Multiple sequence alignment - TraesCS1A01G087800

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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 TraesCS1A01G087800 chr1A 100.000 5330 0 0 1 5330 75715543 75710214 0.000000e+00 9843.0
1 TraesCS1A01G087800 chr1A 87.163 1223 144 8 1567 2787 440923625 440924836 0.000000e+00 1376.0
2 TraesCS1A01G087800 chr1A 83.088 1153 174 14 2924 4063 440924896 440926040 0.000000e+00 1029.0
3 TraesCS1A01G087800 chr1A 98.016 252 5 0 342 593 75710555 75710806 6.340000e-119 438.0
4 TraesCS1A01G087800 chr1A 98.016 252 5 0 4738 4989 75714951 75715202 6.340000e-119 438.0
5 TraesCS1A01G087800 chr1A 93.878 49 3 0 2803 2851 75712698 75712650 2.060000e-09 75.0
6 TraesCS1A01G087800 chr1A 93.878 49 3 0 2846 2894 75712741 75712693 2.060000e-09 75.0
7 TraesCS1A01G087800 chr1A 100.000 35 0 0 4115 4149 75711399 75711365 1.240000e-06 65.8
8 TraesCS1A01G087800 chr1A 100.000 35 0 0 4145 4179 75711429 75711395 1.240000e-06 65.8
9 TraesCS1A01G087800 chr7A 98.329 1735 29 0 1160 2894 430256881 430255147 0.000000e+00 3044.0
10 TraesCS1A01G087800 chr7A 98.678 1362 17 1 2803 4164 430255195 430253835 0.000000e+00 2414.0
11 TraesCS1A01G087800 chr7A 95.433 832 34 2 337 1164 430266203 430265372 0.000000e+00 1323.0
12 TraesCS1A01G087800 chr7A 97.025 773 22 1 4153 4925 430245219 430244448 0.000000e+00 1299.0
13 TraesCS1A01G087800 chr7A 82.726 521 82 7 3546 4063 275272493 275271978 1.750000e-124 457.0
14 TraesCS1A01G087800 chr7A 96.047 253 9 1 4738 4989 430265946 430266198 1.380000e-110 411.0
15 TraesCS1A01G087800 chr7A 94.681 188 10 0 406 593 430244448 430244635 5.220000e-75 292.0
16 TraesCS1A01G087800 chr7A 93.878 49 3 0 2846 2894 430255238 430255190 2.060000e-09 75.0
17 TraesCS1A01G087800 chr7A 100.000 35 0 0 4145 4179 430253884 430253850 1.240000e-06 65.8
18 TraesCS1A01G087800 chr1B 88.661 1270 91 24 1420 2682 684792295 684791072 0.000000e+00 1498.0
19 TraesCS1A01G087800 chr1B 90.400 500 26 6 3111 3610 684791066 684790589 5.820000e-179 638.0
20 TraesCS1A01G087800 chr1B 78.580 873 141 33 337 1185 684793350 684792500 7.860000e-148 534.0
21 TraesCS1A01G087800 chr1B 92.857 350 21 3 3709 4058 684790591 684790246 6.160000e-139 505.0
22 TraesCS1A01G087800 chr5D 86.266 1165 154 5 1624 2787 479790548 479791707 0.000000e+00 1260.0
23 TraesCS1A01G087800 chr5D 81.622 925 142 23 3145 4063 479868125 479869027 0.000000e+00 741.0
24 TraesCS1A01G087800 chr5D 83.636 220 36 0 2932 3151 479791775 479791994 1.950000e-49 207.0
25 TraesCS1A01G087800 chr5D 72.016 486 116 17 2982 3458 412105129 412104655 5.600000e-25 126.0
26 TraesCS1A01G087800 chr2B 87.475 1006 123 3 1624 2627 748143911 748142907 0.000000e+00 1157.0
27 TraesCS1A01G087800 chr2B 98.214 336 6 0 4995 5330 479988851 479989186 5.950000e-164 588.0
28 TraesCS1A01G087800 chr2B 95.536 336 15 0 1 336 479988524 479988859 6.070000e-149 538.0
29 TraesCS1A01G087800 chr2B 83.333 96 14 2 2974 3068 588157454 588157548 2.640000e-13 87.9
30 TraesCS1A01G087800 chr5B 86.419 994 131 4 1624 2616 587477722 587478712 0.000000e+00 1085.0
31 TraesCS1A01G087800 chr5B 81.493 978 158 16 3090 4063 587595459 587596417 0.000000e+00 782.0
32 TraesCS1A01G087800 chr5B 81.787 582 92 12 3486 4063 815435 814864 4.830000e-130 475.0
33 TraesCS1A01G087800 chr5B 83.929 336 38 9 1 334 482991927 482992248 1.860000e-79 307.0
34 TraesCS1A01G087800 chr5B 91.071 56 5 0 2974 3029 255356066 255356011 5.720000e-10 76.8
35 TraesCS1A01G087800 chr3B 98.810 336 4 0 4995 5330 767297592 767297927 2.750000e-167 599.0
36 TraesCS1A01G087800 chr3B 97.619 336 8 0 1 336 767297265 767297600 1.290000e-160 577.0
37 TraesCS1A01G087800 chr3A 96.450 338 10 1 4995 5330 697226869 697227206 1.680000e-154 556.0
38 TraesCS1A01G087800 chr3A 96.154 338 11 1 4995 5330 444718667 444719004 7.800000e-153 551.0
39 TraesCS1A01G087800 chr6A 95.882 340 10 1 4995 5330 215028671 215028332 1.010000e-151 547.0
40 TraesCS1A01G087800 chr6A 95.536 336 15 0 4995 5330 606772526 606772861 6.070000e-149 538.0
41 TraesCS1A01G087800 chr6A 94.940 336 17 0 4995 5330 556913961 556914296 1.310000e-145 527.0
42 TraesCS1A01G087800 chr6A 82.534 521 83 7 3546 4063 70917415 70916900 8.140000e-123 451.0
43 TraesCS1A01G087800 chr5A 95.266 338 13 2 4995 5330 657209127 657208791 2.830000e-147 532.0
44 TraesCS1A01G087800 chr5A 71.919 495 95 33 3207 3676 692756343 692756818 2.630000e-18 104.0
45 TraesCS1A01G087800 chr2A 94.955 337 16 1 4995 5330 44021120 44020784 1.310000e-145 527.0
46 TraesCS1A01G087800 chr2A 82.726 521 82 7 3546 4063 277143917 277144432 1.750000e-124 457.0
47 TraesCS1A01G087800 chr2A 75.032 773 175 18 2944 3707 334903568 334902805 5.110000e-90 342.0
48 TraesCS1A01G087800 chr7D 82.726 521 82 7 3546 4063 22532465 22532980 1.750000e-124 457.0
49 TraesCS1A01G087800 chr7D 84.314 357 23 13 1 336 40735628 40735972 8.610000e-83 318.0
50 TraesCS1A01G087800 chr7D 84.179 335 39 6 3 336 569206432 569206753 4.010000e-81 313.0
51 TraesCS1A01G087800 chr7D 82.865 356 30 10 1 336 7721297 7720953 1.880000e-74 291.0
52 TraesCS1A01G087800 chr7D 96.970 33 0 1 2997 3028 618663554 618663522 3.000000e-03 54.7
53 TraesCS1A01G087800 chr6D 85.112 356 23 11 1 336 38239811 38240156 2.380000e-88 337.0
54 TraesCS1A01G087800 chr6D 85.417 336 36 5 1 336 428600564 428600886 2.380000e-88 337.0
55 TraesCS1A01G087800 chr6D 84.524 336 36 7 1 336 286638778 286639097 8.610000e-83 318.0
56 TraesCS1A01G087800 chr6D 83.662 355 29 10 1 336 408146081 408146425 1.860000e-79 307.0
57 TraesCS1A01G087800 chr4D 85.112 356 22 12 1 336 396743843 396744187 8.550000e-88 335.0
58 TraesCS1A01G087800 chr4D 84.273 337 37 6 1 336 504377447 504377126 1.110000e-81 315.0
59 TraesCS1A01G087800 chr4D 83.976 337 40 6 1 336 504406823 504406500 1.440000e-80 311.0
60 TraesCS1A01G087800 chr4D 82.584 356 29 13 1 336 464131713 464131371 3.140000e-72 283.0
61 TraesCS1A01G087800 chr2D 84.524 336 37 6 1 336 24526524 24526844 8.610000e-83 318.0
62 TraesCS1A01G087800 chr4B 84.348 345 31 11 1 336 624427019 624427349 3.100000e-82 316.0
63 TraesCS1A01G087800 chr3D 71.340 485 122 15 2982 3458 608430569 608431044 5.640000e-20 110.0


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 TraesCS1A01G087800 chr1A 75710214 75715543 5329 True 9843.00 9843 100.00000 1 5330 1 chr1A.!!$R1 5329
1 TraesCS1A01G087800 chr1A 440923625 440926040 2415 False 1202.50 1376 85.12550 1567 4063 2 chr1A.!!$F3 2496
2 TraesCS1A01G087800 chr7A 430253835 430256881 3046 True 1399.70 3044 97.72125 1160 4179 4 chr7A.!!$R4 3019
3 TraesCS1A01G087800 chr7A 430265372 430266203 831 True 1323.00 1323 95.43300 337 1164 1 chr7A.!!$R3 827
4 TraesCS1A01G087800 chr7A 430244448 430245219 771 True 1299.00 1299 97.02500 4153 4925 1 chr7A.!!$R2 772
5 TraesCS1A01G087800 chr7A 275271978 275272493 515 True 457.00 457 82.72600 3546 4063 1 chr7A.!!$R1 517
6 TraesCS1A01G087800 chr1B 684790246 684793350 3104 True 793.75 1498 87.62450 337 4058 4 chr1B.!!$R1 3721
7 TraesCS1A01G087800 chr5D 479868125 479869027 902 False 741.00 741 81.62200 3145 4063 1 chr5D.!!$F1 918
8 TraesCS1A01G087800 chr5D 479790548 479791994 1446 False 733.50 1260 84.95100 1624 3151 2 chr5D.!!$F2 1527
9 TraesCS1A01G087800 chr2B 748142907 748143911 1004 True 1157.00 1157 87.47500 1624 2627 1 chr2B.!!$R1 1003
10 TraesCS1A01G087800 chr2B 479988524 479989186 662 False 563.00 588 96.87500 1 5330 2 chr2B.!!$F2 5329
11 TraesCS1A01G087800 chr5B 587477722 587478712 990 False 1085.00 1085 86.41900 1624 2616 1 chr5B.!!$F2 992
12 TraesCS1A01G087800 chr5B 587595459 587596417 958 False 782.00 782 81.49300 3090 4063 1 chr5B.!!$F3 973
13 TraesCS1A01G087800 chr5B 814864 815435 571 True 475.00 475 81.78700 3486 4063 1 chr5B.!!$R1 577
14 TraesCS1A01G087800 chr3B 767297265 767297927 662 False 588.00 599 98.21450 1 5330 2 chr3B.!!$F1 5329
15 TraesCS1A01G087800 chr6A 70916900 70917415 515 True 451.00 451 82.53400 3546 4063 1 chr6A.!!$R1 517
16 TraesCS1A01G087800 chr2A 277143917 277144432 515 False 457.00 457 82.72600 3546 4063 1 chr2A.!!$F1 517
17 TraesCS1A01G087800 chr2A 334902805 334903568 763 True 342.00 342 75.03200 2944 3707 1 chr2A.!!$R2 763
18 TraesCS1A01G087800 chr7D 22532465 22532980 515 False 457.00 457 82.72600 3546 4063 1 chr7D.!!$F1 517

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
141 142 0.463620 AGCAAAAATGCCCACACGTT 59.536 45.000 0.00 0.00 34.9 3.99 F
751 762 1.019673 TGGAGACTCGTATGTACCGC 58.980 55.000 0.00 0.00 0.0 5.68 F
1557 1668 1.484240 GTGAAGAGAGGTAGCAGCCAT 59.516 52.381 0.00 0.00 0.0 4.40 F
2427 2549 2.503356 ACTAGTGAGAAGCAATCCTGGG 59.497 50.000 0.00 0.00 0.0 4.45 F
3040 3207 1.980765 TGGAGAAAGGTGCACAGAGAT 59.019 47.619 20.43 0.41 0.0 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1557 1668 4.016444 GTGATTTCCCTTTGTCCTGCATA 58.984 43.478 0.00 0.0 0.00 3.14 R
2427 2549 3.044305 GTCACCGCCACTGTGCTC 61.044 66.667 1.29 0.0 33.71 4.26 R
2865 3032 2.054232 TCACCACCTATCTCCTCGAC 57.946 55.000 0.00 0.0 0.00 4.20 R
4246 4423 1.098050 CTTGAATTTCCTGGAGCGGG 58.902 55.000 0.00 0.0 0.00 6.13 R
4986 5163 0.618458 TGTGGCAAGTAGGGGCTAAG 59.382 55.000 0.00 0.0 0.00 2.18 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
141 142 0.463620 AGCAAAAATGCCCACACGTT 59.536 45.000 0.00 0.00 34.90 3.99
184 185 4.495565 ACCCCACCGGATGACTATTTATA 58.504 43.478 9.46 0.00 34.64 0.98
271 272 3.719268 AGTTGCCATGTCTAACCATGA 57.281 42.857 0.00 0.00 43.99 3.07
378 380 6.408107 CCTAGAACTATCAGTTAAGGGACC 57.592 45.833 10.20 0.00 38.80 4.46
446 448 2.162608 TGTCAAACCAGACAAAACACCG 59.837 45.455 0.00 0.00 44.92 4.94
513 515 4.284550 GCCAGGACAAGCCCACCA 62.285 66.667 0.00 0.00 37.37 4.17
534 536 3.152400 GGCCACGTCGATAGGGGT 61.152 66.667 12.76 0.00 0.00 4.95
535 537 2.106332 GCCACGTCGATAGGGGTG 59.894 66.667 12.76 5.55 38.71 4.61
550 552 2.835895 GTGGGTTTGGGTGCGGTT 60.836 61.111 0.00 0.00 0.00 4.44
562 564 1.087771 GTGCGGTTTAGATGACCCCG 61.088 60.000 0.00 0.00 41.50 5.73
639 650 1.351017 TGTTCGCCTTTCCAATCTCCT 59.649 47.619 0.00 0.00 0.00 3.69
645 656 2.422093 GCCTTTCCAATCTCCTTCCGAT 60.422 50.000 0.00 0.00 0.00 4.18
739 750 5.241949 GGTTAGTCACATCGATATGGAGACT 59.758 44.000 15.19 15.19 46.01 3.24
748 759 6.092396 ACATCGATATGGAGACTCGTATGTAC 59.908 42.308 0.00 0.00 37.43 2.90
751 762 1.019673 TGGAGACTCGTATGTACCGC 58.980 55.000 0.00 0.00 0.00 5.68
780 794 4.718961 TCCCTCCTTTCTTCTCTGTTTTG 58.281 43.478 0.00 0.00 0.00 2.44
875 889 7.986085 ATGTAGTGCTTGATTCTGTAGTTTT 57.014 32.000 0.00 0.00 0.00 2.43
884 898 7.750903 GCTTGATTCTGTAGTTTTTGTATGACC 59.249 37.037 0.00 0.00 0.00 4.02
891 905 8.673711 TCTGTAGTTTTTGTATGACCATTATGC 58.326 33.333 0.00 0.00 0.00 3.14
952 970 8.621532 TTTAGTTATGACTGAACTGAAAGCAT 57.378 30.769 0.00 0.00 37.68 3.79
1173 1191 5.121811 GCAGACCATGTTAGATGTTCAGAT 58.878 41.667 0.00 0.00 0.00 2.90
1356 1395 5.191426 CCTGATGACTTTTCACAGGATGAT 58.809 41.667 0.00 0.00 45.07 2.45
1380 1419 3.076621 TGCAGAGGAACATCAACATCAC 58.923 45.455 0.00 0.00 0.00 3.06
1498 1609 4.159135 CAGAAGCTTGGCAATACTCCAATT 59.841 41.667 2.10 0.00 42.18 2.32
1557 1668 1.484240 GTGAAGAGAGGTAGCAGCCAT 59.516 52.381 0.00 0.00 0.00 4.40
1899 2019 6.865834 AGTGATGGAGAGATAAGTGAAGTT 57.134 37.500 0.00 0.00 0.00 2.66
2112 2232 2.763039 TGTCCTTGGAGCATCTATGGA 58.237 47.619 0.00 0.00 45.48 3.41
2427 2549 2.503356 ACTAGTGAGAAGCAATCCTGGG 59.497 50.000 0.00 0.00 0.00 4.45
2685 2807 4.055710 TGACTCATGGTACTGGTTCCTA 57.944 45.455 0.00 0.00 0.00 2.94
2862 3029 7.107542 GGTGGACCTAGTCACATGTTATAAAA 58.892 38.462 0.00 0.00 33.68 1.52
2865 3032 9.173021 TGGACCTAGTCACATGTTATAAAATTG 57.827 33.333 0.00 0.00 33.68 2.32
3040 3207 1.980765 TGGAGAAAGGTGCACAGAGAT 59.019 47.619 20.43 0.41 0.00 2.75
3123 3291 2.576191 ACAATAGAGCCAAACTAGCCCA 59.424 45.455 0.00 0.00 0.00 5.36
4197 4374 6.159988 ACAAGCTTCTCAACATACTGTAGAC 58.840 40.000 0.00 0.00 0.00 2.59
4202 4379 6.529829 GCTTCTCAACATACTGTAGACAGAAG 59.470 42.308 16.44 14.36 46.59 2.85
4246 4423 2.028567 AGAGTAGGTTCAAGCTCACAGC 60.029 50.000 0.00 0.00 42.84 4.40
4248 4425 0.324943 TAGGTTCAAGCTCACAGCCC 59.675 55.000 0.00 0.00 43.77 5.19
4292 4469 1.879380 TCACATGCAAGTGCCAACTAC 59.121 47.619 17.03 0.00 41.18 2.73
4308 4485 1.339438 ACTACTGACAGGCTGCAATGG 60.339 52.381 15.89 8.20 0.00 3.16
4341 4518 4.022849 GGAGAAAGGTGAATGTCCAGTTTG 60.023 45.833 0.00 0.00 0.00 2.93
4353 4530 3.072330 TGTCCAGTTTGCTTATCAGTGGA 59.928 43.478 0.00 0.00 32.00 4.02
4358 4535 5.106396 CCAGTTTGCTTATCAGTGGAGAAAG 60.106 44.000 0.00 0.00 0.00 2.62
4360 4537 5.471456 AGTTTGCTTATCAGTGGAGAAAGTG 59.529 40.000 0.00 0.00 0.00 3.16
4435 4612 4.803088 GCAACATCAAGTTACTTGCACAAA 59.197 37.500 19.24 3.21 40.84 2.83
4510 4687 3.974642 AGACCTTAAGAAGTTGTCAGGGT 59.025 43.478 3.36 0.00 0.00 4.34
4645 4822 5.664294 ATGAACATAGCAATTTTCTGGCA 57.336 34.783 0.00 0.00 0.00 4.92
4776 4953 4.899239 CAGCTCGGCGGGGTCATC 62.899 72.222 9.28 0.00 0.00 2.92
4779 4956 2.792947 GCTCGGCGGGGTCATCTAA 61.793 63.158 9.67 0.00 0.00 2.10
4795 4972 0.824182 CTAAACCGCACCCAAACCCA 60.824 55.000 0.00 0.00 0.00 4.51
4815 4992 3.524606 CCTATCGACGTGGCCGGT 61.525 66.667 1.90 0.00 38.78 5.28
4816 4993 2.493030 CTATCGACGTGGCCGGTT 59.507 61.111 1.90 0.00 38.78 4.44
4884 5061 0.186386 ACTCGAGATGGGTCTAGGGG 59.814 60.000 21.68 0.00 32.38 4.79
4925 5102 6.098409 TGACATAGTTCAGGGGATTAAGTCTC 59.902 42.308 0.00 0.00 0.00 3.36
4926 5103 6.206042 ACATAGTTCAGGGGATTAAGTCTCT 58.794 40.000 0.00 0.00 0.00 3.10
4927 5104 6.098982 ACATAGTTCAGGGGATTAAGTCTCTG 59.901 42.308 2.29 2.29 32.97 3.35
4928 5105 3.777522 AGTTCAGGGGATTAAGTCTCTGG 59.222 47.826 7.58 0.00 32.74 3.86
4929 5106 3.491766 TCAGGGGATTAAGTCTCTGGT 57.508 47.619 7.58 0.00 32.74 4.00
4930 5107 3.803340 TCAGGGGATTAAGTCTCTGGTT 58.197 45.455 7.58 0.00 32.74 3.67
4931 5108 4.175962 TCAGGGGATTAAGTCTCTGGTTT 58.824 43.478 7.58 0.00 32.74 3.27
4932 5109 4.601857 TCAGGGGATTAAGTCTCTGGTTTT 59.398 41.667 7.58 0.00 32.74 2.43
4933 5110 5.788533 TCAGGGGATTAAGTCTCTGGTTTTA 59.211 40.000 7.58 0.00 32.74 1.52
4934 5111 6.070194 TCAGGGGATTAAGTCTCTGGTTTTAG 60.070 42.308 7.58 0.00 32.74 1.85
4935 5112 6.030082 AGGGGATTAAGTCTCTGGTTTTAGA 58.970 40.000 0.00 0.00 0.00 2.10
4936 5113 6.070136 AGGGGATTAAGTCTCTGGTTTTAGAC 60.070 42.308 0.00 0.00 42.02 2.59
4937 5114 5.811100 GGGATTAAGTCTCTGGTTTTAGACG 59.189 44.000 0.00 0.00 45.47 4.18
4938 5115 6.396450 GGATTAAGTCTCTGGTTTTAGACGT 58.604 40.000 0.00 0.00 45.47 4.34
4939 5116 6.310711 GGATTAAGTCTCTGGTTTTAGACGTG 59.689 42.308 0.00 0.00 45.47 4.49
4940 5117 3.662247 AGTCTCTGGTTTTAGACGTGG 57.338 47.619 0.00 0.00 45.47 4.94
4941 5118 2.299297 AGTCTCTGGTTTTAGACGTGGG 59.701 50.000 0.00 0.00 45.47 4.61
4942 5119 1.621814 TCTCTGGTTTTAGACGTGGGG 59.378 52.381 0.00 0.00 0.00 4.96
4943 5120 0.688487 TCTGGTTTTAGACGTGGGGG 59.312 55.000 0.00 0.00 0.00 5.40
4961 5138 3.572632 GGGGGTTATCTGTCCCTTAAC 57.427 52.381 0.00 0.00 43.00 2.01
4962 5139 3.120898 GGGGGTTATCTGTCCCTTAACT 58.879 50.000 0.00 0.00 43.00 2.24
4963 5140 3.118000 GGGGGTTATCTGTCCCTTAACTG 60.118 52.174 0.00 0.00 43.00 3.16
4964 5141 3.778629 GGGGTTATCTGTCCCTTAACTGA 59.221 47.826 0.00 0.00 43.00 3.41
4965 5142 4.412528 GGGGTTATCTGTCCCTTAACTGAT 59.587 45.833 0.00 0.00 43.00 2.90
4966 5143 5.605488 GGGGTTATCTGTCCCTTAACTGATA 59.395 44.000 0.00 0.00 43.00 2.15
4967 5144 6.239629 GGGGTTATCTGTCCCTTAACTGATAG 60.240 46.154 0.00 0.00 43.00 2.08
4968 5145 6.326843 GGGTTATCTGTCCCTTAACTGATAGT 59.673 42.308 0.00 0.00 39.62 2.12
4969 5146 7.147532 GGGTTATCTGTCCCTTAACTGATAGTT 60.148 40.741 0.00 0.00 39.62 2.24
4970 5147 7.927092 GGTTATCTGTCCCTTAACTGATAGTTC 59.073 40.741 0.00 0.00 39.62 3.01
4971 5148 8.697292 GTTATCTGTCCCTTAACTGATAGTTCT 58.303 37.037 0.00 0.00 39.62 3.01
4972 5149 6.531503 TCTGTCCCTTAACTGATAGTTCTG 57.468 41.667 0.00 0.00 39.51 3.02
4973 5150 5.422331 TCTGTCCCTTAACTGATAGTTCTGG 59.578 44.000 0.00 2.47 39.51 3.86
4974 5151 4.469945 TGTCCCTTAACTGATAGTTCTGGG 59.530 45.833 18.17 18.17 44.84 4.45
4975 5152 4.037927 TCCCTTAACTGATAGTTCTGGGG 58.962 47.826 21.27 18.05 44.23 4.96
4976 5153 3.136626 CCCTTAACTGATAGTTCTGGGGG 59.863 52.174 17.20 12.04 42.30 5.40
4998 5175 6.089808 GGGTATCTATACTTAGCCCCTACT 57.910 45.833 0.46 0.00 33.81 2.57
4999 5176 6.501237 GGGTATCTATACTTAGCCCCTACTT 58.499 44.000 0.46 0.00 33.81 2.24
5000 5177 6.380560 GGGTATCTATACTTAGCCCCTACTTG 59.619 46.154 0.46 0.00 33.81 3.16
5001 5178 6.127394 GGTATCTATACTTAGCCCCTACTTGC 60.127 46.154 0.46 0.00 33.81 4.01
5002 5179 4.158015 TCTATACTTAGCCCCTACTTGCC 58.842 47.826 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 1.600636 AATGTCCGCCCACACACAG 60.601 57.895 0.00 0.00 0.00 3.66
169 170 7.909121 CGGCTAACTACTATAAATAGTCATCCG 59.091 40.741 5.92 8.22 42.31 4.18
184 185 2.761786 TACCATCCCGGCTAACTACT 57.238 50.000 0.00 0.00 39.03 2.57
357 358 5.759059 TCGGTCCCTTAACTGATAGTTCTA 58.241 41.667 0.00 0.00 39.51 2.10
446 448 0.671251 CACTCGAGATGGGTCTAGGC 59.329 60.000 21.68 0.00 33.97 3.93
489 491 3.160585 CTTGTCCTGGCCTCCACA 58.839 61.111 3.32 0.00 0.00 4.17
513 515 2.493030 CTATCGACGTGGCCGGTT 59.507 61.111 1.90 0.00 38.78 4.44
534 536 0.824182 CTAAACCGCACCCAAACCCA 60.824 55.000 0.00 0.00 0.00 4.51
535 537 0.537828 TCTAAACCGCACCCAAACCC 60.538 55.000 0.00 0.00 0.00 4.11
550 552 2.792947 GCTCGGCGGGGTCATCTAA 61.793 63.158 9.67 0.00 0.00 2.10
676 687 1.089920 GATGCTCAGTTCATGCCGTT 58.910 50.000 0.00 0.00 0.00 4.44
712 723 3.990469 CCATATCGATGTGACTAACCTGC 59.010 47.826 22.23 0.00 0.00 4.85
739 750 2.223876 GGATTTCAGGCGGTACATACGA 60.224 50.000 0.00 0.00 0.00 3.43
748 759 0.034089 AAAGGAGGGATTTCAGGCGG 60.034 55.000 0.00 0.00 0.00 6.13
751 762 4.227073 AGAGAAGAAAGGAGGGATTTCAGG 59.773 45.833 1.73 0.00 38.79 3.86
780 794 4.559153 CAAAATCACATCAACTCCAACCC 58.441 43.478 0.00 0.00 0.00 4.11
884 898 4.142790 AGGGAAATCAGAGCAGCATAATG 58.857 43.478 0.00 0.00 0.00 1.90
891 905 2.690497 TCTACGAGGGAAATCAGAGCAG 59.310 50.000 0.00 0.00 0.00 4.24
1173 1191 6.238266 GCAGTGTACTGTTGTTTAGTGCTTTA 60.238 38.462 13.08 0.00 45.45 1.85
1356 1395 5.355071 GTGATGTTGATGTTCCTCTGCATAA 59.645 40.000 0.00 0.00 0.00 1.90
1380 1419 6.102897 TGAAGTTCTTGTTCCTCCTCTAAG 57.897 41.667 4.17 0.00 0.00 2.18
1498 1609 4.202223 GCTACTGCTAGGCTGGTAATACAA 60.202 45.833 0.00 0.00 36.03 2.41
1557 1668 4.016444 GTGATTTCCCTTTGTCCTGCATA 58.984 43.478 0.00 0.00 0.00 3.14
1806 1923 6.267242 TGTCTTCTCCATCTGAATCATCTAGG 59.733 42.308 0.00 0.00 0.00 3.02
1899 2019 5.104693 TCTGTGTGTTGTTTTCCTCCTTCTA 60.105 40.000 0.00 0.00 0.00 2.10
2112 2232 6.271857 ACCAATCAGATCTGCTACTAATGGAT 59.728 38.462 18.36 0.00 0.00 3.41
2427 2549 3.044305 GTCACCGCCACTGTGCTC 61.044 66.667 1.29 0.00 33.71 4.26
2685 2807 7.859540 TCTGAAGATCCTTCTGAAGAAATGAT 58.140 34.615 18.68 11.91 33.07 2.45
2862 3029 2.695666 CACCACCTATCTCCTCGACAAT 59.304 50.000 0.00 0.00 0.00 2.71
2865 3032 2.054232 TCACCACCTATCTCCTCGAC 57.946 55.000 0.00 0.00 0.00 4.20
2921 3088 7.092935 ACCCTGCCAAATGATATAAACATGTTT 60.093 33.333 25.99 25.99 36.63 2.83
4197 4374 2.500910 ACTCCTCATCCTGCTTCTTCTG 59.499 50.000 0.00 0.00 0.00 3.02
4202 4379 2.106566 TCTGACTCCTCATCCTGCTTC 58.893 52.381 0.00 0.00 0.00 3.86
4246 4423 1.098050 CTTGAATTTCCTGGAGCGGG 58.902 55.000 0.00 0.00 0.00 6.13
4248 4425 1.399791 GAGCTTGAATTTCCTGGAGCG 59.600 52.381 0.00 0.00 35.41 5.03
4255 4432 5.063060 GCATGTGAATTGAGCTTGAATTTCC 59.937 40.000 6.21 2.41 0.00 3.13
4292 4469 1.654954 GAGCCATTGCAGCCTGTCAG 61.655 60.000 0.00 0.00 41.13 3.51
4341 4518 4.569943 TGACACTTTCTCCACTGATAAGC 58.430 43.478 0.00 0.00 0.00 3.09
4353 4530 6.291377 ACACATCAAGTACATGACACTTTCT 58.709 36.000 2.33 3.67 33.99 2.52
4358 4535 6.779115 TGTTACACATCAAGTACATGACAC 57.221 37.500 2.33 0.00 30.82 3.67
4435 4612 2.795231 ACAGACATTGGCATGCTACT 57.205 45.000 18.92 2.10 33.05 2.57
4499 4676 6.976934 AACATCAAATTTACCCTGACAACT 57.023 33.333 0.00 0.00 0.00 3.16
4767 4944 1.087771 GTGCGGTTTAGATGACCCCG 61.088 60.000 0.00 0.00 41.50 5.73
4776 4953 0.824182 TGGGTTTGGGTGCGGTTTAG 60.824 55.000 0.00 0.00 0.00 1.85
4779 4956 2.835895 GTGGGTTTGGGTGCGGTT 60.836 61.111 0.00 0.00 0.00 4.44
4795 4972 3.152400 GGCCACGTCGATAGGGGT 61.152 66.667 12.76 0.00 0.00 4.95
4815 4992 3.636231 CCAGGACGAGCCCACCAA 61.636 66.667 0.00 0.00 37.37 3.67
4884 5061 3.859411 TGTCAAACCAGACAAAACACC 57.141 42.857 0.00 0.00 44.92 4.16
4925 5102 3.243128 CCCCCACGTCTAAAACCAG 57.757 57.895 0.00 0.00 0.00 4.00
4941 5118 3.118000 CAGTTAAGGGACAGATAACCCCC 60.118 52.174 0.00 0.00 46.64 5.40
4942 5119 3.778629 TCAGTTAAGGGACAGATAACCCC 59.221 47.826 0.00 0.00 46.64 4.95
4943 5120 5.632034 ATCAGTTAAGGGACAGATAACCC 57.368 43.478 0.00 0.00 45.88 4.11
4944 5121 7.362802 ACTATCAGTTAAGGGACAGATAACC 57.637 40.000 0.00 0.00 30.71 2.85
4945 5122 8.697292 AGAACTATCAGTTAAGGGACAGATAAC 58.303 37.037 0.00 0.00 38.80 1.89
4946 5123 8.696374 CAGAACTATCAGTTAAGGGACAGATAA 58.304 37.037 0.00 0.00 38.80 1.75
4947 5124 7.287927 CCAGAACTATCAGTTAAGGGACAGATA 59.712 40.741 0.00 0.00 38.80 1.98
4948 5125 6.098982 CCAGAACTATCAGTTAAGGGACAGAT 59.901 42.308 0.00 0.00 38.80 2.90
4949 5126 5.422331 CCAGAACTATCAGTTAAGGGACAGA 59.578 44.000 0.00 0.00 38.80 3.41
4950 5127 5.395768 CCCAGAACTATCAGTTAAGGGACAG 60.396 48.000 17.31 0.00 46.88 3.51
4951 5128 4.469945 CCCAGAACTATCAGTTAAGGGACA 59.530 45.833 17.31 0.00 46.88 4.02
4952 5129 4.141688 CCCCAGAACTATCAGTTAAGGGAC 60.142 50.000 21.27 0.00 46.88 4.46
4953 5130 4.037927 CCCCAGAACTATCAGTTAAGGGA 58.962 47.826 21.27 0.00 46.88 4.20
4954 5131 3.136626 CCCCCAGAACTATCAGTTAAGGG 59.863 52.174 16.08 16.08 45.10 3.95
4955 5132 4.423625 CCCCCAGAACTATCAGTTAAGG 57.576 50.000 0.00 0.00 38.80 2.69
4973 5150 3.013763 AGGGGCTAAGTATAGATACCCCC 59.986 52.174 17.10 17.10 44.44 5.40
4974 5151 4.349564 AGGGGCTAAGTATAGATACCCC 57.650 50.000 6.06 6.06 44.03 4.95
4975 5152 6.089808 AGTAGGGGCTAAGTATAGATACCC 57.910 45.833 0.00 0.00 38.44 3.69
4976 5153 6.127394 GCAAGTAGGGGCTAAGTATAGATACC 60.127 46.154 0.00 0.00 33.79 2.73
4977 5154 6.127394 GGCAAGTAGGGGCTAAGTATAGATAC 60.127 46.154 0.00 0.00 0.00 2.24
4978 5155 5.956563 GGCAAGTAGGGGCTAAGTATAGATA 59.043 44.000 0.00 0.00 0.00 1.98
4979 5156 4.778427 GGCAAGTAGGGGCTAAGTATAGAT 59.222 45.833 0.00 0.00 0.00 1.98
4980 5157 4.158015 GGCAAGTAGGGGCTAAGTATAGA 58.842 47.826 0.00 0.00 0.00 1.98
4981 5158 3.901844 TGGCAAGTAGGGGCTAAGTATAG 59.098 47.826 0.00 0.00 0.00 1.31
4982 5159 3.644738 GTGGCAAGTAGGGGCTAAGTATA 59.355 47.826 0.00 0.00 0.00 1.47
4983 5160 2.438392 GTGGCAAGTAGGGGCTAAGTAT 59.562 50.000 0.00 0.00 0.00 2.12
4984 5161 1.835531 GTGGCAAGTAGGGGCTAAGTA 59.164 52.381 0.00 0.00 0.00 2.24
4985 5162 0.618981 GTGGCAAGTAGGGGCTAAGT 59.381 55.000 0.00 0.00 0.00 2.24
4986 5163 0.618458 TGTGGCAAGTAGGGGCTAAG 59.382 55.000 0.00 0.00 0.00 2.18
4987 5164 1.295020 ATGTGGCAAGTAGGGGCTAA 58.705 50.000 0.00 0.00 0.00 3.09
4988 5165 2.184088 TATGTGGCAAGTAGGGGCTA 57.816 50.000 0.00 0.00 0.00 3.93
4989 5166 1.143684 CATATGTGGCAAGTAGGGGCT 59.856 52.381 0.00 0.00 0.00 5.19
4990 5167 1.142870 TCATATGTGGCAAGTAGGGGC 59.857 52.381 1.90 0.00 0.00 5.80
4991 5168 3.072915 TGATCATATGTGGCAAGTAGGGG 59.927 47.826 1.90 0.00 0.00 4.79
4992 5169 4.356405 TGATCATATGTGGCAAGTAGGG 57.644 45.455 1.90 0.00 0.00 3.53
4993 5170 6.095300 TGTTTTGATCATATGTGGCAAGTAGG 59.905 38.462 1.90 0.00 0.00 3.18
4994 5171 7.087409 TGTTTTGATCATATGTGGCAAGTAG 57.913 36.000 1.90 0.00 0.00 2.57
4995 5172 6.658816 ACTGTTTTGATCATATGTGGCAAGTA 59.341 34.615 1.90 0.00 0.00 2.24
4996 5173 5.477984 ACTGTTTTGATCATATGTGGCAAGT 59.522 36.000 1.90 0.00 0.00 3.16
4997 5174 5.957798 ACTGTTTTGATCATATGTGGCAAG 58.042 37.500 1.90 0.00 0.00 4.01
4998 5175 5.981088 ACTGTTTTGATCATATGTGGCAA 57.019 34.783 1.90 3.44 0.00 4.52
4999 5176 6.179756 ACTACTGTTTTGATCATATGTGGCA 58.820 36.000 1.90 0.00 0.00 4.92
5000 5177 6.683974 ACTACTGTTTTGATCATATGTGGC 57.316 37.500 1.90 0.00 0.00 5.01
5001 5178 8.044060 ACAACTACTGTTTTGATCATATGTGG 57.956 34.615 1.90 0.00 32.99 4.17
5002 5179 8.720562 TGACAACTACTGTTTTGATCATATGTG 58.279 33.333 1.90 0.00 38.84 3.21


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

AutoCloner maintained by Alex Coulton.