Multiple sequence alignment - TraesCS5A01G109800

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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 TraesCS5A01G109800 chr5A 100.000 2339 0 0 1 2339 205827561 205825223 0.000000e+00 4320.0
1 TraesCS5A01G109800 chr5A 85.921 554 63 11 4 543 293475308 293474756 5.600000e-161 577.0
2 TraesCS5A01G109800 chr5A 87.356 87 11 0 1927 2013 292797680 292797594 1.480000e-17 100.0
3 TraesCS5A01G109800 chr5D 92.184 1177 89 3 1163 2339 150271039 150272212 0.000000e+00 1661.0
4 TraesCS5A01G109800 chr5D 90.017 1182 97 13 1 1167 150265876 150267051 0.000000e+00 1509.0
5 TraesCS5A01G109800 chr5D 83.622 635 81 14 4 618 399130666 399130035 2.020000e-160 575.0
6 TraesCS5A01G109800 chr5D 84.426 488 71 5 883 1367 135093288 135093773 2.100000e-130 475.0
7 TraesCS5A01G109800 chr5D 76.172 256 42 14 1772 2015 256189159 256188911 1.470000e-22 117.0
8 TraesCS5A01G109800 chr5D 74.453 274 43 21 1437 1698 320320677 320320419 2.470000e-15 93.5
9 TraesCS5A01G109800 chr5D 87.692 65 5 3 1495 1558 281695183 281695121 3.220000e-09 73.1
10 TraesCS5A01G109800 chr2D 85.072 623 76 12 4 614 474483688 474484305 9.180000e-174 619.0
11 TraesCS5A01G109800 chr2D 83.937 635 81 13 4 620 311691753 311692384 2.590000e-164 588.0
12 TraesCS5A01G109800 chr2D 81.684 677 91 21 6 655 288619741 288619071 1.230000e-147 532.0
13 TraesCS5A01G109800 chr2D 76.700 691 103 24 1364 2014 588433492 588432820 4.820000e-87 331.0
14 TraesCS5A01G109800 chr2D 85.408 233 28 5 644 872 474484487 474484717 1.080000e-58 237.0
15 TraesCS5A01G109800 chr2D 86.559 186 21 4 471 654 508353556 508353373 3.940000e-48 202.0
16 TraesCS5A01G109800 chr2D 80.645 248 34 11 1402 1648 485592147 485591913 1.850000e-41 180.0
17 TraesCS5A01G109800 chr2D 79.839 248 36 11 1402 1648 485635350 485635116 4.000000e-38 169.0
18 TraesCS5A01G109800 chr2D 77.432 257 45 13 1768 2020 73961601 73961848 8.710000e-30 141.0
19 TraesCS5A01G109800 chr2D 89.189 74 7 1 1943 2015 596149950 596149877 8.900000e-15 91.6
20 TraesCS5A01G109800 chr3D 84.360 633 84 5 1 621 180146868 180147497 7.150000e-170 606.0
21 TraesCS5A01G109800 chr3D 84.094 635 84 6 1 621 180186878 180186247 4.300000e-167 597.0
22 TraesCS5A01G109800 chr3D 83.683 619 78 15 4 601 404176098 404175482 1.570000e-156 562.0
23 TraesCS5A01G109800 chr3D 83.617 470 71 2 883 1352 414911139 414911602 9.920000e-119 436.0
24 TraesCS5A01G109800 chr3D 82.569 436 72 3 878 1312 88434109 88433677 4.720000e-102 381.0
25 TraesCS5A01G109800 chr3D 84.188 234 27 9 644 872 180147685 180147913 3.910000e-53 219.0
26 TraesCS5A01G109800 chr3D 83.761 234 28 9 644 872 180186059 180185831 1.820000e-51 213.0
27 TraesCS5A01G109800 chr3D 80.345 290 45 12 1364 1646 14380715 14380999 2.360000e-50 209.0
28 TraesCS5A01G109800 chr2A 83.159 671 88 18 6 656 348121932 348121267 7.200000e-165 590.0
29 TraesCS5A01G109800 chr7A 84.375 608 77 12 29 620 123119000 123119605 4.330000e-162 580.0
30 TraesCS5A01G109800 chr7A 83.142 611 86 12 4 601 86476674 86476068 2.040000e-150 542.0
31 TraesCS5A01G109800 chr7A 81.804 632 92 16 4 620 66762618 66761995 2.070000e-140 508.0
32 TraesCS5A01G109800 chr7A 80.795 453 83 4 878 1327 241371499 241371048 3.700000e-93 351.0
33 TraesCS5A01G109800 chr7A 76.023 342 71 10 1364 1698 517571366 517571703 1.440000e-37 167.0
34 TraesCS5A01G109800 chr6D 79.970 674 103 20 1364 2019 277734398 277735057 3.520000e-128 468.0
35 TraesCS5A01G109800 chr6D 77.888 502 86 17 1364 1848 86893206 86893699 2.940000e-74 289.0
36 TraesCS5A01G109800 chr6D 80.000 275 42 12 1436 1703 334211400 334211668 8.530000e-45 191.0
37 TraesCS5A01G109800 chr7B 79.529 679 113 18 1361 2018 704252953 704252280 5.890000e-126 460.0
38 TraesCS5A01G109800 chr3A 85.581 430 52 6 929 1358 595920104 595920523 2.130000e-120 442.0
39 TraesCS5A01G109800 chr4A 83.019 477 67 12 151 623 534764006 534763540 1.000000e-113 420.0
40 TraesCS5A01G109800 chr4A 78.571 686 100 34 1364 2015 599463662 599464334 2.160000e-110 409.0
41 TraesCS5A01G109800 chr4A 80.471 297 48 10 1364 1651 408938488 408938193 3.910000e-53 219.0
42 TraesCS5A01G109800 chr4A 77.557 352 59 13 1364 1703 704938449 704938106 6.600000e-46 195.0
43 TraesCS5A01G109800 chr4A 76.771 353 63 13 1364 1703 705100564 705100218 1.850000e-41 180.0
44 TraesCS5A01G109800 chr6B 78.647 665 100 23 1379 2019 439590657 439591303 1.010000e-108 403.0
45 TraesCS5A01G109800 chr6B 78.112 466 77 18 1364 1810 164640035 164640494 2.960000e-69 272.0
46 TraesCS5A01G109800 chr6B 83.761 234 30 7 644 872 574817851 574818081 5.060000e-52 215.0
47 TraesCS5A01G109800 chr6B 83.125 160 22 5 1399 1555 274722375 274722532 8.710000e-30 141.0
48 TraesCS5A01G109800 chr1D 81.212 495 69 12 873 1366 182636834 182637305 6.100000e-101 377.0
49 TraesCS5A01G109800 chr1D 79.942 344 57 10 1364 1699 400788488 400788149 2.320000e-60 243.0
50 TraesCS5A01G109800 chr1D 77.551 245 44 11 1418 1655 354442402 354442642 1.130000e-28 137.0
51 TraesCS5A01G109800 chr1D 89.041 73 8 0 1943 2015 199562647 199562575 8.900000e-15 91.6
52 TraesCS5A01G109800 chr1D 83.133 83 13 1 1929 2011 457780286 457780367 8.960000e-10 75.0
53 TraesCS5A01G109800 chr3B 80.913 482 85 6 872 1353 137852721 137852247 7.890000e-100 374.0
54 TraesCS5A01G109800 chr3B 82.057 418 69 5 885 1300 390215571 390215984 3.700000e-93 351.0
55 TraesCS5A01G109800 chr4D 80.204 490 94 3 878 1366 208370534 208370047 4.750000e-97 364.0
56 TraesCS5A01G109800 chr4D 79.429 175 33 3 1529 1703 15816814 15816643 1.140000e-23 121.0
57 TraesCS5A01G109800 chr4D 88.889 63 3 4 1495 1554 238608972 238608911 8.960000e-10 75.0
58 TraesCS5A01G109800 chr2B 76.912 693 99 25 1364 2014 711865231 711864558 1.040000e-88 337.0
59 TraesCS5A01G109800 chr2B 83.039 283 40 8 1381 1658 762359778 762360057 1.390000e-62 250.0
60 TraesCS5A01G109800 chr2B 85.345 232 29 5 644 872 525154095 525154324 3.890000e-58 235.0
61 TraesCS5A01G109800 chr2B 75.340 588 88 31 1452 2013 298232907 298233463 1.810000e-56 230.0
62 TraesCS5A01G109800 chr2B 78.187 353 58 15 1361 1704 724689876 724689534 8.470000e-50 207.0
63 TraesCS5A01G109800 chr2B 88.000 75 6 3 1943 2015 724689274 724689201 4.140000e-13 86.1
64 TraesCS5A01G109800 chr5B 83.226 310 46 6 1364 1668 308996099 308995791 1.770000e-71 279.0
65 TraesCS5A01G109800 chr5B 85.153 229 31 2 644 870 214851590 214851817 5.030000e-57 231.0
66 TraesCS5A01G109800 chr5B 85.268 224 29 3 653 872 423926767 423926544 6.500000e-56 228.0
67 TraesCS5A01G109800 chr7D 80.233 344 58 9 1364 1702 156781889 156781551 1.390000e-62 250.0
68 TraesCS5A01G109800 chr7D 80.126 317 48 11 1362 1675 595737023 595736719 3.030000e-54 222.0
69 TraesCS5A01G109800 chr7D 83.889 180 27 2 471 649 422214686 422214508 1.110000e-38 171.0
70 TraesCS5A01G109800 chr7D 82.645 121 19 2 1439 1557 244461420 244461300 3.180000e-19 106.0
71 TraesCS5A01G109800 chr4B 84.615 234 27 8 644 872 142720202 142720431 8.410000e-55 224.0
72 TraesCS5A01G109800 chr1B 76.453 344 67 13 1364 1698 476012368 476012706 8.590000e-40 174.0
73 TraesCS5A01G109800 chr1B 84.762 105 13 2 1913 2015 419988128 419988231 4.110000e-18 102.0
74 TraesCS5A01G109800 chr1B 96.774 31 1 0 1588 1618 67646357 67646387 4.000000e-03 52.8
75 TraesCS5A01G109800 chr6A 82.051 195 31 4 1364 1555 193452442 193452635 1.860000e-36 163.0
76 TraesCS5A01G109800 chr1A 75.988 329 63 14 1379 1698 453845180 453845501 3.110000e-34 156.0
77 TraesCS5A01G109800 chr1A 86.842 76 6 4 1943 2015 497079648 497079574 5.360000e-12 82.4


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 TraesCS5A01G109800 chr5A 205825223 205827561 2338 True 4320.0 4320 100.0000 1 2339 1 chr5A.!!$R1 2338
1 TraesCS5A01G109800 chr5A 293474756 293475308 552 True 577.0 577 85.9210 4 543 1 chr5A.!!$R3 539
2 TraesCS5A01G109800 chr5D 150265876 150272212 6336 False 1585.0 1661 91.1005 1 2339 2 chr5D.!!$F2 2338
3 TraesCS5A01G109800 chr5D 399130035 399130666 631 True 575.0 575 83.6220 4 618 1 chr5D.!!$R4 614
4 TraesCS5A01G109800 chr2D 311691753 311692384 631 False 588.0 588 83.9370 4 620 1 chr2D.!!$F2 616
5 TraesCS5A01G109800 chr2D 288619071 288619741 670 True 532.0 532 81.6840 6 655 1 chr2D.!!$R1 649
6 TraesCS5A01G109800 chr2D 474483688 474484717 1029 False 428.0 619 85.2400 4 872 2 chr2D.!!$F3 868
7 TraesCS5A01G109800 chr2D 588432820 588433492 672 True 331.0 331 76.7000 1364 2014 1 chr2D.!!$R5 650
8 TraesCS5A01G109800 chr3D 404175482 404176098 616 True 562.0 562 83.6830 4 601 1 chr3D.!!$R2 597
9 TraesCS5A01G109800 chr3D 180146868 180147913 1045 False 412.5 606 84.2740 1 872 2 chr3D.!!$F3 871
10 TraesCS5A01G109800 chr3D 180185831 180186878 1047 True 405.0 597 83.9275 1 872 2 chr3D.!!$R3 871
11 TraesCS5A01G109800 chr2A 348121267 348121932 665 True 590.0 590 83.1590 6 656 1 chr2A.!!$R1 650
12 TraesCS5A01G109800 chr7A 123119000 123119605 605 False 580.0 580 84.3750 29 620 1 chr7A.!!$F1 591
13 TraesCS5A01G109800 chr7A 86476068 86476674 606 True 542.0 542 83.1420 4 601 1 chr7A.!!$R2 597
14 TraesCS5A01G109800 chr7A 66761995 66762618 623 True 508.0 508 81.8040 4 620 1 chr7A.!!$R1 616
15 TraesCS5A01G109800 chr6D 277734398 277735057 659 False 468.0 468 79.9700 1364 2019 1 chr6D.!!$F2 655
16 TraesCS5A01G109800 chr7B 704252280 704252953 673 True 460.0 460 79.5290 1361 2018 1 chr7B.!!$R1 657
17 TraesCS5A01G109800 chr4A 599463662 599464334 672 False 409.0 409 78.5710 1364 2015 1 chr4A.!!$F1 651
18 TraesCS5A01G109800 chr6B 439590657 439591303 646 False 403.0 403 78.6470 1379 2019 1 chr6B.!!$F3 640
19 TraesCS5A01G109800 chr2B 711864558 711865231 673 True 337.0 337 76.9120 1364 2014 1 chr2B.!!$R1 650
20 TraesCS5A01G109800 chr2B 298232907 298233463 556 False 230.0 230 75.3400 1452 2013 1 chr2B.!!$F1 561

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
924 1140 0.601311 GTCTGCTAAGGGGCATAGCG 60.601 60.0 10.33 6.67 46.93 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2149 6442 0.685097 GGTCACTACCAAGCTCCACA 59.315 55.0 0.0 0.0 45.98 4.17 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
51 53 4.603131 ACCACTATCCAACATGCATCTTT 58.397 39.130 0.00 0.00 0.00 2.52
163 172 7.539366 CCCATTGTTTTACCATTAGTAACAACG 59.461 37.037 0.00 0.00 40.70 4.10
301 316 8.827177 AGTTAGATAGATCAGAGAGAAGTACG 57.173 38.462 0.00 0.00 0.00 3.67
318 333 7.553334 AGAAGTACGAGGCTATAAAATCACAA 58.447 34.615 0.00 0.00 0.00 3.33
409 426 1.407936 TCCCAACAAACACACCATGG 58.592 50.000 11.19 11.19 0.00 3.66
416 433 5.279910 CCAACAAACACACCATGGGAATTAT 60.280 40.000 18.09 0.00 0.00 1.28
452 469 7.681679 TCTCCGAAGAGATGAGTATACTACAT 58.318 38.462 5.09 10.86 44.42 2.29
521 563 5.066117 GGAACTACTCACACGTCATCATAGA 59.934 44.000 0.00 0.00 0.00 1.98
522 564 5.743026 ACTACTCACACGTCATCATAGAG 57.257 43.478 0.00 0.00 0.00 2.43
523 565 4.576873 ACTACTCACACGTCATCATAGAGG 59.423 45.833 0.00 0.00 0.00 3.69
524 566 3.357203 ACTCACACGTCATCATAGAGGT 58.643 45.455 0.00 0.00 37.12 3.85
548 595 3.696051 GCAAGGTTGATGAAGATTGCCTA 59.304 43.478 3.50 0.00 37.62 3.93
562 609 0.780637 TGCCTACCCAATGGTTTCCA 59.219 50.000 0.00 0.00 44.75 3.53
578 625 4.031611 GTTTCCACCTCCCATAGAGTACT 58.968 47.826 0.00 0.00 41.47 2.73
626 673 5.690464 AGAAGAACAGAGGCTTATGACAT 57.310 39.130 0.00 0.00 0.00 3.06
628 675 7.187824 AGAAGAACAGAGGCTTATGACATTA 57.812 36.000 0.00 0.00 0.00 1.90
641 853 9.508567 GGCTTATGACATTAGAAGAATTGTTTC 57.491 33.333 5.64 0.00 0.00 2.78
642 854 9.508567 GCTTATGACATTAGAAGAATTGTTTCC 57.491 33.333 5.64 0.00 31.84 3.13
651 863 4.530946 AGAAGAATTGTTTCCGGTCTCCTA 59.469 41.667 0.00 0.00 31.84 2.94
661 873 1.323412 CGGTCTCCTATGGTCCAGAG 58.677 60.000 6.53 6.53 0.00 3.35
671 883 4.080356 CCTATGGTCCAGAGAAAATCACCA 60.080 45.833 15.38 0.00 36.31 4.17
675 887 6.078456 TGGTCCAGAGAAAATCACCATAAT 57.922 37.500 0.00 0.00 29.00 1.28
713 925 4.459337 GGACTTCCTTTGGTATGGTTTCTG 59.541 45.833 0.00 0.00 0.00 3.02
909 1125 3.349927 TGCTTCCTTTGATCATGGTCTG 58.650 45.455 7.64 0.00 0.00 3.51
924 1140 0.601311 GTCTGCTAAGGGGCATAGCG 60.601 60.000 10.33 6.67 46.93 4.26
925 1141 1.302033 CTGCTAAGGGGCATAGCGG 60.302 63.158 9.62 9.62 46.93 5.52
957 1173 7.161773 TCTCATGGATGACAAAGGAAATTTC 57.838 36.000 9.83 9.83 32.50 2.17
959 1175 7.233144 TCTCATGGATGACAAAGGAAATTTCAA 59.767 33.333 19.49 0.00 32.50 2.69
979 1195 0.965439 TGTTGGCGGAAATTGGAAGG 59.035 50.000 0.00 0.00 0.00 3.46
992 1208 5.391312 AATTGGAAGGTAGATTGTTGTGC 57.609 39.130 0.00 0.00 0.00 4.57
998 1214 2.027192 AGGTAGATTGTTGTGCGGATGT 60.027 45.455 0.00 0.00 0.00 3.06
1000 1216 3.936453 GGTAGATTGTTGTGCGGATGTTA 59.064 43.478 0.00 0.00 0.00 2.41
1011 1227 1.940613 GCGGATGTTATGACAAGGGAC 59.059 52.381 0.00 0.00 39.66 4.46
1032 1248 2.303175 GTGTTGGTGCTTAGGTTTGGA 58.697 47.619 0.00 0.00 0.00 3.53
1063 1279 1.345415 CACAAAAGGCAGGCTCCAATT 59.655 47.619 0.00 0.00 0.00 2.32
1069 1285 1.034292 GGCAGGCTCCAATTGTCTCC 61.034 60.000 4.43 2.07 0.00 3.71
1099 1315 4.422073 TCTGACAACATGGAAGTCACTT 57.578 40.909 11.54 0.00 37.36 3.16
1113 1329 6.183360 TGGAAGTCACTTACACAATGAACAAC 60.183 38.462 0.00 0.00 28.11 3.32
1119 1335 5.007234 CACTTACACAATGAACAACGAAGGA 59.993 40.000 0.00 0.00 0.00 3.36
1120 1336 3.963383 ACACAATGAACAACGAAGGAC 57.037 42.857 0.00 0.00 0.00 3.85
1124 1340 4.911610 CACAATGAACAACGAAGGACATTC 59.088 41.667 0.00 0.00 34.31 2.67
1196 5404 7.741785 TGTGATTTTCCTCTTACTAGGTTTGA 58.258 34.615 0.00 0.00 37.91 2.69
1214 5422 6.152831 AGGTTTGAACATTGTAATAGGGAAGC 59.847 38.462 0.00 0.00 0.00 3.86
1251 5459 2.829720 TGAGCTCGCTAGGTTAGGAAAA 59.170 45.455 9.64 0.00 32.30 2.29
1252 5460 3.259876 TGAGCTCGCTAGGTTAGGAAAAA 59.740 43.478 9.64 0.00 32.30 1.94
1307 5515 6.719829 CCTATGGGAAATATTGTACCCTTTCC 59.280 42.308 19.50 13.22 43.79 3.13
1330 5538 8.821686 TCCTATTGATGATGTAACCATTGTTT 57.178 30.769 0.00 0.00 35.87 2.83
1331 5539 8.902806 TCCTATTGATGATGTAACCATTGTTTC 58.097 33.333 0.00 0.00 35.87 2.78
1449 5658 3.358111 TGAACACAGGGTGAAGACAAA 57.642 42.857 2.98 0.00 36.96 2.83
1487 5742 9.448438 TTCATGTCACTACTTAATGCAATACTT 57.552 29.630 0.00 0.00 0.00 2.24
1523 5778 8.929260 AATACTTTGAGATGCATGATGGATAA 57.071 30.769 2.46 0.00 0.00 1.75
1527 5782 4.648651 TGAGATGCATGATGGATAACTGG 58.351 43.478 2.46 0.00 0.00 4.00
1629 5889 8.741603 TTATGCCATGGATAATCATACTCATG 57.258 34.615 18.40 0.00 33.78 3.07
1675 5935 6.257630 GCCAAACTGTAATTTGTTCAACACAT 59.742 34.615 0.00 0.00 37.79 3.21
1787 6074 5.657745 TGTTGCAATCAAATCCTCCATACAT 59.342 36.000 0.59 0.00 33.37 2.29
1840 6127 3.526534 GCTAGTGAGATTGACAACCTCC 58.473 50.000 7.11 0.00 0.00 4.30
1876 6165 4.546570 GGACACAAGGACATTTAGTTTGC 58.453 43.478 0.00 0.00 0.00 3.68
2029 6322 7.186021 TGAGAGGAAGAAATTACGTTTTGTC 57.814 36.000 0.00 0.00 0.00 3.18
2030 6323 6.764085 TGAGAGGAAGAAATTACGTTTTGTCA 59.236 34.615 0.00 0.00 0.00 3.58
2048 6341 7.624360 TTTGTCAATATGTGGTACCTTCATC 57.376 36.000 20.51 10.77 0.00 2.92
2079 6372 7.760794 TCATTTTCATATGTTCAATGCAGAACC 59.239 33.333 14.29 0.61 45.62 3.62
2133 6426 7.582719 AGGGCAAATAGGTTATGTCAGATAAA 58.417 34.615 0.00 0.00 0.00 1.40
2147 6440 1.282157 AGATAAAGAAGGGCAAGGCGT 59.718 47.619 0.00 0.00 0.00 5.68
2149 6442 1.989706 TAAAGAAGGGCAAGGCGTTT 58.010 45.000 3.11 0.00 0.00 3.60
2158 6451 2.032981 CAAGGCGTTTGTGGAGCTT 58.967 52.632 0.00 0.00 31.92 3.74
2160 6453 1.455383 AAGGCGTTTGTGGAGCTTGG 61.455 55.000 0.00 0.00 0.00 3.61
2166 6459 2.805295 CGTTTGTGGAGCTTGGTAGTGA 60.805 50.000 0.00 0.00 0.00 3.41
2190 6483 4.902448 CCCTAAGAGGCCTAAGAACTACAT 59.098 45.833 4.42 0.00 32.73 2.29
2200 6493 5.297029 GCCTAAGAACTACATCCATTTCCAC 59.703 44.000 0.00 0.00 0.00 4.02
2201 6494 6.414732 CCTAAGAACTACATCCATTTCCACA 58.585 40.000 0.00 0.00 0.00 4.17
2214 6507 4.396166 CCATTTCCACAAGTGCTACCTAAG 59.604 45.833 0.00 0.00 0.00 2.18
2234 6527 9.268282 ACCTAAGACTCTGGTTTATTCTATTCA 57.732 33.333 0.00 0.00 0.00 2.57
2265 6558 9.672086 GTTAGTTTAAGACATTTGCATTGTACA 57.328 29.630 3.03 0.00 0.00 2.90
2282 6575 9.893305 GCATTGTACAGTTAGTTTAAGACATTT 57.107 29.630 0.00 0.00 0.00 2.32
2295 6588 9.816354 AGTTTAAGACATTTATGCAAGTGTTTT 57.184 25.926 0.00 0.00 35.00 2.43
2322 6615 5.360144 TGTTCCTATGACTGCTACCTAAGAC 59.640 44.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
163 172 4.095610 GTTGCAAGGCACGTATTTGTATC 58.904 43.478 0.00 0.00 38.71 2.24
278 292 8.092068 CCTCGTACTTCTCTCTGATCTATCTAA 58.908 40.741 0.00 0.00 0.00 2.10
376 393 6.041865 TGTTTGTTGGGATCTGATGAATTGTT 59.958 34.615 0.00 0.00 0.00 2.83
452 469 5.602561 AGCAGTACTCTCTCTCTCTCTGATA 59.397 44.000 0.00 0.00 0.00 2.15
511 553 4.946478 ACCTTGCTACCTCTATGATGAC 57.054 45.455 0.00 0.00 0.00 3.06
521 563 4.851639 ATCTTCATCAACCTTGCTACCT 57.148 40.909 0.00 0.00 0.00 3.08
522 564 4.439289 GCAATCTTCATCAACCTTGCTACC 60.439 45.833 0.00 0.00 36.83 3.18
523 565 4.439289 GGCAATCTTCATCAACCTTGCTAC 60.439 45.833 5.22 0.00 39.08 3.58
524 566 3.696051 GGCAATCTTCATCAACCTTGCTA 59.304 43.478 5.22 0.00 39.08 3.49
562 609 2.224818 CCGCTAGTACTCTATGGGAGGT 60.225 54.545 0.00 0.00 45.83 3.85
626 673 5.012768 AGGAGACCGGAAACAATTCTTCTAA 59.987 40.000 9.46 0.00 35.79 2.10
628 675 3.328050 AGGAGACCGGAAACAATTCTTCT 59.672 43.478 9.46 0.00 35.79 2.85
641 853 0.106167 TCTGGACCATAGGAGACCGG 60.106 60.000 0.00 0.00 0.00 5.28
642 854 1.133761 TCTCTGGACCATAGGAGACCG 60.134 57.143 7.64 0.00 31.02 4.79
651 863 4.598036 ATGGTGATTTTCTCTGGACCAT 57.402 40.909 0.00 0.00 38.98 3.55
671 883 9.657419 GGAAGTCCAAACATGATGAAAAATTAT 57.343 29.630 0.00 0.00 35.64 1.28
675 887 6.729690 AGGAAGTCCAAACATGATGAAAAA 57.270 33.333 0.00 0.00 38.89 1.94
742 955 4.407365 ACTTAGTGCCTAGTGCCATTTTT 58.593 39.130 1.42 0.00 40.16 1.94
746 959 4.837093 TTAACTTAGTGCCTAGTGCCAT 57.163 40.909 0.00 0.00 40.16 4.40
795 1008 2.164827 TCTTGCATGCTTTATGTGCCAG 59.835 45.455 20.33 0.00 39.08 4.85
865 1081 5.482163 TCCACACTCAACTCAATGATACA 57.518 39.130 0.00 0.00 0.00 2.29
909 1125 2.032681 CCCGCTATGCCCCTTAGC 59.967 66.667 0.00 0.00 38.94 3.09
924 1140 3.181451 TGTCATCCATGAGAATAGCACCC 60.181 47.826 0.00 0.00 37.51 4.61
925 1141 4.077300 TGTCATCCATGAGAATAGCACC 57.923 45.455 0.00 0.00 37.51 5.01
957 1173 2.739885 TCCAATTTCCGCCAACATTG 57.260 45.000 0.00 0.00 0.00 2.82
959 1175 1.550072 CCTTCCAATTTCCGCCAACAT 59.450 47.619 0.00 0.00 0.00 2.71
979 1195 5.293324 TCATAACATCCGCACAACAATCTAC 59.707 40.000 0.00 0.00 0.00 2.59
992 1208 2.201732 CGTCCCTTGTCATAACATCCG 58.798 52.381 0.00 0.00 34.73 4.18
998 1214 2.105134 ACCAACACGTCCCTTGTCATAA 59.895 45.455 0.00 0.00 0.00 1.90
1000 1216 0.472471 ACCAACACGTCCCTTGTCAT 59.528 50.000 0.00 0.00 0.00 3.06
1011 1227 1.001815 CCAAACCTAAGCACCAACACG 60.002 52.381 0.00 0.00 0.00 4.49
1019 1235 4.142182 GCAGCAATAATCCAAACCTAAGCA 60.142 41.667 0.00 0.00 0.00 3.91
1020 1236 4.363138 GCAGCAATAATCCAAACCTAAGC 58.637 43.478 0.00 0.00 0.00 3.09
1058 1274 7.824289 TGTCAGAATTACTAAGGAGACAATTGG 59.176 37.037 10.83 0.00 32.46 3.16
1063 1279 7.297936 TGTTGTCAGAATTACTAAGGAGACA 57.702 36.000 0.00 0.00 33.44 3.41
1069 1285 8.553459 ACTTCCATGTTGTCAGAATTACTAAG 57.447 34.615 0.00 0.00 0.00 2.18
1099 1315 4.443621 TGTCCTTCGTTGTTCATTGTGTA 58.556 39.130 0.00 0.00 0.00 2.90
1113 1329 1.649664 CTCCTGCAGAATGTCCTTCG 58.350 55.000 17.39 0.00 38.98 3.79
1119 1335 2.437359 GCCGCTCCTGCAGAATGT 60.437 61.111 17.39 0.00 39.31 2.71
1120 1336 3.570638 CGCCGCTCCTGCAGAATG 61.571 66.667 17.39 5.73 39.64 2.67
1251 5459 3.973305 ACCAATCCCTTGTCACCAAATTT 59.027 39.130 0.00 0.00 0.00 1.82
1252 5460 3.586429 ACCAATCCCTTGTCACCAAATT 58.414 40.909 0.00 0.00 0.00 1.82
1253 5461 3.258722 ACCAATCCCTTGTCACCAAAT 57.741 42.857 0.00 0.00 0.00 2.32
1523 5778 0.550147 ATACTCCACCCCAAGCCAGT 60.550 55.000 0.00 0.00 0.00 4.00
1527 5782 1.490910 AGCTAATACTCCACCCCAAGC 59.509 52.381 0.00 0.00 0.00 4.01
1675 5935 9.063615 GGTTTCTCTCCAAAAAGATAGTAACAA 57.936 33.333 0.00 0.00 28.29 2.83
1759 6046 4.773674 TGGAGGATTTGATTGCAACAAGAT 59.226 37.500 0.00 5.47 32.79 2.40
1787 6074 3.088532 ACAAAGGAACTGAAAGCACACA 58.911 40.909 0.00 0.00 40.86 3.72
1840 6127 4.324267 CTTGTGTCCCCAACTAAACTAGG 58.676 47.826 0.00 0.00 0.00 3.02
1907 6196 4.257267 TCGTATCCATGAGATTTGCGAT 57.743 40.909 0.00 0.00 36.33 4.58
2015 6308 9.615295 GTACCACATATTGACAAAACGTAATTT 57.385 29.630 0.00 0.00 0.00 1.82
2029 6322 4.750098 GGTCGATGAAGGTACCACATATTG 59.250 45.833 15.94 11.85 32.04 1.90
2030 6323 4.654262 AGGTCGATGAAGGTACCACATATT 59.346 41.667 15.94 0.00 34.29 1.28
2048 6341 6.415867 GCATTGAACATATGAAAATGAGGTCG 59.584 38.462 22.40 6.27 31.34 4.79
2079 6372 0.893270 TTCCCCGAGGCAACATTGTG 60.893 55.000 0.00 0.00 41.41 3.33
2116 6409 6.385759 TGCCCTTCTTTATCTGACATAACCTA 59.614 38.462 0.00 0.00 0.00 3.08
2118 6411 5.437060 TGCCCTTCTTTATCTGACATAACC 58.563 41.667 0.00 0.00 0.00 2.85
2133 6426 1.152756 ACAAACGCCTTGCCCTTCT 60.153 52.632 0.00 0.00 38.75 2.85
2147 6440 2.486548 GGTCACTACCAAGCTCCACAAA 60.487 50.000 0.00 0.00 45.98 2.83
2149 6442 0.685097 GGTCACTACCAAGCTCCACA 59.315 55.000 0.00 0.00 45.98 4.17
2160 6453 2.162264 AGGCCTCTTAGGGTCACTAC 57.838 55.000 0.00 0.00 35.37 2.73
2166 6459 3.493475 AGTTCTTAGGCCTCTTAGGGT 57.507 47.619 9.68 0.00 35.37 4.34
2190 6483 2.375174 AGGTAGCACTTGTGGAAATGGA 59.625 45.455 2.81 0.00 0.00 3.41
2200 6493 3.511934 ACCAGAGTCTTAGGTAGCACTTG 59.488 47.826 0.26 0.00 32.92 3.16
2201 6494 3.780626 ACCAGAGTCTTAGGTAGCACTT 58.219 45.455 0.26 0.00 32.92 3.16
2214 6507 9.167311 ACAACATGAATAGAATAAACCAGAGTC 57.833 33.333 0.00 0.00 0.00 3.36
2233 6526 8.572828 TGCAAATGTCTTAAACTAACAACATG 57.427 30.769 0.00 0.00 0.00 3.21
2234 6527 9.762933 AATGCAAATGTCTTAAACTAACAACAT 57.237 25.926 0.00 0.00 0.00 2.71
2247 6540 7.510549 ACTAACTGTACAATGCAAATGTCTT 57.489 32.000 11.34 3.63 32.27 3.01
2294 6587 5.876357 AGGTAGCAGTCATAGGAACAAAAA 58.124 37.500 0.00 0.00 0.00 1.94
2295 6588 5.499004 AGGTAGCAGTCATAGGAACAAAA 57.501 39.130 0.00 0.00 0.00 2.44
2305 6598 6.008696 ACTAGAGTCTTAGGTAGCAGTCAT 57.991 41.667 0.00 0.00 0.00 3.06
2309 6602 7.013846 AGCATAAACTAGAGTCTTAGGTAGCAG 59.986 40.741 0.00 0.00 0.00 4.24


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

AutoCloner maintained by Alex Coulton.