Multiple sequence alignment - TraesCS5B01G028800

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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 TraesCS5B01G028800 chr5B 100.000 2938 0 0 1 2938 27811976 27814913 0.000000e+00 5426.0
1 TraesCS5B01G028800 chr5B 91.176 510 41 3 1 506 66996148 66996657 0.000000e+00 689.0
2 TraesCS5B01G028800 chr5B 96.875 32 1 0 599 630 308922305 308922336 1.000000e-03 54.7
3 TraesCS5B01G028800 chr5D 90.631 1537 58 36 916 2403 37201663 37203162 0.000000e+00 1962.0
4 TraesCS5B01G028800 chr5D 90.463 367 23 6 506 861 37201110 37201475 9.530000e-130 473.0
5 TraesCS5B01G028800 chr5D 90.746 335 9 4 2505 2817 37203453 37203787 7.520000e-116 427.0
6 TraesCS5B01G028800 chr5D 98.276 58 1 0 2398 2455 37203199 37203256 5.180000e-18 102.0
7 TraesCS5B01G028800 chr5D 97.297 37 1 0 2452 2488 37203385 37203421 2.440000e-06 63.9
8 TraesCS5B01G028800 chr7A 91.639 909 39 21 1065 1939 31591777 31592682 0.000000e+00 1223.0
9 TraesCS5B01G028800 chr7A 87.100 876 93 13 1065 1938 63384272 63383415 0.000000e+00 974.0
10 TraesCS5B01G028800 chr7A 83.405 928 118 23 1036 1938 63378083 63378999 0.000000e+00 828.0
11 TraesCS5B01G028800 chr7A 77.533 227 17 14 2548 2771 31654602 31654797 4.000000e-19 106.0
12 TraesCS5B01G028800 chr7D 89.455 825 44 20 1153 1939 31119413 31120232 0.000000e+00 1002.0
13 TraesCS5B01G028800 chr7D 85.871 913 103 20 1036 1938 58843181 58842285 0.000000e+00 948.0
14 TraesCS5B01G028800 chr7D 83.988 968 113 27 995 1938 58829464 58830413 0.000000e+00 891.0
15 TraesCS5B01G028800 chr7D 95.434 219 9 1 1065 1282 31107434 31107216 6.030000e-92 348.0
16 TraesCS5B01G028800 chr4A 84.940 923 103 23 1036 1932 675932274 675933186 0.000000e+00 902.0
17 TraesCS5B01G028800 chr4A 89.286 588 61 2 1352 1938 675955100 675954514 0.000000e+00 736.0
18 TraesCS5B01G028800 chr6B 91.016 512 39 4 1 506 640129016 640129526 0.000000e+00 684.0
19 TraesCS5B01G028800 chr6B 90.234 512 44 6 1 512 577360639 577360134 0.000000e+00 664.0
20 TraesCS5B01G028800 chr7B 90.711 506 39 5 1 506 454236402 454236899 0.000000e+00 667.0
21 TraesCS5B01G028800 chr7B 90.278 504 43 6 3 506 376806248 376806745 0.000000e+00 654.0
22 TraesCS5B01G028800 chr7B 90.119 506 42 6 1 506 477607779 477607282 0.000000e+00 651.0
23 TraesCS5B01G028800 chr3D 90.316 506 43 5 1 506 84506874 84507373 0.000000e+00 658.0
24 TraesCS5B01G028800 chr3D 90.335 507 42 6 1 506 609879868 609880368 0.000000e+00 658.0
25 TraesCS5B01G028800 chr4D 89.980 509 48 3 1 509 437944841 437944336 0.000000e+00 654.0
26 TraesCS5B01G028800 chr1D 82.286 175 26 3 1108 1281 469052822 469052992 2.360000e-31 147.0
27 TraesCS5B01G028800 chr2D 100.000 39 0 0 936 974 555096619 555096581 4.060000e-09 73.1


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 TraesCS5B01G028800 chr5B 27811976 27814913 2937 False 5426.00 5426 100.0000 1 2938 1 chr5B.!!$F1 2937
1 TraesCS5B01G028800 chr5B 66996148 66996657 509 False 689.00 689 91.1760 1 506 1 chr5B.!!$F2 505
2 TraesCS5B01G028800 chr5D 37201110 37203787 2677 False 605.58 1962 93.4826 506 2817 5 chr5D.!!$F1 2311
3 TraesCS5B01G028800 chr7A 31591777 31592682 905 False 1223.00 1223 91.6390 1065 1939 1 chr7A.!!$F1 874
4 TraesCS5B01G028800 chr7A 63383415 63384272 857 True 974.00 974 87.1000 1065 1938 1 chr7A.!!$R1 873
5 TraesCS5B01G028800 chr7A 63378083 63378999 916 False 828.00 828 83.4050 1036 1938 1 chr7A.!!$F3 902
6 TraesCS5B01G028800 chr7D 31119413 31120232 819 False 1002.00 1002 89.4550 1153 1939 1 chr7D.!!$F1 786
7 TraesCS5B01G028800 chr7D 58842285 58843181 896 True 948.00 948 85.8710 1036 1938 1 chr7D.!!$R2 902
8 TraesCS5B01G028800 chr7D 58829464 58830413 949 False 891.00 891 83.9880 995 1938 1 chr7D.!!$F2 943
9 TraesCS5B01G028800 chr4A 675932274 675933186 912 False 902.00 902 84.9400 1036 1932 1 chr4A.!!$F1 896
10 TraesCS5B01G028800 chr4A 675954514 675955100 586 True 736.00 736 89.2860 1352 1938 1 chr4A.!!$R1 586
11 TraesCS5B01G028800 chr6B 640129016 640129526 510 False 684.00 684 91.0160 1 506 1 chr6B.!!$F1 505
12 TraesCS5B01G028800 chr6B 577360134 577360639 505 True 664.00 664 90.2340 1 512 1 chr6B.!!$R1 511
13 TraesCS5B01G028800 chr3D 609879868 609880368 500 False 658.00 658 90.3350 1 506 1 chr3D.!!$F2 505
14 TraesCS5B01G028800 chr4D 437944336 437944841 505 True 654.00 654 89.9800 1 509 1 chr4D.!!$R1 508

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
350 357 0.096976 GCATGGTGTCCGTTTCATCG 59.903 55.0 0.0 0.0 0.0 3.84 F
352 359 0.321210 ATGGTGTCCGTTTCATCGCA 60.321 50.0 0.0 0.0 0.0 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1341 1521 0.330604 AGCTGCACCATGAACTCCAT 59.669 50.0 1.02 0.0 35.44 3.41 R
2167 2472 0.391263 GGGACGGCGAATTCAGAGTT 60.391 55.0 16.62 0.0 0.00 3.01 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
146 147 3.797353 GAAGGGGCTGGGCGATCA 61.797 66.667 0.00 0.00 0.00 2.92
206 213 0.321671 CGGCAAGAGAAAGAGTGGGA 59.678 55.000 0.00 0.00 0.00 4.37
224 231 1.978580 GGAAAGAGTGGGGAAGAGTGA 59.021 52.381 0.00 0.00 0.00 3.41
253 260 4.467107 GCCGGAGAGAGGGAGGGT 62.467 72.222 5.05 0.00 0.00 4.34
256 263 2.781406 GGAGAGAGGGAGGGTGGT 59.219 66.667 0.00 0.00 0.00 4.16
276 283 1.631388 TGGATAGAAAAAGGCCCGTCA 59.369 47.619 0.00 0.00 0.00 4.35
289 296 1.447663 CCGTCATGTGCCATCGACA 60.448 57.895 0.00 0.00 0.00 4.35
317 324 2.125512 GGAAGGACACGCGCAGAT 60.126 61.111 5.73 0.00 0.00 2.90
348 355 0.321210 TCGCATGGTGTCCGTTTCAT 60.321 50.000 0.00 0.00 0.00 2.57
350 357 0.096976 GCATGGTGTCCGTTTCATCG 59.903 55.000 0.00 0.00 0.00 3.84
352 359 0.321210 ATGGTGTCCGTTTCATCGCA 60.321 50.000 0.00 0.00 0.00 5.10
356 363 2.307049 GTGTCCGTTTCATCGCAAAAG 58.693 47.619 0.00 0.00 0.00 2.27
357 364 1.327507 GTCCGTTTCATCGCAAAAGC 58.672 50.000 0.00 0.00 0.00 3.51
405 413 1.265905 GAAAGCGGACACAAAACGGAT 59.734 47.619 0.00 0.00 0.00 4.18
490 498 3.399181 GGACAGGATGGGGTCGCA 61.399 66.667 0.00 0.00 43.62 5.10
496 504 4.077184 GATGGGGTCGCACGGTGA 62.077 66.667 13.29 0.00 0.00 4.02
506 514 2.908073 GCACGGTGAAGTTGGCCTG 61.908 63.158 13.29 0.00 0.00 4.85
507 515 1.227823 CACGGTGAAGTTGGCCTGA 60.228 57.895 3.32 0.00 0.00 3.86
508 516 1.071471 ACGGTGAAGTTGGCCTGAG 59.929 57.895 3.32 0.00 0.00 3.35
509 517 2.328099 CGGTGAAGTTGGCCTGAGC 61.328 63.158 3.32 0.00 38.76 4.26
523 531 1.202639 CCTGAGCGGCACCACATATAA 60.203 52.381 1.45 0.00 0.00 0.98
526 534 0.880278 AGCGGCACCACATATAAGCG 60.880 55.000 1.45 0.00 0.00 4.68
529 537 0.878523 GGCACCACATATAAGCGCGA 60.879 55.000 12.10 0.00 0.00 5.87
551 559 5.570034 CGAAGAAATAGGGGTAGACCACAAA 60.570 44.000 3.26 0.00 43.57 2.83
553 561 6.402981 AGAAATAGGGGTAGACCACAAATT 57.597 37.500 3.26 0.00 43.57 1.82
554 562 7.519347 AGAAATAGGGGTAGACCACAAATTA 57.481 36.000 3.26 0.00 43.57 1.40
556 564 8.218488 AGAAATAGGGGTAGACCACAAATTATC 58.782 37.037 3.26 4.25 43.57 1.75
565 573 8.258708 GGTAGACCACAAATTATCTCTAACAGT 58.741 37.037 0.00 0.00 35.64 3.55
604 612 9.941664 CAATAGCATGAAATATATTCGGATTCC 57.058 33.333 0.00 0.00 0.00 3.01
643 651 6.585702 TGTCAGATTTTTAATCACGGCAAATG 59.414 34.615 2.60 0.00 0.00 2.32
644 652 5.576384 TCAGATTTTTAATCACGGCAAATGC 59.424 36.000 0.00 0.00 41.14 3.56
689 703 1.031571 TAGATTTTGCAGGCGGCTGG 61.032 55.000 36.25 20.25 45.15 4.85
706 720 2.722094 CTGGGGCAGCAAAATGTACTA 58.278 47.619 0.00 0.00 0.00 1.82
707 721 3.290710 CTGGGGCAGCAAAATGTACTAT 58.709 45.455 0.00 0.00 0.00 2.12
708 722 4.460263 CTGGGGCAGCAAAATGTACTATA 58.540 43.478 0.00 0.00 0.00 1.31
800 819 6.017934 GTGGCAAATTCATAGTATCACGATGT 60.018 38.462 0.00 0.00 33.69 3.06
850 869 4.322385 GCGCAAAAACGTCCGCCT 62.322 61.111 0.30 0.00 40.51 5.52
877 922 0.681564 ACCAAACAAACCGGACAGCA 60.682 50.000 9.46 0.00 0.00 4.41
926 1078 2.033448 TGCGGCCACCTAACCAAG 59.967 61.111 2.24 0.00 0.00 3.61
944 1096 3.197766 CCAAGCACACTGGAGTTATCCTA 59.802 47.826 0.00 0.00 46.80 2.94
945 1097 4.184629 CAAGCACACTGGAGTTATCCTAC 58.815 47.826 0.00 0.00 46.80 3.18
986 1138 2.102252 CACTAGCTAGCCTCCAAGAAGG 59.898 54.545 20.91 0.00 39.62 3.46
1003 1160 0.616964 AGGAGAGCAGAGCACCATGA 60.617 55.000 0.00 0.00 0.00 3.07
1283 1443 2.489329 CCGTCACCTCCTTCTACGTAAA 59.511 50.000 0.00 0.00 31.87 2.01
1295 1455 5.584649 CCTTCTACGTAAAGCATTCCATTCA 59.415 40.000 0.00 0.00 0.00 2.57
1300 1460 6.266168 ACGTAAAGCATTCCATTCAATTCA 57.734 33.333 0.00 0.00 0.00 2.57
1323 1483 6.478016 TCAATTCAGATTCGAGCACAGAATAG 59.522 38.462 2.10 0.11 38.32 1.73
1337 1517 9.787532 GAGCACAGAATAGATATAGTTCAGATC 57.212 37.037 0.00 0.00 0.00 2.75
1338 1518 8.458052 AGCACAGAATAGATATAGTTCAGATCG 58.542 37.037 0.00 0.00 29.78 3.69
1340 1520 9.767684 CACAGAATAGATATAGTTCAGATCGAC 57.232 37.037 0.00 0.00 29.78 4.20
1341 1521 9.508642 ACAGAATAGATATAGTTCAGATCGACA 57.491 33.333 0.00 0.00 29.78 4.35
1344 1524 9.729023 GAATAGATATAGTTCAGATCGACATGG 57.271 37.037 0.00 0.00 29.78 3.66
1345 1525 9.467796 AATAGATATAGTTCAGATCGACATGGA 57.532 33.333 0.00 0.00 29.78 3.41
1346 1526 7.389803 AGATATAGTTCAGATCGACATGGAG 57.610 40.000 0.00 0.00 29.78 3.86
1347 1527 6.945435 AGATATAGTTCAGATCGACATGGAGT 59.055 38.462 0.00 0.00 29.78 3.85
1348 1528 5.860941 ATAGTTCAGATCGACATGGAGTT 57.139 39.130 0.00 0.00 0.00 3.01
1349 1529 4.116747 AGTTCAGATCGACATGGAGTTC 57.883 45.455 0.00 0.00 0.00 3.01
1350 1530 3.511540 AGTTCAGATCGACATGGAGTTCA 59.488 43.478 0.00 0.00 0.00 3.18
1675 1908 4.087892 CAGCTACTGGGCCACGCT 62.088 66.667 0.00 8.38 0.00 5.07
1676 1909 3.775654 AGCTACTGGGCCACGCTC 61.776 66.667 0.00 0.00 0.00 5.03
1945 2250 4.025401 CCGCGCCTGAACACAACC 62.025 66.667 0.00 0.00 0.00 3.77
1971 2276 1.697432 AGATTTGAGTTCACGTCCCCA 59.303 47.619 0.00 0.00 0.00 4.96
1988 2293 1.271597 CCCAATCCCCCGATGAGATTC 60.272 57.143 0.00 0.00 0.00 2.52
1992 2297 2.011122 TCCCCCGATGAGATTCTACC 57.989 55.000 0.00 0.00 0.00 3.18
1995 2300 2.037772 CCCCCGATGAGATTCTACCTTG 59.962 54.545 0.00 0.00 0.00 3.61
2008 2313 7.856415 AGATTCTACCTTGTTAGCTTGATTCT 58.144 34.615 0.00 0.00 0.00 2.40
2030 2335 3.715628 TTTTCTGGTTTCTTCAGCAGC 57.284 42.857 0.00 0.00 41.29 5.25
2032 2337 0.603707 TCTGGTTTCTTCAGCAGCCG 60.604 55.000 0.00 0.00 41.29 5.52
2033 2338 1.580845 CTGGTTTCTTCAGCAGCCGG 61.581 60.000 0.00 0.00 35.58 6.13
2052 2357 2.750135 CGGCTCCTCTACCTCTATGTGT 60.750 54.545 0.00 0.00 0.00 3.72
2053 2358 3.301274 GGCTCCTCTACCTCTATGTGTT 58.699 50.000 0.00 0.00 0.00 3.32
2054 2359 3.319689 GGCTCCTCTACCTCTATGTGTTC 59.680 52.174 0.00 0.00 0.00 3.18
2067 2372 6.018262 CCTCTATGTGTTCTTGTTTTCGTCAA 60.018 38.462 0.00 0.00 0.00 3.18
2091 2396 7.939784 AAAAACCTCTCTCTGTTAAGTGTTT 57.060 32.000 0.00 0.00 0.00 2.83
2092 2397 7.939784 AAAACCTCTCTCTGTTAAGTGTTTT 57.060 32.000 0.00 0.00 0.00 2.43
2093 2398 7.939784 AAACCTCTCTCTGTTAAGTGTTTTT 57.060 32.000 0.00 0.00 0.00 1.94
2181 2486 9.062674 GTATTTAAAAGAAACTCTGAATTCGCC 57.937 33.333 0.04 0.00 0.00 5.54
2276 2581 6.414732 TGGATTACTTTGGGATTCACTGTAG 58.585 40.000 0.00 0.00 0.00 2.74
2279 2584 4.307032 ACTTTGGGATTCACTGTAGCAT 57.693 40.909 0.00 0.00 0.00 3.79
2280 2585 5.435686 ACTTTGGGATTCACTGTAGCATA 57.564 39.130 0.00 0.00 0.00 3.14
2299 2604 6.462552 GCATAGAGCAGTAGATCCATATCA 57.537 41.667 0.00 0.00 44.79 2.15
2302 2607 8.637099 GCATAGAGCAGTAGATCCATATCATTA 58.363 37.037 0.00 0.00 44.79 1.90
2305 2610 8.835550 AGAGCAGTAGATCCATATCATTATGA 57.164 34.615 0.00 0.00 37.94 2.15
2306 2611 9.264653 AGAGCAGTAGATCCATATCATTATGAA 57.735 33.333 0.00 0.00 37.94 2.57
2307 2612 9.881649 GAGCAGTAGATCCATATCATTATGAAA 57.118 33.333 0.00 0.00 37.94 2.69
2308 2613 9.664332 AGCAGTAGATCCATATCATTATGAAAC 57.336 33.333 0.00 0.00 37.94 2.78
2309 2614 9.664332 GCAGTAGATCCATATCATTATGAAACT 57.336 33.333 0.00 0.00 37.94 2.66
2336 2663 5.049886 CGTAATAGATGACGTAGGTGTAGCA 60.050 44.000 0.00 0.00 34.39 3.49
2384 2711 7.264947 TCTTCCTGAACTTCAAATTTTGGTTC 58.735 34.615 17.40 17.40 34.48 3.62
2399 2726 1.341852 TGGTTCGGTCAGTCGATTTCA 59.658 47.619 0.00 0.00 39.03 2.69
2488 2990 3.742013 GCCCCGAATGAAAGTAACGGATA 60.742 47.826 0.00 0.00 45.31 2.59
2489 2991 3.805971 CCCCGAATGAAAGTAACGGATAC 59.194 47.826 0.00 0.00 45.31 2.24
2490 2992 4.435425 CCCGAATGAAAGTAACGGATACA 58.565 43.478 0.00 0.00 45.31 2.29
2491 2993 4.871557 CCCGAATGAAAGTAACGGATACAA 59.128 41.667 0.00 0.00 45.31 2.41
2492 2994 5.352016 CCCGAATGAAAGTAACGGATACAAA 59.648 40.000 0.00 0.00 45.31 2.83
2493 2995 6.128227 CCCGAATGAAAGTAACGGATACAAAA 60.128 38.462 0.00 0.00 45.31 2.44
2494 2996 6.739550 CCGAATGAAAGTAACGGATACAAAAC 59.260 38.462 0.00 0.00 45.31 2.43
2495 2997 7.360607 CCGAATGAAAGTAACGGATACAAAACT 60.361 37.037 0.00 0.00 45.31 2.66
2496 2998 8.013378 CGAATGAAAGTAACGGATACAAAACTT 58.987 33.333 0.00 0.00 36.94 2.66
2499 3001 7.987649 TGAAAGTAACGGATACAAAACTTGTT 58.012 30.769 0.00 0.00 42.22 2.83
2500 3002 8.460428 TGAAAGTAACGGATACAAAACTTGTTT 58.540 29.630 0.00 0.00 42.22 2.83
2502 3004 8.845942 AAGTAACGGATACAAAACTTGTTTTC 57.154 30.769 8.33 0.00 42.22 2.29
2528 3045 9.570488 CATTCTTTTTCAAAATTTTGGCTTGAA 57.430 25.926 26.45 21.98 38.66 2.69
2568 3085 3.901797 CTTTCTGGAAGGCGCCGGT 62.902 63.158 23.20 13.96 35.72 5.28
2709 3236 3.776158 TGGTGGTGCCAGATTTGC 58.224 55.556 0.00 0.00 43.61 3.68
2776 3303 1.066787 GCCCTTAAACTCGCTCAGACT 60.067 52.381 0.00 0.00 0.00 3.24
2777 3304 2.165845 GCCCTTAAACTCGCTCAGACTA 59.834 50.000 0.00 0.00 0.00 2.59
2805 3344 4.692625 CACCACTGTATATATTGGAGCTGC 59.307 45.833 12.05 0.00 33.02 5.25
2818 3357 4.724074 TGGAGCTGCCAAAATATCTTTG 57.276 40.909 1.53 4.38 45.87 2.77
2819 3358 3.448301 TGGAGCTGCCAAAATATCTTTGG 59.552 43.478 17.91 17.91 45.87 3.28
2826 3365 4.900635 CCAAAATATCTTTGGTCGGAGG 57.099 45.455 15.63 0.00 42.92 4.30
2827 3366 4.270008 CCAAAATATCTTTGGTCGGAGGT 58.730 43.478 15.63 0.00 42.92 3.85
2828 3367 4.335594 CCAAAATATCTTTGGTCGGAGGTC 59.664 45.833 15.63 0.00 42.92 3.85
2829 3368 3.840124 AATATCTTTGGTCGGAGGTCC 57.160 47.619 0.00 0.00 0.00 4.46
2830 3369 1.492764 TATCTTTGGTCGGAGGTCCC 58.507 55.000 0.00 0.00 0.00 4.46
2839 3378 4.393778 GGAGGTCCCGGTCCAGGA 62.394 72.222 14.08 0.00 32.55 3.86
2840 3379 2.760385 GAGGTCCCGGTCCAGGAG 60.760 72.222 14.08 0.00 32.84 3.69
2841 3380 3.273654 AGGTCCCGGTCCAGGAGA 61.274 66.667 14.08 0.00 32.84 3.71
2842 3381 3.075641 GGTCCCGGTCCAGGAGAC 61.076 72.222 0.00 0.00 45.51 3.36
2849 3388 2.486042 GTCCAGGAGACGACGAGC 59.514 66.667 0.00 0.00 35.30 5.03
2867 3406 4.595538 GTCGACGGTGGTGTGCCA 62.596 66.667 0.00 0.00 43.73 4.92
2875 3414 4.269523 TGGTGTGCCAGGACCTGC 62.270 66.667 16.72 11.98 40.46 4.85
2912 3451 4.329545 GAGGCTGCACGGTGGGAA 62.330 66.667 10.60 0.00 0.00 3.97
2913 3452 3.842925 GAGGCTGCACGGTGGGAAA 62.843 63.158 10.60 0.00 0.00 3.13
2914 3453 2.909965 GGCTGCACGGTGGGAAAA 60.910 61.111 10.60 0.00 0.00 2.29
2916 3455 2.919494 GCTGCACGGTGGGAAAAGG 61.919 63.158 10.60 0.00 0.00 3.11
2918 3457 4.038080 GCACGGTGGGAAAAGGCG 62.038 66.667 10.60 0.00 0.00 5.52
2923 3462 1.074248 GGTGGGAAAAGGCGGAGAA 59.926 57.895 0.00 0.00 0.00 2.87
2924 3463 1.241990 GGTGGGAAAAGGCGGAGAAC 61.242 60.000 0.00 0.00 0.00 3.01
2925 3464 1.074248 TGGGAAAAGGCGGAGAACC 59.926 57.895 0.00 0.00 0.00 3.62
2926 3465 1.379146 GGGAAAAGGCGGAGAACCT 59.621 57.895 0.00 0.00 40.02 3.50
2927 3466 0.677098 GGGAAAAGGCGGAGAACCTC 60.677 60.000 0.00 0.00 36.14 3.85
2928 3467 0.677098 GGAAAAGGCGGAGAACCTCC 60.677 60.000 2.97 2.97 46.44 4.30
2935 3474 3.377656 GGAGAACCTCCGTGAGCA 58.622 61.111 0.00 0.00 41.08 4.26
2936 3475 1.079750 GGAGAACCTCCGTGAGCAC 60.080 63.158 0.00 0.00 41.08 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 2.499685 GGATCCGGTCGGTCTTGG 59.500 66.667 9.36 0.00 36.47 3.61
144 145 4.273257 TGCAACTCGGACGCGTGA 62.273 61.111 20.70 8.01 0.00 4.35
191 198 4.202409 CCACTCTTTCCCACTCTTTCTCTT 60.202 45.833 0.00 0.00 0.00 2.85
194 201 2.373502 CCCACTCTTTCCCACTCTTTCT 59.626 50.000 0.00 0.00 0.00 2.52
206 213 3.049344 ACTTCACTCTTCCCCACTCTTT 58.951 45.455 0.00 0.00 0.00 2.52
243 250 0.266152 CTATCCACCACCCTCCCTCT 59.734 60.000 0.00 0.00 0.00 3.69
253 260 1.340600 CGGGCCTTTTTCTATCCACCA 60.341 52.381 0.84 0.00 0.00 4.17
256 263 1.631388 TGACGGGCCTTTTTCTATCCA 59.369 47.619 0.84 0.00 0.00 3.41
301 308 2.456119 CCATCTGCGCGTGTCCTTC 61.456 63.158 8.43 0.00 0.00 3.46
327 334 0.110373 GAAACGGACACCATGCGAAC 60.110 55.000 0.00 0.00 46.80 3.95
329 336 0.321210 ATGAAACGGACACCATGCGA 60.321 50.000 0.00 0.00 46.80 5.10
333 340 0.321210 TGCGATGAAACGGACACCAT 60.321 50.000 0.00 0.00 0.00 3.55
350 357 2.237066 AAGTTTGCGCCGCTTTTGC 61.237 52.632 11.67 0.00 43.23 3.68
352 359 1.591327 CCAAGTTTGCGCCGCTTTT 60.591 52.632 11.67 0.00 0.00 2.27
376 384 0.672401 TGTCCGCTTTCGACCCATTC 60.672 55.000 0.00 0.00 38.10 2.67
377 385 0.953960 GTGTCCGCTTTCGACCCATT 60.954 55.000 0.00 0.00 38.10 3.16
405 413 1.515081 CGGGAGCAAACGGACTTTTA 58.485 50.000 0.00 0.00 0.00 1.52
435 443 1.614413 GTAAAACGGACAAATGGGGCA 59.386 47.619 0.00 0.00 0.00 5.36
441 449 4.325028 GTTTGGGGTAAAACGGACAAAT 57.675 40.909 0.00 0.00 30.90 2.32
472 480 3.399181 GCGACCCCATCCTGTCCA 61.399 66.667 0.00 0.00 0.00 4.02
486 494 2.970324 GCCAACTTCACCGTGCGA 60.970 61.111 0.00 0.00 0.00 5.10
490 498 1.071471 CTCAGGCCAACTTCACCGT 59.929 57.895 5.01 0.00 0.00 4.83
506 514 0.868406 GCTTATATGTGGTGCCGCTC 59.132 55.000 3.31 0.00 0.00 5.03
507 515 0.880278 CGCTTATATGTGGTGCCGCT 60.880 55.000 3.31 0.00 0.00 5.52
508 516 1.569493 CGCTTATATGTGGTGCCGC 59.431 57.895 0.00 0.00 0.00 6.53
509 517 1.569493 GCGCTTATATGTGGTGCCG 59.431 57.895 0.00 0.00 0.00 5.69
514 522 4.732285 ATTTCTTCGCGCTTATATGTGG 57.268 40.909 5.56 0.00 0.00 4.17
518 526 4.020485 ACCCCTATTTCTTCGCGCTTATAT 60.020 41.667 5.56 0.00 0.00 0.86
519 527 3.322828 ACCCCTATTTCTTCGCGCTTATA 59.677 43.478 5.56 0.00 0.00 0.98
523 531 1.068741 CTACCCCTATTTCTTCGCGCT 59.931 52.381 5.56 0.00 0.00 5.92
526 534 2.433239 TGGTCTACCCCTATTTCTTCGC 59.567 50.000 0.00 0.00 34.29 4.70
529 537 5.853572 TTTGTGGTCTACCCCTATTTCTT 57.146 39.130 0.00 0.00 34.29 2.52
597 605 9.144747 CTGACATTAGATTTATAGTGGAATCCG 57.855 37.037 0.00 0.00 33.72 4.18
616 624 6.266168 TGCCGTGATTAAAAATCTGACATT 57.734 33.333 1.70 0.00 0.00 2.71
652 666 8.567221 CAAAATCTATCGAATTTTGACGTCAAC 58.433 33.333 29.74 17.23 43.88 3.18
656 670 6.607689 TGCAAAATCTATCGAATTTTGACGT 58.392 32.000 26.56 0.00 43.88 4.34
664 678 2.549754 CCGCCTGCAAAATCTATCGAAT 59.450 45.455 0.00 0.00 0.00 3.34
666 680 1.581934 CCGCCTGCAAAATCTATCGA 58.418 50.000 0.00 0.00 0.00 3.59
689 703 9.981114 AAAAATATATAGTACATTTTGCTGCCC 57.019 29.630 0.00 0.00 33.38 5.36
730 749 3.611549 CGGAATATCTCATGCTCATCACG 59.388 47.826 0.00 0.00 0.00 4.35
850 869 0.173708 GGTTTGTTTGGTGTCGGCAA 59.826 50.000 0.00 0.00 0.00 4.52
877 922 3.386237 GGCAGGAGTCGGTGCTCT 61.386 66.667 13.97 0.00 39.76 4.09
896 941 3.499737 CCGCACATGAAGACGGCC 61.500 66.667 0.00 0.00 39.08 6.13
904 949 1.376683 GTTAGGTGGCCGCACATGA 60.377 57.895 19.98 0.00 0.00 3.07
926 1078 2.766828 AGGTAGGATAACTCCAGTGTGC 59.233 50.000 0.00 0.00 27.12 4.57
944 1096 1.534235 AAGTGGAGTGGAGCGAGGT 60.534 57.895 0.00 0.00 0.00 3.85
945 1097 1.216710 GAAGTGGAGTGGAGCGAGG 59.783 63.158 0.00 0.00 0.00 4.63
986 1138 0.805322 CGTCATGGTGCTCTGCTCTC 60.805 60.000 0.00 0.00 0.00 3.20
1283 1443 7.177832 TCTGAATTGAATTGAATGGAATGCT 57.822 32.000 0.00 0.00 0.00 3.79
1295 1455 5.645067 TCTGTGCTCGAATCTGAATTGAATT 59.355 36.000 0.00 0.00 0.00 2.17
1300 1460 6.577103 TCTATTCTGTGCTCGAATCTGAATT 58.423 36.000 15.48 0.00 33.89 2.17
1323 1483 7.151999 ACTCCATGTCGATCTGAACTATATC 57.848 40.000 0.00 0.00 0.00 1.63
1341 1521 0.330604 AGCTGCACCATGAACTCCAT 59.669 50.000 1.02 0.00 35.44 3.41
1344 1524 0.801251 GACAGCTGCACCATGAACTC 59.199 55.000 15.27 0.00 0.00 3.01
1345 1525 0.952497 CGACAGCTGCACCATGAACT 60.952 55.000 15.27 0.00 0.00 3.01
1346 1526 1.230635 ACGACAGCTGCACCATGAAC 61.231 55.000 15.27 0.00 0.00 3.18
1347 1527 0.950555 GACGACAGCTGCACCATGAA 60.951 55.000 15.27 0.00 0.00 2.57
1348 1528 1.374631 GACGACAGCTGCACCATGA 60.375 57.895 15.27 0.00 0.00 3.07
1349 1529 2.733671 CGACGACAGCTGCACCATG 61.734 63.158 15.27 0.00 0.00 3.66
1350 1530 2.433145 CGACGACAGCTGCACCAT 60.433 61.111 15.27 0.00 0.00 3.55
1621 1848 2.359850 GCACGGACATGGGCTTGA 60.360 61.111 0.00 0.00 0.00 3.02
1716 1949 4.253257 GGCGCGGTAGGAGACGAG 62.253 72.222 8.83 0.00 0.00 4.18
1940 2245 5.049405 GTGAACTCAAATCTCAATCGGTTGT 60.049 40.000 8.54 0.00 36.69 3.32
1945 2250 4.201628 GGACGTGAACTCAAATCTCAATCG 60.202 45.833 0.00 0.00 0.00 3.34
1971 2276 2.907042 GGTAGAATCTCATCGGGGGATT 59.093 50.000 3.22 3.22 33.13 3.01
2027 2332 2.443016 AGGTAGAGGAGCCGGCTG 60.443 66.667 38.41 0.00 0.00 4.85
2028 2333 1.354168 TAGAGGTAGAGGAGCCGGCT 61.354 60.000 33.48 33.48 0.00 5.52
2030 2335 1.202952 ACATAGAGGTAGAGGAGCCGG 60.203 57.143 0.00 0.00 0.00 6.13
2032 2337 2.952116 ACACATAGAGGTAGAGGAGCC 58.048 52.381 0.00 0.00 0.00 4.70
2033 2338 4.211920 AGAACACATAGAGGTAGAGGAGC 58.788 47.826 0.00 0.00 0.00 4.70
2036 2341 5.923733 ACAAGAACACATAGAGGTAGAGG 57.076 43.478 0.00 0.00 0.00 3.69
2039 2344 6.645415 ACGAAAACAAGAACACATAGAGGTAG 59.355 38.462 0.00 0.00 0.00 3.18
2041 2346 5.365619 ACGAAAACAAGAACACATAGAGGT 58.634 37.500 0.00 0.00 0.00 3.85
2067 2372 7.939784 AAACACTTAACAGAGAGAGGTTTTT 57.060 32.000 0.00 0.00 0.00 1.94
2091 2396 6.042437 AGAGTTAACCCCTCTCGTTAAGAAAA 59.958 38.462 0.88 0.00 36.59 2.29
2092 2397 5.541484 AGAGTTAACCCCTCTCGTTAAGAAA 59.459 40.000 0.88 0.00 36.59 2.52
2093 2398 5.082425 AGAGTTAACCCCTCTCGTTAAGAA 58.918 41.667 0.88 0.00 36.59 2.52
2094 2399 4.670765 AGAGTTAACCCCTCTCGTTAAGA 58.329 43.478 0.88 0.00 36.59 2.10
2095 2400 6.328714 GTTAGAGTTAACCCCTCTCGTTAAG 58.671 44.000 0.88 0.00 39.86 1.85
2096 2401 5.106157 CGTTAGAGTTAACCCCTCTCGTTAA 60.106 44.000 0.88 0.00 39.86 2.01
2105 2410 7.706607 ACGTTTATTATCGTTAGAGTTAACCCC 59.293 37.037 0.88 0.00 36.60 4.95
2155 2460 9.062674 GGCGAATTCAGAGTTTCTTTTAAATAC 57.937 33.333 6.22 0.00 0.00 1.89
2156 2461 7.960738 CGGCGAATTCAGAGTTTCTTTTAAATA 59.039 33.333 0.00 0.00 0.00 1.40
2157 2462 6.801862 CGGCGAATTCAGAGTTTCTTTTAAAT 59.198 34.615 0.00 0.00 0.00 1.40
2159 2464 5.237779 ACGGCGAATTCAGAGTTTCTTTTAA 59.762 36.000 16.62 0.00 0.00 1.52
2160 2465 4.753107 ACGGCGAATTCAGAGTTTCTTTTA 59.247 37.500 16.62 0.00 0.00 1.52
2163 2468 2.737252 GACGGCGAATTCAGAGTTTCTT 59.263 45.455 16.62 0.00 0.00 2.52
2165 2470 1.393883 GGACGGCGAATTCAGAGTTTC 59.606 52.381 16.62 0.00 0.00 2.78
2166 2471 1.439679 GGACGGCGAATTCAGAGTTT 58.560 50.000 16.62 0.00 0.00 2.66
2167 2472 0.391263 GGGACGGCGAATTCAGAGTT 60.391 55.000 16.62 0.00 0.00 3.01
2168 2473 1.218316 GGGACGGCGAATTCAGAGT 59.782 57.895 16.62 1.34 0.00 3.24
2169 2474 4.110493 GGGACGGCGAATTCAGAG 57.890 61.111 16.62 0.00 0.00 3.35
2232 2537 3.128242 CCAAATCAGAGTGGATCAACAGC 59.872 47.826 2.34 0.00 37.03 4.40
2234 2539 4.639078 TCCAAATCAGAGTGGATCAACA 57.361 40.909 2.34 0.00 39.04 3.33
2276 2581 6.462552 TGATATGGATCTACTGCTCTATGC 57.537 41.667 0.00 0.00 36.17 3.14
2279 2584 9.927081 TCATAATGATATGGATCTACTGCTCTA 57.073 33.333 0.00 0.00 39.54 2.43
2280 2585 8.835550 TCATAATGATATGGATCTACTGCTCT 57.164 34.615 0.00 0.00 39.54 4.09
2347 2674 4.772100 AGTTCAGGAAGAGAGAGGAGAAAG 59.228 45.833 0.00 0.00 0.00 2.62
2351 2678 4.085733 TGAAGTTCAGGAAGAGAGAGGAG 58.914 47.826 0.08 0.00 0.00 3.69
2352 2679 4.119556 TGAAGTTCAGGAAGAGAGAGGA 57.880 45.455 0.08 0.00 0.00 3.71
2360 2687 6.198966 CGAACCAAAATTTGAAGTTCAGGAAG 59.801 38.462 19.90 6.84 37.31 3.46
2384 2711 2.028045 CGACATTGAAATCGACTGACCG 59.972 50.000 0.00 0.00 40.86 4.79
2399 2726 0.179134 GCCTCGCTGTAGACGACATT 60.179 55.000 0.00 0.00 37.45 2.71
2500 3002 9.570488 CAAGCCAAAATTTTGAAAAAGAATGAA 57.430 25.926 28.44 0.00 40.55 2.57
2502 3004 9.570488 TTCAAGCCAAAATTTTGAAAAAGAATG 57.430 25.926 28.44 15.72 40.55 2.67
2525 3042 3.228453 ACTCTGACTAAACCGTCCTTCA 58.772 45.455 0.00 0.00 32.97 3.02
2528 3045 2.561858 GGAACTCTGACTAAACCGTCCT 59.438 50.000 0.00 0.00 32.97 3.85
2586 3103 2.888594 CACGACATCAACCGGAATAGT 58.111 47.619 9.46 0.00 0.00 2.12
2649 3176 7.507277 TGATGATAAGAGTAGGTAGCATCAAGT 59.493 37.037 8.67 0.00 45.32 3.16
2776 3303 8.204160 GCTCCAATATATACAGTGGTGCATATA 58.796 37.037 17.08 0.00 45.54 0.86
2777 3304 7.050377 GCTCCAATATATACAGTGGTGCATAT 58.950 38.462 17.08 0.00 45.54 1.78
2822 3361 4.393778 TCCTGGACCGGGACCTCC 62.394 72.222 18.94 11.10 33.41 4.30
2823 3362 2.760385 CTCCTGGACCGGGACCTC 60.760 72.222 18.94 1.54 33.41 3.85
2824 3363 3.273654 TCTCCTGGACCGGGACCT 61.274 66.667 18.94 0.00 33.41 3.85
2825 3364 3.075641 GTCTCCTGGACCGGGACC 61.076 72.222 18.94 8.70 38.93 4.46
2826 3365 3.450115 CGTCTCCTGGACCGGGAC 61.450 72.222 18.94 9.50 41.64 4.46
2827 3366 3.654143 TCGTCTCCTGGACCGGGA 61.654 66.667 21.44 21.44 41.64 5.14
2828 3367 3.450115 GTCGTCTCCTGGACCGGG 61.450 72.222 13.92 13.92 41.64 5.73
2829 3368 3.812019 CGTCGTCTCCTGGACCGG 61.812 72.222 0.00 0.00 41.64 5.28
2830 3369 2.745100 TCGTCGTCTCCTGGACCG 60.745 66.667 0.00 0.00 41.64 4.79
2831 3370 3.053849 GCTCGTCGTCTCCTGGACC 62.054 68.421 0.00 0.00 41.64 4.46
2832 3371 2.486042 GCTCGTCGTCTCCTGGAC 59.514 66.667 0.00 0.00 41.28 4.02
2833 3372 3.125573 CGCTCGTCGTCTCCTGGA 61.126 66.667 0.00 0.00 0.00 3.86
2846 3385 4.338539 ACACCACCGTCGACGCTC 62.339 66.667 31.73 0.00 38.18 5.03
2847 3386 4.640855 CACACCACCGTCGACGCT 62.641 66.667 31.73 16.93 38.18 5.07
2850 3389 4.595538 TGGCACACCACCGTCGAC 62.596 66.667 5.18 5.18 42.67 4.20
2851 3390 4.293648 CTGGCACACCACCGTCGA 62.294 66.667 0.00 0.00 42.67 4.20
2853 3392 3.936203 TCCTGGCACACCACCGTC 61.936 66.667 0.00 0.00 42.67 4.79
2854 3393 4.250305 GTCCTGGCACACCACCGT 62.250 66.667 0.00 0.00 42.67 4.83
2856 3395 3.570212 AGGTCCTGGCACACCACC 61.570 66.667 12.36 0.00 42.67 4.61
2857 3396 2.281761 CAGGTCCTGGCACACCAC 60.282 66.667 11.46 0.00 42.67 4.16
2858 3397 4.269523 GCAGGTCCTGGCACACCA 62.270 66.667 20.72 0.00 46.51 4.17
2881 3420 4.742201 CCTCGCCGTGACCCACTG 62.742 72.222 0.00 0.00 31.34 3.66
2899 3438 2.919494 GCCTTTTCCCACCGTGCAG 61.919 63.158 0.00 0.00 0.00 4.41
2900 3439 2.909965 GCCTTTTCCCACCGTGCA 60.910 61.111 0.00 0.00 0.00 4.57
2918 3457 1.079750 GTGCTCACGGAGGTTCTCC 60.080 63.158 3.96 3.96 46.44 3.71


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

AutoCloner maintained by Alex Coulton.