Multiple sequence alignment - TraesCS6B01G025500

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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 TraesCS6B01G025500 chr6B 100.000 2675 0 0 1 2675 15382050 15379376 0.000000e+00 4940
1 TraesCS6B01G025500 chr6B 93.542 1409 88 3 1268 2675 16321334 16322740 0.000000e+00 2095
2 TraesCS6B01G025500 chr6B 86.645 1565 156 28 540 2090 670592672 670591147 0.000000e+00 1683
3 TraesCS6B01G025500 chr6B 86.470 1456 178 9 641 2090 15397820 15396378 0.000000e+00 1580
4 TraesCS6B01G025500 chr6B 92.090 531 42 0 1 531 58155861 58155331 0.000000e+00 749
5 TraesCS6B01G025500 chr6B 91.948 534 40 1 1 531 567664424 567663891 0.000000e+00 745
6 TraesCS6B01G025500 chr6B 77.140 1028 188 33 546 1553 15744037 15743037 1.080000e-153 553
7 TraesCS6B01G025500 chr6B 76.703 1013 199 26 527 1522 14340469 14341461 1.820000e-146 529
8 TraesCS6B01G025500 chr6A 88.708 2152 216 18 534 2675 9461476 9463610 0.000000e+00 2603
9 TraesCS6B01G025500 chr6A 86.927 1461 169 12 638 2090 9355310 9356756 0.000000e+00 1620
10 TraesCS6B01G025500 chr5B 94.373 1564 84 2 530 2090 556795736 556794174 0.000000e+00 2398
11 TraesCS6B01G025500 chr5B 85.547 1626 211 13 530 2143 621238266 621236653 0.000000e+00 1679
12 TraesCS6B01G025500 chr5B 91.948 534 39 2 1 531 378790981 378791513 0.000000e+00 745
13 TraesCS6B01G025500 chr1B 91.753 1637 110 7 527 2150 662037330 662038954 0.000000e+00 2252
14 TraesCS6B01G025500 chr1B 92.669 532 36 1 1 529 436980506 436979975 0.000000e+00 763
15 TraesCS6B01G025500 chr5D 84.879 1574 201 13 530 2092 499865059 499863512 0.000000e+00 1554
16 TraesCS6B01G025500 chr5D 80.447 1478 250 26 528 1989 42076074 42077528 0.000000e+00 1092
17 TraesCS6B01G025500 chr6D 83.881 1582 230 15 635 2206 8987358 8988924 0.000000e+00 1485
18 TraesCS6B01G025500 chr6D 96.790 405 13 0 2271 2675 8988932 8989336 0.000000e+00 676
19 TraesCS6B01G025500 chr2B 81.929 1555 231 25 644 2191 54043880 54042369 0.000000e+00 1269
20 TraesCS6B01G025500 chr4B 93.597 531 33 1 1 531 94864748 94865277 0.000000e+00 791
21 TraesCS6B01G025500 chr4B 92.135 534 39 1 1 531 492274302 492273769 0.000000e+00 750
22 TraesCS6B01G025500 chr4B 91.963 535 40 1 1 532 125088868 125089402 0.000000e+00 747
23 TraesCS6B01G025500 chr4B 91.948 534 39 2 1 531 45860677 45860145 0.000000e+00 745
24 TraesCS6B01G025500 chr7B 84.236 812 95 19 540 1342 32348042 32347255 0.000000e+00 760
25 TraesCS6B01G025500 chr7B 92.135 534 39 1 1 531 53133264 53133797 0.000000e+00 750


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 TraesCS6B01G025500 chr6B 15379376 15382050 2674 True 4940.0 4940 100.0000 1 2675 1 chr6B.!!$R1 2674
1 TraesCS6B01G025500 chr6B 16321334 16322740 1406 False 2095.0 2095 93.5420 1268 2675 1 chr6B.!!$F2 1407
2 TraesCS6B01G025500 chr6B 670591147 670592672 1525 True 1683.0 1683 86.6450 540 2090 1 chr6B.!!$R6 1550
3 TraesCS6B01G025500 chr6B 15396378 15397820 1442 True 1580.0 1580 86.4700 641 2090 1 chr6B.!!$R2 1449
4 TraesCS6B01G025500 chr6B 58155331 58155861 530 True 749.0 749 92.0900 1 531 1 chr6B.!!$R4 530
5 TraesCS6B01G025500 chr6B 567663891 567664424 533 True 745.0 745 91.9480 1 531 1 chr6B.!!$R5 530
6 TraesCS6B01G025500 chr6B 15743037 15744037 1000 True 553.0 553 77.1400 546 1553 1 chr6B.!!$R3 1007
7 TraesCS6B01G025500 chr6B 14340469 14341461 992 False 529.0 529 76.7030 527 1522 1 chr6B.!!$F1 995
8 TraesCS6B01G025500 chr6A 9461476 9463610 2134 False 2603.0 2603 88.7080 534 2675 1 chr6A.!!$F2 2141
9 TraesCS6B01G025500 chr6A 9355310 9356756 1446 False 1620.0 1620 86.9270 638 2090 1 chr6A.!!$F1 1452
10 TraesCS6B01G025500 chr5B 556794174 556795736 1562 True 2398.0 2398 94.3730 530 2090 1 chr5B.!!$R1 1560
11 TraesCS6B01G025500 chr5B 621236653 621238266 1613 True 1679.0 1679 85.5470 530 2143 1 chr5B.!!$R2 1613
12 TraesCS6B01G025500 chr5B 378790981 378791513 532 False 745.0 745 91.9480 1 531 1 chr5B.!!$F1 530
13 TraesCS6B01G025500 chr1B 662037330 662038954 1624 False 2252.0 2252 91.7530 527 2150 1 chr1B.!!$F1 1623
14 TraesCS6B01G025500 chr1B 436979975 436980506 531 True 763.0 763 92.6690 1 529 1 chr1B.!!$R1 528
15 TraesCS6B01G025500 chr5D 499863512 499865059 1547 True 1554.0 1554 84.8790 530 2092 1 chr5D.!!$R1 1562
16 TraesCS6B01G025500 chr5D 42076074 42077528 1454 False 1092.0 1092 80.4470 528 1989 1 chr5D.!!$F1 1461
17 TraesCS6B01G025500 chr6D 8987358 8989336 1978 False 1080.5 1485 90.3355 635 2675 2 chr6D.!!$F1 2040
18 TraesCS6B01G025500 chr2B 54042369 54043880 1511 True 1269.0 1269 81.9290 644 2191 1 chr2B.!!$R1 1547
19 TraesCS6B01G025500 chr4B 94864748 94865277 529 False 791.0 791 93.5970 1 531 1 chr4B.!!$F1 530
20 TraesCS6B01G025500 chr4B 492273769 492274302 533 True 750.0 750 92.1350 1 531 1 chr4B.!!$R2 530
21 TraesCS6B01G025500 chr4B 125088868 125089402 534 False 747.0 747 91.9630 1 532 1 chr4B.!!$F2 531
22 TraesCS6B01G025500 chr4B 45860145 45860677 532 True 745.0 745 91.9480 1 531 1 chr4B.!!$R1 530
23 TraesCS6B01G025500 chr7B 32347255 32348042 787 True 760.0 760 84.2360 540 1342 1 chr7B.!!$R1 802
24 TraesCS6B01G025500 chr7B 53133264 53133797 533 False 750.0 750 92.1350 1 531 1 chr7B.!!$F1 530

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
819 842 1.358152 CCAAGGACCCACTGTTCCTA 58.642 55.0 0.14 0.0 31.42 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2146 2209 1.035385 GGTGAATTAACCCTGGGCCG 61.035 60.0 14.08 0.0 33.79 6.13 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
233 234 2.803670 GTCGCGACGTGCTGCTAA 60.804 61.111 25.19 0.00 43.27 3.09
508 512 2.669569 GGCGCCTCAAGCAGAACA 60.670 61.111 22.15 0.00 44.04 3.18
619 635 2.682136 TCTCCGCCATCGTCCCAA 60.682 61.111 0.00 0.00 0.00 4.12
810 833 3.691342 CTCGTCGCCAAGGACCCA 61.691 66.667 0.00 0.00 33.30 4.51
819 842 1.358152 CCAAGGACCCACTGTTCCTA 58.642 55.000 0.14 0.00 31.42 2.94
1101 1142 1.742831 GGTGACTGCGATATTGCCAAA 59.257 47.619 12.54 0.00 0.00 3.28
1109 1150 2.282290 GCGATATTGCCAAATTGTGCAC 59.718 45.455 10.75 10.75 37.18 4.57
1111 1152 2.360553 TATTGCCAAATTGTGCACCG 57.639 45.000 15.69 0.00 37.18 4.94
1249 1290 3.796111 TCATCTCTTGGGAAAGAGGAGT 58.204 45.455 13.91 0.97 44.86 3.85
1318 1359 1.609210 TGGACGGATGCTGAGGTGA 60.609 57.895 0.00 0.00 0.00 4.02
1319 1360 1.191489 TGGACGGATGCTGAGGTGAA 61.191 55.000 0.00 0.00 0.00 3.18
1412 1453 1.414061 ATCTCCGAGATGGGCTTGGG 61.414 60.000 10.23 0.00 46.73 4.12
1501 1547 4.861462 GGTACTACGCTGTAAAGTTTCTCC 59.139 45.833 0.00 0.00 0.00 3.71
1504 1550 3.746045 ACGCTGTAAAGTTTCTCCAGA 57.254 42.857 11.84 0.00 0.00 3.86
1512 1558 7.049799 TGTAAAGTTTCTCCAGAAAAATGGG 57.950 36.000 3.27 0.00 44.58 4.00
1561 1607 4.684484 ACTGTTTTTAAGGAGTCCGACT 57.316 40.909 2.76 0.00 0.00 4.18
1566 1612 3.396260 TTTAAGGAGTCCGACTTGGTG 57.604 47.619 2.76 0.00 39.52 4.17
1588 1634 6.483640 GGTGTTCAAGAAGAAGTTCATACACT 59.516 38.462 5.50 0.00 36.78 3.55
1601 1647 7.962995 AGTTCATACACTCTCATAAGGAAGA 57.037 36.000 0.00 0.00 0.00 2.87
1627 1673 2.875933 CCGCACCTTGAAAAAGACTACA 59.124 45.455 0.00 0.00 0.00 2.74
1629 1675 4.279659 CGCACCTTGAAAAAGACTACAAC 58.720 43.478 0.00 0.00 0.00 3.32
1729 1781 1.033202 TGTCCGCTGCCGTATGTCTA 61.033 55.000 0.00 0.00 0.00 2.59
1811 1863 8.150945 GGATACTGATATGTAATGTCACCACTT 58.849 37.037 0.00 0.00 39.67 3.16
1832 1884 4.008074 TGTCAGAGAAGAAACCATGGAC 57.992 45.455 21.47 9.43 0.00 4.02
1865 1921 4.853743 GCTTTTTCGTCCTCATTCATGTTC 59.146 41.667 0.00 0.00 0.00 3.18
1867 1924 5.611796 TTTTCGTCCTCATTCATGTTCTG 57.388 39.130 0.00 0.00 0.00 3.02
1898 1958 6.220930 TGTATTGGAACTGAGTAAGTGTGAC 58.779 40.000 0.00 0.00 39.81 3.67
2146 2209 5.063060 CCTGGTGTTAGCGTTTCTTATGTAC 59.937 44.000 0.00 0.00 0.00 2.90
2414 2478 5.519722 AGCCGAAACTAGACACAAAATTTG 58.480 37.500 3.89 3.89 0.00 2.32
2610 2674 2.185004 TTCCTGCCTGCACTAAGAAC 57.815 50.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
233 234 4.400961 GAGCTCTGCCACCCGCTT 62.401 66.667 6.43 0.00 38.78 4.68
619 635 1.606313 CAAATCCGGTGCTTGGGGT 60.606 57.895 0.00 0.00 0.00 4.95
810 833 1.450312 GCTGGCGCATAGGAACAGT 60.450 57.895 10.83 0.00 35.78 3.55
868 892 2.203509 ACGCGATAGGCCTAGGCT 60.204 61.111 32.18 20.26 42.39 4.58
902 927 4.436998 GGTCGGTGAGTGAGGCGG 62.437 72.222 0.00 0.00 0.00 6.13
1101 1142 2.616330 CGGTCTTGCGGTGCACAAT 61.616 57.895 20.43 0.00 38.71 2.71
1109 1150 3.376935 ATCAGCCTCGGTCTTGCGG 62.377 63.158 0.00 0.00 0.00 5.69
1111 1152 1.880340 CGATCAGCCTCGGTCTTGC 60.880 63.158 0.00 0.00 35.03 4.01
1318 1359 7.201644 CGATGGATACTTAGAAACAGCAATGTT 60.202 37.037 0.00 0.00 37.61 2.71
1319 1360 6.258727 CGATGGATACTTAGAAACAGCAATGT 59.741 38.462 0.00 0.00 37.61 2.71
1412 1453 0.179045 ATGAGCAATGTAGGGCGGTC 60.179 55.000 0.00 0.00 34.54 4.79
1501 1547 4.053295 CACTTGAGCAACCCATTTTTCTG 58.947 43.478 0.00 0.00 0.00 3.02
1504 1550 3.450457 TCACACTTGAGCAACCCATTTTT 59.550 39.130 0.00 0.00 0.00 1.94
1561 1607 6.826231 TGTATGAACTTCTTCTTGAACACCAA 59.174 34.615 0.00 0.00 0.00 3.67
1566 1612 7.653713 TGAGAGTGTATGAACTTCTTCTTGAAC 59.346 37.037 0.00 0.00 0.00 3.18
1588 1634 2.483714 GCGGTGCATCTTCCTTATGAGA 60.484 50.000 0.00 0.00 0.00 3.27
1601 1647 0.749649 TTTTTCAAGGTGCGGTGCAT 59.250 45.000 0.00 0.00 41.91 3.96
1720 1766 6.146184 CCAAACCAGCATCTAATAGACATACG 59.854 42.308 0.00 0.00 0.00 3.06
1729 1781 3.456380 ACCACCAAACCAGCATCTAAT 57.544 42.857 0.00 0.00 0.00 1.73
1811 1863 3.648067 AGTCCATGGTTTCTTCTCTGACA 59.352 43.478 12.58 0.00 0.00 3.58
1832 1884 4.003648 AGGACGAAAAAGCTCATAACCAG 58.996 43.478 0.00 0.00 0.00 4.00
1842 1896 4.425577 ACATGAATGAGGACGAAAAAGC 57.574 40.909 0.00 0.00 0.00 3.51
1865 1921 6.166279 ACTCAGTTCCAATACATGTGTACAG 58.834 40.000 9.11 0.00 32.72 2.74
1867 1924 7.817962 ACTTACTCAGTTCCAATACATGTGTAC 59.182 37.037 9.11 0.00 28.91 2.90
1898 1958 2.953648 TGCATTACAGAATGGCCTGATG 59.046 45.455 3.32 0.00 43.62 3.07
2146 2209 1.035385 GGTGAATTAACCCTGGGCCG 61.035 60.000 14.08 0.00 33.79 6.13
2610 2674 8.768019 CATGTCAAACAGGACTATATATGTGTG 58.232 37.037 0.00 0.00 38.61 3.82


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

AutoCloner maintained by Alex Coulton.