Multiple sequence alignment - TraesCS2D01G551500

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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 TraesCS2D01G551500 chr2D 100.000 7321 0 0 1 7321 627158353 627165673 0.000000e+00 13520.0
1 TraesCS2D01G551500 chr2D 90.909 121 10 1 7127 7247 627231333 627231452 2.110000e-35 161.0
2 TraesCS2D01G551500 chr2D 83.036 112 13 2 6509 6614 188888394 188888283 6.050000e-16 97.1
3 TraesCS2D01G551500 chr7D 99.079 3693 22 5 1710 5401 612451712 612448031 0.000000e+00 6621.0
4 TraesCS2D01G551500 chr7D 92.632 95 7 0 279 373 252265185 252265279 3.560000e-28 137.0
5 TraesCS2D01G551500 chrUn 99.052 3693 23 5 1710 5401 299169425 299173106 0.000000e+00 6615.0
6 TraesCS2D01G551500 chrUn 96.003 2377 68 7 2235 4609 71458286 71460637 0.000000e+00 3838.0
7 TraesCS2D01G551500 chrUn 99.503 1409 5 1 3995 5403 320392815 320391409 0.000000e+00 2562.0
8 TraesCS2D01G551500 chr2A 96.403 3698 83 15 1710 5403 3423497 3419846 0.000000e+00 6047.0
9 TraesCS2D01G551500 chr2A 94.267 1343 59 7 379 1709 757897663 757898999 0.000000e+00 2037.0
10 TraesCS2D01G551500 chr2A 93.988 865 30 4 5403 6252 757898992 757899849 0.000000e+00 1290.0
11 TraesCS2D01G551500 chr2A 90.247 851 47 12 6247 7077 757899874 757900708 0.000000e+00 1079.0
12 TraesCS2D01G551500 chr2A 94.857 175 8 1 7074 7248 757900795 757900968 9.360000e-69 272.0
13 TraesCS2D01G551500 chr2A 93.506 154 9 1 2 154 757895706 757895859 2.050000e-55 228.0
14 TraesCS2D01G551500 chr2A 96.809 94 3 0 144 237 757897306 757897399 2.730000e-34 158.0
15 TraesCS2D01G551500 chr2A 84.496 129 9 6 7130 7247 757926007 757926135 4.640000e-22 117.0
16 TraesCS2D01G551500 chr5A 96.112 3704 88 20 1710 5403 535688250 535691907 0.000000e+00 5991.0
17 TraesCS2D01G551500 chr3D 95.945 3699 121 14 1707 5401 51797113 51800786 0.000000e+00 5973.0
18 TraesCS2D01G551500 chr3D 91.837 98 6 2 279 376 463184429 463184334 1.280000e-27 135.0
19 TraesCS2D01G551500 chr3D 96.875 32 1 0 577 608 524783168 524783199 4.000000e-03 54.7
20 TraesCS2D01G551500 chr7A 95.943 3697 101 17 1710 5402 695712934 695716585 0.000000e+00 5951.0
21 TraesCS2D01G551500 chr6A 94.730 3700 113 31 1708 5402 10197357 10200979 0.000000e+00 5677.0
22 TraesCS2D01G551500 chr6A 95.735 2204 86 6 3201 5402 134861027 134863224 0.000000e+00 3542.0
23 TraesCS2D01G551500 chr6A 92.513 1496 79 7 1710 3205 134855357 134856819 0.000000e+00 2111.0
24 TraesCS2D01G551500 chr6A 92.708 96 6 1 288 383 101438278 101438372 3.560000e-28 137.0
25 TraesCS2D01G551500 chr2B 91.759 1978 85 26 5403 7320 768610312 768612271 0.000000e+00 2678.0
26 TraesCS2D01G551500 chr2B 94.974 1174 40 7 540 1709 768609161 768610319 0.000000e+00 1823.0
27 TraesCS2D01G551500 chr2B 91.022 323 14 2 1 321 768593111 768593420 8.780000e-114 422.0
28 TraesCS2D01G551500 chr2B 94.068 236 6 3 315 547 768607947 768608177 1.170000e-92 351.0
29 TraesCS2D01G551500 chr2B 92.562 121 9 0 7127 7247 769044692 769044812 2.720000e-39 174.0
30 TraesCS2D01G551500 chr2B 86.111 108 9 1 6513 6614 161412326 161412219 2.160000e-20 111.0
31 TraesCS2D01G551500 chr2B 82.609 115 13 2 6511 6618 547540474 547540360 2.170000e-15 95.3
32 TraesCS2D01G551500 chr1A 93.941 1634 52 12 1710 3338 535860387 535861978 0.000000e+00 2425.0
33 TraesCS2D01G551500 chr1A 82.031 128 14 4 6504 6624 583884801 583884676 4.670000e-17 100.0
34 TraesCS2D01G551500 chr5B 92.381 105 6 2 284 387 307068601 307068704 1.650000e-31 148.0
35 TraesCS2D01G551500 chr5B 95.402 87 4 0 286 372 429030694 429030608 9.900000e-29 139.0
36 TraesCS2D01G551500 chr5B 85.981 107 9 1 6512 6612 316708824 316708930 7.770000e-20 110.0
37 TraesCS2D01G551500 chr3B 90.476 105 9 1 278 381 472309450 472309346 3.560000e-28 137.0
38 TraesCS2D01G551500 chr3B 91.837 98 8 0 281 378 737755454 737755551 3.560000e-28 137.0
39 TraesCS2D01G551500 chr3B 100.000 32 0 0 577 608 692221695 692221726 7.930000e-05 60.2
40 TraesCS2D01G551500 chr7B 90.291 103 8 2 282 383 551488107 551488208 4.610000e-27 134.0
41 TraesCS2D01G551500 chr6B 84.906 106 10 3 6514 6613 42775731 42775626 1.300000e-17 102.0
42 TraesCS2D01G551500 chr5D 84.112 107 11 1 6512 6612 282007012 282007118 1.680000e-16 99.0
43 TraesCS2D01G551500 chr1B 100.000 35 0 0 6250 6284 17960754 17960720 1.700000e-06 65.8
44 TraesCS2D01G551500 chr3A 100.000 32 0 0 577 608 659159946 659159977 7.930000e-05 60.2


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 TraesCS2D01G551500 chr2D 627158353 627165673 7320 False 13520.000000 13520 100.000000 1 7321 1 chr2D.!!$F1 7320
1 TraesCS2D01G551500 chr7D 612448031 612451712 3681 True 6621.000000 6621 99.079000 1710 5401 1 chr7D.!!$R1 3691
2 TraesCS2D01G551500 chrUn 299169425 299173106 3681 False 6615.000000 6615 99.052000 1710 5401 1 chrUn.!!$F2 3691
3 TraesCS2D01G551500 chrUn 71458286 71460637 2351 False 3838.000000 3838 96.003000 2235 4609 1 chrUn.!!$F1 2374
4 TraesCS2D01G551500 chrUn 320391409 320392815 1406 True 2562.000000 2562 99.503000 3995 5403 1 chrUn.!!$R1 1408
5 TraesCS2D01G551500 chr2A 3419846 3423497 3651 True 6047.000000 6047 96.403000 1710 5403 1 chr2A.!!$R1 3693
6 TraesCS2D01G551500 chr2A 757895706 757900968 5262 False 844.000000 2037 93.945667 2 7248 6 chr2A.!!$F2 7246
7 TraesCS2D01G551500 chr5A 535688250 535691907 3657 False 5991.000000 5991 96.112000 1710 5403 1 chr5A.!!$F1 3693
8 TraesCS2D01G551500 chr3D 51797113 51800786 3673 False 5973.000000 5973 95.945000 1707 5401 1 chr3D.!!$F1 3694
9 TraesCS2D01G551500 chr7A 695712934 695716585 3651 False 5951.000000 5951 95.943000 1710 5402 1 chr7A.!!$F1 3692
10 TraesCS2D01G551500 chr6A 10197357 10200979 3622 False 5677.000000 5677 94.730000 1708 5402 1 chr6A.!!$F1 3694
11 TraesCS2D01G551500 chr6A 134861027 134863224 2197 False 3542.000000 3542 95.735000 3201 5402 1 chr6A.!!$F4 2201
12 TraesCS2D01G551500 chr6A 134855357 134856819 1462 False 2111.000000 2111 92.513000 1710 3205 1 chr6A.!!$F3 1495
13 TraesCS2D01G551500 chr2B 768607947 768612271 4324 False 1617.333333 2678 93.600333 315 7320 3 chr2B.!!$F3 7005
14 TraesCS2D01G551500 chr1A 535860387 535861978 1591 False 2425.000000 2425 93.941000 1710 3338 1 chr1A.!!$F1 1628

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
92 94 1.230281 TGGAGGGCTGGGAAGGATT 60.230 57.895 0.00 0.0 0.00 3.01 F
1366 4045 1.468506 GGTTGCGTCCATGGGGTTTT 61.469 55.000 13.02 0.0 34.93 2.43 F
2467 5169 0.036732 TTGGATTGCTTGCCGACTCT 59.963 50.000 0.00 0.0 0.00 3.24 F
4857 7611 0.537143 TTGCCAGTCTCAACGGCATT 60.537 50.000 2.75 0.0 46.69 3.56 F
5507 8264 1.077787 CCATGCCGAGCTACCCAAA 60.078 57.895 0.00 0.0 0.00 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1496 4180 0.468400 GTTTAACCCACCCTGCACCA 60.468 55.000 0.00 0.0 0.00 4.17 R
3960 6713 8.219769 GCTGATCTAAGATATTTTGATGACGTG 58.780 37.037 0.00 0.0 0.00 4.49 R
5059 7813 3.296854 AGATAGAATGGAGCGTACCACA 58.703 45.455 4.98 0.0 43.03 4.17 R
6036 8811 0.394938 TTGCACGGACCAGTGTACAT 59.605 50.000 14.95 0.0 43.61 2.29 R
7263 10226 0.593128 CTTGCTGCGTTAAAGTGGCT 59.407 50.000 0.00 0.0 0.00 4.75 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
59 61 3.870723 TCACAAAATCAAACGGTCGAG 57.129 42.857 0.00 0.00 0.00 4.04
83 85 2.439701 CATGGCACTGGAGGGCTG 60.440 66.667 0.00 0.00 0.00 4.85
91 93 1.695597 CTGGAGGGCTGGGAAGGAT 60.696 63.158 0.00 0.00 0.00 3.24
92 94 1.230281 TGGAGGGCTGGGAAGGATT 60.230 57.895 0.00 0.00 0.00 3.01
196 1655 8.795513 TGGTACATTAAAGATATGATGCATTGG 58.204 33.333 0.00 0.00 0.00 3.16
203 1662 4.649692 AGATATGATGCATTGGGAGTGTC 58.350 43.478 0.00 0.00 0.00 3.67
237 1696 7.398024 ACTCCCAATGCATTATATCTTAGACC 58.602 38.462 12.53 0.00 0.00 3.85
239 1698 7.932134 TCCCAATGCATTATATCTTAGACCAT 58.068 34.615 12.53 0.00 0.00 3.55
240 1699 9.056799 TCCCAATGCATTATATCTTAGACCATA 57.943 33.333 12.53 0.00 0.00 2.74
241 1700 9.857656 CCCAATGCATTATATCTTAGACCATAT 57.142 33.333 12.53 0.00 0.00 1.78
282 1959 7.739444 TGAACTCAGATATAACCCCTCCAATAT 59.261 37.037 0.00 0.00 0.00 1.28
283 1960 9.268282 GAACTCAGATATAACCCCTCCAATATA 57.732 37.037 0.00 0.00 0.00 0.86
284 1961 9.805204 AACTCAGATATAACCCCTCCAATATAT 57.195 33.333 0.00 0.00 0.00 0.86
285 1962 9.805204 ACTCAGATATAACCCCTCCAATATATT 57.195 33.333 0.00 0.00 0.00 1.28
287 1964 9.574577 TCAGATATAACCCCTCCAATATATTGT 57.425 33.333 21.20 6.28 36.06 2.71
293 1970 6.449830 ACCCCTCCAATATATTGTACTTCC 57.550 41.667 21.20 0.00 36.06 3.46
294 1971 6.158260 ACCCCTCCAATATATTGTACTTCCT 58.842 40.000 21.20 0.00 36.06 3.36
295 1972 6.272558 ACCCCTCCAATATATTGTACTTCCTC 59.727 42.308 21.20 0.00 36.06 3.71
296 1973 6.296489 CCCCTCCAATATATTGTACTTCCTCC 60.296 46.154 21.20 0.00 36.06 4.30
297 1974 6.502158 CCCTCCAATATATTGTACTTCCTCCT 59.498 42.308 21.20 0.00 36.06 3.69
298 1975 7.017651 CCCTCCAATATATTGTACTTCCTCCTT 59.982 40.741 21.20 0.00 36.06 3.36
299 1976 8.097662 CCTCCAATATATTGTACTTCCTCCTTC 58.902 40.741 21.20 0.00 36.06 3.46
300 1977 7.974504 TCCAATATATTGTACTTCCTCCTTCC 58.025 38.462 21.20 0.00 36.06 3.46
301 1978 7.017254 TCCAATATATTGTACTTCCTCCTTCCC 59.983 40.741 21.20 0.00 36.06 3.97
302 1979 7.202186 CCAATATATTGTACTTCCTCCTTCCCA 60.202 40.741 21.20 0.00 36.06 4.37
303 1980 8.386264 CAATATATTGTACTTCCTCCTTCCCAT 58.614 37.037 16.03 0.00 33.22 4.00
304 1981 9.629649 AATATATTGTACTTCCTCCTTCCCATA 57.370 33.333 0.00 0.00 0.00 2.74
305 1982 7.947782 ATATTGTACTTCCTCCTTCCCATAA 57.052 36.000 0.00 0.00 0.00 1.90
306 1983 6.848562 ATTGTACTTCCTCCTTCCCATAAT 57.151 37.500 0.00 0.00 0.00 1.28
307 1984 5.630415 TGTACTTCCTCCTTCCCATAATG 57.370 43.478 0.00 0.00 0.00 1.90
308 1985 5.036916 TGTACTTCCTCCTTCCCATAATGT 58.963 41.667 0.00 0.00 0.00 2.71
309 1986 6.206787 TGTACTTCCTCCTTCCCATAATGTA 58.793 40.000 0.00 0.00 0.00 2.29
310 1987 5.896073 ACTTCCTCCTTCCCATAATGTAG 57.104 43.478 0.00 0.00 0.00 2.74
311 1988 4.660771 ACTTCCTCCTTCCCATAATGTAGG 59.339 45.833 0.00 0.00 0.00 3.18
312 1989 4.569676 TCCTCCTTCCCATAATGTAGGA 57.430 45.455 0.00 0.00 34.07 2.94
313 1990 4.232091 TCCTCCTTCCCATAATGTAGGAC 58.768 47.826 0.00 0.00 31.92 3.85
531 2208 4.173256 ACATAATTTGTTTGCTTAGGCGC 58.827 39.130 0.00 0.00 36.81 6.53
987 3661 2.186076 CACTTCTCTTCGATACCACGC 58.814 52.381 0.00 0.00 0.00 5.34
1197 3871 1.672356 CCGTCCTCCTGCTGGTTTG 60.672 63.158 9.73 1.81 34.23 2.93
1205 3879 2.887152 CTCCTGCTGGTTTGCTACTTTT 59.113 45.455 9.73 0.00 34.23 2.27
1277 3951 5.367302 TCATATGAGCAATGGTGATCGAAA 58.633 37.500 0.00 0.00 43.37 3.46
1366 4045 1.468506 GGTTGCGTCCATGGGGTTTT 61.469 55.000 13.02 0.00 34.93 2.43
1419 4098 4.820284 AGCAAGCTGTAGTTGAACTTTC 57.180 40.909 1.97 0.00 0.00 2.62
1595 4279 2.184830 CGAGCATGGGCATCACTGG 61.185 63.158 0.00 0.00 44.61 4.00
1671 4355 2.434884 AATGAGGTGGCGCGTGAG 60.435 61.111 8.43 0.00 0.00 3.51
1931 4616 1.843368 AACAATCAGATGGGCCACAG 58.157 50.000 9.28 0.98 0.00 3.66
1996 4693 6.573664 AGAAGAATCTGAATCGATCGATCT 57.426 37.500 29.48 18.59 33.59 2.75
2226 4923 0.108804 GACGGTCAAGATCGGAAGCA 60.109 55.000 7.71 0.00 39.68 3.91
2463 5165 1.249469 TGCATTGGATTGCTTGCCGA 61.249 50.000 0.00 0.00 43.18 5.54
2464 5166 0.803380 GCATTGGATTGCTTGCCGAC 60.803 55.000 0.00 0.00 39.57 4.79
2465 5167 0.813184 CATTGGATTGCTTGCCGACT 59.187 50.000 0.00 0.00 0.00 4.18
2466 5168 1.098050 ATTGGATTGCTTGCCGACTC 58.902 50.000 0.00 0.00 0.00 3.36
2467 5169 0.036732 TTGGATTGCTTGCCGACTCT 59.963 50.000 0.00 0.00 0.00 3.24
2468 5170 0.901827 TGGATTGCTTGCCGACTCTA 59.098 50.000 0.00 0.00 0.00 2.43
2469 5171 1.291132 GGATTGCTTGCCGACTCTAC 58.709 55.000 0.00 0.00 0.00 2.59
3960 6713 0.985490 AGGGATTCACTGAGGGAGGC 60.985 60.000 0.00 0.00 0.00 4.70
4673 7427 3.444034 TGGAGATTTCTCTAGTGGTGACG 59.556 47.826 7.47 0.00 42.48 4.35
4857 7611 0.537143 TTGCCAGTCTCAACGGCATT 60.537 50.000 2.75 0.00 46.69 3.56
5059 7813 5.749032 GCCCAGGTCCAATTAGCATATTACT 60.749 44.000 0.00 0.00 0.00 2.24
5060 7814 5.707298 CCCAGGTCCAATTAGCATATTACTG 59.293 44.000 0.00 0.00 0.00 2.74
5507 8264 1.077787 CCATGCCGAGCTACCCAAA 60.078 57.895 0.00 0.00 0.00 3.28
5610 8367 1.671054 CCTGACCGCGTTGATTGGT 60.671 57.895 4.92 0.00 39.12 3.67
5678 8435 1.743623 CGCATGTTGGGCCTTCGTA 60.744 57.895 4.53 0.00 0.00 3.43
5886 8643 2.436646 GTCGGTGCCACATGAGGG 60.437 66.667 11.42 7.51 0.00 4.30
6036 8811 1.549243 TTACAGCGAGGACATGGGCA 61.549 55.000 0.00 0.00 0.00 5.36
6077 8858 3.894547 AACCATCACCCACGCCGTC 62.895 63.158 0.00 0.00 0.00 4.79
6078 8859 4.082523 CCATCACCCACGCCGTCT 62.083 66.667 0.00 0.00 0.00 4.18
6079 8860 2.047274 CATCACCCACGCCGTCTT 60.047 61.111 0.00 0.00 0.00 3.01
6080 8861 2.047274 ATCACCCACGCCGTCTTG 60.047 61.111 0.00 0.00 0.00 3.02
6081 8862 3.605749 ATCACCCACGCCGTCTTGG 62.606 63.158 0.00 0.00 42.50 3.61
6082 8863 4.619227 CACCCACGCCGTCTTGGT 62.619 66.667 0.00 0.00 41.21 3.67
6098 8879 2.584608 GTGGTCGGCTATGGCACT 59.415 61.111 2.58 0.00 40.87 4.40
6160 8941 1.218854 GCACCAAATGGGGTCATGC 59.781 57.895 3.21 0.00 41.84 4.06
6299 9110 1.550327 TCTTCGGTCTGCATCTGTCT 58.450 50.000 0.00 0.00 0.00 3.41
6368 9179 3.464907 AGTGCATGTGATGATCTGTAGC 58.535 45.455 0.00 0.00 0.00 3.58
6477 9292 3.753272 GCTCCTTGCTCATTGTTCTTGTA 59.247 43.478 0.00 0.00 38.95 2.41
6478 9293 4.397417 GCTCCTTGCTCATTGTTCTTGTAT 59.603 41.667 0.00 0.00 38.95 2.29
6479 9294 5.586243 GCTCCTTGCTCATTGTTCTTGTATA 59.414 40.000 0.00 0.00 38.95 1.47
6480 9295 6.238320 GCTCCTTGCTCATTGTTCTTGTATAG 60.238 42.308 0.00 0.00 38.95 1.31
6481 9296 5.586243 TCCTTGCTCATTGTTCTTGTATAGC 59.414 40.000 0.00 0.00 0.00 2.97
6482 9297 5.220931 CCTTGCTCATTGTTCTTGTATAGCC 60.221 44.000 0.00 0.00 0.00 3.93
6525 9345 5.045651 TCAATTCTGCTACTCCCTTTGATCA 60.046 40.000 0.00 0.00 0.00 2.92
6530 9350 6.763355 TCTGCTACTCCCTTTGATCAATATC 58.237 40.000 9.40 0.00 0.00 1.63
6568 9388 7.268199 ACGGATGTATCTAGACGTATTTCAA 57.732 36.000 0.00 0.00 32.30 2.69
6571 9391 7.201359 CGGATGTATCTAGACGTATTTCAATGC 60.201 40.741 0.00 0.00 0.00 3.56
6575 9395 9.841880 TGTATCTAGACGTATTTCAATGCTATC 57.158 33.333 0.00 0.00 0.00 2.08
6601 9426 6.562270 CGTTTGAGCGACAACTAATATGGATC 60.562 42.308 0.00 0.00 38.29 3.36
6671 9512 1.918957 AGTAGCCCAGCTTTCAGGATT 59.081 47.619 0.00 0.00 40.44 3.01
6674 9515 0.323725 GCCCAGCTTTCAGGATTGGA 60.324 55.000 0.00 0.00 0.00 3.53
6693 9534 9.832445 GGATTGGATCTGTTTCTACTTGTATTA 57.168 33.333 0.00 0.00 0.00 0.98
6727 9568 3.229293 TGCATTTGGATTGGACTTGACA 58.771 40.909 0.00 0.00 0.00 3.58
6770 9612 5.898606 CGATTCGAATGAAACTGATTAGCAC 59.101 40.000 16.96 0.00 37.71 4.40
6863 9710 5.941058 TCACAGAGTCAAAGAGGTAGTCTAG 59.059 44.000 0.00 0.00 32.65 2.43
6870 9717 8.339344 AGTCAAAGAGGTAGTCTAGACTAAAC 57.661 38.462 29.75 24.49 43.68 2.01
7059 9911 6.919775 ATATACCATGGTAAGAGGACTGTC 57.080 41.667 27.93 0.00 33.99 3.51
7238 10181 5.456921 AAGGAAGAAATATTCAGGCCTCA 57.543 39.130 0.00 0.00 0.00 3.86
7286 10249 2.032799 CCACTTTAACGCAGCAAGTCAA 59.967 45.455 0.00 0.00 0.00 3.18
7292 10255 2.405892 ACGCAGCAAGTCAATTTCAC 57.594 45.000 0.00 0.00 0.00 3.18
7294 10257 2.098934 ACGCAGCAAGTCAATTTCACAA 59.901 40.909 0.00 0.00 0.00 3.33
7298 10261 5.464168 GCAGCAAGTCAATTTCACAACTAT 58.536 37.500 0.00 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.022589 CCATCAGATATGTTGTGCAATCCC 60.023 45.833 0.00 0.00 0.00 3.85
43 44 2.349155 GCGTTCTCGACCGTTTGATTTT 60.349 45.455 0.00 0.00 39.71 1.82
59 61 1.915614 CTCCAGTGCCATGTGCGTTC 61.916 60.000 0.00 0.00 45.60 3.95
64 66 2.753043 GCCCTCCAGTGCCATGTG 60.753 66.667 0.00 0.00 0.00 3.21
66 68 2.439701 CAGCCCTCCAGTGCCATG 60.440 66.667 0.00 0.00 0.00 3.66
83 85 6.070995 AGGAAATTAAAACCGAAATCCTTCCC 60.071 38.462 0.00 0.00 32.25 3.97
91 93 7.385478 GCCACATTTAGGAAATTAAAACCGAAA 59.615 33.333 0.00 0.00 34.15 3.46
92 94 6.869388 GCCACATTTAGGAAATTAAAACCGAA 59.131 34.615 0.00 0.00 0.00 4.30
172 1631 9.013229 TCCCAATGCATCATATCTTTAATGTAC 57.987 33.333 0.00 0.00 0.00 2.90
282 1959 7.349859 ACATTATGGGAAGGAGGAAGTACAATA 59.650 37.037 0.00 0.00 0.00 1.90
283 1960 6.160459 ACATTATGGGAAGGAGGAAGTACAAT 59.840 38.462 0.00 0.00 0.00 2.71
284 1961 5.491078 ACATTATGGGAAGGAGGAAGTACAA 59.509 40.000 0.00 0.00 0.00 2.41
285 1962 5.036916 ACATTATGGGAAGGAGGAAGTACA 58.963 41.667 0.00 0.00 0.00 2.90
286 1963 5.632034 ACATTATGGGAAGGAGGAAGTAC 57.368 43.478 0.00 0.00 0.00 2.73
287 1964 5.844516 CCTACATTATGGGAAGGAGGAAGTA 59.155 44.000 0.00 0.00 0.00 2.24
288 1965 4.660771 CCTACATTATGGGAAGGAGGAAGT 59.339 45.833 0.00 0.00 0.00 3.01
289 1966 4.907875 TCCTACATTATGGGAAGGAGGAAG 59.092 45.833 8.49 0.00 34.36 3.46
290 1967 4.658901 GTCCTACATTATGGGAAGGAGGAA 59.341 45.833 11.68 0.00 40.22 3.36
291 1968 4.232091 GTCCTACATTATGGGAAGGAGGA 58.768 47.826 11.68 0.00 40.22 3.71
292 1969 3.006967 CGTCCTACATTATGGGAAGGAGG 59.993 52.174 11.68 13.06 40.22 4.30
293 1970 3.641906 ACGTCCTACATTATGGGAAGGAG 59.358 47.826 11.68 9.34 40.22 3.69
294 1971 3.649843 ACGTCCTACATTATGGGAAGGA 58.350 45.455 8.49 8.49 40.22 3.36
295 1972 4.417426 AACGTCCTACATTATGGGAAGG 57.583 45.455 7.88 6.37 40.22 3.46
296 1973 6.753107 AAAAACGTCCTACATTATGGGAAG 57.247 37.500 0.00 0.00 40.22 3.46
343 2020 5.072329 CCCTCTGTCCCATAATGTAAGATGT 59.928 44.000 0.00 0.00 0.00 3.06
344 2021 5.307976 TCCCTCTGTCCCATAATGTAAGATG 59.692 44.000 0.00 0.00 0.00 2.90
345 2022 5.476983 TCCCTCTGTCCCATAATGTAAGAT 58.523 41.667 0.00 0.00 0.00 2.40
531 2208 6.543465 TGCCTTTGACCATATCTTAGTCATTG 59.457 38.462 0.00 0.00 40.06 2.82
771 3445 4.402155 TCCAATGGCACTTCAAATGTATCC 59.598 41.667 0.00 0.00 0.00 2.59
1197 3871 9.900264 CAAAATAAAACAGTGACAAAAAGTAGC 57.100 29.630 0.00 0.00 0.00 3.58
1205 3879 9.092876 GAAATCCACAAAATAAAACAGTGACAA 57.907 29.630 0.00 0.00 32.14 3.18
1293 3967 8.146053 TCTAAGACAGAATGGTCAATAAGGAA 57.854 34.615 0.00 0.00 43.62 3.36
1302 3976 5.046231 AGGAAACCTCTAAGACAGAATGGTC 60.046 44.000 0.00 0.00 43.62 4.02
1382 4061 1.904287 TGCTTTGCAGGGTAACGAAT 58.096 45.000 0.00 0.00 33.32 3.34
1419 4098 8.882415 ACTAATAGACATTAATTGTACCGGTG 57.118 34.615 19.93 0.00 39.18 4.94
1481 4165 6.043822 ACCCTGCACCACACAACATATATATA 59.956 38.462 0.00 0.00 0.00 0.86
1482 4166 5.163099 ACCCTGCACCACACAACATATATAT 60.163 40.000 0.00 0.00 0.00 0.86
1483 4167 4.165180 ACCCTGCACCACACAACATATATA 59.835 41.667 0.00 0.00 0.00 0.86
1484 4168 3.053693 ACCCTGCACCACACAACATATAT 60.054 43.478 0.00 0.00 0.00 0.86
1496 4180 0.468400 GTTTAACCCACCCTGCACCA 60.468 55.000 0.00 0.00 0.00 4.17
1497 4181 0.468400 TGTTTAACCCACCCTGCACC 60.468 55.000 0.00 0.00 0.00 5.01
1595 4279 2.018515 CCTCCGACTCTAGGTCTTGAC 58.981 57.143 8.96 0.00 42.44 3.18
1648 4332 2.480555 CGCCACCTCATTGAACGC 59.519 61.111 0.00 0.00 0.00 4.84
1671 4355 0.659957 GCATCAACTTCTCATCGGGC 59.340 55.000 0.00 0.00 0.00 6.13
1701 4385 1.247567 AATCCGCCACTGGTTTGAAG 58.752 50.000 0.00 0.00 0.00 3.02
1702 4386 1.698506 AAATCCGCCACTGGTTTGAA 58.301 45.000 0.00 0.00 0.00 2.69
1703 4387 2.156098 GTAAATCCGCCACTGGTTTGA 58.844 47.619 0.00 0.00 0.00 2.69
1704 4388 1.201414 GGTAAATCCGCCACTGGTTTG 59.799 52.381 0.00 0.00 0.00 2.93
1705 4389 1.541379 GGTAAATCCGCCACTGGTTT 58.459 50.000 0.00 0.00 0.00 3.27
1706 4390 3.259592 GGTAAATCCGCCACTGGTT 57.740 52.632 0.00 0.00 0.00 3.67
1996 4693 1.403647 CGAACAGGCGACTTGTGGATA 60.404 52.381 0.00 0.00 40.21 2.59
2094 4791 1.395826 GGCGGCAGTCTCTACCTCAT 61.396 60.000 3.07 0.00 0.00 2.90
3960 6713 8.219769 GCTGATCTAAGATATTTTGATGACGTG 58.780 37.037 0.00 0.00 0.00 4.49
3993 6746 6.617371 ACCTCTTCCACTAAATATCTCACCAT 59.383 38.462 0.00 0.00 0.00 3.55
4673 7427 4.184629 AGTTCGTCTCTTATGATTGCACC 58.815 43.478 0.00 0.00 0.00 5.01
4770 7524 6.713762 AATGTTTCTCAGTTTCAACCATCA 57.286 33.333 0.00 0.00 0.00 3.07
5059 7813 3.296854 AGATAGAATGGAGCGTACCACA 58.703 45.455 4.98 0.00 43.03 4.17
5060 7814 5.449107 TTAGATAGAATGGAGCGTACCAC 57.551 43.478 4.98 0.00 43.03 4.16
5145 7899 1.896220 ACGTTCATCCTTGTGCACAT 58.104 45.000 22.39 1.80 0.00 3.21
5507 8264 2.846371 GGTGCAATCAGCTTCGACT 58.154 52.632 0.00 0.00 45.94 4.18
5865 8622 3.792047 CATGTGGCACCGACGCTG 61.792 66.667 16.26 0.00 0.00 5.18
6008 8783 3.130516 TGTCCTCGCTGTAATAGTGGAAG 59.869 47.826 0.00 0.00 37.51 3.46
6036 8811 0.394938 TTGCACGGACCAGTGTACAT 59.605 50.000 14.95 0.00 43.61 2.29
6077 8858 1.819632 GCCATAGCCGACCACCAAG 60.820 63.158 0.00 0.00 0.00 3.61
6078 8859 2.270850 GCCATAGCCGACCACCAA 59.729 61.111 0.00 0.00 0.00 3.67
6079 8860 3.006133 TGCCATAGCCGACCACCA 61.006 61.111 0.00 0.00 38.69 4.17
6080 8861 2.513897 GTGCCATAGCCGACCACC 60.514 66.667 0.00 0.00 38.69 4.61
6081 8862 1.815421 CAGTGCCATAGCCGACCAC 60.815 63.158 0.00 0.00 38.69 4.16
6082 8863 1.987306 TCAGTGCCATAGCCGACCA 60.987 57.895 0.00 0.00 38.69 4.02
6098 8879 3.630769 AGTATCTTCGTAGGAATGCGTCA 59.369 43.478 0.00 0.00 0.00 4.35
6160 8941 1.581934 CGCCATGTACATGTACCCTG 58.418 55.000 29.25 24.18 37.11 4.45
6299 9110 9.684448 CTTCGTTATCTGCTCTGAATAAGATAA 57.316 33.333 10.16 10.16 38.61 1.75
6340 9151 3.866883 TCATCACATGCACTTAGACGA 57.133 42.857 0.00 0.00 0.00 4.20
6368 9179 7.637552 CGCTTAACGATCACAATCCATTGTTG 61.638 42.308 2.01 0.06 46.41 3.33
6477 9292 3.492102 ATGTAAATGTCGGCAGGCTAT 57.508 42.857 0.00 0.00 0.00 2.97
6478 9293 3.275617 AATGTAAATGTCGGCAGGCTA 57.724 42.857 0.00 0.00 0.00 3.93
6479 9294 2.128771 AATGTAAATGTCGGCAGGCT 57.871 45.000 0.00 0.00 0.00 4.58
6480 9295 2.939460 AAATGTAAATGTCGGCAGGC 57.061 45.000 0.00 0.00 0.00 4.85
6481 9296 5.749596 TGATAAATGTAAATGTCGGCAGG 57.250 39.130 0.00 0.00 0.00 4.85
6482 9297 8.131100 AGAATTGATAAATGTAAATGTCGGCAG 58.869 33.333 0.00 0.00 0.00 4.85
6525 9345 7.121168 ACATCCGTTTGAGTGACAATTGATATT 59.879 33.333 13.59 0.00 38.36 1.28
6530 9350 4.488126 ACATCCGTTTGAGTGACAATTG 57.512 40.909 3.24 3.24 38.36 2.32
6538 9358 4.639310 ACGTCTAGATACATCCGTTTGAGT 59.361 41.667 0.00 0.00 0.00 3.41
6541 9361 7.646526 TGAAATACGTCTAGATACATCCGTTTG 59.353 37.037 8.82 0.00 0.00 2.93
6568 9388 1.134818 TGTCGCTCAAACGGATAGCAT 60.135 47.619 0.00 0.00 35.98 3.79
6571 9391 2.607187 AGTTGTCGCTCAAACGGATAG 58.393 47.619 0.00 0.00 37.81 2.08
6574 9394 2.512485 TTAGTTGTCGCTCAAACGGA 57.488 45.000 0.00 0.00 37.81 4.69
6575 9395 4.260212 CCATATTAGTTGTCGCTCAAACGG 60.260 45.833 0.00 0.00 37.81 4.44
6601 9426 3.244215 TGCAAGAAACAGTACTCCCTCAG 60.244 47.826 0.00 0.00 0.00 3.35
6693 9534 7.439381 CAATCCAAATGCAAGGCTAAGAATAT 58.561 34.615 0.00 0.00 0.00 1.28
7037 9885 6.027025 AGACAGTCCTCTTACCATGGTATA 57.973 41.667 25.12 15.10 0.00 1.47
7059 9911 1.002087 ACGGTACCAAGAGCCTGAAAG 59.998 52.381 13.54 0.00 0.00 2.62
7072 9924 1.891150 TCTCTCACCTTCAACGGTACC 59.109 52.381 0.16 0.16 34.94 3.34
7157 10100 8.262227 TCATTAAGTAATTTCCTTTAGCTCCGA 58.738 33.333 0.00 0.00 0.00 4.55
7238 10181 1.228367 CCTGTCCAACAAGCTGCCT 60.228 57.895 0.00 0.00 0.00 4.75
7263 10226 0.593128 CTTGCTGCGTTAAAGTGGCT 59.407 50.000 0.00 0.00 0.00 4.75
7271 10234 3.313803 TGTGAAATTGACTTGCTGCGTTA 59.686 39.130 0.00 0.00 0.00 3.18
7272 10235 2.098934 TGTGAAATTGACTTGCTGCGTT 59.901 40.909 0.00 0.00 0.00 4.84
7273 10236 1.675483 TGTGAAATTGACTTGCTGCGT 59.325 42.857 0.00 0.00 0.00 5.24
7286 10249 7.765695 ATGGTTGAAGACATAGTTGTGAAAT 57.234 32.000 0.00 0.00 35.79 2.17


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

AutoCloner maintained by Alex Coulton.