Multiple sequence alignment - TraesCS7D01G258800

Loading Multiple Alignment...

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 TraesCS7D01G258800 chr7D 100.000 3742 0 0 1 3742 234393542 234397283 0.000000e+00 6911
1 TraesCS7D01G258800 chr7D 96.324 1986 67 5 1572 3552 370463534 370461550 0.000000e+00 3258
2 TraesCS7D01G258800 chr7D 95.210 1670 74 4 1 1669 370465153 370463489 0.000000e+00 2636
3 TraesCS7D01G258800 chr7D 99.490 196 1 0 3547 3742 370461519 370461324 1.280000e-94 357
4 TraesCS7D01G258800 chr1D 95.838 3556 119 16 1 3549 238010233 238013766 0.000000e+00 5720
5 TraesCS7D01G258800 chr1D 97.449 196 4 1 3547 3742 238013800 238013994 2.150000e-87 333
6 TraesCS7D01G258800 chr2D 93.987 3559 174 21 1 3549 273055761 273059289 0.000000e+00 5350
7 TraesCS7D01G258800 chr7A 93.519 3564 202 25 1 3552 315495796 315492250 0.000000e+00 5275
8 TraesCS7D01G258800 chr7A 92.432 3515 217 34 60 3549 583021591 583025081 0.000000e+00 4972
9 TraesCS7D01G258800 chr7A 97.449 196 5 0 3547 3742 315492220 315492025 5.990000e-88 335
10 TraesCS7D01G258800 chr6A 91.893 3565 235 27 1 3549 446428189 446431715 0.000000e+00 4933
11 TraesCS7D01G258800 chr6A 92.166 2502 182 11 1059 3552 175158603 175156108 0.000000e+00 3522
12 TraesCS7D01G258800 chr3A 91.865 3565 206 44 1 3552 217243207 217239714 0.000000e+00 4900
13 TraesCS7D01G258800 chr3A 96.939 196 6 0 3547 3742 217239689 217239494 2.790000e-86 329
14 TraesCS7D01G258800 chr2A 91.633 3514 233 36 60 3549 378112026 378115502 0.000000e+00 4804
15 TraesCS7D01G258800 chr2A 90.827 3565 249 43 15 3552 116993618 116990105 0.000000e+00 4700
16 TraesCS7D01G258800 chr2A 93.651 2079 117 14 1481 3549 434157269 434155196 0.000000e+00 3094
17 TraesCS7D01G258800 chr2A 86.067 567 66 11 1 558 384171195 384170633 6.920000e-167 597
18 TraesCS7D01G258800 chr6D 93.342 2253 113 15 1 2251 186932752 186930535 0.000000e+00 3295
19 TraesCS7D01G258800 chr3D 95.455 2068 85 6 1488 3549 428373413 428375477 0.000000e+00 3290
20 TraesCS7D01G258800 chr3D 96.939 196 6 0 3547 3742 428375510 428375705 2.790000e-86 329
21 TraesCS7D01G258800 chr1A 92.631 1547 106 7 329 1871 379613305 379614847 0.000000e+00 2218
22 TraesCS7D01G258800 chr1A 98.980 196 2 0 3547 3742 379095642 379095447 5.950000e-93 351
23 TraesCS7D01G258800 chr2B 88.515 505 45 7 1 502 497415224 497415718 1.920000e-167 599
24 TraesCS7D01G258800 chr2B 86.705 519 57 10 1 511 506420573 506420059 1.950000e-157 566
25 TraesCS7D01G258800 chr5D 97.959 196 3 1 3547 3742 211785838 211785644 4.630000e-89 339
26 TraesCS7D01G258800 chr5D 97.449 196 5 0 3547 3742 205329849 205330044 5.990000e-88 335
27 TraesCS7D01G258800 chr4D 96.939 196 5 1 3547 3742 274367979 274368173 1.000000e-85 327


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 TraesCS7D01G258800 chr7D 234393542 234397283 3741 False 6911.000000 6911 100.0000 1 3742 1 chr7D.!!$F1 3741
1 TraesCS7D01G258800 chr7D 370461324 370465153 3829 True 2083.666667 3258 97.0080 1 3742 3 chr7D.!!$R1 3741
2 TraesCS7D01G258800 chr1D 238010233 238013994 3761 False 3026.500000 5720 96.6435 1 3742 2 chr1D.!!$F1 3741
3 TraesCS7D01G258800 chr2D 273055761 273059289 3528 False 5350.000000 5350 93.9870 1 3549 1 chr2D.!!$F1 3548
4 TraesCS7D01G258800 chr7A 583021591 583025081 3490 False 4972.000000 4972 92.4320 60 3549 1 chr7A.!!$F1 3489
5 TraesCS7D01G258800 chr7A 315492025 315495796 3771 True 2805.000000 5275 95.4840 1 3742 2 chr7A.!!$R1 3741
6 TraesCS7D01G258800 chr6A 446428189 446431715 3526 False 4933.000000 4933 91.8930 1 3549 1 chr6A.!!$F1 3548
7 TraesCS7D01G258800 chr6A 175156108 175158603 2495 True 3522.000000 3522 92.1660 1059 3552 1 chr6A.!!$R1 2493
8 TraesCS7D01G258800 chr3A 217239494 217243207 3713 True 2614.500000 4900 94.4020 1 3742 2 chr3A.!!$R1 3741
9 TraesCS7D01G258800 chr2A 378112026 378115502 3476 False 4804.000000 4804 91.6330 60 3549 1 chr2A.!!$F1 3489
10 TraesCS7D01G258800 chr2A 116990105 116993618 3513 True 4700.000000 4700 90.8270 15 3552 1 chr2A.!!$R1 3537
11 TraesCS7D01G258800 chr2A 434155196 434157269 2073 True 3094.000000 3094 93.6510 1481 3549 1 chr2A.!!$R3 2068
12 TraesCS7D01G258800 chr2A 384170633 384171195 562 True 597.000000 597 86.0670 1 558 1 chr2A.!!$R2 557
13 TraesCS7D01G258800 chr6D 186930535 186932752 2217 True 3295.000000 3295 93.3420 1 2251 1 chr6D.!!$R1 2250
14 TraesCS7D01G258800 chr3D 428373413 428375705 2292 False 1809.500000 3290 96.1970 1488 3742 2 chr3D.!!$F1 2254
15 TraesCS7D01G258800 chr1A 379613305 379614847 1542 False 2218.000000 2218 92.6310 329 1871 1 chr1A.!!$F1 1542
16 TraesCS7D01G258800 chr2B 506420059 506420573 514 True 566.000000 566 86.7050 1 511 1 chr2B.!!$R1 510

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
527 556 1.303643 GAGCAACAACTCCCAGGGG 60.304 63.158 5.33 0.92 0.0 4.79 F
1193 1239 0.462581 GCCGATGAGGTGATGAGCAA 60.463 55.000 0.00 0.00 43.7 3.91 F
2392 2566 0.465705 ACCTCATCATGTACGCAGGG 59.534 55.000 0.00 0.00 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2392 2566 2.065993 ACGTGGCGTATGCATCTATC 57.934 50.000 0.19 0.0 45.35 2.08 R
2401 2575 2.536365 CATGACTTGTACGTGGCGTAT 58.464 47.619 0.00 0.0 44.12 3.06 R
3603 3843 9.180678 CATAGTAAAAGTTAAAGCACTGGTTTG 57.819 33.333 15.08 0.0 34.94 2.93 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
426 453 3.118408 TCAGTTCACACAGCACTAAACCT 60.118 43.478 0.00 0.00 0.00 3.50
527 556 1.303643 GAGCAACAACTCCCAGGGG 60.304 63.158 5.33 0.92 0.00 4.79
695 728 7.715249 GTGGGATTTAGCAGATCATAAGTACAA 59.285 37.037 0.00 0.00 0.00 2.41
719 752 4.607293 TGACAAGACTACTCAGTGCAAT 57.393 40.909 0.00 0.00 34.21 3.56
741 777 4.665833 AGTAAAAACCCTTTGTCTTGGC 57.334 40.909 0.00 0.00 0.00 4.52
876 912 3.379445 ATCCCCGTCGACGCACTT 61.379 61.111 31.73 13.56 38.18 3.16
917 956 2.573009 TCCATCTCTGCCTCATTCACAA 59.427 45.455 0.00 0.00 0.00 3.33
1063 1109 1.810031 CGGACAAGAGCAACAACCTCA 60.810 52.381 0.00 0.00 0.00 3.86
1193 1239 0.462581 GCCGATGAGGTGATGAGCAA 60.463 55.000 0.00 0.00 43.70 3.91
1396 1442 7.790027 TCTGTTGTACTAGTACTACTCCCTAG 58.210 42.308 32.84 25.17 40.64 3.02
1505 1551 4.794003 GCATTTCTGAAACTGTGAAGTGGG 60.794 45.833 4.73 0.00 31.18 4.61
1565 1663 7.816031 ACTGGATTAGCATTCTGAAAAATGTTG 59.184 33.333 0.00 0.00 38.60 3.33
2100 2270 4.691359 CCCTTGCAGGCCCAAGCT 62.691 66.667 14.46 0.00 40.62 3.74
2106 2276 2.045536 CAGGCCCAAGCTCCTCAC 60.046 66.667 0.00 0.00 39.73 3.51
2197 2367 3.138283 TGGACAAGTCTGGTTTGGAGATT 59.862 43.478 0.00 0.00 0.00 2.40
2392 2566 0.465705 ACCTCATCATGTACGCAGGG 59.534 55.000 0.00 0.00 0.00 4.45
2401 2575 1.408969 TGTACGCAGGGATAGATGCA 58.591 50.000 0.00 0.00 42.68 3.96
2563 2738 2.029728 CGCTTCTGCTTGTCCTTAATCG 59.970 50.000 0.00 0.00 36.97 3.34
2607 2782 3.880490 TGCTTTCGTTATGTTGAACCAGT 59.120 39.130 0.00 0.00 0.00 4.00
2629 2804 7.148474 CCAGTTACCTTATGTTATGTGTGTCAC 60.148 40.741 0.00 0.00 34.56 3.67
2973 3166 4.673441 CCGAGGACAACATTCAGTACTAG 58.327 47.826 0.00 0.00 0.00 2.57
3038 3234 5.118286 CAACAGGAAAAGCAAAGAACCATT 58.882 37.500 0.00 0.00 0.00 3.16
3148 3344 3.292492 AGGAACGGGAAGTTTCAGTTT 57.708 42.857 0.95 0.00 44.35 2.66
3400 3601 7.102993 AGGCACTAGTTTCAAACAACAAAAAT 58.897 30.769 2.41 0.00 36.02 1.82
3603 3843 7.740246 GGCTATCCGTTAAATGTAGCTAATTC 58.260 38.462 0.00 0.00 38.22 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
222 226 1.798223 CGTTCGTTGATGTGTGGACAT 59.202 47.619 0.00 0.00 46.01 3.06
344 371 2.666190 CAGTGGTGTGAGTGGCCG 60.666 66.667 0.00 0.00 0.00 6.13
495 524 5.185056 AGTTGTTGCTCAAAACTGGTACTTT 59.815 36.000 0.00 0.00 37.81 2.66
695 728 3.384789 TGCACTGAGTAGTCTTGTCAAGT 59.615 43.478 12.30 0.00 34.07 3.16
719 752 4.585581 GGCCAAGACAAAGGGTTTTTACTA 59.414 41.667 0.00 0.00 0.00 1.82
741 777 0.392595 GGCCTGGAAGAACTAACCGG 60.393 60.000 0.00 0.00 34.07 5.28
876 912 5.398236 TGGAAGACAATGGGGTATTTTTGA 58.602 37.500 0.00 0.00 0.00 2.69
917 956 1.665442 GAAGCGGCAATGGTGGTTT 59.335 52.632 1.45 0.00 0.00 3.27
1086 1132 1.136611 GTTCTTGTGTACTCGCGCTTG 60.137 52.381 5.56 0.00 0.00 4.01
1193 1239 2.739996 CCGCCCTTCATCCTGAGCT 61.740 63.158 0.00 0.00 0.00 4.09
1396 1442 8.600625 GTTGGGAAACAAGTTTAATGAAGTTTC 58.399 33.333 0.00 0.00 42.27 2.78
1505 1551 5.886960 AGATGCTAATCTGGTGAAACAAC 57.113 39.130 0.00 0.00 41.80 3.32
1565 1663 6.317140 TGGTGCATCAAGTTCAGAATTCTATC 59.683 38.462 7.86 1.87 0.00 2.08
2085 2255 3.066814 GGAGCTTGGGCCTGCAAG 61.067 66.667 20.52 15.32 39.73 4.01
2197 2367 3.181453 TGTCGATGAAGTTGTTGGGGTTA 60.181 43.478 0.00 0.00 0.00 2.85
2293 2464 5.497464 TCATGTCTTTGTAGAATGGGTGA 57.503 39.130 0.00 0.00 30.65 4.02
2392 2566 2.065993 ACGTGGCGTATGCATCTATC 57.934 50.000 0.19 0.00 45.35 2.08
2401 2575 2.536365 CATGACTTGTACGTGGCGTAT 58.464 47.619 0.00 0.00 44.12 3.06
2563 2738 6.751888 AGCAAACTACAAATCTGAAACAACAC 59.248 34.615 0.00 0.00 0.00 3.32
2607 2782 5.870433 CCGTGACACACATAACATAAGGTAA 59.130 40.000 6.37 0.00 33.40 2.85
2629 2804 2.577449 AGGCAAACTTGTTCAAACCG 57.423 45.000 0.00 0.00 0.00 4.44
2996 3189 7.389607 TCCTGTTGCAGTACTTAGTAAATTTCC 59.610 37.037 0.00 0.00 0.00 3.13
3038 3234 7.275183 TGCTAGTGACTAGGAAATACGTACTA 58.725 38.462 20.24 0.00 34.88 1.82
3148 3344 4.582240 TGTGTCACTGTTTTATGGAATGCA 59.418 37.500 4.27 0.00 0.00 3.96
3603 3843 9.180678 CATAGTAAAAGTTAAAGCACTGGTTTG 57.819 33.333 15.08 0.00 34.94 2.93


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

AutoCloner maintained by Alex Coulton.