Multiple sequence alignment - TraesCS5B01G017500

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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 TraesCS5B01G017500 chr5B 100.000 2717 0 0 1 2717 16198571 16201287 0.000000e+00 5018.0
1 TraesCS5B01G017500 chr5B 83.616 1178 135 34 563 1717 16173359 16174501 0.000000e+00 1053.0
2 TraesCS5B01G017500 chr5B 87.380 935 84 17 863 1782 16369056 16368141 0.000000e+00 1042.0
3 TraesCS5B01G017500 chr5B 89.698 728 54 11 1077 1801 16185696 16186405 0.000000e+00 909.0
4 TraesCS5B01G017500 chr5B 89.399 566 44 4 69 629 16386498 16385944 0.000000e+00 699.0
5 TraesCS5B01G017500 chr5B 92.282 298 15 6 276 567 16172226 16172521 1.500000e-112 416.0
6 TraesCS5B01G017500 chr5B 90.000 130 11 2 1795 1923 16368091 16367963 1.670000e-37 167.0
7 TraesCS5B01G017500 chr5B 86.131 137 17 1 637 771 16370555 16370419 2.180000e-31 147.0
8 TraesCS5B01G017500 chr5B 81.022 137 21 5 1801 1935 669292583 669292716 1.330000e-18 104.0
9 TraesCS5B01G017500 chr5B 88.372 86 4 2 1715 1799 16174594 16174674 6.190000e-17 99.0
10 TraesCS5B01G017500 chr5D 92.723 907 43 7 831 1717 23011477 23010574 0.000000e+00 1288.0
11 TraesCS5B01G017500 chr5D 85.877 963 89 21 863 1806 23058229 23057295 0.000000e+00 981.0
12 TraesCS5B01G017500 chr5D 85.995 764 66 19 4 755 23059024 23058290 0.000000e+00 780.0
13 TraesCS5B01G017500 chr5D 87.478 575 48 10 1 564 23014638 23014077 2.280000e-180 641.0
14 TraesCS5B01G017500 chr5D 91.315 426 35 2 2292 2716 22965467 22965043 5.040000e-162 580.0
15 TraesCS5B01G017500 chr5D 85.377 212 15 6 559 761 23011665 23011461 3.550000e-49 206.0
16 TraesCS5B01G017500 chr5D 88.618 123 10 3 1715 1837 23010493 23010375 2.180000e-31 147.0
17 TraesCS5B01G017500 chrUn 87.343 877 77 17 921 1782 312425225 312426082 0.000000e+00 974.0
18 TraesCS5B01G017500 chrUn 90.000 130 11 2 1795 1923 312426132 312426260 1.670000e-37 167.0
19 TraesCS5B01G017500 chr5A 86.589 768 70 16 4 755 16839649 16838899 0.000000e+00 817.0
20 TraesCS5B01G017500 chr5A 91.078 538 23 3 1211 1744 16734743 16734227 0.000000e+00 704.0
21 TraesCS5B01G017500 chr5A 89.696 427 42 2 2292 2717 16730362 16729937 6.620000e-151 544.0
22 TraesCS5B01G017500 chr5A 83.574 554 57 17 1 548 16735536 16735011 3.140000e-134 488.0
23 TraesCS5B01G017500 chr5A 91.321 265 18 3 584 844 16735012 16734749 9.250000e-95 357.0
24 TraesCS5B01G017500 chr5A 82.412 199 25 6 863 1061 16838817 16838629 6.020000e-37 165.0
25 TraesCS5B01G017500 chr3B 77.666 694 112 30 840 1501 18305776 18306458 1.530000e-102 383.0
26 TraesCS5B01G017500 chr3B 77.169 657 111 26 874 1501 18484421 18485067 2.000000e-91 346.0
27 TraesCS5B01G017500 chr3D 82.759 406 58 9 1099 1501 12848511 12848907 4.300000e-93 351.0
28 TraesCS5B01G017500 chr3D 81.381 333 53 6 1171 1501 12841343 12841668 2.070000e-66 263.0
29 TraesCS5B01G017500 chr3D 78.344 157 19 9 1572 1726 12836231 12836374 1.340000e-13 87.9
30 TraesCS5B01G017500 chr7B 89.362 47 5 0 1955 2001 13651613 13651659 2.920000e-05 60.2


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 TraesCS5B01G017500 chr5B 16198571 16201287 2716 False 5018.000000 5018 100.00000 1 2717 1 chr5B.!!$F2 2716
1 TraesCS5B01G017500 chr5B 16185696 16186405 709 False 909.000000 909 89.69800 1077 1801 1 chr5B.!!$F1 724
2 TraesCS5B01G017500 chr5B 16385944 16386498 554 True 699.000000 699 89.39900 69 629 1 chr5B.!!$R1 560
3 TraesCS5B01G017500 chr5B 16172226 16174674 2448 False 522.666667 1053 88.09000 276 1799 3 chr5B.!!$F4 1523
4 TraesCS5B01G017500 chr5B 16367963 16370555 2592 True 452.000000 1042 87.83700 637 1923 3 chr5B.!!$R2 1286
5 TraesCS5B01G017500 chr5D 23057295 23059024 1729 True 880.500000 981 85.93600 4 1806 2 chr5D.!!$R3 1802
6 TraesCS5B01G017500 chr5D 23010375 23014638 4263 True 570.500000 1288 88.54900 1 1837 4 chr5D.!!$R2 1836
7 TraesCS5B01G017500 chrUn 312425225 312426260 1035 False 570.500000 974 88.67150 921 1923 2 chrUn.!!$F1 1002
8 TraesCS5B01G017500 chr5A 16729937 16735536 5599 True 523.250000 704 88.91725 1 2717 4 chr5A.!!$R1 2716
9 TraesCS5B01G017500 chr5A 16838629 16839649 1020 True 491.000000 817 84.50050 4 1061 2 chr5A.!!$R2 1057
10 TraesCS5B01G017500 chr3B 18305776 18306458 682 False 383.000000 383 77.66600 840 1501 1 chr3B.!!$F1 661
11 TraesCS5B01G017500 chr3B 18484421 18485067 646 False 346.000000 346 77.16900 874 1501 1 chr3B.!!$F2 627

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
996 4751 0.174389 TGTCTCGAAGCTGCAGATCC 59.826 55.0 20.43 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2272 9743 0.25589 TACAAAGAGGGGCAGATGGC 59.744 55.0 0.0 0.0 43.74 4.4 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
60 61 1.311859 GATTCCATTCGCATGAGGCA 58.688 50.000 0.00 0.00 45.17 4.75
64 65 2.517875 ATTCGCATGAGGCAGCCC 60.518 61.111 8.22 0.00 45.17 5.19
65 66 3.052909 ATTCGCATGAGGCAGCCCT 62.053 57.895 8.22 0.00 46.74 5.19
82 83 0.179100 CCTGCGGAAGATCATCGTGT 60.179 55.000 0.00 0.00 0.00 4.49
85 86 1.812214 GCGGAAGATCATCGTGTCGC 61.812 60.000 4.11 4.11 35.34 5.19
130 131 4.803426 CCCCTGCTCGTGCTCGTC 62.803 72.222 11.19 2.52 40.48 4.20
168 169 4.462483 AGGAAATGGTTATGTTTGATGCGT 59.538 37.500 0.00 0.00 0.00 5.24
198 199 3.010361 AGGGAGTAGGATCGAATCGGTAT 59.990 47.826 1.76 0.00 0.00 2.73
211 212 1.262417 TCGGTATGTGAGTGGCAAGA 58.738 50.000 0.00 0.00 0.00 3.02
360 382 5.106157 ACCTTTGGTCTCGATTATGCTTTTG 60.106 40.000 0.00 0.00 0.00 2.44
401 423 2.128507 GCCAAACCAAACGGACCCA 61.129 57.895 0.00 0.00 0.00 4.51
402 424 1.737201 CCAAACCAAACGGACCCAC 59.263 57.895 0.00 0.00 0.00 4.61
403 425 0.753848 CCAAACCAAACGGACCCACT 60.754 55.000 0.00 0.00 0.00 4.00
404 426 1.477195 CCAAACCAAACGGACCCACTA 60.477 52.381 0.00 0.00 0.00 2.74
471 498 6.179756 TGAACTAAAGCACATATCACCACAT 58.820 36.000 0.00 0.00 0.00 3.21
504 531 9.178427 CTTATTCAGAAGAAACAAGAGCAAAAG 57.822 33.333 0.00 0.00 37.29 2.27
593 3042 8.693504 CAACAAACTATTTTGCAAGTCACATAG 58.306 33.333 0.00 4.97 45.32 2.23
597 3046 5.939883 ACTATTTTGCAAGTCACATAGCTGA 59.060 36.000 0.00 0.00 0.00 4.26
629 3078 9.740239 AGATCGTATACGCTAATTTTTAGTGAA 57.260 29.630 20.42 0.00 39.60 3.18
630 3079 9.990888 GATCGTATACGCTAATTTTTAGTGAAG 57.009 33.333 20.42 2.46 39.60 3.02
632 3081 8.800972 TCGTATACGCTAATTTTTAGTGAAGTG 58.199 33.333 20.42 0.00 39.60 3.16
633 3082 8.800972 CGTATACGCTAATTTTTAGTGAAGTGA 58.199 33.333 13.08 0.00 0.00 3.41
634 3083 9.897349 GTATACGCTAATTTTTAGTGAAGTGAC 57.103 33.333 13.21 2.80 0.00 3.67
635 3084 6.237313 ACGCTAATTTTTAGTGAAGTGACC 57.763 37.500 13.21 0.00 0.00 4.02
689 3145 6.948353 ACACACACTTCGAATGAATATATGC 58.052 36.000 0.00 0.00 32.61 3.14
692 3148 7.374228 CACACACTTCGAATGAATATATGCAAC 59.626 37.037 0.00 0.00 32.61 4.17
750 3209 2.046314 ACTAATGCGCCGGTTGCT 60.046 55.556 19.32 5.33 38.05 3.91
845 4230 5.012664 TCAAATCTGGGTTGTAAGAGCTGTA 59.987 40.000 0.00 0.00 0.00 2.74
871 4620 8.671384 TTGGATATAATTTCCGGTTGTAGAAG 57.329 34.615 0.00 0.00 35.94 2.85
912 4661 1.006922 GTTGCTTTGTCTGCAGGCC 60.007 57.895 17.28 6.61 41.71 5.19
983 4738 0.242825 TACGTCCCTGCTTTGTCTCG 59.757 55.000 0.00 0.00 0.00 4.04
985 4740 0.319555 CGTCCCTGCTTTGTCTCGAA 60.320 55.000 0.00 0.00 0.00 3.71
996 4751 0.174389 TGTCTCGAAGCTGCAGATCC 59.826 55.000 20.43 0.00 0.00 3.36
997 4752 0.869454 GTCTCGAAGCTGCAGATCCG 60.869 60.000 20.43 12.35 0.00 4.18
1033 4808 0.592247 CGAACCAGCAAAGCACACAC 60.592 55.000 0.00 0.00 0.00 3.82
1034 4809 0.455410 GAACCAGCAAAGCACACACA 59.545 50.000 0.00 0.00 0.00 3.72
1039 4814 1.019673 AGCAAAGCACACACAGACAG 58.980 50.000 0.00 0.00 0.00 3.51
1047 4830 0.179045 ACACACAGACAGAGGGCAAC 60.179 55.000 0.00 0.00 0.00 4.17
1311 5128 1.161843 TCATAGTGTCGCTGTCGTCA 58.838 50.000 0.00 0.00 36.96 4.35
1643 5470 2.808206 GGGGTATGCCTCAGTCCCG 61.808 68.421 0.00 0.00 39.06 5.14
1697 5524 1.373497 CTTCGGAGCAGAGCACGTT 60.373 57.895 0.00 0.00 34.08 3.99
1747 5701 4.100084 TCCGTGGAGCCCTGCATG 62.100 66.667 2.41 2.41 37.62 4.06
1806 5799 2.825532 AGGCGTGGTGAATTGCTTTATT 59.174 40.909 0.00 0.00 0.00 1.40
1881 5874 1.134007 TGGAGAGCCTGCCATATGTTG 60.134 52.381 1.24 0.00 34.31 3.33
1894 5887 3.480470 CATATGTTGGATCTGTCCCACC 58.520 50.000 0.00 0.00 44.41 4.61
1899 5892 1.923395 GGATCTGTCCCACCCACCA 60.923 63.158 0.00 0.00 38.69 4.17
1905 5898 3.465832 TCTGTCCCACCCACCATAAATA 58.534 45.455 0.00 0.00 0.00 1.40
1931 5924 9.661563 ATGAAGATTTTGCAATATTGTTCATGT 57.338 25.926 24.49 13.23 0.00 3.21
1995 5988 2.831685 TGTTGTAGTGGCAACTCGAT 57.168 45.000 0.00 0.00 46.33 3.59
2006 5999 1.159285 CAACTCGATGGTGCACACAT 58.841 50.000 20.43 18.64 0.00 3.21
2036 6029 7.616103 TTTTTGCAACATAACGTCTATTGTG 57.384 32.000 0.00 0.00 0.00 3.33
2042 6035 8.079203 TGCAACATAACGTCTATTGTGAAAAAT 58.921 29.630 0.00 0.00 0.00 1.82
2043 6036 8.365210 GCAACATAACGTCTATTGTGAAAAATG 58.635 33.333 0.00 0.00 0.00 2.32
2044 6037 9.605955 CAACATAACGTCTATTGTGAAAAATGA 57.394 29.630 0.00 0.00 0.00 2.57
2134 9604 6.708949 GGAACATGACCTCTGTTACAAAACTA 59.291 38.462 0.00 0.00 37.39 2.24
2157 9628 9.841295 ACTATTTGTTTGTAGACTCCAAGTAAA 57.159 29.630 0.00 0.00 0.00 2.01
2169 9640 6.719370 AGACTCCAAGTAAATGTAAAATGCCA 59.281 34.615 0.00 0.00 0.00 4.92
2177 9648 8.546597 AGTAAATGTAAAATGCCAAATCAACC 57.453 30.769 0.00 0.00 0.00 3.77
2183 9654 6.667414 TGTAAAATGCCAAATCAACCTCCTAT 59.333 34.615 0.00 0.00 0.00 2.57
2189 9660 5.103728 TGCCAAATCAACCTCCTATCCATTA 60.104 40.000 0.00 0.00 0.00 1.90
2191 9662 6.494835 GCCAAATCAACCTCCTATCCATTATT 59.505 38.462 0.00 0.00 0.00 1.40
2197 9668 6.389869 TCAACCTCCTATCCATTATTTCCACT 59.610 38.462 0.00 0.00 0.00 4.00
2206 9677 6.573664 TCCATTATTTCCACTGAACACAAG 57.426 37.500 0.00 0.00 0.00 3.16
2225 9696 1.137872 AGCATTGAGGGACGCTAGAAG 59.862 52.381 0.00 0.00 31.60 2.85
2247 9718 3.904234 GCGAATTTTTGTACTGTTCGTCC 59.096 43.478 14.81 2.87 42.45 4.79
2255 9726 3.064207 TGTACTGTTCGTCCAAAGCATC 58.936 45.455 0.00 0.00 0.00 3.91
2256 9727 1.148310 ACTGTTCGTCCAAAGCATCG 58.852 50.000 0.00 0.00 0.00 3.84
2257 9728 1.148310 CTGTTCGTCCAAAGCATCGT 58.852 50.000 0.00 0.00 0.00 3.73
2258 9729 1.126846 CTGTTCGTCCAAAGCATCGTC 59.873 52.381 0.00 0.00 0.00 4.20
2259 9730 0.442699 GTTCGTCCAAAGCATCGTCC 59.557 55.000 0.00 0.00 0.00 4.79
2260 9731 0.034198 TTCGTCCAAAGCATCGTCCA 59.966 50.000 0.00 0.00 0.00 4.02
2261 9732 0.389817 TCGTCCAAAGCATCGTCCAG 60.390 55.000 0.00 0.00 0.00 3.86
2262 9733 1.361668 CGTCCAAAGCATCGTCCAGG 61.362 60.000 0.00 0.00 0.00 4.45
2263 9734 1.026718 GTCCAAAGCATCGTCCAGGG 61.027 60.000 0.00 0.00 0.00 4.45
2264 9735 1.002134 CCAAAGCATCGTCCAGGGT 60.002 57.895 0.00 0.00 0.00 4.34
2265 9736 1.308069 CCAAAGCATCGTCCAGGGTG 61.308 60.000 0.00 0.00 0.00 4.61
2266 9737 1.675641 AAAGCATCGTCCAGGGTGC 60.676 57.895 0.00 0.00 37.84 5.01
2267 9738 3.005539 AGCATCGTCCAGGGTGCT 61.006 61.111 1.09 1.09 42.66 4.40
2268 9739 2.045926 GCATCGTCCAGGGTGCTT 60.046 61.111 0.00 0.00 34.85 3.91
2269 9740 1.220749 GCATCGTCCAGGGTGCTTA 59.779 57.895 0.00 0.00 34.85 3.09
2270 9741 1.090052 GCATCGTCCAGGGTGCTTAC 61.090 60.000 0.00 0.00 34.85 2.34
2271 9742 0.537188 CATCGTCCAGGGTGCTTACT 59.463 55.000 0.00 0.00 0.00 2.24
2272 9743 0.537188 ATCGTCCAGGGTGCTTACTG 59.463 55.000 0.00 0.00 34.54 2.74
2273 9744 1.741770 CGTCCAGGGTGCTTACTGC 60.742 63.158 0.00 0.00 43.25 4.40
2274 9745 1.377333 GTCCAGGGTGCTTACTGCC 60.377 63.158 0.00 0.00 42.00 4.85
2275 9746 1.845664 TCCAGGGTGCTTACTGCCA 60.846 57.895 0.00 0.00 42.00 4.92
2276 9747 1.207488 TCCAGGGTGCTTACTGCCAT 61.207 55.000 0.00 0.00 42.00 4.40
2277 9748 0.749454 CCAGGGTGCTTACTGCCATC 60.749 60.000 0.00 0.00 42.00 3.51
2278 9749 0.254178 CAGGGTGCTTACTGCCATCT 59.746 55.000 0.00 0.00 42.00 2.90
2279 9750 0.254178 AGGGTGCTTACTGCCATCTG 59.746 55.000 0.00 0.00 42.00 2.90
2280 9751 1.379642 GGGTGCTTACTGCCATCTGC 61.380 60.000 0.00 0.00 42.00 4.26
2281 9752 1.379642 GGTGCTTACTGCCATCTGCC 61.380 60.000 0.00 0.00 42.00 4.85
2282 9753 1.077501 TGCTTACTGCCATCTGCCC 60.078 57.895 0.00 0.00 42.00 5.36
2283 9754 1.825622 GCTTACTGCCATCTGCCCC 60.826 63.158 0.00 0.00 40.16 5.80
2284 9755 1.918253 CTTACTGCCATCTGCCCCT 59.082 57.895 0.00 0.00 40.16 4.79
2285 9756 0.179034 CTTACTGCCATCTGCCCCTC 60.179 60.000 0.00 0.00 40.16 4.30
2286 9757 0.621571 TTACTGCCATCTGCCCCTCT 60.622 55.000 0.00 0.00 40.16 3.69
2287 9758 0.621571 TACTGCCATCTGCCCCTCTT 60.622 55.000 0.00 0.00 40.16 2.85
2288 9759 1.305623 CTGCCATCTGCCCCTCTTT 59.694 57.895 0.00 0.00 40.16 2.52
2289 9760 1.000521 TGCCATCTGCCCCTCTTTG 60.001 57.895 0.00 0.00 40.16 2.77
2290 9761 1.000396 GCCATCTGCCCCTCTTTGT 60.000 57.895 0.00 0.00 0.00 2.83
2291 9762 0.255890 GCCATCTGCCCCTCTTTGTA 59.744 55.000 0.00 0.00 0.00 2.41
2292 9763 1.133668 GCCATCTGCCCCTCTTTGTAT 60.134 52.381 0.00 0.00 0.00 2.29
2296 9767 3.634397 TCTGCCCCTCTTTGTATTCTG 57.366 47.619 0.00 0.00 0.00 3.02
2306 9777 4.406456 TCTTTGTATTCTGTTGGCACCAT 58.594 39.130 0.00 0.00 0.00 3.55
2307 9778 4.458989 TCTTTGTATTCTGTTGGCACCATC 59.541 41.667 0.00 0.00 0.00 3.51
2319 9790 1.789078 GCACCATCGATGCCACATCC 61.789 60.000 20.25 0.00 37.08 3.51
2320 9791 0.464193 CACCATCGATGCCACATCCA 60.464 55.000 20.25 0.00 0.00 3.41
2323 9794 1.475571 CCATCGATGCCACATCCAGAA 60.476 52.381 20.25 0.00 0.00 3.02
2327 9798 2.945008 TCGATGCCACATCCAGAAATTC 59.055 45.455 2.15 0.00 0.00 2.17
2342 9814 5.006649 CCAGAAATTCGCATCGATTTCTGTA 59.993 40.000 27.37 1.60 45.62 2.74
2343 9815 5.898606 CAGAAATTCGCATCGATTTCTGTAC 59.101 40.000 24.95 0.00 44.32 2.90
2344 9816 4.795970 AATTCGCATCGATTTCTGTACC 57.204 40.909 0.00 0.00 35.23 3.34
2349 9821 3.006940 GCATCGATTTCTGTACCCACAA 58.993 45.455 0.00 0.00 33.22 3.33
2363 9835 7.181305 TCTGTACCCACAAAGATAGTTTATCCA 59.819 37.037 0.00 0.00 33.13 3.41
2382 9854 5.227569 TCCATCTTTCTTAAGTGTGAGCA 57.772 39.130 1.63 0.00 32.98 4.26
2392 9864 7.658179 TCTTAAGTGTGAGCAAATAGAGTTG 57.342 36.000 1.63 0.00 0.00 3.16
2427 9899 3.077359 GCATTCACCCAGCATACCTATC 58.923 50.000 0.00 0.00 0.00 2.08
2431 9903 1.774254 CACCCAGCATACCTATCCCAA 59.226 52.381 0.00 0.00 0.00 4.12
2433 9905 3.587061 CACCCAGCATACCTATCCCAATA 59.413 47.826 0.00 0.00 0.00 1.90
2443 9915 7.659390 GCATACCTATCCCAATATAGATCTTGC 59.341 40.741 0.00 0.00 32.13 4.01
2461 9933 3.266510 TGCAGATTCCTAGCGAAATGT 57.733 42.857 0.00 0.00 33.08 2.71
2464 9936 3.797039 CAGATTCCTAGCGAAATGTCCA 58.203 45.455 0.00 0.00 33.08 4.02
2494 9966 6.040842 ACTCAACCTGAAAATGTTAGCACAAT 59.959 34.615 0.00 0.00 36.16 2.71
2505 9977 9.979578 AAAATGTTAGCACAATGATTTCAGTTA 57.020 25.926 0.00 0.00 36.16 2.24
2509 9981 7.860373 TGTTAGCACAATGATTTCAGTTAACAC 59.140 33.333 8.61 0.00 0.00 3.32
2513 9985 7.596248 AGCACAATGATTTCAGTTAACACATTC 59.404 33.333 8.61 0.00 0.00 2.67
2514 9986 7.148755 GCACAATGATTTCAGTTAACACATTCC 60.149 37.037 8.61 0.00 0.00 3.01
2521 9993 9.271828 GATTTCAGTTAACACATTCCCAAAATT 57.728 29.630 8.61 0.00 0.00 1.82
2524 9996 8.472007 TCAGTTAACACATTCCCAAAATTAGT 57.528 30.769 8.61 0.00 0.00 2.24
2558 10030 3.129113 TGGCACATGCAGCAGTAAAATAG 59.871 43.478 12.17 0.00 44.36 1.73
2561 10033 5.032863 GCACATGCAGCAGTAAAATAGAAG 58.967 41.667 0.00 0.00 41.59 2.85
2574 10046 9.307121 CAGTAAAATAGAAGATCACACACCTAG 57.693 37.037 0.00 0.00 0.00 3.02
2624 10096 1.510492 TATTCCCTGCATCAGCCTCA 58.490 50.000 0.00 0.00 41.13 3.86
2625 10097 0.183014 ATTCCCTGCATCAGCCTCAG 59.817 55.000 0.00 0.00 41.13 3.35
2657 10129 2.224426 TGCTTCGAGGGTCAGCTAAAAA 60.224 45.455 7.50 0.00 34.42 1.94
2688 10160 0.608640 ACATCACCTCTTCGTCCACC 59.391 55.000 0.00 0.00 0.00 4.61
2689 10161 0.898320 CATCACCTCTTCGTCCACCT 59.102 55.000 0.00 0.00 0.00 4.00
2690 10162 1.276421 CATCACCTCTTCGTCCACCTT 59.724 52.381 0.00 0.00 0.00 3.50
2691 10163 0.679505 TCACCTCTTCGTCCACCTTG 59.320 55.000 0.00 0.00 0.00 3.61
2700 10172 2.989639 TCCACCTTGGAGCATCGG 59.010 61.111 0.00 0.00 42.67 4.18
2705 10177 1.452108 CCTTGGAGCATCGGGGTTC 60.452 63.158 0.00 0.00 34.37 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 2.403252 ATGGAATCCTTCACGTGACC 57.597 50.000 19.90 15.47 0.00 4.02
64 65 1.203928 GACACGATGATCTTCCGCAG 58.796 55.000 3.19 0.00 0.00 5.18
65 66 0.525455 CGACACGATGATCTTCCGCA 60.525 55.000 3.19 0.00 0.00 5.69
67 68 1.209275 GGCGACACGATGATCTTCCG 61.209 60.000 3.19 2.59 0.00 4.30
73 74 2.413351 CTCCGGCGACACGATGAT 59.587 61.111 9.30 0.00 35.47 2.45
85 86 3.391665 CTTGCCACTAGCCCTCCGG 62.392 68.421 0.00 0.00 42.71 5.14
102 103 1.512735 GAGCAGGGGATAGGGTTTCT 58.487 55.000 0.00 0.00 0.00 2.52
130 131 0.709992 TTCCTCCTTTCCCCCATTGG 59.290 55.000 0.00 0.00 0.00 3.16
168 169 2.487445 CGATCCTACTCCCTGTAGCTCA 60.487 54.545 0.00 0.00 45.44 4.26
174 175 2.231529 CGATTCGATCCTACTCCCTGT 58.768 52.381 0.00 0.00 0.00 4.00
198 199 1.357137 TACCCATCTTGCCACTCACA 58.643 50.000 0.00 0.00 0.00 3.58
211 212 5.357032 CCAACTTCTAAGCGAAATTACCCAT 59.643 40.000 0.00 0.00 0.00 4.00
264 265 1.035139 CCACAGCTTTTCCACAGCTT 58.965 50.000 0.00 0.00 45.82 3.74
266 267 1.032014 TTCCACAGCTTTTCCACAGC 58.968 50.000 0.00 0.00 37.56 4.40
267 268 3.799281 TTTTCCACAGCTTTTCCACAG 57.201 42.857 0.00 0.00 0.00 3.66
268 269 3.740764 GCATTTTCCACAGCTTTTCCACA 60.741 43.478 0.00 0.00 0.00 4.17
269 270 2.802247 GCATTTTCCACAGCTTTTCCAC 59.198 45.455 0.00 0.00 0.00 4.02
270 271 2.433604 TGCATTTTCCACAGCTTTTCCA 59.566 40.909 0.00 0.00 0.00 3.53
271 272 2.802247 GTGCATTTTCCACAGCTTTTCC 59.198 45.455 0.00 0.00 33.50 3.13
272 273 3.721035 AGTGCATTTTCCACAGCTTTTC 58.279 40.909 0.00 0.00 35.69 2.29
273 274 3.825143 AGTGCATTTTCCACAGCTTTT 57.175 38.095 0.00 0.00 35.69 2.27
274 275 4.584325 TCTTAGTGCATTTTCCACAGCTTT 59.416 37.500 0.00 0.00 35.69 3.51
360 382 5.551760 TTCTAAGCTAACTTCTGCATTGC 57.448 39.130 0.46 0.46 37.33 3.56
401 423 2.151202 CAAACAGACGGGCATGTTAGT 58.849 47.619 0.00 0.00 38.66 2.24
402 424 2.151202 ACAAACAGACGGGCATGTTAG 58.849 47.619 0.00 0.00 38.66 2.34
403 425 2.264005 ACAAACAGACGGGCATGTTA 57.736 45.000 0.00 0.00 38.66 2.41
404 426 2.151202 CTACAAACAGACGGGCATGTT 58.849 47.619 0.00 0.00 41.28 2.71
471 498 9.948964 TCTTGTTTCTTCTGAATAAGATCATCA 57.051 29.630 0.00 0.00 35.48 3.07
478 505 9.178427 CTTTTGCTCTTGTTTCTTCTGAATAAG 57.822 33.333 0.00 0.00 32.65 1.73
593 3042 5.154932 AGCGTATACGATCTAATGTTCAGC 58.845 41.667 28.66 5.54 43.02 4.26
629 3078 7.639113 TTTGAAAAACAATGACTAGGTCACT 57.361 32.000 2.34 0.00 45.65 3.41
630 3079 8.871686 AATTTGAAAAACAATGACTAGGTCAC 57.128 30.769 2.34 0.00 45.65 3.67
633 3082 9.883142 TCAAAATTTGAAAAACAATGACTAGGT 57.117 25.926 5.87 0.00 38.36 3.08
689 3145 2.553086 ACAAAAGCTTGTGCATGGTTG 58.447 42.857 16.88 8.93 44.28 3.77
692 3148 3.922240 GTGATACAAAAGCTTGTGCATGG 59.078 43.478 16.88 0.00 45.53 3.66
771 3230 5.538849 TGTTCACATAGTACTCACCACAA 57.461 39.130 0.00 0.00 0.00 3.33
774 3233 6.605471 AAGATGTTCACATAGTACTCACCA 57.395 37.500 0.00 0.00 36.57 4.17
845 4230 9.284968 CTTCTACAACCGGAAATTATATCCAAT 57.715 33.333 9.46 0.00 36.74 3.16
871 4620 1.448540 CTGTCCCGATGTCACCAGC 60.449 63.158 0.00 0.00 0.00 4.85
912 4661 5.818336 TGTCTCGTCTAAGAATCCTGTCTAG 59.182 44.000 0.00 0.00 0.00 2.43
983 4738 2.032860 TAGGCCGGATCTGCAGCTTC 62.033 60.000 9.47 8.39 0.00 3.86
985 4740 0.542938 TATAGGCCGGATCTGCAGCT 60.543 55.000 9.47 0.00 0.00 4.24
996 4751 4.483311 GTTCGAGGAGTTTATATAGGCCG 58.517 47.826 0.00 0.00 0.00 6.13
997 4752 4.282703 TGGTTCGAGGAGTTTATATAGGCC 59.717 45.833 0.00 0.00 0.00 5.19
1033 4808 0.107945 GCTAGGTTGCCCTCTGTCTG 60.108 60.000 0.00 0.00 41.45 3.51
1034 4809 0.252467 AGCTAGGTTGCCCTCTGTCT 60.252 55.000 0.00 0.00 41.45 3.41
1039 4814 3.206964 GTTTATCAGCTAGGTTGCCCTC 58.793 50.000 0.00 0.00 41.45 4.30
1047 4830 3.386078 TCAGCTCCTGTTTATCAGCTAGG 59.614 47.826 0.00 0.00 42.38 3.02
1090 4904 1.734388 AAAACCACTGCGACCTTGGC 61.734 55.000 0.00 0.00 33.25 4.52
1311 5128 3.849951 CCGCCGGCATACCACTCT 61.850 66.667 28.98 0.00 34.57 3.24
1333 5150 1.675641 GGATCAACTTGCCGCACCT 60.676 57.895 0.00 0.00 0.00 4.00
1643 5470 2.167900 AGTAACGGCCCTGAGACATTAC 59.832 50.000 0.00 0.00 0.00 1.89
1881 5874 1.281925 ATGGTGGGTGGGACAGATCC 61.282 60.000 0.00 0.00 41.80 3.36
1884 5877 1.748732 TTTATGGTGGGTGGGACAGA 58.251 50.000 0.00 0.00 41.80 3.41
1886 5879 3.788708 TCATATTTATGGTGGGTGGGACA 59.211 43.478 0.00 0.00 34.50 4.02
1894 5887 8.945481 TTGCAAAATCTTCATATTTATGGTGG 57.055 30.769 0.00 0.00 34.50 4.61
1905 5898 9.661563 ACATGAACAATATTGCAAAATCTTCAT 57.338 25.926 15.48 16.11 29.57 2.57
1938 5931 6.969043 AGACACATGGATGATACCCTAAAAA 58.031 36.000 0.00 0.00 0.00 1.94
1939 5932 6.575244 AGACACATGGATGATACCCTAAAA 57.425 37.500 0.00 0.00 0.00 1.52
1940 5933 7.684317 TTAGACACATGGATGATACCCTAAA 57.316 36.000 0.00 0.00 0.00 1.85
1941 5934 7.684317 TTTAGACACATGGATGATACCCTAA 57.316 36.000 0.00 0.00 0.00 2.69
1942 5935 7.126573 TGTTTTAGACACATGGATGATACCCTA 59.873 37.037 0.00 0.00 32.00 3.53
1943 5936 6.069673 TGTTTTAGACACATGGATGATACCCT 60.070 38.462 0.00 0.00 32.00 4.34
1944 5937 6.119536 TGTTTTAGACACATGGATGATACCC 58.880 40.000 0.00 0.00 32.00 3.69
1945 5938 7.642669 CATGTTTTAGACACATGGATGATACC 58.357 38.462 0.00 0.00 45.34 2.73
1955 5948 6.899393 ACATTCCACATGTTTTAGACACAT 57.101 33.333 0.00 0.00 42.04 3.21
1956 5949 6.096141 ACAACATTCCACATGTTTTAGACACA 59.904 34.615 0.00 0.00 42.04 3.72
1957 5950 6.503524 ACAACATTCCACATGTTTTAGACAC 58.496 36.000 0.00 0.00 42.04 3.67
1958 5951 6.707440 ACAACATTCCACATGTTTTAGACA 57.293 33.333 0.00 0.00 39.94 3.41
1959 5952 7.803189 CACTACAACATTCCACATGTTTTAGAC 59.197 37.037 20.18 0.00 41.32 2.59
2031 6024 9.582431 CTTATCTTGCAGATCATTTTTCACAAT 57.418 29.630 0.00 0.00 36.20 2.71
2036 6029 9.286946 CAGAACTTATCTTGCAGATCATTTTTC 57.713 33.333 0.00 0.00 36.20 2.29
2042 6035 5.122869 GCAACAGAACTTATCTTGCAGATCA 59.877 40.000 0.00 0.00 38.46 2.92
2043 6036 5.122869 TGCAACAGAACTTATCTTGCAGATC 59.877 40.000 0.00 0.00 41.56 2.75
2044 6037 5.005740 TGCAACAGAACTTATCTTGCAGAT 58.994 37.500 0.00 4.45 41.56 2.90
2045 6038 4.388485 TGCAACAGAACTTATCTTGCAGA 58.612 39.130 0.00 0.00 41.56 4.26
2072 6065 9.209175 TGTAGCAAAAATTGTGTTGTAGTTTTT 57.791 25.926 0.00 0.00 33.63 1.94
2106 6101 5.241403 TGTAACAGAGGTCATGTTCCAAT 57.759 39.130 11.03 0.00 41.08 3.16
2107 6102 4.698201 TGTAACAGAGGTCATGTTCCAA 57.302 40.909 11.03 0.00 41.08 3.53
2110 6105 6.619801 AGTTTTGTAACAGAGGTCATGTTC 57.380 37.500 0.00 0.00 41.08 3.18
2134 9604 9.131791 ACATTTACTTGGAGTCTACAAACAAAT 57.868 29.630 0.00 4.99 0.00 2.32
2150 9621 9.810231 GTTGATTTGGCATTTTACATTTACTTG 57.190 29.630 0.00 0.00 0.00 3.16
2153 9624 8.546597 AGGTTGATTTGGCATTTTACATTTAC 57.453 30.769 0.00 0.00 0.00 2.01
2157 9628 5.484998 AGGAGGTTGATTTGGCATTTTACAT 59.515 36.000 0.00 0.00 0.00 2.29
2158 9629 4.837860 AGGAGGTTGATTTGGCATTTTACA 59.162 37.500 0.00 0.00 0.00 2.41
2164 9635 3.205056 TGGATAGGAGGTTGATTTGGCAT 59.795 43.478 0.00 0.00 0.00 4.40
2169 9640 8.288812 TGGAAATAATGGATAGGAGGTTGATTT 58.711 33.333 0.00 0.00 0.00 2.17
2177 9648 7.227512 GTGTTCAGTGGAAATAATGGATAGGAG 59.772 40.741 0.00 0.00 34.13 3.69
2183 9654 5.048083 GCTTGTGTTCAGTGGAAATAATGGA 60.048 40.000 0.00 0.00 34.13 3.41
2189 9660 4.341806 TCAATGCTTGTGTTCAGTGGAAAT 59.658 37.500 0.00 0.00 34.13 2.17
2191 9662 3.286353 TCAATGCTTGTGTTCAGTGGAA 58.714 40.909 0.00 0.00 0.00 3.53
2197 9668 2.229792 GTCCCTCAATGCTTGTGTTCA 58.770 47.619 0.00 0.00 0.00 3.18
2206 9677 1.576356 CTTCTAGCGTCCCTCAATGC 58.424 55.000 0.00 0.00 0.00 3.56
2225 9696 3.904234 GGACGAACAGTACAAAAATTCGC 59.096 43.478 13.41 8.60 44.53 4.70
2239 9710 1.144969 GACGATGCTTTGGACGAACA 58.855 50.000 0.00 0.00 0.00 3.18
2247 9718 1.926511 GCACCCTGGACGATGCTTTG 61.927 60.000 0.00 0.00 35.16 2.77
2255 9726 1.741770 GCAGTAAGCACCCTGGACG 60.742 63.158 0.00 0.00 44.79 4.79
2256 9727 4.303257 GCAGTAAGCACCCTGGAC 57.697 61.111 0.00 0.00 44.79 4.02
2272 9743 0.255890 TACAAAGAGGGGCAGATGGC 59.744 55.000 0.00 0.00 43.74 4.40
2273 9744 3.117738 AGAATACAAAGAGGGGCAGATGG 60.118 47.826 0.00 0.00 0.00 3.51
2274 9745 3.881688 CAGAATACAAAGAGGGGCAGATG 59.118 47.826 0.00 0.00 0.00 2.90
2275 9746 3.525199 ACAGAATACAAAGAGGGGCAGAT 59.475 43.478 0.00 0.00 0.00 2.90
2276 9747 2.912956 ACAGAATACAAAGAGGGGCAGA 59.087 45.455 0.00 0.00 0.00 4.26
2277 9748 3.356529 ACAGAATACAAAGAGGGGCAG 57.643 47.619 0.00 0.00 0.00 4.85
2278 9749 3.420893 CAACAGAATACAAAGAGGGGCA 58.579 45.455 0.00 0.00 0.00 5.36
2279 9750 2.755103 CCAACAGAATACAAAGAGGGGC 59.245 50.000 0.00 0.00 0.00 5.80
2280 9751 2.755103 GCCAACAGAATACAAAGAGGGG 59.245 50.000 0.00 0.00 0.00 4.79
2281 9752 3.191371 GTGCCAACAGAATACAAAGAGGG 59.809 47.826 0.00 0.00 0.00 4.30
2282 9753 3.191371 GGTGCCAACAGAATACAAAGAGG 59.809 47.826 0.00 0.00 0.00 3.69
2283 9754 3.820467 TGGTGCCAACAGAATACAAAGAG 59.180 43.478 0.00 0.00 0.00 2.85
2284 9755 3.826524 TGGTGCCAACAGAATACAAAGA 58.173 40.909 0.00 0.00 0.00 2.52
2285 9756 4.672542 CGATGGTGCCAACAGAATACAAAG 60.673 45.833 0.00 0.00 0.00 2.77
2286 9757 3.190327 CGATGGTGCCAACAGAATACAAA 59.810 43.478 0.00 0.00 0.00 2.83
2287 9758 2.746904 CGATGGTGCCAACAGAATACAA 59.253 45.455 0.00 0.00 0.00 2.41
2288 9759 2.027653 TCGATGGTGCCAACAGAATACA 60.028 45.455 0.00 0.00 0.00 2.29
2289 9760 2.627945 TCGATGGTGCCAACAGAATAC 58.372 47.619 0.00 0.00 0.00 1.89
2290 9761 3.205338 CATCGATGGTGCCAACAGAATA 58.795 45.455 17.96 0.00 0.00 1.75
2291 9762 2.019249 CATCGATGGTGCCAACAGAAT 58.981 47.619 17.96 0.00 0.00 2.40
2292 9763 1.452110 CATCGATGGTGCCAACAGAA 58.548 50.000 17.96 0.00 0.00 3.02
2306 9777 2.715749 ATTTCTGGATGTGGCATCGA 57.284 45.000 0.00 0.00 0.00 3.59
2307 9778 2.286595 CGAATTTCTGGATGTGGCATCG 60.287 50.000 0.00 0.00 0.00 3.84
2320 9791 5.006746 GGTACAGAAATCGATGCGAATTTCT 59.993 40.000 0.00 15.04 40.48 2.52
2323 9794 3.560068 GGGTACAGAAATCGATGCGAATT 59.440 43.478 0.00 0.00 39.99 2.17
2327 9798 1.593006 GTGGGTACAGAAATCGATGCG 59.407 52.381 0.00 0.00 0.00 4.73
2342 9814 7.213178 AGATGGATAAACTATCTTTGTGGGT 57.787 36.000 0.00 0.00 42.75 4.51
2363 9835 9.160496 CTCTATTTGCTCACACTTAAGAAAGAT 57.840 33.333 10.09 0.00 36.50 2.40
2382 9854 7.260603 GCAATTGGTATCTTGCAACTCTATTT 58.739 34.615 7.72 0.00 45.50 1.40
2392 9864 4.114794 GGTGAATGCAATTGGTATCTTGC 58.885 43.478 7.72 0.51 46.19 4.01
2443 9915 3.797039 TGGACATTTCGCTAGGAATCTG 58.203 45.455 0.00 0.00 33.85 2.90
2461 9933 4.705110 TTTTCAGGTTGAGTCTGATGGA 57.295 40.909 0.00 0.00 40.46 3.41
2464 9936 6.150140 GCTAACATTTTCAGGTTGAGTCTGAT 59.850 38.462 0.00 0.00 40.46 2.90
2494 9966 6.968263 TTGGGAATGTGTTAACTGAAATCA 57.032 33.333 7.22 0.00 0.00 2.57
2534 10006 1.097232 TTACTGCTGCATGTGCCATC 58.903 50.000 1.31 0.00 41.18 3.51
2545 10017 7.413438 GGTGTGTGATCTTCTATTTTACTGCTG 60.413 40.741 0.00 0.00 0.00 4.41
2549 10021 9.256228 TCTAGGTGTGTGATCTTCTATTTTACT 57.744 33.333 0.00 0.00 0.00 2.24
2558 10030 6.701145 TGATACTCTAGGTGTGTGATCTTC 57.299 41.667 0.00 0.00 0.00 2.87
2603 10075 2.224695 TGAGGCTGATGCAGGGAATATG 60.225 50.000 0.00 0.00 41.91 1.78
2624 10096 2.033550 CCTCGAAGCAGTAGATTACGCT 59.966 50.000 0.00 0.00 39.13 5.07
2625 10097 2.386249 CCTCGAAGCAGTAGATTACGC 58.614 52.381 0.00 0.00 0.00 4.42
2657 10129 6.037940 CGAAGAGGTGATGTCATCATTTGAAT 59.962 38.462 18.32 4.56 42.04 2.57
2688 10160 0.745845 CTGAACCCCGATGCTCCAAG 60.746 60.000 0.00 0.00 0.00 3.61
2689 10161 1.299648 CTGAACCCCGATGCTCCAA 59.700 57.895 0.00 0.00 0.00 3.53
2690 10162 2.989639 CTGAACCCCGATGCTCCA 59.010 61.111 0.00 0.00 0.00 3.86
2691 10163 2.514824 GCTGAACCCCGATGCTCC 60.515 66.667 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.