Multiple sequence alignment - TraesCS2D01G361000

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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 TraesCS2D01G361000 chr2D 100.000 3337 0 0 1 3337 463053184 463056520 0.000000e+00 6163
1 TraesCS2D01G361000 chr3B 95.127 3345 143 11 1 3337 546254165 546250833 0.000000e+00 5256
2 TraesCS2D01G361000 chr3B 94.065 3218 173 8 129 3337 310884432 310887640 0.000000e+00 4868
3 TraesCS2D01G361000 chr3B 95.316 1644 67 5 1703 3337 171422645 171421003 0.000000e+00 2601
4 TraesCS2D01G361000 chr3B 93.867 1712 92 8 1 1708 171436531 171434829 0.000000e+00 2567
5 TraesCS2D01G361000 chr7B 94.635 3355 159 8 1 3337 292477735 292481086 0.000000e+00 5179
6 TraesCS2D01G361000 chr7B 94.381 3346 164 20 1 3337 179646485 179649815 0.000000e+00 5116
7 TraesCS2D01G361000 chr7B 93.791 1836 106 5 1508 3337 172906970 172905137 0.000000e+00 2752
8 TraesCS2D01G361000 chr7B 93.714 1718 103 2 1 1713 253131065 253132782 0.000000e+00 2569
9 TraesCS2D01G361000 chr2B 94.224 3324 164 19 25 3337 515534013 515537319 0.000000e+00 5049
10 TraesCS2D01G361000 chr2B 93.946 3221 178 10 129 3337 433375381 433378596 0.000000e+00 4852
11 TraesCS2D01G361000 chr2B 94.763 2807 130 6 1 2790 251179774 251176968 0.000000e+00 4353
12 TraesCS2D01G361000 chr2B 94.723 2293 109 5 1047 3331 570354486 570356774 0.000000e+00 3554
13 TraesCS2D01G361000 chr2B 94.264 1848 86 11 1506 3337 486051368 486049525 0.000000e+00 2808
14 TraesCS2D01G361000 chr2B 96.699 515 15 2 2823 3337 251176972 251176460 0.000000e+00 856
15 TraesCS2D01G361000 chr5B 94.444 144 7 1 1 144 98917536 98917678 1.560000e-53 220
16 TraesCS2D01G361000 chr4B 93.750 144 8 1 1 144 333757038 333757180 7.250000e-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 TraesCS2D01G361000 chr2D 463053184 463056520 3336 False 6163.0 6163 100.000 1 3337 1 chr2D.!!$F1 3336
1 TraesCS2D01G361000 chr3B 546250833 546254165 3332 True 5256.0 5256 95.127 1 3337 1 chr3B.!!$R3 3336
2 TraesCS2D01G361000 chr3B 310884432 310887640 3208 False 4868.0 4868 94.065 129 3337 1 chr3B.!!$F1 3208
3 TraesCS2D01G361000 chr3B 171421003 171422645 1642 True 2601.0 2601 95.316 1703 3337 1 chr3B.!!$R1 1634
4 TraesCS2D01G361000 chr3B 171434829 171436531 1702 True 2567.0 2567 93.867 1 1708 1 chr3B.!!$R2 1707
5 TraesCS2D01G361000 chr7B 292477735 292481086 3351 False 5179.0 5179 94.635 1 3337 1 chr7B.!!$F3 3336
6 TraesCS2D01G361000 chr7B 179646485 179649815 3330 False 5116.0 5116 94.381 1 3337 1 chr7B.!!$F1 3336
7 TraesCS2D01G361000 chr7B 172905137 172906970 1833 True 2752.0 2752 93.791 1508 3337 1 chr7B.!!$R1 1829
8 TraesCS2D01G361000 chr7B 253131065 253132782 1717 False 2569.0 2569 93.714 1 1713 1 chr7B.!!$F2 1712
9 TraesCS2D01G361000 chr2B 515534013 515537319 3306 False 5049.0 5049 94.224 25 3337 1 chr2B.!!$F2 3312
10 TraesCS2D01G361000 chr2B 433375381 433378596 3215 False 4852.0 4852 93.946 129 3337 1 chr2B.!!$F1 3208
11 TraesCS2D01G361000 chr2B 570354486 570356774 2288 False 3554.0 3554 94.723 1047 3331 1 chr2B.!!$F3 2284
12 TraesCS2D01G361000 chr2B 486049525 486051368 1843 True 2808.0 2808 94.264 1506 3337 1 chr2B.!!$R1 1831
13 TraesCS2D01G361000 chr2B 251176460 251179774 3314 True 2604.5 4353 95.731 1 3337 2 chr2B.!!$R2 3336

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
814 823 0.817634 CCACAAGGGAGTGCAAACGA 60.818 55.000 0.0 0.0 40.01 3.85 F
947 960 1.738099 CCGCTTTCGTCTCCACCAG 60.738 63.158 0.0 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1977 2005 1.006337 TGCTGAAACCGGCAAATGC 60.006 52.632 0.0 1.22 42.48 3.56 R
2473 2510 1.859383 TCGACAATGACAAGCACGAA 58.141 45.000 0.0 0.00 0.00 3.85 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
103 104 9.738832 GTTACCAAAACTTATTTAGCTTTGTCA 57.261 29.630 0.00 0.00 37.95 3.58
529 535 1.346395 TCACCAGTCCAAGTAACGCAT 59.654 47.619 0.00 0.00 0.00 4.73
548 554 5.638234 ACGCATTAGAGAAGTACAAAACTCC 59.362 40.000 0.00 0.00 37.50 3.85
549 555 5.637810 CGCATTAGAGAAGTACAAAACTCCA 59.362 40.000 0.00 0.00 37.50 3.86
550 556 6.313905 CGCATTAGAGAAGTACAAAACTCCAT 59.686 38.462 0.00 0.00 37.50 3.41
664 673 3.443925 CCCTGAGACGAGCGCAGA 61.444 66.667 11.47 0.00 46.01 4.26
770 779 2.240510 TGGTTCTTCCAAGCCACCT 58.759 52.632 8.30 0.00 44.12 4.00
814 823 0.817634 CCACAAGGGAGTGCAAACGA 60.818 55.000 0.00 0.00 40.01 3.85
856 865 4.444838 CGTCCCCGATGAACCGCA 62.445 66.667 0.00 0.00 35.63 5.69
935 948 3.055719 CACCACCATCGCCGCTTT 61.056 61.111 0.00 0.00 0.00 3.51
947 960 1.738099 CCGCTTTCGTCTCCACCAG 60.738 63.158 0.00 0.00 0.00 4.00
1182 1195 1.827399 AACCAGACAAGGCCGACGAT 61.827 55.000 0.00 0.00 0.00 3.73
1190 1203 2.300152 ACAAGGCCGACGATATGATCAT 59.700 45.455 13.81 13.81 0.00 2.45
1431 1449 8.934023 ATTCAAACTTGTTTCCCAACTAGATA 57.066 30.769 0.00 0.00 37.81 1.98
1677 1705 8.166061 AGCAATGGTATGTATTGTCCTATTCAT 58.834 33.333 0.00 0.00 37.73 2.57
1977 2005 3.666374 GCTGAAGCATGAGAAGTTGTTCG 60.666 47.826 0.00 0.00 41.59 3.95
2024 2052 5.486526 AGCGACAAAGAGAAGATGAAGATT 58.513 37.500 0.00 0.00 0.00 2.40
2252 2280 4.253685 AGTACGCAGCAAAAGATGTGTAT 58.746 39.130 9.84 0.00 42.49 2.29
2336 2364 1.861982 GGGAGGCTGACCACTACTAA 58.138 55.000 0.00 0.00 39.06 2.24
2430 2467 5.107875 GCTTGCCTTTTATCTTGTTGTTTCG 60.108 40.000 0.00 0.00 0.00 3.46
2473 2510 7.913789 TGTTAGGTTGAACCAGTATGACTATT 58.086 34.615 17.83 0.00 41.95 1.73
2955 3013 8.033038 AGTACAAAGAAGCATCAGTTCGTAATA 58.967 33.333 0.00 0.00 0.00 0.98
2961 3019 2.158871 GCATCAGTTCGTAATACCCCCA 60.159 50.000 0.00 0.00 0.00 4.96
3301 3367 0.318445 CGGCGAACCCCTAGTAATCG 60.318 60.000 0.00 0.00 32.89 3.34
3323 3389 4.912395 AACGCAGGGCCAGCCAAA 62.912 61.111 15.88 0.00 37.98 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
529 535 8.593679 TGATGATGGAGTTTTGTACTTCTCTAA 58.406 33.333 0.00 0.00 37.17 2.10
548 554 2.086869 GTGTCAGGGTTGGTGATGATG 58.913 52.381 0.00 0.00 0.00 3.07
549 555 1.339055 CGTGTCAGGGTTGGTGATGAT 60.339 52.381 0.00 0.00 0.00 2.45
550 556 0.034756 CGTGTCAGGGTTGGTGATGA 59.965 55.000 0.00 0.00 0.00 2.92
664 673 7.844779 TCTGTACTTATCAGTTCCTTTATCCCT 59.155 37.037 0.00 0.00 34.06 4.20
703 712 8.314751 CCAGGGTATTAATCTAATCGAACTGAT 58.685 37.037 0.00 0.00 39.67 2.90
770 779 4.248842 CCAGTGTGTGGCGTGGGA 62.249 66.667 0.00 0.00 40.39 4.37
805 814 2.174969 TGGGTGTCGTCGTTTGCAC 61.175 57.895 0.00 0.00 0.00 4.57
814 823 1.529010 TAGTGGTCGTGGGTGTCGT 60.529 57.895 0.00 0.00 0.00 4.34
856 865 0.627170 TGGATGGGGATGTGTGGGAT 60.627 55.000 0.00 0.00 0.00 3.85
947 960 5.596845 AGAGAGAAGTTTCTGTGTTGTCTC 58.403 41.667 0.00 0.00 39.65 3.36
1182 1195 3.171528 CCTCCAGAGCCTGATGATCATA 58.828 50.000 8.54 0.00 32.44 2.15
1190 1203 1.992277 GCCTTCCTCCAGAGCCTGA 60.992 63.158 4.00 0.00 32.44 3.86
1431 1449 5.763204 CCACTTTCACAAACCACAGTAGTAT 59.237 40.000 0.00 0.00 0.00 2.12
1437 1455 3.796504 GCATCCACTTTCACAAACCACAG 60.797 47.826 0.00 0.00 0.00 3.66
1903 1931 6.445139 AGGGGAGAGACATTTTGAAGATTAGA 59.555 38.462 0.00 0.00 0.00 2.10
1977 2005 1.006337 TGCTGAAACCGGCAAATGC 60.006 52.632 0.00 1.22 42.48 3.56
2024 2052 3.596214 GTTGATCGTTGGAAGGCTAGAA 58.404 45.455 0.00 0.00 0.00 2.10
2252 2280 2.627791 CCATGACTTGAACGTGGCA 58.372 52.632 0.00 0.00 37.56 4.92
2430 2467 6.147328 ACCTAACAAGAGCAAACTACGAATTC 59.853 38.462 0.00 0.00 0.00 2.17
2473 2510 1.859383 TCGACAATGACAAGCACGAA 58.141 45.000 0.00 0.00 0.00 3.85
3289 3355 1.805120 CGTTGTGCCGATTACTAGGGG 60.805 57.143 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.