Multiple sequence alignment - TraesCS5B01G139000

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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 TraesCS5B01G139000 chr5B 100.000 4133 0 0 1 4133 262822978 262818846 0.000000e+00 7633
1 TraesCS5B01G139000 chr5B 88.158 152 15 2 3437 3586 262819065 262818915 1.180000e-40 178
2 TraesCS5B01G139000 chr5B 88.158 152 15 2 3914 4064 262819542 262819393 1.180000e-40 178
3 TraesCS5B01G139000 chr5A 95.473 4109 118 29 1 4064 312920049 312915964 0.000000e+00 6495
4 TraesCS5B01G139000 chr5A 85.424 295 28 8 3624 3905 669912879 669913171 4.040000e-75 292
5 TraesCS5B01G139000 chr5A 93.567 171 9 2 3891 4059 669922215 669922385 1.910000e-63 254
6 TraesCS5B01G139000 chr5A 84.354 147 20 2 3437 3581 669922240 669922385 1.550000e-29 141
7 TraesCS5B01G139000 chr5D 94.712 4179 154 34 1 4132 240849750 240853908 0.000000e+00 6431
8 TraesCS5B01G139000 chr5D 89.143 175 15 3 3437 3609 240853690 240853862 9.000000e-52 215


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 TraesCS5B01G139000 chr5B 262818846 262822978 4132 True 7633 7633 100.0000 1 4133 1 chr5B.!!$R1 4132
1 TraesCS5B01G139000 chr5A 312915964 312920049 4085 True 6495 6495 95.4730 1 4064 1 chr5A.!!$R1 4063
2 TraesCS5B01G139000 chr5D 240849750 240853908 4158 False 3323 6431 91.9275 1 4132 2 chr5D.!!$F1 4131

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
179 181 1.135402 GGCTCGGCAATTAACCAACTG 60.135 52.381 0.0 0.0 0.0 3.16 F
1097 1115 0.543277 CTCAAGGCCATGGAGCAGTA 59.457 55.000 18.4 0.0 0.0 2.74 F
1141 1159 0.032815 GCCTCTCCACTTCCGCTATC 59.967 60.000 0.0 0.0 0.0 2.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1141 1159 1.371635 CAAACGGCCGGAGCAAAAG 60.372 57.895 31.76 6.14 42.56 2.27 R
2857 2887 2.295885 CTCCATCTGCCAAAGGATGTC 58.704 52.381 0.00 0.00 38.02 3.06 R
3135 3165 0.396811 GTAGGCCAGTCCACACAACT 59.603 55.000 5.01 0.00 37.29 3.16 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
36 38 6.370994 CAGCATGTCTAACATTCAGACTCTTT 59.629 38.462 4.32 0.00 42.43 2.52
108 110 4.771114 TGGTGGGGTAATCATTCACTAG 57.229 45.455 0.00 0.00 0.00 2.57
118 120 8.475639 GGGTAATCATTCACTAGTACAAGAAGA 58.524 37.037 0.00 0.00 0.00 2.87
145 147 2.431057 ACAGAACTGAACAAGAGGTCGT 59.569 45.455 8.87 0.00 0.00 4.34
158 160 2.301870 AGAGGTCGTATCTTGCAACCAA 59.698 45.455 0.00 0.00 32.25 3.67
179 181 1.135402 GGCTCGGCAATTAACCAACTG 60.135 52.381 0.00 0.00 0.00 3.16
182 184 1.801771 TCGGCAATTAACCAACTGACG 59.198 47.619 0.00 0.00 41.73 4.35
249 251 2.354510 GCAACTAATAGCGTTGGCATCA 59.645 45.455 5.23 0.00 41.45 3.07
772 783 5.010282 GGTTCTAGAAAATTCCAGAGCCAA 58.990 41.667 15.76 0.00 42.66 4.52
1020 1038 1.299165 GTCGTACATGCGAGGCGAT 60.299 57.895 0.00 0.00 41.85 4.58
1097 1115 0.543277 CTCAAGGCCATGGAGCAGTA 59.457 55.000 18.40 0.00 0.00 2.74
1108 1126 2.162264 GGAGCAGTAAGTACTCCCCT 57.838 55.000 0.00 0.00 43.54 4.79
1141 1159 0.032815 GCCTCTCCACTTCCGCTATC 59.967 60.000 0.00 0.00 0.00 2.08
1292 1313 6.306643 TGGTATTGTCCACAACATCATCTA 57.693 37.500 0.00 0.00 38.86 1.98
1362 1383 8.671384 ATGATTGCATTTCCTTTATCATTTGG 57.329 30.769 1.30 0.00 30.76 3.28
1407 1428 5.771666 AGATGAAAGAAGGCAGAATTGTTGA 59.228 36.000 0.00 0.00 0.00 3.18
1438 1459 3.810310 AGTCCCATTTTCTAGAGCGAG 57.190 47.619 0.00 0.00 0.00 5.03
1543 1564 4.634012 TTCCTAGGCAAGCTTCAAACTA 57.366 40.909 2.96 0.00 0.00 2.24
1544 1565 4.634012 TCCTAGGCAAGCTTCAAACTAA 57.366 40.909 2.96 0.00 0.00 2.24
1596 1617 5.185454 TGTTTCAGTTATGCTCGATCCAAT 58.815 37.500 0.00 0.00 0.00 3.16
1674 1695 2.861147 ACTCTGCCCTACCTTTTCAC 57.139 50.000 0.00 0.00 0.00 3.18
1678 1699 1.351017 CTGCCCTACCTTTTCACCTGA 59.649 52.381 0.00 0.00 0.00 3.86
1719 1740 1.846439 ACTATGCAGTGCCATAAGGGT 59.154 47.619 13.72 3.03 39.65 4.34
1720 1741 3.045634 ACTATGCAGTGCCATAAGGGTA 58.954 45.455 13.72 0.00 39.65 3.69
1721 1742 3.458118 ACTATGCAGTGCCATAAGGGTAA 59.542 43.478 13.72 0.00 39.65 2.85
1722 1743 3.600448 ATGCAGTGCCATAAGGGTAAT 57.400 42.857 13.72 0.00 39.65 1.89
1743 1764 6.530019 AATTTTACATCATCCACTTGGTCC 57.470 37.500 0.00 0.00 36.34 4.46
1942 1971 7.360017 GGTTTAATTGCCATTTGCTGTAAACTC 60.360 37.037 0.00 0.00 39.03 3.01
2314 2343 9.971922 ACAATTTCCTTTTGAGAAGTTAATGAG 57.028 29.630 0.00 0.00 0.00 2.90
2583 2613 7.180229 TCTGTTTCACTCCCAGATATTGTCTTA 59.820 37.037 0.00 0.00 34.00 2.10
3135 3165 4.081642 GCATCAGGTGAAGGACAGTAACTA 60.082 45.833 0.00 0.00 0.00 2.24
3152 3182 0.687354 CTAGTTGTGTGGACTGGCCT 59.313 55.000 3.32 0.00 37.63 5.19
3201 3231 8.786826 TCAACCAACTGATATTTAAACTCGAT 57.213 30.769 0.00 0.00 0.00 3.59
3367 3398 8.696043 TGATTTCATCTCCCATATTGGTTTAG 57.304 34.615 0.00 0.00 35.17 1.85
3371 3402 4.706842 TCTCCCATATTGGTTTAGCCTC 57.293 45.455 0.00 0.00 35.17 4.70
3485 3516 6.509199 CGAGCATTTTAGTAATCTGAGCACTG 60.509 42.308 4.65 0.00 0.00 3.66
3505 3536 0.804989 GTTCAATTGGTGCTCCCTCG 59.195 55.000 5.42 0.00 0.00 4.63
3643 3674 6.914259 GCATTAGCACCTCTTTACTCTTTTT 58.086 36.000 0.00 0.00 41.58 1.94
3713 3758 9.360901 TGCCTGCAAAAATAGTATGGAAATATA 57.639 29.630 0.00 0.00 0.00 0.86
3821 3879 6.374417 TCCTATATCCTTAATGCTGGGTTC 57.626 41.667 0.00 0.00 0.00 3.62
3908 3966 8.210946 TCTTCACTTTTCTCTCCTTATTTGTGA 58.789 33.333 0.00 0.00 0.00 3.58
3993 4051 1.846712 GCTCCCTTTCAGCCCTCTGT 61.847 60.000 0.00 0.00 41.10 3.41
4064 4122 2.617308 GCATTCTGAGTGACATGATGGG 59.383 50.000 0.00 0.00 0.00 4.00
4065 4123 3.211865 CATTCTGAGTGACATGATGGGG 58.788 50.000 0.00 0.00 0.00 4.96
4066 4124 1.206878 TCTGAGTGACATGATGGGGG 58.793 55.000 0.00 0.00 0.00 5.40
4067 4125 1.206878 CTGAGTGACATGATGGGGGA 58.793 55.000 0.00 0.00 0.00 4.81
4068 4126 0.911769 TGAGTGACATGATGGGGGAC 59.088 55.000 0.00 0.00 0.00 4.46
4069 4127 0.911769 GAGTGACATGATGGGGGACA 59.088 55.000 0.00 0.00 0.00 4.02
4070 4128 0.620556 AGTGACATGATGGGGGACAC 59.379 55.000 0.00 0.00 0.00 3.67
4075 4137 2.755103 GACATGATGGGGGACACTTTTC 59.245 50.000 0.00 0.00 0.00 2.29
4083 4145 2.764010 GGGGGACACTTTTCTTGTTGTT 59.236 45.455 0.00 0.00 0.00 2.83
4086 4148 3.194755 GGGACACTTTTCTTGTTGTTGGT 59.805 43.478 0.00 0.00 0.00 3.67
4095 4157 9.841295 ACTTTTCTTGTTGTTGGTTACTCTATA 57.159 29.630 0.00 0.00 0.00 1.31
4099 4161 9.444600 TTCTTGTTGTTGGTTACTCTATATTCC 57.555 33.333 0.00 0.00 0.00 3.01
4100 4162 8.044908 TCTTGTTGTTGGTTACTCTATATTCCC 58.955 37.037 0.00 0.00 0.00 3.97
4102 4164 8.612486 TGTTGTTGGTTACTCTATATTCCCTA 57.388 34.615 0.00 0.00 0.00 3.53
4103 4165 9.220906 TGTTGTTGGTTACTCTATATTCCCTAT 57.779 33.333 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 38 9.409312 CAGTCAATGTAATATTGCACAAGAAAA 57.591 29.630 8.50 0.00 0.00 2.29
108 110 6.706270 TCAGTTCTGTTTGGATCTTCTTGTAC 59.294 38.462 0.00 0.00 0.00 2.90
118 120 4.823989 CCTCTTGTTCAGTTCTGTTTGGAT 59.176 41.667 0.00 0.00 0.00 3.41
145 147 1.678728 CCGAGCCTTGGTTGCAAGATA 60.679 52.381 0.00 0.00 34.26 1.98
152 154 1.173043 TAATTGCCGAGCCTTGGTTG 58.827 50.000 0.00 0.00 0.00 3.77
158 160 1.173913 GTTGGTTAATTGCCGAGCCT 58.826 50.000 0.00 0.00 0.00 4.58
179 181 0.804933 GCATGGGTTCGGTAGTCGTC 60.805 60.000 0.00 0.00 40.32 4.20
182 184 1.090052 GCAGCATGGGTTCGGTAGTC 61.090 60.000 0.00 0.00 35.86 2.59
249 251 0.036010 CCTCATCTGCCAGGTTCGTT 60.036 55.000 0.00 0.00 0.00 3.85
414 416 3.264450 GGACCTCTTCTTCATTCCTTGGA 59.736 47.826 0.00 0.00 0.00 3.53
607 618 2.757508 CCTCTCCAGCTCCGCTCA 60.758 66.667 0.00 0.00 36.40 4.26
616 627 4.168291 GGGCCGCTTCCTCTCCAG 62.168 72.222 0.00 0.00 0.00 3.86
635 646 4.020617 CTCCGAGGCCCACTGCAA 62.021 66.667 0.00 0.00 43.89 4.08
772 783 8.515414 GTTTAGTTTATTCATTCACTGCCTCTT 58.485 33.333 0.00 0.00 0.00 2.85
785 798 5.249780 TGAGCCCAGGTTTAGTTTATTCA 57.750 39.130 0.00 0.00 0.00 2.57
853 868 2.566111 TAAATGGGCCGGGCTGAAGG 62.566 60.000 28.80 0.00 0.00 3.46
987 1005 1.517257 CGACATCTCGCCTCCACAC 60.517 63.158 0.00 0.00 31.91 3.82
1020 1038 2.126850 CGCGTCTTCGTCAGCAGA 60.127 61.111 0.00 0.00 39.49 4.26
1097 1115 2.426561 GCTAGGGATCAGGGGAGTACTT 60.427 54.545 0.00 0.00 0.00 2.24
1105 1123 3.784573 CGGAGCTAGGGATCAGGG 58.215 66.667 0.00 0.00 0.00 4.45
1141 1159 1.371635 CAAACGGCCGGAGCAAAAG 60.372 57.895 31.76 6.14 42.56 2.27
1394 1415 6.790285 ACATTGATTTTCAACAATTCTGCC 57.210 33.333 0.00 0.00 39.45 4.85
1403 1424 8.831715 AAAATGGGACTACATTGATTTTCAAC 57.168 30.769 0.00 0.00 39.45 3.18
1407 1428 9.753674 TCTAGAAAATGGGACTACATTGATTTT 57.246 29.630 0.00 0.00 40.71 1.82
1438 1459 2.214387 AAAGCAAAACAGAGCACAGC 57.786 45.000 0.00 0.00 0.00 4.40
1505 1526 1.476488 GGAAATGTATGCGGGTTTGCT 59.524 47.619 0.00 0.00 35.36 3.91
1512 1533 2.254546 TGCCTAGGAAATGTATGCGG 57.745 50.000 14.75 0.00 0.00 5.69
1562 1583 7.715657 AGCATAACTGAAACAAGATTTGACAA 58.284 30.769 0.00 0.00 0.00 3.18
1567 1588 6.801539 TCGAGCATAACTGAAACAAGATTT 57.198 33.333 0.00 0.00 0.00 2.17
1674 1695 2.849942 TCAGTCCACAAATGTGTCAGG 58.150 47.619 12.21 0.00 44.21 3.86
1678 1699 3.565482 GTGTGATCAGTCCACAAATGTGT 59.435 43.478 12.21 0.00 44.91 3.72
1715 1736 6.607198 CCAAGTGGATGATGTAAAATTACCCT 59.393 38.462 0.00 0.00 37.39 4.34
1719 1740 7.178573 TGGACCAAGTGGATGATGTAAAATTA 58.821 34.615 3.83 0.00 38.94 1.40
1720 1741 6.015918 TGGACCAAGTGGATGATGTAAAATT 58.984 36.000 3.83 0.00 38.94 1.82
1721 1742 5.579047 TGGACCAAGTGGATGATGTAAAAT 58.421 37.500 3.83 0.00 38.94 1.82
1722 1743 4.991776 TGGACCAAGTGGATGATGTAAAA 58.008 39.130 3.83 0.00 38.94 1.52
1942 1971 8.843733 CAAACATCTTCAGTTCACAAATATTCG 58.156 33.333 0.00 0.00 0.00 3.34
2583 2613 4.630184 ACAGTATGACACAAAAAGTGGGGT 60.630 41.667 0.00 0.00 46.86 4.95
2683 2713 6.049149 CCTGTTCTTTCAACTCTAAGACACA 58.951 40.000 0.00 0.00 30.53 3.72
2857 2887 2.295885 CTCCATCTGCCAAAGGATGTC 58.704 52.381 0.00 0.00 38.02 3.06
3135 3165 0.396811 GTAGGCCAGTCCACACAACT 59.603 55.000 5.01 0.00 37.29 3.16
3152 3182 5.789521 TGTCATAAGCAACAGCAACTAGTA 58.210 37.500 0.00 0.00 0.00 1.82
3367 3398 4.708726 AACTTTCATACAGCATTGAGGC 57.291 40.909 0.00 0.00 0.00 4.70
3371 3402 5.122239 TCGGAGAAACTTTCATACAGCATTG 59.878 40.000 4.34 0.00 0.00 2.82
3485 3516 1.177401 GAGGGAGCACCAATTGAACC 58.823 55.000 7.12 2.76 43.89 3.62
3505 3536 1.889829 ACCTCACAGCAGAGTACTGAC 59.110 52.381 0.00 0.00 46.03 3.51
3643 3674 7.284944 TCCAACGGAAGGAAACTATTTTACAAA 59.715 33.333 0.00 0.00 42.68 2.83
3644 3675 6.771749 TCCAACGGAAGGAAACTATTTTACAA 59.228 34.615 0.00 0.00 42.68 2.41
3646 3677 6.429078 ACTCCAACGGAAGGAAACTATTTTAC 59.571 38.462 0.00 0.00 42.68 2.01
3652 3683 3.135167 ACAACTCCAACGGAAGGAAACTA 59.865 43.478 0.00 0.00 42.68 2.24
3851 3909 7.607991 GGATAGTACCATCCTGTCAATATTTGG 59.392 40.741 12.58 0.00 41.24 3.28
3885 3943 8.924511 AATCACAAATAAGGAGAGAAAAGTGA 57.075 30.769 0.00 0.00 36.80 3.41
3908 3966 4.881850 GGGACAGATGGAAATTACACGAAT 59.118 41.667 0.00 0.00 0.00 3.34
3993 4051 1.124780 TGGTTCCTTCGACCTCACAA 58.875 50.000 0.00 0.00 38.04 3.33
4064 4122 3.194755 ACCAACAACAAGAAAAGTGTCCC 59.805 43.478 0.00 0.00 0.00 4.46
4065 4123 4.450082 ACCAACAACAAGAAAAGTGTCC 57.550 40.909 0.00 0.00 0.00 4.02
4066 4124 6.617879 AGTAACCAACAACAAGAAAAGTGTC 58.382 36.000 0.00 0.00 0.00 3.67
4067 4125 6.433093 AGAGTAACCAACAACAAGAAAAGTGT 59.567 34.615 0.00 0.00 0.00 3.55
4068 4126 6.852664 AGAGTAACCAACAACAAGAAAAGTG 58.147 36.000 0.00 0.00 0.00 3.16
4069 4127 8.747538 ATAGAGTAACCAACAACAAGAAAAGT 57.252 30.769 0.00 0.00 0.00 2.66
4075 4137 8.047310 AGGGAATATAGAGTAACCAACAACAAG 58.953 37.037 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.