Multiple sequence alignment - TraesCS3A01G044600

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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 TraesCS3A01G044600 chr3A 100.000 5372 0 0 1 5372 24010136 24015507 0.000000e+00 9921
1 TraesCS3A01G044600 chr3D 93.618 4983 204 50 125 5011 13181903 13176939 0.000000e+00 7336
2 TraesCS3A01G044600 chr3D 86.630 359 28 7 5014 5372 13176896 13176558 3.930000e-101 379
3 TraesCS3A01G044600 chr3D 96.825 126 4 0 1 126 13182110 13181985 1.520000e-50 211
4 TraesCS3A01G044600 chr3B 94.551 4276 178 29 1 4255 18863204 18858963 0.000000e+00 6554
5 TraesCS3A01G044600 chr3B 84.016 757 53 31 4304 5011 18858772 18858035 0.000000e+00 665
6 TraesCS3A01G044600 chr3B 86.667 165 10 6 5019 5181 18857990 18857836 7.150000e-39 172
7 TraesCS3A01G044600 chr6A 76.973 2167 435 56 2079 4208 9577945 9575806 0.000000e+00 1179
8 TraesCS3A01G044600 chr6A 80.019 1051 197 13 458 1503 9579529 9578487 0.000000e+00 765
9 TraesCS3A01G044600 chr5D 78.372 1757 334 29 2057 3785 43962333 43964071 0.000000e+00 1098
10 TraesCS3A01G044600 chr5D 80.583 1030 194 6 471 1497 43960697 43961723 0.000000e+00 789
11 TraesCS3A01G044600 chr5A 83.231 978 162 2 2076 3052 33929430 33930406 0.000000e+00 896
12 TraesCS3A01G044600 chr2D 81.331 1082 196 5 458 1536 592622917 592621839 0.000000e+00 874
13 TraesCS3A01G044600 chr2D 80.773 1113 198 13 2089 3193 592621048 592619944 0.000000e+00 856
14 TraesCS3A01G044600 chr2B 81.513 1071 190 7 2089 3155 718588631 718587565 0.000000e+00 874
15 TraesCS3A01G044600 chr2B 81.273 1084 196 5 457 1538 718590437 718589359 0.000000e+00 870
16 TraesCS3A01G044600 chr2A 81.232 1071 193 6 2089 3155 727175349 727174283 0.000000e+00 857
17 TraesCS3A01G044600 chr2A 80.869 1082 202 3 458 1538 727177286 727176209 0.000000e+00 846
18 TraesCS3A01G044600 chr2A 96.053 76 2 1 1 76 364478384 364478310 7.310000e-24 122
19 TraesCS3A01G044600 chr1B 73.614 2164 511 53 2079 4208 628618566 628616429 0.000000e+00 778
20 TraesCS3A01G044600 chr4D 80.483 1035 180 20 2126 3149 1697850 1698873 0.000000e+00 773
21 TraesCS3A01G044600 chr4D 75.786 1049 233 17 458 1497 1872486 1873522 1.330000e-140 510
22 TraesCS3A01G044600 chr4D 74.686 877 186 26 3205 4060 2129877 2129016 1.840000e-94 357
23 TraesCS3A01G044600 chr1A 73.513 2186 502 68 2066 4208 550636099 550633948 0.000000e+00 758
24 TraesCS3A01G044600 chr5B 75.165 1663 361 36 2553 4196 41910414 41912043 0.000000e+00 736
25 TraesCS3A01G044600 chr5B 86.492 459 60 2 2057 2514 41907235 41907692 2.230000e-138 503
26 TraesCS3A01G044600 chr5B 93.750 80 3 2 1 80 325074045 325073968 9.450000e-23 119
27 TraesCS3A01G044600 chr4B 81.310 840 153 4 664 1501 3714556 3713719 0.000000e+00 678
28 TraesCS3A01G044600 chr4B 83.259 448 71 4 2078 2523 3305698 3305253 5.010000e-110 409
29 TraesCS3A01G044600 chr4B 95.833 72 3 0 1 72 552857629 552857558 3.400000e-22 117
30 TraesCS3A01G044600 chr4B 95.714 70 3 0 1 70 601527588 601527657 4.400000e-21 113
31 TraesCS3A01G044600 chrUn 76.667 1050 219 19 458 1497 47450837 47451870 4.700000e-155 558
32 TraesCS3A01G044600 chr4A 76.331 1052 222 23 458 1497 602870810 602871846 6.120000e-149 538
33 TraesCS3A01G044600 chr4A 81.917 553 98 2 647 1198 603053638 603053087 2.930000e-127 466
34 TraesCS3A01G044600 chr6B 97.222 72 2 0 1 72 284652682 284652753 7.310000e-24 122
35 TraesCS3A01G044600 chr7D 95.890 73 3 0 1 73 262364765 262364693 9.450000e-23 119
36 TraesCS3A01G044600 chr7D 94.444 72 4 0 1 72 506007023 506006952 1.580000e-20 111
37 TraesCS3A01G044600 chr7A 94.444 72 4 0 1 72 573432776 573432705 1.580000e-20 111


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 TraesCS3A01G044600 chr3A 24010136 24015507 5371 False 9921.000000 9921 100.000000 1 5372 1 chr3A.!!$F1 5371
1 TraesCS3A01G044600 chr3D 13176558 13182110 5552 True 2642.000000 7336 92.357667 1 5372 3 chr3D.!!$R1 5371
2 TraesCS3A01G044600 chr3B 18857836 18863204 5368 True 2463.666667 6554 88.411333 1 5181 3 chr3B.!!$R1 5180
3 TraesCS3A01G044600 chr6A 9575806 9579529 3723 True 972.000000 1179 78.496000 458 4208 2 chr6A.!!$R1 3750
4 TraesCS3A01G044600 chr5D 43960697 43964071 3374 False 943.500000 1098 79.477500 471 3785 2 chr5D.!!$F1 3314
5 TraesCS3A01G044600 chr5A 33929430 33930406 976 False 896.000000 896 83.231000 2076 3052 1 chr5A.!!$F1 976
6 TraesCS3A01G044600 chr2D 592619944 592622917 2973 True 865.000000 874 81.052000 458 3193 2 chr2D.!!$R1 2735
7 TraesCS3A01G044600 chr2B 718587565 718590437 2872 True 872.000000 874 81.393000 457 3155 2 chr2B.!!$R1 2698
8 TraesCS3A01G044600 chr2A 727174283 727177286 3003 True 851.500000 857 81.050500 458 3155 2 chr2A.!!$R2 2697
9 TraesCS3A01G044600 chr1B 628616429 628618566 2137 True 778.000000 778 73.614000 2079 4208 1 chr1B.!!$R1 2129
10 TraesCS3A01G044600 chr4D 1697850 1698873 1023 False 773.000000 773 80.483000 2126 3149 1 chr4D.!!$F1 1023
11 TraesCS3A01G044600 chr4D 1872486 1873522 1036 False 510.000000 510 75.786000 458 1497 1 chr4D.!!$F2 1039
12 TraesCS3A01G044600 chr4D 2129016 2129877 861 True 357.000000 357 74.686000 3205 4060 1 chr4D.!!$R1 855
13 TraesCS3A01G044600 chr1A 550633948 550636099 2151 True 758.000000 758 73.513000 2066 4208 1 chr1A.!!$R1 2142
14 TraesCS3A01G044600 chr5B 41907235 41912043 4808 False 619.500000 736 80.828500 2057 4196 2 chr5B.!!$F1 2139
15 TraesCS3A01G044600 chr4B 3713719 3714556 837 True 678.000000 678 81.310000 664 1501 1 chr4B.!!$R2 837
16 TraesCS3A01G044600 chrUn 47450837 47451870 1033 False 558.000000 558 76.667000 458 1497 1 chrUn.!!$F1 1039
17 TraesCS3A01G044600 chr4A 602870810 602871846 1036 False 538.000000 538 76.331000 458 1497 1 chr4A.!!$F1 1039
18 TraesCS3A01G044600 chr4A 603053087 603053638 551 True 466.000000 466 81.917000 647 1198 1 chr4A.!!$R1 551

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
753 846 1.308877 AGGACATGGGGTGCCTTAAT 58.691 50.000 0.00 0.00 38.89 1.40 F
1368 1470 2.045926 CCCTTTAGCCACAGCGCT 60.046 61.111 2.64 2.64 46.67 5.92 F
2053 2743 0.027979 CGCTCCAGTGTGTTTGTGTG 59.972 55.000 0.00 0.00 0.00 3.82 F
3156 6570 0.533032 GGGACCTCTTTCTCACCTCG 59.467 60.000 0.00 0.00 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1606 1873 1.296727 GGCGGATGCACTTAAGGTAC 58.703 55.0 7.53 0.0 45.35 3.34 R
3044 6458 1.755179 CACAGAAACCCCTAGGCATG 58.245 55.0 2.05 0.0 36.11 4.06 R
3552 6975 0.680618 TGCACAAATTCAGGCCCAAG 59.319 50.0 0.00 0.0 0.00 3.61 R
5015 8650 0.108585 GAGTCTGTCCAACCAGGCAA 59.891 55.0 0.00 0.0 39.56 4.52 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
88 97 6.191315 AGGGAGTAGTATATACCATGCAGAG 58.809 44.000 9.32 0.00 0.00 3.35
122 131 8.670135 GGGCTTTCTACTCTTTATTTTTCTCTC 58.330 37.037 0.00 0.00 0.00 3.20
150 243 7.584987 AGTAATGTTGTGCTTGAGTGTAATTC 58.415 34.615 0.00 0.00 0.00 2.17
377 470 4.459390 TTCAAGCATTCATGGGATTGTG 57.541 40.909 9.56 0.00 0.00 3.33
753 846 1.308877 AGGACATGGGGTGCCTTAAT 58.691 50.000 0.00 0.00 38.89 1.40
1006 1099 3.356290 AGGGCACTTGTTCATATGTTCC 58.644 45.455 1.90 0.00 0.00 3.62
1368 1470 2.045926 CCCTTTAGCCACAGCGCT 60.046 61.111 2.64 2.64 46.67 5.92
1682 1984 5.900865 TGTTTGATGAATGATGCTGCTAA 57.099 34.783 0.00 0.00 0.00 3.09
1841 2328 0.310543 TGTTCAAGCGGCATGTTCAC 59.689 50.000 1.45 0.72 0.00 3.18
1957 2509 3.311110 TCCCCGTGAGTGGAGCAC 61.311 66.667 0.00 0.00 34.10 4.40
1987 2647 8.882415 TCAGTTATTAATCAACGGATAGTTCC 57.118 34.615 0.00 0.00 42.02 3.62
2050 2740 2.186826 GCCGCTCCAGTGTGTTTGT 61.187 57.895 0.00 0.00 0.00 2.83
2053 2743 0.027979 CGCTCCAGTGTGTTTGTGTG 59.972 55.000 0.00 0.00 0.00 3.82
2064 2754 4.148000 GTGTGTTTGTGTGTGTGTTTCTTG 59.852 41.667 0.00 0.00 0.00 3.02
2453 3178 6.493166 TGTTCATGGGGACTCTGATAAATTT 58.507 36.000 0.00 0.00 0.00 1.82
2455 3180 5.448654 TCATGGGGACTCTGATAAATTTGG 58.551 41.667 0.00 0.00 0.00 3.28
2774 6187 5.488262 TCAAGATTCAGTCTGGTGATTCA 57.512 39.130 0.00 0.00 37.23 2.57
3044 6458 5.445939 CCTTGACGACACATGTGTAAATAGC 60.446 44.000 30.63 16.15 45.05 2.97
3156 6570 0.533032 GGGACCTCTTTCTCACCTCG 59.467 60.000 0.00 0.00 0.00 4.63
3355 6778 1.751924 ACTCTATCCTCCGTCTTGCAC 59.248 52.381 0.00 0.00 0.00 4.57
3641 7064 4.290711 TCCAAGACTGCATCAGATGAAA 57.709 40.909 15.12 0.38 35.18 2.69
3673 7096 1.852157 TGCAATGGGAGGACTGGGT 60.852 57.895 0.00 0.00 0.00 4.51
3882 7305 1.133482 TGCCCGAGATGACTAGGATCA 60.133 52.381 0.00 0.00 40.57 2.92
3924 7347 4.490899 AATCTTGAGATCAGCTTCTGCT 57.509 40.909 0.00 0.00 41.46 4.24
3981 7404 3.551082 CAGAAGACTTGCGCTGAATCTAG 59.449 47.826 9.73 0.00 0.00 2.43
4001 7424 6.309357 TCTAGGGTACAGTGAGAAACAACTA 58.691 40.000 0.00 0.00 0.00 2.24
4005 7428 2.480845 ACAGTGAGAAACAACTACCGC 58.519 47.619 0.00 0.00 0.00 5.68
4078 7501 1.134371 GGTACTCACCTCCATGGCTTC 60.134 57.143 6.96 0.00 42.11 3.86
4102 7525 0.693049 AAATCTGGCTCGGAGTGGTT 59.307 50.000 6.90 0.00 0.00 3.67
4132 7555 1.615116 CCACATCCAGCATGTTGAGGT 60.615 52.381 11.60 3.22 43.89 3.85
4158 7581 2.691526 GCAAATGATGGAGGCAATGAGA 59.308 45.455 0.00 0.00 0.00 3.27
4224 7648 4.771590 ACAAATGTTGTGCAGGTGATAG 57.228 40.909 0.00 0.00 43.48 2.08
4336 7902 9.491675 TGAATGAACATATTTCATGTTGCTTTT 57.508 25.926 7.32 0.00 41.76 2.27
4341 7907 9.415544 GAACATATTTCATGTTGCTTTTTCTCT 57.584 29.630 7.32 0.00 41.76 3.10
4402 7968 5.426325 ACCATAAGGAGAGGAAGGACTAT 57.574 43.478 0.00 0.00 38.69 2.12
4411 7977 4.294347 AGAGGAAGGACTATGGAAGGAAG 58.706 47.826 0.00 0.00 0.00 3.46
4414 7980 3.977326 GGAAGGACTATGGAAGGAAGGAT 59.023 47.826 0.00 0.00 0.00 3.24
4447 8013 8.097038 TCATCCAAGGTTATATGTGATAGAAGC 58.903 37.037 0.00 0.00 35.37 3.86
4448 8014 7.373617 TCCAAGGTTATATGTGATAGAAGCA 57.626 36.000 0.00 0.00 37.03 3.91
4449 8015 7.445121 TCCAAGGTTATATGTGATAGAAGCAG 58.555 38.462 0.00 0.00 37.03 4.24
4450 8016 7.290014 TCCAAGGTTATATGTGATAGAAGCAGA 59.710 37.037 0.00 0.00 37.03 4.26
4451 8017 7.933577 CCAAGGTTATATGTGATAGAAGCAGAA 59.066 37.037 0.00 0.00 37.03 3.02
4452 8018 8.986847 CAAGGTTATATGTGATAGAAGCAGAAG 58.013 37.037 0.00 0.00 37.03 2.85
4487 8056 6.539464 GTCTTCTGCTGCTACTAGTACTTCTA 59.461 42.308 0.00 0.00 0.00 2.10
4561 8130 3.241067 TGCCGTGAATAGTGGTACTTC 57.759 47.619 0.00 0.00 0.00 3.01
4569 8138 7.119262 CCGTGAATAGTGGTACTTCTTTTTCAT 59.881 37.037 0.00 0.00 0.00 2.57
4570 8140 8.169268 CGTGAATAGTGGTACTTCTTTTTCATC 58.831 37.037 0.00 1.72 0.00 2.92
4671 8268 7.004086 TGAAAAGGAGATTTGGTAACTGTCAT 58.996 34.615 0.00 0.00 37.61 3.06
4794 8409 2.041265 GCCTCCCCCTCTTCCTGA 59.959 66.667 0.00 0.00 0.00 3.86
4828 8443 2.738846 GCGGCTCATACATATCAAGTGG 59.261 50.000 0.00 0.00 0.00 4.00
4843 8458 2.051518 GTGGGCGCATCCATGGAAA 61.052 57.895 20.67 0.00 39.26 3.13
4869 8493 5.215903 ACGATACAGTATGAAAGCGAGATG 58.784 41.667 0.00 0.00 39.69 2.90
4887 8511 6.292596 GCGAGATGGAGAAAATGATACTGAAC 60.293 42.308 0.00 0.00 0.00 3.18
4942 8577 8.816894 TGTATTAAAATTATCCAACCCTTGCAA 58.183 29.630 0.00 0.00 0.00 4.08
4944 8579 4.824479 AAATTATCCAACCCTTGCAAGG 57.176 40.909 34.60 34.60 46.06 3.61
4946 8581 0.324275 TATCCAACCCTTGCAAGGCC 60.324 55.000 35.85 0.00 45.10 5.19
4947 8582 2.384933 ATCCAACCCTTGCAAGGCCA 62.385 55.000 35.85 18.62 45.10 5.36
4948 8583 1.914764 CCAACCCTTGCAAGGCCAT 60.915 57.895 35.85 21.90 45.10 4.40
5003 8638 1.204146 TATGAGCCCCTGGTCTGTTC 58.796 55.000 0.00 0.00 39.75 3.18
5011 8646 3.621558 CCCCTGGTCTGTTCCTTTATTC 58.378 50.000 0.00 0.00 0.00 1.75
5012 8647 3.267031 CCCCTGGTCTGTTCCTTTATTCT 59.733 47.826 0.00 0.00 0.00 2.40
5014 8649 5.045140 CCCCTGGTCTGTTCCTTTATTCTTA 60.045 44.000 0.00 0.00 0.00 2.10
5015 8650 6.353951 CCCCTGGTCTGTTCCTTTATTCTTAT 60.354 42.308 0.00 0.00 0.00 1.73
5016 8651 7.119387 CCCTGGTCTGTTCCTTTATTCTTATT 58.881 38.462 0.00 0.00 0.00 1.40
5059 8737 2.475155 TGATGAGCAGGTGAGGAAGAT 58.525 47.619 0.00 0.00 0.00 2.40
5067 8745 7.013220 TGAGCAGGTGAGGAAGATAATAGTAT 58.987 38.462 0.00 0.00 0.00 2.12
5068 8746 8.170730 TGAGCAGGTGAGGAAGATAATAGTATA 58.829 37.037 0.00 0.00 0.00 1.47
5069 8747 8.356000 AGCAGGTGAGGAAGATAATAGTATAC 57.644 38.462 0.00 0.00 0.00 1.47
5070 8748 7.950684 AGCAGGTGAGGAAGATAATAGTATACA 59.049 37.037 5.50 0.00 0.00 2.29
5071 8749 8.754080 GCAGGTGAGGAAGATAATAGTATACAT 58.246 37.037 5.50 0.00 0.00 2.29
5138 8818 2.359900 GCCAAGCAGCTGTATACAGTT 58.640 47.619 28.95 22.87 45.45 3.16
5141 8821 3.753272 CCAAGCAGCTGTATACAGTTTGT 59.247 43.478 28.95 13.22 45.45 2.83
5143 8823 4.271696 AGCAGCTGTATACAGTTTGTGA 57.728 40.909 28.95 0.00 45.45 3.58
5144 8824 4.248859 AGCAGCTGTATACAGTTTGTGAG 58.751 43.478 28.95 14.92 45.45 3.51
5146 8826 3.061295 CAGCTGTATACAGTTTGTGAGCG 59.939 47.826 28.95 9.93 45.45 5.03
5154 8834 2.159156 ACAGTTTGTGAGCGTAGTGTCA 60.159 45.455 0.00 0.00 0.00 3.58
5157 8837 4.090066 CAGTTTGTGAGCGTAGTGTCATAC 59.910 45.833 0.00 0.00 0.00 2.39
5168 8848 6.486993 AGCGTAGTGTCATACATATTCAGAGA 59.513 38.462 0.00 0.00 0.00 3.10
5169 8849 6.799441 GCGTAGTGTCATACATATTCAGAGAG 59.201 42.308 0.00 0.00 0.00 3.20
5173 8853 6.041409 AGTGTCATACATATTCAGAGAGGGTG 59.959 42.308 0.00 0.00 0.00 4.61
5221 8901 5.738909 TCTCTGGAGACAATGGAATTCTTC 58.261 41.667 5.23 0.00 42.06 2.87
5251 8931 2.307363 CGTGTCGCCATATCCCAAC 58.693 57.895 0.00 0.00 0.00 3.77
5257 8937 0.664761 CGCCATATCCCAACTTGCTG 59.335 55.000 0.00 0.00 0.00 4.41
5263 8943 1.067295 ATCCCAACTTGCTGTCTGGA 58.933 50.000 10.54 0.00 34.26 3.86
5267 8947 2.553904 CCCAACTTGCTGTCTGGATTCT 60.554 50.000 10.54 0.00 32.38 2.40
5268 8948 2.486982 CCAACTTGCTGTCTGGATTCTG 59.513 50.000 0.00 0.00 32.38 3.02
5269 8949 2.486472 ACTTGCTGTCTGGATTCTGG 57.514 50.000 0.00 0.00 0.00 3.86
5270 8950 1.980765 ACTTGCTGTCTGGATTCTGGA 59.019 47.619 0.00 0.00 0.00 3.86
5271 8951 2.373169 ACTTGCTGTCTGGATTCTGGAA 59.627 45.455 0.00 0.00 0.00 3.53
5272 8952 2.775911 TGCTGTCTGGATTCTGGAAG 57.224 50.000 0.00 0.00 0.00 3.46
5273 8953 1.280133 TGCTGTCTGGATTCTGGAAGG 59.720 52.381 0.00 0.00 0.00 3.46
5274 8954 2.016096 GCTGTCTGGATTCTGGAAGGC 61.016 57.143 0.00 0.00 0.00 4.35
5275 8955 1.280133 CTGTCTGGATTCTGGAAGGCA 59.720 52.381 0.00 0.00 0.00 4.75
5276 8956 1.704628 TGTCTGGATTCTGGAAGGCAA 59.295 47.619 0.00 0.00 0.00 4.52
5277 8957 2.309755 TGTCTGGATTCTGGAAGGCAAT 59.690 45.455 0.00 0.00 0.00 3.56
5304 8984 9.177608 CAAATGAAGTTGGTCTCTGGATTATTA 57.822 33.333 0.00 0.00 0.00 0.98
5305 8985 9.927081 AAATGAAGTTGGTCTCTGGATTATTAT 57.073 29.630 0.00 0.00 0.00 1.28
5339 9019 9.498176 GAAACAGGAAACTAGTAATTCAGGTTA 57.502 33.333 9.06 0.00 40.21 2.85
5340 9020 9.503399 AAACAGGAAACTAGTAATTCAGGTTAG 57.497 33.333 9.06 0.00 40.21 2.34
5342 9022 8.657712 ACAGGAAACTAGTAATTCAGGTTAGTT 58.342 33.333 9.06 0.00 40.21 2.24
5343 9023 8.936864 CAGGAAACTAGTAATTCAGGTTAGTTG 58.063 37.037 9.06 0.00 40.21 3.16
5344 9024 8.101419 AGGAAACTAGTAATTCAGGTTAGTTGG 58.899 37.037 9.06 0.00 40.61 3.77
5345 9025 7.881751 GGAAACTAGTAATTCAGGTTAGTTGGT 59.118 37.037 9.06 0.00 35.42 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 131 4.997395 ACACTCAAGCACAACATTACTAGG 59.003 41.667 0.00 0.00 0.00 3.02
215 308 5.848833 TTCAAACATGCATGCCATATACA 57.151 34.783 26.53 0.59 31.47 2.29
422 515 0.102120 TGTTTTTGCTGCCAGAACGG 59.898 50.000 0.00 0.00 38.11 4.44
616 709 5.402398 CACACTCTCGTCTGTGATATTCAA 58.598 41.667 10.28 0.00 40.28 2.69
617 710 4.675408 GCACACTCTCGTCTGTGATATTCA 60.675 45.833 10.28 0.00 40.28 2.57
621 714 1.130561 CGCACACTCTCGTCTGTGATA 59.869 52.381 10.28 0.00 40.28 2.15
753 846 0.251354 GCATGCAGAAGAGGAGTGGA 59.749 55.000 14.21 0.00 0.00 4.02
946 1039 2.348104 CCCCGACCACACTCGATCA 61.348 63.158 0.00 0.00 35.58 2.92
1231 1333 2.358898 GCAAAGCTTTGTCTTGAGACCA 59.641 45.455 33.47 0.00 44.15 4.02
1368 1470 1.076923 GAGGACTCGGCTACCAGGA 60.077 63.158 0.00 0.00 0.00 3.86
1606 1873 1.296727 GGCGGATGCACTTAAGGTAC 58.703 55.000 7.53 0.00 45.35 3.34
1682 1984 6.921857 CCGTGGTAAACATACTAATCGAATCT 59.078 38.462 0.00 0.00 0.00 2.40
1957 2509 6.935741 TCCGTTGATTAATAACTGATTGGG 57.064 37.500 0.00 0.00 0.00 4.12
1987 2647 9.528018 ACTCATAAGTTACCAAACAAAAACATG 57.472 29.630 0.00 0.00 38.12 3.21
2050 2740 6.874664 TGTAGAGTTAACAAGAAACACACACA 59.125 34.615 8.61 0.00 0.00 3.72
2053 2743 6.851330 GCATGTAGAGTTAACAAGAAACACAC 59.149 38.462 8.61 0.00 0.00 3.82
2064 2754 7.365840 AGCAGTTTAAGCATGTAGAGTTAAC 57.634 36.000 0.00 0.00 0.00 2.01
2453 3178 6.884472 TGGTACTCATTTCCTAATTCTCCA 57.116 37.500 0.00 0.00 0.00 3.86
2455 3180 9.495572 CCTTATGGTACTCATTTCCTAATTCTC 57.504 37.037 2.73 0.00 37.30 2.87
2737 6150 9.880157 ACTGAATCTTGAAATTCCCAATTATTG 57.120 29.630 0.00 0.00 35.23 1.90
3044 6458 1.755179 CACAGAAACCCCTAGGCATG 58.245 55.000 2.05 0.00 36.11 4.06
3156 6570 6.210584 TCCAAACCCTTTAATCCAAGATGAAC 59.789 38.462 0.00 0.00 0.00 3.18
3552 6975 0.680618 TGCACAAATTCAGGCCCAAG 59.319 50.000 0.00 0.00 0.00 3.61
3673 7096 1.059584 TTGCACTTCCTCCTCCCACA 61.060 55.000 0.00 0.00 0.00 4.17
3882 7305 7.910584 AGATTTTGCAATTTGGGAAGATTAGT 58.089 30.769 0.00 0.00 0.00 2.24
3924 7347 5.048013 TCTGCTCAAGTAACTCGATCTTTGA 60.048 40.000 0.00 0.00 0.00 2.69
3930 7353 3.452474 GCATCTGCTCAAGTAACTCGAT 58.548 45.455 0.00 0.00 38.21 3.59
3981 7404 4.313282 GGTAGTTGTTTCTCACTGTACCC 58.687 47.826 0.00 0.00 0.00 3.69
4001 7424 1.329256 CAGCCTGTAGGTATAGCGGT 58.671 55.000 0.00 0.00 37.57 5.68
4005 7428 3.983741 GCTTCACAGCCTGTAGGTATAG 58.016 50.000 0.00 0.00 40.61 1.31
4078 7501 0.811616 CTCCGAGCCAGATTTTCCCG 60.812 60.000 0.00 0.00 0.00 5.14
4102 7525 1.883638 GCTGGATGTGGCTGAACTTGA 60.884 52.381 0.00 0.00 0.00 3.02
4132 7555 5.128991 TCATTGCCTCCATCATTTGCATAAA 59.871 36.000 0.00 0.00 0.00 1.40
4224 7648 5.757850 ATGTTTGGAAAGAGTGACAGAAC 57.242 39.130 0.00 0.00 0.00 3.01
4307 7873 6.019318 GCAACATGAAATATGTTCATTCAGGC 60.019 38.462 0.00 0.00 39.94 4.85
4336 7902 8.321353 TGAGTAATCCTGCAATTTAAGAGAGAA 58.679 33.333 0.00 0.00 0.00 2.87
4338 7904 7.984050 TCTGAGTAATCCTGCAATTTAAGAGAG 59.016 37.037 0.00 0.00 0.00 3.20
4341 7907 8.267183 TCATCTGAGTAATCCTGCAATTTAAGA 58.733 33.333 0.00 0.00 0.00 2.10
4402 7968 2.041485 TGATGTTGCATCCTTCCTTCCA 59.959 45.455 6.65 0.00 0.00 3.53
4414 7980 6.039605 CACATATAACCTTGGATGATGTTGCA 59.960 38.462 0.00 0.00 0.00 4.08
4448 8014 5.879223 CAGCAGAAGACATACATTTCCTTCT 59.121 40.000 0.00 0.00 42.82 2.85
4449 8015 5.448360 GCAGCAGAAGACATACATTTCCTTC 60.448 44.000 0.00 0.00 34.92 3.46
4450 8016 4.397417 GCAGCAGAAGACATACATTTCCTT 59.603 41.667 0.00 0.00 0.00 3.36
4451 8017 3.944015 GCAGCAGAAGACATACATTTCCT 59.056 43.478 0.00 0.00 0.00 3.36
4452 8018 3.944015 AGCAGCAGAAGACATACATTTCC 59.056 43.478 0.00 0.00 0.00 3.13
4487 8056 7.932683 AGGGTATGAAAATAAGGCTAGTAGT 57.067 36.000 0.00 0.00 0.00 2.73
4528 8097 2.555123 ACGGCAAATGTAGCAGTGG 58.445 52.632 0.00 0.00 38.92 4.00
4569 8138 8.586744 TCCAGATGTCAATTCAATTCAATTTGA 58.413 29.630 0.00 0.00 33.89 2.69
4570 8140 8.766000 TCCAGATGTCAATTCAATTCAATTTG 57.234 30.769 0.00 0.00 0.00 2.32
4587 8157 5.505181 ACCTTAACAACAGATCCAGATGT 57.495 39.130 0.00 0.00 0.00 3.06
4588 8158 6.406370 TGTACCTTAACAACAGATCCAGATG 58.594 40.000 0.00 0.00 0.00 2.90
4623 8193 8.389779 TCAGTTGAAAAGCTTGTAATGACATA 57.610 30.769 0.00 0.00 34.86 2.29
4809 8424 3.077359 GCCCACTTGATATGTATGAGCC 58.923 50.000 0.00 0.00 0.00 4.70
4810 8425 2.738846 CGCCCACTTGATATGTATGAGC 59.261 50.000 0.00 0.00 0.00 4.26
4811 8426 2.738846 GCGCCCACTTGATATGTATGAG 59.261 50.000 0.00 0.00 0.00 2.90
4828 8443 2.112198 TCGTTTCCATGGATGCGCC 61.112 57.895 24.86 9.19 37.10 6.53
4843 8458 3.064408 TCGCTTTCATACTGTATCGTCGT 59.936 43.478 0.00 0.00 0.00 4.34
4900 8527 4.423625 AATACATGGCCTACACCTTCTC 57.576 45.455 3.32 0.00 0.00 2.87
4907 8534 9.647918 TTGGATAATTTTAATACATGGCCTACA 57.352 29.630 3.32 0.00 0.00 2.74
4909 8536 9.084533 GGTTGGATAATTTTAATACATGGCCTA 57.915 33.333 3.32 0.00 0.00 3.93
4942 8577 9.845396 CAGTACTCTGTTTTGTAAGGATGGCCT 62.845 44.444 3.32 0.00 40.50 5.19
4944 8579 5.122396 CAGTACTCTGTTTTGTAAGGATGGC 59.878 44.000 0.00 0.00 36.97 4.40
4980 8615 2.909006 ACAGACCAGGGGCTCATATATG 59.091 50.000 6.36 6.36 0.00 1.78
5003 8638 5.656416 TCCAACCAGGCAATAAGAATAAAGG 59.344 40.000 0.00 0.00 37.29 3.11
5011 8646 2.749621 GTCTGTCCAACCAGGCAATAAG 59.250 50.000 0.00 0.00 37.04 1.73
5012 8647 2.375174 AGTCTGTCCAACCAGGCAATAA 59.625 45.455 0.00 0.00 39.56 1.40
5014 8649 0.773644 AGTCTGTCCAACCAGGCAAT 59.226 50.000 0.00 0.00 39.56 3.56
5015 8650 0.108585 GAGTCTGTCCAACCAGGCAA 59.891 55.000 0.00 0.00 39.56 4.52
5016 8651 1.053835 TGAGTCTGTCCAACCAGGCA 61.054 55.000 0.00 0.00 39.56 4.75
5072 8750 9.640952 AACAGTAAAAGCCACCATATATGTAAT 57.359 29.630 11.73 0.00 0.00 1.89
5073 8751 9.116067 GAACAGTAAAAGCCACCATATATGTAA 57.884 33.333 11.73 0.00 0.00 2.41
5138 8818 3.926821 TGTATGACACTACGCTCACAA 57.073 42.857 0.00 0.00 0.00 3.33
5141 8821 6.262273 TCTGAATATGTATGACACTACGCTCA 59.738 38.462 0.00 0.00 0.00 4.26
5143 8823 6.486993 TCTCTGAATATGTATGACACTACGCT 59.513 38.462 0.00 0.00 0.00 5.07
5144 8824 6.669278 TCTCTGAATATGTATGACACTACGC 58.331 40.000 0.00 0.00 0.00 4.42
5146 8826 7.231722 ACCCTCTCTGAATATGTATGACACTAC 59.768 40.741 0.00 0.00 0.00 2.73
5154 8834 6.377080 TCAGTCACCCTCTCTGAATATGTAT 58.623 40.000 0.00 0.00 35.65 2.29
5157 8837 5.362143 TCTTCAGTCACCCTCTCTGAATATG 59.638 44.000 7.18 0.00 43.86 1.78
5168 8848 2.770802 CCATCTGATCTTCAGTCACCCT 59.229 50.000 4.56 0.00 44.58 4.34
5169 8849 2.744494 GCCATCTGATCTTCAGTCACCC 60.744 54.545 4.56 0.00 44.58 4.61
5173 8853 2.159184 TCGTGCCATCTGATCTTCAGTC 60.159 50.000 4.56 0.00 44.58 3.51
5185 8865 0.531532 CCAGAGACCATCGTGCCATC 60.532 60.000 0.00 0.00 0.00 3.51
5189 8869 2.193532 TCTCCAGAGACCATCGTGC 58.806 57.895 0.00 0.00 31.41 5.34
5236 8916 0.663153 GCAAGTTGGGATATGGCGAC 59.337 55.000 4.75 0.00 0.00 5.19
5242 8922 2.846206 TCCAGACAGCAAGTTGGGATAT 59.154 45.455 4.75 0.00 32.58 1.63
5251 8931 2.775911 TCCAGAATCCAGACAGCAAG 57.224 50.000 0.00 0.00 0.00 4.01
5257 8937 2.496899 TTGCCTTCCAGAATCCAGAC 57.503 50.000 0.00 0.00 0.00 3.51
5263 8943 5.482878 ACTTCATTTGATTGCCTTCCAGAAT 59.517 36.000 0.00 0.00 0.00 2.40
5267 8947 4.262549 CCAACTTCATTTGATTGCCTTCCA 60.263 41.667 0.00 0.00 0.00 3.53
5268 8948 4.248058 CCAACTTCATTTGATTGCCTTCC 58.752 43.478 0.00 0.00 0.00 3.46
5269 8949 4.886579 ACCAACTTCATTTGATTGCCTTC 58.113 39.130 0.00 0.00 0.00 3.46
5270 8950 4.590222 AGACCAACTTCATTTGATTGCCTT 59.410 37.500 0.00 0.00 0.00 4.35
5271 8951 4.154942 AGACCAACTTCATTTGATTGCCT 58.845 39.130 0.00 0.00 0.00 4.75
5272 8952 4.219288 AGAGACCAACTTCATTTGATTGCC 59.781 41.667 0.00 0.00 0.00 4.52
5273 8953 5.159209 CAGAGACCAACTTCATTTGATTGC 58.841 41.667 0.00 0.00 0.00 3.56
5274 8954 5.474532 TCCAGAGACCAACTTCATTTGATTG 59.525 40.000 0.00 0.00 0.00 2.67
5275 8955 5.634118 TCCAGAGACCAACTTCATTTGATT 58.366 37.500 0.00 0.00 0.00 2.57
5276 8956 5.246981 TCCAGAGACCAACTTCATTTGAT 57.753 39.130 0.00 0.00 0.00 2.57
5277 8957 4.705110 TCCAGAGACCAACTTCATTTGA 57.295 40.909 0.00 0.00 0.00 2.69
5304 8984 6.373759 ACTAGTTTCCTGTTTCCTTCCAAAT 58.626 36.000 0.00 0.00 0.00 2.32
5305 8985 5.762279 ACTAGTTTCCTGTTTCCTTCCAAA 58.238 37.500 0.00 0.00 0.00 3.28
5323 9003 6.271624 ACCACCAACTAACCTGAATTACTAGT 59.728 38.462 0.00 0.00 0.00 2.57
5339 9019 2.024414 GCAGTTTCAGAACCACCAACT 58.976 47.619 0.00 0.00 36.39 3.16
5340 9020 1.748493 TGCAGTTTCAGAACCACCAAC 59.252 47.619 0.00 0.00 36.39 3.77
5342 9022 1.748493 GTTGCAGTTTCAGAACCACCA 59.252 47.619 0.00 0.00 36.39 4.17
5343 9023 2.024414 AGTTGCAGTTTCAGAACCACC 58.976 47.619 0.00 0.00 36.39 4.61
5344 9024 2.682856 TCAGTTGCAGTTTCAGAACCAC 59.317 45.455 0.00 0.00 36.39 4.16
5345 9025 2.997980 TCAGTTGCAGTTTCAGAACCA 58.002 42.857 0.00 0.00 36.39 3.67


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

AutoCloner maintained by Alex Coulton.