Multiple sequence alignment - TraesCS3B01G202100

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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 TraesCS3B01G202100 chr3B 100.000 7503 0 0 1 7503 236194112 236186610 0.000000e+00 13856
1 TraesCS3B01G202100 chr3B 95.730 4403 131 38 1 4394 555267937 555263583 0.000000e+00 7036
2 TraesCS3B01G202100 chr3B 88.691 5659 515 90 1 5630 642076081 642081643 0.000000e+00 6789
3 TraesCS3B01G202100 chr3B 95.201 1917 64 18 5590 7503 555253840 555251949 0.000000e+00 3005
4 TraesCS3B01G202100 chr7B 97.766 7521 145 17 1 7503 746797761 746790246 0.000000e+00 12936
5 TraesCS3B01G202100 chr7B 95.705 5611 189 42 1 5595 734939946 734934372 0.000000e+00 8979
6 TraesCS3B01G202100 chr7B 89.938 3886 310 55 1759 5630 697158465 697154647 0.000000e+00 4935
7 TraesCS3B01G202100 chr7B 95.720 1869 55 15 5638 7503 734925693 734923847 0.000000e+00 2985
8 TraesCS3B01G202100 chr7B 90.043 1627 109 37 5879 7503 697154489 697152914 0.000000e+00 2058
9 TraesCS3B01G202100 chr2B 97.034 7519 167 27 1 7503 130641872 130649350 0.000000e+00 12598
10 TraesCS3B01G202100 chr2B 90.628 5666 409 73 1 5630 132063360 132068939 0.000000e+00 7409
11 TraesCS3B01G202100 chr2B 90.492 5669 431 80 1 5630 800708850 800703251 0.000000e+00 7384
12 TraesCS3B01G202100 chr2B 92.025 1630 85 29 5878 7503 132069099 132070687 0.000000e+00 2248
13 TraesCS3B01G202100 chr2B 91.845 1631 87 27 5878 7503 800703091 800701502 0.000000e+00 2233
14 TraesCS3B01G202100 chr2B 91.166 283 21 4 5590 5870 132068853 132069133 1.530000e-101 381
15 TraesCS3B01G202100 chr2B 91.166 283 21 4 5590 5870 800703337 800703057 1.530000e-101 381
16 TraesCS3B01G202100 chr6B 94.429 5672 232 65 1 5630 239605245 239610874 0.000000e+00 8647
17 TraesCS3B01G202100 chr6B 94.108 1918 79 22 5590 7503 239610787 239612674 0.000000e+00 2885
18 TraesCS3B01G202100 chr5B 91.827 5653 365 69 1 5630 218929199 218934777 0.000000e+00 7790
19 TraesCS3B01G202100 chr5B 91.013 5664 408 72 1 5630 172605684 172611280 0.000000e+00 7546
20 TraesCS3B01G202100 chr5B 93.055 1627 74 29 5879 7503 218934939 218936528 0.000000e+00 2342
21 TraesCS3B01G202100 chr5B 93.059 1628 69 26 5878 7503 172611440 172613025 0.000000e+00 2340
22 TraesCS3B01G202100 chr5B 92.580 283 17 4 5590 5870 172611194 172611474 3.260000e-108 403
23 TraesCS3B01G202100 chr5B 92.254 284 17 5 5590 5870 218934691 218934972 1.520000e-106 398
24 TraesCS3B01G202100 chr5B 91.815 281 19 4 5592 5870 157581901 157582179 9.130000e-104 388


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 TraesCS3B01G202100 chr3B 236186610 236194112 7502 True 13856.000000 13856 100.000000 1 7503 1 chr3B.!!$R1 7502
1 TraesCS3B01G202100 chr3B 555263583 555267937 4354 True 7036.000000 7036 95.730000 1 4394 1 chr3B.!!$R3 4393
2 TraesCS3B01G202100 chr3B 642076081 642081643 5562 False 6789.000000 6789 88.691000 1 5630 1 chr3B.!!$F1 5629
3 TraesCS3B01G202100 chr3B 555251949 555253840 1891 True 3005.000000 3005 95.201000 5590 7503 1 chr3B.!!$R2 1913
4 TraesCS3B01G202100 chr7B 746790246 746797761 7515 True 12936.000000 12936 97.766000 1 7503 1 chr7B.!!$R3 7502
5 TraesCS3B01G202100 chr7B 734934372 734939946 5574 True 8979.000000 8979 95.705000 1 5595 1 chr7B.!!$R2 5594
6 TraesCS3B01G202100 chr7B 697152914 697158465 5551 True 3496.500000 4935 89.990500 1759 7503 2 chr7B.!!$R4 5744
7 TraesCS3B01G202100 chr7B 734923847 734925693 1846 True 2985.000000 2985 95.720000 5638 7503 1 chr7B.!!$R1 1865
8 TraesCS3B01G202100 chr2B 130641872 130649350 7478 False 12598.000000 12598 97.034000 1 7503 1 chr2B.!!$F1 7502
9 TraesCS3B01G202100 chr2B 132063360 132070687 7327 False 3346.000000 7409 91.273000 1 7503 3 chr2B.!!$F2 7502
10 TraesCS3B01G202100 chr2B 800701502 800708850 7348 True 3332.666667 7384 91.167667 1 7503 3 chr2B.!!$R1 7502
11 TraesCS3B01G202100 chr6B 239605245 239612674 7429 False 5766.000000 8647 94.268500 1 7503 2 chr6B.!!$F1 7502
12 TraesCS3B01G202100 chr5B 218929199 218936528 7329 False 3510.000000 7790 92.378667 1 7503 3 chr5B.!!$F3 7502
13 TraesCS3B01G202100 chr5B 172605684 172613025 7341 False 3429.666667 7546 92.217333 1 7503 3 chr5B.!!$F2 7502

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
65 69 0.169009 GAGGTTGAATCAGTTGCCGC 59.831 55.000 0.00 0.0 0.00 6.53 F
430 448 1.165907 CGTGAACAGGTGTGTGGCAT 61.166 55.000 0.00 0.0 36.84 4.40 F
1591 1634 1.077265 CCTGGGTTGGAGGCAATGT 59.923 57.895 0.00 0.0 0.00 2.71 F
2385 2443 1.153353 GCCTACGCACAAGTTTGCTA 58.847 50.000 7.94 0.0 40.62 3.49 F
2990 3068 1.705997 AACAGTTCCCAAGAGCCCGT 61.706 55.000 0.00 0.0 0.00 5.28 F
4273 4380 0.457035 GGCACCCGTCGACAATACTA 59.543 55.000 17.16 0.0 0.00 1.82 F
4504 4611 0.311165 CGCTCCCGAGACGAACATAT 59.689 55.000 0.00 0.0 36.29 1.78 F
5046 5156 1.404181 GCTGATACCGCTGACAAGACA 60.404 52.381 0.00 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1591 1634 0.039798 GCCAGTACAGACGTGTTCGA 60.040 55.000 0.0 0.0 38.19 3.71 R
2385 2443 1.742761 CTGATGGTCCACGCAGAAAT 58.257 50.000 15.4 0.0 0.00 2.17 R
3492 3578 1.267806 CACCTTTGTTCAAGCGAGCAT 59.732 47.619 0.0 0.0 31.87 3.79 R
3961 4059 2.139917 CAGTAGTTGCCGTGTTTAGCA 58.860 47.619 0.0 0.0 37.18 3.49 R
4456 4563 1.075482 CACTTGCTGATGGGGTGGT 59.925 57.895 0.0 0.0 0.00 4.16 R
5148 5258 1.127343 GCCTCTCATTCCTACTGGCT 58.873 55.000 0.0 0.0 36.32 4.75 R
5769 5894 1.461559 TGCCATGTCGCATCAAATGA 58.538 45.000 0.0 0.0 32.62 2.57 R
6681 6897 1.012086 CATGATGACCTTGTCGGCAG 58.988 55.000 0.0 0.0 34.95 4.85 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
65 69 0.169009 GAGGTTGAATCAGTTGCCGC 59.831 55.000 0.00 0.00 0.00 6.53
430 448 1.165907 CGTGAACAGGTGTGTGGCAT 61.166 55.000 0.00 0.00 36.84 4.40
595 618 4.817318 TGAGATAGTTGCCACATACACA 57.183 40.909 0.00 0.00 0.00 3.72
1544 1587 6.867293 GTCCCGTATGAGGTTAATAATGAGAC 59.133 42.308 0.00 0.00 0.00 3.36
1591 1634 1.077265 CCTGGGTTGGAGGCAATGT 59.923 57.895 0.00 0.00 0.00 2.71
1684 1727 6.405619 GCTGCTCATGTATCTCATATCAGCTA 60.406 42.308 14.49 0.00 42.28 3.32
2133 2183 4.712051 ACTGCCTTCATATTAGCATGGA 57.288 40.909 0.00 0.00 34.16 3.41
2385 2443 1.153353 GCCTACGCACAAGTTTGCTA 58.847 50.000 7.94 0.00 40.62 3.49
2845 2923 2.707902 GGAATGACCGGATTGCTCC 58.292 57.895 9.46 3.29 38.29 4.70
2946 3024 3.408020 CGTACACACCGGCCAACG 61.408 66.667 0.00 0.54 43.80 4.10
2990 3068 1.705997 AACAGTTCCCAAGAGCCCGT 61.706 55.000 0.00 0.00 0.00 5.28
3162 3245 4.372656 CGGAGAAAGTGAAAGAACAGACT 58.627 43.478 0.00 0.00 0.00 3.24
3367 3452 1.732259 CTTTCTATTGTCAAGCGCGGT 59.268 47.619 4.23 4.23 0.00 5.68
3431 3517 4.082081 CCTCCATCTGTTATTTTTGCAGCA 60.082 41.667 0.00 0.00 0.00 4.41
3492 3578 2.111460 AACGCCAACCCGTGCTTA 59.889 55.556 0.00 0.00 41.90 3.09
4273 4380 0.457035 GGCACCCGTCGACAATACTA 59.543 55.000 17.16 0.00 0.00 1.82
4456 4563 1.227943 GAAGCCACAGTGAGCCACA 60.228 57.895 0.62 0.00 36.74 4.17
4504 4611 0.311165 CGCTCCCGAGACGAACATAT 59.689 55.000 0.00 0.00 36.29 1.78
4509 4616 1.593006 CCCGAGACGAACATATGCAAC 59.407 52.381 1.58 0.00 0.00 4.17
4512 4619 2.214244 CGAGACGAACATATGCAACGAG 59.786 50.000 18.58 2.83 0.00 4.18
5046 5156 1.404181 GCTGATACCGCTGACAAGACA 60.404 52.381 0.00 0.00 0.00 3.41
5148 5258 1.561717 CGCAAATCGTTCGTGGTCCA 61.562 55.000 0.00 0.00 0.00 4.02
5574 5691 3.005684 TGAAGTTGATTCACCATGGCAAC 59.994 43.478 19.02 19.02 43.09 4.17
5575 5692 2.880443 AGTTGATTCACCATGGCAACT 58.120 42.857 22.00 22.00 42.92 3.16
5576 5693 2.559668 AGTTGATTCACCATGGCAACTG 59.440 45.455 25.08 12.51 45.12 3.16
5577 5694 2.557924 GTTGATTCACCATGGCAACTGA 59.442 45.455 19.25 10.84 36.73 3.41
5579 5696 2.821378 TGATTCACCATGGCAACTGAAG 59.179 45.455 13.04 0.00 31.53 3.02
5580 5697 2.363306 TTCACCATGGCAACTGAAGT 57.637 45.000 13.04 0.00 37.61 3.01
5962 6160 6.040504 TCCTACCTACATGTCACATCATACAC 59.959 42.308 0.00 0.00 0.00 2.90
6537 6753 7.762159 TGTTATGTCGTTTTCATACAGCTCATA 59.238 33.333 0.00 0.00 0.00 2.15
6681 6897 5.698089 ACATCACCAATCACATCGATATGTC 59.302 40.000 3.17 0.00 44.70 3.06
7042 7266 5.009610 GGATGGCAACTTTTCTTCAACTACA 59.990 40.000 0.00 0.00 37.61 2.74
7301 7528 4.183865 CTGATTCAGATCTTACCACGCAA 58.816 43.478 8.00 0.00 32.44 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
430 448 6.488344 TGCCACATTTGTTCATGTAGTTTAGA 59.512 34.615 0.00 0.00 35.51 2.10
696 726 7.206687 TCAAAAGTATGGAAACTTTCGCAAAT 58.793 30.769 2.73 0.00 46.40 2.32
704 734 7.232534 TGGCAACTATCAAAAGTATGGAAACTT 59.767 33.333 0.00 0.00 38.37 2.66
1544 1587 2.748268 GCGAACAGCTCTTCCTCAG 58.252 57.895 0.00 0.00 44.04 3.35
1591 1634 0.039798 GCCAGTACAGACGTGTTCGA 60.040 55.000 0.00 0.00 38.19 3.71
2133 2183 3.614092 CATCCTACTGTGATGGCAGTTT 58.386 45.455 4.01 0.00 46.45 2.66
2385 2443 1.742761 CTGATGGTCCACGCAGAAAT 58.257 50.000 15.40 0.00 0.00 2.17
2845 2923 2.264794 CCCCTCGACCAACTTCCG 59.735 66.667 0.00 0.00 0.00 4.30
2990 3068 4.671766 CGTCTACATCATCTTGTGTGTCGA 60.672 45.833 0.00 0.00 0.00 4.20
3127 3208 3.087253 CTCCGGTGGTGGGGCATA 61.087 66.667 0.00 0.00 0.00 3.14
3353 3438 1.632046 CCGTTACCGCGCTTGACAAT 61.632 55.000 5.56 0.00 0.00 2.71
3367 3452 5.838531 AATGTCAGAAAACAAACCCGTTA 57.161 34.783 0.00 0.00 31.81 3.18
3492 3578 1.267806 CACCTTTGTTCAAGCGAGCAT 59.732 47.619 0.00 0.00 31.87 3.79
3961 4059 2.139917 CAGTAGTTGCCGTGTTTAGCA 58.860 47.619 0.00 0.00 37.18 3.49
4273 4380 2.433145 CGTCATCGGTGCAGCAGT 60.433 61.111 17.33 0.00 0.00 4.40
4444 4551 2.510906 GGTGGTGTGGCTCACTGT 59.489 61.111 18.07 0.00 45.50 3.55
4456 4563 1.075482 CACTTGCTGATGGGGTGGT 59.925 57.895 0.00 0.00 0.00 4.16
4512 4619 2.165437 AGTGTCTGAAGAGAGCGAATCC 59.835 50.000 0.00 0.00 0.00 3.01
4520 4630 3.229697 TGGAGTCAGTGTCTGAAGAGA 57.770 47.619 0.88 0.00 42.46 3.10
4718 4828 3.332034 GGTACGACTGTTGGTTGCTTAT 58.668 45.455 0.00 0.00 32.66 1.73
5046 5156 4.531426 TTGTTTGCAGGGCGGGGT 62.531 61.111 0.00 0.00 0.00 4.95
5148 5258 1.127343 GCCTCTCATTCCTACTGGCT 58.873 55.000 0.00 0.00 36.32 4.75
5527 5642 4.152647 TGCCATGTGTTTACCCAAATGTA 58.847 39.130 0.00 0.00 29.51 2.29
5574 5691 2.821378 TGCCATGGTGAATCAACTTCAG 59.179 45.455 14.67 0.00 44.44 3.02
5575 5692 2.874014 TGCCATGGTGAATCAACTTCA 58.126 42.857 14.67 0.00 41.61 3.02
5576 5693 3.256631 AGTTGCCATGGTGAATCAACTTC 59.743 43.478 22.00 5.00 43.09 3.01
5577 5694 3.006110 CAGTTGCCATGGTGAATCAACTT 59.994 43.478 24.01 12.27 43.09 2.66
5579 5696 2.557924 TCAGTTGCCATGGTGAATCAAC 59.442 45.455 19.02 19.02 37.78 3.18
5580 5697 2.874014 TCAGTTGCCATGGTGAATCAA 58.126 42.857 14.67 5.59 0.00 2.57
5582 5699 2.821969 ACTTCAGTTGCCATGGTGAATC 59.178 45.455 14.67 0.00 0.00 2.52
5583 5700 2.880443 ACTTCAGTTGCCATGGTGAAT 58.120 42.857 14.67 0.00 0.00 2.57
5769 5894 1.461559 TGCCATGTCGCATCAAATGA 58.538 45.000 0.00 0.00 32.62 2.57
5962 6160 2.501316 GGATTGTGAGGAAAAATGGGGG 59.499 50.000 0.00 0.00 0.00 5.40
6032 6231 2.679837 GGCTGCAATGATTCGAGAAGAA 59.320 45.455 0.50 0.00 43.93 2.52
6033 6232 2.283298 GGCTGCAATGATTCGAGAAGA 58.717 47.619 0.50 0.00 0.00 2.87
6484 6699 6.095440 GGAAGAATCATGCCTGCTAAGTAAAA 59.905 38.462 0.00 0.00 0.00 1.52
6681 6897 1.012086 CATGATGACCTTGTCGGCAG 58.988 55.000 0.00 0.00 34.95 4.85
7042 7266 2.390225 TTTTTGGCTATGGTGTGGGT 57.610 45.000 0.00 0.00 0.00 4.51


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

AutoCloner maintained by Alex Coulton.