Multiple sequence alignment - TraesCS3B01G573800

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 TraesCS3B01G573800 chr3B 100.000 2252 0 0 1 2252 804247666 804249917 0.000000e+00 4159
1 TraesCS3B01G573800 chr3A 92.084 2274 135 20 1 2252 727477637 727479887 0.000000e+00 3160
2 TraesCS3B01G573800 chr3D 91.680 1226 67 14 431 1631 597420736 597421951 0.000000e+00 1666
3 TraesCS3B01G573800 chr3D 81.536 1354 118 54 719 1998 597546747 597548042 0.000000e+00 994
4 TraesCS3B01G573800 chr3D 90.566 318 28 2 1796 2111 597422189 597422506 9.620000e-114 420
5 TraesCS3B01G573800 chr3D 88.496 226 11 3 3 228 597420346 597420556 2.220000e-65 259
6 TraesCS3B01G573800 chr3D 83.688 282 34 4 4 274 597546217 597546497 2.870000e-64 255
7 TraesCS3B01G573800 chr3D 88.750 160 15 1 212 371 597420572 597420728 2.280000e-45 193
8 TraesCS3B01G573800 chr3D 84.615 169 22 4 2059 2223 597548067 597548235 4.980000e-37 165
9 TraesCS3B01G573800 chr2A 92.095 1012 50 10 453 1437 605116258 605115250 0.000000e+00 1399
10 TraesCS3B01G573800 chr2A 92.841 433 23 3 1 433 605120302 605119878 2.460000e-174 621
11 TraesCS3B01G573800 chr2A 88.764 267 23 4 1570 1836 605114925 605114666 1.000000e-83 320


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 TraesCS3B01G573800 chr3B 804247666 804249917 2251 False 4159.000000 4159 100.000000 1 2252 1 chr3B.!!$F1 2251
1 TraesCS3B01G573800 chr3A 727477637 727479887 2250 False 3160.000000 3160 92.084000 1 2252 1 chr3A.!!$F1 2251
2 TraesCS3B01G573800 chr3D 597420346 597422506 2160 False 634.500000 1666 89.873000 3 2111 4 chr3D.!!$F1 2108
3 TraesCS3B01G573800 chr3D 597546217 597548235 2018 False 471.333333 994 83.279667 4 2223 3 chr3D.!!$F2 2219
4 TraesCS3B01G573800 chr2A 605114666 605120302 5636 True 780.000000 1399 91.233333 1 1836 3 chr2A.!!$R1 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
919 4587 3.253432 CGCTAGGCTTCCAAAGAAAACTT 59.747 43.478 0.0 0.0 0.0 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2150 6184 0.376852 CATGGCACGTCGGGTAATTG 59.623 55.0 0.0 0.0 0.0 2.32 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
25 26 5.182950 ACGGAGTGCATATAGAGATTCTCTG 59.817 44.000 23.60 10.64 42.51 3.35
98 110 7.670364 CACACATGGTAGGATCTGATATACAA 58.330 38.462 12.13 4.28 0.00 2.41
355 397 9.622004 CATGCACATATTCCAAGATCTAAATTC 57.378 33.333 0.00 0.00 0.00 2.17
358 400 8.844244 GCACATATTCCAAGATCTAAATTCACT 58.156 33.333 0.00 0.00 0.00 3.41
455 4103 9.950496 ATATGAATCCAAAGATCATAGGTGTAC 57.050 33.333 0.00 0.00 31.72 2.90
459 4107 6.174720 TCCAAAGATCATAGGTGTACCATC 57.825 41.667 3.56 0.00 38.89 3.51
476 4124 4.526970 ACCATCTTTGTGTCACTTGACTT 58.473 39.130 10.63 0.00 44.99 3.01
523 4171 7.500992 TGGTAAAACATAATTTTCTGTTGCCA 58.499 30.769 2.64 7.74 35.82 4.92
552 4201 4.202050 GCCTTGCATTTTTAGATGACGGAT 60.202 41.667 0.00 0.00 0.00 4.18
649 4300 4.523943 TGTTTTCATGCATTCCTACTTGCT 59.476 37.500 0.00 0.00 39.60 3.91
706 4360 8.240682 TGGACAATGAAACATTAACTAATTCCG 58.759 33.333 0.00 0.00 0.00 4.30
717 4371 8.024865 ACATTAACTAATTCCGTTGTTTAAGGC 58.975 33.333 3.93 0.00 0.00 4.35
766 4420 4.340950 TCATGGATCTACACAACTCGCATA 59.659 41.667 0.00 0.00 0.00 3.14
770 4424 5.768164 TGGATCTACACAACTCGCATAGATA 59.232 40.000 0.00 0.00 33.70 1.98
919 4587 3.253432 CGCTAGGCTTCCAAAGAAAACTT 59.747 43.478 0.00 0.00 0.00 2.66
927 4595 6.374578 GCTTCCAAAGAAAACTTACTAGCTG 58.625 40.000 0.00 0.00 0.00 4.24
1017 4686 0.173481 CGATGTCGTCCATGGACTGT 59.827 55.000 35.84 21.50 42.54 3.55
1089 4758 2.125512 GAAGTCGTCGCCATGGCT 60.126 61.111 33.07 13.87 39.32 4.75
1200 4890 5.221621 GGGGTCGACTCACTACTACTACTAT 60.222 48.000 18.98 0.00 0.00 2.12
1334 5035 9.013229 TGAGTAATAATGAAATTCAGTGCTTGT 57.987 29.630 6.17 0.00 37.87 3.16
1338 5039 8.693542 AATAATGAAATTCAGTGCTTGTTAGC 57.306 30.769 6.17 0.00 42.07 3.09
1339 5040 7.452880 TAATGAAATTCAGTGCTTGTTAGCT 57.547 32.000 6.17 0.00 42.16 3.32
1352 5062 2.076100 TGTTAGCTACATGTGCACTGC 58.924 47.619 19.41 13.63 0.00 4.40
1406 5123 7.772292 ACATAGTAATTGATCACTCTTGCATGT 59.228 33.333 0.00 0.00 0.00 3.21
1523 5253 6.405842 GGTGTCCATTTGTGTTTCTTTCTTCT 60.406 38.462 0.00 0.00 0.00 2.85
1528 5258 7.339212 TCCATTTGTGTTTCTTTCTTCTCTTGA 59.661 33.333 0.00 0.00 0.00 3.02
1633 5654 9.725019 CTCCAGTGGTTTATAGAATGCATATAA 57.275 33.333 9.54 0.00 0.00 0.98
1682 5703 4.023107 TCGAGAGAGAACAGACACGAATTT 60.023 41.667 0.00 0.00 34.84 1.82
1685 5706 6.085555 AGAGAGAACAGACACGAATTTGTA 57.914 37.500 0.00 0.00 0.00 2.41
1734 5758 6.031964 TCCTACATAGGTGGATCTTCTTCT 57.968 41.667 4.86 0.00 44.02 2.85
1738 5762 6.380079 ACATAGGTGGATCTTCTTCTTTGT 57.620 37.500 0.00 0.00 0.00 2.83
1748 5772 6.128063 GGATCTTCTTCTTTGTTGATGTCCAG 60.128 42.308 0.00 0.00 0.00 3.86
1757 5781 6.775142 TCTTTGTTGATGTCCAGGTTTTATCA 59.225 34.615 0.00 0.00 0.00 2.15
1772 5796 7.700656 CAGGTTTTATCATTCGGGTTGTTATTC 59.299 37.037 0.00 0.00 0.00 1.75
1820 5844 9.774742 GTATTATCAATTTGCGGATATTTCTCC 57.225 33.333 0.00 0.00 0.00 3.71
1821 5845 8.641498 ATTATCAATTTGCGGATATTTCTCCT 57.359 30.769 0.00 0.00 32.77 3.69
1822 5846 9.739276 ATTATCAATTTGCGGATATTTCTCCTA 57.261 29.630 0.00 0.00 32.77 2.94
1846 5873 9.583765 CTAGTAGTCCAACTAATTTAGTTCACC 57.416 37.037 17.00 8.89 45.38 4.02
1899 5926 8.341903 TGTTGTTTCTGTATATTGTTCACTGTG 58.658 33.333 0.17 0.17 0.00 3.66
1901 5928 6.484977 TGTTTCTGTATATTGTTCACTGTGCA 59.515 34.615 2.12 0.00 0.00 4.57
1915 5942 4.214758 TCACTGTGCATGTGATTTCTGAAG 59.785 41.667 17.70 0.00 39.23 3.02
2188 6223 5.450965 GCCATGTAATCTATTGCAACAGCTT 60.451 40.000 0.00 0.00 36.04 3.74
2211 6246 6.283544 TGTGATGCATTGGTTGTGAAATAT 57.716 33.333 0.00 0.00 0.00 1.28
2223 6258 7.424803 TGGTTGTGAAATATCAAACTGTTCAG 58.575 34.615 0.00 0.00 37.30 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 110 8.540388 TGTTCTATTGACAAAAGAGCTAGGTAT 58.460 33.333 0.00 0.0 0.00 2.73
355 397 9.546909 CACATTTACAAGTCTAATTGCTAAGTG 57.453 33.333 0.00 0.0 33.28 3.16
386 428 7.975058 CAGATGCCATTTGTGTTTCACATATTA 59.025 33.333 3.43 0.0 44.16 0.98
449 4097 8.156720 GTCAAGTGACACAAAGATGGTACACC 62.157 46.154 8.59 0.0 43.18 4.16
450 4098 5.277345 GTCAAGTGACACAAAGATGGTACAC 60.277 44.000 8.59 0.0 43.18 2.90
451 4099 4.814234 GTCAAGTGACACAAAGATGGTACA 59.186 41.667 8.59 0.0 44.05 2.90
523 4171 5.356751 TCATCTAAAAATGCAAGGCGTACAT 59.643 36.000 0.00 0.0 0.00 2.29
552 4201 6.764308 AGTACGACTTGTAGTTATGGCTAA 57.236 37.500 0.00 0.0 32.65 3.09
625 4274 5.186409 AGCAAGTAGGAATGCATGAAAACAT 59.814 36.000 0.00 0.0 44.95 2.71
643 4294 2.816087 CAGTAAGCATGTTGGAGCAAGT 59.184 45.455 0.00 0.0 0.00 3.16
649 4300 6.237901 AGTTAATCACAGTAAGCATGTTGGA 58.762 36.000 0.00 0.0 0.00 3.53
704 4358 6.905578 ACTATTTGTAAGCCTTAAACAACGG 58.094 36.000 0.00 0.0 33.10 4.44
766 4420 1.270826 CGATGGCCGTCTGATGTATCT 59.729 52.381 22.53 0.0 0.00 1.98
770 4424 2.501128 CCGATGGCCGTCTGATGT 59.499 61.111 22.53 0.0 36.31 3.06
834 4493 1.003718 ACGGCAGGTAGGTTGCTTC 60.004 57.895 0.00 0.0 41.27 3.86
927 4595 0.658897 CCGACGACTAGCTTCTCTCC 59.341 60.000 0.00 0.0 0.00 3.71
1017 4686 4.002506 AGCACCACGTGGATCGCA 62.003 61.111 40.21 0.0 44.19 5.10
1113 4782 4.681978 GAGAACCGCACGGCCACT 62.682 66.667 9.43 6.0 39.32 4.00
1156 4825 3.239253 GACCACCTGTGTCGGGGT 61.239 66.667 0.00 0.0 33.40 4.95
1164 4833 2.603776 GACCCCGAGACCACCTGT 60.604 66.667 0.00 0.0 0.00 4.00
1334 5035 2.470983 TGCAGTGCACATGTAGCTAA 57.529 45.000 21.04 0.0 31.71 3.09
1523 5253 7.022055 TCAAAACAAAAACGAGCTATCAAGA 57.978 32.000 0.00 0.0 0.00 3.02
1528 5258 6.575162 ATCCTCAAAACAAAAACGAGCTAT 57.425 33.333 0.00 0.0 0.00 2.97
1588 5499 8.925338 CACTGGAGGATTATAGGTTTAGTAGTT 58.075 37.037 0.00 0.0 0.00 2.24
1590 5501 7.509659 ACCACTGGAGGATTATAGGTTTAGTAG 59.490 40.741 0.71 0.0 0.00 2.57
1591 5502 7.367828 ACCACTGGAGGATTATAGGTTTAGTA 58.632 38.462 0.71 0.0 0.00 1.82
1597 5508 8.239478 TCTATAAACCACTGGAGGATTATAGGT 58.761 37.037 22.89 0.0 46.45 3.08
1650 5671 6.431543 TGTCTGTTCTCTCTCGATTCTACTTT 59.568 38.462 0.00 0.0 0.00 2.66
1654 5675 4.330347 CGTGTCTGTTCTCTCTCGATTCTA 59.670 45.833 0.00 0.0 0.00 2.10
1685 5706 7.730084 TGCACTCTATTGCTATATTCAGAGTT 58.270 34.615 8.12 0.0 43.41 3.01
1734 5758 6.968263 TGATAAAACCTGGACATCAACAAA 57.032 33.333 0.00 0.0 0.00 2.83
1738 5762 5.356751 CCGAATGATAAAACCTGGACATCAA 59.643 40.000 0.00 0.0 0.00 2.57
1748 5772 7.540299 TGAATAACAACCCGAATGATAAAACC 58.460 34.615 0.00 0.0 0.00 3.27
1757 5781 3.312421 CAGCGATGAATAACAACCCGAAT 59.688 43.478 0.00 0.0 0.00 3.34
1816 5840 9.765295 AACTAAATTAGTTGGACTACTAGGAGA 57.235 33.333 16.69 0.0 46.58 3.71
1846 5873 5.462398 CCAAGAATCCGGTAATTAGTTCTCG 59.538 44.000 0.00 0.0 0.00 4.04
1899 5926 5.522456 TCAAACACTTCAGAAATCACATGC 58.478 37.500 0.00 0.0 0.00 4.06
1901 5928 7.756395 AGATCAAACACTTCAGAAATCACAT 57.244 32.000 0.00 0.0 0.00 3.21
1915 5942 7.265673 TGATTACAGGCTAGTAGATCAAACAC 58.734 38.462 0.00 0.0 0.00 3.32
2017 6047 8.052748 TGAATGCTTACAATCCTAAGTGGTATT 58.947 33.333 0.00 0.0 37.07 1.89
2150 6184 0.376852 CATGGCACGTCGGGTAATTG 59.623 55.000 0.00 0.0 0.00 2.32
2158 6192 3.362986 GCAATAGATTACATGGCACGTCG 60.363 47.826 0.00 0.0 0.00 5.12
2188 6223 4.603989 ATTTCACAACCAATGCATCACA 57.396 36.364 0.00 0.0 0.00 3.58
2196 6231 8.420222 TGAACAGTTTGATATTTCACAACCAAT 58.580 29.630 0.00 0.0 0.00 3.16


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

AutoCloner maintained by Alex Coulton.