Multiple sequence alignment - TraesCS2B01G294900

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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 TraesCS2B01G294900 chr2B 100.000 2768 0 0 1 2768 412057553 412054786 0 5112
1 TraesCS2B01G294900 chr2B 90.957 1692 144 1 41 1723 262528501 262526810 0 2268
2 TraesCS2B01G294900 chr2B 90.673 1694 147 4 28 1711 704813904 704815596 0 2242
3 TraesCS2B01G294900 chr2B 89.669 1694 157 7 28 1711 675366806 675365121 0 2143
4 TraesCS2B01G294900 chr2B 89.087 1686 161 10 54 1721 577245402 577247082 0 2073
5 TraesCS2B01G294900 chr2B 92.455 1047 79 0 1722 2768 704816119 704817165 0 1496
6 TraesCS2B01G294900 chr2B 91.604 1060 86 3 1711 2768 262526311 262525253 0 1461
7 TraesCS2B01G294900 chr2B 90.935 1048 95 0 1721 2768 577247633 577248680 0 1410
8 TraesCS2B01G294900 chr2B 90.875 1052 95 1 1717 2768 675364602 675363552 0 1410
9 TraesCS2B01G294900 chr7B 92.753 1711 102 10 28 1718 368143636 368141928 0 2453
10 TraesCS2B01G294900 chr7B 97.459 905 23 0 1864 2768 560512936 560512032 0 1544
11 TraesCS2B01G294900 chr7B 92.015 1052 83 1 1717 2768 368141386 368140336 0 1476
12 TraesCS2B01G294900 chr3B 89.906 1694 154 5 28 1711 605004306 605005992 0 2165
13 TraesCS2B01G294900 chr3B 93.679 1060 63 4 1711 2768 162625468 162626525 0 1583
14 TraesCS2B01G294900 chr3B 93.821 1052 62 3 1717 2768 462592986 462594034 0 1580
15 TraesCS2B01G294900 chr3B 93.404 1031 55 3 694 1711 162623912 162624942 0 1515
16 TraesCS2B01G294900 chr5B 86.815 1661 197 13 56 1711 437771052 437769409 0 1834
17 TraesCS2B01G294900 chr3A 87.888 1255 141 5 458 1711 332221537 332222781 0 1465
18 TraesCS2B01G294900 chr1A 90.779 1052 96 1 1717 2768 25580592 25579542 0 1404


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 TraesCS2B01G294900 chr2B 412054786 412057553 2767 True 5112.0 5112 100.0000 1 2768 1 chr2B.!!$R1 2767
1 TraesCS2B01G294900 chr2B 704813904 704817165 3261 False 1869.0 2242 91.5640 28 2768 2 chr2B.!!$F2 2740
2 TraesCS2B01G294900 chr2B 262525253 262528501 3248 True 1864.5 2268 91.2805 41 2768 2 chr2B.!!$R2 2727
3 TraesCS2B01G294900 chr2B 675363552 675366806 3254 True 1776.5 2143 90.2720 28 2768 2 chr2B.!!$R3 2740
4 TraesCS2B01G294900 chr2B 577245402 577248680 3278 False 1741.5 2073 90.0110 54 2768 2 chr2B.!!$F1 2714
5 TraesCS2B01G294900 chr7B 368140336 368143636 3300 True 1964.5 2453 92.3840 28 2768 2 chr7B.!!$R2 2740
6 TraesCS2B01G294900 chr7B 560512032 560512936 904 True 1544.0 1544 97.4590 1864 2768 1 chr7B.!!$R1 904
7 TraesCS2B01G294900 chr3B 605004306 605005992 1686 False 2165.0 2165 89.9060 28 1711 1 chr3B.!!$F2 1683
8 TraesCS2B01G294900 chr3B 462592986 462594034 1048 False 1580.0 1580 93.8210 1717 2768 1 chr3B.!!$F1 1051
9 TraesCS2B01G294900 chr3B 162623912 162626525 2613 False 1549.0 1583 93.5415 694 2768 2 chr3B.!!$F3 2074
10 TraesCS2B01G294900 chr5B 437769409 437771052 1643 True 1834.0 1834 86.8150 56 1711 1 chr5B.!!$R1 1655
11 TraesCS2B01G294900 chr3A 332221537 332222781 1244 False 1465.0 1465 87.8880 458 1711 1 chr3A.!!$F1 1253
12 TraesCS2B01G294900 chr1A 25579542 25580592 1050 True 1404.0 1404 90.7790 1717 2768 1 chr1A.!!$R1 1051

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
172 173 0.970937 CCTCTCCACTAGTGCCGGAA 60.971 60.000 17.86 0.0 0.0 4.30 F
890 901 1.474498 GGACTTTCTGGTGGTGTTCGT 60.474 52.381 0.00 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1193 1204 0.604511 CGGCTCCGTAACCCAAAGTT 60.605 55.0 0.00 0.0 42.83 2.66 R
1881 2474 0.959553 GGAACAGACAGACCGAGTCA 59.040 55.0 6.78 0.0 38.46 3.41 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
84 85 4.496336 GGATCTGCAAGCCCGGCT 62.496 66.667 5.94 5.94 42.56 5.52
163 164 1.656092 ATCCGAGGGCCTCTCCACTA 61.656 60.000 29.81 9.93 39.30 2.74
172 173 0.970937 CCTCTCCACTAGTGCCGGAA 60.971 60.000 17.86 0.00 0.00 4.30
890 901 1.474498 GGACTTTCTGGTGGTGTTCGT 60.474 52.381 0.00 0.00 0.00 3.85
961 972 6.038714 GCATGGCTACTTTAAGCTATTTGTCT 59.961 38.462 0.00 0.00 40.39 3.41
1227 1238 2.272146 CCGGTGATGGTTGGAGGG 59.728 66.667 0.00 0.00 0.00 4.30
1254 1265 2.362503 AGGTCGCCCACATCTCGA 60.363 61.111 0.00 0.00 0.00 4.04
1331 1346 2.659610 GGAGCGCTGGTTGAGACT 59.340 61.111 18.48 0.00 0.00 3.24
1512 1527 1.275421 TGATGGGGCGTATTGGACCA 61.275 55.000 0.00 0.00 36.52 4.02
1569 1584 3.487202 GCGAAGATTCACGCGCCA 61.487 61.111 5.73 0.00 44.91 5.69
1713 1755 1.566211 CTGAGGTGATGGACAGGACT 58.434 55.000 0.00 0.00 0.00 3.85
1783 2376 5.278957 GCTGGGTAACATCAAAACATTCTGT 60.279 40.000 0.00 0.00 39.74 3.41
1785 2378 5.596361 TGGGTAACATCAAAACATTCTGTGT 59.404 36.000 0.00 0.00 40.64 3.72
1809 2402 3.119137 GGGTTGTTGAAGAAACTTGTGCT 60.119 43.478 0.00 0.00 39.70 4.40
1881 2474 0.740868 CCATTCACACCTCGACGCAT 60.741 55.000 0.00 0.00 0.00 4.73
1978 2571 6.709846 CCTTAGGATTTGATTGTGAGGATCTC 59.290 42.308 0.00 0.00 34.92 2.75
1990 2583 0.965866 AGGATCTCGCCGTGTCTGAA 60.966 55.000 0.00 0.00 0.00 3.02
2120 2713 1.839191 GCAGGGATGGATGTGCCTA 59.161 57.895 0.00 0.00 37.92 3.93
2235 2828 1.680989 GCCTTAACAACCCGGCCAT 60.681 57.895 2.24 0.00 36.56 4.40
2275 2868 0.320050 TTGTAGACTCGGTGCATGCA 59.680 50.000 18.46 18.46 0.00 3.96
2359 2952 3.688126 GCATGGGACCAAACTATGATGGA 60.688 47.826 0.00 0.00 39.12 3.41
2711 3304 2.760634 TAACAATGCGCTCAAGGAGA 57.239 45.000 9.73 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 0.665369 GAGCGAACGAGAACGGGAAA 60.665 55.000 0.00 0.00 44.46 3.13
37 38 2.506438 GGGAGCGAACGAGAACGG 60.506 66.667 0.00 0.00 44.46 4.44
84 85 1.115467 GGAGCTTGGAGGAGATCGAA 58.885 55.000 0.00 0.00 32.97 3.71
88 89 1.344191 GGCTGGAGCTTGGAGGAGAT 61.344 60.000 0.00 0.00 41.70 2.75
354 361 3.837146 TGAAGCAGAGACCAAAGAGATCT 59.163 43.478 0.00 0.00 0.00 2.75
540 551 4.570663 GCCTGCGTCGACGGCTAT 62.571 66.667 36.13 0.00 40.62 2.97
655 666 4.752879 GGCTGCAACCGACGCCTA 62.753 66.667 0.50 0.00 39.42 3.93
848 859 0.404040 GGGATGGAACTTGTGGACCA 59.596 55.000 0.00 0.00 36.83 4.02
1193 1204 0.604511 CGGCTCCGTAACCCAAAGTT 60.605 55.000 0.00 0.00 42.83 2.66
1194 1205 1.004200 CGGCTCCGTAACCCAAAGT 60.004 57.895 0.00 0.00 34.35 2.66
1204 1215 3.319198 AACCATCACCGGCTCCGT 61.319 61.111 0.00 0.00 37.81 4.69
1248 1259 3.136345 CTCCAGCAGCGCTCGAGAT 62.136 63.158 18.75 0.00 44.49 2.75
1254 1265 1.079543 CTTGTACTCCAGCAGCGCT 60.080 57.895 2.64 2.64 40.77 5.92
1331 1346 1.043816 GCTACCATCTGAGCTAGGCA 58.956 55.000 0.00 0.00 35.73 4.75
1367 1382 2.894126 GAGAAGTCACCAGAGTCCTCAA 59.106 50.000 0.00 0.00 0.00 3.02
1416 1431 1.810532 GCGAACTCCTCTCGACCAT 59.189 57.895 0.00 0.00 38.61 3.55
1649 1691 2.761416 GCCTTCCTCCCTGGATCATCTA 60.761 54.545 0.00 0.00 45.68 1.98
1731 2324 3.992943 TCTCCTTGGCCGAAAGATTTA 57.007 42.857 4.40 0.00 0.00 1.40
1783 2376 2.993937 AGTTTCTTCAACAACCCGACA 58.006 42.857 0.00 0.00 37.93 4.35
1785 2378 3.127895 CACAAGTTTCTTCAACAACCCGA 59.872 43.478 0.00 0.00 37.93 5.14
1809 2402 1.902508 CAAACTCCCTGAGTAGAGGCA 59.097 52.381 0.00 0.00 42.59 4.75
1881 2474 0.959553 GGAACAGACAGACCGAGTCA 59.040 55.000 6.78 0.00 38.46 3.41
1978 2571 3.470567 GCGTCTTCAGACACGGCG 61.471 66.667 4.80 4.80 44.99 6.46
2120 2713 1.411246 TCGAACCTACTGCGCCATAAT 59.589 47.619 4.18 0.00 0.00 1.28
2235 2828 2.623418 TCCTCTAAGTGCCTTCCTCA 57.377 50.000 0.00 0.00 0.00 3.86
2359 2952 3.383761 CGACGCCGGTAAATAGGTAAAT 58.616 45.455 1.90 0.00 0.00 1.40
2575 3168 2.146724 CCATGGCCCCGGACATAGA 61.147 63.158 0.73 0.00 42.92 1.98
2711 3304 1.747355 CTTTCGCCCATGCAAGAAGAT 59.253 47.619 0.00 0.00 37.32 2.40


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

AutoCloner maintained by Alex Coulton.