Multiple sequence alignment - TraesCS7B01G448700

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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 TraesCS7B01G448700 chr7B 100.000 2483 0 0 1 2483 711434161 711431679 0.000000e+00 4586.0
1 TraesCS7B01G448700 chr7A 94.447 2143 98 8 223 2352 14896678 14894544 0.000000e+00 3278.0
2 TraesCS7B01G448700 chr7A 80.758 712 133 4 696 1405 91294607 91295316 1.000000e-153 553.0
3 TraesCS7B01G448700 chr7A 79.805 718 134 11 695 1406 14821106 14820394 1.700000e-141 512.0
4 TraesCS7B01G448700 chr7A 91.716 169 13 1 7 175 14896855 14896688 1.480000e-57 233.0
5 TraesCS7B01G448700 chr7A 77.311 119 23 4 536 652 5108995 5109111 1.590000e-07 67.6
6 TraesCS7B01G448700 chr4A 93.620 2116 112 13 249 2352 718967831 718969935 0.000000e+00 3138.0
7 TraesCS7B01G448700 chr4A 93.620 2116 112 13 249 2352 718980078 718982182 0.000000e+00 3138.0
8 TraesCS7B01G448700 chr7D 93.202 2133 116 14 223 2352 16060667 16058561 0.000000e+00 3109.0
9 TraesCS7B01G448700 chr7D 79.555 719 134 13 695 1406 15912960 15912248 3.690000e-138 501.0
10 TraesCS7B01G448700 chr7D 89.894 188 16 1 2165 2352 16007627 16007443 3.190000e-59 239.0
11 TraesCS7B01G448700 chr7D 89.362 188 17 1 2165 2352 16016218 16016034 1.480000e-57 233.0
12 TraesCS7B01G448700 chr3D 92.847 1454 91 5 891 2343 584823548 584824989 0.000000e+00 2097.0
13 TraesCS7B01G448700 chr3D 95.168 683 28 4 214 895 584817702 584818380 0.000000e+00 1074.0
14 TraesCS7B01G448700 chr3D 79.037 706 137 11 707 1406 584932134 584932834 8.040000e-130 473.0
15 TraesCS7B01G448700 chrUn 89.894 188 16 1 2156 2343 457338120 457338304 3.190000e-59 239.0
16 TraesCS7B01G448700 chrUn 89.894 188 16 1 2165 2352 462295653 462295469 3.190000e-59 239.0
17 TraesCS7B01G448700 chr2D 95.763 118 5 0 2342 2459 375031541 375031658 9.060000e-45 191.0
18 TraesCS7B01G448700 chr1D 97.297 111 3 0 2349 2459 73690879 73690769 3.260000e-44 189.0
19 TraesCS7B01G448700 chr6B 95.690 116 3 2 2347 2462 224863382 224863495 4.220000e-43 185.0
20 TraesCS7B01G448700 chr5D 96.460 113 3 1 2352 2463 391376987 391376875 4.220000e-43 185.0
21 TraesCS7B01G448700 chr1A 95.690 116 4 1 2351 2466 387511462 387511348 4.220000e-43 185.0
22 TraesCS7B01G448700 chr6A 94.915 118 5 1 2342 2459 408886192 408886076 1.520000e-42 183.0
23 TraesCS7B01G448700 chr3B 94.915 118 5 1 2344 2461 70582219 70582103 1.520000e-42 183.0
24 TraesCS7B01G448700 chr5B 94.167 120 6 1 2350 2468 678513929 678514048 5.460000e-42 182.0
25 TraesCS7B01G448700 chr5B 90.977 133 6 5 2338 2466 559999874 559999744 9.130000e-40 174.0


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 TraesCS7B01G448700 chr7B 711431679 711434161 2482 True 4586.0 4586 100.0000 1 2483 1 chr7B.!!$R1 2482
1 TraesCS7B01G448700 chr7A 14894544 14896855 2311 True 1755.5 3278 93.0815 7 2352 2 chr7A.!!$R2 2345
2 TraesCS7B01G448700 chr7A 91294607 91295316 709 False 553.0 553 80.7580 696 1405 1 chr7A.!!$F2 709
3 TraesCS7B01G448700 chr7A 14820394 14821106 712 True 512.0 512 79.8050 695 1406 1 chr7A.!!$R1 711
4 TraesCS7B01G448700 chr4A 718967831 718969935 2104 False 3138.0 3138 93.6200 249 2352 1 chr4A.!!$F1 2103
5 TraesCS7B01G448700 chr4A 718980078 718982182 2104 False 3138.0 3138 93.6200 249 2352 1 chr4A.!!$F2 2103
6 TraesCS7B01G448700 chr7D 16058561 16060667 2106 True 3109.0 3109 93.2020 223 2352 1 chr7D.!!$R4 2129
7 TraesCS7B01G448700 chr7D 15912248 15912960 712 True 501.0 501 79.5550 695 1406 1 chr7D.!!$R1 711
8 TraesCS7B01G448700 chr3D 584823548 584824989 1441 False 2097.0 2097 92.8470 891 2343 1 chr3D.!!$F2 1452
9 TraesCS7B01G448700 chr3D 584817702 584818380 678 False 1074.0 1074 95.1680 214 895 1 chr3D.!!$F1 681
10 TraesCS7B01G448700 chr3D 584932134 584932834 700 False 473.0 473 79.0370 707 1406 1 chr3D.!!$F3 699

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
221 222 0.030908 CCTTCGGACTATCACGAGCC 59.969 60.0 0.00 0.0 40.51 4.70 F
923 937 0.233848 CTGTTTCGGCGTGTTGGTAC 59.766 55.0 6.85 0.0 0.00 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1453 1467 0.987081 ACAGAGAGCATGCTGGGGAT 60.987 55.0 28.27 4.58 36.47 3.85 R
2441 2466 0.033796 ACATACTCCCTCCGTTCGGA 60.034 55.0 13.34 13.34 0.00 4.55 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
23 24 0.174389 CCGCTAGAGTGCTGATGTGT 59.826 55.000 0.00 0.00 0.00 3.72
37 38 3.402110 TGATGTGTTCAGGATGTGACAC 58.598 45.455 0.00 0.00 46.44 3.67
56 57 3.949113 ACACCCGTTCAATGTTTACACTT 59.051 39.130 0.00 0.00 0.00 3.16
59 60 4.825085 ACCCGTTCAATGTTTACACTTCAT 59.175 37.500 0.00 0.00 0.00 2.57
65 66 5.953183 TCAATGTTTACACTTCATGGATGC 58.047 37.500 0.00 0.00 0.00 3.91
71 72 5.628797 TTACACTTCATGGATGCTGGATA 57.371 39.130 0.00 0.00 0.00 2.59
74 75 3.190744 CACTTCATGGATGCTGGATATGC 59.809 47.826 0.00 0.00 0.00 3.14
148 149 5.982890 AGTACTTTGCTGGTTTATTGCAT 57.017 34.783 0.00 0.00 36.55 3.96
200 201 4.706527 GCATCTATGTGCTTCGAATTAGC 58.293 43.478 0.00 0.00 41.82 3.09
201 202 4.212004 GCATCTATGTGCTTCGAATTAGCA 59.788 41.667 6.18 6.18 45.78 3.49
207 208 1.999735 TGCTTCGAATTAGCACCTTCG 59.000 47.619 6.18 7.88 43.30 3.79
208 209 1.327764 GCTTCGAATTAGCACCTTCGG 59.672 52.381 0.00 2.22 43.29 4.30
209 210 2.888594 CTTCGAATTAGCACCTTCGGA 58.111 47.619 0.00 5.38 43.29 4.55
210 211 2.288961 TCGAATTAGCACCTTCGGAC 57.711 50.000 12.55 0.00 43.29 4.79
211 212 1.822990 TCGAATTAGCACCTTCGGACT 59.177 47.619 12.55 0.00 43.29 3.85
212 213 3.018856 TCGAATTAGCACCTTCGGACTA 58.981 45.455 12.55 0.00 43.29 2.59
216 217 3.795623 TTAGCACCTTCGGACTATCAC 57.204 47.619 0.00 0.00 0.00 3.06
219 220 1.534175 GCACCTTCGGACTATCACGAG 60.534 57.143 0.00 0.00 40.51 4.18
221 222 0.030908 CCTTCGGACTATCACGAGCC 59.969 60.000 0.00 0.00 40.51 4.70
242 243 4.863491 CCATACATGCACTGGCTATTTTC 58.137 43.478 0.00 0.00 41.91 2.29
257 258 6.714810 TGGCTATTTTCTTTCTTAGCACTTCA 59.285 34.615 0.00 0.00 39.01 3.02
258 259 7.394359 TGGCTATTTTCTTTCTTAGCACTTCAT 59.606 33.333 0.00 0.00 39.01 2.57
397 410 3.563808 GTCTTTGTGTGTAAGCCATGTCA 59.436 43.478 0.00 0.00 0.00 3.58
434 447 1.920835 GACCTCCCAGAAGGCCTGT 60.921 63.158 5.69 0.00 41.33 4.00
441 454 1.521450 CCAGAAGGCCTGTTGCACTG 61.521 60.000 5.69 9.44 43.89 3.66
570 583 2.170187 CTCTCCTTCTCCAACCTGATGG 59.830 54.545 0.00 0.00 42.12 3.51
585 598 1.274069 TGATGGCTCTTCTTCCCCTCT 60.274 52.381 0.00 0.00 0.00 3.69
669 682 1.688197 CAAAGTCAACCAAGGTGCCAT 59.312 47.619 0.00 0.00 0.00 4.40
724 737 0.783206 TTTCCTTCATGGGGGCTTCA 59.217 50.000 0.00 0.00 36.20 3.02
910 924 3.378427 GGCTGGACCACATAATCTGTTTC 59.622 47.826 0.00 0.00 35.29 2.78
923 937 0.233848 CTGTTTCGGCGTGTTGGTAC 59.766 55.000 6.85 0.00 0.00 3.34
983 997 2.548057 TCAAGCAAATCGTGGTCTTCAC 59.452 45.455 0.00 0.00 42.74 3.18
1167 1181 1.541233 GGCTGTCGGGGATCTATTGTG 60.541 57.143 0.00 0.00 0.00 3.33
1372 1386 3.403038 CAGGAGTCTGAACGTTGGATTT 58.597 45.455 5.00 0.00 43.49 2.17
1416 1430 5.105595 GCTGCAGGGAGATGTCTTTATTTTT 60.106 40.000 17.12 0.00 0.00 1.94
1471 1485 1.054231 TATCCCCAGCATGCTCTCTG 58.946 55.000 19.68 7.54 31.97 3.35
1565 1580 7.395772 TGCAAGGATGTTTAAGAATTATCCACA 59.604 33.333 0.00 0.00 39.76 4.17
1701 1716 2.287487 TGTTCGGTGATGTTGTTGCATG 60.287 45.455 0.00 0.00 0.00 4.06
1752 1767 4.142600 GCGCATGTAGTGAATTCCTTTCTT 60.143 41.667 0.30 0.00 35.23 2.52
1978 2002 1.016130 ATTGTGCTTCGTGCTCCTCG 61.016 55.000 5.00 0.00 43.37 4.63
2066 2090 0.460987 TTGCAGCGGGTTTGGTTTTG 60.461 50.000 0.00 0.00 0.00 2.44
2115 2139 6.918892 ACTTTTGGTTTGCTAAATTTGGTC 57.081 33.333 0.00 0.00 0.00 4.02
2119 2143 9.271828 CTTTTGGTTTGCTAAATTTGGTCTTAT 57.728 29.630 0.00 0.00 0.00 1.73
2227 2252 6.665992 AAACCCCTAAAAATCTTCAGGAAC 57.334 37.500 0.00 0.00 0.00 3.62
2295 2320 3.006967 TCCAGTAACTCTGCCAGACTTTC 59.993 47.826 0.00 0.00 42.38 2.62
2332 2357 1.586028 CAATGGAAACTGTGGGCGG 59.414 57.895 0.00 0.00 0.00 6.13
2343 2368 4.974438 TGGGCGGGACCTGGTTCT 62.974 66.667 4.84 0.00 39.10 3.01
2345 2370 2.732619 GGGCGGGACCTGGTTCTAG 61.733 68.421 4.84 0.99 39.10 2.43
2352 2377 2.504175 GGGACCTGGTTCTAGCAATGTA 59.496 50.000 4.84 0.00 0.00 2.29
2353 2378 3.532542 GGACCTGGTTCTAGCAATGTAC 58.467 50.000 0.00 0.00 0.00 2.90
2354 2379 3.197983 GGACCTGGTTCTAGCAATGTACT 59.802 47.826 0.00 0.00 0.00 2.73
2355 2380 4.434520 GACCTGGTTCTAGCAATGTACTC 58.565 47.826 0.00 0.00 0.00 2.59
2356 2381 3.197983 ACCTGGTTCTAGCAATGTACTCC 59.802 47.826 0.00 0.00 0.00 3.85
2357 2382 3.432326 CCTGGTTCTAGCAATGTACTCCC 60.432 52.174 0.00 0.00 0.00 4.30
2358 2383 3.450904 TGGTTCTAGCAATGTACTCCCT 58.549 45.455 0.00 0.00 0.00 4.20
2359 2384 3.451178 TGGTTCTAGCAATGTACTCCCTC 59.549 47.826 0.00 0.00 0.00 4.30
2360 2385 3.181464 GGTTCTAGCAATGTACTCCCTCC 60.181 52.174 0.00 0.00 0.00 4.30
2361 2386 2.307768 TCTAGCAATGTACTCCCTCCG 58.692 52.381 0.00 0.00 0.00 4.63
2362 2387 2.032620 CTAGCAATGTACTCCCTCCGT 58.967 52.381 0.00 0.00 0.00 4.69
2363 2388 1.276622 AGCAATGTACTCCCTCCGTT 58.723 50.000 0.00 0.00 0.00 4.44
2364 2389 1.207329 AGCAATGTACTCCCTCCGTTC 59.793 52.381 0.00 0.00 0.00 3.95
2365 2390 1.922570 CAATGTACTCCCTCCGTTCG 58.077 55.000 0.00 0.00 0.00 3.95
2366 2391 0.822164 AATGTACTCCCTCCGTTCGG 59.178 55.000 4.74 4.74 0.00 4.30
2367 2392 0.033796 ATGTACTCCCTCCGTTCGGA 60.034 55.000 13.34 13.34 0.00 4.55
2368 2393 0.251297 TGTACTCCCTCCGTTCGGAA 60.251 55.000 14.79 0.04 33.41 4.30
2369 2394 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
2370 2395 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
2371 2396 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
2372 2397 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
2373 2398 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
2374 2399 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
2375 2400 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
2376 2401 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
2377 2402 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
2378 2403 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
2379 2404 1.060122 CCGTTCGGAATTACTTGTCGC 59.940 52.381 5.19 0.00 0.00 5.19
2380 2405 1.266211 CGTTCGGAATTACTTGTCGCG 60.266 52.381 0.00 0.00 0.00 5.87
2381 2406 1.060122 GTTCGGAATTACTTGTCGCGG 59.940 52.381 6.13 0.00 0.00 6.46
2382 2407 0.527113 TCGGAATTACTTGTCGCGGA 59.473 50.000 6.13 0.00 0.00 5.54
2383 2408 1.067706 TCGGAATTACTTGTCGCGGAA 60.068 47.619 6.13 0.00 0.00 4.30
2384 2409 1.727880 CGGAATTACTTGTCGCGGAAA 59.272 47.619 6.13 0.00 0.00 3.13
2385 2410 2.350498 CGGAATTACTTGTCGCGGAAAT 59.650 45.455 6.13 0.00 0.00 2.17
2386 2411 3.680789 GGAATTACTTGTCGCGGAAATG 58.319 45.455 6.13 0.00 0.00 2.32
2387 2412 3.372822 GGAATTACTTGTCGCGGAAATGA 59.627 43.478 6.13 0.00 0.00 2.57
2388 2413 4.142773 GGAATTACTTGTCGCGGAAATGAA 60.143 41.667 6.13 0.00 0.00 2.57
2389 2414 5.448632 GGAATTACTTGTCGCGGAAATGAAT 60.449 40.000 6.13 0.00 0.00 2.57
2390 2415 2.900122 ACTTGTCGCGGAAATGAATG 57.100 45.000 6.13 0.00 0.00 2.67
2391 2416 2.151202 ACTTGTCGCGGAAATGAATGT 58.849 42.857 6.13 0.00 0.00 2.71
2392 2417 3.331150 ACTTGTCGCGGAAATGAATGTA 58.669 40.909 6.13 0.00 0.00 2.29
2393 2418 3.938963 ACTTGTCGCGGAAATGAATGTAT 59.061 39.130 6.13 0.00 0.00 2.29
2394 2419 4.034048 ACTTGTCGCGGAAATGAATGTATC 59.966 41.667 6.13 0.00 0.00 2.24
2395 2420 3.792401 TGTCGCGGAAATGAATGTATCT 58.208 40.909 6.13 0.00 0.00 1.98
2396 2421 4.939271 TGTCGCGGAAATGAATGTATCTA 58.061 39.130 6.13 0.00 0.00 1.98
2397 2422 4.982295 TGTCGCGGAAATGAATGTATCTAG 59.018 41.667 6.13 0.00 0.00 2.43
2398 2423 5.220381 GTCGCGGAAATGAATGTATCTAGA 58.780 41.667 6.13 0.00 0.00 2.43
2399 2424 5.117287 GTCGCGGAAATGAATGTATCTAGAC 59.883 44.000 6.13 0.00 0.00 2.59
2400 2425 4.088638 CGCGGAAATGAATGTATCTAGACG 59.911 45.833 0.00 0.00 0.00 4.18
2401 2426 4.982916 GCGGAAATGAATGTATCTAGACGT 59.017 41.667 0.00 0.00 0.00 4.34
2402 2427 6.147581 GCGGAAATGAATGTATCTAGACGTA 58.852 40.000 0.00 0.00 0.00 3.57
2403 2428 6.807230 GCGGAAATGAATGTATCTAGACGTAT 59.193 38.462 0.00 0.00 0.00 3.06
2404 2429 7.328737 GCGGAAATGAATGTATCTAGACGTATT 59.671 37.037 0.00 0.00 0.00 1.89
2405 2430 9.193133 CGGAAATGAATGTATCTAGACGTATTT 57.807 33.333 0.00 0.00 0.00 1.40
2437 2462 9.739276 TTAGATACATCCATTTTTGAGACAAGT 57.261 29.630 0.00 0.00 0.00 3.16
2439 2464 9.739276 AGATACATCCATTTTTGAGACAAGTAA 57.261 29.630 0.00 0.00 0.00 2.24
2443 2468 8.306761 ACATCCATTTTTGAGACAAGTAATTCC 58.693 33.333 0.00 0.00 0.00 3.01
2444 2469 6.908825 TCCATTTTTGAGACAAGTAATTCCG 58.091 36.000 0.00 0.00 0.00 4.30
2445 2470 6.712998 TCCATTTTTGAGACAAGTAATTCCGA 59.287 34.615 0.00 0.00 0.00 4.55
2446 2471 7.229707 TCCATTTTTGAGACAAGTAATTCCGAA 59.770 33.333 0.00 0.00 0.00 4.30
2447 2472 7.326063 CCATTTTTGAGACAAGTAATTCCGAAC 59.674 37.037 0.00 0.00 0.00 3.95
2448 2473 5.585500 TTTGAGACAAGTAATTCCGAACG 57.415 39.130 0.00 0.00 0.00 3.95
2449 2474 3.581755 TGAGACAAGTAATTCCGAACGG 58.418 45.455 6.94 6.94 0.00 4.44
2450 2475 3.256383 TGAGACAAGTAATTCCGAACGGA 59.744 43.478 12.04 12.04 43.52 4.69
2451 2476 3.846360 AGACAAGTAATTCCGAACGGAG 58.154 45.455 15.34 5.60 46.06 4.63
2452 2477 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
2453 2478 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
2454 2479 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
2455 2480 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
2456 2481 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
2457 2482 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
2458 2483 2.083628 ATTCCGAACGGAGGGAGTAT 57.916 50.000 15.34 3.38 46.06 2.12
2459 2484 1.108776 TTCCGAACGGAGGGAGTATG 58.891 55.000 15.34 0.00 46.06 2.39
2460 2485 0.033796 TCCGAACGGAGGGAGTATGT 60.034 55.000 12.04 0.00 39.76 2.29
2461 2486 0.822164 CCGAACGGAGGGAGTATGTT 59.178 55.000 7.53 0.00 37.50 2.71
2462 2487 1.470979 CCGAACGGAGGGAGTATGTTG 60.471 57.143 7.53 0.00 37.50 3.33
2463 2488 1.475280 CGAACGGAGGGAGTATGTTGA 59.525 52.381 0.00 0.00 0.00 3.18
2464 2489 2.100916 CGAACGGAGGGAGTATGTTGAT 59.899 50.000 0.00 0.00 0.00 2.57
2465 2490 3.317149 CGAACGGAGGGAGTATGTTGATA 59.683 47.826 0.00 0.00 0.00 2.15
2466 2491 4.618965 GAACGGAGGGAGTATGTTGATAC 58.381 47.826 0.00 0.00 35.54 2.24
2467 2492 3.912248 ACGGAGGGAGTATGTTGATACT 58.088 45.455 0.00 0.00 46.34 2.12
2468 2493 4.287552 ACGGAGGGAGTATGTTGATACTT 58.712 43.478 0.00 0.00 44.14 2.24
2469 2494 4.099573 ACGGAGGGAGTATGTTGATACTTG 59.900 45.833 0.00 0.00 44.14 3.16
2470 2495 4.341235 CGGAGGGAGTATGTTGATACTTGA 59.659 45.833 0.00 0.00 44.14 3.02
2471 2496 5.508153 CGGAGGGAGTATGTTGATACTTGAG 60.508 48.000 0.00 0.00 44.14 3.02
2472 2497 5.364157 GGAGGGAGTATGTTGATACTTGAGT 59.636 44.000 0.00 0.00 44.14 3.41
2473 2498 6.550108 GGAGGGAGTATGTTGATACTTGAGTA 59.450 42.308 0.00 0.00 44.14 2.59
2474 2499 7.349412 AGGGAGTATGTTGATACTTGAGTAC 57.651 40.000 0.00 0.00 44.14 2.73
2475 2500 7.126733 AGGGAGTATGTTGATACTTGAGTACT 58.873 38.462 0.00 0.00 44.14 2.73
2476 2501 7.068839 AGGGAGTATGTTGATACTTGAGTACTG 59.931 40.741 0.00 0.00 44.14 2.74
2477 2502 7.068348 GGGAGTATGTTGATACTTGAGTACTGA 59.932 40.741 0.00 0.00 44.14 3.41
2478 2503 8.467598 GGAGTATGTTGATACTTGAGTACTGAA 58.532 37.037 0.00 0.00 44.14 3.02
2479 2504 9.291664 GAGTATGTTGATACTTGAGTACTGAAC 57.708 37.037 0.00 0.00 44.14 3.18
2480 2505 9.026121 AGTATGTTGATACTTGAGTACTGAACT 57.974 33.333 0.00 0.00 41.86 3.01
2481 2506 9.077674 GTATGTTGATACTTGAGTACTGAACTG 57.922 37.037 0.00 0.00 33.86 3.16
2482 2507 7.284919 TGTTGATACTTGAGTACTGAACTGA 57.715 36.000 0.00 0.00 39.07 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.467384 ATCAGCACTCTAGCGGCATT 59.533 50.000 1.45 0.00 40.15 3.56
1 2 0.249784 CATCAGCACTCTAGCGGCAT 60.250 55.000 1.45 0.00 40.15 4.40
2 3 1.142531 CATCAGCACTCTAGCGGCA 59.857 57.895 1.45 0.00 40.15 5.69
3 4 1.142748 ACATCAGCACTCTAGCGGC 59.857 57.895 0.00 0.00 40.15 6.53
4 5 0.174389 ACACATCAGCACTCTAGCGG 59.826 55.000 0.00 0.00 40.15 5.52
5 6 1.923204 GAACACATCAGCACTCTAGCG 59.077 52.381 0.00 0.00 40.15 4.26
23 24 0.762418 AACGGGTGTCACATCCTGAA 59.238 50.000 5.29 0.00 31.31 3.02
37 38 4.822036 TGAAGTGTAAACATTGAACGGG 57.178 40.909 0.00 0.00 0.00 5.28
56 57 3.801307 AAGCATATCCAGCATCCATGA 57.199 42.857 0.00 0.00 0.00 3.07
59 60 6.214208 ACTTCTATAAGCATATCCAGCATCCA 59.786 38.462 0.00 0.00 36.05 3.41
95 96 9.958180 TGACTAGATTTGAATGAACTATTTCCA 57.042 29.630 0.00 0.00 0.00 3.53
178 179 4.212004 TGCTAATTCGAAGCACATAGATGC 59.788 41.667 6.18 0.00 44.78 3.91
179 180 5.912360 TGCTAATTCGAAGCACATAGATG 57.088 39.130 6.18 0.00 44.78 2.90
203 204 0.738975 TGGCTCGTGATAGTCCGAAG 59.261 55.000 0.00 0.00 31.92 3.79
204 205 1.399714 ATGGCTCGTGATAGTCCGAA 58.600 50.000 0.00 0.00 31.92 4.30
205 206 1.878088 GTATGGCTCGTGATAGTCCGA 59.122 52.381 0.00 0.00 0.00 4.55
206 207 1.607148 TGTATGGCTCGTGATAGTCCG 59.393 52.381 0.00 0.00 0.00 4.79
207 208 3.579709 CATGTATGGCTCGTGATAGTCC 58.420 50.000 0.00 0.00 0.00 3.85
208 209 2.989840 GCATGTATGGCTCGTGATAGTC 59.010 50.000 0.00 0.00 0.00 2.59
209 210 2.365293 TGCATGTATGGCTCGTGATAGT 59.635 45.455 0.00 0.00 0.00 2.12
210 211 2.733552 GTGCATGTATGGCTCGTGATAG 59.266 50.000 0.00 0.00 0.00 2.08
211 212 2.365293 AGTGCATGTATGGCTCGTGATA 59.635 45.455 0.00 0.00 0.00 2.15
212 213 1.139654 AGTGCATGTATGGCTCGTGAT 59.860 47.619 0.00 0.00 0.00 3.06
216 217 2.314256 CCAGTGCATGTATGGCTCG 58.686 57.895 0.00 0.00 0.00 5.03
221 222 5.762825 AGAAAATAGCCAGTGCATGTATG 57.237 39.130 0.00 0.00 41.13 2.39
242 243 9.512588 AATGGGATATATGAAGTGCTAAGAAAG 57.487 33.333 0.00 0.00 0.00 2.62
321 325 6.488006 AGCTTCTCTGCAGAACATTAGAAAAA 59.512 34.615 18.85 0.00 34.71 1.94
333 338 3.517100 AGTAATTCCAGCTTCTCTGCAGA 59.483 43.478 17.19 17.19 41.50 4.26
434 447 1.559831 CGAGCGATGATACAGTGCAA 58.440 50.000 0.00 0.00 0.00 4.08
499 512 2.436115 GTACCCCAAGAGCGGCAC 60.436 66.667 1.45 0.00 0.00 5.01
570 583 3.118075 AGCATTAAGAGGGGAAGAAGAGC 60.118 47.826 0.00 0.00 0.00 4.09
585 598 3.943671 TGCTAAAGGGGCTAGCATTAA 57.056 42.857 18.24 0.00 45.24 1.40
669 682 4.647564 AGAGGAATTTCAGAGCAAAGGA 57.352 40.909 0.00 0.00 0.00 3.36
724 737 5.999205 TGTACAAAATGAGATGGCCAAAT 57.001 34.783 10.96 0.00 0.00 2.32
910 924 1.689352 GAATCGGTACCAACACGCCG 61.689 60.000 13.54 0.00 44.95 6.46
923 937 2.627515 ACATCTCACCCATGAATCGG 57.372 50.000 0.00 0.00 33.30 4.18
927 941 4.142160 CGAGTAGAACATCTCACCCATGAA 60.142 45.833 0.00 0.00 33.30 2.57
983 997 0.040157 CATGCCAAACACACGTCCTG 60.040 55.000 0.00 0.00 0.00 3.86
1167 1181 4.018688 ACTTCAAAGGTTACCCCTGATACC 60.019 45.833 0.00 0.00 45.47 2.73
1353 1367 3.186613 GTGAAATCCAACGTTCAGACTCC 59.813 47.826 0.00 0.00 34.52 3.85
1372 1386 4.681421 CTTGCCGAGCTCAAGTGA 57.319 55.556 15.40 0.00 36.93 3.41
1416 1430 1.357420 ACCTTGCCATCACAACCCATA 59.643 47.619 0.00 0.00 0.00 2.74
1453 1467 0.987081 ACAGAGAGCATGCTGGGGAT 60.987 55.000 28.27 4.58 36.47 3.85
1471 1485 7.874528 TCATGATCATCATAATCACCTACACAC 59.125 37.037 4.86 0.00 34.28 3.82
1565 1580 3.119743 TCGACGATCGACAACTACCAAAT 60.120 43.478 24.34 0.00 44.82 2.32
1615 1630 9.300681 TGAAATTTAGAATCTGTTGAGACCAAT 57.699 29.630 0.00 0.00 34.39 3.16
1701 1716 3.241426 CGAAATTTGCAACATCACGATGC 60.241 43.478 0.00 0.00 43.41 3.91
1716 1731 3.502191 ACATGCGCATTACCGAAATTT 57.498 38.095 22.81 0.00 0.00 1.82
1752 1767 6.678568 ACCCATTGAACACCAATTAATCAA 57.321 33.333 0.00 0.00 42.55 2.57
1978 2002 3.257127 AGAACAGTTCTAGTGCTCAGGTC 59.743 47.826 14.58 0.00 38.49 3.85
2115 2139 3.997021 GGTTGTCACACCTCAGTCATAAG 59.003 47.826 0.00 0.00 33.50 1.73
2119 2143 1.138859 CAGGTTGTCACACCTCAGTCA 59.861 52.381 4.32 0.00 44.63 3.41
2308 2333 3.306641 GCCCACAGTTTCCATTGCATAAA 60.307 43.478 0.00 0.00 0.00 1.40
2309 2334 2.233431 GCCCACAGTTTCCATTGCATAA 59.767 45.455 0.00 0.00 0.00 1.90
2310 2335 1.824230 GCCCACAGTTTCCATTGCATA 59.176 47.619 0.00 0.00 0.00 3.14
2332 2357 2.789409 ACATTGCTAGAACCAGGTCC 57.211 50.000 0.00 0.00 0.00 4.46
2343 2368 2.154567 ACGGAGGGAGTACATTGCTA 57.845 50.000 0.00 0.00 0.00 3.49
2345 2370 1.653151 GAACGGAGGGAGTACATTGC 58.347 55.000 0.00 0.00 0.00 3.56
2352 2377 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
2353 2378 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
2354 2379 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
2355 2380 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
2356 2381 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
2357 2382 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
2358 2383 2.598589 CGACAAGTAATTCCGAACGGA 58.401 47.619 12.04 12.04 43.52 4.69
2359 2384 1.060122 GCGACAAGTAATTCCGAACGG 59.940 52.381 6.94 6.94 0.00 4.44
2360 2385 1.266211 CGCGACAAGTAATTCCGAACG 60.266 52.381 0.00 0.00 0.00 3.95
2361 2386 1.060122 CCGCGACAAGTAATTCCGAAC 59.940 52.381 8.23 0.00 0.00 3.95
2362 2387 1.067706 TCCGCGACAAGTAATTCCGAA 60.068 47.619 8.23 0.00 0.00 4.30
2363 2388 0.527113 TCCGCGACAAGTAATTCCGA 59.473 50.000 8.23 0.00 0.00 4.55
2364 2389 1.352114 TTCCGCGACAAGTAATTCCG 58.648 50.000 8.23 0.00 0.00 4.30
2365 2390 3.372822 TCATTTCCGCGACAAGTAATTCC 59.627 43.478 8.23 0.00 0.00 3.01
2366 2391 4.593597 TCATTTCCGCGACAAGTAATTC 57.406 40.909 8.23 0.00 0.00 2.17
2367 2392 5.106317 ACATTCATTTCCGCGACAAGTAATT 60.106 36.000 8.23 0.00 0.00 1.40
2368 2393 4.394920 ACATTCATTTCCGCGACAAGTAAT 59.605 37.500 8.23 1.19 0.00 1.89
2369 2394 3.749088 ACATTCATTTCCGCGACAAGTAA 59.251 39.130 8.23 0.00 0.00 2.24
2370 2395 3.331150 ACATTCATTTCCGCGACAAGTA 58.669 40.909 8.23 0.00 0.00 2.24
2371 2396 2.151202 ACATTCATTTCCGCGACAAGT 58.849 42.857 8.23 0.00 0.00 3.16
2372 2397 2.900122 ACATTCATTTCCGCGACAAG 57.100 45.000 8.23 0.00 0.00 3.16
2373 2398 4.188462 AGATACATTCATTTCCGCGACAA 58.812 39.130 8.23 0.00 0.00 3.18
2374 2399 3.792401 AGATACATTCATTTCCGCGACA 58.208 40.909 8.23 0.00 0.00 4.35
2375 2400 5.117287 GTCTAGATACATTCATTTCCGCGAC 59.883 44.000 8.23 0.00 0.00 5.19
2376 2401 5.220381 GTCTAGATACATTCATTTCCGCGA 58.780 41.667 8.23 0.00 0.00 5.87
2377 2402 4.088638 CGTCTAGATACATTCATTTCCGCG 59.911 45.833 0.00 0.00 0.00 6.46
2378 2403 4.982916 ACGTCTAGATACATTCATTTCCGC 59.017 41.667 0.00 0.00 0.00 5.54
2379 2404 8.744008 AATACGTCTAGATACATTCATTTCCG 57.256 34.615 0.00 0.00 0.00 4.30
2411 2436 9.739276 ACTTGTCTCAAAAATGGATGTATCTAA 57.261 29.630 0.00 0.00 0.00 2.10
2413 2438 9.739276 TTACTTGTCTCAAAAATGGATGTATCT 57.261 29.630 0.00 0.00 0.00 1.98
2417 2442 8.306761 GGAATTACTTGTCTCAAAAATGGATGT 58.693 33.333 0.00 0.00 0.00 3.06
2418 2443 7.485913 CGGAATTACTTGTCTCAAAAATGGATG 59.514 37.037 0.00 0.00 0.00 3.51
2419 2444 7.393234 TCGGAATTACTTGTCTCAAAAATGGAT 59.607 33.333 0.00 0.00 0.00 3.41
2420 2445 6.712998 TCGGAATTACTTGTCTCAAAAATGGA 59.287 34.615 0.00 0.00 0.00 3.41
2421 2446 6.908825 TCGGAATTACTTGTCTCAAAAATGG 58.091 36.000 0.00 0.00 0.00 3.16
2422 2447 7.059488 CGTTCGGAATTACTTGTCTCAAAAATG 59.941 37.037 0.00 0.00 0.00 2.32
2423 2448 7.075741 CGTTCGGAATTACTTGTCTCAAAAAT 58.924 34.615 0.00 0.00 0.00 1.82
2424 2449 6.423862 CGTTCGGAATTACTTGTCTCAAAAA 58.576 36.000 0.00 0.00 0.00 1.94
2425 2450 5.049954 CCGTTCGGAATTACTTGTCTCAAAA 60.050 40.000 5.19 0.00 0.00 2.44
2426 2451 4.449743 CCGTTCGGAATTACTTGTCTCAAA 59.550 41.667 5.19 0.00 0.00 2.69
2427 2452 3.991773 CCGTTCGGAATTACTTGTCTCAA 59.008 43.478 5.19 0.00 0.00 3.02
2428 2453 3.256383 TCCGTTCGGAATTACTTGTCTCA 59.744 43.478 11.66 0.00 0.00 3.27
2429 2454 3.841643 TCCGTTCGGAATTACTTGTCTC 58.158 45.455 11.66 0.00 0.00 3.36
2430 2455 3.368116 CCTCCGTTCGGAATTACTTGTCT 60.368 47.826 14.79 0.00 33.41 3.41
2431 2456 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
2432 2457 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
2433 2458 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
2434 2459 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
2435 2460 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
2436 2461 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
2437 2462 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
2438 2463 1.856629 TACTCCCTCCGTTCGGAATT 58.143 50.000 14.79 0.00 33.41 2.17
2439 2464 1.687123 CATACTCCCTCCGTTCGGAAT 59.313 52.381 14.79 2.14 33.41 3.01
2440 2465 1.108776 CATACTCCCTCCGTTCGGAA 58.891 55.000 14.79 0.00 33.41 4.30
2441 2466 0.033796 ACATACTCCCTCCGTTCGGA 60.034 55.000 13.34 13.34 0.00 4.55
2442 2467 0.822164 AACATACTCCCTCCGTTCGG 59.178 55.000 4.74 4.74 0.00 4.30
2443 2468 1.475280 TCAACATACTCCCTCCGTTCG 59.525 52.381 0.00 0.00 0.00 3.95
2444 2469 3.821421 ATCAACATACTCCCTCCGTTC 57.179 47.619 0.00 0.00 0.00 3.95
2445 2470 4.287552 AGTATCAACATACTCCCTCCGTT 58.712 43.478 0.00 0.00 41.33 4.44
2446 2471 3.912248 AGTATCAACATACTCCCTCCGT 58.088 45.455 0.00 0.00 41.33 4.69
2447 2472 4.341235 TCAAGTATCAACATACTCCCTCCG 59.659 45.833 0.00 0.00 43.94 4.63
2448 2473 5.364157 ACTCAAGTATCAACATACTCCCTCC 59.636 44.000 0.00 0.00 43.94 4.30
2449 2474 6.472686 ACTCAAGTATCAACATACTCCCTC 57.527 41.667 0.00 0.00 43.94 4.30
2450 2475 7.068839 CAGTACTCAAGTATCAACATACTCCCT 59.931 40.741 0.00 0.00 43.94 4.20
2451 2476 7.068348 TCAGTACTCAAGTATCAACATACTCCC 59.932 40.741 0.00 0.00 43.94 4.30
2452 2477 7.997482 TCAGTACTCAAGTATCAACATACTCC 58.003 38.462 0.00 0.00 43.94 3.85
2453 2478 9.291664 GTTCAGTACTCAAGTATCAACATACTC 57.708 37.037 0.00 0.00 43.94 2.59
2454 2479 9.026121 AGTTCAGTACTCAAGTATCAACATACT 57.974 33.333 0.00 0.00 38.94 2.12
2455 2480 9.077674 CAGTTCAGTACTCAAGTATCAACATAC 57.922 37.037 0.00 0.00 33.85 2.39
2456 2481 9.020731 TCAGTTCAGTACTCAAGTATCAACATA 57.979 33.333 0.00 0.00 33.85 2.29
2457 2482 7.896811 TCAGTTCAGTACTCAAGTATCAACAT 58.103 34.615 0.00 0.00 33.85 2.71
2458 2483 7.284919 TCAGTTCAGTACTCAAGTATCAACA 57.715 36.000 0.00 0.00 33.85 3.33


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

AutoCloner maintained by Alex Coulton.