Multiple sequence alignment - TraesCS5D01G101800

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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 TraesCS5D01G101800 chr5D 100.000 2927 0 0 1 2927 114601212 114598286 0.000000e+00 5406.0
1 TraesCS5D01G101800 chr5A 94.538 1721 68 13 895 2598 119862495 119860784 0.000000e+00 2634.0
2 TraesCS5D01G101800 chr5A 88.764 890 91 7 14 896 119863706 119862819 0.000000e+00 1081.0
3 TraesCS5D01G101800 chr5A 90.909 165 12 2 2594 2756 119848238 119848075 4.910000e-53 219.0
4 TraesCS5D01G101800 chr5A 96.296 54 2 0 2755 2808 119847992 119847939 4.020000e-14 89.8
5 TraesCS5D01G101800 chr5B 95.368 1360 55 3 821 2172 125798342 125796983 0.000000e+00 2156.0
6 TraesCS5D01G101800 chr5B 85.790 753 90 7 4 752 125829329 125828590 0.000000e+00 782.0
7 TraesCS5D01G101800 chr5B 85.833 360 49 2 1 358 652820539 652820180 5.920000e-102 381.0
8 TraesCS5D01G101800 chr5B 92.670 191 11 2 2594 2782 125793591 125793402 3.720000e-69 272.0
9 TraesCS5D01G101800 chr5B 91.371 197 7 4 2405 2598 125794619 125794430 8.050000e-66 261.0
10 TraesCS5D01G101800 chr5B 93.382 136 6 3 2278 2413 125796853 125796721 6.400000e-47 198.0
11 TraesCS5D01G101800 chr4A 81.717 361 63 2 1 360 617364195 617363837 6.130000e-77 298.0
12 TraesCS5D01G101800 chr4A 77.016 248 32 17 1069 1293 429980167 429980412 5.120000e-23 119.0
13 TraesCS5D01G101800 chr7A 78.763 372 76 3 1 370 49470379 49470749 2.250000e-61 246.0
14 TraesCS5D01G101800 chr7A 78.202 367 74 6 1 364 163363483 163363120 2.270000e-56 230.0
15 TraesCS5D01G101800 chr7A 89.147 129 11 3 2800 2927 426578921 426579047 1.090000e-34 158.0
16 TraesCS5D01G101800 chr1D 85.903 227 28 4 1 225 371216630 371216854 3.770000e-59 239.0
17 TraesCS5D01G101800 chr7D 78.814 354 68 7 1 353 64566813 64566466 6.310000e-57 231.0
18 TraesCS5D01G101800 chr7D 88.806 134 11 4 2797 2927 334407769 334407901 8.390000e-36 161.0
19 TraesCS5D01G101800 chr3B 76.127 377 78 10 1 372 466663662 466663293 1.380000e-43 187.0
20 TraesCS5D01G101800 chr3B 88.550 131 12 3 2798 2927 558199263 558199391 3.910000e-34 156.0
21 TraesCS5D01G101800 chr3B 88.462 130 12 3 2799 2927 466661447 466661574 1.400000e-33 154.0
22 TraesCS5D01G101800 chr7B 89.630 135 10 4 2795 2927 750059193 750059061 5.020000e-38 169.0
23 TraesCS5D01G101800 chr1A 90.152 132 10 3 2797 2927 54017257 54017386 5.020000e-38 169.0
24 TraesCS5D01G101800 chr1A 89.231 130 11 3 2800 2927 307480580 307480708 3.020000e-35 159.0
25 TraesCS5D01G101800 chr1A 89.062 128 13 1 2800 2927 32535057 32534931 1.090000e-34 158.0
26 TraesCS5D01G101800 chr2A 89.062 128 11 3 2800 2926 46834603 46834728 3.910000e-34 156.0
27 TraesCS5D01G101800 chr4D 75.497 302 47 18 1048 1326 132292426 132292129 3.960000e-24 122.0
28 TraesCS5D01G101800 chr4B 76.923 247 32 15 1069 1292 164918387 164918631 1.840000e-22 117.0


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 TraesCS5D01G101800 chr5D 114598286 114601212 2926 True 5406.00 5406 100.00000 1 2927 1 chr5D.!!$R1 2926
1 TraesCS5D01G101800 chr5A 119860784 119863706 2922 True 1857.50 2634 91.65100 14 2598 2 chr5A.!!$R2 2584
2 TraesCS5D01G101800 chr5B 125828590 125829329 739 True 782.00 782 85.79000 4 752 1 chr5B.!!$R1 748
3 TraesCS5D01G101800 chr5B 125793402 125798342 4940 True 721.75 2156 93.19775 821 2782 4 chr5B.!!$R3 1961

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
143 145 0.245266 TCGAAACTCGGCATAGCACA 59.755 50.0 0.0 0.0 40.88 4.57 F
416 418 0.606604 GTGGAGACTTTAGCGGGTCA 59.393 55.0 0.0 0.0 35.18 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1707 2046 0.916809 CCGGGATAGGGTTCTTGGTT 59.083 55.0 0.0 0.0 0.00 3.67 R
2350 2792 0.027979 CTCACCAACAAGTGTGTGCG 59.972 55.0 0.0 0.0 38.27 5.34 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 4.685169 ACAAATTGCGACGAATCTGAAT 57.315 36.364 0.00 0.00 0.00 2.57
106 108 2.158623 TGCACTTGAAGAACACCCATCT 60.159 45.455 0.00 0.00 0.00 2.90
107 109 2.227388 GCACTTGAAGAACACCCATCTG 59.773 50.000 0.00 0.00 0.00 2.90
143 145 0.245266 TCGAAACTCGGCATAGCACA 59.755 50.000 0.00 0.00 40.88 4.57
147 149 2.113860 AACTCGGCATAGCACATGTT 57.886 45.000 0.00 0.00 0.00 2.71
159 161 1.674322 ACATGTTGCGGGTAGTGGC 60.674 57.895 0.00 0.00 0.00 5.01
224 226 4.373116 GTTGAGCCAGGCCGACGA 62.373 66.667 8.22 0.00 0.00 4.20
250 252 2.809601 CGTAGCTGTGTCGGTGGC 60.810 66.667 0.00 0.00 0.00 5.01
285 287 4.896829 CCGAGCGCCTAGGGGAGA 62.897 72.222 28.92 0.00 34.16 3.71
317 319 1.687494 GATGCGGTGCAGACTCGTTC 61.687 60.000 0.00 0.00 43.65 3.95
318 320 2.049063 GCGGTGCAGACTCGTTCT 60.049 61.111 0.00 0.00 33.33 3.01
360 362 1.677518 CCGTCGAATCCATCCCAAACA 60.678 52.381 0.00 0.00 0.00 2.83
401 403 2.760477 CAAATCCGGGTGGGTGGA 59.240 61.111 0.00 0.00 38.95 4.02
405 407 2.765705 AATCCGGGTGGGTGGAGACT 62.766 60.000 0.00 0.00 37.76 3.24
406 408 2.765705 ATCCGGGTGGGTGGAGACTT 62.766 60.000 0.00 0.00 37.76 3.01
416 418 0.606604 GTGGAGACTTTAGCGGGTCA 59.393 55.000 0.00 0.00 35.18 4.02
565 569 3.197983 GGCGGAGGAGTATATTTAGGCAT 59.802 47.826 0.00 0.00 0.00 4.40
669 677 7.010771 ACCAAAATTTTACTCCTCTAAAGCCT 58.989 34.615 2.44 0.00 0.00 4.58
686 695 2.908351 AGCCTTTTAGGGGTTCGACTAA 59.092 45.455 0.00 0.00 35.37 2.24
700 713 2.100252 TCGACTAAAGATGCCCGGTAAG 59.900 50.000 0.00 0.00 0.00 2.34
701 714 2.159142 CGACTAAAGATGCCCGGTAAGT 60.159 50.000 0.00 0.00 0.00 2.24
702 715 3.067180 CGACTAAAGATGCCCGGTAAGTA 59.933 47.826 0.00 0.00 0.00 2.24
703 716 4.440525 CGACTAAAGATGCCCGGTAAGTAA 60.441 45.833 0.00 0.00 0.00 2.24
763 777 2.632996 TGACTAGCCTAGCAACAACACT 59.367 45.455 0.00 0.00 0.00 3.55
764 778 3.071023 TGACTAGCCTAGCAACAACACTT 59.929 43.478 0.00 0.00 0.00 3.16
779 793 7.171337 GCAACAACACTTCAATACCAATCAAAT 59.829 33.333 0.00 0.00 0.00 2.32
781 795 7.725251 ACAACACTTCAATACCAATCAAATGT 58.275 30.769 0.00 0.00 0.00 2.71
804 818 5.067283 GTGCCATAATCGGAAAATGTTAGGT 59.933 40.000 0.00 0.00 0.00 3.08
817 831 7.494625 GGAAAATGTTAGGTGATGACGATCTTA 59.505 37.037 0.00 0.00 0.00 2.10
879 893 6.585702 TCCAAAATTAATGTTGTGCTTCATCG 59.414 34.615 15.67 0.00 0.00 3.84
971 1310 3.370315 CCTTTCTCACCTTCCCATCTCAG 60.370 52.174 0.00 0.00 0.00 3.35
1158 1497 2.434884 GGCTACTGCTTCAGCGCA 60.435 61.111 11.47 0.00 45.83 6.09
1221 1560 2.476126 TCGACTTCGACTTCTCCTCT 57.524 50.000 0.00 0.00 44.22 3.69
1509 1848 2.124695 GCCCCGGCGAAAGAATCT 60.125 61.111 9.30 0.00 0.00 2.40
1579 1918 4.790962 CGTCCGGGTCCTCCTCGA 62.791 72.222 0.00 0.00 32.09 4.04
1638 1977 2.419297 GCTCATCCATCCGAACAAGTCT 60.419 50.000 0.00 0.00 0.00 3.24
1693 2032 1.201429 ATGCCCCAAGACGAACTCCT 61.201 55.000 0.00 0.00 0.00 3.69
1709 2048 3.123620 CTCGCTGGCAGCTCCAAC 61.124 66.667 34.17 7.68 46.01 3.77
1719 2058 0.111253 CAGCTCCAACCAAGAACCCT 59.889 55.000 0.00 0.00 0.00 4.34
1721 2060 2.025887 CAGCTCCAACCAAGAACCCTAT 60.026 50.000 0.00 0.00 0.00 2.57
1953 2299 2.027751 GCCGACGCCTCCATAGAC 59.972 66.667 0.00 0.00 0.00 2.59
1954 2300 2.491022 GCCGACGCCTCCATAGACT 61.491 63.158 0.00 0.00 0.00 3.24
2149 2498 7.967908 ACAAAATTGGTGTTTTATATGTCCCA 58.032 30.769 0.00 0.00 30.56 4.37
2168 2517 3.305608 CCCAAATGCTCCTTCTTGTTGTC 60.306 47.826 0.00 0.00 0.00 3.18
2181 2623 7.505585 TCCTTCTTGTTGTCCTCAATGTTTATT 59.494 33.333 0.00 0.00 35.92 1.40
2235 2677 1.868713 TGTTTCTATACCAGGGGCGA 58.131 50.000 0.00 0.00 0.00 5.54
2306 2748 3.426525 CGATTTTCTGTTTTGAGCTTGCC 59.573 43.478 0.00 0.00 0.00 4.52
2358 2800 5.029650 TGAAAGATAAATGACGCACACAC 57.970 39.130 0.00 0.00 0.00 3.82
2490 5050 1.740025 GTGAACTGCTCCTACATTGGC 59.260 52.381 0.00 0.00 0.00 4.52
2491 5051 1.340017 TGAACTGCTCCTACATTGGCC 60.340 52.381 0.00 0.00 0.00 5.36
2514 5074 3.662759 TTAATTAAGGGCAGGGACAGG 57.337 47.619 0.00 0.00 0.00 4.00
2515 5075 1.382914 AATTAAGGGCAGGGACAGGT 58.617 50.000 0.00 0.00 0.00 4.00
2516 5076 0.919710 ATTAAGGGCAGGGACAGGTC 59.080 55.000 0.00 0.00 0.00 3.85
2517 5077 0.474854 TTAAGGGCAGGGACAGGTCA 60.475 55.000 1.41 0.00 0.00 4.02
2518 5078 1.198759 TAAGGGCAGGGACAGGTCAC 61.199 60.000 1.41 0.00 0.00 3.67
2519 5079 3.249189 GGGCAGGGACAGGTCACA 61.249 66.667 4.27 0.00 34.87 3.58
2520 5080 2.348998 GGCAGGGACAGGTCACAG 59.651 66.667 4.27 0.00 34.87 3.66
2587 5147 8.268605 TGGGTTTAGTAACATAATCATAGCACA 58.731 33.333 0.00 0.00 35.92 4.57
2594 5154 5.830799 ACATAATCATAGCACAGGGATGA 57.169 39.130 0.00 0.00 34.25 2.92
2598 5158 4.620589 ATCATAGCACAGGGATGAGAAG 57.379 45.455 0.00 0.00 33.29 2.85
2607 6010 5.450137 GCACAGGGATGAGAAGATTTCATTG 60.450 44.000 0.00 0.00 35.50 2.82
2727 6132 5.502089 TTCGATTTCCTACAAAACCCCTA 57.498 39.130 0.00 0.00 0.00 3.53
2744 6149 8.401955 AAACCCCTATCCTGTAGAATTCTTAA 57.598 34.615 14.36 1.38 0.00 1.85
2745 6150 8.401955 AACCCCTATCCTGTAGAATTCTTAAA 57.598 34.615 14.36 0.00 0.00 1.52
2782 6187 5.451354 ACAAAGGAAGCTTTAACCTTGGTA 58.549 37.500 19.23 0.00 43.53 3.25
2783 6188 5.535030 ACAAAGGAAGCTTTAACCTTGGTAG 59.465 40.000 19.23 12.02 43.53 3.18
2784 6189 5.578157 AAGGAAGCTTTAACCTTGGTAGA 57.422 39.130 15.26 0.00 41.64 2.59
2785 6190 4.907809 AGGAAGCTTTAACCTTGGTAGAC 58.092 43.478 0.00 0.00 0.00 2.59
2786 6191 4.349930 AGGAAGCTTTAACCTTGGTAGACA 59.650 41.667 0.00 0.00 0.00 3.41
2787 6192 4.695928 GGAAGCTTTAACCTTGGTAGACAG 59.304 45.833 0.00 0.00 0.00 3.51
2788 6193 5.512576 GGAAGCTTTAACCTTGGTAGACAGA 60.513 44.000 0.00 0.00 0.00 3.41
2789 6194 5.763876 AGCTTTAACCTTGGTAGACAGAT 57.236 39.130 0.00 0.00 0.00 2.90
2790 6195 5.735766 AGCTTTAACCTTGGTAGACAGATC 58.264 41.667 0.00 0.00 0.00 2.75
2791 6196 5.485708 AGCTTTAACCTTGGTAGACAGATCT 59.514 40.000 0.00 0.00 39.15 2.75
2792 6197 6.013293 AGCTTTAACCTTGGTAGACAGATCTT 60.013 38.462 0.00 0.00 36.29 2.40
2793 6198 6.314152 GCTTTAACCTTGGTAGACAGATCTTC 59.686 42.308 0.00 0.00 36.29 2.87
2794 6199 6.928348 TTAACCTTGGTAGACAGATCTTCA 57.072 37.500 0.00 0.00 36.29 3.02
2795 6200 5.413309 AACCTTGGTAGACAGATCTTCAG 57.587 43.478 0.00 0.00 36.29 3.02
2796 6201 4.678256 ACCTTGGTAGACAGATCTTCAGA 58.322 43.478 0.00 0.00 36.29 3.27
2797 6202 5.087323 ACCTTGGTAGACAGATCTTCAGAA 58.913 41.667 0.00 0.00 36.29 3.02
2798 6203 5.046950 ACCTTGGTAGACAGATCTTCAGAAC 60.047 44.000 0.00 0.00 36.29 3.01
2799 6204 5.186797 CCTTGGTAGACAGATCTTCAGAACT 59.813 44.000 0.00 0.00 36.29 3.01
2800 6205 6.378564 CCTTGGTAGACAGATCTTCAGAACTA 59.621 42.308 0.00 0.00 36.29 2.24
2801 6206 6.761099 TGGTAGACAGATCTTCAGAACTAC 57.239 41.667 0.00 0.00 36.29 2.73
2802 6207 6.486056 TGGTAGACAGATCTTCAGAACTACT 58.514 40.000 0.00 0.00 36.29 2.57
2803 6208 6.600032 TGGTAGACAGATCTTCAGAACTACTC 59.400 42.308 0.00 0.00 36.29 2.59
2804 6209 6.038936 GGTAGACAGATCTTCAGAACTACTCC 59.961 46.154 0.00 0.00 36.29 3.85
2805 6210 4.953579 AGACAGATCTTCAGAACTACTCCC 59.046 45.833 0.00 0.00 0.00 4.30
2806 6211 4.941713 ACAGATCTTCAGAACTACTCCCT 58.058 43.478 0.00 0.00 0.00 4.20
2807 6212 4.953579 ACAGATCTTCAGAACTACTCCCTC 59.046 45.833 0.00 0.00 0.00 4.30
2808 6213 4.036262 CAGATCTTCAGAACTACTCCCTCG 59.964 50.000 0.00 0.00 0.00 4.63
2809 6214 2.724454 TCTTCAGAACTACTCCCTCGG 58.276 52.381 0.00 0.00 0.00 4.63
2810 6215 1.135333 CTTCAGAACTACTCCCTCGGC 59.865 57.143 0.00 0.00 0.00 5.54
2811 6216 0.331954 TCAGAACTACTCCCTCGGCT 59.668 55.000 0.00 0.00 0.00 5.52
2812 6217 1.187087 CAGAACTACTCCCTCGGCTT 58.813 55.000 0.00 0.00 0.00 4.35
2813 6218 1.550976 CAGAACTACTCCCTCGGCTTT 59.449 52.381 0.00 0.00 0.00 3.51
2814 6219 2.758979 CAGAACTACTCCCTCGGCTTTA 59.241 50.000 0.00 0.00 0.00 1.85
2815 6220 3.194968 CAGAACTACTCCCTCGGCTTTAA 59.805 47.826 0.00 0.00 0.00 1.52
2816 6221 3.836562 AGAACTACTCCCTCGGCTTTAAA 59.163 43.478 0.00 0.00 0.00 1.52
2817 6222 4.285260 AGAACTACTCCCTCGGCTTTAAAA 59.715 41.667 0.00 0.00 0.00 1.52
2818 6223 4.838904 ACTACTCCCTCGGCTTTAAAAT 57.161 40.909 0.00 0.00 0.00 1.82
2819 6224 5.945144 ACTACTCCCTCGGCTTTAAAATA 57.055 39.130 0.00 0.00 0.00 1.40
2820 6225 6.496144 ACTACTCCCTCGGCTTTAAAATAT 57.504 37.500 0.00 0.00 0.00 1.28
2821 6226 7.607615 ACTACTCCCTCGGCTTTAAAATATA 57.392 36.000 0.00 0.00 0.00 0.86
2822 6227 7.668492 ACTACTCCCTCGGCTTTAAAATATAG 58.332 38.462 0.00 0.00 0.00 1.31
2823 6228 6.496144 ACTCCCTCGGCTTTAAAATATAGT 57.504 37.500 0.00 0.00 0.00 2.12
2824 6229 6.289064 ACTCCCTCGGCTTTAAAATATAGTG 58.711 40.000 0.00 0.00 0.00 2.74
2825 6230 5.061179 TCCCTCGGCTTTAAAATATAGTGC 58.939 41.667 0.00 0.00 0.00 4.40
2826 6231 4.215613 CCCTCGGCTTTAAAATATAGTGCC 59.784 45.833 3.01 3.01 35.94 5.01
2827 6232 4.215613 CCTCGGCTTTAAAATATAGTGCCC 59.784 45.833 6.76 0.00 35.89 5.36
2828 6233 4.139038 TCGGCTTTAAAATATAGTGCCCC 58.861 43.478 6.76 0.00 35.89 5.80
2829 6234 3.254903 CGGCTTTAAAATATAGTGCCCCC 59.745 47.826 6.76 0.00 35.89 5.40
2830 6235 3.254903 GGCTTTAAAATATAGTGCCCCCG 59.745 47.826 1.85 0.00 33.45 5.73
2831 6236 3.887110 GCTTTAAAATATAGTGCCCCCGT 59.113 43.478 0.00 0.00 0.00 5.28
2832 6237 4.261447 GCTTTAAAATATAGTGCCCCCGTG 60.261 45.833 0.00 0.00 0.00 4.94
2833 6238 1.687563 AAAATATAGTGCCCCCGTGC 58.312 50.000 0.00 0.00 0.00 5.34
2834 6239 0.843984 AAATATAGTGCCCCCGTGCT 59.156 50.000 0.00 0.00 0.00 4.40
2835 6240 0.843984 AATATAGTGCCCCCGTGCTT 59.156 50.000 0.00 0.00 0.00 3.91
2836 6241 0.843984 ATATAGTGCCCCCGTGCTTT 59.156 50.000 0.00 0.00 0.00 3.51
2837 6242 0.179468 TATAGTGCCCCCGTGCTTTC 59.821 55.000 0.00 0.00 0.00 2.62
2838 6243 2.552231 ATAGTGCCCCCGTGCTTTCC 62.552 60.000 0.00 0.00 0.00 3.13
2841 6246 4.796495 GCCCCCGTGCTTTCCGAT 62.796 66.667 0.00 0.00 0.00 4.18
2842 6247 2.824041 CCCCCGTGCTTTCCGATG 60.824 66.667 0.00 0.00 0.00 3.84
2843 6248 2.046314 CCCCGTGCTTTCCGATGT 60.046 61.111 0.00 0.00 0.00 3.06
2844 6249 2.106683 CCCCGTGCTTTCCGATGTC 61.107 63.158 0.00 0.00 0.00 3.06
2845 6250 1.079127 CCCGTGCTTTCCGATGTCT 60.079 57.895 0.00 0.00 0.00 3.41
2846 6251 0.174845 CCCGTGCTTTCCGATGTCTA 59.825 55.000 0.00 0.00 0.00 2.59
2847 6252 1.404986 CCCGTGCTTTCCGATGTCTAA 60.405 52.381 0.00 0.00 0.00 2.10
2848 6253 1.659098 CCGTGCTTTCCGATGTCTAAC 59.341 52.381 0.00 0.00 0.00 2.34
2849 6254 2.607187 CGTGCTTTCCGATGTCTAACT 58.393 47.619 0.00 0.00 0.00 2.24
2850 6255 2.993899 CGTGCTTTCCGATGTCTAACTT 59.006 45.455 0.00 0.00 0.00 2.66
2851 6256 3.432252 CGTGCTTTCCGATGTCTAACTTT 59.568 43.478 0.00 0.00 0.00 2.66
2852 6257 4.666655 CGTGCTTTCCGATGTCTAACTTTG 60.667 45.833 0.00 0.00 0.00 2.77
2853 6258 4.451096 GTGCTTTCCGATGTCTAACTTTGA 59.549 41.667 0.00 0.00 0.00 2.69
2854 6259 5.122396 GTGCTTTCCGATGTCTAACTTTGAT 59.878 40.000 0.00 0.00 0.00 2.57
2855 6260 5.351465 TGCTTTCCGATGTCTAACTTTGATC 59.649 40.000 0.00 0.00 0.00 2.92
2856 6261 5.351465 GCTTTCCGATGTCTAACTTTGATCA 59.649 40.000 0.00 0.00 0.00 2.92
2857 6262 6.037610 GCTTTCCGATGTCTAACTTTGATCAT 59.962 38.462 0.00 0.00 0.00 2.45
2858 6263 7.224753 GCTTTCCGATGTCTAACTTTGATCATA 59.775 37.037 0.00 0.00 0.00 2.15
2859 6264 9.098355 CTTTCCGATGTCTAACTTTGATCATAA 57.902 33.333 0.00 0.00 0.00 1.90
2860 6265 9.443323 TTTCCGATGTCTAACTTTGATCATAAA 57.557 29.630 0.00 0.00 0.00 1.40
2861 6266 9.613428 TTCCGATGTCTAACTTTGATCATAAAT 57.387 29.630 0.00 0.00 0.00 1.40
2862 6267 9.613428 TCCGATGTCTAACTTTGATCATAAATT 57.387 29.630 0.00 0.00 0.00 1.82
2873 6278 9.840427 ACTTTGATCATAAATTTAACCAACGAG 57.160 29.630 1.21 3.35 0.00 4.18
2877 6282 8.547894 TGATCATAAATTTAACCAACGAGATCG 58.452 33.333 1.21 0.00 46.33 3.69
2878 6283 8.657074 ATCATAAATTTAACCAACGAGATCGA 57.343 30.769 9.58 0.00 43.02 3.59
2879 6284 7.902032 TCATAAATTTAACCAACGAGATCGAC 58.098 34.615 9.58 0.00 43.02 4.20
2880 6285 7.762615 TCATAAATTTAACCAACGAGATCGACT 59.237 33.333 9.58 0.00 43.02 4.18
2881 6286 5.779806 AATTTAACCAACGAGATCGACTG 57.220 39.130 9.58 5.77 43.02 3.51
2882 6287 2.273370 TAACCAACGAGATCGACTGC 57.727 50.000 9.58 0.00 43.02 4.40
2883 6288 0.732880 AACCAACGAGATCGACTGCG 60.733 55.000 9.58 0.00 43.02 5.18
2884 6289 1.874019 CCAACGAGATCGACTGCGG 60.874 63.158 9.58 0.00 43.02 5.69
2885 6290 2.202623 AACGAGATCGACTGCGGC 60.203 61.111 9.58 0.00 43.02 6.53
2886 6291 4.538283 ACGAGATCGACTGCGGCG 62.538 66.667 9.58 0.51 43.02 6.46
2888 6293 4.933064 GAGATCGACTGCGGCGGG 62.933 72.222 14.26 2.36 38.28 6.13
2890 6295 4.933064 GATCGACTGCGGCGGGAG 62.933 72.222 14.26 11.31 38.28 4.30
2893 6298 4.735132 CGACTGCGGCGGGAGAAA 62.735 66.667 19.55 0.00 35.29 2.52
2894 6299 2.358247 GACTGCGGCGGGAGAAAA 60.358 61.111 19.55 0.00 35.29 2.29
2895 6300 1.964373 GACTGCGGCGGGAGAAAAA 60.964 57.895 19.55 0.00 35.29 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.465781 GCTTATTGTTTGCTCAAAATTGTGTGT 60.466 33.333 0.00 0.00 31.33 3.72
1 2 6.847289 GCTTATTGTTTGCTCAAAATTGTGTG 59.153 34.615 0.00 0.00 31.33 3.82
2 3 6.762661 AGCTTATTGTTTGCTCAAAATTGTGT 59.237 30.769 0.00 0.00 30.41 3.72
7 8 8.885494 TTTGTAGCTTATTGTTTGCTCAAAAT 57.115 26.923 0.00 0.00 38.15 1.82
49 50 2.614983 GTGCTTGTTTCTCCGGTTGTTA 59.385 45.455 0.00 0.00 0.00 2.41
143 145 2.045340 GGCCACTACCCGCAACAT 60.045 61.111 0.00 0.00 0.00 2.71
147 149 4.323477 GTGTGGCCACTACCCGCA 62.323 66.667 34.75 11.81 40.34 5.69
159 161 1.131126 GTTGCCGATCATCAAGTGTGG 59.869 52.381 0.00 0.00 0.00 4.17
224 226 3.138625 ACAGCTACGCACTGTGGT 58.861 55.556 10.21 8.35 46.38 4.16
229 231 2.258591 CCGACACAGCTACGCACT 59.741 61.111 0.00 0.00 0.00 4.40
250 252 0.030908 GGAGCTCAGTTATCGACCGG 59.969 60.000 17.19 0.00 0.00 5.28
259 261 4.443266 GGCGCTCGGAGCTCAGTT 62.443 66.667 25.96 0.00 39.60 3.16
285 287 1.069765 CGCATCTCGGTATGGCCTT 59.930 57.895 3.32 0.00 34.25 4.35
311 313 2.742372 CGCAACCCCCAGAACGAG 60.742 66.667 0.00 0.00 0.00 4.18
360 362 1.095807 TCTCTCATCGGCGACATCGT 61.096 55.000 13.76 0.00 42.22 3.73
452 454 2.174319 GCTTGTCGATTCCCGCCTC 61.174 63.158 0.00 0.00 38.37 4.70
471 473 4.569023 CGCGCCGCATCTACTCCA 62.569 66.667 10.75 0.00 0.00 3.86
519 521 0.179054 GGCGGACTACCAAATCTCCC 60.179 60.000 0.00 0.00 35.59 4.30
521 523 1.152383 GCGGCGGACTACCAAATCTC 61.152 60.000 9.78 0.00 35.59 2.75
565 569 0.035725 TTACTCCTCGACTCGGCAGA 60.036 55.000 0.00 0.00 0.00 4.26
664 672 1.703513 AGTCGAACCCCTAAAAGGCTT 59.296 47.619 0.00 0.00 32.73 4.35
669 677 4.939439 GCATCTTTAGTCGAACCCCTAAAA 59.061 41.667 7.21 1.42 33.91 1.52
673 681 1.209747 GGCATCTTTAGTCGAACCCCT 59.790 52.381 0.00 0.00 0.00 4.79
674 683 1.664873 GGCATCTTTAGTCGAACCCC 58.335 55.000 0.00 0.00 0.00 4.95
686 695 5.881923 TCTATTTACTTACCGGGCATCTT 57.118 39.130 6.32 0.00 0.00 2.40
736 749 3.007940 TGTTGCTAGGCTAGTCACAATGT 59.992 43.478 21.92 0.00 0.00 2.71
763 777 5.735285 TGGCACATTTGATTGGTATTGAA 57.265 34.783 0.00 0.00 0.00 2.69
781 795 5.067153 CACCTAACATTTTCCGATTATGGCA 59.933 40.000 0.00 0.00 0.00 4.92
804 818 7.281999 TGCAATGGTAAATTAAGATCGTCATCA 59.718 33.333 0.00 0.00 0.00 3.07
879 893 8.133627 CCCTTGATGATAAATGTGAATGAACTC 58.866 37.037 0.00 0.00 0.00 3.01
971 1310 1.618447 AGTGGGGTGGTGGGGATAC 60.618 63.158 0.00 0.00 0.00 2.24
1305 1644 2.338015 CGGACGGAGGAGGAACGAA 61.338 63.158 0.00 0.00 0.00 3.85
1416 1755 4.201679 CGATGCACCGACCGGCTA 62.202 66.667 8.55 0.00 39.32 3.93
1579 1918 2.048127 GCCGCAACTCTTCGAGGT 60.048 61.111 0.00 0.00 33.35 3.85
1638 1977 3.113514 TTGGTGCTTGGAGCCGTCA 62.114 57.895 0.00 0.00 41.51 4.35
1674 2013 1.201429 AGGAGTTCGTCTTGGGGCAT 61.201 55.000 0.00 0.00 0.00 4.40
1707 2046 0.916809 CCGGGATAGGGTTCTTGGTT 59.083 55.000 0.00 0.00 0.00 3.67
1709 2048 1.148498 GCCGGGATAGGGTTCTTGG 59.852 63.158 2.18 0.00 0.00 3.61
1734 2073 2.202810 CTCCTTCTCCCGCGCTTC 60.203 66.667 5.56 0.00 0.00 3.86
1950 2296 1.003812 ACTCGTGAGCTAGTGGAGTCT 59.996 52.381 0.00 0.00 32.86 3.24
1953 2299 1.131504 GACACTCGTGAGCTAGTGGAG 59.868 57.143 16.69 9.84 45.94 3.86
1954 2300 1.166129 GACACTCGTGAGCTAGTGGA 58.834 55.000 16.69 0.00 45.94 4.02
2149 2498 3.823304 GAGGACAACAAGAAGGAGCATTT 59.177 43.478 0.00 0.00 0.00 2.32
2168 2517 6.588719 TTCCTGGAACAATAAACATTGAGG 57.411 37.500 4.68 1.44 38.70 3.86
2181 2623 1.813862 CGTTCTTGGCTTCCTGGAACA 60.814 52.381 4.68 0.00 36.42 3.18
2227 2669 6.451064 AAAAATAAATTACTCTCGCCCCTG 57.549 37.500 0.00 0.00 0.00 4.45
2228 2670 7.114095 TGTAAAAATAAATTACTCTCGCCCCT 58.886 34.615 0.00 0.00 34.94 4.79
2270 2712 2.693797 AAATCGCAGTTGCTGAAGTG 57.306 45.000 2.29 0.00 39.32 3.16
2349 2791 0.675208 TCACCAACAAGTGTGTGCGT 60.675 50.000 0.00 0.00 38.27 5.24
2350 2792 0.027979 CTCACCAACAAGTGTGTGCG 59.972 55.000 0.00 0.00 38.27 5.34
2358 2800 2.260844 TGGAGAAGCTCACCAACAAG 57.739 50.000 4.38 0.00 34.19 3.16
2515 5075 2.437651 TGTCATTTCCAGTCACCTGTGA 59.562 45.455 0.00 0.00 36.95 3.58
2516 5076 2.549754 GTGTCATTTCCAGTCACCTGTG 59.450 50.000 0.00 0.00 36.95 3.66
2517 5077 2.439507 AGTGTCATTTCCAGTCACCTGT 59.560 45.455 0.00 0.00 36.95 4.00
2518 5078 3.131709 AGTGTCATTTCCAGTCACCTG 57.868 47.619 0.00 0.00 38.50 4.00
2519 5079 3.392616 AGAAGTGTCATTTCCAGTCACCT 59.607 43.478 4.57 0.00 0.00 4.00
2520 5080 3.744660 AGAAGTGTCATTTCCAGTCACC 58.255 45.455 4.57 0.00 0.00 4.02
2587 5147 4.479796 TCCCAATGAAATCTTCTCATCCCT 59.520 41.667 0.00 0.00 32.26 4.20
2594 5154 4.313020 AGCAGTCCCAATGAAATCTTCT 57.687 40.909 0.00 0.00 0.00 2.85
2598 5158 5.841957 ACATTAGCAGTCCCAATGAAATC 57.158 39.130 0.00 0.00 34.48 2.17
2640 6045 3.516586 TGTAGGTGGTTCTCATCCTTCA 58.483 45.455 0.00 0.00 32.11 3.02
2684 6089 6.910433 TCGAAATTCTTTCTGCACTTTTGTAC 59.090 34.615 0.00 0.00 37.52 2.90
2689 6094 6.642540 GGAAATCGAAATTCTTTCTGCACTTT 59.357 34.615 12.38 0.00 37.52 2.66
2691 6096 5.474876 AGGAAATCGAAATTCTTTCTGCACT 59.525 36.000 12.38 0.00 37.52 4.40
2693 6098 5.964958 AGGAAATCGAAATTCTTTCTGCA 57.035 34.783 12.38 0.00 37.52 4.41
2694 6099 6.842163 TGTAGGAAATCGAAATTCTTTCTGC 58.158 36.000 12.38 7.04 37.52 4.26
2750 6155 8.967918 GGTTAAAGCTTCCTTTGTTTATAGGAT 58.032 33.333 0.00 0.00 41.24 3.24
2782 6187 4.953579 GGGAGTAGTTCTGAAGATCTGTCT 59.046 45.833 0.00 1.20 35.82 3.41
2783 6188 4.953579 AGGGAGTAGTTCTGAAGATCTGTC 59.046 45.833 0.00 0.00 0.00 3.51
2784 6189 4.941713 AGGGAGTAGTTCTGAAGATCTGT 58.058 43.478 0.00 0.00 0.00 3.41
2785 6190 4.036262 CGAGGGAGTAGTTCTGAAGATCTG 59.964 50.000 0.00 0.00 0.00 2.90
2786 6191 4.204012 CGAGGGAGTAGTTCTGAAGATCT 58.796 47.826 0.00 0.00 0.00 2.75
2787 6192 3.316868 CCGAGGGAGTAGTTCTGAAGATC 59.683 52.174 0.00 0.00 0.00 2.75
2788 6193 3.292460 CCGAGGGAGTAGTTCTGAAGAT 58.708 50.000 0.00 0.00 0.00 2.40
2789 6194 2.724454 CCGAGGGAGTAGTTCTGAAGA 58.276 52.381 0.00 0.00 0.00 2.87
2790 6195 1.135333 GCCGAGGGAGTAGTTCTGAAG 59.865 57.143 0.00 0.00 0.00 3.02
2791 6196 1.183549 GCCGAGGGAGTAGTTCTGAA 58.816 55.000 0.00 0.00 0.00 3.02
2792 6197 0.331954 AGCCGAGGGAGTAGTTCTGA 59.668 55.000 0.00 0.00 0.00 3.27
2793 6198 1.187087 AAGCCGAGGGAGTAGTTCTG 58.813 55.000 0.00 0.00 0.00 3.02
2794 6199 1.939980 AAAGCCGAGGGAGTAGTTCT 58.060 50.000 0.00 0.00 0.00 3.01
2795 6200 3.881937 TTAAAGCCGAGGGAGTAGTTC 57.118 47.619 0.00 0.00 0.00 3.01
2796 6201 4.628963 TTTTAAAGCCGAGGGAGTAGTT 57.371 40.909 0.00 0.00 0.00 2.24
2797 6202 4.838904 ATTTTAAAGCCGAGGGAGTAGT 57.161 40.909 0.00 0.00 0.00 2.73
2798 6203 7.599245 CACTATATTTTAAAGCCGAGGGAGTAG 59.401 40.741 0.00 0.00 0.00 2.57
2799 6204 7.439381 CACTATATTTTAAAGCCGAGGGAGTA 58.561 38.462 0.00 0.00 0.00 2.59
2800 6205 6.289064 CACTATATTTTAAAGCCGAGGGAGT 58.711 40.000 0.00 0.00 0.00 3.85
2801 6206 5.179555 GCACTATATTTTAAAGCCGAGGGAG 59.820 44.000 0.00 0.00 0.00 4.30
2802 6207 5.061179 GCACTATATTTTAAAGCCGAGGGA 58.939 41.667 0.00 0.00 0.00 4.20
2803 6208 4.215613 GGCACTATATTTTAAAGCCGAGGG 59.784 45.833 0.00 0.00 0.00 4.30
2804 6209 4.215613 GGGCACTATATTTTAAAGCCGAGG 59.784 45.833 6.36 0.00 41.43 4.63
2805 6210 4.215613 GGGGCACTATATTTTAAAGCCGAG 59.784 45.833 6.36 0.00 41.43 4.63
2806 6211 4.139038 GGGGCACTATATTTTAAAGCCGA 58.861 43.478 6.36 0.00 41.43 5.54
2807 6212 3.254903 GGGGGCACTATATTTTAAAGCCG 59.745 47.826 6.36 0.00 41.43 5.52
2808 6213 3.254903 CGGGGGCACTATATTTTAAAGCC 59.745 47.826 4.27 4.27 39.86 4.35
2809 6214 3.887110 ACGGGGGCACTATATTTTAAAGC 59.113 43.478 0.00 0.00 0.00 3.51
2810 6215 4.261447 GCACGGGGGCACTATATTTTAAAG 60.261 45.833 0.00 0.00 0.00 1.85
2811 6216 3.633065 GCACGGGGGCACTATATTTTAAA 59.367 43.478 0.00 0.00 0.00 1.52
2812 6217 3.117813 AGCACGGGGGCACTATATTTTAA 60.118 43.478 0.00 0.00 35.83 1.52
2813 6218 2.440253 AGCACGGGGGCACTATATTTTA 59.560 45.455 0.00 0.00 35.83 1.52
2814 6219 1.214424 AGCACGGGGGCACTATATTTT 59.786 47.619 0.00 0.00 35.83 1.82
2815 6220 0.843984 AGCACGGGGGCACTATATTT 59.156 50.000 0.00 0.00 35.83 1.40
2816 6221 0.843984 AAGCACGGGGGCACTATATT 59.156 50.000 0.00 0.00 35.83 1.28
2817 6222 0.843984 AAAGCACGGGGGCACTATAT 59.156 50.000 0.00 0.00 35.83 0.86
2818 6223 0.179468 GAAAGCACGGGGGCACTATA 59.821 55.000 0.00 0.00 35.83 1.31
2819 6224 1.077716 GAAAGCACGGGGGCACTAT 60.078 57.895 0.00 0.00 35.83 2.12
2820 6225 2.349755 GAAAGCACGGGGGCACTA 59.650 61.111 0.00 0.00 35.83 2.74
2821 6226 4.660938 GGAAAGCACGGGGGCACT 62.661 66.667 0.00 0.00 35.83 4.40
2824 6229 4.796495 ATCGGAAAGCACGGGGGC 62.796 66.667 0.00 0.00 0.00 5.80
2825 6230 2.824041 CATCGGAAAGCACGGGGG 60.824 66.667 0.00 0.00 0.00 5.40
2826 6231 2.046314 ACATCGGAAAGCACGGGG 60.046 61.111 0.00 0.00 0.00 5.73
2827 6232 0.174845 TAGACATCGGAAAGCACGGG 59.825 55.000 0.00 0.00 0.00 5.28
2828 6233 1.659098 GTTAGACATCGGAAAGCACGG 59.341 52.381 0.00 0.00 0.00 4.94
2829 6234 2.607187 AGTTAGACATCGGAAAGCACG 58.393 47.619 0.00 0.00 0.00 5.34
2830 6235 4.451096 TCAAAGTTAGACATCGGAAAGCAC 59.549 41.667 0.00 0.00 0.00 4.40
2831 6236 4.637276 TCAAAGTTAGACATCGGAAAGCA 58.363 39.130 0.00 0.00 0.00 3.91
2832 6237 5.351465 TGATCAAAGTTAGACATCGGAAAGC 59.649 40.000 0.00 0.00 0.00 3.51
2833 6238 6.968131 TGATCAAAGTTAGACATCGGAAAG 57.032 37.500 0.00 0.00 0.00 2.62
2834 6239 9.443323 TTTATGATCAAAGTTAGACATCGGAAA 57.557 29.630 0.00 0.00 0.00 3.13
2835 6240 9.613428 ATTTATGATCAAAGTTAGACATCGGAA 57.387 29.630 0.00 0.00 0.00 4.30
2836 6241 9.613428 AATTTATGATCAAAGTTAGACATCGGA 57.387 29.630 0.00 0.00 0.00 4.55
2847 6252 9.840427 CTCGTTGGTTAAATTTATGATCAAAGT 57.160 29.630 0.00 0.00 0.00 2.66
2851 6256 8.547894 CGATCTCGTTGGTTAAATTTATGATCA 58.452 33.333 0.00 0.00 34.11 2.92
2852 6257 8.761497 TCGATCTCGTTGGTTAAATTTATGATC 58.239 33.333 0.00 0.00 40.80 2.92
2853 6258 8.548721 GTCGATCTCGTTGGTTAAATTTATGAT 58.451 33.333 0.00 0.00 40.80 2.45
2854 6259 7.762615 AGTCGATCTCGTTGGTTAAATTTATGA 59.237 33.333 0.00 0.00 40.80 2.15
2855 6260 7.846107 CAGTCGATCTCGTTGGTTAAATTTATG 59.154 37.037 0.00 0.00 40.80 1.90
2856 6261 7.465513 GCAGTCGATCTCGTTGGTTAAATTTAT 60.466 37.037 0.00 0.00 40.80 1.40
2857 6262 6.183360 GCAGTCGATCTCGTTGGTTAAATTTA 60.183 38.462 0.00 0.00 40.80 1.40
2858 6263 5.390567 GCAGTCGATCTCGTTGGTTAAATTT 60.391 40.000 0.00 0.00 40.80 1.82
2859 6264 4.092968 GCAGTCGATCTCGTTGGTTAAATT 59.907 41.667 0.00 0.00 40.80 1.82
2860 6265 3.617263 GCAGTCGATCTCGTTGGTTAAAT 59.383 43.478 0.00 0.00 40.80 1.40
2861 6266 2.991190 GCAGTCGATCTCGTTGGTTAAA 59.009 45.455 0.00 0.00 40.80 1.52
2862 6267 2.602878 GCAGTCGATCTCGTTGGTTAA 58.397 47.619 0.00 0.00 40.80 2.01
2863 6268 1.466866 CGCAGTCGATCTCGTTGGTTA 60.467 52.381 0.00 0.00 40.80 2.85
2864 6269 0.732880 CGCAGTCGATCTCGTTGGTT 60.733 55.000 0.00 0.00 40.80 3.67
2865 6270 1.154016 CGCAGTCGATCTCGTTGGT 60.154 57.895 0.00 0.00 40.80 3.67
2866 6271 1.874019 CCGCAGTCGATCTCGTTGG 60.874 63.158 0.00 0.00 40.80 3.77
2867 6272 2.508891 GCCGCAGTCGATCTCGTTG 61.509 63.158 0.00 1.72 40.80 4.10
2868 6273 2.202623 GCCGCAGTCGATCTCGTT 60.203 61.111 0.00 0.00 40.80 3.85
2869 6274 4.538283 CGCCGCAGTCGATCTCGT 62.538 66.667 0.00 0.00 40.80 4.18
2871 6276 4.933064 CCCGCCGCAGTCGATCTC 62.933 72.222 0.00 0.00 38.10 2.75
2873 6278 4.933064 CTCCCGCCGCAGTCGATC 62.933 72.222 0.00 0.00 38.10 3.69
2876 6281 4.735132 TTTCTCCCGCCGCAGTCG 62.735 66.667 0.00 0.00 0.00 4.18
2877 6282 1.964373 TTTTTCTCCCGCCGCAGTC 60.964 57.895 0.00 0.00 0.00 3.51
2878 6283 2.112297 TTTTTCTCCCGCCGCAGT 59.888 55.556 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.