Multiple sequence alignment - TraesCS6B01G150700

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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 TraesCS6B01G150700 chr6B 100.000 3397 0 0 1 3397 151881865 151885261 0.000000e+00 6274
1 TraesCS6B01G150700 chr6B 97.990 2587 38 8 417 2994 80798629 80801210 0.000000e+00 4477
2 TraesCS6B01G150700 chr6B 97.907 430 8 1 1 429 80789666 80790095 0.000000e+00 743
3 TraesCS6B01G150700 chr6B 98.737 396 5 0 3002 3397 80801330 80801725 0.000000e+00 704
4 TraesCS6B01G150700 chr2B 98.482 3426 22 5 1 3397 657484657 657481233 0.000000e+00 6011
5 TraesCS6B01G150700 chr2A 98.118 3401 32 5 1 3397 441101229 441104601 0.000000e+00 5897
6 TraesCS6B01G150700 chr5B 98.666 2999 33 4 1 2994 535103392 535100396 0.000000e+00 5310
7 TraesCS6B01G150700 chr5B 96.934 3001 74 11 1 2994 52316370 52319359 0.000000e+00 5016
8 TraesCS6B01G150700 chr5B 98.485 396 6 0 3002 3397 535100276 535099881 0.000000e+00 699
9 TraesCS6B01G150700 chr5B 97.468 395 9 1 3002 3396 52319479 52319872 0.000000e+00 673
10 TraesCS6B01G150700 chr5A 96.984 2719 63 7 293 2994 32955199 32952483 0.000000e+00 4549
11 TraesCS6B01G150700 chr5A 98.228 395 6 1 3002 3396 32952363 32951970 0.000000e+00 689
12 TraesCS6B01G150700 chr5A 93.939 99 4 2 2722 2819 696955264 696955361 7.590000e-32 148
13 TraesCS6B01G150700 chr3A 95.553 1799 67 8 927 2718 58067626 58069418 0.000000e+00 2867
14 TraesCS6B01G150700 chr3A 97.310 1673 41 2 1323 2991 336007343 336005671 0.000000e+00 2837
15 TraesCS6B01G150700 chr3A 97.074 991 22 6 293 1280 336008330 336007344 0.000000e+00 1663
16 TraesCS6B01G150700 chr3A 98.228 395 6 1 3002 3396 336005549 336005156 0.000000e+00 689
17 TraesCS6B01G150700 chr7A 95.000 1780 75 12 949 2718 107709781 107711556 0.000000e+00 2782
18 TraesCS6B01G150700 chr7A 96.300 919 23 3 1 919 107678021 107678928 0.000000e+00 1498
19 TraesCS6B01G150700 chr7A 85.799 169 21 1 2820 2985 424318406 424318238 3.480000e-40 176
20 TraesCS6B01G150700 chr7B 97.715 919 18 3 1 919 472920086 472919171 0.000000e+00 1578
21 TraesCS6B01G150700 chr7B 97.715 919 18 2 1 919 606364671 606365586 0.000000e+00 1578
22 TraesCS6B01G150700 chr7B 84.877 972 89 33 1740 2689 140714341 140713406 0.000000e+00 928
23 TraesCS6B01G150700 chr7B 96.429 168 5 1 2552 2718 606368878 606369045 3.340000e-70 276
24 TraesCS6B01G150700 chrUn 95.912 636 14 4 1 636 73439939 73440562 0.000000e+00 1020
25 TraesCS6B01G150700 chrUn 96.456 395 13 1 3002 3396 73441760 73442153 0.000000e+00 651
26 TraesCS6B01G150700 chr3B 82.031 768 76 21 1760 2496 545830907 545831643 6.270000e-167 597
27 TraesCS6B01G150700 chr7D 89.951 408 25 7 3002 3394 287708547 287708141 2.340000e-141 512
28 TraesCS6B01G150700 chr4A 89.706 408 25 8 3003 3394 216809780 216810186 3.910000e-139 505
29 TraesCS6B01G150700 chr4B 96.000 75 2 1 2744 2818 446514696 446514769 1.660000e-23 121


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 TraesCS6B01G150700 chr6B 151881865 151885261 3396 False 6274.000000 6274 100.000000 1 3397 1 chr6B.!!$F2 3396
1 TraesCS6B01G150700 chr6B 80798629 80801725 3096 False 2590.500000 4477 98.363500 417 3397 2 chr6B.!!$F3 2980
2 TraesCS6B01G150700 chr2B 657481233 657484657 3424 True 6011.000000 6011 98.482000 1 3397 1 chr2B.!!$R1 3396
3 TraesCS6B01G150700 chr2A 441101229 441104601 3372 False 5897.000000 5897 98.118000 1 3397 1 chr2A.!!$F1 3396
4 TraesCS6B01G150700 chr5B 535099881 535103392 3511 True 3004.500000 5310 98.575500 1 3397 2 chr5B.!!$R1 3396
5 TraesCS6B01G150700 chr5B 52316370 52319872 3502 False 2844.500000 5016 97.201000 1 3396 2 chr5B.!!$F1 3395
6 TraesCS6B01G150700 chr5A 32951970 32955199 3229 True 2619.000000 4549 97.606000 293 3396 2 chr5A.!!$R1 3103
7 TraesCS6B01G150700 chr3A 58067626 58069418 1792 False 2867.000000 2867 95.553000 927 2718 1 chr3A.!!$F1 1791
8 TraesCS6B01G150700 chr3A 336005156 336008330 3174 True 1729.666667 2837 97.537333 293 3396 3 chr3A.!!$R1 3103
9 TraesCS6B01G150700 chr7A 107709781 107711556 1775 False 2782.000000 2782 95.000000 949 2718 1 chr7A.!!$F2 1769
10 TraesCS6B01G150700 chr7A 107678021 107678928 907 False 1498.000000 1498 96.300000 1 919 1 chr7A.!!$F1 918
11 TraesCS6B01G150700 chr7B 472919171 472920086 915 True 1578.000000 1578 97.715000 1 919 1 chr7B.!!$R2 918
12 TraesCS6B01G150700 chr7B 140713406 140714341 935 True 928.000000 928 84.877000 1740 2689 1 chr7B.!!$R1 949
13 TraesCS6B01G150700 chr7B 606364671 606369045 4374 False 927.000000 1578 97.072000 1 2718 2 chr7B.!!$F1 2717
14 TraesCS6B01G150700 chrUn 73439939 73442153 2214 False 835.500000 1020 96.184000 1 3396 2 chrUn.!!$F1 3395
15 TraesCS6B01G150700 chr3B 545830907 545831643 736 False 597.000000 597 82.031000 1760 2496 1 chr3B.!!$F1 736

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
974 1186 3.445008 ACCAAGATCAGCAGGACTAAGA 58.555 45.455 0.0 0.0 0.0 2.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2990 5536 1.045407 AGCTGAAGGTACGTGGACAA 58.955 50.0 0.0 0.0 0.0 3.18 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
199 201 6.173339 ACCAAATAGTGATGTCAGGTGTAAG 58.827 40.000 0.00 0.0 0.00 2.34
454 456 6.547880 TGTATTCAAGCTCCCAACAAAGTTAA 59.452 34.615 0.00 0.0 0.00 2.01
974 1186 3.445008 ACCAAGATCAGCAGGACTAAGA 58.555 45.455 0.00 0.0 0.00 2.10
1548 3913 4.537751 TCTGGGTTGTGTGGATTTGTTTA 58.462 39.130 0.00 0.0 0.00 2.01
2142 4534 4.698201 TGTTCTGGGTCTGATACAACAA 57.302 40.909 0.00 0.0 0.00 2.83
2988 5534 9.726438 ACTAATCAGTAGTCTTGTATGCTTTTT 57.274 29.630 0.00 0.0 38.84 1.94
3008 5554 1.873698 TTTGTCCACGTACCTTCAGC 58.126 50.000 0.00 0.0 0.00 4.26
3009 5555 1.045407 TTGTCCACGTACCTTCAGCT 58.955 50.000 0.00 0.0 0.00 4.24
3010 5556 1.045407 TGTCCACGTACCTTCAGCTT 58.955 50.000 0.00 0.0 0.00 3.74
3112 5658 7.605449 ACTCACCATTGGATCAAAACTATTTG 58.395 34.615 10.37 0.0 45.92 2.32
3224 5770 1.964223 CAGGCTATCCACCGTCTACAT 59.036 52.381 0.00 0.0 33.74 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
199 201 6.863126 CAGAAACCAACTATTGTTCATGGAAC 59.137 38.462 3.88 2.25 42.26 3.62
254 256 5.163258 CCTGCTTAGTCACCAATCCTAGAAT 60.163 44.000 0.00 0.00 0.00 2.40
1548 3913 8.846943 TTATCAGTAATTCGTTATGCATGGAT 57.153 30.769 10.16 4.68 0.00 3.41
2987 5533 2.614983 GCTGAAGGTACGTGGACAAAAA 59.385 45.455 0.00 0.00 0.00 1.94
2988 5534 2.158871 AGCTGAAGGTACGTGGACAAAA 60.159 45.455 0.00 0.00 0.00 2.44
2989 5535 1.414919 AGCTGAAGGTACGTGGACAAA 59.585 47.619 0.00 0.00 0.00 2.83
2990 5536 1.045407 AGCTGAAGGTACGTGGACAA 58.955 50.000 0.00 0.00 0.00 3.18
2991 5537 1.045407 AAGCTGAAGGTACGTGGACA 58.955 50.000 0.00 0.00 0.00 4.02
2992 5538 3.521947 ATAAGCTGAAGGTACGTGGAC 57.478 47.619 0.00 0.00 0.00 4.02
2993 5539 4.708421 ACTAATAAGCTGAAGGTACGTGGA 59.292 41.667 0.00 0.00 0.00 4.02
2994 5540 5.007385 ACTAATAAGCTGAAGGTACGTGG 57.993 43.478 0.00 0.00 0.00 4.94
2995 5541 6.034683 GTCAACTAATAAGCTGAAGGTACGTG 59.965 42.308 0.00 0.00 29.83 4.49
2996 5542 6.098017 GTCAACTAATAAGCTGAAGGTACGT 58.902 40.000 0.00 0.00 29.83 3.57
2997 5543 5.519206 GGTCAACTAATAAGCTGAAGGTACG 59.481 44.000 0.00 0.00 29.83 3.67
2998 5544 5.519206 CGGTCAACTAATAAGCTGAAGGTAC 59.481 44.000 0.00 0.00 29.83 3.34
2999 5545 5.186409 ACGGTCAACTAATAAGCTGAAGGTA 59.814 40.000 0.00 0.00 29.83 3.08
3000 5546 4.020485 ACGGTCAACTAATAAGCTGAAGGT 60.020 41.667 0.00 0.00 29.83 3.50
3001 5547 4.504858 ACGGTCAACTAATAAGCTGAAGG 58.495 43.478 0.00 0.00 29.83 3.46
3002 5548 6.481954 AAACGGTCAACTAATAAGCTGAAG 57.518 37.500 0.00 0.00 29.83 3.02
3003 5549 6.930164 TGTAAACGGTCAACTAATAAGCTGAA 59.070 34.615 0.00 0.00 29.83 3.02
3004 5550 6.457355 TGTAAACGGTCAACTAATAAGCTGA 58.543 36.000 0.00 0.00 0.00 4.26
3005 5551 6.715344 TGTAAACGGTCAACTAATAAGCTG 57.285 37.500 0.00 0.00 0.00 4.24
3006 5552 6.877322 ACATGTAAACGGTCAACTAATAAGCT 59.123 34.615 0.00 0.00 0.00 3.74
3007 5553 7.068692 ACATGTAAACGGTCAACTAATAAGC 57.931 36.000 0.00 0.00 0.00 3.09
3008 5554 9.325150 CAAACATGTAAACGGTCAACTAATAAG 57.675 33.333 0.00 0.00 0.00 1.73
3009 5555 9.053840 TCAAACATGTAAACGGTCAACTAATAA 57.946 29.630 0.00 0.00 0.00 1.40
3010 5556 8.604640 TCAAACATGTAAACGGTCAACTAATA 57.395 30.769 0.00 0.00 0.00 0.98
3224 5770 3.054139 AGCATCCTTTGTGAATCCTGCTA 60.054 43.478 0.00 0.00 36.98 3.49


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

AutoCloner maintained by Alex Coulton.