Multiple sequence alignment - TraesCS3B01G236100

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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 TraesCS3B01G236100 chr3B 100.000 2369 0 0 1 2369 368854328 368851960 0 4375
1 TraesCS3B01G236100 chr7D 96.508 2377 75 3 1 2369 203518115 203520491 0 3923
2 TraesCS3B01G236100 chr7B 96.299 2378 79 4 1 2369 644470080 644472457 0 3895
3 TraesCS3B01G236100 chr7A 96.173 2378 82 4 1 2369 60120929 60118552 0 3879
4 TraesCS3B01G236100 chr7A 95.963 2378 86 5 1 2369 63429288 63431664 0 3851
5 TraesCS3B01G236100 chr7A 95.837 2378 90 4 1 2369 46394307 46391930 0 3834
6 TraesCS3B01G236100 chr7A 95.791 2376 93 5 1 2369 211272571 211270196 0 3827
7 TraesCS3B01G236100 chr3A 96.088 2377 84 4 1 2369 633113887 633116262 0 3866
8 TraesCS3B01G236100 chr6B 96.002 2376 88 2 1 2369 306993351 306990976 0 3855
9 TraesCS3B01G236100 chr1B 95.837 2378 90 4 1 2369 638698027 638695650 0 3834


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 TraesCS3B01G236100 chr3B 368851960 368854328 2368 True 4375 4375 100.000 1 2369 1 chr3B.!!$R1 2368
1 TraesCS3B01G236100 chr7D 203518115 203520491 2376 False 3923 3923 96.508 1 2369 1 chr7D.!!$F1 2368
2 TraesCS3B01G236100 chr7B 644470080 644472457 2377 False 3895 3895 96.299 1 2369 1 chr7B.!!$F1 2368
3 TraesCS3B01G236100 chr7A 60118552 60120929 2377 True 3879 3879 96.173 1 2369 1 chr7A.!!$R2 2368
4 TraesCS3B01G236100 chr7A 63429288 63431664 2376 False 3851 3851 95.963 1 2369 1 chr7A.!!$F1 2368
5 TraesCS3B01G236100 chr7A 46391930 46394307 2377 True 3834 3834 95.837 1 2369 1 chr7A.!!$R1 2368
6 TraesCS3B01G236100 chr7A 211270196 211272571 2375 True 3827 3827 95.791 1 2369 1 chr7A.!!$R3 2368
7 TraesCS3B01G236100 chr3A 633113887 633116262 2375 False 3866 3866 96.088 1 2369 1 chr3A.!!$F1 2368
8 TraesCS3B01G236100 chr6B 306990976 306993351 2375 True 3855 3855 96.002 1 2369 1 chr6B.!!$R1 2368
9 TraesCS3B01G236100 chr1B 638695650 638698027 2377 True 3834 3834 95.837 1 2369 1 chr1B.!!$R1 2368

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
471 474 0.461961 CTTCTGAAGGGGGCTACTCG 59.538 60.0 9.57 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1619 1625 1.657804 ACTTCTCTTCGGGATGGGTT 58.342 50.0 0.0 0.0 0.0 4.11 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
210 213 1.909302 CTCTTTCCAGGAGGTTGGCTA 59.091 52.381 0.00 0.00 38.16 3.93
266 269 4.868734 CCCTTGTTCGATCTGGTTTAGTAC 59.131 45.833 0.00 0.00 0.00 2.73
306 309 7.108841 TCTGTTTCTATATATATGGGTCCGC 57.891 40.000 5.44 0.00 0.00 5.54
424 427 3.181459 TGTTTCAGTCACCTTTCGATGGA 60.181 43.478 11.32 0.00 0.00 3.41
471 474 0.461961 CTTCTGAAGGGGGCTACTCG 59.538 60.000 9.57 0.00 0.00 4.18
570 573 6.213600 CCAGCCTAATTTCTAGAATAGGGCTA 59.786 42.308 26.46 7.18 44.46 3.93
572 575 6.787957 AGCCTAATTTCTAGAATAGGGCTACA 59.212 38.462 26.10 5.42 44.44 2.74
594 597 1.691196 CAGGAGGGCTTTGTTTGTGA 58.309 50.000 0.00 0.00 0.00 3.58
636 639 4.077184 TCCGGCGAACCTGCGATT 62.077 61.111 9.30 0.00 35.06 3.34
856 859 1.838077 GGCACCTGTAGGGATTAGTGT 59.162 52.381 2.53 0.00 40.27 3.55
951 954 2.676822 ACAAGAGCGAGGCGAGGA 60.677 61.111 0.00 0.00 0.00 3.71
1007 1010 1.304282 GGGCTTTGGAGATGAGGCA 59.696 57.895 0.00 0.00 37.67 4.75
1014 1017 2.905415 TGGAGATGAGGCATTTTGGT 57.095 45.000 0.00 0.00 0.00 3.67
1062 1065 3.876309 ACCCTGCAACTAAGGAAAAGA 57.124 42.857 0.00 0.00 36.91 2.52
1126 1129 1.573108 CCTCCAAAGGTGCCTAGAGA 58.427 55.000 11.94 0.99 37.94 3.10
1128 1131 2.507471 CCTCCAAAGGTGCCTAGAGAAT 59.493 50.000 11.94 0.00 37.94 2.40
1193 1196 2.997315 CAGGGGCACAGGAGACGA 60.997 66.667 0.00 0.00 0.00 4.20
1229 1232 0.033504 CACGACCTACAGGCAACACT 59.966 55.000 0.00 0.00 39.32 3.55
1231 1234 0.317160 CGACCTACAGGCAACACTGA 59.683 55.000 0.00 0.00 40.97 3.41
1233 1236 1.344763 GACCTACAGGCAACACTGACT 59.655 52.381 0.00 0.00 44.10 3.41
1389 1395 4.520874 TGATTTGATTCGGCACAACCTAAA 59.479 37.500 0.00 0.00 35.61 1.85
1515 1521 4.954089 AGTCAATCTCCTTTACTCCTCCT 58.046 43.478 0.00 0.00 0.00 3.69
1552 1558 4.390264 AGAAAATCCCTTAATCTAGGCGC 58.610 43.478 0.00 0.00 33.73 6.53
1581 1587 1.003696 GCCTACTCAGGGAGCAACTTT 59.996 52.381 0.00 0.00 42.88 2.66
1587 1593 3.074538 ACTCAGGGAGCAACTTTTACCAT 59.925 43.478 0.00 0.00 32.04 3.55
1619 1625 4.715534 TTATCTCCCACAAAGACCAACA 57.284 40.909 0.00 0.00 0.00 3.33
1640 1646 2.829023 ACCCATCCCGAAGAGAAGTTA 58.171 47.619 0.00 0.00 0.00 2.24
1648 1654 3.057736 CCCGAAGAGAAGTTAACTGACGA 60.058 47.826 9.34 0.00 0.00 4.20
1709 1715 6.718912 TCCCAAATCAAACATACATTGACAGA 59.281 34.615 0.00 0.00 39.43 3.41
1734 1740 5.359756 GTTGCCAACAAAAAGAGAGGAAAT 58.640 37.500 1.91 0.00 37.58 2.17
1761 1767 6.465894 GGCCCTAGTGAATTTGATATGGTACT 60.466 42.308 0.00 0.00 0.00 2.73
1816 1822 5.278364 GCCAAAATGCAAAATGTTGAATGGA 60.278 36.000 0.00 0.00 32.85 3.41
2001 2007 0.168788 ATGACACTTTCAATGCGCGG 59.831 50.000 8.83 0.00 37.92 6.46
2052 2058 1.242989 TGCTGCAGCCGTTTTATTCA 58.757 45.000 34.64 10.20 41.18 2.57
2055 2061 2.418628 GCTGCAGCCGTTTTATTCACTA 59.581 45.455 28.76 0.00 34.31 2.74
2166 2179 6.484643 CGATCCACTCTCATTTAAATGATGGT 59.515 38.462 30.58 25.79 43.87 3.55
2188 2201 0.331278 TGGGCCATACCAACCTTCAG 59.669 55.000 0.00 0.00 42.05 3.02
2192 2205 3.014623 GGCCATACCAACCTTCAGTTAC 58.985 50.000 0.00 0.00 36.18 2.50
2294 2307 2.239654 GTCCCTTCCCACAGAATCATCA 59.760 50.000 0.00 0.00 32.82 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
159 162 1.123928 GACTGGGTGAGTAGGGATGG 58.876 60.000 0.00 0.00 33.83 3.51
210 213 5.788014 GGAAATGGGAAGATCTAGGATAGGT 59.212 44.000 0.00 0.00 39.78 3.08
266 269 6.867550 AGAAACAGAAAAAGAAGAACCTTGG 58.132 36.000 0.00 0.00 0.00 3.61
306 309 1.136529 CGATATCGTGGAAATGCTGCG 60.137 52.381 17.06 0.00 34.11 5.18
331 334 3.384467 CGGCCAAGTCCCATTAATTGATT 59.616 43.478 2.24 0.00 0.00 2.57
424 427 3.721575 TCCTGGCACATACATTAAGGGAT 59.278 43.478 0.00 0.00 38.20 3.85
471 474 2.046023 GGGCAGGGCATTTTTGGC 60.046 61.111 0.00 0.00 36.73 4.52
570 573 2.011617 AACAAAGCCCTCCTGCCTGT 62.012 55.000 0.00 0.00 31.26 4.00
572 575 0.829182 CAAACAAAGCCCTCCTGCCT 60.829 55.000 0.00 0.00 0.00 4.75
594 597 0.598065 GGGTGTTGCGAGCAAGATTT 59.402 50.000 11.09 0.00 36.52 2.17
636 639 1.280133 AGCATTCAGTTAGAGGCAGCA 59.720 47.619 0.00 0.00 32.62 4.41
856 859 1.811645 TTGTGGATCGCGGTCTCACA 61.812 55.000 28.33 28.33 36.68 3.58
897 900 4.537688 TCCCTTCTTCCATTCTCAAGTCAT 59.462 41.667 0.00 0.00 0.00 3.06
1014 1017 1.885887 CCCGAAATTGACTTGGCTTCA 59.114 47.619 0.00 0.00 0.00 3.02
1126 1129 4.349503 TGCTGCGTCTGGCCCATT 62.350 61.111 0.00 0.00 42.61 3.16
1172 1175 3.324930 CTCCTGTGCCCCTGCTCA 61.325 66.667 0.00 0.00 38.57 4.26
1182 1185 0.099613 CGAGATGGTCGTCTCCTGTG 59.900 60.000 12.89 0.00 44.20 3.66
1193 1196 0.176680 GTGATGTGCCTCGAGATGGT 59.823 55.000 15.71 0.00 0.00 3.55
1229 1232 3.438183 GTTACCTTCCTGGGTCTAGTCA 58.562 50.000 0.00 0.00 40.48 3.41
1231 1234 2.561526 GGGTTACCTTCCTGGGTCTAGT 60.562 54.545 0.00 0.00 40.48 2.57
1233 1236 1.620524 CGGGTTACCTTCCTGGGTCTA 60.621 57.143 0.00 0.00 40.48 2.59
1318 1321 6.249192 CAGAAAAGAGATCCCTTACCCTTTT 58.751 40.000 0.00 0.00 36.79 2.27
1362 1368 1.885233 TGTGCCGAATCAAATCAGCAA 59.115 42.857 0.00 0.00 34.71 3.91
1374 1380 4.274602 TGTATCTTTAGGTTGTGCCGAA 57.725 40.909 0.00 0.00 43.70 4.30
1389 1395 8.853126 CACAAATCATTGGTATTGGATGTATCT 58.147 33.333 0.00 0.00 41.01 1.98
1515 1521 5.248640 GGATTTTCTCATCTTGAGGTGTCA 58.751 41.667 4.78 0.00 44.39 3.58
1552 1558 4.529219 TGAGTAGGCATGGGCGCG 62.529 66.667 0.00 0.00 42.47 6.86
1581 1587 5.368145 GAGATAATGTGTCAGCCATGGTAA 58.632 41.667 14.67 0.00 0.00 2.85
1587 1593 2.092968 GTGGGAGATAATGTGTCAGCCA 60.093 50.000 0.00 0.00 0.00 4.75
1619 1625 1.657804 ACTTCTCTTCGGGATGGGTT 58.342 50.000 0.00 0.00 0.00 4.11
1648 1654 4.467795 TGGAATTTCTTCTCGAGACATCCT 59.532 41.667 16.36 0.00 34.23 3.24
1709 1715 2.695147 CCTCTCTTTTTGTTGGCAACCT 59.305 45.455 26.31 0.00 33.82 3.50
1734 1740 5.610982 ACCATATCAAATTCACTAGGGCCTA 59.389 40.000 13.73 13.73 0.00 3.93
1816 1822 2.105993 GTGTTGTTCAGGGTTCCCTACT 59.894 50.000 10.33 0.00 34.60 2.57
2001 2007 4.434330 CGCACTCTAACTCAAAACGGATTC 60.434 45.833 0.00 0.00 0.00 2.52
2052 2058 9.220767 CTTCCATTTTAGAAAGTAGCAAGTAGT 57.779 33.333 0.00 0.00 0.00 2.73
2055 2061 8.870075 ATCTTCCATTTTAGAAAGTAGCAAGT 57.130 30.769 0.00 0.00 0.00 3.16
2166 2179 2.583101 TGAAGGTTGGTATGGCCCAATA 59.417 45.455 0.00 0.00 45.79 1.90
2237 2250 4.038763 CCTTTTTCCTTCCTTTTTACGCCT 59.961 41.667 0.00 0.00 0.00 5.52
2294 2307 4.399219 GGAAAGTAAGGAAAGTCAAGCCT 58.601 43.478 0.00 0.00 0.00 4.58


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

AutoCloner maintained by Alex Coulton.