Multiple sequence alignment - TraesCS2D01G102600

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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 TraesCS2D01G102600 chr2D 100.000 3407 0 0 1 3407 55314353 55317759 0.000000e+00 6292.0
1 TraesCS2D01G102600 chr2D 91.201 1648 103 18 865 2486 39832241 39830610 0.000000e+00 2202.0
2 TraesCS2D01G102600 chr2D 99.057 1060 9 1 1 1060 55299855 55300913 0.000000e+00 1901.0
3 TraesCS2D01G102600 chr2D 88.128 657 54 15 1781 2427 55357307 55356665 0.000000e+00 760.0
4 TraesCS2D01G102600 chr2D 88.222 433 39 7 1343 1775 55357766 55357346 1.090000e-139 507.0
5 TraesCS2D01G102600 chr2D 88.000 400 33 9 897 1292 55360420 55360032 3.100000e-125 459.0
6 TraesCS2D01G102600 chr2D 77.745 683 133 17 1056 1730 476912925 476913596 5.300000e-108 401.0
7 TraesCS2D01G102600 chr2D 96.591 88 3 0 771 858 39832366 39832279 2.740000e-31 147.0
8 TraesCS2D01G102600 chr2D 81.818 165 19 6 620 773 55267157 55266993 9.920000e-26 128.0
9 TraesCS2D01G102600 chr2D 100.000 33 0 0 715 747 318260516 318260484 1.020000e-05 62.1
10 TraesCS2D01G102600 chr2A 93.116 1598 70 17 905 2477 56916535 56918117 0.000000e+00 2305.0
11 TraesCS2D01G102600 chr2A 77.147 687 134 20 1056 1730 619238295 619238970 8.920000e-101 377.0
12 TraesCS2D01G102600 chr2A 92.308 104 6 1 771 874 44396109 44396008 2.740000e-31 147.0
13 TraesCS2D01G102600 chr2B 91.631 932 55 11 856 1775 87841082 87842002 0.000000e+00 1267.0
14 TraesCS2D01G102600 chr2B 87.360 712 61 17 1781 2480 87842041 87842735 0.000000e+00 789.0
15 TraesCS2D01G102600 chr2B 78.660 642 102 26 2570 3194 24106501 24105878 8.860000e-106 394.0
16 TraesCS2D01G102600 chr4B 89.296 682 69 4 1055 1734 96630519 96631198 0.000000e+00 852.0
17 TraesCS2D01G102600 chr4B 82.558 516 79 7 1894 2399 96631418 96631932 8.680000e-121 444.0
18 TraesCS2D01G102600 chr4B 87.356 87 5 5 710 790 33621134 33621220 1.010000e-15 95.3
19 TraesCS2D01G102600 chr4A 83.333 924 115 28 838 1741 529635255 529634351 0.000000e+00 817.0
20 TraesCS2D01G102600 chr4A 87.435 191 22 2 3217 3407 141570942 141570754 5.720000e-53 219.0
21 TraesCS2D01G102600 chr4A 74.208 442 84 21 2727 3162 614421474 614421891 1.270000e-34 158.0
22 TraesCS2D01G102600 chr4D 88.270 682 76 4 1055 1734 65860509 65861188 0.000000e+00 813.0
23 TraesCS2D01G102600 chr4D 82.376 505 78 8 1905 2399 65861380 65861883 2.430000e-116 429.0
24 TraesCS2D01G102600 chr4D 76.091 527 85 23 2674 3194 45713339 45713830 1.580000e-58 237.0
25 TraesCS2D01G102600 chr4D 83.182 220 25 11 3196 3407 485773403 485773188 1.250000e-44 191.0
26 TraesCS2D01G102600 chr6D 92.750 400 29 0 1 400 399407858 399408257 2.280000e-161 579.0
27 TraesCS2D01G102600 chr6D 86.486 222 21 8 3186 3404 429877396 429877611 5.680000e-58 235.0
28 TraesCS2D01G102600 chr6A 91.228 399 35 0 1 399 545532909 545533307 8.310000e-151 544.0
29 TraesCS2D01G102600 chr6A 87.978 183 20 2 3227 3407 399723214 399723396 7.400000e-52 215.0
30 TraesCS2D01G102600 chr6A 92.593 54 3 1 705 758 231703390 231703338 3.650000e-10 76.8
31 TraesCS2D01G102600 chr3A 90.323 403 35 2 1 402 729170672 729170273 3.010000e-145 525.0
32 TraesCS2D01G102600 chr3A 88.119 404 48 0 1 404 13274269 13273866 6.610000e-132 481.0
33 TraesCS2D01G102600 chr3A 84.577 201 26 4 3211 3407 9974109 9973910 9.650000e-46 195.0
34 TraesCS2D01G102600 chr3A 91.034 145 12 1 417 561 66010175 66010318 9.650000e-46 195.0
35 TraesCS2D01G102600 chr3A 80.751 213 32 9 2572 2782 91470623 91470418 1.270000e-34 158.0
36 TraesCS2D01G102600 chr1D 89.901 406 40 1 1 405 58523404 58522999 3.900000e-144 521.0
37 TraesCS2D01G102600 chr1D 91.034 145 12 1 417 561 51919273 51919416 9.650000e-46 195.0
38 TraesCS2D01G102600 chr1D 73.866 463 80 28 2674 3127 84564466 84564036 2.740000e-31 147.0
39 TraesCS2D01G102600 chr1D 93.258 89 6 0 418 506 293820076 293820164 7.670000e-27 132.0
40 TraesCS2D01G102600 chr1B 89.234 418 41 4 1 417 108558928 108559342 1.400000e-143 520.0
41 TraesCS2D01G102600 chr1B 95.833 48 2 0 710 757 198660374 198660421 1.010000e-10 78.7
42 TraesCS2D01G102600 chr5D 88.279 401 45 2 1 400 513887220 513886821 2.380000e-131 479.0
43 TraesCS2D01G102600 chr5D 75.040 629 73 41 2572 3194 180466243 180465693 7.400000e-52 215.0
44 TraesCS2D01G102600 chr5A 87.147 389 48 2 14 401 378498643 378499030 1.120000e-119 440.0
45 TraesCS2D01G102600 chr7B 78.469 627 89 35 2572 3190 87409384 87409972 5.370000e-98 368.0
46 TraesCS2D01G102600 chr7B 88.333 180 20 1 3228 3407 692195900 692196078 7.400000e-52 215.0
47 TraesCS2D01G102600 chr7B 79.808 104 10 5 667 759 227007888 227007785 7.890000e-07 65.8
48 TraesCS2D01G102600 chr3D 81.395 430 49 22 2571 2995 138216525 138216928 4.240000e-84 322.0
49 TraesCS2D01G102600 chrUn 76.907 485 68 25 2772 3233 23661483 23661946 5.680000e-58 235.0
50 TraesCS2D01G102600 chr7A 84.906 212 28 4 3195 3404 671496748 671496539 9.580000e-51 211.0
51 TraesCS2D01G102600 chr7D 87.222 180 21 2 3227 3405 603341132 603341310 1.600000e-48 204.0
52 TraesCS2D01G102600 chr7D 90.210 143 14 0 419 561 584562337 584562195 1.610000e-43 187.0
53 TraesCS2D01G102600 chr6B 85.938 192 24 2 3211 3400 88656828 88657018 5.760000e-48 202.0
54 TraesCS2D01G102600 chr6B 75.145 346 52 24 2691 3024 19317108 19317431 7.670000e-27 132.0
55 TraesCS2D01G102600 chr6B 91.837 49 4 0 710 758 294736830 294736878 6.100000e-08 69.4
56 TraesCS2D01G102600 chr6B 90.000 50 5 0 710 759 274505978 274505929 7.890000e-07 65.8
57 TraesCS2D01G102600 chr3B 93.478 46 3 0 2200 2245 799449240 799449285 6.100000e-08 69.4


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 TraesCS2D01G102600 chr2D 55314353 55317759 3406 False 6292.000000 6292 100.000000 1 3407 1 chr2D.!!$F2 3406
1 TraesCS2D01G102600 chr2D 55299855 55300913 1058 False 1901.000000 1901 99.057000 1 1060 1 chr2D.!!$F1 1059
2 TraesCS2D01G102600 chr2D 39830610 39832366 1756 True 1174.500000 2202 93.896000 771 2486 2 chr2D.!!$R3 1715
3 TraesCS2D01G102600 chr2D 55356665 55360420 3755 True 575.333333 760 88.116667 897 2427 3 chr2D.!!$R4 1530
4 TraesCS2D01G102600 chr2D 476912925 476913596 671 False 401.000000 401 77.745000 1056 1730 1 chr2D.!!$F3 674
5 TraesCS2D01G102600 chr2A 56916535 56918117 1582 False 2305.000000 2305 93.116000 905 2477 1 chr2A.!!$F1 1572
6 TraesCS2D01G102600 chr2A 619238295 619238970 675 False 377.000000 377 77.147000 1056 1730 1 chr2A.!!$F2 674
7 TraesCS2D01G102600 chr2B 87841082 87842735 1653 False 1028.000000 1267 89.495500 856 2480 2 chr2B.!!$F1 1624
8 TraesCS2D01G102600 chr2B 24105878 24106501 623 True 394.000000 394 78.660000 2570 3194 1 chr2B.!!$R1 624
9 TraesCS2D01G102600 chr4B 96630519 96631932 1413 False 648.000000 852 85.927000 1055 2399 2 chr4B.!!$F2 1344
10 TraesCS2D01G102600 chr4A 529634351 529635255 904 True 817.000000 817 83.333000 838 1741 1 chr4A.!!$R2 903
11 TraesCS2D01G102600 chr4D 65860509 65861883 1374 False 621.000000 813 85.323000 1055 2399 2 chr4D.!!$F2 1344
12 TraesCS2D01G102600 chr5D 180465693 180466243 550 True 215.000000 215 75.040000 2572 3194 1 chr5D.!!$R1 622
13 TraesCS2D01G102600 chr7B 87409384 87409972 588 False 368.000000 368 78.469000 2572 3190 1 chr7B.!!$F1 618

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
752 753 1.686355 GGGTGTCCATTGTGTCACAA 58.314 50.0 20.28 20.28 42.95 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2568 5012 0.539986 CGGGCCCTTCTGCTAGTAAA 59.46 55.0 22.43 0.0 0.0 2.01 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
502 503 8.731275 ATTATGTGGAAAGACGTATTCAATGA 57.269 30.769 13.66 4.11 0.00 2.57
698 699 3.394674 TTAATGTTCGCTCACACAGGA 57.605 42.857 0.00 0.00 0.00 3.86
731 732 3.667282 CCGGACGAGTCGTGTGGT 61.667 66.667 25.31 0.00 41.37 4.16
752 753 1.686355 GGGTGTCCATTGTGTCACAA 58.314 50.000 20.28 20.28 42.95 3.33
1568 3862 0.963962 AACGCCGTCTACTTCAAGGA 59.036 50.000 0.00 0.00 0.00 3.36
1735 4029 1.829222 TCGAGTACAAGATGGGGGAAC 59.171 52.381 0.00 0.00 0.00 3.62
1957 4377 1.272816 TGTGTATCTTCCTCCCGGACA 60.273 52.381 0.73 0.00 39.60 4.02
1960 4380 0.337082 TATCTTCCTCCCGGACACCA 59.663 55.000 0.73 0.00 39.60 4.17
1995 4415 3.918220 CTGCTCGACGCGATTGCC 61.918 66.667 15.93 0.00 43.27 4.52
2328 4770 0.104120 ATTTCGTCGCCGATCATCCA 59.896 50.000 0.00 0.00 43.80 3.41
2358 4800 1.447838 CATTGTGGACGAGGGGACG 60.448 63.158 0.00 0.00 39.31 4.79
2409 4852 5.480772 CCTAGACCCCTCGACACAATAATAT 59.519 44.000 0.00 0.00 0.00 1.28
2410 4853 6.662234 CCTAGACCCCTCGACACAATAATATA 59.338 42.308 0.00 0.00 0.00 0.86
2411 4854 6.591750 AGACCCCTCGACACAATAATATAG 57.408 41.667 0.00 0.00 0.00 1.31
2412 4855 6.312529 AGACCCCTCGACACAATAATATAGA 58.687 40.000 0.00 0.00 0.00 1.98
2413 4856 6.434652 AGACCCCTCGACACAATAATATAGAG 59.565 42.308 0.00 0.00 0.00 2.43
2414 4857 5.047235 ACCCCTCGACACAATAATATAGAGC 60.047 44.000 0.00 0.00 0.00 4.09
2415 4858 5.047306 CCCCTCGACACAATAATATAGAGCA 60.047 44.000 0.00 0.00 0.00 4.26
2416 4859 6.455647 CCCTCGACACAATAATATAGAGCAA 58.544 40.000 0.00 0.00 0.00 3.91
2480 4924 4.944962 TGCGTTTGAAATAGATGACCAG 57.055 40.909 0.00 0.00 0.00 4.00
2481 4925 3.126858 TGCGTTTGAAATAGATGACCAGC 59.873 43.478 0.00 0.00 0.00 4.85
2486 4930 7.526608 CGTTTGAAATAGATGACCAGCTTTTA 58.473 34.615 0.00 0.00 0.00 1.52
2487 4931 7.481798 CGTTTGAAATAGATGACCAGCTTTTAC 59.518 37.037 0.00 0.00 0.00 2.01
2488 4932 7.994425 TTGAAATAGATGACCAGCTTTTACA 57.006 32.000 0.00 0.00 0.00 2.41
2489 4933 8.579850 TTGAAATAGATGACCAGCTTTTACAT 57.420 30.769 0.00 0.00 0.00 2.29
2490 4934 9.679661 TTGAAATAGATGACCAGCTTTTACATA 57.320 29.630 0.00 0.00 0.00 2.29
2491 4935 9.851686 TGAAATAGATGACCAGCTTTTACATAT 57.148 29.630 0.00 0.00 0.00 1.78
2515 4959 7.894753 TTAATAATTGCACTCCATGAATCCA 57.105 32.000 0.00 0.00 0.00 3.41
2516 4960 6.989155 AATAATTGCACTCCATGAATCCAT 57.011 33.333 0.00 0.00 0.00 3.41
2517 4961 9.585369 TTAATAATTGCACTCCATGAATCCATA 57.415 29.630 0.00 0.00 0.00 2.74
2518 4962 8.660295 AATAATTGCACTCCATGAATCCATAT 57.340 30.769 0.00 0.00 0.00 1.78
2519 4963 6.989155 AATTGCACTCCATGAATCCATATT 57.011 33.333 0.00 0.00 0.00 1.28
2520 4964 9.758021 ATAATTGCACTCCATGAATCCATATTA 57.242 29.630 0.00 0.00 0.00 0.98
2521 4965 6.882610 TTGCACTCCATGAATCCATATTAC 57.117 37.500 0.00 0.00 0.00 1.89
2522 4966 6.191657 TGCACTCCATGAATCCATATTACT 57.808 37.500 0.00 0.00 0.00 2.24
2523 4967 6.233434 TGCACTCCATGAATCCATATTACTC 58.767 40.000 0.00 0.00 0.00 2.59
2524 4968 6.183361 TGCACTCCATGAATCCATATTACTCA 60.183 38.462 0.00 0.00 0.00 3.41
2525 4969 6.712095 GCACTCCATGAATCCATATTACTCAA 59.288 38.462 0.00 0.00 0.00 3.02
2526 4970 7.308229 GCACTCCATGAATCCATATTACTCAAC 60.308 40.741 0.00 0.00 0.00 3.18
2527 4971 6.931281 ACTCCATGAATCCATATTACTCAACG 59.069 38.462 0.00 0.00 0.00 4.10
2528 4972 7.061566 TCCATGAATCCATATTACTCAACGA 57.938 36.000 0.00 0.00 0.00 3.85
2529 4973 7.679783 TCCATGAATCCATATTACTCAACGAT 58.320 34.615 0.00 0.00 0.00 3.73
2530 4974 8.811994 TCCATGAATCCATATTACTCAACGATA 58.188 33.333 0.00 0.00 0.00 2.92
2531 4975 9.435688 CCATGAATCCATATTACTCAACGATAA 57.564 33.333 0.00 0.00 0.00 1.75
2568 5012 9.816787 TGGAAAAGAGTATTAAGGTTTATTGGT 57.183 29.630 0.00 0.00 0.00 3.67
2589 5033 0.616679 TACTAGCAGAAGGGCCCGTT 60.617 55.000 18.44 11.45 0.00 4.44
2654 5100 2.460757 AACATTTTGCTGCATCACCC 57.539 45.000 1.84 0.00 0.00 4.61
2665 5111 4.708909 TGCTGCATCACCCATAACATTTTA 59.291 37.500 0.00 0.00 0.00 1.52
2667 5113 6.127111 TGCTGCATCACCCATAACATTTTAAT 60.127 34.615 0.00 0.00 0.00 1.40
2670 5116 7.264221 TGCATCACCCATAACATTTTAATGAC 58.736 34.615 9.32 0.00 39.67 3.06
2672 5118 7.417797 GCATCACCCATAACATTTTAATGACCT 60.418 37.037 9.32 0.00 39.67 3.85
3001 5460 1.581954 CCAAACGGGCGCAATTGTA 59.418 52.632 10.83 0.00 0.00 2.41
3007 5466 0.307760 CGGGCGCAATTGTATCTTCC 59.692 55.000 10.83 0.00 0.00 3.46
3010 5469 1.680338 GCGCAATTGTATCTTCCCCT 58.320 50.000 0.30 0.00 0.00 4.79
3013 5472 3.403038 CGCAATTGTATCTTCCCCTAGG 58.597 50.000 7.40 0.06 0.00 3.02
3014 5473 3.149981 GCAATTGTATCTTCCCCTAGGC 58.850 50.000 2.05 0.00 0.00 3.93
3015 5474 3.435026 GCAATTGTATCTTCCCCTAGGCA 60.435 47.826 2.05 0.00 0.00 4.75
3016 5475 4.751028 GCAATTGTATCTTCCCCTAGGCAT 60.751 45.833 2.05 0.00 0.00 4.40
3017 5476 4.647564 ATTGTATCTTCCCCTAGGCATG 57.352 45.455 2.05 0.00 0.00 4.06
3018 5477 1.699634 TGTATCTTCCCCTAGGCATGC 59.300 52.381 9.90 9.90 0.00 4.06
3020 5479 0.769873 ATCTTCCCCTAGGCATGCAG 59.230 55.000 21.36 9.17 0.00 4.41
3021 5480 0.326522 TCTTCCCCTAGGCATGCAGA 60.327 55.000 21.36 8.04 0.00 4.26
3022 5481 0.108207 CTTCCCCTAGGCATGCAGAG 59.892 60.000 21.36 15.13 0.00 3.35
3023 5482 1.987807 TTCCCCTAGGCATGCAGAGC 61.988 60.000 21.36 5.41 0.00 4.09
3024 5483 2.749584 CCCCTAGGCATGCAGAGCA 61.750 63.158 21.36 0.00 44.86 4.26
3025 5484 1.525535 CCCTAGGCATGCAGAGCAC 60.526 63.158 21.36 0.00 43.04 4.40
3026 5485 1.525535 CCTAGGCATGCAGAGCACC 60.526 63.158 21.36 0.00 43.04 5.01
3027 5486 1.222661 CTAGGCATGCAGAGCACCA 59.777 57.895 21.36 0.00 43.04 4.17
3028 5487 0.179026 CTAGGCATGCAGAGCACCAT 60.179 55.000 21.36 1.96 43.04 3.55
3029 5488 1.071228 CTAGGCATGCAGAGCACCATA 59.929 52.381 21.36 2.88 43.04 2.74
3118 5582 5.023452 TCACTTATAGGTGACATCAGTGGT 58.977 41.667 13.28 0.00 40.72 4.16
3134 5598 8.893727 ACATCAGTGGTTAATATTTAGCAACTC 58.106 33.333 7.83 0.00 0.00 3.01
3167 5631 1.288127 GTGACGTACCGCCAGAAGT 59.712 57.895 0.00 0.00 0.00 3.01
3170 5634 0.807496 GACGTACCGCCAGAAGTACT 59.193 55.000 0.00 0.00 37.33 2.73
3171 5635 2.009774 GACGTACCGCCAGAAGTACTA 58.990 52.381 0.00 0.00 37.33 1.82
3172 5636 2.420022 GACGTACCGCCAGAAGTACTAA 59.580 50.000 0.00 0.00 37.33 2.24
3184 5648 8.753175 CGCCAGAAGTACTAATAATGACTTTAC 58.247 37.037 0.00 0.00 32.37 2.01
3201 5665 9.863650 ATGACTTTACTATTAGGTAGACTAGCA 57.136 33.333 13.89 0.00 34.38 3.49
3202 5666 9.690913 TGACTTTACTATTAGGTAGACTAGCAA 57.309 33.333 13.89 6.71 34.38 3.91
3209 5673 8.978472 ACTATTAGGTAGACTAGCAAACAATCA 58.022 33.333 13.89 0.00 34.38 2.57
3210 5674 9.250624 CTATTAGGTAGACTAGCAAACAATCAC 57.749 37.037 13.89 0.00 32.16 3.06
3211 5675 4.495422 AGGTAGACTAGCAAACAATCACG 58.505 43.478 13.89 0.00 0.00 4.35
3212 5676 4.021368 AGGTAGACTAGCAAACAATCACGT 60.021 41.667 13.89 0.00 0.00 4.49
3213 5677 4.091509 GGTAGACTAGCAAACAATCACGTG 59.908 45.833 9.94 9.94 0.00 4.49
3214 5678 2.480419 AGACTAGCAAACAATCACGTGC 59.520 45.455 11.67 0.00 37.26 5.34
3215 5679 2.217750 ACTAGCAAACAATCACGTGCA 58.782 42.857 11.67 0.00 39.50 4.57
3216 5680 2.813754 ACTAGCAAACAATCACGTGCAT 59.186 40.909 11.67 2.50 39.50 3.96
3217 5681 2.798976 AGCAAACAATCACGTGCATT 57.201 40.000 11.67 8.92 39.50 3.56
3218 5682 2.396601 AGCAAACAATCACGTGCATTG 58.603 42.857 25.69 25.69 39.50 2.82
3219 5683 1.136557 GCAAACAATCACGTGCATTGC 60.137 47.619 26.53 23.17 37.43 3.56
3220 5684 2.125685 CAAACAATCACGTGCATTGCA 58.874 42.857 26.53 7.38 35.02 4.08
3221 5685 2.505628 AACAATCACGTGCATTGCAA 57.494 40.000 26.53 0.00 41.47 4.08
3222 5686 2.728690 ACAATCACGTGCATTGCAAT 57.271 40.000 26.53 5.99 41.47 3.56
3223 5687 2.330286 ACAATCACGTGCATTGCAATG 58.670 42.857 30.92 30.92 41.47 2.82
3224 5688 1.656594 CAATCACGTGCATTGCAATGG 59.343 47.619 34.23 22.66 41.47 3.16
3225 5689 0.173935 ATCACGTGCATTGCAATGGG 59.826 50.000 34.23 14.96 41.47 4.00
3226 5690 0.892814 TCACGTGCATTGCAATGGGA 60.893 50.000 34.23 16.96 41.47 4.37
3227 5691 0.038435 CACGTGCATTGCAATGGGAA 60.038 50.000 34.23 7.44 41.47 3.97
3228 5692 0.678395 ACGTGCATTGCAATGGGAAA 59.322 45.000 34.23 5.25 41.47 3.13
3229 5693 1.069823 ACGTGCATTGCAATGGGAAAA 59.930 42.857 34.23 0.00 41.47 2.29
3230 5694 2.141517 CGTGCATTGCAATGGGAAAAA 58.858 42.857 34.23 0.00 41.47 1.94
3269 5733 4.374843 GTCATGACCATATTTTGCTGCA 57.625 40.909 15.31 0.00 0.00 4.41
3270 5734 4.940463 GTCATGACCATATTTTGCTGCAT 58.060 39.130 15.31 0.00 0.00 3.96
3271 5735 5.353938 GTCATGACCATATTTTGCTGCATT 58.646 37.500 15.31 0.00 0.00 3.56
3272 5736 6.506147 GTCATGACCATATTTTGCTGCATTA 58.494 36.000 15.31 0.00 0.00 1.90
3273 5737 7.149973 GTCATGACCATATTTTGCTGCATTAT 58.850 34.615 15.31 2.64 0.00 1.28
3274 5738 7.654520 GTCATGACCATATTTTGCTGCATTATT 59.345 33.333 15.31 0.00 0.00 1.40
3275 5739 7.654116 TCATGACCATATTTTGCTGCATTATTG 59.346 33.333 1.84 0.87 0.00 1.90
3276 5740 7.110043 TGACCATATTTTGCTGCATTATTGA 57.890 32.000 1.84 0.00 0.00 2.57
3277 5741 7.204604 TGACCATATTTTGCTGCATTATTGAG 58.795 34.615 1.84 0.00 0.00 3.02
3278 5742 7.068470 TGACCATATTTTGCTGCATTATTGAGA 59.932 33.333 1.84 0.00 0.00 3.27
3279 5743 7.959175 ACCATATTTTGCTGCATTATTGAGAT 58.041 30.769 1.84 0.00 0.00 2.75
3280 5744 9.081204 ACCATATTTTGCTGCATTATTGAGATA 57.919 29.630 1.84 0.00 0.00 1.98
3281 5745 9.350357 CCATATTTTGCTGCATTATTGAGATAC 57.650 33.333 1.84 0.00 0.00 2.24
3282 5746 9.902196 CATATTTTGCTGCATTATTGAGATACA 57.098 29.630 1.84 0.00 0.00 2.29
3283 5747 9.903682 ATATTTTGCTGCATTATTGAGATACAC 57.096 29.630 1.84 0.00 0.00 2.90
3284 5748 7.395190 TTTTGCTGCATTATTGAGATACACT 57.605 32.000 1.84 0.00 0.00 3.55
3285 5749 8.504812 TTTTGCTGCATTATTGAGATACACTA 57.495 30.769 1.84 0.00 0.00 2.74
3286 5750 8.681486 TTTGCTGCATTATTGAGATACACTAT 57.319 30.769 1.84 0.00 0.00 2.12
3287 5751 7.895975 TGCTGCATTATTGAGATACACTATC 57.104 36.000 0.00 0.00 35.41 2.08
3288 5752 7.444299 TGCTGCATTATTGAGATACACTATCA 58.556 34.615 0.00 0.00 37.65 2.15
3289 5753 7.386025 TGCTGCATTATTGAGATACACTATCAC 59.614 37.037 0.00 0.00 37.65 3.06
3290 5754 7.601886 GCTGCATTATTGAGATACACTATCACT 59.398 37.037 0.00 0.00 37.65 3.41
3291 5755 9.138062 CTGCATTATTGAGATACACTATCACTC 57.862 37.037 0.00 0.00 37.65 3.51
3292 5756 8.864087 TGCATTATTGAGATACACTATCACTCT 58.136 33.333 0.00 0.00 37.65 3.24
3293 5757 9.352784 GCATTATTGAGATACACTATCACTCTC 57.647 37.037 0.00 0.00 37.65 3.20
3299 5763 9.809096 TTGAGATACACTATCACTCTCAATTTC 57.191 33.333 8.73 0.00 44.03 2.17
3300 5764 8.971073 TGAGATACACTATCACTCTCAATTTCA 58.029 33.333 0.00 0.00 39.37 2.69
3301 5765 9.979578 GAGATACACTATCACTCTCAATTTCAT 57.020 33.333 0.00 0.00 37.65 2.57
3302 5766 9.761504 AGATACACTATCACTCTCAATTTCATG 57.238 33.333 0.00 0.00 37.65 3.07
3303 5767 9.755804 GATACACTATCACTCTCAATTTCATGA 57.244 33.333 0.00 0.00 35.28 3.07
3305 5769 8.853077 ACACTATCACTCTCAATTTCATGAAA 57.147 30.769 22.52 22.52 34.46 2.69
3306 5770 9.458727 ACACTATCACTCTCAATTTCATGAAAT 57.541 29.630 24.83 24.83 42.35 2.17
3307 5771 9.932699 CACTATCACTCTCAATTTCATGAAATC 57.067 33.333 29.08 0.00 39.88 2.17
3308 5772 9.676861 ACTATCACTCTCAATTTCATGAAATCA 57.323 29.630 29.08 19.15 39.88 2.57
3366 5830 8.900511 AACTCGTGAACATATTTGAAATCATG 57.099 30.769 0.00 0.47 0.00 3.07
3367 5831 8.267620 ACTCGTGAACATATTTGAAATCATGA 57.732 30.769 0.00 0.00 33.19 3.07
3368 5832 8.729756 ACTCGTGAACATATTTGAAATCATGAA 58.270 29.630 0.00 0.00 33.50 2.57
3369 5833 8.894409 TCGTGAACATATTTGAAATCATGAAC 57.106 30.769 0.00 0.00 32.26 3.18
3370 5834 8.510505 TCGTGAACATATTTGAAATCATGAACA 58.489 29.630 0.00 0.00 32.26 3.18
3371 5835 9.292846 CGTGAACATATTTGAAATCATGAACAT 57.707 29.630 0.00 0.00 0.00 2.71
3383 5847 9.543783 TGAAATCATGAACATGTTTCAAATTCA 57.456 25.926 24.58 15.15 40.88 2.57
3391 5855 9.814899 TGAACATGTTTCAAATTCATTAACACT 57.185 25.926 13.36 0.00 32.20 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
464 465 7.348274 TCTTTCCACATAATTCTGTAGGGATCT 59.652 37.037 4.49 0.00 0.00 2.75
502 503 4.000988 CTCCAAGCCGTACATACAACTTT 58.999 43.478 0.00 0.00 0.00 2.66
698 699 2.036387 TCCGGTCGTATTCCACATGAT 58.964 47.619 0.00 0.00 0.00 2.45
731 732 0.250124 GTGACACAATGGACACCCGA 60.250 55.000 0.00 0.00 34.29 5.14
752 753 3.096852 TGACTCCGATATTCACCACACT 58.903 45.455 0.00 0.00 0.00 3.55
1842 4169 3.407657 GCGGCAGCATGAGAGAAG 58.592 61.111 3.18 0.00 44.35 2.85
1889 4276 1.344942 GCTGTAGCTGTCGTTGGACG 61.345 60.000 0.00 0.00 46.49 4.79
1890 4277 2.446341 GCTGTAGCTGTCGTTGGAC 58.554 57.895 0.00 0.00 43.71 4.02
1921 4341 0.877071 CACATGGAGAACTGTGTGGC 59.123 55.000 0.00 0.00 38.56 5.01
2196 4617 1.081892 CTTTGTGGATGACCTCGCTG 58.918 55.000 0.00 0.00 37.04 5.18
2328 4770 3.270877 GTCCACAATGAAGTAGGCGAAT 58.729 45.455 0.00 0.00 0.00 3.34
2437 4880 6.063640 CATGCAATGTATTCGAAATCCAGA 57.936 37.500 0.00 0.00 40.20 3.86
2489 4933 9.585369 TGGATTCATGGAGTGCAATTATTAATA 57.415 29.630 0.00 0.00 0.00 0.98
2490 4934 8.481492 TGGATTCATGGAGTGCAATTATTAAT 57.519 30.769 0.00 0.00 0.00 1.40
2491 4935 7.894753 TGGATTCATGGAGTGCAATTATTAA 57.105 32.000 0.00 0.00 0.00 1.40
2492 4936 9.758021 ATATGGATTCATGGAGTGCAATTATTA 57.242 29.630 0.00 0.00 34.96 0.98
2493 4937 6.989155 ATGGATTCATGGAGTGCAATTATT 57.011 33.333 0.00 0.00 31.34 1.40
2494 4938 8.660295 AATATGGATTCATGGAGTGCAATTAT 57.340 30.769 0.00 0.00 34.96 1.28
2495 4939 9.013229 GTAATATGGATTCATGGAGTGCAATTA 57.987 33.333 0.00 0.00 34.96 1.40
2496 4940 6.989155 AATATGGATTCATGGAGTGCAATT 57.011 33.333 0.00 0.00 34.96 2.32
2497 4941 7.236529 AGTAATATGGATTCATGGAGTGCAAT 58.763 34.615 0.00 0.00 34.96 3.56
2498 4942 6.604171 AGTAATATGGATTCATGGAGTGCAA 58.396 36.000 0.00 0.00 34.96 4.08
2499 4943 6.183361 TGAGTAATATGGATTCATGGAGTGCA 60.183 38.462 0.00 0.00 34.96 4.57
2500 4944 6.233434 TGAGTAATATGGATTCATGGAGTGC 58.767 40.000 0.00 0.00 34.96 4.40
2501 4945 7.095481 CGTTGAGTAATATGGATTCATGGAGTG 60.095 40.741 0.00 0.00 34.96 3.51
2502 4946 6.931281 CGTTGAGTAATATGGATTCATGGAGT 59.069 38.462 0.00 0.00 34.96 3.85
2503 4947 7.154656 TCGTTGAGTAATATGGATTCATGGAG 58.845 38.462 0.00 0.00 34.96 3.86
2504 4948 7.061566 TCGTTGAGTAATATGGATTCATGGA 57.938 36.000 0.00 0.00 34.96 3.41
2505 4949 7.912056 ATCGTTGAGTAATATGGATTCATGG 57.088 36.000 0.00 0.00 34.96 3.66
2542 4986 9.816787 ACCAATAAACCTTAATACTCTTTTCCA 57.183 29.630 0.00 0.00 0.00 3.53
2553 4997 9.969001 TCTGCTAGTAAACCAATAAACCTTAAT 57.031 29.630 0.00 0.00 0.00 1.40
2554 4998 9.796180 TTCTGCTAGTAAACCAATAAACCTTAA 57.204 29.630 0.00 0.00 0.00 1.85
2555 4999 9.444600 CTTCTGCTAGTAAACCAATAAACCTTA 57.555 33.333 0.00 0.00 0.00 2.69
2556 5000 7.393515 CCTTCTGCTAGTAAACCAATAAACCTT 59.606 37.037 0.00 0.00 0.00 3.50
2557 5001 6.884836 CCTTCTGCTAGTAAACCAATAAACCT 59.115 38.462 0.00 0.00 0.00 3.50
2558 5002 6.095021 CCCTTCTGCTAGTAAACCAATAAACC 59.905 42.308 0.00 0.00 0.00 3.27
2559 5003 6.404403 GCCCTTCTGCTAGTAAACCAATAAAC 60.404 42.308 0.00 0.00 0.00 2.01
2560 5004 5.650703 GCCCTTCTGCTAGTAAACCAATAAA 59.349 40.000 0.00 0.00 0.00 1.40
2561 5005 5.190677 GCCCTTCTGCTAGTAAACCAATAA 58.809 41.667 0.00 0.00 0.00 1.40
2562 5006 4.384868 GGCCCTTCTGCTAGTAAACCAATA 60.385 45.833 0.00 0.00 0.00 1.90
2563 5007 3.621558 GCCCTTCTGCTAGTAAACCAAT 58.378 45.455 0.00 0.00 0.00 3.16
2564 5008 2.290705 GGCCCTTCTGCTAGTAAACCAA 60.291 50.000 0.00 0.00 0.00 3.67
2565 5009 1.280998 GGCCCTTCTGCTAGTAAACCA 59.719 52.381 0.00 0.00 0.00 3.67
2566 5010 1.408405 GGGCCCTTCTGCTAGTAAACC 60.408 57.143 17.04 0.00 0.00 3.27
2567 5011 1.742750 CGGGCCCTTCTGCTAGTAAAC 60.743 57.143 22.43 0.00 0.00 2.01
2568 5012 0.539986 CGGGCCCTTCTGCTAGTAAA 59.460 55.000 22.43 0.00 0.00 2.01
2578 5022 0.603439 TTGTAACGAACGGGCCCTTC 60.603 55.000 22.43 20.20 0.00 3.46
2622 5068 6.035327 GCAGCAAAATGTTATCATTGTCTTCC 59.965 38.462 0.00 0.00 42.60 3.46
2623 5069 6.587226 TGCAGCAAAATGTTATCATTGTCTTC 59.413 34.615 0.00 0.00 42.60 2.87
2629 5075 5.813672 GGTGATGCAGCAAAATGTTATCATT 59.186 36.000 6.05 0.00 44.94 2.57
2665 5111 9.883142 TTAATGAAACTGAACAAAAAGGTCATT 57.117 25.926 0.00 0.00 44.51 2.57
2667 5113 8.307483 TGTTAATGAAACTGAACAAAAAGGTCA 58.693 29.630 0.00 0.00 42.91 4.02
2939 5398 8.502387 CGGCCTGATTTGAAATTTAATTTTTGA 58.498 29.630 0.00 0.00 31.47 2.69
2940 5399 7.271008 GCGGCCTGATTTGAAATTTAATTTTTG 59.729 33.333 0.00 0.00 31.47 2.44
2947 5406 3.096092 AGGCGGCCTGATTTGAAATTTA 58.904 40.909 23.19 0.00 29.57 1.40
2995 5454 4.751028 GCATGCCTAGGGGAAGATACAATT 60.751 45.833 11.72 0.00 33.58 2.32
2996 5455 3.245052 GCATGCCTAGGGGAAGATACAAT 60.245 47.826 11.72 0.00 33.58 2.71
3001 5460 0.769873 CTGCATGCCTAGGGGAAGAT 59.230 55.000 16.68 0.00 33.58 2.40
3007 5466 1.525535 GTGCTCTGCATGCCTAGGG 60.526 63.158 16.68 7.99 41.91 3.53
3010 5469 1.130777 TATGGTGCTCTGCATGCCTA 58.869 50.000 16.68 1.59 41.91 3.93
3013 5472 4.778534 ATATTTATGGTGCTCTGCATGC 57.221 40.909 11.82 11.82 41.91 4.06
3014 5473 6.175471 TCCTATATTTATGGTGCTCTGCATG 58.825 40.000 0.00 0.00 41.91 4.06
3015 5474 6.378661 TCCTATATTTATGGTGCTCTGCAT 57.621 37.500 0.00 0.00 41.91 3.96
3016 5475 5.280164 CCTCCTATATTTATGGTGCTCTGCA 60.280 44.000 0.00 0.00 35.60 4.41
3017 5476 5.181748 CCTCCTATATTTATGGTGCTCTGC 58.818 45.833 0.00 0.00 0.00 4.26
3018 5477 6.365970 ACCTCCTATATTTATGGTGCTCTG 57.634 41.667 0.00 0.00 0.00 3.35
3020 5479 5.485708 AGGACCTCCTATATTTATGGTGCTC 59.514 44.000 0.00 0.00 46.48 4.26
3021 5480 5.415961 AGGACCTCCTATATTTATGGTGCT 58.584 41.667 0.00 0.00 46.48 4.40
3022 5481 5.763876 AGGACCTCCTATATTTATGGTGC 57.236 43.478 0.00 0.00 46.48 5.01
3108 5572 8.807948 AGTTGCTAAATATTAACCACTGATGT 57.192 30.769 0.00 0.00 0.00 3.06
3118 5582 5.137551 GCCCCCAGAGTTGCTAAATATTAA 58.862 41.667 0.00 0.00 0.00 1.40
3127 5591 0.178924 AAATTGCCCCCAGAGTTGCT 60.179 50.000 0.00 0.00 0.00 3.91
3134 5598 1.405105 CGTCACATAAATTGCCCCCAG 59.595 52.381 0.00 0.00 0.00 4.45
3184 5648 9.250624 GTGATTGTTTGCTAGTCTACCTAATAG 57.749 37.037 0.00 0.00 0.00 1.73
3194 5658 2.223144 TGCACGTGATTGTTTGCTAGTC 59.777 45.455 22.23 0.00 35.91 2.59
3195 5659 2.217750 TGCACGTGATTGTTTGCTAGT 58.782 42.857 22.23 0.00 35.91 2.57
3196 5660 2.967459 TGCACGTGATTGTTTGCTAG 57.033 45.000 22.23 0.00 35.91 3.42
3197 5661 3.563508 CAATGCACGTGATTGTTTGCTA 58.436 40.909 22.23 0.00 35.91 3.49
3198 5662 2.396601 CAATGCACGTGATTGTTTGCT 58.603 42.857 22.23 0.00 35.91 3.91
3199 5663 1.136557 GCAATGCACGTGATTGTTTGC 60.137 47.619 26.69 22.82 33.96 3.68
3200 5664 2.125685 TGCAATGCACGTGATTGTTTG 58.874 42.857 26.69 19.16 33.96 2.93
3201 5665 2.505628 TGCAATGCACGTGATTGTTT 57.494 40.000 26.69 10.86 33.96 2.83
3202 5666 2.505628 TTGCAATGCACGTGATTGTT 57.494 40.000 26.69 12.99 38.71 2.83
3203 5667 2.330286 CATTGCAATGCACGTGATTGT 58.670 42.857 25.50 14.38 38.71 2.71
3204 5668 1.656594 CCATTGCAATGCACGTGATTG 59.343 47.619 30.15 23.61 38.71 2.67
3205 5669 1.404449 CCCATTGCAATGCACGTGATT 60.404 47.619 30.15 13.10 38.71 2.57
3206 5670 0.173935 CCCATTGCAATGCACGTGAT 59.826 50.000 30.15 7.22 38.71 3.06
3207 5671 0.892814 TCCCATTGCAATGCACGTGA 60.893 50.000 30.15 18.03 38.71 4.35
3208 5672 0.038435 TTCCCATTGCAATGCACGTG 60.038 50.000 30.15 17.52 38.71 4.49
3209 5673 0.678395 TTTCCCATTGCAATGCACGT 59.322 45.000 30.15 0.00 38.71 4.49
3210 5674 1.793258 TTTTCCCATTGCAATGCACG 58.207 45.000 30.15 19.80 38.71 5.34
3248 5712 4.374843 TGCAGCAAAATATGGTCATGAC 57.625 40.909 17.91 17.91 37.77 3.06
3249 5713 5.601583 AATGCAGCAAAATATGGTCATGA 57.398 34.783 0.00 0.00 37.77 3.07
3250 5714 7.654116 TCAATAATGCAGCAAAATATGGTCATG 59.346 33.333 0.00 0.00 37.77 3.07
3251 5715 7.728148 TCAATAATGCAGCAAAATATGGTCAT 58.272 30.769 0.00 0.00 37.77 3.06
3252 5716 7.068470 TCTCAATAATGCAGCAAAATATGGTCA 59.932 33.333 0.00 0.00 37.77 4.02
3253 5717 7.428020 TCTCAATAATGCAGCAAAATATGGTC 58.572 34.615 0.00 0.00 37.77 4.02
3254 5718 7.350744 TCTCAATAATGCAGCAAAATATGGT 57.649 32.000 0.00 0.00 41.41 3.55
3255 5719 9.350357 GTATCTCAATAATGCAGCAAAATATGG 57.650 33.333 0.00 0.00 0.00 2.74
3256 5720 9.902196 TGTATCTCAATAATGCAGCAAAATATG 57.098 29.630 0.00 0.00 0.00 1.78
3257 5721 9.903682 GTGTATCTCAATAATGCAGCAAAATAT 57.096 29.630 0.00 0.00 0.00 1.28
3258 5722 9.123902 AGTGTATCTCAATAATGCAGCAAAATA 57.876 29.630 0.00 0.00 0.00 1.40
3259 5723 8.004087 AGTGTATCTCAATAATGCAGCAAAAT 57.996 30.769 0.00 0.00 0.00 1.82
3260 5724 7.395190 AGTGTATCTCAATAATGCAGCAAAA 57.605 32.000 0.00 0.00 0.00 2.44
3261 5725 8.681486 ATAGTGTATCTCAATAATGCAGCAAA 57.319 30.769 0.00 0.00 30.44 3.68
3262 5726 7.933033 TGATAGTGTATCTCAATAATGCAGCAA 59.067 33.333 0.00 0.00 36.17 3.91
3263 5727 7.386025 GTGATAGTGTATCTCAATAATGCAGCA 59.614 37.037 0.00 0.00 36.17 4.41
3264 5728 7.601886 AGTGATAGTGTATCTCAATAATGCAGC 59.398 37.037 0.00 0.00 36.17 5.25
3265 5729 9.138062 GAGTGATAGTGTATCTCAATAATGCAG 57.862 37.037 0.00 0.00 36.17 4.41
3266 5730 8.864087 AGAGTGATAGTGTATCTCAATAATGCA 58.136 33.333 0.00 0.00 36.17 3.96
3267 5731 9.352784 GAGAGTGATAGTGTATCTCAATAATGC 57.647 37.037 0.00 0.00 37.07 3.56
3274 5738 8.971073 TGAAATTGAGAGTGATAGTGTATCTCA 58.029 33.333 0.00 0.00 43.38 3.27
3275 5739 9.979578 ATGAAATTGAGAGTGATAGTGTATCTC 57.020 33.333 0.00 0.00 37.50 2.75
3276 5740 9.761504 CATGAAATTGAGAGTGATAGTGTATCT 57.238 33.333 0.00 0.00 36.17 1.98
3277 5741 9.755804 TCATGAAATTGAGAGTGATAGTGTATC 57.244 33.333 0.00 0.00 35.74 2.24
3279 5743 9.942850 TTTCATGAAATTGAGAGTGATAGTGTA 57.057 29.630 16.91 0.00 0.00 2.90
3280 5744 8.853077 TTTCATGAAATTGAGAGTGATAGTGT 57.147 30.769 16.91 0.00 0.00 3.55
3281 5745 9.932699 GATTTCATGAAATTGAGAGTGATAGTG 57.067 33.333 29.44 0.00 40.77 2.74
3282 5746 9.676861 TGATTTCATGAAATTGAGAGTGATAGT 57.323 29.630 29.44 7.83 40.77 2.12
3340 5804 9.345517 CATGATTTCAAATATGTTCACGAGTTT 57.654 29.630 0.00 0.00 0.00 2.66
3341 5805 8.729756 TCATGATTTCAAATATGTTCACGAGTT 58.270 29.630 0.00 0.00 0.00 3.01
3342 5806 8.267620 TCATGATTTCAAATATGTTCACGAGT 57.732 30.769 0.00 0.00 0.00 4.18
3343 5807 9.003112 GTTCATGATTTCAAATATGTTCACGAG 57.997 33.333 0.00 0.00 0.00 4.18
3344 5808 8.510505 TGTTCATGATTTCAAATATGTTCACGA 58.489 29.630 0.00 0.00 0.00 4.35
3345 5809 8.672214 TGTTCATGATTTCAAATATGTTCACG 57.328 30.769 0.00 0.00 0.00 4.35
3357 5821 9.543783 TGAATTTGAAACATGTTCATGATTTCA 57.456 25.926 22.95 22.95 37.47 2.69
3365 5829 9.814899 AGTGTTAATGAATTTGAAACATGTTCA 57.185 25.926 12.39 8.91 33.10 3.18


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

AutoCloner maintained by Alex Coulton.