Multiple sequence alignment - TraesCS6A01G333700

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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 TraesCS6A01G333700 chr6A 100.000 2734 0 0 1 2734 564725842 564723109 0.000000e+00 5049.0
1 TraesCS6A01G333700 chr6B 85.192 2080 111 95 588 2581 635176899 635174931 0.000000e+00 1953.0
2 TraesCS6A01G333700 chr6B 85.608 403 33 15 1 398 635177588 635177206 1.530000e-107 399.0
3 TraesCS6A01G333700 chr6B 88.298 94 6 4 446 539 635177076 635176988 1.040000e-19 108.0
4 TraesCS6A01G333700 chr6B 100.000 44 0 0 2689 2732 635174883 635174840 6.270000e-12 82.4
5 TraesCS6A01G333700 chr6D 91.545 887 26 24 620 1493 421888700 421887850 0.000000e+00 1177.0
6 TraesCS6A01G333700 chr6D 87.834 1011 51 28 1601 2581 421887743 421886775 0.000000e+00 1120.0
7 TraesCS6A01G333700 chr6D 87.059 595 44 17 1 592 421889258 421888694 2.300000e-180 641.0
8 TraesCS6A01G333700 chr6D 93.289 149 9 1 2584 2732 421886744 421886597 4.580000e-53 219.0
9 TraesCS6A01G333700 chr5D 90.357 560 34 11 912 1467 319327027 319327570 0.000000e+00 717.0
10 TraesCS6A01G333700 chr5D 96.341 82 3 0 1639 1720 319327565 319327646 4.750000e-28 135.0
11 TraesCS6A01G333700 chr4B 94.562 331 17 1 1038 1368 629748574 629748903 6.750000e-141 510.0


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 TraesCS6A01G333700 chr6A 564723109 564725842 2733 True 5049.00 5049 100.00000 1 2734 1 chr6A.!!$R1 2733
1 TraesCS6A01G333700 chr6B 635174840 635177588 2748 True 635.60 1953 89.77450 1 2732 4 chr6B.!!$R1 2731
2 TraesCS6A01G333700 chr6D 421886597 421889258 2661 True 789.25 1177 89.93175 1 2732 4 chr6D.!!$R1 2731
3 TraesCS6A01G333700 chr5D 319327027 319327646 619 False 426.00 717 93.34900 912 1720 2 chr5D.!!$F1 808

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
750 888 0.036671 GAGGAAATCCCACCGTTCGT 60.037 55.0 0.0 0.0 37.41 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1797 2016 0.106708 TTCTTCTGCGTCTGCTGGTT 59.893 50.0 0.0 0.0 43.34 3.67 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 4.591998 GAGTTGGATCTCGCTCTTTTTC 57.408 45.455 0.00 0.00 0.00 2.29
28 29 3.339141 AGTTGGATCTCGCTCTTTTTCC 58.661 45.455 0.00 0.00 0.00 3.13
30 31 2.977914 TGGATCTCGCTCTTTTTCCTG 58.022 47.619 0.00 0.00 0.00 3.86
31 32 1.668237 GGATCTCGCTCTTTTTCCTGC 59.332 52.381 0.00 0.00 0.00 4.85
44 46 0.175760 TTCCTGCCGGAAGATTCTCG 59.824 55.000 12.53 0.00 44.28 4.04
54 56 2.474359 GGAAGATTCTCGATGCATGTCG 59.526 50.000 2.46 2.95 42.74 4.35
98 101 3.201290 AGATTCTCCATGCATGTCGAAC 58.799 45.455 24.58 17.52 0.00 3.95
99 102 1.358877 TTCTCCATGCATGTCGAACG 58.641 50.000 24.58 8.85 0.00 3.95
100 103 0.530288 TCTCCATGCATGTCGAACGA 59.470 50.000 24.58 12.58 0.00 3.85
102 105 1.524355 CTCCATGCATGTCGAACGATC 59.476 52.381 24.58 0.00 0.00 3.69
103 106 1.134848 TCCATGCATGTCGAACGATCA 60.135 47.619 24.58 1.64 0.00 2.92
107 110 0.721154 GCATGTCGAACGATCAGCAA 59.279 50.000 0.00 0.00 0.00 3.91
110 113 3.728864 GCATGTCGAACGATCAGCAAAAT 60.729 43.478 0.00 0.00 0.00 1.82
111 114 4.406069 CATGTCGAACGATCAGCAAAATT 58.594 39.130 0.00 0.00 0.00 1.82
127 130 5.153513 GCAAAATTGCGACACTCTTATGAA 58.846 37.500 1.90 0.00 45.11 2.57
196 201 0.880278 CCACCGGCCTGACATAATCG 60.880 60.000 0.00 0.00 0.00 3.34
268 273 1.153489 CCCTCTCCACTGTGATGCG 60.153 63.158 9.86 0.00 0.00 4.73
317 327 0.249280 ACGTTCGTGTGATGCACTCA 60.249 50.000 0.00 0.00 45.57 3.41
329 339 1.882912 TGCACTCACCAACTAAGCTG 58.117 50.000 0.00 0.00 0.00 4.24
331 341 2.038952 TGCACTCACCAACTAAGCTGAT 59.961 45.455 0.00 0.00 0.00 2.90
346 356 3.809905 AGCTGATTTATTCCCGAGGAAC 58.190 45.455 7.42 0.00 45.07 3.62
354 364 0.978907 TTCCCGAGGAACTACCAACC 59.021 55.000 1.68 0.00 41.55 3.77
359 369 3.007635 CCGAGGAACTACCAACCAATTC 58.992 50.000 0.00 0.00 41.55 2.17
361 371 2.418976 GAGGAACTACCAACCAATTCGC 59.581 50.000 0.00 0.00 41.55 4.70
370 380 1.312371 AACCAATTCGCCCATCCACG 61.312 55.000 0.00 0.00 0.00 4.94
400 428 1.966493 CTCCCACGCATTTTCGACGG 61.966 60.000 0.00 0.00 0.00 4.79
401 429 2.478746 CCACGCATTTTCGACGGG 59.521 61.111 0.00 0.00 0.00 5.28
418 446 1.743394 CGGGATTTTAGCCAACTGACC 59.257 52.381 0.00 0.00 0.00 4.02
479 571 3.257561 CGCACGCGAGGATTCAGG 61.258 66.667 15.93 0.00 42.83 3.86
481 573 2.202932 CACGCGAGGATTCAGGGG 60.203 66.667 15.93 0.00 0.00 4.79
503 595 0.880278 ATCCGAATCCAACCGCGATG 60.880 55.000 8.23 6.24 0.00 3.84
504 596 1.520564 CCGAATCCAACCGCGATGA 60.521 57.895 8.23 0.00 0.00 2.92
505 597 0.880278 CCGAATCCAACCGCGATGAT 60.880 55.000 8.23 0.16 0.00 2.45
506 598 1.604438 CCGAATCCAACCGCGATGATA 60.604 52.381 8.23 0.00 0.00 2.15
539 631 0.650512 CAAATGCCGCACCGTAGTAG 59.349 55.000 0.00 0.00 0.00 2.57
540 632 0.248289 AAATGCCGCACCGTAGTAGT 59.752 50.000 0.00 0.00 0.00 2.73
543 635 1.105457 TGCCGCACCGTAGTAGTAAT 58.895 50.000 0.00 0.00 0.00 1.89
544 636 2.296792 TGCCGCACCGTAGTAGTAATA 58.703 47.619 0.00 0.00 0.00 0.98
545 637 2.033299 TGCCGCACCGTAGTAGTAATAC 59.967 50.000 0.00 0.00 0.00 1.89
546 638 2.908634 CCGCACCGTAGTAGTAATACG 58.091 52.381 20.25 20.25 44.29 3.06
613 751 3.315765 TTGTACTGCAAGGGGAACG 57.684 52.632 0.00 0.00 39.30 3.95
618 756 1.750399 CTGCAAGGGGAACGATGGG 60.750 63.158 0.00 0.00 0.00 4.00
625 763 1.711942 AGGGGAACGATGGGGTTAAAA 59.288 47.619 0.00 0.00 0.00 1.52
626 764 2.097036 GGGGAACGATGGGGTTAAAAG 58.903 52.381 0.00 0.00 0.00 2.27
627 765 2.555892 GGGGAACGATGGGGTTAAAAGT 60.556 50.000 0.00 0.00 0.00 2.66
628 766 3.159472 GGGAACGATGGGGTTAAAAGTT 58.841 45.455 0.00 0.00 0.00 2.66
629 767 3.057104 GGGAACGATGGGGTTAAAAGTTG 60.057 47.826 0.00 0.00 0.00 3.16
630 768 3.057104 GGAACGATGGGGTTAAAAGTTGG 60.057 47.826 0.00 0.00 0.00 3.77
631 769 2.521126 ACGATGGGGTTAAAAGTTGGG 58.479 47.619 0.00 0.00 0.00 4.12
713 851 4.321452 CCCGAATCAATGCCCAATAATGAG 60.321 45.833 0.00 0.00 0.00 2.90
750 888 0.036671 GAGGAAATCCCACCGTTCGT 60.037 55.000 0.00 0.00 37.41 3.85
754 892 0.952010 AAATCCCACCGTTCGTTCCG 60.952 55.000 0.00 0.00 0.00 4.30
755 893 2.103339 AATCCCACCGTTCGTTCCGT 62.103 55.000 0.00 0.00 0.00 4.69
756 894 2.496828 ATCCCACCGTTCGTTCCGTC 62.497 60.000 0.00 0.00 0.00 4.79
757 895 2.735857 CCACCGTTCGTTCCGTCC 60.736 66.667 0.00 0.00 0.00 4.79
758 896 3.101428 CACCGTTCGTTCCGTCCG 61.101 66.667 0.00 0.00 0.00 4.79
762 900 3.110178 GTTCGTTCCGTCCGCCAG 61.110 66.667 0.00 0.00 0.00 4.85
763 901 4.367023 TTCGTTCCGTCCGCCAGG 62.367 66.667 0.00 0.00 39.46 4.45
801 948 4.957296 GGGGTATATATCAGCCCGTTATG 58.043 47.826 8.37 0.00 43.48 1.90
1482 1656 0.744414 CCCCAGGTACGCACATTCAG 60.744 60.000 0.00 0.00 0.00 3.02
1483 1657 0.036388 CCCAGGTACGCACATTCAGT 60.036 55.000 0.00 0.00 0.00 3.41
1484 1658 1.610624 CCCAGGTACGCACATTCAGTT 60.611 52.381 0.00 0.00 0.00 3.16
1485 1659 1.732259 CCAGGTACGCACATTCAGTTC 59.268 52.381 0.00 0.00 0.00 3.01
1486 1660 1.390123 CAGGTACGCACATTCAGTTCG 59.610 52.381 0.00 0.00 42.69 3.95
1487 1661 0.719465 GGTACGCACATTCAGTTCGG 59.281 55.000 0.00 0.00 41.28 4.30
1488 1662 1.425412 GTACGCACATTCAGTTCGGT 58.575 50.000 0.00 0.00 41.28 4.69
1489 1663 1.796459 GTACGCACATTCAGTTCGGTT 59.204 47.619 0.00 0.00 41.28 4.44
1490 1664 1.305201 ACGCACATTCAGTTCGGTTT 58.695 45.000 0.00 0.00 41.28 3.27
1491 1665 1.263217 ACGCACATTCAGTTCGGTTTC 59.737 47.619 0.00 0.00 41.28 2.78
1492 1666 1.262950 CGCACATTCAGTTCGGTTTCA 59.737 47.619 0.00 0.00 33.12 2.69
1493 1667 2.662791 CGCACATTCAGTTCGGTTTCAG 60.663 50.000 0.00 0.00 33.12 3.02
1494 1668 2.548057 GCACATTCAGTTCGGTTTCAGA 59.452 45.455 0.00 0.00 0.00 3.27
1495 1669 3.189287 GCACATTCAGTTCGGTTTCAGAT 59.811 43.478 0.00 0.00 0.00 2.90
1496 1670 4.320494 GCACATTCAGTTCGGTTTCAGATT 60.320 41.667 0.00 0.00 0.00 2.40
1497 1671 5.762045 CACATTCAGTTCGGTTTCAGATTT 58.238 37.500 0.00 0.00 0.00 2.17
1498 1672 5.853282 CACATTCAGTTCGGTTTCAGATTTC 59.147 40.000 0.00 0.00 0.00 2.17
1499 1673 5.530915 ACATTCAGTTCGGTTTCAGATTTCA 59.469 36.000 0.00 0.00 0.00 2.69
1500 1674 5.673337 TTCAGTTCGGTTTCAGATTTCAG 57.327 39.130 0.00 0.00 0.00 3.02
1501 1675 3.498397 TCAGTTCGGTTTCAGATTTCAGC 59.502 43.478 0.00 0.00 0.00 4.26
1502 1676 3.250762 CAGTTCGGTTTCAGATTTCAGCA 59.749 43.478 0.00 0.00 0.00 4.41
1503 1677 3.499918 AGTTCGGTTTCAGATTTCAGCAG 59.500 43.478 0.00 0.00 0.00 4.24
1504 1678 3.401033 TCGGTTTCAGATTTCAGCAGA 57.599 42.857 0.00 0.00 0.00 4.26
1505 1679 3.329386 TCGGTTTCAGATTTCAGCAGAG 58.671 45.455 0.00 0.00 0.00 3.35
1506 1680 3.070018 CGGTTTCAGATTTCAGCAGAGT 58.930 45.455 0.00 0.00 0.00 3.24
1507 1681 3.499918 CGGTTTCAGATTTCAGCAGAGTT 59.500 43.478 0.00 0.00 0.00 3.01
1508 1682 4.377841 CGGTTTCAGATTTCAGCAGAGTTC 60.378 45.833 0.00 0.00 0.00 3.01
1509 1683 4.759183 GGTTTCAGATTTCAGCAGAGTTCT 59.241 41.667 0.00 0.00 0.00 3.01
1510 1684 5.334724 GGTTTCAGATTTCAGCAGAGTTCTG 60.335 44.000 11.72 11.72 46.40 3.02
1518 1692 2.828933 GCAGAGTTCTGGTTCGGTC 58.171 57.895 10.88 0.00 43.94 4.79
1541 1715 8.149647 GGTCTCATCTGATCTGTTGATTAGATT 58.850 37.037 12.20 0.00 46.98 2.40
1547 1721 8.451908 TCTGATCTGTTGATTAGATTAGACGA 57.548 34.615 5.65 0.00 40.34 4.20
1548 1722 8.563732 TCTGATCTGTTGATTAGATTAGACGAG 58.436 37.037 5.65 0.00 40.34 4.18
1549 1723 7.142021 TGATCTGTTGATTAGATTAGACGAGC 58.858 38.462 0.00 0.00 35.14 5.03
1550 1724 5.511571 TCTGTTGATTAGATTAGACGAGCG 58.488 41.667 0.00 0.00 0.00 5.03
1551 1725 4.607955 TGTTGATTAGATTAGACGAGCGG 58.392 43.478 0.00 0.00 0.00 5.52
1552 1726 4.097437 TGTTGATTAGATTAGACGAGCGGT 59.903 41.667 0.00 0.00 0.00 5.68
1553 1727 4.485024 TGATTAGATTAGACGAGCGGTC 57.515 45.455 4.06 4.06 46.45 4.79
1577 1768 6.263168 TCTCTGAATTTCTCTTCAACCAAACC 59.737 38.462 0.00 0.00 34.86 3.27
1595 1786 6.096695 CCAAACCCGAATAAATTTCGATTGT 58.903 36.000 9.14 1.59 43.97 2.71
1599 1805 7.852971 ACCCGAATAAATTTCGATTGTTAGA 57.147 32.000 9.14 0.00 43.97 2.10
1609 1815 4.118093 TCGATTGTTAGAGCGATTGGAA 57.882 40.909 0.00 0.00 0.00 3.53
1610 1816 3.863424 TCGATTGTTAGAGCGATTGGAAC 59.137 43.478 0.00 0.00 0.00 3.62
1797 2016 2.028112 CGAATTCAGAGGAGGGACAACA 60.028 50.000 6.22 0.00 0.00 3.33
1799 2018 2.930826 TTCAGAGGAGGGACAACAAC 57.069 50.000 0.00 0.00 0.00 3.32
1801 2020 0.764890 CAGAGGAGGGACAACAACCA 59.235 55.000 0.00 0.00 0.00 3.67
1802 2021 1.059913 AGAGGAGGGACAACAACCAG 58.940 55.000 0.00 0.00 0.00 4.00
1803 2022 0.606673 GAGGAGGGACAACAACCAGC 60.607 60.000 0.00 0.00 0.00 4.85
1804 2023 1.150536 GGAGGGACAACAACCAGCA 59.849 57.895 0.00 0.00 0.00 4.41
1829 2048 3.065925 CGCAGAAGAAAAGAATCATCCCC 59.934 47.826 0.00 0.00 0.00 4.81
1862 2081 2.029380 TCGAGATCGAAGAAGCAACCAA 60.029 45.455 1.76 0.00 46.30 3.67
1863 2082 2.932614 CGAGATCGAAGAAGCAACCAAT 59.067 45.455 0.00 0.00 43.58 3.16
1864 2083 3.242220 CGAGATCGAAGAAGCAACCAATG 60.242 47.826 0.00 0.00 43.58 2.82
1913 2132 1.035932 ATCTACCAGGTGTCGTCGGG 61.036 60.000 0.76 0.00 0.00 5.14
1986 2205 4.657236 GCTATAGCTTTAGCCTGCTGCTG 61.657 52.174 21.60 0.00 44.18 4.41
1999 2218 1.733912 TGCTGCTGCTAATCGACTTTG 59.266 47.619 17.00 0.00 40.48 2.77
2031 2250 5.849081 TGTTTATCGTTGAGCAATTCGAAAC 59.151 36.000 0.00 0.00 35.99 2.78
2049 2269 4.555313 CGAAACTATACTCCGTAATCCGCA 60.555 45.833 0.00 0.00 34.38 5.69
2050 2270 3.911661 ACTATACTCCGTAATCCGCAC 57.088 47.619 0.00 0.00 34.38 5.34
2052 2272 3.501445 ACTATACTCCGTAATCCGCACTC 59.499 47.826 0.00 0.00 34.38 3.51
2055 2275 2.108362 CCGTAATCCGCACTCCCC 59.892 66.667 0.00 0.00 34.38 4.81
2069 2289 4.072839 GCACTCCCCCTGTTATAATTAGC 58.927 47.826 0.00 0.00 0.00 3.09
2074 2294 4.844655 TCCCCCTGTTATAATTAGCTCCTC 59.155 45.833 0.00 0.00 0.00 3.71
2075 2295 4.019231 CCCCCTGTTATAATTAGCTCCTCC 60.019 50.000 0.00 0.00 0.00 4.30
2076 2296 4.846940 CCCCTGTTATAATTAGCTCCTCCT 59.153 45.833 0.00 0.00 0.00 3.69
2077 2297 5.046231 CCCCTGTTATAATTAGCTCCTCCTC 60.046 48.000 0.00 0.00 0.00 3.71
2078 2298 5.046231 CCCTGTTATAATTAGCTCCTCCTCC 60.046 48.000 0.00 0.00 0.00 4.30
2089 2309 4.548513 CTCCTCCCCTCCCCTCCG 62.549 77.778 0.00 0.00 0.00 4.63
2107 2327 3.267860 CTGATCTTCAGCCGCGGC 61.268 66.667 42.34 42.34 37.72 6.53
2149 2372 0.831307 ACCTCCCCTGATTTCGTAGC 59.169 55.000 0.00 0.00 0.00 3.58
2151 2374 1.202580 CCTCCCCTGATTTCGTAGCAG 60.203 57.143 0.00 0.00 0.00 4.24
2152 2375 1.482593 CTCCCCTGATTTCGTAGCAGT 59.517 52.381 5.21 0.00 0.00 4.40
2153 2376 2.693591 CTCCCCTGATTTCGTAGCAGTA 59.306 50.000 5.21 0.00 0.00 2.74
2154 2377 3.101437 TCCCCTGATTTCGTAGCAGTAA 58.899 45.455 5.21 0.00 0.00 2.24
2155 2378 3.709653 TCCCCTGATTTCGTAGCAGTAAT 59.290 43.478 5.21 0.00 0.00 1.89
2156 2379 4.897076 TCCCCTGATTTCGTAGCAGTAATA 59.103 41.667 5.21 0.00 0.00 0.98
2157 2380 5.364446 TCCCCTGATTTCGTAGCAGTAATAA 59.636 40.000 5.21 0.00 0.00 1.40
2158 2381 6.042781 TCCCCTGATTTCGTAGCAGTAATAAT 59.957 38.462 5.21 0.00 0.00 1.28
2159 2382 6.710744 CCCCTGATTTCGTAGCAGTAATAATT 59.289 38.462 5.21 0.00 0.00 1.40
2173 2396 9.601217 AGCAGTAATAATTTACTTTCGACATCT 57.399 29.630 0.00 0.00 44.48 2.90
2193 2417 1.860326 TCTGTACATTGCGCATCATCG 59.140 47.619 12.75 0.10 0.00 3.84
2240 2464 7.870665 TTAGATTAATTTCAATTCGCGTTCG 57.129 32.000 5.77 0.00 0.00 3.95
2263 2491 7.247728 TCGTGGAATTGATAATAAACTGTTGC 58.752 34.615 0.00 0.00 0.00 4.17
2291 2519 1.000938 CAGTTGCTGTTGCTTCTTCCC 60.001 52.381 0.00 0.00 40.48 3.97
2305 2533 5.012975 TGCTTCTTCCCCTTGCAAAATAATT 59.987 36.000 0.00 0.00 0.00 1.40
2306 2534 5.939883 GCTTCTTCCCCTTGCAAAATAATTT 59.060 36.000 0.00 0.00 0.00 1.82
2319 2547 4.654091 AAATAATTTGACCAGCGATGGG 57.346 40.909 25.79 6.10 0.00 4.00
2353 2581 1.851304 TTGCTCACCCAATCAATCCC 58.149 50.000 0.00 0.00 0.00 3.85
2426 2654 0.942962 CGATCCTTTGCCTCATCTGC 59.057 55.000 0.00 0.00 0.00 4.26
2427 2655 1.744798 CGATCCTTTGCCTCATCTGCA 60.745 52.381 0.00 0.00 36.84 4.41
2428 2656 2.372264 GATCCTTTGCCTCATCTGCAA 58.628 47.619 0.00 0.00 46.30 4.08
2556 2824 3.311596 TGACGACACGGATAGATACTGTG 59.688 47.826 0.00 0.00 46.29 3.66
2575 2843 1.941999 GCCACCATCCTTTCTGCAGC 61.942 60.000 9.47 0.00 0.00 5.25
2581 2849 0.392193 ATCCTTTCTGCAGCGGTGAG 60.392 55.000 20.69 12.78 0.00 3.51
2602 2898 3.829026 AGGTGCAGAGAAAATTCCCTTTC 59.171 43.478 0.00 0.00 35.85 2.62
2613 2909 1.722011 TTCCCTTTCTCGCGAATGAC 58.278 50.000 11.33 0.00 0.00 3.06
2666 2962 0.104304 CGTATGGGAACGGGAGGAAG 59.896 60.000 0.00 0.00 39.19 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 4.397348 TCCGGCAGGAAAAAGAGC 57.603 55.556 1.89 0.00 45.12 4.09
27 28 0.390860 ATCGAGAATCTTCCGGCAGG 59.609 55.000 0.00 0.00 39.46 4.85
28 29 1.495878 CATCGAGAATCTTCCGGCAG 58.504 55.000 0.00 0.00 0.00 4.85
30 31 0.530650 TGCATCGAGAATCTTCCGGC 60.531 55.000 0.00 0.00 0.00 6.13
31 32 1.797046 CATGCATCGAGAATCTTCCGG 59.203 52.381 0.00 0.00 0.00 5.14
44 46 0.598419 TGCGATCCTCGACATGCATC 60.598 55.000 0.00 0.00 43.74 3.91
54 56 0.179097 GGACAACTCCTGCGATCCTC 60.179 60.000 0.00 0.00 33.07 3.71
70 73 1.134401 TGCATGGAGAATCTTCCGGAC 60.134 52.381 1.83 0.00 40.27 4.79
103 106 8.908436 TCTTCATAAGAGTGTCGCAATTTTGCT 61.908 37.037 12.97 0.00 41.26 3.91
107 110 6.603095 GTTCTTCATAAGAGTGTCGCAATTT 58.397 36.000 0.00 0.00 39.03 1.82
110 113 3.673338 CGTTCTTCATAAGAGTGTCGCAA 59.327 43.478 0.00 0.00 39.03 4.85
111 114 3.242518 CGTTCTTCATAAGAGTGTCGCA 58.757 45.455 0.00 0.00 39.03 5.10
116 119 4.500837 CGATCCACGTTCTTCATAAGAGTG 59.499 45.833 0.00 0.00 39.03 3.51
123 126 2.483714 CCCATCGATCCACGTTCTTCAT 60.484 50.000 0.00 0.00 43.13 2.57
127 130 1.144057 GCCCATCGATCCACGTTCT 59.856 57.895 0.00 0.00 43.13 3.01
196 201 3.475774 CACCTAACCGACGTGCGC 61.476 66.667 0.00 0.00 39.11 6.09
317 327 4.881850 CGGGAATAAATCAGCTTAGTTGGT 59.118 41.667 0.00 0.00 0.00 3.67
322 332 5.215252 TCCTCGGGAATAAATCAGCTTAG 57.785 43.478 0.00 0.00 0.00 2.18
323 333 5.130477 AGTTCCTCGGGAATAAATCAGCTTA 59.870 40.000 8.36 0.00 44.04 3.09
324 334 4.080299 AGTTCCTCGGGAATAAATCAGCTT 60.080 41.667 8.36 0.00 44.04 3.74
325 335 3.456277 AGTTCCTCGGGAATAAATCAGCT 59.544 43.478 8.36 0.00 44.04 4.24
326 336 3.809905 AGTTCCTCGGGAATAAATCAGC 58.190 45.455 8.36 0.00 44.04 4.26
329 339 5.286267 TGGTAGTTCCTCGGGAATAAATC 57.714 43.478 8.36 0.46 44.04 2.17
331 341 4.323715 GGTTGGTAGTTCCTCGGGAATAAA 60.324 45.833 8.36 0.00 44.04 1.40
346 356 1.676006 GATGGGCGAATTGGTTGGTAG 59.324 52.381 0.00 0.00 0.00 3.18
354 364 1.024046 TGTCGTGGATGGGCGAATTG 61.024 55.000 0.00 0.00 38.91 2.32
359 369 2.822418 TTACGTGTCGTGGATGGGCG 62.822 60.000 0.00 0.00 41.39 6.13
361 371 1.931172 GAATTACGTGTCGTGGATGGG 59.069 52.381 0.00 0.00 41.39 4.00
370 380 0.997196 GCGTGGGAGAATTACGTGTC 59.003 55.000 0.00 0.00 39.79 3.67
400 428 1.743394 CCGGTCAGTTGGCTAAAATCC 59.257 52.381 0.00 0.00 0.00 3.01
418 446 0.653323 CGTGTCTTGTTTTCACGCCG 60.653 55.000 4.16 0.00 45.66 6.46
483 575 0.600255 ATCGCGGTTGGATTCGGATC 60.600 55.000 6.13 0.00 0.00 3.36
484 576 0.880278 CATCGCGGTTGGATTCGGAT 60.880 55.000 6.13 0.00 0.00 4.18
503 595 4.418392 CATTTGAGCTGGCTGTTTGTATC 58.582 43.478 0.00 0.00 0.00 2.24
504 596 3.367703 GCATTTGAGCTGGCTGTTTGTAT 60.368 43.478 0.00 0.00 0.00 2.29
505 597 2.030007 GCATTTGAGCTGGCTGTTTGTA 60.030 45.455 0.00 0.00 0.00 2.41
506 598 1.269936 GCATTTGAGCTGGCTGTTTGT 60.270 47.619 0.00 0.00 0.00 2.83
569 707 7.116805 AGTGTTTTGAACTTTTGCTCAAAGAAG 59.883 33.333 13.87 0.00 44.40 2.85
570 708 6.928492 AGTGTTTTGAACTTTTGCTCAAAGAA 59.072 30.769 13.87 0.00 44.40 2.52
571 709 6.454795 AGTGTTTTGAACTTTTGCTCAAAGA 58.545 32.000 13.87 0.00 44.40 2.52
609 747 3.057104 CCCAACTTTTAACCCCATCGTTC 60.057 47.826 0.00 0.00 0.00 3.95
613 751 2.897350 ACCCCAACTTTTAACCCCATC 58.103 47.619 0.00 0.00 0.00 3.51
618 756 3.762407 ATGCAACCCCAACTTTTAACC 57.238 42.857 0.00 0.00 0.00 2.85
625 763 1.677633 GCCGTATGCAACCCCAACT 60.678 57.895 0.00 0.00 40.77 3.16
626 764 2.706834 GGCCGTATGCAACCCCAAC 61.707 63.158 0.00 0.00 43.89 3.77
627 765 2.361865 GGCCGTATGCAACCCCAA 60.362 61.111 0.00 0.00 43.89 4.12
628 766 4.787286 CGGCCGTATGCAACCCCA 62.787 66.667 19.50 0.00 43.89 4.96
629 767 4.789123 ACGGCCGTATGCAACCCC 62.789 66.667 33.34 0.00 43.89 4.95
630 768 2.748647 AACGGCCGTATGCAACCC 60.749 61.111 34.44 0.00 43.89 4.11
631 769 2.757056 GGAACGGCCGTATGCAACC 61.757 63.158 34.44 22.17 43.89 3.77
733 871 0.800631 GAACGAACGGTGGGATTTCC 59.199 55.000 0.00 0.00 0.00 3.13
765 903 4.838152 CCCCTCGTGGATGCGTGG 62.838 72.222 4.76 0.00 42.90 4.94
766 904 2.028125 ATACCCCTCGTGGATGCGTG 62.028 60.000 4.76 0.00 35.39 5.34
767 905 0.468585 TATACCCCTCGTGGATGCGT 60.469 55.000 4.76 0.00 35.39 5.24
768 906 0.895530 ATATACCCCTCGTGGATGCG 59.104 55.000 4.76 0.00 35.39 4.73
780 921 4.377897 GCATAACGGGCTGATATATACCC 58.622 47.826 0.00 7.58 39.12 3.69
781 922 4.049186 CGCATAACGGGCTGATATATACC 58.951 47.826 0.00 0.00 38.44 2.73
819 967 1.739338 CTTAGCGGATCGGGTGCTCT 61.739 60.000 14.54 0.00 40.06 4.09
820 968 1.300233 CTTAGCGGATCGGGTGCTC 60.300 63.158 14.54 0.00 40.06 4.26
972 1136 2.904866 CTCCTCCTCCTCCGCGAG 60.905 72.222 8.23 2.69 0.00 5.03
973 1137 4.507916 CCTCCTCCTCCTCCGCGA 62.508 72.222 8.23 0.00 0.00 5.87
1482 1656 3.498397 TCTGCTGAAATCTGAAACCGAAC 59.502 43.478 0.00 0.00 0.00 3.95
1483 1657 3.738982 TCTGCTGAAATCTGAAACCGAA 58.261 40.909 0.00 0.00 0.00 4.30
1484 1658 3.244215 ACTCTGCTGAAATCTGAAACCGA 60.244 43.478 0.00 0.00 0.00 4.69
1485 1659 3.070018 ACTCTGCTGAAATCTGAAACCG 58.930 45.455 0.00 0.00 0.00 4.44
1486 1660 4.759183 AGAACTCTGCTGAAATCTGAAACC 59.241 41.667 6.92 0.00 0.00 3.27
1487 1661 5.334724 CCAGAACTCTGCTGAAATCTGAAAC 60.335 44.000 24.73 2.73 42.47 2.78
1488 1662 4.758674 CCAGAACTCTGCTGAAATCTGAAA 59.241 41.667 24.73 0.00 42.47 2.69
1489 1663 4.202398 ACCAGAACTCTGCTGAAATCTGAA 60.202 41.667 24.73 0.00 42.47 3.02
1490 1664 3.326006 ACCAGAACTCTGCTGAAATCTGA 59.674 43.478 24.73 0.00 42.47 3.27
1491 1665 3.672808 ACCAGAACTCTGCTGAAATCTG 58.327 45.455 19.87 19.87 42.47 2.90
1492 1666 4.322567 GAACCAGAACTCTGCTGAAATCT 58.677 43.478 0.89 0.00 42.47 2.40
1493 1667 3.124297 CGAACCAGAACTCTGCTGAAATC 59.876 47.826 0.89 0.00 42.47 2.17
1494 1668 3.070018 CGAACCAGAACTCTGCTGAAAT 58.930 45.455 0.89 0.00 42.47 2.17
1495 1669 2.483876 CGAACCAGAACTCTGCTGAAA 58.516 47.619 0.89 0.00 42.47 2.69
1496 1670 1.270305 CCGAACCAGAACTCTGCTGAA 60.270 52.381 0.89 0.00 42.47 3.02
1497 1671 0.318441 CCGAACCAGAACTCTGCTGA 59.682 55.000 0.89 0.00 42.47 4.26
1498 1672 0.034059 ACCGAACCAGAACTCTGCTG 59.966 55.000 0.89 0.00 42.47 4.41
1499 1673 0.318762 GACCGAACCAGAACTCTGCT 59.681 55.000 0.89 0.00 42.47 4.24
1500 1674 0.318762 AGACCGAACCAGAACTCTGC 59.681 55.000 0.89 0.00 42.47 4.26
1501 1675 1.613925 TGAGACCGAACCAGAACTCTG 59.386 52.381 0.00 0.00 43.40 3.35
1502 1676 1.996798 TGAGACCGAACCAGAACTCT 58.003 50.000 0.00 0.00 0.00 3.24
1503 1677 2.494073 AGATGAGACCGAACCAGAACTC 59.506 50.000 0.00 0.00 0.00 3.01
1504 1678 2.232452 CAGATGAGACCGAACCAGAACT 59.768 50.000 0.00 0.00 0.00 3.01
1505 1679 2.231478 TCAGATGAGACCGAACCAGAAC 59.769 50.000 0.00 0.00 0.00 3.01
1506 1680 2.525368 TCAGATGAGACCGAACCAGAA 58.475 47.619 0.00 0.00 0.00 3.02
1507 1681 2.215942 TCAGATGAGACCGAACCAGA 57.784 50.000 0.00 0.00 0.00 3.86
1508 1682 2.692557 AGATCAGATGAGACCGAACCAG 59.307 50.000 0.00 0.00 0.00 4.00
1509 1683 2.428530 CAGATCAGATGAGACCGAACCA 59.571 50.000 0.00 0.00 0.00 3.67
1510 1684 2.428890 ACAGATCAGATGAGACCGAACC 59.571 50.000 0.00 0.00 0.00 3.62
1515 1689 7.048629 TCTAATCAACAGATCAGATGAGACC 57.951 40.000 4.48 0.00 26.87 3.85
1543 1717 1.921230 GAAATTCAGAGACCGCTCGTC 59.079 52.381 0.00 0.00 45.98 4.20
1544 1718 1.546476 AGAAATTCAGAGACCGCTCGT 59.454 47.619 0.00 0.00 45.98 4.18
1547 1721 3.259374 TGAAGAGAAATTCAGAGACCGCT 59.741 43.478 0.00 0.00 34.31 5.52
1548 1722 3.589988 TGAAGAGAAATTCAGAGACCGC 58.410 45.455 0.00 0.00 34.31 5.68
1549 1723 4.390297 GGTTGAAGAGAAATTCAGAGACCG 59.610 45.833 0.00 0.00 40.16 4.79
1550 1724 5.308825 TGGTTGAAGAGAAATTCAGAGACC 58.691 41.667 0.00 3.08 40.16 3.85
1551 1725 6.867662 TTGGTTGAAGAGAAATTCAGAGAC 57.132 37.500 0.00 0.00 40.16 3.36
1552 1726 6.263168 GGTTTGGTTGAAGAGAAATTCAGAGA 59.737 38.462 0.00 0.00 40.16 3.10
1553 1727 6.442112 GGTTTGGTTGAAGAGAAATTCAGAG 58.558 40.000 0.00 0.00 40.16 3.35
1554 1728 5.301805 GGGTTTGGTTGAAGAGAAATTCAGA 59.698 40.000 0.00 0.00 40.16 3.27
1555 1729 5.532557 GGGTTTGGTTGAAGAGAAATTCAG 58.467 41.667 0.00 0.00 40.16 3.02
1557 1731 4.277423 TCGGGTTTGGTTGAAGAGAAATTC 59.723 41.667 0.00 0.00 0.00 2.17
1558 1732 4.211920 TCGGGTTTGGTTGAAGAGAAATT 58.788 39.130 0.00 0.00 0.00 1.82
1559 1733 3.827722 TCGGGTTTGGTTGAAGAGAAAT 58.172 40.909 0.00 0.00 0.00 2.17
1577 1768 6.570058 CGCTCTAACAATCGAAATTTATTCGG 59.430 38.462 10.29 0.00 41.78 4.30
1595 1786 6.092670 CAGATCAAAAGTTCCAATCGCTCTAA 59.907 38.462 0.00 0.00 0.00 2.10
1599 1805 4.154918 GTCAGATCAAAAGTTCCAATCGCT 59.845 41.667 0.00 0.00 0.00 4.93
1609 1815 3.058914 CGCCGAAAAGTCAGATCAAAAGT 60.059 43.478 0.00 0.00 0.00 2.66
1610 1816 3.482786 CGCCGAAAAGTCAGATCAAAAG 58.517 45.455 0.00 0.00 0.00 2.27
1642 1854 1.225704 GGGTCATCTGCAGGGAAGG 59.774 63.158 15.13 0.00 0.00 3.46
1643 1855 1.153289 CGGGTCATCTGCAGGGAAG 60.153 63.158 15.13 1.52 0.00 3.46
1644 1856 2.989639 CGGGTCATCTGCAGGGAA 59.010 61.111 15.13 0.00 0.00 3.97
1645 1857 3.785859 GCGGGTCATCTGCAGGGA 61.786 66.667 15.13 9.43 46.73 4.20
1771 1990 2.965831 TCCCTCCTCTGAATTCGGTATG 59.034 50.000 13.95 6.05 0.00 2.39
1797 2016 0.106708 TTCTTCTGCGTCTGCTGGTT 59.893 50.000 0.00 0.00 43.34 3.67
1799 2018 1.196354 CTTTTCTTCTGCGTCTGCTGG 59.804 52.381 0.00 0.00 43.34 4.85
1801 2020 2.533266 TCTTTTCTTCTGCGTCTGCT 57.467 45.000 0.00 0.00 43.34 4.24
1802 2021 3.187227 TGATTCTTTTCTTCTGCGTCTGC 59.813 43.478 0.00 0.00 43.20 4.26
1803 2022 4.997905 TGATTCTTTTCTTCTGCGTCTG 57.002 40.909 0.00 0.00 0.00 3.51
1804 2023 4.633565 GGATGATTCTTTTCTTCTGCGTCT 59.366 41.667 0.00 0.00 0.00 4.18
1829 2048 1.825281 GATCTCGAGGCAGGGATGGG 61.825 65.000 13.56 0.00 30.13 4.00
1832 2051 1.151679 TCGATCTCGAGGCAGGGAT 59.848 57.895 13.56 0.00 44.22 3.85
1862 2081 2.375146 TGCTTGCTTGCTCATCATCAT 58.625 42.857 3.47 0.00 0.00 2.45
1863 2082 1.828979 TGCTTGCTTGCTCATCATCA 58.171 45.000 3.47 0.00 0.00 3.07
1864 2083 2.527100 GTTGCTTGCTTGCTCATCATC 58.473 47.619 3.47 0.00 0.00 2.92
1923 2142 2.825836 CAGATGTGGAAGGCGGCC 60.826 66.667 12.11 12.11 0.00 6.13
1999 2218 4.084066 TGCTCAACGATAAACATGTGACAC 60.084 41.667 0.00 0.00 0.00 3.67
2049 2269 4.597940 GGAGCTAATTATAACAGGGGGAGT 59.402 45.833 0.00 0.00 0.00 3.85
2050 2270 4.846940 AGGAGCTAATTATAACAGGGGGAG 59.153 45.833 0.00 0.00 0.00 4.30
2052 2272 4.019231 GGAGGAGCTAATTATAACAGGGGG 60.019 50.000 0.00 0.00 0.00 5.40
2055 2275 5.046231 GGGAGGAGGAGCTAATTATAACAGG 60.046 48.000 0.00 0.00 0.00 4.00
2069 2289 3.039526 AGGGGAGGGGAGGAGGAG 61.040 72.222 0.00 0.00 0.00 3.69
2077 2297 4.888325 ATCAGCGGAGGGGAGGGG 62.888 72.222 0.00 0.00 0.00 4.79
2078 2298 3.237741 GATCAGCGGAGGGGAGGG 61.238 72.222 0.00 0.00 0.00 4.30
2156 2379 9.436957 AATGTACAGAGATGTCGAAAGTAAATT 57.563 29.630 0.33 0.00 0.00 1.82
2157 2380 8.873830 CAATGTACAGAGATGTCGAAAGTAAAT 58.126 33.333 0.33 0.00 0.00 1.40
2158 2381 7.148639 GCAATGTACAGAGATGTCGAAAGTAAA 60.149 37.037 0.33 0.00 0.00 2.01
2159 2382 6.310467 GCAATGTACAGAGATGTCGAAAGTAA 59.690 38.462 0.33 0.00 0.00 2.24
2162 2385 4.259570 CGCAATGTACAGAGATGTCGAAAG 60.260 45.833 0.33 0.00 0.00 2.62
2173 2396 1.860326 CGATGATGCGCAATGTACAGA 59.140 47.619 17.11 0.00 0.00 3.41
2193 2417 1.688772 ACCTGCTGATGATTGATGGC 58.311 50.000 0.00 0.00 0.00 4.40
2240 2464 7.489113 CAGGCAACAGTTTATTATCAATTCCAC 59.511 37.037 0.00 0.00 41.41 4.02
2291 2519 4.091800 CGCTGGTCAAATTATTTTGCAAGG 59.908 41.667 0.00 0.00 41.66 3.61
2305 2533 2.359850 GCACCCATCGCTGGTCAA 60.360 61.111 4.31 0.00 41.37 3.18
2306 2534 3.321648 AGCACCCATCGCTGGTCA 61.322 61.111 4.31 0.00 41.37 4.02
2311 2539 3.650298 AATGGCAGCACCCATCGCT 62.650 57.895 8.40 0.00 44.68 4.93
2319 2547 1.668793 GCAAACCCAATGGCAGCAC 60.669 57.895 0.00 0.00 33.59 4.40
2353 2581 2.438434 GCCAATGACACGAGGGGG 60.438 66.667 0.00 0.00 0.00 5.40
2360 2588 1.376609 GATCGGGTGGCCAATGACAC 61.377 60.000 7.24 0.00 36.89 3.67
2475 2727 4.591929 TGGATCATGAATCACACACACAT 58.408 39.130 0.00 0.00 35.96 3.21
2556 2824 1.941999 GCTGCAGAAAGGATGGTGGC 61.942 60.000 20.43 0.00 0.00 5.01
2575 2843 1.813513 ATTTTCTCTGCACCTCACCG 58.186 50.000 0.00 0.00 0.00 4.94
2581 2849 3.829026 AGAAAGGGAATTTTCTCTGCACC 59.171 43.478 0.00 0.00 42.22 5.01
2602 2898 1.874019 CTGTCCCGTCATTCGCGAG 60.874 63.158 9.59 0.00 38.35 5.03
2613 2909 4.394712 GGACCACAGCCTGTCCCG 62.395 72.222 0.00 0.00 44.32 5.14
2666 2962 0.107945 AAACCTGCTCTCCATCTCGC 60.108 55.000 0.00 0.00 0.00 5.03


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

AutoCloner maintained by Alex Coulton.