Multiple sequence alignment - TraesCS7A01G092200

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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 TraesCS7A01G092200 chr7A 100.000 2375 0 0 1 2375 56073899 56076273 0.000000e+00 4386.0
1 TraesCS7A01G092200 chr2A 96.089 2327 70 8 1 2324 610789242 610791550 0.000000e+00 3773.0
2 TraesCS7A01G092200 chr2A 91.885 764 53 6 1567 2327 442545682 442544925 0.000000e+00 1059.0
3 TraesCS7A01G092200 chr2A 92.754 69 4 1 2308 2375 298386718 298386650 5.400000e-17 99.0
4 TraesCS7A01G092200 chr4D 93.755 2354 113 11 1 2328 236672657 236670312 0.000000e+00 3502.0
5 TraesCS7A01G092200 chr4D 86.639 1437 119 29 905 2328 239784686 239783310 0.000000e+00 1522.0
6 TraesCS7A01G092200 chr4D 93.535 727 34 2 901 1614 125802840 125802114 0.000000e+00 1070.0
7 TraesCS7A01G092200 chr4D 89.891 643 32 15 901 1542 261222784 261222174 0.000000e+00 797.0
8 TraesCS7A01G092200 chr4D 89.368 348 17 13 1491 1828 125802203 125801866 1.020000e-113 420.0
9 TraesCS7A01G092200 chr4D 92.641 231 11 2 1390 1614 125903980 125903750 6.330000e-86 327.0
10 TraesCS7A01G092200 chr4D 93.671 79 1 1 1435 1513 196955416 196955490 5.360000e-22 115.0
11 TraesCS7A01G092200 chr1D 93.473 2344 117 21 1 2324 463793643 463791316 0.000000e+00 3448.0
12 TraesCS7A01G092200 chr2D 92.223 2366 111 24 1 2324 645236663 645234329 0.000000e+00 3282.0
13 TraesCS7A01G092200 chr4A 92.413 2346 96 31 1 2324 129030524 129032809 0.000000e+00 3271.0
14 TraesCS7A01G092200 chr4A 95.543 920 37 4 1 918 433607523 433606606 0.000000e+00 1469.0
15 TraesCS7A01G092200 chr4A 92.424 66 3 2 2311 2375 541714325 541714389 2.510000e-15 93.5
16 TraesCS7A01G092200 chr5A 92.088 2351 131 13 1 2324 235675095 235677417 0.000000e+00 3260.0
17 TraesCS7A01G092200 chr5A 92.537 67 2 3 2311 2375 49137863 49137928 2.510000e-15 93.5
18 TraesCS7A01G092200 chr5B 93.402 2122 80 24 1 2114 56336221 56338290 0.000000e+00 3088.0
19 TraesCS7A01G092200 chr5B 92.424 66 4 1 2311 2375 606210322 606210387 2.510000e-15 93.5
20 TraesCS7A01G092200 chr5B 92.424 66 4 1 2311 2375 694740490 694740555 2.510000e-15 93.5
21 TraesCS7A01G092200 chr3B 90.283 2223 155 35 1 2212 753431277 753429105 0.000000e+00 2852.0
22 TraesCS7A01G092200 chr2B 88.870 2363 198 47 1 2324 149803143 149805479 0.000000e+00 2846.0
23 TraesCS7A01G092200 chr2B 93.548 62 3 1 2315 2375 52011338 52011277 9.040000e-15 91.6
24 TraesCS7A01G092200 chr5D 93.733 1452 56 13 904 2326 384511181 384509736 0.000000e+00 2145.0
25 TraesCS7A01G092200 chr5D 91.757 1468 73 17 901 2325 140952322 140950860 0.000000e+00 1997.0
26 TraesCS7A01G092200 chr5D 91.757 1468 71 14 901 2325 29766743 29765283 0.000000e+00 1995.0
27 TraesCS7A01G092200 chr5D 96.746 922 30 0 1 922 384512118 384511197 0.000000e+00 1537.0
28 TraesCS7A01G092200 chr7D 91.162 1584 82 22 1 1557 501764135 501765687 0.000000e+00 2097.0
29 TraesCS7A01G092200 chr6D 92.764 1451 68 20 901 2324 297170564 297169124 0.000000e+00 2063.0
30 TraesCS7A01G092200 chr6D 92.436 1441 60 32 904 2328 446363468 446362061 0.000000e+00 2012.0
31 TraesCS7A01G092200 chr6D 95.879 922 38 0 1 922 297171498 297170577 0.000000e+00 1493.0
32 TraesCS7A01G092200 chr3A 93.157 833 52 3 546 1375 706571677 706570847 0.000000e+00 1218.0
33 TraesCS7A01G092200 chr7B 89.588 874 78 11 1459 2324 551236441 551237309 0.000000e+00 1098.0
34 TraesCS7A01G092200 chr3D 92.063 63 5 0 2313 2375 157009308 157009246 3.250000e-14 89.8
35 TraesCS7A01G092200 chr6A 90.909 66 5 1 2311 2375 552273511 552273576 1.170000e-13 87.9
36 TraesCS7A01G092200 chr1A 92.063 63 4 1 2314 2375 80957181 80957119 1.170000e-13 87.9


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 TraesCS7A01G092200 chr7A 56073899 56076273 2374 False 4386 4386 100.0000 1 2375 1 chr7A.!!$F1 2374
1 TraesCS7A01G092200 chr2A 610789242 610791550 2308 False 3773 3773 96.0890 1 2324 1 chr2A.!!$F1 2323
2 TraesCS7A01G092200 chr2A 442544925 442545682 757 True 1059 1059 91.8850 1567 2327 1 chr2A.!!$R2 760
3 TraesCS7A01G092200 chr4D 236670312 236672657 2345 True 3502 3502 93.7550 1 2328 1 chr4D.!!$R2 2327
4 TraesCS7A01G092200 chr4D 239783310 239784686 1376 True 1522 1522 86.6390 905 2328 1 chr4D.!!$R3 1423
5 TraesCS7A01G092200 chr4D 261222174 261222784 610 True 797 797 89.8910 901 1542 1 chr4D.!!$R4 641
6 TraesCS7A01G092200 chr4D 125801866 125802840 974 True 745 1070 91.4515 901 1828 2 chr4D.!!$R5 927
7 TraesCS7A01G092200 chr1D 463791316 463793643 2327 True 3448 3448 93.4730 1 2324 1 chr1D.!!$R1 2323
8 TraesCS7A01G092200 chr2D 645234329 645236663 2334 True 3282 3282 92.2230 1 2324 1 chr2D.!!$R1 2323
9 TraesCS7A01G092200 chr4A 129030524 129032809 2285 False 3271 3271 92.4130 1 2324 1 chr4A.!!$F1 2323
10 TraesCS7A01G092200 chr4A 433606606 433607523 917 True 1469 1469 95.5430 1 918 1 chr4A.!!$R1 917
11 TraesCS7A01G092200 chr5A 235675095 235677417 2322 False 3260 3260 92.0880 1 2324 1 chr5A.!!$F2 2323
12 TraesCS7A01G092200 chr5B 56336221 56338290 2069 False 3088 3088 93.4020 1 2114 1 chr5B.!!$F1 2113
13 TraesCS7A01G092200 chr3B 753429105 753431277 2172 True 2852 2852 90.2830 1 2212 1 chr3B.!!$R1 2211
14 TraesCS7A01G092200 chr2B 149803143 149805479 2336 False 2846 2846 88.8700 1 2324 1 chr2B.!!$F1 2323
15 TraesCS7A01G092200 chr5D 140950860 140952322 1462 True 1997 1997 91.7570 901 2325 1 chr5D.!!$R2 1424
16 TraesCS7A01G092200 chr5D 29765283 29766743 1460 True 1995 1995 91.7570 901 2325 1 chr5D.!!$R1 1424
17 TraesCS7A01G092200 chr5D 384509736 384512118 2382 True 1841 2145 95.2395 1 2326 2 chr5D.!!$R3 2325
18 TraesCS7A01G092200 chr7D 501764135 501765687 1552 False 2097 2097 91.1620 1 1557 1 chr7D.!!$F1 1556
19 TraesCS7A01G092200 chr6D 446362061 446363468 1407 True 2012 2012 92.4360 904 2328 1 chr6D.!!$R1 1424
20 TraesCS7A01G092200 chr6D 297169124 297171498 2374 True 1778 2063 94.3215 1 2324 2 chr6D.!!$R2 2323
21 TraesCS7A01G092200 chr3A 706570847 706571677 830 True 1218 1218 93.1570 546 1375 1 chr3A.!!$R1 829
22 TraesCS7A01G092200 chr7B 551236441 551237309 868 False 1098 1098 89.5880 1459 2324 1 chr7B.!!$F1 865

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
743 804 0.758734 TGATCGGCTCAATCGGGAAT 59.241 50.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2343 2662 0.108138 CTTTGCTCTACTGGACGGGG 60.108 60.0 0.0 0.0 0.0 5.73 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
70 71 1.115467 GTCCCAGATCTGACGGATGT 58.885 55.000 24.62 0.00 34.33 3.06
105 106 1.078823 TGGTGGAGATGTGGTCTACCT 59.921 52.381 7.11 0.00 36.93 3.08
322 324 7.011382 AGAACTTTTCTCTAGAGACCTTACCA 58.989 38.462 22.25 2.83 37.14 3.25
340 342 7.069085 ACCTTACCATTTGATCCTCATTGAATG 59.931 37.037 0.00 0.00 0.00 2.67
551 582 6.071221 TGTTTGATTCATAGCCAGCTTTGATT 60.071 34.615 12.58 9.65 34.84 2.57
599 658 4.338118 TGTTGTTTGATTCAGAACCAGTCC 59.662 41.667 8.33 0.00 0.00 3.85
743 804 0.758734 TGATCGGCTCAATCGGGAAT 59.241 50.000 0.00 0.00 0.00 3.01
801 863 7.800155 TGAAGCGATCATATTGTTCCAATTA 57.200 32.000 0.00 0.00 31.50 1.40
819 881 3.961480 TTACATGTCTCCAGGTCACAG 57.039 47.619 0.00 0.00 36.83 3.66
1108 1217 1.536766 TCAAGCAAAGCACATTCCTCG 59.463 47.619 0.00 0.00 0.00 4.63
1244 1353 3.191371 GTGATTCAAGAAGAATTGGCGGT 59.809 43.478 0.00 0.00 46.76 5.68
1378 1487 4.101114 TGGAGCTAAGGTAGTTTGATGGA 58.899 43.478 0.00 0.00 0.00 3.41
1535 1719 0.991920 GGGATCTTGTGAACCTGGGA 59.008 55.000 0.00 0.00 35.70 4.37
1754 2037 2.675658 TGACTAAAAAGGCTTGGGCT 57.324 45.000 0.00 0.00 41.24 5.19
1908 2201 3.102204 CAGAAAAAGGCTCCATTCCCAT 58.898 45.455 0.00 0.00 0.00 4.00
1969 2265 5.933463 AGATGAGCAAAACAAAGAGAGAGAG 59.067 40.000 0.00 0.00 0.00 3.20
2079 2385 2.806244 GTTGTAATTCTGCCACGTCAGT 59.194 45.455 4.38 0.00 35.63 3.41
2094 2400 0.888736 TCAGTTTGCCACGGTGGATG 60.889 55.000 30.65 18.03 40.96 3.51
2216 2524 7.765307 AGGTCATTAATTCTAGTTTACGACGA 58.235 34.615 0.00 0.00 0.00 4.20
2220 2528 8.192774 TCATTAATTCTAGTTTACGACGACCAT 58.807 33.333 0.00 0.00 0.00 3.55
2328 2647 7.445402 AGTTGACATATTTCTTGTAGTGCTTGT 59.555 33.333 0.00 0.00 0.00 3.16
2329 2648 7.744087 TGACATATTTCTTGTAGTGCTTGTT 57.256 32.000 0.00 0.00 0.00 2.83
2330 2649 7.806690 TGACATATTTCTTGTAGTGCTTGTTC 58.193 34.615 0.00 0.00 0.00 3.18
2331 2650 6.831769 ACATATTTCTTGTAGTGCTTGTTCG 58.168 36.000 0.00 0.00 0.00 3.95
2332 2651 4.749245 ATTTCTTGTAGTGCTTGTTCGG 57.251 40.909 0.00 0.00 0.00 4.30
2333 2652 2.163818 TCTTGTAGTGCTTGTTCGGG 57.836 50.000 0.00 0.00 0.00 5.14
2334 2653 1.156736 CTTGTAGTGCTTGTTCGGGG 58.843 55.000 0.00 0.00 0.00 5.73
2335 2654 0.470766 TTGTAGTGCTTGTTCGGGGT 59.529 50.000 0.00 0.00 0.00 4.95
2336 2655 1.340088 TGTAGTGCTTGTTCGGGGTA 58.660 50.000 0.00 0.00 0.00 3.69
2337 2656 1.903860 TGTAGTGCTTGTTCGGGGTAT 59.096 47.619 0.00 0.00 0.00 2.73
2338 2657 2.093869 TGTAGTGCTTGTTCGGGGTATC 60.094 50.000 0.00 0.00 0.00 2.24
2339 2658 1.276622 AGTGCTTGTTCGGGGTATCT 58.723 50.000 0.00 0.00 0.00 1.98
2340 2659 1.628846 AGTGCTTGTTCGGGGTATCTT 59.371 47.619 0.00 0.00 0.00 2.40
2341 2660 2.007608 GTGCTTGTTCGGGGTATCTTC 58.992 52.381 0.00 0.00 0.00 2.87
2342 2661 1.626321 TGCTTGTTCGGGGTATCTTCA 59.374 47.619 0.00 0.00 0.00 3.02
2343 2662 2.007608 GCTTGTTCGGGGTATCTTCAC 58.992 52.381 0.00 0.00 0.00 3.18
2344 2663 2.629051 CTTGTTCGGGGTATCTTCACC 58.371 52.381 0.00 0.00 37.91 4.02
2351 2670 2.599216 GGTATCTTCACCCCGTCCA 58.401 57.895 0.00 0.00 31.91 4.02
2352 2671 0.464452 GGTATCTTCACCCCGTCCAG 59.536 60.000 0.00 0.00 31.91 3.86
2353 2672 1.192428 GTATCTTCACCCCGTCCAGT 58.808 55.000 0.00 0.00 0.00 4.00
2354 2673 2.381911 GTATCTTCACCCCGTCCAGTA 58.618 52.381 0.00 0.00 0.00 2.74
2355 2674 1.486211 ATCTTCACCCCGTCCAGTAG 58.514 55.000 0.00 0.00 0.00 2.57
2356 2675 0.406750 TCTTCACCCCGTCCAGTAGA 59.593 55.000 0.00 0.00 0.00 2.59
2357 2676 0.818296 CTTCACCCCGTCCAGTAGAG 59.182 60.000 0.00 0.00 0.00 2.43
2358 2677 1.255667 TTCACCCCGTCCAGTAGAGC 61.256 60.000 0.00 0.00 0.00 4.09
2359 2678 1.982395 CACCCCGTCCAGTAGAGCA 60.982 63.158 0.00 0.00 0.00 4.26
2360 2679 1.229082 ACCCCGTCCAGTAGAGCAA 60.229 57.895 0.00 0.00 0.00 3.91
2361 2680 0.834687 ACCCCGTCCAGTAGAGCAAA 60.835 55.000 0.00 0.00 0.00 3.68
2362 2681 0.108138 CCCCGTCCAGTAGAGCAAAG 60.108 60.000 0.00 0.00 0.00 2.77
2363 2682 0.895530 CCCGTCCAGTAGAGCAAAGA 59.104 55.000 0.00 0.00 0.00 2.52
2364 2683 1.482593 CCCGTCCAGTAGAGCAAAGAT 59.517 52.381 0.00 0.00 0.00 2.40
2365 2684 2.093447 CCCGTCCAGTAGAGCAAAGATT 60.093 50.000 0.00 0.00 0.00 2.40
2366 2685 3.600388 CCGTCCAGTAGAGCAAAGATTT 58.400 45.455 0.00 0.00 0.00 2.17
2367 2686 3.372206 CCGTCCAGTAGAGCAAAGATTTG 59.628 47.826 0.84 0.84 41.03 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 71 1.250328 CACCAGAGCTTGCCATTCAA 58.750 50.000 0.00 0.0 0.00 2.69
222 224 5.749588 TGTACACGACTTTTTCTCGATTCAA 59.250 36.000 0.00 0.0 35.08 2.69
340 342 8.239314 TGTTATTCAGCAAGAATCAGAAATGTC 58.761 33.333 7.57 0.0 43.42 3.06
551 582 6.983984 TCAAATCATCAAAGCATCAAACAGA 58.016 32.000 0.00 0.0 0.00 3.41
743 804 8.742125 AGAATGGTGGTTCTATATAAGATGGA 57.258 34.615 0.00 0.0 36.71 3.41
801 863 2.015456 TCTGTGACCTGGAGACATGT 57.985 50.000 0.00 0.0 42.24 3.21
819 881 9.151471 TGACAGCATTATTTGACTAGTAACTTC 57.849 33.333 0.00 0.0 0.00 3.01
1108 1217 0.681243 GACTGGAGCCCAACATTCCC 60.681 60.000 0.00 0.0 30.80 3.97
1227 1336 4.584874 TGATTACCGCCAATTCTTCTTGA 58.415 39.130 0.00 0.0 0.00 3.02
1244 1353 4.753516 TCTTCCGCCTTCATCTTGATTA 57.246 40.909 0.00 0.0 0.00 1.75
1302 1411 1.069204 TGCTCTTGAGACTTCTTGCGT 59.931 47.619 1.30 0.0 0.00 5.24
1378 1487 7.936847 TCATAGGTTCAAAGACAAACTACACAT 59.063 33.333 0.00 0.0 0.00 3.21
1535 1719 0.109342 CTCCCAGGTTCACAAGTGCT 59.891 55.000 0.00 0.0 0.00 4.40
1969 2265 8.839343 CCCAATAATTCAGCCCATTTAATTTTC 58.161 33.333 0.00 0.0 0.00 2.29
2079 2385 1.149401 TCACATCCACCGTGGCAAA 59.851 52.632 13.19 0.0 37.47 3.68
2196 2504 8.411683 AGATGGTCGTCGTAAACTAGAATTAAT 58.588 33.333 0.00 0.0 0.00 1.40
2216 2524 5.675684 AAAACAGTTGGTCAAAAGATGGT 57.324 34.783 0.00 0.0 0.00 3.55
2333 2652 0.464452 CTGGACGGGGTGAAGATACC 59.536 60.000 0.00 0.0 40.10 2.73
2334 2653 1.192428 ACTGGACGGGGTGAAGATAC 58.808 55.000 0.00 0.0 0.00 2.24
2335 2654 2.242965 TCTACTGGACGGGGTGAAGATA 59.757 50.000 0.00 0.0 0.00 1.98
2336 2655 1.006758 TCTACTGGACGGGGTGAAGAT 59.993 52.381 0.00 0.0 0.00 2.40
2337 2656 0.406750 TCTACTGGACGGGGTGAAGA 59.593 55.000 0.00 0.0 0.00 2.87
2338 2657 0.818296 CTCTACTGGACGGGGTGAAG 59.182 60.000 0.00 0.0 0.00 3.02
2339 2658 1.255667 GCTCTACTGGACGGGGTGAA 61.256 60.000 0.00 0.0 0.00 3.18
2340 2659 1.681327 GCTCTACTGGACGGGGTGA 60.681 63.158 0.00 0.0 0.00 4.02
2341 2660 1.541310 TTGCTCTACTGGACGGGGTG 61.541 60.000 0.00 0.0 0.00 4.61
2342 2661 0.834687 TTTGCTCTACTGGACGGGGT 60.835 55.000 0.00 0.0 0.00 4.95
2343 2662 0.108138 CTTTGCTCTACTGGACGGGG 60.108 60.000 0.00 0.0 0.00 5.73
2344 2663 0.895530 TCTTTGCTCTACTGGACGGG 59.104 55.000 0.00 0.0 0.00 5.28
2345 2664 2.969628 ATCTTTGCTCTACTGGACGG 57.030 50.000 0.00 0.0 0.00 4.79
2346 2665 4.590400 CAAATCTTTGCTCTACTGGACG 57.410 45.455 0.00 0.0 0.00 4.79


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

AutoCloner maintained by Alex Coulton.