Multiple sequence alignment - TraesCS3D01G256400

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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 TraesCS3D01G256400 chr3D 100.000 3401 0 0 1 3401 358187040 358190440 0.000000e+00 6281.0
1 TraesCS3D01G256400 chr3D 91.685 914 65 4 2497 3399 386722688 386723601 0.000000e+00 1256.0
2 TraesCS3D01G256400 chr3D 80.266 978 171 17 1015 1984 358176873 358177836 0.000000e+00 717.0
3 TraesCS3D01G256400 chr3D 78.306 968 186 20 1035 1993 358504478 358503526 1.350000e-168 603.0
4 TraesCS3D01G256400 chr3D 96.667 90 3 0 461 550 400749700 400749611 2.110000e-32 150.0
5 TraesCS3D01G256400 chr3A 94.260 1812 74 13 575 2364 477430086 477431889 0.000000e+00 2743.0
6 TraesCS3D01G256400 chr3A 79.779 994 178 15 1001 1984 477427517 477428497 0.000000e+00 701.0
7 TraesCS3D01G256400 chr3A 87.213 305 13 4 159 461 477429800 477430080 1.180000e-84 324.0
8 TraesCS3D01G256400 chr3A 93.333 120 8 0 2381 2500 477431872 477431991 9.700000e-41 178.0
9 TraesCS3D01G256400 chr3A 95.789 95 3 1 462 555 123306339 123306433 5.880000e-33 152.0
10 TraesCS3D01G256400 chr3A 95.506 89 4 0 462 550 696284968 696285056 3.540000e-30 143.0
11 TraesCS3D01G256400 chr3B 93.326 1828 77 23 544 2364 462890066 462891855 0.000000e+00 2658.0
12 TraesCS3D01G256400 chr3B 80.201 995 169 22 1001 1984 462866352 462867329 0.000000e+00 721.0
13 TraesCS3D01G256400 chr3B 92.060 466 18 3 1 447 462889593 462890058 3.700000e-179 638.0
14 TraesCS3D01G256400 chr3B 93.333 120 8 0 2381 2500 462891838 462891957 9.700000e-41 178.0
15 TraesCS3D01G256400 chr4D 92.560 914 52 7 2502 3400 506341230 506342142 0.000000e+00 1297.0
16 TraesCS3D01G256400 chr1D 91.740 908 63 7 2503 3400 448219642 448218737 0.000000e+00 1251.0
17 TraesCS3D01G256400 chr1D 76.507 962 209 16 1035 1983 450462940 450461983 3.030000e-140 508.0
18 TraesCS3D01G256400 chr1D 93.069 101 7 0 951 1051 246507053 246507153 7.600000e-32 148.0
19 TraesCS3D01G256400 chr2D 93.773 819 46 3 2587 3400 76625529 76626347 0.000000e+00 1225.0
20 TraesCS3D01G256400 chr6D 90.273 915 76 6 2498 3400 465948887 465947974 0.000000e+00 1184.0
21 TraesCS3D01G256400 chr7D 90.294 917 69 9 2500 3400 219705637 219704725 0.000000e+00 1182.0
22 TraesCS3D01G256400 chr7D 87.288 118 11 4 440 555 330808109 330808224 7.660000e-27 132.0
23 TraesCS3D01G256400 chr5A 90.252 913 77 6 2500 3400 457877961 457877049 0.000000e+00 1182.0
24 TraesCS3D01G256400 chr5A 89.923 913 77 8 2500 3400 523460949 523461858 0.000000e+00 1162.0
25 TraesCS3D01G256400 chr5A 93.000 100 7 0 458 557 453187925 453187826 2.730000e-31 147.0
26 TraesCS3D01G256400 chr4A 90.755 887 68 7 2526 3400 136247572 136248456 0.000000e+00 1171.0
27 TraesCS3D01G256400 chr4A 94.792 96 4 1 463 557 112585131 112585036 7.600000e-32 148.0
28 TraesCS3D01G256400 chr4B 89.629 916 73 11 2502 3400 423354222 423353312 0.000000e+00 1146.0
29 TraesCS3D01G256400 chr4B 94.737 95 5 0 465 559 2431980 2431886 7.600000e-32 148.0
30 TraesCS3D01G256400 chr7A 88.804 911 75 11 2500 3400 442588311 442589204 0.000000e+00 1092.0
31 TraesCS3D01G256400 chr7A 86.241 923 96 16 2500 3400 683638252 683639165 0.000000e+00 972.0
32 TraesCS3D01G256400 chr6B 85.908 887 100 11 2537 3400 460203221 460204105 0.000000e+00 922.0
33 TraesCS3D01G256400 chr1A 77.075 964 200 19 1035 1983 545649139 545648182 1.390000e-148 536.0
34 TraesCS3D01G256400 chr1A 91.919 99 7 1 459 557 577481113 577481210 1.650000e-28 137.0
35 TraesCS3D01G256400 chr1B 76.611 962 202 18 1035 1983 617968615 617967664 3.030000e-140 508.0
36 TraesCS3D01G256400 chr5B 92.000 100 7 1 462 560 696179018 696178919 4.580000e-29 139.0
37 TraesCS3D01G256400 chr2A 92.063 63 5 0 989 1051 702196684 702196746 4.670000e-14 89.8


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 TraesCS3D01G256400 chr3D 358187040 358190440 3400 False 6281.0 6281 100.000000 1 3401 1 chr3D.!!$F2 3400
1 TraesCS3D01G256400 chr3D 386722688 386723601 913 False 1256.0 1256 91.685000 2497 3399 1 chr3D.!!$F3 902
2 TraesCS3D01G256400 chr3D 358176873 358177836 963 False 717.0 717 80.266000 1015 1984 1 chr3D.!!$F1 969
3 TraesCS3D01G256400 chr3D 358503526 358504478 952 True 603.0 603 78.306000 1035 1993 1 chr3D.!!$R1 958
4 TraesCS3D01G256400 chr3A 477427517 477431991 4474 False 986.5 2743 88.646250 159 2500 4 chr3A.!!$F3 2341
5 TraesCS3D01G256400 chr3B 462889593 462891957 2364 False 1158.0 2658 92.906333 1 2500 3 chr3B.!!$F2 2499
6 TraesCS3D01G256400 chr3B 462866352 462867329 977 False 721.0 721 80.201000 1001 1984 1 chr3B.!!$F1 983
7 TraesCS3D01G256400 chr4D 506341230 506342142 912 False 1297.0 1297 92.560000 2502 3400 1 chr4D.!!$F1 898
8 TraesCS3D01G256400 chr1D 448218737 448219642 905 True 1251.0 1251 91.740000 2503 3400 1 chr1D.!!$R1 897
9 TraesCS3D01G256400 chr1D 450461983 450462940 957 True 508.0 508 76.507000 1035 1983 1 chr1D.!!$R2 948
10 TraesCS3D01G256400 chr2D 76625529 76626347 818 False 1225.0 1225 93.773000 2587 3400 1 chr2D.!!$F1 813
11 TraesCS3D01G256400 chr6D 465947974 465948887 913 True 1184.0 1184 90.273000 2498 3400 1 chr6D.!!$R1 902
12 TraesCS3D01G256400 chr7D 219704725 219705637 912 True 1182.0 1182 90.294000 2500 3400 1 chr7D.!!$R1 900
13 TraesCS3D01G256400 chr5A 457877049 457877961 912 True 1182.0 1182 90.252000 2500 3400 1 chr5A.!!$R2 900
14 TraesCS3D01G256400 chr5A 523460949 523461858 909 False 1162.0 1162 89.923000 2500 3400 1 chr5A.!!$F1 900
15 TraesCS3D01G256400 chr4A 136247572 136248456 884 False 1171.0 1171 90.755000 2526 3400 1 chr4A.!!$F1 874
16 TraesCS3D01G256400 chr4B 423353312 423354222 910 True 1146.0 1146 89.629000 2502 3400 1 chr4B.!!$R2 898
17 TraesCS3D01G256400 chr7A 442588311 442589204 893 False 1092.0 1092 88.804000 2500 3400 1 chr7A.!!$F1 900
18 TraesCS3D01G256400 chr7A 683638252 683639165 913 False 972.0 972 86.241000 2500 3400 1 chr7A.!!$F2 900
19 TraesCS3D01G256400 chr6B 460203221 460204105 884 False 922.0 922 85.908000 2537 3400 1 chr6B.!!$F1 863
20 TraesCS3D01G256400 chr1A 545648182 545649139 957 True 536.0 536 77.075000 1035 1983 1 chr1A.!!$R1 948
21 TraesCS3D01G256400 chr1B 617967664 617968615 951 True 508.0 508 76.611000 1035 1983 1 chr1B.!!$R1 948

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
355 368 0.319641 CCTTATCGGTTAGGCTCGGC 60.320 60.0 0.00 0.0 0.0 5.54 F
931 952 0.392461 AAATACACCTCGCGCACCAT 60.392 50.0 8.75 0.0 0.0 3.55 F
2058 5112 0.323629 TCGTTTGGCCCGAAGAATCT 59.676 50.0 0.00 0.0 0.0 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1742 4796 1.449070 TGATCCAAGAGCTGCGCTG 60.449 57.895 9.73 10.04 39.88 5.18 R
2394 5451 0.038618 TCGAACCCTCACGTCACATG 60.039 55.000 0.00 0.00 0.00 3.21 R
2933 6016 0.176910 TGTGGCGAGACTTGTGTTGA 59.823 50.000 0.00 0.00 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
53 54 5.347907 CAGGAACGATGGACAAGTAACTAAC 59.652 44.000 0.00 0.00 0.00 2.34
79 80 1.743252 CAGCTTCAGCCGAACTCCC 60.743 63.158 0.00 0.00 43.38 4.30
106 107 1.527034 GCTGTGCTGTCCAAAGATCA 58.473 50.000 0.00 0.00 29.57 2.92
117 118 3.055094 GTCCAAAGATCAGTCAGGGCTTA 60.055 47.826 0.00 0.00 0.00 3.09
122 123 2.093447 AGATCAGTCAGGGCTTAAACCG 60.093 50.000 0.00 0.00 0.00 4.44
123 124 1.344065 TCAGTCAGGGCTTAAACCGA 58.656 50.000 0.00 0.00 0.00 4.69
185 186 1.347320 GAACGAAACGTGCCTCTAGG 58.653 55.000 0.00 0.00 39.99 3.02
188 189 1.342174 ACGAAACGTGCCTCTAGGAAA 59.658 47.619 0.00 0.00 39.18 3.13
224 225 1.276138 TGATGATGGACGTGTCTTGCT 59.724 47.619 0.00 0.00 0.00 3.91
272 285 2.037251 ACTGCAAAGCCTAACGAGAGAA 59.963 45.455 0.00 0.00 0.00 2.87
301 314 1.593296 GCGAGACTGGGACGTAACCT 61.593 60.000 9.84 0.00 0.00 3.50
313 326 1.404391 ACGTAACCTCGAGGCACATAG 59.596 52.381 31.56 18.99 39.32 2.23
326 339 1.624487 CACATAGCTAACACGACGCA 58.376 50.000 0.00 0.00 0.00 5.24
329 342 2.159296 ACATAGCTAACACGACGCATCA 60.159 45.455 0.00 0.00 0.00 3.07
334 347 1.920574 CTAACACGACGCATCAAGGAG 59.079 52.381 0.00 0.00 0.00 3.69
354 367 3.888093 CCTTATCGGTTAGGCTCGG 57.112 57.895 0.00 0.00 0.00 4.63
355 368 0.319641 CCTTATCGGTTAGGCTCGGC 60.320 60.000 0.00 0.00 0.00 5.54
494 514 9.750783 TCCCTCTATAAACTAATATAAGAGCGT 57.249 33.333 0.00 0.00 0.00 5.07
573 593 6.668645 AGTTATTATCCATTGGGTTACTGCA 58.331 36.000 2.09 0.00 34.93 4.41
575 595 8.444783 AGTTATTATCCATTGGGTTACTGCATA 58.555 33.333 2.09 0.00 34.93 3.14
630 650 1.218875 GCATCACGTGACGTCCACAA 61.219 55.000 22.71 0.00 45.98 3.33
678 698 0.755079 CTGAAGCCGATCCAGATCCA 59.245 55.000 2.11 0.00 34.40 3.41
711 731 0.512952 CAGCAGAAAAACGACGGGAG 59.487 55.000 0.00 0.00 0.00 4.30
713 733 1.202604 AGCAGAAAAACGACGGGAGAA 60.203 47.619 0.00 0.00 0.00 2.87
715 735 1.798813 CAGAAAAACGACGGGAGAAGG 59.201 52.381 0.00 0.00 0.00 3.46
717 737 1.226030 AAAAACGACGGGAGAAGGCG 61.226 55.000 0.00 0.00 0.00 5.52
781 801 2.034066 CCTTCCTTTGCAGCCGGA 59.966 61.111 5.05 0.00 0.00 5.14
855 876 0.670546 CCATTCTCGCACGTGTTCCT 60.671 55.000 18.38 0.00 0.00 3.36
856 877 1.148310 CATTCTCGCACGTGTTCCTT 58.852 50.000 18.38 0.00 0.00 3.36
857 878 1.126846 CATTCTCGCACGTGTTCCTTC 59.873 52.381 18.38 0.00 0.00 3.46
858 879 0.599204 TTCTCGCACGTGTTCCTTCC 60.599 55.000 18.38 0.00 0.00 3.46
859 880 2.355363 TCGCACGTGTTCCTTCCG 60.355 61.111 18.38 10.20 0.00 4.30
918 939 4.062293 GCCACTCCGCACATATAAATACA 58.938 43.478 0.00 0.00 0.00 2.29
927 948 3.738791 CACATATAAATACACCTCGCGCA 59.261 43.478 8.75 0.00 0.00 6.09
931 952 0.392461 AAATACACCTCGCGCACCAT 60.392 50.000 8.75 0.00 0.00 3.55
944 965 2.061790 GCACCATCCCTCCATCCTCC 62.062 65.000 0.00 0.00 0.00 4.30
948 969 0.990374 CATCCCTCCATCCTCCCATC 59.010 60.000 0.00 0.00 0.00 3.51
949 970 0.546267 ATCCCTCCATCCTCCCATCG 60.546 60.000 0.00 0.00 0.00 3.84
950 971 2.746359 CCTCCATCCTCCCATCGC 59.254 66.667 0.00 0.00 0.00 4.58
970 993 3.181526 CGCATACAAAGTCAGCTCAGAAC 60.182 47.826 0.00 0.00 0.00 3.01
978 1001 2.027377 AGTCAGCTCAGAACCAATCCAG 60.027 50.000 0.00 0.00 0.00 3.86
1089 1116 4.287781 TGGCTTGCGTCCGACGAA 62.288 61.111 24.78 11.90 46.05 3.85
1119 1149 2.266055 CTCCTGGCCGTCAAGTCC 59.734 66.667 0.00 0.00 0.00 3.85
1719 4773 0.614697 TGGACGGATGCTTCAGGAGA 60.615 55.000 4.84 0.00 0.00 3.71
1732 4786 4.459089 GGAGACAGCCCAGCGACC 62.459 72.222 0.00 0.00 0.00 4.79
1764 4818 1.300963 GCAGCTCTTGGATCACCCA 59.699 57.895 0.00 0.00 44.93 4.51
1803 4857 2.735237 GCCGGCGACTATAAGGCT 59.265 61.111 12.58 0.00 44.06 4.58
1842 4896 1.367471 CACGTCTCCCAAGAGCACA 59.633 57.895 0.00 0.00 40.22 4.57
1883 4937 4.773117 GGACACCGACGACGAGGC 62.773 72.222 9.28 2.80 42.66 4.70
1893 4947 2.024871 GACGAGGCGGACGAGATG 59.975 66.667 8.47 0.00 34.70 2.90
1894 4948 2.750637 ACGAGGCGGACGAGATGT 60.751 61.111 8.47 0.00 34.70 3.06
1987 5041 3.545481 GCTGGATCGACGTGTGCG 61.545 66.667 0.00 0.00 44.93 5.34
2003 5057 2.627737 GCGACGAGGTCCACAGAGT 61.628 63.158 0.00 0.00 0.00 3.24
2005 5059 1.884444 GACGAGGTCCACAGAGTCC 59.116 63.158 0.00 0.00 0.00 3.85
2007 5061 2.352032 CGAGGTCCACAGAGTCCCC 61.352 68.421 0.00 0.00 0.00 4.81
2058 5112 0.323629 TCGTTTGGCCCGAAGAATCT 59.676 50.000 0.00 0.00 0.00 2.40
2109 5163 0.710567 CTGACGACAGCAACGACATC 59.289 55.000 1.13 0.00 37.33 3.06
2136 5190 2.048127 GCAGTGGTGACCGACTCC 60.048 66.667 0.00 0.00 0.00 3.85
2149 5203 0.745845 CGACTCCTCCATTTGGCAGG 60.746 60.000 8.13 8.13 34.44 4.85
2190 5244 4.096984 GTGCATTTAGGCAGCTGTAGAAAT 59.903 41.667 16.64 14.37 45.96 2.17
2191 5245 4.336433 TGCATTTAGGCAGCTGTAGAAATC 59.664 41.667 16.64 11.60 39.25 2.17
2195 5249 7.486647 CATTTAGGCAGCTGTAGAAATCAATT 58.513 34.615 16.64 0.00 0.00 2.32
2208 5262 5.772521 AGAAATCAATTTCACCCGTTTCAG 58.227 37.500 15.75 0.00 46.50 3.02
2211 5265 3.815809 TCAATTTCACCCGTTTCAGTCT 58.184 40.909 0.00 0.00 0.00 3.24
2226 5280 2.076863 CAGTCTGACGGGGATGAAAAC 58.923 52.381 1.52 0.00 0.00 2.43
2232 5286 2.370519 TGACGGGGATGAAAACTTGAGA 59.629 45.455 0.00 0.00 0.00 3.27
2238 5292 5.126061 CGGGGATGAAAACTTGAGATTTGAT 59.874 40.000 0.00 0.00 0.00 2.57
2243 5297 5.915857 TGAAAACTTGAGATTTGATCGTCG 58.084 37.500 0.00 0.00 0.00 5.12
2306 5360 2.376808 ATCTCAAAGTCTGCGACCAG 57.623 50.000 5.29 0.00 40.54 4.00
2362 5419 3.520290 TTTCGTTACAGATCCGAGCAT 57.480 42.857 0.00 0.00 31.54 3.79
2363 5420 2.492019 TCGTTACAGATCCGAGCATG 57.508 50.000 0.00 0.00 0.00 4.06
2364 5421 0.855349 CGTTACAGATCCGAGCATGC 59.145 55.000 10.51 10.51 0.00 4.06
2365 5422 1.536922 CGTTACAGATCCGAGCATGCT 60.537 52.381 22.92 22.92 0.00 3.79
2366 5423 2.131183 GTTACAGATCCGAGCATGCTC 58.869 52.381 33.47 33.47 39.55 4.26
2367 5424 1.697284 TACAGATCCGAGCATGCTCT 58.303 50.000 37.44 24.07 40.69 4.09
2368 5425 0.829333 ACAGATCCGAGCATGCTCTT 59.171 50.000 37.44 25.11 40.69 2.85
2369 5426 1.209019 ACAGATCCGAGCATGCTCTTT 59.791 47.619 37.44 24.79 40.69 2.52
2370 5427 2.286872 CAGATCCGAGCATGCTCTTTT 58.713 47.619 37.44 24.47 40.69 2.27
2371 5428 2.681848 CAGATCCGAGCATGCTCTTTTT 59.318 45.455 37.44 22.89 40.69 1.94
2391 5448 1.522668 TTTTGCAGGTGACAGATCCG 58.477 50.000 0.00 0.00 0.00 4.18
2392 5449 0.684535 TTTGCAGGTGACAGATCCGA 59.315 50.000 0.00 0.00 0.00 4.55
2393 5450 0.247460 TTGCAGGTGACAGATCCGAG 59.753 55.000 0.00 0.00 0.00 4.63
2394 5451 1.520342 GCAGGTGACAGATCCGAGC 60.520 63.158 0.00 0.00 0.00 5.03
2395 5452 1.893062 CAGGTGACAGATCCGAGCA 59.107 57.895 0.00 0.00 0.00 4.26
2399 5456 1.284657 GTGACAGATCCGAGCATGTG 58.715 55.000 0.00 0.00 0.00 3.21
2406 5463 0.179127 ATCCGAGCATGTGACGTGAG 60.179 55.000 9.33 0.00 0.00 3.51
2438 5495 2.736721 TCAGTTACTTGAAGCGACATGC 59.263 45.455 0.00 0.00 46.98 4.06
2454 5511 0.028242 ATGCGAGTGACGTCGAGATC 59.972 55.000 11.62 5.16 42.85 2.75
2456 5513 0.028242 GCGAGTGACGTCGAGATCAT 59.972 55.000 11.62 0.00 42.85 2.45
2478 5535 0.890996 CTCCTGTGTTCCAGCCAACC 60.891 60.000 0.00 0.00 40.06 3.77
2492 5549 2.026262 AGCCAACCTGGATCGTATTTGT 60.026 45.455 0.00 0.00 40.96 2.83
2521 5578 1.202313 GGCGTGTTTGGTTGCAGTTTA 60.202 47.619 0.00 0.00 0.00 2.01
2523 5580 2.105659 CGTGTTTGGTTGCAGTTTACG 58.894 47.619 0.00 0.00 0.00 3.18
2551 5608 3.259876 AGTTGCATTGCATGTCCATCTTT 59.740 39.130 12.95 0.00 38.76 2.52
2561 5618 4.443457 GCATGTCCATCTTTAGTCAGCCTA 60.443 45.833 0.00 0.00 0.00 3.93
2613 5676 3.696051 ACTTATTTGATTGCCTGCATCGT 59.304 39.130 0.00 0.00 0.00 3.73
2623 5686 2.136791 CTGCATCGTATGGAGGGGT 58.863 57.895 7.98 0.00 43.98 4.95
2631 5695 2.515429 TCGTATGGAGGGGTACTTACCT 59.485 50.000 5.41 4.36 45.72 3.08
2761 5832 2.423373 GGCCTTACCACCACATGATCAT 60.423 50.000 1.18 1.18 38.86 2.45
2789 5861 4.660789 AGCAAGATCAAACAAAGCAAGT 57.339 36.364 0.00 0.00 0.00 3.16
2816 5898 6.315891 CCCAAATGAAATCAAACACAACAAGT 59.684 34.615 0.00 0.00 0.00 3.16
2837 5919 8.850156 ACAAGTAAGAAAATGACAGCAAACTAT 58.150 29.630 0.00 0.00 0.00 2.12
2850 5932 9.938280 TGACAGCAAACTATTTAACTACATAGT 57.062 29.630 0.00 0.00 37.75 2.12
2933 6016 5.997129 CCTGGCCAAAATATGAACAAGTTTT 59.003 36.000 7.01 0.00 0.00 2.43
3081 6180 4.283722 AGTCGTGGTTAGATCTGAACCTTT 59.716 41.667 23.24 10.26 45.63 3.11
3163 6262 2.253403 GAAGTAGTTCCAGCCCCGGG 62.253 65.000 15.80 15.80 0.00 5.73
3202 6301 0.846693 AAAGTTCTGGACCTGCACCT 59.153 50.000 0.00 0.00 0.00 4.00
3231 6330 3.036084 CGCTTGTTCGCCGACAGT 61.036 61.111 0.00 0.00 0.00 3.55
3237 6336 1.286260 GTTCGCCGACAGTCTGACT 59.714 57.895 6.91 4.06 0.00 3.41
3335 6434 2.758979 GGTCCTCGTTGTCCTTGATCTA 59.241 50.000 0.00 0.00 0.00 1.98
3347 6446 4.402793 GTCCTTGATCTACTGGTAGAAGCA 59.597 45.833 13.45 11.75 44.44 3.91
3400 6500 0.178998 CCTCGGAGATCGTCCCCTTA 60.179 60.000 6.58 0.00 43.47 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 2.380084 TACTTGTCCATCGTTCCTGC 57.620 50.000 0.00 0.00 0.00 4.85
53 54 1.153005 GGCTGAAGCTGATGGAGGG 60.153 63.158 1.74 0.00 41.70 4.30
92 93 2.354259 CCTGACTGATCTTTGGACAGC 58.646 52.381 0.00 0.00 35.38 4.40
106 107 0.323957 GGTCGGTTTAAGCCCTGACT 59.676 55.000 13.40 0.00 0.00 3.41
185 186 0.462047 ATCCAGTCCATCGCCGTTTC 60.462 55.000 0.00 0.00 0.00 2.78
188 189 1.402896 ATCATCCAGTCCATCGCCGT 61.403 55.000 0.00 0.00 0.00 5.68
224 225 3.441922 CGTGGAGATGTCTCAGAAGAAGA 59.558 47.826 11.78 0.00 44.60 2.87
272 285 0.036010 CCAGTCTCGCCTTGGACATT 60.036 55.000 0.00 0.00 35.18 2.71
301 314 1.202256 CGTGTTAGCTATGTGCCTCGA 60.202 52.381 0.00 0.00 44.23 4.04
313 326 0.370273 CCTTGATGCGTCGTGTTAGC 59.630 55.000 0.58 0.00 0.00 3.09
326 339 1.807814 ACCGATAAGGCCTCCTTGAT 58.192 50.000 5.23 0.00 44.44 2.57
329 342 2.047830 CCTAACCGATAAGGCCTCCTT 58.952 52.381 5.23 3.40 46.63 3.36
355 368 4.039357 ACGTGACGTGCTCCGGAG 62.039 66.667 27.83 27.83 39.18 4.63
468 488 9.750783 ACGCTCTTATATTAGTTTATAGAGGGA 57.249 33.333 16.73 0.00 37.30 4.20
519 539 8.882736 CCCTCCGTAAACTAATATAAAAACGTT 58.117 33.333 0.00 0.00 0.00 3.99
520 540 8.257306 TCCCTCCGTAAACTAATATAAAAACGT 58.743 33.333 0.00 0.00 0.00 3.99
521 541 8.647143 TCCCTCCGTAAACTAATATAAAAACG 57.353 34.615 0.00 0.00 0.00 3.60
522 542 9.605275 ACTCCCTCCGTAAACTAATATAAAAAC 57.395 33.333 0.00 0.00 0.00 2.43
525 545 9.646522 ACTACTCCCTCCGTAAACTAATATAAA 57.353 33.333 0.00 0.00 0.00 1.40
526 546 9.646522 AACTACTCCCTCCGTAAACTAATATAA 57.353 33.333 0.00 0.00 0.00 0.98
528 548 9.819754 ATAACTACTCCCTCCGTAAACTAATAT 57.180 33.333 0.00 0.00 0.00 1.28
529 549 9.646522 AATAACTACTCCCTCCGTAAACTAATA 57.353 33.333 0.00 0.00 0.00 0.98
530 550 8.544687 AATAACTACTCCCTCCGTAAACTAAT 57.455 34.615 0.00 0.00 0.00 1.73
531 551 7.961326 AATAACTACTCCCTCCGTAAACTAA 57.039 36.000 0.00 0.00 0.00 2.24
532 552 9.289782 GATAATAACTACTCCCTCCGTAAACTA 57.710 37.037 0.00 0.00 0.00 2.24
533 553 7.232330 GGATAATAACTACTCCCTCCGTAAACT 59.768 40.741 0.00 0.00 0.00 2.66
534 554 7.014615 TGGATAATAACTACTCCCTCCGTAAAC 59.985 40.741 0.00 0.00 0.00 2.01
535 555 7.068702 TGGATAATAACTACTCCCTCCGTAAA 58.931 38.462 0.00 0.00 0.00 2.01
536 556 6.613699 TGGATAATAACTACTCCCTCCGTAA 58.386 40.000 0.00 0.00 0.00 3.18
537 557 6.204852 TGGATAATAACTACTCCCTCCGTA 57.795 41.667 0.00 0.00 0.00 4.02
538 558 5.070823 TGGATAATAACTACTCCCTCCGT 57.929 43.478 0.00 0.00 0.00 4.69
539 559 6.398918 CAATGGATAATAACTACTCCCTCCG 58.601 44.000 0.00 0.00 0.00 4.63
540 560 6.296489 CCCAATGGATAATAACTACTCCCTCC 60.296 46.154 0.00 0.00 0.00 4.30
541 561 6.272558 ACCCAATGGATAATAACTACTCCCTC 59.727 42.308 0.00 0.00 34.81 4.30
542 562 6.158260 ACCCAATGGATAATAACTACTCCCT 58.842 40.000 0.00 0.00 34.81 4.20
573 593 6.959871 GTCGACGTATACGATGATCATTGTAT 59.040 38.462 35.10 35.10 45.57 2.29
575 595 5.145059 GTCGACGTATACGATGATCATTGT 58.855 41.667 30.77 27.65 43.02 2.71
630 650 0.664761 CATCGGCGCCTGAATTGAAT 59.335 50.000 26.68 4.49 0.00 2.57
678 698 0.385390 CTGCTGCCTTTTCGTTTGGT 59.615 50.000 0.00 0.00 0.00 3.67
711 731 0.800683 GGTATTTTTGGCGCGCCTTC 60.801 55.000 45.79 25.44 36.94 3.46
713 733 1.319614 ATGGTATTTTTGGCGCGCCT 61.320 50.000 45.79 30.43 36.94 5.52
715 735 0.179150 TCATGGTATTTTTGGCGCGC 60.179 50.000 25.94 25.94 0.00 6.86
717 737 1.203523 TGGTCATGGTATTTTTGGCGC 59.796 47.619 0.00 0.00 0.00 6.53
751 771 2.144482 AGGAAGGTGTAACGAACGTG 57.856 50.000 0.00 0.00 38.12 4.49
781 801 5.253991 AGAAATGAAAAGCCTTCTCCTCT 57.746 39.130 0.00 0.00 0.00 3.69
927 948 1.073397 GGGAGGATGGAGGGATGGT 60.073 63.158 0.00 0.00 0.00 3.55
931 952 1.152247 CGATGGGAGGATGGAGGGA 60.152 63.158 0.00 0.00 0.00 4.20
944 965 2.283298 AGCTGACTTTGTATGCGATGG 58.717 47.619 0.00 0.00 0.00 3.51
948 969 2.610433 TCTGAGCTGACTTTGTATGCG 58.390 47.619 0.00 0.00 0.00 4.73
949 970 3.126000 GGTTCTGAGCTGACTTTGTATGC 59.874 47.826 0.00 0.00 0.00 3.14
950 971 4.318332 TGGTTCTGAGCTGACTTTGTATG 58.682 43.478 0.00 0.00 0.00 2.39
970 993 3.508840 GCGTTCCGGCTGGATTGG 61.509 66.667 16.96 8.86 45.91 3.16
985 1008 3.541831 CATCGTTGGTCGTCGGCG 61.542 66.667 1.15 1.15 40.80 6.46
986 1009 2.901051 ATCCATCGTTGGTCGTCGGC 62.901 60.000 12.19 0.00 44.06 5.54
1077 1104 4.415332 GAGGCTTCGTCGGACGCA 62.415 66.667 24.76 14.22 42.21 5.24
1221 1254 4.436998 AGCTGGTACTCGCCGCAC 62.437 66.667 0.00 0.00 33.01 5.34
1742 4796 1.449070 TGATCCAAGAGCTGCGCTG 60.449 57.895 9.73 10.04 39.88 5.18
1883 4937 3.872728 TCGCCGACATCTCGTCCG 61.873 66.667 0.00 0.00 42.07 4.79
1945 4999 4.135153 CGAGTCCCAGTCCGGCAG 62.135 72.222 0.00 0.00 0.00 4.85
1987 5041 1.596895 GGGACTCTGTGGACCTCGTC 61.597 65.000 0.00 0.00 0.00 4.20
2105 5159 3.511595 CTGCATTGCGCGGGATGT 61.512 61.111 8.83 0.00 46.97 3.06
2136 5190 1.915141 AACTGTCCTGCCAAATGGAG 58.085 50.000 2.98 0.00 37.39 3.86
2149 5203 2.048503 AGGGCGCACGTAACTGTC 60.049 61.111 10.83 0.00 0.00 3.51
2190 5244 3.563808 CAGACTGAAACGGGTGAAATTGA 59.436 43.478 0.00 0.00 0.00 2.57
2191 5245 3.563808 TCAGACTGAAACGGGTGAAATTG 59.436 43.478 1.64 0.00 0.00 2.32
2195 5249 1.537348 CGTCAGACTGAAACGGGTGAA 60.537 52.381 6.76 0.00 32.96 3.18
2208 5262 2.474410 AGTTTTCATCCCCGTCAGAC 57.526 50.000 0.00 0.00 0.00 3.51
2211 5265 2.370519 TCTCAAGTTTTCATCCCCGTCA 59.629 45.455 0.00 0.00 0.00 4.35
2226 5280 4.910746 ACAACGACGATCAAATCTCAAG 57.089 40.909 0.00 0.00 0.00 3.02
2232 5286 6.018588 TGTCTTTGTTACAACGACGATCAAAT 60.019 34.615 23.13 0.00 0.00 2.32
2238 5292 4.031418 TCTGTCTTTGTTACAACGACGA 57.969 40.909 23.13 20.06 0.00 4.20
2243 5297 7.724305 TCCATTACTCTGTCTTTGTTACAAC 57.276 36.000 0.00 0.00 0.00 3.32
2306 5360 2.368221 AGGAATGTAGCAGAGAGATGGC 59.632 50.000 0.00 0.00 0.00 4.40
2371 5428 1.879380 CGGATCTGTCACCTGCAAAAA 59.121 47.619 0.00 0.00 0.00 1.94
2372 5429 1.071542 TCGGATCTGTCACCTGCAAAA 59.928 47.619 0.42 0.00 0.00 2.44
2373 5430 0.684535 TCGGATCTGTCACCTGCAAA 59.315 50.000 0.42 0.00 0.00 3.68
2374 5431 0.247460 CTCGGATCTGTCACCTGCAA 59.753 55.000 0.42 0.00 0.00 4.08
2375 5432 1.893062 CTCGGATCTGTCACCTGCA 59.107 57.895 0.42 0.00 0.00 4.41
2376 5433 1.520342 GCTCGGATCTGTCACCTGC 60.520 63.158 0.42 0.00 0.00 4.85
2377 5434 0.463204 ATGCTCGGATCTGTCACCTG 59.537 55.000 0.42 0.00 0.00 4.00
2378 5435 0.463204 CATGCTCGGATCTGTCACCT 59.537 55.000 0.42 0.00 0.00 4.00
2379 5436 0.176680 ACATGCTCGGATCTGTCACC 59.823 55.000 0.42 0.00 0.00 4.02
2380 5437 1.134995 TCACATGCTCGGATCTGTCAC 60.135 52.381 0.42 0.00 0.00 3.67
2381 5438 1.134995 GTCACATGCTCGGATCTGTCA 60.135 52.381 0.42 1.74 0.00 3.58
2382 5439 1.565305 GTCACATGCTCGGATCTGTC 58.435 55.000 0.42 0.00 0.00 3.51
2383 5440 0.179127 CGTCACATGCTCGGATCTGT 60.179 55.000 0.42 0.00 0.00 3.41
2384 5441 0.179127 ACGTCACATGCTCGGATCTG 60.179 55.000 0.00 0.00 0.00 2.90
2385 5442 0.179127 CACGTCACATGCTCGGATCT 60.179 55.000 0.00 0.00 0.00 2.75
2386 5443 0.179137 TCACGTCACATGCTCGGATC 60.179 55.000 0.00 0.00 0.00 3.36
2387 5444 0.179127 CTCACGTCACATGCTCGGAT 60.179 55.000 0.00 0.00 0.00 4.18
2388 5445 1.212751 CTCACGTCACATGCTCGGA 59.787 57.895 0.00 0.00 0.00 4.55
2389 5446 1.807165 CCTCACGTCACATGCTCGG 60.807 63.158 0.00 0.00 0.00 4.63
2390 5447 1.807165 CCCTCACGTCACATGCTCG 60.807 63.158 0.00 0.00 0.00 5.03
2391 5448 0.320771 AACCCTCACGTCACATGCTC 60.321 55.000 0.00 0.00 0.00 4.26
2392 5449 0.320771 GAACCCTCACGTCACATGCT 60.321 55.000 0.00 0.00 0.00 3.79
2393 5450 1.626654 CGAACCCTCACGTCACATGC 61.627 60.000 0.00 0.00 0.00 4.06
2394 5451 0.038618 TCGAACCCTCACGTCACATG 60.039 55.000 0.00 0.00 0.00 3.21
2395 5452 0.243907 CTCGAACCCTCACGTCACAT 59.756 55.000 0.00 0.00 0.00 3.21
2399 5456 1.201647 TGAATCTCGAACCCTCACGTC 59.798 52.381 0.00 0.00 0.00 4.34
2406 5463 4.817517 TCAAGTAACTGAATCTCGAACCC 58.182 43.478 0.00 0.00 0.00 4.11
2438 5495 2.660631 GCTATGATCTCGACGTCACTCG 60.661 54.545 17.16 1.66 46.00 4.18
2478 5535 4.568359 CCTCAGTGAACAAATACGATCCAG 59.432 45.833 0.00 0.00 0.00 3.86
2492 5549 0.817634 CCAAACACGCCCTCAGTGAA 60.818 55.000 3.20 0.00 41.83 3.18
2521 5578 1.877637 TGCAATGCAACTACTGTCGT 58.122 45.000 5.01 0.00 34.76 4.34
2551 5608 5.767665 TGCATTTCAAAAACTAGGCTGACTA 59.232 36.000 0.00 0.00 0.00 2.59
2600 5663 1.544093 CCTCCATACGATGCAGGCAAT 60.544 52.381 0.00 0.00 0.00 3.56
2623 5686 6.072175 GCAATCAAACAACATGGAGGTAAGTA 60.072 38.462 0.00 0.00 0.00 2.24
2631 5695 1.959985 ACGGCAATCAAACAACATGGA 59.040 42.857 0.00 0.00 0.00 3.41
2634 5698 4.633565 ACAAAAACGGCAATCAAACAACAT 59.366 33.333 0.00 0.00 0.00 2.71
2761 5832 6.151691 GCTTTGTTTGATCTTGCTATTGTGA 58.848 36.000 0.00 0.00 0.00 3.58
2789 5861 6.878317 TGTTGTGTTTGATTTCATTTGGGTA 58.122 32.000 0.00 0.00 0.00 3.69
2850 5932 6.014499 GCCCCTGCTGTTAATCTAGACTTATA 60.014 42.308 0.00 0.00 33.53 0.98
2933 6016 0.176910 TGTGGCGAGACTTGTGTTGA 59.823 50.000 0.00 0.00 0.00 3.18
3081 6180 1.681538 GCATCTCAGGACTCGGACTA 58.318 55.000 0.00 0.00 0.00 2.59
3202 6301 1.890876 AACAAGCGGTGCATGTTCTA 58.109 45.000 6.58 0.00 45.21 2.10
3231 6330 3.506096 CTCCCGCGCGTAGTCAGA 61.506 66.667 29.95 13.55 0.00 3.27
3335 6434 1.293498 CCGCTGTGCTTCTACCAGT 59.707 57.895 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.