Multiple sequence alignment - TraesCS3B01G135700

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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 TraesCS3B01G135700 chr3B 100.000 4484 0 0 1 4484 118507968 118503485 0.000000e+00 8281.0
1 TraesCS3B01G135700 chr3B 90.299 134 12 1 567 700 655635116 655634984 1.660000e-39 174.0
2 TraesCS3B01G135700 chr3B 80.282 142 23 5 564 703 679632686 679632824 7.940000e-18 102.0
3 TraesCS3B01G135700 chr3B 77.844 167 27 10 3497 3655 477605695 477605859 1.330000e-15 95.3
4 TraesCS3B01G135700 chr3A 92.393 4036 210 35 482 4447 86124603 86120595 0.000000e+00 5662.0
5 TraesCS3B01G135700 chr3D 92.645 3712 201 32 1 3671 73207556 73203876 0.000000e+00 5276.0
6 TraesCS3B01G135700 chr3D 88.302 265 14 7 4183 4446 73197326 73197078 7.290000e-78 302.0
7 TraesCS3B01G135700 chr3D 80.282 142 23 5 564 703 516202345 516202483 7.940000e-18 102.0
8 TraesCS3B01G135700 chr5B 92.136 1208 78 9 1661 2857 563519829 563518628 0.000000e+00 1688.0
9 TraesCS3B01G135700 chr5B 84.058 69 11 0 823 891 506203937 506203869 2.890000e-07 67.6
10 TraesCS3B01G135700 chr4B 91.083 471 40 2 1108 1577 615715613 615716082 1.760000e-178 636.0
11 TraesCS3B01G135700 chr4B 87.234 141 17 1 558 698 184302602 184302741 4.640000e-35 159.0
12 TraesCS3B01G135700 chr4B 78.107 169 21 15 3498 3655 52577861 52577698 4.780000e-15 93.5
13 TraesCS3B01G135700 chr4B 78.571 140 27 3 564 700 487272910 487273049 6.180000e-14 89.8
14 TraesCS3B01G135700 chr4B 96.154 52 2 0 1576 1627 615764985 615765036 7.990000e-13 86.1
15 TraesCS3B01G135700 chr7B 89.781 137 14 0 564 700 106804235 106804099 4.610000e-40 176.0
16 TraesCS3B01G135700 chr4A 82.482 137 15 8 758 892 86932908 86932779 1.320000e-20 111.0
17 TraesCS3B01G135700 chr4A 87.234 94 12 0 607 700 449398524 449398431 1.710000e-19 108.0
18 TraesCS3B01G135700 chr4A 88.406 69 5 3 3497 3564 562300975 562301041 3.720000e-11 80.5
19 TraesCS3B01G135700 chr7D 85.714 98 9 5 360 457 471206340 471206432 1.030000e-16 99.0
20 TraesCS3B01G135700 chr7D 78.014 141 28 3 753 891 246365863 246365724 7.990000e-13 86.1
21 TraesCS3B01G135700 chr7D 88.571 70 5 3 3498 3566 136113577 136113644 1.030000e-11 82.4
22 TraesCS3B01G135700 chr7D 85.714 70 9 1 320 388 555566441 555566372 6.220000e-09 73.1
23 TraesCS3B01G135700 chr7A 78.616 159 25 8 234 388 721201823 721201670 3.690000e-16 97.1
24 TraesCS3B01G135700 chr4D 87.654 81 10 0 813 893 21700260 21700340 1.330000e-15 95.3
25 TraesCS3B01G135700 chr2B 90.278 72 4 3 3497 3567 683006028 683005959 1.720000e-14 91.6
26 TraesCS3B01G135700 chr6D 83.721 86 13 1 822 906 301049680 301049595 3.720000e-11 80.5
27 TraesCS3B01G135700 chr5D 94.340 53 2 1 3498 3550 565353581 565353530 3.720000e-11 80.5
28 TraesCS3B01G135700 chr1B 76.761 142 27 6 755 891 445667762 445667902 1.730000e-09 75.0
29 TraesCS3B01G135700 chr2D 100.000 30 0 0 360 389 485665501 485665472 6.270000e-04 56.5
30 TraesCS3B01G135700 chr5A 84.906 53 8 0 839 891 666158416 666158468 2.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G135700 chr3B 118503485 118507968 4483 True 8281 8281 100.000 1 4484 1 chr3B.!!$R1 4483
1 TraesCS3B01G135700 chr3A 86120595 86124603 4008 True 5662 5662 92.393 482 4447 1 chr3A.!!$R1 3965
2 TraesCS3B01G135700 chr3D 73203876 73207556 3680 True 5276 5276 92.645 1 3671 1 chr3D.!!$R2 3670
3 TraesCS3B01G135700 chr5B 563518628 563519829 1201 True 1688 1688 92.136 1661 2857 1 chr5B.!!$R2 1196

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
811 827 1.406065 CGATCCTGTGGCCTCCAGAT 61.406 60.0 20.54 13.68 32.34 2.90 F
1440 1462 0.602562 TTTGCTGAATTTGGCCGAGG 59.397 50.0 0.00 0.00 0.00 4.63 F
2793 2826 0.034477 CCTGTAAACTCCCCGCCAAT 60.034 55.0 0.00 0.00 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1650 1672 0.518636 CCCAACTGACGCTGTTGATG 59.481 55.0 21.8 13.31 42.93 3.07 R
3026 3059 1.151668 CAAGAGACGCAGACAAAGGG 58.848 55.0 0.0 0.00 0.00 3.95 R
3738 3797 0.103390 TCCGCACGTCTTCAACAGAA 59.897 50.0 0.0 0.00 31.28 3.02 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
172 178 5.748402 ACATGGTCAATATTTCTCTGCAGA 58.252 37.500 17.19 17.19 0.00 4.26
173 179 5.587844 ACATGGTCAATATTTCTCTGCAGAC 59.412 40.000 13.74 0.00 0.00 3.51
182 188 9.844790 CAATATTTCTCTGCAGACATTTAACAA 57.155 29.630 13.74 0.00 0.00 2.83
296 302 5.459762 ACATTTTTGAACAGCTTGATCAACG 59.540 36.000 3.38 2.41 38.58 4.10
306 312 6.272318 ACAGCTTGATCAACGATTTTCAAAA 58.728 32.000 3.38 0.00 0.00 2.44
312 318 5.691305 TGATCAACGATTTTCAAAAGCAAGG 59.309 36.000 0.00 0.00 0.00 3.61
373 379 7.945033 ACACATTTCGCATTTTTCAAATACT 57.055 28.000 0.00 0.00 0.00 2.12
374 380 8.364129 ACACATTTCGCATTTTTCAAATACTT 57.636 26.923 0.00 0.00 0.00 2.24
375 381 8.274939 ACACATTTCGCATTTTTCAAATACTTG 58.725 29.630 0.00 0.00 0.00 3.16
376 382 7.266756 CACATTTCGCATTTTTCAAATACTTGC 59.733 33.333 0.00 0.00 32.14 4.01
377 383 7.171337 ACATTTCGCATTTTTCAAATACTTGCT 59.829 29.630 0.00 0.00 32.14 3.91
378 384 7.475771 TTTCGCATTTTTCAAATACTTGCTT 57.524 28.000 0.00 0.00 32.14 3.91
379 385 8.581057 TTTCGCATTTTTCAAATACTTGCTTA 57.419 26.923 0.00 0.00 32.14 3.09
380 386 8.581057 TTCGCATTTTTCAAATACTTGCTTAA 57.419 26.923 0.00 0.00 32.14 1.85
381 387 8.002433 TCGCATTTTTCAAATACTTGCTTAAC 57.998 30.769 0.00 0.00 32.14 2.01
501 507 8.772705 ACACATTTAACATTTTTCGAATGCATT 58.227 25.926 12.83 12.83 0.00 3.56
561 567 7.838079 TTTGTAATATATGCCCATGCTTTCT 57.162 32.000 0.00 0.00 38.71 2.52
575 581 7.088905 CCCATGCTTTCTGAATTATAAGATGC 58.911 38.462 0.00 0.00 0.00 3.91
595 601 8.716674 AGATGCTTTGGATATTTCAATATGGT 57.283 30.769 0.00 0.00 31.96 3.55
617 623 6.826741 TGGTCTAGATACAAACTAAAATGGGC 59.173 38.462 0.00 0.00 0.00 5.36
621 627 7.990886 TCTAGATACAAACTAAAATGGGCGAAT 59.009 33.333 0.00 0.00 0.00 3.34
703 712 3.343941 TTGGAACCGAGGGAGTATTTG 57.656 47.619 0.00 0.00 0.00 2.32
706 715 3.073356 TGGAACCGAGGGAGTATTTGTTT 59.927 43.478 0.00 0.00 0.00 2.83
811 827 1.406065 CGATCCTGTGGCCTCCAGAT 61.406 60.000 20.54 13.68 32.34 2.90
1000 1021 3.894547 TTCGCCTTCACCTTCGCCC 62.895 63.158 0.00 0.00 0.00 6.13
1398 1420 1.144093 TCTTTGTGATTCCCGGTGGTT 59.856 47.619 0.00 0.00 0.00 3.67
1416 1438 5.105351 GGTGGTTTAGGATTGAGAATTTGGG 60.105 44.000 0.00 0.00 0.00 4.12
1440 1462 0.602562 TTTGCTGAATTTGGCCGAGG 59.397 50.000 0.00 0.00 0.00 4.63
1643 1665 7.094463 GGAGAATTAACAGCTGCAGCATATTAT 60.094 37.037 38.24 24.11 45.16 1.28
1650 1672 4.093115 CAGCTGCAGCATATTATAGAGTGC 59.907 45.833 38.24 8.43 45.16 4.40
1696 1718 2.294449 TCCGGTGATCTCTATGGGAG 57.706 55.000 0.00 0.00 43.12 4.30
1783 1805 1.539827 GGCAGTGTGGTGGTAATGTTC 59.460 52.381 0.00 0.00 0.00 3.18
1939 1962 4.046938 TGATGACAGGAATCGACTTAGC 57.953 45.455 0.00 0.00 0.00 3.09
1945 1968 3.693085 ACAGGAATCGACTTAGCGTTCTA 59.307 43.478 0.00 0.00 0.00 2.10
1946 1969 4.201930 ACAGGAATCGACTTAGCGTTCTAG 60.202 45.833 0.00 0.00 0.00 2.43
1947 1970 3.946558 AGGAATCGACTTAGCGTTCTAGT 59.053 43.478 0.00 0.00 0.00 2.57
1948 1971 5.007430 CAGGAATCGACTTAGCGTTCTAGTA 59.993 44.000 0.00 0.00 0.00 1.82
1959 1984 7.607991 ACTTAGCGTTCTAGTAAGTGGTAAGTA 59.392 37.037 17.46 0.00 44.21 2.24
2008 2033 5.249393 AGTTGTAGGTGGAATCTGTTCAGAT 59.751 40.000 9.22 9.22 36.01 2.90
2357 2382 9.883142 ATCTCTTTTTGGTTCAGAGTAAGATAG 57.117 33.333 0.00 0.00 36.27 2.08
2390 2415 6.715718 TCACAAAATCATTCATTTGCCCATTT 59.284 30.769 0.00 0.00 39.55 2.32
2548 2581 2.914695 ATGAGATTGAGAGCAGAGGC 57.085 50.000 0.00 0.00 41.61 4.70
2739 2772 1.885887 TCCTTCACAGCAAAATTCCCG 59.114 47.619 0.00 0.00 0.00 5.14
2793 2826 0.034477 CCTGTAAACTCCCCGCCAAT 60.034 55.000 0.00 0.00 0.00 3.16
3010 3043 4.884961 ACTAGAGGTACATGTGATTCCCT 58.115 43.478 9.11 5.62 0.00 4.20
3026 3059 1.625818 TCCCTTCCAGAACTCTCTTGC 59.374 52.381 0.00 0.00 0.00 4.01
3105 3138 4.293662 TCTGGCACCATGTACATAACAA 57.706 40.909 8.32 0.00 42.70 2.83
3156 3189 1.775039 ATTGCGGATTGCGATCACCG 61.775 55.000 15.92 12.40 44.84 4.94
3163 3196 1.705337 ATTGCGATCACCGGCTTTCG 61.705 55.000 14.19 14.19 39.04 3.46
3205 3238 3.699894 CCTGCAGGCTGTCTCGGT 61.700 66.667 22.33 0.00 0.00 4.69
3211 3244 3.227614 TGCAGGCTGTCTCGGTATAATA 58.772 45.455 17.16 0.00 0.00 0.98
3362 3395 0.099436 CCTGTAAAAGATGCAGCGGC 59.901 55.000 0.31 0.31 40.14 6.53
3489 3541 9.607988 AAATAATATACAGTTGACGATGGTTGA 57.392 29.630 0.00 0.00 0.00 3.18
3698 3757 2.079170 ATCAGCAATCTCTCCGAGGA 57.921 50.000 0.00 0.00 0.00 3.71
3708 3767 1.680735 CTCTCCGAGGATCTGGTTCTG 59.319 57.143 0.00 0.00 32.04 3.02
3709 3768 0.749649 CTCCGAGGATCTGGTTCTGG 59.250 60.000 0.00 0.00 32.04 3.86
3752 3811 6.698380 ACTTGGTATATTCTGTTGAAGACGT 58.302 36.000 0.00 0.00 35.44 4.34
3762 3821 1.798813 GTTGAAGACGTGCGGATTTCT 59.201 47.619 0.00 0.00 0.00 2.52
3804 3863 1.134037 TGTAGCAACGACAAAAGGGGT 60.134 47.619 0.00 0.00 0.00 4.95
3822 3881 1.009449 TCAAAGCCGCGTTTTTCCG 60.009 52.632 4.92 0.00 0.00 4.30
3864 3923 1.984570 CGAAGCCACCAGGAGAGGA 60.985 63.158 0.00 0.00 36.89 3.71
3867 3926 0.768221 AAGCCACCAGGAGAGGAACA 60.768 55.000 0.00 0.00 36.89 3.18
3875 3934 4.163078 CACCAGGAGAGGAACATATCTTGT 59.837 45.833 0.00 0.00 41.53 3.16
3881 3940 7.175119 CAGGAGAGGAACATATCTTGTATCGTA 59.825 40.741 0.00 0.00 37.68 3.43
3903 3962 3.310774 AGAGCATTGCACATATGTTCGAC 59.689 43.478 11.91 0.00 38.01 4.20
3913 3972 1.170442 TATGTTCGACGCTGTCCTCA 58.830 50.000 0.00 2.05 0.00 3.86
3915 3974 0.109272 TGTTCGACGCTGTCCTCATC 60.109 55.000 0.00 0.00 0.00 2.92
3936 3995 3.009033 TCCTGCAGGCAAGTATAACAAGT 59.991 43.478 28.91 0.00 34.44 3.16
3938 3997 3.343617 TGCAGGCAAGTATAACAAGTCC 58.656 45.455 0.00 0.00 0.00 3.85
3954 4013 0.951040 GTCCAAGTCTGGTCTTGCGG 60.951 60.000 0.00 0.00 43.97 5.69
3955 4014 1.118965 TCCAAGTCTGGTCTTGCGGA 61.119 55.000 0.00 0.00 43.97 5.54
3986 4045 4.222810 TGGCACAGTGATATGAGTTACAGT 59.777 41.667 4.15 0.00 0.00 3.55
3989 4048 6.045318 GCACAGTGATATGAGTTACAGTGAT 58.955 40.000 4.15 0.00 37.21 3.06
3990 4049 6.019237 GCACAGTGATATGAGTTACAGTGATG 60.019 42.308 4.15 0.00 37.21 3.07
4009 4068 2.807631 GATGTTGTGCCGCAAGCCAG 62.808 60.000 0.00 0.00 42.71 4.85
4010 4069 3.286751 GTTGTGCCGCAAGCCAGA 61.287 61.111 0.00 0.00 42.71 3.86
4069 4128 4.769488 AGATAGATGCAGCGAAAGGAGATA 59.231 41.667 0.00 0.00 0.00 1.98
4074 4133 4.142609 TGCAGCGAAAGGAGATATTTCT 57.857 40.909 0.00 0.00 35.05 2.52
4079 4138 6.507900 CAGCGAAAGGAGATATTTCTAGTCA 58.492 40.000 0.00 0.00 35.05 3.41
4080 4139 6.419413 CAGCGAAAGGAGATATTTCTAGTCAC 59.581 42.308 0.00 0.00 35.05 3.67
4083 4142 6.920758 CGAAAGGAGATATTTCTAGTCACTGG 59.079 42.308 0.00 0.00 35.05 4.00
4086 4145 5.069781 AGGAGATATTTCTAGTCACTGGCAC 59.930 44.000 0.00 0.00 30.30 5.01
4110 4169 0.459585 ATTGATACACCGAGCGCGTT 60.460 50.000 8.43 0.00 35.23 4.84
4111 4170 1.348538 TTGATACACCGAGCGCGTTG 61.349 55.000 8.43 7.60 35.90 4.10
4128 4187 0.173935 TTGTATACACGCCCGAGGTG 59.826 55.000 4.68 2.39 41.15 4.00
4129 4188 1.066918 GTATACACGCCCGAGGTGG 59.933 63.158 0.00 1.07 39.69 4.61
4160 4219 3.376859 CACACAAAAGTGGCAGTTGTCTA 59.623 43.478 8.61 0.00 33.27 2.59
4186 4245 1.271543 CCCACTGAACAGAGGCAATGA 60.272 52.381 11.71 0.00 37.78 2.57
4188 4247 2.497138 CACTGAACAGAGGCAATGACA 58.503 47.619 8.87 0.00 0.00 3.58
4189 4248 2.483106 CACTGAACAGAGGCAATGACAG 59.517 50.000 8.87 13.84 34.52 3.51
4190 4249 2.369860 ACTGAACAGAGGCAATGACAGA 59.630 45.455 8.87 0.00 33.52 3.41
4191 4250 3.008813 ACTGAACAGAGGCAATGACAGAT 59.991 43.478 8.87 7.94 33.52 2.90
4194 4253 2.983229 ACAGAGGCAATGACAGATCAC 58.017 47.619 0.00 0.00 37.79 3.06
4195 4254 2.570752 ACAGAGGCAATGACAGATCACT 59.429 45.455 0.00 0.00 37.79 3.41
4196 4255 3.008813 ACAGAGGCAATGACAGATCACTT 59.991 43.478 0.00 0.00 37.79 3.16
4197 4256 3.374367 CAGAGGCAATGACAGATCACTTG 59.626 47.826 0.00 0.00 37.79 3.16
4198 4257 3.262660 AGAGGCAATGACAGATCACTTGA 59.737 43.478 0.00 0.00 37.79 3.02
4199 4258 4.005650 GAGGCAATGACAGATCACTTGAA 58.994 43.478 0.00 0.00 37.79 2.69
4200 4259 3.755378 AGGCAATGACAGATCACTTGAAC 59.245 43.478 0.00 0.00 37.79 3.18
4201 4260 3.119708 GGCAATGACAGATCACTTGAACC 60.120 47.826 0.00 0.00 37.79 3.62
4222 4302 2.353323 GGTTCACCGTCCTTATGTTCC 58.647 52.381 0.00 0.00 0.00 3.62
4239 4319 1.143183 CCGGGTATGAACCTCCACG 59.857 63.158 0.00 0.00 45.95 4.94
4240 4320 1.610554 CCGGGTATGAACCTCCACGT 61.611 60.000 0.00 0.00 45.95 4.49
4260 4340 4.081642 ACGTAGTTGTAGATCATTGGCACT 60.082 41.667 0.00 0.00 37.78 4.40
4261 4341 5.126545 ACGTAGTTGTAGATCATTGGCACTA 59.873 40.000 0.00 0.00 37.78 2.74
4297 4378 2.095212 GCGGTCCCTCAGAACAAAATTC 60.095 50.000 0.00 0.00 29.87 2.17
4344 4425 3.094484 ACAAGGTTGTCAACTTTCCCA 57.906 42.857 15.17 0.00 36.50 4.37
4352 4433 5.281727 GTTGTCAACTTTCCCATCAAACTC 58.718 41.667 8.53 0.00 0.00 3.01
4362 4443 2.749076 CCCATCAAACTCGAAGCATCAA 59.251 45.455 0.00 0.00 0.00 2.57
4398 4479 5.482163 AGATTCTTAATGCCTAGCTCTCC 57.518 43.478 0.00 0.00 0.00 3.71
4443 4524 2.214376 TTCCAGGCCACCAAATACTG 57.786 50.000 5.01 0.00 0.00 2.74
4444 4525 1.072266 TCCAGGCCACCAAATACTGT 58.928 50.000 5.01 0.00 0.00 3.55
4446 4527 1.463674 CAGGCCACCAAATACTGTCC 58.536 55.000 5.01 0.00 0.00 4.02
4447 4528 0.035439 AGGCCACCAAATACTGTCCG 60.035 55.000 5.01 0.00 0.00 4.79
4448 4529 1.654023 GGCCACCAAATACTGTCCGC 61.654 60.000 0.00 0.00 0.00 5.54
4449 4530 1.654023 GCCACCAAATACTGTCCGCC 61.654 60.000 0.00 0.00 0.00 6.13
4450 4531 0.322098 CCACCAAATACTGTCCGCCA 60.322 55.000 0.00 0.00 0.00 5.69
4451 4532 1.681780 CCACCAAATACTGTCCGCCAT 60.682 52.381 0.00 0.00 0.00 4.40
4452 4533 2.091541 CACCAAATACTGTCCGCCATT 58.908 47.619 0.00 0.00 0.00 3.16
4453 4534 2.097466 CACCAAATACTGTCCGCCATTC 59.903 50.000 0.00 0.00 0.00 2.67
4454 4535 2.290641 ACCAAATACTGTCCGCCATTCA 60.291 45.455 0.00 0.00 0.00 2.57
4455 4536 2.097466 CCAAATACTGTCCGCCATTCAC 59.903 50.000 0.00 0.00 0.00 3.18
4456 4537 3.009723 CAAATACTGTCCGCCATTCACT 58.990 45.455 0.00 0.00 0.00 3.41
4457 4538 2.604046 ATACTGTCCGCCATTCACTC 57.396 50.000 0.00 0.00 0.00 3.51
4458 4539 0.535335 TACTGTCCGCCATTCACTCC 59.465 55.000 0.00 0.00 0.00 3.85
4459 4540 1.296392 CTGTCCGCCATTCACTCCA 59.704 57.895 0.00 0.00 0.00 3.86
4460 4541 1.003839 TGTCCGCCATTCACTCCAC 60.004 57.895 0.00 0.00 0.00 4.02
4461 4542 1.745489 GTCCGCCATTCACTCCACC 60.745 63.158 0.00 0.00 0.00 4.61
4462 4543 2.438434 CCGCCATTCACTCCACCC 60.438 66.667 0.00 0.00 0.00 4.61
4463 4544 2.671070 CGCCATTCACTCCACCCT 59.329 61.111 0.00 0.00 0.00 4.34
4464 4545 1.002134 CGCCATTCACTCCACCCTT 60.002 57.895 0.00 0.00 0.00 3.95
4465 4546 1.026718 CGCCATTCACTCCACCCTTC 61.027 60.000 0.00 0.00 0.00 3.46
4466 4547 1.026718 GCCATTCACTCCACCCTTCG 61.027 60.000 0.00 0.00 0.00 3.79
4467 4548 1.026718 CCATTCACTCCACCCTTCGC 61.027 60.000 0.00 0.00 0.00 4.70
4468 4549 1.026718 CATTCACTCCACCCTTCGCC 61.027 60.000 0.00 0.00 0.00 5.54
4469 4550 2.521958 ATTCACTCCACCCTTCGCCG 62.522 60.000 0.00 0.00 0.00 6.46
4479 4560 4.082523 CTTCGCCGCCCAGAGGAA 62.083 66.667 0.00 0.00 33.47 3.36
4480 4561 3.391665 CTTCGCCGCCCAGAGGAAT 62.392 63.158 0.00 0.00 33.47 3.01
4481 4562 3.680620 TTCGCCGCCCAGAGGAATG 62.681 63.158 0.00 0.00 33.47 2.67
4482 4563 4.161295 CGCCGCCCAGAGGAATGA 62.161 66.667 0.00 0.00 33.47 2.57
4483 4564 2.272146 GCCGCCCAGAGGAATGAA 59.728 61.111 0.00 0.00 33.47 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
155 161 9.230122 TGTTAAATGTCTGCAGAGAAATATTGA 57.770 29.630 18.89 4.74 0.00 2.57
280 286 5.451908 TGAAAATCGTTGATCAAGCTGTTC 58.548 37.500 8.80 9.58 0.00 3.18
283 289 6.614999 GCTTTTGAAAATCGTTGATCAAGCTG 60.615 38.462 8.80 2.09 33.71 4.24
284 290 5.403466 GCTTTTGAAAATCGTTGATCAAGCT 59.597 36.000 8.80 0.00 33.71 3.74
286 292 6.752335 TGCTTTTGAAAATCGTTGATCAAG 57.248 33.333 8.80 3.55 33.71 3.02
350 356 7.266756 GCAAGTATTTGAAAAATGCGAAATGTG 59.733 33.333 1.56 0.00 36.36 3.21
357 363 7.782242 TGTTAAGCAAGTATTTGAAAAATGCG 58.218 30.769 1.56 0.00 36.36 4.73
549 555 6.639632 TCTTATAATTCAGAAAGCATGGGC 57.360 37.500 0.00 0.00 41.61 5.36
595 601 6.880484 TCGCCCATTTTAGTTTGTATCTAGA 58.120 36.000 0.00 0.00 0.00 2.43
605 611 5.123344 GTGTGTAGATTCGCCCATTTTAGTT 59.877 40.000 0.00 0.00 0.00 2.24
615 621 3.064207 TGTTTCAGTGTGTAGATTCGCC 58.936 45.455 0.00 0.00 0.00 5.54
617 623 5.845985 ACATGTTTCAGTGTGTAGATTCG 57.154 39.130 0.00 0.00 0.00 3.34
621 627 9.419297 GTATCTAAACATGTTTCAGTGTGTAGA 57.581 33.333 26.46 19.83 44.78 2.59
672 678 7.883311 ACTCCCTCGGTTCCAAAATATAATATG 59.117 37.037 0.00 0.00 0.00 1.78
684 690 2.262637 ACAAATACTCCCTCGGTTCCA 58.737 47.619 0.00 0.00 0.00 3.53
828 845 2.664851 CGTCAAGGGCAGCACGAA 60.665 61.111 0.00 0.00 34.06 3.85
853 870 1.488527 CTTATAGCGACACGAAGGGC 58.511 55.000 0.00 0.00 0.00 5.19
1078 1100 3.009714 GGACCCCGCTTCTTCCCT 61.010 66.667 0.00 0.00 0.00 4.20
1374 1396 2.884639 CACCGGGAATCACAAAGAACTT 59.115 45.455 6.32 0.00 0.00 2.66
1398 1420 5.796502 AGGACCCAAATTCTCAATCCTAA 57.203 39.130 0.00 0.00 33.29 2.69
1416 1438 2.416747 GGCCAAATTCAGCAAAAGGAC 58.583 47.619 0.00 0.00 0.00 3.85
1440 1462 0.883833 CCAGCACCACACCAAGAATC 59.116 55.000 0.00 0.00 0.00 2.52
1643 1665 1.272212 TGACGCTGTTGATGCACTCTA 59.728 47.619 0.00 0.00 0.00 2.43
1650 1672 0.518636 CCCAACTGACGCTGTTGATG 59.481 55.000 21.80 13.31 42.93 3.07
1696 1718 1.439679 CCAACCGAAGCACCTCTTAC 58.560 55.000 0.00 0.00 34.56 2.34
1734 1756 1.539388 TGCCGCGACATCAAAAGAATT 59.461 42.857 8.23 0.00 0.00 2.17
1783 1805 4.814771 AGTCTCTTAACCCACTTGAAAACG 59.185 41.667 0.00 0.00 0.00 3.60
1903 1926 5.519927 CCTGTCATCAAAAGGTTTGTGAAAC 59.480 40.000 0.98 0.00 40.65 2.78
1939 1962 7.120432 AGACCTTACTTACCACTTACTAGAACG 59.880 40.741 0.00 0.00 0.00 3.95
1945 1968 7.289549 AGACAAAGACCTTACTTACCACTTACT 59.710 37.037 0.00 0.00 0.00 2.24
1946 1969 7.384387 CAGACAAAGACCTTACTTACCACTTAC 59.616 40.741 0.00 0.00 0.00 2.34
1947 1970 7.288389 TCAGACAAAGACCTTACTTACCACTTA 59.712 37.037 0.00 0.00 0.00 2.24
1948 1971 6.099269 TCAGACAAAGACCTTACTTACCACTT 59.901 38.462 0.00 0.00 0.00 3.16
1959 1984 0.603975 GCCGCTCAGACAAAGACCTT 60.604 55.000 0.00 0.00 0.00 3.50
2222 2247 7.605691 ACAGATTAAGAGAATTGGTTGAGACAG 59.394 37.037 0.00 0.00 0.00 3.51
2357 2382 9.588774 CAAATGAATGATTTTGTGATGTTTGTC 57.411 29.630 0.00 0.00 31.41 3.18
2390 2415 3.627577 GCTACCAGCAGCTTTAGCATTTA 59.372 43.478 21.22 0.00 45.16 1.40
2468 2493 9.167311 CCAGATAACAATAGCAAGAACTAAAGT 57.833 33.333 0.00 0.00 0.00 2.66
2475 2500 4.207165 GGGCCAGATAACAATAGCAAGAA 58.793 43.478 4.39 0.00 0.00 2.52
2548 2581 2.825836 GAAGACCCTGCCATGCCG 60.826 66.667 0.00 0.00 0.00 5.69
2793 2826 1.267574 ATCCCGAGCTCTGCTTCCAA 61.268 55.000 12.85 0.00 39.88 3.53
2920 2953 5.630680 CCAATAAACTGACTGATGTTGTTGC 59.369 40.000 0.00 0.00 0.00 4.17
2926 2959 5.880901 AGGTTCCAATAAACTGACTGATGT 58.119 37.500 0.00 0.00 0.00 3.06
3010 3043 1.734655 AGGGCAAGAGAGTTCTGGAA 58.265 50.000 0.00 0.00 32.79 3.53
3026 3059 1.151668 CAAGAGACGCAGACAAAGGG 58.848 55.000 0.00 0.00 0.00 3.95
3105 3138 4.430441 AGACCAGAAGGATAGTTTCAGGT 58.570 43.478 2.27 2.27 44.19 4.00
3163 3196 1.515736 GCTTCCATTCAGCAAGCGC 60.516 57.895 0.00 0.00 30.01 5.92
3205 3238 6.433847 ACTGGTAATGCAGGCACTATTATA 57.566 37.500 0.00 0.00 36.02 0.98
3211 3244 1.352352 AGAACTGGTAATGCAGGCACT 59.648 47.619 0.00 0.00 43.88 4.40
3362 3395 4.499183 ACAAGGTTCTATCTCTTTCTGCG 58.501 43.478 0.00 0.00 0.00 5.18
3447 3489 9.216117 GTATATTATTTCGGTGCTTATTCAGGT 57.784 33.333 0.00 0.00 0.00 4.00
3560 3612 1.966451 CACCCGGTGCAAACCTCTC 60.966 63.158 4.16 0.00 0.00 3.20
3576 3629 4.531332 GTTCTTTGCTCAGATGTTCACAC 58.469 43.478 0.00 0.00 0.00 3.82
3698 3757 1.980765 TGTTCAGCTCCAGAACCAGAT 59.019 47.619 11.64 0.00 43.57 2.90
3735 3794 2.930040 CCGCACGTCTTCAACAGAATAT 59.070 45.455 0.00 0.00 31.28 1.28
3738 3797 0.103390 TCCGCACGTCTTCAACAGAA 59.897 50.000 0.00 0.00 31.28 3.02
3752 3811 1.541147 CTGGAAGCAAAGAAATCCGCA 59.459 47.619 0.00 0.00 34.60 5.69
3792 3851 0.313987 GGCTTTGACCCCTTTTGTCG 59.686 55.000 0.00 0.00 35.46 4.35
3796 3855 2.561037 CGCGGCTTTGACCCCTTTT 61.561 57.895 0.00 0.00 0.00 2.27
3804 3863 1.009449 CGGAAAAACGCGGCTTTGA 60.009 52.632 12.47 0.00 0.00 2.69
3822 3881 5.220758 GCTCTAGAACTAATTTCAGCAAGGC 60.221 44.000 0.00 0.00 36.57 4.35
3864 3923 7.116948 GCAATGCTCTACGATACAAGATATGTT 59.883 37.037 0.00 0.00 43.63 2.71
3867 3926 6.587990 GTGCAATGCTCTACGATACAAGATAT 59.412 38.462 6.82 0.00 0.00 1.63
3875 3934 5.783111 ACATATGTGCAATGCTCTACGATA 58.217 37.500 7.78 0.00 0.00 2.92
3881 3940 3.310774 GTCGAACATATGTGCAATGCTCT 59.689 43.478 14.37 0.00 0.00 4.09
3903 3962 1.521010 CTGCAGGATGAGGACAGCG 60.521 63.158 5.57 0.00 39.69 5.18
3913 3972 3.931907 TGTTATACTTGCCTGCAGGAT 57.068 42.857 37.21 21.83 37.39 3.24
3915 3974 3.347216 ACTTGTTATACTTGCCTGCAGG 58.653 45.455 29.34 29.34 38.53 4.85
3938 3997 2.533318 GTCCGCAAGACCAGACTTG 58.467 57.895 5.64 5.64 46.69 3.16
3969 4028 8.016301 ACATCATCACTGTAACTCATATCACT 57.984 34.615 0.00 0.00 0.00 3.41
3971 4030 8.260114 ACAACATCATCACTGTAACTCATATCA 58.740 33.333 0.00 0.00 0.00 2.15
3986 4045 0.522626 CTTGCGGCACAACATCATCA 59.477 50.000 0.05 0.00 33.68 3.07
3989 4048 2.644418 GCTTGCGGCACAACATCA 59.356 55.556 0.05 0.00 41.35 3.07
3990 4049 2.126346 GGCTTGCGGCACAACATC 60.126 61.111 0.05 0.00 44.01 3.06
4009 4068 6.417930 GCACCTTTGAAGTGTAAATCTTTGTC 59.582 38.462 0.00 0.00 37.56 3.18
4010 4069 6.273071 GCACCTTTGAAGTGTAAATCTTTGT 58.727 36.000 0.00 0.00 37.56 2.83
4069 4128 2.704572 GCTGTGCCAGTGACTAGAAAT 58.295 47.619 0.00 0.00 33.43 2.17
4083 4142 0.378257 CGGTGTATCAATGGCTGTGC 59.622 55.000 0.00 0.00 0.00 4.57
4086 4145 0.940126 GCTCGGTGTATCAATGGCTG 59.060 55.000 0.00 0.00 0.00 4.85
4110 4169 1.669049 CCACCTCGGGCGTGTATACA 61.669 60.000 0.08 0.08 0.00 2.29
4111 4170 1.066918 CCACCTCGGGCGTGTATAC 59.933 63.158 0.00 0.00 0.00 1.47
4129 4188 1.067916 CTTTTGTGTGGCCCTGTGC 59.932 57.895 0.00 0.00 40.16 4.57
4141 4200 2.612212 CGTAGACAACTGCCACTTTTGT 59.388 45.455 0.00 0.00 36.16 2.83
4160 4219 0.898320 CTCTGTTCAGTGGGATCCGT 59.102 55.000 5.45 0.00 0.00 4.69
4186 4245 2.104111 TGAACCGGTTCAAGTGATCTGT 59.896 45.455 40.69 6.95 45.56 3.41
4221 4301 1.143183 CGTGGAGGTTCATACCCGG 59.857 63.158 0.00 0.00 46.28 5.73
4222 4302 1.066605 CTACGTGGAGGTTCATACCCG 59.933 57.143 0.00 0.00 46.28 5.28
4239 4319 6.986817 ACATAGTGCCAATGATCTACAACTAC 59.013 38.462 0.00 0.00 0.00 2.73
4240 4320 7.124573 ACATAGTGCCAATGATCTACAACTA 57.875 36.000 0.00 0.00 0.00 2.24
4297 4378 2.438434 GGTTGGAGATGGCCACCG 60.438 66.667 8.16 0.00 37.75 4.94
4344 4425 3.755378 AGCTTTGATGCTTCGAGTTTGAT 59.245 39.130 0.00 0.00 40.93 2.57
4373 4454 7.041107 GGAGAGCTAGGCATTAAGAATCTATG 58.959 42.308 0.00 0.00 0.00 2.23
4374 4455 6.127479 CGGAGAGCTAGGCATTAAGAATCTAT 60.127 42.308 0.00 0.00 0.00 1.98
4386 4467 1.329913 TTGCATCGGAGAGCTAGGCA 61.330 55.000 6.75 0.00 43.63 4.75
4398 4479 3.084579 GCAGGTCGACTTGCATCG 58.915 61.111 38.27 12.12 46.60 3.84
4443 4524 1.745489 GGTGGAGTGAATGGCGGAC 60.745 63.158 0.00 0.00 0.00 4.79
4444 4525 2.668632 GGTGGAGTGAATGGCGGA 59.331 61.111 0.00 0.00 0.00 5.54
4446 4527 1.002134 AAGGGTGGAGTGAATGGCG 60.002 57.895 0.00 0.00 0.00 5.69
4447 4528 1.026718 CGAAGGGTGGAGTGAATGGC 61.027 60.000 0.00 0.00 0.00 4.40
4448 4529 1.026718 GCGAAGGGTGGAGTGAATGG 61.027 60.000 0.00 0.00 0.00 3.16
4449 4530 1.026718 GGCGAAGGGTGGAGTGAATG 61.027 60.000 0.00 0.00 0.00 2.67
4450 4531 1.299976 GGCGAAGGGTGGAGTGAAT 59.700 57.895 0.00 0.00 0.00 2.57
4451 4532 2.747686 GGCGAAGGGTGGAGTGAA 59.252 61.111 0.00 0.00 0.00 3.18
4452 4533 3.691342 CGGCGAAGGGTGGAGTGA 61.691 66.667 0.00 0.00 0.00 3.41
4462 4543 3.391665 ATTCCTCTGGGCGGCGAAG 62.392 63.158 12.98 4.49 0.00 3.79
4463 4544 3.399181 ATTCCTCTGGGCGGCGAA 61.399 61.111 12.98 0.18 0.00 4.70
4464 4545 4.161295 CATTCCTCTGGGCGGCGA 62.161 66.667 12.98 0.00 0.00 5.54
4465 4546 3.680620 TTCATTCCTCTGGGCGGCG 62.681 63.158 0.51 0.51 0.00 6.46
4466 4547 2.272146 TTCATTCCTCTGGGCGGC 59.728 61.111 0.00 0.00 0.00 6.53


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

AutoCloner maintained by Alex Coulton.