Multiple sequence alignment - TraesCS5B01G031400

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 TraesCS5B01G031400 chr5B 100.000 2288 0 0 1 2288 34490388 34492675 0.000000e+00 4226
1 TraesCS5B01G031400 chr5B 87.330 442 31 11 1731 2152 34253899 34254335 1.230000e-132 483
2 TraesCS5B01G031400 chr5B 81.475 610 50 16 1730 2288 34010141 34010738 2.090000e-120 442
3 TraesCS5B01G031400 chr5B 84.580 441 42 8 1730 2149 34561437 34561872 4.550000e-112 414
4 TraesCS5B01G031400 chr5B 80.721 555 59 22 1757 2269 34591219 34591767 2.760000e-104 388
5 TraesCS5B01G031400 chr5B 81.818 440 37 20 1730 2149 34549456 34549872 1.690000e-86 329
6 TraesCS5B01G031400 chr5B 83.803 284 42 3 1869 2152 34725057 34725336 1.350000e-67 267
7 TraesCS5B01G031400 chr5B 88.000 150 15 3 2141 2288 34254389 34254537 8.400000e-40 174
8 TraesCS5B01G031400 chr5B 89.344 122 12 1 2146 2266 34561955 34562076 3.940000e-33 152
9 TraesCS5B01G031400 chr3D 92.614 1733 97 10 2 1728 449746642 449748349 0.000000e+00 2462
10 TraesCS5B01G031400 chr3D 88.761 1735 142 28 2 1729 113913341 113911653 0.000000e+00 2074
11 TraesCS5B01G031400 chr4D 92.707 1618 105 8 114 1729 56941670 56943276 0.000000e+00 2322
12 TraesCS5B01G031400 chr5D 90.435 1725 136 14 7 1729 416789961 416791658 0.000000e+00 2244
13 TraesCS5B01G031400 chr5D 91.156 441 20 7 1730 2152 40748793 40749232 4.240000e-162 580
14 TraesCS5B01G031400 chr5D 91.232 422 18 1 1730 2132 40721415 40721836 7.140000e-155 556
15 TraesCS5B01G031400 chr5D 91.765 255 16 5 1900 2152 40721946 40722197 1.300000e-92 350
16 TraesCS5B01G031400 chr5D 77.803 437 67 11 1730 2143 40784823 40785252 2.270000e-60 243
17 TraesCS5B01G031400 chr5D 88.535 157 12 1 1900 2056 40768152 40768302 3.880000e-43 185
18 TraesCS5B01G031400 chr3A 90.254 1734 141 18 2 1729 418765649 418763938 0.000000e+00 2241
19 TraesCS5B01G031400 chr4A 90.724 1617 136 9 113 1726 78819558 78817953 0.000000e+00 2143
20 TraesCS5B01G031400 chr6D 89.319 1704 141 19 2 1703 469235228 469236892 0.000000e+00 2100
21 TraesCS5B01G031400 chr1B 88.242 1735 171 23 1 1729 192470101 192468394 0.000000e+00 2043
22 TraesCS5B01G031400 chr1B 86.012 1730 184 28 7 1729 311135931 311134253 0.000000e+00 1801
23 TraesCS5B01G031400 chr2B 89.018 1548 138 18 189 1729 495053922 495055444 0.000000e+00 1888
24 TraesCS5B01G031400 chr5A 88.772 570 24 6 1730 2274 28897031 28897585 0.000000e+00 662
25 TraesCS5B01G031400 chr5A 86.456 443 35 11 1730 2152 28710264 28710701 1.600000e-126 462


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 TraesCS5B01G031400 chr5B 34490388 34492675 2287 False 4226.0 4226 100.0000 1 2288 1 chr5B.!!$F2 2287
1 TraesCS5B01G031400 chr5B 34010141 34010738 597 False 442.0 442 81.4750 1730 2288 1 chr5B.!!$F1 558
2 TraesCS5B01G031400 chr5B 34591219 34591767 548 False 388.0 388 80.7210 1757 2269 1 chr5B.!!$F4 512
3 TraesCS5B01G031400 chr5B 34253899 34254537 638 False 328.5 483 87.6650 1731 2288 2 chr5B.!!$F6 557
4 TraesCS5B01G031400 chr5B 34561437 34562076 639 False 283.0 414 86.9620 1730 2266 2 chr5B.!!$F7 536
5 TraesCS5B01G031400 chr3D 449746642 449748349 1707 False 2462.0 2462 92.6140 2 1728 1 chr3D.!!$F1 1726
6 TraesCS5B01G031400 chr3D 113911653 113913341 1688 True 2074.0 2074 88.7610 2 1729 1 chr3D.!!$R1 1727
7 TraesCS5B01G031400 chr4D 56941670 56943276 1606 False 2322.0 2322 92.7070 114 1729 1 chr4D.!!$F1 1615
8 TraesCS5B01G031400 chr5D 416789961 416791658 1697 False 2244.0 2244 90.4350 7 1729 1 chr5D.!!$F4 1722
9 TraesCS5B01G031400 chr5D 40721415 40722197 782 False 453.0 556 91.4985 1730 2152 2 chr5D.!!$F5 422
10 TraesCS5B01G031400 chr3A 418763938 418765649 1711 True 2241.0 2241 90.2540 2 1729 1 chr3A.!!$R1 1727
11 TraesCS5B01G031400 chr4A 78817953 78819558 1605 True 2143.0 2143 90.7240 113 1726 1 chr4A.!!$R1 1613
12 TraesCS5B01G031400 chr6D 469235228 469236892 1664 False 2100.0 2100 89.3190 2 1703 1 chr6D.!!$F1 1701
13 TraesCS5B01G031400 chr1B 192468394 192470101 1707 True 2043.0 2043 88.2420 1 1729 1 chr1B.!!$R1 1728
14 TraesCS5B01G031400 chr1B 311134253 311135931 1678 True 1801.0 1801 86.0120 7 1729 1 chr1B.!!$R2 1722
15 TraesCS5B01G031400 chr2B 495053922 495055444 1522 False 1888.0 1888 89.0180 189 1729 1 chr2B.!!$F1 1540
16 TraesCS5B01G031400 chr5A 28897031 28897585 554 False 662.0 662 88.7720 1730 2274 1 chr5A.!!$F2 544

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
161 165 0.417841 TCCTCTTTAGGCTCCCCACT 59.582 55.0 0.0 0.0 43.31 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1604 1643 0.034089 GGTTGCCTACATGCCCTCTT 60.034 55.0 0.0 0.0 0.0 2.85 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
67 68 1.446618 TCGTCGTCGTCATCCTCGA 60.447 57.895 1.33 0.00 38.33 4.04
147 151 3.176924 TGCACTAGTTCTTCCTCCTCT 57.823 47.619 0.00 0.00 0.00 3.69
161 165 0.417841 TCCTCTTTAGGCTCCCCACT 59.582 55.000 0.00 0.00 43.31 4.00
382 388 0.618680 AGTGGCCCTCATGAGCACTA 60.619 55.000 24.50 12.28 30.88 2.74
424 430 4.301505 GCATGGAGCCGAAGTTCA 57.698 55.556 3.32 0.00 37.23 3.18
521 527 2.478803 CCCAAGGGAAGGGGTTGGT 61.479 63.158 0.00 0.00 42.90 3.67
670 678 5.822519 AGAGTGACAGTCATGCAGTTTTAAA 59.177 36.000 6.51 0.00 0.00 1.52
735 743 3.945921 CTCCATGAATTGTGTGCAGATCT 59.054 43.478 0.00 0.00 0.00 2.75
738 746 4.880120 CCATGAATTGTGTGCAGATCTAGT 59.120 41.667 0.00 0.00 0.00 2.57
749 757 5.303845 TGTGCAGATCTAGTAGAGCAATGAT 59.696 40.000 17.31 0.00 31.99 2.45
841 850 3.164977 TTGTCGCCCACCACCTGA 61.165 61.111 0.00 0.00 0.00 3.86
842 851 3.177194 TTGTCGCCCACCACCTGAG 62.177 63.158 0.00 0.00 0.00 3.35
843 852 4.394712 GTCGCCCACCACCTGAGG 62.395 72.222 0.00 0.00 0.00 3.86
846 855 4.729918 GCCCACCACCTGAGGCTG 62.730 72.222 0.00 0.00 42.34 4.85
847 856 4.039092 CCCACCACCTGAGGCTGG 62.039 72.222 15.60 15.60 32.70 4.85
848 857 4.729918 CCACCACCTGAGGCTGGC 62.730 72.222 16.69 0.00 30.64 4.85
851 860 3.790437 CCACCTGAGGCTGGCGAT 61.790 66.667 0.00 0.00 0.00 4.58
893 902 1.878069 CGATGACGAGCGCATGGAA 60.878 57.895 11.47 0.00 42.66 3.53
925 939 1.069296 GCAACAAGCATCGCAACTACA 60.069 47.619 0.00 0.00 44.79 2.74
969 983 2.301346 CCAACTCACTTCTGCAAGGTT 58.699 47.619 0.00 0.00 33.37 3.50
984 998 2.871096 AGGTTATCCTTGCACCGAAA 57.129 45.000 0.00 0.00 42.12 3.46
1070 1084 0.320374 CTCAGGAACAACACCGGCTA 59.680 55.000 0.00 0.00 0.00 3.93
1080 1094 0.617820 ACACCGGCTACTCCTGGAAT 60.618 55.000 0.00 0.00 34.18 3.01
1085 1099 1.414181 CGGCTACTCCTGGAATGTGAT 59.586 52.381 0.00 0.00 0.00 3.06
1112 1126 0.107508 CTGATGAACGGCAGGGTGAT 60.108 55.000 0.00 0.00 0.00 3.06
1186 1200 1.070758 ACATGGTGACGTTCAAGCTCT 59.929 47.619 0.00 0.00 0.00 4.09
1314 1328 2.185387 GGCACCTCCTTCCTAAGTACA 58.815 52.381 0.00 0.00 0.00 2.90
1397 1424 7.710907 GTGTGGTACTGCTTATCTGAAATATGA 59.289 37.037 0.00 0.00 0.00 2.15
1516 1554 1.414919 GAGGTTACCACACACCAGACA 59.585 52.381 3.51 0.00 35.25 3.41
1580 1619 1.457455 AGGCAACCAAACACCAGGG 60.457 57.895 0.00 0.00 37.17 4.45
1600 1639 0.467844 AGTGTTGTTCAGCCCATGCA 60.468 50.000 0.00 0.00 41.13 3.96
1601 1640 0.038892 GTGTTGTTCAGCCCATGCAG 60.039 55.000 0.00 0.00 41.13 4.41
1602 1641 1.180456 TGTTGTTCAGCCCATGCAGG 61.180 55.000 0.00 0.00 41.13 4.85
1610 1649 2.441532 CCCATGCAGGCAAGAGGG 60.442 66.667 13.15 13.15 35.39 4.30
1611 1650 3.145551 CCATGCAGGCAAGAGGGC 61.146 66.667 0.00 0.00 43.80 5.19
1612 1651 2.361992 CATGCAGGCAAGAGGGCA 60.362 61.111 0.00 0.00 46.44 5.36
1613 1652 2.687902 ATGCAGGCAAGAGGGCAT 59.312 55.556 0.00 0.00 46.44 4.40
1615 1654 2.362120 GCAGGCAAGAGGGCATGT 60.362 61.111 1.76 0.00 46.51 3.21
1627 1682 1.194218 GGGCATGTAGGCAACCAAAT 58.806 50.000 0.00 0.00 46.44 2.32
1861 1917 2.500098 GGAGCTCTTGTATACACCACCA 59.500 50.000 14.64 0.00 0.00 4.17
2023 2104 3.006752 TGCAAGAAACATTTCCCCATGAC 59.993 43.478 0.00 0.00 37.92 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.242220 CGATGAACAAGAAGATGAAGGCG 60.242 47.826 0.00 0.00 0.00 5.52
126 127 3.718723 AGAGGAGGAAGAACTAGTGCAT 58.281 45.455 3.00 0.00 0.00 3.96
147 151 1.965414 TCATCAGTGGGGAGCCTAAA 58.035 50.000 0.00 0.00 0.00 1.85
329 335 0.036388 GACGCTGATTCCTGACCCAA 60.036 55.000 0.00 0.00 0.00 4.12
382 388 5.748402 TGACATGCAGAAGGAATCTAATGT 58.252 37.500 0.00 5.94 42.76 2.71
466 472 2.678934 CTTCCTCGGGTGGTCGGA 60.679 66.667 0.00 0.00 0.00 4.55
547 553 0.787084 ACCTTCCTCCTCTCCACTGA 59.213 55.000 0.00 0.00 0.00 3.41
550 556 1.276705 GTCAACCTTCCTCCTCTCCAC 59.723 57.143 0.00 0.00 0.00 4.02
670 678 6.301486 TCATGGCTTATTGAAGAGCATGTAT 58.699 36.000 5.83 0.00 40.63 2.29
735 743 4.321974 CGTGCCCATATCATTGCTCTACTA 60.322 45.833 0.00 0.00 0.00 1.82
738 746 2.289631 CCGTGCCCATATCATTGCTCTA 60.290 50.000 0.00 0.00 0.00 2.43
841 850 1.555075 TCTTTAGTTCATCGCCAGCCT 59.445 47.619 0.00 0.00 0.00 4.58
842 851 1.666189 GTCTTTAGTTCATCGCCAGCC 59.334 52.381 0.00 0.00 0.00 4.85
843 852 1.324736 CGTCTTTAGTTCATCGCCAGC 59.675 52.381 0.00 0.00 0.00 4.85
844 853 1.324736 GCGTCTTTAGTTCATCGCCAG 59.675 52.381 0.00 0.00 38.16 4.85
845 854 1.355971 GCGTCTTTAGTTCATCGCCA 58.644 50.000 0.00 0.00 38.16 5.69
847 856 1.324736 CAGGCGTCTTTAGTTCATCGC 59.675 52.381 0.00 0.00 42.32 4.58
848 857 2.854777 CTCAGGCGTCTTTAGTTCATCG 59.145 50.000 0.00 0.00 0.00 3.84
851 860 1.337823 GCCTCAGGCGTCTTTAGTTCA 60.338 52.381 0.00 0.00 39.62 3.18
915 929 1.687660 TGGTAGTGGTTGTAGTTGCGA 59.312 47.619 0.00 0.00 0.00 5.10
925 939 2.642171 TCCTCCTCATGGTAGTGGTT 57.358 50.000 0.00 0.00 34.23 3.67
969 983 3.244422 ACTCAAGTTTCGGTGCAAGGATA 60.244 43.478 0.00 0.00 0.00 2.59
984 998 0.682209 GCATGGGGATGCACTCAAGT 60.682 55.000 2.14 0.00 46.25 3.16
1042 1056 3.378427 GTGTTGTTCCTGAGCTTGAACTT 59.622 43.478 19.17 0.00 41.10 2.66
1070 1084 2.269023 TCACCATCACATTCCAGGAGT 58.731 47.619 0.00 0.00 0.00 3.85
1080 1094 3.076621 GTTCATCAGCTTCACCATCACA 58.923 45.455 0.00 0.00 0.00 3.58
1085 1099 0.955428 GCCGTTCATCAGCTTCACCA 60.955 55.000 0.00 0.00 0.00 4.17
1186 1200 0.761323 TTGAGGGTGTCGGGAGTGAA 60.761 55.000 0.00 0.00 0.00 3.18
1218 1232 0.820482 CCTCAATGCCATCGCCATCA 60.820 55.000 0.00 0.00 0.00 3.07
1314 1328 3.733337 ACAGTTCAAAGCAGACTCGATT 58.267 40.909 0.00 0.00 0.00 3.34
1358 1372 6.070194 AGCAGTACCACACCTCATAATAGTTT 60.070 38.462 0.00 0.00 0.00 2.66
1363 1377 4.844349 AAGCAGTACCACACCTCATAAT 57.156 40.909 0.00 0.00 0.00 1.28
1370 1396 3.887621 TCAGATAAGCAGTACCACACC 57.112 47.619 0.00 0.00 0.00 4.16
1397 1424 7.986085 AAACAGAGCATCAACTACTTAACAT 57.014 32.000 0.00 0.00 37.82 2.71
1516 1554 4.567971 CATGGTGTTTGGTTGTATGCAAT 58.432 39.130 0.00 0.00 36.92 3.56
1580 1619 0.242017 GCATGGGCTGAACAACACTC 59.758 55.000 0.00 0.00 36.96 3.51
1600 1639 1.918253 CCTACATGCCCTCTTGCCT 59.082 57.895 0.00 0.00 0.00 4.75
1601 1640 1.825622 GCCTACATGCCCTCTTGCC 60.826 63.158 0.00 0.00 0.00 4.52
1602 1641 0.680921 TTGCCTACATGCCCTCTTGC 60.681 55.000 0.00 0.00 0.00 4.01
1603 1642 1.098050 GTTGCCTACATGCCCTCTTG 58.902 55.000 0.00 0.00 0.00 3.02
1604 1643 0.034089 GGTTGCCTACATGCCCTCTT 60.034 55.000 0.00 0.00 0.00 2.85
1605 1644 1.207488 TGGTTGCCTACATGCCCTCT 61.207 55.000 0.00 0.00 0.00 3.69
1606 1645 0.323360 TTGGTTGCCTACATGCCCTC 60.323 55.000 0.00 0.00 0.00 4.30
1607 1646 0.114168 TTTGGTTGCCTACATGCCCT 59.886 50.000 0.00 0.00 0.00 5.19
1608 1647 1.194218 ATTTGGTTGCCTACATGCCC 58.806 50.000 0.00 0.00 0.00 5.36
1609 1648 3.447229 AGTTATTTGGTTGCCTACATGCC 59.553 43.478 0.00 0.00 0.00 4.40
1610 1649 4.718940 AGTTATTTGGTTGCCTACATGC 57.281 40.909 0.00 0.00 0.00 4.06
1611 1650 4.864247 GCAAGTTATTTGGTTGCCTACATG 59.136 41.667 0.00 0.00 40.61 3.21
1612 1651 4.526262 TGCAAGTTATTTGGTTGCCTACAT 59.474 37.500 3.98 0.00 44.90 2.29
1613 1652 3.891977 TGCAAGTTATTTGGTTGCCTACA 59.108 39.130 3.98 0.00 44.90 2.74
1614 1653 4.217550 TCTGCAAGTTATTTGGTTGCCTAC 59.782 41.667 3.98 0.00 44.90 3.18
1615 1654 4.402829 TCTGCAAGTTATTTGGTTGCCTA 58.597 39.130 3.98 0.00 44.90 3.93
1697 1752 6.599356 TTGGTTGCAGTAGTGAATAGTAGA 57.401 37.500 0.42 0.00 0.00 2.59
1832 1888 1.853963 TACAAGAGCTCCTCCTGGTC 58.146 55.000 10.93 0.00 34.23 4.02
1835 1891 3.068873 GGTGTATACAAGAGCTCCTCCTG 59.931 52.174 10.93 5.65 0.00 3.86
1861 1917 6.766467 ACATCTGGAAAAAGTTAGTTTCGTCT 59.234 34.615 0.00 0.00 36.11 4.18


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

AutoCloner maintained by Alex Coulton.