Multiple sequence alignment - TraesCS6D01G080500

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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 TraesCS6D01G080500 chr6D 100.000 5959 0 0 1 5959 46053981 46048023 0.000000e+00 11005.0
1 TraesCS6D01G080500 chr6D 82.791 1813 266 36 3088 4872 385663802 385665596 0.000000e+00 1578.0
2 TraesCS6D01G080500 chr6D 83.333 120 20 0 1824 1943 385663148 385663267 1.760000e-20 111.0
3 TraesCS6D01G080500 chr6D 100.000 28 0 0 1613 1640 102120511 102120538 1.100000e-02 52.8
4 TraesCS6D01G080500 chr6D 100.000 28 0 0 1613 1640 347157178 347157151 1.100000e-02 52.8
5 TraesCS6D01G080500 chr6B 96.246 2291 68 9 2932 5207 114509533 114507246 0.000000e+00 3738.0
6 TraesCS6D01G080500 chr6B 82.084 1814 278 35 3088 4872 576017602 576019397 0.000000e+00 1506.0
7 TraesCS6D01G080500 chr6B 92.784 873 35 10 729 1578 114511617 114510750 0.000000e+00 1238.0
8 TraesCS6D01G080500 chr6B 94.980 737 35 2 5225 5959 706000873 706000137 0.000000e+00 1155.0
9 TraesCS6D01G080500 chr6B 94.488 635 23 7 1636 2266 114510746 114510120 0.000000e+00 968.0
10 TraesCS6D01G080500 chr6B 88.451 736 43 19 7 721 114512387 114511673 0.000000e+00 850.0
11 TraesCS6D01G080500 chr6B 95.020 502 13 6 2424 2924 114510086 114509596 0.000000e+00 778.0
12 TraesCS6D01G080500 chr6B 84.000 200 24 7 2732 2924 576017218 576017416 1.020000e-42 185.0
13 TraesCS6D01G080500 chr6B 82.576 132 21 2 1811 1942 576016828 576016957 1.360000e-21 115.0
14 TraesCS6D01G080500 chr6B 89.888 89 5 3 290 375 576014603 576014690 1.760000e-20 111.0
15 TraesCS6D01G080500 chr6A 94.146 2306 108 14 2932 5226 60224834 60222545 0.000000e+00 3485.0
16 TraesCS6D01G080500 chr6A 94.204 1294 40 18 1643 2924 60226170 60224900 0.000000e+00 1941.0
17 TraesCS6D01G080500 chr6A 82.645 1815 267 37 3088 4872 530122267 530124063 0.000000e+00 1563.0
18 TraesCS6D01G080500 chr6A 95.929 737 26 3 5226 5959 493725935 493726670 0.000000e+00 1192.0
19 TraesCS6D01G080500 chr6A 90.449 869 52 20 729 1578 60227037 60226181 0.000000e+00 1116.0
20 TraesCS6D01G080500 chr6A 93.409 531 22 5 206 728 60227621 60227096 0.000000e+00 774.0
21 TraesCS6D01G080500 chr6A 84.000 200 24 7 2732 2924 530121883 530122081 1.020000e-42 185.0
22 TraesCS6D01G080500 chr6A 89.888 89 5 2 290 375 530119526 530119613 1.760000e-20 111.0
23 TraesCS6D01G080500 chr6A 81.513 119 22 0 1824 1942 530121610 530121728 1.370000e-16 99.0
24 TraesCS6D01G080500 chr6A 100.000 28 0 0 1613 1640 100424285 100424312 1.100000e-02 52.8
25 TraesCS6D01G080500 chr4B 96.332 736 24 3 5227 5959 187621256 187621991 0.000000e+00 1206.0
26 TraesCS6D01G080500 chr4B 96.054 735 26 3 5228 5959 567184108 567184842 0.000000e+00 1194.0
27 TraesCS6D01G080500 chr4A 96.201 737 25 3 5226 5959 667313177 667312441 0.000000e+00 1203.0
28 TraesCS6D01G080500 chr3A 96.190 735 25 3 5228 5959 234972295 234973029 0.000000e+00 1199.0
29 TraesCS6D01G080500 chr3A 95.652 736 29 3 5227 5959 429486178 429486913 0.000000e+00 1179.0
30 TraesCS6D01G080500 chr5B 95.924 736 26 4 5227 5959 197093895 197093161 0.000000e+00 1190.0
31 TraesCS6D01G080500 chr2D 95.516 736 30 3 5226 5959 643739851 643740585 0.000000e+00 1173.0
32 TraesCS6D01G080500 chr5D 94.444 36 0 1 1607 1640 328727394 328727429 3.000000e-03 54.7
33 TraesCS6D01G080500 chr2B 96.875 32 1 0 1613 1644 201247814 201247783 3.000000e-03 54.7
34 TraesCS6D01G080500 chrUn 100.000 28 0 0 1613 1640 32314053 32314026 1.100000e-02 52.8
35 TraesCS6D01G080500 chr7A 96.774 31 1 0 1614 1644 122346940 122346910 1.100000e-02 52.8
36 TraesCS6D01G080500 chr5A 100.000 28 0 0 1613 1640 619607358 619607385 1.100000e-02 52.8
37 TraesCS6D01G080500 chr1A 100.000 28 0 0 1613 1640 371910514 371910487 1.100000e-02 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 TraesCS6D01G080500 chr6D 46048023 46053981 5958 True 11005.00 11005 100.0000 1 5959 1 chr6D.!!$R1 5958
1 TraesCS6D01G080500 chr6D 385663148 385665596 2448 False 844.50 1578 83.0620 1824 4872 2 chr6D.!!$F2 3048
2 TraesCS6D01G080500 chr6B 114507246 114512387 5141 True 1514.40 3738 93.3978 7 5207 5 chr6B.!!$R2 5200
3 TraesCS6D01G080500 chr6B 706000137 706000873 736 True 1155.00 1155 94.9800 5225 5959 1 chr6B.!!$R1 734
4 TraesCS6D01G080500 chr6B 576014603 576019397 4794 False 479.25 1506 84.6370 290 4872 4 chr6B.!!$F1 4582
5 TraesCS6D01G080500 chr6A 60222545 60227621 5076 True 1829.00 3485 93.0520 206 5226 4 chr6A.!!$R1 5020
6 TraesCS6D01G080500 chr6A 493725935 493726670 735 False 1192.00 1192 95.9290 5226 5959 1 chr6A.!!$F2 733
7 TraesCS6D01G080500 chr6A 530119526 530124063 4537 False 489.50 1563 84.5115 290 4872 4 chr6A.!!$F3 4582
8 TraesCS6D01G080500 chr4B 187621256 187621991 735 False 1206.00 1206 96.3320 5227 5959 1 chr4B.!!$F1 732
9 TraesCS6D01G080500 chr4B 567184108 567184842 734 False 1194.00 1194 96.0540 5228 5959 1 chr4B.!!$F2 731
10 TraesCS6D01G080500 chr4A 667312441 667313177 736 True 1203.00 1203 96.2010 5226 5959 1 chr4A.!!$R1 733
11 TraesCS6D01G080500 chr3A 234972295 234973029 734 False 1199.00 1199 96.1900 5228 5959 1 chr3A.!!$F1 731
12 TraesCS6D01G080500 chr3A 429486178 429486913 735 False 1179.00 1179 95.6520 5227 5959 1 chr3A.!!$F2 732
13 TraesCS6D01G080500 chr5B 197093161 197093895 734 True 1190.00 1190 95.9240 5227 5959 1 chr5B.!!$R1 732
14 TraesCS6D01G080500 chr2D 643739851 643740585 734 False 1173.00 1173 95.5160 5226 5959 1 chr2D.!!$F1 733

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
63 64 0.042581 TGGGACAGAGATGGCACCTA 59.957 55.000 0.00 0.00 0.00 3.08 F
64 65 0.755686 GGGACAGAGATGGCACCTAG 59.244 60.000 0.00 0.00 0.00 3.02 F
1616 2708 0.179142 GCCGTTAGTTCGAGGACCTC 60.179 60.000 11.87 11.87 0.00 3.85 F
1752 2845 0.920664 GGCTTTGCACGTGTGTTTTC 59.079 50.000 18.38 0.00 0.00 2.29 F
2670 3887 2.289382 TGCACGGTAGCATGAAAAGAGA 60.289 45.455 0.00 0.00 40.11 3.10 F
4228 5540 0.530288 TCGTTGGCATGTCAGATCGA 59.470 50.000 16.13 16.13 0.00 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1597 2689 0.179142 GAGGTCCTCGAACTAACGGC 60.179 60.000 2.28 0.00 25.20 5.68 R
1736 2828 0.888619 TGGGAAAACACACGTGCAAA 59.111 45.000 17.22 0.00 0.00 3.68 R
2670 3887 2.093711 TGCAAGAGTGTATGCACCGTAT 60.094 45.455 10.59 0.00 46.87 3.06 R
2963 4246 4.574421 TGTGAACAAAGGACATACTGTGTG 59.426 41.667 2.78 2.78 42.36 3.82 R
4472 5791 1.901833 GGCCAATTGATTCACTTGGGT 59.098 47.619 27.49 0.00 42.14 4.51 R
5436 6769 1.475034 GGGTGGCAGCATAATCTTCGA 60.475 52.381 19.48 0.00 0.00 3.71 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
19 20 3.056458 CCACCGCAGACACCACTA 58.944 61.111 0.00 0.00 0.00 2.74
37 38 3.511146 CACTAGGCACATCCCAACAATTT 59.489 43.478 0.00 0.00 34.51 1.82
53 54 4.392940 ACAATTTCTTGAGTGGGACAGAG 58.607 43.478 0.00 0.00 35.87 3.35
54 55 4.103153 ACAATTTCTTGAGTGGGACAGAGA 59.897 41.667 0.00 0.00 35.87 3.10
55 56 5.222007 ACAATTTCTTGAGTGGGACAGAGAT 60.222 40.000 0.00 0.00 35.87 2.75
56 57 3.969287 TTCTTGAGTGGGACAGAGATG 57.031 47.619 0.00 0.00 41.80 2.90
57 58 2.182827 TCTTGAGTGGGACAGAGATGG 58.817 52.381 0.00 0.00 41.80 3.51
59 60 0.545071 TGAGTGGGACAGAGATGGCA 60.545 55.000 0.00 0.00 41.80 4.92
60 61 0.107945 GAGTGGGACAGAGATGGCAC 60.108 60.000 0.00 0.00 41.80 5.01
61 62 1.078143 GTGGGACAGAGATGGCACC 60.078 63.158 0.00 0.00 41.80 5.01
62 63 1.229625 TGGGACAGAGATGGCACCT 60.230 57.895 0.00 0.00 0.00 4.00
63 64 0.042581 TGGGACAGAGATGGCACCTA 59.957 55.000 0.00 0.00 0.00 3.08
64 65 0.755686 GGGACAGAGATGGCACCTAG 59.244 60.000 0.00 0.00 0.00 3.02
65 66 1.689575 GGGACAGAGATGGCACCTAGA 60.690 57.143 0.00 0.00 0.00 2.43
66 67 1.686052 GGACAGAGATGGCACCTAGAG 59.314 57.143 0.00 0.00 0.00 2.43
67 68 1.686052 GACAGAGATGGCACCTAGAGG 59.314 57.143 0.00 0.00 42.17 3.69
106 111 2.668457 CACGAGTTGAGAAGGTGCATAC 59.332 50.000 0.00 0.00 0.00 2.39
113 118 3.472652 TGAGAAGGTGCATACAAAACGT 58.527 40.909 0.00 0.00 0.00 3.99
130 135 5.597813 AAACGTCATGAAGTTCAGCTAAG 57.402 39.130 24.22 4.35 32.04 2.18
146 151 1.753073 CTAAGCCAGCTCCCAAAATGG 59.247 52.381 0.00 0.00 37.25 3.16
164 169 2.858745 TGGTAAAGTTGCTTCCAGTCC 58.141 47.619 0.00 0.00 0.00 3.85
200 209 3.303924 GCTAGAGCTTGCTACGTACTACC 60.304 52.174 0.00 0.00 38.21 3.18
201 210 3.002038 AGAGCTTGCTACGTACTACCT 57.998 47.619 0.00 0.00 0.00 3.08
202 211 2.683867 AGAGCTTGCTACGTACTACCTG 59.316 50.000 0.00 0.00 0.00 4.00
203 212 2.422832 GAGCTTGCTACGTACTACCTGT 59.577 50.000 0.00 0.00 0.00 4.00
204 213 2.422832 AGCTTGCTACGTACTACCTGTC 59.577 50.000 0.00 0.00 0.00 3.51
356 370 2.718073 GGGCTCGATGGGTACGTGT 61.718 63.158 0.00 0.00 0.00 4.49
436 450 2.746277 GGGAACGCGCATGGAAGT 60.746 61.111 5.73 0.00 0.00 3.01
490 513 3.254654 CACGTACGCTGCCATCGG 61.255 66.667 16.72 0.00 0.00 4.18
493 516 2.585247 GTACGCTGCCATCGGACC 60.585 66.667 0.00 0.00 34.87 4.46
596 770 2.955402 GTCACGAGACGACCAGCT 59.045 61.111 0.00 0.00 34.60 4.24
632 901 1.818642 GTCATGGCTGAGAAGTTGCT 58.181 50.000 0.00 0.00 30.18 3.91
818 1169 1.294857 GTGGCACCGCAATTGTTTTT 58.705 45.000 6.29 0.00 0.00 1.94
952 1339 1.376037 CTCCTTCCTCCGTGTTGCC 60.376 63.158 0.00 0.00 0.00 4.52
954 1341 1.376037 CCTTCCTCCGTGTTGCCTC 60.376 63.158 0.00 0.00 0.00 4.70
1035 1442 5.673337 TGGTTTCTCTCTTTTGATCGTTG 57.327 39.130 0.00 0.00 0.00 4.10
1036 1443 5.364778 TGGTTTCTCTCTTTTGATCGTTGA 58.635 37.500 0.00 0.00 0.00 3.18
1042 1449 6.102663 TCTCTCTTTTGATCGTTGAAGATCC 58.897 40.000 4.75 0.00 44.72 3.36
1397 1819 2.611225 ATCAGCCGATTGTTCTCCTC 57.389 50.000 0.00 0.00 0.00 3.71
1411 1833 6.748333 TGTTCTCCTCTTATTTGCTGAATG 57.252 37.500 0.00 0.00 0.00 2.67
1578 2670 5.811100 CCCAAGCTAGTTTGTAGTAGTAAGC 59.189 44.000 16.87 0.00 31.14 3.09
1579 2671 6.351117 CCCAAGCTAGTTTGTAGTAGTAAGCT 60.351 42.308 16.87 0.00 31.14 3.74
1580 2672 7.147949 CCCAAGCTAGTTTGTAGTAGTAAGCTA 60.148 40.741 16.87 0.00 31.14 3.32
1581 2673 7.916450 CCAAGCTAGTTTGTAGTAGTAAGCTAG 59.084 40.741 16.87 10.92 39.34 3.42
1585 2677 8.441312 CTAGTTTGTAGTAGTAAGCTAGCTCT 57.559 38.462 19.65 14.36 33.21 4.09
1586 2678 9.545105 CTAGTTTGTAGTAGTAAGCTAGCTCTA 57.455 37.037 19.65 13.25 33.21 2.43
1587 2679 8.441312 AGTTTGTAGTAGTAAGCTAGCTCTAG 57.559 38.462 19.65 0.00 36.29 2.43
1588 2680 8.266473 AGTTTGTAGTAGTAAGCTAGCTCTAGA 58.734 37.037 19.65 10.24 35.21 2.43
1589 2681 9.059260 GTTTGTAGTAGTAAGCTAGCTCTAGAT 57.941 37.037 19.65 4.14 35.21 1.98
1600 2692 7.504924 AGCTAGCTCTAGATATATTTAGCCG 57.495 40.000 12.68 1.75 35.21 5.52
1601 2693 7.057894 AGCTAGCTCTAGATATATTTAGCCGT 58.942 38.462 12.68 0.00 35.21 5.68
1602 2694 7.558444 AGCTAGCTCTAGATATATTTAGCCGTT 59.442 37.037 12.68 1.54 35.21 4.44
1603 2695 8.838365 GCTAGCTCTAGATATATTTAGCCGTTA 58.162 37.037 7.70 2.40 35.21 3.18
1605 2697 8.810990 AGCTCTAGATATATTTAGCCGTTAGT 57.189 34.615 5.58 0.00 0.00 2.24
1606 2698 9.245481 AGCTCTAGATATATTTAGCCGTTAGTT 57.755 33.333 5.58 0.00 0.00 2.24
1607 2699 9.505995 GCTCTAGATATATTTAGCCGTTAGTTC 57.494 37.037 5.58 0.00 0.00 3.01
1608 2700 9.705471 CTCTAGATATATTTAGCCGTTAGTTCG 57.295 37.037 5.58 0.00 0.00 3.95
1609 2701 9.440773 TCTAGATATATTTAGCCGTTAGTTCGA 57.559 33.333 5.58 0.00 0.00 3.71
1610 2702 9.705471 CTAGATATATTTAGCCGTTAGTTCGAG 57.295 37.037 0.00 0.00 0.00 4.04
1611 2703 7.536855 AGATATATTTAGCCGTTAGTTCGAGG 58.463 38.462 0.00 0.00 0.00 4.63
1612 2704 5.779529 ATATTTAGCCGTTAGTTCGAGGA 57.220 39.130 0.00 0.00 0.00 3.71
1613 2705 2.927553 TTAGCCGTTAGTTCGAGGAC 57.072 50.000 0.00 0.00 0.00 3.85
1614 2706 1.098050 TAGCCGTTAGTTCGAGGACC 58.902 55.000 0.00 0.00 0.00 4.46
1615 2707 0.611340 AGCCGTTAGTTCGAGGACCT 60.611 55.000 0.00 0.00 0.00 3.85
1616 2708 0.179142 GCCGTTAGTTCGAGGACCTC 60.179 60.000 11.87 11.87 0.00 3.85
1617 2709 1.461559 CCGTTAGTTCGAGGACCTCT 58.538 55.000 19.39 3.08 0.00 3.69
1618 2710 1.132643 CCGTTAGTTCGAGGACCTCTG 59.867 57.143 19.39 12.59 0.00 3.35
1619 2711 2.082231 CGTTAGTTCGAGGACCTCTGA 58.918 52.381 19.39 14.59 0.00 3.27
1620 2712 2.486982 CGTTAGTTCGAGGACCTCTGAA 59.513 50.000 19.39 19.01 0.00 3.02
1621 2713 3.057736 CGTTAGTTCGAGGACCTCTGAAA 60.058 47.826 22.16 11.66 30.14 2.69
1622 2714 4.380655 CGTTAGTTCGAGGACCTCTGAAAT 60.381 45.833 22.85 22.85 31.23 2.17
1623 2715 5.163683 CGTTAGTTCGAGGACCTCTGAAATA 60.164 44.000 22.16 21.79 29.97 1.40
1624 2716 4.993029 AGTTCGAGGACCTCTGAAATAG 57.007 45.455 22.16 7.04 30.14 1.73
1625 2717 4.345854 AGTTCGAGGACCTCTGAAATAGT 58.654 43.478 22.16 10.60 30.14 2.12
1626 2718 4.773149 AGTTCGAGGACCTCTGAAATAGTT 59.227 41.667 22.16 9.54 30.14 2.24
1627 2719 4.985538 TCGAGGACCTCTGAAATAGTTC 57.014 45.455 19.39 0.00 0.00 3.01
1628 2720 3.377485 TCGAGGACCTCTGAAATAGTTCG 59.623 47.826 19.39 2.62 36.46 3.95
1629 2721 3.377485 CGAGGACCTCTGAAATAGTTCGA 59.623 47.826 19.39 0.00 36.46 3.71
1630 2722 4.496673 CGAGGACCTCTGAAATAGTTCGAG 60.497 50.000 19.39 13.91 36.46 4.04
1632 2724 3.700038 GGACCTCTGAAATAGTTCGAGGA 59.300 47.826 31.48 16.50 46.43 3.71
1633 2725 4.440387 GGACCTCTGAAATAGTTCGAGGAC 60.440 50.000 31.48 27.30 46.43 3.85
1634 2726 3.447944 ACCTCTGAAATAGTTCGAGGACC 59.552 47.826 31.48 0.97 46.43 4.46
1635 2727 3.702045 CCTCTGAAATAGTTCGAGGACCT 59.298 47.826 25.82 0.00 46.43 3.85
1636 2728 4.888239 CCTCTGAAATAGTTCGAGGACCTA 59.112 45.833 25.82 0.00 46.43 3.08
1637 2729 5.536916 CCTCTGAAATAGTTCGAGGACCTAT 59.463 44.000 25.82 0.00 46.43 2.57
1638 2730 6.392625 TCTGAAATAGTTCGAGGACCTATG 57.607 41.667 0.00 0.00 36.46 2.23
1639 2731 6.127101 TCTGAAATAGTTCGAGGACCTATGA 58.873 40.000 0.00 0.00 36.46 2.15
1640 2732 6.039493 TCTGAAATAGTTCGAGGACCTATGAC 59.961 42.308 0.00 0.00 36.46 3.06
1641 2733 5.655090 TGAAATAGTTCGAGGACCTATGACA 59.345 40.000 0.00 0.00 36.46 3.58
1645 2737 4.533815 AGTTCGAGGACCTATGACACATA 58.466 43.478 0.00 0.00 0.00 2.29
1736 2828 4.365368 TCTACATATCCATATGCCAGGCT 58.635 43.478 14.15 0.35 42.98 4.58
1752 2845 0.920664 GGCTTTGCACGTGTGTTTTC 59.079 50.000 18.38 0.00 0.00 2.29
1938 3032 5.368989 GGTGGTAAGATTCAGAACCCTATG 58.631 45.833 0.00 0.00 0.00 2.23
2161 3369 7.906199 AAGATTAGTTACTCCAGTGAGCTAT 57.094 36.000 0.00 0.00 42.74 2.97
2238 3448 5.063691 TGCCCGTTAATAGTTGAATTGTACG 59.936 40.000 0.00 0.00 32.58 3.67
2266 3476 3.181443 GGGGGAGGAATAACAGTATGGTG 60.181 52.174 0.00 0.00 35.42 4.17
2283 3493 5.715439 ATGGTGAAACTATCTTGGGATCA 57.285 39.130 0.00 0.00 28.92 2.92
2284 3494 5.715439 TGGTGAAACTATCTTGGGATCAT 57.285 39.130 0.00 0.00 36.74 2.45
2345 3555 8.227791 GCGAAATATTTTGTACAAGACTCAAGA 58.772 33.333 15.40 0.00 0.00 3.02
2369 3579 3.243068 GGTGAAAAGAAAGTCATGCACGT 60.243 43.478 0.00 0.00 0.00 4.49
2372 3582 4.572795 TGAAAAGAAAGTCATGCACGTACA 59.427 37.500 0.00 0.00 0.00 2.90
2462 3678 4.100498 GGTAATGGAAGTGTAGAATCGGGA 59.900 45.833 0.00 0.00 0.00 5.14
2550 3767 3.714391 ACAAGTTCACCGAGAAGTACAC 58.286 45.455 0.00 0.00 38.96 2.90
2579 3796 9.315363 CCACTATAGGAAGTGTAGGAAGAATAT 57.685 37.037 4.43 0.00 44.45 1.28
2595 3812 8.221251 AGGAAGAATATGATAGAAAAAGGTCCC 58.779 37.037 0.00 0.00 0.00 4.46
2603 3820 2.958818 AGAAAAAGGTCCCCCAAGAAC 58.041 47.619 0.00 0.00 0.00 3.01
2670 3887 2.289382 TGCACGGTAGCATGAAAAGAGA 60.289 45.455 0.00 0.00 40.11 3.10
2703 3920 3.928992 ACACTCTTGCATGACTGATAACG 59.071 43.478 13.68 0.00 0.00 3.18
2849 4072 9.155975 CTTAGACTGCAATGTTTAAGTGTCTAT 57.844 33.333 7.75 0.00 36.23 1.98
3021 4306 6.016527 CAGTCAATACATGCAGCCATATTCTT 60.017 38.462 0.00 0.00 0.00 2.52
3120 4408 5.428253 TCACATATTAAGAGGCAACACTCC 58.572 41.667 0.00 0.00 36.02 3.85
4077 5378 2.191400 CTGGAGTCTGAGGGGATCAAA 58.809 52.381 0.00 0.00 37.52 2.69
4228 5540 0.530288 TCGTTGGCATGTCAGATCGA 59.470 50.000 16.13 16.13 0.00 3.59
4472 5791 3.207265 TGCCTTGTTCTTAACTGCAGA 57.793 42.857 23.35 0.00 31.24 4.26
4681 6000 4.186077 TCTAGACAGGATGGGTTCTAGG 57.814 50.000 4.98 0.00 43.62 3.02
4701 6020 2.224305 GGACAGCAACCTCTAGTGTTGT 60.224 50.000 20.91 12.71 43.86 3.32
4708 6027 3.963428 ACCTCTAGTGTTGTGATGGTC 57.037 47.619 0.00 0.00 0.00 4.02
4774 6093 7.148018 CCAACAAGTGATGCTATTTACTGGATT 60.148 37.037 0.00 0.00 0.00 3.01
4789 6108 1.834896 TGGATTCCAAGCTTAGCCGTA 59.165 47.619 1.94 0.00 0.00 4.02
4807 6126 2.120232 GTAGATGATGACCGCTTCACG 58.880 52.381 0.00 0.00 36.92 4.35
4956 6276 4.277515 TCTGGTATTGCATCTAGATGGC 57.722 45.455 29.43 22.10 39.16 4.40
5017 6343 7.554959 TCTTCTCTAAGAACACCCTAAATGT 57.445 36.000 0.00 0.00 38.81 2.71
5085 6414 9.525826 GTAAATGATTAAAGGGAGATGGATCAT 57.474 33.333 0.00 0.00 35.07 2.45
5143 6472 4.732355 GCGCAAAGTCTTAAGGTCACAAAA 60.732 41.667 0.30 0.00 0.00 2.44
5210 6539 4.704540 ACGAAGTCCATGCCAATTATTCAA 59.295 37.500 0.00 0.00 29.74 2.69
5439 6772 2.975536 GGTGGTGGACCGATTCGA 59.024 61.111 7.83 0.00 39.43 3.71
5464 6797 2.283101 GCTGCCACCCATGTTGGA 60.283 61.111 13.59 0.37 40.96 3.53
5500 6833 1.091771 CACCTGCTCCAACCGCATAG 61.092 60.000 0.00 0.00 36.70 2.23
5508 6841 1.739929 CAACCGCATAGACACCGCA 60.740 57.895 0.00 0.00 0.00 5.69
5531 6864 0.690762 AACAGCGGTTGGTACTCCAT 59.309 50.000 0.00 0.00 43.91 3.41
5542 6875 2.563620 TGGTACTCCATTCGTTGTAGCA 59.436 45.455 0.00 0.00 39.86 3.49
5550 6883 4.100963 TCCATTCGTTGTAGCATAGACCAT 59.899 41.667 0.00 0.00 0.00 3.55
5559 6892 4.643334 TGTAGCATAGACCATGTACGAAGT 59.357 41.667 0.00 0.00 38.90 3.01
5585 6918 4.388469 GTGCGTACAACGGAAAATAACCTA 59.612 41.667 0.00 0.00 45.07 3.08
5665 6999 0.956633 TAGTAAGGCATACGCTCCCG 59.043 55.000 0.00 0.00 39.62 5.14
5767 7101 6.885735 ACAAATTTAACGCTATTTGGATGC 57.114 33.333 12.62 0.00 42.96 3.91
5825 7159 7.410120 AAAAGAGGTGTTTGATTGTCTCTTT 57.590 32.000 9.48 9.48 46.80 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.234630 TAGTGGTGTCTGCGGTGGC 62.235 63.158 0.00 0.00 40.52 5.01
2 3 1.079819 CTAGTGGTGTCTGCGGTGG 60.080 63.158 0.00 0.00 0.00 4.61
3 4 1.079819 CCTAGTGGTGTCTGCGGTG 60.080 63.158 0.00 0.00 0.00 4.94
4 5 2.943978 GCCTAGTGGTGTCTGCGGT 61.944 63.158 0.00 0.00 35.27 5.68
5 6 2.125512 GCCTAGTGGTGTCTGCGG 60.126 66.667 0.00 0.00 35.27 5.69
17 18 4.019174 AGAAATTGTTGGGATGTGCCTAG 58.981 43.478 0.00 0.00 36.66 3.02
19 20 2.893424 AGAAATTGTTGGGATGTGCCT 58.107 42.857 0.00 0.00 36.66 4.75
37 38 2.182827 CCATCTCTGTCCCACTCAAGA 58.817 52.381 0.00 0.00 0.00 3.02
53 54 1.892474 CTCTAGCCTCTAGGTGCCATC 59.108 57.143 0.00 0.00 37.57 3.51
54 55 2.008242 CTCTAGCCTCTAGGTGCCAT 57.992 55.000 0.00 0.00 37.57 4.40
55 56 0.757188 GCTCTAGCCTCTAGGTGCCA 60.757 60.000 0.00 0.00 37.57 4.92
56 57 2.046108 GCTCTAGCCTCTAGGTGCC 58.954 63.158 0.00 0.00 37.57 5.01
67 68 4.933483 CGACAGATCGGCTCTAGC 57.067 61.111 0.00 0.00 44.99 3.42
106 111 4.214980 AGCTGAACTTCATGACGTTTTG 57.785 40.909 17.63 13.96 0.00 2.44
113 118 3.603532 CTGGCTTAGCTGAACTTCATGA 58.396 45.455 3.59 0.00 0.00 3.07
130 135 1.555967 TTACCATTTTGGGAGCTGGC 58.444 50.000 0.00 0.00 43.37 4.85
137 142 4.202305 TGGAAGCAACTTTACCATTTTGGG 60.202 41.667 0.00 0.00 43.37 4.12
146 151 3.440522 GGATGGACTGGAAGCAACTTTAC 59.559 47.826 0.00 0.00 37.60 2.01
196 205 3.446516 AGCCGTTAGTTTAGGACAGGTAG 59.553 47.826 0.00 0.00 0.00 3.18
200 209 5.220605 GCATTTAGCCGTTAGTTTAGGACAG 60.221 44.000 0.00 0.00 37.23 3.51
201 210 4.632688 GCATTTAGCCGTTAGTTTAGGACA 59.367 41.667 0.00 0.00 37.23 4.02
202 211 4.632688 TGCATTTAGCCGTTAGTTTAGGAC 59.367 41.667 0.00 0.00 44.83 3.85
203 212 4.834534 TGCATTTAGCCGTTAGTTTAGGA 58.165 39.130 0.00 0.00 44.83 2.94
204 213 5.527582 AGATGCATTTAGCCGTTAGTTTAGG 59.472 40.000 0.00 0.00 44.83 2.69
356 370 3.268603 CGTCACCTTGTGCACGCA 61.269 61.111 13.13 0.00 33.43 5.24
427 441 6.085555 TGTACTGCTACTATACTTCCATGC 57.914 41.667 0.00 0.00 0.00 4.06
596 770 4.380973 CCATGACGAAGAAGACTTGCTCTA 60.381 45.833 0.00 0.00 36.39 2.43
632 901 2.203480 GCTTGGGTTGGTGCAGGA 60.203 61.111 0.00 0.00 0.00 3.86
818 1169 4.748102 AGCTTTTGTCGTCGACAGAAAATA 59.252 37.500 25.69 11.11 43.69 1.40
875 1226 3.243434 CCTGAAGCCGTATATATAGCCCG 60.243 52.174 0.00 0.00 0.00 6.13
952 1339 2.811873 GCAGCTAGGGAGAGAGAGAGAG 60.812 59.091 0.00 0.00 0.00 3.20
954 1341 1.609208 GCAGCTAGGGAGAGAGAGAG 58.391 60.000 0.00 0.00 0.00 3.20
1001 1391 3.373830 AGAGAAACCAGCTAGCAGATCT 58.626 45.455 18.83 15.38 0.00 2.75
1035 1442 5.523188 CACAGACATCTTAGCTTGGATCTTC 59.477 44.000 0.00 0.00 0.00 2.87
1036 1443 5.426504 CACAGACATCTTAGCTTGGATCTT 58.573 41.667 0.00 0.00 0.00 2.40
1042 1449 2.610433 TCGCACAGACATCTTAGCTTG 58.390 47.619 0.00 0.00 0.00 4.01
1077 1488 1.522580 GCCCTGCTCGTCATCTTCC 60.523 63.158 0.00 0.00 0.00 3.46
1351 1773 2.981400 ATCGTTACCCGCAAACAAAG 57.019 45.000 0.00 0.00 36.19 2.77
1355 1777 4.870221 AAATCTATCGTTACCCGCAAAC 57.130 40.909 0.00 0.00 36.19 2.93
1377 1799 3.300388 AGAGGAGAACAATCGGCTGATA 58.700 45.455 8.86 0.00 33.40 2.15
1397 1819 6.949352 ACAGGTATCCATTCAGCAAATAAG 57.051 37.500 0.00 0.00 0.00 1.73
1579 2671 9.902684 ACTAACGGCTAAATATATCTAGAGCTA 57.097 33.333 0.00 0.00 0.00 3.32
1580 2672 8.810990 ACTAACGGCTAAATATATCTAGAGCT 57.189 34.615 0.00 0.00 0.00 4.09
1581 2673 9.505995 GAACTAACGGCTAAATATATCTAGAGC 57.494 37.037 0.00 0.00 0.00 4.09
1582 2674 9.705471 CGAACTAACGGCTAAATATATCTAGAG 57.295 37.037 0.00 0.00 0.00 2.43
1584 2676 9.705471 CTCGAACTAACGGCTAAATATATCTAG 57.295 37.037 0.00 0.00 0.00 2.43
1585 2677 8.671921 CCTCGAACTAACGGCTAAATATATCTA 58.328 37.037 0.00 0.00 0.00 1.98
1586 2678 7.392673 TCCTCGAACTAACGGCTAAATATATCT 59.607 37.037 0.00 0.00 0.00 1.98
1587 2679 7.484324 GTCCTCGAACTAACGGCTAAATATATC 59.516 40.741 0.00 0.00 0.00 1.63
1588 2680 7.311408 GTCCTCGAACTAACGGCTAAATATAT 58.689 38.462 0.00 0.00 0.00 0.86
1589 2681 6.294176 GGTCCTCGAACTAACGGCTAAATATA 60.294 42.308 0.00 0.00 0.00 0.86
1590 2682 5.508657 GGTCCTCGAACTAACGGCTAAATAT 60.509 44.000 0.00 0.00 0.00 1.28
1591 2683 4.202050 GGTCCTCGAACTAACGGCTAAATA 60.202 45.833 0.00 0.00 0.00 1.40
1592 2684 3.429960 GGTCCTCGAACTAACGGCTAAAT 60.430 47.826 0.00 0.00 0.00 1.40
1593 2685 2.094545 GGTCCTCGAACTAACGGCTAAA 60.095 50.000 0.00 0.00 0.00 1.85
1594 2686 1.474077 GGTCCTCGAACTAACGGCTAA 59.526 52.381 0.00 0.00 0.00 3.09
1595 2687 1.098050 GGTCCTCGAACTAACGGCTA 58.902 55.000 0.00 0.00 0.00 3.93
1596 2688 0.611340 AGGTCCTCGAACTAACGGCT 60.611 55.000 0.00 0.00 0.00 5.52
1597 2689 0.179142 GAGGTCCTCGAACTAACGGC 60.179 60.000 2.28 0.00 25.20 5.68
1598 2690 1.132643 CAGAGGTCCTCGAACTAACGG 59.867 57.143 13.41 0.00 35.36 4.44
1599 2691 2.082231 TCAGAGGTCCTCGAACTAACG 58.918 52.381 13.41 0.00 35.36 3.18
1600 2692 4.516365 TTTCAGAGGTCCTCGAACTAAC 57.484 45.455 19.38 0.00 35.36 2.34
1601 2693 5.950549 ACTATTTCAGAGGTCCTCGAACTAA 59.049 40.000 19.38 10.35 35.36 2.24
1602 2694 5.507637 ACTATTTCAGAGGTCCTCGAACTA 58.492 41.667 19.38 17.39 35.36 2.24
1603 2695 4.345854 ACTATTTCAGAGGTCCTCGAACT 58.654 43.478 19.38 17.25 35.36 3.01
1604 2696 4.722361 ACTATTTCAGAGGTCCTCGAAC 57.278 45.455 19.38 0.00 35.36 3.95
1605 2697 4.142447 CGAACTATTTCAGAGGTCCTCGAA 60.142 45.833 13.41 15.62 35.36 3.71
1606 2698 3.377485 CGAACTATTTCAGAGGTCCTCGA 59.623 47.826 13.41 10.75 35.36 4.04
1607 2699 3.377485 TCGAACTATTTCAGAGGTCCTCG 59.623 47.826 13.41 8.60 35.36 4.63
1608 2700 4.202070 CCTCGAACTATTTCAGAGGTCCTC 60.202 50.000 11.31 11.31 42.05 3.71
1609 2701 3.702045 CCTCGAACTATTTCAGAGGTCCT 59.298 47.826 17.61 0.00 42.05 3.85
1610 2702 3.700038 TCCTCGAACTATTTCAGAGGTCC 59.300 47.826 21.48 0.00 44.46 4.46
1611 2703 4.440387 GGTCCTCGAACTATTTCAGAGGTC 60.440 50.000 21.48 18.28 44.46 3.85
1612 2704 3.447944 GGTCCTCGAACTATTTCAGAGGT 59.552 47.826 21.48 0.00 44.46 3.85
1613 2705 3.702045 AGGTCCTCGAACTATTTCAGAGG 59.298 47.826 18.80 18.80 44.93 3.69
1614 2706 4.993029 AGGTCCTCGAACTATTTCAGAG 57.007 45.455 0.00 7.31 34.68 3.35
1615 2707 6.039493 GTCATAGGTCCTCGAACTATTTCAGA 59.961 42.308 0.00 0.00 39.24 3.27
1616 2708 6.183360 TGTCATAGGTCCTCGAACTATTTCAG 60.183 42.308 0.00 0.00 39.24 3.02
1617 2709 5.655090 TGTCATAGGTCCTCGAACTATTTCA 59.345 40.000 0.00 0.00 39.24 2.69
1618 2710 5.978322 GTGTCATAGGTCCTCGAACTATTTC 59.022 44.000 0.00 0.00 39.24 2.17
1619 2711 5.421056 TGTGTCATAGGTCCTCGAACTATTT 59.579 40.000 0.00 0.00 39.24 1.40
1620 2712 4.954202 TGTGTCATAGGTCCTCGAACTATT 59.046 41.667 0.00 0.00 39.24 1.73
1621 2713 4.533815 TGTGTCATAGGTCCTCGAACTAT 58.466 43.478 0.00 0.00 42.55 2.12
1622 2714 3.959293 TGTGTCATAGGTCCTCGAACTA 58.041 45.455 0.00 0.00 36.22 2.24
1623 2715 2.803956 TGTGTCATAGGTCCTCGAACT 58.196 47.619 0.00 0.00 32.68 3.01
1624 2716 3.802948 ATGTGTCATAGGTCCTCGAAC 57.197 47.619 0.00 0.00 0.00 3.95
1625 2717 7.002276 TCTTATATGTGTCATAGGTCCTCGAA 58.998 38.462 0.00 0.00 0.00 3.71
1626 2718 6.540083 TCTTATATGTGTCATAGGTCCTCGA 58.460 40.000 0.00 0.00 0.00 4.04
1627 2719 6.819397 TCTTATATGTGTCATAGGTCCTCG 57.181 41.667 0.00 0.00 0.00 4.63
1628 2720 8.588290 AGATCTTATATGTGTCATAGGTCCTC 57.412 38.462 0.00 0.00 0.00 3.71
1629 2721 8.397957 AGAGATCTTATATGTGTCATAGGTCCT 58.602 37.037 0.00 0.00 0.00 3.85
1630 2722 8.465999 CAGAGATCTTATATGTGTCATAGGTCC 58.534 40.741 0.00 0.00 0.00 4.46
1631 2723 9.019656 ACAGAGATCTTATATGTGTCATAGGTC 57.980 37.037 0.00 0.00 0.00 3.85
1632 2724 8.948401 ACAGAGATCTTATATGTGTCATAGGT 57.052 34.615 0.00 0.00 0.00 3.08
1633 2725 9.241919 AGACAGAGATCTTATATGTGTCATAGG 57.758 37.037 12.48 0.00 44.36 2.57
1736 2828 0.888619 TGGGAAAACACACGTGCAAA 59.111 45.000 17.22 0.00 0.00 3.68
2072 3171 8.506168 AAAAGTGATAGGAATTCGCTATTTCA 57.494 30.769 14.09 9.13 33.72 2.69
2161 3369 1.632920 TGCACCTACACCATGGAATCA 59.367 47.619 21.47 0.00 0.00 2.57
2238 3448 3.522343 ACTGTTATTCCTCCCCCTTGTAC 59.478 47.826 0.00 0.00 0.00 2.90
2345 3555 4.498009 CGTGCATGACTTTCTTTTCACCTT 60.498 41.667 0.00 0.00 0.00 3.50
2346 3556 3.003689 CGTGCATGACTTTCTTTTCACCT 59.996 43.478 0.00 0.00 0.00 4.00
2347 3557 3.243068 ACGTGCATGACTTTCTTTTCACC 60.243 43.478 14.17 0.00 0.00 4.02
2348 3558 3.952535 ACGTGCATGACTTTCTTTTCAC 58.047 40.909 14.17 0.00 0.00 3.18
2369 3579 7.759489 ACTTCTCTACCAATTTTTGCATGTA 57.241 32.000 0.00 0.00 0.00 2.29
2372 3582 8.635765 TCTTACTTCTCTACCAATTTTTGCAT 57.364 30.769 0.00 0.00 0.00 3.96
2380 3590 9.877178 CACTAACAATCTTACTTCTCTACCAAT 57.123 33.333 0.00 0.00 0.00 3.16
2462 3678 4.023980 TCCGTGATGAAAGATCTGTACCT 58.976 43.478 0.00 0.00 0.00 3.08
2595 3812 7.488322 TGAACACAATTTTTCTAGTTCTTGGG 58.512 34.615 0.00 0.00 37.03 4.12
2603 3820 6.317789 TGAGGCTGAACACAATTTTTCTAG 57.682 37.500 0.00 0.00 0.00 2.43
2670 3887 2.093711 TGCAAGAGTGTATGCACCGTAT 60.094 45.455 10.59 0.00 46.87 3.06
2849 4072 7.166851 TCCCGTACCTAAATGTTAACATGAAA 58.833 34.615 21.46 9.28 36.56 2.69
2952 4234 5.700832 GGACATACTGTGTGAAGAATGACAA 59.299 40.000 11.67 0.00 42.36 3.18
2963 4246 4.574421 TGTGAACAAAGGACATACTGTGTG 59.426 41.667 2.78 2.78 42.36 3.82
3021 4306 9.237187 TGAATATGTTGCAACCTATTACTTTGA 57.763 29.630 28.83 9.53 32.34 2.69
3059 4344 8.602472 AATAGCCCAATGGTGTTAAATTAAGA 57.398 30.769 0.00 0.00 0.00 2.10
3110 4398 6.759497 AAGAGTAATATTTGGAGTGTTGCC 57.241 37.500 0.00 0.00 0.00 4.52
3957 5258 6.091034 GCTTCTTGTACACTAGTAAAGAAGGC 59.909 42.308 28.59 22.45 43.87 4.35
3962 5263 8.870879 GGTAATGCTTCTTGTACACTAGTAAAG 58.129 37.037 0.00 0.00 30.67 1.85
4077 5378 3.553828 TTCAAGAAGTCCTGGACGTTT 57.446 42.857 20.49 10.49 37.67 3.60
4155 5462 7.400439 ACACTACTATGAACTGTAGTACCTGA 58.600 38.462 5.63 0.00 45.01 3.86
4228 5540 3.576078 TTGAGTGTTGTCCTCCATTGT 57.424 42.857 0.00 0.00 0.00 2.71
4472 5791 1.901833 GGCCAATTGATTCACTTGGGT 59.098 47.619 27.49 0.00 42.14 4.51
4701 6020 7.071196 AGGAGTTATTGCTATTAGTGACCATCA 59.929 37.037 0.00 0.00 0.00 3.07
4774 6093 2.384828 TCATCTACGGCTAAGCTTGGA 58.615 47.619 14.82 0.00 0.00 3.53
4789 6108 0.532573 ACGTGAAGCGGTCATCATCT 59.467 50.000 0.00 0.00 46.52 2.90
4807 6126 3.493503 CGAGGTTTGTAGAGTTGTTCCAC 59.506 47.826 0.00 0.00 0.00 4.02
4891 6211 3.431922 TCTCGTTCGTAATGGATCACC 57.568 47.619 0.00 0.00 0.00 4.02
4938 6258 2.738846 CACGCCATCTAGATGCAATACC 59.261 50.000 24.81 8.77 37.49 2.73
4982 6303 9.430623 GTGTTCTTAGAGAAGAGCTAAATTTCT 57.569 33.333 0.00 0.00 42.66 2.52
5051 6377 9.053472 TCTCCCTTTAATCATTTACTACCTTGA 57.947 33.333 0.00 0.00 0.00 3.02
5085 6414 8.556213 AACCGCTGAAGTAAATCTTATGTTTA 57.444 30.769 0.00 0.00 36.40 2.01
5104 6433 1.644786 GCGCCAACAATCTAACCGCT 61.645 55.000 0.00 0.00 37.27 5.52
5233 6563 7.817418 TGAGATAATAAAAGCGCCCTTTATT 57.183 32.000 27.43 27.43 40.30 1.40
5374 6707 5.416326 GGTCTATATGACTCTATTGTCGCCT 59.584 44.000 0.00 0.00 44.74 5.52
5436 6769 1.475034 GGGTGGCAGCATAATCTTCGA 60.475 52.381 19.48 0.00 0.00 3.71
5439 6772 2.313317 CATGGGTGGCAGCATAATCTT 58.687 47.619 19.48 0.00 0.00 2.40
5464 6797 2.574824 AGGTGGCTACGGAGGTTTTTAT 59.425 45.455 0.00 0.00 0.00 1.40
5500 6833 4.847255 GCTGTTCAATGCGGTGTC 57.153 55.556 0.00 0.00 0.00 3.67
5508 6841 2.423577 GAGTACCAACCGCTGTTCAAT 58.576 47.619 0.00 0.00 30.42 2.57
5531 6864 4.465632 ACATGGTCTATGCTACAACGAA 57.534 40.909 0.00 0.00 40.59 3.85
5542 6875 4.440250 GCACTCACTTCGTACATGGTCTAT 60.440 45.833 0.00 0.00 0.00 1.98
5559 6892 1.937278 TTTTCCGTTGTACGCACTCA 58.063 45.000 0.00 0.00 40.91 3.41
5585 6918 8.203485 TCAATAACAAAAATGCTTCTCCTTTGT 58.797 29.630 0.00 0.00 40.87 2.83
5825 7159 6.449635 AGAAGTGTTGTTTTTGCACTCATA 57.550 33.333 0.00 0.00 41.94 2.15


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

AutoCloner maintained by Alex Coulton.