Multiple sequence alignment - TraesCS5D01G415200

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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 TraesCS5D01G415200 chr5D 100.000 5826 0 0 1 5826 477377002 477382827 0.000000e+00 10759.0
1 TraesCS5D01G415200 chr5D 91.566 664 43 2 5175 5826 536342779 536342117 0.000000e+00 904.0
2 TraesCS5D01G415200 chr5D 92.361 144 11 0 671 814 477377637 477377780 7.650000e-49 206.0
3 TraesCS5D01G415200 chr5D 92.361 144 11 0 636 779 477377672 477377815 7.650000e-49 206.0
4 TraesCS5D01G415200 chr5D 94.495 109 6 0 706 814 477377637 477377745 1.000000e-37 169.0
5 TraesCS5D01G415200 chr5D 94.495 109 6 0 636 744 477377707 477377815 1.000000e-37 169.0
6 TraesCS5D01G415200 chr5D 89.412 85 7 2 731 814 477377627 477377710 7.980000e-19 106.0
7 TraesCS5D01G415200 chr5D 89.412 85 7 2 626 709 477377732 477377815 7.980000e-19 106.0
8 TraesCS5D01G415200 chr5A 95.266 4478 148 13 706 5156 596564909 596569349 0.000000e+00 7036.0
9 TraesCS5D01G415200 chr5A 92.011 751 42 7 11 744 596564268 596565017 0.000000e+00 1038.0
10 TraesCS5D01G415200 chr5A 94.595 74 4 0 636 709 596564944 596565017 1.330000e-21 115.0
11 TraesCS5D01G415200 chr5B 95.988 2418 54 11 1169 3570 585005290 585007680 0.000000e+00 3888.0
12 TraesCS5D01G415200 chr5B 96.557 1394 45 3 3567 4958 585007996 585009388 0.000000e+00 2305.0
13 TraesCS5D01G415200 chr5B 89.840 748 38 16 11 744 585004154 585004877 0.000000e+00 926.0
14 TraesCS5D01G415200 chr5B 93.291 313 21 0 822 1134 585004978 585005290 4.110000e-126 462.0
15 TraesCS5D01G415200 chr5B 92.857 210 14 1 4947 5156 585009405 585009613 2.640000e-78 303.0
16 TraesCS5D01G415200 chr1B 78.849 2397 371 79 1014 3336 676151235 676148901 0.000000e+00 1493.0
17 TraesCS5D01G415200 chr1B 95.359 668 18 6 5171 5826 7180439 7181105 0.000000e+00 1050.0
18 TraesCS5D01G415200 chr1B 95.060 668 20 6 5171 5826 7140439 7141105 0.000000e+00 1038.0
19 TraesCS5D01G415200 chr1B 81.040 1366 200 27 2016 3364 676118986 676120309 0.000000e+00 1033.0
20 TraesCS5D01G415200 chr1B 78.947 722 106 24 859 1545 676118244 676118954 3.200000e-122 449.0
21 TraesCS5D01G415200 chr1B 73.253 744 151 34 2261 2975 676458540 676457816 1.630000e-55 228.0
22 TraesCS5D01G415200 chr1B 80.081 246 35 5 205 436 676161695 676161450 2.790000e-38 171.0
23 TraesCS5D01G415200 chr1B 89.744 78 6 1 3415 3490 676120458 676120535 1.340000e-16 99.0
24 TraesCS5D01G415200 chr1A 81.213 1501 217 33 1880 3363 583115843 583117295 0.000000e+00 1149.0
25 TraesCS5D01G415200 chr1A 80.791 1213 186 24 2128 3323 583130792 583129610 0.000000e+00 905.0
26 TraesCS5D01G415200 chr1A 76.585 1025 153 44 790 1760 583114324 583115315 3.160000e-132 483.0
27 TraesCS5D01G415200 chr1A 75.740 878 165 37 2006 2851 583297431 583296570 1.180000e-106 398.0
28 TraesCS5D01G415200 chr1A 79.930 573 76 22 1514 2077 583131435 583130893 9.160000e-103 385.0
29 TraesCS5D01G415200 chr1A 79.920 249 33 5 205 436 583132598 583132350 3.610000e-37 167.0
30 TraesCS5D01G415200 chr1A 80.822 219 33 7 3390 3606 583117297 583117508 4.670000e-36 163.0
31 TraesCS5D01G415200 chr1A 86.667 120 13 3 334 450 583299296 583299177 4.740000e-26 130.0
32 TraesCS5D01G415200 chr4A 91.717 664 26 3 5175 5826 689262024 689261378 0.000000e+00 894.0
33 TraesCS5D01G415200 chr4A 84.756 164 17 6 3030 3193 46639290 46639135 2.170000e-34 158.0
34 TraesCS5D01G415200 chr4A 84.536 97 14 1 3439 3535 46625581 46625486 1.730000e-15 95.3
35 TraesCS5D01G415200 chr4A 88.889 72 8 0 2778 2849 46639418 46639489 8.040000e-14 89.8
36 TraesCS5D01G415200 chr3B 88.404 664 62 8 5175 5825 762971783 762971122 0.000000e+00 785.0
37 TraesCS5D01G415200 chr3B 83.562 219 27 4 206 421 438112305 438112517 4.610000e-46 196.0
38 TraesCS5D01G415200 chr7B 87.068 665 72 9 5175 5825 153571393 153570729 0.000000e+00 739.0
39 TraesCS5D01G415200 chr7B 89.362 141 15 0 281 421 610529178 610529038 1.670000e-40 178.0
40 TraesCS5D01G415200 chr1D 87.478 567 70 1 5260 5825 435135778 435136344 0.000000e+00 652.0
41 TraesCS5D01G415200 chr1D 74.270 890 167 45 1986 2844 485712178 485711320 9.420000e-83 318.0
42 TraesCS5D01G415200 chr1D 86.047 129 14 4 325 450 485713701 485713574 1.020000e-27 135.0
43 TraesCS5D01G415200 chr2A 94.958 357 6 1 5177 5521 77235614 77235258 3.070000e-152 549.0
44 TraesCS5D01G415200 chr2A 95.455 286 5 1 5549 5826 77234890 77234605 3.200000e-122 449.0
45 TraesCS5D01G415200 chr2A 88.630 343 15 4 5175 5516 698143621 698143302 4.230000e-106 396.0
46 TraesCS5D01G415200 chr2A 79.412 408 64 15 3089 3493 93885625 93885235 2.680000e-68 270.0
47 TraesCS5D01G415200 chr6A 93.176 381 13 2 5176 5543 1941439 1941059 1.100000e-151 547.0
48 TraesCS5D01G415200 chr6A 93.860 342 8 5 5176 5504 592529583 592529242 2.420000e-138 503.0
49 TraesCS5D01G415200 chr6A 96.098 205 8 0 5622 5826 592528683 592528479 9.350000e-88 335.0
50 TraesCS5D01G415200 chr2B 80.210 763 117 19 4104 4855 712953146 712953885 5.140000e-150 542.0
51 TraesCS5D01G415200 chr2B 84.878 205 27 3 3842 4044 712911915 712912117 2.750000e-48 204.0
52 TraesCS5D01G415200 chr2B 86.525 141 16 3 281 421 756030677 756030540 1.010000e-32 152.0
53 TraesCS5D01G415200 chr7A 88.596 342 6 2 5173 5502 45919222 45918902 9.160000e-103 385.0
54 TraesCS5D01G415200 chr7A 78.589 397 65 9 3845 4224 498940890 498940497 1.620000e-60 244.0
55 TraesCS5D01G415200 chr4B 84.343 198 30 1 224 421 338331111 338331307 5.960000e-45 193.0
56 TraesCS5D01G415200 chr4B 89.916 119 11 1 286 404 670390325 670390442 1.010000e-32 152.0
57 TraesCS5D01G415200 chr4D 83.178 107 17 1 3429 3535 418208253 418208358 4.810000e-16 97.1


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 TraesCS5D01G415200 chr5D 477377002 477382827 5825 False 10759.000000 10759 100.000000 1 5826 1 chr5D.!!$F1 5825
1 TraesCS5D01G415200 chr5D 536342117 536342779 662 True 904.000000 904 91.566000 5175 5826 1 chr5D.!!$R1 651
2 TraesCS5D01G415200 chr5A 596564268 596569349 5081 False 4037.000000 7036 93.638500 11 5156 2 chr5A.!!$F2 5145
3 TraesCS5D01G415200 chr5B 585004154 585009613 5459 False 1576.800000 3888 93.706600 11 5156 5 chr5B.!!$F1 5145
4 TraesCS5D01G415200 chr1B 676148901 676151235 2334 True 1493.000000 1493 78.849000 1014 3336 1 chr1B.!!$R1 2322
5 TraesCS5D01G415200 chr1B 7180439 7181105 666 False 1050.000000 1050 95.359000 5171 5826 1 chr1B.!!$F2 655
6 TraesCS5D01G415200 chr1B 7140439 7141105 666 False 1038.000000 1038 95.060000 5171 5826 1 chr1B.!!$F1 655
7 TraesCS5D01G415200 chr1B 676118244 676120535 2291 False 527.000000 1033 83.243667 859 3490 3 chr1B.!!$F3 2631
8 TraesCS5D01G415200 chr1B 676457816 676458540 724 True 228.000000 228 73.253000 2261 2975 1 chr1B.!!$R3 714
9 TraesCS5D01G415200 chr1A 583114324 583117508 3184 False 598.333333 1149 79.540000 790 3606 3 chr1A.!!$F1 2816
10 TraesCS5D01G415200 chr1A 583129610 583132598 2988 True 485.666667 905 80.213667 205 3323 3 chr1A.!!$R1 3118
11 TraesCS5D01G415200 chr1A 583296570 583299296 2726 True 264.000000 398 81.203500 334 2851 2 chr1A.!!$R2 2517
12 TraesCS5D01G415200 chr4A 689261378 689262024 646 True 894.000000 894 91.717000 5175 5826 1 chr4A.!!$R3 651
13 TraesCS5D01G415200 chr3B 762971122 762971783 661 True 785.000000 785 88.404000 5175 5825 1 chr3B.!!$R1 650
14 TraesCS5D01G415200 chr7B 153570729 153571393 664 True 739.000000 739 87.068000 5175 5825 1 chr7B.!!$R1 650
15 TraesCS5D01G415200 chr1D 435135778 435136344 566 False 652.000000 652 87.478000 5260 5825 1 chr1D.!!$F1 565
16 TraesCS5D01G415200 chr1D 485711320 485713701 2381 True 226.500000 318 80.158500 325 2844 2 chr1D.!!$R1 2519
17 TraesCS5D01G415200 chr2A 77234605 77235614 1009 True 499.000000 549 95.206500 5177 5826 2 chr2A.!!$R3 649
18 TraesCS5D01G415200 chr6A 592528479 592529583 1104 True 419.000000 503 94.979000 5176 5826 2 chr6A.!!$R2 650
19 TraesCS5D01G415200 chr2B 712953146 712953885 739 False 542.000000 542 80.210000 4104 4855 1 chr2B.!!$F2 751

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
776 1425 0.039618 AATGTCCCCTTCCGCAATGT 59.960 50.000 0.00 0.00 0.00 2.71 F
778 1427 0.693622 TGTCCCCTTCCGCAATGTAA 59.306 50.000 0.00 0.00 0.00 2.41 F
780 1429 1.065709 GTCCCCTTCCGCAATGTAAGA 60.066 52.381 0.00 0.00 0.00 2.10 F
1819 2731 0.317770 ATTGCACCGCGAAAACTGTG 60.318 50.000 8.23 7.18 0.00 3.66 F
2938 4347 0.392336 GGGCACATCAGTTTGGCAAA 59.608 50.000 8.93 8.93 40.00 3.68 F
3916 5660 0.811616 CGCTTGGTCCTAGCATGGTC 60.812 60.000 22.68 0.00 38.55 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1792 2704 2.823196 TCGCGGTGCAATTGAAATAG 57.177 45.000 10.34 0.0 0.00 1.73 R
1819 2731 6.961359 AAAACACCAAAAGAACAAGCTTAC 57.039 33.333 0.00 0.0 0.00 2.34 R
2506 3889 9.793259 TTACCTTGTGAAGAAGTCTGAATAATT 57.207 29.630 0.00 0.0 0.00 1.40 R
3323 4741 1.546476 ACAGAGGTAAACAGGAGAGCG 59.454 52.381 0.00 0.0 0.00 5.03 R
3970 5714 1.070134 GGATGGCAATGAGCAATGCAT 59.930 47.619 8.35 0.0 43.94 3.96 R
5007 6785 0.178967 TCAGCAAATGCCCTCCACAA 60.179 50.000 0.94 0.0 43.38 3.33 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
23 24 3.304659 CGGAATTTTGATTATCGGGGCTG 60.305 47.826 0.00 0.00 0.00 4.85
28 29 1.199615 TGATTATCGGGGCTGTGTCA 58.800 50.000 0.00 0.00 0.00 3.58
149 151 0.745128 AAAAACCTCACCGCGACACA 60.745 50.000 8.23 0.00 0.00 3.72
269 272 1.458777 ATGGCCCCGGATAAGACGA 60.459 57.895 0.73 0.00 0.00 4.20
272 275 2.779033 GCCCCGGATAAGACGACGT 61.779 63.158 0.73 0.00 0.00 4.34
534 1177 5.436175 CTCATATTGTTGGTGTGGTATGGA 58.564 41.667 0.00 0.00 0.00 3.41
556 1202 6.812160 TGGACGCTTAGTTCTTCTTCTATTTC 59.188 38.462 0.00 0.00 0.00 2.17
563 1209 5.725362 AGTTCTTCTTCTATTTCCGGTCTG 58.275 41.667 0.00 0.00 0.00 3.51
600 1249 4.283978 TGGTTTAGTACTGATTTCGACCCA 59.716 41.667 5.39 0.00 0.00 4.51
614 1263 8.195436 TGATTTCGACCCAATTTACTACTAGAG 58.805 37.037 0.00 0.00 0.00 2.43
631 1280 4.586421 ACTAGAGCTATGTCATGCTTAGCA 59.414 41.667 23.72 10.09 46.93 3.49
740 1389 5.121221 GGAAAATATCCCCTTACGCAATG 57.879 43.478 0.00 0.00 43.00 2.82
741 1390 4.583073 GGAAAATATCCCCTTACGCAATGT 59.417 41.667 0.00 0.00 43.00 2.71
742 1391 5.766174 GGAAAATATCCCCTTACGCAATGTA 59.234 40.000 0.00 0.00 43.00 2.29
743 1392 6.263617 GGAAAATATCCCCTTACGCAATGTAA 59.736 38.462 0.00 0.00 43.00 2.41
744 1393 7.521585 GGAAAATATCCCCTTACGCAATGTAAG 60.522 40.741 7.63 7.63 46.98 2.34
753 1402 5.794687 TTACGCAATGTAAGATTGTCAGG 57.205 39.130 0.00 0.00 38.12 3.86
754 1403 3.009723 ACGCAATGTAAGATTGTCAGGG 58.990 45.455 0.00 0.00 0.00 4.45
755 1404 3.270027 CGCAATGTAAGATTGTCAGGGA 58.730 45.455 0.00 0.00 0.00 4.20
756 1405 3.689161 CGCAATGTAAGATTGTCAGGGAA 59.311 43.478 0.00 0.00 0.00 3.97
757 1406 4.155826 CGCAATGTAAGATTGTCAGGGAAA 59.844 41.667 0.00 0.00 0.00 3.13
758 1407 5.335583 CGCAATGTAAGATTGTCAGGGAAAA 60.336 40.000 0.00 0.00 0.00 2.29
759 1408 6.625740 CGCAATGTAAGATTGTCAGGGAAAAT 60.626 38.462 0.00 0.00 0.00 1.82
760 1409 6.532657 GCAATGTAAGATTGTCAGGGAAAATG 59.467 38.462 0.00 0.00 0.00 2.32
761 1410 7.605449 CAATGTAAGATTGTCAGGGAAAATGT 58.395 34.615 0.00 0.00 0.00 2.71
762 1411 6.817765 TGTAAGATTGTCAGGGAAAATGTC 57.182 37.500 0.00 0.00 0.00 3.06
771 1420 2.189833 GGAAAATGTCCCCTTCCGC 58.810 57.895 0.00 0.00 41.10 5.54
772 1421 0.610785 GGAAAATGTCCCCTTCCGCA 60.611 55.000 0.00 0.00 41.10 5.69
773 1422 1.253100 GAAAATGTCCCCTTCCGCAA 58.747 50.000 0.00 0.00 0.00 4.85
774 1423 1.824852 GAAAATGTCCCCTTCCGCAAT 59.175 47.619 0.00 0.00 0.00 3.56
775 1424 1.185315 AAATGTCCCCTTCCGCAATG 58.815 50.000 0.00 0.00 0.00 2.82
776 1425 0.039618 AATGTCCCCTTCCGCAATGT 59.960 50.000 0.00 0.00 0.00 2.71
777 1426 0.916086 ATGTCCCCTTCCGCAATGTA 59.084 50.000 0.00 0.00 0.00 2.29
778 1427 0.693622 TGTCCCCTTCCGCAATGTAA 59.306 50.000 0.00 0.00 0.00 2.41
779 1428 1.339631 TGTCCCCTTCCGCAATGTAAG 60.340 52.381 0.00 0.00 0.00 2.34
780 1429 1.065709 GTCCCCTTCCGCAATGTAAGA 60.066 52.381 0.00 0.00 0.00 2.10
781 1430 1.843851 TCCCCTTCCGCAATGTAAGAT 59.156 47.619 0.00 0.00 0.00 2.40
782 1431 2.241176 TCCCCTTCCGCAATGTAAGATT 59.759 45.455 0.00 0.00 0.00 2.40
783 1432 2.358898 CCCCTTCCGCAATGTAAGATTG 59.641 50.000 0.00 0.00 0.00 2.67
883 1635 7.680442 TTTCAGTTCCATTTCGATGTGATAA 57.320 32.000 0.00 0.00 0.00 1.75
905 1660 3.244215 ACGATGTTGATGTGTCTGACCTT 60.244 43.478 5.17 0.00 0.00 3.50
906 1661 3.124128 CGATGTTGATGTGTCTGACCTTG 59.876 47.826 5.17 0.00 0.00 3.61
907 1662 3.558931 TGTTGATGTGTCTGACCTTGT 57.441 42.857 5.17 0.00 0.00 3.16
930 1685 3.610040 TTCTTATCATCGCAGGTGTGT 57.390 42.857 0.00 0.00 0.00 3.72
948 1703 1.070914 TGTAACCGCAACATCTCCACA 59.929 47.619 0.00 0.00 0.00 4.17
1037 1792 2.827642 GCTCATGGGTCTGCTGCC 60.828 66.667 0.00 0.00 0.00 4.85
1151 1906 3.618507 GCTCAAGTGCACCATCTACTCTT 60.619 47.826 14.63 0.00 0.00 2.85
1164 1919 4.018484 TCTACTCTTCCTACGCCTATCC 57.982 50.000 0.00 0.00 0.00 2.59
1358 2167 2.839486 TCCTTGGCGGTATGATCATC 57.161 50.000 12.53 4.10 0.00 2.92
1380 2200 8.462811 TCATCGCTTCTCAACTAATATCCTATC 58.537 37.037 0.00 0.00 0.00 2.08
1792 2704 8.794335 ATAGATTTTGGACTTCTTCTGGTTAC 57.206 34.615 0.00 0.00 0.00 2.50
1810 2722 2.542766 ACTATTTCAATTGCACCGCG 57.457 45.000 0.00 0.00 0.00 6.46
1819 2731 0.317770 ATTGCACCGCGAAAACTGTG 60.318 50.000 8.23 7.18 0.00 3.66
1930 3213 3.026707 AGGTTGTGGGTTTGTAGCTTT 57.973 42.857 0.00 0.00 0.00 3.51
2077 3370 7.816995 TGCTTGTATATTTTGTTTTGTCCCATC 59.183 33.333 0.00 0.00 0.00 3.51
2506 3889 2.362717 CCTTTTTGAAACTACGCCCCAA 59.637 45.455 0.00 0.00 0.00 4.12
2938 4347 0.392336 GGGCACATCAGTTTGGCAAA 59.608 50.000 8.93 8.93 40.00 3.68
2986 4395 4.139786 ACTTTCTGCTGTTCATCACATGT 58.860 39.130 0.00 0.00 33.76 3.21
3424 4843 7.589958 ATTATCGTGTACTCTTGGATCTCTT 57.410 36.000 0.00 0.00 0.00 2.85
3738 5482 8.548877 GGATCCTCAAACCTATATAAGCCAATA 58.451 37.037 3.84 0.00 0.00 1.90
3802 5546 6.782000 ACATGGCTTTTATAAGGGCAATATGA 59.218 34.615 16.33 0.00 38.89 2.15
3916 5660 0.811616 CGCTTGGTCCTAGCATGGTC 60.812 60.000 22.68 0.00 38.55 4.02
3970 5714 3.572642 TGTTTCCAGTCTCAGTAGGTCA 58.427 45.455 0.00 0.00 0.00 4.02
3980 5724 2.871022 CTCAGTAGGTCATGCATTGCTC 59.129 50.000 10.49 0.00 0.00 4.26
4274 6018 3.711704 GGTGAGGGATTCAATCTAGGTGA 59.288 47.826 0.00 0.00 37.61 4.02
4402 6147 3.104512 ACTGATATCACCCTTCGTTGGA 58.895 45.455 0.00 0.00 0.00 3.53
4585 6333 3.489355 TCAAGATGTGTGCATTCCTGTT 58.511 40.909 0.00 0.00 35.07 3.16
4719 6468 2.730094 CAGCTTTGGCCTTTGCGT 59.270 55.556 3.32 0.00 39.73 5.24
4826 6575 3.842869 GTTGGAGACGGAAGCTGAT 57.157 52.632 0.00 0.00 0.00 2.90
4846 6595 5.788450 TGATGACTCTTTTCTGAGGACTTC 58.212 41.667 0.00 0.00 38.32 3.01
4874 6624 5.773575 TGTAGCAGTTAGTTCACTTCAGAG 58.226 41.667 0.00 0.00 0.00 3.35
4903 6653 7.657761 GGATAGGGTGAGTAATATCAACACTTG 59.342 40.741 0.00 0.00 38.73 3.16
4935 6685 4.927049 ACGGGAAGGAATATATAGGTCGA 58.073 43.478 0.00 0.00 0.00 4.20
4941 6691 7.147932 GGGAAGGAATATATAGGTCGAGTTACC 60.148 44.444 0.00 0.00 40.06 2.85
4988 6766 4.048504 GTTCCAAACAGACAAATTTCCCG 58.951 43.478 0.00 0.00 0.00 5.14
4991 6769 0.596082 AACAGACAAATTTCCCGCGG 59.404 50.000 21.04 21.04 0.00 6.46
5007 6785 2.546778 CGCGGAACTTGTACATATGGT 58.453 47.619 7.80 0.00 0.00 3.55
5083 6873 2.030274 AGTTTGCATACTTGTTTCCGCC 60.030 45.455 3.73 0.00 0.00 6.13
5095 6885 2.731691 TTTCCGCCTCACAGCTGACC 62.732 60.000 23.35 2.34 0.00 4.02
5156 6946 2.375174 ACTGGCTGAACCCAATGAGTTA 59.625 45.455 0.00 0.00 37.83 2.24
5157 6947 3.012518 CTGGCTGAACCCAATGAGTTAG 58.987 50.000 0.00 0.00 37.83 2.34
5158 6948 2.642311 TGGCTGAACCCAATGAGTTAGA 59.358 45.455 0.00 0.00 37.83 2.10
5159 6949 3.274288 GGCTGAACCCAATGAGTTAGAG 58.726 50.000 0.00 0.00 0.00 2.43
5160 6950 2.680339 GCTGAACCCAATGAGTTAGAGC 59.320 50.000 0.00 0.00 0.00 4.09
5161 6951 3.869912 GCTGAACCCAATGAGTTAGAGCA 60.870 47.826 6.34 0.00 34.86 4.26
5162 6952 4.521146 CTGAACCCAATGAGTTAGAGCAT 58.479 43.478 0.00 0.00 0.00 3.79
5163 6953 4.922206 TGAACCCAATGAGTTAGAGCATT 58.078 39.130 0.00 0.00 35.24 3.56
5164 6954 4.701651 TGAACCCAATGAGTTAGAGCATTG 59.298 41.667 0.00 0.00 46.71 2.82
5171 6961 4.890158 TGAGTTAGAGCATTGAAGTGGA 57.110 40.909 0.00 0.00 0.00 4.02
5172 6962 4.825422 TGAGTTAGAGCATTGAAGTGGAG 58.175 43.478 0.00 0.00 0.00 3.86
5717 7963 1.812525 CGCTCTGCTTCCTCTGCTA 59.187 57.895 0.00 0.00 0.00 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.882137 GCCCCGATAATCAAAATTCCGA 59.118 45.455 0.00 0.00 0.00 4.55
1 2 2.884639 AGCCCCGATAATCAAAATTCCG 59.115 45.455 0.00 0.00 0.00 4.30
2 3 3.636764 ACAGCCCCGATAATCAAAATTCC 59.363 43.478 0.00 0.00 0.00 3.01
3 4 4.097892 ACACAGCCCCGATAATCAAAATTC 59.902 41.667 0.00 0.00 0.00 2.17
4 5 4.023291 ACACAGCCCCGATAATCAAAATT 58.977 39.130 0.00 0.00 0.00 1.82
5 6 3.631250 ACACAGCCCCGATAATCAAAAT 58.369 40.909 0.00 0.00 0.00 1.82
6 7 3.013921 GACACAGCCCCGATAATCAAAA 58.986 45.455 0.00 0.00 0.00 2.44
7 8 2.026729 TGACACAGCCCCGATAATCAAA 60.027 45.455 0.00 0.00 0.00 2.69
8 9 1.557371 TGACACAGCCCCGATAATCAA 59.443 47.619 0.00 0.00 0.00 2.57
9 10 1.138859 CTGACACAGCCCCGATAATCA 59.861 52.381 0.00 0.00 0.00 2.57
23 24 9.190858 CAGCTGTTATTATTAGATCTCTGACAC 57.809 37.037 5.25 0.00 0.00 3.67
149 151 4.363999 CTTCTCTTCGTCACACAACTTCT 58.636 43.478 0.00 0.00 0.00 2.85
272 275 1.138568 CTCCTCCCCCTCGTAGTCTA 58.861 60.000 0.00 0.00 0.00 2.59
445 478 3.127533 GAAGCACGCGCCTGGAAT 61.128 61.111 5.73 0.00 39.83 3.01
534 1177 5.805994 CGGAAATAGAAGAAGAACTAAGCGT 59.194 40.000 0.00 0.00 0.00 5.07
556 1202 3.005261 CAGATGAATCTAGACCAGACCGG 59.995 52.174 0.00 0.00 35.62 5.28
563 1209 8.138712 CAGTACTAAACCAGATGAATCTAGACC 58.861 40.741 0.00 0.00 34.85 3.85
600 1249 8.865090 AGCATGACATAGCTCTAGTAGTAAATT 58.135 33.333 0.00 0.00 36.00 1.82
631 1280 1.929494 TCCCCTGGCAATCTTACCAAT 59.071 47.619 0.00 0.00 34.96 3.16
638 1287 3.532641 GGATATTTCCCCTGGCAATCT 57.467 47.619 0.00 0.00 35.84 2.40
731 1380 4.634004 CCCTGACAATCTTACATTGCGTAA 59.366 41.667 0.00 0.00 37.76 3.18
732 1381 4.081365 TCCCTGACAATCTTACATTGCGTA 60.081 41.667 0.00 0.00 32.55 4.42
733 1382 3.009723 CCCTGACAATCTTACATTGCGT 58.990 45.455 0.00 0.00 32.55 5.24
734 1383 3.270027 TCCCTGACAATCTTACATTGCG 58.730 45.455 0.00 0.00 32.55 4.85
735 1384 5.643379 TTTCCCTGACAATCTTACATTGC 57.357 39.130 0.00 0.00 32.55 3.56
736 1385 7.605449 ACATTTTCCCTGACAATCTTACATTG 58.395 34.615 0.00 0.00 35.29 2.82
737 1386 7.093771 GGACATTTTCCCTGACAATCTTACATT 60.094 37.037 0.00 0.00 38.70 2.71
738 1387 6.378280 GGACATTTTCCCTGACAATCTTACAT 59.622 38.462 0.00 0.00 38.70 2.29
739 1388 5.710099 GGACATTTTCCCTGACAATCTTACA 59.290 40.000 0.00 0.00 38.70 2.41
740 1389 6.196079 GGACATTTTCCCTGACAATCTTAC 57.804 41.667 0.00 0.00 38.70 2.34
753 1402 0.610785 TGCGGAAGGGGACATTTTCC 60.611 55.000 0.00 0.00 45.00 3.13
754 1403 1.253100 TTGCGGAAGGGGACATTTTC 58.747 50.000 0.00 0.00 0.00 2.29
755 1404 1.550072 CATTGCGGAAGGGGACATTTT 59.450 47.619 0.00 0.00 0.00 1.82
756 1405 1.185315 CATTGCGGAAGGGGACATTT 58.815 50.000 0.00 0.00 0.00 2.32
757 1406 0.039618 ACATTGCGGAAGGGGACATT 59.960 50.000 6.23 0.00 0.00 2.71
758 1407 0.916086 TACATTGCGGAAGGGGACAT 59.084 50.000 6.23 0.00 0.00 3.06
759 1408 0.693622 TTACATTGCGGAAGGGGACA 59.306 50.000 6.23 0.00 0.00 4.02
760 1409 1.065709 TCTTACATTGCGGAAGGGGAC 60.066 52.381 6.23 0.00 0.00 4.46
761 1410 1.281419 TCTTACATTGCGGAAGGGGA 58.719 50.000 6.23 0.00 0.00 4.81
762 1411 2.348411 ATCTTACATTGCGGAAGGGG 57.652 50.000 6.23 0.00 0.00 4.79
763 1412 2.223572 GCAATCTTACATTGCGGAAGGG 60.224 50.000 6.23 0.00 43.80 3.95
764 1413 3.070429 GCAATCTTACATTGCGGAAGG 57.930 47.619 0.00 0.00 43.80 3.46
771 1420 5.404466 TTTTCCCTGGCAATCTTACATTG 57.596 39.130 0.00 0.00 0.00 2.82
772 1421 7.687592 GCATATTTTCCCTGGCAATCTTACATT 60.688 37.037 0.00 0.00 0.00 2.71
773 1422 6.239402 GCATATTTTCCCTGGCAATCTTACAT 60.239 38.462 0.00 0.00 0.00 2.29
774 1423 5.068987 GCATATTTTCCCTGGCAATCTTACA 59.931 40.000 0.00 0.00 0.00 2.41
775 1424 5.509670 GGCATATTTTCCCTGGCAATCTTAC 60.510 44.000 0.00 0.00 35.68 2.34
776 1425 4.588528 GGCATATTTTCCCTGGCAATCTTA 59.411 41.667 0.00 0.00 35.68 2.10
777 1426 3.389002 GGCATATTTTCCCTGGCAATCTT 59.611 43.478 0.00 0.00 35.68 2.40
778 1427 2.967887 GGCATATTTTCCCTGGCAATCT 59.032 45.455 0.00 0.00 35.68 2.40
779 1428 2.037641 GGGCATATTTTCCCTGGCAATC 59.962 50.000 0.00 0.00 39.46 2.67
780 1429 2.049372 GGGCATATTTTCCCTGGCAAT 58.951 47.619 0.00 0.00 39.46 3.56
781 1430 1.494960 GGGCATATTTTCCCTGGCAA 58.505 50.000 0.00 0.00 39.46 4.52
782 1431 3.222287 GGGCATATTTTCCCTGGCA 57.778 52.632 0.00 0.00 39.46 4.92
787 1436 2.387757 TGCAGAAGGGCATATTTTCCC 58.612 47.619 0.00 0.00 39.25 3.97
788 1437 4.141869 ACATTGCAGAAGGGCATATTTTCC 60.142 41.667 0.00 0.00 44.48 3.13
838 1580 7.950512 TGAAAATGAGTTCAACATAACCACAT 58.049 30.769 0.00 0.00 34.59 3.21
883 1635 2.300152 AGGTCAGACACATCAACATCGT 59.700 45.455 2.17 0.00 0.00 3.73
905 1660 4.759693 ACACCTGCGATGATAAGAAAAACA 59.240 37.500 0.00 0.00 0.00 2.83
906 1661 5.088739 CACACCTGCGATGATAAGAAAAAC 58.911 41.667 0.00 0.00 0.00 2.43
907 1662 4.759693 ACACACCTGCGATGATAAGAAAAA 59.240 37.500 0.00 0.00 0.00 1.94
930 1685 1.803334 GTGTGGAGATGTTGCGGTTA 58.197 50.000 0.00 0.00 0.00 2.85
937 1692 1.546476 GAGAGGACGTGTGGAGATGTT 59.454 52.381 0.00 0.00 0.00 2.71
948 1703 3.507009 GCGGCGTAGAGAGGACGT 61.507 66.667 9.37 0.00 43.98 4.34
1052 1807 1.691976 ACTCCCAAACGACACAGATGA 59.308 47.619 0.00 0.00 0.00 2.92
1151 1906 0.820891 GGTCACGGATAGGCGTAGGA 60.821 60.000 0.00 0.00 0.00 2.94
1164 1919 2.809861 AAGCAGGGATGCAGGTCACG 62.810 60.000 2.73 0.00 37.25 4.35
1358 2167 7.540400 CACAGATAGGATATTAGTTGAGAAGCG 59.460 40.741 0.00 0.00 0.00 4.68
1562 2420 7.228906 CCAGGATAATACACTTCGAACTAGAGA 59.771 40.741 0.00 0.00 0.00 3.10
1792 2704 2.823196 TCGCGGTGCAATTGAAATAG 57.177 45.000 10.34 0.00 0.00 1.73
1810 2722 7.201435 CCAAAAGAACAAGCTTACACAGTTTTC 60.201 37.037 0.00 0.00 0.00 2.29
1819 2731 6.961359 AAAACACCAAAAGAACAAGCTTAC 57.039 33.333 0.00 0.00 0.00 2.34
2506 3889 9.793259 TTACCTTGTGAAGAAGTCTGAATAATT 57.207 29.630 0.00 0.00 0.00 1.40
2938 4347 3.072476 TCTGCAAAGTTTAGTAGTGGCCT 59.928 43.478 3.32 0.00 0.00 5.19
2986 4395 4.323417 ACTGTTTTGCCAATGAGATACGA 58.677 39.130 0.00 0.00 0.00 3.43
3323 4741 1.546476 ACAGAGGTAAACAGGAGAGCG 59.454 52.381 0.00 0.00 0.00 5.03
3424 4843 7.763985 TGTCATCGCTTAATAAATTGACAGAGA 59.236 33.333 0.00 0.00 37.62 3.10
3738 5482 8.960591 CATTATTTGGATTCAGTACCTCACTTT 58.039 33.333 0.00 0.00 34.26 2.66
3802 5546 3.441572 CGAAGAGCCCTTTTCACATGATT 59.558 43.478 0.00 0.00 31.62 2.57
3868 5612 2.125461 TCGAACAGCAGCATATCTCG 57.875 50.000 0.00 0.00 0.00 4.04
3916 5660 5.118357 GCAGAATAGAATATCACAGCAGTCG 59.882 44.000 0.00 0.00 0.00 4.18
3970 5714 1.070134 GGATGGCAATGAGCAATGCAT 59.930 47.619 8.35 0.00 43.94 3.96
3980 5724 2.191513 CAGCGGAGGGATGGCAATG 61.192 63.158 0.00 0.00 0.00 2.82
4402 6147 5.507637 AGAGCTGGAAAATCATCATCAGTT 58.492 37.500 0.00 0.00 0.00 3.16
4585 6333 1.725641 CAACGAGTAGCTTCATGGCA 58.274 50.000 0.00 0.00 34.17 4.92
4719 6468 4.777896 ACACCTTGCCAAGATAGTAGAAGA 59.222 41.667 5.89 0.00 0.00 2.87
4826 6575 5.878406 AAGAAGTCCTCAGAAAAGAGTCA 57.122 39.130 0.00 0.00 33.75 3.41
4846 6595 7.693952 TGAAGTGAACTAACTGCTACAAAAAG 58.306 34.615 0.00 0.00 0.00 2.27
4874 6624 6.497259 TGTTGATATTACTCACCCTATCCCTC 59.503 42.308 0.00 0.00 0.00 4.30
4903 6653 1.374758 CCTTCCCGTCTGCACACTC 60.375 63.158 0.00 0.00 0.00 3.51
4935 6685 1.139058 GCATCCATCCTGTCGGTAACT 59.861 52.381 0.00 0.00 0.00 2.24
4941 6691 2.289820 CTCATTTGCATCCATCCTGTCG 59.710 50.000 0.00 0.00 0.00 4.35
4988 6766 3.687698 ACAACCATATGTACAAGTTCCGC 59.312 43.478 0.00 0.00 0.00 5.54
4991 6769 5.354234 CCTCCACAACCATATGTACAAGTTC 59.646 44.000 0.00 0.00 30.84 3.01
5007 6785 0.178967 TCAGCAAATGCCCTCCACAA 60.179 50.000 0.94 0.00 43.38 3.33
5083 6873 0.315251 TGAACTCGGTCAGCTGTGAG 59.685 55.000 22.74 22.74 31.53 3.51
5095 6885 3.570926 TGCTAAGTGTACCTGAACTCG 57.429 47.619 0.00 0.00 0.00 4.18
5156 6946 3.307339 GGAAGACTCCACTTCAATGCTCT 60.307 47.826 0.00 0.00 45.39 4.09
5157 6947 3.006247 GGAAGACTCCACTTCAATGCTC 58.994 50.000 0.00 0.00 45.39 4.26
5158 6948 2.641815 AGGAAGACTCCACTTCAATGCT 59.358 45.455 0.00 0.00 45.24 3.79
5159 6949 3.006247 GAGGAAGACTCCACTTCAATGC 58.994 50.000 0.00 0.00 45.24 3.56
5170 6960 2.490685 GTCGCGGGAGGAAGACTC 59.509 66.667 6.13 0.00 45.84 3.36
5171 6961 3.441290 CGTCGCGGGAGGAAGACT 61.441 66.667 16.26 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.