Multiple sequence alignment - TraesCS2B01G610400

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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 TraesCS2B01G610400 chr2B 100.000 2621 0 0 1 2621 789963609 789966229 0.000000e+00 4841.0
1 TraesCS2B01G610400 chr2B 83.176 636 95 3 998 1621 649750233 649749598 2.930000e-159 571.0
2 TraesCS2B01G610400 chr2B 83.176 636 95 3 998 1621 649756122 649755487 2.930000e-159 571.0
3 TraesCS2B01G610400 chr2B 82.759 638 94 6 998 1622 649708242 649707608 2.950000e-154 555.0
4 TraesCS2B01G610400 chr2B 82.704 636 98 9 998 1621 649714073 649713438 2.950000e-154 555.0
5 TraesCS2B01G610400 chr2B 95.238 63 1 2 2370 2432 135771236 135771296 5.970000e-17 99.0
6 TraesCS2B01G610400 chr2D 90.348 1896 83 52 546 2388 645662294 645660446 0.000000e+00 2396.0
7 TraesCS2B01G610400 chr2D 81.291 759 114 17 883 1621 544464990 544464240 8.080000e-165 590.0
8 TraesCS2B01G610400 chr2D 87.381 420 23 6 144 549 645662722 645662319 3.080000e-124 455.0
9 TraesCS2B01G610400 chr2D 94.161 137 7 1 1 137 645663097 645662962 9.510000e-50 207.0
10 TraesCS2B01G610400 chr2D 89.809 157 11 5 2467 2621 645660438 645660285 2.060000e-46 196.0
11 TraesCS2B01G610400 chr2A 89.718 1595 74 50 570 2106 771339560 771341122 0.000000e+00 1954.0
12 TraesCS2B01G610400 chr2A 81.506 757 116 15 883 1621 686802027 686801277 3.730000e-168 601.0
13 TraesCS2B01G610400 chr2A 81.374 757 105 20 883 1621 686812502 686811764 3.760000e-163 584.0
14 TraesCS2B01G610400 chr2A 82.712 671 96 12 966 1621 686805671 686805006 1.750000e-161 579.0
15 TraesCS2B01G610400 chr2A 83.067 313 16 16 135 440 771339112 771339394 1.560000e-62 250.0
16 TraesCS2B01G610400 chr2A 91.765 85 5 2 2467 2550 771341542 771341625 1.650000e-22 117.0
17 TraesCS2B01G610400 chr7B 93.846 65 3 1 2386 2449 428486208 428486272 2.150000e-16 97.1
18 TraesCS2B01G610400 chr7B 91.549 71 3 3 2364 2432 159510579 159510648 7.720000e-16 95.3
19 TraesCS2B01G610400 chr6D 95.161 62 2 1 2372 2433 94664987 94665047 2.150000e-16 97.1
20 TraesCS2B01G610400 chr5D 93.750 64 2 1 2386 2449 340640279 340640340 7.720000e-16 95.3
21 TraesCS2B01G610400 chr4D 93.750 64 2 1 2386 2449 87655588 87655649 7.720000e-16 95.3
22 TraesCS2B01G610400 chr4D 93.750 64 2 1 2386 2449 363958121 363958060 7.720000e-16 95.3
23 TraesCS2B01G610400 chr4D 90.411 73 3 3 2379 2449 290071622 290071552 2.780000e-15 93.5
24 TraesCS2B01G610400 chr1D 93.750 64 2 1 2386 2449 201373354 201373415 7.720000e-16 95.3


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 TraesCS2B01G610400 chr2B 789963609 789966229 2620 False 4841.000000 4841 100.000000 1 2621 1 chr2B.!!$F2 2620
1 TraesCS2B01G610400 chr2B 649749598 649750233 635 True 571.000000 571 83.176000 998 1621 1 chr2B.!!$R3 623
2 TraesCS2B01G610400 chr2B 649755487 649756122 635 True 571.000000 571 83.176000 998 1621 1 chr2B.!!$R4 623
3 TraesCS2B01G610400 chr2B 649707608 649708242 634 True 555.000000 555 82.759000 998 1622 1 chr2B.!!$R1 624
4 TraesCS2B01G610400 chr2B 649713438 649714073 635 True 555.000000 555 82.704000 998 1621 1 chr2B.!!$R2 623
5 TraesCS2B01G610400 chr2D 645660285 645663097 2812 True 813.500000 2396 90.424750 1 2621 4 chr2D.!!$R2 2620
6 TraesCS2B01G610400 chr2D 544464240 544464990 750 True 590.000000 590 81.291000 883 1621 1 chr2D.!!$R1 738
7 TraesCS2B01G610400 chr2A 771339112 771341625 2513 False 773.666667 1954 88.183333 135 2550 3 chr2A.!!$F1 2415
8 TraesCS2B01G610400 chr2A 686801277 686805671 4394 True 590.000000 601 82.109000 883 1621 2 chr2A.!!$R2 738
9 TraesCS2B01G610400 chr2A 686811764 686812502 738 True 584.000000 584 81.374000 883 1621 1 chr2A.!!$R1 738

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
424 678 0.034477 AAACCCAAAGGCCGATCGAT 60.034 50.0 18.66 0.0 36.11 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1680 4488 0.182061 ATCACGAGGGAAGCATGCAT 59.818 50.0 21.98 8.13 0.0 3.96 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
78 79 6.798315 TGTCTACATAGCGGAGTATCTAAC 57.202 41.667 0.00 0.00 33.73 2.34
180 414 6.258230 TCATCACCATTTCAATGAACACTC 57.742 37.500 0.00 0.00 38.70 3.51
245 479 2.282391 ATGCACTGCCGGAAAGCA 60.282 55.556 5.05 9.04 41.46 3.91
250 484 0.169672 CACTGCCGGAAAGCAATCTG 59.830 55.000 5.05 0.00 43.52 2.90
254 488 1.876497 GCCGGAAAGCAATCTGCCAA 61.876 55.000 5.05 0.00 46.52 4.52
305 539 1.369839 GAAAACAGCTAGCTCCCCGC 61.370 60.000 16.15 0.66 39.57 6.13
311 551 3.019003 GCTAGCTCCCCGCAACAGA 62.019 63.158 7.70 0.00 42.61 3.41
327 567 3.320673 ACAGAAACTCTAAAGCCCGAG 57.679 47.619 0.00 0.00 0.00 4.63
380 634 5.994668 TGCATGACGGCAATAATAATACTGA 59.005 36.000 0.00 0.00 41.65 3.41
408 662 4.391830 TCGACTCATATGTGCAAGGAAAAC 59.608 41.667 1.90 0.00 0.00 2.43
422 676 0.170339 GAAAACCCAAAGGCCGATCG 59.830 55.000 8.51 8.51 36.11 3.69
424 678 0.034477 AAACCCAAAGGCCGATCGAT 60.034 50.000 18.66 0.00 36.11 3.59
425 679 0.834612 AACCCAAAGGCCGATCGATA 59.165 50.000 18.66 0.00 36.11 2.92
483 765 4.135153 TCGCCTCGCCAAGCTCTC 62.135 66.667 0.00 0.00 0.00 3.20
561 881 2.421739 GAGCTGTGTCCGTGTGGT 59.578 61.111 0.00 0.00 36.30 4.16
566 886 1.942677 CTGTGTCCGTGTGGTTGTAA 58.057 50.000 0.00 0.00 36.30 2.41
631 951 6.603599 GGAATGGATGGGTTAATAATCTAGGC 59.396 42.308 0.00 0.00 0.00 3.93
705 1025 7.201688 GGATGTCAAAAGAGAGGAAAAGATAGC 60.202 40.741 0.00 0.00 0.00 2.97
714 1034 4.821805 AGAGGAAAAGATAGCGAGAGAGAG 59.178 45.833 0.00 0.00 0.00 3.20
715 1035 4.787551 AGGAAAAGATAGCGAGAGAGAGA 58.212 43.478 0.00 0.00 0.00 3.10
809 1129 0.815615 GAACCTCAGCGCTAATGGGG 60.816 60.000 10.99 11.75 44.51 4.96
855 1175 3.345808 CACACGCAACACCCTCCG 61.346 66.667 0.00 0.00 0.00 4.63
927 3702 0.533032 GTCCTCCACACTACTGCCTC 59.467 60.000 0.00 0.00 0.00 4.70
929 3704 0.616111 CCTCCACACTACTGCCTCCT 60.616 60.000 0.00 0.00 0.00 3.69
947 3722 3.315142 TTGCCTGCTACCTGCCTCG 62.315 63.158 0.00 0.00 42.00 4.63
967 3754 0.034767 CACCACTGCCACCATCTCAT 60.035 55.000 0.00 0.00 0.00 2.90
1392 4200 4.821589 GCCCTCGCCTTCTCCGTG 62.822 72.222 0.00 0.00 0.00 4.94
1674 4482 2.747822 CCGTCACCGATCGTCGTCT 61.748 63.158 15.09 0.00 38.40 4.18
1675 4483 1.296722 CGTCACCGATCGTCGTCTC 60.297 63.158 15.09 0.72 38.40 3.36
1679 4487 1.818785 ACCGATCGTCGTCTCCTCC 60.819 63.158 15.09 0.00 38.40 4.30
1680 4488 1.818363 CCGATCGTCGTCTCCTCCA 60.818 63.158 15.09 0.00 38.40 3.86
1681 4489 1.167155 CCGATCGTCGTCTCCTCCAT 61.167 60.000 15.09 0.00 38.40 3.41
1682 4490 0.040870 CGATCGTCGTCTCCTCCATG 60.041 60.000 7.03 0.00 34.72 3.66
1690 4498 1.307097 GTCTCCTCCATGCATGCTTC 58.693 55.000 21.69 3.27 0.00 3.86
1705 4513 0.030908 GCTTCCCTCGTGATCCTACG 59.969 60.000 0.00 0.00 44.98 3.51
1813 4644 7.468084 CGTCTCTTCCCTAGTTAATTCTCTCTG 60.468 44.444 0.00 0.00 0.00 3.35
1829 4662 6.691754 TCTCTCTGTCTCTACTGCTATTTG 57.308 41.667 0.00 0.00 0.00 2.32
1847 4680 5.840243 ATTTGCTAGTCTTTGCATGCATA 57.160 34.783 23.37 16.39 39.07 3.14
1848 4681 5.840243 TTTGCTAGTCTTTGCATGCATAT 57.160 34.783 23.37 8.43 39.07 1.78
1924 4764 7.241663 TGCTATAGTATTTTTACTTGCACCG 57.758 36.000 0.84 0.00 30.72 4.94
1984 4838 3.859386 GTGACAAGGTTGTTGCAAGAAAG 59.141 43.478 11.02 4.45 42.43 2.62
1986 4840 2.204237 CAAGGTTGTTGCAAGAAAGGC 58.796 47.619 11.02 0.00 0.00 4.35
1987 4841 1.484038 AGGTTGTTGCAAGAAAGGCA 58.516 45.000 11.02 0.00 40.00 4.75
1989 4843 1.538849 GGTTGTTGCAAGAAAGGCAGG 60.539 52.381 11.02 0.00 43.05 4.85
1990 4844 0.104671 TTGTTGCAAGAAAGGCAGGC 59.895 50.000 6.55 0.00 43.05 4.85
1998 4857 5.634118 TGCAAGAAAGGCAGGCTATATATT 58.366 37.500 0.00 0.00 36.11 1.28
2043 4903 0.605050 TGCAAGTCAAGCCGTATGCA 60.605 50.000 0.00 0.00 44.83 3.96
2044 4904 0.734889 GCAAGTCAAGCCGTATGCAT 59.265 50.000 3.79 3.79 44.83 3.96
2045 4905 1.939934 GCAAGTCAAGCCGTATGCATA 59.060 47.619 1.16 1.16 44.83 3.14
2046 4906 2.549754 GCAAGTCAAGCCGTATGCATAT 59.450 45.455 10.16 0.00 44.83 1.78
2047 4907 3.607775 GCAAGTCAAGCCGTATGCATATG 60.608 47.826 17.55 17.55 44.83 1.78
2048 4908 2.146342 AGTCAAGCCGTATGCATATGC 58.854 47.619 21.09 21.09 44.83 3.14
2139 5026 3.456280 GCAAAGAATCAGGTTGTTGCAA 58.544 40.909 0.00 0.00 37.38 4.08
2140 5027 3.492011 GCAAAGAATCAGGTTGTTGCAAG 59.508 43.478 0.00 0.00 37.38 4.01
2144 5031 3.005155 AGAATCAGGTTGTTGCAAGAAGC 59.995 43.478 25.97 25.97 45.96 3.86
2160 5047 5.731686 GCAAGAAGCCAAGTTCTACATATGC 60.732 44.000 1.58 0.00 35.65 3.14
2169 5056 9.706691 GCCAAGTTCTACATATGCTACTAATTA 57.293 33.333 1.58 0.00 0.00 1.40
2250 5237 4.778842 AAGAATAATTAGCAGCGTGACG 57.221 40.909 0.00 0.00 0.00 4.35
2317 5306 0.464036 GAGTCACTCCACACCACACA 59.536 55.000 0.00 0.00 0.00 3.72
2373 5378 6.752335 TTAAAGCATGCATAATTCGCAATC 57.248 33.333 21.98 2.61 43.84 2.67
2388 5393 1.947678 GCAATCTGCCACACAGCTACT 60.948 52.381 0.00 0.00 46.76 2.57
2389 5394 2.005451 CAATCTGCCACACAGCTACTC 58.995 52.381 0.00 0.00 46.76 2.59
2390 5395 0.539051 ATCTGCCACACAGCTACTCC 59.461 55.000 0.00 0.00 46.76 3.85
2391 5396 1.078848 CTGCCACACAGCTACTCCC 60.079 63.158 0.00 0.00 40.19 4.30
2392 5397 1.536418 TGCCACACAGCTACTCCCT 60.536 57.895 0.00 0.00 0.00 4.20
2394 5399 1.901085 CCACACAGCTACTCCCTCC 59.099 63.158 0.00 0.00 0.00 4.30
2395 5400 1.513158 CACACAGCTACTCCCTCCG 59.487 63.158 0.00 0.00 0.00 4.63
2396 5401 1.076906 ACACAGCTACTCCCTCCGT 59.923 57.895 0.00 0.00 0.00 4.69
2397 5402 0.542232 ACACAGCTACTCCCTCCGTT 60.542 55.000 0.00 0.00 0.00 4.44
2398 5403 0.173708 CACAGCTACTCCCTCCGTTC 59.826 60.000 0.00 0.00 0.00 3.95
2399 5404 0.971447 ACAGCTACTCCCTCCGTTCC 60.971 60.000 0.00 0.00 0.00 3.62
2400 5405 0.970937 CAGCTACTCCCTCCGTTCCA 60.971 60.000 0.00 0.00 0.00 3.53
2401 5406 0.252103 AGCTACTCCCTCCGTTCCAA 60.252 55.000 0.00 0.00 0.00 3.53
2402 5407 0.611714 GCTACTCCCTCCGTTCCAAA 59.388 55.000 0.00 0.00 0.00 3.28
2403 5408 1.002773 GCTACTCCCTCCGTTCCAAAA 59.997 52.381 0.00 0.00 0.00 2.44
2404 5409 2.355818 GCTACTCCCTCCGTTCCAAAAT 60.356 50.000 0.00 0.00 0.00 1.82
2405 5410 3.118519 GCTACTCCCTCCGTTCCAAAATA 60.119 47.826 0.00 0.00 0.00 1.40
2406 5411 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2407 5412 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2408 5413 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
2409 5414 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
2410 5415 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
2411 5416 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
2412 5417 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
2413 5418 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
2414 5419 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
2415 5420 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
2416 5421 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
2417 5422 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
2418 5423 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
2419 5424 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
2420 5425 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
2421 5426 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
2422 5427 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
2423 5428 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
2424 5429 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
2434 5439 9.268268 TGACTCAACTTTGTACTAACTTTATGG 57.732 33.333 0.00 0.00 0.00 2.74
2435 5440 9.485206 GACTCAACTTTGTACTAACTTTATGGA 57.515 33.333 0.00 0.00 0.00 3.41
2436 5441 9.841295 ACTCAACTTTGTACTAACTTTATGGAA 57.159 29.630 0.00 0.00 0.00 3.53
2438 5443 8.767085 TCAACTTTGTACTAACTTTATGGAACG 58.233 33.333 0.00 0.00 0.00 3.95
2439 5444 8.767085 CAACTTTGTACTAACTTTATGGAACGA 58.233 33.333 0.00 0.00 0.00 3.85
2440 5445 8.891671 ACTTTGTACTAACTTTATGGAACGAA 57.108 30.769 0.00 0.00 0.00 3.85
2441 5446 8.985805 ACTTTGTACTAACTTTATGGAACGAAG 58.014 33.333 0.00 0.00 34.64 3.79
2442 5447 7.894376 TTGTACTAACTTTATGGAACGAAGG 57.106 36.000 0.00 0.00 0.00 3.46
2443 5448 6.400568 TGTACTAACTTTATGGAACGAAGGG 58.599 40.000 0.00 0.00 0.00 3.95
2444 5449 5.750352 ACTAACTTTATGGAACGAAGGGA 57.250 39.130 0.00 0.00 0.00 4.20
2445 5450 5.731591 ACTAACTTTATGGAACGAAGGGAG 58.268 41.667 0.00 0.00 0.00 4.30
2446 5451 4.635699 AACTTTATGGAACGAAGGGAGT 57.364 40.909 0.00 0.00 0.00 3.85
2447 5452 5.750352 AACTTTATGGAACGAAGGGAGTA 57.250 39.130 0.00 0.00 0.00 2.59
2448 5453 5.082251 ACTTTATGGAACGAAGGGAGTAC 57.918 43.478 0.00 0.00 0.00 2.73
2449 5454 3.788333 TTATGGAACGAAGGGAGTACG 57.212 47.619 0.00 0.00 0.00 3.67
2450 5455 1.553706 ATGGAACGAAGGGAGTACGT 58.446 50.000 0.00 0.00 41.97 3.57
2451 5456 2.198827 TGGAACGAAGGGAGTACGTA 57.801 50.000 0.00 0.00 39.31 3.57
2452 5457 1.812571 TGGAACGAAGGGAGTACGTAC 59.187 52.381 18.10 18.10 39.31 3.67
2453 5458 1.133216 GGAACGAAGGGAGTACGTACC 59.867 57.143 21.80 13.02 39.31 3.34
2454 5459 2.087646 GAACGAAGGGAGTACGTACCT 58.912 52.381 21.80 9.71 39.31 3.08
2455 5460 3.270877 GAACGAAGGGAGTACGTACCTA 58.729 50.000 21.80 0.00 39.31 3.08
2456 5461 2.911484 ACGAAGGGAGTACGTACCTAG 58.089 52.381 21.80 11.95 38.47 3.02
2457 5462 1.601430 CGAAGGGAGTACGTACCTAGC 59.399 57.143 21.80 9.17 33.37 3.42
2458 5463 2.744494 CGAAGGGAGTACGTACCTAGCT 60.744 54.545 21.80 2.90 33.37 3.32
2459 5464 3.286353 GAAGGGAGTACGTACCTAGCTT 58.714 50.000 21.80 6.96 33.37 3.74
2460 5465 4.455606 GAAGGGAGTACGTACCTAGCTTA 58.544 47.826 21.80 0.00 33.37 3.09
2461 5466 4.084011 AGGGAGTACGTACCTAGCTTAG 57.916 50.000 21.80 0.00 31.53 2.18
2478 5483 5.812286 AGCTTAGGTAGAGAGCTAGGATAC 58.188 45.833 0.00 0.00 44.41 2.24
2499 5504 7.336931 GGATACTATTTCAAGCTTCTTGTCCAA 59.663 37.037 0.00 0.50 0.00 3.53
2500 5505 8.814038 ATACTATTTCAAGCTTCTTGTCCAAT 57.186 30.769 0.00 6.56 0.00 3.16
2501 5506 7.150783 ACTATTTCAAGCTTCTTGTCCAATC 57.849 36.000 0.00 0.00 0.00 2.67
2503 5508 3.795688 TCAAGCTTCTTGTCCAATCCT 57.204 42.857 0.00 0.00 0.00 3.24
2545 5551 2.353858 TCGGGTCCGAGCTTAACAA 58.646 52.632 8.14 0.00 44.01 2.83
2546 5552 0.037975 TCGGGTCCGAGCTTAACAAC 60.038 55.000 8.14 0.00 44.01 3.32
2549 5555 2.223745 GGGTCCGAGCTTAACAACAAA 58.776 47.619 0.00 0.00 0.00 2.83
2551 5557 3.254903 GGGTCCGAGCTTAACAACAAAAT 59.745 43.478 0.00 0.00 0.00 1.82
2553 5559 4.473199 GTCCGAGCTTAACAACAAAATCC 58.527 43.478 0.00 0.00 0.00 3.01
2554 5560 4.215613 GTCCGAGCTTAACAACAAAATCCT 59.784 41.667 0.00 0.00 0.00 3.24
2555 5561 5.410439 GTCCGAGCTTAACAACAAAATCCTA 59.590 40.000 0.00 0.00 0.00 2.94
2556 5562 5.642063 TCCGAGCTTAACAACAAAATCCTAG 59.358 40.000 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 7.817418 TGTAGACAAAAGGAAAGCTAAACAT 57.183 32.000 0.00 0.00 0.00 2.71
42 43 6.312918 CGCTATGTAGACAAAAGGAAAGCTAA 59.687 38.462 0.00 0.00 0.00 3.09
78 79 5.105635 ACCAATTATGCATCTGGTTCAACAG 60.106 40.000 17.94 0.00 39.14 3.16
180 414 3.303132 GCCTGTTTTGTGTCTCGTAAGTG 60.303 47.826 0.00 0.00 39.48 3.16
238 472 0.247460 GGGTTGGCAGATTGCTTTCC 59.753 55.000 0.67 1.68 44.28 3.13
245 479 1.686115 GGCATAGTGGGTTGGCAGATT 60.686 52.381 0.00 0.00 38.23 2.40
250 484 2.418083 GCTGGCATAGTGGGTTGGC 61.418 63.158 0.00 0.00 38.77 4.52
254 488 0.112218 TTTGTGCTGGCATAGTGGGT 59.888 50.000 0.00 0.00 0.00 4.51
305 539 3.399330 TCGGGCTTTAGAGTTTCTGTTG 58.601 45.455 0.00 0.00 0.00 3.33
311 551 0.984995 AGGCTCGGGCTTTAGAGTTT 59.015 50.000 7.48 0.00 33.67 2.66
327 567 1.357761 AGAGATCTAGCTAGGGGAGGC 59.642 57.143 20.58 6.11 0.00 4.70
374 628 6.676700 GCACATATGAGTCGATCGATCAGTAT 60.677 42.308 22.50 17.84 0.00 2.12
376 630 4.614764 GCACATATGAGTCGATCGATCAGT 60.615 45.833 22.50 15.28 0.00 3.41
377 631 3.850837 GCACATATGAGTCGATCGATCAG 59.149 47.826 22.50 16.57 0.00 2.90
378 632 3.253188 TGCACATATGAGTCGATCGATCA 59.747 43.478 22.50 22.92 0.00 2.92
380 634 3.923017 TGCACATATGAGTCGATCGAT 57.077 42.857 22.50 10.34 0.00 3.59
408 662 0.679505 TCTATCGATCGGCCTTTGGG 59.320 55.000 16.41 0.00 0.00 4.12
422 676 1.139058 AGGGAACATGGCACGTCTATC 59.861 52.381 0.00 0.00 0.00 2.08
424 678 0.981183 AAGGGAACATGGCACGTCTA 59.019 50.000 0.00 0.00 0.00 2.59
425 679 0.606401 CAAGGGAACATGGCACGTCT 60.606 55.000 0.00 0.00 0.00 4.18
466 748 4.135153 GAGAGCTTGGCGAGGCGA 62.135 66.667 3.44 0.00 0.00 5.54
468 750 4.135153 TCGAGAGCTTGGCGAGGC 62.135 66.667 3.44 0.00 0.00 4.70
469 751 2.103934 CTCGAGAGCTTGGCGAGG 59.896 66.667 19.70 7.14 45.54 4.63
483 765 3.082548 TCTGGTCCTGTCTAACTTCTCG 58.917 50.000 0.00 0.00 0.00 4.04
554 874 5.278604 TCGATCATATCTTACAACCACACG 58.721 41.667 0.00 0.00 0.00 4.49
561 881 8.846211 TGAGTGTACATCGATCATATCTTACAA 58.154 33.333 0.00 0.00 0.00 2.41
566 886 5.474876 TGCTGAGTGTACATCGATCATATCT 59.525 40.000 0.00 0.00 0.00 1.98
631 951 0.100682 CGATCGACCACACACCTAGG 59.899 60.000 10.26 7.41 0.00 3.02
705 1025 1.541233 GCCCTCTCTCTCTCTCTCTCG 60.541 61.905 0.00 0.00 0.00 4.04
714 1034 1.251527 TTGACACGGCCCTCTCTCTC 61.252 60.000 0.00 0.00 0.00 3.20
715 1035 0.616111 ATTGACACGGCCCTCTCTCT 60.616 55.000 0.00 0.00 0.00 3.10
809 1129 0.178301 CTCTCCGCCTACCTTTTCCC 59.822 60.000 0.00 0.00 0.00 3.97
811 1131 0.806492 CGCTCTCCGCCTACCTTTTC 60.806 60.000 0.00 0.00 34.21 2.29
855 1175 4.767255 CTCTGCCCGGTCAGGTGC 62.767 72.222 13.45 1.35 38.74 5.01
967 3754 1.483004 AGATCGAGAGTGAGACGGAGA 59.517 52.381 0.00 0.00 0.00 3.71
1074 3882 4.351938 CCCGCGAAGTCCACGTCA 62.352 66.667 8.23 0.00 0.00 4.35
1626 4434 0.816421 AAAAACCTCGTCCACCGGTG 60.816 55.000 28.26 28.26 37.11 4.94
1628 4436 4.468007 AAAAACCTCGTCCACCGG 57.532 55.556 0.00 0.00 37.11 5.28
1644 4452 1.997669 GGTGACGGCAACAACAAAAA 58.002 45.000 0.00 0.00 0.00 1.94
1674 4482 1.228228 GGGAAGCATGCATGGAGGA 59.772 57.895 27.34 0.00 0.00 3.71
1675 4483 0.822532 GAGGGAAGCATGCATGGAGG 60.823 60.000 27.34 2.89 0.00 4.30
1679 4487 0.745486 TCACGAGGGAAGCATGCATG 60.745 55.000 22.70 22.70 0.00 4.06
1680 4488 0.182061 ATCACGAGGGAAGCATGCAT 59.818 50.000 21.98 8.13 0.00 3.96
1681 4489 0.462581 GATCACGAGGGAAGCATGCA 60.463 55.000 21.98 0.00 0.00 3.96
1682 4490 1.162800 GGATCACGAGGGAAGCATGC 61.163 60.000 10.51 10.51 0.00 4.06
1690 4498 0.585357 CGTACGTAGGATCACGAGGG 59.415 60.000 9.66 0.00 44.69 4.30
1705 4513 2.430582 TTGGCGCCACGTACGTAC 60.431 61.111 32.95 15.90 0.00 3.67
1717 4525 2.033194 GGGGAAGAAGACGTTGGCG 61.033 63.158 0.00 0.00 44.93 5.69
1749 4557 1.811645 TTCCATGCACGGACGTCAGA 61.812 55.000 22.71 0.00 33.75 3.27
1868 4701 0.381801 GCCAATGTTACATCAGCGGG 59.618 55.000 0.00 0.00 0.00 6.13
1869 4702 0.381801 GGCCAATGTTACATCAGCGG 59.618 55.000 0.00 6.21 0.00 5.52
1871 4704 1.202336 GCTGGCCAATGTTACATCAGC 60.202 52.381 16.94 16.94 39.13 4.26
1872 4705 2.098607 CAGCTGGCCAATGTTACATCAG 59.901 50.000 7.01 2.98 0.00 2.90
1873 4706 2.093890 CAGCTGGCCAATGTTACATCA 58.906 47.619 7.01 0.00 0.00 3.07
1874 4707 1.202336 GCAGCTGGCCAATGTTACATC 60.202 52.381 17.12 0.00 36.11 3.06
1924 4764 5.346822 CCAATCACTACCAGTAACGTTACAC 59.653 44.000 33.43 16.10 36.12 2.90
1937 4777 1.580059 TCCACCTCCCAATCACTACC 58.420 55.000 0.00 0.00 0.00 3.18
2021 4881 2.009051 CATACGGCTTGACTTGCATGA 58.991 47.619 6.60 0.00 0.00 3.07
2048 4908 7.012138 AGCTTACTTGAACAATGAGCATATCTG 59.988 37.037 14.35 0.00 0.00 2.90
2049 4909 7.052873 AGCTTACTTGAACAATGAGCATATCT 58.947 34.615 14.35 0.00 0.00 1.98
2098 4962 4.507710 TGCCTGCTACTATTGTTCTCAAG 58.492 43.478 0.00 0.00 36.97 3.02
2111 4985 2.716217 ACCTGATTCTTTGCCTGCTAC 58.284 47.619 0.00 0.00 0.00 3.58
2118 4992 3.096489 TGCAACAACCTGATTCTTTGC 57.904 42.857 0.00 0.00 37.06 3.68
2139 5026 5.365021 AGCATATGTAGAACTTGGCTTCT 57.635 39.130 4.29 0.00 34.72 2.85
2140 5027 6.284459 AGTAGCATATGTAGAACTTGGCTTC 58.716 40.000 4.29 0.00 0.00 3.86
2228 5206 4.034048 CCGTCACGCTGCTAATTATTCTTT 59.966 41.667 0.00 0.00 0.00 2.52
2229 5207 3.555956 CCGTCACGCTGCTAATTATTCTT 59.444 43.478 0.00 0.00 0.00 2.52
2230 5208 3.123804 CCGTCACGCTGCTAATTATTCT 58.876 45.455 0.00 0.00 0.00 2.40
2231 5209 2.864343 ACCGTCACGCTGCTAATTATTC 59.136 45.455 0.00 0.00 0.00 1.75
2232 5210 2.607635 CACCGTCACGCTGCTAATTATT 59.392 45.455 0.00 0.00 0.00 1.40
2250 5237 2.158449 CGTGATTCTTTGTCTCTGCACC 59.842 50.000 0.00 0.00 0.00 5.01
2317 5306 6.017523 CGGTGCATCGATCATATCTATCTACT 60.018 42.308 15.97 0.00 0.00 2.57
2388 5393 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
2389 5394 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
2390 5395 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
2391 5396 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
2392 5397 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
2394 5399 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
2395 5400 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
2396 5401 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
2397 5402 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
2398 5403 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
2408 5413 9.268268 CCATAAAGTTAGTACAAAGTTGAGTCA 57.732 33.333 0.00 0.00 0.00 3.41
2409 5414 9.485206 TCCATAAAGTTAGTACAAAGTTGAGTC 57.515 33.333 0.00 0.00 0.00 3.36
2410 5415 9.841295 TTCCATAAAGTTAGTACAAAGTTGAGT 57.159 29.630 0.00 0.00 0.00 3.41
2412 5417 8.767085 CGTTCCATAAAGTTAGTACAAAGTTGA 58.233 33.333 0.00 0.00 0.00 3.18
2413 5418 8.767085 TCGTTCCATAAAGTTAGTACAAAGTTG 58.233 33.333 0.00 0.00 0.00 3.16
2414 5419 8.891671 TCGTTCCATAAAGTTAGTACAAAGTT 57.108 30.769 0.00 0.00 0.00 2.66
2415 5420 8.891671 TTCGTTCCATAAAGTTAGTACAAAGT 57.108 30.769 0.00 0.00 0.00 2.66
2416 5421 8.440833 CCTTCGTTCCATAAAGTTAGTACAAAG 58.559 37.037 0.00 0.00 0.00 2.77
2417 5422 7.388500 CCCTTCGTTCCATAAAGTTAGTACAAA 59.612 37.037 0.00 0.00 0.00 2.83
2418 5423 6.875195 CCCTTCGTTCCATAAAGTTAGTACAA 59.125 38.462 0.00 0.00 0.00 2.41
2419 5424 6.211184 TCCCTTCGTTCCATAAAGTTAGTACA 59.789 38.462 0.00 0.00 0.00 2.90
2420 5425 6.633856 TCCCTTCGTTCCATAAAGTTAGTAC 58.366 40.000 0.00 0.00 0.00 2.73
2421 5426 6.438425 ACTCCCTTCGTTCCATAAAGTTAGTA 59.562 38.462 0.00 0.00 0.00 1.82
2422 5427 5.247792 ACTCCCTTCGTTCCATAAAGTTAGT 59.752 40.000 0.00 0.00 0.00 2.24
2423 5428 5.731591 ACTCCCTTCGTTCCATAAAGTTAG 58.268 41.667 0.00 0.00 0.00 2.34
2424 5429 5.750352 ACTCCCTTCGTTCCATAAAGTTA 57.250 39.130 0.00 0.00 0.00 2.24
2425 5430 4.635699 ACTCCCTTCGTTCCATAAAGTT 57.364 40.909 0.00 0.00 0.00 2.66
2426 5431 4.381292 CGTACTCCCTTCGTTCCATAAAGT 60.381 45.833 0.00 0.00 0.00 2.66
2427 5432 4.110482 CGTACTCCCTTCGTTCCATAAAG 58.890 47.826 0.00 0.00 0.00 1.85
2428 5433 3.511146 ACGTACTCCCTTCGTTCCATAAA 59.489 43.478 0.00 0.00 34.07 1.40
2429 5434 3.091545 ACGTACTCCCTTCGTTCCATAA 58.908 45.455 0.00 0.00 34.07 1.90
2430 5435 2.726821 ACGTACTCCCTTCGTTCCATA 58.273 47.619 0.00 0.00 34.07 2.74
2431 5436 1.553706 ACGTACTCCCTTCGTTCCAT 58.446 50.000 0.00 0.00 34.07 3.41
2432 5437 1.812571 GTACGTACTCCCTTCGTTCCA 59.187 52.381 18.47 0.00 38.69 3.53
2433 5438 1.133216 GGTACGTACTCCCTTCGTTCC 59.867 57.143 24.07 0.22 37.70 3.62
2434 5439 2.087646 AGGTACGTACTCCCTTCGTTC 58.912 52.381 24.07 4.60 38.69 3.95
2435 5440 2.206576 AGGTACGTACTCCCTTCGTT 57.793 50.000 24.07 0.00 38.69 3.85
2436 5441 2.911484 CTAGGTACGTACTCCCTTCGT 58.089 52.381 24.07 1.94 40.78 3.85
2437 5442 1.601430 GCTAGGTACGTACTCCCTTCG 59.399 57.143 24.07 9.67 0.00 3.79
2438 5443 2.929641 AGCTAGGTACGTACTCCCTTC 58.070 52.381 24.07 7.42 0.00 3.46
2439 5444 3.378861 AAGCTAGGTACGTACTCCCTT 57.621 47.619 24.07 17.13 0.00 3.95
2440 5445 3.181446 CCTAAGCTAGGTACGTACTCCCT 60.181 52.174 24.07 15.83 41.18 4.20
2441 5446 3.145286 CCTAAGCTAGGTACGTACTCCC 58.855 54.545 24.07 9.06 41.18 4.30
2454 5459 6.731919 AGTATCCTAGCTCTCTACCTAAGCTA 59.268 42.308 0.00 3.56 44.28 3.32
2456 5461 5.812286 AGTATCCTAGCTCTCTACCTAAGC 58.188 45.833 0.00 0.00 36.27 3.09
2457 5462 9.969001 AAATAGTATCCTAGCTCTCTACCTAAG 57.031 37.037 0.00 0.00 0.00 2.18
2458 5463 9.962809 GAAATAGTATCCTAGCTCTCTACCTAA 57.037 37.037 0.00 0.00 0.00 2.69
2459 5464 9.113797 TGAAATAGTATCCTAGCTCTCTACCTA 57.886 37.037 0.00 0.00 0.00 3.08
2460 5465 7.991174 TGAAATAGTATCCTAGCTCTCTACCT 58.009 38.462 0.00 0.00 0.00 3.08
2461 5466 8.638629 TTGAAATAGTATCCTAGCTCTCTACC 57.361 38.462 0.00 0.00 0.00 3.18
2462 5467 8.241367 GCTTGAAATAGTATCCTAGCTCTCTAC 58.759 40.741 0.00 0.00 0.00 2.59
2463 5468 8.167392 AGCTTGAAATAGTATCCTAGCTCTCTA 58.833 37.037 12.33 0.00 31.92 2.43
2464 5469 7.010160 AGCTTGAAATAGTATCCTAGCTCTCT 58.990 38.462 12.33 0.00 31.92 3.10
2465 5470 7.227049 AGCTTGAAATAGTATCCTAGCTCTC 57.773 40.000 12.33 0.00 31.92 3.20
2478 5483 6.376581 AGGATTGGACAAGAAGCTTGAAATAG 59.623 38.462 2.10 0.00 0.00 1.73
2545 5551 9.688592 GTACGTAGCAATATACTAGGATTTTGT 57.311 33.333 16.63 8.44 31.56 2.83
2546 5552 9.136952 GGTACGTAGCAATATACTAGGATTTTG 57.863 37.037 19.43 12.45 31.56 2.44
2549 5555 6.950041 TGGGTACGTAGCAATATACTAGGATT 59.050 38.462 24.76 0.00 31.56 3.01
2551 5557 5.879763 TGGGTACGTAGCAATATACTAGGA 58.120 41.667 24.76 0.00 31.56 2.94
2553 5559 7.120873 AGTGATGGGTACGTAGCAATATACTAG 59.879 40.741 24.76 0.00 0.00 2.57
2554 5560 6.944290 AGTGATGGGTACGTAGCAATATACTA 59.056 38.462 24.76 3.40 0.00 1.82
2555 5561 5.773680 AGTGATGGGTACGTAGCAATATACT 59.226 40.000 24.76 21.18 0.00 2.12
2556 5562 5.862323 CAGTGATGGGTACGTAGCAATATAC 59.138 44.000 24.76 19.61 0.00 1.47
2596 5602 2.437413 CCCTCCAAAAGTTGCTACCTC 58.563 52.381 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.