Multiple sequence alignment - TraesCS7B01G069400

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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 TraesCS7B01G069400 chr7B 100.000 3831 0 0 1 3831 74776678 74772848 0.000000e+00 7075.0
1 TraesCS7B01G069400 chr7B 95.899 2682 96 10 520 3191 720361565 720358888 0.000000e+00 4331.0
2 TraesCS7B01G069400 chr7B 92.743 689 41 7 3014 3698 392018365 392017682 0.000000e+00 987.0
3 TraesCS7B01G069400 chr7B 94.643 560 27 2 3142 3698 720358697 720358138 0.000000e+00 865.0
4 TraesCS7B01G069400 chr7B 95.543 516 21 2 1 515 720362399 720361885 0.000000e+00 824.0
5 TraesCS7B01G069400 chr7B 93.333 135 8 1 3697 3831 720358084 720357951 8.390000e-47 198.0
6 TraesCS7B01G069400 chr7B 97.368 38 1 0 3656 3693 21187974 21187937 8.880000e-07 65.8
7 TraesCS7B01G069400 chr1B 95.436 3199 113 9 1 3191 178492233 178489060 0.000000e+00 5068.0
8 TraesCS7B01G069400 chr1B 97.309 2750 68 6 1 2748 653855297 653858042 0.000000e+00 4663.0
9 TraesCS7B01G069400 chr1B 91.388 1916 123 18 1083 2985 24033685 24031799 0.000000e+00 2586.0
10 TraesCS7B01G069400 chr1B 92.086 139 7 1 3697 3831 178488269 178488131 3.910000e-45 193.0
11 TraesCS7B01G069400 chr2B 95.137 3002 128 8 1 2986 651660985 651657986 0.000000e+00 4719.0
12 TraesCS7B01G069400 chr2B 89.071 183 19 1 329 510 359277413 359277595 3.850000e-55 226.0
13 TraesCS7B01G069400 chr2B 85.455 165 11 9 542 706 359277921 359278072 3.960000e-35 159.0
14 TraesCS7B01G069400 chr4B 95.247 2567 116 4 421 2982 524150241 524147676 0.000000e+00 4060.0
15 TraesCS7B01G069400 chr4B 91.399 686 52 6 3014 3696 141026731 141027412 0.000000e+00 933.0
16 TraesCS7B01G069400 chr4B 94.987 379 18 1 1 378 524150620 524150242 9.160000e-166 593.0
17 TraesCS7B01G069400 chr4B 94.937 158 8 0 751 908 77074500 77074657 8.220000e-62 248.0
18 TraesCS7B01G069400 chr6B 97.001 2034 48 5 1801 3831 113023793 113025816 0.000000e+00 3406.0
19 TraesCS7B01G069400 chr6B 97.343 1769 44 3 1 1767 113022027 113023794 0.000000e+00 3003.0
20 TraesCS7B01G069400 chr6B 93.420 1915 113 8 1083 2986 55638794 55636882 0.000000e+00 2826.0
21 TraesCS7B01G069400 chr4D 93.873 2089 115 7 909 2986 502619662 502621748 0.000000e+00 3136.0
22 TraesCS7B01G069400 chr4D 82.836 268 22 3 641 908 502958698 502958941 6.440000e-53 219.0
23 TraesCS7B01G069400 chr4D 100.000 35 0 0 1 35 129498473 129498439 8.880000e-07 65.8
24 TraesCS7B01G069400 chr4D 100.000 35 0 0 1 35 459399501 459399467 8.880000e-07 65.8
25 TraesCS7B01G069400 chr2D 93.831 2091 114 9 909 2986 82249709 82247621 0.000000e+00 3133.0
26 TraesCS7B01G069400 chr2D 89.051 685 72 3 3015 3698 633366411 633367093 0.000000e+00 846.0
27 TraesCS7B01G069400 chr2D 88.502 661 70 6 3014 3672 373403324 373403980 0.000000e+00 795.0
28 TraesCS7B01G069400 chrUn 93.777 2089 117 7 909 2986 134332847 134330761 0.000000e+00 3125.0
29 TraesCS7B01G069400 chrUn 89.051 685 72 3 3015 3698 31817147 31817829 0.000000e+00 846.0
30 TraesCS7B01G069400 chrUn 88.905 685 73 3 3015 3698 361750674 361751356 0.000000e+00 841.0
31 TraesCS7B01G069400 chr3D 93.777 2089 117 7 909 2986 579345527 579347613 0.000000e+00 3125.0
32 TraesCS7B01G069400 chr3B 96.135 802 28 2 1 799 26466048 26466849 0.000000e+00 1306.0
33 TraesCS7B01G069400 chr3B 94.304 158 9 0 751 908 750374515 750374358 3.820000e-60 243.0
34 TraesCS7B01G069400 chr3B 94.815 135 7 0 3697 3831 26469990 26470124 1.080000e-50 211.0
35 TraesCS7B01G069400 chr1D 89.811 687 65 5 3014 3698 406708142 406707459 0.000000e+00 876.0
36 TraesCS7B01G069400 chr5D 88.824 689 69 8 3014 3698 448508406 448507722 0.000000e+00 839.0
37 TraesCS7B01G069400 chr5D 83.582 268 20 6 641 908 324724197 324723954 2.980000e-56 230.0
38 TraesCS7B01G069400 chr6D 94.170 223 13 0 39 261 413797169 413797391 1.320000e-89 340.0
39 TraesCS7B01G069400 chr6D 81.199 367 31 14 542 908 413799289 413799617 1.060000e-65 261.0
40 TraesCS7B01G069400 chr3A 93.722 223 14 0 42 264 562953348 562953126 6.130000e-88 335.0
41 TraesCS7B01G069400 chr6A 89.071 183 19 1 329 510 35122489 35122307 3.850000e-55 226.0
42 TraesCS7B01G069400 chr6A 84.848 165 11 9 542 706 35121981 35121831 1.840000e-33 154.0
43 TraesCS7B01G069400 chr4A 88.525 183 20 1 329 510 675001047 675001229 1.790000e-53 220.0
44 TraesCS7B01G069400 chr2A 96.000 50 2 0 3601 3650 207109731 207109682 8.820000e-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 TraesCS7B01G069400 chr7B 74772848 74776678 3830 True 7075.0 7075 100.0000 1 3831 1 chr7B.!!$R2 3830
1 TraesCS7B01G069400 chr7B 720357951 720362399 4448 True 1554.5 4331 94.8545 1 3831 4 chr7B.!!$R4 3830
2 TraesCS7B01G069400 chr7B 392017682 392018365 683 True 987.0 987 92.7430 3014 3698 1 chr7B.!!$R3 684
3 TraesCS7B01G069400 chr1B 653855297 653858042 2745 False 4663.0 4663 97.3090 1 2748 1 chr1B.!!$F1 2747
4 TraesCS7B01G069400 chr1B 178488131 178492233 4102 True 2630.5 5068 93.7610 1 3831 2 chr1B.!!$R2 3830
5 TraesCS7B01G069400 chr1B 24031799 24033685 1886 True 2586.0 2586 91.3880 1083 2985 1 chr1B.!!$R1 1902
6 TraesCS7B01G069400 chr2B 651657986 651660985 2999 True 4719.0 4719 95.1370 1 2986 1 chr2B.!!$R1 2985
7 TraesCS7B01G069400 chr4B 524147676 524150620 2944 True 2326.5 4060 95.1170 1 2982 2 chr4B.!!$R1 2981
8 TraesCS7B01G069400 chr4B 141026731 141027412 681 False 933.0 933 91.3990 3014 3696 1 chr4B.!!$F2 682
9 TraesCS7B01G069400 chr6B 113022027 113025816 3789 False 3204.5 3406 97.1720 1 3831 2 chr6B.!!$F1 3830
10 TraesCS7B01G069400 chr6B 55636882 55638794 1912 True 2826.0 2826 93.4200 1083 2986 1 chr6B.!!$R1 1903
11 TraesCS7B01G069400 chr4D 502619662 502621748 2086 False 3136.0 3136 93.8730 909 2986 1 chr4D.!!$F1 2077
12 TraesCS7B01G069400 chr2D 82247621 82249709 2088 True 3133.0 3133 93.8310 909 2986 1 chr2D.!!$R1 2077
13 TraesCS7B01G069400 chr2D 633366411 633367093 682 False 846.0 846 89.0510 3015 3698 1 chr2D.!!$F2 683
14 TraesCS7B01G069400 chr2D 373403324 373403980 656 False 795.0 795 88.5020 3014 3672 1 chr2D.!!$F1 658
15 TraesCS7B01G069400 chrUn 134330761 134332847 2086 True 3125.0 3125 93.7770 909 2986 1 chrUn.!!$R1 2077
16 TraesCS7B01G069400 chrUn 31817147 31817829 682 False 846.0 846 89.0510 3015 3698 1 chrUn.!!$F1 683
17 TraesCS7B01G069400 chrUn 361750674 361751356 682 False 841.0 841 88.9050 3015 3698 1 chrUn.!!$F2 683
18 TraesCS7B01G069400 chr3D 579345527 579347613 2086 False 3125.0 3125 93.7770 909 2986 1 chr3D.!!$F1 2077
19 TraesCS7B01G069400 chr3B 26466048 26470124 4076 False 758.5 1306 95.4750 1 3831 2 chr3B.!!$F1 3830
20 TraesCS7B01G069400 chr1D 406707459 406708142 683 True 876.0 876 89.8110 3014 3698 1 chr1D.!!$R1 684
21 TraesCS7B01G069400 chr5D 448507722 448508406 684 True 839.0 839 88.8240 3014 3698 1 chr5D.!!$R2 684
22 TraesCS7B01G069400 chr6D 413797169 413799617 2448 False 300.5 340 87.6845 39 908 2 chr6D.!!$F1 869

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
950 2636 0.896923 TTTTGCTGCATCCACATCCC 59.103 50.0 1.84 0.0 0.0 3.85 F
2253 4092 3.176411 TCTATCCCGGACTCCTCGTATA 58.824 50.0 0.73 0.0 0.0 1.47 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2774 4618 0.329261 TGAGGGATGTTTCCAGCAGG 59.671 55.000 0.0 0.0 44.6 4.85 R
3766 5930 1.912731 TCCCCAATACAGCAGCAACTA 59.087 47.619 0.0 0.0 0.0 2.24 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
303 914 1.412710 CTGCCACGCTAGGAATTAGGA 59.587 52.381 0.00 0.00 0.00 2.94
310 921 2.989840 CGCTAGGAATTAGGAATGAGCG 59.010 50.000 0.00 0.00 44.51 5.03
342 1577 7.079451 TGTAAGGAATTTGGGGATCTCTATC 57.921 40.000 0.00 0.00 0.00 2.08
346 1581 4.352298 GGAATTTGGGGATCTCTATCTGGT 59.648 45.833 0.00 0.00 32.29 4.00
374 1610 5.815222 ACATAGTTTTTGGTGCCTTTTTGTC 59.185 36.000 0.00 0.00 0.00 3.18
811 2495 9.100197 TGGTAGAACTATATTCAGCCATGATTA 57.900 33.333 0.00 0.00 34.73 1.75
894 2578 1.632920 CCCTCTCCTTGCTCTTCCTTT 59.367 52.381 0.00 0.00 0.00 3.11
950 2636 0.896923 TTTTGCTGCATCCACATCCC 59.103 50.000 1.84 0.00 0.00 3.85
1339 3025 3.882444 AGGTCGTACACAGCATACTCTA 58.118 45.455 0.00 0.00 0.00 2.43
1351 3037 8.037758 ACACAGCATACTCTATTGAATATAGGC 58.962 37.037 3.17 0.00 0.00 3.93
1542 3228 9.909644 AGCTTAATGTCCTTACTATATTGTACG 57.090 33.333 0.00 0.00 0.00 3.67
1916 3607 6.093219 CACACTATTTCATACTTCAGCAAGCT 59.907 38.462 0.00 0.00 32.09 3.74
2231 4070 7.341805 ACCTTCTGTAGTATCTACTTCCGTTA 58.658 38.462 8.13 0.00 37.73 3.18
2253 4092 3.176411 TCTATCCCGGACTCCTCGTATA 58.824 50.000 0.73 0.00 0.00 1.47
2254 4093 3.779183 TCTATCCCGGACTCCTCGTATAT 59.221 47.826 0.73 0.00 0.00 0.86
2370 4209 8.125978 AGAGATGATGAAGGAGATCACTATTC 57.874 38.462 0.00 0.00 32.68 1.75
2625 4464 3.457380 AGCATGACCTGGATGAACACTAT 59.543 43.478 0.00 0.00 0.00 2.12
2774 4618 6.985188 TGCTTATGGTGAAAGACAATCTAC 57.015 37.500 0.00 0.00 0.00 2.59
2967 4825 6.293698 AGTTTTGGTACTACTACAAGTTGGG 58.706 40.000 7.96 2.29 0.00 4.12
2974 4832 5.556006 ACTACTACAAGTTGGGTTTGCTA 57.444 39.130 7.96 0.00 0.00 3.49
3287 5389 1.317613 TTTCAGACATTGCGTGCCTT 58.682 45.000 0.00 0.00 0.00 4.35
3386 5488 7.039011 TCGGTAATAATCACATTCCAGCTAGAT 60.039 37.037 0.00 0.00 0.00 1.98
3745 5909 0.476771 GGGGAGTGAAAGGTGTTGGA 59.523 55.000 0.00 0.00 0.00 3.53
3752 5916 3.117512 AGTGAAAGGTGTTGGATCCTTGT 60.118 43.478 14.23 0.00 42.38 3.16
3759 5923 3.412386 GTGTTGGATCCTTGTAGTTGCT 58.588 45.455 14.23 0.00 0.00 3.91
3766 5930 6.245408 TGGATCCTTGTAGTTGCTTGTTATT 58.755 36.000 14.23 0.00 0.00 1.40
3784 5948 5.356751 TGTTATTAGTTGCTGCTGTATTGGG 59.643 40.000 0.00 0.00 0.00 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
303 914 3.081804 CCTTACAGTTTTCCCGCTCATT 58.918 45.455 0.00 0.00 0.00 2.57
310 921 4.020573 CCCCAAATTCCTTACAGTTTTCCC 60.021 45.833 0.00 0.00 0.00 3.97
342 1577 5.335661 GGCACCAAAAACTATGTTCTACCAG 60.336 44.000 0.00 0.00 0.00 4.00
346 1581 6.969993 AAAGGCACCAAAAACTATGTTCTA 57.030 33.333 0.00 0.00 0.00 2.10
374 1610 7.806690 TGCCTAGAAAGCTATAAATATTTGCG 58.193 34.615 11.05 0.60 0.00 4.85
510 1746 9.650539 GGATCTCGATGCAGCATATATATAAAT 57.349 33.333 8.22 0.00 0.00 1.40
811 2495 1.129058 CGGGGAATAACTGGGTAGCT 58.871 55.000 0.00 0.00 0.00 3.32
862 2546 1.075896 GAGAGGGAGGACGGATGGT 60.076 63.158 0.00 0.00 0.00 3.55
950 2636 0.523072 CCGAGGTGTCTTGGCAATTG 59.477 55.000 0.00 0.00 37.71 2.32
975 2661 2.032924 TGATCGATACGCGTGAGTGATT 59.967 45.455 24.59 0.00 46.66 2.57
1144 2830 1.388133 GCAAATCCTCCTGGGGGTT 59.612 57.895 13.53 0.17 35.33 4.11
1339 3025 9.618890 AAGCAATATCATACGCCTATATTCAAT 57.381 29.630 0.00 0.00 0.00 2.57
1438 3124 0.515127 TGTGCAACGGAAATACTGCG 59.485 50.000 0.00 0.00 45.77 5.18
1720 3410 8.814931 AGATAATCTAACAGCTATGAGCAGAAT 58.185 33.333 0.64 0.00 45.56 2.40
2231 4070 0.772384 ACGAGGAGTCCGGGATAGAT 59.228 55.000 0.00 0.00 0.00 1.98
2253 4092 6.884832 TCATCCGATTTACCACAAGTAGAAT 58.115 36.000 0.00 0.00 30.92 2.40
2254 4093 6.288941 TCATCCGATTTACCACAAGTAGAA 57.711 37.500 0.00 0.00 30.92 2.10
2370 4209 5.008415 ACACTTCATTGAGTTCTTGCTTCAG 59.992 40.000 0.00 0.00 0.00 3.02
2551 4390 6.266103 TCTCTTGTAGAACTAAGAAACCCGAA 59.734 38.462 0.00 0.00 32.96 4.30
2589 4428 2.076100 TCATGCTACGCAAAGAACCTG 58.924 47.619 0.00 0.00 43.62 4.00
2774 4618 0.329261 TGAGGGATGTTTCCAGCAGG 59.671 55.000 0.00 0.00 44.60 4.85
2967 4825 8.184192 ACAGCAGTCAACAATATAATAGCAAAC 58.816 33.333 0.00 0.00 0.00 2.93
2974 4832 7.201732 GCCAACTACAGCAGTCAACAATATAAT 60.202 37.037 0.00 0.00 36.04 1.28
3745 5909 8.730680 CAACTAATAACAAGCAACTACAAGGAT 58.269 33.333 0.00 0.00 0.00 3.24
3752 5916 5.705441 AGCAGCAACTAATAACAAGCAACTA 59.295 36.000 0.00 0.00 0.00 2.24
3759 5923 6.127758 CCCAATACAGCAGCAACTAATAACAA 60.128 38.462 0.00 0.00 0.00 2.83
3766 5930 1.912731 TCCCCAATACAGCAGCAACTA 59.087 47.619 0.00 0.00 0.00 2.24
3784 5948 3.536075 AGTAGCTAATCCTCCTCCTCC 57.464 52.381 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.