Multiple sequence alignment - TraesCS4D01G154000

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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 TraesCS4D01G154000 chr4D 100.000 3080 0 0 1 3080 198581690 198584769 0.000000e+00 5688
1 TraesCS4D01G154000 chr7A 98.336 3005 42 4 80 3080 613710813 613713813 0.000000e+00 5265
2 TraesCS4D01G154000 chr7A 98.474 1114 13 2 1971 3080 712101793 712102906 0.000000e+00 1960
3 TraesCS4D01G154000 chr7A 98.179 604 11 0 80 683 712099195 712099798 0.000000e+00 1055
4 TraesCS4D01G154000 chr7A 97.068 614 18 0 704 1317 712099787 712100400 0.000000e+00 1035
5 TraesCS4D01G154000 chr7A 87.149 498 30 17 2615 3080 449710831 449711326 4.520000e-148 534
6 TraesCS4D01G154000 chr7A 94.690 113 6 0 1480 1592 672597472 672597360 3.160000e-40 176
7 TraesCS4D01G154000 chr7A 100.000 82 0 0 1 82 613710684 613710765 5.320000e-33 152
8 TraesCS4D01G154000 chr5B 96.008 3006 93 11 80 3080 386152740 386155723 0.000000e+00 4861
9 TraesCS4D01G154000 chr5B 96.341 82 3 0 1 82 386152610 386152691 5.360000e-28 135
10 TraesCS4D01G154000 chr4A 95.806 3004 118 5 80 3080 658607660 658610658 0.000000e+00 4843
11 TraesCS4D01G154000 chr4A 96.429 252 9 0 2249 2500 374575844 374576095 1.710000e-112 416
12 TraesCS4D01G154000 chr4A 92.683 82 6 0 1 82 658607534 658607615 5.400000e-23 119
13 TraesCS4D01G154000 chr2A 95.933 2213 80 7 872 3080 596501776 596499570 0.000000e+00 3579
14 TraesCS4D01G154000 chr2A 94.763 802 25 5 80 876 595998410 595999199 0.000000e+00 1232
15 TraesCS4D01G154000 chr2A 91.252 503 32 9 1851 2349 207107984 207108478 0.000000e+00 675
16 TraesCS4D01G154000 chr2A 88.663 344 27 8 80 413 58012625 58012966 2.860000e-110 409
17 TraesCS4D01G154000 chr2A 83.462 260 32 9 1275 1533 595998950 595999199 6.640000e-57 231
18 TraesCS4D01G154000 chr2A 97.531 81 2 0 2 82 595998277 595998357 4.140000e-29 139
19 TraesCS4D01G154000 chr2A 98.333 60 1 0 1 60 58012489 58012548 4.200000e-19 106
20 TraesCS4D01G154000 chr3B 95.675 1549 61 5 80 1626 534149511 534147967 0.000000e+00 2484
21 TraesCS4D01G154000 chr3B 93.889 180 11 0 1614 1793 534143206 534143027 3.910000e-69 272
22 TraesCS4D01G154000 chr3B 95.833 72 3 0 9 80 534149640 534149569 1.940000e-22 117
23 TraesCS4D01G154000 chr6A 90.130 1844 129 24 442 2249 36691061 36692887 0.000000e+00 2348
24 TraesCS4D01G154000 chr6B 91.352 1642 115 16 623 2250 67994962 67996590 0.000000e+00 2220
25 TraesCS4D01G154000 chr6B 96.838 854 25 1 80 933 254030407 254029556 0.000000e+00 1426
26 TraesCS4D01G154000 chr6B 94.182 275 16 0 2806 3080 711437687 711437961 1.320000e-113 420
27 TraesCS4D01G154000 chr5A 98.205 1114 16 2 1971 3080 605038449 605039562 0.000000e+00 1943
28 TraesCS4D01G154000 chr5A 97.848 604 13 0 80 683 605035851 605036454 0.000000e+00 1044
29 TraesCS4D01G154000 chr5A 97.068 614 18 0 704 1317 605036443 605037056 0.000000e+00 1035
30 TraesCS4D01G154000 chr5A 93.548 527 32 2 1349 1874 174257363 174257888 0.000000e+00 784
31 TraesCS4D01G154000 chr5A 86.747 498 32 17 2615 3080 641407272 641407767 9.790000e-145 523
32 TraesCS4D01G154000 chr2D 91.633 502 29 10 1851 2349 107760340 107760831 0.000000e+00 682
33 TraesCS4D01G154000 chr2D 85.301 449 28 21 1 414 56639777 56640222 2.190000e-116 429
34 TraesCS4D01G154000 chr2D 86.104 367 38 9 2257 2614 605564232 605563870 1.730000e-102 383
35 TraesCS4D01G154000 chr1A 92.000 375 27 1 2249 2620 218981623 218981997 9.790000e-145 523
36 TraesCS4D01G154000 chr5D 93.426 289 19 0 2792 3080 64813546 64813834 2.190000e-116 429
37 TraesCS4D01G154000 chr1B 93.080 289 20 0 2792 3080 580159303 580159591 1.020000e-114 424
38 TraesCS4D01G154000 chr2B 96.825 252 8 0 2249 2500 190041027 190040776 3.670000e-114 422
39 TraesCS4D01G154000 chr2B 89.521 334 28 4 83 414 66809192 66808864 1.710000e-112 416
40 TraesCS4D01G154000 chr2B 88.201 339 24 9 85 414 89702614 89702945 1.040000e-104 390
41 TraesCS4D01G154000 chr2B 92.683 82 5 1 1 82 66809322 66809242 1.940000e-22 117
42 TraesCS4D01G154000 chr2B 96.970 66 1 1 1 65 89702489 89702554 3.250000e-20 110
43 TraesCS4D01G154000 chrUn 92.982 171 11 1 2619 2788 39528803 39528633 6.600000e-62 248


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 TraesCS4D01G154000 chr4D 198581690 198584769 3079 False 5688.000000 5688 100.000000 1 3080 1 chr4D.!!$F1 3079
1 TraesCS4D01G154000 chr7A 613710684 613713813 3129 False 2708.500000 5265 99.168000 1 3080 2 chr7A.!!$F2 3079
2 TraesCS4D01G154000 chr7A 712099195 712102906 3711 False 1350.000000 1960 97.907000 80 3080 3 chr7A.!!$F3 3000
3 TraesCS4D01G154000 chr5B 386152610 386155723 3113 False 2498.000000 4861 96.174500 1 3080 2 chr5B.!!$F1 3079
4 TraesCS4D01G154000 chr4A 658607534 658610658 3124 False 2481.000000 4843 94.244500 1 3080 2 chr4A.!!$F2 3079
5 TraesCS4D01G154000 chr2A 596499570 596501776 2206 True 3579.000000 3579 95.933000 872 3080 1 chr2A.!!$R1 2208
6 TraesCS4D01G154000 chr2A 595998277 595999199 922 False 534.000000 1232 91.918667 2 1533 3 chr2A.!!$F3 1531
7 TraesCS4D01G154000 chr3B 534147967 534149640 1673 True 1300.500000 2484 95.754000 9 1626 2 chr3B.!!$R2 1617
8 TraesCS4D01G154000 chr6A 36691061 36692887 1826 False 2348.000000 2348 90.130000 442 2249 1 chr6A.!!$F1 1807
9 TraesCS4D01G154000 chr6B 67994962 67996590 1628 False 2220.000000 2220 91.352000 623 2250 1 chr6B.!!$F1 1627
10 TraesCS4D01G154000 chr6B 254029556 254030407 851 True 1426.000000 1426 96.838000 80 933 1 chr6B.!!$R1 853
11 TraesCS4D01G154000 chr5A 605035851 605039562 3711 False 1340.666667 1943 97.707000 80 3080 3 chr5A.!!$F3 3000
12 TraesCS4D01G154000 chr5A 174257363 174257888 525 False 784.000000 784 93.548000 1349 1874 1 chr5A.!!$F1 525

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
262 327 2.695147 AGCAGTTTTTCAGAAAGGTGGG 59.305 45.455 0.00 0.0 0.0 4.61 F
1167 1272 5.371526 CTGATGCTCCTTAAGATTTGGCTA 58.628 41.667 3.36 0.0 0.0 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1098 1202 1.700186 GGATCATTGAGGTAGTCCCCC 59.300 57.143 0.00 0.0 0.00 5.4 R
2560 3701 1.002069 TCCTGGGCCATGAACAGATT 58.998 50.000 6.72 0.0 34.21 2.4 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
262 327 2.695147 AGCAGTTTTTCAGAAAGGTGGG 59.305 45.455 0.00 0.00 0.00 4.61
1167 1272 5.371526 CTGATGCTCCTTAAGATTTGGCTA 58.628 41.667 3.36 0.00 0.00 3.93
1579 2681 6.894682 TGCTTGTCTGGGTGAACAATATATA 58.105 36.000 0.00 0.00 0.00 0.86
1992 3126 7.630026 TCATTTTGTTATATTCAGCGCTGTAG 58.370 34.615 34.70 12.36 0.00 2.74
2124 3261 1.969256 CGAATTGCGTGAAAAGGAACG 59.031 47.619 0.00 0.00 42.61 3.95
2560 3701 1.281867 CCCACTTCTGTTCATGCCCTA 59.718 52.381 0.00 0.00 0.00 3.53
2664 3805 4.341806 TCATTGTTGCTTTGACCATCTGTT 59.658 37.500 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
257 322 3.637273 AGCCGAGTCAACCCCACC 61.637 66.667 0.00 0.0 0.00 4.61
262 327 0.815734 TAGCTACAGCCGAGTCAACC 59.184 55.000 0.00 0.0 43.38 3.77
1098 1202 1.700186 GGATCATTGAGGTAGTCCCCC 59.300 57.143 0.00 0.0 0.00 5.40
1202 1307 4.636249 AGTCCTGTAGAAAAAGCAGAGTG 58.364 43.478 0.00 0.0 32.39 3.51
1279 1386 2.449137 AATCATGAAAGGAGGCAGGG 57.551 50.000 0.00 0.0 0.00 4.45
1579 2681 5.945784 TCCCTGAAAAATCAAATCGTGATCT 59.054 36.000 0.00 0.0 46.80 2.75
2055 3190 7.011109 CCTTAACAATAGTCGTTAACCTGGATG 59.989 40.741 0.00 0.0 34.68 3.51
2124 3261 2.385315 GAAGGCGCAAGAACTTCAAAC 58.615 47.619 10.83 0.0 45.90 2.93
2560 3701 1.002069 TCCTGGGCCATGAACAGATT 58.998 50.000 6.72 0.0 34.21 2.40
2664 3805 6.262944 CCATTGGTTCTTCGATAATTGATGGA 59.737 38.462 0.00 0.0 32.85 3.41


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

AutoCloner maintained by Alex Coulton.