Multiple sequence alignment - TraesCS7D01G022700

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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 TraesCS7D01G022700 chr7D 100.000 4009 0 0 1 4009 10711167 10715175 0.000000e+00 7404.0
1 TraesCS7D01G022700 chr7A 94.011 4041 167 28 2 4006 9750961 9754962 0.000000e+00 6052.0
2 TraesCS7D01G022700 chr4A 92.748 1834 78 28 1470 3285 728089650 728087854 0.000000e+00 2599.0
3 TraesCS7D01G022700 chr4A 92.818 1462 64 20 2 1432 728091100 728089649 0.000000e+00 2080.0
4 TraesCS7D01G022700 chr4A 92.201 718 36 8 3311 4009 728087856 728087140 0.000000e+00 998.0
5 TraesCS7D01G022700 chr4A 89.006 473 33 8 965 1432 728065014 728064556 5.810000e-158 568.0
6 TraesCS7D01G022700 chr4A 88.095 84 4 3 1464 1546 728064563 728064485 1.190000e-15 95.3


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 TraesCS7D01G022700 chr7D 10711167 10715175 4008 False 7404.000000 7404 100.0000 1 4009 1 chr7D.!!$F1 4008
1 TraesCS7D01G022700 chr7A 9750961 9754962 4001 False 6052.000000 6052 94.0110 2 4006 1 chr7A.!!$F1 4004
2 TraesCS7D01G022700 chr4A 728087140 728091100 3960 True 1892.333333 2599 92.5890 2 4009 3 chr4A.!!$R2 4007
3 TraesCS7D01G022700 chr4A 728064485 728065014 529 True 331.650000 568 88.5505 965 1546 2 chr4A.!!$R1 581

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
889 918 1.200020 CACTAGCGCCTTTTCTTTGGG 59.800 52.381 2.29 0.0 0.0 4.12 F
1214 1247 1.072331 GCCACAGTCTTCCTTTCTCCA 59.928 52.381 0.00 0.0 0.0 3.86 F
2017 2073 0.108424 CAGCACTCTACTCCAGCACC 60.108 60.000 0.00 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1885 1941 0.037160 TCTTGCCAGATTCTGCTGCA 59.963 50.0 11.98 11.98 34.56 4.41 R
2236 2292 0.477597 ATCCCACTCCAGACCCCAAA 60.478 55.0 0.00 0.00 0.00 3.28 R
3510 3581 0.395724 AGGTCCGGAAAATGGCATCC 60.396 55.0 5.23 0.00 0.00 3.51 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
58 59 5.512749 GCACTCTCATGAATCACCATCCTAT 60.513 44.000 0.00 0.00 0.00 2.57
85 86 7.592938 TCCTGAACAATGTTAATTTGCTAGTG 58.407 34.615 0.00 0.00 0.00 2.74
86 87 6.808212 CCTGAACAATGTTAATTTGCTAGTGG 59.192 38.462 0.00 0.00 0.00 4.00
116 117 6.212589 TGATCCAGTAAGTTACCTGAACATGA 59.787 38.462 9.46 1.63 40.86 3.07
142 143 3.515602 ATTCTCCAGGTGGGCATAATC 57.484 47.619 0.00 0.00 36.21 1.75
157 158 4.132336 GCATAATCCAGCATCTTGTCTGA 58.868 43.478 0.00 0.00 32.26 3.27
163 164 3.009363 TCCAGCATCTTGTCTGAATCCAA 59.991 43.478 0.00 0.00 32.26 3.53
168 169 5.104193 AGCATCTTGTCTGAATCCAATACCT 60.104 40.000 0.00 0.00 0.00 3.08
172 190 3.371034 TGTCTGAATCCAATACCTCGGA 58.629 45.455 0.00 0.00 35.27 4.55
266 290 2.752903 GGGAATTTTATGTCACCGCACT 59.247 45.455 0.00 0.00 0.00 4.40
395 420 1.226746 GCAGCAAAGTGTAGTTCCGT 58.773 50.000 0.00 0.00 0.00 4.69
465 490 1.826340 TTCGCAACTGGGAGCTGCTA 61.826 55.000 0.15 0.00 38.26 3.49
606 631 1.856265 GACAGCACCGCCTTTTCTGG 61.856 60.000 0.00 0.00 0.00 3.86
855 884 5.650266 ACCGTTTCATGCCAATAAGTAATCA 59.350 36.000 0.00 0.00 0.00 2.57
889 918 1.200020 CACTAGCGCCTTTTCTTTGGG 59.800 52.381 2.29 0.00 0.00 4.12
934 963 4.927978 ATCCTCCGTGACATCTCTTTAG 57.072 45.455 0.00 0.00 0.00 1.85
943 972 6.090088 CCGTGACATCTCTTTAGTTTTCAGAG 59.910 42.308 0.00 0.00 36.19 3.35
1035 1068 5.049474 TGAAGGTGTGTCAAAGATTCATTCG 60.049 40.000 0.00 0.00 0.00 3.34
1095 1128 1.815003 CCGGTGATCGCAATGCTGA 60.815 57.895 8.82 2.80 37.59 4.26
1199 1232 2.203139 CGTCAACTGGTGGCCACA 60.203 61.111 35.78 20.93 0.00 4.17
1214 1247 1.072331 GCCACAGTCTTCCTTTCTCCA 59.928 52.381 0.00 0.00 0.00 3.86
1240 1273 5.466058 TCGCATTTTTCAAAGAACGGTACTA 59.534 36.000 0.00 0.00 0.00 1.82
1271 1308 2.751259 TGAATTGCAGAAGATGACCAGC 59.249 45.455 0.00 0.00 0.00 4.85
1272 1309 2.502142 ATTGCAGAAGATGACCAGCA 57.498 45.000 0.00 0.00 0.00 4.41
1273 1310 1.817357 TTGCAGAAGATGACCAGCAG 58.183 50.000 0.00 0.00 33.14 4.24
1439 1479 8.654997 AGCAATCACTTCCTCATATTAGTACAT 58.345 33.333 0.00 0.00 0.00 2.29
1441 1481 9.987272 CAATCACTTCCTCATATTAGTACATCA 57.013 33.333 0.00 0.00 0.00 3.07
1448 1488 5.011738 CCTCATATTAGTACATCAACCCGGT 59.988 44.000 0.00 0.00 0.00 5.28
1458 1498 7.970102 AGTACATCAACCCGGTTATATAATGT 58.030 34.615 1.43 10.11 0.00 2.71
1468 1508 5.995282 CCGGTTATATAATGTTCTGCCAGAA 59.005 40.000 2.24 2.24 0.00 3.02
1494 1534 9.582431 AATGATTCTGTTTGATTCATCATTGAC 57.418 29.630 8.04 0.00 41.91 3.18
1495 1535 8.344446 TGATTCTGTTTGATTCATCATTGACT 57.656 30.769 0.00 0.00 36.56 3.41
1496 1536 8.799367 TGATTCTGTTTGATTCATCATTGACTT 58.201 29.630 0.00 0.00 36.56 3.01
1497 1537 9.635520 GATTCTGTTTGATTCATCATTGACTTT 57.364 29.630 0.00 0.00 36.56 2.66
1498 1538 9.635520 ATTCTGTTTGATTCATCATTGACTTTC 57.364 29.630 0.00 0.00 36.56 2.62
1641 1682 1.510480 GGTCTTGCTCAGGTGTGTGC 61.510 60.000 0.00 0.00 42.45 4.57
1643 1684 3.245948 CTTGCTCAGGTGTGTGCGC 62.246 63.158 0.00 0.00 44.59 6.09
1644 1685 4.544047 TGCTCAGGTGTGTGCGCA 62.544 61.111 5.66 5.66 44.59 6.09
1664 1709 5.381477 CGCAAATTTTCAAATTTACCTGGC 58.619 37.500 9.41 7.94 44.38 4.85
1671 1719 5.622346 TTCAAATTTACCTGGCACCTTTT 57.378 34.783 0.00 0.00 0.00 2.27
1699 1747 6.845302 TGCACTTTGTTCTTGCTAATATCTG 58.155 36.000 0.00 0.00 37.16 2.90
1729 1785 2.157738 GGGAATACTGCTCATGGATGC 58.842 52.381 0.00 0.00 0.00 3.91
1967 2023 1.143684 TGTGCTTCTCCTTTTGGCTCT 59.856 47.619 0.00 0.00 40.12 4.09
2017 2073 0.108424 CAGCACTCTACTCCAGCACC 60.108 60.000 0.00 0.00 0.00 5.01
2160 2216 8.903820 AGTAAGATCTTTTTGTTGCAGTTTACT 58.096 29.630 14.36 2.67 0.00 2.24
2236 2292 5.999205 TGTTTCATATGTTGCAGGGAATT 57.001 34.783 1.90 0.00 0.00 2.17
2377 2433 7.126061 TCTTTCTCCATGAGAACATCTACCTA 58.874 38.462 6.05 0.00 46.54 3.08
2405 2461 6.012745 AGGTAAACCTGATTTGCTTCAGATT 58.987 36.000 0.00 9.32 46.55 2.40
2406 2462 7.175104 AGGTAAACCTGATTTGCTTCAGATTA 58.825 34.615 0.00 8.62 46.55 1.75
2442 2498 9.131791 ACAATCTCATGATCATTCATTCATTCA 57.868 29.630 5.16 0.00 40.70 2.57
2503 2560 8.107729 TCAGTTTAGAGTGAGTCTATCCACTTA 58.892 37.037 0.00 0.00 43.02 2.24
2512 2569 4.446371 AGTCTATCCACTTATGCACTTGC 58.554 43.478 0.00 0.00 42.50 4.01
2577 2634 1.769026 TGTTTTGGCCTTGCAGTGTA 58.231 45.000 3.32 0.00 0.00 2.90
2598 2655 6.437477 GTGTACTGGGATCCATACTGATGATA 59.563 42.308 15.23 0.00 34.73 2.15
2709 2766 5.579511 GCAAATCAAATCATGAGGACCAAAG 59.420 40.000 0.09 0.00 42.53 2.77
2729 2786 6.127647 CCAAAGCTATGCAATTCTTAGGTTGA 60.128 38.462 8.94 0.00 40.21 3.18
3095 3162 7.060633 CGATTTGATTTGGACTTAAAGAAACGG 59.939 37.037 0.00 0.00 0.00 4.44
3133 3200 1.637553 AGACAGTGGGCATTGGATCTT 59.362 47.619 0.00 0.00 0.00 2.40
3134 3201 2.019984 GACAGTGGGCATTGGATCTTC 58.980 52.381 0.00 0.00 0.00 2.87
3155 3222 2.795329 GAACTTTCTCATGGGAAGGCA 58.205 47.619 16.85 0.00 0.00 4.75
3184 3251 5.427481 CCTAAATTGGTCCTTGTAGGTCCTA 59.573 44.000 9.80 0.00 42.97 2.94
3217 3285 6.286758 TCATGCCAAAATTTTCAGTGCTAAA 58.713 32.000 0.00 0.00 0.00 1.85
3328 3399 4.389374 CAGAGCCTTACTTTGTTCCTTCA 58.611 43.478 0.00 0.00 0.00 3.02
3346 3417 4.083110 CCTTCACACTGTGCAATAAAGAGG 60.083 45.833 7.90 1.10 32.98 3.69
3364 3435 1.415659 AGGCAGCTATTCGATTCAGCT 59.584 47.619 9.44 9.44 46.36 4.24
3385 3456 1.135699 GGTGCGCAATTTGCTCGATG 61.136 55.000 14.00 4.53 42.25 3.84
3465 3536 1.678728 CGGGCCATGTTTTAGCTCTCA 60.679 52.381 4.39 0.00 0.00 3.27
3566 3637 5.838521 ACCCCTATAAAAACCATGGCATAAG 59.161 40.000 13.04 0.00 0.00 1.73
3620 3702 1.464997 GACGGACTGAAAATGTGGAGC 59.535 52.381 0.00 0.00 0.00 4.70
3847 3929 3.986277 AGCAAAGGCAAAAACAGATCAG 58.014 40.909 0.00 0.00 44.61 2.90
3919 4007 3.317603 TTTCACTGTCGCTGATCATGA 57.682 42.857 0.00 0.00 0.00 3.07
3920 4008 2.573941 TCACTGTCGCTGATCATGAG 57.426 50.000 0.09 0.00 0.00 2.90
3922 4010 0.822811 ACTGTCGCTGATCATGAGCT 59.177 50.000 12.92 0.00 34.03 4.09
3925 4013 0.304098 GTCGCTGATCATGAGCTTGC 59.696 55.000 12.92 14.66 34.03 4.01
3926 4014 1.149964 TCGCTGATCATGAGCTTGCG 61.150 55.000 30.66 30.66 39.85 4.85
3993 4082 5.640189 AAGATCACTGCTGAAATCTTTGG 57.360 39.130 14.59 0.00 25.92 3.28
3994 4083 4.914983 AGATCACTGCTGAAATCTTTGGA 58.085 39.130 0.00 0.00 0.00 3.53
4006 4095 5.945784 TGAAATCTTTGGATACCTGTTCCTG 59.054 40.000 0.00 0.00 34.17 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.922058 ATGAATCTTTATCAACTGATTTGCAC 57.078 30.769 0.00 0.00 36.05 4.57
58 59 8.637986 ACTAGCAAATTAACATTGTTCAGGAAA 58.362 29.630 5.07 0.00 0.00 3.13
116 117 1.133668 GCCCACCTGGAGAATAGCATT 60.134 52.381 0.00 0.00 37.39 3.56
142 143 2.995283 TGGATTCAGACAAGATGCTGG 58.005 47.619 0.00 0.00 33.05 4.85
232 250 1.545841 AATTCCCCGAGGTTTTGCTC 58.454 50.000 0.00 0.00 0.00 4.26
233 251 2.009681 AAATTCCCCGAGGTTTTGCT 57.990 45.000 0.00 0.00 0.00 3.91
266 290 1.567649 ACCGGTAGTAGATCCAGACCA 59.432 52.381 4.49 0.00 0.00 4.02
395 420 3.813143 CGGCATTGGCGCACATGA 61.813 61.111 19.95 0.00 45.68 3.07
606 631 2.675348 GGTGCAGAGCTATTCAGTTGTC 59.325 50.000 0.00 0.00 0.00 3.18
889 918 2.496070 GCAGAAATGACCCTTTTACCCC 59.504 50.000 0.00 0.00 0.00 4.95
934 963 2.498078 AGACGGAGATCCCTCTGAAAAC 59.502 50.000 8.13 0.00 46.42 2.43
943 972 3.840124 ATTTTACCAGACGGAGATCCC 57.160 47.619 0.00 0.00 35.59 3.85
1095 1128 1.686052 GGCAGAGATGAGGTCGAAGAT 59.314 52.381 0.00 0.00 40.67 2.40
1199 1232 2.303022 TGCGATTGGAGAAAGGAAGACT 59.697 45.455 0.00 0.00 0.00 3.24
1214 1247 4.616953 ACCGTTCTTTGAAAAATGCGATT 58.383 34.783 0.00 0.00 0.00 3.34
1240 1273 9.932207 TCATCTTCTGCAATTCAAAATTTATGT 57.068 25.926 0.00 0.00 0.00 2.29
1253 1287 2.026542 TCTGCTGGTCATCTTCTGCAAT 60.027 45.455 0.00 0.00 37.38 3.56
1285 1322 8.093307 ACAACAGTAGCATCATATTCTAGGATG 58.907 37.037 0.00 4.82 46.53 3.51
1439 1479 5.761234 GCAGAACATTATATAACCGGGTTGA 59.239 40.000 22.44 10.50 0.00 3.18
1441 1481 5.067954 GGCAGAACATTATATAACCGGGTT 58.932 41.667 17.83 17.83 0.00 4.11
1468 1508 9.582431 GTCAATGATGAATCAAACAGAATCATT 57.418 29.630 0.00 0.00 44.82 2.57
1494 1534 5.622233 CGCTAAAATGGGAGGAAAAGGAAAG 60.622 44.000 0.00 0.00 0.00 2.62
1495 1535 4.219725 CGCTAAAATGGGAGGAAAAGGAAA 59.780 41.667 0.00 0.00 0.00 3.13
1496 1536 3.761752 CGCTAAAATGGGAGGAAAAGGAA 59.238 43.478 0.00 0.00 0.00 3.36
1497 1537 3.352648 CGCTAAAATGGGAGGAAAAGGA 58.647 45.455 0.00 0.00 0.00 3.36
1498 1538 2.159240 GCGCTAAAATGGGAGGAAAAGG 60.159 50.000 0.00 0.00 0.00 3.11
1577 1618 3.157087 AGCCAGGTTGGTGAAAGTTATG 58.843 45.455 0.00 0.00 40.46 1.90
1641 1682 5.049818 TGCCAGGTAAATTTGAAAATTTGCG 60.050 36.000 19.28 9.72 45.73 4.85
1643 1684 6.486320 AGGTGCCAGGTAAATTTGAAAATTTG 59.514 34.615 19.28 7.25 45.38 2.32
1644 1685 6.600388 AGGTGCCAGGTAAATTTGAAAATTT 58.400 32.000 15.82 15.82 46.85 1.82
1664 1709 5.111293 AGAACAAAGTGCATGAAAAAGGTG 58.889 37.500 0.00 0.00 0.00 4.00
1671 1719 5.512753 TTAGCAAGAACAAAGTGCATGAA 57.487 34.783 0.00 0.00 40.83 2.57
1699 1747 3.431415 AGCAGTATTCCCAAAGGGTTTC 58.569 45.455 1.36 0.00 44.74 2.78
1729 1785 0.758734 TGTTCAGTGACTCCACCCTG 59.241 55.000 0.00 0.00 44.22 4.45
1881 1937 1.994507 GCCAGATTCTGCTGCAGCTG 61.995 60.000 36.61 34.64 42.66 4.24
1885 1941 0.037160 TCTTGCCAGATTCTGCTGCA 59.963 50.000 11.98 11.98 34.56 4.41
1967 2023 1.148949 TGAGCTTGGACTGCAGCAA 59.851 52.632 15.27 10.10 38.61 3.91
2017 2073 2.222678 GCTGATGAGGAACATGTATGCG 59.777 50.000 0.00 0.00 39.56 4.73
2089 2145 0.607489 CTGGCTTTGTGAGGACCCAG 60.607 60.000 0.00 0.00 34.54 4.45
2192 2248 4.965119 AGTGTTCTTTGGTTCAGTCAAC 57.035 40.909 0.00 0.00 0.00 3.18
2236 2292 0.477597 ATCCCACTCCAGACCCCAAA 60.478 55.000 0.00 0.00 0.00 3.28
2377 2433 4.388577 AGCAAATCAGGTTTACCTTCCT 57.611 40.909 0.00 0.00 46.09 3.36
2512 2569 0.524862 GACCAGCCATTGCAGTTCTG 59.475 55.000 0.00 0.00 41.13 3.02
2577 2634 6.069789 CCATTATCATCAGTATGGATCCCAGT 60.070 42.308 9.90 0.00 39.93 4.00
2598 2655 3.654806 ACAGCAGAATATAGAGGCCCATT 59.345 43.478 0.00 0.00 0.00 3.16
2709 2766 7.814587 AGTTTTTCAACCTAAGAATTGCATAGC 59.185 33.333 0.00 0.00 32.70 2.97
2997 3064 4.336532 ACAAAAATCGTGCGGAGAATAC 57.663 40.909 0.00 0.00 0.00 1.89
3095 3162 5.238214 ACTGTCTCTTCTTTGATGAGCAAAC 59.762 40.000 0.00 0.00 41.37 2.93
3133 3200 2.615493 GCCTTCCCATGAGAAAGTTCGA 60.615 50.000 0.00 0.00 0.00 3.71
3134 3201 1.740025 GCCTTCCCATGAGAAAGTTCG 59.260 52.381 0.00 0.00 0.00 3.95
3155 3222 4.692523 ACAAGGACCAATTTAGGGGAAT 57.307 40.909 0.00 0.00 0.00 3.01
3169 3236 3.593096 CCGTTTTAGGACCTACAAGGAC 58.407 50.000 17.73 5.62 37.67 3.85
3328 3399 2.816087 CTGCCTCTTTATTGCACAGTGT 59.184 45.455 1.61 0.00 0.00 3.55
3385 3456 5.121454 TGAATAATTGTGGAAAATTTGCCGC 59.879 36.000 20.35 20.35 32.16 6.53
3465 3536 0.802994 TCGTTTTCGCACACGTGACT 60.803 50.000 25.01 0.00 43.73 3.41
3505 3576 3.648528 GGAAAATGGCATCCGAAGC 57.351 52.632 0.00 0.00 0.00 3.86
3510 3581 0.395724 AGGTCCGGAAAATGGCATCC 60.396 55.000 5.23 0.00 0.00 3.51
3566 3637 4.801891 TCTGATGAGCAATTTGTTTCTGC 58.198 39.130 0.00 0.00 36.29 4.26
3581 3652 2.295629 GTCTGCCTCGATGATCTGATGA 59.704 50.000 0.00 0.00 0.00 2.92
3847 3929 2.805845 CAGCTGCTTTTATCACCATGC 58.194 47.619 0.00 0.00 0.00 4.06


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

AutoCloner maintained by Alex Coulton.