Multiple sequence alignment - TraesCS3D01G442900

Loading Multiple Alignment...

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 TraesCS3D01G442900 chr3D 100.000 3385 0 0 1 3385 552718538 552715154 0.000000e+00 6252.0
1 TraesCS3D01G442900 chr3D 90.931 419 28 9 2946 3362 552574280 552573870 3.820000e-154 555.0
2 TraesCS3D01G442900 chr3D 83.079 656 58 21 2737 3385 552618065 552617456 6.390000e-152 547.0
3 TraesCS3D01G442900 chr3D 82.848 653 65 24 2737 3385 552611710 552611101 2.970000e-150 542.0
4 TraesCS3D01G442900 chr3D 82.219 658 71 23 2746 3385 552630872 552630243 2.990000e-145 525.0
5 TraesCS3D01G442900 chr3D 84.868 304 32 8 3089 3385 552577657 552577361 9.190000e-76 294.0
6 TraesCS3D01G442900 chr3D 81.361 338 33 18 2737 3061 552578261 552577941 7.250000e-62 248.0
7 TraesCS3D01G442900 chr3D 78.409 176 24 7 3215 3385 552436856 552436690 5.980000e-18 102.0
8 TraesCS3D01G442900 chr4A 90.950 1116 88 3 1 1105 479384261 479383148 0.000000e+00 1489.0
9 TraesCS3D01G442900 chr4A 90.303 330 29 3 1513 1841 353109765 353109438 2.410000e-116 429.0
10 TraesCS3D01G442900 chr4A 80.426 235 44 2 563 796 593458574 593458807 9.650000e-41 178.0
11 TraesCS3D01G442900 chr4A 86.486 111 15 0 210 320 102388516 102388406 4.590000e-24 122.0
12 TraesCS3D01G442900 chr5D 88.686 1096 102 13 751 1841 298136469 298137547 0.000000e+00 1317.0
13 TraesCS3D01G442900 chr5D 87.740 677 82 1 26 702 298135710 298136385 0.000000e+00 789.0
14 TraesCS3D01G442900 chr5D 79.600 250 47 4 550 798 85136194 85136440 3.470000e-40 176.0
15 TraesCS3D01G442900 chr6D 88.588 885 63 16 1859 2733 336836189 336835333 0.000000e+00 1040.0
16 TraesCS3D01G442900 chr6D 84.539 304 40 6 1120 1419 255101611 255101311 9.190000e-76 294.0
17 TraesCS3D01G442900 chr3A 90.701 785 62 6 1840 2613 46216246 46215462 0.000000e+00 1035.0
18 TraesCS3D01G442900 chr3A 88.359 524 45 11 2865 3382 688988775 688988262 1.730000e-172 616.0
19 TraesCS3D01G442900 chr3A 89.351 385 35 5 2746 3130 688980680 688980302 2.360000e-131 479.0
20 TraesCS3D01G442900 chr3A 87.833 263 22 6 3126 3385 688980144 688979889 1.970000e-77 300.0
21 TraesCS3D01G442900 chr3A 77.841 176 25 7 3215 3385 688918080 688917914 2.780000e-16 97.1
22 TraesCS3D01G442900 chr6B 87.583 902 75 16 1859 2733 42818912 42818021 0.000000e+00 1011.0
23 TraesCS3D01G442900 chr6B 86.000 850 97 11 982 1827 101740966 101740135 0.000000e+00 891.0
24 TraesCS3D01G442900 chr6B 86.545 825 90 11 1922 2733 101740109 101739293 0.000000e+00 889.0
25 TraesCS3D01G442900 chr6B 80.417 240 45 2 560 798 19599817 19599579 7.460000e-42 182.0
26 TraesCS3D01G442900 chr6B 80.417 240 45 2 560 798 19636413 19636175 7.460000e-42 182.0
27 TraesCS3D01G442900 chr6B 80.426 235 44 2 562 795 700100360 700100593 9.650000e-41 178.0
28 TraesCS3D01G442900 chr2A 86.971 875 95 11 1872 2733 197558817 197559685 0.000000e+00 966.0
29 TraesCS3D01G442900 chr2A 84.740 865 97 15 982 1841 197557986 197558820 0.000000e+00 833.0
30 TraesCS3D01G442900 chr2A 83.565 791 86 17 1054 1841 59741505 59742254 0.000000e+00 701.0
31 TraesCS3D01G442900 chr2A 90.083 484 40 6 2251 2733 398762872 398762396 3.710000e-174 621.0
32 TraesCS3D01G442900 chr2A 83.333 690 85 19 2067 2733 4026282 4026964 8.030000e-171 610.0
33 TraesCS3D01G442900 chr2A 89.050 484 45 6 2251 2733 398503916 398503440 8.090000e-166 593.0
34 TraesCS3D01G442900 chr2A 88.592 412 38 5 1875 2277 59742253 59742664 3.030000e-135 492.0
35 TraesCS3D01G442900 chr2A 86.237 465 49 9 611 1075 4025725 4026174 1.090000e-134 490.0
36 TraesCS3D01G442900 chr2A 88.182 110 13 0 210 319 753468307 753468198 7.620000e-27 132.0
37 TraesCS3D01G442900 chr5A 86.667 900 77 13 1856 2733 601238330 601239208 0.000000e+00 957.0
38 TraesCS3D01G442900 chr5A 84.971 865 96 15 982 1841 671546492 671547327 0.000000e+00 846.0
39 TraesCS3D01G442900 chr5A 89.300 486 40 9 2252 2736 54761067 54761541 1.740000e-167 599.0
40 TraesCS3D01G442900 chr5A 85.806 465 51 7 611 1075 11950610 11951059 2.360000e-131 479.0
41 TraesCS3D01G442900 chr5A 77.758 571 78 24 1130 1696 450225363 450224838 4.240000e-79 305.0
42 TraesCS3D01G442900 chr5A 80.936 299 43 11 1134 1424 602964266 602963974 1.220000e-54 224.0
43 TraesCS3D01G442900 chr5A 85.586 111 16 0 210 320 552595966 552596076 2.130000e-22 117.0
44 TraesCS3D01G442900 chr6A 87.161 849 77 15 1911 2733 599216509 599215667 0.000000e+00 935.0
45 TraesCS3D01G442900 chr6A 83.056 301 43 7 1120 1416 329910660 329910956 2.000000e-67 267.0
46 TraesCS3D01G442900 chr6A 87.387 111 14 0 210 320 467050242 467050132 9.860000e-26 128.0
47 TraesCS3D01G442900 chr2B 85.218 893 70 22 1856 2733 789011469 789012314 0.000000e+00 861.0
48 TraesCS3D01G442900 chr1D 82.993 1029 90 36 1729 2733 421660371 421661338 0.000000e+00 852.0
49 TraesCS3D01G442900 chr1D 86.348 564 73 4 1 563 328835680 328835120 2.230000e-171 612.0
50 TraesCS3D01G442900 chr1D 90.672 268 22 3 1507 1773 421660105 421660370 1.490000e-93 353.0
51 TraesCS3D01G442900 chr3B 88.333 660 46 18 2737 3385 733000113 732999474 0.000000e+00 763.0
52 TraesCS3D01G442900 chr3B 86.469 606 59 8 2784 3380 733005075 733004484 0.000000e+00 643.0
53 TraesCS3D01G442900 chr3B 89.135 497 40 7 2737 3232 733268038 733267555 1.040000e-169 606.0
54 TraesCS3D01G442900 chr3B 83.817 655 58 19 2737 3382 733219304 733218689 2.260000e-161 579.0
55 TraesCS3D01G442900 chr3B 83.013 624 66 18 2737 3359 733327994 733327410 2.310000e-146 529.0
56 TraesCS3D01G442900 chr3B 87.069 464 60 0 611 1074 738292583 738292120 2.990000e-145 525.0
57 TraesCS3D01G442900 chr3B 83.666 551 75 7 2067 2609 738292048 738291505 3.900000e-139 505.0
58 TraesCS3D01G442900 chr7D 90.807 533 38 6 2067 2589 58188934 58188403 0.000000e+00 702.0
59 TraesCS3D01G442900 chr7D 92.453 318 21 2 324 639 58189329 58189013 5.150000e-123 451.0
60 TraesCS3D01G442900 chr7D 89.231 325 22 3 14 325 58192949 58192625 8.800000e-106 394.0
61 TraesCS3D01G442900 chr7D 80.478 251 44 5 550 798 243296055 243295808 1.600000e-43 187.0
62 TraesCS3D01G442900 chr2D 88.069 461 45 7 2276 2734 612961230 612961682 3.840000e-149 538.0
63 TraesCS3D01G442900 chr2D 82.412 597 88 4 907 1486 463919955 463920551 3.900000e-139 505.0
64 TraesCS3D01G442900 chr1A 81.926 592 85 8 907 1489 9752177 9751599 6.570000e-132 481.0
65 TraesCS3D01G442900 chr7A 90.909 330 27 3 1513 1841 269088314 269087987 1.110000e-119 440.0
66 TraesCS3D01G442900 chr1B 82.844 443 53 8 633 1073 20207028 20207449 3.190000e-100 375.0


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 TraesCS3D01G442900 chr3D 552715154 552718538 3384 True 6252.000000 6252 100.000000 1 3385 1 chr3D.!!$R5 3384
1 TraesCS3D01G442900 chr3D 552617456 552618065 609 True 547.000000 547 83.079000 2737 3385 1 chr3D.!!$R3 648
2 TraesCS3D01G442900 chr3D 552611101 552611710 609 True 542.000000 542 82.848000 2737 3385 1 chr3D.!!$R2 648
3 TraesCS3D01G442900 chr3D 552630243 552630872 629 True 525.000000 525 82.219000 2746 3385 1 chr3D.!!$R4 639
4 TraesCS3D01G442900 chr3D 552573870 552578261 4391 True 365.666667 555 85.720000 2737 3385 3 chr3D.!!$R6 648
5 TraesCS3D01G442900 chr4A 479383148 479384261 1113 True 1489.000000 1489 90.950000 1 1105 1 chr4A.!!$R3 1104
6 TraesCS3D01G442900 chr5D 298135710 298137547 1837 False 1053.000000 1317 88.213000 26 1841 2 chr5D.!!$F2 1815
7 TraesCS3D01G442900 chr6D 336835333 336836189 856 True 1040.000000 1040 88.588000 1859 2733 1 chr6D.!!$R2 874
8 TraesCS3D01G442900 chr3A 46215462 46216246 784 True 1035.000000 1035 90.701000 1840 2613 1 chr3A.!!$R1 773
9 TraesCS3D01G442900 chr3A 688988262 688988775 513 True 616.000000 616 88.359000 2865 3382 1 chr3A.!!$R3 517
10 TraesCS3D01G442900 chr3A 688979889 688980680 791 True 389.500000 479 88.592000 2746 3385 2 chr3A.!!$R4 639
11 TraesCS3D01G442900 chr6B 42818021 42818912 891 True 1011.000000 1011 87.583000 1859 2733 1 chr6B.!!$R3 874
12 TraesCS3D01G442900 chr6B 101739293 101740966 1673 True 890.000000 891 86.272500 982 2733 2 chr6B.!!$R4 1751
13 TraesCS3D01G442900 chr2A 197557986 197559685 1699 False 899.500000 966 85.855500 982 2733 2 chr2A.!!$F3 1751
14 TraesCS3D01G442900 chr2A 59741505 59742664 1159 False 596.500000 701 86.078500 1054 2277 2 chr2A.!!$F2 1223
15 TraesCS3D01G442900 chr2A 4025725 4026964 1239 False 550.000000 610 84.785000 611 2733 2 chr2A.!!$F1 2122
16 TraesCS3D01G442900 chr5A 601238330 601239208 878 False 957.000000 957 86.667000 1856 2733 1 chr5A.!!$F4 877
17 TraesCS3D01G442900 chr5A 671546492 671547327 835 False 846.000000 846 84.971000 982 1841 1 chr5A.!!$F5 859
18 TraesCS3D01G442900 chr5A 450224838 450225363 525 True 305.000000 305 77.758000 1130 1696 1 chr5A.!!$R1 566
19 TraesCS3D01G442900 chr6A 599215667 599216509 842 True 935.000000 935 87.161000 1911 2733 1 chr6A.!!$R2 822
20 TraesCS3D01G442900 chr2B 789011469 789012314 845 False 861.000000 861 85.218000 1856 2733 1 chr2B.!!$F1 877
21 TraesCS3D01G442900 chr1D 328835120 328835680 560 True 612.000000 612 86.348000 1 563 1 chr1D.!!$R1 562
22 TraesCS3D01G442900 chr1D 421660105 421661338 1233 False 602.500000 852 86.832500 1507 2733 2 chr1D.!!$F1 1226
23 TraesCS3D01G442900 chr3B 732999474 733000113 639 True 763.000000 763 88.333000 2737 3385 1 chr3B.!!$R1 648
24 TraesCS3D01G442900 chr3B 733004484 733005075 591 True 643.000000 643 86.469000 2784 3380 1 chr3B.!!$R2 596
25 TraesCS3D01G442900 chr3B 733218689 733219304 615 True 579.000000 579 83.817000 2737 3382 1 chr3B.!!$R3 645
26 TraesCS3D01G442900 chr3B 733327410 733327994 584 True 529.000000 529 83.013000 2737 3359 1 chr3B.!!$R5 622
27 TraesCS3D01G442900 chr3B 738291505 738292583 1078 True 515.000000 525 85.367500 611 2609 2 chr3B.!!$R6 1998
28 TraesCS3D01G442900 chr7D 58188403 58192949 4546 True 515.666667 702 90.830333 14 2589 3 chr7D.!!$R2 2575
29 TraesCS3D01G442900 chr2D 463919955 463920551 596 False 505.000000 505 82.412000 907 1486 1 chr2D.!!$F1 579
30 TraesCS3D01G442900 chr1A 9751599 9752177 578 True 481.000000 481 81.926000 907 1489 1 chr1A.!!$R1 582

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
24 25 0.800631 CCCGCTTTCCGTTTTACTCC 59.199 55.000 0.00 0.0 34.38 3.85 F
958 4355 1.490490 TGGTGAGCTTGAAGACCACTT 59.510 47.619 13.99 0.0 39.24 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1063 4461 0.179124 TGGTTTGGCAAACGTCTTGC 60.179 50.0 30.45 18.83 42.29 4.01 R
2838 6489 0.031616 ACAGACAGGGAGGGGATCTC 60.032 60.0 0.00 0.00 41.71 2.75 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
24 25 0.800631 CCCGCTTTCCGTTTTACTCC 59.199 55.000 0.00 0.00 34.38 3.85
73 74 2.054021 TGTTTCACCATCTCCAGTGGA 58.946 47.619 12.40 12.40 39.12 4.02
157 158 5.541953 ATGAGCAGCAAGAGTACATCATA 57.458 39.130 0.00 0.00 0.00 2.15
161 162 2.797156 CAGCAAGAGTACATCATACGCC 59.203 50.000 0.00 0.00 0.00 5.68
181 184 4.588278 GCCGTGAGCACATAACTTATTTC 58.412 43.478 1.20 0.00 42.97 2.17
231 234 3.820467 CTCACAGCTTCATAACCAACCAA 59.180 43.478 0.00 0.00 0.00 3.67
403 3715 8.755018 CAATGTTTGTTTCCTTTTGTAGTCATC 58.245 33.333 0.00 0.00 0.00 2.92
404 3716 7.639113 TGTTTGTTTCCTTTTGTAGTCATCT 57.361 32.000 0.00 0.00 0.00 2.90
427 3739 2.188062 TCAGCATGTCAGACAATGCA 57.812 45.000 26.39 13.31 36.10 3.96
430 3742 2.082231 AGCATGTCAGACAATGCAGAC 58.918 47.619 26.39 0.00 36.10 3.51
473 3785 7.602644 TCGTTTGTGCTTTCTCTATTCTACAAT 59.397 33.333 0.00 0.00 0.00 2.71
606 3921 2.654896 AGGCTACCCTCCCAAAATTCTT 59.345 45.455 0.00 0.00 36.46 2.52
693 4008 1.629043 AGCCGACCTTTGTCACTCTA 58.371 50.000 0.00 0.00 41.85 2.43
718 4104 1.571460 CACACGAGCAAGTTCCAGC 59.429 57.895 0.00 0.00 0.00 4.85
958 4355 1.490490 TGGTGAGCTTGAAGACCACTT 59.510 47.619 13.99 0.00 39.24 3.16
1048 4446 3.883830 AGAGCCAGACATCAAGTACTG 57.116 47.619 0.00 0.00 0.00 2.74
1049 4447 3.435275 AGAGCCAGACATCAAGTACTGA 58.565 45.455 0.00 0.00 38.81 3.41
1112 4588 6.772233 AGTATATGGTATGCTCAAATGCACAA 59.228 34.615 0.00 0.00 46.33 3.33
1118 4594 4.644103 ATGCTCAAATGCACAACCTATC 57.356 40.909 0.00 0.00 46.33 2.08
1218 4710 9.645059 TTAACAGAAAACATGTTGATTGTTTCA 57.355 25.926 26.20 17.02 44.32 2.69
1238 4730 8.462811 TGTTTCAAACTGAGTATTTGTGCTTTA 58.537 29.630 1.10 0.00 38.08 1.85
1239 4731 9.463443 GTTTCAAACTGAGTATTTGTGCTTTAT 57.537 29.630 0.00 0.00 38.08 1.40
1240 4732 9.677567 TTTCAAACTGAGTATTTGTGCTTTATC 57.322 29.630 0.00 0.00 38.08 1.75
1286 4778 0.324552 TGCTTTAGTGCCATGCCCAT 60.325 50.000 0.00 0.00 0.00 4.00
1287 4779 0.103572 GCTTTAGTGCCATGCCCATG 59.896 55.000 1.28 1.28 38.51 3.66
1306 4798 5.163488 CCCATGCTGTATGTGAAAATGACAT 60.163 40.000 5.04 0.00 37.75 3.06
1317 4820 7.887996 TGTGAAAATGACATATTTGCTTTCC 57.112 32.000 5.86 0.56 0.00 3.13
1318 4821 7.669427 TGTGAAAATGACATATTTGCTTTCCT 58.331 30.769 5.86 0.00 0.00 3.36
1319 4822 8.801299 TGTGAAAATGACATATTTGCTTTCCTA 58.199 29.630 5.86 0.00 0.00 2.94
1320 4823 9.076596 GTGAAAATGACATATTTGCTTTCCTAC 57.923 33.333 5.86 0.00 0.00 3.18
1321 4824 7.967854 TGAAAATGACATATTTGCTTTCCTACG 59.032 33.333 5.86 0.00 0.00 3.51
1322 4825 7.391148 AAATGACATATTTGCTTTCCTACGT 57.609 32.000 0.00 0.00 0.00 3.57
1323 4826 6.604735 ATGACATATTTGCTTTCCTACGTC 57.395 37.500 0.00 0.00 0.00 4.34
1324 4827 5.730550 TGACATATTTGCTTTCCTACGTCT 58.269 37.500 0.00 0.00 0.00 4.18
1325 4828 5.810587 TGACATATTTGCTTTCCTACGTCTC 59.189 40.000 0.00 0.00 0.00 3.36
1326 4829 5.978814 ACATATTTGCTTTCCTACGTCTCT 58.021 37.500 0.00 0.00 0.00 3.10
1327 4830 6.407202 ACATATTTGCTTTCCTACGTCTCTT 58.593 36.000 0.00 0.00 0.00 2.85
1472 4978 2.613390 GACCATTCGATTACCCGCC 58.387 57.895 0.00 0.00 0.00 6.13
1518 5024 4.887748 TCCTCTACTGCTTCACTCTTTTG 58.112 43.478 0.00 0.00 0.00 2.44
1548 5054 6.095440 GCTTCACCAGCCATTTTAGAGAATAA 59.905 38.462 0.00 0.00 43.65 1.40
1555 5061 7.707893 CCAGCCATTTTAGAGAATAAACAATGG 59.292 37.037 0.00 0.00 0.00 3.16
1619 5126 4.454161 TGTGATGATACAAACGAAGGTTGG 59.546 41.667 2.77 0.00 36.25 3.77
1626 5133 2.616842 ACAAACGAAGGTTGGCTTACAG 59.383 45.455 2.77 0.00 36.25 2.74
1721 5229 4.815269 ACAGTCAGCAGTTTAGTCATCTC 58.185 43.478 0.00 0.00 0.00 2.75
1770 5322 8.628630 TCTCACTGTATACCAGATAGATCAAG 57.371 38.462 0.00 0.00 44.49 3.02
1805 5357 5.841810 TGTTATTTTTCTCCTGCCACTTTG 58.158 37.500 0.00 0.00 0.00 2.77
1809 5361 2.276732 TTCTCCTGCCACTTTGGAAG 57.723 50.000 0.00 0.00 43.22 3.46
1810 5362 1.140312 TCTCCTGCCACTTTGGAAGT 58.860 50.000 0.00 0.00 41.94 3.01
1913 5469 4.158579 TCTCTGCTCATACACTAGGTTGTG 59.841 45.833 0.00 0.00 43.07 3.33
1950 5506 6.127647 TGTCAATTGGAGACCAGAAATATTGC 60.128 38.462 5.42 0.00 33.81 3.56
1963 5522 6.810182 CCAGAAATATTGCCTTCTCTTTGTTG 59.190 38.462 0.00 0.00 29.29 3.33
1977 5536 6.003326 TCTCTTTGTTGTTTCATCAGCCATA 58.997 36.000 0.00 0.00 0.00 2.74
2115 5676 8.203485 ACACAACAATTTCTGTCCATGTAAATT 58.797 29.630 0.00 0.00 37.23 1.82
2145 5706 6.569179 TTTCTTGTACCAGTATTTTCAGGC 57.431 37.500 0.00 0.00 0.00 4.85
2170 5742 1.896465 AGAGAACCTGCTGGACTACAC 59.104 52.381 17.64 4.17 37.04 2.90
2172 5744 3.090037 GAGAACCTGCTGGACTACACTA 58.910 50.000 17.64 0.00 37.04 2.74
2298 5879 1.227409 TCTGAGTTTTGTCGCCGCA 60.227 52.632 0.00 0.00 0.00 5.69
2405 5986 2.346766 TGCACCATTGAAGACACTGT 57.653 45.000 0.00 0.00 0.00 3.55
2551 6169 7.921786 TGCTTATGTAAAGTGCACTATTCTT 57.078 32.000 22.01 13.28 0.00 2.52
2639 6283 8.639428 GCTGCTAAGTTTCTTAATTAAAGCAAC 58.361 33.333 15.59 10.11 40.41 4.17
2652 6296 0.185901 AAGCAACCATCCCACACACT 59.814 50.000 0.00 0.00 0.00 3.55
2706 6350 1.116536 TCGACTACAACCAGGCACCA 61.117 55.000 0.00 0.00 0.00 4.17
2778 6427 9.476202 CGATGAGGTGTCATATTCTGTTTATTA 57.524 33.333 0.00 0.00 43.92 0.98
2838 6489 0.037882 TCAGCAAGCTCACCTTCTCG 60.038 55.000 0.00 0.00 0.00 4.04
2849 6500 0.105913 ACCTTCTCGAGATCCCCTCC 60.106 60.000 17.44 0.00 38.71 4.30
2868 6519 4.040461 CCTCCCTGTCTGTCTCTTGTAAAA 59.960 45.833 0.00 0.00 0.00 1.52
2899 6565 7.819644 AGTAGTGTATCACATACGTACAAACA 58.180 34.615 0.00 0.00 38.59 2.83
2907 6574 5.966503 TCACATACGTACAAACAGTTTTTGC 59.033 36.000 0.00 0.00 32.93 3.68
2922 6589 5.927689 CAGTTTTTGCATGCTATCTCCAAAA 59.072 36.000 20.33 12.04 34.65 2.44
3023 6691 2.096220 AGAGTTGCTGATCTGCACAG 57.904 50.000 24.94 0.07 43.20 3.66
3056 6726 0.905809 ATGGCATGCCCTTGCTTTGA 60.906 50.000 33.44 12.32 42.38 2.69
3076 10525 0.323302 TTAACACTGCATCTCCGGCA 59.677 50.000 0.00 0.00 39.32 5.69
3114 10565 5.441718 TCTTCTCAGTTGGGCTAATCAAT 57.558 39.130 0.00 0.00 0.00 2.57
3365 11001 1.893137 AGCTACGTGGAGTGACATCAA 59.107 47.619 1.81 0.00 0.00 2.57
3369 11005 1.000955 ACGTGGAGTGACATCAAGGAC 59.999 52.381 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.800631 GGAGTAAAACGGAAAGCGGG 59.199 55.000 0.00 0.00 0.00 6.13
8 9 4.514066 TGAAAGAGGAGTAAAACGGAAAGC 59.486 41.667 0.00 0.00 0.00 3.51
122 123 3.766051 TGCTGCTCATTCTCTTCAGTCTA 59.234 43.478 0.00 0.00 0.00 2.59
157 158 0.320421 AAGTTATGTGCTCACGGCGT 60.320 50.000 6.77 6.77 45.43 5.68
161 162 7.298122 ACAAAGAAATAAGTTATGTGCTCACG 58.702 34.615 0.00 0.00 0.00 4.35
231 234 9.737427 CAGTCGATAAAGAAATACACTGATACT 57.263 33.333 0.00 0.00 33.30 2.12
403 3715 2.756840 TGTCTGACATGCTGAAGGAG 57.243 50.000 6.36 0.00 0.00 3.69
404 3716 3.340928 CATTGTCTGACATGCTGAAGGA 58.659 45.455 11.86 0.00 0.00 3.36
427 3739 4.141846 ACGATTGCATACAGATTCAGGTCT 60.142 41.667 0.00 0.00 0.00 3.85
430 3742 5.163723 ACAAACGATTGCATACAGATTCAGG 60.164 40.000 5.20 0.00 40.34 3.86
595 3910 2.403259 GTGAACGGCAAGAATTTTGGG 58.597 47.619 0.00 0.00 0.00 4.12
606 3921 1.739929 CACGCTATGGTGAACGGCA 60.740 57.895 0.00 0.00 40.38 5.69
693 4008 3.368116 GGAACTTGCTCGTGTGGTACTAT 60.368 47.826 0.00 0.00 0.00 2.12
718 4104 7.221452 CAGAATTTTGGTGAAGAAAACTGTGAG 59.779 37.037 0.00 0.00 0.00 3.51
788 4174 0.910088 AGGCTGGGTGTTAGGGTCTC 60.910 60.000 0.00 0.00 0.00 3.36
791 4177 0.118547 AGTAGGCTGGGTGTTAGGGT 59.881 55.000 0.00 0.00 0.00 4.34
829 4215 5.534654 TGTCATAGTTTGTTTGGGAAAGGAG 59.465 40.000 0.00 0.00 0.00 3.69
958 4355 4.566907 GCTTCACCTCATTACCCCAGTAAA 60.567 45.833 0.00 0.00 41.68 2.01
999 4397 5.717119 CCAAAACATAGCAAAGAGAGCATT 58.283 37.500 0.00 0.00 0.00 3.56
1048 4446 1.875514 TCTTGCTGATTGTGCACACTC 59.124 47.619 25.64 25.64 40.40 3.51
1049 4447 1.605710 GTCTTGCTGATTGTGCACACT 59.394 47.619 21.56 15.47 40.40 3.55
1063 4461 0.179124 TGGTTTGGCAAACGTCTTGC 60.179 50.000 30.45 18.83 42.29 4.01
1112 4588 9.396022 CATGAAGTTAGTAAACATTGGATAGGT 57.604 33.333 0.00 0.00 38.12 3.08
1214 4706 9.677567 GATAAAGCACAAATACTCAGTTTGAAA 57.322 29.630 5.69 0.00 38.51 2.69
1218 4710 8.409358 AAGGATAAAGCACAAATACTCAGTTT 57.591 30.769 0.00 0.00 0.00 2.66
1238 4730 8.164070 AGTAGTGGTGTTCAAAAGATAAAGGAT 58.836 33.333 0.00 0.00 0.00 3.24
1239 4731 7.514721 AGTAGTGGTGTTCAAAAGATAAAGGA 58.485 34.615 0.00 0.00 0.00 3.36
1240 4732 7.745620 AGTAGTGGTGTTCAAAAGATAAAGG 57.254 36.000 0.00 0.00 0.00 3.11
1286 4778 7.488792 GCAAATATGTCATTTTCACATACAGCA 59.511 33.333 0.00 0.00 39.09 4.41
1287 4779 7.703621 AGCAAATATGTCATTTTCACATACAGC 59.296 33.333 0.00 0.00 39.09 4.40
1306 4798 6.228258 ACAAAGAGACGTAGGAAAGCAAATA 58.772 36.000 0.00 0.00 0.00 1.40
1317 4820 3.587797 TGGGCTTACAAAGAGACGTAG 57.412 47.619 0.00 0.00 0.00 3.51
1318 4821 4.546829 ATTGGGCTTACAAAGAGACGTA 57.453 40.909 0.00 0.00 33.48 3.57
1319 4822 2.922740 TTGGGCTTACAAAGAGACGT 57.077 45.000 0.00 0.00 0.00 4.34
1320 4823 4.766404 AAATTGGGCTTACAAAGAGACG 57.234 40.909 0.00 0.00 33.48 4.18
1346 4851 1.351017 AGAGTGGGAAAGAATGCCGAA 59.649 47.619 0.00 0.00 43.91 4.30
1391 4896 8.524870 AATATTGCAAAAGTGAGTTCAATGAC 57.475 30.769 1.71 0.00 0.00 3.06
1441 4947 2.531206 GAATGGTCGACTACAGCAGAC 58.469 52.381 16.46 0.00 0.00 3.51
1500 5006 5.616424 GCACATCAAAAGAGTGAAGCAGTAG 60.616 44.000 0.00 0.00 35.33 2.57
1541 5047 9.994432 CATAAGAGAACACCATTGTTTATTCTC 57.006 33.333 4.06 4.06 46.43 2.87
1676 5184 8.185506 TGTTAGGTAGTATGAACAGAACAAGA 57.814 34.615 0.00 0.00 0.00 3.02
1696 5204 6.393990 AGATGACTAAACTGCTGACTGTTAG 58.606 40.000 0.00 0.00 37.00 2.34
1721 5229 8.531146 AGAAAGGGAACATAATTGGTATTTGTG 58.469 33.333 0.00 0.00 0.00 3.33
1770 5322 6.294010 GGAGAAAAATAACAACAGACCAGGTC 60.294 42.308 12.25 12.25 0.00 3.85
1896 5448 5.907207 AGTATGCACAACCTAGTGTATGAG 58.093 41.667 7.73 0.00 43.26 2.90
1913 5469 6.749118 GTCTCCAATTGACAATTTGAGTATGC 59.251 38.462 28.05 18.33 40.01 3.14
1936 5492 6.151817 ACAAAGAGAAGGCAATATTTCTGGTC 59.848 38.462 0.00 0.00 33.97 4.02
1950 5506 5.218139 GCTGATGAAACAACAAAGAGAAGG 58.782 41.667 0.00 0.00 0.00 3.46
1963 5522 6.038603 TGCTCAAGTAATATGGCTGATGAAAC 59.961 38.462 0.00 0.00 0.00 2.78
1977 5536 8.310122 ACCCAATTTATGAATGCTCAAGTAAT 57.690 30.769 0.00 0.00 34.49 1.89
2115 5676 8.685838 AAAATACTGGTACAAGAAAGCAAGTA 57.314 30.769 3.64 0.00 38.70 2.24
2145 5706 0.318441 TCCAGCAGGTTCTCTTCGTG 59.682 55.000 0.00 0.00 35.89 4.35
2170 5742 8.347771 CCATGAGTGTATCATTGTTTGGATTAG 58.652 37.037 0.00 0.00 46.97 1.73
2172 5744 6.664816 ACCATGAGTGTATCATTGTTTGGATT 59.335 34.615 0.00 0.00 46.97 3.01
2298 5879 2.104111 TGTCTCCTTCGTGAATGTTGGT 59.896 45.455 0.00 0.00 0.00 3.67
2405 5986 7.291416 TGCTAGATTATATTGACACAGGGGTTA 59.709 37.037 0.00 0.00 0.00 2.85
2468 6084 2.501316 GAGGGCCCAAAAGCAAACATAT 59.499 45.455 27.56 0.00 0.00 1.78
2551 6169 6.407412 GGATCTGAACATGAACCATCTGACTA 60.407 42.308 0.00 0.00 0.00 2.59
2639 6283 5.614324 TCTAATTAGAGTGTGTGGGATGG 57.386 43.478 11.24 0.00 0.00 3.51
2681 6325 1.749634 CCTGGTTGTAGTCGACCCTAG 59.250 57.143 13.01 6.18 45.19 3.02
2682 6326 1.843368 CCTGGTTGTAGTCGACCCTA 58.157 55.000 13.01 0.00 45.19 3.53
2683 6327 1.542187 GCCTGGTTGTAGTCGACCCT 61.542 60.000 13.01 0.00 45.19 4.34
2684 6328 1.079336 GCCTGGTTGTAGTCGACCC 60.079 63.158 13.01 6.38 45.19 4.46
2706 6350 2.612115 CTTGAGGGGGAGCTGGGT 60.612 66.667 0.00 0.00 0.00 4.51
2733 6378 4.655762 TCGATTGGATGAGAACTAGGTG 57.344 45.455 0.00 0.00 0.00 4.00
2778 6427 7.075851 TCTCTGCAAGATATGGAAATCAGAT 57.924 36.000 0.00 0.00 45.62 2.90
2779 6428 6.490241 TCTCTGCAAGATATGGAAATCAGA 57.510 37.500 0.00 0.00 45.62 3.27
2780 6429 7.563888 TTTCTCTGCAAGATATGGAAATCAG 57.436 36.000 0.00 0.00 45.62 2.90
2781 6430 6.039047 GCTTTCTCTGCAAGATATGGAAATCA 59.961 38.462 0.00 0.00 45.62 2.57
2782 6431 6.437094 GCTTTCTCTGCAAGATATGGAAATC 58.563 40.000 0.00 0.00 45.62 2.17
2838 6489 0.031616 ACAGACAGGGAGGGGATCTC 60.032 60.000 0.00 0.00 41.71 2.75
2875 6541 7.752239 ACTGTTTGTACGTATGTGATACACTAC 59.248 37.037 0.00 0.00 35.48 2.73
2895 6561 5.010922 TGGAGATAGCATGCAAAAACTGTTT 59.989 36.000 21.98 0.00 0.00 2.83
2899 6565 5.726980 TTTGGAGATAGCATGCAAAAACT 57.273 34.783 21.98 11.18 35.42 2.66
2907 6574 8.127327 CACAGTTAATCTTTTGGAGATAGCATG 58.873 37.037 0.00 0.00 44.41 4.06
2958 6625 3.408634 TCATTTGGACGGGAAACTTCTC 58.591 45.455 0.00 0.00 0.00 2.87
2965 6632 7.174253 GCATAAACTATATCATTTGGACGGGAA 59.826 37.037 0.00 0.00 0.00 3.97
3023 6691 2.196245 GCCATGAAATCGGGAGCCC 61.196 63.158 0.00 0.00 0.00 5.19
3056 6726 1.065491 TGCCGGAGATGCAGTGTTAAT 60.065 47.619 5.05 0.00 34.05 1.40
3087 10538 3.515602 AGCCCAACTGAGAAGAACAAT 57.484 42.857 0.00 0.00 0.00 2.71
3114 10565 9.585369 TGCATGGTTCTGAATATATTTATTGGA 57.415 29.630 0.00 0.00 0.00 3.53
3165 10780 8.408601 GCAGTTTGTGATGATGACCTAATTAAT 58.591 33.333 0.00 0.00 0.00 1.40
3267 10894 5.843673 TGGCAATTGACAGAGTAACAAAA 57.156 34.783 10.79 0.00 0.00 2.44
3317 10953 3.370978 CACGACCCACATCATGAACTAAC 59.629 47.826 0.00 0.00 0.00 2.34


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

AutoCloner maintained by Alex Coulton.