Multiple sequence alignment - TraesCS2D01G056600

Loading Multiple Alignment...

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 TraesCS2D01G056600 chr2D 100.000 4917 0 0 1 4917 22512305 22507389 0.000000e+00 9081.0
1 TraesCS2D01G056600 chr2D 82.442 2973 442 51 990 3919 30449632 30446697 0.000000e+00 2525.0
2 TraesCS2D01G056600 chr2D 82.403 1398 235 10 1850 3243 22820228 22818838 0.000000e+00 1208.0
3 TraesCS2D01G056600 chr2D 90.646 588 55 0 3333 3920 22818751 22818164 0.000000e+00 782.0
4 TraesCS2D01G056600 chr2D 78.278 778 140 21 982 1740 22440268 22441035 1.600000e-129 473.0
5 TraesCS2D01G056600 chr2D 83.373 415 59 6 1446 1852 22820500 22820088 4.650000e-100 375.0
6 TraesCS2D01G056600 chr2D 81.696 224 41 0 1017 1240 22820907 22820684 2.340000e-43 187.0
7 TraesCS2D01G056600 chr2D 80.519 154 21 5 275 420 22484414 22484262 5.200000e-20 110.0
8 TraesCS2D01G056600 chr2D 89.394 66 7 0 840 905 22440088 22440153 3.150000e-12 84.2
9 TraesCS2D01G056600 chr2D 100.000 31 0 0 611 641 22439782 22439812 1.910000e-04 58.4
10 TraesCS2D01G056600 chr2B 94.548 3008 118 23 1516 4506 39184434 39187412 0.000000e+00 4604.0
11 TraesCS2D01G056600 chr2B 85.572 2211 295 19 1711 3915 39339962 39337770 0.000000e+00 2294.0
12 TraesCS2D01G056600 chr2B 82.218 2092 336 23 1849 3919 38417220 38419296 0.000000e+00 1770.0
13 TraesCS2D01G056600 chr2B 84.478 1791 243 25 1711 3491 49900548 49898783 0.000000e+00 1735.0
14 TraesCS2D01G056600 chr2B 81.414 2093 345 36 1850 3920 37677759 37679829 0.000000e+00 1670.0
15 TraesCS2D01G056600 chr2B 81.334 2084 357 27 1850 3920 38034384 38036448 0.000000e+00 1664.0
16 TraesCS2D01G056600 chr2B 80.718 1644 289 23 2293 3920 39087024 39088655 0.000000e+00 1254.0
17 TraesCS2D01G056600 chr2B 81.903 1398 239 11 1850 3243 38074070 38075457 0.000000e+00 1168.0
18 TraesCS2D01G056600 chr2B 88.095 588 70 0 3333 3920 38075556 38076143 0.000000e+00 699.0
19 TraesCS2D01G056600 chr2B 76.243 1368 239 43 686 1990 39341303 39339959 0.000000e+00 647.0
20 TraesCS2D01G056600 chr2B 78.503 1042 176 29 984 1990 49901573 49900545 1.490000e-179 640.0
21 TraesCS2D01G056600 chr2B 79.496 595 104 14 1267 1852 37677314 37677899 1.650000e-109 407.0
22 TraesCS2D01G056600 chr2B 91.901 284 15 2 1171 1446 39184158 39184441 1.660000e-104 390.0
23 TraesCS2D01G056600 chr2B 92.417 211 11 5 4697 4905 39187612 39187819 3.720000e-76 296.0
24 TraesCS2D01G056600 chr2B 77.187 583 71 38 4232 4773 39335419 39334858 2.900000e-72 283.0
25 TraesCS2D01G056600 chr2B 80.645 248 48 0 990 1237 38073115 38073362 5.020000e-45 193.0
26 TraesCS2D01G056600 chr2B 80.242 248 49 0 990 1237 38033631 38033878 2.340000e-43 187.0
27 TraesCS2D01G056600 chr2B 97.059 34 1 0 611 644 39341425 39341392 1.910000e-04 58.4
28 TraesCS2D01G056600 chr2B 94.444 36 2 0 4508 4543 39187597 39187632 6.880000e-04 56.5
29 TraesCS2D01G056600 chr2A 98.032 1728 32 2 980 2707 24309389 24307664 0.000000e+00 3001.0
30 TraesCS2D01G056600 chr2A 85.507 2208 299 16 1711 3913 24174241 24176432 0.000000e+00 2285.0
31 TraesCS2D01G056600 chr2A 82.609 2093 326 28 1850 3920 24411822 24409746 0.000000e+00 1814.0
32 TraesCS2D01G056600 chr2A 91.774 778 46 5 129 891 24310228 24309454 0.000000e+00 1066.0
33 TraesCS2D01G056600 chr2A 81.164 584 89 16 1281 1852 24412256 24411682 2.700000e-122 449.0
34 TraesCS2D01G056600 chr2A 88.356 146 13 4 4632 4773 24180252 24180397 6.540000e-39 172.0
35 TraesCS2D01G056600 chr2A 86.614 127 17 0 3938 4064 24176423 24176549 1.850000e-29 141.0
36 TraesCS2D01G056600 chr2A 83.974 156 11 7 4632 4773 24275748 24275903 2.390000e-28 137.0
37 TraesCS2D01G056600 chr2A 96.104 77 3 0 1 77 24310305 24310229 5.170000e-25 126.0
38 TraesCS2D01G056600 chr2A 81.379 145 18 6 4312 4452 24179976 24180115 5.200000e-20 110.0
39 TraesCS2D01G056600 chr7B 86.209 1414 174 14 982 2385 744137109 744138511 0.000000e+00 1511.0
40 TraesCS2D01G056600 chr7B 82.008 1534 232 31 2394 3919 744138571 744140068 0.000000e+00 1264.0
41 TraesCS2D01G056600 chr7B 82.623 305 40 8 6 301 744134718 744135018 1.760000e-64 257.0
42 TraesCS2D01G056600 chr7B 84.892 139 9 4 770 896 744136912 744137050 3.990000e-26 130.0
43 TraesCS2D01G056600 chr7B 79.048 210 27 9 4427 4627 744140759 744140960 1.440000e-25 128.0


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 TraesCS2D01G056600 chr2D 22507389 22512305 4916 True 9081.000000 9081 100.000000 1 4917 1 chr2D.!!$R2 4916
1 TraesCS2D01G056600 chr2D 30446697 30449632 2935 True 2525.000000 2525 82.442000 990 3919 1 chr2D.!!$R3 2929
2 TraesCS2D01G056600 chr2D 22818164 22820907 2743 True 638.000000 1208 84.529500 1017 3920 4 chr2D.!!$R4 2903
3 TraesCS2D01G056600 chr2D 22439782 22441035 1253 False 205.200000 473 89.224000 611 1740 3 chr2D.!!$F1 1129
4 TraesCS2D01G056600 chr2B 38417220 38419296 2076 False 1770.000000 1770 82.218000 1849 3919 1 chr2B.!!$F1 2070
5 TraesCS2D01G056600 chr2B 39184158 39187819 3661 False 1336.625000 4604 93.327500 1171 4905 4 chr2B.!!$F6 3734
6 TraesCS2D01G056600 chr2B 39087024 39088655 1631 False 1254.000000 1254 80.718000 2293 3920 1 chr2B.!!$F2 1627
7 TraesCS2D01G056600 chr2B 49898783 49901573 2790 True 1187.500000 1735 81.490500 984 3491 2 chr2B.!!$R2 2507
8 TraesCS2D01G056600 chr2B 37677314 37679829 2515 False 1038.500000 1670 80.455000 1267 3920 2 chr2B.!!$F3 2653
9 TraesCS2D01G056600 chr2B 38033631 38036448 2817 False 925.500000 1664 80.788000 990 3920 2 chr2B.!!$F4 2930
10 TraesCS2D01G056600 chr2B 39334858 39341425 6567 True 820.600000 2294 84.015250 611 4773 4 chr2B.!!$R1 4162
11 TraesCS2D01G056600 chr2B 38073115 38076143 3028 False 686.666667 1168 83.547667 990 3920 3 chr2B.!!$F5 2930
12 TraesCS2D01G056600 chr2A 24307664 24310305 2641 True 1397.666667 3001 95.303333 1 2707 3 chr2A.!!$R1 2706
13 TraesCS2D01G056600 chr2A 24409746 24412256 2510 True 1131.500000 1814 81.886500 1281 3920 2 chr2A.!!$R2 2639
14 TraesCS2D01G056600 chr2A 24174241 24180397 6156 False 677.000000 2285 85.464000 1711 4773 4 chr2A.!!$F2 3062
15 TraesCS2D01G056600 chr7B 744134718 744140960 6242 False 658.000000 1511 82.956000 6 4627 5 chr7B.!!$F1 4621

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
53 54 0.106149 AGTCCACAAAGTGTCGGGAC 59.894 55.000 8.97 8.97 41.28 4.46 F
1253 2857 0.038310 CTTTCCCAGGACTTGACCCC 59.962 60.000 0.00 0.00 0.00 4.95 F
1750 3622 5.529791 CATTTGAGATCCAATGGATTGAGC 58.470 41.667 16.90 3.35 43.27 4.26 F
3246 5742 1.203162 TGGTGGCATTCCATTTGGACT 60.203 47.619 0.00 0.00 45.39 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1742 3614 1.069935 GGAGGCTACCGCTCAATCC 59.930 63.158 0.0 0.0 36.09 3.01 R
2773 5267 2.758979 GTCCAGTTCTCCCGACATCTTA 59.241 50.000 0.0 0.0 0.00 2.10 R
3255 5751 4.216257 GCCAACCATCGTATTCATAAGCAT 59.784 41.667 0.0 0.0 0.00 3.79 R
4079 8668 0.535780 CTTGCAGGGACACAGCTTCA 60.536 55.000 0.0 0.0 0.00 3.02 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
49 50 2.285220 CACTCAAGTCCACAAAGTGTCG 59.715 50.000 0.00 0.00 34.14 4.35
53 54 0.106149 AGTCCACAAAGTGTCGGGAC 59.894 55.000 8.97 8.97 41.28 4.46
91 94 4.100808 TGCCCAAGATTAATGGTTAATGGC 59.899 41.667 11.55 11.55 39.52 4.40
92 95 4.795962 GCCCAAGATTAATGGTTAATGGCG 60.796 45.833 0.00 0.00 36.04 5.69
93 96 4.298332 CCAAGATTAATGGTTAATGGCGC 58.702 43.478 0.00 0.00 36.04 6.53
94 97 4.202101 CCAAGATTAATGGTTAATGGCGCA 60.202 41.667 10.83 0.00 36.04 6.09
95 98 4.568152 AGATTAATGGTTAATGGCGCAC 57.432 40.909 10.83 0.00 36.04 5.34
96 99 3.317993 AGATTAATGGTTAATGGCGCACC 59.682 43.478 10.83 8.54 36.04 5.01
107 110 1.152963 GGCGCACCCATAGTCCAAT 60.153 57.895 10.83 0.00 0.00 3.16
109 112 0.663153 GCGCACCCATAGTCCAATTC 59.337 55.000 0.30 0.00 0.00 2.17
113 116 2.357154 GCACCCATAGTCCAATTCTGGT 60.357 50.000 0.00 0.00 43.97 4.00
119 122 5.453903 CCCATAGTCCAATTCTGGTCACTAG 60.454 48.000 0.00 0.00 43.97 2.57
121 124 6.323996 CCATAGTCCAATTCTGGTCACTAGTA 59.676 42.308 0.00 0.00 43.97 1.82
127 130 5.468072 CCAATTCTGGTCACTAGTATCATGC 59.532 44.000 0.00 0.00 38.00 4.06
170 175 5.012354 ACAAAATGTTCCTCAATGAGCCAAT 59.988 36.000 4.40 0.00 0.00 3.16
176 181 4.174704 TCCTCAATGAGCCAATAATGCT 57.825 40.909 4.40 0.00 43.03 3.79
215 220 5.516996 TCTACAATCTAAGCATACGTTCCG 58.483 41.667 0.00 0.00 0.00 4.30
235 240 3.188460 CCGTGACCATGGACTAAACTTTG 59.812 47.826 21.47 0.00 39.90 2.77
263 270 6.851609 ACGAAGCAAGTTTATAATCATGCAA 58.148 32.000 20.09 0.00 36.30 4.08
320 370 2.820059 AGCACGTCTCATGTTCTCAA 57.180 45.000 0.00 0.00 0.00 3.02
323 373 4.177026 AGCACGTCTCATGTTCTCAATAC 58.823 43.478 0.00 0.00 0.00 1.89
352 402 3.808466 AGCTGAACTGATGCGATAAGA 57.192 42.857 0.00 0.00 0.00 2.10
386 436 4.517285 TCTTTGAAGTGGGCAGCTATTAG 58.483 43.478 0.00 0.00 0.00 1.73
454 504 9.362539 ACTAGATCATGTTTTCAATTTCAATGC 57.637 29.630 0.00 0.00 0.00 3.56
480 530 1.472878 TCTTCCCACTCTGAATCGACG 59.527 52.381 0.00 0.00 0.00 5.12
496 546 2.434359 CGAAAGGGTGTCCTCGGC 60.434 66.667 0.00 0.00 44.07 5.54
553 610 4.116238 GCATAACTAACACTCTCAGCTCC 58.884 47.826 0.00 0.00 0.00 4.70
563 620 4.081752 ACACTCTCAGCTCCTTATTGTCTG 60.082 45.833 0.00 0.00 0.00 3.51
565 622 4.774726 ACTCTCAGCTCCTTATTGTCTGAA 59.225 41.667 0.00 0.00 33.93 3.02
609 669 4.959596 TGCTTGATCTCTTCATTTCTGC 57.040 40.909 0.00 0.00 33.34 4.26
701 809 3.967987 AGTGGAGGAGCTTCGGTAATAAT 59.032 43.478 0.00 0.00 0.00 1.28
774 2275 2.637382 TCCTTAGTGGTGCAGTCATTGA 59.363 45.455 0.00 0.00 37.07 2.57
778 2279 0.593128 GTGGTGCAGTCATTGACCAC 59.407 55.000 13.14 13.84 43.78 4.16
793 2294 1.644913 CCACGTTTGGTCGTTGGTC 59.355 57.895 0.00 0.00 42.27 4.02
873 2419 3.909776 TGAAGTTGCTTTGCTGATCAG 57.090 42.857 18.84 18.84 0.00 2.90
905 2451 4.389374 CTTGACCATGGACTAAACTGTGT 58.611 43.478 21.47 0.00 0.00 3.72
906 2452 4.431416 TGACCATGGACTAAACTGTGTT 57.569 40.909 21.47 0.00 0.00 3.32
907 2453 5.554437 TGACCATGGACTAAACTGTGTTA 57.446 39.130 21.47 0.00 0.00 2.41
908 2454 5.931294 TGACCATGGACTAAACTGTGTTAA 58.069 37.500 21.47 0.00 0.00 2.01
909 2455 6.539173 TGACCATGGACTAAACTGTGTTAAT 58.461 36.000 21.47 0.00 0.00 1.40
910 2456 7.001674 TGACCATGGACTAAACTGTGTTAATT 58.998 34.615 21.47 0.00 0.00 1.40
911 2457 7.040755 TGACCATGGACTAAACTGTGTTAATTG 60.041 37.037 21.47 0.00 0.00 2.32
937 2483 4.325084 AGTCTATAGTCTAGGGATGGCC 57.675 50.000 0.00 0.00 0.00 5.36
939 2485 4.108124 AGTCTATAGTCTAGGGATGGCCAA 59.892 45.833 10.96 0.00 35.15 4.52
940 2486 4.221041 GTCTATAGTCTAGGGATGGCCAAC 59.779 50.000 10.96 7.12 35.15 3.77
954 2528 3.472652 TGGCCAACTATAAATAGGCACG 58.527 45.455 0.61 0.00 46.96 5.34
971 2545 2.202987 GCATCCTGCTCCCAGACG 60.203 66.667 0.00 0.00 41.77 4.18
974 2565 1.610673 ATCCTGCTCCCAGACGTGT 60.611 57.895 0.00 0.00 41.77 4.49
976 2567 1.215647 CCTGCTCCCAGACGTGTAC 59.784 63.158 0.00 0.00 41.77 2.90
994 2586 5.895483 CGTGTACAACGTGAAAACCTTTTCA 60.895 40.000 8.79 8.79 46.80 2.69
1011 2603 7.275920 ACCTTTTCATCGAAATGAGCTACTAT 58.724 34.615 0.00 0.00 42.72 2.12
1012 2604 7.225538 ACCTTTTCATCGAAATGAGCTACTATG 59.774 37.037 0.00 0.00 42.72 2.23
1086 2678 0.598065 GTTGTTCGGGCTGCTTCATT 59.402 50.000 0.00 0.00 0.00 2.57
1253 2857 0.038310 CTTTCCCAGGACTTGACCCC 59.962 60.000 0.00 0.00 0.00 4.95
1742 3614 5.685954 CGAGAATTGCATTTGAGATCCAATG 59.314 40.000 0.00 3.00 34.23 2.82
1750 3622 5.529791 CATTTGAGATCCAATGGATTGAGC 58.470 41.667 16.90 3.35 43.27 4.26
2773 5267 6.317312 AGCCATCATGGATTTACATGGTAAT 58.683 36.000 8.30 0.00 46.33 1.89
2888 5382 5.118510 CACCGAGGAATTTGCAAATTAACAC 59.881 40.000 31.79 23.90 38.64 3.32
2896 5390 8.992073 GGAATTTGCAAATTAACACTTCTTGAT 58.008 29.630 31.79 9.78 38.64 2.57
3082 5578 3.658398 AGGCAACCTTGACTGGATG 57.342 52.632 0.00 0.00 46.96 3.51
3107 5603 9.719355 TGCTTTATCTTACTCAAATCAGTGTAA 57.281 29.630 0.00 0.00 0.00 2.41
3246 5742 1.203162 TGGTGGCATTCCATTTGGACT 60.203 47.619 0.00 0.00 45.39 3.85
3254 5750 4.441079 GCATTCCATTTGGACTCCTTGATG 60.441 45.833 0.00 0.25 45.39 3.07
3255 5751 4.656100 TTCCATTTGGACTCCTTGATGA 57.344 40.909 0.00 0.00 45.39 2.92
3327 5847 1.143073 GGGGGATTATGGTGTGGACTC 59.857 57.143 0.00 0.00 0.00 3.36
3328 5848 1.843851 GGGGATTATGGTGTGGACTCA 59.156 52.381 0.00 0.00 0.00 3.41
3353 5873 5.696030 TGTATAGCAGTGAGTATGACCTCT 58.304 41.667 0.00 0.00 32.50 3.69
3496 6019 3.603532 GAATCTGAGCCACATCAAGTCA 58.396 45.455 0.00 0.00 0.00 3.41
3710 6234 4.805719 GTCAGTTCAGCACATTCGATATGA 59.194 41.667 12.53 0.00 0.00 2.15
3920 6444 8.251721 AGCGTCTTATTCTCAAACTGTAATAGT 58.748 33.333 0.00 0.00 42.89 2.12
4052 8511 5.909610 GCTTTCCGATAATGTTTGTATCTGC 59.090 40.000 0.00 0.00 0.00 4.26
4079 8668 9.816354 AAACTATGTTATCTTTTGTTGCTTGTT 57.184 25.926 0.00 0.00 0.00 2.83
4178 12060 1.202382 GCAAGAGATTGGAATGCTGGC 60.202 52.381 0.00 0.00 34.29 4.85
4212 12126 0.872021 CGCCTGCGAGTAGAATGGTC 60.872 60.000 5.43 0.00 42.83 4.02
4220 12134 2.921754 CGAGTAGAATGGTCGGTGTTTC 59.078 50.000 0.00 0.00 0.00 2.78
4295 12236 2.856760 ATCTTCCTACAGAGCAGGGA 57.143 50.000 0.00 0.00 33.66 4.20
4310 12251 1.007118 CAGGGAGGCCTGGGTTTTAAT 59.993 52.381 12.00 0.00 34.47 1.40
4311 12252 1.288037 AGGGAGGCCTGGGTTTTAATC 59.712 52.381 12.00 0.00 0.00 1.75
4312 12253 1.288037 GGGAGGCCTGGGTTTTAATCT 59.712 52.381 12.00 0.00 0.00 2.40
4325 12354 7.666623 TGGGTTTTAATCTTCTTTTTAGCAGG 58.333 34.615 0.00 0.00 0.00 4.85
4334 12363 5.998363 TCTTCTTTTTAGCAGGGAAGAGTTC 59.002 40.000 0.00 0.00 37.88 3.01
4391 12420 2.648059 AGAACTATGAATGGTGGCTGC 58.352 47.619 0.00 0.00 0.00 5.25
4402 12431 1.750399 GTGGCTGCAATCATCGGGT 60.750 57.895 0.50 0.00 0.00 5.28
4464 12497 2.282462 GGTGGTGGGCAGTTGAGG 60.282 66.667 0.00 0.00 0.00 3.86
4507 12545 9.495572 GGTTCTGCATAGCTCTTTATTTACTAT 57.504 33.333 0.00 0.00 0.00 2.12
4554 12775 4.199310 TGAACTTTCTTTAGCACTGCTGT 58.801 39.130 14.15 0.00 40.10 4.40
4566 12788 7.582667 TTAGCACTGCTGTAGTCTCATAATA 57.417 36.000 14.15 0.00 40.10 0.98
4641 12896 1.035139 AAGCTGCAACCCTTTGTGAG 58.965 50.000 1.02 0.00 34.90 3.51
4672 12929 1.917872 AGTCGTCTTCCTCTGCTTCT 58.082 50.000 0.00 0.00 0.00 2.85
4673 12930 1.816224 AGTCGTCTTCCTCTGCTTCTC 59.184 52.381 0.00 0.00 0.00 2.87
4687 12944 7.453752 TCCTCTGCTTCTCCTTTACTTTACTTA 59.546 37.037 0.00 0.00 0.00 2.24
4692 12949 8.380099 TGCTTCTCCTTTACTTTACTTATTCCA 58.620 33.333 0.00 0.00 0.00 3.53
4774 13037 3.781079 TGCCGAGATTTATGCAAAAGG 57.219 42.857 0.00 0.00 0.00 3.11
4782 13045 1.846007 TTATGCAAAAGGCCCACGAT 58.154 45.000 0.00 0.00 43.89 3.73
4801 13064 0.612174 TGAAGAGGACCTCAGTCGGG 60.612 60.000 23.60 0.00 44.54 5.14
4839 13102 7.226523 TGTTCCATATTGAACGATCGAATCAAT 59.773 33.333 33.83 33.83 46.04 2.57
4874 13137 8.806146 AGTTTCTTATTGGCTATGTTGTTTGAT 58.194 29.630 0.00 0.00 0.00 2.57
4879 13142 8.929827 TTATTGGCTATGTTGTTTGATTGATG 57.070 30.769 0.00 0.00 0.00 3.07
4881 13144 6.343716 TGGCTATGTTGTTTGATTGATGTT 57.656 33.333 0.00 0.00 0.00 2.71
4882 13145 6.757237 TGGCTATGTTGTTTGATTGATGTTT 58.243 32.000 0.00 0.00 0.00 2.83
4883 13146 7.215789 TGGCTATGTTGTTTGATTGATGTTTT 58.784 30.769 0.00 0.00 0.00 2.43
4912 13175 9.593134 TTAGCACAATCAAATTTGTTTACAACT 57.407 25.926 17.47 12.32 37.73 3.16
4914 13177 9.030301 AGCACAATCAAATTTGTTTACAACTAC 57.970 29.630 17.47 3.22 37.73 2.73
4915 13178 7.995998 GCACAATCAAATTTGTTTACAACTACG 59.004 33.333 17.47 4.58 37.73 3.51
4916 13179 9.227490 CACAATCAAATTTGTTTACAACTACGA 57.773 29.630 17.47 0.00 37.73 3.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 9.436957 CTTGGGCATATATAATATTATCGTCCC 57.563 37.037 11.28 14.60 0.00 4.46
80 83 0.396974 ATGGGTGCGCCATTAACCAT 60.397 50.000 19.98 12.19 35.56 3.55
83 86 1.602377 GACTATGGGTGCGCCATTAAC 59.398 52.381 19.98 0.00 36.17 2.01
91 94 1.942657 CAGAATTGGACTATGGGTGCG 59.057 52.381 0.00 0.00 39.22 5.34
107 110 4.290093 AGGCATGATACTAGTGACCAGAA 58.710 43.478 5.39 0.00 0.00 3.02
109 112 4.679373 AAGGCATGATACTAGTGACCAG 57.321 45.455 5.39 0.00 0.00 4.00
113 116 4.199310 GCCAAAAGGCATGATACTAGTGA 58.801 43.478 5.39 0.00 34.62 3.41
127 130 5.452078 TTGTTTGAGTCTATGCCAAAAGG 57.548 39.130 0.00 0.00 32.44 3.11
135 138 7.874940 TGAGGAACATTTTGTTTGAGTCTATG 58.125 34.615 0.00 0.00 41.28 2.23
215 220 5.767816 AACAAAGTTTAGTCCATGGTCAC 57.232 39.130 12.58 3.19 0.00 3.67
235 240 8.734030 GCATGATTATAAACTTGCTTCGTAAAC 58.266 33.333 19.87 0.00 35.37 2.01
258 265 5.890985 TGGTGTTTATAAGTGGCTATTGCAT 59.109 36.000 0.66 0.00 41.91 3.96
263 270 5.885912 CCTTGTGGTGTTTATAAGTGGCTAT 59.114 40.000 0.00 0.00 0.00 2.97
320 370 4.290093 TCAGTTCAGCTGGGATGTAGTAT 58.710 43.478 15.13 0.00 45.08 2.12
323 373 3.464907 CATCAGTTCAGCTGGGATGTAG 58.535 50.000 15.13 3.97 45.08 2.74
352 402 6.687901 GCCCACTTCAAAGAAAAGGGTTTTAT 60.688 38.462 14.10 0.00 37.16 1.40
372 422 4.040461 TCCTCAATACTAATAGCTGCCCAC 59.960 45.833 0.00 0.00 0.00 4.61
386 436 3.705043 CAGGCAATGCTTCCTCAATAC 57.295 47.619 4.82 0.00 0.00 1.89
418 468 5.563876 AACATGATCTAGTCCATGCTCAT 57.436 39.130 19.57 7.63 42.77 2.90
454 504 4.510711 CGATTCAGAGTGGGAAGAATGATG 59.489 45.833 0.00 0.00 31.35 3.07
480 530 1.079057 GAGCCGAGGACACCCTTTC 60.079 63.158 0.00 0.00 44.53 2.62
496 546 1.405256 GGGCATATCATGAGCGAGGAG 60.405 57.143 0.09 0.00 0.00 3.69
542 599 4.348486 TCAGACAATAAGGAGCTGAGAGT 58.652 43.478 0.00 0.00 32.36 3.24
553 610 8.218338 AGCAACTGGATTATTCAGACAATAAG 57.782 34.615 7.61 0.00 36.22 1.73
563 620 8.814235 CAATCAAATGAAGCAACTGGATTATTC 58.186 33.333 0.00 0.00 0.00 1.75
565 622 6.759827 GCAATCAAATGAAGCAACTGGATTAT 59.240 34.615 6.40 0.00 31.95 1.28
609 669 9.791820 TTGAATGCTTGTGTTGATATAAGATTG 57.208 29.630 0.00 0.00 0.00 2.67
778 2279 0.237235 CATGGACCAACGACCAAACG 59.763 55.000 0.00 0.00 39.69 3.60
873 2419 1.299541 CATGGTCAAGGACGTATGCC 58.700 55.000 0.00 0.00 32.65 4.40
905 2451 9.742144 CCCTAGACTATAGACTAGCTCAATTAA 57.258 37.037 25.08 0.39 38.48 1.40
906 2452 9.113797 TCCCTAGACTATAGACTAGCTCAATTA 57.886 37.037 25.08 8.80 38.48 1.40
907 2453 7.991174 TCCCTAGACTATAGACTAGCTCAATT 58.009 38.462 25.08 0.00 38.48 2.32
908 2454 7.576978 TCCCTAGACTATAGACTAGCTCAAT 57.423 40.000 25.08 0.00 38.48 2.57
909 2455 7.398829 CATCCCTAGACTATAGACTAGCTCAA 58.601 42.308 25.08 14.31 38.48 3.02
910 2456 6.069905 CCATCCCTAGACTATAGACTAGCTCA 60.070 46.154 25.08 15.10 38.48 4.26
911 2457 6.354130 CCATCCCTAGACTATAGACTAGCTC 58.646 48.000 25.08 5.87 38.48 4.09
922 2468 2.868964 AGTTGGCCATCCCTAGACTA 57.131 50.000 6.09 0.00 0.00 2.59
937 2483 4.997395 AGGATGCGTGCCTATTTATAGTTG 59.003 41.667 0.00 0.00 32.92 3.16
939 2485 4.569943 CAGGATGCGTGCCTATTTATAGT 58.430 43.478 0.00 0.00 33.51 2.12
971 2545 5.920085 GAAAAGGTTTTCACGTTGTACAC 57.080 39.130 9.80 0.00 44.48 2.90
994 2586 6.149129 TGACACATAGTAGCTCATTTCGAT 57.851 37.500 0.00 0.00 0.00 3.59
1011 2603 5.882000 CAGGAATAAACATCTCCATGACACA 59.118 40.000 0.00 0.00 33.72 3.72
1012 2604 5.297776 CCAGGAATAAACATCTCCATGACAC 59.702 44.000 0.00 0.00 33.72 3.67
1086 2678 1.381056 GAGGGCTGCTCTCTCCTCA 60.381 63.158 22.03 0.00 43.78 3.86
1275 2909 5.763444 TCAAGTTAAGATTCGAGCTTTCG 57.237 39.130 7.75 0.00 0.00 3.46
1742 3614 1.069935 GGAGGCTACCGCTCAATCC 59.930 63.158 0.00 0.00 36.09 3.01
1750 3622 1.690219 AAGATGCAGGGAGGCTACCG 61.690 60.000 10.90 6.68 34.04 4.02
2380 4810 7.551974 AGAGATATGTTCACCAGTTTGAGATTG 59.448 37.037 0.00 0.00 0.00 2.67
2723 5217 3.115390 CCCCAGACAGATTTCTAGGGAA 58.885 50.000 0.00 0.00 45.07 3.97
2773 5267 2.758979 GTCCAGTTCTCCCGACATCTTA 59.241 50.000 0.00 0.00 0.00 2.10
2868 5362 8.490355 CAAGAAGTGTTAATTTGCAAATTCCTC 58.510 33.333 34.40 25.35 39.24 3.71
2888 5382 9.462174 GTCTGACAGATCTAACATATCAAGAAG 57.538 37.037 8.73 0.00 0.00 2.85
2896 5390 8.809468 AGTAGTTGTCTGACAGATCTAACATA 57.191 34.615 21.75 13.42 0.00 2.29
3246 5742 6.758254 TCGTATTCATAAGCATCATCAAGGA 58.242 36.000 0.00 0.00 0.00 3.36
3254 5750 5.617751 GCCAACCATCGTATTCATAAGCATC 60.618 44.000 0.00 0.00 0.00 3.91
3255 5751 4.216257 GCCAACCATCGTATTCATAAGCAT 59.784 41.667 0.00 0.00 0.00 3.79
3710 6234 5.336929 GGTTGTTGTTCCCTTTGTAACTGTT 60.337 40.000 0.00 0.00 0.00 3.16
3939 6463 7.887381 TCTCTTTTTACCTCTTACAGTCTGAG 58.113 38.462 6.91 0.00 0.00 3.35
3951 6475 3.772572 AGCCCTCTCTCTCTTTTTACCTC 59.227 47.826 0.00 0.00 0.00 3.85
4052 8511 9.248291 ACAAGCAACAAAAGATAACATAGTTTG 57.752 29.630 0.00 0.00 35.72 2.93
4079 8668 0.535780 CTTGCAGGGACACAGCTTCA 60.536 55.000 0.00 0.00 0.00 3.02
4178 12060 2.867429 CAGGCGGCAAAATCTTAACTG 58.133 47.619 13.08 0.00 0.00 3.16
4194 12076 0.872021 CGACCATTCTACTCGCAGGC 60.872 60.000 0.00 0.00 0.00 4.85
4212 12126 2.279582 ATGAGCTACGAGAAACACCG 57.720 50.000 0.00 0.00 0.00 4.94
4220 12134 5.034554 TGCAAAAGAAAATGAGCTACGAG 57.965 39.130 0.00 0.00 0.00 4.18
4252 12183 4.162040 ACTTCCTCCCACATCATTCATC 57.838 45.455 0.00 0.00 0.00 2.92
4295 12236 4.404185 AAGAAGATTAAAACCCAGGCCT 57.596 40.909 0.00 0.00 0.00 5.19
4310 12251 5.568620 ACTCTTCCCTGCTAAAAAGAAGA 57.431 39.130 0.00 0.00 40.35 2.87
4311 12252 6.000840 AGAACTCTTCCCTGCTAAAAAGAAG 58.999 40.000 0.00 0.00 36.19 2.85
4312 12253 5.765182 CAGAACTCTTCCCTGCTAAAAAGAA 59.235 40.000 0.00 0.00 0.00 2.52
4325 12354 5.674933 ACAAAATTCGACAGAACTCTTCC 57.325 39.130 0.00 0.00 39.48 3.46
4334 12363 9.663904 TGATTCTTCTTTAACAAAATTCGACAG 57.336 29.630 0.00 0.00 0.00 3.51
4391 12420 1.066002 GCATCCAACACCCGATGATTG 59.934 52.381 1.34 0.00 38.53 2.67
4402 12431 1.042229 AGCAGCAAAAGCATCCAACA 58.958 45.000 0.00 0.00 0.00 3.33
4464 12497 5.563671 GCAGAACCAAGAATCCTCTCAAAAC 60.564 44.000 0.00 0.00 0.00 2.43
4539 12760 3.826729 TGAGACTACAGCAGTGCTAAAGA 59.173 43.478 25.08 9.32 37.72 2.52
4566 12788 4.889409 ACCGAATCATCCAGCATTACAAAT 59.111 37.500 0.00 0.00 0.00 2.32
4578 12800 1.964223 TCCTCAGCTACCGAATCATCC 59.036 52.381 0.00 0.00 0.00 3.51
4581 12803 4.081142 TCAAAATCCTCAGCTACCGAATCA 60.081 41.667 0.00 0.00 0.00 2.57
4582 12804 4.442706 TCAAAATCCTCAGCTACCGAATC 58.557 43.478 0.00 0.00 0.00 2.52
4583 12805 4.446371 CTCAAAATCCTCAGCTACCGAAT 58.554 43.478 0.00 0.00 0.00 3.34
4672 12929 9.720769 CAAGAGTGGAATAAGTAAAGTAAAGGA 57.279 33.333 0.00 0.00 0.00 3.36
4673 12930 9.503399 ACAAGAGTGGAATAAGTAAAGTAAAGG 57.497 33.333 0.00 0.00 0.00 3.11
4687 12944 3.144506 CAGTTGCTGACAAGAGTGGAAT 58.855 45.455 0.00 0.00 36.16 3.01
4692 12949 3.136763 CACATCAGTTGCTGACAAGAGT 58.863 45.455 0.53 0.00 43.63 3.24
4774 13037 1.153349 GGTCCTCTTCATCGTGGGC 60.153 63.158 0.00 0.00 0.00 5.36
4782 13045 0.612174 CCCGACTGAGGTCCTCTTCA 60.612 60.000 19.82 0.00 39.15 3.02


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

AutoCloner maintained by Alex Coulton.