Multiple sequence alignment - TraesCS5B01G025500

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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 TraesCS5B01G025500 chr5B 100.000 4009 0 0 1 4009 24148071 24144063 0.000000e+00 7404.0
1 TraesCS5B01G025500 chr5B 90.006 1541 122 19 351 1883 24775957 24774441 0.000000e+00 1964.0
2 TraesCS5B01G025500 chr5B 90.800 1250 88 15 645 1890 24108035 24109261 0.000000e+00 1646.0
3 TraesCS5B01G025500 chr5B 93.075 982 66 2 2139 3118 24773863 24772882 0.000000e+00 1435.0
4 TraesCS5B01G025500 chr5B 89.558 1130 79 14 2139 3242 24109826 24110942 0.000000e+00 1397.0
5 TraesCS5B01G025500 chr5B 90.382 863 70 9 374 1231 24806333 24807187 0.000000e+00 1122.0
6 TraesCS5B01G025500 chr5B 98.214 336 6 0 351 686 24805992 24806327 4.460000e-164 588.0
7 TraesCS5B01G025500 chr5B 90.114 263 20 4 1879 2141 24109312 24109568 1.780000e-88 337.0
8 TraesCS5B01G025500 chr5B 89.474 266 17 5 1882 2141 24774380 24774120 3.860000e-85 326.0
9 TraesCS5B01G025500 chr5B 95.455 44 2 0 272 315 24285153 24285110 2.000000e-08 71.3
10 TraesCS5B01G025500 chr5B 95.455 44 2 0 272 315 24776083 24776040 2.000000e-08 71.3
11 TraesCS5B01G025500 chr5B 92.157 51 2 2 265 315 24805861 24805909 2.000000e-08 71.3
12 TraesCS5B01G025500 chr5D 92.085 2906 166 28 351 3242 33658263 33655408 0.000000e+00 4034.0
13 TraesCS5B01G025500 chr5D 89.508 1544 118 22 351 1883 37046488 37047998 0.000000e+00 1914.0
14 TraesCS5B01G025500 chr5D 89.501 1543 119 23 351 1883 33049328 33047819 0.000000e+00 1912.0
15 TraesCS5B01G025500 chr5D 91.215 1366 100 11 519 1883 37040257 37041603 0.000000e+00 1840.0
16 TraesCS5B01G025500 chr5D 90.849 1366 104 12 519 1883 33055549 33054204 0.000000e+00 1810.0
17 TraesCS5B01G025500 chr5D 91.312 1128 78 14 2139 3253 33047246 33046126 0.000000e+00 1522.0
18 TraesCS5B01G025500 chr5D 90.691 1128 74 17 2139 3239 37042173 37043296 0.000000e+00 1472.0
19 TraesCS5B01G025500 chr5D 90.539 1131 76 18 2139 3242 33053634 33052508 0.000000e+00 1467.0
20 TraesCS5B01G025500 chr5D 92.879 983 63 6 2139 3118 37048571 37049549 0.000000e+00 1421.0
21 TraesCS5B01G025500 chr5D 93.462 260 12 3 1882 2141 33047758 33047504 8.130000e-102 381.0
22 TraesCS5B01G025500 chr5D 92.395 263 15 3 1879 2141 37048056 37048313 1.760000e-98 370.0
23 TraesCS5B01G025500 chr5D 91.538 260 15 5 1882 2141 33054143 33053891 6.370000e-93 351.0
24 TraesCS5B01G025500 chr5D 91.255 263 16 5 1879 2141 37041661 37041916 6.370000e-93 351.0
25 TraesCS5B01G025500 chr5D 82.558 430 27 30 89 515 37039799 37040183 6.420000e-88 335.0
26 TraesCS5B01G025500 chr5D 81.818 429 31 28 89 515 33056006 33055623 2.330000e-82 316.0
27 TraesCS5B01G025500 chr5D 89.583 240 20 4 3184 3422 33031211 33030976 2.340000e-77 300.0
28 TraesCS5B01G025500 chr5A 92.001 2788 158 27 515 3290 21440733 21437999 0.000000e+00 3853.0
29 TraesCS5B01G025500 chr5A 90.518 1371 82 18 515 1883 22059797 22058473 0.000000e+00 1768.0
30 TraesCS5B01G025500 chr5A 90.653 1134 75 9 2139 3242 22057901 22056769 0.000000e+00 1478.0
31 TraesCS5B01G025500 chr5A 92.692 260 14 3 1882 2141 22058412 22058158 1.760000e-98 370.0
32 TraesCS5B01G025500 chr5A 92.121 165 13 0 351 515 22060031 22059867 2.410000e-57 233.0
33 TraesCS5B01G025500 chr5A 84.874 238 16 13 192 419 21441070 21440843 5.210000e-54 222.0
34 TraesCS5B01G025500 chr5A 89.655 145 8 6 15 158 21441209 21441071 1.140000e-40 178.0
35 TraesCS5B01G025500 chr6D 95.408 588 23 2 3422 4009 175423683 175424266 0.000000e+00 933.0
36 TraesCS5B01G025500 chr3D 95.238 588 28 0 3422 4009 523400411 523400998 0.000000e+00 931.0
37 TraesCS5B01G025500 chr3D 94.915 590 28 2 3422 4009 160913034 160913623 0.000000e+00 922.0
38 TraesCS5B01G025500 chr3D 94.737 589 30 1 3422 4009 20288618 20289206 0.000000e+00 915.0
39 TraesCS5B01G025500 chr3D 93.559 590 30 6 3422 4009 532071287 532070704 0.000000e+00 872.0
40 TraesCS5B01G025500 chr7D 94.941 593 22 5 3422 4009 540442133 540442722 0.000000e+00 922.0
41 TraesCS5B01G025500 chr7D 93.012 601 32 8 3412 4009 526288215 526288808 0.000000e+00 869.0
42 TraesCS5B01G025500 chr2D 94.764 592 25 3 3422 4009 513034140 513033551 0.000000e+00 917.0
43 TraesCS5B01G025500 chr4D 93.220 590 32 8 3422 4009 391455571 391456154 0.000000e+00 861.0


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 TraesCS5B01G025500 chr5B 24144063 24148071 4008 True 7404.000000 7404 100.000000 1 4009 1 chr5B.!!$R1 4008
1 TraesCS5B01G025500 chr5B 24108035 24110942 2907 False 1126.666667 1646 90.157333 645 3242 3 chr5B.!!$F1 2597
2 TraesCS5B01G025500 chr5B 24772882 24776083 3201 True 949.075000 1964 92.002500 272 3118 4 chr5B.!!$R3 2846
3 TraesCS5B01G025500 chr5B 24805861 24807187 1326 False 593.766667 1122 93.584333 265 1231 3 chr5B.!!$F2 966
4 TraesCS5B01G025500 chr5D 33655408 33658263 2855 True 4034.000000 4034 92.085000 351 3242 1 chr5D.!!$R2 2891
5 TraesCS5B01G025500 chr5D 33046126 33056006 9880 True 1108.428571 1912 89.859857 89 3253 7 chr5D.!!$R3 3164
6 TraesCS5B01G025500 chr5D 37039799 37049549 9750 False 1100.428571 1914 90.071571 89 3239 7 chr5D.!!$F1 3150
7 TraesCS5B01G025500 chr5A 21437999 21441209 3210 True 1417.666667 3853 88.843333 15 3290 3 chr5A.!!$R1 3275
8 TraesCS5B01G025500 chr5A 22056769 22060031 3262 True 962.250000 1768 91.496000 351 3242 4 chr5A.!!$R2 2891
9 TraesCS5B01G025500 chr6D 175423683 175424266 583 False 933.000000 933 95.408000 3422 4009 1 chr6D.!!$F1 587
10 TraesCS5B01G025500 chr3D 523400411 523400998 587 False 931.000000 931 95.238000 3422 4009 1 chr3D.!!$F3 587
11 TraesCS5B01G025500 chr3D 160913034 160913623 589 False 922.000000 922 94.915000 3422 4009 1 chr3D.!!$F2 587
12 TraesCS5B01G025500 chr3D 20288618 20289206 588 False 915.000000 915 94.737000 3422 4009 1 chr3D.!!$F1 587
13 TraesCS5B01G025500 chr3D 532070704 532071287 583 True 872.000000 872 93.559000 3422 4009 1 chr3D.!!$R1 587
14 TraesCS5B01G025500 chr7D 540442133 540442722 589 False 922.000000 922 94.941000 3422 4009 1 chr7D.!!$F2 587
15 TraesCS5B01G025500 chr7D 526288215 526288808 593 False 869.000000 869 93.012000 3412 4009 1 chr7D.!!$F1 597
16 TraesCS5B01G025500 chr2D 513033551 513034140 589 True 917.000000 917 94.764000 3422 4009 1 chr2D.!!$R1 587
17 TraesCS5B01G025500 chr4D 391455571 391456154 583 False 861.000000 861 93.220000 3422 4009 1 chr4D.!!$F1 587

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
206 207 0.185175 AAAAAGAGCTCCCCACGGTT 59.815 50.000 10.93 0.0 0.00 4.44 F
696 1147 1.849039 AGCCAGGATGCTCCACTTATT 59.151 47.619 0.00 0.0 39.61 1.40 F
2616 9798 0.902531 ACCTGAGTACCCATTCACGG 59.097 55.000 0.00 0.0 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1749 8597 2.001872 TGACAATCACGCACTGCTATG 58.998 47.619 0.0 0.0 0.00 2.23 R
2655 9837 2.202756 CCAGCGAACGAGGGCTAC 60.203 66.667 0.0 0.0 37.41 3.58 R
3740 11199 0.173708 CTCGTACTGGAGCAAGGGAC 59.826 60.000 0.0 0.0 0.00 4.46 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
60 61 0.382158 TCCTGAACGAGCAGCGATAG 59.618 55.000 5.99 1.66 44.57 2.08
163 164 1.909986 GGTCTAAAAGAGCTCCCCACT 59.090 52.381 10.93 0.00 39.50 4.00
164 165 2.306219 GGTCTAAAAGAGCTCCCCACTT 59.694 50.000 10.93 0.00 39.50 3.16
166 167 3.262151 GTCTAAAAGAGCTCCCCACTTCT 59.738 47.826 10.93 0.00 0.00 2.85
167 168 4.466726 GTCTAAAAGAGCTCCCCACTTCTA 59.533 45.833 10.93 0.00 0.00 2.10
168 169 3.704800 AAAAGAGCTCCCCACTTCTAC 57.295 47.619 10.93 0.00 0.00 2.59
169 170 2.632763 AAGAGCTCCCCACTTCTACT 57.367 50.000 10.93 0.00 0.00 2.57
170 171 2.153034 AGAGCTCCCCACTTCTACTC 57.847 55.000 10.93 0.00 0.00 2.59
176 177 3.753797 GCTCCCCACTTCTACTCAAAAAG 59.246 47.826 0.00 0.00 0.00 2.27
179 180 6.008696 TCCCCACTTCTACTCAAAAAGAAA 57.991 37.500 0.00 0.00 31.61 2.52
181 182 6.893005 TCCCCACTTCTACTCAAAAAGAAAAA 59.107 34.615 0.00 0.00 31.61 1.94
182 183 7.068226 TCCCCACTTCTACTCAAAAAGAAAAAG 59.932 37.037 0.00 0.00 31.61 2.27
183 184 7.068226 CCCCACTTCTACTCAAAAAGAAAAAGA 59.932 37.037 0.00 0.00 31.61 2.52
184 185 8.466798 CCCACTTCTACTCAAAAAGAAAAAGAA 58.533 33.333 0.00 0.00 31.61 2.52
185 186 9.855021 CCACTTCTACTCAAAAAGAAAAAGAAA 57.145 29.630 0.00 0.00 31.61 2.52
206 207 0.185175 AAAAAGAGCTCCCCACGGTT 59.815 50.000 10.93 0.00 0.00 4.44
220 221 2.656069 CGGTTCGGGGTGTGGAGAT 61.656 63.158 0.00 0.00 0.00 2.75
261 263 3.747976 GCCGCCGCTTGGTTGATT 61.748 61.111 0.00 0.00 34.16 2.57
593 1040 7.462571 ACTTTTTGGTATCTTGGTATTGTCC 57.537 36.000 0.00 0.00 0.00 4.02
594 1041 7.007723 ACTTTTTGGTATCTTGGTATTGTCCA 58.992 34.615 0.00 0.00 35.49 4.02
605 1052 6.657541 TCTTGGTATTGTCCATTGTAGTTTCC 59.342 38.462 0.00 0.00 37.33 3.13
616 1063 4.718858 TTGTAGTTTCCGTCATGTTTCG 57.281 40.909 0.00 0.00 0.00 3.46
634 1081 3.663995 TCGTCTATTTGGACCGTCAAA 57.336 42.857 0.00 0.00 40.37 2.69
671 1122 9.822185 AAATTCTAGATTTATTGGGCAATGTTC 57.178 29.630 0.00 0.00 32.50 3.18
680 1131 2.533916 TGGGCAATGTTCAATAAGCCA 58.466 42.857 0.00 0.00 43.72 4.75
696 1147 1.849039 AGCCAGGATGCTCCACTTATT 59.151 47.619 0.00 0.00 39.61 1.40
701 1152 3.819337 CAGGATGCTCCACTTATTCCATG 59.181 47.826 5.21 0.00 39.61 3.66
800 1252 5.026121 TGGATCTGGAATGAGACTAACACT 58.974 41.667 0.00 0.00 0.00 3.55
813 1265 6.152154 TGAGACTAACACTGAATAATGACCGA 59.848 38.462 0.00 0.00 0.00 4.69
1515 8351 6.959311 CACAAATAGGTATTGACAAGCGTAAC 59.041 38.462 0.00 0.00 0.00 2.50
1608 8456 2.302733 TCATGAAGCACAACTAGAGCCA 59.697 45.455 0.00 0.00 33.99 4.75
1803 8651 8.942338 TGCTTAATTATGTCTTCAATCGTAGT 57.058 30.769 0.84 0.00 0.00 2.73
2188 9369 2.751259 TGCATGTGCTTTGAGGATCTTC 59.249 45.455 6.55 0.00 42.66 2.87
2206 9388 8.734386 AGGATCTTCTACAATGATGTGTTTTTC 58.266 33.333 0.00 0.00 40.84 2.29
2224 9406 6.268847 TGTTTTTCCCTTTGCATATGTTAGGT 59.731 34.615 4.29 0.00 0.00 3.08
2384 9566 7.517614 TCTGTTGTCAATTGGCATAAAGTAA 57.482 32.000 14.57 0.00 0.00 2.24
2417 9599 9.679661 TGCTTCACATATTTCTTACTTTCCATA 57.320 29.630 0.00 0.00 0.00 2.74
2616 9798 0.902531 ACCTGAGTACCCATTCACGG 59.097 55.000 0.00 0.00 0.00 4.94
2655 9837 2.476051 GCGCGGTTGACATCACTG 59.524 61.111 8.83 0.00 0.00 3.66
2669 9851 1.805945 CACTGTAGCCCTCGTTCGC 60.806 63.158 0.00 0.00 0.00 4.70
2789 9971 4.336889 TGAGATTCAACTCTTTCGTGGT 57.663 40.909 0.00 0.00 37.73 4.16
2808 9990 4.211374 GTGGTAGTGTTGTTGAGTCATGTC 59.789 45.833 0.00 0.00 0.00 3.06
2878 10060 4.873746 TGAAGTTCAAGGTAGGTCAGAG 57.126 45.455 2.20 0.00 0.00 3.35
2879 10061 4.480115 TGAAGTTCAAGGTAGGTCAGAGA 58.520 43.478 2.20 0.00 0.00 3.10
2883 10065 5.642165 AGTTCAAGGTAGGTCAGAGAAGTA 58.358 41.667 0.00 0.00 0.00 2.24
2969 10151 0.679002 TCATGCTTGAGCTTGCCTCC 60.679 55.000 12.51 0.00 43.38 4.30
2984 10166 1.280421 GCCTCCATCTCAGTGAAGGTT 59.720 52.381 9.12 0.00 35.23 3.50
3038 10221 6.234920 TCTTTCATATTCGAACTTGGGTTGA 58.765 36.000 0.00 0.00 35.58 3.18
3059 10242 7.383300 GGTTGAGTTACTAGTTGAATGTACGTT 59.617 37.037 0.00 0.00 0.00 3.99
3075 10258 3.305398 ACGTTTGTTGCCACAGAAAAA 57.695 38.095 0.00 0.00 33.22 1.94
3223 10434 9.295825 TGTGAGTTCAGATTTGTACCATTTTAT 57.704 29.630 0.00 0.00 0.00 1.40
3300 10593 4.936802 AGAAGAGCAGGTAGAGGTAGAAA 58.063 43.478 0.00 0.00 0.00 2.52
3301 10594 5.524535 AGAAGAGCAGGTAGAGGTAGAAAT 58.475 41.667 0.00 0.00 0.00 2.17
3302 10595 5.362430 AGAAGAGCAGGTAGAGGTAGAAATG 59.638 44.000 0.00 0.00 0.00 2.32
3303 10596 3.386402 AGAGCAGGTAGAGGTAGAAATGC 59.614 47.826 0.00 0.00 0.00 3.56
3304 10597 2.436173 AGCAGGTAGAGGTAGAAATGCC 59.564 50.000 0.00 0.00 32.95 4.40
3305 10598 2.803492 GCAGGTAGAGGTAGAAATGCCG 60.803 54.545 0.00 0.00 0.00 5.69
3309 10602 2.918712 AGAGGTAGAAATGCCGATGG 57.081 50.000 0.00 0.00 0.00 3.51
3311 10604 2.158900 AGAGGTAGAAATGCCGATGGTG 60.159 50.000 0.00 0.00 0.00 4.17
3312 10605 1.559682 AGGTAGAAATGCCGATGGTGT 59.440 47.619 0.00 0.00 0.00 4.16
3313 10606 1.670811 GGTAGAAATGCCGATGGTGTG 59.329 52.381 0.00 0.00 0.00 3.82
3315 10608 1.167851 AGAAATGCCGATGGTGTGTG 58.832 50.000 0.00 0.00 0.00 3.82
3316 10609 1.164411 GAAATGCCGATGGTGTGTGA 58.836 50.000 0.00 0.00 0.00 3.58
3317 10610 1.539388 GAAATGCCGATGGTGTGTGAA 59.461 47.619 0.00 0.00 0.00 3.18
3318 10611 1.167851 AATGCCGATGGTGTGTGAAG 58.832 50.000 0.00 0.00 0.00 3.02
3319 10612 0.324614 ATGCCGATGGTGTGTGAAGA 59.675 50.000 0.00 0.00 0.00 2.87
3320 10613 0.107643 TGCCGATGGTGTGTGAAGAA 59.892 50.000 0.00 0.00 0.00 2.52
3321 10614 1.271325 TGCCGATGGTGTGTGAAGAAT 60.271 47.619 0.00 0.00 0.00 2.40
3323 10616 3.206150 GCCGATGGTGTGTGAAGAATAT 58.794 45.455 0.00 0.00 0.00 1.28
3324 10617 4.141824 TGCCGATGGTGTGTGAAGAATATA 60.142 41.667 0.00 0.00 0.00 0.86
3325 10618 4.997395 GCCGATGGTGTGTGAAGAATATAT 59.003 41.667 0.00 0.00 0.00 0.86
3326 10619 5.120830 GCCGATGGTGTGTGAAGAATATATC 59.879 44.000 0.00 0.00 0.00 1.63
3327 10620 6.459066 CCGATGGTGTGTGAAGAATATATCT 58.541 40.000 0.00 0.00 41.32 1.98
3328 10621 6.367149 CCGATGGTGTGTGAAGAATATATCTG 59.633 42.308 0.00 0.00 38.79 2.90
3329 10622 6.128715 CGATGGTGTGTGAAGAATATATCTGC 60.129 42.308 0.00 0.00 38.79 4.26
3330 10623 5.988287 TGGTGTGTGAAGAATATATCTGCA 58.012 37.500 0.00 0.00 41.76 4.41
3345 10711 3.935872 GCACGTGCACAAGTCGCA 61.936 61.111 34.52 0.00 41.59 5.10
3369 10735 2.868583 CTGTATTGAAGCGGAGACATGG 59.131 50.000 0.00 0.00 0.00 3.66
3370 10736 1.599542 GTATTGAAGCGGAGACATGGC 59.400 52.381 0.00 0.00 0.00 4.40
3381 10747 0.622136 AGACATGGCTGGCTCATCAA 59.378 50.000 0.00 0.00 34.92 2.57
3400 10766 3.077556 AGTCGGCCGGAGAGCAAT 61.078 61.111 27.83 0.00 0.00 3.56
3402 10768 2.125147 TCGGCCGGAGAGCAATTG 60.125 61.111 27.83 0.00 0.00 2.32
3403 10769 2.436646 CGGCCGGAGAGCAATTGT 60.437 61.111 20.10 0.00 0.00 2.71
3404 10770 2.464459 CGGCCGGAGAGCAATTGTC 61.464 63.158 20.10 3.80 0.00 3.18
3406 10772 1.372087 GGCCGGAGAGCAATTGTCTG 61.372 60.000 5.05 1.97 0.00 3.51
3407 10773 1.986575 GCCGGAGAGCAATTGTCTGC 61.987 60.000 5.05 12.17 42.97 4.26
3408 10774 0.674581 CCGGAGAGCAATTGTCTGCA 60.675 55.000 20.66 0.00 45.18 4.41
3409 10775 1.376543 CGGAGAGCAATTGTCTGCAT 58.623 50.000 20.66 5.17 45.18 3.96
3410 10776 1.063616 CGGAGAGCAATTGTCTGCATG 59.936 52.381 20.66 8.84 45.18 4.06
3411 10777 2.089980 GGAGAGCAATTGTCTGCATGT 58.910 47.619 17.98 0.00 45.18 3.21
3412 10778 2.159421 GGAGAGCAATTGTCTGCATGTG 60.159 50.000 17.98 0.00 45.18 3.21
3413 10779 2.745821 GAGAGCAATTGTCTGCATGTGA 59.254 45.455 7.40 0.00 45.18 3.58
3414 10780 2.486982 AGAGCAATTGTCTGCATGTGAC 59.513 45.455 7.40 12.11 45.18 3.67
3416 10782 2.030540 AGCAATTGTCTGCATGTGACAC 60.031 45.455 18.55 0.00 45.18 3.67
3418 10784 3.302555 CAATTGTCTGCATGTGACACAC 58.697 45.455 11.22 0.00 43.13 3.82
3419 10785 0.936600 TTGTCTGCATGTGACACACG 59.063 50.000 11.22 3.28 43.13 4.49
3509 10877 1.002251 TCAAAAAGCTACCAAACGCGG 60.002 47.619 12.47 0.00 0.00 6.46
3573 10941 6.551736 CGATTTAACCATTTTTCTGACGGAT 58.448 36.000 0.00 0.00 0.00 4.18
3720 11093 1.211449 CACTCTCTCGTGCTCGCTT 59.789 57.895 2.69 0.00 36.96 4.68
3740 11199 1.958902 GCTCACTCCCCTGCTCTCAG 61.959 65.000 0.00 0.00 40.02 3.35
3745 11204 2.040278 CCCCTGCTCTCAGTCCCT 59.960 66.667 0.00 0.00 38.66 4.20
3811 11298 4.675029 CGTCGACCCCTTTGCCGT 62.675 66.667 10.58 0.00 0.00 5.68
3929 12287 3.184628 GGTTAGGGTTAGGGTTAGGTGT 58.815 50.000 0.00 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.452287 AAGCTAATGGTTTACGGTTTTTATAGA 57.548 29.630 0.00 0.00 0.00 1.98
5 6 9.498307 CAAGCTAATGGTTTACGGTTTTTATAG 57.502 33.333 0.00 0.00 0.00 1.31
6 7 7.969508 GCAAGCTAATGGTTTACGGTTTTTATA 59.030 33.333 0.00 0.00 0.00 0.98
7 8 6.809689 GCAAGCTAATGGTTTACGGTTTTTAT 59.190 34.615 0.00 0.00 0.00 1.40
9 10 4.986034 GCAAGCTAATGGTTTACGGTTTTT 59.014 37.500 0.00 0.00 0.00 1.94
10 11 4.279922 AGCAAGCTAATGGTTTACGGTTTT 59.720 37.500 0.00 0.00 0.00 2.43
11 12 3.824443 AGCAAGCTAATGGTTTACGGTTT 59.176 39.130 0.00 0.00 0.00 3.27
12 13 3.190535 CAGCAAGCTAATGGTTTACGGTT 59.809 43.478 0.00 0.00 0.00 4.44
13 14 2.747446 CAGCAAGCTAATGGTTTACGGT 59.253 45.455 0.00 0.00 0.00 4.83
43 44 1.752753 CTCTATCGCTGCTCGTTCAG 58.247 55.000 0.00 3.01 39.67 3.02
91 92 4.609018 ATTCCCATCGCTCGCCCG 62.609 66.667 0.00 0.00 0.00 6.13
93 94 3.654020 GCATTCCCATCGCTCGCC 61.654 66.667 0.00 0.00 0.00 5.54
94 95 4.005472 CGCATTCCCATCGCTCGC 62.005 66.667 0.00 0.00 0.00 5.03
95 96 4.005472 GCGCATTCCCATCGCTCG 62.005 66.667 0.30 0.00 44.79 5.03
104 105 3.599704 GGCCCATCAGCGCATTCC 61.600 66.667 11.47 0.00 0.00 3.01
187 188 0.185175 AACCGTGGGGAGCTCTTTTT 59.815 50.000 14.64 0.00 36.97 1.94
188 189 0.250770 GAACCGTGGGGAGCTCTTTT 60.251 55.000 14.64 0.00 36.97 2.27
189 190 1.375326 GAACCGTGGGGAGCTCTTT 59.625 57.895 14.64 0.00 36.97 2.52
190 191 2.943978 CGAACCGTGGGGAGCTCTT 61.944 63.158 14.64 0.00 36.97 2.85
206 207 4.263550 TGAATTTTTATCTCCACACCCCGA 60.264 41.667 0.00 0.00 0.00 5.14
220 221 5.866633 CCGCCAAAATACTGCTGAATTTTTA 59.133 36.000 0.00 0.00 34.01 1.52
323 365 4.925861 GGATCGCAGGAGCAGGCC 62.926 72.222 0.00 0.00 42.27 5.19
324 366 4.925861 GGGATCGCAGGAGCAGGC 62.926 72.222 4.64 0.00 42.27 4.85
325 367 4.598894 CGGGATCGCAGGAGCAGG 62.599 72.222 10.70 0.00 42.27 4.85
336 378 4.899239 CAGGTGCGAGGCGGGATC 62.899 72.222 0.00 0.00 0.00 3.36
453 509 5.023533 ACTGGACACATACACATGATACC 57.976 43.478 0.00 0.00 35.96 2.73
563 1010 6.327279 ACCAAGATACCAAAAAGTAGCAAC 57.673 37.500 0.00 0.00 30.97 4.17
593 1040 5.079406 CGAAACATGACGGAAACTACAATG 58.921 41.667 0.00 0.00 0.00 2.82
594 1041 4.753107 ACGAAACATGACGGAAACTACAAT 59.247 37.500 0.00 0.00 0.00 2.71
605 1052 4.201685 GGTCCAAATAGACGAAACATGACG 60.202 45.833 0.00 4.93 37.66 4.35
616 1063 5.622770 AATGTTTGACGGTCCAAATAGAC 57.377 39.130 5.55 0.00 38.18 2.59
719 1171 2.571212 ACAGAAGGTCAAAACGCATCA 58.429 42.857 0.00 0.00 0.00 3.07
720 1172 3.994392 TCTACAGAAGGTCAAAACGCATC 59.006 43.478 0.00 0.00 0.00 3.91
721 1173 4.002906 TCTACAGAAGGTCAAAACGCAT 57.997 40.909 0.00 0.00 0.00 4.73
800 1252 7.224753 GCAATCTTAGAACTCGGTCATTATTCA 59.775 37.037 0.00 0.00 0.00 2.57
813 1265 5.703130 GTCACCAAAGAGCAATCTTAGAACT 59.297 40.000 0.00 0.00 0.00 3.01
883 1335 3.364549 TGCCCCAATTATTCACTCCTTG 58.635 45.455 0.00 0.00 0.00 3.61
1489 8325 5.001232 ACGCTTGTCAATACCTATTTGTGT 58.999 37.500 0.00 0.00 0.00 3.72
1608 8456 3.118775 TCGTGGGATTCGAGAACATCATT 60.119 43.478 0.00 0.00 33.38 2.57
1676 8524 6.829229 TCAGTGAGAAAATCTGCATCATTT 57.171 33.333 0.00 0.00 0.00 2.32
1677 8525 6.829229 TTCAGTGAGAAAATCTGCATCATT 57.171 33.333 0.00 0.00 32.05 2.57
1749 8597 2.001872 TGACAATCACGCACTGCTATG 58.998 47.619 0.00 0.00 0.00 2.23
2022 8934 3.005897 AGCACAAGATTAGAGTGTCACGT 59.994 43.478 0.00 0.00 35.75 4.49
2092 9005 3.758023 CACCATCAGCAACACCTCAAATA 59.242 43.478 0.00 0.00 0.00 1.40
2188 9369 6.146021 GCAAAGGGAAAAACACATCATTGTAG 59.854 38.462 0.00 0.00 33.76 2.74
2206 9388 7.093945 ACAAACTTACCTAACATATGCAAAGGG 60.094 37.037 18.04 10.00 0.00 3.95
2616 9798 3.120199 CCACAATCGCCATTAATCCGATC 60.120 47.826 16.50 0.00 40.43 3.69
2655 9837 2.202756 CCAGCGAACGAGGGCTAC 60.203 66.667 0.00 0.00 37.41 3.58
2789 9971 3.057019 GCGACATGACTCAACAACACTA 58.943 45.455 0.00 0.00 0.00 2.74
2808 9990 6.018425 ACAGCAATCACATATCTTCTTAAGCG 60.018 38.462 0.00 0.00 0.00 4.68
2969 10151 4.899502 ACCAAGTAACCTTCACTGAGATG 58.100 43.478 0.00 0.00 0.00 2.90
2984 10166 2.875933 CCTTTGCAAGTTCGACCAAGTA 59.124 45.455 0.00 0.00 0.00 2.24
3009 10191 6.371548 CCCAAGTTCGAATATGAAAGAGTGAA 59.628 38.462 0.00 0.00 0.00 3.18
3032 10215 6.309737 CGTACATTCAACTAGTAACTCAACCC 59.690 42.308 0.00 0.00 0.00 4.11
3038 10221 8.545420 CAACAAACGTACATTCAACTAGTAACT 58.455 33.333 0.00 0.00 0.00 2.24
3182 10393 6.390721 TGAACTCACACAACTCTAATAGAGC 58.609 40.000 16.62 0.00 46.12 4.09
3242 10453 9.661187 CCGTCCGATAGTCATACAAATATATAC 57.339 37.037 0.00 0.00 0.00 1.47
3265 10558 4.099170 CTTCTCGCCGTCGTCCGT 62.099 66.667 0.00 0.00 36.96 4.69
3300 10593 0.324614 TCTTCACACACCATCGGCAT 59.675 50.000 0.00 0.00 0.00 4.40
3301 10594 0.107643 TTCTTCACACACCATCGGCA 59.892 50.000 0.00 0.00 0.00 5.69
3302 10595 1.453155 ATTCTTCACACACCATCGGC 58.547 50.000 0.00 0.00 0.00 5.54
3303 10596 6.367149 CAGATATATTCTTCACACACCATCGG 59.633 42.308 0.00 0.00 29.93 4.18
3304 10597 6.128715 GCAGATATATTCTTCACACACCATCG 60.129 42.308 0.00 0.00 29.93 3.84
3305 10598 6.707608 TGCAGATATATTCTTCACACACCATC 59.292 38.462 0.00 0.00 29.93 3.51
3309 10602 5.520288 ACGTGCAGATATATTCTTCACACAC 59.480 40.000 13.53 0.00 45.54 3.82
3311 10604 5.557136 GCACGTGCAGATATATTCTTCACAC 60.557 44.000 34.52 0.00 45.54 3.82
3312 10605 4.507756 GCACGTGCAGATATATTCTTCACA 59.492 41.667 34.52 1.33 45.54 3.58
3313 10606 5.011451 GCACGTGCAGATATATTCTTCAC 57.989 43.478 34.52 0.00 42.91 3.18
3328 10621 3.935872 TGCGACTTGTGCACGTGC 61.936 61.111 33.11 33.11 37.44 5.34
3333 10626 2.962697 TACAGCGTGCGACTTGTGCA 62.963 55.000 0.00 0.00 40.70 4.57
3338 10704 1.726791 CTTCAATACAGCGTGCGACTT 59.273 47.619 0.00 0.00 0.00 3.01
3369 10735 1.364626 CCGACTGTTGATGAGCCAGC 61.365 60.000 0.00 0.00 0.00 4.85
3370 10736 1.364626 GCCGACTGTTGATGAGCCAG 61.365 60.000 0.00 0.00 0.00 4.85
3378 10744 2.599281 TCTCCGGCCGACTGTTGA 60.599 61.111 30.73 13.47 0.00 3.18
3400 10766 0.936600 CGTGTGTCACATGCAGACAA 59.063 50.000 19.51 10.00 46.50 3.18
3402 10768 0.233074 CACGTGTGTCACATGCAGAC 59.767 55.000 22.50 10.97 38.65 3.51
3403 10769 0.103937 TCACGTGTGTCACATGCAGA 59.896 50.000 22.50 17.78 38.65 4.26
3404 10770 0.509929 CTCACGTGTGTCACATGCAG 59.490 55.000 22.50 16.02 38.65 4.41
3406 10772 1.778334 TACTCACGTGTGTCACATGC 58.222 50.000 25.06 4.45 38.65 4.06
3407 10773 4.990543 ATTTACTCACGTGTGTCACATG 57.009 40.909 25.06 21.25 40.80 3.21
3408 10774 4.625742 GCTATTTACTCACGTGTGTCACAT 59.374 41.667 25.06 17.09 33.40 3.21
3409 10775 3.985279 GCTATTTACTCACGTGTGTCACA 59.015 43.478 25.06 11.77 33.40 3.58
3410 10776 3.985279 TGCTATTTACTCACGTGTGTCAC 59.015 43.478 25.06 10.86 0.00 3.67
3411 10777 4.245845 TGCTATTTACTCACGTGTGTCA 57.754 40.909 25.06 13.17 0.00 3.58
3412 10778 6.880822 TTATGCTATTTACTCACGTGTGTC 57.119 37.500 25.06 11.42 0.00 3.67
3413 10779 7.386848 AGTTTTATGCTATTTACTCACGTGTGT 59.613 33.333 24.76 24.76 0.00 3.72
3414 10780 7.739295 AGTTTTATGCTATTTACTCACGTGTG 58.261 34.615 16.51 16.06 0.00 3.82
3416 10782 9.084164 AGTAGTTTTATGCTATTTACTCACGTG 57.916 33.333 9.94 9.94 0.00 4.49
3492 10860 1.520600 CCCCGCGTTTGGTAGCTTTT 61.521 55.000 4.92 0.00 0.00 2.27
3538 10906 2.492881 TGGTTAAATCGCTAGTCACCGA 59.507 45.455 0.00 0.00 37.91 4.69
3559 10927 1.379527 GCCCGATCCGTCAGAAAAAT 58.620 50.000 0.00 0.00 0.00 1.82
3560 10928 0.675522 GGCCCGATCCGTCAGAAAAA 60.676 55.000 0.00 0.00 0.00 1.94
3573 10941 3.785859 GCTGACAGATGGGCCCGA 61.786 66.667 19.37 6.86 0.00 5.14
3614 10982 2.816520 GGCCGTTAATGTCCGCGT 60.817 61.111 4.92 0.00 0.00 6.01
3695 11068 1.917782 GCACGAGAGAGTGAGCGAGT 61.918 60.000 0.88 0.00 44.43 4.18
3701 11074 1.237954 AAGCGAGCACGAGAGAGTGA 61.238 55.000 8.01 0.00 44.43 3.41
3720 11093 1.986757 GAGAGCAGGGGAGTGAGCA 60.987 63.158 0.00 0.00 0.00 4.26
3740 11199 0.173708 CTCGTACTGGAGCAAGGGAC 59.826 60.000 0.00 0.00 0.00 4.46
3802 11289 0.455815 GGAAGGCATTACGGCAAAGG 59.544 55.000 0.00 0.00 44.47 3.11
3811 11298 1.404986 CGTCGTTCCAGGAAGGCATTA 60.405 52.381 16.00 0.00 37.29 1.90


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

AutoCloner maintained by Alex Coulton.