Multiple sequence alignment - TraesCS2A01G538300

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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 TraesCS2A01G538300 chr2A 100.000 4884 0 0 1 4884 751266535 751271418 0.000000e+00 9020
1 TraesCS2A01G538300 chr2A 99.620 3949 13 2 681 4627 751236827 751240775 0.000000e+00 7208
2 TraesCS2A01G538300 chr2A 99.638 2209 7 1 1 2208 751287460 751289668 0.000000e+00 4034
3 TraesCS2A01G538300 chr2A 88.135 3270 328 34 685 3928 751207462 751210697 0.000000e+00 3834
4 TraesCS2A01G538300 chr2A 86.122 1996 216 42 2205 4172 751233166 751235128 0.000000e+00 2095
5 TraesCS2A01G538300 chr2A 82.080 2154 301 49 1973 4093 719730717 719728616 0.000000e+00 1760
6 TraesCS2A01G538300 chr2A 85.792 1464 184 16 697 2141 751231693 751233151 0.000000e+00 1530
7 TraesCS2A01G538300 chr2A 98.895 181 2 0 4625 4805 722747256 722747076 1.700000e-84 324
8 TraesCS2A01G538300 chr2A 100.000 80 0 0 4805 4884 751240760 751240839 1.100000e-31 148
9 TraesCS2A01G538300 chr2D 95.721 3482 139 8 697 4172 619700955 619704432 0.000000e+00 5596
10 TraesCS2A01G538300 chr2D 88.795 1767 162 25 2177 3924 619664417 619666166 0.000000e+00 2134
11 TraesCS2A01G538300 chr2D 81.653 2033 271 67 2186 4175 585687837 585685864 0.000000e+00 1594
12 TraesCS2A01G538300 chr2D 86.186 1332 169 7 796 2121 619663094 619664416 0.000000e+00 1426
13 TraesCS2A01G538300 chr2D 93.316 374 22 3 4256 4627 619704363 619704735 2.570000e-152 549
14 TraesCS2A01G538300 chr2D 98.343 181 3 0 4625 4805 442882399 442882579 7.890000e-83 318
15 TraesCS2A01G538300 chr2D 97.500 80 2 0 4805 4884 619704720 619704799 2.370000e-28 137
16 TraesCS2A01G538300 chr2B 95.531 3468 139 13 697 4159 759439130 759442586 0.000000e+00 5531
17 TraesCS2A01G538300 chr2B 87.664 3275 338 37 685 3928 759344876 759348115 0.000000e+00 3749
18 TraesCS2A01G538300 chr2B 82.328 2156 294 53 1973 4092 706732014 706729910 0.000000e+00 1790
19 TraesCS2A01G538300 chr2B 82.208 2147 295 52 1981 4092 706923939 706921845 0.000000e+00 1768
20 TraesCS2A01G538300 chr2B 93.950 281 16 1 4348 4627 759442584 759442864 1.630000e-114 424
21 TraesCS2A01G538300 chr2B 98.370 184 3 0 4625 4808 331010219 331010402 1.700000e-84 324
22 TraesCS2A01G538300 chr2B 88.199 161 15 2 4213 4369 759348150 759348310 6.450000e-44 189
23 TraesCS2A01G538300 chr2B 94.805 77 4 0 4806 4882 759442850 759442926 2.390000e-23 121
24 TraesCS2A01G538300 chrUn 99.593 2209 8 1 1 2208 337510833 337513041 0.000000e+00 4028
25 TraesCS2A01G538300 chrUn 99.271 686 5 0 1 686 304917328 304916643 0.000000e+00 1240
26 TraesCS2A01G538300 chrUn 95.918 686 26 2 3 686 63467305 63466620 0.000000e+00 1110
27 TraesCS2A01G538300 chrUn 95.912 685 27 1 3 686 63543379 63544063 0.000000e+00 1109
28 TraesCS2A01G538300 chrUn 95.906 684 26 2 3 686 63476500 63475819 0.000000e+00 1107
29 TraesCS2A01G538300 chr3B 99.125 686 6 0 1 686 713753563 713752878 0.000000e+00 1234
30 TraesCS2A01G538300 chr3B 97.849 186 3 1 4624 4808 766145187 766145372 2.190000e-83 320
31 TraesCS2A01G538300 chr5A 96.053 684 26 1 3 686 647601925 647601243 0.000000e+00 1112
32 TraesCS2A01G538300 chr5A 95.906 684 28 0 3 686 3646273 3645590 0.000000e+00 1109
33 TraesCS2A01G538300 chr3A 98.378 185 3 0 4625 4809 724319107 724318923 4.710000e-85 326
34 TraesCS2A01G538300 chr6B 98.895 181 2 0 4626 4806 46961800 46961980 1.700000e-84 324
35 TraesCS2A01G538300 chr4A 98.370 184 3 0 4625 4808 420020379 420020562 1.700000e-84 324
36 TraesCS2A01G538300 chr5B 98.370 184 2 1 4625 4808 654755743 654755925 6.100000e-84 322
37 TraesCS2A01G538300 chr1A 95.000 200 8 2 4607 4804 486340225 486340026 3.670000e-81 313


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 TraesCS2A01G538300 chr2A 751266535 751271418 4883 False 9020.000000 9020 100.000000 1 4884 1 chr2A.!!$F2 4883
1 TraesCS2A01G538300 chr2A 751287460 751289668 2208 False 4034.000000 4034 99.638000 1 2208 1 chr2A.!!$F3 2207
2 TraesCS2A01G538300 chr2A 751207462 751210697 3235 False 3834.000000 3834 88.135000 685 3928 1 chr2A.!!$F1 3243
3 TraesCS2A01G538300 chr2A 751231693 751240839 9146 False 2745.250000 7208 92.883500 681 4884 4 chr2A.!!$F4 4203
4 TraesCS2A01G538300 chr2A 719728616 719730717 2101 True 1760.000000 1760 82.080000 1973 4093 1 chr2A.!!$R1 2120
5 TraesCS2A01G538300 chr2D 619700955 619704799 3844 False 2094.000000 5596 95.512333 697 4884 3 chr2D.!!$F3 4187
6 TraesCS2A01G538300 chr2D 619663094 619666166 3072 False 1780.000000 2134 87.490500 796 3924 2 chr2D.!!$F2 3128
7 TraesCS2A01G538300 chr2D 585685864 585687837 1973 True 1594.000000 1594 81.653000 2186 4175 1 chr2D.!!$R1 1989
8 TraesCS2A01G538300 chr2B 759439130 759442926 3796 False 2025.333333 5531 94.762000 697 4882 3 chr2B.!!$F3 4185
9 TraesCS2A01G538300 chr2B 759344876 759348310 3434 False 1969.000000 3749 87.931500 685 4369 2 chr2B.!!$F2 3684
10 TraesCS2A01G538300 chr2B 706729910 706732014 2104 True 1790.000000 1790 82.328000 1973 4092 1 chr2B.!!$R1 2119
11 TraesCS2A01G538300 chr2B 706921845 706923939 2094 True 1768.000000 1768 82.208000 1981 4092 1 chr2B.!!$R2 2111
12 TraesCS2A01G538300 chrUn 337510833 337513041 2208 False 4028.000000 4028 99.593000 1 2208 1 chrUn.!!$F2 2207
13 TraesCS2A01G538300 chrUn 304916643 304917328 685 True 1240.000000 1240 99.271000 1 686 1 chrUn.!!$R3 685
14 TraesCS2A01G538300 chrUn 63466620 63467305 685 True 1110.000000 1110 95.918000 3 686 1 chrUn.!!$R1 683
15 TraesCS2A01G538300 chrUn 63543379 63544063 684 False 1109.000000 1109 95.912000 3 686 1 chrUn.!!$F1 683
16 TraesCS2A01G538300 chrUn 63475819 63476500 681 True 1107.000000 1107 95.906000 3 686 1 chrUn.!!$R2 683
17 TraesCS2A01G538300 chr3B 713752878 713753563 685 True 1234.000000 1234 99.125000 1 686 1 chr3B.!!$R1 685
18 TraesCS2A01G538300 chr5A 647601243 647601925 682 True 1112.000000 1112 96.053000 3 686 1 chr5A.!!$R2 683
19 TraesCS2A01G538300 chr5A 3645590 3646273 683 True 1109.000000 1109 95.906000 3 686 1 chr5A.!!$R1 683

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
627 630 0.546122 AGTCTGGAAGTGTTGTGGCA 59.454 50.000 0.00 0.0 33.76 4.92 F
764 5220 4.314440 TGCAAAGCCGCTCTCCGT 62.314 61.111 0.00 0.0 34.38 4.69 F
2640 7143 3.541996 AAGGTGGCTTTGGAAAAGTTG 57.458 42.857 2.01 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2640 7143 9.952188 GATCAGCCTAAAAATTATTACCTTGTC 57.048 33.333 0.00 0.00 0.0 3.18 R
3353 7872 1.067142 TCAGGTGACATGTAACCGCTC 60.067 52.381 24.27 3.16 39.2 5.03 R
4791 9342 0.033699 GCAAGATGAAGGGGAGCCTT 60.034 55.000 0.00 0.00 0.0 4.35 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
627 630 0.546122 AGTCTGGAAGTGTTGTGGCA 59.454 50.000 0.00 0.00 33.76 4.92
764 5220 4.314440 TGCAAAGCCGCTCTCCGT 62.314 61.111 0.00 0.00 34.38 4.69
2492 6995 9.543018 CGAATCAAGGAAACTAAGAACAAATAC 57.457 33.333 0.00 0.00 42.68 1.89
2640 7143 3.541996 AAGGTGGCTTTGGAAAAGTTG 57.458 42.857 2.01 0.00 0.00 3.16
4623 9174 2.548178 CAAGTGATCTTGCGCCTGT 58.452 52.632 4.18 0.00 43.34 4.00
4624 9175 1.725641 CAAGTGATCTTGCGCCTGTA 58.274 50.000 4.18 0.00 43.34 2.74
4625 9176 2.076100 CAAGTGATCTTGCGCCTGTAA 58.924 47.619 4.18 0.00 43.34 2.41
4626 9177 2.015736 AGTGATCTTGCGCCTGTAAG 57.984 50.000 4.18 1.07 38.96 2.34
4627 9178 2.936993 AAGTGATCTTGCGCCTGTAAGG 60.937 50.000 4.18 0.00 44.74 2.69
4644 9195 4.794648 GGCAGCCCGGTGCATGTA 62.795 66.667 19.47 0.00 45.93 2.29
4645 9196 3.204827 GCAGCCCGGTGCATGTAG 61.205 66.667 13.70 0.91 43.41 2.74
4646 9197 3.204827 CAGCCCGGTGCATGTAGC 61.205 66.667 15.92 2.56 44.83 3.58
4647 9198 3.402681 AGCCCGGTGCATGTAGCT 61.403 61.111 15.92 4.82 45.94 3.32
4648 9199 2.897350 GCCCGGTGCATGTAGCTC 60.897 66.667 11.25 0.00 45.94 4.09
4654 9205 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
4655 9206 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
4656 9207 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
4657 9208 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
4660 9211 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
4672 9223 4.785453 GCGCAGGGTCCAGGGAAG 62.785 72.222 0.30 0.00 0.00 3.46
4673 9224 4.101448 CGCAGGGTCCAGGGAAGG 62.101 72.222 0.00 0.00 0.00 3.46
4674 9225 3.732849 GCAGGGTCCAGGGAAGGG 61.733 72.222 0.00 0.00 0.00 3.95
4675 9226 2.204151 CAGGGTCCAGGGAAGGGT 60.204 66.667 0.00 0.00 0.00 4.34
4676 9227 2.125225 AGGGTCCAGGGAAGGGTC 59.875 66.667 0.00 0.00 0.00 4.46
4677 9228 3.015753 GGGTCCAGGGAAGGGTCC 61.016 72.222 0.00 0.00 44.10 4.46
4678 9229 3.400054 GGTCCAGGGAAGGGTCCG 61.400 72.222 0.00 0.00 46.04 4.79
4679 9230 2.284405 GTCCAGGGAAGGGTCCGA 60.284 66.667 0.00 0.00 46.04 4.55
4680 9231 2.284405 TCCAGGGAAGGGTCCGAC 60.284 66.667 0.00 0.00 46.04 4.79
4681 9232 3.400054 CCAGGGAAGGGTCCGACC 61.400 72.222 9.30 9.30 46.04 4.79
4682 9233 2.606519 CAGGGAAGGGTCCGACCA 60.607 66.667 19.43 0.00 46.04 4.02
4683 9234 2.606826 AGGGAAGGGTCCGACCAC 60.607 66.667 19.43 8.70 46.04 4.16
4684 9235 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
4685 9236 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
4686 9237 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
4687 9238 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
4688 9239 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
4689 9240 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
4690 9241 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
4700 9251 4.996788 ACCACTTTGGGTCTATAGTACG 57.003 45.455 0.00 0.00 43.37 3.67
4701 9252 3.131755 ACCACTTTGGGTCTATAGTACGC 59.868 47.826 0.00 6.13 43.37 4.42
4702 9253 3.131577 CCACTTTGGGTCTATAGTACGCA 59.868 47.826 13.98 13.98 37.94 5.24
4703 9254 4.360563 CACTTTGGGTCTATAGTACGCAG 58.639 47.826 16.00 11.29 40.36 5.18
4704 9255 3.181478 ACTTTGGGTCTATAGTACGCAGC 60.181 47.826 16.00 2.07 40.36 5.25
4705 9256 1.325355 TGGGTCTATAGTACGCAGCC 58.675 55.000 13.98 8.23 35.18 4.85
4706 9257 1.133575 TGGGTCTATAGTACGCAGCCT 60.134 52.381 13.98 0.00 35.18 4.58
4707 9258 1.962100 GGGTCTATAGTACGCAGCCTT 59.038 52.381 0.00 0.00 0.00 4.35
4708 9259 2.364647 GGGTCTATAGTACGCAGCCTTT 59.635 50.000 0.00 0.00 0.00 3.11
4709 9260 3.552478 GGGTCTATAGTACGCAGCCTTTC 60.552 52.174 0.00 0.00 0.00 2.62
4710 9261 3.552478 GGTCTATAGTACGCAGCCTTTCC 60.552 52.174 0.00 0.00 0.00 3.13
4711 9262 2.626743 TCTATAGTACGCAGCCTTTCCC 59.373 50.000 0.00 0.00 0.00 3.97
4712 9263 1.497161 ATAGTACGCAGCCTTTCCCT 58.503 50.000 0.00 0.00 0.00 4.20
4713 9264 2.148446 TAGTACGCAGCCTTTCCCTA 57.852 50.000 0.00 0.00 0.00 3.53
4714 9265 0.535797 AGTACGCAGCCTTTCCCTAC 59.464 55.000 0.00 0.00 0.00 3.18
4715 9266 0.248289 GTACGCAGCCTTTCCCTACA 59.752 55.000 0.00 0.00 0.00 2.74
4716 9267 1.134491 GTACGCAGCCTTTCCCTACAT 60.134 52.381 0.00 0.00 0.00 2.29
4717 9268 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
4718 9269 1.271926 ACGCAGCCTTTCCCTACATTT 60.272 47.619 0.00 0.00 0.00 2.32
4719 9270 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
4720 9271 2.728007 GCAGCCTTTCCCTACATTTCT 58.272 47.619 0.00 0.00 0.00 2.52
4721 9272 2.424956 GCAGCCTTTCCCTACATTTCTG 59.575 50.000 0.00 0.00 0.00 3.02
4722 9273 3.690460 CAGCCTTTCCCTACATTTCTGT 58.310 45.455 0.00 0.00 39.49 3.41
4723 9274 4.843728 CAGCCTTTCCCTACATTTCTGTA 58.156 43.478 0.00 0.00 36.79 2.74
4724 9275 5.253330 CAGCCTTTCCCTACATTTCTGTAA 58.747 41.667 0.00 0.00 37.41 2.41
4725 9276 5.355350 CAGCCTTTCCCTACATTTCTGTAAG 59.645 44.000 0.00 0.00 37.41 2.34
4726 9277 5.250774 AGCCTTTCCCTACATTTCTGTAAGA 59.749 40.000 0.00 0.00 44.68 2.10
4739 9290 4.873746 TCTGTAAGAGACTGTTTCCAGG 57.126 45.455 10.10 0.00 39.91 4.45
4740 9291 4.480115 TCTGTAAGAGACTGTTTCCAGGA 58.520 43.478 10.10 0.00 39.91 3.86
4741 9292 4.281182 TCTGTAAGAGACTGTTTCCAGGAC 59.719 45.833 10.10 0.00 39.91 3.85
4742 9293 4.223953 TGTAAGAGACTGTTTCCAGGACT 58.776 43.478 0.00 0.00 43.36 3.85
4743 9294 4.654262 TGTAAGAGACTGTTTCCAGGACTT 59.346 41.667 0.00 0.00 43.36 3.01
4744 9295 3.760580 AGAGACTGTTTCCAGGACTTG 57.239 47.619 0.00 0.00 43.36 3.16
4745 9296 3.309296 AGAGACTGTTTCCAGGACTTGA 58.691 45.455 0.00 0.00 43.36 3.02
4746 9297 3.711704 AGAGACTGTTTCCAGGACTTGAA 59.288 43.478 0.00 0.00 43.36 2.69
4747 9298 3.809905 AGACTGTTTCCAGGACTTGAAC 58.190 45.455 0.00 0.00 43.36 3.18
4748 9299 2.879026 GACTGTTTCCAGGACTTGAACC 59.121 50.000 0.00 0.00 43.36 3.62
4749 9300 2.230660 CTGTTTCCAGGACTTGAACCC 58.769 52.381 0.00 0.00 34.90 4.11
4750 9301 1.235724 GTTTCCAGGACTTGAACCCG 58.764 55.000 0.00 0.00 0.00 5.28
4751 9302 0.841289 TTTCCAGGACTTGAACCCGT 59.159 50.000 0.00 0.00 0.00 5.28
4752 9303 0.107831 TTCCAGGACTTGAACCCGTG 59.892 55.000 0.00 0.00 0.00 4.94
4753 9304 0.761323 TCCAGGACTTGAACCCGTGA 60.761 55.000 0.00 0.00 0.00 4.35
4754 9305 0.602905 CCAGGACTTGAACCCGTGAC 60.603 60.000 0.00 0.00 0.00 3.67
4755 9306 0.602905 CAGGACTTGAACCCGTGACC 60.603 60.000 0.00 0.00 0.00 4.02
4756 9307 0.763223 AGGACTTGAACCCGTGACCT 60.763 55.000 0.00 0.00 0.00 3.85
4757 9308 0.320508 GGACTTGAACCCGTGACCTC 60.321 60.000 0.00 0.00 0.00 3.85
4758 9309 0.391597 GACTTGAACCCGTGACCTCA 59.608 55.000 0.00 0.00 0.00 3.86
4759 9310 1.002087 GACTTGAACCCGTGACCTCAT 59.998 52.381 0.00 0.00 0.00 2.90
4760 9311 1.270839 ACTTGAACCCGTGACCTCATG 60.271 52.381 0.00 0.00 0.00 3.07
4771 9322 2.154139 ACCTCATGGTCACAAGGCA 58.846 52.632 0.00 0.00 44.78 4.75
4772 9323 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.00 44.78 4.85
4773 9324 1.310933 CCTCATGGTCACAAGGCAGC 61.311 60.000 0.00 0.00 0.00 5.25
4774 9325 0.607217 CTCATGGTCACAAGGCAGCA 60.607 55.000 0.00 0.00 0.00 4.41
4775 9326 0.607217 TCATGGTCACAAGGCAGCAG 60.607 55.000 0.00 0.00 0.00 4.24
4776 9327 1.975407 ATGGTCACAAGGCAGCAGC 60.975 57.895 0.00 0.00 41.10 5.25
4777 9328 2.282040 GGTCACAAGGCAGCAGCT 60.282 61.111 0.00 0.00 41.70 4.24
4778 9329 1.900498 GGTCACAAGGCAGCAGCTT 60.900 57.895 0.00 0.00 41.70 3.74
4779 9330 1.458639 GGTCACAAGGCAGCAGCTTT 61.459 55.000 0.00 0.00 41.17 3.51
4780 9331 1.238439 GTCACAAGGCAGCAGCTTTA 58.762 50.000 0.00 0.00 38.07 1.85
4781 9332 1.068954 GTCACAAGGCAGCAGCTTTAC 60.069 52.381 0.00 0.00 38.07 2.01
4782 9333 0.242017 CACAAGGCAGCAGCTTTACC 59.758 55.000 0.00 0.00 38.07 2.85
4783 9334 0.178992 ACAAGGCAGCAGCTTTACCA 60.179 50.000 0.00 0.00 38.07 3.25
4784 9335 0.242017 CAAGGCAGCAGCTTTACCAC 59.758 55.000 0.00 0.00 38.07 4.16
4785 9336 0.111253 AAGGCAGCAGCTTTACCACT 59.889 50.000 0.00 0.00 38.40 4.00
4786 9337 0.607489 AGGCAGCAGCTTTACCACTG 60.607 55.000 0.00 0.00 41.70 3.66
4790 9341 2.870372 CAGCTTTACCACTGCGCC 59.130 61.111 4.18 0.00 0.00 6.53
4791 9342 1.965930 CAGCTTTACCACTGCGCCA 60.966 57.895 4.18 0.00 0.00 5.69
4792 9343 1.228124 AGCTTTACCACTGCGCCAA 60.228 52.632 4.18 0.00 0.00 4.52
4793 9344 1.210155 GCTTTACCACTGCGCCAAG 59.790 57.895 4.18 0.00 0.00 3.61
4794 9345 1.875963 CTTTACCACTGCGCCAAGG 59.124 57.895 4.18 6.21 0.00 3.61
4795 9346 2.200170 CTTTACCACTGCGCCAAGGC 62.200 60.000 4.18 0.00 37.85 4.35
4796 9347 2.690653 TTTACCACTGCGCCAAGGCT 62.691 55.000 4.18 0.00 39.32 4.58
4797 9348 3.605749 TACCACTGCGCCAAGGCTC 62.606 63.158 4.18 1.20 39.32 4.70
4810 9361 1.611965 AGGCTCCCCTTCATCTTGC 59.388 57.895 0.00 0.00 38.74 4.01
4811 9362 1.821332 GGCTCCCCTTCATCTTGCG 60.821 63.158 0.00 0.00 0.00 4.85
4812 9363 2.476320 GCTCCCCTTCATCTTGCGC 61.476 63.158 0.00 0.00 0.00 6.09
4813 9364 1.821332 CTCCCCTTCATCTTGCGCC 60.821 63.158 4.18 0.00 0.00 6.53
4814 9365 2.262774 CTCCCCTTCATCTTGCGCCT 62.263 60.000 4.18 0.00 0.00 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2640 7143 9.952188 GATCAGCCTAAAAATTATTACCTTGTC 57.048 33.333 0.00 0.00 0.00 3.18
3353 7872 1.067142 TCAGGTGACATGTAACCGCTC 60.067 52.381 24.27 3.16 39.20 5.03
4627 9178 4.794648 TACATGCACCGGGCTGCC 62.795 66.667 11.05 11.05 45.15 4.85
4628 9179 3.204827 CTACATGCACCGGGCTGC 61.205 66.667 6.32 8.50 45.15 5.25
4629 9180 3.204827 GCTACATGCACCGGGCTG 61.205 66.667 6.32 9.21 45.15 4.85
4630 9181 3.391665 GAGCTACATGCACCGGGCT 62.392 63.158 6.32 0.81 45.94 5.19
4631 9182 2.897350 GAGCTACATGCACCGGGC 60.897 66.667 6.32 7.25 45.94 6.13
4632 9183 2.203070 GGAGCTACATGCACCGGG 60.203 66.667 6.32 0.00 42.21 5.73
4655 9206 4.785453 CTTCCCTGGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
4656 9207 4.101448 CCTTCCCTGGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
4657 9208 3.732849 CCCTTCCCTGGACCCTGC 61.733 72.222 0.00 0.00 0.00 4.85
4658 9209 2.204151 ACCCTTCCCTGGACCCTG 60.204 66.667 0.00 0.00 0.00 4.45
4659 9210 2.125225 GACCCTTCCCTGGACCCT 59.875 66.667 0.00 0.00 0.00 4.34
4660 9211 3.015753 GGACCCTTCCCTGGACCC 61.016 72.222 0.00 0.00 35.57 4.46
4661 9212 3.400054 CGGACCCTTCCCTGGACC 61.400 72.222 0.00 0.00 38.99 4.46
4662 9213 2.284405 TCGGACCCTTCCCTGGAC 60.284 66.667 0.00 0.00 38.99 4.02
4663 9214 2.284405 GTCGGACCCTTCCCTGGA 60.284 66.667 0.00 0.00 38.99 3.86
4664 9215 3.400054 GGTCGGACCCTTCCCTGG 61.400 72.222 16.55 0.00 38.99 4.45
4665 9216 2.606519 TGGTCGGACCCTTCCCTG 60.607 66.667 23.81 0.00 38.99 4.45
4666 9217 2.606826 GTGGTCGGACCCTTCCCT 60.607 66.667 23.81 0.00 38.99 4.20
4667 9218 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
4668 9219 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
4669 9220 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
4670 9221 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
4671 9222 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
4672 9223 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
4673 9224 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
4674 9225 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
4679 9230 3.131755 GCGTACTATAGACCCAAAGTGGT 59.868 47.826 6.78 0.00 42.79 4.16
4680 9231 3.131577 TGCGTACTATAGACCCAAAGTGG 59.868 47.826 6.78 0.00 37.25 4.00
4681 9232 4.360563 CTGCGTACTATAGACCCAAAGTG 58.639 47.826 6.78 0.00 0.00 3.16
4682 9233 3.181478 GCTGCGTACTATAGACCCAAAGT 60.181 47.826 6.78 0.00 0.00 2.66
4683 9234 3.381949 GCTGCGTACTATAGACCCAAAG 58.618 50.000 6.78 0.00 0.00 2.77
4684 9235 2.101917 GGCTGCGTACTATAGACCCAAA 59.898 50.000 6.78 0.00 0.00 3.28
4685 9236 1.684983 GGCTGCGTACTATAGACCCAA 59.315 52.381 6.78 0.00 0.00 4.12
4686 9237 1.133575 AGGCTGCGTACTATAGACCCA 60.134 52.381 6.78 0.00 0.00 4.51
4687 9238 1.618487 AGGCTGCGTACTATAGACCC 58.382 55.000 6.78 0.00 0.00 4.46
4688 9239 3.552478 GGAAAGGCTGCGTACTATAGACC 60.552 52.174 6.78 0.00 0.00 3.85
4689 9240 3.552478 GGGAAAGGCTGCGTACTATAGAC 60.552 52.174 6.78 0.00 0.00 2.59
4690 9241 2.626743 GGGAAAGGCTGCGTACTATAGA 59.373 50.000 6.78 0.00 0.00 1.98
4691 9242 2.628657 AGGGAAAGGCTGCGTACTATAG 59.371 50.000 0.00 0.00 0.00 1.31
4692 9243 2.674420 AGGGAAAGGCTGCGTACTATA 58.326 47.619 0.00 0.00 0.00 1.31
4693 9244 1.497161 AGGGAAAGGCTGCGTACTAT 58.503 50.000 0.00 0.00 0.00 2.12
4694 9245 1.753073 GTAGGGAAAGGCTGCGTACTA 59.247 52.381 0.00 0.00 34.81 1.82
4695 9246 0.535797 GTAGGGAAAGGCTGCGTACT 59.464 55.000 0.00 0.00 34.81 2.73
4696 9247 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.000 0.00 0.00 37.28 3.67
4697 9248 1.200519 ATGTAGGGAAAGGCTGCGTA 58.799 50.000 0.00 0.00 0.00 4.42
4698 9249 0.328258 AATGTAGGGAAAGGCTGCGT 59.672 50.000 0.00 0.00 0.00 5.24
4699 9250 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
4700 9251 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
4701 9252 3.690460 ACAGAAATGTAGGGAAAGGCTG 58.310 45.455 0.00 0.00 0.00 4.85
4702 9253 5.250774 TCTTACAGAAATGTAGGGAAAGGCT 59.749 40.000 0.00 0.00 0.00 4.58
4703 9254 5.497474 TCTTACAGAAATGTAGGGAAAGGC 58.503 41.667 0.00 0.00 0.00 4.35
4704 9255 6.819146 GTCTCTTACAGAAATGTAGGGAAAGG 59.181 42.308 0.00 0.00 30.72 3.11
4705 9256 7.547370 CAGTCTCTTACAGAAATGTAGGGAAAG 59.453 40.741 0.00 0.00 30.72 2.62
4706 9257 7.016268 ACAGTCTCTTACAGAAATGTAGGGAAA 59.984 37.037 0.00 0.00 33.46 3.13
4707 9258 6.497259 ACAGTCTCTTACAGAAATGTAGGGAA 59.503 38.462 0.00 0.00 33.46 3.97
4708 9259 6.017192 ACAGTCTCTTACAGAAATGTAGGGA 58.983 40.000 0.00 0.00 33.46 4.20
4709 9260 6.287589 ACAGTCTCTTACAGAAATGTAGGG 57.712 41.667 0.00 0.00 33.46 3.53
4710 9261 7.332182 GGAAACAGTCTCTTACAGAAATGTAGG 59.668 40.741 0.00 0.00 33.89 3.18
4711 9262 7.872993 TGGAAACAGTCTCTTACAGAAATGTAG 59.127 37.037 0.00 0.00 33.89 2.74
4712 9263 7.732025 TGGAAACAGTCTCTTACAGAAATGTA 58.268 34.615 0.00 0.00 33.89 2.29
4713 9264 6.591935 TGGAAACAGTCTCTTACAGAAATGT 58.408 36.000 0.00 0.00 35.66 2.71
4730 9281 1.476110 CGGGTTCAAGTCCTGGAAACA 60.476 52.381 0.00 0.00 32.36 2.83
4731 9282 1.235724 CGGGTTCAAGTCCTGGAAAC 58.764 55.000 0.00 0.00 0.00 2.78
4732 9283 0.841289 ACGGGTTCAAGTCCTGGAAA 59.159 50.000 0.00 0.00 35.79 3.13
4733 9284 0.107831 CACGGGTTCAAGTCCTGGAA 59.892 55.000 0.00 0.00 35.79 3.53
4734 9285 0.761323 TCACGGGTTCAAGTCCTGGA 60.761 55.000 0.00 0.00 35.79 3.86
4735 9286 0.602905 GTCACGGGTTCAAGTCCTGG 60.603 60.000 0.00 0.00 35.79 4.45
4736 9287 0.602905 GGTCACGGGTTCAAGTCCTG 60.603 60.000 0.00 0.00 37.36 3.86
4737 9288 0.763223 AGGTCACGGGTTCAAGTCCT 60.763 55.000 0.00 0.00 0.00 3.85
4738 9289 0.320508 GAGGTCACGGGTTCAAGTCC 60.321 60.000 0.00 0.00 0.00 3.85
4739 9290 0.391597 TGAGGTCACGGGTTCAAGTC 59.608 55.000 0.00 0.00 0.00 3.01
4740 9291 1.056660 ATGAGGTCACGGGTTCAAGT 58.943 50.000 0.00 0.00 0.00 3.16
4741 9292 1.442769 CATGAGGTCACGGGTTCAAG 58.557 55.000 0.00 0.00 0.00 3.02
4742 9293 0.036164 CCATGAGGTCACGGGTTCAA 59.964 55.000 0.00 0.00 0.00 2.69
4743 9294 1.676968 CCATGAGGTCACGGGTTCA 59.323 57.895 0.00 0.00 0.00 3.18
4744 9295 4.617875 CCATGAGGTCACGGGTTC 57.382 61.111 0.00 0.00 0.00 3.62
4754 9305 1.310933 GCTGCCTTGTGACCATGAGG 61.311 60.000 0.00 0.00 42.21 3.86
4755 9306 0.607217 TGCTGCCTTGTGACCATGAG 60.607 55.000 0.00 0.00 0.00 2.90
4756 9307 0.607217 CTGCTGCCTTGTGACCATGA 60.607 55.000 0.00 0.00 0.00 3.07
4757 9308 1.880894 CTGCTGCCTTGTGACCATG 59.119 57.895 0.00 0.00 0.00 3.66
4758 9309 1.975407 GCTGCTGCCTTGTGACCAT 60.975 57.895 3.85 0.00 0.00 3.55
4759 9310 2.595463 GCTGCTGCCTTGTGACCA 60.595 61.111 3.85 0.00 0.00 4.02
4760 9311 1.458639 AAAGCTGCTGCCTTGTGACC 61.459 55.000 12.44 0.00 40.80 4.02
4761 9312 1.068954 GTAAAGCTGCTGCCTTGTGAC 60.069 52.381 12.44 0.00 40.80 3.67
4762 9313 1.238439 GTAAAGCTGCTGCCTTGTGA 58.762 50.000 12.44 0.00 40.80 3.58
4763 9314 0.242017 GGTAAAGCTGCTGCCTTGTG 59.758 55.000 12.44 0.00 40.80 3.33
4764 9315 0.178992 TGGTAAAGCTGCTGCCTTGT 60.179 50.000 12.44 0.00 40.80 3.16
4765 9316 0.242017 GTGGTAAAGCTGCTGCCTTG 59.758 55.000 12.44 0.00 40.80 3.61
4766 9317 0.111253 AGTGGTAAAGCTGCTGCCTT 59.889 50.000 12.44 8.34 40.80 4.35
4767 9318 0.607489 CAGTGGTAAAGCTGCTGCCT 60.607 55.000 12.44 2.45 40.80 4.75
4768 9319 1.878775 CAGTGGTAAAGCTGCTGCC 59.121 57.895 12.44 7.07 40.80 4.85
4773 9324 1.514678 TTGGCGCAGTGGTAAAGCTG 61.515 55.000 10.83 0.00 35.93 4.24
4774 9325 1.228124 TTGGCGCAGTGGTAAAGCT 60.228 52.632 10.83 0.00 0.00 3.74
4775 9326 1.210155 CTTGGCGCAGTGGTAAAGC 59.790 57.895 10.83 0.00 0.00 3.51
4776 9327 1.875963 CCTTGGCGCAGTGGTAAAG 59.124 57.895 10.83 0.71 0.00 1.85
4777 9328 2.265182 GCCTTGGCGCAGTGGTAAA 61.265 57.895 10.83 0.00 0.00 2.01
4778 9329 2.671619 GCCTTGGCGCAGTGGTAA 60.672 61.111 10.83 0.00 0.00 2.85
4779 9330 3.605749 GAGCCTTGGCGCAGTGGTA 62.606 63.158 10.83 0.00 0.00 3.25
4787 9338 3.350031 ATGAAGGGGAGCCTTGGCG 62.350 63.158 5.95 0.00 0.00 5.69
4788 9339 1.454663 GATGAAGGGGAGCCTTGGC 60.455 63.158 2.97 2.97 0.00 4.52
4789 9340 0.627986 AAGATGAAGGGGAGCCTTGG 59.372 55.000 0.00 0.00 0.00 3.61
4790 9341 1.760192 CAAGATGAAGGGGAGCCTTG 58.240 55.000 0.00 0.00 0.00 3.61
4791 9342 0.033699 GCAAGATGAAGGGGAGCCTT 60.034 55.000 0.00 0.00 0.00 4.35
4792 9343 1.611965 GCAAGATGAAGGGGAGCCT 59.388 57.895 0.00 0.00 0.00 4.58
4793 9344 1.821332 CGCAAGATGAAGGGGAGCC 60.821 63.158 0.00 0.00 43.02 4.70
4794 9345 2.476320 GCGCAAGATGAAGGGGAGC 61.476 63.158 0.30 0.00 43.02 4.70
4795 9346 1.821332 GGCGCAAGATGAAGGGGAG 60.821 63.158 10.83 0.00 43.02 4.30
4796 9347 2.272146 GGCGCAAGATGAAGGGGA 59.728 61.111 10.83 0.00 43.02 4.81
4797 9348 2.117156 CAGGCGCAAGATGAAGGGG 61.117 63.158 10.83 0.00 43.02 4.79
4798 9349 0.107703 TACAGGCGCAAGATGAAGGG 60.108 55.000 10.83 0.00 43.02 3.95
4799 9350 1.667724 CTTACAGGCGCAAGATGAAGG 59.332 52.381 10.83 0.00 43.02 3.46
4800 9351 2.349886 GTCTTACAGGCGCAAGATGAAG 59.650 50.000 10.83 4.70 43.02 3.02
4801 9352 2.346803 GTCTTACAGGCGCAAGATGAA 58.653 47.619 10.83 0.00 43.02 2.57
4802 9353 1.405526 GGTCTTACAGGCGCAAGATGA 60.406 52.381 10.83 0.00 43.02 2.92
4803 9354 1.009829 GGTCTTACAGGCGCAAGATG 58.990 55.000 10.83 4.52 43.02 2.90
4804 9355 0.613260 TGGTCTTACAGGCGCAAGAT 59.387 50.000 10.83 0.00 43.02 2.40
4805 9356 0.037326 CTGGTCTTACAGGCGCAAGA 60.037 55.000 10.83 6.79 41.00 3.02
4806 9357 0.037326 TCTGGTCTTACAGGCGCAAG 60.037 55.000 10.83 3.97 38.98 4.01
4807 9358 0.613260 ATCTGGTCTTACAGGCGCAA 59.387 50.000 10.83 0.00 38.98 4.85
4808 9359 0.613260 AATCTGGTCTTACAGGCGCA 59.387 50.000 10.83 0.00 38.98 6.09
4809 9360 2.596904 TAATCTGGTCTTACAGGCGC 57.403 50.000 0.00 0.00 38.98 6.53
4810 9361 5.360591 AGATTTAATCTGGTCTTACAGGCG 58.639 41.667 6.67 0.00 38.44 5.52
4811 9362 6.458888 GCAAGATTTAATCTGGTCTTACAGGC 60.459 42.308 8.34 0.00 40.13 4.85
4812 9363 6.038714 GGCAAGATTTAATCTGGTCTTACAGG 59.961 42.308 8.34 0.00 40.13 4.00
4813 9364 6.599244 TGGCAAGATTTAATCTGGTCTTACAG 59.401 38.462 14.20 0.00 40.13 2.74
4814 9365 6.480763 TGGCAAGATTTAATCTGGTCTTACA 58.519 36.000 14.20 3.16 40.13 2.41


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

AutoCloner maintained by Alex Coulton.