Multiple sequence alignment - TraesCS5D01G349500

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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 TraesCS5D01G349500 chr5D 100.000 2330 0 0 1 2330 434472457 434470128 0.000000e+00 4303
1 TraesCS5D01G349500 chr5D 93.712 1479 70 11 864 2330 159652050 159650583 0.000000e+00 2194
2 TraesCS5D01G349500 chr5A 91.415 2353 162 18 3 2330 520469968 520467631 0.000000e+00 3190
3 TraesCS5D01G349500 chr5A 88.983 354 33 6 1 350 708852091 708852442 1.280000e-117 433
4 TraesCS5D01G349500 chr5A 87.042 355 37 6 1 350 677937214 677936864 2.170000e-105 392
5 TraesCS5D01G349500 chr3B 89.260 2244 166 40 137 2330 810463288 810465506 0.000000e+00 2739
6 TraesCS5D01G349500 chr3B 93.041 1480 82 11 868 2330 763007348 763005873 0.000000e+00 2143
7 TraesCS5D01G349500 chr3B 90.832 1538 104 19 670 2181 827648464 827646938 0.000000e+00 2025
8 TraesCS5D01G349500 chr3B 90.702 1538 106 19 670 2181 827103216 827101690 0.000000e+00 2013
9 TraesCS5D01G349500 chr1A 91.129 1905 137 15 447 2330 60028906 60030799 0.000000e+00 2553
10 TraesCS5D01G349500 chr1A 89.573 422 37 2 1 416 60028485 60028905 1.590000e-146 529
11 TraesCS5D01G349500 chr1B 90.694 1687 113 27 670 2330 309928276 309929944 0.000000e+00 2206
12 TraesCS5D01G349500 chr1B 89.232 1718 135 28 643 2330 66183507 66185204 0.000000e+00 2102
13 TraesCS5D01G349500 chr7D 91.009 1646 114 24 701 2330 101182780 101181153 0.000000e+00 2189
14 TraesCS5D01G349500 chr7D 87.302 504 51 8 1 496 558793336 558793834 4.350000e-157 564
15 TraesCS5D01G349500 chr6B 90.468 1689 114 27 668 2330 553384297 553385964 0.000000e+00 2183
16 TraesCS5D01G349500 chr3A 93.113 1481 77 10 868 2330 601364995 601363522 0.000000e+00 2146
17 TraesCS5D01G349500 chr3A 91.474 1513 114 9 827 2330 25255565 25254059 0.000000e+00 2065
18 TraesCS5D01G349500 chr2D 89.825 1710 116 33 647 2330 71956716 71955039 0.000000e+00 2141
19 TraesCS5D01G349500 chr6A 91.299 1586 96 23 443 1995 209854353 209852777 0.000000e+00 2126
20 TraesCS5D01G349500 chr6A 90.265 452 36 3 2 447 209854881 209854432 3.340000e-163 584
21 TraesCS5D01G349500 chr2A 89.480 1692 129 27 647 2310 759649610 759651280 0.000000e+00 2093
22 TraesCS5D01G349500 chr2A 91.579 1235 75 13 1113 2330 726320085 726321307 0.000000e+00 1677
23 TraesCS5D01G349500 chr2A 84.531 1642 176 54 121 1712 702303106 702301493 0.000000e+00 1554
24 TraesCS5D01G349500 chr2A 92.393 631 38 5 1708 2330 702299777 702299149 0.000000e+00 891
25 TraesCS5D01G349500 chr2A 87.216 352 39 6 1 349 759648895 759649243 1.680000e-106 396
26 TraesCS5D01G349500 chr6D 88.979 1724 129 41 642 2330 319012159 319010462 0.000000e+00 2074
27 TraesCS5D01G349500 chr7A 88.967 1713 137 28 646 2330 494280245 494278557 0.000000e+00 2069
28 TraesCS5D01G349500 chr5B 91.852 1485 89 11 864 2330 35398180 35396710 0.000000e+00 2043
29 TraesCS5D01G349500 chr4B 76.923 1365 254 40 1000 2330 386759216 386757879 0.000000e+00 719
30 TraesCS5D01G349500 chr4A 88.102 353 37 4 2 350 8505133 8505484 4.630000e-112 414


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 TraesCS5D01G349500 chr5D 434470128 434472457 2329 True 4303.0 4303 100.000 1 2330 1 chr5D.!!$R2 2329
1 TraesCS5D01G349500 chr5D 159650583 159652050 1467 True 2194.0 2194 93.712 864 2330 1 chr5D.!!$R1 1466
2 TraesCS5D01G349500 chr5A 520467631 520469968 2337 True 3190.0 3190 91.415 3 2330 1 chr5A.!!$R1 2327
3 TraesCS5D01G349500 chr3B 810463288 810465506 2218 False 2739.0 2739 89.260 137 2330 1 chr3B.!!$F1 2193
4 TraesCS5D01G349500 chr3B 763005873 763007348 1475 True 2143.0 2143 93.041 868 2330 1 chr3B.!!$R1 1462
5 TraesCS5D01G349500 chr3B 827646938 827648464 1526 True 2025.0 2025 90.832 670 2181 1 chr3B.!!$R3 1511
6 TraesCS5D01G349500 chr3B 827101690 827103216 1526 True 2013.0 2013 90.702 670 2181 1 chr3B.!!$R2 1511
7 TraesCS5D01G349500 chr1A 60028485 60030799 2314 False 1541.0 2553 90.351 1 2330 2 chr1A.!!$F1 2329
8 TraesCS5D01G349500 chr1B 309928276 309929944 1668 False 2206.0 2206 90.694 670 2330 1 chr1B.!!$F2 1660
9 TraesCS5D01G349500 chr1B 66183507 66185204 1697 False 2102.0 2102 89.232 643 2330 1 chr1B.!!$F1 1687
10 TraesCS5D01G349500 chr7D 101181153 101182780 1627 True 2189.0 2189 91.009 701 2330 1 chr7D.!!$R1 1629
11 TraesCS5D01G349500 chr6B 553384297 553385964 1667 False 2183.0 2183 90.468 668 2330 1 chr6B.!!$F1 1662
12 TraesCS5D01G349500 chr3A 601363522 601364995 1473 True 2146.0 2146 93.113 868 2330 1 chr3A.!!$R2 1462
13 TraesCS5D01G349500 chr3A 25254059 25255565 1506 True 2065.0 2065 91.474 827 2330 1 chr3A.!!$R1 1503
14 TraesCS5D01G349500 chr2D 71955039 71956716 1677 True 2141.0 2141 89.825 647 2330 1 chr2D.!!$R1 1683
15 TraesCS5D01G349500 chr6A 209852777 209854881 2104 True 1355.0 2126 90.782 2 1995 2 chr6A.!!$R1 1993
16 TraesCS5D01G349500 chr2A 726320085 726321307 1222 False 1677.0 1677 91.579 1113 2330 1 chr2A.!!$F1 1217
17 TraesCS5D01G349500 chr2A 759648895 759651280 2385 False 1244.5 2093 88.348 1 2310 2 chr2A.!!$F2 2309
18 TraesCS5D01G349500 chr2A 702299149 702303106 3957 True 1222.5 1554 88.462 121 2330 2 chr2A.!!$R1 2209
19 TraesCS5D01G349500 chr6D 319010462 319012159 1697 True 2074.0 2074 88.979 642 2330 1 chr6D.!!$R1 1688
20 TraesCS5D01G349500 chr7A 494278557 494280245 1688 True 2069.0 2069 88.967 646 2330 1 chr7A.!!$R1 1684
21 TraesCS5D01G349500 chr5B 35396710 35398180 1470 True 2043.0 2043 91.852 864 2330 1 chr5B.!!$R1 1466
22 TraesCS5D01G349500 chr4B 386757879 386759216 1337 True 719.0 719 76.923 1000 2330 1 chr4B.!!$R1 1330

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
885 1200 0.174845 TTTGGTAGATCGCGGACTGG 59.825 55.0 6.13 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1703 2067 0.108585 GCACCACCCTTCAGTTCTGA 59.891 55.0 0.0 0.0 0.0 3.27 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
27 28 2.931386 GGATTCGGCTTGCGATCG 59.069 61.111 11.69 11.69 0.00 3.69
219 220 0.777446 ACTGTTATGGCAGGGTTGGT 59.223 50.000 0.00 0.00 40.59 3.67
306 310 3.306917 TGAGCTGTTCGTCGGAATTTA 57.693 42.857 0.00 0.00 34.05 1.40
488 646 2.549992 GGGATACATGCATGAGCGGTTA 60.550 50.000 32.75 13.83 41.49 2.85
640 932 3.263425 AGATTCCTGGTAAACGGTGACAT 59.737 43.478 0.00 0.00 0.00 3.06
757 1059 1.247567 ATTGTTTGCGAGTTCAGGGG 58.752 50.000 0.00 0.00 0.00 4.79
866 1180 5.838521 AGAAAGGTTGTGTGGGTCATATTTT 59.161 36.000 0.00 0.00 0.00 1.82
885 1200 0.174845 TTTGGTAGATCGCGGACTGG 59.825 55.000 6.13 0.00 0.00 4.00
913 1228 0.458669 TTCAGACGAGGAATACGGGC 59.541 55.000 0.00 0.00 34.93 6.13
989 1304 1.674817 CGGCAACAGGTCGGTTAGATT 60.675 52.381 0.00 0.00 42.02 2.40
1148 1470 1.008538 CAGCCAAGGTTGACAACGC 60.009 57.895 12.07 9.62 0.00 4.84
1242 1579 3.361786 TGTCATGGACGAAGATACTCCA 58.638 45.455 0.00 0.00 38.47 3.86
1280 1618 6.919721 ACAAGTTGGCAAATCGTTATATGTT 58.080 32.000 7.96 0.00 0.00 2.71
1298 1637 0.250124 TTCAAGTCGGCGACCAACAT 60.250 50.000 34.04 14.64 32.18 2.71
1328 1668 6.892658 TTTGAAGCAAAAGTTCTATGGCTA 57.107 33.333 0.00 0.00 29.89 3.93
1504 1851 7.523293 TTACATTGACACATGGAAAGACAAT 57.477 32.000 0.00 0.20 0.00 2.71
1562 1909 5.068855 TGGACATGAGTTGATGAAGCAAAAA 59.931 36.000 0.00 0.00 0.00 1.94
1581 1928 3.672767 AAAAATGCTGCAGAAAGGGAG 57.327 42.857 20.43 0.00 0.00 4.30
1585 1932 1.644509 TGCTGCAGAAAGGGAGAGTA 58.355 50.000 20.43 0.00 0.00 2.59
1586 1933 1.276421 TGCTGCAGAAAGGGAGAGTAC 59.724 52.381 20.43 0.00 0.00 2.73
1703 2067 4.043435 GGGGACATATAAAGAGGGAATGCT 59.957 45.833 0.00 0.00 0.00 3.79
1720 3804 0.398318 GCTCAGAACTGAAGGGTGGT 59.602 55.000 6.01 0.00 39.39 4.16
1785 3869 8.989980 CAGTGATAGTGATGTTCTCGTAGTATA 58.010 37.037 0.00 0.00 0.00 1.47
1850 3937 1.195448 CTTGCTCTTTTCATGCGACGT 59.805 47.619 0.00 0.00 0.00 4.34
1938 4033 1.066858 CGTGTTGCTGGAGTAGGTGAT 60.067 52.381 0.00 0.00 0.00 3.06
1961 4056 3.920446 TCAAAATCAAGATGGTCGACGA 58.080 40.909 9.92 5.99 0.00 4.20
2001 4097 1.130054 AGTCAGGCATGTGTCAGGGT 61.130 55.000 0.00 0.00 0.00 4.34
2048 4144 5.190726 TGGTGTTCTTCATGATGGTGGTATA 59.809 40.000 8.60 0.00 0.00 1.47
2049 4145 6.126507 TGGTGTTCTTCATGATGGTGGTATAT 60.127 38.462 8.60 0.00 0.00 0.86
2059 4156 5.879763 TGATGGTGGTATATGGAATTCTGG 58.120 41.667 5.23 0.00 0.00 3.86
2089 4186 6.423182 TCGGGATAAGAAGACCATGAAAATT 58.577 36.000 0.00 0.00 0.00 1.82
2125 4222 5.379706 TGACTGTGATGATAGGAGAGAGA 57.620 43.478 0.00 0.00 0.00 3.10
2134 4231 1.765230 TAGGAGAGAGAACGGCTTCC 58.235 55.000 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 1.153061 ACTCCGATCTATCCGGCCA 59.847 57.895 2.24 0.00 46.10 5.36
219 220 2.253051 TCGCACGTACTCACCGACA 61.253 57.895 0.00 0.00 0.00 4.35
336 341 5.450550 GCAGCACAGTAACTTTCCTTTTCTT 60.451 40.000 0.00 0.00 0.00 2.52
496 654 2.301346 CCTGGCCACACATATCTTTCC 58.699 52.381 0.00 0.00 0.00 3.13
498 656 1.063717 CCCCTGGCCACACATATCTTT 60.064 52.381 0.00 0.00 0.00 2.52
501 659 0.179018 GTCCCCTGGCCACACATATC 60.179 60.000 0.00 0.00 0.00 1.63
504 665 2.430704 CTTGTCCCCTGGCCACACAT 62.431 60.000 0.00 0.00 0.00 3.21
640 932 5.319140 TGATACGGAAATCGAGTCTGAAA 57.681 39.130 13.25 3.36 42.43 2.69
757 1059 0.319641 AACTCGTCCGCTCCACTTTC 60.320 55.000 0.00 0.00 0.00 2.62
866 1180 0.174845 CCAGTCCGCGATCTACCAAA 59.825 55.000 8.23 0.00 0.00 3.28
885 1200 4.373116 TCGTCTGAAGCCACGCCC 62.373 66.667 0.00 0.00 35.93 6.13
913 1228 5.578727 CCTCCTCACGAAAAAGATCACTAAG 59.421 44.000 0.00 0.00 0.00 2.18
1077 1396 1.416030 TGCTGCGCCAGAATATCCTTA 59.584 47.619 4.18 0.00 32.44 2.69
1148 1470 0.179048 TTGCATATCCTCCCACGCAG 60.179 55.000 0.00 0.00 0.00 5.18
1242 1579 3.390967 CCAACTTGTCCCAAATTCCCTTT 59.609 43.478 0.00 0.00 0.00 3.11
1280 1618 0.948623 CATGTTGGTCGCCGACTTGA 60.949 55.000 17.76 0.38 42.33 3.02
1298 1637 6.147864 AGAACTTTTGCTTCAAATACAGCA 57.852 33.333 0.00 0.00 44.43 4.41
1328 1668 1.604378 CGACCCCTCCTGCATCTTT 59.396 57.895 0.00 0.00 0.00 2.52
1504 1851 5.819379 GCAGTGACTTCCTCATTATTGATGA 59.181 40.000 0.00 0.00 42.42 2.92
1562 1909 2.824341 CTCTCCCTTTCTGCAGCATTTT 59.176 45.455 9.47 0.00 0.00 1.82
1565 1912 0.990374 ACTCTCCCTTTCTGCAGCAT 59.010 50.000 9.47 0.00 0.00 3.79
1586 1933 0.961753 GCCAACTCCAAACCTTGAGG 59.038 55.000 0.00 0.00 42.17 3.86
1599 1946 4.459337 GCTGATAACCTTTAACTGCCAACT 59.541 41.667 0.00 0.00 0.00 3.16
1703 2067 0.108585 GCACCACCCTTCAGTTCTGA 59.891 55.000 0.00 0.00 0.00 3.27
1720 3804 0.392327 TAGCCGCATTAGCACTTGCA 60.392 50.000 3.62 0.00 45.16 4.08
1785 3869 2.997303 GTTTTTGTTGACCGCCTGTTTT 59.003 40.909 0.00 0.00 0.00 2.43
1850 3937 2.589720 TGTACGAAGAGAACCACTGGA 58.410 47.619 0.71 0.00 0.00 3.86
1938 4033 5.656480 TCGTCGACCATCTTGATTTTGATA 58.344 37.500 10.58 0.00 0.00 2.15
1961 4056 1.134965 CCTCGAAGATCCGCTCAACTT 60.135 52.381 0.00 0.00 33.89 2.66
2001 4097 6.542370 CCAAGCGAAATTAGATTCCTCCTTAA 59.458 38.462 0.00 0.00 0.00 1.85
2048 4144 2.105477 CCCGATCAGACCAGAATTCCAT 59.895 50.000 0.65 0.00 0.00 3.41
2049 4145 1.486310 CCCGATCAGACCAGAATTCCA 59.514 52.381 0.65 0.00 0.00 3.53
2059 4156 3.637229 TGGTCTTCTTATCCCGATCAGAC 59.363 47.826 0.00 0.00 0.00 3.51
2089 4186 4.297768 TCACAGTCATCCCATCTTCCATA 58.702 43.478 0.00 0.00 0.00 2.74
2125 4222 2.871096 TGTAAAGATGGGAAGCCGTT 57.129 45.000 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.