Multiple sequence alignment - TraesCS3D01G263800

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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 TraesCS3D01G263800 chr3D 100.000 3037 0 0 3391 6427 365790323 365787287 0.000000e+00 5609.0
1 TraesCS3D01G263800 chr3D 100.000 2961 0 0 1 2961 365793713 365790753 0.000000e+00 5469.0
2 TraesCS3D01G263800 chr3D 90.132 152 13 2 3699 3850 467283660 467283511 5.080000e-46 196.0
3 TraesCS3D01G263800 chr3D 94.872 39 2 0 3894 3932 135376565 135376527 1.930000e-05 62.1
4 TraesCS3D01G263800 chr3A 92.852 3050 103 41 3391 6403 487459999 487457028 0.000000e+00 4318.0
5 TraesCS3D01G263800 chr3A 93.724 2422 67 21 551 2960 487462796 487460448 0.000000e+00 3552.0
6 TraesCS3D01G263800 chr3A 94.326 141 8 0 551 691 487462948 487462808 3.900000e-52 217.0
7 TraesCS3D01G263800 chr3A 86.813 182 14 5 3699 3880 609951129 609950958 1.830000e-45 195.0
8 TraesCS3D01G263800 chr3B 97.716 2364 41 8 574 2927 476295364 476293004 0.000000e+00 4054.0
9 TraesCS3D01G263800 chr3B 95.251 2274 82 10 3880 6141 476291465 476289206 0.000000e+00 3578.0
10 TraesCS3D01G263800 chr3B 94.622 502 16 4 3394 3884 476292742 476292241 0.000000e+00 767.0
11 TraesCS3D01G263800 chr2D 98.734 553 7 0 1 553 598861084 598861636 0.000000e+00 983.0
12 TraesCS3D01G263800 chr1D 98.370 552 8 1 1 551 314333069 314333620 0.000000e+00 968.0
13 TraesCS3D01G263800 chr1D 98.004 551 10 1 1 551 421848759 421848210 0.000000e+00 955.0
14 TraesCS3D01G263800 chr7D 98.185 551 10 0 1 551 546237739 546238289 0.000000e+00 963.0
15 TraesCS3D01G263800 chr7D 97.653 554 13 0 1 554 214903916 214903363 0.000000e+00 952.0
16 TraesCS3D01G263800 chr7D 90.000 150 13 2 3701 3850 126649570 126649717 6.580000e-45 193.0
17 TraesCS3D01G263800 chr6D 98.007 552 10 1 1 552 83000438 83000988 0.000000e+00 957.0
18 TraesCS3D01G263800 chr6D 97.822 551 12 0 1 551 159351605 159351055 0.000000e+00 952.0
19 TraesCS3D01G263800 chr6D 93.590 78 5 0 3597 3674 445729990 445729913 4.070000e-22 117.0
20 TraesCS3D01G263800 chr4D 98.007 552 10 1 1 551 365050280 365050831 0.000000e+00 957.0
21 TraesCS3D01G263800 chr4D 92.405 79 6 0 3596 3674 23322749 23322827 5.270000e-21 113.0
22 TraesCS3D01G263800 chr5D 97.645 552 13 0 1 552 27014915 27014364 0.000000e+00 948.0
23 TraesCS3D01G263800 chr5D 98.438 64 1 0 4263 4326 268905743 268905680 5.270000e-21 113.0
24 TraesCS3D01G263800 chr5D 96.875 64 2 0 4263 4326 125808334 125808271 2.450000e-19 108.0
25 TraesCS3D01G263800 chr7A 90.667 150 11 3 3702 3850 696172085 696171938 5.080000e-46 196.0
26 TraesCS3D01G263800 chr7A 89.404 151 14 2 3699 3849 68090226 68090374 8.510000e-44 189.0
27 TraesCS3D01G263800 chr2B 90.604 149 12 2 3702 3850 602995247 602995393 5.080000e-46 196.0
28 TraesCS3D01G263800 chr2B 95.000 40 0 2 3894 3932 622914075 622914113 1.930000e-05 62.1
29 TraesCS3D01G263800 chr5B 89.474 152 14 2 3699 3850 573003717 573003568 2.370000e-44 191.0
30 TraesCS3D01G263800 chr5B 98.438 64 1 0 4263 4326 223130192 223130129 5.270000e-21 113.0
31 TraesCS3D01G263800 chr4A 89.474 152 14 2 3699 3850 584667431 584667580 2.370000e-44 191.0
32 TraesCS3D01G263800 chr4A 93.671 79 5 0 3596 3674 216809662 216809740 1.130000e-22 119.0
33 TraesCS3D01G263800 chr4A 92.405 79 6 0 3596 3674 606539302 606539380 5.270000e-21 113.0
34 TraesCS3D01G263800 chr4A 88.136 59 7 0 6025 6083 460458752 460458810 3.210000e-08 71.3
35 TraesCS3D01G263800 chr5A 93.750 80 5 0 3595 3674 255600558 255600637 3.150000e-23 121.0
36 TraesCS3D01G263800 chr5A 93.590 78 5 0 3597 3674 591138675 591138752 4.070000e-22 117.0
37 TraesCS3D01G263800 chr5A 98.438 64 1 0 4263 4326 271053375 271053312 5.270000e-21 113.0
38 TraesCS3D01G263800 chr6B 92.405 79 6 0 3596 3674 331039815 331039737 5.270000e-21 113.0
39 TraesCS3D01G263800 chr6B 90.196 51 3 2 3893 3941 530560431 530560481 1.500000e-06 65.8
40 TraesCS3D01G263800 chr6B 95.000 40 1 1 3894 3932 518389039 518389078 1.930000e-05 62.1
41 TraesCS3D01G263800 chr4B 98.438 64 1 0 4263 4326 142929753 142929690 5.270000e-21 113.0
42 TraesCS3D01G263800 chr4B 98.438 64 1 0 4263 4326 411631051 411631114 5.270000e-21 113.0
43 TraesCS3D01G263800 chr7B 98.438 64 0 1 4263 4326 254836751 254836689 1.890000e-20 111.0
44 TraesCS3D01G263800 chr2A 95.349 43 1 1 3891 3932 738435354 738435396 4.160000e-07 67.6
45 TraesCS3D01G263800 chr1B 100.000 36 0 0 3896 3931 150361132 150361097 4.160000e-07 67.6
46 TraesCS3D01G263800 chr6A 95.238 42 0 2 3894 3934 604890720 604890760 1.500000e-06 65.8


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 TraesCS3D01G263800 chr3D 365787287 365793713 6426 True 5539.000000 5609 100.000 1 6427 2 chr3D.!!$R3 6426
1 TraesCS3D01G263800 chr3A 487457028 487462948 5920 True 2695.666667 4318 93.634 551 6403 3 chr3A.!!$R2 5852
2 TraesCS3D01G263800 chr3B 476289206 476295364 6158 True 2799.666667 4054 95.863 574 6141 3 chr3B.!!$R1 5567
3 TraesCS3D01G263800 chr2D 598861084 598861636 552 False 983.000000 983 98.734 1 553 1 chr2D.!!$F1 552
4 TraesCS3D01G263800 chr1D 314333069 314333620 551 False 968.000000 968 98.370 1 551 1 chr1D.!!$F1 550
5 TraesCS3D01G263800 chr1D 421848210 421848759 549 True 955.000000 955 98.004 1 551 1 chr1D.!!$R1 550
6 TraesCS3D01G263800 chr7D 546237739 546238289 550 False 963.000000 963 98.185 1 551 1 chr7D.!!$F2 550
7 TraesCS3D01G263800 chr7D 214903363 214903916 553 True 952.000000 952 97.653 1 554 1 chr7D.!!$R1 553
8 TraesCS3D01G263800 chr6D 83000438 83000988 550 False 957.000000 957 98.007 1 552 1 chr6D.!!$F1 551
9 TraesCS3D01G263800 chr6D 159351055 159351605 550 True 952.000000 952 97.822 1 551 1 chr6D.!!$R1 550
10 TraesCS3D01G263800 chr4D 365050280 365050831 551 False 957.000000 957 98.007 1 551 1 chr4D.!!$F2 550
11 TraesCS3D01G263800 chr5D 27014364 27014915 551 True 948.000000 948 97.645 1 552 1 chr5D.!!$R1 551

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
394 397 1.293498 CGACTGAGGGAGGGTGTTG 59.707 63.158 0.00 0.00 0.00 3.33 F
872 1027 1.801178 GTCCTCCAGCTCTTTTGTTCG 59.199 52.381 0.00 0.00 0.00 3.95 F
1178 1357 2.479275 GCTGTAGTCCGTTTGAGGAAAC 59.521 50.000 0.00 0.00 42.77 2.78 F
2551 2730 2.107204 ACCTTCTGAACTTCTGGTGCAT 59.893 45.455 0.00 0.00 32.16 3.96 F
3749 3947 0.037605 CTTGTGTAGGGTCCGACCAC 60.038 60.000 19.43 10.17 41.02 4.16 F
4066 5055 0.464554 GTTGGCCTCTGTAGCATCCC 60.465 60.000 3.32 0.00 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2344 2523 2.118313 TTGGAGCATGTGAGATGTGG 57.882 50.000 0.00 0.00 0.00 4.17 R
2464 2643 4.316205 TGGATTTTGATGCATCATGAGC 57.684 40.909 29.13 21.41 36.56 4.26 R
2582 2761 6.197655 CAGATGACACATTTTGACACAAACAG 59.802 38.462 0.00 0.00 32.48 3.16 R
4016 5005 0.671781 GGCGTGTCTGAGTGAGCAAT 60.672 55.000 0.00 0.00 0.00 3.56 R
5330 6321 1.377725 CCCCATCATAGCCATCGCC 60.378 63.158 0.00 0.00 34.57 5.54 R
6014 7026 1.048601 TCGATCTACATCCAAGGGCC 58.951 55.000 0.00 0.00 0.00 5.80 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
333 335 3.136260 AGGATTGCCATCTCCTCTCTTTC 59.864 47.826 0.00 0.00 37.30 2.62
394 397 1.293498 CGACTGAGGGAGGGTGTTG 59.707 63.158 0.00 0.00 0.00 3.33
473 477 8.746530 CCTTGTATAGGTGTCCGTATATTGTAT 58.253 37.037 0.00 0.00 39.39 2.29
628 632 6.001460 TCATACAAGGGTCAAAGTTTACCAG 58.999 40.000 13.06 5.78 37.51 4.00
867 1022 3.297134 TTGTTGTCCTCCAGCTCTTTT 57.703 42.857 0.00 0.00 0.00 2.27
868 1023 2.575532 TGTTGTCCTCCAGCTCTTTTG 58.424 47.619 0.00 0.00 0.00 2.44
872 1027 1.801178 GTCCTCCAGCTCTTTTGTTCG 59.199 52.381 0.00 0.00 0.00 3.95
1031 1210 3.069443 GGTGCTTCCAAAAGATTTGGTGA 59.931 43.478 18.54 9.90 40.40 4.02
1032 1211 4.301628 GTGCTTCCAAAAGATTTGGTGAG 58.698 43.478 18.54 17.33 40.40 3.51
1033 1212 4.037923 GTGCTTCCAAAAGATTTGGTGAGA 59.962 41.667 18.54 0.30 40.40 3.27
1034 1213 4.648762 TGCTTCCAAAAGATTTGGTGAGAA 59.351 37.500 18.54 11.34 40.40 2.87
1035 1214 5.305128 TGCTTCCAAAAGATTTGGTGAGAAT 59.695 36.000 18.54 0.00 40.40 2.40
1036 1215 5.636543 GCTTCCAAAAGATTTGGTGAGAATG 59.363 40.000 18.54 5.71 40.40 2.67
1037 1216 6.517194 GCTTCCAAAAGATTTGGTGAGAATGA 60.517 38.462 18.54 0.00 40.40 2.57
1038 1217 6.975196 TCCAAAAGATTTGGTGAGAATGAA 57.025 33.333 18.54 0.00 40.40 2.57
1039 1218 6.985117 TCCAAAAGATTTGGTGAGAATGAAG 58.015 36.000 18.54 0.00 40.40 3.02
1040 1219 6.777091 TCCAAAAGATTTGGTGAGAATGAAGA 59.223 34.615 18.54 0.00 40.40 2.87
1041 1220 6.865205 CCAAAAGATTTGGTGAGAATGAAGAC 59.135 38.462 12.63 0.00 34.92 3.01
1042 1221 7.255730 CCAAAAGATTTGGTGAGAATGAAGACT 60.256 37.037 12.63 0.00 34.92 3.24
1043 1222 7.830099 AAAGATTTGGTGAGAATGAAGACTT 57.170 32.000 0.00 0.00 0.00 3.01
1044 1223 7.830099 AAGATTTGGTGAGAATGAAGACTTT 57.170 32.000 0.00 0.00 0.00 2.66
1045 1224 7.211966 AGATTTGGTGAGAATGAAGACTTTG 57.788 36.000 0.00 0.00 0.00 2.77
1046 1225 7.000472 AGATTTGGTGAGAATGAAGACTTTGA 59.000 34.615 0.00 0.00 0.00 2.69
1047 1226 7.503566 AGATTTGGTGAGAATGAAGACTTTGAA 59.496 33.333 0.00 0.00 0.00 2.69
1048 1227 6.377327 TTGGTGAGAATGAAGACTTTGAAC 57.623 37.500 0.00 0.00 0.00 3.18
1049 1228 5.684704 TGGTGAGAATGAAGACTTTGAACT 58.315 37.500 0.00 0.00 0.00 3.01
1050 1229 6.122277 TGGTGAGAATGAAGACTTTGAACTT 58.878 36.000 0.00 0.00 0.00 2.66
1051 1230 6.260936 TGGTGAGAATGAAGACTTTGAACTTC 59.739 38.462 0.00 0.00 41.67 3.01
1052 1231 6.484977 GGTGAGAATGAAGACTTTGAACTTCT 59.515 38.462 0.00 0.00 41.79 2.85
1053 1232 7.351223 GTGAGAATGAAGACTTTGAACTTCTG 58.649 38.462 0.00 0.00 41.79 3.02
1178 1357 2.479275 GCTGTAGTCCGTTTGAGGAAAC 59.521 50.000 0.00 0.00 42.77 2.78
1476 1655 8.635765 TTTCTGTACATAAGCCTTCAGATTTT 57.364 30.769 0.00 0.00 33.10 1.82
1567 1746 8.149647 TGTTTGCAATCAATAGGAAAATTGACT 58.850 29.630 7.74 0.00 45.90 3.41
1863 2042 5.012239 TCTTGCAGCAAGGATGAAACTAAT 58.988 37.500 30.71 0.00 41.33 1.73
2013 2192 6.418057 AGATGCCAAAAACAACAGGATTTA 57.582 33.333 0.00 0.00 0.00 1.40
2211 2390 5.047021 CACAGAGATCTCCAAGTTACTGGAA 60.047 44.000 19.30 0.00 44.97 3.53
2312 2491 2.675658 AGCAAGCAAAAAGGGTCCTA 57.324 45.000 0.00 0.00 0.00 2.94
2344 2523 7.653647 TGAAATGTTAACAGTACCATCCAAAC 58.346 34.615 14.65 0.00 0.00 2.93
2464 2643 5.973651 AACAGATACATTGTACAGCGATG 57.026 39.130 0.00 0.00 43.18 3.84
2551 2730 2.107204 ACCTTCTGAACTTCTGGTGCAT 59.893 45.455 0.00 0.00 32.16 3.96
2582 2761 8.718102 TGACAGAACTTAAGTATTTATCAGGC 57.282 34.615 8.92 2.12 0.00 4.85
2601 2780 3.195396 AGGCTGTTTGTGTCAAAATGTGT 59.805 39.130 0.00 0.00 0.00 3.72
2853 3032 8.637281 TTTATTCTTGTATGAAAGCATGCATG 57.363 30.769 22.70 22.70 44.73 4.06
2953 3133 4.843728 ACAAACATATCAATCAGACGGGT 58.156 39.130 0.00 0.00 0.00 5.28
2960 3140 4.819105 ATCAATCAGACGGGTAAGAACA 57.181 40.909 0.00 0.00 0.00 3.18
3554 3752 6.122850 TGCATGCTACTGTAAATCAACATC 57.877 37.500 20.33 0.00 0.00 3.06
3609 3807 3.445008 TCTGATTGCTTGAGTAGGGTCT 58.555 45.455 0.00 0.00 0.00 3.85
3745 3943 2.642254 CCGCTTGTGTAGGGTCCGA 61.642 63.158 0.00 0.00 35.13 4.55
3746 3944 1.445582 CGCTTGTGTAGGGTCCGAC 60.446 63.158 0.00 0.00 32.41 4.79
3747 3945 1.079336 GCTTGTGTAGGGTCCGACC 60.079 63.158 9.30 9.30 37.60 4.79
3749 3947 0.037605 CTTGTGTAGGGTCCGACCAC 60.038 60.000 19.43 10.17 41.02 4.16
3750 3948 0.470456 TTGTGTAGGGTCCGACCACT 60.470 55.000 19.43 15.07 41.02 4.00
3808 4017 4.620723 TCTGTAAGAGGCTATTTCCAGGA 58.379 43.478 16.33 0.00 38.67 3.86
3824 4033 1.111116 AGGACTCGAACCCGTGACAA 61.111 55.000 4.92 0.00 37.05 3.18
3873 4082 3.551496 TACTGCTGCGCCAAGGCTT 62.551 57.895 4.18 0.00 39.32 4.35
4016 5005 3.502595 CACAGTCTCGAAGGTTCTGAGTA 59.497 47.826 0.00 0.00 33.08 2.59
4066 5055 0.464554 GTTGGCCTCTGTAGCATCCC 60.465 60.000 3.32 0.00 0.00 3.85
4127 5116 1.606737 GGTGCCACTCTCTCAACTCAC 60.607 57.143 0.00 0.00 0.00 3.51
4128 5117 1.342819 GTGCCACTCTCTCAACTCACT 59.657 52.381 0.00 0.00 0.00 3.41
4294 5285 1.619654 CCAACTCATGGTTCTGGCAA 58.380 50.000 0.00 0.00 44.85 4.52
4381 5372 1.689258 GGGGGCCTATGATGCACTTTT 60.689 52.381 0.84 0.00 31.13 2.27
4598 5589 6.047511 ACTTTCTGTTGCTCATAGTCTGAT 57.952 37.500 0.00 0.00 32.10 2.90
4849 5840 7.224297 ACTTGTGCTAGTAAGAAAGAATGGAA 58.776 34.615 9.51 0.00 0.00 3.53
5066 6057 3.709834 TCCTGGAGGAGCATGTACA 57.290 52.632 0.00 0.00 39.78 2.90
5182 6173 1.531149 ACAAAACCAAGATGCGTCTCG 59.469 47.619 9.35 5.18 32.15 4.04
5330 6321 0.179215 GTCAGTTTCCAAGCATCGCG 60.179 55.000 0.00 0.00 0.00 5.87
5369 6360 2.066262 CGTGTAATGAACAAGCTCCGT 58.934 47.619 0.00 0.00 40.63 4.69
5471 6462 3.443045 GCCATCGGCTGTGGGTTG 61.443 66.667 13.79 0.00 46.69 3.77
5547 6544 7.066284 TGTTTCCTCACAGAAGAAGAGAAAAAG 59.934 37.037 0.00 0.00 0.00 2.27
5587 6584 7.338800 TCATTCCAAGGAGAGAAAAATATGC 57.661 36.000 0.00 0.00 0.00 3.14
5590 6587 5.253330 TCCAAGGAGAGAAAAATATGCGTT 58.747 37.500 0.00 0.00 0.00 4.84
5608 6605 3.810373 CGTTGTTTCTACCAATCACAGC 58.190 45.455 0.00 0.00 0.00 4.40
5680 6677 1.450312 CATCGTCTGAAGGGTGCCC 60.450 63.158 0.00 0.00 0.00 5.36
5718 6715 7.465916 CGTGACCAAACAGATATTCATAACTGG 60.466 40.741 8.48 0.00 37.45 4.00
5837 6835 3.181487 ACATTGTCGCTGTGCTTTTCTTT 60.181 39.130 0.00 0.00 0.00 2.52
5854 6852 0.250901 TTTGGAGCTGCTGGAAGGAC 60.251 55.000 7.01 0.00 0.00 3.85
5940 6938 3.334583 TCTTATGAAGCAGAAGCCGTT 57.665 42.857 0.00 0.00 43.56 4.44
5999 7011 3.347216 GCTGTGGTTGAATATCCTGTGT 58.653 45.455 0.00 0.00 0.00 3.72
6049 7061 0.735471 TCGAACGATCAGCTGAGGAG 59.265 55.000 22.96 16.97 0.00 3.69
6072 7084 4.019792 TGCTGGACTTGTGTGTAATGAT 57.980 40.909 0.00 0.00 0.00 2.45
6073 7085 5.159273 TGCTGGACTTGTGTGTAATGATA 57.841 39.130 0.00 0.00 0.00 2.15
6095 7107 1.602377 GACTCGTTGTGGGTTTTCTGG 59.398 52.381 0.00 0.00 0.00 3.86
6102 7114 4.440802 CGTTGTGGGTTTTCTGGAAATTCA 60.441 41.667 0.00 0.00 0.00 2.57
6106 7118 3.645212 TGGGTTTTCTGGAAATTCATGCA 59.355 39.130 0.00 0.00 0.00 3.96
6117 7129 3.939740 AATTCATGCAAGCTCTCCCTA 57.060 42.857 0.00 0.00 0.00 3.53
6121 7133 2.977580 TCATGCAAGCTCTCCCTATGAT 59.022 45.455 0.00 0.00 0.00 2.45
6150 7162 1.409427 CTAGGGAACTTAGGTGCTCCG 59.591 57.143 0.00 0.00 43.67 4.63
6152 7164 1.262640 GGGAACTTAGGTGCTCCGGA 61.263 60.000 2.93 2.93 39.05 5.14
6167 7179 4.802876 CTCCGGAAGCACAAGATATTTC 57.197 45.455 5.23 0.00 0.00 2.17
6170 7182 2.287915 CGGAAGCACAAGATATTTCCCG 59.712 50.000 0.00 0.00 35.07 5.14
6172 7184 3.279434 GAAGCACAAGATATTTCCCGGT 58.721 45.455 0.00 0.00 0.00 5.28
6174 7186 1.947456 GCACAAGATATTTCCCGGTCC 59.053 52.381 0.00 0.00 0.00 4.46
6195 7207 2.631428 CGTTGCACGGTGAGGTTG 59.369 61.111 13.29 0.00 38.08 3.77
6196 7208 2.892334 CGTTGCACGGTGAGGTTGG 61.892 63.158 13.29 0.00 38.08 3.77
6205 7217 1.198759 GGTGAGGTTGGTGGCTCCTA 61.199 60.000 7.19 0.00 37.07 2.94
6240 7252 0.112995 ACCATCACATTGGCTGGTGT 59.887 50.000 6.34 0.00 40.43 4.16
6242 7254 1.536940 CATCACATTGGCTGGTGTCA 58.463 50.000 0.00 0.00 36.43 3.58
6264 7276 4.758251 TGCTGCCCGATCACGTGG 62.758 66.667 17.00 0.00 37.88 4.94
6307 7319 2.591429 CTGGCAACACGGTGCTCA 60.591 61.111 8.30 2.79 46.17 4.26
6316 7328 3.055719 CGGTGCTCATGGGCGTTT 61.056 61.111 14.07 0.00 34.52 3.60
6353 7366 0.494551 TGTGAGGGGGAAGGAGGTTA 59.505 55.000 0.00 0.00 0.00 2.85
6359 7372 1.345112 GGGGGAAGGAGGTTATGGAGA 60.345 57.143 0.00 0.00 0.00 3.71
6382 7395 4.675303 CCTCACCCTCCACCCCCA 62.675 72.222 0.00 0.00 0.00 4.96
6396 7409 1.285280 CCCCCAGGTCATGTTCTACA 58.715 55.000 0.00 0.00 0.00 2.74
6399 7412 1.407437 CCCAGGTCATGTTCTACAGGC 60.407 57.143 0.00 0.00 28.67 4.85
6400 7413 1.645034 CAGGTCATGTTCTACAGGCG 58.355 55.000 0.00 0.00 28.67 5.52
6401 7414 1.204704 CAGGTCATGTTCTACAGGCGA 59.795 52.381 0.00 0.00 28.67 5.54
6404 7417 2.673368 GGTCATGTTCTACAGGCGAAAG 59.327 50.000 0.00 0.00 28.67 2.62
6419 7432 2.611518 CGAAAGCCTAAGACTCTGGTG 58.388 52.381 0.00 0.00 0.00 4.17
6420 7433 2.028930 CGAAAGCCTAAGACTCTGGTGT 60.029 50.000 0.00 0.00 0.00 4.16
6421 7434 3.192844 CGAAAGCCTAAGACTCTGGTGTA 59.807 47.826 0.00 0.00 0.00 2.90
6422 7435 4.675671 CGAAAGCCTAAGACTCTGGTGTAG 60.676 50.000 0.00 0.00 0.00 2.74
6423 7436 2.741145 AGCCTAAGACTCTGGTGTAGG 58.259 52.381 0.00 0.00 34.96 3.18
6424 7437 2.043252 AGCCTAAGACTCTGGTGTAGGT 59.957 50.000 4.22 0.00 34.62 3.08
6425 7438 2.427812 GCCTAAGACTCTGGTGTAGGTC 59.572 54.545 4.22 0.00 34.62 3.85
6426 7439 2.683867 CCTAAGACTCTGGTGTAGGTCG 59.316 54.545 0.00 0.00 34.06 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
333 335 2.770164 AGACTGTCCCGAAAATCCAG 57.230 50.000 3.76 0.00 0.00 3.86
473 477 4.491676 GTTACAAGGCAGAGTTCGTATCA 58.508 43.478 0.00 0.00 0.00 2.15
609 613 5.592104 AAACTGGTAAACTTTGACCCTTG 57.408 39.130 0.00 0.00 34.58 3.61
612 616 6.994496 ACTAGTAAACTGGTAAACTTTGACCC 59.006 38.462 0.00 0.00 35.84 4.46
841 996 2.093235 AGCTGGAGGACAACAATAGCTC 60.093 50.000 0.00 0.00 35.29 4.09
867 1022 8.441312 AAACCAGTATAAAGAAGAAACGAACA 57.559 30.769 0.00 0.00 0.00 3.18
868 1023 8.553696 TGAAACCAGTATAAAGAAGAAACGAAC 58.446 33.333 0.00 0.00 0.00 3.95
1031 1210 6.017275 CAGCAGAAGTTCAAAGTCTTCATTCT 60.017 38.462 5.50 0.00 41.46 2.40
1032 1211 6.017605 TCAGCAGAAGTTCAAAGTCTTCATTC 60.018 38.462 5.50 0.00 41.46 2.67
1033 1212 5.824624 TCAGCAGAAGTTCAAAGTCTTCATT 59.175 36.000 5.50 0.00 41.46 2.57
1034 1213 5.371526 TCAGCAGAAGTTCAAAGTCTTCAT 58.628 37.500 5.50 0.00 41.46 2.57
1035 1214 4.769688 TCAGCAGAAGTTCAAAGTCTTCA 58.230 39.130 5.50 0.00 41.46 3.02
1036 1215 4.319405 GCTCAGCAGAAGTTCAAAGTCTTC 60.319 45.833 5.50 0.00 39.93 2.87
1037 1216 3.563390 GCTCAGCAGAAGTTCAAAGTCTT 59.437 43.478 5.50 0.00 0.00 3.01
1038 1217 3.137533 GCTCAGCAGAAGTTCAAAGTCT 58.862 45.455 5.50 0.00 0.00 3.24
1039 1218 2.874701 TGCTCAGCAGAAGTTCAAAGTC 59.125 45.455 0.00 0.00 33.32 3.01
1040 1219 2.923121 TGCTCAGCAGAAGTTCAAAGT 58.077 42.857 0.00 0.00 33.32 2.66
1041 1220 3.976793 TTGCTCAGCAGAAGTTCAAAG 57.023 42.857 0.00 0.00 40.61 2.77
1042 1221 4.675510 CTTTTGCTCAGCAGAAGTTCAAA 58.324 39.130 19.60 6.07 43.01 2.69
1043 1222 4.297299 CTTTTGCTCAGCAGAAGTTCAA 57.703 40.909 19.60 0.00 43.01 2.69
1044 1223 3.976793 CTTTTGCTCAGCAGAAGTTCA 57.023 42.857 19.60 0.00 43.01 3.18
1049 1228 5.247862 TGATATCACTTTTGCTCAGCAGAA 58.752 37.500 0.00 0.00 40.61 3.02
1050 1229 4.835678 TGATATCACTTTTGCTCAGCAGA 58.164 39.130 0.00 0.00 40.61 4.26
1051 1230 4.874396 TCTGATATCACTTTTGCTCAGCAG 59.126 41.667 0.00 0.00 40.61 4.24
1052 1231 4.835678 TCTGATATCACTTTTGCTCAGCA 58.164 39.130 0.00 0.00 36.47 4.41
1053 1232 5.114780 TCTCTGATATCACTTTTGCTCAGC 58.885 41.667 0.00 0.00 32.20 4.26
1476 1655 8.690203 TCAAAAGTTTATGAGAATCCACAGAA 57.310 30.769 0.00 0.00 0.00 3.02
1567 1746 3.167485 ACCGTCTTGGGTTGAGTATACA 58.833 45.455 5.50 0.00 44.64 2.29
1848 2027 5.716703 ACCAAGGGAATTAGTTTCATCCTTG 59.283 40.000 11.07 11.07 44.83 3.61
2013 2192 7.676683 TGGCTCATAAAATACTACTTCCTCT 57.323 36.000 0.00 0.00 0.00 3.69
2211 2390 7.278875 TCATTACTGGTGCCTTTTCAATTTTT 58.721 30.769 0.00 0.00 0.00 1.94
2344 2523 2.118313 TTGGAGCATGTGAGATGTGG 57.882 50.000 0.00 0.00 0.00 4.17
2464 2643 4.316205 TGGATTTTGATGCATCATGAGC 57.684 40.909 29.13 21.41 36.56 4.26
2569 2748 6.237901 TGACACAAACAGCCTGATAAATACT 58.762 36.000 0.00 0.00 0.00 2.12
2582 2761 6.197655 CAGATGACACATTTTGACACAAACAG 59.802 38.462 0.00 0.00 32.48 3.16
3554 3752 4.766891 TGAAAGGTAGGAATCTTTTGCAGG 59.233 41.667 0.00 0.00 33.85 4.85
3609 3807 1.846124 GTGGTCAGACCCTTCCCCA 60.846 63.158 17.59 0.00 37.50 4.96
3745 3943 4.142337 CGTACAAAAAGACCCAAAAGTGGT 60.142 41.667 0.00 0.00 44.30 4.16
3746 3944 4.356289 CGTACAAAAAGACCCAAAAGTGG 58.644 43.478 0.00 0.00 45.53 4.00
3747 3945 3.794564 GCGTACAAAAAGACCCAAAAGTG 59.205 43.478 0.00 0.00 0.00 3.16
3749 3947 4.035278 TGCGTACAAAAAGACCCAAAAG 57.965 40.909 0.00 0.00 0.00 2.27
3750 3948 3.735514 GCTGCGTACAAAAAGACCCAAAA 60.736 43.478 0.00 0.00 0.00 2.44
3808 4017 1.299620 CGTTGTCACGGGTTCGAGT 60.300 57.895 0.00 0.00 43.16 4.18
3824 4033 1.078072 TGTTGCCTTGTGACCACGT 60.078 52.632 0.00 0.00 0.00 4.49
3826 4035 1.103398 AGCTGTTGCCTTGTGACCAC 61.103 55.000 0.00 0.00 40.80 4.16
3873 4082 1.004277 GCATGTGTTGGTAGGAAGGGA 59.996 52.381 0.00 0.00 0.00 4.20
3884 4093 2.054687 AATTGTCGCTGCATGTGTTG 57.945 45.000 0.00 0.00 0.00 3.33
3885 4094 3.913548 TTAATTGTCGCTGCATGTGTT 57.086 38.095 0.00 0.00 0.00 3.32
4016 5005 0.671781 GGCGTGTCTGAGTGAGCAAT 60.672 55.000 0.00 0.00 0.00 3.56
4105 5094 1.070758 GAGTTGAGAGAGTGGCACCAA 59.929 52.381 15.27 8.09 0.00 3.67
4127 5116 1.134965 GTGTCATTCGGTCCCTCAGAG 60.135 57.143 0.00 0.00 0.00 3.35
4128 5117 0.895530 GTGTCATTCGGTCCCTCAGA 59.104 55.000 0.00 0.00 0.00 3.27
4251 5242 6.347483 GGTTTCGAGATCTTAACTTGAACCAC 60.347 42.308 0.00 0.00 37.46 4.16
4849 5840 2.577700 TGCTTGACGTTTTGGGTATGT 58.422 42.857 0.00 0.00 0.00 2.29
5066 6057 2.722094 TCAAGCACTTGACCAAACACT 58.278 42.857 8.99 0.00 43.90 3.55
5330 6321 1.377725 CCCCATCATAGCCATCGCC 60.378 63.158 0.00 0.00 34.57 5.54
5369 6360 3.071602 CCCTCTTCTCAAGTTCACAAGGA 59.928 47.826 0.00 0.00 0.00 3.36
5471 6462 4.445452 TTCTCTCCTGCATGCAAATTTC 57.555 40.909 22.88 0.00 0.00 2.17
5516 6512 5.760253 TCTTCTTCTGTGAGGAAACAATCAC 59.240 40.000 0.00 0.00 44.88 3.06
5547 6544 7.173907 CCTTGGAATGATATTCACACTACCATC 59.826 40.741 4.19 0.00 0.00 3.51
5587 6584 3.664276 CGCTGTGATTGGTAGAAACAACG 60.664 47.826 0.00 0.00 0.00 4.10
5590 6587 2.805671 CACGCTGTGATTGGTAGAAACA 59.194 45.455 3.04 0.00 35.23 2.83
5608 6605 6.903479 CACAATCAACACATCAATCTATCACG 59.097 38.462 0.00 0.00 0.00 4.35
5680 6677 4.512198 TGTTTGGTCACGGTACACAAATAG 59.488 41.667 0.00 0.00 34.11 1.73
5718 6715 6.715347 AATATAAACTGAATGCAACCTCCC 57.285 37.500 0.00 0.00 0.00 4.30
5758 6755 5.302360 TCTGGAAGCAACATAACGTAACTT 58.698 37.500 0.00 0.00 0.00 2.66
5837 6835 1.418097 TTGTCCTTCCAGCAGCTCCA 61.418 55.000 0.00 0.00 0.00 3.86
5854 6852 8.682016 CAGAAAACATTAGCGTCTAAACTTTTG 58.318 33.333 14.80 7.99 0.00 2.44
5915 6913 6.058183 ACGGCTTCTGCTTCATAAGATTTAT 58.942 36.000 0.00 0.00 39.59 1.40
5940 6938 3.809775 GCGCCATTGCTACGCCAA 61.810 61.111 0.00 0.00 46.63 4.52
6014 7026 1.048601 TCGATCTACATCCAAGGGCC 58.951 55.000 0.00 0.00 0.00 5.80
6016 7028 2.361119 TCGTTCGATCTACATCCAAGGG 59.639 50.000 0.00 0.00 0.00 3.95
6049 7061 3.563808 TCATTACACACAAGTCCAGCAAC 59.436 43.478 0.00 0.00 0.00 4.17
6072 7084 2.701951 AGAAAACCCACAACGAGTCCTA 59.298 45.455 0.00 0.00 0.00 2.94
6073 7085 1.489230 AGAAAACCCACAACGAGTCCT 59.511 47.619 0.00 0.00 0.00 3.85
6095 7107 3.022406 AGGGAGAGCTTGCATGAATTTC 58.978 45.455 3.33 0.00 0.00 2.17
6102 7114 3.137913 ACAATCATAGGGAGAGCTTGCAT 59.862 43.478 0.00 0.00 0.00 3.96
6106 7118 2.441001 CCCACAATCATAGGGAGAGCTT 59.559 50.000 0.00 0.00 45.80 3.74
6117 7129 4.310740 AGTTCCCTAGATCCCACAATCAT 58.689 43.478 0.00 0.00 0.00 2.45
6121 7133 4.037927 CCTAAGTTCCCTAGATCCCACAA 58.962 47.826 0.00 0.00 0.00 3.33
6150 7162 2.618709 CCGGGAAATATCTTGTGCTTCC 59.381 50.000 0.00 0.00 35.76 3.46
6152 7164 3.279434 GACCGGGAAATATCTTGTGCTT 58.721 45.455 6.32 0.00 0.00 3.91
6157 7169 1.878953 CCGGACCGGGAAATATCTTG 58.121 55.000 26.15 0.00 44.15 3.02
6183 7195 2.978010 GCCACCAACCTCACCGTG 60.978 66.667 0.00 0.00 0.00 4.94
6184 7196 3.168528 AGCCACCAACCTCACCGT 61.169 61.111 0.00 0.00 0.00 4.83
6185 7197 2.358737 GAGCCACCAACCTCACCG 60.359 66.667 0.00 0.00 0.00 4.94
6186 7198 1.198759 TAGGAGCCACCAACCTCACC 61.199 60.000 0.00 0.00 42.04 4.02
6188 7200 1.541310 CGTAGGAGCCACCAACCTCA 61.541 60.000 0.00 0.00 42.04 3.86
6189 7201 1.218316 CGTAGGAGCCACCAACCTC 59.782 63.158 0.00 0.00 42.04 3.85
6190 7202 1.535687 ACGTAGGAGCCACCAACCT 60.536 57.895 0.00 0.00 42.04 3.50
6192 7204 0.249398 ATCACGTAGGAGCCACCAAC 59.751 55.000 0.00 0.00 42.04 3.77
6193 7205 0.249120 CATCACGTAGGAGCCACCAA 59.751 55.000 0.00 0.00 42.04 3.67
6194 7206 1.613317 CCATCACGTAGGAGCCACCA 61.613 60.000 0.00 0.00 42.04 4.17
6195 7207 1.144057 CCATCACGTAGGAGCCACC 59.856 63.158 0.00 0.00 39.35 4.61
6196 7208 1.521681 GCCATCACGTAGGAGCCAC 60.522 63.158 5.16 0.00 0.00 5.01
6240 7252 3.356639 GATCGGGCAGCACGTCTGA 62.357 63.158 18.55 0.00 45.72 3.27
6242 7254 3.381983 TGATCGGGCAGCACGTCT 61.382 61.111 18.55 5.68 0.00 4.18
6264 7276 3.775654 CTCGGAGCAGTCCACCCC 61.776 72.222 0.00 0.00 44.18 4.95
6267 7279 2.765250 TTTCGCTCGGAGCAGTCCAC 62.765 60.000 27.83 0.00 44.18 4.02
6288 7300 2.896801 GAGCACCGTGTTGCCAGTG 61.897 63.158 0.00 0.00 44.14 3.66
6290 7302 1.968017 ATGAGCACCGTGTTGCCAG 60.968 57.895 0.00 0.00 44.14 4.85
6307 7319 0.178975 TGGAGGAAACAAACGCCCAT 60.179 50.000 0.00 0.00 0.00 4.00
6316 7328 2.687425 CACACACACATTGGAGGAAACA 59.313 45.455 0.00 0.00 0.00 2.83
6359 7372 0.545548 GGTGGAGGGTGAGGAAGACT 60.546 60.000 0.00 0.00 0.00 3.24
6382 7395 1.557099 TCGCCTGTAGAACATGACCT 58.443 50.000 0.00 0.00 0.00 3.85
6399 7412 2.028930 ACACCAGAGTCTTAGGCTTTCG 60.029 50.000 0.00 0.00 0.00 3.46
6400 7413 3.686916 ACACCAGAGTCTTAGGCTTTC 57.313 47.619 0.00 0.00 0.00 2.62
6401 7414 3.515901 CCTACACCAGAGTCTTAGGCTTT 59.484 47.826 0.00 0.00 0.00 3.51
6404 7417 2.427812 GACCTACACCAGAGTCTTAGGC 59.572 54.545 13.46 5.40 34.15 3.93
6405 7418 2.683867 CGACCTACACCAGAGTCTTAGG 59.316 54.545 12.35 12.35 35.86 2.69


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

AutoCloner maintained by Alex Coulton.