Multiple sequence alignment - TraesCS3D01G042000

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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 TraesCS3D01G042000 chr3D 100.000 2492 0 0 1 2492 16121524 16119033 0.000000e+00 4602
1 TraesCS3D01G042000 chr3D 96.233 1513 39 5 3 1503 468665808 468664302 0.000000e+00 2462
2 TraesCS3D01G042000 chr3D 92.027 1505 70 17 2 1503 356977894 356976437 0.000000e+00 2069
3 TraesCS3D01G042000 chr3D 92.829 1018 33 11 1503 2492 468658515 468657510 0.000000e+00 1439
4 TraesCS3D01G042000 chr3D 97.066 818 24 0 686 1503 578322983 578322166 0.000000e+00 1378
5 TraesCS3D01G042000 chr3D 93.720 844 24 5 2 842 182085063 182085880 0.000000e+00 1238
6 TraesCS3D01G042000 chr3D 93.321 539 23 2 1503 2028 152708785 152709323 0.000000e+00 784
7 TraesCS3D01G042000 chr4A 93.896 1540 50 19 1 1503 693356499 693354967 0.000000e+00 2283
8 TraesCS3D01G042000 chr4A 90.607 1022 44 12 1503 2492 693351781 693350780 0.000000e+00 1308
9 TraesCS3D01G042000 chr7D 93.714 1543 41 13 1 1503 154001804 154003330 0.000000e+00 2261
10 TraesCS3D01G042000 chr7D 92.815 1016 37 8 1503 2492 154007742 154008747 0.000000e+00 1439
11 TraesCS3D01G042000 chr7D 95.616 844 22 3 2 842 574241218 574240387 0.000000e+00 1339
12 TraesCS3D01G042000 chr7D 93.135 539 24 2 1503 2028 508809465 508810003 0.000000e+00 778
13 TraesCS3D01G042000 chr1D 91.960 1505 66 17 2 1503 346200148 346198696 0.000000e+00 2058
14 TraesCS3D01G042000 chr1D 81.798 445 42 24 2071 2491 346194266 346193837 1.100000e-88 337
15 TraesCS3D01G042000 chr2B 91.905 1013 33 11 1503 2492 54447216 54446230 0.000000e+00 1371
16 TraesCS3D01G042000 chr2B 91.143 700 33 15 1 671 54453502 54452803 0.000000e+00 922
17 TraesCS3D01G042000 chr6B 91.609 1013 36 5 1503 2492 149430585 149431571 0.000000e+00 1354
18 TraesCS3D01G042000 chr6B 90.602 681 45 7 1 662 149424467 149425147 0.000000e+00 885
19 TraesCS3D01G042000 chr6B 94.094 491 16 1 1503 1980 169163471 169162981 0.000000e+00 734
20 TraesCS3D01G042000 chr6B 94.094 491 16 1 1503 1980 558309087 558308597 0.000000e+00 734
21 TraesCS3D01G042000 chr5D 91.115 1013 54 9 1503 2491 284891120 284892120 0.000000e+00 1339
22 TraesCS3D01G042000 chr5D 95.926 761 31 0 743 1503 284885981 284886741 0.000000e+00 1234
23 TraesCS3D01G042000 chr5D 93.602 844 25 5 2 842 78754935 78755752 0.000000e+00 1232
24 TraesCS3D01G042000 chr5D 95.325 770 36 0 734 1503 489756318 489757087 0.000000e+00 1223
25 TraesCS3D01G042000 chr5D 95.157 702 34 0 802 1503 525156593 525157294 0.000000e+00 1109
26 TraesCS3D01G042000 chr5D 81.798 445 42 23 2071 2491 78757982 78758411 1.100000e-88 337
27 TraesCS3D01G042000 chr5D 81.839 446 40 24 2071 2491 125664184 125664613 1.100000e-88 337
28 TraesCS3D01G042000 chr3A 90.693 1010 62 19 1509 2492 670752539 670751536 0.000000e+00 1315
29 TraesCS3D01G042000 chr6D 94.689 772 37 4 734 1503 100211333 100210564 0.000000e+00 1195
30 TraesCS3D01G042000 chr7B 94.767 707 36 1 802 1508 719468145 719467440 0.000000e+00 1099
31 TraesCS3D01G042000 chr7B 85.433 1016 75 34 1508 2491 719463229 719462255 0.000000e+00 989
32 TraesCS3D01G042000 chr7B 87.124 466 24 11 2037 2492 145530676 145530237 1.720000e-136 496
33 TraesCS3D01G042000 chr7B 86.325 468 28 13 2034 2492 506554669 506555109 6.240000e-131 477
34 TraesCS3D01G042000 chr7B 84.080 201 31 1 2284 2483 351449566 351449766 2.530000e-45 193
35 TraesCS3D01G042000 chr3B 87.360 981 61 24 552 1502 392293144 392292197 0.000000e+00 1066
36 TraesCS3D01G042000 chr3B 86.036 222 26 5 2264 2483 391883768 391883550 1.490000e-57 233
37 TraesCS3D01G042000 chr5B 94.758 496 13 1 1503 1985 696498776 696498281 0.000000e+00 760
38 TraesCS3D01G042000 chr5B 92.208 462 30 6 2034 2492 696498282 696497824 0.000000e+00 649
39 TraesCS3D01G042000 chr5B 87.339 466 23 11 2037 2492 567000306 566999867 3.700000e-138 501
40 TraesCS3D01G042000 chr1B 93.890 491 17 1 1503 1980 649434277 649434767 0.000000e+00 728
41 TraesCS3D01G042000 chr1B 90.614 554 40 8 1 545 61450463 61449913 0.000000e+00 725
42 TraesCS3D01G042000 chr1B 86.994 469 25 12 2034 2492 649434775 649435217 1.720000e-136 496
43 TraesCS3D01G042000 chr1B 86.910 466 25 12 2034 2489 438165565 438166004 8.010000e-135 490
44 TraesCS3D01G042000 chr1B 86.141 469 29 12 2034 2492 61445015 61444573 8.070000e-130 473


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 TraesCS3D01G042000 chr3D 16119033 16121524 2491 True 4602.0 4602 100.0000 1 2492 1 chr3D.!!$R1 2491
1 TraesCS3D01G042000 chr3D 468664302 468665808 1506 True 2462.0 2462 96.2330 3 1503 1 chr3D.!!$R4 1500
2 TraesCS3D01G042000 chr3D 356976437 356977894 1457 True 2069.0 2069 92.0270 2 1503 1 chr3D.!!$R2 1501
3 TraesCS3D01G042000 chr3D 468657510 468658515 1005 True 1439.0 1439 92.8290 1503 2492 1 chr3D.!!$R3 989
4 TraesCS3D01G042000 chr3D 578322166 578322983 817 True 1378.0 1378 97.0660 686 1503 1 chr3D.!!$R5 817
5 TraesCS3D01G042000 chr3D 182085063 182085880 817 False 1238.0 1238 93.7200 2 842 1 chr3D.!!$F2 840
6 TraesCS3D01G042000 chr3D 152708785 152709323 538 False 784.0 784 93.3210 1503 2028 1 chr3D.!!$F1 525
7 TraesCS3D01G042000 chr4A 693350780 693356499 5719 True 1795.5 2283 92.2515 1 2492 2 chr4A.!!$R1 2491
8 TraesCS3D01G042000 chr7D 154001804 154003330 1526 False 2261.0 2261 93.7140 1 1503 1 chr7D.!!$F1 1502
9 TraesCS3D01G042000 chr7D 154007742 154008747 1005 False 1439.0 1439 92.8150 1503 2492 1 chr7D.!!$F2 989
10 TraesCS3D01G042000 chr7D 574240387 574241218 831 True 1339.0 1339 95.6160 2 842 1 chr7D.!!$R1 840
11 TraesCS3D01G042000 chr7D 508809465 508810003 538 False 778.0 778 93.1350 1503 2028 1 chr7D.!!$F3 525
12 TraesCS3D01G042000 chr1D 346198696 346200148 1452 True 2058.0 2058 91.9600 2 1503 1 chr1D.!!$R2 1501
13 TraesCS3D01G042000 chr2B 54446230 54447216 986 True 1371.0 1371 91.9050 1503 2492 1 chr2B.!!$R1 989
14 TraesCS3D01G042000 chr2B 54452803 54453502 699 True 922.0 922 91.1430 1 671 1 chr2B.!!$R2 670
15 TraesCS3D01G042000 chr6B 149430585 149431571 986 False 1354.0 1354 91.6090 1503 2492 1 chr6B.!!$F2 989
16 TraesCS3D01G042000 chr6B 149424467 149425147 680 False 885.0 885 90.6020 1 662 1 chr6B.!!$F1 661
17 TraesCS3D01G042000 chr5D 284891120 284892120 1000 False 1339.0 1339 91.1150 1503 2491 1 chr5D.!!$F3 988
18 TraesCS3D01G042000 chr5D 284885981 284886741 760 False 1234.0 1234 95.9260 743 1503 1 chr5D.!!$F2 760
19 TraesCS3D01G042000 chr5D 489756318 489757087 769 False 1223.0 1223 95.3250 734 1503 1 chr5D.!!$F4 769
20 TraesCS3D01G042000 chr5D 525156593 525157294 701 False 1109.0 1109 95.1570 802 1503 1 chr5D.!!$F5 701
21 TraesCS3D01G042000 chr5D 78754935 78758411 3476 False 784.5 1232 87.7000 2 2491 2 chr5D.!!$F6 2489
22 TraesCS3D01G042000 chr3A 670751536 670752539 1003 True 1315.0 1315 90.6930 1509 2492 1 chr3A.!!$R1 983
23 TraesCS3D01G042000 chr6D 100210564 100211333 769 True 1195.0 1195 94.6890 734 1503 1 chr6D.!!$R1 769
24 TraesCS3D01G042000 chr7B 719467440 719468145 705 True 1099.0 1099 94.7670 802 1508 1 chr7B.!!$R3 706
25 TraesCS3D01G042000 chr7B 719462255 719463229 974 True 989.0 989 85.4330 1508 2491 1 chr7B.!!$R2 983
26 TraesCS3D01G042000 chr3B 392292197 392293144 947 True 1066.0 1066 87.3600 552 1502 1 chr3B.!!$R2 950
27 TraesCS3D01G042000 chr5B 696497824 696498776 952 True 704.5 760 93.4830 1503 2492 2 chr5B.!!$R2 989
28 TraesCS3D01G042000 chr1B 61449913 61450463 550 True 725.0 725 90.6140 1 545 1 chr1B.!!$R2 544
29 TraesCS3D01G042000 chr1B 649434277 649435217 940 False 612.0 728 90.4420 1503 2492 2 chr1B.!!$F2 989

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
33 34 1.825474 GTGGAACGATGGAGAGGAGAA 59.175 52.381 0.0 0.0 0.00 2.87 F
1037 1246 1.335810 CCATGGCAGAATGATTGACCG 59.664 52.381 0.0 0.0 39.69 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1372 1581 1.962807 CTCTATCAGCCAGTCCCTCTG 59.037 57.143 0.0 0.0 43.27 3.35 R
2424 7177 1.821332 CGCAAGATCAGGGCTTCCC 60.821 63.158 0.0 0.0 42.67 3.97 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
33 34 1.825474 GTGGAACGATGGAGAGGAGAA 59.175 52.381 0.00 0.00 0.00 2.87
119 129 2.558974 AGGGTTAGGGTTAGGGTTCAG 58.441 52.381 0.00 0.00 0.00 3.02
223 234 3.497405 CCTGGCACCACTATAGATGCATT 60.497 47.826 21.48 0.00 39.92 3.56
731 899 3.951775 TGCAGTGACCAAACTTGTTTT 57.048 38.095 0.00 0.00 0.00 2.43
735 903 5.866633 TGCAGTGACCAAACTTGTTTTTAAG 59.133 36.000 0.00 0.00 0.00 1.85
996 1205 6.885918 TGCAAAGATGTTTGGAGAAGATATGA 59.114 34.615 16.29 0.00 42.99 2.15
1037 1246 1.335810 CCATGGCAGAATGATTGACCG 59.664 52.381 0.00 0.00 39.69 4.79
1135 1344 4.728772 TGAGGATGTCACCAAGATGTTTT 58.271 39.130 0.00 0.00 0.00 2.43
1167 1376 2.972021 TCAGAACAACAGGGTCATGAGA 59.028 45.455 0.00 0.00 0.00 3.27
1372 1581 3.369997 GGAGAGGGATGACTTCAAGGAAC 60.370 52.174 0.00 0.00 0.00 3.62
1495 1704 5.813383 AGTCAATCCTTGATGAGTGAACAT 58.187 37.500 0.00 0.00 40.59 2.71
1960 6407 7.286546 TCATCCAAACTACACAAAATTGAGGAA 59.713 33.333 0.00 0.00 0.00 3.36
2117 6774 7.502226 TCATGCATAAAACCATAAACCTAGAGG 59.498 37.037 0.00 0.00 42.17 3.69
2202 6882 6.456795 AACAGCCCTAAAATAATCTTCAGC 57.543 37.500 0.00 0.00 0.00 4.26
2424 7177 4.473520 ATGGCCTTCTCCCACGCG 62.474 66.667 3.53 3.53 34.68 6.01
2483 7236 1.296392 CGCTCAATGTCCCACTCCA 59.704 57.895 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
119 129 5.402270 CCATTGTTTCAAATCGAAGAACACC 59.598 40.000 0.00 0.0 43.58 4.16
223 234 1.547820 CTGCAGCTCTACCACAGAAGA 59.452 52.381 0.00 0.0 31.12 2.87
735 903 9.934190 AATTGCAAAATCACTGTTAAAAACATC 57.066 25.926 1.71 0.0 41.26 3.06
996 1205 4.533707 TGGTTCTCCTCATGAAACATCTCT 59.466 41.667 9.57 0.0 36.36 3.10
1037 1246 8.524487 TCTCCAACTCTTTCTTATACTTCTCAC 58.476 37.037 0.00 0.0 0.00 3.51
1135 1344 4.264253 CTGTTGTTCTGATCTGCCCAATA 58.736 43.478 0.00 0.0 0.00 1.90
1167 1376 4.002316 GCTTCTGCTTGAACTCTTCATCT 58.998 43.478 0.00 0.0 39.84 2.90
1372 1581 1.962807 CTCTATCAGCCAGTCCCTCTG 59.037 57.143 0.00 0.0 43.27 3.35
1495 1704 4.713553 TGTAGAGCCAGTTGAAACATCAA 58.286 39.130 0.00 0.0 0.00 2.57
1506 4901 2.867109 ATTGCTGTTGTAGAGCCAGT 57.133 45.000 0.00 0.0 35.43 4.00
1960 6407 9.768662 AAAACTGAATCAATCAAGCACTAATTT 57.231 25.926 0.00 0.0 37.67 1.82
2202 6882 5.975693 TTAGGGCTTTGTTTACTGGATTG 57.024 39.130 0.00 0.0 0.00 2.67
2337 7080 2.092914 CACCCCTCTCTTCCATGTTACC 60.093 54.545 0.00 0.0 0.00 2.85
2424 7177 1.821332 CGCAAGATCAGGGCTTCCC 60.821 63.158 0.00 0.0 42.67 3.97


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

AutoCloner maintained by Alex Coulton.