Multiple sequence alignment - TraesCS7B01G304900

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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 TraesCS7B01G304900 chr7B 100.000 3103 0 0 2359 5461 546020753 546017651 0 5731
1 TraesCS7B01G304900 chr7B 100.000 2059 0 0 1 2059 546023111 546021053 0 3803
2 TraesCS7B01G304900 chr7D 93.518 2530 120 26 2482 4984 515473385 515470873 0 3723
3 TraesCS7B01G304900 chr7D 95.236 2078 77 8 1 2059 515475579 515473505 0 3269
4 TraesCS7B01G304900 chr7D 96.040 404 13 1 5061 5461 515470884 515470481 0 654
5 TraesCS7B01G304900 chr7A 94.674 2272 99 11 2482 4743 589139031 589136772 0 3506
6 TraesCS7B01G304900 chr7A 94.436 2085 88 12 1 2059 589141233 589139151 0 3182
7 TraesCS7B01G304900 chr7A 93.508 724 35 7 4750 5461 589136162 589135439 0 1066


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 TraesCS7B01G304900 chr7B 546017651 546023111 5460 True 4767.000000 5731 100.000000 1 5461 2 chr7B.!!$R1 5460
1 TraesCS7B01G304900 chr7D 515470481 515475579 5098 True 2548.666667 3723 94.931333 1 5461 3 chr7D.!!$R1 5460
2 TraesCS7B01G304900 chr7A 589135439 589141233 5794 True 2584.666667 3506 94.206000 1 5461 3 chr7A.!!$R1 5460

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
977 999 0.250424 TGCATGATCACCTATGGCCG 60.250 55.000 0.00 0.00 0.00 6.13 F
1063 1085 0.896940 ATGTGGGTCTTTGCTGCAGG 60.897 55.000 17.12 0.00 0.00 4.85 F
1751 1776 1.538950 GGAACAGCTCTGCAGGAAAAG 59.461 52.381 15.13 4.69 0.00 2.27 F
2481 2506 0.629596 TGGATCGGAGGGAGTACAGT 59.370 55.000 0.00 0.00 0.00 3.55 F
3188 3214 0.771127 TGCACCCTAAAGGCTGAACT 59.229 50.000 0.00 0.00 40.58 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2462 2487 0.629596 ACTGTACTCCCTCCGATCCA 59.370 55.0 0.00 0.0 0.0 3.41 R
2463 2488 2.653234 TACTGTACTCCCTCCGATCC 57.347 55.0 0.00 0.0 0.0 3.36 R
3134 3160 1.099689 CACGGGTGAACAACAAAGGT 58.900 50.0 0.00 0.0 0.0 3.50 R
4265 4300 0.033699 GAGGGCCAGGCATCTTCTTT 60.034 55.0 15.19 0.0 0.0 2.52 R
5055 5714 0.322546 CCCACAAGGTAAGCAGTCCC 60.323 60.0 0.00 0.0 0.0 4.46 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
37 38 1.000896 CCTGGGGTTTCTTGGCGAT 60.001 57.895 0.00 0.00 0.00 4.58
56 57 1.757508 TTGGACTAGGGGTCAGGGGT 61.758 60.000 0.00 0.00 46.16 4.95
73 74 0.397564 GGTGGTTTCTTGGTCCCGTA 59.602 55.000 0.00 0.00 0.00 4.02
144 145 2.427812 GGGTTTTGTCGGGTTTCTTGAA 59.572 45.455 0.00 0.00 0.00 2.69
202 206 1.454276 GCGATTTCGTTGTGTTCTCGA 59.546 47.619 1.55 0.00 42.22 4.04
285 289 3.183574 CGCCGGAAATTTTGGACTTTTTC 59.816 43.478 5.05 0.00 0.00 2.29
305 310 8.887036 TTTTTCTTTTGGAATTTAGGAGCTTC 57.113 30.769 0.00 0.00 33.53 3.86
326 331 5.054390 TCAACAGAATCGGGTAATTTTGC 57.946 39.130 0.00 0.00 0.00 3.68
371 376 4.703897 TCGTATGCCTAGAAATTCCAAGG 58.296 43.478 7.43 7.43 0.00 3.61
390 395 4.635699 AGGAGGTCGTTATGGTTTTCTT 57.364 40.909 0.00 0.00 0.00 2.52
394 399 5.702209 GGAGGTCGTTATGGTTTTCTTGTTA 59.298 40.000 0.00 0.00 0.00 2.41
395 400 6.205270 GGAGGTCGTTATGGTTTTCTTGTTAA 59.795 38.462 0.00 0.00 0.00 2.01
709 728 5.134202 TCGAAGTGATTCAGTCTGCTTTA 57.866 39.130 0.00 0.00 0.00 1.85
727 746 9.719355 TCTGCTTTAAGAGTATCACAACAATAA 57.281 29.630 0.00 0.00 37.82 1.40
805 825 6.684613 GCATCATACCATGAAAATTCAGGCTT 60.685 38.462 2.43 0.00 43.50 4.35
872 894 6.074888 GCTTCATTGTTTGTGTAATGTGTGTC 60.075 38.462 0.00 0.00 36.09 3.67
907 929 1.014044 TGGCGCTCGAAGTGAACATC 61.014 55.000 7.64 0.00 0.00 3.06
973 995 8.959705 ATCTTGTATATGCATGATCACCTATG 57.040 34.615 10.16 0.00 30.53 2.23
977 999 0.250424 TGCATGATCACCTATGGCCG 60.250 55.000 0.00 0.00 0.00 6.13
1011 1033 1.992557 TGACCTAAAATGGGAGTGGCT 59.007 47.619 0.00 0.00 0.00 4.75
1063 1085 0.896940 ATGTGGGTCTTTGCTGCAGG 60.897 55.000 17.12 0.00 0.00 4.85
1112 1135 7.749666 TCCCTCCCTCTAAGAATTATCATTTG 58.250 38.462 0.00 0.00 0.00 2.32
1186 1210 4.927425 CCATTTCAACTCCTTTGCATCAAG 59.073 41.667 0.00 0.00 34.88 3.02
1292 1316 1.929836 GTTGGTGAGAGCGATGATGAC 59.070 52.381 0.00 0.00 0.00 3.06
1457 1481 3.055094 TGGGAGAACTGTCTATTTCTGGC 60.055 47.826 0.00 0.00 32.80 4.85
1518 1542 3.370953 CCCATCTCAACCTAGGTCCTTTG 60.371 52.174 16.64 10.08 0.00 2.77
1528 1552 8.647796 TCAACCTAGGTCCTTTGTATATACATG 58.352 37.037 16.64 11.73 35.89 3.21
1574 1598 4.240096 ACTCCGTACTTAATGGTTTGTCG 58.760 43.478 0.00 0.00 35.53 4.35
1751 1776 1.538950 GGAACAGCTCTGCAGGAAAAG 59.461 52.381 15.13 4.69 0.00 2.27
1885 1910 4.574013 ACGAGGATGATCTTTCAATGAAGC 59.426 41.667 0.00 0.00 34.96 3.86
1886 1911 4.318618 CGAGGATGATCTTTCAATGAAGCG 60.319 45.833 0.00 0.00 34.96 4.68
1941 1966 5.955959 ACTTCAAAAGGAAAAGGTTGGTACT 59.044 36.000 0.00 0.00 34.44 2.73
1958 1983 5.428253 TGGTACTGATTCCATAGTTTGCTC 58.572 41.667 0.00 0.00 0.00 4.26
1992 2017 2.030805 GGTTCTGTTCTGTTCATGTGCC 60.031 50.000 0.00 0.00 0.00 5.01
1996 2021 3.253921 TCTGTTCTGTTCATGTGCCAATG 59.746 43.478 0.00 0.00 0.00 2.82
2005 2030 2.697229 TCATGTGCCAATGTTCCAAACA 59.303 40.909 0.00 0.00 46.94 2.83
2416 2441 4.525996 ACTGTGGCATTAGCACATAATCA 58.474 39.130 0.00 0.00 44.61 2.57
2422 2447 6.205464 GTGGCATTAGCACATAATCATGTACT 59.795 38.462 0.00 0.00 43.73 2.73
2423 2448 6.427853 TGGCATTAGCACATAATCATGTACTC 59.572 38.462 0.00 0.00 43.73 2.59
2424 2449 6.128172 GGCATTAGCACATAATCATGTACTCC 60.128 42.308 0.00 0.00 43.73 3.85
2425 2450 6.128172 GCATTAGCACATAATCATGTACTCCC 60.128 42.308 0.00 0.00 43.73 4.30
2427 2452 5.220710 AGCACATAATCATGTACTCCCTC 57.779 43.478 0.00 0.00 43.73 4.30
2428 2453 4.904251 AGCACATAATCATGTACTCCCTCT 59.096 41.667 0.00 0.00 43.73 3.69
2429 2454 4.993584 GCACATAATCATGTACTCCCTCTG 59.006 45.833 0.00 0.00 43.73 3.35
2430 2455 5.221521 GCACATAATCATGTACTCCCTCTGA 60.222 44.000 0.00 0.00 43.73 3.27
2431 2456 6.519721 GCACATAATCATGTACTCCCTCTGAT 60.520 42.308 0.00 0.00 43.73 2.90
2432 2457 7.095910 CACATAATCATGTACTCCCTCTGATC 58.904 42.308 0.00 0.00 43.73 2.92
2433 2458 6.212388 ACATAATCATGTACTCCCTCTGATCC 59.788 42.308 0.00 0.00 43.74 3.36
2434 2459 3.688049 TCATGTACTCCCTCTGATCCA 57.312 47.619 0.00 0.00 0.00 3.41
2435 2460 3.994317 TCATGTACTCCCTCTGATCCAA 58.006 45.455 0.00 0.00 0.00 3.53
2436 2461 4.361783 TCATGTACTCCCTCTGATCCAAA 58.638 43.478 0.00 0.00 0.00 3.28
2437 2462 4.406972 TCATGTACTCCCTCTGATCCAAAG 59.593 45.833 0.00 0.00 0.00 2.77
2438 2463 4.061131 TGTACTCCCTCTGATCCAAAGA 57.939 45.455 0.00 0.00 0.00 2.52
2439 2464 4.425772 TGTACTCCCTCTGATCCAAAGAA 58.574 43.478 0.00 0.00 0.00 2.52
2440 2465 4.844085 TGTACTCCCTCTGATCCAAAGAAA 59.156 41.667 0.00 0.00 0.00 2.52
2441 2466 4.566426 ACTCCCTCTGATCCAAAGAAAG 57.434 45.455 0.00 0.00 0.00 2.62
2442 2467 3.913163 ACTCCCTCTGATCCAAAGAAAGT 59.087 43.478 0.00 0.00 0.00 2.66
2443 2468 4.260170 CTCCCTCTGATCCAAAGAAAGTG 58.740 47.826 0.00 0.00 0.00 3.16
2444 2469 3.652869 TCCCTCTGATCCAAAGAAAGTGT 59.347 43.478 0.00 0.00 0.00 3.55
2445 2470 4.006319 CCCTCTGATCCAAAGAAAGTGTC 58.994 47.826 0.00 0.00 0.00 3.67
2446 2471 4.505566 CCCTCTGATCCAAAGAAAGTGTCA 60.506 45.833 0.00 0.00 0.00 3.58
2447 2472 5.251764 CCTCTGATCCAAAGAAAGTGTCAT 58.748 41.667 0.00 0.00 0.00 3.06
2448 2473 5.123502 CCTCTGATCCAAAGAAAGTGTCATG 59.876 44.000 0.00 0.00 0.00 3.07
2449 2474 4.456911 TCTGATCCAAAGAAAGTGTCATGC 59.543 41.667 0.00 0.00 0.00 4.06
2450 2475 4.143543 TGATCCAAAGAAAGTGTCATGCA 58.856 39.130 0.00 0.00 0.00 3.96
2459 2484 3.495124 GTGTCATGCACGGCAATTT 57.505 47.368 0.00 0.00 43.62 1.82
2460 2485 1.782044 GTGTCATGCACGGCAATTTT 58.218 45.000 0.00 0.00 43.62 1.82
2461 2486 2.134346 GTGTCATGCACGGCAATTTTT 58.866 42.857 0.00 0.00 43.62 1.94
2478 2503 3.622166 TTTTTGGATCGGAGGGAGTAC 57.378 47.619 0.00 0.00 0.00 2.73
2479 2504 2.241281 TTTGGATCGGAGGGAGTACA 57.759 50.000 0.00 0.00 0.00 2.90
2480 2505 1.776662 TTGGATCGGAGGGAGTACAG 58.223 55.000 0.00 0.00 0.00 2.74
2481 2506 0.629596 TGGATCGGAGGGAGTACAGT 59.370 55.000 0.00 0.00 0.00 3.55
2482 2507 1.848388 TGGATCGGAGGGAGTACAGTA 59.152 52.381 0.00 0.00 0.00 2.74
2483 2508 2.445905 TGGATCGGAGGGAGTACAGTAT 59.554 50.000 0.00 0.00 0.00 2.12
2484 2509 3.654321 TGGATCGGAGGGAGTACAGTATA 59.346 47.826 0.00 0.00 0.00 1.47
2485 2510 4.105217 TGGATCGGAGGGAGTACAGTATAA 59.895 45.833 0.00 0.00 0.00 0.98
2486 2511 5.075493 GGATCGGAGGGAGTACAGTATAAA 58.925 45.833 0.00 0.00 0.00 1.40
2487 2512 5.715753 GGATCGGAGGGAGTACAGTATAAAT 59.284 44.000 0.00 0.00 0.00 1.40
2488 2513 6.350277 GGATCGGAGGGAGTACAGTATAAATG 60.350 46.154 0.00 0.00 0.00 2.32
2489 2514 5.698104 TCGGAGGGAGTACAGTATAAATGA 58.302 41.667 0.00 0.00 0.00 2.57
2534 2559 4.607293 AGCTGATGACAGTCAGTGTAAA 57.393 40.909 9.64 0.00 45.80 2.01
2536 2561 4.039730 AGCTGATGACAGTCAGTGTAAAGT 59.960 41.667 9.64 0.00 45.80 2.66
2539 2564 5.532557 TGATGACAGTCAGTGTAAAGTCTG 58.467 41.667 9.64 0.00 40.56 3.51
2540 2565 3.717707 TGACAGTCAGTGTAAAGTCTGC 58.282 45.455 0.00 0.00 40.56 4.26
2547 2572 1.961394 AGTGTAAAGTCTGCGGTCTGA 59.039 47.619 0.00 0.00 0.00 3.27
2548 2573 2.364324 AGTGTAAAGTCTGCGGTCTGAA 59.636 45.455 0.00 0.00 0.00 3.02
2549 2574 3.006967 AGTGTAAAGTCTGCGGTCTGAAT 59.993 43.478 0.00 0.00 0.00 2.57
2556 2581 4.375272 AGTCTGCGGTCTGAATGATTATG 58.625 43.478 0.00 0.00 0.00 1.90
2563 2588 7.639039 TGCGGTCTGAATGATTATGTAAAATC 58.361 34.615 0.00 0.00 36.57 2.17
2564 2589 7.498900 TGCGGTCTGAATGATTATGTAAAATCT 59.501 33.333 0.00 0.00 36.90 2.40
2579 2604 8.868522 ATGTAAAATCTCCTGACTTGAAATGA 57.131 30.769 0.00 0.00 0.00 2.57
2582 2607 7.771927 AAAATCTCCTGACTTGAAATGACAT 57.228 32.000 0.00 0.00 0.00 3.06
2644 2669 4.965814 AGATTCTTGACTTTGTGAGCTCA 58.034 39.130 13.74 13.74 0.00 4.26
2701 2726 3.644265 TCTTGGCCACTGTTACTGAAGTA 59.356 43.478 3.88 0.00 0.00 2.24
2725 2750 3.445008 TCCTAGCCTCAATGACTCTGTT 58.555 45.455 0.00 0.00 0.00 3.16
2815 2840 8.834749 TTAAAGAAGAGAAAGTTAAGAGGCTC 57.165 34.615 6.34 6.34 0.00 4.70
2836 2861 3.254657 TCGGAAAGGTAAATTTGCAGTGG 59.745 43.478 8.59 0.00 31.47 4.00
2843 2868 1.260544 AAATTTGCAGTGGAGCCTCC 58.739 50.000 2.98 2.98 36.96 4.30
2844 2869 0.962356 AATTTGCAGTGGAGCCTCCG 60.962 55.000 6.21 0.00 40.17 4.63
2869 2894 6.428465 GGTTATTGCTTATCCTCTCTTTAGGC 59.572 42.308 0.00 0.00 36.51 3.93
2882 2907 6.239176 CCTCTCTTTAGGCGTCTTTGATATCT 60.239 42.308 0.00 0.00 0.00 1.98
2887 2912 7.822334 TCTTTAGGCGTCTTTGATATCTTTTCA 59.178 33.333 0.00 0.00 0.00 2.69
3080 3105 5.338365 GCTTTGGCTCTTGATGTAATTGAG 58.662 41.667 0.00 0.00 35.22 3.02
3136 3162 9.662947 AGTTTGGTGTATTGATAAAGTAGTACC 57.337 33.333 0.00 0.00 0.00 3.34
3137 3163 9.662947 GTTTGGTGTATTGATAAAGTAGTACCT 57.337 33.333 0.00 0.00 0.00 3.08
3150 3176 4.711399 AGTAGTACCTTTGTTGTTCACCC 58.289 43.478 0.00 0.00 0.00 4.61
3155 3181 1.746220 CCTTTGTTGTTCACCCGTGAA 59.254 47.619 6.17 6.17 46.27 3.18
3188 3214 0.771127 TGCACCCTAAAGGCTGAACT 59.229 50.000 0.00 0.00 40.58 3.01
3471 3497 2.481104 GCTAGCATGCGAAGAAGAGAGT 60.481 50.000 22.53 0.56 0.00 3.24
3502 3528 3.006967 AGACTATAGCCGGGTATGCAAAG 59.993 47.826 31.54 23.37 0.00 2.77
3508 3534 1.000394 GCCGGGTATGCAAAGTTTGTT 60.000 47.619 16.70 7.76 0.00 2.83
3521 3547 7.331791 TGCAAAGTTTGTTATGTTACCCTTTT 58.668 30.769 16.70 0.00 0.00 2.27
3522 3548 7.278868 TGCAAAGTTTGTTATGTTACCCTTTTG 59.721 33.333 16.70 0.00 0.00 2.44
3563 3595 5.220491 GCTCGAAGATATCAAGTGTGTTTCC 60.220 44.000 5.32 0.00 33.89 3.13
3611 3643 4.872124 GCATTGTTCTTCCAATTCCATTCC 59.128 41.667 0.00 0.00 32.81 3.01
3888 3920 1.736032 CGTGAGTGCTAGTGCTAACCC 60.736 57.143 0.00 0.00 40.48 4.11
3977 4009 3.360867 TGGGAACAAGAACACAACACAT 58.639 40.909 0.00 0.00 37.44 3.21
4006 4038 3.173240 GACGGTGTCGCGCTTCTC 61.173 66.667 5.56 0.00 40.63 2.87
4072 4104 2.569404 AGAGAAGCGAAGAATGAGGGTT 59.431 45.455 0.00 0.00 0.00 4.11
4077 4109 5.364157 AGAAGCGAAGAATGAGGGTTAGTAT 59.636 40.000 0.00 0.00 0.00 2.12
4078 4110 4.950050 AGCGAAGAATGAGGGTTAGTATG 58.050 43.478 0.00 0.00 0.00 2.39
4088 4120 4.010349 GAGGGTTAGTATGCTTTTGTGCT 58.990 43.478 0.00 0.00 0.00 4.40
4090 4122 3.501950 GGTTAGTATGCTTTTGTGCTGC 58.498 45.455 0.00 0.00 0.00 5.25
4098 4130 1.862827 GCTTTTGTGCTGCTCCTTTTG 59.137 47.619 0.00 0.00 0.00 2.44
4099 4131 2.739609 GCTTTTGTGCTGCTCCTTTTGT 60.740 45.455 0.00 0.00 0.00 2.83
4144 4177 1.126488 ATCATCTCTGCGTCCCATGT 58.874 50.000 0.00 0.00 0.00 3.21
4235 4270 1.446272 GGAGAAGCTGTTCGGGTCG 60.446 63.158 0.00 0.00 37.79 4.79
4272 4307 1.230635 GCCGCAGTCTGCAAAGAAGA 61.231 55.000 24.13 0.00 45.36 2.87
4474 4509 1.330655 ACCTGACACCTGGCCTATCG 61.331 60.000 3.32 0.00 35.04 2.92
4520 4555 5.077564 TGTGCAGTAGTCGGGAGATTATAT 58.922 41.667 0.00 0.00 43.27 0.86
4521 4556 6.243148 TGTGCAGTAGTCGGGAGATTATATA 58.757 40.000 0.00 0.00 43.27 0.86
4567 4606 3.368236 GTGGAGCGAGAGTTTAATGTGAC 59.632 47.826 0.00 0.00 0.00 3.67
4726 4767 2.937799 GTGACCAACTTTTACACGACCA 59.062 45.455 0.00 0.00 0.00 4.02
4743 4784 2.017049 ACCAACTTGTCAGTCTTGCAC 58.983 47.619 0.00 0.00 30.45 4.57
4778 5422 5.478407 TCGAATCATCTAACACTTCAGCAA 58.522 37.500 0.00 0.00 0.00 3.91
4857 5502 5.009110 TCAGGATCTGAAGAAGCTATGTACG 59.991 44.000 0.00 0.00 37.57 3.67
4861 5506 4.982999 TCTGAAGAAGCTATGTACGTCAC 58.017 43.478 0.00 0.00 0.00 3.67
4866 5511 3.128938 AGAAGCTATGTACGTCACTCCAC 59.871 47.826 0.00 0.00 0.00 4.02
4892 5537 1.648504 GGTTTCAGTAATCCGTCGGG 58.351 55.000 12.29 0.00 0.00 5.14
4910 5555 4.603946 GGCTGGCGGGGATCGTAC 62.604 72.222 0.00 0.00 41.72 3.67
4986 5640 1.876156 CCTTCTTGCTCACCTTGTCAC 59.124 52.381 0.00 0.00 0.00 3.67
4988 5642 2.936919 TCTTGCTCACCTTGTCACAT 57.063 45.000 0.00 0.00 0.00 3.21
4995 5649 1.693606 TCACCTTGTCACATCAGAGCA 59.306 47.619 0.00 0.00 0.00 4.26
4998 5652 4.020307 TCACCTTGTCACATCAGAGCATTA 60.020 41.667 0.00 0.00 0.00 1.90
5014 5668 3.131396 GCATTACGGAATCAGTACAGGG 58.869 50.000 0.00 0.00 0.00 4.45
5016 5670 1.855295 TACGGAATCAGTACAGGGCA 58.145 50.000 0.00 0.00 0.00 5.36
5017 5671 1.204146 ACGGAATCAGTACAGGGCAT 58.796 50.000 0.00 0.00 0.00 4.40
5020 5674 2.565841 GGAATCAGTACAGGGCATCAC 58.434 52.381 0.00 0.00 0.00 3.06
5023 5677 1.937191 TCAGTACAGGGCATCACTGA 58.063 50.000 8.57 8.57 43.77 3.41
5027 5681 2.433604 AGTACAGGGCATCACTGATGAG 59.566 50.000 21.20 10.33 42.09 2.90
5042 5701 0.607489 ATGAGGCTAATCATGGCGGC 60.607 55.000 0.00 0.00 38.49 6.53
5044 5703 2.280797 GGCTAATCATGGCGGCGA 60.281 61.111 12.98 0.00 33.05 5.54
5055 5714 4.933064 GCGGCGACTCGAGGGATG 62.933 72.222 18.41 4.27 0.00 3.51
5060 5719 1.454111 CGACTCGAGGGATGGGACT 60.454 63.158 18.41 0.00 0.00 3.85
5062 5721 2.022240 GACTCGAGGGATGGGACTGC 62.022 65.000 18.41 0.00 0.00 4.40
5094 5753 3.365265 CTTGGTTGGAGCCGGTGC 61.365 66.667 1.90 0.00 37.95 5.01
5178 5840 2.664081 GGGCCTGTAGCAGCTGAGT 61.664 63.158 20.43 6.02 46.50 3.41
5429 6091 4.787280 CTCCCCCTGCTCCGACCT 62.787 72.222 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 1.497309 ATCGCCAAGAAACCCCAGGA 61.497 55.000 0.00 0.00 0.00 3.86
37 38 1.082206 CCCCTGACCCCTAGTCCAA 59.918 63.158 0.00 0.00 45.68 3.53
56 57 0.688487 CCTACGGGACCAAGAAACCA 59.312 55.000 0.00 0.00 33.58 3.67
73 74 5.600669 AAATCCCTAGAAAGAAACCACCT 57.399 39.130 0.00 0.00 0.00 4.00
202 206 3.767630 AAACAGGCAACCGGACGCT 62.768 57.895 9.46 0.00 37.17 5.07
285 289 6.748132 TGTTGAAGCTCCTAAATTCCAAAAG 58.252 36.000 0.00 0.00 0.00 2.27
305 310 4.173256 GGCAAAATTACCCGATTCTGTTG 58.827 43.478 0.00 0.00 0.00 3.33
339 344 3.759086 TCTAGGCATACGAGCTATTCCAG 59.241 47.826 0.00 0.00 34.17 3.86
371 376 5.684550 AACAAGAAAACCATAACGACCTC 57.315 39.130 0.00 0.00 0.00 3.85
390 395 8.006298 ACAATTCTCCACAAAGAACATTAACA 57.994 30.769 0.00 0.00 38.06 2.41
395 400 9.696917 GATTTAACAATTCTCCACAAAGAACAT 57.303 29.630 0.00 0.00 38.06 2.71
474 479 4.882671 ATGGACGTTCAGATAATGTTGC 57.117 40.909 1.50 0.00 0.00 4.17
622 641 3.580895 TGGGCAAGACTACACAATACAGA 59.419 43.478 0.00 0.00 0.00 3.41
709 728 9.825972 CACGAAATTTATTGTTGTGATACTCTT 57.174 29.630 0.00 0.00 0.00 2.85
872 894 4.351192 AGCGCCATAAAAATCTAAAAGCG 58.649 39.130 2.29 0.00 43.58 4.68
907 929 7.052873 ACTCTGAAACTATCATGATTCAAGGG 58.947 38.462 14.65 8.55 37.44 3.95
973 995 1.202114 TCAAAATCTGCAATGACGGCC 59.798 47.619 0.00 0.00 0.00 6.13
977 999 7.063780 CCATTTTAGGTCAAAATCTGCAATGAC 59.936 37.037 7.38 7.38 43.51 3.06
1011 1033 2.631160 ACAAAGGATCGTTGTGACCA 57.369 45.000 11.45 0.00 37.80 4.02
1063 1085 1.604604 TGGCAAAGCACCTGTAGTTC 58.395 50.000 0.00 0.00 0.00 3.01
1112 1135 4.142160 ACCTCTCAAAAAGTGCAAGGAAAC 60.142 41.667 2.37 0.00 34.42 2.78
1119 1143 6.707440 TCAATTTACCTCTCAAAAAGTGCA 57.293 33.333 0.00 0.00 30.54 4.57
1161 1185 5.076182 TGATGCAAAGGAGTTGAAATGGTA 58.924 37.500 0.00 0.00 39.87 3.25
1292 1316 2.333926 TGAAGTAACATCTTGTCGCGG 58.666 47.619 6.13 0.00 0.00 6.46
1491 1515 2.840651 ACCTAGGTTGAGATGGGAGTTG 59.159 50.000 9.21 0.00 0.00 3.16
1566 1590 9.537848 CAGAAGTAAAATAATGTACGACAAACC 57.462 33.333 0.00 0.00 0.00 3.27
1651 1676 3.913799 TGTAAATCAGGAGAAAGGGGACA 59.086 43.478 0.00 0.00 0.00 4.02
1751 1776 4.882842 AACTCTTTCACCCTCTTCTCTC 57.117 45.455 0.00 0.00 0.00 3.20
1941 1966 3.691118 GTGCAGAGCAAACTATGGAATCA 59.309 43.478 0.00 0.00 41.47 2.57
1958 1983 2.292267 ACAGAACCAGTTCTTGTGCAG 58.708 47.619 10.32 1.61 46.95 4.41
1985 2010 3.109044 TGTTTGGAACATTGGCACATG 57.891 42.857 7.73 7.73 39.30 3.21
1996 2021 2.030805 AGCGAGCTTTGATGTTTGGAAC 60.031 45.455 0.00 0.00 0.00 3.62
2380 2405 5.181690 TGCCACAGTTTAGATTTCAACAC 57.818 39.130 0.00 0.00 0.00 3.32
2388 2413 4.588899 TGTGCTAATGCCACAGTTTAGAT 58.411 39.130 0.00 0.00 38.71 1.98
2416 2441 4.624913 TCTTTGGATCAGAGGGAGTACAT 58.375 43.478 0.00 0.00 0.00 2.29
2422 2447 3.652869 ACACTTTCTTTGGATCAGAGGGA 59.347 43.478 0.00 0.00 0.00 4.20
2423 2448 4.006319 GACACTTTCTTTGGATCAGAGGG 58.994 47.826 0.00 0.00 0.00 4.30
2424 2449 4.645535 TGACACTTTCTTTGGATCAGAGG 58.354 43.478 0.00 0.00 0.00 3.69
2425 2450 5.391736 GCATGACACTTTCTTTGGATCAGAG 60.392 44.000 0.00 0.00 0.00 3.35
2427 2452 4.216902 TGCATGACACTTTCTTTGGATCAG 59.783 41.667 0.00 0.00 0.00 2.90
2428 2453 4.022935 GTGCATGACACTTTCTTTGGATCA 60.023 41.667 11.51 0.00 46.41 2.92
2429 2454 4.479619 GTGCATGACACTTTCTTTGGATC 58.520 43.478 11.51 0.00 46.41 3.36
2430 2455 4.510038 GTGCATGACACTTTCTTTGGAT 57.490 40.909 11.51 0.00 46.41 3.41
2431 2456 3.988379 GTGCATGACACTTTCTTTGGA 57.012 42.857 11.51 0.00 46.41 3.53
2441 2466 1.782044 AAAATTGCCGTGCATGACAC 58.218 45.000 7.72 3.38 46.45 3.67
2442 2467 2.522836 AAAAATTGCCGTGCATGACA 57.477 40.000 7.72 0.00 38.76 3.58
2458 2483 2.907696 TGTACTCCCTCCGATCCAAAAA 59.092 45.455 0.00 0.00 0.00 1.94
2459 2484 2.500098 CTGTACTCCCTCCGATCCAAAA 59.500 50.000 0.00 0.00 0.00 2.44
2460 2485 2.108168 CTGTACTCCCTCCGATCCAAA 58.892 52.381 0.00 0.00 0.00 3.28
2461 2486 1.006758 ACTGTACTCCCTCCGATCCAA 59.993 52.381 0.00 0.00 0.00 3.53
2462 2487 0.629596 ACTGTACTCCCTCCGATCCA 59.370 55.000 0.00 0.00 0.00 3.41
2463 2488 2.653234 TACTGTACTCCCTCCGATCC 57.347 55.000 0.00 0.00 0.00 3.36
2464 2489 6.433404 TCATTTATACTGTACTCCCTCCGATC 59.567 42.308 0.00 0.00 0.00 3.69
2465 2490 6.208994 GTCATTTATACTGTACTCCCTCCGAT 59.791 42.308 0.00 0.00 0.00 4.18
2466 2491 5.533903 GTCATTTATACTGTACTCCCTCCGA 59.466 44.000 0.00 0.00 0.00 4.55
2467 2492 5.278858 GGTCATTTATACTGTACTCCCTCCG 60.279 48.000 0.00 0.00 0.00 4.63
2468 2493 5.601313 TGGTCATTTATACTGTACTCCCTCC 59.399 44.000 0.00 0.00 0.00 4.30
2469 2494 6.726490 TGGTCATTTATACTGTACTCCCTC 57.274 41.667 0.00 0.00 0.00 4.30
2470 2495 7.504926 TTTGGTCATTTATACTGTACTCCCT 57.495 36.000 0.00 0.00 0.00 4.20
2471 2496 6.260271 GCTTTGGTCATTTATACTGTACTCCC 59.740 42.308 0.00 0.00 0.00 4.30
2472 2497 6.821665 TGCTTTGGTCATTTATACTGTACTCC 59.178 38.462 0.00 0.00 0.00 3.85
2473 2498 7.843490 TGCTTTGGTCATTTATACTGTACTC 57.157 36.000 0.00 0.00 0.00 2.59
2474 2499 8.807948 ATTGCTTTGGTCATTTATACTGTACT 57.192 30.769 0.00 0.00 0.00 2.73
2476 2501 9.337396 CCTATTGCTTTGGTCATTTATACTGTA 57.663 33.333 0.00 0.00 0.00 2.74
2477 2502 7.201821 GCCTATTGCTTTGGTCATTTATACTGT 60.202 37.037 0.00 0.00 36.87 3.55
2478 2503 7.141363 GCCTATTGCTTTGGTCATTTATACTG 58.859 38.462 0.00 0.00 36.87 2.74
2479 2504 7.277174 GCCTATTGCTTTGGTCATTTATACT 57.723 36.000 0.00 0.00 36.87 2.12
2534 2559 4.141846 ACATAATCATTCAGACCGCAGACT 60.142 41.667 0.00 0.00 0.00 3.24
2536 2561 4.406648 ACATAATCATTCAGACCGCAGA 57.593 40.909 0.00 0.00 0.00 4.26
2539 2564 7.865707 AGATTTTACATAATCATTCAGACCGC 58.134 34.615 0.00 0.00 37.06 5.68
2540 2565 8.499162 GGAGATTTTACATAATCATTCAGACCG 58.501 37.037 0.00 0.00 37.06 4.79
2549 2574 9.958180 TTCAAGTCAGGAGATTTTACATAATCA 57.042 29.630 0.00 0.00 37.06 2.57
2556 2581 8.099364 TGTCATTTCAAGTCAGGAGATTTTAC 57.901 34.615 0.00 0.00 0.00 2.01
2563 2588 6.814506 AAGAATGTCATTTCAAGTCAGGAG 57.185 37.500 0.00 0.00 0.00 3.69
2564 2589 8.868522 ATTAAGAATGTCATTTCAAGTCAGGA 57.131 30.769 0.00 0.00 0.00 3.86
2592 2617 7.629222 GCAACCTATCACTCTGCAATACAAAAT 60.629 37.037 0.00 0.00 33.19 1.82
2644 2669 2.802816 GACAGAACAAAGATCGTGCACT 59.197 45.455 16.19 0.00 0.00 4.40
2701 2726 3.387374 CAGAGTCATTGAGGCTAGGATGT 59.613 47.826 0.00 0.00 27.31 3.06
2725 2750 2.840199 ACTCTTGGAGTGAGCACCA 58.160 52.632 0.00 0.00 41.76 4.17
2815 2840 3.254657 TCCACTGCAAATTTACCTTTCCG 59.745 43.478 0.00 0.00 0.00 4.30
2843 2868 6.647067 CCTAAAGAGAGGATAAGCAATAACCG 59.353 42.308 0.00 0.00 39.15 4.44
2844 2869 6.428465 GCCTAAAGAGAGGATAAGCAATAACC 59.572 42.308 0.00 0.00 39.15 2.85
2907 2932 8.011844 TGAATCTAAGAGAGCATAGCACTTAA 57.988 34.615 0.00 0.00 28.14 1.85
2942 2967 3.137544 TCCAAAGTTCAGTTAGCTGGGAA 59.862 43.478 6.75 0.00 42.78 3.97
2957 2982 4.220602 GTGGCATCCATTAAGTTCCAAAGT 59.779 41.667 0.00 0.00 35.28 2.66
3080 3105 5.703130 AGAGAAGAAACACATCTTAACCTGC 59.297 40.000 0.00 0.00 39.70 4.85
3134 3160 1.099689 CACGGGTGAACAACAAAGGT 58.900 50.000 0.00 0.00 0.00 3.50
3172 3198 4.386424 AACTTCAAGTTCAGCCTTTAGGGT 60.386 41.667 0.00 0.00 37.44 4.34
3173 3199 3.756117 ACTTCAAGTTCAGCCTTTAGGG 58.244 45.455 0.00 0.00 35.18 3.53
3174 3200 4.821805 TCAACTTCAAGTTCAGCCTTTAGG 59.178 41.667 0.00 0.00 36.03 2.69
3188 3214 3.822735 CTGATCCAGCCTTTCAACTTCAA 59.177 43.478 0.00 0.00 0.00 2.69
3502 3528 6.277605 ACAGCAAAAGGGTAACATAACAAAC 58.722 36.000 0.00 0.00 39.74 2.93
3508 3534 4.042311 TGGAGACAGCAAAAGGGTAACATA 59.958 41.667 0.00 0.00 34.39 2.29
3611 3643 3.799917 GCAAGTGGTTTCAACTTCATGGG 60.800 47.826 0.00 0.00 0.00 4.00
3881 3913 3.667360 TGAAAAGTTAGGTCGGGTTAGC 58.333 45.455 0.00 0.00 0.00 3.09
3888 3920 6.851222 AGATATGCATGAAAAGTTAGGTCG 57.149 37.500 10.16 0.00 0.00 4.79
4006 4038 0.869880 TGTATTCGTCCAGCATCGCG 60.870 55.000 0.00 0.00 0.00 5.87
4072 4104 3.009723 GGAGCAGCACAAAAGCATACTA 58.990 45.455 0.00 0.00 36.85 1.82
4077 4109 1.113788 AAAGGAGCAGCACAAAAGCA 58.886 45.000 0.00 0.00 36.85 3.91
4078 4110 1.862827 CAAAAGGAGCAGCACAAAAGC 59.137 47.619 0.00 0.00 0.00 3.51
4088 4120 0.843309 TGGACAGGACAAAAGGAGCA 59.157 50.000 0.00 0.00 0.00 4.26
4090 4122 1.873591 CGTTGGACAGGACAAAAGGAG 59.126 52.381 0.00 0.00 0.00 3.69
4098 4130 0.249398 ACATAGCCGTTGGACAGGAC 59.751 55.000 0.00 0.00 0.00 3.85
4099 4131 0.535335 GACATAGCCGTTGGACAGGA 59.465 55.000 0.00 0.00 0.00 3.86
4144 4177 4.216257 GGCAGATAGAACAGTTGAGCAAAA 59.784 41.667 0.00 0.00 0.00 2.44
4256 4291 1.135460 GGCATCTTCTTTGCAGACTGC 60.135 52.381 20.86 20.86 45.29 4.40
4265 4300 0.033699 GAGGGCCAGGCATCTTCTTT 60.034 55.000 15.19 0.00 0.00 2.52
4474 4509 1.673808 ATACTTCTCCGACCGGCACC 61.674 60.000 0.00 0.00 34.68 5.01
4567 4606 1.714794 GATTCCCGCCATGACTATCG 58.285 55.000 0.00 0.00 0.00 2.92
4726 4767 6.509418 TTTTAAGTGCAAGACTGACAAGTT 57.491 33.333 0.00 0.00 36.52 2.66
4743 4784 8.820933 TGTTAGATGATTCGAGCTGATTTTAAG 58.179 33.333 0.00 0.00 0.00 1.85
4778 5422 7.391148 TTTCTCTTACTTTTCAGTTGCTTGT 57.609 32.000 0.00 0.00 34.06 3.16
4822 5466 4.824479 TCAGATCCTGATTGCTGTGTTA 57.176 40.909 0.00 0.00 35.39 2.41
4857 5502 0.674534 AACCGAGACAGTGGAGTGAC 59.325 55.000 0.00 0.00 0.00 3.67
4861 5506 1.341531 ACTGAAACCGAGACAGTGGAG 59.658 52.381 0.00 0.00 42.18 3.86
4866 5511 3.179830 CGGATTACTGAAACCGAGACAG 58.820 50.000 0.00 0.00 46.94 3.51
4923 5574 1.334243 GCTGCAGAAGGATCATCAAGC 59.666 52.381 20.43 0.00 0.00 4.01
4986 5640 4.375272 ACTGATTCCGTAATGCTCTGATG 58.625 43.478 0.00 0.00 0.00 3.07
4988 5642 4.401202 TGTACTGATTCCGTAATGCTCTGA 59.599 41.667 0.00 0.00 0.00 3.27
4995 5649 2.769663 TGCCCTGTACTGATTCCGTAAT 59.230 45.455 0.60 0.00 0.00 1.89
4998 5652 1.139058 GATGCCCTGTACTGATTCCGT 59.861 52.381 0.60 0.00 0.00 4.69
5014 5668 3.736720 TGATTAGCCTCATCAGTGATGC 58.263 45.455 25.53 15.66 43.68 3.91
5016 5670 4.806625 GCCATGATTAGCCTCATCAGTGAT 60.807 45.833 0.00 0.00 34.12 3.06
5017 5671 3.495629 GCCATGATTAGCCTCATCAGTGA 60.496 47.826 0.00 0.00 34.12 3.41
5020 5674 2.074576 CGCCATGATTAGCCTCATCAG 58.925 52.381 0.00 0.00 34.12 2.90
5023 5677 0.607489 GCCGCCATGATTAGCCTCAT 60.607 55.000 0.00 0.00 36.29 2.90
5027 5681 2.280797 TCGCCGCCATGATTAGCC 60.281 61.111 0.00 0.00 0.00 3.93
5029 5683 1.278172 CGAGTCGCCGCCATGATTAG 61.278 60.000 0.00 0.00 0.00 1.73
5030 5684 1.299850 CGAGTCGCCGCCATGATTA 60.300 57.895 0.00 0.00 0.00 1.75
5042 5701 1.454111 AGTCCCATCCCTCGAGTCG 60.454 63.158 12.31 6.09 0.00 4.18
5044 5703 2.060980 GCAGTCCCATCCCTCGAGT 61.061 63.158 12.31 0.00 0.00 4.18
5053 5712 1.004745 CCACAAGGTAAGCAGTCCCAT 59.995 52.381 0.00 0.00 0.00 4.00
5055 5714 0.322546 CCCACAAGGTAAGCAGTCCC 60.323 60.000 0.00 0.00 0.00 4.46
5060 5719 2.290896 CCAAGATCCCACAAGGTAAGCA 60.291 50.000 0.00 0.00 36.75 3.91
5062 5721 3.721087 ACCAAGATCCCACAAGGTAAG 57.279 47.619 0.00 0.00 36.75 2.34


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

AutoCloner maintained by Alex Coulton.