Multiple sequence alignment - TraesCS7A01G446600

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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 TraesCS7A01G446600 chr7A 100.000 2526 0 0 1 2526 641404514 641401989 0.000000e+00 4665
1 TraesCS7A01G446600 chr4D 97.497 1878 33 7 1 1871 379508837 379506967 0.000000e+00 3195
2 TraesCS7A01G446600 chr1A 97.161 1867 44 5 1 1862 520787029 520788891 0.000000e+00 3145
3 TraesCS7A01G446600 chr3A 97.367 1823 36 7 1 1816 170229599 170227782 0.000000e+00 3090
4 TraesCS7A01G446600 chr4B 95.024 1869 86 6 1 1862 575618931 575617063 0.000000e+00 2929
5 TraesCS7A01G446600 chr3B 93.948 1867 107 5 1 1861 62531660 62529794 0.000000e+00 2817
6 TraesCS7A01G446600 chr3B 93.006 1058 66 6 806 1859 612314088 612315141 0.000000e+00 1537
7 TraesCS7A01G446600 chr3B 92.743 1061 72 4 806 1861 605446113 605445053 0.000000e+00 1528
8 TraesCS7A01G446600 chr3B 85.265 509 67 7 1 505 629796968 629797472 3.720000e-143 518
9 TraesCS7A01G446600 chr5B 92.884 1883 112 14 1 1878 395331224 395333089 0.000000e+00 2715
10 TraesCS7A01G446600 chr2A 97.756 1025 21 2 1 1023 123740561 123739537 0.000000e+00 1764
11 TraesCS7A01G446600 chr1D 94.227 1074 56 6 806 1874 467476026 467474954 0.000000e+00 1635
12 TraesCS7A01G446600 chr7D 88.314 522 43 9 1869 2382 554576816 554577327 5.970000e-171 610
13 TraesCS7A01G446600 chr7B 86.564 521 40 13 1870 2382 602099525 602099027 4.750000e-152 547
14 TraesCS7A01G446600 chr7B 88.377 456 38 7 1870 2310 602111230 602110775 3.700000e-148 534
15 TraesCS7A01G446600 chr2D 86.106 511 61 9 1 505 344565436 344565942 2.210000e-150 542


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 TraesCS7A01G446600 chr7A 641401989 641404514 2525 True 4665 4665 100.000 1 2526 1 chr7A.!!$R1 2525
1 TraesCS7A01G446600 chr4D 379506967 379508837 1870 True 3195 3195 97.497 1 1871 1 chr4D.!!$R1 1870
2 TraesCS7A01G446600 chr1A 520787029 520788891 1862 False 3145 3145 97.161 1 1862 1 chr1A.!!$F1 1861
3 TraesCS7A01G446600 chr3A 170227782 170229599 1817 True 3090 3090 97.367 1 1816 1 chr3A.!!$R1 1815
4 TraesCS7A01G446600 chr4B 575617063 575618931 1868 True 2929 2929 95.024 1 1862 1 chr4B.!!$R1 1861
5 TraesCS7A01G446600 chr3B 62529794 62531660 1866 True 2817 2817 93.948 1 1861 1 chr3B.!!$R1 1860
6 TraesCS7A01G446600 chr3B 612314088 612315141 1053 False 1537 1537 93.006 806 1859 1 chr3B.!!$F1 1053
7 TraesCS7A01G446600 chr3B 605445053 605446113 1060 True 1528 1528 92.743 806 1861 1 chr3B.!!$R2 1055
8 TraesCS7A01G446600 chr3B 629796968 629797472 504 False 518 518 85.265 1 505 1 chr3B.!!$F2 504
9 TraesCS7A01G446600 chr5B 395331224 395333089 1865 False 2715 2715 92.884 1 1878 1 chr5B.!!$F1 1877
10 TraesCS7A01G446600 chr2A 123739537 123740561 1024 True 1764 1764 97.756 1 1023 1 chr2A.!!$R1 1022
11 TraesCS7A01G446600 chr1D 467474954 467476026 1072 True 1635 1635 94.227 806 1874 1 chr1D.!!$R1 1068
12 TraesCS7A01G446600 chr7D 554576816 554577327 511 False 610 610 88.314 1869 2382 1 chr7D.!!$F1 513
13 TraesCS7A01G446600 chr2D 344565436 344565942 506 False 542 542 86.106 1 505 1 chr2D.!!$F1 504

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
328 331 2.115343 AATCCCGGACTTCTGCTTTC 57.885 50.0 0.73 0.0 0.0 2.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2034 2054 0.949105 CGAACCCTCCAACAACTCCG 60.949 60.0 0.0 0.0 0.0 4.63 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
202 203 9.161629 GCAATTATAGTTAGGTTGCCAATTTTT 57.838 29.630 0.00 0.00 39.27 1.94
239 242 2.742428 ATGGTGGCTGTTATGCTCAT 57.258 45.000 0.00 0.00 0.00 2.90
328 331 2.115343 AATCCCGGACTTCTGCTTTC 57.885 50.000 0.73 0.00 0.00 2.62
1031 1042 7.041916 TGGGTACGCTGAAAATATATAAAACCG 60.042 37.037 11.59 0.00 0.00 4.44
1209 1221 4.426112 CTCCACTGCGCGCTCTCA 62.426 66.667 33.29 11.13 0.00 3.27
1485 1498 2.497675 AGGACATGTACCTGCACTACAG 59.502 50.000 3.84 0.00 46.77 2.74
1864 1882 2.096980 CGCAACGAGTCATCTAGTACCA 59.903 50.000 0.00 0.00 0.00 3.25
1899 1917 5.878406 TTGGTTGGTAAATTTGGTCATGT 57.122 34.783 0.00 0.00 0.00 3.21
1904 1922 5.543507 TGGTAAATTTGGTCATGTTGCTT 57.456 34.783 0.00 0.00 0.00 3.91
1905 1923 5.295950 TGGTAAATTTGGTCATGTTGCTTG 58.704 37.500 0.00 0.00 0.00 4.01
1907 1925 5.757808 GGTAAATTTGGTCATGTTGCTTGTT 59.242 36.000 0.00 0.00 0.00 2.83
1929 1947 3.118454 GGACCGTGGCGATGTGTG 61.118 66.667 0.00 0.00 0.00 3.82
1937 1955 0.948623 TGGCGATGTGTGAAAGTCGG 60.949 55.000 0.00 0.00 34.85 4.79
1949 1967 3.001414 TGAAAGTCGGACGAAAACACAA 58.999 40.909 1.89 0.00 0.00 3.33
1951 1969 3.394313 AAGTCGGACGAAAACACAAAC 57.606 42.857 1.89 0.00 0.00 2.93
1955 1973 4.099824 GTCGGACGAAAACACAAACAAAT 58.900 39.130 0.00 0.00 0.00 2.32
1973 1993 3.760580 AATTATCCGAGGGAAGAGCAG 57.239 47.619 0.00 0.00 34.34 4.24
1984 2004 1.950973 GAAGAGCAGTCGGAGGGTCC 61.951 65.000 5.48 0.00 32.12 4.46
2032 2052 0.681564 TCTGAAGAGAGTCGGAGGCC 60.682 60.000 0.00 0.00 0.00 5.19
2034 2054 2.364448 AAGAGAGTCGGAGGCCCC 60.364 66.667 0.00 0.00 0.00 5.80
2091 2117 4.170449 AGGAAATTGGGCAAAGGAAGAAT 58.830 39.130 0.00 0.00 0.00 2.40
2092 2118 4.019950 AGGAAATTGGGCAAAGGAAGAATG 60.020 41.667 0.00 0.00 0.00 2.67
2093 2119 3.986996 AATTGGGCAAAGGAAGAATGG 57.013 42.857 0.00 0.00 0.00 3.16
2094 2120 1.643310 TTGGGCAAAGGAAGAATGGG 58.357 50.000 0.00 0.00 0.00 4.00
2095 2121 0.252193 TGGGCAAAGGAAGAATGGGG 60.252 55.000 0.00 0.00 0.00 4.96
2096 2122 1.617018 GGGCAAAGGAAGAATGGGGC 61.617 60.000 0.00 0.00 0.00 5.80
2097 2123 0.615827 GGCAAAGGAAGAATGGGGCT 60.616 55.000 0.00 0.00 0.00 5.19
2098 2124 1.269958 GCAAAGGAAGAATGGGGCTT 58.730 50.000 0.00 0.00 0.00 4.35
2099 2125 1.625315 GCAAAGGAAGAATGGGGCTTT 59.375 47.619 0.00 0.00 0.00 3.51
2110 2136 1.886422 TGGGGCTTTTGAGGGTTTTT 58.114 45.000 0.00 0.00 0.00 1.94
2114 2140 2.224281 GGGCTTTTGAGGGTTTTTGGAG 60.224 50.000 0.00 0.00 0.00 3.86
2127 2153 5.361571 GGGTTTTTGGAGTTTGGTCTCTAAA 59.638 40.000 0.00 0.00 40.98 1.85
2133 2159 5.751586 TGGAGTTTGGTCTCTAAACACTTT 58.248 37.500 10.32 0.00 39.78 2.66
2134 2160 5.588648 TGGAGTTTGGTCTCTAAACACTTTG 59.411 40.000 10.32 0.00 39.78 2.77
2135 2161 5.500645 AGTTTGGTCTCTAAACACTTTGC 57.499 39.130 10.32 0.00 39.78 3.68
2140 2166 5.890334 TGGTCTCTAAACACTTTGCAAAAG 58.110 37.500 13.84 11.15 0.00 2.27
2149 2175 4.485163 ACACTTTGCAAAAGACACTTCAC 58.515 39.130 13.84 0.00 0.00 3.18
2159 2185 7.115663 TGCAAAAGACACTTCACTTAACAAAAC 59.884 33.333 0.00 0.00 0.00 2.43
2182 2208 8.537728 AACCAATATCCTTTTTGATAGCATCA 57.462 30.769 0.00 0.00 37.55 3.07
2183 2209 8.537728 ACCAATATCCTTTTTGATAGCATCAA 57.462 30.769 7.27 7.27 46.77 2.57
2198 2224 5.283457 AGCATCAACATACCTAAGGACTC 57.717 43.478 0.00 0.00 0.00 3.36
2234 2260 6.662414 TCACTAAAGGCTATGAAAATGTCG 57.338 37.500 0.00 0.00 0.00 4.35
2237 2263 6.742718 CACTAAAGGCTATGAAAATGTCGTTG 59.257 38.462 0.00 0.00 0.00 4.10
2239 2265 6.515272 AAAGGCTATGAAAATGTCGTTGAT 57.485 33.333 0.00 0.00 0.00 2.57
2244 2270 5.294306 GCTATGAAAATGTCGTTGATCCTGA 59.706 40.000 0.00 0.00 0.00 3.86
2252 2278 4.744570 TGTCGTTGATCCTGATAACACTC 58.255 43.478 0.00 0.00 0.00 3.51
2256 2282 4.438880 CGTTGATCCTGATAACACTCGTCT 60.439 45.833 0.00 0.00 0.00 4.18
2303 2329 2.879103 TCTTTTGGGGTCTAAGCTGG 57.121 50.000 0.00 0.00 0.00 4.85
2314 2340 4.504340 GGGTCTAAGCTGGTCAACACTTTA 60.504 45.833 0.00 0.00 0.00 1.85
2317 2343 6.535508 GGTCTAAGCTGGTCAACACTTTATAG 59.464 42.308 0.00 0.00 0.00 1.31
2320 2346 5.746990 AGCTGGTCAACACTTTATAGAGT 57.253 39.130 0.00 0.00 0.00 3.24
2324 2350 7.603024 AGCTGGTCAACACTTTATAGAGTAAAC 59.397 37.037 0.00 0.00 0.00 2.01
2325 2351 7.386848 GCTGGTCAACACTTTATAGAGTAAACA 59.613 37.037 0.00 0.00 0.00 2.83
2326 2352 9.436957 CTGGTCAACACTTTATAGAGTAAACAT 57.563 33.333 0.00 0.00 0.00 2.71
2348 2374 5.772393 TTAGTCCCTTTAATCAAGCTGGA 57.228 39.130 0.00 0.00 0.00 3.86
2382 2408 7.054124 TCAAAAACCACTATAGGGCAATAGAG 58.946 38.462 4.43 5.25 34.22 2.43
2383 2409 4.625607 AACCACTATAGGGCAATAGAGC 57.374 45.455 4.43 0.00 34.22 4.09
2384 2410 3.863086 ACCACTATAGGGCAATAGAGCT 58.137 45.455 4.43 0.00 34.22 4.09
2385 2411 5.011982 ACCACTATAGGGCAATAGAGCTA 57.988 43.478 4.43 0.00 34.22 3.32
2386 2412 5.594777 ACCACTATAGGGCAATAGAGCTAT 58.405 41.667 4.43 0.00 34.22 2.97
2387 2413 5.423610 ACCACTATAGGGCAATAGAGCTATG 59.576 44.000 4.43 1.67 34.22 2.23
2388 2414 5.355596 CACTATAGGGCAATAGAGCTATGC 58.644 45.833 4.43 0.00 34.22 3.14
2389 2415 5.026121 ACTATAGGGCAATAGAGCTATGCA 58.974 41.667 4.43 0.00 34.22 3.96
2390 2416 5.664908 ACTATAGGGCAATAGAGCTATGCAT 59.335 40.000 3.79 3.79 34.22 3.96
2391 2417 3.803186 AGGGCAATAGAGCTATGCATT 57.197 42.857 3.54 0.00 34.17 3.56
2392 2418 3.418995 AGGGCAATAGAGCTATGCATTG 58.581 45.455 3.54 3.55 34.17 2.82
2394 2420 3.213249 GCAATAGAGCTATGCATTGCC 57.787 47.619 26.14 18.22 44.71 4.52
2395 2421 2.094854 GCAATAGAGCTATGCATTGCCC 60.095 50.000 26.14 17.11 44.71 5.36
2396 2422 3.151554 CAATAGAGCTATGCATTGCCCA 58.848 45.455 26.14 13.89 0.00 5.36
2397 2423 3.733883 ATAGAGCTATGCATTGCCCAT 57.266 42.857 26.14 16.03 0.00 4.00
2398 2424 1.906990 AGAGCTATGCATTGCCCATC 58.093 50.000 26.14 18.19 0.00 3.51
2399 2425 1.144298 AGAGCTATGCATTGCCCATCA 59.856 47.619 26.14 0.00 0.00 3.07
2400 2426 1.958579 GAGCTATGCATTGCCCATCAA 59.041 47.619 26.14 0.00 39.32 2.57
2401 2427 2.363038 GAGCTATGCATTGCCCATCAAA 59.637 45.455 26.14 0.00 38.34 2.69
2402 2428 2.364324 AGCTATGCATTGCCCATCAAAG 59.636 45.455 26.14 5.54 38.34 2.77
2403 2429 2.547218 GCTATGCATTGCCCATCAAAGG 60.547 50.000 20.63 0.00 38.34 3.11
2404 2430 1.575419 ATGCATTGCCCATCAAAGGT 58.425 45.000 6.12 0.00 38.34 3.50
2405 2431 0.609151 TGCATTGCCCATCAAAGGTG 59.391 50.000 6.12 0.00 38.34 4.00
2406 2432 0.896923 GCATTGCCCATCAAAGGTGA 59.103 50.000 0.00 0.00 38.34 4.02
2407 2433 1.275856 GCATTGCCCATCAAAGGTGAA 59.724 47.619 0.00 0.00 38.34 3.18
2408 2434 2.675889 GCATTGCCCATCAAAGGTGAAG 60.676 50.000 0.00 0.00 38.34 3.02
2409 2435 0.968405 TTGCCCATCAAAGGTGAAGC 59.032 50.000 0.00 0.00 37.30 3.86
2410 2436 1.243342 TGCCCATCAAAGGTGAAGCG 61.243 55.000 0.00 0.00 37.30 4.68
2411 2437 0.960364 GCCCATCAAAGGTGAAGCGA 60.960 55.000 0.00 0.00 37.30 4.93
2412 2438 0.804989 CCCATCAAAGGTGAAGCGAC 59.195 55.000 0.00 0.00 37.30 5.19
2413 2439 0.443869 CCATCAAAGGTGAAGCGACG 59.556 55.000 0.00 0.00 37.30 5.12
2414 2440 0.443869 CATCAAAGGTGAAGCGACGG 59.556 55.000 0.00 0.00 37.30 4.79
2415 2441 0.034896 ATCAAAGGTGAAGCGACGGT 59.965 50.000 0.00 0.00 37.30 4.83
2416 2442 0.878523 TCAAAGGTGAAGCGACGGTG 60.879 55.000 0.00 0.00 0.00 4.94
2417 2443 2.251642 AAAGGTGAAGCGACGGTGC 61.252 57.895 0.00 0.00 0.00 5.01
2430 2456 4.307908 GGTGCGCCACGACACAAC 62.308 66.667 12.58 0.00 36.32 3.32
2431 2457 4.307908 GTGCGCCACGACACAACC 62.308 66.667 4.18 0.00 35.35 3.77
2432 2458 4.539083 TGCGCCACGACACAACCT 62.539 61.111 4.18 0.00 0.00 3.50
2433 2459 3.276846 GCGCCACGACACAACCTT 61.277 61.111 0.00 0.00 0.00 3.50
2434 2460 2.830285 GCGCCACGACACAACCTTT 61.830 57.895 0.00 0.00 0.00 3.11
2435 2461 1.010125 CGCCACGACACAACCTTTG 60.010 57.895 0.00 0.00 0.00 2.77
2436 2462 1.358759 GCCACGACACAACCTTTGG 59.641 57.895 0.00 0.00 34.12 3.28
2437 2463 1.381165 GCCACGACACAACCTTTGGT 61.381 55.000 0.00 0.00 37.65 3.67
2447 2473 2.009681 AACCTTTGGTTGGGATGTCC 57.990 50.000 0.71 0.00 45.07 4.02
2448 2474 1.158007 ACCTTTGGTTGGGATGTCCT 58.842 50.000 0.00 0.00 36.20 3.85
2449 2475 1.075536 ACCTTTGGTTGGGATGTCCTC 59.924 52.381 0.00 0.00 36.20 3.71
2450 2476 1.453155 CTTTGGTTGGGATGTCCTCG 58.547 55.000 0.00 0.00 36.20 4.63
2451 2477 1.003118 CTTTGGTTGGGATGTCCTCGA 59.997 52.381 0.00 0.00 36.20 4.04
2452 2478 1.285280 TTGGTTGGGATGTCCTCGAT 58.715 50.000 0.00 0.00 36.20 3.59
2453 2479 0.541392 TGGTTGGGATGTCCTCGATG 59.459 55.000 0.00 0.00 36.20 3.84
2454 2480 0.541863 GGTTGGGATGTCCTCGATGT 59.458 55.000 0.00 0.00 36.20 3.06
2455 2481 1.065418 GGTTGGGATGTCCTCGATGTT 60.065 52.381 0.00 0.00 36.20 2.71
2456 2482 2.009774 GTTGGGATGTCCTCGATGTTG 58.990 52.381 0.00 0.00 36.20 3.33
2457 2483 0.107703 TGGGATGTCCTCGATGTTGC 60.108 55.000 0.00 0.00 36.20 4.17
2458 2484 0.107703 GGGATGTCCTCGATGTTGCA 60.108 55.000 0.00 0.00 35.95 4.08
2459 2485 1.475751 GGGATGTCCTCGATGTTGCAT 60.476 52.381 0.00 0.00 35.95 3.96
2460 2486 1.600957 GGATGTCCTCGATGTTGCATG 59.399 52.381 0.00 0.00 0.00 4.06
2461 2487 2.283298 GATGTCCTCGATGTTGCATGT 58.717 47.619 0.00 0.00 0.00 3.21
2462 2488 1.441738 TGTCCTCGATGTTGCATGTG 58.558 50.000 0.00 0.00 0.00 3.21
2463 2489 0.097674 GTCCTCGATGTTGCATGTGC 59.902 55.000 0.00 0.00 42.50 4.57
2464 2490 1.061411 CCTCGATGTTGCATGTGCG 59.939 57.895 0.01 0.00 45.83 5.34
2465 2491 1.638388 CCTCGATGTTGCATGTGCGT 61.638 55.000 0.01 0.00 45.83 5.24
2466 2492 0.519792 CTCGATGTTGCATGTGCGTG 60.520 55.000 0.01 0.00 45.83 5.34
2467 2493 1.207339 CGATGTTGCATGTGCGTGT 59.793 52.632 0.01 0.00 45.83 4.49
2468 2494 1.061262 CGATGTTGCATGTGCGTGTG 61.061 55.000 0.01 0.00 45.83 3.82
2469 2495 0.040157 GATGTTGCATGTGCGTGTGT 60.040 50.000 0.01 0.00 45.83 3.72
2470 2496 0.318022 ATGTTGCATGTGCGTGTGTG 60.318 50.000 0.01 0.00 45.83 3.82
2471 2497 1.063972 GTTGCATGTGCGTGTGTGT 59.936 52.632 0.01 0.00 45.83 3.72
2472 2498 1.063811 TTGCATGTGCGTGTGTGTG 59.936 52.632 0.01 0.00 45.83 3.82
2473 2499 1.652167 TTGCATGTGCGTGTGTGTGT 61.652 50.000 0.01 0.00 45.83 3.72
2474 2500 1.655046 GCATGTGCGTGTGTGTGTG 60.655 57.895 0.00 0.00 0.00 3.82
2475 2501 1.720894 CATGTGCGTGTGTGTGTGT 59.279 52.632 0.00 0.00 0.00 3.72
2476 2502 0.589479 CATGTGCGTGTGTGTGTGTG 60.589 55.000 0.00 0.00 0.00 3.82
2477 2503 1.024046 ATGTGCGTGTGTGTGTGTGT 61.024 50.000 0.00 0.00 0.00 3.72
2478 2504 1.231296 TGTGCGTGTGTGTGTGTGTT 61.231 50.000 0.00 0.00 0.00 3.32
2479 2505 0.109964 GTGCGTGTGTGTGTGTGTTT 60.110 50.000 0.00 0.00 0.00 2.83
2480 2506 0.593618 TGCGTGTGTGTGTGTGTTTT 59.406 45.000 0.00 0.00 0.00 2.43
2481 2507 1.255767 GCGTGTGTGTGTGTGTTTTC 58.744 50.000 0.00 0.00 0.00 2.29
2482 2508 1.135803 GCGTGTGTGTGTGTGTTTTCT 60.136 47.619 0.00 0.00 0.00 2.52
2483 2509 2.667171 GCGTGTGTGTGTGTGTTTTCTT 60.667 45.455 0.00 0.00 0.00 2.52
2484 2510 3.560503 CGTGTGTGTGTGTGTTTTCTTT 58.439 40.909 0.00 0.00 0.00 2.52
2485 2511 3.360463 CGTGTGTGTGTGTGTTTTCTTTG 59.640 43.478 0.00 0.00 0.00 2.77
2486 2512 3.672867 GTGTGTGTGTGTGTTTTCTTTGG 59.327 43.478 0.00 0.00 0.00 3.28
2487 2513 3.249917 GTGTGTGTGTGTTTTCTTTGGG 58.750 45.455 0.00 0.00 0.00 4.12
2488 2514 2.894126 TGTGTGTGTGTTTTCTTTGGGT 59.106 40.909 0.00 0.00 0.00 4.51
2489 2515 3.249917 GTGTGTGTGTTTTCTTTGGGTG 58.750 45.455 0.00 0.00 0.00 4.61
2490 2516 2.267426 GTGTGTGTTTTCTTTGGGTGC 58.733 47.619 0.00 0.00 0.00 5.01
2491 2517 1.205893 TGTGTGTTTTCTTTGGGTGCC 59.794 47.619 0.00 0.00 0.00 5.01
2492 2518 1.480545 GTGTGTTTTCTTTGGGTGCCT 59.519 47.619 0.00 0.00 0.00 4.75
2493 2519 2.691011 GTGTGTTTTCTTTGGGTGCCTA 59.309 45.455 0.00 0.00 0.00 3.93
2494 2520 2.691011 TGTGTTTTCTTTGGGTGCCTAC 59.309 45.455 0.00 0.00 0.00 3.18
2495 2521 2.691011 GTGTTTTCTTTGGGTGCCTACA 59.309 45.455 0.00 0.00 0.00 2.74
2496 2522 2.955660 TGTTTTCTTTGGGTGCCTACAG 59.044 45.455 0.00 0.00 0.00 2.74
2497 2523 2.286365 TTTCTTTGGGTGCCTACAGG 57.714 50.000 0.00 0.00 38.53 4.00
2498 2524 1.145571 TTCTTTGGGTGCCTACAGGT 58.854 50.000 0.00 0.00 37.57 4.00
2499 2525 1.145571 TCTTTGGGTGCCTACAGGTT 58.854 50.000 0.00 0.00 37.57 3.50
2500 2526 1.497286 TCTTTGGGTGCCTACAGGTTT 59.503 47.619 0.00 0.00 37.57 3.27
2501 2527 1.613437 CTTTGGGTGCCTACAGGTTTG 59.387 52.381 0.00 0.00 37.57 2.93
2502 2528 0.553819 TTGGGTGCCTACAGGTTTGT 59.446 50.000 0.00 0.00 41.39 2.83
2503 2529 0.179004 TGGGTGCCTACAGGTTTGTG 60.179 55.000 0.00 0.00 38.23 3.33
2504 2530 0.179001 GGGTGCCTACAGGTTTGTGT 60.179 55.000 0.00 0.00 38.23 3.72
2505 2531 1.235724 GGTGCCTACAGGTTTGTGTC 58.764 55.000 0.00 0.00 38.23 3.67
2506 2532 0.865769 GTGCCTACAGGTTTGTGTCG 59.134 55.000 0.00 0.00 38.23 4.35
2507 2533 0.250124 TGCCTACAGGTTTGTGTCGG 60.250 55.000 0.00 0.00 38.23 4.79
2508 2534 0.250166 GCCTACAGGTTTGTGTCGGT 60.250 55.000 0.00 0.00 38.23 4.69
2509 2535 1.508632 CCTACAGGTTTGTGTCGGTG 58.491 55.000 0.00 0.00 38.23 4.94
2510 2536 1.202604 CCTACAGGTTTGTGTCGGTGT 60.203 52.381 0.00 0.00 38.23 4.16
2511 2537 2.557317 CTACAGGTTTGTGTCGGTGTT 58.443 47.619 0.00 0.00 38.23 3.32
2512 2538 1.828979 ACAGGTTTGTGTCGGTGTTT 58.171 45.000 0.00 0.00 35.83 2.83
2513 2539 2.164338 ACAGGTTTGTGTCGGTGTTTT 58.836 42.857 0.00 0.00 35.83 2.43
2514 2540 2.559231 ACAGGTTTGTGTCGGTGTTTTT 59.441 40.909 0.00 0.00 35.83 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
202 203 6.405731 GCCACCATTAAATGCAGTTATGAAGA 60.406 38.462 7.53 0.00 0.00 2.87
239 242 5.659440 AGACAACCTTTCTTTGAGCAAAA 57.341 34.783 0.00 0.00 0.00 2.44
328 331 7.883229 ACAAAATTAGTAAATTTCGGCCAAG 57.117 32.000 2.24 0.00 43.04 3.61
1031 1042 8.988934 GGGAAACAAATTATCCAAAAGAAGAAC 58.011 33.333 0.00 0.00 34.82 3.01
1485 1498 2.280052 GCAGCCCAGATCTCTCGC 60.280 66.667 0.00 0.00 0.00 5.03
1899 1917 1.135257 CACGGTCCAAACAACAAGCAA 60.135 47.619 0.00 0.00 0.00 3.91
1904 1922 2.473760 CGCCACGGTCCAAACAACA 61.474 57.895 0.00 0.00 0.00 3.33
1905 1923 1.512156 ATCGCCACGGTCCAAACAAC 61.512 55.000 0.00 0.00 0.00 3.32
1907 1925 1.963855 CATCGCCACGGTCCAAACA 60.964 57.895 0.00 0.00 0.00 2.83
1929 1947 3.661758 TTGTGTTTTCGTCCGACTTTC 57.338 42.857 0.00 0.00 0.00 2.62
1937 1955 6.633634 TCGGATAATTTGTTTGTGTTTTCGTC 59.366 34.615 0.00 0.00 0.00 4.20
1949 1967 4.200092 GCTCTTCCCTCGGATAATTTGTT 58.800 43.478 0.00 0.00 0.00 2.83
1951 1969 3.808728 TGCTCTTCCCTCGGATAATTTG 58.191 45.455 0.00 0.00 0.00 2.32
1955 1973 2.032620 GACTGCTCTTCCCTCGGATAA 58.967 52.381 0.00 0.00 0.00 1.75
1984 2004 2.995466 ATTTGTCTGTGTGCCATTCG 57.005 45.000 0.00 0.00 0.00 3.34
1985 2005 5.376854 AGTAATTTGTCTGTGTGCCATTC 57.623 39.130 0.00 0.00 0.00 2.67
2032 2052 2.064242 AACCCTCCAACAACTCCGGG 62.064 60.000 0.00 0.00 37.70 5.73
2034 2054 0.949105 CGAACCCTCCAACAACTCCG 60.949 60.000 0.00 0.00 0.00 4.63
2040 2066 1.210967 ACTTGTTCGAACCCTCCAACA 59.789 47.619 24.78 1.72 0.00 3.33
2091 2117 1.488393 CAAAAACCCTCAAAAGCCCCA 59.512 47.619 0.00 0.00 0.00 4.96
2092 2118 1.202758 CCAAAAACCCTCAAAAGCCCC 60.203 52.381 0.00 0.00 0.00 5.80
2093 2119 1.765904 TCCAAAAACCCTCAAAAGCCC 59.234 47.619 0.00 0.00 0.00 5.19
2094 2120 2.434336 ACTCCAAAAACCCTCAAAAGCC 59.566 45.455 0.00 0.00 0.00 4.35
2095 2121 3.819564 ACTCCAAAAACCCTCAAAAGC 57.180 42.857 0.00 0.00 0.00 3.51
2096 2122 4.875536 CCAAACTCCAAAAACCCTCAAAAG 59.124 41.667 0.00 0.00 0.00 2.27
2097 2123 4.287326 ACCAAACTCCAAAAACCCTCAAAA 59.713 37.500 0.00 0.00 0.00 2.44
2098 2124 3.841255 ACCAAACTCCAAAAACCCTCAAA 59.159 39.130 0.00 0.00 0.00 2.69
2099 2125 3.445987 ACCAAACTCCAAAAACCCTCAA 58.554 40.909 0.00 0.00 0.00 3.02
2110 2136 5.367945 AAGTGTTTAGAGACCAAACTCCA 57.632 39.130 0.00 0.00 36.92 3.86
2114 2140 5.243426 TGCAAAGTGTTTAGAGACCAAAC 57.757 39.130 0.00 0.00 36.60 2.93
2127 2153 4.218417 AGTGAAGTGTCTTTTGCAAAGTGT 59.782 37.500 12.41 0.00 0.00 3.55
2133 2159 5.888691 TGTTAAGTGAAGTGTCTTTTGCA 57.111 34.783 0.00 0.00 0.00 4.08
2134 2160 7.411480 GGTTTTGTTAAGTGAAGTGTCTTTTGC 60.411 37.037 0.00 0.00 0.00 3.68
2135 2161 7.596995 TGGTTTTGTTAAGTGAAGTGTCTTTTG 59.403 33.333 0.00 0.00 0.00 2.44
2140 2166 9.394477 GATATTGGTTTTGTTAAGTGAAGTGTC 57.606 33.333 0.00 0.00 0.00 3.67
2182 2208 3.705051 TCACCGAGTCCTTAGGTATGTT 58.295 45.455 0.00 0.00 36.34 2.71
2183 2209 3.377253 TCACCGAGTCCTTAGGTATGT 57.623 47.619 0.00 0.00 36.34 2.29
2234 2260 5.000012 AGACGAGTGTTATCAGGATCAAC 58.000 43.478 0.00 0.00 0.00 3.18
2237 2263 5.651530 TCAAAGACGAGTGTTATCAGGATC 58.348 41.667 0.00 0.00 0.00 3.36
2239 2265 5.243060 TCTTCAAAGACGAGTGTTATCAGGA 59.757 40.000 0.00 0.00 0.00 3.86
2244 2270 7.171678 CCTCTTTTCTTCAAAGACGAGTGTTAT 59.828 37.037 0.00 0.00 45.12 1.89
2252 2278 3.498777 GTCCCCTCTTTTCTTCAAAGACG 59.501 47.826 0.00 0.00 45.12 4.18
2256 2282 6.262056 AGTTAGTCCCCTCTTTTCTTCAAA 57.738 37.500 0.00 0.00 0.00 2.69
2273 2299 6.449830 AGACCCCAAAAGATACAAGTTAGT 57.550 37.500 0.00 0.00 0.00 2.24
2278 2304 5.355350 CAGCTTAGACCCCAAAAGATACAAG 59.645 44.000 0.00 0.00 0.00 3.16
2320 2346 8.956426 CAGCTTGATTAAAGGGACTAATGTTTA 58.044 33.333 0.00 0.00 38.49 2.01
2324 2350 6.122277 TCCAGCTTGATTAAAGGGACTAATG 58.878 40.000 0.00 0.00 38.49 1.90
2325 2351 6.327386 TCCAGCTTGATTAAAGGGACTAAT 57.673 37.500 0.00 0.00 38.49 1.73
2326 2352 5.772393 TCCAGCTTGATTAAAGGGACTAA 57.228 39.130 0.00 0.00 38.49 2.24
2333 2359 9.281371 TGATGATCTATTCCAGCTTGATTAAAG 57.719 33.333 0.00 0.00 39.07 1.85
2340 2366 6.976925 GGTTTTTGATGATCTATTCCAGCTTG 59.023 38.462 0.00 0.00 0.00 4.01
2343 2369 6.096001 AGTGGTTTTTGATGATCTATTCCAGC 59.904 38.462 0.00 0.00 0.00 4.85
2348 2374 9.799106 CCCTATAGTGGTTTTTGATGATCTATT 57.201 33.333 0.00 0.00 0.00 1.73
2382 2408 2.547218 CCTTTGATGGGCAATGCATAGC 60.547 50.000 7.79 0.00 36.15 2.97
2383 2409 2.696707 ACCTTTGATGGGCAATGCATAG 59.303 45.455 7.79 0.00 36.15 2.23
2384 2410 2.431419 CACCTTTGATGGGCAATGCATA 59.569 45.455 7.79 0.00 36.15 3.14
2385 2411 1.208535 CACCTTTGATGGGCAATGCAT 59.791 47.619 7.79 0.00 36.15 3.96
2386 2412 0.609151 CACCTTTGATGGGCAATGCA 59.391 50.000 7.79 0.00 36.15 3.96
2387 2413 0.896923 TCACCTTTGATGGGCAATGC 59.103 50.000 0.00 0.00 36.15 3.56
2388 2414 2.675889 GCTTCACCTTTGATGGGCAATG 60.676 50.000 0.00 0.00 36.15 2.82
2389 2415 1.551883 GCTTCACCTTTGATGGGCAAT 59.448 47.619 0.00 0.00 36.15 3.56
2390 2416 0.968405 GCTTCACCTTTGATGGGCAA 59.032 50.000 0.00 0.00 33.88 4.52
2391 2417 1.243342 CGCTTCACCTTTGATGGGCA 61.243 55.000 0.00 0.00 34.43 5.36
2392 2418 0.960364 TCGCTTCACCTTTGATGGGC 60.960 55.000 0.00 0.00 38.82 5.36
2393 2419 0.804989 GTCGCTTCACCTTTGATGGG 59.195 55.000 0.00 0.00 39.75 4.00
2394 2420 0.443869 CGTCGCTTCACCTTTGATGG 59.556 55.000 0.00 0.00 0.00 3.51
2395 2421 0.443869 CCGTCGCTTCACCTTTGATG 59.556 55.000 0.00 0.00 0.00 3.07
2396 2422 0.034896 ACCGTCGCTTCACCTTTGAT 59.965 50.000 0.00 0.00 0.00 2.57
2397 2423 0.878523 CACCGTCGCTTCACCTTTGA 60.879 55.000 0.00 0.00 0.00 2.69
2398 2424 1.569493 CACCGTCGCTTCACCTTTG 59.431 57.895 0.00 0.00 0.00 2.77
2399 2425 2.251642 GCACCGTCGCTTCACCTTT 61.252 57.895 0.00 0.00 0.00 3.11
2400 2426 2.665185 GCACCGTCGCTTCACCTT 60.665 61.111 0.00 0.00 0.00 3.50
2413 2439 4.307908 GTTGTGTCGTGGCGCACC 62.308 66.667 10.83 0.00 34.76 5.01
2414 2440 4.307908 GGTTGTGTCGTGGCGCAC 62.308 66.667 10.83 4.68 35.63 5.34
2415 2441 4.539083 AGGTTGTGTCGTGGCGCA 62.539 61.111 10.83 0.00 0.00 6.09
2416 2442 2.830285 AAAGGTTGTGTCGTGGCGC 61.830 57.895 0.00 0.00 0.00 6.53
2417 2443 1.010125 CAAAGGTTGTGTCGTGGCG 60.010 57.895 0.00 0.00 0.00 5.69
2418 2444 1.358759 CCAAAGGTTGTGTCGTGGC 59.641 57.895 0.00 0.00 0.00 5.01
2419 2445 1.099689 AACCAAAGGTTGTGTCGTGG 58.900 50.000 0.00 0.00 45.07 4.94
2429 2455 1.075536 GAGGACATCCCAACCAAAGGT 59.924 52.381 0.00 0.00 34.91 3.50
2430 2456 1.839424 GAGGACATCCCAACCAAAGG 58.161 55.000 0.00 0.00 37.41 3.11
2431 2457 1.003118 TCGAGGACATCCCAACCAAAG 59.997 52.381 0.00 0.00 37.41 2.77
2432 2458 1.060729 TCGAGGACATCCCAACCAAA 58.939 50.000 0.00 0.00 37.41 3.28
2433 2459 1.065491 CATCGAGGACATCCCAACCAA 60.065 52.381 0.00 0.00 37.41 3.67
2434 2460 0.541392 CATCGAGGACATCCCAACCA 59.459 55.000 0.00 0.00 37.41 3.67
2435 2461 0.541863 ACATCGAGGACATCCCAACC 59.458 55.000 3.06 0.00 37.41 3.77
2436 2462 2.009774 CAACATCGAGGACATCCCAAC 58.990 52.381 3.06 0.00 37.41 3.77
2437 2463 1.678728 GCAACATCGAGGACATCCCAA 60.679 52.381 3.06 0.00 37.41 4.12
2438 2464 0.107703 GCAACATCGAGGACATCCCA 60.108 55.000 3.06 0.00 37.41 4.37
2439 2465 0.107703 TGCAACATCGAGGACATCCC 60.108 55.000 3.06 0.00 36.42 3.85
2440 2466 1.600957 CATGCAACATCGAGGACATCC 59.399 52.381 3.06 0.00 0.00 3.51
2441 2467 2.031314 CACATGCAACATCGAGGACATC 59.969 50.000 3.06 0.00 0.00 3.06
2442 2468 2.011947 CACATGCAACATCGAGGACAT 58.988 47.619 3.06 1.46 0.00 3.06
2443 2469 1.441738 CACATGCAACATCGAGGACA 58.558 50.000 3.06 0.00 0.00 4.02
2444 2470 0.097674 GCACATGCAACATCGAGGAC 59.902 55.000 3.06 0.00 41.59 3.85
2445 2471 1.360931 CGCACATGCAACATCGAGGA 61.361 55.000 3.06 0.00 42.21 3.71
2446 2472 1.061411 CGCACATGCAACATCGAGG 59.939 57.895 4.49 0.00 42.21 4.63
2447 2473 0.519792 CACGCACATGCAACATCGAG 60.520 55.000 4.49 0.00 42.21 4.04
2448 2474 1.227342 ACACGCACATGCAACATCGA 61.227 50.000 4.49 0.00 42.21 3.59
2449 2475 1.061262 CACACGCACATGCAACATCG 61.061 55.000 4.49 0.00 42.21 3.84
2450 2476 0.040157 ACACACGCACATGCAACATC 60.040 50.000 4.49 0.00 42.21 3.06
2451 2477 0.318022 CACACACGCACATGCAACAT 60.318 50.000 4.49 0.00 42.21 2.71
2452 2478 1.063811 CACACACGCACATGCAACA 59.936 52.632 4.49 0.00 42.21 3.33
2453 2479 1.063972 ACACACACGCACATGCAAC 59.936 52.632 4.49 0.00 42.21 4.17
2454 2480 1.063811 CACACACACGCACATGCAA 59.936 52.632 4.49 0.00 42.21 4.08
2455 2481 2.111582 ACACACACACGCACATGCA 61.112 52.632 4.49 0.00 42.21 3.96
2456 2482 1.655046 CACACACACACGCACATGC 60.655 57.895 0.00 0.00 37.78 4.06
2457 2483 0.589479 CACACACACACACGCACATG 60.589 55.000 0.00 0.00 0.00 3.21
2458 2484 1.024046 ACACACACACACACGCACAT 61.024 50.000 0.00 0.00 0.00 3.21
2459 2485 1.231296 AACACACACACACACGCACA 61.231 50.000 0.00 0.00 0.00 4.57
2460 2486 0.109964 AAACACACACACACACGCAC 60.110 50.000 0.00 0.00 0.00 5.34
2461 2487 0.593618 AAAACACACACACACACGCA 59.406 45.000 0.00 0.00 0.00 5.24
2462 2488 1.135803 AGAAAACACACACACACACGC 60.136 47.619 0.00 0.00 0.00 5.34
2463 2489 2.892373 AGAAAACACACACACACACG 57.108 45.000 0.00 0.00 0.00 4.49
2464 2490 3.672867 CCAAAGAAAACACACACACACAC 59.327 43.478 0.00 0.00 0.00 3.82
2465 2491 3.305676 CCCAAAGAAAACACACACACACA 60.306 43.478 0.00 0.00 0.00 3.72
2466 2492 3.249917 CCCAAAGAAAACACACACACAC 58.750 45.455 0.00 0.00 0.00 3.82
2467 2493 2.894126 ACCCAAAGAAAACACACACACA 59.106 40.909 0.00 0.00 0.00 3.72
2468 2494 3.249917 CACCCAAAGAAAACACACACAC 58.750 45.455 0.00 0.00 0.00 3.82
2469 2495 2.353208 GCACCCAAAGAAAACACACACA 60.353 45.455 0.00 0.00 0.00 3.72
2470 2496 2.267426 GCACCCAAAGAAAACACACAC 58.733 47.619 0.00 0.00 0.00 3.82
2471 2497 1.205893 GGCACCCAAAGAAAACACACA 59.794 47.619 0.00 0.00 0.00 3.72
2472 2498 1.480545 AGGCACCCAAAGAAAACACAC 59.519 47.619 0.00 0.00 0.00 3.82
2473 2499 1.859302 AGGCACCCAAAGAAAACACA 58.141 45.000 0.00 0.00 0.00 3.72
2474 2500 2.691011 TGTAGGCACCCAAAGAAAACAC 59.309 45.455 0.00 0.00 0.00 3.32
2475 2501 2.955660 CTGTAGGCACCCAAAGAAAACA 59.044 45.455 0.00 0.00 0.00 2.83
2476 2502 2.296190 CCTGTAGGCACCCAAAGAAAAC 59.704 50.000 0.00 0.00 0.00 2.43
2477 2503 2.091555 ACCTGTAGGCACCCAAAGAAAA 60.092 45.455 0.00 0.00 39.32 2.29
2478 2504 1.497286 ACCTGTAGGCACCCAAAGAAA 59.503 47.619 0.00 0.00 39.32 2.52
2479 2505 1.145571 ACCTGTAGGCACCCAAAGAA 58.854 50.000 0.00 0.00 39.32 2.52
2480 2506 1.145571 AACCTGTAGGCACCCAAAGA 58.854 50.000 0.00 0.00 39.32 2.52
2481 2507 1.613437 CAAACCTGTAGGCACCCAAAG 59.387 52.381 0.00 0.00 39.32 2.77
2482 2508 1.063567 ACAAACCTGTAGGCACCCAAA 60.064 47.619 0.00 0.00 39.32 3.28
2483 2509 0.553819 ACAAACCTGTAGGCACCCAA 59.446 50.000 0.00 0.00 39.32 4.12
2484 2510 0.179004 CACAAACCTGTAGGCACCCA 60.179 55.000 0.00 0.00 39.32 4.51
2485 2511 0.179001 ACACAAACCTGTAGGCACCC 60.179 55.000 0.00 0.00 39.32 4.61
2486 2512 1.235724 GACACAAACCTGTAGGCACC 58.764 55.000 0.00 0.00 39.32 5.01
2487 2513 0.865769 CGACACAAACCTGTAGGCAC 59.134 55.000 0.00 0.00 39.32 5.01
2488 2514 0.250124 CCGACACAAACCTGTAGGCA 60.250 55.000 0.00 0.00 39.32 4.75
2489 2515 0.250166 ACCGACACAAACCTGTAGGC 60.250 55.000 0.00 0.00 39.81 3.93
2490 2516 1.202604 ACACCGACACAAACCTGTAGG 60.203 52.381 0.00 0.00 41.43 3.18
2491 2517 2.234300 ACACCGACACAAACCTGTAG 57.766 50.000 0.00 0.00 33.22 2.74
2492 2518 2.695127 AACACCGACACAAACCTGTA 57.305 45.000 0.00 0.00 33.22 2.74
2493 2519 1.828979 AAACACCGACACAAACCTGT 58.171 45.000 0.00 0.00 35.63 4.00
2494 2520 2.931512 AAAACACCGACACAAACCTG 57.068 45.000 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.