Multiple sequence alignment - TraesCS6D01G238600

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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 TraesCS6D01G238600 chr6D 100.000 2339 0 0 1 2339 338919671 338922009 0.000000e+00 4320.0
1 TraesCS6D01G238600 chr5D 96.047 1366 51 3 1 1363 383585976 383587341 0.000000e+00 2220.0
2 TraesCS6D01G238600 chr5D 95.604 1365 55 4 1 1362 473452341 473453703 0.000000e+00 2183.0
3 TraesCS6D01G238600 chr5D 85.686 503 56 11 1852 2339 87387232 87387733 1.240000e-142 516.0
4 TraesCS6D01G238600 chr2B 95.757 1367 53 5 1 1364 390803530 390802166 0.000000e+00 2198.0
5 TraesCS6D01G238600 chr2B 83.032 996 137 18 1362 2339 190883511 190882530 0.000000e+00 874.0
6 TraesCS6D01G238600 chr1A 95.751 1365 54 4 1 1362 213935671 213937034 0.000000e+00 2196.0
7 TraesCS6D01G238600 chr5B 95.614 1368 57 3 1 1365 59780962 59779595 0.000000e+00 2191.0
8 TraesCS6D01G238600 chr5B 81.413 807 112 19 1362 2168 599698358 599697590 1.970000e-175 625.0
9 TraesCS6D01G238600 chr4B 95.611 1367 57 3 1 1364 613148848 613150214 0.000000e+00 2189.0
10 TraesCS6D01G238600 chr4B 78.218 707 121 26 1637 2327 660868866 660868177 2.780000e-114 422.0
11 TraesCS6D01G238600 chr4B 81.454 399 66 7 1637 2027 660743057 660742659 1.040000e-83 320.0
12 TraesCS6D01G238600 chr1B 95.608 1366 56 4 1 1363 92336394 92337758 0.000000e+00 2187.0
13 TraesCS6D01G238600 chr1B 95.269 1374 59 6 1 1371 482480371 482481741 0.000000e+00 2172.0
14 TraesCS6D01G238600 chr3B 95.538 1367 58 3 1 1364 161678848 161677482 0.000000e+00 2183.0
15 TraesCS6D01G238600 chr3B 90.674 193 17 1 2148 2339 807860619 807860811 2.980000e-64 255.0
16 TraesCS6D01G238600 chr7B 82.917 1001 107 23 1362 2339 506555671 506556630 0.000000e+00 843.0
17 TraesCS6D01G238600 chr2D 81.145 1013 136 29 1362 2339 573984988 573983996 0.000000e+00 761.0
18 TraesCS6D01G238600 chr7D 79.727 878 133 30 1494 2339 433283886 433284750 5.570000e-166 593.0
19 TraesCS6D01G238600 chr1D 87.354 514 55 4 1835 2339 337223945 337224457 4.330000e-162 580.0
20 TraesCS6D01G238600 chr6A 80.507 749 107 23 1416 2141 30885865 30886597 2.640000e-149 538.0
21 TraesCS6D01G238600 chr6A 100.000 31 0 0 1362 1392 30885831 30885861 9.030000e-05 58.4
22 TraesCS6D01G238600 chr4D 83.766 462 65 7 1362 1821 14967276 14966823 1.660000e-116 429.0
23 TraesCS6D01G238600 chr7A 89.538 325 32 1 1844 2168 128908339 128908017 6.020000e-111 411.0
24 TraesCS6D01G238600 chr7A 82.500 200 6 11 2161 2339 128907994 128907803 5.210000e-32 148.0
25 TraesCS6D01G238600 chr4A 89.894 188 17 2 2152 2339 648622576 648622391 8.350000e-60 241.0
26 TraesCS6D01G238600 chr4A 86.979 192 20 5 2152 2339 82746771 82746961 6.550000e-51 211.0
27 TraesCS6D01G238600 chr3A 92.547 161 12 0 2152 2312 624166072 624165912 5.030000e-57 231.0


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 TraesCS6D01G238600 chr6D 338919671 338922009 2338 False 4320.0 4320 100.0000 1 2339 1 chr6D.!!$F1 2338
1 TraesCS6D01G238600 chr5D 383585976 383587341 1365 False 2220.0 2220 96.0470 1 1363 1 chr5D.!!$F2 1362
2 TraesCS6D01G238600 chr5D 473452341 473453703 1362 False 2183.0 2183 95.6040 1 1362 1 chr5D.!!$F3 1361
3 TraesCS6D01G238600 chr5D 87387232 87387733 501 False 516.0 516 85.6860 1852 2339 1 chr5D.!!$F1 487
4 TraesCS6D01G238600 chr2B 390802166 390803530 1364 True 2198.0 2198 95.7570 1 1364 1 chr2B.!!$R2 1363
5 TraesCS6D01G238600 chr2B 190882530 190883511 981 True 874.0 874 83.0320 1362 2339 1 chr2B.!!$R1 977
6 TraesCS6D01G238600 chr1A 213935671 213937034 1363 False 2196.0 2196 95.7510 1 1362 1 chr1A.!!$F1 1361
7 TraesCS6D01G238600 chr5B 59779595 59780962 1367 True 2191.0 2191 95.6140 1 1365 1 chr5B.!!$R1 1364
8 TraesCS6D01G238600 chr5B 599697590 599698358 768 True 625.0 625 81.4130 1362 2168 1 chr5B.!!$R2 806
9 TraesCS6D01G238600 chr4B 613148848 613150214 1366 False 2189.0 2189 95.6110 1 1364 1 chr4B.!!$F1 1363
10 TraesCS6D01G238600 chr4B 660868177 660868866 689 True 422.0 422 78.2180 1637 2327 1 chr4B.!!$R2 690
11 TraesCS6D01G238600 chr1B 92336394 92337758 1364 False 2187.0 2187 95.6080 1 1363 1 chr1B.!!$F1 1362
12 TraesCS6D01G238600 chr1B 482480371 482481741 1370 False 2172.0 2172 95.2690 1 1371 1 chr1B.!!$F2 1370
13 TraesCS6D01G238600 chr3B 161677482 161678848 1366 True 2183.0 2183 95.5380 1 1364 1 chr3B.!!$R1 1363
14 TraesCS6D01G238600 chr7B 506555671 506556630 959 False 843.0 843 82.9170 1362 2339 1 chr7B.!!$F1 977
15 TraesCS6D01G238600 chr2D 573983996 573984988 992 True 761.0 761 81.1450 1362 2339 1 chr2D.!!$R1 977
16 TraesCS6D01G238600 chr7D 433283886 433284750 864 False 593.0 593 79.7270 1494 2339 1 chr7D.!!$F1 845
17 TraesCS6D01G238600 chr1D 337223945 337224457 512 False 580.0 580 87.3540 1835 2339 1 chr1D.!!$F1 504
18 TraesCS6D01G238600 chr6A 30885831 30886597 766 False 298.2 538 90.2535 1362 2141 2 chr6A.!!$F1 779
19 TraesCS6D01G238600 chr7A 128907803 128908339 536 True 279.5 411 86.0190 1844 2339 2 chr7A.!!$R1 495

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
428 431 1.772063 GCGAACACTTCACGGCACTT 61.772 55.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1873 1918 0.106868 CCTCGGATGGGGGTAAAACC 60.107 60.0 0.0 0.0 37.6 3.27 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
61 62 4.503643 CCTGGATTCCAAATTGTGCAAACT 60.504 41.667 6.88 0.00 30.80 2.66
97 98 2.509964 CCTAAGGGAGGCCAGTTGTTAT 59.490 50.000 5.01 0.00 38.96 1.89
181 182 6.126652 ACAGACTCTATGGCCTATTGATGTTT 60.127 38.462 3.32 0.00 0.00 2.83
185 186 6.183361 ACTCTATGGCCTATTGATGTTTAGCA 60.183 38.462 3.32 0.00 0.00 3.49
412 415 9.646427 AGCAAAGGTTAAAATATTATTTTGCGA 57.354 25.926 19.88 7.24 41.67 5.10
428 431 1.772063 GCGAACACTTCACGGCACTT 61.772 55.000 0.00 0.00 0.00 3.16
471 474 9.593134 CTTAGCTAATAGACATGTGAAAGTCTT 57.407 33.333 1.15 0.00 42.12 3.01
508 511 1.890552 ACTCATCTGGGCCAGAAGAT 58.109 50.000 37.86 23.97 44.04 2.40
537 540 7.566760 AACATCTGTTGTTTCTATGTGACAA 57.433 32.000 0.00 0.00 46.51 3.18
816 820 4.322650 GCCAATTTTGTTAATGCCTCCTCA 60.323 41.667 0.00 0.00 0.00 3.86
960 964 2.007608 GACAAAGGTAGGTTCATCGGC 58.992 52.381 0.00 0.00 0.00 5.54
1010 1014 3.430042 AGATGTGTTGATGGCTGAAGT 57.570 42.857 0.00 0.00 0.00 3.01
1263 1268 6.721208 AGTTGGCTAGATTTTCCTTCATTTCA 59.279 34.615 0.00 0.00 0.00 2.69
1395 1400 4.082523 GGCCCACGAGCTACTGCA 62.083 66.667 0.00 0.00 42.74 4.41
1396 1401 2.047274 GCCCACGAGCTACTGCAA 60.047 61.111 0.00 0.00 42.74 4.08
1449 1456 2.029073 CCACACGTGGCTCTTCGT 59.971 61.111 21.57 0.00 44.73 3.85
1456 1463 2.108157 TGGCTCTTCGTTGCACGT 59.892 55.556 8.22 0.00 43.14 4.49
1513 1527 0.396417 CTCCCCCTCTCTCGTGTCAT 60.396 60.000 0.00 0.00 0.00 3.06
1516 1530 1.032657 CCCCTCTCTCGTGTCATCGT 61.033 60.000 0.00 0.00 0.00 3.73
1551 1565 1.216710 CACGCTTCCTCACTCTCCC 59.783 63.158 0.00 0.00 0.00 4.30
1566 1580 2.046892 CCCTCTCACCGCCTGTTG 60.047 66.667 0.00 0.00 0.00 3.33
1574 1598 2.348998 CCGCCTGTTGCTCTCCTT 59.651 61.111 0.00 0.00 38.05 3.36
1598 1622 3.287222 CTCTCCTCTCCTTCGATGAGTT 58.713 50.000 11.06 0.00 30.61 3.01
1601 1625 3.636300 CTCCTCTCCTTCGATGAGTTGAT 59.364 47.826 11.06 0.00 0.00 2.57
1602 1626 4.026744 TCCTCTCCTTCGATGAGTTGATT 58.973 43.478 11.06 0.00 0.00 2.57
1606 1630 2.027285 TCCTTCGATGAGTTGATTGCCA 60.027 45.455 0.00 0.00 0.00 4.92
1704 1742 1.402896 GGGGTCGATCTCATGCAGGA 61.403 60.000 0.00 0.00 0.00 3.86
1734 1772 1.214062 CGTCTCCTCTCTGCACCAC 59.786 63.158 0.00 0.00 0.00 4.16
1856 1895 3.114616 CACCGCTGCTCAGAACCG 61.115 66.667 0.29 0.00 0.00 4.44
1904 1950 0.616679 ATCCGAGGGTTTTCTCCGGA 60.617 55.000 2.93 2.93 39.15 5.14
1929 1975 4.408821 GCAGGCCCATGGACGACA 62.409 66.667 15.22 0.00 34.63 4.35
2031 2083 2.028125 CTTCGCCCGCCATCTCCTTA 62.028 60.000 0.00 0.00 0.00 2.69
2035 2087 1.447643 CCCGCCATCTCCTTACCAG 59.552 63.158 0.00 0.00 0.00 4.00
2037 2089 1.522092 CGCCATCTCCTTACCAGCA 59.478 57.895 0.00 0.00 0.00 4.41
2102 2155 3.014304 GGTAAGAACCAAATCTCCCCC 57.986 52.381 0.00 0.00 45.98 5.40
2142 2195 9.613428 TGTAGATTAGGGTTTTCATCATTAGTG 57.387 33.333 0.00 0.00 0.00 2.74
2279 2444 3.492102 AGATTGGTGTGTGCTTAGTGT 57.508 42.857 0.00 0.00 0.00 3.55
2320 2485 2.487746 TGGGCATGGTAGATAGGTGA 57.512 50.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 5.590259 CGTCCTCCCAAATGTCAATATTCTT 59.410 40.000 0.00 0.00 0.00 2.52
97 98 5.178096 TCAATCAAATCTGCTACCTTCCA 57.822 39.130 0.00 0.00 0.00 3.53
185 186 0.464036 TATCGGGATCGCAAGCACTT 59.536 50.000 10.70 0.00 36.13 3.16
269 270 6.657541 GTCCCATTCCACAAAATAAGTAGACA 59.342 38.462 0.00 0.00 0.00 3.41
408 411 2.202946 TGCCGTGAAGTGTTCGCA 60.203 55.556 1.51 0.00 40.11 5.10
412 415 1.404035 GGAAAAGTGCCGTGAAGTGTT 59.596 47.619 0.00 0.00 0.00 3.32
428 431 3.490526 GCTAAGTTAACACGACACGGAAA 59.509 43.478 8.61 0.00 0.00 3.13
471 474 0.902531 GTAGGCAGGACACTTAGGCA 59.097 55.000 0.00 0.00 0.00 4.75
537 540 5.041191 TCTTCTCCAGACTTCTTTTGCTT 57.959 39.130 0.00 0.00 0.00 3.91
589 592 5.279506 CCTCACCCGCATAGTCTATTTACAT 60.280 44.000 0.00 0.00 0.00 2.29
644 648 5.701290 GTGCCCATAATACATAGTTCCTGAC 59.299 44.000 0.00 0.00 0.00 3.51
816 820 2.162681 CTTTTCATGGAAGCCTTCGGT 58.837 47.619 0.00 0.00 0.00 4.69
868 872 9.575783 AAAAGAAGCATCAACGTTAAGTTTAAA 57.424 25.926 0.00 0.00 42.02 1.52
960 964 2.949644 GTCAATCTTACCATTTCCCCCG 59.050 50.000 0.00 0.00 0.00 5.73
1010 1014 6.647067 CGATAGGCCAAATTTTAACACCAAAA 59.353 34.615 5.01 0.00 0.00 2.44
1263 1268 0.250513 GTGGTTCCTCGAGCCAATCT 59.749 55.000 11.30 0.00 44.05 2.40
1449 1456 4.373116 GCTCCCCGAGACGTGCAA 62.373 66.667 0.00 0.00 0.00 4.08
1468 1475 1.063642 AGATGTCTCATCCGTCTCCCA 60.064 52.381 6.18 0.00 0.00 4.37
1481 1489 3.208692 AGAGGGGGAGTTATGAGATGTCT 59.791 47.826 0.00 0.00 0.00 3.41
1513 1527 0.391597 GTGTGAAAGGGAGTGGACGA 59.608 55.000 0.00 0.00 0.00 4.20
1516 1530 0.472471 GTGGTGTGAAAGGGAGTGGA 59.528 55.000 0.00 0.00 0.00 4.02
1566 1580 2.031870 GAGAGGAGAGGAAAGGAGAGC 58.968 57.143 0.00 0.00 0.00 4.09
1574 1598 2.242452 TCATCGAAGGAGAGGAGAGGAA 59.758 50.000 0.00 0.00 0.00 3.36
1704 1742 2.202492 GAGACGACGCGTGCAGAT 60.202 61.111 20.70 0.00 41.37 2.90
1779 1817 0.878523 CACGAGGTCCGAAAACAGCA 60.879 55.000 0.00 0.00 41.76 4.41
1850 1889 3.953775 CCCACCCACAGCGGTTCT 61.954 66.667 0.00 0.00 32.17 3.01
1873 1918 0.106868 CCTCGGATGGGGGTAAAACC 60.107 60.000 0.00 0.00 37.60 3.27
1874 1919 0.106868 CCCTCGGATGGGGGTAAAAC 60.107 60.000 0.00 0.00 43.45 2.43
1904 1950 3.975591 ATGGGCCTGCTGTGCTGT 61.976 61.111 4.53 0.00 0.00 4.40
2037 2089 2.600470 GGCCGGGCAGAAAAACCT 60.600 61.111 25.33 0.00 0.00 3.50
2101 2154 4.592485 ATCTACAAATCTACGAGCAGGG 57.408 45.455 0.00 0.00 0.00 4.45
2102 2155 6.153067 CCTAATCTACAAATCTACGAGCAGG 58.847 44.000 0.00 0.00 0.00 4.85
2279 2444 6.127675 CCCATGAACACATTGTACATCATGAA 60.128 38.462 25.78 1.34 41.83 2.57


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

AutoCloner maintained by Alex Coulton.