Multiple sequence alignment - TraesCS7D01G402400

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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 TraesCS7D01G402400 chr7D 100.000 2468 0 0 1 2468 519746679 519749146 0 4558
1 TraesCS7D01G402400 chr7D 90.543 1491 107 18 999 2468 531066600 531065123 0 1941
2 TraesCS7D01G402400 chr7D 95.896 999 41 0 1 999 519688362 519689360 0 1618
3 TraesCS7D01G402400 chr7D 95.604 1001 43 1 1 1000 212701201 212702201 0 1604
4 TraesCS7D01G402400 chr7D 95.346 795 34 2 999 1790 503837045 503836251 0 1260
5 TraesCS7D01G402400 chr7D 92.377 669 48 3 1802 2468 503836202 503835535 0 950
6 TraesCS7D01G402400 chr1D 90.763 1494 105 20 999 2466 316242842 316241356 0 1964
7 TraesCS7D01G402400 chr1D 95.904 1001 39 2 1 999 216241539 216242539 0 1620
8 TraesCS7D01G402400 chr1D 95.613 1003 40 4 1 999 110348891 110349893 0 1605
9 TraesCS7D01G402400 chr1D 95.691 998 42 1 2 999 333202880 333203876 0 1604
10 TraesCS7D01G402400 chr6D 90.715 1497 102 23 999 2468 25732440 25733926 0 1960
11 TraesCS7D01G402400 chr5D 90.642 1496 107 20 999 2468 333090242 333091730 0 1956
12 TraesCS7D01G402400 chr4D 90.642 1496 107 20 999 2468 491382617 491384105 0 1956
13 TraesCS7D01G402400 chr4D 95.800 1000 41 1 1 999 121409870 121410869 0 1613
14 TraesCS7D01G402400 chr4D 95.604 1001 41 3 1 999 20544237 20543238 0 1602
15 TraesCS7D01G402400 chr4D 95.586 793 33 2 999 1790 470183501 470182710 0 1269
16 TraesCS7D01G402400 chr3D 90.642 1496 107 19 999 2468 335260 336748 0 1956
17 TraesCS7D01G402400 chr3D 95.704 1001 41 2 1 999 532050696 532051696 0 1609
18 TraesCS7D01G402400 chr3D 91.940 670 51 3 1802 2468 383171080 383170411 0 935
19 TraesCS7D01G402400 chr2D 90.575 1496 108 21 999 2468 130078003 130076515 0 1951
20 TraesCS7D01G402400 chr7A 89.519 1498 114 24 999 2468 70255751 70254269 0 1857
21 TraesCS7D01G402400 chr6A 95.696 999 41 1 1 999 595694687 595695683 0 1605
22 TraesCS7D01G402400 chr1A 95.586 793 28 4 999 1790 518114572 518115358 0 1264
23 TraesCS7D01G402400 chr7B 91.955 808 56 6 999 1801 156407232 156406429 0 1123
24 TraesCS7D01G402400 chr7B 92.191 794 59 2 999 1789 43571245 43572038 0 1120
25 TraesCS7D01G402400 chr7B 91.905 803 57 6 999 1798 730311275 730312072 0 1116
26 TraesCS7D01G402400 chr6B 91.688 794 62 4 999 1790 142983750 142982959 0 1098
27 TraesCS7D01G402400 chr4B 91.169 804 63 4 999 1801 88350787 88349991 0 1085


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 TraesCS7D01G402400 chr7D 519746679 519749146 2467 False 4558 4558 100.0000 1 2468 1 chr7D.!!$F3 2467
1 TraesCS7D01G402400 chr7D 531065123 531066600 1477 True 1941 1941 90.5430 999 2468 1 chr7D.!!$R1 1469
2 TraesCS7D01G402400 chr7D 519688362 519689360 998 False 1618 1618 95.8960 1 999 1 chr7D.!!$F2 998
3 TraesCS7D01G402400 chr7D 212701201 212702201 1000 False 1604 1604 95.6040 1 1000 1 chr7D.!!$F1 999
4 TraesCS7D01G402400 chr7D 503835535 503837045 1510 True 1105 1260 93.8615 999 2468 2 chr7D.!!$R2 1469
5 TraesCS7D01G402400 chr1D 316241356 316242842 1486 True 1964 1964 90.7630 999 2466 1 chr1D.!!$R1 1467
6 TraesCS7D01G402400 chr1D 216241539 216242539 1000 False 1620 1620 95.9040 1 999 1 chr1D.!!$F2 998
7 TraesCS7D01G402400 chr1D 110348891 110349893 1002 False 1605 1605 95.6130 1 999 1 chr1D.!!$F1 998
8 TraesCS7D01G402400 chr1D 333202880 333203876 996 False 1604 1604 95.6910 2 999 1 chr1D.!!$F3 997
9 TraesCS7D01G402400 chr6D 25732440 25733926 1486 False 1960 1960 90.7150 999 2468 1 chr6D.!!$F1 1469
10 TraesCS7D01G402400 chr5D 333090242 333091730 1488 False 1956 1956 90.6420 999 2468 1 chr5D.!!$F1 1469
11 TraesCS7D01G402400 chr4D 491382617 491384105 1488 False 1956 1956 90.6420 999 2468 1 chr4D.!!$F2 1469
12 TraesCS7D01G402400 chr4D 121409870 121410869 999 False 1613 1613 95.8000 1 999 1 chr4D.!!$F1 998
13 TraesCS7D01G402400 chr4D 20543238 20544237 999 True 1602 1602 95.6040 1 999 1 chr4D.!!$R1 998
14 TraesCS7D01G402400 chr4D 470182710 470183501 791 True 1269 1269 95.5860 999 1790 1 chr4D.!!$R2 791
15 TraesCS7D01G402400 chr3D 335260 336748 1488 False 1956 1956 90.6420 999 2468 1 chr3D.!!$F1 1469
16 TraesCS7D01G402400 chr3D 532050696 532051696 1000 False 1609 1609 95.7040 1 999 1 chr3D.!!$F2 998
17 TraesCS7D01G402400 chr3D 383170411 383171080 669 True 935 935 91.9400 1802 2468 1 chr3D.!!$R1 666
18 TraesCS7D01G402400 chr2D 130076515 130078003 1488 True 1951 1951 90.5750 999 2468 1 chr2D.!!$R1 1469
19 TraesCS7D01G402400 chr7A 70254269 70255751 1482 True 1857 1857 89.5190 999 2468 1 chr7A.!!$R1 1469
20 TraesCS7D01G402400 chr6A 595694687 595695683 996 False 1605 1605 95.6960 1 999 1 chr6A.!!$F1 998
21 TraesCS7D01G402400 chr1A 518114572 518115358 786 False 1264 1264 95.5860 999 1790 1 chr1A.!!$F1 791
22 TraesCS7D01G402400 chr7B 156406429 156407232 803 True 1123 1123 91.9550 999 1801 1 chr7B.!!$R1 802
23 TraesCS7D01G402400 chr7B 43571245 43572038 793 False 1120 1120 92.1910 999 1789 1 chr7B.!!$F1 790
24 TraesCS7D01G402400 chr7B 730311275 730312072 797 False 1116 1116 91.9050 999 1798 1 chr7B.!!$F2 799
25 TraesCS7D01G402400 chr6B 142982959 142983750 791 True 1098 1098 91.6880 999 1790 1 chr6B.!!$R1 791
26 TraesCS7D01G402400 chr4B 88349991 88350787 796 True 1085 1085 91.1690 999 1801 1 chr4B.!!$R1 802

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
176 180 1.340088 TTAAGTGTGCGGACCCTACA 58.66 50.0 4.04 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2079 2150 0.616111 AGACGAAGAGGAGGTGCCAT 60.616 55.0 0.0 0.0 40.02 4.4 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
176 180 1.340088 TTAAGTGTGCGGACCCTACA 58.660 50.000 4.04 0.00 0.00 2.74
454 458 6.615264 ACTCATTAGTCATATTGCTTGCAG 57.385 37.500 0.00 0.00 0.00 4.41
560 564 1.362355 CCCAACAAACACCTTCGGC 59.638 57.895 0.00 0.00 0.00 5.54
610 614 3.304391 CCCAGTTACGTTGTGACATTTGG 60.304 47.826 0.00 0.00 0.00 3.28
629 633 1.476110 GGTAGCACACAAGGTGTTCCA 60.476 52.381 0.00 0.00 45.08 3.53
917 925 7.148355 TCAAGTTTCCGGTTAATACAATTCC 57.852 36.000 0.00 0.00 0.00 3.01
1089 1098 3.771479 TGCAGAAGGAGCTTGATTCTCTA 59.229 43.478 6.16 0.00 30.99 2.43
1145 1154 5.048083 TGTCCAAGTTGTTTGATTATCAGGC 60.048 40.000 1.45 0.00 39.21 4.85
1311 1320 8.883954 TTCAGAGTCAAGCTGATATAATCAAG 57.116 34.615 0.00 0.00 41.60 3.02
1341 1350 3.586618 GGAAGGCCATGAAGGAGATAGAT 59.413 47.826 5.01 0.00 41.22 1.98
1377 1386 7.446769 ACCTCCTTAAAGAAGAGAAGAAGAAC 58.553 38.462 0.00 0.00 34.25 3.01
1378 1387 7.071321 ACCTCCTTAAAGAAGAGAAGAAGAACA 59.929 37.037 0.00 0.00 34.25 3.18
1453 1462 4.287067 AGCTGGACAAGATCAAGGAAGTTA 59.713 41.667 0.00 0.00 0.00 2.24
1542 1559 2.751259 GACTGATCAGCCTGATGCAAAA 59.249 45.455 22.83 0.00 44.83 2.44
1606 1625 7.340487 AGAACTGGAATGGGTTTAGATCATTTC 59.660 37.037 0.00 0.00 32.05 2.17
1616 1635 5.391629 GGTTTAGATCATTTCGGTTGGTGTC 60.392 44.000 0.00 0.00 0.00 3.67
1646 1667 3.355378 TGTTTGCCCTGATCTGTAATGG 58.645 45.455 0.00 0.00 0.00 3.16
1657 1678 7.094205 CCCTGATCTGTAATGGCCAAATATTAC 60.094 40.741 10.96 14.79 39.21 1.89
1676 1697 0.747283 CCCTGATGCTGAGAACTGGC 60.747 60.000 0.00 0.00 0.00 4.85
1790 1812 3.830755 AGAAAATGCTTCATCACAGGCTT 59.169 39.130 0.00 0.00 0.00 4.35
1792 1835 4.708726 AAATGCTTCATCACAGGCTTAC 57.291 40.909 0.00 0.00 0.00 2.34
1794 1837 3.354948 TGCTTCATCACAGGCTTACAT 57.645 42.857 0.00 0.00 0.00 2.29
1796 1839 4.445453 TGCTTCATCACAGGCTTACATAG 58.555 43.478 0.00 0.00 0.00 2.23
1799 1842 6.041979 TGCTTCATCACAGGCTTACATAGATA 59.958 38.462 0.00 0.00 0.00 1.98
1800 1843 6.589523 GCTTCATCACAGGCTTACATAGATAG 59.410 42.308 0.00 0.00 0.00 2.08
1921 1980 2.558359 AGATTGCAAACACCCTGCTAAC 59.442 45.455 1.71 0.00 40.59 2.34
1922 1981 0.665835 TTGCAAACACCCTGCTAACG 59.334 50.000 0.00 0.00 40.59 3.18
1964 2025 5.929058 AACTGAATCTCACATAGAGCTGA 57.071 39.130 0.00 0.00 44.35 4.26
2032 2103 4.552365 TCCTGCCCTGCTATGCGC 62.552 66.667 0.00 0.00 39.77 6.09
2079 2150 1.990060 GAGTGGGAGGTGGCAGCTA 60.990 63.158 20.63 0.54 0.00 3.32
2131 2202 3.140225 GATGGGAGGAGGACGTCGC 62.140 68.421 9.92 3.87 41.78 5.19
2166 2237 0.034186 GGTGGGGTGATGATCTGCAA 60.034 55.000 0.00 0.00 0.00 4.08
2201 2272 1.776975 GCCCATAGCAGCTGGAGGAT 61.777 60.000 17.12 0.00 42.97 3.24
2290 2361 1.454479 CGCCTCCTTCATTGCCCAT 60.454 57.895 0.00 0.00 0.00 4.00
2291 2362 1.039233 CGCCTCCTTCATTGCCCATT 61.039 55.000 0.00 0.00 0.00 3.16
2293 2364 1.856629 CCTCCTTCATTGCCCATTGT 58.143 50.000 0.00 0.00 0.00 2.71
2368 2440 1.897225 GCTGCTTCTCCTGAGCCTCA 61.897 60.000 0.00 0.00 0.00 3.86
2410 2482 1.078143 GCATCCACGAGCCCTTCTT 60.078 57.895 0.00 0.00 0.00 2.52
2438 2510 4.272991 GCTGTATCTCTTGGCAATCTTCAG 59.727 45.833 0.00 6.65 0.00 3.02
2459 2531 4.096081 CAGGTAGTCGACGAATAGGTCTTT 59.904 45.833 10.46 0.00 34.75 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 70 1.134367 GATCACGGACATGACGAGGAA 59.866 52.381 18.41 4.34 34.93 3.36
176 180 5.886474 TCATGTCTACATAGTTCTCGAACCT 59.114 40.000 6.20 0.00 36.90 3.50
443 447 4.136796 CACTATAAGCCCTGCAAGCAATA 58.863 43.478 10.73 7.07 0.00 1.90
454 458 4.455877 GGTAATGCACATCACTATAAGCCC 59.544 45.833 0.00 0.00 0.00 5.19
518 522 5.843673 TGGCATAGATCGAGATTAGGATC 57.156 43.478 0.00 0.00 39.44 3.36
560 564 2.949451 AAGATGCTCTACAGGTGTCG 57.051 50.000 0.00 0.00 0.00 4.35
610 614 1.961793 TGGAACACCTTGTGTGCTAC 58.038 50.000 5.38 0.00 46.79 3.58
629 633 0.402504 TGCAACTCCCAAATACCGGT 59.597 50.000 13.98 13.98 0.00 5.28
1089 1098 3.434167 CCAGTTGGCTATACTGATTGGCT 60.434 47.826 13.87 0.00 44.52 4.75
1120 1129 6.516527 GCCTGATAATCAAACAACTTGGACAA 60.517 38.462 0.00 0.00 35.56 3.18
1311 1320 1.909700 TCATGGCCTTCCTTGTGTTC 58.090 50.000 3.32 0.00 38.34 3.18
1341 1350 2.992847 TAAGGAGGTCTCTGTCCACA 57.007 50.000 0.00 0.00 35.02 4.17
1377 1386 3.243101 GCTCAGCAATGACATTCTCCATG 60.243 47.826 0.00 0.00 39.07 3.66
1378 1387 2.950309 GCTCAGCAATGACATTCTCCAT 59.050 45.455 0.00 0.00 0.00 3.41
1453 1462 1.211457 GCCACTTCACTCCTCCATCAT 59.789 52.381 0.00 0.00 0.00 2.45
1577 1596 7.110155 TGATCTAAACCCATTCCAGTTCTTAC 58.890 38.462 0.00 0.00 0.00 2.34
1646 1667 4.144297 TCAGCATCAGGGTAATATTTGGC 58.856 43.478 0.00 0.00 0.00 4.52
1657 1678 0.747283 GCCAGTTCTCAGCATCAGGG 60.747 60.000 0.00 0.00 0.00 4.45
1726 1747 7.656412 AGCAACAAATTATGATACACACACAA 58.344 30.769 0.00 0.00 0.00 3.33
1790 1812 8.901472 ATGGGAGACTAAATGCTATCTATGTA 57.099 34.615 0.00 0.00 0.00 2.29
1792 1835 9.194972 TCTATGGGAGACTAAATGCTATCTATG 57.805 37.037 0.00 0.00 0.00 2.23
1796 1839 8.141268 GCTATCTATGGGAGACTAAATGCTATC 58.859 40.741 0.00 0.00 36.87 2.08
1799 1842 5.782331 TGCTATCTATGGGAGACTAAATGCT 59.218 40.000 0.00 0.00 36.87 3.79
1800 1843 6.042638 TGCTATCTATGGGAGACTAAATGC 57.957 41.667 0.00 0.00 36.87 3.56
1921 1980 6.089551 CAGTTATGTCTGTTTAGTTCTGTCCG 59.910 42.308 0.00 0.00 0.00 4.79
1922 1981 7.152645 TCAGTTATGTCTGTTTAGTTCTGTCC 58.847 38.462 0.00 0.00 36.85 4.02
1964 2025 5.807520 CAGATTCAGTTACAGCAGTTATCGT 59.192 40.000 0.00 0.00 0.00 3.73
2032 2103 4.436998 GAGGTGCGACGGTCAGGG 62.437 72.222 9.10 0.00 0.00 4.45
2079 2150 0.616111 AGACGAAGAGGAGGTGCCAT 60.616 55.000 0.00 0.00 40.02 4.40
2154 2225 1.827344 ACGAGGACTTGCAGATCATCA 59.173 47.619 12.58 0.00 0.00 3.07
2166 2237 2.254651 GCAACGACGACGAGGACT 59.745 61.111 15.32 0.00 42.66 3.85
2290 2361 0.251634 TGCCCATCGACATGCTACAA 59.748 50.000 0.00 0.00 0.00 2.41
2291 2362 0.469494 ATGCCCATCGACATGCTACA 59.531 50.000 0.00 0.00 0.00 2.74
2293 2364 0.758123 TCATGCCCATCGACATGCTA 59.242 50.000 8.47 0.00 42.72 3.49
2368 2440 3.716872 TCAAAAGAGGTGAGGAAGAAGGT 59.283 43.478 0.00 0.00 0.00 3.50
2410 2482 0.107508 GCCAAGAGATACAGCAGCCA 60.108 55.000 0.00 0.00 0.00 4.75
2438 2510 4.142513 ACAAAGACCTATTCGTCGACTACC 60.143 45.833 14.70 0.00 37.85 3.18


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

AutoCloner maintained by Alex Coulton.