Multiple sequence alignment - TraesCS7B01G216200

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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 TraesCS7B01G216200 chr7B 100.000 2728 0 0 1 2728 398610431 398613158 0.000000e+00 5038
1 TraesCS7B01G216200 chr7B 95.152 2104 90 7 625 2728 144868558 144866467 0.000000e+00 3310
2 TraesCS7B01G216200 chr7B 92.960 625 44 0 1 625 174094110 174094734 0.000000e+00 911
3 TraesCS7B01G216200 chr7B 92.915 621 44 0 5 625 691612296 691612916 0.000000e+00 904
4 TraesCS7B01G216200 chr6A 95.485 2104 83 4 626 2728 557669503 557671595 0.000000e+00 3349
5 TraesCS7B01G216200 chr6B 93.619 2100 132 2 628 2726 363476811 363478909 0.000000e+00 3134
6 TraesCS7B01G216200 chr6B 93.109 624 43 0 1 624 151706788 151706165 0.000000e+00 915
7 TraesCS7B01G216200 chr6B 92.640 625 46 0 1 625 556614341 556613717 0.000000e+00 900
8 TraesCS7B01G216200 chrUn 94.505 1747 94 2 620 2365 155229175 155230920 0.000000e+00 2693
9 TraesCS7B01G216200 chr1B 94.111 1749 99 2 620 2365 36186152 36187899 0.000000e+00 2656
10 TraesCS7B01G216200 chr1B 93.406 1562 99 3 626 2187 595831219 595832776 0.000000e+00 2311
11 TraesCS7B01G216200 chr1B 93.278 1562 101 3 626 2187 595882633 595884190 0.000000e+00 2300
12 TraesCS7B01G216200 chr1B 96.085 1405 53 1 945 2349 284048246 284046844 0.000000e+00 2289
13 TraesCS7B01G216200 chr1B 95.386 1257 53 2 1472 2728 235395192 235396443 0.000000e+00 1995
14 TraesCS7B01G216200 chr1B 96.559 494 15 2 2235 2728 595832784 595833275 0.000000e+00 817
15 TraesCS7B01G216200 chr1B 96.356 494 15 3 2235 2728 595884198 595884688 0.000000e+00 809
16 TraesCS7B01G216200 chr1B 98.201 389 7 0 2340 2728 284046249 284045861 0.000000e+00 680
17 TraesCS7B01G216200 chr1B 90.520 327 28 2 625 949 284057460 284057135 1.940000e-116 429
18 TraesCS7B01G216200 chr1D 94.169 1715 84 8 1018 2728 38867046 38868748 0.000000e+00 2599
19 TraesCS7B01G216200 chr1A 92.529 1566 109 3 626 2185 300543235 300541672 0.000000e+00 2237
20 TraesCS7B01G216200 chr1A 97.175 531 15 0 2198 2728 300528288 300527758 0.000000e+00 898
21 TraesCS7B01G216200 chr3D 89.010 919 72 9 626 1538 517387813 517388708 0.000000e+00 1110
22 TraesCS7B01G216200 chr2B 93.920 625 38 0 1 625 714585582 714586206 0.000000e+00 944
23 TraesCS7B01G216200 chr2B 93.120 625 42 1 1 625 714716148 714716771 0.000000e+00 915
24 TraesCS7B01G216200 chr3B 93.280 625 42 0 1 625 160448778 160448154 0.000000e+00 922
25 TraesCS7B01G216200 chr5B 92.812 626 42 3 1 625 407063135 407062512 0.000000e+00 904
26 TraesCS7B01G216200 chr5B 92.480 625 45 2 1 625 585535252 585535874 0.000000e+00 893
27 TraesCS7B01G216200 chr2D 86.182 275 37 1 626 899 621171324 621171050 2.050000e-76 296


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 TraesCS7B01G216200 chr7B 398610431 398613158 2727 False 5038.0 5038 100.0000 1 2728 1 chr7B.!!$F2 2727
1 TraesCS7B01G216200 chr7B 144866467 144868558 2091 True 3310.0 3310 95.1520 625 2728 1 chr7B.!!$R1 2103
2 TraesCS7B01G216200 chr7B 174094110 174094734 624 False 911.0 911 92.9600 1 625 1 chr7B.!!$F1 624
3 TraesCS7B01G216200 chr7B 691612296 691612916 620 False 904.0 904 92.9150 5 625 1 chr7B.!!$F3 620
4 TraesCS7B01G216200 chr6A 557669503 557671595 2092 False 3349.0 3349 95.4850 626 2728 1 chr6A.!!$F1 2102
5 TraesCS7B01G216200 chr6B 363476811 363478909 2098 False 3134.0 3134 93.6190 628 2726 1 chr6B.!!$F1 2098
6 TraesCS7B01G216200 chr6B 151706165 151706788 623 True 915.0 915 93.1090 1 624 1 chr6B.!!$R1 623
7 TraesCS7B01G216200 chr6B 556613717 556614341 624 True 900.0 900 92.6400 1 625 1 chr6B.!!$R2 624
8 TraesCS7B01G216200 chrUn 155229175 155230920 1745 False 2693.0 2693 94.5050 620 2365 1 chrUn.!!$F1 1745
9 TraesCS7B01G216200 chr1B 36186152 36187899 1747 False 2656.0 2656 94.1110 620 2365 1 chr1B.!!$F1 1745
10 TraesCS7B01G216200 chr1B 235395192 235396443 1251 False 1995.0 1995 95.3860 1472 2728 1 chr1B.!!$F2 1256
11 TraesCS7B01G216200 chr1B 595831219 595833275 2056 False 1564.0 2311 94.9825 626 2728 2 chr1B.!!$F3 2102
12 TraesCS7B01G216200 chr1B 595882633 595884688 2055 False 1554.5 2300 94.8170 626 2728 2 chr1B.!!$F4 2102
13 TraesCS7B01G216200 chr1B 284045861 284048246 2385 True 1484.5 2289 97.1430 945 2728 2 chr1B.!!$R2 1783
14 TraesCS7B01G216200 chr1D 38867046 38868748 1702 False 2599.0 2599 94.1690 1018 2728 1 chr1D.!!$F1 1710
15 TraesCS7B01G216200 chr1A 300541672 300543235 1563 True 2237.0 2237 92.5290 626 2185 1 chr1A.!!$R2 1559
16 TraesCS7B01G216200 chr1A 300527758 300528288 530 True 898.0 898 97.1750 2198 2728 1 chr1A.!!$R1 530
17 TraesCS7B01G216200 chr3D 517387813 517388708 895 False 1110.0 1110 89.0100 626 1538 1 chr3D.!!$F1 912
18 TraesCS7B01G216200 chr2B 714585582 714586206 624 False 944.0 944 93.9200 1 625 1 chr2B.!!$F1 624
19 TraesCS7B01G216200 chr2B 714716148 714716771 623 False 915.0 915 93.1200 1 625 1 chr2B.!!$F2 624
20 TraesCS7B01G216200 chr3B 160448154 160448778 624 True 922.0 922 93.2800 1 625 1 chr3B.!!$R1 624
21 TraesCS7B01G216200 chr5B 407062512 407063135 623 True 904.0 904 92.8120 1 625 1 chr5B.!!$R1 624
22 TraesCS7B01G216200 chr5B 585535252 585535874 622 False 893.0 893 92.4800 1 625 1 chr5B.!!$F1 624

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
765 770 0.038166 GGAGTGTTTCCCATCAGCCA 59.962 55.0 0.0 0.0 40.37 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1784 1804 0.039618 GGTTGGGGCTTTGAGGATGA 59.96 55.0 0.0 0.0 0.0 2.92 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
18 19 2.823628 GGTGGCACTGACTTACGTC 58.176 57.895 18.45 0.00 40.64 4.34
47 48 0.546598 ACCGGCTTAAGGCATTAGCT 59.453 50.000 26.61 0.00 44.01 3.32
62 63 4.339247 GCATTAGCTGCCTCATTTTTCCTA 59.661 41.667 0.00 0.00 45.66 2.94
89 90 5.380900 TCAATGTGTTCCACTTGATAACCA 58.619 37.500 0.00 0.00 35.11 3.67
96 97 5.048083 TGTTCCACTTGATAACCATTGAAGC 60.048 40.000 0.00 0.00 0.00 3.86
202 203 1.528292 AAGTCTGAGTCGCCGAAGCT 61.528 55.000 0.00 0.00 36.60 3.74
203 204 0.677098 AGTCTGAGTCGCCGAAGCTA 60.677 55.000 0.00 0.00 36.60 3.32
232 233 4.099573 CCGGCTTAAACTCATCTCCTTAGA 59.900 45.833 0.00 0.00 35.80 2.10
324 325 9.930693 TTAAAACATAACAAAACTTGTCACCTT 57.069 25.926 0.00 0.00 44.59 3.50
329 330 3.963129 ACAAAACTTGTCACCTTGAGGA 58.037 40.909 3.59 0.00 40.56 3.71
439 440 1.221293 GCATCTGCAGCTCTGTCCT 59.779 57.895 9.47 0.00 41.59 3.85
592 593 3.456277 CCTAAGGGAGCAGAACTAACCAT 59.544 47.826 0.00 0.00 33.58 3.55
658 659 0.749454 GGATCTTTGCCGTCAGCCAT 60.749 55.000 0.00 0.00 42.71 4.40
755 760 1.871676 GGACGACAAAGGGAGTGTTTC 59.128 52.381 0.00 0.00 0.00 2.78
765 770 0.038166 GGAGTGTTTCCCATCAGCCA 59.962 55.000 0.00 0.00 40.37 4.75
771 776 1.210478 GTTTCCCATCAGCCAGCTCTA 59.790 52.381 0.00 0.00 0.00 2.43
777 782 2.728443 ATCAGCCAGCTCTATGCCGC 62.728 60.000 0.00 0.00 44.23 6.53
833 838 1.143183 GCGGACGGCAAAGAGGATA 59.857 57.895 0.00 0.00 42.87 2.59
848 853 1.209621 GGATAGGTGGCCCACTAACA 58.790 55.000 14.71 0.00 34.40 2.41
855 860 1.818674 GTGGCCCACTAACAAGAATGG 59.181 52.381 6.63 0.00 0.00 3.16
864 869 4.630069 CACTAACAAGAATGGTCTAACGGG 59.370 45.833 0.00 0.00 32.16 5.28
899 904 1.813862 TTTGCTAGCAGACGGCAAAGT 60.814 47.619 18.45 0.00 46.45 2.66
998 1006 1.750399 GCAGCCATGGACACGGATT 60.750 57.895 18.40 0.00 0.00 3.01
1024 1032 4.514585 GGCACACACCCACCCACA 62.515 66.667 0.00 0.00 0.00 4.17
1197 1214 0.032615 CACCACCTAGCTCTCCTCCT 60.033 60.000 0.00 0.00 0.00 3.69
1262 1279 3.160047 CTCGCCCAGGAGAGCCAT 61.160 66.667 4.42 0.00 35.47 4.40
1358 1375 2.351276 GGCGTGGTCAGGATGGTT 59.649 61.111 0.00 0.00 36.16 3.67
1392 1409 2.125552 CTCAATGGCGGCGTCTCA 60.126 61.111 14.51 7.64 0.00 3.27
1548 1565 1.455217 CATCCGGTACCTCGACCCT 60.455 63.158 10.90 0.00 35.95 4.34
1552 1569 1.676635 CGGTACCTCGACCCTGACA 60.677 63.158 10.90 0.00 35.95 3.58
1580 1597 0.953471 GACAAGGTATGTGTGCCGCA 60.953 55.000 0.00 0.00 44.12 5.69
1694 1714 2.513666 GCGGTGCATTGGATCCGA 60.514 61.111 14.67 3.49 44.86 4.55
1756 1776 2.050350 CCCTCGTCGGTGCCTTCTA 61.050 63.158 0.00 0.00 0.00 2.10
1761 1781 0.030908 CGTCGGTGCCTTCTAGATCC 59.969 60.000 0.00 0.00 0.00 3.36
1762 1782 1.404843 GTCGGTGCCTTCTAGATCCT 58.595 55.000 0.00 0.00 0.00 3.24
1765 1785 1.052617 GGTGCCTTCTAGATCCTCCC 58.947 60.000 0.00 0.00 0.00 4.30
1784 1804 1.081277 GTCAGTCCCTCCCTCCCTT 59.919 63.158 0.00 0.00 0.00 3.95
2150 2170 6.219473 CGCTTTCTCTGGTATTAGATGTGAT 58.781 40.000 0.00 0.00 0.00 3.06
2265 2296 3.677596 GCTCTTAGTTTCTCTGTGCTCAC 59.322 47.826 0.00 0.00 0.00 3.51
2386 3021 6.461509 CCAAATATGAGGTGCCCTTTATTCAC 60.462 42.308 0.00 0.00 31.76 3.18
2429 3064 2.158475 TGACTGCTTCAAACCCAATCCT 60.158 45.455 0.00 0.00 0.00 3.24
2458 3093 9.443283 CTTGCTGTTTAGTGAATAAATATGCTC 57.557 33.333 7.99 0.00 35.83 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 4.214986 TGATCGTAGGAAAAATGAGGCA 57.785 40.909 0.00 0.00 0.00 4.75
89 90 1.027357 CTATTGCTGGGCGCTTCAAT 58.973 50.000 7.64 18.95 40.11 2.57
96 97 0.029834 GTTGATGCTATTGCTGGGCG 59.970 55.000 0.00 0.00 40.48 6.13
202 203 4.652421 AGATGAGTTTAAGCCGGGTATGTA 59.348 41.667 6.57 0.00 0.00 2.29
203 204 3.454812 AGATGAGTTTAAGCCGGGTATGT 59.545 43.478 6.57 0.00 0.00 2.29
232 233 0.179000 GCTCCATGGTCTTCGGATGT 59.821 55.000 12.58 0.00 0.00 3.06
324 325 3.093057 GAGTGGTCTTAGCTTCTCCTCA 58.907 50.000 0.00 0.00 0.00 3.86
329 330 2.303311 GGTTGGAGTGGTCTTAGCTTCT 59.697 50.000 0.00 0.00 0.00 2.85
439 440 5.565242 GCACTTGTGGATTTCATCAATGACA 60.565 40.000 2.81 0.00 36.36 3.58
592 593 8.742125 ATATTTTCTAGGTCATCCCATCACTA 57.258 34.615 0.00 0.00 34.66 2.74
630 631 2.290896 ACGGCAAAGATCCTGATTCCAA 60.291 45.455 0.00 0.00 0.00 3.53
755 760 0.605860 GCATAGAGCTGGCTGATGGG 60.606 60.000 0.00 0.00 41.15 4.00
765 770 1.814772 CTAGCTGGCGGCATAGAGCT 61.815 60.000 23.48 23.48 44.05 4.09
771 776 3.473647 TCAGCTAGCTGGCGGCAT 61.474 61.111 37.60 8.27 43.75 4.40
777 782 0.319383 CTATGCCGTCAGCTAGCTGG 60.319 60.000 37.60 26.07 43.75 4.85
833 838 1.145571 TTCTTGTTAGTGGGCCACCT 58.854 50.000 32.30 21.16 37.76 4.00
848 853 9.470399 AAAAATAATACCCGTTAGACCATTCTT 57.530 29.630 0.00 0.00 32.75 2.52
855 860 5.065090 ACGGCAAAAATAATACCCGTTAGAC 59.935 40.000 0.00 0.00 45.70 2.59
998 1006 0.537143 GGGTGTGTGCCAAGTCATCA 60.537 55.000 0.00 0.00 0.00 3.07
1358 1375 1.352017 TGAGAATCTTGAAGGGCTGCA 59.648 47.619 0.50 0.00 34.92 4.41
1415 1432 2.431454 ATGTACCCGCCGATGCTCA 61.431 57.895 0.00 0.00 34.43 4.26
1548 1565 1.758280 ACCTTGTCCAAGTACGTGTCA 59.242 47.619 8.02 4.29 36.72 3.58
1552 1569 3.322828 ACACATACCTTGTCCAAGTACGT 59.677 43.478 6.31 0.00 36.00 3.57
1748 1768 0.261991 ACGGGAGGATCTAGAAGGCA 59.738 55.000 0.00 0.00 33.73 4.75
1756 1776 1.075896 GGGACTGACGGGAGGATCT 60.076 63.158 0.00 0.00 33.73 2.75
1761 1781 2.760385 GGGAGGGACTGACGGGAG 60.760 72.222 0.00 0.00 41.55 4.30
1762 1782 3.273654 AGGGAGGGACTGACGGGA 61.274 66.667 0.00 0.00 41.55 5.14
1765 1785 2.760385 GGGAGGGAGGGACTGACG 60.760 72.222 0.00 0.00 41.55 4.35
1784 1804 0.039618 GGTTGGGGCTTTGAGGATGA 59.960 55.000 0.00 0.00 0.00 2.92
2284 2315 3.623703 TCATACATCAGCAGCCATTTGT 58.376 40.909 0.00 0.00 0.00 2.83
2429 3064 9.571810 CATATTTATTCACTAAACAGCAAGCAA 57.428 29.630 0.00 0.00 32.23 3.91
2458 3093 7.775729 ATTACGAAGTTTGCAATTTTCTACG 57.224 32.000 16.63 11.61 37.78 3.51
2507 3143 7.587757 GCGAATACAATTTTAATCTTCATCGCT 59.412 33.333 0.00 0.00 44.06 4.93


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

AutoCloner maintained by Alex Coulton.