Multiple sequence alignment - TraesCS4D01G067200

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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 TraesCS4D01G067200 chr4D 100.000 2650 0 0 1 2650 42333874 42336523 0 4894
1 TraesCS4D01G067200 chr4D 91.873 1009 81 1 1643 2650 297023591 297024599 0 1408
2 TraesCS4D01G067200 chr4D 91.774 1009 82 1 1642 2650 259005121 259006128 0 1402
3 TraesCS4D01G067200 chr1D 96.902 1646 42 5 1 1641 96036114 96034473 0 2748
4 TraesCS4D01G067200 chr1D 96.100 1641 56 3 1 1638 64335921 64337556 0 2669
5 TraesCS4D01G067200 chr1D 95.975 1118 30 10 524 1638 439404020 439405125 0 1801
6 TraesCS4D01G067200 chr4A 94.608 1632 58 11 1 1629 557664144 557662540 0 2499
7 TraesCS4D01G067200 chr4A 94.427 1633 60 13 1 1629 554698175 554699780 0 2483
8 TraesCS4D01G067200 chr6A 94.035 1643 58 16 3 1641 121725555 121723949 0 2455
9 TraesCS4D01G067200 chr7D 93.685 1647 53 14 1 1641 600062940 600064541 0 2418
10 TraesCS4D01G067200 chr7B 95.476 1481 54 4 1 1478 6998570 7000040 0 2351
11 TraesCS4D01G067200 chr3A 93.088 1360 72 11 281 1638 638855301 638853962 0 1971
12 TraesCS4D01G067200 chr1B 95.349 1118 32 11 524 1638 596176023 596177123 0 1759
13 TraesCS4D01G067200 chr1B 95.012 421 17 2 1 418 596175559 596175978 0 658
14 TraesCS4D01G067200 chr2B 85.939 1650 175 35 1 1637 760892134 760890529 0 1709
15 TraesCS4D01G067200 chr2B 93.100 1116 50 9 526 1634 755329850 755330945 0 1609
16 TraesCS4D01G067200 chr6D 93.905 1132 50 6 1 1129 68973815 68974930 0 1690
17 TraesCS4D01G067200 chr6D 92.779 1011 71 2 1642 2650 212528696 212527686 0 1461
18 TraesCS4D01G067200 chr6D 91.309 1024 87 2 1628 2650 163875030 163874008 0 1397
19 TraesCS4D01G067200 chr6D 91.386 1010 86 1 1641 2650 286313552 286314560 0 1382
20 TraesCS4D01G067200 chr2D 89.600 1125 101 12 518 1637 620512053 620510940 0 1415
21 TraesCS4D01G067200 chr2D 90.927 1025 89 4 1629 2650 329898947 329899970 0 1375
22 TraesCS4D01G067200 chr2D 90.750 1027 92 3 1626 2650 114593668 114594693 0 1367
23 TraesCS4D01G067200 chr2D 90.954 1017 88 4 1628 2641 356331744 356332759 0 1365
24 TraesCS4D01G067200 chr2D 90.732 1025 92 3 1628 2650 328926642 328927665 0 1363


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 TraesCS4D01G067200 chr4D 42333874 42336523 2649 False 4894.0 4894 100.0000 1 2650 1 chr4D.!!$F1 2649
1 TraesCS4D01G067200 chr4D 297023591 297024599 1008 False 1408.0 1408 91.8730 1643 2650 1 chr4D.!!$F3 1007
2 TraesCS4D01G067200 chr4D 259005121 259006128 1007 False 1402.0 1402 91.7740 1642 2650 1 chr4D.!!$F2 1008
3 TraesCS4D01G067200 chr1D 96034473 96036114 1641 True 2748.0 2748 96.9020 1 1641 1 chr1D.!!$R1 1640
4 TraesCS4D01G067200 chr1D 64335921 64337556 1635 False 2669.0 2669 96.1000 1 1638 1 chr1D.!!$F1 1637
5 TraesCS4D01G067200 chr1D 439404020 439405125 1105 False 1801.0 1801 95.9750 524 1638 1 chr1D.!!$F2 1114
6 TraesCS4D01G067200 chr4A 557662540 557664144 1604 True 2499.0 2499 94.6080 1 1629 1 chr4A.!!$R1 1628
7 TraesCS4D01G067200 chr4A 554698175 554699780 1605 False 2483.0 2483 94.4270 1 1629 1 chr4A.!!$F1 1628
8 TraesCS4D01G067200 chr6A 121723949 121725555 1606 True 2455.0 2455 94.0350 3 1641 1 chr6A.!!$R1 1638
9 TraesCS4D01G067200 chr7D 600062940 600064541 1601 False 2418.0 2418 93.6850 1 1641 1 chr7D.!!$F1 1640
10 TraesCS4D01G067200 chr7B 6998570 7000040 1470 False 2351.0 2351 95.4760 1 1478 1 chr7B.!!$F1 1477
11 TraesCS4D01G067200 chr3A 638853962 638855301 1339 True 1971.0 1971 93.0880 281 1638 1 chr3A.!!$R1 1357
12 TraesCS4D01G067200 chr1B 596175559 596177123 1564 False 1208.5 1759 95.1805 1 1638 2 chr1B.!!$F1 1637
13 TraesCS4D01G067200 chr2B 760890529 760892134 1605 True 1709.0 1709 85.9390 1 1637 1 chr2B.!!$R1 1636
14 TraesCS4D01G067200 chr2B 755329850 755330945 1095 False 1609.0 1609 93.1000 526 1634 1 chr2B.!!$F1 1108
15 TraesCS4D01G067200 chr6D 68973815 68974930 1115 False 1690.0 1690 93.9050 1 1129 1 chr6D.!!$F1 1128
16 TraesCS4D01G067200 chr6D 212527686 212528696 1010 True 1461.0 1461 92.7790 1642 2650 1 chr6D.!!$R2 1008
17 TraesCS4D01G067200 chr6D 163874008 163875030 1022 True 1397.0 1397 91.3090 1628 2650 1 chr6D.!!$R1 1022
18 TraesCS4D01G067200 chr6D 286313552 286314560 1008 False 1382.0 1382 91.3860 1641 2650 1 chr6D.!!$F2 1009
19 TraesCS4D01G067200 chr2D 620510940 620512053 1113 True 1415.0 1415 89.6000 518 1637 1 chr2D.!!$R1 1119
20 TraesCS4D01G067200 chr2D 329898947 329899970 1023 False 1375.0 1375 90.9270 1629 2650 1 chr2D.!!$F3 1021
21 TraesCS4D01G067200 chr2D 114593668 114594693 1025 False 1367.0 1367 90.7500 1626 2650 1 chr2D.!!$F1 1024
22 TraesCS4D01G067200 chr2D 356331744 356332759 1015 False 1365.0 1365 90.9540 1628 2641 1 chr2D.!!$F4 1013
23 TraesCS4D01G067200 chr2D 328926642 328927665 1023 False 1363.0 1363 90.7320 1628 2650 1 chr2D.!!$F2 1022

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
574 591 3.813724 GTCACCTGTTTTCCTTGGTCTAC 59.186 47.826 0.0 0.0 0.0 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2197 2242 0.743701 GGTCTCGACGGAGCTAGTCA 60.744 60.0 18.3 7.72 40.26 3.41 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
498 514 5.755409 ACATGAACAGTACCATCCTAACA 57.245 39.130 0.00 0.00 0.00 2.41
574 591 3.813724 GTCACCTGTTTTCCTTGGTCTAC 59.186 47.826 0.00 0.00 0.00 2.59
902 926 3.853671 CGCAGCAAATATGACTTGTTTCC 59.146 43.478 0.00 0.00 0.00 3.13
904 928 4.860907 GCAGCAAATATGACTTGTTTCCTG 59.139 41.667 0.00 0.00 0.00 3.86
927 955 5.118990 GCTCATACTTGACTGGCTTCATAA 58.881 41.667 0.00 0.00 0.00 1.90
1105 1135 1.142870 TGGATTATCCCTTCAAGCCCG 59.857 52.381 8.98 0.00 35.03 6.13
1244 1279 4.388469 GCTGCTGCTTGCTATCTTATCTAC 59.612 45.833 8.53 0.00 43.37 2.59
1552 1593 1.197721 CCTGTCAATCTGTTCGTTGCC 59.802 52.381 0.00 0.00 0.00 4.52
1667 1708 3.056749 CGTAGGGCTGTTACTTCTTCTGT 60.057 47.826 0.00 0.00 0.00 3.41
1713 1754 3.243941 TGCGTGTACAACTTCACCATAGT 60.244 43.478 0.00 0.00 0.00 2.12
1765 1807 6.071334 CCCATTCTACTGTCAGACTTAGAACA 60.071 42.308 19.62 6.87 34.27 3.18
1812 1855 3.476552 CAGGTGTCTTAGCAACTTTCCA 58.523 45.455 0.00 0.00 33.52 3.53
2059 2104 2.259818 CGCAGTGTCTTCGCTCCT 59.740 61.111 0.00 0.00 31.46 3.69
2184 2229 1.883275 CCGATGAATCTCTCTACGGCT 59.117 52.381 0.00 0.00 36.94 5.52
2197 2242 2.230508 TCTACGGCTTGTTCGATCTGTT 59.769 45.455 0.00 0.00 0.00 3.16
2202 2247 3.585862 GGCTTGTTCGATCTGTTGACTA 58.414 45.455 0.00 0.00 0.00 2.59
2391 2438 0.390472 GCAGAGGGAGGAACTTCACG 60.390 60.000 0.00 0.00 41.55 4.35
2561 2608 2.142357 CTGAGTCCAGTCGACGGCAA 62.142 60.000 17.95 3.72 46.92 4.52
2602 2649 1.063867 ACCTCAGGTATACCGCACTCT 60.064 52.381 16.31 0.00 42.08 3.24
2619 2666 5.578336 CGCACTCTGATTCAGAATCTTACAA 59.422 40.000 21.44 2.86 40.18 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
433 449 7.978975 ACACAACATTAACAATGCTAAAGTTGT 59.021 29.630 18.47 18.47 45.14 3.32
498 514 6.991531 GCCACTCTTGATGATTCTCTCTATTT 59.008 38.462 0.00 0.00 0.00 1.40
837 861 6.856426 GCTTTAGTTATGTGTGAACAAGTTCC 59.144 38.462 10.19 3.15 38.77 3.62
902 926 2.687700 AGCCAGTCAAGTATGAGCAG 57.312 50.000 0.00 0.00 35.88 4.24
904 928 2.977914 TGAAGCCAGTCAAGTATGAGC 58.022 47.619 0.00 0.00 35.88 4.26
927 955 4.158394 ACACAACAGTCAGACAAGCATTTT 59.842 37.500 2.66 0.00 0.00 1.82
1105 1135 1.445871 ACACCGGAAATTACCTTCGC 58.554 50.000 9.46 0.00 0.00 4.70
1667 1708 1.344065 TTACGAGTTCAGGCCCTTCA 58.656 50.000 0.00 0.00 0.00 3.02
1765 1807 1.822186 GTGGGTGCCAACTGTCGTT 60.822 57.895 0.00 0.00 34.18 3.85
1812 1855 4.411256 TCGGAAAAACTACAACCTCACT 57.589 40.909 0.00 0.00 0.00 3.41
2045 2090 2.569134 GCGAGGAGCGAAGACACT 59.431 61.111 0.00 0.00 44.57 3.55
2184 2229 4.486090 GAGCTAGTCAACAGATCGAACAA 58.514 43.478 0.00 0.00 0.00 2.83
2197 2242 0.743701 GGTCTCGACGGAGCTAGTCA 60.744 60.000 18.30 7.72 40.26 3.41
2202 2247 2.752238 CAGGGTCTCGACGGAGCT 60.752 66.667 12.88 0.00 40.26 4.09
2428 2475 1.077068 CGAGCCTCAGAGGTCTCCT 60.077 63.158 24.23 12.75 37.80 3.69
2429 2476 2.124693 CCGAGCCTCAGAGGTCTCC 61.125 68.421 24.23 8.87 37.80 3.71
2561 2608 2.280592 GGCGGGAACAGTTGTCGT 60.281 61.111 0.00 0.00 0.00 4.34
2602 2649 5.122869 GCTGCAGTTGTAAGATTCTGAATCA 59.877 40.000 27.06 9.29 40.42 2.57
2619 2666 1.443407 CTGCTATACGGGCTGCAGT 59.557 57.895 16.64 3.46 45.31 4.40


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

AutoCloner maintained by Alex Coulton.