Multiple sequence alignment - TraesCS2D01G266800

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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 TraesCS2D01G266800 chr2D 100.000 3505 0 0 1 3505 325761442 325757938 0.000000e+00 6473.0
1 TraesCS2D01G266800 chr2A 94.646 3026 109 26 516 3505 392449040 392452048 0.000000e+00 4641.0
2 TraesCS2D01G266800 chr2B 94.625 2437 70 20 463 2894 394952824 394950444 0.000000e+00 3718.0
3 TraesCS2D01G266800 chr2B 92.172 511 17 5 3017 3505 394949844 394949335 0.000000e+00 701.0
4 TraesCS2D01G266800 chr2B 91.898 469 30 6 1 467 394953445 394952983 0.000000e+00 649.0
5 TraesCS2D01G266800 chr2B 95.489 133 6 0 2887 3019 394950405 394950273 2.740000e-51 213.0
6 TraesCS2D01G266800 chr1D 76.077 209 42 7 57 260 487867739 487867944 6.190000e-18 102.0
7 TraesCS2D01G266800 chr4A 76.596 188 32 10 58 237 552857296 552857113 3.730000e-15 93.5
8 TraesCS2D01G266800 chr5B 87.500 72 7 2 155 224 545621023 545620952 8.060000e-12 82.4
9 TraesCS2D01G266800 chr5B 79.787 94 18 1 209 301 60907283 60907376 2.260000e-07 67.6
10 TraesCS2D01G266800 chr5B 78.378 111 8 13 160 260 708186800 708186904 1.360000e-04 58.4
11 TraesCS2D01G266800 chr1B 74.016 254 43 17 57 301 121833849 121833610 8.060000e-12 82.4
12 TraesCS2D01G266800 chr3A 87.879 66 5 3 176 238 208722599 208722534 1.350000e-09 75.0
13 TraesCS2D01G266800 chr6B 81.111 90 14 2 155 241 6257433 6257344 6.280000e-08 69.4
14 TraesCS2D01G266800 chr5A 79.787 94 14 2 209 301 45448417 45448328 2.920000e-06 63.9
15 TraesCS2D01G266800 chr4B 73.043 230 43 12 88 301 532763414 532763640 2.920000e-06 63.9
16 TraesCS2D01G266800 chr7A 83.099 71 9 2 173 240 729184994 729184924 1.050000e-05 62.1
17 TraesCS2D01G266800 chrUn 96.970 33 1 0 161 193 146256767 146256735 4.890000e-04 56.5


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 TraesCS2D01G266800 chr2D 325757938 325761442 3504 True 6473.00 6473 100.000 1 3505 1 chr2D.!!$R1 3504
1 TraesCS2D01G266800 chr2A 392449040 392452048 3008 False 4641.00 4641 94.646 516 3505 1 chr2A.!!$F1 2989
2 TraesCS2D01G266800 chr2B 394949335 394953445 4110 True 1320.25 3718 93.546 1 3505 4 chr2B.!!$R1 3504

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
298 301 0.179225 GCATCTGCGTTTGTACCGTG 60.179 55.0 0.00 0.0 0.00 4.94 F
505 671 0.900421 TCGACCGGAGAGTCTGACTA 59.100 55.0 9.46 0.0 34.46 2.59 F
1989 2186 0.037734 TTCTTCTTTTCCCCCTCGGC 59.962 55.0 0.00 0.0 0.00 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1740 1937 3.817084 CTCTTTCACTTGATGCTGGTGAA 59.183 43.478 0.00 0.0 44.69 3.18 R
2316 2514 5.555966 TCAAACATCATGCACTAGGTTACA 58.444 37.500 0.00 0.0 0.00 2.41 R
3479 4182 1.879575 AATGGTGGCAGCTAGAGGTA 58.120 50.000 18.53 0.0 0.00 3.08 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
48 49 2.852449 AGCTTCCCTATGATGGAACCAA 59.148 45.455 0.00 0.00 36.97 3.67
51 52 2.858644 TCCCTATGATGGAACCAACCT 58.141 47.619 0.00 0.00 0.00 3.50
54 55 3.716872 CCCTATGATGGAACCAACCTACT 59.283 47.826 0.00 0.00 0.00 2.57
55 56 4.202367 CCCTATGATGGAACCAACCTACTC 60.202 50.000 0.00 0.00 0.00 2.59
69 70 3.771216 ACCTACTCGGTTCAAGTCCTAA 58.229 45.455 0.00 0.00 46.37 2.69
77 78 2.549349 GGTTCAAGTCCTAAACTCGGCA 60.549 50.000 0.00 0.00 37.17 5.69
96 97 3.492421 CACAGGTGCTCGCATATTTTT 57.508 42.857 0.00 0.00 0.00 1.94
133 134 3.052455 TGTCCTGCGCTATTCTTTCAA 57.948 42.857 9.73 0.00 0.00 2.69
141 142 4.275689 TGCGCTATTCTTTCAATGGGTATG 59.724 41.667 9.73 0.00 0.00 2.39
142 143 4.320494 GCGCTATTCTTTCAATGGGTATGG 60.320 45.833 0.00 0.00 0.00 2.74
171 174 2.542595 GTCAACTACGAGGTGTTTGTGG 59.457 50.000 0.00 0.00 33.77 4.17
179 182 1.597663 GAGGTGTTTGTGGTGACTTCG 59.402 52.381 0.00 0.00 0.00 3.79
183 186 2.417239 GTGTTTGTGGTGACTTCGTCAA 59.583 45.455 0.00 0.00 44.49 3.18
198 201 7.067494 TGACTTCGTCAATCTCAAGATCTATCA 59.933 37.037 0.00 0.00 39.78 2.15
199 202 7.424803 ACTTCGTCAATCTCAAGATCTATCAG 58.575 38.462 0.00 0.00 32.75 2.90
225 228 0.390860 CCCTCGAAGGTGCTCATAGG 59.609 60.000 0.00 0.00 31.93 2.57
264 267 0.391130 TGTTCATAGGGTGAGCGTGC 60.391 55.000 0.00 0.00 40.58 5.34
298 301 0.179225 GCATCTGCGTTTGTACCGTG 60.179 55.000 0.00 0.00 0.00 4.94
309 312 4.345288 GTTTGTACCGTGTTTCTCCAAAC 58.655 43.478 0.00 0.00 42.16 2.93
433 436 5.854157 ACAAAACGAACATATGTTAGCTCG 58.146 37.500 23.62 22.06 38.56 5.03
438 441 6.068473 ACGAACATATGTTAGCTCGTGATA 57.932 37.500 24.90 0.00 38.56 2.15
439 442 6.143496 ACGAACATATGTTAGCTCGTGATAG 58.857 40.000 24.90 4.51 38.56 2.08
505 671 0.900421 TCGACCGGAGAGTCTGACTA 59.100 55.000 9.46 0.00 34.46 2.59
506 672 1.008329 CGACCGGAGAGTCTGACTAC 58.992 60.000 9.46 7.99 34.46 2.73
507 673 1.675116 CGACCGGAGAGTCTGACTACA 60.675 57.143 9.46 0.00 34.46 2.74
508 674 2.645802 GACCGGAGAGTCTGACTACAT 58.354 52.381 9.46 0.00 33.79 2.29
509 675 3.018149 GACCGGAGAGTCTGACTACATT 58.982 50.000 9.46 0.00 33.79 2.71
510 676 4.197750 GACCGGAGAGTCTGACTACATTA 58.802 47.826 9.46 0.00 33.79 1.90
511 677 4.794334 ACCGGAGAGTCTGACTACATTAT 58.206 43.478 9.46 0.00 0.00 1.28
512 678 5.938279 ACCGGAGAGTCTGACTACATTATA 58.062 41.667 9.46 0.00 0.00 0.98
513 679 6.544650 ACCGGAGAGTCTGACTACATTATAT 58.455 40.000 9.46 0.00 0.00 0.86
514 680 6.431543 ACCGGAGAGTCTGACTACATTATATG 59.568 42.308 9.46 0.00 0.00 1.78
515 681 6.431543 CCGGAGAGTCTGACTACATTATATGT 59.568 42.308 10.86 0.00 46.92 2.29
516 682 7.606839 CCGGAGAGTCTGACTACATTATATGTA 59.393 40.741 10.86 0.00 44.38 2.29
580 746 5.917462 AGATTGGGCAATTATTAGGCAAAC 58.083 37.500 0.00 0.00 0.00 2.93
586 752 5.450550 GGGCAATTATTAGGCAAACTGAGAC 60.451 44.000 0.00 0.00 0.00 3.36
587 753 5.450550 GGCAATTATTAGGCAAACTGAGACC 60.451 44.000 0.00 0.00 0.00 3.85
601 767 7.367285 CAAACTGAGACCGAATCCAAATTAAA 58.633 34.615 0.00 0.00 0.00 1.52
653 819 5.007136 GTCATGTTTCTCATTACCTAGCAGC 59.993 44.000 0.00 0.00 34.09 5.25
671 837 6.002062 AGCAGCTGAAAGTATTGTGTAAAC 57.998 37.500 20.43 0.00 35.30 2.01
673 839 5.853282 GCAGCTGAAAGTATTGTGTAAACAG 59.147 40.000 20.43 0.00 35.30 3.16
675 841 7.639039 CAGCTGAAAGTATTGTGTAAACAGAA 58.361 34.615 8.42 0.00 35.30 3.02
722 888 4.219288 GCATCCACTGGAGTTGAAAGAAAT 59.781 41.667 3.62 0.00 34.05 2.17
734 900 9.314321 GGAGTTGAAAGAAATCTATCGTTATGA 57.686 33.333 0.00 0.00 0.00 2.15
867 1060 7.724305 TTAGCTAGTGGTAAACAGACAAAAG 57.276 36.000 0.00 0.00 33.79 2.27
880 1073 6.995511 ACAGACAAAAGCACTGTAAACTAA 57.004 33.333 0.00 0.00 42.01 2.24
1024 1218 6.121776 TCTTCCTACATCTTAACTTGGCAA 57.878 37.500 0.00 0.00 0.00 4.52
1219 1416 3.018149 ACTACCAGTAGTACAGCTGCTC 58.982 50.000 15.27 7.15 43.98 4.26
1365 1562 2.344203 CCGAGAGTTCCGGTCTGCT 61.344 63.158 0.00 0.00 41.91 4.24
1989 2186 0.037734 TTCTTCTTTTCCCCCTCGGC 59.962 55.000 0.00 0.00 0.00 5.54
1999 2196 1.755384 CCCCTCGGCCTCTATTTCC 59.245 63.158 0.00 0.00 0.00 3.13
2311 2509 2.291365 TGTGCTTCCATGGATCATTCG 58.709 47.619 17.06 1.54 0.00 3.34
2316 2514 4.130118 GCTTCCATGGATCATTCGTAGTT 58.870 43.478 17.06 0.00 0.00 2.24
2360 2558 5.620206 TGATCAGGAAACAAAGAGCTGTTA 58.380 37.500 0.00 0.00 38.59 2.41
2398 2596 5.807011 ACAAAATGTGAAGCAGAAACTCAAC 59.193 36.000 0.00 0.00 0.00 3.18
2422 2621 8.519492 ACTTAATTGACAAAACATCAAATCGG 57.481 30.769 0.00 0.00 39.43 4.18
2930 3180 8.940397 ACTAGGCCAATTAGCACATAATAATT 57.060 30.769 5.01 0.00 32.71 1.40
2999 3249 7.722949 ATAATGGTGTGAAATGAGGAAATGT 57.277 32.000 0.00 0.00 0.00 2.71
3247 3928 2.456119 CGTCCCGCTGTGAATCTGC 61.456 63.158 0.00 0.00 37.59 4.26
3322 4003 7.522901 CAGATATACTTCTATCTGCACATGC 57.477 40.000 7.86 0.00 44.78 4.06
3357 4042 4.899239 CTGCTAGCTTCCCGCCCG 62.899 72.222 17.23 0.00 40.39 6.13
3442 4143 3.203040 AGTGCATGGGGAGCTAATTAACT 59.797 43.478 0.00 0.00 0.00 2.24
3454 4155 7.095017 GGGAGCTAATTAACTAATTGCTGCTAG 60.095 40.741 21.99 0.00 41.60 3.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 7.717436 AGGGAAGCTAATCATCTAAACTAAAGC 59.283 37.037 0.00 0.00 0.00 3.51
32 33 3.716872 AGTAGGTTGGTTCCATCATAGGG 59.283 47.826 0.00 0.00 0.00 3.53
48 49 6.218572 AGTTTAGGACTTGAACCGAGTAGGT 61.219 44.000 0.00 0.00 46.83 3.08
51 52 4.083110 CGAGTTTAGGACTTGAACCGAGTA 60.083 45.833 0.00 0.00 41.59 2.59
54 55 2.029649 CCGAGTTTAGGACTTGAACCGA 60.030 50.000 5.27 0.00 41.59 4.69
55 56 2.334838 CCGAGTTTAGGACTTGAACCG 58.665 52.381 0.00 0.00 41.59 4.44
119 120 4.320494 CCATACCCATTGAAAGAATAGCGC 60.320 45.833 0.00 0.00 0.00 5.92
133 134 0.178068 GACGAGCACACCATACCCAT 59.822 55.000 0.00 0.00 0.00 4.00
160 163 1.065709 ACGAAGTCACCACAAACACCT 60.066 47.619 0.00 0.00 29.74 4.00
179 182 5.858049 CGAGCTGATAGATCTTGAGATTGAC 59.142 44.000 0.00 0.00 34.37 3.18
183 186 5.357878 GGATCGAGCTGATAGATCTTGAGAT 59.642 44.000 14.14 0.00 39.34 2.75
198 201 1.076632 ACCTTCGAGGGATCGAGCT 60.077 57.895 22.01 0.00 43.33 4.09
199 202 1.066587 CACCTTCGAGGGATCGAGC 59.933 63.158 22.01 0.00 43.33 5.03
218 221 3.576118 CACACACTCCCTATCCCTATGAG 59.424 52.174 0.00 0.00 0.00 2.90
225 228 1.527370 GGGCACACACTCCCTATCC 59.473 63.158 0.00 0.00 39.46 2.59
245 248 0.391130 GCACGCTCACCCTATGAACA 60.391 55.000 0.00 0.00 36.69 3.18
264 267 2.798847 CAGATGCTCACATACATCCACG 59.201 50.000 0.00 0.00 43.01 4.94
269 272 2.609427 ACGCAGATGCTCACATACAT 57.391 45.000 2.95 0.00 36.35 2.29
287 290 4.142643 TGTTTGGAGAAACACGGTACAAAC 60.143 41.667 0.00 0.00 45.26 2.93
358 361 6.297080 TCGTCCCCAGTTAACATATGTTAA 57.703 37.500 28.96 28.96 45.18 2.01
373 376 4.649705 TTCCTGGCCTCGTCCCCA 62.650 66.667 3.32 0.00 0.00 4.96
488 654 2.110901 TGTAGTCAGACTCTCCGGTC 57.889 55.000 6.27 0.00 36.56 4.79
554 720 6.558488 TGCCTAATAATTGCCCAATCTTTT 57.442 33.333 0.00 0.00 0.00 2.27
555 721 6.558488 TTGCCTAATAATTGCCCAATCTTT 57.442 33.333 0.00 0.00 0.00 2.52
556 722 6.156775 AGTTTGCCTAATAATTGCCCAATCTT 59.843 34.615 0.00 0.00 0.00 2.40
557 723 5.662657 AGTTTGCCTAATAATTGCCCAATCT 59.337 36.000 0.00 0.00 0.00 2.40
563 729 5.450550 GGTCTCAGTTTGCCTAATAATTGCC 60.451 44.000 0.00 0.00 0.00 4.52
580 746 5.648092 ACCTTTAATTTGGATTCGGTCTCAG 59.352 40.000 0.00 0.00 0.00 3.35
586 752 9.248291 CATTATCAACCTTTAATTTGGATTCGG 57.752 33.333 0.00 0.00 0.00 4.30
587 753 8.755018 GCATTATCAACCTTTAATTTGGATTCG 58.245 33.333 0.00 0.00 0.00 3.34
601 767 5.245751 TGTTTGGAACATGCATTATCAACCT 59.754 36.000 0.00 0.00 39.30 3.50
637 803 4.467795 ACTTTCAGCTGCTAGGTAATGAGA 59.532 41.667 9.47 0.00 0.00 3.27
638 804 4.764172 ACTTTCAGCTGCTAGGTAATGAG 58.236 43.478 9.47 0.00 0.00 2.90
639 805 4.826274 ACTTTCAGCTGCTAGGTAATGA 57.174 40.909 9.47 0.00 0.00 2.57
645 811 4.256920 ACACAATACTTTCAGCTGCTAGG 58.743 43.478 9.47 2.43 0.00 3.02
653 819 8.767944 GTGTTCTGTTTACACAATACTTTCAG 57.232 34.615 0.00 0.00 44.08 3.02
675 841 8.580720 TGCAAACATAACCTAATTGTAATGTGT 58.419 29.630 0.00 0.00 0.00 3.72
695 861 2.229792 TCAACTCCAGTGGATGCAAAC 58.770 47.619 13.56 0.00 0.00 2.93
722 888 8.110860 TCAGCAGACATATTCATAACGATAGA 57.889 34.615 0.00 0.00 41.38 1.98
838 1031 8.812513 TGTCTGTTTACCACTAGCTAATACTA 57.187 34.615 0.00 0.00 0.00 1.82
839 1032 7.713734 TGTCTGTTTACCACTAGCTAATACT 57.286 36.000 0.00 0.00 0.00 2.12
840 1033 8.767478 TTTGTCTGTTTACCACTAGCTAATAC 57.233 34.615 0.00 0.00 0.00 1.89
867 1060 6.376581 TCCTCTACCTAGTTAGTTTACAGTGC 59.623 42.308 0.00 0.00 0.00 4.40
880 1073 6.358991 GTGAGATACACTTCCTCTACCTAGT 58.641 44.000 0.00 0.00 45.13 2.57
915 1108 5.681954 GCATAGCTAGCTGGGAGATGAATAG 60.682 48.000 27.68 5.67 0.00 1.73
964 1157 9.557606 GTTTTTGTTGTTTGCGTTTATATGTAC 57.442 29.630 0.00 0.00 0.00 2.90
1056 1253 4.400120 ACCAGTACTAGATGGCTAGCTAC 58.600 47.826 15.72 7.28 46.55 3.58
1089 1286 2.072298 GTTTGATCGAGCTCTGCACTT 58.928 47.619 12.85 0.00 0.00 3.16
1740 1937 3.817084 CTCTTTCACTTGATGCTGGTGAA 59.183 43.478 0.00 0.00 44.69 3.18
1989 2186 8.286191 AGAATTAAGCACAAAGGAAATAGAGG 57.714 34.615 0.00 0.00 0.00 3.69
1999 2196 7.799914 GGCAATCAAAAAGAATTAAGCACAAAG 59.200 33.333 0.00 0.00 0.00 2.77
2311 2509 6.106673 ACATCATGCACTAGGTTACAACTAC 58.893 40.000 0.00 0.00 0.00 2.73
2316 2514 5.555966 TCAAACATCATGCACTAGGTTACA 58.444 37.500 0.00 0.00 0.00 2.41
2398 2596 8.427012 CACCGATTTGATGTTTTGTCAATTAAG 58.573 33.333 0.00 0.00 35.68 1.85
2422 2621 9.537848 CGTTAACAGATAATTAGTTTGGAACAC 57.462 33.333 6.39 0.00 39.29 3.32
2514 2714 5.960113 AGCTATATATGTCCTCTTTCGCAG 58.040 41.667 0.00 0.00 0.00 5.18
2866 3070 8.561738 TTCCTGTTTATCAACCTAATCTTGAC 57.438 34.615 0.00 0.00 30.46 3.18
3349 4034 4.853142 ATACTCTGCCGGGCGGGA 62.853 66.667 26.86 19.08 38.47 5.14
3357 4042 6.072728 TGACACACATAAAACAATACTCTGCC 60.073 38.462 0.00 0.00 0.00 4.85
3424 4125 6.491403 AGCAATTAGTTAATTAGCTCCCCATG 59.509 38.462 4.97 1.70 36.37 3.66
3442 4143 5.357596 TGCATTGATTGACTAGCAGCAATTA 59.642 36.000 0.00 2.14 35.05 1.40
3479 4182 1.879575 AATGGTGGCAGCTAGAGGTA 58.120 50.000 18.53 0.00 0.00 3.08


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

AutoCloner maintained by Alex Coulton.