Multiple sequence alignment - TraesCS3D01G015300

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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 TraesCS3D01G015300 chr3D 100.000 5672 0 0 1 5672 5411203 5405532 0.000000e+00 10475.0
1 TraesCS3D01G015300 chr3D 85.409 2015 245 29 932 2934 41427096 41425119 0.000000e+00 2047.0
2 TraesCS3D01G015300 chr3D 84.775 2069 259 28 886 2931 5328517 5330552 0.000000e+00 2025.0
3 TraesCS3D01G015300 chr3D 85.174 2010 249 25 932 2934 41596801 41594834 0.000000e+00 2015.0
4 TraesCS3D01G015300 chr3D 84.343 1980 267 24 976 2931 5376599 5374639 0.000000e+00 1899.0
5 TraesCS3D01G015300 chr3D 87.316 1561 172 13 3178 4724 5374464 5372916 0.000000e+00 1762.0
6 TraesCS3D01G015300 chr3D 84.549 1618 200 26 3147 4750 41424901 41423320 0.000000e+00 1557.0
7 TraesCS3D01G015300 chr3D 82.768 1770 219 43 3150 4875 41594617 41592890 0.000000e+00 1500.0
8 TraesCS3D01G015300 chr3D 93.243 74 5 0 4786 4859 41423000 41422927 6.010000e-20 110.0
9 TraesCS3D01G015300 chr3D 90.196 51 1 1 5486 5532 41589884 41589834 4.740000e-06 63.9
10 TraesCS3D01G015300 chr3B 95.228 3311 141 10 1714 5019 13413561 13416859 0.000000e+00 5223.0
11 TraesCS3D01G015300 chr3B 87.576 2624 225 46 3060 5667 12935394 12937932 0.000000e+00 2946.0
12 TraesCS3D01G015300 chr3B 87.823 2398 205 40 592 2931 13245622 13247990 0.000000e+00 2730.0
13 TraesCS3D01G015300 chr3B 87.159 2165 207 33 782 2931 12933216 12935324 0.000000e+00 2392.0
14 TraesCS3D01G015300 chr3B 83.600 2250 281 44 691 2931 12472212 12474382 0.000000e+00 2030.0
15 TraesCS3D01G015300 chr3B 84.928 2017 259 19 932 2934 12843170 12841185 0.000000e+00 1999.0
16 TraesCS3D01G015300 chr3B 82.672 1841 234 35 3060 4875 13248060 13249840 0.000000e+00 1554.0
17 TraesCS3D01G015300 chr3B 84.398 1596 186 31 3150 4724 12840968 12839415 0.000000e+00 1509.0
18 TraesCS3D01G015300 chr3B 89.619 761 59 12 1 748 12547147 12546394 0.000000e+00 950.0
19 TraesCS3D01G015300 chr3B 85.140 821 67 24 1 791 13409342 13410137 0.000000e+00 789.0
20 TraesCS3D01G015300 chr3B 89.610 462 23 3 5229 5667 13419506 13419965 1.070000e-156 564.0
21 TraesCS3D01G015300 chr3B 82.178 505 61 12 3150 3643 12474598 12475084 1.900000e-109 407.0
22 TraesCS3D01G015300 chr3B 90.833 240 16 6 20 256 13241342 13241578 3.300000e-82 316.0
23 TraesCS3D01G015300 chr3B 95.833 120 4 1 5058 5177 13416864 13416982 5.800000e-45 193.0
24 TraesCS3D01G015300 chr3B 95.745 47 2 0 5197 5243 13416981 13417027 6.090000e-10 76.8
25 TraesCS3D01G015300 chr3B 100.000 30 0 0 5485 5514 12478922 12478951 7.940000e-04 56.5
26 TraesCS3D01G015300 chr3A 88.794 2588 191 38 3060 5629 16011199 16013705 0.000000e+00 3081.0
27 TraesCS3D01G015300 chr3A 88.299 2034 176 22 756 2771 16009014 16011003 0.000000e+00 2381.0
28 TraesCS3D01G015300 chr3A 83.987 2473 308 57 508 2931 17330917 17333350 0.000000e+00 2292.0
29 TraesCS3D01G015300 chr3A 84.883 1958 258 19 988 2931 17379908 17377975 0.000000e+00 1941.0
30 TraesCS3D01G015300 chr3A 84.604 1968 268 21 988 2931 16234688 16232732 0.000000e+00 1923.0
31 TraesCS3D01G015300 chr3A 84.377 1997 254 33 945 2931 15835605 15837553 0.000000e+00 1906.0
32 TraesCS3D01G015300 chr3A 88.526 1560 154 13 3178 4724 17333525 17335072 0.000000e+00 1866.0
33 TraesCS3D01G015300 chr3A 85.304 1810 192 34 2931 4724 16232762 16231011 0.000000e+00 1801.0
34 TraesCS3D01G015300 chr3A 87.060 1561 176 15 3178 4724 17377800 17376252 0.000000e+00 1740.0
35 TraesCS3D01G015300 chr3A 84.296 1592 191 29 3150 4724 15837769 15839318 0.000000e+00 1500.0
36 TraesCS3D01G015300 chr3A 88.594 754 57 14 3 730 16008265 16009015 0.000000e+00 889.0
37 TraesCS3D01G015300 chr3A 89.413 699 24 9 4971 5667 16334935 16335585 0.000000e+00 835.0
38 TraesCS3D01G015300 chr3A 94.763 401 15 3 4579 4976 16321339 16321736 2.240000e-173 619.0
39 TraesCS3D01G015300 chr3A 95.122 41 2 0 687 727 16234837 16234797 1.320000e-06 65.8
40 TraesCS3D01G015300 chr3A 95.122 41 2 0 687 727 17380057 17380017 1.320000e-06 65.8
41 TraesCS3D01G015300 chr1A 81.633 147 24 2 178 323 387860823 387860679 9.980000e-23 119.0
42 TraesCS3D01G015300 chr7A 78.378 148 30 2 176 322 694024607 694024461 1.680000e-15 95.3


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 TraesCS3D01G015300 chr3D 5405532 5411203 5671 True 10475.000000 10475 100.000000 1 5672 1 chr3D.!!$R1 5671
1 TraesCS3D01G015300 chr3D 5328517 5330552 2035 False 2025.000000 2025 84.775000 886 2931 1 chr3D.!!$F1 2045
2 TraesCS3D01G015300 chr3D 5372916 5376599 3683 True 1830.500000 1899 85.829500 976 4724 2 chr3D.!!$R2 3748
3 TraesCS3D01G015300 chr3D 41422927 41427096 4169 True 1238.000000 2047 87.733667 932 4859 3 chr3D.!!$R3 3927
4 TraesCS3D01G015300 chr3D 41589834 41596801 6967 True 1192.966667 2015 86.046000 932 5532 3 chr3D.!!$R4 4600
5 TraesCS3D01G015300 chr3B 12933216 12937932 4716 False 2669.000000 2946 87.367500 782 5667 2 chr3B.!!$F3 4885
6 TraesCS3D01G015300 chr3B 13245622 13249840 4218 False 2142.000000 2730 85.247500 592 4875 2 chr3B.!!$F4 4283
7 TraesCS3D01G015300 chr3B 12839415 12843170 3755 True 1754.000000 1999 84.663000 932 4724 2 chr3B.!!$R2 3792
8 TraesCS3D01G015300 chr3B 13409342 13419965 10623 False 1369.160000 5223 92.311200 1 5667 5 chr3B.!!$F5 5666
9 TraesCS3D01G015300 chr3B 12546394 12547147 753 True 950.000000 950 89.619000 1 748 1 chr3B.!!$R1 747
10 TraesCS3D01G015300 chr3B 12472212 12478951 6739 False 831.166667 2030 88.592667 691 5514 3 chr3B.!!$F2 4823
11 TraesCS3D01G015300 chr3A 16008265 16013705 5440 False 2117.000000 3081 88.562333 3 5629 3 chr3A.!!$F4 5626
12 TraesCS3D01G015300 chr3A 17330917 17335072 4155 False 2079.000000 2292 86.256500 508 4724 2 chr3A.!!$F5 4216
13 TraesCS3D01G015300 chr3A 15835605 15839318 3713 False 1703.000000 1906 84.336500 945 4724 2 chr3A.!!$F3 3779
14 TraesCS3D01G015300 chr3A 16231011 16234837 3826 True 1263.266667 1923 88.343333 687 4724 3 chr3A.!!$R1 4037
15 TraesCS3D01G015300 chr3A 17376252 17380057 3805 True 1248.933333 1941 89.021667 687 4724 3 chr3A.!!$R2 4037
16 TraesCS3D01G015300 chr3A 16334935 16335585 650 False 835.000000 835 89.413000 4971 5667 1 chr3A.!!$F2 696

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
127 140 0.596082 TCGTCGTCAGCAACAGATCA 59.404 50.000 0.00 0.00 0.00 2.92 F
1479 3885 0.536260 GAGCTGTCTGCAGGATCACT 59.464 55.000 15.13 5.38 45.94 3.41 F
1620 4044 1.895798 TCACTCTTCAAGGATGCTCGT 59.104 47.619 0.00 0.00 0.00 4.18 F
2956 5653 1.123077 TGCTAGAGGACGATGGCATT 58.877 50.000 0.00 0.00 0.00 3.56 F
4104 6945 2.290531 TCTTCTTCGATCTGCAGCTG 57.709 50.000 10.11 10.11 0.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1917 4561 0.689412 CCTCCCACTCCTCCTCCTTC 60.689 65.000 0.00 0.0 0.00 3.46 R
2389 5084 0.320683 CTCTTGACGATGCCCACACA 60.321 55.000 0.00 0.0 0.00 3.72 R
3214 6012 0.912528 GACGCCTTCGACATCGTTAC 59.087 55.000 0.54 0.0 40.80 2.50 R
4257 7098 0.671781 CAACGACTTGGAGGAGGCTG 60.672 60.000 0.00 0.0 0.00 4.85 R
5630 13960 1.431633 CAAAAGGTTTACCCCCTCCCT 59.568 52.381 0.00 0.0 36.42 4.20 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
25 26 1.536284 CGGGAGAGCGTGAATTAGGTC 60.536 57.143 0.00 0.63 35.33 3.85
90 91 2.303022 GGGTCATCTTCTGTCCAAGTCA 59.697 50.000 0.00 0.00 35.03 3.41
127 140 0.596082 TCGTCGTCAGCAACAGATCA 59.404 50.000 0.00 0.00 0.00 2.92
151 176 1.079405 AACAACGTCGATCCCGCAT 60.079 52.632 0.00 0.00 35.37 4.73
168 193 3.807622 CCGCATCAACTAATGAACCGTAT 59.192 43.478 0.00 0.00 42.54 3.06
185 210 3.920412 CCGTATGTCCATCGTGATATGTG 59.080 47.826 0.00 0.00 0.00 3.21
277 303 3.303395 GCTAGACCGTTGCATGCTATTTC 60.303 47.826 20.33 9.07 0.00 2.17
385 415 2.906354 ACTAATCGGAACACAGGCATC 58.094 47.619 0.00 0.00 0.00 3.91
463 493 1.322538 TAGGGTCGCCGGTAAAGTCC 61.323 60.000 1.90 0.00 0.00 3.85
474 504 1.135053 GGTAAAGTCCGGAGTGAGAGC 60.135 57.143 13.86 7.15 0.00 4.09
481 511 1.018226 CCGGAGTGAGAGCTTGCTTG 61.018 60.000 0.00 0.00 0.00 4.01
518 548 7.327214 GTCTGAGGAAGAAACTATTGAGATGT 58.673 38.462 0.00 0.00 36.40 3.06
524 554 8.816894 AGGAAGAAACTATTGAGATGTGTTCTA 58.183 33.333 0.00 0.00 33.74 2.10
553 583 4.262506 CCCGAAAGAGTGTACTTCCTTCTT 60.263 45.833 0.00 0.00 0.00 2.52
555 585 5.758784 CCGAAAGAGTGTACTTCCTTCTTTT 59.241 40.000 0.00 0.00 37.99 2.27
612 652 1.407712 GGAATTTTCGATCGGGGGACA 60.408 52.381 16.41 0.00 0.00 4.02
765 839 5.847111 TCTATACAGCTTCCGTATTGTGT 57.153 39.130 0.97 0.00 32.01 3.72
834 2032 9.108284 GTCCGAGTAGTATTATATAGGAACTCC 57.892 40.741 0.00 0.00 41.75 3.85
896 2239 1.134367 CACCGGACGAGATCTAGCAAA 59.866 52.381 9.46 0.00 0.00 3.68
1357 3415 1.681327 GTGTCCCCGTCTAGCCTGA 60.681 63.158 0.00 0.00 0.00 3.86
1479 3885 0.536260 GAGCTGTCTGCAGGATCACT 59.464 55.000 15.13 5.38 45.94 3.41
1488 3906 3.941081 AGGATCACTGACGCGGAT 58.059 55.556 12.47 2.12 0.00 4.18
1578 4002 2.793317 AATTCCACCAGGGGCAGCAG 62.793 60.000 0.00 0.00 37.22 4.24
1582 4006 4.990910 ACCAGGGGCAGCAGGTCT 62.991 66.667 0.00 0.00 0.00 3.85
1589 4013 3.123620 GCAGCAGGTCTCCTTGCG 61.124 66.667 0.00 0.00 34.52 4.85
1620 4044 1.895798 TCACTCTTCAAGGATGCTCGT 59.104 47.619 0.00 0.00 0.00 4.18
1797 4440 2.531206 GATCTTACGTTCTTCTGCGCT 58.469 47.619 9.73 0.00 0.00 5.92
1890 4534 4.142315 GCAGCATGTACACCTGATCAAAAT 60.142 41.667 22.76 0.00 39.31 1.82
1892 4536 6.404623 GCAGCATGTACACCTGATCAAAATAA 60.405 38.462 22.76 0.00 39.31 1.40
1893 4537 7.191551 CAGCATGTACACCTGATCAAAATAAG 58.808 38.462 16.53 0.00 0.00 1.73
1894 4538 7.066163 CAGCATGTACACCTGATCAAAATAAGA 59.934 37.037 16.53 0.00 0.00 2.10
1895 4539 7.611467 AGCATGTACACCTGATCAAAATAAGAA 59.389 33.333 0.00 0.00 0.00 2.52
1896 4540 7.698130 GCATGTACACCTGATCAAAATAAGAAC 59.302 37.037 0.00 0.00 0.00 3.01
1917 4561 5.729974 ACAACAACGATGATGATGATGAG 57.270 39.130 9.88 0.00 33.82 2.90
1920 4564 6.036844 ACAACAACGATGATGATGATGAGAAG 59.963 38.462 9.88 0.00 33.82 2.85
1930 4574 3.052262 TGATGATGAGAAGGAGGAGGAGT 60.052 47.826 0.00 0.00 0.00 3.85
1931 4575 2.744760 TGATGAGAAGGAGGAGGAGTG 58.255 52.381 0.00 0.00 0.00 3.51
2059 4752 2.618053 CGAGGTTTTATCGGAAGCAGT 58.382 47.619 0.00 0.00 36.54 4.40
2630 5325 3.497262 CCGTTACAGGGAAACAAGAAGAC 59.503 47.826 0.00 0.00 0.00 3.01
2759 5454 9.901172 TGGATAGTTTCTAATACCTTTCCTTTC 57.099 33.333 0.00 0.00 0.00 2.62
2811 5508 6.398234 TCTCTACTCAACTCATTAGCCATC 57.602 41.667 0.00 0.00 0.00 3.51
2860 5557 1.153086 GCCCCATGAGATCGCTGTT 60.153 57.895 0.00 0.00 0.00 3.16
2956 5653 1.123077 TGCTAGAGGACGATGGCATT 58.877 50.000 0.00 0.00 0.00 3.56
3054 5755 2.689983 CAATGAGGTATGGGGACTTTGC 59.310 50.000 0.00 0.00 0.00 3.68
3176 5974 6.573434 TCAACTGATGTGGCTATAAGTACAG 58.427 40.000 0.00 0.00 0.00 2.74
3350 6153 3.240134 GAACTGGCAGCCCTCGTCA 62.240 63.158 15.89 0.00 0.00 4.35
3351 6154 2.731691 GAACTGGCAGCCCTCGTCAA 62.732 60.000 15.89 0.00 0.00 3.18
3387 6196 4.954970 AGTTGCCAGTGCCCACGG 62.955 66.667 0.00 5.37 36.33 4.94
3514 6332 2.577449 TGCTGCGACGAATCATTCTA 57.423 45.000 0.00 0.00 0.00 2.10
3536 6354 8.058667 TCTACTTTCCATGTTTCGATGTACTA 57.941 34.615 0.00 0.00 0.00 1.82
3673 6494 4.684214 TTGTTTGCACAATATGGTTTGCCA 60.684 37.500 0.00 0.00 42.74 4.92
3848 6684 5.598005 TCCTCTCTTTTTCAAGGAAATGCAA 59.402 36.000 0.00 0.00 35.01 4.08
3952 6788 3.058570 GTGCACATGAAAATACACGGTCA 60.059 43.478 13.17 0.00 0.00 4.02
3972 6811 5.807011 GGTCAATGCATGGTTAGAAATGAAC 59.193 40.000 0.00 0.00 0.00 3.18
4104 6945 2.290531 TCTTCTTCGATCTGCAGCTG 57.709 50.000 10.11 10.11 0.00 4.24
4533 7374 2.365293 GTGGCTTCAGGGAAATGTTGTT 59.635 45.455 0.00 0.00 0.00 2.83
4804 7988 6.485313 TCCGTGGATATATGATTTTTGGTGAC 59.515 38.462 0.00 0.00 0.00 3.67
4809 7993 6.485313 GGATATATGATTTTTGGTGACGGTGA 59.515 38.462 0.00 0.00 0.00 4.02
4937 8124 9.987272 TGGACTACATCATTTATCTATCAACAG 57.013 33.333 0.00 0.00 0.00 3.16
4953 8140 5.036117 TCAACAGATATAAAGGCTGGGTC 57.964 43.478 0.00 0.00 34.05 4.46
5040 8227 5.052481 TCATCTATATATCGCCAAGCATGC 58.948 41.667 10.51 10.51 0.00 4.06
5041 8228 4.743057 TCTATATATCGCCAAGCATGCT 57.257 40.909 16.30 16.30 0.00 3.79
5042 8229 4.686972 TCTATATATCGCCAAGCATGCTC 58.313 43.478 22.93 7.83 0.00 4.26
5043 8230 2.837532 TATATCGCCAAGCATGCTCA 57.162 45.000 22.93 3.12 0.00 4.26
5044 8231 2.195741 ATATCGCCAAGCATGCTCAT 57.804 45.000 22.93 2.64 0.00 2.90
5045 8232 1.971481 TATCGCCAAGCATGCTCATT 58.029 45.000 22.93 1.73 0.00 2.57
5046 8233 0.384309 ATCGCCAAGCATGCTCATTG 59.616 50.000 22.93 15.78 0.00 2.82
5047 8234 0.677414 TCGCCAAGCATGCTCATTGA 60.677 50.000 22.93 14.13 0.00 2.57
5048 8235 0.171679 CGCCAAGCATGCTCATTGAA 59.828 50.000 22.93 0.00 0.00 2.69
5049 8236 1.202371 CGCCAAGCATGCTCATTGAAT 60.202 47.619 22.93 0.00 0.00 2.57
5050 8237 2.033675 CGCCAAGCATGCTCATTGAATA 59.966 45.455 22.93 0.00 0.00 1.75
5051 8238 3.639538 GCCAAGCATGCTCATTGAATAG 58.360 45.455 22.93 4.20 0.00 1.73
5052 8239 3.067742 GCCAAGCATGCTCATTGAATAGT 59.932 43.478 22.93 0.00 0.00 2.12
5053 8240 4.607955 CCAAGCATGCTCATTGAATAGTG 58.392 43.478 22.93 11.12 0.00 2.74
5054 8241 3.984508 AGCATGCTCATTGAATAGTGC 57.015 42.857 16.30 5.38 0.00 4.40
5055 8242 3.284617 AGCATGCTCATTGAATAGTGCA 58.715 40.909 16.30 7.55 38.42 4.57
5056 8243 3.315470 AGCATGCTCATTGAATAGTGCAG 59.685 43.478 16.30 4.16 37.62 4.41
5057 8244 3.314357 GCATGCTCATTGAATAGTGCAGA 59.686 43.478 11.37 0.00 37.62 4.26
5058 8245 4.554919 GCATGCTCATTGAATAGTGCAGAG 60.555 45.833 11.37 0.00 37.62 3.35
5059 8246 2.941064 TGCTCATTGAATAGTGCAGAGC 59.059 45.455 10.81 10.81 45.23 4.09
5060 8247 2.941064 GCTCATTGAATAGTGCAGAGCA 59.059 45.455 12.37 0.00 44.60 4.26
5061 8248 3.564644 GCTCATTGAATAGTGCAGAGCAT 59.435 43.478 12.37 0.00 44.60 3.79
5062 8249 4.554919 GCTCATTGAATAGTGCAGAGCATG 60.555 45.833 12.37 0.00 44.60 4.06
5063 8250 4.773013 TCATTGAATAGTGCAGAGCATGA 58.227 39.130 0.00 0.00 41.91 3.07
5175 8363 2.040278 AGGTTAAGCATGCACTTCCAGA 59.960 45.455 21.98 0.00 0.00 3.86
5176 8364 3.019564 GGTTAAGCATGCACTTCCAGAT 58.980 45.455 21.98 0.00 0.00 2.90
5177 8365 3.181493 GGTTAAGCATGCACTTCCAGATG 60.181 47.826 21.98 0.00 0.00 2.90
5178 8366 2.502142 AAGCATGCACTTCCAGATGA 57.498 45.000 21.98 0.00 0.00 2.92
5179 8367 1.747709 AGCATGCACTTCCAGATGAC 58.252 50.000 21.98 0.00 0.00 3.06
5180 8368 0.737219 GCATGCACTTCCAGATGACC 59.263 55.000 14.21 0.00 0.00 4.02
5181 8369 1.012086 CATGCACTTCCAGATGACCG 58.988 55.000 0.00 0.00 0.00 4.79
5182 8370 0.615331 ATGCACTTCCAGATGACCGT 59.385 50.000 0.00 0.00 0.00 4.83
5183 8371 0.396435 TGCACTTCCAGATGACCGTT 59.604 50.000 0.00 0.00 0.00 4.44
5184 8372 1.202758 TGCACTTCCAGATGACCGTTT 60.203 47.619 0.00 0.00 0.00 3.60
5185 8373 2.037902 TGCACTTCCAGATGACCGTTTA 59.962 45.455 0.00 0.00 0.00 2.01
5186 8374 3.270877 GCACTTCCAGATGACCGTTTAT 58.729 45.455 0.00 0.00 0.00 1.40
5187 8375 4.081365 TGCACTTCCAGATGACCGTTTATA 60.081 41.667 0.00 0.00 0.00 0.98
5188 8376 5.057149 GCACTTCCAGATGACCGTTTATAT 58.943 41.667 0.00 0.00 0.00 0.86
5189 8377 6.183360 TGCACTTCCAGATGACCGTTTATATA 60.183 38.462 0.00 0.00 0.00 0.86
5190 8378 6.145696 GCACTTCCAGATGACCGTTTATATAC 59.854 42.308 0.00 0.00 0.00 1.47
5191 8379 6.645415 CACTTCCAGATGACCGTTTATATACC 59.355 42.308 0.00 0.00 0.00 2.73
5192 8380 5.733620 TCCAGATGACCGTTTATATACCC 57.266 43.478 0.00 0.00 0.00 3.69
5193 8381 4.529377 TCCAGATGACCGTTTATATACCCC 59.471 45.833 0.00 0.00 0.00 4.95
5194 8382 4.285003 CCAGATGACCGTTTATATACCCCA 59.715 45.833 0.00 0.00 0.00 4.96
5195 8383 5.045869 CCAGATGACCGTTTATATACCCCAT 60.046 44.000 0.00 0.00 0.00 4.00
5236 8463 9.691362 GCAAAAGAAATGAGGTTTAACTGAATA 57.309 29.630 0.00 0.00 0.00 1.75
5272 10992 6.131544 ACACTGTTTGGTGTAAAGCTTTAG 57.868 37.500 19.16 8.54 46.89 1.85
5318 11040 9.685276 TCAAGTAGATCATCACCATTTGTTTAT 57.315 29.630 0.00 0.00 0.00 1.40
5630 13960 6.166279 CAGCAAACTAGTTCATAGACCAAGA 58.834 40.000 8.95 0.00 35.30 3.02
5656 13986 4.694512 AGGGGGTAAACCTTTTGCAATAT 58.305 39.130 0.00 0.00 40.03 1.28
5657 13987 4.714802 AGGGGGTAAACCTTTTGCAATATC 59.285 41.667 0.00 0.00 40.03 1.63
5660 13990 6.468543 GGGGTAAACCTTTTGCAATATCAAA 58.531 36.000 0.00 0.00 40.03 2.69
5662 13992 6.593770 GGGTAAACCTTTTGCAATATCAAAGG 59.406 38.462 20.45 20.45 37.27 3.11
5663 13993 6.092122 GGTAAACCTTTTGCAATATCAAAGGC 59.908 38.462 21.52 9.24 37.27 4.35
5665 13995 5.226194 ACCTTTTGCAATATCAAAGGCAA 57.774 34.783 21.52 0.00 43.79 4.52
5669 13999 3.932545 TGCAATATCAAAGGCAAACGT 57.067 38.095 0.00 0.00 32.54 3.99
5670 14000 4.250116 TGCAATATCAAAGGCAAACGTT 57.750 36.364 0.00 0.00 32.54 3.99
5671 14001 4.626042 TGCAATATCAAAGGCAAACGTTT 58.374 34.783 7.96 7.96 34.30 3.60
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 5.470368 GCTTCCCAAAAAGACCTAATTCAC 58.530 41.667 0.00 0.00 0.00 3.18
25 26 0.387750 GCAGAGCGCTTCCCAAAAAG 60.388 55.000 13.26 0.00 37.77 2.27
90 91 1.000163 CGATGATAAGTAGCACCGCCT 60.000 52.381 0.00 0.00 0.00 5.52
127 140 1.674817 GGGATCGACGTTGTTGGTGAT 60.675 52.381 1.96 0.00 0.00 3.06
151 176 5.408880 TGGACATACGGTTCATTAGTTGA 57.591 39.130 0.00 0.00 26.83 3.18
168 193 2.977772 TGCACATATCACGATGGACA 57.022 45.000 0.00 0.00 0.00 4.02
185 210 6.106673 ACAACAACTATAGGTAGACACATGC 58.893 40.000 4.43 0.00 0.00 4.06
261 287 4.836125 AATAGGAAATAGCATGCAACGG 57.164 40.909 21.98 0.00 0.00 4.44
262 288 6.425114 ACTCTAATAGGAAATAGCATGCAACG 59.575 38.462 21.98 0.00 0.00 4.10
333 363 4.961438 TTAGGGTTGTTTAGTCCTCGTT 57.039 40.909 0.00 0.00 0.00 3.85
417 447 0.976590 GCCTTCCCTCTACCTTCCGT 60.977 60.000 0.00 0.00 0.00 4.69
425 455 2.103153 ATGGATTCGCCTTCCCTCTA 57.897 50.000 0.00 0.00 37.63 2.43
463 493 1.018226 CCAAGCAAGCTCTCACTCCG 61.018 60.000 0.00 0.00 0.00 4.63
474 504 1.026718 CCTTAGGCGGTCCAAGCAAG 61.027 60.000 0.00 0.00 36.08 4.01
498 528 7.684529 AGAACACATCTCAATAGTTTCTTCCT 58.315 34.615 0.00 0.00 30.46 3.36
518 548 4.082190 CACTCTTTCGGGAGATGTAGAACA 60.082 45.833 7.69 0.00 39.57 3.18
524 554 3.432378 AGTACACTCTTTCGGGAGATGT 58.568 45.455 0.00 9.52 39.57 3.06
553 583 1.570813 CAGCGCCGATGTAGATGAAA 58.429 50.000 2.29 0.00 0.00 2.69
555 585 1.300156 GCAGCGCCGATGTAGATGA 60.300 57.895 2.29 0.00 0.00 2.92
584 624 1.035385 ATCGAAAATTCCCACCGCCC 61.035 55.000 0.00 0.00 0.00 6.13
612 652 2.022129 CGCAAGCGTTCGTCTCCTT 61.022 57.895 6.25 0.00 34.35 3.36
760 834 3.676291 TCCAACAGATCGATCACACAA 57.324 42.857 26.47 5.36 0.00 3.33
765 839 8.559536 GCTTAATTAATTCCAACAGATCGATCA 58.440 33.333 26.47 5.00 0.00 2.92
834 2032 3.724374 ACCACGTACGGATTGGATTATG 58.276 45.455 25.14 8.90 34.24 1.90
1209 3267 2.284405 ACCACCTGTCCGGGGTAG 60.284 66.667 0.00 0.00 35.38 3.18
1232 3290 2.124612 CGCCCATGTCAGATGCCA 60.125 61.111 0.00 0.00 0.00 4.92
1488 3906 2.154798 CTCTCGCCAGGTTCGTGGAA 62.155 60.000 14.54 2.28 40.44 3.53
1589 4013 0.793250 GAAGAGTGAACAAGCGCCTC 59.207 55.000 2.29 0.85 0.00 4.70
1620 4044 1.005332 TGCCAGTAGCCATTAAGCCAA 59.995 47.619 0.00 0.00 42.71 4.52
1876 4520 7.581213 TGTTGTTCTTATTTTGATCAGGTGT 57.419 32.000 0.00 0.00 0.00 4.16
1878 4522 7.012894 TCGTTGTTGTTCTTATTTTGATCAGGT 59.987 33.333 0.00 0.00 0.00 4.00
1890 4534 7.548780 TCATCATCATCATCGTTGTTGTTCTTA 59.451 33.333 4.84 0.00 0.00 2.10
1892 4536 5.876460 TCATCATCATCATCGTTGTTGTTCT 59.124 36.000 4.84 0.00 0.00 3.01
1893 4537 6.036408 TCTCATCATCATCATCGTTGTTGTTC 59.964 38.462 4.84 0.00 0.00 3.18
1894 4538 5.876460 TCTCATCATCATCATCGTTGTTGTT 59.124 36.000 4.84 0.00 0.00 2.83
1895 4539 5.422145 TCTCATCATCATCATCGTTGTTGT 58.578 37.500 4.84 0.00 0.00 3.32
1896 4540 5.978934 TCTCATCATCATCATCGTTGTTG 57.021 39.130 0.00 0.00 0.00 3.33
1917 4561 0.689412 CCTCCCACTCCTCCTCCTTC 60.689 65.000 0.00 0.00 0.00 3.46
1920 4564 1.075600 CTCCTCCCACTCCTCCTCC 60.076 68.421 0.00 0.00 0.00 4.30
1930 4574 4.024984 CCCCTCCCACTCCTCCCA 62.025 72.222 0.00 0.00 0.00 4.37
1931 4575 4.825679 CCCCCTCCCACTCCTCCC 62.826 77.778 0.00 0.00 0.00 4.30
2059 4752 2.029649 CCTCAAAGACGACCTTCCGTAA 60.030 50.000 0.00 0.00 43.49 3.18
2105 4800 4.437239 CACCTCCACATGTCTCATTACTC 58.563 47.826 0.00 0.00 0.00 2.59
2302 4997 3.840666 ACATGGTCTCCTGTAGTGTCAAT 59.159 43.478 0.00 0.00 0.00 2.57
2389 5084 0.320683 CTCTTGACGATGCCCACACA 60.321 55.000 0.00 0.00 0.00 3.72
2609 5304 4.124238 TGTCTTCTTGTTTCCCTGTAACG 58.876 43.478 0.00 0.00 0.00 3.18
2630 5325 1.197721 GATCGGCGGGAATAGCATTTG 59.802 52.381 7.21 0.00 36.08 2.32
2811 5508 1.782044 CACGCCCAAACAAATCAAGG 58.218 50.000 0.00 0.00 0.00 3.61
2860 5557 1.324383 TGTAGTGCTCGTCCTTGACA 58.676 50.000 0.00 0.00 32.09 3.58
2956 5653 1.678728 GGTTCTTCGGGTGCATCATCA 60.679 52.381 0.00 0.00 0.00 3.07
3176 5974 9.566432 AGATCAATGTCCTAAAATCAGATAACC 57.434 33.333 0.00 0.00 0.00 2.85
3214 6012 0.912528 GACGCCTTCGACATCGTTAC 59.087 55.000 0.54 0.00 40.80 2.50
3245 6043 3.325716 ACCCTAAAAGGCTTGTACTCGAA 59.674 43.478 0.00 0.00 32.73 3.71
3350 6153 1.338973 TCTGAGCTTGGTAACGACGTT 59.661 47.619 18.47 18.47 42.51 3.99
3351 6154 0.956633 TCTGAGCTTGGTAACGACGT 59.043 50.000 0.00 0.00 42.51 4.34
3514 6332 6.460781 TGTAGTACATCGAAACATGGAAAGT 58.539 36.000 0.00 0.00 0.00 2.66
3536 6354 1.918262 TGATCCAAAGGGCTGATCTGT 59.082 47.619 1.27 0.00 36.65 3.41
3673 6494 2.947652 CTGCAGATGGATTCCAACGATT 59.052 45.455 8.42 0.00 36.95 3.34
3720 6544 7.944000 AGCCAAAGGGATTCAATTTTATTTTGT 59.056 29.630 0.00 0.00 35.59 2.83
3848 6684 2.044252 TTCCCTCGACTAGCGCCT 60.044 61.111 2.29 0.00 40.61 5.52
3952 6788 6.209192 TGTCTGTTCATTTCTAACCATGCATT 59.791 34.615 0.00 0.00 0.00 3.56
3972 6811 5.687285 GGTTTCTGCACATTAAAGTTGTCTG 59.313 40.000 0.00 0.00 0.00 3.51
4257 7098 0.671781 CAACGACTTGGAGGAGGCTG 60.672 60.000 0.00 0.00 0.00 4.85
4533 7374 2.438254 GTGGCATGGGCATCGTCA 60.438 61.111 0.00 0.00 43.71 4.35
4804 7988 4.875536 TGAATGATTACAAGACCATCACCG 59.124 41.667 0.00 0.00 29.74 4.94
4809 7993 9.426837 CAAAAATGTGAATGATTACAAGACCAT 57.573 29.630 0.00 0.00 0.00 3.55
5040 8227 4.814771 TCATGCTCTGCACTATTCAATGAG 59.185 41.667 0.00 0.00 43.04 2.90
5041 8228 4.773013 TCATGCTCTGCACTATTCAATGA 58.227 39.130 0.00 0.00 43.04 2.57
5042 8229 5.238650 TGATCATGCTCTGCACTATTCAATG 59.761 40.000 0.00 0.00 43.04 2.82
5043 8230 5.374071 TGATCATGCTCTGCACTATTCAAT 58.626 37.500 0.00 0.00 43.04 2.57
5044 8231 4.773013 TGATCATGCTCTGCACTATTCAA 58.227 39.130 0.00 0.00 43.04 2.69
5045 8232 4.411256 TGATCATGCTCTGCACTATTCA 57.589 40.909 0.00 0.00 43.04 2.57
5046 8233 5.284428 CATGATCATGCTCTGCACTATTC 57.716 43.478 22.20 0.00 43.04 1.75
5059 8246 4.731961 GCACGTTCTTAAAGCATGATCATG 59.268 41.667 28.04 28.04 41.60 3.07
5060 8247 4.395854 TGCACGTTCTTAAAGCATGATCAT 59.604 37.500 1.18 1.18 0.00 2.45
5061 8248 3.750652 TGCACGTTCTTAAAGCATGATCA 59.249 39.130 0.00 0.00 0.00 2.92
5062 8249 4.340894 TGCACGTTCTTAAAGCATGATC 57.659 40.909 0.00 0.00 0.00 2.92
5063 8250 4.455533 TCTTGCACGTTCTTAAAGCATGAT 59.544 37.500 0.00 0.00 35.39 2.45
5176 8364 9.940974 ACTATATATGGGGTATATAAACGGTCA 57.059 33.333 0.80 0.00 37.63 4.02
5187 8375 9.778479 TTGCAGTAACTACTATATATGGGGTAT 57.222 33.333 0.80 0.00 34.13 2.73
5188 8376 9.604569 TTTGCAGTAACTACTATATATGGGGTA 57.395 33.333 0.80 0.00 34.13 3.69
5189 8377 8.500667 TTTGCAGTAACTACTATATATGGGGT 57.499 34.615 0.80 0.00 34.13 4.95
5190 8378 9.436957 CTTTTGCAGTAACTACTATATATGGGG 57.563 37.037 0.80 0.00 34.13 4.96
5318 11040 7.097192 AGTAGCAGATTGAATTCTGAAACGTA 58.903 34.615 7.05 0.00 44.88 3.57
5353 13186 1.671845 TCAACTTTACACCGGTGCAAC 59.328 47.619 34.26 0.00 0.00 4.17
5359 13192 3.074412 AGCAAGATCAACTTTACACCGG 58.926 45.455 0.00 0.00 36.61 5.28
5630 13960 1.431633 CAAAAGGTTTACCCCCTCCCT 59.568 52.381 0.00 0.00 36.42 4.20


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

AutoCloner maintained by Alex Coulton.