Multiple sequence alignment - TraesCS4B01G334400

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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 TraesCS4B01G334400 chr4B 100.000 2530 0 0 1 2530 625335058 625337587 0.000000e+00 4673.0
1 TraesCS4B01G334400 chr4B 94.712 1286 54 6 4 1277 625332993 625331710 0.000000e+00 1986.0
2 TraesCS4B01G334400 chr4B 94.855 1244 57 6 1294 2530 625331632 625330389 0.000000e+00 1936.0
3 TraesCS4B01G334400 chr4B 100.000 28 0 0 1321 1348 625331679 625331652 5.000000e-03 52.8
4 TraesCS4B01G334400 chr7D 92.570 2113 126 26 1 2092 521969924 521967822 0.000000e+00 3003.0
5 TraesCS4B01G334400 chr7D 85.604 389 35 18 2095 2466 521967781 521967397 3.050000e-104 388.0
6 TraesCS4B01G334400 chr5D 92.714 1249 68 14 858 2092 499709548 499710787 0.000000e+00 1781.0
7 TraesCS4B01G334400 chr6B 87.919 298 34 2 1797 2092 453940165 453939868 1.440000e-92 350.0
8 TraesCS4B01G334400 chr1B 87.402 254 32 0 1797 2050 557101935 557102188 2.460000e-75 292.0
9 TraesCS4B01G334400 chr1B 88.514 148 9 6 102 247 57102121 57101980 3.350000e-39 172.0
10 TraesCS4B01G334400 chr1B 90.476 63 5 1 2028 2089 557107708 557107770 5.800000e-12 82.4
11 TraesCS4B01G334400 chr3A 90.476 189 13 5 2309 2493 735480022 735479835 6.990000e-61 244.0
12 TraesCS4B01G334400 chr3A 90.374 187 13 5 2309 2491 735477686 735477501 9.040000e-60 241.0
13 TraesCS4B01G334400 chr3A 79.191 173 19 12 328 486 719624614 719624783 1.240000e-18 104.0
14 TraesCS4B01G334400 chr3A 78.916 166 18 12 328 480 645617910 645618071 2.070000e-16 97.1


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 TraesCS4B01G334400 chr4B 625335058 625337587 2529 False 4673.000000 4673 100.000000 1 2530 1 chr4B.!!$F1 2529
1 TraesCS4B01G334400 chr4B 625330389 625332993 2604 True 1324.933333 1986 96.522333 4 2530 3 chr4B.!!$R1 2526
2 TraesCS4B01G334400 chr7D 521967397 521969924 2527 True 1695.500000 3003 89.087000 1 2466 2 chr7D.!!$R1 2465
3 TraesCS4B01G334400 chr5D 499709548 499710787 1239 False 1781.000000 1781 92.714000 858 2092 1 chr5D.!!$F1 1234
4 TraesCS4B01G334400 chr3A 735477501 735480022 2521 True 242.500000 244 90.425000 2309 2493 2 chr3A.!!$R1 184

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
272 274 0.609151 TTCGTCTCCCCGTTATTGCA 59.391 50.0 0.0 0.0 0.0 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1910 2014 0.319083 GTCATGGTCCGTGTGGTACA 59.681 55.0 10.97 0.0 36.3 2.9 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
112 114 8.544597 GTTTATGCCGTTCTACATTTTTGTTTT 58.455 29.630 0.00 0.0 0.00 2.43
243 245 5.310409 TCTCCAAACAGAGGTGAAAGATT 57.690 39.130 0.00 0.0 34.46 2.40
267 269 2.299582 TGATTGTTTCGTCTCCCCGTTA 59.700 45.455 0.00 0.0 0.00 3.18
272 274 0.609151 TTCGTCTCCCCGTTATTGCA 59.391 50.000 0.00 0.0 0.00 4.08
324 335 5.638133 ACTGTAGGTGTAGTAGGAAGTTCA 58.362 41.667 5.01 0.0 0.00 3.18
392 405 4.849926 CACTGCAATTCATTGTTTCTCTCG 59.150 41.667 1.59 0.0 39.88 4.04
396 409 4.853743 GCAATTCATTGTTTCTCTCGTTCC 59.146 41.667 1.59 0.0 39.88 3.62
518 531 4.553429 GTGCCATTTTATTCAGTTTCGTCG 59.447 41.667 0.00 0.0 0.00 5.12
528 541 3.635331 TCAGTTTCGTCGGTAGTTTCAG 58.365 45.455 0.00 0.0 0.00 3.02
539 552 4.099881 TCGGTAGTTTCAGTGTTAGGTGTT 59.900 41.667 0.00 0.0 0.00 3.32
661 675 5.100259 CGGTCGTGTAGTTGATTTACTCAT 58.900 41.667 0.00 0.0 32.72 2.90
778 794 8.164070 AGTTATGAACTGAAAACCCTGATACTT 58.836 33.333 0.00 0.0 41.01 2.24
938 961 8.725148 CAGTTTGCTTACTCTGAAAACATATCT 58.275 33.333 0.00 0.0 34.05 1.98
953 976 9.118300 GAAAACATATCTGTCCTGATGATTCTT 57.882 33.333 0.00 0.0 33.36 2.52
1066 1091 3.120060 GCAGACTTTTCGCATTGTCATCT 60.120 43.478 0.00 0.0 32.41 2.90
1253 1285 7.989947 AGGAATAGGTTTAACCAGATGTCTA 57.010 36.000 17.10 0.0 41.95 2.59
1271 1303 4.039488 TGTCTAGGTTGAACTTTAAGGCGA 59.961 41.667 0.00 0.0 0.00 5.54
1391 1484 3.740832 GCAGGGCAATGTAGTTGTTTTTC 59.259 43.478 0.00 0.0 40.07 2.29
1427 1520 5.106317 CGAACAACAAAGGTATATGTGGCTT 60.106 40.000 0.00 0.0 0.00 4.35
1457 1550 2.952702 GCTGAAGAAGAGGGAGGAGCTA 60.953 54.545 0.00 0.0 0.00 3.32
1496 1589 5.312079 CAGTTGATGAAGAGGAAGAGGTTT 58.688 41.667 0.00 0.0 0.00 3.27
1602 1695 2.968574 TGGAGCTCATTCTCACTATCCC 59.031 50.000 17.19 0.0 34.84 3.85
1795 1899 2.398754 ACCCTCCCCTTTTTCCTTTG 57.601 50.000 0.00 0.0 0.00 2.77
1848 1952 4.041198 CCCAAGAAGGTAGTTGAACCACTA 59.959 45.833 0.00 0.0 42.40 2.74
1910 2014 2.308570 TGGGAGATGTTATGCAGGTTGT 59.691 45.455 0.00 0.0 0.00 3.32
1953 2057 0.248296 GCGTCGTTTTCAACCAAGCA 60.248 50.000 0.00 0.0 0.00 3.91
1956 2060 2.540769 CGTCGTTTTCAACCAAGCATGT 60.541 45.455 0.00 0.0 0.00 3.21
1972 2076 2.035832 GCATGTGGTGTTTTTGTAGCCT 59.964 45.455 0.00 0.0 0.00 4.58
2066 2170 1.155889 TGCGTCGTCAATGCTTTGAT 58.844 45.000 17.04 0.0 43.49 2.57
2131 2273 2.787473 TCTAATGGTGTGGCAGAAGG 57.213 50.000 0.00 0.0 0.00 3.46
2194 2341 7.995463 TTTACTTTTGTTGTTTATGAGGTGC 57.005 32.000 0.00 0.0 0.00 5.01
2255 2412 5.895534 ACTATGAACTGGGAATGAAATGCAT 59.104 36.000 0.00 0.0 39.43 3.96
2412 4913 7.581213 ATGATTAAGTGTTGGTTCTTGAACA 57.419 32.000 14.38 0.0 0.00 3.18
2518 5020 2.676839 CAGTCTTGACCTGCTGCATTAG 59.323 50.000 1.31 0.0 0.00 1.73
2519 5021 2.568956 AGTCTTGACCTGCTGCATTAGA 59.431 45.455 1.31 0.0 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 114 6.708949 ACTACGCTTTTCCTTGAACTAAATGA 59.291 34.615 0.00 0.00 0.00 2.57
243 245 2.611971 CGGGGAGACGAAACAATCAGAA 60.612 50.000 0.00 0.00 35.47 3.02
267 269 2.893424 ACTCACCCCAAGAAATGCAAT 58.107 42.857 0.00 0.00 0.00 3.56
272 274 3.308473 GGAAGCTACTCACCCCAAGAAAT 60.308 47.826 0.00 0.00 0.00 2.17
392 405 9.713713 AGAACTTAGTCTTGAAGAAATAGGAAC 57.286 33.333 0.00 0.00 0.00 3.62
396 409 9.581099 GAGGAGAACTTAGTCTTGAAGAAATAG 57.419 37.037 0.00 0.00 0.00 1.73
518 531 7.974482 AATAACACCTAACACTGAAACTACC 57.026 36.000 0.00 0.00 0.00 3.18
661 675 6.463995 AGACTATCTGCCAAAACACAAAAA 57.536 33.333 0.00 0.00 0.00 1.94
724 738 3.440173 AGTCGTAAATCAAATGGGCACTG 59.560 43.478 0.00 0.00 0.00 3.66
725 739 3.686016 AGTCGTAAATCAAATGGGCACT 58.314 40.909 0.00 0.00 0.00 4.40
726 740 5.751243 ATAGTCGTAAATCAAATGGGCAC 57.249 39.130 0.00 0.00 0.00 5.01
727 741 6.119536 AGAATAGTCGTAAATCAAATGGGCA 58.880 36.000 0.00 0.00 0.00 5.36
728 742 6.619801 AGAATAGTCGTAAATCAAATGGGC 57.380 37.500 0.00 0.00 0.00 5.36
756 772 9.533831 AAATAAGTATCAGGGTTTTCAGTTCAT 57.466 29.630 0.00 0.00 0.00 2.57
778 794 7.962995 TGCCATATTGGAACACCTAAAAATA 57.037 32.000 0.00 0.00 40.96 1.40
853 869 5.907197 TCGACAGAGCAAAAAGTAGAAAG 57.093 39.130 0.00 0.00 0.00 2.62
938 961 4.564782 AAGCAGAAGAATCATCAGGACA 57.435 40.909 0.00 0.00 0.00 4.02
1066 1091 4.174009 GCTAAAGCTTCGTAGTCATCACA 58.826 43.478 0.00 0.00 38.21 3.58
1253 1285 2.546789 CGTTCGCCTTAAAGTTCAACCT 59.453 45.455 0.00 0.00 0.00 3.50
1271 1303 0.609662 ACAACATACCTACGGCCGTT 59.390 50.000 38.94 22.03 0.00 4.44
1292 1385 1.344065 TCGTGTCCCCTGTACACATT 58.656 50.000 7.10 0.00 46.05 2.71
1391 1484 2.209273 TGTTGTTCGTCCAGTCATGTG 58.791 47.619 0.00 0.00 0.00 3.21
1427 1520 2.301296 CCTCTTCTTCAGCCTCAACTCA 59.699 50.000 0.00 0.00 0.00 3.41
1457 1550 5.581126 TCAACTGCAACAACTTCTTCATT 57.419 34.783 0.00 0.00 0.00 2.57
1496 1589 2.684374 CAAGCCCGTGATCATCATTGAA 59.316 45.455 0.00 0.00 34.96 2.69
1602 1695 3.432046 GGGTGGGCCAATGAATAAATGTG 60.432 47.826 8.40 0.00 36.17 3.21
1910 2014 0.319083 GTCATGGTCCGTGTGGTACA 59.681 55.000 10.97 0.00 36.30 2.90
1953 2057 4.980573 TCTAGGCTACAAAAACACCACAT 58.019 39.130 0.00 0.00 0.00 3.21
1956 2060 4.139038 GGTTCTAGGCTACAAAAACACCA 58.861 43.478 0.00 0.00 0.00 4.17
1997 2101 3.691575 TCCCTGAAGTTGAACACAACAA 58.308 40.909 14.03 0.00 44.14 2.83
2066 2170 1.451927 CCTTATGCTTCTGCCGGCA 60.452 57.895 30.59 30.59 42.80 5.69
2131 2273 5.179368 TGTCAGTAGCACTGCTAACATTTTC 59.821 40.000 12.46 0.00 45.54 2.29
2308 2466 8.761575 TTATCAATCAAAAATCAAGCTGTTCC 57.238 30.769 0.00 0.00 0.00 3.62
2310 2468 9.768662 AACTTATCAATCAAAAATCAAGCTGTT 57.231 25.926 0.00 0.00 0.00 3.16
2311 2469 9.199982 CAACTTATCAATCAAAAATCAAGCTGT 57.800 29.630 0.00 0.00 0.00 4.40
2312 2470 9.199982 ACAACTTATCAATCAAAAATCAAGCTG 57.800 29.630 0.00 0.00 0.00 4.24
2353 4850 3.715628 AAAGTTTCATGCTGTGGACAC 57.284 42.857 0.00 0.00 0.00 3.67
2412 4913 8.526147 AGCTGCAAAAATTAAATCTCACTACAT 58.474 29.630 1.02 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.