Multiple sequence alignment - TraesCS4B01G289500

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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 TraesCS4B01G289500 chr4B 100.000 2498 0 0 1 2498 574293585 574291088 0.000000e+00 4614
1 TraesCS4B01G289500 chr6B 94.812 2506 109 14 1 2498 653200607 653198115 0.000000e+00 3888
2 TraesCS4B01G289500 chr7A 92.227 1814 117 13 225 2035 348725719 348727511 0.000000e+00 2547
3 TraesCS4B01G289500 chr7A 91.351 1110 92 3 936 2043 595398201 595397094 0.000000e+00 1515
4 TraesCS4B01G289500 chr7A 94.231 156 8 1 785 940 595407760 595407606 1.150000e-58 237
5 TraesCS4B01G289500 chr1B 92.474 1754 127 4 750 2498 50302697 50304450 0.000000e+00 2503
6 TraesCS4B01G289500 chr1B 98.864 88 1 0 665 752 50258090 50258177 9.250000e-35 158
7 TraesCS4B01G289500 chr4A 92.720 989 67 5 1049 2035 636128179 636127194 0.000000e+00 1423
8 TraesCS4B01G289500 chr4A 93.381 695 42 3 1808 2498 731998043 731997349 0.000000e+00 1026
9 TraesCS4B01G289500 chr4A 95.122 287 13 1 234 520 636216235 636215950 3.790000e-123 451
10 TraesCS4B01G289500 chr4A 96.190 210 8 0 666 875 636128388 636128179 6.610000e-91 344
11 TraesCS4B01G289500 chr4A 95.484 155 5 2 518 670 636197678 636197524 1.920000e-61 246
12 TraesCS4B01G289500 chr5B 91.700 988 79 3 1043 2028 488979308 488980294 0.000000e+00 1367
13 TraesCS4B01G289500 chr3D 95.401 674 27 4 234 905 41135464 41136135 0.000000e+00 1070
14 TraesCS4B01G289500 chr3D 92.915 621 39 4 1413 2031 41146795 41147412 0.000000e+00 898
15 TraesCS4B01G289500 chr3D 92.816 515 37 0 906 1420 41141427 41141941 0.000000e+00 747
16 TraesCS4B01G289500 chr2B 85.207 1014 130 15 704 1713 593014163 593015160 0.000000e+00 1024
17 TraesCS4B01G289500 chr2B 87.792 557 60 6 1946 2496 680187643 680188197 0.000000e+00 645
18 TraesCS4B01G289500 chr2B 96.842 95 3 0 30 124 680104499 680104593 2.570000e-35 159
19 TraesCS4B01G289500 chr2D 84.578 1031 131 22 704 1724 505837835 505838847 0.000000e+00 998
20 TraesCS4B01G289500 chr2D 87.342 632 57 12 1888 2498 41232774 41233403 0.000000e+00 702
21 TraesCS4B01G289500 chr2D 87.120 559 58 7 1946 2495 290557789 290557236 2.730000e-174 621
22 TraesCS4B01G289500 chr2D 80.220 364 52 13 217 571 341666836 341667188 3.190000e-64 255
23 TraesCS4B01G289500 chr2D 86.620 142 16 1 30 168 417218522 417218663 1.200000e-33 154
24 TraesCS4B01G289500 chr6D 89.253 763 60 12 1751 2498 46496048 46495293 0.000000e+00 935
25 TraesCS4B01G289500 chr6D 93.194 382 24 2 191 571 46496614 46496234 6.030000e-156 560
26 TraesCS4B01G289500 chr6D 94.578 166 9 0 30 195 46496974 46496809 8.870000e-65 257
27 TraesCS4B01G289500 chr6D 89.222 167 15 1 30 193 431058569 431058735 3.260000e-49 206
28 TraesCS4B01G289500 chr7D 87.362 633 60 9 1884 2498 83949056 83949686 0.000000e+00 708
29 TraesCS4B01G289500 chr7D 87.362 633 60 9 1884 2498 83971695 83972325 0.000000e+00 708
30 TraesCS4B01G289500 chr2A 85.345 696 80 17 1026 1715 650256699 650257378 0.000000e+00 701
31 TraesCS4B01G289500 chr2A 93.455 382 20 4 191 571 674139207 674139584 1.680000e-156 562
32 TraesCS4B01G289500 chr2A 95.783 166 6 1 30 195 674138848 674139012 1.470000e-67 267
33 TraesCS4B01G289500 chr5D 90.751 173 15 1 269 441 481218067 481218238 1.930000e-56 230
34 TraesCS4B01G289500 chr3A 90.173 173 16 1 269 441 370984940 370984769 8.990000e-55 224
35 TraesCS4B01G289500 chr1A 95.789 95 4 0 30 124 585740056 585739962 1.200000e-33 154


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 TraesCS4B01G289500 chr4B 574291088 574293585 2497 True 4614.0 4614 100.000000 1 2498 1 chr4B.!!$R1 2497
1 TraesCS4B01G289500 chr6B 653198115 653200607 2492 True 3888.0 3888 94.812000 1 2498 1 chr6B.!!$R1 2497
2 TraesCS4B01G289500 chr7A 348725719 348727511 1792 False 2547.0 2547 92.227000 225 2035 1 chr7A.!!$F1 1810
3 TraesCS4B01G289500 chr7A 595397094 595398201 1107 True 1515.0 1515 91.351000 936 2043 1 chr7A.!!$R1 1107
4 TraesCS4B01G289500 chr1B 50302697 50304450 1753 False 2503.0 2503 92.474000 750 2498 1 chr1B.!!$F2 1748
5 TraesCS4B01G289500 chr4A 731997349 731998043 694 True 1026.0 1026 93.381000 1808 2498 1 chr4A.!!$R3 690
6 TraesCS4B01G289500 chr4A 636127194 636128388 1194 True 883.5 1423 94.455000 666 2035 2 chr4A.!!$R4 1369
7 TraesCS4B01G289500 chr5B 488979308 488980294 986 False 1367.0 1367 91.700000 1043 2028 1 chr5B.!!$F1 985
8 TraesCS4B01G289500 chr3D 41135464 41136135 671 False 1070.0 1070 95.401000 234 905 1 chr3D.!!$F1 671
9 TraesCS4B01G289500 chr3D 41146795 41147412 617 False 898.0 898 92.915000 1413 2031 1 chr3D.!!$F3 618
10 TraesCS4B01G289500 chr3D 41141427 41141941 514 False 747.0 747 92.816000 906 1420 1 chr3D.!!$F2 514
11 TraesCS4B01G289500 chr2B 593014163 593015160 997 False 1024.0 1024 85.207000 704 1713 1 chr2B.!!$F1 1009
12 TraesCS4B01G289500 chr2B 680187643 680188197 554 False 645.0 645 87.792000 1946 2496 1 chr2B.!!$F3 550
13 TraesCS4B01G289500 chr2D 505837835 505838847 1012 False 998.0 998 84.578000 704 1724 1 chr2D.!!$F4 1020
14 TraesCS4B01G289500 chr2D 41232774 41233403 629 False 702.0 702 87.342000 1888 2498 1 chr2D.!!$F1 610
15 TraesCS4B01G289500 chr2D 290557236 290557789 553 True 621.0 621 87.120000 1946 2495 1 chr2D.!!$R1 549
16 TraesCS4B01G289500 chr6D 46495293 46496974 1681 True 584.0 935 92.341667 30 2498 3 chr6D.!!$R1 2468
17 TraesCS4B01G289500 chr7D 83949056 83949686 630 False 708.0 708 87.362000 1884 2498 1 chr7D.!!$F1 614
18 TraesCS4B01G289500 chr7D 83971695 83972325 630 False 708.0 708 87.362000 1884 2498 1 chr7D.!!$F2 614
19 TraesCS4B01G289500 chr2A 650256699 650257378 679 False 701.0 701 85.345000 1026 1715 1 chr2A.!!$F1 689
20 TraesCS4B01G289500 chr2A 674138848 674139584 736 False 414.5 562 94.619000 30 571 2 chr2A.!!$F2 541

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
256 456 0.042581 TAGTCATCCCCAGGAGTGCA 59.957 55.0 0.0 0.0 34.05 4.57 F
1318 1528 2.198827 TGCCTCTGTGTTTGGTATGG 57.801 50.0 0.0 0.0 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1360 1570 0.110486 ACAAGAGGGTCGGCAATGTT 59.890 50.0 0.0 0.0 0.00 2.71 R
2419 2665 0.694771 TGATGCAGTCTCTGGGCTTT 59.305 50.0 0.0 0.0 31.21 3.51 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
256 456 0.042581 TAGTCATCCCCAGGAGTGCA 59.957 55.000 0.00 0.00 34.05 4.57
323 523 3.611766 ACCATAGCAGTTTTACGCTCT 57.388 42.857 0.00 0.00 39.70 4.09
411 611 4.946157 ACAGTAGCATAAGCAAGCTTGATT 59.054 37.500 30.48 30.48 45.49 2.57
587 791 7.630242 TGCATTAGAATTTTTAGAGGACTGG 57.370 36.000 0.00 0.00 0.00 4.00
683 887 5.674525 TCAGGGTTTATGAAGTCTATGCTG 58.325 41.667 0.00 0.00 0.00 4.41
835 1040 3.605634 ACATGTACTCTTGGCGCAAATA 58.394 40.909 10.83 0.00 0.00 1.40
908 1113 5.831525 TGAGTTAGACAGGTTCAGACTACAA 59.168 40.000 0.00 0.00 0.00 2.41
911 1116 7.379750 AGTTAGACAGGTTCAGACTACAAATC 58.620 38.462 0.00 0.00 0.00 2.17
1023 1228 3.135994 GAGGACGGCTAGAAACAAAACA 58.864 45.455 0.00 0.00 0.00 2.83
1067 1272 6.519679 TTCATTGCTCATACTTGCTGATTT 57.480 33.333 0.00 0.00 0.00 2.17
1073 1278 5.218139 GCTCATACTTGCTGATTTTATGGC 58.782 41.667 0.00 0.00 0.00 4.40
1127 1335 6.098409 TGAGAGAATCCACACCTTAGTAATCC 59.902 42.308 0.00 0.00 33.66 3.01
1135 1343 5.897824 CCACACCTTAGTAATCCTCTTCCTA 59.102 44.000 0.00 0.00 0.00 2.94
1181 1389 2.746362 TCATTATGTGTGCGAACATGCA 59.254 40.909 0.00 0.00 40.93 3.96
1286 1496 2.362077 GCGATGCTATTGGATTTGGGTT 59.638 45.455 0.00 0.00 0.00 4.11
1294 1504 2.926778 TGGATTTGGGTTTGCCTTTG 57.073 45.000 0.00 0.00 34.45 2.77
1318 1528 2.198827 TGCCTCTGTGTTTGGTATGG 57.801 50.000 0.00 0.00 0.00 2.74
1360 1570 5.221702 TGCATCTTCATGAAATCGGGATCTA 60.222 40.000 9.88 0.00 30.57 1.98
1376 1586 1.568504 TCTAACATTGCCGACCCTCT 58.431 50.000 0.00 0.00 0.00 3.69
1398 1610 3.093814 TGTTCGTTCAGGTATCAGGCTA 58.906 45.455 0.00 0.00 0.00 3.93
1505 1717 4.318332 CAAGACAAGGTGTGAGCTAATCA 58.682 43.478 0.00 0.00 34.79 2.57
1520 1732 5.211973 AGCTAATCACCTGACCATCTCTAA 58.788 41.667 0.00 0.00 0.00 2.10
1595 1811 3.369546 AAAAATTTGGGACTGAGCACG 57.630 42.857 0.00 0.00 0.00 5.34
1625 1844 2.549349 GCGTTCCTCCCAAAGTTGTAGA 60.549 50.000 0.00 0.00 0.00 2.59
1734 1954 3.333414 GCAGTTGCAGTTGCTCGA 58.667 55.556 14.99 0.00 42.66 4.04
1879 2100 3.562176 CCCCTTGCTTGAAACTCCTATGT 60.562 47.826 0.00 0.00 0.00 2.29
1897 2118 6.328934 TCCTATGTTGAATTAGAGGGTATGCA 59.671 38.462 0.00 0.00 0.00 3.96
1996 2227 6.331369 ACCAACATTATCTTTTCCTGTGTG 57.669 37.500 0.00 0.00 0.00 3.82
2003 2234 8.641541 ACATTATCTTTTCCTGTGTGTCAAAAT 58.358 29.630 0.00 0.00 0.00 1.82
2031 2262 7.063780 GTCAACCTGGCTCATAAAATGATTTTG 59.936 37.037 13.08 0.00 38.85 2.44
2230 2472 1.876799 CGTGCAACAAGTATGGACCAA 59.123 47.619 0.00 0.00 35.93 3.67
2305 2547 2.426522 CTGCTGGATTTGAACGAGGAA 58.573 47.619 0.00 0.00 0.00 3.36
2358 2600 0.960364 GGTGCATGGGTGATTGACGT 60.960 55.000 0.00 0.00 0.00 4.34
2396 2642 2.802816 GTGAGTGTCGTGCTCTTCAAAT 59.197 45.455 0.00 0.00 34.30 2.32
2404 2650 3.057104 TCGTGCTCTTCAAATACTCGGAA 60.057 43.478 0.00 0.00 0.00 4.30
2484 2737 4.176851 GTCGGAGGTCGTCGAGGC 62.177 72.222 0.00 0.00 40.32 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
162 163 4.486125 TGTTAGCAGCACATCCAGAATA 57.514 40.909 0.00 0.00 0.00 1.75
256 456 9.700831 ACAATTAGCTATATGGAAGGAAAAGTT 57.299 29.630 10.12 0.00 0.00 2.66
297 497 4.205792 GCGTAAAACTGCTATGGTACTACG 59.794 45.833 0.00 0.00 33.97 3.51
318 518 9.477484 AGTATATCTGTAACCATAAAAAGAGCG 57.523 33.333 0.00 0.00 0.00 5.03
411 611 7.503549 TGAGAAGAGCAAGCATCATAATTCTA 58.496 34.615 0.00 0.00 0.00 2.10
587 791 5.298026 GCTCCAAGAAAGGAATCAGGAATAC 59.702 44.000 0.00 0.00 37.20 1.89
630 834 7.172868 TGCCATAGAATGTGATTCAAAATGT 57.827 32.000 0.00 0.00 41.71 2.71
683 887 3.955650 TGTGCTACTGAGTTAGAACCC 57.044 47.619 0.00 0.00 0.00 4.11
835 1040 3.307762 GGTAGGAACCAATGAGCTCACTT 60.308 47.826 20.97 11.77 45.98 3.16
945 1150 9.499479 CTCTCTTTAATGCATAATACACCATCT 57.501 33.333 0.00 0.00 0.00 2.90
981 1186 1.191535 TGGCGTTGTACCTGCTCTAT 58.808 50.000 0.00 0.00 0.00 1.98
1067 1272 4.778213 AGCTCAGTAAGAATGGCCATAA 57.222 40.909 21.15 1.93 0.00 1.90
1073 1278 6.521151 AAAATCCAAGCTCAGTAAGAATGG 57.479 37.500 0.00 0.00 34.94 3.16
1127 1335 4.462508 TCAGAGTGCACAATAGGAAGAG 57.537 45.455 21.04 0.00 0.00 2.85
1135 1343 6.701340 TCACTAGTAAATCAGAGTGCACAAT 58.299 36.000 21.04 3.43 39.33 2.71
1181 1389 8.462016 GTTAAGCCATGAAAACAATCTATGAGT 58.538 33.333 0.00 0.00 0.00 3.41
1286 1496 1.136695 CAGAGGCAAACACAAAGGCAA 59.863 47.619 0.00 0.00 0.00 4.52
1294 1504 1.476488 ACCAAACACAGAGGCAAACAC 59.524 47.619 0.00 0.00 0.00 3.32
1318 1528 1.600916 AGGCGCAAAGAGGGTGAAC 60.601 57.895 10.83 0.00 0.00 3.18
1360 1570 0.110486 ACAAGAGGGTCGGCAATGTT 59.890 50.000 0.00 0.00 0.00 2.71
1376 1586 2.301870 AGCCTGATACCTGAACGAACAA 59.698 45.455 0.00 0.00 0.00 2.83
1398 1610 3.244112 GCACTAGCTTCCGGGTATTGTAT 60.244 47.826 0.00 0.00 37.91 2.29
1505 1717 6.380079 ACAGAAAATTAGAGATGGTCAGGT 57.620 37.500 0.00 0.00 0.00 4.00
1520 1732 7.095017 GCTTCTTCAGTTAGCAGTACAGAAAAT 60.095 37.037 0.00 0.00 35.05 1.82
1605 1821 3.396260 TCTACAACTTTGGGAGGAACG 57.604 47.619 0.00 0.00 0.00 3.95
1625 1844 4.649218 ACTAAATGCTGTTTGTTGGGACTT 59.351 37.500 0.00 0.00 0.00 3.01
1661 1880 3.872511 CCACAGCTTATCATTGGCAAA 57.127 42.857 3.01 0.00 0.00 3.68
1734 1954 7.704578 TCTATTAGTAACTGCAACTGAGTCT 57.295 36.000 0.00 0.00 0.00 3.24
1779 1999 5.007039 CACAGTACTAATGTCCATGTGATGC 59.993 44.000 0.00 0.00 36.74 3.91
1879 2100 5.065914 GCATCTGCATACCCTCTAATTCAA 58.934 41.667 0.00 0.00 41.59 2.69
1897 2118 7.712639 CACCAACAATGATTAGTAGTAGCATCT 59.287 37.037 0.00 0.00 0.00 2.90
1950 2177 7.041372 TGGTAACAGTCTTCATTAGCAAGAAAC 60.041 37.037 0.00 0.00 46.17 2.78
1985 2216 6.030548 TGACAATTTTGACACACAGGAAAA 57.969 33.333 0.00 0.00 0.00 2.29
1996 2227 3.068024 TGAGCCAGGTTGACAATTTTGAC 59.932 43.478 0.00 0.00 0.00 3.18
2003 2234 5.076182 TCATTTTATGAGCCAGGTTGACAA 58.924 37.500 0.00 0.00 33.59 3.18
2121 2359 1.614824 CCAGCTCCCCTCCTTCTGT 60.615 63.158 0.00 0.00 0.00 3.41
2193 2433 1.289066 CGAGACGTGAAGAAGGCCA 59.711 57.895 5.01 0.00 0.00 5.36
2230 2472 7.016153 TGAATCAATAGTAACAACCAGAGGT 57.984 36.000 0.00 0.00 37.65 3.85
2404 2650 1.679032 GGCTTTATGGTGAAGTCCGCT 60.679 52.381 0.00 0.00 0.00 5.52
2419 2665 0.694771 TGATGCAGTCTCTGGGCTTT 59.305 50.000 0.00 0.00 31.21 3.51


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

AutoCloner maintained by Alex Coulton.