Multiple sequence alignment - TraesCS6D01G187800

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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 TraesCS6D01G187800 chr6D 100.000 2927 0 0 1 2927 254550548 254553474 0.000000e+00 5406.0
1 TraesCS6D01G187800 chr6D 91.166 283 23 2 2646 2927 254629901 254630182 1.650000e-102 383.0
2 TraesCS6D01G187800 chr6D 95.652 46 2 0 1993 2038 277047847 277047802 1.130000e-09 75.0
3 TraesCS6D01G187800 chr6D 92.157 51 4 0 1989 2039 14268400 14268350 4.050000e-09 73.1
4 TraesCS6D01G187800 chr6B 94.133 1125 48 4 853 1960 354954881 354956004 0.000000e+00 1696.0
5 TraesCS6D01G187800 chr6B 86.481 540 70 3 2039 2577 354956062 354956599 9.030000e-165 590.0
6 TraesCS6D01G187800 chr6B 78.107 169 33 4 2313 2479 60076613 60076447 1.430000e-18 104.0
7 TraesCS6D01G187800 chr6B 95.745 47 2 0 1989 2035 676283864 676283910 3.130000e-10 76.8
8 TraesCS6D01G187800 chr6A 95.545 1055 33 2 920 1960 364308136 364307082 0.000000e+00 1676.0
9 TraesCS6D01G187800 chr6A 91.685 890 71 2 2040 2927 364307023 364306135 0.000000e+00 1230.0
10 TraesCS6D01G187800 chr6A 89.070 430 40 5 504 928 364312263 364311836 7.180000e-146 527.0
11 TraesCS6D01G187800 chr6A 82.051 273 41 7 2648 2918 349538679 349538413 2.940000e-55 226.0
12 TraesCS6D01G187800 chr6A 97.872 47 1 0 1989 2035 214801926 214801880 6.720000e-12 82.4
13 TraesCS6D01G187800 chr4D 92.799 1111 65 6 863 1960 20897872 20898980 0.000000e+00 1594.0
14 TraesCS6D01G187800 chr4D 90.000 260 26 0 2666 2925 233837129 233837388 1.300000e-88 337.0
15 TraesCS6D01G187800 chr4D 86.014 286 39 1 2640 2925 233798079 233798363 3.660000e-79 305.0
16 TraesCS6D01G187800 chr5D 87.915 753 77 11 5 751 464907653 464906909 0.000000e+00 874.0
17 TraesCS6D01G187800 chr7B 78.692 474 82 17 90 553 107103038 107103502 6.130000e-77 298.0
18 TraesCS6D01G187800 chr7B 76.786 168 35 4 2313 2478 670218619 670218454 1.120000e-14 91.6
19 TraesCS6D01G187800 chr7B 97.872 47 1 0 1989 2035 89972033 89972079 6.720000e-12 82.4
20 TraesCS6D01G187800 chr7B 75.155 161 40 0 2345 2505 649298740 649298580 3.130000e-10 76.8
21 TraesCS6D01G187800 chr1D 85.556 270 36 2 2646 2913 305511487 305511219 2.220000e-71 279.0
22 TraesCS6D01G187800 chr2B 83.396 265 40 4 2646 2909 443972178 443972439 2.910000e-60 243.0
23 TraesCS6D01G187800 chr2B 77.852 149 27 5 2313 2458 749185550 749185695 1.450000e-13 87.9
24 TraesCS6D01G187800 chr2B 77.241 145 29 4 2313 2455 200223423 200223565 6.720000e-12 82.4
25 TraesCS6D01G187800 chr2B 93.617 47 3 0 1989 2035 255504826 255504872 1.460000e-08 71.3
26 TraesCS6D01G187800 chr4A 81.915 282 45 5 2646 2926 281757418 281757694 1.750000e-57 233.0
27 TraesCS6D01G187800 chr4A 95.745 47 2 0 1989 2035 429228534 429228580 3.130000e-10 76.8
28 TraesCS6D01G187800 chr2D 81.404 285 48 5 2638 2922 141585950 141585671 8.160000e-56 228.0
29 TraesCS6D01G187800 chr2D 95.918 49 2 0 1989 2037 537526673 537526721 2.420000e-11 80.5
30 TraesCS6D01G187800 chr7A 82.759 116 17 3 143 257 297441192 297441079 1.860000e-17 100.0
31 TraesCS6D01G187800 chr7A 94.231 52 3 0 1989 2040 164643759 164643708 2.420000e-11 80.5
32 TraesCS6D01G187800 chr3A 82.759 116 17 3 143 257 726089731 726089618 1.860000e-17 100.0
33 TraesCS6D01G187800 chr3A 81.148 122 20 3 137 257 732789639 732789758 8.640000e-16 95.3
34 TraesCS6D01G187800 chrUn 77.852 149 27 5 2313 2458 2021000 2021145 1.450000e-13 87.9
35 TraesCS6D01G187800 chr5A 79.508 122 22 3 137 257 403874705 403874824 1.870000e-12 84.2
36 TraesCS6D01G187800 chr3B 97.872 47 1 0 1990 2036 7236846 7236800 6.720000e-12 82.4
37 TraesCS6D01G187800 chr3B 76.871 147 32 2 2313 2458 124115281 124115136 6.720000e-12 82.4
38 TraesCS6D01G187800 chr5B 95.833 48 2 0 1994 2041 327604148 327604101 8.700000e-11 78.7
39 TraesCS6D01G187800 chr5B 95.745 47 2 0 1989 2035 526558541 526558587 3.130000e-10 76.8
40 TraesCS6D01G187800 chr7D 93.878 49 3 0 1989 2037 64692464 64692416 1.130000e-09 75.0
41 TraesCS6D01G187800 chr4B 93.878 49 3 0 1989 2037 22595516 22595468 1.130000e-09 75.0
42 TraesCS6D01G187800 chr1B 95.556 45 2 0 1989 2033 629468891 629468847 4.050000e-09 73.1
43 TraesCS6D01G187800 chr1B 90.196 51 4 1 1989 2038 343986278 343986328 6.770000e-07 65.8
44 TraesCS6D01G187800 chr1B 100.000 29 0 0 1989 2017 13892539 13892567 1.000000e-03 54.7
45 TraesCS6D01G187800 chr1A 75.641 156 30 6 95 249 99651821 99651969 1.460000e-08 71.3
46 TraesCS6D01G187800 chr1A 100.000 28 0 0 1990 2017 514030039 514030066 5.000000e-03 52.8


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 TraesCS6D01G187800 chr6D 254550548 254553474 2926 False 5406.000000 5406 100.000 1 2927 1 chr6D.!!$F1 2926
1 TraesCS6D01G187800 chr6B 354954881 354956599 1718 False 1143.000000 1696 90.307 853 2577 2 chr6B.!!$F2 1724
2 TraesCS6D01G187800 chr6A 364306135 364312263 6128 True 1144.333333 1676 92.100 504 2927 3 chr6A.!!$R3 2423
3 TraesCS6D01G187800 chr4D 20897872 20898980 1108 False 1594.000000 1594 92.799 863 1960 1 chr4D.!!$F1 1097
4 TraesCS6D01G187800 chr5D 464906909 464907653 744 True 874.000000 874 87.915 5 751 1 chr5D.!!$R1 746

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
89 90 0.106894 GTCCCAATCCTAAGAGGCCG 59.893 60.0 0.0 0.0 34.61 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2018 5773 0.035152 TAGTACTCCCTGCGTCCGAA 60.035 55.0 0.0 0.0 0.0 4.3 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
33 34 2.292569 TGACTACGACGACAAAGAGCTT 59.707 45.455 0.00 0.00 0.00 3.74
38 39 1.579808 CGACGACAAAGAGCTTCGATC 59.420 52.381 11.49 4.95 36.58 3.69
44 45 4.914420 AGAGCTTCGATCGCGGCG 62.914 66.667 17.70 17.70 38.28 6.46
45 46 4.907034 GAGCTTCGATCGCGGCGA 62.907 66.667 28.46 28.46 41.13 5.54
62 63 0.940126 CGATGCAAGGCTACATGGAC 59.060 55.000 7.60 0.00 0.00 4.02
85 86 3.274288 GTGCTTGTCCCAATCCTAAGAG 58.726 50.000 0.00 0.00 0.00 2.85
88 89 1.213296 TGTCCCAATCCTAAGAGGCC 58.787 55.000 0.00 0.00 34.61 5.19
89 90 0.106894 GTCCCAATCCTAAGAGGCCG 59.893 60.000 0.00 0.00 34.61 6.13
106 108 0.660595 CCGGAGATGTGCGACGATAC 60.661 60.000 5.03 0.00 40.58 2.24
123 125 0.539986 TACGGATGAAAGTCCTGCCC 59.460 55.000 0.00 0.00 36.07 5.36
131 133 1.002773 GAAAGTCCTGCCCGGTTTCTA 59.997 52.381 0.00 0.00 29.53 2.10
186 188 2.586792 GCTCCTTGGAGGCATCGT 59.413 61.111 17.33 0.00 34.61 3.73
187 189 1.522580 GCTCCTTGGAGGCATCGTC 60.523 63.158 17.33 0.00 34.61 4.20
188 190 1.227089 CTCCTTGGAGGCATCGTCG 60.227 63.158 8.74 0.00 34.61 5.12
193 195 2.105128 GGAGGCATCGTCGAGGTG 59.895 66.667 8.86 0.00 0.00 4.00
216 218 0.250234 CGGCATCTCCCTTGTTCTCA 59.750 55.000 0.00 0.00 0.00 3.27
221 223 3.201290 CATCTCCCTTGTTCTCATTCGG 58.799 50.000 0.00 0.00 0.00 4.30
230 232 3.921677 TGTTCTCATTCGGAGTTGGTAC 58.078 45.455 0.00 0.00 44.40 3.34
272 274 1.384989 ATTCAGAGTCGGATCGGCGT 61.385 55.000 6.85 0.00 36.23 5.68
274 276 3.518998 AGAGTCGGATCGGCGTGG 61.519 66.667 6.85 0.00 36.23 4.94
300 302 3.582743 GTCCTCGACGTTGTTCCTT 57.417 52.632 1.96 0.00 0.00 3.36
303 305 1.137479 TCCTCGACGTTGTTCCTTTGT 59.863 47.619 1.96 0.00 0.00 2.83
310 312 2.436911 ACGTTGTTCCTTTGTAGGGAGT 59.563 45.455 0.00 0.00 42.26 3.85
314 316 5.337330 CGTTGTTCCTTTGTAGGGAGTATCT 60.337 44.000 0.00 0.00 42.26 1.98
315 317 6.473758 GTTGTTCCTTTGTAGGGAGTATCTT 58.526 40.000 0.00 0.00 42.26 2.40
333 335 1.676006 CTTGTTTGGAGACACGGCTTT 59.324 47.619 0.00 0.00 42.67 3.51
337 339 0.250295 TTGGAGACACGGCTTTGAGG 60.250 55.000 0.00 0.00 42.67 3.86
354 356 2.575735 TGAGGTCCAATGTAGCATTCCA 59.424 45.455 0.00 0.00 0.00 3.53
355 357 3.202818 TGAGGTCCAATGTAGCATTCCAT 59.797 43.478 0.00 0.00 0.00 3.41
357 359 2.549754 GGTCCAATGTAGCATTCCATCG 59.450 50.000 0.00 0.00 0.00 3.84
361 363 3.205338 CAATGTAGCATTCCATCGGTGA 58.795 45.455 0.00 0.00 0.00 4.02
364 366 2.061773 GTAGCATTCCATCGGTGATCG 58.938 52.381 0.00 0.00 40.90 3.69
366 368 1.134401 AGCATTCCATCGGTGATCGTT 60.134 47.619 0.00 0.00 40.32 3.85
368 370 2.279741 CATTCCATCGGTGATCGTTGT 58.720 47.619 0.00 0.00 40.32 3.32
369 371 2.465860 TTCCATCGGTGATCGTTGTT 57.534 45.000 0.00 0.00 40.32 2.83
382 384 5.003160 TGATCGTTGTTGTCCAAGATTGAT 58.997 37.500 0.00 0.00 32.51 2.57
394 396 0.531532 AGATTGATCTTGAGCGGCGG 60.532 55.000 9.78 0.00 31.97 6.13
399 401 0.811616 GATCTTGAGCGGCGGAATGT 60.812 55.000 9.78 0.00 0.00 2.71
412 414 1.512734 GAATGTACGTCGTCGCCGT 60.513 57.895 6.55 6.55 42.06 5.68
480 482 0.984230 ATTTGCCACCTCCTTCTCGA 59.016 50.000 0.00 0.00 0.00 4.04
483 485 1.079750 GCCACCTCCTTCTCGACAC 60.080 63.158 0.00 0.00 0.00 3.67
504 506 2.439409 CAAGAGTGGATGGTGCATTGA 58.561 47.619 0.00 0.00 0.00 2.57
515 517 2.040947 TGGTGCATTGACATGGGAGTTA 59.959 45.455 0.00 0.00 0.00 2.24
556 563 2.750637 AGGTGACCGCGTCGAGAT 60.751 61.111 4.92 0.00 34.95 2.75
558 565 2.178521 GTGACCGCGTCGAGATGT 59.821 61.111 4.92 0.00 34.95 3.06
580 587 2.104963 GGCCTTGGTGATTAGTCTAGGG 59.895 54.545 0.00 0.00 0.00 3.53
584 591 3.398318 TGGTGATTAGTCTAGGGCAGA 57.602 47.619 0.00 0.00 0.00 4.26
625 632 2.142357 CTGTCGGTGGCTGTCTTCGA 62.142 60.000 0.00 0.00 0.00 3.71
638 645 0.179067 TCTTCGAACGTGCCTTGGTT 60.179 50.000 0.00 0.00 0.00 3.67
666 673 2.108700 CGTACTGCACTTGTTGTTTGC 58.891 47.619 0.00 0.00 36.76 3.68
722 729 6.954944 TGCCTTCTACAAAAATATGATACGC 58.045 36.000 0.00 0.00 0.00 4.42
726 733 9.268268 CCTTCTACAAAAATATGATACGCCTTA 57.732 33.333 0.00 0.00 0.00 2.69
846 853 0.605589 GGATGGAGGGAGTAGCATCG 59.394 60.000 0.00 0.00 0.00 3.84
848 855 1.271102 GATGGAGGGAGTAGCATCGTC 59.729 57.143 0.00 0.00 0.00 4.20
1031 4748 0.696143 TCCTGGACCTGGACACCAAA 60.696 55.000 15.82 0.00 30.80 3.28
1075 4792 5.273208 ACATACTCCACTCCACTAACTGAT 58.727 41.667 0.00 0.00 0.00 2.90
1485 5214 1.386533 CAATGCTGGAGACCATGTCC 58.613 55.000 0.00 0.00 32.18 4.02
1548 5277 1.972223 CGACCTCGACCTCACCACT 60.972 63.158 0.00 0.00 43.02 4.00
1863 5598 7.553334 TGTGTTTGTAGGTCTAGGAATGTATC 58.447 38.462 0.00 0.00 0.00 2.24
1899 5634 6.183360 CCTTCCGTGAAGTGTCAATATTTACC 60.183 42.308 11.21 0.00 37.92 2.85
1968 5723 0.895530 ATGCATATACTCCCCGTCCG 59.104 55.000 0.00 0.00 0.00 4.79
1970 5725 0.963962 GCATATACTCCCCGTCCGAA 59.036 55.000 0.00 0.00 0.00 4.30
1996 5751 9.502091 AAAAACTTGTATGCACTTCTAGATACA 57.498 29.630 0.00 0.00 31.07 2.29
1997 5752 9.672673 AAAACTTGTATGCACTTCTAGATACAT 57.327 29.630 0.00 0.00 32.69 2.29
1998 5753 8.879342 AACTTGTATGCACTTCTAGATACATC 57.121 34.615 0.00 0.00 32.69 3.06
1999 5754 7.437748 ACTTGTATGCACTTCTAGATACATCC 58.562 38.462 0.00 0.00 32.69 3.51
2000 5755 6.976934 TGTATGCACTTCTAGATACATCCA 57.023 37.500 0.00 0.00 0.00 3.41
2001 5756 7.544804 TGTATGCACTTCTAGATACATCCAT 57.455 36.000 0.00 0.00 0.00 3.41
2002 5757 7.966812 TGTATGCACTTCTAGATACATCCATT 58.033 34.615 0.00 0.00 0.00 3.16
2003 5758 8.432013 TGTATGCACTTCTAGATACATCCATTT 58.568 33.333 0.00 0.00 0.00 2.32
2004 5759 7.741027 ATGCACTTCTAGATACATCCATTTG 57.259 36.000 0.00 0.00 0.00 2.32
2005 5760 6.888105 TGCACTTCTAGATACATCCATTTGA 58.112 36.000 0.00 0.00 0.00 2.69
2006 5761 6.988580 TGCACTTCTAGATACATCCATTTGAG 59.011 38.462 0.00 0.00 0.00 3.02
2007 5762 6.426328 GCACTTCTAGATACATCCATTTGAGG 59.574 42.308 0.00 0.00 0.00 3.86
2008 5763 6.933521 CACTTCTAGATACATCCATTTGAGGG 59.066 42.308 0.00 0.00 0.00 4.30
2009 5764 6.846505 ACTTCTAGATACATCCATTTGAGGGA 59.153 38.462 0.00 0.00 39.14 4.20
2010 5765 6.672266 TCTAGATACATCCATTTGAGGGAC 57.328 41.667 0.00 0.00 37.23 4.46
2011 5766 6.143206 TCTAGATACATCCATTTGAGGGACA 58.857 40.000 0.00 0.00 37.23 4.02
2012 5767 5.715439 AGATACATCCATTTGAGGGACAA 57.285 39.130 0.00 0.00 37.23 3.18
2032 5787 4.371975 TTTTTCGGACGCAGGGAG 57.628 55.556 0.00 0.00 0.00 4.30
2033 5788 1.448497 TTTTTCGGACGCAGGGAGT 59.552 52.632 0.00 0.00 0.00 3.85
2034 5789 0.680618 TTTTTCGGACGCAGGGAGTA 59.319 50.000 0.00 0.00 0.00 2.59
2035 5790 0.037975 TTTTCGGACGCAGGGAGTAC 60.038 55.000 0.00 0.00 0.00 2.73
2036 5791 0.896940 TTTCGGACGCAGGGAGTACT 60.897 55.000 0.00 0.00 0.00 2.73
2037 5792 0.035152 TTCGGACGCAGGGAGTACTA 60.035 55.000 0.00 0.00 0.00 1.82
2063 5818 0.039165 GCTTTCCTGGTTGCTTTCCG 60.039 55.000 0.00 0.00 0.00 4.30
2066 5821 0.106419 TTCCTGGTTGCTTTCCGGTT 60.106 50.000 0.00 0.00 0.00 4.44
2071 5826 1.889829 TGGTTGCTTTCCGGTTTATGG 59.110 47.619 0.00 0.00 0.00 2.74
2075 5830 1.340600 TGCTTTCCGGTTTATGGAGGG 60.341 52.381 0.00 0.00 36.72 4.30
2102 5859 4.932268 TTAAAGAAAAGGCATACGTCCG 57.068 40.909 0.00 0.00 0.00 4.79
2222 5979 0.890542 AACACAGTCACGGCATGCAT 60.891 50.000 21.36 3.56 0.00 3.96
2260 6017 0.108804 TAACAGGAAGGAGAAGCGCG 60.109 55.000 0.00 0.00 0.00 6.86
2297 6054 1.004745 ACCATCAGGATTTTGCGGAGT 59.995 47.619 0.00 0.00 38.69 3.85
2304 6061 0.675522 GATTTTGCGGAGTCGGGGAA 60.676 55.000 0.00 0.00 36.79 3.97
2311 6068 2.031465 GAGTCGGGGAAACGGCAA 59.969 61.111 0.00 0.00 41.73 4.52
2355 6112 1.918262 ACCTTCAGAGCATCCCAATCA 59.082 47.619 0.00 0.00 33.66 2.57
2371 6128 5.045213 TCCCAATCAGCAACCTTAGTCAATA 60.045 40.000 0.00 0.00 0.00 1.90
2417 6174 6.178239 ACACATTTTAAATAGACCGTCAGC 57.822 37.500 0.40 0.00 0.00 4.26
2479 6236 3.237268 TGGTTGTCTACAAAGCCCAAT 57.763 42.857 0.00 0.00 37.63 3.16
2559 6316 0.599558 GCACATGGAGCTCTGCAAAA 59.400 50.000 18.00 0.00 33.77 2.44
2593 6350 0.722676 AGGACACCCCCATCTAGGAA 59.277 55.000 0.00 0.00 41.22 3.36
2644 6401 8.250332 GCCAAGACACATCCAAAGAAAATATTA 58.750 33.333 0.00 0.00 0.00 0.98
2684 6441 2.486727 GGACCCAAGAAAGGTTCGAACT 60.487 50.000 26.32 8.28 37.88 3.01
2691 6448 0.250770 AAAGGTTCGAACTCTGGGGC 60.251 55.000 26.32 9.09 0.00 5.80
2701 6458 2.032528 TCTGGGGCGTGCTTGAAG 59.967 61.111 0.00 0.00 0.00 3.02
2731 6488 3.054802 CCAAACTCTAGTTCTCTGCCCAT 60.055 47.826 0.00 0.00 37.25 4.00
2738 6495 0.322816 GTTCTCTGCCCATTGCCTCA 60.323 55.000 0.00 0.00 40.16 3.86
2744 6501 2.264480 CCCATTGCCTCACGACGA 59.736 61.111 0.00 0.00 0.00 4.20
2746 6503 2.444624 CCATTGCCTCACGACGACG 61.445 63.158 5.58 5.58 45.75 5.12
2749 6506 3.891586 TTGCCTCACGACGACGCTC 62.892 63.158 7.30 0.00 43.96 5.03
2752 6509 3.785499 CTCACGACGACGCTCCGA 61.785 66.667 7.30 0.00 43.96 4.55
2753 6510 3.097137 CTCACGACGACGCTCCGAT 62.097 63.158 7.30 0.00 43.96 4.18
2754 6511 1.759293 CTCACGACGACGCTCCGATA 61.759 60.000 7.30 0.00 43.96 2.92
2835 6592 1.180029 TGCGGTGTAAGACCCTACTC 58.820 55.000 0.00 0.00 42.62 2.59
2839 6596 1.481363 GGTGTAAGACCCTACTCCTGC 59.519 57.143 0.00 0.00 39.10 4.85
2840 6597 2.176889 GTGTAAGACCCTACTCCTGCA 58.823 52.381 0.00 0.00 0.00 4.41
2848 6605 1.679944 CCCTACTCCTGCATTGTGGTG 60.680 57.143 0.00 0.00 0.00 4.17
2851 6608 0.250901 ACTCCTGCATTGTGGTGGAC 60.251 55.000 0.00 0.00 0.00 4.02
2862 6619 4.373116 GGTGGACTGCCTCGCGAA 62.373 66.667 11.33 0.00 34.31 4.70
2895 6652 8.539544 TGAATATGAGTGTACAAGGAAGATGAA 58.460 33.333 0.00 0.00 0.00 2.57
2896 6653 9.553064 GAATATGAGTGTACAAGGAAGATGAAT 57.447 33.333 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.878088 AGCTCTTTGTCGTCGTAGTCA 59.122 47.619 0.00 0.00 0.00 3.41
33 34 4.863925 TTGCATCGCCGCGATCGA 62.864 61.111 25.03 21.58 45.19 3.59
44 45 0.940126 CGTCCATGTAGCCTTGCATC 59.060 55.000 0.00 0.00 0.00 3.91
45 46 0.464373 CCGTCCATGTAGCCTTGCAT 60.464 55.000 0.00 0.00 0.00 3.96
88 89 0.992263 CGTATCGTCGCACATCTCCG 60.992 60.000 0.00 0.00 0.00 4.63
89 90 0.660595 CCGTATCGTCGCACATCTCC 60.661 60.000 0.00 0.00 0.00 3.71
102 104 2.484889 GGCAGGACTTTCATCCGTATC 58.515 52.381 0.00 0.00 44.22 2.24
106 108 1.815421 CGGGCAGGACTTTCATCCG 60.815 63.158 0.00 0.00 44.22 4.18
123 125 1.887707 GCCAGCCCGATAGAAACCG 60.888 63.158 0.00 0.00 39.76 4.44
166 168 2.688666 ATGCCTCCAAGGAGCGGA 60.689 61.111 10.68 6.01 37.67 5.54
169 171 1.522580 GACGATGCCTCCAAGGAGC 60.523 63.158 10.68 7.04 37.67 4.70
182 184 2.875485 CCGACACACCTCGACGAT 59.125 61.111 0.00 0.00 35.58 3.73
186 188 1.934220 GAGATGCCGACACACCTCGA 61.934 60.000 0.00 0.00 35.58 4.04
187 189 1.517257 GAGATGCCGACACACCTCG 60.517 63.158 0.00 0.00 0.00 4.63
188 190 1.153549 GGAGATGCCGACACACCTC 60.154 63.158 0.00 0.00 0.00 3.85
193 195 0.321653 AACAAGGGAGATGCCGACAC 60.322 55.000 0.00 0.00 37.63 3.67
216 218 3.056035 GGAGACAAGTACCAACTCCGAAT 60.056 47.826 0.00 0.00 37.87 3.34
221 223 1.067071 CCCGGAGACAAGTACCAACTC 60.067 57.143 0.73 0.00 33.75 3.01
230 232 2.391389 GCTTTCGCCCGGAGACAAG 61.391 63.158 0.73 9.61 0.00 3.16
300 302 5.783360 TCTCCAAACAAGATACTCCCTACAA 59.217 40.000 0.00 0.00 0.00 2.41
303 305 5.187186 GTGTCTCCAAACAAGATACTCCCTA 59.813 44.000 0.00 0.00 33.52 3.53
310 312 2.301870 AGCCGTGTCTCCAAACAAGATA 59.698 45.455 0.00 0.00 31.29 1.98
314 316 1.403679 CAAAGCCGTGTCTCCAAACAA 59.596 47.619 0.00 0.00 0.00 2.83
315 317 1.021202 CAAAGCCGTGTCTCCAAACA 58.979 50.000 0.00 0.00 0.00 2.83
333 335 2.575735 TGGAATGCTACATTGGACCTCA 59.424 45.455 0.00 0.00 0.00 3.86
337 339 2.549754 CCGATGGAATGCTACATTGGAC 59.450 50.000 5.21 0.00 47.00 4.02
354 356 1.001520 TGGACAACAACGATCACCGAT 59.998 47.619 0.00 0.00 41.76 4.18
355 357 0.389757 TGGACAACAACGATCACCGA 59.610 50.000 0.00 0.00 41.76 4.69
357 359 2.489971 TCTTGGACAACAACGATCACC 58.510 47.619 0.00 0.00 34.76 4.02
361 363 5.248640 AGATCAATCTTGGACAACAACGAT 58.751 37.500 0.00 0.00 34.76 3.73
382 384 0.459585 GTACATTCCGCCGCTCAAGA 60.460 55.000 0.00 0.00 0.00 3.02
386 388 2.202703 ACGTACATTCCGCCGCTC 60.203 61.111 0.00 0.00 0.00 5.03
412 414 1.002624 GGCACCGTCTTGGATTCCA 60.003 57.895 0.00 0.00 42.00 3.53
453 455 1.205417 GGAGGTGGCAAATGAATGGTG 59.795 52.381 0.00 0.00 0.00 4.17
454 456 1.077663 AGGAGGTGGCAAATGAATGGT 59.922 47.619 0.00 0.00 0.00 3.55
483 485 1.475280 CAATGCACCATCCACTCTTGG 59.525 52.381 0.00 0.00 45.56 3.61
504 506 0.545787 TCCCACGGTAACTCCCATGT 60.546 55.000 0.00 0.00 0.00 3.21
515 517 2.027469 GGAGAATAACAACTCCCACGGT 60.027 50.000 0.00 0.00 44.70 4.83
548 550 1.811266 CCAAGGCCACATCTCGACG 60.811 63.158 5.01 0.00 0.00 5.12
556 563 1.985159 AGACTAATCACCAAGGCCACA 59.015 47.619 5.01 0.00 0.00 4.17
558 565 2.771943 CCTAGACTAATCACCAAGGCCA 59.228 50.000 5.01 0.00 0.00 5.36
580 587 2.623416 ACTACAAAGCAAAAGGGTCTGC 59.377 45.455 0.00 0.00 38.91 4.26
584 591 3.430236 GCACAACTACAAAGCAAAAGGGT 60.430 43.478 0.00 0.00 0.00 4.34
625 632 0.395173 ACTCCAAACCAAGGCACGTT 60.395 50.000 0.00 0.00 0.00 3.99
638 645 2.159014 ACAAGTGCAGTACGAACTCCAA 60.159 45.455 0.00 0.00 31.97 3.53
666 673 1.979469 CAAGACGACTACAACTCGCTG 59.021 52.381 0.00 0.00 34.34 5.18
783 790 8.918202 ATGTGTTTCTAAGATTGTCCTTTACA 57.082 30.769 0.00 0.00 35.88 2.41
786 793 9.793259 TCTAATGTGTTTCTAAGATTGTCCTTT 57.207 29.630 0.00 0.00 0.00 3.11
789 796 8.779354 AGTCTAATGTGTTTCTAAGATTGTCC 57.221 34.615 0.00 0.00 0.00 4.02
846 853 5.181622 AGGTTCATAGGAGATATTCGACGAC 59.818 44.000 0.00 0.00 0.00 4.34
848 855 5.181433 TGAGGTTCATAGGAGATATTCGACG 59.819 44.000 0.00 0.00 0.00 5.12
1031 4748 0.317479 CGAACGAGGGTGAGGTTCTT 59.683 55.000 0.00 0.00 38.27 2.52
1374 5103 3.078097 CTCGAAGAACCTCTCTCTGACA 58.922 50.000 0.00 0.00 34.09 3.58
1485 5214 4.645956 CGTAGAACAGTACGTACTTCCAG 58.354 47.826 25.35 16.20 40.75 3.86
1642 5375 2.705154 GCACAAGTTCAACGTCAAGAC 58.295 47.619 0.00 0.00 0.00 3.01
1659 5392 5.874892 TTAACAAATAAACTGTTGCGCAC 57.125 34.783 11.12 6.28 37.56 5.34
1863 5598 3.912907 CGGAAGGGATCGACGGGG 61.913 72.222 0.00 0.00 0.00 5.73
1970 5725 9.502091 TGTATCTAGAAGTGCATACAAGTTTTT 57.498 29.630 0.00 0.00 30.48 1.94
1975 5730 7.436933 TGGATGTATCTAGAAGTGCATACAAG 58.563 38.462 6.82 0.00 35.79 3.16
1977 5732 6.976934 TGGATGTATCTAGAAGTGCATACA 57.023 37.500 5.49 5.49 36.43 2.29
1979 5734 8.650490 TCAAATGGATGTATCTAGAAGTGCATA 58.350 33.333 0.00 0.00 0.00 3.14
1981 5736 6.888105 TCAAATGGATGTATCTAGAAGTGCA 58.112 36.000 0.00 0.00 0.00 4.57
1985 5740 7.158021 GTCCCTCAAATGGATGTATCTAGAAG 58.842 42.308 0.00 0.00 33.65 2.85
1989 5744 6.823286 TTGTCCCTCAAATGGATGTATCTA 57.177 37.500 0.00 0.00 33.65 1.98
2015 5770 0.680618 TACTCCCTGCGTCCGAAAAA 59.319 50.000 0.00 0.00 0.00 1.94
2016 5771 0.037975 GTACTCCCTGCGTCCGAAAA 60.038 55.000 0.00 0.00 0.00 2.29
2017 5772 0.896940 AGTACTCCCTGCGTCCGAAA 60.897 55.000 0.00 0.00 0.00 3.46
2018 5773 0.035152 TAGTACTCCCTGCGTCCGAA 60.035 55.000 0.00 0.00 0.00 4.30
2019 5774 0.463295 CTAGTACTCCCTGCGTCCGA 60.463 60.000 0.00 0.00 0.00 4.55
2020 5775 0.463295 TCTAGTACTCCCTGCGTCCG 60.463 60.000 0.00 0.00 0.00 4.79
2021 5776 1.609555 CATCTAGTACTCCCTGCGTCC 59.390 57.143 0.00 0.00 0.00 4.79
2022 5777 2.291190 GTCATCTAGTACTCCCTGCGTC 59.709 54.545 0.00 0.00 0.00 5.19
2023 5778 2.299521 GTCATCTAGTACTCCCTGCGT 58.700 52.381 0.00 0.00 0.00 5.24
2024 5779 1.264557 CGTCATCTAGTACTCCCTGCG 59.735 57.143 0.00 0.60 0.00 5.18
2025 5780 1.001158 GCGTCATCTAGTACTCCCTGC 60.001 57.143 0.00 0.00 0.00 4.85
2026 5781 2.577700 AGCGTCATCTAGTACTCCCTG 58.422 52.381 0.00 0.00 0.00 4.45
2027 5782 3.300239 AAGCGTCATCTAGTACTCCCT 57.700 47.619 0.00 0.00 0.00 4.20
2028 5783 3.243468 GGAAAGCGTCATCTAGTACTCCC 60.243 52.174 0.00 0.00 0.00 4.30
2029 5784 3.633065 AGGAAAGCGTCATCTAGTACTCC 59.367 47.826 0.00 0.00 0.00 3.85
2030 5785 4.498345 CCAGGAAAGCGTCATCTAGTACTC 60.498 50.000 0.00 0.00 0.00 2.59
2031 5786 3.381908 CCAGGAAAGCGTCATCTAGTACT 59.618 47.826 0.00 0.00 0.00 2.73
2032 5787 3.130693 ACCAGGAAAGCGTCATCTAGTAC 59.869 47.826 0.00 0.00 0.00 2.73
2033 5788 3.362706 ACCAGGAAAGCGTCATCTAGTA 58.637 45.455 0.00 0.00 0.00 1.82
2034 5789 2.180276 ACCAGGAAAGCGTCATCTAGT 58.820 47.619 0.00 0.00 0.00 2.57
2035 5790 2.932614 CAACCAGGAAAGCGTCATCTAG 59.067 50.000 0.00 0.00 0.00 2.43
2036 5791 2.935238 GCAACCAGGAAAGCGTCATCTA 60.935 50.000 0.00 0.00 0.00 1.98
2037 5792 1.813513 CAACCAGGAAAGCGTCATCT 58.186 50.000 0.00 0.00 0.00 2.90
2118 5875 6.365247 GCTCTGTTTCATACTCTGTTTAACGA 59.635 38.462 0.00 0.00 0.00 3.85
2120 5877 7.421530 TGCTCTGTTTCATACTCTGTTTAAC 57.578 36.000 0.00 0.00 0.00 2.01
2124 5881 4.453819 GCTTGCTCTGTTTCATACTCTGTT 59.546 41.667 0.00 0.00 0.00 3.16
2125 5882 3.999663 GCTTGCTCTGTTTCATACTCTGT 59.000 43.478 0.00 0.00 0.00 3.41
2133 5890 1.761449 TGGTTGCTTGCTCTGTTTCA 58.239 45.000 0.00 0.00 0.00 2.69
2260 6017 0.179054 GGTCGGGCTCATTCCTAACC 60.179 60.000 0.00 0.00 0.00 2.85
2297 6054 2.557372 GCTTTTGCCGTTTCCCCGA 61.557 57.895 0.00 0.00 40.15 5.14
2311 6068 4.083590 GCTGATTGAGAAAGTTCGAGCTTT 60.084 41.667 24.82 24.82 40.94 3.51
2355 6112 6.069963 AGTGGAGATTATTGACTAAGGTTGCT 60.070 38.462 0.00 0.00 0.00 3.91
2371 6128 2.157738 GTTCTTGCAGCAGTGGAGATT 58.842 47.619 0.00 0.00 0.00 2.40
2411 6168 0.165944 CTTTAACAAGCCCGCTGACG 59.834 55.000 0.00 0.00 39.67 4.35
2417 6174 3.670627 GCATCTGTTCTTTAACAAGCCCG 60.671 47.826 0.00 0.00 44.79 6.13
2467 6224 4.224147 TGCTACTCTGTATTGGGCTTTGTA 59.776 41.667 0.00 0.00 0.00 2.41
2479 6236 2.039348 GGTTGGGGTTTGCTACTCTGTA 59.961 50.000 0.00 0.00 0.00 2.74
2578 6335 3.496870 GCATTAGTTCCTAGATGGGGGTG 60.497 52.174 0.00 0.00 36.20 4.61
2593 6350 2.512692 TGGCCTGATGTTGCATTAGT 57.487 45.000 3.32 0.00 0.00 2.24
2663 6420 1.878088 GTTCGAACCTTTCTTGGGTCC 59.122 52.381 17.68 0.00 40.60 4.46
2684 6441 2.032528 CTTCAAGCACGCCCCAGA 59.967 61.111 0.00 0.00 0.00 3.86
2701 6458 2.165319 ACTAGAGTTTGGCGTGGTTC 57.835 50.000 0.00 0.00 0.00 3.62
2708 6465 2.351455 GGCAGAGAACTAGAGTTTGGC 58.649 52.381 0.00 0.35 38.56 4.52
2738 6495 1.278937 CATATCGGAGCGTCGTCGT 59.721 57.895 3.66 0.00 39.49 4.34
2744 6501 0.598680 GCTCAAGCATATCGGAGCGT 60.599 55.000 0.00 0.00 42.72 5.07
2749 6506 2.032549 CCTTTTCGCTCAAGCATATCGG 60.033 50.000 2.50 0.00 42.21 4.18
2752 6509 4.333926 GTCTTCCTTTTCGCTCAAGCATAT 59.666 41.667 2.50 0.00 42.21 1.78
2753 6510 3.684788 GTCTTCCTTTTCGCTCAAGCATA 59.315 43.478 2.50 0.00 42.21 3.14
2754 6511 2.485814 GTCTTCCTTTTCGCTCAAGCAT 59.514 45.455 2.50 0.00 42.21 3.79
2835 6592 1.870055 GCAGTCCACCACAATGCAGG 61.870 60.000 0.00 0.00 36.88 4.85
2839 6596 1.300971 CGAGGCAGTCCACCACAATG 61.301 60.000 0.00 0.00 33.74 2.82
2840 6597 1.003355 CGAGGCAGTCCACCACAAT 60.003 57.895 0.00 0.00 33.74 2.71
2848 6605 3.296709 TTCCTTCGCGAGGCAGTCC 62.297 63.158 13.49 0.00 45.87 3.85
2851 6608 1.142748 ATCTTCCTTCGCGAGGCAG 59.857 57.895 13.49 14.19 45.87 4.85
2862 6619 7.345653 TCCTTGTACACTCATATTCATCTTCCT 59.654 37.037 0.00 0.00 0.00 3.36
2866 6623 8.311395 TCTTCCTTGTACACTCATATTCATCT 57.689 34.615 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.