Multiple sequence alignment - TraesCS6A01G237200

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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 TraesCS6A01G237200 chr6A 100.000 3875 0 0 1 3875 446732725 446728851 0.000000e+00 7156.0
1 TraesCS6A01G237200 chr6D 94.051 1580 65 18 2319 3875 309955224 309953651 0.000000e+00 2370.0
2 TraesCS6A01G237200 chr6D 85.467 750 22 25 3 734 309959780 309959100 0.000000e+00 701.0
3 TraesCS6A01G237200 chr6D 89.312 552 30 7 1781 2321 309955830 309955297 0.000000e+00 665.0
4 TraesCS6A01G237200 chr6D 88.717 452 31 12 1244 1687 309956653 309956214 5.700000e-148 534.0
5 TraesCS6A01G237200 chr6D 89.510 429 13 12 738 1166 309957262 309956866 7.420000e-142 514.0
6 TraesCS6A01G237200 chr6D 95.349 43 1 1 1195 1236 309956722 309956680 2.500000e-07 67.6
7 TraesCS6A01G237200 chr6B 89.017 1730 89 42 3 1698 477794597 477792935 0.000000e+00 2049.0
8 TraesCS6A01G237200 chr6B 83.130 901 93 29 2228 3108 477792183 477791322 0.000000e+00 767.0
9 TraesCS6A01G237200 chr6B 94.541 403 20 1 3461 3863 477790974 477790574 4.250000e-174 621.0
10 TraesCS6A01G237200 chr6B 90.262 267 24 2 1781 2046 477792605 477792340 7.970000e-92 348.0
11 TraesCS6A01G237200 chr6B 84.709 327 20 14 3160 3464 477791326 477791008 2.260000e-77 300.0
12 TraesCS6A01G237200 chr2D 93.023 43 0 2 1118 1160 470907376 470907415 4.180000e-05 60.2
13 TraesCS6A01G237200 chr2B 93.023 43 0 2 1118 1160 550040231 550040270 4.180000e-05 60.2
14 TraesCS6A01G237200 chr2A 93.023 43 0 2 1118 1160 612418969 612419008 4.180000e-05 60.2


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 TraesCS6A01G237200 chr6A 446728851 446732725 3874 True 7156.0 7156 100.0000 1 3875 1 chr6A.!!$R1 3874
1 TraesCS6A01G237200 chr6D 309953651 309959780 6129 True 808.6 2370 90.4010 3 3875 6 chr6D.!!$R1 3872
2 TraesCS6A01G237200 chr6B 477790574 477794597 4023 True 817.0 2049 88.3318 3 3863 5 chr6B.!!$R1 3860

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
117 118 0.032130 GATTGGAGGATCGCGCTGTA 59.968 55.0 5.56 0.0 34.37 2.74 F
118 119 0.032678 ATTGGAGGATCGCGCTGTAG 59.967 55.0 5.56 0.0 34.37 2.74 F
1370 3388 0.110192 GAAGCTGCCGAAAAACCTCG 60.110 55.0 0.00 0.0 38.58 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1703 3729 0.244721 GGCTGGCCAGTGAAACATTC 59.755 55.0 32.81 13.25 41.43 2.67 R
1773 3802 0.630673 ATGGGGGCAGTGAATAGCAA 59.369 50.0 0.00 0.00 0.00 3.91 R
3264 5773 0.169009 GGAAACAGGCATGAAGTCGC 59.831 55.0 4.84 0.00 0.00 5.19 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
27 28 3.690745 GGGACGGGAAAGAGACGA 58.309 61.111 0.00 0.00 0.00 4.20
31 32 0.456995 GACGGGAAAGAGACGAGCTG 60.457 60.000 0.00 0.00 0.00 4.24
82 83 1.153842 GTGGTGGGCTTTAATGCGC 60.154 57.895 19.63 19.63 44.63 6.09
112 113 3.191903 CAGAGATTGGAGGATCGCG 57.808 57.895 0.00 0.00 34.37 5.87
113 114 0.943359 CAGAGATTGGAGGATCGCGC 60.943 60.000 0.00 0.00 34.37 6.86
117 118 0.032130 GATTGGAGGATCGCGCTGTA 59.968 55.000 5.56 0.00 34.37 2.74
118 119 0.032678 ATTGGAGGATCGCGCTGTAG 59.967 55.000 5.56 0.00 34.37 2.74
119 120 1.320344 TTGGAGGATCGCGCTGTAGT 61.320 55.000 5.56 0.00 34.37 2.73
120 121 0.464916 TGGAGGATCGCGCTGTAGTA 60.465 55.000 5.56 0.00 34.37 1.82
121 122 0.238817 GGAGGATCGCGCTGTAGTAG 59.761 60.000 5.56 0.00 34.37 2.57
122 123 3.651262 GGAGGATCGCGCTGTAGTAGC 62.651 61.905 5.56 0.00 42.68 3.58
141 142 3.815809 AGCAGTTTAGTGTGGCTTACAA 58.184 40.909 0.00 0.00 41.89 2.41
146 147 2.443887 TAGTGTGGCTTACAACCGTC 57.556 50.000 0.00 0.00 41.89 4.79
208 212 0.467384 CAGGAGCGAATCAGTGGGAT 59.533 55.000 0.00 0.00 38.05 3.85
210 214 0.465705 GGAGCGAATCAGTGGGATGA 59.534 55.000 0.00 0.00 36.02 2.92
211 215 1.539929 GGAGCGAATCAGTGGGATGAG 60.540 57.143 0.00 0.00 36.02 2.90
212 216 1.410517 GAGCGAATCAGTGGGATGAGA 59.589 52.381 0.00 0.00 36.02 3.27
213 217 1.833630 AGCGAATCAGTGGGATGAGAA 59.166 47.619 0.00 0.00 36.02 2.87
214 218 2.237143 AGCGAATCAGTGGGATGAGAAA 59.763 45.455 0.00 0.00 36.02 2.52
215 219 3.009723 GCGAATCAGTGGGATGAGAAAA 58.990 45.455 0.00 0.00 36.02 2.29
271 275 4.386652 ACGTCGATTGTATTGTACCAACAC 59.613 41.667 0.00 0.00 34.61 3.32
272 276 4.386350 CGTCGATTGTATTGTACCAACACA 59.614 41.667 0.00 0.00 34.61 3.72
273 277 5.107414 CGTCGATTGTATTGTACCAACACAA 60.107 40.000 3.59 3.59 42.32 3.33
274 278 6.304126 GTCGATTGTATTGTACCAACACAAG 58.696 40.000 6.90 0.00 41.48 3.16
275 279 5.410132 TCGATTGTATTGTACCAACACAAGG 59.590 40.000 6.90 2.58 41.48 3.61
276 280 4.839668 TTGTATTGTACCAACACAAGGC 57.160 40.909 0.00 0.00 41.48 4.35
277 281 3.821748 TGTATTGTACCAACACAAGGCA 58.178 40.909 0.00 0.00 41.48 4.75
287 291 0.461135 ACACAAGGCAAAGGCAACAG 59.539 50.000 0.00 0.00 43.71 3.16
381 389 3.069079 TCCCTAGGATTCGATAGTCCG 57.931 52.381 11.48 0.00 39.54 4.79
436 444 3.641906 ACCTGTGAGAATTATACTCCCCG 59.358 47.826 0.00 0.00 33.95 5.73
471 479 2.047844 CTGCACTGTCCCTGTCCG 60.048 66.667 0.00 0.00 0.00 4.79
472 480 3.596066 CTGCACTGTCCCTGTCCGG 62.596 68.421 0.00 0.00 0.00 5.14
474 482 3.314331 CACTGTCCCTGTCCGGCT 61.314 66.667 0.00 0.00 0.00 5.52
475 483 3.314331 ACTGTCCCTGTCCGGCTG 61.314 66.667 0.00 0.00 0.00 4.85
476 484 3.314331 CTGTCCCTGTCCGGCTGT 61.314 66.667 0.00 0.00 0.00 4.40
477 485 3.302347 CTGTCCCTGTCCGGCTGTC 62.302 68.421 0.00 0.00 0.00 3.51
478 486 4.083862 GTCCCTGTCCGGCTGTCC 62.084 72.222 0.00 0.00 0.00 4.02
481 489 4.087892 CCTGTCCGGCTGTCCCTG 62.088 72.222 0.00 0.00 0.00 4.45
482 490 4.767255 CTGTCCGGCTGTCCCTGC 62.767 72.222 0.00 0.00 0.00 4.85
536 553 3.682315 CGCGATGTCCGATGCGTC 61.682 66.667 0.00 0.00 45.12 5.19
734 775 2.167662 GCTAAAAGCAGCCCCACTAAA 58.832 47.619 0.00 0.00 41.89 1.85
735 776 2.760650 GCTAAAAGCAGCCCCACTAAAT 59.239 45.455 0.00 0.00 41.89 1.40
736 777 3.951680 GCTAAAAGCAGCCCCACTAAATA 59.048 43.478 0.00 0.00 41.89 1.40
755 2630 5.810080 AATAAGCTCCCGGATATATAGCC 57.190 43.478 0.73 6.98 33.63 3.93
756 2631 3.406512 AAGCTCCCGGATATATAGCCT 57.593 47.619 14.88 0.00 33.63 4.58
757 2632 4.537945 AAGCTCCCGGATATATAGCCTA 57.462 45.455 14.88 0.18 33.63 3.93
815 2691 1.304464 CCAACCTTTCCTCCAGGCC 60.304 63.158 0.00 0.00 34.32 5.19
932 2811 1.269444 CGCGGTTGAGTATCGCTAGC 61.269 60.000 4.06 4.06 46.23 3.42
967 2846 1.784062 CAGCTGCGGAAGTTTCTCG 59.216 57.895 0.00 0.00 0.00 4.04
1166 3049 4.033702 CGTCGACAGCAGTGAGTATACTAA 59.966 45.833 17.16 0.00 0.00 2.24
1167 3050 5.264712 GTCGACAGCAGTGAGTATACTAAC 58.735 45.833 12.01 12.01 0.00 2.34
1242 3260 4.080356 TGAAGAGGGTTCATATGTGGAAGG 60.080 45.833 1.90 0.00 0.00 3.46
1250 3268 6.409234 GGGTTCATATGTGGAAGGATCAACTA 60.409 42.308 1.90 0.00 30.17 2.24
1295 3313 6.262273 TGTTTTCTATCTGTTCCACAAGGTTC 59.738 38.462 0.00 0.00 35.89 3.62
1297 3315 5.152623 TCTATCTGTTCCACAAGGTTCAG 57.847 43.478 0.00 0.00 37.72 3.02
1327 3345 0.798776 CACCGCACCTGATTTCTGAC 59.201 55.000 0.00 0.00 0.00 3.51
1370 3388 0.110192 GAAGCTGCCGAAAAACCTCG 60.110 55.000 0.00 0.00 38.58 4.63
1431 3449 5.879223 AGGTGACTGAATGATGATTCAACTC 59.121 40.000 8.96 7.06 45.89 3.01
1432 3450 5.065731 GGTGACTGAATGATGATTCAACTCC 59.934 44.000 8.96 11.36 45.89 3.85
1599 3618 4.214332 CCAAGGCTGAGAACAAGTAAGTTC 59.786 45.833 0.00 0.00 46.35 3.01
1624 3650 4.170468 ACAATAGATCCATTGTCACCCC 57.830 45.455 12.98 0.00 43.96 4.95
1642 3668 1.457346 CCTTCATTCTGCACTGGGAC 58.543 55.000 0.00 0.00 0.00 4.46
1658 3684 1.834263 GGGACTGTCAGTTAGCTGGAT 59.166 52.381 7.00 0.00 42.78 3.41
1664 3690 2.302733 TGTCAGTTAGCTGGATCAAGCA 59.697 45.455 24.11 7.45 46.08 3.91
1665 3691 3.054875 TGTCAGTTAGCTGGATCAAGCAT 60.055 43.478 24.11 11.43 46.08 3.79
1666 3692 3.559242 GTCAGTTAGCTGGATCAAGCATC 59.441 47.826 24.11 12.90 46.08 3.91
1693 3719 1.154430 TTTTAGCACCCCTCCCTGTT 58.846 50.000 0.00 0.00 0.00 3.16
1694 3720 0.696501 TTTAGCACCCCTCCCTGTTC 59.303 55.000 0.00 0.00 0.00 3.18
1695 3721 0.474854 TTAGCACCCCTCCCTGTTCA 60.475 55.000 0.00 0.00 0.00 3.18
1696 3722 0.909610 TAGCACCCCTCCCTGTTCAG 60.910 60.000 0.00 0.00 0.00 3.02
1697 3723 2.529744 GCACCCCTCCCTGTTCAGT 61.530 63.158 0.00 0.00 0.00 3.41
1698 3724 1.198759 GCACCCCTCCCTGTTCAGTA 61.199 60.000 0.00 0.00 0.00 2.74
1699 3725 1.358152 CACCCCTCCCTGTTCAGTAA 58.642 55.000 0.00 0.00 0.00 2.24
1700 3726 1.916181 CACCCCTCCCTGTTCAGTAAT 59.084 52.381 0.00 0.00 0.00 1.89
1701 3727 2.092914 CACCCCTCCCTGTTCAGTAATC 60.093 54.545 0.00 0.00 0.00 1.75
1702 3728 2.225908 ACCCCTCCCTGTTCAGTAATCT 60.226 50.000 0.00 0.00 0.00 2.40
1703 3729 2.171448 CCCCTCCCTGTTCAGTAATCTG 59.829 54.545 0.00 0.00 42.54 2.90
1717 3743 5.412594 TCAGTAATCTGAATGTTTCACTGGC 59.587 40.000 0.00 0.00 46.17 4.85
1737 3763 1.528129 CAGCCCTGGAAAACTCTGTC 58.472 55.000 0.00 0.00 0.00 3.51
1741 3768 2.498167 CCCTGGAAAACTCTGTCACAG 58.502 52.381 0.00 0.00 0.00 3.66
1747 3774 5.984725 TGGAAAACTCTGTCACAGACTTAA 58.015 37.500 2.36 0.00 35.39 1.85
1748 3775 6.411376 TGGAAAACTCTGTCACAGACTTAAA 58.589 36.000 2.36 0.00 35.39 1.52
1751 3778 6.679327 AAACTCTGTCACAGACTTAAAACC 57.321 37.500 2.36 0.00 35.39 3.27
1765 3792 4.945543 ACTTAAAACCGGAAAGTTGTCACT 59.054 37.500 9.46 0.00 29.25 3.41
1766 3793 3.775661 AAAACCGGAAAGTTGTCACTG 57.224 42.857 9.46 0.00 31.60 3.66
1767 3794 1.675552 AACCGGAAAGTTGTCACTGG 58.324 50.000 9.46 0.00 31.60 4.00
1773 3802 2.952310 GGAAAGTTGTCACTGGAAGCTT 59.048 45.455 0.00 0.00 37.60 3.74
1783 4127 3.753272 TCACTGGAAGCTTTGCTATTCAC 59.247 43.478 0.00 0.00 38.25 3.18
1792 4136 0.630673 TTGCTATTCACTGCCCCCAT 59.369 50.000 0.00 0.00 0.00 4.00
1798 4142 3.443045 CACTGCCCCCATTGCGTC 61.443 66.667 0.00 0.00 0.00 5.19
1813 4157 5.931724 CCATTGCGTCACAACATCCTATATA 59.068 40.000 0.00 0.00 42.27 0.86
1817 4161 8.926715 TTGCGTCACAACATCCTATATATATC 57.073 34.615 0.00 0.00 31.73 1.63
1818 4162 7.193595 TGCGTCACAACATCCTATATATATCG 58.806 38.462 0.00 0.00 0.00 2.92
1949 4294 1.882623 GGGAGAACACAAAGAAGGCAG 59.117 52.381 0.00 0.00 0.00 4.85
2079 4469 5.876460 CCTTTCTTTATTGCTGGGGATTTTG 59.124 40.000 0.00 0.00 0.00 2.44
2125 4522 5.679734 CCATGAGTGGTCTGCATATTTAC 57.320 43.478 0.00 0.00 40.83 2.01
2142 4539 9.815936 GCATATTTACCGGTACATTTACAATAC 57.184 33.333 18.00 2.64 0.00 1.89
2150 4547 7.066525 ACCGGTACATTTACAATACTTCCATTG 59.933 37.037 4.49 0.00 40.93 2.82
2215 4613 5.650543 TGCAAACAAGGAAGTTCTTCTTTC 58.349 37.500 11.53 0.98 36.40 2.62
2236 4634 9.372369 TCTTTCCTTCGAGAAAAAGAATCTATC 57.628 33.333 12.83 0.00 35.43 2.08
2265 4682 3.508744 CCACATCAAGGCAATACAACC 57.491 47.619 0.00 0.00 0.00 3.77
2266 4683 2.824936 CCACATCAAGGCAATACAACCA 59.175 45.455 0.00 0.00 0.00 3.67
2267 4684 3.448301 CCACATCAAGGCAATACAACCAT 59.552 43.478 0.00 0.00 0.00 3.55
2268 4685 4.644234 CCACATCAAGGCAATACAACCATA 59.356 41.667 0.00 0.00 0.00 2.74
2269 4686 5.126869 CCACATCAAGGCAATACAACCATAA 59.873 40.000 0.00 0.00 0.00 1.90
2270 4687 6.267817 CACATCAAGGCAATACAACCATAAG 58.732 40.000 0.00 0.00 0.00 1.73
2271 4688 6.095300 CACATCAAGGCAATACAACCATAAGA 59.905 38.462 0.00 0.00 0.00 2.10
2272 4689 6.319658 ACATCAAGGCAATACAACCATAAGAG 59.680 38.462 0.00 0.00 0.00 2.85
2273 4690 5.815581 TCAAGGCAATACAACCATAAGAGT 58.184 37.500 0.00 0.00 0.00 3.24
2274 4691 6.245408 TCAAGGCAATACAACCATAAGAGTT 58.755 36.000 0.00 0.00 0.00 3.01
2275 4692 6.719370 TCAAGGCAATACAACCATAAGAGTTT 59.281 34.615 0.00 0.00 0.00 2.66
2276 4693 7.885922 TCAAGGCAATACAACCATAAGAGTTTA 59.114 33.333 0.00 0.00 0.00 2.01
2277 4694 7.625828 AGGCAATACAACCATAAGAGTTTAC 57.374 36.000 0.00 0.00 0.00 2.01
2322 4814 3.738982 TCCCACAGACACAACATTACAG 58.261 45.455 0.00 0.00 0.00 2.74
2351 4843 7.466746 ACAATAAAGTTCAGCCATAACATGT 57.533 32.000 0.00 0.00 0.00 3.21
2392 4892 5.067805 CACAAAAGGAAACAGCTTAAGGTCT 59.932 40.000 3.68 0.00 0.00 3.85
2483 4983 5.221106 CCACCTTGGCACATAATATGAACAG 60.221 44.000 7.33 0.00 39.30 3.16
2568 5069 1.895798 TGGTGACCTTGACTAGCTGAG 59.104 52.381 2.11 0.00 0.00 3.35
2619 5120 2.581246 TGTAGCCACTTCTCCTAGAGGA 59.419 50.000 0.00 0.00 43.08 3.71
2723 5225 3.583806 ACGCTGAGAAGATGAAGAACAG 58.416 45.455 0.00 0.00 0.00 3.16
2892 5394 5.767168 GGCATAAGAAGCACCTCAATCTTAT 59.233 40.000 0.00 0.00 42.74 1.73
3092 5601 1.135972 GCATTGTTCGCGTTGTCTGAT 60.136 47.619 5.77 0.00 0.00 2.90
3219 5728 2.490903 ACTTCATGGCTTTCTGCATGAC 59.509 45.455 0.00 0.00 45.15 3.06
3255 5764 5.954153 ATGATCTCTTCTTGACTCATGGT 57.046 39.130 0.00 0.00 0.00 3.55
3256 5765 5.336150 TGATCTCTTCTTGACTCATGGTC 57.664 43.478 7.22 7.22 44.70 4.02
3260 5769 5.022122 TCTCTTCTTGACTCATGGTCTGAT 58.978 41.667 13.32 0.00 44.74 2.90
3261 5770 5.082251 TCTTCTTGACTCATGGTCTGATG 57.918 43.478 13.32 12.49 44.74 3.07
3263 5772 5.716703 TCTTCTTGACTCATGGTCTGATGTA 59.283 40.000 13.32 0.00 44.74 2.29
3264 5773 5.588958 TCTTGACTCATGGTCTGATGTAG 57.411 43.478 13.32 0.00 44.74 2.74
3265 5774 3.808466 TGACTCATGGTCTGATGTAGC 57.192 47.619 13.32 0.00 44.74 3.58
3266 5775 2.099756 TGACTCATGGTCTGATGTAGCG 59.900 50.000 13.32 0.00 44.74 4.26
3267 5776 2.359214 GACTCATGGTCTGATGTAGCGA 59.641 50.000 6.98 0.00 41.46 4.93
3268 5777 2.099921 ACTCATGGTCTGATGTAGCGAC 59.900 50.000 0.00 0.00 32.10 5.19
3270 5779 2.760650 TCATGGTCTGATGTAGCGACTT 59.239 45.455 0.00 0.00 0.00 3.01
3271 5780 2.941453 TGGTCTGATGTAGCGACTTC 57.059 50.000 5.99 5.99 0.00 3.01
3276 5806 1.863454 CTGATGTAGCGACTTCATGCC 59.137 52.381 14.38 0.00 38.62 4.40
3326 5856 5.550011 TGGTAATGTGGGCATATGTAGGTAT 59.450 40.000 4.29 0.00 34.39 2.73
3365 5895 7.861629 ACAGGATATATGAAAGACAACAAGGA 58.138 34.615 0.00 0.00 0.00 3.36
3445 5980 6.980978 TGGTCTCAGAGCTCTTATTTATTTCG 59.019 38.462 15.27 0.00 0.00 3.46
3452 5987 6.767902 AGAGCTCTTATTTATTTCGATGGCAA 59.232 34.615 11.45 0.00 0.00 4.52
3482 6054 5.126061 ACCATGTTAGAGGATGCATTTTGAC 59.874 40.000 0.00 0.00 0.00 3.18
3550 6122 4.561752 ACATCCCTAGCCTCTACAATTCT 58.438 43.478 0.00 0.00 0.00 2.40
3553 6125 2.703007 CCCTAGCCTCTACAATTCTGCT 59.297 50.000 0.00 0.00 0.00 4.24
3558 6130 4.026744 AGCCTCTACAATTCTGCTAGTGA 58.973 43.478 0.00 0.00 0.00 3.41
3592 6164 6.128849 CCTTTGCATAAACAAGATTTTGACGG 60.129 38.462 2.48 0.00 37.73 4.79
3642 6214 1.801178 GAACTGCAAGCACTACAGGTC 59.199 52.381 3.67 3.67 40.63 3.85
3838 6410 1.229951 ATCCTCAGCCTTGGGACCA 60.230 57.895 0.00 0.00 31.48 4.02
3868 6440 6.625740 GCAGCAACAACATACCAATGATAAGT 60.626 38.462 0.00 0.00 36.54 2.24
3872 6444 8.620416 GCAACAACATACCAATGATAAGTGATA 58.380 33.333 0.00 0.00 36.54 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.511768 CTCGTCTCTTTCCCGTCCC 59.488 63.158 0.00 0.00 0.00 4.46
22 23 2.336478 CGGTCTCACCAGCTCGTCT 61.336 63.158 0.00 0.00 38.47 4.18
23 24 2.179517 CGGTCTCACCAGCTCGTC 59.820 66.667 0.00 0.00 38.47 4.20
24 25 3.374402 CCGGTCTCACCAGCTCGT 61.374 66.667 0.00 0.00 38.47 4.18
27 28 1.979693 GTCTCCGGTCTCACCAGCT 60.980 63.158 0.00 0.00 38.47 4.24
31 32 1.521450 TTCGTGTCTCCGGTCTCACC 61.521 60.000 0.00 0.00 34.05 4.02
82 83 4.272489 TCCAATCTCTGGGCTGTATTTTG 58.728 43.478 0.00 0.00 46.44 2.44
113 114 3.927142 GCCACACTAAACTGCTACTACAG 59.073 47.826 0.00 0.00 43.59 2.74
117 118 3.771577 AAGCCACACTAAACTGCTACT 57.228 42.857 0.00 0.00 0.00 2.57
118 119 4.312443 TGTAAGCCACACTAAACTGCTAC 58.688 43.478 0.00 0.00 30.04 3.58
119 120 4.610605 TGTAAGCCACACTAAACTGCTA 57.389 40.909 0.00 0.00 30.04 3.49
120 121 3.485463 TGTAAGCCACACTAAACTGCT 57.515 42.857 0.00 0.00 30.04 4.24
121 122 3.304458 GGTTGTAAGCCACACTAAACTGC 60.304 47.826 0.00 0.00 36.69 4.40
122 123 3.059188 CGGTTGTAAGCCACACTAAACTG 60.059 47.826 0.00 0.00 36.69 3.16
123 124 3.135994 CGGTTGTAAGCCACACTAAACT 58.864 45.455 0.00 0.00 36.69 2.66
124 125 2.874086 ACGGTTGTAAGCCACACTAAAC 59.126 45.455 0.00 0.00 36.69 2.01
125 126 3.132925 GACGGTTGTAAGCCACACTAAA 58.867 45.455 0.00 0.00 36.69 1.85
126 127 2.366266 AGACGGTTGTAAGCCACACTAA 59.634 45.455 0.00 0.00 36.69 2.24
208 212 1.981256 AAGCCGCCTTCTTTTTCTCA 58.019 45.000 0.00 0.00 0.00 3.27
210 214 2.039879 TCCTAAGCCGCCTTCTTTTTCT 59.960 45.455 0.00 0.00 32.47 2.52
211 215 2.433436 TCCTAAGCCGCCTTCTTTTTC 58.567 47.619 0.00 0.00 32.47 2.29
212 216 2.579410 TCCTAAGCCGCCTTCTTTTT 57.421 45.000 0.00 0.00 32.47 1.94
213 217 2.579410 TTCCTAAGCCGCCTTCTTTT 57.421 45.000 0.00 0.00 32.47 2.27
214 218 2.026262 TCATTCCTAAGCCGCCTTCTTT 60.026 45.455 0.00 0.00 32.47 2.52
215 219 1.559682 TCATTCCTAAGCCGCCTTCTT 59.440 47.619 0.00 0.00 32.47 2.52
271 275 4.348857 GCTGTTGCCTTTGCCTTG 57.651 55.556 0.00 0.00 36.33 3.61
287 291 0.179076 AAAACAGCACAAGCAAGGGC 60.179 50.000 0.00 0.00 45.49 5.19
381 389 2.064014 GAGCACAGTACGGTACAAACC 58.936 52.381 19.62 6.10 42.95 3.27
436 444 0.040425 AGCGTTGAATTGGCACGTTC 60.040 50.000 5.16 5.16 0.00 3.95
529 546 4.933064 CGCCTCCTCCGACGCATC 62.933 72.222 0.00 0.00 0.00 3.91
636 667 2.309764 AATGAAATGACGCGCGCCTC 62.310 55.000 32.58 23.96 0.00 4.70
734 775 5.081315 AGGCTATATATCCGGGAGCTTAT 57.919 43.478 0.00 0.00 33.57 1.73
735 776 4.537945 AGGCTATATATCCGGGAGCTTA 57.462 45.455 0.00 0.00 33.57 3.09
736 777 3.406512 AGGCTATATATCCGGGAGCTT 57.593 47.619 0.00 0.00 33.57 3.74
777 2652 4.332543 AGCGGGGAGGTGGAAGGA 62.333 66.667 0.00 0.00 0.00 3.36
778 2653 4.101448 CAGCGGGGAGGTGGAAGG 62.101 72.222 0.00 0.00 44.14 3.46
842 2718 0.915364 AGCCTGGCCTAGAGGAAAAG 59.085 55.000 16.57 0.00 37.39 2.27
843 2719 2.238898 GTTAGCCTGGCCTAGAGGAAAA 59.761 50.000 16.57 1.93 37.39 2.29
932 2811 1.135046 CTGCTTCACTGTCTGTCACG 58.865 55.000 0.00 0.00 0.00 4.35
967 2846 3.595758 ACAGGTGCTTGTTGCGGC 61.596 61.111 0.00 0.00 46.63 6.53
1005 2888 1.078143 CTTCTTGGCTTCCTCCCCG 60.078 63.158 0.00 0.00 0.00 5.73
1053 2936 4.070552 ACGTCCTTCTCTGCGGCC 62.071 66.667 0.00 0.00 0.00 6.13
1115 2998 2.989639 CCTTGGAGTCATCGGCCA 59.010 61.111 2.24 0.00 0.00 5.36
1116 2999 2.514824 GCCTTGGAGTCATCGGCC 60.515 66.667 0.00 0.00 35.25 6.13
1117 3000 2.514824 GGCCTTGGAGTCATCGGC 60.515 66.667 0.00 7.14 38.39 5.54
1118 3001 2.190578 GGGCCTTGGAGTCATCGG 59.809 66.667 0.84 0.00 0.00 4.18
1119 3002 1.144936 GAGGGCCTTGGAGTCATCG 59.855 63.158 7.89 0.00 0.00 3.84
1120 3003 1.144936 CGAGGGCCTTGGAGTCATC 59.855 63.158 13.46 0.00 0.00 2.92
1193 3191 3.785486 TGAGAATGGTTAGCATGTCTCG 58.215 45.455 20.26 0.00 35.36 4.04
1242 3260 3.878778 ACAGGACAGGCAATAGTTGATC 58.121 45.455 0.00 0.00 0.00 2.92
1250 3268 1.675641 GGCGAACAGGACAGGCAAT 60.676 57.895 0.00 0.00 0.00 3.56
1295 3313 0.249447 TGCGGTGACTTGACTGACTG 60.249 55.000 0.00 0.00 0.00 3.51
1297 3315 1.222115 GGTGCGGTGACTTGACTGAC 61.222 60.000 0.00 0.00 0.00 3.51
1327 3345 1.676006 ACAAGAAACCGGAGCAAAGTG 59.324 47.619 9.46 0.00 0.00 3.16
1362 3380 1.056660 TCTTCTCAGGGCGAGGTTTT 58.943 50.000 0.00 0.00 42.55 2.43
1370 3388 1.003580 TGTGGATGTTCTTCTCAGGGC 59.996 52.381 0.00 0.00 0.00 5.19
1431 3449 1.813786 AGAGACGAGAAGAAGGAACGG 59.186 52.381 0.00 0.00 0.00 4.44
1432 3450 2.857618 CAGAGACGAGAAGAAGGAACG 58.142 52.381 0.00 0.00 0.00 3.95
1474 3492 8.553459 AAGCAGGTTATATTATGTATGCTGTC 57.447 34.615 0.00 0.00 41.61 3.51
1624 3650 2.082231 CAGTCCCAGTGCAGAATGAAG 58.918 52.381 3.52 0.00 39.69 3.02
1680 3706 1.358152 TTACTGAACAGGGAGGGGTG 58.642 55.000 6.76 0.00 0.00 4.61
1693 3719 5.412594 GCCAGTGAAACATTCAGATTACTGA 59.587 40.000 0.00 0.00 45.39 3.41
1694 3720 5.392380 GGCCAGTGAAACATTCAGATTACTG 60.392 44.000 0.00 0.00 41.01 2.74
1695 3721 4.702131 GGCCAGTGAAACATTCAGATTACT 59.298 41.667 0.00 0.00 41.01 2.24
1696 3722 4.458989 TGGCCAGTGAAACATTCAGATTAC 59.541 41.667 0.00 0.00 41.01 1.89
1697 3723 4.661222 TGGCCAGTGAAACATTCAGATTA 58.339 39.130 0.00 0.00 41.01 1.75
1698 3724 3.499338 TGGCCAGTGAAACATTCAGATT 58.501 40.909 0.00 0.00 41.01 2.40
1699 3725 3.087031 CTGGCCAGTGAAACATTCAGAT 58.913 45.455 25.53 0.00 41.01 2.90
1700 3726 2.507484 CTGGCCAGTGAAACATTCAGA 58.493 47.619 25.53 0.00 41.01 3.27
1701 3727 1.068055 GCTGGCCAGTGAAACATTCAG 60.068 52.381 32.81 4.95 41.01 3.02
1702 3728 0.961019 GCTGGCCAGTGAAACATTCA 59.039 50.000 32.81 0.00 41.43 2.57
1703 3729 0.244721 GGCTGGCCAGTGAAACATTC 59.755 55.000 32.81 13.25 41.43 2.67
1704 3730 1.187567 GGGCTGGCCAGTGAAACATT 61.188 55.000 32.81 0.00 41.43 2.71
1705 3731 1.607467 GGGCTGGCCAGTGAAACAT 60.607 57.895 32.81 0.00 41.43 2.71
1706 3732 2.203480 GGGCTGGCCAGTGAAACA 60.203 61.111 32.81 0.00 41.43 2.83
1707 3733 2.116125 AGGGCTGGCCAGTGAAAC 59.884 61.111 32.81 16.23 37.98 2.78
1708 3734 2.115910 CAGGGCTGGCCAGTGAAA 59.884 61.111 32.81 0.00 37.98 2.69
1709 3735 3.970410 CCAGGGCTGGCCAGTGAA 61.970 66.667 32.81 0.00 44.73 3.18
1730 3756 4.369182 CGGTTTTAAGTCTGTGACAGAGT 58.631 43.478 16.76 16.79 44.91 3.24
1731 3757 3.741344 CCGGTTTTAAGTCTGTGACAGAG 59.259 47.826 16.76 0.52 41.46 3.35
1732 3758 3.385433 TCCGGTTTTAAGTCTGTGACAGA 59.615 43.478 11.93 11.93 38.25 3.41
1737 3763 5.163693 ACAACTTTCCGGTTTTAAGTCTGTG 60.164 40.000 0.00 5.89 31.26 3.66
1741 3768 5.065602 AGTGACAACTTTCCGGTTTTAAGTC 59.934 40.000 0.00 5.63 30.14 3.01
1747 3774 2.021457 CCAGTGACAACTTTCCGGTTT 58.979 47.619 0.00 0.00 32.98 3.27
1748 3775 1.210967 TCCAGTGACAACTTTCCGGTT 59.789 47.619 0.00 0.00 32.98 4.44
1751 3778 1.264288 GCTTCCAGTGACAACTTTCCG 59.736 52.381 0.00 0.00 32.98 4.30
1765 3792 2.489329 GCAGTGAATAGCAAAGCTTCCA 59.511 45.455 0.00 0.00 40.44 3.53
1766 3793 2.159324 GGCAGTGAATAGCAAAGCTTCC 60.159 50.000 0.00 0.00 40.44 3.46
1767 3794 2.159324 GGGCAGTGAATAGCAAAGCTTC 60.159 50.000 0.00 0.00 40.44 3.86
1773 3802 0.630673 ATGGGGGCAGTGAATAGCAA 59.369 50.000 0.00 0.00 0.00 3.91
1783 4127 3.443045 GTGACGCAATGGGGGCAG 61.443 66.667 0.00 0.00 46.90 4.85
1792 4136 7.700656 CGATATATATAGGATGTTGTGACGCAA 59.299 37.037 0.00 0.00 34.16 4.85
1813 4157 8.450578 TGATTTGCAACTTATTTCCTCGATAT 57.549 30.769 0.00 0.00 0.00 1.63
1817 4161 8.184192 AGTTATGATTTGCAACTTATTTCCTCG 58.816 33.333 0.00 0.00 0.00 4.63
1818 4162 9.508567 GAGTTATGATTTGCAACTTATTTCCTC 57.491 33.333 0.00 0.00 32.79 3.71
1859 4204 8.366359 AGACAGCAAGGGATTAAATTTATTGT 57.634 30.769 0.00 0.00 0.00 2.71
1862 4207 9.646522 ACATAGACAGCAAGGGATTAAATTTAT 57.353 29.630 0.00 0.00 0.00 1.40
1863 4208 9.120538 GACATAGACAGCAAGGGATTAAATTTA 57.879 33.333 0.00 0.00 0.00 1.40
1866 4211 6.543831 GTGACATAGACAGCAAGGGATTAAAT 59.456 38.462 0.00 0.00 0.00 1.40
1875 4220 3.434641 CCTGTTGTGACATAGACAGCAAG 59.565 47.826 9.75 0.00 38.48 4.01
1918 4263 5.710513 TTGTGTTCTCCCATGAAAGAATG 57.289 39.130 11.40 0.00 34.26 2.67
1949 4294 4.201990 CCTTTTGAGTTGAGCATCTATGGC 60.202 45.833 0.00 0.00 34.92 4.40
1966 4311 5.004448 GGAGGACTTACTTCCTTCCTTTTG 58.996 45.833 0.00 0.00 46.80 2.44
1993 4338 9.865321 ATCATAACTTGAGAAACATGAAATTGG 57.135 29.630 0.00 0.00 37.89 3.16
2125 4522 7.281324 TCAATGGAAGTATTGTAAATGTACCGG 59.719 37.037 0.00 0.00 38.77 5.28
2142 4539 9.132521 GTGTGAAAATATGAAGTTCAATGGAAG 57.867 33.333 10.14 0.00 33.29 3.46
2145 4542 9.480053 AAAGTGTGAAAATATGAAGTTCAATGG 57.520 29.630 10.14 0.00 33.29 3.16
2178 4575 3.937814 TGTTTGCATCCTACTCGAACAT 58.062 40.909 0.00 0.00 31.30 2.71
2179 4576 3.394674 TGTTTGCATCCTACTCGAACA 57.605 42.857 0.00 0.00 33.19 3.18
2180 4577 3.125316 CCTTGTTTGCATCCTACTCGAAC 59.875 47.826 0.00 0.00 0.00 3.95
2181 4578 3.007506 TCCTTGTTTGCATCCTACTCGAA 59.992 43.478 0.00 0.00 0.00 3.71
2183 4580 2.972625 TCCTTGTTTGCATCCTACTCG 58.027 47.619 0.00 0.00 0.00 4.18
2236 4634 1.081892 CCTTGATGTGGCAAGAGTCG 58.918 55.000 5.74 0.00 46.31 4.18
2262 4679 4.324331 GGCTGGGAGTAAACTCTTATGGTT 60.324 45.833 9.84 0.00 42.48 3.67
2263 4680 3.200165 GGCTGGGAGTAAACTCTTATGGT 59.800 47.826 9.84 0.00 42.48 3.55
2264 4681 3.456277 AGGCTGGGAGTAAACTCTTATGG 59.544 47.826 9.84 0.00 42.48 2.74
2265 4682 4.762289 AGGCTGGGAGTAAACTCTTATG 57.238 45.455 9.84 0.77 42.48 1.90
2266 4683 5.221742 GCATAGGCTGGGAGTAAACTCTTAT 60.222 44.000 9.84 0.00 38.89 1.73
2267 4684 4.101119 GCATAGGCTGGGAGTAAACTCTTA 59.899 45.833 9.84 0.00 38.89 2.10
2268 4685 3.118223 GCATAGGCTGGGAGTAAACTCTT 60.118 47.826 9.84 0.00 38.89 2.85
2269 4686 2.436173 GCATAGGCTGGGAGTAAACTCT 59.564 50.000 9.84 0.00 38.89 3.24
2270 4687 2.170607 TGCATAGGCTGGGAGTAAACTC 59.829 50.000 0.00 1.30 41.91 3.01
2271 4688 2.196595 TGCATAGGCTGGGAGTAAACT 58.803 47.619 0.00 0.00 41.91 2.66
2272 4689 2.710096 TGCATAGGCTGGGAGTAAAC 57.290 50.000 0.00 0.00 41.91 2.01
2273 4690 4.412199 ACTTATGCATAGGCTGGGAGTAAA 59.588 41.667 15.25 0.00 41.91 2.01
2274 4691 3.973973 ACTTATGCATAGGCTGGGAGTAA 59.026 43.478 15.25 0.00 41.91 2.24
2275 4692 3.587498 ACTTATGCATAGGCTGGGAGTA 58.413 45.455 15.25 0.00 41.91 2.59
2276 4693 2.412591 ACTTATGCATAGGCTGGGAGT 58.587 47.619 15.25 7.37 41.91 3.85
2277 4694 3.834813 TCTACTTATGCATAGGCTGGGAG 59.165 47.826 15.25 6.75 41.91 4.30
2322 4814 2.298729 TGGCTGAACTTTATTGTTGGCC 59.701 45.455 0.00 0.00 41.45 5.36
2351 4843 9.107177 TCCTTTTGTGTTTAAACTATGTCGTTA 57.893 29.630 18.72 0.00 0.00 3.18
2392 4892 1.897133 TCTTTCGGATCGGTCTTCCAA 59.103 47.619 0.00 0.00 32.45 3.53
2407 4907 4.909880 GCATGGACAACGTTTTAGTCTTTC 59.090 41.667 14.61 2.45 32.98 2.62
2531 5032 4.989168 GTCACCAGAAGACATAAACGAGTT 59.011 41.667 0.00 0.00 36.06 3.01
2619 5120 4.201812 CGATCAGTGGACGCACATAAAATT 60.202 41.667 0.00 0.00 0.00 1.82
2892 5394 1.296392 CAGATCACCTCCAACGCCA 59.704 57.895 0.00 0.00 0.00 5.69
2893 5395 0.321653 AACAGATCACCTCCAACGCC 60.322 55.000 0.00 0.00 0.00 5.68
2932 5435 7.765695 ACAGGACACATTTTCAGAACATAAT 57.234 32.000 0.00 0.00 0.00 1.28
3120 5629 9.662947 GATTCAACATGTATGATATCATGGAGA 57.337 33.333 25.44 7.98 43.68 3.71
3140 5649 9.265901 GAAAAGTAGAGCAGCTATATGATTCAA 57.734 33.333 0.00 0.00 0.00 2.69
3152 5661 7.363431 ACATTACAAAAGAAAAGTAGAGCAGC 58.637 34.615 0.00 0.00 0.00 5.25
3219 5728 7.156000 AGAAGAGATCATATGCTCTGAACATG 58.844 38.462 13.65 0.00 40.43 3.21
3255 5764 2.481969 GGCATGAAGTCGCTACATCAGA 60.482 50.000 0.00 0.00 36.81 3.27
3256 5765 1.863454 GGCATGAAGTCGCTACATCAG 59.137 52.381 0.00 0.00 36.81 2.90
3260 5769 0.608130 ACAGGCATGAAGTCGCTACA 59.392 50.000 4.84 0.00 0.00 2.74
3261 5770 1.726853 AACAGGCATGAAGTCGCTAC 58.273 50.000 4.84 0.00 0.00 3.58
3263 5772 1.160137 GAAACAGGCATGAAGTCGCT 58.840 50.000 4.84 0.00 0.00 4.93
3264 5773 0.169009 GGAAACAGGCATGAAGTCGC 59.831 55.000 4.84 0.00 0.00 5.19
3265 5774 1.734465 GAGGAAACAGGCATGAAGTCG 59.266 52.381 4.84 0.00 0.00 4.18
3266 5775 3.064900 AGAGGAAACAGGCATGAAGTC 57.935 47.619 4.84 0.00 0.00 3.01
3267 5776 3.416156 GAAGAGGAAACAGGCATGAAGT 58.584 45.455 4.84 0.00 0.00 3.01
3268 5777 2.751806 GGAAGAGGAAACAGGCATGAAG 59.248 50.000 4.84 0.00 0.00 3.02
3270 5779 1.704628 TGGAAGAGGAAACAGGCATGA 59.295 47.619 4.84 0.00 0.00 3.07
3271 5780 2.089980 CTGGAAGAGGAAACAGGCATG 58.910 52.381 0.00 0.00 34.07 4.06
3276 5806 2.874701 CACACACTGGAAGAGGAAACAG 59.125 50.000 0.00 0.00 37.43 3.16
3326 5856 9.782900 TCATATATCCTGTATTCCTGTATTCCA 57.217 33.333 0.00 0.00 0.00 3.53
3351 5881 4.448060 CGGTAAGTCTCCTTGTTGTCTTTC 59.552 45.833 0.00 0.00 31.89 2.62
3365 5895 6.527423 TGTTAGGTTCAAATTCGGTAAGTCT 58.473 36.000 0.00 0.00 0.00 3.24
3445 5980 5.964758 TCTAACATGGTGAAAATTGCCATC 58.035 37.500 0.00 0.00 40.68 3.51
3452 5987 5.263599 TGCATCCTCTAACATGGTGAAAAT 58.736 37.500 0.00 0.00 0.00 1.82
3592 6164 7.649306 ACTCATGTATGTTTGTGCTTTTCTTTC 59.351 33.333 0.00 0.00 0.00 2.62
3642 6214 4.678509 TTTTGGCTTCTGTATGTTAGCG 57.321 40.909 0.00 0.00 34.50 4.26
3838 6410 1.270550 GGTATGTTGTTGCTGCAGCTT 59.729 47.619 36.61 15.95 42.66 3.74


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

AutoCloner maintained by Alex Coulton.