Multiple sequence alignment - TraesCS1D01G246100

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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 TraesCS1D01G246100 chr1D 100.000 6339 0 0 1 6339 338519170 338525508 0.000000e+00 11707.0
1 TraesCS1D01G246100 chr1D 84.215 1077 116 25 3727 4762 338534263 338535326 0.000000e+00 998.0
2 TraesCS1D01G246100 chr1D 87.869 610 57 10 4592 5192 338539941 338540542 0.000000e+00 701.0
3 TraesCS1D01G246100 chr1D 89.222 167 17 1 2353 2518 338537010 338537176 2.320000e-49 207.0
4 TraesCS1D01G246100 chr1A 94.081 5558 175 47 892 6338 437582638 437588152 0.000000e+00 8299.0
5 TraesCS1D01G246100 chr1A 83.893 447 52 13 2353 2794 437592085 437592516 5.920000e-110 409.0
6 TraesCS1D01G246100 chr1A 93.200 250 13 4 1 247 437581292 437581540 1.300000e-96 364.0
7 TraesCS1D01G246100 chr1A 80.714 420 56 14 2857 3262 437692282 437691874 2.870000e-78 303.0
8 TraesCS1D01G246100 chr1A 88.571 245 24 2 353 593 437581596 437581840 1.730000e-75 294.0
9 TraesCS1D01G246100 chr1A 79.903 413 42 15 5903 6314 437712209 437712581 1.360000e-66 265.0
10 TraesCS1D01G246100 chr1A 78.964 309 33 20 5191 5482 437590217 437590510 1.400000e-41 182.0
11 TraesCS1D01G246100 chr1A 94.915 59 3 0 268 326 437581537 437581595 6.770000e-15 93.5
12 TraesCS1D01G246100 chr1A 92.857 42 2 1 5903 5944 437590906 437590946 6.860000e-05 60.2
13 TraesCS1D01G246100 chr1B 95.957 1781 45 13 3684 5441 453191472 453193248 0.000000e+00 2865.0
14 TraesCS1D01G246100 chr1B 97.095 1549 29 3 2146 3685 453189638 453191179 0.000000e+00 2597.0
15 TraesCS1D01G246100 chr1B 87.821 1634 121 37 591 2166 453188014 453189627 0.000000e+00 1844.0
16 TraesCS1D01G246100 chr1B 94.783 920 20 14 5431 6338 453193398 453194301 0.000000e+00 1408.0
17 TraesCS1D01G246100 chr1B 86.277 685 65 18 3727 4393 453200574 453201247 0.000000e+00 717.0
18 TraesCS1D01G246100 chr1B 87.728 603 50 16 4 593 453180751 453181342 0.000000e+00 682.0
19 TraesCS1D01G246100 chr1B 87.797 590 56 11 4613 5192 453202645 453203228 0.000000e+00 676.0
20 TraesCS1D01G246100 chr1B 89.414 529 51 3 4592 5118 453276110 453276635 0.000000e+00 662.0
21 TraesCS1D01G246100 chr1B 81.179 441 53 11 2353 2789 453212141 453212555 1.700000e-85 327.0
22 TraesCS1D01G246100 chr1B 91.034 145 11 1 6194 6338 453317161 453317303 1.800000e-45 195.0
23 TraesCS1D01G246100 chr1B 84.810 79 10 2 5289 5367 453208386 453208462 1.890000e-10 78.7
24 TraesCS1D01G246100 chr1B 93.182 44 2 1 5903 5946 453209100 453209142 5.310000e-06 63.9
25 TraesCS1D01G246100 chr2B 95.349 86 4 0 3418 3503 679898336 679898251 3.080000e-28 137.0
26 TraesCS1D01G246100 chr2A 95.349 86 4 0 3418 3503 706752991 706752906 3.080000e-28 137.0
27 TraesCS1D01G246100 chr7A 89.091 110 7 4 3401 3506 60731065 60731173 1.430000e-26 132.0
28 TraesCS1D01G246100 chr7A 90.722 97 8 1 3415 3510 202994989 202995085 1.850000e-25 128.0
29 TraesCS1D01G246100 chr2D 94.186 86 5 0 3418 3503 566989088 566989003 1.430000e-26 132.0
30 TraesCS1D01G246100 chr3B 89.899 99 8 2 3413 3510 685063034 685063131 6.670000e-25 126.0
31 TraesCS1D01G246100 chr3D 88.889 99 9 2 3413 3510 520220518 520220615 3.100000e-23 121.0


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 TraesCS1D01G246100 chr1D 338519170 338525508 6338 False 11707.000000 11707 100.000000 1 6339 1 chr1D.!!$F1 6338
1 TraesCS1D01G246100 chr1D 338534263 338540542 6279 False 635.333333 998 87.102000 2353 5192 3 chr1D.!!$F2 2839
2 TraesCS1D01G246100 chr1A 437581292 437592516 11224 False 1385.957143 8299 89.497286 1 6338 7 chr1A.!!$F2 6337
3 TraesCS1D01G246100 chr1B 453188014 453194301 6287 False 2178.500000 2865 93.914000 591 6338 4 chr1B.!!$F4 5747
4 TraesCS1D01G246100 chr1B 453200574 453203228 2654 False 696.500000 717 87.037000 3727 5192 2 chr1B.!!$F5 1465
5 TraesCS1D01G246100 chr1B 453180751 453181342 591 False 682.000000 682 87.728000 4 593 1 chr1B.!!$F1 589
6 TraesCS1D01G246100 chr1B 453276110 453276635 525 False 662.000000 662 89.414000 4592 5118 1 chr1B.!!$F2 526

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
559 574 0.107508 AACATCCTCAGCATCACCCG 60.108 55.000 0.00 0.00 0.00 5.28 F
813 1309 0.519961 GGCAAACGTTCGTTGGCTAT 59.480 50.000 28.17 5.60 42.80 2.97 F
924 1636 0.855349 GAGTCGTGACAAGCACTGTG 59.145 55.000 2.76 2.76 45.49 3.66 F
1256 1968 1.940613 ACGAAACTCGCTTCAGCTTTT 59.059 42.857 0.00 0.00 45.12 2.27 F
1746 2470 1.461127 GACGAATCGGCATCATTAGGC 59.539 52.381 2.47 0.00 33.63 3.93 F
2157 2908 0.178992 ATGAGTTGTGTGTGGGGGTG 60.179 55.000 0.00 0.00 0.00 4.61 F
2876 3668 0.241213 GTCTGTGACGCTCTAGCACA 59.759 55.000 2.44 0.00 42.21 4.57 F
3027 3820 2.664851 TGCCGAAGCCAACTGTCG 60.665 61.111 0.00 0.00 38.69 4.35 F
3623 4419 3.664107 AGCGTGCAGTCATTCTTCTTTA 58.336 40.909 0.00 0.00 0.00 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1406 2123 0.926846 GTGCGATAAGAGCAGCTCAC 59.073 55.000 24.64 8.7 46.10 3.51 R
1641 2365 3.190738 AAAGCACCGCTGCCCACTA 62.191 57.895 0.00 0.0 45.53 2.74 R
1729 2453 3.931578 AGTAGCCTAATGATGCCGATTC 58.068 45.455 0.00 0.0 0.00 2.52 R
2098 2849 4.375272 ACTGAGATTAACAGCGATGATGG 58.625 43.478 8.12 0.0 38.74 3.51 R
3539 4335 2.236146 TGGTTCTACATGCACCTTCGAT 59.764 45.455 0.00 0.0 33.01 3.59 R
4072 5174 3.071874 TGTGGGCAGAAACCTCTAATG 57.928 47.619 0.00 0.0 0.00 1.90 R
4700 11856 6.385176 TCTCTGGAGTCAATTTACCATGAGAT 59.615 38.462 0.00 0.0 34.82 2.75 R
5006 12169 1.035932 ACTCCGGGTCGTATCCAGTG 61.036 60.000 0.00 0.0 0.00 3.66 R
5432 12623 0.867753 CTGGCTTGTACTAGCTCGCG 60.868 60.000 24.97 0.0 40.99 5.87 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
248 253 9.419297 GCAAATATATATCCGACACACTAAAGA 57.581 33.333 0.00 0.00 0.00 2.52
251 256 9.529823 AATATATATCCGACACACTAAAGAGGA 57.470 33.333 0.00 0.00 0.00 3.71
318 323 6.805016 AGTCATCCAGATAATCTGTCTTGT 57.195 37.500 0.00 0.00 42.80 3.16
334 339 4.513692 TGTCTTGTCCGGACATACAAAAAG 59.486 41.667 34.06 27.56 41.52 2.27
338 343 3.244422 TGTCCGGACATACAAAAAGAGCT 60.244 43.478 33.23 0.00 36.21 4.09
347 352 8.462016 GGACATACAAAAAGAGCTAAACATGAT 58.538 33.333 0.00 0.00 0.00 2.45
372 377 7.535139 TGTTTGATCTTCCGTCAATATTTTCC 58.465 34.615 0.00 0.00 35.68 3.13
380 386 5.104374 TCCGTCAATATTTTCCGTACACTC 58.896 41.667 0.00 0.00 0.00 3.51
392 398 2.732500 CCGTACACTCGTTTGTTATGCA 59.267 45.455 0.00 0.00 0.00 3.96
400 406 6.592220 ACACTCGTTTGTTATGCATGTATACA 59.408 34.615 10.16 8.27 0.00 2.29
491 506 2.852495 CTACGCACGCTGGGGTGAAT 62.852 60.000 19.39 9.78 40.38 2.57
509 524 4.039124 GTGAATATCCCGAATTTGGCCATT 59.961 41.667 6.09 0.00 0.00 3.16
522 537 1.272928 TGGCCATTAAGCACATTGGGA 60.273 47.619 0.00 0.00 0.00 4.37
559 574 0.107508 AACATCCTCAGCATCACCCG 60.108 55.000 0.00 0.00 0.00 5.28
565 580 2.438975 CAGCATCACCCGGCATGT 60.439 61.111 0.00 0.00 0.00 3.21
634 1111 4.839121 AGGACACTTATAATTGGCGAACA 58.161 39.130 7.63 0.00 0.00 3.18
651 1128 3.926527 CGAACATTCGTCAAAGAGGATGA 59.073 43.478 5.85 0.00 45.09 2.92
658 1135 4.641396 TCGTCAAAGAGGATGACATTTGT 58.359 39.130 7.36 0.00 45.90 2.83
663 1140 7.148423 CGTCAAAGAGGATGACATTTGTGAATA 60.148 37.037 7.36 0.00 45.90 1.75
669 1146 7.123098 AGAGGATGACATTTGTGAATATTTGCA 59.877 33.333 0.00 0.00 0.00 4.08
695 1186 4.097892 ACAGTTTTAGTTGAAAGTGGCAGG 59.902 41.667 9.27 0.00 41.86 4.85
707 1198 1.074405 AGTGGCAGGCATCTCTTTGAA 59.926 47.619 0.00 0.00 0.00 2.69
712 1203 3.446516 GGCAGGCATCTCTTTGAAAAGAT 59.553 43.478 5.97 0.34 43.52 2.40
744 1237 6.950428 CGTTTAAACTGTCATCTTTGATCTCG 59.050 38.462 16.01 0.00 33.56 4.04
753 1246 8.322906 TGTCATCTTTGATCTCGTTTTACAAT 57.677 30.769 0.00 0.00 33.56 2.71
786 1282 2.531522 AAAGATGGTTTGCTTGCCAC 57.468 45.000 0.00 0.00 37.62 5.01
789 1285 2.490993 GATGGTTTGCTTGCCACCCG 62.491 60.000 8.13 0.00 37.62 5.28
811 1307 2.719354 GGCAAACGTTCGTTGGCT 59.281 55.556 28.17 6.24 42.80 4.75
812 1308 1.833434 CGGCAAACGTTCGTTGGCTA 61.833 55.000 28.17 0.00 42.80 3.93
813 1309 0.519961 GGCAAACGTTCGTTGGCTAT 59.480 50.000 28.17 5.60 42.80 2.97
824 1320 6.985645 ACGTTCGTTGGCTATTATTATTACCA 59.014 34.615 0.00 0.00 0.00 3.25
825 1321 7.042523 ACGTTCGTTGGCTATTATTATTACCAC 60.043 37.037 0.00 0.00 0.00 4.16
826 1322 7.569957 CGTTCGTTGGCTATTATTATTACCACC 60.570 40.741 0.00 0.00 0.00 4.61
847 1343 7.178628 ACCACCGATCTATACAGCTATTATTGT 59.821 37.037 0.00 0.00 0.00 2.71
859 1534 8.340618 ACAGCTATTATTGTCAAAGACATTGT 57.659 30.769 0.12 0.00 42.40 2.71
866 1541 8.669946 TTATTGTCAAAGACATTGTCACTGTA 57.330 30.769 18.57 6.65 42.40 2.74
868 1543 5.423886 TGTCAAAGACATTGTCACTGTACA 58.576 37.500 18.57 15.15 37.67 2.90
869 1544 5.877564 TGTCAAAGACATTGTCACTGTACAA 59.122 36.000 18.57 0.00 43.16 2.41
870 1545 6.183360 TGTCAAAGACATTGTCACTGTACAAC 60.183 38.462 18.57 9.23 41.89 3.32
871 1546 5.877564 TCAAAGACATTGTCACTGTACAACA 59.122 36.000 18.57 0.00 41.89 3.33
872 1547 6.542005 TCAAAGACATTGTCACTGTACAACAT 59.458 34.615 18.57 0.00 41.89 2.71
873 1548 7.713073 TCAAAGACATTGTCACTGTACAACATA 59.287 33.333 18.57 0.00 41.89 2.29
874 1549 8.506437 CAAAGACATTGTCACTGTACAACATAT 58.494 33.333 18.57 0.00 41.89 1.78
875 1550 9.719355 AAAGACATTGTCACTGTACAACATATA 57.281 29.630 18.57 0.00 41.89 0.86
876 1551 8.703604 AGACATTGTCACTGTACAACATATAC 57.296 34.615 18.57 0.00 41.89 1.47
877 1552 8.531982 AGACATTGTCACTGTACAACATATACT 58.468 33.333 18.57 0.00 41.89 2.12
878 1553 8.703604 ACATTGTCACTGTACAACATATACTC 57.296 34.615 0.00 0.00 41.89 2.59
879 1554 8.531982 ACATTGTCACTGTACAACATATACTCT 58.468 33.333 0.00 0.00 41.89 3.24
910 1585 3.997319 TCAAAAATCGCTCATGAGTCG 57.003 42.857 23.38 24.00 0.00 4.18
921 1633 1.341209 TCATGAGTCGTGACAAGCACT 59.659 47.619 11.11 0.00 45.49 4.40
922 1634 1.458445 CATGAGTCGTGACAAGCACTG 59.542 52.381 6.49 0.00 45.49 3.66
924 1636 0.855349 GAGTCGTGACAAGCACTGTG 59.145 55.000 2.76 2.76 45.49 3.66
933 1645 2.492773 AAGCACTGTGGCAGCCAAC 61.493 57.895 18.28 11.38 34.18 3.77
1256 1968 1.940613 ACGAAACTCGCTTCAGCTTTT 59.059 42.857 0.00 0.00 45.12 2.27
1359 2071 2.220593 CCGAGTTCTACGACGAGGTATC 59.779 54.545 0.00 0.00 0.00 2.24
1385 2102 3.511934 AGTAGTTCTCAGAGGCATTTCGT 59.488 43.478 0.00 0.00 0.00 3.85
1444 2161 2.430244 CGGAGCGCGTACTTGTGT 60.430 61.111 8.43 0.00 0.00 3.72
1455 2175 5.544621 CGCGTACTTGTGTTTATAAACTCC 58.455 41.667 24.81 16.94 39.59 3.85
1746 2470 1.461127 GACGAATCGGCATCATTAGGC 59.539 52.381 2.47 0.00 33.63 3.93
1784 2513 5.174037 TGGTCCTTCCGTATCATTTTCTT 57.826 39.130 0.00 0.00 39.52 2.52
1928 2657 5.195940 CACACATCTCTATTCACCCCAAAT 58.804 41.667 0.00 0.00 0.00 2.32
2022 2773 4.806342 TGTTTTCTTCTGTTACTTCGCC 57.194 40.909 0.00 0.00 0.00 5.54
2029 2780 3.863142 TCTGTTACTTCGCCTACCTTC 57.137 47.619 0.00 0.00 0.00 3.46
2089 2840 6.183361 TGAGCATACATCTCCATCTGATTCAA 60.183 38.462 0.00 0.00 0.00 2.69
2098 2849 9.894783 CATCTCCATCTGATTCAAATATTCAAC 57.105 33.333 0.00 0.00 0.00 3.18
2149 2900 9.809096 ATTGTCTAGACTTATATGAGTTGTGTG 57.191 33.333 23.01 0.00 0.00 3.82
2150 2901 8.349568 TGTCTAGACTTATATGAGTTGTGTGT 57.650 34.615 23.01 0.00 0.00 3.72
2151 2902 8.244113 TGTCTAGACTTATATGAGTTGTGTGTG 58.756 37.037 23.01 0.00 0.00 3.82
2153 2904 5.734720 AGACTTATATGAGTTGTGTGTGGG 58.265 41.667 1.15 0.00 0.00 4.61
2155 2906 2.806945 ATATGAGTTGTGTGTGGGGG 57.193 50.000 0.00 0.00 0.00 5.40
2156 2907 1.440618 TATGAGTTGTGTGTGGGGGT 58.559 50.000 0.00 0.00 0.00 4.95
2157 2908 0.178992 ATGAGTTGTGTGTGGGGGTG 60.179 55.000 0.00 0.00 0.00 4.61
2187 2971 7.386299 GGGATTATACTTATGTGAGTTGAGCTG 59.614 40.741 0.00 0.00 0.00 4.24
2206 2990 3.758554 GCTGTCACATCCATGGTTTTACT 59.241 43.478 12.58 0.00 0.00 2.24
2509 3293 8.911662 CATTTGGACTCTTACAAATTTAAACCG 58.088 33.333 0.00 0.00 42.78 4.44
2522 3306 3.899052 TTAAACCGTACTGCTATGCCT 57.101 42.857 0.00 0.00 0.00 4.75
2565 3349 4.844349 TCTGGACCAAGAATTAAGGGAG 57.156 45.455 0.00 0.00 0.00 4.30
2581 3365 7.624360 TTAAGGGAGCTACACAAAATACATG 57.376 36.000 0.00 0.00 0.00 3.21
2876 3668 0.241213 GTCTGTGACGCTCTAGCACA 59.759 55.000 2.44 0.00 42.21 4.57
2972 3765 7.123355 ACAAAATCATGGAAAAGGAAGTTCA 57.877 32.000 5.01 0.00 0.00 3.18
3027 3820 2.664851 TGCCGAAGCCAACTGTCG 60.665 61.111 0.00 0.00 38.69 4.35
3188 3981 6.311445 CGTGATGTATGTAAAAGCTCTGTTCT 59.689 38.462 0.00 0.00 0.00 3.01
3189 3982 7.488150 CGTGATGTATGTAAAAGCTCTGTTCTA 59.512 37.037 0.00 0.00 0.00 2.10
3190 3983 9.151471 GTGATGTATGTAAAAGCTCTGTTCTAA 57.849 33.333 0.00 0.00 0.00 2.10
3191 3984 9.151471 TGATGTATGTAAAAGCTCTGTTCTAAC 57.849 33.333 0.00 0.00 0.00 2.34
3192 3985 9.372369 GATGTATGTAAAAGCTCTGTTCTAACT 57.628 33.333 0.00 0.00 0.00 2.24
3193 3986 9.726438 ATGTATGTAAAAGCTCTGTTCTAACTT 57.274 29.630 0.00 0.00 0.00 2.66
3194 3987 9.204570 TGTATGTAAAAGCTCTGTTCTAACTTC 57.795 33.333 0.00 0.00 0.00 3.01
3539 4335 4.106663 AGGAACTACCCATAAACAAACCCA 59.893 41.667 0.00 0.00 36.02 4.51
3623 4419 3.664107 AGCGTGCAGTCATTCTTCTTTA 58.336 40.909 0.00 0.00 0.00 1.85
3884 4981 4.998671 TTTTGACTTGTCCTCATTGCAA 57.001 36.364 0.00 0.00 0.00 4.08
4680 7055 6.530019 AAAGAACATAAAGTATTGCAGGGG 57.470 37.500 0.00 0.00 0.00 4.79
4683 7058 5.888161 AGAACATAAAGTATTGCAGGGGAAG 59.112 40.000 0.00 0.00 0.00 3.46
4700 11856 8.494433 GCAGGGGAAGGATATTATTATCACATA 58.506 37.037 6.89 0.00 36.68 2.29
4793 11950 8.921205 CATTCCCTAATTGGATTCTGAATTTCT 58.079 33.333 4.11 0.00 38.35 2.52
5006 12169 3.251972 AGCAAGAAAAGAGTAAGCTGCAC 59.748 43.478 1.02 0.00 0.00 4.57
5182 12350 1.442526 GCATCGACTTGCCTGGATGG 61.443 60.000 0.00 0.00 37.38 3.51
5306 12497 9.719355 AAAATGTATACATTATATGCGTGGAGA 57.281 29.630 27.15 0.00 45.06 3.71
5307 12498 9.719355 AAATGTATACATTATATGCGTGGAGAA 57.281 29.630 27.15 0.00 45.06 2.87
5308 12499 8.703604 ATGTATACATTATATGCGTGGAGAAC 57.296 34.615 12.75 0.00 31.37 3.01
5309 12500 7.892609 TGTATACATTATATGCGTGGAGAACT 58.107 34.615 0.08 0.00 0.00 3.01
5310 12501 7.812669 TGTATACATTATATGCGTGGAGAACTG 59.187 37.037 0.08 0.00 0.00 3.16
5311 12502 4.380531 ACATTATATGCGTGGAGAACTGG 58.619 43.478 0.00 0.00 0.00 4.00
5432 12623 2.011947 GGGTATTCCGGTGCTTGTAAC 58.988 52.381 0.00 0.00 33.83 2.50
5665 13016 4.991153 TCTCATAAGCTAGGACACTGTG 57.009 45.455 6.19 6.19 0.00 3.66
5840 13193 0.978146 AATAGCTCCCACCGCTGAGT 60.978 55.000 0.00 0.00 38.38 3.41
5960 13322 4.216257 GTCTGCCAAATTCTGAAGCTGTTA 59.784 41.667 0.00 0.00 0.00 2.41
5964 13326 5.068987 TGCCAAATTCTGAAGCTGTTACTTT 59.931 36.000 0.00 0.00 0.00 2.66
5965 13327 5.631096 GCCAAATTCTGAAGCTGTTACTTTC 59.369 40.000 0.00 0.00 0.00 2.62
6047 13411 3.011760 GCGAAACCAAGTCGGCTCG 62.012 63.158 0.00 0.00 43.24 5.03
6170 13534 2.845363 TGCTCTTCTCAGATGTTGCA 57.155 45.000 6.82 6.82 0.00 4.08
6261 13625 1.621317 TCACCACTGCAAAGATCCGTA 59.379 47.619 0.00 0.00 0.00 4.02
6338 13702 1.684983 ACGAAAACTCACCGGAGAAGA 59.315 47.619 9.46 0.00 44.26 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
235 240 8.928270 AATACTATTTCCTCTTTAGTGTGTCG 57.072 34.615 0.00 0.00 0.00 4.35
318 323 3.695830 AGCTCTTTTTGTATGTCCGGA 57.304 42.857 0.00 0.00 0.00 5.14
347 352 7.535139 GGAAAATATTGACGGAAGATCAAACA 58.465 34.615 0.00 0.00 39.43 2.83
372 377 4.143200 ACATGCATAACAAACGAGTGTACG 60.143 41.667 0.00 0.00 39.31 3.67
380 386 7.341446 TCGATTGTATACATGCATAACAAACG 58.659 34.615 24.10 24.10 34.73 3.60
400 406 7.431249 AGCAATGAAAAGCATATCAATCGATT 58.569 30.769 4.39 4.39 35.78 3.34
491 506 3.572255 GCTTAATGGCCAAATTCGGGATA 59.428 43.478 10.96 0.00 0.00 2.59
496 511 3.229276 TGTGCTTAATGGCCAAATTCG 57.771 42.857 10.96 0.00 0.00 3.34
509 524 2.550606 GTGTTCGTTCCCAATGTGCTTA 59.449 45.455 0.00 0.00 0.00 3.09
522 537 1.018148 TTCACGCCAATGTGTTCGTT 58.982 45.000 0.00 0.00 40.74 3.85
611 638 5.979993 TGTTCGCCAATTATAAGTGTCCTA 58.020 37.500 11.63 0.00 0.00 2.94
634 1111 5.707298 ACAAATGTCATCCTCTTTGACGAAT 59.293 36.000 3.46 0.00 45.14 3.34
642 1119 7.977853 GCAAATATTCACAAATGTCATCCTCTT 59.022 33.333 0.00 0.00 0.00 2.85
648 1125 8.035984 TGTCATGCAAATATTCACAAATGTCAT 58.964 29.630 0.00 0.00 0.00 3.06
651 1128 7.380536 ACTGTCATGCAAATATTCACAAATGT 58.619 30.769 0.00 0.00 0.00 2.71
658 1135 9.409312 CAACTAAAACTGTCATGCAAATATTCA 57.591 29.630 0.00 0.00 0.00 2.57
663 1140 7.981225 ACTTTCAACTAAAACTGTCATGCAAAT 59.019 29.630 0.00 0.00 0.00 2.32
669 1146 5.359576 TGCCACTTTCAACTAAAACTGTCAT 59.640 36.000 0.00 0.00 0.00 3.06
753 1246 8.555361 GCAAACCATCTTTACTTGCAATTTTAA 58.445 29.630 0.00 0.00 41.55 1.52
762 1255 3.989817 GGCAAGCAAACCATCTTTACTTG 59.010 43.478 0.00 0.00 36.87 3.16
794 1290 0.519961 ATAGCCAACGAACGTTTGCC 59.480 50.000 24.57 12.34 44.59 4.52
807 1303 7.490657 AGATCGGTGGTAATAATAATAGCCA 57.509 36.000 0.00 0.00 0.00 4.75
813 1309 9.251440 AGCTGTATAGATCGGTGGTAATAATAA 57.749 33.333 0.00 0.00 0.00 1.40
824 1320 8.349568 TGACAATAATAGCTGTATAGATCGGT 57.650 34.615 0.00 0.00 0.00 4.69
825 1321 9.639601 TTTGACAATAATAGCTGTATAGATCGG 57.360 33.333 0.00 0.00 0.00 4.18
847 1343 5.877564 TGTTGTACAGTGACAATGTCTTTGA 59.122 36.000 12.49 0.00 41.21 2.69
874 1549 8.971321 GCGATTTTTGAAACCGTATATAGAGTA 58.029 33.333 0.00 0.00 0.00 2.59
875 1550 7.709613 AGCGATTTTTGAAACCGTATATAGAGT 59.290 33.333 0.00 0.00 0.00 3.24
876 1551 8.073355 AGCGATTTTTGAAACCGTATATAGAG 57.927 34.615 0.00 0.00 0.00 2.43
877 1552 7.707464 TGAGCGATTTTTGAAACCGTATATAGA 59.293 33.333 0.00 0.00 0.00 1.98
878 1553 7.847487 TGAGCGATTTTTGAAACCGTATATAG 58.153 34.615 0.00 0.00 0.00 1.31
879 1554 7.773864 TGAGCGATTTTTGAAACCGTATATA 57.226 32.000 0.00 0.00 0.00 0.86
880 1555 6.671614 TGAGCGATTTTTGAAACCGTATAT 57.328 33.333 0.00 0.00 0.00 0.86
881 1556 6.314152 TCATGAGCGATTTTTGAAACCGTATA 59.686 34.615 0.00 0.00 0.00 1.47
882 1557 5.123186 TCATGAGCGATTTTTGAAACCGTAT 59.877 36.000 0.00 0.00 0.00 3.06
883 1558 4.452795 TCATGAGCGATTTTTGAAACCGTA 59.547 37.500 0.00 0.00 0.00 4.02
884 1559 3.252215 TCATGAGCGATTTTTGAAACCGT 59.748 39.130 0.00 0.00 0.00 4.83
885 1560 3.820689 TCATGAGCGATTTTTGAAACCG 58.179 40.909 0.00 0.00 0.00 4.44
886 1561 4.798574 ACTCATGAGCGATTTTTGAAACC 58.201 39.130 22.83 0.00 0.00 3.27
887 1562 4.551126 CGACTCATGAGCGATTTTTGAAAC 59.449 41.667 25.52 3.74 32.49 2.78
888 1563 4.213270 ACGACTCATGAGCGATTTTTGAAA 59.787 37.500 31.93 0.00 34.06 2.69
889 1564 3.745975 ACGACTCATGAGCGATTTTTGAA 59.254 39.130 31.93 0.00 34.06 2.69
890 1565 3.123453 CACGACTCATGAGCGATTTTTGA 59.877 43.478 31.93 0.00 34.06 2.69
910 1585 1.650912 CTGCCACAGTGCTTGTCAC 59.349 57.895 0.00 0.00 45.98 3.67
933 1645 1.642215 GATGCAGTGATGCTCGCAG 59.358 57.895 0.00 0.00 35.72 5.18
951 1663 2.837371 GAAACCCGAGCCGACAGAGG 62.837 65.000 0.00 0.00 0.00 3.69
1143 1855 2.179517 GTGCAGACGAGACGGAGG 59.820 66.667 0.00 0.00 0.00 4.30
1406 2123 0.926846 GTGCGATAAGAGCAGCTCAC 59.073 55.000 24.64 8.70 46.10 3.51
1444 2161 3.358118 CCAAAGGGGCGGAGTTTATAAA 58.642 45.455 0.00 0.00 0.00 1.40
1511 2233 1.691196 TGTCCCAAGCAAAAGGTCAG 58.309 50.000 0.00 0.00 0.00 3.51
1641 2365 3.190738 AAAGCACCGCTGCCCACTA 62.191 57.895 0.00 0.00 45.53 2.74
1729 2453 3.931578 AGTAGCCTAATGATGCCGATTC 58.068 45.455 0.00 0.00 0.00 2.52
1746 2470 5.776173 AGGACCATCGACAAATCTAGTAG 57.224 43.478 0.00 0.00 0.00 2.57
1808 2537 8.687242 CCCTCGTGATGATTCTATATAAGCTAA 58.313 37.037 0.00 0.00 0.00 3.09
1928 2657 5.178623 GGTATTCGTGTGTTCAACTCATCAA 59.821 40.000 0.00 0.00 0.00 2.57
2022 2773 9.765795 AGAGATAATACCAATTTTCGAAGGTAG 57.234 33.333 16.36 2.47 39.74 3.18
2029 2780 9.542462 TGTTAGGAGAGATAATACCAATTTTCG 57.458 33.333 0.00 0.00 30.81 3.46
2089 2840 7.566760 TTAACAGCGATGATGGTTGAATATT 57.433 32.000 8.12 0.00 0.00 1.28
2098 2849 4.375272 ACTGAGATTAACAGCGATGATGG 58.625 43.478 8.12 0.00 38.74 3.51
2105 2856 5.349817 AGACAATGAACTGAGATTAACAGCG 59.650 40.000 0.00 0.00 38.74 5.18
2187 2971 9.783256 GTAAAATAGTAAAACCATGGATGTGAC 57.217 33.333 21.47 9.44 0.00 3.67
2509 3293 4.508662 AGAGAAACAAGGCATAGCAGTAC 58.491 43.478 0.00 0.00 0.00 2.73
2554 3338 8.276252 TGTATTTTGTGTAGCTCCCTTAATTC 57.724 34.615 0.00 0.00 0.00 2.17
2565 3349 6.968904 CCATCTGTTCATGTATTTTGTGTAGC 59.031 38.462 0.00 0.00 0.00 3.58
2581 3365 5.185635 TGGATCACAATTTTCCCATCTGTTC 59.814 40.000 0.00 0.00 0.00 3.18
3408 4201 7.041098 GCGACAATTAATTTGGATCAGGAGTAT 60.041 37.037 0.00 0.00 39.80 2.12
3539 4335 2.236146 TGGTTCTACATGCACCTTCGAT 59.764 45.455 0.00 0.00 33.01 3.59
3623 4419 9.558648 GTGTTTCAATTTCTTGCAAAATTCTTT 57.441 25.926 0.00 0.00 36.86 2.52
4072 5174 3.071874 TGTGGGCAGAAACCTCTAATG 57.928 47.619 0.00 0.00 0.00 1.90
4583 6956 6.867662 ATTAGATGTATAACAGCTTGGCAC 57.132 37.500 2.86 0.00 43.03 5.01
4700 11856 6.385176 TCTCTGGAGTCAATTTACCATGAGAT 59.615 38.462 0.00 0.00 34.82 2.75
4858 12015 8.055986 GCTGAAAAGAAAAACAATACGGAAAAG 58.944 33.333 0.00 0.00 0.00 2.27
5006 12169 1.035932 ACTCCGGGTCGTATCCAGTG 61.036 60.000 0.00 0.00 0.00 3.66
5182 12350 4.261197 CCACAAAGAAACAGCTAGTGGAAC 60.261 45.833 0.00 0.00 42.32 3.62
5304 12495 5.194432 ACATCACTACGTATCTCCAGTTCT 58.806 41.667 0.00 0.00 0.00 3.01
5305 12496 5.502153 ACATCACTACGTATCTCCAGTTC 57.498 43.478 0.00 0.00 0.00 3.01
5306 12497 5.884232 TGTACATCACTACGTATCTCCAGTT 59.116 40.000 0.00 0.00 0.00 3.16
5307 12498 5.434408 TGTACATCACTACGTATCTCCAGT 58.566 41.667 0.00 0.00 0.00 4.00
5308 12499 6.561737 ATGTACATCACTACGTATCTCCAG 57.438 41.667 1.41 0.00 0.00 3.86
5309 12500 6.954487 AATGTACATCACTACGTATCTCCA 57.046 37.500 9.23 0.00 0.00 3.86
5310 12501 6.144080 GCAAATGTACATCACTACGTATCTCC 59.856 42.308 9.23 0.00 0.00 3.71
5311 12502 6.695713 TGCAAATGTACATCACTACGTATCTC 59.304 38.462 9.23 0.00 0.00 2.75
5432 12623 0.867753 CTGGCTTGTACTAGCTCGCG 60.868 60.000 24.97 0.00 40.99 5.87
5605 12956 6.845782 GCAAAACTGCAATTACTTTTACAAGC 59.154 34.615 0.00 0.00 32.02 4.01
5634 12985 7.554118 TGTCCTAGCTTATGAGATTTCCAAAAG 59.446 37.037 0.00 0.00 0.00 2.27
5683 13034 1.736126 CAGTAAGCACATGGAGCACAG 59.264 52.381 13.81 0.00 0.00 3.66
5840 13193 4.639310 CGAACCTTGGTCTAGCTAGTTAGA 59.361 45.833 20.10 11.90 0.00 2.10
5960 13322 0.323178 CAGGGCAGCCATGAGAAAGT 60.323 55.000 22.14 0.00 37.52 2.66
5964 13326 1.491274 TTGACAGGGCAGCCATGAGA 61.491 55.000 32.50 14.88 37.52 3.27
5965 13327 0.395311 ATTGACAGGGCAGCCATGAG 60.395 55.000 32.50 7.56 37.52 2.90
6047 13411 3.257127 AGTGGCGAGCCTAGAGAATAATC 59.743 47.826 15.75 0.00 36.94 1.75
6170 13534 1.400494 GACGTTGTTTGCACCTTGTCT 59.600 47.619 0.00 0.00 0.00 3.41
6261 13625 3.326297 GGCTCTCAATACTATTGCCCTCT 59.674 47.826 4.13 0.00 33.45 3.69


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

AutoCloner maintained by Alex Coulton.