Multiple sequence alignment - TraesCS2A01G053100

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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 TraesCS2A01G053100 chr2A 100.000 4064 0 0 1 4064 21255544 21251481 0.000000e+00 7505.0
1 TraesCS2A01G053100 chr2A 86.979 3072 341 25 434 3468 21231358 21228309 0.000000e+00 3402.0
2 TraesCS2A01G053100 chr2B 89.359 3665 323 26 373 4001 33842241 33838608 0.000000e+00 4545.0
3 TraesCS2A01G053100 chr2B 86.548 394 27 13 1 384 33842673 33842296 1.050000e-110 411.0
4 TraesCS2A01G053100 chr2B 83.279 305 35 8 2754 3056 33734594 33734304 2.410000e-67 267.0
5 TraesCS2A01G053100 chr2D 92.323 2983 205 16 373 3347 20771119 20768153 0.000000e+00 4218.0
6 TraesCS2A01G053100 chr2D 87.978 2903 288 36 229 3104 20608262 20605394 0.000000e+00 3371.0
7 TraesCS2A01G053100 chr2D 89.572 2666 243 22 330 2971 20634468 20631814 0.000000e+00 3350.0
8 TraesCS2A01G053100 chr2D 87.798 2688 281 19 399 3065 20427446 20424785 0.000000e+00 3103.0
9 TraesCS2A01G053100 chr2D 83.252 412 38 11 1 388 20771580 20771176 2.320000e-92 350.0
10 TraesCS2A01G053100 chr2D 83.276 293 42 3 2826 3114 20615959 20615670 3.120000e-66 263.0
11 TraesCS2A01G053100 chr2D 91.139 79 7 0 139 217 20634622 20634544 1.540000e-19 108.0
12 TraesCS2A01G053100 chr2D 91.379 58 5 0 85 142 20608395 20608338 3.370000e-11 80.5


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 TraesCS2A01G053100 chr2A 21251481 21255544 4063 True 7505.00 7505 100.0000 1 4064 1 chr2A.!!$R2 4063
1 TraesCS2A01G053100 chr2A 21228309 21231358 3049 True 3402.00 3402 86.9790 434 3468 1 chr2A.!!$R1 3034
2 TraesCS2A01G053100 chr2B 33838608 33842673 4065 True 2478.00 4545 87.9535 1 4001 2 chr2B.!!$R2 4000
3 TraesCS2A01G053100 chr2D 20424785 20427446 2661 True 3103.00 3103 87.7980 399 3065 1 chr2D.!!$R1 2666
4 TraesCS2A01G053100 chr2D 20768153 20771580 3427 True 2284.00 4218 87.7875 1 3347 2 chr2D.!!$R5 3346
5 TraesCS2A01G053100 chr2D 20631814 20634622 2808 True 1729.00 3350 90.3555 139 2971 2 chr2D.!!$R4 2832
6 TraesCS2A01G053100 chr2D 20605394 20608395 3001 True 1725.75 3371 89.6785 85 3104 2 chr2D.!!$R3 3019

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
19 20 0.035317 TCACAGCCGAGCAGTTCAAT 59.965 50.0 0.0 0.0 0.00 2.57 F
20 21 0.167470 CACAGCCGAGCAGTTCAATG 59.833 55.0 0.0 0.0 0.00 2.82 F
952 1103 0.179111 CTCGCTTCGCAACCCATCTA 60.179 55.0 0.0 0.0 0.00 1.98 F
1700 1851 0.107993 CTGAATGAGGAAGCAGCGGA 60.108 55.0 0.0 0.0 0.00 5.54 F
1910 2064 0.179108 GCGGAAAGCGTAGACAGGAT 60.179 55.0 0.0 0.0 35.41 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1200 1351 0.999406 CGGCAACTGGATAGAACACG 59.001 55.000 0.00 0.0 0.0 4.49 R
1453 1604 1.272928 TGTCCATTGCAAGCCCCATAA 60.273 47.619 4.94 0.0 0.0 1.90 R
2188 2342 0.251341 AGCACCTCATGGAAACCACC 60.251 55.000 0.00 0.0 35.8 4.61 R
2646 2800 0.937304 CGGTGTTTGTCTGTGTCTGG 59.063 55.000 0.00 0.0 0.0 3.86 R
3721 3888 0.036765 GTTCGACACCAGCCCATACA 60.037 55.000 0.00 0.0 0.0 2.29 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
19 20 0.035317 TCACAGCCGAGCAGTTCAAT 59.965 50.000 0.00 0.00 0.00 2.57
20 21 0.167470 CACAGCCGAGCAGTTCAATG 59.833 55.000 0.00 0.00 0.00 2.82
21 22 1.136147 CAGCCGAGCAGTTCAATGC 59.864 57.895 0.00 0.00 46.88 3.56
128 137 4.022849 CCAAGTCAAGTCAATGGAAACTCC 60.023 45.833 0.00 0.00 36.96 3.85
134 143 6.655003 GTCAAGTCAATGGAAACTCCTGAATA 59.345 38.462 0.00 0.00 37.46 1.75
142 164 4.080356 TGGAAACTCCTGAATACCATGAGG 60.080 45.833 0.00 0.00 40.48 3.86
172 194 7.203218 TCATAATTGACAAGTAGGAGACGATG 58.797 38.462 5.96 0.00 0.00 3.84
183 206 0.659957 GAGACGATGGCCAGAATTGC 59.340 55.000 13.05 0.00 0.00 3.56
279 306 3.249559 GTGTTTTCTCAGTTCCTCTGCAG 59.750 47.826 7.63 7.63 43.32 4.41
284 311 3.935315 TCTCAGTTCCTCTGCAGAAATG 58.065 45.455 18.85 12.67 43.32 2.32
288 315 4.889409 TCAGTTCCTCTGCAGAAATGTTTT 59.111 37.500 18.85 0.00 43.32 2.43
309 336 0.954452 GGAACCAGACTGGCACTTTG 59.046 55.000 21.95 0.00 42.67 2.77
384 488 0.320596 AGCTCAGAACAGTCAGCAGC 60.321 55.000 0.00 0.00 34.08 5.25
397 501 3.172919 GCAGCGAGACCTTTCTGC 58.827 61.111 8.08 8.08 43.95 4.26
524 652 1.217882 CCACACTGTTCCACGAAGAC 58.782 55.000 0.00 0.00 0.00 3.01
625 762 1.010419 GCAAAAGCAATGGCACCTCG 61.010 55.000 0.00 0.00 44.61 4.63
670 810 1.910580 TTGCTACTACTGCTGGGGGC 61.911 60.000 0.00 0.00 42.22 5.80
731 871 4.649705 TCCTTGACGCCCCAGGGA 62.650 66.667 7.25 0.49 39.59 4.20
881 1032 2.484417 CCAAGAGCAGTCAAGACACACT 60.484 50.000 2.72 0.00 0.00 3.55
952 1103 0.179111 CTCGCTTCGCAACCCATCTA 60.179 55.000 0.00 0.00 0.00 1.98
979 1130 3.596799 TCTGGAGTCCCCGGGTCA 61.597 66.667 21.85 1.57 41.84 4.02
1005 1156 2.825836 GCCTACGCCAGCATGCTT 60.826 61.111 19.98 6.10 31.97 3.91
1066 1217 4.546674 ACCAAAGTGGAAGACCTTTGATT 58.453 39.130 12.36 0.00 46.65 2.57
1152 1303 2.413351 CGTCTCATCGCCACGGAT 59.587 61.111 0.00 0.00 0.00 4.18
1200 1351 4.024218 GCTGTGCAATCTGATGGTAATCTC 60.024 45.833 0.00 0.00 33.61 2.75
1279 1430 2.092429 GGTACAGATGGGAATGGCTCAA 60.092 50.000 0.00 0.00 0.00 3.02
1320 1471 4.130118 CTGGCAGGATATACTTCACAACC 58.870 47.826 6.61 0.00 0.00 3.77
1362 1513 1.067295 TCACTTCAGCAGGGGTGAAT 58.933 50.000 10.80 0.71 46.49 2.57
1376 1527 4.016666 AGGGGTGAATTCAATGGGTGATTA 60.017 41.667 10.35 0.00 35.70 1.75
1448 1599 2.359230 AAAGAGCAGACAGGCCGC 60.359 61.111 0.00 0.00 0.00 6.53
1453 1604 2.437359 GCAGACAGGCCGCAAGAT 60.437 61.111 0.00 0.00 43.02 2.40
1481 1632 0.821301 TTGCAATGGACAGCGGTGAA 60.821 50.000 23.44 6.74 0.00 3.18
1579 1730 1.304713 AGCTTTGATGGCACCCAGG 60.305 57.895 0.00 0.00 36.75 4.45
1608 1759 2.034124 ACAATATGCCAATGCCCAGAC 58.966 47.619 0.00 0.00 36.33 3.51
1623 1774 3.826729 GCCCAGACCATTACAAGTTCTTT 59.173 43.478 0.00 0.00 0.00 2.52
1700 1851 0.107993 CTGAATGAGGAAGCAGCGGA 60.108 55.000 0.00 0.00 0.00 5.54
1701 1852 0.324614 TGAATGAGGAAGCAGCGGAA 59.675 50.000 0.00 0.00 0.00 4.30
1777 1931 2.829120 GAGGAGTACAGCCCCATAGATC 59.171 54.545 0.00 0.00 0.00 2.75
1787 1941 4.529769 CAGCCCCATAGATCTGACTGAATA 59.470 45.833 5.18 0.00 0.00 1.75
1910 2064 0.179108 GCGGAAAGCGTAGACAGGAT 60.179 55.000 0.00 0.00 35.41 3.24
1928 2082 2.614057 GGATGGTTCTTATCAAGGTGCG 59.386 50.000 0.00 0.00 0.00 5.34
1950 2104 2.688507 AGGAGCAACAATACACAGTCG 58.311 47.619 0.00 0.00 0.00 4.18
1986 2140 4.142293 GGCTCTAGCAAATGGAAAAAGGAG 60.142 45.833 4.07 0.00 44.36 3.69
2184 2338 2.206576 ACAATGAACTGGAGAAGGCC 57.793 50.000 0.00 0.00 0.00 5.19
2188 2342 1.376037 GAACTGGAGAAGGCCACCG 60.376 63.158 5.01 2.51 33.52 4.94
2478 2632 2.045926 GCTCGGCCACATTGGAGT 60.046 61.111 2.24 0.00 40.96 3.85
2646 2800 0.440371 CGAAGCTTCTTCGAGCCAAC 59.560 55.000 23.50 0.00 43.74 3.77
2724 2878 4.200092 GGTTCAAGAACATAGGGATCACC 58.800 47.826 14.25 0.00 42.85 4.02
2763 2917 1.202976 AGCTTTGGTGTGATCCTGCTT 60.203 47.619 0.00 0.00 0.00 3.91
2799 2953 3.107601 CAGGAGGAATGTGGAGGTAGAA 58.892 50.000 0.00 0.00 0.00 2.10
2804 2958 4.030913 AGGAATGTGGAGGTAGAAATCGA 58.969 43.478 0.00 0.00 0.00 3.59
2994 3148 4.539870 CAACCATGCTTAAAGTGACACAG 58.460 43.478 8.59 0.00 0.00 3.66
3060 3214 4.347876 TCTTCCTTCATCAGTTCACTTCCA 59.652 41.667 0.00 0.00 0.00 3.53
3083 3237 6.071952 CCATAGTGACCTGCTTGTTAACAAAT 60.072 38.462 20.89 5.86 35.15 2.32
3084 3238 7.120579 CCATAGTGACCTGCTTGTTAACAAATA 59.879 37.037 20.89 12.05 35.15 1.40
3085 3239 8.677300 CATAGTGACCTGCTTGTTAACAAATAT 58.323 33.333 20.89 4.91 35.15 1.28
3086 3240 6.913170 AGTGACCTGCTTGTTAACAAATATG 58.087 36.000 20.89 11.02 35.15 1.78
3159 3313 8.225603 ACTGTTTTCTATTGAAGCTTCAGAAA 57.774 30.769 26.30 26.30 38.61 2.52
3166 3320 7.934457 TCTATTGAAGCTTCAGAAATAATGGC 58.066 34.615 27.02 0.00 38.61 4.40
3358 3520 9.745880 ACATTCTATACAATACCTCGTAAACAG 57.254 33.333 0.00 0.00 0.00 3.16
3392 3554 6.593759 TTCTCTACACTAGAAGAGGGGTAT 57.406 41.667 16.23 0.00 39.79 2.73
3458 3620 6.465439 TTATATATCTACATGGTCTGGGCG 57.535 41.667 0.00 0.00 0.00 6.13
3476 3638 1.199789 GCGACTGGCATCAAACAATCA 59.800 47.619 0.00 0.00 42.87 2.57
3486 3648 5.870433 GGCATCAAACAATCATTCAATGTGA 59.130 36.000 0.00 0.00 0.00 3.58
3489 3651 6.954616 TCAAACAATCATTCAATGTGATGC 57.045 33.333 0.00 0.00 36.49 3.91
3495 3657 8.178313 ACAATCATTCAATGTGATGCTGATAT 57.822 30.769 0.00 0.00 36.49 1.63
3500 3662 9.122779 TCATTCAATGTGATGCTGATATGTAAA 57.877 29.630 0.00 0.00 0.00 2.01
3503 3665 7.696755 TCAATGTGATGCTGATATGTAAACAC 58.303 34.615 0.00 0.00 0.00 3.32
3523 3685 8.925161 AAACACTGAATCAAGAAAAATTTCGA 57.075 26.923 0.00 0.00 41.92 3.71
3525 3687 9.533253 AACACTGAATCAAGAAAAATTTCGATT 57.467 25.926 8.04 8.04 41.92 3.34
3544 3710 9.988350 TTTCGATTAGACTTTGAAGAATAATGC 57.012 29.630 0.00 0.00 0.00 3.56
3564 3730 3.245087 TGCCTACCTTGTATTTCAGGCAA 60.245 43.478 10.51 0.00 46.48 4.52
3579 3745 0.938008 GGCAATTACGTCTAGCTGCC 59.062 55.000 10.18 10.18 42.28 4.85
3582 3748 2.616960 CAATTACGTCTAGCTGCCACA 58.383 47.619 0.00 0.00 0.00 4.17
3589 3755 1.594862 GTCTAGCTGCCACAAATAGCG 59.405 52.381 0.00 0.00 42.10 4.26
3598 3765 3.252215 TGCCACAAATAGCGCCATAATAC 59.748 43.478 2.29 0.00 0.00 1.89
3601 3768 5.689819 CCACAAATAGCGCCATAATACTTC 58.310 41.667 2.29 0.00 0.00 3.01
3603 3770 6.365839 CACAAATAGCGCCATAATACTTCTG 58.634 40.000 2.29 0.00 0.00 3.02
3610 3777 6.159988 AGCGCCATAATACTTCTGTATCTTC 58.840 40.000 2.29 0.00 38.33 2.87
3614 3781 8.491152 CGCCATAATACTTCTGTATCTTCTTTG 58.509 37.037 0.00 0.00 38.33 2.77
3633 3800 7.935338 TCTTTGTTTCTTCAGAAAATGCATC 57.065 32.000 0.00 0.00 44.58 3.91
3634 3801 7.490840 TCTTTGTTTCTTCAGAAAATGCATCA 58.509 30.769 0.00 0.00 44.58 3.07
3637 3804 6.210796 TGTTTCTTCAGAAAATGCATCAGTG 58.789 36.000 0.00 0.00 44.58 3.66
3646 3813 6.745907 CAGAAAATGCATCAGTGTCTGTATTG 59.254 38.462 0.00 0.12 38.51 1.90
3655 3822 6.976934 TCAGTGTCTGTATTGATATGCCTA 57.023 37.500 0.00 0.00 32.61 3.93
3659 3826 8.715998 CAGTGTCTGTATTGATATGCCTAATTC 58.284 37.037 0.00 0.00 0.00 2.17
3689 3856 5.698832 TGCTGAATCCATTTTAGTCAAACG 58.301 37.500 0.00 0.00 0.00 3.60
3696 3863 4.888239 TCCATTTTAGTCAAACGTTCCCAA 59.112 37.500 0.00 0.00 0.00 4.12
3700 3867 5.838531 TTTAGTCAAACGTTCCCAACAAT 57.161 34.783 0.00 0.00 0.00 2.71
3702 3869 4.729227 AGTCAAACGTTCCCAACAATTT 57.271 36.364 0.00 0.00 0.00 1.82
3707 3874 7.863877 AGTCAAACGTTCCCAACAATTTAATAC 59.136 33.333 0.00 0.00 0.00 1.89
3712 3879 6.150474 ACGTTCCCAACAATTTAATACTCAGG 59.850 38.462 0.00 0.00 0.00 3.86
3713 3880 6.330278 GTTCCCAACAATTTAATACTCAGGC 58.670 40.000 0.00 0.00 0.00 4.85
3714 3881 4.638421 TCCCAACAATTTAATACTCAGGCG 59.362 41.667 0.00 0.00 0.00 5.52
3721 3888 8.677148 ACAATTTAATACTCAGGCGTGAATAT 57.323 30.769 10.76 7.56 30.14 1.28
3736 3903 3.815401 GTGAATATGTATGGGCTGGTGTC 59.185 47.826 0.00 0.00 0.00 3.67
3740 3907 0.036765 TGTATGGGCTGGTGTCGAAC 60.037 55.000 0.00 0.00 0.00 3.95
3747 3914 1.298859 GCTGGTGTCGAACATCCCAC 61.299 60.000 0.00 0.00 0.00 4.61
3750 3917 1.156736 GGTGTCGAACATCCCACAAG 58.843 55.000 4.29 0.00 0.00 3.16
3759 3926 1.985159 ACATCCCACAAGACCTTGCTA 59.015 47.619 9.48 0.00 44.03 3.49
3764 3931 6.101150 ACATCCCACAAGACCTTGCTAATATA 59.899 38.462 9.48 0.00 44.03 0.86
3774 3941 5.853936 ACCTTGCTAATATACAAGCGATGA 58.146 37.500 7.29 0.00 41.56 2.92
3790 3957 8.081633 ACAAGCGATGAATCAAGAAAAATGTTA 58.918 29.630 0.00 0.00 0.00 2.41
3822 3989 9.066892 AGCATATTTTGAGTACTTTCAGAACAA 57.933 29.630 0.00 0.00 0.00 2.83
3827 3994 8.909708 TTTTGAGTACTTTCAGAACAACATTG 57.090 30.769 0.00 0.00 0.00 2.82
3828 3995 6.060028 TGAGTACTTTCAGAACAACATTGC 57.940 37.500 0.00 0.00 0.00 3.56
3831 3998 7.443879 TGAGTACTTTCAGAACAACATTGCATA 59.556 33.333 0.00 0.00 0.00 3.14
3833 4000 8.796475 AGTACTTTCAGAACAACATTGCATATT 58.204 29.630 0.00 0.00 0.00 1.28
3834 4001 9.065871 GTACTTTCAGAACAACATTGCATATTC 57.934 33.333 0.00 0.00 0.00 1.75
3837 4004 6.441093 TCAGAACAACATTGCATATTCTCC 57.559 37.500 0.00 0.00 0.00 3.71
3838 4005 5.945191 TCAGAACAACATTGCATATTCTCCA 59.055 36.000 0.00 0.00 0.00 3.86
3839 4006 6.433716 TCAGAACAACATTGCATATTCTCCAA 59.566 34.615 0.00 0.00 0.00 3.53
3841 4008 7.599621 CAGAACAACATTGCATATTCTCCAAAA 59.400 33.333 0.00 0.00 0.00 2.44
3842 4009 7.816031 AGAACAACATTGCATATTCTCCAAAAG 59.184 33.333 0.00 0.00 0.00 2.27
3844 4011 7.318141 ACAACATTGCATATTCTCCAAAAGAG 58.682 34.615 0.00 0.00 44.75 2.85
3890 4057 8.370493 TCTTCACTGTAAAAATTCAGAGAGTG 57.630 34.615 0.00 0.00 34.16 3.51
3891 4058 6.545504 TCACTGTAAAAATTCAGAGAGTGC 57.454 37.500 0.00 0.00 35.84 4.40
3892 4059 6.054941 TCACTGTAAAAATTCAGAGAGTGCA 58.945 36.000 0.00 0.00 35.84 4.57
3894 4061 7.066887 TCACTGTAAAAATTCAGAGAGTGCAAA 59.933 33.333 0.00 0.00 35.84 3.68
3895 4062 7.864379 CACTGTAAAAATTCAGAGAGTGCAAAT 59.136 33.333 0.00 0.00 35.84 2.32
3896 4063 9.066892 ACTGTAAAAATTCAGAGAGTGCAAATA 57.933 29.630 0.00 0.00 35.84 1.40
3910 4077 7.710896 AGAGTGCAAATATTTCTTATGAAGGC 58.289 34.615 0.00 0.00 33.28 4.35
3912 4079 8.752005 AGTGCAAATATTTCTTATGAAGGCTA 57.248 30.769 0.00 0.00 33.28 3.93
3940 4107 4.335594 AGAAACTAATTAGCCGCATTGGTC 59.664 41.667 12.54 0.00 41.21 4.02
3980 4155 5.880341 AGAAACAAACAACTTCTTTCCGAG 58.120 37.500 0.00 0.00 0.00 4.63
4023 4198 2.958818 TGGTACTTCCACTCACTCACT 58.041 47.619 0.00 0.00 41.93 3.41
4024 4199 2.628178 TGGTACTTCCACTCACTCACTG 59.372 50.000 0.00 0.00 41.93 3.66
4025 4200 2.891580 GGTACTTCCACTCACTCACTGA 59.108 50.000 0.00 0.00 35.97 3.41
4026 4201 3.321111 GGTACTTCCACTCACTCACTGAA 59.679 47.826 0.00 0.00 35.97 3.02
4027 4202 4.021016 GGTACTTCCACTCACTCACTGAAT 60.021 45.833 0.00 0.00 35.97 2.57
4028 4203 4.696479 ACTTCCACTCACTCACTGAATT 57.304 40.909 0.00 0.00 0.00 2.17
4029 4204 5.041191 ACTTCCACTCACTCACTGAATTT 57.959 39.130 0.00 0.00 0.00 1.82
4030 4205 5.059833 ACTTCCACTCACTCACTGAATTTC 58.940 41.667 0.00 0.00 0.00 2.17
4031 4206 3.653344 TCCACTCACTCACTGAATTTCG 58.347 45.455 0.00 0.00 0.00 3.46
4032 4207 2.158449 CCACTCACTCACTGAATTTCGC 59.842 50.000 0.00 0.00 0.00 4.70
4033 4208 2.158449 CACTCACTCACTGAATTTCGCC 59.842 50.000 0.00 0.00 0.00 5.54
4034 4209 2.224281 ACTCACTCACTGAATTTCGCCA 60.224 45.455 0.00 0.00 0.00 5.69
4035 4210 2.807967 CTCACTCACTGAATTTCGCCAA 59.192 45.455 0.00 0.00 0.00 4.52
4036 4211 3.210227 TCACTCACTGAATTTCGCCAAA 58.790 40.909 0.00 0.00 0.00 3.28
4037 4212 3.629855 TCACTCACTGAATTTCGCCAAAA 59.370 39.130 0.00 0.00 0.00 2.44
4038 4213 4.278170 TCACTCACTGAATTTCGCCAAAAT 59.722 37.500 0.00 0.00 39.30 1.82
4040 4215 6.016693 TCACTCACTGAATTTCGCCAAAATTA 60.017 34.615 4.84 0.00 45.47 1.40
4041 4216 6.306356 CACTCACTGAATTTCGCCAAAATTAG 59.694 38.462 4.84 0.00 45.47 1.73
4042 4217 6.016276 ACTCACTGAATTTCGCCAAAATTAGT 60.016 34.615 4.84 0.00 45.47 2.24
4043 4218 6.148948 TCACTGAATTTCGCCAAAATTAGTG 58.851 36.000 9.53 9.53 45.47 2.74
4044 4219 5.345741 CACTGAATTTCGCCAAAATTAGTGG 59.654 40.000 8.34 4.08 45.47 4.00
4045 4220 4.815269 TGAATTTCGCCAAAATTAGTGGG 58.185 39.130 9.53 1.77 45.47 4.61
4046 4221 4.180817 GAATTTCGCCAAAATTAGTGGGG 58.819 43.478 15.41 15.41 45.47 4.96
4047 4222 0.892063 TTCGCCAAAATTAGTGGGGC 59.108 50.000 16.31 7.64 46.07 5.80
4048 4223 0.251386 TCGCCAAAATTAGTGGGGCA 60.251 50.000 16.31 6.69 46.07 5.36
4049 4224 0.605589 CGCCAAAATTAGTGGGGCAA 59.394 50.000 10.94 0.00 44.82 4.52
4050 4225 1.001406 CGCCAAAATTAGTGGGGCAAA 59.999 47.619 10.94 0.00 44.82 3.68
4051 4226 2.548920 CGCCAAAATTAGTGGGGCAAAA 60.549 45.455 10.94 0.00 44.82 2.44
4052 4227 3.481453 GCCAAAATTAGTGGGGCAAAAA 58.519 40.909 9.53 0.00 44.01 1.94
4053 4228 4.078537 GCCAAAATTAGTGGGGCAAAAAT 58.921 39.130 9.53 0.00 44.01 1.82
4054 4229 4.155826 GCCAAAATTAGTGGGGCAAAAATC 59.844 41.667 9.53 0.00 44.01 2.17
4055 4230 4.699735 CCAAAATTAGTGGGGCAAAAATCC 59.300 41.667 0.88 0.00 32.03 3.01
4056 4231 4.568072 AAATTAGTGGGGCAAAAATCCC 57.432 40.909 0.00 0.00 43.42 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.236616 TGGTGGCATTGAACTGCTCG 61.237 55.000 0.00 0.00 41.95 5.03
19 20 1.152984 CAACAGGTCAGTGGTGGCA 60.153 57.895 0.00 0.00 30.89 4.92
20 21 3.749981 CAACAGGTCAGTGGTGGC 58.250 61.111 0.00 0.00 30.89 5.01
134 143 7.959658 TGTCAATTATGATTTTCCTCATGGT 57.040 32.000 0.00 0.00 38.01 3.55
155 177 1.202428 GGCCATCGTCTCCTACTTGTC 60.202 57.143 0.00 0.00 0.00 3.18
172 194 0.893447 AAGCTTCAGCAATTCTGGCC 59.107 50.000 0.00 0.00 45.16 5.36
183 206 8.729805 ACTCTAAATCCTGATAAAAGCTTCAG 57.270 34.615 0.00 2.34 39.25 3.02
188 211 8.608317 GTCTGAACTCTAAATCCTGATAAAAGC 58.392 37.037 0.00 0.00 0.00 3.51
279 306 5.049828 CCAGTCTGGTTCCAAAAACATTTC 58.950 41.667 11.09 0.00 29.94 2.17
284 311 1.754226 TGCCAGTCTGGTTCCAAAAAC 59.246 47.619 20.24 0.80 40.46 2.43
288 315 0.550914 AAGTGCCAGTCTGGTTCCAA 59.449 50.000 20.24 0.00 40.46 3.53
309 336 5.160641 ACCATCAACATACGTTTCAAATGC 58.839 37.500 0.00 0.00 31.13 3.56
384 488 0.737367 TCATGCGCAGAAAGGTCTCG 60.737 55.000 18.32 0.00 28.78 4.04
524 652 2.152699 GGTCAGTCATCACGCGTCG 61.153 63.158 9.86 5.44 0.00 5.12
638 775 3.686916 AGTAGCAAGAACTGGAGGAAC 57.313 47.619 0.00 0.00 0.00 3.62
881 1032 1.604308 CTGGATGGCACTTGCACCA 60.604 57.895 3.15 8.38 44.36 4.17
909 1060 0.037303 ACCCATCAGTTGTGAGCTGG 59.963 55.000 0.00 0.00 35.66 4.85
952 1103 1.187087 GGACTCCAGACCTCATCGTT 58.813 55.000 0.00 0.00 0.00 3.85
999 1150 0.952497 AGTCGCCTGTGTCAAGCATG 60.952 55.000 0.00 0.00 0.00 4.06
1005 1156 1.367471 CCTGAAGTCGCCTGTGTCA 59.633 57.895 0.00 0.00 0.00 3.58
1054 1205 1.075536 AGCCGGGAAATCAAAGGTCTT 59.924 47.619 2.18 0.00 0.00 3.01
1066 1217 2.142220 GGATGGTATCAGCCGGGAA 58.858 57.895 2.18 0.00 39.86 3.97
1119 1270 4.592942 TGAGACGGCTTCTAAGTACCTTA 58.407 43.478 0.00 0.00 33.22 2.69
1200 1351 0.999406 CGGCAACTGGATAGAACACG 59.001 55.000 0.00 0.00 0.00 4.49
1258 1409 1.490490 TGAGCCATTCCCATCTGTACC 59.510 52.381 0.00 0.00 0.00 3.34
1259 1410 3.281727 TTGAGCCATTCCCATCTGTAC 57.718 47.619 0.00 0.00 0.00 2.90
1265 1416 2.181975 CCAACTTTGAGCCATTCCCAT 58.818 47.619 0.00 0.00 0.00 4.00
1272 1423 2.136298 TGAACACCAACTTTGAGCCA 57.864 45.000 0.00 0.00 0.00 4.75
1279 1430 4.680440 GCCAGTTTCATTGAACACCAACTT 60.680 41.667 0.00 0.00 37.63 2.66
1320 1471 6.319405 TGATATTGATCTGTGTCCCATTTGTG 59.681 38.462 0.00 0.00 32.79 3.33
1362 1513 5.943416 ACGATTGAAGTAATCACCCATTGAA 59.057 36.000 0.00 0.00 44.42 2.69
1376 1527 1.301716 AGCGTGGCACGATTGAAGT 60.302 52.632 40.94 13.99 46.05 3.01
1448 1599 3.493699 CCATTGCAAGCCCCATAATCTTG 60.494 47.826 4.94 0.00 39.95 3.02
1453 1604 1.272928 TGTCCATTGCAAGCCCCATAA 60.273 47.619 4.94 0.00 0.00 1.90
1517 1668 1.373246 CCACTGCCGGCATTGTTTG 60.373 57.895 35.76 24.12 0.00 2.93
1579 1730 4.980434 GCATTGGCATATTGTTGTCTGATC 59.020 41.667 0.00 0.00 40.72 2.92
1608 1759 4.994852 TCCTCGTCAAAGAACTTGTAATGG 59.005 41.667 0.00 0.00 36.34 3.16
1623 1774 5.479306 CCTTTGTATTTTCTCTCCTCGTCA 58.521 41.667 0.00 0.00 0.00 4.35
1700 1851 2.373169 TGAGTCATCTCAAACTGGGCTT 59.627 45.455 0.00 0.00 46.17 4.35
1701 1852 1.980765 TGAGTCATCTCAAACTGGGCT 59.019 47.619 0.00 0.00 46.17 5.19
1725 1876 4.443457 GCTAGAGGCCAGTCAACATTATCA 60.443 45.833 5.01 0.00 34.27 2.15
1729 1880 2.409948 GCTAGAGGCCAGTCAACATT 57.590 50.000 5.01 0.00 34.27 2.71
1777 1931 2.755655 ACAGTCTCCGGTATTCAGTCAG 59.244 50.000 0.00 0.00 0.00 3.51
1787 1941 5.871396 ATCAATTATACACAGTCTCCGGT 57.129 39.130 0.00 0.00 0.00 5.28
1910 2064 2.851263 ACGCACCTTGATAAGAACCA 57.149 45.000 0.00 0.00 0.00 3.67
1928 2082 3.612860 CGACTGTGTATTGTTGCTCCTAC 59.387 47.826 0.00 0.00 0.00 3.18
1942 2096 2.356793 GCTGAGCTGCGACTGTGT 60.357 61.111 0.00 0.00 0.00 3.72
1986 2140 6.418946 ACTCCCAAGAATCCAATACTTCTTC 58.581 40.000 0.00 0.00 39.15 2.87
2184 2338 0.960364 CCTCATGGAAACCACCGGTG 60.960 60.000 28.26 28.26 35.80 4.94
2188 2342 0.251341 AGCACCTCATGGAAACCACC 60.251 55.000 0.00 0.00 35.80 4.61
2478 2632 3.731136 GCAACTTGCACACGGAGA 58.269 55.556 8.97 0.00 44.26 3.71
2646 2800 0.937304 CGGTGTTTGTCTGTGTCTGG 59.063 55.000 0.00 0.00 0.00 3.86
2724 2878 3.997021 AGCTGTAAACATCGACTTTGGAG 59.003 43.478 0.00 0.00 0.00 3.86
2763 2917 1.895231 CCTGCAGCACACAAGCTCA 60.895 57.895 8.66 0.00 44.54 4.26
2799 2953 1.804372 GCCTGCTCTTCATCGTCGATT 60.804 52.381 4.63 0.00 0.00 3.34
2804 2958 1.032794 TATCGCCTGCTCTTCATCGT 58.967 50.000 0.00 0.00 0.00 3.73
3060 3214 8.677300 CATATTTGTTAACAAGCAGGTCACTAT 58.323 33.333 19.72 9.86 37.15 2.12
3083 3237 7.102993 TCTTGCTTCATGCTACAACTTACATA 58.897 34.615 0.00 0.00 43.37 2.29
3084 3238 5.939883 TCTTGCTTCATGCTACAACTTACAT 59.060 36.000 0.00 0.00 43.37 2.29
3085 3239 5.304778 TCTTGCTTCATGCTACAACTTACA 58.695 37.500 0.00 0.00 43.37 2.41
3086 3240 5.862924 TCTTGCTTCATGCTACAACTTAC 57.137 39.130 0.00 0.00 43.37 2.34
3183 3337 9.573133 GTTCAGCTAAACATAAGTGCATTAATT 57.427 29.630 0.00 0.00 0.00 1.40
3184 3338 8.739039 TGTTCAGCTAAACATAAGTGCATTAAT 58.261 29.630 0.00 0.00 34.31 1.40
3185 3339 8.105097 TGTTCAGCTAAACATAAGTGCATTAA 57.895 30.769 0.00 0.00 34.31 1.40
3186 3340 7.680442 TGTTCAGCTAAACATAAGTGCATTA 57.320 32.000 0.00 0.00 34.31 1.90
3187 3341 6.573664 TGTTCAGCTAAACATAAGTGCATT 57.426 33.333 0.00 0.00 34.31 3.56
3188 3342 6.573664 TTGTTCAGCTAAACATAAGTGCAT 57.426 33.333 2.52 0.00 38.83 3.96
3189 3343 6.384258 TTTGTTCAGCTAAACATAAGTGCA 57.616 33.333 2.52 0.00 38.83 4.57
3305 3461 8.777865 TGACAAAAACAGGTCAGAGATATAAG 57.222 34.615 0.00 0.00 39.00 1.73
3364 3526 7.147105 ACCCCTCTTCTAGTGTAGAGAATGATA 60.147 40.741 15.92 0.00 39.23 2.15
3458 3620 5.063180 TGAATGATTGTTTGATGCCAGTC 57.937 39.130 0.00 0.00 0.00 3.51
3476 3638 8.905850 TGTTTACATATCAGCATCACATTGAAT 58.094 29.630 0.00 0.00 0.00 2.57
3486 3648 8.510243 TTGATTCAGTGTTTACATATCAGCAT 57.490 30.769 0.00 0.00 0.00 3.79
3521 3683 8.147642 AGGCATTATTCTTCAAAGTCTAATCG 57.852 34.615 0.00 0.00 0.00 3.34
3523 3685 9.343539 GGTAGGCATTATTCTTCAAAGTCTAAT 57.656 33.333 0.00 0.00 0.00 1.73
3525 3687 8.090788 AGGTAGGCATTATTCTTCAAAGTCTA 57.909 34.615 0.00 0.00 0.00 2.59
3527 3689 7.121315 ACAAGGTAGGCATTATTCTTCAAAGTC 59.879 37.037 0.00 0.00 0.00 3.01
3529 3691 7.396540 ACAAGGTAGGCATTATTCTTCAAAG 57.603 36.000 0.00 0.00 0.00 2.77
3544 3710 6.238374 CGTAATTGCCTGAAATACAAGGTAGG 60.238 42.308 0.00 0.00 0.00 3.18
3564 3730 3.328382 TTTGTGGCAGCTAGACGTAAT 57.672 42.857 0.00 0.00 0.00 1.89
3579 3745 6.017934 ACAGAAGTATTATGGCGCTATTTGTG 60.018 38.462 12.84 10.84 42.67 3.33
3582 3748 8.314751 AGATACAGAAGTATTATGGCGCTATTT 58.685 33.333 12.84 0.00 42.67 1.40
3589 3755 9.331282 ACAAAGAAGATACAGAAGTATTATGGC 57.669 33.333 0.00 0.00 42.67 4.40
3598 3765 9.265901 TCTGAAGAAACAAAGAAGATACAGAAG 57.734 33.333 0.00 0.00 0.00 2.85
3610 3777 7.437267 ACTGATGCATTTTCTGAAGAAACAAAG 59.563 33.333 0.00 5.96 43.01 2.77
3614 3781 6.211515 ACACTGATGCATTTTCTGAAGAAAC 58.788 36.000 0.00 0.00 43.01 2.78
3618 3785 5.048921 ACAGACACTGATGCATTTTCTGAAG 60.049 40.000 21.22 6.69 35.18 3.02
3633 3800 8.613060 AATTAGGCATATCAATACAGACACTG 57.387 34.615 0.00 0.00 37.52 3.66
3634 3801 8.654997 AGAATTAGGCATATCAATACAGACACT 58.345 33.333 0.00 0.00 0.00 3.55
3646 3813 8.783833 TCAGCAAAGATAGAATTAGGCATATC 57.216 34.615 0.00 0.00 0.00 1.63
3659 3826 8.896744 TGACTAAAATGGATTCAGCAAAGATAG 58.103 33.333 0.00 0.00 0.00 2.08
3663 3830 7.148918 CGTTTGACTAAAATGGATTCAGCAAAG 60.149 37.037 0.00 0.00 32.05 2.77
3668 3835 6.801862 GGAACGTTTGACTAAAATGGATTCAG 59.198 38.462 0.46 0.00 38.83 3.02
3689 3856 6.330278 GCCTGAGTATTAAATTGTTGGGAAC 58.670 40.000 0.00 0.00 0.00 3.62
3696 3863 8.559536 CATATTCACGCCTGAGTATTAAATTGT 58.440 33.333 0.00 0.00 29.15 2.71
3700 3867 9.203421 CATACATATTCACGCCTGAGTATTAAA 57.797 33.333 0.00 0.00 29.15 1.52
3702 3869 7.320399 CCATACATATTCACGCCTGAGTATTA 58.680 38.462 0.00 0.00 29.15 0.98
3707 3874 3.329386 CCCATACATATTCACGCCTGAG 58.671 50.000 0.00 0.00 0.00 3.35
3712 3879 1.806542 CCAGCCCATACATATTCACGC 59.193 52.381 0.00 0.00 0.00 5.34
3713 3880 2.807967 CACCAGCCCATACATATTCACG 59.192 50.000 0.00 0.00 0.00 4.35
3714 3881 3.815401 GACACCAGCCCATACATATTCAC 59.185 47.826 0.00 0.00 0.00 3.18
3721 3888 0.036765 GTTCGACACCAGCCCATACA 60.037 55.000 0.00 0.00 0.00 2.29
3736 3903 1.806542 CAAGGTCTTGTGGGATGTTCG 59.193 52.381 2.74 0.00 35.92 3.95
3740 3907 2.787473 TAGCAAGGTCTTGTGGGATG 57.213 50.000 11.71 0.00 42.31 3.51
3747 3914 5.753438 TCGCTTGTATATTAGCAAGGTCTTG 59.247 40.000 6.36 6.36 41.54 3.02
3750 3917 5.926542 TCATCGCTTGTATATTAGCAAGGTC 59.073 40.000 12.91 1.85 41.54 3.85
3764 3931 6.449698 ACATTTTTCTTGATTCATCGCTTGT 58.550 32.000 0.00 0.00 0.00 3.16
3790 3957 9.461312 TGAAAGTACTCAAAATATGCTGGTAAT 57.539 29.630 0.00 0.00 0.00 1.89
3795 3962 8.506437 TGTTCTGAAAGTACTCAAAATATGCTG 58.494 33.333 0.00 0.00 35.04 4.41
3802 3969 7.487829 GCAATGTTGTTCTGAAAGTACTCAAAA 59.512 33.333 0.00 0.00 35.04 2.44
3808 3975 8.970691 AATATGCAATGTTGTTCTGAAAGTAC 57.029 30.769 0.00 0.00 34.49 2.73
3811 3978 7.487189 GGAGAATATGCAATGTTGTTCTGAAAG 59.513 37.037 2.22 0.00 0.00 2.62
3834 4001 9.748708 TTATTTTGACATGTTTCTCTTTTGGAG 57.251 29.630 0.00 0.00 43.12 3.86
3868 4035 6.054941 TGCACTCTCTGAATTTTTACAGTGA 58.945 36.000 0.00 0.00 36.01 3.41
3884 4051 7.859875 GCCTTCATAAGAAATATTTGCACTCTC 59.140 37.037 5.17 0.00 32.35 3.20
3887 4054 7.651027 AGCCTTCATAAGAAATATTTGCACT 57.349 32.000 5.17 0.00 32.35 4.40
3897 4064 9.520515 AGTTTCTGAATTAGCCTTCATAAGAAA 57.479 29.630 0.00 0.00 34.76 2.52
3910 4077 7.246674 TGCGGCTAATTAGTTTCTGAATTAG 57.753 36.000 13.91 9.13 43.74 1.73
3912 4079 6.699575 ATGCGGCTAATTAGTTTCTGAATT 57.300 33.333 13.91 0.00 0.00 2.17
3920 4087 2.949644 GGACCAATGCGGCTAATTAGTT 59.050 45.455 13.91 0.00 39.03 2.24
3922 4089 2.571212 TGGACCAATGCGGCTAATTAG 58.429 47.619 8.20 8.20 39.03 1.73
3927 4094 1.961793 GTAATGGACCAATGCGGCTA 58.038 50.000 0.00 0.00 39.03 3.93
3928 4095 2.793831 GTAATGGACCAATGCGGCT 58.206 52.632 0.00 0.00 39.03 5.52
3951 4118 8.653338 GGAAAGAAGTTGTTTGTTTCTTTTACC 58.347 33.333 2.21 6.82 45.87 2.85
3958 4125 5.511729 CACTCGGAAAGAAGTTGTTTGTTTC 59.488 40.000 2.21 2.08 44.24 2.78
3980 4155 1.080298 GCTGGTTGCTGGCAATCAC 60.080 57.895 16.04 10.20 41.52 3.06
4003 4178 5.177337 TTCAGTGAGTGAGTGGAAGTACCA 61.177 45.833 0.00 0.00 40.73 3.25
4004 4179 2.891580 TCAGTGAGTGAGTGGAAGTACC 59.108 50.000 0.00 0.00 39.54 3.34
4005 4180 4.585955 TTCAGTGAGTGAGTGGAAGTAC 57.414 45.455 0.00 0.00 36.21 2.73
4006 4181 5.808366 AATTCAGTGAGTGAGTGGAAGTA 57.192 39.130 0.00 0.00 36.21 2.24
4007 4182 4.696479 AATTCAGTGAGTGAGTGGAAGT 57.304 40.909 0.00 0.00 36.21 3.01
4008 4183 4.151335 CGAAATTCAGTGAGTGAGTGGAAG 59.849 45.833 0.00 0.00 36.21 3.46
4009 4184 4.058124 CGAAATTCAGTGAGTGAGTGGAA 58.942 43.478 0.00 0.00 36.21 3.53
4010 4185 3.653344 CGAAATTCAGTGAGTGAGTGGA 58.347 45.455 0.00 0.00 36.21 4.02
4011 4186 2.158449 GCGAAATTCAGTGAGTGAGTGG 59.842 50.000 0.00 0.00 36.21 4.00
4012 4187 2.158449 GGCGAAATTCAGTGAGTGAGTG 59.842 50.000 0.00 0.00 36.21 3.51
4013 4188 2.224281 TGGCGAAATTCAGTGAGTGAGT 60.224 45.455 0.00 0.00 36.21 3.41
4014 4189 2.416747 TGGCGAAATTCAGTGAGTGAG 58.583 47.619 0.00 0.00 36.21 3.51
4015 4190 2.542020 TGGCGAAATTCAGTGAGTGA 57.458 45.000 0.00 0.00 0.00 3.41
4016 4191 3.624326 TTTGGCGAAATTCAGTGAGTG 57.376 42.857 0.00 0.00 0.00 3.51
4017 4192 4.853924 ATTTTGGCGAAATTCAGTGAGT 57.146 36.364 6.89 0.00 34.27 3.41
4018 4193 6.306356 CACTAATTTTGGCGAAATTCAGTGAG 59.694 38.462 30.14 23.44 42.81 3.51
4019 4194 6.148948 CACTAATTTTGGCGAAATTCAGTGA 58.851 36.000 30.14 17.15 42.81 3.41
4020 4195 5.345741 CCACTAATTTTGGCGAAATTCAGTG 59.654 40.000 28.84 28.84 42.81 3.66
4021 4196 5.469479 CCACTAATTTTGGCGAAATTCAGT 58.531 37.500 24.90 21.29 42.81 3.41
4022 4197 4.864247 CCCACTAATTTTGGCGAAATTCAG 59.136 41.667 24.90 20.80 42.81 3.02
4023 4198 4.322349 CCCCACTAATTTTGGCGAAATTCA 60.322 41.667 24.90 12.88 42.81 2.57
4024 4199 4.180817 CCCCACTAATTTTGGCGAAATTC 58.819 43.478 24.90 0.00 42.81 2.17
4025 4200 3.618752 GCCCCACTAATTTTGGCGAAATT 60.619 43.478 24.64 24.64 46.75 1.82
4026 4201 2.093711 GCCCCACTAATTTTGGCGAAAT 60.094 45.455 6.89 6.89 39.63 2.17
4027 4202 1.273886 GCCCCACTAATTTTGGCGAAA 59.726 47.619 1.66 1.66 32.13 3.46
4028 4203 0.892063 GCCCCACTAATTTTGGCGAA 59.108 50.000 0.00 0.00 32.13 4.70
4029 4204 0.251386 TGCCCCACTAATTTTGGCGA 60.251 50.000 0.00 0.00 45.12 5.54
4030 4205 0.605589 TTGCCCCACTAATTTTGGCG 59.394 50.000 0.00 0.00 45.12 5.69
4031 4206 2.849294 TTTGCCCCACTAATTTTGGC 57.151 45.000 0.00 0.00 42.49 4.52
4032 4207 4.699735 GGATTTTTGCCCCACTAATTTTGG 59.300 41.667 0.00 0.00 0.00 3.28
4033 4208 4.699735 GGGATTTTTGCCCCACTAATTTTG 59.300 41.667 0.00 0.00 42.24 2.44
4034 4209 4.917385 GGGATTTTTGCCCCACTAATTTT 58.083 39.130 0.00 0.00 42.24 1.82
4035 4210 4.568072 GGGATTTTTGCCCCACTAATTT 57.432 40.909 0.00 0.00 42.24 1.82


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

AutoCloner maintained by Alex Coulton.