Multiple sequence alignment - TraesCS2B01G620600

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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 TraesCS2B01G620600 chr2B 100.000 4801 0 0 1 4801 795049475 795044675 0.000000e+00 8866.0
1 TraesCS2B01G620600 chr2B 93.939 66 4 0 1 66 523781490 523781555 3.060000e-17 100.0
2 TraesCS2B01G620600 chr2A 90.221 4612 265 86 1 4496 762314673 762319214 0.000000e+00 5847.0
3 TraesCS2B01G620600 chr2A 78.406 690 76 35 1235 1910 753815290 753815920 9.750000e-102 381.0
4 TraesCS2B01G620600 chr2A 80.777 515 64 15 2869 3369 762323959 762324452 2.110000e-98 370.0
5 TraesCS2B01G620600 chr2A 92.683 164 12 0 4526 4689 762319213 762319376 2.230000e-58 237.0
6 TraesCS2B01G620600 chr2A 99.138 116 1 0 4686 4801 762324414 762324529 4.870000e-50 209.0
7 TraesCS2B01G620600 chr2D 89.709 4460 277 79 1 4328 637635263 637630854 0.000000e+00 5526.0
8 TraesCS2B01G620600 chr2D 85.846 650 52 19 2820 3456 637606936 637606314 0.000000e+00 654.0
9 TraesCS2B01G620600 chr2D 91.237 194 14 1 2473 2666 637607279 637607089 1.330000e-65 261.0
10 TraesCS2B01G620600 chr2D 97.590 83 1 1 2302 2384 637608185 637608104 1.800000e-29 141.0
11 TraesCS2B01G620600 chr2D 94.286 70 3 1 2728 2797 637607068 637607000 6.570000e-19 106.0
12 TraesCS2B01G620600 chr2D 87.356 87 7 1 4719 4801 637606305 637606219 3.950000e-16 97.1
13 TraesCS2B01G620600 chr1A 84.192 563 58 18 165 707 168548644 168548093 7.120000e-143 518.0
14 TraesCS2B01G620600 chr1A 77.667 900 129 35 1188 2065 96731926 96732775 2.600000e-132 483.0
15 TraesCS2B01G620600 chr1A 95.588 68 3 0 1 68 168548731 168548664 5.080000e-20 110.0
16 TraesCS2B01G620600 chr1A 97.872 47 0 1 1709 1754 561117067 561117113 3.980000e-11 80.5
17 TraesCS2B01G620600 chr3A 77.855 578 83 21 1418 1977 572536662 572537212 2.790000e-82 316.0
18 TraesCS2B01G620600 chr1D 77.122 542 71 21 1414 1947 468126494 468126990 1.020000e-66 265.0


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 TraesCS2B01G620600 chr2B 795044675 795049475 4800 True 8866.00 8866 100.0000 1 4801 1 chr2B.!!$R1 4800
1 TraesCS2B01G620600 chr2A 762314673 762319376 4703 False 3042.00 5847 91.4520 1 4689 2 chr2A.!!$F2 4688
2 TraesCS2B01G620600 chr2A 753815290 753815920 630 False 381.00 381 78.4060 1235 1910 1 chr2A.!!$F1 675
3 TraesCS2B01G620600 chr2A 762323959 762324529 570 False 289.50 370 89.9575 2869 4801 2 chr2A.!!$F3 1932
4 TraesCS2B01G620600 chr2D 637630854 637635263 4409 True 5526.00 5526 89.7090 1 4328 1 chr2D.!!$R1 4327
5 TraesCS2B01G620600 chr2D 637606219 637608185 1966 True 251.82 654 91.2630 2302 4801 5 chr2D.!!$R2 2499
6 TraesCS2B01G620600 chr1A 96731926 96732775 849 False 483.00 483 77.6670 1188 2065 1 chr1A.!!$F1 877
7 TraesCS2B01G620600 chr1A 168548093 168548731 638 True 314.00 518 89.8900 1 707 2 chr1A.!!$R1 706
8 TraesCS2B01G620600 chr3A 572536662 572537212 550 False 316.00 316 77.8550 1418 1977 1 chr3A.!!$F1 559

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
561 610 1.151668 CCGTCTTCTTCCACAGCTTG 58.848 55.0 0.00 0.0 0.00 4.01 F
1430 1564 0.979709 TACGACGAGGAGGAGGAGGA 60.980 60.0 0.00 0.0 0.00 3.71 F
2971 3925 0.247736 CCTGCTTAGCAACTCTCGGT 59.752 55.0 8.68 0.0 38.41 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1861 2031 1.200948 GCAATCCAGCCACTGAAGTTC 59.799 52.381 0.0 0.0 32.44 3.01 R
3375 4350 0.240945 ATACACAAAGCAACAGCCGC 59.759 50.000 0.0 0.0 0.00 6.53 R
4629 5634 0.952280 GCATCATCATCCAGGCAGTG 59.048 55.000 0.0 0.0 0.00 3.66 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
93 94 3.395858 GAGTGAGTCGATTGCAAATGG 57.604 47.619 1.71 0.00 0.00 3.16
94 95 1.470098 AGTGAGTCGATTGCAAATGGC 59.530 47.619 1.71 0.00 45.13 4.40
111 112 6.089954 GCAAATGGCAAACTGAACTATCTTTC 59.910 38.462 0.00 0.00 43.97 2.62
127 145 8.256356 ACTATCTTTCACTAGAGGTATGCAAT 57.744 34.615 0.00 0.00 0.00 3.56
128 146 8.709308 ACTATCTTTCACTAGAGGTATGCAATT 58.291 33.333 0.00 0.00 0.00 2.32
185 221 4.019321 TGAGAATTCTACAAGGGGTCCAAG 60.019 45.833 8.25 0.00 0.00 3.61
187 223 4.019231 AGAATTCTACAAGGGGTCCAAGTC 60.019 45.833 6.06 0.00 0.00 3.01
234 273 1.216710 GCTGAGCTTACTGCCGAGT 59.783 57.895 0.00 0.00 44.23 4.18
239 278 2.143925 GAGCTTACTGCCGAGTTTGTT 58.856 47.619 0.00 0.00 44.23 2.83
367 406 1.351076 TCAGAGCAGACCACCATCAA 58.649 50.000 0.00 0.00 0.00 2.57
370 409 2.093075 CAGAGCAGACCACCATCAATCT 60.093 50.000 0.00 0.00 0.00 2.40
375 414 4.080129 AGCAGACCACCATCAATCTAACAT 60.080 41.667 0.00 0.00 0.00 2.71
379 418 5.190528 AGACCACCATCAATCTAACATCAGT 59.809 40.000 0.00 0.00 0.00 3.41
382 421 6.384015 ACCACCATCAATCTAACATCAGTAGA 59.616 38.462 0.00 0.00 0.00 2.59
401 440 7.067615 TCAGTAGAAGAAAGATAGCAGTAGGTG 59.932 40.741 0.00 0.00 0.00 4.00
402 441 5.606348 AGAAGAAAGATAGCAGTAGGTGG 57.394 43.478 0.00 0.00 0.00 4.61
403 442 5.026790 AGAAGAAAGATAGCAGTAGGTGGT 58.973 41.667 0.00 0.00 40.92 4.16
561 610 1.151668 CCGTCTTCTTCCACAGCTTG 58.848 55.000 0.00 0.00 0.00 4.01
601 655 3.819920 TCTGCGAGCAGAGCGGAG 61.820 66.667 22.28 0.00 46.80 4.63
798 890 2.179517 CCACGACGACTCTCTGGC 59.820 66.667 0.00 0.00 0.00 4.85
806 898 1.441311 GACTCTCTGGCCTGCTAGC 59.559 63.158 8.10 8.10 0.00 3.42
871 981 4.228567 GGCTCTAGGTGGGCTCGC 62.229 72.222 0.00 0.00 0.00 5.03
909 1019 1.301558 CAGATGAGATGAGGCCCGC 60.302 63.158 0.00 0.00 0.00 6.13
913 1023 4.959596 GAGATGAGGCCCGCGAGC 62.960 72.222 8.23 5.53 0.00 5.03
964 1074 5.124776 CACTCTGTTATCTCCTCGTCTTCTT 59.875 44.000 0.00 0.00 0.00 2.52
1042 1152 4.962836 GGATGGGGATGGCGGCTG 62.963 72.222 11.43 0.00 0.00 4.85
1221 1343 3.319198 GGCGAAGACCAGGGTCCA 61.319 66.667 14.67 0.00 45.59 4.02
1389 1514 2.492090 CGGGAGGAGCAGTTCGAG 59.508 66.667 0.00 0.00 0.00 4.04
1430 1564 0.979709 TACGACGAGGAGGAGGAGGA 60.980 60.000 0.00 0.00 0.00 3.71
1560 1695 3.676049 GCATAGTCACCATCGTCAGTTGA 60.676 47.826 0.00 0.00 0.00 3.18
1582 1719 7.634671 TGATTCACATTCAGCTTTGTCATAT 57.365 32.000 0.00 0.00 0.00 1.78
1583 1720 8.735692 TGATTCACATTCAGCTTTGTCATATA 57.264 30.769 0.00 0.00 0.00 0.86
1584 1721 8.833493 TGATTCACATTCAGCTTTGTCATATAG 58.167 33.333 0.00 0.00 0.00 1.31
1596 1733 8.715998 AGCTTTGTCATATAGCTAATTCATTCG 58.284 33.333 0.00 0.00 43.08 3.34
1624 1765 6.872628 TGAAATGCATTATCCTAAGCTCAG 57.127 37.500 13.39 0.00 0.00 3.35
1649 1790 4.593597 GCAAATTTGTGCAGATTGATGG 57.406 40.909 19.03 0.00 44.29 3.51
1755 1906 5.163893 GGTCGACATGTAATTAACCACACTG 60.164 44.000 18.91 0.00 0.00 3.66
1758 1909 5.178623 CGACATGTAATTAACCACACTGTGT 59.821 40.000 7.80 7.80 0.00 3.72
1760 1911 7.064134 CGACATGTAATTAACCACACTGTGTAT 59.936 37.037 13.89 5.77 0.00 2.29
1791 1944 6.381481 TTGATTGCAATGTCCATAGATGAC 57.619 37.500 18.59 0.00 0.00 3.06
1804 1957 4.283212 CCATAGATGACTCCCCTCTTCTTC 59.717 50.000 0.00 0.00 0.00 2.87
1805 1958 3.774842 AGATGACTCCCCTCTTCTTCT 57.225 47.619 0.00 0.00 0.00 2.85
1806 1959 3.373830 AGATGACTCCCCTCTTCTTCTG 58.626 50.000 0.00 0.00 0.00 3.02
1807 1960 1.270907 TGACTCCCCTCTTCTTCTGC 58.729 55.000 0.00 0.00 0.00 4.26
1808 1961 1.203237 TGACTCCCCTCTTCTTCTGCT 60.203 52.381 0.00 0.00 0.00 4.24
1809 1962 1.905894 GACTCCCCTCTTCTTCTGCTT 59.094 52.381 0.00 0.00 0.00 3.91
1810 1963 3.100671 GACTCCCCTCTTCTTCTGCTTA 58.899 50.000 0.00 0.00 0.00 3.09
1811 1964 3.103742 ACTCCCCTCTTCTTCTGCTTAG 58.896 50.000 0.00 0.00 0.00 2.18
1812 1965 3.103742 CTCCCCTCTTCTTCTGCTTAGT 58.896 50.000 0.00 0.00 0.00 2.24
1813 1966 4.264442 ACTCCCCTCTTCTTCTGCTTAGTA 60.264 45.833 0.00 0.00 0.00 1.82
1814 1967 4.684724 TCCCCTCTTCTTCTGCTTAGTAA 58.315 43.478 0.00 0.00 0.00 2.24
1815 1968 4.466726 TCCCCTCTTCTTCTGCTTAGTAAC 59.533 45.833 0.00 0.00 0.00 2.50
1816 1969 4.223032 CCCCTCTTCTTCTGCTTAGTAACA 59.777 45.833 0.00 0.00 0.00 2.41
1817 1970 5.415221 CCCTCTTCTTCTGCTTAGTAACAG 58.585 45.833 6.28 6.28 35.15 3.16
1818 1971 5.046950 CCCTCTTCTTCTGCTTAGTAACAGT 60.047 44.000 10.38 0.00 35.37 3.55
1819 1972 6.459923 CCTCTTCTTCTGCTTAGTAACAGTT 58.540 40.000 10.38 0.00 35.37 3.16
1820 1973 6.931840 CCTCTTCTTCTGCTTAGTAACAGTTT 59.068 38.462 0.00 0.00 35.37 2.66
1924 2096 0.923403 TTTCATCGATTGAGCGCTCG 59.077 50.000 30.75 20.60 35.27 5.03
1929 2101 0.930282 TCGATTGAGCGCTCGATTCG 60.930 55.000 34.87 33.68 38.86 3.34
1933 2105 0.713883 TTGAGCGCTCGATTCGTTTC 59.286 50.000 30.75 5.96 0.00 2.78
1961 2133 6.441093 TCAAGCATGATTTCAGTTGATACC 57.559 37.500 0.00 0.00 0.00 2.73
2002 2179 6.653320 TCTCCATGTGGTGTTTAATGAAGTAC 59.347 38.462 0.00 0.00 36.34 2.73
2010 2187 8.561212 GTGGTGTTTAATGAAGTACACAATGTA 58.439 33.333 7.85 0.00 41.94 2.29
2132 2310 3.873910 CGGGTAAGGATCACACAGAAAT 58.126 45.455 0.00 0.00 0.00 2.17
2201 2380 4.099881 AGGGCATTACAAATGCTTATGTGG 59.900 41.667 20.47 0.00 44.02 4.17
2243 2422 4.749598 TGCTTATGTAACACACTGACACTG 59.250 41.667 0.00 0.00 0.00 3.66
2411 3291 3.326880 AGAATTCCACGGTAACCAGAAGT 59.673 43.478 0.65 0.00 0.00 3.01
2450 3330 5.506730 TTATTGTGTCAGTAATCACCCCA 57.493 39.130 0.00 0.00 34.14 4.96
2471 3351 3.525268 AAAAACAGGTTCCTGCTTGTG 57.475 42.857 17.55 0.00 37.57 3.33
2525 3437 9.965824 CTATGAATTTAAAAGTTGGTGTGTCTT 57.034 29.630 0.00 0.00 0.00 3.01
2528 3440 8.930760 TGAATTTAAAAGTTGGTGTGTCTTTTG 58.069 29.630 10.90 0.00 40.21 2.44
2553 3465 6.019479 GTGTGATGTGCTTCTAGTTGTATAGC 60.019 42.308 0.00 0.00 0.00 2.97
2654 3566 2.224018 TGCAACTTCAATTTGGTGAGCC 60.224 45.455 0.00 0.00 0.00 4.70
2656 3568 3.383761 CAACTTCAATTTGGTGAGCCAC 58.616 45.455 0.00 0.00 46.01 5.01
2657 3569 1.608590 ACTTCAATTTGGTGAGCCACG 59.391 47.619 0.00 0.00 46.01 4.94
2665 3577 1.557099 TGGTGAGCCACGTAGATTCT 58.443 50.000 0.00 0.00 40.46 2.40
2673 3585 5.637810 TGAGCCACGTAGATTCTTTTACTTG 59.362 40.000 0.00 0.00 0.00 3.16
2690 3602 3.697166 ACTTGTCTTCCTGTTTTGTGGT 58.303 40.909 0.00 0.00 0.00 4.16
2971 3925 0.247736 CCTGCTTAGCAACTCTCGGT 59.752 55.000 8.68 0.00 38.41 4.69
3095 4052 6.527057 AGATGTTAGTCCAGTTACCACTAC 57.473 41.667 0.00 0.00 0.00 2.73
3156 4113 5.355630 TGCAACTTAGAAGCACTTTGTGTAA 59.644 36.000 0.00 0.00 35.75 2.41
3157 4114 6.127869 TGCAACTTAGAAGCACTTTGTGTAAA 60.128 34.615 0.00 0.00 35.75 2.01
3166 4123 5.418676 AGCACTTTGTGTAAAAACAGCAAT 58.581 33.333 0.00 0.00 35.75 3.56
3170 4127 6.954852 CACTTTGTGTAAAAACAGCAATTGTG 59.045 34.615 7.40 6.87 40.74 3.33
3219 4176 0.830648 GATCTGATGGACGACCCCAA 59.169 55.000 0.34 0.00 40.04 4.12
3250 4207 2.097629 CGCCATAGACGAAGAGACAGAA 59.902 50.000 0.00 0.00 0.00 3.02
3288 4250 2.896854 TCAGCCGGCGATTGCATC 60.897 61.111 23.20 0.00 45.35 3.91
3319 4288 5.459505 TCTTTCTAGTTGGCTCCTAGCTAT 58.540 41.667 0.00 0.00 41.99 2.97
3371 4346 3.131933 TGACTGGTGTTTGATGTTTTGGG 59.868 43.478 0.00 0.00 0.00 4.12
3372 4347 2.158971 ACTGGTGTTTGATGTTTTGGGC 60.159 45.455 0.00 0.00 0.00 5.36
3373 4348 1.202463 TGGTGTTTGATGTTTTGGGCG 60.202 47.619 0.00 0.00 0.00 6.13
3374 4349 1.202475 GGTGTTTGATGTTTTGGGCGT 60.202 47.619 0.00 0.00 0.00 5.68
3375 4350 1.857837 GTGTTTGATGTTTTGGGCGTG 59.142 47.619 0.00 0.00 0.00 5.34
3376 4351 0.858583 GTTTGATGTTTTGGGCGTGC 59.141 50.000 0.00 0.00 0.00 5.34
3377 4352 0.596083 TTTGATGTTTTGGGCGTGCG 60.596 50.000 0.00 0.00 0.00 5.34
3378 4353 2.126502 GATGTTTTGGGCGTGCGG 60.127 61.111 0.00 0.00 0.00 5.69
3379 4354 4.356442 ATGTTTTGGGCGTGCGGC 62.356 61.111 9.70 9.70 42.51 6.53
3381 4356 4.999939 GTTTTGGGCGTGCGGCTG 63.000 66.667 17.11 0.00 42.94 4.85
3596 4575 1.434555 TACACATACGTTGGTGCTGC 58.565 50.000 16.36 0.00 38.57 5.25
3639 4618 3.368236 GTGTAGGTTAAGAAGAAGCTGCG 59.632 47.826 0.00 0.00 40.94 5.18
3743 4722 7.036220 ACATTATTTGTCTACGAGTTGGAGAG 58.964 38.462 0.00 0.00 30.89 3.20
3866 4845 2.416747 CATCGTGCAAGGAAAGAGACA 58.583 47.619 0.00 0.00 32.76 3.41
4100 5103 5.922544 GCAAAAAGCACTTGTGATAGTTGAT 59.077 36.000 14.52 0.00 44.79 2.57
4348 5352 7.397476 TGTGGTATTTGTTAATGGATAGGCAAA 59.603 33.333 0.00 0.00 0.00 3.68
4496 5501 0.111061 ATTGAACAGCCTCAGGTGCA 59.889 50.000 0.00 0.00 45.66 4.57
4497 5502 0.819259 TTGAACAGCCTCAGGTGCAC 60.819 55.000 8.80 8.80 45.66 4.57
4498 5503 1.968540 GAACAGCCTCAGGTGCACC 60.969 63.158 29.22 29.22 45.66 5.01
4507 5512 4.730487 AGGTGCACCTGATGAAGC 57.270 55.556 37.39 6.73 46.55 3.86
4508 5513 2.073232 AGGTGCACCTGATGAAGCT 58.927 52.632 37.39 10.40 46.55 3.74
4509 5514 0.322277 AGGTGCACCTGATGAAGCTG 60.322 55.000 37.39 0.00 43.59 4.24
4510 5515 0.321919 GGTGCACCTGATGAAGCTGA 60.322 55.000 29.12 0.00 30.81 4.26
4511 5516 1.085091 GTGCACCTGATGAAGCTGAG 58.915 55.000 5.22 0.00 0.00 3.35
4512 5517 0.035725 TGCACCTGATGAAGCTGAGG 60.036 55.000 0.00 0.00 0.00 3.86
4513 5518 0.251354 GCACCTGATGAAGCTGAGGA 59.749 55.000 0.00 0.00 0.00 3.71
4514 5519 1.134159 GCACCTGATGAAGCTGAGGAT 60.134 52.381 0.00 0.00 0.00 3.24
4515 5520 2.683152 GCACCTGATGAAGCTGAGGATT 60.683 50.000 0.00 0.00 0.00 3.01
4516 5521 3.618351 CACCTGATGAAGCTGAGGATTT 58.382 45.455 0.00 0.00 0.00 2.17
4517 5522 3.377485 CACCTGATGAAGCTGAGGATTTG 59.623 47.826 0.00 0.00 0.00 2.32
4518 5523 3.009916 ACCTGATGAAGCTGAGGATTTGT 59.990 43.478 0.00 0.00 0.00 2.83
4519 5524 4.015084 CCTGATGAAGCTGAGGATTTGTT 58.985 43.478 0.00 0.00 0.00 2.83
4520 5525 4.461781 CCTGATGAAGCTGAGGATTTGTTT 59.538 41.667 0.00 0.00 0.00 2.83
4521 5526 5.649395 CCTGATGAAGCTGAGGATTTGTTTA 59.351 40.000 0.00 0.00 0.00 2.01
4522 5527 6.151648 CCTGATGAAGCTGAGGATTTGTTTAA 59.848 38.462 0.00 0.00 0.00 1.52
4523 5528 7.309377 CCTGATGAAGCTGAGGATTTGTTTAAA 60.309 37.037 0.00 0.00 0.00 1.52
4524 5529 7.596494 TGATGAAGCTGAGGATTTGTTTAAAG 58.404 34.615 0.00 0.00 0.00 1.85
4525 5530 6.331369 TGAAGCTGAGGATTTGTTTAAAGG 57.669 37.500 0.00 0.00 0.00 3.11
4526 5531 4.790765 AGCTGAGGATTTGTTTAAAGGC 57.209 40.909 0.00 0.00 0.00 4.35
4614 5619 4.460382 TCTGCTCTTATTTCCTTTGCTTGG 59.540 41.667 0.00 0.00 0.00 3.61
4622 5627 0.704076 TCCTTTGCTTGGGCCATACT 59.296 50.000 7.26 0.00 37.74 2.12
4629 5634 1.207089 GCTTGGGCCATACTTTTTCCC 59.793 52.381 7.26 0.00 37.49 3.97
4644 5649 0.256752 TTCCCACTGCCTGGATGATG 59.743 55.000 0.00 0.00 43.95 3.07
4645 5650 0.621280 TCCCACTGCCTGGATGATGA 60.621 55.000 0.00 0.00 43.95 2.92
4659 5664 3.057033 GGATGATGATGCAGCCCATTTAC 60.057 47.826 0.00 0.00 38.38 2.01
4663 5668 4.038282 TGATGATGCAGCCCATTTACATTC 59.962 41.667 0.00 0.00 33.29 2.67
4682 5687 2.344592 TCAAGGCCTAAGGACCAGAAA 58.655 47.619 5.16 0.00 0.00 2.52
4684 5689 2.040412 CAAGGCCTAAGGACCAGAAAGT 59.960 50.000 5.16 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 7.270757 ACATCTAAACTTGTGTGCAATTGTA 57.729 32.000 7.40 0.00 33.65 2.41
93 94 7.064016 CCTCTAGTGAAAGATAGTTCAGTTTGC 59.936 40.741 0.94 0.00 40.73 3.68
94 95 8.091449 ACCTCTAGTGAAAGATAGTTCAGTTTG 58.909 37.037 0.94 0.00 40.73 2.93
111 112 8.506168 TCCTTAAAAATTGCATACCTCTAGTG 57.494 34.615 0.00 0.00 0.00 2.74
164 189 3.916989 ACTTGGACCCCTTGTAGAATTCT 59.083 43.478 13.56 13.56 0.00 2.40
216 255 0.390472 AACTCGGCAGTAAGCTCAGC 60.390 55.000 0.00 0.00 44.79 4.26
234 273 0.854062 CGGACGAAGCGTACAACAAA 59.146 50.000 2.92 0.00 41.29 2.83
239 278 1.002142 CCATATCGGACGAAGCGTACA 60.002 52.381 0.00 0.00 41.29 2.90
370 409 8.972127 ACTGCTATCTTTCTTCTACTGATGTTA 58.028 33.333 0.00 0.00 0.00 2.41
375 414 7.067615 CACCTACTGCTATCTTTCTTCTACTGA 59.932 40.741 0.00 0.00 0.00 3.41
379 418 6.096987 CACCACCTACTGCTATCTTTCTTCTA 59.903 42.308 0.00 0.00 0.00 2.10
382 421 4.624125 GCACCACCTACTGCTATCTTTCTT 60.624 45.833 0.00 0.00 0.00 2.52
392 431 0.674895 CCTCTTGCACCACCTACTGC 60.675 60.000 0.00 0.00 0.00 4.40
401 440 0.747283 CCTGCATCTCCTCTTGCACC 60.747 60.000 0.00 0.00 43.54 5.01
402 441 0.035630 ACCTGCATCTCCTCTTGCAC 60.036 55.000 0.00 0.00 43.54 4.57
403 442 0.035725 CACCTGCATCTCCTCTTGCA 60.036 55.000 0.00 0.00 46.03 4.08
561 610 2.435059 GTGGAGGCGCTCAAGGAC 60.435 66.667 7.64 0.00 31.08 3.85
613 667 0.032678 CTCATCTCTAATGGCGGCGT 59.967 55.000 9.37 0.00 0.00 5.68
674 757 3.471244 CTCCGACATCCGCGTCTCC 62.471 68.421 4.92 0.00 36.84 3.71
757 840 1.215647 GCCGGAGACATGTCGAAGT 59.784 57.895 19.85 2.34 34.09 3.01
883 993 1.117749 TCATCTCATCTGAGCCCGGG 61.118 60.000 19.09 19.09 41.80 5.73
909 1019 3.573772 TTGCTCCAGTGGACGCTCG 62.574 63.158 24.73 11.67 30.89 5.03
913 1023 2.868583 CAGATATTTGCTCCAGTGGACG 59.131 50.000 8.12 6.02 0.00 4.79
964 1074 2.757099 GTTAGCGGGTCGGGAGGA 60.757 66.667 0.00 0.00 0.00 3.71
1381 1503 2.202492 CGCCTCGTCCTCGAACTG 60.202 66.667 0.00 0.00 45.61 3.16
1402 1527 2.758089 CCTCGTCGTAGTCCCCGTG 61.758 68.421 0.00 0.00 0.00 4.94
1405 1530 1.823041 CCTCCTCGTCGTAGTCCCC 60.823 68.421 0.00 0.00 0.00 4.81
1542 1677 3.006859 TGAATCAACTGACGATGGTGACT 59.993 43.478 0.00 0.00 0.00 3.41
1560 1695 7.501559 AGCTATATGACAAAGCTGAATGTGAAT 59.498 33.333 8.94 2.50 44.67 2.57
1582 1719 8.335356 GCATTTCAAGTACGAATGAATTAGCTA 58.665 33.333 14.32 0.00 35.63 3.32
1583 1720 7.148255 TGCATTTCAAGTACGAATGAATTAGCT 60.148 33.333 18.96 0.00 35.63 3.32
1584 1721 6.966632 TGCATTTCAAGTACGAATGAATTAGC 59.033 34.615 14.32 14.95 35.63 3.09
1596 1733 8.159344 AGCTTAGGATAATGCATTTCAAGTAC 57.841 34.615 18.75 2.10 0.00 2.73
1767 1918 6.776116 AGTCATCTATGGACATTGCAATCAAT 59.224 34.615 9.53 1.81 43.31 2.57
1770 1921 5.180868 GGAGTCATCTATGGACATTGCAATC 59.819 44.000 9.53 0.00 37.74 2.67
1781 1934 3.855668 AGAAGAGGGGAGTCATCTATGG 58.144 50.000 0.00 0.00 35.17 2.74
1786 1939 2.158971 GCAGAAGAAGAGGGGAGTCATC 60.159 54.545 0.00 0.00 0.00 2.92
1787 1940 1.836802 GCAGAAGAAGAGGGGAGTCAT 59.163 52.381 0.00 0.00 0.00 3.06
1791 1944 3.103742 ACTAAGCAGAAGAAGAGGGGAG 58.896 50.000 0.00 0.00 0.00 4.30
1804 1957 9.813080 GAAGTAATCAAAACTGTTACTAAGCAG 57.187 33.333 0.00 0.00 37.60 4.24
1805 1958 9.555727 AGAAGTAATCAAAACTGTTACTAAGCA 57.444 29.630 0.00 0.00 37.60 3.91
1811 1964 9.665264 CCTGAAAGAAGTAATCAAAACTGTTAC 57.335 33.333 0.00 0.00 34.07 2.50
1812 1965 8.349983 GCCTGAAAGAAGTAATCAAAACTGTTA 58.650 33.333 0.00 0.00 34.07 2.41
1813 1966 7.203218 GCCTGAAAGAAGTAATCAAAACTGTT 58.797 34.615 0.00 0.00 34.07 3.16
1814 1967 6.239036 GGCCTGAAAGAAGTAATCAAAACTGT 60.239 38.462 0.00 0.00 34.07 3.55
1815 1968 6.015940 AGGCCTGAAAGAAGTAATCAAAACTG 60.016 38.462 3.11 0.00 34.07 3.16
1816 1969 6.015940 CAGGCCTGAAAGAAGTAATCAAAACT 60.016 38.462 29.88 0.00 34.07 2.66
1817 1970 6.152379 CAGGCCTGAAAGAAGTAATCAAAAC 58.848 40.000 29.88 0.00 34.07 2.43
1818 1971 5.833131 ACAGGCCTGAAAGAAGTAATCAAAA 59.167 36.000 39.19 0.00 34.07 2.44
1819 1972 5.241506 CACAGGCCTGAAAGAAGTAATCAAA 59.758 40.000 39.19 0.00 34.07 2.69
1820 1973 4.761739 CACAGGCCTGAAAGAAGTAATCAA 59.238 41.667 39.19 0.00 34.07 2.57
1861 2031 1.200948 GCAATCCAGCCACTGAAGTTC 59.799 52.381 0.00 0.00 32.44 3.01
1924 2096 6.408858 TCATGCTTGAACTAGAAACGAATC 57.591 37.500 0.00 0.00 0.00 2.52
1929 2101 7.588512 ACTGAAATCATGCTTGAACTAGAAAC 58.411 34.615 6.36 0.00 34.96 2.78
1933 2105 7.137490 TCAACTGAAATCATGCTTGAACTAG 57.863 36.000 6.36 5.85 34.96 2.57
1984 2161 7.422399 ACATTGTGTACTTCATTAAACACCAC 58.578 34.615 3.97 0.00 41.17 4.16
2132 2310 8.107095 AGGTTAGAAGTTTGCATTTCTATGGTA 58.893 33.333 13.39 1.29 36.20 3.25
2201 2380 4.794169 AGCAATGAACACGGTTAAATGTC 58.206 39.130 0.00 0.00 0.00 3.06
2456 3336 2.260844 TTCTCACAAGCAGGAACCTG 57.739 50.000 15.64 15.64 46.15 4.00
2516 3428 3.694734 CACATCACACAAAAGACACACC 58.305 45.455 0.00 0.00 0.00 4.16
2525 3437 4.881273 ACAACTAGAAGCACATCACACAAA 59.119 37.500 0.00 0.00 0.00 2.83
2528 3440 6.019479 GCTATACAACTAGAAGCACATCACAC 60.019 42.308 0.00 0.00 33.38 3.82
2579 3491 1.003118 ACCGCCACTAGAATCTGCAAA 59.997 47.619 0.00 0.00 0.00 3.68
2654 3566 7.599245 AGGAAGACAAGTAAAAGAATCTACGTG 59.401 37.037 0.00 0.00 34.78 4.49
2656 3568 7.599245 ACAGGAAGACAAGTAAAAGAATCTACG 59.401 37.037 0.00 0.00 0.00 3.51
2657 3569 8.834749 ACAGGAAGACAAGTAAAAGAATCTAC 57.165 34.615 0.00 0.00 0.00 2.59
2665 3577 6.209788 ACCACAAAACAGGAAGACAAGTAAAA 59.790 34.615 0.00 0.00 0.00 1.52
2673 3585 4.497507 GCTACAACCACAAAACAGGAAGAC 60.498 45.833 0.00 0.00 0.00 3.01
2690 3602 6.260050 GTCGGAATATGATTCTTTGGCTACAA 59.740 38.462 0.00 0.00 34.07 2.41
3095 4052 5.511088 AAACGTTGTTCAGCGTATAAGAG 57.489 39.130 14.11 0.00 40.70 2.85
3166 4123 5.643348 CACAGATCACCATAAGTAAGCACAA 59.357 40.000 0.00 0.00 0.00 3.33
3170 4127 5.874810 TGTTCACAGATCACCATAAGTAAGC 59.125 40.000 0.00 0.00 0.00 3.09
3219 4176 0.249073 GTCTATGGCGCTCACGATGT 60.249 55.000 7.64 0.00 43.93 3.06
3250 4207 1.459450 GTACCACCAATGCCGTGAAT 58.541 50.000 0.00 0.00 32.77 2.57
3288 4250 5.182190 GGAGCCAACTAGAAAGAAAGAAAGG 59.818 44.000 0.00 0.00 0.00 3.11
3371 4346 4.629115 AAAGCAACAGCCGCACGC 62.629 61.111 0.00 0.00 37.98 5.34
3372 4347 2.726912 CAAAGCAACAGCCGCACG 60.727 61.111 0.00 0.00 0.00 5.34
3373 4348 1.945662 CACAAAGCAACAGCCGCAC 60.946 57.895 0.00 0.00 0.00 5.34
3374 4349 1.098129 TACACAAAGCAACAGCCGCA 61.098 50.000 0.00 0.00 0.00 5.69
3375 4350 0.240945 ATACACAAAGCAACAGCCGC 59.759 50.000 0.00 0.00 0.00 6.53
3376 4351 1.967762 CATACACAAAGCAACAGCCG 58.032 50.000 0.00 0.00 0.00 5.52
3377 4352 1.000385 TGCATACACAAAGCAACAGCC 60.000 47.619 0.00 0.00 34.97 4.85
3378 4353 2.322161 CTGCATACACAAAGCAACAGC 58.678 47.619 0.00 0.00 37.89 4.40
3379 4354 2.553602 TCCTGCATACACAAAGCAACAG 59.446 45.455 0.00 0.00 37.89 3.16
3380 4355 2.553602 CTCCTGCATACACAAAGCAACA 59.446 45.455 0.00 0.00 37.89 3.33
3381 4356 2.095059 CCTCCTGCATACACAAAGCAAC 60.095 50.000 0.00 0.00 37.89 4.17
3470 4448 5.886474 ACTCTACGTATCCTCACATTCTCAA 59.114 40.000 0.00 0.00 0.00 3.02
3510 4488 5.010012 ACAACACATTCTCCAAACAGAATCC 59.990 40.000 0.00 0.00 40.52 3.01
3517 4495 7.440523 AGATCTAACAACACATTCTCCAAAC 57.559 36.000 0.00 0.00 0.00 2.93
3596 4575 5.050363 ACACTCGCTTTACAAACACATACAG 60.050 40.000 0.00 0.00 0.00 2.74
3639 4618 3.701664 ACATCCTCCAAATTCAAGACCC 58.298 45.455 0.00 0.00 0.00 4.46
3732 4711 5.354767 TCATTCATCAATCTCTCCAACTCG 58.645 41.667 0.00 0.00 0.00 4.18
3743 4722 9.553064 ACTACTAAATCCACTCATTCATCAATC 57.447 33.333 0.00 0.00 0.00 2.67
4191 5194 8.853077 TCATGACTCTAAAAAGATCACATTGT 57.147 30.769 0.00 0.00 0.00 2.71
4480 5485 1.968540 GGTGCACCTGAGGCTGTTC 60.969 63.158 29.12 0.00 0.00 3.18
4496 5501 3.009916 ACAAATCCTCAGCTTCATCAGGT 59.990 43.478 0.00 0.00 0.00 4.00
4497 5502 3.618351 ACAAATCCTCAGCTTCATCAGG 58.382 45.455 0.00 0.00 0.00 3.86
4498 5503 5.640189 AAACAAATCCTCAGCTTCATCAG 57.360 39.130 0.00 0.00 0.00 2.90
4499 5504 7.309377 CCTTTAAACAAATCCTCAGCTTCATCA 60.309 37.037 0.00 0.00 0.00 3.07
4500 5505 7.031975 CCTTTAAACAAATCCTCAGCTTCATC 58.968 38.462 0.00 0.00 0.00 2.92
4501 5506 6.573094 GCCTTTAAACAAATCCTCAGCTTCAT 60.573 38.462 0.00 0.00 0.00 2.57
4502 5507 5.278957 GCCTTTAAACAAATCCTCAGCTTCA 60.279 40.000 0.00 0.00 0.00 3.02
4503 5508 5.164233 GCCTTTAAACAAATCCTCAGCTTC 58.836 41.667 0.00 0.00 0.00 3.86
4504 5509 4.021104 GGCCTTTAAACAAATCCTCAGCTT 60.021 41.667 0.00 0.00 0.00 3.74
4505 5510 3.511540 GGCCTTTAAACAAATCCTCAGCT 59.488 43.478 0.00 0.00 0.00 4.24
4506 5511 3.368427 GGGCCTTTAAACAAATCCTCAGC 60.368 47.826 0.84 0.00 0.00 4.26
4507 5512 3.831911 TGGGCCTTTAAACAAATCCTCAG 59.168 43.478 4.53 0.00 0.00 3.35
4508 5513 3.850752 TGGGCCTTTAAACAAATCCTCA 58.149 40.909 4.53 0.00 0.00 3.86
4509 5514 5.420725 AATGGGCCTTTAAACAAATCCTC 57.579 39.130 4.53 0.00 0.00 3.71
4510 5515 6.443527 ACATAATGGGCCTTTAAACAAATCCT 59.556 34.615 15.00 0.00 0.00 3.24
4511 5516 6.649155 ACATAATGGGCCTTTAAACAAATCC 58.351 36.000 15.00 0.00 0.00 3.01
4512 5517 7.413988 GCAACATAATGGGCCTTTAAACAAATC 60.414 37.037 15.00 0.44 0.00 2.17
4513 5518 6.374053 GCAACATAATGGGCCTTTAAACAAAT 59.626 34.615 15.00 0.00 0.00 2.32
4514 5519 5.703130 GCAACATAATGGGCCTTTAAACAAA 59.297 36.000 15.00 0.00 0.00 2.83
4515 5520 5.012561 AGCAACATAATGGGCCTTTAAACAA 59.987 36.000 15.00 0.00 0.00 2.83
4516 5521 4.530161 AGCAACATAATGGGCCTTTAAACA 59.470 37.500 15.00 0.00 0.00 2.83
4517 5522 5.084818 AGCAACATAATGGGCCTTTAAAC 57.915 39.130 15.00 4.64 0.00 2.01
4518 5523 5.247110 TGAAGCAACATAATGGGCCTTTAAA 59.753 36.000 15.00 0.00 0.00 1.52
4519 5524 4.774726 TGAAGCAACATAATGGGCCTTTAA 59.225 37.500 15.00 0.82 0.00 1.52
4520 5525 4.348486 TGAAGCAACATAATGGGCCTTTA 58.652 39.130 13.60 13.60 0.00 1.85
4521 5526 3.172339 TGAAGCAACATAATGGGCCTTT 58.828 40.909 4.53 7.62 0.00 3.11
4522 5527 2.762327 CTGAAGCAACATAATGGGCCTT 59.238 45.455 4.53 0.00 0.00 4.35
4523 5528 2.291800 ACTGAAGCAACATAATGGGCCT 60.292 45.455 4.53 0.00 0.00 5.19
4524 5529 2.102578 ACTGAAGCAACATAATGGGCC 58.897 47.619 0.00 0.00 0.00 5.80
4525 5530 3.056607 ACAACTGAAGCAACATAATGGGC 60.057 43.478 0.00 0.00 0.00 5.36
4526 5531 4.789012 ACAACTGAAGCAACATAATGGG 57.211 40.909 0.00 0.00 0.00 4.00
4614 5619 1.204704 GCAGTGGGAAAAAGTATGGCC 59.795 52.381 0.00 0.00 0.00 5.36
4629 5634 0.952280 GCATCATCATCCAGGCAGTG 59.048 55.000 0.00 0.00 0.00 3.66
4644 5649 4.365723 CTTGAATGTAAATGGGCTGCATC 58.634 43.478 0.50 0.00 0.00 3.91
4645 5650 3.133362 CCTTGAATGTAAATGGGCTGCAT 59.867 43.478 0.50 0.00 0.00 3.96
4659 5664 2.239654 TCTGGTCCTTAGGCCTTGAATG 59.760 50.000 12.58 0.00 0.00 2.67
4663 5668 2.040412 ACTTTCTGGTCCTTAGGCCTTG 59.960 50.000 12.58 4.20 0.00 3.61
4682 5687 7.930325 CACATCAGTACCAGAATATGATCAACT 59.070 37.037 0.00 0.00 0.00 3.16
4684 5689 7.712205 CACACATCAGTACCAGAATATGATCAA 59.288 37.037 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.