Multiple sequence alignment - TraesCS7D01G038900

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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 TraesCS7D01G038900 chr7D 100.000 3340 0 0 1 3340 19906517 19909856 0.000000e+00 6168
1 TraesCS7D01G038900 chr7D 96.653 3346 104 7 1 3340 19834540 19837883 0.000000e+00 5552
2 TraesCS7D01G038900 chr7D 95.872 3343 109 16 1 3340 19773072 19776388 0.000000e+00 5382
3 TraesCS7D01G038900 chr7D 91.822 2568 172 18 780 3340 19742123 19744659 0.000000e+00 3544
4 TraesCS7D01G038900 chr7D 92.486 1850 129 6 1496 3340 19863185 19865029 0.000000e+00 2638
5 TraesCS7D01G038900 chr7D 92.378 1640 121 4 1496 3131 19817009 19818648 0.000000e+00 2333
6 TraesCS7D01G038900 chr7D 90.711 1421 117 10 1298 2717 19861782 19863188 0.000000e+00 1879
7 TraesCS7D01G038900 chr7D 90.429 1421 121 11 1298 2717 19815606 19817012 0.000000e+00 1857
8 TraesCS7D01G038900 chr7D 90.389 1207 102 9 1298 2503 19925006 19926199 0.000000e+00 1574
9 TraesCS7D01G038900 chr7D 86.940 781 77 10 2 779 19741283 19742041 0.000000e+00 854
10 TraesCS7D01G038900 chr7D 89.557 632 44 13 643 1267 19814991 19815607 0.000000e+00 782
11 TraesCS7D01G038900 chr7D 92.029 276 18 2 995 1267 19861509 19861783 5.230000e-103 385
12 TraesCS7D01G038900 chr7D 83.750 320 21 13 643 956 19924245 19924539 1.180000e-69 274
13 TraesCS7D01G038900 chr7D 93.443 183 11 1 1085 1267 19924826 19925007 1.530000e-68 270
14 TraesCS7D01G038900 chr7A 89.852 1350 101 18 1155 2502 20025060 20026375 0.000000e+00 1701
15 TraesCS7D01G038900 chr7A 87.832 1167 99 19 1 1155 20021862 20022997 0.000000e+00 1328
16 TraesCS7D01G038900 chrUn 88.223 1384 101 27 1 1371 50648069 50646735 0.000000e+00 1596
17 TraesCS7D01G038900 chrUn 95.848 843 32 3 2501 3340 306812001 306811159 0.000000e+00 1360
18 TraesCS7D01G038900 chrUn 89.873 1027 103 1 1478 2503 50646690 50645664 0.000000e+00 1319
19 TraesCS7D01G038900 chr2D 95.724 842 33 3 2502 3340 443396847 443396006 0.000000e+00 1352
20 TraesCS7D01G038900 chr4D 95.606 842 32 3 2501 3340 58029936 58029098 0.000000e+00 1345
21 TraesCS7D01G038900 chr3D 95.492 843 35 3 2501 3340 47120700 47119858 0.000000e+00 1343
22 TraesCS7D01G038900 chr5B 89.549 421 43 1 89 509 263520802 263521221 1.760000e-147 532
23 TraesCS7D01G038900 chr5A 91.293 379 33 0 89 467 313879063 313879441 4.940000e-143 518
24 TraesCS7D01G038900 chr5D 90.765 379 35 0 89 467 240086049 240085671 1.070000e-139 507
25 TraesCS7D01G038900 chr1D 86.588 425 54 3 89 511 17643358 17643781 1.810000e-127 466
26 TraesCS7D01G038900 chr2B 77.966 413 84 6 92 501 776761613 776762021 5.530000e-63 252


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 TraesCS7D01G038900 chr7D 19906517 19909856 3339 False 6168.000000 6168 100.000 1 3340 1 chr7D.!!$F3 3339
1 TraesCS7D01G038900 chr7D 19834540 19837883 3343 False 5552.000000 5552 96.653 1 3340 1 chr7D.!!$F2 3339
2 TraesCS7D01G038900 chr7D 19773072 19776388 3316 False 5382.000000 5382 95.872 1 3340 1 chr7D.!!$F1 3339
3 TraesCS7D01G038900 chr7D 19741283 19744659 3376 False 2199.000000 3544 89.381 2 3340 2 chr7D.!!$F4 3338
4 TraesCS7D01G038900 chr7D 19814991 19818648 3657 False 1657.333333 2333 90.788 643 3131 3 chr7D.!!$F5 2488
5 TraesCS7D01G038900 chr7D 19861509 19865029 3520 False 1634.000000 2638 91.742 995 3340 3 chr7D.!!$F6 2345
6 TraesCS7D01G038900 chr7D 19924245 19926199 1954 False 706.000000 1574 89.194 643 2503 3 chr7D.!!$F7 1860
7 TraesCS7D01G038900 chr7A 20021862 20026375 4513 False 1514.500000 1701 88.842 1 2502 2 chr7A.!!$F1 2501
8 TraesCS7D01G038900 chrUn 50645664 50648069 2405 True 1457.500000 1596 89.048 1 2503 2 chrUn.!!$R2 2502
9 TraesCS7D01G038900 chrUn 306811159 306812001 842 True 1360.000000 1360 95.848 2501 3340 1 chrUn.!!$R1 839
10 TraesCS7D01G038900 chr2D 443396006 443396847 841 True 1352.000000 1352 95.724 2502 3340 1 chr2D.!!$R1 838
11 TraesCS7D01G038900 chr4D 58029098 58029936 838 True 1345.000000 1345 95.606 2501 3340 1 chr4D.!!$R1 839
12 TraesCS7D01G038900 chr3D 47119858 47120700 842 True 1343.000000 1343 95.492 2501 3340 1 chr3D.!!$R1 839

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
516 526 0.393808 GAACGGGGCCTTAGCATGAA 60.394 55.0 0.84 0.0 42.56 2.57 F
1392 3725 0.963962 AAGGCAGAGCACCACATTTG 59.036 50.0 0.00 0.0 0.00 2.32 F
1396 3729 1.241165 CAGAGCACCACATTTGAGCA 58.759 50.0 0.00 0.0 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1739 5303 0.546747 TCGAGGATGTTGGTCCCCTT 60.547 55.0 0.00 0.00 39.17 3.95 R
2247 7035 1.034292 GGAGTTCTCCATTGGCAGCC 61.034 60.0 3.66 3.66 0.00 4.85 R
2534 7322 1.481901 TAAGCGGCACTAACACCCCA 61.482 55.0 1.45 0.00 0.00 4.96 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
55 56 7.423844 TCCTTTCAGTATATGCTTCTCTTCA 57.576 36.000 0.00 0.00 0.00 3.02
149 153 3.324713 CTTCCCGGGAAGCCAGAT 58.675 61.111 42.55 0.00 43.95 2.90
162 166 1.827969 AGCCAGATGTCGCTAGTTTCT 59.172 47.619 0.00 0.00 32.26 2.52
430 440 2.637872 TCGTTCTCCAGAAGTGGGATTT 59.362 45.455 0.00 0.00 45.11 2.17
516 526 0.393808 GAACGGGGCCTTAGCATGAA 60.394 55.000 0.84 0.00 42.56 2.57
551 561 6.368779 TGTCTAGTACAATAAGGTTTGCCT 57.631 37.500 0.00 0.00 40.46 4.75
560 570 2.282180 GGTTTGCCTGGCTCCGAA 60.282 61.111 21.03 2.25 0.00 4.30
564 574 1.480212 TTTGCCTGGCTCCGAAGAGA 61.480 55.000 21.03 0.00 43.39 3.10
684 699 8.908903 TGTTCTTTGTATTACCTTCACAATTGT 58.091 29.630 4.92 4.92 32.57 2.71
744 759 5.860941 TCTTGAAGTTGCAACCCAATTTA 57.139 34.783 25.62 14.26 34.04 1.40
745 760 5.596845 TCTTGAAGTTGCAACCCAATTTAC 58.403 37.500 25.62 8.96 34.04 2.01
1156 3488 2.290896 GGGATCAACCATTGTCAGGTCA 60.291 50.000 0.00 0.00 38.76 4.02
1189 3521 2.987355 TTTCTTGCCACCCCGAACCC 62.987 60.000 0.00 0.00 0.00 4.11
1392 3725 0.963962 AAGGCAGAGCACCACATTTG 59.036 50.000 0.00 0.00 0.00 2.32
1396 3729 1.241165 CAGAGCACCACATTTGAGCA 58.759 50.000 0.00 0.00 0.00 4.26
1429 3762 3.697045 CGTCCTCTTCAACATCTCCTAGT 59.303 47.826 0.00 0.00 0.00 2.57
1606 3939 2.507944 GTGGGGATGCTGCTCGAT 59.492 61.111 0.00 0.00 0.00 3.59
1622 3955 1.437573 GATGTCACCGGCGAGATCA 59.562 57.895 21.25 4.39 36.09 2.92
1670 4009 3.885521 GGGACTACCTCGCCGACG 61.886 72.222 0.00 0.00 42.01 5.12
1671 4010 4.549516 GGACTACCTCGCCGACGC 62.550 72.222 0.00 0.00 39.84 5.19
1672 4011 4.549516 GACTACCTCGCCGACGCC 62.550 72.222 0.00 0.00 39.84 5.68
1739 5303 1.977854 AGCTCAAGGGTGTCATGTACA 59.022 47.619 0.00 0.00 35.06 2.90
1865 5429 2.051518 TTCGCCCATGACATTGGCC 61.052 57.895 21.55 0.00 42.29 5.36
1977 5541 3.692406 GACCGGCCGACCTTCTGT 61.692 66.667 30.73 14.54 0.00 3.41
1994 5558 2.915659 TGGCTGACCGGAAGACGT 60.916 61.111 9.46 0.00 42.24 4.34
2009 5573 1.829222 AGACGTATCCGGTGTTGGAAT 59.171 47.619 0.00 0.00 42.46 3.01
2045 5610 5.300539 TCGGTGAGAAGATTGAAGAGGATAG 59.699 44.000 0.00 0.00 0.00 2.08
2165 5732 1.991264 GGTCTTTAACGACGAGGAAGC 59.009 52.381 0.00 0.00 34.75 3.86
2247 7035 0.742505 TACTAAGGTCGGCCATCACG 59.257 55.000 9.71 0.00 37.19 4.35
2280 7068 0.689623 AACTCCCTGCAACTCCAGAG 59.310 55.000 0.00 0.00 34.77 3.35
2294 7082 6.518032 GCAACTCCAGAGATATCTATGCTTGA 60.518 42.308 19.84 11.84 34.08 3.02
2391 7179 3.385111 GGACCTCATTACTCAATCGTCCT 59.615 47.826 0.00 0.00 33.21 3.85
2497 7285 2.428491 ACCACCGCATCGACAAATTAA 58.572 42.857 0.00 0.00 0.00 1.40
2534 7322 3.686726 CGCCAGAAAAGAGCTTAGTTGAT 59.313 43.478 0.00 0.00 0.00 2.57
2702 7490 6.159575 TGGATGACCTAAGGTTTATCAATCCA 59.840 38.462 0.00 0.00 35.25 3.41
3312 8105 2.711547 AGAGTGCCCCAAAGTTTCTACT 59.288 45.455 0.00 0.00 35.68 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 1.396996 GCGCACGAGAATAACAACCAT 59.603 47.619 0.30 0.00 0.00 3.55
148 152 1.482593 CCCCTCAGAAACTAGCGACAT 59.517 52.381 0.00 0.00 0.00 3.06
149 153 0.895530 CCCCTCAGAAACTAGCGACA 59.104 55.000 0.00 0.00 0.00 4.35
162 166 0.984230 AACGCATCTTTCTCCCCTCA 59.016 50.000 0.00 0.00 0.00 3.86
330 340 3.645687 AGGGGAAGTTGCTTTAAATTGCA 59.354 39.130 0.00 0.00 36.57 4.08
516 526 2.614134 ACTAGACAGCCAGGAAGTCT 57.386 50.000 16.04 16.04 44.25 3.24
551 561 0.967887 CACCTCTCTCTTCGGAGCCA 60.968 60.000 0.00 0.00 41.58 4.75
560 570 1.380403 CCGTGATCGCACCTCTCTCT 61.380 60.000 7.12 0.00 42.09 3.10
564 574 3.362399 CTGCCGTGATCGCACCTCT 62.362 63.158 7.12 0.00 42.09 3.69
744 759 8.842280 TCGTGTGAACAATAAATTCCTAAAAGT 58.158 29.630 0.00 0.00 0.00 2.66
745 760 9.672086 TTCGTGTGAACAATAAATTCCTAAAAG 57.328 29.630 0.00 0.00 0.00 2.27
1156 3488 2.290577 GCAAGAAAGGGATCTGACCTGT 60.291 50.000 0.00 0.00 38.63 4.00
1396 3729 5.116882 GTTGAAGAGGACGGTAGCAATTAT 58.883 41.667 0.00 0.00 0.00 1.28
1429 3762 1.211703 TGTGTTTGGCTTCCAGACTCA 59.788 47.619 7.83 7.42 39.09 3.41
1606 3939 1.080093 GTTGATCTCGCCGGTGACA 60.080 57.895 15.21 8.27 0.00 3.58
1622 3955 1.900498 GCTTGTCCTGCAGGCTGTT 60.900 57.895 28.91 0.00 45.42 3.16
1670 4009 3.567797 GATGCGCTTCCTGTCGGC 61.568 66.667 9.73 0.00 0.00 5.54
1671 4010 2.125552 TGATGCGCTTCCTGTCGG 60.126 61.111 19.40 0.00 0.00 4.79
1672 4011 2.456119 GGTGATGCGCTTCCTGTCG 61.456 63.158 19.40 0.00 0.00 4.35
1673 4012 2.456119 CGGTGATGCGCTTCCTGTC 61.456 63.158 19.40 8.17 0.00 3.51
1739 5303 0.546747 TCGAGGATGTTGGTCCCCTT 60.547 55.000 0.00 0.00 39.17 3.95
1865 5429 3.267860 GAGCTTCCTGATGCGGCG 61.268 66.667 0.51 0.51 36.69 6.46
1892 5456 2.228582 CCAATTTGCAGATGTCGTCCAA 59.771 45.455 0.00 0.00 0.00 3.53
1977 5541 0.968901 ATACGTCTTCCGGTCAGCCA 60.969 55.000 0.00 0.00 42.24 4.75
1994 5558 1.472552 CGAGCATTCCAACACCGGATA 60.473 52.381 9.46 0.00 34.19 2.59
2009 5573 4.794439 CACCGACGATGCCGAGCA 62.794 66.667 0.00 1.01 44.86 4.26
2045 5610 1.346068 ACTCCTCAACCAGTGCTCTTC 59.654 52.381 0.00 0.00 0.00 2.87
2165 5732 4.808364 TCTTCTTTTCAAATTTGGGTTGCG 59.192 37.500 17.90 3.18 0.00 4.85
2247 7035 1.034292 GGAGTTCTCCATTGGCAGCC 61.034 60.000 3.66 3.66 0.00 4.85
2280 7068 2.622436 GCCGGGTCAAGCATAGATATC 58.378 52.381 2.18 0.00 0.00 1.63
2294 7082 2.677228 CATTGAGAAGGGCCGGGT 59.323 61.111 2.18 0.00 0.00 5.28
2534 7322 1.481901 TAAGCGGCACTAACACCCCA 61.482 55.000 1.45 0.00 0.00 4.96
2702 7490 3.421394 TCTTCATCCTACACCTCCCAT 57.579 47.619 0.00 0.00 0.00 4.00
3251 8042 9.809096 TGTTAGTTGAATAGATGAATCTGAGAC 57.191 33.333 2.99 0.00 37.76 3.36
3312 8105 4.119862 CAAGTTTTCGTCTTGACTCTCCA 58.880 43.478 0.00 0.00 43.17 3.86


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

AutoCloner maintained by Alex Coulton.