0.00 0.00 3.51
274 275 1.063174 CTACGCTCAGCTTGCAAATCC 59.937 52.381 0.00 0.00 0.00 3.01
277 278 1.138247 CTCAGCTTGCAAATCCCGC 59.862 57.895 0.00 0.00 0.00 6.13
282 283 3.266230 CTTGCAAATCCCGCGCACA 62.266 57.895 8.75 0.00 34.87 4.57
286 287 2.593148 AAATCCCGCGCACACACA 60.593 55.556 8.75 0.00 0.00 3.72
296 297 0.386352 CGCACACACAAGCAATCCAG 60.386 55.000 0.00 0.00 0.00 3.86
297 298 0.953727 GCACACACAAGCAATCCAGA 59.046 50.000 0.00 0.00 0.00 3.86
335 336 6.094603 AGTTTAGATTTTATGAGCAGGCACAG 59.905 38.462 0.00 0.00 0.00 3.66
380 404 4.700365 TGACGACGCGCACTCTGG 62.700 66.667 5.73 0.00 0.00 3.86
475 507 3.978855 CCGACGGAAAAAGAAACAAATCC 59.021 43.478 8.64 0.00 0.00 3.01
532 567 2.118951 GCCCATATGCCCAGCCAT 59.881 61.111 0.00 0.00 0.00 4.40
536 571 0.040646 CCATATGCCCAGCCATCCAT 59.959 55.000 0.00 0.00 0.00 3.41
683 719 4.152284 CCCCCAGTTAATTCAGGTACTC 57.848 50.000 0.00 0.00 34.60 2.59
701 737 1.476891 CTCTAGCCGTGTGTGTACCAT 59.523 52.381 0.00 0.00 0.00 3.55
814 850 3.231207 TCATTTGGTCGGAAAAAGGGA 57.769 42.857 0.98 0.00 0.00 4.20
815 851 3.773560 TCATTTGGTCGGAAAAAGGGAT 58.226 40.909 0.98 0.00 0.00 3.85
818 854 4.329462 TTTGGTCGGAAAAAGGGATTTG 57.671 40.909 0.00 0.00 0.00 2.32
819 855 2.952116 TGGTCGGAAAAAGGGATTTGT 58.048 42.857 0.00 0.00 0.00 2.83
865 921 6.091305 GCTTAAAATTGCTTGGAGGAATTCAC 59.909 38.462 7.93 0.58 43.92 3.18
882 938 1.962822 ACCGCTGATATGCATGCCG 60.963 57.895 16.68 9.28 0.00 5.69
883 939 2.175078 CGCTGATATGCATGCCGC 59.825 61.111 16.68 8.45 42.89 6.53
885 941 2.865308 CTGATATGCATGCCGCCG 59.135 61.111 16.68 0.00 41.33 6.46
886 942 2.669229 TGATATGCATGCCGCCGG 60.669 61.111 16.68 0.00 41.33 6.13
1239 1301 3.770040 CCGGAGATGGCACCGTGA 61.770 66.667 13.15 0.00 45.26 4.35
1244 1306 2.887568 GATGGCACCGTGAGCTCG 60.888 66.667 9.64 0.00 0.00 5.03
1292 1354 2.954753 GCCGTGCCAGAACGACTTG 61.955 63.158 0.00 0.00 46.49 3.16
1457 1519 2.969238 CCTGATGATCCCGCGCAC 60.969 66.667 8.75 0.00 0.00 5.34
1553 1615 1.283793 CGAGTCCAACACGTACGGT 59.716 57.895 21.06 11.73 0.00 4.83
1634 1699 0.253160 AGATTAGTCAGGTGGCCCCA 60.253 55.000 12.24 0.00 34.66 4.96
1664 1729 0.035056 AAGGGAACAAGATGCCGGAG 60.035 55.000 5.05 0.00 35.66 4.63
1758 1841 2.264480 CCAGCATCACGTTCGGGA 59.736 61.111 0.00 0.00 0.00 5.14
1865 1948 3.329889 TTGCCCAGCCTGACCGAT 61.330 61.111 0.00 0.00 0.00 4.18
2171 2257 1.592131 GTCGGTGCAACGGTACACA 60.592 57.895 26.21 0.00 38.57 3.72
2298 2384 5.900425 ACATGAACATGCAGTTGTAACAAA 58.100 33.333 13.71 0.00 41.51 2.83
2347 2433 2.926200 GTGGTGACATGAGATCGAAGTG 59.074 50.000 0.00 0.00 46.14 3.16
2353 2439 4.889995 TGACATGAGATCGAAGTGTATCCT 59.110 41.667 0.00 0.00 0.00 3.24
2358 2444 4.895889 TGAGATCGAAGTGTATCCTTCCAT 59.104 41.667 0.00 0.00 38.05 3.41
2359 2445 5.010112 TGAGATCGAAGTGTATCCTTCCATC 59.990 44.000 0.00 0.00 38.55 3.51
2360 2446 3.710326 TCGAAGTGTATCCTTCCATCG 57.290 47.619 0.00 0.00 38.05 3.84
2361 2447 2.361119 TCGAAGTGTATCCTTCCATCGG 59.639 50.000 0.00 0.00 38.05 4.18
2486 2648 2.493278 ACTTGGGAATTGATGGAAAGCG 59.507 45.455 0.00 0.00 0.00 4.68
2487 2649 2.214376 TGGGAATTGATGGAAAGCGT 57.786 45.000 0.00 0.00 0.00 5.07
2493 2655 5.394115 GGGAATTGATGGAAAGCGTTGTAAT 60.394 40.000 0.00 0.00 0.00 1.89
2494 2656 5.516339 GGAATTGATGGAAAGCGTTGTAATG 59.484 40.000 0.00 0.00 0.00 1.90
2509 2673 6.632834 GCGTTGTAATGTAATCATGGATGAAC 59.367 38.462 0.00 0.00 40.69 3.18
2569 2738 6.763135 TGTACTAAGATTGATGGCTTGCTAAG 59.237 38.462 0.00 0.00 0.00 2.18
2583 2752 0.444260 GCTAAGAGCAACTCCAACGC 59.556 55.000 0.00 0.00 41.89 4.84
2584 2753 1.795768 CTAAGAGCAACTCCAACGCA 58.204 50.000 0.00 0.00 0.00 5.24
2586 2755 0.106708 AAGAGCAACTCCAACGCAGA 59.893 50.000 0.00 0.00 0.00 4.26
2588 2757 1.905922 GAGCAACTCCAACGCAGAGC 61.906 60.000 0.00 0.00 34.56 4.09
2594 2763 2.825836 CCAACGCAGAGCCCCATC 60.826 66.667 0.00 0.00 0.00 3.51
2600 2769 1.606531 GCAGAGCCCCATCTTGTCT 59.393 57.895 0.00 0.00 0.00 3.41
2601 2770 0.747283 GCAGAGCCCCATCTTGTCTG 60.747 60.000 0.00 0.00 38.14 3.51
2614 2783 1.073763 CTTGTCTGGTTGGGTCATCCA 59.926 52.381 0.00 0.00 45.43 3.41
2626 2795 2.101415 GGGTCATCCAGCCATAAAAAGC 59.899 50.000 0.00 0.00 42.97 3.51
2651 2823 2.462898 GACGACCGAAACGAACGC 59.537 61.111 0.00 0.00 34.70 4.84
2652 2824 3.312349 GACGACCGAAACGAACGCG 62.312 63.158 3.53 3.53 44.79 6.01
2654 2826 3.694394 GACCGAAACGAACGCGCA 61.694 61.111 5.73 0.00 42.48 6.09
2672 2844 2.034879 ATGTCCGCTTTGCTGTCCG 61.035 57.895 0.00 0.00 0.00 4.79
2674 2846 2.357034 TCCGCTTTGCTGTCCGTC 60.357 61.111 0.00 0.00 0.00 4.79
2676 2848 2.671177 CCGCTTTGCTGTCCGTCTG 61.671 63.158 0.00 0.00 0.00 3.51
2679 2851 1.508632 GCTTTGCTGTCCGTCTGTTA 58.491 50.000 0.00 0.00 0.00 2.41
2682 2854 2.380084 TTGCTGTCCGTCTGTTATCC 57.620 50.000 0.00 0.00 0.00 2.59
2683 2855 0.172578 TGCTGTCCGTCTGTTATCCG 59.827 55.000 0.00 0.00 0.00 4.18
2684 2856 0.172803 GCTGTCCGTCTGTTATCCGT 59.827 55.000 0.00 0.00 0.00 4.69
2685 2857 1.403780 GCTGTCCGTCTGTTATCCGTT 60.404 52.381 0.00 0.00 0.00 4.44
2687 2859 1.203052 TGTCCGTCTGTTATCCGTTCC 59.797 52.381 0.00 0.00 0.00 3.62
2690 2862 1.542544 CGTCTGTTATCCGTTCCGAC 58.457 55.000 0.00 0.00 0.00 4.79
2713 2885 4.747810 CCAAACTTGGTCCAAATATGAGC 58.252 43.478 5.64 0.00 43.43 4.26
2714 2886 4.381932 CCAAACTTGGTCCAAATATGAGCC 60.382 45.833 5.64 0.00 43.43 4.70
2715 2887 2.643551 ACTTGGTCCAAATATGAGCCG 58.356 47.619 5.64 0.00 0.00 5.52
2726 2898 2.949177 TATGAGCCGCAAATGGGTAT 57.051 45.000 0.00 0.00 40.53 2.73
2728 2900 0.751277 TGAGCCGCAAATGGGTATGG 60.751 55.000 0.00 0.00 40.53 2.74
2730 2902 0.033601 AGCCGCAAATGGGTATGGAA 60.034 50.000 0.00 0.00 38.14 3.53
2731 2903 1.039856 GCCGCAAATGGGTATGGAAT 58.960 50.000 0.00 0.00 0.00 3.01
2737 2909 3.450457 GCAAATGGGTATGGAATGGACAA 59.550 43.478 0.00 0.00 0.00 3.18
2738 2910 4.441913 GCAAATGGGTATGGAATGGACAAG 60.442 45.833 0.00 0.00 0.00 3.16
2741 2913 3.189606 TGGGTATGGAATGGACAAGAGT 58.810 45.455 0.00 0.00 0.00 3.24
2742 2914 3.054434 TGGGTATGGAATGGACAAGAGTG 60.054 47.826 0.00 0.00 0.00 3.51
2743 2915 3.199946 GGGTATGGAATGGACAAGAGTGA 59.800 47.826 0.00 0.00 0.00 3.41
2763 2935 1.297012 CGCTCTCGTCACTCGCTAC 60.297 63.158 0.00 0.00 39.67 3.58
2804 2976 1.272872 GGTCCTACCTACCAGTGACCA 60.273 57.143 0.00 0.00 41.46 4.02
2826 3014 1.294857 CGCATCTCTCGTCTCTCTCA 58.705 55.000 0.00 0.00 0.00 3.27
2832 3020 5.048782 GCATCTCTCGTCTCTCTCATACAAT 60.049 44.000 0.00 0.00 0.00 2.71
2843 3031 8.686334 GTCTCTCTCATACAATTTTCTCTCTCT 58.314 37.037 0.00 0.00 0.00 3.10
2844 3032 8.902806 TCTCTCTCATACAATTTTCTCTCTCTC 58.097 37.037 0.00 0.00 0.00 3.20
2847 3035 7.702386 TCTCATACAATTTTCTCTCTCTCTCG 58.298 38.462 0.00 0.00 0.00 4.04
2848 3036 7.554476 TCTCATACAATTTTCTCTCTCTCTCGA 59.446 37.037 0.00 0.00 0.00 4.04
2851 3039 5.901552 ACAATTTTCTCTCTCTCTCGATCC 58.098 41.667 0.00 0.00 0.00 3.36
2852 3040 5.163457 ACAATTTTCTCTCTCTCTCGATCCC 60.163 44.000 0.00 0.00 0.00 3.85
2855 3043 1.697432 TCTCTCTCTCTCGATCCCCTC 59.303 57.143 0.00 0.00 0.00 4.30
2856 3044 1.699634 CTCTCTCTCTCGATCCCCTCT 59.300 57.143 0.00 0.00 0.00 3.69
2857 3045 1.419762 TCTCTCTCTCGATCCCCTCTG 59.580 57.143 0.00 0.00 0.00 3.35
2858 3046 1.142870 CTCTCTCTCGATCCCCTCTGT 59.857 57.143 0.00 0.00 0.00 3.41
2859 3047 1.566703 TCTCTCTCGATCCCCTCTGTT 59.433 52.381 0.00 0.00 0.00 3.16
2860 3048 1.680735 CTCTCTCGATCCCCTCTGTTG 59.319 57.143 0.00 0.00 0.00 3.33
2861 3049 0.103937 CTCTCGATCCCCTCTGTTGC 59.896 60.000 0.00 0.00 0.00 4.17
2878 3066 3.117372 CCTACGTCGGCCGATTCT 58.883 61.111 33.58 18.58 40.70 2.40
2880 3068 1.299165 CTACGTCGGCCGATTCTGG 60.299 63.158 33.58 19.65 40.70 3.86
2897 3085 3.394836 GCTGGAACGGAGAGGCCT 61.395 66.667 3.86 3.86 36.31 5.19
2922 3110 4.172232 CGATGGGGAGGGGGAGGA 62.172 72.222 0.00 0.00 0.00 3.71
2923 3111 2.122189 GATGGGGAGGGGGAGGAG 60.122 72.222 0.00 0.00 0.00 3.69
2928 3116 4.825679 GGAGGGGGAGGAGGGTGG 62.826 77.778 0.00 0.00 0.00 4.61
2976 3164 3.596066 GAAGCGGAGAGGCACAGCA 62.596 63.158 0.00 0.00 34.64 4.41
3023 3211 1.680651 CGACTGGAGTGGAGAGGCT 60.681 63.158 0.00 0.00 0.00 4.58
3202 4717 2.267961 GTTGACCACCCGGCCTAG 59.732 66.667 0.00 0.00 34.57 3.02
3208 4723 3.066190 CACCCGGCCTAGTGTCGA 61.066 66.667 12.61 0.00 0.00 4.20
3218 4733 0.247894 CTAGTGTCGAGTCGAGCAGC 60.248 60.000 17.12 4.58 36.23 5.25
3220 4735 1.799519 GTGTCGAGTCGAGCAGCAG 60.800 63.158 17.12 0.00 36.23 4.24
3224 4739 2.508887 GAGTCGAGCAGCAGCCAG 60.509 66.667 0.00 0.00 43.56 4.85
3243 4758 1.080230 CTCAGTGTGAGCTCCACCG 60.080 63.158 23.51 17.22 45.09 4.94
3263 4793 4.847444 GCCGAGAAGCCCTCCTGC 62.847 72.222 0.00 0.00 38.71 4.85
3318 4848 1.524621 CGACATGATGCAGACCCCC 60.525 63.158 0.00 0.00 0.00 5.40
3332 4862 2.282462 CCCCTTGTGGTGCAGGTC 60.282 66.667 0.00 0.00 0.00 3.85
3348 4878 3.870955 TCCACTGCGGAGACAAGT 58.129 55.556 12.26 0.00 39.64 3.16
3384 4914 4.436998 GCGACTGTGGCCGTAGCT 62.437 66.667 3.14 0.00 39.73 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.670627 GCTTGCGTTTTTAGGGATGAGTG 60.671 47.826 0.00 0.00 0.00 3.51
1 2 2.488153 GCTTGCGTTTTTAGGGATGAGT 59.512 45.455 0.00 0.00 0.00 3.41
2 3 2.476185 CGCTTGCGTTTTTAGGGATGAG 60.476 50.000 6.86 0.00 0.00 2.90
3 4 1.466950 CGCTTGCGTTTTTAGGGATGA 59.533 47.619 6.86 0.00 0.00 2.92
4 5 1.895051 CGCTTGCGTTTTTAGGGATG 58.105 50.000 6.86 0.00 0.00 3.51
5 6 0.170339 GCGCTTGCGTTTTTAGGGAT 59.830 50.000 16.38 0.00 0.00 3.85
6 7 1.577421 GCGCTTGCGTTTTTAGGGA 59.423 52.632 16.38 0.00 0.00 4.20
7 8 1.443702 GGCGCTTGCGTTTTTAGGG 60.444 57.895 16.38 0.00 40.46 3.53
8 9 1.443702 GGGCGCTTGCGTTTTTAGG 60.444 57.895 16.38 0.00 40.46 2.69
9 10 0.109319 ATGGGCGCTTGCGTTTTTAG 60.109 50.000 16.38 0.00 40.46 1.85
10 11 1.135632 GTATGGGCGCTTGCGTTTTTA 60.136 47.619 16.38 2.07 40.46 1.52
11 12 0.388006 GTATGGGCGCTTGCGTTTTT 60.388 50.000 16.38 2.95 40.46 1.94
12 13 1.211709 GTATGGGCGCTTGCGTTTT 59.788 52.632 16.38 2.62 40.46 2.43
13 14 2.696759 GGTATGGGCGCTTGCGTTT 61.697 57.895 16.38 2.30 40.46 3.60
18 19 1.227853 GGTAGGGTATGGGCGCTTG 60.228 63.158 7.64 0.00 33.59 4.01
23 24 2.955200 TATAGGGGTAGGGTATGGGC 57.045 55.000 0.00 0.00 0.00 5.36
28 29 4.389034 GGAGGTGTTTATAGGGGTAGGGTA 60.389 50.000 0.00 0.00 0.00 3.69
52 53 6.647229 AGATGATGTGTGAGCTCAATTTCTA 58.353 36.000 20.19 4.67 0.00 2.10
56 57 7.876936 ATTAAGATGATGTGTGAGCTCAATT 57.123 32.000 20.19 3.13 0.00 2.32
65 66 9.608617 GCTTCATCAATATTAAGATGATGTGTG 57.391 33.333 20.82 14.10 47.00 3.82
71 72 7.229306 GTGGTGGCTTCATCAATATTAAGATGA 59.771 37.037 12.26 12.26 46.38 2.92
75 76 6.543465 TCTGTGGTGGCTTCATCAATATTAAG 59.457 38.462 0.00 0.00 32.66 1.85
80 81 3.609853 GTCTGTGGTGGCTTCATCAATA 58.390 45.455 0.00 0.00 32.66 1.90
86 87 2.280797 GCGTCTGTGGTGGCTTCA 60.281 61.111 0.00 0.00 0.00 3.02
91 92 2.357517 GTGAGGCGTCTGTGGTGG 60.358 66.667 8.06 0.00 0.00 4.61
131 132 9.832445 AGACTTTCTGACAATTTTAGTTCAGTA 57.168 29.630 0.00 0.00 0.00 2.74
132 133 8.738645 AGACTTTCTGACAATTTTAGTTCAGT 57.261 30.769 0.00 0.00 0.00 3.41
202 203 7.110155 GGTAGAATCAGTTCACCAGGATTTAA 58.890 38.462 0.00 0.00 36.44 1.52
208 209 3.007940 TGTGGTAGAATCAGTTCACCAGG 59.992 47.826 10.56 0.00 41.66 4.45
209 210 4.271696 TGTGGTAGAATCAGTTCACCAG 57.728 45.455 10.56 0.00 41.66 4.00
215 216 5.680619 TCTTGTGTTGTGGTAGAATCAGTT 58.319 37.500 0.00 0.00 0.00 3.16
232 233 3.262420 CTCGGATGTTAGGGTTCTTGTG 58.738 50.000 0.00 0.00 0.00 3.33
234 235 2.093447 AGCTCGGATGTTAGGGTTCTTG 60.093 50.000 0.00 0.00 0.00 3.02
237 238 2.543238 CGTAGCTCGGATGTTAGGGTTC 60.543 54.545 0.00 0.00 35.71 3.62
238 239 1.407979 CGTAGCTCGGATGTTAGGGTT 59.592 52.381 0.00 0.00 35.71 4.11
240 241 3.867723 CGTAGCTCGGATGTTAGGG 57.132 57.895 0.00 0.00 35.71 3.53
261 262 2.202518 CGCGGGATTTGCAAGCTG 60.203 61.111 0.00 0.00 0.00 4.24
263 264 4.418401 TGCGCGGGATTTGCAAGC 62.418 61.111 8.83 0.00 35.33 4.01
266 267 4.036804 GTGTGCGCGGGATTTGCA 62.037 61.111 8.83 0.00 36.02 4.08
274 275 3.541093 ATTGCTTGTGTGTGCGCGG 62.541 57.895 8.83 0.00 0.00 6.46
277 278 0.386352 CTGGATTGCTTGTGTGTGCG 60.386 55.000 0.00 0.00 0.00 5.34
282 283 2.936919 TCTGTCTGGATTGCTTGTGT 57.063 45.000 0.00 0.00 0.00 3.72
286 287 8.270744 ACTATAGAATTTCTGTCTGGATTGCTT 58.729 33.333 6.78 0.00 0.00 3.91
318 319 3.689347 ACATCTGTGCCTGCTCATAAAA 58.311 40.909 0.00 0.00 0.00 1.52
335 336 2.604914 CGTGCAGATTCACAGGTACATC 59.395 50.000 0.00 0.00 36.80 3.06
380 404 2.617274 GGTTTCAGCTGGCGGACAC 61.617 63.158 15.13 0.00 0.00 3.67
390 414 2.437895 GTAGGGGGCGGTTTCAGC 60.438 66.667 0.00 0.00 0.00 4.26
392 416 1.128809 TTCTGTAGGGGGCGGTTTCA 61.129 55.000 0.00 0.00 0.00 2.69
489 524 2.769663 TCTTTTTATAGCCGGCCTGAGA 59.230 45.455 26.15 13.98 0.00 3.27
492 527 1.597663 CGTCTTTTTATAGCCGGCCTG 59.402 52.381 26.15 4.52 0.00 4.85
716 752 5.200368 TCAAGAAAAGGAAGCCACAAATC 57.800 39.130 0.00 0.00 0.00 2.17
720 756 3.565307 ACATCAAGAAAAGGAAGCCACA 58.435 40.909 0.00 0.00 0.00 4.17
721 757 4.301628 CAACATCAAGAAAAGGAAGCCAC 58.698 43.478 0.00 0.00 0.00 5.01
728 764 3.004734 AGCGAACCAACATCAAGAAAAGG 59.995 43.478 0.00 0.00 0.00 3.11
814 850 7.264221 TCAAAGCTAACATGAACACAACAAAT 58.736 30.769 0.00 0.00 0.00 2.32
815 851 6.625362 TCAAAGCTAACATGAACACAACAAA 58.375 32.000 0.00 0.00 0.00 2.83
818 854 4.676924 GCTCAAAGCTAACATGAACACAAC 59.323 41.667 0.00 0.00 38.45 3.32
819 855 4.858935 GCTCAAAGCTAACATGAACACAA 58.141 39.130 0.00 0.00 38.45 3.33
845 885 3.056607 CGGTGAATTCCTCCAAGCAATTT 60.057 43.478 14.35 0.00 0.00 1.82
865 921 2.865308 CGGCATGCATATCAGCGG 59.135 61.111 21.36 0.00 37.31 5.52
882 938 2.286418 CGATGAGAAACATTAAGCCGGC 60.286 50.000 21.89 21.89 39.56 6.13
883 939 3.194861 TCGATGAGAAACATTAAGCCGG 58.805 45.455 0.00 0.00 39.56 6.13
885 941 8.316640 AGATAATCGATGAGAAACATTAAGCC 57.683 34.615 0.00 0.00 39.56 4.35
888 944 9.406828 CGGTAGATAATCGATGAGAAACATTAA 57.593 33.333 0.00 0.00 39.56 1.40
890 946 6.868864 CCGGTAGATAATCGATGAGAAACATT 59.131 38.462 0.00 0.00 39.56 2.71
891 947 6.015350 ACCGGTAGATAATCGATGAGAAACAT 60.015 38.462 4.49 0.00 42.47 2.71
1034 1096 3.119101 TCGATCCCAACTTGCTAGTTCTC 60.119 47.826 10.73 5.28 42.67 2.87
1036 1098 3.190874 CTCGATCCCAACTTGCTAGTTC 58.809 50.000 10.73 0.00 42.67 3.01
1226 1288 2.581354 GAGCTCACGGTGCCATCT 59.419 61.111 9.40 0.00 0.00 2.90
1239 1301 3.450115 GTGGTAGGCGTCCGAGCT 61.450 66.667 8.90 0.00 37.29 4.09
1275 1337 1.284982 CTCAAGTCGTTCTGGCACGG 61.285 60.000 0.00 0.00 40.74 4.94
1285 1347 2.659610 GCAGGAGGCTCAAGTCGT 59.340 61.111 17.69 0.00 40.25 4.34
1347 1409 0.034896 AGAAAGACGTTGGATGGCGT 59.965 50.000 0.00 0.00 44.50 5.68
1350 1412 1.993370 GTCGAGAAAGACGTTGGATGG 59.007 52.381 0.00 0.00 0.00 3.51
1352 1414 2.414293 CGAGTCGAGAAAGACGTTGGAT 60.414 50.000 6.73 0.00 45.26 3.41
1475 1537 1.449778 GCTGTAACCGGAGAAGGCC 60.450 63.158 9.46 0.00 33.69 5.19
1553 1615 4.460683 GTATCGTGCCCGCCACCA 62.461 66.667 0.00 0.00 41.53 4.17
1634 1699 2.527374 TTCCCTTTCGTCGGGGGT 60.527 61.111 14.96 0.00 42.73 4.95
1736 1819 1.282248 CGAACGTGATGCTGGTCGTT 61.282 55.000 9.19 9.19 46.51 3.85
1787 1870 2.805546 GCTATCGCCTCCGTGTCA 59.194 61.111 0.00 0.00 35.54 3.58
2018 2101 1.144936 GTCCATCTTGCTCCCTCCG 59.855 63.158 0.00 0.00 0.00 4.63
2347 2433 1.339151 GGCATCCCGATGGAAGGATAC 60.339 57.143 6.81 0.00 45.98 2.24
2353 2439 1.121407 ATCGAGGCATCCCGATGGAA 61.121 55.000 6.81 0.00 45.98 3.53
2358 2444 1.587043 GATCGATCGAGGCATCCCGA 61.587 60.000 23.84 7.43 39.25 5.14
2359 2445 1.153939 GATCGATCGAGGCATCCCG 60.154 63.158 23.84 0.00 35.76 5.14
2360 2446 0.108898 CAGATCGATCGAGGCATCCC 60.109 60.000 23.84 6.28 0.00 3.85
2361 2447 0.108898 CCAGATCGATCGAGGCATCC 60.109 60.000 23.84 7.92 0.00 3.51
2486 2648 9.113838 AGAGTTCATCCATGATTACATTACAAC 57.886 33.333 0.00 0.00 36.56 3.32
2493 2655 9.029368 CCTAGATAGAGTTCATCCATGATTACA 57.971 37.037 0.00 0.00 36.56 2.41
2494 2656 9.030452 ACCTAGATAGAGTTCATCCATGATTAC 57.970 37.037 0.00 0.00 36.56 1.89
2569 2738 1.905922 GCTCTGCGTTGGAGTTGCTC 61.906 60.000 0.00 0.00 33.73 4.26
2581 2750 1.817099 GACAAGATGGGGCTCTGCG 60.817 63.158 0.00 0.00 0.00 5.18
2583 2752 0.107312 CCAGACAAGATGGGGCTCTG 60.107 60.000 0.00 0.00 33.94 3.35
2584 2753 0.548682 ACCAGACAAGATGGGGCTCT 60.549 55.000 0.00 0.00 42.48 4.09
2586 2755 0.038744 CAACCAGACAAGATGGGGCT 59.961 55.000 0.00 0.00 42.48 5.19
2588 2757 0.323725 CCCAACCAGACAAGATGGGG 60.324 60.000 1.08 0.00 45.72 4.96
2594 2763 1.073763 TGGATGACCCAACCAGACAAG 59.926 52.381 0.00 0.00 43.29 3.16
2614 2783 0.894835 CCGTTGGGCTTTTTATGGCT 59.105 50.000 0.00 0.00 0.00 4.75
2616 2785 1.203758 GTCCCGTTGGGCTTTTTATGG 59.796 52.381 0.00 0.00 43.94 2.74
2641 2813 1.509162 GGACATGCGCGTTCGTTTC 60.509 57.895 8.43 0.00 38.14 2.78
2647 2819 3.353836 AAAGCGGACATGCGCGTT 61.354 55.556 12.58 12.58 40.67 4.84
2651 2823 2.202388 CAGCAAAGCGGACATGCG 60.202 61.111 0.00 0.00 44.60 4.73
2652 2824 1.154150 GACAGCAAAGCGGACATGC 60.154 57.895 0.00 0.00 40.34 4.06
2654 2826 2.034879 CGGACAGCAAAGCGGACAT 61.035 57.895 0.00 0.00 0.00 3.06
2662 2834 2.695359 GGATAACAGACGGACAGCAAA 58.305 47.619 0.00 0.00 0.00 3.68
2663 2835 1.403647 CGGATAACAGACGGACAGCAA 60.404 52.381 0.00 0.00 0.00 3.91
2701 2873 2.361757 CCATTTGCGGCTCATATTTGGA 59.638 45.455 0.00 0.00 0.00 3.53
2708 2880 1.321474 CATACCCATTTGCGGCTCAT 58.679 50.000 0.00 0.00 0.00 2.90
2711 2883 0.033601 TTCCATACCCATTTGCGGCT 60.034 50.000 0.00 0.00 0.00 5.52
2713 2885 1.340889 CCATTCCATACCCATTTGCGG 59.659 52.381 0.00 0.00 0.00 5.69
2714 2886 2.034558 GTCCATTCCATACCCATTTGCG 59.965 50.000 0.00 0.00 0.00 4.85
2715 2887 3.030291 TGTCCATTCCATACCCATTTGC 58.970 45.455 0.00 0.00 0.00 3.68
2726 2898 2.766313 CGTTCACTCTTGTCCATTCCA 58.234 47.619 0.00 0.00 0.00 3.53
2728 2900 2.413453 GAGCGTTCACTCTTGTCCATTC 59.587 50.000 0.00 0.00 33.69 2.67
2730 2902 1.620819 AGAGCGTTCACTCTTGTCCAT 59.379 47.619 1.01 0.00 44.76 3.41
2731 2903 1.040646 AGAGCGTTCACTCTTGTCCA 58.959 50.000 1.01 0.00 44.76 4.02
2755 2927 3.507009 GAGCGGACGGTAGCGAGT 61.507 66.667 22.88 0.00 38.61 4.18
2799 2971 2.181777 GAGAGATGCGCGTGGTCA 59.818 61.111 6.97 0.00 0.00 4.02
2843 3031 1.330655 GGCAACAGAGGGGATCGAGA 61.331 60.000 0.00 0.00 0.00 4.04
2844 3032 1.144936 GGCAACAGAGGGGATCGAG 59.855 63.158 0.00 0.00 0.00 4.04
2847 3035 0.105039 CGTAGGCAACAGAGGGGATC 59.895 60.000 0.00 0.00 41.41 3.36
2848 3036 0.617820 ACGTAGGCAACAGAGGGGAT 60.618 55.000 0.00 0.00 41.41 3.85
2851 3039 1.153823 CGACGTAGGCAACAGAGGG 60.154 63.158 0.00 0.00 41.41 4.30
2852 3040 1.153823 CCGACGTAGGCAACAGAGG 60.154 63.158 0.39 0.00 41.41 3.69
2861 3049 1.299165 CAGAATCGGCCGACGTAGG 60.299 63.158 33.75 15.58 44.69 3.18
2878 3066 3.706373 GCCTCTCCGTTCCAGCCA 61.706 66.667 0.00 0.00 0.00 4.75
2880 3068 3.394836 AGGCCTCTCCGTTCCAGC 61.395 66.667 0.00 0.00 40.77 4.85
2918 3106 4.394712 CCGTGTGCCACCCTCCTC 62.395 72.222 0.00 0.00 0.00 3.71
2919 3107 4.954118 TCCGTGTGCCACCCTCCT 62.954 66.667 0.00 0.00 0.00 3.69
2949 3137 4.521062 CTCCGCTTCCCCTCGCAG 62.521 72.222 0.00 0.00 0.00 5.18
2997 3185 3.753434 ACTCCAGTCGCCGCTGAG 61.753 66.667 9.57 7.78 38.70 3.35
2998 3186 4.056125 CACTCCAGTCGCCGCTGA 62.056 66.667 9.57 0.00 38.70 4.26
3001 3189 4.803426 CTCCACTCCAGTCGCCGC 62.803 72.222 0.00 0.00 0.00 6.53
3002 3190 3.057547 CTCTCCACTCCAGTCGCCG 62.058 68.421 0.00 0.00 0.00 6.46
3003 3191 2.716017 CCTCTCCACTCCAGTCGCC 61.716 68.421 0.00 0.00 0.00 5.54
3004 3192 2.888863 CCTCTCCACTCCAGTCGC 59.111 66.667 0.00 0.00 0.00 5.19
3005 3193 1.254284 AAGCCTCTCCACTCCAGTCG 61.254 60.000 0.00 0.00 0.00 4.18
3006 3194 0.248843 CAAGCCTCTCCACTCCAGTC 59.751 60.000 0.00 0.00 0.00 3.51
3007 3195 1.197430 CCAAGCCTCTCCACTCCAGT 61.197 60.000 0.00 0.00 0.00 4.00
3008 3196 1.601171 CCAAGCCTCTCCACTCCAG 59.399 63.158 0.00 0.00 0.00 3.86
3202 4717 1.799519 CTGCTGCTCGACTCGACAC 60.800 63.158 0.00 0.00 0.00 3.67
3208 4723 4.756458 GCTGGCTGCTGCTCGACT 62.756 66.667 15.64 0.00 39.59 4.18
3218 4733 4.280676 CTCACACTGAGCTGGCTG 57.719 61.111 0.00 0.00 37.72 4.85
3282 4812 2.430921 CGCGTGGTGGAGACAGAC 60.431 66.667 0.00 0.00 44.46 3.51
3332 4862 1.734477 CGACTTGTCTCCGCAGTGG 60.734 63.158 0.00 0.00 40.09 4.00
3338 4868 2.125912 CCAGGCGACTTGTCTCCG 60.126 66.667 0.00 0.88 40.21 4.63
3399 4929 2.422591 GACGTGTTCCCGTTCCCA 59.577 61.111 0.00 0.00 41.98 4.37


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

AutoCloner maintained by Alex Coulton.