Multiple sequence alignment - TraesCS2D01G587100

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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 TraesCS2D01G587100 chr2D 100.000 4815 0 0 1 4815 645013324 645008510 0.000000e+00 8892.0
1 TraesCS2D01G587100 chr2D 85.398 767 68 27 4064 4802 591977832 591978582 0.000000e+00 756.0
2 TraesCS2D01G587100 chr2D 84.123 781 81 22 4067 4815 426918574 426917805 0.000000e+00 715.0
3 TraesCS2D01G587100 chr2D 95.122 82 2 1 2543 2622 24916184 24916265 1.410000e-25 128.0
4 TraesCS2D01G587100 chr2B 94.505 2111 96 12 1582 3687 790584654 790586749 0.000000e+00 3238.0
5 TraesCS2D01G587100 chr2B 91.121 687 32 11 181 847 790583268 790583945 0.000000e+00 904.0
6 TraesCS2D01G587100 chr2B 84.319 778 82 25 4067 4815 741379723 741380489 0.000000e+00 725.0
7 TraesCS2D01G587100 chr2B 82.918 802 66 36 4062 4810 1911477 1910694 0.000000e+00 656.0
8 TraesCS2D01G587100 chr2B 90.670 418 15 8 951 1350 790584007 790584418 7.090000e-148 534.0
9 TraesCS2D01G587100 chr2B 91.713 181 11 4 1376 1555 790584476 790584653 1.030000e-61 248.0
10 TraesCS2D01G587100 chr2B 89.222 167 14 3 3713 3876 790586746 790586911 6.320000e-49 206.0
11 TraesCS2D01G587100 chr2B 85.641 195 16 2 1 186 790582458 790582649 1.370000e-45 195.0
12 TraesCS2D01G587100 chr2B 88.722 133 9 3 3875 4007 790587787 790587913 1.790000e-34 158.0
13 TraesCS2D01G587100 chr3B 95.253 1896 76 8 1634 3520 48888465 48886575 0.000000e+00 2990.0
14 TraesCS2D01G587100 chr3B 92.355 484 36 1 3002 3484 48803254 48802771 0.000000e+00 688.0
15 TraesCS2D01G587100 chr3B 92.952 454 28 3 3517 3968 48886473 48886022 0.000000e+00 658.0
16 TraesCS2D01G587100 chr3B 90.968 465 21 8 402 853 48889421 48888965 1.480000e-169 606.0
17 TraesCS2D01G587100 chr3B 91.127 417 19 6 951 1364 48888909 48888508 2.530000e-152 549.0
18 TraesCS2D01G587100 chr3B 88.396 293 21 4 1 281 48889726 48889435 1.660000e-89 340.0
19 TraesCS2D01G587100 chr2A 91.944 1651 89 22 1379 3000 770360821 770359186 0.000000e+00 2272.0
20 TraesCS2D01G587100 chr2A 93.420 1079 55 11 3006 4073 770359079 770358006 0.000000e+00 1585.0
21 TraesCS2D01G587100 chr2A 88.802 1277 57 34 158 1364 770362134 770360874 0.000000e+00 1487.0
22 TraesCS2D01G587100 chr5D 85.987 785 66 25 4067 4815 498435959 498436735 0.000000e+00 800.0
23 TraesCS2D01G587100 chr5D 85.313 783 69 27 4067 4815 513910726 513909956 0.000000e+00 767.0
24 TraesCS2D01G587100 chr5D 86.789 545 32 18 4067 4575 242648496 242647956 5.410000e-159 571.0
25 TraesCS2D01G587100 chr5D 84.068 590 63 15 4066 4633 12067460 12068040 1.520000e-149 540.0
26 TraesCS2D01G587100 chr7D 85.917 774 70 23 4068 4815 1605162 1604402 0.000000e+00 789.0
27 TraesCS2D01G587100 chr7D 83.333 798 72 37 4067 4815 14555700 14554915 0.000000e+00 680.0
28 TraesCS2D01G587100 chr7D 84.637 703 57 22 4066 4743 164759068 164758392 0.000000e+00 652.0
29 TraesCS2D01G587100 chr7D 83.932 529 42 17 4065 4567 579636347 579635836 2.620000e-127 466.0
30 TraesCS2D01G587100 chr4B 84.685 777 81 21 4068 4815 30744975 30745742 0.000000e+00 741.0
31 TraesCS2D01G587100 chr3D 84.556 777 77 26 4068 4815 36363289 36364051 0.000000e+00 730.0
32 TraesCS2D01G587100 chr3D 94.839 155 7 1 4066 4220 547460539 547460692 1.730000e-59 241.0
33 TraesCS2D01G587100 chr3D 82.069 145 21 4 1490 1632 590329749 590329890 8.470000e-23 119.0
34 TraesCS2D01G587100 chr3A 84.264 788 73 30 4066 4815 165341063 165340289 0.000000e+00 721.0
35 TraesCS2D01G587100 chr1D 83.313 809 68 32 4067 4815 359477536 359478337 0.000000e+00 684.0
36 TraesCS2D01G587100 chr6D 84.834 633 48 18 4058 4651 28284101 28284724 1.150000e-165 593.0
37 TraesCS2D01G587100 chr1B 82.979 94 14 2 3566 3658 28764935 28764843 3.090000e-12 84.2
38 TraesCS2D01G587100 chr1B 95.122 41 2 0 1456 1496 34203009 34202969 1.120000e-06 65.8
39 TraesCS2D01G587100 chr1B 97.368 38 0 1 3565 3602 492307399 492307435 4.020000e-06 63.9


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 TraesCS2D01G587100 chr2D 645008510 645013324 4814 True 8892.000000 8892 100.000000 1 4815 1 chr2D.!!$R2 4814
1 TraesCS2D01G587100 chr2D 591977832 591978582 750 False 756.000000 756 85.398000 4064 4802 1 chr2D.!!$F2 738
2 TraesCS2D01G587100 chr2D 426917805 426918574 769 True 715.000000 715 84.123000 4067 4815 1 chr2D.!!$R1 748
3 TraesCS2D01G587100 chr2B 790582458 790587913 5455 False 783.285714 3238 90.227714 1 4007 7 chr2B.!!$F2 4006
4 TraesCS2D01G587100 chr2B 741379723 741380489 766 False 725.000000 725 84.319000 4067 4815 1 chr2B.!!$F1 748
5 TraesCS2D01G587100 chr2B 1910694 1911477 783 True 656.000000 656 82.918000 4062 4810 1 chr2B.!!$R1 748
6 TraesCS2D01G587100 chr3B 48886022 48889726 3704 True 1028.600000 2990 91.739200 1 3968 5 chr3B.!!$R2 3967
7 TraesCS2D01G587100 chr2A 770358006 770362134 4128 True 1781.333333 2272 91.388667 158 4073 3 chr2A.!!$R1 3915
8 TraesCS2D01G587100 chr5D 498435959 498436735 776 False 800.000000 800 85.987000 4067 4815 1 chr5D.!!$F2 748
9 TraesCS2D01G587100 chr5D 513909956 513910726 770 True 767.000000 767 85.313000 4067 4815 1 chr5D.!!$R2 748
10 TraesCS2D01G587100 chr5D 242647956 242648496 540 True 571.000000 571 86.789000 4067 4575 1 chr5D.!!$R1 508
11 TraesCS2D01G587100 chr5D 12067460 12068040 580 False 540.000000 540 84.068000 4066 4633 1 chr5D.!!$F1 567
12 TraesCS2D01G587100 chr7D 1604402 1605162 760 True 789.000000 789 85.917000 4068 4815 1 chr7D.!!$R1 747
13 TraesCS2D01G587100 chr7D 14554915 14555700 785 True 680.000000 680 83.333000 4067 4815 1 chr7D.!!$R2 748
14 TraesCS2D01G587100 chr7D 164758392 164759068 676 True 652.000000 652 84.637000 4066 4743 1 chr7D.!!$R3 677
15 TraesCS2D01G587100 chr7D 579635836 579636347 511 True 466.000000 466 83.932000 4065 4567 1 chr7D.!!$R4 502
16 TraesCS2D01G587100 chr4B 30744975 30745742 767 False 741.000000 741 84.685000 4068 4815 1 chr4B.!!$F1 747
17 TraesCS2D01G587100 chr3D 36363289 36364051 762 False 730.000000 730 84.556000 4068 4815 1 chr3D.!!$F1 747
18 TraesCS2D01G587100 chr3A 165340289 165341063 774 True 721.000000 721 84.264000 4066 4815 1 chr3A.!!$R1 749
19 TraesCS2D01G587100 chr1D 359477536 359478337 801 False 684.000000 684 83.313000 4067 4815 1 chr1D.!!$F1 748
20 TraesCS2D01G587100 chr6D 28284101 28284724 623 False 593.000000 593 84.834000 4058 4651 1 chr6D.!!$F1 593

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
138 139 0.533308 GTGCAACCCGTGGTTACAGA 60.533 55.0 8.47 0.0 45.01 3.41 F
1266 2003 0.318120 ACCATCTTTTTGCCTTGCCG 59.682 50.0 0.00 0.0 0.00 5.69 F
1364 2101 0.555769 GGTGGCAGGGGATTATTGGA 59.444 55.0 0.00 0.0 0.00 3.53 F
2503 3311 0.823356 TTGGTCCTGGCAGTGCTTTC 60.823 55.0 16.11 0.0 0.00 2.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1365 2102 0.827368 GCAGAGAACCTACTCCCTGG 59.173 60.000 0.0 0.0 37.6 4.45 R
2973 3783 1.399440 CTTGGAGTGCATGAACATCGG 59.601 52.381 6.6 0.0 0.0 4.18 R
3313 4229 0.250727 ACCCTGATGACAACCAACCG 60.251 55.000 0.0 0.0 0.0 4.44 R
4020 5927 0.033601 ACCAGGACAGCAACCAAACA 60.034 50.000 0.0 0.0 0.0 2.83 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
35 36 4.788521 GCTCGGATTTTCGAACAACAAGTT 60.789 41.667 0.00 0.00 44.93 2.66
67 68 2.844946 TGATCCTTGTGAGCGAAAACA 58.155 42.857 0.00 0.00 29.76 2.83
74 75 3.840890 TGTGAGCGAAAACAACAAACT 57.159 38.095 0.00 0.00 0.00 2.66
97 98 2.034104 TCCGTCGTGTATCTAGCACT 57.966 50.000 0.00 0.00 34.91 4.40
108 109 5.812642 GTGTATCTAGCACTTGCAACACTAT 59.187 40.000 3.62 0.00 45.16 2.12
137 138 0.534203 AGTGCAACCCGTGGTTACAG 60.534 55.000 8.47 0.00 45.01 2.74
138 139 0.533308 GTGCAACCCGTGGTTACAGA 60.533 55.000 8.47 0.00 45.01 3.41
144 145 2.868839 AACCCGTGGTTACAGAATGTCG 60.869 50.000 6.53 0.00 42.10 4.35
188 822 1.132640 GCGTGCGCCTCTTTTACAG 59.867 57.895 4.18 0.00 34.56 2.74
200 834 6.710744 CGCCTCTTTTACAGGGATACAATAAT 59.289 38.462 0.00 0.00 39.74 1.28
365 1010 8.461222 TGGACAGCATAAAAATACAAAGAGATG 58.539 33.333 0.00 0.00 0.00 2.90
428 1079 5.927115 GGGACTGATCGGTGACTAAATAATC 59.073 44.000 13.13 0.00 0.00 1.75
477 1128 1.404391 GCAATCAGCATTCACTCCCTG 59.596 52.381 0.00 0.00 44.79 4.45
639 1327 1.276145 GCGTCGATCCGATACAAGGC 61.276 60.000 0.00 0.00 38.42 4.35
656 1344 2.585247 CGGTTAGCTAGGCGCCAC 60.585 66.667 31.54 16.91 40.39 5.01
672 1368 1.800805 CCACTGTCGATTTGCTCTGT 58.199 50.000 0.00 0.00 0.00 3.41
782 1478 1.305465 TAGGCGTGGCTAGGAACCA 60.305 57.895 0.00 0.00 33.84 3.67
813 1509 1.340114 GGGTCAAAAGGGGCTACTCTG 60.340 57.143 0.00 0.00 0.00 3.35
814 1510 1.454201 GTCAAAAGGGGCTACTCTGC 58.546 55.000 0.00 0.00 0.00 4.26
815 1511 1.003696 GTCAAAAGGGGCTACTCTGCT 59.996 52.381 0.00 0.00 0.00 4.24
816 1512 1.279271 TCAAAAGGGGCTACTCTGCTC 59.721 52.381 0.00 0.00 0.00 4.26
817 1513 1.280421 CAAAAGGGGCTACTCTGCTCT 59.720 52.381 0.00 0.00 33.17 4.09
899 1596 7.829211 CAGGGAAAGAAACTATCTACCATGAAA 59.171 37.037 0.00 0.00 43.15 2.69
981 1678 1.646189 GAGGTCTGATTCGTGGCTTC 58.354 55.000 0.00 0.00 0.00 3.86
982 1679 0.976641 AGGTCTGATTCGTGGCTTCA 59.023 50.000 0.00 0.00 0.00 3.02
983 1680 1.556911 AGGTCTGATTCGTGGCTTCAT 59.443 47.619 0.00 0.00 0.00 2.57
984 1681 1.936547 GGTCTGATTCGTGGCTTCATC 59.063 52.381 0.00 0.00 0.00 2.92
986 1683 3.265791 GTCTGATTCGTGGCTTCATCTT 58.734 45.455 0.00 0.00 0.00 2.40
987 1684 3.063180 GTCTGATTCGTGGCTTCATCTTG 59.937 47.826 0.00 0.00 0.00 3.02
988 1685 2.353889 CTGATTCGTGGCTTCATCTTGG 59.646 50.000 0.00 0.00 0.00 3.61
989 1686 2.290260 TGATTCGTGGCTTCATCTTGGT 60.290 45.455 0.00 0.00 0.00 3.67
990 1687 3.055458 TGATTCGTGGCTTCATCTTGGTA 60.055 43.478 0.00 0.00 0.00 3.25
1026 1723 4.872485 GAGGACTCGACGAGCGCG 62.872 72.222 24.38 8.75 44.79 6.86
1119 1834 1.269988 CCGTGGCATGATCTCGAGATT 60.270 52.381 27.90 11.53 34.37 2.40
1163 1896 6.405176 CCTTTTCTCCATTACTGAATGCCTTC 60.405 42.308 0.00 0.00 41.09 3.46
1166 1899 6.499106 TCTCCATTACTGAATGCCTTCATA 57.501 37.500 4.81 0.00 40.52 2.15
1266 2003 0.318120 ACCATCTTTTTGCCTTGCCG 59.682 50.000 0.00 0.00 0.00 5.69
1304 2041 9.653287 TCGTCAGTTAAGATATTTGATGTTCTT 57.347 29.630 0.00 0.00 33.29 2.52
1312 2049 6.250819 AGATATTTGATGTTCTTTTGTCGCG 58.749 36.000 0.00 0.00 0.00 5.87
1332 2069 4.390909 CGCGAAGTAAATTAGGAAGTTGGT 59.609 41.667 0.00 0.00 0.00 3.67
1357 2094 2.765969 CAAGTGGTGGCAGGGGAT 59.234 61.111 0.00 0.00 0.00 3.85
1364 2101 0.555769 GGTGGCAGGGGATTATTGGA 59.444 55.000 0.00 0.00 0.00 3.53
1365 2102 1.692411 GTGGCAGGGGATTATTGGAC 58.308 55.000 0.00 0.00 0.00 4.02
1366 2103 0.555769 TGGCAGGGGATTATTGGACC 59.444 55.000 0.00 0.00 0.00 4.46
1367 2104 0.555769 GGCAGGGGATTATTGGACCA 59.444 55.000 0.00 0.00 0.00 4.02
1368 2105 1.479389 GGCAGGGGATTATTGGACCAG 60.479 57.143 0.00 0.00 0.00 4.00
1369 2106 1.479389 GCAGGGGATTATTGGACCAGG 60.479 57.143 0.00 0.00 0.00 4.45
1370 2107 1.145738 CAGGGGATTATTGGACCAGGG 59.854 57.143 0.00 0.00 0.00 4.45
1372 2109 1.425448 GGGGATTATTGGACCAGGGAG 59.575 57.143 0.00 0.00 0.00 4.30
1373 2110 2.136026 GGGATTATTGGACCAGGGAGT 58.864 52.381 0.00 0.00 0.00 3.85
1375 2112 3.328050 GGGATTATTGGACCAGGGAGTAG 59.672 52.174 0.00 0.00 0.00 2.57
1377 2114 3.502051 TTATTGGACCAGGGAGTAGGT 57.498 47.619 0.00 0.00 41.83 3.08
1429 2204 5.561145 GCACAATTTTGATGCTTCATTGCAA 60.561 36.000 0.00 0.00 46.61 4.08
1491 2266 6.271566 TCAGTGAGATCTCGATGAAATTCAG 58.728 40.000 21.22 2.86 0.00 3.02
1494 2269 6.038985 GTGAGATCTCGATGAAATTCAGTGA 58.961 40.000 17.76 1.06 0.00 3.41
1759 2541 7.420800 GGCTATGTCTGAATCAAAATAACTGG 58.579 38.462 0.00 0.00 0.00 4.00
1944 2734 4.726583 AGCATGATACATGGAATTCAGCT 58.273 39.130 7.93 0.00 0.00 4.24
2199 3004 7.453752 TGTGATTTTAGACCTGTAGTTACCTCT 59.546 37.037 0.00 0.00 0.00 3.69
2426 3234 4.732285 AATTGCTTCTCAGTAACACACG 57.268 40.909 0.00 0.00 0.00 4.49
2427 3235 2.882927 TGCTTCTCAGTAACACACGT 57.117 45.000 0.00 0.00 0.00 4.49
2428 3236 3.994204 TGCTTCTCAGTAACACACGTA 57.006 42.857 0.00 0.00 0.00 3.57
2447 3255 6.984474 ACACGTATATATTGAGTGGTCTTTGG 59.016 38.462 14.92 0.00 37.16 3.28
2449 3257 8.139350 CACGTATATATTGAGTGGTCTTTGGTA 58.861 37.037 0.00 0.00 0.00 3.25
2473 3281 4.274421 TCTGTTAACGATGCTAGACTCG 57.726 45.455 11.47 11.47 40.62 4.18
2503 3311 0.823356 TTGGTCCTGGCAGTGCTTTC 60.823 55.000 16.11 0.00 0.00 2.62
2504 3312 1.073897 GGTCCTGGCAGTGCTTTCT 59.926 57.895 16.11 0.00 0.00 2.52
2515 3323 4.142730 GGCAGTGCTTTCTAACTCATGAAG 60.143 45.833 16.11 0.00 0.00 3.02
2622 3430 4.003648 GGACTGATTAAGGTGTGTTCTGG 58.996 47.826 0.00 0.00 0.00 3.86
2775 3585 7.452880 TGTGCTTGCTAAATTGATTTAGTCT 57.547 32.000 19.29 0.00 46.78 3.24
2826 3636 8.947940 GCTATTTTTCGTCAAAGCATAATGTAG 58.052 33.333 0.00 0.00 0.00 2.74
2830 3640 8.722342 TTTTCGTCAAAGCATAATGTAGTTTC 57.278 30.769 0.00 0.00 0.00 2.78
2894 3704 8.712228 TGTACTCATCAGTTGTATATCCTCAT 57.288 34.615 0.00 0.00 33.62 2.90
3147 4062 1.867363 ACAGAGGGGGTAGTGATCAC 58.133 55.000 18.47 18.47 0.00 3.06
3154 4069 2.615493 GGGGGTAGTGATCACTGTGTTG 60.615 54.545 33.76 0.00 42.52 3.33
3261 4177 4.943705 GGTATTCCTTGTTCATTCTCTGCA 59.056 41.667 0.00 0.00 0.00 4.41
3313 4229 3.421844 ACCTTGTTTTACTGAGGATGGC 58.578 45.455 0.00 0.00 33.47 4.40
3332 4248 0.250727 CGGTTGGTTGTCATCAGGGT 60.251 55.000 0.00 0.00 0.00 4.34
3674 4695 8.705134 CAATGTAAGTACAGTTTCGTGTTGATA 58.295 33.333 0.00 0.00 39.92 2.15
3724 4745 9.685276 TTAGTTTCATAAGTGATGATGGTGAAT 57.315 29.630 0.00 0.00 44.23 2.57
3729 4750 6.539826 TCATAAGTGATGATGGTGAATGTGTC 59.460 38.462 0.00 0.00 39.78 3.67
3741 4762 4.973663 GGTGAATGTGTCTTTTGGTTTACG 59.026 41.667 0.00 0.00 0.00 3.18
3756 4777 3.964347 GGTTTACGTTGACGCTTCTTTTC 59.036 43.478 3.05 0.00 44.43 2.29
3784 4809 2.584064 CGCAGGGACCTGTATGCA 59.416 61.111 18.86 0.00 45.24 3.96
3828 4853 1.808411 CAGTAGCATGTCGGTGGTTT 58.192 50.000 0.00 0.00 0.00 3.27
3869 4897 8.603304 TCTATTAATAATAAGTGGGGAAGAGCC 58.397 37.037 0.00 0.00 0.00 4.70
4011 5918 8.718158 TGTGCCCAATTCATATATCCATTTTA 57.282 30.769 0.00 0.00 0.00 1.52
4012 5919 8.805175 TGTGCCCAATTCATATATCCATTTTAG 58.195 33.333 0.00 0.00 0.00 1.85
4038 5945 0.670162 CTGTTTGGTTGCTGTCCTGG 59.330 55.000 0.00 0.00 0.00 4.45
4039 5946 0.033601 TGTTTGGTTGCTGTCCTGGT 60.034 50.000 0.00 0.00 0.00 4.00
4052 5959 0.469331 TCCTGGTCAACTCGACTGGT 60.469 55.000 0.00 0.00 44.70 4.00
4124 6032 2.672996 CAACTCCCCAGGTTGCGG 60.673 66.667 0.00 0.00 37.76 5.69
4232 6163 5.305585 TCTCTCAAACCGCTTTCACTATTT 58.694 37.500 0.00 0.00 0.00 1.40
4289 6221 5.125417 CCCATGTTGATAGGTTTTGACGAAT 59.875 40.000 0.00 0.00 0.00 3.34
4388 6378 2.548057 GTGCCTCTCACGAAATCACAAA 59.452 45.455 0.00 0.00 35.76 2.83
4395 6385 0.041663 ACGAAATCACAAACGTGCCG 60.042 50.000 0.00 0.00 37.58 5.69
4396 6386 1.327292 CGAAATCACAAACGTGCCGC 61.327 55.000 0.00 0.00 34.20 6.53
4397 6387 0.040425 GAAATCACAAACGTGCCGCT 60.040 50.000 0.00 0.00 34.20 5.52
4521 6528 2.496341 CATGCCTCTCGCGGAAGA 59.504 61.111 6.13 0.90 42.08 2.87
4728 7013 1.191647 CGGAAAGAAAACCGTGACTCG 59.808 52.381 0.00 0.00 43.53 4.18
4731 7016 2.589798 AAGAAAACCGTGACTCGTGA 57.410 45.000 0.00 0.00 37.94 4.35
4734 7020 2.606272 AGAAAACCGTGACTCGTGAAAC 59.394 45.455 0.00 0.00 37.94 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.449525 TTCGAAAATCCGAGCCGCG 61.450 57.895 0.00 0.00 39.90 6.46
17 18 4.502645 CCACCAACTTGTTGTTCGAAAATC 59.497 41.667 0.00 0.00 36.63 2.17
67 68 2.078392 ACACGACGGAAACAGTTTGTT 58.922 42.857 2.34 0.00 43.41 2.83
74 75 2.488937 TGCTAGATACACGACGGAAACA 59.511 45.455 0.00 0.00 0.00 2.83
137 138 1.372582 TCAATCTGGCTGCGACATTC 58.627 50.000 0.00 0.00 0.00 2.67
138 139 2.048444 ATCAATCTGGCTGCGACATT 57.952 45.000 0.00 0.00 0.00 2.71
144 145 6.161381 CCCATTAATTTATCAATCTGGCTGC 58.839 40.000 0.00 0.00 0.00 5.25
188 822 8.293699 AGAAAAGGAACACATTATTGTATCCC 57.706 34.615 13.89 6.04 39.88 3.85
200 834 7.340743 TCAAGGAACATAAAGAAAAGGAACACA 59.659 33.333 0.00 0.00 0.00 3.72
248 888 2.361567 GCAAAAGATGGCCAGGGGG 61.362 63.158 13.05 0.00 37.18 5.40
336 979 8.177119 TCTTTGTATTTTTATGCTGTCCAACT 57.823 30.769 0.00 0.00 0.00 3.16
338 981 8.402798 TCTCTTTGTATTTTTATGCTGTCCAA 57.597 30.769 0.00 0.00 0.00 3.53
339 982 7.994425 TCTCTTTGTATTTTTATGCTGTCCA 57.006 32.000 0.00 0.00 0.00 4.02
340 983 8.677300 TCATCTCTTTGTATTTTTATGCTGTCC 58.323 33.333 0.00 0.00 0.00 4.02
342 985 9.236006 ACTCATCTCTTTGTATTTTTATGCTGT 57.764 29.630 0.00 0.00 0.00 4.40
345 988 9.638300 CGTACTCATCTCTTTGTATTTTTATGC 57.362 33.333 0.00 0.00 0.00 3.14
365 1010 4.670227 AACGAGTAACCACTACGTACTC 57.330 45.455 2.89 2.89 37.47 2.59
370 1015 2.421424 AGCCTAACGAGTAACCACTACG 59.579 50.000 0.00 0.00 34.21 3.51
414 1065 4.058817 CCCTGCTCGATTATTTAGTCACC 58.941 47.826 0.00 0.00 0.00 4.02
477 1128 1.873572 CGCAGGCGCTTAAAATGGC 60.874 57.895 7.64 0.00 35.30 4.40
496 1151 0.458889 CTCTGCTCTGCTCACTCTGC 60.459 60.000 0.00 0.00 0.00 4.26
554 1229 0.386858 CCTCTTGAAACGACGAGCGA 60.387 55.000 0.00 0.00 44.57 4.93
656 1344 3.062763 ACAAGACAGAGCAAATCGACAG 58.937 45.455 0.00 0.00 0.00 3.51
672 1368 1.447140 CGGCGAAATCGGGACAAGA 60.447 57.895 0.00 0.00 40.23 3.02
813 1509 4.086178 CGTGCACAGCAGCAGAGC 62.086 66.667 18.64 0.00 46.69 4.09
814 1510 3.420606 CCGTGCACAGCAGCAGAG 61.421 66.667 18.64 0.00 46.69 3.35
815 1511 4.994471 CCCGTGCACAGCAGCAGA 62.994 66.667 18.64 0.00 46.69 4.26
899 1596 1.201414 GTTGGTTTCATCCGGCGAAAT 59.799 47.619 18.23 0.00 35.01 2.17
981 1678 0.543277 TCCTGCTGCCTACCAAGATG 59.457 55.000 0.00 0.00 0.00 2.90
982 1679 1.142465 CATCCTGCTGCCTACCAAGAT 59.858 52.381 0.00 0.00 0.00 2.40
983 1680 0.543277 CATCCTGCTGCCTACCAAGA 59.457 55.000 0.00 0.00 0.00 3.02
984 1681 0.543277 TCATCCTGCTGCCTACCAAG 59.457 55.000 0.00 0.00 0.00 3.61
986 1683 1.976132 GCTCATCCTGCTGCCTACCA 61.976 60.000 0.00 0.00 0.00 3.25
987 1684 1.227793 GCTCATCCTGCTGCCTACC 60.228 63.158 0.00 0.00 0.00 3.18
988 1685 1.227793 GGCTCATCCTGCTGCCTAC 60.228 63.158 0.00 0.00 41.92 3.18
989 1686 1.273986 TTGGCTCATCCTGCTGCCTA 61.274 55.000 0.00 0.00 45.11 3.93
990 1687 2.553765 CTTGGCTCATCCTGCTGCCT 62.554 60.000 0.00 0.00 45.11 4.75
1006 1703 1.226156 CGCTCGTCGAGTCCTCTTG 60.226 63.158 22.61 0.00 41.67 3.02
1041 1756 1.153745 CCTCTCGTTGAGCTTCGGG 60.154 63.158 0.00 0.00 41.35 5.14
1119 1834 2.039624 GGCTCCTCCTCCTCACCA 59.960 66.667 0.00 0.00 0.00 4.17
1266 2003 2.086054 ACTGACGAAGATGTTCAGCC 57.914 50.000 3.24 0.00 32.36 4.85
1304 2041 5.697633 ACTTCCTAATTTACTTCGCGACAAA 59.302 36.000 9.15 10.31 0.00 2.83
1312 2049 8.297426 CCAAGAACCAACTTCCTAATTTACTTC 58.703 37.037 0.00 0.00 0.00 3.01
1332 2069 1.832167 GCCACCACTTGCCCAAGAA 60.832 57.895 14.46 0.00 40.79 2.52
1357 2094 3.502051 ACCTACTCCCTGGTCCAATAA 57.498 47.619 0.00 0.00 29.18 1.40
1364 2101 1.897647 GCAGAGAACCTACTCCCTGGT 60.898 57.143 0.00 0.00 37.60 4.00
1365 2102 0.827368 GCAGAGAACCTACTCCCTGG 59.173 60.000 0.00 0.00 37.60 4.45
1366 2103 1.480137 CTGCAGAGAACCTACTCCCTG 59.520 57.143 8.42 0.00 37.60 4.45
1367 2104 1.621072 CCTGCAGAGAACCTACTCCCT 60.621 57.143 17.39 0.00 37.60 4.20
1368 2105 0.827368 CCTGCAGAGAACCTACTCCC 59.173 60.000 17.39 0.00 37.60 4.30
1369 2106 1.853963 TCCTGCAGAGAACCTACTCC 58.146 55.000 17.39 0.00 37.60 3.85
1370 2107 2.482839 GCATCCTGCAGAGAACCTACTC 60.483 54.545 17.39 0.00 44.26 2.59
1372 2109 1.946745 GCATCCTGCAGAGAACCTAC 58.053 55.000 17.39 0.00 44.26 3.18
1429 2204 5.269991 TGTTGCCTACTTCCTAGTACAGAT 58.730 41.667 0.00 0.00 35.78 2.90
1557 2333 9.619316 CCGTAACATTCACTTGAATTATTTGAA 57.381 29.630 1.52 0.00 42.41 2.69
1559 2335 7.009174 GGCCGTAACATTCACTTGAATTATTTG 59.991 37.037 1.52 0.00 42.41 2.32
1561 2337 6.405397 GGGCCGTAACATTCACTTGAATTATT 60.405 38.462 1.52 3.28 42.41 1.40
1759 2541 6.489675 ACAATTGCAATACTGATCGAACATC 58.510 36.000 13.39 0.00 0.00 3.06
1801 2583 5.982890 AACGGATGAGGAAAACATTGAAT 57.017 34.783 0.00 0.00 0.00 2.57
1944 2734 6.594788 AGTATAAAACAGTGAGAACCGGTA 57.405 37.500 8.00 0.00 0.00 4.02
2343 3151 7.015226 TGTTGCACAACTATATATCAACTGC 57.985 36.000 14.16 4.83 41.67 4.40
2447 3255 7.096966 CGAGTCTAGCATCGTTAACAGAAATAC 60.097 40.741 6.39 0.00 34.30 1.89
2449 3257 5.744345 CGAGTCTAGCATCGTTAACAGAAAT 59.256 40.000 6.39 0.00 34.30 2.17
2473 3281 4.076394 TGCCAGGACCAACTTTACATAAC 58.924 43.478 0.00 0.00 0.00 1.89
2716 3526 3.872511 TTATGCTGGTGGATGCTTTTG 57.127 42.857 0.00 0.00 0.00 2.44
2894 3704 5.188163 TGTCCTCGGAATGAAACCATAGTTA 59.812 40.000 0.00 0.00 34.19 2.24
2973 3783 1.399440 CTTGGAGTGCATGAACATCGG 59.601 52.381 6.60 0.00 0.00 4.18
3081 3995 7.595819 ATTTGTCTCAAGTCAAACCCATAAA 57.404 32.000 4.88 0.00 36.30 1.40
3147 4062 5.698089 TGTGAGAGATAAAAGAGCAACACAG 59.302 40.000 0.00 0.00 32.27 3.66
3154 4069 4.119136 GCTCCTGTGAGAGATAAAAGAGC 58.881 47.826 0.00 0.00 41.42 4.09
3261 4177 2.104967 TCGTTCATCTCCCATTACCGT 58.895 47.619 0.00 0.00 0.00 4.83
3313 4229 0.250727 ACCCTGATGACAACCAACCG 60.251 55.000 0.00 0.00 0.00 4.44
3332 4248 6.417258 TGCTATGATCTTGTCATCCTTTTCA 58.583 36.000 0.00 0.00 44.23 2.69
3543 4564 2.093869 AGTTACGGCTAAGGATGCGAAA 60.094 45.455 0.00 0.00 0.00 3.46
3717 4738 5.449314 CGTAAACCAAAAGACACATTCACCA 60.449 40.000 0.00 0.00 0.00 4.17
3724 4745 4.435784 CGTCAACGTAAACCAAAAGACACA 60.436 41.667 0.00 0.00 34.11 3.72
3729 4750 3.328237 AGCGTCAACGTAAACCAAAAG 57.672 42.857 4.29 0.00 42.22 2.27
3784 4809 6.038714 GCCTTAAGCTCTGCAAAATATACTGT 59.961 38.462 0.00 0.00 38.99 3.55
3854 4882 0.040646 TCTCGGCTCTTCCCCACTTA 59.959 55.000 0.00 0.00 0.00 2.24
3984 5889 6.594788 ATGGATATATGAATTGGGCACAAC 57.405 37.500 1.86 0.00 39.87 3.32
4011 5918 1.355720 AGCAACCAAACAGGCCTATCT 59.644 47.619 3.98 0.00 43.14 1.98
4012 5919 1.474077 CAGCAACCAAACAGGCCTATC 59.526 52.381 3.98 0.00 43.14 2.08
4015 5922 1.076044 ACAGCAACCAAACAGGCCT 60.076 52.632 0.00 0.00 43.14 5.19
4016 5923 1.363807 GACAGCAACCAAACAGGCC 59.636 57.895 0.00 0.00 43.14 5.19
4017 5924 1.109323 AGGACAGCAACCAAACAGGC 61.109 55.000 0.00 0.00 43.14 4.85
4018 5925 0.670162 CAGGACAGCAACCAAACAGG 59.330 55.000 0.00 0.00 45.67 4.00
4019 5926 0.670162 CCAGGACAGCAACCAAACAG 59.330 55.000 0.00 0.00 0.00 3.16
4020 5927 0.033601 ACCAGGACAGCAACCAAACA 60.034 50.000 0.00 0.00 0.00 2.83
4039 5946 1.816863 GCCTGGACCAGTCGAGTTGA 61.817 60.000 20.24 0.00 34.20 3.18
4232 6163 1.751351 AGATCTCAACGCGAGGAATCA 59.249 47.619 15.93 0.00 42.55 2.57
4395 6385 1.592336 GTTTTACTTGCGCGAGAAGC 58.408 50.000 31.19 13.76 43.95 3.86
4396 6386 1.461888 CGGTTTTACTTGCGCGAGAAG 60.462 52.381 31.19 17.59 0.00 2.85
4397 6387 0.509499 CGGTTTTACTTGCGCGAGAA 59.491 50.000 31.19 17.00 0.00 2.87
4405 6395 1.796459 CGAGGGTCACGGTTTTACTTG 59.204 52.381 0.00 0.00 0.00 3.16
4521 6528 2.420722 TCTTTTGCGAGTCACGGTTTTT 59.579 40.909 0.00 0.00 42.83 1.94
4565 6578 2.225491 CCGTGCCTCTCGAAAATGAAAA 59.775 45.455 0.00 0.00 0.00 2.29
4713 6998 4.817289 CGTTTCACGAGTCACGGTTTTCT 61.817 47.826 0.00 0.00 46.05 2.52


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

AutoCloner maintained by Alex Coulton.