Multiple sequence alignment - TraesCS1B01G374300

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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 TraesCS1B01G374300 chr1B 100.000 3708 0 0 1 3708 604564924 604561217 0.000000e+00 6848
1 TraesCS1B01G374300 chr1B 87.342 711 57 17 2567 3273 604645361 604644680 0.000000e+00 784
2 TraesCS1B01G374300 chr1D 96.100 1718 63 4 1 1717 444385000 444383286 0.000000e+00 2798
3 TraesCS1B01G374300 chr1D 95.943 1627 59 5 1778 3403 444383284 444381664 0.000000e+00 2632
4 TraesCS1B01G374300 chr1D 95.806 310 11 1 3399 3708 444377212 444376905 1.990000e-137 499
5 TraesCS1B01G374300 chr1A 95.732 1640 60 8 2066 3704 540063334 540061704 0.000000e+00 2632
6 TraesCS1B01G374300 chr1A 95.224 1633 63 4 87 1717 540065204 540063585 0.000000e+00 2569
7 TraesCS1B01G374300 chr1A 96.109 257 10 0 1778 2034 540063583 540063327 1.590000e-113 420
8 TraesCS1B01G374300 chr7A 76.471 612 128 13 2141 2749 88176280 88175682 5.980000e-83 318


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 TraesCS1B01G374300 chr1B 604561217 604564924 3707 True 6848.000000 6848 100.000000 1 3708 1 chr1B.!!$R1 3707
1 TraesCS1B01G374300 chr1B 604644680 604645361 681 True 784.000000 784 87.342000 2567 3273 1 chr1B.!!$R2 706
2 TraesCS1B01G374300 chr1D 444381664 444385000 3336 True 2715.000000 2798 96.021500 1 3403 2 chr1D.!!$R2 3402
3 TraesCS1B01G374300 chr1A 540061704 540065204 3500 True 1873.666667 2632 95.688333 87 3704 3 chr1A.!!$R1 3617
4 TraesCS1B01G374300 chr7A 88175682 88176280 598 True 318.000000 318 76.471000 2141 2749 1 chr7A.!!$R1 608

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
727 729 0.037419 AATTGCATGTCGCCAAACCC 60.037 50.0 0.00 0.0 41.33 4.11 F
1389 1392 0.179012 GGGTACGAGAGGAGGAGGAG 60.179 65.0 0.00 0.0 0.00 3.69 F
2473 2476 0.865769 CGCAAACGCTTGGTTCTACT 59.134 50.0 0.02 0.0 38.08 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2248 2251 0.731417 CACGACCGTAGACACCTAGG 59.269 60.000 7.41 7.41 0.00 3.02 R
2679 2682 2.942804 TGCCAAGAGGAAAACATGTCA 58.057 42.857 0.00 0.00 36.89 3.58 R
3556 3562 1.491754 ACACTACCCCGTGTTTCCTTT 59.508 47.619 0.00 0.00 45.27 3.11 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
174 175 8.574309 AAATTATTTGGAGAGAGATAGAGGGT 57.426 34.615 0.00 0.00 0.00 4.34
189 190 1.153706 GGGTGCTGCAACATCATGC 60.154 57.895 20.65 0.00 46.58 4.06
200 201 5.057819 TGCAACATCATGCTGTCAATTTTT 58.942 33.333 2.07 0.00 46.54 1.94
340 341 5.519927 TGTGTTGTATGCGAGATAAGTGATG 59.480 40.000 0.00 0.00 0.00 3.07
413 414 5.528870 TCATATGTGTGGCATAGTTACTCG 58.471 41.667 1.90 0.00 42.68 4.18
414 415 5.300792 TCATATGTGTGGCATAGTTACTCGA 59.699 40.000 1.90 0.00 42.68 4.04
461 462 7.114882 TGCAAATATGTACACAACAAAATGC 57.885 32.000 0.00 2.26 42.70 3.56
511 512 3.307691 CGACATTGATATATGGGCCACCT 60.308 47.826 9.28 0.57 37.76 4.00
516 517 6.160992 ACATTGATATATGGGCCACCTATGAT 59.839 38.462 9.28 3.00 37.76 2.45
611 612 3.255395 CGATGAGAGGAGCACATATGTCT 59.745 47.826 5.07 6.46 0.00 3.41
623 624 2.610833 ACATATGTCTCGCATGCACAAG 59.389 45.455 19.57 11.69 38.47 3.16
676 677 4.901197 TTATCAACACTCAACAGGCCTA 57.099 40.909 3.98 0.00 0.00 3.93
727 729 0.037419 AATTGCATGTCGCCAAACCC 60.037 50.000 0.00 0.00 41.33 4.11
787 790 1.048601 ACATGTGTCGGTGTCTTCCT 58.951 50.000 0.00 0.00 0.00 3.36
857 860 1.408266 GGCCCGACAATCTACCAATGT 60.408 52.381 0.00 0.00 0.00 2.71
886 889 9.834628 CAAATTAATTAGCGAAAGTAGGTTTCA 57.165 29.630 0.01 0.00 44.38 2.69
980 983 6.495872 AGTTCATACTACCCACAAGTCTGTAA 59.504 38.462 0.00 0.00 30.54 2.41
1058 1061 0.392327 GAAGAGGAGGCAAGGTCAGC 60.392 60.000 0.00 0.00 0.00 4.26
1193 1196 7.707035 GGTAACAGATCTTTATGTCAATCTCGT 59.293 37.037 0.00 0.00 0.00 4.18
1203 1206 2.230266 TGTCAATCTCGTCGTGGAATCA 59.770 45.455 0.00 0.00 0.00 2.57
1219 1222 6.510638 CGTGGAATCATATATGATGCATTCGG 60.511 42.308 27.85 12.87 46.22 4.30
1243 1246 3.260884 GGAGGAGAGACATGTTGTTGGTA 59.739 47.826 0.00 0.00 0.00 3.25
1257 1260 2.811431 TGTTGGTAGCAACACACATAGC 59.189 45.455 31.08 7.64 39.80 2.97
1389 1392 0.179012 GGGTACGAGAGGAGGAGGAG 60.179 65.000 0.00 0.00 0.00 3.69
1451 1454 3.055530 GCATTGGAGGATACGAGGATCAT 60.056 47.826 0.00 0.00 46.39 2.45
1663 1666 9.679661 ACCATACACTAATTAATCATGTTGTGA 57.320 29.630 6.49 0.00 42.06 3.58
1800 1803 5.475719 TCCCATACAAGTTTTAGACTGACG 58.524 41.667 0.00 0.00 39.00 4.35
1823 1826 8.433421 ACGAACTTACATCCCTTACATTTATG 57.567 34.615 0.00 0.00 0.00 1.90
1829 1832 9.342308 CTTACATCCCTTACATTTATGTGTGAT 57.658 33.333 5.64 0.56 41.89 3.06
1896 1899 6.530019 AAATAAGGCCAGTAAACTCCAATG 57.470 37.500 5.01 0.00 0.00 2.82
1964 1967 7.707104 ACCATACAAAATTGCTAAGATAGTGC 58.293 34.615 0.00 0.00 0.00 4.40
2099 2102 7.491048 GTGTGTTGTTGAAATGGTTAGAAACAT 59.509 33.333 0.00 0.00 0.00 2.71
2138 2141 7.848128 AGTCGGGATATTTTGTCTCTCTAAAA 58.152 34.615 0.00 0.00 0.00 1.52
2248 2251 1.154197 GTAGGTTGTTTCTCCGTGGC 58.846 55.000 0.00 0.00 0.00 5.01
2473 2476 0.865769 CGCAAACGCTTGGTTCTACT 59.134 50.000 0.02 0.00 38.08 2.57
2497 2500 5.592282 TGGTCTCAACAATGAAACAAGCTTA 59.408 36.000 0.00 0.00 34.49 3.09
2513 2516 3.622060 TTAGGGTTGCAGGCTCCGC 62.622 63.158 0.00 0.00 0.00 5.54
2679 2682 3.875369 GCTCCTCCATGTCAACAAGGATT 60.875 47.826 7.50 0.00 42.12 3.01
2755 2758 7.716799 TTGGGAAATGTTTGTGAAGCTATAT 57.283 32.000 0.00 0.00 0.00 0.86
3043 3048 6.146021 CAGGATTGTTGCCTTCATTACAAAAC 59.854 38.462 0.00 0.00 34.54 2.43
3355 3361 3.008375 TGCTCCTCATTGTATATCCCAGC 59.992 47.826 0.00 0.00 0.00 4.85
3373 3379 3.884091 CCAGCTGTCTCGTAGTATTACCT 59.116 47.826 13.81 0.00 0.00 3.08
3430 3436 2.552155 GGGCAATGACCAACACTCACTA 60.552 50.000 0.00 0.00 0.00 2.74
3452 3458 7.907045 CACTAGTATTCATTTTGTCATGCTCAC 59.093 37.037 0.00 0.00 0.00 3.51
3454 3460 7.218228 AGTATTCATTTTGTCATGCTCACAA 57.782 32.000 0.00 0.00 31.76 3.33
3466 3472 2.897350 TGCTCACAAGACCTAGGGTTA 58.103 47.619 14.81 0.00 35.25 2.85
3554 3560 5.615289 ACATATACTGGCATGGAAGTCTTC 58.385 41.667 3.80 3.80 0.00 2.87
3556 3562 6.554982 ACATATACTGGCATGGAAGTCTTCTA 59.445 38.462 12.31 6.83 0.00 2.10
3591 3597 7.884354 ACGGGGTAGTGTTTTATTATTCTTTCA 59.116 33.333 0.00 0.00 0.00 2.69
3593 3599 8.188799 GGGGTAGTGTTTTATTATTCTTTCAGC 58.811 37.037 0.00 0.00 0.00 4.26
3627 3633 8.394121 GTTGATTCAATCCTACTGAAGTTCATC 58.606 37.037 5.91 0.00 36.30 2.92
3662 3668 9.461312 TGTAACTTGGTTGATAGCTCATATTTT 57.539 29.630 0.00 0.00 0.00 1.82
3663 3669 9.937175 GTAACTTGGTTGATAGCTCATATTTTC 57.063 33.333 0.00 0.00 0.00 2.29
3664 3670 8.579850 AACTTGGTTGATAGCTCATATTTTCA 57.420 30.769 0.00 0.00 0.00 2.69
3665 3671 8.757982 ACTTGGTTGATAGCTCATATTTTCAT 57.242 30.769 0.00 0.00 0.00 2.57
3704 3710 7.255277 GGTTAATATGAGCATTTCTTGGGAGTC 60.255 40.741 0.00 0.00 0.00 3.36
3705 3711 5.643421 ATATGAGCATTTCTTGGGAGTCT 57.357 39.130 0.00 0.00 0.00 3.24
3706 3712 3.063510 TGAGCATTTCTTGGGAGTCTG 57.936 47.619 0.00 0.00 0.00 3.51
3707 3713 2.373169 TGAGCATTTCTTGGGAGTCTGT 59.627 45.455 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 8.087982 ACTATGAACATAACAGTTGACAACAG 57.912 34.615 20.08 14.55 0.00 3.16
143 144 7.579761 ATCTCTCTCCAAATAATTTCAAGGC 57.420 36.000 0.00 0.00 0.00 4.35
174 175 0.524414 GACAGCATGATGTTGCAGCA 59.476 50.000 19.10 5.46 45.23 4.41
200 201 9.902684 ATGCATTTAATAACCCATGAATTCAAA 57.097 25.926 13.09 0.00 0.00 2.69
367 368 6.823182 TGATCCACTCATTACCAGTAAATGTG 59.177 38.462 10.96 10.96 0.00 3.21
373 374 7.290014 ACACATATGATCCACTCATTACCAGTA 59.710 37.037 10.38 0.00 42.07 2.74
445 446 3.128764 TCAACGGCATTTTGTTGTGTACA 59.871 39.130 0.00 0.00 44.43 2.90
461 462 2.663808 TGTACGTACACATGTCAACGG 58.336 47.619 24.10 12.79 39.57 4.44
511 512 7.339212 ACAAGATTTTCATCCGGTTTGATCATA 59.661 33.333 0.00 0.00 0.00 2.15
516 517 4.582656 ACACAAGATTTTCATCCGGTTTGA 59.417 37.500 0.00 3.23 0.00 2.69
611 612 1.071299 ACCTGTCTTGTGCATGCGA 59.929 52.632 14.09 0.40 0.00 5.10
641 642 7.609146 TGAGTGTTGATAAATCTCAATCTTGCT 59.391 33.333 12.93 0.00 37.47 3.91
980 983 7.921041 TCCATGAGACTAGATAGGTCAAAAT 57.079 36.000 0.00 0.00 36.29 1.82
1058 1061 0.171903 GCTGTTGTGCCTAGCAATGG 59.828 55.000 0.00 0.00 41.47 3.16
1193 1196 6.256321 CGAATGCATCATATATGATTCCACGA 59.744 38.462 22.97 5.68 44.70 4.35
1203 1206 3.137176 CCTCCCCCGAATGCATCATATAT 59.863 47.826 0.00 0.00 0.00 0.86
1219 1222 1.280457 ACAACATGTCTCTCCTCCCC 58.720 55.000 0.00 0.00 0.00 4.81
1257 1260 1.064979 ACTAGGTTAATGGGGCCAACG 60.065 52.381 4.39 0.00 0.00 4.10
1361 1364 2.143594 CTCTCGTACCCCATAGCCGC 62.144 65.000 0.00 0.00 0.00 6.53
1389 1392 4.304110 CATTATCATTCATGGTTGCTGCC 58.696 43.478 0.00 0.00 0.00 4.85
1412 1415 6.751157 TCCAATGCATGACCAAATATCAATC 58.249 36.000 0.00 0.00 0.00 2.67
1451 1454 1.118965 TGGTGCTTCCTTCGTCTCCA 61.119 55.000 0.80 0.00 37.07 3.86
1554 1557 2.482721 GTGTTCGTCGATGGTCCAAAAT 59.517 45.455 4.48 0.00 0.00 1.82
1635 1638 8.902806 ACAACATGATTAATTAGTGTATGGTGG 58.097 33.333 17.06 6.42 36.39 4.61
1673 1676 8.709646 CACAAACTTAACCTAACTCTCACATAC 58.290 37.037 0.00 0.00 0.00 2.39
1754 1757 8.838741 GGGAAGTATTATTTACCACCCCATATA 58.161 37.037 0.00 0.00 31.63 0.86
1755 1758 7.298552 TGGGAAGTATTATTTACCACCCCATAT 59.701 37.037 0.00 0.00 34.59 1.78
1756 1759 6.624440 TGGGAAGTATTATTTACCACCCCATA 59.376 38.462 0.00 0.00 34.59 2.74
1757 1760 5.437043 TGGGAAGTATTATTTACCACCCCAT 59.563 40.000 0.00 0.00 34.59 4.00
1758 1761 4.794616 TGGGAAGTATTATTTACCACCCCA 59.205 41.667 0.00 0.00 34.59 4.96
1759 1762 5.391577 TGGGAAGTATTATTTACCACCCC 57.608 43.478 0.00 0.00 34.59 4.95
1760 1763 7.519927 TGTATGGGAAGTATTATTTACCACCC 58.480 38.462 5.09 0.00 35.41 4.61
1761 1764 8.983702 TTGTATGGGAAGTATTATTTACCACC 57.016 34.615 5.09 1.05 0.00 4.61
1762 1765 9.623000 ACTTGTATGGGAAGTATTATTTACCAC 57.377 33.333 5.09 0.00 31.72 4.16
1771 1774 9.449719 CAGTCTAAAACTTGTATGGGAAGTATT 57.550 33.333 0.00 0.00 35.45 1.89
1772 1775 8.822805 TCAGTCTAAAACTTGTATGGGAAGTAT 58.177 33.333 0.00 0.00 35.45 2.12
1773 1776 8.092687 GTCAGTCTAAAACTTGTATGGGAAGTA 58.907 37.037 0.00 0.00 35.45 2.24
1774 1777 6.935208 GTCAGTCTAAAACTTGTATGGGAAGT 59.065 38.462 0.00 0.00 35.45 3.01
1775 1778 6.090898 CGTCAGTCTAAAACTTGTATGGGAAG 59.909 42.308 0.00 0.00 35.45 3.46
1776 1779 5.929992 CGTCAGTCTAAAACTTGTATGGGAA 59.070 40.000 0.00 0.00 35.45 3.97
1800 1803 9.174166 ACACATAAATGTAAGGGATGTAAGTTC 57.826 33.333 0.00 0.00 39.39 3.01
1885 1888 6.266168 CAAGTAATGCCACATTGGAGTTTA 57.734 37.500 3.11 0.00 40.96 2.01
1964 1967 6.811253 TGGCCATAACAAACTACAACTAAG 57.189 37.500 0.00 0.00 0.00 2.18
2029 2032 9.499585 GTTATGGTACTACATAGTATGTATGCG 57.500 37.037 20.65 13.09 44.11 4.73
2051 2054 8.677300 CACACATGCTTATTTTAGTGGAGTTAT 58.323 33.333 0.00 0.00 0.00 1.89
2055 2058 6.500684 ACACACATGCTTATTTTAGTGGAG 57.499 37.500 0.00 0.00 0.00 3.86
2099 2102 9.453572 AAATATCCCGACTTACGTAGATATACA 57.546 33.333 11.14 0.00 41.11 2.29
2248 2251 0.731417 CACGACCGTAGACACCTAGG 59.269 60.000 7.41 7.41 0.00 3.02
2473 2476 3.953612 AGCTTGTTTCATTGTTGAGACCA 59.046 39.130 0.00 0.00 36.41 4.02
2513 2516 6.519382 TGTTCATGACTATGGATGAGCTTAG 58.481 40.000 0.00 0.00 34.97 2.18
2679 2682 2.942804 TGCCAAGAGGAAAACATGTCA 58.057 42.857 0.00 0.00 36.89 3.58
2683 2686 5.716228 TCATACATTGCCAAGAGGAAAACAT 59.284 36.000 0.00 0.00 35.55 2.71
2768 2771 7.666388 TCTTTTGGAGGGAAATTCGTTTATACA 59.334 33.333 0.00 0.00 0.00 2.29
2908 2913 3.981211 CAGGGACCTGAAACAAACATTG 58.019 45.455 13.06 0.00 46.30 2.82
3043 3048 5.920273 GTGTTTTGTCATTGGGTGATTACAG 59.080 40.000 0.00 0.00 39.48 2.74
3293 3299 7.179338 AGCTATTTGGGGACTATGTATAGTGAG 59.821 40.741 9.15 0.00 43.27 3.51
3355 3361 8.433126 CAAACAAAAGGTAATACTACGAGACAG 58.567 37.037 0.00 0.00 0.00 3.51
3373 3379 7.040478 CCATTCTCCACTATCAGACAAACAAAA 60.040 37.037 0.00 0.00 0.00 2.44
3390 3396 2.440627 CCCATGATGTCTCCATTCTCCA 59.559 50.000 0.00 0.00 0.00 3.86
3421 3427 8.939929 CATGACAAAATGAATACTAGTGAGTGT 58.060 33.333 5.39 0.00 36.28 3.55
3430 3436 6.822667 TGTGAGCATGACAAAATGAATACT 57.177 33.333 0.00 0.00 0.00 2.12
3452 3458 4.159879 ACGTCATTCTAACCCTAGGTCTTG 59.840 45.833 8.29 0.00 33.12 3.02
3454 3460 3.978610 ACGTCATTCTAACCCTAGGTCT 58.021 45.455 8.29 0.00 33.12 3.85
3466 3472 5.791336 TTCTCCTATGCATACGTCATTCT 57.209 39.130 1.16 0.00 0.00 2.40
3554 3560 3.244318 ACACTACCCCGTGTTTCCTTTAG 60.244 47.826 0.00 0.00 45.27 1.85
3556 3562 1.491754 ACACTACCCCGTGTTTCCTTT 59.508 47.619 0.00 0.00 45.27 3.11
3591 3597 3.624861 GGATTGAATCAACTCATGTCGCT 59.375 43.478 7.56 0.00 0.00 4.93
3593 3599 6.019237 CAGTAGGATTGAATCAACTCATGTCG 60.019 42.308 7.56 0.00 0.00 4.35
3627 3633 1.923356 ACCAAGTTACAATGGCCCAG 58.077 50.000 0.00 0.00 40.51 4.45
3674 3680 7.255381 CCCAAGAAATGCTCATATTAACCAGAG 60.255 40.741 0.00 0.00 0.00 3.35
3684 3690 4.225942 ACAGACTCCCAAGAAATGCTCATA 59.774 41.667 0.00 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.