Multiple sequence alignment - TraesCS4D01G243200

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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 TraesCS4D01G243200 chr4D 100.000 2339 0 0 1 2339 405775472 405773134 0.000000e+00 4320
1 TraesCS4D01G243200 chr4B 95.556 1530 34 12 20 1543 504944531 504943030 0.000000e+00 2418
2 TraesCS4D01G243200 chr4B 87.467 383 29 10 1952 2328 504942463 504942094 7.730000e-115 424
3 TraesCS4D01G243200 chr4B 81.922 437 30 30 1559 1961 504943044 504942623 8.060000e-85 324
4 TraesCS4D01G243200 chr4A 94.308 1423 43 17 145 1543 63544647 63543239 0.000000e+00 2145
5 TraesCS4D01G243200 chr4A 91.803 427 32 2 1894 2318 63541283 63540858 2.000000e-165 592
6 TraesCS4D01G243200 chr4A 88.630 343 16 16 1559 1894 63543253 63542927 1.680000e-106 396
7 TraesCS4D01G243200 chr6B 77.825 938 202 6 394 1328 659616792 659615858 2.020000e-160 575
8 TraesCS4D01G243200 chr2A 75.455 1043 199 45 427 1439 183551760 183550745 2.740000e-124 455
9 TraesCS4D01G243200 chr2B 75.264 1043 201 45 427 1439 231234902 231233887 5.930000e-121 444
10 TraesCS4D01G243200 chr2D 74.904 1040 198 49 427 1433 166608429 166609438 1.290000e-112 416
11 TraesCS4D01G243200 chr5B 73.958 1056 227 45 423 1457 400562816 400563844 1.310000e-102 383
12 TraesCS4D01G243200 chr5A 84.028 288 39 7 423 708 442290826 442291108 1.070000e-68 270
13 TraesCS4D01G243200 chr5D 83.333 288 41 7 423 708 341075306 341075588 2.310000e-65 259


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 TraesCS4D01G243200 chr4D 405773134 405775472 2338 True 4320.000000 4320 100.000000 1 2339 1 chr4D.!!$R1 2338
1 TraesCS4D01G243200 chr4B 504942094 504944531 2437 True 1055.333333 2418 88.315000 20 2328 3 chr4B.!!$R1 2308
2 TraesCS4D01G243200 chr4A 63540858 63544647 3789 True 1044.333333 2145 91.580333 145 2318 3 chr4A.!!$R1 2173
3 TraesCS4D01G243200 chr6B 659615858 659616792 934 True 575.000000 575 77.825000 394 1328 1 chr6B.!!$R1 934
4 TraesCS4D01G243200 chr2A 183550745 183551760 1015 True 455.000000 455 75.455000 427 1439 1 chr2A.!!$R1 1012
5 TraesCS4D01G243200 chr2B 231233887 231234902 1015 True 444.000000 444 75.264000 427 1439 1 chr2B.!!$R1 1012
6 TraesCS4D01G243200 chr2D 166608429 166609438 1009 False 416.000000 416 74.904000 427 1433 1 chr2D.!!$F1 1006
7 TraesCS4D01G243200 chr5B 400562816 400563844 1028 False 383.000000 383 73.958000 423 1457 1 chr5B.!!$F1 1034

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
196 202 0.179137 CTGCTGTTCCTCGTCGCATA 60.179 55.0 0.0 0.0 0.0 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1559 1594 0.035152 TCGTTCAGGCCATCTGCATT 60.035 50.0 5.01 0.0 43.06 3.56 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
17 18 4.941609 ACAGGTAGGCTCGCATTG 57.058 55.556 0.00 0.00 0.00 2.82
18 19 1.983224 ACAGGTAGGCTCGCATTGT 59.017 52.632 0.00 0.00 0.00 2.71
78 82 8.026341 GGATACTACCACTAAACAAGAAACAC 57.974 38.462 0.00 0.00 0.00 3.32
87 91 7.411274 CACTAAACAAGAAACACCGAAATACA 58.589 34.615 0.00 0.00 0.00 2.29
98 102 4.219070 ACACCGAAATACACTACACTGCTA 59.781 41.667 0.00 0.00 0.00 3.49
125 129 4.083003 TCTGTCCCAAAATAATTGACGTGC 60.083 41.667 0.00 0.00 0.00 5.34
142 146 2.433436 GTGCTTATTTTGGGACCGAGT 58.567 47.619 0.00 0.00 0.00 4.18
196 202 0.179137 CTGCTGTTCCTCGTCGCATA 60.179 55.000 0.00 0.00 0.00 3.14
197 203 0.459899 TGCTGTTCCTCGTCGCATAT 59.540 50.000 0.00 0.00 0.00 1.78
198 204 0.855349 GCTGTTCCTCGTCGCATATG 59.145 55.000 0.00 0.00 0.00 1.78
199 205 1.491670 CTGTTCCTCGTCGCATATGG 58.508 55.000 4.56 0.00 0.00 2.74
200 206 1.067060 CTGTTCCTCGTCGCATATGGA 59.933 52.381 4.56 0.00 0.00 3.41
201 207 1.478916 TGTTCCTCGTCGCATATGGAA 59.521 47.619 4.56 0.00 34.81 3.53
202 208 2.093921 TGTTCCTCGTCGCATATGGAAA 60.094 45.455 4.56 0.00 38.35 3.13
203 209 3.131396 GTTCCTCGTCGCATATGGAAAT 58.869 45.455 4.56 0.00 38.35 2.17
214 220 3.797865 GCATATGGAAATGGAAGCAGTGC 60.798 47.826 7.13 7.13 0.00 4.40
259 282 2.288186 GTGTCTGCACTCGATCGAGATA 59.712 50.000 42.97 28.00 44.53 1.98
846 878 1.672030 CAGGAACATCTGCACGCCA 60.672 57.895 0.00 0.00 0.00 5.69
969 1001 3.479269 GCGTCGCTCTTGAACCCG 61.479 66.667 10.68 0.00 0.00 5.28
1506 1541 9.453325 GTATAGTAAGAAGAAATTCTGAGACGG 57.547 37.037 0.00 0.00 0.00 4.79
1543 1578 2.028876 TCATCAAATGCAGATGGCCTG 58.971 47.619 3.32 0.00 42.38 4.85
1544 1579 1.754803 CATCAAATGCAGATGGCCTGT 59.245 47.619 3.32 0.00 44.71 4.00
1545 1580 1.466856 TCAAATGCAGATGGCCTGTC 58.533 50.000 3.32 1.89 44.71 3.51
1546 1581 0.458669 CAAATGCAGATGGCCTGTCC 59.541 55.000 3.32 0.00 44.71 4.02
1547 1582 0.685458 AAATGCAGATGGCCTGTCCC 60.685 55.000 3.32 0.00 44.71 4.46
1548 1583 2.578586 AATGCAGATGGCCTGTCCCC 62.579 60.000 3.32 0.00 44.71 4.81
1549 1584 4.864334 GCAGATGGCCTGTCCCCG 62.864 72.222 3.32 0.00 44.71 5.73
1550 1585 4.864334 CAGATGGCCTGTCCCCGC 62.864 72.222 3.32 0.00 38.10 6.13
1552 1587 4.424711 GATGGCCTGTCCCCGCAA 62.425 66.667 3.32 0.00 0.00 4.85
1553 1588 3.936772 GATGGCCTGTCCCCGCAAA 62.937 63.158 3.32 0.00 0.00 3.68
1554 1589 3.521765 ATGGCCTGTCCCCGCAAAA 62.522 57.895 3.32 0.00 0.00 2.44
1555 1590 2.915137 GGCCTGTCCCCGCAAAAA 60.915 61.111 0.00 0.00 0.00 1.94
1608 1644 1.683319 GGCCAGAATGTTCTCTTCCCC 60.683 57.143 0.00 0.00 34.74 4.81
1668 1724 4.030913 ACCTAGCATGCTTTCCTACTGTA 58.969 43.478 28.02 1.95 0.00 2.74
1699 1757 2.764010 TCACCTTAGCATGTGACCGTAT 59.236 45.455 0.00 0.00 36.62 3.06
1702 1760 5.069914 TCACCTTAGCATGTGACCGTATAAT 59.930 40.000 0.00 0.00 36.62 1.28
1716 1774 8.378421 GTGACCGTATAATTAAAGTGTCAGAAC 58.622 37.037 9.95 0.01 32.68 3.01
1723 1781 0.107410 AAAGTGTCAGAACCGCACCA 60.107 50.000 0.00 0.00 33.96 4.17
1757 1816 3.134458 CGGAATCTCTTAATCAGTGGGC 58.866 50.000 0.00 0.00 0.00 5.36
1825 1887 5.748670 ATGATCTACTCCTACTCGAGCTA 57.251 43.478 13.61 3.50 32.79 3.32
1866 1928 0.666274 TGTCTTGCCTGCTTCGTACG 60.666 55.000 9.53 9.53 0.00 3.67
1867 1929 1.080093 TCTTGCCTGCTTCGTACGG 60.080 57.895 16.52 0.69 0.00 4.02
1868 1930 1.080093 CTTGCCTGCTTCGTACGGA 60.080 57.895 16.52 5.54 0.00 4.69
1911 3616 9.533253 ACGCCTTTATATTATACAAGTACGTTT 57.467 29.630 0.00 0.00 0.00 3.60
1912 3617 9.787626 CGCCTTTATATTATACAAGTACGTTTG 57.212 33.333 0.00 0.00 0.00 2.93
1971 3852 1.747709 ACTCATGCTCAATCAGTGCC 58.252 50.000 0.00 0.00 35.92 5.01
2182 4070 4.724798 TGGTCCAGGCCTAAGTTTATGTAT 59.275 41.667 3.98 0.00 0.00 2.29
2247 4135 1.485514 CTACACGTGAACAACCGCG 59.514 57.895 25.01 0.00 44.66 6.46
2268 4156 3.682858 CGCCTGCTTGCTACTACTAAAAA 59.317 43.478 0.00 0.00 0.00 1.94
2298 4186 2.683968 ACACACACGATAGATTTGCGT 58.316 42.857 0.00 0.00 39.04 5.24
2328 4218 0.249073 ACGATCCTACATGACAGCGC 60.249 55.000 0.00 0.00 0.00 5.92
2329 4219 0.941463 CGATCCTACATGACAGCGCC 60.941 60.000 2.29 0.00 0.00 6.53
2330 4220 0.104855 GATCCTACATGACAGCGCCA 59.895 55.000 2.29 0.00 0.00 5.69
2331 4221 0.179073 ATCCTACATGACAGCGCCAC 60.179 55.000 2.29 0.00 0.00 5.01
2332 4222 1.079197 CCTACATGACAGCGCCACA 60.079 57.895 2.29 1.87 0.00 4.17
2333 4223 1.086067 CCTACATGACAGCGCCACAG 61.086 60.000 2.29 0.00 0.00 3.66
2334 4224 1.699656 CTACATGACAGCGCCACAGC 61.700 60.000 2.29 0.00 37.41 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.108138 GACAATGCGAGCCTACCTGT 60.108 55.000 0.00 0.00 0.00 4.00
1 2 0.108186 TGACAATGCGAGCCTACCTG 60.108 55.000 0.00 0.00 0.00 4.00
2 3 0.176680 CTGACAATGCGAGCCTACCT 59.823 55.000 0.00 0.00 0.00 3.08
3 4 0.175760 TCTGACAATGCGAGCCTACC 59.824 55.000 0.00 0.00 0.00 3.18
4 5 1.135139 TCTCTGACAATGCGAGCCTAC 59.865 52.381 0.00 0.00 0.00 3.18
5 6 1.135139 GTCTCTGACAATGCGAGCCTA 59.865 52.381 0.00 0.00 32.09 3.93
6 7 0.108424 GTCTCTGACAATGCGAGCCT 60.108 55.000 0.00 0.00 32.09 4.58
7 8 1.086634 GGTCTCTGACAATGCGAGCC 61.087 60.000 0.00 0.00 33.68 4.70
8 9 0.390340 TGGTCTCTGACAATGCGAGC 60.390 55.000 0.00 0.00 33.68 5.03
9 10 1.728971 GTTGGTCTCTGACAATGCGAG 59.271 52.381 0.00 0.00 33.68 5.03
10 11 1.344438 AGTTGGTCTCTGACAATGCGA 59.656 47.619 0.00 0.00 33.68 5.10
11 12 1.800805 AGTTGGTCTCTGACAATGCG 58.199 50.000 0.07 0.00 33.68 4.73
12 13 2.485814 GGAAGTTGGTCTCTGACAATGC 59.514 50.000 0.07 0.00 33.68 3.56
13 14 3.743521 TGGAAGTTGGTCTCTGACAATG 58.256 45.455 0.07 0.00 33.68 2.82
14 15 4.437682 TTGGAAGTTGGTCTCTGACAAT 57.562 40.909 0.07 0.00 33.68 2.71
15 16 3.924114 TTGGAAGTTGGTCTCTGACAA 57.076 42.857 0.07 0.00 33.68 3.18
16 17 3.054728 TGTTTGGAAGTTGGTCTCTGACA 60.055 43.478 0.07 0.00 33.68 3.58
17 18 3.541632 TGTTTGGAAGTTGGTCTCTGAC 58.458 45.455 0.00 0.00 0.00 3.51
18 19 3.924114 TGTTTGGAAGTTGGTCTCTGA 57.076 42.857 0.00 0.00 0.00 3.27
62 66 7.375017 GTGTATTTCGGTGTTTCTTGTTTAGTG 59.625 37.037 0.00 0.00 0.00 2.74
78 82 4.110482 GGTAGCAGTGTAGTGTATTTCGG 58.890 47.826 0.00 0.00 0.00 4.30
87 91 2.448453 GACAGAGGGTAGCAGTGTAGT 58.552 52.381 0.00 0.00 0.00 2.73
98 102 5.016831 GTCAATTATTTTGGGACAGAGGGT 58.983 41.667 0.00 0.00 42.39 4.34
125 129 8.582437 TCTATATACACTCGGTCCCAAAATAAG 58.418 37.037 0.00 0.00 0.00 1.73
196 202 1.927487 TGCACTGCTTCCATTTCCAT 58.073 45.000 1.98 0.00 0.00 3.41
197 203 1.702182 TTGCACTGCTTCCATTTCCA 58.298 45.000 1.98 0.00 0.00 3.53
198 204 3.445096 ACTATTGCACTGCTTCCATTTCC 59.555 43.478 1.98 0.00 0.00 3.13
199 205 4.708726 ACTATTGCACTGCTTCCATTTC 57.291 40.909 1.98 0.00 0.00 2.17
200 206 4.322198 CCAACTATTGCACTGCTTCCATTT 60.322 41.667 1.98 0.00 0.00 2.32
201 207 3.194116 CCAACTATTGCACTGCTTCCATT 59.806 43.478 1.98 0.00 0.00 3.16
202 208 2.756760 CCAACTATTGCACTGCTTCCAT 59.243 45.455 1.98 0.00 0.00 3.41
203 209 2.161855 CCAACTATTGCACTGCTTCCA 58.838 47.619 1.98 0.00 0.00 3.53
214 220 0.460284 AGTCGCGAGCCCAACTATTG 60.460 55.000 10.24 0.00 0.00 1.90
259 282 7.816995 GGATACTGAGCTTTATCAATCGATCTT 59.183 37.037 0.00 0.00 32.73 2.40
268 291 8.027524 AGAAAGATGGATACTGAGCTTTATCA 57.972 34.615 11.13 0.00 37.61 2.15
969 1001 4.901627 GTGCTGTTCAACACGCTC 57.098 55.556 11.63 6.09 0.00 5.03
1485 1520 5.721232 TCCCGTCTCAGAATTTCTTCTTAC 58.279 41.667 0.00 0.00 39.78 2.34
1487 1522 4.891992 TCCCGTCTCAGAATTTCTTCTT 57.108 40.909 0.00 0.00 39.78 2.52
1489 1524 5.643777 TGATTTCCCGTCTCAGAATTTCTTC 59.356 40.000 0.00 0.00 0.00 2.87
1490 1525 5.412904 GTGATTTCCCGTCTCAGAATTTCTT 59.587 40.000 0.00 0.00 0.00 2.52
1499 1534 2.823924 TTTCGTGATTTCCCGTCTCA 57.176 45.000 0.00 0.00 0.00 3.27
1502 1537 1.400494 CCCATTTCGTGATTTCCCGTC 59.600 52.381 0.00 0.00 0.00 4.79
1506 1541 3.694072 TGATGACCCATTTCGTGATTTCC 59.306 43.478 0.00 0.00 0.00 3.13
1556 1591 2.353011 CGTTCAGGCCATCTGCATTTTT 60.353 45.455 5.01 0.00 43.06 1.94
1557 1592 1.203052 CGTTCAGGCCATCTGCATTTT 59.797 47.619 5.01 0.00 43.06 1.82
1558 1593 0.813184 CGTTCAGGCCATCTGCATTT 59.187 50.000 5.01 0.00 43.06 2.32
1559 1594 0.035152 TCGTTCAGGCCATCTGCATT 60.035 50.000 5.01 0.00 43.06 3.56
1560 1595 0.463295 CTCGTTCAGGCCATCTGCAT 60.463 55.000 5.01 0.00 43.06 3.96
1561 1596 1.078918 CTCGTTCAGGCCATCTGCA 60.079 57.895 5.01 0.00 43.06 4.41
1562 1597 1.817099 CCTCGTTCAGGCCATCTGC 60.817 63.158 5.01 0.00 43.06 4.26
1563 1598 4.528674 CCTCGTTCAGGCCATCTG 57.471 61.111 5.01 0.00 44.68 2.90
1570 1605 1.750399 CCAATGGGCCTCGTTCAGG 60.750 63.158 4.53 0.00 46.82 3.86
1571 1606 1.750399 CCCAATGGGCCTCGTTCAG 60.750 63.158 4.89 0.00 35.35 3.02
1572 1607 2.354729 CCCAATGGGCCTCGTTCA 59.645 61.111 4.89 0.00 35.35 3.18
1681 1739 7.956420 TTAATTATACGGTCACATGCTAAGG 57.044 36.000 0.00 0.00 0.00 2.69
1682 1740 9.042008 ACTTTAATTATACGGTCACATGCTAAG 57.958 33.333 0.00 0.00 0.00 2.18
1683 1741 8.822855 CACTTTAATTATACGGTCACATGCTAA 58.177 33.333 0.00 0.00 0.00 3.09
1684 1742 7.982919 ACACTTTAATTATACGGTCACATGCTA 59.017 33.333 0.00 0.00 0.00 3.49
1685 1743 6.821665 ACACTTTAATTATACGGTCACATGCT 59.178 34.615 0.00 0.00 0.00 3.79
1686 1744 7.011828 ACACTTTAATTATACGGTCACATGC 57.988 36.000 0.00 0.00 0.00 4.06
1687 1745 8.192068 TGACACTTTAATTATACGGTCACATG 57.808 34.615 0.00 0.00 0.00 3.21
1688 1746 8.255206 TCTGACACTTTAATTATACGGTCACAT 58.745 33.333 0.00 0.00 31.47 3.21
1689 1747 7.604549 TCTGACACTTTAATTATACGGTCACA 58.395 34.615 0.00 0.00 31.47 3.58
1699 1757 4.453136 GGTGCGGTTCTGACACTTTAATTA 59.547 41.667 0.00 0.00 34.70 1.40
1702 1760 2.215196 GGTGCGGTTCTGACACTTTAA 58.785 47.619 0.00 0.00 34.70 1.52
1716 1774 0.107214 ATGGTGATAGGTTGGTGCGG 60.107 55.000 0.00 0.00 0.00 5.69
1723 1781 4.227197 AGAGATTCCGATGGTGATAGGTT 58.773 43.478 0.00 0.00 0.00 3.50
1757 1816 2.691409 TTCCACCGCTTCTGATTAGG 57.309 50.000 0.00 0.00 0.00 2.69
1866 1928 5.474189 AGGCGTCTAGACTCAATTATACTCC 59.526 44.000 20.34 0.00 25.16 3.85
1867 1929 6.563222 AGGCGTCTAGACTCAATTATACTC 57.437 41.667 20.34 0.00 25.16 2.59
1868 1930 6.963083 AAGGCGTCTAGACTCAATTATACT 57.037 37.500 20.34 0.96 37.06 2.12
1886 1948 9.787626 CAAACGTACTTGTATAATATAAAGGCG 57.212 33.333 0.00 12.90 0.00 5.52
1955 3667 2.089201 TCAAGGCACTGATTGAGCATG 58.911 47.619 0.00 0.00 40.86 4.06
1971 3852 6.923508 TGCATTAGATTACTACACGGATCAAG 59.076 38.462 0.00 0.00 0.00 3.02
2084 3965 2.325082 CCTTCCTTGCCGAACACCG 61.325 63.158 0.00 0.00 38.18 4.94
2085 3966 0.536460 TTCCTTCCTTGCCGAACACC 60.536 55.000 0.00 0.00 0.00 4.16
2093 3976 2.568623 TCTTCTGGTTCCTTCCTTGC 57.431 50.000 0.00 0.00 0.00 4.01
2182 4070 5.239351 CGAGCCTAGCTGATAGAGTAGTTA 58.761 45.833 0.67 0.00 39.88 2.24
2232 4120 4.659874 GGCGCGGTTGTTCACGTG 62.660 66.667 9.94 9.94 42.90 4.49
2280 4168 1.917955 CGACGCAAATCTATCGTGTGT 59.082 47.619 0.00 0.00 38.64 3.72
2298 4186 0.106868 TAGGATCGTTCAGGCCTCGA 60.107 55.000 16.42 16.42 37.96 4.04


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

AutoCloner maintained by Alex Coulton.