Multiple sequence alignment - TraesCS1A01G047500

Loading Multiple Alignment...

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 TraesCS1A01G047500 chr1A 100.000 6219 0 0 1 6219 29606704 29612922 0.000000e+00 11485.0
1 TraesCS1A01G047500 chr1A 83.155 374 48 13 41 402 473413746 473414116 1.670000e-85 327.0
2 TraesCS1A01G047500 chr1A 74.807 647 130 22 1323 1962 50845316 50844696 1.720000e-65 261.0
3 TraesCS1A01G047500 chr1A 74.615 650 127 26 1323 1962 29883621 29883000 1.030000e-62 252.0
4 TraesCS1A01G047500 chr1A 82.632 190 27 6 1317 1503 50841072 50840886 4.990000e-36 163.0
5 TraesCS1A01G047500 chr1A 72.926 458 90 24 1066 1503 29993509 29993952 1.820000e-25 128.0
6 TraesCS1A01G047500 chr1A 75.735 136 28 5 1370 1503 29875125 29874993 5.200000e-06 63.9
7 TraesCS1A01G047500 chr1D 94.632 3316 113 18 2047 5329 28486752 28490035 0.000000e+00 5077.0
8 TraesCS1A01G047500 chr1D 94.511 3316 115 20 2047 5329 28501582 28504863 0.000000e+00 5053.0
9 TraesCS1A01G047500 chr1D 93.447 2045 93 20 3302 5313 28969508 28967472 0.000000e+00 2996.0
10 TraesCS1A01G047500 chr1D 94.091 1117 46 7 918 2022 28485646 28486754 0.000000e+00 1679.0
11 TraesCS1A01G047500 chr1D 94.307 1089 22 6 942 2022 28500528 28501584 0.000000e+00 1631.0
12 TraesCS1A01G047500 chr1D 90.404 1261 81 15 910 2155 28978872 28977637 0.000000e+00 1622.0
13 TraesCS1A01G047500 chr1D 91.474 997 44 17 1 960 28498072 28499064 0.000000e+00 1332.0
14 TraesCS1A01G047500 chr1D 93.561 528 24 6 5475 5994 28490033 28490558 0.000000e+00 778.0
15 TraesCS1A01G047500 chr1D 96.734 398 11 1 5475 5870 28504861 28505258 0.000000e+00 662.0
16 TraesCS1A01G047500 chr1D 84.903 616 87 6 4636 5248 29479057 29479669 8.860000e-173 617.0
17 TraesCS1A01G047500 chr1D 92.449 437 19 3 2880 3307 28975874 28975443 4.120000e-171 612.0
18 TraesCS1A01G047500 chr1D 82.323 594 77 18 5574 6157 28967242 28966667 2.010000e-134 490.0
19 TraesCS1A01G047500 chr1D 94.684 301 10 4 5860 6157 28506087 28506384 4.390000e-126 462.0
20 TraesCS1A01G047500 chr1D 84.309 376 32 12 2195 2570 28977628 28977280 5.970000e-90 342.0
21 TraesCS1A01G047500 chr1D 86.598 194 12 6 2568 2758 28977170 28976988 1.060000e-47 202.0
22 TraesCS1A01G047500 chr1B 95.304 2321 65 11 2156 4466 47161545 47163831 0.000000e+00 3642.0
23 TraesCS1A01G047500 chr1B 95.981 1692 53 9 4477 6157 47163920 47165607 0.000000e+00 2734.0
24 TraesCS1A01G047500 chr1B 94.286 1260 50 9 918 2163 47160136 47161387 0.000000e+00 1908.0
25 TraesCS1A01G047500 chr1B 87.879 429 46 4 4478 4902 46914878 46914452 3.350000e-137 499.0
26 TraesCS1A01G047500 chr1B 75.562 667 144 18 4519 5176 47391316 47390660 1.680000e-80 311.0
27 TraesCS1A01G047500 chr1B 79.478 268 39 12 1323 1584 47392975 47392718 6.410000e-40 176.0
28 TraesCS1A01G047500 chr1B 85.075 134 18 2 1317 1449 47544325 47544457 1.090000e-27 135.0
29 TraesCS1A01G047500 chr1B 100.000 30 0 0 4361 4390 47163828 47163857 8.710000e-04 56.5
30 TraesCS1A01G047500 chr2A 83.422 374 47 12 37 402 144021498 144021132 3.590000e-87 333.0
31 TraesCS1A01G047500 chrUn 82.521 349 54 7 57 399 286629471 286629124 3.640000e-77 300.0
32 TraesCS1A01G047500 chr7B 82.521 349 54 7 57 399 649451780 649451433 3.640000e-77 300.0
33 TraesCS1A01G047500 chr7B 82.353 357 47 15 57 402 49423749 49423398 4.710000e-76 296.0
34 TraesCS1A01G047500 chr7D 82.507 343 51 9 67 402 562435411 562435751 6.100000e-75 292.0
35 TraesCS1A01G047500 chr7D 85.629 167 15 6 398 563 589659472 589659314 3.860000e-37 167.0
36 TraesCS1A01G047500 chr7D 83.708 178 23 5 5976 6153 8911175 8911346 4.990000e-36 163.0
37 TraesCS1A01G047500 chr2D 80.412 388 46 27 40 407 39105660 39105283 1.030000e-67 268.0
38 TraesCS1A01G047500 chr4A 81.633 245 28 8 5920 6154 642603687 642603924 2.960000e-43 187.0
39 TraesCS1A01G047500 chr6D 76.946 334 58 12 40 364 3470080 3470403 8.290000e-39 172.0
40 TraesCS1A01G047500 chr4B 85.870 92 8 3 5689 5776 650956414 650956504 6.640000e-15 93.5
41 TraesCS1A01G047500 chr5A 88.333 60 5 2 4657 4715 513282919 513282977 3.110000e-08 71.3
42 TraesCS1A01G047500 chr7A 78.302 106 20 3 4609 4711 138532288 138532183 1.450000e-06 65.8
43 TraesCS1A01G047500 chr7A 96.774 31 1 0 6124 6154 710489103 710489133 1.100000e-02 52.8


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 TraesCS1A01G047500 chr1A 29606704 29612922 6218 False 11485.000000 11485 100.000000 1 6219 1 chr1A.!!$F1 6218
1 TraesCS1A01G047500 chr1A 29883000 29883621 621 True 252.000000 252 74.615000 1323 1962 1 chr1A.!!$R2 639
2 TraesCS1A01G047500 chr1A 50840886 50845316 4430 True 212.000000 261 78.719500 1317 1962 2 chr1A.!!$R3 645
3 TraesCS1A01G047500 chr1D 28485646 28490558 4912 False 2511.333333 5077 94.094667 918 5994 3 chr1D.!!$F2 5076
4 TraesCS1A01G047500 chr1D 28498072 28506384 8312 False 1828.000000 5053 94.342000 1 6157 5 chr1D.!!$F3 6156
5 TraesCS1A01G047500 chr1D 28966667 28969508 2841 True 1743.000000 2996 87.885000 3302 6157 2 chr1D.!!$R1 2855
6 TraesCS1A01G047500 chr1D 28975443 28978872 3429 True 694.500000 1622 88.440000 910 3307 4 chr1D.!!$R2 2397
7 TraesCS1A01G047500 chr1D 29479057 29479669 612 False 617.000000 617 84.903000 4636 5248 1 chr1D.!!$F1 612
8 TraesCS1A01G047500 chr1B 47160136 47165607 5471 False 2085.125000 3642 96.392750 918 6157 4 chr1B.!!$F2 5239
9 TraesCS1A01G047500 chr1B 47390660 47392975 2315 True 243.500000 311 77.520000 1323 5176 2 chr1B.!!$R2 3853

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
440 463 5.382618 ACCTGAACATTTTCTGAATGAGC 57.617 39.130 5.82 0.0 33.56 4.26 F
1257 2801 1.676746 CGAGGACGAGGGAGATTGTA 58.323 55.000 0.00 0.0 42.66 2.41 F
2303 4216 0.896940 CCTGTGCCACAAGCCTGATT 60.897 55.000 0.00 0.0 42.71 2.57 F
3427 6488 1.134371 GCTTCACCCTCCCATACACTC 60.134 57.143 0.00 0.0 0.00 3.51 F
3437 6498 1.630126 CCATACACTCCCCAGCTGCT 61.630 60.000 8.66 0.0 0.00 4.24 F
4897 8075 1.477553 TCCGAGGTGTATTTACCGCT 58.522 50.000 0.00 0.0 45.56 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1810 3386 1.139256 TGTAGTCCCGCAACTTTGACA 59.861 47.619 0.0 0.0 0.00 3.58 R
2807 4924 0.039527 ACAGGTTTTCCAAATCGCGC 60.040 50.000 0.0 0.0 43.73 6.86 R
4046 7122 0.617820 ACAGACCAGGGGACGCTATT 60.618 55.000 0.0 0.0 0.00 1.73 R
4897 8075 0.949397 CGTCTATGCTGGCGGTAGTA 59.051 55.000 0.0 0.0 0.00 1.82 R
5217 8395 1.490069 AGCCAAACCAAAGCCACATTT 59.510 42.857 0.0 0.0 0.00 2.32 R
6193 11087 0.323178 GACCGACAGTGACCCTCCTA 60.323 60.000 0.0 0.0 0.00 2.94 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 7.386848 ACTCGGTTACCATACACATTAATATGC 59.613 37.037 1.13 0.00 35.03 3.14
85 86 8.761575 ACATTTTCATATTTCATCGCAAAAGT 57.238 26.923 0.00 0.00 0.00 2.66
125 128 9.667989 CATTTTTGGGAATCTCAAACATTTTTC 57.332 29.630 7.94 0.00 34.34 2.29
249 252 7.856145 AGTGCCAACATTTTTCAAAATTACA 57.144 28.000 0.00 0.00 36.52 2.41
268 271 9.701098 AAATTACAGACATACTTTCAAGACGTA 57.299 29.630 0.00 0.00 0.00 3.57
281 284 8.122952 ACTTTCAAGACGTAAACATTTTCTGAG 58.877 33.333 0.00 0.00 0.00 3.35
284 287 7.981142 TCAAGACGTAAACATTTTCTGAGTTT 58.019 30.769 0.00 0.00 38.79 2.66
440 463 5.382618 ACCTGAACATTTTCTGAATGAGC 57.617 39.130 5.82 0.00 33.56 4.26
581 604 6.088085 GCAAACATCACTTGGAATTCTAAACG 59.912 38.462 5.70 0.29 0.00 3.60
582 605 6.877611 AACATCACTTGGAATTCTAAACGT 57.122 33.333 5.70 0.00 0.00 3.99
583 606 6.877611 ACATCACTTGGAATTCTAAACGTT 57.122 33.333 5.70 0.00 0.00 3.99
601 624 9.442033 CTAAACGTTTTTAGAATTTCCGAAACT 57.558 29.630 20.19 0.00 44.99 2.66
656 679 8.633075 AATAATAAAATTGAACATGCGGACAG 57.367 30.769 0.00 0.00 0.00 3.51
704 736 6.260936 TGGAAAACAACAACAACAACAACAAT 59.739 30.769 0.00 0.00 0.00 2.71
707 739 9.818796 GAAAACAACAACAACAACAACAATAAT 57.181 25.926 0.00 0.00 0.00 1.28
757 789 9.631452 AAAAGAGAAACAGAAACAGAAAAGAAG 57.369 29.630 0.00 0.00 0.00 2.85
1032 2552 4.821589 GCGGAGGCGGAAGTGGAG 62.822 72.222 0.00 0.00 0.00 3.86
1214 2740 4.135153 CGTCAGCGAGGTGGGGAG 62.135 72.222 2.30 0.00 41.33 4.30
1215 2741 4.459089 GTCAGCGAGGTGGGGAGC 62.459 72.222 2.30 0.00 0.00 4.70
1217 2743 4.463879 CAGCGAGGTGGGGAGCAG 62.464 72.222 0.00 0.00 0.00 4.24
1257 2801 1.676746 CGAGGACGAGGGAGATTGTA 58.323 55.000 0.00 0.00 42.66 2.41
1605 3149 6.431722 TCTTTATCCCAAATCCTTCGGAAAT 58.568 36.000 0.00 0.00 34.34 2.17
1609 3153 4.411927 TCCCAAATCCTTCGGAAATTTCA 58.588 39.130 19.49 0.00 34.34 2.69
2303 4216 0.896940 CCTGTGCCACAAGCCTGATT 60.897 55.000 0.00 0.00 42.71 2.57
2304 4217 1.614051 CCTGTGCCACAAGCCTGATTA 60.614 52.381 0.00 0.00 42.71 1.75
2305 4218 2.161855 CTGTGCCACAAGCCTGATTAA 58.838 47.619 0.00 0.00 42.71 1.40
2309 4222 3.005791 GTGCCACAAGCCTGATTAAGTTT 59.994 43.478 0.00 0.00 42.71 2.66
2310 4223 3.005684 TGCCACAAGCCTGATTAAGTTTG 59.994 43.478 0.00 0.00 42.71 2.93
2312 4225 4.501400 GCCACAAGCCTGATTAAGTTTGTT 60.501 41.667 0.00 0.00 32.47 2.83
2313 4226 5.278758 GCCACAAGCCTGATTAAGTTTGTTA 60.279 40.000 0.00 0.00 32.47 2.41
2314 4227 6.737346 GCCACAAGCCTGATTAAGTTTGTTAA 60.737 38.462 0.00 0.00 32.47 2.01
2315 4228 7.378181 CCACAAGCCTGATTAAGTTTGTTAAT 58.622 34.615 0.00 0.00 32.47 1.40
2316 4229 7.872483 CCACAAGCCTGATTAAGTTTGTTAATT 59.128 33.333 0.00 0.00 32.47 1.40
2317 4230 9.906660 CACAAGCCTGATTAAGTTTGTTAATTA 57.093 29.630 0.00 0.00 32.47 1.40
2321 4234 9.586435 AGCCTGATTAAGTTTGTTAATTAATGC 57.414 29.630 0.31 0.00 31.10 3.56
2322 4235 9.586435 GCCTGATTAAGTTTGTTAATTAATGCT 57.414 29.630 0.31 0.00 31.10 3.79
2333 4246 9.859427 TTTGTTAATTAATGCTTCAGAAGATGG 57.141 29.630 14.86 0.00 0.00 3.51
2334 4247 8.579850 TGTTAATTAATGCTTCAGAAGATGGT 57.420 30.769 14.86 0.00 0.00 3.55
2335 4248 9.023962 TGTTAATTAATGCTTCAGAAGATGGTT 57.976 29.630 14.86 4.96 0.00 3.67
2353 4273 4.272489 TGGTTAATGGATGCTTCAGAAGG 58.728 43.478 12.30 0.00 0.00 3.46
2415 4335 3.067180 AGCAAGTGATGTGTTGGTTCAAG 59.933 43.478 0.00 0.00 30.28 3.02
2433 4353 7.450014 TGGTTCAAGCACCTCTTTAATTATTGA 59.550 33.333 0.00 0.00 37.75 2.57
2618 4652 7.661437 TGCACTCTGTAATATGAATATGAACCC 59.339 37.037 0.00 0.00 0.00 4.11
2806 4923 3.014036 CGTCCAGTGTGTGTGTGC 58.986 61.111 0.00 0.00 0.00 4.57
2807 4924 2.870341 CGTCCAGTGTGTGTGTGCG 61.870 63.158 0.00 0.00 0.00 5.34
2808 4925 2.894879 TCCAGTGTGTGTGTGCGC 60.895 61.111 0.00 0.00 0.00 6.09
2914 5961 3.888930 ACTTTCGTTCAATCCAACCATGT 59.111 39.130 0.00 0.00 0.00 3.21
3093 6150 1.270305 ACCATCAGACAGTGTCAACCG 60.270 52.381 24.73 10.32 34.60 4.44
3427 6488 1.134371 GCTTCACCCTCCCATACACTC 60.134 57.143 0.00 0.00 0.00 3.51
3437 6498 1.630126 CCATACACTCCCCAGCTGCT 61.630 60.000 8.66 0.00 0.00 4.24
3609 6676 2.555757 GCCCAGGTATCAATGAATCTGC 59.444 50.000 0.00 0.00 0.00 4.26
3632 6699 5.699143 CTTCATTCCCCAGTTATCCTCATT 58.301 41.667 0.00 0.00 0.00 2.57
3751 6822 6.183361 TGGCATTCCATTCTTCCTTTTTCTTT 60.183 34.615 0.00 0.00 37.47 2.52
3752 6823 6.369890 GGCATTCCATTCTTCCTTTTTCTTTC 59.630 38.462 0.00 0.00 0.00 2.62
3786 6857 3.915437 TTTCTCTGGCGAATTGTTTCC 57.085 42.857 0.00 0.00 0.00 3.13
3788 6861 3.973206 TCTCTGGCGAATTGTTTCCTA 57.027 42.857 0.00 0.00 0.00 2.94
3880 6956 6.551085 TGGGGCAATTATAATCATAGCAAGA 58.449 36.000 0.00 0.00 0.00 3.02
3881 6957 7.009550 TGGGGCAATTATAATCATAGCAAGAA 58.990 34.615 0.00 0.00 0.00 2.52
4003 7079 3.954258 CCCTTTGAGAATACATTGGACCC 59.046 47.826 0.00 0.00 0.00 4.46
4120 7198 7.493320 TGTTACTTTGTCGTGTTCTCTTGTAAT 59.507 33.333 0.00 0.00 0.00 1.89
4285 7372 9.414295 CAAGTTATGTTTTCATTGTGATGATGT 57.586 29.630 0.00 0.00 41.71 3.06
4298 7391 4.523558 TGTGATGATGTTCAATGCCTTTGA 59.476 37.500 0.00 0.00 42.62 2.69
4566 7742 7.650504 CGGTCCTATTTGAGATAAACGATACAA 59.349 37.037 0.00 0.00 0.00 2.41
4897 8075 1.477553 TCCGAGGTGTATTTACCGCT 58.522 50.000 0.00 0.00 45.56 5.52
4928 8106 4.105486 CAGCATAGACGACGAGAAAATCA 58.895 43.478 0.00 0.00 0.00 2.57
5217 8395 2.897326 ACATGCCGTGTCCTAGCATATA 59.103 45.455 0.00 0.00 45.16 0.86
5417 8685 6.016610 TGGTTGTTCCAGTCTTTTATACAAGC 60.017 38.462 0.00 0.00 41.93 4.01
5507 8775 5.923733 TGCACCGGGAAAATAATTATGTT 57.076 34.783 6.32 0.17 0.00 2.71
5511 8781 6.983890 GCACCGGGAAAATAATTATGTTCATT 59.016 34.615 23.73 7.31 32.67 2.57
6086 10980 4.159557 ACCATACCACAAAAGCCATTTCT 58.840 39.130 0.00 0.00 0.00 2.52
6091 10985 3.160269 CCACAAAAGCCATTTCTCCTCT 58.840 45.455 0.00 0.00 0.00 3.69
6172 11066 5.988310 TTTTCGATACAGAGGGAGTACAA 57.012 39.130 0.00 0.00 0.00 2.41
6174 11068 4.498894 TCGATACAGAGGGAGTACAAGA 57.501 45.455 0.00 0.00 0.00 3.02
6175 11069 5.050126 TCGATACAGAGGGAGTACAAGAT 57.950 43.478 0.00 0.00 0.00 2.40
6177 11071 4.580995 CGATACAGAGGGAGTACAAGATGT 59.419 45.833 0.00 0.00 0.00 3.06
6178 11072 5.278071 CGATACAGAGGGAGTACAAGATGTC 60.278 48.000 0.00 0.00 0.00 3.06
6179 11073 3.100671 ACAGAGGGAGTACAAGATGTCC 58.899 50.000 0.00 0.00 0.00 4.02
6180 11074 2.099921 CAGAGGGAGTACAAGATGTCCG 59.900 54.545 0.00 0.00 0.00 4.79
6181 11075 2.025226 AGAGGGAGTACAAGATGTCCGA 60.025 50.000 0.00 0.00 0.00 4.55
6182 11076 2.099427 GAGGGAGTACAAGATGTCCGAC 59.901 54.545 0.00 0.00 0.00 4.79
6185 11079 2.753452 GGAGTACAAGATGTCCGACAGA 59.247 50.000 7.41 0.00 0.00 3.41
6186 11080 3.192844 GGAGTACAAGATGTCCGACAGAA 59.807 47.826 7.41 0.00 0.00 3.02
6187 11081 4.142138 GGAGTACAAGATGTCCGACAGAAT 60.142 45.833 7.41 0.00 0.00 2.40
6188 11082 5.067413 GGAGTACAAGATGTCCGACAGAATA 59.933 44.000 7.41 0.00 0.00 1.75
6189 11083 6.239064 GGAGTACAAGATGTCCGACAGAATAT 60.239 42.308 7.41 0.00 0.00 1.28
6190 11084 6.740110 AGTACAAGATGTCCGACAGAATATC 58.260 40.000 7.41 0.00 0.00 1.63
6193 11087 5.127845 ACAAGATGTCCGACAGAATATCAGT 59.872 40.000 7.41 0.49 0.00 3.41
6198 11092 4.822350 TGTCCGACAGAATATCAGTAGGAG 59.178 45.833 0.00 0.00 38.07 3.69
6200 11094 3.508012 CCGACAGAATATCAGTAGGAGGG 59.492 52.174 0.00 0.00 31.98 4.30
6201 11095 4.145807 CGACAGAATATCAGTAGGAGGGT 58.854 47.826 0.00 0.00 0.00 4.34
6202 11096 4.216687 CGACAGAATATCAGTAGGAGGGTC 59.783 50.000 0.00 0.00 0.00 4.46
6203 11097 5.141182 GACAGAATATCAGTAGGAGGGTCA 58.859 45.833 0.00 0.00 0.00 4.02
6205 11099 5.144100 CAGAATATCAGTAGGAGGGTCACT 58.856 45.833 0.00 0.00 0.00 3.41
6206 11100 5.010516 CAGAATATCAGTAGGAGGGTCACTG 59.989 48.000 0.00 0.00 40.83 3.66
6207 11101 2.930109 ATCAGTAGGAGGGTCACTGT 57.070 50.000 0.00 0.00 40.44 3.55
6208 11102 2.217510 TCAGTAGGAGGGTCACTGTC 57.782 55.000 0.00 0.00 40.44 3.51
6210 11104 0.323542 AGTAGGAGGGTCACTGTCGG 60.324 60.000 0.00 0.00 0.00 4.79
6211 11105 0.611340 GTAGGAGGGTCACTGTCGGT 60.611 60.000 0.00 0.00 0.00 4.69
6213 11107 1.906824 GGAGGGTCACTGTCGGTCA 60.907 63.158 0.00 0.00 0.00 4.02
6214 11108 1.258445 GGAGGGTCACTGTCGGTCAT 61.258 60.000 0.00 0.00 0.00 3.06
6215 11109 0.608640 GAGGGTCACTGTCGGTCATT 59.391 55.000 0.00 0.00 0.00 2.57
6216 11110 0.608640 AGGGTCACTGTCGGTCATTC 59.391 55.000 0.00 0.00 0.00 2.67
6217 11111 0.608640 GGGTCACTGTCGGTCATTCT 59.391 55.000 0.00 0.00 0.00 2.40
6218 11112 1.673033 GGGTCACTGTCGGTCATTCTG 60.673 57.143 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 4.326548 TGTTTCGGGTTTTTAACTTTTGCG 59.673 37.500 0.00 0.00 0.00 4.85
84 85 6.315642 TCCCAAAAATGTTTCGGGTTTTTAAC 59.684 34.615 12.81 0.00 36.85 2.01
85 86 6.412214 TCCCAAAAATGTTTCGGGTTTTTAA 58.588 32.000 12.81 0.00 36.85 1.52
249 252 8.603242 AATGTTTACGTCTTGAAAGTATGTCT 57.397 30.769 0.00 0.00 0.00 3.41
256 259 8.122952 ACTCAGAAAATGTTTACGTCTTGAAAG 58.877 33.333 0.00 0.00 0.00 2.62
268 271 3.314080 TCGGCGAAACTCAGAAAATGTTT 59.686 39.130 7.35 0.00 36.73 2.83
281 284 2.733517 TCCAAAAATGTTCGGCGAAAC 58.266 42.857 25.48 18.01 0.00 2.78
284 287 3.004839 TGAATTCCAAAAATGTTCGGCGA 59.995 39.130 4.99 4.99 0.00 5.54
394 397 9.497030 GGTAAATTTGTTTGAAAAATGTTCACC 57.503 29.630 0.00 0.00 0.00 4.02
437 460 7.373966 TGTTCGTATTTTAGTTTTTGTTCGCTC 59.626 33.333 0.00 0.00 0.00 5.03
547 570 7.230849 TCCAAGTGATGTTTGCTTATTTCAT 57.769 32.000 0.00 0.00 0.00 2.57
548 571 6.647334 TCCAAGTGATGTTTGCTTATTTCA 57.353 33.333 0.00 0.00 0.00 2.69
553 576 6.899393 AGAATTCCAAGTGATGTTTGCTTA 57.101 33.333 0.65 0.00 0.00 3.09
632 655 7.771183 ACTGTCCGCATGTTCAATTTTATTAT 58.229 30.769 0.00 0.00 0.00 1.28
737 769 7.762382 TCCTTCTTCTTTTCTGTTTCTGTTTC 58.238 34.615 0.00 0.00 0.00 2.78
740 772 7.611855 TCTTTCCTTCTTCTTTTCTGTTTCTGT 59.388 33.333 0.00 0.00 0.00 3.41
741 773 7.989826 TCTTTCCTTCTTCTTTTCTGTTTCTG 58.010 34.615 0.00 0.00 0.00 3.02
830 868 2.031870 CATATCCAGTCGGTGTCTCCA 58.968 52.381 0.00 0.00 35.57 3.86
882 920 0.100682 AACAGATCGATCGACACCGG 59.899 55.000 22.06 14.99 36.24 5.28
1032 2552 8.421784 TCCATCAACAGATAGTTAATGTAGGAC 58.578 37.037 0.00 0.00 38.74 3.85
1128 2651 2.059541 GTCTCCGTCTTCCGTTTCTTG 58.940 52.381 0.00 0.00 33.66 3.02
1211 2737 4.496336 ATTCCGCTGGGCTGCTCC 62.496 66.667 0.00 0.00 0.00 4.70
1212 2738 2.899339 GATTCCGCTGGGCTGCTC 60.899 66.667 0.00 0.00 0.00 4.26
1213 2739 3.406200 AGATTCCGCTGGGCTGCT 61.406 61.111 0.00 0.00 0.00 4.24
1214 2740 2.955022 ATCAGATTCCGCTGGGCTGC 62.955 60.000 0.00 0.00 36.55 5.25
1215 2741 0.465097 AATCAGATTCCGCTGGGCTG 60.465 55.000 0.00 0.00 36.55 4.85
1216 2742 0.257039 AAATCAGATTCCGCTGGGCT 59.743 50.000 0.00 0.00 36.55 5.19
1217 2743 0.383231 CAAATCAGATTCCGCTGGGC 59.617 55.000 0.00 0.00 36.55 5.36
1218 2744 1.027357 CCAAATCAGATTCCGCTGGG 58.973 55.000 0.00 0.00 36.55 4.45
1219 2745 0.383231 GCCAAATCAGATTCCGCTGG 59.617 55.000 7.10 7.10 36.55 4.85
1220 2746 0.028505 CGCCAAATCAGATTCCGCTG 59.971 55.000 10.97 0.00 37.24 5.18
1221 2747 0.107703 TCGCCAAATCAGATTCCGCT 60.108 50.000 10.97 0.00 0.00 5.52
1222 2748 0.305922 CTCGCCAAATCAGATTCCGC 59.694 55.000 0.00 0.48 0.00 5.54
1223 2749 0.940126 CCTCGCCAAATCAGATTCCG 59.060 55.000 0.00 0.77 0.00 4.30
1257 2801 4.269523 TTGGCCGTGGCTGCTTCT 62.270 61.111 11.25 0.00 41.60 2.85
1605 3149 3.315191 GCAGCTTACTGTTGTCCTTGAAA 59.685 43.478 0.00 0.00 46.30 2.69
1609 3153 1.142870 TGGCAGCTTACTGTTGTCCTT 59.857 47.619 0.00 0.00 46.30 3.36
1810 3386 1.139256 TGTAGTCCCGCAACTTTGACA 59.861 47.619 0.00 0.00 0.00 3.58
2309 4222 8.579850 ACCATCTTCTGAAGCATTAATTAACA 57.420 30.769 12.54 0.00 0.00 2.41
2314 4227 8.636213 CCATTAACCATCTTCTGAAGCATTAAT 58.364 33.333 12.54 14.11 0.00 1.40
2315 4228 7.833682 TCCATTAACCATCTTCTGAAGCATTAA 59.166 33.333 12.54 12.79 0.00 1.40
2316 4229 7.345691 TCCATTAACCATCTTCTGAAGCATTA 58.654 34.615 12.54 5.69 0.00 1.90
2317 4230 6.189859 TCCATTAACCATCTTCTGAAGCATT 58.810 36.000 12.54 6.54 0.00 3.56
2318 4231 5.759059 TCCATTAACCATCTTCTGAAGCAT 58.241 37.500 12.54 4.81 0.00 3.79
2319 4232 5.178096 TCCATTAACCATCTTCTGAAGCA 57.822 39.130 12.54 2.66 0.00 3.91
2320 4233 5.506982 GCATCCATTAACCATCTTCTGAAGC 60.507 44.000 12.54 0.00 0.00 3.86
2321 4234 5.826737 AGCATCCATTAACCATCTTCTGAAG 59.173 40.000 11.18 11.18 0.00 3.02
2322 4235 5.759059 AGCATCCATTAACCATCTTCTGAA 58.241 37.500 0.00 0.00 0.00 3.02
2323 4236 5.378230 AGCATCCATTAACCATCTTCTGA 57.622 39.130 0.00 0.00 0.00 3.27
2324 4237 5.591472 TGAAGCATCCATTAACCATCTTCTG 59.409 40.000 0.00 0.00 32.36 3.02
2325 4238 5.759059 TGAAGCATCCATTAACCATCTTCT 58.241 37.500 0.00 0.00 32.36 2.85
2326 4239 5.824624 TCTGAAGCATCCATTAACCATCTTC 59.175 40.000 0.00 0.00 0.00 2.87
2327 4240 5.759059 TCTGAAGCATCCATTAACCATCTT 58.241 37.500 0.00 0.00 0.00 2.40
2328 4241 5.378230 TCTGAAGCATCCATTAACCATCT 57.622 39.130 0.00 0.00 0.00 2.90
2329 4242 5.009410 CCTTCTGAAGCATCCATTAACCATC 59.991 44.000 11.93 0.00 0.00 3.51
2330 4243 4.891756 CCTTCTGAAGCATCCATTAACCAT 59.108 41.667 11.93 0.00 0.00 3.55
2331 4244 4.272489 CCTTCTGAAGCATCCATTAACCA 58.728 43.478 11.93 0.00 0.00 3.67
2332 4245 3.067320 GCCTTCTGAAGCATCCATTAACC 59.933 47.826 11.93 0.00 0.00 2.85
2333 4246 3.696051 TGCCTTCTGAAGCATCCATTAAC 59.304 43.478 11.93 0.00 33.08 2.01
2334 4247 3.966979 TGCCTTCTGAAGCATCCATTAA 58.033 40.909 11.93 0.00 33.08 1.40
2335 4248 3.650281 TGCCTTCTGAAGCATCCATTA 57.350 42.857 11.93 0.00 33.08 1.90
2336 4249 2.519771 TGCCTTCTGAAGCATCCATT 57.480 45.000 11.93 0.00 33.08 3.16
2415 4335 6.404734 CCTGTGGTCAATAATTAAAGAGGTGC 60.405 42.308 0.00 0.00 0.00 5.01
2433 4353 3.023832 CAAGAACTTTGTTCCCTGTGGT 58.976 45.455 6.80 0.00 0.00 4.16
2505 4425 6.150976 CAGTGTGCTCCAACCAGATATTTTTA 59.849 38.462 0.00 0.00 0.00 1.52
2618 4652 5.523916 ACCGCATACTGCATACTCTTAAAAG 59.476 40.000 0.00 0.00 45.36 2.27
2730 4847 4.048970 ACACATACTCTACCACACTCCT 57.951 45.455 0.00 0.00 0.00 3.69
2806 4923 1.065031 CAGGTTTTCCAAATCGCGCG 61.065 55.000 26.76 26.76 43.73 6.86
2807 4924 0.039527 ACAGGTTTTCCAAATCGCGC 60.040 50.000 0.00 0.00 43.73 6.86
2808 4925 2.287308 TGAACAGGTTTTCCAAATCGCG 60.287 45.455 0.00 0.00 43.73 5.87
2914 5961 0.110295 AGCAGGGTGTGTGCACAATA 59.890 50.000 23.59 11.27 46.95 1.90
3093 6150 4.563786 CCACTTAGGGAAGAAGTCTCAACC 60.564 50.000 0.00 0.00 34.90 3.77
3135 6192 2.771372 GAGCTTCAGGAGAGGGAAGATT 59.229 50.000 5.64 0.00 39.62 2.40
3609 6676 4.778213 TGAGGATAACTGGGGAATGAAG 57.222 45.455 0.00 0.00 0.00 3.02
3738 6809 2.229062 GGAGGCGGAAAGAAAAAGGAAG 59.771 50.000 0.00 0.00 0.00 3.46
3751 6822 1.003233 GAGAAAAAGAAGGGAGGCGGA 59.997 52.381 0.00 0.00 0.00 5.54
3752 6823 1.003696 AGAGAAAAAGAAGGGAGGCGG 59.996 52.381 0.00 0.00 0.00 6.13
3786 6857 4.471904 TTGTCCAGTGCATAAGAGGTAG 57.528 45.455 0.00 0.00 0.00 3.18
3788 6861 3.560025 CCTTTGTCCAGTGCATAAGAGGT 60.560 47.826 0.00 0.00 0.00 3.85
3860 6936 9.390795 CACACTTCTTGCTATGATTATAATTGC 57.609 33.333 0.00 3.63 0.00 3.56
3890 6966 1.134280 CCGCTCTCTCAAATGGGATGT 60.134 52.381 0.00 0.00 0.00 3.06
4003 7079 2.270352 TGTGGGAGCACAACTAAAGG 57.730 50.000 0.00 0.00 31.35 3.11
4046 7122 0.617820 ACAGACCAGGGGACGCTATT 60.618 55.000 0.00 0.00 0.00 1.73
4103 7181 5.846473 GCAGAAAATTACAAGAGAACACGAC 59.154 40.000 0.00 0.00 0.00 4.34
4120 7198 8.787391 CTGTGTTCAGCATTTTCAAGCAGAAAA 61.787 37.037 16.21 16.21 44.98 2.29
4541 7717 8.882415 TTGTATCGTTTATCTCAAATAGGACC 57.118 34.615 0.00 0.00 0.00 4.46
4897 8075 0.949397 CGTCTATGCTGGCGGTAGTA 59.051 55.000 0.00 0.00 0.00 1.82
4928 8106 2.614057 CGTCTCTGAAACCAAGCAACTT 59.386 45.455 0.00 0.00 0.00 2.66
4943 8121 2.549754 CAACAGGCAATTTGTCGTCTCT 59.450 45.455 0.00 0.00 0.00 3.10
5217 8395 1.490069 AGCCAAACCAAAGCCACATTT 59.510 42.857 0.00 0.00 0.00 2.32
5375 8643 4.248859 CAACCATCGAATCTGAACTGTCT 58.751 43.478 0.00 0.00 0.00 3.41
5417 8685 9.144747 GTAACTCATCATACAAGCATATACAGG 57.855 37.037 0.00 0.00 0.00 4.00
5916 10745 4.099266 TGGCACAATAAGTCAAGTTTGCTT 59.901 37.500 0.00 6.72 31.92 3.91
6157 11051 4.279145 GGACATCTTGTACTCCCTCTGTA 58.721 47.826 0.00 0.00 0.00 2.74
6158 11052 3.100671 GGACATCTTGTACTCCCTCTGT 58.899 50.000 0.00 0.00 0.00 3.41
6159 11053 2.099921 CGGACATCTTGTACTCCCTCTG 59.900 54.545 0.00 0.00 0.00 3.35
6160 11054 2.025226 TCGGACATCTTGTACTCCCTCT 60.025 50.000 0.00 0.00 0.00 3.69
6162 11056 2.100989 GTCGGACATCTTGTACTCCCT 58.899 52.381 2.62 0.00 0.00 4.20
6164 11058 2.753452 TCTGTCGGACATCTTGTACTCC 59.247 50.000 11.86 0.00 0.00 3.85
6165 11059 4.436242 TTCTGTCGGACATCTTGTACTC 57.564 45.455 11.86 0.00 0.00 2.59
6166 11060 6.321435 TGATATTCTGTCGGACATCTTGTACT 59.679 38.462 11.86 0.00 0.00 2.73
6167 11061 6.504398 TGATATTCTGTCGGACATCTTGTAC 58.496 40.000 11.86 2.44 0.00 2.90
6168 11062 6.321435 ACTGATATTCTGTCGGACATCTTGTA 59.679 38.462 11.86 1.93 0.00 2.41
6169 11063 5.127845 ACTGATATTCTGTCGGACATCTTGT 59.872 40.000 11.86 6.67 0.00 3.16
6170 11064 5.595885 ACTGATATTCTGTCGGACATCTTG 58.404 41.667 11.86 0.00 0.00 3.02
6172 11066 5.475220 CCTACTGATATTCTGTCGGACATCT 59.525 44.000 11.86 2.17 34.52 2.90
6174 11068 5.386060 TCCTACTGATATTCTGTCGGACAT 58.614 41.667 11.86 0.00 36.02 3.06
6175 11069 4.788679 TCCTACTGATATTCTGTCGGACA 58.211 43.478 10.88 10.88 36.02 4.02
6177 11071 4.399219 CCTCCTACTGATATTCTGTCGGA 58.601 47.826 7.32 7.32 37.67 4.55
6178 11072 3.508012 CCCTCCTACTGATATTCTGTCGG 59.492 52.174 0.45 0.45 34.11 4.79
6179 11073 4.145807 ACCCTCCTACTGATATTCTGTCG 58.854 47.826 0.00 0.00 31.00 4.35
6180 11074 5.010213 GTGACCCTCCTACTGATATTCTGTC 59.990 48.000 0.00 0.00 31.00 3.51
6181 11075 4.896482 GTGACCCTCCTACTGATATTCTGT 59.104 45.833 0.00 0.00 33.13 3.41
6182 11076 5.010516 CAGTGACCCTCCTACTGATATTCTG 59.989 48.000 0.00 0.00 43.35 3.02
6185 11079 4.884961 ACAGTGACCCTCCTACTGATATT 58.115 43.478 10.24 0.00 43.35 1.28
6186 11080 4.475345 GACAGTGACCCTCCTACTGATAT 58.525 47.826 10.24 0.00 43.35 1.63
6187 11081 3.684697 CGACAGTGACCCTCCTACTGATA 60.685 52.174 10.24 0.00 43.35 2.15
6188 11082 2.741145 GACAGTGACCCTCCTACTGAT 58.259 52.381 10.24 0.00 43.35 2.90
6189 11083 1.613520 CGACAGTGACCCTCCTACTGA 60.614 57.143 10.24 0.00 43.35 3.41
6190 11084 0.811915 CGACAGTGACCCTCCTACTG 59.188 60.000 0.00 0.00 45.48 2.74
6193 11087 0.323178 GACCGACAGTGACCCTCCTA 60.323 60.000 0.00 0.00 0.00 2.94
6198 11092 0.608640 AGAATGACCGACAGTGACCC 59.391 55.000 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.