Multiple sequence alignment - TraesCS4B01G172900

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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 TraesCS4B01G172900 chr4B 100.000 8310 0 0 1 8310 377802728 377794419 0.000000e+00 15346.0
1 TraesCS4B01G172900 chr4B 88.400 1000 82 13 4518 5507 427507315 427508290 0.000000e+00 1173.0
2 TraesCS4B01G172900 chr4D 93.990 2945 101 33 1 2890 303082475 303079552 0.000000e+00 4388.0
3 TraesCS4B01G172900 chr4D 92.708 2208 91 32 5635 7800 303077728 303075549 0.000000e+00 3121.0
4 TraesCS4B01G172900 chr4D 92.217 1529 77 17 4122 5634 303079259 303077757 0.000000e+00 2126.0
5 TraesCS4B01G172900 chr4D 88.669 353 27 4 7971 8310 303072344 303071992 1.290000e-112 418.0
6 TraesCS4B01G172900 chr4D 93.981 216 12 1 3908 4123 303079555 303079341 8.040000e-85 326.0
7 TraesCS4B01G172900 chr4D 95.322 171 8 0 7802 7972 303075514 303075344 1.060000e-68 272.0
8 TraesCS4B01G172900 chr4A 93.778 1784 62 10 4745 6499 176540475 176542238 0.000000e+00 2634.0
9 TraesCS4B01G172900 chr4A 94.777 1685 47 14 2 1664 176536675 176538340 0.000000e+00 2586.0
10 TraesCS4B01G172900 chr4A 96.803 1251 28 8 1656 2895 176538367 176539616 0.000000e+00 2078.0
11 TraesCS4B01G172900 chr4A 95.083 1322 49 6 6490 7800 176542548 176543864 0.000000e+00 2067.0
12 TraesCS4B01G172900 chr4A 94.395 892 24 6 3908 4797 176539607 176540474 0.000000e+00 1347.0
13 TraesCS4B01G172900 chr4A 91.256 446 21 6 7880 8310 176544763 176545205 7.180000e-165 592.0
14 TraesCS4B01G172900 chr4A 95.238 84 4 0 7799 7882 176543897 176543980 5.230000e-27 134.0
15 TraesCS4B01G172900 chr4A 100.000 28 0 0 5521 5548 306291184 306291157 1.500000e-02 52.8
16 TraesCS4B01G172900 chr2D 96.881 1026 29 3 2892 3915 520039140 520040164 0.000000e+00 1714.0
17 TraesCS4B01G172900 chr2D 88.342 995 83 12 4524 5507 380417607 380416635 0.000000e+00 1164.0
18 TraesCS4B01G172900 chr5B 95.262 1013 46 2 2896 3907 710360418 710361429 0.000000e+00 1604.0
19 TraesCS4B01G172900 chr5B 94.587 1016 50 5 2896 3908 608349662 608348649 0.000000e+00 1567.0
20 TraesCS4B01G172900 chr5B 88.229 994 83 15 4518 5507 192865704 192866667 0.000000e+00 1157.0
21 TraesCS4B01G172900 chr2B 94.980 1016 44 7 2896 3907 406113735 406114747 0.000000e+00 1587.0
22 TraesCS4B01G172900 chr3B 94.794 1018 48 5 2896 3910 761204941 761203926 0.000000e+00 1581.0
23 TraesCS4B01G172900 chr3B 94.867 1013 46 5 2898 3908 549034841 549033833 0.000000e+00 1578.0
24 TraesCS4B01G172900 chr3B 94.175 1030 55 5 2886 3913 421109655 421110681 0.000000e+00 1565.0
25 TraesCS4B01G172900 chr3B 93.957 1026 56 6 2893 3916 800070668 800069647 0.000000e+00 1546.0
26 TraesCS4B01G172900 chr3B 86.573 998 109 17 4518 5507 115332219 115331239 0.000000e+00 1077.0
27 TraesCS4B01G172900 chr7B 94.477 1014 51 5 2897 3908 721415935 721414925 0.000000e+00 1557.0
28 TraesCS4B01G172900 chr7B 85.200 1000 113 13 4518 5508 354255744 354256717 0.000000e+00 994.0
29 TraesCS4B01G172900 chr2A 88.844 995 78 14 4524 5507 515952721 515951749 0.000000e+00 1192.0
30 TraesCS4B01G172900 chr2A 90.741 54 5 0 7883 7936 760341082 760341135 1.160000e-08 73.1
31 TraesCS4B01G172900 chr5A 88.318 993 91 10 4518 5507 524722867 524723837 0.000000e+00 1168.0
32 TraesCS4B01G172900 chr5A 88.117 993 93 13 4518 5507 68818834 68817864 0.000000e+00 1157.0
33 TraesCS4B01G172900 chr3D 87.988 999 89 15 4518 5507 182650571 182651547 0.000000e+00 1151.0
34 TraesCS4B01G172900 chr3D 87.726 994 95 13 4518 5507 496779330 496780300 0.000000e+00 1134.0
35 TraesCS4B01G172900 chr1A 86.228 1002 109 21 4518 5512 59955203 59954224 0.000000e+00 1059.0
36 TraesCS4B01G172900 chr1A 100.000 28 0 0 5521 5548 418941321 418941294 1.500000e-02 52.8
37 TraesCS4B01G172900 chr6B 85.306 490 52 16 5037 5520 503532389 503532864 9.690000e-134 488.0
38 TraesCS4B01G172900 chr6B 84.884 86 12 1 2529 2613 134825708 134825623 1.490000e-12 86.1
39 TraesCS4B01G172900 chr1D 82.338 385 57 7 5127 5506 289394213 289393835 2.890000e-84 324.0
40 TraesCS4B01G172900 chr6D 84.884 86 12 1 2529 2613 60547442 60547357 1.490000e-12 86.1
41 TraesCS4B01G172900 chr6A 83.721 86 13 1 2529 2613 77538010 77537925 6.910000e-11 80.5
42 TraesCS4B01G172900 chr3A 83.721 86 11 2 2529 2613 149983356 149983439 2.490000e-10 78.7


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 TraesCS4B01G172900 chr4B 377794419 377802728 8309 True 15346.000000 15346 100.000000 1 8310 1 chr4B.!!$R1 8309
1 TraesCS4B01G172900 chr4B 427507315 427508290 975 False 1173.000000 1173 88.400000 4518 5507 1 chr4B.!!$F1 989
2 TraesCS4B01G172900 chr4D 303071992 303082475 10483 True 1775.166667 4388 92.814500 1 8310 6 chr4D.!!$R1 8309
3 TraesCS4B01G172900 chr4A 176536675 176545205 8530 False 1634.000000 2634 94.475714 2 8310 7 chr4A.!!$F1 8308
4 TraesCS4B01G172900 chr2D 520039140 520040164 1024 False 1714.000000 1714 96.881000 2892 3915 1 chr2D.!!$F1 1023
5 TraesCS4B01G172900 chr2D 380416635 380417607 972 True 1164.000000 1164 88.342000 4524 5507 1 chr2D.!!$R1 983
6 TraesCS4B01G172900 chr5B 710360418 710361429 1011 False 1604.000000 1604 95.262000 2896 3907 1 chr5B.!!$F2 1011
7 TraesCS4B01G172900 chr5B 608348649 608349662 1013 True 1567.000000 1567 94.587000 2896 3908 1 chr5B.!!$R1 1012
8 TraesCS4B01G172900 chr5B 192865704 192866667 963 False 1157.000000 1157 88.229000 4518 5507 1 chr5B.!!$F1 989
9 TraesCS4B01G172900 chr2B 406113735 406114747 1012 False 1587.000000 1587 94.980000 2896 3907 1 chr2B.!!$F1 1011
10 TraesCS4B01G172900 chr3B 761203926 761204941 1015 True 1581.000000 1581 94.794000 2896 3910 1 chr3B.!!$R3 1014
11 TraesCS4B01G172900 chr3B 549033833 549034841 1008 True 1578.000000 1578 94.867000 2898 3908 1 chr3B.!!$R2 1010
12 TraesCS4B01G172900 chr3B 421109655 421110681 1026 False 1565.000000 1565 94.175000 2886 3913 1 chr3B.!!$F1 1027
13 TraesCS4B01G172900 chr3B 800069647 800070668 1021 True 1546.000000 1546 93.957000 2893 3916 1 chr3B.!!$R4 1023
14 TraesCS4B01G172900 chr3B 115331239 115332219 980 True 1077.000000 1077 86.573000 4518 5507 1 chr3B.!!$R1 989
15 TraesCS4B01G172900 chr7B 721414925 721415935 1010 True 1557.000000 1557 94.477000 2897 3908 1 chr7B.!!$R1 1011
16 TraesCS4B01G172900 chr7B 354255744 354256717 973 False 994.000000 994 85.200000 4518 5508 1 chr7B.!!$F1 990
17 TraesCS4B01G172900 chr2A 515951749 515952721 972 True 1192.000000 1192 88.844000 4524 5507 1 chr2A.!!$R1 983
18 TraesCS4B01G172900 chr5A 524722867 524723837 970 False 1168.000000 1168 88.318000 4518 5507 1 chr5A.!!$F1 989
19 TraesCS4B01G172900 chr5A 68817864 68818834 970 True 1157.000000 1157 88.117000 4518 5507 1 chr5A.!!$R1 989
20 TraesCS4B01G172900 chr3D 182650571 182651547 976 False 1151.000000 1151 87.988000 4518 5507 1 chr3D.!!$F1 989
21 TraesCS4B01G172900 chr3D 496779330 496780300 970 False 1134.000000 1134 87.726000 4518 5507 1 chr3D.!!$F2 989
22 TraesCS4B01G172900 chr1A 59954224 59955203 979 True 1059.000000 1059 86.228000 4518 5512 1 chr1A.!!$R1 994

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
320 333 1.954382 TCGATGGTAGGAAGATGGTCG 59.046 52.381 0.00 0.00 0.00 4.79 F
1321 1357 2.165167 CTTTTGCTCCTCAGCCATCAA 58.835 47.619 0.00 0.00 46.26 2.57 F
2278 2356 1.202879 TGGTTCAGCCTTCCAATTCGT 60.203 47.619 0.00 0.00 38.35 3.85 F
2463 2541 2.224499 TGAAAGTATGTCTGCAGTGCCA 60.224 45.455 14.67 9.62 0.00 4.92 F
3525 3610 1.206578 CGCGTACCCTGCAAAACAG 59.793 57.895 0.00 0.00 46.77 3.16 F
3811 3898 0.172803 GCCAGTCCTACGTGGTACTG 59.827 60.000 16.24 16.24 40.47 2.74 F
4719 4898 1.221840 CGGATGAGGTCACAAGGGG 59.778 63.158 0.00 0.00 0.00 4.79 F
5516 5816 1.609580 GGTGCGTGGAACCATGAGTTA 60.610 52.381 16.11 0.00 39.40 2.24 F
6640 7298 0.108615 ATCTTACTGAAGCGCTGCGT 60.109 50.000 24.04 14.49 32.21 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1365 1401 0.255890 ACCAAGTTGCCTCAGTGTGT 59.744 50.000 0.00 0.00 0.00 3.72 R
3084 3166 0.103208 GAGGTACGAGGCCTGACATG 59.897 60.000 12.00 0.00 36.29 3.21 R
3509 3593 1.468520 CCATCTGTTTTGCAGGGTACG 59.531 52.381 0.00 0.00 45.08 3.67 R
3811 3898 2.663119 GCACGAATCTTGGCATGTTTTC 59.337 45.455 0.00 4.94 0.00 2.29 R
5521 5821 0.641275 CAACGACGACGACAACAACA 59.359 50.000 15.32 0.00 42.66 3.33 R
5522 5822 0.641783 ACAACGACGACGACAACAAC 59.358 50.000 15.32 0.00 42.66 3.32 R
5523 5823 0.915904 GACAACGACGACGACAACAA 59.084 50.000 15.32 0.00 42.66 2.83 R
7096 7778 0.112995 TTCTGGTTGCAGGATGGCTT 59.887 50.000 0.00 0.00 35.86 4.35 R
8069 12581 0.946221 GACTCAACCAGCTGGACGTG 60.946 60.000 39.19 29.07 38.94 4.49 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
94 95 4.079787 CCTGGGGTTTAATTCAGATCCTCA 60.080 45.833 0.00 0.00 0.00 3.86
137 139 4.202161 CCTGTCATCCTGCGAGTTAATAGT 60.202 45.833 0.00 0.00 0.00 2.12
225 227 8.206325 ACATAGATTGCACAGTGAATAGAAAG 57.794 34.615 4.15 0.00 0.00 2.62
280 293 7.661437 TGTTGTTGTATTATGAAGCTTCAGAGT 59.339 33.333 31.14 25.78 41.08 3.24
295 308 6.543831 AGCTTCAGAGTGTGAATAAAAGTTGT 59.456 34.615 2.77 0.00 44.44 3.32
296 309 6.853362 GCTTCAGAGTGTGAATAAAAGTTGTC 59.147 38.462 2.77 0.00 44.44 3.18
297 310 6.525121 TCAGAGTGTGAATAAAAGTTGTCG 57.475 37.500 0.00 0.00 29.64 4.35
320 333 1.954382 TCGATGGTAGGAAGATGGTCG 59.046 52.381 0.00 0.00 0.00 4.79
376 389 3.609256 TCTCTAGAGGATCCTGCATGT 57.391 47.619 22.02 0.00 33.66 3.21
479 493 2.355756 GCGCTCCTTTGAGATTGCAATA 59.644 45.455 12.97 0.00 41.42 1.90
678 705 5.674052 AATTTAATATGTTGCTGGCCACA 57.326 34.783 0.00 1.92 0.00 4.17
754 787 3.998099 TGCTCGTGAGATCCTAATCAG 57.002 47.619 0.00 0.00 40.84 2.90
831 864 7.445121 TGCTTGATATATTAGCTACAGTTGCT 58.555 34.615 14.20 14.20 43.79 3.91
866 899 5.477510 TGGTTACAATTCGTACGGTGTAAT 58.522 37.500 27.17 15.16 38.37 1.89
867 900 6.625362 TGGTTACAATTCGTACGGTGTAATA 58.375 36.000 27.17 20.78 38.37 0.98
868 901 6.751425 TGGTTACAATTCGTACGGTGTAATAG 59.249 38.462 27.17 11.57 38.37 1.73
1271 1307 2.706339 AATCCTCTTGATTCTGCGCT 57.294 45.000 9.73 0.00 39.56 5.92
1321 1357 2.165167 CTTTTGCTCCTCAGCCATCAA 58.835 47.619 0.00 0.00 46.26 2.57
1326 1362 4.174704 TGCTCCTCAGCCATCAAATATT 57.825 40.909 0.00 0.00 46.26 1.28
1373 1409 1.546738 TCCCTGGAGGACACACTGA 59.453 57.895 0.00 0.00 40.93 3.41
1583 1619 4.017958 TCCCCAGTCAAAGGTATGCAAATA 60.018 41.667 0.00 0.00 0.00 1.40
1588 1624 7.151308 CCAGTCAAAGGTATGCAAATAAAACA 58.849 34.615 0.00 0.00 0.00 2.83
1603 1639 9.143631 GCAAATAAAACAGCATAAAGAGTCATT 57.856 29.630 0.00 0.00 0.00 2.57
1947 2018 7.385752 CACCAGTAAATGATTTCTTGTTTGCAT 59.614 33.333 0.00 0.00 0.00 3.96
1980 2051 6.264970 AGAGGGTCGTTATTAGATTGACTACC 59.735 42.308 0.00 0.00 0.00 3.18
2084 2156 4.428209 TGCTGCTTCTTCTCTAATTCTCG 58.572 43.478 0.00 0.00 0.00 4.04
2210 2288 3.734902 GCTTTTGGTAAGCCCATTCGATG 60.735 47.826 0.00 0.00 44.74 3.84
2253 2331 6.085555 TGTTTGTTGTCACCTTTGTTGTAA 57.914 33.333 0.00 0.00 0.00 2.41
2278 2356 1.202879 TGGTTCAGCCTTCCAATTCGT 60.203 47.619 0.00 0.00 38.35 3.85
2463 2541 2.224499 TGAAAGTATGTCTGCAGTGCCA 60.224 45.455 14.67 9.62 0.00 4.92
2883 2964 9.605951 ATTTTTATGATAATGGTTAGGGCTGAT 57.394 29.630 0.00 0.00 0.00 2.90
3283 3365 5.362717 CCATGTATGGTCTGGTCTACTGTAA 59.637 44.000 2.66 0.00 43.05 2.41
3525 3610 1.206578 CGCGTACCCTGCAAAACAG 59.793 57.895 0.00 0.00 46.77 3.16
3559 3645 5.701290 CGGATAAAAAGAGAGTTGTCACCTT 59.299 40.000 0.00 0.00 0.00 3.50
3807 3894 2.119832 AGGCCAGTCCTACGTGGT 59.880 61.111 5.01 0.00 45.41 4.16
3811 3898 0.172803 GCCAGTCCTACGTGGTACTG 59.827 60.000 16.24 16.24 40.47 2.74
3952 4039 4.988540 TCTCAGGACGCGATATTATTTTGG 59.011 41.667 15.93 0.00 0.00 3.28
4101 4188 4.337145 ACTCTAGACCTGAAATCGTGAGT 58.663 43.478 0.00 0.00 32.57 3.41
4333 4503 9.236006 AGAAAACTGATGCTGATATAAGTTTGT 57.764 29.630 7.95 1.96 37.77 2.83
4514 4684 1.640670 AGGAACTTACATGCCCACCAT 59.359 47.619 0.00 0.00 27.25 3.55
4515 4685 2.042979 AGGAACTTACATGCCCACCATT 59.957 45.455 0.00 0.00 27.25 3.16
4719 4898 1.221840 CGGATGAGGTCACAAGGGG 59.778 63.158 0.00 0.00 0.00 4.79
4756 4935 2.372264 CCATGGTGTATGCTCTTTGCT 58.628 47.619 2.57 0.00 43.37 3.91
4846 5078 6.954487 ACTTTGGAATCGAAAGGTTTTAGT 57.046 33.333 19.22 0.00 32.13 2.24
4901 5136 3.665190 GGTTTCAGTACTGCTAAGCACT 58.335 45.455 18.45 0.00 33.79 4.40
4997 5233 4.098349 GCTGCAAAAAGGATGGTGATATCA 59.902 41.667 0.00 0.00 0.00 2.15
5152 5389 4.603535 GGTGCTGGGTGTTGGCCT 62.604 66.667 3.32 0.00 0.00 5.19
5205 5442 1.980951 GCGGAGATGCGCATGTTGAA 61.981 55.000 30.76 0.00 0.00 2.69
5466 5743 3.756082 AGAGAGATCTGAAGGACTGGT 57.244 47.619 0.00 0.00 0.00 4.00
5474 5752 2.492088 TCTGAAGGACTGGTATGTCACG 59.508 50.000 0.00 0.00 38.61 4.35
5516 5816 1.609580 GGTGCGTGGAACCATGAGTTA 60.610 52.381 16.11 0.00 39.40 2.24
5521 5821 3.252458 GCGTGGAACCATGAGTTAGTTTT 59.748 43.478 16.11 0.00 39.40 2.43
5522 5822 4.783242 CGTGGAACCATGAGTTAGTTTTG 58.217 43.478 7.21 0.00 39.40 2.44
5523 5823 4.274950 CGTGGAACCATGAGTTAGTTTTGT 59.725 41.667 7.21 0.00 39.40 2.83
5524 5824 5.220970 CGTGGAACCATGAGTTAGTTTTGTT 60.221 40.000 7.21 0.00 39.40 2.83
5530 5830 6.560711 ACCATGAGTTAGTTTTGTTGTTGTC 58.439 36.000 0.00 0.00 0.00 3.18
5539 5839 1.348276 TTGTTGTTGTCGTCGTCGTT 58.652 45.000 1.33 0.00 38.33 3.85
5588 5888 5.753438 GGCACGTTCAGTTATGATATCAAGA 59.247 40.000 9.99 0.00 34.73 3.02
5753 6092 7.840931 AGAAGGGGAATGATTTATGTTTTGAC 58.159 34.615 0.00 0.00 0.00 3.18
5907 6246 3.731652 TTTTGGAATTCTGTGCACCAG 57.268 42.857 15.69 11.86 42.97 4.00
5913 6252 4.009675 GGAATTCTGTGCACCAGTTATGA 58.990 43.478 15.69 0.00 42.19 2.15
6019 6358 4.816385 TGGTCTTGATGTTTTCAGTGTCTC 59.184 41.667 0.00 0.00 35.27 3.36
6020 6359 5.059833 GGTCTTGATGTTTTCAGTGTCTCT 58.940 41.667 0.00 0.00 35.27 3.10
6075 6414 7.168302 CACTTAGCTGACTGGAAAGATATAACG 59.832 40.741 0.00 0.00 0.00 3.18
6229 6568 3.056607 ACACATTTTATTGGCACTGGAGC 60.057 43.478 0.00 0.00 0.00 4.70
6233 6572 2.772077 TTATTGGCACTGGAGCGTTA 57.228 45.000 0.00 0.00 34.64 3.18
6379 6718 6.366061 TCACAGTTATGTTCTTTGATGTCGAG 59.634 38.462 0.00 0.00 37.65 4.04
6391 6730 5.784750 TTGATGTCGAGCTCACAATTAAG 57.215 39.130 15.40 0.00 0.00 1.85
6504 6843 7.973944 GTCCTGTTGAACCCAATTTATATTCAC 59.026 37.037 0.00 0.00 34.39 3.18
6526 7184 3.986970 CTGTTGGGCCAGGAAAAAC 57.013 52.632 6.23 0.78 0.00 2.43
6596 7254 7.442364 GTCAGCCATGATTAACACTATACATGT 59.558 37.037 2.69 2.69 37.87 3.21
6640 7298 0.108615 ATCTTACTGAAGCGCTGCGT 60.109 50.000 24.04 14.49 32.21 5.24
6739 7411 1.475403 AGGTGATGTCTAGGTGACCG 58.525 55.000 0.00 0.00 44.75 4.79
6808 7489 5.447144 GGAAACATTGTTCTTTTTGCACACC 60.447 40.000 1.83 0.00 0.00 4.16
6858 7539 5.924475 ACTCTACAAAAGAAACATCCACG 57.076 39.130 0.00 0.00 32.46 4.94
6890 7571 5.499004 TGGTCTTTACATGATATAGGCCC 57.501 43.478 0.00 0.00 29.50 5.80
6938 7620 6.603237 TGAAACACACATAGTCTGAACTTG 57.397 37.500 0.00 0.00 36.92 3.16
6946 7628 6.596888 ACACATAGTCTGAACTTGATTCCATG 59.403 38.462 0.00 0.00 36.36 3.66
6976 7658 2.092429 ACAGACCCAGAGAAAGTTGCAA 60.092 45.455 0.00 0.00 0.00 4.08
7042 7724 7.072177 TGAAAAGCAGTCTAAATCCAATACG 57.928 36.000 0.00 0.00 0.00 3.06
7096 7778 4.042809 ACAACAACCCTATCATCTGAACCA 59.957 41.667 0.00 0.00 0.00 3.67
7122 7804 1.284785 TCCTGCAACCAGAAATAGGGG 59.715 52.381 0.00 0.00 41.77 4.79
7124 7806 2.094675 CTGCAACCAGAAATAGGGGTG 58.905 52.381 0.00 0.00 44.90 4.61
7240 7922 1.991965 GCAGAAAGCGAGTCTTCTGAG 59.008 52.381 19.54 0.92 34.63 3.35
7267 7949 6.461509 CCCTTGCAAATACTAATGATGGTTCC 60.462 42.308 0.00 0.00 0.00 3.62
7350 8032 5.047092 TCAGATGATAGCAGTTCAGTCAACA 60.047 40.000 0.00 0.00 37.48 3.33
7523 8211 8.909923 GGTAATTGGTAAATAAGTATGCCTTGT 58.090 33.333 0.00 0.00 34.46 3.16
7536 8224 1.762957 TGCCTTGTGGTCTAGCTATCC 59.237 52.381 0.00 0.82 35.27 2.59
7706 8397 6.424812 CGTATTGGCTGAACTCATGATGATTA 59.575 38.462 0.00 0.00 0.00 1.75
7738 8429 7.931578 TTGTGTTATAAGATGGTAACTTGGG 57.068 36.000 0.00 0.00 33.17 4.12
7741 8432 6.541278 GTGTTATAAGATGGTAACTTGGGTCC 59.459 42.308 0.00 0.00 33.17 4.46
7755 8446 3.757947 TGGGTCCACTTCTCTGAGATA 57.242 47.619 8.42 0.00 0.00 1.98
7773 8464 6.753180 TGAGATATGTACTGCTTGAAGATCC 58.247 40.000 0.00 0.00 0.00 3.36
7800 8491 7.092079 TCATCTTTATTTGTTCTGCCATGTTG 58.908 34.615 0.00 0.00 0.00 3.33
7892 9403 3.994392 GGCTTGTTTCTCAGATTACACGA 59.006 43.478 0.00 0.00 0.00 4.35
7923 9434 2.353406 CGGTTTTCGATACACACCTCCT 60.353 50.000 0.00 0.00 42.43 3.69
7990 12502 0.243907 AATGAGTACGAGCGCACACT 59.756 50.000 11.47 3.41 0.00 3.55
8022 12534 0.617413 CTGGAGGCACACAGGAAGAT 59.383 55.000 0.00 0.00 33.09 2.40
8106 12618 1.135489 GTCGGCGACTAGTTGTGATCA 60.135 52.381 31.15 0.00 0.00 2.92
8107 12619 1.542472 TCGGCGACTAGTTGTGATCAA 59.458 47.619 4.99 0.00 0.00 2.57
8132 12644 3.204827 CGAGGCGGCCATTGAAGG 61.205 66.667 23.09 0.00 0.00 3.46
8263 12785 2.214216 CGGACCCCAACTCCTGACA 61.214 63.158 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.137543 GGCACCTAATTCTCCCATAACAG 58.862 47.826 0.00 0.00 0.00 3.16
137 139 3.952967 TGGTACGCATGTGGTACTATGTA 59.047 43.478 20.89 0.00 40.04 2.29
225 227 4.024641 CCTTTTTCAACAGAAAATGGCAGC 60.025 41.667 17.20 0.00 43.51 5.25
280 293 7.201487 CCATCGATACGACAACTTTTATTCACA 60.201 37.037 0.00 0.00 39.18 3.58
295 308 3.756963 CCATCTTCCTACCATCGATACGA 59.243 47.826 0.00 0.00 41.13 3.43
296 309 3.506455 ACCATCTTCCTACCATCGATACG 59.494 47.826 0.00 0.00 0.00 3.06
297 310 4.379603 CGACCATCTTCCTACCATCGATAC 60.380 50.000 0.00 0.00 0.00 2.24
320 333 0.323725 ATGTCCTGATGTGGGGCAAC 60.324 55.000 0.00 0.00 42.03 4.17
376 389 4.452114 GTCATGTTTCTGCATAGACACACA 59.548 41.667 0.00 0.00 44.01 3.72
457 471 0.321919 TGCAATCTCAAAGGAGCGCT 60.322 50.000 11.27 11.27 41.13 5.92
479 493 8.814038 AATAGAACAGAAGCAGATTAAACCAT 57.186 30.769 0.00 0.00 0.00 3.55
580 607 5.163120 ACTCCAATGGCAGATCATATCTTGT 60.163 40.000 0.00 0.00 37.58 3.16
581 608 5.314529 ACTCCAATGGCAGATCATATCTTG 58.685 41.667 0.00 0.00 37.58 3.02
582 609 5.579753 ACTCCAATGGCAGATCATATCTT 57.420 39.130 0.00 0.00 37.58 2.40
583 610 6.021672 TCTACTCCAATGGCAGATCATATCT 58.978 40.000 0.00 0.00 41.15 1.98
584 611 6.105333 GTCTACTCCAATGGCAGATCATATC 58.895 44.000 0.00 0.00 0.00 1.63
585 612 5.545335 TGTCTACTCCAATGGCAGATCATAT 59.455 40.000 0.00 0.00 0.00 1.78
586 613 4.901250 TGTCTACTCCAATGGCAGATCATA 59.099 41.667 0.00 0.00 0.00 2.15
587 614 3.713248 TGTCTACTCCAATGGCAGATCAT 59.287 43.478 0.00 0.00 0.00 2.45
588 615 3.106827 TGTCTACTCCAATGGCAGATCA 58.893 45.455 0.00 0.00 0.00 2.92
589 616 3.827008 TGTCTACTCCAATGGCAGATC 57.173 47.619 0.00 0.00 0.00 2.75
590 617 4.574674 TTTGTCTACTCCAATGGCAGAT 57.425 40.909 0.00 0.00 0.00 2.90
591 618 4.365514 TTTTGTCTACTCCAATGGCAGA 57.634 40.909 0.00 0.00 0.00 4.26
592 619 5.649782 ATTTTTGTCTACTCCAATGGCAG 57.350 39.130 0.00 0.00 0.00 4.85
593 620 6.096705 CCATATTTTTGTCTACTCCAATGGCA 59.903 38.462 0.00 0.00 0.00 4.92
594 621 6.507023 CCATATTTTTGTCTACTCCAATGGC 58.493 40.000 0.00 0.00 0.00 4.40
595 622 6.322201 AGCCATATTTTTGTCTACTCCAATGG 59.678 38.462 0.00 0.00 0.00 3.16
678 705 6.073765 CGTGTTAGCAAGAGTCATAAAGTTGT 60.074 38.462 0.00 0.00 0.00 3.32
1271 1307 4.101585 CCATAGACTGCCTCTCATGGTTAA 59.898 45.833 0.00 0.00 31.67 2.01
1365 1401 0.255890 ACCAAGTTGCCTCAGTGTGT 59.744 50.000 0.00 0.00 0.00 3.72
1583 1619 8.396272 ACTACAATGACTCTTTATGCTGTTTT 57.604 30.769 0.00 0.00 0.00 2.43
1588 1624 7.069331 AGAGCTACTACAATGACTCTTTATGCT 59.931 37.037 0.00 0.00 30.52 3.79
1603 1639 3.170991 ACCCAAGACAGAGCTACTACA 57.829 47.619 0.00 0.00 0.00 2.74
1606 1642 2.564947 CAGAACCCAAGACAGAGCTACT 59.435 50.000 0.00 0.00 0.00 2.57
1660 1696 5.067283 ACTGGCAAAGAACTTACGTGAAATT 59.933 36.000 0.00 0.00 0.00 1.82
1947 2018 9.729281 AATCTAATAACGACCCTCTTTAAACAA 57.271 29.630 0.00 0.00 0.00 2.83
2084 2156 5.231991 CCGCATATTTCTATTTTGTGCCAAC 59.768 40.000 0.00 0.00 0.00 3.77
2210 2288 8.878769 ACAAACATTTGGTCATAAAAGAAACAC 58.121 29.630 9.09 0.00 42.34 3.32
2253 2331 1.002069 TGGAAGGCTGAACCATGGAT 58.998 50.000 21.47 6.44 43.14 3.41
2463 2541 7.678837 TCTAAAATGCACTTTTGGGAATCAAT 58.321 30.769 0.00 0.00 37.61 2.57
2514 2592 5.595952 AGCTTCTGAAGGACAAGACAAAAAT 59.404 36.000 18.38 0.00 0.00 1.82
2779 2860 4.264460 CCTGTGCAGGGAAGATCTATAC 57.736 50.000 10.28 0.00 44.87 1.47
3084 3166 0.103208 GAGGTACGAGGCCTGACATG 59.897 60.000 12.00 0.00 36.29 3.21
3283 3365 8.912988 TCCTAAAGTTTTGAAATCATGACAACT 58.087 29.630 0.00 0.00 0.00 3.16
3509 3593 1.468520 CCATCTGTTTTGCAGGGTACG 59.531 52.381 0.00 0.00 45.08 3.67
3525 3610 4.876107 TCTCTTTTTATCCGAGTTGCCATC 59.124 41.667 0.00 0.00 0.00 3.51
3559 3645 4.469945 ACTGCCCTAGTGTGCTTTATAAGA 59.530 41.667 0.00 0.00 38.49 2.10
3807 3894 4.759693 ACGAATCTTGGCATGTTTTCAGTA 59.240 37.500 14.24 0.00 0.00 2.74
3811 3898 2.663119 GCACGAATCTTGGCATGTTTTC 59.337 45.455 0.00 4.94 0.00 2.29
3934 4021 5.467735 ACCTTACCAAAATAATATCGCGTCC 59.532 40.000 5.77 0.00 0.00 4.79
3952 4039 9.899226 GAATTCTATGCAATAATGGAACCTTAC 57.101 33.333 0.00 0.00 30.88 2.34
4139 4309 6.728164 AGATGGGTATCATGCTAGAGTACAAT 59.272 38.462 0.00 0.00 35.97 2.71
4244 4414 8.387190 ACAAACTAAACCACCATCTTAACTAC 57.613 34.615 0.00 0.00 0.00 2.73
4333 4503 5.483231 TCCCCATTAAAATGCAGTTGAATCA 59.517 36.000 6.50 0.00 35.08 2.57
4514 4684 2.175202 GGCCCACCACATGACATTTAA 58.825 47.619 0.00 0.00 35.26 1.52
4515 4685 1.357420 AGGCCCACCACATGACATTTA 59.643 47.619 0.00 0.00 39.06 1.40
4719 4898 6.213600 ACACCATGGGATATCTCCTTGTATAC 59.786 42.308 18.09 0.00 41.74 1.47
4756 4935 3.979101 TTGACTAGCACCACATCATCA 57.021 42.857 0.00 0.00 0.00 3.07
5152 5389 3.046968 TGCACATGTCGCCTTTTAGTA 57.953 42.857 14.85 0.00 0.00 1.82
5205 5442 3.010472 TCTTGGGTGATCACACATCCATT 59.990 43.478 30.51 0.00 45.26 3.16
5474 5752 3.209410 CCTGTCCATGGCTAGTCATTTC 58.791 50.000 7.21 1.86 0.00 2.17
5516 5816 2.222640 CGACGACGACAACAACAAAACT 60.223 45.455 0.00 0.00 42.66 2.66
5521 5821 0.641275 CAACGACGACGACAACAACA 59.359 50.000 15.32 0.00 42.66 3.33
5522 5822 0.641783 ACAACGACGACGACAACAAC 59.358 50.000 15.32 0.00 42.66 3.32
5523 5823 0.915904 GACAACGACGACGACAACAA 59.084 50.000 15.32 0.00 42.66 2.83
5524 5824 1.195513 CGACAACGACGACGACAACA 61.196 55.000 15.32 0.00 42.66 3.33
5530 5830 1.195513 TGACAACGACAACGACGACG 61.196 55.000 5.58 5.58 42.66 5.12
5539 5839 1.789506 TGCGATGAATGACAACGACA 58.210 45.000 0.00 0.00 45.29 4.35
5588 5888 5.013183 ACAGGACCAAGTTTAATAGAGCTGT 59.987 40.000 0.00 0.00 0.00 4.40
5753 6092 7.706281 CTGCAAGTAGTAGAATCCTGTATTG 57.294 40.000 0.00 0.00 30.56 1.90
6019 6358 6.348213 CGAAATGTACCCAACCTCTTGTTAAG 60.348 42.308 0.00 0.00 34.69 1.85
6020 6359 5.470777 CGAAATGTACCCAACCTCTTGTTAA 59.529 40.000 0.00 0.00 34.69 2.01
6075 6414 1.062148 GACATAAGCTCCGGAAAACGC 59.938 52.381 5.23 5.27 42.52 4.84
6229 6568 9.530129 GATTTAGAACAGACAGAAAATGTAACG 57.470 33.333 0.00 0.00 44.17 3.18
6379 6718 6.265577 ACAACAACACTTCTTAATTGTGAGC 58.734 36.000 8.84 0.00 35.51 4.26
6391 6730 3.179048 GGAGCACAAACAACAACACTTC 58.821 45.455 0.00 0.00 0.00 3.01
6526 7184 8.733458 TGTCTCACAATGAATCCTCAAAAATAG 58.267 33.333 0.00 0.00 34.49 1.73
6596 7254 9.866655 ATCCATGCTCCTGTATAAGAAAAATAA 57.133 29.630 0.00 0.00 0.00 1.40
6808 7489 9.844790 TCACTGCAGTCAAAATTTGATTTATAG 57.155 29.630 18.64 9.30 42.47 1.31
6822 7503 5.722021 TTGTAGAGTATCACTGCAGTCAA 57.278 39.130 18.64 11.89 37.82 3.18
6890 7571 2.688446 TGGTAATAGTCTGACTGAGCCG 59.312 50.000 20.19 0.00 0.00 5.52
6938 7620 5.529060 GGGTCTGTCATAGAAACATGGAATC 59.471 44.000 0.00 0.00 37.12 2.52
6946 7628 5.407407 TTCTCTGGGTCTGTCATAGAAAC 57.593 43.478 0.00 0.00 37.12 2.78
6976 7658 3.826157 TCCCTTGTTCTTCAATTCGCAAT 59.174 39.130 0.00 0.00 35.35 3.56
7042 7724 2.301583 GGATAGATCCTGCACCTTCTCC 59.698 54.545 0.98 0.00 43.73 3.71
7096 7778 0.112995 TTCTGGTTGCAGGATGGCTT 59.887 50.000 0.00 0.00 35.86 4.35
7122 7804 1.602851 GGTCATCAGCTGCATCATCAC 59.397 52.381 9.47 0.00 0.00 3.06
7124 7806 2.257691 AGGTCATCAGCTGCATCATC 57.742 50.000 9.47 0.00 0.00 2.92
7240 7922 4.262164 CCATCATTAGTATTTGCAAGGGGC 60.262 45.833 0.00 0.00 45.13 5.80
7267 7949 2.034066 TTCTCTTGCGGGGCCTTG 59.966 61.111 0.84 0.00 0.00 3.61
7381 8069 0.575859 CTTGCAGATCAGCATCGACG 59.424 55.000 14.03 0.00 45.19 5.12
7556 8247 3.242518 GCCGCTTGAAACCTCAAATAAC 58.757 45.455 0.00 0.00 41.05 1.89
7557 8248 2.887783 TGCCGCTTGAAACCTCAAATAA 59.112 40.909 0.00 0.00 41.05 1.40
7558 8249 2.487762 CTGCCGCTTGAAACCTCAAATA 59.512 45.455 0.00 0.00 41.05 1.40
7623 8314 3.833070 ACGGGGTCAGGTATCTCAATATC 59.167 47.826 0.00 0.00 0.00 1.63
7631 8322 1.003928 ACCAAAACGGGGTCAGGTATC 59.996 52.381 0.00 0.00 40.22 2.24
7738 8429 6.734137 CAGTACATATCTCAGAGAAGTGGAC 58.266 44.000 17.41 17.41 30.88 4.02
7741 8432 6.389830 AGCAGTACATATCTCAGAGAAGTG 57.610 41.667 3.63 8.84 0.00 3.16
7755 8446 5.426689 TGAAGGATCTTCAAGCAGTACAT 57.573 39.130 7.77 0.00 0.00 2.29
7773 8464 7.318141 ACATGGCAGAACAAATAAAGATGAAG 58.682 34.615 0.00 0.00 0.00 3.02
7800 8491 5.067954 TCTTTTACAGGGGTTTTCTGCTAC 58.932 41.667 0.00 0.00 35.78 3.58
7892 9403 2.188062 TCGAAAACCGGCCAAATACT 57.812 45.000 0.00 0.00 39.14 2.12
7923 9434 2.640826 ACGTGGGAGAAAAACTATGGGA 59.359 45.455 0.00 0.00 0.00 4.37
8022 12534 2.125552 CCGGAGATCGCTGTTGCA 60.126 61.111 0.00 0.00 39.64 4.08
8069 12581 0.946221 GACTCAACCAGCTGGACGTG 60.946 60.000 39.19 29.07 38.94 4.49
8106 12618 2.048127 GCCGCCTCGTCTGACTTT 60.048 61.111 6.21 0.00 0.00 2.66
8107 12619 4.070552 GGCCGCCTCGTCTGACTT 62.071 66.667 0.71 0.00 0.00 3.01
8132 12644 2.820037 GCCACCTAGTCCTTGCGC 60.820 66.667 0.00 0.00 0.00 6.09
8228 12750 1.599047 CGAGATCCACCAGGTTGCT 59.401 57.895 0.00 0.00 35.89 3.91
8263 12785 4.021925 GTCAGGCGCAAGGACCCT 62.022 66.667 10.83 0.00 38.28 4.34


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

AutoCloner maintained by Alex Coulton.