Multiple sequence alignment - TraesCS3B01G063300

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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 TraesCS3B01G063300 chr3B 100.000 2297 0 0 1 2297 35516977 35519273 0.000000e+00 4242.0
1 TraesCS3B01G063300 chr3B 93.542 1471 68 7 3 1473 35457952 35459395 0.000000e+00 2165.0
2 TraesCS3B01G063300 chr3B 97.185 817 21 2 1482 2297 34516336 34515521 0.000000e+00 1380.0
3 TraesCS3B01G063300 chr3B 96.450 817 28 1 1482 2297 35479292 35480108 0.000000e+00 1347.0
4 TraesCS3B01G063300 chr3B 96.459 819 24 3 1482 2297 35650540 35651356 0.000000e+00 1347.0
5 TraesCS3B01G063300 chr3B 96.337 819 25 3 1482 2297 35584602 35585418 0.000000e+00 1341.0
6 TraesCS3B01G063300 chr3B 92.121 825 45 10 666 1470 35570780 35571604 0.000000e+00 1146.0
7 TraesCS3B01G063300 chr3B 92.327 808 39 8 670 1472 34470571 34469782 0.000000e+00 1127.0
8 TraesCS3B01G063300 chr3B 95.082 671 31 2 3 672 35545682 35546351 0.000000e+00 1055.0
9 TraesCS3B01G063300 chr3B 94.776 670 35 0 3 672 35729012 35729681 0.000000e+00 1044.0
10 TraesCS3B01G063300 chr3B 94.776 670 35 0 3 672 35800702 35801371 0.000000e+00 1044.0
11 TraesCS3B01G063300 chr3B 94.478 670 37 0 3 672 34543372 34542703 0.000000e+00 1033.0
12 TraesCS3B01G063300 chr3B 94.039 671 38 2 3 672 34489225 34488556 0.000000e+00 1016.0
13 TraesCS3B01G063300 chr3B 92.368 642 31 6 832 1473 35732068 35732691 0.000000e+00 898.0
14 TraesCS3B01G063300 chr3B 92.579 539 37 3 1482 2019 34461777 34461241 0.000000e+00 771.0
15 TraesCS3B01G063300 chr3B 93.980 299 16 2 1177 1473 35695047 35695345 3.480000e-123 451.0
16 TraesCS3B01G063300 chr3B 95.406 283 12 1 670 951 34525700 34525418 1.250000e-122 449.0
17 TraesCS3B01G063300 chr3B 94.771 153 8 0 670 822 35731368 35731520 2.950000e-59 239.0
18 TraesCS3B01G063300 chr3B 94.805 77 4 0 670 746 99279183 99279259 1.110000e-23 121.0
19 TraesCS3B01G063300 chr3B 94.286 70 4 0 670 739 35803058 35803127 8.680000e-20 108.0
20 TraesCS3B01G063300 chrUn 98.409 817 12 1 1482 2297 168706094 168705278 0.000000e+00 1435.0
21 TraesCS3B01G063300 chrUn 97.797 817 17 1 1482 2297 419123118 419123934 0.000000e+00 1408.0
22 TraesCS3B01G063300 chrUn 94.321 810 40 5 670 1473 296042006 296041197 0.000000e+00 1236.0
23 TraesCS3B01G063300 chrUn 94.154 804 43 3 672 1473 265761374 265762175 0.000000e+00 1221.0
24 TraesCS3B01G063300 chrUn 94.569 626 31 2 849 1473 389921898 389921275 0.000000e+00 965.0
25 TraesCS3B01G063300 chrUn 95.618 502 22 0 171 672 377176741 377177242 0.000000e+00 806.0
26 TraesCS3B01G063300 chrUn 96.486 370 9 4 819 1186 205343600 205343233 1.950000e-170 608.0
27 TraesCS3B01G063300 chrUn 96.216 370 10 4 819 1186 168657548 168657181 9.080000e-169 603.0
28 TraesCS3B01G063300 chrUn 87.927 439 41 3 1804 2242 44556800 44556374 7.320000e-140 507.0
29 TraesCS3B01G063300 chrUn 94.769 325 17 0 3 327 202809178 202808854 7.320000e-140 507.0
30 TraesCS3B01G063300 chrUn 94.769 325 17 0 3 327 241048759 241048435 7.320000e-140 507.0
31 TraesCS3B01G063300 chrUn 86.547 446 47 4 1797 2242 44289090 44289522 1.600000e-131 479.0
32 TraesCS3B01G063300 chrUn 94.667 300 14 1 1174 1473 477392323 477392620 4.470000e-127 464.0
33 TraesCS3B01G063300 chrUn 85.237 359 44 4 1575 1925 282845219 282844862 6.030000e-96 361.0
34 TraesCS3B01G063300 chrUn 85.237 359 44 4 1575 1925 282851945 282851588 6.030000e-96 361.0
35 TraesCS3B01G063300 chrUn 95.181 83 3 1 1482 1563 338662564 338662646 1.850000e-26 130.0
36 TraesCS3B01G063300 chrUn 95.181 83 3 1 1482 1563 390052158 390052076 1.850000e-26 130.0
37 TraesCS3B01G063300 chr7B 88.439 346 40 0 176 521 334197373 334197028 3.530000e-113 418.0
38 TraesCS3B01G063300 chr5A 98.182 55 1 0 2243 2297 1337894 1337948 1.880000e-16 97.1
39 TraesCS3B01G063300 chr1D 98.182 55 1 0 2243 2297 470555175 470555121 1.880000e-16 97.1
40 TraesCS3B01G063300 chr1A 98.182 55 1 0 2243 2297 44363355 44363409 1.880000e-16 97.1


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 TraesCS3B01G063300 chr3B 35516977 35519273 2296 False 4242 4242 100.000000 1 2297 1 chr3B.!!$F3 2296
1 TraesCS3B01G063300 chr3B 35457952 35459395 1443 False 2165 2165 93.542000 3 1473 1 chr3B.!!$F1 1470
2 TraesCS3B01G063300 chr3B 34515521 34516336 815 True 1380 1380 97.185000 1482 2297 1 chr3B.!!$R4 815
3 TraesCS3B01G063300 chr3B 35479292 35480108 816 False 1347 1347 96.450000 1482 2297 1 chr3B.!!$F2 815
4 TraesCS3B01G063300 chr3B 35650540 35651356 816 False 1347 1347 96.459000 1482 2297 1 chr3B.!!$F7 815
5 TraesCS3B01G063300 chr3B 35584602 35585418 816 False 1341 1341 96.337000 1482 2297 1 chr3B.!!$F6 815
6 TraesCS3B01G063300 chr3B 35570780 35571604 824 False 1146 1146 92.121000 666 1470 1 chr3B.!!$F5 804
7 TraesCS3B01G063300 chr3B 34469782 34470571 789 True 1127 1127 92.327000 670 1472 1 chr3B.!!$R2 802
8 TraesCS3B01G063300 chr3B 35545682 35546351 669 False 1055 1055 95.082000 3 672 1 chr3B.!!$F4 669
9 TraesCS3B01G063300 chr3B 34542703 34543372 669 True 1033 1033 94.478000 3 672 1 chr3B.!!$R6 669
10 TraesCS3B01G063300 chr3B 34488556 34489225 669 True 1016 1016 94.039000 3 672 1 chr3B.!!$R3 669
11 TraesCS3B01G063300 chr3B 34461241 34461777 536 True 771 771 92.579000 1482 2019 1 chr3B.!!$R1 537
12 TraesCS3B01G063300 chr3B 35729012 35732691 3679 False 727 1044 93.971667 3 1473 3 chr3B.!!$F10 1470
13 TraesCS3B01G063300 chr3B 35800702 35803127 2425 False 576 1044 94.531000 3 739 2 chr3B.!!$F11 736
14 TraesCS3B01G063300 chrUn 168705278 168706094 816 True 1435 1435 98.409000 1482 2297 1 chrUn.!!$R3 815
15 TraesCS3B01G063300 chrUn 419123118 419123934 816 False 1408 1408 97.797000 1482 2297 1 chrUn.!!$F5 815
16 TraesCS3B01G063300 chrUn 296041197 296042006 809 True 1236 1236 94.321000 670 1473 1 chrUn.!!$R9 803
17 TraesCS3B01G063300 chrUn 265761374 265762175 801 False 1221 1221 94.154000 672 1473 1 chrUn.!!$F2 801
18 TraesCS3B01G063300 chrUn 389921275 389921898 623 True 965 965 94.569000 849 1473 1 chrUn.!!$R10 624
19 TraesCS3B01G063300 chrUn 377176741 377177242 501 False 806 806 95.618000 171 672 1 chrUn.!!$F4 501

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
51 52 0.456221 CGCTGTCCATAGTCGACCTT 59.544 55.0 13.01 0.0 0.0 3.5 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1344 3587 0.167908 GTGTGTGTGTGTGTGTGTGG 59.832 55.0 0.0 0.0 0.0 4.17 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
51 52 0.456221 CGCTGTCCATAGTCGACCTT 59.544 55.000 13.01 0.00 0.00 3.50
120 122 1.400846 CCAGATCACATCAGCACAAGC 59.599 52.381 0.00 0.00 42.56 4.01
204 206 4.672587 AGCTCCAAGAATTACGCTATCA 57.327 40.909 0.00 0.00 0.00 2.15
407 409 3.947132 GCAGCAGAGAGCCGCAAGA 62.947 63.158 0.00 0.00 46.01 3.02
561 563 1.777878 TGCCAAACTGGAAGACCCTTA 59.222 47.619 0.00 0.00 40.96 2.69
576 578 8.364894 GGAAGACCCTTACATGTGTTTTATTTT 58.635 33.333 9.11 0.00 0.00 1.82
705 2396 5.212532 TCAAAATTGCTTAGTTGGCATGT 57.787 34.783 0.00 0.00 39.54 3.21
733 2424 8.398743 TGATACTACCTATGATACTCCCATTGA 58.601 37.037 0.00 0.00 0.00 2.57
784 2475 4.699735 TCGTAAATGCACTCAATTCCATGT 59.300 37.500 0.00 0.00 0.00 3.21
804 2495 5.408880 TGTCCGGTCACTTGTATTAATCA 57.591 39.130 0.00 0.00 0.00 2.57
816 2507 8.450180 CACTTGTATTAATCAGTTGTGCATACA 58.550 33.333 0.00 0.00 34.31 2.29
891 3121 2.698797 CCTCCCGGTACAATCACATAGT 59.301 50.000 0.00 0.00 0.00 2.12
1034 3265 3.592814 CGACGCGGCCATCTCCTA 61.593 66.667 12.47 0.00 0.00 2.94
1104 3335 3.370231 GGCGCCAACCCGATTGTT 61.370 61.111 24.80 0.00 36.47 2.83
1218 3449 2.314647 GCTCAACGCTGGCAACGTA 61.315 57.895 17.02 0.75 44.30 3.57
1321 3554 2.107378 ACCAATGGTCACCATGTGTACA 59.893 45.455 11.08 0.00 44.40 2.90
1344 3587 1.822186 GGTCACACCCACACACACC 60.822 63.158 0.00 0.00 30.04 4.16
1366 3617 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1442 3693 0.985490 GAAGAGGAGCAGGTGGGGAT 60.985 60.000 0.00 0.00 0.00 3.85
1473 3724 1.002011 GAAGTTGGAGGGGGAGCAC 60.002 63.158 0.00 0.00 0.00 4.40
1474 3725 1.774217 AAGTTGGAGGGGGAGCACA 60.774 57.895 0.00 0.00 0.00 4.57
1475 3726 1.360393 AAGTTGGAGGGGGAGCACAA 61.360 55.000 0.00 0.00 0.00 3.33
1476 3727 1.603739 GTTGGAGGGGGAGCACAAC 60.604 63.158 0.00 0.00 35.28 3.32
1477 3728 2.081787 TTGGAGGGGGAGCACAACA 61.082 57.895 0.00 0.00 0.00 3.33
1478 3729 1.650242 TTGGAGGGGGAGCACAACAA 61.650 55.000 0.00 0.00 0.00 2.83
1479 3730 1.303643 GGAGGGGGAGCACAACAAG 60.304 63.158 0.00 0.00 0.00 3.16
1480 3731 1.761174 GAGGGGGAGCACAACAAGA 59.239 57.895 0.00 0.00 0.00 3.02
1481 3732 0.329596 GAGGGGGAGCACAACAAGAT 59.670 55.000 0.00 0.00 0.00 2.40
1482 3733 1.559682 GAGGGGGAGCACAACAAGATA 59.440 52.381 0.00 0.00 0.00 1.98
1483 3734 2.173569 GAGGGGGAGCACAACAAGATAT 59.826 50.000 0.00 0.00 0.00 1.63
1484 3735 2.582636 AGGGGGAGCACAACAAGATATT 59.417 45.455 0.00 0.00 0.00 1.28
1485 3736 3.011708 AGGGGGAGCACAACAAGATATTT 59.988 43.478 0.00 0.00 0.00 1.40
1486 3737 3.769300 GGGGGAGCACAACAAGATATTTT 59.231 43.478 0.00 0.00 0.00 1.82
1489 3740 6.461509 GGGGGAGCACAACAAGATATTTTATG 60.462 42.308 0.00 0.00 0.00 1.90
1845 4098 7.065324 TCGTGAGACTAACTTTCACAAATTTGT 59.935 33.333 18.13 18.13 40.88 2.83
2070 4325 6.469782 AAGACACATTTTGAAGACATTGGT 57.530 33.333 0.00 0.00 0.00 3.67
2217 4474 2.894126 ACCAAAATAACATGGGCGTGAA 59.106 40.909 0.00 0.00 41.17 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.056313 GCCGAAACCTGCCTCATGC 62.056 63.158 0.00 0.00 41.77 4.06
1 2 2.753966 CGCCGAAACCTGCCTCATG 61.754 63.158 0.00 0.00 0.00 3.07
51 52 3.893763 CGTTTGGTTGGCGGTGCA 61.894 61.111 0.00 0.00 0.00 4.57
196 198 0.105593 CTCCATGCCAGTGATAGCGT 59.894 55.000 0.00 0.00 0.00 5.07
204 206 3.341629 CACCCCCTCCATGCCAGT 61.342 66.667 0.00 0.00 0.00 4.00
232 234 3.988525 GCAACGCATGGGTTGGCA 61.989 61.111 39.95 0.00 45.72 4.92
234 236 2.768503 CTTGGCAACGCATGGGTTGG 62.769 60.000 39.95 26.88 45.72 3.77
328 330 2.341875 TGGATCGACGGCCGTAACA 61.342 57.895 34.36 21.80 39.75 2.41
330 332 2.491152 GTGGATCGACGGCCGTAA 59.509 61.111 34.36 23.32 39.75 3.18
407 409 1.207570 CATGAGAGTCAGAGCCTTGCT 59.792 52.381 0.00 0.00 43.88 3.91
423 425 3.700539 CTGTAAATGCCCATTCCACATGA 59.299 43.478 0.00 0.00 30.40 3.07
561 563 5.776173 TCCCGTCAAAATAAAACACATGT 57.224 34.783 0.00 0.00 0.00 3.21
733 2424 3.217626 GCTTGATTACTAATGCTGCCCT 58.782 45.455 0.00 0.00 0.00 5.19
784 2475 5.670792 ACTGATTAATACAAGTGACCGGA 57.329 39.130 9.46 0.00 0.00 5.14
804 2495 1.075374 ACCCATGGTGTATGCACAACT 59.925 47.619 16.11 0.00 46.95 3.16
891 3121 8.255111 TGAAGATGATAAGAAGGCTAGATTCA 57.745 34.615 9.88 0.00 0.00 2.57
981 3211 2.294170 TAGCTAGCGGCCACTAGGGT 62.294 60.000 25.56 15.50 43.05 4.34
1034 3265 1.007721 AGGTAGAGCTCACCTGTCCAT 59.992 52.381 27.00 10.35 44.89 3.41
1218 3449 0.693049 ACTTGAAGGGAATGTCGGCT 59.307 50.000 0.00 0.00 0.00 5.52
1321 3554 0.843309 TGTGTGGGTGTGACCTCAAT 59.157 50.000 0.00 0.00 38.64 2.57
1344 3587 0.167908 GTGTGTGTGTGTGTGTGTGG 59.832 55.000 0.00 0.00 0.00 4.17
1387 3638 1.059006 GCCACCTCCTCCTCCATGAT 61.059 60.000 0.00 0.00 0.00 2.45
1442 3693 1.553417 CCAACTTCTCCTCCTCCTCCA 60.553 57.143 0.00 0.00 0.00 3.86
1473 3724 9.811655 CCTACGCATACATAAAATATCTTGTTG 57.188 33.333 0.00 0.00 0.00 3.33
1474 3725 9.772973 TCCTACGCATACATAAAATATCTTGTT 57.227 29.630 0.00 0.00 0.00 2.83
1475 3726 9.204570 GTCCTACGCATACATAAAATATCTTGT 57.795 33.333 0.00 0.00 0.00 3.16
1476 3727 9.424319 AGTCCTACGCATACATAAAATATCTTG 57.576 33.333 0.00 0.00 0.00 3.02
1482 3733 8.639761 ACTCTTAGTCCTACGCATACATAAAAT 58.360 33.333 0.00 0.00 0.00 1.82
1483 3734 8.004087 ACTCTTAGTCCTACGCATACATAAAA 57.996 34.615 0.00 0.00 0.00 1.52
1484 3735 7.578310 ACTCTTAGTCCTACGCATACATAAA 57.422 36.000 0.00 0.00 0.00 1.40
1485 3736 7.255381 GGAACTCTTAGTCCTACGCATACATAA 60.255 40.741 0.00 0.00 0.00 1.90
1486 3737 6.206243 GGAACTCTTAGTCCTACGCATACATA 59.794 42.308 0.00 0.00 0.00 2.29
1489 3740 4.261530 GGGAACTCTTAGTCCTACGCATAC 60.262 50.000 0.00 0.00 0.00 2.39
1675 3926 2.109128 TCATGCCCCTGTTTTAGGTTCA 59.891 45.455 0.00 0.00 45.80 3.18
1712 3963 1.153647 CTGCGTGGTCCAGCGATTA 60.154 57.895 15.29 3.27 35.87 1.75
2070 4325 1.671054 GCAACGCCAACCTCTGCTA 60.671 57.895 0.00 0.00 0.00 3.49


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

AutoCloner maintained by Alex Coulton.