Multiple sequence alignment - TraesCS5D01G454500

Loading Multiple Alignment...

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 TraesCS5D01G454500 chr5D 100.000 2611 0 0 1 2611 501451070 501448460 0.000000e+00 4822.0
1 TraesCS5D01G454500 chr5D 87.740 938 78 18 783 1695 517213174 517214099 0.000000e+00 1061.0
2 TraesCS5D01G454500 chr5D 86.917 986 78 24 877 1836 495199783 495200743 0.000000e+00 1059.0
3 TraesCS5D01G454500 chr5D 93.364 648 28 9 991 1629 296965061 296965702 0.000000e+00 944.0
4 TraesCS5D01G454500 chr5D 85.905 823 73 20 1049 1836 509024449 509023635 0.000000e+00 837.0
5 TraesCS5D01G454500 chr5D 89.431 369 30 7 641 1008 296963282 296963642 8.520000e-125 457.0
6 TraesCS5D01G454500 chr5D 91.667 240 11 4 111 350 296959444 296959674 9.010000e-85 324.0
7 TraesCS5D01G454500 chr5D 89.583 192 11 2 1663 1854 296965702 296965884 4.340000e-58 235.0
8 TraesCS5D01G454500 chr5D 97.297 111 3 0 445 555 296959673 296959783 3.430000e-44 189.0
9 TraesCS5D01G454500 chr5D 93.750 96 5 1 560 654 296960028 296960123 2.710000e-30 143.0
10 TraesCS5D01G454500 chr5D 90.909 66 4 2 6 71 520718662 520718599 1.290000e-13 87.9
11 TraesCS5D01G454500 chr5B 91.979 1309 78 12 560 1854 628724855 628723560 0.000000e+00 1810.0
12 TraesCS5D01G454500 chr5B 88.835 1245 90 25 560 1770 629953648 629952419 0.000000e+00 1483.0
13 TraesCS5D01G454500 chr5B 86.887 1243 101 32 621 1854 629926712 629925523 0.000000e+00 1336.0
14 TraesCS5D01G454500 chr5B 98.287 759 13 0 1853 2611 633257066 633257824 0.000000e+00 1330.0
15 TraesCS5D01G454500 chr5B 92.244 851 50 8 1004 1854 633171391 633172225 0.000000e+00 1192.0
16 TraesCS5D01G454500 chr5B 86.406 1074 105 24 769 1820 649498261 649499315 0.000000e+00 1136.0
17 TraesCS5D01G454500 chr5B 89.636 878 77 9 875 1746 611677573 611678442 0.000000e+00 1105.0
18 TraesCS5D01G454500 chr5B 92.988 656 38 7 560 1209 625134201 625133548 0.000000e+00 950.0
19 TraesCS5D01G454500 chr5B 90.909 660 40 6 1205 1854 625131203 625130554 0.000000e+00 869.0
20 TraesCS5D01G454500 chr5B 94.414 555 23 6 1 555 625134992 625134446 0.000000e+00 846.0
21 TraesCS5D01G454500 chr5B 94.414 555 23 6 1 555 628725646 628725100 0.000000e+00 846.0
22 TraesCS5D01G454500 chr5B 86.156 744 59 22 767 1497 649694141 649694853 0.000000e+00 763.0
23 TraesCS5D01G454500 chr5B 91.525 295 24 1 2318 2611 623152904 623152610 3.130000e-109 405.0
24 TraesCS5D01G454500 chr5B 91.186 295 25 1 2318 2611 626817828 626817534 1.460000e-107 399.0
25 TraesCS5D01G454500 chr5B 91.349 289 24 1 2318 2605 625094281 625093993 6.770000e-106 394.0
26 TraesCS5D01G454500 chr5B 91.349 289 24 1 2318 2605 628673830 628673542 6.770000e-106 394.0
27 TraesCS5D01G454500 chr5B 90.476 294 28 0 2318 2611 629861392 629861099 3.150000e-104 388.0
28 TraesCS5D01G454500 chr5B 93.130 262 11 5 295 555 633170460 633170715 6.820000e-101 377.0
29 TraesCS5D01G454500 chr5B 95.000 200 9 1 560 759 633170960 633171158 1.950000e-81 313.0
30 TraesCS5D01G454500 chr5B 92.537 201 11 4 808 1008 633171156 633171352 4.250000e-73 285.0
31 TraesCS5D01G454500 chr5B 79.381 388 53 16 1455 1836 639670610 639670244 5.580000e-62 248.0
32 TraesCS5D01G454500 chr5A 93.035 761 46 4 1853 2611 625754649 625755404 0.000000e+00 1105.0
33 TraesCS5D01G454500 chr5A 85.584 1096 111 24 769 1836 644310158 644311234 0.000000e+00 1105.0
34 TraesCS5D01G454500 chr5A 88.594 868 59 20 991 1836 625715372 625716221 0.000000e+00 1018.0
35 TraesCS5D01G454500 chr5A 92.500 560 24 8 1 555 625714159 625714705 0.000000e+00 785.0
36 TraesCS5D01G454500 chr5A 94.500 200 10 1 560 759 625714951 625715149 9.080000e-80 307.0
37 TraesCS5D01G454500 chr5A 95.082 183 8 1 808 989 625715147 625715329 1.180000e-73 287.0
38 TraesCS5D01G454500 chr2A 91.176 68 5 1 3 69 767166161 767166094 9.950000e-15 91.6
39 TraesCS5D01G454500 chr2A 94.828 58 2 1 15 72 749054815 749054759 3.580000e-14 89.8
40 TraesCS5D01G454500 chr4D 92.063 63 5 0 7 69 64375876 64375938 3.580000e-14 89.8
41 TraesCS5D01G454500 chr1D 93.333 60 4 0 8 67 250210535 250210476 3.580000e-14 89.8
42 TraesCS5D01G454500 chr6A 90.625 64 4 2 20 82 601670951 601670889 1.670000e-12 84.2


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 TraesCS5D01G454500 chr5D 501448460 501451070 2610 True 4822.000000 4822 100.000000 1 2611 1 chr5D.!!$R1 2610
1 TraesCS5D01G454500 chr5D 517213174 517214099 925 False 1061.000000 1061 87.740000 783 1695 1 chr5D.!!$F2 912
2 TraesCS5D01G454500 chr5D 495199783 495200743 960 False 1059.000000 1059 86.917000 877 1836 1 chr5D.!!$F1 959
3 TraesCS5D01G454500 chr5D 509023635 509024449 814 True 837.000000 837 85.905000 1049 1836 1 chr5D.!!$R2 787
4 TraesCS5D01G454500 chr5D 296959444 296965884 6440 False 382.000000 944 92.515333 111 1854 6 chr5D.!!$F3 1743
5 TraesCS5D01G454500 chr5B 629952419 629953648 1229 True 1483.000000 1483 88.835000 560 1770 1 chr5B.!!$R7 1210
6 TraesCS5D01G454500 chr5B 629925523 629926712 1189 True 1336.000000 1336 86.887000 621 1854 1 chr5B.!!$R6 1233
7 TraesCS5D01G454500 chr5B 633257066 633257824 758 False 1330.000000 1330 98.287000 1853 2611 1 chr5B.!!$F2 758
8 TraesCS5D01G454500 chr5B 628723560 628725646 2086 True 1328.000000 1810 93.196500 1 1854 2 chr5B.!!$R10 1853
9 TraesCS5D01G454500 chr5B 649498261 649499315 1054 False 1136.000000 1136 86.406000 769 1820 1 chr5B.!!$F3 1051
10 TraesCS5D01G454500 chr5B 611677573 611678442 869 False 1105.000000 1105 89.636000 875 1746 1 chr5B.!!$F1 871
11 TraesCS5D01G454500 chr5B 625130554 625134992 4438 True 888.333333 950 92.770333 1 1854 3 chr5B.!!$R9 1853
12 TraesCS5D01G454500 chr5B 649694141 649694853 712 False 763.000000 763 86.156000 767 1497 1 chr5B.!!$F4 730
13 TraesCS5D01G454500 chr5B 633170460 633172225 1765 False 541.750000 1192 93.227750 295 1854 4 chr5B.!!$F5 1559
14 TraesCS5D01G454500 chr5A 625754649 625755404 755 False 1105.000000 1105 93.035000 1853 2611 1 chr5A.!!$F1 758
15 TraesCS5D01G454500 chr5A 644310158 644311234 1076 False 1105.000000 1105 85.584000 769 1836 1 chr5A.!!$F2 1067
16 TraesCS5D01G454500 chr5A 625714159 625716221 2062 False 599.250000 1018 92.669000 1 1836 4 chr5A.!!$F3 1835

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
230 231 1.253100 CACATACCCAACCCAACCAC 58.747 55.000 0.0 0.0 0.0 4.16 F
1047 6055 1.066002 CCATCGCGCCAAATCTCAAAT 59.934 47.619 0.0 0.0 0.0 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1446 8823 0.676151 GTCTTCTTGGGGAGCAGCAG 60.676 60.000 0.0 0.0 0.00 4.24 R
2287 9731 1.893137 TGCTGCTTTCTCTAAGGACGA 59.107 47.619 0.0 0.0 34.26 4.20 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
230 231 1.253100 CACATACCCAACCCAACCAC 58.747 55.000 0.00 0.0 0.00 4.16
271 272 4.785453 GGGCAGCTCAGGGTTCCG 62.785 72.222 0.00 0.0 0.00 4.30
276 277 1.306141 AGCTCAGGGTTCCGATCCA 60.306 57.895 0.00 0.0 0.00 3.41
363 460 5.933617 TCACAAAGATAGATGAATGAGGGG 58.066 41.667 0.00 0.0 0.00 4.79
508 606 5.090757 CCGGCTTTTTATTTCCGTTTAGTC 58.909 41.667 0.00 0.0 40.23 2.59
558 656 9.638176 ATGAGAAATTCAAGCCTAAAGTATGAT 57.362 29.630 0.00 0.0 39.77 2.45
598 940 3.886505 ACGCCCATACAAAACAAAAGAGA 59.113 39.130 0.00 0.0 0.00 3.10
634 977 3.493334 ACCTGGCATGTCATATGGATTG 58.507 45.455 10.79 0.0 0.00 2.67
666 4181 8.996024 ACATAACCAATTTATAACTTTGTGGC 57.004 30.769 6.59 0.0 0.00 5.01
903 4471 2.125106 GTCCACTCGCCACCCATC 60.125 66.667 0.00 0.0 0.00 3.51
999 4571 2.514824 GCCCGCCTTCTCATCACC 60.515 66.667 0.00 0.0 0.00 4.02
1001 4573 1.299648 CCCGCCTTCTCATCACCAA 59.700 57.895 0.00 0.0 0.00 3.67
1047 6055 1.066002 CCATCGCGCCAAATCTCAAAT 59.934 47.619 0.00 0.0 0.00 2.32
1446 8823 1.984026 CTGCCCAACATCAACCCCC 60.984 63.158 0.00 0.0 0.00 5.40
1713 9135 0.464036 TACATCTGTGCGGTGGGATC 59.536 55.000 0.00 0.0 0.00 3.36
1749 9181 7.652727 TCTACCAATCGTCTGAATCTGATAAG 58.347 38.462 0.00 0.0 0.00 1.73
1753 9185 6.983307 CCAATCGTCTGAATCTGATAAGTTCT 59.017 38.462 0.00 0.0 0.00 3.01
1759 9191 7.327214 GTCTGAATCTGATAAGTTCTCTTGGT 58.673 38.462 0.00 0.0 35.36 3.67
1760 9192 7.491048 GTCTGAATCTGATAAGTTCTCTTGGTC 59.509 40.741 0.00 0.0 35.36 4.02
1761 9193 7.398618 TCTGAATCTGATAAGTTCTCTTGGTCT 59.601 37.037 0.00 0.0 35.36 3.85
1762 9194 7.326454 TGAATCTGATAAGTTCTCTTGGTCTG 58.674 38.462 0.00 0.0 35.36 3.51
1763 9195 5.667539 TCTGATAAGTTCTCTTGGTCTGG 57.332 43.478 0.00 0.0 35.36 3.86
1764 9196 5.087323 TCTGATAAGTTCTCTTGGTCTGGT 58.913 41.667 0.00 0.0 35.36 4.00
1766 9198 6.153000 TCTGATAAGTTCTCTTGGTCTGGTAC 59.847 42.308 0.00 0.0 35.36 3.34
2195 9639 2.996168 AAGCGCTCGTGTTTCTGCCT 62.996 55.000 12.06 0.0 0.00 4.75
2287 9731 2.023888 ACTGCTCCAGTAGTACCCATCT 60.024 50.000 0.00 0.0 43.46 2.90
2378 9822 2.696526 TGTCCCTTCACTACTCACCT 57.303 50.000 0.00 0.0 0.00 4.00
2587 10032 2.574006 ATGATGGACCCCGATTGATG 57.426 50.000 0.00 0.0 0.00 3.07
2599 10044 4.022416 CCCCGATTGATGAACAAAAAGTGA 60.022 41.667 0.00 0.0 42.03 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
276 277 5.006261 GCATCGTTACCAAAAGCTTGTTTTT 59.994 36.000 0.00 0.0 0.00 1.94
363 460 7.114953 GCTTTGCTTTTGAGTGTAGTAAATTCC 59.885 37.037 0.00 0.0 0.00 3.01
891 4459 4.530857 GGTCGGATGGGTGGCGAG 62.531 72.222 0.00 0.0 0.00 5.03
903 4471 2.819595 CAGGCAATGGACGGTCGG 60.820 66.667 1.43 0.0 0.00 4.79
999 4571 0.035458 AGAAGGCGGGAGAGTGTTTG 59.965 55.000 0.00 0.0 0.00 2.93
1001 4573 0.832135 TGAGAAGGCGGGAGAGTGTT 60.832 55.000 0.00 0.0 0.00 3.32
1047 6055 2.844362 CATGGCGGCTAGAGGGGA 60.844 66.667 11.43 0.0 0.00 4.81
1401 8778 3.498834 GTGCGCGATGGTGATGCA 61.499 61.111 12.10 0.0 0.00 3.96
1446 8823 0.676151 GTCTTCTTGGGGAGCAGCAG 60.676 60.000 0.00 0.0 0.00 4.24
1570 8968 4.022762 AGAGCATACTACATCGACACCATC 60.023 45.833 0.00 0.0 0.00 3.51
1713 9135 8.135529 TCAGACGATTGGTAGATACAACTATTG 58.864 37.037 0.00 0.0 0.00 1.90
1749 9181 3.056465 CCAGAGTACCAGACCAAGAGAAC 60.056 52.174 0.00 0.0 0.00 3.01
1753 9185 2.696526 ACCAGAGTACCAGACCAAGA 57.303 50.000 0.00 0.0 0.00 3.02
1759 9191 7.508296 AGTTTTTCTAGTAACCAGAGTACCAGA 59.492 37.037 0.00 0.0 0.00 3.86
1760 9192 7.668492 AGTTTTTCTAGTAACCAGAGTACCAG 58.332 38.462 0.00 0.0 0.00 4.00
1761 9193 7.607615 AGTTTTTCTAGTAACCAGAGTACCA 57.392 36.000 0.00 0.0 0.00 3.25
1762 9194 9.018582 TCTAGTTTTTCTAGTAACCAGAGTACC 57.981 37.037 0.00 0.0 44.59 3.34
1766 9198 9.628746 GACTTCTAGTTTTTCTAGTAACCAGAG 57.371 37.037 0.00 0.0 44.59 3.35
2287 9731 1.893137 TGCTGCTTTCTCTAAGGACGA 59.107 47.619 0.00 0.0 34.26 4.20
2378 9822 3.985019 TTCGCCTAAACCATTCTACCA 57.015 42.857 0.00 0.0 0.00 3.25


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

AutoCloner maintained by Alex Coulton.