Multiple sequence alignment - TraesCS1B01G378900

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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 TraesCS1B01G378900 chr1B 100.000 4025 0 0 1 4025 611522524 611526548 0.000000e+00 7433.0
1 TraesCS1B01G378900 chr1B 87.941 2720 274 29 747 3435 543469009 543466313 0.000000e+00 3157.0
2 TraesCS1B01G378900 chr1D 97.867 3797 56 9 251 4025 446708747 446704954 0.000000e+00 6540.0
3 TraesCS1B01G378900 chr1D 87.771 2723 278 27 747 3435 403948356 403945655 0.000000e+00 3133.0
4 TraesCS1B01G378900 chr1D 94.606 241 13 0 446 686 7770790 7770550 1.370000e-99 374.0
5 TraesCS1B01G378900 chr1D 89.344 244 20 6 446 689 82332863 82333100 6.540000e-78 302.0
6 TraesCS1B01G378900 chr1A 96.858 3374 68 11 674 4025 542440324 542436967 0.000000e+00 5609.0
7 TraesCS1B01G378900 chr1A 87.757 2728 280 32 747 3435 499623889 499621177 0.000000e+00 3138.0
8 TraesCS1B01G378900 chr1A 96.499 457 15 1 1 457 542440841 542440386 0.000000e+00 754.0
9 TraesCS1B01G378900 chr1A 92.946 241 15 1 446 686 9205614 9205376 2.300000e-92 350.0
10 TraesCS1B01G378900 chr1A 87.967 241 28 1 446 686 22251262 22251501 2.370000e-72 283.0
11 TraesCS1B01G378900 chr3D 78.080 1469 296 20 1496 2951 442040140 442041595 0.000000e+00 905.0
12 TraesCS1B01G378900 chr3B 77.332 1469 307 19 1496 2951 579284921 579286376 0.000000e+00 845.0
13 TraesCS1B01G378900 chr3B 77.332 1469 307 19 1496 2951 579301578 579303033 0.000000e+00 845.0
14 TraesCS1B01G378900 chr7D 91.667 240 19 1 446 685 471219405 471219167 8.340000e-87 331.0
15 TraesCS1B01G378900 chr7D 90.455 220 20 1 445 664 294421798 294422016 5.090000e-74 289.0
16 TraesCS1B01G378900 chr2D 90.496 242 22 1 446 687 518007135 518006895 6.490000e-83 318.0
17 TraesCS1B01G378900 chr5D 86.975 238 29 2 448 685 214614310 214614545 2.380000e-67 267.0
18 TraesCS1B01G378900 chr5B 94.444 54 1 2 1250 1301 429846290 429846237 9.270000e-12 82.4
19 TraesCS1B01G378900 chr2B 94.444 54 1 2 1250 1301 36363415 36363362 9.270000e-12 82.4


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 TraesCS1B01G378900 chr1B 611522524 611526548 4024 False 7433.0 7433 100.0000 1 4025 1 chr1B.!!$F1 4024
1 TraesCS1B01G378900 chr1B 543466313 543469009 2696 True 3157.0 3157 87.9410 747 3435 1 chr1B.!!$R1 2688
2 TraesCS1B01G378900 chr1D 446704954 446708747 3793 True 6540.0 6540 97.8670 251 4025 1 chr1D.!!$R3 3774
3 TraesCS1B01G378900 chr1D 403945655 403948356 2701 True 3133.0 3133 87.7710 747 3435 1 chr1D.!!$R2 2688
4 TraesCS1B01G378900 chr1A 542436967 542440841 3874 True 3181.5 5609 96.6785 1 4025 2 chr1A.!!$R3 4024
5 TraesCS1B01G378900 chr1A 499621177 499623889 2712 True 3138.0 3138 87.7570 747 3435 1 chr1A.!!$R2 2688
6 TraesCS1B01G378900 chr3D 442040140 442041595 1455 False 905.0 905 78.0800 1496 2951 1 chr3D.!!$F1 1455
7 TraesCS1B01G378900 chr3B 579284921 579286376 1455 False 845.0 845 77.3320 1496 2951 1 chr3B.!!$F1 1455
8 TraesCS1B01G378900 chr3B 579301578 579303033 1455 False 845.0 845 77.3320 1496 2951 1 chr3B.!!$F2 1455

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
62 63 0.841289 AACCCGTCCCTGTCTTTTCA 59.159 50.000 0.00 0.00 0.00 2.69 F
1214 1220 1.004161 TGGATCATTCGCCACCTTCAA 59.996 47.619 0.00 0.00 0.00 2.69 F
2718 2733 1.767759 AATGGAATTTCGGGCCTGAG 58.232 50.000 15.42 0.22 26.74 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1402 1414 1.488393 GGCCTTAACTCCATCTGAGCT 59.512 52.381 0.0 0.0 45.61 4.09 R
2718 2733 2.030946 CGTGCTTTGCTCACCTATAAGC 59.969 50.000 0.0 0.0 41.10 3.09 R
3682 3732 0.821301 TCGCAGAAACCAATGCCACA 60.821 50.000 0.0 0.0 39.30 4.17 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
37 38 3.391382 GCTCCAGCACCCTACCGT 61.391 66.667 0.00 0.00 41.59 4.83
47 48 1.079612 CCCTACCGTCAACGAACCC 60.080 63.158 3.71 0.00 43.02 4.11
62 63 0.841289 AACCCGTCCCTGTCTTTTCA 59.159 50.000 0.00 0.00 0.00 2.69
153 154 8.380099 AGGATTATTGTGTAGTGGAACAGTTAA 58.620 33.333 0.00 0.00 40.27 2.01
213 214 5.936187 TGTTATGCAACCCAAATCATGAT 57.064 34.783 1.18 1.18 33.41 2.45
304 305 1.064803 TGCAACGTACAAGCACTTTGG 59.935 47.619 0.00 0.00 41.25 3.28
366 367 7.671302 TGTCCTAGTATTCTTCCATTATCAGC 58.329 38.462 0.00 0.00 0.00 4.26
471 472 2.354403 CCTCCGTCCTCGTTTATTGGTT 60.354 50.000 0.00 0.00 35.01 3.67
537 538 7.701539 AAGAAAATACTAATGCATGTCACCA 57.298 32.000 0.00 0.00 0.00 4.17
647 648 7.528996 AATCATGGTCAAAGAATGAAACTGA 57.471 32.000 0.00 0.00 40.50 3.41
648 649 6.957920 TCATGGTCAAAGAATGAAACTGAA 57.042 33.333 0.00 0.00 40.50 3.02
649 650 6.738114 TCATGGTCAAAGAATGAAACTGAAC 58.262 36.000 0.00 0.00 40.50 3.18
678 679 4.383880 GGGGACTAATAAACCAGGACAGAC 60.384 50.000 0.00 0.00 0.00 3.51
701 702 4.508124 CGTAGTACATGGAAGGAAATGCTC 59.492 45.833 0.00 0.00 0.00 4.26
823 825 7.516198 AAGATCAATGAGTAACAAAAGCAGT 57.484 32.000 0.00 0.00 0.00 4.40
1214 1220 1.004161 TGGATCATTCGCCACCTTCAA 59.996 47.619 0.00 0.00 0.00 2.69
2718 2733 1.767759 AATGGAATTTCGGGCCTGAG 58.232 50.000 15.42 0.22 26.74 3.35
3098 3130 4.339748 TGCCTGATTGGTTTGCTGTATTA 58.660 39.130 0.00 0.00 38.35 0.98
3385 3435 0.181114 TACCCATAGCCAAGCTGCAG 59.819 55.000 10.11 10.11 40.10 4.41
3682 3732 6.041751 GGTGCTACCTAGATTGTACCTATGTT 59.958 42.308 0.00 0.00 34.73 2.71
3685 3735 6.924060 GCTACCTAGATTGTACCTATGTTGTG 59.076 42.308 0.00 0.00 0.00 3.33
3686 3736 6.235231 ACCTAGATTGTACCTATGTTGTGG 57.765 41.667 0.00 0.00 0.00 4.17
3931 3996 1.228215 TGGCTGTTAGCTGCTTGCA 60.228 52.632 7.79 6.57 45.94 4.08
3939 4004 0.867746 TAGCTGCTTGCAACTTGTCG 59.132 50.000 7.79 0.00 45.94 4.35
3961 4026 0.716108 CTCGGTGCTCGCTGTTAAAG 59.284 55.000 0.00 0.00 39.05 1.85
4017 4082 3.628008 TGTGTCTATGATACCCACTCGT 58.372 45.455 0.00 0.00 0.00 4.18
4018 4083 3.630769 TGTGTCTATGATACCCACTCGTC 59.369 47.826 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 4.157817 CGGGTTCGTTGACGGTAG 57.842 61.111 3.48 0.00 40.29 3.18
153 154 5.535030 GGTTTCACCACAATTTTAGTCCTCT 59.465 40.000 0.00 0.00 38.42 3.69
282 283 4.489683 GTGCTTGTACGTTGCACG 57.510 55.556 17.44 7.07 45.62 5.34
366 367 7.201145 ACATCAGTACCATTTACTAACTAGCG 58.799 38.462 0.00 0.00 0.00 4.26
396 397 3.243724 AGCAGAGGGTAGAAGAACAGTT 58.756 45.455 0.00 0.00 0.00 3.16
471 472 5.067273 ACATTGACACAAAATACGAAGGGA 58.933 37.500 0.00 0.00 0.00 4.20
637 638 2.504367 CCCCTCGTGTTCAGTTTCATT 58.496 47.619 0.00 0.00 0.00 2.57
642 643 0.763223 AGTCCCCCTCGTGTTCAGTT 60.763 55.000 0.00 0.00 0.00 3.16
647 648 3.054875 GGTTTATTAGTCCCCCTCGTGTT 60.055 47.826 0.00 0.00 0.00 3.32
648 649 2.502947 GGTTTATTAGTCCCCCTCGTGT 59.497 50.000 0.00 0.00 0.00 4.49
649 650 2.502538 TGGTTTATTAGTCCCCCTCGTG 59.497 50.000 0.00 0.00 0.00 4.35
678 679 4.442706 AGCATTTCCTTCCATGTACTACG 58.557 43.478 0.00 0.00 0.00 3.51
823 825 8.570068 AGTTAAACACCAAACTAAAGTCTCAA 57.430 30.769 0.00 0.00 34.23 3.02
1214 1220 3.119990 CGAAAAACCATTCACGGTAGCAT 60.120 43.478 0.00 0.00 38.76 3.79
1402 1414 1.488393 GGCCTTAACTCCATCTGAGCT 59.512 52.381 0.00 0.00 45.61 4.09
2718 2733 2.030946 CGTGCTTTGCTCACCTATAAGC 59.969 50.000 0.00 0.00 41.10 3.09
3280 3319 1.072489 TGCGGTCCCATGTTCTTACAA 59.928 47.619 0.00 0.00 37.91 2.41
3385 3435 4.738740 CGCTGTAGCTAGTATAAACACACC 59.261 45.833 0.00 0.00 39.32 4.16
3408 3458 2.732412 GAAAGCCAAGCCTTTCTTCC 57.268 50.000 7.25 0.00 44.51 3.46
3530 3580 5.159273 ACCCGCAATTAATCCAAAAATGT 57.841 34.783 0.00 0.00 0.00 2.71
3658 3708 6.651975 ACATAGGTACAATCTAGGTAGCAC 57.348 41.667 8.80 0.00 40.67 4.40
3682 3732 0.821301 TCGCAGAAACCAATGCCACA 60.821 50.000 0.00 0.00 39.30 4.17
3685 3735 0.881118 TCTTCGCAGAAACCAATGCC 59.119 50.000 0.00 0.00 45.90 4.40
3686 3736 2.523015 CATCTTCGCAGAAACCAATGC 58.477 47.619 0.00 0.00 45.90 3.56
3710 3760 2.035961 TGTCTTCTCACTCCAGAAACGG 59.964 50.000 0.00 0.00 31.86 4.44
3931 3996 1.300697 GCACCGAGTCCGACAAGTT 60.301 57.895 0.40 0.00 38.22 2.66
3939 4004 2.209064 TAACAGCGAGCACCGAGTCC 62.209 60.000 2.63 0.00 41.76 3.85
3961 4026 1.156736 AGTACAACCAAGCGACATGC 58.843 50.000 0.00 0.00 46.98 4.06


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

AutoCloner maintained by Alex Coulton.