Multiple sequence alignment - TraesCS2D01G245500

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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 TraesCS2D01G245500 chr2D 100.000 8852 0 0 1 8852 280657061 280648210 0.000000e+00 16347.0
1 TraesCS2D01G245500 chr2D 96.000 50 2 0 8438 8487 280648563 280648514 2.050000e-11 82.4
2 TraesCS2D01G245500 chr2D 96.000 50 2 0 8499 8548 280648624 280648575 2.050000e-11 82.4
3 TraesCS2D01G245500 chr2B 96.356 4555 123 17 3809 8349 326677528 326682053 0.000000e+00 7452.0
4 TraesCS2D01G245500 chr2B 95.085 2177 60 21 852 3005 326675393 326677545 0.000000e+00 3384.0
5 TraesCS2D01G245500 chr2B 89.014 355 33 4 8499 8852 326682103 326682452 1.360000e-117 435.0
6 TraesCS2D01G245500 chr2B 95.604 91 4 0 8395 8485 326682060 326682150 7.160000e-31 147.0
7 TraesCS2D01G245500 chr2B 100.000 48 0 0 7633 7680 104943309 104943356 1.220000e-13 89.8
8 TraesCS2D01G245500 chr2A 96.611 2921 65 12 428 3339 334598792 334595897 0.000000e+00 4815.0
9 TraesCS2D01G245500 chr2A 98.427 1653 25 1 5922 7573 334592254 334590602 0.000000e+00 2907.0
10 TraesCS2D01G245500 chr2A 97.523 1292 20 7 3749 5039 334594289 334593009 0.000000e+00 2198.0
11 TraesCS2D01G245500 chr2A 97.759 714 13 2 5080 5790 334593006 334592293 0.000000e+00 1227.0
12 TraesCS2D01G245500 chr2A 91.954 609 23 9 8244 8852 334590602 334590020 0.000000e+00 830.0
13 TraesCS2D01G245500 chr2A 99.022 409 3 1 3346 3753 334594723 334594315 0.000000e+00 732.0
14 TraesCS2D01G245500 chr2A 98.077 52 1 0 5918 5969 334592301 334592250 3.400000e-14 91.6
15 TraesCS2D01G245500 chr4D 93.354 632 39 3 3119 3749 465059094 465058465 0.000000e+00 931.0
16 TraesCS2D01G245500 chr4D 91.453 117 6 4 3005 3117 465063397 465063281 3.310000e-34 158.0
17 TraesCS2D01G245500 chr4D 98.039 51 1 0 3747 3797 465058437 465058387 1.220000e-13 89.8
18 TraesCS2D01G245500 chr7B 88.841 699 67 8 1 689 749293828 749294525 0.000000e+00 848.0
19 TraesCS2D01G245500 chr3B 88.588 701 70 7 1 692 784154504 784153805 0.000000e+00 843.0
20 TraesCS2D01G245500 chr3B 87.714 700 72 10 1 689 207054490 207055186 0.000000e+00 804.0
21 TraesCS2D01G245500 chr3B 91.045 67 5 1 7632 7698 172008078 172008013 1.220000e-13 89.8
22 TraesCS2D01G245500 chr1B 88.126 699 71 9 1 689 205499950 205500646 0.000000e+00 821.0
23 TraesCS2D01G245500 chr3A 87.214 743 62 18 3013 3749 684591185 684591900 0.000000e+00 815.0
24 TraesCS2D01G245500 chr3A 87.536 698 77 8 1 689 746839064 746838368 0.000000e+00 798.0
25 TraesCS2D01G245500 chr3A 87.536 698 77 8 1 689 748076349 748075653 0.000000e+00 798.0
26 TraesCS2D01G245500 chr3A 95.161 62 3 0 3747 3808 684591928 684591989 2.030000e-16 99.0
27 TraesCS2D01G245500 chr3A 84.810 79 8 3 7630 7707 149572363 149572288 9.530000e-10 76.8
28 TraesCS2D01G245500 chr3A 86.957 69 8 1 4007 4074 483152034 483152102 9.530000e-10 76.8
29 TraesCS2D01G245500 chr4A 86.963 698 81 8 1 689 490152889 490153585 0.000000e+00 776.0
30 TraesCS2D01G245500 chr1A 86.963 698 81 8 1 689 592540285 592539589 0.000000e+00 776.0
31 TraesCS2D01G245500 chr1A 90.769 65 1 1 7634 7698 53412016 53412075 2.050000e-11 82.4
32 TraesCS2D01G245500 chr6B 85.673 698 87 8 1 689 71220709 71221402 0.000000e+00 723.0
33 TraesCS2D01G245500 chr6B 84.768 302 41 3 3444 3745 135870568 135870272 1.870000e-76 298.0
34 TraesCS2D01G245500 chr6B 77.698 139 24 5 3929 4061 615992803 615992666 2.650000e-10 78.7
35 TraesCS2D01G245500 chr3D 88.571 70 5 3 4007 4074 362727871 362727939 2.050000e-11 82.4
36 TraesCS2D01G245500 chr3D 87.324 71 5 1 7632 7698 525535676 525535606 2.650000e-10 78.7
37 TraesCS2D01G245500 chr6D 88.889 63 7 0 3999 4061 409775715 409775653 2.650000e-10 78.7
38 TraesCS2D01G245500 chr5A 86.076 79 4 6 7631 7708 342045715 342045643 2.650000e-10 78.7
39 TraesCS2D01G245500 chr6A 84.615 78 10 2 3999 4074 555245226 555245149 9.530000e-10 76.8
40 TraesCS2D01G245500 chr1D 89.231 65 2 2 7634 7698 53403107 53403166 9.530000e-10 76.8
41 TraesCS2D01G245500 chr1D 84.000 75 11 1 4007 4080 346018924 346018850 4.430000e-08 71.3
42 TraesCS2D01G245500 chr5D 85.000 80 5 3 4007 4079 509887005 509886926 3.430000e-09 75.0
43 TraesCS2D01G245500 chr7A 83.544 79 9 3 7630 7707 388489311 388489386 4.430000e-08 71.3


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G245500 chr2D 280648210 280657061 8851 True 16347.000000 16347 100.000000 1 8852 1 chr2D.!!$R1 8851
1 TraesCS2D01G245500 chr2B 326675393 326682452 7059 False 2854.500000 7452 94.014750 852 8852 4 chr2B.!!$F2 8000
2 TraesCS2D01G245500 chr2A 334590020 334598792 8772 True 1828.657143 4815 97.053286 428 8852 7 chr2A.!!$R1 8424
3 TraesCS2D01G245500 chr4D 465058387 465059094 707 True 510.400000 931 95.696500 3119 3797 2 chr4D.!!$R2 678
4 TraesCS2D01G245500 chr7B 749293828 749294525 697 False 848.000000 848 88.841000 1 689 1 chr7B.!!$F1 688
5 TraesCS2D01G245500 chr3B 784153805 784154504 699 True 843.000000 843 88.588000 1 692 1 chr3B.!!$R2 691
6 TraesCS2D01G245500 chr3B 207054490 207055186 696 False 804.000000 804 87.714000 1 689 1 chr3B.!!$F1 688
7 TraesCS2D01G245500 chr1B 205499950 205500646 696 False 821.000000 821 88.126000 1 689 1 chr1B.!!$F1 688
8 TraesCS2D01G245500 chr3A 746838368 746839064 696 True 798.000000 798 87.536000 1 689 1 chr3A.!!$R2 688
9 TraesCS2D01G245500 chr3A 748075653 748076349 696 True 798.000000 798 87.536000 1 689 1 chr3A.!!$R3 688
10 TraesCS2D01G245500 chr3A 684591185 684591989 804 False 457.000000 815 91.187500 3013 3808 2 chr3A.!!$F2 795
11 TraesCS2D01G245500 chr4A 490152889 490153585 696 False 776.000000 776 86.963000 1 689 1 chr4A.!!$F1 688
12 TraesCS2D01G245500 chr1A 592539589 592540285 696 True 776.000000 776 86.963000 1 689 1 chr1A.!!$R1 688
13 TraesCS2D01G245500 chr6B 71220709 71221402 693 False 723.000000 723 85.673000 1 689 1 chr6B.!!$F1 688


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
182 187 0.251386 AGTTCAGCAGTCTCCTCCGA 60.251 55.000 0.00 0.0 0.00 4.55 F
570 578 0.260230 TGGAAACCCAGTCTGCCAAA 59.740 50.000 0.00 0.0 0.00 3.28 F
1326 1339 1.479021 GGTGCGGAGGTAGAGGTAGAT 60.479 57.143 0.00 0.0 0.00 1.98 F
1801 1814 0.458025 GGAGCTTGACCGGTTCTACG 60.458 60.000 9.42 0.0 0.00 3.51 F
2880 2912 1.005037 CAACCGACAGTGGCAGCTA 60.005 57.895 0.00 0.0 0.00 3.32 F
3745 4953 0.610232 GGTGCAAAGCTCCAGGACAT 60.610 55.000 5.31 0.0 41.27 3.06 F
4663 5910 5.339008 ACACGAGCCTGAATGATAGTTTA 57.661 39.130 0.00 0.0 0.00 2.01 F
4919 6174 1.472990 ACTTTTGCGCGTAACTTTGC 58.527 45.000 9.79 0.0 0.00 3.68 F
5876 7133 4.432712 ACAGTGAAAGTCCATTTTTGCAC 58.567 39.130 0.00 0.0 0.00 4.57 F
6781 8042 2.595750 TTGTACTGTTTCCCCATGGG 57.404 50.000 25.30 25.3 46.11 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1326 1339 1.813753 GGCATCGCCTAAACGCTCA 60.814 57.895 0.00 0.0 46.69 4.26 R
1548 1561 2.923035 ACCCTGACCTCGGTGTGG 60.923 66.667 0.00 0.0 0.00 4.17 R
2844 2876 1.299976 GTCACGAAATCCTGGGGCT 59.700 57.895 0.00 0.0 0.00 5.19 R
2987 3019 1.404315 GGTTCACGATCTGTCACCCTC 60.404 57.143 0.00 0.0 0.00 4.30 R
4663 5910 0.111061 TGCTTCCTCTGCACATGGTT 59.889 50.000 0.00 0.0 35.31 3.67 R
4756 6003 4.134563 TGACTTTCCTCTTAAGCAACCAC 58.865 43.478 0.00 0.0 0.00 4.16 R
5865 7122 5.355596 TCACAAGTTTAGGTGCAAAAATGG 58.644 37.500 0.00 0.0 35.04 3.16 R
6699 7960 6.865834 AAATGAGATACTCACAGTTCTCCT 57.134 37.500 3.54 0.0 43.63 3.69 R
7156 8417 0.035881 CAAGTTGCTCAGGCTCTCCA 59.964 55.000 0.00 0.0 39.59 3.86 R
7895 9158 0.957362 AAGAGCCTTGAAGCAGCAAC 59.043 50.000 0.00 0.0 34.23 4.17 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
20 25 1.616865 CTTCCCTACTTGACGTGGACA 59.383 52.381 0.00 0.00 0.00 4.02
74 79 4.837896 AAGATCGAGCGAGATTGTATGA 57.162 40.909 0.00 0.00 0.00 2.15
99 104 9.988815 GATGAACAGACAGTATATAGTCCAAAT 57.011 33.333 4.47 0.00 35.38 2.32
113 118 1.361668 CCAAATCGAGTGTGAGGCCG 61.362 60.000 0.00 0.00 0.00 6.13
125 130 3.190535 GTGTGAGGCCGATACACAAAATT 59.809 43.478 25.38 0.00 44.21 1.82
182 187 0.251386 AGTTCAGCAGTCTCCTCCGA 60.251 55.000 0.00 0.00 0.00 4.55
218 224 3.188460 ACATTTTCTTCGTCCAATGACCG 59.812 43.478 0.00 0.00 38.32 4.79
229 235 1.086696 CAATGACCGTGTCCATCCAC 58.913 55.000 2.23 0.00 0.00 4.02
253 259 5.293324 CGAGGCAACACACTTTAGCATATTA 59.707 40.000 0.00 0.00 41.41 0.98
256 262 6.828273 AGGCAACACACTTTAGCATATTATGA 59.172 34.615 7.87 0.00 41.41 2.15
281 287 9.696917 GAAATTGAAAATAGAGTCCACAACATT 57.303 29.630 0.00 0.00 0.00 2.71
286 292 7.658167 TGAAAATAGAGTCCACAACATTTACGA 59.342 33.333 0.00 0.00 0.00 3.43
290 296 3.343617 AGTCCACAACATTTACGATGGG 58.656 45.455 0.00 0.00 0.00 4.00
305 311 2.227757 TGGGCGTCCAGGAATCCAA 61.228 57.895 3.51 0.00 38.32 3.53
307 313 0.472471 GGGCGTCCAGGAATCCAATA 59.528 55.000 0.00 0.00 0.00 1.90
347 353 3.198417 CCTTTTGGCCATTAGCAATTCCT 59.802 43.478 6.09 0.00 46.50 3.36
355 361 3.885297 CCATTAGCAATTCCTCACCGAAT 59.115 43.478 0.00 0.00 33.84 3.34
365 371 1.656652 CTCACCGAATACCAGCCTTG 58.343 55.000 0.00 0.00 0.00 3.61
468 476 8.743714 GTGGAGAAAATAATGTCCTTTGAGAAT 58.256 33.333 0.00 0.00 0.00 2.40
528 536 4.943705 CCAACATTGTCTACCAAGCATAGT 59.056 41.667 0.00 0.00 36.25 2.12
564 572 5.011023 GTGAAAAATCATGGAAACCCAGTCT 59.989 40.000 0.00 0.00 37.09 3.24
565 573 5.010922 TGAAAAATCATGGAAACCCAGTCTG 59.989 40.000 0.00 0.00 37.09 3.51
570 578 0.260230 TGGAAACCCAGTCTGCCAAA 59.740 50.000 0.00 0.00 0.00 3.28
604 613 2.088423 GGTAACCATTCCATGAACGCA 58.912 47.619 0.00 0.00 0.00 5.24
630 640 6.937465 GGTGAAGTTTCCTCTTACATCTTCTT 59.063 38.462 0.00 0.00 33.41 2.52
639 649 6.903534 TCCTCTTACATCTTCTTTATCCCACT 59.096 38.462 0.00 0.00 0.00 4.00
704 714 3.163467 GGGTATACGCAGGGAGTTCTAT 58.837 50.000 14.60 0.00 0.00 1.98
1252 1265 2.198287 GGCGACGCCCTAGTGGATA 61.198 63.158 28.74 0.00 44.06 2.59
1326 1339 1.479021 GGTGCGGAGGTAGAGGTAGAT 60.479 57.143 0.00 0.00 0.00 1.98
1548 1561 5.824624 TGATAAAGCAGGAAATGGAGATGAC 59.175 40.000 0.00 0.00 0.00 3.06
1801 1814 0.458025 GGAGCTTGACCGGTTCTACG 60.458 60.000 9.42 0.00 0.00 3.51
2157 2173 7.101652 TGTGGTTTGCTTACTTAATGAACAA 57.898 32.000 0.00 0.00 0.00 2.83
2677 2709 1.227263 GTGCTCGTCATGCCGGTAT 60.227 57.895 1.90 0.00 0.00 2.73
2701 2733 1.137086 GCCACCGAGATCAGCTTCTTA 59.863 52.381 0.00 0.00 0.00 2.10
2725 2757 2.202783 GCACAAATGGCGCCCATC 60.203 61.111 26.77 0.00 44.40 3.51
2844 2876 2.192861 CCTGAAAACTGCACCGCCA 61.193 57.895 0.00 0.00 0.00 5.69
2880 2912 1.005037 CAACCGACAGTGGCAGCTA 60.005 57.895 0.00 0.00 0.00 3.32
2987 3019 1.202533 AGGAGACACAAGTTGGTCACG 60.203 52.381 19.93 3.21 36.50 4.35
2989 3021 2.128035 GAGACACAAGTTGGTCACGAG 58.872 52.381 19.93 0.00 36.50 4.18
3232 3270 4.407621 TCGGAATAAGATGGTCCTGCTTTA 59.592 41.667 2.76 0.00 0.00 1.85
3292 3330 2.084930 AGTTGGCCCCCTGTGTCTT 61.085 57.895 0.00 0.00 0.00 3.01
3295 3333 3.971702 GGCCCCCTGTGTCTTGCT 61.972 66.667 0.00 0.00 0.00 3.91
3552 4760 1.402984 GCAGACCGTTCAATCGACTCT 60.403 52.381 0.00 0.00 0.00 3.24
3649 4857 2.722487 GCGACGATGGAGTCCGAT 59.278 61.111 4.30 0.00 37.85 4.18
3745 4953 0.610232 GGTGCAAAGCTCCAGGACAT 60.610 55.000 5.31 0.00 41.27 3.06
3790 5029 9.469807 GTTATTTGTTGAATGAACATGTGGTAA 57.530 29.630 0.00 0.00 44.23 2.85
3800 5039 5.491070 TGAACATGTGGTAATTCCTCTCAG 58.509 41.667 0.00 0.00 37.07 3.35
4072 5318 8.783660 ATAGGACCTCTGATACATTTTACTCA 57.216 34.615 0.00 0.00 0.00 3.41
4073 5319 7.682787 AGGACCTCTGATACATTTTACTCAT 57.317 36.000 0.00 0.00 0.00 2.90
4074 5320 7.731054 AGGACCTCTGATACATTTTACTCATC 58.269 38.462 0.00 0.00 0.00 2.92
4075 5321 7.566879 AGGACCTCTGATACATTTTACTCATCT 59.433 37.037 0.00 0.00 0.00 2.90
4076 5322 8.207545 GGACCTCTGATACATTTTACTCATCTT 58.792 37.037 0.00 0.00 0.00 2.40
4077 5323 9.606631 GACCTCTGATACATTTTACTCATCTTT 57.393 33.333 0.00 0.00 0.00 2.52
4591 5837 7.035840 ACCTTATTGAGCAAATCAGCATAAG 57.964 36.000 0.00 0.00 39.68 1.73
4663 5910 5.339008 ACACGAGCCTGAATGATAGTTTA 57.661 39.130 0.00 0.00 0.00 2.01
4756 6003 4.471373 TGCATACACAATTAGCAAACACG 58.529 39.130 0.00 0.00 31.42 4.49
4919 6174 1.472990 ACTTTTGCGCGTAACTTTGC 58.527 45.000 9.79 0.00 0.00 3.68
5133 6388 5.048991 GGAGTTGGAACGTAATTGACATGTT 60.049 40.000 0.00 0.00 0.00 2.71
5876 7133 4.432712 ACAGTGAAAGTCCATTTTTGCAC 58.567 39.130 0.00 0.00 0.00 4.57
5882 7139 6.019075 GTGAAAGTCCATTTTTGCACCTAAAC 60.019 38.462 0.00 0.00 0.00 2.01
5884 7141 5.869649 AGTCCATTTTTGCACCTAAACTT 57.130 34.783 0.00 0.00 0.00 2.66
6256 7515 6.950842 TCTGGACATCATTTGTTAGACATCT 58.049 36.000 0.00 0.00 39.18 2.90
6699 7960 6.889177 TGCTGATTGGGTGAAGATAAATGTTA 59.111 34.615 0.00 0.00 0.00 2.41
6781 8042 2.595750 TTGTACTGTTTCCCCATGGG 57.404 50.000 25.30 25.30 46.11 4.00
7135 8396 3.452627 AGGTACATGTTCAGTCAGATCCC 59.547 47.826 2.30 0.00 0.00 3.85
7156 8417 1.473434 GCTGGCCGCTTGATAGTTACT 60.473 52.381 11.61 0.00 35.14 2.24
7174 8435 0.324285 CTGGAGAGCCTGAGCAACTT 59.676 55.000 0.00 0.00 43.56 2.66
7335 8596 1.280421 GATCCTCACCAAACCTCAGCT 59.720 52.381 0.00 0.00 0.00 4.24
7518 8780 9.893305 TCTAAGAAAGAACGGAAAATGAATTTC 57.107 29.630 0.00 0.00 45.55 2.17
7610 8872 4.632153 AGCACTAGATTGTTTCACGAGTT 58.368 39.130 0.00 0.00 0.00 3.01
7622 8884 7.151999 TGTTTCACGAGTTATAAATGGCAAT 57.848 32.000 0.00 0.00 0.00 3.56
7703 8965 1.309006 GGGACGGAGGGAGGAGTAA 59.691 63.158 0.00 0.00 0.00 2.24
7704 8966 0.105607 GGGACGGAGGGAGGAGTAAT 60.106 60.000 0.00 0.00 0.00 1.89
7705 8967 1.146566 GGGACGGAGGGAGGAGTAATA 59.853 57.143 0.00 0.00 0.00 0.98
7740 9002 0.105709 TCTGGTCTGGTCACAGTGGA 60.106 55.000 0.00 0.00 45.14 4.02
7795 9058 5.930135 ACACAGAACACTTATCTTCCAACT 58.070 37.500 0.00 0.00 0.00 3.16
7796 9059 5.760253 ACACAGAACACTTATCTTCCAACTG 59.240 40.000 0.00 0.00 0.00 3.16
7797 9060 4.757149 ACAGAACACTTATCTTCCAACTGC 59.243 41.667 0.00 0.00 0.00 4.40
7798 9061 4.154918 CAGAACACTTATCTTCCAACTGCC 59.845 45.833 0.00 0.00 0.00 4.85
7799 9062 3.788227 ACACTTATCTTCCAACTGCCA 57.212 42.857 0.00 0.00 0.00 4.92
7800 9063 3.412386 ACACTTATCTTCCAACTGCCAC 58.588 45.455 0.00 0.00 0.00 5.01
7801 9064 3.181445 ACACTTATCTTCCAACTGCCACA 60.181 43.478 0.00 0.00 0.00 4.17
7802 9065 3.189287 CACTTATCTTCCAACTGCCACAC 59.811 47.826 0.00 0.00 0.00 3.82
7803 9066 3.181445 ACTTATCTTCCAACTGCCACACA 60.181 43.478 0.00 0.00 0.00 3.72
7804 9067 1.609208 ATCTTCCAACTGCCACACAC 58.391 50.000 0.00 0.00 0.00 3.82
7805 9068 0.465460 TCTTCCAACTGCCACACACC 60.465 55.000 0.00 0.00 0.00 4.16
7806 9069 0.466189 CTTCCAACTGCCACACACCT 60.466 55.000 0.00 0.00 0.00 4.00
7807 9070 0.033601 TTCCAACTGCCACACACCTT 60.034 50.000 0.00 0.00 0.00 3.50
7808 9071 0.751277 TCCAACTGCCACACACCTTG 60.751 55.000 0.00 0.00 0.00 3.61
7809 9072 0.751277 CCAACTGCCACACACCTTGA 60.751 55.000 0.00 0.00 0.00 3.02
7810 9073 0.381801 CAACTGCCACACACCTTGAC 59.618 55.000 0.00 0.00 0.00 3.18
7811 9074 0.255890 AACTGCCACACACCTTGACT 59.744 50.000 0.00 0.00 0.00 3.41
7812 9075 0.255890 ACTGCCACACACCTTGACTT 59.744 50.000 0.00 0.00 0.00 3.01
7813 9076 1.488812 ACTGCCACACACCTTGACTTA 59.511 47.619 0.00 0.00 0.00 2.24
7814 9077 1.873591 CTGCCACACACCTTGACTTAC 59.126 52.381 0.00 0.00 0.00 2.34
7815 9078 1.235724 GCCACACACCTTGACTTACC 58.764 55.000 0.00 0.00 0.00 2.85
7895 9158 4.559251 CCTGATCTTTGTTCGTCTAGTTCG 59.441 45.833 0.00 0.00 0.00 3.95
7918 9181 1.881498 GCTGCTTCAAGGCTCTTCAGT 60.881 52.381 0.00 0.00 0.00 3.41
7942 9205 4.935205 GGTGCTGTATGTTCTGTGTATTGA 59.065 41.667 0.00 0.00 0.00 2.57
7947 9210 9.394767 TGCTGTATGTTCTGTGTATTGATTAAT 57.605 29.630 0.00 0.00 0.00 1.40
8007 9270 4.449743 TGTGACATTTAGCGTAAGTTCCAC 59.550 41.667 0.00 0.00 41.68 4.02
8017 9280 1.351350 GTAAGTTCCACCCTCCAAGCT 59.649 52.381 0.00 0.00 0.00 3.74
8071 9334 5.184287 TCATGGTTTATTCGTTCCCTTTTCC 59.816 40.000 0.00 0.00 0.00 3.13
8090 9353 4.764050 TCCGTTTAGCCATCAAAGGATA 57.236 40.909 0.00 0.00 30.87 2.59
8092 9355 5.690865 TCCGTTTAGCCATCAAAGGATAAT 58.309 37.500 0.00 0.00 39.10 1.28
8146 9409 9.823647 CCTAATACTTGAGTTTGTCATCATACT 57.176 33.333 0.00 0.00 38.25 2.12
8151 9414 4.503910 TGAGTTTGTCATCATACTTCCGG 58.496 43.478 0.00 0.00 36.34 5.14
8221 9484 2.818130 ACAAAACCATTGCATTCGCT 57.182 40.000 0.00 0.00 39.64 4.93
8234 9497 5.369685 TGCATTCGCTTGACTGAAAATAA 57.630 34.783 0.00 0.00 39.64 1.40
8259 9522 5.836358 TGGTTCTTTAGGCCTTGTACAATTT 59.164 36.000 12.58 0.00 0.00 1.82
8270 9533 6.090783 GCCTTGTACAATTTAAGGTGCTTAC 58.909 40.000 9.13 0.00 42.30 2.34
8331 9594 2.582052 ACGCATTGGTCCTTCAGAAAA 58.418 42.857 0.00 0.00 0.00 2.29
8332 9595 2.955660 ACGCATTGGTCCTTCAGAAAAA 59.044 40.909 0.00 0.00 0.00 1.94
8333 9596 3.243401 ACGCATTGGTCCTTCAGAAAAAC 60.243 43.478 0.00 0.00 0.00 2.43
8334 9597 3.653344 GCATTGGTCCTTCAGAAAAACC 58.347 45.455 6.65 6.65 0.00 3.27
8335 9598 3.554960 GCATTGGTCCTTCAGAAAAACCC 60.555 47.826 9.98 0.00 0.00 4.11
8336 9599 3.390175 TTGGTCCTTCAGAAAAACCCA 57.610 42.857 9.98 0.36 0.00 4.51
8337 9600 2.944129 TGGTCCTTCAGAAAAACCCAG 58.056 47.619 9.98 0.00 0.00 4.45
8338 9601 2.243736 TGGTCCTTCAGAAAAACCCAGT 59.756 45.455 9.98 0.00 0.00 4.00
8339 9602 3.296854 GGTCCTTCAGAAAAACCCAGTT 58.703 45.455 3.15 0.00 0.00 3.16
8340 9603 3.704566 GGTCCTTCAGAAAAACCCAGTTT 59.295 43.478 3.15 0.00 37.34 2.66
8341 9604 4.202121 GGTCCTTCAGAAAAACCCAGTTTC 60.202 45.833 3.15 0.00 34.43 2.78
8342 9605 4.645136 GTCCTTCAGAAAAACCCAGTTTCT 59.355 41.667 0.00 0.00 44.30 2.52
8343 9606 5.127194 GTCCTTCAGAAAAACCCAGTTTCTT 59.873 40.000 0.00 0.00 41.47 2.52
8344 9607 5.719563 TCCTTCAGAAAAACCCAGTTTCTTT 59.280 36.000 0.00 0.00 41.47 2.52
8345 9608 6.212589 TCCTTCAGAAAAACCCAGTTTCTTTT 59.787 34.615 0.00 0.00 41.47 2.27
8346 9609 6.878923 CCTTCAGAAAAACCCAGTTTCTTTTT 59.121 34.615 0.00 0.00 41.47 1.94
8347 9610 7.064609 CCTTCAGAAAAACCCAGTTTCTTTTTC 59.935 37.037 6.70 6.70 41.47 2.29
8349 9612 7.676004 TCAGAAAAACCCAGTTTCTTTTTCTT 58.324 30.769 12.46 0.39 45.49 2.52
8350 9613 8.154203 TCAGAAAAACCCAGTTTCTTTTTCTTT 58.846 29.630 12.46 0.00 45.49 2.52
8351 9614 8.783093 CAGAAAAACCCAGTTTCTTTTTCTTTT 58.217 29.630 12.46 0.00 45.49 2.27
8352 9615 9.349713 AGAAAAACCCAGTTTCTTTTTCTTTTT 57.650 25.926 10.23 0.00 45.49 1.94
8408 9678 1.583054 CTTAGCATTGTACGAGGCCC 58.417 55.000 15.94 0.00 0.00 5.80
8412 9682 2.686106 ATTGTACGAGGCCCGGGT 60.686 61.111 24.63 1.57 43.93 5.28
8510 9780 2.490217 CTACAGGCCGAGGACACG 59.510 66.667 0.00 0.00 0.00 4.49
8658 9928 1.677052 GTAACCCCGAAGTTGTTGCAA 59.323 47.619 0.00 0.00 0.00 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.603842 CAGTATGGCTGGCTGTCCA 59.396 57.895 2.00 9.24 41.42 4.02
26 31 8.048534 AGATTTCTTTTCATCACACAGTATGG 57.951 34.615 0.00 0.00 43.62 2.74
74 79 9.988815 GATTTGGACTATATACTGTCTGTTCAT 57.011 33.333 6.83 0.00 34.01 2.57
99 104 0.678684 TGTATCGGCCTCACACTCGA 60.679 55.000 0.00 0.00 36.07 4.04
113 118 6.261826 CCATGGAGGAGAGAATTTTGTGTATC 59.738 42.308 5.56 0.00 41.22 2.24
125 130 0.262876 TAGCAGCCATGGAGGAGAGA 59.737 55.000 18.40 0.00 41.22 3.10
218 224 1.003839 TTGCCTCGTGGATGGACAC 60.004 57.895 7.92 0.00 37.99 3.67
229 235 1.225855 TGCTAAAGTGTGTTGCCTCG 58.774 50.000 0.00 0.00 0.00 4.63
253 259 8.859090 TGTTGTGGACTCTATTTTCAATTTCAT 58.141 29.630 0.00 0.00 0.00 2.57
262 268 7.972832 TCGTAAATGTTGTGGACTCTATTTT 57.027 32.000 0.00 0.00 0.00 1.82
272 278 1.202132 CGCCCATCGTAAATGTTGTGG 60.202 52.381 0.00 0.00 0.00 4.17
286 292 1.570857 TTGGATTCCTGGACGCCCAT 61.571 55.000 3.95 0.00 42.59 4.00
290 296 5.003804 ACATATTATTGGATTCCTGGACGC 58.996 41.667 3.95 0.00 0.00 5.19
307 313 9.382275 GCCAAAAGGTTAAAATCATGACATATT 57.618 29.630 0.00 0.00 0.00 1.28
347 353 1.066430 GTCAAGGCTGGTATTCGGTGA 60.066 52.381 0.00 0.00 0.00 4.02
355 361 1.276421 GAGAGCTTGTCAAGGCTGGTA 59.724 52.381 14.40 0.00 39.05 3.25
365 371 0.747255 TCTATGGCCGAGAGCTTGTC 59.253 55.000 3.06 0.00 43.05 3.18
424 430 2.126467 CACTGCAATTTTTGGGACACG 58.874 47.619 0.00 0.00 39.29 4.49
425 431 2.102252 TCCACTGCAATTTTTGGGACAC 59.898 45.455 0.00 0.00 39.29 3.67
426 432 2.364970 CTCCACTGCAATTTTTGGGACA 59.635 45.455 0.00 0.00 0.00 4.02
468 476 4.067896 GCCAGATTCTCTTTGTGTTCAGA 58.932 43.478 0.00 0.00 0.00 3.27
528 536 6.016024 CCATGATTTTTCACTCTTCAACCAGA 60.016 38.462 0.00 0.00 0.00 3.86
604 613 6.271159 AGAAGATGTAAGAGGAAACTTCACCT 59.729 38.462 0.00 0.00 44.43 4.00
630 640 6.040391 GCTGTTGCCAATTATTAGTGGGATAA 59.960 38.462 0.00 0.00 39.65 1.75
633 643 3.699038 GCTGTTGCCAATTATTAGTGGGA 59.301 43.478 0.00 0.00 39.89 4.37
639 649 9.748708 GATGAAATAAGCTGTTGCCAATTATTA 57.251 29.630 0.00 0.00 40.80 0.98
646 656 2.760092 GGGATGAAATAAGCTGTTGCCA 59.240 45.455 0.00 0.00 40.80 4.92
647 657 3.026694 AGGGATGAAATAAGCTGTTGCC 58.973 45.455 0.00 0.00 40.80 4.52
660 670 5.887598 CCATTTCTACATGTGAAGGGATGAA 59.112 40.000 9.11 0.00 0.00 2.57
711 721 7.201974 CCAACGGTCTATCCTCTTTTTATAGGA 60.202 40.741 0.00 0.00 45.76 2.94
712 722 6.929606 CCAACGGTCTATCCTCTTTTTATAGG 59.070 42.308 0.00 0.00 0.00 2.57
1316 1329 3.568853 GCCTAAACGCTCATCTACCTCTA 59.431 47.826 0.00 0.00 0.00 2.43
1326 1339 1.813753 GGCATCGCCTAAACGCTCA 60.814 57.895 0.00 0.00 46.69 4.26
1548 1561 2.923035 ACCCTGACCTCGGTGTGG 60.923 66.667 0.00 0.00 0.00 4.17
1801 1814 6.074142 GGCTTGAATTCCATTAATTTCATCGC 60.074 38.462 2.27 7.20 37.93 4.58
2157 2173 6.147000 GCGGACAAACATTTCCAAACATAATT 59.853 34.615 0.00 0.00 0.00 1.40
2677 2709 2.981302 CTGATCTCGGTGGCCACA 59.019 61.111 35.78 17.29 0.00 4.17
2701 2733 3.683937 GCCATTTGTGCAGGGCGT 61.684 61.111 0.00 0.00 36.58 5.68
2725 2757 3.082579 GCACCTCTGGGTCTAGCGG 62.083 68.421 0.00 0.00 45.41 5.52
2844 2876 1.299976 GTCACGAAATCCTGGGGCT 59.700 57.895 0.00 0.00 0.00 5.19
2880 2912 2.203728 TGTGTAGCGGGTCCAGGT 60.204 61.111 0.00 0.00 0.00 4.00
2987 3019 1.404315 GGTTCACGATCTGTCACCCTC 60.404 57.143 0.00 0.00 0.00 4.30
2989 3021 3.139029 GGTTCACGATCTGTCACCC 57.861 57.895 0.00 0.00 0.00 4.61
3232 3270 3.009115 CATCACCGAGGTGGGGGT 61.009 66.667 20.79 3.94 43.65 4.95
3286 3324 4.094590 CAGATCTGAAATCCAGCAAGACAC 59.905 45.833 18.34 0.00 42.62 3.67
3292 3330 2.497273 TCGTCAGATCTGAAATCCAGCA 59.503 45.455 26.70 0.00 41.85 4.41
3295 3333 4.743057 ACATCGTCAGATCTGAAATCCA 57.257 40.909 26.70 9.51 41.85 3.41
3649 4857 5.653330 TGCAAATCCAATCTCTTAAGCATCA 59.347 36.000 0.00 0.00 0.00 3.07
4071 5317 8.915654 GCACAGAGGTTGTTAAATTAAAAGATG 58.084 33.333 0.00 0.00 38.16 2.90
4072 5318 8.860088 AGCACAGAGGTTGTTAAATTAAAAGAT 58.140 29.630 0.00 0.00 38.16 2.40
4073 5319 8.232913 AGCACAGAGGTTGTTAAATTAAAAGA 57.767 30.769 0.00 0.00 38.16 2.52
4074 5320 8.871686 AAGCACAGAGGTTGTTAAATTAAAAG 57.128 30.769 0.00 0.00 38.16 2.27
4075 5321 9.660180 AAAAGCACAGAGGTTGTTAAATTAAAA 57.340 25.926 0.00 0.00 38.16 1.52
4076 5322 9.092876 CAAAAGCACAGAGGTTGTTAAATTAAA 57.907 29.630 0.00 0.00 38.16 1.52
4077 5323 8.254508 ACAAAAGCACAGAGGTTGTTAAATTAA 58.745 29.630 0.00 0.00 38.16 1.40
4088 5334 3.577805 AGGTAACAAAAGCACAGAGGT 57.422 42.857 0.00 0.00 41.41 3.85
4255 5501 7.099764 ACGAGGATTATAAACAGCATATGGAG 58.900 38.462 4.56 0.00 0.00 3.86
4591 5837 8.691797 TCTGGGTTTGCAATAAATCCTTATTAC 58.308 33.333 0.00 0.00 35.88 1.89
4663 5910 0.111061 TGCTTCCTCTGCACATGGTT 59.889 50.000 0.00 0.00 35.31 3.67
4756 6003 4.134563 TGACTTTCCTCTTAAGCAACCAC 58.865 43.478 0.00 0.00 0.00 4.16
4919 6174 8.279970 TCAACCTCACATTGATAAAGGTTATG 57.720 34.615 4.88 0.00 46.04 1.90
5133 6388 7.121463 GTGATAGGAGAGAGTACAGAAAGAACA 59.879 40.741 0.00 0.00 0.00 3.18
5802 7059 6.805016 ACACATGACTCCTCTCTATTTGAT 57.195 37.500 0.00 0.00 0.00 2.57
5860 7117 6.233905 AGTTTAGGTGCAAAAATGGACTTT 57.766 33.333 0.00 0.00 0.00 2.66
5865 7122 5.355596 TCACAAGTTTAGGTGCAAAAATGG 58.644 37.500 0.00 0.00 35.04 3.16
5876 7133 8.571336 ACTTCAAAGAATGATCACAAGTTTAGG 58.429 33.333 0.00 0.00 38.03 2.69
5884 7141 9.591792 CTCATACTACTTCAAAGAATGATCACA 57.408 33.333 0.00 0.00 38.03 3.58
6699 7960 6.865834 AAATGAGATACTCACAGTTCTCCT 57.134 37.500 3.54 0.00 43.63 3.69
6781 8042 7.553402 TGTACTGAGAACTATTGGAGTAGAGAC 59.447 40.741 0.00 0.00 37.44 3.36
7156 8417 0.035881 CAAGTTGCTCAGGCTCTCCA 59.964 55.000 0.00 0.00 39.59 3.86
7174 8435 4.165372 GGAGTAACACCCCAAGGATTATCA 59.835 45.833 0.00 0.00 36.73 2.15
7335 8596 0.036732 GCCCATGGAGAGTGACAACA 59.963 55.000 15.22 0.00 0.00 3.33
7518 8780 6.309712 ACATTCCTCAATAATGCATCTTCG 57.690 37.500 0.00 0.00 37.77 3.79
7616 8878 7.149202 AGGGAGTATTATTTCAGTATTGCCA 57.851 36.000 0.00 0.00 0.00 4.92
7622 8884 6.500751 GGGATGGAGGGAGTATTATTTCAGTA 59.499 42.308 0.00 0.00 0.00 2.74
7633 8895 7.844779 GTCTTATATTATGGGATGGAGGGAGTA 59.155 40.741 0.00 0.00 0.00 2.59
7740 9002 5.697633 GCAAATGAAAATGATGAACACAGGT 59.302 36.000 0.00 0.00 0.00 4.00
7795 9058 1.476110 GGTAAGTCAAGGTGTGTGGCA 60.476 52.381 0.00 0.00 0.00 4.92
7796 9059 1.202770 AGGTAAGTCAAGGTGTGTGGC 60.203 52.381 0.00 0.00 0.00 5.01
7797 9060 2.930826 AGGTAAGTCAAGGTGTGTGG 57.069 50.000 0.00 0.00 0.00 4.17
7798 9061 4.073293 AGAAGGTAAGTCAAGGTGTGTG 57.927 45.455 0.00 0.00 0.00 3.82
7799 9062 4.704965 GAAGAAGGTAAGTCAAGGTGTGT 58.295 43.478 0.00 0.00 0.00 3.72
7800 9063 3.741344 CGAAGAAGGTAAGTCAAGGTGTG 59.259 47.826 0.00 0.00 0.00 3.82
7801 9064 3.387050 ACGAAGAAGGTAAGTCAAGGTGT 59.613 43.478 0.00 0.00 0.00 4.16
7802 9065 3.741344 CACGAAGAAGGTAAGTCAAGGTG 59.259 47.826 0.00 0.00 0.00 4.00
7803 9066 3.802675 GCACGAAGAAGGTAAGTCAAGGT 60.803 47.826 0.00 0.00 0.00 3.50
7804 9067 2.737252 GCACGAAGAAGGTAAGTCAAGG 59.263 50.000 0.00 0.00 0.00 3.61
7805 9068 3.390135 TGCACGAAGAAGGTAAGTCAAG 58.610 45.455 0.00 0.00 0.00 3.02
7806 9069 3.390135 CTGCACGAAGAAGGTAAGTCAA 58.610 45.455 0.00 0.00 0.00 3.18
7807 9070 2.288825 CCTGCACGAAGAAGGTAAGTCA 60.289 50.000 0.00 0.00 0.00 3.41
7808 9071 2.288886 ACCTGCACGAAGAAGGTAAGTC 60.289 50.000 10.06 0.00 42.59 3.01
7809 9072 1.692519 ACCTGCACGAAGAAGGTAAGT 59.307 47.619 10.06 0.00 42.59 2.24
7810 9073 2.457366 ACCTGCACGAAGAAGGTAAG 57.543 50.000 10.06 0.00 42.59 2.34
7811 9074 2.489971 CAACCTGCACGAAGAAGGTAA 58.510 47.619 11.80 0.00 43.62 2.85
7812 9075 1.876416 GCAACCTGCACGAAGAAGGTA 60.876 52.381 11.80 0.00 43.62 3.08
7813 9076 1.166531 GCAACCTGCACGAAGAAGGT 61.167 55.000 6.49 6.49 46.40 3.50
7814 9077 1.576421 GCAACCTGCACGAAGAAGG 59.424 57.895 5.29 5.29 44.26 3.46
7895 9158 0.957362 AAGAGCCTTGAAGCAGCAAC 59.043 50.000 0.00 0.00 34.23 4.17
7918 9181 2.928801 ACACAGAACATACAGCACCA 57.071 45.000 0.00 0.00 0.00 4.17
7963 9226 1.401905 GGCAATGCACAGTACTAAGCC 59.598 52.381 7.79 7.99 0.00 4.35
8007 9270 1.139853 CTAGGCTACAAGCTTGGAGGG 59.860 57.143 34.45 16.20 41.99 4.30
8017 9280 2.170607 GCATCAGGAACCTAGGCTACAA 59.829 50.000 9.30 0.00 0.00 2.41
8071 9334 6.618287 TCATTATCCTTTGATGGCTAAACG 57.382 37.500 0.00 0.00 32.18 3.60
8090 9353 5.880054 AAGCTACAACGCTACAAATCATT 57.120 34.783 0.00 0.00 39.86 2.57
8092 9355 6.978343 ATAAAGCTACAACGCTACAAATCA 57.022 33.333 0.00 0.00 39.86 2.57
8138 9401 4.867047 GCATCTATGTCCGGAAGTATGATG 59.133 45.833 21.33 21.33 33.93 3.07
8139 9402 4.380973 CGCATCTATGTCCGGAAGTATGAT 60.381 45.833 5.23 3.99 0.00 2.45
8140 9403 3.057526 CGCATCTATGTCCGGAAGTATGA 60.058 47.826 5.23 1.37 0.00 2.15
8146 9409 2.815384 TCCGCATCTATGTCCGGAA 58.185 52.632 5.23 0.00 45.79 4.30
8151 9414 5.106791 CCAGAATTTCATCCGCATCTATGTC 60.107 44.000 0.00 0.00 0.00 3.06
8221 9484 8.303876 GCCTAAAGAACCATTATTTTCAGTCAA 58.696 33.333 0.00 0.00 0.00 3.18
8234 9497 4.650972 TGTACAAGGCCTAAAGAACCAT 57.349 40.909 5.16 0.00 0.00 3.55
8259 9522 3.512724 GTGTACCCTCTGTAAGCACCTTA 59.487 47.826 0.00 0.00 0.00 2.69
8270 9533 6.034591 CGTCTAATTAAGTGTGTACCCTCTG 58.965 44.000 0.00 0.00 0.00 3.35
8351 9614 9.157104 GAAAAATAAACTGGGTTGTCTCAAAAA 57.843 29.630 0.00 0.00 0.00 1.94
8352 9615 8.536175 AGAAAAATAAACTGGGTTGTCTCAAAA 58.464 29.630 0.00 0.00 0.00 2.44
8353 9616 8.073467 AGAAAAATAAACTGGGTTGTCTCAAA 57.927 30.769 0.00 0.00 0.00 2.69
8354 9617 7.654022 AGAAAAATAAACTGGGTTGTCTCAA 57.346 32.000 0.00 0.00 0.00 3.02
8355 9618 8.754991 TTAGAAAAATAAACTGGGTTGTCTCA 57.245 30.769 0.00 0.00 0.00 3.27
8356 9619 9.459640 GTTTAGAAAAATAAACTGGGTTGTCTC 57.540 33.333 2.85 0.00 40.77 3.36
8357 9620 8.973182 TGTTTAGAAAAATAAACTGGGTTGTCT 58.027 29.630 9.88 0.00 43.17 3.41
8358 9621 9.027129 GTGTTTAGAAAAATAAACTGGGTTGTC 57.973 33.333 9.88 0.00 43.17 3.18
8359 9622 7.982919 GGTGTTTAGAAAAATAAACTGGGTTGT 59.017 33.333 9.88 0.00 43.17 3.32
8360 9623 7.982354 TGGTGTTTAGAAAAATAAACTGGGTTG 59.018 33.333 9.88 0.00 43.17 3.77
8408 9678 2.743928 GAGTCCAAGCAGCACCCG 60.744 66.667 0.00 0.00 0.00 5.28
8523 9793 2.308039 GGTCGAAGCACCACACGTC 61.308 63.158 0.00 0.00 36.32 4.34
8820 10090 3.680937 CGTATTCTTTTACAACGGCCTGA 59.319 43.478 0.00 0.00 0.00 3.86



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

AutoCloner maintained by Alex Coulton.