Multiple sequence alignment - TraesCS7B01G427500

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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 TraesCS7B01G427500 chr7B 100.000 1944 0 0 891 2834 696899066 696897123 0.000000e+00 3591.0
1 TraesCS7B01G427500 chr7B 92.909 1946 100 20 919 2833 693248759 693246821 0.000000e+00 2795.0
2 TraesCS7B01G427500 chr7B 89.651 1778 125 23 1086 2831 693867536 693865786 0.000000e+00 2209.0
3 TraesCS7B01G427500 chr7B 86.407 2001 177 38 891 2833 697256627 697254664 0.000000e+00 2100.0
4 TraesCS7B01G427500 chr7B 100.000 622 0 0 1 622 696899956 696899335 0.000000e+00 1149.0
5 TraesCS7B01G427500 chr7B 91.994 637 31 14 1 622 693249479 693248848 0.000000e+00 876.0
6 TraesCS7B01G427500 chr7B 91.983 237 16 1 388 621 697256976 697256740 2.100000e-86 329.0
7 TraesCS7B01G427500 chr7B 91.358 162 13 1 900 1061 693904473 693904313 1.320000e-53 220.0
8 TraesCS7B01G427500 chr7B 96.739 92 3 0 267 358 697257376 697257285 1.360000e-33 154.0
9 TraesCS7B01G427500 chr7B 79.487 195 28 8 893 1075 697034262 697034456 8.240000e-26 128.0
10 TraesCS7B01G427500 chrUn 92.199 1974 113 23 891 2834 77648240 77646278 0.000000e+00 2754.0
11 TraesCS7B01G427500 chrUn 93.280 1250 69 2 891 2125 83440911 83439662 0.000000e+00 1829.0
12 TraesCS7B01G427500 chrUn 87.997 1333 125 22 1316 2633 317940740 317942052 0.000000e+00 1543.0
13 TraesCS7B01G427500 chrUn 92.888 689 20 7 2162 2834 83439665 83438990 0.000000e+00 974.0
14 TraesCS7B01G427500 chrUn 82.570 1004 124 27 1859 2834 317942050 317943030 0.000000e+00 837.0
15 TraesCS7B01G427500 chrUn 86.322 658 44 17 1 622 77648999 77648352 0.000000e+00 675.0
16 TraesCS7B01G427500 chrUn 92.219 347 22 3 280 622 373622204 373622549 1.180000e-133 486.0
17 TraesCS7B01G427500 chrUn 86.434 258 22 9 378 622 83441280 83441023 1.290000e-68 270.0
18 TraesCS7B01G427500 chrUn 91.011 178 16 0 891 1068 373622661 373622838 1.010000e-59 241.0
19 TraesCS7B01G427500 chr7D 90.419 1983 126 24 891 2834 607614868 607612911 0.000000e+00 2551.0
20 TraesCS7B01G427500 chr7D 90.206 1991 123 24 891 2834 610214675 610216640 0.000000e+00 2531.0
21 TraesCS7B01G427500 chr7D 87.281 629 45 11 14 622 607615593 607614980 0.000000e+00 686.0
22 TraesCS7B01G427500 chr7D 86.825 630 45 15 14 622 610213951 610214563 0.000000e+00 669.0
23 TraesCS7B01G427500 chr7A 86.610 1053 87 20 891 1914 699842162 699841135 0.000000e+00 1114.0
24 TraesCS7B01G427500 chr7A 94.878 449 21 2 1934 2380 699841150 699840702 0.000000e+00 701.0
25 TraesCS7B01G427500 chr7A 90.188 479 37 5 153 622 699842751 699842274 1.440000e-172 616.0
26 TraesCS7B01G427500 chr7A 97.753 178 3 1 2658 2834 699840329 699840152 3.550000e-79 305.0
27 TraesCS7B01G427500 chr3A 84.615 117 12 2 1786 1899 673508947 673508834 8.300000e-21 111.0
28 TraesCS7B01G427500 chr2A 72.945 292 52 19 1701 1984 193550745 193550473 3.030000e-10 76.8


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 TraesCS7B01G427500 chr7B 696897123 696899956 2833 True 2370.000000 3591 100.000000 1 2834 2 chr7B.!!$R4 2833
1 TraesCS7B01G427500 chr7B 693865786 693867536 1750 True 2209.000000 2209 89.651000 1086 2831 1 chr7B.!!$R1 1745
2 TraesCS7B01G427500 chr7B 693246821 693249479 2658 True 1835.500000 2795 92.451500 1 2833 2 chr7B.!!$R3 2832
3 TraesCS7B01G427500 chr7B 697254664 697257376 2712 True 861.000000 2100 91.709667 267 2833 3 chr7B.!!$R5 2566
4 TraesCS7B01G427500 chrUn 77646278 77648999 2721 True 1714.500000 2754 89.260500 1 2834 2 chrUn.!!$R1 2833
5 TraesCS7B01G427500 chrUn 317940740 317943030 2290 False 1190.000000 1543 85.283500 1316 2834 2 chrUn.!!$F1 1518
6 TraesCS7B01G427500 chrUn 83438990 83441280 2290 True 1024.333333 1829 90.867333 378 2834 3 chrUn.!!$R2 2456
7 TraesCS7B01G427500 chrUn 373622204 373622838 634 False 363.500000 486 91.615000 280 1068 2 chrUn.!!$F2 788
8 TraesCS7B01G427500 chr7D 607612911 607615593 2682 True 1618.500000 2551 88.850000 14 2834 2 chr7D.!!$R1 2820
9 TraesCS7B01G427500 chr7D 610213951 610216640 2689 False 1600.000000 2531 88.515500 14 2834 2 chr7D.!!$F1 2820
10 TraesCS7B01G427500 chr7A 699840152 699842751 2599 True 684.000000 1114 92.357250 153 2834 4 chr7A.!!$R1 2681

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
227 230 0.379669 GCCTGAAGATGACCATTGCG 59.62 55.0 0.00 0.0 0.0 4.85 F
1000 1317 0.249868 CCAAGTGTTCACGGAGCTCA 60.25 55.0 17.19 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1449 1782 1.207791 CCTCCACAATGGCTAGACCT 58.792 55.0 0.0 0.0 37.47 3.85 R
2515 3718 0.400213 ATTTGCCGTTCACTGGGAGA 59.600 50.0 0.0 0.0 0.00 3.71 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
225 228 1.019673 CGGCCTGAAGATGACCATTG 58.980 55.000 0.00 0.00 0.00 2.82
227 230 0.379669 GCCTGAAGATGACCATTGCG 59.620 55.000 0.00 0.00 0.00 4.85
252 255 1.133253 CATTTCGGCAGCACGACAG 59.867 57.895 5.58 0.00 43.37 3.51
360 370 4.028993 TCCAGTTCAAAATACCAGGGTC 57.971 45.455 0.00 0.00 0.00 4.46
364 374 1.761711 TCAAAATACCAGGGTCCCCA 58.238 50.000 3.51 0.00 38.92 4.96
425 726 2.125147 CAGCCGCCCTCGAATTCA 60.125 61.111 6.22 0.00 38.10 2.57
563 880 4.819761 GATCTCGCCCGCACAGCA 62.820 66.667 0.00 0.00 0.00 4.41
1000 1317 0.249868 CCAAGTGTTCACGGAGCTCA 60.250 55.000 17.19 0.00 0.00 4.26
1189 1518 2.033801 GTGGTCATGATAGCACATTGCC 59.966 50.000 10.83 0.00 46.52 4.52
1209 1538 3.850098 AACTGGTCCGGCTGCCTTG 62.850 63.158 17.92 7.94 0.00 3.61
1223 1552 1.000955 TGCCTTGGTCTTCTCTTCGAC 59.999 52.381 0.00 0.00 0.00 4.20
1364 1697 2.747446 GCTGCTTTTATTTGGAGTCCGA 59.253 45.455 4.30 0.00 0.00 4.55
1449 1782 4.025563 CCACGTGAAACTTCGAACATGTTA 60.026 41.667 19.30 0.00 31.43 2.41
1482 1815 1.992277 GGAGGCAGGAGAAGGCAGA 60.992 63.158 0.00 0.00 0.00 4.26
1537 1870 3.264193 AGGTGGCAAATGTGATCTCTGTA 59.736 43.478 0.00 0.00 0.00 2.74
1585 1926 2.769095 AGTTCTAGCCAGTGGAAGATCC 59.231 50.000 15.20 8.39 36.96 3.36
1699 2055 3.894427 GTCCATAAGCTCATCTCTGGAGA 59.106 47.826 2.63 2.63 42.37 3.71
1975 2382 6.007076 TGGTTATTTATCTTGTGCTTGTGGA 58.993 36.000 0.00 0.00 0.00 4.02
2126 2537 8.859090 TCATGAAATCACAAAAATGGTAGAACT 58.141 29.630 0.00 0.00 0.00 3.01
2252 2665 3.506067 TCAAGCACGACTCATCTTGTCTA 59.494 43.478 0.00 0.00 37.68 2.59
2316 2741 5.831702 AGATTTTGAGGCATCTTCACATC 57.168 39.130 0.00 0.00 0.00 3.06
2420 3613 5.621555 GCACAAGCTGTTTGATCTGAATCAT 60.622 40.000 11.31 0.00 38.57 2.45
2513 3716 1.014564 CCCGTGCTTCTTTCCGAGTC 61.015 60.000 0.00 0.00 0.00 3.36
2514 3717 1.344942 CCGTGCTTCTTTCCGAGTCG 61.345 60.000 5.29 5.29 0.00 4.18
2515 3718 0.663568 CGTGCTTCTTTCCGAGTCGT 60.664 55.000 12.31 0.00 0.00 4.34
2562 3765 3.510388 TGCAAAATTTGTCGGTTGTGA 57.490 38.095 7.60 0.00 0.00 3.58
2564 3767 3.119316 TGCAAAATTTGTCGGTTGTGACT 60.119 39.130 7.60 0.00 39.64 3.41
2682 4041 1.885887 GGCTGCAACACAAATCTACCA 59.114 47.619 0.50 0.00 0.00 3.25
2708 4068 6.811253 TTTGCATGATCTAAGTTTTACCGT 57.189 33.333 0.00 0.00 0.00 4.83
2789 4151 7.081349 TGCAAATTACACTGCTAAACACATAC 58.919 34.615 1.83 0.00 39.38 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 0.250234 TGATACAGCAGCTCCGCTTT 59.750 50.000 0.00 0.00 41.38 3.51
22 23 1.226686 CCATGATACAGCAGCTCCGC 61.227 60.000 0.00 0.00 0.00 5.54
252 255 3.360867 TGGAGTCTGGAGAGAGTGATTC 58.639 50.000 0.00 0.00 31.47 2.52
425 726 0.546988 GAGAGTGGTTGGGGGTAGGT 60.547 60.000 0.00 0.00 0.00 3.08
462 773 3.381136 GGCCATTTGCTTGCCGGA 61.381 61.111 5.05 0.00 40.92 5.14
471 788 1.091771 ATCAGCGACGAGGCCATTTG 61.092 55.000 5.01 0.00 0.00 2.32
563 880 3.612247 GATGGTGACGCAGGTGGCT 62.612 63.158 0.00 0.00 41.67 4.75
579 896 2.835705 CGGCTACGACTCTGCGGAT 61.836 63.158 0.00 0.00 44.60 4.18
1189 1518 3.365265 GGCAGCCGGACCAGTTTG 61.365 66.667 5.05 0.00 0.00 2.93
1223 1552 2.819595 CTCGCCATTGTCGGGTGG 60.820 66.667 0.00 0.00 36.56 4.61
1364 1697 8.819974 CAAACACAAGCAACTTCTTATTCATTT 58.180 29.630 0.00 0.00 0.00 2.32
1437 1770 3.512329 TGGCTAGACCTAACATGTTCGAA 59.488 43.478 15.85 0.00 40.22 3.71
1449 1782 1.207791 CCTCCACAATGGCTAGACCT 58.792 55.000 0.00 0.00 37.47 3.85
1482 1815 2.689658 TGGATATCCAACATCCCGAGT 58.310 47.619 22.52 0.00 44.35 4.18
1537 1870 9.838339 CTCACCTATGTTTCCTCTAATGTAATT 57.162 33.333 0.00 0.00 41.28 1.40
1556 1889 3.357203 CACTGGCTAGAACTCTCACCTA 58.643 50.000 3.17 0.00 0.00 3.08
1585 1926 7.776107 TCATAAGGTAGTGAGATTGTCTTCTG 58.224 38.462 0.00 0.00 0.00 3.02
1699 2055 5.163311 TGACGTCCATTGAGACATATTCCAT 60.163 40.000 14.12 0.00 36.52 3.41
2011 2420 9.607285 GAAAGCGATTAGAACATAGAAAACAAA 57.393 29.630 0.00 0.00 0.00 2.83
2019 2428 4.617959 TCCGGAAAGCGATTAGAACATAG 58.382 43.478 0.00 0.00 0.00 2.23
2021 2430 3.132289 TCTCCGGAAAGCGATTAGAACAT 59.868 43.478 5.23 0.00 0.00 2.71
2420 3613 4.460731 CGCCTATCAGTGATCTTATGAGGA 59.539 45.833 17.89 0.00 0.00 3.71
2485 3688 4.939439 GGAAAGAAGCACGGGAAATAGTTA 59.061 41.667 0.00 0.00 0.00 2.24
2501 3704 0.886563 GGGAGACGACTCGGAAAGAA 59.113 55.000 8.76 0.00 43.44 2.52
2513 3716 2.432628 GCCGTTCACTGGGAGACG 60.433 66.667 7.38 7.38 0.00 4.18
2514 3717 0.534203 TTTGCCGTTCACTGGGAGAC 60.534 55.000 0.00 0.00 0.00 3.36
2515 3718 0.400213 ATTTGCCGTTCACTGGGAGA 59.600 50.000 0.00 0.00 0.00 3.71
2682 4041 8.303876 ACGGTAAAACTTAGATCATGCAAAAAT 58.696 29.630 0.00 0.00 0.00 1.82
2708 4068 9.899661 AGGCATGTAAACATAAGTAAATGAGTA 57.100 29.630 0.00 0.00 34.26 2.59
2789 4151 4.863689 TGTGCAACATCAAAACTTCACTTG 59.136 37.500 0.00 0.00 45.67 3.16


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

AutoCloner maintained by Alex Coulton.