Multiple sequence alignment - TraesCS2D01G385800

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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 TraesCS2D01G385800 chr2D 100.000 6963 0 0 1 6963 490617816 490624778 0.000000e+00 12859.0
1 TraesCS2D01G385800 chr2D 97.505 3527 81 7 3440 6963 178318106 178314584 0.000000e+00 6019.0
2 TraesCS2D01G385800 chr2D 87.997 1258 109 25 2213 3440 490567981 490569226 0.000000e+00 1448.0
3 TraesCS2D01G385800 chr2D 89.281 737 42 12 2684 3410 490644167 490644876 0.000000e+00 889.0
4 TraesCS2D01G385800 chr2D 87.048 525 49 6 825 1333 490564809 490565330 6.060000e-160 575.0
5 TraesCS2D01G385800 chr2D 88.591 298 28 4 1912 2206 490567590 490567884 2.390000e-94 357.0
6 TraesCS2D01G385800 chr2D 84.123 359 42 7 2390 2746 490130705 490130360 4.020000e-87 333.0
7 TraesCS2D01G385800 chr2D 81.108 397 44 13 404 780 490564346 490564731 8.840000e-74 289.0
8 TraesCS2D01G385800 chr2D 84.345 313 18 18 2213 2510 490569040 490569336 1.910000e-70 278.0
9 TraesCS2D01G385800 chr2D 84.454 238 28 6 1975 2206 490568566 490568800 7.030000e-55 226.0
10 TraesCS2D01G385800 chr2D 79.693 261 42 5 1402 1654 490568778 490569035 2.000000e-40 178.0
11 TraesCS2D01G385800 chr2D 88.506 87 7 3 1827 1911 568755192 568755107 1.240000e-17 102.0
12 TraesCS2D01G385800 chr4D 97.822 3535 67 10 3436 6963 387341605 387345136 0.000000e+00 6093.0
13 TraesCS2D01G385800 chr4D 85.417 96 7 3 1823 1911 253767550 253767455 7.440000e-15 93.5
14 TraesCS2D01G385800 chr7D 97.649 3530 72 11 3439 6963 42860964 42864487 0.000000e+00 6048.0
15 TraesCS2D01G385800 chr7D 97.620 3530 73 9 3440 6963 246594428 246590904 0.000000e+00 6043.0
16 TraesCS2D01G385800 chr7D 97.534 3528 79 7 3440 6963 87521794 87518271 0.000000e+00 6026.0
17 TraesCS2D01G385800 chr7D 97.506 3528 81 6 3440 6963 282916052 282912528 0.000000e+00 6021.0
18 TraesCS2D01G385800 chr7D 96.721 61 1 1 1 61 606444938 606444997 4.440000e-17 100.0
19 TraesCS2D01G385800 chr7D 87.500 88 3 4 1829 1909 529689603 529689689 2.070000e-15 95.3
20 TraesCS2D01G385800 chr5D 97.563 3529 75 9 3438 6963 132316564 132313044 0.000000e+00 6030.0
21 TraesCS2D01G385800 chr5D 97.477 3528 81 8 3440 6963 272639040 272642563 0.000000e+00 6015.0
22 TraesCS2D01G385800 chr5D 96.875 64 2 0 1 64 462463902 462463839 2.660000e-19 108.0
23 TraesCS2D01G385800 chr5D 100.000 55 0 0 1 55 408359874 408359928 1.240000e-17 102.0
24 TraesCS2D01G385800 chr5D 87.097 93 6 2 1823 1910 115124593 115124502 4.440000e-17 100.0
25 TraesCS2D01G385800 chr3D 97.477 3528 83 6 3439 6963 543561035 543564559 0.000000e+00 6017.0
26 TraesCS2D01G385800 chr2B 90.623 1749 91 19 110 1832 575114681 575116382 0.000000e+00 2254.0
27 TraesCS2D01G385800 chr2B 92.812 960 35 15 1908 2847 575116381 575117326 0.000000e+00 1360.0
28 TraesCS2D01G385800 chr2B 89.958 946 61 12 404 1333 574708486 574709413 0.000000e+00 1190.0
29 TraesCS2D01G385800 chr2B 84.478 670 70 20 2213 2870 574663995 574664642 1.270000e-176 630.0
30 TraesCS2D01G385800 chr2B 79.979 939 117 27 925 1830 574661022 574661922 1.650000e-175 627.0
31 TraesCS2D01G385800 chr2B 86.364 550 50 14 2838 3369 574710986 574711528 1.680000e-160 577.0
32 TraesCS2D01G385800 chr2B 92.199 282 16 2 110 386 574707821 574708101 1.820000e-105 394.0
33 TraesCS2D01G385800 chr2B 88.485 165 13 5 617 780 574660667 574660826 1.980000e-45 195.0
34 TraesCS2D01G385800 chr2B 80.077 261 41 5 1402 1654 574711153 574711410 4.290000e-42 183.0
35 TraesCS2D01G385800 chr2B 96.970 99 3 0 3342 3440 574711529 574711627 4.320000e-37 167.0
36 TraesCS2D01G385800 chr2B 96.774 62 2 0 1 62 570173374 570173313 3.440000e-18 104.0
37 TraesCS2D01G385800 chr2B 92.308 65 5 0 53 117 574707743 574707807 7.440000e-15 93.5
38 TraesCS2D01G385800 chr2A 90.814 1437 66 23 437 1833 634598676 634600086 0.000000e+00 1862.0
39 TraesCS2D01G385800 chr2A 94.243 1216 53 11 1971 3172 634600989 634602201 0.000000e+00 1842.0
40 TraesCS2D01G385800 chr2A 95.459 1079 33 10 1904 2967 634600087 634601164 0.000000e+00 1707.0
41 TraesCS2D01G385800 chr2A 87.015 1186 110 26 2213 3366 634098640 634099813 0.000000e+00 1297.0
42 TraesCS2D01G385800 chr2A 85.333 525 60 5 825 1333 634091433 634091956 1.720000e-145 527.0
43 TraesCS2D01G385800 chr2A 85.924 341 40 8 2403 2739 634602477 634602813 2.390000e-94 357.0
44 TraesCS2D01G385800 chr2A 87.584 298 31 4 1912 2206 634098249 634098543 2.410000e-89 340.0
45 TraesCS2D01G385800 chr2A 81.980 394 42 11 404 780 634090974 634091355 2.440000e-79 307.0
46 TraesCS2D01G385800 chr2A 86.760 287 19 6 110 386 634597871 634598148 1.140000e-77 302.0
47 TraesCS2D01G385800 chr2A 83.613 238 30 6 1975 2206 634099229 634099463 1.520000e-51 215.0
48 TraesCS2D01G385800 chr2A 80.077 261 41 5 1402 1654 634099441 634099698 4.290000e-42 183.0
49 TraesCS2D01G385800 chr2A 83.422 187 24 5 2799 2980 634600158 634600342 4.320000e-37 167.0
50 TraesCS2D01G385800 chr1A 90.640 203 12 3 148 345 512490586 512490386 5.360000e-66 263.0
51 TraesCS2D01G385800 chr5B 87.179 195 20 1 153 342 610130443 610130637 4.230000e-52 217.0
52 TraesCS2D01G385800 chr5B 92.857 70 2 2 1 70 473611012 473610946 1.600000e-16 99.0
53 TraesCS2D01G385800 chrUn 81.768 181 25 5 2394 2566 259673171 259672991 2.020000e-30 145.0
54 TraesCS2D01G385800 chrUn 100.000 55 0 0 1 55 30075309 30075363 1.240000e-17 102.0
55 TraesCS2D01G385800 chrUn 84.783 92 9 2 1823 1909 16761851 16761942 3.460000e-13 87.9
56 TraesCS2D01G385800 chr6A 92.208 77 5 1 1820 1895 511530087 511530163 2.660000e-19 108.0
57 TraesCS2D01G385800 chr1B 100.000 56 0 0 1 56 33006472 33006417 3.440000e-18 104.0
58 TraesCS2D01G385800 chr1B 92.647 68 3 2 1 66 32873350 32873417 5.750000e-16 97.1
59 TraesCS2D01G385800 chr7B 89.412 85 4 1 1830 1909 203031544 203031460 1.240000e-17 102.0
60 TraesCS2D01G385800 chr7B 87.805 82 9 1 1827 1907 254488573 254488492 2.070000e-15 95.3
61 TraesCS2D01G385800 chr1D 100.000 55 0 0 1 55 469464409 469464463 1.240000e-17 102.0
62 TraesCS2D01G385800 chr3A 85.567 97 6 5 1823 1912 17365047 17364952 2.070000e-15 95.3
63 TraesCS2D01G385800 chr6D 100.000 29 0 0 1401 1429 37451177 37451205 4.000000e-03 54.7


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 TraesCS2D01G385800 chr2D 490617816 490624778 6962 False 12859.000000 12859 100.00000 1 6963 1 chr2D.!!$F1 6962
1 TraesCS2D01G385800 chr2D 178314584 178318106 3522 True 6019.000000 6019 97.50500 3440 6963 1 chr2D.!!$R1 3523
2 TraesCS2D01G385800 chr2D 490644167 490644876 709 False 889.000000 889 89.28100 2684 3410 1 chr2D.!!$F2 726
3 TraesCS2D01G385800 chr2D 490564346 490569336 4990 False 478.714286 1448 84.74800 404 3440 7 chr2D.!!$F3 3036
4 TraesCS2D01G385800 chr4D 387341605 387345136 3531 False 6093.000000 6093 97.82200 3436 6963 1 chr4D.!!$F1 3527
5 TraesCS2D01G385800 chr7D 42860964 42864487 3523 False 6048.000000 6048 97.64900 3439 6963 1 chr7D.!!$F1 3524
6 TraesCS2D01G385800 chr7D 246590904 246594428 3524 True 6043.000000 6043 97.62000 3440 6963 1 chr7D.!!$R2 3523
7 TraesCS2D01G385800 chr7D 87518271 87521794 3523 True 6026.000000 6026 97.53400 3440 6963 1 chr7D.!!$R1 3523
8 TraesCS2D01G385800 chr7D 282912528 282916052 3524 True 6021.000000 6021 97.50600 3440 6963 1 chr7D.!!$R3 3523
9 TraesCS2D01G385800 chr5D 132313044 132316564 3520 True 6030.000000 6030 97.56300 3438 6963 1 chr5D.!!$R2 3525
10 TraesCS2D01G385800 chr5D 272639040 272642563 3523 False 6015.000000 6015 97.47700 3440 6963 1 chr5D.!!$F1 3523
11 TraesCS2D01G385800 chr3D 543561035 543564559 3524 False 6017.000000 6017 97.47700 3439 6963 1 chr3D.!!$F1 3524
12 TraesCS2D01G385800 chr2B 575114681 575117326 2645 False 1807.000000 2254 91.71750 110 2847 2 chr2B.!!$F3 2737
13 TraesCS2D01G385800 chr2B 574660667 574664642 3975 False 484.000000 630 84.31400 617 2870 3 chr2B.!!$F1 2253
14 TraesCS2D01G385800 chr2B 574707743 574711627 3884 False 434.083333 1190 89.64600 53 3440 6 chr2B.!!$F2 3387
15 TraesCS2D01G385800 chr2A 634597871 634602813 4942 False 1039.500000 1862 89.43700 110 3172 6 chr2A.!!$F3 3062
16 TraesCS2D01G385800 chr2A 634098249 634099813 1564 False 508.750000 1297 84.57225 1402 3366 4 chr2A.!!$F2 1964
17 TraesCS2D01G385800 chr2A 634090974 634091956 982 False 417.000000 527 83.65650 404 1333 2 chr2A.!!$F1 929

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
52 53 0.396139 TAGGGTGCGATTCCGGTAGT 60.396 55.000 0.0 0.0 36.06 2.73 F
1360 2295 0.252513 TCCACGGAAGAAGGATGGGA 60.253 55.000 0.0 0.0 34.81 4.37 F
1907 4359 0.702902 TCTTACAGGACGGAGGGAGT 59.297 55.000 0.0 0.0 0.00 3.85 F
1910 4362 1.293062 TACAGGACGGAGGGAGTAGT 58.707 55.000 0.0 0.0 0.00 2.73 F
3247 7191 0.856982 TGGAGGAAAAAGGGAAGCCA 59.143 50.000 0.0 0.0 0.00 4.75 F
3692 7668 0.247736 GATCCAGCCGAGTGTTGAGT 59.752 55.000 0.0 0.0 0.00 3.41 F
4729 8715 1.348036 AGTACCTTTGGAGACACCTGC 59.652 52.381 0.0 0.0 42.67 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1368 2303 0.247736 CTGAAGTAGCACGGGAAGCT 59.752 55.000 0.00 0.0 45.77 3.74 R
3236 7177 0.991920 TCCTTCGATGGCTTCCCTTT 59.008 50.000 12.42 0.0 0.00 3.11 R
3247 7191 1.220206 CACAGGCAGCTCCTTCGAT 59.780 57.895 2.32 0.0 44.75 3.59 R
3433 7409 2.165030 ACTACGTTCCCCAACAGATACG 59.835 50.000 0.00 0.0 32.14 3.06 R
4316 8302 0.390209 GTAGGGTCCGCACGCTTAAA 60.390 55.000 0.00 0.0 43.11 1.52 R
5133 9123 4.307259 TGAAGGAAATATGCCCTAGAGGT 58.693 43.478 0.00 0.0 38.26 3.85 R
6654 10808 4.603131 AGTGGTACGGTAATCCTGTTCTA 58.397 43.478 0.00 0.0 0.00 2.10 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
47 48 3.642755 GCATAGGGTGCGATTCCG 58.357 61.111 0.00 0.00 45.23 4.30
48 49 1.961277 GCATAGGGTGCGATTCCGG 60.961 63.158 0.00 0.00 45.23 5.14
49 50 1.445942 CATAGGGTGCGATTCCGGT 59.554 57.895 0.00 0.00 36.06 5.28
50 51 0.677288 CATAGGGTGCGATTCCGGTA 59.323 55.000 0.00 0.00 36.06 4.02
51 52 0.966920 ATAGGGTGCGATTCCGGTAG 59.033 55.000 0.00 0.00 36.06 3.18
52 53 0.396139 TAGGGTGCGATTCCGGTAGT 60.396 55.000 0.00 0.00 36.06 2.73
53 54 1.520787 GGGTGCGATTCCGGTAGTG 60.521 63.158 0.00 0.00 36.06 2.74
54 55 1.217244 GGTGCGATTCCGGTAGTGT 59.783 57.895 0.00 0.00 36.06 3.55
55 56 0.804933 GGTGCGATTCCGGTAGTGTC 60.805 60.000 0.00 0.00 36.06 3.67
56 57 0.804933 GTGCGATTCCGGTAGTGTCC 60.805 60.000 0.00 0.00 36.06 4.02
70 71 4.979388 GTAGTGTCCGTTCTACCTAACAG 58.021 47.826 0.00 0.00 32.83 3.16
147 169 2.520741 CCTCTCCCTCTCCCTCGC 60.521 72.222 0.00 0.00 0.00 5.03
396 428 3.430098 GCATCCCATAATGCGACCAAAAA 60.430 43.478 0.00 0.00 42.33 1.94
402 434 5.448632 CCCATAATGCGACCAAAAACTAGAC 60.449 44.000 0.00 0.00 0.00 2.59
584 1161 8.709499 GAAATAATTTCCAGCCAAAAATGGGCA 61.709 37.037 6.17 0.00 42.59 5.36
621 1199 8.957466 GTATTTCCAGCTAAGAATACCAAGTTT 58.043 33.333 11.41 0.00 31.83 2.66
644 1222 9.908152 GTTTATTTGCTTTTACACTAGTGGATT 57.092 29.630 26.12 8.69 34.19 3.01
730 1311 0.889994 TTGGATGCACTGCCAATGTC 59.110 50.000 12.12 0.00 39.14 3.06
784 1365 8.241367 ACGAATTAAAACTTGCTAAATACTGGG 58.759 33.333 0.00 0.00 0.00 4.45
785 1366 7.700656 CGAATTAAAACTTGCTAAATACTGGGG 59.299 37.037 0.00 0.00 0.00 4.96
786 1367 8.430573 AATTAAAACTTGCTAAATACTGGGGT 57.569 30.769 0.00 0.00 0.00 4.95
787 1368 9.536510 AATTAAAACTTGCTAAATACTGGGGTA 57.463 29.630 0.00 0.00 0.00 3.69
788 1369 9.709387 ATTAAAACTTGCTAAATACTGGGGTAT 57.291 29.630 0.00 0.00 40.03 2.73
791 1372 8.691661 AAACTTGCTAAATACTGGGGTATATG 57.308 34.615 0.00 0.00 37.63 1.78
792 1373 6.238648 ACTTGCTAAATACTGGGGTATATGC 58.761 40.000 0.00 0.00 37.63 3.14
793 1374 5.834281 TGCTAAATACTGGGGTATATGCA 57.166 39.130 0.00 0.00 37.63 3.96
794 1375 6.194285 TGCTAAATACTGGGGTATATGCAA 57.806 37.500 0.00 0.00 37.63 4.08
795 1376 6.606069 TGCTAAATACTGGGGTATATGCAAA 58.394 36.000 0.00 0.00 37.63 3.68
796 1377 7.237982 TGCTAAATACTGGGGTATATGCAAAT 58.762 34.615 0.00 0.00 37.63 2.32
826 1451 4.746535 TTGGAGCACTATTCCGTCAATA 57.253 40.909 0.00 0.00 37.54 1.90
829 1454 3.495001 GGAGCACTATTCCGTCAATAAGC 59.505 47.826 0.00 0.00 32.15 3.09
851 1476 0.529992 CCGTTGGATAGCTTCCCGAC 60.530 60.000 12.23 12.23 44.77 4.79
867 1492 0.528924 CGACGTGGAGTGTTCCCATA 59.471 55.000 0.00 0.00 43.33 2.74
919 1544 1.330521 TCTCGCAAAATATTCGGCTGC 59.669 47.619 8.96 0.00 0.00 5.25
1030 1698 4.680237 CACGCGCTCCAGGTTCCA 62.680 66.667 5.73 0.00 0.00 3.53
1360 2295 0.252513 TCCACGGAAGAAGGATGGGA 60.253 55.000 0.00 0.00 34.81 4.37
1363 2298 1.555075 CACGGAAGAAGGATGGGAAGA 59.445 52.381 0.00 0.00 0.00 2.87
1364 2299 1.834263 ACGGAAGAAGGATGGGAAGAG 59.166 52.381 0.00 0.00 0.00 2.85
1368 2303 2.260639 AGAAGGATGGGAAGAGAGCA 57.739 50.000 0.00 0.00 0.00 4.26
1463 2431 4.742201 TGCGCTGAAGTCTCCCGC 62.742 66.667 9.73 0.00 40.01 6.13
1524 2492 1.338200 CCGTTTCCCCTCTCAACTGAG 60.338 57.143 0.00 0.00 43.36 3.35
1604 2581 5.130809 AGAAGGAGAAGAAGAATGGATGGAG 59.869 44.000 0.00 0.00 0.00 3.86
1605 2582 3.136260 AGGAGAAGAAGAATGGATGGAGC 59.864 47.826 0.00 0.00 0.00 4.70
1839 2821 7.964666 AGTATGCTAGAATAATACTCCCTCC 57.035 40.000 0.00 0.00 32.89 4.30
1840 2822 5.923733 ATGCTAGAATAATACTCCCTCCG 57.076 43.478 0.00 0.00 0.00 4.63
1842 2824 4.765856 TGCTAGAATAATACTCCCTCCGTC 59.234 45.833 0.00 0.00 0.00 4.79
1843 2825 5.011586 GCTAGAATAATACTCCCTCCGTCT 58.988 45.833 0.00 0.00 0.00 4.18
1844 2826 5.124297 GCTAGAATAATACTCCCTCCGTCTC 59.876 48.000 0.00 0.00 0.00 3.36
1845 2827 5.063017 AGAATAATACTCCCTCCGTCTCA 57.937 43.478 0.00 0.00 0.00 3.27
1846 2828 5.646215 AGAATAATACTCCCTCCGTCTCAT 58.354 41.667 0.00 0.00 0.00 2.90
1849 2831 7.896496 AGAATAATACTCCCTCCGTCTCATAAT 59.104 37.037 0.00 0.00 0.00 1.28
1851 2833 6.837471 AATACTCCCTCCGTCTCATAATAC 57.163 41.667 0.00 0.00 0.00 1.89
1853 2835 4.543689 ACTCCCTCCGTCTCATAATACAA 58.456 43.478 0.00 0.00 0.00 2.41
1854 2836 4.585162 ACTCCCTCCGTCTCATAATACAAG 59.415 45.833 0.00 0.00 0.00 3.16
1856 2838 4.583489 TCCCTCCGTCTCATAATACAAGAC 59.417 45.833 0.00 0.00 36.82 3.01
1865 2847 8.861277 GTCTCATAATACAAGACGTTTTTGAC 57.139 34.615 17.33 2.26 31.01 3.18
1866 2848 8.492748 GTCTCATAATACAAGACGTTTTTGACA 58.507 33.333 17.33 7.60 31.01 3.58
1867 2849 8.492748 TCTCATAATACAAGACGTTTTTGACAC 58.507 33.333 17.33 0.00 0.00 3.67
1868 2850 8.373048 TCATAATACAAGACGTTTTTGACACT 57.627 30.769 17.33 1.75 0.00 3.55
1869 2851 9.478768 TCATAATACAAGACGTTTTTGACACTA 57.521 29.630 17.33 3.55 0.00 2.74
1870 2852 9.741168 CATAATACAAGACGTTTTTGACACTAG 57.259 33.333 17.33 0.00 0.00 2.57
1871 2853 7.781548 AATACAAGACGTTTTTGACACTAGT 57.218 32.000 17.33 0.00 0.00 2.57
1888 4340 5.511234 ACTAGTGTAGTGTCAAGAAACGT 57.489 39.130 0.00 0.00 37.69 3.99
1891 4343 5.007385 AGTGTAGTGTCAAGAAACGTCTT 57.993 39.130 0.00 0.00 45.36 3.01
1893 4345 5.975939 AGTGTAGTGTCAAGAAACGTCTTAC 59.024 40.000 0.00 0.00 42.45 2.34
1894 4346 5.745294 GTGTAGTGTCAAGAAACGTCTTACA 59.255 40.000 0.00 0.00 42.45 2.41
1895 4347 5.975344 TGTAGTGTCAAGAAACGTCTTACAG 59.025 40.000 0.00 0.00 42.45 2.74
1896 4348 4.369182 AGTGTCAAGAAACGTCTTACAGG 58.631 43.478 0.00 0.00 42.45 4.00
1897 4349 4.098960 AGTGTCAAGAAACGTCTTACAGGA 59.901 41.667 0.00 0.00 42.45 3.86
1898 4350 4.208666 GTGTCAAGAAACGTCTTACAGGAC 59.791 45.833 0.00 0.00 42.45 3.85
1905 4357 3.277962 GTCTTACAGGACGGAGGGA 57.722 57.895 0.00 0.00 0.00 4.20
1906 4358 1.104630 GTCTTACAGGACGGAGGGAG 58.895 60.000 0.00 0.00 0.00 4.30
1907 4359 0.702902 TCTTACAGGACGGAGGGAGT 59.297 55.000 0.00 0.00 0.00 3.85
1909 4361 2.092538 TCTTACAGGACGGAGGGAGTAG 60.093 54.545 0.00 0.00 0.00 2.57
1910 4362 1.293062 TACAGGACGGAGGGAGTAGT 58.707 55.000 0.00 0.00 0.00 2.73
2026 4817 9.778741 GTGTATTCATCAGGAATTAATCTGGTA 57.221 33.333 0.00 0.00 43.76 3.25
2276 6149 2.571212 TCAAGTGATGTCCAAAACGCT 58.429 42.857 0.00 0.00 0.00 5.07
2572 6459 1.412074 GGAGGGGCATTCATGGTCAAT 60.412 52.381 0.00 0.00 0.00 2.57
2938 6835 1.768870 GCCCAGCCAGGATTAAGACTA 59.231 52.381 0.00 0.00 41.22 2.59
3058 6968 2.050351 CGCGGAAGTCTCGTGTGT 60.050 61.111 0.00 0.00 33.99 3.72
3132 7042 7.604549 TCTCCAGTTAAATATGTTGTCGTGTA 58.395 34.615 0.00 0.00 0.00 2.90
3197 7138 4.787534 AGGTTCAGAAGGAGAAGAATGGAT 59.212 41.667 0.00 0.00 0.00 3.41
3236 7177 4.104738 AGAAGATGAAGTTGGTGGAGGAAA 59.895 41.667 0.00 0.00 0.00 3.13
3247 7191 0.856982 TGGAGGAAAAAGGGAAGCCA 59.143 50.000 0.00 0.00 0.00 4.75
3295 7239 7.025963 CACTGAATATTGTGAAGAGGAAAAGC 58.974 38.462 0.00 0.00 36.38 3.51
3358 7302 6.861065 TCGGTAAGAATTTCCTATGCATTC 57.139 37.500 3.54 0.00 32.75 2.67
3692 7668 0.247736 GATCCAGCCGAGTGTTGAGT 59.752 55.000 0.00 0.00 0.00 3.41
3797 7773 6.734502 TTATCGAGGTGTAATATGGTGGAA 57.265 37.500 0.00 0.00 0.00 3.53
3829 7806 4.565166 CGCACACGGTTAAGAGATCAATAA 59.435 41.667 0.00 0.00 34.97 1.40
4588 8574 2.736721 CCGTAATACATCATCCCGCAAG 59.263 50.000 0.00 0.00 0.00 4.01
4729 8715 1.348036 AGTACCTTTGGAGACACCTGC 59.652 52.381 0.00 0.00 42.67 4.85
5314 9305 7.268586 AGTCAATAATCTAGTTCACATCGCTT 58.731 34.615 0.00 0.00 0.00 4.68
5594 9742 8.608844 AATCGAGAAACATATCCTTATTCCAC 57.391 34.615 0.00 0.00 0.00 4.02
6207 10360 1.942657 TCGCTGGAGCTTGCATATTTC 59.057 47.619 7.80 0.00 39.32 2.17
6360 10513 8.209584 ACATGATTCAGACAGACTTAAGCATAT 58.790 33.333 0.00 0.00 36.92 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 0.677288 TACCGGAATCGCACCCTATG 59.323 55.000 9.46 0.00 34.56 2.23
32 33 0.966920 CTACCGGAATCGCACCCTAT 59.033 55.000 9.46 0.00 34.56 2.57
33 34 0.396139 ACTACCGGAATCGCACCCTA 60.396 55.000 9.46 0.00 34.56 3.53
34 35 1.684734 ACTACCGGAATCGCACCCT 60.685 57.895 9.46 0.00 34.56 4.34
35 36 1.520787 CACTACCGGAATCGCACCC 60.521 63.158 9.46 0.00 34.56 4.61
36 37 0.804933 GACACTACCGGAATCGCACC 60.805 60.000 9.46 0.00 34.56 5.01
37 38 0.804933 GGACACTACCGGAATCGCAC 60.805 60.000 9.46 0.00 34.56 5.34
38 39 1.514087 GGACACTACCGGAATCGCA 59.486 57.895 9.46 0.00 34.56 5.10
39 40 4.414732 GGACACTACCGGAATCGC 57.585 61.111 9.46 0.00 34.56 4.58
48 49 4.673841 GCTGTTAGGTAGAACGGACACTAC 60.674 50.000 0.00 0.00 37.83 2.73
49 50 3.441572 GCTGTTAGGTAGAACGGACACTA 59.558 47.826 0.00 0.00 37.83 2.74
50 51 2.230750 GCTGTTAGGTAGAACGGACACT 59.769 50.000 0.00 0.00 37.83 3.55
51 52 2.603953 GCTGTTAGGTAGAACGGACAC 58.396 52.381 0.00 0.00 37.83 3.67
52 53 1.547372 GGCTGTTAGGTAGAACGGACA 59.453 52.381 0.00 0.00 42.47 4.02
53 54 1.468736 CGGCTGTTAGGTAGAACGGAC 60.469 57.143 0.00 0.00 39.93 4.79
54 55 0.813184 CGGCTGTTAGGTAGAACGGA 59.187 55.000 0.00 0.00 37.83 4.69
55 56 0.813184 TCGGCTGTTAGGTAGAACGG 59.187 55.000 0.00 0.00 38.51 4.44
56 57 2.257034 GTTCGGCTGTTAGGTAGAACG 58.743 52.381 0.00 0.00 31.59 3.95
57 58 2.095059 TCGTTCGGCTGTTAGGTAGAAC 60.095 50.000 0.00 0.00 35.85 3.01
58 59 2.161855 TCGTTCGGCTGTTAGGTAGAA 58.838 47.619 0.00 0.00 0.00 2.10
59 60 1.741706 CTCGTTCGGCTGTTAGGTAGA 59.258 52.381 0.00 0.00 0.00 2.59
60 61 1.741706 TCTCGTTCGGCTGTTAGGTAG 59.258 52.381 0.00 0.00 0.00 3.18
61 62 1.741706 CTCTCGTTCGGCTGTTAGGTA 59.258 52.381 0.00 0.00 0.00 3.08
62 63 0.526662 CTCTCGTTCGGCTGTTAGGT 59.473 55.000 0.00 0.00 0.00 3.08
63 64 0.809385 TCTCTCGTTCGGCTGTTAGG 59.191 55.000 0.00 0.00 0.00 2.69
64 65 1.199327 TGTCTCTCGTTCGGCTGTTAG 59.801 52.381 0.00 0.00 0.00 2.34
65 66 1.241165 TGTCTCTCGTTCGGCTGTTA 58.759 50.000 0.00 0.00 0.00 2.41
66 67 0.387929 TTGTCTCTCGTTCGGCTGTT 59.612 50.000 0.00 0.00 0.00 3.16
67 68 0.387929 TTTGTCTCTCGTTCGGCTGT 59.612 50.000 0.00 0.00 0.00 4.40
68 69 1.497991 TTTTGTCTCTCGTTCGGCTG 58.502 50.000 0.00 0.00 0.00 4.85
69 70 2.135933 CTTTTTGTCTCTCGTTCGGCT 58.864 47.619 0.00 0.00 0.00 5.52
70 71 2.132762 TCTTTTTGTCTCTCGTTCGGC 58.867 47.619 0.00 0.00 0.00 5.54
119 141 1.839296 GGGAGAGGGGGAGGAATCG 60.839 68.421 0.00 0.00 0.00 3.34
147 169 4.789012 AGTTTGTGTCAATATTGGCAGG 57.211 40.909 22.67 0.00 44.42 4.85
426 825 8.580720 CACAGGTGTGCTAATCTATCTATTAGT 58.419 37.037 0.00 0.00 40.23 2.24
584 1161 3.019564 GCTGGAAATACATTCAGTGCCT 58.980 45.455 0.00 0.00 39.98 4.75
621 1199 9.953565 AGTAATCCACTAGTGTAAAAGCAAATA 57.046 29.630 21.18 0.00 34.98 1.40
730 1311 4.038402 ACAGTTGATTTTTCTGGAAGGCTG 59.962 41.667 0.00 0.00 34.02 4.85
782 1363 9.561069 CCAATCTAGTATATTTGCATATACCCC 57.439 37.037 12.01 0.00 45.01 4.95
787 1368 9.388506 GTGCTCCAATCTAGTATATTTGCATAT 57.611 33.333 0.00 0.00 0.00 1.78
788 1369 8.597167 AGTGCTCCAATCTAGTATATTTGCATA 58.403 33.333 0.00 0.00 0.00 3.14
789 1370 7.456725 AGTGCTCCAATCTAGTATATTTGCAT 58.543 34.615 0.00 0.00 0.00 3.96
790 1371 6.830912 AGTGCTCCAATCTAGTATATTTGCA 58.169 36.000 0.00 0.00 0.00 4.08
791 1372 9.442047 AATAGTGCTCCAATCTAGTATATTTGC 57.558 33.333 0.00 0.00 0.00 3.68
794 1375 8.470805 CGGAATAGTGCTCCAATCTAGTATATT 58.529 37.037 0.00 0.00 32.77 1.28
795 1376 7.616150 ACGGAATAGTGCTCCAATCTAGTATAT 59.384 37.037 0.00 0.00 32.77 0.86
796 1377 6.946583 ACGGAATAGTGCTCCAATCTAGTATA 59.053 38.462 0.00 0.00 32.77 1.47
826 1451 2.513897 GCTATCCAACGGCGGCTT 60.514 61.111 13.24 0.00 0.00 4.35
829 1454 3.719214 GAAGCTATCCAACGGCGG 58.281 61.111 13.24 0.00 0.00 6.13
867 1492 2.129146 TGTTGACTGGACGGTCGGT 61.129 57.895 6.78 3.67 38.91 4.69
928 1581 3.488721 GCGCCTCGTCTAAATCTGAAGTA 60.489 47.826 0.00 0.00 0.00 2.24
1030 1698 4.778143 GGCGATGGAGTTGGCGGT 62.778 66.667 0.00 0.00 0.00 5.68
1360 2295 1.294780 CACGGGAAGCTGCTCTCTT 59.705 57.895 1.00 0.00 0.00 2.85
1363 2298 1.984570 TAGCACGGGAAGCTGCTCT 60.985 57.895 1.00 0.00 42.86 4.09
1364 2299 1.811679 GTAGCACGGGAAGCTGCTC 60.812 63.158 1.00 0.00 42.86 4.26
1368 2303 0.247736 CTGAAGTAGCACGGGAAGCT 59.752 55.000 0.00 0.00 45.77 3.74
1445 2413 2.185350 CGGGAGACTTCAGCGCAT 59.815 61.111 11.47 0.00 0.00 4.73
1463 2431 2.960129 GCGTAGTGGAATCGCCCG 60.960 66.667 0.00 0.00 43.41 6.13
1524 2492 1.090052 ATTAGGCGAGCGGCAACTTC 61.090 55.000 18.53 0.00 46.16 3.01
1605 2582 6.320171 CACTTTGATCTTCTTAGCACCATTG 58.680 40.000 0.00 0.00 0.00 2.82
1626 2603 1.633774 TCTCTTCTTTCTCCGCCACT 58.366 50.000 0.00 0.00 0.00 4.00
1667 2644 2.262423 AGCAGTGTTGAGTCTTTCCC 57.738 50.000 0.00 0.00 0.00 3.97
1673 2650 2.543777 TACCCAAGCAGTGTTGAGTC 57.456 50.000 6.92 0.00 0.00 3.36
1834 2816 4.872664 GTCTTGTATTATGAGACGGAGGG 58.127 47.826 0.00 0.00 31.54 4.30
1840 2822 8.492748 TGTCAAAAACGTCTTGTATTATGAGAC 58.507 33.333 9.44 0.00 37.13 3.36
1842 2824 8.495949 AGTGTCAAAAACGTCTTGTATTATGAG 58.504 33.333 9.44 0.00 0.00 2.90
1843 2825 8.373048 AGTGTCAAAAACGTCTTGTATTATGA 57.627 30.769 9.44 0.00 0.00 2.15
1844 2826 9.741168 CTAGTGTCAAAAACGTCTTGTATTATG 57.259 33.333 9.44 0.00 0.00 1.90
1845 2827 9.485206 ACTAGTGTCAAAAACGTCTTGTATTAT 57.515 29.630 0.00 0.00 0.00 1.28
1846 2828 8.757789 CACTAGTGTCAAAAACGTCTTGTATTA 58.242 33.333 15.06 3.12 0.00 0.98
1849 2831 6.101332 ACACTAGTGTCAAAAACGTCTTGTA 58.899 36.000 22.95 0.23 40.24 2.41
1851 2833 5.464965 ACACTAGTGTCAAAAACGTCTTG 57.535 39.130 22.95 4.38 40.24 3.02
1853 2835 5.899299 ACTACACTAGTGTCAAAAACGTCT 58.101 37.500 31.11 5.64 43.74 4.18
1866 2848 5.298777 AGACGTTTCTTGACACTACACTAGT 59.701 40.000 0.00 0.00 40.28 2.57
1867 2849 5.759963 AGACGTTTCTTGACACTACACTAG 58.240 41.667 0.00 0.00 0.00 2.57
1868 2850 5.762825 AGACGTTTCTTGACACTACACTA 57.237 39.130 0.00 0.00 0.00 2.74
1869 2851 4.650754 AGACGTTTCTTGACACTACACT 57.349 40.909 0.00 0.00 0.00 3.55
1870 2852 5.745294 TGTAAGACGTTTCTTGACACTACAC 59.255 40.000 0.00 0.00 42.41 2.90
1871 2853 5.893687 TGTAAGACGTTTCTTGACACTACA 58.106 37.500 0.00 0.00 42.41 2.74
1877 4329 4.968660 GTCCTGTAAGACGTTTCTTGAC 57.031 45.455 0.00 0.00 42.41 3.18
1888 4340 0.702902 ACTCCCTCCGTCCTGTAAGA 59.297 55.000 0.00 0.00 34.07 2.10
1891 4343 1.293062 ACTACTCCCTCCGTCCTGTA 58.707 55.000 0.00 0.00 0.00 2.74
1893 4345 2.431954 TAACTACTCCCTCCGTCCTG 57.568 55.000 0.00 0.00 0.00 3.86
1894 4346 3.684408 ATTAACTACTCCCTCCGTCCT 57.316 47.619 0.00 0.00 0.00 3.85
1895 4347 6.244654 ACTATATTAACTACTCCCTCCGTCC 58.755 44.000 0.00 0.00 0.00 4.79
1896 4348 8.891720 CATACTATATTAACTACTCCCTCCGTC 58.108 40.741 0.00 0.00 0.00 4.79
1897 4349 8.389366 ACATACTATATTAACTACTCCCTCCGT 58.611 37.037 0.00 0.00 0.00 4.69
1898 4350 8.804912 ACATACTATATTAACTACTCCCTCCG 57.195 38.462 0.00 0.00 0.00 4.63
2026 4817 9.899661 TGTACTTTTATATTGATACCAGCAACT 57.100 29.630 0.00 0.00 0.00 3.16
2053 4847 9.705103 AGGTATGTTAAGTACTTCATAGGTGTA 57.295 33.333 12.39 0.00 0.00 2.90
2063 4859 8.191534 ACTGAGACAAGGTATGTTAAGTACTT 57.808 34.615 13.68 13.68 44.12 2.24
2191 4996 1.915078 CGGCTCCACATTCCCCTTCT 61.915 60.000 0.00 0.00 0.00 2.85
2276 6149 4.894784 AGAAAATTCTCACCGAAGCAGTA 58.105 39.130 0.00 0.00 34.56 2.74
2572 6459 3.648009 GTCCGCAATCCAAAATTCAACA 58.352 40.909 0.00 0.00 0.00 3.33
2730 6622 7.013834 AGGAAAGGGTTGTAATTTGTGGATAA 58.986 34.615 0.00 0.00 0.00 1.75
2739 6631 9.816787 TTTCAGTATTAGGAAAGGGTTGTAATT 57.183 29.630 0.00 0.00 0.00 1.40
3058 6968 2.892374 CTGATGTGTAGTGGAATCGCA 58.108 47.619 0.00 0.00 0.00 5.10
3132 7042 4.899502 ACATGTGCTTACTCTGCTTTAGT 58.100 39.130 0.00 0.00 0.00 2.24
3173 7114 5.342017 TCCATTCTTCTCCTTCTGAACCTA 58.658 41.667 0.00 0.00 0.00 3.08
3197 7138 7.523293 TCATCTTCTTAGAACCATTTTTGCA 57.477 32.000 0.00 0.00 33.20 4.08
3236 7177 0.991920 TCCTTCGATGGCTTCCCTTT 59.008 50.000 12.42 0.00 0.00 3.11
3247 7191 1.220206 CACAGGCAGCTCCTTCGAT 59.780 57.895 2.32 0.00 44.75 3.59
3266 7210 8.463930 TTCCTCTTCACAATATTCAGTGTTTT 57.536 30.769 5.98 0.00 37.07 2.43
3295 7239 7.540400 TCGGCATTTTGTACATTACTTGATTTG 59.460 33.333 0.00 0.00 0.00 2.32
3358 7302 4.874970 ACAAATAGTGCAGGCTGAAAAAG 58.125 39.130 20.86 1.98 0.00 2.27
3433 7409 2.165030 ACTACGTTCCCCAACAGATACG 59.835 50.000 0.00 0.00 32.14 3.06
3829 7806 5.185635 CACCCCATAGACACAACAATTGATT 59.814 40.000 13.59 0.00 0.00 2.57
4016 8000 0.759346 CCGAATTGGACTAGGGAGGG 59.241 60.000 0.00 0.00 42.00 4.30
4017 8001 1.789523 TCCGAATTGGACTAGGGAGG 58.210 55.000 0.00 0.00 43.74 4.30
4316 8302 0.390209 GTAGGGTCCGCACGCTTAAA 60.390 55.000 0.00 0.00 43.11 1.52
4729 8715 4.780815 TGGGTGATTATAAAGGTGCTCTG 58.219 43.478 0.00 0.00 0.00 3.35
5133 9123 4.307259 TGAAGGAAATATGCCCTAGAGGT 58.693 43.478 0.00 0.00 38.26 3.85
5328 9319 4.841813 TGATCACACCTTAGTACCCTTTGA 59.158 41.667 0.00 0.00 0.00 2.69
5334 9325 6.622896 GCAAAACATGATCACACCTTAGTACC 60.623 42.308 0.00 0.00 0.00 3.34
5593 9741 5.497474 ACAGCGGTCAAAATTATCCTTAGT 58.503 37.500 0.00 0.00 0.00 2.24
5594 9742 5.007724 GGACAGCGGTCAAAATTATCCTTAG 59.992 44.000 18.81 0.00 46.17 2.18
5799 9948 4.718961 AGAGTTCTTGCCTGTGTTACAAT 58.281 39.130 0.00 0.00 0.00 2.71
5978 10131 8.752005 ATTATTCTGCAAAGCATAAAGGAGTA 57.248 30.769 0.00 0.00 38.13 2.59
6207 10360 5.856126 TGTCAATCCTAAAAGTGCTAACG 57.144 39.130 0.00 0.00 0.00 3.18
6654 10808 4.603131 AGTGGTACGGTAATCCTGTTCTA 58.397 43.478 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.