Multiple sequence alignment - TraesCS6D01G081700

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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 TraesCS6D01G081700 chr6D 100.000 6539 0 0 1 6539 47255760 47262298 0.000000e+00 12076.0
1 TraesCS6D01G081700 chr6D 83.876 645 65 20 3370 3988 230782882 230783513 4.400000e-161 579.0
2 TraesCS6D01G081700 chr6D 90.300 433 33 6 3522 3949 200870014 200870442 5.730000e-155 558.0
3 TraesCS6D01G081700 chr6D 91.519 283 10 1 1 269 454832485 454832767 1.720000e-100 377.0
4 TraesCS6D01G081700 chr6D 94.979 239 12 0 494 732 454832767 454833005 6.190000e-100 375.0
5 TraesCS6D01G081700 chr6D 93.443 61 4 0 673 733 419450012 419449952 2.510000e-14 91.6
6 TraesCS6D01G081700 chr6D 93.443 61 4 0 673 733 419450593 419450533 2.510000e-14 91.6
7 TraesCS6D01G081700 chr6B 94.380 2687 81 18 732 3364 124480730 124478060 0.000000e+00 4061.0
8 TraesCS6D01G081700 chr6B 95.407 1829 38 14 3984 5796 124478065 124476267 0.000000e+00 2870.0
9 TraesCS6D01G081700 chr6B 93.948 727 22 4 5835 6539 124472043 124471317 0.000000e+00 1079.0
10 TraesCS6D01G081700 chr6B 87.405 524 38 13 3466 3981 707319235 707318732 1.580000e-160 577.0
11 TraesCS6D01G081700 chr6B 81.918 365 65 1 375 738 452180535 452180171 2.290000e-79 307.0
12 TraesCS6D01G081700 chr6B 86.800 250 16 5 3356 3601 55345084 55345320 5.030000e-66 263.0
13 TraesCS6D01G081700 chr6B 97.826 46 1 0 5794 5839 124474863 124474818 5.440000e-11 80.5
14 TraesCS6D01G081700 chr6A 97.757 1694 37 1 1672 3364 68515113 68513420 0.000000e+00 2916.0
15 TraesCS6D01G081700 chr6A 97.480 873 19 3 4925 5796 68512267 68511397 0.000000e+00 1487.0
16 TraesCS6D01G081700 chr6A 94.726 948 16 7 3982 4924 68513427 68512509 0.000000e+00 1443.0
17 TraesCS6D01G081700 chr6A 92.551 792 21 14 732 1506 68515893 68515123 0.000000e+00 1101.0
18 TraesCS6D01G081700 chr6A 90.409 636 31 12 3365 3983 13663442 13664064 0.000000e+00 809.0
19 TraesCS6D01G081700 chr6A 88.948 561 40 10 3426 3981 284811427 284810884 0.000000e+00 673.0
20 TraesCS6D01G081700 chr6A 90.385 364 21 2 5833 6182 68511256 68510893 3.570000e-127 466.0
21 TraesCS6D01G081700 chr6A 94.595 37 1 1 5802 5837 68511371 68511335 1.000000e-03 56.5
22 TraesCS6D01G081700 chr7A 91.465 2144 94 32 748 2833 387172073 387174185 0.000000e+00 2863.0
23 TraesCS6D01G081700 chr7A 94.005 1201 65 6 4564 5763 387175360 387176554 0.000000e+00 1812.0
24 TraesCS6D01G081700 chr7A 91.869 578 34 10 3982 4552 387174699 387175270 0.000000e+00 795.0
25 TraesCS6D01G081700 chr7A 92.010 413 30 2 2955 3364 387174294 387174706 1.580000e-160 577.0
26 TraesCS6D01G081700 chr7B 91.797 1914 84 29 968 2833 356698720 356700608 0.000000e+00 2597.0
27 TraesCS6D01G081700 chr7B 93.766 1203 67 6 4564 5763 356701529 356702726 0.000000e+00 1799.0
28 TraesCS6D01G081700 chr7B 92.788 513 28 8 3982 4488 356701017 356701526 0.000000e+00 734.0
29 TraesCS6D01G081700 chr7B 90.676 429 29 2 2937 3364 356700606 356701024 1.590000e-155 560.0
30 TraesCS6D01G081700 chr7B 77.635 389 82 3 349 732 590102832 590102444 1.420000e-56 231.0
31 TraesCS6D01G081700 chr4D 96.558 552 13 4 3365 3913 214750856 214751404 0.000000e+00 909.0
32 TraesCS6D01G081700 chr4D 79.500 400 73 9 336 732 220897486 220897093 6.460000e-70 276.0
33 TraesCS6D01G081700 chr3B 91.024 635 36 13 3365 3981 302357330 302357961 0.000000e+00 837.0
34 TraesCS6D01G081700 chr3B 82.842 373 64 0 364 736 456624522 456624150 1.050000e-87 335.0
35 TraesCS6D01G081700 chr3B 83.152 184 21 9 3798 3976 766361828 766361650 6.790000e-35 159.0
36 TraesCS6D01G081700 chr1B 90.536 634 30 12 3365 3981 612990892 612990272 0.000000e+00 811.0
37 TraesCS6D01G081700 chr5A 84.873 747 98 7 1 733 619521644 619522389 0.000000e+00 739.0
38 TraesCS6D01G081700 chr5A 84.337 747 97 11 1 732 123474463 123475204 0.000000e+00 713.0
39 TraesCS6D01G081700 chr5A 91.546 414 30 3 6131 6539 697925 698338 3.420000e-157 566.0
40 TraesCS6D01G081700 chr3A 88.486 634 29 13 3365 3981 8934739 8935345 0.000000e+00 726.0
41 TraesCS6D01G081700 chr3A 90.974 421 35 2 3542 3962 131766025 131766442 1.230000e-156 564.0
42 TraesCS6D01G081700 chr3A 92.473 186 9 3 3365 3545 131765500 131765685 1.810000e-65 261.0
43 TraesCS6D01G081700 chr5D 85.196 716 91 7 1 702 437036429 437037143 0.000000e+00 721.0
44 TraesCS6D01G081700 chr5D 91.726 423 32 2 3554 3976 120338979 120339398 9.450000e-163 584.0
45 TraesCS6D01G081700 chr5D 91.019 412 31 4 6131 6537 521839872 521840282 9.580000e-153 551.0
46 TraesCS6D01G081700 chr5D 89.928 417 32 6 6130 6537 447190248 447190663 4.490000e-146 529.0
47 TraesCS6D01G081700 chr5D 80.808 495 88 7 245 737 538102712 538103201 1.330000e-101 381.0
48 TraesCS6D01G081700 chr5D 79.200 500 93 10 241 736 438182695 438183187 2.920000e-88 337.0
49 TraesCS6D01G081700 chr5D 78.842 501 92 9 241 735 541689580 541689088 6.320000e-85 326.0
50 TraesCS6D01G081700 chr5D 78.226 496 97 10 241 732 412127959 412127471 2.290000e-79 307.0
51 TraesCS6D01G081700 chr3D 84.021 751 103 11 1 736 582580985 582580237 0.000000e+00 706.0
52 TraesCS6D01G081700 chr3D 90.840 262 15 5 3365 3621 543102056 543101799 6.280000e-90 342.0
53 TraesCS6D01G081700 chr4A 82.626 754 110 17 1 735 4855523 4854772 0.000000e+00 647.0
54 TraesCS6D01G081700 chr4A 91.304 46 2 2 4179 4224 539154368 539154325 1.970000e-05 62.1
55 TraesCS6D01G081700 chr4A 100.000 30 0 0 4191 4220 610309418 610309389 1.000000e-03 56.5
56 TraesCS6D01G081700 chr5B 92.048 415 23 4 6132 6539 391809558 391809147 5.690000e-160 575.0
57 TraesCS6D01G081700 chr5B 91.063 414 29 2 6132 6538 659553237 659552825 2.660000e-153 553.0
58 TraesCS6D01G081700 chr5B 79.372 446 80 11 292 732 549652190 549652628 2.960000e-78 303.0
59 TraesCS6D01G081700 chr2D 90.639 438 34 5 3540 3976 533795940 533796371 5.690000e-160 575.0
60 TraesCS6D01G081700 chr2D 91.607 417 26 2 6132 6539 633256981 633256565 9.520000e-158 568.0
61 TraesCS6D01G081700 chr2D 91.607 417 26 2 6132 6539 633284336 633283920 9.520000e-158 568.0
62 TraesCS6D01G081700 chr2D 89.236 288 19 8 3359 3644 533795718 533795995 3.750000e-92 350.0
63 TraesCS6D01G081700 chr2D 75.159 471 85 24 4798 5251 576281659 576282114 6.690000e-45 193.0
64 TraesCS6D01G081700 chr2D 76.168 214 43 6 1956 2165 196455886 196456095 8.970000e-19 106.0
65 TraesCS6D01G081700 chr1A 91.084 415 29 4 6131 6539 31907766 31908178 7.410000e-154 555.0
66 TraesCS6D01G081700 chr1A 80.418 383 71 4 356 735 82086385 82086004 8.300000e-74 289.0
67 TraesCS6D01G081700 chr1A 83.256 215 34 1 520 732 581936073 581935859 5.170000e-46 196.0
68 TraesCS6D01G081700 chr1A 91.071 112 10 0 624 735 71774470 71774359 1.140000e-32 152.0
69 TraesCS6D01G081700 chr2B 81.298 647 100 10 101 732 798588088 798588728 7.570000e-139 505.0
70 TraesCS6D01G081700 chr2B 81.211 644 100 11 106 732 798733968 798733329 3.520000e-137 499.0
71 TraesCS6D01G081700 chr2B 74.576 472 88 24 4798 5251 692462553 692463010 1.870000e-40 178.0
72 TraesCS6D01G081700 chr2B 75.701 214 44 6 1956 2165 254011066 254011275 4.170000e-17 100.0
73 TraesCS6D01G081700 chr1D 82.245 490 82 5 245 732 209736011 209735525 1.010000e-112 418.0
74 TraesCS6D01G081700 chr7D 78.968 504 93 12 241 740 58069614 58070108 1.360000e-86 331.0
75 TraesCS6D01G081700 chr2A 74.894 470 87 25 4798 5251 714330588 714331042 1.120000e-42 185.0
76 TraesCS6D01G081700 chr2A 75.701 214 44 6 1956 2165 212644015 212644224 4.170000e-17 100.0
77 TraesCS6D01G081700 chr4B 91.304 46 2 2 4179 4224 86087984 86088027 1.970000e-05 62.1


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 TraesCS6D01G081700 chr6D 47255760 47262298 6538 False 12076.000000 12076 100.000000 1 6539 1 chr6D.!!$F1 6538
1 TraesCS6D01G081700 chr6D 230782882 230783513 631 False 579.000000 579 83.876000 3370 3988 1 chr6D.!!$F3 618
2 TraesCS6D01G081700 chr6D 454832485 454833005 520 False 376.000000 377 93.249000 1 732 2 chr6D.!!$F4 731
3 TraesCS6D01G081700 chr6B 124471317 124480730 9413 True 2022.625000 4061 95.390250 732 6539 4 chr6B.!!$R3 5807
4 TraesCS6D01G081700 chr6B 707318732 707319235 503 True 577.000000 577 87.405000 3466 3981 1 chr6B.!!$R2 515
5 TraesCS6D01G081700 chr6A 68510893 68515893 5000 True 1244.916667 2916 94.582333 732 6182 6 chr6A.!!$R2 5450
6 TraesCS6D01G081700 chr6A 13663442 13664064 622 False 809.000000 809 90.409000 3365 3983 1 chr6A.!!$F1 618
7 TraesCS6D01G081700 chr6A 284810884 284811427 543 True 673.000000 673 88.948000 3426 3981 1 chr6A.!!$R1 555
8 TraesCS6D01G081700 chr7A 387172073 387176554 4481 False 1511.750000 2863 92.337250 748 5763 4 chr7A.!!$F1 5015
9 TraesCS6D01G081700 chr7B 356698720 356702726 4006 False 1422.500000 2597 92.256750 968 5763 4 chr7B.!!$F1 4795
10 TraesCS6D01G081700 chr4D 214750856 214751404 548 False 909.000000 909 96.558000 3365 3913 1 chr4D.!!$F1 548
11 TraesCS6D01G081700 chr3B 302357330 302357961 631 False 837.000000 837 91.024000 3365 3981 1 chr3B.!!$F1 616
12 TraesCS6D01G081700 chr1B 612990272 612990892 620 True 811.000000 811 90.536000 3365 3981 1 chr1B.!!$R1 616
13 TraesCS6D01G081700 chr5A 619521644 619522389 745 False 739.000000 739 84.873000 1 733 1 chr5A.!!$F3 732
14 TraesCS6D01G081700 chr5A 123474463 123475204 741 False 713.000000 713 84.337000 1 732 1 chr5A.!!$F2 731
15 TraesCS6D01G081700 chr3A 8934739 8935345 606 False 726.000000 726 88.486000 3365 3981 1 chr3A.!!$F1 616
16 TraesCS6D01G081700 chr3A 131765500 131766442 942 False 412.500000 564 91.723500 3365 3962 2 chr3A.!!$F2 597
17 TraesCS6D01G081700 chr5D 437036429 437037143 714 False 721.000000 721 85.196000 1 702 1 chr5D.!!$F2 701
18 TraesCS6D01G081700 chr3D 582580237 582580985 748 True 706.000000 706 84.021000 1 736 1 chr3D.!!$R2 735
19 TraesCS6D01G081700 chr4A 4854772 4855523 751 True 647.000000 647 82.626000 1 735 1 chr4A.!!$R1 734
20 TraesCS6D01G081700 chr2D 533795718 533796371 653 False 462.500000 575 89.937500 3359 3976 2 chr2D.!!$F3 617
21 TraesCS6D01G081700 chr2B 798588088 798588728 640 False 505.000000 505 81.298000 101 732 1 chr2B.!!$F3 631
22 TraesCS6D01G081700 chr2B 798733329 798733968 639 True 499.000000 499 81.211000 106 732 1 chr2B.!!$R1 626

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
394 409 0.388649 CTCCGACCCTCGAAACACTG 60.389 60.000 0.00 0.0 43.74 3.66 F
653 673 0.827925 TGGCCGCCATGTTTGGTTAA 60.828 50.000 8.43 0.0 45.57 2.01 F
1201 1317 1.594310 GAGGTCAGGACACTCTGGC 59.406 63.158 1.41 0.0 38.55 4.85 F
2200 2347 2.108157 GCCCATGCGTATCGGACA 59.892 61.111 0.41 0.0 0.00 4.02 F
3150 3395 1.077930 CACACATCCTCTGCCTGGG 60.078 63.158 0.00 0.0 0.00 4.45 F
3612 4256 1.152652 GATCTGCCGGAGAGGAGGA 60.153 63.158 5.05 0.0 45.00 3.71 F
3976 4682 1.741706 GCCTTAGGGACGCCTTAAAAC 59.258 52.381 0.00 0.0 33.58 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1201 1317 1.115467 CAGTACTGCAGGTCCCCTAG 58.885 60.000 19.93 0.00 29.64 3.02 R
1612 1736 1.271102 GTTCGCAAAATACCTTGGCCA 59.729 47.619 0.00 0.00 0.00 5.36 R
2988 3230 0.323629 CACAAAGAGCCTCCGGGTAA 59.676 55.000 0.00 0.00 31.55 2.85 R
3612 4256 0.977108 CCTCTCTGGCAGCTTCTCCT 60.977 60.000 10.34 0.00 0.00 3.69 R
5148 6189 1.079987 AGGGCTTCCTCTGCAGAGA 59.920 57.895 39.34 24.37 44.74 3.10 R
5522 6566 2.656560 AAGTCAGACGGCATCTACAC 57.343 50.000 0.00 0.00 35.15 2.90 R
5907 11148 0.462789 AGCCGGACCTAACGTAATGG 59.537 55.000 5.05 0.00 0.00 3.16 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
281 296 7.036996 TGAACATTGATGCTGTTGTTTCTAA 57.963 32.000 0.00 0.00 36.98 2.10
282 297 7.487484 TGAACATTGATGCTGTTGTTTCTAAA 58.513 30.769 0.00 0.00 36.98 1.85
294 309 3.602483 TGTTTCTAAACGAGGGTATGGC 58.398 45.455 0.00 0.00 41.74 4.40
312 327 1.378762 CTCGGTGGGGGTGATTTGT 59.621 57.895 0.00 0.00 0.00 2.83
323 338 3.053619 GGGGTGATTTGTAGGGATCAAGT 60.054 47.826 0.00 0.00 34.34 3.16
340 355 0.540597 AGTTGGAGCTTTCTTGGGGC 60.541 55.000 0.00 0.00 0.00 5.80
360 375 2.742774 CCTTCGGCCTTTTTGTTTCAG 58.257 47.619 0.00 0.00 0.00 3.02
391 406 2.280552 CCCTCCGACCCTCGAAACA 61.281 63.158 0.00 0.00 43.74 2.83
394 409 0.388649 CTCCGACCCTCGAAACACTG 60.389 60.000 0.00 0.00 43.74 3.66
421 436 2.174349 GAAGCTCTTGCGTTGGCG 59.826 61.111 0.00 0.00 45.42 5.69
469 484 2.089887 TTACGTCCGACTGCAAGCCA 62.090 55.000 0.00 0.00 37.60 4.75
481 496 1.569479 GCAAGCCAGTGACGGAAGAC 61.569 60.000 0.00 0.00 0.00 3.01
598 614 7.796054 AGTTTAGGAGCTCTAATTATGAAGCA 58.204 34.615 14.64 0.00 37.74 3.91
608 624 8.450964 GCTCTAATTATGAAGCACACAACTTAA 58.549 33.333 8.84 0.00 0.00 1.85
626 646 4.757149 ACTTAACGAAGCATGCTCTTTCTT 59.243 37.500 22.93 12.75 35.97 2.52
653 673 0.827925 TGGCCGCCATGTTTGGTTAA 60.828 50.000 8.43 0.00 45.57 2.01
662 682 3.895041 CCATGTTTGGTTAAGACACCCTT 59.105 43.478 0.00 0.00 38.30 3.95
688 708 4.847990 TTTACCATCCGTCCCTGTAAAT 57.152 40.909 0.00 0.00 0.00 1.40
881 906 5.299582 CGGATTTGTTACCGTAACCAAAT 57.700 39.130 16.98 18.91 43.53 2.32
909 934 5.125739 ACTTCACAAAAACCAATCACCGTAA 59.874 36.000 0.00 0.00 0.00 3.18
912 937 3.700038 ACAAAAACCAATCACCGTAACCA 59.300 39.130 0.00 0.00 0.00 3.67
913 938 4.159879 ACAAAAACCAATCACCGTAACCAA 59.840 37.500 0.00 0.00 0.00 3.67
914 939 5.109903 CAAAAACCAATCACCGTAACCAAA 58.890 37.500 0.00 0.00 0.00 3.28
915 940 3.994204 AACCAATCACCGTAACCAAAC 57.006 42.857 0.00 0.00 0.00 2.93
916 941 2.933573 ACCAATCACCGTAACCAAACA 58.066 42.857 0.00 0.00 0.00 2.83
1201 1317 1.594310 GAGGTCAGGACACTCTGGC 59.406 63.158 1.41 0.00 38.55 4.85
1288 1408 4.863925 GTGCCTCTCGCTCTCCGC 62.864 72.222 0.00 0.00 38.78 5.54
1290 1410 4.264638 GCCTCTCGCTCTCCGCTC 62.265 72.222 0.00 0.00 36.73 5.03
1437 1559 6.799441 TGATGATGTAAAACACGTTTATGTGC 59.201 34.615 2.08 0.00 43.74 4.57
1678 1822 5.471456 ACTGGTTGACTGATTCAGATTTGTC 59.529 40.000 20.33 8.18 34.94 3.18
1769 1913 7.778470 ATTGATCTTTCGTATTGTCCTCTTC 57.222 36.000 0.00 0.00 0.00 2.87
2016 2163 2.353109 GCTGCTGATGTCACAGACTACA 60.353 50.000 13.22 0.00 39.94 2.74
2037 2184 8.267894 ACTACATATTGCAAGAGACATTTAGGT 58.732 33.333 4.94 0.13 0.00 3.08
2200 2347 2.108157 GCCCATGCGTATCGGACA 59.892 61.111 0.41 0.00 0.00 4.02
2405 2552 5.008712 CCTTCTGTGGTTCAGTTTCCTTTAC 59.991 44.000 0.00 0.00 43.97 2.01
2540 2688 4.693566 TCATAAACTCCCATTGTGTCGAAC 59.306 41.667 0.00 0.00 0.00 3.95
2988 3230 6.610830 TCTTAGGAATGGTCAGAACCTTTTT 58.389 36.000 0.00 0.00 46.60 1.94
3066 3311 3.296943 CGTGCACACATAACGTAATTTGC 59.703 43.478 18.64 0.00 32.79 3.68
3150 3395 1.077930 CACACATCCTCTGCCTGGG 60.078 63.158 0.00 0.00 0.00 4.45
3261 3506 5.529791 GTCACAGCTAGTTGTTGAGTTCTA 58.470 41.667 9.81 0.00 0.00 2.10
3279 3524 8.128582 TGAGTTCTAGTGTTTGTTTATTTGCTG 58.871 33.333 0.00 0.00 0.00 4.41
3303 3549 7.452562 TGATCAGCTTATTCTGTGGCATAATA 58.547 34.615 0.00 0.00 35.63 0.98
3311 3557 9.701098 CTTATTCTGTGGCATAATATTGCAAAT 57.299 29.630 1.71 0.00 44.59 2.32
3612 4256 1.152652 GATCTGCCGGAGAGGAGGA 60.153 63.158 5.05 0.00 45.00 3.71
3625 4269 1.992277 GGAGGAGGAGAAGCTGCCA 60.992 63.158 0.00 0.00 0.00 4.92
3924 4629 3.636231 CGCCTTGTGACCTGGGGA 61.636 66.667 0.00 0.00 36.10 4.81
3976 4682 1.741706 GCCTTAGGGACGCCTTAAAAC 59.258 52.381 0.00 0.00 33.58 2.43
3977 4683 2.876892 GCCTTAGGGACGCCTTAAAACA 60.877 50.000 0.00 0.00 33.58 2.83
3978 4684 3.414269 CCTTAGGGACGCCTTAAAACAA 58.586 45.455 0.00 0.00 33.58 2.83
3979 4685 4.014406 CCTTAGGGACGCCTTAAAACAAT 58.986 43.478 0.00 0.00 33.58 2.71
3980 4686 4.142469 CCTTAGGGACGCCTTAAAACAATG 60.142 45.833 0.00 0.00 33.58 2.82
3981 4687 2.167662 AGGGACGCCTTAAAACAATGG 58.832 47.619 0.00 0.00 0.00 3.16
3982 4688 1.890489 GGGACGCCTTAAAACAATGGT 59.110 47.619 0.00 0.00 0.00 3.55
4150 4857 5.636123 TGAAAAGGTGGGTCTAGCAAAATA 58.364 37.500 0.00 0.00 0.00 1.40
4151 4858 6.071984 TGAAAAGGTGGGTCTAGCAAAATAA 58.928 36.000 0.00 0.00 0.00 1.40
4322 5032 5.406477 GGCCTGAGTAATTTTCAAAAGCAAG 59.594 40.000 0.00 0.00 0.00 4.01
4336 5051 7.698836 TCAAAAGCAAGCTCTGAAATTTAAC 57.301 32.000 0.00 0.00 0.00 2.01
4604 5399 6.593770 TGCTTGATACTGCGGTATATATTTGG 59.406 38.462 18.20 6.15 38.60 3.28
4659 5454 5.313520 TGACATGGCATTTGTATGAACAG 57.686 39.130 0.00 0.00 36.83 3.16
4691 5486 4.038402 ACCAAGCATTCCTTTTCAAGTCAG 59.962 41.667 0.00 0.00 0.00 3.51
4843 5643 4.210331 ACAATGATCCTAGCAATTCCACC 58.790 43.478 0.00 0.00 0.00 4.61
4901 5701 3.961408 ACTAGCCTACTGACTGGTTATGG 59.039 47.826 0.00 0.00 0.00 2.74
5004 6045 5.473504 ACAAGTTTTCACTCCATATGGTGAC 59.526 40.000 26.62 15.24 41.36 3.67
5522 6566 7.519002 CAGGAACCTGTAAAATCTTCGTTAAG 58.481 38.462 12.21 0.00 39.10 1.85
5731 6784 3.003394 TGGTATGATGAAGTGGCTTGG 57.997 47.619 0.00 0.00 0.00 3.61
5763 6816 3.765511 ACTGCACACAATTGGCTCATAAT 59.234 39.130 10.83 0.00 0.00 1.28
5764 6817 4.949238 ACTGCACACAATTGGCTCATAATA 59.051 37.500 10.83 0.00 0.00 0.98
5807 8269 8.993121 TGAACAATTAAATCTCAGAGTCAAGAC 58.007 33.333 0.00 0.00 0.00 3.01
5893 11134 8.642908 TGATCTACTACGTTTTATGAACATGG 57.357 34.615 0.00 0.00 0.00 3.66
5919 11160 6.746745 ACCATTTTACACCATTACGTTAGG 57.253 37.500 0.00 0.00 0.00 2.69
6059 11300 4.744631 GCTAGAGCAATTAGAGCTTCTGAC 59.255 45.833 0.00 0.00 43.58 3.51
6376 11639 5.351465 TGTCGATATTTTTGGCTCTGAACTC 59.649 40.000 0.00 0.00 0.00 3.01
6461 11724 6.659242 AGTGGAATATTTAGTTTGACCAGTGG 59.341 38.462 7.91 7.91 0.00 4.00
6522 11785 2.837591 GGTTATTTGGTGGGCCTTTCAT 59.162 45.455 4.53 0.00 35.27 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 3.104512 CCCAGAGAGTAACCACCATACA 58.895 50.000 0.00 0.00 0.00 2.29
294 309 0.616371 TACAAATCACCCCCACCGAG 59.384 55.000 0.00 0.00 0.00 4.63
312 327 3.846588 AGAAAGCTCCAACTTGATCCCTA 59.153 43.478 0.00 0.00 0.00 3.53
323 338 1.228862 GGCCCCAAGAAAGCTCCAA 60.229 57.895 0.00 0.00 0.00 3.53
360 375 1.221021 GGAGGGTCCACGATGTTCC 59.779 63.158 0.00 0.00 36.28 3.62
391 406 0.540923 GAGCTTCTCTGATGGCCAGT 59.459 55.000 13.05 0.00 43.38 4.00
394 409 1.666054 CAAGAGCTTCTCTGATGGCC 58.334 55.000 0.00 0.00 40.28 5.36
421 436 7.771361 TGAATACGTCTCAGATATAGATCCTCC 59.229 40.741 0.00 0.00 31.81 4.30
452 467 3.865929 CTGGCTTGCAGTCGGACGT 62.866 63.158 1.89 0.00 0.00 4.34
457 472 2.661566 CGTCACTGGCTTGCAGTCG 61.662 63.158 0.00 0.00 0.00 4.18
469 484 3.306088 CCTTGTGTATGTCTTCCGTCACT 60.306 47.826 0.00 0.00 0.00 3.41
474 489 3.868757 TCTCCTTGTGTATGTCTTCCG 57.131 47.619 0.00 0.00 0.00 4.30
481 496 2.026822 AGCCAGGTTCTCCTTGTGTATG 60.027 50.000 0.00 0.00 43.07 2.39
598 614 2.878406 AGCATGCTTCGTTAAGTTGTGT 59.122 40.909 16.30 0.00 34.99 3.72
608 624 2.158449 CGAAAGAAAGAGCATGCTTCGT 59.842 45.455 23.61 11.09 0.00 3.85
653 673 4.569865 GGATGGTAAATTCCAAGGGTGTCT 60.570 45.833 0.00 0.00 41.09 3.41
662 682 2.092646 CAGGGACGGATGGTAAATTCCA 60.093 50.000 0.00 0.00 42.01 3.53
881 906 6.459024 CGGTGATTGGTTTTTGTGAAGTTCTA 60.459 38.462 4.17 0.00 0.00 2.10
909 934 2.470057 ATGGGGTTGTTCTGTTTGGT 57.530 45.000 0.00 0.00 0.00 3.67
912 937 6.542370 CGAGATATTATGGGGTTGTTCTGTTT 59.458 38.462 0.00 0.00 0.00 2.83
913 938 6.055588 CGAGATATTATGGGGTTGTTCTGTT 58.944 40.000 0.00 0.00 0.00 3.16
914 939 5.611374 CGAGATATTATGGGGTTGTTCTGT 58.389 41.667 0.00 0.00 0.00 3.41
915 940 4.452455 GCGAGATATTATGGGGTTGTTCTG 59.548 45.833 0.00 0.00 0.00 3.02
916 941 4.642429 GCGAGATATTATGGGGTTGTTCT 58.358 43.478 0.00 0.00 0.00 3.01
956 983 1.538204 GCGCGAAGAGATTGGGATGTA 60.538 52.381 12.10 0.00 0.00 2.29
1095 1160 4.828296 GGCTGGCCCCACATCTGG 62.828 72.222 0.00 0.00 37.29 3.86
1178 1294 0.674534 GAGTGTCCTGACCTCGTTGT 59.325 55.000 0.00 0.00 0.00 3.32
1201 1317 1.115467 CAGTACTGCAGGTCCCCTAG 58.885 60.000 19.93 0.00 29.64 3.02
1288 1408 2.025767 CTGAGGAGATGGCACCGGAG 62.026 65.000 9.46 0.00 0.00 4.63
1289 1409 2.038813 TGAGGAGATGGCACCGGA 59.961 61.111 9.46 0.00 0.00 5.14
1290 1410 1.617018 TTCTGAGGAGATGGCACCGG 61.617 60.000 0.00 0.00 0.00 5.28
1417 1539 5.049954 AGACGCACATAAACGTGTTTTACAT 60.050 36.000 2.97 0.00 43.71 2.29
1418 1540 4.270566 AGACGCACATAAACGTGTTTTACA 59.729 37.500 2.97 0.00 43.71 2.41
1419 1541 4.605594 CAGACGCACATAAACGTGTTTTAC 59.394 41.667 2.97 0.00 43.71 2.01
1437 1559 3.551496 TTTGGAGCTGGGCCAGACG 62.551 63.158 37.07 12.74 36.64 4.18
1612 1736 1.271102 GTTCGCAAAATACCTTGGCCA 59.729 47.619 0.00 0.00 0.00 5.36
1678 1822 9.738832 TTGCAGAACACATGATGATAAATAATG 57.261 29.630 0.00 0.00 0.00 1.90
1769 1913 5.375417 TCACAGATTGCACCTACAAATTG 57.625 39.130 0.00 0.00 32.27 2.32
1907 2053 4.122046 TCAATCTGTATGCCATCTCAACG 58.878 43.478 0.00 0.00 0.00 4.10
2016 2163 7.226720 CCGTAACCTAAATGTCTCTTGCAATAT 59.773 37.037 0.00 0.00 0.00 1.28
2200 2347 4.128643 TGCTTTTTGCTTATTTGCAGCTT 58.871 34.783 0.00 0.00 44.27 3.74
2339 2486 4.686091 GCAAGAACAACTAAGGGCAAAATC 59.314 41.667 0.00 0.00 0.00 2.17
2346 2493 5.063880 AGTAACTGCAAGAACAACTAAGGG 58.936 41.667 0.00 0.00 37.43 3.95
2405 2552 6.366332 AGCTTCGACACATTTTCAACTAGTAG 59.634 38.462 0.00 0.00 0.00 2.57
2540 2688 2.971330 AGAGAGCCTGTTGATATCCTGG 59.029 50.000 0.00 0.74 0.00 4.45
2766 2914 1.204704 CGTTCTGCCACAGATCCTACA 59.795 52.381 0.00 0.00 40.39 2.74
2930 3079 1.341080 AACCCATGTTTGGAAGGCTG 58.659 50.000 0.00 0.00 46.92 4.85
2988 3230 0.323629 CACAAAGAGCCTCCGGGTAA 59.676 55.000 0.00 0.00 31.55 2.85
3066 3311 6.900189 AGTATATAGAAATGTCACGACTCCG 58.100 40.000 0.00 0.00 42.50 4.63
3225 3470 1.266718 GCTGTGACGCCAAATCTCAAA 59.733 47.619 0.00 0.00 0.00 2.69
3279 3524 6.814506 ATTATGCCACAGAATAAGCTGATC 57.185 37.500 0.00 0.00 39.20 2.92
3303 3549 7.121759 ACAATAAGACAGCTGAGTATTTGCAAT 59.878 33.333 23.35 0.00 0.00 3.56
3311 3557 7.093354 CAGAAAGACAATAAGACAGCTGAGTA 58.907 38.462 23.35 9.40 0.00 2.59
3358 3605 5.741011 ACCGCCTTAAAAACATAGATCTCA 58.259 37.500 0.00 0.00 0.00 3.27
3359 3606 7.041984 CCTTACCGCCTTAAAAACATAGATCTC 60.042 40.741 0.00 0.00 0.00 2.75
3360 3607 6.766467 CCTTACCGCCTTAAAAACATAGATCT 59.234 38.462 0.00 0.00 0.00 2.75
3361 3608 6.512903 GCCTTACCGCCTTAAAAACATAGATC 60.513 42.308 0.00 0.00 0.00 2.75
3362 3609 5.298527 GCCTTACCGCCTTAAAAACATAGAT 59.701 40.000 0.00 0.00 0.00 1.98
3363 3610 4.637091 GCCTTACCGCCTTAAAAACATAGA 59.363 41.667 0.00 0.00 0.00 1.98
3612 4256 0.977108 CCTCTCTGGCAGCTTCTCCT 60.977 60.000 10.34 0.00 0.00 3.69
3625 4269 1.228215 AGCTTCTCCCCCTCCTCTCT 61.228 60.000 0.00 0.00 0.00 3.10
3976 4682 6.860080 AGTGCTCAAAATATCTCAACCATTG 58.140 36.000 0.00 0.00 0.00 2.82
3977 4683 8.579850 TTAGTGCTCAAAATATCTCAACCATT 57.420 30.769 0.00 0.00 0.00 3.16
3978 4684 8.757982 ATTAGTGCTCAAAATATCTCAACCAT 57.242 30.769 0.00 0.00 0.00 3.55
3979 4685 9.679661 TTATTAGTGCTCAAAATATCTCAACCA 57.320 29.630 0.00 0.00 0.00 3.67
3980 4686 9.937175 GTTATTAGTGCTCAAAATATCTCAACC 57.063 33.333 0.00 0.00 0.00 3.77
3981 4687 9.638300 CGTTATTAGTGCTCAAAATATCTCAAC 57.362 33.333 0.00 0.00 0.00 3.18
3982 4688 9.594478 TCGTTATTAGTGCTCAAAATATCTCAA 57.406 29.630 0.00 0.00 0.00 3.02
4049 4755 9.303537 CTCTACTAGAGTTGCTATAAAACCAAC 57.696 37.037 0.00 0.00 37.57 3.77
4150 4857 1.224592 GATGGAGCACGGGATGGTT 59.775 57.895 0.00 0.00 39.82 3.67
4151 4858 2.911143 GATGGAGCACGGGATGGT 59.089 61.111 0.00 0.00 43.43 3.55
4295 5005 5.177511 GCTTTTGAAAATTACTCAGGCCAAC 59.822 40.000 5.01 0.00 0.00 3.77
4336 5051 9.878599 AGAAGACGAATAACAAACTTTAACATG 57.121 29.630 0.00 0.00 0.00 3.21
4604 5399 8.091449 ACACATTCTATCTAGCAATAACTAGGC 58.909 37.037 0.00 0.00 40.13 3.93
4659 5454 4.192429 AGGAATGCTTGGTAAATGCAAC 57.808 40.909 0.00 0.00 40.24 4.17
4691 5486 6.593382 TGCCATGCAGGTTATAAATTTTCAAC 59.407 34.615 0.00 1.14 40.61 3.18
4843 5643 4.084013 AGGAAATAGAACAAAGAACGCACG 60.084 41.667 0.00 0.00 0.00 5.34
5004 6045 4.119862 CAGGTATCTTAACATGGACCACG 58.880 47.826 0.00 0.00 0.00 4.94
5148 6189 1.079987 AGGGCTTCCTCTGCAGAGA 59.920 57.895 39.34 24.37 44.74 3.10
5230 6271 5.913137 TCACCTGAACTTGTTTGTTTGAT 57.087 34.783 0.00 0.00 0.00 2.57
5522 6566 2.656560 AAGTCAGACGGCATCTACAC 57.343 50.000 0.00 0.00 35.15 2.90
5731 6784 5.156355 CAATTGTGTGCAGTGGTAATTCTC 58.844 41.667 0.00 0.00 0.00 2.87
5763 6816 4.101898 TGTTCAACCTGGCTACTCAACTTA 59.898 41.667 0.00 0.00 0.00 2.24
5764 6817 3.118038 TGTTCAACCTGGCTACTCAACTT 60.118 43.478 0.00 0.00 0.00 2.66
5893 11134 8.553696 CCTAACGTAATGGTGTAAAATGGTATC 58.446 37.037 0.00 0.00 0.00 2.24
5907 11148 0.462789 AGCCGGACCTAACGTAATGG 59.537 55.000 5.05 0.00 0.00 3.16
5919 11160 1.737793 CAAATGTTGGACTAGCCGGAC 59.262 52.381 5.05 0.00 40.66 4.79
6096 11337 8.813643 ATACAGAAGACGTAAATAGCCAATAC 57.186 34.615 0.00 0.00 0.00 1.89
6345 11608 4.336433 AGCCAAAAATATCGACATCCACAG 59.664 41.667 0.00 0.00 0.00 3.66
6436 11699 6.659242 CCACTGGTCAAACTAAATATTCCACT 59.341 38.462 0.00 0.00 0.00 4.00
6437 11700 6.127730 CCCACTGGTCAAACTAAATATTCCAC 60.128 42.308 0.00 0.00 0.00 4.02
6461 11724 1.207791 ACACACTCCATCATCTCCCC 58.792 55.000 0.00 0.00 0.00 4.81


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

AutoCloner maintained by Alex Coulton.