Multiple sequence alignment - TraesCS5D01G102600

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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 TraesCS5D01G102600 chr5D 100.000 5839 0 0 1 5839 115946799 115952637 0.000000e+00 10783.0
1 TraesCS5D01G102600 chr5A 95.701 5187 166 30 1 5164 122952907 122958059 0.000000e+00 8290.0
2 TraesCS5D01G102600 chr5A 88.563 717 42 20 845 1559 504720520 504719842 0.000000e+00 833.0
3 TraesCS5D01G102600 chr5A 88.208 212 5 2 5106 5317 122958050 122958241 9.780000e-58 235.0
4 TraesCS5D01G102600 chr5A 89.017 173 17 2 5587 5759 122958817 122958987 4.580000e-51 213.0
5 TraesCS5D01G102600 chr5A 97.500 40 1 0 5499 5538 122958611 122958650 1.050000e-07 69.4
6 TraesCS5D01G102600 chr5B 95.126 4924 130 29 222 5104 127501054 127505908 0.000000e+00 7662.0
7 TraesCS5D01G102600 chr5B 92.564 2676 156 12 943 3612 252302842 252300204 0.000000e+00 3799.0
8 TraesCS5D01G102600 chr5B 93.885 785 31 8 2831 3612 704278576 704277806 0.000000e+00 1168.0
9 TraesCS5D01G102600 chr5B 88.802 768 42 10 1260 2026 704279303 704278579 0.000000e+00 902.0
10 TraesCS5D01G102600 chr5B 95.547 247 10 1 1249 1494 678674092 678673846 1.530000e-105 394.0
11 TraesCS5D01G102600 chr5B 96.591 88 3 0 5108 5195 127505988 127506075 4.720000e-31 147.0
12 TraesCS5D01G102600 chr5B 87.611 113 8 4 5727 5839 127506668 127506774 6.140000e-25 126.0
13 TraesCS5D01G102600 chr5B 94.444 72 0 1 5356 5427 127506224 127506291 2.220000e-19 108.0
14 TraesCS5D01G102600 chr5B 100.000 46 0 0 5430 5475 127506327 127506372 1.040000e-12 86.1
15 TraesCS5D01G102600 chr4A 91.190 1555 90 11 1432 2982 321175767 321174256 0.000000e+00 2069.0
16 TraesCS5D01G102600 chr4A 92.891 633 45 0 2980 3612 321129404 321128772 0.000000e+00 920.0
17 TraesCS5D01G102600 chr4A 90.355 591 32 13 847 1435 321184646 321184079 0.000000e+00 752.0
18 TraesCS5D01G102600 chr4A 80.119 1011 187 13 3790 4796 721384825 721385825 0.000000e+00 741.0
19 TraesCS5D01G102600 chr1A 89.720 1070 58 11 845 1914 483640780 483641797 0.000000e+00 1319.0
20 TraesCS5D01G102600 chr1B 92.034 954 47 10 1073 2026 332154903 332153979 0.000000e+00 1314.0
21 TraesCS5D01G102600 chr1B 93.121 785 44 4 2831 3612 332153976 332153199 0.000000e+00 1142.0
22 TraesCS5D01G102600 chr1B 94.098 610 26 5 2282 2883 122923476 122922869 0.000000e+00 918.0
23 TraesCS5D01G102600 chr1B 88.427 769 43 23 1260 2026 169942250 169941526 0.000000e+00 885.0
24 TraesCS5D01G102600 chr1B 95.695 511 16 3 3102 3612 169941322 169940818 0.000000e+00 817.0
25 TraesCS5D01G102600 chr1B 90.476 483 21 5 852 1333 122924313 122923855 1.080000e-171 614.0
26 TraesCS5D01G102600 chr1B 91.204 216 9 4 2831 3043 169941523 169941315 9.580000e-73 285.0
27 TraesCS5D01G102600 chr4B 93.631 785 34 7 2831 3612 564198134 564197363 0.000000e+00 1158.0
28 TraesCS5D01G102600 chr4B 93.376 785 36 7 2831 3612 175549169 175548398 0.000000e+00 1147.0
29 TraesCS5D01G102600 chr4B 90.091 767 34 4 1260 2026 175549896 175549172 0.000000e+00 957.0
30 TraesCS5D01G102600 chr4B 89.831 767 36 3 1260 2026 564198861 564198137 0.000000e+00 946.0
31 TraesCS5D01G102600 chr7B 92.475 598 38 3 2282 2873 623471067 623470471 0.000000e+00 848.0
32 TraesCS5D01G102600 chr7B 79.093 1081 194 28 3729 4796 451354362 451355423 0.000000e+00 715.0
33 TraesCS5D01G102600 chr7B 94.949 396 18 2 940 1333 623268369 623267974 2.310000e-173 619.0
34 TraesCS5D01G102600 chr7B 93.846 260 15 1 2282 2541 623266263 623266005 1.970000e-104 390.0
35 TraesCS5D01G102600 chr7B 74.341 569 128 16 2152 2711 451352908 451353467 5.890000e-55 226.0
36 TraesCS5D01G102600 chr7A 80.313 1021 167 31 3790 4796 484595959 484596959 0.000000e+00 741.0
37 TraesCS5D01G102600 chr7A 79.010 1010 200 11 3790 4796 14190524 14189524 0.000000e+00 680.0
38 TraesCS5D01G102600 chr7A 89.157 166 16 2 3751 3916 474812322 474812485 7.670000e-49 206.0
39 TraesCS5D01G102600 chr7A 77.551 245 47 8 2333 2573 727433681 727433441 2.190000e-29 141.0
40 TraesCS5D01G102600 chr7D 79.070 1118 200 30 3693 4796 434148763 434149860 0.000000e+00 737.0
41 TraesCS5D01G102600 chr7D 79.208 1010 198 11 3790 4796 14881448 14880448 0.000000e+00 691.0
42 TraesCS5D01G102600 chr7D 71.615 842 208 27 3879 4706 366451927 366452751 9.920000e-48 202.0
43 TraesCS5D01G102600 chr2B 75.862 232 48 8 2333 2560 798723510 798723737 1.720000e-20 111.0
44 TraesCS5D01G102600 chr2B 96.970 33 1 0 5771 5803 19117 19149 8.170000e-04 56.5
45 TraesCS5D01G102600 chr4D 72.653 245 56 8 5587 5827 71436933 71436696 2.920000e-08 71.3
46 TraesCS5D01G102600 chr3D 79.612 103 17 2 5704 5803 611301655 611301756 2.920000e-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 TraesCS5D01G102600 chr5D 115946799 115952637 5838 False 10783.000000 10783 100.000000 1 5839 1 chr5D.!!$F1 5838
1 TraesCS5D01G102600 chr5A 122952907 122958987 6080 False 2201.850000 8290 92.606500 1 5759 4 chr5A.!!$F1 5758
2 TraesCS5D01G102600 chr5A 504719842 504720520 678 True 833.000000 833 88.563000 845 1559 1 chr5A.!!$R1 714
3 TraesCS5D01G102600 chr5B 252300204 252302842 2638 True 3799.000000 3799 92.564000 943 3612 1 chr5B.!!$R1 2669
4 TraesCS5D01G102600 chr5B 127501054 127506774 5720 False 1625.820000 7662 94.754400 222 5839 5 chr5B.!!$F1 5617
5 TraesCS5D01G102600 chr5B 704277806 704279303 1497 True 1035.000000 1168 91.343500 1260 3612 2 chr5B.!!$R3 2352
6 TraesCS5D01G102600 chr4A 321174256 321175767 1511 True 2069.000000 2069 91.190000 1432 2982 1 chr4A.!!$R2 1550
7 TraesCS5D01G102600 chr4A 321128772 321129404 632 True 920.000000 920 92.891000 2980 3612 1 chr4A.!!$R1 632
8 TraesCS5D01G102600 chr4A 321184079 321184646 567 True 752.000000 752 90.355000 847 1435 1 chr4A.!!$R3 588
9 TraesCS5D01G102600 chr4A 721384825 721385825 1000 False 741.000000 741 80.119000 3790 4796 1 chr4A.!!$F1 1006
10 TraesCS5D01G102600 chr1A 483640780 483641797 1017 False 1319.000000 1319 89.720000 845 1914 1 chr1A.!!$F1 1069
11 TraesCS5D01G102600 chr1B 332153199 332154903 1704 True 1228.000000 1314 92.577500 1073 3612 2 chr1B.!!$R3 2539
12 TraesCS5D01G102600 chr1B 122922869 122924313 1444 True 766.000000 918 92.287000 852 2883 2 chr1B.!!$R1 2031
13 TraesCS5D01G102600 chr1B 169940818 169942250 1432 True 662.333333 885 91.775333 1260 3612 3 chr1B.!!$R2 2352
14 TraesCS5D01G102600 chr4B 175548398 175549896 1498 True 1052.000000 1147 91.733500 1260 3612 2 chr4B.!!$R1 2352
15 TraesCS5D01G102600 chr4B 564197363 564198861 1498 True 1052.000000 1158 91.731000 1260 3612 2 chr4B.!!$R2 2352
16 TraesCS5D01G102600 chr7B 623470471 623471067 596 True 848.000000 848 92.475000 2282 2873 1 chr7B.!!$R1 591
17 TraesCS5D01G102600 chr7B 623266005 623268369 2364 True 504.500000 619 94.397500 940 2541 2 chr7B.!!$R2 1601
18 TraesCS5D01G102600 chr7B 451352908 451355423 2515 False 470.500000 715 76.717000 2152 4796 2 chr7B.!!$F1 2644
19 TraesCS5D01G102600 chr7A 484595959 484596959 1000 False 741.000000 741 80.313000 3790 4796 1 chr7A.!!$F2 1006
20 TraesCS5D01G102600 chr7A 14189524 14190524 1000 True 680.000000 680 79.010000 3790 4796 1 chr7A.!!$R1 1006
21 TraesCS5D01G102600 chr7D 434148763 434149860 1097 False 737.000000 737 79.070000 3693 4796 1 chr7D.!!$F2 1103
22 TraesCS5D01G102600 chr7D 14880448 14881448 1000 True 691.000000 691 79.208000 3790 4796 1 chr7D.!!$R1 1006
23 TraesCS5D01G102600 chr7D 366451927 366452751 824 False 202.000000 202 71.615000 3879 4706 1 chr7D.!!$F1 827

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
936 952 0.392327 GTTCTTGAGCTCAGCCTCCC 60.392 60.0 17.43 0.68 0.00 4.30 F
2006 2614 0.389391 CTCAGCCCATACAGGTACCG 59.611 60.0 6.18 4.16 34.66 4.02 F
2085 2719 0.459411 GTCGCTTCTTCCTCTGCTCC 60.459 60.0 0.00 0.00 0.00 4.70 F
2422 3792 0.831288 CCATCCTCTCCATCCTCGCT 60.831 60.0 0.00 0.00 0.00 4.93 F
4046 5448 0.250858 TCAACCTCACCGACCGTCTA 60.251 55.0 0.00 0.00 0.00 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2599 3970 0.884704 GCCGCACCTTGTTCTTGAGA 60.885 55.000 0.00 0.0 0.00 3.27 R
3140 4532 0.179225 GCGAAACGTACACCAGCATG 60.179 55.000 0.00 0.0 0.00 4.06 R
3589 4984 1.215647 CTGTCCGTCTTCTTCCCCG 59.784 63.158 0.00 0.0 0.00 5.73 R
4257 5659 0.471211 AGGAAGACCAGGAACGTGGA 60.471 55.000 18.36 0.0 40.44 4.02 R
5539 7323 0.178944 TGACCTTCCTCCCTCGTGAA 60.179 55.000 0.00 0.0 0.00 3.18 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 21 1.278238 CGGTCCGACACAATAGAAGC 58.722 55.000 4.91 0.00 0.00 3.86
22 23 0.645868 GTCCGACACAATAGAAGCGC 59.354 55.000 0.00 0.00 0.00 5.92
24 25 1.429148 CCGACACAATAGAAGCGCCC 61.429 60.000 2.29 0.00 0.00 6.13
30 31 1.202382 ACAATAGAAGCGCCCGAGTAC 60.202 52.381 2.29 0.00 0.00 2.73
33 34 1.709147 TAGAAGCGCCCGAGTACGTC 61.709 60.000 2.29 0.00 37.88 4.34
42 43 2.099831 GAGTACGTCCGTGCCTCG 59.900 66.667 1.98 0.00 39.52 4.63
48 49 1.298413 CGTCCGTGCCTCGACATAG 60.298 63.158 0.02 0.00 42.86 2.23
51 52 2.655364 CGTGCCTCGACATAGCCG 60.655 66.667 0.00 0.00 42.86 5.52
55 56 0.459585 TGCCTCGACATAGCCGTTTC 60.460 55.000 0.00 0.00 0.00 2.78
69 70 5.746040 AGCCGTTTCGGATTTAGGCTTGA 62.746 47.826 12.48 0.00 45.97 3.02
103 104 1.659098 GGTCAATTTAGACGACTGCGG 59.341 52.381 0.00 0.00 43.17 5.69
121 122 2.537625 GCGGTCGATTTGAAGAGATCAG 59.462 50.000 0.00 0.00 39.77 2.90
141 142 8.045507 AGATCAGACTGTATCATGATTTTGTGT 58.954 33.333 14.65 6.06 32.68 3.72
143 144 7.389232 TCAGACTGTATCATGATTTTGTGTCT 58.611 34.615 14.65 15.90 0.00 3.41
153 154 3.068024 TGATTTTGTGTCTGGGCTTTGAC 59.932 43.478 0.00 0.00 0.00 3.18
181 182 2.504244 CGTCGGCTCGGTCAGTTC 60.504 66.667 0.00 0.00 0.00 3.01
246 251 9.786105 TCTAACACACAACGATCGTAAATTATA 57.214 29.630 23.04 8.90 0.00 0.98
413 422 3.926821 TTCCAAAATCTTTACCACCGC 57.073 42.857 0.00 0.00 0.00 5.68
414 423 2.164338 TCCAAAATCTTTACCACCGCC 58.836 47.619 0.00 0.00 0.00 6.13
415 424 1.889829 CCAAAATCTTTACCACCGCCA 59.110 47.619 0.00 0.00 0.00 5.69
416 425 2.297597 CCAAAATCTTTACCACCGCCAA 59.702 45.455 0.00 0.00 0.00 4.52
419 428 2.799126 ATCTTTACCACCGCCAATCA 57.201 45.000 0.00 0.00 0.00 2.57
463 473 0.472471 ACGAGCTCAACCCCAAGAAA 59.528 50.000 15.40 0.00 0.00 2.52
485 495 2.284995 GTGGCAGGTCCCTCTCCT 60.285 66.667 0.00 0.00 35.45 3.69
486 496 2.039624 TGGCAGGTCCCTCTCCTC 59.960 66.667 0.00 0.00 32.37 3.71
509 519 2.732016 CACGTGGTTCACTCCCGA 59.268 61.111 7.95 0.00 31.34 5.14
653 667 1.508545 CACGTCAGAGCCGACTCAT 59.491 57.895 0.35 0.00 46.09 2.90
820 835 4.722700 CACCGCCCCACCTTCAGG 62.723 72.222 0.00 0.00 42.17 3.86
849 865 5.570973 CAGATCTCGCTATAATTTCGACCAG 59.429 44.000 0.00 0.00 0.00 4.00
855 871 4.381411 GCTATAATTTCGACCAGCCTTCT 58.619 43.478 0.00 0.00 0.00 2.85
932 948 1.304509 GCTGGTTCTTGAGCTCAGCC 61.305 60.000 17.43 16.98 43.36 4.85
936 952 0.392327 GTTCTTGAGCTCAGCCTCCC 60.392 60.000 17.43 0.68 0.00 4.30
984 1000 2.614013 ATTTGGAGGAGGCGGGGT 60.614 61.111 0.00 0.00 0.00 4.95
2006 2614 0.389391 CTCAGCCCATACAGGTACCG 59.611 60.000 6.18 4.16 34.66 4.02
2085 2719 0.459411 GTCGCTTCTTCCTCTGCTCC 60.459 60.000 0.00 0.00 0.00 4.70
2422 3792 0.831288 CCATCCTCTCCATCCTCGCT 60.831 60.000 0.00 0.00 0.00 4.93
2599 3970 2.046285 CGGCCAGAAGCGGGATTTT 61.046 57.895 2.24 0.00 45.17 1.82
2829 4215 4.410400 GACTGGGGCCGTGAAGGG 62.410 72.222 0.00 0.00 41.48 3.95
2878 4264 4.329545 GGCACTTGGCTCACCGGA 62.330 66.667 9.46 0.00 44.01 5.14
2943 4329 5.936372 AGGTGATTGATCGAATCCATACATG 59.064 40.000 12.43 0.00 40.00 3.21
2944 4330 5.934043 GGTGATTGATCGAATCCATACATGA 59.066 40.000 0.00 0.00 40.00 3.07
2945 4331 6.596888 GGTGATTGATCGAATCCATACATGAT 59.403 38.462 0.00 0.00 40.00 2.45
2946 4332 7.765819 GGTGATTGATCGAATCCATACATGATA 59.234 37.037 0.00 0.00 40.00 2.15
3140 4532 2.109181 GTAGACATCCGGCTGCCC 59.891 66.667 14.12 0.00 0.00 5.36
3170 4562 1.796355 CGTTTCGCGCGAGAAGAGA 60.796 57.895 32.74 14.63 0.00 3.10
3470 4862 2.737881 GCAGGGCCCCATGTACGTA 61.738 63.158 21.43 0.00 0.00 3.57
3560 4952 1.983224 CTGGCTCGGGAGGAAGAAA 59.017 57.895 0.00 0.00 0.00 2.52
3589 4984 1.779061 TTCCTGAGGAAGCCCACCAC 61.779 60.000 10.46 0.00 36.71 4.16
3740 5142 2.570181 GTGTCGTCGATCCCCGTT 59.430 61.111 0.00 0.00 39.75 4.44
4046 5448 0.250858 TCAACCTCACCGACCGTCTA 60.251 55.000 0.00 0.00 0.00 2.59
4106 5508 2.966309 CTTCTCCCGCAACAACGCC 61.966 63.158 0.00 0.00 0.00 5.68
4268 5670 1.079543 CCTGAGCTCCACGTTCCTG 60.080 63.158 12.15 0.00 0.00 3.86
4843 6248 1.822990 CTTCAGCTTCCCGTAGTGGTA 59.177 52.381 0.00 0.00 35.15 3.25
4983 6390 7.445121 TGCTCTACCAAGATATTAAGACATGG 58.555 38.462 0.00 0.00 0.00 3.66
5104 6511 7.100409 AGCTAGAAATACTTGGAGTTCAGTTC 58.900 38.462 0.00 0.00 0.00 3.01
5128 6614 5.868801 CACAACTTTGGTCACTTGTGAATTT 59.131 36.000 4.93 0.00 41.42 1.82
5200 6686 8.470805 CAGGATTACTGTAGGATATGACCATAC 58.529 40.741 0.00 0.00 42.42 2.39
5204 6690 8.637196 TTACTGTAGGATATGACCATACTCAG 57.363 38.462 0.00 0.00 0.00 3.35
5252 6738 6.016360 TGTTCACTTATGAATTTGACACCCTG 60.016 38.462 0.00 0.00 46.43 4.45
5253 6739 4.458989 TCACTTATGAATTTGACACCCTGC 59.541 41.667 0.00 0.00 0.00 4.85
5254 6740 4.460382 CACTTATGAATTTGACACCCTGCT 59.540 41.667 0.00 0.00 0.00 4.24
5390 6922 7.197071 ACTTTCACACGAAATACAAGCATAA 57.803 32.000 0.00 0.00 40.32 1.90
5391 6923 7.644490 ACTTTCACACGAAATACAAGCATAAA 58.356 30.769 0.00 0.00 40.32 1.40
5392 6924 8.132362 ACTTTCACACGAAATACAAGCATAAAA 58.868 29.630 0.00 0.00 40.32 1.52
5393 6925 7.845617 TTCACACGAAATACAAGCATAAAAC 57.154 32.000 0.00 0.00 0.00 2.43
5428 6993 9.912634 AACACTCATATACCTCAAACAATTTTG 57.087 29.630 0.00 0.00 43.17 2.44
5485 7050 6.530120 TGTGGTGTTGTTGTCTAATACAGAT 58.470 36.000 0.00 0.00 39.87 2.90
5494 7059 3.068165 TGTCTAATACAGATCTGCCACCG 59.932 47.826 22.83 8.87 35.17 4.94
5495 7060 2.628178 TCTAATACAGATCTGCCACCGG 59.372 50.000 22.83 0.00 0.00 5.28
5533 7317 2.887568 GGATGGTGCGAGACTGCG 60.888 66.667 0.00 0.00 37.81 5.18
5538 7322 2.691771 GGTGCGAGACTGCGAGAGA 61.692 63.158 0.00 0.00 37.81 3.10
5539 7323 1.431440 GTGCGAGACTGCGAGAGAT 59.569 57.895 0.00 0.00 37.81 2.75
5542 7326 0.099613 GCGAGACTGCGAGAGATTCA 59.900 55.000 0.00 0.00 0.00 2.57
5543 7327 1.821336 CGAGACTGCGAGAGATTCAC 58.179 55.000 0.00 0.00 0.00 3.18
5546 7330 1.400142 AGACTGCGAGAGATTCACGAG 59.600 52.381 0.00 0.00 32.24 4.18
5547 7331 0.453793 ACTGCGAGAGATTCACGAGG 59.546 55.000 0.00 0.00 32.24 4.63
5549 7333 0.679960 TGCGAGAGATTCACGAGGGA 60.680 55.000 0.00 0.00 32.24 4.20
5552 7336 1.747552 CGAGAGATTCACGAGGGAGGA 60.748 57.143 0.00 0.00 32.24 3.71
5554 7338 2.360801 GAGAGATTCACGAGGGAGGAAG 59.639 54.545 0.00 0.00 0.00 3.46
5555 7339 1.410882 GAGATTCACGAGGGAGGAAGG 59.589 57.143 0.00 0.00 0.00 3.46
5557 7341 1.137282 GATTCACGAGGGAGGAAGGTC 59.863 57.143 0.00 0.00 0.00 3.85
5558 7342 0.178944 TTCACGAGGGAGGAAGGTCA 60.179 55.000 0.00 0.00 0.00 4.02
5559 7343 0.898789 TCACGAGGGAGGAAGGTCAC 60.899 60.000 0.00 0.00 0.00 3.67
5561 7345 0.900647 ACGAGGGAGGAAGGTCACTG 60.901 60.000 0.00 0.00 26.92 3.66
5566 7350 0.531200 GGAGGAAGGTCACTGGTACG 59.469 60.000 0.00 0.00 0.00 3.67
5568 7352 1.079336 GGAAGGTCACTGGTACGGC 60.079 63.158 0.00 0.00 39.14 5.68
5569 7353 1.079336 GAAGGTCACTGGTACGGCC 60.079 63.158 0.00 0.00 39.14 6.13
5570 7354 1.823169 GAAGGTCACTGGTACGGCCA 61.823 60.000 2.24 1.10 46.95 5.36
5578 7362 1.768349 TGGTACGGCCAAAATCCCA 59.232 52.632 2.24 0.00 45.94 4.37
5580 7364 0.609681 GGTACGGCCAAAATCCCACA 60.610 55.000 2.24 0.00 37.17 4.17
5581 7365 1.470051 GTACGGCCAAAATCCCACAT 58.530 50.000 2.24 0.00 0.00 3.21
5583 7367 0.894835 ACGGCCAAAATCCCACATTC 59.105 50.000 2.24 0.00 0.00 2.67
5584 7368 0.894141 CGGCCAAAATCCCACATTCA 59.106 50.000 2.24 0.00 0.00 2.57
5585 7369 1.135024 CGGCCAAAATCCCACATTCAG 60.135 52.381 2.24 0.00 0.00 3.02
5588 7372 2.094026 GCCAAAATCCCACATTCAGGAC 60.094 50.000 0.00 0.00 34.20 3.85
5589 7373 3.164268 CCAAAATCCCACATTCAGGACA 58.836 45.455 0.00 0.00 34.20 4.02
5604 7517 4.002982 TCAGGACAACACATGCATACTTC 58.997 43.478 0.00 0.00 0.00 3.01
5636 7549 4.278419 GGTGCTTTTCAAGTACATGGTCTT 59.722 41.667 6.99 0.00 44.66 3.01
5642 7555 4.623932 TCAAGTACATGGTCTTGAGCTT 57.376 40.909 22.12 3.73 43.02 3.74
5645 7558 2.093973 AGTACATGGTCTTGAGCTTCGG 60.094 50.000 0.00 0.00 0.00 4.30
5653 7566 1.909302 TCTTGAGCTTCGGGGAGAAAT 59.091 47.619 0.00 0.00 38.57 2.17
5686 7599 2.705658 CCCTAGTTGGTCATATCAGGCA 59.294 50.000 0.00 0.00 0.00 4.75
5695 7608 4.067896 GGTCATATCAGGCAAATGACGAT 58.932 43.478 8.19 0.67 46.75 3.73
5699 7612 5.589855 TCATATCAGGCAAATGACGATGTTT 59.410 36.000 0.00 0.00 31.95 2.83
5700 7613 3.829886 TCAGGCAAATGACGATGTTTC 57.170 42.857 0.00 0.00 0.00 2.78
5703 7616 2.489329 AGGCAAATGACGATGTTTCCTG 59.511 45.455 0.00 0.00 0.00 3.86
5782 7695 3.053395 TGAAAGCCCATGATCTAGCCTTT 60.053 43.478 0.00 0.00 0.00 3.11
5783 7696 2.653234 AGCCCATGATCTAGCCTTTG 57.347 50.000 0.00 0.00 0.00 2.77
5784 7697 2.130193 AGCCCATGATCTAGCCTTTGA 58.870 47.619 0.00 0.00 0.00 2.69
5788 7701 3.181436 CCCATGATCTAGCCTTTGATGGT 60.181 47.826 0.00 0.00 0.00 3.55
5789 7702 4.467769 CCATGATCTAGCCTTTGATGGTT 58.532 43.478 0.00 0.00 0.00 3.67
5790 7703 4.277672 CCATGATCTAGCCTTTGATGGTTG 59.722 45.833 0.00 0.00 0.00 3.77
5791 7704 3.889815 TGATCTAGCCTTTGATGGTTGG 58.110 45.455 0.00 0.00 0.00 3.77
5792 7705 3.523157 TGATCTAGCCTTTGATGGTTGGA 59.477 43.478 0.00 0.00 33.06 3.53
5793 7706 4.166725 TGATCTAGCCTTTGATGGTTGGAT 59.833 41.667 0.00 0.00 40.16 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.488527 GTACTCGGGCGCTTCTATTG 58.511 55.000 7.64 0.00 0.00 1.90
12 13 0.030369 CGTACTCGGGCGCTTCTATT 59.970 55.000 7.64 0.00 0.00 1.73
20 21 4.824166 CACGGACGTACTCGGGCG 62.824 72.222 0.00 0.00 41.85 6.13
22 23 4.487412 GGCACGGACGTACTCGGG 62.487 72.222 0.00 0.00 41.85 5.14
24 25 2.099831 GAGGCACGGACGTACTCG 59.900 66.667 11.22 0.00 43.34 4.18
30 31 1.298413 CTATGTCGAGGCACGGACG 60.298 63.158 4.15 0.00 42.82 4.79
33 34 2.279517 GGCTATGTCGAGGCACGG 60.280 66.667 4.15 0.00 41.55 4.94
51 52 5.949735 TCAAATCAAGCCTAAATCCGAAAC 58.050 37.500 0.00 0.00 0.00 2.78
55 56 3.316308 CCCTCAAATCAAGCCTAAATCCG 59.684 47.826 0.00 0.00 0.00 4.18
57 58 4.098501 CACCCCTCAAATCAAGCCTAAATC 59.901 45.833 0.00 0.00 0.00 2.17
69 70 2.075355 TTGACCGGCACCCCTCAAAT 62.075 55.000 0.00 0.00 0.00 2.32
103 104 5.406649 ACAGTCTGATCTCTTCAAATCGAC 58.593 41.667 6.91 0.00 32.78 4.20
121 122 6.183360 CCCAGACACAAAATCATGATACAGTC 60.183 42.308 9.04 12.34 0.00 3.51
141 142 1.455849 CACCCAGTCAAAGCCCAGA 59.544 57.895 0.00 0.00 0.00 3.86
143 144 2.391130 ACCACCCAGTCAAAGCCCA 61.391 57.895 0.00 0.00 0.00 5.36
185 186 1.080974 AGACGAACTACAACCCGCG 60.081 57.895 0.00 0.00 0.00 6.46
186 187 0.319297 ACAGACGAACTACAACCCGC 60.319 55.000 0.00 0.00 0.00 6.13
187 188 1.268899 AGACAGACGAACTACAACCCG 59.731 52.381 0.00 0.00 0.00 5.28
246 251 1.303806 TCACATGTGCATGCTGGCT 60.304 52.632 21.38 0.00 42.39 4.75
269 274 0.469917 ATTGATCTGCCGGGGTAGTG 59.530 55.000 2.18 0.00 0.00 2.74
364 372 5.784177 TCTTTGTCTTGTCCAGCTTAGTAG 58.216 41.667 0.00 0.00 0.00 2.57
413 422 6.427853 GGTTTCCATTTCTTTCCTTTGATTGG 59.572 38.462 0.00 0.00 0.00 3.16
414 423 6.427853 GGGTTTCCATTTCTTTCCTTTGATTG 59.572 38.462 0.00 0.00 0.00 2.67
415 424 6.101005 TGGGTTTCCATTTCTTTCCTTTGATT 59.899 34.615 0.00 0.00 38.32 2.57
416 425 5.606329 TGGGTTTCCATTTCTTTCCTTTGAT 59.394 36.000 0.00 0.00 38.32 2.57
419 428 5.966853 TTGGGTTTCCATTTCTTTCCTTT 57.033 34.783 0.00 0.00 43.63 3.11
485 495 3.164977 TGAACCACGTGGGCCAGA 61.165 61.111 36.47 14.07 42.05 3.86
486 496 2.978010 GTGAACCACGTGGGCCAG 60.978 66.667 36.47 13.26 42.05 4.85
509 519 1.131928 AAGGGAGGTAGCCGTTTGGT 61.132 55.000 0.00 0.00 37.67 3.67
653 667 3.372730 CAACGGTCGGGTCGGGTA 61.373 66.667 0.00 0.00 0.00 3.69
705 720 1.970092 CGGGGCGTTATTTATTCCCA 58.030 50.000 0.00 0.00 38.72 4.37
820 835 6.637254 TCGAAATTATAGCGAGATCTGTGAAC 59.363 38.462 0.00 0.00 0.00 3.18
824 839 5.009710 TGGTCGAAATTATAGCGAGATCTGT 59.990 40.000 0.00 0.00 34.41 3.41
849 865 3.641436 TCAAAGAAAGGGGAAAAGAAGGC 59.359 43.478 0.00 0.00 0.00 4.35
855 871 1.339929 GCGCTCAAAGAAAGGGGAAAA 59.660 47.619 0.00 0.00 0.00 2.29
932 948 1.726853 AACGATCAAAGAAGCGGGAG 58.273 50.000 0.00 0.00 0.00 4.30
936 952 2.480419 ACTCCAAACGATCAAAGAAGCG 59.520 45.455 0.00 0.00 0.00 4.68
984 1000 1.131303 ACATCCCTCCACCGGTTCAA 61.131 55.000 2.97 0.00 0.00 2.69
1788 2364 4.973055 CACCGGGCGTGGTCGAAA 62.973 66.667 6.32 0.00 41.38 3.46
2599 3970 0.884704 GCCGCACCTTGTTCTTGAGA 60.885 55.000 0.00 0.00 0.00 3.27
2829 4215 1.517832 CCGTCAGACATCCAGGTCC 59.482 63.158 0.41 0.00 38.59 4.46
2943 4329 3.189080 TGTCAGCTGCAACAACATGTATC 59.811 43.478 9.47 0.00 0.00 2.24
2944 4330 3.058016 GTGTCAGCTGCAACAACATGTAT 60.058 43.478 9.47 0.00 0.00 2.29
2945 4331 2.290367 GTGTCAGCTGCAACAACATGTA 59.710 45.455 9.47 0.00 0.00 2.29
2946 4332 1.066002 GTGTCAGCTGCAACAACATGT 59.934 47.619 9.47 0.00 0.00 3.21
3125 4517 3.092511 ATGGGCAGCCGGATGTCT 61.093 61.111 25.34 1.27 0.00 3.41
3140 4532 0.179225 GCGAAACGTACACCAGCATG 60.179 55.000 0.00 0.00 0.00 4.06
3170 4562 2.523902 TTGTGGTCGTACCCGGGT 60.524 61.111 32.66 32.66 37.50 5.28
3560 4952 3.683802 CTTCCTCAGGAACAGCTTGATT 58.316 45.455 0.34 0.00 36.71 2.57
3589 4984 1.215647 CTGTCCGTCTTCTTCCCCG 59.784 63.158 0.00 0.00 0.00 5.73
3740 5142 1.306141 CCTCCCCTGGTACTCTGCA 60.306 63.158 0.00 0.00 0.00 4.41
4046 5448 3.941188 CACCGGAGCACCTGGTGT 61.941 66.667 26.48 14.20 45.92 4.16
4257 5659 0.471211 AGGAAGACCAGGAACGTGGA 60.471 55.000 18.36 0.00 40.44 4.02
4268 5670 2.559440 GTGATGATGAGCAGGAAGACC 58.441 52.381 0.00 0.00 0.00 3.85
4843 6248 4.623932 TCAGATGAACTTGGTAACTGCT 57.376 40.909 0.00 0.00 37.61 4.24
5128 6614 4.259356 CAATGGCTCTGAATCACTCTGAA 58.741 43.478 0.00 0.00 32.19 3.02
5204 6690 2.894387 GCTCACATCGGCTCTGCC 60.894 66.667 0.00 0.00 46.75 4.85
5212 6698 3.607422 TGAACAAAGTTGCTCACATCG 57.393 42.857 0.00 0.00 29.11 3.84
5252 6738 3.119990 ACATTGTTTGTATACACCGCAGC 60.120 43.478 4.68 0.00 36.57 5.25
5253 6739 4.391830 AGACATTGTTTGTATACACCGCAG 59.608 41.667 4.68 0.00 39.18 5.18
5254 6740 4.320023 AGACATTGTTTGTATACACCGCA 58.680 39.130 4.68 2.22 39.18 5.69
5334 6830 5.879223 AGCAATTTGGTTTTGTGACAAATGA 59.121 32.000 11.97 0.00 42.21 2.57
5390 6922 9.959721 AGGTATATGAGTGTTTAATCACTGTTT 57.040 29.630 21.09 9.75 46.81 2.83
5391 6923 9.601217 GAGGTATATGAGTGTTTAATCACTGTT 57.399 33.333 21.09 11.76 46.81 3.16
5392 6924 8.758829 TGAGGTATATGAGTGTTTAATCACTGT 58.241 33.333 21.09 12.90 46.81 3.55
5393 6925 9.599866 TTGAGGTATATGAGTGTTTAATCACTG 57.400 33.333 21.09 0.00 46.81 3.66
5427 6992 8.314021 AGTAAATCACTGACTGATCAACATACA 58.686 33.333 0.00 0.00 38.82 2.29
5428 6993 8.709386 AGTAAATCACTGACTGATCAACATAC 57.291 34.615 0.00 0.00 38.82 2.39
5494 7059 1.382695 TAGGTCCTAGGTGGCAGCC 60.383 63.158 13.95 3.66 35.26 4.85
5495 7060 1.403687 CCTAGGTCCTAGGTGGCAGC 61.404 65.000 30.49 9.02 46.15 5.25
5496 7061 2.827715 CCTAGGTCCTAGGTGGCAG 58.172 63.158 30.49 9.50 46.15 4.85
5533 7317 2.060050 TCCTCCCTCGTGAATCTCTC 57.940 55.000 0.00 0.00 0.00 3.20
5538 7322 1.196012 GACCTTCCTCCCTCGTGAAT 58.804 55.000 0.00 0.00 0.00 2.57
5539 7323 0.178944 TGACCTTCCTCCCTCGTGAA 60.179 55.000 0.00 0.00 0.00 3.18
5542 7326 0.900647 CAGTGACCTTCCTCCCTCGT 60.901 60.000 0.00 0.00 0.00 4.18
5543 7327 1.608717 CCAGTGACCTTCCTCCCTCG 61.609 65.000 0.00 0.00 0.00 4.63
5546 7330 0.903236 GTACCAGTGACCTTCCTCCC 59.097 60.000 0.00 0.00 0.00 4.30
5547 7331 0.531200 CGTACCAGTGACCTTCCTCC 59.469 60.000 0.00 0.00 0.00 4.30
5549 7333 1.542187 GCCGTACCAGTGACCTTCCT 61.542 60.000 0.00 0.00 0.00 3.36
5552 7336 1.839747 TGGCCGTACCAGTGACCTT 60.840 57.895 0.00 0.00 46.36 3.50
5561 7345 0.609681 TGTGGGATTTTGGCCGTACC 60.610 55.000 0.00 0.00 39.84 3.34
5566 7350 1.207811 CCTGAATGTGGGATTTTGGCC 59.792 52.381 0.00 0.00 0.00 5.36
5568 7352 3.164268 TGTCCTGAATGTGGGATTTTGG 58.836 45.455 0.00 0.00 33.89 3.28
5569 7353 4.039004 TGTTGTCCTGAATGTGGGATTTTG 59.961 41.667 0.00 0.00 33.89 2.44
5570 7354 4.039124 GTGTTGTCCTGAATGTGGGATTTT 59.961 41.667 0.00 0.00 33.89 1.82
5572 7356 3.157087 GTGTTGTCCTGAATGTGGGATT 58.843 45.455 0.00 0.00 33.89 3.01
5573 7357 2.108075 TGTGTTGTCCTGAATGTGGGAT 59.892 45.455 0.00 0.00 33.89 3.85
5575 7359 1.979855 TGTGTTGTCCTGAATGTGGG 58.020 50.000 0.00 0.00 0.00 4.61
5578 7362 2.585330 TGCATGTGTTGTCCTGAATGT 58.415 42.857 0.00 0.00 0.00 2.71
5580 7364 4.592942 AGTATGCATGTGTTGTCCTGAAT 58.407 39.130 10.16 0.00 0.00 2.57
5581 7365 4.019792 AGTATGCATGTGTTGTCCTGAA 57.980 40.909 10.16 0.00 0.00 3.02
5583 7367 3.181517 CGAAGTATGCATGTGTTGTCCTG 60.182 47.826 10.16 0.00 0.00 3.86
5584 7368 3.002791 CGAAGTATGCATGTGTTGTCCT 58.997 45.455 10.16 0.00 0.00 3.85
5585 7369 3.000041 TCGAAGTATGCATGTGTTGTCC 59.000 45.455 10.16 0.00 0.00 4.02
5588 7372 4.794762 CCAAATCGAAGTATGCATGTGTTG 59.205 41.667 10.16 2.61 0.00 3.33
5589 7373 4.458989 ACCAAATCGAAGTATGCATGTGTT 59.541 37.500 10.16 0.00 0.00 3.32
5604 7517 2.791383 TGAAAAGCACCACCAAATCG 57.209 45.000 0.00 0.00 0.00 3.34
5636 7549 0.541863 GGATTTCTCCCCGAAGCTCA 59.458 55.000 0.00 0.00 35.28 4.26
5642 7555 0.763223 GGCCTAGGATTTCTCCCCGA 60.763 60.000 14.75 0.00 43.21 5.14
5645 7558 1.418264 GTCAGGCCTAGGATTTCTCCC 59.582 57.143 14.75 1.52 43.21 4.30
5653 7566 1.016415 AACTAGGGTCAGGCCTAGGA 58.984 55.000 14.75 0.00 39.98 2.94
5684 7597 2.253603 GCAGGAAACATCGTCATTTGC 58.746 47.619 0.00 0.00 0.00 3.68
5686 7599 4.361451 GATGCAGGAAACATCGTCATTT 57.639 40.909 0.00 0.00 35.03 2.32
5695 7608 2.811431 CAAGGTAACGATGCAGGAAACA 59.189 45.455 0.00 0.00 46.39 2.83
5699 7612 2.037902 TGAACAAGGTAACGATGCAGGA 59.962 45.455 0.00 0.00 46.39 3.86
5700 7613 2.422597 TGAACAAGGTAACGATGCAGG 58.577 47.619 0.00 0.00 46.39 4.85
5770 7683 3.523157 TCCAACCATCAAAGGCTAGATCA 59.477 43.478 0.00 0.00 0.00 2.92
5776 7689 1.683011 CGGATCCAACCATCAAAGGCT 60.683 52.381 13.41 0.00 0.00 4.58
5782 7695 2.189257 CGCCGGATCCAACCATCA 59.811 61.111 13.41 0.00 0.00 3.07
5783 7696 1.887707 GTCGCCGGATCCAACCATC 60.888 63.158 13.41 0.00 0.00 3.51
5784 7697 2.189521 GTCGCCGGATCCAACCAT 59.810 61.111 13.41 0.00 0.00 3.55
5788 7701 4.485834 CGTCGTCGCCGGATCCAA 62.486 66.667 13.41 0.00 33.95 3.53
5790 7703 4.901520 GTCGTCGTCGCCGGATCC 62.902 72.222 5.05 0.00 36.96 3.36
5791 7704 4.170062 TGTCGTCGTCGCCGGATC 62.170 66.667 5.05 0.00 36.96 3.36
5792 7705 4.471726 GTGTCGTCGTCGCCGGAT 62.472 66.667 5.05 0.00 36.96 4.18
5807 7720 2.450609 AAGGGCACTACGTGTAAGTG 57.549 50.000 11.77 11.77 35.75 3.16
5808 7721 2.103601 ACAAAGGGCACTACGTGTAAGT 59.896 45.455 0.00 0.00 35.75 2.24


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

AutoCloner maintained by Alex Coulton.