Multiple sequence alignment - TraesCS5B01G414500

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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 TraesCS5B01G414500 chr5B 100.000 3981 0 0 1 3981 588831720 588835700 0.000000e+00 7352.0
1 TraesCS5B01G414500 chr5B 87.155 1448 146 20 2016 3433 588779621 588781058 0.000000e+00 1607.0
2 TraesCS5B01G414500 chr5B 87.030 1010 88 27 1 987 588777419 588778408 0.000000e+00 1099.0
3 TraesCS5B01G414500 chr5B 84.972 905 87 18 1080 1942 588778607 588779504 0.000000e+00 872.0
4 TraesCS5B01G414500 chr5B 95.547 539 23 1 3443 3981 355621400 355621937 0.000000e+00 861.0
5 TraesCS5B01G414500 chr5B 94.640 541 28 1 3441 3981 554767303 554767842 0.000000e+00 837.0
6 TraesCS5B01G414500 chr5B 86.420 324 35 6 3105 3424 588691034 588691352 2.940000e-91 346.0
7 TraesCS5B01G414500 chr5A 87.803 1443 136 22 2020 3433 599452366 599453797 0.000000e+00 1653.0
8 TraesCS5B01G414500 chr5A 92.543 979 58 12 4 977 599448189 599449157 0.000000e+00 1389.0
9 TraesCS5B01G414500 chr5A 91.121 901 46 23 1080 1960 599451238 599452124 0.000000e+00 1190.0
10 TraesCS5B01G414500 chr5A 88.649 881 71 17 4 881 599389649 599390503 0.000000e+00 1046.0
11 TraesCS5B01G414500 chr5A 88.682 751 74 8 2312 3059 599392207 599392949 0.000000e+00 905.0
12 TraesCS5B01G414500 chr5A 86.649 749 58 18 1080 1821 599390814 599391527 0.000000e+00 791.0
13 TraesCS5B01G414500 chr5A 93.255 341 22 1 3094 3433 599393236 599393576 5.940000e-138 501.0
14 TraesCS5B01G414500 chr5A 85.802 324 38 5 3105 3424 599254004 599254323 1.770000e-88 337.0
15 TraesCS5B01G414500 chr5A 89.333 75 3 2 1007 1076 599390710 599390784 5.480000e-14 89.8
16 TraesCS5B01G414500 chr5A 92.982 57 2 2 983 1037 599451161 599451217 9.170000e-12 82.4
17 TraesCS5B01G414500 chr6B 95.264 549 22 4 3434 3981 710925665 710925120 0.000000e+00 867.0
18 TraesCS5B01G414500 chr6B 94.353 549 27 4 3434 3981 710952386 710951841 0.000000e+00 839.0
19 TraesCS5B01G414500 chr6B 79.114 158 33 0 1320 1477 691783627 691783470 4.210000e-20 110.0
20 TraesCS5B01G414500 chr6B 85.437 103 15 0 1130 1232 692016788 692016686 1.510000e-19 108.0
21 TraesCS5B01G414500 chr6B 84.466 103 16 0 1130 1232 691795203 691795101 7.040000e-18 102.0
22 TraesCS5B01G414500 chr2D 95.009 541 26 1 3441 3981 159336012 159335473 0.000000e+00 848.0
23 TraesCS5B01G414500 chr2D 77.959 490 77 15 255 734 7718700 7719168 1.090000e-70 278.0
24 TraesCS5B01G414500 chr5D 94.991 539 26 1 3443 3981 220683830 220684367 0.000000e+00 845.0
25 TraesCS5B01G414500 chr5D 86.916 321 35 5 3105 3424 480493829 480494143 1.760000e-93 353.0
26 TraesCS5B01G414500 chr3B 94.649 542 26 3 3441 3981 44328333 44328872 0.000000e+00 837.0
27 TraesCS5B01G414500 chr3B 94.640 541 28 1 3441 3981 802623324 802623863 0.000000e+00 837.0
28 TraesCS5B01G414500 chr1B 94.569 534 28 1 3448 3981 542604870 542605402 0.000000e+00 824.0
29 TraesCS5B01G414500 chr2B 79.093 904 139 32 1 867 4186081 4185191 9.590000e-161 577.0
30 TraesCS5B01G414500 chr2B 79.070 903 140 33 1 867 3907075 3906186 3.450000e-160 575.0
31 TraesCS5B01G414500 chr7D 88.934 244 26 1 3187 3430 199129942 199130184 2.330000e-77 300.0
32 TraesCS5B01G414500 chr7B 87.200 250 31 1 3184 3433 163010965 163011213 2.340000e-72 283.0
33 TraesCS5B01G414500 chr7A 87.449 247 30 1 3187 3433 208526356 208526601 2.340000e-72 283.0
34 TraesCS5B01G414500 chr6D 85.000 100 15 0 1130 1229 454734291 454734390 7.040000e-18 102.0
35 TraesCS5B01G414500 chr6D 81.553 103 19 0 1130 1232 454926849 454926747 7.090000e-13 86.1
36 TraesCS5B01G414500 chr6A 80.488 123 24 0 1107 1229 600978135 600978013 1.180000e-15 95.3
37 TraesCS5B01G414500 chr6A 78.740 127 27 0 1107 1233 601033070 601032944 7.090000e-13 86.1


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 TraesCS5B01G414500 chr5B 588831720 588835700 3980 False 7352.000000 7352 100.000000 1 3981 1 chr5B.!!$F4 3980
1 TraesCS5B01G414500 chr5B 588777419 588781058 3639 False 1192.666667 1607 86.385667 1 3433 3 chr5B.!!$F5 3432
2 TraesCS5B01G414500 chr5B 355621400 355621937 537 False 861.000000 861 95.547000 3443 3981 1 chr5B.!!$F1 538
3 TraesCS5B01G414500 chr5B 554767303 554767842 539 False 837.000000 837 94.640000 3441 3981 1 chr5B.!!$F2 540
4 TraesCS5B01G414500 chr5A 599448189 599453797 5608 False 1078.600000 1653 91.112250 4 3433 4 chr5A.!!$F3 3429
5 TraesCS5B01G414500 chr5A 599389649 599393576 3927 False 666.560000 1046 89.313600 4 3433 5 chr5A.!!$F2 3429
6 TraesCS5B01G414500 chr6B 710925120 710925665 545 True 867.000000 867 95.264000 3434 3981 1 chr6B.!!$R4 547
7 TraesCS5B01G414500 chr6B 710951841 710952386 545 True 839.000000 839 94.353000 3434 3981 1 chr6B.!!$R5 547
8 TraesCS5B01G414500 chr2D 159335473 159336012 539 True 848.000000 848 95.009000 3441 3981 1 chr2D.!!$R1 540
9 TraesCS5B01G414500 chr5D 220683830 220684367 537 False 845.000000 845 94.991000 3443 3981 1 chr5D.!!$F1 538
10 TraesCS5B01G414500 chr3B 44328333 44328872 539 False 837.000000 837 94.649000 3441 3981 1 chr3B.!!$F1 540
11 TraesCS5B01G414500 chr3B 802623324 802623863 539 False 837.000000 837 94.640000 3441 3981 1 chr3B.!!$F2 540
12 TraesCS5B01G414500 chr1B 542604870 542605402 532 False 824.000000 824 94.569000 3448 3981 1 chr1B.!!$F1 533
13 TraesCS5B01G414500 chr2B 4185191 4186081 890 True 577.000000 577 79.093000 1 867 1 chr2B.!!$R2 866
14 TraesCS5B01G414500 chr2B 3906186 3907075 889 True 575.000000 575 79.070000 1 867 1 chr2B.!!$R1 866

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
374 408 1.280457 AAACTGAGTCCAGGCTAGGG 58.720 55.0 0.0 0.0 44.60 3.53 F
1243 3342 0.036164 AGGTACGCATCTTGCACCAA 59.964 50.0 10.5 0.0 45.36 3.67 F
1248 3347 0.244450 CGCATCTTGCACCAAACCAT 59.756 50.0 0.0 0.0 45.36 3.55 F
2567 5041 0.318441 CCATCTATGCCGACATCCGT 59.682 55.0 0.0 0.0 37.74 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1298 3401 0.316442 GATTGATGCACGACGCCATG 60.316 55.0 6.35 0.00 41.33 3.66 R
2522 4996 0.037734 CGTTGGGGTAGGCCTTCTTT 59.962 55.0 12.58 0.00 34.45 2.52 R
2831 5311 0.174845 TTGGAGAATCTGTACGGGCG 59.825 55.0 0.85 0.00 33.73 6.13 R
3904 6649 0.244994 AGTTTCTCGCTCGAGCACAT 59.755 50.0 34.69 13.05 41.71 3.21 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
145 152 2.100631 CACCGTTCCATCGTCTGCC 61.101 63.158 0.00 0.00 0.00 4.85
185 194 1.872952 TGCTGACATGGACTGAAAACG 59.127 47.619 0.00 0.00 0.00 3.60
287 321 3.257393 CTTGATCGTCTCCTGGTTGAAG 58.743 50.000 0.00 0.00 0.00 3.02
323 357 4.421479 CGGCGTCGCTTCCAGTCT 62.421 66.667 18.11 0.00 0.00 3.24
325 359 2.383527 GGCGTCGCTTCCAGTCTTG 61.384 63.158 18.11 0.00 0.00 3.02
353 387 1.683629 GCAAATATGACCCCGTTCCCA 60.684 52.381 0.00 0.00 0.00 4.37
355 389 3.093057 CAAATATGACCCCGTTCCCAAA 58.907 45.455 0.00 0.00 0.00 3.28
358 392 1.334160 ATGACCCCGTTCCCAAAAAC 58.666 50.000 0.00 0.00 0.00 2.43
371 405 2.224769 CCCAAAAACTGAGTCCAGGCTA 60.225 50.000 0.00 0.00 44.60 3.93
374 408 1.280457 AAACTGAGTCCAGGCTAGGG 58.720 55.000 0.00 0.00 44.60 3.53
383 417 2.168728 GTCCAGGCTAGGGTTCAAGTAG 59.831 54.545 0.00 0.00 0.00 2.57
386 420 2.168728 CAGGCTAGGGTTCAAGTAGTCC 59.831 54.545 0.00 0.00 0.00 3.85
389 423 3.118702 GGCTAGGGTTCAAGTAGTCCTTC 60.119 52.174 0.00 0.00 0.00 3.46
398 432 3.964688 TCAAGTAGTCCTTCTGGAACACA 59.035 43.478 0.00 0.00 45.18 3.72
408 442 2.608623 TCTGGAACACATCTGTCCTGA 58.391 47.619 0.00 0.00 0.00 3.86
703 744 1.842562 ACAAGCATCCTATGGCACTCT 59.157 47.619 0.00 0.00 0.00 3.24
805 846 4.973168 TCCAAATCAGATACCATACTGCC 58.027 43.478 0.00 0.00 34.57 4.85
852 893 4.060667 GGCCAGGGCTTGCCCTAA 62.061 66.667 30.31 0.00 41.97 2.69
877 918 2.119495 GGCTCCATGACTCTCCCTTTA 58.881 52.381 0.00 0.00 0.00 1.85
883 924 5.590818 TCCATGACTCTCCCTTTAGTACTT 58.409 41.667 0.00 0.00 0.00 2.24
884 925 5.422331 TCCATGACTCTCCCTTTAGTACTTG 59.578 44.000 0.00 0.00 0.00 3.16
885 926 4.803098 TGACTCTCCCTTTAGTACTTGC 57.197 45.455 0.00 0.00 0.00 4.01
891 943 6.046290 TCTCCCTTTAGTACTTGCTTAACC 57.954 41.667 0.00 0.00 0.00 2.85
893 945 6.955851 TCTCCCTTTAGTACTTGCTTAACCTA 59.044 38.462 0.00 0.00 0.00 3.08
906 958 5.437060 TGCTTAACCTATGATTGTTCTCCC 58.563 41.667 0.00 0.00 0.00 4.30
919 971 1.804748 GTTCTCCCGTAGCAGTTTTGG 59.195 52.381 0.00 0.00 0.00 3.28
945 1000 3.967326 ACTTATATAGCAGCACTGGACCA 59.033 43.478 0.00 0.00 0.00 4.02
950 1005 1.968540 GCAGCACTGGACCAAGACC 60.969 63.158 0.00 0.00 0.00 3.85
979 1036 5.045140 ACCCACTTGCCTAGCTTCTTTATAA 60.045 40.000 0.00 0.00 0.00 0.98
1038 3094 1.603455 CACGGCAACCCACAAGGAT 60.603 57.895 0.00 0.00 39.89 3.24
1039 3095 1.152830 ACGGCAACCCACAAGGATT 59.847 52.632 0.00 0.00 39.89 3.01
1061 3122 6.431198 TTGTTTGTGTAGTGGAAAGAGAAC 57.569 37.500 0.00 0.00 0.00 3.01
1076 3137 7.162082 GGAAAGAGAACCAATTTAGTCTCTCA 58.838 38.462 10.49 0.00 33.97 3.27
1077 3138 7.333174 GGAAAGAGAACCAATTTAGTCTCTCAG 59.667 40.741 10.49 0.00 33.97 3.35
1078 3139 6.926630 AGAGAACCAATTTAGTCTCTCAGT 57.073 37.500 5.94 0.00 33.31 3.41
1165 3252 1.682344 GGGGGCTTCATTGGGTCAC 60.682 63.158 0.00 0.00 0.00 3.67
1240 3339 1.369091 CCCAGGTACGCATCTTGCAC 61.369 60.000 0.00 0.00 45.36 4.57
1241 3340 1.369091 CCAGGTACGCATCTTGCACC 61.369 60.000 0.00 0.97 45.36 5.01
1242 3341 0.673333 CAGGTACGCATCTTGCACCA 60.673 55.000 10.50 0.00 45.36 4.17
1243 3342 0.036164 AGGTACGCATCTTGCACCAA 59.964 50.000 10.50 0.00 45.36 3.67
1244 3343 0.878416 GGTACGCATCTTGCACCAAA 59.122 50.000 4.60 0.00 45.36 3.28
1245 3344 1.401018 GGTACGCATCTTGCACCAAAC 60.401 52.381 4.60 0.00 45.36 2.93
1246 3345 0.878416 TACGCATCTTGCACCAAACC 59.122 50.000 0.00 0.00 45.36 3.27
1247 3346 1.106351 ACGCATCTTGCACCAAACCA 61.106 50.000 0.00 0.00 45.36 3.67
1248 3347 0.244450 CGCATCTTGCACCAAACCAT 59.756 50.000 0.00 0.00 45.36 3.55
1249 3348 1.717194 GCATCTTGCACCAAACCATG 58.283 50.000 0.00 0.00 44.26 3.66
1250 3349 1.717194 CATCTTGCACCAAACCATGC 58.283 50.000 0.00 0.00 42.40 4.06
1254 3353 3.054679 TGCACCAAACCATGCATCT 57.945 47.368 0.00 0.00 46.63 2.90
1255 3354 2.212812 TGCACCAAACCATGCATCTA 57.787 45.000 0.00 0.00 46.63 1.98
1256 3355 2.523245 TGCACCAAACCATGCATCTAA 58.477 42.857 0.00 0.00 46.63 2.10
1257 3356 3.098377 TGCACCAAACCATGCATCTAAT 58.902 40.909 0.00 0.00 46.63 1.73
1262 3361 7.233144 TGCACCAAACCATGCATCTAATTATAT 59.767 33.333 0.00 0.00 46.63 0.86
1298 3401 3.845781 TCTAATCCATCACCTGCTTCC 57.154 47.619 0.00 0.00 0.00 3.46
1367 3470 2.785389 AAACCTTGGAGGGGGCCA 60.785 61.111 4.39 0.00 40.58 5.36
1386 3489 2.158711 CCAATGAGAGGCTATCCTTGCA 60.159 50.000 18.11 0.00 44.46 4.08
1390 3493 0.978146 AGAGGCTATCCTTGCACCGT 60.978 55.000 0.00 0.00 44.46 4.83
1697 3832 0.800683 TCACTTCTTCGTATGGCGCG 60.801 55.000 0.00 0.00 41.07 6.86
1724 3859 1.152830 GAACCCCAACAGAAGCCCA 59.847 57.895 0.00 0.00 0.00 5.36
1821 3956 6.258160 AGCGACTTAACATTCATTGCAATAC 58.742 36.000 12.53 0.00 0.00 1.89
1822 3957 6.094048 AGCGACTTAACATTCATTGCAATACT 59.906 34.615 12.53 0.00 0.00 2.12
1823 3958 7.279981 AGCGACTTAACATTCATTGCAATACTA 59.720 33.333 12.53 0.55 0.00 1.82
1824 3959 8.070171 GCGACTTAACATTCATTGCAATACTAT 58.930 33.333 12.53 3.07 0.00 2.12
1825 3960 9.935682 CGACTTAACATTCATTGCAATACTATT 57.064 29.630 12.53 6.05 0.00 1.73
1864 3999 9.386010 ACAAAAGGGTAAATTAAGGTGAAAAAC 57.614 29.630 0.00 0.00 0.00 2.43
1887 4049 7.149569 ACAACAGTATTTGGATCAATCACAG 57.850 36.000 0.00 0.00 0.00 3.66
1925 4087 3.080319 GCAATCAGCTGGGATAGATTCC 58.920 50.000 15.13 0.00 41.43 3.01
1926 4088 3.497405 GCAATCAGCTGGGATAGATTCCA 60.497 47.826 15.13 0.00 42.94 3.53
1944 4107 1.918293 AACAGCCACCTCCGATCCA 60.918 57.895 0.00 0.00 0.00 3.41
1960 4123 5.014123 TCCGATCCATTATCCTATGGCTTTT 59.986 40.000 0.00 0.00 43.94 2.27
1965 4128 5.063204 CCATTATCCTATGGCTTTTCGACA 58.937 41.667 0.00 0.00 38.75 4.35
1966 4129 5.180117 CCATTATCCTATGGCTTTTCGACAG 59.820 44.000 0.00 0.00 38.75 3.51
1967 4130 5.607939 TTATCCTATGGCTTTTCGACAGA 57.392 39.130 0.00 0.00 31.10 3.41
1968 4131 4.696479 ATCCTATGGCTTTTCGACAGAT 57.304 40.909 0.00 0.00 31.10 2.90
1975 4188 4.000988 TGGCTTTTCGACAGATTCCTAAC 58.999 43.478 0.00 0.00 0.00 2.34
1994 4208 6.960542 TCCTAACTGGAGAATTAGAGTTTCCT 59.039 38.462 0.00 0.00 40.56 3.36
2049 4394 7.669722 TCCAAATGAAAGTGATACTAAAAGGCT 59.330 33.333 0.00 0.00 0.00 4.58
2072 4417 6.918569 GCTATCATAGCGTCTTAGAAACTTGA 59.081 38.462 0.00 0.00 42.62 3.02
2113 4458 3.068873 GGTGCAGTGTTTGTTCCCAATTA 59.931 43.478 0.00 0.00 0.00 1.40
2160 4505 2.894126 ACAATTAATTTGTGGCACCCGA 59.106 40.909 16.26 0.79 46.80 5.14
2167 4512 0.817634 TTGTGGCACCCGAAAGTCAG 60.818 55.000 16.26 0.00 0.00 3.51
2169 4514 0.951040 GTGGCACCCGAAAGTCAGAG 60.951 60.000 6.29 0.00 0.00 3.35
2233 4581 0.639943 ACCCAAAACCTCCCAAACCT 59.360 50.000 0.00 0.00 0.00 3.50
2251 4606 6.070251 CCAAACCTATAGGAAAAGGCCAATTT 60.070 38.462 26.01 5.77 36.24 1.82
2300 4655 1.134220 TGGCCCGAAGCTAATTACCAG 60.134 52.381 0.00 0.00 43.05 4.00
2310 4665 7.870954 CCGAAGCTAATTACCAGACATAATACA 59.129 37.037 0.00 0.00 0.00 2.29
2409 4883 2.435586 CAGCAACGGAGGAGGCAG 60.436 66.667 0.00 0.00 0.00 4.85
2496 4970 2.561419 TCTCTAAACGGCAGCAACTACT 59.439 45.455 0.00 0.00 0.00 2.57
2498 4972 3.841643 TCTAAACGGCAGCAACTACTAC 58.158 45.455 0.00 0.00 0.00 2.73
2519 4993 1.819632 CGCAAGGTACCTGATGGGC 60.820 63.158 17.14 13.16 39.10 5.36
2522 4996 0.327924 CAAGGTACCTGATGGGCACA 59.672 55.000 17.14 0.00 39.10 4.57
2562 5036 1.067416 GTCGCCATCTATGCCGACA 59.933 57.895 18.32 0.00 46.57 4.35
2567 5041 0.318441 CCATCTATGCCGACATCCGT 59.682 55.000 0.00 0.00 37.74 4.69
2608 5082 2.202440 CGTCTACGAGCACCACCG 60.202 66.667 0.00 0.00 43.02 4.94
2711 5185 7.203910 CACACTATCCTATCACTTCCAAGTAC 58.796 42.308 0.00 0.00 37.08 2.73
2713 5187 3.795623 TCCTATCACTTCCAAGTACGC 57.204 47.619 0.00 0.00 37.08 4.42
2723 5197 4.274214 ACTTCCAAGTACGCTTTGTTTACC 59.726 41.667 0.00 0.00 37.52 2.85
2749 5223 2.238521 TGAATTGTCAACCTTCTGCCC 58.761 47.619 0.00 0.00 0.00 5.36
2750 5224 2.238521 GAATTGTCAACCTTCTGCCCA 58.761 47.619 0.00 0.00 0.00 5.36
2751 5225 2.380064 ATTGTCAACCTTCTGCCCAA 57.620 45.000 0.00 0.00 0.00 4.12
2772 5246 5.983118 CCAAATGCGCGTCCATATCTATATA 59.017 40.000 8.43 0.00 0.00 0.86
2831 5311 2.200170 GAACGACAAGCCCATGGTGC 62.200 60.000 11.73 13.78 0.00 5.01
2851 5331 1.202533 CGCCCGTACAGATTCTCCAAT 60.203 52.381 0.00 0.00 0.00 3.16
2860 5340 6.035435 CGTACAGATTCTCCAATCAAAGACTG 59.965 42.308 0.00 0.00 41.03 3.51
2861 5341 6.119240 ACAGATTCTCCAATCAAAGACTGA 57.881 37.500 0.00 0.00 41.03 3.41
2887 5367 5.501156 GACTTGGGGTTAGAATTCACTGAT 58.499 41.667 8.44 0.00 0.00 2.90
2888 5368 5.256474 ACTTGGGGTTAGAATTCACTGATG 58.744 41.667 8.44 0.00 0.00 3.07
2889 5369 5.014123 ACTTGGGGTTAGAATTCACTGATGA 59.986 40.000 8.44 0.00 0.00 2.92
2908 5388 8.200792 ACTGATGACATGAGGAAAACTCTATAC 58.799 37.037 6.85 0.00 46.72 1.47
2960 5449 0.321475 TGTGCGTCTCATCATGCCAA 60.321 50.000 0.00 0.00 0.00 4.52
2967 5456 2.686405 GTCTCATCATGCCAAATCAGCA 59.314 45.455 0.00 0.00 45.94 4.41
3002 5491 1.278985 TCAGGATGAAGTGCGACCAAT 59.721 47.619 0.00 0.00 45.97 3.16
3059 5548 6.039270 CCTTCTCAAAAGTAATTGTGTGGACA 59.961 38.462 0.00 0.00 0.00 4.02
3066 5555 7.817418 AAAGTAATTGTGTGGACATGTAAGT 57.183 32.000 0.00 0.00 30.13 2.24
3067 5556 6.801539 AGTAATTGTGTGGACATGTAAGTG 57.198 37.500 0.00 0.00 30.13 3.16
3068 5557 5.705441 AGTAATTGTGTGGACATGTAAGTGG 59.295 40.000 0.00 0.00 30.13 4.00
3074 5563 4.522789 GTGTGGACATGTAAGTGGGAAAAT 59.477 41.667 0.00 0.00 0.00 1.82
3076 5565 5.943416 TGTGGACATGTAAGTGGGAAAATAG 59.057 40.000 0.00 0.00 0.00 1.73
3086 5583 8.988060 TGTAAGTGGGAAAATAGTCAGATATCA 58.012 33.333 5.32 0.00 0.00 2.15
3127 5869 7.176490 TGCATTGGAATGGATGTATCATGATA 58.824 34.615 11.49 11.49 36.90 2.15
3178 5920 7.538334 TGCAAGATGTTATGAAAATTGAAGACG 59.462 33.333 0.00 0.00 0.00 4.18
3182 5925 5.379003 TGTTATGAAAATTGAAGACGCGAC 58.621 37.500 15.93 6.86 0.00 5.19
3240 5983 9.823647 TTACAAAAGGTTGAAAATCAATTAGCA 57.176 25.926 0.00 0.00 38.79 3.49
3437 6182 5.401531 AAAGCCTCAGATTACGAGTGTTA 57.598 39.130 0.00 0.00 0.00 2.41
3446 6191 6.602009 TCAGATTACGAGTGTTAGGAATGAGA 59.398 38.462 0.00 0.00 0.00 3.27
3492 6237 7.201902 CCAAAGGCCAATACATATACATGTGTT 60.202 37.037 9.11 0.00 44.52 3.32
3543 6288 0.257905 GGGATAAGCCGAAAAGGGGT 59.742 55.000 0.00 0.00 41.48 4.95
3553 6298 4.164604 AGCCGAAAAGGGGTTATACACATA 59.835 41.667 0.00 0.00 41.48 2.29
3620 6365 5.745312 TGGAGAGAAGAAAACTATGCTGA 57.255 39.130 0.00 0.00 0.00 4.26
3664 6409 4.820894 AGAAGTCCGCCAACTATAACTT 57.179 40.909 0.00 0.00 0.00 2.66
3668 6413 6.324254 AGAAGTCCGCCAACTATAACTTAGAT 59.676 38.462 0.00 0.00 0.00 1.98
3670 6415 5.597182 AGTCCGCCAACTATAACTTAGATGA 59.403 40.000 0.00 0.00 0.00 2.92
3677 6422 9.542462 GCCAACTATAACTTAGATGACACATAA 57.458 33.333 0.00 0.00 0.00 1.90
3694 6439 5.105554 ACACATAATGAAGAGCGAGAGTCTT 60.106 40.000 0.00 0.00 36.95 3.01
3908 6653 1.284657 CTCGCAACTCAGCCTATGTG 58.715 55.000 0.00 0.00 0.00 3.21
3945 6690 3.206150 GCAGTCTGTTTCTTGGTCTTCA 58.794 45.455 0.93 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 128 2.358247 GATGGAACGGTGGTGCGT 60.358 61.111 0.00 0.00 0.00 5.24
246 280 9.176460 GATCAAGGTTACTACTTAGTCACTACT 57.824 37.037 0.00 0.00 37.73 2.57
247 281 8.121708 CGATCAAGGTTACTACTTAGTCACTAC 58.878 40.741 0.00 0.00 37.73 2.73
248 282 7.826252 ACGATCAAGGTTACTACTTAGTCACTA 59.174 37.037 0.00 0.00 37.73 2.74
249 283 6.658391 ACGATCAAGGTTACTACTTAGTCACT 59.342 38.462 0.00 0.00 37.73 3.41
250 284 6.850555 ACGATCAAGGTTACTACTTAGTCAC 58.149 40.000 0.00 0.00 37.73 3.67
251 285 6.883217 AGACGATCAAGGTTACTACTTAGTCA 59.117 38.462 0.00 0.00 37.73 3.41
252 286 7.319142 AGACGATCAAGGTTACTACTTAGTC 57.681 40.000 0.00 0.00 37.73 2.59
253 287 6.318396 GGAGACGATCAAGGTTACTACTTAGT 59.682 42.308 0.00 0.00 40.24 2.24
254 288 6.543100 AGGAGACGATCAAGGTTACTACTTAG 59.457 42.308 0.00 0.00 0.00 2.18
287 321 2.360726 AAATTCGTCCACCCGGCC 60.361 61.111 0.00 0.00 0.00 6.13
323 357 3.057174 GGGTCATATTTGCAAACGGACAA 60.057 43.478 27.12 4.95 0.00 3.18
325 359 2.159296 GGGGTCATATTTGCAAACGGAC 60.159 50.000 15.41 19.76 0.00 4.79
353 387 2.040412 CCCTAGCCTGGACTCAGTTTTT 59.960 50.000 0.00 0.00 39.31 1.94
355 389 1.280457 CCCTAGCCTGGACTCAGTTT 58.720 55.000 0.00 0.00 39.31 2.66
358 392 0.827368 GAACCCTAGCCTGGACTCAG 59.173 60.000 0.00 0.00 40.59 3.35
371 405 2.907042 CCAGAAGGACTACTTGAACCCT 59.093 50.000 0.00 0.00 40.21 4.34
374 408 4.750598 GTGTTCCAGAAGGACTACTTGAAC 59.249 45.833 0.00 0.00 45.73 3.18
383 417 3.330267 GACAGATGTGTTCCAGAAGGAC 58.670 50.000 0.00 0.00 45.73 3.85
386 420 3.007290 TCAGGACAGATGTGTTCCAGAAG 59.993 47.826 12.00 2.62 36.88 2.85
389 423 2.693069 GTCAGGACAGATGTGTTCCAG 58.307 52.381 12.00 6.09 36.88 3.86
398 432 1.338107 TGTTCACCGTCAGGACAGAT 58.662 50.000 0.00 0.00 41.02 2.90
408 442 2.774439 GTGAAGCAAATGTTCACCGT 57.226 45.000 13.30 0.00 45.42 4.83
500 534 5.163163 ACAATCCCATATCTATGTGCTGTGT 60.163 40.000 0.00 0.00 31.82 3.72
703 744 2.520458 CTTGTTGGGTCCCTGCCA 59.480 61.111 10.00 0.00 0.00 4.92
805 846 1.091771 CGCTGCTGGTGACCATAAGG 61.092 60.000 4.03 0.00 42.21 2.69
852 893 2.393646 GGAGAGTCATGGAGCCTAACT 58.606 52.381 0.00 0.00 0.00 2.24
877 918 8.322091 AGAACAATCATAGGTTAAGCAAGTACT 58.678 33.333 7.52 0.00 0.00 2.73
883 924 5.437060 GGGAGAACAATCATAGGTTAAGCA 58.563 41.667 7.52 0.00 0.00 3.91
884 925 4.511826 CGGGAGAACAATCATAGGTTAAGC 59.488 45.833 0.00 0.00 0.00 3.09
885 926 5.671493 ACGGGAGAACAATCATAGGTTAAG 58.329 41.667 0.00 0.00 0.00 1.85
891 943 4.202161 ACTGCTACGGGAGAACAATCATAG 60.202 45.833 0.00 0.00 34.86 2.23
893 945 2.501723 ACTGCTACGGGAGAACAATCAT 59.498 45.455 0.00 0.00 34.86 2.45
906 958 2.467566 AGTACCCCAAAACTGCTACG 57.532 50.000 0.00 0.00 0.00 3.51
919 971 4.527038 TCCAGTGCTGCTATATAAGTACCC 59.473 45.833 0.00 0.00 30.18 3.69
945 1000 1.208776 GGCAAGTGGGTATACGGTCTT 59.791 52.381 0.00 0.00 0.00 3.01
950 1005 1.687123 AGCTAGGCAAGTGGGTATACG 59.313 52.381 0.00 0.00 0.00 3.06
979 1036 7.013846 GCTCATACCTGTGTCTCTATCTAACTT 59.986 40.741 0.00 0.00 0.00 2.66
987 2918 3.131223 GCAAGCTCATACCTGTGTCTCTA 59.869 47.826 0.00 0.00 0.00 2.43
988 2919 2.093764 GCAAGCTCATACCTGTGTCTCT 60.094 50.000 0.00 0.00 0.00 3.10
989 2920 2.275318 GCAAGCTCATACCTGTGTCTC 58.725 52.381 0.00 0.00 0.00 3.36
990 2921 1.625315 TGCAAGCTCATACCTGTGTCT 59.375 47.619 0.00 0.00 0.00 3.41
991 2922 2.099141 TGCAAGCTCATACCTGTGTC 57.901 50.000 0.00 0.00 0.00 3.67
992 2923 2.795231 ATGCAAGCTCATACCTGTGT 57.205 45.000 0.00 0.00 0.00 3.72
993 2924 6.866010 TTATAATGCAAGCTCATACCTGTG 57.134 37.500 0.00 0.00 0.00 3.66
994 2925 9.003658 GTATTTATAATGCAAGCTCATACCTGT 57.996 33.333 0.00 0.00 0.00 4.00
1038 3094 5.355910 GGTTCTCTTTCCACTACACAAACAA 59.644 40.000 0.00 0.00 0.00 2.83
1039 3095 4.879545 GGTTCTCTTTCCACTACACAAACA 59.120 41.667 0.00 0.00 0.00 2.83
1049 3105 6.937465 AGAGACTAAATTGGTTCTCTTTCCAC 59.063 38.462 7.01 0.00 31.35 4.02
1050 3106 7.079451 AGAGACTAAATTGGTTCTCTTTCCA 57.921 36.000 7.01 0.00 31.35 3.53
1061 3122 7.443575 CCATGGAATACTGAGAGACTAAATTGG 59.556 40.741 5.56 0.00 0.00 3.16
1076 3137 3.891366 GCTGTTATTGGCCATGGAATACT 59.109 43.478 18.40 0.00 0.00 2.12
1077 3138 3.636300 TGCTGTTATTGGCCATGGAATAC 59.364 43.478 18.40 2.31 0.00 1.89
1078 3139 3.890756 CTGCTGTTATTGGCCATGGAATA 59.109 43.478 18.40 8.91 0.00 1.75
1121 3208 0.865769 CGTCACACAAACTAGCACCC 59.134 55.000 0.00 0.00 0.00 4.61
1124 3211 0.753867 TCCCGTCACACAAACTAGCA 59.246 50.000 0.00 0.00 0.00 3.49
1165 3252 2.266055 GAGCTCCTTCACCACCCG 59.734 66.667 0.87 0.00 0.00 5.28
1187 3274 1.597797 CCTTACACGGTAGCCACGGA 61.598 60.000 0.00 0.00 35.23 4.69
1240 3339 8.680903 GGAGATATAATTAGATGCATGGTTTGG 58.319 37.037 2.46 0.00 0.00 3.28
1241 3340 9.458727 AGGAGATATAATTAGATGCATGGTTTG 57.541 33.333 2.46 0.00 0.00 2.93
1244 3343 8.428063 GCTAGGAGATATAATTAGATGCATGGT 58.572 37.037 2.46 0.00 0.00 3.55
1245 3344 8.649591 AGCTAGGAGATATAATTAGATGCATGG 58.350 37.037 2.46 0.00 0.00 3.66
1248 3347 9.137459 GGTAGCTAGGAGATATAATTAGATGCA 57.863 37.037 0.00 0.00 0.00 3.96
1249 3348 9.362151 AGGTAGCTAGGAGATATAATTAGATGC 57.638 37.037 0.00 0.00 0.00 3.91
1262 3361 6.441222 TGGATTAGAAAAGGTAGCTAGGAGA 58.559 40.000 0.00 0.00 0.00 3.71
1298 3401 0.316442 GATTGATGCACGACGCCATG 60.316 55.000 6.35 0.00 41.33 3.66
1367 3470 2.158696 GGTGCAAGGATAGCCTCTCATT 60.159 50.000 0.00 0.00 46.28 2.57
1390 3493 2.981302 CAGTCCAGGACATCGGCA 59.019 61.111 22.31 0.00 34.60 5.69
1569 3700 2.282958 AGTCGGCCGAGAACAGGA 60.283 61.111 31.97 0.00 0.00 3.86
1620 3755 1.350310 ACCACGTTTCTGGTCCCCTT 61.350 55.000 0.00 0.00 40.91 3.95
1666 3801 2.052782 AGAAGTGAAAACAAGGCGGT 57.947 45.000 0.00 0.00 0.00 5.68
1697 3832 1.112315 TGTTGGGGTTCATGTGCACC 61.112 55.000 15.69 0.00 0.00 5.01
1844 3979 7.982919 ACTGTTGTTTTTCACCTTAATTTACCC 59.017 33.333 0.00 0.00 0.00 3.69
1864 3999 7.381766 TCTGTGATTGATCCAAATACTGTTG 57.618 36.000 0.00 0.00 0.00 3.33
1887 4049 7.178741 GCTGATTGCTCGTCATTATTATGATC 58.821 38.462 0.00 0.00 39.65 2.92
1925 4087 1.450312 GGATCGGAGGTGGCTGTTG 60.450 63.158 0.00 0.00 0.00 3.33
1926 4088 1.274703 ATGGATCGGAGGTGGCTGTT 61.275 55.000 0.00 0.00 0.00 3.16
1929 4091 1.625818 GATAATGGATCGGAGGTGGCT 59.374 52.381 0.00 0.00 0.00 4.75
1944 4107 6.174720 TCTGTCGAAAAGCCATAGGATAAT 57.825 37.500 0.00 0.00 0.00 1.28
1968 4131 7.458170 AGGAAACTCTAATTCTCCAGTTAGGAA 59.542 37.037 0.00 0.00 41.84 3.36
1992 4206 9.838339 ATACCATCTTATTTCAGTCAGTTTAGG 57.162 33.333 0.00 0.00 0.00 2.69
2049 4394 9.894783 GTATCAAGTTTCTAAGACGCTATGATA 57.105 33.333 0.00 0.00 0.00 2.15
2072 4417 2.037251 ACCTGCGGAAAGATATGCGTAT 59.963 45.455 0.00 0.00 36.44 3.06
2220 4568 5.281558 CCTTTTCCTATAGGTTTGGGAGGTT 60.282 44.000 18.51 0.00 36.34 3.50
2233 4581 8.285891 TCCTTGATAAATTGGCCTTTTCCTATA 58.714 33.333 3.32 0.00 0.00 1.31
2251 4606 7.526192 GCTTGTGAGCTCCTTATATCCTTGATA 60.526 40.741 12.15 0.00 45.65 2.15
2300 4655 8.083462 TGACAGACACTGTTTTGTATTATGTC 57.917 34.615 5.88 0.00 45.44 3.06
2310 4665 6.174720 TCCTAAGATGACAGACACTGTTTT 57.825 37.500 5.88 0.00 45.44 2.43
2387 4861 1.596934 CTCCTCCGTTGCTGCCTTA 59.403 57.895 0.00 0.00 0.00 2.69
2389 4863 3.710722 CCTCCTCCGTTGCTGCCT 61.711 66.667 0.00 0.00 0.00 4.75
2496 4970 1.133598 CATCAGGTACCTTGCGACGTA 59.866 52.381 13.15 0.00 0.00 3.57
2498 4972 0.806102 CCATCAGGTACCTTGCGACG 60.806 60.000 13.15 0.00 0.00 5.12
2519 4993 0.404040 TGGGGTAGGCCTTCTTTGTG 59.596 55.000 12.58 0.00 34.45 3.33
2522 4996 0.037734 CGTTGGGGTAGGCCTTCTTT 59.962 55.000 12.58 0.00 34.45 2.52
2562 5036 0.524816 GCACGTACGACATCACGGAT 60.525 55.000 24.41 0.00 42.35 4.18
2567 5041 0.179121 GATGGGCACGTACGACATCA 60.179 55.000 24.41 14.46 38.20 3.07
2665 5139 1.613925 GAAAAAGACCCCTGAGCAACC 59.386 52.381 0.00 0.00 0.00 3.77
2711 5185 4.497473 TTCATTCAGGGTAAACAAAGCG 57.503 40.909 0.00 0.00 0.00 4.68
2713 5187 7.432869 TGACAATTCATTCAGGGTAAACAAAG 58.567 34.615 0.00 0.00 0.00 2.77
2723 5197 5.706916 CAGAAGGTTGACAATTCATTCAGG 58.293 41.667 6.13 0.00 0.00 3.86
2749 5223 5.973651 ATATAGATATGGACGCGCATTTG 57.026 39.130 5.73 0.00 0.00 2.32
2750 5224 7.210174 ACATATATAGATATGGACGCGCATTT 58.790 34.615 18.96 0.00 46.42 2.32
2751 5225 6.749139 ACATATATAGATATGGACGCGCATT 58.251 36.000 18.96 0.00 46.42 3.56
2772 5246 6.131961 AGGTAGTAAATGGTAGTCGGTACAT 58.868 40.000 0.00 0.00 32.62 2.29
2831 5311 0.174845 TTGGAGAATCTGTACGGGCG 59.825 55.000 0.85 0.00 33.73 6.13
2851 5331 2.106511 CCCCAAGTCCTTCAGTCTTTGA 59.893 50.000 0.00 0.00 0.00 2.69
2860 5340 4.700692 GTGAATTCTAACCCCAAGTCCTTC 59.299 45.833 7.05 0.00 0.00 3.46
2861 5341 4.354087 AGTGAATTCTAACCCCAAGTCCTT 59.646 41.667 7.05 0.00 0.00 3.36
2887 5367 6.769134 TCGTATAGAGTTTTCCTCATGTCA 57.231 37.500 0.00 0.00 43.12 3.58
2888 5368 7.760340 AGTTTCGTATAGAGTTTTCCTCATGTC 59.240 37.037 0.00 0.00 43.12 3.06
2889 5369 7.545965 CAGTTTCGTATAGAGTTTTCCTCATGT 59.454 37.037 0.00 0.00 43.12 3.21
2908 5388 4.142708 TGTTGCAGGCATATTACAGTTTCG 60.143 41.667 0.00 0.00 0.00 3.46
2960 5449 6.695429 TGATCTATAAGCTCGAATGCTGATT 58.305 36.000 2.05 0.00 43.24 2.57
2967 5456 7.178274 ACTTCATCCTGATCTATAAGCTCGAAT 59.822 37.037 0.00 0.00 0.00 3.34
2990 5479 1.686355 TGTGGAAATTGGTCGCACTT 58.314 45.000 0.00 0.00 0.00 3.16
3002 5491 3.791953 TTTCTTCCGGGTATGTGGAAA 57.208 42.857 0.00 0.00 43.35 3.13
3067 5556 9.323985 GCATATCTGATATCTGACTATTTTCCC 57.676 37.037 13.85 0.00 0.00 3.97
3127 5869 6.711645 ACTGCAGGCACAATTTTCATAATTTT 59.288 30.769 19.93 0.00 0.00 1.82
3140 5882 0.824595 ATCTTGCACTGCAGGCACAA 60.825 50.000 23.92 19.30 41.75 3.33
3142 5884 1.211969 CATCTTGCACTGCAGGCAC 59.788 57.895 23.92 11.70 41.75 5.01
3178 5920 2.473609 TCATGTGTACTTTTCGTGTCGC 59.526 45.455 0.00 0.00 0.00 5.19
3182 5925 6.086765 GCTTGAATTCATGTGTACTTTTCGTG 59.913 38.462 19.25 0.00 0.00 4.35
3185 5928 7.115378 CCTTGCTTGAATTCATGTGTACTTTTC 59.885 37.037 19.25 3.89 0.00 2.29
3194 5937 2.893424 ACCCCTTGCTTGAATTCATGT 58.107 42.857 19.25 0.00 0.00 3.21
3437 6182 8.367660 TCTAGTGAATGTAGTTTCTCATTCCT 57.632 34.615 13.00 11.78 45.11 3.36
3446 6191 3.844211 TGGCCCTCTAGTGAATGTAGTTT 59.156 43.478 0.00 0.00 0.00 2.66
3492 6237 1.073284 GGGTCTCTTGCACTTTACCCA 59.927 52.381 17.58 0.00 44.94 4.51
3531 6276 2.713877 TGTGTATAACCCCTTTTCGGC 58.286 47.619 0.00 0.00 0.00 5.54
3620 6365 1.080434 GAAGGCTCAGACTCGCGTT 60.080 57.895 5.77 0.00 37.00 4.84
3664 6409 6.263168 TCTCGCTCTTCATTATGTGTCATCTA 59.737 38.462 0.00 0.00 0.00 1.98
3668 6413 4.158579 ACTCTCGCTCTTCATTATGTGTCA 59.841 41.667 0.00 0.00 0.00 3.58
3670 6415 4.400884 AGACTCTCGCTCTTCATTATGTGT 59.599 41.667 0.00 0.00 0.00 3.72
3677 6422 4.278170 CAGGATAAGACTCTCGCTCTTCAT 59.722 45.833 0.00 0.00 0.00 2.57
3904 6649 0.244994 AGTTTCTCGCTCGAGCACAT 59.755 50.000 34.69 13.05 41.71 3.21
3908 6653 1.681945 CTGCAGTTTCTCGCTCGAGC 61.682 60.000 27.64 27.64 41.71 5.03
3945 6690 1.635487 TGGTGGCTCTCTTATTGCCTT 59.365 47.619 0.00 0.00 46.23 4.35


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

AutoCloner maintained by Alex Coulton.