Multiple sequence alignment - TraesCS3D01G460100

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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 TraesCS3D01G460100 chr3D 100.000 2414 0 0 1 2414 565242723 565245136 0.000000e+00 4458
1 TraesCS3D01G460100 chr3D 93.737 958 43 8 1460 2414 565197199 565198142 0.000000e+00 1421
2 TraesCS3D01G460100 chr3D 95.863 556 16 4 1858 2411 100728721 100729271 0.000000e+00 893
3 TraesCS3D01G460100 chr3D 93.393 560 30 5 1858 2414 574996476 574995921 0.000000e+00 822
4 TraesCS3D01G460100 chr3D 87.800 459 56 0 1 459 28587858 28587400 2.730000e-149 538
5 TraesCS3D01G460100 chr3D 90.750 400 34 3 1463 1859 468765162 468765561 4.570000e-147 531
6 TraesCS3D01G460100 chr3D 88.630 387 38 4 1473 1858 596878599 596878980 1.310000e-127 466
7 TraesCS3D01G460100 chr3D 89.591 269 27 1 461 729 28585895 28585628 8.270000e-90 340
8 TraesCS3D01G460100 chr3A 91.144 1434 123 4 5 1438 21354284 21352855 0.000000e+00 1941
9 TraesCS3D01G460100 chr3A 90.301 732 70 1 709 1440 112923285 112924015 0.000000e+00 957
10 TraesCS3D01G460100 chr7D 90.978 1441 126 3 1 1440 609177331 609178768 0.000000e+00 1938
11 TraesCS3D01G460100 chr7D 96.071 560 16 4 1858 2414 166969276 166969832 0.000000e+00 907
12 TraesCS3D01G460100 chr7D 93.972 564 24 8 1854 2414 569907627 569907071 0.000000e+00 845
13 TraesCS3D01G460100 chr7D 93.900 541 31 2 1876 2414 581133332 581132792 0.000000e+00 815
14 TraesCS3D01G460100 chr7D 93.900 541 31 2 1876 2414 581135411 581134871 0.000000e+00 815
15 TraesCS3D01G460100 chr7D 90.513 390 26 5 1473 1861 414276531 414276152 2.770000e-139 505
16 TraesCS3D01G460100 chr5D 90.777 1442 129 3 1 1441 7611659 7610221 0.000000e+00 1923
17 TraesCS3D01G460100 chr5D 80.909 1430 253 18 20 1440 548272784 548274202 0.000000e+00 1110
18 TraesCS3D01G460100 chr7A 87.578 1441 177 2 1 1440 580627131 580628570 0.000000e+00 1668
19 TraesCS3D01G460100 chr5A 86.954 1441 176 4 5 1443 608863820 608862390 0.000000e+00 1609
20 TraesCS3D01G460100 chr4D 86.667 1440 191 1 1 1440 486555385 486556823 0.000000e+00 1594
21 TraesCS3D01G460100 chr1B 83.183 1439 227 8 5 1439 270328066 270329493 0.000000e+00 1303
22 TraesCS3D01G460100 chr2B 82.349 1439 247 7 8 1443 217269761 217268327 0.000000e+00 1243
23 TraesCS3D01G460100 chr2D 96.422 559 18 1 1858 2414 566717093 566717651 0.000000e+00 920
24 TraesCS3D01G460100 chr2D 94.444 558 25 5 1858 2412 615326209 615325655 0.000000e+00 854
25 TraesCS3D01G460100 chr2D 92.208 385 29 1 1475 1858 391101514 391101898 5.870000e-151 544
26 TraesCS3D01G460100 chr2D 90.155 386 34 3 1473 1855 323088067 323088451 1.290000e-137 499
27 TraesCS3D01G460100 chrUn 94.624 558 26 4 1857 2412 104107669 104107114 0.000000e+00 861
28 TraesCS3D01G460100 chr1D 90.933 386 25 7 1475 1859 447778585 447778961 5.950000e-141 510
29 TraesCS3D01G460100 chr3B 90.130 385 36 2 1475 1858 237321438 237321821 1.290000e-137 499
30 TraesCS3D01G460100 chr2A 86.082 388 37 11 1475 1858 70146095 70145721 3.740000e-108 401


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 TraesCS3D01G460100 chr3D 565242723 565245136 2413 False 4458 4458 100.0000 1 2414 1 chr3D.!!$F4 2413
1 TraesCS3D01G460100 chr3D 565197199 565198142 943 False 1421 1421 93.7370 1460 2414 1 chr3D.!!$F3 954
2 TraesCS3D01G460100 chr3D 100728721 100729271 550 False 893 893 95.8630 1858 2411 1 chr3D.!!$F1 553
3 TraesCS3D01G460100 chr3D 574995921 574996476 555 True 822 822 93.3930 1858 2414 1 chr3D.!!$R1 556
4 TraesCS3D01G460100 chr3D 28585628 28587858 2230 True 439 538 88.6955 1 729 2 chr3D.!!$R2 728
5 TraesCS3D01G460100 chr3A 21352855 21354284 1429 True 1941 1941 91.1440 5 1438 1 chr3A.!!$R1 1433
6 TraesCS3D01G460100 chr3A 112923285 112924015 730 False 957 957 90.3010 709 1440 1 chr3A.!!$F1 731
7 TraesCS3D01G460100 chr7D 609177331 609178768 1437 False 1938 1938 90.9780 1 1440 1 chr7D.!!$F2 1439
8 TraesCS3D01G460100 chr7D 166969276 166969832 556 False 907 907 96.0710 1858 2414 1 chr7D.!!$F1 556
9 TraesCS3D01G460100 chr7D 569907071 569907627 556 True 845 845 93.9720 1854 2414 1 chr7D.!!$R2 560
10 TraesCS3D01G460100 chr7D 581132792 581135411 2619 True 815 815 93.9000 1876 2414 2 chr7D.!!$R3 538
11 TraesCS3D01G460100 chr5D 7610221 7611659 1438 True 1923 1923 90.7770 1 1441 1 chr5D.!!$R1 1440
12 TraesCS3D01G460100 chr5D 548272784 548274202 1418 False 1110 1110 80.9090 20 1440 1 chr5D.!!$F1 1420
13 TraesCS3D01G460100 chr7A 580627131 580628570 1439 False 1668 1668 87.5780 1 1440 1 chr7A.!!$F1 1439
14 TraesCS3D01G460100 chr5A 608862390 608863820 1430 True 1609 1609 86.9540 5 1443 1 chr5A.!!$R1 1438
15 TraesCS3D01G460100 chr4D 486555385 486556823 1438 False 1594 1594 86.6670 1 1440 1 chr4D.!!$F1 1439
16 TraesCS3D01G460100 chr1B 270328066 270329493 1427 False 1303 1303 83.1830 5 1439 1 chr1B.!!$F1 1434
17 TraesCS3D01G460100 chr2B 217268327 217269761 1434 True 1243 1243 82.3490 8 1443 1 chr2B.!!$R1 1435
18 TraesCS3D01G460100 chr2D 566717093 566717651 558 False 920 920 96.4220 1858 2414 1 chr2D.!!$F3 556
19 TraesCS3D01G460100 chr2D 615325655 615326209 554 True 854 854 94.4440 1858 2412 1 chr2D.!!$R1 554
20 TraesCS3D01G460100 chrUn 104107114 104107669 555 True 861 861 94.6240 1857 2412 1 chrUn.!!$R1 555

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
607 2110 0.816018 TTGGGTGAACATGCGTCGTT 60.816 50.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1450 2958 0.323725 ATAAGCAAGGCCTGGTGTGG 60.324 55.0 5.69 0.0 35.42 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
84 85 2.507071 ACATGGAGGGATCCTTGGATT 58.493 47.619 12.58 0.00 38.71 3.01
86 87 1.131638 TGGAGGGATCCTTGGATTCG 58.868 55.000 12.58 0.00 31.76 3.34
131 132 6.378280 CCAATTACTCCTAAAAGGAACTGCAT 59.622 38.462 0.00 0.00 45.28 3.96
269 270 2.223711 GCCAACGTGGTGATTTTCTGTT 60.224 45.455 0.00 0.00 40.46 3.16
318 319 3.312421 TCACAGTCAAAAGTGCTTACAGC 59.688 43.478 0.00 0.00 42.82 4.40
405 406 0.951040 GCTCCTTGTGGAACCTCGTG 60.951 60.000 0.00 0.00 42.66 4.35
420 421 2.878406 CCTCGTGTGGAAATCTGTTGTT 59.122 45.455 0.00 0.00 0.00 2.83
607 2110 0.816018 TTGGGTGAACATGCGTCGTT 60.816 50.000 0.00 0.00 0.00 3.85
657 2160 5.471456 GCTTCTTGACTCTGGAAAAGAATGA 59.529 40.000 0.00 0.00 37.84 2.57
711 2217 9.271921 ACAGATGTGAGGGATATGCTAATTATA 57.728 33.333 0.00 0.00 0.00 0.98
748 2254 2.009774 GGCAGATGCGTAATGACTTGT 58.990 47.619 0.00 0.00 43.26 3.16
961 2467 3.093057 ACGGTAGCTCTCTCAGTTGATT 58.907 45.455 0.00 0.00 0.00 2.57
1022 2528 4.842531 TGGTGCTAAGGAATTCAGATGA 57.157 40.909 7.93 0.00 0.00 2.92
1075 2581 1.134075 CACTGCAATGACTCGCTGC 59.866 57.895 0.00 0.00 36.60 5.25
1284 2791 7.419711 TCCTCTAAAGATTAACCGTTCTCAT 57.580 36.000 0.00 0.00 0.00 2.90
1348 2855 3.551454 GCGAACTACTACTGTGTGGTTGA 60.551 47.826 13.55 0.00 40.76 3.18
1361 2868 1.419381 TGGTTGAGCTCAGTACCACA 58.581 50.000 28.74 13.20 33.23 4.17
1454 2962 2.452600 AAAAAGGTTCTGAGGCCACA 57.547 45.000 5.01 3.31 0.00 4.17
1455 2963 1.692411 AAAAGGTTCTGAGGCCACAC 58.308 50.000 5.01 0.00 0.00 3.82
1456 2964 0.178990 AAAGGTTCTGAGGCCACACC 60.179 55.000 5.01 2.33 39.61 4.16
1457 2965 1.352622 AAGGTTCTGAGGCCACACCA 61.353 55.000 5.01 0.00 43.14 4.17
1458 2966 1.302832 GGTTCTGAGGCCACACCAG 60.303 63.158 5.01 6.83 43.14 4.00
1459 2967 1.302832 GTTCTGAGGCCACACCAGG 60.303 63.158 5.01 0.00 43.14 4.45
1467 2975 2.203538 CCACACCAGGCCTTGCTT 60.204 61.111 0.00 0.00 0.00 3.91
1468 2976 1.074775 CCACACCAGGCCTTGCTTA 59.925 57.895 0.00 0.00 0.00 3.09
1469 2977 0.323725 CCACACCAGGCCTTGCTTAT 60.324 55.000 0.00 0.00 0.00 1.73
1470 2978 1.549203 CACACCAGGCCTTGCTTATT 58.451 50.000 0.00 0.00 0.00 1.40
1505 3013 1.602237 CAGACCCCGCATAAGTGGT 59.398 57.895 0.00 0.00 44.14 4.16
1510 3018 0.808755 CCCCGCATAAGTGGTCAAAC 59.191 55.000 0.00 0.00 44.14 2.93
1512 3020 0.808755 CCGCATAAGTGGTCAAACCC 59.191 55.000 0.00 0.00 40.63 4.11
1522 3030 3.054166 GTGGTCAAACCCGCAAAATAAC 58.946 45.455 0.00 0.00 37.50 1.89
1566 3075 0.321996 AAAGAGCCCGAACAGACCTC 59.678 55.000 0.00 0.00 0.00 3.85
1579 3088 0.320374 AGACCTCGCAAAATCGTCCA 59.680 50.000 0.00 0.00 0.00 4.02
1589 3098 4.623002 GCAAAATCGTCCAACCCTTAAAA 58.377 39.130 0.00 0.00 0.00 1.52
1590 3099 5.051153 GCAAAATCGTCCAACCCTTAAAAA 58.949 37.500 0.00 0.00 0.00 1.94
1595 3104 7.722795 AATCGTCCAACCCTTAAAAATTTTG 57.277 32.000 3.73 0.00 0.00 2.44
1612 3121 6.451064 AATTTTGAAGGAGCCCTATAAACG 57.549 37.500 0.00 0.00 31.13 3.60
1629 3138 3.573558 GCGAATGCGAAACCCTCA 58.426 55.556 0.00 0.00 40.82 3.86
1636 3145 5.005779 GCGAATGCGAAACCCTCATATATAG 59.994 44.000 0.00 0.00 40.82 1.31
1645 3154 9.542462 CGAAACCCTCATATATAGAGTTTTGAA 57.458 33.333 6.05 0.00 0.00 2.69
2213 5809 8.378172 TCACTCATTTCAAATCGTCTAACTTT 57.622 30.769 0.00 0.00 0.00 2.66
2280 5876 6.616237 TTAACTTCGGAGTTCTATTCCCTT 57.384 37.500 13.67 0.00 44.75 3.95
2299 5895 3.253432 CCTTTACTTTCCAAGTCTGCACC 59.747 47.826 0.00 0.00 41.77 5.01
2312 5908 3.118038 AGTCTGCACCTGTTGTTTTCCTA 60.118 43.478 0.00 0.00 0.00 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 3.521560 CTCCATGTACGTATTGCAGTGT 58.478 45.455 0.00 0.00 0.00 3.55
84 85 0.959372 GGAACGAGTCAGGTCTCCGA 60.959 60.000 0.00 0.00 0.00 4.55
318 319 2.260844 TGTGTTCCTGAGAAGCAAGG 57.739 50.000 0.00 0.00 30.91 3.61
565 2068 5.904614 AAAGAATTCTTGCATGCGTACATGG 60.905 40.000 21.15 0.00 43.57 3.66
657 2160 5.355350 GCACTTGCTCAATAAGGACAATAGT 59.645 40.000 0.00 0.00 38.21 2.12
711 2217 1.203162 TGCCAAATCCTCCACACCAAT 60.203 47.619 0.00 0.00 0.00 3.16
748 2254 2.935238 GCGTACTCTCTTTCCCATGCAA 60.935 50.000 0.00 0.00 0.00 4.08
934 2440 1.076632 AGAGAGCTACCGTCCCAGG 60.077 63.158 0.00 0.00 37.30 4.45
1043 2549 5.122239 TCATTGCAGTGGAAGATAAAACGAG 59.878 40.000 9.56 0.00 0.00 4.18
1075 2581 4.170062 CGCATGCAGTTCCGCCTG 62.170 66.667 19.57 0.00 35.49 4.85
1284 2791 3.004419 CCAGTCGATCGGCAACTCTATTA 59.996 47.826 23.45 0.00 0.00 0.98
1336 2843 0.833287 ACTGAGCTCAACCACACAGT 59.167 50.000 18.85 6.51 34.46 3.55
1348 2855 3.832490 TCAATACACTGTGGTACTGAGCT 59.168 43.478 13.09 0.00 27.58 4.09
1361 2868 3.010584 AGGCCACAAATCCTCAATACACT 59.989 43.478 5.01 0.00 0.00 3.55
1440 2948 1.302832 CTGGTGTGGCCTCAGAACC 60.303 63.158 7.99 6.87 38.35 3.62
1443 2951 3.640407 GCCTGGTGTGGCCTCAGA 61.640 66.667 7.99 0.00 46.82 3.27
1450 2958 0.323725 ATAAGCAAGGCCTGGTGTGG 60.324 55.000 5.69 0.00 35.42 4.17
1451 2959 1.474077 GAATAAGCAAGGCCTGGTGTG 59.526 52.381 5.69 0.61 35.42 3.82
1452 2960 1.355720 AGAATAAGCAAGGCCTGGTGT 59.644 47.619 5.69 0.00 35.42 4.16
1453 2961 2.134789 AGAATAAGCAAGGCCTGGTG 57.865 50.000 5.69 2.04 35.42 4.17
1454 2962 3.523564 TCTTAGAATAAGCAAGGCCTGGT 59.476 43.478 5.69 3.10 37.35 4.00
1455 2963 4.133078 CTCTTAGAATAAGCAAGGCCTGG 58.867 47.826 5.69 3.35 0.00 4.45
1456 2964 3.563390 GCTCTTAGAATAAGCAAGGCCTG 59.437 47.826 5.69 1.10 36.06 4.85
1457 2965 3.200825 TGCTCTTAGAATAAGCAAGGCCT 59.799 43.478 0.00 0.00 42.71 5.19
1458 2966 3.545703 TGCTCTTAGAATAAGCAAGGCC 58.454 45.455 0.00 0.00 42.71 5.19
1464 2972 6.686630 TGCTAGAGATGCTCTTAGAATAAGC 58.313 40.000 1.88 4.55 41.50 3.09
1465 2973 8.023128 GTCTGCTAGAGATGCTCTTAGAATAAG 58.977 40.741 1.88 0.00 41.50 1.73
1466 2974 7.040062 GGTCTGCTAGAGATGCTCTTAGAATAA 60.040 40.741 1.88 0.00 41.50 1.40
1467 2975 6.432783 GGTCTGCTAGAGATGCTCTTAGAATA 59.567 42.308 1.88 0.00 41.50 1.75
1468 2976 5.243730 GGTCTGCTAGAGATGCTCTTAGAAT 59.756 44.000 1.88 0.00 41.50 2.40
1469 2977 4.582656 GGTCTGCTAGAGATGCTCTTAGAA 59.417 45.833 1.88 0.00 41.50 2.10
1470 2978 4.141287 GGTCTGCTAGAGATGCTCTTAGA 58.859 47.826 1.88 2.76 41.50 2.10
1505 3013 1.955080 ACGGTTATTTTGCGGGTTTGA 59.045 42.857 0.00 0.00 0.00 2.69
1566 3075 0.596082 AAGGGTTGGACGATTTTGCG 59.404 50.000 0.00 0.00 37.29 4.85
1579 3088 6.296026 GGCTCCTTCAAAATTTTTAAGGGTT 58.704 36.000 30.30 0.00 40.36 4.11
1589 3098 5.163550 GCGTTTATAGGGCTCCTTCAAAATT 60.164 40.000 0.00 0.00 34.61 1.82
1590 3099 4.338400 GCGTTTATAGGGCTCCTTCAAAAT 59.662 41.667 0.00 0.00 34.61 1.82
1595 3104 1.068127 TCGCGTTTATAGGGCTCCTTC 59.932 52.381 5.77 0.00 34.61 3.46
1612 3121 1.295792 TATGAGGGTTTCGCATTCGC 58.704 50.000 0.00 0.00 37.15 4.70
1636 3145 4.743493 TGGCAAAGTTGTCTTCAAAACTC 58.257 39.130 0.00 0.00 35.60 3.01
1645 3154 1.531602 GGCCCTGGCAAAGTTGTCT 60.532 57.895 10.86 0.00 44.11 3.41
1826 3335 3.471244 CTCCGTTCTAGAGCCGCGG 62.471 68.421 24.05 24.05 43.32 6.46


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

AutoCloner maintained by Alex Coulton.