Multiple sequence alignment - TraesCS6B01G403200

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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 TraesCS6B01G403200 chr6B 100.000 2804 0 0 1 2804 678840792 678843595 0.000000e+00 5179
1 TraesCS6B01G403200 chr6B 97.130 2787 66 7 21 2804 678821581 678824356 0.000000e+00 4691
2 TraesCS6B01G403200 chr6B 91.438 292 25 0 2088 2379 716950029 716950320 4.350000e-108 401
3 TraesCS6B01G403200 chr3B 95.286 2100 86 11 1 2093 154423002 154420909 0.000000e+00 3317
4 TraesCS6B01G403200 chr3B 95.086 2096 85 10 1 2093 151117092 151115012 0.000000e+00 3284
5 TraesCS6B01G403200 chr3B 88.611 720 46 10 2088 2804 791302206 791301520 0.000000e+00 843
6 TraesCS6B01G403200 chr5B 95.134 2096 87 8 1 2093 75081144 75083227 0.000000e+00 3291
7 TraesCS6B01G403200 chr5B 95.088 2097 87 8 1 2094 67028340 67026257 0.000000e+00 3288
8 TraesCS6B01G403200 chr5B 86.878 724 59 20 2084 2804 539321911 539321221 0.000000e+00 778
9 TraesCS6B01G403200 chr5B 94.051 353 20 1 2452 2804 579162296 579161945 4.110000e-148 534
10 TraesCS6B01G403200 chr5B 91.186 295 26 0 2085 2379 588621310 588621604 4.350000e-108 401
11 TraesCS6B01G403200 chr5B 89.347 291 31 0 2089 2379 579162587 579162297 1.590000e-97 366
12 TraesCS6B01G403200 chr4B 94.516 2097 105 7 1 2093 561750373 561748283 0.000000e+00 3227
13 TraesCS6B01G403200 chr4B 88.268 716 62 12 2089 2801 57956240 57956936 0.000000e+00 837
14 TraesCS6B01G403200 chr4B 88.203 729 49 8 2079 2804 347572410 347571716 0.000000e+00 835
15 TraesCS6B01G403200 chr4B 86.220 537 50 6 2089 2615 455600052 455599530 6.780000e-156 560
16 TraesCS6B01G403200 chr2B 94.323 2096 101 10 1 2093 480006191 480008271 0.000000e+00 3195
17 TraesCS6B01G403200 chr2B 95.186 1994 90 6 4 1997 72935137 72937124 0.000000e+00 3145
18 TraesCS6B01G403200 chr1B 94.137 2098 104 6 1 2093 630554802 630552719 0.000000e+00 3175
19 TraesCS6B01G403200 chr4D 86.382 727 69 11 2089 2804 417403786 417403079 0.000000e+00 767
20 TraesCS6B01G403200 chr5A 93.820 356 21 1 2449 2804 576073504 576073858 4.110000e-148 534
21 TraesCS6B01G403200 chr5A 90.068 292 28 1 2088 2379 576073216 576073506 7.330000e-101 377
22 TraesCS6B01G403200 chr3D 93.277 357 21 2 2449 2804 302256625 302256979 8.900000e-145 523
23 TraesCS6B01G403200 chr2D 93.484 353 22 1 2452 2804 85835216 85834865 8.900000e-145 523
24 TraesCS6B01G403200 chr4A 90.785 293 26 1 2088 2379 32695205 32695497 9.420000e-105 390
25 TraesCS6B01G403200 chr5D 87.611 339 37 5 2089 2425 50730379 50730044 3.390000e-104 388
26 TraesCS6B01G403200 chr6A 89.691 291 30 0 2089 2379 543491222 543491512 3.410000e-99 372
27 TraesCS6B01G403200 chr1A 89.723 253 25 1 2087 2338 568015285 568015537 3.480000e-84 322


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 TraesCS6B01G403200 chr6B 678840792 678843595 2803 False 5179.0 5179 100.000 1 2804 1 chr6B.!!$F2 2803
1 TraesCS6B01G403200 chr6B 678821581 678824356 2775 False 4691.0 4691 97.130 21 2804 1 chr6B.!!$F1 2783
2 TraesCS6B01G403200 chr3B 154420909 154423002 2093 True 3317.0 3317 95.286 1 2093 1 chr3B.!!$R2 2092
3 TraesCS6B01G403200 chr3B 151115012 151117092 2080 True 3284.0 3284 95.086 1 2093 1 chr3B.!!$R1 2092
4 TraesCS6B01G403200 chr3B 791301520 791302206 686 True 843.0 843 88.611 2088 2804 1 chr3B.!!$R3 716
5 TraesCS6B01G403200 chr5B 75081144 75083227 2083 False 3291.0 3291 95.134 1 2093 1 chr5B.!!$F1 2092
6 TraesCS6B01G403200 chr5B 67026257 67028340 2083 True 3288.0 3288 95.088 1 2094 1 chr5B.!!$R1 2093
7 TraesCS6B01G403200 chr5B 539321221 539321911 690 True 778.0 778 86.878 2084 2804 1 chr5B.!!$R2 720
8 TraesCS6B01G403200 chr5B 579161945 579162587 642 True 450.0 534 91.699 2089 2804 2 chr5B.!!$R3 715
9 TraesCS6B01G403200 chr4B 561748283 561750373 2090 True 3227.0 3227 94.516 1 2093 1 chr4B.!!$R3 2092
10 TraesCS6B01G403200 chr4B 57956240 57956936 696 False 837.0 837 88.268 2089 2801 1 chr4B.!!$F1 712
11 TraesCS6B01G403200 chr4B 347571716 347572410 694 True 835.0 835 88.203 2079 2804 1 chr4B.!!$R1 725
12 TraesCS6B01G403200 chr4B 455599530 455600052 522 True 560.0 560 86.220 2089 2615 1 chr4B.!!$R2 526
13 TraesCS6B01G403200 chr2B 480006191 480008271 2080 False 3195.0 3195 94.323 1 2093 1 chr2B.!!$F2 2092
14 TraesCS6B01G403200 chr2B 72935137 72937124 1987 False 3145.0 3145 95.186 4 1997 1 chr2B.!!$F1 1993
15 TraesCS6B01G403200 chr1B 630552719 630554802 2083 True 3175.0 3175 94.137 1 2093 1 chr1B.!!$R1 2092
16 TraesCS6B01G403200 chr4D 417403079 417403786 707 True 767.0 767 86.382 2089 2804 1 chr4D.!!$R1 715
17 TraesCS6B01G403200 chr5A 576073216 576073858 642 False 455.5 534 91.944 2088 2804 2 chr5A.!!$F1 716

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
814 829 4.020128 ACACCCAGAGACCAATAGAAAGAC 60.020 45.833 0.00 0.0 0.00 3.01 F
1553 1569 2.143122 CAGGCGCACCATATTCGTATT 58.857 47.619 10.83 0.0 39.06 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1801 1817 0.100682 CGCAGGCGAAACTCTAGCTA 59.899 55.0 8.15 0.0 42.83 3.32 R
2379 2420 0.543277 CTGCCTTCCCAGTCTGCATA 59.457 55.0 0.00 0.0 0.00 3.14 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
106 107 5.338300 GGAACGTAAATACCTGGGGTTTAGA 60.338 44.000 0.00 0.0 37.09 2.10
293 294 5.277250 TCCATCACCAAGTAGGATCAGTAA 58.723 41.667 0.00 0.0 41.22 2.24
593 604 7.611213 TCGAAAAGAAGTCAAAGGGATATTC 57.389 36.000 0.00 0.0 0.00 1.75
594 605 7.394816 TCGAAAAGAAGTCAAAGGGATATTCT 58.605 34.615 0.00 0.0 36.52 2.40
814 829 4.020128 ACACCCAGAGACCAATAGAAAGAC 60.020 45.833 0.00 0.0 0.00 3.01
1311 1327 2.679342 CGGCCCTCCCATTCCAGAA 61.679 63.158 0.00 0.0 0.00 3.02
1371 1387 2.964925 GGTGACACGCTGTTCGCA 60.965 61.111 0.00 0.0 43.23 5.10
1519 1535 4.138290 GGACGAGATGATCTTCTCCTACA 58.862 47.826 25.14 0.0 39.19 2.74
1553 1569 2.143122 CAGGCGCACCATATTCGTATT 58.857 47.619 10.83 0.0 39.06 1.89
1574 1590 3.075005 GTGGAGCAGGGCGGTCTA 61.075 66.667 0.00 0.0 42.06 2.59
1665 1681 2.762234 CCGAGGCTACTTCGACGCT 61.762 63.158 0.27 0.0 0.00 5.07
1801 1817 1.481802 GGATGTGGATCCCATGGCATT 60.482 52.381 17.42 0.0 42.42 3.56
1827 1843 2.047655 TTTCGCCTGCGTCGGATT 60.048 55.556 11.68 0.0 40.74 3.01
1861 1878 1.843734 GAGTATCGAGGAGTCGCCGG 61.844 65.000 0.00 0.0 46.39 6.13
2379 2420 7.544804 AGGCTTTGTTGAATTAGGAAGATTT 57.455 32.000 0.00 0.0 0.00 2.17
2591 2644 8.501580 TCTATCAAGCGATGATCAATGATTTTC 58.498 33.333 10.75 0.0 45.91 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 1.482593 CGGTGGAAATGCTACTCCTCT 59.517 52.381 0.00 0.00 32.51 3.69
559 570 8.447787 TTTGACTTCTTTTCGAAAAAGACAAG 57.552 30.769 24.91 22.32 36.14 3.16
990 1006 1.348775 GCTTAGACATCCAGCCCCCT 61.349 60.000 0.00 0.00 0.00 4.79
1171 1187 0.388649 CCACGCTCAGGTGACACTAC 60.389 60.000 5.39 0.00 40.38 2.73
1311 1327 1.900498 GGAGCCACAAAGCAGTGCT 60.900 57.895 13.14 13.14 42.56 4.40
1467 1483 1.741401 CGTCGGCATGCTTCTCCAA 60.741 57.895 18.92 0.00 0.00 3.53
1534 1550 2.037251 AGAATACGAATATGGTGCGCCT 59.963 45.455 18.96 5.67 35.27 5.52
1665 1681 0.817654 CGACCCATGTGTCTAGCTCA 59.182 55.000 6.75 0.00 32.97 4.26
1755 1771 1.901085 GTCGGCCATCTTCCACTCT 59.099 57.895 2.24 0.00 0.00 3.24
1801 1817 0.100682 CGCAGGCGAAACTCTAGCTA 59.899 55.000 8.15 0.00 42.83 3.32
1861 1878 4.864334 CCAGGCCCTGTCCGATGC 62.864 72.222 10.47 0.00 0.00 3.91
1993 2010 1.659098 CATTAACACGTTCCTCTCGCC 59.341 52.381 0.00 0.00 0.00 5.54
2006 2026 6.932356 TTTTTGTACACGGTACCATTAACA 57.068 33.333 13.54 7.82 0.00 2.41
2123 2143 4.067972 ACTTGGTCATAACGTTGTGACT 57.932 40.909 39.19 26.04 45.22 3.41
2133 2153 6.048732 TGAGCATTCACTACTTGGTCATAA 57.951 37.500 0.35 0.00 41.45 1.90
2379 2420 0.543277 CTGCCTTCCCAGTCTGCATA 59.457 55.000 0.00 0.00 0.00 3.14


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

AutoCloner maintained by Alex Coulton.