Multiple sequence alignment - TraesCS3B01G009900

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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 TraesCS3B01G009900 chr3B 100.000 3372 0 0 1 3372 4664478 4661107 0.000000e+00 6228
1 TraesCS3B01G009900 chr3B 98.814 3372 40 0 1 3372 3764005 3760634 0.000000e+00 6006
2 TraesCS3B01G009900 chr3B 94.901 2824 80 16 575 3372 60270841 60273626 0.000000e+00 4359
3 TraesCS3B01G009900 chr3B 96.168 548 19 1 13 560 3773251 3773796 0.000000e+00 894
4 TraesCS3B01G009900 chr3B 96.168 548 19 1 13 560 4673855 4674400 0.000000e+00 894
5 TraesCS3B01G009900 chr3B 78.185 518 96 12 47 560 4640675 4640171 7.020000e-82 315
6 TraesCS3B01G009900 chr3B 97.753 178 4 0 1 178 4632054 4632231 1.180000e-79 307
7 TraesCS3B01G009900 chr3B 96.629 178 6 0 1 178 5148579 5148402 2.540000e-76 296
8 TraesCS3B01G009900 chr3B 75.510 343 46 24 240 560 720958719 720959045 2.110000e-27 134
9 TraesCS3B01G009900 chr7B 96.254 2803 73 3 570 3372 714531572 714528802 0.000000e+00 4566
10 TraesCS3B01G009900 chr5B 95.623 2833 82 17 576 3372 455290989 455288163 0.000000e+00 4506
11 TraesCS3B01G009900 chr5B 95.935 1894 47 2 570 2437 670107859 670105970 0.000000e+00 3044
12 TraesCS3B01G009900 chr5B 95.891 1582 54 3 1791 3372 14354567 14356137 0.000000e+00 2551
13 TraesCS3B01G009900 chrUn 95.363 2825 74 23 574 3372 8808796 8806003 0.000000e+00 4438
14 TraesCS3B01G009900 chrUn 96.168 548 19 1 13 560 344719152 344718607 0.000000e+00 894
15 TraesCS3B01G009900 chr5A 95.361 2824 73 15 575 3372 44279440 44276649 0.000000e+00 4436
16 TraesCS3B01G009900 chr7A 95.220 2824 76 16 575 3372 13133456 13130666 0.000000e+00 4412
17 TraesCS3B01G009900 chr7A 95.007 2824 83 15 575 3372 707670450 707673241 0.000000e+00 4381
18 TraesCS3B01G009900 chr6B 94.592 2829 88 25 570 3372 704743233 704746022 0.000000e+00 4316
19 TraesCS3B01G009900 chr2A 94.372 2825 94 25 575 3372 2768049 2765263 0.000000e+00 4276
20 TraesCS3B01G009900 chr4B 93.839 2824 83 14 575 3372 621762622 621759864 0.000000e+00 4167
21 TraesCS3B01G009900 chr4B 94.846 1824 60 14 1549 3372 661151327 661149538 0.000000e+00 2817
22 TraesCS3B01G009900 chr1B 90.300 2835 204 40 575 3370 591152712 591155514 0.000000e+00 3646
23 TraesCS3B01G009900 chr1B 96.083 1889 44 2 575 2437 39899055 39897171 0.000000e+00 3051
24 TraesCS3B01G009900 chr1B 92.739 1818 98 16 1575 3371 637633954 637632150 0.000000e+00 2595
25 TraesCS3B01G009900 chr1B 96.207 1582 47 4 1791 3372 141731527 141729959 0.000000e+00 2577
26 TraesCS3B01G009900 chr6A 94.956 1824 46 5 1549 3372 223587500 223585723 0.000000e+00 2817
27 TraesCS3B01G009900 chr3A 79.020 510 94 9 53 560 7350274 7349776 1.500000e-88 337
28 TraesCS3B01G009900 chr3D 78.320 512 98 9 51 560 1652336 1652836 5.430000e-83 318


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 TraesCS3B01G009900 chr3B 4661107 4664478 3371 True 6228 6228 100.000 1 3372 1 chr3B.!!$R3 3371
1 TraesCS3B01G009900 chr3B 3760634 3764005 3371 True 6006 6006 98.814 1 3372 1 chr3B.!!$R1 3371
2 TraesCS3B01G009900 chr3B 60270841 60273626 2785 False 4359 4359 94.901 575 3372 1 chr3B.!!$F4 2797
3 TraesCS3B01G009900 chr3B 3773251 3773796 545 False 894 894 96.168 13 560 1 chr3B.!!$F1 547
4 TraesCS3B01G009900 chr3B 4673855 4674400 545 False 894 894 96.168 13 560 1 chr3B.!!$F3 547
5 TraesCS3B01G009900 chr3B 4640171 4640675 504 True 315 315 78.185 47 560 1 chr3B.!!$R2 513
6 TraesCS3B01G009900 chr7B 714528802 714531572 2770 True 4566 4566 96.254 570 3372 1 chr7B.!!$R1 2802
7 TraesCS3B01G009900 chr5B 455288163 455290989 2826 True 4506 4506 95.623 576 3372 1 chr5B.!!$R1 2796
8 TraesCS3B01G009900 chr5B 670105970 670107859 1889 True 3044 3044 95.935 570 2437 1 chr5B.!!$R2 1867
9 TraesCS3B01G009900 chr5B 14354567 14356137 1570 False 2551 2551 95.891 1791 3372 1 chr5B.!!$F1 1581
10 TraesCS3B01G009900 chrUn 8806003 8808796 2793 True 4438 4438 95.363 574 3372 1 chrUn.!!$R1 2798
11 TraesCS3B01G009900 chrUn 344718607 344719152 545 True 894 894 96.168 13 560 1 chrUn.!!$R2 547
12 TraesCS3B01G009900 chr5A 44276649 44279440 2791 True 4436 4436 95.361 575 3372 1 chr5A.!!$R1 2797
13 TraesCS3B01G009900 chr7A 13130666 13133456 2790 True 4412 4412 95.220 575 3372 1 chr7A.!!$R1 2797
14 TraesCS3B01G009900 chr7A 707670450 707673241 2791 False 4381 4381 95.007 575 3372 1 chr7A.!!$F1 2797
15 TraesCS3B01G009900 chr6B 704743233 704746022 2789 False 4316 4316 94.592 570 3372 1 chr6B.!!$F1 2802
16 TraesCS3B01G009900 chr2A 2765263 2768049 2786 True 4276 4276 94.372 575 3372 1 chr2A.!!$R1 2797
17 TraesCS3B01G009900 chr4B 621759864 621762622 2758 True 4167 4167 93.839 575 3372 1 chr4B.!!$R1 2797
18 TraesCS3B01G009900 chr4B 661149538 661151327 1789 True 2817 2817 94.846 1549 3372 1 chr4B.!!$R2 1823
19 TraesCS3B01G009900 chr1B 591152712 591155514 2802 False 3646 3646 90.300 575 3370 1 chr1B.!!$F1 2795
20 TraesCS3B01G009900 chr1B 39897171 39899055 1884 True 3051 3051 96.083 575 2437 1 chr1B.!!$R1 1862
21 TraesCS3B01G009900 chr1B 637632150 637633954 1804 True 2595 2595 92.739 1575 3371 1 chr1B.!!$R3 1796
22 TraesCS3B01G009900 chr1B 141729959 141731527 1568 True 2577 2577 96.207 1791 3372 1 chr1B.!!$R2 1581
23 TraesCS3B01G009900 chr6A 223585723 223587500 1777 True 2817 2817 94.956 1549 3372 1 chr6A.!!$R1 1823
24 TraesCS3B01G009900 chr3D 1652336 1652836 500 False 318 318 78.320 51 560 1 chr3D.!!$F1 509

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
90 91 0.742281 CTTGGACTGGGATCTGCACG 60.742 60.000 0.00 0.0 0.00 5.34 F
763 765 1.226575 CGAATCAGTCGCCACGCTA 60.227 57.895 0.00 0.0 44.14 4.26 F
1982 2186 0.250727 GGTGGCCAAGCTACACAAGA 60.251 55.000 7.24 0.0 41.80 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1532 1585 8.753175 GTTAACAGCTATATTCTCAGGTTAACG 58.247 37.037 11.13 0.00 39.29 3.18 R
2206 2410 4.941657 TCCTCATGTTCTGAATGATCTCG 58.058 43.478 0.00 0.00 33.69 4.04 R
2996 3208 2.436824 GAAGAAGAGGGTGGCCGC 60.437 66.667 8.12 8.12 0.00 6.53 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
90 91 0.742281 CTTGGACTGGGATCTGCACG 60.742 60.000 0.00 0.0 0.00 5.34
238 239 4.382320 GCCGGGCCACTAACGACA 62.382 66.667 8.12 0.0 0.00 4.35
347 348 1.877637 CATCGTTGTGTTGGAGGTCA 58.122 50.000 0.00 0.0 0.00 4.02
565 566 2.828095 TGGTGCACGCACTTGCTT 60.828 55.556 20.65 0.0 45.52 3.91
605 606 5.923733 ACCAAAAACTACCACAATTGTCA 57.076 34.783 8.48 0.0 0.00 3.58
661 662 8.475331 TTTTGTGCGAAAAACTACCAAATTTA 57.525 26.923 0.00 0.0 0.00 1.40
763 765 1.226575 CGAATCAGTCGCCACGCTA 60.227 57.895 0.00 0.0 44.14 4.26
932 938 2.197324 CTCCCTCTCCCTCTCCCG 59.803 72.222 0.00 0.0 0.00 5.14
1532 1585 7.868415 CCTACAAGCAGATATCTTTAGTGTACC 59.132 40.741 1.33 0.0 0.00 3.34
1535 1588 6.466885 AGCAGATATCTTTAGTGTACCGTT 57.533 37.500 1.33 0.0 0.00 4.44
1982 2186 0.250727 GGTGGCCAAGCTACACAAGA 60.251 55.000 7.24 0.0 41.80 3.02
2206 2410 1.001181 TGCATTCTTCAAAGCCAAGCC 59.999 47.619 0.00 0.0 0.00 4.35
2582 2790 7.519057 AGACCTACTATGCTAAGTACTCATGA 58.481 38.462 0.00 0.0 0.00 3.07
3146 3361 0.398098 GTTCCTATCCCCCTCCACGA 60.398 60.000 0.00 0.0 0.00 4.35
3247 3477 1.064685 TCGTCAGAGGGCTCATCACTA 60.065 52.381 0.00 0.0 0.00 2.74
3351 3587 2.422597 CCAGTAGGCGTTGTTGATTGA 58.577 47.619 0.00 0.0 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 91 0.249238 CTCTGTGTGGAGATAGCGCC 60.249 60.000 2.29 0.00 35.52 6.53
238 239 1.228552 GGTGCCCATGACAACCTGT 60.229 57.895 0.00 0.00 0.00 4.00
379 380 3.733960 GCTTTGTCGGCCGGTTCC 61.734 66.667 27.83 11.61 0.00 3.62
565 566 2.568062 TGGTTAAATACTCGACCAGCCA 59.432 45.455 0.00 0.00 37.26 4.75
603 604 4.268405 GGTAGTTTTTCGTCACGTTTCTGA 59.732 41.667 0.00 0.00 0.00 3.27
605 606 4.033243 GTGGTAGTTTTTCGTCACGTTTCT 59.967 41.667 0.00 0.00 0.00 2.52
932 938 2.203806 GACCTAGGTCAGAGCACCC 58.796 63.158 32.91 6.38 44.02 4.61
1532 1585 8.753175 GTTAACAGCTATATTCTCAGGTTAACG 58.247 37.037 11.13 0.00 39.29 3.18
1535 1588 9.197306 TCAGTTAACAGCTATATTCTCAGGTTA 57.803 33.333 8.61 0.00 0.00 2.85
1667 1802 9.453572 AGCATCAGAGATAAATTCAGTTAACAA 57.546 29.630 8.61 0.00 0.00 2.83
2206 2410 4.941657 TCCTCATGTTCTGAATGATCTCG 58.058 43.478 0.00 0.00 33.69 4.04
2996 3208 2.436824 GAAGAAGAGGGTGGCCGC 60.437 66.667 8.12 8.12 0.00 6.53


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

AutoCloner maintained by Alex Coulton.