Multiple sequence alignment - TraesCS5D01G128900

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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 TraesCS5D01G128900 chr5D 100.000 2288 0 0 1 2288 201837672 201839959 0 4226
1 TraesCS5D01G128900 chr5D 97.252 837 20 3 1 835 192936161 192936996 0 1415
2 TraesCS5D01G128900 chr5D 97.139 839 21 3 1 836 192943174 192944012 0 1413
3 TraesCS5D01G128900 chr5D 96.905 840 23 3 1 837 71571724 71572563 0 1404
4 TraesCS5D01G128900 chr5D 96.535 837 27 2 1 835 39684081 39683245 0 1384
5 TraesCS5D01G128900 chr5D 96.879 737 23 0 836 1572 353958164 353958900 0 1234
6 TraesCS5D01G128900 chr5D 98.946 664 7 0 1625 2288 201847062 201847725 0 1188
7 TraesCS5D01G128900 chr5D 98.647 665 8 1 1625 2288 199771308 199770644 0 1177
8 TraesCS5D01G128900 chr5D 95.387 737 31 1 836 1572 39090680 39091413 0 1170
9 TraesCS5D01G128900 chr5D 98.346 665 10 1 1625 2288 199762668 199762004 0 1166
10 TraesCS5D01G128900 chr6D 97.255 838 20 3 1 836 391522295 391523131 0 1417
11 TraesCS5D01G128900 chr6D 97.451 667 14 2 1625 2288 453895438 453896104 0 1134
12 TraesCS5D01G128900 chr1D 96.897 838 22 4 1 835 69522377 69521541 0 1400
13 TraesCS5D01G128900 chr1D 96.901 839 21 4 1 835 386383703 386384540 0 1400
14 TraesCS5D01G128900 chr1D 96.894 837 23 3 1 835 386390705 386391540 0 1399
15 TraesCS5D01G128900 chr1D 95.522 737 33 0 836 1572 481926411 481927147 0 1179
16 TraesCS5D01G128900 chr1D 95.522 737 28 1 836 1572 467435074 467435805 0 1173
17 TraesCS5D01G128900 chr1D 97.748 666 14 1 1624 2288 152258534 152257869 0 1146
18 TraesCS5D01G128900 chr3D 96.774 837 25 2 1 835 105057318 105056482 0 1395
19 TraesCS5D01G128900 chr3D 96.201 737 28 0 836 1572 55370010 55370746 0 1206
20 TraesCS5D01G128900 chr4D 95.799 738 31 0 836 1573 487078790 487078053 0 1192
21 TraesCS5D01G128900 chr4D 95.387 737 34 0 836 1572 39368940 39368204 0 1173
22 TraesCS5D01G128900 chr7D 95.387 737 32 2 836 1572 474490608 474489874 0 1171
23 TraesCS5D01G128900 chr7D 97.605 668 12 4 1625 2288 35109746 35110413 0 1142
24 TraesCS5D01G128900 chr7D 97.598 666 14 2 1625 2288 606417065 606417730 0 1140
25 TraesCS5D01G128900 chr7D 97.455 668 13 4 1625 2288 35101617 35102284 0 1136
26 TraesCS5D01G128900 chr7B 95.251 737 35 0 836 1572 603839894 603840630 0 1168
27 TraesCS5D01G128900 chr2D 97.455 668 13 3 1625 2288 459573814 459574481 0 1136


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 TraesCS5D01G128900 chr5D 201837672 201839959 2287 False 4226 4226 100.000 1 2288 1 chr5D.!!$F5 2287
1 TraesCS5D01G128900 chr5D 192936161 192936996 835 False 1415 1415 97.252 1 835 1 chr5D.!!$F3 834
2 TraesCS5D01G128900 chr5D 192943174 192944012 838 False 1413 1413 97.139 1 836 1 chr5D.!!$F4 835
3 TraesCS5D01G128900 chr5D 71571724 71572563 839 False 1404 1404 96.905 1 837 1 chr5D.!!$F2 836
4 TraesCS5D01G128900 chr5D 39683245 39684081 836 True 1384 1384 96.535 1 835 1 chr5D.!!$R1 834
5 TraesCS5D01G128900 chr5D 353958164 353958900 736 False 1234 1234 96.879 836 1572 1 chr5D.!!$F7 736
6 TraesCS5D01G128900 chr5D 201847062 201847725 663 False 1188 1188 98.946 1625 2288 1 chr5D.!!$F6 663
7 TraesCS5D01G128900 chr5D 199770644 199771308 664 True 1177 1177 98.647 1625 2288 1 chr5D.!!$R3 663
8 TraesCS5D01G128900 chr5D 39090680 39091413 733 False 1170 1170 95.387 836 1572 1 chr5D.!!$F1 736
9 TraesCS5D01G128900 chr5D 199762004 199762668 664 True 1166 1166 98.346 1625 2288 1 chr5D.!!$R2 663
10 TraesCS5D01G128900 chr6D 391522295 391523131 836 False 1417 1417 97.255 1 836 1 chr6D.!!$F1 835
11 TraesCS5D01G128900 chr6D 453895438 453896104 666 False 1134 1134 97.451 1625 2288 1 chr6D.!!$F2 663
12 TraesCS5D01G128900 chr1D 69521541 69522377 836 True 1400 1400 96.897 1 835 1 chr1D.!!$R1 834
13 TraesCS5D01G128900 chr1D 386383703 386384540 837 False 1400 1400 96.901 1 835 1 chr1D.!!$F1 834
14 TraesCS5D01G128900 chr1D 386390705 386391540 835 False 1399 1399 96.894 1 835 1 chr1D.!!$F2 834
15 TraesCS5D01G128900 chr1D 481926411 481927147 736 False 1179 1179 95.522 836 1572 1 chr1D.!!$F4 736
16 TraesCS5D01G128900 chr1D 467435074 467435805 731 False 1173 1173 95.522 836 1572 1 chr1D.!!$F3 736
17 TraesCS5D01G128900 chr1D 152257869 152258534 665 True 1146 1146 97.748 1624 2288 1 chr1D.!!$R2 664
18 TraesCS5D01G128900 chr3D 105056482 105057318 836 True 1395 1395 96.774 1 835 1 chr3D.!!$R1 834
19 TraesCS5D01G128900 chr3D 55370010 55370746 736 False 1206 1206 96.201 836 1572 1 chr3D.!!$F1 736
20 TraesCS5D01G128900 chr4D 487078053 487078790 737 True 1192 1192 95.799 836 1573 1 chr4D.!!$R2 737
21 TraesCS5D01G128900 chr4D 39368204 39368940 736 True 1173 1173 95.387 836 1572 1 chr4D.!!$R1 736
22 TraesCS5D01G128900 chr7D 474489874 474490608 734 True 1171 1171 95.387 836 1572 1 chr7D.!!$R1 736
23 TraesCS5D01G128900 chr7D 35109746 35110413 667 False 1142 1142 97.605 1625 2288 1 chr7D.!!$F2 663
24 TraesCS5D01G128900 chr7D 606417065 606417730 665 False 1140 1140 97.598 1625 2288 1 chr7D.!!$F3 663
25 TraesCS5D01G128900 chr7D 35101617 35102284 667 False 1136 1136 97.455 1625 2288 1 chr7D.!!$F1 663
26 TraesCS5D01G128900 chr7B 603839894 603840630 736 False 1168 1168 95.251 836 1572 1 chr7B.!!$F1 736
27 TraesCS5D01G128900 chr2D 459573814 459574481 667 False 1136 1136 97.455 1625 2288 1 chr2D.!!$F1 663

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
990 997 0.036732 TCCTTGCACCGAAGCTTGAT 59.963 50.0 2.1 0.0 34.99 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1794 1807 4.380841 TCCGCTGTTATCGTTTAGATGT 57.619 40.909 0.0 0.0 40.4 3.06 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
52 53 0.962489 GATGAGATCCCGGACGTCAT 59.038 55.000 18.91 11.61 0.00 3.06
600 607 1.299648 CTGGATCAAGGCGTGGGAA 59.700 57.895 0.00 0.00 0.00 3.97
662 669 1.705337 CGTTCGGCGCTTGGATCATT 61.705 55.000 7.64 0.00 0.00 2.57
753 760 4.033709 ACAAGGGTATGTAGATGCACTCT 58.966 43.478 0.00 0.00 38.06 3.24
755 762 4.679373 AGGGTATGTAGATGCACTCTTG 57.321 45.455 0.00 0.00 35.28 3.02
769 776 0.739112 CTCTTGCCCTCTCGTTGCTC 60.739 60.000 0.00 0.00 0.00 4.26
869 876 1.840635 GGAAGACCCTAAGATGCCTGT 59.159 52.381 0.00 0.00 0.00 4.00
926 933 1.234615 AACAAGCGCCGCAACTATGT 61.235 50.000 13.36 5.25 0.00 2.29
931 938 2.461110 CGCCGCAACTATGTCCACC 61.461 63.158 0.00 0.00 0.00 4.61
953 960 2.971331 ATCAGGAGGATGGCCCAAT 58.029 52.632 0.00 0.00 37.41 3.16
968 975 2.517959 CCCAATTCACTTCTGCAAGGA 58.482 47.619 0.00 0.00 33.37 3.36
990 997 0.036732 TCCTTGCACCGAAGCTTGAT 59.963 50.000 2.10 0.00 34.99 2.57
1026 1033 1.605710 CTGGACTTCACCAAGCACTTG 59.394 52.381 3.32 3.32 39.59 3.16
1406 1419 9.736414 ATATCTGAATTATGCTAGTTGATGCTT 57.264 29.630 0.00 0.00 0.00 3.91
1542 1555 3.586470 TGGGTTTGTCCACTAACATGT 57.414 42.857 0.00 0.00 38.11 3.21
1573 1586 0.880278 CACCAGACAGTGTGGTTCGG 60.880 60.000 19.82 5.50 46.73 4.30
1574 1587 1.046472 ACCAGACAGTGTGGTTCGGA 61.046 55.000 16.80 0.00 46.73 4.55
1575 1588 0.600255 CCAGACAGTGTGGTTCGGAC 60.600 60.000 8.67 0.00 0.00 4.79
1576 1589 0.939577 CAGACAGTGTGGTTCGGACG 60.940 60.000 0.00 0.00 0.00 4.79
1577 1590 1.105167 AGACAGTGTGGTTCGGACGA 61.105 55.000 0.00 0.00 0.00 4.20
1578 1591 0.249155 GACAGTGTGGTTCGGACGAA 60.249 55.000 0.00 2.62 0.00 3.85
1579 1592 0.176219 ACAGTGTGGTTCGGACGAAA 59.824 50.000 8.88 0.00 35.75 3.46
1580 1593 0.580104 CAGTGTGGTTCGGACGAAAC 59.420 55.000 15.01 15.01 41.83 2.78
1581 1594 0.462789 AGTGTGGTTCGGACGAAACT 59.537 50.000 21.25 12.57 41.98 2.66
1582 1595 1.134610 AGTGTGGTTCGGACGAAACTT 60.135 47.619 21.25 4.31 41.98 2.66
1583 1596 1.004292 GTGTGGTTCGGACGAAACTTG 60.004 52.381 21.25 0.00 41.98 3.16
1584 1597 0.041576 GTGGTTCGGACGAAACTTGC 60.042 55.000 21.25 9.51 41.98 4.01
1585 1598 1.161563 TGGTTCGGACGAAACTTGCC 61.162 55.000 21.25 12.65 41.98 4.52
1586 1599 0.883370 GGTTCGGACGAAACTTGCCT 60.883 55.000 14.64 0.00 38.67 4.75
1587 1600 0.234884 GTTCGGACGAAACTTGCCTG 59.765 55.000 8.88 0.00 35.75 4.85
1588 1601 1.503818 TTCGGACGAAACTTGCCTGC 61.504 55.000 4.47 0.00 0.00 4.85
1589 1602 1.961277 CGGACGAAACTTGCCTGCT 60.961 57.895 0.00 0.00 0.00 4.24
1590 1603 1.869690 GGACGAAACTTGCCTGCTC 59.130 57.895 0.00 0.00 0.00 4.26
1591 1604 0.603975 GGACGAAACTTGCCTGCTCT 60.604 55.000 0.00 0.00 0.00 4.09
1592 1605 0.793250 GACGAAACTTGCCTGCTCTC 59.207 55.000 0.00 0.00 0.00 3.20
1593 1606 0.394565 ACGAAACTTGCCTGCTCTCT 59.605 50.000 0.00 0.00 0.00 3.10
1594 1607 1.202698 ACGAAACTTGCCTGCTCTCTT 60.203 47.619 0.00 0.00 0.00 2.85
1595 1608 1.462670 CGAAACTTGCCTGCTCTCTTC 59.537 52.381 0.00 0.00 0.00 2.87
1596 1609 1.809547 GAAACTTGCCTGCTCTCTTCC 59.190 52.381 0.00 0.00 0.00 3.46
1597 1610 0.037447 AACTTGCCTGCTCTCTTCCC 59.963 55.000 0.00 0.00 0.00 3.97
1598 1611 1.130054 ACTTGCCTGCTCTCTTCCCA 61.130 55.000 0.00 0.00 0.00 4.37
1599 1612 0.255318 CTTGCCTGCTCTCTTCCCAT 59.745 55.000 0.00 0.00 0.00 4.00
1600 1613 0.034767 TTGCCTGCTCTCTTCCCATG 60.035 55.000 0.00 0.00 0.00 3.66
1601 1614 1.203441 TGCCTGCTCTCTTCCCATGT 61.203 55.000 0.00 0.00 0.00 3.21
1602 1615 0.034670 GCCTGCTCTCTTCCCATGTT 60.035 55.000 0.00 0.00 0.00 2.71
1603 1616 2.016096 GCCTGCTCTCTTCCCATGTTC 61.016 57.143 0.00 0.00 0.00 3.18
1604 1617 1.558756 CCTGCTCTCTTCCCATGTTCT 59.441 52.381 0.00 0.00 0.00 3.01
1605 1618 2.419851 CCTGCTCTCTTCCCATGTTCTC 60.420 54.545 0.00 0.00 0.00 2.87
1606 1619 2.235650 CTGCTCTCTTCCCATGTTCTCA 59.764 50.000 0.00 0.00 0.00 3.27
1607 1620 2.842496 TGCTCTCTTCCCATGTTCTCAT 59.158 45.455 0.00 0.00 34.21 2.90
1608 1621 3.118482 TGCTCTCTTCCCATGTTCTCATC 60.118 47.826 0.00 0.00 31.15 2.92
1609 1622 3.743899 GCTCTCTTCCCATGTTCTCATCC 60.744 52.174 0.00 0.00 31.15 3.51
1610 1623 2.432146 TCTCTTCCCATGTTCTCATCCG 59.568 50.000 0.00 0.00 31.15 4.18
1611 1624 2.169352 CTCTTCCCATGTTCTCATCCGT 59.831 50.000 0.00 0.00 31.15 4.69
1612 1625 2.093500 TCTTCCCATGTTCTCATCCGTG 60.093 50.000 0.00 0.00 31.15 4.94
1613 1626 0.107703 TCCCATGTTCTCATCCGTGC 60.108 55.000 0.00 0.00 31.15 5.34
1614 1627 0.107508 CCCATGTTCTCATCCGTGCT 60.108 55.000 0.00 0.00 31.15 4.40
1615 1628 1.293924 CCATGTTCTCATCCGTGCTC 58.706 55.000 0.00 0.00 31.15 4.26
1616 1629 1.293924 CATGTTCTCATCCGTGCTCC 58.706 55.000 0.00 0.00 31.15 4.70
1617 1630 0.179000 ATGTTCTCATCCGTGCTCCC 59.821 55.000 0.00 0.00 0.00 4.30
1618 1631 1.519455 GTTCTCATCCGTGCTCCCG 60.519 63.158 0.00 0.00 0.00 5.14
1619 1632 3.371097 TTCTCATCCGTGCTCCCGC 62.371 63.158 0.00 0.00 0.00 6.13
1620 1633 4.147449 CTCATCCGTGCTCCCGCA 62.147 66.667 0.00 0.00 45.60 5.69
1674 1687 1.904852 GCTGTGCACCAGTGTCATCG 61.905 60.000 15.69 0.00 43.55 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 1.909302 GGACCATTCCAGAACTCCTCA 59.091 52.381 0.00 0.00 42.30 3.86
417 424 1.214305 AAAGGTATGGCTGCCCTCCA 61.214 55.000 17.53 0.00 38.09 3.86
630 637 3.998672 GAACGGACGGCACCTCCA 61.999 66.667 0.00 0.00 34.01 3.86
753 760 1.529152 TACGAGCAACGAGAGGGCAA 61.529 55.000 10.05 0.00 45.77 4.52
755 762 0.389426 TTTACGAGCAACGAGAGGGC 60.389 55.000 10.05 0.00 45.77 5.19
769 776 6.986817 ACCAAGATCAATCTATGGAGTTTACG 59.013 38.462 19.34 0.00 37.92 3.18
819 826 1.952102 GCGGTGTTGGGGATCGTAGA 61.952 60.000 0.00 0.00 45.75 2.59
926 933 2.502068 ATCCTCCTGATGATGGTGGA 57.498 50.000 6.11 6.11 46.95 4.02
953 960 2.373169 AGGATGTCCTTGCAGAAGTGAA 59.627 45.455 0.00 0.00 46.09 3.18
968 975 0.250901 AAGCTTCGGTGCAAGGATGT 60.251 50.000 0.00 0.00 34.99 3.06
1041 1054 3.118261 TGTTGTTCCTGAGCTTGAACTCT 60.118 43.478 19.17 0.00 41.10 3.24
1249 1262 3.916392 CTTCGTCGTGCTTCCCGCT 62.916 63.158 0.00 0.00 40.11 5.52
1329 1342 7.148641 TCAACGCATAAACCATAAACATGTTT 58.851 30.769 25.99 25.99 36.63 2.83
1406 1419 8.840833 TCATAAGCACAACAGAGTATAAACAA 57.159 30.769 0.00 0.00 0.00 2.83
1542 1555 1.213182 TGTCTGGTGTTTGGTTGCCTA 59.787 47.619 0.00 0.00 0.00 3.93
1573 1586 0.793250 GAGAGCAGGCAAGTTTCGTC 59.207 55.000 0.00 0.00 0.00 4.20
1574 1587 0.394565 AGAGAGCAGGCAAGTTTCGT 59.605 50.000 0.00 0.00 0.00 3.85
1575 1588 1.462670 GAAGAGAGCAGGCAAGTTTCG 59.537 52.381 0.00 0.00 0.00 3.46
1576 1589 1.809547 GGAAGAGAGCAGGCAAGTTTC 59.190 52.381 0.00 0.00 0.00 2.78
1577 1590 1.546548 GGGAAGAGAGCAGGCAAGTTT 60.547 52.381 0.00 0.00 0.00 2.66
1578 1591 0.037447 GGGAAGAGAGCAGGCAAGTT 59.963 55.000 0.00 0.00 0.00 2.66
1579 1592 1.130054 TGGGAAGAGAGCAGGCAAGT 61.130 55.000 0.00 0.00 0.00 3.16
1580 1593 0.255318 ATGGGAAGAGAGCAGGCAAG 59.745 55.000 0.00 0.00 0.00 4.01
1581 1594 0.034767 CATGGGAAGAGAGCAGGCAA 60.035 55.000 0.00 0.00 0.00 4.52
1582 1595 1.203441 ACATGGGAAGAGAGCAGGCA 61.203 55.000 0.00 0.00 0.00 4.75
1583 1596 0.034670 AACATGGGAAGAGAGCAGGC 60.035 55.000 0.00 0.00 0.00 4.85
1584 1597 1.558756 AGAACATGGGAAGAGAGCAGG 59.441 52.381 0.00 0.00 0.00 4.85
1585 1598 2.235650 TGAGAACATGGGAAGAGAGCAG 59.764 50.000 0.00 0.00 0.00 4.24
1586 1599 2.259917 TGAGAACATGGGAAGAGAGCA 58.740 47.619 0.00 0.00 0.00 4.26
1587 1600 3.465871 GATGAGAACATGGGAAGAGAGC 58.534 50.000 0.00 0.00 36.82 4.09
1588 1601 3.492309 CGGATGAGAACATGGGAAGAGAG 60.492 52.174 0.00 0.00 36.82 3.20
1589 1602 2.432146 CGGATGAGAACATGGGAAGAGA 59.568 50.000 0.00 0.00 36.82 3.10
1590 1603 2.169352 ACGGATGAGAACATGGGAAGAG 59.831 50.000 0.00 0.00 36.82 2.85
1591 1604 2.093500 CACGGATGAGAACATGGGAAGA 60.093 50.000 0.00 0.00 36.82 2.87
1592 1605 2.283298 CACGGATGAGAACATGGGAAG 58.717 52.381 0.00 0.00 36.82 3.46
1593 1606 1.678728 GCACGGATGAGAACATGGGAA 60.679 52.381 0.00 0.00 36.82 3.97
1594 1607 0.107703 GCACGGATGAGAACATGGGA 60.108 55.000 0.00 0.00 36.82 4.37
1595 1608 0.107508 AGCACGGATGAGAACATGGG 60.108 55.000 0.00 0.00 36.82 4.00
1596 1609 1.293924 GAGCACGGATGAGAACATGG 58.706 55.000 0.00 0.00 36.82 3.66
1597 1610 1.293924 GGAGCACGGATGAGAACATG 58.706 55.000 0.00 0.00 36.82 3.21
1598 1611 0.179000 GGGAGCACGGATGAGAACAT 59.821 55.000 0.00 0.00 39.67 2.71
1599 1612 1.596934 GGGAGCACGGATGAGAACA 59.403 57.895 0.00 0.00 0.00 3.18
1600 1613 1.519455 CGGGAGCACGGATGAGAAC 60.519 63.158 0.00 0.00 0.00 3.01
1601 1614 2.892640 CGGGAGCACGGATGAGAA 59.107 61.111 0.00 0.00 0.00 2.87
1618 1631 1.536284 GGTCTGGTCGCTACAGTATGC 60.536 57.143 0.00 0.00 42.53 3.14
1619 1632 2.025155 AGGTCTGGTCGCTACAGTATG 58.975 52.381 0.00 0.00 46.00 2.39
1620 1633 2.299521 GAGGTCTGGTCGCTACAGTAT 58.700 52.381 0.00 0.00 37.25 2.12
1621 1634 1.003928 TGAGGTCTGGTCGCTACAGTA 59.996 52.381 0.00 0.00 37.25 2.74
1622 1635 0.251209 TGAGGTCTGGTCGCTACAGT 60.251 55.000 0.00 0.00 37.25 3.55
1794 1807 4.380841 TCCGCTGTTATCGTTTAGATGT 57.619 40.909 0.00 0.00 40.40 3.06


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

AutoCloner maintained by Alex Coulton.