Multiple sequence alignment - TraesCS2B01G316100

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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 TraesCS2B01G316100 chr2B 100.000 4675 0 0 1 4675 451453085 451457759 0.000000e+00 8634.0
1 TraesCS2B01G316100 chr2B 77.098 882 187 13 2506 3378 4752725 4751850 3.250000e-136 496.0
2 TraesCS2B01G316100 chr2D 94.041 4195 152 37 1 4170 380077172 380081293 0.000000e+00 6272.0
3 TraesCS2B01G316100 chr2D 80.008 2391 424 40 1082 3442 380088838 380091204 0.000000e+00 1718.0
4 TraesCS2B01G316100 chr2D 88.147 599 41 6 4027 4619 380092152 380092726 0.000000e+00 686.0
5 TraesCS2B01G316100 chr2D 76.810 884 186 16 2506 3378 8347359 8346484 3.270000e-131 479.0
6 TraesCS2B01G316100 chr2D 82.734 278 18 15 3676 3948 380091436 380091688 2.190000e-53 220.0
7 TraesCS2B01G316100 chr2A 96.371 2811 86 10 941 3748 515302338 515305135 0.000000e+00 4612.0
8 TraesCS2B01G316100 chr2A 79.958 2390 423 39 1082 3440 515308902 515311266 0.000000e+00 1709.0
9 TraesCS2B01G316100 chr2A 80.857 1494 248 27 1946 3411 16347289 16345806 0.000000e+00 1140.0
10 TraesCS2B01G316100 chr2A 80.040 1498 259 27 1946 3411 2819090 2817601 0.000000e+00 1074.0
11 TraesCS2B01G316100 chr2A 89.118 680 39 13 4016 4666 515312180 515312853 0.000000e+00 813.0
12 TraesCS2B01G316100 chr2A 90.476 336 23 6 106 440 515301343 515301670 7.180000e-118 435.0
13 TraesCS2B01G316100 chr2A 92.357 314 10 4 581 889 515302023 515302327 7.180000e-118 435.0
14 TraesCS2B01G316100 chr2A 84.848 165 12 9 438 596 141506316 141506473 2.250000e-33 154.0
15 TraesCS2B01G316100 chr2A 85.401 137 14 5 460 592 330080207 330080073 2.270000e-28 137.0
16 TraesCS2B01G316100 chr1D 75.441 908 192 27 2494 3382 107196310 107195415 3.370000e-111 412.0
17 TraesCS2B01G316100 chr1D 85.526 152 13 8 446 592 277352504 277352357 2.910000e-32 150.0
18 TraesCS2B01G316100 chr4A 74.834 902 204 21 2493 3378 738515574 738516468 2.040000e-103 387.0
19 TraesCS2B01G316100 chr4A 83.660 153 13 7 446 592 636663067 636663213 2.930000e-27 134.0
20 TraesCS2B01G316100 chr4A 80.583 103 10 9 1063 1161 738514074 738514170 2.330000e-08 71.3
21 TraesCS2B01G316100 chr3A 84.177 158 17 6 439 592 401026584 401026737 3.770000e-31 147.0
22 TraesCS2B01G316100 chr5D 84.314 153 15 7 445 592 175300052 175299904 1.750000e-29 141.0
23 TraesCS2B01G316100 chr3D 84.211 152 16 6 445 592 85449373 85449520 1.750000e-29 141.0
24 TraesCS2B01G316100 chr3B 83.117 154 15 8 445 592 135687309 135687457 3.800000e-26 130.0
25 TraesCS2B01G316100 chr3B 77.305 141 19 9 1094 1223 805337604 805337742 2.330000e-08 71.3
26 TraesCS2B01G316100 chr7D 95.455 44 2 0 1118 1161 491790826 491790783 2.330000e-08 71.3
27 TraesCS2B01G316100 chr7A 95.455 44 2 0 1118 1161 558082423 558082380 2.330000e-08 71.3


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 TraesCS2B01G316100 chr2B 451453085 451457759 4674 False 8634.000000 8634 100.000000 1 4675 1 chr2B.!!$F1 4674
1 TraesCS2B01G316100 chr2B 4751850 4752725 875 True 496.000000 496 77.098000 2506 3378 1 chr2B.!!$R1 872
2 TraesCS2B01G316100 chr2D 380077172 380081293 4121 False 6272.000000 6272 94.041000 1 4170 1 chr2D.!!$F1 4169
3 TraesCS2B01G316100 chr2D 380088838 380092726 3888 False 874.666667 1718 83.629667 1082 4619 3 chr2D.!!$F2 3537
4 TraesCS2B01G316100 chr2D 8346484 8347359 875 True 479.000000 479 76.810000 2506 3378 1 chr2D.!!$R1 872
5 TraesCS2B01G316100 chr2A 515301343 515312853 11510 False 1600.800000 4612 89.656000 106 4666 5 chr2A.!!$F2 4560
6 TraesCS2B01G316100 chr2A 16345806 16347289 1483 True 1140.000000 1140 80.857000 1946 3411 1 chr2A.!!$R2 1465
7 TraesCS2B01G316100 chr2A 2817601 2819090 1489 True 1074.000000 1074 80.040000 1946 3411 1 chr2A.!!$R1 1465
8 TraesCS2B01G316100 chr1D 107195415 107196310 895 True 412.000000 412 75.441000 2494 3382 1 chr1D.!!$R1 888
9 TraesCS2B01G316100 chr4A 738514074 738516468 2394 False 229.150000 387 77.708500 1063 3378 2 chr4A.!!$F2 2315

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
931 1204 0.391130 TAGTTGTGCATCACGCCTCC 60.391 55.000 0.00 0.0 41.33 4.30 F
933 1206 0.391130 GTTGTGCATCACGCCTCCTA 60.391 55.000 0.00 0.0 41.33 2.94 F
1162 1438 1.004320 TTCGCGCTGGGCTTCTTTA 60.004 52.632 14.94 0.0 40.44 1.85 F
1634 1964 1.071471 CCCGGTTCAGTCTTGCAGT 59.929 57.895 0.00 0.0 0.00 4.40 F
1649 1979 1.269723 TGCAGTACTGAACTCGTCCAG 59.730 52.381 27.08 0.0 35.76 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1880 2270 0.965363 ATCACAATGGTCGTTGGGGC 60.965 55.000 5.46 0.0 33.31 5.80 R
2653 3070 3.554934 TGATATGCTGAATGGTCCCAAC 58.445 45.455 0.00 0.0 0.00 3.77 R
3299 3735 9.613428 CAAGATATTGAACTACTTCACCCATTA 57.387 33.333 0.00 0.0 36.06 1.90 R
3573 4036 2.728690 TCGGCTACACGTACACAAAT 57.271 45.000 0.00 0.0 34.94 2.32 R
3821 10721 4.018490 AGAGTACAAATGATTGCCATGCA 58.982 39.130 0.00 0.0 40.34 3.96 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
22 23 4.963318 AACACAGAGACAAGATCTTCCA 57.037 40.909 4.57 0.00 38.00 3.53
23 24 4.963318 ACACAGAGACAAGATCTTCCAA 57.037 40.909 4.57 0.00 38.00 3.53
24 25 4.892433 ACACAGAGACAAGATCTTCCAAG 58.108 43.478 4.57 0.00 38.00 3.61
26 27 5.163258 ACACAGAGACAAGATCTTCCAAGTT 60.163 40.000 4.57 0.00 38.00 2.66
27 28 5.407995 CACAGAGACAAGATCTTCCAAGTTC 59.592 44.000 4.57 2.31 38.00 3.01
28 29 4.624882 CAGAGACAAGATCTTCCAAGTTCG 59.375 45.833 4.57 0.00 38.00 3.95
75 76 3.195698 GATGGTCTTCGCCACGCC 61.196 66.667 0.00 0.00 41.94 5.68
78 79 1.966901 ATGGTCTTCGCCACGCCATA 61.967 55.000 0.00 0.00 41.94 2.74
112 113 1.341383 CCCATGGTTCTTCCCTTGAGG 60.341 57.143 11.73 0.00 32.74 3.86
128 129 6.161348 TCCCTTGAGGATATTTTTCCCACATA 59.839 38.462 0.00 0.00 40.93 2.29
166 167 7.110216 GTCTTATTATTGATGTACTTTTGCGCG 59.890 37.037 0.00 0.00 0.00 6.86
168 169 2.308347 TTGATGTACTTTTGCGCGTG 57.692 45.000 8.43 0.00 0.00 5.34
188 189 7.587757 GCGCGTGAGATAAATCTTGATAAATTT 59.412 33.333 8.43 0.00 37.25 1.82
210 211 7.925043 TTTAAGGCCTTAATACAAATCGACA 57.075 32.000 33.16 14.73 35.27 4.35
211 212 8.514330 TTTAAGGCCTTAATACAAATCGACAT 57.486 30.769 33.16 2.80 35.27 3.06
212 213 6.619801 AAGGCCTTAATACAAATCGACATC 57.380 37.500 18.87 0.00 0.00 3.06
213 214 4.750098 AGGCCTTAATACAAATCGACATCG 59.250 41.667 0.00 0.00 41.45 3.84
215 216 4.510340 GCCTTAATACAAATCGACATCGGT 59.490 41.667 0.73 0.00 40.29 4.69
232 234 5.768164 ACATCGGTTAAACCTCAAAGTCAAT 59.232 36.000 0.00 0.00 35.66 2.57
234 236 4.449743 TCGGTTAAACCTCAAAGTCAATCG 59.550 41.667 0.00 0.00 35.66 3.34
248 250 7.542477 TCAAAGTCAATCGTCTGATTAGAGAAC 59.458 37.037 0.00 0.00 42.94 3.01
257 259 6.653740 TCGTCTGATTAGAGAACTCTTGTACA 59.346 38.462 9.64 0.00 40.93 2.90
258 260 7.174426 TCGTCTGATTAGAGAACTCTTGTACAA 59.826 37.037 8.28 8.28 40.93 2.41
271 273 8.747538 AACTCTTGTACAAATAAACTTCCAGT 57.252 30.769 10.03 0.00 0.00 4.00
353 355 3.420893 TCCCTTAATTTCACTGCAGTGG 58.579 45.455 39.04 23.98 45.65 4.00
354 356 3.073798 TCCCTTAATTTCACTGCAGTGGA 59.926 43.478 39.04 32.66 45.65 4.02
355 357 4.019174 CCCTTAATTTCACTGCAGTGGAT 58.981 43.478 39.04 30.16 45.65 3.41
356 358 4.096984 CCCTTAATTTCACTGCAGTGGATC 59.903 45.833 39.04 0.00 45.65 3.36
441 699 6.287589 ACTGGAACACTCCTTGATAAGTAG 57.712 41.667 0.00 0.00 42.94 2.57
457 715 7.801104 TGATAAGTAGTGCCTCCATTCATAAA 58.199 34.615 0.00 0.00 0.00 1.40
458 716 8.439971 TGATAAGTAGTGCCTCCATTCATAAAT 58.560 33.333 0.00 0.00 0.00 1.40
497 755 8.902540 TGGATATTTCAACATGGACTACATAC 57.097 34.615 0.00 0.00 37.84 2.39
508 766 6.322969 ACATGGACTACATACGGACTGAAATA 59.677 38.462 0.00 0.00 37.84 1.40
516 774 6.460781 ACATACGGACTGAAATAAGTGAACA 58.539 36.000 0.00 0.00 0.00 3.18
607 866 6.452757 AGGGAGTAGTACCTAGGAGTAATC 57.547 45.833 17.98 13.86 34.71 1.75
612 871 9.230122 GGAGTAGTACCTAGGAGTAATCAATAC 57.770 40.741 17.98 3.98 34.52 1.89
684 943 2.203480 GAGCACAGGTTTGGCCCA 60.203 61.111 0.00 0.00 38.26 5.36
699 958 2.693871 CCCATTCTCCACCCCAGGG 61.694 68.421 0.00 0.00 42.03 4.45
725 984 1.593787 ACGATGTGTGAGCTCCAGG 59.406 57.895 12.15 1.44 0.00 4.45
734 993 1.332889 TGAGCTCCAGGCATGATCGT 61.333 55.000 12.15 0.00 44.79 3.73
778 1042 9.784680 GACATATATATTTCAGTCGTATTCGGT 57.215 33.333 4.34 0.00 37.69 4.69
906 1177 0.739112 CTCAGCTTGCTCCCTTCGTC 60.739 60.000 0.00 0.00 0.00 4.20
921 1194 3.431626 CCTTCGTCCCATATAGTTGTGCA 60.432 47.826 0.00 0.00 0.00 4.57
922 1195 4.380531 CTTCGTCCCATATAGTTGTGCAT 58.619 43.478 0.00 0.00 0.00 3.96
923 1196 3.990092 TCGTCCCATATAGTTGTGCATC 58.010 45.455 0.00 0.00 0.00 3.91
924 1197 3.386402 TCGTCCCATATAGTTGTGCATCA 59.614 43.478 0.00 0.00 0.00 3.07
925 1198 3.494626 CGTCCCATATAGTTGTGCATCAC 59.505 47.826 0.00 0.00 34.56 3.06
926 1199 3.494626 GTCCCATATAGTTGTGCATCACG 59.505 47.826 0.00 0.00 37.14 4.35
927 1200 2.224079 CCCATATAGTTGTGCATCACGC 59.776 50.000 0.00 0.00 37.14 5.34
928 1201 2.224079 CCATATAGTTGTGCATCACGCC 59.776 50.000 0.00 0.00 41.33 5.68
929 1202 2.979814 TATAGTTGTGCATCACGCCT 57.020 45.000 0.00 0.00 41.33 5.52
930 1203 1.656652 ATAGTTGTGCATCACGCCTC 58.343 50.000 0.00 0.00 41.33 4.70
931 1204 0.391130 TAGTTGTGCATCACGCCTCC 60.391 55.000 0.00 0.00 41.33 4.30
932 1205 1.672356 GTTGTGCATCACGCCTCCT 60.672 57.895 0.00 0.00 41.33 3.69
933 1206 0.391130 GTTGTGCATCACGCCTCCTA 60.391 55.000 0.00 0.00 41.33 2.94
934 1207 0.391130 TTGTGCATCACGCCTCCTAC 60.391 55.000 0.00 0.00 41.33 3.18
935 1208 1.218047 GTGCATCACGCCTCCTACA 59.782 57.895 0.00 0.00 41.33 2.74
936 1209 1.084370 GTGCATCACGCCTCCTACAC 61.084 60.000 0.00 0.00 41.33 2.90
937 1210 1.257750 TGCATCACGCCTCCTACACT 61.258 55.000 0.00 0.00 41.33 3.55
979 1252 5.896106 TCCTCATCTCAAGAAATAGAGCAGA 59.104 40.000 0.00 0.00 0.00 4.26
982 1255 7.716123 CCTCATCTCAAGAAATAGAGCAGAAAT 59.284 37.037 0.00 0.00 0.00 2.17
985 1258 7.856145 TCTCAAGAAATAGAGCAGAAATTCC 57.144 36.000 0.00 0.00 0.00 3.01
990 1263 7.622893 AGAAATAGAGCAGAAATTCCAGTTC 57.377 36.000 0.00 0.00 0.00 3.01
991 1264 7.401246 AGAAATAGAGCAGAAATTCCAGTTCT 58.599 34.615 7.35 7.35 35.69 3.01
1041 1317 2.197875 GCCTACGGCCTCCTCCTA 59.802 66.667 0.00 0.00 44.06 2.94
1161 1437 2.281484 TTCGCGCTGGGCTTCTTT 60.281 55.556 14.94 0.00 40.44 2.52
1162 1438 1.004320 TTCGCGCTGGGCTTCTTTA 60.004 52.632 14.94 0.00 40.44 1.85
1269 1557 1.526225 GGCCAACGGAGATAAGCCC 60.526 63.158 0.00 0.00 34.23 5.19
1274 1562 2.354773 CGGAGATAAGCCCGTCGC 60.355 66.667 0.00 0.00 40.78 5.19
1365 1674 2.771943 GTCCATCATCTGGTCTACCCAA 59.228 50.000 0.00 0.00 44.65 4.12
1450 1771 2.912956 AGCACCTCAAACTCTTCCCATA 59.087 45.455 0.00 0.00 0.00 2.74
1527 1857 1.228337 TCGAGACAAGGTCACCGGA 60.228 57.895 9.46 0.00 34.60 5.14
1559 1889 4.024809 CCGTCTTGTTTCCAGAAAGAACTC 60.025 45.833 0.00 0.00 32.03 3.01
1578 1908 1.145945 TCGATAGATCCTGCTCCTGGT 59.854 52.381 0.00 0.00 42.67 4.00
1634 1964 1.071471 CCCGGTTCAGTCTTGCAGT 59.929 57.895 0.00 0.00 0.00 4.40
1649 1979 1.269723 TGCAGTACTGAACTCGTCCAG 59.730 52.381 27.08 0.00 35.76 3.86
1713 2043 4.896482 GGTTCTATACCAGAGATGTCAGGT 59.104 45.833 11.79 11.79 46.92 4.00
1720 2080 1.520342 GAGATGTCAGGTCGCCAGC 60.520 63.158 0.00 0.00 0.00 4.85
2355 2757 2.313317 AGGAACAGGCGACGGATAATA 58.687 47.619 0.00 0.00 0.00 0.98
2653 3070 4.453177 TTCAGAGCTGAAGTGAGATCAG 57.547 45.455 8.76 0.00 43.90 2.90
3299 3735 3.912496 TCATGAGTTTGATCGACCCAT 57.088 42.857 0.00 0.00 0.00 4.00
3569 4032 4.646040 AGCATGCCTAACTTGCATCATTTA 59.354 37.500 15.66 0.00 46.04 1.40
3573 4036 7.652909 GCATGCCTAACTTGCATCATTTATTTA 59.347 33.333 6.36 0.00 46.04 1.40
3775 10675 9.722056 CGCTATTAGCATTTCTGAAACTAAATT 57.278 29.630 15.64 5.29 42.58 1.82
3818 10718 9.077885 ACTGTGTTTTTCAGGATATATTGTTGT 57.922 29.630 0.00 0.00 37.25 3.32
3827 10727 8.339344 TCAGGATATATTGTTGTATTGCATGG 57.661 34.615 0.00 0.00 0.00 3.66
3828 10728 7.031372 CAGGATATATTGTTGTATTGCATGGC 58.969 38.462 0.00 0.00 0.00 4.40
3829 10729 6.720748 AGGATATATTGTTGTATTGCATGGCA 59.279 34.615 0.00 0.00 36.47 4.92
3998 10922 4.794278 TTTGGCTAGTGATCGTTGTCTA 57.206 40.909 0.00 0.00 0.00 2.59
4008 11400 5.031578 GTGATCGTTGTCTATGAGTCACTC 58.968 45.833 0.00 0.00 32.93 3.51
4009 11401 3.741805 TCGTTGTCTATGAGTCACTCG 57.258 47.619 0.00 0.00 32.35 4.18
4010 11402 2.418976 TCGTTGTCTATGAGTCACTCGG 59.581 50.000 0.00 0.00 32.35 4.63
4011 11403 2.161808 CGTTGTCTATGAGTCACTCGGT 59.838 50.000 0.00 0.00 32.35 4.69
4012 11404 3.373130 CGTTGTCTATGAGTCACTCGGTA 59.627 47.826 0.00 0.00 32.35 4.02
4013 11405 4.142752 CGTTGTCTATGAGTCACTCGGTAA 60.143 45.833 0.00 0.00 32.35 2.85
4014 11406 5.333513 GTTGTCTATGAGTCACTCGGTAAG 58.666 45.833 0.00 0.00 32.35 2.34
4015 11407 4.586884 TGTCTATGAGTCACTCGGTAAGT 58.413 43.478 0.00 0.00 39.44 2.24
4255 11647 2.281484 GCTTCCCGGCTTCACACA 60.281 61.111 0.00 0.00 0.00 3.72
4283 11675 1.578206 GGCCTTGCGAGAAACAGGAC 61.578 60.000 1.22 0.00 0.00 3.85
4297 11689 2.112297 GGACAAGTTGCGGTGGGA 59.888 61.111 1.81 0.00 0.00 4.37
4325 11717 1.216710 GGTCTTCCTGCTCCTGTCG 59.783 63.158 0.00 0.00 0.00 4.35
4389 11784 2.595536 CGTGGTCGGTAGAAATTGTACG 59.404 50.000 0.00 0.00 0.00 3.67
4390 11785 2.346545 GTGGTCGGTAGAAATTGTACGC 59.653 50.000 0.00 0.00 0.00 4.42
4397 11794 4.040376 GGTAGAAATTGTACGCCTAGACG 58.960 47.826 0.00 0.00 39.50 4.18
4408 11805 1.262640 GCCTAGACGGAGGGGTTTCA 61.263 60.000 0.00 0.00 37.06 2.69
4413 11810 1.460689 ACGGAGGGGTTTCAGGACA 60.461 57.895 0.00 0.00 0.00 4.02
4428 11825 4.402528 ACACCGCCGCAATGCCTA 62.403 61.111 0.00 0.00 0.00 3.93
4466 11863 2.518587 GGTATTTCGGGGCAGGGC 60.519 66.667 0.00 0.00 0.00 5.19
4505 11903 2.510691 CGTGGCCGTGGTATCACC 60.511 66.667 0.00 0.00 40.65 4.02
4506 11904 2.510691 GTGGCCGTGGTATCACCG 60.511 66.667 0.00 0.00 42.58 4.94
4507 11905 2.680707 TGGCCGTGGTATCACCGA 60.681 61.111 0.00 0.00 42.58 4.69
4508 11906 2.106332 GGCCGTGGTATCACCGAG 59.894 66.667 0.00 0.00 42.58 4.63
4509 11907 2.106332 GCCGTGGTATCACCGAGG 59.894 66.667 0.00 0.00 42.58 4.63
4528 11932 0.397957 GTTTGGGGTTTCAGGGTGGT 60.398 55.000 0.00 0.00 0.00 4.16
4580 11988 4.828925 TGGCGCGGCGATGATTGA 62.829 61.111 28.54 4.33 0.00 2.57
4666 12091 2.788589 GAGGGGGAGGGGAGTTCT 59.211 66.667 0.00 0.00 0.00 3.01
4667 12092 1.690985 GAGGGGGAGGGGAGTTCTG 60.691 68.421 0.00 0.00 0.00 3.02
4668 12093 2.182858 GAGGGGGAGGGGAGTTCTGA 62.183 65.000 0.00 0.00 0.00 3.27
4669 12094 1.229853 GGGGGAGGGGAGTTCTGAA 60.230 63.158 0.00 0.00 0.00 3.02
4670 12095 1.275421 GGGGGAGGGGAGTTCTGAAG 61.275 65.000 0.00 0.00 0.00 3.02
4671 12096 0.252742 GGGGAGGGGAGTTCTGAAGA 60.253 60.000 0.00 0.00 0.00 2.87
4672 12097 1.626631 GGGGAGGGGAGTTCTGAAGAT 60.627 57.143 0.00 0.00 0.00 2.40
4673 12098 1.765904 GGGAGGGGAGTTCTGAAGATC 59.234 57.143 0.00 0.00 0.00 2.75
4674 12099 1.410882 GGAGGGGAGTTCTGAAGATCG 59.589 57.143 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 4.016706 ACCTCGCCCCCGAACTTG 62.017 66.667 0.00 0.00 43.87 3.16
22 23 4.016706 CACCTCGCCCCCGAACTT 62.017 66.667 0.00 0.00 43.87 2.66
24 25 2.814913 AAATCACCTCGCCCCCGAAC 62.815 60.000 0.00 0.00 43.87 3.95
26 27 3.006728 AAATCACCTCGCCCCCGA 61.007 61.111 0.00 0.00 42.01 5.14
27 28 2.824041 CAAATCACCTCGCCCCCG 60.824 66.667 0.00 0.00 0.00 5.73
28 29 3.140814 GCAAATCACCTCGCCCCC 61.141 66.667 0.00 0.00 0.00 5.40
75 76 1.394266 GGGTGGCTGGGTGCATTATG 61.394 60.000 0.00 0.00 45.15 1.90
78 79 3.242492 ATGGGTGGCTGGGTGCATT 62.242 57.895 0.00 0.00 45.15 3.56
112 113 9.665719 ACCAAATTTGTATGTGGGAAAAATATC 57.334 29.630 16.73 0.00 42.66 1.63
139 140 7.908082 GCGCAAAAGTACATCAATAATAAGACA 59.092 33.333 0.30 0.00 0.00 3.41
154 155 3.984018 TTATCTCACGCGCAAAAGTAC 57.016 42.857 5.73 0.00 0.00 2.73
188 189 6.422701 CGATGTCGATTTGTATTAAGGCCTTA 59.577 38.462 21.68 21.68 43.02 2.69
200 201 4.320870 AGGTTTAACCGATGTCGATTTGT 58.679 39.130 8.63 0.00 44.90 2.83
205 206 3.663995 TTGAGGTTTAACCGATGTCGA 57.336 42.857 8.63 0.00 44.90 4.20
206 207 3.744426 ACTTTGAGGTTTAACCGATGTCG 59.256 43.478 8.63 0.00 44.90 4.35
207 208 4.753107 TGACTTTGAGGTTTAACCGATGTC 59.247 41.667 8.63 14.79 44.90 3.06
210 211 5.121768 CGATTGACTTTGAGGTTTAACCGAT 59.878 40.000 8.63 0.00 44.90 4.18
211 212 4.449743 CGATTGACTTTGAGGTTTAACCGA 59.550 41.667 8.63 0.00 44.90 4.69
212 213 4.212636 ACGATTGACTTTGAGGTTTAACCG 59.787 41.667 8.63 0.00 44.90 4.44
213 214 5.469084 AGACGATTGACTTTGAGGTTTAACC 59.531 40.000 5.91 5.91 38.99 2.85
215 216 6.285224 TCAGACGATTGACTTTGAGGTTTAA 58.715 36.000 0.00 0.00 0.00 1.52
232 234 6.653740 TGTACAAGAGTTCTCTAATCAGACGA 59.346 38.462 2.63 0.00 0.00 4.20
234 236 9.646427 ATTTGTACAAGAGTTCTCTAATCAGAC 57.354 33.333 8.56 0.00 0.00 3.51
271 273 2.421619 TGAACGCTCACATGTGCATTA 58.578 42.857 21.38 2.72 34.50 1.90
353 355 0.454600 TTGCCTAGGTGACGTCGATC 59.545 55.000 11.31 3.92 0.00 3.69
354 356 0.456221 CTTGCCTAGGTGACGTCGAT 59.544 55.000 11.31 1.47 0.00 3.59
355 357 0.607217 TCTTGCCTAGGTGACGTCGA 60.607 55.000 11.31 0.00 0.00 4.20
356 358 0.242825 TTCTTGCCTAGGTGACGTCG 59.757 55.000 11.31 0.00 0.00 5.12
383 385 1.204704 GCCTGGGTTGATTAGTTTGGC 59.795 52.381 0.00 0.00 0.00 4.52
395 397 4.178956 TCTTGAAACTAAAGCCTGGGTT 57.821 40.909 5.07 5.07 0.00 4.11
484 742 4.649088 TTCAGTCCGTATGTAGTCCATG 57.351 45.455 0.00 0.00 34.86 3.66
487 745 6.696148 CACTTATTTCAGTCCGTATGTAGTCC 59.304 42.308 0.00 0.00 0.00 3.85
488 746 7.478322 TCACTTATTTCAGTCCGTATGTAGTC 58.522 38.462 0.00 0.00 0.00 2.59
497 755 5.907391 GTGTTTGTTCACTTATTTCAGTCCG 59.093 40.000 0.00 0.00 35.68 4.79
508 766 9.730420 GATATGTTTTAGTGTGTTTGTTCACTT 57.270 29.630 3.25 0.00 43.39 3.16
562 821 6.764085 CCCTCCGTTCACAAATGTATAACATA 59.236 38.462 9.99 0.28 37.97 2.29
565 824 5.180271 TCCCTCCGTTCACAAATGTATAAC 58.820 41.667 0.00 0.00 0.00 1.89
566 825 5.046159 ACTCCCTCCGTTCACAAATGTATAA 60.046 40.000 0.00 0.00 0.00 0.98
607 866 3.770666 CTGGGACGTCACTACTGTATTG 58.229 50.000 20.37 0.00 0.00 1.90
612 871 0.171455 GAGCTGGGACGTCACTACTG 59.829 60.000 20.37 7.75 0.00 2.74
684 943 2.128226 AGCCCTGGGGTGGAGAAT 59.872 61.111 18.34 0.00 37.65 2.40
699 958 4.450122 CACACATCGTGCCGCAGC 62.450 66.667 0.00 0.00 39.19 5.25
725 984 3.165058 TGTCTGAAGGTACGATCATGC 57.835 47.619 0.00 0.00 0.00 4.06
734 993 1.180456 TCGGCGGTTGTCTGAAGGTA 61.180 55.000 7.21 0.00 0.00 3.08
778 1042 4.563061 GAGTACGACTGGCTTTAAAGGAA 58.437 43.478 16.78 0.00 0.00 3.36
906 1177 2.224079 GCGTGATGCACAACTATATGGG 59.776 50.000 0.00 0.00 45.45 4.00
921 1194 0.818296 GTGAGTGTAGGAGGCGTGAT 59.182 55.000 0.00 0.00 0.00 3.06
922 1195 1.583495 CGTGAGTGTAGGAGGCGTGA 61.583 60.000 0.00 0.00 0.00 4.35
923 1196 1.154016 CGTGAGTGTAGGAGGCGTG 60.154 63.158 0.00 0.00 0.00 5.34
924 1197 2.991076 GCGTGAGTGTAGGAGGCGT 61.991 63.158 0.00 0.00 0.00 5.68
925 1198 2.202623 GCGTGAGTGTAGGAGGCG 60.203 66.667 0.00 0.00 0.00 5.52
926 1199 2.184579 GGCGTGAGTGTAGGAGGC 59.815 66.667 0.00 0.00 0.00 4.70
927 1200 1.994507 CTCGGCGTGAGTGTAGGAGG 61.995 65.000 6.85 0.00 40.03 4.30
928 1201 1.429825 CTCGGCGTGAGTGTAGGAG 59.570 63.158 6.85 0.00 40.03 3.69
929 1202 2.044555 CCTCGGCGTGAGTGTAGGA 61.045 63.158 10.96 0.00 43.64 2.94
930 1203 2.490217 CCTCGGCGTGAGTGTAGG 59.510 66.667 10.96 2.01 43.64 3.18
931 1204 2.202623 GCCTCGGCGTGAGTGTAG 60.203 66.667 10.96 0.00 43.64 2.74
932 1205 2.986979 TGCCTCGGCGTGAGTGTA 60.987 61.111 10.96 0.00 43.64 2.90
933 1206 4.363990 CTGCCTCGGCGTGAGTGT 62.364 66.667 10.96 0.00 43.64 3.55
936 1209 4.827087 ATGCTGCCTCGGCGTGAG 62.827 66.667 10.96 0.00 45.51 3.51
937 1210 3.899981 AAATGCTGCCTCGGCGTGA 62.900 57.895 10.96 0.00 45.51 4.35
960 1233 8.051535 TGGAATTTCTGCTCTATTTCTTGAGAT 58.948 33.333 0.00 0.00 32.44 2.75
979 1252 1.963515 GGTGGTGCAGAACTGGAATTT 59.036 47.619 3.99 0.00 31.21 1.82
982 1255 0.478072 ATGGTGGTGCAGAACTGGAA 59.522 50.000 3.99 0.00 31.21 3.53
985 1258 1.582968 GCATGGTGGTGCAGAACTG 59.417 57.895 0.00 0.00 44.43 3.16
990 1263 2.672651 TTCGGCATGGTGGTGCAG 60.673 61.111 0.00 0.00 46.81 4.41
991 1264 2.983030 GTTCGGCATGGTGGTGCA 60.983 61.111 0.00 0.00 46.81 4.57
1080 1356 1.908340 GCCCAGCTGAGATGGTGTCT 61.908 60.000 17.39 0.00 40.81 3.41
1161 1437 3.005554 CGAGGACTTACTGTTCGGTCTA 58.994 50.000 0.00 0.00 0.00 2.59
1162 1438 1.811359 CGAGGACTTACTGTTCGGTCT 59.189 52.381 0.00 0.00 0.00 3.85
1269 1557 3.414700 GAAGTGGTGCCAGCGACG 61.415 66.667 0.00 0.00 0.00 5.12
1278 1566 4.379243 AGCTCCGGCGAAGTGGTG 62.379 66.667 9.30 0.00 44.37 4.17
1279 1567 4.070552 GAGCTCCGGCGAAGTGGT 62.071 66.667 9.30 0.00 44.37 4.16
1365 1674 0.969917 TGTTTGCTGTGGTGTTGGCT 60.970 50.000 0.00 0.00 0.00 4.75
1450 1771 4.612264 AATCAAAGCTTTGCCACAAGAT 57.388 36.364 30.35 16.06 38.05 2.40
1527 1857 0.463116 AAACAAGACGGCGGTTCAGT 60.463 50.000 13.24 0.00 0.00 3.41
1559 1889 1.626686 ACCAGGAGCAGGATCTATCG 58.373 55.000 0.00 0.00 0.00 2.92
1578 1908 9.612066 TTCTCATGCAACTCATAAACATACATA 57.388 29.630 0.00 0.00 33.19 2.29
1634 1964 2.281539 TGGTCTGGACGAGTTCAGTA 57.718 50.000 10.97 0.00 33.13 2.74
1665 1995 2.106683 GTGCCCGTTCCATTCTCCG 61.107 63.158 0.00 0.00 0.00 4.63
1713 2043 3.342719 TGTAAAATCAATCAGCTGGCGA 58.657 40.909 15.13 8.46 0.00 5.54
1720 2080 8.726650 TTGTTGACGAATGTAAAATCAATCAG 57.273 30.769 0.00 0.00 32.30 2.90
1880 2270 0.965363 ATCACAATGGTCGTTGGGGC 60.965 55.000 5.46 0.00 33.31 5.80
2653 3070 3.554934 TGATATGCTGAATGGTCCCAAC 58.445 45.455 0.00 0.00 0.00 3.77
3299 3735 9.613428 CAAGATATTGAACTACTTCACCCATTA 57.387 33.333 0.00 0.00 36.06 1.90
3465 3911 4.310769 ACACATCTCGCTGCTTATATTCC 58.689 43.478 0.00 0.00 0.00 3.01
3511 3974 7.672983 ATTGACATACCATAGGCTTTTATCG 57.327 36.000 0.00 0.00 0.00 2.92
3569 4032 5.170021 TCGGCTACACGTACACAAATAAAT 58.830 37.500 0.00 0.00 34.94 1.40
3573 4036 2.728690 TCGGCTACACGTACACAAAT 57.271 45.000 0.00 0.00 34.94 2.32
3821 10721 4.018490 AGAGTACAAATGATTGCCATGCA 58.982 39.130 0.00 0.00 40.34 3.96
3822 10722 4.096833 TGAGAGTACAAATGATTGCCATGC 59.903 41.667 0.00 0.00 40.34 4.06
3823 10723 5.823209 TGAGAGTACAAATGATTGCCATG 57.177 39.130 0.00 0.00 40.34 3.66
3824 10724 6.124340 TGATGAGAGTACAAATGATTGCCAT 58.876 36.000 0.00 0.00 40.34 4.40
3825 10725 5.499313 TGATGAGAGTACAAATGATTGCCA 58.501 37.500 0.00 0.00 40.34 4.92
3826 10726 6.441093 TTGATGAGAGTACAAATGATTGCC 57.559 37.500 0.00 0.00 40.34 4.52
3827 10727 6.971184 CCTTTGATGAGAGTACAAATGATTGC 59.029 38.462 0.00 0.00 40.34 3.56
3828 10728 8.048534 ACCTTTGATGAGAGTACAAATGATTG 57.951 34.615 0.00 0.00 42.46 2.67
3829 10729 7.065085 CGACCTTTGATGAGAGTACAAATGATT 59.935 37.037 0.00 0.00 33.97 2.57
3830 10730 6.536582 CGACCTTTGATGAGAGTACAAATGAT 59.463 38.462 0.00 0.00 33.97 2.45
3831 10731 5.869344 CGACCTTTGATGAGAGTACAAATGA 59.131 40.000 0.00 0.00 33.97 2.57
3832 10732 5.446473 GCGACCTTTGATGAGAGTACAAATG 60.446 44.000 0.00 0.00 33.97 2.32
3833 10733 4.631813 GCGACCTTTGATGAGAGTACAAAT 59.368 41.667 0.00 0.00 33.97 2.32
3834 10734 3.994392 GCGACCTTTGATGAGAGTACAAA 59.006 43.478 0.00 0.00 33.49 2.83
3966 10890 9.998106 ACGATCACTAGCCAAATTATACTATTT 57.002 29.630 0.00 0.00 0.00 1.40
3967 10891 9.998106 AACGATCACTAGCCAAATTATACTATT 57.002 29.630 0.00 0.00 0.00 1.73
3998 10922 1.743958 CCGACTTACCGAGTGACTCAT 59.256 52.381 13.67 2.46 39.19 2.90
4008 11400 6.732154 TGAATTCTATTCTACCGACTTACCG 58.268 40.000 7.05 0.00 0.00 4.02
4009 11401 6.641723 GCTGAATTCTATTCTACCGACTTACC 59.358 42.308 7.05 0.00 0.00 2.85
4010 11402 6.641723 GGCTGAATTCTATTCTACCGACTTAC 59.358 42.308 7.05 0.00 0.00 2.34
4011 11403 6.514541 CGGCTGAATTCTATTCTACCGACTTA 60.515 42.308 19.61 0.00 38.76 2.24
4012 11404 5.602628 GGCTGAATTCTATTCTACCGACTT 58.397 41.667 7.05 0.00 0.00 3.01
4013 11405 4.261656 CGGCTGAATTCTATTCTACCGACT 60.262 45.833 19.61 0.00 38.76 4.18
4014 11406 3.982058 CGGCTGAATTCTATTCTACCGAC 59.018 47.826 19.61 2.90 38.76 4.79
4015 11407 3.635373 ACGGCTGAATTCTATTCTACCGA 59.365 43.478 25.78 0.67 39.30 4.69
4229 11621 3.953775 CCGGGAAGCCACACCACT 61.954 66.667 0.00 0.00 0.00 4.00
4269 11661 1.939934 CAACTTGTCCTGTTTCTCGCA 59.060 47.619 0.00 0.00 0.00 5.10
4273 11665 1.308998 CCGCAACTTGTCCTGTTTCT 58.691 50.000 0.00 0.00 0.00 2.52
4283 11675 0.036010 AGATCTCCCACCGCAACTTG 60.036 55.000 0.00 0.00 0.00 3.16
4297 11689 1.076632 AGGAAGACCGGCGAGATCT 60.077 57.895 9.30 5.36 41.83 2.75
4369 11764 2.346545 GCGTACAATTTCTACCGACCAC 59.653 50.000 0.00 0.00 0.00 4.16
4372 11767 2.884827 AGGCGTACAATTTCTACCGAC 58.115 47.619 0.00 0.00 0.00 4.79
4373 11768 3.947196 TCTAGGCGTACAATTTCTACCGA 59.053 43.478 0.00 0.00 0.00 4.69
4389 11784 1.262640 TGAAACCCCTCCGTCTAGGC 61.263 60.000 0.00 0.00 40.77 3.93
4390 11785 0.824759 CTGAAACCCCTCCGTCTAGG 59.175 60.000 0.00 0.00 42.97 3.02
4397 11794 1.379146 GGTGTCCTGAAACCCCTCC 59.621 63.158 0.00 0.00 0.00 4.30
4505 11903 0.893727 CCCTGAAACCCCAAACCTCG 60.894 60.000 0.00 0.00 0.00 4.63
4506 11904 0.187606 ACCCTGAAACCCCAAACCTC 59.812 55.000 0.00 0.00 0.00 3.85
4507 11905 0.105709 CACCCTGAAACCCCAAACCT 60.106 55.000 0.00 0.00 0.00 3.50
4508 11906 1.118965 CCACCCTGAAACCCCAAACC 61.119 60.000 0.00 0.00 0.00 3.27
4509 11907 0.397957 ACCACCCTGAAACCCCAAAC 60.398 55.000 0.00 0.00 0.00 2.93
4580 11988 2.365635 CCTCCCGTCTCCACCCAT 60.366 66.667 0.00 0.00 0.00 4.00
4613 12021 1.382420 CTCTCCACTCCCTCCCCAG 60.382 68.421 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.