Multiple sequence alignment - TraesCS2B01G388800

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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 TraesCS2B01G388800 chr2B 100.000 4034 0 0 1 4034 551636327 551632294 0.000000e+00 7450
1 TraesCS2B01G388800 chr2B 77.490 1928 377 42 1070 2959 551637862 551639770 0.000000e+00 1103
2 TraesCS2B01G388800 chr2B 100.000 67 0 0 3 69 732347464 732347398 1.520000e-24 124
3 TraesCS2B01G388800 chr2B 98.551 69 1 0 3 71 67537490 67537558 5.480000e-24 122
4 TraesCS2B01G388800 chr2D 92.202 3655 158 52 71 3674 472469944 472466366 0.000000e+00 5053
5 TraesCS2B01G388800 chr2D 76.808 1936 385 47 1070 2959 472470497 472472414 0.000000e+00 1029
6 TraesCS2B01G388800 chr2D 86.667 270 14 7 3770 4034 472452390 472452138 3.070000e-71 279
7 TraesCS2B01G388800 chr2D 73.482 626 163 3 1955 2577 75754979 75755604 2.420000e-57 233
8 TraesCS2B01G388800 chr2A 92.694 2806 113 36 758 3516 613990076 613987316 0.000000e+00 3962
9 TraesCS2B01G388800 chr2A 76.489 1948 385 50 1065 2959 613991493 613993420 0.000000e+00 992
10 TraesCS2B01G388800 chr2A 87.406 532 39 17 3511 4034 613986580 613986069 1.620000e-163 586
11 TraesCS2B01G388800 chr2A 77.184 561 61 24 176 712 613990926 613990409 8.600000e-67 265
12 TraesCS2B01G388800 chr2A 73.046 627 164 5 1955 2577 75635004 75634379 2.440000e-52 217
13 TraesCS2B01G388800 chr5B 76.529 1913 376 54 1087 2952 586359925 586358039 0.000000e+00 977
14 TraesCS2B01G388800 chr5B 97.101 69 2 0 1 69 412691108 412691176 2.550000e-22 117
15 TraesCS2B01G388800 chr5A 77.669 1630 304 47 1358 2952 597687906 597686302 0.000000e+00 939
16 TraesCS2B01G388800 chr5A 85.625 160 14 7 2000 2156 18923063 18923216 4.170000e-35 159
17 TraesCS2B01G388800 chr5A 100.000 69 0 0 3 71 523834390 523834458 1.180000e-25 128
18 TraesCS2B01G388800 chr1D 76.444 1575 320 43 1081 2634 192569413 192570957 0.000000e+00 806
19 TraesCS2B01G388800 chr5D 81.003 1037 160 25 1847 2859 478594578 478595601 0.000000e+00 789
20 TraesCS2B01G388800 chr7A 75.947 1584 322 46 1091 2637 49991149 49989588 0.000000e+00 760
21 TraesCS2B01G388800 chr3D 92.035 113 9 0 2249 2361 13323682 13323570 4.170000e-35 159
22 TraesCS2B01G388800 chr3A 92.035 113 9 0 2249 2361 23775094 23775206 4.170000e-35 159
23 TraesCS2B01G388800 chr3A 100.000 68 0 0 3 70 20559416 20559483 4.230000e-25 126
24 TraesCS2B01G388800 chr7D 84.049 163 17 6 2000 2159 49820398 49820242 9.030000e-32 148
25 TraesCS2B01G388800 chr7B 100.000 69 0 0 1 69 638416456 638416388 1.180000e-25 128
26 TraesCS2B01G388800 chr6B 98.551 69 1 0 3 71 568475214 568475146 5.480000e-24 122
27 TraesCS2B01G388800 chr3B 98.551 69 1 0 3 71 133387974 133388042 5.480000e-24 122
28 TraesCS2B01G388800 chr3B 97.143 70 2 0 3 72 697132874 697132805 7.080000e-23 119


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 TraesCS2B01G388800 chr2B 551632294 551636327 4033 True 7450.000000 7450 100.000000 1 4034 1 chr2B.!!$R1 4033
1 TraesCS2B01G388800 chr2B 551637862 551639770 1908 False 1103.000000 1103 77.490000 1070 2959 1 chr2B.!!$F2 1889
2 TraesCS2B01G388800 chr2D 472466366 472469944 3578 True 5053.000000 5053 92.202000 71 3674 1 chr2D.!!$R2 3603
3 TraesCS2B01G388800 chr2D 472470497 472472414 1917 False 1029.000000 1029 76.808000 1070 2959 1 chr2D.!!$F2 1889
4 TraesCS2B01G388800 chr2D 75754979 75755604 625 False 233.000000 233 73.482000 1955 2577 1 chr2D.!!$F1 622
5 TraesCS2B01G388800 chr2A 613986069 613990926 4857 True 1604.333333 3962 85.761333 176 4034 3 chr2A.!!$R2 3858
6 TraesCS2B01G388800 chr2A 613991493 613993420 1927 False 992.000000 992 76.489000 1065 2959 1 chr2A.!!$F1 1894
7 TraesCS2B01G388800 chr2A 75634379 75635004 625 True 217.000000 217 73.046000 1955 2577 1 chr2A.!!$R1 622
8 TraesCS2B01G388800 chr5B 586358039 586359925 1886 True 977.000000 977 76.529000 1087 2952 1 chr5B.!!$R1 1865
9 TraesCS2B01G388800 chr5A 597686302 597687906 1604 True 939.000000 939 77.669000 1358 2952 1 chr5A.!!$R1 1594
10 TraesCS2B01G388800 chr1D 192569413 192570957 1544 False 806.000000 806 76.444000 1081 2634 1 chr1D.!!$F1 1553
11 TraesCS2B01G388800 chr5D 478594578 478595601 1023 False 789.000000 789 81.003000 1847 2859 1 chr5D.!!$F1 1012
12 TraesCS2B01G388800 chr7A 49989588 49991149 1561 True 760.000000 760 75.947000 1091 2637 1 chr7A.!!$R1 1546

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
686 720 0.254178 CCCACTGGAGCACTAGCATT 59.746 55.0 0.0 0.0 45.49 3.56 F
1290 1666 0.320374 TCGCCATCGTCTCCAACTTT 59.680 50.0 0.0 0.0 36.96 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2883 3304 1.001597 GTATAGCTGAGGAACGTCGGG 60.002 57.143 0.0 0.0 0.0 5.14 R
3469 3930 0.674581 CGCAGAAATCCAGTGAGCCA 60.675 55.000 0.0 0.0 0.0 4.75 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
44 45 8.839310 ACTAGTTTATTTCATATAGCCTGCTG 57.161 34.615 0.97 0.00 0.00 4.41
45 46 8.651389 ACTAGTTTATTTCATATAGCCTGCTGA 58.349 33.333 0.97 0.00 0.00 4.26
46 47 7.736447 AGTTTATTTCATATAGCCTGCTGAC 57.264 36.000 0.97 0.00 0.00 3.51
47 48 7.512992 AGTTTATTTCATATAGCCTGCTGACT 58.487 34.615 0.97 0.00 0.00 3.41
48 49 7.659390 AGTTTATTTCATATAGCCTGCTGACTC 59.341 37.037 0.97 0.00 0.00 3.36
49 50 5.557576 ATTTCATATAGCCTGCTGACTCA 57.442 39.130 0.97 0.00 0.00 3.41
50 51 5.557576 TTTCATATAGCCTGCTGACTCAT 57.442 39.130 0.97 0.00 0.00 2.90
51 52 4.797800 TCATATAGCCTGCTGACTCATC 57.202 45.455 0.97 0.00 0.00 2.92
52 53 4.414677 TCATATAGCCTGCTGACTCATCT 58.585 43.478 0.97 0.00 0.00 2.90
53 54 4.462132 TCATATAGCCTGCTGACTCATCTC 59.538 45.833 0.97 0.00 0.00 2.75
54 55 2.450867 TAGCCTGCTGACTCATCTCT 57.549 50.000 0.97 0.00 0.00 3.10
55 56 2.450867 AGCCTGCTGACTCATCTCTA 57.549 50.000 0.00 0.00 0.00 2.43
56 57 2.961510 AGCCTGCTGACTCATCTCTAT 58.038 47.619 0.00 0.00 0.00 1.98
57 58 3.307506 AGCCTGCTGACTCATCTCTATT 58.692 45.455 0.00 0.00 0.00 1.73
58 59 4.478203 AGCCTGCTGACTCATCTCTATTA 58.522 43.478 0.00 0.00 0.00 0.98
59 60 5.085920 AGCCTGCTGACTCATCTCTATTAT 58.914 41.667 0.00 0.00 0.00 1.28
60 61 6.252233 AGCCTGCTGACTCATCTCTATTATA 58.748 40.000 0.00 0.00 0.00 0.98
61 62 6.152661 AGCCTGCTGACTCATCTCTATTATAC 59.847 42.308 0.00 0.00 0.00 1.47
62 63 6.152661 GCCTGCTGACTCATCTCTATTATACT 59.847 42.308 0.00 0.00 0.00 2.12
63 64 7.309744 GCCTGCTGACTCATCTCTATTATACTT 60.310 40.741 0.00 0.00 0.00 2.24
64 65 8.028354 CCTGCTGACTCATCTCTATTATACTTG 58.972 40.741 0.00 0.00 0.00 3.16
65 66 7.374272 TGCTGACTCATCTCTATTATACTTGC 58.626 38.462 0.00 0.00 0.00 4.01
66 67 7.232330 TGCTGACTCATCTCTATTATACTTGCT 59.768 37.037 0.00 0.00 0.00 3.91
67 68 7.754924 GCTGACTCATCTCTATTATACTTGCTC 59.245 40.741 0.00 0.00 0.00 4.26
68 69 8.932434 TGACTCATCTCTATTATACTTGCTCT 57.068 34.615 0.00 0.00 0.00 4.09
69 70 9.360901 TGACTCATCTCTATTATACTTGCTCTT 57.639 33.333 0.00 0.00 0.00 2.85
162 168 1.147153 GCTCCTATCCTTTGCGGCT 59.853 57.895 0.00 0.00 0.00 5.52
174 180 4.117372 GCGGCTCGTTCGTTCGTG 62.117 66.667 0.00 2.00 0.00 4.35
200 206 3.390639 ACCTTCCATGTCTCATCTCATCC 59.609 47.826 0.00 0.00 0.00 3.51
204 210 2.224233 CCATGTCTCATCTCATCCGCTT 60.224 50.000 0.00 0.00 0.00 4.68
266 276 2.303549 GACCCATCCACTCGCCTCAG 62.304 65.000 0.00 0.00 0.00 3.35
324 334 7.332003 CAGATTTGTATCTATCTGCTTCGAC 57.668 40.000 0.00 0.00 40.74 4.20
362 372 5.118510 CGCCAATTCTTTTGAACATTGTACC 59.881 40.000 0.00 0.00 41.77 3.34
428 438 4.124238 CCTGACACGAGTGGTAAGAAAAA 58.876 43.478 8.19 0.00 34.19 1.94
456 466 0.534412 ATGTGCCGAGGAGAAGTCAG 59.466 55.000 0.00 0.00 0.00 3.51
497 509 0.319555 TTCGTCGCAGTTAGCAGCTT 60.320 50.000 0.00 0.00 46.13 3.74
498 510 0.319555 TCGTCGCAGTTAGCAGCTTT 60.320 50.000 0.00 0.00 46.13 3.51
502 514 1.000843 TCGCAGTTAGCAGCTTTCTCA 59.999 47.619 0.00 0.00 46.13 3.27
513 525 4.818546 AGCAGCTTTCTCAAATGCGTATAT 59.181 37.500 0.00 0.00 41.69 0.86
656 685 1.733399 TACAATGCACGCGTACGCA 60.733 52.632 36.44 23.98 45.53 5.24
658 687 4.147322 AATGCACGCGTACGCAGC 62.147 61.111 34.29 34.29 45.53 5.25
681 715 4.130255 GTCCCCACTGGAGCACTA 57.870 61.111 0.00 0.00 46.38 2.74
686 720 0.254178 CCCACTGGAGCACTAGCATT 59.746 55.000 0.00 0.00 45.49 3.56
712 746 3.573967 TGTCTCTGTACTGTGATCTTGCA 59.426 43.478 7.63 0.00 0.00 4.08
714 748 3.573967 TCTCTGTACTGTGATCTTGCACA 59.426 43.478 0.00 0.00 45.80 4.57
814 1146 2.689983 CAATCTTGATTACTGGCACCCC 59.310 50.000 0.00 0.00 0.00 4.95
878 1211 0.957888 TCGCACCATCGCCAAAATCA 60.958 50.000 0.00 0.00 0.00 2.57
997 1337 2.916502 AAGCAACGCACGGACACTCA 62.917 55.000 0.00 0.00 0.00 3.41
1027 1367 2.202810 GCCGCTTTCTCCTCCTCG 60.203 66.667 0.00 0.00 0.00 4.63
1028 1368 2.202810 CCGCTTTCTCCTCCTCGC 60.203 66.667 0.00 0.00 0.00 5.03
1029 1369 2.580867 CGCTTTCTCCTCCTCGCG 60.581 66.667 0.00 0.00 34.50 5.87
1050 1393 2.272797 CTCCTCGTCCTCCTCGGT 59.727 66.667 0.00 0.00 0.00 4.69
1053 1396 2.752238 CTCGTCCTCCTCGGTGCT 60.752 66.667 0.00 0.00 0.00 4.40
1054 1397 2.750637 TCGTCCTCCTCGGTGCTC 60.751 66.667 0.00 0.00 0.00 4.26
1062 1405 1.377725 CCTCGGTGCTCATGGCTTT 60.378 57.895 7.54 0.00 42.39 3.51
1115 1458 2.126228 CTACAACGGCTTCGCGGA 60.126 61.111 6.13 0.00 37.41 5.54
1290 1666 0.320374 TCGCCATCGTCTCCAACTTT 59.680 50.000 0.00 0.00 36.96 2.66
1389 1768 2.444624 CGGCATCCTCAACGTCACG 61.445 63.158 0.00 0.00 0.00 4.35
1539 1921 3.830192 GCCGGGTGGTACGACGAT 61.830 66.667 2.18 0.00 37.67 3.73
1989 2380 1.609501 CGAGGACTGGGAGGTGGAA 60.610 63.158 0.00 0.00 0.00 3.53
2901 3322 0.395311 TCCCGACGTTCCTCAGCTAT 60.395 55.000 0.00 0.00 0.00 2.97
3053 3478 6.263168 AGGTGAATAAACAAGGACAAGAAGTG 59.737 38.462 0.00 0.00 0.00 3.16
3056 3481 7.227910 GTGAATAAACAAGGACAAGAAGTGGTA 59.772 37.037 0.00 0.00 0.00 3.25
3059 3484 4.338379 ACAAGGACAAGAAGTGGTAGTC 57.662 45.455 0.00 0.00 0.00 2.59
3061 3486 1.272769 AGGACAAGAAGTGGTAGTCGC 59.727 52.381 0.00 0.00 0.00 5.19
3062 3487 1.672145 GGACAAGAAGTGGTAGTCGCC 60.672 57.143 0.00 0.00 0.00 5.54
3070 3504 4.849329 GGTAGTCGCCGCGTGAGG 62.849 72.222 13.39 0.00 0.00 3.86
3121 3560 4.082190 ACGTACTCATCTGCTGTAACATGT 60.082 41.667 0.00 0.00 0.00 3.21
3124 3579 4.437239 ACTCATCTGCTGTAACATGTAGC 58.563 43.478 11.44 11.44 37.93 3.58
3197 3652 4.997395 TGATGTTTTTCTAGTCTGCACTCC 59.003 41.667 0.00 0.00 33.62 3.85
3198 3653 3.390135 TGTTTTTCTAGTCTGCACTCCG 58.610 45.455 0.00 0.00 33.62 4.63
3199 3654 3.181469 TGTTTTTCTAGTCTGCACTCCGT 60.181 43.478 0.00 0.00 33.62 4.69
3200 3655 3.299340 TTTTCTAGTCTGCACTCCGTC 57.701 47.619 0.00 0.00 33.62 4.79
3201 3656 1.905637 TTCTAGTCTGCACTCCGTCA 58.094 50.000 0.00 0.00 33.62 4.35
3202 3657 2.130272 TCTAGTCTGCACTCCGTCAT 57.870 50.000 0.00 0.00 33.62 3.06
3203 3658 1.745653 TCTAGTCTGCACTCCGTCATG 59.254 52.381 0.00 0.00 33.62 3.07
3204 3659 1.474478 CTAGTCTGCACTCCGTCATGT 59.526 52.381 0.00 0.00 33.62 3.21
3205 3660 0.037882 AGTCTGCACTCCGTCATGTG 60.038 55.000 0.00 0.00 37.26 3.21
3226 3681 1.601419 AACATCAGTGCCATGCCTGC 61.601 55.000 0.00 0.00 30.75 4.85
3267 3722 5.476091 AACGAAAAATTAATCTTGGGCCA 57.524 34.783 0.00 0.00 0.00 5.36
3311 3766 8.338259 GGAGTGCACAATAACTATGTTATCTTG 58.662 37.037 21.04 3.71 0.00 3.02
3316 3771 7.520614 GCACAATAACTATGTTATCTTGGAGCC 60.521 40.741 3.81 0.00 0.00 4.70
3327 3782 2.920384 TGGAGCCACCACTGCGTA 60.920 61.111 0.00 0.00 44.64 4.42
3329 3784 2.434359 GAGCCACCACTGCGTACC 60.434 66.667 0.00 0.00 0.00 3.34
3420 3875 4.680237 CGAGTGGGCAAGCACGGA 62.680 66.667 0.00 0.00 0.00 4.69
3421 3876 3.050275 GAGTGGGCAAGCACGGAC 61.050 66.667 0.00 0.00 0.00 4.79
3422 3877 4.988598 AGTGGGCAAGCACGGACG 62.989 66.667 0.00 0.00 0.00 4.79
3489 3950 0.674895 GGCTCACTGGATTTCTGCGT 60.675 55.000 0.00 0.00 0.00 5.24
3507 3968 1.874739 CGTCCGCCTGTTGTTTTCCTA 60.875 52.381 0.00 0.00 0.00 2.94
3509 3970 2.161609 GTCCGCCTGTTGTTTTCCTATG 59.838 50.000 0.00 0.00 0.00 2.23
3536 4738 4.348081 GTTGCACATGCGACGATG 57.652 55.556 8.45 2.33 44.53 3.84
3556 4758 1.299850 GCGTGGTTTCAGTTTGGCC 60.300 57.895 0.00 0.00 0.00 5.36
3577 4782 1.613437 CCTTTGCCGGTTCTGTTCATT 59.387 47.619 1.90 0.00 0.00 2.57
3579 4784 3.492482 CCTTTGCCGGTTCTGTTCATTTT 60.492 43.478 1.90 0.00 0.00 1.82
3580 4785 2.791383 TGCCGGTTCTGTTCATTTTG 57.209 45.000 1.90 0.00 0.00 2.44
3601 4811 6.653526 TTGTTTTCACAATGGACATGAGAT 57.346 33.333 0.00 0.00 38.03 2.75
3652 4867 2.029200 TGTAACGTGTTGATCCGGCTTA 60.029 45.455 0.00 0.00 0.00 3.09
3663 4878 6.208599 TGTTGATCCGGCTTAAGAAAGATTTT 59.791 34.615 6.67 0.00 34.37 1.82
3675 4890 4.920376 AGAAAGATTTTGTGACGTGTTGG 58.080 39.130 0.00 0.00 0.00 3.77
3676 4891 3.708563 AAGATTTTGTGACGTGTTGGG 57.291 42.857 0.00 0.00 0.00 4.12
3678 4893 3.811083 AGATTTTGTGACGTGTTGGGTA 58.189 40.909 0.00 0.00 0.00 3.69
3680 4895 1.301423 TTTGTGACGTGTTGGGTAGC 58.699 50.000 0.00 0.00 0.00 3.58
3683 4898 1.301401 TGACGTGTTGGGTAGCAGC 60.301 57.895 0.00 0.00 0.00 5.25
3684 4899 1.301401 GACGTGTTGGGTAGCAGCA 60.301 57.895 0.00 0.00 0.00 4.41
3685 4900 1.291877 GACGTGTTGGGTAGCAGCAG 61.292 60.000 0.00 0.00 0.00 4.24
3686 4901 2.680913 CGTGTTGGGTAGCAGCAGC 61.681 63.158 0.00 0.00 42.56 5.25
3758 4977 2.943653 CACCGGTGGCGTCTTTTC 59.056 61.111 27.57 0.00 0.00 2.29
3767 4986 2.066262 TGGCGTCTTTTCTTAAGCTCG 58.934 47.619 0.00 0.00 0.00 5.03
3773 4992 4.322274 CGTCTTTTCTTAAGCTCGACTCTG 59.678 45.833 0.00 0.00 0.00 3.35
3795 5014 1.914051 CTACTGTTCAGTCGTCATGCG 59.086 52.381 8.80 3.55 43.01 4.73
3797 5016 1.284297 CTGTTCAGTCGTCATGCGCA 61.284 55.000 14.96 14.96 41.07 6.09
3805 5024 3.052082 GTCATGCGCACTGCCTGT 61.052 61.111 14.90 0.00 45.60 4.00
3809 5028 2.911484 ATGCGCACTGCCTGTTGTG 61.911 57.895 14.90 0.00 45.60 3.33
3820 5039 1.068333 GCCTGTTGTGTGCCATACAAG 60.068 52.381 7.30 0.00 41.89 3.16
3821 5040 2.229792 CCTGTTGTGTGCCATACAAGT 58.770 47.619 7.30 0.00 41.89 3.16
3822 5041 2.622942 CCTGTTGTGTGCCATACAAGTT 59.377 45.455 7.30 0.00 41.89 2.66
3823 5042 3.818210 CCTGTTGTGTGCCATACAAGTTA 59.182 43.478 7.30 0.00 41.89 2.24
3825 5044 4.200092 TGTTGTGTGCCATACAAGTTACA 58.800 39.130 7.30 0.12 41.89 2.41
3826 5045 4.640647 TGTTGTGTGCCATACAAGTTACAA 59.359 37.500 7.30 0.00 41.89 2.41
3827 5046 4.822036 TGTGTGCCATACAAGTTACAAC 57.178 40.909 0.00 0.00 41.89 3.32
3828 5047 3.566322 TGTGTGCCATACAAGTTACAACC 59.434 43.478 0.00 0.00 41.89 3.77
3830 5049 4.217550 GTGTGCCATACAAGTTACAACCAT 59.782 41.667 0.00 0.00 41.89 3.55
3831 5050 4.457603 TGTGCCATACAAGTTACAACCATC 59.542 41.667 0.00 0.00 36.06 3.51
3832 5051 3.687212 TGCCATACAAGTTACAACCATCG 59.313 43.478 0.00 0.00 0.00 3.84
3833 5052 3.687698 GCCATACAAGTTACAACCATCGT 59.312 43.478 0.00 0.00 0.00 3.73
3834 5053 4.871557 GCCATACAAGTTACAACCATCGTA 59.128 41.667 0.00 0.00 0.00 3.43
3835 5054 5.220529 GCCATACAAGTTACAACCATCGTAC 60.221 44.000 0.00 0.00 0.00 3.67
3836 5055 5.870433 CCATACAAGTTACAACCATCGTACA 59.130 40.000 0.00 0.00 0.00 2.90
3837 5056 6.537301 CCATACAAGTTACAACCATCGTACAT 59.463 38.462 0.00 0.00 0.00 2.29
3838 5057 5.856126 ACAAGTTACAACCATCGTACATG 57.144 39.130 0.00 0.00 0.00 3.21
3839 5058 4.153475 ACAAGTTACAACCATCGTACATGC 59.847 41.667 0.00 0.00 0.00 4.06
3851 5070 3.791245 TCGTACATGCTGATATGCACAA 58.209 40.909 0.00 0.00 46.33 3.33
3861 5080 6.876155 TGCTGATATGCACAACCAAAATATT 58.124 32.000 0.00 0.00 38.12 1.28
3862 5081 6.757478 TGCTGATATGCACAACCAAAATATTG 59.243 34.615 0.00 0.00 38.12 1.90
3863 5082 6.757947 GCTGATATGCACAACCAAAATATTGT 59.242 34.615 0.00 0.00 39.63 2.71
3937 5160 0.679960 ATTCAGCGGGCAAGGGTAAC 60.680 55.000 0.00 0.00 0.00 2.50
3947 5170 1.838396 AAGGGTAACGTGGTCGGGT 60.838 57.895 0.00 0.00 41.85 5.28
3948 5171 1.820010 AAGGGTAACGTGGTCGGGTC 61.820 60.000 0.00 0.00 41.85 4.46
3959 5182 0.462789 GGTCGGGTCGGTGTTCATAT 59.537 55.000 0.00 0.00 0.00 1.78
3961 5184 2.624636 GTCGGGTCGGTGTTCATATTT 58.375 47.619 0.00 0.00 0.00 1.40
3986 5209 7.707104 TCCATATCTATATACATGCACAGTCG 58.293 38.462 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 9.929180 CAGCAGGCTATATGAAATAAACTAGTA 57.071 33.333 0.00 0.00 29.06 1.82
19 20 8.651389 TCAGCAGGCTATATGAAATAAACTAGT 58.349 33.333 0.00 0.00 29.06 2.57
20 21 8.930760 GTCAGCAGGCTATATGAAATAAACTAG 58.069 37.037 0.00 0.00 29.06 2.57
21 22 8.651389 AGTCAGCAGGCTATATGAAATAAACTA 58.349 33.333 0.00 0.00 29.06 2.24
22 23 7.512992 AGTCAGCAGGCTATATGAAATAAACT 58.487 34.615 0.00 0.00 29.06 2.66
23 24 7.442364 TGAGTCAGCAGGCTATATGAAATAAAC 59.558 37.037 0.00 0.00 29.06 2.01
24 25 7.508687 TGAGTCAGCAGGCTATATGAAATAAA 58.491 34.615 0.00 0.00 29.06 1.40
25 26 7.066307 TGAGTCAGCAGGCTATATGAAATAA 57.934 36.000 0.00 0.00 29.06 1.40
26 27 6.670695 TGAGTCAGCAGGCTATATGAAATA 57.329 37.500 0.00 0.00 0.00 1.40
27 28 5.557576 TGAGTCAGCAGGCTATATGAAAT 57.442 39.130 0.00 0.00 0.00 2.17
28 29 5.306419 AGATGAGTCAGCAGGCTATATGAAA 59.694 40.000 11.60 0.00 0.00 2.69
29 30 4.837298 AGATGAGTCAGCAGGCTATATGAA 59.163 41.667 11.60 0.00 0.00 2.57
30 31 4.414677 AGATGAGTCAGCAGGCTATATGA 58.585 43.478 11.60 0.00 0.00 2.15
31 32 4.463539 AGAGATGAGTCAGCAGGCTATATG 59.536 45.833 11.60 0.00 0.00 1.78
32 33 4.676109 AGAGATGAGTCAGCAGGCTATAT 58.324 43.478 11.60 0.00 0.00 0.86
33 34 4.111255 AGAGATGAGTCAGCAGGCTATA 57.889 45.455 11.60 0.00 0.00 1.31
34 35 2.961510 AGAGATGAGTCAGCAGGCTAT 58.038 47.619 11.60 0.00 0.00 2.97
35 36 2.450867 AGAGATGAGTCAGCAGGCTA 57.549 50.000 11.60 0.00 0.00 3.93
36 37 2.450867 TAGAGATGAGTCAGCAGGCT 57.549 50.000 11.60 7.34 0.00 4.58
37 38 3.749665 AATAGAGATGAGTCAGCAGGC 57.250 47.619 11.60 0.00 0.00 4.85
38 39 7.701539 AGTATAATAGAGATGAGTCAGCAGG 57.298 40.000 11.60 0.00 0.00 4.85
39 40 7.541783 GCAAGTATAATAGAGATGAGTCAGCAG 59.458 40.741 11.60 0.00 0.00 4.24
40 41 7.232330 AGCAAGTATAATAGAGATGAGTCAGCA 59.768 37.037 11.60 0.00 0.00 4.41
41 42 7.601856 AGCAAGTATAATAGAGATGAGTCAGC 58.398 38.462 0.00 0.00 0.00 4.26
42 43 9.013229 AGAGCAAGTATAATAGAGATGAGTCAG 57.987 37.037 0.00 0.00 0.00 3.51
43 44 8.932434 AGAGCAAGTATAATAGAGATGAGTCA 57.068 34.615 0.00 0.00 0.00 3.41
52 53 9.233649 GCCTCTAGTAAGAGCAAGTATAATAGA 57.766 37.037 0.00 0.00 46.84 1.98
53 54 9.238368 AGCCTCTAGTAAGAGCAAGTATAATAG 57.762 37.037 0.00 0.00 46.84 1.73
54 55 9.015367 CAGCCTCTAGTAAGAGCAAGTATAATA 57.985 37.037 0.00 0.00 46.84 0.98
55 56 7.524698 GCAGCCTCTAGTAAGAGCAAGTATAAT 60.525 40.741 0.00 0.00 46.84 1.28
56 57 6.239064 GCAGCCTCTAGTAAGAGCAAGTATAA 60.239 42.308 0.00 0.00 46.84 0.98
57 58 5.241949 GCAGCCTCTAGTAAGAGCAAGTATA 59.758 44.000 0.00 0.00 46.84 1.47
58 59 4.038642 GCAGCCTCTAGTAAGAGCAAGTAT 59.961 45.833 0.00 0.00 46.84 2.12
59 60 3.381908 GCAGCCTCTAGTAAGAGCAAGTA 59.618 47.826 0.00 0.00 46.84 2.24
60 61 2.167487 GCAGCCTCTAGTAAGAGCAAGT 59.833 50.000 0.00 0.00 46.84 3.16
61 62 2.167281 TGCAGCCTCTAGTAAGAGCAAG 59.833 50.000 0.00 0.00 46.84 4.01
62 63 2.179427 TGCAGCCTCTAGTAAGAGCAA 58.821 47.619 0.00 0.00 46.84 3.91
63 64 1.852633 TGCAGCCTCTAGTAAGAGCA 58.147 50.000 0.00 0.00 46.84 4.26
64 65 2.753296 CATGCAGCCTCTAGTAAGAGC 58.247 52.381 0.00 0.00 46.84 4.09
65 66 3.799574 CTGCATGCAGCCTCTAGTAAGAG 60.800 52.174 33.18 7.09 44.83 2.85
66 67 2.102084 CTGCATGCAGCCTCTAGTAAGA 59.898 50.000 33.18 0.00 44.83 2.10
67 68 2.481854 CTGCATGCAGCCTCTAGTAAG 58.518 52.381 33.18 7.76 44.83 2.34
68 69 2.609427 CTGCATGCAGCCTCTAGTAA 57.391 50.000 33.18 0.00 44.83 2.24
162 168 4.324424 GTTCCCACGAACGAACGA 57.676 55.556 11.97 0.00 39.14 3.85
185 191 2.288091 CGAAGCGGATGAGATGAGACAT 60.288 50.000 0.00 0.00 0.00 3.06
266 276 1.602605 CCTCAACCACCGGGGAAAC 60.603 63.158 4.41 0.00 41.15 2.78
324 334 5.395642 AGAATTGGCGTGGTATTAAAAACG 58.604 37.500 0.00 0.00 39.00 3.60
362 372 2.094675 AGACCCGGAAATTGCAAGATG 58.905 47.619 0.73 0.00 0.00 2.90
456 466 2.032681 AGTTGGTGCGCCCTTCTC 59.967 61.111 15.15 0.00 0.00 2.87
497 509 6.761242 AGCAACACTATATACGCATTTGAGAA 59.239 34.615 0.00 0.00 0.00 2.87
498 510 6.280643 AGCAACACTATATACGCATTTGAGA 58.719 36.000 0.00 0.00 0.00 3.27
502 514 5.466728 CAGGAGCAACACTATATACGCATTT 59.533 40.000 0.00 0.00 0.00 2.32
513 525 0.602638 CCGCAACAGGAGCAACACTA 60.603 55.000 0.00 0.00 0.00 2.74
542 559 1.668151 GAGTGAGTGGTTGGGCGTC 60.668 63.158 0.00 0.00 0.00 5.19
543 560 2.426023 GAGTGAGTGGTTGGGCGT 59.574 61.111 0.00 0.00 0.00 5.68
544 561 2.358737 GGAGTGAGTGGTTGGGCG 60.359 66.667 0.00 0.00 0.00 6.13
545 562 1.302832 CAGGAGTGAGTGGTTGGGC 60.303 63.158 0.00 0.00 0.00 5.36
546 563 0.035458 GACAGGAGTGAGTGGTTGGG 59.965 60.000 0.00 0.00 0.00 4.12
547 564 0.758734 TGACAGGAGTGAGTGGTTGG 59.241 55.000 0.00 0.00 0.00 3.77
681 715 4.512944 CACAGTACAGAGACAAACAATGCT 59.487 41.667 0.00 0.00 0.00 3.79
686 720 5.791336 AGATCACAGTACAGAGACAAACA 57.209 39.130 0.00 0.00 0.00 2.83
712 746 3.194542 GTGGAGAGTACAATCAGAGCTGT 59.805 47.826 0.00 0.00 0.00 4.40
714 748 2.763448 GGTGGAGAGTACAATCAGAGCT 59.237 50.000 0.00 0.00 0.00 4.09
718 760 2.417379 CGTGGGTGGAGAGTACAATCAG 60.417 54.545 0.00 0.00 0.00 2.90
814 1146 3.272439 TCGTTCAAAATCTGCTGCTTG 57.728 42.857 0.00 0.00 0.00 4.01
878 1211 0.802222 CGTGTGAACGATGCGATCCT 60.802 55.000 0.00 0.00 34.64 3.24
904 1237 7.256286 GTTTGTAGTGTAGAGTGTATAGTGGG 58.744 42.308 0.00 0.00 0.00 4.61
909 1242 5.415389 TGCGGTTTGTAGTGTAGAGTGTATA 59.585 40.000 0.00 0.00 0.00 1.47
1027 1367 2.557372 GGAGGACGAGGAGGATCGC 61.557 68.421 0.00 0.00 46.60 4.58
1029 1369 0.887387 CGAGGAGGACGAGGAGGATC 60.887 65.000 0.00 0.00 0.00 3.36
1240 1616 2.651361 CGAGAAGGACTGCACGGT 59.349 61.111 0.00 0.00 0.00 4.83
1290 1666 1.372499 GTTGTCGCTCAGCACGGTA 60.372 57.895 0.00 0.00 0.00 4.02
1485 1864 2.743928 CGCAGGCTGTTGAGGTCC 60.744 66.667 17.16 0.00 0.00 4.46
2883 3304 1.001597 GTATAGCTGAGGAACGTCGGG 60.002 57.143 0.00 0.00 0.00 5.14
3021 3442 2.570415 TGTTTATTCACCTTCCGCCA 57.430 45.000 0.00 0.00 0.00 5.69
3053 3478 4.849329 CCTCACGCGGCGACTACC 62.849 72.222 30.94 0.00 0.00 3.18
3070 3504 6.789403 CGATAGATGAGAAATCAAATCAACGC 59.211 38.462 0.00 0.00 39.76 4.84
3076 3510 6.980978 ACGTCACGATAGATGAGAAATCAAAT 59.019 34.615 2.91 0.00 41.38 2.32
3121 3560 3.094572 ACTACTAGGAAAAGTGCCGCTA 58.905 45.455 0.00 0.00 0.00 4.26
3124 3579 2.232941 TCCACTACTAGGAAAAGTGCCG 59.767 50.000 9.88 1.41 39.42 5.69
3197 3652 2.413239 GGCACTGATGTTTCACATGACG 60.413 50.000 0.00 0.00 39.27 4.35
3198 3653 2.553602 TGGCACTGATGTTTCACATGAC 59.446 45.455 0.00 0.00 39.27 3.06
3199 3654 2.861274 TGGCACTGATGTTTCACATGA 58.139 42.857 0.00 0.00 39.27 3.07
3200 3655 3.507786 CATGGCACTGATGTTTCACATG 58.492 45.455 0.00 0.00 39.27 3.21
3201 3656 2.094390 GCATGGCACTGATGTTTCACAT 60.094 45.455 0.00 0.00 42.43 3.21
3202 3657 1.270274 GCATGGCACTGATGTTTCACA 59.730 47.619 0.00 0.00 0.00 3.58
3203 3658 1.403249 GGCATGGCACTGATGTTTCAC 60.403 52.381 15.47 0.00 0.00 3.18
3204 3659 0.889994 GGCATGGCACTGATGTTTCA 59.110 50.000 15.47 0.00 0.00 2.69
3205 3660 1.135199 CAGGCATGGCACTGATGTTTC 60.135 52.381 22.64 0.00 36.86 2.78
3238 3693 7.254590 CCCAAGATTAATTTTTCGTTTGCAACA 60.255 33.333 0.00 0.00 0.00 3.33
3243 3698 5.698545 TGGCCCAAGATTAATTTTTCGTTTG 59.301 36.000 0.00 0.00 0.00 2.93
3249 3704 4.568072 GGGTGGCCCAAGATTAATTTTT 57.432 40.909 0.00 0.00 44.65 1.94
3311 3766 2.434359 GTACGCAGTGGTGGCTCC 60.434 66.667 0.00 0.00 45.73 4.70
3358 3813 3.257561 CAAGCCGAGACGCCATCG 61.258 66.667 0.00 0.00 42.43 3.84
3385 3840 2.395690 CTTTCGTCATGTCGCGCC 59.604 61.111 0.00 0.00 0.00 6.53
3394 3849 2.357034 GCCCACTCGCTTTCGTCA 60.357 61.111 0.00 0.00 36.96 4.35
3422 3877 4.864334 CACGGCCATCCTCTGCCC 62.864 72.222 2.24 0.00 45.07 5.36
3423 3878 3.785859 TCACGGCCATCCTCTGCC 61.786 66.667 2.24 0.00 44.41 4.85
3424 3879 2.512515 GTCACGGCCATCCTCTGC 60.513 66.667 2.24 0.00 0.00 4.26
3469 3930 0.674581 CGCAGAAATCCAGTGAGCCA 60.675 55.000 0.00 0.00 0.00 4.75
3489 3950 2.224670 ACATAGGAAAACAACAGGCGGA 60.225 45.455 0.00 0.00 0.00 5.54
3507 3968 2.831685 TGTGCAACGGACTCTTACAT 57.168 45.000 0.00 0.00 42.39 2.29
3509 3970 1.128692 GCATGTGCAACGGACTCTTAC 59.871 52.381 0.00 0.00 42.39 2.34
3534 4736 0.673437 CAAACTGAAACCACGCCCAT 59.327 50.000 0.00 0.00 0.00 4.00
3536 4738 1.362355 CCAAACTGAAACCACGCCC 59.638 57.895 0.00 0.00 0.00 6.13
3556 4758 0.821711 TGAACAGAACCGGCAAAGGG 60.822 55.000 0.00 0.00 35.02 3.95
3577 4782 6.462552 TCTCATGTCCATTGTGAAAACAAA 57.537 33.333 0.00 0.00 32.94 2.83
3579 4784 6.127925 GCTATCTCATGTCCATTGTGAAAACA 60.128 38.462 0.00 0.00 0.00 2.83
3580 4785 6.261118 GCTATCTCATGTCCATTGTGAAAAC 58.739 40.000 0.00 0.00 0.00 2.43
3601 4811 2.817834 GCGTCGGCAACATGGCTA 60.818 61.111 0.00 0.00 41.25 3.93
3652 4867 5.339990 CCAACACGTCACAAAATCTTTCTT 58.660 37.500 0.00 0.00 0.00 2.52
3663 4878 0.249699 CTGCTACCCAACACGTCACA 60.250 55.000 0.00 0.00 0.00 3.58
3683 4898 9.388506 CCCCATAGAACAAGATTATATAAGCTG 57.611 37.037 13.75 10.33 31.47 4.24
3684 4899 9.117223 ACCCCATAGAACAAGATTATATAAGCT 57.883 33.333 7.44 7.44 32.57 3.74
3685 4900 9.167311 CACCCCATAGAACAAGATTATATAAGC 57.833 37.037 2.40 2.40 0.00 3.09
3689 4904 7.831193 GCATCACCCCATAGAACAAGATTATAT 59.169 37.037 0.00 0.00 0.00 0.86
3690 4905 7.168219 GCATCACCCCATAGAACAAGATTATA 58.832 38.462 0.00 0.00 0.00 0.98
3691 4906 6.006449 GCATCACCCCATAGAACAAGATTAT 58.994 40.000 0.00 0.00 0.00 1.28
3692 4907 5.376625 GCATCACCCCATAGAACAAGATTA 58.623 41.667 0.00 0.00 0.00 1.75
3693 4908 4.210331 GCATCACCCCATAGAACAAGATT 58.790 43.478 0.00 0.00 0.00 2.40
3694 4909 3.745480 CGCATCACCCCATAGAACAAGAT 60.745 47.826 0.00 0.00 0.00 2.40
3695 4910 2.419990 CGCATCACCCCATAGAACAAGA 60.420 50.000 0.00 0.00 0.00 3.02
3696 4911 1.942657 CGCATCACCCCATAGAACAAG 59.057 52.381 0.00 0.00 0.00 3.16
3697 4912 1.557371 TCGCATCACCCCATAGAACAA 59.443 47.619 0.00 0.00 0.00 2.83
3698 4913 1.199615 TCGCATCACCCCATAGAACA 58.800 50.000 0.00 0.00 0.00 3.18
3699 4914 2.325583 TTCGCATCACCCCATAGAAC 57.674 50.000 0.00 0.00 0.00 3.01
3745 4964 2.152016 AGCTTAAGAAAAGACGCCACC 58.848 47.619 6.67 0.00 0.00 4.61
3758 4977 4.393680 ACAGTAGACAGAGTCGAGCTTAAG 59.606 45.833 0.00 0.00 37.67 1.85
3767 4986 3.499157 ACGACTGAACAGTAGACAGAGTC 59.501 47.826 18.63 0.00 42.66 3.36
3773 4992 2.917971 GCATGACGACTGAACAGTAGAC 59.082 50.000 18.63 13.86 42.66 2.59
3797 5016 2.275089 TGGCACACAACAGGCAGT 59.725 55.556 0.00 0.00 35.21 4.40
3809 5028 4.436852 CGATGGTTGTAACTTGTATGGCAC 60.437 45.833 0.00 0.00 0.00 5.01
3820 5039 3.930229 TCAGCATGTACGATGGTTGTAAC 59.070 43.478 7.10 0.00 37.40 2.50
3821 5040 4.195225 TCAGCATGTACGATGGTTGTAA 57.805 40.909 7.10 0.00 37.40 2.41
3822 5041 3.878160 TCAGCATGTACGATGGTTGTA 57.122 42.857 7.10 0.00 37.40 2.41
3823 5042 2.760634 TCAGCATGTACGATGGTTGT 57.239 45.000 7.10 0.00 37.40 3.32
3825 5044 3.748048 GCATATCAGCATGTACGATGGTT 59.252 43.478 7.10 0.00 37.40 3.67
3826 5045 3.244181 TGCATATCAGCATGTACGATGGT 60.244 43.478 0.00 4.75 40.11 3.55
3827 5046 3.328505 TGCATATCAGCATGTACGATGG 58.671 45.455 0.00 0.00 40.11 3.51
3837 5056 4.804868 ATTTTGGTTGTGCATATCAGCA 57.195 36.364 0.00 0.00 43.35 4.41
3838 5057 6.757947 ACAATATTTTGGTTGTGCATATCAGC 59.242 34.615 0.00 0.00 37.19 4.26
3839 5058 8.122306 CACAATATTTTGGTTGTGCATATCAG 57.878 34.615 5.44 0.00 45.75 2.90
3851 5070 4.522789 GGTCAGTGTCCACAATATTTTGGT 59.477 41.667 18.05 0.00 37.15 3.67
3937 5160 4.289245 AACACCGACCCGACCACG 62.289 66.667 0.00 0.00 39.43 4.94
3959 5182 9.875691 GACTGTGCATGTATATAGATATGGAAA 57.124 33.333 6.28 0.00 0.00 3.13
3961 5184 7.682021 GCGACTGTGCATGTATATAGATATGGA 60.682 40.741 6.28 0.64 34.15 3.41
3974 5197 1.257750 TAGGGAGCGACTGTGCATGT 61.258 55.000 0.00 0.00 37.31 3.21
3986 5209 3.181465 TGCTTGTGCTAGTTATAGGGAGC 60.181 47.826 0.00 0.00 40.48 4.70


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

AutoCloner maintained by Alex Coulton.