Multiple sequence alignment - TraesCS7A01G359400

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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 TraesCS7A01G359400 chr7A 100.000 2558 0 0 1 2558 533369139 533366582 0.000000e+00 4724
1 TraesCS7A01G359400 chr7A 95.107 981 46 2 807 1786 342306033 342305054 0.000000e+00 1544
2 TraesCS7A01G359400 chr7A 95.924 785 24 4 1780 2558 621359624 621360406 0.000000e+00 1266
3 TraesCS7A01G359400 chr7A 81.034 1160 147 40 1 1146 67883753 67884853 0.000000e+00 856
4 TraesCS7A01G359400 chr7A 94.872 546 24 4 1 542 342307275 342306730 0.000000e+00 850
5 TraesCS7A01G359400 chr2D 94.715 1192 50 10 605 1786 397963553 397962365 0.000000e+00 1840
6 TraesCS7A01G359400 chr2D 94.444 900 40 5 893 1783 54392198 54393096 0.000000e+00 1376
7 TraesCS7A01G359400 chr2D 93.578 545 28 7 2 542 54391011 54391552 0.000000e+00 806
8 TraesCS7A01G359400 chr2D 96.013 301 12 0 1482 1782 250920886 250920586 8.220000e-135 490
9 TraesCS7A01G359400 chr2D 83.304 569 40 26 1255 1783 100318539 100317986 8.280000e-130 473
10 TraesCS7A01G359400 chr1D 93.513 1187 68 6 605 1783 465259659 465260844 0.000000e+00 1757
11 TraesCS7A01G359400 chr3A 96.662 779 23 3 1781 2558 456342813 456343589 0.000000e+00 1291
12 TraesCS7A01G359400 chr3A 96.021 779 28 3 1781 2558 243815556 243816332 0.000000e+00 1264
13 TraesCS7A01G359400 chr3A 87.179 507 48 12 2 496 549258120 549257619 6.180000e-156 560
14 TraesCS7A01G359400 chr5A 96.203 790 25 5 1772 2558 344056611 344055824 0.000000e+00 1288
15 TraesCS7A01G359400 chr5A 90.494 547 45 7 1 542 675834754 675835298 0.000000e+00 715
16 TraesCS7A01G359400 chr5A 85.980 699 60 19 787 1479 675835738 675836404 0.000000e+00 713
17 TraesCS7A01G359400 chr4A 96.392 776 26 2 1784 2558 489030611 489029837 0.000000e+00 1277
18 TraesCS7A01G359400 chr2A 96.392 776 24 4 1784 2558 605839375 605838603 0.000000e+00 1275
19 TraesCS7A01G359400 chr2A 96.263 776 27 2 1784 2558 342056567 342057341 0.000000e+00 1271
20 TraesCS7A01G359400 chr2A 96.144 778 24 5 1782 2558 142924791 142925563 0.000000e+00 1266
21 TraesCS7A01G359400 chr2A 96.005 776 28 3 1784 2558 544767206 544766433 0.000000e+00 1258
22 TraesCS7A01G359400 chr2A 86.067 445 33 17 665 1098 5146365 5146791 3.880000e-123 451
23 TraesCS7A01G359400 chr6A 80.723 1162 150 41 1 1146 39897269 39896166 0.000000e+00 837
24 TraesCS7A01G359400 chr6A 80.519 1155 145 40 1 1146 402588572 402589655 0.000000e+00 813
25 TraesCS7A01G359400 chr6A 81.862 623 67 24 529 1146 69498764 69498183 1.380000e-132 483
26 TraesCS7A01G359400 chr7B 85.979 756 66 16 816 1565 359363786 359364507 0.000000e+00 773
27 TraesCS7A01G359400 chr7B 89.111 551 48 9 1 542 359362781 359363328 0.000000e+00 675
28 TraesCS7A01G359400 chr7B 89.259 540 50 6 1 536 675595770 675595235 0.000000e+00 669
29 TraesCS7A01G359400 chr7B 85.629 167 15 7 1255 1413 29687741 29687906 1.570000e-37 167
30 TraesCS7A01G359400 chr3B 84.968 785 68 22 787 1565 762576222 762576962 0.000000e+00 750
31 TraesCS7A01G359400 chr3B 88.889 468 48 3 3 467 699403880 699404346 7.940000e-160 573
32 TraesCS7A01G359400 chr3B 82.873 543 49 21 1258 1786 245922964 245922452 5.020000e-122 448
33 TraesCS7A01G359400 chr2B 85.811 740 64 25 3 705 49635116 49635851 0.000000e+00 747
34 TraesCS7A01G359400 chr1B 86.727 663 52 19 909 1565 126506643 126507275 0.000000e+00 704
35 TraesCS7A01G359400 chr5B 87.810 484 57 1 1 484 528390480 528389999 1.330000e-157 566
36 TraesCS7A01G359400 chr6D 96.026 302 12 0 1482 1783 288070271 288070572 2.290000e-135 492
37 TraesCS7A01G359400 chr7D 82.667 600 58 27 555 1146 271123925 271124486 8.220000e-135 490
38 TraesCS7A01G359400 chr7D 92.333 300 22 1 1485 1783 157759016 157759315 2.350000e-115 425
39 TraesCS7A01G359400 chr7D 88.757 338 31 4 529 865 611959013 611959344 8.520000e-110 407
40 TraesCS7A01G359400 chr7D 89.456 294 19 3 1311 1604 157758736 157759017 6.730000e-96 361
41 TraesCS7A01G359400 chr6B 81.481 621 73 21 529 1146 149348764 149349345 2.980000e-129 472
42 TraesCS7A01G359400 chr3D 82.353 289 26 13 1255 1531 284206241 284205966 7.120000e-56 228


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 TraesCS7A01G359400 chr7A 533366582 533369139 2557 True 4724 4724 100.0000 1 2558 1 chr7A.!!$R1 2557
1 TraesCS7A01G359400 chr7A 621359624 621360406 782 False 1266 1266 95.9240 1780 2558 1 chr7A.!!$F2 778
2 TraesCS7A01G359400 chr7A 342305054 342307275 2221 True 1197 1544 94.9895 1 1786 2 chr7A.!!$R2 1785
3 TraesCS7A01G359400 chr7A 67883753 67884853 1100 False 856 856 81.0340 1 1146 1 chr7A.!!$F1 1145
4 TraesCS7A01G359400 chr2D 397962365 397963553 1188 True 1840 1840 94.7150 605 1786 1 chr2D.!!$R3 1181
5 TraesCS7A01G359400 chr2D 54391011 54393096 2085 False 1091 1376 94.0110 2 1783 2 chr2D.!!$F1 1781
6 TraesCS7A01G359400 chr2D 100317986 100318539 553 True 473 473 83.3040 1255 1783 1 chr2D.!!$R1 528
7 TraesCS7A01G359400 chr1D 465259659 465260844 1185 False 1757 1757 93.5130 605 1783 1 chr1D.!!$F1 1178
8 TraesCS7A01G359400 chr3A 456342813 456343589 776 False 1291 1291 96.6620 1781 2558 1 chr3A.!!$F2 777
9 TraesCS7A01G359400 chr3A 243815556 243816332 776 False 1264 1264 96.0210 1781 2558 1 chr3A.!!$F1 777
10 TraesCS7A01G359400 chr3A 549257619 549258120 501 True 560 560 87.1790 2 496 1 chr3A.!!$R1 494
11 TraesCS7A01G359400 chr5A 344055824 344056611 787 True 1288 1288 96.2030 1772 2558 1 chr5A.!!$R1 786
12 TraesCS7A01G359400 chr5A 675834754 675836404 1650 False 714 715 88.2370 1 1479 2 chr5A.!!$F1 1478
13 TraesCS7A01G359400 chr4A 489029837 489030611 774 True 1277 1277 96.3920 1784 2558 1 chr4A.!!$R1 774
14 TraesCS7A01G359400 chr2A 605838603 605839375 772 True 1275 1275 96.3920 1784 2558 1 chr2A.!!$R2 774
15 TraesCS7A01G359400 chr2A 342056567 342057341 774 False 1271 1271 96.2630 1784 2558 1 chr2A.!!$F3 774
16 TraesCS7A01G359400 chr2A 142924791 142925563 772 False 1266 1266 96.1440 1782 2558 1 chr2A.!!$F2 776
17 TraesCS7A01G359400 chr2A 544766433 544767206 773 True 1258 1258 96.0050 1784 2558 1 chr2A.!!$R1 774
18 TraesCS7A01G359400 chr6A 39896166 39897269 1103 True 837 837 80.7230 1 1146 1 chr6A.!!$R1 1145
19 TraesCS7A01G359400 chr6A 402588572 402589655 1083 False 813 813 80.5190 1 1146 1 chr6A.!!$F1 1145
20 TraesCS7A01G359400 chr6A 69498183 69498764 581 True 483 483 81.8620 529 1146 1 chr6A.!!$R2 617
21 TraesCS7A01G359400 chr7B 359362781 359364507 1726 False 724 773 87.5450 1 1565 2 chr7B.!!$F2 1564
22 TraesCS7A01G359400 chr7B 675595235 675595770 535 True 669 669 89.2590 1 536 1 chr7B.!!$R1 535
23 TraesCS7A01G359400 chr3B 762576222 762576962 740 False 750 750 84.9680 787 1565 1 chr3B.!!$F2 778
24 TraesCS7A01G359400 chr3B 245922452 245922964 512 True 448 448 82.8730 1258 1786 1 chr3B.!!$R1 528
25 TraesCS7A01G359400 chr2B 49635116 49635851 735 False 747 747 85.8110 3 705 1 chr2B.!!$F1 702
26 TraesCS7A01G359400 chr1B 126506643 126507275 632 False 704 704 86.7270 909 1565 1 chr1B.!!$F1 656
27 TraesCS7A01G359400 chr7D 271123925 271124486 561 False 490 490 82.6670 555 1146 1 chr7D.!!$F1 591
28 TraesCS7A01G359400 chr7D 157758736 157759315 579 False 393 425 90.8945 1311 1783 2 chr7D.!!$F3 472
29 TraesCS7A01G359400 chr6B 149348764 149349345 581 False 472 472 81.4810 529 1146 1 chr6B.!!$F1 617

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
817 1278 0.978146 CCGACCTCCCTCCACATCTT 60.978 60.0 0.0 0.0 0.0 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2304 2971 0.107214 ATTGTGGATCGCCGGTGAAT 60.107 50.0 23.72 10.72 36.79 2.57 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
135 137 7.308229 GCAACAAATATATGGTAGCTCCTTCAG 60.308 40.741 0.00 0.00 37.07 3.02
354 374 8.610248 TCGTGAAAACCTTATCTTTGATTACA 57.390 30.769 0.00 0.00 0.00 2.41
358 378 9.362151 TGAAAACCTTATCTTTGATTACAACCT 57.638 29.630 0.00 0.00 35.63 3.50
425 445 3.551846 TGGTCTATAGACATCTCACGCA 58.448 45.455 29.36 15.33 46.47 5.24
447 467 2.519377 TCGTTCATCAAACACCGTCT 57.481 45.000 0.00 0.00 37.77 4.18
708 771 2.534272 CCTCTTCCCCAACCCCCA 60.534 66.667 0.00 0.00 0.00 4.96
811 1272 4.753662 CCGACCGACCTCCCTCCA 62.754 72.222 0.00 0.00 0.00 3.86
817 1278 0.978146 CCGACCTCCCTCCACATCTT 60.978 60.000 0.00 0.00 0.00 2.40
894 1355 4.193893 CTGGCGATGGATGGGGCA 62.194 66.667 0.00 0.00 34.85 5.36
1112 1609 0.895100 AGACGCCCAAGGTACGTACA 60.895 55.000 26.02 0.00 40.69 2.90
1161 1658 4.978863 TGCGTGGCTTGCGTGCTA 62.979 61.111 0.92 0.00 34.24 3.49
1167 1664 0.321564 TGGCTTGCGTGCTACAGATT 60.322 50.000 0.92 0.00 0.00 2.40
1174 1672 2.027561 TGCGTGCTACAGATTTAACCCT 60.028 45.455 0.00 0.00 0.00 4.34
1175 1673 2.351726 GCGTGCTACAGATTTAACCCTG 59.648 50.000 0.00 0.00 36.53 4.45
1283 1781 1.352352 CCCTCCTTGTTCACATCACCT 59.648 52.381 0.00 0.00 0.00 4.00
1480 2013 6.930667 TGTTTAAACTTCACAGTAGGTTCC 57.069 37.500 18.72 0.00 30.68 3.62
1486 2019 3.077088 ACTTCACAGTAGGTTCCCTCCTA 59.923 47.826 0.00 0.00 38.86 2.94
1697 2354 1.076549 GATGCACCTTGGGGGAACA 59.923 57.895 0.00 0.00 38.76 3.18
2036 2703 3.198409 AGCAGTCACACAATGAAGACA 57.802 42.857 0.00 0.00 39.72 3.41
2055 2722 9.979578 TGAAGACAAAATAACTAATGCAAACAT 57.020 25.926 0.00 0.00 38.49 2.71
2128 2795 1.143305 CAGTGGCTCGTTGAAGACAG 58.857 55.000 0.00 0.00 34.09 3.51
2145 2812 1.956477 ACAGTGATTTGTTGGACCAGC 59.044 47.619 0.49 0.49 0.00 4.85
2231 2898 4.225267 GTCTTCACCTTATTCCCCTTGAGA 59.775 45.833 0.00 0.00 0.00 3.27
2304 2971 3.924114 TCCAAACCTTCACAGACTTCA 57.076 42.857 0.00 0.00 0.00 3.02
2437 3104 4.833390 ACTTAAGTGATGCCTAACACTCC 58.167 43.478 7.48 0.00 44.94 3.85
2521 3189 3.181500 GGTTGCTCTCAAACGACAAAAGT 60.181 43.478 0.00 0.00 33.37 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 103 9.311916 GCTACCATATATTTGTTGCAAAATTGA 57.688 29.630 0.00 0.00 32.16 2.57
354 374 8.568617 AGACCTTATGACCATCTAAATAGGTT 57.431 34.615 0.00 0.00 35.36 3.50
425 445 2.993899 GACGGTGTTTGATGAACGATCT 59.006 45.455 0.00 0.00 41.29 2.75
447 467 1.065491 CCGTTGGATCCTGGACAATCA 60.065 52.381 14.23 0.00 0.00 2.57
586 649 4.648626 AGGGTCGTCGACGGTGGA 62.649 66.667 35.05 15.53 40.29 4.02
708 771 2.122768 AGCGGAGATTGGAGAGGAATT 58.877 47.619 0.00 0.00 0.00 2.17
811 1272 1.371467 TGGGTGGATGGACAAGATGT 58.629 50.000 0.00 0.00 0.00 3.06
894 1355 1.557099 TCCATCGCTAGAACTGGTGT 58.443 50.000 0.00 0.00 30.47 4.16
1112 1609 1.594331 GAAGAGTTGGCAAGAACGGT 58.406 50.000 0.00 0.00 0.00 4.83
1161 1658 4.273318 GAAGGATGCAGGGTTAAATCTGT 58.727 43.478 0.00 0.00 33.81 3.41
1167 1664 2.025321 GGAAGGAAGGATGCAGGGTTAA 60.025 50.000 0.00 0.00 0.00 2.01
1174 1672 1.425066 ACACAAGGAAGGAAGGATGCA 59.575 47.619 0.00 0.00 0.00 3.96
1175 1673 2.206576 ACACAAGGAAGGAAGGATGC 57.793 50.000 0.00 0.00 0.00 3.91
1262 1760 1.073923 GGTGATGTGAACAAGGAGGGT 59.926 52.381 0.00 0.00 0.00 4.34
1283 1781 1.219213 TCCAAGGGAAAGCAAAGGGAA 59.781 47.619 0.00 0.00 0.00 3.97
1480 2013 0.460311 ACGGAATCACGCTTAGGAGG 59.540 55.000 0.00 0.00 37.37 4.30
1486 2019 0.179161 CTCTCGACGGAATCACGCTT 60.179 55.000 0.00 0.00 37.37 4.68
1524 2178 1.201181 TGCAAAAGCACGTTCAACACT 59.799 42.857 0.00 0.00 0.00 3.55
1697 2354 5.714806 AGAAAATAACCGGGAAACATGACAT 59.285 36.000 6.32 0.00 0.00 3.06
1736 2395 6.790285 AATTGCTTTTGTAAATTCTGCAGG 57.210 33.333 15.13 0.00 0.00 4.85
2055 2722 2.229792 GGTCCTTGTGAAGTCATTGCA 58.770 47.619 0.00 0.00 0.00 4.08
2128 2795 1.541588 GGAGCTGGTCCAACAAATCAC 59.458 52.381 20.44 0.00 46.10 3.06
2304 2971 0.107214 ATTGTGGATCGCCGGTGAAT 60.107 50.000 23.72 10.72 36.79 2.57
2437 3104 1.614317 CCCTAAACACCCAGAGCCAAG 60.614 57.143 0.00 0.00 0.00 3.61
2521 3189 2.161808 GCTGCTCAGAGTTAGTGTACGA 59.838 50.000 0.29 0.00 0.00 3.43


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

AutoCloner maintained by Alex Coulton.