Multiple sequence alignment - TraesCS1D01G353600

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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 TraesCS1D01G353600 chr1D 100.000 2462 0 0 1 2462 439163751 439166212 0.000000e+00 4547
1 TraesCS1D01G353600 chr1D 97.959 147 3 0 2316 2462 439167283 439167137 3.140000e-64 255
2 TraesCS1D01G353600 chr3D 94.069 1332 70 7 983 2310 542835481 542836807 0.000000e+00 2013
3 TraesCS1D01G353600 chr3D 93.534 1330 71 6 983 2310 543500152 543501468 0.000000e+00 1965
4 TraesCS1D01G353600 chr3D 93.318 1332 83 5 983 2310 461560471 461561800 0.000000e+00 1962
5 TraesCS1D01G353600 chr3D 93.168 1332 86 4 983 2310 478121184 478122514 0.000000e+00 1951
6 TraesCS1D01G353600 chr3D 95.661 991 34 3 1 983 543499052 543500041 0.000000e+00 1583
7 TraesCS1D01G353600 chr3D 97.959 147 3 0 2316 2462 268048435 268048581 3.140000e-64 255
8 TraesCS1D01G353600 chr3D 97.959 147 3 0 2316 2462 508163734 508163588 3.140000e-64 255
9 TraesCS1D01G353600 chr5D 93.844 1332 77 4 983 2310 238122958 238124288 0.000000e+00 2001
10 TraesCS1D01G353600 chr5D 94.939 988 45 2 1 983 218193869 218194856 0.000000e+00 1543
11 TraesCS1D01G353600 chr5D 97.987 149 3 0 2314 2462 497816991 497816843 2.430000e-65 259
12 TraesCS1D01G353600 chr2D 93.764 1331 76 6 986 2310 634062270 634060941 0.000000e+00 1991
13 TraesCS1D01G353600 chr2D 95.243 988 41 3 1 982 462189996 462189009 0.000000e+00 1559
14 TraesCS1D01G353600 chr2D 95.040 988 43 4 1 986 634063364 634062381 0.000000e+00 1548
15 TraesCS1D01G353600 chr2D 97.403 154 3 1 2309 2462 82833032 82833184 6.750000e-66 261
16 TraesCS1D01G353600 chr1A 93.638 1336 72 8 979 2310 549599650 549598324 0.000000e+00 1984
17 TraesCS1D01G353600 chr5A 93.398 1333 83 4 979 2308 469233380 469232050 0.000000e+00 1969
18 TraesCS1D01G353600 chr7D 93.473 1333 73 9 983 2310 116648995 116650318 0.000000e+00 1967
19 TraesCS1D01G353600 chr7D 95.035 987 43 4 1 983 116647900 116648884 0.000000e+00 1546
20 TraesCS1D01G353600 chr7D 98.693 153 2 0 2310 2462 599722963 599723115 3.120000e-69 272
21 TraesCS1D01G353600 chr7D 98.658 149 2 0 2314 2462 199048911 199048763 5.220000e-67 265
22 TraesCS1D01G353600 chr7D 98.639 147 2 0 2316 2462 199047686 199047832 6.750000e-66 261
23 TraesCS1D01G353600 chr7D 96.815 157 4 1 2306 2462 599724186 599724031 6.750000e-66 261
24 TraesCS1D01G353600 chr4D 95.156 991 42 3 1 986 479373020 479372031 0.000000e+00 1559
25 TraesCS1D01G353600 chr4D 94.939 988 44 3 1 982 303072848 303073835 0.000000e+00 1543
26 TraesCS1D01G353600 chr4D 94.822 985 45 3 4 986 130443235 130442255 0.000000e+00 1531
27 TraesCS1D01G353600 chr4B 94.833 987 46 3 1 982 519348574 519349560 0.000000e+00 1535


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 TraesCS1D01G353600 chr1D 439163751 439166212 2461 False 4547.0 4547 100.0000 1 2462 1 chr1D.!!$F1 2461
1 TraesCS1D01G353600 chr3D 542835481 542836807 1326 False 2013.0 2013 94.0690 983 2310 1 chr3D.!!$F4 1327
2 TraesCS1D01G353600 chr3D 461560471 461561800 1329 False 1962.0 1962 93.3180 983 2310 1 chr3D.!!$F2 1327
3 TraesCS1D01G353600 chr3D 478121184 478122514 1330 False 1951.0 1951 93.1680 983 2310 1 chr3D.!!$F3 1327
4 TraesCS1D01G353600 chr3D 543499052 543501468 2416 False 1774.0 1965 94.5975 1 2310 2 chr3D.!!$F5 2309
5 TraesCS1D01G353600 chr5D 238122958 238124288 1330 False 2001.0 2001 93.8440 983 2310 1 chr5D.!!$F2 1327
6 TraesCS1D01G353600 chr5D 218193869 218194856 987 False 1543.0 1543 94.9390 1 983 1 chr5D.!!$F1 982
7 TraesCS1D01G353600 chr2D 634060941 634063364 2423 True 1769.5 1991 94.4020 1 2310 2 chr2D.!!$R2 2309
8 TraesCS1D01G353600 chr2D 462189009 462189996 987 True 1559.0 1559 95.2430 1 982 1 chr2D.!!$R1 981
9 TraesCS1D01G353600 chr1A 549598324 549599650 1326 True 1984.0 1984 93.6380 979 2310 1 chr1A.!!$R1 1331
10 TraesCS1D01G353600 chr5A 469232050 469233380 1330 True 1969.0 1969 93.3980 979 2308 1 chr5A.!!$R1 1329
11 TraesCS1D01G353600 chr7D 116647900 116650318 2418 False 1756.5 1967 94.2540 1 2310 2 chr7D.!!$F3 2309
12 TraesCS1D01G353600 chr4D 479372031 479373020 989 True 1559.0 1559 95.1560 1 986 1 chr4D.!!$R2 985
13 TraesCS1D01G353600 chr4D 303072848 303073835 987 False 1543.0 1543 94.9390 1 982 1 chr4D.!!$F1 981
14 TraesCS1D01G353600 chr4D 130442255 130443235 980 True 1531.0 1531 94.8220 4 986 1 chr4D.!!$R1 982
15 TraesCS1D01G353600 chr4B 519348574 519349560 986 False 1535.0 1535 94.8330 1 982 1 chr4B.!!$F1 981

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
513 520 0.237235 TTTGCTCCATCGTTTGTCGC 59.763 50.0 0.0 0.0 39.67 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2397 2533 0.248702 TTTTTGAAACAGCCGACGCC 60.249 50.0 0.0 0.0 34.57 5.68 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
124 127 1.016627 TTGATTGCTATGCTGCGGTC 58.983 50.000 0.00 0.00 35.36 4.79
126 129 1.835483 GATTGCTATGCTGCGGTCGG 61.835 60.000 0.00 0.00 35.36 4.79
132 135 1.670811 CTATGCTGCGGTCGGAATTTT 59.329 47.619 0.00 0.00 0.00 1.82
137 140 1.000717 CTGCGGTCGGAATTTTTGGTT 60.001 47.619 0.00 0.00 0.00 3.67
176 179 5.244178 AGCATGTGGTAGGCTAGATTAGTAC 59.756 44.000 0.00 0.00 46.08 2.73
274 279 7.306515 CCATTTGTAGCATGTTGTTTGTTGTAC 60.307 37.037 0.00 0.00 0.00 2.90
280 285 6.800543 AGCATGTTGTTTGTTGTACATGTAA 58.199 32.000 7.25 0.00 45.92 2.41
298 303 8.023021 ACATGTAAGTTCCTGCTCATAGATTA 57.977 34.615 0.00 0.00 0.00 1.75
310 315 5.046529 GCTCATAGATTATCCGGTATGCTG 58.953 45.833 0.00 0.00 0.00 4.41
399 406 1.745232 TGGATTGTCCGGTATGTTGC 58.255 50.000 0.00 0.00 40.17 4.17
400 407 1.003696 TGGATTGTCCGGTATGTTGCA 59.996 47.619 0.00 0.00 40.17 4.08
513 520 0.237235 TTTGCTCCATCGTTTGTCGC 59.763 50.000 0.00 0.00 39.67 5.19
685 704 3.194005 AGGTCGAACAACATGAAGTGT 57.806 42.857 1.87 0.00 44.84 3.55
788 807 1.301423 GGTGCACTTGAACACCGTTA 58.699 50.000 17.98 0.00 46.32 3.18
820 839 0.756294 TCGAGTTCTGTGGGCAAGAA 59.244 50.000 0.00 0.00 0.00 2.52
955 974 1.276421 GTTCTGGAGGCAGAGCACTAA 59.724 52.381 0.00 0.00 33.45 2.24
968 987 1.078497 CACTAAGCCGGCCATGTCA 60.078 57.895 26.15 0.42 0.00 3.58
1027 1157 0.826715 CATCTTCTCCTTCGGGCTGA 59.173 55.000 0.00 0.00 34.44 4.26
1075 1205 1.925972 GAGCCTCTTGGTTCCCCCT 60.926 63.158 0.00 0.00 37.58 4.79
1168 1298 0.893270 CAAGCCATTTGACCCCGTCA 60.893 55.000 0.00 0.00 41.09 4.35
1332 1462 2.450502 ACCCAGGGTGGCTTCAGT 60.451 61.111 11.70 0.00 35.79 3.41
1342 1472 1.004440 GGCTTCAGTGACGAGGCTT 60.004 57.895 10.37 0.00 38.05 4.35
1384 1514 3.873781 CTTGATAACAAGGCCCGGA 57.126 52.632 0.73 0.00 46.67 5.14
1420 1551 1.832608 ATGGCCGACGCTCATAGGA 60.833 57.895 0.00 0.00 34.44 2.94
1554 1685 4.609947 TGACGACGTACATTTTGTGTAGT 58.390 39.130 0.00 0.00 43.70 2.73
1583 1714 5.574443 GCTCAAAAACTATTTCATGGTCTGC 59.426 40.000 0.00 0.00 0.00 4.26
1608 1739 7.120726 GCATATTTTGGTGAGGTGGTATATACC 59.879 40.741 22.97 22.97 46.62 2.73
1711 1842 4.467795 AGTGCTAGGAAGAACTTGCTATGA 59.532 41.667 14.20 4.04 38.62 2.15
1776 1909 5.063204 TGTTTGTGTGCTACTTTGCTCTAT 58.937 37.500 0.00 0.00 0.00 1.98
1781 1914 5.179368 TGTGTGCTACTTTGCTCTATTTGTC 59.821 40.000 0.00 0.00 0.00 3.18
1786 1919 5.123027 GCTACTTTGCTCTATTTGTCTGCTT 59.877 40.000 0.00 0.00 0.00 3.91
1895 2030 1.361204 TCATGGGAAGAAGCCAGTGA 58.639 50.000 0.00 0.00 0.00 3.41
1900 2035 1.609072 GGGAAGAAGCCAGTGAACAAC 59.391 52.381 0.00 0.00 0.00 3.32
1922 2057 1.528586 GGCATCGTATAGCAACAGCAG 59.471 52.381 0.00 0.00 0.00 4.24
2017 2152 0.396435 TGACAGTCGCAAGGTTGGAT 59.604 50.000 0.00 0.00 38.47 3.41
2127 2262 0.392595 GTGCTAGGTGTGGGTAAGCC 60.393 60.000 0.00 0.00 32.14 4.35
2156 2291 5.030820 ACTAGGGTAGAAGGTAAGCACAAT 58.969 41.667 0.00 0.00 0.00 2.71
2174 2309 4.062293 ACAATATGTACGCCGTATGCAAT 58.938 39.130 0.00 0.00 41.33 3.56
2265 2400 0.841961 TGCAGGAAGCCTAGATGCAT 59.158 50.000 0.00 0.00 41.65 3.96
2296 2432 3.501828 ACAACTTGCAGATGACGCATTTA 59.498 39.130 2.91 0.00 39.58 1.40
2310 2446 2.154772 CGCATTTAGGGTTGTTTTTGCG 59.845 45.455 0.00 0.00 44.39 4.85
2311 2447 3.385577 GCATTTAGGGTTGTTTTTGCGA 58.614 40.909 0.00 0.00 0.00 5.10
2312 2448 3.804873 GCATTTAGGGTTGTTTTTGCGAA 59.195 39.130 0.00 0.00 0.00 4.70
2313 2449 4.450757 GCATTTAGGGTTGTTTTTGCGAAT 59.549 37.500 0.00 0.00 0.00 3.34
2314 2450 5.614449 GCATTTAGGGTTGTTTTTGCGAATG 60.614 40.000 0.00 0.00 0.00 2.67
2315 2451 4.920640 TTAGGGTTGTTTTTGCGAATGA 57.079 36.364 0.00 0.00 0.00 2.57
2316 2452 3.810310 AGGGTTGTTTTTGCGAATGAA 57.190 38.095 0.00 0.00 0.00 2.57
2317 2453 4.335400 AGGGTTGTTTTTGCGAATGAAT 57.665 36.364 0.00 0.00 0.00 2.57
2318 2454 5.461032 AGGGTTGTTTTTGCGAATGAATA 57.539 34.783 0.00 0.00 0.00 1.75
2319 2455 5.469479 AGGGTTGTTTTTGCGAATGAATAG 58.531 37.500 0.00 0.00 0.00 1.73
2320 2456 4.091365 GGGTTGTTTTTGCGAATGAATAGC 59.909 41.667 0.00 0.00 0.00 2.97
2321 2457 4.683781 GGTTGTTTTTGCGAATGAATAGCA 59.316 37.500 0.00 0.00 39.33 3.49
2322 2458 5.348451 GGTTGTTTTTGCGAATGAATAGCAT 59.652 36.000 0.00 0.00 40.83 3.79
2323 2459 6.529829 GGTTGTTTTTGCGAATGAATAGCATA 59.470 34.615 0.00 0.00 40.83 3.14
2324 2460 7.062839 GGTTGTTTTTGCGAATGAATAGCATAA 59.937 33.333 0.00 0.00 40.83 1.90
2325 2461 8.431593 GTTGTTTTTGCGAATGAATAGCATAAA 58.568 29.630 0.00 2.23 40.83 1.40
2326 2462 8.526218 TGTTTTTGCGAATGAATAGCATAAAA 57.474 26.923 6.80 6.36 41.05 1.52
2327 2463 8.431593 TGTTTTTGCGAATGAATAGCATAAAAC 58.568 29.630 19.94 19.94 41.05 2.43
2328 2464 8.647226 GTTTTTGCGAATGAATAGCATAAAACT 58.353 29.630 19.72 0.00 41.05 2.66
2329 2465 9.847706 TTTTTGCGAATGAATAGCATAAAACTA 57.152 25.926 3.57 0.00 38.28 2.24
2330 2466 8.835467 TTTGCGAATGAATAGCATAAAACTAC 57.165 30.769 0.00 0.00 40.83 2.73
2331 2467 6.954944 TGCGAATGAATAGCATAAAACTACC 58.045 36.000 0.00 0.00 35.78 3.18
2332 2468 6.540551 TGCGAATGAATAGCATAAAACTACCA 59.459 34.615 0.00 0.00 35.78 3.25
2333 2469 7.228507 TGCGAATGAATAGCATAAAACTACCAT 59.771 33.333 0.00 0.00 35.78 3.55
2334 2470 8.076178 GCGAATGAATAGCATAAAACTACCATT 58.924 33.333 0.00 0.00 35.78 3.16
2335 2471 9.950680 CGAATGAATAGCATAAAACTACCATTT 57.049 29.630 0.00 0.00 35.78 2.32
2339 2475 9.781834 TGAATAGCATAAAACTACCATTTTTCG 57.218 29.630 0.00 0.00 33.80 3.46
2340 2476 9.783256 GAATAGCATAAAACTACCATTTTTCGT 57.217 29.630 0.00 0.00 33.80 3.85
2341 2477 9.783256 AATAGCATAAAACTACCATTTTTCGTC 57.217 29.630 0.00 0.00 33.80 4.20
2342 2478 6.617879 AGCATAAAACTACCATTTTTCGTCC 58.382 36.000 0.00 0.00 33.80 4.79
2343 2479 6.433093 AGCATAAAACTACCATTTTTCGTCCT 59.567 34.615 0.00 0.00 33.80 3.85
2344 2480 7.608761 AGCATAAAACTACCATTTTTCGTCCTA 59.391 33.333 0.00 0.00 33.80 2.94
2345 2481 8.403236 GCATAAAACTACCATTTTTCGTCCTAT 58.597 33.333 0.00 0.00 33.80 2.57
2348 2484 7.754851 AAACTACCATTTTTCGTCCTATTGT 57.245 32.000 0.00 0.00 0.00 2.71
2349 2485 7.754851 AACTACCATTTTTCGTCCTATTGTT 57.245 32.000 0.00 0.00 0.00 2.83
2350 2486 7.373778 ACTACCATTTTTCGTCCTATTGTTC 57.626 36.000 0.00 0.00 0.00 3.18
2351 2487 5.638596 ACCATTTTTCGTCCTATTGTTCC 57.361 39.130 0.00 0.00 0.00 3.62
2352 2488 5.074115 ACCATTTTTCGTCCTATTGTTCCA 58.926 37.500 0.00 0.00 0.00 3.53
2353 2489 5.536916 ACCATTTTTCGTCCTATTGTTCCAA 59.463 36.000 0.00 0.00 0.00 3.53
2354 2490 6.041069 ACCATTTTTCGTCCTATTGTTCCAAA 59.959 34.615 0.00 0.00 0.00 3.28
2355 2491 6.926272 CCATTTTTCGTCCTATTGTTCCAAAA 59.074 34.615 0.00 0.00 0.00 2.44
2356 2492 7.439655 CCATTTTTCGTCCTATTGTTCCAAAAA 59.560 33.333 0.00 0.00 0.00 1.94
2378 2514 8.608844 AAAAACTACCACATTTTTGTTTGTGA 57.391 26.923 4.70 0.00 44.74 3.58
2379 2515 7.589574 AAACTACCACATTTTTGTTTGTGAC 57.410 32.000 4.70 0.00 44.74 3.67
2380 2516 6.524101 ACTACCACATTTTTGTTTGTGACT 57.476 33.333 4.70 0.00 44.74 3.41
2381 2517 6.329496 ACTACCACATTTTTGTTTGTGACTG 58.671 36.000 4.70 0.00 44.74 3.51
2382 2518 5.398603 ACCACATTTTTGTTTGTGACTGA 57.601 34.783 4.70 0.00 44.74 3.41
2383 2519 5.976458 ACCACATTTTTGTTTGTGACTGAT 58.024 33.333 4.70 0.00 44.74 2.90
2384 2520 7.106439 ACCACATTTTTGTTTGTGACTGATA 57.894 32.000 4.70 0.00 44.74 2.15
2385 2521 7.551585 ACCACATTTTTGTTTGTGACTGATAA 58.448 30.769 4.70 0.00 44.74 1.75
2386 2522 7.491048 ACCACATTTTTGTTTGTGACTGATAAC 59.509 33.333 4.70 0.00 44.74 1.89
2387 2523 7.706179 CCACATTTTTGTTTGTGACTGATAACT 59.294 33.333 4.70 0.00 44.74 2.24
2388 2524 9.729023 CACATTTTTGTTTGTGACTGATAACTA 57.271 29.630 0.00 0.00 44.74 2.24
2389 2525 9.730420 ACATTTTTGTTTGTGACTGATAACTAC 57.270 29.630 0.00 0.00 0.00 2.73
2390 2526 9.180678 CATTTTTGTTTGTGACTGATAACTACC 57.819 33.333 0.00 0.00 0.00 3.18
2391 2527 6.533819 TTTGTTTGTGACTGATAACTACCG 57.466 37.500 0.00 0.00 0.00 4.02
2392 2528 5.456548 TGTTTGTGACTGATAACTACCGA 57.543 39.130 0.00 0.00 0.00 4.69
2393 2529 5.845103 TGTTTGTGACTGATAACTACCGAA 58.155 37.500 0.00 0.00 0.00 4.30
2394 2530 6.282167 TGTTTGTGACTGATAACTACCGAAA 58.718 36.000 0.00 0.00 0.00 3.46
2395 2531 6.201425 TGTTTGTGACTGATAACTACCGAAAC 59.799 38.462 0.00 0.00 0.00 2.78
2396 2532 4.813027 TGTGACTGATAACTACCGAAACC 58.187 43.478 0.00 0.00 0.00 3.27
2397 2533 3.855950 GTGACTGATAACTACCGAAACCG 59.144 47.826 0.00 0.00 0.00 4.44
2413 2549 3.342627 CGGCGTCGGCTGTTTCAA 61.343 61.111 17.35 0.00 40.80 2.69
2414 2550 2.887889 CGGCGTCGGCTGTTTCAAA 61.888 57.895 17.35 0.00 40.80 2.69
2415 2551 1.357334 GGCGTCGGCTGTTTCAAAA 59.643 52.632 12.17 0.00 39.81 2.44
2416 2552 0.248702 GGCGTCGGCTGTTTCAAAAA 60.249 50.000 12.17 0.00 39.81 1.94
2430 2566 4.838046 AAAAACCCAAAACGCCCG 57.162 50.000 0.00 0.00 0.00 6.13
2431 2567 1.898885 AAAAACCCAAAACGCCCGT 59.101 47.368 0.00 0.00 0.00 5.28
2432 2568 0.460459 AAAAACCCAAAACGCCCGTG 60.460 50.000 0.00 0.00 0.00 4.94
2433 2569 2.299503 AAAACCCAAAACGCCCGTGG 62.300 55.000 0.00 0.00 0.00 4.94
2447 2583 3.766151 GCCCGTGGCTAAGAAATTAAAC 58.234 45.455 7.58 0.00 46.69 2.01
2448 2584 3.428452 GCCCGTGGCTAAGAAATTAAACC 60.428 47.826 7.58 0.00 46.69 3.27
2449 2585 3.181504 CCCGTGGCTAAGAAATTAAACCG 60.182 47.826 0.00 0.00 0.00 4.44
2450 2586 3.181504 CCGTGGCTAAGAAATTAAACCGG 60.182 47.826 0.00 0.00 0.00 5.28
2451 2587 3.437741 CGTGGCTAAGAAATTAAACCGGT 59.562 43.478 0.00 0.00 0.00 5.28
2452 2588 4.083164 CGTGGCTAAGAAATTAAACCGGTT 60.083 41.667 15.86 15.86 0.00 4.44
2453 2589 5.563280 CGTGGCTAAGAAATTAAACCGGTTT 60.563 40.000 33.42 33.42 36.63 3.27
2454 2590 6.348376 CGTGGCTAAGAAATTAAACCGGTTTA 60.348 38.462 31.25 31.25 34.23 2.01
2455 2591 7.541162 GTGGCTAAGAAATTAAACCGGTTTAT 58.459 34.615 34.14 22.75 35.27 1.40
2456 2592 7.486870 GTGGCTAAGAAATTAAACCGGTTTATG 59.513 37.037 34.14 18.96 35.27 1.90
2457 2593 7.393796 TGGCTAAGAAATTAAACCGGTTTATGA 59.606 33.333 34.14 23.49 35.27 2.15
2458 2594 7.699391 GGCTAAGAAATTAAACCGGTTTATGAC 59.301 37.037 34.14 24.74 35.27 3.06
2459 2595 8.238631 GCTAAGAAATTAAACCGGTTTATGACA 58.761 33.333 34.14 22.51 35.27 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
124 127 2.823154 TCTAGCCCAACCAAAAATTCCG 59.177 45.455 0.00 0.00 0.00 4.30
126 129 5.405935 ACATCTAGCCCAACCAAAAATTC 57.594 39.130 0.00 0.00 0.00 2.17
132 135 3.420893 CTTGAACATCTAGCCCAACCAA 58.579 45.455 0.00 0.00 0.00 3.67
137 140 2.025981 ACATGCTTGAACATCTAGCCCA 60.026 45.455 6.60 0.00 43.03 5.36
176 179 7.012421 AGCACAAGGTTTAACTTCAAACTCTAG 59.988 37.037 0.00 0.00 38.27 2.43
191 194 3.951775 TTCAACACAAGCACAAGGTTT 57.048 38.095 0.00 0.00 32.07 3.27
274 279 9.149225 GATAATCTATGAGCAGGAACTTACATG 57.851 37.037 0.00 0.00 34.60 3.21
280 285 4.221703 CCGGATAATCTATGAGCAGGAACT 59.778 45.833 0.00 0.00 43.88 3.01
298 303 0.984230 CCATACCCAGCATACCGGAT 59.016 55.000 9.46 0.00 0.00 4.18
310 315 1.070134 TGCTTCATCGCTACCATACCC 59.930 52.381 0.00 0.00 0.00 3.69
399 406 4.534168 GCATTGACAGTAAGCATAGCATG 58.466 43.478 0.00 0.00 0.00 4.06
400 407 3.249320 CGCATTGACAGTAAGCATAGCAT 59.751 43.478 0.00 0.00 0.00 3.79
513 520 1.299468 GACATAGGCTGCGAGTCCG 60.299 63.158 0.00 0.00 39.16 4.79
685 704 1.374125 CGTGGACATGAACGGCTGA 60.374 57.895 0.00 0.00 36.17 4.26
788 807 0.104304 AACTCGAACACCTGCTTCGT 59.896 50.000 5.15 0.00 41.08 3.85
968 987 1.899814 TCTGGATTGTGAGCTAACCGT 59.100 47.619 0.00 0.00 0.00 4.83
1027 1157 0.251922 ATGGCATGCTTCCCAGTTGT 60.252 50.000 18.92 0.00 34.01 3.32
1071 1201 2.234296 AGGGAAGTCTGGCAAGGGG 61.234 63.158 0.00 0.00 0.00 4.79
1168 1298 6.036926 TCCTCTCTTCCTCTTCCTATCATT 57.963 41.667 0.00 0.00 0.00 2.57
1332 1462 0.674581 CTGCCATCAAAGCCTCGTCA 60.675 55.000 0.00 0.00 0.00 4.35
1342 1472 4.631773 GCTGAGAGCTGCCATCAA 57.368 55.556 0.00 0.00 38.45 2.57
1382 1512 1.652563 GCAACGAACCCAACACTCC 59.347 57.895 0.00 0.00 0.00 3.85
1384 1514 0.467290 ATGGCAACGAACCCAACACT 60.467 50.000 0.00 0.00 42.51 3.55
1473 1604 1.026182 GGGATCATGCACGCTCACAA 61.026 55.000 0.00 0.00 0.00 3.33
1518 1649 0.445043 TCGTCATCGTCATCGTCGTT 59.555 50.000 0.00 0.00 38.33 3.85
1554 1685 6.723977 ACCATGAAATAGTTTTTGAGCCCTAA 59.276 34.615 0.00 0.00 0.00 2.69
1583 1714 8.561738 GGTATATACCACCTCACCAAAATATG 57.438 38.462 24.46 0.00 45.73 1.78
1608 1739 1.746615 CCATCAGCGTGAGGGGTTG 60.747 63.158 9.82 0.00 44.05 3.77
1711 1842 1.939974 AAGCACGCATGATCATACGT 58.060 45.000 24.86 24.86 41.05 3.57
1725 1856 3.682377 GGAGCAGAAGAGAAGTAAAGCAC 59.318 47.826 0.00 0.00 0.00 4.40
1776 1909 4.986034 CAGCAAATCAATGAAGCAGACAAA 59.014 37.500 8.07 0.00 0.00 2.83
1781 1914 3.232213 AGCAGCAAATCAATGAAGCAG 57.768 42.857 0.00 2.22 0.00 4.24
1786 1919 4.521639 AGAGTTGAAGCAGCAAATCAATGA 59.478 37.500 17.24 0.00 43.21 2.57
1895 2030 3.260475 TGCTATACGATGCCAGTTGTT 57.740 42.857 0.00 0.00 0.00 2.83
1900 2035 1.528586 GCTGTTGCTATACGATGCCAG 59.471 52.381 0.00 0.00 36.03 4.85
1922 2057 3.070302 CCTAGTCTTGAACCCTCTATGGC 59.930 52.174 0.00 0.00 0.00 4.40
1997 2132 0.249868 TCCAACCTTGCGACTGTCAG 60.250 55.000 8.73 0.00 0.00 3.51
2017 2152 1.000843 CTGACGATCCACCTTGACACA 59.999 52.381 0.00 0.00 0.00 3.72
2127 2262 2.547990 ACCTTCTACCCTAGTTGGTGG 58.452 52.381 1.21 0.00 39.53 4.61
2142 2277 4.025145 GGCGTACATATTGTGCTTACCTTC 60.025 45.833 0.00 0.00 30.49 3.46
2174 2309 1.004398 GCACATGAACACGACGTTTGA 60.004 47.619 0.00 0.00 38.19 2.69
2208 2343 1.134848 GCACTTTGTTTGGTTGCCTGA 60.135 47.619 0.00 0.00 0.00 3.86
2252 2387 1.341285 TGGTTGCATGCATCTAGGCTT 60.341 47.619 23.37 0.00 34.04 4.35
2254 2389 1.105457 TTGGTTGCATGCATCTAGGC 58.895 50.000 23.37 8.39 0.00 3.93
2296 2432 3.810310 TTCATTCGCAAAAACAACCCT 57.190 38.095 0.00 0.00 0.00 4.34
2300 2436 8.526218 TTTATGCTATTCATTCGCAAAAACAA 57.474 26.923 0.00 0.00 37.20 2.83
2313 2449 9.781834 CGAAAAATGGTAGTTTTATGCTATTCA 57.218 29.630 0.00 0.00 31.43 2.57
2314 2450 9.783256 ACGAAAAATGGTAGTTTTATGCTATTC 57.217 29.630 0.00 0.00 31.43 1.75
2315 2451 9.783256 GACGAAAAATGGTAGTTTTATGCTATT 57.217 29.630 0.00 0.00 31.43 1.73
2316 2452 8.403236 GGACGAAAAATGGTAGTTTTATGCTAT 58.597 33.333 0.00 0.00 31.43 2.97
2317 2453 7.608761 AGGACGAAAAATGGTAGTTTTATGCTA 59.391 33.333 0.00 0.00 31.43 3.49
2318 2454 6.433093 AGGACGAAAAATGGTAGTTTTATGCT 59.567 34.615 0.00 0.00 31.43 3.79
2319 2455 6.617879 AGGACGAAAAATGGTAGTTTTATGC 58.382 36.000 0.00 0.00 31.43 3.14
2322 2458 9.287373 ACAATAGGACGAAAAATGGTAGTTTTA 57.713 29.630 0.00 0.00 31.43 1.52
2323 2459 8.173542 ACAATAGGACGAAAAATGGTAGTTTT 57.826 30.769 0.00 0.00 32.94 2.43
2324 2460 7.754851 ACAATAGGACGAAAAATGGTAGTTT 57.245 32.000 0.00 0.00 0.00 2.66
2325 2461 7.094506 GGAACAATAGGACGAAAAATGGTAGTT 60.095 37.037 0.00 0.00 0.00 2.24
2326 2462 6.373495 GGAACAATAGGACGAAAAATGGTAGT 59.627 38.462 0.00 0.00 0.00 2.73
2327 2463 6.373216 TGGAACAATAGGACGAAAAATGGTAG 59.627 38.462 0.00 0.00 31.92 3.18
2328 2464 6.239396 TGGAACAATAGGACGAAAAATGGTA 58.761 36.000 0.00 0.00 31.92 3.25
2329 2465 5.074115 TGGAACAATAGGACGAAAAATGGT 58.926 37.500 0.00 0.00 31.92 3.55
2330 2466 5.637006 TGGAACAATAGGACGAAAAATGG 57.363 39.130 0.00 0.00 31.92 3.16
2353 2489 8.499967 GTCACAAACAAAAATGTGGTAGTTTTT 58.500 29.630 6.11 0.00 45.41 1.94
2354 2490 7.875554 AGTCACAAACAAAAATGTGGTAGTTTT 59.124 29.630 6.11 0.00 45.41 2.43
2355 2491 7.330700 CAGTCACAAACAAAAATGTGGTAGTTT 59.669 33.333 6.11 0.00 45.41 2.66
2356 2492 6.811170 CAGTCACAAACAAAAATGTGGTAGTT 59.189 34.615 6.11 0.00 45.41 2.24
2357 2493 6.151985 TCAGTCACAAACAAAAATGTGGTAGT 59.848 34.615 6.11 0.00 45.41 2.73
2358 2494 6.559810 TCAGTCACAAACAAAAATGTGGTAG 58.440 36.000 6.11 0.00 45.41 3.18
2359 2495 6.516739 TCAGTCACAAACAAAAATGTGGTA 57.483 33.333 6.11 0.00 45.41 3.25
2360 2496 5.398603 TCAGTCACAAACAAAAATGTGGT 57.601 34.783 6.11 0.00 45.41 4.16
2361 2497 7.706179 AGTTATCAGTCACAAACAAAAATGTGG 59.294 33.333 6.11 0.00 45.41 4.17
2362 2498 8.633075 AGTTATCAGTCACAAACAAAAATGTG 57.367 30.769 0.00 0.00 46.44 3.21
2363 2499 9.730420 GTAGTTATCAGTCACAAACAAAAATGT 57.270 29.630 0.00 0.00 0.00 2.71
2364 2500 9.180678 GGTAGTTATCAGTCACAAACAAAAATG 57.819 33.333 0.00 0.00 0.00 2.32
2365 2501 8.073768 CGGTAGTTATCAGTCACAAACAAAAAT 58.926 33.333 0.00 0.00 0.00 1.82
2366 2502 7.280428 TCGGTAGTTATCAGTCACAAACAAAAA 59.720 33.333 0.00 0.00 0.00 1.94
2367 2503 6.762187 TCGGTAGTTATCAGTCACAAACAAAA 59.238 34.615 0.00 0.00 0.00 2.44
2368 2504 6.282167 TCGGTAGTTATCAGTCACAAACAAA 58.718 36.000 0.00 0.00 0.00 2.83
2369 2505 5.845103 TCGGTAGTTATCAGTCACAAACAA 58.155 37.500 0.00 0.00 0.00 2.83
2370 2506 5.456548 TCGGTAGTTATCAGTCACAAACA 57.543 39.130 0.00 0.00 0.00 2.83
2371 2507 6.347160 GGTTTCGGTAGTTATCAGTCACAAAC 60.347 42.308 0.00 0.00 0.00 2.93
2372 2508 5.697633 GGTTTCGGTAGTTATCAGTCACAAA 59.302 40.000 0.00 0.00 0.00 2.83
2373 2509 5.232463 GGTTTCGGTAGTTATCAGTCACAA 58.768 41.667 0.00 0.00 0.00 3.33
2374 2510 4.616604 CGGTTTCGGTAGTTATCAGTCACA 60.617 45.833 0.00 0.00 0.00 3.58
2375 2511 3.855950 CGGTTTCGGTAGTTATCAGTCAC 59.144 47.826 0.00 0.00 0.00 3.67
2376 2512 4.100707 CGGTTTCGGTAGTTATCAGTCA 57.899 45.455 0.00 0.00 0.00 3.41
2396 2532 2.381665 TTTTGAAACAGCCGACGCCG 62.382 55.000 0.00 0.00 34.57 6.46
2397 2533 0.248702 TTTTTGAAACAGCCGACGCC 60.249 50.000 0.00 0.00 34.57 5.68
2398 2534 3.243855 TTTTTGAAACAGCCGACGC 57.756 47.368 0.00 0.00 0.00 5.19
2413 2549 0.460459 CACGGGCGTTTTGGGTTTTT 60.460 50.000 0.00 0.00 0.00 1.94
2414 2550 1.142097 CACGGGCGTTTTGGGTTTT 59.858 52.632 0.00 0.00 0.00 2.43
2415 2551 2.787567 CCACGGGCGTTTTGGGTTT 61.788 57.895 0.00 0.00 0.00 3.27
2416 2552 3.220658 CCACGGGCGTTTTGGGTT 61.221 61.111 0.00 0.00 0.00 4.11
2427 2563 3.181504 CGGTTTAATTTCTTAGCCACGGG 60.182 47.826 0.00 0.00 0.00 5.28
2428 2564 3.181504 CCGGTTTAATTTCTTAGCCACGG 60.182 47.826 0.00 0.00 0.00 4.94
2429 2565 3.437741 ACCGGTTTAATTTCTTAGCCACG 59.562 43.478 0.00 0.00 0.00 4.94
2430 2566 5.381174 AACCGGTTTAATTTCTTAGCCAC 57.619 39.130 15.86 0.00 0.00 5.01
2431 2567 7.393796 TCATAAACCGGTTTAATTTCTTAGCCA 59.606 33.333 36.33 16.70 38.38 4.75
2432 2568 7.699391 GTCATAAACCGGTTTAATTTCTTAGCC 59.301 37.037 36.33 15.45 38.38 3.93
2433 2569 8.238631 TGTCATAAACCGGTTTAATTTCTTAGC 58.761 33.333 36.33 20.56 38.38 3.09


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

AutoCloner maintained by Alex Coulton.