Multiple sequence alignment - TraesCS4A01G386400

Loading Multiple Alignment...

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 TraesCS4A01G386400 chr4A 100.000 2909 0 0 1 2909 663985138 663988046 0.000000e+00 5373.0
1 TraesCS4A01G386400 chr4A 80.488 861 89 34 999 1849 664153150 664153941 1.160000e-163 586.0
2 TraesCS4A01G386400 chr4A 92.638 163 11 1 1 162 598291504 598291342 1.740000e-57 233.0
3 TraesCS4A01G386400 chr7A 90.766 888 66 8 471 1351 52278373 52279251 0.000000e+00 1171.0
4 TraesCS4A01G386400 chr7A 91.274 848 33 11 1429 2257 52279264 52280089 0.000000e+00 1118.0
5 TraesCS4A01G386400 chr7A 85.200 750 75 10 999 1742 52386913 52387632 0.000000e+00 737.0
6 TraesCS4A01G386400 chr7A 81.871 513 61 16 1 482 52277820 52278331 1.260000e-108 403.0
7 TraesCS4A01G386400 chr7A 80.591 541 74 23 1778 2306 52387720 52388241 3.520000e-104 388.0
8 TraesCS4A01G386400 chr7A 77.333 750 100 34 839 1566 50389280 50388579 2.120000e-101 379.0
9 TraesCS4A01G386400 chr7A 91.429 175 14 1 1569 1742 50388520 50388346 3.750000e-59 239.0
10 TraesCS4A01G386400 chr7D 89.509 896 65 13 471 1351 49380636 49381517 0.000000e+00 1107.0
11 TraesCS4A01G386400 chr7D 93.223 546 20 8 1805 2342 49381981 49382517 0.000000e+00 787.0
12 TraesCS4A01G386400 chr7D 83.988 687 70 17 1569 2235 47763350 47762684 8.850000e-175 623.0
13 TraesCS4A01G386400 chr7D 84.828 580 76 7 2341 2909 631182615 631183193 9.040000e-160 573.0
14 TraesCS4A01G386400 chr7D 88.089 403 26 5 1433 1819 49635923 49636319 2.640000e-125 459.0
15 TraesCS4A01G386400 chr7D 86.423 383 29 6 1431 1806 49381533 49381899 5.840000e-107 398.0
16 TraesCS4A01G386400 chr7D 89.444 180 16 3 1 177 269892743 269892564 1.050000e-54 224.0
17 TraesCS4A01G386400 chr7D 87.000 200 21 3 1845 2041 49636515 49636712 1.360000e-53 220.0
18 TraesCS4A01G386400 chr2B 94.271 576 24 6 2341 2907 571513438 571512863 0.000000e+00 872.0
19 TraesCS4A01G386400 chr2B 92.683 164 11 1 1 163 177780398 177780235 4.850000e-58 235.0
20 TraesCS4A01G386400 chr1D 88.256 579 50 11 2341 2909 462360164 462360734 0.000000e+00 676.0
21 TraesCS4A01G386400 chr6A 84.629 579 78 8 2341 2909 13045631 13045054 1.510000e-157 566.0
22 TraesCS4A01G386400 chr2A 84.602 578 78 7 2342 2909 133503917 133503341 5.440000e-157 564.0
23 TraesCS4A01G386400 chr2A 84.859 568 77 6 2339 2897 750110739 750111306 5.440000e-157 564.0
24 TraesCS4A01G386400 chr4B 84.256 578 78 12 2343 2909 660293451 660292876 4.240000e-153 551.0
25 TraesCS4A01G386400 chr4B 89.444 180 16 3 1 177 389088733 389088554 1.050000e-54 224.0
26 TraesCS4A01G386400 chr1A 85.038 528 76 3 2342 2868 482276900 482276375 4.270000e-148 534.0
27 TraesCS4A01G386400 chr6B 83.419 585 82 11 2338 2909 101464243 101464825 1.990000e-146 529.0
28 TraesCS4A01G386400 chr5D 90.000 180 15 3 1 177 175606240 175606061 2.250000e-56 230.0
29 TraesCS4A01G386400 chr5D 91.463 164 13 1 1 163 355110111 355110274 1.050000e-54 224.0
30 TraesCS4A01G386400 chr5D 89.381 113 12 0 1000 1112 329796631 329796519 3.020000e-30 143.0
31 TraesCS4A01G386400 chr3D 92.073 164 12 1 1 163 417979603 417979766 2.250000e-56 230.0
32 TraesCS4A01G386400 chr3D 89.444 180 16 3 1 177 433974750 433974571 1.050000e-54 224.0
33 TraesCS4A01G386400 chr2D 89.444 180 16 3 1 177 466989990 466989811 1.050000e-54 224.0
34 TraesCS4A01G386400 chr5A 86.614 127 15 2 1000 1126 426903901 426904025 3.910000e-29 139.0
35 TraesCS4A01G386400 chr5B 91.398 93 8 0 1000 1092 382909954 382909862 8.460000e-26 128.0
36 TraesCS4A01G386400 chr5B 100.000 33 0 0 1672 1704 382909497 382909465 8.700000e-06 62.1


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 TraesCS4A01G386400 chr4A 663985138 663988046 2908 False 5373.000000 5373 100.000000 1 2909 1 chr4A.!!$F1 2908
1 TraesCS4A01G386400 chr4A 664153150 664153941 791 False 586.000000 586 80.488000 999 1849 1 chr4A.!!$F2 850
2 TraesCS4A01G386400 chr7A 52277820 52280089 2269 False 897.333333 1171 87.970333 1 2257 3 chr7A.!!$F1 2256
3 TraesCS4A01G386400 chr7A 52386913 52388241 1328 False 562.500000 737 82.895500 999 2306 2 chr7A.!!$F2 1307
4 TraesCS4A01G386400 chr7A 50388346 50389280 934 True 309.000000 379 84.381000 839 1742 2 chr7A.!!$R1 903
5 TraesCS4A01G386400 chr7D 49380636 49382517 1881 False 764.000000 1107 89.718333 471 2342 3 chr7D.!!$F2 1871
6 TraesCS4A01G386400 chr7D 47762684 47763350 666 True 623.000000 623 83.988000 1569 2235 1 chr7D.!!$R1 666
7 TraesCS4A01G386400 chr7D 631182615 631183193 578 False 573.000000 573 84.828000 2341 2909 1 chr7D.!!$F1 568
8 TraesCS4A01G386400 chr7D 49635923 49636712 789 False 339.500000 459 87.544500 1433 2041 2 chr7D.!!$F3 608
9 TraesCS4A01G386400 chr2B 571512863 571513438 575 True 872.000000 872 94.271000 2341 2907 1 chr2B.!!$R2 566
10 TraesCS4A01G386400 chr1D 462360164 462360734 570 False 676.000000 676 88.256000 2341 2909 1 chr1D.!!$F1 568
11 TraesCS4A01G386400 chr6A 13045054 13045631 577 True 566.000000 566 84.629000 2341 2909 1 chr6A.!!$R1 568
12 TraesCS4A01G386400 chr2A 133503341 133503917 576 True 564.000000 564 84.602000 2342 2909 1 chr2A.!!$R1 567
13 TraesCS4A01G386400 chr2A 750110739 750111306 567 False 564.000000 564 84.859000 2339 2897 1 chr2A.!!$F1 558
14 TraesCS4A01G386400 chr4B 660292876 660293451 575 True 551.000000 551 84.256000 2343 2909 1 chr4B.!!$R2 566
15 TraesCS4A01G386400 chr1A 482276375 482276900 525 True 534.000000 534 85.038000 2342 2868 1 chr1A.!!$R1 526
16 TraesCS4A01G386400 chr6B 101464243 101464825 582 False 529.000000 529 83.419000 2338 2909 1 chr6B.!!$F1 571


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
717 822 0.31812 CATGGTGGGCACAAAACCTC 59.682 55.0 0.0 0.0 34.9 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1969 2505 0.534203 ACGAACACACGGCCTCAAAT 60.534 50.0 0.0 0.0 37.61 2.32 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
32 33 4.154942 AGACTCATTTTGCATTGGGAAGT 58.845 39.130 0.00 0.00 0.00 3.01
33 34 4.021719 AGACTCATTTTGCATTGGGAAGTG 60.022 41.667 0.00 0.00 0.00 3.16
48 49 3.877508 GGGAAGTGCTATGTGATGGTAAC 59.122 47.826 0.00 0.00 0.00 2.50
107 108 7.878477 AACTACTTGCAACATCATCATTTTG 57.122 32.000 0.00 0.00 0.00 2.44
108 109 6.392354 ACTACTTGCAACATCATCATTTTGG 58.608 36.000 0.00 0.00 0.00 3.28
113 114 7.879160 ACTTGCAACATCATCATTTTGGTTTAT 59.121 29.630 0.00 0.00 0.00 1.40
116 117 7.117956 TGCAACATCATCATTTTGGTTTATGTG 59.882 33.333 0.00 0.00 0.00 3.21
155 159 5.598830 ACCTATGTTACTCCACTATGACCAG 59.401 44.000 0.00 0.00 0.00 4.00
162 166 1.764723 TCCACTATGACCAGCCTCATG 59.235 52.381 0.00 0.00 32.86 3.07
178 182 1.528824 ATGGCCGGACATGAGGAAG 59.471 57.895 25.71 0.00 0.00 3.46
190 219 8.537016 CCGGACATGAGGAAGGTATTAATTATA 58.463 37.037 0.00 0.00 0.00 0.98
205 234 9.654663 GTATTAATTATACCTCAAGAGCCGAAT 57.345 33.333 0.00 0.00 34.25 3.34
218 247 1.366111 GCCGAATGAGCACCGCTTAA 61.366 55.000 0.00 0.00 39.88 1.85
223 252 4.518217 CGAATGAGCACCGCTTAATTTAG 58.482 43.478 0.00 0.00 39.88 1.85
230 259 7.049133 TGAGCACCGCTTAATTTAGGTAAATA 58.951 34.615 0.00 0.00 39.88 1.40
265 294 5.642063 CGTTATGTTTATATGGAATCCGCCT 59.358 40.000 0.00 0.00 0.00 5.52
282 311 4.081752 TCCGCCTATGTTTGCATGAATTTT 60.082 37.500 0.00 0.00 36.58 1.82
285 314 7.013750 TCCGCCTATGTTTGCATGAATTTTATA 59.986 33.333 0.00 0.00 36.58 0.98
286 315 7.814107 CCGCCTATGTTTGCATGAATTTTATAT 59.186 33.333 0.00 0.00 36.58 0.86
288 317 9.480053 GCCTATGTTTGCATGAATTTTATATGT 57.520 29.630 0.00 0.00 36.58 2.29
320 349 6.858993 GCAAAAGTGTTTGAAATGTATACGGA 59.141 34.615 3.44 0.00 45.99 4.69
329 358 7.795482 TTGAAATGTATACGGATAAGGTTGG 57.205 36.000 0.00 0.00 0.00 3.77
337 366 1.815408 CGGATAAGGTTGGATGGCAGG 60.815 57.143 0.00 0.00 0.00 4.85
343 372 3.008517 TTGGATGGCAGGCTCCGA 61.009 61.111 0.00 0.00 34.05 4.55
347 376 1.153086 GATGGCAGGCTCCGACATT 60.153 57.895 0.00 0.00 0.00 2.71
349 378 1.913951 ATGGCAGGCTCCGACATTCA 61.914 55.000 0.00 0.00 0.00 2.57
351 380 1.442526 GGCAGGCTCCGACATTCATG 61.443 60.000 0.00 0.00 0.00 3.07
353 382 1.473257 GCAGGCTCCGACATTCATGTA 60.473 52.381 0.00 0.00 41.95 2.29
357 386 1.588404 GCTCCGACATTCATGTACACG 59.412 52.381 0.00 0.00 41.95 4.49
363 392 2.930040 GACATTCATGTACACGGACTGG 59.070 50.000 16.22 5.94 41.95 4.00
375 404 3.827898 GACTGGTCCCGCCTCTCG 61.828 72.222 0.00 0.00 38.35 4.04
393 422 2.588314 GCAGGCAGATGCGAGAGG 60.588 66.667 0.00 0.00 43.26 3.69
400 429 3.118261 AGGCAGATGCGAGAGGAAATTTA 60.118 43.478 0.00 0.00 43.26 1.40
402 431 3.623060 GCAGATGCGAGAGGAAATTTACA 59.377 43.478 2.58 0.00 32.68 2.41
404 433 3.873952 AGATGCGAGAGGAAATTTACAGC 59.126 43.478 2.58 3.47 32.68 4.40
405 434 3.334583 TGCGAGAGGAAATTTACAGCT 57.665 42.857 2.58 0.00 0.00 4.24
410 439 2.027192 AGAGGAAATTTACAGCTCGCCA 60.027 45.455 2.58 0.00 0.00 5.69
412 441 2.684881 AGGAAATTTACAGCTCGCCATG 59.315 45.455 2.58 0.00 0.00 3.66
413 442 2.223572 GGAAATTTACAGCTCGCCATGG 60.224 50.000 7.63 7.63 0.00 3.66
415 444 0.546122 ATTTACAGCTCGCCATGGGA 59.454 50.000 15.13 8.30 0.00 4.37
441 470 3.190874 CCCTTAGAGCAACATCGAAGAC 58.809 50.000 0.00 0.00 42.51 3.01
453 485 2.542020 TCGAAGACCATTGCAACTCA 57.458 45.000 0.00 0.00 0.00 3.41
459 491 0.667993 ACCATTGCAACTCAACACCG 59.332 50.000 0.00 0.00 37.53 4.94
482 514 4.213059 GGAGCTCTCACTTGTTTCTTCTTG 59.787 45.833 14.64 0.00 0.00 3.02
550 642 5.416947 GTCGAGCCTATCCTAAAAGAAACA 58.583 41.667 0.00 0.00 0.00 2.83
564 656 7.925483 CCTAAAAGAAACAAATCAACATCACCA 59.075 33.333 0.00 0.00 0.00 4.17
630 722 2.035832 CGTTTTCCCTCTGCAAACCAAT 59.964 45.455 0.00 0.00 0.00 3.16
671 763 0.324830 AGGACTAGACCCCACTGCTC 60.325 60.000 7.68 0.00 0.00 4.26
672 764 1.668101 GGACTAGACCCCACTGCTCG 61.668 65.000 0.00 0.00 0.00 5.03
673 765 0.680280 GACTAGACCCCACTGCTCGA 60.680 60.000 0.00 0.00 0.00 4.04
676 768 0.680280 TAGACCCCACTGCTCGAGAC 60.680 60.000 18.75 8.32 0.00 3.36
683 775 0.999228 CACTGCTCGAGACACGACAC 60.999 60.000 18.75 0.00 46.45 3.67
697 789 0.729116 CGACACAGATGGTTGATGGC 59.271 55.000 0.00 0.00 0.00 4.40
706 811 2.059786 GGTTGATGGCCATGGTGGG 61.060 63.158 26.56 0.00 38.19 4.61
716 821 1.120795 CCATGGTGGGCACAAAACCT 61.121 55.000 2.57 0.00 34.90 3.50
717 822 0.318120 CATGGTGGGCACAAAACCTC 59.682 55.000 0.00 0.00 34.90 3.85
729 836 1.686587 CAAAACCTCTTCCCAACCCAC 59.313 52.381 0.00 0.00 0.00 4.61
740 847 0.674269 CCAACCCACCAAATGCATGC 60.674 55.000 11.82 11.82 0.00 4.06
742 849 0.609662 AACCCACCAAATGCATGCTC 59.390 50.000 20.33 0.00 0.00 4.26
748 855 0.458669 CCAAATGCATGCTCCAGGAC 59.541 55.000 20.33 0.00 0.00 3.85
790 897 1.301795 GAAGATCCGAATCCCGCCC 60.302 63.158 0.00 0.00 36.84 6.13
791 898 2.733319 GAAGATCCGAATCCCGCCCC 62.733 65.000 0.00 0.00 36.84 5.80
792 899 3.556306 GATCCGAATCCCGCCCCA 61.556 66.667 0.00 0.00 36.84 4.96
846 953 1.118838 ATCCACCTCTGCTGCTCTAC 58.881 55.000 0.00 0.00 0.00 2.59
915 1022 1.586042 CGCGCTCTTCTCTCTCTGC 60.586 63.158 5.56 0.00 0.00 4.26
1093 1201 2.093106 GCAAGTACTCCTCCTTCTCGA 58.907 52.381 0.00 0.00 0.00 4.04
1190 1304 2.435234 CCCGTCCGGCGAATCAAA 60.435 61.111 17.96 0.00 44.77 2.69
1203 1317 0.250124 AATCAAACTCCGTGCCGTCA 60.250 50.000 0.00 0.00 0.00 4.35
1206 1320 0.948623 CAAACTCCGTGCCGTCATCA 60.949 55.000 0.00 0.00 0.00 3.07
1217 1331 2.436646 GTCATCACCGGCCAGTGG 60.437 66.667 19.04 4.20 38.34 4.00
1247 1361 2.521708 GTTGGCAGCAGGTGGGTT 60.522 61.111 0.86 0.00 0.00 4.11
1304 1423 6.069705 TCCATTCTTTAATTAGGACCGGTT 57.930 37.500 9.42 0.00 0.00 4.44
1336 1469 0.522626 TAGCGTTGATCGACCGTGAA 59.477 50.000 7.54 0.00 42.86 3.18
1351 1484 1.531149 CGTGAACGCTTCTGTTGGATT 59.469 47.619 0.00 0.00 30.75 3.01
1354 1487 2.151202 GAACGCTTCTGTTGGATTGGA 58.849 47.619 0.00 0.00 30.75 3.53
1355 1488 2.496899 ACGCTTCTGTTGGATTGGAT 57.503 45.000 0.00 0.00 0.00 3.41
1356 1489 2.359900 ACGCTTCTGTTGGATTGGATC 58.640 47.619 0.00 0.00 0.00 3.36
1357 1490 2.026822 ACGCTTCTGTTGGATTGGATCT 60.027 45.455 0.00 0.00 0.00 2.75
1358 1491 2.353889 CGCTTCTGTTGGATTGGATCTG 59.646 50.000 0.00 0.00 0.00 2.90
1381 1514 4.694012 GATGTGTCGATTCGTTGGTATC 57.306 45.455 5.89 2.46 0.00 2.24
1382 1515 2.883574 TGTGTCGATTCGTTGGTATCC 58.116 47.619 5.89 0.00 0.00 2.59
1383 1516 2.199236 GTGTCGATTCGTTGGTATCCC 58.801 52.381 5.89 0.00 0.00 3.85
1384 1517 1.826096 TGTCGATTCGTTGGTATCCCA 59.174 47.619 5.89 0.00 39.65 4.37
1385 1518 2.432874 TGTCGATTCGTTGGTATCCCAT 59.567 45.455 5.89 0.00 41.49 4.00
1386 1519 2.800544 GTCGATTCGTTGGTATCCCATG 59.199 50.000 5.89 0.00 41.49 3.66
1387 1520 2.696187 TCGATTCGTTGGTATCCCATGA 59.304 45.455 5.89 0.00 41.49 3.07
1388 1521 3.133183 TCGATTCGTTGGTATCCCATGAA 59.867 43.478 5.89 0.00 41.49 2.57
1389 1522 3.874543 CGATTCGTTGGTATCCCATGAAA 59.125 43.478 0.00 0.00 41.49 2.69
1477 1613 4.114073 CAGAATCAGATCTGTGAGCAGTC 58.886 47.826 21.92 11.10 41.54 3.51
1479 1615 1.189752 TCAGATCTGTGAGCAGTCCC 58.810 55.000 21.92 0.00 43.05 4.46
1480 1616 0.900421 CAGATCTGTGAGCAGTCCCA 59.100 55.000 14.95 0.00 43.05 4.37
1481 1617 1.134759 CAGATCTGTGAGCAGTCCCAG 60.135 57.143 14.95 0.00 43.05 4.45
1482 1618 1.189752 GATCTGTGAGCAGTCCCAGA 58.810 55.000 0.00 0.00 43.05 3.86
1483 1619 1.136695 GATCTGTGAGCAGTCCCAGAG 59.863 57.143 0.00 0.00 43.05 3.35
1484 1620 0.113190 TCTGTGAGCAGTCCCAGAGA 59.887 55.000 0.00 0.00 43.05 3.10
1661 1855 4.131088 GTCGTCCAGTCGGAGGCC 62.131 72.222 0.00 0.00 43.99 5.19
1809 2070 9.784680 CTGACCAATCATTCAGAAAAATAGAAG 57.215 33.333 0.00 0.00 41.65 2.85
1969 2505 2.103373 CAGAGGAGCTTAGCTGGTGTA 58.897 52.381 13.01 0.00 39.88 2.90
1992 2528 1.352156 GAGGCCGTGTGTTCGTCATC 61.352 60.000 0.00 0.00 0.00 2.92
2044 2583 7.644490 TCGTTGTGTTAATTAGATGCACTTTT 58.356 30.769 0.00 0.00 0.00 2.27
2189 2734 2.697751 GTGTATGTGGAGGAGATGAGCT 59.302 50.000 0.00 0.00 0.00 4.09
2192 2737 2.244486 TGTGGAGGAGATGAGCTCTT 57.756 50.000 16.19 8.82 43.43 2.85
2212 2757 5.653507 TCTTAAATGAGGATGCAATGCAAC 58.346 37.500 13.45 9.92 43.62 4.17
2275 2820 5.872617 TGTACTGTAATTGAGTACCATGTGC 59.127 40.000 19.34 2.97 43.51 4.57
2283 2828 0.973632 AGTACCATGTGCGTCTGGAA 59.026 50.000 5.36 0.00 36.35 3.53
2288 2833 3.009723 ACCATGTGCGTCTGGAATTAAG 58.990 45.455 5.36 0.00 36.35 1.85
2445 2992 2.434359 CGACCAGAGGGAAACGCC 60.434 66.667 0.00 0.00 38.05 5.68
2525 3072 8.504005 ACGAAAACTAATCCTTACAAAGTCATG 58.496 33.333 0.00 0.00 0.00 3.07
2534 3081 6.108687 TCCTTACAAAGTCATGCATAGACTG 58.891 40.000 23.56 17.76 45.11 3.51
2578 3126 3.566322 AGCGTATGAAGATAGCGTTCTCT 59.434 43.478 0.00 0.00 0.00 3.10
2579 3127 4.036971 AGCGTATGAAGATAGCGTTCTCTT 59.963 41.667 0.00 0.00 34.48 2.85
2648 3199 0.592148 GTGACGTTGAGGTCTCTCGT 59.408 55.000 16.20 16.20 42.79 4.18
2690 3241 1.457346 GCATGTGCTTCAAGGCTAGT 58.543 50.000 0.00 0.00 38.21 2.57
2815 3366 0.883370 GGCCCCGTCGACATTAATCC 60.883 60.000 17.16 4.69 0.00 3.01
2819 3370 3.556423 GCCCCGTCGACATTAATCCTAAT 60.556 47.826 17.16 0.00 0.00 1.73
2873 3433 2.203998 CTCTGGGGAGGTGGTGGT 60.204 66.667 0.00 0.00 36.03 4.16
2882 3442 1.152756 AGGTGGTGGTTGGCTTCAC 60.153 57.895 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 5.076182 TCCCAATGCAAAATGAGTCTACAA 58.924 37.500 0.00 0.00 0.00 2.41
107 108 8.943002 GGTAGTAACATATATGCCACATAAACC 58.057 37.037 12.79 11.77 0.00 3.27
108 109 9.720769 AGGTAGTAACATATATGCCACATAAAC 57.279 33.333 12.79 7.67 0.00 2.01
113 114 8.430573 ACATAGGTAGTAACATATATGCCACA 57.569 34.615 12.79 0.00 31.04 4.17
137 140 2.766828 AGGCTGGTCATAGTGGAGTAAC 59.233 50.000 0.00 0.00 0.00 2.50
162 166 1.335132 TACCTTCCTCATGTCCGGCC 61.335 60.000 0.00 0.00 0.00 6.13
190 219 0.107945 GCTCATTCGGCTCTTGAGGT 60.108 55.000 8.76 0.00 37.84 3.85
205 234 3.343941 ACCTAAATTAAGCGGTGCTCA 57.656 42.857 0.00 0.00 38.25 4.26
236 265 9.373603 CGGATTCCATATAAACATAACGGATTA 57.626 33.333 3.09 0.00 0.00 1.75
240 269 5.163794 GGCGGATTCCATATAAACATAACGG 60.164 44.000 3.09 0.00 0.00 4.44
244 273 7.857456 ACATAGGCGGATTCCATATAAACATA 58.143 34.615 3.09 0.00 0.00 2.29
256 285 2.618241 TCATGCAAACATAGGCGGATTC 59.382 45.455 0.00 0.00 33.67 2.52
260 289 3.441496 AATTCATGCAAACATAGGCGG 57.559 42.857 0.00 0.00 33.67 6.13
261 290 8.641155 CATATAAAATTCATGCAAACATAGGCG 58.359 33.333 0.00 0.00 33.67 5.52
282 311 9.371136 TCAAACACTTTTGCAACAAAACATATA 57.629 25.926 0.00 0.00 41.78 0.86
285 314 6.551385 TCAAACACTTTTGCAACAAAACAT 57.449 29.167 0.00 0.00 41.78 2.71
286 315 5.991328 TCAAACACTTTTGCAACAAAACA 57.009 30.435 0.00 0.00 41.78 2.83
288 317 7.420800 ACATTTCAAACACTTTTGCAACAAAA 58.579 26.923 0.00 5.47 41.78 2.44
320 349 0.929244 AGCCTGCCATCCAACCTTAT 59.071 50.000 0.00 0.00 0.00 1.73
329 358 1.153086 AATGTCGGAGCCTGCCATC 60.153 57.895 0.00 0.00 0.00 3.51
337 366 1.588404 CGTGTACATGAATGTCGGAGC 59.412 52.381 9.62 0.00 41.97 4.70
343 372 2.301870 ACCAGTCCGTGTACATGAATGT 59.698 45.455 16.87 0.95 44.48 2.71
347 376 0.892755 GGACCAGTCCGTGTACATGA 59.107 55.000 16.87 5.32 40.36 3.07
375 404 2.588314 CTCTCGCATCTGCCTGCC 60.588 66.667 0.00 0.00 39.00 4.85
380 409 3.623060 TGTAAATTTCCTCTCGCATCTGC 59.377 43.478 0.00 0.00 37.78 4.26
393 422 2.223572 CCCATGGCGAGCTGTAAATTTC 60.224 50.000 6.09 0.00 0.00 2.17
400 429 2.068821 ATCTCCCATGGCGAGCTGT 61.069 57.895 19.87 9.62 0.00 4.40
402 431 2.827423 CATCTCCCATGGCGAGCT 59.173 61.111 19.87 11.45 0.00 4.09
404 433 2.281345 GGCATCTCCCATGGCGAG 60.281 66.667 19.03 19.03 34.93 5.03
413 442 1.210478 TGTTGCTCTAAGGGCATCTCC 59.790 52.381 0.00 0.00 39.54 3.71
415 444 2.484417 CGATGTTGCTCTAAGGGCATCT 60.484 50.000 0.00 0.00 39.54 2.90
426 455 2.476854 GCAATGGTCTTCGATGTTGCTC 60.477 50.000 13.68 0.00 38.97 4.26
441 470 0.039256 CCGGTGTTGAGTTGCAATGG 60.039 55.000 0.59 0.00 39.03 3.16
453 485 0.034059 CAAGTGAGAGCTCCGGTGTT 59.966 55.000 10.93 0.00 0.00 3.32
459 491 4.001618 AGAAGAAACAAGTGAGAGCTCC 57.998 45.455 10.93 2.40 0.00 4.70
482 514 0.243095 GGACGATGCGGATAGTACCC 59.757 60.000 2.07 0.00 0.00 3.69
564 656 3.438087 CCAGAGTTGAAATCTTGCATCGT 59.562 43.478 0.00 0.00 0.00 3.73
650 742 1.361543 AGCAGTGGGGTCTAGTCCTTA 59.638 52.381 5.97 0.00 0.00 2.69
671 763 0.241213 ACCATCTGTGTCGTGTCTCG 59.759 55.000 0.00 0.00 41.41 4.04
672 764 2.061773 CAACCATCTGTGTCGTGTCTC 58.938 52.381 0.00 0.00 0.00 3.36
673 765 1.686587 TCAACCATCTGTGTCGTGTCT 59.313 47.619 0.00 0.00 0.00 3.41
676 768 1.733912 CCATCAACCATCTGTGTCGTG 59.266 52.381 0.00 0.00 0.00 4.35
683 775 1.037493 CCATGGCCATCAACCATCTG 58.963 55.000 17.61 2.18 44.85 2.90
697 789 1.120795 AGGTTTTGTGCCCACCATGG 61.121 55.000 11.19 11.19 37.25 3.66
706 811 1.068588 GGTTGGGAAGAGGTTTTGTGC 59.931 52.381 0.00 0.00 0.00 4.57
716 821 2.008242 CATTTGGTGGGTTGGGAAGA 57.992 50.000 0.00 0.00 0.00 2.87
717 822 0.321346 GCATTTGGTGGGTTGGGAAG 59.679 55.000 0.00 0.00 0.00 3.46
729 836 0.458669 GTCCTGGAGCATGCATTTGG 59.541 55.000 21.98 15.96 34.26 3.28
740 847 2.358737 GTGTTGCCGGTCCTGGAG 60.359 66.667 1.90 0.00 0.00 3.86
742 849 2.358737 GAGTGTTGCCGGTCCTGG 60.359 66.667 1.90 0.00 0.00 4.45
748 855 3.041940 GACGTGGAGTGTTGCCGG 61.042 66.667 0.00 0.00 0.00 6.13
790 897 1.798725 CGTGCGCTGATTTGCTTGG 60.799 57.895 9.73 0.00 0.00 3.61
791 898 2.430942 GCGTGCGCTGATTTGCTTG 61.431 57.895 9.73 0.00 38.26 4.01
792 899 2.126734 GCGTGCGCTGATTTGCTT 60.127 55.556 9.73 0.00 38.26 3.91
958 1065 1.403323 GTTCCGTTCCGTCTACCTAGG 59.597 57.143 7.41 7.41 0.00 3.02
997 1105 4.554036 GTCGAGGAGCCCCATGCC 62.554 72.222 0.00 0.00 42.71 4.40
1158 1272 2.684735 GGGAGAGAGAGGGACGGT 59.315 66.667 0.00 0.00 0.00 4.83
1164 1278 2.517402 CCGGACGGGAGAGAGAGG 60.517 72.222 0.00 0.00 38.47 3.69
1170 1284 3.524606 GATTCGCCGGACGGGAGA 61.525 66.667 5.05 7.18 43.50 3.71
1233 1347 2.991540 GGAAACCCACCTGCTGCC 60.992 66.667 0.00 0.00 0.00 4.85
1247 1361 1.073923 GGCCAAGAAACAGAGGAGGAA 59.926 52.381 0.00 0.00 0.00 3.36
1299 1418 2.404215 CTACACAGAGTCACAAACCGG 58.596 52.381 0.00 0.00 0.00 5.28
1304 1423 2.100087 TCAACGCTACACAGAGTCACAA 59.900 45.455 0.00 0.00 33.17 3.33
1336 1469 2.026822 AGATCCAATCCAACAGAAGCGT 60.027 45.455 0.00 0.00 0.00 5.07
1351 1484 4.812814 CGACACATCGCAGATCCA 57.187 55.556 0.00 0.00 45.12 3.41
1383 1516 4.820716 TGTTTTTCTTGCCCCATTTTCATG 59.179 37.500 0.00 0.00 0.00 3.07
1384 1517 5.046288 TGTTTTTCTTGCCCCATTTTCAT 57.954 34.783 0.00 0.00 0.00 2.57
1385 1518 4.494091 TGTTTTTCTTGCCCCATTTTCA 57.506 36.364 0.00 0.00 0.00 2.69
1386 1519 4.216042 CCATGTTTTTCTTGCCCCATTTTC 59.784 41.667 0.00 0.00 0.00 2.29
1387 1520 4.141298 TCCATGTTTTTCTTGCCCCATTTT 60.141 37.500 0.00 0.00 0.00 1.82
1388 1521 3.393941 TCCATGTTTTTCTTGCCCCATTT 59.606 39.130 0.00 0.00 0.00 2.32
1389 1522 2.978278 TCCATGTTTTTCTTGCCCCATT 59.022 40.909 0.00 0.00 0.00 3.16
1472 1608 1.610673 TCTGGGTCTCTGGGACTGC 60.611 63.158 7.74 0.00 43.97 4.40
1475 1611 3.007973 GCGTCTGGGTCTCTGGGAC 62.008 68.421 0.00 0.00 43.79 4.46
1477 1613 2.997315 TGCGTCTGGGTCTCTGGG 60.997 66.667 0.00 0.00 0.00 4.45
1479 1615 0.962855 TCTCTGCGTCTGGGTCTCTG 60.963 60.000 0.00 0.00 0.00 3.35
1480 1616 0.033601 ATCTCTGCGTCTGGGTCTCT 60.034 55.000 0.00 0.00 0.00 3.10
1481 1617 0.102120 CATCTCTGCGTCTGGGTCTC 59.898 60.000 0.00 0.00 0.00 3.36
1482 1618 0.613292 ACATCTCTGCGTCTGGGTCT 60.613 55.000 0.00 0.00 0.00 3.85
1483 1619 0.179124 GACATCTCTGCGTCTGGGTC 60.179 60.000 0.00 0.00 0.00 4.46
1484 1620 1.893786 GACATCTCTGCGTCTGGGT 59.106 57.895 0.00 0.00 0.00 4.51
1618 1812 1.202177 CGTTGGCCATCTTGGATTTCG 60.202 52.381 6.09 0.00 40.96 3.46
1809 2070 4.632153 ACCGTCTGCCATATGTTCTTATC 58.368 43.478 1.24 0.00 0.00 1.75
1969 2505 0.534203 ACGAACACACGGCCTCAAAT 60.534 50.000 0.00 0.00 37.61 2.32
2010 2549 8.821147 TCTAATTAACACAACGATTACACAGT 57.179 30.769 0.00 0.00 0.00 3.55
2011 2550 9.689075 CATCTAATTAACACAACGATTACACAG 57.311 33.333 0.00 0.00 0.00 3.66
2012 2551 8.172484 GCATCTAATTAACACAACGATTACACA 58.828 33.333 0.00 0.00 0.00 3.72
2117 2657 1.278985 ACATCTCGATTGCCTCAACCA 59.721 47.619 0.00 0.00 0.00 3.67
2169 2714 2.961741 GAGCTCATCTCCTCCACATACA 59.038 50.000 9.40 0.00 35.77 2.29
2170 2715 3.230134 AGAGCTCATCTCCTCCACATAC 58.770 50.000 17.77 0.00 42.90 2.39
2171 2716 3.609256 AGAGCTCATCTCCTCCACATA 57.391 47.619 17.77 0.00 42.90 2.29
2172 2717 2.475339 AGAGCTCATCTCCTCCACAT 57.525 50.000 17.77 0.00 42.90 3.21
2173 2718 2.244486 AAGAGCTCATCTCCTCCACA 57.756 50.000 17.77 0.00 42.90 4.17
2174 2719 4.744795 TTTAAGAGCTCATCTCCTCCAC 57.255 45.455 17.77 0.00 42.90 4.02
2189 2734 5.419788 AGTTGCATTGCATCCTCATTTAAGA 59.580 36.000 12.95 0.00 38.76 2.10
2192 2737 4.463539 ACAGTTGCATTGCATCCTCATTTA 59.536 37.500 12.95 0.00 38.76 1.40
2212 2757 5.455392 AGAAAACGAAGCATGATTGAACAG 58.545 37.500 0.00 0.00 0.00 3.16
2275 2820 4.481930 TTGTTGCACTTAATTCCAGACG 57.518 40.909 0.00 0.00 0.00 4.18
2283 2828 6.909550 TTTAGGGTGATTGTTGCACTTAAT 57.090 33.333 0.00 0.00 36.53 1.40
2288 2833 4.782019 TGATTTAGGGTGATTGTTGCAC 57.218 40.909 0.00 0.00 35.56 4.57
2534 3081 8.129211 ACGCTTTGGTTATAGATGAAATAAAGC 58.871 33.333 0.00 0.00 42.20 3.51
2578 3126 1.346395 AGTAGTGGCGGACATCAACAA 59.654 47.619 0.00 0.00 0.00 2.83
2579 3127 0.973632 AGTAGTGGCGGACATCAACA 59.026 50.000 0.00 0.00 0.00 3.33
2648 3199 3.226429 AACGAGGCTCTTGCGCTGA 62.226 57.895 13.50 6.21 40.82 4.26
2815 3366 3.441222 TGCACCAGTGAAGATGCAATTAG 59.559 43.478 0.99 0.00 44.72 1.73
2819 3370 3.418022 TGCACCAGTGAAGATGCAA 57.582 47.368 0.99 0.00 44.72 4.08
2873 3433 2.638480 AGCTACTGTTGTGAAGCCAA 57.362 45.000 0.00 0.00 35.54 4.52
2882 3442 5.911752 AGGATCTTGACATAGCTACTGTTG 58.088 41.667 0.00 0.00 0.00 3.33



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

AutoCloner maintained by Alex Coulton.