Multiple sequence alignment - TraesCS7D01G290900

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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 TraesCS7D01G290900 chr7D 100.000 2273 0 0 1 2273 346185852 346183580 0.000000e+00 4198
1 TraesCS7D01G290900 chr7D 93.884 932 19 8 686 1580 354527196 354528126 0.000000e+00 1371
2 TraesCS7D01G290900 chr7D 95.038 786 25 2 808 1580 195395561 195396345 0.000000e+00 1223
3 TraesCS7D01G290900 chr7D 96.366 688 19 4 1587 2273 354528163 354528845 0.000000e+00 1127
4 TraesCS7D01G290900 chr7D 95.924 687 18 3 1587 2273 195396383 195397059 0.000000e+00 1105
5 TraesCS7D01G290900 chr7D 92.436 661 50 0 1 661 394652855 394652195 0.000000e+00 944
6 TraesCS7D01G290900 chr7D 90.415 699 38 15 888 1565 588678969 588678279 0.000000e+00 893
7 TraesCS7D01G290900 chr7D 87.786 131 7 3 1444 1565 588841162 588841292 6.540000e-31 145
8 TraesCS7D01G290900 chr4B 91.458 878 52 7 715 1570 141079891 141080767 0.000000e+00 1184
9 TraesCS7D01G290900 chr4B 93.421 608 32 6 1668 2273 141080926 141081527 0.000000e+00 894
10 TraesCS7D01G290900 chr4B 94.231 416 20 4 1861 2273 621660522 621660936 1.150000e-177 632
11 TraesCS7D01G290900 chr7B 91.892 777 49 2 808 1570 253264583 253263807 0.000000e+00 1074
12 TraesCS7D01G290900 chr7B 94.554 606 26 6 1670 2273 253263646 253263046 0.000000e+00 929
13 TraesCS7D01G290900 chr7B 90.665 707 36 12 888 1565 663107699 663108404 0.000000e+00 913
14 TraesCS7D01G290900 chr2B 90.851 776 57 2 809 1570 311334443 311335218 0.000000e+00 1027
15 TraesCS7D01G290900 chr2B 92.092 607 40 4 1668 2273 311335377 311335976 0.000000e+00 848
16 TraesCS7D01G290900 chr2D 92.598 662 47 2 1 661 236105113 236105773 0.000000e+00 950
17 TraesCS7D01G290900 chr2D 94.667 150 8 0 680 829 274709752 274709603 1.360000e-57 233
18 TraesCS7D01G290900 chr5B 90.055 724 69 3 1 723 700896995 700897716 0.000000e+00 935
19 TraesCS7D01G290900 chr5B 88.780 205 15 4 1668 1864 308024021 308023817 6.270000e-61 244
20 TraesCS7D01G290900 chr7A 91.336 681 58 1 8 688 204135476 204136155 0.000000e+00 929
21 TraesCS7D01G290900 chr7A 88.705 726 77 5 1 723 689121275 689121998 0.000000e+00 881
22 TraesCS7D01G290900 chr7A 88.906 658 43 13 920 1554 680406716 680407366 0.000000e+00 784
23 TraesCS7D01G290900 chr7A 89.820 167 13 3 1665 1830 238547034 238547197 6.360000e-51 211
24 TraesCS7D01G290900 chr3D 91.692 662 51 3 1 661 316103989 316104647 0.000000e+00 915
25 TraesCS7D01G290900 chr3D 93.243 148 9 1 683 829 368369509 368369362 1.370000e-52 217
26 TraesCS7D01G290900 chr5D 89.546 727 64 9 1 723 410018165 410017447 0.000000e+00 911
27 TraesCS7D01G290900 chr3A 89.928 695 64 5 1 694 225320381 225319692 0.000000e+00 891
28 TraesCS7D01G290900 chr3A 88.705 726 77 5 1 723 526911052 526911775 0.000000e+00 881
29 TraesCS7D01G290900 chr4D 95.864 411 14 2 1865 2273 35719764 35720173 0.000000e+00 662
30 TraesCS7D01G290900 chr4D 96.958 263 7 1 1628 1889 35659421 35659159 7.450000e-120 440
31 TraesCS7D01G290900 chr4D 96.947 262 7 1 1628 1889 35645040 35644780 2.680000e-119 438
32 TraesCS7D01G290900 chr4D 95.333 150 7 0 680 829 310939838 310939689 2.920000e-59 239
33 TraesCS7D01G290900 chr3B 94.231 416 20 4 1861 2273 658959599 658960013 1.150000e-177 632
34 TraesCS7D01G290900 chr3B 90.132 152 11 2 691 839 538767365 538767215 6.410000e-46 195
35 TraesCS7D01G290900 chr1B 93.046 417 23 6 1861 2273 30060643 30061057 2.500000e-169 604
36 TraesCS7D01G290900 chr1B 93.590 156 5 2 696 851 616926911 616926761 6.320000e-56 228
37 TraesCS7D01G290900 chr6A 93.373 166 3 1 686 843 468509444 468509609 2.920000e-59 239
38 TraesCS7D01G290900 chr6A 93.750 160 3 3 685 843 385100617 385100770 1.360000e-57 233
39 TraesCS7D01G290900 chr6A 91.329 173 8 4 682 852 330782372 330782205 1.760000e-56 230


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 TraesCS7D01G290900 chr7D 346183580 346185852 2272 True 4198.0 4198 100.0000 1 2273 1 chr7D.!!$R1 2272
1 TraesCS7D01G290900 chr7D 354527196 354528845 1649 False 1249.0 1371 95.1250 686 2273 2 chr7D.!!$F3 1587
2 TraesCS7D01G290900 chr7D 195395561 195397059 1498 False 1164.0 1223 95.4810 808 2273 2 chr7D.!!$F2 1465
3 TraesCS7D01G290900 chr7D 394652195 394652855 660 True 944.0 944 92.4360 1 661 1 chr7D.!!$R2 660
4 TraesCS7D01G290900 chr7D 588678279 588678969 690 True 893.0 893 90.4150 888 1565 1 chr7D.!!$R3 677
5 TraesCS7D01G290900 chr4B 141079891 141081527 1636 False 1039.0 1184 92.4395 715 2273 2 chr4B.!!$F2 1558
6 TraesCS7D01G290900 chr7B 253263046 253264583 1537 True 1001.5 1074 93.2230 808 2273 2 chr7B.!!$R1 1465
7 TraesCS7D01G290900 chr7B 663107699 663108404 705 False 913.0 913 90.6650 888 1565 1 chr7B.!!$F1 677
8 TraesCS7D01G290900 chr2B 311334443 311335976 1533 False 937.5 1027 91.4715 809 2273 2 chr2B.!!$F1 1464
9 TraesCS7D01G290900 chr2D 236105113 236105773 660 False 950.0 950 92.5980 1 661 1 chr2D.!!$F1 660
10 TraesCS7D01G290900 chr5B 700896995 700897716 721 False 935.0 935 90.0550 1 723 1 chr5B.!!$F1 722
11 TraesCS7D01G290900 chr7A 204135476 204136155 679 False 929.0 929 91.3360 8 688 1 chr7A.!!$F1 680
12 TraesCS7D01G290900 chr7A 689121275 689121998 723 False 881.0 881 88.7050 1 723 1 chr7A.!!$F4 722
13 TraesCS7D01G290900 chr7A 680406716 680407366 650 False 784.0 784 88.9060 920 1554 1 chr7A.!!$F3 634
14 TraesCS7D01G290900 chr3D 316103989 316104647 658 False 915.0 915 91.6920 1 661 1 chr3D.!!$F1 660
15 TraesCS7D01G290900 chr5D 410017447 410018165 718 True 911.0 911 89.5460 1 723 1 chr5D.!!$R1 722
16 TraesCS7D01G290900 chr3A 225319692 225320381 689 True 891.0 891 89.9280 1 694 1 chr3A.!!$R1 693
17 TraesCS7D01G290900 chr3A 526911052 526911775 723 False 881.0 881 88.7050 1 723 1 chr3A.!!$F1 722

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
40 41 0.320771 TTGGTCCTCGAAGAAGCAGC 60.321 55.0 0.0 0.0 34.09 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1617 1770 0.320697 GGGTCGAACTAACTGCCTGT 59.679 55.0 0.0 0.0 0.0 4.0 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
40 41 0.320771 TTGGTCCTCGAAGAAGCAGC 60.321 55.000 0.00 0.00 34.09 5.25
44 45 1.202582 GTCCTCGAAGAAGCAGCACTA 59.797 52.381 0.00 0.00 34.09 2.74
46 47 1.067565 CCTCGAAGAAGCAGCACTACA 60.068 52.381 0.00 0.00 34.09 2.74
80 81 5.984695 ACTACTGAAGCTGAGTACATTGA 57.015 39.130 0.00 0.00 0.00 2.57
95 96 3.689347 ACATTGATGCTGGTTCTTGCTA 58.311 40.909 0.00 0.00 0.00 3.49
106 107 4.081406 TGGTTCTTGCTATGCTCAATTGT 58.919 39.130 5.13 0.00 0.00 2.71
205 206 4.646040 CCATCAAGATTGCTCATAACCCAA 59.354 41.667 0.00 0.00 0.00 4.12
246 247 2.286294 GCACATCCAGATTCGTCATCAC 59.714 50.000 1.13 0.00 33.75 3.06
294 295 2.791560 CGACATCTCCATCGAACATGTC 59.208 50.000 0.00 12.20 40.86 3.06
346 347 2.097825 CAAAGCCCTTGGATGAGAAGG 58.902 52.381 0.00 0.00 39.92 3.46
371 372 1.008079 GCAAGTTGCAGTGTGAGCC 60.008 57.895 22.90 0.00 44.26 4.70
399 400 6.917217 ATCTTGGAATCTTCGAATGTTCTC 57.083 37.500 17.10 10.81 0.00 2.87
515 517 8.622948 AACCCTCTAAGTGTGAAGAAATTAAG 57.377 34.615 0.00 0.00 0.00 1.85
542 544 7.510675 AGAATTTGATTCTCCTAACCCTACA 57.489 36.000 0.00 0.00 46.17 2.74
579 581 7.350467 CGGTGTCTGAAATCATCATTCTTATG 58.650 38.462 0.00 0.00 37.44 1.90
613 615 5.734720 TGCCACCAACAAAAGTTGAAAATA 58.265 33.333 9.73 0.00 36.50 1.40
648 670 8.825064 AGTTTTTCTTCATTTTTGCAAATTCG 57.175 26.923 13.65 4.37 29.41 3.34
747 769 3.526430 GTGGGACTATTTAGAAACCCCCT 59.474 47.826 0.00 0.00 35.58 4.79
1132 1225 1.903877 GAGGAGCTGCCCTTACTGCA 61.904 60.000 0.00 0.00 36.49 4.41
1511 1630 1.217882 CTCCGTTGCTCGTGAGTTTT 58.782 50.000 0.00 0.00 37.94 2.43
1575 1696 7.651304 AGATGATGCGATACAGTTCTTCTTAAG 59.349 37.037 0.00 0.00 0.00 1.85
1580 1701 8.821147 TGCGATACAGTTCTTCTTAAGTTTTA 57.179 30.769 1.63 0.00 0.00 1.52
1581 1702 8.922676 TGCGATACAGTTCTTCTTAAGTTTTAG 58.077 33.333 1.63 0.00 0.00 1.85
1582 1703 8.923683 GCGATACAGTTCTTCTTAAGTTTTAGT 58.076 33.333 1.63 0.00 0.00 2.24
1617 1770 5.598830 CCCTAGACAGTTAGCTATTTCAGGA 59.401 44.000 0.00 0.00 0.00 3.86
1619 1772 6.096987 CCTAGACAGTTAGCTATTTCAGGACA 59.903 42.308 0.00 0.00 0.00 4.02
1733 1950 6.623549 GCCTGATCAGTCGAAAAATGAATGAA 60.624 38.462 21.11 0.00 42.79 2.57
1734 1951 7.307694 CCTGATCAGTCGAAAAATGAATGAAA 58.692 34.615 21.11 0.00 42.79 2.69
1735 1952 7.484007 CCTGATCAGTCGAAAAATGAATGAAAG 59.516 37.037 21.11 0.00 42.79 2.62
1873 2093 1.471851 CGGTTACCCATACACGCATGA 60.472 52.381 0.00 0.00 0.00 3.07
1973 2194 6.713762 AAATCTCTCTCTATCTCTGTGTGG 57.286 41.667 0.00 0.00 0.00 4.17
1992 2213 0.905357 GGGAAGTTAGCAGGCAGAGA 59.095 55.000 0.00 0.00 0.00 3.10
2068 2290 7.068103 TGTTTCTATTGGTGTTTCAGTTGTCAT 59.932 33.333 0.00 0.00 0.00 3.06
2137 2359 8.869897 GTTAATTTCGAGTGTGATATCAGTTCA 58.130 33.333 5.42 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 6.819146 TCAGTAGTAGAGAGTGACATGTAGTG 59.181 42.308 0.00 0.00 0.00 2.74
44 45 5.124776 GCTTCAGTAGTAGAGAGTGACATGT 59.875 44.000 0.00 0.00 0.00 3.21
46 47 5.356751 CAGCTTCAGTAGTAGAGAGTGACAT 59.643 44.000 0.00 0.00 0.00 3.06
80 81 2.295885 GAGCATAGCAAGAACCAGCAT 58.704 47.619 0.00 0.00 0.00 3.79
95 96 4.619863 GCTTCATCCACAACAATTGAGCAT 60.620 41.667 13.59 0.00 0.00 3.79
106 107 3.819368 TGAGAGTTTGCTTCATCCACAA 58.181 40.909 0.00 0.00 0.00 3.33
165 166 1.738099 GGCACTCTCGTTGTCGCAT 60.738 57.895 0.00 0.00 36.96 4.73
205 206 3.056536 TGCTTAGTCTTCGAGTGCTGAAT 60.057 43.478 0.00 0.00 0.00 2.57
246 247 7.027760 CCTTCAACACATGATCATGAAGAAAG 58.972 38.462 36.37 27.41 46.16 2.62
294 295 2.665537 CGCTAGCTGTTCTTCAGTCTTG 59.334 50.000 13.93 0.00 45.23 3.02
346 347 3.253188 TCACACTGCAACTTGCTAAATCC 59.747 43.478 14.78 0.00 45.31 3.01
371 372 9.443283 GAACATTCGAAGATTCCAAGATATTTG 57.557 33.333 3.35 0.00 35.04 2.32
399 400 4.452455 GTGTTAGGATGTGTGTCCTTTCAG 59.548 45.833 0.15 0.00 46.45 3.02
532 534 4.201647 CGCGTACAATTGTTGTAGGGTTAG 60.202 45.833 17.78 0.00 45.99 2.34
533 535 3.679025 CGCGTACAATTGTTGTAGGGTTA 59.321 43.478 17.78 0.00 45.99 2.85
542 544 1.529438 CAGACACCGCGTACAATTGTT 59.471 47.619 17.78 0.95 0.00 2.83
648 670 7.250569 TGAAGAACATCAGTTGAAAAGTTGAC 58.749 34.615 0.00 0.00 38.30 3.18
865 919 2.700773 GCCTGTTGCCGGAATCCAC 61.701 63.158 5.05 0.00 0.00 4.02
1114 1207 1.920325 TGCAGTAAGGGCAGCTCCT 60.920 57.895 0.00 0.00 36.11 3.69
1511 1630 3.741245 AGAAGGACTGTAGCCAGACTA 57.259 47.619 0.00 0.00 41.50 2.59
1599 1752 4.624125 GCCTGTCCTGAAATAGCTAACTGT 60.624 45.833 0.00 0.00 0.00 3.55
1617 1770 0.320697 GGGTCGAACTAACTGCCTGT 59.679 55.000 0.00 0.00 0.00 4.00
1619 1772 1.002087 CTTGGGTCGAACTAACTGCCT 59.998 52.381 0.00 0.00 0.00 4.75
1803 2023 4.836825 ACTGCTACAGTAGACGGTAACTA 58.163 43.478 12.15 0.00 43.46 2.24
1873 2093 1.603456 TGCACAAACACATCCGATGT 58.397 45.000 8.28 8.28 46.22 3.06
1973 2194 0.905357 TCTCTGCCTGCTAACTTCCC 59.095 55.000 0.00 0.00 0.00 3.97
1992 2213 4.463050 TCATTTTCCCCTAACTGTTGGT 57.537 40.909 2.69 0.00 0.00 3.67
2038 2260 6.795399 ACTGAAACACCAATAGAAACAACAG 58.205 36.000 0.00 0.00 0.00 3.16
2068 2290 7.719633 GGATAACTGCTGAATTTTCATACCCTA 59.280 37.037 0.00 0.00 36.46 3.53


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

AutoCloner maintained by Alex Coulton.