Multiple sequence alignment - TraesCS2A01G131200

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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 TraesCS2A01G131200 chr2A 100.000 2471 0 0 1 2471 78774097 78771627 0.000000e+00 4564.0
1 TraesCS2A01G131200 chr2A 89.235 771 57 13 731 1483 78756645 78755883 0.000000e+00 941.0
2 TraesCS2A01G131200 chr2A 84.673 796 75 23 745 1520 78742268 78741500 0.000000e+00 750.0
3 TraesCS2A01G131200 chr2A 91.273 550 34 2 982 1517 78323386 78323935 0.000000e+00 737.0
4 TraesCS2A01G131200 chr2A 90.406 542 40 4 981 1520 78263033 78263564 0.000000e+00 702.0
5 TraesCS2A01G131200 chr2A 86.719 640 48 13 526 1135 78234043 78234675 0.000000e+00 676.0
6 TraesCS2A01G131200 chr2A 91.223 376 24 5 1124 1498 78255292 78255659 1.020000e-138 503.0
7 TraesCS2A01G131200 chr2A 92.500 200 11 4 537 735 78762886 78762690 1.450000e-72 283.0
8 TraesCS2A01G131200 chr2A 98.077 52 0 1 1586 1637 78255658 78255708 3.380000e-14 89.8
9 TraesCS2A01G131200 chr2A 95.652 46 0 2 634 678 78742430 78742386 3.410000e-09 73.1
10 TraesCS2A01G131200 chr2A 90.196 51 5 0 435 485 17927530 17927480 1.590000e-07 67.6
11 TraesCS2A01G131200 chr4A 93.176 850 42 3 1634 2471 590315530 590316375 0.000000e+00 1234.0
12 TraesCS2A01G131200 chr4A 93.176 850 42 3 1634 2471 590326901 590327746 0.000000e+00 1234.0
13 TraesCS2A01G131200 chr2D 88.557 1005 54 18 564 1523 78509375 78508387 0.000000e+00 1162.0
14 TraesCS2A01G131200 chr2D 83.750 880 83 33 667 1523 78436402 78435560 0.000000e+00 778.0
15 TraesCS2A01G131200 chr2D 87.048 332 34 7 1 327 78510282 78509955 1.400000e-97 366.0
16 TraesCS2A01G131200 chr2D 84.444 90 5 6 603 684 78502855 78502767 2.040000e-11 80.5
17 TraesCS2A01G131200 chr2B 87.712 1001 72 23 564 1520 121483652 121482659 0.000000e+00 1120.0
18 TraesCS2A01G131200 chr2B 87.542 899 52 13 671 1520 121479015 121478128 0.000000e+00 985.0
19 TraesCS2A01G131200 chr2B 89.881 672 39 6 865 1518 121475104 121474444 0.000000e+00 837.0
20 TraesCS2A01G131200 chr2B 86.233 661 58 12 880 1523 121383280 121382636 0.000000e+00 686.0
21 TraesCS2A01G131200 chr2B 88.727 550 47 7 979 1523 121433012 121432473 0.000000e+00 658.0
22 TraesCS2A01G131200 chr2B 90.604 149 14 0 179 327 121479427 121479279 5.390000e-47 198.0
23 TraesCS2A01G131200 chr2B 93.407 91 6 0 1546 1636 121482667 121482577 4.290000e-28 135.0
24 TraesCS2A01G131200 chr2B 83.916 143 14 7 1 137 121479570 121479431 7.170000e-26 128.0
25 TraesCS2A01G131200 chr2B 91.304 92 8 0 1546 1637 121478136 121478045 2.580000e-25 126.0
26 TraesCS2A01G131200 chr2B 92.537 67 5 0 603 669 121383602 121383536 2.020000e-16 97.1
27 TraesCS2A01G131200 chr2B 87.500 80 6 4 613 689 121438722 121438644 3.380000e-14 89.8
28 TraesCS2A01G131200 chr2B 91.803 61 2 2 1576 1636 121474415 121474358 5.660000e-12 82.4
29 TraesCS2A01G131200 chr2B 90.566 53 4 1 431 482 634019931 634019983 4.410000e-08 69.4
30 TraesCS2A01G131200 chr2B 90.566 53 4 1 431 482 634052511 634052563 4.410000e-08 69.4
31 TraesCS2A01G131200 chr2B 91.837 49 4 0 435 483 788199793 788199745 4.410000e-08 69.4
32 TraesCS2A01G131200 chr5A 94.000 50 3 0 435 484 50752652 50752603 2.640000e-10 76.8
33 TraesCS2A01G131200 chr3B 95.745 47 2 0 441 487 222064705 222064751 2.640000e-10 76.8
34 TraesCS2A01G131200 chr1A 89.831 59 5 1 435 493 354667011 354666954 9.480000e-10 75.0
35 TraesCS2A01G131200 chr1B 91.837 49 4 0 441 489 355102828 355102876 4.410000e-08 69.4
36 TraesCS2A01G131200 chr4B 85.484 62 7 2 435 494 187091114 187091053 2.050000e-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 TraesCS2A01G131200 chr2A 78771627 78774097 2470 True 4564.000 4564 100.000000 1 2471 1 chr2A.!!$R4 2470
1 TraesCS2A01G131200 chr2A 78755883 78756645 762 True 941.000 941 89.235000 731 1483 1 chr2A.!!$R2 752
2 TraesCS2A01G131200 chr2A 78323386 78323935 549 False 737.000 737 91.273000 982 1517 1 chr2A.!!$F3 535
3 TraesCS2A01G131200 chr2A 78263033 78263564 531 False 702.000 702 90.406000 981 1520 1 chr2A.!!$F2 539
4 TraesCS2A01G131200 chr2A 78234043 78234675 632 False 676.000 676 86.719000 526 1135 1 chr2A.!!$F1 609
5 TraesCS2A01G131200 chr2A 78741500 78742430 930 True 411.550 750 90.162500 634 1520 2 chr2A.!!$R5 886
6 TraesCS2A01G131200 chr4A 590315530 590316375 845 False 1234.000 1234 93.176000 1634 2471 1 chr4A.!!$F1 837
7 TraesCS2A01G131200 chr4A 590326901 590327746 845 False 1234.000 1234 93.176000 1634 2471 1 chr4A.!!$F2 837
8 TraesCS2A01G131200 chr2D 78435560 78436402 842 True 778.000 778 83.750000 667 1523 1 chr2D.!!$R1 856
9 TraesCS2A01G131200 chr2D 78508387 78510282 1895 True 764.000 1162 87.802500 1 1523 2 chr2D.!!$R3 1522
10 TraesCS2A01G131200 chr2B 121432473 121433012 539 True 658.000 658 88.727000 979 1523 1 chr2B.!!$R1 544
11 TraesCS2A01G131200 chr2B 121474358 121483652 9294 True 451.425 1120 89.521125 1 1637 8 chr2B.!!$R5 1636
12 TraesCS2A01G131200 chr2B 121382636 121383602 966 True 391.550 686 89.385000 603 1523 2 chr2B.!!$R4 920

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
259 4354 0.109723 GGTGTGGAAGCAAGTGGGTA 59.89 55.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1849 8723 0.592637 TTTGGCACTTGCGTGAGATG 59.407 50.0 0.0 0.0 43.97 2.9 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
24 4107 6.309357 TCGCTAGGGAAGTATATGGACTAAA 58.691 40.000 7.09 0.00 0.00 1.85
46 4129 1.613928 TACATGGCCTTGGGGTCGA 60.614 57.895 21.67 0.00 40.80 4.20
55 4138 0.839946 CTTGGGGTCGATGGAAGGAT 59.160 55.000 0.00 0.00 0.00 3.24
56 4139 0.837272 TTGGGGTCGATGGAAGGATC 59.163 55.000 0.00 0.00 0.00 3.36
57 4140 1.367840 GGGGTCGATGGAAGGATCG 59.632 63.158 0.00 0.00 45.43 3.69
69 4152 2.165030 GGAAGGATCGAAGTACCAACGA 59.835 50.000 8.58 8.58 40.18 3.85
93 4186 1.066002 CAAGGATTGGTGCATTAGGCG 59.934 52.381 0.00 0.00 44.53 5.52
94 4187 4.156313 CAAGGATTGGTGCATTAGGCGG 62.156 54.545 0.00 0.00 44.53 6.13
140 4233 7.464830 AAGACGACACATGCTATATGTTTAC 57.535 36.000 0.00 0.00 0.00 2.01
177 4270 4.083003 GCTATGAAAACATCGGAACACCAA 60.083 41.667 0.00 0.00 0.00 3.67
196 4289 3.119531 CCAACGTGTTTATGATGCCATGT 60.120 43.478 0.00 0.00 34.31 3.21
197 4292 4.097714 CAACGTGTTTATGATGCCATGTC 58.902 43.478 0.00 0.00 34.31 3.06
203 4298 1.298602 TATGATGCCATGTCGTGTGC 58.701 50.000 0.00 0.00 34.31 4.57
204 4299 1.708193 ATGATGCCATGTCGTGTGCG 61.708 55.000 0.00 0.00 39.92 5.34
231 4326 3.119245 AGGTGTTACGATGTATTGCGAGT 60.119 43.478 0.00 0.00 0.00 4.18
234 4329 4.503007 GTGTTACGATGTATTGCGAGTGAT 59.497 41.667 0.00 0.00 0.00 3.06
259 4354 0.109723 GGTGTGGAAGCAAGTGGGTA 59.890 55.000 0.00 0.00 0.00 3.69
382 4504 1.704641 GTGGTGCTCTTTCCCCTTTT 58.295 50.000 0.00 0.00 0.00 2.27
383 4505 2.490168 GGTGGTGCTCTTTCCCCTTTTA 60.490 50.000 0.00 0.00 0.00 1.52
400 4522 5.358090 CCTTTTATTCTACTCCCTCCGTTC 58.642 45.833 0.00 0.00 0.00 3.95
405 4527 7.909485 TTATTCTACTCCCTCCGTTCTAAAT 57.091 36.000 0.00 0.00 0.00 1.40
434 4556 9.826574 AGTGTCTCAATTTTGTACTAAGTTGTA 57.173 29.630 19.20 10.23 0.00 2.41
438 4560 9.485206 TCTCAATTTTGTACTAAGTTGTACTCC 57.515 33.333 19.20 0.00 42.22 3.85
439 4561 9.268268 CTCAATTTTGTACTAAGTTGTACTCCA 57.732 33.333 19.20 4.46 42.22 3.86
440 4562 9.268268 TCAATTTTGTACTAAGTTGTACTCCAG 57.732 33.333 19.20 0.00 42.22 3.86
441 4563 9.052759 CAATTTTGTACTAAGTTGTACTCCAGT 57.947 33.333 14.21 0.00 42.22 4.00
443 4565 9.924650 ATTTTGTACTAAGTTGTACTCCAGTAG 57.075 33.333 13.28 0.00 42.22 2.57
444 4566 8.469309 TTTGTACTAAGTTGTACTCCAGTAGT 57.531 34.615 13.28 0.00 42.22 2.73
445 4567 7.444629 TGTACTAAGTTGTACTCCAGTAGTG 57.555 40.000 13.28 0.00 42.22 2.74
446 4568 5.388408 ACTAAGTTGTACTCCAGTAGTGC 57.612 43.478 0.00 0.00 39.39 4.40
447 4569 3.679824 AAGTTGTACTCCAGTAGTGCC 57.320 47.619 0.00 0.00 39.88 5.01
448 4570 2.605257 AGTTGTACTCCAGTAGTGCCA 58.395 47.619 0.00 0.00 39.88 4.92
449 4571 2.969950 AGTTGTACTCCAGTAGTGCCAA 59.030 45.455 0.00 0.00 39.88 4.52
450 4572 3.389983 AGTTGTACTCCAGTAGTGCCAAA 59.610 43.478 0.00 0.00 39.88 3.28
451 4573 4.131596 GTTGTACTCCAGTAGTGCCAAAA 58.868 43.478 0.00 0.00 39.88 2.44
452 4574 4.425180 TGTACTCCAGTAGTGCCAAAAA 57.575 40.909 0.00 0.00 39.88 1.94
531 4668 7.972832 AGAAGGAGAGAGTATATTACACTCG 57.027 40.000 0.00 0.00 46.58 4.18
600 5041 5.320549 TGATTCCGTAGTTCCTTGTAGAC 57.679 43.478 0.00 0.00 0.00 2.59
669 5117 5.076182 TGGATGACCAAAATTGAGCTAACA 58.924 37.500 0.00 0.00 43.91 2.41
698 5238 2.472861 CGTATCTGATCATGCAACGTCC 59.527 50.000 0.00 0.00 0.00 4.79
759 5326 3.425359 CGCTAAATCTGACAACTGCTTGG 60.425 47.826 0.00 0.00 0.00 3.61
857 5425 2.037772 AGCACGACTCAGATTTGTTCCT 59.962 45.455 0.00 0.00 0.00 3.36
902 5508 2.816012 TCGTCAACGAAGCACCCA 59.184 55.556 2.18 0.00 46.30 4.51
903 5509 1.300620 TCGTCAACGAAGCACCCAG 60.301 57.895 2.18 0.00 46.30 4.45
904 5510 1.594293 CGTCAACGAAGCACCCAGT 60.594 57.895 0.00 0.00 43.02 4.00
905 5511 1.831389 CGTCAACGAAGCACCCAGTG 61.831 60.000 0.00 0.00 43.02 3.66
964 5582 3.392440 CCGTAATACGCGAGCGCC 61.392 66.667 15.93 0.00 44.19 6.53
1091 5738 2.050934 GGTTCTACGGGAGCGAGGT 61.051 63.158 0.00 0.00 0.00 3.85
1123 5770 1.070615 TGCTCAAAGTGCTACCGCA 59.929 52.632 0.00 0.00 45.60 5.69
1135 5782 0.034896 CTACCGCAACCACCTCAAGT 59.965 55.000 0.00 0.00 0.00 3.16
1185 5835 1.541233 GGGAAGATCAATGCCGACGAT 60.541 52.381 0.00 0.00 0.00 3.73
1212 5862 0.391597 TCGCCTTCAAGAAGTCGGTT 59.608 50.000 12.48 0.00 39.85 4.44
1219 5869 2.244695 TCAAGAAGTCGGTTAGCCTGA 58.755 47.619 0.00 0.00 0.00 3.86
1473 6135 6.263344 CAAGCTCCACAACAAGATATGAATG 58.737 40.000 0.00 0.00 0.00 2.67
1483 6145 5.759059 ACAAGATATGAATGAAGGCAGGAA 58.241 37.500 0.00 0.00 0.00 3.36
1523 6189 6.854496 ACAGTTTTAGTTTACTCATTCGCA 57.146 33.333 0.00 0.00 0.00 5.10
1526 6192 7.855904 ACAGTTTTAGTTTACTCATTCGCAAAG 59.144 33.333 0.00 0.00 0.00 2.77
1527 6193 7.855904 CAGTTTTAGTTTACTCATTCGCAAAGT 59.144 33.333 0.00 0.00 0.00 2.66
1528 6194 8.403236 AGTTTTAGTTTACTCATTCGCAAAGTT 58.597 29.630 0.00 0.00 0.00 2.66
1529 6195 9.016623 GTTTTAGTTTACTCATTCGCAAAGTTT 57.983 29.630 0.00 0.00 0.00 2.66
1530 6196 8.776680 TTTAGTTTACTCATTCGCAAAGTTTC 57.223 30.769 0.00 0.00 0.00 2.78
1531 6197 6.619801 AGTTTACTCATTCGCAAAGTTTCT 57.380 33.333 0.00 0.00 0.00 2.52
1532 6198 7.027778 AGTTTACTCATTCGCAAAGTTTCTT 57.972 32.000 0.00 0.00 0.00 2.52
1533 6199 7.480810 AGTTTACTCATTCGCAAAGTTTCTTT 58.519 30.769 0.00 0.00 0.00 2.52
1534 6200 7.432252 AGTTTACTCATTCGCAAAGTTTCTTTG 59.568 33.333 15.22 15.22 0.00 2.77
1535 6201 5.248870 ACTCATTCGCAAAGTTTCTTTGT 57.751 34.783 18.94 2.01 0.00 2.83
1536 6202 6.371809 ACTCATTCGCAAAGTTTCTTTGTA 57.628 33.333 18.94 8.79 0.00 2.41
1537 6203 6.430451 ACTCATTCGCAAAGTTTCTTTGTAG 58.570 36.000 18.94 14.56 0.00 2.74
1538 6204 5.212194 TCATTCGCAAAGTTTCTTTGTAGC 58.788 37.500 18.94 8.00 0.00 3.58
1539 6205 3.619233 TCGCAAAGTTTCTTTGTAGCC 57.381 42.857 18.94 6.03 0.00 3.93
1540 6206 3.211045 TCGCAAAGTTTCTTTGTAGCCT 58.789 40.909 18.94 0.00 0.00 4.58
1541 6207 3.003275 TCGCAAAGTTTCTTTGTAGCCTG 59.997 43.478 18.94 7.02 0.00 4.85
1542 6208 3.243068 CGCAAAGTTTCTTTGTAGCCTGT 60.243 43.478 18.94 0.00 0.00 4.00
1543 6209 4.290969 GCAAAGTTTCTTTGTAGCCTGTC 58.709 43.478 18.94 1.95 0.00 3.51
1544 6210 4.793028 GCAAAGTTTCTTTGTAGCCTGTCC 60.793 45.833 18.94 1.41 0.00 4.02
1545 6211 4.439253 AAGTTTCTTTGTAGCCTGTCCT 57.561 40.909 0.00 0.00 0.00 3.85
1546 6212 4.439253 AGTTTCTTTGTAGCCTGTCCTT 57.561 40.909 0.00 0.00 0.00 3.36
1547 6213 5.562298 AGTTTCTTTGTAGCCTGTCCTTA 57.438 39.130 0.00 0.00 0.00 2.69
1548 6214 5.306394 AGTTTCTTTGTAGCCTGTCCTTAC 58.694 41.667 0.00 0.00 0.00 2.34
1549 6215 5.071923 AGTTTCTTTGTAGCCTGTCCTTACT 59.928 40.000 0.00 0.00 0.00 2.24
1550 6216 4.803098 TCTTTGTAGCCTGTCCTTACTC 57.197 45.455 0.00 0.00 0.00 2.59
1551 6217 4.157246 TCTTTGTAGCCTGTCCTTACTCA 58.843 43.478 0.00 0.00 0.00 3.41
1552 6218 4.777896 TCTTTGTAGCCTGTCCTTACTCAT 59.222 41.667 0.00 0.00 0.00 2.90
1553 6219 5.248477 TCTTTGTAGCCTGTCCTTACTCATT 59.752 40.000 0.00 0.00 0.00 2.57
1554 6220 5.499004 TTGTAGCCTGTCCTTACTCATTT 57.501 39.130 0.00 0.00 0.00 2.32
1555 6221 4.832248 TGTAGCCTGTCCTTACTCATTTG 58.168 43.478 0.00 0.00 0.00 2.32
1556 6222 2.716217 AGCCTGTCCTTACTCATTTGC 58.284 47.619 0.00 0.00 0.00 3.68
1557 6223 2.307098 AGCCTGTCCTTACTCATTTGCT 59.693 45.455 0.00 0.00 0.00 3.91
1558 6224 3.084786 GCCTGTCCTTACTCATTTGCTT 58.915 45.455 0.00 0.00 0.00 3.91
1559 6225 3.507622 GCCTGTCCTTACTCATTTGCTTT 59.492 43.478 0.00 0.00 0.00 3.51
1567 6233 6.874134 TCCTTACTCATTTGCTTTACTGTCTC 59.126 38.462 0.00 0.00 0.00 3.36
1568 6234 6.876257 CCTTACTCATTTGCTTTACTGTCTCT 59.124 38.462 0.00 0.00 0.00 3.10
1580 6246 7.014905 TGCTTTACTGTCTCTCCTGTACTTAAA 59.985 37.037 0.00 0.00 0.00 1.52
1623 6289 6.508777 AGCTCGATATAAGTTGAAGAAGGTC 58.491 40.000 0.00 0.00 0.00 3.85
1674 6498 6.523676 AGCGTTTGAATGTTTTACAATTGG 57.476 33.333 10.83 0.00 0.00 3.16
1736 8598 2.033602 GTCCAAGACCAACCCCCG 59.966 66.667 0.00 0.00 0.00 5.73
1828 8702 3.300590 GCACTTGAACACAAAACAGAACG 59.699 43.478 0.00 0.00 0.00 3.95
1839 8713 0.179073 AACAGAACGCACAGCTGTCT 60.179 50.000 18.64 7.89 41.65 3.41
1849 8723 2.724349 CACAGCTGTCTTTGAACTTGC 58.276 47.619 18.64 0.00 0.00 4.01
1850 8724 2.097954 CACAGCTGTCTTTGAACTTGCA 59.902 45.455 18.64 0.00 0.00 4.08
1948 9011 1.270678 GCACACCCTAAAACGGAGACT 60.271 52.381 0.00 0.00 0.00 3.24
1967 9030 4.473520 CGCCATGGGAGAAGCGGT 62.474 66.667 15.13 0.00 44.64 5.68
1993 9056 6.214412 AGAGGAAGATGAAAGAACTGTACCAT 59.786 38.462 0.00 0.00 0.00 3.55
2001 9064 3.550437 AGAACTGTACCATGGCAGATC 57.450 47.619 22.01 19.26 35.59 2.75
2019 9082 6.126940 GGCAGATCCAGAATCTTATAGCCATA 60.127 42.308 8.46 0.00 44.03 2.74
2095 9158 2.441750 AGGCCAGGAACACTCTTAACAA 59.558 45.455 5.01 0.00 0.00 2.83
2104 9167 6.940867 AGGAACACTCTTAACAAATTCCTACC 59.059 38.462 0.80 0.00 42.03 3.18
2124 9187 3.117512 ACCGCAAATAATCTTGATCCCCT 60.118 43.478 0.00 0.00 0.00 4.79
2140 9203 1.285962 CCCCTTCATCAGGTTCACCAT 59.714 52.381 0.00 0.00 42.02 3.55
2185 9248 8.318412 TGCTTCACCTATTACATTAGAGAAACA 58.682 33.333 0.00 0.00 0.00 2.83
2211 9642 3.555966 ACAAAAGGAAACCCAGAGACAG 58.444 45.455 0.00 0.00 0.00 3.51
2242 9673 7.226325 AGACTATGCTGATCACTAGAAAAATGC 59.774 37.037 0.00 0.00 0.00 3.56
2264 9695 9.598517 AATGCAAAACTCTGAAATTACAGAAAA 57.401 25.926 0.00 0.00 44.62 2.29
2265 9696 8.994429 TGCAAAACTCTGAAATTACAGAAAAA 57.006 26.923 0.00 0.00 44.62 1.94
2331 9762 9.322773 GGTACCTAGTAATTTCCAGTGTAAATC 57.677 37.037 4.06 0.00 0.00 2.17
2444 9875 3.833559 AATCCCAGGAAATTCCAGTGT 57.166 42.857 15.21 0.00 39.61 3.55
2454 9885 7.611855 CCAGGAAATTCCAGTGTAAATTAGACT 59.388 37.037 15.21 0.00 39.61 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 4095 7.016914 AGGCCATGTAGACTTTAGTCCATATA 58.983 38.462 5.01 0.00 45.85 0.86
13 4096 5.846714 AGGCCATGTAGACTTTAGTCCATAT 59.153 40.000 5.01 0.00 45.85 1.78
24 4107 0.550147 ACCCCAAGGCCATGTAGACT 60.550 55.000 5.01 0.00 36.11 3.24
46 4129 3.430374 CGTTGGTACTTCGATCCTTCCAT 60.430 47.826 0.00 0.00 0.00 3.41
55 4138 3.571571 CTTGATGTCGTTGGTACTTCGA 58.428 45.455 0.00 0.00 33.11 3.71
56 4139 2.666508 CCTTGATGTCGTTGGTACTTCG 59.333 50.000 0.00 0.00 0.00 3.79
57 4140 3.921677 TCCTTGATGTCGTTGGTACTTC 58.078 45.455 0.00 0.00 0.00 3.01
58 4141 4.553330 ATCCTTGATGTCGTTGGTACTT 57.447 40.909 0.00 0.00 0.00 2.24
59 4142 4.253685 CAATCCTTGATGTCGTTGGTACT 58.746 43.478 0.00 0.00 0.00 2.73
69 4152 3.956199 CCTAATGCACCAATCCTTGATGT 59.044 43.478 0.00 0.00 0.00 3.06
93 4186 2.600470 GTTGACCAAGGTGCCCCC 60.600 66.667 0.00 0.00 0.00 5.40
94 4187 1.456705 TTGTTGACCAAGGTGCCCC 60.457 57.895 0.00 0.00 0.00 5.80
140 4233 4.944619 TTCATAGCTCCCACATGACTAG 57.055 45.455 0.00 0.00 0.00 2.57
177 4270 2.351418 CGACATGGCATCATAAACACGT 59.649 45.455 0.00 0.00 31.33 4.49
188 4281 3.803082 GCGCACACGACATGGCAT 61.803 61.111 0.30 0.00 43.93 4.40
203 4298 2.508439 ATCGTAACACCTGCCGCG 60.508 61.111 0.00 0.00 0.00 6.46
204 4299 0.458889 TACATCGTAACACCTGCCGC 60.459 55.000 0.00 0.00 0.00 6.53
214 4309 6.267070 TGTAATCACTCGCAATACATCGTAA 58.733 36.000 0.00 0.00 0.00 3.18
231 4326 3.500448 TGCTTCCACACCTTGTAATCA 57.500 42.857 0.00 0.00 0.00 2.57
234 4329 2.948979 CACTTGCTTCCACACCTTGTAA 59.051 45.455 0.00 0.00 0.00 2.41
382 4504 7.909485 AATTTAGAACGGAGGGAGTAGAATA 57.091 36.000 0.00 0.00 0.00 1.75
383 4505 6.809976 AATTTAGAACGGAGGGAGTAGAAT 57.190 37.500 0.00 0.00 0.00 2.40
422 4544 6.320944 GCACTACTGGAGTACAACTTAGTAC 58.679 44.000 0.00 0.00 43.61 2.73
427 4549 2.969950 TGGCACTACTGGAGTACAACTT 59.030 45.455 0.00 0.00 35.64 2.66
429 4551 3.396260 TTGGCACTACTGGAGTACAAC 57.604 47.619 5.51 0.00 35.64 3.32
449 4571 7.513371 TTGTCCCATAATGTAAGACGTTTTT 57.487 32.000 0.00 0.00 0.00 1.94
450 4572 7.308951 CCTTTGTCCCATAATGTAAGACGTTTT 60.309 37.037 0.00 0.00 0.00 2.43
451 4573 6.150474 CCTTTGTCCCATAATGTAAGACGTTT 59.850 38.462 0.00 0.00 0.00 3.60
452 4574 5.646360 CCTTTGTCCCATAATGTAAGACGTT 59.354 40.000 0.00 0.00 0.00 3.99
453 4575 5.046159 TCCTTTGTCCCATAATGTAAGACGT 60.046 40.000 0.00 0.00 0.00 4.34
454 4576 5.424757 TCCTTTGTCCCATAATGTAAGACG 58.575 41.667 0.00 0.00 0.00 4.18
455 4577 6.884836 ACTTCCTTTGTCCCATAATGTAAGAC 59.115 38.462 0.00 0.00 0.00 3.01
463 4585 9.762381 ATGTTTAATACTTCCTTTGTCCCATAA 57.238 29.630 0.00 0.00 0.00 1.90
492 4614 9.936759 CTCTCTCCTTCTAAAAATAAGTGTCTT 57.063 33.333 0.00 0.00 0.00 3.01
506 4643 8.649591 ACGAGTGTAATATACTCTCTCCTTCTA 58.350 37.037 13.85 0.00 43.50 2.10
510 4647 5.470777 GCACGAGTGTAATATACTCTCTCCT 59.529 44.000 13.85 0.00 43.50 3.69
600 5041 1.425448 ACAACTCCTCCCTTTTCCCAG 59.575 52.381 0.00 0.00 0.00 4.45
669 5117 6.575162 TGCATGATCAGATACGTACATACT 57.425 37.500 0.09 0.00 0.00 2.12
759 5326 1.519455 CTGTGTCCCGATCCGAAGC 60.519 63.158 0.00 0.00 0.00 3.86
964 5582 2.627863 GATCGAGGATGGATCGTCTG 57.372 55.000 7.53 2.73 40.46 3.51
984 5617 1.016130 CCATGTATCGCCGCTGATCC 61.016 60.000 0.00 0.00 0.00 3.36
1091 5738 1.303561 GAGCACATGCCCTTGGTCA 60.304 57.895 8.01 0.00 43.38 4.02
1123 5770 1.507140 TCTGTGGACTTGAGGTGGTT 58.493 50.000 0.00 0.00 0.00 3.67
1185 5835 1.852633 TCTTGAAGGCGAGGATGAGA 58.147 50.000 0.00 0.00 0.00 3.27
1212 5862 2.022754 GCGGTAGAGTCCTTCAGGCTA 61.023 57.143 0.00 0.00 34.44 3.93
1219 5869 1.324005 GCCTCAGCGGTAGAGTCCTT 61.324 60.000 11.34 0.00 34.25 3.36
1473 6135 2.568623 TTCCAACTCTTCCTGCCTTC 57.431 50.000 0.00 0.00 0.00 3.46
1483 6145 7.404671 AAAACTGTACATGTTTTCCAACTCT 57.595 32.000 20.78 6.23 41.90 3.24
1520 6186 3.243068 ACAGGCTACAAAGAAACTTTGCG 60.243 43.478 19.64 13.71 32.93 4.85
1523 6189 4.793201 AGGACAGGCTACAAAGAAACTTT 58.207 39.130 0.00 0.00 0.00 2.66
1526 6192 5.306394 AGTAAGGACAGGCTACAAAGAAAC 58.694 41.667 0.00 0.00 0.00 2.78
1527 6193 5.071250 TGAGTAAGGACAGGCTACAAAGAAA 59.929 40.000 0.00 0.00 0.00 2.52
1528 6194 4.591498 TGAGTAAGGACAGGCTACAAAGAA 59.409 41.667 0.00 0.00 0.00 2.52
1529 6195 4.157246 TGAGTAAGGACAGGCTACAAAGA 58.843 43.478 0.00 0.00 0.00 2.52
1530 6196 4.537135 TGAGTAAGGACAGGCTACAAAG 57.463 45.455 0.00 0.00 0.00 2.77
1531 6197 5.499004 AATGAGTAAGGACAGGCTACAAA 57.501 39.130 0.00 0.00 0.00 2.83
1532 6198 5.245531 CAAATGAGTAAGGACAGGCTACAA 58.754 41.667 0.00 0.00 0.00 2.41
1533 6199 4.832248 CAAATGAGTAAGGACAGGCTACA 58.168 43.478 0.00 0.00 0.00 2.74
1534 6200 3.623510 GCAAATGAGTAAGGACAGGCTAC 59.376 47.826 0.00 0.00 0.00 3.58
1535 6201 3.519510 AGCAAATGAGTAAGGACAGGCTA 59.480 43.478 0.00 0.00 0.00 3.93
1536 6202 2.307098 AGCAAATGAGTAAGGACAGGCT 59.693 45.455 0.00 0.00 0.00 4.58
1537 6203 2.716217 AGCAAATGAGTAAGGACAGGC 58.284 47.619 0.00 0.00 0.00 4.85
1538 6204 5.940470 AGTAAAGCAAATGAGTAAGGACAGG 59.060 40.000 0.00 0.00 0.00 4.00
1539 6205 6.428159 ACAGTAAAGCAAATGAGTAAGGACAG 59.572 38.462 0.00 0.00 0.00 3.51
1540 6206 6.296026 ACAGTAAAGCAAATGAGTAAGGACA 58.704 36.000 0.00 0.00 0.00 4.02
1541 6207 6.651225 AGACAGTAAAGCAAATGAGTAAGGAC 59.349 38.462 0.00 0.00 0.00 3.85
1542 6208 6.769512 AGACAGTAAAGCAAATGAGTAAGGA 58.230 36.000 0.00 0.00 0.00 3.36
1543 6209 6.876257 AGAGACAGTAAAGCAAATGAGTAAGG 59.124 38.462 0.00 0.00 0.00 2.69
1544 6210 7.064016 GGAGAGACAGTAAAGCAAATGAGTAAG 59.936 40.741 0.00 0.00 0.00 2.34
1545 6211 6.874134 GGAGAGACAGTAAAGCAAATGAGTAA 59.126 38.462 0.00 0.00 0.00 2.24
1546 6212 6.211584 AGGAGAGACAGTAAAGCAAATGAGTA 59.788 38.462 0.00 0.00 0.00 2.59
1547 6213 5.012561 AGGAGAGACAGTAAAGCAAATGAGT 59.987 40.000 0.00 0.00 0.00 3.41
1548 6214 5.350914 CAGGAGAGACAGTAAAGCAAATGAG 59.649 44.000 0.00 0.00 0.00 2.90
1549 6215 5.221722 ACAGGAGAGACAGTAAAGCAAATGA 60.222 40.000 0.00 0.00 0.00 2.57
1550 6216 4.999950 ACAGGAGAGACAGTAAAGCAAATG 59.000 41.667 0.00 0.00 0.00 2.32
1551 6217 5.234466 ACAGGAGAGACAGTAAAGCAAAT 57.766 39.130 0.00 0.00 0.00 2.32
1552 6218 4.689612 ACAGGAGAGACAGTAAAGCAAA 57.310 40.909 0.00 0.00 0.00 3.68
1553 6219 4.833380 AGTACAGGAGAGACAGTAAAGCAA 59.167 41.667 0.00 0.00 0.00 3.91
1554 6220 4.408276 AGTACAGGAGAGACAGTAAAGCA 58.592 43.478 0.00 0.00 0.00 3.91
1555 6221 5.394224 AAGTACAGGAGAGACAGTAAAGC 57.606 43.478 0.00 0.00 0.00 3.51
1556 6222 9.930693 AATTTAAGTACAGGAGAGACAGTAAAG 57.069 33.333 0.00 0.00 0.00 1.85
1559 6225 9.970553 TCTAATTTAAGTACAGGAGAGACAGTA 57.029 33.333 0.00 0.00 0.00 2.74
1623 6289 4.100189 AGACACTCCCCAAAGATAAGATCG 59.900 45.833 0.00 0.00 0.00 3.69
1704 8566 2.877097 TGGACATACAAGTGGCATGT 57.123 45.000 0.00 0.00 35.65 3.21
1736 8598 7.223971 TGAAATACAGCTACATACAATTCGGAC 59.776 37.037 0.00 0.00 0.00 4.79
1828 8702 2.724349 CAAGTTCAAAGACAGCTGTGC 58.276 47.619 27.27 15.71 28.90 4.57
1839 8713 1.946081 TGCGTGAGATGCAAGTTCAAA 59.054 42.857 0.00 0.00 37.15 2.69
1849 8723 0.592637 TTTGGCACTTGCGTGAGATG 59.407 50.000 0.00 0.00 43.97 2.90
1850 8724 0.593128 GTTTGGCACTTGCGTGAGAT 59.407 50.000 0.00 0.00 43.97 2.75
1886 8760 1.602377 GAAATGTATGTGTAGGGCCGC 59.398 52.381 0.00 0.00 0.00 6.53
1887 8761 3.131396 GAGAAATGTATGTGTAGGGCCG 58.869 50.000 0.00 0.00 0.00 6.13
1888 8762 3.477530 GGAGAAATGTATGTGTAGGGCC 58.522 50.000 0.00 0.00 0.00 5.80
1889 8763 3.136626 AGGGAGAAATGTATGTGTAGGGC 59.863 47.826 0.00 0.00 0.00 5.19
1948 9011 4.161295 CGCTTCTCCCATGGCGGA 62.161 66.667 6.09 3.29 43.25 5.54
1967 9030 6.724441 TGGTACAGTTCTTTCATCTTCCTCTA 59.276 38.462 0.00 0.00 0.00 2.43
1993 9056 4.019860 GGCTATAAGATTCTGGATCTGCCA 60.020 45.833 16.33 0.31 44.41 4.92
2001 9064 7.364585 CCTTCTCCTATGGCTATAAGATTCTGG 60.365 44.444 0.00 0.00 0.00 3.86
2019 9082 1.229658 CCTCCCCACACCTTCTCCT 60.230 63.158 0.00 0.00 0.00 3.69
2057 9120 1.211457 GCCTGTGAATCCTGTGATCCT 59.789 52.381 0.00 0.00 0.00 3.24
2095 9158 7.040409 GGATCAAGATTATTTGCGGTAGGAATT 60.040 37.037 0.00 0.00 0.00 2.17
2104 9167 4.580167 TGAAGGGGATCAAGATTATTTGCG 59.420 41.667 0.00 0.00 0.00 4.85
2157 9220 7.898014 TCTCTAATGTAATAGGTGAAGCAGA 57.102 36.000 0.00 0.00 0.00 4.26
2185 9248 5.593095 GTCTCTGGGTTTCCTTTTGTAAGTT 59.407 40.000 0.00 0.00 0.00 2.66
2211 9642 2.364970 AGTGATCAGCATAGTCTCCTGC 59.635 50.000 0.00 0.11 38.69 4.85
2258 9689 7.194607 TCAGAGTAGACAGCAAATTTTTCTG 57.805 36.000 13.05 13.05 0.00 3.02
2264 9695 8.798859 ACATATTTCAGAGTAGACAGCAAATT 57.201 30.769 0.00 0.00 0.00 1.82
2265 9696 8.671921 CAACATATTTCAGAGTAGACAGCAAAT 58.328 33.333 0.00 0.00 0.00 2.32
2286 9717 8.142485 AGGTACCTACAGTGTAAATACAACAT 57.858 34.615 14.41 3.83 38.04 2.71


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

AutoCloner maintained by Alex Coulton.