Multiple sequence alignment - TraesCS5D01G169400

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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 TraesCS5D01G169400 chr5D 100.000 2721 0 0 403 3123 265953494 265956214 0.000000e+00 5025.0
1 TraesCS5D01G169400 chr5D 97.845 2691 49 4 441 3123 486198748 486201437 0.000000e+00 4639.0
2 TraesCS5D01G169400 chr5D 100.000 170 0 0 1 170 265953092 265953261 6.500000e-82 315.0
3 TraesCS5D01G169400 chr5D 97.059 170 5 0 1 170 168659010 168658841 1.420000e-73 287.0
4 TraesCS5D01G169400 chr2D 97.689 2726 52 6 409 3123 548732405 548735130 0.000000e+00 4674.0
5 TraesCS5D01G169400 chr2D 97.539 2722 53 9 411 3123 35040440 35043156 0.000000e+00 4643.0
6 TraesCS5D01G169400 chr2D 97.069 2729 66 11 403 3123 375589094 375586372 0.000000e+00 4584.0
7 TraesCS5D01G169400 chr2D 97.056 2717 67 10 413 3123 10438827 10441536 0.000000e+00 4562.0
8 TraesCS5D01G169400 chr2D 97.459 2676 53 11 454 3123 396654041 396656707 0.000000e+00 4551.0
9 TraesCS5D01G169400 chr2D 97.059 170 5 0 1 170 575238045 575237876 1.420000e-73 287.0
10 TraesCS5D01G169400 chr2D 94.776 134 7 0 4 137 83952160 83952027 3.160000e-50 209.0
11 TraesCS5D01G169400 chr6D 97.633 2704 50 11 428 3123 429954557 429957254 0.000000e+00 4626.0
12 TraesCS5D01G169400 chr6D 97.250 2727 66 8 403 3123 26591344 26594067 0.000000e+00 4612.0
13 TraesCS5D01G169400 chr6D 98.148 54 1 0 1 54 12486130 12486077 9.220000e-16 95.3
14 TraesCS5D01G169400 chr6D 100.000 51 0 0 1 51 62261374 62261424 9.220000e-16 95.3
15 TraesCS5D01G169400 chr6D 100.000 51 0 0 1 51 429953945 429953995 9.220000e-16 95.3
16 TraesCS5D01G169400 chr3D 97.771 2692 47 6 440 3123 86230496 86233182 0.000000e+00 4626.0
17 TraesCS5D01G169400 chr7D 95.882 170 7 0 1 170 571893449 571893280 3.070000e-70 276.0
18 TraesCS5D01G169400 chr4D 96.951 164 5 0 1 164 67447171 67447334 3.070000e-70 276.0
19 TraesCS5D01G169400 chr1D 100.000 51 0 0 1 51 342836394 342836444 9.220000e-16 95.3


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 TraesCS5D01G169400 chr5D 265953092 265956214 3122 False 2670.00 5025 100.0000 1 3123 2 chr5D.!!$F2 3122
1 TraesCS5D01G169400 chr5D 486198748 486201437 2689 False 4639.00 4639 97.8450 441 3123 1 chr5D.!!$F1 2682
2 TraesCS5D01G169400 chr2D 548732405 548735130 2725 False 4674.00 4674 97.6890 409 3123 1 chr2D.!!$F4 2714
3 TraesCS5D01G169400 chr2D 35040440 35043156 2716 False 4643.00 4643 97.5390 411 3123 1 chr2D.!!$F2 2712
4 TraesCS5D01G169400 chr2D 375586372 375589094 2722 True 4584.00 4584 97.0690 403 3123 1 chr2D.!!$R2 2720
5 TraesCS5D01G169400 chr2D 10438827 10441536 2709 False 4562.00 4562 97.0560 413 3123 1 chr2D.!!$F1 2710
6 TraesCS5D01G169400 chr2D 396654041 396656707 2666 False 4551.00 4551 97.4590 454 3123 1 chr2D.!!$F3 2669
7 TraesCS5D01G169400 chr6D 26591344 26594067 2723 False 4612.00 4612 97.2500 403 3123 1 chr6D.!!$F1 2720
8 TraesCS5D01G169400 chr6D 429953945 429957254 3309 False 2360.65 4626 98.8165 1 3123 2 chr6D.!!$F3 3122
9 TraesCS5D01G169400 chr3D 86230496 86233182 2686 False 4626.00 4626 97.7710 440 3123 1 chr3D.!!$F1 2683

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
51 52 1.518572 CCAGATGACGCCGTACCAC 60.519 63.158 0.0 0.00 0.00 4.16 F
52 53 1.872234 CAGATGACGCCGTACCACG 60.872 63.158 0.0 0.94 42.11 4.94 F
107 108 2.202623 CCGTAGCACTCTGCCGAC 60.203 66.667 0.0 0.00 46.52 4.79 F
1910 2412 1.343985 TGATTGCTACTCCCCCTGCTA 60.344 52.381 0.0 0.00 0.00 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1003 1496 1.003118 CTCCTTGTGGACAATTCCGGA 59.997 52.381 0.00 0.00 46.37 5.14 R
1303 1796 1.196766 ATCCACTCTGCCTCTGCACA 61.197 55.000 0.00 0.00 44.23 4.57 R
1945 2447 1.544825 TAGAGACCGCCAAAGCTGCT 61.545 55.000 0.00 0.00 36.60 4.24 R
2888 3390 3.519510 TCAGGATTCGGGAAGTTCTTCAT 59.480 43.478 13.44 0.04 0.00 2.57 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
51 52 1.518572 CCAGATGACGCCGTACCAC 60.519 63.158 0.00 0.00 0.00 4.16
52 53 1.872234 CAGATGACGCCGTACCACG 60.872 63.158 0.00 0.94 42.11 4.94
53 54 3.252484 GATGACGCCGTACCACGC 61.252 66.667 0.00 0.00 40.91 5.34
54 55 4.807039 ATGACGCCGTACCACGCC 62.807 66.667 0.00 0.00 40.91 5.68
56 57 4.807039 GACGCCGTACCACGCCAT 62.807 66.667 0.00 0.00 40.91 4.40
57 58 4.807039 ACGCCGTACCACGCCATC 62.807 66.667 0.00 0.00 40.91 3.51
58 59 4.805231 CGCCGTACCACGCCATCA 62.805 66.667 0.00 0.00 40.91 3.07
59 60 2.435234 GCCGTACCACGCCATCAA 60.435 61.111 0.00 0.00 40.91 2.57
60 61 2.746803 GCCGTACCACGCCATCAAC 61.747 63.158 0.00 0.00 40.91 3.18
61 62 2.449525 CCGTACCACGCCATCAACG 61.450 63.158 0.00 0.00 40.91 4.10
62 63 2.449525 CGTACCACGCCATCAACGG 61.450 63.158 0.00 0.00 33.65 4.44
101 102 4.778415 CACGCGCCGTAGCACTCT 62.778 66.667 5.73 0.00 38.32 3.24
102 103 4.778415 ACGCGCCGTAGCACTCTG 62.778 66.667 5.73 0.00 38.73 3.35
106 107 4.129737 GCCGTAGCACTCTGCCGA 62.130 66.667 0.00 0.00 46.52 5.54
107 108 2.202623 CCGTAGCACTCTGCCGAC 60.203 66.667 0.00 0.00 46.52 4.79
108 109 2.202623 CGTAGCACTCTGCCGACC 60.203 66.667 0.00 0.00 46.52 4.79
109 110 2.202623 GTAGCACTCTGCCGACCG 60.203 66.667 0.00 0.00 46.52 4.79
110 111 4.129737 TAGCACTCTGCCGACCGC 62.130 66.667 0.00 0.00 46.52 5.68
751 1244 6.660887 AATGCGTATTTGGGCTTAAAAATG 57.339 33.333 0.00 0.00 0.00 2.32
998 1491 5.682422 TCTCATGATTTTTGCATAAATCGCG 59.318 36.000 26.86 21.99 43.99 5.87
1003 1496 3.773860 TTTTGCATAAATCGCGGATGT 57.226 38.095 6.13 0.00 0.00 3.06
1303 1796 3.668447 CTGAAGTACACTGTGAAGCCAT 58.332 45.455 15.86 0.00 0.00 4.40
1910 2412 1.343985 TGATTGCTACTCCCCCTGCTA 60.344 52.381 0.00 0.00 0.00 3.49
2156 2658 4.704540 TGGTTATCATGATTCCGTGCTTTT 59.295 37.500 14.65 0.00 0.00 2.27
2656 3158 2.223112 CGATGATGAAAACGGCAAGGAG 60.223 50.000 0.00 0.00 0.00 3.69
2888 3390 3.282885 TCGCATGGCCATAATGTTAACA 58.717 40.909 20.30 11.41 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 90 4.129737 TCGGCAGAGTGCTACGGC 62.130 66.667 0.00 0.00 44.28 5.68
90 91 2.202623 GTCGGCAGAGTGCTACGG 60.203 66.667 0.00 0.00 44.28 4.02
91 92 2.202623 GGTCGGCAGAGTGCTACG 60.203 66.667 0.00 0.00 44.28 3.51
92 93 2.202623 CGGTCGGCAGAGTGCTAC 60.203 66.667 0.00 0.00 44.28 3.58
93 94 4.129737 GCGGTCGGCAGAGTGCTA 62.130 66.667 0.00 0.00 44.28 3.49
643 1132 3.061205 GCGCAAAAACTGAAAACTACAGC 60.061 43.478 0.30 0.00 38.74 4.40
751 1244 3.261580 CCAAAAATTGAATTCCCGAGGC 58.738 45.455 2.27 0.00 0.00 4.70
998 1491 1.339631 TGTGGACAATTCCGGACATCC 60.340 52.381 1.83 9.65 46.37 3.51
1003 1496 1.003118 CTCCTTGTGGACAATTCCGGA 59.997 52.381 0.00 0.00 46.37 5.14
1047 1540 2.093447 GGACCATGACAGGTAGTTCAGG 60.093 54.545 0.00 0.00 43.38 3.86
1303 1796 1.196766 ATCCACTCTGCCTCTGCACA 61.197 55.000 0.00 0.00 44.23 4.57
1498 1992 4.106197 CAACTCTGAATACCTCGTGTAGC 58.894 47.826 0.00 0.00 31.61 3.58
1945 2447 1.544825 TAGAGACCGCCAAAGCTGCT 61.545 55.000 0.00 0.00 36.60 4.24
2180 2682 7.244166 CTCTCATAGAGCTTACAACCAAATG 57.756 40.000 0.00 0.00 35.30 2.32
2207 2709 8.638565 CAATCGCCAAAGTAAAGAATAAGTTTG 58.361 33.333 0.00 0.00 36.31 2.93
2459 2961 4.307432 CCGGCGATTGTCATAATACTTCT 58.693 43.478 9.30 0.00 0.00 2.85
2656 3158 1.394917 CGCTTTGTGATGAGTAGGCAC 59.605 52.381 0.00 0.00 0.00 5.01
2888 3390 3.519510 TCAGGATTCGGGAAGTTCTTCAT 59.480 43.478 13.44 0.04 0.00 2.57


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

AutoCloner maintained by Alex Coulton.