Multiple sequence alignment - TraesCS4D01G277600

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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 TraesCS4D01G277600 chr4D 100.000 2228 0 0 1 2228 449740397 449738170 0.000000e+00 4115.0
1 TraesCS4D01G277600 chr4D 87.716 578 48 9 926 1489 449854433 449853865 0.000000e+00 652.0
2 TraesCS4D01G277600 chr4D 86.833 281 34 2 982 1262 449887539 449887262 5.970000e-81 311.0
3 TraesCS4D01G277600 chr4D 81.087 423 51 20 848 1263 449946224 449946624 5.970000e-81 311.0
4 TraesCS4D01G277600 chr4D 86.517 267 20 8 673 933 449854740 449854484 1.680000e-71 279.0
5 TraesCS4D01G277600 chr4D 76.667 270 42 18 662 925 449962752 449963006 1.800000e-26 130.0
6 TraesCS4D01G277600 chr4A 92.637 747 50 4 922 1667 17256536 17257278 0.000000e+00 1070.0
7 TraesCS4D01G277600 chr4A 93.223 664 23 1 1 664 603120486 603121127 0.000000e+00 957.0
8 TraesCS4D01G277600 chr4A 83.049 997 93 38 789 1742 17032397 17033360 0.000000e+00 835.0
9 TraesCS4D01G277600 chr4A 92.172 396 29 2 958 1352 17253372 17253766 1.930000e-155 558.0
10 TraesCS4D01G277600 chr4A 91.756 279 11 6 661 935 17256225 17256495 5.810000e-101 377.0
11 TraesCS4D01G277600 chr4A 91.489 235 17 2 1705 1938 17257276 17257508 9.930000e-84 320.0
12 TraesCS4D01G277600 chr4A 86.552 290 36 2 973 1262 17018283 17018569 1.280000e-82 316.0
13 TraesCS4D01G277600 chr4A 95.000 80 3 1 661 739 17234164 17234243 8.350000e-25 124.0
14 TraesCS4D01G277600 chr4A 86.250 80 9 2 848 926 16981314 16981236 3.940000e-13 86.1
15 TraesCS4D01G277600 chr6D 95.633 664 7 1 1 664 143963035 143963676 0.000000e+00 1046.0
16 TraesCS4D01G277600 chr1D 93.646 661 20 1 4 664 441063182 441062544 0.000000e+00 968.0
17 TraesCS4D01G277600 chr2D 93.495 661 21 1 4 664 597841141 597840503 0.000000e+00 963.0
18 TraesCS4D01G277600 chr2D 93.495 661 21 1 4 664 641886358 641885720 0.000000e+00 963.0
19 TraesCS4D01G277600 chr2B 93.495 661 21 1 4 664 727677320 727676682 0.000000e+00 963.0
20 TraesCS4D01G277600 chr2B 94.273 227 12 1 2003 2228 691789299 691789073 1.640000e-91 346.0
21 TraesCS4D01G277600 chr7D 93.495 661 13 5 4 664 114587576 114586946 0.000000e+00 955.0
22 TraesCS4D01G277600 chr4B 85.143 976 86 31 673 1612 562419683 562418731 0.000000e+00 944.0
23 TraesCS4D01G277600 chr4B 86.429 700 41 18 922 1596 562361284 562360614 0.000000e+00 717.0
24 TraesCS4D01G277600 chr4B 90.794 315 20 5 1633 1938 562360610 562360296 1.590000e-111 412.0
25 TraesCS4D01G277600 chr4B 86.176 340 34 7 964 1299 562436349 562436019 2.720000e-94 355.0
26 TraesCS4D01G277600 chr4B 94.012 167 8 2 769 935 562361489 562361325 3.670000e-63 252.0
27 TraesCS4D01G277600 chr4B 87.342 79 6 4 848 925 562628613 562628688 1.100000e-13 87.9
28 TraesCS4D01G277600 chr3B 92.738 661 26 1 4 664 787404267 787403629 0.000000e+00 935.0
29 TraesCS4D01G277600 chr3B 96.035 227 8 1 2003 2228 641989409 641989635 3.500000e-98 368.0
30 TraesCS4D01G277600 chr7A 81.997 661 97 8 4 664 714064855 714064217 1.950000e-150 542.0
31 TraesCS4D01G277600 chr5D 96.035 227 5 2 2003 2228 75921718 75921941 1.260000e-97 366.0
32 TraesCS4D01G277600 chr3A 97.345 113 3 0 1 113 725562165 725562277 2.260000e-45 193.0


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 TraesCS4D01G277600 chr4D 449738170 449740397 2227 True 4115.000000 4115 100.000000 1 2228 1 chr4D.!!$R1 2227
1 TraesCS4D01G277600 chr4D 449853865 449854740 875 True 465.500000 652 87.116500 673 1489 2 chr4D.!!$R3 816
2 TraesCS4D01G277600 chr4A 603120486 603121127 641 False 957.000000 957 93.223000 1 664 1 chr4A.!!$F4 663
3 TraesCS4D01G277600 chr4A 17032397 17033360 963 False 835.000000 835 83.049000 789 1742 1 chr4A.!!$F2 953
4 TraesCS4D01G277600 chr4A 17253372 17257508 4136 False 581.250000 1070 92.013500 661 1938 4 chr4A.!!$F5 1277
5 TraesCS4D01G277600 chr6D 143963035 143963676 641 False 1046.000000 1046 95.633000 1 664 1 chr6D.!!$F1 663
6 TraesCS4D01G277600 chr1D 441062544 441063182 638 True 968.000000 968 93.646000 4 664 1 chr1D.!!$R1 660
7 TraesCS4D01G277600 chr2D 597840503 597841141 638 True 963.000000 963 93.495000 4 664 1 chr2D.!!$R1 660
8 TraesCS4D01G277600 chr2D 641885720 641886358 638 True 963.000000 963 93.495000 4 664 1 chr2D.!!$R2 660
9 TraesCS4D01G277600 chr2B 727676682 727677320 638 True 963.000000 963 93.495000 4 664 1 chr2B.!!$R2 660
10 TraesCS4D01G277600 chr7D 114586946 114587576 630 True 955.000000 955 93.495000 4 664 1 chr7D.!!$R1 660
11 TraesCS4D01G277600 chr4B 562418731 562419683 952 True 944.000000 944 85.143000 673 1612 1 chr4B.!!$R1 939
12 TraesCS4D01G277600 chr4B 562360296 562361489 1193 True 460.333333 717 90.411667 769 1938 3 chr4B.!!$R3 1169
13 TraesCS4D01G277600 chr3B 787403629 787404267 638 True 935.000000 935 92.738000 4 664 1 chr3B.!!$R1 660
14 TraesCS4D01G277600 chr7A 714064217 714064855 638 True 542.000000 542 81.997000 4 664 1 chr7A.!!$R1 660

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
736 2932 0.543277 CCATTCTACAGGCTGGCTCA 59.457 55.0 20.34 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1961 4297 0.033504 GCTTGTCACGGTCTTCTGGA 59.966 55.0 0.0 0.0 0.0 3.86 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
368 369 3.074390 ACAAGTCTTCATCCCATGAACCA 59.926 43.478 0.00 0.00 43.84 3.67
440 441 7.067496 TCTTAATGATATCACCTTCCTGTCC 57.933 40.000 7.78 0.00 0.00 4.02
441 442 4.342862 AATGATATCACCTTCCTGTCCG 57.657 45.455 7.78 0.00 0.00 4.79
443 444 1.344763 GATATCACCTTCCTGTCCGGG 59.655 57.143 0.00 0.00 0.00 5.73
445 446 3.322466 CACCTTCCTGTCCGGGCT 61.322 66.667 7.97 0.00 0.00 5.19
446 447 1.987855 CACCTTCCTGTCCGGGCTA 60.988 63.158 7.97 0.00 0.00 3.93
448 449 2.501610 CTTCCTGTCCGGGCTAGC 59.498 66.667 7.97 6.04 0.00 3.42
450 451 2.303549 CTTCCTGTCCGGGCTAGCTG 62.304 65.000 15.72 7.61 0.00 4.24
451 452 3.854669 CCTGTCCGGGCTAGCTGG 61.855 72.222 15.72 16.67 0.00 4.85
452 453 3.854669 CTGTCCGGGCTAGCTGGG 61.855 72.222 21.34 18.64 0.00 4.45
455 456 2.524394 TCCGGGCTAGCTGGGATC 60.524 66.667 21.34 2.72 0.00 3.36
457 458 2.844362 CGGGCTAGCTGGGATCCA 60.844 66.667 15.72 0.00 0.00 3.41
459 460 1.377994 GGGCTAGCTGGGATCCATG 59.622 63.158 15.72 6.47 30.82 3.66
664 665 4.214119 GCACTCTAGCACACAAAGATTCAA 59.786 41.667 0.00 0.00 0.00 2.69
671 2865 6.463995 AGCACACAAAGATTCAACCTTAAA 57.536 33.333 0.00 0.00 0.00 1.52
731 2927 1.148157 CGCGTCCATTCTACAGGCTG 61.148 60.000 14.16 14.16 0.00 4.85
732 2928 0.811616 GCGTCCATTCTACAGGCTGG 60.812 60.000 20.34 1.44 0.00 4.85
733 2929 0.811616 CGTCCATTCTACAGGCTGGC 60.812 60.000 20.34 0.00 0.00 4.85
734 2930 0.543749 GTCCATTCTACAGGCTGGCT 59.456 55.000 20.34 0.00 0.00 4.75
735 2931 0.833287 TCCATTCTACAGGCTGGCTC 59.167 55.000 20.34 0.00 0.00 4.70
736 2932 0.543277 CCATTCTACAGGCTGGCTCA 59.457 55.000 20.34 0.00 0.00 4.26
766 2962 5.288015 ACGAGAGCAGATCATACAATCAAG 58.712 41.667 0.00 0.00 0.00 3.02
772 2968 4.572389 GCAGATCATACAATCAAGTCCGTT 59.428 41.667 0.00 0.00 0.00 4.44
814 3012 8.582657 TCATTTCCCATTCGTTATAGGAAAAA 57.417 30.769 13.35 6.11 43.95 1.94
817 3015 7.576861 TTCCCATTCGTTATAGGAAAAATCC 57.423 36.000 0.00 0.00 32.04 3.01
894 3100 1.342819 CAACCATCGATCTCTCCTCCC 59.657 57.143 0.00 0.00 0.00 4.30
1053 3331 2.480610 CCAGTGCTGCAACGTGGTT 61.481 57.895 2.77 0.00 0.00 3.67
1256 3537 2.455032 CGGAGCTCGACTAGTCAATTG 58.545 52.381 22.37 6.44 42.43 2.32
1299 3580 4.995487 ACGTACATGCGTAGATAGAGATCA 59.005 41.667 0.00 0.00 43.83 2.92
1336 3633 7.595130 GTCTGGTTTGATTAATTCTTTGTCCAC 59.405 37.037 0.00 0.00 0.00 4.02
1355 3656 6.154363 TGTCCACTGGTTCTTTCATTCTTTTT 59.846 34.615 0.00 0.00 0.00 1.94
1358 3659 7.777910 TCCACTGGTTCTTTCATTCTTTTTAGA 59.222 33.333 0.00 0.00 0.00 2.10
1359 3660 8.579863 CCACTGGTTCTTTCATTCTTTTTAGAT 58.420 33.333 0.00 0.00 0.00 1.98
1360 3661 9.403110 CACTGGTTCTTTCATTCTTTTTAGATG 57.597 33.333 0.00 0.00 0.00 2.90
1361 3662 9.136323 ACTGGTTCTTTCATTCTTTTTAGATGT 57.864 29.630 0.00 0.00 0.00 3.06
1392 3696 6.844097 ATTATTTTAGGGCTTCCGTGAAAA 57.156 33.333 0.82 0.00 32.38 2.29
1418 3722 2.362077 GAGCCCAAGAAGCTGTTCAAAA 59.638 45.455 0.00 0.00 41.75 2.44
1588 3911 5.641636 GGAAGGAGAGAAACAGACTCATTTC 59.358 44.000 0.00 0.00 35.39 2.17
1776 4110 1.220749 GACAATGCTCCGGCTGGTA 59.779 57.895 12.43 0.00 39.59 3.25
1830 4166 7.060600 TGTTCGTTGTTTTGATATAGCTCAG 57.939 36.000 0.00 0.00 0.00 3.35
1839 4175 7.283807 TGTTTTGATATAGCTCAGCATTCATGT 59.716 33.333 0.00 0.00 0.00 3.21
1865 4201 9.058174 TCGAATGGTAAAAATGTTTCTACTCAA 57.942 29.630 0.00 0.00 0.00 3.02
1870 4206 4.766404 AAAATGTTTCTACTCAAGGCGG 57.234 40.909 0.00 0.00 0.00 6.13
1917 4253 0.318699 CGAGGAAGCGTGTTCAGTCA 60.319 55.000 2.66 0.00 0.00 3.41
1932 4268 7.855409 CGTGTTCAGTCAAATTCAAATTGTAGA 59.145 33.333 0.00 0.00 0.00 2.59
1938 4274 8.971321 CAGTCAAATTCAAATTGTAGAGTTTGG 58.029 33.333 16.48 0.00 40.04 3.28
1939 4275 8.695456 AGTCAAATTCAAATTGTAGAGTTTGGT 58.305 29.630 16.48 7.88 40.04 3.67
1940 4276 8.968242 GTCAAATTCAAATTGTAGAGTTTGGTC 58.032 33.333 16.48 10.58 40.04 4.02
1941 4277 8.141268 TCAAATTCAAATTGTAGAGTTTGGTCC 58.859 33.333 16.48 0.00 40.04 4.46
1942 4278 6.590234 ATTCAAATTGTAGAGTTTGGTCCC 57.410 37.500 7.81 0.00 36.30 4.46
1943 4279 4.403734 TCAAATTGTAGAGTTTGGTCCCC 58.596 43.478 7.81 0.00 36.30 4.81
1944 4280 3.451402 AATTGTAGAGTTTGGTCCCCC 57.549 47.619 0.00 0.00 0.00 5.40
1945 4281 1.822425 TTGTAGAGTTTGGTCCCCCA 58.178 50.000 0.00 0.00 39.65 4.96
1952 4288 3.681129 TTGGTCCCCCAAGCTCAA 58.319 55.556 0.00 0.00 45.93 3.02
1953 4289 2.172900 TTGGTCCCCCAAGCTCAAT 58.827 52.632 0.00 0.00 45.93 2.57
1954 4290 1.377690 TTGGTCCCCCAAGCTCAATA 58.622 50.000 0.00 0.00 45.93 1.90
1955 4291 1.377690 TGGTCCCCCAAGCTCAATAA 58.622 50.000 0.00 0.00 37.98 1.40
1956 4292 1.929494 TGGTCCCCCAAGCTCAATAAT 59.071 47.619 0.00 0.00 37.98 1.28
1957 4293 2.310538 GGTCCCCCAAGCTCAATAATG 58.689 52.381 0.00 0.00 0.00 1.90
1958 4294 2.091885 GGTCCCCCAAGCTCAATAATGA 60.092 50.000 0.00 0.00 0.00 2.57
1959 4295 3.627237 GGTCCCCCAAGCTCAATAATGAA 60.627 47.826 0.00 0.00 34.49 2.57
1960 4296 3.381590 GTCCCCCAAGCTCAATAATGAAC 59.618 47.826 0.00 0.00 34.49 3.18
1961 4297 3.269381 TCCCCCAAGCTCAATAATGAACT 59.731 43.478 0.00 0.00 33.44 3.01
1962 4298 3.633986 CCCCCAAGCTCAATAATGAACTC 59.366 47.826 0.00 0.00 30.81 3.01
1963 4299 3.633986 CCCCAAGCTCAATAATGAACTCC 59.366 47.826 0.00 0.00 30.81 3.85
1964 4300 4.272489 CCCAAGCTCAATAATGAACTCCA 58.728 43.478 0.00 0.00 30.81 3.86
1965 4301 4.337555 CCCAAGCTCAATAATGAACTCCAG 59.662 45.833 0.00 0.00 30.81 3.86
1966 4302 5.188434 CCAAGCTCAATAATGAACTCCAGA 58.812 41.667 0.00 0.00 30.81 3.86
1967 4303 5.649395 CCAAGCTCAATAATGAACTCCAGAA 59.351 40.000 0.00 0.00 30.81 3.02
1968 4304 6.183360 CCAAGCTCAATAATGAACTCCAGAAG 60.183 42.308 0.00 0.00 30.81 2.85
1969 4305 6.305272 AGCTCAATAATGAACTCCAGAAGA 57.695 37.500 0.00 0.00 34.49 2.87
1970 4306 6.112058 AGCTCAATAATGAACTCCAGAAGAC 58.888 40.000 0.00 0.00 34.49 3.01
1971 4307 5.295540 GCTCAATAATGAACTCCAGAAGACC 59.704 44.000 0.00 0.00 34.49 3.85
1972 4308 5.419542 TCAATAATGAACTCCAGAAGACCG 58.580 41.667 0.00 0.00 30.99 4.79
1973 4309 5.046591 TCAATAATGAACTCCAGAAGACCGT 60.047 40.000 0.00 0.00 30.99 4.83
1974 4310 2.751166 ATGAACTCCAGAAGACCGTG 57.249 50.000 0.00 0.00 0.00 4.94
1975 4311 1.699730 TGAACTCCAGAAGACCGTGA 58.300 50.000 0.00 0.00 0.00 4.35
1976 4312 1.340248 TGAACTCCAGAAGACCGTGAC 59.660 52.381 0.00 0.00 0.00 3.67
1977 4313 1.340248 GAACTCCAGAAGACCGTGACA 59.660 52.381 0.00 0.00 0.00 3.58
1978 4314 1.410004 ACTCCAGAAGACCGTGACAA 58.590 50.000 0.00 0.00 0.00 3.18
1979 4315 1.341531 ACTCCAGAAGACCGTGACAAG 59.658 52.381 0.00 0.00 0.00 3.16
1980 4316 0.033504 TCCAGAAGACCGTGACAAGC 59.966 55.000 0.00 0.00 0.00 4.01
1981 4317 0.034059 CCAGAAGACCGTGACAAGCT 59.966 55.000 0.00 0.00 0.00 3.74
1982 4318 1.423395 CAGAAGACCGTGACAAGCTC 58.577 55.000 0.00 0.00 0.00 4.09
1983 4319 0.318762 AGAAGACCGTGACAAGCTCC 59.681 55.000 0.00 0.00 0.00 4.70
1984 4320 0.318762 GAAGACCGTGACAAGCTCCT 59.681 55.000 0.00 0.00 0.00 3.69
1985 4321 0.034059 AAGACCGTGACAAGCTCCTG 59.966 55.000 0.00 0.00 0.00 3.86
1986 4322 2.029844 GACCGTGACAAGCTCCTGC 61.030 63.158 0.00 0.00 40.05 4.85
1996 4332 2.886124 GCTCCTGCTTCCGTACGC 60.886 66.667 10.49 0.00 36.03 4.42
1997 4333 2.571757 CTCCTGCTTCCGTACGCA 59.428 61.111 10.49 0.88 34.54 5.24
2001 4337 3.997397 TGCTTCCGTACGCAGGCA 61.997 61.111 12.41 12.41 0.00 4.75
2002 4338 2.740826 GCTTCCGTACGCAGGCAA 60.741 61.111 8.60 0.00 0.00 4.52
2003 4339 3.023591 GCTTCCGTACGCAGGCAAC 62.024 63.158 8.60 0.00 0.00 4.17
2004 4340 1.666553 CTTCCGTACGCAGGCAACA 60.667 57.895 10.49 0.00 41.41 3.33
2005 4341 1.897398 CTTCCGTACGCAGGCAACAC 61.897 60.000 10.49 0.00 41.41 3.32
2006 4342 3.773630 CCGTACGCAGGCAACACG 61.774 66.667 10.49 0.00 43.22 4.49
2007 4343 3.773630 CGTACGCAGGCAACACGG 61.774 66.667 0.52 0.00 42.05 4.94
2008 4344 4.084888 GTACGCAGGCAACACGGC 62.085 66.667 0.00 0.00 42.05 5.68
2027 4363 3.896133 CCCGCGTCGCCTAGCTTA 61.896 66.667 12.44 0.00 0.00 3.09
2028 4364 2.353607 CCGCGTCGCCTAGCTTAG 60.354 66.667 12.44 0.00 0.00 2.18
2036 4372 4.711980 CCTAGCTTAGGCGACACG 57.288 61.111 0.00 0.00 44.37 4.49
2037 4373 1.065928 CCTAGCTTAGGCGACACGG 59.934 63.158 0.00 0.00 44.37 4.94
2038 4374 1.065928 CTAGCTTAGGCGACACGGG 59.934 63.158 0.00 0.00 44.37 5.28
2039 4375 2.955751 CTAGCTTAGGCGACACGGGC 62.956 65.000 0.00 0.00 44.37 6.13
2071 4407 4.479993 GCCGTCCAGCAGCTCCAT 62.480 66.667 0.00 0.00 0.00 3.41
2072 4408 2.202987 CCGTCCAGCAGCTCCATC 60.203 66.667 0.00 0.00 0.00 3.51
2073 4409 2.202987 CGTCCAGCAGCTCCATCC 60.203 66.667 0.00 0.00 0.00 3.51
2074 4410 2.993008 GTCCAGCAGCTCCATCCA 59.007 61.111 0.00 0.00 0.00 3.41
2075 4411 1.451028 GTCCAGCAGCTCCATCCAC 60.451 63.158 0.00 0.00 0.00 4.02
2076 4412 2.124403 CCAGCAGCTCCATCCACC 60.124 66.667 0.00 0.00 0.00 4.61
2077 4413 2.513204 CAGCAGCTCCATCCACCG 60.513 66.667 0.00 0.00 0.00 4.94
2078 4414 3.790437 AGCAGCTCCATCCACCGG 61.790 66.667 0.00 0.00 0.00 5.28
2079 4415 4.101448 GCAGCTCCATCCACCGGT 62.101 66.667 0.00 0.00 0.00 5.28
2080 4416 2.124983 CAGCTCCATCCACCGGTG 60.125 66.667 28.26 28.26 0.00 4.94
2081 4417 4.101448 AGCTCCATCCACCGGTGC 62.101 66.667 29.75 15.98 42.15 5.01
2083 4419 3.402681 CTCCATCCACCGGTGCCT 61.403 66.667 29.75 15.09 0.00 4.75
2084 4420 3.391665 CTCCATCCACCGGTGCCTC 62.392 68.421 29.75 0.00 0.00 4.70
2085 4421 4.489771 CCATCCACCGGTGCCTCC 62.490 72.222 29.75 0.00 0.00 4.30
2086 4422 3.402681 CATCCACCGGTGCCTCCT 61.403 66.667 29.75 7.87 0.00 3.69
2087 4423 3.083997 ATCCACCGGTGCCTCCTC 61.084 66.667 29.75 0.00 0.00 3.71
2184 4520 4.101448 CCTTCCTGGGGGTCGCAG 62.101 72.222 5.19 5.19 42.81 5.18
2185 4521 4.785453 CTTCCTGGGGGTCGCAGC 62.785 72.222 6.47 0.00 42.02 5.25
2206 4542 4.241715 GAGCGCTCGATCCAGATG 57.758 61.111 23.61 0.00 0.00 2.90
2207 4543 2.021039 GAGCGCTCGATCCAGATGC 61.021 63.158 23.61 0.00 0.00 3.91
2209 4545 3.401411 CGCTCGATCCAGATGCGC 61.401 66.667 0.00 0.00 40.15 6.09
2210 4546 3.040763 GCTCGATCCAGATGCGCC 61.041 66.667 4.18 0.00 0.00 6.53
2211 4547 2.356793 CTCGATCCAGATGCGCCC 60.357 66.667 4.18 0.00 0.00 6.13
2212 4548 4.284860 TCGATCCAGATGCGCCCG 62.285 66.667 4.18 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 0.889994 GTGCATGCCCAATCTGTCAA 59.110 50.000 16.68 0.00 0.00 3.18
368 369 1.194781 AGCTCATCGACCCCAACACT 61.195 55.000 0.00 0.00 0.00 3.55
440 441 2.219875 ATGGATCCCAGCTAGCCCG 61.220 63.158 12.13 2.51 36.75 6.13
441 442 1.377994 CATGGATCCCAGCTAGCCC 59.622 63.158 12.13 4.68 36.75 5.19
443 444 0.036022 GGACATGGATCCCAGCTAGC 59.964 60.000 9.90 6.62 36.75 3.42
445 446 1.121407 CCGGACATGGATCCCAGCTA 61.121 60.000 9.90 0.00 36.75 3.32
446 447 2.446848 CCGGACATGGATCCCAGCT 61.447 63.158 9.90 0.00 36.75 4.24
448 449 2.831770 CCCGGACATGGATCCCAG 59.168 66.667 9.90 3.95 36.75 4.45
450 451 1.831652 CTAGCCCGGACATGGATCCC 61.832 65.000 9.90 0.00 35.03 3.85
451 452 1.674057 CTAGCCCGGACATGGATCC 59.326 63.158 0.73 4.20 35.16 3.36
452 453 1.004440 GCTAGCCCGGACATGGATC 60.004 63.158 0.73 0.00 0.00 3.36
455 456 2.109799 CAGCTAGCCCGGACATGG 59.890 66.667 12.13 0.00 0.00 3.66
457 458 2.972589 ATCCCAGCTAGCCCGGACAT 62.973 60.000 19.81 9.95 0.00 3.06
459 460 2.844839 ATCCCAGCTAGCCCGGAC 60.845 66.667 19.81 0.00 0.00 4.79
664 665 4.660771 CCCAGTCCATCTCCTATTTAAGGT 59.339 45.833 0.00 0.00 46.62 3.50
671 2865 3.051803 TCTCAACCCAGTCCATCTCCTAT 60.052 47.826 0.00 0.00 0.00 2.57
717 2911 0.543277 TGAGCCAGCCTGTAGAATGG 59.457 55.000 0.00 0.00 35.84 3.16
718 2912 1.474677 CCTGAGCCAGCCTGTAGAATG 60.475 57.143 0.00 0.00 0.00 2.67
719 2913 0.835941 CCTGAGCCAGCCTGTAGAAT 59.164 55.000 0.00 0.00 0.00 2.40
720 2914 1.903877 GCCTGAGCCAGCCTGTAGAA 61.904 60.000 0.00 0.00 0.00 2.10
731 2927 3.119709 CTCTCGTCGAGCCTGAGCC 62.120 68.421 17.61 0.00 41.25 4.70
732 2928 2.407210 CTCTCGTCGAGCCTGAGC 59.593 66.667 17.61 0.00 40.32 4.26
756 2952 6.281405 GTCTATCCAACGGACTTGATTGTAT 58.719 40.000 0.00 0.00 32.98 2.29
766 2962 1.136500 GACCTGGTCTATCCAACGGAC 59.864 57.143 19.53 0.00 46.59 4.79
772 2968 2.866923 TGATGGACCTGGTCTATCCA 57.133 50.000 35.69 25.54 45.66 3.41
814 3012 0.535797 GGTCGTCCGAGGAAAAGGAT 59.464 55.000 0.00 0.00 38.97 3.24
894 3100 3.119531 TGACCTTGCTTGAAGTTGTTGTG 60.120 43.478 0.00 0.00 0.00 3.33
1256 3537 2.202518 GTCACGCACATGCATGCC 60.203 61.111 26.53 16.21 42.99 4.40
1299 3580 6.884280 AATCAAACCAGACGAAAAAGAGAT 57.116 33.333 0.00 0.00 0.00 2.75
1306 3602 8.410141 ACAAAGAATTAATCAAACCAGACGAAA 58.590 29.630 0.00 0.00 0.00 3.46
1363 3664 9.802039 TCACGGAAGCCCTAAAATAATTATAAT 57.198 29.630 0.00 0.00 0.00 1.28
1364 3665 9.629878 TTCACGGAAGCCCTAAAATAATTATAA 57.370 29.630 0.00 0.00 0.00 0.98
1365 3666 9.629878 TTTCACGGAAGCCCTAAAATAATTATA 57.370 29.630 0.00 0.00 0.00 0.98
1366 3667 8.528044 TTTCACGGAAGCCCTAAAATAATTAT 57.472 30.769 0.00 0.00 0.00 1.28
1392 3696 0.255318 CAGCTTCTTGGGCTCCATCT 59.745 55.000 0.00 0.00 38.03 2.90
1624 3947 3.197766 TGTGGATTATCTCGCTTTGGTCT 59.802 43.478 0.00 0.00 0.00 3.85
1670 3995 5.479306 CCCTGATACAAATCTACATACCCG 58.521 45.833 0.00 0.00 32.93 5.28
1776 4110 9.507280 CAATGCATAGAAACATTTTACGAAGAT 57.493 29.630 0.00 0.00 34.32 2.40
1839 4175 8.610248 TGAGTAGAAACATTTTTACCATTCGA 57.390 30.769 2.37 0.00 30.49 3.71
1865 4201 3.825328 AGATATTCATTTCAAGCCGCCT 58.175 40.909 0.00 0.00 0.00 5.52
1917 4253 7.441836 GGGACCAAACTCTACAATTTGAATTT 58.558 34.615 2.79 0.00 37.91 1.82
1938 4274 3.297134 TCATTATTGAGCTTGGGGGAC 57.703 47.619 0.00 0.00 0.00 4.46
1939 4275 3.269381 AGTTCATTATTGAGCTTGGGGGA 59.731 43.478 0.00 0.00 40.12 4.81
1940 4276 3.633986 GAGTTCATTATTGAGCTTGGGGG 59.366 47.826 5.60 0.00 42.72 5.40
1941 4277 3.633986 GGAGTTCATTATTGAGCTTGGGG 59.366 47.826 5.60 0.00 42.72 4.96
1942 4278 4.272489 TGGAGTTCATTATTGAGCTTGGG 58.728 43.478 5.60 0.00 42.72 4.12
1943 4279 5.188434 TCTGGAGTTCATTATTGAGCTTGG 58.812 41.667 5.60 1.22 42.72 3.61
1944 4280 6.596888 TCTTCTGGAGTTCATTATTGAGCTTG 59.403 38.462 5.60 1.48 42.72 4.01
1945 4281 6.597280 GTCTTCTGGAGTTCATTATTGAGCTT 59.403 38.462 5.60 0.00 42.72 3.74
1946 4282 6.112058 GTCTTCTGGAGTTCATTATTGAGCT 58.888 40.000 3.93 3.93 45.01 4.09
1947 4283 5.295540 GGTCTTCTGGAGTTCATTATTGAGC 59.704 44.000 0.00 0.00 32.27 4.26
1948 4284 5.521735 CGGTCTTCTGGAGTTCATTATTGAG 59.478 44.000 0.00 0.00 32.27 3.02
1949 4285 5.046591 ACGGTCTTCTGGAGTTCATTATTGA 60.047 40.000 0.00 0.00 0.00 2.57
1950 4286 5.063944 CACGGTCTTCTGGAGTTCATTATTG 59.936 44.000 0.00 0.00 0.00 1.90
1951 4287 5.046591 TCACGGTCTTCTGGAGTTCATTATT 60.047 40.000 0.00 0.00 0.00 1.40
1952 4288 4.466370 TCACGGTCTTCTGGAGTTCATTAT 59.534 41.667 0.00 0.00 0.00 1.28
1953 4289 3.830178 TCACGGTCTTCTGGAGTTCATTA 59.170 43.478 0.00 0.00 0.00 1.90
1954 4290 2.632996 TCACGGTCTTCTGGAGTTCATT 59.367 45.455 0.00 0.00 0.00 2.57
1955 4291 2.028930 GTCACGGTCTTCTGGAGTTCAT 60.029 50.000 0.00 0.00 0.00 2.57
1956 4292 1.340248 GTCACGGTCTTCTGGAGTTCA 59.660 52.381 0.00 0.00 0.00 3.18
1957 4293 1.340248 TGTCACGGTCTTCTGGAGTTC 59.660 52.381 0.00 0.00 0.00 3.01
1958 4294 1.410004 TGTCACGGTCTTCTGGAGTT 58.590 50.000 0.00 0.00 0.00 3.01
1959 4295 1.341531 CTTGTCACGGTCTTCTGGAGT 59.658 52.381 0.00 0.00 0.00 3.85
1960 4296 1.937108 GCTTGTCACGGTCTTCTGGAG 60.937 57.143 0.00 0.00 0.00 3.86
1961 4297 0.033504 GCTTGTCACGGTCTTCTGGA 59.966 55.000 0.00 0.00 0.00 3.86
1962 4298 0.034059 AGCTTGTCACGGTCTTCTGG 59.966 55.000 0.00 0.00 0.00 3.86
1963 4299 1.423395 GAGCTTGTCACGGTCTTCTG 58.577 55.000 1.51 0.00 0.00 3.02
1964 4300 0.318762 GGAGCTTGTCACGGTCTTCT 59.681 55.000 8.25 0.00 0.00 2.85
1965 4301 0.318762 AGGAGCTTGTCACGGTCTTC 59.681 55.000 8.25 0.00 0.00 2.87
1966 4302 0.034059 CAGGAGCTTGTCACGGTCTT 59.966 55.000 8.25 0.00 0.00 3.01
1967 4303 1.668294 CAGGAGCTTGTCACGGTCT 59.332 57.895 8.25 0.00 0.00 3.85
1968 4304 2.029844 GCAGGAGCTTGTCACGGTC 61.030 63.158 0.05 0.05 37.91 4.79
1969 4305 2.031163 GCAGGAGCTTGTCACGGT 59.969 61.111 0.00 0.00 37.91 4.83
1979 4315 2.886124 GCGTACGGAAGCAGGAGC 60.886 66.667 18.39 0.00 42.56 4.70
1980 4316 2.571757 TGCGTACGGAAGCAGGAG 59.428 61.111 18.39 0.00 38.59 3.69
1984 4320 3.523087 TTGCCTGCGTACGGAAGCA 62.523 57.895 26.31 26.31 41.55 3.91
1985 4321 2.740826 TTGCCTGCGTACGGAAGC 60.741 61.111 21.72 21.72 0.00 3.86
1986 4322 1.666553 TGTTGCCTGCGTACGGAAG 60.667 57.895 18.39 9.47 0.00 3.46
1987 4323 1.957186 GTGTTGCCTGCGTACGGAA 60.957 57.895 18.39 0.00 0.00 4.30
1988 4324 2.356553 GTGTTGCCTGCGTACGGA 60.357 61.111 18.39 14.19 0.00 4.69
1989 4325 3.773630 CGTGTTGCCTGCGTACGG 61.774 66.667 18.39 1.04 0.00 4.02
1990 4326 3.773630 CCGTGTTGCCTGCGTACG 61.774 66.667 11.84 11.84 34.78 3.67
1991 4327 4.084888 GCCGTGTTGCCTGCGTAC 62.085 66.667 0.00 0.00 0.00 3.67
2010 4346 3.825833 CTAAGCTAGGCGACGCGGG 62.826 68.421 14.61 2.38 0.00 6.13
2011 4347 2.353607 CTAAGCTAGGCGACGCGG 60.354 66.667 14.61 7.69 0.00 6.46
2012 4348 2.353607 CCTAAGCTAGGCGACGCG 60.354 66.667 14.61 3.53 39.48 6.01
2020 4356 1.065928 CCCGTGTCGCCTAAGCTAG 59.934 63.158 0.00 0.00 36.60 3.42
2021 4357 3.072486 GCCCGTGTCGCCTAAGCTA 62.072 63.158 0.00 0.00 36.60 3.32
2022 4358 4.452733 GCCCGTGTCGCCTAAGCT 62.453 66.667 0.00 0.00 36.60 3.74
2055 4391 2.202987 GATGGAGCTGCTGGACGG 60.203 66.667 7.01 0.00 0.00 4.79
2056 4392 2.202987 GGATGGAGCTGCTGGACG 60.203 66.667 7.01 0.00 0.00 4.79
2057 4393 1.451028 GTGGATGGAGCTGCTGGAC 60.451 63.158 7.01 0.00 0.00 4.02
2058 4394 2.673200 GGTGGATGGAGCTGCTGGA 61.673 63.158 7.01 0.00 0.00 3.86
2059 4395 2.124403 GGTGGATGGAGCTGCTGG 60.124 66.667 7.01 0.00 0.00 4.85
2060 4396 2.513204 CGGTGGATGGAGCTGCTG 60.513 66.667 7.01 0.00 0.00 4.41
2061 4397 3.790437 CCGGTGGATGGAGCTGCT 61.790 66.667 6.82 0.00 0.00 4.24
2062 4398 4.101448 ACCGGTGGATGGAGCTGC 62.101 66.667 6.12 0.00 0.00 5.25
2063 4399 2.124983 CACCGGTGGATGGAGCTG 60.125 66.667 27.57 0.00 0.00 4.24
2064 4400 4.101448 GCACCGGTGGATGGAGCT 62.101 66.667 34.58 0.00 39.62 4.09
2066 4402 3.391665 GAGGCACCGGTGGATGGAG 62.392 68.421 34.58 9.21 0.00 3.86
2067 4403 3.399181 GAGGCACCGGTGGATGGA 61.399 66.667 34.58 0.00 0.00 3.41
2068 4404 4.489771 GGAGGCACCGGTGGATGG 62.490 72.222 34.58 10.83 0.00 3.51
2069 4405 3.391665 GAGGAGGCACCGGTGGATG 62.392 68.421 34.58 11.31 44.74 3.51
2070 4406 3.083997 GAGGAGGCACCGGTGGAT 61.084 66.667 34.58 9.01 44.74 3.41
2167 4503 4.101448 CTGCGACCCCCAGGAAGG 62.101 72.222 0.00 0.00 36.73 3.46
2168 4504 4.785453 GCTGCGACCCCCAGGAAG 62.785 72.222 0.00 0.00 36.73 3.46
2182 4518 4.218578 ATCGAGCGCTCCCAGCTG 62.219 66.667 30.66 16.02 46.13 4.24
2184 4520 4.959596 GGATCGAGCGCTCCCAGC 62.960 72.222 30.66 19.85 38.02 4.85
2185 4521 3.496875 CTGGATCGAGCGCTCCCAG 62.497 68.421 32.86 32.86 38.48 4.45
2186 4522 3.531207 CTGGATCGAGCGCTCCCA 61.531 66.667 30.66 27.98 29.93 4.37
2187 4523 2.569354 ATCTGGATCGAGCGCTCCC 61.569 63.158 30.66 25.12 29.93 4.30
2188 4524 1.372748 CATCTGGATCGAGCGCTCC 60.373 63.158 30.66 18.69 0.00 4.70
2189 4525 2.021039 GCATCTGGATCGAGCGCTC 61.021 63.158 27.64 27.64 0.00 5.03
2190 4526 2.028778 GCATCTGGATCGAGCGCT 59.971 61.111 11.27 11.27 0.00 5.92
2191 4527 3.401411 CGCATCTGGATCGAGCGC 61.401 66.667 0.00 0.00 41.95 5.92
2193 4529 3.040763 GGCGCATCTGGATCGAGC 61.041 66.667 10.83 0.00 0.00 5.03
2194 4530 2.356793 GGGCGCATCTGGATCGAG 60.357 66.667 10.83 0.00 0.00 4.04
2195 4531 4.284860 CGGGCGCATCTGGATCGA 62.285 66.667 10.83 0.00 0.00 3.59


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

AutoCloner maintained by Alex Coulton.