Multiple sequence alignment - TraesCS3B01G393000

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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 TraesCS3B01G393000 chr3B 100.000 4123 0 0 1 4123 618444089 618439967 0.000000e+00 7614.0
1 TraesCS3B01G393000 chr3B 79.951 1227 209 33 1911 3119 618155767 618154560 0.000000e+00 869.0
2 TraesCS3B01G393000 chr3B 78.358 134 29 0 1690 1823 618156440 618156307 2.040000e-13 87.9
3 TraesCS3B01G393000 chr3A 92.675 3522 154 42 76 3536 608349222 608345744 0.000000e+00 4979.0
4 TraesCS3B01G393000 chr3A 80.476 1219 205 29 1911 3119 608195759 608194564 0.000000e+00 902.0
5 TraesCS3B01G393000 chr3A 90.500 200 16 3 3914 4112 608343564 608343367 1.140000e-65 261.0
6 TraesCS3B01G393000 chr3A 92.073 164 12 1 3706 3869 608345374 608345212 3.210000e-56 230.0
7 TraesCS3B01G393000 chr3D 92.174 3514 137 54 76 3551 465028949 465025536 0.000000e+00 4839.0
8 TraesCS3B01G393000 chr3D 80.898 1225 200 28 1911 3119 464808961 464807755 0.000000e+00 935.0
9 TraesCS3B01G393000 chr3D 84.239 552 43 22 3551 4093 465025572 465025056 7.960000e-137 497.0
10 TraesCS3B01G393000 chr3D 97.368 76 2 0 1 76 58425749 58425824 3.340000e-26 130.0
11 TraesCS3B01G393000 chr3D 83.529 85 12 2 3710 3793 122451331 122451414 1.230000e-10 78.7
12 TraesCS3B01G393000 chr1D 80.478 1255 181 46 1917 3123 381019561 381020799 0.000000e+00 902.0
13 TraesCS3B01G393000 chr1D 97.368 76 2 0 1 76 232138740 232138665 3.340000e-26 130.0
14 TraesCS3B01G393000 chr1D 97.368 76 2 0 1 76 363511628 363511553 3.340000e-26 130.0
15 TraesCS3B01G393000 chr1D 97.368 76 2 0 1 76 363528991 363528916 3.340000e-26 130.0
16 TraesCS3B01G393000 chr1D 95.062 81 4 0 2 82 475799423 475799343 1.200000e-25 128.0
17 TraesCS3B01G393000 chr7D 79.392 1218 216 28 1692 2894 149181675 149182872 0.000000e+00 826.0
18 TraesCS3B01G393000 chr7D 97.368 76 2 0 1 76 507802314 507802389 3.340000e-26 130.0
19 TraesCS3B01G393000 chr7D 96.053 76 3 0 1 76 13363806 13363881 1.560000e-24 124.0
20 TraesCS3B01G393000 chr7D 95.745 47 2 0 3710 3756 133233770 133233724 4.420000e-10 76.8
21 TraesCS3B01G393000 chr2D 76.090 1468 283 55 1692 3123 165484966 165483531 0.000000e+00 704.0
22 TraesCS3B01G393000 chr2D 85.405 370 52 2 1209 1577 165485351 165484983 2.330000e-102 383.0
23 TraesCS3B01G393000 chr2D 76.923 689 135 19 1692 2367 165334028 165334705 1.810000e-98 370.0
24 TraesCS3B01G393000 chr2D 95.062 81 4 0 4 84 644523508 644523428 1.200000e-25 128.0
25 TraesCS3B01G393000 chr2D 86.111 72 7 3 3708 3778 548247622 548247553 1.590000e-09 75.0
26 TraesCS3B01G393000 chr2B 75.758 1452 298 37 1692 3123 232290926 232289509 0.000000e+00 682.0
27 TraesCS3B01G393000 chr2B 76.645 1216 258 24 1692 2894 232261908 232263110 0.000000e+00 649.0
28 TraesCS3B01G393000 chr2B 85.942 377 49 4 1209 1583 232291311 232290937 2.310000e-107 399.0
29 TraesCS3B01G393000 chr2B 85.175 371 51 4 1209 1577 232261523 232261891 1.080000e-100 377.0
30 TraesCS3B01G393000 chr2A 85.135 370 53 2 1209 1577 185264932 185265300 1.080000e-100 377.0
31 TraesCS3B01G393000 chr5B 84.103 390 58 4 1209 1596 679311152 679311539 1.400000e-99 374.0
32 TraesCS3B01G393000 chr5B 87.879 132 16 0 1692 1823 679311537 679311668 5.520000e-34 156.0
33 TraesCS3B01G393000 chr7A 83.791 401 56 7 1188 1584 150021865 150022260 5.030000e-99 372.0
34 TraesCS3B01G393000 chr7A 97.872 47 1 0 3710 3756 131842452 131842406 9.500000e-12 82.4
35 TraesCS3B01G393000 chr5D 84.062 389 58 4 1210 1596 538255194 538255580 5.030000e-99 372.0
36 TraesCS3B01G393000 chr6D 97.368 76 2 0 1 76 460494934 460495009 3.340000e-26 130.0
37 TraesCS3B01G393000 chr4D 83.088 136 21 2 2989 3123 360453016 360453150 5.600000e-24 122.0
38 TraesCS3B01G393000 chr4D 95.000 40 2 0 3708 3747 499588241 499588202 3.440000e-06 63.9
39 TraesCS3B01G393000 chrUn 80.460 87 14 2 3708 3793 229995875 229995959 3.440000e-06 63.9
40 TraesCS3B01G393000 chrUn 80.460 87 14 2 3708 3793 245749941 245750025 3.440000e-06 63.9


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 TraesCS3B01G393000 chr3B 618439967 618444089 4122 True 7614.000000 7614 100.000000 1 4123 1 chr3B.!!$R1 4122
1 TraesCS3B01G393000 chr3B 618154560 618156440 1880 True 478.450000 869 79.154500 1690 3119 2 chr3B.!!$R2 1429
2 TraesCS3B01G393000 chr3A 608343367 608349222 5855 True 1823.333333 4979 91.749333 76 4112 3 chr3A.!!$R2 4036
3 TraesCS3B01G393000 chr3A 608194564 608195759 1195 True 902.000000 902 80.476000 1911 3119 1 chr3A.!!$R1 1208
4 TraesCS3B01G393000 chr3D 465025056 465028949 3893 True 2668.000000 4839 88.206500 76 4093 2 chr3D.!!$R2 4017
5 TraesCS3B01G393000 chr3D 464807755 464808961 1206 True 935.000000 935 80.898000 1911 3119 1 chr3D.!!$R1 1208
6 TraesCS3B01G393000 chr1D 381019561 381020799 1238 False 902.000000 902 80.478000 1917 3123 1 chr1D.!!$F1 1206
7 TraesCS3B01G393000 chr7D 149181675 149182872 1197 False 826.000000 826 79.392000 1692 2894 1 chr7D.!!$F2 1202
8 TraesCS3B01G393000 chr2D 165483531 165485351 1820 True 543.500000 704 80.747500 1209 3123 2 chr2D.!!$R3 1914
9 TraesCS3B01G393000 chr2D 165334028 165334705 677 False 370.000000 370 76.923000 1692 2367 1 chr2D.!!$F1 675
10 TraesCS3B01G393000 chr2B 232289509 232291311 1802 True 540.500000 682 80.850000 1209 3123 2 chr2B.!!$R1 1914
11 TraesCS3B01G393000 chr2B 232261523 232263110 1587 False 513.000000 649 80.910000 1209 2894 2 chr2B.!!$F1 1685
12 TraesCS3B01G393000 chr5B 679311152 679311668 516 False 265.000000 374 85.991000 1209 1823 2 chr5B.!!$F1 614

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
164 167 0.108281 GCCCGAGTAGGAAGACCAAC 60.108 60.0 0.0 0.0 45.0 3.77 F
1127 1184 0.454196 ACCGTTGTTCAGTTGTTGCC 59.546 50.0 0.0 0.0 0.0 4.52 F
1768 1831 0.755686 GAGGCCCGAATGTCTCTGAT 59.244 55.0 0.0 0.0 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2131 2696 0.032912 TCATGTAGTAGGTCGCCCCA 60.033 55.0 0.0 0.0 34.66 4.96 R
2290 2855 0.109086 AGCTCGTGTCGTTGATCTGG 60.109 55.0 0.0 0.0 0.00 3.86 R
3546 4237 0.457035 CTGGCCATGGAATTTGGACG 59.543 55.0 18.4 0.0 46.01 4.79 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
30 31 3.507009 GTCTACGACGCTCGCCCT 61.507 66.667 0.00 0.00 45.12 5.19
31 32 3.200593 TCTACGACGCTCGCCCTC 61.201 66.667 0.00 0.00 45.12 4.30
32 33 4.592936 CTACGACGCTCGCCCTCG 62.593 72.222 0.00 0.00 45.12 4.63
44 45 3.458163 CCCTCGCTCCGCAACCTA 61.458 66.667 0.00 0.00 0.00 3.08
45 46 2.105128 CCTCGCTCCGCAACCTAG 59.895 66.667 0.00 0.00 0.00 3.02
46 47 2.105128 CTCGCTCCGCAACCTAGG 59.895 66.667 7.41 7.41 0.00 3.02
47 48 2.361992 TCGCTCCGCAACCTAGGA 60.362 61.111 17.98 0.00 34.93 2.94
48 49 2.202756 CGCTCCGCAACCTAGGAC 60.203 66.667 17.98 3.31 32.33 3.85
49 50 2.187163 GCTCCGCAACCTAGGACC 59.813 66.667 17.98 1.75 32.33 4.46
50 51 2.494918 CTCCGCAACCTAGGACCG 59.505 66.667 17.98 13.98 32.33 4.79
51 52 3.072468 TCCGCAACCTAGGACCGG 61.072 66.667 23.92 23.92 40.25 5.28
52 53 3.072468 CCGCAACCTAGGACCGGA 61.072 66.667 24.96 0.00 41.34 5.14
53 54 2.432300 CCGCAACCTAGGACCGGAT 61.432 63.158 24.96 0.00 41.34 4.18
54 55 1.520666 CGCAACCTAGGACCGGATT 59.479 57.895 17.98 0.00 0.00 3.01
55 56 0.529992 CGCAACCTAGGACCGGATTC 60.530 60.000 17.98 0.00 0.00 2.52
56 57 0.529992 GCAACCTAGGACCGGATTCG 60.530 60.000 17.98 0.00 0.00 3.34
57 58 0.529992 CAACCTAGGACCGGATTCGC 60.530 60.000 17.98 0.00 34.56 4.70
58 59 1.683418 AACCTAGGACCGGATTCGCC 61.683 60.000 17.98 0.67 34.56 5.54
67 68 4.832608 GGATTCGCCGGCGGAGTT 62.833 66.667 44.95 26.89 40.25 3.01
68 69 3.564027 GATTCGCCGGCGGAGTTG 61.564 66.667 44.95 19.83 40.25 3.16
103 104 5.047306 TCAACCCGATACTATGGCAGAATAG 60.047 44.000 0.00 0.00 36.40 1.73
125 128 0.891904 TCCTTTACCGTTGGCAAGCC 60.892 55.000 0.00 3.61 0.00 4.35
133 136 2.597217 TTGGCAAGCCCCGTTGAG 60.597 61.111 8.89 0.00 34.56 3.02
164 167 0.108281 GCCCGAGTAGGAAGACCAAC 60.108 60.000 0.00 0.00 45.00 3.77
173 176 3.441500 AGGAAGACCAACAATTCTCCC 57.558 47.619 0.00 0.00 38.94 4.30
230 233 4.836736 CCCTCTCCAAATATCATGCCATTT 59.163 41.667 0.00 0.00 0.00 2.32
262 265 3.947196 CAGGCTTATTTGATGTGCCACTA 59.053 43.478 0.00 0.00 45.42 2.74
279 282 3.555956 CCACTAGCACGTACAAATCATCC 59.444 47.826 0.00 0.00 0.00 3.51
338 342 9.634163 GTTTTTCTTTTCTCCTTTGAGTAAACA 57.366 29.630 0.00 0.00 39.75 2.83
359 363 2.296190 AGCACTTCATACACGTGACTCA 59.704 45.455 25.01 4.40 0.00 3.41
437 446 4.236935 ACGGCTAAATCAATTTGTTGCAG 58.763 39.130 0.00 4.21 0.00 4.41
442 451 6.346838 GGCTAAATCAATTTGTTGCAGTGTTC 60.347 38.462 0.00 0.00 0.00 3.18
443 452 5.989551 AAATCAATTTGTTGCAGTGTTCC 57.010 34.783 0.00 0.00 0.00 3.62
448 457 1.686355 TTGTTGCAGTGTTCCCGATT 58.314 45.000 0.00 0.00 0.00 3.34
487 496 9.624697 GCAATTAAGTCAAGATGTATGAAAACA 57.375 29.630 0.00 0.00 0.00 2.83
513 546 3.869246 GGTCCACATTCGTTGGTATACAG 59.131 47.826 5.01 0.00 0.00 2.74
579 612 1.207791 TGGAAAGGCCAGAGAGGATC 58.792 55.000 5.01 0.00 43.33 3.36
620 653 1.040339 AGAGCCCGATCAGAGTGACC 61.040 60.000 0.00 0.00 0.00 4.02
745 788 1.153939 GTGCTCGTGCTCGATCAGT 60.154 57.895 14.24 0.00 45.21 3.41
962 1011 1.418334 TTGGCTATCCAGAGCTCTCC 58.582 55.000 14.96 11.67 44.53 3.71
996 1045 1.892474 GCTAGCTAGCTGAGGCATAGT 59.108 52.381 33.71 0.00 45.62 2.12
1095 1144 2.345641 CCAGTTCGATGTAAGTTGCTCG 59.654 50.000 0.00 6.52 0.00 5.03
1099 1148 2.602878 TCGATGTAAGTTGCTCGGTTC 58.397 47.619 10.89 0.00 0.00 3.62
1127 1184 0.454196 ACCGTTGTTCAGTTGTTGCC 59.546 50.000 0.00 0.00 0.00 4.52
1139 1196 3.191371 CAGTTGTTGCCTATTCAGGTTCC 59.809 47.826 0.00 0.00 44.68 3.62
1140 1197 3.153919 GTTGTTGCCTATTCAGGTTCCA 58.846 45.455 0.00 0.00 44.68 3.53
1343 1401 2.421388 GGCCCAGTACAACATGAGCATA 60.421 50.000 0.00 0.00 0.00 3.14
1403 1461 4.157120 GGGCCGGCGTACATCACT 62.157 66.667 22.54 0.00 0.00 3.41
1503 1561 2.685017 ACATCTCCTGGCTCCGCA 60.685 61.111 0.00 0.00 0.00 5.69
1584 1642 1.923395 CCCTACAAGGAGGTGCCCA 60.923 63.158 0.00 0.00 37.67 5.36
1642 1700 2.703536 TGGTGACTGGTGATAAGTGTGT 59.296 45.455 0.00 0.00 0.00 3.72
1660 1723 3.189921 GCGCATGCATGAAGGACA 58.810 55.556 30.64 0.00 42.15 4.02
1671 1734 7.707893 GCATGCATGAAGGACATAAGTTTATTT 59.292 33.333 30.64 0.00 37.46 1.40
1765 1828 3.635510 GGAGGCCCGAATGTCTCT 58.364 61.111 0.00 0.00 0.00 3.10
1768 1831 0.755686 GAGGCCCGAATGTCTCTGAT 59.244 55.000 0.00 0.00 0.00 2.90
1833 1899 0.869880 GCCAAAGGTTTGTGTCGTGC 60.870 55.000 1.94 0.00 36.45 5.34
2131 2696 3.400054 GCCAAGCCGTCCTACCCT 61.400 66.667 0.00 0.00 0.00 4.34
2470 3053 4.394078 CCGACGAACGACAGCCGA 62.394 66.667 0.00 0.00 45.77 5.54
2581 3164 3.562232 TCCAACTTCCCCGCCGTT 61.562 61.111 0.00 0.00 0.00 4.44
2968 3578 7.663081 TGAGTAAGAAAACTGATGATCTGCTTT 59.337 33.333 1.15 1.15 0.00 3.51
2979 3589 9.788889 ACTGATGATCTGCTTTTGATATTGATA 57.211 29.630 0.00 0.00 0.00 2.15
3340 4031 3.265479 AGCAAGAGCCTTAGGACTTTCAT 59.735 43.478 0.69 0.00 43.56 2.57
3387 4078 2.818130 TTTGTAACGTACGGGAGCTT 57.182 45.000 21.06 6.76 0.00 3.74
3536 4227 4.715792 ACAAATTCCATGGCCATTGTATGA 59.284 37.500 17.92 5.03 29.89 2.15
3537 4228 5.367352 ACAAATTCCATGGCCATTGTATGAT 59.633 36.000 17.92 2.50 29.89 2.45
3539 4230 6.594788 AATTCCATGGCCATTGTATGATAC 57.405 37.500 17.92 0.00 0.00 2.24
3540 4231 4.999469 TCCATGGCCATTGTATGATACT 57.001 40.909 17.92 0.00 0.00 2.12
3541 4232 5.323382 TCCATGGCCATTGTATGATACTT 57.677 39.130 17.92 0.00 0.00 2.24
3542 4233 5.316167 TCCATGGCCATTGTATGATACTTC 58.684 41.667 17.92 0.00 0.00 3.01
3543 4234 5.073554 TCCATGGCCATTGTATGATACTTCT 59.926 40.000 17.92 0.00 0.00 2.85
3544 4235 5.771666 CCATGGCCATTGTATGATACTTCTT 59.228 40.000 17.92 0.00 0.00 2.52
3545 4236 6.072286 CCATGGCCATTGTATGATACTTCTTC 60.072 42.308 17.92 0.00 0.00 2.87
3546 4237 5.376625 TGGCCATTGTATGATACTTCTTCC 58.623 41.667 0.00 1.40 0.00 3.46
3547 4238 4.452455 GGCCATTGTATGATACTTCTTCCG 59.548 45.833 0.00 0.00 0.00 4.30
3548 4239 5.057149 GCCATTGTATGATACTTCTTCCGT 58.943 41.667 4.03 0.00 0.00 4.69
3549 4240 5.177696 GCCATTGTATGATACTTCTTCCGTC 59.822 44.000 4.03 0.00 0.00 4.79
3550 4241 5.696724 CCATTGTATGATACTTCTTCCGTCC 59.303 44.000 4.03 0.00 0.00 4.79
3551 4242 5.925506 TTGTATGATACTTCTTCCGTCCA 57.074 39.130 4.03 0.00 0.00 4.02
3555 4246 7.335627 TGTATGATACTTCTTCCGTCCAAATT 58.664 34.615 4.03 0.00 0.00 1.82
3556 4247 6.927294 ATGATACTTCTTCCGTCCAAATTC 57.073 37.500 0.00 0.00 0.00 2.17
3557 4248 5.183228 TGATACTTCTTCCGTCCAAATTCC 58.817 41.667 0.00 0.00 0.00 3.01
3558 4249 3.502123 ACTTCTTCCGTCCAAATTCCA 57.498 42.857 0.00 0.00 0.00 3.53
3559 4250 4.034285 ACTTCTTCCGTCCAAATTCCAT 57.966 40.909 0.00 0.00 0.00 3.41
3560 4251 3.758554 ACTTCTTCCGTCCAAATTCCATG 59.241 43.478 0.00 0.00 0.00 3.66
3561 4252 2.722094 TCTTCCGTCCAAATTCCATGG 58.278 47.619 4.97 4.97 39.41 3.66
3562 4253 1.134946 CTTCCGTCCAAATTCCATGGC 59.865 52.381 6.96 0.00 37.88 4.40
3563 4254 0.682855 TCCGTCCAAATTCCATGGCC 60.683 55.000 6.96 0.00 37.88 5.36
3564 4255 0.969917 CCGTCCAAATTCCATGGCCA 60.970 55.000 8.56 8.56 37.88 5.36
3567 4258 1.205417 GTCCAAATTCCATGGCCAGTG 59.795 52.381 13.05 9.85 37.88 3.66
3569 4260 2.042297 TCCAAATTCCATGGCCAGTGTA 59.958 45.455 13.05 0.00 37.88 2.90
3570 4261 3.033184 CCAAATTCCATGGCCAGTGTAT 58.967 45.455 13.05 0.67 0.00 2.29
3571 4262 3.181473 CCAAATTCCATGGCCAGTGTATG 60.181 47.826 13.05 3.50 0.00 2.39
3572 4263 3.668141 AATTCCATGGCCAGTGTATGA 57.332 42.857 13.05 0.00 0.00 2.15
3597 4391 3.244665 ACTTCTTCCGTCCGGGTTTATTT 60.245 43.478 0.00 0.00 37.00 1.40
3602 4396 3.753815 TCCGTCCGGGTTTATTTTTCTT 58.246 40.909 0.00 0.00 37.00 2.52
3603 4397 3.502979 TCCGTCCGGGTTTATTTTTCTTG 59.497 43.478 0.00 0.00 37.00 3.02
3605 4403 4.455190 CCGTCCGGGTTTATTTTTCTTGTA 59.545 41.667 0.00 0.00 0.00 2.41
3624 4422 5.024768 TGTATTGTGTCGAATTTTGACCG 57.975 39.130 13.12 0.00 35.46 4.79
3629 4427 4.835344 TGTGTCGAATTTTGACCGTAAAC 58.165 39.130 13.12 5.96 35.46 2.01
3635 4433 8.011106 TGTCGAATTTTGACCGTAAACTTAATC 58.989 33.333 13.12 0.00 35.46 1.75
3638 4436 8.624028 CGAATTTTGACCGTAAACTTAATCAAC 58.376 33.333 0.00 0.00 0.00 3.18
3681 4479 9.221775 CTATTAAAAATAACACTGCGAATCCAC 57.778 33.333 0.00 0.00 0.00 4.02
3756 4653 9.880157 AATCTATGGTCAAAATTTGATCCAAAG 57.120 29.630 23.41 15.31 40.09 2.77
3758 4655 8.869109 TCTATGGTCAAAATTTGATCCAAAGTT 58.131 29.630 23.41 14.77 42.13 2.66
3815 4712 2.100605 ACATTCCACTCCGAAGAAGC 57.899 50.000 0.00 0.00 0.00 3.86
3868 6377 5.425539 TCTCTCCAGGGTGAAAACCTATTAG 59.574 44.000 0.00 0.00 36.32 1.73
3870 6379 3.053917 TCCAGGGTGAAAACCTATTAGCC 60.054 47.826 0.00 0.00 36.32 3.93
3873 6382 2.294979 GGTGAAAACCTATTAGCCGGG 58.705 52.381 2.18 0.00 0.00 5.73
3909 6418 1.064017 TGGCTGAGGAGGTGTTGTTTT 60.064 47.619 0.00 0.00 0.00 2.43
3910 6419 1.338020 GGCTGAGGAGGTGTTGTTTTG 59.662 52.381 0.00 0.00 0.00 2.44
3912 6421 2.654863 CTGAGGAGGTGTTGTTTTGGT 58.345 47.619 0.00 0.00 0.00 3.67
3922 6431 4.697828 GGTGTTGTTTTGGTGTTTTGGATT 59.302 37.500 0.00 0.00 0.00 3.01
3937 6446 4.811555 TTGGATTCTCACTTGTTTGTCG 57.188 40.909 0.00 0.00 0.00 4.35
3938 6447 3.138304 TGGATTCTCACTTGTTTGTCGG 58.862 45.455 0.00 0.00 0.00 4.79
3956 6465 1.278127 CGGGAGGTGTATGTCTTTGGT 59.722 52.381 0.00 0.00 0.00 3.67
3957 6466 2.711542 GGGAGGTGTATGTCTTTGGTG 58.288 52.381 0.00 0.00 0.00 4.17
3959 6468 2.084546 GAGGTGTATGTCTTTGGTGGC 58.915 52.381 0.00 0.00 0.00 5.01
3960 6469 1.423541 AGGTGTATGTCTTTGGTGGCA 59.576 47.619 0.00 0.00 0.00 4.92
3961 6470 1.539827 GGTGTATGTCTTTGGTGGCAC 59.460 52.381 9.70 9.70 0.00 5.01
3965 6474 0.675633 ATGTCTTTGGTGGCACTTGC 59.324 50.000 18.45 1.07 41.14 4.01
3987 6497 4.472286 CGCCACGTTATGATTTTGTCTTT 58.528 39.130 0.00 0.00 0.00 2.52
4014 6524 4.154015 TGACATACCGAATGAGTTTTGCAG 59.846 41.667 4.93 0.00 39.07 4.41
4040 6550 3.744238 AAAACCTTGGATGAAAACCCG 57.256 42.857 0.00 0.00 0.00 5.28
4045 6555 0.251430 TTGGATGAAAACCCGGACCC 60.251 55.000 0.73 0.00 0.00 4.46
4106 6616 0.605589 AGCATCGCCTCTAGTATGGC 59.394 55.000 12.02 12.02 45.25 4.40
4112 6622 1.262417 GCCTCTAGTATGGCCTCCTC 58.738 60.000 3.32 0.00 43.11 3.71
4113 6623 1.540267 CCTCTAGTATGGCCTCCTCG 58.460 60.000 3.32 0.00 0.00 4.63
4114 6624 1.540267 CTCTAGTATGGCCTCCTCGG 58.460 60.000 3.32 0.00 0.00 4.63
4115 6625 0.112606 TCTAGTATGGCCTCCTCGGG 59.887 60.000 3.32 0.00 0.00 5.14
4116 6626 0.112606 CTAGTATGGCCTCCTCGGGA 59.887 60.000 3.32 0.00 0.00 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 3.200593 GAGGGCGAGCGTCGTAGA 61.201 66.667 8.72 0.00 42.81 2.59
15 16 4.592936 CGAGGGCGAGCGTCGTAG 62.593 72.222 9.42 0.00 42.81 3.51
33 34 2.494918 CGGTCCTAGGTTGCGGAG 59.505 66.667 9.08 0.00 0.00 4.63
34 35 2.866523 ATCCGGTCCTAGGTTGCGGA 62.867 60.000 9.08 11.29 0.00 5.54
35 36 1.968050 AATCCGGTCCTAGGTTGCGG 61.968 60.000 9.08 5.19 0.00 5.69
36 37 0.529992 GAATCCGGTCCTAGGTTGCG 60.530 60.000 9.08 0.00 0.00 4.85
37 38 0.529992 CGAATCCGGTCCTAGGTTGC 60.530 60.000 9.08 0.40 0.00 4.17
38 39 0.529992 GCGAATCCGGTCCTAGGTTG 60.530 60.000 9.08 0.00 36.06 3.77
39 40 1.683418 GGCGAATCCGGTCCTAGGTT 61.683 60.000 9.08 0.00 36.06 3.50
40 41 2.132352 GGCGAATCCGGTCCTAGGT 61.132 63.158 9.08 0.00 36.06 3.08
41 42 2.735237 GGCGAATCCGGTCCTAGG 59.265 66.667 0.82 0.82 36.06 3.02
59 60 2.746277 ATGTTCCGCAACTCCGCC 60.746 61.111 0.00 0.00 33.17 6.13
60 61 1.369091 ATCATGTTCCGCAACTCCGC 61.369 55.000 0.00 0.00 33.17 5.54
61 62 0.652592 GATCATGTTCCGCAACTCCG 59.347 55.000 0.00 0.00 33.17 4.63
62 63 1.737838 TGATCATGTTCCGCAACTCC 58.262 50.000 0.00 0.00 33.17 3.85
63 64 2.159517 GGTTGATCATGTTCCGCAACTC 60.160 50.000 0.00 0.00 38.95 3.01
64 65 1.812571 GGTTGATCATGTTCCGCAACT 59.187 47.619 0.00 0.00 38.95 3.16
65 66 1.135402 GGGTTGATCATGTTCCGCAAC 60.135 52.381 0.00 0.00 38.40 4.17
66 67 1.173043 GGGTTGATCATGTTCCGCAA 58.827 50.000 0.00 0.00 0.00 4.85
67 68 1.024046 CGGGTTGATCATGTTCCGCA 61.024 55.000 0.00 0.00 0.00 5.69
68 69 0.742990 TCGGGTTGATCATGTTCCGC 60.743 55.000 16.55 3.88 37.65 5.54
69 70 1.953559 ATCGGGTTGATCATGTTCCG 58.046 50.000 15.72 15.72 38.92 4.30
70 71 4.073293 AGTATCGGGTTGATCATGTTCC 57.927 45.455 0.00 0.00 38.57 3.62
71 72 5.639506 CCATAGTATCGGGTTGATCATGTTC 59.360 44.000 0.00 0.00 38.57 3.18
72 73 5.551233 CCATAGTATCGGGTTGATCATGTT 58.449 41.667 0.00 0.00 38.57 2.71
73 74 4.563580 GCCATAGTATCGGGTTGATCATGT 60.564 45.833 0.00 0.00 38.57 3.21
74 75 3.935203 GCCATAGTATCGGGTTGATCATG 59.065 47.826 0.00 0.00 38.57 3.07
103 104 0.891904 TTGCCAACGGTAAAGGAGGC 60.892 55.000 0.00 0.00 42.32 4.70
142 145 0.971447 GGTCTTCCTACTCGGGCTGT 60.971 60.000 0.00 0.00 0.00 4.40
144 147 0.252103 TTGGTCTTCCTACTCGGGCT 60.252 55.000 0.00 0.00 34.23 5.19
164 167 6.509418 TTCGGTTAATTTCTGGGAGAATTG 57.491 37.500 0.00 0.00 33.67 2.32
173 176 6.259167 TCCGTCCATAATTCGGTTAATTTCTG 59.741 38.462 2.84 0.00 43.94 3.02
230 233 4.343231 TCAAATAAGCCTGGCATTTGAGA 58.657 39.130 29.03 16.86 41.40 3.27
262 265 2.665649 TCGGATGATTTGTACGTGCT 57.334 45.000 4.97 0.00 0.00 4.40
268 271 6.464222 ACAGAGAAACTTCGGATGATTTGTA 58.536 36.000 0.00 0.00 0.00 2.41
279 282 0.784778 GCACGGACAGAGAAACTTCG 59.215 55.000 0.00 0.00 0.00 3.79
338 342 2.296190 TGAGTCACGTGTATGAAGTGCT 59.704 45.455 16.51 1.38 34.33 4.40
359 363 4.766375 AGCCATTTTACGCTACATGTACT 58.234 39.130 0.08 0.00 32.26 2.73
448 457 2.971660 TAATTGCTCGACGATTCCCA 57.028 45.000 0.00 0.00 34.09 4.37
487 496 2.593026 ACCAACGAATGTGGACCATTT 58.407 42.857 0.00 0.00 43.87 2.32
513 546 8.882415 TGTCCGGTCTTAATTATCAAGATTAC 57.118 34.615 0.00 0.00 34.67 1.89
620 653 1.005294 CGTCTGTTTACCCGTCACCG 61.005 60.000 0.00 0.00 0.00 4.94
633 671 3.785189 AAGTCAACCGCGCGTCTGT 62.785 57.895 29.95 17.06 0.00 3.41
733 776 1.071605 GTTGGTCACTGATCGAGCAC 58.928 55.000 0.00 0.00 40.37 4.40
745 788 1.454847 GTTGGTGCAGGGTTGGTCA 60.455 57.895 0.00 0.00 0.00 4.02
962 1011 2.034048 GCTAGCTCCCCTTCTTCCCG 62.034 65.000 7.70 0.00 0.00 5.14
992 1041 1.609208 GATGGCCGCCATTTCACTAT 58.391 50.000 25.80 1.47 45.26 2.12
996 1045 1.453745 GAGGATGGCCGCCATTTCA 60.454 57.895 25.80 0.00 45.26 2.69
1095 1144 3.636282 ACAACGGTAATTGCAAGAACC 57.364 42.857 18.66 18.66 32.47 3.62
1099 1148 4.223320 ACTGAACAACGGTAATTGCAAG 57.777 40.909 4.94 0.00 36.20 4.01
1127 1184 2.798499 CGTAGGCGTGGAACCTGAATAG 60.798 54.545 0.00 0.00 38.26 1.73
1517 1575 1.459539 GGGGAGGATGACGATGGGA 60.460 63.158 0.00 0.00 0.00 4.37
1584 1642 3.587797 AGAACACGTACCGAACATGAT 57.412 42.857 0.00 0.00 0.00 2.45
1602 1660 5.836898 TCACCACCTTGTAAGACTAAGAAGA 59.163 40.000 0.00 0.00 0.00 2.87
1603 1661 5.927115 GTCACCACCTTGTAAGACTAAGAAG 59.073 44.000 0.00 0.00 0.00 2.85
1604 1662 5.601313 AGTCACCACCTTGTAAGACTAAGAA 59.399 40.000 0.00 0.00 34.83 2.52
1605 1663 5.010719 CAGTCACCACCTTGTAAGACTAAGA 59.989 44.000 0.00 0.00 34.83 2.10
1606 1664 5.230942 CAGTCACCACCTTGTAAGACTAAG 58.769 45.833 0.00 0.00 34.83 2.18
1609 1667 2.368875 CCAGTCACCACCTTGTAAGACT 59.631 50.000 0.00 0.00 36.84 3.24
1613 1671 2.120312 TCACCAGTCACCACCTTGTAA 58.880 47.619 0.00 0.00 0.00 2.41
1671 1734 3.549423 GCCTGAGCACGTACGTATCAATA 60.549 47.826 26.16 11.69 39.53 1.90
1672 1735 2.798499 GCCTGAGCACGTACGTATCAAT 60.798 50.000 26.16 11.66 39.53 2.57
1674 1737 0.099968 GCCTGAGCACGTACGTATCA 59.900 55.000 25.23 25.23 39.53 2.15
1675 1738 0.928908 CGCCTGAGCACGTACGTATC 60.929 60.000 22.34 21.06 39.83 2.24
1676 1739 1.063649 CGCCTGAGCACGTACGTAT 59.936 57.895 22.34 12.98 39.83 3.06
1765 1828 2.380941 CCATTGATGGTGAAGGCATCA 58.619 47.619 1.73 0.00 43.05 3.07
1833 1899 2.054363 CGCATGTAGGTAGATGAAGCG 58.946 52.381 0.00 0.00 36.62 4.68
2015 2580 2.483745 GTCGACGATGGTGAGCGA 59.516 61.111 0.00 0.00 34.27 4.93
2131 2696 0.032912 TCATGTAGTAGGTCGCCCCA 60.033 55.000 0.00 0.00 34.66 4.96
2290 2855 0.109086 AGCTCGTGTCGTTGATCTGG 60.109 55.000 0.00 0.00 0.00 3.86
2581 3164 1.595929 GTTGAACGGCGACTTGGGA 60.596 57.895 16.62 0.00 0.00 4.37
2585 3168 1.494824 GTGTAGTTGAACGGCGACTT 58.505 50.000 16.62 0.00 41.55 3.01
2828 3411 4.657824 CACGCCGACGGTGTTCCT 62.658 66.667 29.66 6.39 44.78 3.36
2947 3557 7.281040 TCAAAAGCAGATCATCAGTTTTCTT 57.719 32.000 0.00 0.00 0.00 2.52
2968 3578 6.487668 CCCTGCAGAACACATATCAATATCAA 59.512 38.462 17.39 0.00 0.00 2.57
2979 3589 0.538057 CACACCCCTGCAGAACACAT 60.538 55.000 17.39 0.00 0.00 3.21
3326 4017 6.681777 CAGTCCAAAAATGAAAGTCCTAAGG 58.318 40.000 0.00 0.00 0.00 2.69
3340 4031 3.188460 GCGACTAATCAGCAGTCCAAAAA 59.812 43.478 0.00 0.00 39.43 1.94
3506 4197 2.417243 GGCCATGGAATTTGTGCAGTAC 60.417 50.000 18.40 0.00 0.00 2.73
3536 4227 5.174037 TGGAATTTGGACGGAAGAAGTAT 57.826 39.130 0.00 0.00 0.00 2.12
3537 4228 4.627284 TGGAATTTGGACGGAAGAAGTA 57.373 40.909 0.00 0.00 0.00 2.24
3539 4230 3.129287 CCATGGAATTTGGACGGAAGAAG 59.871 47.826 5.56 0.00 36.26 2.85
3540 4231 3.088532 CCATGGAATTTGGACGGAAGAA 58.911 45.455 5.56 0.00 36.26 2.52
3541 4232 2.722094 CCATGGAATTTGGACGGAAGA 58.278 47.619 5.56 0.00 36.26 2.87
3542 4233 1.134946 GCCATGGAATTTGGACGGAAG 59.865 52.381 18.40 0.00 36.26 3.46
3543 4234 1.181786 GCCATGGAATTTGGACGGAA 58.818 50.000 18.40 0.00 36.26 4.30
3544 4235 0.682855 GGCCATGGAATTTGGACGGA 60.683 55.000 18.40 0.00 36.26 4.69
3545 4236 0.969917 TGGCCATGGAATTTGGACGG 60.970 55.000 18.40 0.00 46.01 4.79
3546 4237 0.457035 CTGGCCATGGAATTTGGACG 59.543 55.000 18.40 0.00 46.01 4.79
3547 4238 1.205417 CACTGGCCATGGAATTTGGAC 59.795 52.381 18.40 0.00 43.11 4.02
3548 4239 1.203162 ACACTGGCCATGGAATTTGGA 60.203 47.619 18.40 0.00 36.26 3.53
3549 4240 1.269012 ACACTGGCCATGGAATTTGG 58.731 50.000 18.40 1.83 37.31 3.28
3550 4241 3.700539 TCATACACTGGCCATGGAATTTG 59.299 43.478 18.40 9.09 0.00 2.32
3551 4242 3.979911 TCATACACTGGCCATGGAATTT 58.020 40.909 18.40 0.00 0.00 1.82
3555 4246 3.716353 AGTATTCATACACTGGCCATGGA 59.284 43.478 18.40 3.91 35.74 3.41
3556 4247 4.090761 AGTATTCATACACTGGCCATGG 57.909 45.455 5.51 7.63 35.74 3.66
3557 4248 5.679734 GAAGTATTCATACACTGGCCATG 57.320 43.478 5.51 9.86 46.62 3.66
3564 4255 8.341395 CCGGACGGAAGAAGTATTCATACACT 62.341 46.154 4.40 0.00 42.67 3.55
3567 4258 4.296690 CCGGACGGAAGAAGTATTCATAC 58.703 47.826 4.40 0.00 42.67 2.39
3569 4260 2.102588 CCCGGACGGAAGAAGTATTCAT 59.897 50.000 13.13 0.00 42.67 2.57
3570 4261 1.479323 CCCGGACGGAAGAAGTATTCA 59.521 52.381 13.13 0.00 42.67 2.57
3571 4262 1.479730 ACCCGGACGGAAGAAGTATTC 59.520 52.381 13.13 0.00 41.20 1.75
3572 4263 1.565067 ACCCGGACGGAAGAAGTATT 58.435 50.000 13.13 0.00 37.50 1.89
3597 4391 7.646130 GGTCAAAATTCGACACAATACAAGAAA 59.354 33.333 9.47 0.00 34.97 2.52
3602 4396 4.512198 ACGGTCAAAATTCGACACAATACA 59.488 37.500 9.47 0.00 34.97 2.29
3603 4397 5.025986 ACGGTCAAAATTCGACACAATAC 57.974 39.130 9.47 0.00 34.97 1.89
3605 4403 5.676532 TTACGGTCAAAATTCGACACAAT 57.323 34.783 9.47 0.00 34.97 2.71
3744 4641 9.147732 AGTTCTTCCTTAAACTTTGGATCAAAT 57.852 29.630 0.00 0.00 31.81 2.32
3756 4653 8.944029 GTCCTGGTTTATAGTTCTTCCTTAAAC 58.056 37.037 0.00 0.00 33.89 2.01
3758 4655 7.325694 CGTCCTGGTTTATAGTTCTTCCTTAA 58.674 38.462 0.00 0.00 0.00 1.85
3759 4656 6.127253 CCGTCCTGGTTTATAGTTCTTCCTTA 60.127 42.308 0.00 0.00 0.00 2.69
3777 4674 2.022934 GTACCTACTTCCTCCGTCCTG 58.977 57.143 0.00 0.00 0.00 3.86
3815 4712 2.704725 ATTAGTTGTGTTGCTTGGCG 57.295 45.000 0.00 0.00 0.00 5.69
3832 4729 3.267031 CCCTGGAGAGAACCCAAAGTATT 59.733 47.826 0.00 0.00 32.53 1.89
3868 6377 2.399356 GCTTGAGCTACAACCCGGC 61.399 63.158 0.00 0.00 38.21 6.13
3870 6379 1.131126 CATTGCTTGAGCTACAACCCG 59.869 52.381 4.44 0.00 42.66 5.28
3873 6382 2.268730 GCCATTGCTTGAGCTACAAC 57.731 50.000 4.44 0.00 42.66 3.32
3909 6418 4.277476 ACAAGTGAGAATCCAAAACACCA 58.723 39.130 0.00 0.00 32.76 4.17
3910 6419 4.918810 ACAAGTGAGAATCCAAAACACC 57.081 40.909 0.00 0.00 32.76 4.16
3912 6421 6.279513 ACAAACAAGTGAGAATCCAAAACA 57.720 33.333 0.00 0.00 0.00 2.83
3922 6431 1.070134 CCTCCCGACAAACAAGTGAGA 59.930 52.381 0.00 0.00 0.00 3.27
3937 6446 2.618045 CCACCAAAGACATACACCTCCC 60.618 54.545 0.00 0.00 0.00 4.30
3938 6447 2.711542 CCACCAAAGACATACACCTCC 58.288 52.381 0.00 0.00 0.00 4.30
3959 6468 0.726827 ATCATAACGTGGCGCAAGTG 59.273 50.000 10.83 0.00 41.68 3.16
3960 6469 1.448985 AATCATAACGTGGCGCAAGT 58.551 45.000 10.83 2.15 41.68 3.16
3961 6470 2.542766 AAATCATAACGTGGCGCAAG 57.457 45.000 10.83 1.38 43.44 4.01
3965 6474 3.740044 AGACAAAATCATAACGTGGCG 57.260 42.857 0.00 0.00 0.00 5.69
3987 6497 2.184533 ACTCATTCGGTATGTCACCCA 58.815 47.619 0.00 0.00 45.52 4.51
4000 6510 4.846779 TTACACCCTGCAAAACTCATTC 57.153 40.909 0.00 0.00 0.00 2.67
4040 6550 1.378119 GTGATTGGTTCCCGGGTCC 60.378 63.158 22.86 23.41 0.00 4.46
4045 6555 1.812571 CAAGAAGGTGATTGGTTCCCG 59.187 52.381 0.00 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.