Multiple sequence alignment - TraesCS6D01G309100

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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 TraesCS6D01G309100 chr6D 100.000 3742 0 0 1 3742 419836336 419840077 0.000000e+00 6911.0
1 TraesCS6D01G309100 chr6D 92.784 194 11 3 3421 3613 97853072 97852881 1.120000e-70 278.0
2 TraesCS6D01G309100 chr6D 100.000 63 0 0 4032 4094 419840367 419840429 2.590000e-22 117.0
3 TraesCS6D01G309100 chr6D 96.875 64 1 1 4032 4094 97852251 97852188 5.600000e-19 106.0
4 TraesCS6D01G309100 chr6D 100.000 33 0 0 1621 1653 419837922 419837954 1.230000e-05 62.1
5 TraesCS6D01G309100 chr6D 100.000 33 0 0 1587 1619 419837956 419837988 1.230000e-05 62.1
6 TraesCS6D01G309100 chr6B 93.621 2618 115 21 820 3420 632848595 632851177 0.000000e+00 3862.0
7 TraesCS6D01G309100 chr6B 90.274 329 24 6 3421 3742 157532089 157531762 1.360000e-114 424.0
8 TraesCS6D01G309100 chr6B 85.596 361 13 9 3421 3742 423079455 423079095 3.920000e-90 342.0
9 TraesCS6D01G309100 chr6B 87.215 219 24 4 3528 3742 94841640 94841422 3.160000e-61 246.0
10 TraesCS6D01G309100 chr6B 100.000 33 0 0 1621 1653 632849346 632849378 1.230000e-05 62.1
11 TraesCS6D01G309100 chr6A 93.581 1480 67 10 1621 3096 562930752 562932207 0.000000e+00 2182.0
12 TraesCS6D01G309100 chr6A 93.467 796 34 8 837 1620 562929996 562930785 0.000000e+00 1166.0
13 TraesCS6D01G309100 chr6A 87.500 336 27 6 3419 3742 572259540 572259208 1.390000e-99 374.0
14 TraesCS6D01G309100 chr1D 88.609 834 90 3 1 832 452108235 452107405 0.000000e+00 1009.0
15 TraesCS6D01G309100 chr1D 86.095 338 27 7 3425 3742 10805057 10804720 3.030000e-91 346.0
16 TraesCS6D01G309100 chr1D 84.641 306 19 16 3464 3742 466347017 466346713 3.120000e-71 279.0
17 TraesCS6D01G309100 chr7B 86.131 822 110 4 1 819 323829916 323829096 0.000000e+00 883.0
18 TraesCS6D01G309100 chr7B 82.388 335 29 15 3421 3742 607052196 607051879 8.730000e-67 265.0
19 TraesCS6D01G309100 chr7B 95.312 64 2 1 4032 4094 607051661 607051598 2.600000e-17 100.0
20 TraesCS6D01G309100 chr2B 80.895 827 141 12 2 820 381830523 381829706 1.610000e-178 636.0
21 TraesCS6D01G309100 chr2B 84.877 324 30 10 3421 3742 693491002 693491308 3.970000e-80 309.0
22 TraesCS6D01G309100 chr2B 82.133 347 32 15 3421 3742 600075346 600075005 1.880000e-68 270.0
23 TraesCS6D01G309100 chr2B 96.875 64 1 1 4032 4094 693491545 693491608 5.600000e-19 106.0
24 TraesCS6D01G309100 chr2B 95.312 64 2 1 4032 4094 77579918 77579855 2.600000e-17 100.0
25 TraesCS6D01G309100 chr1B 80.458 742 131 12 84 819 473708467 473707734 4.620000e-154 555.0
26 TraesCS6D01G309100 chr5D 87.135 342 25 9 3420 3742 65964275 65964616 1.800000e-98 370.0
27 TraesCS6D01G309100 chr5D 86.207 348 22 10 3421 3742 526623638 526623985 1.810000e-93 353.0
28 TraesCS6D01G309100 chr5D 95.312 64 2 1 4032 4094 472516228 472516165 2.600000e-17 100.0
29 TraesCS6D01G309100 chr4A 87.273 330 25 7 3414 3742 740414326 740414013 1.080000e-95 361.0
30 TraesCS6D01G309100 chr7D 86.087 345 24 19 3421 3742 54971964 54972307 2.340000e-92 350.0
31 TraesCS6D01G309100 chr3D 85.434 357 18 10 3420 3742 175422834 175422478 1.410000e-89 340.0
32 TraesCS6D01G309100 chr3D 96.875 64 1 1 4032 4094 570599348 570599285 5.600000e-19 106.0
33 TraesCS6D01G309100 chr3D 96.875 64 1 1 4032 4094 613552727 613552790 5.600000e-19 106.0
34 TraesCS6D01G309100 chr5B 92.268 194 11 2 3419 3611 672949996 672949806 5.210000e-69 272.0
35 TraesCS6D01G309100 chr5B 95.312 64 2 1 4032 4094 672914653 672914590 2.600000e-17 100.0
36 TraesCS6D01G309100 chr3B 95.312 64 2 1 4032 4094 692068385 692068448 2.600000e-17 100.0


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 TraesCS6D01G309100 chr6D 419836336 419840429 4093 False 1788.05 6911 100.0000 1 4094 4 chr6D.!!$F1 4093
1 TraesCS6D01G309100 chr6B 632848595 632851177 2582 False 1962.05 3862 96.8105 820 3420 2 chr6B.!!$F1 2600
2 TraesCS6D01G309100 chr6A 562929996 562932207 2211 False 1674.00 2182 93.5240 837 3096 2 chr6A.!!$F1 2259
3 TraesCS6D01G309100 chr1D 452107405 452108235 830 True 1009.00 1009 88.6090 1 832 1 chr1D.!!$R2 831
4 TraesCS6D01G309100 chr7B 323829096 323829916 820 True 883.00 883 86.1310 1 819 1 chr7B.!!$R1 818
5 TraesCS6D01G309100 chr2B 381829706 381830523 817 True 636.00 636 80.8950 2 820 1 chr2B.!!$R2 818
6 TraesCS6D01G309100 chr2B 693491002 693491608 606 False 207.50 309 90.8760 3421 4094 2 chr2B.!!$F1 673
7 TraesCS6D01G309100 chr1B 473707734 473708467 733 True 555.00 555 80.4580 84 819 1 chr1B.!!$R1 735

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
406 407 0.461870 GGCATCGGCTGTATGTCACA 60.462 55.0 0.0 0.0 40.87 3.58 F
1180 1193 0.614134 GTACGAGTCCCACCCCTCTT 60.614 60.0 0.0 0.0 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2269 2297 1.094785 GCAAATTCCTAAGCTCGGCA 58.905 50.0 0.00 0.0 0.00 5.69 R
3104 3141 0.376852 GGCTAATGCGCAACATCGAA 59.623 50.0 17.11 0.0 38.34 3.71 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
79 80 7.560368 AGTCTTGGTAGAAAATCTGTCTATGG 58.440 38.462 0.00 0.00 30.52 2.74
80 81 6.763610 GTCTTGGTAGAAAATCTGTCTATGGG 59.236 42.308 0.00 0.00 30.52 4.00
305 306 3.683281 GCAAGGAATATTGGGGTACGACA 60.683 47.826 0.00 0.00 0.00 4.35
308 309 3.778629 AGGAATATTGGGGTACGACAAGT 59.221 43.478 0.00 0.00 30.14 3.16
319 320 4.062991 GGTACGACAAGTTGAGTGGATTT 58.937 43.478 10.54 0.00 0.00 2.17
333 334 3.776731 TGGATTTCTCCACTAGAGGGA 57.223 47.619 6.35 7.01 46.95 4.20
361 362 0.932399 AATAAATACGGACGCGGCAC 59.068 50.000 17.00 1.36 0.00 5.01
405 406 1.490693 CGGCATCGGCTGTATGTCAC 61.491 60.000 9.30 1.10 41.67 3.67
406 407 0.461870 GGCATCGGCTGTATGTCACA 60.462 55.000 0.00 0.00 40.87 3.58
435 436 1.538047 GCAAGTTCTTGGGAGCATCA 58.462 50.000 13.35 0.00 36.25 3.07
447 448 2.648059 GGAGCATCAGCCATAACTGTT 58.352 47.619 0.00 0.00 43.56 3.16
465 466 7.775729 AACTGTTAAATTTTTATCAGACGCG 57.224 32.000 20.19 3.53 40.42 6.01
471 472 1.552226 TTTTATCAGACGCGGCTACG 58.448 50.000 17.67 2.52 44.63 3.51
502 503 1.146263 GCGATCCGGGAAGGTCAAT 59.854 57.895 0.00 0.00 41.99 2.57
627 628 8.395633 GCTATTTTACATGAAATTACAGGTCGT 58.604 33.333 0.00 0.00 36.27 4.34
630 631 6.730960 TTACATGAAATTACAGGTCGTTCC 57.269 37.500 0.00 0.00 36.27 3.62
632 633 5.253330 ACATGAAATTACAGGTCGTTCCAT 58.747 37.500 0.00 0.00 39.02 3.41
696 697 3.372206 CGAATTTCGAGCCTCACAATCTT 59.628 43.478 13.45 0.00 43.74 2.40
721 722 5.348724 GCTAAGTTTGCTTTAAATCTTGGGC 59.651 40.000 1.79 0.00 36.22 5.36
733 734 1.271856 TCTTGGGCTTGGACGTCATA 58.728 50.000 18.91 2.38 0.00 2.15
760 761 0.620556 GGGCCAACCTGAGAATCTGA 59.379 55.000 4.39 0.00 35.94 3.27
807 810 6.205464 TGGATTCAATAAAGATTGGCGAGATC 59.795 38.462 0.00 0.00 42.45 2.75
910 917 4.699522 GCCTCCCACCCACGTCAC 62.700 72.222 0.00 0.00 0.00 3.67
939 952 2.125753 CACGACTGCAGCTCCCTC 60.126 66.667 15.27 1.97 0.00 4.30
940 953 3.386237 ACGACTGCAGCTCCCTCC 61.386 66.667 15.27 0.00 0.00 4.30
941 954 4.154347 CGACTGCAGCTCCCTCCC 62.154 72.222 15.27 0.00 0.00 4.30
942 955 2.686835 GACTGCAGCTCCCTCCCT 60.687 66.667 15.27 0.00 0.00 4.20
943 956 2.686835 ACTGCAGCTCCCTCCCTC 60.687 66.667 15.27 0.00 0.00 4.30
944 957 3.478274 CTGCAGCTCCCTCCCTCC 61.478 72.222 0.00 0.00 0.00 4.30
946 959 4.814041 GCAGCTCCCTCCCTCCCT 62.814 72.222 0.00 0.00 0.00 4.20
1179 1192 1.000107 GTACGAGTCCCACCCCTCT 60.000 63.158 0.00 0.00 0.00 3.69
1180 1193 0.614134 GTACGAGTCCCACCCCTCTT 60.614 60.000 0.00 0.00 0.00 2.85
1188 1201 3.717294 CACCCCTCTTCCCACCCG 61.717 72.222 0.00 0.00 0.00 5.28
1192 1205 3.400054 CCTCTTCCCACCCGACCC 61.400 72.222 0.00 0.00 0.00 4.46
1264 1282 5.176407 ACAGATAGATTCTACTGTGCGAC 57.824 43.478 19.35 0.00 41.16 5.19
1270 1288 2.273370 TTCTACTGTGCGACGGATTC 57.727 50.000 0.00 0.00 0.00 2.52
1283 1301 5.205565 GCGACGGATTCTTTTCATTTATCC 58.794 41.667 0.00 0.00 33.09 2.59
1325 1343 2.883574 TCAAGTTGATTACGCGGTAGG 58.116 47.619 12.47 0.00 0.00 3.18
1329 1347 3.256558 AGTTGATTACGCGGTAGGTTTC 58.743 45.455 12.47 0.00 0.00 2.78
1358 1379 1.290639 GGAGCAGCGGTATAGAGGC 59.709 63.158 0.00 0.00 0.00 4.70
1359 1380 1.182385 GGAGCAGCGGTATAGAGGCT 61.182 60.000 0.00 0.00 37.55 4.58
1361 1382 1.182385 AGCAGCGGTATAGAGGCTCC 61.182 60.000 11.71 0.00 34.13 4.70
1510 1531 6.306596 CGATATGACGACAGTAGAATGAATGG 59.693 42.308 0.00 0.00 35.09 3.16
1517 1538 4.589908 ACAGTAGAATGAATGGTGGTTCC 58.410 43.478 0.00 0.00 0.00 3.62
1641 1662 7.615039 AATGGTCTGATGAGATCACTAGATT 57.385 36.000 0.00 0.00 42.33 2.40
1724 1745 1.191489 TTCCAGGACATCACTCGCCA 61.191 55.000 0.00 0.00 0.00 5.69
1765 1786 1.134401 TGATTCGGCTCACAGGATTCC 60.134 52.381 0.00 0.00 0.00 3.01
1795 1816 7.360575 TGCTTTTCTACCGACTTCTTTATTC 57.639 36.000 0.00 0.00 0.00 1.75
1796 1817 6.090358 TGCTTTTCTACCGACTTCTTTATTCG 59.910 38.462 0.00 0.00 0.00 3.34
1883 1906 7.775053 TGACAGAGCAAATTAAATAAAGGGT 57.225 32.000 0.00 0.00 0.00 4.34
2124 2147 8.761575 AATTTACTTTGATTTGTGCTACATGG 57.238 30.769 0.00 0.00 0.00 3.66
2140 2163 6.164176 GCTACATGGTGAACAGTACTTAGTT 58.836 40.000 0.00 0.00 0.00 2.24
2152 2175 5.419155 ACAGTACTTAGTTCTGCAGCTGATA 59.581 40.000 20.43 4.20 34.96 2.15
2199 2222 3.684693 GCTTGGCCAGCTTTTGAAA 57.315 47.368 16.95 0.00 46.27 2.69
2200 2223 1.220529 GCTTGGCCAGCTTTTGAAAC 58.779 50.000 16.95 0.00 46.27 2.78
2201 2224 1.473080 GCTTGGCCAGCTTTTGAAACA 60.473 47.619 16.95 0.00 46.27 2.83
2204 2227 3.340814 TGGCCAGCTTTTGAAACAAAA 57.659 38.095 0.00 8.89 0.00 2.44
2207 2230 5.431765 TGGCCAGCTTTTGAAACAAAATTA 58.568 33.333 0.00 0.00 0.00 1.40
2208 2231 5.295540 TGGCCAGCTTTTGAAACAAAATTAC 59.704 36.000 0.00 4.25 0.00 1.89
2209 2232 5.527214 GGCCAGCTTTTGAAACAAAATTACT 59.473 36.000 0.00 6.02 0.00 2.24
2211 2234 6.562086 GCCAGCTTTTGAAACAAAATTACTCG 60.562 38.462 9.52 3.81 0.00 4.18
2265 2293 1.183676 AGTCCTAGTCCAACCGCGTT 61.184 55.000 4.92 0.00 0.00 4.84
2266 2294 1.012486 GTCCTAGTCCAACCGCGTTG 61.012 60.000 4.92 9.81 42.49 4.10
2267 2295 1.180456 TCCTAGTCCAACCGCGTTGA 61.180 55.000 18.69 2.15 45.28 3.18
2268 2296 0.320073 CCTAGTCCAACCGCGTTGAA 60.320 55.000 18.69 0.34 45.28 2.69
2269 2297 1.674817 CCTAGTCCAACCGCGTTGAAT 60.675 52.381 18.69 6.36 45.28 2.57
2270 2298 1.393539 CTAGTCCAACCGCGTTGAATG 59.606 52.381 18.69 5.25 45.28 2.67
2271 2299 1.442017 GTCCAACCGCGTTGAATGC 60.442 57.895 18.69 0.00 45.28 3.56
2272 2300 2.126502 CCAACCGCGTTGAATGCC 60.127 61.111 18.69 0.00 45.28 4.40
2280 2308 0.026803 GCGTTGAATGCCGAGCTTAG 59.973 55.000 0.00 0.00 0.00 2.18
2376 2404 6.831353 CCATATGGGTACACCTTACATGAAAA 59.169 38.462 14.52 0.00 41.11 2.29
2380 2408 4.401202 GGGTACACCTTACATGAAAATGGG 59.599 45.833 0.00 0.00 35.85 4.00
2506 2534 9.358872 GTAAATCTTGATTGGAAAACTGGAATC 57.641 33.333 0.00 0.00 0.00 2.52
2587 2615 1.812571 GCCAAACAACCGATCAGTCAT 59.187 47.619 0.00 0.00 0.00 3.06
2596 2624 1.202348 CCGATCAGTCATGTCTCGCTT 60.202 52.381 0.00 0.00 33.95 4.68
2606 2634 1.446966 GTCTCGCTTGGCTCCAGTC 60.447 63.158 0.00 0.00 0.00 3.51
2776 2804 7.936496 TTGACATAAGTTTCAGGCAATATCA 57.064 32.000 0.00 0.00 0.00 2.15
2791 2819 5.063817 GGCAATATCATTTGTTGCTTGAACC 59.936 40.000 8.90 0.00 45.56 3.62
2792 2820 5.638657 GCAATATCATTTGTTGCTTGAACCA 59.361 36.000 2.36 0.00 43.56 3.67
2832 2860 1.885887 GCTTTTGGTGTATGACTGGCA 59.114 47.619 0.00 0.00 0.00 4.92
2903 2940 3.609103 AAATGTGTCGTGCAAGACTTC 57.391 42.857 28.76 21.86 41.47 3.01
2906 2943 2.739292 TGTGTCGTGCAAGACTTCTAC 58.261 47.619 28.76 20.09 41.47 2.59
3066 3103 1.109323 AGTTGTGGCACCTTCAAGGC 61.109 55.000 16.26 0.00 39.63 4.35
3102 3139 4.803452 AGAAGCTCATCTAGACTAAGCCT 58.197 43.478 15.58 6.48 33.43 4.58
3104 3141 3.909732 AGCTCATCTAGACTAAGCCTGT 58.090 45.455 15.58 0.26 33.43 4.00
3139 3176 2.664402 AGCCCAGATTGTTGTTCACT 57.336 45.000 0.00 0.00 0.00 3.41
3181 3218 6.152661 AGAGTTGTTTCTTCATGTTTGGTTCA 59.847 34.615 0.00 0.00 0.00 3.18
3207 3244 1.063327 CACGCTAGTGGAGAGCTCG 59.937 63.158 8.37 0.00 44.34 5.03
3208 3245 2.025441 CGCTAGTGGAGAGCTCGC 59.975 66.667 9.23 9.23 37.81 5.03
3223 3260 1.191944 CTCGCAGCATGTACTGTACG 58.808 55.000 12.87 1.47 39.96 3.67
3261 3298 7.500892 TGATCCATTTTAGCCGTGTTGTATTAT 59.499 33.333 0.00 0.00 0.00 1.28
3262 3299 7.022055 TCCATTTTAGCCGTGTTGTATTATG 57.978 36.000 0.00 0.00 0.00 1.90
3263 3300 6.824196 TCCATTTTAGCCGTGTTGTATTATGA 59.176 34.615 0.00 0.00 0.00 2.15
3264 3301 7.500892 TCCATTTTAGCCGTGTTGTATTATGAT 59.499 33.333 0.00 0.00 0.00 2.45
3265 3302 7.803189 CCATTTTAGCCGTGTTGTATTATGATC 59.197 37.037 0.00 0.00 0.00 2.92
3311 3349 5.200483 TCACTTTGGTCTTGTCCATCTTTT 58.800 37.500 0.00 0.00 37.33 2.27
3312 3350 5.067674 TCACTTTGGTCTTGTCCATCTTTTG 59.932 40.000 0.00 0.00 37.33 2.44
3313 3351 4.956075 ACTTTGGTCTTGTCCATCTTTTGT 59.044 37.500 0.00 0.00 37.33 2.83
3314 3352 6.039270 CACTTTGGTCTTGTCCATCTTTTGTA 59.961 38.462 0.00 0.00 37.33 2.41
3315 3353 6.039382 ACTTTGGTCTTGTCCATCTTTTGTAC 59.961 38.462 0.00 0.00 37.33 2.90
3413 3451 4.082354 AGCGTACTGGTACCTCTTTAACAG 60.082 45.833 14.36 1.53 41.82 3.16
3415 3453 5.393896 GCGTACTGGTACCTCTTTAACAGAT 60.394 44.000 14.36 0.00 38.86 2.90
3464 3502 1.741770 CCCACTAGTGCAACCGAGC 60.742 63.158 17.86 0.00 37.80 5.03
3484 3522 1.972752 GCCGGCCGAAAAGGGTAAA 60.973 57.895 30.73 0.00 41.48 2.01
3486 3524 1.588824 CCGGCCGAAAAGGGTAAACC 61.589 60.000 30.73 0.00 41.48 3.27
3513 3552 0.517316 CCGCGGAACAGAAAAGGAAG 59.483 55.000 24.07 0.00 0.00 3.46
3517 3556 1.202891 CGGAACAGAAAAGGAAGGGGT 60.203 52.381 0.00 0.00 0.00 4.95
3526 3565 1.231963 AAGGAAGGGGTCACCAAACT 58.768 50.000 0.00 0.00 43.89 2.66
3527 3566 0.478507 AGGAAGGGGTCACCAAACTG 59.521 55.000 0.00 0.00 43.89 3.16
3528 3567 0.476771 GGAAGGGGTCACCAAACTGA 59.523 55.000 0.00 0.00 43.89 3.41
3529 3568 1.605753 GAAGGGGTCACCAAACTGAC 58.394 55.000 0.00 0.00 43.89 3.51
3535 3574 1.068474 GTCACCAAACTGACCGATCG 58.932 55.000 8.51 8.51 35.44 3.69
3536 3575 0.963225 TCACCAAACTGACCGATCGA 59.037 50.000 18.66 0.00 0.00 3.59
3537 3576 1.067846 TCACCAAACTGACCGATCGAG 60.068 52.381 18.66 8.84 0.00 4.04
3538 3577 0.389948 ACCAAACTGACCGATCGAGC 60.390 55.000 18.66 8.49 0.00 5.03
3539 3578 1.413767 CCAAACTGACCGATCGAGCG 61.414 60.000 17.57 17.57 0.00 5.03
3546 3585 3.822192 CCGATCGAGCGGTCACCA 61.822 66.667 32.79 0.00 46.07 4.17
3547 3586 2.180769 CGATCGAGCGGTCACCAA 59.819 61.111 16.65 0.00 0.00 3.67
3548 3587 1.445410 CGATCGAGCGGTCACCAAA 60.445 57.895 16.65 0.00 0.00 3.28
3549 3588 1.683790 CGATCGAGCGGTCACCAAAC 61.684 60.000 16.65 0.00 0.00 2.93
3579 3618 2.700773 GCGGCCACCAACAGAATCC 61.701 63.158 2.24 0.00 0.00 3.01
3653 3700 3.345414 CTGCCTTCTTCTTCTTCTGCAT 58.655 45.455 0.00 0.00 0.00 3.96
3656 3703 3.345414 CCTTCTTCTTCTTCTGCATGCT 58.655 45.455 20.33 0.00 0.00 3.79
3713 3760 2.037367 TCCTCCTACACAGCCGCT 59.963 61.111 0.00 0.00 0.00 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 0.035881 ACCATATGCTCCTCGCCATG 59.964 55.000 0.00 0.00 38.05 3.66
79 80 2.959507 AACAACCAGTTCTTTGCACC 57.040 45.000 0.00 0.00 34.74 5.01
80 81 3.789224 CGTAAACAACCAGTTCTTTGCAC 59.211 43.478 0.00 0.00 40.26 4.57
274 275 3.371917 CCAATATTCCTTGCCCAGACTGA 60.372 47.826 3.32 0.00 0.00 3.41
280 281 1.014804 ACCCCAATATTCCTTGCCCA 58.985 50.000 0.00 0.00 0.00 5.36
319 320 8.798975 ATTTTTACATATCCCTCTAGTGGAGA 57.201 34.615 12.54 6.63 44.45 3.71
333 334 7.512297 CCGCGTCCGTATTTATTTTTACATAT 58.488 34.615 4.92 0.00 0.00 1.78
361 362 0.312416 AACGAGCCTGCTATCGCTAG 59.688 55.000 0.00 0.00 42.61 3.42
405 406 1.826385 AGAACTTGCCTTCCCGATTG 58.174 50.000 0.00 0.00 0.00 2.67
406 407 2.162681 CAAGAACTTGCCTTCCCGATT 58.837 47.619 1.60 0.00 33.45 3.34
447 448 5.276489 CGTAGCCGCGTCTGATAAAAATTTA 60.276 40.000 4.92 0.00 0.00 1.40
465 466 4.452733 AGCGCCTCCAACGTAGCC 62.453 66.667 2.29 0.00 0.00 3.93
480 481 4.918201 CCTTCCCGGATCGCCAGC 62.918 72.222 0.73 0.00 33.16 4.85
502 503 6.840527 TGACATATAAATCCTCTGCCAATGA 58.159 36.000 0.00 0.00 0.00 2.57
620 621 4.829064 TTGAAAAAGATGGAACGACCTG 57.171 40.909 0.00 0.00 39.86 4.00
685 686 4.217118 AGCAAACTTAGCAAGATTGTGAGG 59.783 41.667 15.11 0.00 41.64 3.86
696 697 6.454795 CCCAAGATTTAAAGCAAACTTAGCA 58.545 36.000 6.19 0.00 34.05 3.49
721 722 3.128589 CCCAACCAAATATGACGTCCAAG 59.871 47.826 14.12 0.00 0.00 3.61
752 753 9.793259 TGTTTACAGGTAAGAAATTCAGATTCT 57.207 29.630 0.00 0.00 38.75 2.40
887 890 3.940480 TGGGTGGGAGGCTCCTGA 61.940 66.667 31.39 16.72 36.57 3.86
939 952 3.744155 GGCTTTGGGGAGGGAGGG 61.744 72.222 0.00 0.00 0.00 4.30
940 953 3.744155 GGGCTTTGGGGAGGGAGG 61.744 72.222 0.00 0.00 0.00 4.30
941 954 3.744155 GGGGCTTTGGGGAGGGAG 61.744 72.222 0.00 0.00 0.00 4.30
944 957 4.115199 CTCGGGGCTTTGGGGAGG 62.115 72.222 0.00 0.00 0.00 4.30
945 958 4.803908 GCTCGGGGCTTTGGGGAG 62.804 72.222 0.00 0.00 38.06 4.30
1192 1205 0.174845 TGGATTACCTTGACGGCGAG 59.825 55.000 16.62 0.00 37.04 5.03
1264 1282 6.942532 TCCAGGATAAATGAAAAGAATCCG 57.057 37.500 0.00 0.00 40.87 4.18
1283 1301 4.505313 TTCGTCCAGATTATCGATCCAG 57.495 45.455 0.00 0.00 35.21 3.86
1358 1379 3.373565 GCCCCAGCAAAACCGGAG 61.374 66.667 9.46 0.00 39.53 4.63
1359 1380 4.986708 GGCCCCAGCAAAACCGGA 62.987 66.667 9.46 0.00 42.56 5.14
1361 1382 3.683937 CAGGCCCCAGCAAAACCG 61.684 66.667 0.00 0.00 42.56 4.44
1724 1745 6.294361 TCAGCCGGTTTATATATATGCTGT 57.706 37.500 20.98 0.00 43.95 4.40
1765 1786 4.663636 AGTCGGTAGAAAAGCAAATTCG 57.336 40.909 0.00 0.00 32.04 3.34
1795 1816 1.484653 TCACACCCATGGGATCTTACG 59.515 52.381 38.07 16.71 31.41 3.18
1796 1817 2.158755 CCTCACACCCATGGGATCTTAC 60.159 54.545 38.07 0.00 37.71 2.34
1913 1936 9.935682 ACATAAAGTAGCATCAAATTAATGTCG 57.064 29.630 0.00 0.00 0.00 4.35
1993 2016 6.826741 CCATGGATGCAATATATCTGATCACA 59.173 38.462 5.56 0.00 0.00 3.58
2124 2147 4.150804 GCTGCAGAACTAAGTACTGTTCAC 59.849 45.833 20.43 15.55 43.38 3.18
2140 2163 6.238566 GCTAACATTCATTTATCAGCTGCAGA 60.239 38.462 20.43 0.00 0.00 4.26
2197 2220 9.581099 AAATTGTCTTGACGAGTAATTTTGTTT 57.419 25.926 11.40 0.00 33.60 2.83
2198 2221 9.019764 CAAATTGTCTTGACGAGTAATTTTGTT 57.980 29.630 13.21 0.00 34.34 2.83
2199 2222 7.167468 GCAAATTGTCTTGACGAGTAATTTTGT 59.833 33.333 13.21 0.00 34.34 2.83
2200 2223 7.167302 TGCAAATTGTCTTGACGAGTAATTTTG 59.833 33.333 13.21 8.52 34.34 2.44
2201 2224 7.199766 TGCAAATTGTCTTGACGAGTAATTTT 58.800 30.769 13.21 0.00 34.34 1.82
2204 2227 5.470098 ACTGCAAATTGTCTTGACGAGTAAT 59.530 36.000 0.00 0.00 0.00 1.89
2207 2230 3.206150 ACTGCAAATTGTCTTGACGAGT 58.794 40.909 0.00 0.00 0.00 4.18
2208 2231 3.885484 ACTGCAAATTGTCTTGACGAG 57.115 42.857 0.00 0.00 0.00 4.18
2209 2232 4.123506 TGTACTGCAAATTGTCTTGACGA 58.876 39.130 0.00 0.00 0.00 4.20
2211 2234 7.535258 CACTATTGTACTGCAAATTGTCTTGAC 59.465 37.037 0.00 0.00 40.91 3.18
2265 2293 3.281727 AATTCCTAAGCTCGGCATTCA 57.718 42.857 0.00 0.00 0.00 2.57
2266 2294 3.793465 GCAAATTCCTAAGCTCGGCATTC 60.793 47.826 0.00 0.00 0.00 2.67
2267 2295 2.099756 GCAAATTCCTAAGCTCGGCATT 59.900 45.455 0.00 0.00 0.00 3.56
2268 2296 1.678101 GCAAATTCCTAAGCTCGGCAT 59.322 47.619 0.00 0.00 0.00 4.40
2269 2297 1.094785 GCAAATTCCTAAGCTCGGCA 58.905 50.000 0.00 0.00 0.00 5.69
2270 2298 1.383523 AGCAAATTCCTAAGCTCGGC 58.616 50.000 0.00 0.00 30.05 5.54
2271 2299 3.009723 TCAAGCAAATTCCTAAGCTCGG 58.990 45.455 0.00 0.00 36.07 4.63
2272 2300 4.889832 ATCAAGCAAATTCCTAAGCTCG 57.110 40.909 0.00 0.00 36.07 5.03
2280 2308 4.563061 AGAGTGCAAATCAAGCAAATTCC 58.437 39.130 0.00 0.00 44.64 3.01
2376 2404 4.380843 TGACCAACTGTAACATTCCCAT 57.619 40.909 0.00 0.00 0.00 4.00
2380 2408 5.982516 TGCAAATTGACCAACTGTAACATTC 59.017 36.000 0.00 0.00 0.00 2.67
2506 2534 1.736696 GCATCCCAATCCTTTGTTGCG 60.737 52.381 0.00 0.00 0.00 4.85
2574 2602 1.469940 GCGAGACATGACTGATCGGTT 60.470 52.381 8.99 0.00 36.40 4.44
2587 2615 2.159819 GACTGGAGCCAAGCGAGACA 62.160 60.000 0.00 0.00 0.00 3.41
2596 2624 2.420547 GCAATACATGAGACTGGAGCCA 60.421 50.000 0.00 0.00 0.00 4.75
2606 2634 8.496751 CAATTAGAGACATGAGCAATACATGAG 58.503 37.037 13.54 0.00 45.22 2.90
2654 2682 0.815734 TCTAGTTCTACGCCCTGCAC 59.184 55.000 0.00 0.00 0.00 4.57
2776 2804 2.435437 AGCCTTGGTTCAAGCAACAAAT 59.565 40.909 0.00 0.00 39.85 2.32
2832 2860 5.497474 AGTGTTAACCATTTTCTAGCGGAT 58.503 37.500 2.48 0.00 0.00 4.18
2903 2940 3.776656 GCTGTACCGCCAACGTAG 58.223 61.111 0.00 0.00 37.70 3.51
3066 3103 6.878389 AGATGAGCTTCTTTTTCCTGAAGTAG 59.122 38.462 0.00 0.00 41.05 2.57
3102 3139 1.202020 GCTAATGCGCAACATCGAACA 60.202 47.619 17.11 0.00 38.34 3.18
3104 3141 0.376852 GGCTAATGCGCAACATCGAA 59.623 50.000 17.11 0.00 38.34 3.71
3154 3191 7.027778 ACCAAACATGAAGAAACAACTCTAC 57.972 36.000 0.00 0.00 0.00 2.59
3158 3195 6.279513 TGAACCAAACATGAAGAAACAACT 57.720 33.333 0.00 0.00 0.00 3.16
3181 3218 3.997021 CTCTCCACTAGCGTGAAATGTTT 59.003 43.478 0.00 0.00 43.97 2.83
3186 3223 1.202582 GAGCTCTCCACTAGCGTGAAA 59.797 52.381 6.43 0.00 44.87 2.69
3203 3240 0.924090 GTACAGTACATGCTGCGAGC 59.076 55.000 5.79 1.70 42.82 5.03
3207 3244 1.075542 TTGCGTACAGTACATGCTGC 58.924 50.000 11.37 6.12 39.96 5.25
3208 3245 2.672874 ACATTGCGTACAGTACATGCTG 59.327 45.455 11.37 5.25 41.92 4.41
3223 3260 7.042523 GGCTAAAATGGATCATTGTTACATTGC 60.043 37.037 6.04 5.73 34.04 3.56
3261 3298 3.071023 AGAAAGAACACTCCAACCGATCA 59.929 43.478 0.00 0.00 0.00 2.92
3262 3299 3.665190 AGAAAGAACACTCCAACCGATC 58.335 45.455 0.00 0.00 0.00 3.69
3263 3300 3.771577 AGAAAGAACACTCCAACCGAT 57.228 42.857 0.00 0.00 0.00 4.18
3264 3301 4.527038 AGATAGAAAGAACACTCCAACCGA 59.473 41.667 0.00 0.00 0.00 4.69
3265 3302 4.822026 AGATAGAAAGAACACTCCAACCG 58.178 43.478 0.00 0.00 0.00 4.44
3311 3349 6.954487 AGGACGTATCAATGATACAGTACA 57.046 37.500 26.93 0.00 43.41 2.90
3312 3350 6.862090 GGAAGGACGTATCAATGATACAGTAC 59.138 42.308 26.93 24.01 43.41 2.73
3313 3351 6.776116 AGGAAGGACGTATCAATGATACAGTA 59.224 38.462 26.93 0.00 43.41 2.74
3314 3352 5.598830 AGGAAGGACGTATCAATGATACAGT 59.401 40.000 26.93 23.97 43.41 3.55
3315 3353 6.015856 AGAGGAAGGACGTATCAATGATACAG 60.016 42.308 26.93 21.67 43.41 2.74
3330 3368 2.035321 GGTCATCATCGAGAGGAAGGAC 59.965 54.545 11.71 11.71 39.01 3.85
3362 3400 0.307760 CGCGGCTTACATTCCAATCC 59.692 55.000 0.00 0.00 0.00 3.01
3413 3451 2.541178 CCACTAGACGCGTCCTACAATC 60.541 54.545 34.08 9.03 0.00 2.67
3415 3453 0.806868 CCACTAGACGCGTCCTACAA 59.193 55.000 34.08 14.54 0.00 2.41
3440 3478 3.899981 TTGCACTAGTGGGCAGCCG 62.900 63.158 23.95 0.00 41.68 5.52
3442 3480 2.335712 GGTTGCACTAGTGGGCAGC 61.336 63.158 23.95 17.40 41.68 5.25
3480 3518 2.045634 GCGGGGGACAGGGTTTAC 60.046 66.667 0.00 0.00 0.00 2.01
3499 3538 2.885266 GTGACCCCTTCCTTTTCTGTTC 59.115 50.000 0.00 0.00 0.00 3.18
3517 3556 0.963225 TCGATCGGTCAGTTTGGTGA 59.037 50.000 16.41 0.00 0.00 4.02
3530 3569 1.445410 TTTGGTGACCGCTCGATCG 60.445 57.895 9.36 9.36 0.00 3.69
3531 3570 1.359459 GGTTTGGTGACCGCTCGATC 61.359 60.000 0.00 0.00 0.00 3.69
3532 3571 1.375523 GGTTTGGTGACCGCTCGAT 60.376 57.895 0.00 0.00 0.00 3.59
3533 3572 2.029964 GGTTTGGTGACCGCTCGA 59.970 61.111 0.00 0.00 0.00 4.04
3540 3579 1.349259 CGATCGGTCGGTTTGGTGAC 61.349 60.000 11.03 0.00 44.00 3.67
3541 3580 1.080366 CGATCGGTCGGTTTGGTGA 60.080 57.895 11.03 0.00 44.00 4.02
3542 3581 3.470267 CGATCGGTCGGTTTGGTG 58.530 61.111 11.03 0.00 44.00 4.17
3626 3673 1.301677 GAAGAAGAAGGCAGCGTGGG 61.302 60.000 0.00 0.00 0.00 4.61
3629 3676 1.346068 AGAAGAAGAAGAAGGCAGCGT 59.654 47.619 0.00 0.00 0.00 5.07
3653 3700 3.713003 TCTGTTGGATCTCCTTCTAGCA 58.287 45.455 0.00 0.00 36.82 3.49
3656 3703 4.202161 GCGATTCTGTTGGATCTCCTTCTA 60.202 45.833 0.00 0.00 36.82 2.10
4050 4097 4.575885 AGTTGCACAGTAATTCGTGGTAT 58.424 39.130 0.00 0.00 33.62 2.73


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

AutoCloner maintained by Alex Coulton.