Multiple sequence alignment - TraesCS3B01G291800

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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 TraesCS3B01G291800 chr3B 100.000 2534 0 0 1 2534 469810331 469807798 0.000000e+00 4680
1 TraesCS3B01G291800 chr3B 88.521 1298 121 16 705 1991 637642759 637641479 0.000000e+00 1546
2 TraesCS3B01G291800 chr3B 95.371 821 36 2 1715 2534 696567019 696567838 0.000000e+00 1304
3 TraesCS3B01G291800 chr3B 92.426 713 44 6 1 709 696564849 696565555 0.000000e+00 1009
4 TraesCS3B01G291800 chr3B 90.616 714 56 9 3 709 749482550 749481841 0.000000e+00 937
5 TraesCS3B01G291800 chr3B 91.358 162 11 3 2375 2534 1651393 1651553 4.240000e-53 219
6 TraesCS3B01G291800 chr5B 94.820 1834 84 9 705 2534 77879229 77881055 0.000000e+00 2850
7 TraesCS3B01G291800 chr5B 89.400 717 66 7 1 709 697910898 697910184 0.000000e+00 894
8 TraesCS3B01G291800 chr2B 95.213 1734 69 11 705 2428 485157907 485156178 0.000000e+00 2730
9 TraesCS3B01G291800 chr2B 91.630 1374 91 15 1171 2531 739343521 739344883 0.000000e+00 1879
10 TraesCS3B01G291800 chr2B 92.587 715 45 5 1 709 485158650 485157938 0.000000e+00 1020
11 TraesCS3B01G291800 chr1B 91.047 1452 110 15 1090 2534 451655504 451656942 0.000000e+00 1943
12 TraesCS3B01G291800 chr1B 92.228 1248 86 9 705 1949 451610446 451611685 0.000000e+00 1757
13 TraesCS3B01G291800 chr1B 92.479 718 42 9 1 709 596114771 596114057 0.000000e+00 1016
14 TraesCS3B01G291800 chr1B 90.350 715 59 8 1 709 18353330 18352620 0.000000e+00 929
15 TraesCS3B01G291800 chr1B 89.679 717 63 8 1 709 39833595 39834308 0.000000e+00 904
16 TraesCS3B01G291800 chr1B 90.588 595 42 10 1949 2534 451611925 451612514 0.000000e+00 776
17 TraesCS3B01G291800 chr1B 93.636 440 26 2 1747 2185 596112786 596112348 0.000000e+00 656
18 TraesCS3B01G291800 chr1B 90.959 365 22 2 2180 2534 596103627 596103264 4.900000e-132 481
19 TraesCS3B01G291800 chr1B 92.593 162 9 3 2375 2534 18294381 18294221 1.960000e-56 230
20 TraesCS3B01G291800 chr2D 89.340 1304 115 17 705 1991 355444971 355443675 0.000000e+00 1616
21 TraesCS3B01G291800 chr2D 90.934 717 55 8 1 709 355445717 355445003 0.000000e+00 955
22 TraesCS3B01G291800 chr2D 91.011 178 10 5 2137 2313 355443610 355443438 4.210000e-58 235
23 TraesCS3B01G291800 chr2D 93.421 76 4 1 1999 2073 355443727 355443652 7.410000e-21 111
24 TraesCS3B01G291800 chr6D 89.264 1304 116 17 705 1991 464546152 464547448 0.000000e+00 1611
25 TraesCS3B01G291800 chr6D 90.934 717 53 10 1 709 464545408 464546120 0.000000e+00 953
26 TraesCS3B01G291800 chr6D 91.925 161 10 3 2375 2534 464547714 464547872 3.280000e-54 222
27 TraesCS3B01G291800 chr5A 87.539 1292 130 22 711 1989 119653266 119651993 0.000000e+00 1465
28 TraesCS3B01G291800 chr5A 86.047 344 31 11 1999 2334 119652042 119651708 1.120000e-93 353


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 TraesCS3B01G291800 chr3B 469807798 469810331 2533 True 4680.000000 4680 100.000000 1 2534 1 chr3B.!!$R1 2533
1 TraesCS3B01G291800 chr3B 637641479 637642759 1280 True 1546.000000 1546 88.521000 705 1991 1 chr3B.!!$R2 1286
2 TraesCS3B01G291800 chr3B 696564849 696567838 2989 False 1156.500000 1304 93.898500 1 2534 2 chr3B.!!$F2 2533
3 TraesCS3B01G291800 chr3B 749481841 749482550 709 True 937.000000 937 90.616000 3 709 1 chr3B.!!$R3 706
4 TraesCS3B01G291800 chr5B 77879229 77881055 1826 False 2850.000000 2850 94.820000 705 2534 1 chr5B.!!$F1 1829
5 TraesCS3B01G291800 chr5B 697910184 697910898 714 True 894.000000 894 89.400000 1 709 1 chr5B.!!$R1 708
6 TraesCS3B01G291800 chr2B 739343521 739344883 1362 False 1879.000000 1879 91.630000 1171 2531 1 chr2B.!!$F1 1360
7 TraesCS3B01G291800 chr2B 485156178 485158650 2472 True 1875.000000 2730 93.900000 1 2428 2 chr2B.!!$R1 2427
8 TraesCS3B01G291800 chr1B 451655504 451656942 1438 False 1943.000000 1943 91.047000 1090 2534 1 chr1B.!!$F2 1444
9 TraesCS3B01G291800 chr1B 451610446 451612514 2068 False 1266.500000 1757 91.408000 705 2534 2 chr1B.!!$F3 1829
10 TraesCS3B01G291800 chr1B 18352620 18353330 710 True 929.000000 929 90.350000 1 709 1 chr1B.!!$R2 708
11 TraesCS3B01G291800 chr1B 39833595 39834308 713 False 904.000000 904 89.679000 1 709 1 chr1B.!!$F1 708
12 TraesCS3B01G291800 chr1B 596112348 596114771 2423 True 836.000000 1016 93.057500 1 2185 2 chr1B.!!$R4 2184
13 TraesCS3B01G291800 chr2D 355443438 355445717 2279 True 729.250000 1616 91.176500 1 2313 4 chr2D.!!$R1 2312
14 TraesCS3B01G291800 chr6D 464545408 464547872 2464 False 928.666667 1611 90.707667 1 2534 3 chr6D.!!$F1 2533
15 TraesCS3B01G291800 chr5A 119651708 119653266 1558 True 909.000000 1465 86.793000 711 2334 2 chr5A.!!$R1 1623

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
364 374 1.068333 GTGCTGTTTGCCATGTTCGAT 60.068 47.619 0.0 0.0 42.00 3.59 F
1234 1329 1.001378 CAACACTAACAGCTTGGTGCC 60.001 52.381 2.1 0.0 41.43 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1337 1432 0.251165 AGGAAAACACCGTGGGGATG 60.251 55.0 3.03 0.0 36.97 3.51 R
2445 3232 4.954202 AGAACAGATTTCATGCACCATCAT 59.046 37.5 0.00 0.0 0.00 2.45 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
134 140 4.938080 TCATCAACGAGCTCTAGGAAATC 58.062 43.478 12.85 0.00 0.00 2.17
137 143 3.381908 TCAACGAGCTCTAGGAAATCTCC 59.618 47.826 12.85 0.00 42.81 3.71
165 174 6.701145 TCATGTTTTGTAAGCAACCTACAA 57.299 33.333 0.00 0.00 33.82 2.41
305 315 1.831736 CCAAGAGGGTGTACGAGGAAT 59.168 52.381 0.00 0.00 0.00 3.01
324 334 5.961421 AGGAATAGAGGTAAGAGCTTTGAGT 59.039 40.000 0.00 0.00 0.00 3.41
364 374 1.068333 GTGCTGTTTGCCATGTTCGAT 60.068 47.619 0.00 0.00 42.00 3.59
371 381 4.023963 TGTTTGCCATGTTCGATTTTCGTA 60.024 37.500 0.00 0.00 41.35 3.43
401 411 2.880822 ATGCGAAACAGATGAACACG 57.119 45.000 0.00 0.00 0.00 4.49
441 452 2.485426 CACACTCATTACAGCAACAGGG 59.515 50.000 0.00 0.00 0.00 4.45
492 503 6.719370 AGGCACACTAAAGGAATAATTTGTCA 59.281 34.615 0.00 0.00 0.00 3.58
501 512 7.976414 AAGGAATAATTTGTCATGGGAATCA 57.024 32.000 0.00 0.00 0.00 2.57
590 601 4.840115 AGGAGGATGAATCAAAGCCAAAAA 59.160 37.500 0.00 0.00 0.00 1.94
605 617 3.372514 GCCAAAAACACCGAAAAACATGT 59.627 39.130 0.00 0.00 0.00 3.21
676 694 9.883142 TTTTTCAAGGTTGTATTGATTTTCTGT 57.117 25.926 0.00 0.00 36.60 3.41
768 858 9.463443 AGCAATGTTGAAGTTATAAGAACAAAC 57.537 29.630 0.00 0.00 30.75 2.93
986 1080 4.654262 AGAGTTTGGAGGTCTGTTACAGAA 59.346 41.667 17.25 0.00 42.46 3.02
1234 1329 1.001378 CAACACTAACAGCTTGGTGCC 60.001 52.381 2.10 0.00 41.43 5.01
1279 1374 4.644685 GGGCAGCAGATAACAATTTCCTAA 59.355 41.667 0.00 0.00 0.00 2.69
1296 1391 1.169661 TAAGTGCTTGGTTGGCGGTG 61.170 55.000 0.00 0.00 0.00 4.94
1337 1432 3.003378 GCTCCTACCACAAGTTTGAACAC 59.997 47.826 0.00 0.00 0.00 3.32
1470 1565 0.308684 ATGCAGTCTGTTGTTGCGTG 59.691 50.000 0.93 0.00 40.62 5.34
1538 1634 7.615757 TCATAGTTTCTCATCTAGTTGACCTCA 59.384 37.037 0.00 0.00 0.00 3.86
1760 2282 3.541071 TGTTTGTGAAGCACATGATCG 57.459 42.857 0.00 0.00 44.16 3.69
1819 2343 6.239008 CCGCCATTTGTTTTGAGGTCATATAT 60.239 38.462 0.00 0.00 0.00 0.86
1834 2358 7.749666 AGGTCATATATATGTCAGGCAACTTT 58.250 34.615 19.78 2.82 38.95 2.66
1851 2375 5.305585 CAACTTTCCAAGTAACTGCTAGGA 58.694 41.667 0.00 0.00 41.91 2.94
1976 2742 5.804639 AGGCAATACAGACACATACTTCAA 58.195 37.500 0.00 0.00 0.00 2.69
1991 2757 7.959651 CACATACTTCAAGCAACTACAGATTTC 59.040 37.037 0.00 0.00 0.00 2.17
1997 2763 9.424319 CTTCAAGCAACTACAGATTTCTAAGTA 57.576 33.333 0.00 0.00 0.00 2.24
2136 2905 9.574516 AATAGAAAAAGTTGTGAATACTCCAGT 57.425 29.630 0.00 0.00 0.00 4.00
2395 3179 7.272978 ACAAGTTCTAATATACGTGCCTCAAT 58.727 34.615 0.00 0.00 0.00 2.57
2445 3232 5.401550 CACAGAAACAAAAGAAGCTTGTCA 58.598 37.500 2.10 0.00 35.98 3.58
2519 3306 4.132122 ACAGGGAATTGGGAAACTTGAT 57.868 40.909 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
134 140 7.254421 GGTTGCTTACAAAACATGAAAAAGGAG 60.254 37.037 0.00 0.00 37.58 3.69
137 143 7.538303 AGGTTGCTTACAAAACATGAAAAAG 57.462 32.000 0.00 0.00 37.58 2.27
141 147 6.701145 TGTAGGTTGCTTACAAAACATGAA 57.299 33.333 0.00 0.00 37.58 2.57
234 244 2.286365 TCCTTGCCTCGGACATTTTT 57.714 45.000 0.00 0.00 0.00 1.94
305 315 4.220821 CCACACTCAAAGCTCTTACCTCTA 59.779 45.833 0.00 0.00 0.00 2.43
324 334 3.899981 GACGCTCCACCATGCCACA 62.900 63.158 0.00 0.00 0.00 4.17
441 452 2.930950 TGTAGCCAATCATAGTTGGGC 58.069 47.619 7.68 0.00 46.97 5.36
471 482 7.893302 TCCCATGACAAATTATTCCTTTAGTGT 59.107 33.333 0.00 0.00 0.00 3.55
501 512 5.802465 CATTGCTATCTATGTCTGATGGGT 58.198 41.667 0.00 0.00 0.00 4.51
590 601 4.098654 TCATTTCCACATGTTTTTCGGTGT 59.901 37.500 0.00 0.00 0.00 4.16
768 858 7.207383 TGTTTGTCCTATACAGAATACCATCG 58.793 38.462 0.00 0.00 39.87 3.84
995 1089 3.133721 ACTTAAGTCTCCTGGCATGCTAG 59.866 47.826 23.17 23.17 0.00 3.42
1207 1302 1.417890 AGCTGTTAGTGTTGGTGAGCT 59.582 47.619 0.00 0.00 0.00 4.09
1234 1329 5.186409 CCCCAGCCATATCCTTAATCATTTG 59.814 44.000 0.00 0.00 0.00 2.32
1279 1374 2.906897 CACCGCCAACCAAGCACT 60.907 61.111 0.00 0.00 0.00 4.40
1296 1391 1.751351 GCAAGGAAACAGGATAAGGCC 59.249 52.381 0.00 0.00 0.00 5.19
1302 1397 2.239907 GGTAGGAGCAAGGAAACAGGAT 59.760 50.000 0.00 0.00 0.00 3.24
1337 1432 0.251165 AGGAAAACACCGTGGGGATG 60.251 55.000 3.03 0.00 36.97 3.51
1470 1565 9.760660 CAAGTTAGACTTACAACTAAATGCATC 57.239 33.333 0.00 0.00 36.03 3.91
1587 1691 5.150715 TCCAATGAGTCCAGATATAGCAGT 58.849 41.667 0.00 0.00 0.00 4.40
1708 1817 1.457009 TACCCGCAACTTGCCAAACC 61.457 55.000 8.20 0.00 41.12 3.27
1760 2282 7.316544 TGAAGAAAAACTAAAGTGACTGACC 57.683 36.000 0.00 0.00 0.00 4.02
1834 2358 4.101898 TGTGTTTCCTAGCAGTTACTTGGA 59.898 41.667 0.00 0.00 39.39 3.53
1851 2375 3.687698 GCCTACGTATGGACAATGTGTTT 59.312 43.478 13.28 0.00 0.00 2.83
1991 2757 8.106247 TGCCTTTGATTGGTTTAACTACTTAG 57.894 34.615 0.00 0.00 0.00 2.18
1997 2763 7.232534 TCTGTATTGCCTTTGATTGGTTTAACT 59.767 33.333 0.00 0.00 0.00 2.24
2445 3232 4.954202 AGAACAGATTTCATGCACCATCAT 59.046 37.500 0.00 0.00 0.00 2.45


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

AutoCloner maintained by Alex Coulton.