Multiple sequence alignment - TraesCS2D01G595400

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 TraesCS2D01G595400 chr2D 100.000 2741 0 0 1 2741 648594034 648596774 0.000000e+00 5062.0
1 TraesCS2D01G595400 chr2D 99.032 930 9 0 1 930 616477004 616477933 0.000000e+00 1668.0
2 TraesCS2D01G595400 chr2D 98.718 936 12 0 1 936 50847662 50846727 0.000000e+00 1663.0
3 TraesCS2D01G595400 chr2D 87.887 710 77 4 991 1693 648572741 648573448 0.000000e+00 826.0
4 TraesCS2D01G595400 chr2D 79.460 1149 176 20 990 2085 648547614 648546473 0.000000e+00 760.0
5 TraesCS2D01G595400 chr2D 100.000 52 0 0 931 982 82840991 82840940 2.250000e-16 97.1
6 TraesCS2D01G595400 chr2D 98.214 56 0 1 931 986 321657780 321657726 2.250000e-16 97.1
7 TraesCS2D01G595400 chr2D 95.000 60 1 2 931 989 315860449 315860391 2.910000e-15 93.5
8 TraesCS2D01G595400 chr2D 91.176 68 4 1 931 996 449927745 449927678 1.050000e-14 91.6
9 TraesCS2D01G595400 chr7D 99.033 931 9 0 1 931 529968810 529967880 0.000000e+00 1670.0
10 TraesCS2D01G595400 chr7D 96.552 58 2 0 931 988 608439228 608439285 2.250000e-16 97.1
11 TraesCS2D01G595400 chr1D 98.926 931 10 0 1 931 395397472 395398402 0.000000e+00 1664.0
12 TraesCS2D01G595400 chr1D 98.926 931 10 0 1 931 492623200 492622270 0.000000e+00 1664.0
13 TraesCS2D01G595400 chr1D 98.925 930 10 0 1 930 471686080 471687009 0.000000e+00 1663.0
14 TraesCS2D01G595400 chr1D 81.481 270 28 13 2160 2418 44612763 44612505 4.630000e-48 202.0
15 TraesCS2D01G595400 chr1D 98.113 53 1 0 931 983 207157483 207157535 2.910000e-15 93.5
16 TraesCS2D01G595400 chr1D 93.548 62 4 0 931 992 344161267 344161328 2.910000e-15 93.5
17 TraesCS2D01G595400 chr3D 98.925 930 9 1 1 930 25317258 25316330 0.000000e+00 1661.0
18 TraesCS2D01G595400 chr4D 98.818 931 11 0 1 931 360226901 360227831 0.000000e+00 1659.0
19 TraesCS2D01G595400 chr4D 96.552 58 0 2 931 986 339054839 339054782 8.080000e-16 95.3
20 TraesCS2D01G595400 chr5D 98.714 933 12 0 1 933 52606527 52605595 0.000000e+00 1657.0
21 TraesCS2D01G595400 chr2B 81.743 1216 176 18 991 2171 784688282 784689486 0.000000e+00 974.0
22 TraesCS2D01G595400 chr2B 85.556 900 109 12 991 1881 784707267 784708154 0.000000e+00 922.0
23 TraesCS2D01G595400 chr2B 78.729 1133 181 27 990 2085 784664374 784665483 0.000000e+00 702.0
24 TraesCS2D01G595400 chr2B 84.543 427 26 17 2330 2741 784689650 784690051 1.190000e-103 387.0
25 TraesCS2D01G595400 chr2B 86.585 164 14 3 2330 2493 784710739 784710894 1.010000e-39 174.0
26 TraesCS2D01G595400 chr2B 86.228 167 7 3 2575 2741 784710918 784711068 1.690000e-37 167.0
27 TraesCS2D01G595400 chr2B 94.872 78 3 1 2160 2237 784710238 784710314 1.330000e-23 121.0
28 TraesCS2D01G595400 chr2A 87.088 728 80 6 991 1711 775763783 775763063 0.000000e+00 811.0
29 TraesCS2D01G595400 chr2A 81.707 902 87 31 1887 2736 775756363 775755488 0.000000e+00 680.0
30 TraesCS2D01G595400 chr2A 82.984 429 60 9 1275 1693 775769714 775769289 2.580000e-100 375.0
31 TraesCS2D01G595400 chr2A 83.099 213 25 6 1890 2094 775762884 775762675 1.680000e-42 183.0
32 TraesCS2D01G595400 chr7A 86.316 190 20 5 1985 2171 66643800 66643986 4.630000e-48 202.0
33 TraesCS2D01G595400 chr5A 86.316 190 20 5 1988 2174 458336943 458336757 4.630000e-48 202.0
34 TraesCS2D01G595400 chr6A 85.789 190 21 5 1988 2174 15468107 15467921 2.150000e-46 196.0
35 TraesCS2D01G595400 chr3B 85.263 190 22 5 1988 2174 9286710 9286524 1.000000e-44 191.0
36 TraesCS2D01G595400 chr4B 96.491 57 2 0 931 987 379090278 379090334 8.080000e-16 95.3


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G595400 chr2D 648594034 648596774 2740 False 5062.0 5062 100.00000 1 2741 1 chr2D.!!$F3 2740
1 TraesCS2D01G595400 chr2D 616477004 616477933 929 False 1668.0 1668 99.03200 1 930 1 chr2D.!!$F1 929
2 TraesCS2D01G595400 chr2D 50846727 50847662 935 True 1663.0 1663 98.71800 1 936 1 chr2D.!!$R1 935
3 TraesCS2D01G595400 chr2D 648572741 648573448 707 False 826.0 826 87.88700 991 1693 1 chr2D.!!$F2 702
4 TraesCS2D01G595400 chr2D 648546473 648547614 1141 True 760.0 760 79.46000 990 2085 1 chr2D.!!$R6 1095
5 TraesCS2D01G595400 chr7D 529967880 529968810 930 True 1670.0 1670 99.03300 1 931 1 chr7D.!!$R1 930
6 TraesCS2D01G595400 chr1D 395397472 395398402 930 False 1664.0 1664 98.92600 1 931 1 chr1D.!!$F3 930
7 TraesCS2D01G595400 chr1D 492622270 492623200 930 True 1664.0 1664 98.92600 1 931 1 chr1D.!!$R2 930
8 TraesCS2D01G595400 chr1D 471686080 471687009 929 False 1663.0 1663 98.92500 1 930 1 chr1D.!!$F4 929
9 TraesCS2D01G595400 chr3D 25316330 25317258 928 True 1661.0 1661 98.92500 1 930 1 chr3D.!!$R1 929
10 TraesCS2D01G595400 chr4D 360226901 360227831 930 False 1659.0 1659 98.81800 1 931 1 chr4D.!!$F1 930
11 TraesCS2D01G595400 chr5D 52605595 52606527 932 True 1657.0 1657 98.71400 1 933 1 chr5D.!!$R1 932
12 TraesCS2D01G595400 chr2B 784664374 784665483 1109 False 702.0 702 78.72900 990 2085 1 chr2B.!!$F1 1095
13 TraesCS2D01G595400 chr2B 784688282 784690051 1769 False 680.5 974 83.14300 991 2741 2 chr2B.!!$F2 1750
14 TraesCS2D01G595400 chr2B 784707267 784711068 3801 False 346.0 922 88.31025 991 2741 4 chr2B.!!$F3 1750
15 TraesCS2D01G595400 chr2A 775755488 775756363 875 True 680.0 680 81.70700 1887 2736 1 chr2A.!!$R1 849
16 TraesCS2D01G595400 chr2A 775762675 775763783 1108 True 497.0 811 85.09350 991 2094 2 chr2A.!!$R3 1103

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
624 625 0.390735 GCGACTAAAGGCTTTCGGGA 60.391 55.000 17.13 0.0 32.04 5.14 F
1017 1018 1.270732 GCAATGCCCACACAAATTGGA 60.271 47.619 0.00 0.0 36.02 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1507 1523 0.033504 ATACCGGTAATGGCTGAGCG 59.966 55.0 20.22 0.0 36.36 5.03 R
2512 4728 0.103572 GAAGACCGCGGCCACTAATA 59.896 55.0 28.58 0.0 0.00 0.98 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
419 420 2.225467 GAGAAAGCTCAAGTGTGGCTT 58.775 47.619 0.00 7.89 40.69 4.35
453 454 3.819368 TCATGTTTGTTTCAGGCTCTCA 58.181 40.909 0.00 0.00 0.00 3.27
617 618 0.955919 GCCAACTGCGACTAAAGGCT 60.956 55.000 0.00 0.00 37.67 4.58
624 625 0.390735 GCGACTAAAGGCTTTCGGGA 60.391 55.000 17.13 0.00 32.04 5.14
941 942 8.418597 TTTTTCTACTAGTGATATATCGGCCT 57.581 34.615 5.39 6.45 0.00 5.19
942 943 9.524496 TTTTTCTACTAGTGATATATCGGCCTA 57.476 33.333 5.39 7.17 0.00 3.93
943 944 9.696572 TTTTCTACTAGTGATATATCGGCCTAT 57.303 33.333 5.39 0.00 0.00 2.57
944 945 8.678593 TTCTACTAGTGATATATCGGCCTATG 57.321 38.462 5.39 5.52 0.00 2.23
945 946 7.225011 TCTACTAGTGATATATCGGCCTATGG 58.775 42.308 5.39 1.57 0.00 2.74
961 962 4.371624 CTATGGCCTCATGGGAATACAA 57.628 45.455 3.32 0.00 37.23 2.41
962 963 2.734755 TGGCCTCATGGGAATACAAG 57.265 50.000 3.32 0.00 37.23 3.16
963 964 1.922447 TGGCCTCATGGGAATACAAGT 59.078 47.619 3.32 0.00 37.23 3.16
964 965 2.311542 TGGCCTCATGGGAATACAAGTT 59.688 45.455 3.32 0.00 37.23 2.66
965 966 2.689983 GGCCTCATGGGAATACAAGTTG 59.310 50.000 0.00 0.00 37.23 3.16
966 967 2.099756 GCCTCATGGGAATACAAGTTGC 59.900 50.000 1.81 0.00 37.23 4.17
967 968 3.624777 CCTCATGGGAATACAAGTTGCT 58.375 45.455 1.81 0.00 37.23 3.91
968 969 4.019174 CCTCATGGGAATACAAGTTGCTT 58.981 43.478 1.81 0.00 37.23 3.91
969 970 5.192927 CCTCATGGGAATACAAGTTGCTTA 58.807 41.667 1.81 0.00 37.23 3.09
970 971 5.829924 CCTCATGGGAATACAAGTTGCTTAT 59.170 40.000 1.81 0.00 37.23 1.73
971 972 6.322201 CCTCATGGGAATACAAGTTGCTTATT 59.678 38.462 1.81 0.58 37.23 1.40
972 973 7.333528 TCATGGGAATACAAGTTGCTTATTC 57.666 36.000 13.88 13.88 0.00 1.75
973 974 6.321181 TCATGGGAATACAAGTTGCTTATTCC 59.679 38.462 24.35 24.35 43.17 3.01
974 975 5.826643 TGGGAATACAAGTTGCTTATTCCT 58.173 37.500 27.77 4.94 43.33 3.36
975 976 6.964464 TGGGAATACAAGTTGCTTATTCCTA 58.036 36.000 27.77 23.73 43.33 2.94
976 977 7.406916 TGGGAATACAAGTTGCTTATTCCTAA 58.593 34.615 27.77 19.95 43.33 2.69
977 978 7.338449 TGGGAATACAAGTTGCTTATTCCTAAC 59.662 37.037 27.77 19.00 43.33 2.34
978 979 7.338449 GGGAATACAAGTTGCTTATTCCTAACA 59.662 37.037 27.77 0.00 43.33 2.41
979 980 8.182227 GGAATACAAGTTGCTTATTCCTAACAC 58.818 37.037 24.74 8.74 41.60 3.32
980 981 8.863872 AATACAAGTTGCTTATTCCTAACACT 57.136 30.769 1.81 0.00 0.00 3.55
981 982 8.863872 ATACAAGTTGCTTATTCCTAACACTT 57.136 30.769 1.81 0.00 0.00 3.16
982 983 7.582667 ACAAGTTGCTTATTCCTAACACTTT 57.417 32.000 1.81 0.00 0.00 2.66
983 984 8.685838 ACAAGTTGCTTATTCCTAACACTTTA 57.314 30.769 1.81 0.00 0.00 1.85
984 985 8.565416 ACAAGTTGCTTATTCCTAACACTTTAC 58.435 33.333 1.81 0.00 0.00 2.01
985 986 8.564574 CAAGTTGCTTATTCCTAACACTTTACA 58.435 33.333 0.00 0.00 0.00 2.41
986 987 8.095937 AGTTGCTTATTCCTAACACTTTACAC 57.904 34.615 0.00 0.00 0.00 2.90
987 988 7.174426 AGTTGCTTATTCCTAACACTTTACACC 59.826 37.037 0.00 0.00 0.00 4.16
988 989 5.640357 TGCTTATTCCTAACACTTTACACCG 59.360 40.000 0.00 0.00 0.00 4.94
1014 1015 3.629548 GGCAATGCCCACACAAATT 57.370 47.368 14.47 0.00 44.06 1.82
1017 1018 1.270732 GCAATGCCCACACAAATTGGA 60.271 47.619 0.00 0.00 36.02 3.53
1039 1040 2.163010 GACATGACAGAATTGCAGGTGG 59.837 50.000 0.00 0.00 29.91 4.61
1078 1085 4.550255 GCGACGGCAGTGAACTAAAATATC 60.550 45.833 0.00 0.00 39.62 1.63
1087 1094 7.281100 GCAGTGAACTAAAATATCTTGGCTACT 59.719 37.037 0.00 0.00 0.00 2.57
1099 1106 4.157246 TCTTGGCTACTTACTCCAGTTGA 58.843 43.478 0.00 0.00 0.00 3.18
1204 1214 2.768253 TCGCTCACTGTCAATCCATT 57.232 45.000 0.00 0.00 0.00 3.16
1237 1253 4.569966 CCGAAGAAGAGAATGAGAATGTGG 59.430 45.833 0.00 0.00 0.00 4.17
1249 1265 6.998968 ATGAGAATGTGGACAAGAAAGATC 57.001 37.500 0.00 0.00 0.00 2.75
1259 1275 3.950395 GACAAGAAAGATCCATCCCCAAG 59.050 47.826 0.00 0.00 0.00 3.61
1314 1330 1.643880 GCCTGAAAAATGGATTGCCG 58.356 50.000 0.00 0.00 36.79 5.69
1329 1345 4.493547 GATTGCCGTCATGGATTGAAAAA 58.506 39.130 0.00 0.00 42.00 1.94
1363 1379 3.033184 ACCAAAATGACCCTGCATATGG 58.967 45.455 4.56 0.00 39.45 2.74
1368 1384 3.882102 ATGACCCTGCATATGGCTTTA 57.118 42.857 4.56 0.00 45.15 1.85
1432 1448 1.758514 TCCTGGCTTAGGCTCCGAG 60.759 63.158 7.43 0.00 46.87 4.63
1433 1449 2.107953 CTGGCTTAGGCTCCGAGC 59.892 66.667 12.27 12.27 41.46 5.03
1507 1523 4.067896 TCTTGAGTTCCTTGACATTGAGC 58.932 43.478 0.00 0.00 0.00 4.26
1563 1579 2.351455 GCCTGTCCTAAGCTGAAGAAC 58.649 52.381 0.00 0.00 0.00 3.01
1564 1580 2.289694 GCCTGTCCTAAGCTGAAGAACA 60.290 50.000 0.00 0.00 0.00 3.18
1599 1615 6.419484 TCTACTGGTGAACAATCTCTTTCA 57.581 37.500 0.00 0.00 0.00 2.69
1614 1630 0.392998 TTTCAGGGATTGAGCGCCTC 60.393 55.000 2.29 1.22 37.07 4.70
1653 3409 2.157738 GAGTTGACAGGCAGCTTTGAT 58.842 47.619 0.00 0.00 38.26 2.57
1660 3416 1.201647 CAGGCAGCTTTGATGTGGAAG 59.798 52.381 0.00 0.00 0.00 3.46
1693 3449 3.069158 AGCAATTGAAGCAAGCAAGAACT 59.931 39.130 10.34 0.00 0.00 3.01
1721 3477 4.771114 TGTTGGAATCATACCCTACCAG 57.229 45.455 0.00 0.00 0.00 4.00
1722 3478 3.458118 TGTTGGAATCATACCCTACCAGG 59.542 47.826 0.00 0.00 34.30 4.45
1723 3479 3.714798 GTTGGAATCATACCCTACCAGGA 59.285 47.826 0.00 0.00 37.67 3.86
1725 3481 2.638363 GGAATCATACCCTACCAGGACC 59.362 54.545 0.00 0.00 37.67 4.46
1730 3487 0.337428 TACCCTACCAGGACCAGGTC 59.663 60.000 12.63 11.70 37.67 3.85
1759 3516 3.128242 GTGATCCACATTTGCTCCTTGAG 59.872 47.826 0.00 0.00 34.08 3.02
1821 3581 6.097412 GGGGCAGAAATGTATCTCAAGAAAAT 59.903 38.462 0.00 0.00 0.00 1.82
1851 3611 1.872952 CTTCGCGGATTATTGCCATCA 59.127 47.619 6.13 0.00 0.00 3.07
1853 3613 2.293170 TCGCGGATTATTGCCATCAAA 58.707 42.857 6.13 0.00 35.56 2.69
1857 3617 4.619973 GCGGATTATTGCCATCAAATTCA 58.380 39.130 0.00 0.00 35.56 2.57
1887 3658 8.533965 CCTGCATATTTGATTTATTTTGTCGTG 58.466 33.333 0.00 0.00 0.00 4.35
1888 3659 7.893824 TGCATATTTGATTTATTTTGTCGTGC 58.106 30.769 0.00 0.00 0.00 5.34
1889 3660 7.543520 TGCATATTTGATTTATTTTGTCGTGCA 59.456 29.630 0.00 0.00 33.55 4.57
1890 3661 7.840797 GCATATTTGATTTATTTTGTCGTGCAC 59.159 33.333 6.82 6.82 0.00 4.57
1907 3708 1.823295 ACTGCAGTGACTGAACCGT 59.177 52.632 20.97 0.00 32.44 4.83
1908 3709 0.178068 ACTGCAGTGACTGAACCGTT 59.822 50.000 20.97 0.00 32.44 4.44
1922 3728 4.663166 TGAACCGTTGTGTGTATTTGTTG 58.337 39.130 0.00 0.00 0.00 3.33
1939 3751 4.963318 TGTTGAGGTCACTCTCAGATTT 57.037 40.909 0.00 0.00 43.64 2.17
1965 3790 1.297598 GTGCTGTGTTGTGTCGTGC 60.298 57.895 0.00 0.00 0.00 5.34
1966 3791 1.743252 TGCTGTGTTGTGTCGTGCA 60.743 52.632 0.00 0.00 0.00 4.57
2001 3827 3.451141 TGCATTTGTTCACCCAGAAAC 57.549 42.857 0.00 0.00 38.13 2.78
2091 3920 5.661312 TGTTGTATTAGGGTGAGTGATAGCT 59.339 40.000 0.00 0.00 0.00 3.32
2127 3961 7.342581 TGATGGGCAAATGTACTACTATTTGA 58.657 34.615 16.47 1.48 43.51 2.69
2128 3962 7.998383 TGATGGGCAAATGTACTACTATTTGAT 59.002 33.333 16.47 5.24 43.51 2.57
2135 3969 9.838975 CAAATGTACTACTATTTGATTTGTGCA 57.161 29.630 9.64 0.00 43.51 4.57
2141 3976 7.810658 ACTACTATTTGATTTGTGCAGTTCAG 58.189 34.615 0.00 0.00 0.00 3.02
2151 3986 1.136147 GCAGTTCAGAATGCCTGCG 59.864 57.895 8.14 0.00 45.73 5.18
2207 4068 7.992033 CCAAGCAATATTCCCCAATTTGAATTA 59.008 33.333 0.00 0.00 33.46 1.40
2231 4414 2.622942 TCGCTGAAATTCCAAGCAAAGT 59.377 40.909 6.21 0.00 0.00 2.66
2281 4464 5.584649 TGTGTCAAGAAGTGTTAACTGAAGG 59.415 40.000 7.22 0.00 36.51 3.46
2282 4465 5.815740 GTGTCAAGAAGTGTTAACTGAAGGA 59.184 40.000 7.22 0.00 36.51 3.36
2283 4466 6.018669 GTGTCAAGAAGTGTTAACTGAAGGAG 60.019 42.308 7.22 0.00 36.51 3.69
2292 4475 5.587844 GTGTTAACTGAAGGAGATCATGCAT 59.412 40.000 7.22 0.00 0.00 3.96
2307 4490 8.507524 AGATCATGCATGGTATTCAGATATTG 57.492 34.615 25.97 0.00 0.00 1.90
2311 4494 7.392393 TCATGCATGGTATTCAGATATTGGAAG 59.608 37.037 25.97 0.00 0.00 3.46
2313 4496 6.006449 GCATGGTATTCAGATATTGGAAGGT 58.994 40.000 0.00 0.00 0.00 3.50
2328 4530 2.427095 GGAAGGTTTGCAAGTTGACACT 59.573 45.455 7.16 0.00 33.11 3.55
2339 4555 3.179443 AGTTGACACTCTGCTCGAAAA 57.821 42.857 0.00 0.00 0.00 2.29
2369 4585 1.556911 ACACCACATCCATCTCCAGTC 59.443 52.381 0.00 0.00 0.00 3.51
2407 4623 8.082242 ACTAAACTGAAATTGGAAAGCATGTAC 58.918 33.333 0.00 0.00 0.00 2.90
2409 4625 6.017400 ACTGAAATTGGAAAGCATGTACTG 57.983 37.500 0.00 0.00 0.00 2.74
2411 4627 6.714810 ACTGAAATTGGAAAGCATGTACTGTA 59.285 34.615 0.00 0.00 0.00 2.74
2412 4628 7.230510 ACTGAAATTGGAAAGCATGTACTGTAA 59.769 33.333 0.00 0.00 0.00 2.41
2416 4632 7.944729 ATTGGAAAGCATGTACTGTAATTCT 57.055 32.000 0.00 0.00 0.00 2.40
2417 4633 7.759489 TTGGAAAGCATGTACTGTAATTCTT 57.241 32.000 0.00 0.00 0.00 2.52
2418 4634 8.856153 TTGGAAAGCATGTACTGTAATTCTTA 57.144 30.769 0.00 0.00 0.00 2.10
2419 4635 9.461312 TTGGAAAGCATGTACTGTAATTCTTAT 57.539 29.630 0.00 0.00 0.00 1.73
2463 4679 5.545063 TGTAATTCTCTCACCTGTGTCAA 57.455 39.130 0.00 0.00 0.00 3.18
2485 4701 3.244249 ACAACAACCTAGAGACTGAAGGC 60.244 47.826 0.00 0.00 33.42 4.35
2487 4703 1.902508 CAACCTAGAGACTGAAGGCCA 59.097 52.381 5.01 0.00 33.42 5.36
2499 4715 3.137360 ACTGAAGGCCAGATTCCTTATCC 59.863 47.826 5.01 0.00 45.78 2.59
2512 4728 6.842807 AGATTCCTTATCCCTTTGATTGCATT 59.157 34.615 0.00 0.00 34.76 3.56
2513 4729 8.006564 AGATTCCTTATCCCTTTGATTGCATTA 58.993 33.333 0.00 0.00 34.76 1.90
2514 4730 8.731591 ATTCCTTATCCCTTTGATTGCATTAT 57.268 30.769 0.00 0.00 34.76 1.28
2515 4731 8.551682 TTCCTTATCCCTTTGATTGCATTATT 57.448 30.769 0.00 0.00 34.76 1.40
2546 4762 1.984570 CTTCTCCAGAGGACGCCCA 60.985 63.158 0.00 0.00 33.88 5.36
2669 4911 4.796231 GCCGAGGTCGACGCACAT 62.796 66.667 9.92 0.00 43.02 3.21
2670 4912 2.880879 CCGAGGTCGACGCACATG 60.881 66.667 9.92 0.00 43.02 3.21
2675 4917 4.077184 GTCGACGCACATGGGGGA 62.077 66.667 20.25 0.00 0.00 4.81
2676 4918 3.080765 TCGACGCACATGGGGGAT 61.081 61.111 20.25 2.72 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
419 420 7.230309 TGAAACAAACATGATATGAAGTGTCCA 59.770 33.333 0.00 0.00 0.00 4.02
453 454 2.489329 CAAGGTGTTCGATGAAATGCCT 59.511 45.455 0.00 0.00 0.00 4.75
604 605 0.672401 CCCGAAAGCCTTTAGTCGCA 60.672 55.000 0.00 0.00 32.21 5.10
617 618 2.865119 GGGACTAAAGGTTCCCGAAA 57.135 50.000 0.00 0.00 37.63 3.46
939 940 2.644299 TGTATTCCCATGAGGCCATAGG 59.356 50.000 5.01 0.21 33.55 2.57
940 941 4.202503 ACTTGTATTCCCATGAGGCCATAG 60.203 45.833 5.01 0.00 34.51 2.23
941 942 3.721575 ACTTGTATTCCCATGAGGCCATA 59.278 43.478 5.01 0.00 34.51 2.74
942 943 2.515429 ACTTGTATTCCCATGAGGCCAT 59.485 45.455 5.01 0.00 34.51 4.40
943 944 1.922447 ACTTGTATTCCCATGAGGCCA 59.078 47.619 5.01 0.00 34.51 5.36
944 945 2.689983 CAACTTGTATTCCCATGAGGCC 59.310 50.000 0.00 0.00 34.51 5.19
945 946 2.099756 GCAACTTGTATTCCCATGAGGC 59.900 50.000 0.00 0.00 34.51 4.70
946 947 3.624777 AGCAACTTGTATTCCCATGAGG 58.375 45.455 0.00 0.00 0.00 3.86
947 948 6.949352 ATAAGCAACTTGTATTCCCATGAG 57.051 37.500 0.00 0.00 0.00 2.90
948 949 6.321181 GGAATAAGCAACTTGTATTCCCATGA 59.679 38.462 14.79 0.00 43.89 3.07
949 950 6.507023 GGAATAAGCAACTTGTATTCCCATG 58.493 40.000 14.79 0.00 43.89 3.66
950 951 6.715347 GGAATAAGCAACTTGTATTCCCAT 57.285 37.500 14.79 0.00 43.89 4.00
954 955 8.947115 AGTGTTAGGAATAAGCAACTTGTATTC 58.053 33.333 0.00 4.57 34.75 1.75
955 956 8.863872 AGTGTTAGGAATAAGCAACTTGTATT 57.136 30.769 0.00 0.00 0.00 1.89
956 957 8.863872 AAGTGTTAGGAATAAGCAACTTGTAT 57.136 30.769 0.00 0.00 0.00 2.29
957 958 8.685838 AAAGTGTTAGGAATAAGCAACTTGTA 57.314 30.769 0.00 0.00 0.00 2.41
958 959 7.582667 AAAGTGTTAGGAATAAGCAACTTGT 57.417 32.000 0.00 0.00 0.00 3.16
959 960 8.564574 TGTAAAGTGTTAGGAATAAGCAACTTG 58.435 33.333 0.00 0.00 0.00 3.16
960 961 8.565416 GTGTAAAGTGTTAGGAATAAGCAACTT 58.435 33.333 0.00 0.00 0.00 2.66
961 962 7.174426 GGTGTAAAGTGTTAGGAATAAGCAACT 59.826 37.037 0.00 0.00 0.00 3.16
962 963 7.303261 GGTGTAAAGTGTTAGGAATAAGCAAC 58.697 38.462 0.00 0.00 0.00 4.17
963 964 6.148150 CGGTGTAAAGTGTTAGGAATAAGCAA 59.852 38.462 0.00 0.00 0.00 3.91
964 965 5.640357 CGGTGTAAAGTGTTAGGAATAAGCA 59.360 40.000 0.00 0.00 0.00 3.91
965 966 5.640783 ACGGTGTAAAGTGTTAGGAATAAGC 59.359 40.000 0.00 0.00 0.00 3.09
966 967 6.869913 TGACGGTGTAAAGTGTTAGGAATAAG 59.130 38.462 0.00 0.00 0.00 1.73
967 968 6.646240 GTGACGGTGTAAAGTGTTAGGAATAA 59.354 38.462 0.00 0.00 0.00 1.40
968 969 6.158598 GTGACGGTGTAAAGTGTTAGGAATA 58.841 40.000 0.00 0.00 0.00 1.75
969 970 4.992951 GTGACGGTGTAAAGTGTTAGGAAT 59.007 41.667 0.00 0.00 0.00 3.01
970 971 4.370917 GTGACGGTGTAAAGTGTTAGGAA 58.629 43.478 0.00 0.00 0.00 3.36
971 972 3.243839 GGTGACGGTGTAAAGTGTTAGGA 60.244 47.826 0.00 0.00 0.00 2.94
972 973 3.062042 GGTGACGGTGTAAAGTGTTAGG 58.938 50.000 0.00 0.00 0.00 2.69
1011 1012 4.768448 TGCAATTCTGTCATGTCTCCAATT 59.232 37.500 0.00 0.00 0.00 2.32
1014 1015 3.340928 CTGCAATTCTGTCATGTCTCCA 58.659 45.455 0.00 0.00 0.00 3.86
1017 1018 3.079578 CACCTGCAATTCTGTCATGTCT 58.920 45.455 0.00 0.00 0.00 3.41
1039 1040 2.663602 CGTCGCCAGCAATATGAGATAC 59.336 50.000 0.00 0.00 0.00 2.24
1078 1085 4.537135 TCAACTGGAGTAAGTAGCCAAG 57.463 45.455 0.00 0.00 0.00 3.61
1087 1094 6.001460 CACCCAACTTAATCAACTGGAGTAA 58.999 40.000 0.00 0.00 35.05 2.24
1099 1106 4.141251 AGAGACAACCACACCCAACTTAAT 60.141 41.667 0.00 0.00 0.00 1.40
1204 1214 2.035449 TCTCTTCTTCGGTTTCTGCGAA 59.965 45.455 0.00 0.00 0.00 4.70
1237 1253 3.652057 TGGGGATGGATCTTTCTTGTC 57.348 47.619 0.00 0.00 0.00 3.18
1249 1265 4.459852 ACTTTGGATATCTTGGGGATGG 57.540 45.455 2.05 0.00 35.98 3.51
1314 1330 4.925646 GCCTTGAGTTTTTCAATCCATGAC 59.074 41.667 0.00 0.00 44.48 3.06
1329 1345 4.278419 GTCATTTTGGTAAGTGCCTTGAGT 59.722 41.667 0.00 0.00 0.00 3.41
1337 1353 2.890311 TGCAGGGTCATTTTGGTAAGTG 59.110 45.455 0.00 0.00 0.00 3.16
1432 1448 3.844577 ACTTTCATTGCATGACTCTGC 57.155 42.857 0.00 0.00 39.39 4.26
1433 1449 5.410746 ACTGTACTTTCATTGCATGACTCTG 59.589 40.000 0.00 0.00 39.39 3.35
1472 1488 4.083590 GGAACTCAAGACTCTGAAATGCAC 60.084 45.833 0.00 0.00 0.00 4.57
1507 1523 0.033504 ATACCGGTAATGGCTGAGCG 59.966 55.000 20.22 0.00 36.36 5.03
1522 1538 4.142381 GGCCTCATTGTCAAAGTTGATACC 60.142 45.833 0.00 0.00 39.73 2.73
1563 1579 3.034635 ACCAGTAGAAGACCAGGCTATG 58.965 50.000 0.00 0.00 0.00 2.23
1564 1580 3.034635 CACCAGTAGAAGACCAGGCTAT 58.965 50.000 0.00 0.00 0.00 2.97
1614 1630 2.175236 GAGCTTTTCGAGGCTTGGG 58.825 57.895 0.97 0.00 39.05 4.12
1624 1640 1.195674 GCCTGTCAACTCGAGCTTTTC 59.804 52.381 13.61 0.30 0.00 2.29
1653 3409 1.748493 GCTTGTTTCACACCTTCCACA 59.252 47.619 0.00 0.00 0.00 4.17
1660 3416 3.245990 GCTTCAATTGCTTGTTTCACACC 59.754 43.478 0.00 0.00 33.87 4.16
1708 3464 1.062428 CCTGGTCCTGGTAGGGTATGA 60.062 57.143 6.63 0.00 35.59 2.15
1722 3478 4.016706 CACACCCCGGACCTGGTC 62.017 72.222 18.65 18.65 30.70 4.02
1723 3479 3.864983 ATCACACCCCGGACCTGGT 62.865 63.158 0.73 0.00 34.40 4.00
1725 3481 2.584608 GATCACACCCCGGACCTG 59.415 66.667 0.73 0.00 0.00 4.00
1736 3493 7.733093 ACTCAAGGAGCAAATGTGGATCACA 62.733 44.000 3.10 3.10 39.94 3.58
1759 3516 2.125106 GGCATCCGGTGAGGTCAC 60.125 66.667 0.00 1.17 45.72 3.67
1821 3581 6.855914 GCAATAATCCGCGAAGAATGAAATTA 59.144 34.615 8.23 0.00 36.07 1.40
1851 3611 4.032310 TCAAATATGCAGGGGCTGAATTT 58.968 39.130 0.00 0.00 41.91 1.82
1853 3613 3.317455 TCAAATATGCAGGGGCTGAAT 57.683 42.857 0.00 0.00 41.91 2.57
1857 3617 6.752285 AAATAAATCAAATATGCAGGGGCT 57.248 33.333 0.00 0.00 41.91 5.19
1887 3658 1.835483 CGGTTCAGTCACTGCAGTGC 61.835 60.000 36.76 30.09 45.25 4.40
1888 3659 0.530650 ACGGTTCAGTCACTGCAGTG 60.531 55.000 36.07 36.07 46.91 3.66
1889 3660 0.178068 AACGGTTCAGTCACTGCAGT 59.822 50.000 15.25 15.25 0.00 4.40
1890 3661 0.583438 CAACGGTTCAGTCACTGCAG 59.417 55.000 13.48 13.48 0.00 4.41
1907 3708 5.189928 AGTGACCTCAACAAATACACACAA 58.810 37.500 0.00 0.00 0.00 3.33
1908 3709 4.776349 AGTGACCTCAACAAATACACACA 58.224 39.130 0.00 0.00 0.00 3.72
1922 3728 4.799564 ACTGAAATCTGAGAGTGACCTC 57.200 45.455 0.00 0.00 38.04 3.85
1939 3751 3.540617 ACACAACACAGCACATAACTGA 58.459 40.909 0.00 0.00 38.55 3.41
1965 3790 2.397777 TGCAAACAATAGCACACGTG 57.602 45.000 15.48 15.48 35.51 4.49
1966 3791 3.641437 AATGCAAACAATAGCACACGT 57.359 38.095 0.00 0.00 44.49 4.49
1981 3806 2.762887 TGTTTCTGGGTGAACAAATGCA 59.237 40.909 0.00 0.00 33.88 3.96
2113 3942 8.615878 AACTGCACAAATCAAATAGTAGTACA 57.384 30.769 2.52 0.00 0.00 2.90
2127 3961 2.895404 AGGCATTCTGAACTGCACAAAT 59.105 40.909 19.19 4.71 40.18 2.32
2128 3962 2.034939 CAGGCATTCTGAACTGCACAAA 59.965 45.455 19.19 0.00 46.18 2.83
2135 3969 1.016130 CGACGCAGGCATTCTGAACT 61.016 55.000 0.00 0.00 46.18 3.01
2141 3976 3.363970 CCATATTAACGACGCAGGCATTC 60.364 47.826 0.00 0.00 0.00 2.67
2207 4068 3.940209 TGCTTGGAATTTCAGCGATTT 57.060 38.095 0.00 0.00 0.00 2.17
2252 4435 7.438160 TCAGTTAACACTTCTTGACACATACAG 59.562 37.037 8.61 0.00 0.00 2.74
2256 4439 6.260936 CCTTCAGTTAACACTTCTTGACACAT 59.739 38.462 8.61 0.00 0.00 3.21
2257 4440 5.584649 CCTTCAGTTAACACTTCTTGACACA 59.415 40.000 8.61 0.00 0.00 3.72
2258 4441 5.815740 TCCTTCAGTTAACACTTCTTGACAC 59.184 40.000 8.61 0.00 0.00 3.67
2259 4442 5.984725 TCCTTCAGTTAACACTTCTTGACA 58.015 37.500 8.61 0.00 0.00 3.58
2260 4443 6.281405 TCTCCTTCAGTTAACACTTCTTGAC 58.719 40.000 8.61 0.00 0.00 3.18
2261 4444 6.479972 TCTCCTTCAGTTAACACTTCTTGA 57.520 37.500 8.61 0.00 0.00 3.02
2262 4445 6.931281 TGATCTCCTTCAGTTAACACTTCTTG 59.069 38.462 8.61 0.00 0.00 3.02
2263 4446 7.067496 TGATCTCCTTCAGTTAACACTTCTT 57.933 36.000 8.61 0.00 0.00 2.52
2264 4447 6.672266 TGATCTCCTTCAGTTAACACTTCT 57.328 37.500 8.61 0.00 0.00 2.85
2265 4448 6.183360 GCATGATCTCCTTCAGTTAACACTTC 60.183 42.308 8.61 0.00 0.00 3.01
2281 4464 8.613482 CAATATCTGAATACCATGCATGATCTC 58.387 37.037 28.31 17.24 0.00 2.75
2282 4465 7.556635 CCAATATCTGAATACCATGCATGATCT 59.443 37.037 28.31 11.94 0.00 2.75
2283 4466 7.555195 TCCAATATCTGAATACCATGCATGATC 59.445 37.037 28.31 18.60 0.00 2.92
2292 4475 6.321181 GCAAACCTTCCAATATCTGAATACCA 59.679 38.462 0.00 0.00 0.00 3.25
2307 4490 2.427095 AGTGTCAACTTGCAAACCTTCC 59.573 45.455 0.00 0.00 30.14 3.46
2311 4494 2.796032 GCAGAGTGTCAACTTGCAAACC 60.796 50.000 0.00 0.00 38.85 3.27
2313 4496 2.355756 GAGCAGAGTGTCAACTTGCAAA 59.644 45.455 0.00 0.00 40.19 3.68
2328 4530 1.508632 CGGTTCCTTTTTCGAGCAGA 58.491 50.000 0.00 0.00 0.00 4.26
2339 4555 0.889186 GATGTGGTGTGCGGTTCCTT 60.889 55.000 0.00 0.00 0.00 3.36
2463 4679 3.244249 GCCTTCAGTCTCTAGGTTGTTGT 60.244 47.826 0.00 0.00 0.00 3.32
2485 4701 5.010415 GCAATCAAAGGGATAAGGAATCTGG 59.990 44.000 0.00 0.00 34.28 3.86
2487 4703 5.769835 TGCAATCAAAGGGATAAGGAATCT 58.230 37.500 0.00 0.00 34.28 2.40
2499 4715 5.291971 GGCCACTAATAATGCAATCAAAGG 58.708 41.667 0.00 0.00 0.00 3.11
2512 4728 0.103572 GAAGACCGCGGCCACTAATA 59.896 55.000 28.58 0.00 0.00 0.98
2513 4729 1.153429 GAAGACCGCGGCCACTAAT 60.153 57.895 28.58 2.52 0.00 1.73
2514 4730 2.221906 GAGAAGACCGCGGCCACTAA 62.222 60.000 28.58 0.00 0.00 2.24
2515 4731 2.678934 AGAAGACCGCGGCCACTA 60.679 61.111 28.58 0.00 0.00 2.74
2578 4808 2.887889 CGCAAACCTCGACCGCAAA 61.888 57.895 0.00 0.00 0.00 3.68
2655 4897 2.509336 CCCATGTGCGTCGACCTC 60.509 66.667 10.58 2.56 0.00 3.85
2658 4900 3.385749 ATCCCCCATGTGCGTCGAC 62.386 63.158 5.18 5.18 0.00 4.20
2659 4901 3.080765 ATCCCCCATGTGCGTCGA 61.081 61.111 0.00 0.00 0.00 4.20
2660 4902 2.896854 CATCCCCCATGTGCGTCG 60.897 66.667 0.00 0.00 0.00 5.12
2661 4903 3.211963 GCATCCCCCATGTGCGTC 61.212 66.667 0.00 0.00 34.56 5.19
2662 4904 4.820744 GGCATCCCCCATGTGCGT 62.821 66.667 0.00 0.00 39.69 5.24


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

AutoCloner maintained by Alex Coulton.