Multiple sequence alignment - TraesCS3B01G243300

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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 TraesCS3B01G243300 chr3B 100.000 2273 0 0 1 2273 384336609 384334337 0 4198
1 TraesCS3B01G243300 chr5B 98.616 1301 17 1 2 1302 666585837 666584538 0 2302
2 TraesCS3B01G243300 chr2B 97.849 1302 28 0 2 1303 296058440 296059741 0 2250
3 TraesCS3B01G243300 chr2B 89.683 1260 128 2 44 1303 109881570 109880313 0 1605
4 TraesCS3B01G243300 chr4A 97.920 1298 27 0 2 1299 169683704 169682407 0 2248
5 TraesCS3B01G243300 chr7B 97.414 1276 33 0 2 1277 14773430 14774705 0 2174
6 TraesCS3B01G243300 chr6B 91.988 1298 104 0 5 1302 177406685 177405388 0 1821
7 TraesCS3B01G243300 chr6B 91.942 1303 95 4 5 1307 690455902 690454610 0 1816
8 TraesCS3B01G243300 chrUn 89.316 1301 139 0 2 1302 336409525 336410825 0 1633
9 TraesCS3B01G243300 chr3D 94.715 965 49 2 1307 2270 291233576 291232613 0 1498
10 TraesCS3B01G243300 chr3D 84.138 1305 199 8 2 1303 570309817 570311116 0 1256


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 TraesCS3B01G243300 chr3B 384334337 384336609 2272 True 4198 4198 100.000 1 2273 1 chr3B.!!$R1 2272
1 TraesCS3B01G243300 chr5B 666584538 666585837 1299 True 2302 2302 98.616 2 1302 1 chr5B.!!$R1 1300
2 TraesCS3B01G243300 chr2B 296058440 296059741 1301 False 2250 2250 97.849 2 1303 1 chr2B.!!$F1 1301
3 TraesCS3B01G243300 chr2B 109880313 109881570 1257 True 1605 1605 89.683 44 1303 1 chr2B.!!$R1 1259
4 TraesCS3B01G243300 chr4A 169682407 169683704 1297 True 2248 2248 97.920 2 1299 1 chr4A.!!$R1 1297
5 TraesCS3B01G243300 chr7B 14773430 14774705 1275 False 2174 2174 97.414 2 1277 1 chr7B.!!$F1 1275
6 TraesCS3B01G243300 chr6B 177405388 177406685 1297 True 1821 1821 91.988 5 1302 1 chr6B.!!$R1 1297
7 TraesCS3B01G243300 chr6B 690454610 690455902 1292 True 1816 1816 91.942 5 1307 1 chr6B.!!$R2 1302
8 TraesCS3B01G243300 chrUn 336409525 336410825 1300 False 1633 1633 89.316 2 1302 1 chrUn.!!$F1 1300
9 TraesCS3B01G243300 chr3D 291232613 291233576 963 True 1498 1498 94.715 1307 2270 1 chr3D.!!$R1 963
10 TraesCS3B01G243300 chr3D 570309817 570311116 1299 False 1256 1256 84.138 2 1303 1 chr3D.!!$F1 1301

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
417 418 0.386352 CGACTACTTTGCGTCACCGA 60.386 55.0 0.0 0.0 35.63 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2069 2078 0.601558 TTCCGCCTCACTCAGTACAC 59.398 55.0 0.0 0.0 0.0 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
414 415 1.977412 GACTCGACTACTTTGCGTCAC 59.023 52.381 0.00 0.00 0.00 3.67
417 418 0.386352 CGACTACTTTGCGTCACCGA 60.386 55.000 0.00 0.00 35.63 4.69
522 523 2.669569 GCGTTCTGGAAGGCTGCA 60.670 61.111 17.25 0.00 45.57 4.41
798 806 2.852075 AAACCACCTGAGGCGGGA 60.852 61.111 15.85 0.00 33.36 5.14
1338 1346 1.419381 TACGCATCATTGGCCTCCTA 58.581 50.000 3.32 0.00 0.00 2.94
1359 1367 1.134580 TGTATTGAGAGAGGCAGCAGC 60.135 52.381 0.00 0.00 41.10 5.25
1376 1384 0.606604 AGCCGGTGACACTCGTAAAT 59.393 50.000 1.90 0.00 0.00 1.40
1382 1390 4.417506 CGGTGACACTCGTAAATGATGTA 58.582 43.478 5.39 0.00 0.00 2.29
1399 1407 6.505039 TGATGTATTCAACTATTACGCACG 57.495 37.500 0.00 0.00 0.00 5.34
1446 1454 3.453717 TCTGTATCAAGAGAGGCTGCAAT 59.546 43.478 0.50 0.00 0.00 3.56
1501 1509 1.546029 CACACCTCTCCAACTCGATCA 59.454 52.381 0.00 0.00 0.00 2.92
1517 1525 4.127907 TCGATCAGTCAATAGCTACTCGT 58.872 43.478 0.00 0.00 0.00 4.18
1638 1646 1.519234 GACAGCCGCACATCGATCA 60.519 57.895 0.00 0.00 41.67 2.92
1660 1668 3.323979 AGTCGGGTTCTGTAATGTGAAGT 59.676 43.478 0.00 0.00 0.00 3.01
1666 1674 5.305585 GGTTCTGTAATGTGAAGTCTCCAA 58.694 41.667 0.00 0.00 0.00 3.53
1696 1704 0.179045 AGTTCTCGCCCATGCATACC 60.179 55.000 0.00 0.00 37.32 2.73
1699 1707 3.157949 TCGCCCATGCATACCGGA 61.158 61.111 9.46 0.00 37.32 5.14
1723 1731 1.754803 TCTAACTACCATGCACGAGGG 59.245 52.381 6.62 0.86 0.00 4.30
1724 1732 0.177141 TAACTACCATGCACGAGGGC 59.823 55.000 6.62 0.00 0.00 5.19
1784 1792 3.419759 GCACCACCGCCAAGTACG 61.420 66.667 0.00 0.00 0.00 3.67
1785 1793 3.419759 CACCACCGCCAAGTACGC 61.420 66.667 0.00 0.00 0.00 4.42
1787 1795 2.435938 CCACCGCCAAGTACGCAT 60.436 61.111 0.00 0.00 0.00 4.73
1802 1810 0.956902 CGCATGCCATGGCTATAGCA 60.957 55.000 35.53 16.49 44.36 3.49
1824 1832 2.115595 GAGCTCACATCGAACGATCAG 58.884 52.381 9.40 5.18 31.62 2.90
1861 1869 7.852945 GTGAAATCTCCAATTTGATTAGTAGCG 59.147 37.037 0.00 0.00 33.17 4.26
1896 1904 1.072678 GGGCCCCTCTAATTACCGC 59.927 63.158 12.23 0.00 0.00 5.68
1900 1908 0.034896 CCCCTCTAATTACCGCGCAT 59.965 55.000 8.75 0.00 0.00 4.73
1984 1993 3.617288 CGAGTCTCACACCCATCAATCAA 60.617 47.826 0.00 0.00 0.00 2.57
2018 2027 1.107114 AGTCTCCAACGCGAGATCAT 58.893 50.000 15.93 0.00 40.89 2.45
2027 2036 1.805261 CGCGAGATCATGCACGACTG 61.805 60.000 0.00 0.00 0.00 3.51
2058 2067 1.003355 AACATCACACTCAGGGCCG 60.003 57.895 0.00 0.00 0.00 6.13
2086 2095 1.154016 CGTGTACTGAGTGAGGCGG 60.154 63.158 0.00 0.00 0.00 6.13
2100 2109 2.507324 GCGGAACTCACTCGAGGC 60.507 66.667 18.41 3.70 44.17 4.70
2103 2112 0.108615 CGGAACTCACTCGAGGCATT 60.109 55.000 18.41 5.29 44.17 3.56
2119 2128 1.064654 GCATTGCCGGAGAATTCTCAC 59.935 52.381 31.29 21.57 44.60 3.51
2142 2151 6.477688 CACCATCATTTCTACCATGAAAATGC 59.522 38.462 13.44 0.00 39.08 3.56
2166 2175 4.069304 TGTCATGGAAGACCCTAAAAACG 58.931 43.478 0.00 0.00 37.73 3.60
2168 2177 4.517832 GTCATGGAAGACCCTAAAAACGTT 59.482 41.667 0.00 0.00 35.38 3.99
2185 2194 1.078497 TTATCCAGGTGTGCGGCTG 60.078 57.895 0.00 0.00 0.00 4.85
2201 2210 4.986708 TGGCCCGCCCAAAGAACC 62.987 66.667 0.00 0.00 41.82 3.62
2229 2238 2.016905 TCTTAGAGATAGCAGGGGGC 57.983 55.000 0.00 0.00 45.30 5.80
2242 2251 1.134431 CAGGGGGCCATTTTATTGCAC 60.134 52.381 4.39 0.00 0.00 4.57
2243 2252 3.778619 GGGGCCATTTTATTGCACC 57.221 52.632 4.39 0.00 42.18 5.01
2270 2279 8.894768 AATTGTGTCTTCTTCCTATATGCTAC 57.105 34.615 0.00 0.00 0.00 3.58
2271 2280 6.406692 TGTGTCTTCTTCCTATATGCTACC 57.593 41.667 0.00 0.00 0.00 3.18
2272 2281 5.009710 TGTGTCTTCTTCCTATATGCTACCG 59.990 44.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.748879 CAGTGTGGGCGTATTGGGG 60.749 63.158 0.00 0.00 0.00 4.96
414 415 1.942657 CCCAACTGCTTGATATGTCGG 59.057 52.381 0.00 0.00 0.00 4.79
417 418 3.521126 AGAGACCCAACTGCTTGATATGT 59.479 43.478 0.00 0.00 0.00 2.29
695 696 0.738389 AACCCACTTCAACGCTTGTG 59.262 50.000 0.00 0.00 0.00 3.33
798 806 6.000219 GCCATCAGTGTTGATAGTAATCCAT 59.000 40.000 2.63 0.00 42.12 3.41
1322 1330 2.283145 ACATAGGAGGCCAATGATGC 57.717 50.000 5.01 0.00 0.00 3.91
1338 1346 2.485124 GCTGCTGCCTCTCTCAATACAT 60.485 50.000 3.85 0.00 0.00 2.29
1359 1367 2.357327 TCATTTACGAGTGTCACCGG 57.643 50.000 15.29 0.00 0.00 5.28
1376 1384 6.197655 GTCGTGCGTAATAGTTGAATACATCA 59.802 38.462 0.00 0.00 35.85 3.07
1382 1390 2.855963 CGGTCGTGCGTAATAGTTGAAT 59.144 45.455 0.00 0.00 0.00 2.57
1399 1407 1.499056 CTGCTGATGTTGCACGGTC 59.501 57.895 0.00 0.00 36.37 4.79
1501 1509 5.465051 CATATGCACGAGTAGCTATTGACT 58.535 41.667 0.00 0.00 0.00 3.41
1517 1525 2.011627 TTGGAGGCCCCCATATGCA 61.012 57.895 6.90 0.00 35.87 3.96
1620 1628 1.485838 CTGATCGATGTGCGGCTGTC 61.486 60.000 0.54 0.00 41.33 3.51
1622 1630 1.485838 GACTGATCGATGTGCGGCTG 61.486 60.000 0.54 0.00 41.33 4.85
1638 1646 3.323979 ACTTCACATTACAGAACCCGACT 59.676 43.478 0.00 0.00 0.00 4.18
1660 1668 6.333416 CGAGAACTACTGATCAAATTGGAGA 58.667 40.000 0.00 0.00 0.00 3.71
1666 1674 3.197766 TGGGCGAGAACTACTGATCAAAT 59.802 43.478 0.00 0.00 0.00 2.32
1696 1704 1.269831 GCATGGTAGTTAGAGGCTCCG 60.270 57.143 11.71 0.00 0.00 4.63
1699 1707 1.137086 CGTGCATGGTAGTTAGAGGCT 59.863 52.381 0.00 0.00 0.00 4.58
1784 1792 1.201647 CTTGCTATAGCCATGGCATGC 59.798 52.381 37.18 30.39 46.58 4.06
1785 1793 2.747989 CTCTTGCTATAGCCATGGCATG 59.252 50.000 37.18 23.21 46.58 4.06
1787 1795 1.544093 GCTCTTGCTATAGCCATGGCA 60.544 52.381 37.18 23.40 45.82 4.92
1802 1810 2.164422 TGATCGTTCGATGTGAGCTCTT 59.836 45.455 16.19 0.00 0.00 2.85
1824 1832 6.817765 TTGGAGATTTCACATTACAGAACC 57.182 37.500 0.00 0.00 0.00 3.62
1861 1869 1.490693 CCCGTATGCATGCGTGAGTC 61.491 60.000 30.70 8.99 33.98 3.36
1896 1904 0.740868 AGACCCGTTGTGATCATGCG 60.741 55.000 0.00 4.14 0.00 4.73
1900 1908 2.753452 GAGTAGAGACCCGTTGTGATCA 59.247 50.000 0.00 0.00 0.00 2.92
1923 1932 5.456192 GATAATTCGAGAACCCATATGCG 57.544 43.478 0.00 0.00 0.00 4.73
1951 1960 3.301906 GTGTGAGACTCGATCAATGTTCG 59.698 47.826 7.34 7.34 37.94 3.95
1991 2000 1.531149 CGCGTTGGAGACTTCACATTT 59.469 47.619 0.00 0.00 0.00 2.32
2036 2045 0.962356 CCCTGAGTGTGATGTTGGGC 60.962 60.000 0.00 0.00 0.00 5.36
2069 2078 0.601558 TTCCGCCTCACTCAGTACAC 59.398 55.000 0.00 0.00 0.00 2.90
2086 2095 0.723981 GCAATGCCTCGAGTGAGTTC 59.276 55.000 12.31 0.00 40.85 3.01
2100 2109 1.672881 GGTGAGAATTCTCCGGCAATG 59.327 52.381 28.40 0.00 42.20 2.82
2103 2112 0.911769 ATGGTGAGAATTCTCCGGCA 59.088 50.000 28.40 15.54 42.20 5.69
2119 2128 6.812998 AGCATTTTCATGGTAGAAATGATGG 58.187 36.000 19.46 3.92 39.44 3.51
2142 2151 5.334879 CGTTTTTAGGGTCTTCCATGACAAG 60.335 44.000 0.00 0.00 38.61 3.16
2166 2175 1.078426 AGCCGCACACCTGGATAAC 60.078 57.895 0.00 0.00 0.00 1.89
2168 2177 2.584064 CAGCCGCACACCTGGATA 59.416 61.111 0.00 0.00 0.00 2.59
2201 2210 2.600731 CTATCTCTAAGAATGGCCGCG 58.399 52.381 0.00 0.00 0.00 6.46
2229 2238 6.427547 AGACACAATTTGGTGCAATAAAATGG 59.572 34.615 13.43 8.89 42.55 3.16
2242 2251 7.284034 AGCATATAGGAAGAAGACACAATTTGG 59.716 37.037 0.78 0.00 0.00 3.28
2243 2252 8.218338 AGCATATAGGAAGAAGACACAATTTG 57.782 34.615 0.00 0.00 0.00 2.32
2244 2253 9.331282 GTAGCATATAGGAAGAAGACACAATTT 57.669 33.333 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.