Multiple sequence alignment - TraesCS3A01G031600

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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 TraesCS3A01G031600 chr3A 100.000 6266 0 0 1 6266 17381038 17374773 0.000000e+00 11572.0
1 TraesCS3A01G031600 chr3A 94.979 4680 198 12 548 5197 16235274 16230602 0.000000e+00 7306.0
2 TraesCS3A01G031600 chr3A 94.808 3794 175 11 1112 4885 17331379 17335170 0.000000e+00 5895.0
3 TraesCS3A01G031600 chr3A 86.471 1870 186 30 2944 4787 16011009 16012837 0.000000e+00 1989.0
4 TraesCS3A01G031600 chr3A 82.982 2133 289 30 1112 3235 15835637 15837704 0.000000e+00 1860.0
5 TraesCS3A01G031600 chr3A 84.537 1772 248 12 1131 2889 16009230 16010988 0.000000e+00 1731.0
6 TraesCS3A01G031600 chr3A 84.887 1555 192 24 3235 4779 15837789 15839310 0.000000e+00 1530.0
7 TraesCS3A01G031600 chr3A 88.793 696 48 8 4923 5602 17335169 17335850 0.000000e+00 826.0
8 TraesCS3A01G031600 chr3A 89.399 566 48 6 5267 5824 16176833 16176272 0.000000e+00 702.0
9 TraesCS3A01G031600 chr3A 91.096 438 38 1 5829 6266 16176238 16175802 5.410000e-165 592.0
10 TraesCS3A01G031600 chr3A 84.810 553 40 17 1 551 16243325 16242815 3.350000e-142 516.0
11 TraesCS3A01G031600 chr3A 85.263 95 11 3 4791 4885 16012898 16012989 1.860000e-15 95.3
12 TraesCS3A01G031600 chr3A 96.429 56 2 0 5212 5267 16183522 16183467 6.690000e-15 93.5
13 TraesCS3A01G031600 chr3A 83.158 95 13 3 4791 4885 16321548 16321639 4.030000e-12 84.2
14 TraesCS3A01G031600 chr3D 95.946 4983 174 17 1 4970 5377705 5372738 0.000000e+00 8058.0
15 TraesCS3A01G031600 chr3D 94.579 3339 138 12 1114 4442 5328604 5331909 0.000000e+00 5123.0
16 TraesCS3A01G031600 chr3D 84.156 2127 254 39 1131 3235 41427036 41424971 0.000000e+00 1984.0
17 TraesCS3A01G031600 chr3D 83.777 2139 268 33 1112 3235 41596756 41594682 0.000000e+00 1954.0
18 TraesCS3A01G031600 chr3D 84.875 1957 260 17 1131 3064 5410216 5408273 0.000000e+00 1941.0
19 TraesCS3A01G031600 chr3D 87.068 1562 174 14 3239 4787 5408026 5406480 0.000000e+00 1740.0
20 TraesCS3A01G031600 chr3D 85.595 1562 177 29 3235 4782 41424878 41423351 0.000000e+00 1594.0
21 TraesCS3A01G031600 chr3D 84.719 1564 188 32 3235 4782 41594597 41593069 0.000000e+00 1517.0
22 TraesCS3A01G031600 chr3D 94.946 930 39 2 4903 5824 5372737 5371808 0.000000e+00 1450.0
23 TraesCS3A01G031600 chr3D 95.399 326 15 0 5829 6154 5371775 5371450 2.590000e-143 520.0
24 TraesCS3A01G031600 chr3D 95.122 41 2 0 982 1022 5410517 5410477 1.460000e-06 65.8
25 TraesCS3A01G031600 chr3B 83.623 3688 489 58 1131 4787 12933426 12937029 0.000000e+00 3358.0
26 TraesCS3A01G031600 chr3B 83.843 2748 337 50 2045 4759 13246986 13249659 0.000000e+00 2516.0
27 TraesCS3A01G031600 chr3B 83.853 2118 272 34 1131 3235 12472473 12474533 0.000000e+00 1953.0
28 TraesCS3A01G031600 chr3B 83.178 2152 275 37 1112 3235 12843125 12841033 0.000000e+00 1888.0
29 TraesCS3A01G031600 chr3B 86.079 1566 185 22 3238 4788 13415023 13416570 0.000000e+00 1653.0
30 TraesCS3A01G031600 chr3B 85.275 1562 183 25 3235 4782 12840948 12839420 0.000000e+00 1567.0
31 TraesCS3A01G031600 chr3B 85.243 1213 153 14 1866 3058 13413561 13414767 0.000000e+00 1225.0
32 TraesCS3A01G031600 chr3B 84.624 930 130 7 1131 2058 13246042 13246960 0.000000e+00 913.0
33 TraesCS3A01G031600 chr3B 85.526 380 32 15 5904 6266 593930588 593930961 5.930000e-100 375.0
34 TraesCS3A01G031600 chr3B 94.828 58 3 0 4828 4885 12937124 12937181 2.410000e-14 91.6
35 TraesCS3A01G031600 chr2D 76.182 1608 323 38 1131 2723 548631023 548632585 0.000000e+00 793.0
36 TraesCS3A01G031600 chr2D 86.595 373 28 9 5909 6266 548900679 548900314 5.890000e-105 392.0
37 TraesCS3A01G031600 chr2D 85.714 378 29 8 5904 6266 493527647 493527280 5.930000e-100 375.0
38 TraesCS3A01G031600 chr2D 85.542 166 18 4 5427 5586 506399394 506399229 1.080000e-37 169.0
39 TraesCS3A01G031600 chr2D 74.662 296 47 13 302 570 321761727 321761433 8.590000e-19 106.0
40 TraesCS3A01G031600 chr2D 84.524 84 13 0 2779 2862 514947390 514947473 4.030000e-12 84.2
41 TraesCS3A01G031600 chr6D 87.131 373 30 6 5904 6260 140222445 140222815 2.100000e-109 407.0
42 TraesCS3A01G031600 chr5D 86.508 378 29 14 5905 6266 385963166 385962795 4.550000e-106 396.0
43 TraesCS3A01G031600 chr5D 84.083 289 26 8 5902 6171 120610017 120610304 1.730000e-65 261.0
44 TraesCS3A01G031600 chr7A 86.053 380 31 14 5904 6266 125920623 125920249 7.620000e-104 388.0
45 TraesCS3A01G031600 chr5A 85.979 378 32 10 5904 6266 216968028 216967657 9.850000e-103 385.0
46 TraesCS3A01G031600 chr5A 85.302 381 34 9 5902 6266 53463136 53462762 2.130000e-99 374.0
47 TraesCS3A01G031600 chr5A 84.718 373 35 7 5909 6265 555946588 555946222 2.780000e-93 353.0
48 TraesCS3A01G031600 chr2A 84.392 378 32 10 5904 6266 640078281 640078646 4.650000e-91 346.0
49 TraesCS3A01G031600 chr2A 88.095 84 10 0 2782 2865 691530998 691531081 4.000000e-17 100.0
50 TraesCS3A01G031600 chr2A 86.207 87 12 0 2782 2868 658907952 658908038 1.860000e-15 95.3
51 TraesCS3A01G031600 chr1A 80.685 321 43 6 5902 6205 248429012 248428694 1.360000e-56 231.0
52 TraesCS3A01G031600 chr2B 86.420 162 16 1 5432 5587 109974475 109974314 8.350000e-39 172.0
53 TraesCS3A01G031600 chrUn 85.380 171 17 5 5431 5594 86671478 86671309 3.000000e-38 171.0
54 TraesCS3A01G031600 chr4B 85.380 171 17 5 5431 5594 115040640 115040809 3.000000e-38 171.0
55 TraesCS3A01G031600 chr4B 85.380 171 18 2 5432 5595 406389457 406389287 3.000000e-38 171.0
56 TraesCS3A01G031600 chr4B 85.380 171 17 5 5431 5594 499224663 499224494 3.000000e-38 171.0


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 TraesCS3A01G031600 chr3A 17374773 17381038 6265 True 11572.000000 11572 100.000000 1 6266 1 chr3A.!!$R4 6265
1 TraesCS3A01G031600 chr3A 16230602 16235274 4672 True 7306.000000 7306 94.979000 548 5197 1 chr3A.!!$R2 4649
2 TraesCS3A01G031600 chr3A 17331379 17335850 4471 False 3360.500000 5895 91.800500 1112 5602 2 chr3A.!!$F4 4490
3 TraesCS3A01G031600 chr3A 15835637 15839310 3673 False 1695.000000 1860 83.934500 1112 4779 2 chr3A.!!$F2 3667
4 TraesCS3A01G031600 chr3A 16009230 16012989 3759 False 1271.766667 1989 85.423667 1131 4885 3 chr3A.!!$F3 3754
5 TraesCS3A01G031600 chr3A 16175802 16176833 1031 True 647.000000 702 90.247500 5267 6266 2 chr3A.!!$R5 999
6 TraesCS3A01G031600 chr3A 16242815 16243325 510 True 516.000000 516 84.810000 1 551 1 chr3A.!!$R3 550
7 TraesCS3A01G031600 chr3D 5328604 5331909 3305 False 5123.000000 5123 94.579000 1114 4442 1 chr3D.!!$F1 3328
8 TraesCS3A01G031600 chr3D 5371450 5377705 6255 True 3342.666667 8058 95.430333 1 6154 3 chr3D.!!$R1 6153
9 TraesCS3A01G031600 chr3D 41423351 41427036 3685 True 1789.000000 1984 84.875500 1131 4782 2 chr3D.!!$R3 3651
10 TraesCS3A01G031600 chr3D 41593069 41596756 3687 True 1735.500000 1954 84.248000 1112 4782 2 chr3D.!!$R4 3670
11 TraesCS3A01G031600 chr3D 5406480 5410517 4037 True 1248.933333 1941 89.021667 982 4787 3 chr3D.!!$R2 3805
12 TraesCS3A01G031600 chr3B 12472473 12474533 2060 False 1953.000000 1953 83.853000 1131 3235 1 chr3B.!!$F1 2104
13 TraesCS3A01G031600 chr3B 12839420 12843125 3705 True 1727.500000 1888 84.226500 1112 4782 2 chr3B.!!$R1 3670
14 TraesCS3A01G031600 chr3B 12933426 12937181 3755 False 1724.800000 3358 89.225500 1131 4885 2 chr3B.!!$F3 3754
15 TraesCS3A01G031600 chr3B 13246042 13249659 3617 False 1714.500000 2516 84.233500 1131 4759 2 chr3B.!!$F4 3628
16 TraesCS3A01G031600 chr3B 13413561 13416570 3009 False 1439.000000 1653 85.661000 1866 4788 2 chr3B.!!$F5 2922
17 TraesCS3A01G031600 chr2D 548631023 548632585 1562 False 793.000000 793 76.182000 1131 2723 1 chr2D.!!$F2 1592

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
604 607 0.673644 GTCCATCCCTTGTCCGTGTG 60.674 60.000 0.00 0.00 0.00 3.82 F
1652 1830 0.834687 AGGCCGTGTCCAAGAACCTA 60.835 55.000 0.00 0.00 0.00 3.08 F
2988 3297 2.421725 AGGTATTGCCCCATGAGATCA 58.578 47.619 0.00 0.00 38.26 2.92 F
3441 4025 0.741221 CAAGCTCAGAGTTACCCGCC 60.741 60.000 0.00 0.00 0.00 6.13 F
4263 4961 0.837272 AGTGTGGTACAGTGTGCCTT 59.163 50.000 27.78 10.77 41.80 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2006 2191 0.322546 AAGTTGCATCCCCTTCGGTC 60.323 55.0 0.0 0.0 0.00 4.79 R
3050 3359 1.096967 GTGCATCATCGGTGCCATCA 61.097 55.0 0.0 0.0 41.83 3.07 R
4073 4691 1.613317 ATCCATGCGGTCCTCGAACA 61.613 55.0 0.0 0.0 42.43 3.18 R
5244 6083 1.519751 TATTTGTGCGTGTGTGGGGC 61.520 55.0 0.0 0.0 0.00 5.80 R
5834 6709 0.402566 AGGGGATTGGAGGGGATCTG 60.403 60.0 0.0 0.0 0.00 2.90 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
31 32 4.039004 AGCATTAAATGGCCATTAATCGCA 59.961 37.500 30.84 11.76 0.00 5.10
56 57 6.744112 TGCCAAAGTCCACTTTAACATTAAG 58.256 36.000 4.38 0.00 43.72 1.85
119 120 2.498941 GCGTCATCATCCTCCCCGA 61.499 63.158 0.00 0.00 0.00 5.14
120 121 2.028125 GCGTCATCATCCTCCCCGAA 62.028 60.000 0.00 0.00 0.00 4.30
130 131 3.316573 CTCCCCGAACAGGTGAGGC 62.317 68.421 0.00 0.00 38.74 4.70
141 142 1.134280 CAGGTGAGGCCGATCAATTCT 60.134 52.381 0.00 0.00 43.70 2.40
168 169 1.543065 GCCCAACCCACATGAATGCA 61.543 55.000 0.00 0.00 0.00 3.96
250 251 3.223589 GCGCTCCTCCTCCTCCTC 61.224 72.222 0.00 0.00 0.00 3.71
286 287 2.292267 GAGCACGACATTCCAATGGAT 58.708 47.619 1.39 0.00 40.70 3.41
289 290 2.620115 GCACGACATTCCAATGGATGAT 59.380 45.455 1.39 0.00 40.70 2.45
342 343 4.927782 AAGCTGGCGCCGTGTGAA 62.928 61.111 23.90 0.87 36.60 3.18
347 348 4.090057 GGCGCCGTGTGAAGCTTC 62.090 66.667 19.89 19.89 0.00 3.86
348 349 3.044305 GCGCCGTGTGAAGCTTCT 61.044 61.111 26.09 0.00 0.00 2.85
398 400 2.051345 GTTTTGGTGTCGCTGGCG 60.051 61.111 8.80 8.80 41.35 5.69
430 432 1.379843 GGCCAAATGTGGACGGGAT 60.380 57.895 5.94 0.00 45.39 3.85
510 513 2.436115 GGAGGTAGGTGGTTGCGC 60.436 66.667 0.00 0.00 0.00 6.09
521 524 1.061566 GTGGTTGCGCTTAATACGACC 59.938 52.381 9.73 4.57 0.00 4.79
530 533 1.947597 TTAATACGACCGCGGGCAGT 61.948 55.000 33.95 29.81 43.17 4.40
535 538 2.813908 GACCGCGGGCAGTAGTTG 60.814 66.667 30.38 0.00 0.00 3.16
536 539 4.388499 ACCGCGGGCAGTAGTTGG 62.388 66.667 31.76 0.00 0.00 3.77
546 549 4.382320 GTAGTTGGGCGGCCGACA 62.382 66.667 40.55 27.13 0.00 4.35
594 597 4.457496 CGCAGCGTGTCCATCCCT 62.457 66.667 6.65 0.00 0.00 4.20
604 607 0.673644 GTCCATCCCTTGTCCGTGTG 60.674 60.000 0.00 0.00 0.00 3.82
607 610 1.442769 CATCCCTTGTCCGTGTGAAG 58.557 55.000 0.00 0.00 0.00 3.02
640 643 9.062524 CGGTCATAAATTTGGGTCTGAAATATA 57.937 33.333 0.00 0.00 0.00 0.86
649 652 4.844085 TGGGTCTGAAATATATCCGGACAT 59.156 41.667 6.12 2.01 0.00 3.06
662 665 1.757118 CCGGACATACACTGAGTGGAT 59.243 52.381 17.92 11.54 37.63 3.41
1599 1777 8.387354 TGTATATCGACATTGATGTGTTGTTTC 58.613 33.333 0.57 0.00 41.95 2.78
1652 1830 0.834687 AGGCCGTGTCCAAGAACCTA 60.835 55.000 0.00 0.00 0.00 3.08
2187 2481 7.472334 AAGCAGAATGATGTGAGGTTTTATT 57.528 32.000 0.00 0.00 39.69 1.40
2419 2713 2.865151 GCATGTTGTCGCGAACGC 60.865 61.111 12.06 9.20 39.84 4.84
2436 2730 4.508124 CGAACGCTCTTCCTATTAATGCTT 59.492 41.667 0.00 0.00 0.00 3.91
2478 2784 7.223582 GTGATCCTAATGACATGACAACTACTG 59.776 40.741 0.00 0.00 0.00 2.74
2674 2980 4.788925 AGATAGACTCTAGCCACTCTGT 57.211 45.455 0.00 0.00 30.26 3.41
2988 3297 2.421725 AGGTATTGCCCCATGAGATCA 58.578 47.619 0.00 0.00 38.26 2.92
3050 3359 1.457831 GGGCGACTGGGTAGAGGAT 60.458 63.158 0.00 0.00 0.00 3.24
3290 3872 8.349983 TCAGAATCTAAATAACGATGTCGATGA 58.650 33.333 9.67 0.00 43.02 2.92
3441 4025 0.741221 CAAGCTCAGAGTTACCCGCC 60.741 60.000 0.00 0.00 0.00 6.13
3471 4055 2.299013 TGATGATAGTATCGGTGGTGCC 59.701 50.000 5.68 0.00 0.00 5.01
3989 4605 1.806623 CGGCTTACCAGGTATGTGAGC 60.807 57.143 11.35 11.35 42.68 4.26
4007 4623 2.420022 GAGCGCACCTCAAAATACACAT 59.580 45.455 11.47 0.00 40.45 3.21
4008 4624 2.162208 AGCGCACCTCAAAATACACATG 59.838 45.455 11.47 0.00 0.00 3.21
4035 4653 9.783256 GGTCCATGTGTCTACAAAATTTAATAC 57.217 33.333 0.00 0.00 40.84 1.89
4073 4691 3.323243 CAGAAACCATTTACGTCCGAGT 58.677 45.455 0.00 0.00 0.00 4.18
4263 4961 0.837272 AGTGTGGTACAGTGTGCCTT 59.163 50.000 27.78 10.77 41.80 4.35
4412 5110 2.357009 GCTATGAGACATTGGTTGGCAG 59.643 50.000 0.00 0.00 34.87 4.85
4491 5189 2.301870 TCGGACTATGCAACACCTTCTT 59.698 45.455 0.00 0.00 0.00 2.52
4674 5372 2.899838 GCACTCACCAACGTGGCA 60.900 61.111 0.00 0.00 42.67 4.92
4797 5553 4.471548 AGACTGAGTAGTTGCGGGTATAT 58.528 43.478 0.00 0.00 37.25 0.86
4817 5573 9.520515 GGTATATGATATTTTGTGATCCTGGTT 57.479 33.333 0.00 0.00 0.00 3.67
5184 6021 4.385310 GGCAGAAGACCATTTATGTACCCT 60.385 45.833 0.00 0.00 0.00 4.34
5244 6083 2.232941 ACAGCCAATTCATCTGCAAAGG 59.767 45.455 0.00 0.00 0.00 3.11
5318 6157 5.003096 AGTGAAGAAATGAACTTCCCCAT 57.997 39.130 0.00 0.00 41.83 4.00
5352 6191 7.827819 TCACTTCCAAAAATCATAGAGTACG 57.172 36.000 0.00 0.00 0.00 3.67
5388 6227 6.658188 TGGGGTTTAATTGGAAAACACTAG 57.342 37.500 4.92 0.00 39.63 2.57
5407 6246 3.314541 AGTTGGTGTAAAGCTACCGAG 57.685 47.619 0.00 0.00 39.87 4.63
5425 6264 3.490078 CCGAGTAAGATGGTTCTGCTCTC 60.490 52.174 0.00 0.00 34.88 3.20
5426 6265 3.701241 GAGTAAGATGGTTCTGCTCTCG 58.299 50.000 0.00 0.00 34.52 4.04
5441 6280 2.427453 GCTCTCGAAAGTACTCCATCCA 59.573 50.000 0.00 0.00 0.00 3.41
5499 6338 4.712829 TGGACTACATACGGAGGAAAATGA 59.287 41.667 0.00 0.00 0.00 2.57
5505 6344 4.935808 ACATACGGAGGAAAATGAGTGAAC 59.064 41.667 0.00 0.00 0.00 3.18
5649 6495 0.744874 TCGAGGGCTCAGATTAACCG 59.255 55.000 0.00 0.00 0.00 4.44
5685 6531 5.415701 TCTTAGGTGTTTCAGAATGCAATCC 59.584 40.000 0.00 0.00 34.76 3.01
5716 6562 6.876155 TGCATCTTAATTGCACCAATGTAAT 58.124 32.000 8.67 0.00 44.73 1.89
5761 6607 4.063967 TGTGCGGACCGAGCGATT 62.064 61.111 20.50 0.00 37.44 3.34
5762 6608 3.554692 GTGCGGACCGAGCGATTG 61.555 66.667 20.50 0.00 37.44 2.67
5765 6611 2.586079 CGGACCGAGCGATTGCAT 60.586 61.111 8.64 0.00 46.23 3.96
5771 6617 1.301244 CGAGCGATTGCATAGCCCT 60.301 57.895 7.90 0.00 46.23 5.19
5808 6654 3.064324 GGCTGCATTCGGTTGGCT 61.064 61.111 0.50 0.00 0.00 4.75
5816 6662 2.879826 CATTCGGTTGGCTTGGATTTC 58.120 47.619 0.00 0.00 0.00 2.17
5826 6672 1.852633 CTTGGATTTCAAGGGGTCCC 58.147 55.000 0.00 0.00 46.81 4.46
5827 6673 0.411848 TTGGATTTCAAGGGGTCCCC 59.588 55.000 20.85 20.85 45.90 4.81
5860 6735 1.589414 CCTCCAATCCCCTTGAGACT 58.411 55.000 0.00 0.00 36.97 3.24
5911 6786 9.764363 GGAGAGTAACAAATTTGAAAGGAAAAT 57.236 29.630 24.64 2.24 0.00 1.82
6042 6917 1.999735 TCTGCTTTATTCAACCTCGCG 59.000 47.619 0.00 0.00 0.00 5.87
6044 6919 0.727398 GCTTTATTCAACCTCGCGCT 59.273 50.000 5.56 0.00 0.00 5.92
6132 7007 0.902531 GAAGATCGAAGTCCCCACCA 59.097 55.000 0.00 0.00 0.00 4.17
6148 7023 3.781760 CAACCATGGTTGCAGCCT 58.218 55.556 37.64 10.94 46.92 4.58
6182 7057 1.208706 CCTCCCCCTTCTTCCTTCTC 58.791 60.000 0.00 0.00 0.00 2.87
6191 7066 3.055458 CCTTCTTCCTTCTCCCTCACTTC 60.055 52.174 0.00 0.00 0.00 3.01
6206 7081 2.112691 TCACTTCCTTTCTCCTCCTCCT 59.887 50.000 0.00 0.00 0.00 3.69
6210 7085 1.289530 TCCTTTCTCCTCCTCCTCCTC 59.710 57.143 0.00 0.00 0.00 3.71
6213 7088 3.449918 CTTTCTCCTCCTCCTCCTCTTT 58.550 50.000 0.00 0.00 0.00 2.52
6240 7115 1.142748 TTTTTGCTGCAACCGGTGG 59.857 52.632 15.72 6.08 0.00 4.61
6257 7132 2.568090 GCAGGCCAAACGTCATGG 59.432 61.111 5.01 14.36 41.08 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 0.537143 AAGTGGACTTTGGCATGCGA 60.537 50.000 12.44 4.51 30.82 5.10
31 32 5.806654 AATGTTAAAGTGGACTTTGGCAT 57.193 34.783 13.87 13.46 45.01 4.40
109 110 1.080354 TCACCTGTTCGGGGAGGAT 59.920 57.895 2.61 0.00 41.43 3.24
119 120 0.620556 ATTGATCGGCCTCACCTGTT 59.379 50.000 0.00 0.00 35.61 3.16
120 121 0.620556 AATTGATCGGCCTCACCTGT 59.379 50.000 0.00 0.00 35.61 4.00
130 131 1.779025 CTGGCGCCAGAATTGATCGG 61.779 60.000 46.72 20.32 46.30 4.18
160 161 1.452651 CGTGGGAGGCTGCATTCAT 60.453 57.895 8.68 0.00 0.00 2.57
161 162 2.046023 CGTGGGAGGCTGCATTCA 60.046 61.111 8.68 0.00 0.00 2.57
248 249 4.087892 CACTGGGCACGGGAGGAG 62.088 72.222 0.00 0.00 0.00 3.69
269 270 3.251729 GGATCATCCATTGGAATGTCGTG 59.748 47.826 9.98 2.36 36.28 4.35
272 273 2.816087 CCGGATCATCCATTGGAATGTC 59.184 50.000 9.98 7.63 35.91 3.06
338 339 2.470983 AGAGCAAGGAGAAGCTTCAC 57.529 50.000 27.57 21.19 42.04 3.18
339 340 2.775890 CAAGAGCAAGGAGAAGCTTCA 58.224 47.619 27.57 0.00 42.04 3.02
340 341 1.468127 GCAAGAGCAAGGAGAAGCTTC 59.532 52.381 19.11 19.11 42.04 3.86
341 342 1.532523 GCAAGAGCAAGGAGAAGCTT 58.467 50.000 0.00 0.00 42.04 3.74
342 343 0.322366 GGCAAGAGCAAGGAGAAGCT 60.322 55.000 0.00 0.00 45.25 3.74
343 344 0.607489 TGGCAAGAGCAAGGAGAAGC 60.607 55.000 0.00 0.00 44.61 3.86
344 345 1.901591 TTGGCAAGAGCAAGGAGAAG 58.098 50.000 0.00 0.00 44.61 2.85
345 346 2.158623 TCTTTGGCAAGAGCAAGGAGAA 60.159 45.455 0.00 0.00 44.61 2.87
347 348 1.901591 TCTTTGGCAAGAGCAAGGAG 58.098 50.000 0.00 0.00 44.61 3.69
348 349 2.362077 GTTTCTTTGGCAAGAGCAAGGA 59.638 45.455 0.00 0.00 44.61 3.36
398 400 1.181098 TTGGCCAAGCTTGCTTCCTC 61.181 55.000 21.43 6.47 0.00 3.71
430 432 4.285790 AAGCACAGGGGAGGGGGA 62.286 66.667 0.00 0.00 0.00 4.81
441 443 1.065600 GCCGTCTTTTGCAAGCACA 59.934 52.632 0.00 0.00 0.00 4.57
465 468 2.820037 GCAGCGGGTAGAAGCACC 60.820 66.667 0.00 0.00 37.91 5.01
510 513 1.213094 CTGCCCGCGGTCGTATTAAG 61.213 60.000 26.12 6.10 0.00 1.85
530 533 4.077184 CTGTCGGCCGCCCAACTA 62.077 66.667 23.51 0.00 0.00 2.24
580 583 1.296715 GACAAGGGATGGACACGCT 59.703 57.895 0.00 0.00 0.00 5.07
592 595 0.817634 TTGCCTTCACACGGACAAGG 60.818 55.000 0.00 0.00 39.91 3.61
594 597 0.736053 GTTTGCCTTCACACGGACAA 59.264 50.000 0.00 0.00 0.00 3.18
604 607 4.450082 AATTTATGACCGGTTTGCCTTC 57.550 40.909 9.42 0.00 0.00 3.46
607 610 3.258228 CCAAATTTATGACCGGTTTGCC 58.742 45.455 9.42 0.00 0.00 4.52
640 643 1.757118 CCACTCAGTGTATGTCCGGAT 59.243 52.381 7.81 0.00 0.00 4.18
649 652 5.221843 ACCTAAAAAGCATCCACTCAGTGTA 60.222 40.000 3.56 0.00 0.00 2.90
662 665 5.124645 TCGTTGACCTAAACCTAAAAAGCA 58.875 37.500 0.00 0.00 0.00 3.91
1599 1777 0.462225 CTGCAGACTGCTCCATCCTG 60.462 60.000 26.94 4.83 45.31 3.86
1652 1830 1.055040 AGCTGTCAGGCACTCTTTCT 58.945 50.000 1.14 0.00 34.60 2.52
1746 1930 2.213499 CGCCTTGAAGACTGAACAACT 58.787 47.619 0.00 0.00 0.00 3.16
1747 1931 1.264288 CCGCCTTGAAGACTGAACAAC 59.736 52.381 0.00 0.00 0.00 3.32
2006 2191 0.322546 AAGTTGCATCCCCTTCGGTC 60.323 55.000 0.00 0.00 0.00 4.79
2187 2481 1.279271 GACCTTCCTTAGCTGCTTCCA 59.721 52.381 7.79 0.00 0.00 3.53
2333 2627 0.401356 TTGCTGAAGGTCTGCCATGA 59.599 50.000 0.00 0.00 40.10 3.07
2414 2708 5.050023 GGAAGCATTAATAGGAAGAGCGTTC 60.050 44.000 0.00 0.00 0.00 3.95
2419 2713 6.018669 GTCAACGGAAGCATTAATAGGAAGAG 60.019 42.308 0.00 0.00 0.00 2.85
2436 2730 1.174078 TCACCAGTAGCGTCAACGGA 61.174 55.000 4.54 0.00 40.23 4.69
2988 3297 1.300697 GCTTGTCCTTGACGACGGT 60.301 57.895 0.00 0.00 34.95 4.83
3050 3359 1.096967 GTGCATCATCGGTGCCATCA 61.097 55.000 0.00 0.00 41.83 3.07
3274 3856 5.234329 GGTTGACATCATCGACATCGTTATT 59.766 40.000 0.54 0.00 42.93 1.40
3290 3872 1.167851 CGACATTGCCAGGTTGACAT 58.832 50.000 0.00 0.00 0.00 3.06
3330 3912 3.988976 TGGAGGAAAGACTGGAATGAG 57.011 47.619 0.00 0.00 0.00 2.90
3441 4025 4.859245 CCGATACTATCATCATTCGTGTGG 59.141 45.833 0.00 0.00 0.00 4.17
3471 4055 1.522355 ATCGCTGGTCTCCATTGCG 60.522 57.895 13.58 13.58 45.39 4.85
3665 4264 1.749634 ACTACCTCCCGTTCTTCATCG 59.250 52.381 0.00 0.00 0.00 3.84
3989 4605 2.159393 CCCATGTGTATTTTGAGGTGCG 60.159 50.000 0.00 0.00 0.00 5.34
4007 4623 3.866703 TTTTGTAGACACATGGACCCA 57.133 42.857 0.00 0.00 33.76 4.51
4008 4624 5.722021 AAATTTTGTAGACACATGGACCC 57.278 39.130 0.00 0.00 33.76 4.46
4035 4653 7.144661 TGGTTTCTGCACATTAAATAGTTGTG 58.855 34.615 2.42 2.42 42.80 3.33
4073 4691 1.613317 ATCCATGCGGTCCTCGAACA 61.613 55.000 0.00 0.00 42.43 3.18
4263 4961 2.027561 ACCGAATGTGTTTAGCAGGCTA 60.028 45.455 0.00 0.00 0.00 3.93
4797 5553 6.009589 ACACAACCAGGATCACAAAATATCA 58.990 36.000 0.00 0.00 0.00 2.15
4817 5573 5.900865 ATGTGCATGATTATCACAACACA 57.099 34.783 20.97 20.97 42.97 3.72
5184 6021 8.491134 ACTTGTAACCCATGAGCACTATATAAA 58.509 33.333 0.00 0.00 0.00 1.40
5244 6083 1.519751 TATTTGTGCGTGTGTGGGGC 61.520 55.000 0.00 0.00 0.00 5.80
5318 6157 8.231692 TGATTTTTGGAAGTGAATAGTTGTGA 57.768 30.769 0.00 0.00 0.00 3.58
5352 6191 2.549064 AACCCCATTTCTTTTGCAGC 57.451 45.000 0.00 0.00 0.00 5.25
5388 6227 3.036075 ACTCGGTAGCTTTACACCAAC 57.964 47.619 4.32 0.00 34.25 3.77
5407 6246 3.784701 TCGAGAGCAGAACCATCTTAC 57.215 47.619 0.00 0.00 32.03 2.34
5425 6264 4.408182 AGGAATGGATGGAGTACTTTCG 57.592 45.455 0.00 0.00 0.00 3.46
5530 6369 8.138074 TGTAGAGATTTGACTACATACAGATGC 58.862 37.037 0.00 0.00 42.27 3.91
5559 6405 7.652554 ACTCCCTCCATTCCTAAATACAATTT 58.347 34.615 0.00 0.00 0.00 1.82
5561 6407 6.848562 ACTCCCTCCATTCCTAAATACAAT 57.151 37.500 0.00 0.00 0.00 2.71
5623 6469 1.847328 TCTGAGCCCTCGATGTGTTA 58.153 50.000 0.00 0.00 0.00 2.41
5709 6555 8.169977 ACAACACTGAAGATCAACATTACATT 57.830 30.769 0.00 0.00 0.00 2.71
5710 6556 7.094634 GGACAACACTGAAGATCAACATTACAT 60.095 37.037 0.00 0.00 0.00 2.29
5716 6562 3.876914 GTGGACAACACTGAAGATCAACA 59.123 43.478 0.00 0.00 46.72 3.33
5753 6599 1.287730 GAGGGCTATGCAATCGCTCG 61.288 60.000 12.14 0.00 41.03 5.03
5761 6607 2.627945 CTGTTTTACGAGGGCTATGCA 58.372 47.619 0.00 0.00 0.00 3.96
5762 6608 1.940613 CCTGTTTTACGAGGGCTATGC 59.059 52.381 0.00 0.00 0.00 3.14
5765 6611 3.846955 GCCTGTTTTACGAGGGCTA 57.153 52.632 0.00 0.00 39.68 3.93
5771 6617 1.279846 CTTAGGGGGCCTGTTTTACGA 59.720 52.381 0.84 0.00 34.61 3.43
5797 6643 2.524306 TGAAATCCAAGCCAACCGAAT 58.476 42.857 0.00 0.00 0.00 3.34
5834 6709 0.402566 AGGGGATTGGAGGGGATCTG 60.403 60.000 0.00 0.00 0.00 2.90
5860 6735 1.310904 GCTTTGTTCGGTTACACCCA 58.689 50.000 0.00 0.00 33.75 4.51
6042 6917 1.540267 TCGTTATAGGGCGAGATCAGC 59.460 52.381 4.80 4.80 32.98 4.26
6044 6919 2.031420 CGTTCGTTATAGGGCGAGATCA 60.031 50.000 0.00 0.00 38.40 2.92
6132 7007 1.973281 CGAGGCTGCAACCATGGTT 60.973 57.895 24.86 24.86 39.13 3.67
6182 7057 1.557371 GGAGGAGAAAGGAAGTGAGGG 59.443 57.143 0.00 0.00 0.00 4.30
6191 7066 1.290732 AGAGGAGGAGGAGGAGAAAGG 59.709 57.143 0.00 0.00 0.00 3.11
6238 7113 2.115052 ATGACGTTTGGCCTGCCA 59.885 55.556 6.80 6.80 45.63 4.92
6240 7115 1.926511 CTCCATGACGTTTGGCCTGC 61.927 60.000 3.32 0.00 34.06 4.85


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

AutoCloner maintained by Alex Coulton.