Multiple sequence alignment - TraesCS5D01G499300

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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 TraesCS5D01G499300 chr5D 100.000 2675 0 0 1 2675 528761225 528763899 0.000000e+00 4940.0
1 TraesCS5D01G499300 chr5D 87.798 1721 163 20 960 2657 528802717 528804413 0.000000e+00 1971.0
2 TraesCS5D01G499300 chr5D 86.344 1157 142 8 1515 2660 528747820 528748971 0.000000e+00 1247.0
3 TraesCS5D01G499300 chr5D 88.730 630 39 17 678 1299 528745478 528746083 0.000000e+00 741.0
4 TraesCS5D01G499300 chr5D 76.774 155 34 2 2503 2656 4051541 4051388 4.740000e-13 86.1
5 TraesCS5D01G499300 chr5B 93.798 1177 59 6 1506 2675 665939082 665940251 0.000000e+00 1757.0
6 TraesCS5D01G499300 chr5B 87.894 1173 118 12 1506 2660 665958679 665959845 0.000000e+00 1358.0
7 TraesCS5D01G499300 chr5B 92.535 777 48 6 596 1366 665938180 665938952 0.000000e+00 1105.0
8 TraesCS5D01G499300 chr5B 91.883 616 30 11 1 599 665912973 665913585 0.000000e+00 843.0
9 TraesCS5D01G499300 chr5B 90.995 422 35 1 945 1366 665958156 665958574 1.390000e-157 566.0
10 TraesCS5D01G499300 chr5B 85.149 101 13 2 2555 2654 6881944 6881845 4.710000e-18 102.0
11 TraesCS5D01G499300 chr6B 83.231 1139 164 13 1538 2660 106509384 106510511 0.000000e+00 1020.0
12 TraesCS5D01G499300 chrUn 82.275 1134 174 13 1538 2655 97782383 97783505 0.000000e+00 955.0
13 TraesCS5D01G499300 chr1D 83.297 910 138 9 1765 2666 476570482 476569579 0.000000e+00 826.0
14 TraesCS5D01G499300 chr1B 83.790 839 124 7 1839 2670 662843672 662842839 0.000000e+00 785.0
15 TraesCS5D01G499300 chr1A 83.439 157 23 3 1873 2028 584840507 584840661 2.780000e-30 143.0


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 TraesCS5D01G499300 chr5D 528761225 528763899 2674 False 4940 4940 100.0000 1 2675 1 chr5D.!!$F1 2674
1 TraesCS5D01G499300 chr5D 528802717 528804413 1696 False 1971 1971 87.7980 960 2657 1 chr5D.!!$F2 1697
2 TraesCS5D01G499300 chr5D 528745478 528748971 3493 False 994 1247 87.5370 678 2660 2 chr5D.!!$F3 1982
3 TraesCS5D01G499300 chr5B 665938180 665940251 2071 False 1431 1757 93.1665 596 2675 2 chr5B.!!$F2 2079
4 TraesCS5D01G499300 chr5B 665958156 665959845 1689 False 962 1358 89.4445 945 2660 2 chr5B.!!$F3 1715
5 TraesCS5D01G499300 chr5B 665912973 665913585 612 False 843 843 91.8830 1 599 1 chr5B.!!$F1 598
6 TraesCS5D01G499300 chr6B 106509384 106510511 1127 False 1020 1020 83.2310 1538 2660 1 chr6B.!!$F1 1122
7 TraesCS5D01G499300 chrUn 97782383 97783505 1122 False 955 955 82.2750 1538 2655 1 chrUn.!!$F1 1117
8 TraesCS5D01G499300 chr1D 476569579 476570482 903 True 826 826 83.2970 1765 2666 1 chr1D.!!$R1 901
9 TraesCS5D01G499300 chr1B 662842839 662843672 833 True 785 785 83.7900 1839 2670 1 chr1B.!!$R1 831

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
980 1008 0.17897 GCCATCAGCCCATCCAAGAT 60.179 55.0 0.0 0.0 34.35 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2115 3725 0.698238 CCCTTTCCCACAGGTCATCA 59.302 55.0 0.0 0.0 0.0 3.07 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
130 135 6.475076 CGTGACCATTTCTTGAAATTGTGAAA 59.525 34.615 14.70 0.00 33.74 2.69
225 231 8.250332 ACCATACAATTTAAAATTCGTGAGCAT 58.750 29.630 0.00 0.00 0.00 3.79
300 308 7.753309 TCATGAACTTTTCTTAAATTCCCGA 57.247 32.000 0.00 0.00 0.00 5.14
305 313 8.079809 TGAACTTTTCTTAAATTCCCGAACATC 58.920 33.333 0.00 0.00 0.00 3.06
336 344 9.750125 ACAAATTCACAAATACTTTTCTTCTCC 57.250 29.630 0.00 0.00 0.00 3.71
383 391 0.612174 TCACCCACTCTCCTTCTCCG 60.612 60.000 0.00 0.00 0.00 4.63
442 458 6.099701 GCCACCTTTGGGGAATAATAGATTTT 59.900 38.462 0.00 0.00 44.15 1.82
444 460 8.860088 CCACCTTTGGGGAATAATAGATTTTAG 58.140 37.037 0.00 0.00 39.57 1.85
462 478 0.679960 AGTAAATTGTCCCCTGGCGC 60.680 55.000 0.00 0.00 0.00 6.53
509 527 0.179034 CAAGCATAGGAGGGTGGCTC 60.179 60.000 0.00 0.00 32.84 4.70
552 570 3.118261 TCGGGTAAGACATACTAGTCCGT 60.118 47.826 0.00 0.00 39.34 4.69
564 582 3.220110 ACTAGTCCGTGAACTCTTGACA 58.780 45.455 0.00 0.00 0.00 3.58
608 626 4.352298 GTCCATCTCCAGATCCCCTAAAAT 59.648 45.833 0.00 0.00 31.21 1.82
614 632 2.175499 CCAGATCCCCTAAAATGAGCCA 59.825 50.000 0.00 0.00 0.00 4.75
718 738 7.668492 ACGTCTTCATAAGTAAAGAAACTCCT 58.332 34.615 0.00 0.00 33.53 3.69
819 847 1.344114 GGTACCCACCAACTTGTACGA 59.656 52.381 0.00 0.00 45.04 3.43
840 868 9.831737 GTACGAGTACTTTATTCTTACTGTCAA 57.168 33.333 0.00 0.00 33.45 3.18
871 899 0.753867 TGTTGACGGTAGACTTGGCA 59.246 50.000 0.00 0.00 0.00 4.92
916 944 3.057876 GCGTGATAAGACCTGATCGATCT 60.058 47.826 25.02 6.15 0.00 2.75
974 1002 2.124024 TGCAGCCATCAGCCCATC 60.124 61.111 0.00 0.00 45.47 3.51
975 1003 2.910994 GCAGCCATCAGCCCATCC 60.911 66.667 0.00 0.00 45.47 3.51
980 1008 0.178970 GCCATCAGCCCATCCAAGAT 60.179 55.000 0.00 0.00 34.35 2.40
982 1010 2.236766 CCATCAGCCCATCCAAGATTC 58.763 52.381 0.00 0.00 0.00 2.52
1001 1029 1.674764 CGAGAGAGGTGAGCAGCCAT 61.675 60.000 0.00 0.00 0.00 4.40
1002 1030 0.179078 GAGAGAGGTGAGCAGCCATG 60.179 60.000 0.00 0.00 0.00 3.66
1003 1031 1.153208 GAGAGGTGAGCAGCCATGG 60.153 63.158 7.63 7.63 0.00 3.66
1004 1032 2.827642 GAGGTGAGCAGCCATGGC 60.828 66.667 30.12 30.12 42.33 4.40
1164 1193 2.439104 GGAGGCCCTGCTCGAAGAT 61.439 63.158 0.00 0.00 33.89 2.40
1333 1362 4.399618 TGAACCAAGACGAAATTTGTCCAA 59.600 37.500 9.61 0.00 37.04 3.53
1340 1373 3.059166 ACGAAATTTGTCCAATGCTTGC 58.941 40.909 0.00 0.00 0.00 4.01
1362 1395 2.866762 GCTCTAATTGTTCTGGGTAGCG 59.133 50.000 0.00 0.00 0.00 4.26
1369 1402 3.472283 TGTTCTGGGTAGCGTTTGTTA 57.528 42.857 0.00 0.00 0.00 2.41
1372 1405 4.251268 GTTCTGGGTAGCGTTTGTTAGAT 58.749 43.478 0.00 0.00 0.00 1.98
1376 1409 4.186159 TGGGTAGCGTTTGTTAGATTAGC 58.814 43.478 0.00 0.00 0.00 3.09
1377 1410 3.558829 GGGTAGCGTTTGTTAGATTAGCC 59.441 47.826 0.00 0.00 0.00 3.93
1380 1413 4.946784 AGCGTTTGTTAGATTAGCCAAG 57.053 40.909 0.00 0.00 0.00 3.61
1431 1480 7.490962 TTTTTGAGAGTCAATGAATGTACGT 57.509 32.000 0.00 0.00 36.11 3.57
1433 1482 8.771920 TTTTGAGAGTCAATGAATGTACGTAT 57.228 30.769 0.00 0.00 36.11 3.06
1434 1483 7.755582 TTGAGAGTCAATGAATGTACGTATG 57.244 36.000 0.00 0.00 30.26 2.39
1435 1484 7.095695 TGAGAGTCAATGAATGTACGTATGA 57.904 36.000 0.00 0.00 0.00 2.15
1436 1485 7.543756 TGAGAGTCAATGAATGTACGTATGAA 58.456 34.615 0.00 0.00 0.00 2.57
1437 1486 7.702348 TGAGAGTCAATGAATGTACGTATGAAG 59.298 37.037 0.00 0.00 0.00 3.02
1438 1487 6.980978 AGAGTCAATGAATGTACGTATGAAGG 59.019 38.462 0.00 0.00 0.00 3.46
1518 3102 3.708563 ACTTATGTTGTGTTGTGGTGC 57.291 42.857 0.00 0.00 0.00 5.01
1531 3118 5.687285 GTGTTGTGGTGCTTGATTTCTAAAG 59.313 40.000 0.00 0.00 0.00 1.85
1534 3121 6.317789 TGTGGTGCTTGATTTCTAAAGAAG 57.682 37.500 0.00 0.00 35.21 2.85
1644 3244 1.251251 AGTGTTGCCCTCAAATCAGC 58.749 50.000 0.00 0.00 33.37 4.26
1827 3437 4.527944 GAGGGATAAGGAAAAACAGGAGG 58.472 47.826 0.00 0.00 0.00 4.30
1829 3439 4.017126 GGGATAAGGAAAAACAGGAGGTG 58.983 47.826 0.00 0.00 0.00 4.00
1938 3548 5.653507 CACGATTGGTTTTCAATGATCCAT 58.346 37.500 0.00 0.00 45.36 3.41
1961 3571 3.506844 AGTTCAAAGAGTACTCTCGGGTC 59.493 47.826 25.34 15.30 44.65 4.46
1967 3577 1.211457 GAGTACTCTCGGGTCTGGGTA 59.789 57.143 15.91 0.00 0.00 3.69
1992 3602 2.875933 GTGTCCCAGACGTTTGATTTGA 59.124 45.455 7.81 0.00 34.95 2.69
2115 3725 7.510675 TGGTAAGAAGGTCCTAATCATCTTT 57.489 36.000 7.86 0.00 0.00 2.52
2130 3740 3.330405 TCATCTTTGATGACCTGTGGGAA 59.670 43.478 6.19 0.00 36.25 3.97
2138 3748 0.476771 GACCTGTGGGAAAGGGAACA 59.523 55.000 0.00 0.00 39.30 3.18
2140 3750 1.289530 ACCTGTGGGAAAGGGAACAAA 59.710 47.619 0.00 0.00 39.30 2.83
2242 3858 8.767478 AGAAAATATTGCACAGAAAATTCAGG 57.233 30.769 0.00 0.00 0.00 3.86
2452 4068 1.600957 CATCTGATGAATGGGTGTCGC 59.399 52.381 12.27 0.00 0.00 5.19
2660 4276 1.133513 TGGACTTGTTGAGCCACCAAT 60.134 47.619 0.00 0.00 30.03 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 60 7.813148 TGAAAACGTGTTTGTAAAATGGAAGAA 59.187 29.630 0.00 0.00 32.36 2.52
56 61 7.313646 TGAAAACGTGTTTGTAAAATGGAAGA 58.686 30.769 0.00 0.00 32.36 2.87
98 103 6.573664 TTCAAGAAATGGTCACGATTTGAT 57.426 33.333 2.01 0.00 36.32 2.57
355 363 0.980231 AGAGTGGGTGAGATGAGGGC 60.980 60.000 0.00 0.00 0.00 5.19
383 391 0.997196 AAAAACGATCTAGCGGCGAC 59.003 50.000 12.98 1.23 35.12 5.19
410 426 1.068921 CCCAAAGGTGGCGGTTTTG 59.931 57.895 0.00 1.79 44.46 2.44
414 430 1.502527 TATTCCCCAAAGGTGGCGGT 61.503 55.000 0.00 0.00 44.46 5.68
442 458 1.407712 GCGCCAGGGGACAATTTACTA 60.408 52.381 7.95 0.00 0.00 1.82
444 460 0.679960 AGCGCCAGGGGACAATTTAC 60.680 55.000 7.95 0.00 0.00 2.01
462 478 3.137176 TGGGCTATTTGGAATGAGAGGAG 59.863 47.826 0.00 0.00 0.00 3.69
521 539 1.138036 TCTTACCCGACATCACGCG 59.862 57.895 3.53 3.53 0.00 6.01
535 553 6.413052 AGAGTTCACGGACTAGTATGTCTTA 58.587 40.000 0.00 0.00 37.16 2.10
552 570 0.104855 AGCGCACTGTCAAGAGTTCA 59.895 50.000 11.47 0.00 0.00 3.18
583 601 2.156425 AGGGGATCTGGAGATGGACTA 58.844 52.381 0.00 0.00 34.37 2.59
608 626 1.559682 GGATGGTTAAGGACTGGCTCA 59.440 52.381 0.00 0.00 0.00 4.26
614 632 3.655777 TGTTTGGAGGATGGTTAAGGACT 59.344 43.478 0.00 0.00 0.00 3.85
718 738 3.433598 CCCTTAAAGCATCTTCATCGGGA 60.434 47.826 0.00 0.00 0.00 5.14
835 863 4.455533 GTCAACAAGTGCCTATCATTGACA 59.544 41.667 8.84 0.00 42.45 3.58
840 868 2.027192 ACCGTCAACAAGTGCCTATCAT 60.027 45.455 0.00 0.00 0.00 2.45
871 899 0.856982 TTGGAGATTGGGGTGGTTGT 59.143 50.000 0.00 0.00 0.00 3.32
908 936 1.757118 TCCTGGTGTGGAAGATCGATC 59.243 52.381 17.91 17.91 32.39 3.69
916 944 1.816863 GACGAGCTCCTGGTGTGGAA 61.817 60.000 8.47 0.00 35.43 3.53
974 1002 2.481104 GCTCACCTCTCTCGAATCTTGG 60.481 54.545 0.00 0.00 0.00 3.61
975 1003 2.165234 TGCTCACCTCTCTCGAATCTTG 59.835 50.000 0.00 0.00 0.00 3.02
980 1008 1.599606 GGCTGCTCACCTCTCTCGAA 61.600 60.000 0.00 0.00 0.00 3.71
982 1010 1.674764 ATGGCTGCTCACCTCTCTCG 61.675 60.000 0.00 0.00 0.00 4.04
1001 1029 4.854924 CCCCGACATGATGCGCCA 62.855 66.667 4.18 0.00 0.00 5.69
1005 1033 4.856801 ACGCCCCCGACATGATGC 62.857 66.667 0.00 0.00 38.29 3.91
1006 1034 2.588877 GACGCCCCCGACATGATG 60.589 66.667 0.00 0.00 38.29 3.07
1007 1035 2.383245 GATGACGCCCCCGACATGAT 62.383 60.000 0.00 0.00 46.62 2.45
1008 1036 3.080765 ATGACGCCCCCGACATGA 61.081 61.111 0.00 0.00 45.36 3.07
1164 1193 2.685017 ATGGACCGCCTCTCAGCA 60.685 61.111 0.00 0.00 34.31 4.41
1340 1373 2.866762 GCTACCCAGAACAATTAGAGCG 59.133 50.000 0.00 0.00 0.00 5.03
1406 1455 8.099364 ACGTACATTCATTGACTCTCAAAAAT 57.901 30.769 0.00 0.00 40.12 1.82
1429 1478 2.120232 GAGCATGACGTCCTTCATACG 58.880 52.381 14.12 0.00 45.64 3.06
1431 1480 2.495669 TGTGAGCATGACGTCCTTCATA 59.504 45.455 14.12 7.02 34.29 2.15
1433 1482 0.678950 TGTGAGCATGACGTCCTTCA 59.321 50.000 14.12 8.54 0.00 3.02
1434 1483 1.337260 ACTGTGAGCATGACGTCCTTC 60.337 52.381 14.12 5.97 0.00 3.46
1435 1484 0.681733 ACTGTGAGCATGACGTCCTT 59.318 50.000 14.12 0.00 0.00 3.36
1436 1485 0.681733 AACTGTGAGCATGACGTCCT 59.318 50.000 14.12 2.34 0.00 3.85
1437 1486 1.071605 GAACTGTGAGCATGACGTCC 58.928 55.000 14.12 0.00 0.00 4.79
1438 1487 1.071605 GGAACTGTGAGCATGACGTC 58.928 55.000 9.11 9.11 0.00 4.34
1499 3083 3.988379 AGCACCACAACACAACATAAG 57.012 42.857 0.00 0.00 0.00 1.73
1513 3097 7.765695 ATTCTTCTTTAGAAATCAAGCACCA 57.234 32.000 0.00 0.00 45.62 4.17
1553 3143 9.699410 AATGAAATATAATTTGACAGTCCTGGA 57.301 29.630 0.00 0.00 34.19 3.86
1607 3205 6.403092 GCAACACTACAAAGGCAACAAATTTT 60.403 34.615 0.00 0.00 41.41 1.82
1608 3206 5.064579 GCAACACTACAAAGGCAACAAATTT 59.935 36.000 0.00 0.00 41.41 1.82
1609 3207 4.570369 GCAACACTACAAAGGCAACAAATT 59.430 37.500 0.00 0.00 41.41 1.82
1610 3208 4.119136 GCAACACTACAAAGGCAACAAAT 58.881 39.130 0.00 0.00 41.41 2.32
1611 3209 3.516615 GCAACACTACAAAGGCAACAAA 58.483 40.909 0.00 0.00 41.41 2.83
1612 3210 2.159170 GGCAACACTACAAAGGCAACAA 60.159 45.455 0.00 0.00 41.41 2.83
1644 3244 1.336795 GGCCATTTCAACCTGGAAACG 60.337 52.381 0.00 0.00 39.40 3.60
1827 3437 3.869065 TCCCAGATAAACGAACCATCAC 58.131 45.455 0.00 0.00 0.00 3.06
1829 3439 2.872858 GCTCCCAGATAAACGAACCATC 59.127 50.000 0.00 0.00 0.00 3.51
1938 3548 4.660168 ACCCGAGAGTACTCTTTGAACTA 58.340 43.478 25.86 0.00 40.61 2.24
1967 3577 3.973206 TCAAACGTCTGGGACACATAT 57.027 42.857 0.00 0.00 32.09 1.78
2090 3700 7.510675 AAGATGATTAGGACCTTCTTACCAA 57.489 36.000 0.00 0.00 0.00 3.67
2115 3725 0.698238 CCCTTTCCCACAGGTCATCA 59.302 55.000 0.00 0.00 0.00 3.07
2130 3740 3.662759 TCCAACTCAGTTTGTTCCCTT 57.337 42.857 0.00 0.00 0.00 3.95
2140 3750 9.918630 CATATTCTTCAATTTTTCCAACTCAGT 57.081 29.630 0.00 0.00 0.00 3.41
2307 3923 5.350091 GTCAGTTCTAGCATCAAAGGAAGTC 59.650 44.000 0.00 0.00 0.00 3.01
2570 4186 6.267471 ACCTTTTGGAAAGATTGCACAATAGA 59.733 34.615 2.15 0.00 44.07 1.98


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

AutoCloner maintained by Alex Coulton.