Multiple sequence alignment - TraesCS7D01G312000

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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 TraesCS7D01G312000 chr7D 100.000 4135 0 0 1 4135 395352720 395348586 0.000000e+00 7637
1 TraesCS7D01G312000 chr7D 98.869 973 11 0 1 973 612278318 612277346 0.000000e+00 1736
2 TraesCS7D01G312000 chr7D 98.770 976 11 1 1 975 484345427 484344452 0.000000e+00 1735
3 TraesCS7D01G312000 chr7A 96.646 2415 58 9 975 3381 448709192 448706793 0.000000e+00 3989
4 TraesCS7D01G312000 chr7A 91.627 418 18 6 3418 3820 448706799 448706384 2.790000e-156 562
5 TraesCS7D01G312000 chr7A 92.982 114 8 0 4020 4133 448706161 448706048 2.560000e-37 167
6 TraesCS7D01G312000 chr7B 95.607 2117 81 7 975 3080 395064499 395062384 0.000000e+00 3384
7 TraesCS7D01G312000 chr7B 93.878 294 14 2 3030 3323 395062383 395062094 1.360000e-119 440
8 TraesCS7D01G312000 chr7B 87.730 326 21 9 3361 3683 395061883 395061574 3.040000e-96 363
9 TraesCS7D01G312000 chr3D 99.381 970 5 1 1 970 253666470 253667438 0.000000e+00 1757
10 TraesCS7D01G312000 chr2D 98.458 973 15 0 1 973 599113825 599112853 0.000000e+00 1714
11 TraesCS7D01G312000 chr2D 97.947 974 17 3 1 973 31037217 31038188 0.000000e+00 1685
12 TraesCS7D01G312000 chr6D 98.053 976 18 1 1 975 58529492 58530467 0.000000e+00 1696
13 TraesCS7D01G312000 chr1D 98.047 973 19 0 1 973 420603152 420604124 0.000000e+00 1692
14 TraesCS7D01G312000 chr5B 97.837 971 21 0 3 973 527602804 527601834 0.000000e+00 1677
15 TraesCS7D01G312000 chr2A 95.267 972 38 6 5 976 610212345 610211382 0.000000e+00 1533


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 TraesCS7D01G312000 chr7D 395348586 395352720 4134 True 7637.000000 7637 100.000000 1 4135 1 chr7D.!!$R1 4134
1 TraesCS7D01G312000 chr7D 612277346 612278318 972 True 1736.000000 1736 98.869000 1 973 1 chr7D.!!$R3 972
2 TraesCS7D01G312000 chr7D 484344452 484345427 975 True 1735.000000 1735 98.770000 1 975 1 chr7D.!!$R2 974
3 TraesCS7D01G312000 chr7A 448706048 448709192 3144 True 1572.666667 3989 93.751667 975 4133 3 chr7A.!!$R1 3158
4 TraesCS7D01G312000 chr7B 395061574 395064499 2925 True 1395.666667 3384 92.405000 975 3683 3 chr7B.!!$R1 2708
5 TraesCS7D01G312000 chr3D 253666470 253667438 968 False 1757.000000 1757 99.381000 1 970 1 chr3D.!!$F1 969
6 TraesCS7D01G312000 chr2D 599112853 599113825 972 True 1714.000000 1714 98.458000 1 973 1 chr2D.!!$R1 972
7 TraesCS7D01G312000 chr2D 31037217 31038188 971 False 1685.000000 1685 97.947000 1 973 1 chr2D.!!$F1 972
8 TraesCS7D01G312000 chr6D 58529492 58530467 975 False 1696.000000 1696 98.053000 1 975 1 chr6D.!!$F1 974
9 TraesCS7D01G312000 chr1D 420603152 420604124 972 False 1692.000000 1692 98.047000 1 973 1 chr1D.!!$F1 972
10 TraesCS7D01G312000 chr5B 527601834 527602804 970 True 1677.000000 1677 97.837000 3 973 1 chr5B.!!$R1 970
11 TraesCS7D01G312000 chr2A 610211382 610212345 963 True 1533.000000 1533 95.267000 5 976 1 chr2A.!!$R1 971

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
228 229 0.823769 TCCATCTCTGGATCGGACGG 60.824 60.000 0.00 0.0 46.95 4.79 F
1078 1081 1.272212 CTTTTGGCGGCTTTGTACCAT 59.728 47.619 11.43 0.0 30.85 3.55 F
2248 2260 0.536260 TGGCATTGGCAATAAGGTGC 59.464 50.000 13.23 13.1 43.71 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1290 1293 0.108615 CCTCGTCGTCTGAAGGCAAT 60.109 55.0 0.00 0.0 0.0 3.56 R
2969 2991 0.617820 TGCCAGGTCTAAGAGTCCCC 60.618 60.0 0.00 0.0 0.0 4.81 R
3591 3835 0.242825 GCAAAGCTCGGGGGTTTAAC 59.757 55.0 4.51 0.0 42.8 2.01 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
228 229 0.823769 TCCATCTCTGGATCGGACGG 60.824 60.000 0.00 0.00 46.95 4.79
531 533 4.228210 TCTCTCTATTTTTGATGGTGGCCT 59.772 41.667 3.32 0.00 0.00 5.19
762 765 3.384146 TGATTCAACAAAGCTTGCTTCCA 59.616 39.130 8.39 0.00 0.00 3.53
1078 1081 1.272212 CTTTTGGCGGCTTTGTACCAT 59.728 47.619 11.43 0.00 30.85 3.55
1180 1183 2.024176 TGGACCTAGCCTGTTTGAGA 57.976 50.000 0.00 0.00 0.00 3.27
1216 1219 4.101790 GCATGTTCCGGCCACACG 62.102 66.667 2.24 2.15 0.00 4.49
1290 1293 3.662759 AAAGGGCCGATTATTGAGGAA 57.337 42.857 0.00 0.00 0.00 3.36
1961 1970 7.285401 GGCATGAGAAATTTGGGAAAGAGTATA 59.715 37.037 0.00 0.00 0.00 1.47
1991 2000 2.292569 GGCACATCATATCAACAGCCAG 59.707 50.000 0.00 0.00 40.50 4.85
2149 2161 2.878406 AGTTCTGGTGGTGATTGTTTCG 59.122 45.455 0.00 0.00 0.00 3.46
2202 2214 1.312815 AGGAAGCAGACACAACAAGC 58.687 50.000 0.00 0.00 0.00 4.01
2248 2260 0.536260 TGGCATTGGCAATAAGGTGC 59.464 50.000 13.23 13.10 43.71 5.01
2303 2315 4.286297 TCTTTGGACTACACCAAGGATG 57.714 45.455 7.91 0.00 46.10 3.51
2326 2338 6.607970 TGAATGATTTAGAGCCATGATTCCT 58.392 36.000 0.00 0.00 0.00 3.36
2473 2485 8.627403 CCTTATTCATGTTGTTTCTGATGCTAT 58.373 33.333 0.00 0.00 0.00 2.97
2650 2666 7.117956 GGTTACTGATAAGTTGAAACTCACTCC 59.882 40.741 0.00 0.00 38.57 3.85
2830 2846 4.866508 AGTTTATCCACGTGAGACAAGA 57.133 40.909 19.30 4.57 0.00 3.02
2919 2938 3.311596 GCCTGTTGTTTTCGTGTTCTAGT 59.688 43.478 0.00 0.00 0.00 2.57
2972 2994 6.710744 ACATTCTTGTTATAGATAAAGCGGGG 59.289 38.462 0.00 0.00 29.55 5.73
2981 3003 3.912248 AGATAAAGCGGGGACTCTTAGA 58.088 45.455 0.00 0.00 0.00 2.10
3153 3226 4.855298 TGATTTCCTCGGGAATTTAGGT 57.145 40.909 6.25 0.00 41.71 3.08
3353 3597 7.121974 ACTTCTGTTTACAAGAACGATCATG 57.878 36.000 0.00 0.00 32.18 3.07
3355 3599 7.226720 ACTTCTGTTTACAAGAACGATCATGTT 59.773 33.333 8.86 0.00 38.39 2.71
3409 3653 3.698040 AGGCTGCATTCCTGTATTTTCTG 59.302 43.478 6.84 0.00 31.53 3.02
3410 3654 3.696051 GGCTGCATTCCTGTATTTTCTGA 59.304 43.478 0.50 0.00 0.00 3.27
3411 3655 4.340381 GGCTGCATTCCTGTATTTTCTGAT 59.660 41.667 0.50 0.00 0.00 2.90
3412 3656 5.279384 GCTGCATTCCTGTATTTTCTGATG 58.721 41.667 0.00 0.00 0.00 3.07
3413 3657 5.163581 GCTGCATTCCTGTATTTTCTGATGT 60.164 40.000 0.00 0.00 0.00 3.06
3414 3658 6.038603 GCTGCATTCCTGTATTTTCTGATGTA 59.961 38.462 0.00 0.00 0.00 2.29
3415 3659 7.320443 TGCATTCCTGTATTTTCTGATGTAC 57.680 36.000 0.00 0.00 0.00 2.90
3479 3723 8.278482 GATTCAATAATCTTCCAAAGCAATCG 57.722 34.615 0.00 0.00 38.79 3.34
3490 3734 3.367630 CCAAAGCAATCGCACCAATTTAC 59.632 43.478 0.00 0.00 42.27 2.01
3572 3816 6.260714 TCGAGTTGCATATTAGTCATTTGCAT 59.739 34.615 3.69 0.00 45.78 3.96
3573 3817 6.914215 CGAGTTGCATATTAGTCATTTGCATT 59.086 34.615 3.69 0.00 45.78 3.56
3601 3845 3.247948 TCAAAAGGAGGTTAAACCCCC 57.752 47.619 0.00 0.00 39.75 5.40
3671 3918 4.172807 TGGGACAAATGTAGTACTCCCTT 58.827 43.478 19.92 0.00 37.10 3.95
3683 3930 9.668497 ATGTAGTACTCCCTTTGTAAAGAAATC 57.332 33.333 0.00 0.00 38.28 2.17
3684 3931 7.816031 TGTAGTACTCCCTTTGTAAAGAAATCG 59.184 37.037 0.00 0.00 38.28 3.34
3685 3932 6.766429 AGTACTCCCTTTGTAAAGAAATCGT 58.234 36.000 5.95 0.00 38.28 3.73
3686 3933 7.222161 AGTACTCCCTTTGTAAAGAAATCGTT 58.778 34.615 5.95 0.00 38.28 3.85
3687 3934 6.954487 ACTCCCTTTGTAAAGAAATCGTTT 57.046 33.333 5.95 0.00 38.28 3.60
3689 3936 8.095937 ACTCCCTTTGTAAAGAAATCGTTTAG 57.904 34.615 5.95 0.00 38.28 1.85
3690 3937 7.935210 ACTCCCTTTGTAAAGAAATCGTTTAGA 59.065 33.333 5.95 0.00 38.28 2.10
3691 3938 8.857694 TCCCTTTGTAAAGAAATCGTTTAGAT 57.142 30.769 5.95 0.00 38.60 1.98
3692 3939 8.943002 TCCCTTTGTAAAGAAATCGTTTAGATC 58.057 33.333 5.95 0.00 37.06 2.75
3693 3940 7.903431 CCCTTTGTAAAGAAATCGTTTAGATCG 59.097 37.037 5.95 0.00 37.06 3.69
3694 3941 7.425595 CCTTTGTAAAGAAATCGTTTAGATCGC 59.574 37.037 5.95 0.00 37.06 4.58
3702 3956 8.922058 AGAAATCGTTTAGATCGCTACTTTAA 57.078 30.769 0.00 0.00 38.98 1.52
3775 4037 3.548014 GCGGAGTGCATAATAAACGCAAT 60.548 43.478 11.82 0.00 45.45 3.56
3833 4236 7.607250 ACTATGACTAAGTTGACTTCTTCTGG 58.393 38.462 0.00 0.00 37.40 3.86
3834 4237 6.672266 ATGACTAAGTTGACTTCTTCTGGA 57.328 37.500 0.00 0.00 37.40 3.86
3835 4238 6.479972 TGACTAAGTTGACTTCTTCTGGAA 57.520 37.500 0.00 0.00 37.40 3.53
3884 4287 4.465512 CGCTGCCGTTGCCATGTC 62.466 66.667 0.00 0.00 36.33 3.06
3885 4288 3.058160 GCTGCCGTTGCCATGTCT 61.058 61.111 0.00 0.00 36.33 3.41
3886 4289 1.745115 GCTGCCGTTGCCATGTCTA 60.745 57.895 0.00 0.00 36.33 2.59
3887 4290 1.709147 GCTGCCGTTGCCATGTCTAG 61.709 60.000 0.00 0.00 36.33 2.43
3888 4291 1.709147 CTGCCGTTGCCATGTCTAGC 61.709 60.000 0.00 0.00 36.33 3.42
3889 4292 2.472909 GCCGTTGCCATGTCTAGCC 61.473 63.158 0.00 0.00 0.00 3.93
3890 4293 2.173669 CCGTTGCCATGTCTAGCCG 61.174 63.158 0.00 0.00 0.00 5.52
3891 4294 1.153647 CGTTGCCATGTCTAGCCGA 60.154 57.895 0.00 0.00 0.00 5.54
3892 4295 0.739462 CGTTGCCATGTCTAGCCGAA 60.739 55.000 0.00 0.00 0.00 4.30
3893 4296 1.009829 GTTGCCATGTCTAGCCGAAG 58.990 55.000 0.00 0.00 0.00 3.79
3894 4297 0.901827 TTGCCATGTCTAGCCGAAGA 59.098 50.000 0.00 0.00 0.00 2.87
3895 4298 0.175760 TGCCATGTCTAGCCGAAGAC 59.824 55.000 4.86 4.86 45.10 3.01
3906 4309 4.354155 CGAAGACGGCCAAGACAA 57.646 55.556 2.24 0.00 35.72 3.18
3907 4310 2.840974 CGAAGACGGCCAAGACAAT 58.159 52.632 2.24 0.00 35.72 2.71
3908 4311 0.443869 CGAAGACGGCCAAGACAATG 59.556 55.000 2.24 0.00 35.72 2.82
3909 4312 1.808411 GAAGACGGCCAAGACAATGA 58.192 50.000 2.24 0.00 0.00 2.57
3910 4313 1.464997 GAAGACGGCCAAGACAATGAC 59.535 52.381 2.24 0.00 0.00 3.06
3911 4314 0.687354 AGACGGCCAAGACAATGACT 59.313 50.000 2.24 0.00 0.00 3.41
3912 4315 1.072331 AGACGGCCAAGACAATGACTT 59.928 47.619 2.24 0.00 0.00 3.01
3913 4316 1.880027 GACGGCCAAGACAATGACTTT 59.120 47.619 2.24 0.00 0.00 2.66
3914 4317 2.293399 GACGGCCAAGACAATGACTTTT 59.707 45.455 2.24 0.00 0.00 2.27
3915 4318 3.482436 ACGGCCAAGACAATGACTTTTA 58.518 40.909 2.24 0.00 0.00 1.52
3916 4319 4.079253 ACGGCCAAGACAATGACTTTTAT 58.921 39.130 2.24 0.00 0.00 1.40
3917 4320 4.156008 ACGGCCAAGACAATGACTTTTATC 59.844 41.667 2.24 0.00 0.00 1.75
3918 4321 4.438744 CGGCCAAGACAATGACTTTTATCC 60.439 45.833 2.24 0.00 0.00 2.59
3919 4322 4.706962 GGCCAAGACAATGACTTTTATCCT 59.293 41.667 0.00 0.00 0.00 3.24
3920 4323 5.393461 GGCCAAGACAATGACTTTTATCCTG 60.393 44.000 0.00 0.00 0.00 3.86
3921 4324 5.393461 GCCAAGACAATGACTTTTATCCTGG 60.393 44.000 0.00 0.00 0.00 4.45
3922 4325 5.711976 CCAAGACAATGACTTTTATCCTGGT 59.288 40.000 0.00 0.00 0.00 4.00
3923 4326 6.209391 CCAAGACAATGACTTTTATCCTGGTT 59.791 38.462 0.00 0.00 0.00 3.67
3924 4327 6.824305 AGACAATGACTTTTATCCTGGTTG 57.176 37.500 0.00 0.00 0.00 3.77
3925 4328 5.183904 AGACAATGACTTTTATCCTGGTTGC 59.816 40.000 0.00 0.00 0.00 4.17
3926 4329 4.832266 ACAATGACTTTTATCCTGGTTGCA 59.168 37.500 0.00 0.00 0.00 4.08
3927 4330 5.163513 CAATGACTTTTATCCTGGTTGCAC 58.836 41.667 0.00 0.00 0.00 4.57
3928 4331 2.811431 TGACTTTTATCCTGGTTGCACG 59.189 45.455 0.00 0.00 0.00 5.34
3929 4332 3.071479 GACTTTTATCCTGGTTGCACGA 58.929 45.455 0.00 0.00 0.00 4.35
3930 4333 2.812011 ACTTTTATCCTGGTTGCACGAC 59.188 45.455 0.00 0.00 0.00 4.34
3931 4334 1.816074 TTTATCCTGGTTGCACGACC 58.184 50.000 0.21 0.21 40.23 4.79
3936 4339 3.038280 TGGTTGCACGACCAATGC 58.962 55.556 7.83 0.00 46.33 3.56
3937 4340 2.258286 GGTTGCACGACCAATGCC 59.742 61.111 2.53 0.00 42.69 4.40
3938 4341 2.126888 GTTGCACGACCAATGCCG 60.127 61.111 0.00 0.00 42.69 5.69
3939 4342 3.361158 TTGCACGACCAATGCCGG 61.361 61.111 0.00 0.00 42.69 6.13
3940 4343 4.634703 TGCACGACCAATGCCGGT 62.635 61.111 1.90 0.00 42.69 5.28
3941 4344 4.101790 GCACGACCAATGCCGGTG 62.102 66.667 1.90 0.00 40.22 4.94
3942 4345 2.358125 CACGACCAATGCCGGTGA 60.358 61.111 1.90 0.00 40.22 4.02
3943 4346 1.745115 CACGACCAATGCCGGTGAT 60.745 57.895 1.90 0.00 40.22 3.06
3944 4347 1.002624 ACGACCAATGCCGGTGATT 60.003 52.632 1.90 0.00 40.22 2.57
3945 4348 1.305219 ACGACCAATGCCGGTGATTG 61.305 55.000 17.09 17.09 40.22 2.67
3946 4349 1.139520 GACCAATGCCGGTGATTGC 59.860 57.895 18.12 6.54 40.22 3.56
3947 4350 1.304381 ACCAATGCCGGTGATTGCT 60.304 52.632 18.12 6.58 38.07 3.91
3948 4351 1.140161 CCAATGCCGGTGATTGCTG 59.860 57.895 18.12 6.54 30.66 4.41
3949 4352 1.517694 CAATGCCGGTGATTGCTGC 60.518 57.895 13.37 0.00 0.00 5.25
3950 4353 2.713967 AATGCCGGTGATTGCTGCC 61.714 57.895 1.90 0.00 0.00 4.85
3951 4354 3.650298 ATGCCGGTGATTGCTGCCT 62.650 57.895 1.90 0.00 0.00 4.75
3952 4355 3.064324 GCCGGTGATTGCTGCCTT 61.064 61.111 1.90 0.00 0.00 4.35
3953 4356 2.879907 CCGGTGATTGCTGCCTTG 59.120 61.111 0.00 0.00 0.00 3.61
3954 4357 1.675310 CCGGTGATTGCTGCCTTGA 60.675 57.895 0.00 0.00 0.00 3.02
3955 4358 1.033746 CCGGTGATTGCTGCCTTGAT 61.034 55.000 0.00 0.00 0.00 2.57
3956 4359 0.379669 CGGTGATTGCTGCCTTGATC 59.620 55.000 0.00 0.00 0.00 2.92
3957 4360 1.466856 GGTGATTGCTGCCTTGATCA 58.533 50.000 0.00 0.00 0.00 2.92
3958 4361 1.820519 GGTGATTGCTGCCTTGATCAA 59.179 47.619 8.12 8.12 31.01 2.57
3959 4362 2.231964 GGTGATTGCTGCCTTGATCAAA 59.768 45.455 9.88 0.00 31.01 2.69
3960 4363 3.508762 GTGATTGCTGCCTTGATCAAAG 58.491 45.455 9.88 4.49 35.47 2.77
3961 4364 3.192001 GTGATTGCTGCCTTGATCAAAGA 59.808 43.478 9.88 0.00 38.24 2.52
3962 4365 3.827876 TGATTGCTGCCTTGATCAAAGAA 59.172 39.130 9.88 0.00 38.24 2.52
3963 4366 4.464951 TGATTGCTGCCTTGATCAAAGAAT 59.535 37.500 9.88 6.37 38.24 2.40
3964 4367 4.877378 TTGCTGCCTTGATCAAAGAATT 57.123 36.364 9.88 0.00 38.24 2.17
3965 4368 4.445452 TGCTGCCTTGATCAAAGAATTC 57.555 40.909 9.88 0.00 38.24 2.17
3966 4369 3.194116 TGCTGCCTTGATCAAAGAATTCC 59.806 43.478 9.88 0.00 38.24 3.01
3967 4370 3.194116 GCTGCCTTGATCAAAGAATTCCA 59.806 43.478 9.88 0.00 38.24 3.53
3968 4371 4.322198 GCTGCCTTGATCAAAGAATTCCAA 60.322 41.667 9.88 0.00 38.24 3.53
3969 4372 5.395682 TGCCTTGATCAAAGAATTCCAAG 57.604 39.130 9.88 7.28 38.24 3.61
3970 4373 5.078949 TGCCTTGATCAAAGAATTCCAAGA 58.921 37.500 16.70 7.38 38.24 3.02
3971 4374 5.718130 TGCCTTGATCAAAGAATTCCAAGAT 59.282 36.000 16.70 11.04 38.24 2.40
3972 4375 6.040878 GCCTTGATCAAAGAATTCCAAGATG 58.959 40.000 16.70 6.61 38.24 2.90
3973 4376 6.350780 GCCTTGATCAAAGAATTCCAAGATGT 60.351 38.462 16.70 0.00 38.24 3.06
3974 4377 7.033791 CCTTGATCAAAGAATTCCAAGATGTG 58.966 38.462 16.70 0.00 38.24 3.21
3975 4378 7.309621 CCTTGATCAAAGAATTCCAAGATGTGT 60.310 37.037 16.70 0.00 38.24 3.72
3976 4379 7.528996 TGATCAAAGAATTCCAAGATGTGTT 57.471 32.000 0.65 0.00 0.00 3.32
3977 4380 7.596494 TGATCAAAGAATTCCAAGATGTGTTC 58.404 34.615 0.65 0.00 0.00 3.18
3978 4381 6.000891 TCAAAGAATTCCAAGATGTGTTCG 57.999 37.500 0.65 0.00 0.00 3.95
3979 4382 5.048782 TCAAAGAATTCCAAGATGTGTTCGG 60.049 40.000 0.65 0.00 0.00 4.30
3980 4383 4.286297 AGAATTCCAAGATGTGTTCGGA 57.714 40.909 0.65 0.00 0.00 4.55
3981 4384 4.256920 AGAATTCCAAGATGTGTTCGGAG 58.743 43.478 0.65 0.00 0.00 4.63
3982 4385 3.981071 ATTCCAAGATGTGTTCGGAGA 57.019 42.857 0.00 0.00 0.00 3.71
3983 4386 3.762407 TTCCAAGATGTGTTCGGAGAA 57.238 42.857 0.00 0.00 45.90 2.87
3984 4387 3.040147 TCCAAGATGTGTTCGGAGAAC 57.960 47.619 6.01 6.01 45.90 3.01
3985 4388 2.076863 CCAAGATGTGTTCGGAGAACC 58.923 52.381 10.00 3.27 45.90 3.62
3986 4389 2.549992 CCAAGATGTGTTCGGAGAACCA 60.550 50.000 10.00 8.08 45.90 3.67
4010 4413 2.975489 AGGATACCACTAATGCCAGAGG 59.025 50.000 0.00 0.00 32.97 3.69
4011 4414 4.832855 AGGATACCACTAATGCCAGAGGC 61.833 52.174 0.00 0.00 44.79 4.70
4026 4429 2.164422 CAGAGGCGACTAGTGAACATCA 59.836 50.000 0.00 0.00 44.43 3.07
4028 4431 1.134965 AGGCGACTAGTGAACATCAGC 60.135 52.381 0.00 0.00 40.61 4.26
4034 4437 4.372656 GACTAGTGAACATCAGCCCATAC 58.627 47.826 0.00 0.00 0.00 2.39
4056 4459 0.031178 GCACAAGCCAGAACACAAGG 59.969 55.000 0.00 0.00 33.58 3.61
4086 4489 5.537674 ACAGAAAAGCAAGTCATGGATCTTT 59.462 36.000 0.00 0.00 0.00 2.52
4095 4498 6.583806 GCAAGTCATGGATCTTTTACAAACAG 59.416 38.462 0.00 0.00 0.00 3.16
4133 4536 1.019673 CCAGTCCATTTGCATCTCCG 58.980 55.000 0.00 0.00 0.00 4.63
4134 4537 1.019673 CAGTCCATTTGCATCTCCGG 58.980 55.000 0.00 0.00 0.00 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
228 229 4.831307 ACATCGAGACGCCGTCGC 62.831 66.667 12.13 11.60 37.67 5.19
531 533 0.909610 CCTCCTCTAGGCCACACCAA 60.910 60.000 5.01 0.00 43.14 3.67
762 765 4.506886 CACTAGTTGGAACGAGAAGAGT 57.493 45.455 6.64 0.00 35.54 3.24
979 982 4.937201 TCTTGTACTGAAGTTCTCTGCA 57.063 40.909 4.17 0.00 0.00 4.41
987 990 4.074970 CCCTTTGCATCTTGTACTGAAGT 58.925 43.478 0.00 0.00 0.00 3.01
1035 1038 0.677288 GAAAAGGGTCCCCAAAACCG 59.323 55.000 3.51 0.00 37.69 4.44
1078 1081 2.915869 ACTGGACATAAGGTTCCCAGA 58.084 47.619 13.00 0.00 41.73 3.86
1180 1183 5.357596 ACATGCTTGAACCAAAAATGCTTTT 59.642 32.000 6.60 0.00 35.02 2.27
1216 1219 2.969262 AGCCTCCTACATTTAGAGCTCC 59.031 50.000 10.93 0.00 0.00 4.70
1290 1293 0.108615 CCTCGTCGTCTGAAGGCAAT 60.109 55.000 0.00 0.00 0.00 3.56
1576 1582 0.253160 AGGGTTCCAGGCCATACAGA 60.253 55.000 5.01 0.00 0.00 3.41
1578 1584 0.844661 ACAGGGTTCCAGGCCATACA 60.845 55.000 5.01 0.00 0.00 2.29
1579 1585 1.134189 GTACAGGGTTCCAGGCCATAC 60.134 57.143 5.01 0.00 0.00 2.39
1626 1632 4.918810 ACTCCAAAACAATCTTGTGGAC 57.081 40.909 0.00 0.00 41.31 4.02
1961 1970 1.142936 TATGATGTGCCAGCCCTGAT 58.857 50.000 0.00 0.00 0.00 2.90
1991 2000 6.398234 TGAGCTCTGAAACATATAGGTCTC 57.602 41.667 16.19 0.00 36.06 3.36
2149 2161 7.103641 TCCATTGTAACCTAGAAGACATTGAC 58.896 38.462 0.00 0.00 0.00 3.18
2202 2214 2.163818 TCCTGTGAGTTGCTTTACCG 57.836 50.000 0.00 0.00 0.00 4.02
2248 2260 2.680841 TGTCTGGGTTGTGAAGAAAACG 59.319 45.455 0.00 0.00 0.00 3.60
2303 2315 7.521871 AAGGAATCATGGCTCTAAATCATTC 57.478 36.000 0.00 0.00 0.00 2.67
2326 2338 1.531128 TGCATGACCCTGCAGCAAA 60.531 52.632 8.66 0.00 46.76 3.68
2633 2648 6.126997 TGGTTACAGGAGTGAGTTTCAACTTA 60.127 38.462 0.00 0.00 39.88 2.24
2650 2666 1.939838 GCCGTGTTCCTCTGGTTACAG 60.940 57.143 0.00 0.00 46.30 2.74
2830 2846 7.534852 AGATAGAGATCTGAACTCAGGGTTAT 58.465 38.462 15.99 5.75 41.12 1.89
2919 2938 3.256704 ACCACTCCAGGGATCAAACTAA 58.743 45.455 0.00 0.00 0.00 2.24
2969 2991 0.617820 TGCCAGGTCTAAGAGTCCCC 60.618 60.000 0.00 0.00 0.00 4.81
2972 2994 2.111384 TGGATGCCAGGTCTAAGAGTC 58.889 52.381 0.00 0.00 0.00 3.36
2981 3003 4.467769 CATTATCTTCTTGGATGCCAGGT 58.532 43.478 0.00 0.00 33.81 4.00
3153 3226 2.435069 TCAAACCGGGAACACAGTTCTA 59.565 45.455 6.32 0.00 0.00 2.10
3325 3569 6.500775 TCGTTCTTGTAAACAGAAGTTACG 57.499 37.500 0.00 0.00 36.84 3.18
3353 3597 4.569564 AGTTACTCAACAGTCGTGGAAAAC 59.430 41.667 0.00 0.00 37.10 2.43
3355 3599 4.395959 AGTTACTCAACAGTCGTGGAAA 57.604 40.909 0.00 0.00 37.10 3.13
3409 3653 6.868864 CCATAGTGCCAACATAGTAGTACATC 59.131 42.308 2.52 0.00 0.00 3.06
3410 3654 6.326583 ACCATAGTGCCAACATAGTAGTACAT 59.673 38.462 2.52 0.00 0.00 2.29
3411 3655 5.659525 ACCATAGTGCCAACATAGTAGTACA 59.340 40.000 2.52 0.00 0.00 2.90
3412 3656 5.983720 CACCATAGTGCCAACATAGTAGTAC 59.016 44.000 0.00 0.00 37.14 2.73
3413 3657 6.156748 CACCATAGTGCCAACATAGTAGTA 57.843 41.667 0.00 0.00 37.14 1.82
3414 3658 5.023533 CACCATAGTGCCAACATAGTAGT 57.976 43.478 0.00 0.00 37.14 2.73
3490 3734 7.670009 ACTAAGCATAGTAGATAGTACACCG 57.330 40.000 0.00 0.00 40.62 4.94
3591 3835 0.242825 GCAAAGCTCGGGGGTTTAAC 59.757 55.000 4.51 0.00 42.80 2.01
3601 3845 2.161012 ACTCACAATGATGCAAAGCTCG 59.839 45.455 0.00 0.00 0.00 5.03
3671 3918 7.591006 AGCGATCTAAACGATTTCTTTACAA 57.409 32.000 0.00 0.00 30.84 2.41
3683 3930 8.508800 AGATCATTAAAGTAGCGATCTAAACG 57.491 34.615 0.00 0.00 40.70 3.60
3689 3936 8.983724 AGCTTTAAGATCATTAAAGTAGCGATC 58.016 33.333 23.50 13.63 41.56 3.69
3690 3937 8.894768 AGCTTTAAGATCATTAAAGTAGCGAT 57.105 30.769 23.50 0.00 41.56 4.58
3691 3938 8.718102 AAGCTTTAAGATCATTAAAGTAGCGA 57.282 30.769 23.50 3.23 41.56 4.93
3692 3939 9.774742 AAAAGCTTTAAGATCATTAAAGTAGCG 57.225 29.630 23.50 10.84 41.56 4.26
3770 4032 5.339177 TGTAATGGCTTAATTGTGATTGCG 58.661 37.500 0.00 0.00 0.00 4.85
3775 4037 7.936496 TCATCTTGTAATGGCTTAATTGTGA 57.064 32.000 0.00 0.00 0.00 3.58
3859 4262 4.927782 AACGGCAGCGCAAGGACA 62.928 61.111 11.47 0.00 38.28 4.02
3868 4271 1.709147 CTAGACATGGCAACGGCAGC 61.709 60.000 0.00 0.00 42.43 5.25
3889 4292 0.443869 CATTGTCTTGGCCGTCTTCG 59.556 55.000 0.00 0.00 0.00 3.79
3890 4293 1.464997 GTCATTGTCTTGGCCGTCTTC 59.535 52.381 0.00 0.00 0.00 2.87
3891 4294 1.072331 AGTCATTGTCTTGGCCGTCTT 59.928 47.619 0.00 0.00 0.00 3.01
3892 4295 0.687354 AGTCATTGTCTTGGCCGTCT 59.313 50.000 0.00 0.00 0.00 4.18
3893 4296 1.523758 AAGTCATTGTCTTGGCCGTC 58.476 50.000 0.00 0.00 0.00 4.79
3894 4297 1.981256 AAAGTCATTGTCTTGGCCGT 58.019 45.000 0.00 0.00 0.00 5.68
3895 4298 4.438744 GGATAAAAGTCATTGTCTTGGCCG 60.439 45.833 0.00 0.00 0.00 6.13
3896 4299 4.706962 AGGATAAAAGTCATTGTCTTGGCC 59.293 41.667 0.00 0.00 0.00 5.36
3897 4300 5.393461 CCAGGATAAAAGTCATTGTCTTGGC 60.393 44.000 2.88 0.00 39.53 4.52
3898 4301 5.711976 ACCAGGATAAAAGTCATTGTCTTGG 59.288 40.000 11.53 11.53 46.37 3.61
3899 4302 6.824305 ACCAGGATAAAAGTCATTGTCTTG 57.176 37.500 0.00 0.00 30.63 3.02
3900 4303 6.294731 GCAACCAGGATAAAAGTCATTGTCTT 60.295 38.462 0.00 0.00 0.00 3.01
3901 4304 5.183904 GCAACCAGGATAAAAGTCATTGTCT 59.816 40.000 0.00 0.00 0.00 3.41
3902 4305 5.048083 TGCAACCAGGATAAAAGTCATTGTC 60.048 40.000 0.00 0.00 0.00 3.18
3903 4306 4.832266 TGCAACCAGGATAAAAGTCATTGT 59.168 37.500 0.00 0.00 0.00 2.71
3904 4307 5.163513 GTGCAACCAGGATAAAAGTCATTG 58.836 41.667 0.00 0.00 0.00 2.82
3905 4308 4.082787 CGTGCAACCAGGATAAAAGTCATT 60.083 41.667 0.00 0.00 0.00 2.57
3906 4309 3.440173 CGTGCAACCAGGATAAAAGTCAT 59.560 43.478 0.00 0.00 0.00 3.06
3907 4310 2.811431 CGTGCAACCAGGATAAAAGTCA 59.189 45.455 0.00 0.00 0.00 3.41
3908 4311 3.071479 TCGTGCAACCAGGATAAAAGTC 58.929 45.455 0.00 0.00 31.43 3.01
3909 4312 2.812011 GTCGTGCAACCAGGATAAAAGT 59.188 45.455 0.00 0.00 38.06 2.66
3910 4313 2.161609 GGTCGTGCAACCAGGATAAAAG 59.838 50.000 2.53 0.00 38.06 2.27
3911 4314 2.156098 GGTCGTGCAACCAGGATAAAA 58.844 47.619 2.53 0.00 38.06 1.52
3912 4315 1.072489 TGGTCGTGCAACCAGGATAAA 59.928 47.619 6.14 0.00 44.40 1.40
3913 4316 0.687920 TGGTCGTGCAACCAGGATAA 59.312 50.000 6.14 0.00 44.40 1.75
3914 4317 2.367529 TGGTCGTGCAACCAGGATA 58.632 52.632 6.14 0.00 44.40 2.59
3915 4318 3.156714 TGGTCGTGCAACCAGGAT 58.843 55.556 6.14 0.00 44.40 3.24
3920 4323 2.258286 GGCATTGGTCGTGCAACC 59.742 61.111 0.21 0.21 44.25 3.77
3921 4324 2.126888 CGGCATTGGTCGTGCAAC 60.127 61.111 0.00 0.00 44.25 4.17
3922 4325 3.361158 CCGGCATTGGTCGTGCAA 61.361 61.111 0.00 0.00 44.25 4.08
3923 4326 4.634703 ACCGGCATTGGTCGTGCA 62.635 61.111 0.00 0.00 44.25 4.57
3924 4327 4.101790 CACCGGCATTGGTCGTGC 62.102 66.667 0.00 0.00 41.38 5.34
3925 4328 1.305219 AATCACCGGCATTGGTCGTG 61.305 55.000 0.00 0.00 41.38 4.35
3926 4329 1.002624 AATCACCGGCATTGGTCGT 60.003 52.632 0.00 0.00 41.38 4.34
3927 4330 1.429021 CAATCACCGGCATTGGTCG 59.571 57.895 15.95 0.00 41.38 4.79
3928 4331 1.139520 GCAATCACCGGCATTGGTC 59.860 57.895 22.21 8.16 41.38 4.02
3929 4332 1.304381 AGCAATCACCGGCATTGGT 60.304 52.632 20.43 20.43 45.21 3.67
3930 4333 1.140161 CAGCAATCACCGGCATTGG 59.860 57.895 22.21 8.16 32.66 3.16
3931 4334 1.517694 GCAGCAATCACCGGCATTG 60.518 57.895 18.44 18.44 34.80 2.82
3932 4335 2.713967 GGCAGCAATCACCGGCATT 61.714 57.895 0.00 0.00 0.00 3.56
3933 4336 3.142838 GGCAGCAATCACCGGCAT 61.143 61.111 0.00 0.00 0.00 4.40
3934 4337 3.866379 AAGGCAGCAATCACCGGCA 62.866 57.895 0.00 0.00 0.00 5.69
3935 4338 3.064324 AAGGCAGCAATCACCGGC 61.064 61.111 0.00 0.00 0.00 6.13
3936 4339 1.033746 ATCAAGGCAGCAATCACCGG 61.034 55.000 0.00 0.00 0.00 5.28
3937 4340 0.379669 GATCAAGGCAGCAATCACCG 59.620 55.000 0.00 0.00 0.00 4.94
3938 4341 1.466856 TGATCAAGGCAGCAATCACC 58.533 50.000 0.00 0.00 0.00 4.02
3939 4342 3.192001 TCTTTGATCAAGGCAGCAATCAC 59.808 43.478 12.50 0.00 32.64 3.06
3940 4343 3.423749 TCTTTGATCAAGGCAGCAATCA 58.576 40.909 12.50 0.00 32.64 2.57
3941 4344 4.445452 TTCTTTGATCAAGGCAGCAATC 57.555 40.909 12.50 0.00 32.64 2.67
3942 4345 5.416271 AATTCTTTGATCAAGGCAGCAAT 57.584 34.783 12.50 4.81 32.64 3.56
3943 4346 4.322198 GGAATTCTTTGATCAAGGCAGCAA 60.322 41.667 12.50 2.65 32.64 3.91
3944 4347 3.194116 GGAATTCTTTGATCAAGGCAGCA 59.806 43.478 12.50 0.00 32.64 4.41
3945 4348 3.194116 TGGAATTCTTTGATCAAGGCAGC 59.806 43.478 12.50 2.62 32.64 5.25
3946 4349 5.184479 TCTTGGAATTCTTTGATCAAGGCAG 59.816 40.000 12.50 6.03 34.23 4.85
3947 4350 5.078949 TCTTGGAATTCTTTGATCAAGGCA 58.921 37.500 12.50 2.34 34.23 4.75
3948 4351 5.649782 TCTTGGAATTCTTTGATCAAGGC 57.350 39.130 12.50 0.00 34.23 4.35
3949 4352 7.033791 CACATCTTGGAATTCTTTGATCAAGG 58.966 38.462 11.18 11.18 34.23 3.61
3950 4353 7.600065 ACACATCTTGGAATTCTTTGATCAAG 58.400 34.615 8.41 9.10 34.61 3.02
3951 4354 7.528996 ACACATCTTGGAATTCTTTGATCAA 57.471 32.000 3.38 3.38 0.00 2.57
3952 4355 7.528996 AACACATCTTGGAATTCTTTGATCA 57.471 32.000 5.23 0.00 0.00 2.92
3953 4356 6.744537 CGAACACATCTTGGAATTCTTTGATC 59.255 38.462 5.23 0.00 0.00 2.92
3954 4357 6.349611 CCGAACACATCTTGGAATTCTTTGAT 60.350 38.462 5.23 3.96 0.00 2.57
3955 4358 5.048782 CCGAACACATCTTGGAATTCTTTGA 60.049 40.000 5.23 1.72 0.00 2.69
3956 4359 5.048782 TCCGAACACATCTTGGAATTCTTTG 60.049 40.000 5.23 0.00 0.00 2.77
3957 4360 5.070001 TCCGAACACATCTTGGAATTCTTT 58.930 37.500 5.23 0.00 0.00 2.52
3958 4361 4.651778 TCCGAACACATCTTGGAATTCTT 58.348 39.130 5.23 0.00 0.00 2.52
3959 4362 4.020218 TCTCCGAACACATCTTGGAATTCT 60.020 41.667 5.23 0.00 0.00 2.40
3960 4363 4.253685 TCTCCGAACACATCTTGGAATTC 58.746 43.478 0.00 0.00 0.00 2.17
3961 4364 4.286297 TCTCCGAACACATCTTGGAATT 57.714 40.909 0.00 0.00 0.00 2.17
3962 4365 3.981071 TCTCCGAACACATCTTGGAAT 57.019 42.857 0.00 0.00 0.00 3.01
3963 4366 3.399330 GTTCTCCGAACACATCTTGGAA 58.601 45.455 2.10 0.00 0.00 3.53
3964 4367 2.289444 GGTTCTCCGAACACATCTTGGA 60.289 50.000 8.76 0.00 0.00 3.53
3965 4368 2.076863 GGTTCTCCGAACACATCTTGG 58.923 52.381 8.76 0.00 0.00 3.61
3966 4369 2.480419 GTGGTTCTCCGAACACATCTTG 59.520 50.000 8.76 0.00 36.30 3.02
3967 4370 2.104111 TGTGGTTCTCCGAACACATCTT 59.896 45.455 8.76 0.00 38.76 2.40
3968 4371 1.691976 TGTGGTTCTCCGAACACATCT 59.308 47.619 8.76 0.00 38.76 2.90
3969 4372 2.163818 TGTGGTTCTCCGAACACATC 57.836 50.000 8.76 0.00 38.76 3.06
3970 4373 2.494059 CTTGTGGTTCTCCGAACACAT 58.506 47.619 8.76 0.00 42.66 3.21
3971 4374 1.474320 CCTTGTGGTTCTCCGAACACA 60.474 52.381 8.76 8.00 41.59 3.72
3972 4375 1.202604 TCCTTGTGGTTCTCCGAACAC 60.203 52.381 8.76 5.94 36.30 3.32
3973 4376 1.124780 TCCTTGTGGTTCTCCGAACA 58.875 50.000 8.76 0.00 36.30 3.18
3974 4377 2.474410 ATCCTTGTGGTTCTCCGAAC 57.526 50.000 0.00 0.00 36.30 3.95
3975 4378 2.235402 GGTATCCTTGTGGTTCTCCGAA 59.765 50.000 0.00 0.00 36.30 4.30
3976 4379 1.829222 GGTATCCTTGTGGTTCTCCGA 59.171 52.381 0.00 0.00 36.30 4.55
3977 4380 1.553248 TGGTATCCTTGTGGTTCTCCG 59.447 52.381 0.00 0.00 36.30 4.63
3978 4381 2.572104 AGTGGTATCCTTGTGGTTCTCC 59.428 50.000 0.00 0.00 34.23 3.71
3979 4382 3.983044 AGTGGTATCCTTGTGGTTCTC 57.017 47.619 0.00 0.00 34.23 2.87
3980 4383 5.745227 CATTAGTGGTATCCTTGTGGTTCT 58.255 41.667 0.00 0.00 34.23 3.01
3981 4384 4.335594 GCATTAGTGGTATCCTTGTGGTTC 59.664 45.833 0.00 0.00 34.23 3.62
3982 4385 4.270008 GCATTAGTGGTATCCTTGTGGTT 58.730 43.478 0.00 0.00 34.23 3.67
3983 4386 3.371595 GGCATTAGTGGTATCCTTGTGGT 60.372 47.826 0.00 0.00 34.23 4.16
3984 4387 3.214328 GGCATTAGTGGTATCCTTGTGG 58.786 50.000 0.00 0.00 0.00 4.17
3985 4388 3.879295 CTGGCATTAGTGGTATCCTTGTG 59.121 47.826 0.00 0.00 0.00 3.33
3986 4389 3.780294 TCTGGCATTAGTGGTATCCTTGT 59.220 43.478 0.00 0.00 0.00 3.16
4010 4413 1.281899 GGCTGATGTTCACTAGTCGC 58.718 55.000 0.00 0.00 0.00 5.19
4011 4414 1.204704 TGGGCTGATGTTCACTAGTCG 59.795 52.381 0.00 0.00 0.00 4.18
4012 4415 3.550437 ATGGGCTGATGTTCACTAGTC 57.450 47.619 0.00 0.00 0.00 2.59
4013 4416 3.774766 TGTATGGGCTGATGTTCACTAGT 59.225 43.478 0.00 0.00 0.00 2.57
4014 4417 4.375272 CTGTATGGGCTGATGTTCACTAG 58.625 47.826 0.00 0.00 0.00 2.57
4015 4418 3.134623 CCTGTATGGGCTGATGTTCACTA 59.865 47.826 0.00 0.00 0.00 2.74
4016 4419 2.092753 CCTGTATGGGCTGATGTTCACT 60.093 50.000 0.00 0.00 0.00 3.41
4017 4420 2.292267 CCTGTATGGGCTGATGTTCAC 58.708 52.381 0.00 0.00 0.00 3.18
4018 4421 2.715749 CCTGTATGGGCTGATGTTCA 57.284 50.000 0.00 0.00 0.00 3.18
4047 4450 2.910688 TCTGTCTCACCCTTGTGTTC 57.089 50.000 0.00 0.00 43.26 3.18
4054 4457 2.173569 ACTTGCTTTTCTGTCTCACCCT 59.826 45.455 0.00 0.00 0.00 4.34
4056 4459 3.206150 TGACTTGCTTTTCTGTCTCACC 58.794 45.455 0.00 0.00 0.00 4.02
4086 4489 3.566322 CGTTGAATCACCCCTGTTTGTAA 59.434 43.478 0.00 0.00 0.00 2.41
4095 4498 1.653151 GAGCTACGTTGAATCACCCC 58.347 55.000 0.00 0.00 0.00 4.95


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

AutoCloner maintained by Alex Coulton.