Multiple sequence alignment - TraesCS4D01G157600

Loading Multiple Alignment...

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 TraesCS4D01G157600 chr4D 100.000 2198 0 0 1 2198 216532975 216535172 0.000000e+00 4060.0
1 TraesCS4D01G157600 chr4B 92.344 1489 55 26 201 1647 245683713 245682242 0.000000e+00 2063.0
2 TraesCS4D01G157600 chr4B 93.088 217 10 2 1 214 245685288 245685074 1.640000e-81 313.0
3 TraesCS4D01G157600 chr4B 92.188 192 11 2 1891 2079 245681708 245681518 3.600000e-68 268.0
4 TraesCS4D01G157600 chr4B 95.161 62 3 0 2018 2079 245681491 245681430 4.990000e-17 99.0
5 TraesCS4D01G157600 chr4A 93.853 1269 58 10 181 1435 414424277 414423015 0.000000e+00 1893.0
6 TraesCS4D01G157600 chr4A 88.800 375 36 5 1825 2196 414231044 414230673 2.570000e-124 455.0
7 TraesCS4D01G157600 chr3D 93.720 207 13 0 993 1199 609922795 609922589 5.890000e-81 311.0
8 TraesCS4D01G157600 chr3D 90.909 231 15 4 976 1200 609929087 609928857 2.740000e-79 305.0
9 TraesCS4D01G157600 chr3D 81.013 158 21 8 1315 1470 609922483 609922333 1.380000e-22 117.0
10 TraesCS4D01G157600 chr3D 91.463 82 7 0 1315 1396 609921553 609921472 1.780000e-21 113.0
11 TraesCS4D01G157600 chr3B 90.909 231 15 4 976 1200 821089558 821089328 2.740000e-79 305.0
12 TraesCS4D01G157600 chr3B 93.171 205 14 0 995 1199 821076983 821076779 3.550000e-78 302.0
13 TraesCS4D01G157600 chr3B 87.349 166 15 2 1753 1912 529407954 529407789 3.730000e-43 185.0
14 TraesCS4D01G157600 chr3B 85.124 121 12 5 1315 1433 821076673 821076557 3.830000e-23 119.0
15 TraesCS4D01G157600 chr3B 79.032 124 13 8 279 394 821091339 821091221 3.030000e-09 73.1
16 TraesCS4D01G157600 chr3A 90.909 231 15 4 976 1200 743758278 743758048 2.740000e-79 305.0
17 TraesCS4D01G157600 chr3A 91.220 205 18 0 995 1199 743674296 743674092 1.660000e-71 279.0
18 TraesCS4D01G157600 chr3A 86.624 157 21 0 1756 1912 738134356 738134512 8.070000e-40 174.0
19 TraesCS4D01G157600 chr5D 87.500 168 14 2 1754 1914 377987999 377988166 1.040000e-43 187.0
20 TraesCS4D01G157600 chr2D 87.730 163 13 2 1757 1912 134301488 134301650 1.340000e-42 183.0
21 TraesCS4D01G157600 chr7A 86.471 170 16 2 1754 1916 59406904 59407073 1.730000e-41 180.0
22 TraesCS4D01G157600 chr1D 86.747 166 14 3 1757 1915 314014422 314014258 6.240000e-41 178.0
23 TraesCS4D01G157600 chr1D 91.463 82 7 0 1315 1396 347311299 347311218 1.780000e-21 113.0
24 TraesCS4D01G157600 chr5A 86.228 167 15 3 1757 1915 558675497 558675663 8.070000e-40 174.0
25 TraesCS4D01G157600 chr1B 86.145 166 13 7 1755 1911 31245241 31245077 1.040000e-38 171.0
26 TraesCS4D01G157600 chr7D 91.463 82 7 0 1315 1396 623714290 623714209 1.780000e-21 113.0
27 TraesCS4D01G157600 chr7B 91.463 82 7 0 1315 1396 123985844 123985763 1.780000e-21 113.0
28 TraesCS4D01G157600 chr5B 91.463 82 7 0 1315 1396 616514035 616514116 1.780000e-21 113.0


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 TraesCS4D01G157600 chr4D 216532975 216535172 2197 False 4060.00 4060 100.00000 1 2198 1 chr4D.!!$F1 2197
1 TraesCS4D01G157600 chr4B 245681430 245685288 3858 True 685.75 2063 93.19525 1 2079 4 chr4B.!!$R1 2078
2 TraesCS4D01G157600 chr4A 414423015 414424277 1262 True 1893.00 1893 93.85300 181 1435 1 chr4A.!!$R2 1254


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
444 1847 0.686441 TGTCACATCCCTCCCCTACG 60.686 60.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1677 3109 0.318107 CAAAACTCCGCACTGGCTTG 60.318 55.0 0.0 0.0 38.1 4.01 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
126 130 9.715121 AAAATTACTAAGGATCGTACAAAGTGA 57.285 29.630 0.00 0.00 0.00 3.41
152 156 8.862325 AAATATCAACATGAACACACCTTCTA 57.138 30.769 0.00 0.00 0.00 2.10
168 172 7.227910 CACACCTTCTAGGCTAAAGTTTGTTTA 59.772 37.037 0.00 0.00 39.63 2.01
176 180 9.886132 CTAGGCTAAAGTTTGTTTATCTAGGAA 57.114 33.333 0.00 0.00 0.00 3.36
266 1656 1.303317 GGCCCAACAGACCATTCGT 60.303 57.895 0.00 0.00 0.00 3.85
275 1665 1.593006 CAGACCATTCGTTCGCATACC 59.407 52.381 0.00 0.00 0.00 2.73
276 1666 0.935196 GACCATTCGTTCGCATACCC 59.065 55.000 0.00 0.00 0.00 3.69
279 1669 1.227438 ATTCGTTCGCATACCCCGG 60.227 57.895 0.00 0.00 0.00 5.73
281 1671 4.524318 CGTTCGCATACCCCGGCT 62.524 66.667 0.00 0.00 0.00 5.52
318 1720 4.142359 CCTTATATAAGCATCGGACGAGCT 60.142 45.833 15.86 11.11 41.03 4.09
444 1847 0.686441 TGTCACATCCCTCCCCTACG 60.686 60.000 0.00 0.00 0.00 3.51
445 1848 1.760875 TCACATCCCTCCCCTACGC 60.761 63.158 0.00 0.00 0.00 4.42
446 1849 2.446036 ACATCCCTCCCCTACGCC 60.446 66.667 0.00 0.00 0.00 5.68
447 1850 2.122813 CATCCCTCCCCTACGCCT 60.123 66.667 0.00 0.00 0.00 5.52
460 1863 0.978667 TACGCCTGCCTATTCACCCA 60.979 55.000 0.00 0.00 0.00 4.51
615 2019 7.277174 ACTCCTTTCATTTTCCACTTGTAAG 57.723 36.000 0.00 0.00 0.00 2.34
671 2075 3.220674 AGATCTCAAATAAGCCCTGGC 57.779 47.619 0.00 0.00 42.33 4.85
770 2174 3.497332 AGCTGTATTATGCCTCGGTAGA 58.503 45.455 0.00 0.00 0.00 2.59
797 2201 2.094597 TGCTGCCGATTTCTTGATTTGG 60.095 45.455 0.00 0.00 0.00 3.28
828 2232 2.309136 AGTATGCAAAACAGGGGCTT 57.691 45.000 0.00 0.00 0.00 4.35
846 2250 4.382362 GGGCTTTGAATTGCTTGCTTATCT 60.382 41.667 0.00 0.00 0.00 1.98
849 2253 6.324819 GCTTTGAATTGCTTGCTTATCTGTA 58.675 36.000 0.00 0.00 0.00 2.74
872 2276 5.864418 ACCGCTTACTTATGGATCACTTA 57.136 39.130 0.00 0.00 0.00 2.24
974 2378 3.320256 TGAATTGTACACCAGCATTTGCA 59.680 39.130 5.20 0.00 45.16 4.08
1251 2655 8.621532 AACTCTACTGCATTTGAATCAACTTA 57.378 30.769 0.00 0.00 0.00 2.24
1252 2656 8.621532 ACTCTACTGCATTTGAATCAACTTAA 57.378 30.769 0.00 0.00 0.00 1.85
1410 2814 8.553696 GGTTATTTGAATTGATTGGATGAATGC 58.446 33.333 0.00 0.00 0.00 3.56
1461 2893 2.922740 TGGTTACCTGTGGTGACTTC 57.077 50.000 2.07 0.00 41.20 3.01
1463 2895 2.104111 TGGTTACCTGTGGTGACTTCTG 59.896 50.000 2.07 0.00 41.20 3.02
1465 2897 3.433173 GGTTACCTGTGGTGACTTCTGTT 60.433 47.826 10.67 0.00 41.20 3.16
1467 2899 2.919228 ACCTGTGGTGACTTCTGTTTC 58.081 47.619 0.00 0.00 32.98 2.78
1468 2900 2.505819 ACCTGTGGTGACTTCTGTTTCT 59.494 45.455 0.00 0.00 32.98 2.52
1469 2901 3.054361 ACCTGTGGTGACTTCTGTTTCTT 60.054 43.478 0.00 0.00 32.98 2.52
1470 2902 3.313526 CCTGTGGTGACTTCTGTTTCTTG 59.686 47.826 0.00 0.00 0.00 3.02
1471 2903 4.191544 CTGTGGTGACTTCTGTTTCTTGA 58.808 43.478 0.00 0.00 0.00 3.02
1494 2926 4.936891 ACACTTGAACTGGAAAATTCAGC 58.063 39.130 0.00 0.00 36.26 4.26
1499 2931 6.321181 ACTTGAACTGGAAAATTCAGCAGTTA 59.679 34.615 13.96 4.06 38.73 2.24
1516 2948 4.333926 GCAGTTATCTCTCACAACAATCCC 59.666 45.833 0.00 0.00 0.00 3.85
1519 2951 0.036388 TCTCTCACAACAATCCCGCC 60.036 55.000 0.00 0.00 0.00 6.13
1552 2984 6.849085 AGTGAATGCAATTTGGGTTACATA 57.151 33.333 0.00 0.00 36.07 2.29
1573 3005 7.141363 ACATACAAAGTTTTCTCTCACAATGC 58.859 34.615 0.00 0.00 0.00 3.56
1587 3019 1.005294 CAATGCTGTGCTCCGTTTGC 61.005 55.000 0.00 0.00 0.00 3.68
1588 3020 1.174712 AATGCTGTGCTCCGTTTGCT 61.175 50.000 0.00 0.00 0.00 3.91
1599 3031 2.808543 CTCCGTTTGCTTAAAGCTGTCT 59.191 45.455 0.00 0.00 42.97 3.41
1612 3044 5.573337 AAAGCTGTCTTATCATCCAAAGC 57.427 39.130 0.00 0.00 31.02 3.51
1617 3049 4.194640 TGTCTTATCATCCAAAGCTGCTC 58.805 43.478 1.00 0.00 0.00 4.26
1624 3056 4.194640 TCATCCAAAGCTGCTCTATGAAC 58.805 43.478 1.00 0.00 0.00 3.18
1640 3072 0.507358 GAACGGAGAACAGCGTTGAC 59.493 55.000 6.16 0.00 0.00 3.18
1647 3079 2.924290 GAGAACAGCGTTGACAGATACC 59.076 50.000 6.16 0.00 0.00 2.73
1648 3080 2.299013 AGAACAGCGTTGACAGATACCA 59.701 45.455 6.16 0.00 0.00 3.25
1649 3081 3.055819 AGAACAGCGTTGACAGATACCAT 60.056 43.478 6.16 0.00 0.00 3.55
1650 3082 4.159693 AGAACAGCGTTGACAGATACCATA 59.840 41.667 6.16 0.00 0.00 2.74
1651 3083 3.782046 ACAGCGTTGACAGATACCATAC 58.218 45.455 6.16 0.00 0.00 2.39
1652 3084 3.447586 ACAGCGTTGACAGATACCATACT 59.552 43.478 6.16 0.00 0.00 2.12
1653 3085 4.643334 ACAGCGTTGACAGATACCATACTA 59.357 41.667 6.16 0.00 0.00 1.82
1654 3086 4.976731 CAGCGTTGACAGATACCATACTAC 59.023 45.833 0.00 0.00 0.00 2.73
1655 3087 4.643334 AGCGTTGACAGATACCATACTACA 59.357 41.667 0.00 0.00 0.00 2.74
1656 3088 4.738740 GCGTTGACAGATACCATACTACAC 59.261 45.833 0.00 0.00 0.00 2.90
1657 3089 4.968181 CGTTGACAGATACCATACTACACG 59.032 45.833 0.00 0.00 0.00 4.49
1658 3090 5.220719 CGTTGACAGATACCATACTACACGA 60.221 44.000 0.00 0.00 0.00 4.35
1659 3091 6.512903 CGTTGACAGATACCATACTACACGAT 60.513 42.308 0.00 0.00 0.00 3.73
1660 3092 6.954487 TGACAGATACCATACTACACGATT 57.046 37.500 0.00 0.00 0.00 3.34
1661 3093 7.342769 TGACAGATACCATACTACACGATTT 57.657 36.000 0.00 0.00 0.00 2.17
1662 3094 7.200455 TGACAGATACCATACTACACGATTTG 58.800 38.462 0.00 0.00 0.00 2.32
1663 3095 6.513180 ACAGATACCATACTACACGATTTGG 58.487 40.000 0.00 0.00 0.00 3.28
1664 3096 5.926542 CAGATACCATACTACACGATTTGGG 59.073 44.000 0.00 0.00 0.00 4.12
1665 3097 5.601313 AGATACCATACTACACGATTTGGGT 59.399 40.000 0.00 0.00 0.00 4.51
1666 3098 4.563140 ACCATACTACACGATTTGGGTT 57.437 40.909 0.00 0.00 0.00 4.11
1667 3099 5.680594 ACCATACTACACGATTTGGGTTA 57.319 39.130 0.00 0.00 0.00 2.85
1668 3100 5.422145 ACCATACTACACGATTTGGGTTAC 58.578 41.667 0.00 0.00 0.00 2.50
1669 3101 5.188359 ACCATACTACACGATTTGGGTTACT 59.812 40.000 0.00 0.00 0.00 2.24
1670 3102 5.751990 CCATACTACACGATTTGGGTTACTC 59.248 44.000 0.00 0.00 0.00 2.59
1671 3103 4.198028 ACTACACGATTTGGGTTACTCC 57.802 45.455 0.00 0.00 0.00 3.85
1672 3104 3.579586 ACTACACGATTTGGGTTACTCCA 59.420 43.478 0.00 0.00 38.11 3.86
1673 3105 3.495434 ACACGATTTGGGTTACTCCAA 57.505 42.857 0.00 2.03 44.29 3.53
1681 3113 1.892474 TGGGTTACTCCAAATGCAAGC 59.108 47.619 0.00 0.00 38.11 4.01
1682 3114 1.204704 GGGTTACTCCAAATGCAAGCC 59.795 52.381 0.00 0.00 38.11 4.35
1683 3115 1.892474 GGTTACTCCAAATGCAAGCCA 59.108 47.619 0.00 0.00 35.97 4.75
1684 3116 2.094545 GGTTACTCCAAATGCAAGCCAG 60.095 50.000 0.00 0.00 35.97 4.85
1685 3117 2.558359 GTTACTCCAAATGCAAGCCAGT 59.442 45.455 0.00 0.00 0.00 4.00
1686 3118 0.963962 ACTCCAAATGCAAGCCAGTG 59.036 50.000 0.00 0.00 0.00 3.66
1687 3119 0.389426 CTCCAAATGCAAGCCAGTGC 60.389 55.000 0.00 0.00 45.15 4.40
1701 3133 1.200020 CCAGTGCGGAGTTTTGGAATC 59.800 52.381 0.00 0.00 36.56 2.52
1736 3169 9.489393 GAAGCCATTTCAAAGTTAAACTTTTTG 57.511 29.630 0.00 1.50 45.38 2.44
1764 3197 9.725206 ACATTTTCTTTACCTATCTACTCCCTA 57.275 33.333 0.00 0.00 0.00 3.53
1814 3269 9.751542 AGAGATTTCAATAAGAACTATGTACGG 57.248 33.333 0.00 0.00 35.56 4.02
1864 3324 6.109359 ACTCATTTTGCTCTGTATGTAGTCC 58.891 40.000 0.00 0.00 0.00 3.85
1874 3334 5.828747 TCTGTATGTAGTCCGCATTAGAAC 58.171 41.667 0.00 0.00 0.00 3.01
1880 3340 4.951715 TGTAGTCCGCATTAGAACCTCTAA 59.048 41.667 0.00 0.00 42.49 2.10
1917 3683 5.896073 AGGAATGGAGGGAGTATAAAGTG 57.104 43.478 0.00 0.00 0.00 3.16
1918 3684 4.103311 AGGAATGGAGGGAGTATAAAGTGC 59.897 45.833 0.00 0.00 0.00 4.40
1925 3691 5.041191 AGGGAGTATAAAGTGCCATTGAG 57.959 43.478 0.00 0.00 38.98 3.02
1937 3703 7.951530 AAGTGCCATTGAGAATAAAGTTTTG 57.048 32.000 0.00 0.00 0.00 2.44
1947 3713 4.835056 AGAATAAAGTTTTGCAAGGAGGCT 59.165 37.500 0.00 0.00 34.04 4.58
1971 3737 2.041701 AGCCAAATGCCTTGTGAAGTT 58.958 42.857 0.00 0.00 42.71 2.66
1972 3738 2.036346 AGCCAAATGCCTTGTGAAGTTC 59.964 45.455 0.00 0.00 42.71 3.01
1983 3749 5.473504 GCCTTGTGAAGTTCTTCCAGAAATA 59.526 40.000 4.17 0.00 35.75 1.40
2086 3855 8.190122 TGATTGATGAAATATTTTAGTTGCGCT 58.810 29.630 9.73 0.00 0.00 5.92
2087 3856 7.739022 TTGATGAAATATTTTAGTTGCGCTG 57.261 32.000 9.73 0.00 0.00 5.18
2089 3858 7.188834 TGATGAAATATTTTAGTTGCGCTGAG 58.811 34.615 9.73 0.00 0.00 3.35
2090 3859 6.735678 TGAAATATTTTAGTTGCGCTGAGA 57.264 33.333 9.73 0.00 0.00 3.27
2091 3860 7.320443 TGAAATATTTTAGTTGCGCTGAGAT 57.680 32.000 9.73 0.00 0.00 2.75
2092 3861 7.188834 TGAAATATTTTAGTTGCGCTGAGATG 58.811 34.615 9.73 0.00 0.00 2.90
2093 3862 5.679734 ATATTTTAGTTGCGCTGAGATGG 57.320 39.130 9.73 0.00 0.00 3.51
2094 3863 2.472695 TTTAGTTGCGCTGAGATGGT 57.527 45.000 9.73 0.00 0.00 3.55
2097 3866 2.472695 AGTTGCGCTGAGATGGTTAA 57.527 45.000 9.73 0.00 0.00 2.01
2098 3867 2.991250 AGTTGCGCTGAGATGGTTAAT 58.009 42.857 9.73 0.00 0.00 1.40
2099 3868 3.347216 AGTTGCGCTGAGATGGTTAATT 58.653 40.909 9.73 0.00 0.00 1.40
2100 3869 3.375299 AGTTGCGCTGAGATGGTTAATTC 59.625 43.478 9.73 0.00 0.00 2.17
2101 3870 2.984562 TGCGCTGAGATGGTTAATTCA 58.015 42.857 9.73 0.00 0.00 2.57
2102 3871 3.342719 TGCGCTGAGATGGTTAATTCAA 58.657 40.909 9.73 0.00 0.00 2.69
2103 3872 3.126858 TGCGCTGAGATGGTTAATTCAAC 59.873 43.478 9.73 0.00 36.32 3.18
2106 3875 5.064707 GCGCTGAGATGGTTAATTCAACTAA 59.935 40.000 0.00 0.00 37.30 2.24
2107 3876 6.709643 CGCTGAGATGGTTAATTCAACTAAG 58.290 40.000 0.00 0.00 37.30 2.18
2108 3877 6.535150 CGCTGAGATGGTTAATTCAACTAAGA 59.465 38.462 7.26 0.00 37.30 2.10
2109 3878 7.254252 CGCTGAGATGGTTAATTCAACTAAGAG 60.254 40.741 7.26 2.31 37.30 2.85
2111 3880 8.777865 TGAGATGGTTAATTCAACTAAGAGTG 57.222 34.615 0.00 0.00 37.30 3.51
2112 3881 8.375506 TGAGATGGTTAATTCAACTAAGAGTGT 58.624 33.333 0.00 0.00 37.30 3.55
2124 3893 9.470399 TTCAACTAAGAGTGTATATGGTAGTGA 57.530 33.333 0.00 0.00 0.00 3.41
2125 3894 9.642343 TCAACTAAGAGTGTATATGGTAGTGAT 57.358 33.333 0.00 0.00 0.00 3.06
2152 3921 2.634982 TCATTTGTGATTTCCTGCGC 57.365 45.000 0.00 0.00 0.00 6.09
2153 3922 1.885233 TCATTTGTGATTTCCTGCGCA 59.115 42.857 10.98 10.98 0.00 6.09
2155 3924 2.879002 TTTGTGATTTCCTGCGCAAA 57.121 40.000 13.05 2.84 40.82 3.68
2156 3925 2.879002 TTGTGATTTCCTGCGCAAAA 57.121 40.000 13.05 11.00 32.21 2.44
2158 3927 3.383620 TGTGATTTCCTGCGCAAAAAT 57.616 38.095 23.15 23.15 0.00 1.82
2160 3929 4.876125 TGTGATTTCCTGCGCAAAAATAA 58.124 34.783 23.04 16.65 0.00 1.40
2163 3932 7.093354 TGTGATTTCCTGCGCAAAAATAAATA 58.907 30.769 23.04 13.82 0.00 1.40
2164 3933 7.600375 TGTGATTTCCTGCGCAAAAATAAATAA 59.400 29.630 23.04 11.08 0.00 1.40
2165 3934 8.439286 GTGATTTCCTGCGCAAAAATAAATAAA 58.561 29.630 23.04 9.91 0.00 1.40
2166 3935 8.655092 TGATTTCCTGCGCAAAAATAAATAAAG 58.345 29.630 23.04 4.31 0.00 1.85
2167 3936 7.954788 TTTCCTGCGCAAAAATAAATAAAGT 57.045 28.000 13.05 0.00 0.00 2.66
2168 3937 9.646427 ATTTCCTGCGCAAAAATAAATAAAGTA 57.354 25.926 22.17 0.00 0.00 2.24
2169 3938 9.646427 TTTCCTGCGCAAAAATAAATAAAGTAT 57.354 25.926 13.05 0.00 0.00 2.12
2170 3939 8.850454 TCCTGCGCAAAAATAAATAAAGTATC 57.150 30.769 13.05 0.00 0.00 2.24
2171 3940 8.462811 TCCTGCGCAAAAATAAATAAAGTATCA 58.537 29.630 13.05 0.00 0.00 2.15
2172 3941 9.248291 CCTGCGCAAAAATAAATAAAGTATCAT 57.752 29.630 13.05 0.00 0.00 2.45
2187 3956 7.945033 AAAGTATCATTTGCGATTTGTTTGT 57.055 28.000 0.00 0.00 0.00 2.83
2189 3958 8.673626 AAGTATCATTTGCGATTTGTTTGTAG 57.326 30.769 0.00 0.00 0.00 2.74
2190 3959 6.747280 AGTATCATTTGCGATTTGTTTGTAGC 59.253 34.615 0.00 0.00 0.00 3.58
2191 3960 4.864633 TCATTTGCGATTTGTTTGTAGCA 58.135 34.783 0.00 0.00 0.00 3.49
2192 3961 4.916831 TCATTTGCGATTTGTTTGTAGCAG 59.083 37.500 0.00 0.00 35.95 4.24
2193 3962 2.330231 TGCGATTTGTTTGTAGCAGC 57.670 45.000 0.00 0.00 0.00 5.25
2194 3963 1.879380 TGCGATTTGTTTGTAGCAGCT 59.121 42.857 0.00 0.00 0.00 4.24
2195 3964 3.070748 TGCGATTTGTTTGTAGCAGCTA 58.929 40.909 0.00 0.00 0.00 3.32
2196 3965 3.689161 TGCGATTTGTTTGTAGCAGCTAT 59.311 39.130 5.14 0.00 0.00 2.97
2197 3966 4.031028 GCGATTTGTTTGTAGCAGCTATG 58.969 43.478 5.14 0.00 0.00 2.23
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 5.065235 GCACCCAAGTTGGTACTTACTAAA 58.935 41.667 20.54 0.00 42.67 1.85
65 66 4.348754 AGCACCCAAGTTGGTACTTACTAA 59.651 41.667 20.54 0.00 42.67 2.24
66 67 3.905591 AGCACCCAAGTTGGTACTTACTA 59.094 43.478 20.54 0.00 42.67 1.82
67 68 2.709397 AGCACCCAAGTTGGTACTTACT 59.291 45.455 20.54 6.27 42.67 2.24
126 130 8.181904 AGAAGGTGTGTTCATGTTGATATTTT 57.818 30.769 0.00 0.00 0.00 1.82
152 156 9.755122 AATTCCTAGATAAACAAACTTTAGCCT 57.245 29.630 0.00 0.00 0.00 4.58
176 180 3.439857 TTGCAACTCTAGGCCTCAAAT 57.560 42.857 9.68 0.00 0.00 2.32
223 1602 1.600023 CCCAAACGAGTGCTGGTTTA 58.400 50.000 11.00 0.00 39.02 2.01
226 1605 2.594592 GCCCAAACGAGTGCTGGT 60.595 61.111 0.00 0.00 0.00 4.00
266 1656 4.849310 GCAGCCGGGGTATGCGAA 62.849 66.667 2.18 0.00 0.00 4.70
444 1847 0.825010 CCATGGGTGAATAGGCAGGC 60.825 60.000 2.85 0.00 0.00 4.85
445 1848 0.825010 GCCATGGGTGAATAGGCAGG 60.825 60.000 15.13 0.00 44.59 4.85
446 1849 2.724520 GCCATGGGTGAATAGGCAG 58.275 57.895 15.13 0.00 44.59 4.85
460 1863 1.068083 CGCAGATCCGTAGTGCCAT 59.932 57.895 0.00 0.00 33.42 4.40
615 2019 1.539827 ACATCGGCACAAAACTAAGCC 59.460 47.619 0.00 0.00 43.61 4.35
770 2174 5.581126 TCAAGAAATCGGCAGCAAAATAT 57.419 34.783 0.00 0.00 0.00 1.28
828 2232 6.620678 GGTTACAGATAAGCAAGCAATTCAA 58.379 36.000 0.00 0.00 38.44 2.69
846 2250 5.128171 AGTGATCCATAAGTAAGCGGTTACA 59.872 40.000 32.21 17.71 41.06 2.41
849 2253 4.755266 AGTGATCCATAAGTAAGCGGTT 57.245 40.909 4.76 4.76 0.00 4.44
872 2276 4.939052 AAGCGAATGCCTACATACTAGT 57.061 40.909 0.00 0.00 44.31 2.57
1251 2655 1.609208 AGACAAAGCCAGCGTTCATT 58.391 45.000 0.00 0.00 0.00 2.57
1252 2656 1.609208 AAGACAAAGCCAGCGTTCAT 58.391 45.000 0.00 0.00 0.00 2.57
1444 2876 3.470645 ACAGAAGTCACCACAGGTAAC 57.529 47.619 0.00 0.00 32.11 2.50
1463 2895 5.560966 TCCAGTTCAAGTGTTCAAGAAAC 57.439 39.130 0.00 0.00 38.43 2.78
1465 2897 6.582677 TTTTCCAGTTCAAGTGTTCAAGAA 57.417 33.333 0.00 0.00 0.00 2.52
1467 2899 7.035004 TGAATTTTCCAGTTCAAGTGTTCAAG 58.965 34.615 0.00 0.00 31.85 3.02
1468 2900 6.929625 TGAATTTTCCAGTTCAAGTGTTCAA 58.070 32.000 0.00 0.00 31.85 2.69
1469 2901 6.522625 TGAATTTTCCAGTTCAAGTGTTCA 57.477 33.333 0.00 0.00 31.85 3.18
1470 2902 5.460091 GCTGAATTTTCCAGTTCAAGTGTTC 59.540 40.000 0.00 0.00 34.26 3.18
1471 2903 5.105392 TGCTGAATTTTCCAGTTCAAGTGTT 60.105 36.000 0.00 0.00 34.26 3.32
1494 2926 4.568359 CGGGATTGTTGTGAGAGATAACTG 59.432 45.833 0.00 0.00 0.00 3.16
1499 2931 1.407437 GGCGGGATTGTTGTGAGAGAT 60.407 52.381 0.00 0.00 0.00 2.75
1516 2948 3.743911 TGCATTCACTATTATTACCGGCG 59.256 43.478 0.00 0.00 0.00 6.46
1519 2951 7.594758 CCCAAATTGCATTCACTATTATTACCG 59.405 37.037 0.00 0.00 0.00 4.02
1552 2984 5.126061 ACAGCATTGTGAGAGAAAACTTTGT 59.874 36.000 0.00 0.00 35.83 2.83
1571 3003 0.533978 TAAGCAAACGGAGCACAGCA 60.534 50.000 0.00 0.00 0.00 4.41
1573 3005 2.918131 GCTTTAAGCAAACGGAGCACAG 60.918 50.000 12.54 0.00 41.89 3.66
1577 3009 1.266989 ACAGCTTTAAGCAAACGGAGC 59.733 47.619 19.63 0.00 45.56 4.70
1581 3013 5.927030 TGATAAGACAGCTTTAAGCAAACG 58.073 37.500 19.63 6.90 45.56 3.60
1587 3019 7.066766 AGCTTTGGATGATAAGACAGCTTTAAG 59.933 37.037 0.00 0.00 35.56 1.85
1588 3020 6.886459 AGCTTTGGATGATAAGACAGCTTTAA 59.114 34.615 0.00 0.00 35.56 1.52
1599 3031 6.178607 TCATAGAGCAGCTTTGGATGATAA 57.821 37.500 0.00 0.00 0.00 1.75
1612 3044 3.443037 CTGTTCTCCGTTCATAGAGCAG 58.557 50.000 0.00 0.00 42.23 4.24
1617 3049 2.279582 ACGCTGTTCTCCGTTCATAG 57.720 50.000 0.00 0.00 33.26 2.23
1624 3056 0.318699 TCTGTCAACGCTGTTCTCCG 60.319 55.000 0.00 0.00 0.00 4.63
1640 3072 5.926542 CCCAAATCGTGTAGTATGGTATCTG 59.073 44.000 0.00 0.00 0.00 2.90
1647 3079 5.751990 GGAGTAACCCAAATCGTGTAGTATG 59.248 44.000 0.00 0.00 0.00 2.39
1648 3080 5.422970 TGGAGTAACCCAAATCGTGTAGTAT 59.577 40.000 0.00 0.00 38.00 2.12
1649 3081 4.771577 TGGAGTAACCCAAATCGTGTAGTA 59.228 41.667 0.00 0.00 38.00 1.82
1650 3082 3.579586 TGGAGTAACCCAAATCGTGTAGT 59.420 43.478 0.00 0.00 38.00 2.73
1651 3083 4.196626 TGGAGTAACCCAAATCGTGTAG 57.803 45.455 0.00 0.00 38.00 2.74
1652 3084 4.620589 TTGGAGTAACCCAAATCGTGTA 57.379 40.909 0.00 0.00 42.75 2.90
1653 3085 3.495434 TTGGAGTAACCCAAATCGTGT 57.505 42.857 0.00 0.00 42.75 4.49
1660 3092 2.298729 GCTTGCATTTGGAGTAACCCAA 59.701 45.455 0.00 0.00 43.90 4.12
1661 3093 1.892474 GCTTGCATTTGGAGTAACCCA 59.108 47.619 0.00 0.00 38.00 4.51
1662 3094 1.204704 GGCTTGCATTTGGAGTAACCC 59.795 52.381 0.00 0.00 38.00 4.11
1663 3095 1.892474 TGGCTTGCATTTGGAGTAACC 59.108 47.619 0.00 0.00 39.54 2.85
1664 3096 2.558359 ACTGGCTTGCATTTGGAGTAAC 59.442 45.455 0.00 0.00 0.00 2.50
1665 3097 2.557924 CACTGGCTTGCATTTGGAGTAA 59.442 45.455 0.00 0.00 0.00 2.24
1666 3098 2.161855 CACTGGCTTGCATTTGGAGTA 58.838 47.619 0.00 0.00 0.00 2.59
1667 3099 0.963962 CACTGGCTTGCATTTGGAGT 59.036 50.000 0.00 0.00 0.00 3.85
1668 3100 0.389426 GCACTGGCTTGCATTTGGAG 60.389 55.000 6.77 0.00 42.49 3.86
1669 3101 1.667151 GCACTGGCTTGCATTTGGA 59.333 52.632 6.77 0.00 42.49 3.53
1670 3102 1.735198 CGCACTGGCTTGCATTTGG 60.735 57.895 11.40 0.00 43.15 3.28
1671 3103 1.735198 CCGCACTGGCTTGCATTTG 60.735 57.895 11.40 0.00 43.15 2.32
1672 3104 1.870055 CTCCGCACTGGCTTGCATTT 61.870 55.000 11.40 0.00 43.15 2.32
1673 3105 2.282391 TCCGCACTGGCTTGCATT 60.282 55.556 11.40 0.00 43.15 3.56
1674 3106 2.749044 CTCCGCACTGGCTTGCAT 60.749 61.111 11.40 0.00 43.15 3.96
1675 3107 3.772853 AACTCCGCACTGGCTTGCA 62.773 57.895 11.40 0.00 43.15 4.08
1676 3108 2.075426 AAAACTCCGCACTGGCTTGC 62.075 55.000 1.98 1.98 39.28 4.01
1677 3109 0.318107 CAAAACTCCGCACTGGCTTG 60.318 55.000 0.00 0.00 38.10 4.01
1678 3110 1.455383 CCAAAACTCCGCACTGGCTT 61.455 55.000 0.00 0.00 38.10 4.35
1679 3111 1.898574 CCAAAACTCCGCACTGGCT 60.899 57.895 0.00 0.00 38.10 4.75
1680 3112 1.452145 TTCCAAAACTCCGCACTGGC 61.452 55.000 0.00 0.00 37.80 4.85
1681 3113 1.200020 GATTCCAAAACTCCGCACTGG 59.800 52.381 0.00 0.00 40.09 4.00
1682 3114 1.200020 GGATTCCAAAACTCCGCACTG 59.800 52.381 0.00 0.00 0.00 3.66
1683 3115 1.202879 TGGATTCCAAAACTCCGCACT 60.203 47.619 1.94 0.00 31.36 4.40
1684 3116 1.200020 CTGGATTCCAAAACTCCGCAC 59.800 52.381 6.88 0.00 30.80 5.34
1685 3117 1.202879 ACTGGATTCCAAAACTCCGCA 60.203 47.619 6.88 0.00 30.80 5.69
1686 3118 1.200020 CACTGGATTCCAAAACTCCGC 59.800 52.381 6.88 0.00 30.80 5.54
1687 3119 2.504367 ACACTGGATTCCAAAACTCCG 58.496 47.619 6.88 0.00 30.80 4.63
1688 3120 4.340950 TCAAACACTGGATTCCAAAACTCC 59.659 41.667 6.88 0.00 30.80 3.85
1689 3121 5.514274 TCAAACACTGGATTCCAAAACTC 57.486 39.130 6.88 0.00 30.80 3.01
1701 3133 3.731652 TGAAATGGCTTCAAACACTGG 57.268 42.857 0.00 0.00 41.21 4.00
1736 3169 9.761504 GGGAGTAGATAGGTAAAGAAAATGTAC 57.238 37.037 0.00 0.00 0.00 2.90
1742 3175 9.725206 AACATAGGGAGTAGATAGGTAAAGAAA 57.275 33.333 0.00 0.00 0.00 2.52
1828 3283 8.559536 CAGAGCAAAATGAGTTACACTCTAAAA 58.440 33.333 5.53 0.00 45.27 1.52
1839 3294 6.595716 GGACTACATACAGAGCAAAATGAGTT 59.404 38.462 0.00 0.00 0.00 3.01
1864 3324 6.969828 AGTCTTTTTAGAGGTTCTAATGCG 57.030 37.500 0.00 0.00 38.60 4.73
1880 3340 9.868160 CCCTCCATTCCTAAATATAAGTCTTTT 57.132 33.333 0.00 0.00 0.00 2.27
1917 3683 6.128472 CCTTGCAAAACTTTATTCTCAATGGC 60.128 38.462 0.00 0.00 0.00 4.40
1918 3684 7.153985 TCCTTGCAAAACTTTATTCTCAATGG 58.846 34.615 0.00 0.00 0.00 3.16
1925 3691 4.925646 CAGCCTCCTTGCAAAACTTTATTC 59.074 41.667 0.00 0.00 0.00 1.75
1971 3737 5.190528 ACTGCAGGAATCTATTTCTGGAAGA 59.809 40.000 19.93 0.00 42.18 2.87
1972 3738 5.435291 ACTGCAGGAATCTATTTCTGGAAG 58.565 41.667 19.93 6.72 42.18 3.46
1983 3749 3.387374 CCTGAGTATGACTGCAGGAATCT 59.613 47.826 19.93 9.35 41.69 2.40
2063 3832 7.534282 TCAGCGCAACTAAAATATTTCATCAA 58.466 30.769 11.47 0.00 0.00 2.57
2079 3848 3.126858 TGAATTAACCATCTCAGCGCAAC 59.873 43.478 11.47 0.00 0.00 4.17
2081 3850 2.984562 TGAATTAACCATCTCAGCGCA 58.015 42.857 11.47 0.00 0.00 6.09
2082 3851 3.375299 AGTTGAATTAACCATCTCAGCGC 59.625 43.478 0.00 0.00 40.24 5.92
2084 3853 7.550906 ACTCTTAGTTGAATTAACCATCTCAGC 59.449 37.037 0.00 0.00 40.24 4.26
2086 3855 8.375506 ACACTCTTAGTTGAATTAACCATCTCA 58.624 33.333 0.00 0.00 40.24 3.27
2087 3856 8.779354 ACACTCTTAGTTGAATTAACCATCTC 57.221 34.615 0.00 0.00 40.24 2.75
2098 3867 9.470399 TCACTACCATATACACTCTTAGTTGAA 57.530 33.333 0.00 0.00 0.00 2.69
2099 3868 9.642343 ATCACTACCATATACACTCTTAGTTGA 57.358 33.333 0.00 0.00 0.00 3.18
2126 3895 7.596248 GCGCAGGAAATCACAAATGATATTAAT 59.404 33.333 0.30 0.00 45.26 1.40
2127 3896 6.917477 GCGCAGGAAATCACAAATGATATTAA 59.083 34.615 0.30 0.00 45.26 1.40
2128 3897 6.039159 TGCGCAGGAAATCACAAATGATATTA 59.961 34.615 5.66 0.00 45.26 0.98
2129 3898 5.163530 TGCGCAGGAAATCACAAATGATATT 60.164 36.000 5.66 0.00 45.26 1.28
2130 3899 4.338964 TGCGCAGGAAATCACAAATGATAT 59.661 37.500 5.66 0.00 45.26 1.63
2133 3902 1.885233 TGCGCAGGAAATCACAAATGA 59.115 42.857 5.66 0.00 39.83 2.57
2134 3903 2.350899 TGCGCAGGAAATCACAAATG 57.649 45.000 5.66 0.00 0.00 2.32
2135 3904 3.383620 TTTGCGCAGGAAATCACAAAT 57.616 38.095 11.31 0.00 44.43 2.32
2136 3905 2.879002 TTTGCGCAGGAAATCACAAA 57.121 40.000 11.31 0.00 44.43 2.83
2144 3913 9.296400 GATACTTTATTTATTTTTGCGCAGGAA 57.704 29.630 11.31 10.21 34.77 3.36
2146 3915 8.627487 TGATACTTTATTTATTTTTGCGCAGG 57.373 30.769 11.31 0.00 0.00 4.85
2163 3932 7.945033 ACAAACAAATCGCAAATGATACTTT 57.055 28.000 0.00 0.00 0.00 2.66
2164 3933 7.273381 GCTACAAACAAATCGCAAATGATACTT 59.727 33.333 0.00 0.00 0.00 2.24
2165 3934 6.747280 GCTACAAACAAATCGCAAATGATACT 59.253 34.615 0.00 0.00 0.00 2.12
2166 3935 6.526325 TGCTACAAACAAATCGCAAATGATAC 59.474 34.615 0.00 0.00 0.00 2.24
2167 3936 6.616017 TGCTACAAACAAATCGCAAATGATA 58.384 32.000 0.00 0.00 0.00 2.15
2168 3937 5.468592 TGCTACAAACAAATCGCAAATGAT 58.531 33.333 0.00 0.00 0.00 2.45
2169 3938 4.864633 TGCTACAAACAAATCGCAAATGA 58.135 34.783 0.00 0.00 0.00 2.57
2170 3939 4.433283 GCTGCTACAAACAAATCGCAAATG 60.433 41.667 0.00 0.00 0.00 2.32
2171 3940 3.674753 GCTGCTACAAACAAATCGCAAAT 59.325 39.130 0.00 0.00 0.00 2.32
2172 3941 3.049206 GCTGCTACAAACAAATCGCAAA 58.951 40.909 0.00 0.00 0.00 3.68
2173 3942 2.293122 AGCTGCTACAAACAAATCGCAA 59.707 40.909 0.00 0.00 0.00 4.85
2174 3943 1.879380 AGCTGCTACAAACAAATCGCA 59.121 42.857 0.00 0.00 0.00 5.10
2175 3944 2.619013 AGCTGCTACAAACAAATCGC 57.381 45.000 0.00 0.00 0.00 4.58



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

AutoCloner maintained by Alex Coulton.