Multiple sequence alignment - TraesCS4D01G024600

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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 TraesCS4D01G024600 chr4D 100.000 2513 0 0 1 2513 10811338 10808826 0.000000e+00 4641.0
1 TraesCS4D01G024600 chr4D 97.189 676 19 0 1 676 10829107 10828432 0.000000e+00 1144.0
2 TraesCS4D01G024600 chr4B 95.221 1088 35 6 519 1593 20354446 20353363 0.000000e+00 1705.0
3 TraesCS4D01G024600 chr4B 90.505 1169 46 24 867 1979 20326185 20325026 0.000000e+00 1483.0
4 TraesCS4D01G024600 chr4B 95.192 520 20 2 1996 2513 20325045 20324529 0.000000e+00 817.0
5 TraesCS4D01G024600 chr4B 94.990 519 25 1 1996 2513 20352952 20352434 0.000000e+00 813.0
6 TraesCS4D01G024600 chr4B 94.847 524 22 3 1 520 20354995 20354473 0.000000e+00 813.0
7 TraesCS4D01G024600 chr4B 94.335 406 9 5 1584 1979 20353334 20352933 5.940000e-171 610.0
8 TraesCS4D01G024600 chr4B 89.712 243 11 6 1540 1777 17179541 17179774 5.260000e-77 298.0
9 TraesCS4D01G024600 chr4B 88.430 242 14 5 1542 1777 17216620 17216853 1.900000e-71 279.0
10 TraesCS4D01G024600 chr4A 90.941 1137 60 16 867 1975 592807413 592808534 0.000000e+00 1489.0
11 TraesCS4D01G024600 chr4A 90.781 1139 60 18 867 1975 593087672 593088795 0.000000e+00 1480.0
12 TraesCS4D01G024600 chr4A 90.464 1143 60 20 867 1975 592521114 592522241 0.000000e+00 1461.0
13 TraesCS4D01G024600 chr4A 90.131 1145 62 17 867 1975 591523194 591522065 0.000000e+00 1441.0
14 TraesCS4D01G024600 chr4A 88.528 523 49 4 1 520 592362143 592362657 7.630000e-175 623.0
15 TraesCS4D01G024600 chr4A 88.654 520 46 5 4 520 591293530 591293021 2.750000e-174 621.0
16 TraesCS4D01G024600 chr4A 88.506 522 48 5 1 519 591674804 591674292 2.750000e-174 621.0
17 TraesCS4D01G024600 chr4A 88.337 523 49 5 1 520 591347300 591346787 3.550000e-173 617.0
18 TraesCS4D01G024600 chr4A 88.145 523 50 5 1 520 592927476 592927989 1.650000e-171 612.0
19 TraesCS4D01G024600 chr4A 88.145 523 49 6 1 520 592335823 592336335 5.940000e-171 610.0
20 TraesCS4D01G024600 chr4A 87.954 523 51 5 1 520 592638092 592638605 7.690000e-170 606.0
21 TraesCS4D01G024600 chr4A 93.633 267 17 0 2000 2266 591522080 591521814 1.400000e-107 399.0
22 TraesCS4D01G024600 chr4A 93.258 267 18 0 2000 2266 593088780 593089046 6.520000e-106 394.0
23 TraesCS4D01G024600 chr4A 92.884 267 19 0 2000 2266 592522226 592522492 3.030000e-104 388.0
24 TraesCS4D01G024600 chr4A 92.884 267 19 0 2000 2266 592808519 592808785 3.030000e-104 388.0
25 TraesCS4D01G024600 chr4A 91.743 218 15 2 2296 2513 592523631 592523845 1.460000e-77 300.0
26 TraesCS4D01G024600 chr4A 91.743 218 15 2 2296 2513 593090185 593090399 1.460000e-77 300.0
27 TraesCS4D01G024600 chr4A 91.284 218 16 2 2296 2513 591520675 591520461 6.800000e-76 294.0
28 TraesCS4D01G024600 chr4A 91.284 218 16 2 2296 2513 592809924 592810138 6.800000e-76 294.0
29 TraesCS4D01G024600 chr4A 93.233 133 8 1 519 651 32715338 32715469 7.090000e-46 195.0
30 TraesCS4D01G024600 chr4A 89.630 135 12 2 519 651 591292994 591292860 1.200000e-38 171.0
31 TraesCS4D01G024600 chr4A 89.630 135 12 2 519 651 591346760 591346626 1.200000e-38 171.0
32 TraesCS4D01G024600 chr4A 89.630 135 12 2 519 651 591416279 591416145 1.200000e-38 171.0
33 TraesCS4D01G024600 chrUn 90.502 737 46 13 867 1593 390753515 390754237 0.000000e+00 952.0
34 TraesCS4D01G024600 chrUn 94.264 401 16 2 1581 1975 406815687 406816086 7.690000e-170 606.0
35 TraesCS4D01G024600 chrUn 93.258 267 18 0 2000 2266 406816071 406816337 6.520000e-106 394.0
36 TraesCS4D01G024600 chrUn 82.486 354 36 18 321 651 256114639 256114289 1.140000e-73 287.0
37 TraesCS4D01G024600 chrUn 77.169 219 42 8 2297 2513 76185220 76185432 1.220000e-23 121.0
38 TraesCS4D01G024600 chr5B 82.353 357 37 18 318 651 660880364 660880717 1.140000e-73 287.0
39 TraesCS4D01G024600 chr5B 82.353 357 37 18 318 651 660926313 660926666 1.140000e-73 287.0
40 TraesCS4D01G024600 chr5B 81.818 220 35 4 2295 2513 399795886 399796101 1.990000e-41 180.0
41 TraesCS4D01G024600 chr5B 79.487 195 32 7 1872 2062 621562269 621562459 5.640000e-27 132.0
42 TraesCS4D01G024600 chr3A 80.000 195 31 7 1872 2062 264954678 264954868 1.210000e-28 137.0
43 TraesCS4D01G024600 chr2B 81.006 179 28 6 2089 2264 23602662 23602837 1.210000e-28 137.0
44 TraesCS4D01G024600 chr1B 84.397 141 13 5 656 794 118428993 118428860 2.030000e-26 130.0
45 TraesCS4D01G024600 chr5A 85.039 127 12 5 656 781 398786993 398787113 3.390000e-24 122.0
46 TraesCS4D01G024600 chr3D 77.439 164 28 5 2297 2455 576317366 576317525 3.440000e-14 89.8
47 TraesCS4D01G024600 chr6D 78.462 130 28 0 2136 2265 68505254 68505125 4.450000e-13 86.1


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 TraesCS4D01G024600 chr4D 10808826 10811338 2512 True 4641.000000 4641 100.000000 1 2513 1 chr4D.!!$R1 2512
1 TraesCS4D01G024600 chr4D 10828432 10829107 675 True 1144.000000 1144 97.189000 1 676 1 chr4D.!!$R2 675
2 TraesCS4D01G024600 chr4B 20324529 20326185 1656 True 1150.000000 1483 92.848500 867 2513 2 chr4B.!!$R1 1646
3 TraesCS4D01G024600 chr4B 20352434 20354995 2561 True 985.250000 1705 94.848250 1 2513 4 chr4B.!!$R2 2512
4 TraesCS4D01G024600 chr4A 593087672 593090399 2727 False 724.666667 1480 91.927333 867 2513 3 chr4A.!!$F8 1646
5 TraesCS4D01G024600 chr4A 592807413 592810138 2725 False 723.666667 1489 91.703000 867 2513 3 chr4A.!!$F7 1646
6 TraesCS4D01G024600 chr4A 592521114 592523845 2731 False 716.333333 1461 91.697000 867 2513 3 chr4A.!!$F6 1646
7 TraesCS4D01G024600 chr4A 591520461 591523194 2733 True 711.333333 1441 91.682667 867 2513 3 chr4A.!!$R5 1646
8 TraesCS4D01G024600 chr4A 592362143 592362657 514 False 623.000000 623 88.528000 1 520 1 chr4A.!!$F3 519
9 TraesCS4D01G024600 chr4A 591674292 591674804 512 True 621.000000 621 88.506000 1 519 1 chr4A.!!$R2 518
10 TraesCS4D01G024600 chr4A 592927476 592927989 513 False 612.000000 612 88.145000 1 520 1 chr4A.!!$F5 519
11 TraesCS4D01G024600 chr4A 592335823 592336335 512 False 610.000000 610 88.145000 1 520 1 chr4A.!!$F2 519
12 TraesCS4D01G024600 chr4A 592638092 592638605 513 False 606.000000 606 87.954000 1 520 1 chr4A.!!$F4 519
13 TraesCS4D01G024600 chr4A 591292860 591293530 670 True 396.000000 621 89.142000 4 651 2 chr4A.!!$R3 647
14 TraesCS4D01G024600 chr4A 591346626 591347300 674 True 394.000000 617 88.983500 1 651 2 chr4A.!!$R4 650
15 TraesCS4D01G024600 chrUn 390753515 390754237 722 False 952.000000 952 90.502000 867 1593 1 chrUn.!!$F2 726
16 TraesCS4D01G024600 chrUn 406815687 406816337 650 False 500.000000 606 93.761000 1581 2266 2 chrUn.!!$F3 685

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
753 792 1.377612 GGGTTACCTGCTTTCCGGT 59.622 57.895 0.0 0.0 37.31 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2366 3630 3.43836 GTTGAATTGGCCGAGCTAATTG 58.562 45.455 19.42 0.0 46.6 2.32 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
97 99 2.074547 TTAAACCCGTGAGCTCTTCG 57.925 50.000 16.19 18.17 0.00 3.79
142 144 6.159988 AGCATTGATTAGATCGCTAACTACC 58.840 40.000 0.00 0.00 39.29 3.18
387 395 8.051468 TGTACCAATCCTCCAAATATATCCAA 57.949 34.615 0.00 0.00 0.00 3.53
416 424 8.634335 TGAAGGATGAAAGACAAAACATGATA 57.366 30.769 0.00 0.00 0.00 2.15
479 487 8.147058 AGATTGTAGCAGATCATAGTTAAGGTG 58.853 37.037 0.00 0.00 0.00 4.00
753 792 1.377612 GGGTTACCTGCTTTCCGGT 59.622 57.895 0.00 0.00 37.31 5.28
1020 1068 0.394762 TGGCCATCATCAAGCAGTCC 60.395 55.000 0.00 0.00 0.00 3.85
1118 1172 0.512952 GACAATCTGTGTGTCGGCAC 59.487 55.000 14.58 14.58 41.96 5.01
1227 1287 0.935196 AAAGCACGTCCAACGAAGAC 59.065 50.000 6.48 0.00 46.05 3.01
1254 1314 3.764049 GTCGCCAACGTCGCACTC 61.764 66.667 8.16 0.00 41.18 3.51
1502 1562 1.252904 GGCAGAGCCCTCATTTGCAA 61.253 55.000 0.00 0.00 44.06 4.08
1532 1592 5.352569 AGTGATCGTTGTCAGGATTTTCATC 59.647 40.000 0.00 0.00 0.00 2.92
1608 1747 8.936070 TGTGTGTGTGATTTAGTATATGGTAC 57.064 34.615 0.00 0.00 0.00 3.34
1749 1892 3.828451 TCAAAAGGAAGCTGGAAATGGAG 59.172 43.478 0.00 0.00 0.00 3.86
1843 1992 7.402811 TGTACTGTAGCGCATTAATTGATAC 57.597 36.000 11.47 0.00 0.00 2.24
1852 2001 5.347635 GCGCATTAATTGATACATACTCCGA 59.652 40.000 0.30 0.00 0.00 4.55
2290 2549 1.559682 GCCTTCACCTCCCACAAGATA 59.440 52.381 0.00 0.00 0.00 1.98
2323 3583 9.444534 CTCGACATAATGCTCATATATGTACTC 57.555 37.037 12.42 1.94 39.64 2.59
2346 3606 6.353323 TCTGTATCCGAATCCATTGCTTTAA 58.647 36.000 0.00 0.00 0.00 1.52
2347 3607 6.826231 TCTGTATCCGAATCCATTGCTTTAAA 59.174 34.615 0.00 0.00 0.00 1.52
2348 3608 7.012327 TCTGTATCCGAATCCATTGCTTTAAAG 59.988 37.037 11.02 11.02 0.00 1.85
2366 3630 7.435488 GCTTTAAAGAAGAAGAAGGGACAAAAC 59.565 37.037 19.48 0.00 0.00 2.43
2398 3662 1.608590 CCAATTCAACGGACACTTGCT 59.391 47.619 0.00 0.00 0.00 3.91
2400 3664 0.593128 ATTCAACGGACACTTGCTGC 59.407 50.000 0.00 0.00 0.00 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 2.335316 AATTTGGGCGCGGTAATCTA 57.665 45.000 8.83 0.00 0.00 1.98
97 99 5.124776 TGCTACTATTATTGGTTTGTGGCAC 59.875 40.000 11.55 11.55 37.09 5.01
142 144 1.365699 CCATCCCACGAGGTTAAACG 58.634 55.000 0.00 0.00 36.75 3.60
387 395 5.360714 TGTTTTGTCTTTCATCCTTCAAGCT 59.639 36.000 0.00 0.00 0.00 3.74
416 424 1.603455 CCCTTCACGTGGCCACAAT 60.603 57.895 34.16 19.81 0.00 2.71
479 487 6.183360 CGCAAGAATTTTAAATGCCAAGTACC 60.183 38.462 5.40 0.00 43.02 3.34
736 775 1.017701 CGACCGGAAAGCAGGTAACC 61.018 60.000 9.46 0.00 42.94 2.85
766 805 3.188786 GCGAGCGTTCCGAGCATT 61.189 61.111 0.00 0.00 37.01 3.56
783 822 1.546834 GAGGACTTACTAGTTGCGCG 58.453 55.000 0.00 0.00 33.84 6.86
1020 1068 1.209019 AGCAGCACTAGGACAATGAGG 59.791 52.381 0.00 0.00 0.00 3.86
1204 1264 2.157834 TCGTTGGACGTGCTTTATGT 57.842 45.000 8.99 0.00 43.14 2.29
1289 1349 1.009829 GAAGCATGGCGTGAAGGTAG 58.990 55.000 11.71 0.00 0.00 3.18
1497 1557 0.179032 ACGATCACTGTGGGTTGCAA 60.179 50.000 8.11 0.00 0.00 4.08
1502 1562 0.756294 TGACAACGATCACTGTGGGT 59.244 50.000 8.11 1.30 0.00 4.51
1532 1592 0.467474 ATCATGGTGCAGCTGATGGG 60.467 55.000 20.43 0.77 0.00 4.00
1608 1747 6.530120 TGGCACAACCATACCATATTACTAG 58.470 40.000 0.00 0.00 46.36 2.57
1749 1892 9.191995 CTTATACAACCAACCATTCTTTTGTTC 57.808 33.333 0.00 0.00 0.00 3.18
1843 1992 3.611766 ACAAAGGGAGTTCGGAGTATG 57.388 47.619 0.00 0.00 0.00 2.39
1852 2001 6.940867 GTGAGTATTTAGGAACAAAGGGAGTT 59.059 38.462 0.00 0.00 0.00 3.01
2024 2173 8.941977 AGTATTTGTAGTGATTGCAATACGAAA 58.058 29.630 12.97 10.06 46.18 3.46
2039 2188 9.924650 CCGCTCCTAAATATAAGTATTTGTAGT 57.075 33.333 4.20 0.00 40.01 2.73
2290 2549 5.268118 TGAGCATTATGTCGAGTCAAGAT 57.732 39.130 0.00 0.00 0.00 2.40
2323 3583 6.618287 TTAAAGCAATGGATTCGGATACAG 57.382 37.500 0.00 0.00 27.13 2.74
2346 3606 7.423844 AATTGTTTTGTCCCTTCTTCTTCTT 57.576 32.000 0.00 0.00 0.00 2.52
2347 3607 7.255625 GCTAATTGTTTTGTCCCTTCTTCTTCT 60.256 37.037 0.00 0.00 0.00 2.85
2348 3608 6.863645 GCTAATTGTTTTGTCCCTTCTTCTTC 59.136 38.462 0.00 0.00 0.00 2.87
2366 3630 3.438360 GTTGAATTGGCCGAGCTAATTG 58.562 45.455 19.42 0.00 46.60 2.32


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

AutoCloner maintained by Alex Coulton.