Multiple sequence alignment - TraesCS7A01G500700

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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 TraesCS7A01G500700 chr7A 100.000 3936 0 0 1 3936 690531257 690535192 0.000000e+00 7269.0
1 TraesCS7A01G500700 chr7A 85.027 2017 232 44 980 2952 682892315 682890325 0.000000e+00 1988.0
2 TraesCS7A01G500700 chr7A 82.570 2008 261 53 990 2939 687953114 687955090 0.000000e+00 1687.0
3 TraesCS7A01G500700 chr7A 85.963 748 72 18 840 1587 690574832 690574118 0.000000e+00 769.0
4 TraesCS7A01G500700 chr7A 84.015 538 74 8 1 531 410719084 410718552 1.260000e-139 507.0
5 TraesCS7A01G500700 chr7D 93.770 1830 102 6 4 1825 598254120 598252295 0.000000e+00 2737.0
6 TraesCS7A01G500700 chr7D 84.956 2054 211 41 990 2961 591806089 591804052 0.000000e+00 1991.0
7 TraesCS7A01G500700 chr7D 92.554 1249 73 8 1815 3047 598252226 598250982 0.000000e+00 1773.0
8 TraesCS7A01G500700 chr7D 82.074 2025 258 59 990 2939 594986779 594988773 0.000000e+00 1631.0
9 TraesCS7A01G500700 chr7D 85.078 516 63 10 27 531 29257732 29257220 7.540000e-142 514.0
10 TraesCS7A01G500700 chr7D 86.264 182 22 3 695 876 591806751 591806573 1.120000e-45 195.0
11 TraesCS7A01G500700 chr7B 92.730 1293 81 3 533 1825 677116060 677114781 0.000000e+00 1855.0
12 TraesCS7A01G500700 chr7B 82.473 2014 256 57 990 2939 666685407 666683427 0.000000e+00 1674.0
13 TraesCS7A01G500700 chr7B 90.779 1052 70 14 2009 3047 677114492 677113455 0.000000e+00 1380.0
14 TraesCS7A01G500700 chr7B 89.747 829 68 10 1163 1977 677158901 677158076 0.000000e+00 1044.0
15 TraesCS7A01G500700 chr7B 87.368 570 54 9 2481 3045 677157705 677157149 4.290000e-179 638.0
16 TraesCS7A01G500700 chr7B 86.728 437 27 16 3528 3936 677113256 677112823 1.290000e-124 457.0
17 TraesCS7A01G500700 chr7B 83.295 437 47 11 3242 3655 677157139 677156706 2.870000e-101 379.0
18 TraesCS7A01G500700 chr7B 90.566 212 17 2 1815 2024 677114716 677114506 1.080000e-70 278.0
19 TraesCS7A01G500700 chr7B 93.125 160 11 0 2316 2475 677158052 677157893 6.580000e-58 235.0
20 TraesCS7A01G500700 chr7B 85.455 220 21 8 3232 3449 677113456 677113246 6.620000e-53 219.0
21 TraesCS7A01G500700 chrUn 93.521 1173 63 6 1 1165 87057626 87056459 0.000000e+00 1733.0
22 TraesCS7A01G500700 chr5D 83.632 1173 143 28 976 2106 476674082 476672917 0.000000e+00 1057.0
23 TraesCS7A01G500700 chr5B 83.418 1176 132 36 976 2101 584096543 584095381 0.000000e+00 1033.0
24 TraesCS7A01G500700 chr5B 83.859 539 74 12 1 531 635797649 635798182 5.870000e-138 501.0
25 TraesCS7A01G500700 chr2A 90.637 534 46 3 1 531 100673091 100672559 0.000000e+00 706.0
26 TraesCS7A01G500700 chr2A 96.465 198 5 2 3033 3230 196517952 196518147 3.790000e-85 326.0
27 TraesCS7A01G500700 chr2A 97.312 186 5 0 3045 3230 195349932 195350117 2.280000e-82 316.0
28 TraesCS7A01G500700 chr6D 85.968 506 61 10 28 531 310123064 310123561 2.080000e-147 532.0
29 TraesCS7A01G500700 chr2B 84.572 538 70 11 1 531 790889545 790890076 4.510000e-144 521.0
30 TraesCS7A01G500700 chr2B 83.333 78 12 1 3794 3870 615329954 615330031 1.960000e-08 71.3
31 TraesCS7A01G500700 chr4A 83.457 538 77 10 1 531 632588702 632589234 1.270000e-134 490.0
32 TraesCS7A01G500700 chr4A 91.743 218 12 6 3025 3239 544173560 544173346 8.270000e-77 298.0
33 TraesCS7A01G500700 chr5A 99.444 180 1 0 3051 3230 473306110 473305931 1.050000e-85 327.0
34 TraesCS7A01G500700 chr5A 95.361 194 8 1 3040 3233 390235317 390235125 1.370000e-79 307.0
35 TraesCS7A01G500700 chr5A 93.627 204 11 2 3028 3230 670826090 670826292 1.780000e-78 303.0
36 TraesCS7A01G500700 chr3A 95.500 200 9 0 3044 3243 517285443 517285244 1.760000e-83 320.0
37 TraesCS7A01G500700 chr3A 96.354 192 5 2 3039 3230 434834906 434835095 8.210000e-82 315.0
38 TraesCS7A01G500700 chr3A 92.558 215 14 2 3026 3238 740079763 740079549 1.370000e-79 307.0
39 TraesCS7A01G500700 chr3A 87.273 55 7 0 3816 3870 697878340 697878286 3.280000e-06 63.9
40 TraesCS7A01G500700 chr6B 86.957 69 8 1 3800 3867 708129487 708129419 4.220000e-10 76.8
41 TraesCS7A01G500700 chr6B 86.765 68 7 2 3797 3863 1936984 1936918 1.520000e-09 75.0
42 TraesCS7A01G500700 chr6B 89.655 58 6 0 3816 3873 705522386 705522329 1.520000e-09 75.0
43 TraesCS7A01G500700 chr6A 84.286 70 10 1 3794 3863 235075148 235075216 2.540000e-07 67.6
44 TraesCS7A01G500700 chr3B 90.196 51 5 0 3820 3870 828085917 828085867 2.540000e-07 67.6
45 TraesCS7A01G500700 chr1B 85.938 64 7 2 3787 3849 645098111 645098173 2.540000e-07 67.6


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 TraesCS7A01G500700 chr7A 690531257 690535192 3935 False 7269.0 7269 100.00000 1 3936 1 chr7A.!!$F2 3935
1 TraesCS7A01G500700 chr7A 682890325 682892315 1990 True 1988.0 1988 85.02700 980 2952 1 chr7A.!!$R2 1972
2 TraesCS7A01G500700 chr7A 687953114 687955090 1976 False 1687.0 1687 82.57000 990 2939 1 chr7A.!!$F1 1949
3 TraesCS7A01G500700 chr7A 690574118 690574832 714 True 769.0 769 85.96300 840 1587 1 chr7A.!!$R3 747
4 TraesCS7A01G500700 chr7A 410718552 410719084 532 True 507.0 507 84.01500 1 531 1 chr7A.!!$R1 530
5 TraesCS7A01G500700 chr7D 598250982 598254120 3138 True 2255.0 2737 93.16200 4 3047 2 chr7D.!!$R3 3043
6 TraesCS7A01G500700 chr7D 594986779 594988773 1994 False 1631.0 1631 82.07400 990 2939 1 chr7D.!!$F1 1949
7 TraesCS7A01G500700 chr7D 591804052 591806751 2699 True 1093.0 1991 85.61000 695 2961 2 chr7D.!!$R2 2266
8 TraesCS7A01G500700 chr7D 29257220 29257732 512 True 514.0 514 85.07800 27 531 1 chr7D.!!$R1 504
9 TraesCS7A01G500700 chr7B 666683427 666685407 1980 True 1674.0 1674 82.47300 990 2939 1 chr7B.!!$R1 1949
10 TraesCS7A01G500700 chr7B 677112823 677116060 3237 True 837.8 1855 89.25160 533 3936 5 chr7B.!!$R2 3403
11 TraesCS7A01G500700 chr7B 677156706 677158901 2195 True 574.0 1044 88.38375 1163 3655 4 chr7B.!!$R3 2492
12 TraesCS7A01G500700 chrUn 87056459 87057626 1167 True 1733.0 1733 93.52100 1 1165 1 chrUn.!!$R1 1164
13 TraesCS7A01G500700 chr5D 476672917 476674082 1165 True 1057.0 1057 83.63200 976 2106 1 chr5D.!!$R1 1130
14 TraesCS7A01G500700 chr5B 584095381 584096543 1162 True 1033.0 1033 83.41800 976 2101 1 chr5B.!!$R1 1125
15 TraesCS7A01G500700 chr5B 635797649 635798182 533 False 501.0 501 83.85900 1 531 1 chr5B.!!$F1 530
16 TraesCS7A01G500700 chr2A 100672559 100673091 532 True 706.0 706 90.63700 1 531 1 chr2A.!!$R1 530
17 TraesCS7A01G500700 chr2B 790889545 790890076 531 False 521.0 521 84.57200 1 531 1 chr2B.!!$F2 530
18 TraesCS7A01G500700 chr4A 632588702 632589234 532 False 490.0 490 83.45700 1 531 1 chr4A.!!$F1 530

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
441 458 1.174712 GGTGTTGGCTGTGTGCATCT 61.175 55.0 0.0 0.00 45.15 2.90 F
1690 2111 0.965866 CCTGTACACGAGGCTCTCCA 60.966 60.0 13.5 1.08 33.74 3.86 F
2607 3396 0.032403 GGCTGTGTTGCTTGCATTCA 59.968 50.0 0.0 0.00 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2178 2769 1.069500 GGAAACGCGTGTGCTGTATTT 60.069 47.619 14.98 0.0 39.65 1.40 R
2923 3778 0.609131 AGGTTCTTCATGCAACCGGG 60.609 55.000 6.32 0.0 45.92 5.73 R
3864 4752 0.852777 CGCGCGCATACTAGTCATTT 59.147 50.000 32.61 0.0 0.00 2.32 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
163 164 2.706555 TGCTCGGATATGCTTAGACG 57.293 50.000 0.00 0.00 0.00 4.18
194 196 3.916989 AGGGTGAAAACCTAGATTCTGGT 59.083 43.478 0.00 0.00 36.32 4.00
441 458 1.174712 GGTGTTGGCTGTGTGCATCT 61.175 55.000 0.00 0.00 45.15 2.90
448 465 3.334691 TGGCTGTGTGCATCTTAGTTAC 58.665 45.455 0.00 0.00 45.15 2.50
475 492 2.634600 GCCGGGTGTGTGTTCATTATA 58.365 47.619 2.18 0.00 0.00 0.98
553 571 1.382522 ATAACTCATGCAGCAACCGG 58.617 50.000 0.00 0.00 0.00 5.28
563 581 4.994415 ATGCAGCAACCGGCAATATTTCA 61.994 43.478 0.00 0.00 45.01 2.69
906 942 4.832266 ACCAACATCTAATGCTTGGAAACA 59.168 37.500 19.18 0.00 40.61 2.83
947 983 7.936847 TCTCCACAAATGTAACAATGTCTACTT 59.063 33.333 0.00 0.00 0.00 2.24
950 986 8.999431 CCACAAATGTAACAATGTCTACTTAGT 58.001 33.333 0.00 0.00 0.00 2.24
971 1007 1.339438 GCCCACTTCTCATCTGCTGAA 60.339 52.381 0.00 0.00 32.14 3.02
972 1008 2.630158 CCCACTTCTCATCTGCTGAAG 58.370 52.381 0.00 0.00 41.87 3.02
974 1010 2.354906 CCACTTCTCATCTGCTGAAGCT 60.355 50.000 3.61 0.00 40.36 3.74
1378 1790 3.461773 CCATCGCCCTCGTCTGGT 61.462 66.667 0.00 0.00 36.00 4.00
1690 2111 0.965866 CCTGTACACGAGGCTCTCCA 60.966 60.000 13.50 1.08 33.74 3.86
1808 2229 2.608261 GGTGAGACGAGTCTTCCTGTTG 60.608 54.545 7.23 0.00 40.61 3.33
1832 2341 8.655651 TGTATCATCTCAACGTATGCATTTTA 57.344 30.769 3.54 0.00 0.00 1.52
1838 2347 8.533965 CATCTCAACGTATGCATTTTAATTTGG 58.466 33.333 3.54 0.00 0.00 3.28
2178 2769 5.586243 GTGTCTCTGCTTTTCCTGCATATAA 59.414 40.000 0.00 0.00 39.86 0.98
2357 2948 4.832590 CGAGGAGGAAGTCGTTACATAT 57.167 45.455 0.00 0.00 0.00 1.78
2402 2993 4.766375 TCGGGGTATCTTTCTTCATTGAC 58.234 43.478 0.00 0.00 0.00 3.18
2433 3035 6.169094 CACACTTCTCTTTCAGGTATCATGT 58.831 40.000 0.00 0.00 0.00 3.21
2450 3052 5.804944 TCATGTGTGAAATTCCCACATTT 57.195 34.783 18.85 0.67 45.01 2.32
2470 3072 6.091169 ACATTTCCACGTATTTACTACAACCG 59.909 38.462 0.00 0.00 0.00 4.44
2478 3080 5.581874 CGTATTTACTACAACCGGGAACATT 59.418 40.000 6.32 0.00 0.00 2.71
2607 3396 0.032403 GGCTGTGTTGCTTGCATTCA 59.968 50.000 0.00 0.00 0.00 2.57
2634 3423 5.662456 TGCATTTGAATGGAATGGTATGTG 58.338 37.500 5.91 0.00 36.90 3.21
2642 3444 6.375174 TGAATGGAATGGTATGTGCTATATGC 59.625 38.462 0.00 0.00 43.25 3.14
2667 3470 6.183360 CCAGCATGAATTTAACATTTCACTGC 60.183 38.462 0.00 13.86 39.69 4.40
2787 3611 2.351726 GCTTGTGTGGATCGTACATTCC 59.648 50.000 4.95 4.47 0.00 3.01
2810 3634 6.216662 TCCATAAACTGGGAGAATGAGGTAAA 59.783 38.462 0.00 0.00 45.98 2.01
2846 3683 4.627035 GCACAGCACCATAAAATTTTCCTC 59.373 41.667 6.72 0.00 0.00 3.71
2909 3764 5.695816 TCAATTAAAGCAAAAGACATGGTGC 59.304 36.000 0.00 0.00 37.26 5.01
2923 3778 4.826556 ACATGGTGCTAGAAACTTCTCTC 58.173 43.478 0.00 0.00 38.70 3.20
3039 3902 9.979897 ATTGTATGCACATTTAGGGATGTATAT 57.020 29.630 0.00 0.00 38.15 0.86
3059 3922 9.031537 TGTATATTACATATGGGTGTGTCTAGG 57.968 37.037 7.80 0.00 32.89 3.02
3060 3923 5.825593 ATTACATATGGGTGTGTCTAGGG 57.174 43.478 7.80 0.00 33.62 3.53
3061 3924 1.768870 ACATATGGGTGTGTCTAGGGC 59.231 52.381 7.80 0.00 0.00 5.19
3062 3925 1.768275 CATATGGGTGTGTCTAGGGCA 59.232 52.381 0.00 0.00 0.00 5.36
3063 3926 1.200519 TATGGGTGTGTCTAGGGCAC 58.799 55.000 10.20 10.20 37.37 5.01
3064 3927 0.840288 ATGGGTGTGTCTAGGGCACA 60.840 55.000 14.22 14.22 43.60 4.57
3065 3928 0.840288 TGGGTGTGTCTAGGGCACAT 60.840 55.000 18.92 0.00 46.66 3.21
3066 3929 0.107654 GGGTGTGTCTAGGGCACATC 60.108 60.000 18.92 18.25 46.66 3.06
3067 3930 0.905357 GGTGTGTCTAGGGCACATCT 59.095 55.000 18.92 0.00 46.66 2.90
3068 3931 2.108168 GGTGTGTCTAGGGCACATCTA 58.892 52.381 18.92 0.21 46.66 1.98
3069 3932 2.101582 GGTGTGTCTAGGGCACATCTAG 59.898 54.545 18.92 0.00 46.66 2.43
3070 3933 3.024547 GTGTGTCTAGGGCACATCTAGA 58.975 50.000 18.92 0.00 46.66 2.43
3071 3934 3.639094 GTGTGTCTAGGGCACATCTAGAT 59.361 47.826 18.92 0.00 46.66 1.98
3072 3935 3.638627 TGTGTCTAGGGCACATCTAGATG 59.361 47.826 27.63 27.63 43.25 2.90
3097 3960 6.878317 TGCTCTAGTTATTGCACATCTAAGT 58.122 36.000 0.00 0.00 0.00 2.24
3098 3961 6.758416 TGCTCTAGTTATTGCACATCTAAGTG 59.242 38.462 0.00 0.00 42.37 3.16
3099 3962 6.980978 GCTCTAGTTATTGCACATCTAAGTGA 59.019 38.462 0.00 0.00 42.05 3.41
3100 3963 7.168972 GCTCTAGTTATTGCACATCTAAGTGAG 59.831 40.741 0.00 0.00 42.05 3.51
3101 3964 8.067751 TCTAGTTATTGCACATCTAAGTGAGT 57.932 34.615 0.00 0.00 42.05 3.41
3102 3965 6.974932 AGTTATTGCACATCTAAGTGAGTG 57.025 37.500 0.00 0.00 42.05 3.51
3103 3966 6.701340 AGTTATTGCACATCTAAGTGAGTGA 58.299 36.000 0.00 0.00 42.05 3.41
3104 3967 7.161404 AGTTATTGCACATCTAAGTGAGTGAA 58.839 34.615 0.00 0.00 42.05 3.18
3105 3968 7.826252 AGTTATTGCACATCTAAGTGAGTGAAT 59.174 33.333 0.00 0.00 42.05 2.57
3106 3969 6.674694 ATTGCACATCTAAGTGAGTGAATC 57.325 37.500 0.00 0.00 42.05 2.52
3107 3970 5.151297 TGCACATCTAAGTGAGTGAATCA 57.849 39.130 0.00 0.00 42.05 2.57
3108 3971 5.550290 TGCACATCTAAGTGAGTGAATCAA 58.450 37.500 0.00 0.00 42.05 2.57
3109 3972 5.640783 TGCACATCTAAGTGAGTGAATCAAG 59.359 40.000 0.00 0.00 42.05 3.02
3110 3973 5.641209 GCACATCTAAGTGAGTGAATCAAGT 59.359 40.000 0.00 0.00 42.05 3.16
3111 3974 6.813649 GCACATCTAAGTGAGTGAATCAAGTA 59.186 38.462 0.00 0.00 42.05 2.24
3112 3975 7.493971 GCACATCTAAGTGAGTGAATCAAGTAT 59.506 37.037 0.00 0.00 42.05 2.12
3156 4019 9.442047 AGAGAAAGAAAATATTCACACGAATCT 57.558 29.630 0.00 0.00 41.09 2.40
3157 4020 9.695884 GAGAAAGAAAATATTCACACGAATCTC 57.304 33.333 0.00 0.00 41.09 2.75
3158 4021 9.219603 AGAAAGAAAATATTCACACGAATCTCA 57.780 29.630 0.00 0.00 41.09 3.27
3159 4022 9.825972 GAAAGAAAATATTCACACGAATCTCAA 57.174 29.630 0.00 0.00 41.09 3.02
3161 4024 9.778993 AAGAAAATATTCACACGAATCTCAATG 57.221 29.630 0.00 0.00 41.09 2.82
3162 4025 8.950210 AGAAAATATTCACACGAATCTCAATGT 58.050 29.630 0.00 0.00 41.09 2.71
3166 4029 9.599866 AATATTCACACGAATCTCAATGTAAGA 57.400 29.630 0.00 0.00 41.09 2.10
3167 4030 9.770097 ATATTCACACGAATCTCAATGTAAGAT 57.230 29.630 0.00 0.00 41.09 2.40
3168 4031 7.525688 TTCACACGAATCTCAATGTAAGATC 57.474 36.000 0.00 0.00 32.29 2.75
3169 4032 6.630071 TCACACGAATCTCAATGTAAGATCA 58.370 36.000 0.00 0.00 32.29 2.92
3170 4033 7.096551 TCACACGAATCTCAATGTAAGATCAA 58.903 34.615 0.00 0.00 32.29 2.57
3171 4034 7.765819 TCACACGAATCTCAATGTAAGATCAAT 59.234 33.333 0.00 0.00 32.29 2.57
3172 4035 7.849515 CACACGAATCTCAATGTAAGATCAATG 59.150 37.037 0.00 0.00 32.29 2.82
3173 4036 7.011763 ACACGAATCTCAATGTAAGATCAATGG 59.988 37.037 0.00 0.00 32.29 3.16
3174 4037 6.017605 ACGAATCTCAATGTAAGATCAATGGC 60.018 38.462 0.00 0.00 32.29 4.40
3175 4038 6.017687 CGAATCTCAATGTAAGATCAATGGCA 60.018 38.462 0.00 0.00 32.29 4.92
3176 4039 7.308408 CGAATCTCAATGTAAGATCAATGGCAT 60.308 37.037 0.00 0.00 32.29 4.40
3177 4040 8.929260 AATCTCAATGTAAGATCAATGGCATA 57.071 30.769 0.00 0.00 32.29 3.14
3178 4041 9.529823 AATCTCAATGTAAGATCAATGGCATAT 57.470 29.630 0.00 0.00 32.29 1.78
3191 4054 9.512435 GATCAATGGCATATAATTTAGATGTGC 57.488 33.333 0.00 3.39 39.82 4.57
3192 4055 8.406730 TCAATGGCATATAATTTAGATGTGCA 57.593 30.769 0.00 0.00 41.66 4.57
3193 4056 8.858094 TCAATGGCATATAATTTAGATGTGCAA 58.142 29.630 0.00 0.63 41.66 4.08
3194 4057 9.647797 CAATGGCATATAATTTAGATGTGCAAT 57.352 29.630 0.00 2.68 41.66 3.56
3197 4060 9.519191 TGGCATATAATTTAGATGTGCAATACT 57.481 29.630 11.54 0.00 41.66 2.12
3204 4067 7.822161 ATTTAGATGTGCAATACTTATGGCA 57.178 32.000 0.00 0.00 40.19 4.92
3270 4133 3.289836 TGAAATACATCCTGCCATGTGG 58.710 45.455 3.84 0.00 37.57 4.17
3273 4136 4.518278 AATACATCCTGCCATGTGGTAA 57.482 40.909 0.35 0.00 37.57 2.85
3430 4315 7.778470 AATTTTCAAGTTCTATCTAGCTCCG 57.222 36.000 0.00 0.00 0.00 4.63
3431 4316 5.916661 TTTCAAGTTCTATCTAGCTCCGT 57.083 39.130 0.00 0.00 0.00 4.69
3450 4335 5.249420 TCCGTATCAAAAATCCACACATCA 58.751 37.500 0.00 0.00 0.00 3.07
3477 4362 6.575083 ATTGTCTATCGAGTGTTTCATTCG 57.425 37.500 8.02 8.02 43.22 3.34
3496 4381 7.595604 TCATTCGCGTGGAATATATACTTGTA 58.404 34.615 5.77 0.00 43.52 2.41
3507 4392 8.936864 GGAATATATACTTGTAGTTGGATGTGC 58.063 37.037 0.00 0.00 0.00 4.57
3509 4394 9.845740 AATATATACTTGTAGTTGGATGTGCAA 57.154 29.630 0.00 0.00 0.00 4.08
3560 4445 3.684788 GTCACAAGCCGATAGTTCAACAT 59.315 43.478 0.00 0.00 0.00 2.71
3561 4446 4.154195 GTCACAAGCCGATAGTTCAACATT 59.846 41.667 0.00 0.00 0.00 2.71
3613 4498 5.290158 GCAATTGAAATAGACCAACATGCAG 59.710 40.000 10.34 0.00 37.88 4.41
3630 4515 7.317842 ACATGCAGATTCAAGATACAAGAAG 57.682 36.000 0.00 0.00 0.00 2.85
3631 4516 6.883217 ACATGCAGATTCAAGATACAAGAAGT 59.117 34.615 0.00 0.00 0.00 3.01
3632 4517 6.732531 TGCAGATTCAAGATACAAGAAGTG 57.267 37.500 0.00 0.00 0.00 3.16
3642 4527 2.103153 ACAAGAAGTGACTCCCTCCA 57.897 50.000 0.00 0.00 0.00 3.86
3652 4537 4.592351 AGTGACTCCCTCCATCTCATAATG 59.408 45.833 0.00 0.00 0.00 1.90
3800 4688 9.472361 TGATCGCCTCAACTAATTAAGTAATAC 57.528 33.333 0.00 0.00 37.50 1.89
3850 4738 5.633830 ATTGACTCAAAATGAAGCATCGT 57.366 34.783 0.00 0.00 0.00 3.73
3858 4746 2.550830 ATGAAGCATCGTGGGGATAC 57.449 50.000 0.00 0.00 32.85 2.24
3863 4751 1.021968 GCATCGTGGGGATACAAACC 58.978 55.000 0.00 0.00 39.74 3.27
3864 4752 1.680555 GCATCGTGGGGATACAAACCA 60.681 52.381 0.00 0.00 39.74 3.67
3885 4796 3.743167 GACTAGTATGCGCGCGCG 61.743 66.667 45.73 45.73 45.51 6.86
3903 4814 1.520564 GCACACACACAGTCCGTCA 60.521 57.895 0.00 0.00 0.00 4.35
3922 4833 5.492854 CGTCATCAACACTATTGAATTCCG 58.507 41.667 2.27 0.00 31.55 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
163 164 3.840991 AGGTTTTCACCCTAAAGAACCC 58.159 45.455 0.00 0.00 45.63 4.11
194 196 1.200519 CCGGATCCAACCACCTAAGA 58.799 55.000 13.41 0.00 0.00 2.10
441 458 1.514087 CCGGCCTCTGCGTAACTAA 59.486 57.895 0.00 0.00 38.85 2.24
475 492 5.378230 TGGAGCATCAAGAGGATACAAAT 57.622 39.130 0.00 0.00 36.25 2.32
521 539 7.533222 GCTGCATGAGTTATTCATTTTCGATAG 59.467 37.037 0.00 0.00 44.14 2.08
542 560 0.894141 AAATATTGCCGGTTGCTGCA 59.106 45.000 1.90 0.00 42.00 4.41
553 571 3.002246 TGAGCCGTCGAATGAAATATTGC 59.998 43.478 0.00 0.00 0.00 3.56
563 581 0.389948 GAAGTGGTGAGCCGTCGAAT 60.390 55.000 0.00 0.00 37.67 3.34
720 738 6.665992 ATGGTGAGTGTTGTTCTTACTAGA 57.334 37.500 0.00 0.00 0.00 2.43
906 942 8.517878 CATTTGTGGAGATCATTTTCTACAGTT 58.482 33.333 0.00 0.00 37.25 3.16
947 983 1.208052 GCAGATGAGAAGTGGGCACTA 59.792 52.381 0.00 0.00 41.58 2.74
950 986 0.035725 CAGCAGATGAGAAGTGGGCA 60.036 55.000 0.00 0.00 0.00 5.36
972 1008 5.297278 TGTGAGCTCTAGTTTACTAGCTAGC 59.703 44.000 20.91 16.79 44.24 3.42
974 1010 7.110810 TCTTGTGAGCTCTAGTTTACTAGCTA 58.889 38.462 16.19 0.00 44.24 3.32
1140 1552 1.742880 CATCACGGACACCAGCTGG 60.743 63.158 31.60 31.60 42.17 4.85
1293 1705 1.982938 GAGGAGGTGGTACTGCCGT 60.983 63.158 0.00 0.00 41.21 5.68
1378 1790 2.598787 GGATCCGGGTGGTGTTGGA 61.599 63.158 0.00 0.00 36.30 3.53
1560 1972 2.355513 GCAGATGAGGATGTGGTTCAGT 60.356 50.000 0.00 0.00 0.00 3.41
1600 2013 1.610086 CTTTGCTCCCCATGCCCAA 60.610 57.895 0.00 0.00 0.00 4.12
1690 2111 4.749310 CGTCCTCTTGCAGGCGCT 62.749 66.667 7.64 0.00 43.08 5.92
2178 2769 1.069500 GGAAACGCGTGTGCTGTATTT 60.069 47.619 14.98 0.00 39.65 1.40
2351 2942 7.995052 AGGTATCATCCTGGCAATATATGTA 57.005 36.000 0.00 0.00 36.35 2.29
2402 2993 3.664107 TGAAAGAGAAGTGTGGATTCCG 58.336 45.455 0.00 0.00 0.00 4.30
2433 3035 3.005261 CGTGGAAATGTGGGAATTTCACA 59.995 43.478 14.90 14.90 44.77 3.58
2450 3052 3.119173 CCCGGTTGTAGTAAATACGTGGA 60.119 47.826 0.00 0.00 37.17 4.02
2607 3396 4.035112 ACCATTCCATTCAAATGCAGGAT 58.965 39.130 0.00 0.00 35.08 3.24
2634 3423 6.680810 TGTTAAATTCATGCTGGCATATAGC 58.319 36.000 7.79 0.00 44.65 2.97
2642 3444 6.183360 GCAGTGAAATGTTAAATTCATGCTGG 60.183 38.462 0.00 0.00 37.82 4.85
2667 3470 1.884579 GGCATGCTCTATTCATGTGGG 59.115 52.381 18.92 0.00 42.34 4.61
2787 3611 7.415653 GCTTTTACCTCATTCTCCCAGTTTATG 60.416 40.741 0.00 0.00 0.00 1.90
2909 3764 3.851098 CAACCGGGAGAGAAGTTTCTAG 58.149 50.000 6.32 0.00 37.73 2.43
2923 3778 0.609131 AGGTTCTTCATGCAACCGGG 60.609 55.000 6.32 0.00 45.92 5.73
2983 3840 3.527253 TCAAAATGGGAGAATGGCCTAGA 59.473 43.478 3.32 0.00 0.00 2.43
3011 3874 7.422465 ACATCCCTAAATGTGCATACAATTT 57.578 32.000 0.00 0.00 40.84 1.82
3012 3875 8.710749 ATACATCCCTAAATGTGCATACAATT 57.289 30.769 0.00 0.00 40.08 2.32
3014 3877 9.806448 AATATACATCCCTAAATGTGCATACAA 57.194 29.630 0.00 0.00 40.08 2.41
3026 3889 9.569074 ACACCCATATGTAATATACATCCCTAA 57.431 33.333 6.30 0.00 45.83 2.69
3039 3902 3.389983 GCCCTAGACACACCCATATGTAA 59.610 47.826 1.24 0.00 0.00 2.41
3047 3910 3.478780 TGTGCCCTAGACACACCC 58.521 61.111 12.81 0.00 42.88 4.61
3051 3914 4.250116 CATCTAGATGTGCCCTAGACAC 57.750 50.000 22.42 8.47 43.57 3.67
3073 3936 6.758416 CACTTAGATGTGCAATAACTAGAGCA 59.242 38.462 0.00 0.00 34.10 4.26
3074 3937 6.980978 TCACTTAGATGTGCAATAACTAGAGC 59.019 38.462 0.00 0.00 37.81 4.09
3075 3938 8.194104 ACTCACTTAGATGTGCAATAACTAGAG 58.806 37.037 0.00 0.00 37.81 2.43
3076 3939 7.976175 CACTCACTTAGATGTGCAATAACTAGA 59.024 37.037 0.00 0.00 37.81 2.43
3077 3940 7.976175 TCACTCACTTAGATGTGCAATAACTAG 59.024 37.037 0.00 0.00 37.81 2.57
3078 3941 7.836842 TCACTCACTTAGATGTGCAATAACTA 58.163 34.615 0.00 0.00 37.81 2.24
3079 3942 6.701340 TCACTCACTTAGATGTGCAATAACT 58.299 36.000 0.00 0.00 37.81 2.24
3080 3943 6.968131 TCACTCACTTAGATGTGCAATAAC 57.032 37.500 0.00 0.00 37.81 1.89
3081 3944 7.823799 TGATTCACTCACTTAGATGTGCAATAA 59.176 33.333 0.00 0.00 37.81 1.40
3082 3945 7.330262 TGATTCACTCACTTAGATGTGCAATA 58.670 34.615 0.00 0.00 37.81 1.90
3083 3946 6.175471 TGATTCACTCACTTAGATGTGCAAT 58.825 36.000 0.00 0.00 37.81 3.56
3084 3947 5.550290 TGATTCACTCACTTAGATGTGCAA 58.450 37.500 0.00 0.00 37.81 4.08
3085 3948 5.151297 TGATTCACTCACTTAGATGTGCA 57.849 39.130 0.00 0.00 37.81 4.57
3086 3949 5.641209 ACTTGATTCACTCACTTAGATGTGC 59.359 40.000 0.00 0.00 37.81 4.57
3087 3950 8.939201 ATACTTGATTCACTCACTTAGATGTG 57.061 34.615 0.00 0.00 39.15 3.21
3130 3993 9.442047 AGATTCGTGTGAATATTTTCTTTCTCT 57.558 29.630 0.00 0.00 44.79 3.10
3131 3994 9.695884 GAGATTCGTGTGAATATTTTCTTTCTC 57.304 33.333 0.00 0.00 44.79 2.87
3132 3995 9.219603 TGAGATTCGTGTGAATATTTTCTTTCT 57.780 29.630 0.00 0.00 44.79 2.52
3133 3996 9.825972 TTGAGATTCGTGTGAATATTTTCTTTC 57.174 29.630 0.00 0.00 44.79 2.62
3135 3998 9.778993 CATTGAGATTCGTGTGAATATTTTCTT 57.221 29.630 0.00 0.00 44.79 2.52
3136 3999 8.950210 ACATTGAGATTCGTGTGAATATTTTCT 58.050 29.630 0.00 0.00 44.79 2.52
3140 4003 9.599866 TCTTACATTGAGATTCGTGTGAATATT 57.400 29.630 0.00 0.00 44.79 1.28
3141 4004 9.770097 ATCTTACATTGAGATTCGTGTGAATAT 57.230 29.630 0.00 0.00 44.79 1.28
3142 4005 9.249457 GATCTTACATTGAGATTCGTGTGAATA 57.751 33.333 0.00 0.00 44.79 1.75
3144 4007 7.096551 TGATCTTACATTGAGATTCGTGTGAA 58.903 34.615 0.00 0.00 38.76 3.18
3145 4008 6.630071 TGATCTTACATTGAGATTCGTGTGA 58.370 36.000 0.00 0.00 34.13 3.58
3146 4009 6.892310 TGATCTTACATTGAGATTCGTGTG 57.108 37.500 0.00 0.00 34.13 3.82
3147 4010 7.011763 CCATTGATCTTACATTGAGATTCGTGT 59.988 37.037 0.00 0.00 34.13 4.49
3148 4011 7.350467 CCATTGATCTTACATTGAGATTCGTG 58.650 38.462 0.00 0.00 34.13 4.35
3149 4012 6.017605 GCCATTGATCTTACATTGAGATTCGT 60.018 38.462 0.00 0.00 34.13 3.85
3150 4013 6.017687 TGCCATTGATCTTACATTGAGATTCG 60.018 38.462 0.00 0.00 34.13 3.34
3151 4014 7.268199 TGCCATTGATCTTACATTGAGATTC 57.732 36.000 0.00 0.00 34.13 2.52
3152 4015 7.834881 ATGCCATTGATCTTACATTGAGATT 57.165 32.000 0.00 0.00 34.13 2.40
3165 4028 9.512435 GCACATCTAAATTATATGCCATTGATC 57.488 33.333 0.00 0.00 0.00 2.92
3166 4029 9.027202 TGCACATCTAAATTATATGCCATTGAT 57.973 29.630 0.00 0.00 0.00 2.57
3167 4030 8.406730 TGCACATCTAAATTATATGCCATTGA 57.593 30.769 0.00 0.00 0.00 2.57
3168 4031 9.647797 ATTGCACATCTAAATTATATGCCATTG 57.352 29.630 0.00 0.00 0.00 2.82
3171 4034 9.519191 AGTATTGCACATCTAAATTATATGCCA 57.481 29.630 0.00 0.00 0.00 4.92
3178 4041 9.348476 TGCCATAAGTATTGCACATCTAAATTA 57.652 29.630 0.00 0.00 30.49 1.40
3179 4042 8.236585 TGCCATAAGTATTGCACATCTAAATT 57.763 30.769 0.00 0.00 30.49 1.82
3180 4043 7.822161 TGCCATAAGTATTGCACATCTAAAT 57.178 32.000 0.00 0.00 30.49 1.40
3189 4052 6.173427 TCTAGATGTGCCATAAGTATTGCA 57.827 37.500 0.00 0.00 32.69 4.08
3190 4053 7.069852 CATCTAGATGTGCCATAAGTATTGC 57.930 40.000 22.42 0.00 34.23 3.56
3423 4308 4.873827 GTGTGGATTTTTGATACGGAGCTA 59.126 41.667 0.00 0.00 0.00 3.32
3457 4342 3.061797 CGCGAATGAAACACTCGATAGAC 60.062 47.826 0.00 0.00 42.67 2.59
3477 4362 7.149973 TCCAACTACAAGTATATATTCCACGC 58.850 38.462 0.00 0.00 0.00 5.34
3496 4381 3.518634 AAACGTTTTGCACATCCAACT 57.481 38.095 7.96 0.00 0.00 3.16
3519 4404 7.135591 TGTGACATTATGTGATTCCTCCATA 57.864 36.000 1.24 0.00 0.00 2.74
3520 4405 6.005066 TGTGACATTATGTGATTCCTCCAT 57.995 37.500 1.24 0.00 0.00 3.41
3521 4406 5.434182 TGTGACATTATGTGATTCCTCCA 57.566 39.130 1.24 0.00 0.00 3.86
3522 4407 5.220931 GCTTGTGACATTATGTGATTCCTCC 60.221 44.000 1.24 0.00 0.00 4.30
3561 4446 8.898761 TGTTGATCTAAGCTTCAGTAACAAAAA 58.101 29.630 0.00 0.00 0.00 1.94
3596 4481 6.660521 TCTTGAATCTGCATGTTGGTCTATTT 59.339 34.615 0.00 0.00 0.00 1.40
3613 4498 6.536941 GGGAGTCACTTCTTGTATCTTGAATC 59.463 42.308 0.00 0.00 0.00 2.52
3630 4515 4.346418 ACATTATGAGATGGAGGGAGTCAC 59.654 45.833 0.00 0.00 0.00 3.67
3631 4516 4.560739 ACATTATGAGATGGAGGGAGTCA 58.439 43.478 0.00 0.00 0.00 3.41
3632 4517 6.495181 TCTTACATTATGAGATGGAGGGAGTC 59.505 42.308 0.00 0.00 0.00 3.36
3642 4527 7.732140 TCTGTCCCAGATCTTACATTATGAGAT 59.268 37.037 0.00 0.00 35.39 2.75
3652 4537 2.696187 GTCCCTCTGTCCCAGATCTTAC 59.304 54.545 0.00 0.00 39.92 2.34
3848 4736 3.085533 TCATTTGGTTTGTATCCCCACG 58.914 45.455 0.00 0.00 0.00 4.94
3850 4738 4.396357 AGTCATTTGGTTTGTATCCCCA 57.604 40.909 0.00 0.00 0.00 4.96
3858 4746 4.342772 GCGCATACTAGTCATTTGGTTTG 58.657 43.478 0.30 0.00 0.00 2.93
3863 4751 1.395944 CGCGCGCATACTAGTCATTTG 60.396 52.381 32.61 5.06 0.00 2.32
3864 4752 0.852777 CGCGCGCATACTAGTCATTT 59.147 50.000 32.61 0.00 0.00 2.32
3885 4796 0.880278 ATGACGGACTGTGTGTGTGC 60.880 55.000 0.00 0.00 0.00 4.57
3894 4805 4.494484 TCAATAGTGTTGATGACGGACTG 58.506 43.478 0.00 0.00 0.00 3.51
3895 4806 4.801330 TCAATAGTGTTGATGACGGACT 57.199 40.909 0.00 0.00 0.00 3.85
3903 4814 4.096382 GCCACGGAATTCAATAGTGTTGAT 59.904 41.667 7.93 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.