Multiple sequence alignment - TraesCS3D01G116700

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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 TraesCS3D01G116700 chr3D 100.000 5030 0 0 1 5030 70241262 70246291 0.000000e+00 9289
1 TraesCS3D01G116700 chr3B 90.948 4231 232 57 907 5022 116108082 116112276 0.000000e+00 5552
2 TraesCS3D01G116700 chr3A 92.314 1275 61 11 2525 3768 81693975 81695243 0.000000e+00 1777
3 TraesCS3D01G116700 chr3A 94.208 1036 51 5 3981 5009 81695239 81696272 0.000000e+00 1572
4 TraesCS3D01G116700 chr3A 90.235 850 53 13 1 847 501656655 501657477 0.000000e+00 1083
5 TraesCS3D01G116700 chr3A 87.284 810 57 22 862 1629 81692016 81692821 0.000000e+00 883
6 TraesCS3D01G116700 chr3A 84.375 800 56 24 1763 2499 81692863 81693656 0.000000e+00 721
7 TraesCS3D01G116700 chr3A 96.429 112 3 1 737 848 491524859 491524749 3.090000e-42 183
8 TraesCS3D01G116700 chr3A 81.618 136 21 4 68 201 491525315 491525182 5.320000e-20 110
9 TraesCS3D01G116700 chr6A 92.732 853 53 8 1 847 461435130 461435979 0.000000e+00 1223
10 TraesCS3D01G116700 chr6A 92.145 853 54 10 4 847 542378431 542377583 0.000000e+00 1192
11 TraesCS3D01G116700 chr6A 85.139 323 41 5 1250 1567 73678826 73679146 1.750000e-84 324
12 TraesCS3D01G116700 chr7A 89.424 851 56 10 4 847 448197033 448196210 0.000000e+00 1042
13 TraesCS3D01G116700 chr5B 90.085 827 42 23 52 847 18414406 18413589 0.000000e+00 1037
14 TraesCS3D01G116700 chr5A 89.151 848 57 22 4 847 601749329 601748513 0.000000e+00 1024
15 TraesCS3D01G116700 chr5D 92.168 715 48 8 137 848 91656950 91657659 0.000000e+00 1003
16 TraesCS3D01G116700 chr2B 90.166 722 55 12 137 847 233338852 233338136 0.000000e+00 926
17 TraesCS3D01G116700 chr4D 86.490 792 87 17 65 848 495990119 495989340 0.000000e+00 852
18 TraesCS3D01G116700 chr1B 77.864 646 120 20 4271 4908 677913912 677914542 3.680000e-101 379
19 TraesCS3D01G116700 chr1A 86.301 292 40 0 4617 4908 584374169 584374460 8.130000e-83 318
20 TraesCS3D01G116700 chr2A 91.818 110 7 1 729 838 98728226 98728119 8.720000e-33 152


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 TraesCS3D01G116700 chr3D 70241262 70246291 5029 False 9289.00 9289 100.00000 1 5030 1 chr3D.!!$F1 5029
1 TraesCS3D01G116700 chr3B 116108082 116112276 4194 False 5552.00 5552 90.94800 907 5022 1 chr3B.!!$F1 4115
2 TraesCS3D01G116700 chr3A 81692016 81696272 4256 False 1238.25 1777 89.54525 862 5009 4 chr3A.!!$F2 4147
3 TraesCS3D01G116700 chr3A 501656655 501657477 822 False 1083.00 1083 90.23500 1 847 1 chr3A.!!$F1 846
4 TraesCS3D01G116700 chr6A 461435130 461435979 849 False 1223.00 1223 92.73200 1 847 1 chr6A.!!$F2 846
5 TraesCS3D01G116700 chr6A 542377583 542378431 848 True 1192.00 1192 92.14500 4 847 1 chr6A.!!$R1 843
6 TraesCS3D01G116700 chr7A 448196210 448197033 823 True 1042.00 1042 89.42400 4 847 1 chr7A.!!$R1 843
7 TraesCS3D01G116700 chr5B 18413589 18414406 817 True 1037.00 1037 90.08500 52 847 1 chr5B.!!$R1 795
8 TraesCS3D01G116700 chr5A 601748513 601749329 816 True 1024.00 1024 89.15100 4 847 1 chr5A.!!$R1 843
9 TraesCS3D01G116700 chr5D 91656950 91657659 709 False 1003.00 1003 92.16800 137 848 1 chr5D.!!$F1 711
10 TraesCS3D01G116700 chr2B 233338136 233338852 716 True 926.00 926 90.16600 137 847 1 chr2B.!!$R1 710
11 TraesCS3D01G116700 chr4D 495989340 495990119 779 True 852.00 852 86.49000 65 848 1 chr4D.!!$R1 783
12 TraesCS3D01G116700 chr1B 677913912 677914542 630 False 379.00 379 77.86400 4271 4908 1 chr1B.!!$F1 637

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
861 981 0.105039 CTCCCGATTGAGCTGTACCC 59.895 60.0 0.00 0.0 0.00 3.69 F
1322 1466 0.036671 ACTGCTACAGCCGGTAAACC 60.037 55.0 1.90 0.0 41.18 3.27 F
1896 2059 0.463295 ACCATGAAGCTGCGATCTGG 60.463 55.0 16.90 16.9 0.00 3.86 F
3416 3951 0.161446 GTTGCGGCATTTTCTTTGCG 59.839 50.0 2.28 0.0 41.07 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1749 1912 0.038166 CAGGAAGCCAACCCTAGCAA 59.962 55.000 0.00 0.0 0.00 3.91 R
3270 3803 2.030007 TCCTTGATTTTGAGGCTTTGCG 60.030 45.455 0.00 0.0 32.93 4.85 R
3891 4460 0.251916 ATCTCCCGCGATTTTCACCA 59.748 50.000 8.23 0.0 0.00 4.17 R
4400 4978 0.531200 ACCAGAAGTCGACGGAATCC 59.469 55.000 10.46 0.0 0.00 3.01 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
510 603 9.934190 AAAAATCGATGAACCTTTTTCATTTTG 57.066 25.926 0.00 0.00 39.08 2.44
626 722 6.514947 TGCACGAAAAGGTTAACTAGAACTA 58.485 36.000 5.42 0.00 0.00 2.24
740 850 8.466798 GCTATCCTCAGGTTTTATTGCTTTTTA 58.533 33.333 0.00 0.00 0.00 1.52
769 888 2.099062 GATTGAGTGCAAGCGCGG 59.901 61.111 8.83 0.00 42.97 6.46
848 968 1.454111 GCTGACTAGGAGCTCCCGA 60.454 63.158 29.54 16.66 40.87 5.14
849 969 0.825840 GCTGACTAGGAGCTCCCGAT 60.826 60.000 29.54 14.62 40.87 4.18
850 970 1.698506 CTGACTAGGAGCTCCCGATT 58.301 55.000 29.54 13.43 40.87 3.34
851 971 1.339610 CTGACTAGGAGCTCCCGATTG 59.660 57.143 29.54 14.21 40.87 2.67
852 972 1.063942 TGACTAGGAGCTCCCGATTGA 60.064 52.381 29.54 6.51 40.87 2.57
853 973 1.611491 GACTAGGAGCTCCCGATTGAG 59.389 57.143 29.54 17.72 40.87 3.02
860 980 3.669354 CTCCCGATTGAGCTGTACC 57.331 57.895 0.00 0.00 0.00 3.34
861 981 0.105039 CTCCCGATTGAGCTGTACCC 59.895 60.000 0.00 0.00 0.00 3.69
862 982 0.616395 TCCCGATTGAGCTGTACCCA 60.616 55.000 0.00 0.00 0.00 4.51
863 983 0.179073 CCCGATTGAGCTGTACCCAG 60.179 60.000 0.00 0.00 41.91 4.45
864 984 0.179073 CCGATTGAGCTGTACCCAGG 60.179 60.000 0.00 0.00 39.22 4.45
865 985 0.811616 CGATTGAGCTGTACCCAGGC 60.812 60.000 0.00 0.00 39.22 4.85
866 986 0.464554 GATTGAGCTGTACCCAGGCC 60.465 60.000 0.00 0.00 39.22 5.19
867 987 1.926426 ATTGAGCTGTACCCAGGCCC 61.926 60.000 0.00 0.00 39.22 5.80
868 988 3.009115 GAGCTGTACCCAGGCCCA 61.009 66.667 0.00 0.00 39.22 5.36
869 989 2.531685 AGCTGTACCCAGGCCCAA 60.532 61.111 0.00 0.00 39.22 4.12
870 990 2.044946 GCTGTACCCAGGCCCAAG 60.045 66.667 0.00 0.00 39.22 3.61
871 991 2.677228 CTGTACCCAGGCCCAAGG 59.323 66.667 0.00 0.00 34.90 3.61
872 992 2.121689 TGTACCCAGGCCCAAGGT 60.122 61.111 13.12 13.12 37.69 3.50
890 1010 4.937201 AGGTGTGGAATGTTTTTCTTCC 57.063 40.909 0.00 0.00 41.13 3.46
919 1039 1.447099 TAGGTTTTGTACAGGGCCCA 58.553 50.000 27.56 0.00 0.00 5.36
1055 1175 2.202851 CTGCGACCTAGCTGCCTG 60.203 66.667 0.00 0.00 38.13 4.85
1212 1356 1.137872 CCTCTGCCTGCTACTACTTGG 59.862 57.143 0.00 0.00 0.00 3.61
1216 1360 1.003118 TGCCTGCTACTACTTGGTTGG 59.997 52.381 0.00 0.00 0.00 3.77
1264 1408 3.747099 CTGGGTAATTTTCTCACGCAG 57.253 47.619 7.67 7.67 43.75 5.18
1284 1428 5.115472 CGCAGTTTTAGTTTTAGCATGTGTG 59.885 40.000 0.00 0.00 0.00 3.82
1290 1434 8.690840 GTTTTAGTTTTAGCATGTGTGTGATTC 58.309 33.333 0.00 0.00 0.00 2.52
1308 1452 6.209192 TGTGATTCAATATGTGGAAAACTGCT 59.791 34.615 0.00 0.00 0.00 4.24
1312 1456 6.741992 TCAATATGTGGAAAACTGCTACAG 57.258 37.500 0.00 0.00 37.52 2.74
1315 1459 0.517316 GTGGAAAACTGCTACAGCCG 59.483 55.000 0.00 0.00 41.18 5.52
1320 1464 2.554370 AAACTGCTACAGCCGGTAAA 57.446 45.000 1.90 0.00 41.18 2.01
1322 1466 0.036671 ACTGCTACAGCCGGTAAACC 60.037 55.000 1.90 0.00 41.18 3.27
1339 1494 8.225603 CGGTAAACCTACTGGAACTAGTTATA 57.774 38.462 8.42 0.00 37.04 0.98
1534 1692 8.208718 TCTATTTTGCTACATCGTTAAGCATT 57.791 30.769 0.00 0.00 45.09 3.56
1646 1808 7.630082 TCTTGGATAGTTATAAGTGCCAAAGT 58.370 34.615 20.71 0.00 33.96 2.66
1692 1855 1.401539 GGCACGAGGTTTGCTTCAATC 60.402 52.381 0.00 0.00 40.07 2.67
1741 1904 3.446873 TGATGTTTCCCAATTTCCATCCG 59.553 43.478 0.00 0.00 0.00 4.18
1745 1908 2.656947 TCCCAATTTCCATCCGGATC 57.343 50.000 15.88 0.00 42.41 3.36
1746 1909 1.144913 TCCCAATTTCCATCCGGATCC 59.855 52.381 15.88 0.00 42.41 3.36
1747 1910 1.133513 CCCAATTTCCATCCGGATCCA 60.134 52.381 15.88 0.00 42.41 3.41
1748 1911 2.233271 CCAATTTCCATCCGGATCCAG 58.767 52.381 15.88 6.65 42.41 3.86
1749 1912 2.423373 CCAATTTCCATCCGGATCCAGT 60.423 50.000 15.88 0.00 42.41 4.00
1750 1913 3.290710 CAATTTCCATCCGGATCCAGTT 58.709 45.455 15.88 3.40 42.41 3.16
1757 1920 1.048724 TCCGGATCCAGTTGCTAGGG 61.049 60.000 13.41 1.08 0.00 3.53
1761 1924 1.408822 GGATCCAGTTGCTAGGGTTGG 60.409 57.143 6.95 0.00 0.00 3.77
1763 1926 1.133809 TCCAGTTGCTAGGGTTGGCT 61.134 55.000 0.00 0.00 0.00 4.75
1772 1935 2.172717 GCTAGGGTTGGCTTCCTGATTA 59.827 50.000 0.00 0.00 34.75 1.75
1792 1955 2.910688 TTCTCTGAAACCTGAACGCT 57.089 45.000 0.00 0.00 0.00 5.07
1825 1988 9.383519 CATAGCAGTTACTAATTTCTTTCCAGA 57.616 33.333 0.00 0.00 0.00 3.86
1839 2002 0.469494 TCCAGAACTGCTGTGCTTCA 59.531 50.000 0.51 0.00 43.33 3.02
1853 2016 3.689161 TGTGCTTCAATCGTTCAATAGGG 59.311 43.478 0.00 0.00 0.00 3.53
1855 2018 4.156008 GTGCTTCAATCGTTCAATAGGGTT 59.844 41.667 0.00 0.00 0.00 4.11
1856 2019 4.764823 TGCTTCAATCGTTCAATAGGGTTT 59.235 37.500 0.00 0.00 0.00 3.27
1857 2020 5.941058 TGCTTCAATCGTTCAATAGGGTTTA 59.059 36.000 0.00 0.00 0.00 2.01
1858 2021 6.128117 TGCTTCAATCGTTCAATAGGGTTTAC 60.128 38.462 0.00 0.00 0.00 2.01
1896 2059 0.463295 ACCATGAAGCTGCGATCTGG 60.463 55.000 16.90 16.90 0.00 3.86
1955 2135 4.889995 TCAGTAGAGGACATAGTGTGATGG 59.110 45.833 0.00 0.00 0.00 3.51
2075 2275 4.020218 TGGATACTCAGCTAGTTTGCTTGT 60.020 41.667 0.00 0.00 39.80 3.16
2087 2287 6.074676 GCTAGTTTGCTTGTTGAAACATTGAG 60.075 38.462 0.00 0.00 38.95 3.02
2137 2345 2.837591 TGCAGAGCTGATGGGTTAGTTA 59.162 45.455 0.85 0.00 0.00 2.24
2148 2356 6.884832 TGATGGGTTAGTTACCTCTTGTATG 58.115 40.000 0.00 0.00 46.86 2.39
2151 2359 6.704310 TGGGTTAGTTACCTCTTGTATGTTC 58.296 40.000 0.00 0.00 46.86 3.18
2152 2360 5.809051 GGGTTAGTTACCTCTTGTATGTTCG 59.191 44.000 0.00 0.00 46.86 3.95
2158 2390 7.215085 AGTTACCTCTTGTATGTTCGAAAACT 58.785 34.615 0.00 0.00 36.30 2.66
2269 2502 3.816523 TGTAGAGGCAAAAGGGTTTTACG 59.183 43.478 0.00 0.00 0.00 3.18
2398 2631 5.047021 TGAAGTAGGTCAAGGTTCTCTCATG 60.047 44.000 0.00 0.00 0.00 3.07
2401 2634 3.515562 AGGTCAAGGTTCTCTCATGTCT 58.484 45.455 0.00 0.00 0.00 3.41
2405 2638 5.639931 GGTCAAGGTTCTCTCATGTCTTAAC 59.360 44.000 0.00 0.00 0.00 2.01
2412 2645 6.535508 GGTTCTCTCATGTCTTAACGCTTATT 59.464 38.462 0.00 0.00 0.00 1.40
2551 3077 5.332743 AGATTCAGCTTGGGGTATTTTGAA 58.667 37.500 0.00 0.00 0.00 2.69
2843 3374 4.142271 GCAGAGCAACTTCTTCTAGCTAGA 60.142 45.833 19.72 19.72 35.36 2.43
2931 3462 5.530915 TCTTATGGTTTGTTCTTGTGTGAGG 59.469 40.000 0.00 0.00 0.00 3.86
3098 3629 3.969976 AGCTGGTAAAGGAGATATGCTCA 59.030 43.478 0.00 0.00 45.81 4.26
3270 3803 3.064207 TGTCGAAGTAGGTTTGATGCAC 58.936 45.455 0.00 0.00 30.78 4.57
3287 3820 1.602668 GCACGCAAAGCCTCAAAATCA 60.603 47.619 0.00 0.00 0.00 2.57
3416 3951 0.161446 GTTGCGGCATTTTCTTTGCG 59.839 50.000 2.28 0.00 41.07 4.85
3422 3957 1.799994 GGCATTTTCTTTGCGTGCAAT 59.200 42.857 8.26 0.00 41.07 3.56
3423 3958 2.223845 GGCATTTTCTTTGCGTGCAATT 59.776 40.909 8.26 0.00 41.07 2.32
3447 3982 5.734855 TTTGAAGTGACTGTTACAGAAGC 57.265 39.130 20.07 8.32 35.18 3.86
3578 4131 5.261209 AGTCATTTCTGATCTCCGAGAAG 57.739 43.478 1.27 0.00 32.98 2.85
3641 4194 3.118112 CCCTTGTCAGCCTCACAGATAAT 60.118 47.826 0.00 0.00 0.00 1.28
3662 4215 4.672587 TCCTAAGTAGCTAGGCACATTG 57.327 45.455 0.00 0.00 38.73 2.82
3710 4266 2.271800 GCCGAGTAGTCCACATGAAAG 58.728 52.381 0.00 0.00 0.00 2.62
3719 4275 2.549754 GTCCACATGAAAGTCACACCTG 59.450 50.000 0.00 0.00 0.00 4.00
3728 4284 3.627395 AAGTCACACCTGAACTGTTCA 57.373 42.857 20.95 20.95 38.17 3.18
3732 4288 3.003689 GTCACACCTGAACTGTTCAATGG 59.996 47.826 25.90 23.63 39.58 3.16
3733 4289 2.951642 CACACCTGAACTGTTCAATGGT 59.048 45.455 25.90 24.11 38.37 3.55
3772 4331 5.356882 TTTCTGGAAACATGTGATTCGAC 57.643 39.130 0.00 0.00 41.51 4.20
3800 4359 4.293415 GAGCAACTGAAATGTTGTTCCTG 58.707 43.478 11.35 0.00 45.76 3.86
3804 4363 5.284079 CAACTGAAATGTTGTTCCTGGAAG 58.716 41.667 9.92 0.00 41.50 3.46
3808 4367 5.076182 TGAAATGTTGTTCCTGGAAGCATA 58.924 37.500 9.92 0.00 0.00 3.14
3814 4373 4.046286 TGTTCCTGGAAGCATATGGTTT 57.954 40.909 20.42 5.56 35.69 3.27
3815 4374 4.016444 TGTTCCTGGAAGCATATGGTTTC 58.984 43.478 20.42 18.91 35.69 2.78
3817 4376 1.949525 CCTGGAAGCATATGGTTTCGG 59.050 52.381 22.87 22.87 37.58 4.30
3820 4379 3.426615 TGGAAGCATATGGTTTCGGTTT 58.573 40.909 20.42 0.00 37.58 3.27
3822 4381 3.428862 GGAAGCATATGGTTTCGGTTTGG 60.429 47.826 20.42 0.00 37.58 3.28
3823 4382 3.080300 AGCATATGGTTTCGGTTTGGA 57.920 42.857 0.40 0.00 0.00 3.53
3824 4383 2.752903 AGCATATGGTTTCGGTTTGGAC 59.247 45.455 0.40 0.00 0.00 4.02
3825 4384 2.477189 GCATATGGTTTCGGTTTGGACG 60.477 50.000 4.56 0.00 0.00 4.79
3826 4385 2.547299 TATGGTTTCGGTTTGGACGT 57.453 45.000 0.00 0.00 0.00 4.34
3827 4386 1.232119 ATGGTTTCGGTTTGGACGTC 58.768 50.000 7.13 7.13 0.00 4.34
3830 4389 1.268184 GGTTTCGGTTTGGACGTCAAC 60.268 52.381 18.91 13.67 34.67 3.18
3833 4392 2.027003 TCGGTTTGGACGTCAACTTT 57.973 45.000 18.91 0.00 34.67 2.66
3844 4403 5.122239 TGGACGTCAACTTTGATCATGATTC 59.878 40.000 18.91 4.08 39.73 2.52
3852 4411 8.124823 TCAACTTTGATCATGATTCTAAATCGC 58.875 33.333 10.14 0.00 31.01 4.58
3854 4413 4.652175 TGATCATGATTCTAAATCGCGC 57.348 40.909 10.14 0.00 0.00 6.86
3856 4415 2.469826 TCATGATTCTAAATCGCGCGT 58.530 42.857 30.98 13.76 0.00 6.01
3858 4417 0.927537 TGATTCTAAATCGCGCGTGG 59.072 50.000 30.98 13.12 0.00 4.94
3862 4421 0.440758 TCTAAATCGCGCGTGGTTTG 59.559 50.000 34.35 24.59 0.00 2.93
3873 4432 3.661911 TGGTTTGGCCATCGTTCG 58.338 55.556 6.09 0.00 43.61 3.95
3875 4434 2.178273 GTTTGGCCATCGTTCGCC 59.822 61.111 6.09 0.00 45.92 5.54
3904 4473 1.135315 CAGGCTGGTGAAAATCGCG 59.865 57.895 6.61 0.00 0.00 5.87
3912 4481 0.577269 GTGAAAATCGCGGGAGATCG 59.423 55.000 6.13 0.00 0.00 3.69
3920 4489 3.604629 CGGGAGATCGCCGGATAT 58.395 61.111 16.62 0.00 31.51 1.63
3921 4490 1.890894 CGGGAGATCGCCGGATATT 59.109 57.895 16.62 0.00 31.51 1.28
3922 4491 0.458543 CGGGAGATCGCCGGATATTG 60.459 60.000 16.62 0.00 31.51 1.90
3923 4492 0.608640 GGGAGATCGCCGGATATTGT 59.391 55.000 5.05 0.00 31.51 2.71
3924 4493 1.673033 GGGAGATCGCCGGATATTGTG 60.673 57.143 5.05 0.00 31.51 3.33
3925 4494 1.071605 GAGATCGCCGGATATTGTGC 58.928 55.000 5.05 0.00 31.51 4.57
3926 4495 0.320771 AGATCGCCGGATATTGTGCC 60.321 55.000 5.05 0.00 31.51 5.01
3927 4496 0.602638 GATCGCCGGATATTGTGCCA 60.603 55.000 5.05 0.00 31.51 4.92
3928 4497 0.179032 ATCGCCGGATATTGTGCCAA 60.179 50.000 5.05 0.00 0.00 4.52
3990 4559 7.940178 ATTTTGTTTCTCCCGTGATTTTAAC 57.060 32.000 0.00 0.00 0.00 2.01
3993 4562 5.074115 TGTTTCTCCCGTGATTTTAACCAT 58.926 37.500 0.00 0.00 0.00 3.55
4012 4581 6.791887 ACCATTGATATTGATTCTACTGCG 57.208 37.500 0.00 0.00 0.00 5.18
4043 4612 1.238439 ATGTCCCGTTCAGTTTGCTG 58.762 50.000 0.00 0.00 43.87 4.41
4060 4634 2.743928 GACAAGTCCAGCGCAGGG 60.744 66.667 19.70 15.42 0.00 4.45
4077 4651 1.153289 GGCAGGACGACAGCATCAT 60.153 57.895 0.00 0.00 0.00 2.45
4078 4652 1.156645 GGCAGGACGACAGCATCATC 61.157 60.000 0.00 0.00 0.00 2.92
4079 4653 0.460811 GCAGGACGACAGCATCATCA 60.461 55.000 0.00 0.00 0.00 3.07
4092 4666 3.635373 AGCATCATCATTGGTAAGGCAAG 59.365 43.478 0.00 0.00 0.00 4.01
4388 4966 0.952280 TAGCAGCGGTATCGGAGAAG 59.048 55.000 0.00 0.00 43.58 2.85
4397 4975 0.032515 TATCGGAGAAGCCCTGGACA 60.033 55.000 0.00 0.00 43.58 4.02
4400 4978 1.298014 GGAGAAGCCCTGGACACTG 59.702 63.158 0.00 0.00 0.00 3.66
4469 5047 2.200337 GCCTCCGTTGGTGCCTTTT 61.200 57.895 0.00 0.00 0.00 2.27
4557 5142 2.613730 TCACTCGTCGTCAAGATCAC 57.386 50.000 0.00 0.00 0.00 3.06
4762 5347 0.462759 CGTCCAGGATCTTGCCCTTC 60.463 60.000 0.00 0.00 0.00 3.46
4925 5510 0.907486 CATGAGCAGGTTCTCCCTCA 59.093 55.000 0.00 0.00 43.86 3.86
4940 5525 1.674764 CCTCATCGGCACTCTGCTCT 61.675 60.000 0.00 0.00 44.28 4.09
4965 5550 0.681733 TCACTCTCCTCTGCCACAAC 59.318 55.000 0.00 0.00 0.00 3.32
5011 5596 7.651027 TCAGATGATCAGATACACTTCTTGA 57.349 36.000 0.09 0.00 0.00 3.02
5014 5599 7.326547 CAGATGATCAGATACACTTCTTGATCG 59.673 40.741 0.09 0.00 35.42 3.69
5022 5607 1.923204 CACTTCTTGATCGCTTCTCGG 59.077 52.381 0.00 0.00 39.05 4.63
5023 5608 1.546476 ACTTCTTGATCGCTTCTCGGT 59.454 47.619 0.00 0.00 39.05 4.69
5029 5614 2.682952 GATCGCTTCTCGGTCGATAA 57.317 50.000 0.00 0.00 42.20 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 64 7.746034 TCGAATTCAGAAAAAGTTCATCGAATG 59.254 33.333 6.22 0.00 36.09 2.67
181 245 5.655488 TCAGAAAAAGTTCGCCAAATTTGA 58.345 33.333 19.86 0.00 38.90 2.69
649 745 5.820947 ACACTAACCACCAGAACAAACTAAG 59.179 40.000 0.00 0.00 0.00 2.18
740 850 3.066621 TGCACTCAATCGCTTTTGAAGTT 59.933 39.130 0.00 0.00 35.31 2.66
848 968 1.609783 GGCCTGGGTACAGCTCAAT 59.390 57.895 0.00 0.00 43.53 2.57
849 969 2.602676 GGGCCTGGGTACAGCTCAA 61.603 63.158 0.84 0.00 43.53 3.02
850 970 3.009115 GGGCCTGGGTACAGCTCA 61.009 66.667 0.84 0.00 43.53 4.26
851 971 2.543067 CTTGGGCCTGGGTACAGCTC 62.543 65.000 4.53 0.00 43.53 4.09
852 972 2.531685 TTGGGCCTGGGTACAGCT 60.532 61.111 4.53 0.00 43.53 4.24
853 973 2.044946 CTTGGGCCTGGGTACAGC 60.045 66.667 4.53 0.00 43.53 4.40
854 974 2.231380 ACCTTGGGCCTGGGTACAG 61.231 63.158 17.01 0.00 44.51 2.74
855 975 2.121689 ACCTTGGGCCTGGGTACA 60.122 61.111 17.01 0.00 0.00 2.90
856 976 2.355115 CACCTTGGGCCTGGGTAC 59.645 66.667 17.82 0.00 0.00 3.34
857 977 2.121689 ACACCTTGGGCCTGGGTA 60.122 61.111 17.82 0.00 0.00 3.69
858 978 3.902112 CACACCTTGGGCCTGGGT 61.902 66.667 17.84 15.85 0.00 4.51
859 979 4.684134 CCACACCTTGGGCCTGGG 62.684 72.222 17.84 15.27 42.54 4.45
860 980 2.445492 ATTCCACACCTTGGGCCTGG 62.445 60.000 4.53 9.97 46.92 4.45
861 981 1.077265 ATTCCACACCTTGGGCCTG 59.923 57.895 4.53 0.00 46.92 4.85
862 982 1.077265 CATTCCACACCTTGGGCCT 59.923 57.895 4.53 0.00 46.92 5.19
863 983 0.831711 AACATTCCACACCTTGGGCC 60.832 55.000 0.00 0.00 46.92 5.80
864 984 1.047801 AAACATTCCACACCTTGGGC 58.952 50.000 0.00 0.00 46.92 5.36
865 985 3.387699 AGAAAAACATTCCACACCTTGGG 59.612 43.478 0.00 0.00 46.92 4.12
867 987 5.049828 GGAAGAAAAACATTCCACACCTTG 58.950 41.667 0.00 0.00 43.75 3.61
868 988 5.276461 GGAAGAAAAACATTCCACACCTT 57.724 39.130 0.00 0.00 43.75 3.50
869 989 4.937201 GGAAGAAAAACATTCCACACCT 57.063 40.909 0.00 0.00 43.75 4.00
904 1024 1.890573 GCATCTGGGCCCTGTACAAAA 60.891 52.381 25.70 5.55 0.00 2.44
912 1032 2.357836 CTGTTGCATCTGGGCCCT 59.642 61.111 25.70 0.00 0.00 5.19
919 1039 1.518056 CGTGTTGGGCTGTTGCATCT 61.518 55.000 0.00 0.00 41.91 2.90
1011 1131 1.859427 CGCAACCAGACTGCTGCAAT 61.859 55.000 21.05 0.00 40.91 3.56
1242 1386 1.202031 GCGTGAGAAAATTACCCAGCG 60.202 52.381 0.00 0.00 0.00 5.18
1264 1408 8.574196 AATCACACACATGCTAAAACTAAAAC 57.426 30.769 0.00 0.00 0.00 2.43
1284 1428 6.624423 AGCAGTTTTCCACATATTGAATCAC 58.376 36.000 0.00 0.00 0.00 3.06
1290 1434 5.335127 GCTGTAGCAGTTTTCCACATATTG 58.665 41.667 0.00 0.00 41.59 1.90
1308 1452 1.826720 CCAGTAGGTTTACCGGCTGTA 59.173 52.381 0.00 0.00 42.08 2.74
1312 1456 1.277273 AGTTCCAGTAGGTTTACCGGC 59.723 52.381 0.00 0.00 42.08 6.13
1315 1459 9.978044 CATATAACTAGTTCCAGTAGGTTTACC 57.022 37.037 12.39 0.00 35.89 2.85
1339 1494 9.574516 TCTACATACACTGATACACATAGACAT 57.425 33.333 0.00 0.00 0.00 3.06
1521 1679 9.559958 AGAATTTTAACTCAATGCTTAACGATG 57.440 29.630 0.00 0.00 0.00 3.84
1672 1835 0.598065 ATTGAAGCAAACCTCGTGCC 59.402 50.000 0.00 0.00 43.27 5.01
1675 1838 2.554032 CCAAGATTGAAGCAAACCTCGT 59.446 45.455 0.00 0.00 0.00 4.18
1676 1839 2.669391 GCCAAGATTGAAGCAAACCTCG 60.669 50.000 0.00 0.00 0.00 4.63
1678 1841 2.560105 GAGCCAAGATTGAAGCAAACCT 59.440 45.455 0.00 0.00 0.00 3.50
1709 1872 0.375106 GGAAACATCAGCGCTACTGC 59.625 55.000 10.99 0.00 46.76 4.40
1719 1882 3.446873 CGGATGGAAATTGGGAAACATCA 59.553 43.478 0.00 0.00 37.14 3.07
1722 1885 2.175202 CCGGATGGAAATTGGGAAACA 58.825 47.619 0.00 0.00 37.49 2.83
1723 1886 2.452505 TCCGGATGGAAATTGGGAAAC 58.547 47.619 0.00 0.00 42.85 2.78
1724 1887 2.909504 TCCGGATGGAAATTGGGAAA 57.090 45.000 0.00 0.00 42.85 3.13
1741 1904 1.408822 CCAACCCTAGCAACTGGATCC 60.409 57.143 4.20 4.20 0.00 3.36
1745 1908 0.251341 AAGCCAACCCTAGCAACTGG 60.251 55.000 0.00 0.00 0.00 4.00
1746 1909 1.168714 GAAGCCAACCCTAGCAACTG 58.831 55.000 0.00 0.00 0.00 3.16
1747 1910 0.038310 GGAAGCCAACCCTAGCAACT 59.962 55.000 0.00 0.00 0.00 3.16
1748 1911 0.038310 AGGAAGCCAACCCTAGCAAC 59.962 55.000 0.00 0.00 0.00 4.17
1749 1912 0.038166 CAGGAAGCCAACCCTAGCAA 59.962 55.000 0.00 0.00 0.00 3.91
1750 1913 0.840288 TCAGGAAGCCAACCCTAGCA 60.840 55.000 0.00 0.00 0.00 3.49
1757 1920 5.431765 TCAGAGAATAATCAGGAAGCCAAC 58.568 41.667 0.00 0.00 0.00 3.77
1761 1924 6.038050 CAGGTTTCAGAGAATAATCAGGAAGC 59.962 42.308 0.00 0.00 0.00 3.86
1763 1926 7.257790 TCAGGTTTCAGAGAATAATCAGGAA 57.742 36.000 0.00 0.00 0.00 3.36
1772 1935 3.409026 AGCGTTCAGGTTTCAGAGAAT 57.591 42.857 0.00 0.00 0.00 2.40
1792 1955 9.422681 AGAAATTAGTAACTGCTATGACCTCTA 57.577 33.333 0.00 0.00 0.00 2.43
1825 1988 1.597742 ACGATTGAAGCACAGCAGTT 58.402 45.000 0.00 0.00 0.00 3.16
1839 2002 7.394923 TGGATTTGTAAACCCTATTGAACGATT 59.605 33.333 0.00 0.00 0.00 3.34
1857 2020 8.768397 TCATGGTCTATAAACTAGTGGATTTGT 58.232 33.333 0.00 0.00 0.00 2.83
1858 2021 9.613428 TTCATGGTCTATAAACTAGTGGATTTG 57.387 33.333 0.00 0.00 0.00 2.32
1879 2042 2.229675 TACCAGATCGCAGCTTCATG 57.770 50.000 0.00 0.00 0.00 3.07
1922 2085 4.274147 TGTCCTCTACTGAAGATCCAGAC 58.726 47.826 6.04 0.00 37.59 3.51
1955 2135 8.682710 TCAACTGATACCCTTATAATGCAAAAC 58.317 33.333 0.00 0.00 0.00 2.43
2048 2247 4.624125 GCAAACTAGCTGAGTATCCAGGTT 60.624 45.833 0.00 0.00 41.58 3.50
2057 2257 3.808728 TCAACAAGCAAACTAGCTGAGT 58.191 40.909 0.00 0.00 45.89 3.41
2087 2287 6.531594 GGCACCAGCAAATCTTATTTAAAGAC 59.468 38.462 0.00 0.00 44.61 3.01
2137 2345 5.820947 ACAAGTTTTCGAACATACAAGAGGT 59.179 36.000 0.00 0.00 0.00 3.85
2148 2356 9.245284 CATACAAAACAAAACAAGTTTTCGAAC 57.755 29.630 7.89 0.00 44.72 3.95
2151 2359 8.428536 TGACATACAAAACAAAACAAGTTTTCG 58.571 29.630 7.89 7.01 44.72 3.46
2158 2390 7.675870 GCAAGCATGACATACAAAACAAAACAA 60.676 33.333 0.00 0.00 0.00 2.83
2269 2502 7.859325 TTTAATAGCCTAATTGGATATCGCC 57.141 36.000 0.00 0.00 45.82 5.54
2385 2618 4.021016 AGCGTTAAGACATGAGAGAACCTT 60.021 41.667 0.00 0.00 0.00 3.50
2398 2631 8.589335 TGGAATAGATCAATAAGCGTTAAGAC 57.411 34.615 0.00 0.00 0.00 3.01
2401 2634 9.337396 ACAATGGAATAGATCAATAAGCGTTAA 57.663 29.630 0.00 0.00 0.00 2.01
2405 2638 7.425577 TCACAATGGAATAGATCAATAAGCG 57.574 36.000 0.00 0.00 0.00 4.68
2412 2645 5.447757 TGGCAATCACAATGGAATAGATCA 58.552 37.500 0.00 0.00 0.00 2.92
2578 3104 6.401955 ACAAAATGTGTTGTGCAAAAGTAC 57.598 33.333 0.00 0.00 40.22 2.73
2843 3374 2.419574 GCAACCCATACGTACCTCATGT 60.420 50.000 0.00 0.00 0.00 3.21
2931 3462 3.904571 TGTCATTTTGCACAAGCTGATC 58.095 40.909 0.00 0.00 42.74 2.92
3270 3803 2.030007 TCCTTGATTTTGAGGCTTTGCG 60.030 45.455 0.00 0.00 32.93 4.85
3287 3820 9.374711 TGAATAAACTTGAAATAAACCCTCCTT 57.625 29.630 0.00 0.00 0.00 3.36
3423 3958 6.374333 AGCTTCTGTAACAGTCACTTCAAAAA 59.626 34.615 0.00 0.00 32.61 1.94
3428 3963 4.621991 TGAGCTTCTGTAACAGTCACTTC 58.378 43.478 0.00 0.00 32.61 3.01
3433 3968 2.300437 ACCCTGAGCTTCTGTAACAGTC 59.700 50.000 0.00 0.00 32.61 3.51
3447 3982 7.756395 ATTGCATAATCATTCTAACCCTGAG 57.244 36.000 0.00 0.00 0.00 3.35
3641 4194 3.181465 GCAATGTGCCTAGCTACTTAGGA 60.181 47.826 4.34 0.00 42.39 2.94
3662 4215 3.756727 GCTGCCTTTGCCTCCTGC 61.757 66.667 0.00 0.00 41.77 4.85
3710 4266 3.003689 CCATTGAACAGTTCAGGTGTGAC 59.996 47.826 15.61 0.00 41.38 3.67
3719 4275 4.305989 TGCTGAAACCATTGAACAGTTC 57.694 40.909 6.32 6.32 0.00 3.01
3765 4324 0.442699 GTTGCTCAACCCGTCGAATC 59.557 55.000 1.45 0.00 35.36 2.52
3771 4330 1.608590 CATTTCAGTTGCTCAACCCGT 59.391 47.619 8.95 0.00 42.06 5.28
3772 4331 1.608590 ACATTTCAGTTGCTCAACCCG 59.391 47.619 8.95 1.99 42.06 5.28
3797 4356 1.949525 CCGAAACCATATGCTTCCAGG 59.050 52.381 0.00 0.00 0.00 4.45
3800 4359 3.428862 CCAAACCGAAACCATATGCTTCC 60.429 47.826 0.00 0.00 0.00 3.46
3804 4363 2.477189 CGTCCAAACCGAAACCATATGC 60.477 50.000 0.00 0.00 0.00 3.14
3808 4367 1.232119 GACGTCCAAACCGAAACCAT 58.768 50.000 3.51 0.00 0.00 3.55
3814 4373 1.666700 CAAAGTTGACGTCCAAACCGA 59.333 47.619 14.12 0.00 36.36 4.69
3815 4374 1.666700 TCAAAGTTGACGTCCAAACCG 59.333 47.619 14.12 3.97 36.36 4.44
3817 4376 4.545823 TGATCAAAGTTGACGTCCAAAC 57.454 40.909 14.12 11.75 40.49 2.93
3820 4379 4.001618 TCATGATCAAAGTTGACGTCCA 57.998 40.909 14.12 0.00 40.49 4.02
3822 4381 6.414408 AGAATCATGATCAAAGTTGACGTC 57.586 37.500 9.06 9.11 40.49 4.34
3823 4382 7.905604 TTAGAATCATGATCAAAGTTGACGT 57.094 32.000 9.06 0.00 40.49 4.34
3824 4383 9.430838 GATTTAGAATCATGATCAAAGTTGACG 57.569 33.333 9.06 0.00 40.49 4.35
3825 4384 9.430838 CGATTTAGAATCATGATCAAAGTTGAC 57.569 33.333 9.06 0.00 40.49 3.18
3826 4385 8.124823 GCGATTTAGAATCATGATCAAAGTTGA 58.875 33.333 9.06 0.00 42.14 3.18
3827 4386 7.111179 CGCGATTTAGAATCATGATCAAAGTTG 59.889 37.037 9.06 5.98 0.00 3.16
3830 4389 5.562998 GCGCGATTTAGAATCATGATCAAAG 59.437 40.000 12.10 0.00 0.00 2.77
3833 4392 3.121778 CGCGCGATTTAGAATCATGATCA 59.878 43.478 28.94 0.00 0.00 2.92
3844 4403 0.520412 CCAAACCACGCGCGATTTAG 60.520 55.000 39.36 20.96 0.00 1.85
3879 4438 0.597568 TTTCACCAGCCTGCAAATCG 59.402 50.000 0.00 0.00 0.00 3.34
3888 4457 2.485122 CCGCGATTTTCACCAGCC 59.515 61.111 8.23 0.00 0.00 4.85
3891 4460 0.251916 ATCTCCCGCGATTTTCACCA 59.748 50.000 8.23 0.00 0.00 4.17
3904 4473 0.608640 ACAATATCCGGCGATCTCCC 59.391 55.000 9.30 0.00 0.00 4.30
3925 4494 5.005682 GCAGCGAAATTTTAGCCTAAATTGG 59.994 40.000 10.15 0.00 37.67 3.16
3926 4495 5.576384 TGCAGCGAAATTTTAGCCTAAATTG 59.424 36.000 10.15 3.35 37.67 2.32
3927 4496 5.719173 TGCAGCGAAATTTTAGCCTAAATT 58.281 33.333 10.15 1.62 38.90 1.82
3928 4497 5.323371 TGCAGCGAAATTTTAGCCTAAAT 57.677 34.783 10.15 0.00 0.00 1.40
3965 4534 8.083462 GGTTAAAATCACGGGAGAAACAAAATA 58.917 33.333 0.00 0.00 0.00 1.40
3970 4539 4.462133 TGGTTAAAATCACGGGAGAAACA 58.538 39.130 0.00 0.00 0.00 2.83
3971 4540 5.638596 ATGGTTAAAATCACGGGAGAAAC 57.361 39.130 0.00 0.00 0.00 2.78
3990 4559 5.702670 ACCGCAGTAGAATCAATATCAATGG 59.297 40.000 0.00 0.00 0.00 3.16
3993 4562 6.811954 TGTACCGCAGTAGAATCAATATCAA 58.188 36.000 0.00 0.00 0.00 2.57
4012 4581 2.774687 ACGGGACATTTCAGTTGTACC 58.225 47.619 0.00 0.00 43.57 3.34
4043 4612 2.743928 CCCTGCGCTGGACTTGTC 60.744 66.667 32.43 0.00 0.00 3.18
4060 4634 0.460811 TGATGATGCTGTCGTCCTGC 60.461 55.000 8.70 1.12 41.35 4.85
4077 4651 2.192664 TTCGCTTGCCTTACCAATGA 57.807 45.000 0.00 0.00 0.00 2.57
4078 4652 3.508744 AATTCGCTTGCCTTACCAATG 57.491 42.857 0.00 0.00 0.00 2.82
4079 4653 4.013728 TGTAATTCGCTTGCCTTACCAAT 58.986 39.130 0.00 0.00 0.00 3.16
4092 4666 3.444916 TCTTCGGAGTCATGTAATTCGC 58.555 45.455 0.00 0.00 0.00 4.70
4172 4750 2.588989 CCCCAGCTCTGCTCTTCC 59.411 66.667 0.00 0.00 36.40 3.46
4200 4778 1.938577 CAAGATGATCACTTCCAGCGG 59.061 52.381 0.00 0.00 0.00 5.52
4388 4966 1.077429 GGAATCCAGTGTCCAGGGC 60.077 63.158 0.00 0.00 33.79 5.19
4397 4975 1.202582 CAGAAGTCGACGGAATCCAGT 59.797 52.381 10.46 0.00 0.00 4.00
4400 4978 0.531200 ACCAGAAGTCGACGGAATCC 59.469 55.000 10.46 0.00 0.00 3.01
4475 5053 3.675619 GAACCACATCCGTCCGGGG 62.676 68.421 0.00 0.00 36.01 5.73
4557 5142 1.474478 ACCGTGCTGTGAGTGATCTAG 59.526 52.381 0.00 0.00 0.00 2.43
4762 5347 2.492090 CCGCTGGACTTCGAGGAG 59.508 66.667 0.00 0.00 0.00 3.69
4925 5510 1.954362 GACCAGAGCAGAGTGCCGAT 61.954 60.000 0.00 0.00 46.52 4.18
4940 5525 1.244697 GCAGAGGAGAGTGACGACCA 61.245 60.000 0.00 0.00 0.00 4.02
4965 5550 5.294060 TGATGTATGATCGATGTGTTTGTGG 59.706 40.000 0.54 0.00 0.00 4.17
4999 5584 4.355437 CGAGAAGCGATCAAGAAGTGTAT 58.645 43.478 0.00 0.00 44.57 2.29


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

AutoCloner maintained by Alex Coulton.