Multiple sequence alignment - TraesCS1B01G106500

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 TraesCS1B01G106500 chr1B 100.000 4471 0 0 1 4471 118132912 118137382 0.000000e+00 8257.0
1 TraesCS1B01G106500 chr1B 99.652 3741 11 2 1 3740 118120241 118116502 0.000000e+00 6835.0
2 TraesCS1B01G106500 chr1B 77.914 489 93 13 3791 4273 626658122 626658601 1.570000e-74 291.0
3 TraesCS1B01G106500 chr1B 96.000 50 2 0 1 50 269041533 269041484 1.030000e-11 82.4
4 TraesCS1B01G106500 chr1A 95.327 3552 126 10 217 3740 74434825 74431286 0.000000e+00 5603.0
5 TraesCS1B01G106500 chr1A 98.198 111 2 0 112 222 74434962 74434852 1.270000e-45 195.0
6 TraesCS1B01G106500 chr1A 96.491 114 4 0 1 114 74435131 74435018 5.900000e-44 189.0
7 TraesCS1B01G106500 chr1D 95.882 2064 56 7 1661 3703 74280180 74282235 0.000000e+00 3314.0
8 TraesCS1B01G106500 chr1D 96.571 1458 38 6 217 1667 74278638 74280090 0.000000e+00 2405.0
9 TraesCS1B01G106500 chr1D 99.099 222 2 0 1 222 74278390 74278611 2.510000e-107 399.0
10 TraesCS1B01G106500 chr1D 94.340 53 2 1 1 52 437299824 437299772 3.710000e-11 80.5
11 TraesCS1B01G106500 chr2B 96.302 703 24 1 3771 4471 598580382 598579680 0.000000e+00 1153.0
12 TraesCS1B01G106500 chr6B 96.148 701 25 1 3771 4469 432362213 432362913 0.000000e+00 1144.0
13 TraesCS1B01G106500 chr6B 82.698 682 108 6 3776 4454 671096715 671097389 8.280000e-167 597.0
14 TraesCS1B01G106500 chr7A 95.197 687 29 3 3782 4465 96095237 96095922 0.000000e+00 1083.0
15 TraesCS1B01G106500 chr7A 94.340 53 2 1 1 52 124795756 124795704 3.710000e-11 80.5
16 TraesCS1B01G106500 chr5B 85.714 693 85 7 3776 4463 706491207 706491890 0.000000e+00 719.0
17 TraesCS1B01G106500 chr4B 81.042 691 104 17 3771 4454 638534767 638534097 3.960000e-145 525.0
18 TraesCS1B01G106500 chr7B 81.014 690 104 17 3772 4454 741669228 741669897 1.420000e-144 523.0
19 TraesCS1B01G106500 chr6A 84.787 447 60 4 3772 4216 27175089 27175529 4.100000e-120 442.0
20 TraesCS1B01G106500 chr6A 83.936 249 40 0 4215 4463 27178184 27178432 5.780000e-59 239.0
21 TraesCS1B01G106500 chr5D 98.077 52 1 0 1 52 510122431 510122380 1.710000e-14 91.6
22 TraesCS1B01G106500 chr7D 94.340 53 2 1 1 52 618868817 618868765 3.710000e-11 80.5
23 TraesCS1B01G106500 chr2D 94.340 53 2 1 1 52 35210431 35210483 3.710000e-11 80.5


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 TraesCS1B01G106500 chr1B 118132912 118137382 4470 False 8257.000000 8257 100.0000 1 4471 1 chr1B.!!$F1 4470
1 TraesCS1B01G106500 chr1B 118116502 118120241 3739 True 6835.000000 6835 99.6520 1 3740 1 chr1B.!!$R1 3739
2 TraesCS1B01G106500 chr1A 74431286 74435131 3845 True 1995.666667 5603 96.6720 1 3740 3 chr1A.!!$R1 3739
3 TraesCS1B01G106500 chr1D 74278390 74282235 3845 False 2039.333333 3314 97.1840 1 3703 3 chr1D.!!$F1 3702
4 TraesCS1B01G106500 chr2B 598579680 598580382 702 True 1153.000000 1153 96.3020 3771 4471 1 chr2B.!!$R1 700
5 TraesCS1B01G106500 chr6B 432362213 432362913 700 False 1144.000000 1144 96.1480 3771 4469 1 chr6B.!!$F1 698
6 TraesCS1B01G106500 chr6B 671096715 671097389 674 False 597.000000 597 82.6980 3776 4454 1 chr6B.!!$F2 678
7 TraesCS1B01G106500 chr7A 96095237 96095922 685 False 1083.000000 1083 95.1970 3782 4465 1 chr7A.!!$F1 683
8 TraesCS1B01G106500 chr5B 706491207 706491890 683 False 719.000000 719 85.7140 3776 4463 1 chr5B.!!$F1 687
9 TraesCS1B01G106500 chr4B 638534097 638534767 670 True 525.000000 525 81.0420 3771 4454 1 chr4B.!!$R1 683
10 TraesCS1B01G106500 chr7B 741669228 741669897 669 False 523.000000 523 81.0140 3772 4454 1 chr7B.!!$F1 682
11 TraesCS1B01G106500 chr6A 27175089 27178432 3343 False 340.500000 442 84.3615 3772 4463 2 chr6A.!!$F1 691

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
688 785 4.333649 CGTGCCTTCATGTCAACATCTTAT 59.666 41.667 0.0 0.0 33.61 1.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3747 3984 5.068987 CCTCTGCAGCTCTCTAAAGAACTAT 59.931 44.0 9.47 0.0 0.0 2.12 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
688 785 4.333649 CGTGCCTTCATGTCAACATCTTAT 59.666 41.667 0.00 0.00 33.61 1.73
689 786 5.163723 CGTGCCTTCATGTCAACATCTTATT 60.164 40.000 0.00 0.00 33.61 1.40
3217 3453 7.226523 TGCATGAACTATACCACACATGAATAC 59.773 37.037 0.00 0.00 37.77 1.89
3740 3977 4.161189 GGAGTCTCCATTCATGAGAGTTCA 59.839 45.833 14.46 0.00 36.28 3.18
3741 3978 5.163322 GGAGTCTCCATTCATGAGAGTTCAT 60.163 44.000 14.46 0.00 39.46 2.57
3742 3979 6.041409 GGAGTCTCCATTCATGAGAGTTCATA 59.959 42.308 14.46 0.00 38.00 2.15
3743 3980 6.815089 AGTCTCCATTCATGAGAGTTCATAC 58.185 40.000 9.55 2.19 42.12 2.39
3744 3981 5.689514 GTCTCCATTCATGAGAGTTCATACG 59.310 44.000 9.55 0.00 42.12 3.06
3745 3982 5.594317 TCTCCATTCATGAGAGTTCATACGA 59.406 40.000 9.55 0.00 42.12 3.43
3746 3983 6.266330 TCTCCATTCATGAGAGTTCATACGAT 59.734 38.462 9.55 0.00 42.12 3.73
3747 3984 7.448469 TCTCCATTCATGAGAGTTCATACGATA 59.552 37.037 9.55 0.00 42.12 2.92
3748 3985 8.127150 TCCATTCATGAGAGTTCATACGATAT 57.873 34.615 0.00 0.00 42.12 1.63
3749 3986 9.243105 TCCATTCATGAGAGTTCATACGATATA 57.757 33.333 0.00 0.00 42.12 0.86
3750 3987 9.513727 CCATTCATGAGAGTTCATACGATATAG 57.486 37.037 0.00 0.00 42.12 1.31
3754 3991 9.508642 TCATGAGAGTTCATACGATATAGTTCT 57.491 33.333 0.00 0.00 42.12 3.01
3764 4001 9.727859 TCATACGATATAGTTCTTTAGAGAGCT 57.272 33.333 5.01 5.01 44.45 4.09
3765 4002 9.767684 CATACGATATAGTTCTTTAGAGAGCTG 57.232 37.037 9.55 0.00 42.56 4.24
3766 4003 6.674066 ACGATATAGTTCTTTAGAGAGCTGC 58.326 40.000 9.55 0.00 42.56 5.25
3767 4004 6.263392 ACGATATAGTTCTTTAGAGAGCTGCA 59.737 38.462 9.55 0.00 42.56 4.41
3768 4005 6.801377 CGATATAGTTCTTTAGAGAGCTGCAG 59.199 42.308 10.11 10.11 42.56 4.41
3769 4006 7.308288 CGATATAGTTCTTTAGAGAGCTGCAGA 60.308 40.741 20.43 0.00 42.56 4.26
3779 4016 2.588314 GCTGCAGAGGATGGCTCG 60.588 66.667 20.43 0.00 0.00 5.03
3823 4060 4.087892 CCGCTCCTCCACCACCAG 62.088 72.222 0.00 0.00 0.00 4.00
3880 4123 1.292242 TCCCAACTCCATCTAGCCTCT 59.708 52.381 0.00 0.00 0.00 3.69
4022 4265 1.002134 AGGTTTGGTCTGCCATCCG 60.002 57.895 0.00 0.00 45.56 4.18
4038 4281 0.259065 TCCGTCAGCCTATCACTCCT 59.741 55.000 0.00 0.00 0.00 3.69
4388 7292 1.227823 CCCACTCACTTTCACGCCA 60.228 57.895 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
551 648 0.179127 CGACATGGCGAGTGATGACT 60.179 55.000 18.41 0.00 33.98 3.41
3740 3977 8.455682 GCAGCTCTCTAAAGAACTATATCGTAT 58.544 37.037 0.00 0.00 0.00 3.06
3741 3978 7.444487 TGCAGCTCTCTAAAGAACTATATCGTA 59.556 37.037 0.00 0.00 0.00 3.43
3742 3979 6.263392 TGCAGCTCTCTAAAGAACTATATCGT 59.737 38.462 0.00 0.00 0.00 3.73
3743 3980 6.673106 TGCAGCTCTCTAAAGAACTATATCG 58.327 40.000 0.00 0.00 0.00 2.92
3744 3981 7.881142 TCTGCAGCTCTCTAAAGAACTATATC 58.119 38.462 9.47 0.00 0.00 1.63
3745 3982 7.039784 CCTCTGCAGCTCTCTAAAGAACTATAT 60.040 40.741 9.47 0.00 0.00 0.86
3746 3983 6.264292 CCTCTGCAGCTCTCTAAAGAACTATA 59.736 42.308 9.47 0.00 0.00 1.31
3747 3984 5.068987 CCTCTGCAGCTCTCTAAAGAACTAT 59.931 44.000 9.47 0.00 0.00 2.12
3748 3985 4.400884 CCTCTGCAGCTCTCTAAAGAACTA 59.599 45.833 9.47 0.00 0.00 2.24
3749 3986 3.195396 CCTCTGCAGCTCTCTAAAGAACT 59.805 47.826 9.47 0.00 0.00 3.01
3750 3987 3.194542 TCCTCTGCAGCTCTCTAAAGAAC 59.805 47.826 9.47 0.00 0.00 3.01
3751 3988 3.435275 TCCTCTGCAGCTCTCTAAAGAA 58.565 45.455 9.47 0.00 0.00 2.52
3752 3989 3.093057 TCCTCTGCAGCTCTCTAAAGA 57.907 47.619 9.47 0.00 0.00 2.52
3753 3990 3.493002 CCATCCTCTGCAGCTCTCTAAAG 60.493 52.174 9.47 0.00 0.00 1.85
3754 3991 2.433604 CCATCCTCTGCAGCTCTCTAAA 59.566 50.000 9.47 0.00 0.00 1.85
3755 3992 2.037901 CCATCCTCTGCAGCTCTCTAA 58.962 52.381 9.47 0.00 0.00 2.10
3756 3993 1.702182 CCATCCTCTGCAGCTCTCTA 58.298 55.000 9.47 0.00 0.00 2.43
3757 3994 1.688269 GCCATCCTCTGCAGCTCTCT 61.688 60.000 9.47 0.00 0.00 3.10
3758 3995 1.227615 GCCATCCTCTGCAGCTCTC 60.228 63.158 9.47 0.00 0.00 3.20
3759 3996 1.688269 GAGCCATCCTCTGCAGCTCT 61.688 60.000 9.47 0.00 45.11 4.09
3760 3997 1.227615 GAGCCATCCTCTGCAGCTC 60.228 63.158 9.47 7.52 42.74 4.09
3761 3998 2.909577 GAGCCATCCTCTGCAGCT 59.090 61.111 9.47 0.40 37.60 4.24
3762 3999 2.588314 CGAGCCATCCTCTGCAGC 60.588 66.667 9.47 0.00 38.49 5.25
3763 4000 2.588314 GCGAGCCATCCTCTGCAG 60.588 66.667 7.63 7.63 38.82 4.41
3764 4001 4.519437 CGCGAGCCATCCTCTGCA 62.519 66.667 0.00 0.00 38.87 4.41
3823 4060 2.386660 GGAGTTGAGACTGCAGCGC 61.387 63.158 15.27 9.23 43.10 5.92
3880 4123 0.246635 GAGCAGAAAGTGGCTACGGA 59.753 55.000 0.00 0.00 41.22 4.69
4022 4265 2.482142 CGGAAAGGAGTGATAGGCTGAC 60.482 54.545 0.00 0.00 0.00 3.51
4038 4281 1.407258 CCTGAGTTTTTGTGGCGGAAA 59.593 47.619 0.00 0.00 0.00 3.13
4388 7292 2.280592 GTCAAACGTGAGCGGGGT 60.281 61.111 0.00 0.00 43.45 4.95


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

AutoCloner maintained by Alex Coulton.