Multiple sequence alignment - TraesCS4B01G329000

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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 TraesCS4B01G329000 chr4B 100.000 3509 0 0 1 3509 619807325 619810833 0 6481
1 TraesCS4B01G329000 chr4B 96.072 2011 58 17 1513 3509 661862677 661864680 0 3256
2 TraesCS4B01G329000 chr2B 97.102 2657 60 7 854 3509 731753531 731750891 0 4464
3 TraesCS4B01G329000 chr2B 97.887 899 19 0 1 899 85862652 85863550 0 1555
4 TraesCS4B01G329000 chr2B 97.775 899 20 0 1 899 87174162 87173264 0 1550
5 TraesCS4B01G329000 chr4A 96.796 2622 66 8 854 3474 723905105 723907709 0 4361
6 TraesCS4B01G329000 chr4A 95.845 2455 60 8 854 3306 668048292 668050706 0 3930
7 TraesCS4B01G329000 chr4A 96.560 1977 49 7 1537 3509 672471993 672470032 0 3256
8 TraesCS4B01G329000 chr5B 96.048 2657 55 15 854 3509 289590195 289587588 0 4279
9 TraesCS4B01G329000 chr5B 97.342 903 19 2 1 899 289591092 289590191 0 1530
10 TraesCS4B01G329000 chr5B 97.133 907 17 5 1 899 462700259 462701164 0 1522
11 TraesCS4B01G329000 chr7B 96.226 2623 75 10 854 3474 530226603 530224003 0 4274
12 TraesCS4B01G329000 chr7B 95.822 2657 77 8 854 3509 604992083 604989460 0 4261
13 TraesCS4B01G329000 chr7B 96.908 1973 44 6 1537 3509 179706020 179704065 0 3290
14 TraesCS4B01G329000 chr7B 96.747 830 18 2 74 899 611580233 611579409 0 1375
15 TraesCS4B01G329000 chr6B 97.333 2400 51 5 854 3252 683850209 683852596 0 4065
16 TraesCS4B01G329000 chr6B 96.709 1975 43 8 1537 3509 158272999 158271045 0 3267
17 TraesCS4B01G329000 chr6B 97.553 899 18 1 1 899 290994812 290995706 0 1535
18 TraesCS4B01G329000 chr6B 99.081 653 6 0 1 653 158274735 158274083 0 1173
19 TraesCS4B01G329000 chr1B 97.257 2297 48 5 854 3148 52888736 52891019 0 3879
20 TraesCS4B01G329000 chr1B 96.424 2153 48 5 459 2611 645044919 645042796 0 3522
21 TraesCS4B01G329000 chr1B 95.897 1974 52 5 1537 3509 593169148 593167203 0 3169
22 TraesCS4B01G329000 chr1B 95.114 2026 64 18 1513 3509 648086522 648088541 0 3160
23 TraesCS4B01G329000 chr1B 98.443 899 14 0 1 899 52887842 52888740 0 1583
24 TraesCS4B01G329000 chr3B 97.302 2150 54 4 854 3002 731044164 731046310 0 3646
25 TraesCS4B01G329000 chr3B 97.564 903 18 1 1 899 731043266 731044168 0 1543


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 TraesCS4B01G329000 chr4B 619807325 619810833 3508 False 6481.0 6481 100.000 1 3509 1 chr4B.!!$F1 3508
1 TraesCS4B01G329000 chr4B 661862677 661864680 2003 False 3256.0 3256 96.072 1513 3509 1 chr4B.!!$F2 1996
2 TraesCS4B01G329000 chr2B 731750891 731753531 2640 True 4464.0 4464 97.102 854 3509 1 chr2B.!!$R2 2655
3 TraesCS4B01G329000 chr2B 85862652 85863550 898 False 1555.0 1555 97.887 1 899 1 chr2B.!!$F1 898
4 TraesCS4B01G329000 chr2B 87173264 87174162 898 True 1550.0 1550 97.775 1 899 1 chr2B.!!$R1 898
5 TraesCS4B01G329000 chr4A 723905105 723907709 2604 False 4361.0 4361 96.796 854 3474 1 chr4A.!!$F2 2620
6 TraesCS4B01G329000 chr4A 668048292 668050706 2414 False 3930.0 3930 95.845 854 3306 1 chr4A.!!$F1 2452
7 TraesCS4B01G329000 chr4A 672470032 672471993 1961 True 3256.0 3256 96.560 1537 3509 1 chr4A.!!$R1 1972
8 TraesCS4B01G329000 chr5B 289587588 289591092 3504 True 2904.5 4279 96.695 1 3509 2 chr5B.!!$R1 3508
9 TraesCS4B01G329000 chr5B 462700259 462701164 905 False 1522.0 1522 97.133 1 899 1 chr5B.!!$F1 898
10 TraesCS4B01G329000 chr7B 530224003 530226603 2600 True 4274.0 4274 96.226 854 3474 1 chr7B.!!$R2 2620
11 TraesCS4B01G329000 chr7B 604989460 604992083 2623 True 4261.0 4261 95.822 854 3509 1 chr7B.!!$R3 2655
12 TraesCS4B01G329000 chr7B 179704065 179706020 1955 True 3290.0 3290 96.908 1537 3509 1 chr7B.!!$R1 1972
13 TraesCS4B01G329000 chr7B 611579409 611580233 824 True 1375.0 1375 96.747 74 899 1 chr7B.!!$R4 825
14 TraesCS4B01G329000 chr6B 683850209 683852596 2387 False 4065.0 4065 97.333 854 3252 1 chr6B.!!$F2 2398
15 TraesCS4B01G329000 chr6B 158271045 158274735 3690 True 2220.0 3267 97.895 1 3509 2 chr6B.!!$R1 3508
16 TraesCS4B01G329000 chr6B 290994812 290995706 894 False 1535.0 1535 97.553 1 899 1 chr6B.!!$F1 898
17 TraesCS4B01G329000 chr1B 645042796 645044919 2123 True 3522.0 3522 96.424 459 2611 1 chr1B.!!$R2 2152
18 TraesCS4B01G329000 chr1B 593167203 593169148 1945 True 3169.0 3169 95.897 1537 3509 1 chr1B.!!$R1 1972
19 TraesCS4B01G329000 chr1B 648086522 648088541 2019 False 3160.0 3160 95.114 1513 3509 1 chr1B.!!$F1 1996
20 TraesCS4B01G329000 chr1B 52887842 52891019 3177 False 2731.0 3879 97.850 1 3148 2 chr1B.!!$F2 3147
21 TraesCS4B01G329000 chr3B 731043266 731046310 3044 False 2594.5 3646 97.433 1 3002 2 chr3B.!!$F1 3001

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
979 1330 0.744771 GGAGGAATCGTGGAGCAACC 60.745 60.000 0.00 0.00 39.54 3.77 F
1303 1655 2.227865 GACAAACCTCCGCAAATTGCTA 59.772 45.455 16.42 3.16 42.25 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2085 2811 2.269241 CGGAGTTCCTTGGGCCTC 59.731 66.667 4.53 0.0 0.0 4.70 R
3090 3819 1.758514 TGCTCGATCCCTCCACTCC 60.759 63.158 0.00 0.0 0.0 3.85 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
63 64 1.466167 CGGAGACATGACCTTTGCAAG 59.534 52.381 0.00 0.00 0.00 4.01
99 100 5.122869 CACGATGGTCTTTCTCAATGTGATT 59.877 40.000 0.00 0.00 0.00 2.57
668 977 0.846427 TCAGAAACAGGAGGGCCCAT 60.846 55.000 27.56 9.36 37.41 4.00
728 1037 2.261729 GTCTCCCCTCCAGAGTTTTCT 58.738 52.381 0.00 0.00 32.93 2.52
979 1330 0.744771 GGAGGAATCGTGGAGCAACC 60.745 60.000 0.00 0.00 39.54 3.77
1073 1424 4.400961 GGCGTCTGGCAAGGAGCT 62.401 66.667 8.29 0.00 46.16 4.09
1160 1512 3.051940 TGATATCCACCTGAAGGAGCT 57.948 47.619 2.62 0.00 38.83 4.09
1303 1655 2.227865 GACAAACCTCCGCAAATTGCTA 59.772 45.455 16.42 3.16 42.25 3.49
1440 1792 8.581057 AGTAGATGCAATAGTTATGAAGTTCG 57.419 34.615 0.00 0.00 0.00 3.95
1665 2378 9.541143 AGTTTCTGAAGTTTTTGAAGTTTTTGA 57.459 25.926 0.00 0.00 0.00 2.69
1668 2381 9.541143 TTCTGAAGTTTTTGAAGTTTTTGAAGT 57.459 25.926 0.00 0.00 0.00 3.01
1669 2382 9.541143 TCTGAAGTTTTTGAAGTTTTTGAAGTT 57.459 25.926 0.00 0.00 0.00 2.66
1674 2387 9.541143 AGTTTTTGAAGTTTTTGAAGTTTCTGA 57.459 25.926 0.00 0.00 0.00 3.27
2085 2811 6.151663 TGATGCACCAGATTAATTTGATGG 57.848 37.500 7.53 7.72 37.07 3.51
2290 3016 0.964358 GTTTGCAGCCAGCCTCATCT 60.964 55.000 0.00 0.00 44.83 2.90
2579 3306 6.767524 AGTTATGTGGTTGAACAAGTTTGA 57.232 33.333 0.00 0.00 32.81 2.69
2681 3408 4.428209 GTCAGTTGACATCATCTCATCGT 58.572 43.478 7.37 0.00 44.18 3.73
2684 3411 4.033702 CAGTTGACATCATCTCATCGTTGG 59.966 45.833 0.00 0.00 0.00 3.77
2839 3566 6.266558 TCCAACCACATAACTTAACTGCAAAT 59.733 34.615 0.00 0.00 0.00 2.32
3113 3842 1.826921 GGAGGGATCGAGCACCGTA 60.827 63.158 0.00 0.00 39.75 4.02
3205 3934 2.442272 GGTGGAGCTCGAGGGCTA 60.442 66.667 15.58 0.00 43.20 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 0.249073 CCATCGTGTCTCCGACCATC 60.249 60.000 0.00 0.00 40.08 3.51
668 977 2.037367 CGTCCAGGAGGGGAGACA 59.963 66.667 0.63 0.00 37.71 3.41
728 1037 4.791069 GGGGAGACGTGGGCCCTA 62.791 72.222 25.70 6.58 41.72 3.53
827 1136 1.213430 ACCTGGACGTGGGAAGAAAAA 59.787 47.619 0.00 0.00 0.00 1.94
953 1304 1.160329 CCACGATTCCTCCGCCATTC 61.160 60.000 0.00 0.00 0.00 2.67
979 1330 4.101448 CTTGGCAGACGGAGGGGG 62.101 72.222 0.00 0.00 0.00 5.40
1073 1424 4.337060 CGTCGTCGACCACCAGCA 62.337 66.667 19.29 0.00 39.71 4.41
1160 1512 1.754226 TGGTGCATACGACATCTAGCA 59.246 47.619 0.00 0.00 0.00 3.49
1440 1792 7.717568 TCAGAACTAGTATTGCATCTACTTCC 58.282 38.462 13.00 3.58 31.96 3.46
1658 2371 8.742554 TCAGAAACTTCAGAAACTTCAAAAAC 57.257 30.769 6.64 0.00 0.00 2.43
1659 2372 9.410556 CTTCAGAAACTTCAGAAACTTCAAAAA 57.589 29.630 6.64 0.00 33.25 1.94
1660 2373 8.576442 ACTTCAGAAACTTCAGAAACTTCAAAA 58.424 29.630 6.64 1.44 33.25 2.44
1661 2374 8.110860 ACTTCAGAAACTTCAGAAACTTCAAA 57.889 30.769 6.64 1.68 33.25 2.69
1662 2375 7.687941 ACTTCAGAAACTTCAGAAACTTCAA 57.312 32.000 6.64 0.00 33.25 2.69
1663 2376 8.258007 TCTACTTCAGAAACTTCAGAAACTTCA 58.742 33.333 6.64 0.00 33.25 3.02
1664 2377 8.649973 TCTACTTCAGAAACTTCAGAAACTTC 57.350 34.615 0.00 0.00 33.25 3.01
1665 2378 9.050601 CATCTACTTCAGAAACTTCAGAAACTT 57.949 33.333 0.00 0.00 36.67 2.66
1666 2379 7.172361 GCATCTACTTCAGAAACTTCAGAAACT 59.828 37.037 0.00 0.00 36.67 2.66
1667 2380 7.041780 TGCATCTACTTCAGAAACTTCAGAAAC 60.042 37.037 0.00 0.00 36.67 2.78
1668 2381 6.992123 TGCATCTACTTCAGAAACTTCAGAAA 59.008 34.615 0.00 0.00 36.67 2.52
1669 2382 6.524734 TGCATCTACTTCAGAAACTTCAGAA 58.475 36.000 0.00 0.00 36.67 3.02
1670 2383 6.101650 TGCATCTACTTCAGAAACTTCAGA 57.898 37.500 0.00 0.00 36.67 3.27
1671 2384 6.791887 TTGCATCTACTTCAGAAACTTCAG 57.208 37.500 0.00 0.00 36.67 3.02
1672 2385 8.097038 ACTATTGCATCTACTTCAGAAACTTCA 58.903 33.333 0.00 0.00 36.67 3.02
1673 2386 8.485976 ACTATTGCATCTACTTCAGAAACTTC 57.514 34.615 0.00 0.00 36.67 3.01
1674 2387 8.854614 AACTATTGCATCTACTTCAGAAACTT 57.145 30.769 0.00 0.00 36.67 2.66
1675 2388 8.317679 AGAACTATTGCATCTACTTCAGAAACT 58.682 33.333 0.00 0.00 36.67 2.66
2085 2811 2.269241 CGGAGTTCCTTGGGCCTC 59.731 66.667 4.53 0.00 0.00 4.70
2290 3016 5.885912 GCTTCATTTTTGAGTAGGATGGGTA 59.114 40.000 0.00 0.00 0.00 3.69
2579 3306 8.491331 AGCAAACTTGTTCAACATAACAAAAT 57.509 26.923 0.00 0.00 45.88 1.82
2681 3408 4.484912 AGGTAAAACTAAACCATGCCCAA 58.515 39.130 0.00 0.00 38.30 4.12
2684 3411 8.063200 AGATAAAGGTAAAACTAAACCATGCC 57.937 34.615 0.00 0.00 38.30 4.40
2726 3453 6.881067 ATATCTTCCATGCCTGAATAGCTA 57.119 37.500 0.00 0.00 0.00 3.32
2839 3566 9.452287 GTGTAACTACAATTTACAGGGGAAATA 57.548 33.333 0.00 0.00 39.53 1.40
3090 3819 1.758514 TGCTCGATCCCTCCACTCC 60.759 63.158 0.00 0.00 0.00 3.85
3092 3821 2.060980 GGTGCTCGATCCCTCCACT 61.061 63.158 0.00 0.00 0.00 4.00
3101 3830 4.570663 GGCGCTACGGTGCTCGAT 62.571 66.667 7.64 0.00 46.94 3.59
3205 3934 4.806339 CCCCTCCCTCGCCTTCCT 62.806 72.222 0.00 0.00 0.00 3.36
3307 4060 3.518998 CGCCTCCGTCTCCATCGT 61.519 66.667 0.00 0.00 0.00 3.73
3431 4192 1.095807 GGTGCGCCATTAGAACCCTC 61.096 60.000 12.58 0.00 34.09 4.30


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

AutoCloner maintained by Alex Coulton.