Multiple sequence alignment - TraesCS2A01G295200

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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 TraesCS2A01G295200 chr2A 100.000 3311 0 0 3487 6797 507695648 507692338 0.000000e+00 6115.0
1 TraesCS2A01G295200 chr2A 100.000 3184 0 0 1 3184 507699134 507695951 0.000000e+00 5880.0
2 TraesCS2A01G295200 chr2A 89.474 57 3 3 3760 3815 723907658 723907712 1.220000e-07 69.4
3 TraesCS2A01G295200 chr2A 91.837 49 1 3 3760 3808 19043533 19043578 1.580000e-06 65.8
4 TraesCS2A01G295200 chr2A 88.679 53 5 1 1750 1801 40955019 40954967 5.690000e-06 63.9
5 TraesCS2A01G295200 chr2D 94.265 2511 78 34 3899 6353 375368077 375365577 0.000000e+00 3779.0
6 TraesCS2A01G295200 chr2D 97.722 1405 30 2 1782 3184 375369918 375368514 0.000000e+00 2416.0
7 TraesCS2A01G295200 chr2D 94.451 883 41 7 902 1781 315478665 315479542 0.000000e+00 1352.0
8 TraesCS2A01G295200 chr2D 96.245 506 12 2 49 551 375370412 375369911 0.000000e+00 822.0
9 TraesCS2A01G295200 chr2D 94.949 396 12 2 3487 3882 375368448 375368061 1.250000e-171 614.0
10 TraesCS2A01G295200 chr2D 90.022 461 30 4 551 1009 315478221 315478667 3.530000e-162 582.0
11 TraesCS2A01G295200 chr2D 91.367 278 12 7 6527 6797 375365367 375365095 2.990000e-98 370.0
12 TraesCS2A01G295200 chr2D 94.667 75 4 0 6431 6505 375365435 375365361 4.310000e-22 117.0
13 TraesCS2A01G295200 chr2D 94.545 55 2 1 6378 6431 375365523 375365469 4.370000e-12 84.2
14 TraesCS2A01G295200 chr2B 92.979 2051 126 7 3899 5938 445689144 445687101 0.000000e+00 2974.0
15 TraesCS2A01G295200 chr2B 91.801 744 39 12 2443 3184 445690133 445689410 0.000000e+00 1016.0
16 TraesCS2A01G295200 chr2B 90.233 686 40 9 1782 2443 445690979 445690297 0.000000e+00 870.0
17 TraesCS2A01G295200 chr2B 96.819 503 12 1 49 551 445691470 445690972 0.000000e+00 837.0
18 TraesCS2A01G295200 chr2B 94.118 374 13 4 6431 6797 445686474 445686103 1.660000e-155 560.0
19 TraesCS2A01G295200 chr2B 81.260 651 108 12 1139 1781 799647475 799646831 1.310000e-141 514.0
20 TraesCS2A01G295200 chr2B 81.667 360 19 22 6105 6436 445686842 445686502 8.750000e-64 255.0
21 TraesCS2A01G295200 chr2B 91.018 167 8 5 5937 6096 445687070 445686904 1.150000e-52 219.0
22 TraesCS2A01G295200 chr2B 85.185 216 27 5 1561 1774 526838740 526838528 4.130000e-52 217.0
23 TraesCS2A01G295200 chr2B 84.112 214 21 7 552 764 799647916 799647715 1.930000e-45 195.0
24 TraesCS2A01G295200 chr2B 93.333 75 4 1 552 625 795480328 795480254 7.210000e-20 110.0
25 TraesCS2A01G295200 chr3D 94.928 1183 45 8 600 1781 131431518 131432686 0.000000e+00 1838.0
26 TraesCS2A01G295200 chr6D 91.174 1235 72 15 548 1778 461738 462939 0.000000e+00 1642.0
27 TraesCS2A01G295200 chr6D 89.796 147 12 2 3614 3759 433481352 433481208 1.160000e-42 185.0
28 TraesCS2A01G295200 chr1D 89.755 1142 89 15 645 1781 59628317 59627199 0.000000e+00 1435.0
29 TraesCS2A01G295200 chr1D 77.303 890 115 45 966 1782 386893650 386894525 1.740000e-120 444.0
30 TraesCS2A01G295200 chr1D 77.303 890 113 46 966 1781 92946215 92945341 6.260000e-120 442.0
31 TraesCS2A01G295200 chr1D 80.387 413 69 9 1378 1782 2209730 2209322 3.080000e-78 303.0
32 TraesCS2A01G295200 chr3B 84.770 1241 134 29 552 1781 257323072 257324268 0.000000e+00 1194.0
33 TraesCS2A01G295200 chr3B 91.781 146 12 0 3614 3759 119087731 119087586 3.210000e-48 204.0
34 TraesCS2A01G295200 chr3B 91.096 146 13 0 3614 3759 136485996 136486141 1.500000e-46 198.0
35 TraesCS2A01G295200 chr3B 87.273 55 4 3 564 617 438584254 438584202 7.360000e-05 60.2
36 TraesCS2A01G295200 chr4A 84.189 974 95 26 552 1511 669353751 669354679 0.000000e+00 891.0
37 TraesCS2A01G295200 chr4A 91.156 147 13 0 3612 3758 160254630 160254776 4.160000e-47 200.0
38 TraesCS2A01G295200 chr6B 80.803 1271 129 56 552 1781 584317751 584318947 0.000000e+00 889.0
39 TraesCS2A01G295200 chr3A 80.606 660 116 11 1137 1789 24479835 24479181 3.660000e-137 499.0
40 TraesCS2A01G295200 chr3A 77.934 213 28 9 3614 3808 623341718 623341929 1.550000e-21 115.0
41 TraesCS2A01G295200 chr1B 81.780 472 58 15 1125 1587 631757487 631757035 2.990000e-98 370.0
42 TraesCS2A01G295200 chr1B 88.660 97 10 1 1028 1123 631766661 631766565 4.310000e-22 117.0
43 TraesCS2A01G295200 chr1B 90.741 54 1 3 3760 3812 77892284 77892234 1.220000e-07 69.4
44 TraesCS2A01G295200 chr7B 90.230 174 12 5 1018 1188 749646006 749645835 8.870000e-54 222.0
45 TraesCS2A01G295200 chr7D 89.726 146 15 0 3614 3759 51414383 51414528 3.240000e-43 187.0
46 TraesCS2A01G295200 chr7D 89.796 147 14 1 3614 3760 551607246 551607101 3.240000e-43 187.0
47 TraesCS2A01G295200 chr7D 89.262 149 13 2 3614 3762 551503355 551503210 4.190000e-42 183.0
48 TraesCS2A01G295200 chr7D 95.652 46 0 2 3760 3805 583063224 583063181 9.460000e-09 73.1
49 TraesCS2A01G295200 chr4D 89.116 147 16 0 3612 3758 315080460 315080314 4.190000e-42 183.0
50 TraesCS2A01G295200 chrUn 93.750 80 5 0 551 630 263687693 263687614 3.330000e-23 121.0
51 TraesCS2A01G295200 chrUn 92.157 51 2 2 3760 3808 49639902 49639852 3.400000e-08 71.3
52 TraesCS2A01G295200 chrUn 88.136 59 3 3 3760 3815 103532038 103531981 4.400000e-07 67.6
53 TraesCS2A01G295200 chr5D 95.349 43 2 0 3760 3802 558587300 558587258 1.220000e-07 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 TraesCS2A01G295200 chr2A 507692338 507699134 6796 True 5997.500000 6115 100.000000 1 6797 2 chr2A.!!$R2 6796
1 TraesCS2A01G295200 chr2D 375365095 375370412 5317 True 1171.742857 3779 94.822857 49 6797 7 chr2D.!!$R1 6748
2 TraesCS2A01G295200 chr2D 315478221 315479542 1321 False 967.000000 1352 92.236500 551 1781 2 chr2D.!!$F1 1230
3 TraesCS2A01G295200 chr2B 445686103 445691470 5367 True 961.571429 2974 91.233571 49 6797 7 chr2B.!!$R3 6748
4 TraesCS2A01G295200 chr2B 799646831 799647916 1085 True 354.500000 514 82.686000 552 1781 2 chr2B.!!$R4 1229
5 TraesCS2A01G295200 chr3D 131431518 131432686 1168 False 1838.000000 1838 94.928000 600 1781 1 chr3D.!!$F1 1181
6 TraesCS2A01G295200 chr6D 461738 462939 1201 False 1642.000000 1642 91.174000 548 1778 1 chr6D.!!$F1 1230
7 TraesCS2A01G295200 chr1D 59627199 59628317 1118 True 1435.000000 1435 89.755000 645 1781 1 chr1D.!!$R2 1136
8 TraesCS2A01G295200 chr1D 386893650 386894525 875 False 444.000000 444 77.303000 966 1782 1 chr1D.!!$F1 816
9 TraesCS2A01G295200 chr1D 92945341 92946215 874 True 442.000000 442 77.303000 966 1781 1 chr1D.!!$R3 815
10 TraesCS2A01G295200 chr3B 257323072 257324268 1196 False 1194.000000 1194 84.770000 552 1781 1 chr3B.!!$F2 1229
11 TraesCS2A01G295200 chr4A 669353751 669354679 928 False 891.000000 891 84.189000 552 1511 1 chr4A.!!$F2 959
12 TraesCS2A01G295200 chr6B 584317751 584318947 1196 False 889.000000 889 80.803000 552 1781 1 chr6B.!!$F1 1229
13 TraesCS2A01G295200 chr3A 24479181 24479835 654 True 499.000000 499 80.606000 1137 1789 1 chr3A.!!$R1 652

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
41 42 0.109272 TCGTGAGACTGAATCGGCAC 60.109 55.000 0.00 0.0 35.43 5.01 F
303 304 0.175760 CTTCTCCTCGCAATCCCGAA 59.824 55.000 0.00 0.0 36.72 4.30 F
943 982 0.593128 CTGAACGGCCAGGAAAACAG 59.407 55.000 2.24 0.0 0.00 3.16 F
1846 2179 1.006102 CGTGTCTGCGGAGGTTTCT 60.006 57.895 3.37 0.0 0.00 2.52 F
2108 2441 3.144506 CTCAATGTGAGGTTCTTGCACT 58.855 45.455 0.00 0.0 40.71 4.40 F
2987 3509 3.611113 GCTGCTGAGCATTTACATTTGTG 59.389 43.478 7.94 0.0 45.46 3.33 F
3868 4395 5.059161 TGAGTATGCTTTGTATCCTCATGC 58.941 41.667 0.00 0.0 0.00 4.06 F
3935 4462 0.321564 TCATGCACCACTTCCTTCCG 60.322 55.000 0.00 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1731 2064 1.398692 GGGCAAGACAACACAAAGGA 58.601 50.000 0.00 0.00 0.00 3.36 R
1834 2167 2.666098 GCCCCTAGAAACCTCCGCA 61.666 63.158 0.00 0.00 0.00 5.69 R
2679 3200 4.498894 TCGATGGAAGTACCTACAGAGA 57.501 45.455 0.00 0.00 39.86 3.10 R
3162 3688 2.430465 AGAAGATGTGCACGCAATTCT 58.570 42.857 13.13 15.05 0.00 2.40 R
3890 4417 1.340502 TGCAATAAGACATTCCCCGCA 60.341 47.619 0.00 0.00 0.00 5.69 R
3891 4418 1.388547 TGCAATAAGACATTCCCCGC 58.611 50.000 0.00 0.00 0.00 6.13 R
5706 6236 1.090625 CCGACCTCGTGATCTCTCGT 61.091 60.000 0.00 0.00 37.74 4.18 R
5871 6409 0.823356 AACATGCTGCTTCCACCGTT 60.823 50.000 0.00 0.00 0.00 4.44 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
24 25 7.580818 CATTTTATCACTACGAGCATTTTCG 57.419 36.000 0.00 0.00 45.70 3.46
32 33 2.776694 CGAGCATTTTCGTGAGACTG 57.223 50.000 0.00 0.00 41.84 3.51
33 34 2.328473 CGAGCATTTTCGTGAGACTGA 58.672 47.619 0.00 0.00 41.84 3.41
34 35 2.731451 CGAGCATTTTCGTGAGACTGAA 59.269 45.455 0.00 0.00 41.84 3.02
35 36 3.369147 CGAGCATTTTCGTGAGACTGAAT 59.631 43.478 0.00 0.00 41.84 2.57
36 37 4.491602 CGAGCATTTTCGTGAGACTGAATC 60.492 45.833 0.00 0.00 41.84 2.52
37 38 3.369147 AGCATTTTCGTGAGACTGAATCG 59.631 43.478 0.00 0.00 41.84 3.34
38 39 3.484229 GCATTTTCGTGAGACTGAATCGG 60.484 47.826 0.00 0.00 41.84 4.18
39 40 1.710013 TTTCGTGAGACTGAATCGGC 58.290 50.000 0.00 0.00 41.84 5.54
40 41 0.601057 TTCGTGAGACTGAATCGGCA 59.399 50.000 0.00 0.00 41.84 5.69
41 42 0.109272 TCGTGAGACTGAATCGGCAC 60.109 55.000 0.00 0.00 35.43 5.01
42 43 0.388520 CGTGAGACTGAATCGGCACA 60.389 55.000 0.00 0.00 37.35 4.57
43 44 1.737029 CGTGAGACTGAATCGGCACAT 60.737 52.381 0.00 0.00 37.35 3.21
44 45 2.350522 GTGAGACTGAATCGGCACATT 58.649 47.619 0.00 0.00 37.41 2.71
45 46 2.349886 GTGAGACTGAATCGGCACATTC 59.650 50.000 0.00 0.85 37.41 2.67
46 47 2.028203 TGAGACTGAATCGGCACATTCA 60.028 45.455 8.75 8.75 39.91 2.57
47 48 3.201290 GAGACTGAATCGGCACATTCAT 58.799 45.455 9.35 2.31 41.06 2.57
81 82 1.568025 GTGCTGGACCGAAACGTTC 59.432 57.895 0.00 0.00 0.00 3.95
82 83 0.878961 GTGCTGGACCGAAACGTTCT 60.879 55.000 0.00 0.00 0.00 3.01
83 84 0.599204 TGCTGGACCGAAACGTTCTC 60.599 55.000 0.00 0.74 0.00 2.87
84 85 0.319641 GCTGGACCGAAACGTTCTCT 60.320 55.000 0.00 0.00 0.00 3.10
204 205 2.787249 CATCGCGTTCCAGGCTTG 59.213 61.111 5.77 0.00 0.00 4.01
278 279 1.817099 GGCGAATCCTGCACCTCTG 60.817 63.158 0.00 0.00 0.00 3.35
303 304 0.175760 CTTCTCCTCGCAATCCCGAA 59.824 55.000 0.00 0.00 36.72 4.30
636 645 2.757868 CCCGATTGCTTGGTTTCCATAA 59.242 45.455 0.00 0.00 31.53 1.90
818 836 2.015090 GCCGATTAGTACGCTCGCC 61.015 63.158 8.62 0.00 0.00 5.54
864 895 2.392613 AAAGTGCAAGCGCTTGACGG 62.393 55.000 45.25 25.06 44.81 4.79
889 921 1.012086 CCTTCATCGATGCCACACAG 58.988 55.000 20.81 8.61 0.00 3.66
890 922 1.012086 CTTCATCGATGCCACACAGG 58.988 55.000 20.81 0.00 41.84 4.00
943 982 0.593128 CTGAACGGCCAGGAAAACAG 59.407 55.000 2.24 0.00 0.00 3.16
948 987 1.142262 ACGGCCAGGAAAACAGTACTT 59.858 47.619 2.24 0.00 0.00 2.24
950 989 2.583143 GGCCAGGAAAACAGTACTTGT 58.417 47.619 0.00 0.00 43.45 3.16
1161 1394 7.191593 TGAAGATCATCCCCATACATATCTG 57.808 40.000 0.00 0.00 0.00 2.90
1163 1396 6.805016 AGATCATCCCCATACATATCTGTC 57.195 41.667 0.00 0.00 36.79 3.51
1174 1409 3.892284 ACATATCTGTCTCTCACTCCGT 58.108 45.455 0.00 0.00 0.00 4.69
1304 1542 3.758554 TGTTCCAAGCCTTTCTTAGCATC 59.241 43.478 0.00 0.00 32.74 3.91
1309 1548 5.047802 TCCAAGCCTTTCTTAGCATCTTTTG 60.048 40.000 0.00 0.00 32.74 2.44
1448 1721 7.928307 TCAGTTTATTGAGATCAAGAAAGGG 57.072 36.000 13.93 10.03 44.46 3.95
1478 1775 8.556213 TTGACATTTTCCTATAACAGGTACAC 57.444 34.615 0.00 0.00 45.71 2.90
1502 1799 5.444218 CGTACTTCTGTTAGAAATTCCGTGC 60.444 44.000 0.00 0.00 33.19 5.34
1606 1913 1.429423 GGCCGATTGAAAAGAGCGG 59.571 57.895 0.00 0.00 40.46 5.52
1731 2064 3.510459 AGAAAAATGTGGCTTTAGGGCT 58.490 40.909 0.00 0.00 41.48 5.19
1846 2179 1.006102 CGTGTCTGCGGAGGTTTCT 60.006 57.895 3.37 0.00 0.00 2.52
2108 2441 3.144506 CTCAATGTGAGGTTCTTGCACT 58.855 45.455 0.00 0.00 40.71 4.40
2147 2480 7.953173 CGTGTTTGATAAAATGTACGAAAGCTA 59.047 33.333 0.00 0.00 32.58 3.32
2207 2540 6.402550 CGTTGATTGTAGAAATTCACTCCCTG 60.403 42.308 0.00 0.00 0.00 4.45
2284 2641 6.061441 CACTGGTAATTGTGCCATCCTAATA 58.939 40.000 0.00 0.00 39.02 0.98
2679 3200 8.327429 CGAAAAATTGTTGTTTACTTGAATGCT 58.673 29.630 0.00 0.00 0.00 3.79
2987 3509 3.611113 GCTGCTGAGCATTTACATTTGTG 59.389 43.478 7.94 0.00 45.46 3.33
3125 3648 8.526147 GGATTGATAATGTTCATAGAATTGGGG 58.474 37.037 0.00 0.00 0.00 4.96
3146 3669 6.962902 TGGGGGTCCAACTAATTAATCATTTT 59.037 34.615 0.00 0.00 40.73 1.82
3862 4389 8.443953 AGAATTTCTGAGTATGCTTTGTATCC 57.556 34.615 0.00 0.00 0.00 2.59
3865 4392 6.544928 TTCTGAGTATGCTTTGTATCCTCA 57.455 37.500 0.00 0.00 0.00 3.86
3866 4393 6.737720 TCTGAGTATGCTTTGTATCCTCAT 57.262 37.500 0.00 0.00 0.00 2.90
3867 4394 6.519382 TCTGAGTATGCTTTGTATCCTCATG 58.481 40.000 0.00 0.00 0.00 3.07
3868 4395 5.059161 TGAGTATGCTTTGTATCCTCATGC 58.941 41.667 0.00 0.00 0.00 4.06
3869 4396 5.163269 TGAGTATGCTTTGTATCCTCATGCT 60.163 40.000 0.00 0.00 33.84 3.79
3870 4397 5.688807 AGTATGCTTTGTATCCTCATGCTT 58.311 37.500 0.00 0.00 28.20 3.91
3871 4398 6.125029 AGTATGCTTTGTATCCTCATGCTTT 58.875 36.000 0.00 0.00 28.20 3.51
3872 4399 7.282585 AGTATGCTTTGTATCCTCATGCTTTA 58.717 34.615 0.00 0.00 28.20 1.85
3873 4400 7.941238 AGTATGCTTTGTATCCTCATGCTTTAT 59.059 33.333 0.00 0.00 28.20 1.40
3874 4401 7.592885 ATGCTTTGTATCCTCATGCTTTATT 57.407 32.000 0.00 0.00 0.00 1.40
3875 4402 6.798482 TGCTTTGTATCCTCATGCTTTATTG 58.202 36.000 0.00 0.00 0.00 1.90
3876 4403 5.689068 GCTTTGTATCCTCATGCTTTATTGC 59.311 40.000 0.00 0.00 0.00 3.56
3935 4462 0.321564 TCATGCACCACTTCCTTCCG 60.322 55.000 0.00 0.00 0.00 4.30
4076 4603 2.158370 TCCCTGAGGTAATCGCCATCTA 60.158 50.000 0.00 0.00 0.00 1.98
4242 4772 6.126409 GGATGATCATGGGGTTTTAGTTACA 58.874 40.000 14.30 0.00 0.00 2.41
4255 4785 8.301720 GGGTTTTAGTTACATTTTTCTAGTGGG 58.698 37.037 0.00 0.00 0.00 4.61
4424 4954 3.881089 CTCATACATCCATGCTGCTTTCA 59.119 43.478 0.00 0.00 0.00 2.69
4708 5238 6.423905 TGCAGAATCTGTAAACAGTCTTACAC 59.576 38.462 12.29 0.00 44.12 2.90
4730 5260 3.975035 CGTTTCACCTTTTTAGCTCAAGC 59.025 43.478 0.00 0.00 42.49 4.01
4799 5329 8.462811 TGATTATCTTCTAAGATGGCTATCGAC 58.537 37.037 14.16 0.00 45.01 4.20
4817 5347 4.383173 TCGACAAACTTCCCTTTTAGGAC 58.617 43.478 0.00 0.00 37.67 3.85
4946 5476 2.602660 CCTTTTGTGTCTTTGCGGTTTG 59.397 45.455 0.00 0.00 0.00 2.93
4972 5502 3.282021 CATCTCATTTGGGGTGTTCGAT 58.718 45.455 0.00 0.00 0.00 3.59
5057 5587 7.367285 TCAGCTTCCAACACACATAATTTAAC 58.633 34.615 0.00 0.00 0.00 2.01
5124 5654 8.553696 GTTTTCATGCATGTTCATTTCTTCTTT 58.446 29.630 25.43 0.00 0.00 2.52
5157 5687 5.704888 TGTTATTTTCCGGTACAATTGCTG 58.295 37.500 5.05 0.00 0.00 4.41
5174 5704 5.574891 TTGCTGAAAATATTGCGTATGGT 57.425 34.783 0.00 0.00 0.00 3.55
5181 5711 4.967084 AATATTGCGTATGGTGACCCTA 57.033 40.909 0.00 0.00 0.00 3.53
5235 5765 1.752498 CTGCTAAGATTGCCAATGCCA 59.248 47.619 0.00 0.00 36.33 4.92
5245 5775 1.273048 TGCCAATGCCAATGAGTTCAC 59.727 47.619 0.00 0.00 36.33 3.18
5259 5789 7.067372 CCAATGAGTTCACTAAGATATTGCCAA 59.933 37.037 0.00 0.00 0.00 4.52
5277 5807 4.836175 TGCCAAAGGGATATGACTCGTATA 59.164 41.667 0.00 0.00 35.59 1.47
5445 5975 0.326595 TCGCAAGGGCAATCTACCAA 59.673 50.000 0.00 0.00 41.24 3.67
5519 6049 3.576118 TCTGAGCTGCTACTGAAAGAAGT 59.424 43.478 0.15 0.00 37.43 3.01
5622 6152 3.081061 TGTTTTCATGATGTTCTCCCCG 58.919 45.455 0.00 0.00 0.00 5.73
5706 6236 6.945218 TGTTTTACTAGAGGGCGGTAAATTA 58.055 36.000 0.00 0.00 36.00 1.40
5965 6536 0.443869 CCAAATCGCTGAACGTCAGG 59.556 55.000 14.19 6.97 44.43 3.86
6037 6610 9.064706 AGAGAATCAGCAAATTAATGGTATGAG 57.935 33.333 0.00 0.00 37.82 2.90
6041 6614 7.514784 TCAGCAAATTAATGGTATGAGATGG 57.485 36.000 0.00 0.00 0.00 3.51
6168 6799 9.935682 CACACAGCTACAAGTATAAAATAATGG 57.064 33.333 0.00 0.00 0.00 3.16
6200 6831 6.290748 CGAAATAATGCGAATCAGAAAGTTGC 60.291 38.462 0.00 0.00 0.00 4.17
6201 6832 3.921119 AATGCGAATCAGAAAGTTGCA 57.079 38.095 0.00 0.00 35.10 4.08
6231 6891 1.667191 AGCTGTGTTGCTCTCTGCG 60.667 57.895 0.00 0.00 46.63 5.18
6289 6949 9.056005 GCATAGTCCTGTGTTTCATGATAAATA 57.944 33.333 0.00 0.00 0.00 1.40
6292 6952 7.861629 AGTCCTGTGTTTCATGATAAATAGGA 58.138 34.615 15.07 15.07 0.00 2.94
6369 7045 8.422973 AACAAGTAAAAATGACGTACAGTACA 57.577 30.769 11.37 0.00 0.00 2.90
6370 7046 8.422973 ACAAGTAAAAATGACGTACAGTACAA 57.577 30.769 11.37 0.00 0.00 2.41
6385 7061 4.219033 CAGTACAAAGCAAAATCGTCACC 58.781 43.478 0.00 0.00 0.00 4.02
6419 7125 4.065321 CCTGTTTGGGCAATGTACAAAA 57.935 40.909 0.00 0.00 36.05 2.44
6437 7177 9.562583 TGTACAAAACACTTGTTCAAGAAATAC 57.437 29.630 17.75 10.31 37.25 1.89
6461 7201 4.142093 GCAATCCTGCCATATTCAACAAGT 60.142 41.667 0.00 0.00 43.26 3.16
6470 7210 4.949238 CCATATTCAACAAGTGGTGATGGA 59.051 41.667 10.67 0.00 40.24 3.41
6511 7251 0.749454 GGCCCTAGCAACATGGAGTG 60.749 60.000 0.00 0.00 42.56 3.51
6523 7263 5.762045 CAACATGGAGTGTCAAAAGTAAGG 58.238 41.667 0.00 0.00 41.14 2.69
6542 7282 4.357918 AGGTAAGCAACACAACAGATCT 57.642 40.909 0.00 0.00 0.00 2.75
6556 7296 4.096190 ACAGATCTTATCCATGCCAAGG 57.904 45.455 0.00 0.00 0.00 3.61
6557 7297 3.461085 ACAGATCTTATCCATGCCAAGGT 59.539 43.478 0.00 0.00 0.00 3.50
6615 7362 0.673022 CAACAGCTGAGACAGGCCTC 60.673 60.000 23.35 0.00 31.21 4.70
6616 7363 0.835543 AACAGCTGAGACAGGCCTCT 60.836 55.000 23.35 0.00 34.38 3.69
6675 7424 4.471386 CCTCAAGGAAGGATCTGAAACCTA 59.529 45.833 7.09 0.00 38.87 3.08
6684 7433 5.219739 AGGATCTGAAACCTATAGAGCCAA 58.780 41.667 10.00 0.00 46.62 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.328473 TCAGTCTCACGAAAATGCTCG 58.672 47.619 0.00 0.00 44.50 5.03
14 15 4.491602 CGATTCAGTCTCACGAAAATGCTC 60.492 45.833 0.00 0.00 0.00 4.26
15 16 3.369147 CGATTCAGTCTCACGAAAATGCT 59.631 43.478 0.00 0.00 0.00 3.79
16 17 3.484229 CCGATTCAGTCTCACGAAAATGC 60.484 47.826 0.00 0.00 0.00 3.56
17 18 3.484229 GCCGATTCAGTCTCACGAAAATG 60.484 47.826 0.00 0.00 0.00 2.32
18 19 2.673368 GCCGATTCAGTCTCACGAAAAT 59.327 45.455 0.00 0.00 0.00 1.82
19 20 2.066262 GCCGATTCAGTCTCACGAAAA 58.934 47.619 0.00 0.00 0.00 2.29
20 21 1.000394 TGCCGATTCAGTCTCACGAAA 60.000 47.619 0.00 0.00 0.00 3.46
21 22 0.601057 TGCCGATTCAGTCTCACGAA 59.399 50.000 0.00 0.00 0.00 3.85
22 23 0.109272 GTGCCGATTCAGTCTCACGA 60.109 55.000 0.00 0.00 0.00 4.35
23 24 0.388520 TGTGCCGATTCAGTCTCACG 60.389 55.000 0.00 0.00 33.44 4.35
24 25 2.015736 ATGTGCCGATTCAGTCTCAC 57.984 50.000 0.00 0.00 0.00 3.51
25 26 2.028203 TGAATGTGCCGATTCAGTCTCA 60.028 45.455 3.89 0.00 37.41 3.27
26 27 2.621338 TGAATGTGCCGATTCAGTCTC 58.379 47.619 3.89 0.00 37.41 3.36
27 28 2.768253 TGAATGTGCCGATTCAGTCT 57.232 45.000 3.89 0.00 37.41 3.24
28 29 5.484173 TTTATGAATGTGCCGATTCAGTC 57.516 39.130 11.78 0.31 43.79 3.51
29 30 5.895636 TTTTATGAATGTGCCGATTCAGT 57.104 34.783 11.78 5.07 43.79 3.41
30 31 5.622448 CGATTTTATGAATGTGCCGATTCAG 59.378 40.000 11.78 0.00 43.79 3.02
31 32 5.505489 CCGATTTTATGAATGTGCCGATTCA 60.505 40.000 9.28 9.28 44.47 2.57
32 33 4.911610 CCGATTTTATGAATGTGCCGATTC 59.088 41.667 0.00 0.00 33.59 2.52
33 34 4.792704 GCCGATTTTATGAATGTGCCGATT 60.793 41.667 0.00 0.00 0.00 3.34
34 35 3.304659 GCCGATTTTATGAATGTGCCGAT 60.305 43.478 0.00 0.00 0.00 4.18
35 36 2.032799 GCCGATTTTATGAATGTGCCGA 59.967 45.455 0.00 0.00 0.00 5.54
36 37 2.223456 TGCCGATTTTATGAATGTGCCG 60.223 45.455 0.00 0.00 0.00 5.69
37 38 3.115554 GTGCCGATTTTATGAATGTGCC 58.884 45.455 0.00 0.00 0.00 5.01
38 39 3.768406 TGTGCCGATTTTATGAATGTGC 58.232 40.909 0.00 0.00 0.00 4.57
39 40 4.985413 ACTGTGCCGATTTTATGAATGTG 58.015 39.130 0.00 0.00 0.00 3.21
40 41 4.201812 CGACTGTGCCGATTTTATGAATGT 60.202 41.667 0.00 0.00 0.00 2.71
41 42 4.201812 ACGACTGTGCCGATTTTATGAATG 60.202 41.667 0.00 0.00 0.00 2.67
42 43 3.938963 ACGACTGTGCCGATTTTATGAAT 59.061 39.130 0.00 0.00 0.00 2.57
43 44 3.124466 CACGACTGTGCCGATTTTATGAA 59.876 43.478 0.00 0.00 39.67 2.57
44 45 2.670905 CACGACTGTGCCGATTTTATGA 59.329 45.455 0.00 0.00 39.67 2.15
45 46 3.038352 CACGACTGTGCCGATTTTATG 57.962 47.619 0.00 0.00 39.67 1.90
66 67 1.269998 AGAGAGAACGTTTCGGTCCAG 59.730 52.381 0.46 0.00 45.54 3.86
81 82 3.445450 TCGGTCAATTGAGAAGGAGAGAG 59.555 47.826 8.80 0.00 0.00 3.20
82 83 3.431415 TCGGTCAATTGAGAAGGAGAGA 58.569 45.455 8.80 0.00 0.00 3.10
83 84 3.876274 TCGGTCAATTGAGAAGGAGAG 57.124 47.619 8.80 0.00 0.00 3.20
84 85 4.826274 AATCGGTCAATTGAGAAGGAGA 57.174 40.909 8.80 2.97 0.00 3.71
278 279 0.678048 ATTGCGAGGAGAAGGTTGGC 60.678 55.000 0.00 0.00 0.00 4.52
303 304 1.355381 TGAGATGCTTGGGGTGAATGT 59.645 47.619 0.00 0.00 0.00 2.71
818 836 3.250744 TGTACGAGAGAATTCAAAGGCG 58.749 45.455 8.44 6.46 0.00 5.52
864 895 4.153117 GTGTGGCATCGATGAAGGATATTC 59.847 45.833 29.20 7.42 0.00 1.75
889 921 2.172483 ATCCCAGAGTCGTGTGTGCC 62.172 60.000 0.00 0.00 0.00 5.01
890 922 0.737715 GATCCCAGAGTCGTGTGTGC 60.738 60.000 0.00 0.00 0.00 4.57
891 923 0.108615 GGATCCCAGAGTCGTGTGTG 60.109 60.000 0.00 0.00 0.00 3.82
892 924 1.595993 CGGATCCCAGAGTCGTGTGT 61.596 60.000 6.06 0.00 0.00 3.72
893 925 1.139734 CGGATCCCAGAGTCGTGTG 59.860 63.158 6.06 0.00 0.00 3.82
894 926 1.001269 TCGGATCCCAGAGTCGTGT 60.001 57.895 6.06 0.00 0.00 4.49
895 927 0.748367 TCTCGGATCCCAGAGTCGTG 60.748 60.000 4.76 0.00 36.03 4.35
896 928 0.183971 ATCTCGGATCCCAGAGTCGT 59.816 55.000 14.76 0.00 36.03 4.34
1161 1394 2.036089 ACAGGAAAACGGAGTGAGAGAC 59.964 50.000 0.00 0.00 45.00 3.36
1163 1396 2.224066 ACACAGGAAAACGGAGTGAGAG 60.224 50.000 0.00 0.00 45.00 3.20
1174 1409 6.843752 TCTAATCCTAACCAACACAGGAAAA 58.156 36.000 0.00 0.00 41.68 2.29
1265 1501 6.560003 TGGAACAAAGATCTAGATGGCTAA 57.440 37.500 10.74 0.00 31.92 3.09
1478 1775 5.444218 GCACGGAATTTCTAACAGAAGTACG 60.444 44.000 0.00 5.31 35.37 3.67
1502 1799 8.641499 TTTTTCAACAGTAACTAAAGGCATTG 57.359 30.769 0.00 0.00 0.00 2.82
1552 1854 3.036075 AGGTTCGTGCCTACACTAAAC 57.964 47.619 0.00 0.00 45.10 2.01
1731 2064 1.398692 GGGCAAGACAACACAAAGGA 58.601 50.000 0.00 0.00 0.00 3.36
1834 2167 2.666098 GCCCCTAGAAACCTCCGCA 61.666 63.158 0.00 0.00 0.00 5.69
2108 2441 5.836821 ATCAAACACGTCTATCTAGCAGA 57.163 39.130 0.00 0.00 0.00 4.26
2207 2540 6.295039 TCAAGTATGAGGAACGTTCAAAAC 57.705 37.500 28.24 17.48 0.00 2.43
2284 2641 9.932207 TTGTCTGCATGAAAATGAGAAATAAAT 57.068 25.926 0.00 0.00 0.00 1.40
2679 3200 4.498894 TCGATGGAAGTACCTACAGAGA 57.501 45.455 0.00 0.00 39.86 3.10
2987 3509 9.001049 CGACGATACAGCATATAGTAAGAATTC 57.999 37.037 0.00 0.00 0.00 2.17
3125 3648 9.803315 GAGGAAAAATGATTAATTAGTTGGACC 57.197 33.333 0.00 0.00 0.00 4.46
3162 3688 2.430465 AGAAGATGTGCACGCAATTCT 58.570 42.857 13.13 15.05 0.00 2.40
3163 3689 2.907910 AGAAGATGTGCACGCAATTC 57.092 45.000 13.13 13.11 0.00 2.17
3494 4020 5.919755 TGCATATTCCGGTACAATAACTCA 58.080 37.500 0.00 0.00 0.00 3.41
3736 4262 9.778993 CACTTTTGACTCATAATTATGGTCAAG 57.221 33.333 32.72 28.90 44.59 3.02
3744 4270 6.719370 ACAAGGCCACTTTTGACTCATAATTA 59.281 34.615 5.01 0.00 33.81 1.40
3886 4413 4.815269 CAATAAGACATTCCCCGCAAAAA 58.185 39.130 0.00 0.00 0.00 1.94
3887 4414 3.367910 GCAATAAGACATTCCCCGCAAAA 60.368 43.478 0.00 0.00 0.00 2.44
3888 4415 2.165437 GCAATAAGACATTCCCCGCAAA 59.835 45.455 0.00 0.00 0.00 3.68
3889 4416 1.748493 GCAATAAGACATTCCCCGCAA 59.252 47.619 0.00 0.00 0.00 4.85
3890 4417 1.340502 TGCAATAAGACATTCCCCGCA 60.341 47.619 0.00 0.00 0.00 5.69
3891 4418 1.388547 TGCAATAAGACATTCCCCGC 58.611 50.000 0.00 0.00 0.00 6.13
3892 4419 2.951642 ACATGCAATAAGACATTCCCCG 59.048 45.455 0.00 0.00 0.00 5.73
3893 4420 4.160252 ACAACATGCAATAAGACATTCCCC 59.840 41.667 0.00 0.00 0.00 4.81
3894 4421 5.105797 TGACAACATGCAATAAGACATTCCC 60.106 40.000 0.00 0.00 0.00 3.97
3895 4422 5.953183 TGACAACATGCAATAAGACATTCC 58.047 37.500 0.00 0.00 0.00 3.01
3896 4423 7.445900 CATGACAACATGCAATAAGACATTC 57.554 36.000 0.00 0.00 45.51 2.67
3935 4462 4.084328 CGTGAGAACCAAATCAAGAGTGTC 60.084 45.833 0.00 0.00 0.00 3.67
4242 4772 5.833131 TCAAGCAGTTTCCCACTAGAAAAAT 59.167 36.000 0.00 0.00 37.49 1.82
4255 4785 6.796426 ACTTCTTTTACCTTCAAGCAGTTTC 58.204 36.000 0.00 0.00 0.00 2.78
4398 4928 2.947652 GCAGCATGGATGTATGAGTTGT 59.052 45.455 0.00 0.00 35.86 3.32
4424 4954 1.885049 ATCCCTCACCTACAGCACAT 58.115 50.000 0.00 0.00 0.00 3.21
4678 5208 5.072741 ACTGTTTACAGATTCTGCACCAAT 58.927 37.500 16.31 0.00 46.59 3.16
4708 5238 3.975035 GCTTGAGCTAAAAAGGTGAAACG 59.025 43.478 0.00 0.00 36.21 3.60
4730 5260 8.059798 AGAAAACCAGAATTCATGATACCAAG 57.940 34.615 8.44 0.00 0.00 3.61
4799 5329 7.775561 AGCTATATGTCCTAAAAGGGAAGTTTG 59.224 37.037 0.00 0.00 37.10 2.93
4946 5476 2.827921 ACACCCCAAATGAGATGCTTTC 59.172 45.455 0.00 0.00 0.00 2.62
5057 5587 8.864069 TGTGTTTAGTCCAACATGTAAAAATG 57.136 30.769 0.00 0.00 38.89 2.32
5124 5654 9.451002 TGTACCGGAAAATAACATCTATGAAAA 57.549 29.630 9.46 0.00 0.00 2.29
5157 5687 4.578928 AGGGTCACCATACGCAATATTTTC 59.421 41.667 0.00 0.00 40.13 2.29
5174 5704 9.439461 CTCATATTAATATCTCCCATAGGGTCA 57.561 37.037 4.93 0.00 44.74 4.02
5235 5765 8.579850 TTTGGCAATATCTTAGTGAACTCATT 57.420 30.769 0.00 0.00 0.00 2.57
5245 5775 8.105829 AGTCATATCCCTTTGGCAATATCTTAG 58.894 37.037 0.00 0.00 0.00 2.18
5259 5789 7.640313 TGTCCTATATACGAGTCATATCCCTT 58.360 38.462 0.00 0.00 0.00 3.95
5277 5807 8.117312 ACTTAAACTAGAACCTCTCTGTCCTAT 58.883 37.037 0.00 0.00 35.41 2.57
5360 5890 4.545610 TGAAACATCGAAACCAATTCAGC 58.454 39.130 0.00 0.00 37.96 4.26
5519 6049 4.098349 GGCTTGCCATCAAATTCATCAGTA 59.902 41.667 6.79 0.00 0.00 2.74
5559 6089 4.142447 TGAAGAACGATACTCCTACTGCAC 60.142 45.833 0.00 0.00 0.00 4.57
5622 6152 4.092383 GCAATGATGACAACCTGAAAATGC 59.908 41.667 0.00 0.00 0.00 3.56
5706 6236 1.090625 CCGACCTCGTGATCTCTCGT 61.091 60.000 0.00 0.00 37.74 4.18
5871 6409 0.823356 AACATGCTGCTTCCACCGTT 60.823 50.000 0.00 0.00 0.00 4.44
5990 6561 4.873827 TCTCTTGTGGCATTATCGTTAACC 59.126 41.667 0.00 0.00 0.00 2.85
6037 6610 9.793252 TTTATACTTGTCGTTAAGTCTACCATC 57.207 33.333 9.65 0.00 41.01 3.51
6085 6663 5.743636 ACAACAGACCAATTTGGCATAAT 57.256 34.783 15.49 0.00 42.67 1.28
6093 6671 7.651704 GCAGTTAACATTACAACAGACCAATTT 59.348 33.333 8.61 0.00 0.00 1.82
6096 6674 5.277586 CGCAGTTAACATTACAACAGACCAA 60.278 40.000 8.61 0.00 0.00 3.67
6098 6676 4.378046 CCGCAGTTAACATTACAACAGACC 60.378 45.833 8.61 0.00 0.00 3.85
6099 6677 4.708601 CCGCAGTTAACATTACAACAGAC 58.291 43.478 8.61 0.00 0.00 3.51
6100 6678 3.187637 GCCGCAGTTAACATTACAACAGA 59.812 43.478 8.61 0.00 0.00 3.41
6101 6679 3.058570 TGCCGCAGTTAACATTACAACAG 60.059 43.478 8.61 0.00 0.00 3.16
6130 6761 1.729276 CTGTGTGCCTGTGTGGTTG 59.271 57.895 0.00 0.00 38.35 3.77
6168 6799 4.975502 TGATTCGCATTATTTCGGCAATTC 59.024 37.500 0.00 0.00 0.00 2.17
6200 6831 2.050714 CAGCTGTGCGCCTGTTTG 60.051 61.111 4.18 0.00 40.39 2.93
6201 6832 2.516930 ACAGCTGTGCGCCTGTTT 60.517 55.556 20.97 0.00 40.39 2.83
6231 6891 1.327764 GCTCGCAGTTACAAGGCATAC 59.672 52.381 0.00 0.00 0.00 2.39
6353 7029 5.994887 TTGCTTTGTACTGTACGTCATTT 57.005 34.783 12.87 0.00 0.00 2.32
6357 7033 5.070862 CGATTTTGCTTTGTACTGTACGTC 58.929 41.667 12.87 3.27 0.00 4.34
6360 7036 5.844396 GTGACGATTTTGCTTTGTACTGTAC 59.156 40.000 10.98 10.98 0.00 2.90
6366 7042 4.902443 TTGGTGACGATTTTGCTTTGTA 57.098 36.364 0.00 0.00 0.00 2.41
6367 7043 3.791973 TTGGTGACGATTTTGCTTTGT 57.208 38.095 0.00 0.00 0.00 2.83
6369 7045 4.111916 CACTTTGGTGACGATTTTGCTTT 58.888 39.130 0.00 0.00 45.61 3.51
6370 7046 3.130340 ACACTTTGGTGACGATTTTGCTT 59.870 39.130 3.06 0.00 45.61 3.91
6385 7061 2.480073 CCAAACAGGCAGACACACTTTG 60.480 50.000 0.00 0.00 0.00 2.77
6419 7125 5.493133 TTGCGTATTTCTTGAACAAGTGT 57.507 34.783 13.15 4.96 39.38 3.55
6461 7201 9.403583 CATTGATATGATATGAATCCATCACCA 57.596 33.333 0.00 0.00 35.84 4.17
6470 7210 6.832384 GGCCACTCCATTGATATGATATGAAT 59.168 38.462 0.00 0.00 33.37 2.57
6511 7251 6.126568 TGTGTTGCTTACCTTACTTTTGAC 57.873 37.500 0.00 0.00 0.00 3.18
6523 7263 6.371548 TGGATAAGATCTGTTGTGTTGCTTAC 59.628 38.462 0.00 0.00 0.00 2.34
6542 7282 3.205815 GGCACCTTGGCATGGATAA 57.794 52.632 24.70 0.00 43.14 1.75
6556 7296 2.684881 CAAGATTGGTCATACTGGGCAC 59.315 50.000 0.00 0.00 0.00 5.01
6557 7297 2.945440 GCAAGATTGGTCATACTGGGCA 60.945 50.000 0.00 0.00 0.00 5.36
6615 7362 6.207810 AGAGTAGCCGAGTTTGGAATATAGAG 59.792 42.308 0.00 0.00 0.00 2.43
6616 7363 6.016192 CAGAGTAGCCGAGTTTGGAATATAGA 60.016 42.308 0.00 0.00 0.00 1.98
6675 7424 1.209019 CACTCTGCTGGTTGGCTCTAT 59.791 52.381 0.00 0.00 0.00 1.98
6684 7433 2.194388 CTGGATGGCACTCTGCTGGT 62.194 60.000 0.00 0.00 44.28 4.00


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

AutoCloner maintained by Alex Coulton.