Multiple sequence alignment - TraesCS2B01G403100

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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 TraesCS2B01G403100 chr2B 100.000 2977 0 0 961 3937 571533529 571530553 0.000000e+00 5498.0
1 TraesCS2B01G403100 chr2B 100.000 627 0 0 1 627 571534489 571533863 0.000000e+00 1158.0
2 TraesCS2B01G403100 chr2B 85.915 71 7 3 3359 3427 572791190 572791121 5.460000e-09 73.1
3 TraesCS2B01G403100 chr2A 91.711 2449 88 51 968 3379 631969356 631966986 0.000000e+00 3291.0
4 TraesCS2B01G403100 chr2A 84.394 660 19 18 1 627 631970040 631969432 4.410000e-159 571.0
5 TraesCS2B01G403100 chr2A 87.532 385 30 9 3400 3768 631966742 631966360 2.810000e-116 429.0
6 TraesCS2B01G403100 chr2A 85.294 68 8 2 3361 3427 158594009 158594075 7.060000e-08 69.4
7 TraesCS2B01G403100 chr2D 90.962 2401 87 40 961 3330 486957513 486955212 0.000000e+00 3112.0
8 TraesCS2B01G403100 chr2D 87.612 783 48 19 1887 2658 643637232 643636488 0.000000e+00 863.0
9 TraesCS2B01G403100 chr2D 90.820 610 18 12 1 589 486958225 486957633 0.000000e+00 782.0
10 TraesCS2B01G403100 chr2D 86.622 299 18 10 3647 3937 486955096 486954812 1.060000e-80 311.0
11 TraesCS2B01G403100 chr2D 87.692 65 5 2 3389 3452 78527751 78527689 5.460000e-09 73.1
12 TraesCS2B01G403100 chr2D 88.525 61 5 2 3368 3427 506139969 506140028 5.460000e-09 73.1
13 TraesCS2B01G403100 chr2D 84.507 71 8 3 3359 3427 489409555 489409486 2.540000e-07 67.6
14 TraesCS2B01G403100 chr5D 88.590 780 41 20 1887 2658 365088062 365088801 0.000000e+00 904.0
15 TraesCS2B01G403100 chr7A 88.462 780 47 17 1887 2658 176279527 176278783 0.000000e+00 902.0
16 TraesCS2B01G403100 chr7A 88.333 780 48 17 1887 2658 670564400 670563656 0.000000e+00 896.0
17 TraesCS2B01G403100 chr3A 87.949 780 48 19 1887 2658 693453531 693452790 0.000000e+00 878.0
18 TraesCS2B01G403100 chrUn 87.786 786 42 21 1887 2653 116830642 116831392 0.000000e+00 870.0
19 TraesCS2B01G403100 chr3B 88.186 237 20 6 1864 2099 32282286 32282057 3.880000e-70 276.0
20 TraesCS2B01G403100 chr3B 83.854 192 16 7 2143 2334 32280465 32280289 6.770000e-38 169.0
21 TraesCS2B01G403100 chr6D 87.069 116 15 0 1241 1356 310523087 310522972 8.880000e-27 132.0
22 TraesCS2B01G403100 chr6D 90.909 55 4 1 3374 3427 8138007 8137953 5.460000e-09 73.1
23 TraesCS2B01G403100 chr6B 87.850 107 12 1 1241 1347 478753292 478753397 1.490000e-24 124.0
24 TraesCS2B01G403100 chr4D 90.909 55 4 1 3374 3427 208558563 208558617 5.460000e-09 73.1
25 TraesCS2B01G403100 chr1D 90.909 55 4 1 3374 3427 211693975 211693921 5.460000e-09 73.1
26 TraesCS2B01G403100 chr5A 87.097 62 6 2 3367 3427 325923655 325923595 7.060000e-08 69.4


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 TraesCS2B01G403100 chr2B 571530553 571534489 3936 True 3328.000000 5498 100.000 1 3937 2 chr2B.!!$R2 3936
1 TraesCS2B01G403100 chr2A 631966360 631970040 3680 True 1430.333333 3291 87.879 1 3768 3 chr2A.!!$R1 3767
2 TraesCS2B01G403100 chr2D 486954812 486958225 3413 True 1401.666667 3112 89.468 1 3937 3 chr2D.!!$R4 3936
3 TraesCS2B01G403100 chr2D 643636488 643637232 744 True 863.000000 863 87.612 1887 2658 1 chr2D.!!$R3 771
4 TraesCS2B01G403100 chr5D 365088062 365088801 739 False 904.000000 904 88.590 1887 2658 1 chr5D.!!$F1 771
5 TraesCS2B01G403100 chr7A 176278783 176279527 744 True 902.000000 902 88.462 1887 2658 1 chr7A.!!$R1 771
6 TraesCS2B01G403100 chr7A 670563656 670564400 744 True 896.000000 896 88.333 1887 2658 1 chr7A.!!$R2 771
7 TraesCS2B01G403100 chr3A 693452790 693453531 741 True 878.000000 878 87.949 1887 2658 1 chr3A.!!$R1 771
8 TraesCS2B01G403100 chrUn 116830642 116831392 750 False 870.000000 870 87.786 1887 2653 1 chrUn.!!$F1 766
9 TraesCS2B01G403100 chr3B 32280289 32282286 1997 True 222.500000 276 86.020 1864 2334 2 chr3B.!!$R1 470

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
569 622 0.035630 ACTGCTCACTCCCAAGCATC 60.036 55.0 0.00 0.0 46.69 3.91 F
572 625 0.106819 GCTCACTCCCAAGCATCCAT 60.107 55.0 0.00 0.0 38.42 3.41 F
1189 1252 0.179111 CTTCCATTCGCAGCTCGGTA 60.179 55.0 5.87 0.0 39.05 4.02 F
2800 4492 0.105246 ATAGGCCCTGAGCAGCTAGT 60.105 55.0 0.00 0.0 46.50 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2200 3864 0.247460 TCAGGAACAGCACGGATCAG 59.753 55.000 0.0 0.0 0.00 2.90 R
2557 4244 1.664321 AAGACCGAACCCGATCCGAG 61.664 60.000 0.0 0.0 38.22 4.63 R
2809 4501 1.003545 CACACAGCACAAAGGAGAACG 60.004 52.381 0.0 0.0 0.00 3.95 R
3769 5709 1.151777 ACGCTTGATATTCCCGTGCG 61.152 55.000 0.0 0.0 46.02 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
168 183 1.768684 GCCACTGTTCCCTGTCCAGA 61.769 60.000 0.00 0.00 0.00 3.86
169 184 0.322975 CCACTGTTCCCTGTCCAGAG 59.677 60.000 0.00 0.00 0.00 3.35
170 185 0.322975 CACTGTTCCCTGTCCAGAGG 59.677 60.000 0.00 0.00 0.00 3.69
181 196 0.106217 GTCCAGAGGGAGGAGAGGAG 60.106 65.000 0.00 0.00 46.12 3.69
182 197 0.253868 TCCAGAGGGAGGAGAGGAGA 60.254 60.000 0.00 0.00 38.64 3.71
183 198 0.185901 CCAGAGGGAGGAGAGGAGAG 59.814 65.000 0.00 0.00 35.59 3.20
184 199 0.185901 CAGAGGGAGGAGAGGAGAGG 59.814 65.000 0.00 0.00 0.00 3.69
185 200 0.998945 AGAGGGAGGAGAGGAGAGGG 60.999 65.000 0.00 0.00 0.00 4.30
186 201 2.018086 AGGGAGGAGAGGAGAGGGG 61.018 68.421 0.00 0.00 0.00 4.79
187 202 2.015726 GGGAGGAGAGGAGAGGGGA 61.016 68.421 0.00 0.00 0.00 4.81
188 203 1.541672 GGAGGAGAGGAGAGGGGAG 59.458 68.421 0.00 0.00 0.00 4.30
189 204 1.541672 GAGGAGAGGAGAGGGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
190 205 0.996762 GAGGAGAGGAGAGGGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
191 206 0.998945 AGGAGAGGAGAGGGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
192 207 0.996762 GGAGAGGAGAGGGGAGGAGA 60.997 65.000 0.00 0.00 0.00 3.71
193 208 0.478507 GAGAGGAGAGGGGAGGAGAG 59.521 65.000 0.00 0.00 0.00 3.20
301 316 1.673767 TCCCATTCCTTGCCTCTCTT 58.326 50.000 0.00 0.00 0.00 2.85
361 377 2.310538 GGATCCCGGCTTTCAAATCAT 58.689 47.619 0.00 0.00 0.00 2.45
375 391 4.143543 TCAAATCATCAGAGGCAACAACA 58.856 39.130 0.00 0.00 41.41 3.33
439 483 3.448301 GGAGTGCCCATCAAATCAAATCA 59.552 43.478 0.00 0.00 34.14 2.57
450 499 4.761739 TCAAATCAAATCACCTCACCTCAC 59.238 41.667 0.00 0.00 0.00 3.51
467 516 0.521735 CACCTCATCACGTCTCGTCA 59.478 55.000 0.00 0.00 38.32 4.35
485 534 9.258826 GTCTCGTCAACAAGACTAGAGTATATA 57.741 37.037 0.00 0.00 46.13 0.86
487 536 8.953368 TCGTCAACAAGACTAGAGTATATACA 57.047 34.615 15.18 0.00 45.32 2.29
489 538 7.792967 CGTCAACAAGACTAGAGTATATACACG 59.207 40.741 15.18 6.88 45.32 4.49
501 554 6.153000 AGAGTATATACACGTCCATTCATCCC 59.847 42.308 15.18 0.00 0.00 3.85
558 611 1.377725 CATCCCCACCACTGCTCAC 60.378 63.158 0.00 0.00 0.00 3.51
559 612 1.539869 ATCCCCACCACTGCTCACT 60.540 57.895 0.00 0.00 0.00 3.41
560 613 1.557269 ATCCCCACCACTGCTCACTC 61.557 60.000 0.00 0.00 0.00 3.51
561 614 2.348998 CCCACCACTGCTCACTCC 59.651 66.667 0.00 0.00 0.00 3.85
562 615 2.348998 CCACCACTGCTCACTCCC 59.651 66.667 0.00 0.00 0.00 4.30
563 616 2.519622 CCACCACTGCTCACTCCCA 61.520 63.158 0.00 0.00 0.00 4.37
564 617 1.451504 CACCACTGCTCACTCCCAA 59.548 57.895 0.00 0.00 0.00 4.12
565 618 0.604780 CACCACTGCTCACTCCCAAG 60.605 60.000 0.00 0.00 0.00 3.61
566 619 1.673665 CCACTGCTCACTCCCAAGC 60.674 63.158 0.00 0.00 39.02 4.01
567 620 1.071987 CACTGCTCACTCCCAAGCA 59.928 57.895 0.00 0.00 45.83 3.91
568 621 0.322277 CACTGCTCACTCCCAAGCAT 60.322 55.000 0.00 0.00 46.69 3.79
569 622 0.035630 ACTGCTCACTCCCAAGCATC 60.036 55.000 0.00 0.00 46.69 3.91
570 623 0.747283 CTGCTCACTCCCAAGCATCC 60.747 60.000 0.00 0.00 46.69 3.51
571 624 1.300963 GCTCACTCCCAAGCATCCA 59.699 57.895 0.00 0.00 38.42 3.41
572 625 0.106819 GCTCACTCCCAAGCATCCAT 60.107 55.000 0.00 0.00 38.42 3.41
1151 1214 3.114650 GGTACGTACGCCTCCTCC 58.885 66.667 16.72 5.29 0.00 4.30
1152 1215 1.750399 GGTACGTACGCCTCCTCCA 60.750 63.158 16.72 0.00 0.00 3.86
1153 1216 1.722636 GGTACGTACGCCTCCTCCAG 61.723 65.000 16.72 0.00 0.00 3.86
1154 1217 1.452651 TACGTACGCCTCCTCCAGG 60.453 63.158 16.72 0.00 46.82 4.45
1161 1224 3.478274 CCTCCTCCAGGCTCCAGC 61.478 72.222 0.00 0.00 34.56 4.85
1174 1237 4.120755 CCAGCCAGCCTCCCTTCC 62.121 72.222 0.00 0.00 0.00 3.46
1181 1244 2.272146 GCCTCCCTTCCATTCGCA 59.728 61.111 0.00 0.00 0.00 5.10
1182 1245 1.821332 GCCTCCCTTCCATTCGCAG 60.821 63.158 0.00 0.00 0.00 5.18
1186 1249 2.176273 CCCTTCCATTCGCAGCTCG 61.176 63.158 0.00 0.00 40.15 5.03
1189 1252 0.179111 CTTCCATTCGCAGCTCGGTA 60.179 55.000 5.87 0.00 39.05 4.02
1211 1278 1.171308 CTCGTTTCCACCCTCGTCTA 58.829 55.000 0.00 0.00 0.00 2.59
1213 1280 1.542915 TCGTTTCCACCCTCGTCTAAG 59.457 52.381 0.00 0.00 0.00 2.18
1220 1287 3.024547 CCACCCTCGTCTAAGAATCTCA 58.975 50.000 0.00 0.00 0.00 3.27
1236 1304 2.048222 CATGCTCGTCCGTGTGGT 60.048 61.111 0.00 0.00 36.30 4.16
1240 1308 3.036084 CTCGTCCGTGTGGTGTGC 61.036 66.667 0.00 0.00 36.30 4.57
1433 1501 2.303022 ACGGCCTCCTGGTATGAATATG 59.697 50.000 0.00 0.00 35.27 1.78
1504 1572 4.951715 TGAACTGATGGCAGATATTTGCTT 59.048 37.500 16.93 6.13 45.17 3.91
1536 1612 2.306805 ACTCCTGCAGGATGAAATGTCA 59.693 45.455 35.11 9.62 44.46 3.58
1735 1811 1.807142 GTAAGTGCCAAGCTCAGTTCC 59.193 52.381 0.00 0.00 0.00 3.62
1760 1836 2.797177 ACCATTCTTCTCTTCCTGCC 57.203 50.000 0.00 0.00 0.00 4.85
1765 1841 2.994995 TTCTCTTCCTGCCGCCGA 60.995 61.111 0.00 0.00 0.00 5.54
1776 1852 2.051882 CCGCCGATCGTACGTACC 60.052 66.667 19.67 5.33 36.19 3.34
1780 1856 1.723273 CCGATCGTACGTACCAGCA 59.277 57.895 19.67 2.19 0.00 4.41
1977 2068 1.202031 GCCGGTTGAATAGTTTGCTCG 60.202 52.381 1.90 0.00 0.00 5.03
1978 2069 1.202031 CCGGTTGAATAGTTTGCTCGC 60.202 52.381 0.00 0.00 0.00 5.03
1979 2070 1.732259 CGGTTGAATAGTTTGCTCGCT 59.268 47.619 0.00 0.00 0.00 4.93
1980 2071 2.222819 CGGTTGAATAGTTTGCTCGCTC 60.223 50.000 0.00 0.00 0.00 5.03
1984 2075 2.289382 TGAATAGTTTGCTCGCTCACCA 60.289 45.455 0.00 0.00 0.00 4.17
2167 3831 6.104877 ATACGACTGTAGGGGTACCAAATGA 61.105 44.000 15.35 0.00 41.31 2.57
2169 3833 9.930468 ATACGACTGTAGGGGTACCAAATGAGA 62.930 44.444 15.35 0.00 41.31 3.27
2200 3864 3.006247 GCACTTGTCTGATCTTTCTCCC 58.994 50.000 0.00 0.00 0.00 4.30
2348 4020 2.676839 CAAGTGAGTGATGATCAGTGGC 59.323 50.000 7.63 0.36 30.75 5.01
2378 4050 2.750712 GTTCCCCGTTTTAGCTTGCATA 59.249 45.455 0.00 0.00 0.00 3.14
2379 4051 3.290948 TCCCCGTTTTAGCTTGCATAT 57.709 42.857 0.00 0.00 0.00 1.78
2380 4052 4.425180 TCCCCGTTTTAGCTTGCATATA 57.575 40.909 0.00 0.00 0.00 0.86
2381 4053 4.980573 TCCCCGTTTTAGCTTGCATATAT 58.019 39.130 0.00 0.00 0.00 0.86
2557 4244 5.522456 TCTCATTCTCAACACACATTTTGC 58.478 37.500 0.00 0.00 0.00 3.68
2572 4259 2.845752 TTTGCTCGGATCGGGTTCGG 62.846 60.000 0.00 0.00 36.95 4.30
2621 4308 4.972286 TTTATCATCGATCGTGTGCATC 57.028 40.909 15.94 0.00 0.00 3.91
2738 4425 2.438392 AGGAGGCCCTAAAACCTAATCG 59.562 50.000 0.00 0.00 42.15 3.34
2743 4430 6.106648 AGGCCCTAAAACCTAATCGTATAC 57.893 41.667 0.00 0.00 33.38 1.47
2744 4431 5.842874 AGGCCCTAAAACCTAATCGTATACT 59.157 40.000 0.00 0.00 33.38 2.12
2800 4492 0.105246 ATAGGCCCTGAGCAGCTAGT 60.105 55.000 0.00 0.00 46.50 2.57
2809 4501 4.261825 CCCTGAGCAGCTAGTACTTATGTC 60.262 50.000 0.00 0.22 0.00 3.06
2810 4502 4.532276 CTGAGCAGCTAGTACTTATGTCG 58.468 47.826 0.00 0.00 0.00 4.35
2811 4503 3.945921 TGAGCAGCTAGTACTTATGTCGT 59.054 43.478 0.00 0.00 0.00 4.34
2829 4521 1.003545 CGTTCTCCTTTGTGCTGTGTG 60.004 52.381 0.00 0.00 0.00 3.82
2879 4572 0.803117 TCAAGGACAGTCTCTACGCG 59.197 55.000 3.53 3.53 0.00 6.01
2944 4637 2.400399 CACTCCGTTTTAGCGTCTTCA 58.600 47.619 0.00 0.00 0.00 3.02
3072 4773 6.988622 TTCGTTGTTTCTTCCTGTCTTTTA 57.011 33.333 0.00 0.00 0.00 1.52
3123 4824 1.131883 CAGCTAATGAGGTTGCTGTGC 59.868 52.381 0.00 0.00 45.31 4.57
3181 4882 3.535280 TCTAGTTGCCGCACATTATCA 57.465 42.857 0.00 0.00 0.00 2.15
3222 4923 3.836562 TCCTAACTCCTTACTTCGGCTTT 59.163 43.478 0.00 0.00 0.00 3.51
3223 4924 4.081807 TCCTAACTCCTTACTTCGGCTTTC 60.082 45.833 0.00 0.00 0.00 2.62
3224 4925 4.081586 CCTAACTCCTTACTTCGGCTTTCT 60.082 45.833 0.00 0.00 0.00 2.52
3225 4926 3.320673 ACTCCTTACTTCGGCTTTCTG 57.679 47.619 0.00 0.00 0.00 3.02
3360 5061 9.803315 CAACATGACACTAGTAATAAAGAGCTA 57.197 33.333 0.00 0.00 0.00 3.32
3387 5088 9.627123 AAATCATATTAACTCCATCCGAAAAGA 57.373 29.630 0.00 0.00 0.00 2.52
3392 5093 6.737254 TTAACTCCATCCGAAAAGATTGTC 57.263 37.500 0.00 0.00 0.00 3.18
3432 5357 4.138290 CGGATGTATCTAGACACCAGACT 58.862 47.826 0.00 0.00 30.52 3.24
3457 5383 5.198207 AGGGGTATAAAATTTGAGGAACCG 58.802 41.667 0.00 0.00 0.00 4.44
3503 5437 7.174946 AGCTAAAATCATAATGGTTATGTCCGG 59.825 37.037 0.00 0.00 42.77 5.14
3520 5454 5.123227 TGTCCGGGAATTTCTATTGCTAAG 58.877 41.667 0.00 0.00 33.09 2.18
3588 5525 7.759489 ATTGTAGATAAGTGTTTGCAAGGAA 57.241 32.000 0.00 0.00 0.00 3.36
3604 5541 4.785341 GCAAGGAACTAAGTCACGTGTTTG 60.785 45.833 16.51 7.10 38.49 2.93
3605 5542 4.395959 AGGAACTAAGTCACGTGTTTGA 57.604 40.909 16.51 0.00 36.02 2.69
3606 5543 4.957296 AGGAACTAAGTCACGTGTTTGAT 58.043 39.130 16.51 0.00 36.02 2.57
3637 5574 3.347216 GTTGGAGGCACACTTATCACAT 58.653 45.455 0.00 0.00 0.00 3.21
3661 5598 9.367160 CATGGTTGGGTAAATTAATCCTCTAAT 57.633 33.333 0.00 0.00 0.00 1.73
3679 5616 5.175859 TCTAATGACCTCCTAAAAAGTGCG 58.824 41.667 0.00 0.00 0.00 5.34
3769 5709 7.145932 ACTTAACCAAACAGACAATCATAGC 57.854 36.000 0.00 0.00 0.00 2.97
3770 5710 4.685169 AACCAAACAGACAATCATAGCG 57.315 40.909 0.00 0.00 0.00 4.26
3772 5712 2.419673 CCAAACAGACAATCATAGCGCA 59.580 45.455 11.47 0.00 0.00 6.09
3773 5713 3.419915 CAAACAGACAATCATAGCGCAC 58.580 45.455 11.47 0.00 0.00 5.34
3774 5714 1.280982 ACAGACAATCATAGCGCACG 58.719 50.000 11.47 0.00 0.00 5.34
3775 5715 0.578683 CAGACAATCATAGCGCACGG 59.421 55.000 11.47 0.00 0.00 4.94
3776 5716 0.530650 AGACAATCATAGCGCACGGG 60.531 55.000 11.47 0.00 0.00 5.28
3777 5717 0.529773 GACAATCATAGCGCACGGGA 60.530 55.000 11.47 1.18 0.00 5.14
3778 5718 0.107897 ACAATCATAGCGCACGGGAA 60.108 50.000 11.47 0.00 0.00 3.97
3779 5719 1.229428 CAATCATAGCGCACGGGAAT 58.771 50.000 11.47 0.00 0.00 3.01
3780 5720 2.224185 ACAATCATAGCGCACGGGAATA 60.224 45.455 11.47 0.00 0.00 1.75
3781 5721 3.002791 CAATCATAGCGCACGGGAATAT 58.997 45.455 11.47 0.00 0.00 1.28
3782 5722 2.363788 TCATAGCGCACGGGAATATC 57.636 50.000 11.47 0.00 0.00 1.63
3783 5723 1.616374 TCATAGCGCACGGGAATATCA 59.384 47.619 11.47 0.00 0.00 2.15
3784 5724 2.036604 TCATAGCGCACGGGAATATCAA 59.963 45.455 11.47 0.00 0.00 2.57
3798 5738 6.347402 CGGGAATATCAAGCGTAACCAAATAG 60.347 42.308 0.00 0.00 0.00 1.73
3801 5741 9.431887 GGAATATCAAGCGTAACCAAATAGATA 57.568 33.333 0.00 0.00 0.00 1.98
3916 5862 1.872952 GCATTTCAACTGGGCCAAAAC 59.127 47.619 8.04 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 93 3.752339 GAAAAGCGGGCAGGGCAG 61.752 66.667 0.00 0.00 0.00 4.85
89 94 4.594854 TGAAAAGCGGGCAGGGCA 62.595 61.111 0.00 0.00 0.00 5.36
168 183 2.018086 CCCCTCTCCTCTCCTCCCT 61.018 68.421 0.00 0.00 0.00 4.20
169 184 2.015726 TCCCCTCTCCTCTCCTCCC 61.016 68.421 0.00 0.00 0.00 4.30
170 185 1.541672 CTCCCCTCTCCTCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
181 196 1.152546 GCTCTCCTCTCCTCCCCTC 60.153 68.421 0.00 0.00 0.00 4.30
182 197 3.024217 GCTCTCCTCTCCTCCCCT 58.976 66.667 0.00 0.00 0.00 4.79
183 198 2.520741 CGCTCTCCTCTCCTCCCC 60.521 72.222 0.00 0.00 0.00 4.81
184 199 2.520741 CCGCTCTCCTCTCCTCCC 60.521 72.222 0.00 0.00 0.00 4.30
185 200 2.520741 CCCGCTCTCCTCTCCTCC 60.521 72.222 0.00 0.00 0.00 4.30
186 201 1.826487 GTCCCGCTCTCCTCTCCTC 60.826 68.421 0.00 0.00 0.00 3.71
187 202 2.277404 GTCCCGCTCTCCTCTCCT 59.723 66.667 0.00 0.00 0.00 3.69
188 203 2.124693 CAGTCCCGCTCTCCTCTCC 61.125 68.421 0.00 0.00 0.00 3.71
189 204 2.124693 CCAGTCCCGCTCTCCTCTC 61.125 68.421 0.00 0.00 0.00 3.20
190 205 2.043450 CCAGTCCCGCTCTCCTCT 60.043 66.667 0.00 0.00 0.00 3.69
191 206 2.043852 TCCAGTCCCGCTCTCCTC 60.044 66.667 0.00 0.00 0.00 3.71
192 207 2.363147 GTCCAGTCCCGCTCTCCT 60.363 66.667 0.00 0.00 0.00 3.69
193 208 3.827898 CGTCCAGTCCCGCTCTCC 61.828 72.222 0.00 0.00 0.00 3.71
361 377 1.295792 GTCGTTGTTGTTGCCTCTGA 58.704 50.000 0.00 0.00 0.00 3.27
375 391 1.134075 CGGATCTGTCGTCGTCGTT 59.866 57.895 1.33 0.00 38.33 3.85
439 483 1.270907 GTGATGAGGTGAGGTGAGGT 58.729 55.000 0.00 0.00 0.00 3.85
450 499 1.068541 TGTTGACGAGACGTGATGAGG 60.069 52.381 0.00 0.00 41.37 3.86
467 516 7.772292 TGGACGTGTATATACTCTAGTCTTGTT 59.228 37.037 13.89 0.00 0.00 2.83
485 534 0.541863 GGAGGGATGAATGGACGTGT 59.458 55.000 0.00 0.00 0.00 4.49
487 536 1.345715 GGGGAGGGATGAATGGACGT 61.346 60.000 0.00 0.00 0.00 4.34
489 538 0.183731 GTGGGGAGGGATGAATGGAC 59.816 60.000 0.00 0.00 0.00 4.02
501 554 2.359975 GGAAACGGCAGTGGGGAG 60.360 66.667 0.00 0.00 0.00 4.30
558 611 1.152368 GGGGATGGATGCTTGGGAG 59.848 63.158 0.00 0.00 0.00 4.30
559 612 1.309013 AGGGGATGGATGCTTGGGA 60.309 57.895 0.00 0.00 0.00 4.37
560 613 1.152368 GAGGGGATGGATGCTTGGG 59.848 63.158 0.00 0.00 0.00 4.12
561 614 0.110104 GAGAGGGGATGGATGCTTGG 59.890 60.000 0.00 0.00 0.00 3.61
562 615 0.110104 GGAGAGGGGATGGATGCTTG 59.890 60.000 0.00 0.00 0.00 4.01
563 616 0.029267 AGGAGAGGGGATGGATGCTT 60.029 55.000 0.00 0.00 0.00 3.91
564 617 0.473501 GAGGAGAGGGGATGGATGCT 60.474 60.000 0.00 0.00 0.00 3.79
565 618 0.473501 AGAGGAGAGGGGATGGATGC 60.474 60.000 0.00 0.00 0.00 3.91
566 619 1.643310 GAGAGGAGAGGGGATGGATG 58.357 60.000 0.00 0.00 0.00 3.51
567 620 0.491371 GGAGAGGAGAGGGGATGGAT 59.509 60.000 0.00 0.00 0.00 3.41
568 621 0.631998 AGGAGAGGAGAGGGGATGGA 60.632 60.000 0.00 0.00 0.00 3.41
569 622 0.178935 GAGGAGAGGAGAGGGGATGG 60.179 65.000 0.00 0.00 0.00 3.51
570 623 0.859760 AGAGGAGAGGAGAGGGGATG 59.140 60.000 0.00 0.00 0.00 3.51
571 624 1.158007 GAGAGGAGAGGAGAGGGGAT 58.842 60.000 0.00 0.00 0.00 3.85
572 625 0.996762 GGAGAGGAGAGGAGAGGGGA 60.997 65.000 0.00 0.00 0.00 4.81
1144 1207 3.478274 GCTGGAGCCTGGAGGAGG 61.478 72.222 0.00 0.00 46.13 4.30
1155 1218 3.013932 AAGGGAGGCTGGCTGGAG 61.014 66.667 9.06 0.00 0.00 3.86
1156 1219 3.011517 GAAGGGAGGCTGGCTGGA 61.012 66.667 9.06 0.00 0.00 3.86
1157 1220 4.120755 GGAAGGGAGGCTGGCTGG 62.121 72.222 9.06 0.00 0.00 4.85
1158 1221 2.220786 AATGGAAGGGAGGCTGGCTG 62.221 60.000 9.06 0.00 0.00 4.85
1159 1222 1.931007 GAATGGAAGGGAGGCTGGCT 61.931 60.000 2.24 2.24 0.00 4.75
1160 1223 1.454663 GAATGGAAGGGAGGCTGGC 60.455 63.158 0.00 0.00 0.00 4.85
1161 1224 1.153086 CGAATGGAAGGGAGGCTGG 60.153 63.158 0.00 0.00 0.00 4.85
1162 1225 1.821332 GCGAATGGAAGGGAGGCTG 60.821 63.158 0.00 0.00 0.00 4.85
1163 1226 2.262774 CTGCGAATGGAAGGGAGGCT 62.263 60.000 0.00 0.00 0.00 4.58
1164 1227 1.821332 CTGCGAATGGAAGGGAGGC 60.821 63.158 0.00 0.00 0.00 4.70
1170 1233 0.179111 TACCGAGCTGCGAATGGAAG 60.179 55.000 0.00 0.00 44.57 3.46
1174 1237 2.860628 GCGTACCGAGCTGCGAATG 61.861 63.158 0.00 0.00 44.57 2.67
1182 1245 2.157073 GGAAACGAGCGTACCGAGC 61.157 63.158 0.00 0.00 0.00 5.03
1186 1249 1.739196 GGGTGGAAACGAGCGTACC 60.739 63.158 10.64 10.64 0.00 3.34
1189 1252 2.342648 GAGGGTGGAAACGAGCGT 59.657 61.111 0.00 0.00 0.00 5.07
1211 1278 1.478510 ACGGACGAGCATGAGATTCTT 59.521 47.619 0.00 0.00 0.00 2.52
1213 1280 1.203928 CACGGACGAGCATGAGATTC 58.796 55.000 0.00 0.00 0.00 2.52
1220 1287 2.048222 CACCACACGGACGAGCAT 60.048 61.111 0.00 0.00 35.59 3.79
1433 1501 7.605449 TCCAACGCATAATAATAGGTAGGTAC 58.395 38.462 0.00 0.00 0.00 3.34
1504 1572 4.157246 TCCTGCAGGAGTCAAGTTAAGTA 58.843 43.478 32.00 3.90 39.78 2.24
1536 1612 2.125106 GACGGCGCTTGGAAGGAT 60.125 61.111 6.90 0.00 0.00 3.24
1539 1615 3.181967 CTCGACGGCGCTTGGAAG 61.182 66.667 5.31 0.00 37.46 3.46
1765 1841 3.012518 ACTAGTTGCTGGTACGTACGAT 58.987 45.455 24.41 8.93 0.00 3.73
1776 1852 2.498167 AGGTGCTTTGACTAGTTGCTG 58.502 47.619 0.00 0.00 0.00 4.41
1780 1856 3.503748 GCATCAAGGTGCTTTGACTAGTT 59.496 43.478 0.00 0.00 39.68 2.24
1885 1975 4.450053 AGAGACAGAATGCATAAAGAGGC 58.550 43.478 0.00 0.00 42.53 4.70
1977 2068 2.432510 AGGTACTATTGAGCTGGTGAGC 59.567 50.000 0.00 0.00 41.54 4.26
1978 2069 4.744795 AAGGTACTATTGAGCTGGTGAG 57.255 45.455 0.00 0.00 38.49 3.51
1979 2070 5.221843 ACAAAAGGTACTATTGAGCTGGTGA 60.222 40.000 0.00 0.00 38.49 4.02
1980 2071 5.003804 ACAAAAGGTACTATTGAGCTGGTG 58.996 41.667 0.00 0.00 38.49 4.17
1984 2075 4.020485 ACGGACAAAAGGTACTATTGAGCT 60.020 41.667 11.10 0.00 38.49 4.09
2021 2113 1.610038 GTTAACGTTGGAGTTTGGGGG 59.390 52.381 11.99 0.00 35.70 5.40
2065 2175 7.490657 TTTAGTTTAGTTCTCCTATGCCTCA 57.509 36.000 0.00 0.00 0.00 3.86
2096 2212 6.946340 TGTTTCTGATTCCTAATGCTCACTA 58.054 36.000 0.00 0.00 0.00 2.74
2167 3831 1.376424 CAAGTGCATCCTGGCGTCT 60.376 57.895 0.00 0.00 36.28 4.18
2169 3833 1.672356 GACAAGTGCATCCTGGCGT 60.672 57.895 0.00 0.00 36.28 5.68
2200 3864 0.247460 TCAGGAACAGCACGGATCAG 59.753 55.000 0.00 0.00 0.00 2.90
2348 4020 4.571176 GCTAAAACGGGGAACTAGAATGAG 59.429 45.833 0.00 0.00 0.00 2.90
2378 4050 5.443283 TGCATTTTGCCAGAGAGAAGATAT 58.557 37.500 0.00 0.00 44.23 1.63
2379 4051 4.847198 TGCATTTTGCCAGAGAGAAGATA 58.153 39.130 0.00 0.00 44.23 1.98
2380 4052 3.693807 TGCATTTTGCCAGAGAGAAGAT 58.306 40.909 0.00 0.00 44.23 2.40
2381 4053 3.144657 TGCATTTTGCCAGAGAGAAGA 57.855 42.857 0.00 0.00 44.23 2.87
2557 4244 1.664321 AAGACCGAACCCGATCCGAG 61.664 60.000 0.00 0.00 38.22 4.63
2621 4308 1.753073 GGAAAATGAGCCCACTGATGG 59.247 52.381 0.00 0.00 46.81 3.51
2738 4425 5.936686 TCTGCACGGACATAGTAGTATAC 57.063 43.478 0.00 0.00 43.47 1.47
2743 4430 4.036852 TCTGATTCTGCACGGACATAGTAG 59.963 45.833 0.00 0.00 0.00 2.57
2744 4431 3.951680 TCTGATTCTGCACGGACATAGTA 59.048 43.478 0.00 0.00 0.00 1.82
2800 4492 4.927425 GCACAAAGGAGAACGACATAAGTA 59.073 41.667 0.00 0.00 0.00 2.24
2809 4501 1.003545 CACACAGCACAAAGGAGAACG 60.004 52.381 0.00 0.00 0.00 3.95
2810 4502 1.268743 GCACACAGCACAAAGGAGAAC 60.269 52.381 0.00 0.00 44.79 3.01
2811 4503 1.024271 GCACACAGCACAAAGGAGAA 58.976 50.000 0.00 0.00 44.79 2.87
2829 4521 4.208686 CCCAGCTCCGTCCTACGC 62.209 72.222 0.00 0.00 40.91 4.42
3072 4773 5.435545 ACATATAGGACTAGGGAAAGGGT 57.564 43.478 0.00 0.00 0.00 4.34
3123 4824 5.059833 GTCCATAAGATAAGAGGTGGCAAG 58.940 45.833 0.00 0.00 0.00 4.01
3222 4923 7.339466 TCAGCAGACATGTAATTAGTAGACAGA 59.661 37.037 0.00 0.00 0.00 3.41
3223 4924 7.484140 TCAGCAGACATGTAATTAGTAGACAG 58.516 38.462 0.00 0.00 0.00 3.51
3224 4925 7.404671 TCAGCAGACATGTAATTAGTAGACA 57.595 36.000 0.00 0.00 0.00 3.41
3225 4926 8.879342 ATTCAGCAGACATGTAATTAGTAGAC 57.121 34.615 0.00 0.00 0.00 2.59
3258 4959 4.554723 CGAAGGATAAAAATCCCGCACATC 60.555 45.833 0.75 0.00 41.65 3.06
3369 5070 6.472887 AGACAATCTTTTCGGATGGAGTTAA 58.527 36.000 0.00 0.00 0.00 2.01
3371 5072 4.911390 AGACAATCTTTTCGGATGGAGTT 58.089 39.130 0.00 0.00 0.00 3.01
3379 5080 7.584987 AGACAAATGTAAGACAATCTTTTCGG 58.415 34.615 0.00 0.00 37.89 4.30
3387 5088 8.692710 TCCGTATCTAGACAAATGTAAGACAAT 58.307 33.333 0.00 0.00 0.00 2.71
3427 5352 6.543831 CCTCAAATTTTATACCCCTCAGTCTG 59.456 42.308 0.00 0.00 0.00 3.51
3432 5357 6.192044 GGTTCCTCAAATTTTATACCCCTCA 58.808 40.000 0.00 0.00 0.00 3.86
3492 5426 5.278315 GCAATAGAAATTCCCGGACATAACC 60.278 44.000 0.73 0.00 0.00 2.85
3557 5491 8.841300 TGCAAACACTTATCTACAATACAAACA 58.159 29.630 0.00 0.00 0.00 2.83
3570 5506 7.041372 TGACTTAGTTCCTTGCAAACACTTATC 60.041 37.037 0.00 2.84 0.00 1.75
3578 5514 3.311322 CACGTGACTTAGTTCCTTGCAAA 59.689 43.478 10.90 0.00 0.00 3.68
3588 5525 8.373048 TGAATTTATCAAACACGTGACTTAGT 57.627 30.769 25.01 9.10 34.30 2.24
3604 5541 3.381590 GTGCCTCCAACCCTGAATTTATC 59.618 47.826 0.00 0.00 0.00 1.75
3605 5542 3.245586 TGTGCCTCCAACCCTGAATTTAT 60.246 43.478 0.00 0.00 0.00 1.40
3606 5543 2.109128 TGTGCCTCCAACCCTGAATTTA 59.891 45.455 0.00 0.00 0.00 1.40
3637 5574 8.561769 TCATTAGAGGATTAATTTACCCAACCA 58.438 33.333 0.00 0.00 0.00 3.67
3661 5598 2.103432 TGACGCACTTTTTAGGAGGTCA 59.897 45.455 0.00 0.00 0.00 4.02
3769 5709 1.151777 ACGCTTGATATTCCCGTGCG 61.152 55.000 0.00 0.00 46.02 5.34
3770 5710 1.860676 TACGCTTGATATTCCCGTGC 58.139 50.000 0.00 0.00 33.79 5.34
3772 5712 2.168936 TGGTTACGCTTGATATTCCCGT 59.831 45.455 0.00 0.00 36.07 5.28
3773 5713 2.828877 TGGTTACGCTTGATATTCCCG 58.171 47.619 0.00 0.00 0.00 5.14
3774 5714 5.767816 ATTTGGTTACGCTTGATATTCCC 57.232 39.130 0.00 0.00 0.00 3.97
3775 5715 7.724305 TCTATTTGGTTACGCTTGATATTCC 57.276 36.000 0.00 0.00 0.00 3.01
3780 5720 9.772973 TGTTATATCTATTTGGTTACGCTTGAT 57.227 29.630 0.00 0.00 0.00 2.57
3781 5721 9.602568 TTGTTATATCTATTTGGTTACGCTTGA 57.397 29.630 0.00 0.00 0.00 3.02
3837 5777 9.095065 GGTCTTACGATGTGATTAACTACATTT 57.905 33.333 7.59 2.71 37.63 2.32
3855 5801 6.696441 AACTAGATGTCTTAGGGTCTTACG 57.304 41.667 0.00 0.00 0.00 3.18
3859 5805 7.741554 ATCAAAACTAGATGTCTTAGGGTCT 57.258 36.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.