Multiple sequence alignment - TraesCS7B01G207000

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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 TraesCS7B01G207000 chr7B 100.000 3600 0 0 1 3600 379432306 379428707 0.000000e+00 6649
1 TraesCS7B01G207000 chr7A 95.185 1973 66 16 555 2507 432981681 432979718 0.000000e+00 3090
2 TraesCS7B01G207000 chr7A 95.924 1104 34 5 2507 3600 432979679 432978577 0.000000e+00 1779
3 TraesCS7B01G207000 chr7A 90.957 564 48 2 1 561 432982511 432981948 0.000000e+00 756
4 TraesCS7B01G207000 chr7D 97.270 1099 23 2 2507 3600 384947382 384946286 0.000000e+00 1857
5 TraesCS7B01G207000 chr7D 93.672 1043 37 9 623 1651 384949580 384948553 0.000000e+00 1533
6 TraesCS7B01G207000 chr7D 93.750 880 27 15 1653 2507 384948290 384947414 0.000000e+00 1295
7 TraesCS7B01G207000 chr7D 89.433 653 44 12 1 629 384976531 384975880 0.000000e+00 800
8 TraesCS7B01G207000 chr2A 80.563 355 54 11 1 348 616218185 616217839 3.570000e-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 TraesCS7B01G207000 chr7B 379428707 379432306 3599 True 6649.000000 6649 100.000000 1 3600 1 chr7B.!!$R1 3599
1 TraesCS7B01G207000 chr7A 432978577 432982511 3934 True 1875.000000 3090 94.022000 1 3600 3 chr7A.!!$R1 3599
2 TraesCS7B01G207000 chr7D 384946286 384949580 3294 True 1561.666667 1857 94.897333 623 3600 3 chr7D.!!$R2 2977
3 TraesCS7B01G207000 chr7D 384975880 384976531 651 True 800.000000 800 89.433000 1 629 1 chr7D.!!$R1 628

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
541 567 0.034337 GGGTGCGGTGACTAAAGTGA 59.966 55.000 0.0 0.0 0.0 3.41 F
1372 1696 1.753073 AGTTGCCCTGCTTCATTATGC 59.247 47.619 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
1516 1840 1.035385 TCTTGATCCTCACCGCGCTA 61.035 55.0 5.56 0.0 0.0 4.26 R
3108 3777 0.240945 CCACAACGTTTCATGCCCTC 59.759 55.0 0.00 0.0 0.0 4.30 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 54 7.519347 ACCCTATCAAACTAACCCAAGATAA 57.481 36.000 0.00 0.00 0.00 1.75
60 62 7.615365 TCAAACTAACCCAAGATAATTGATGCT 59.385 33.333 0.00 0.00 0.00 3.79
125 127 4.340617 TGACGAAAAAGATTGGGGCTTAT 58.659 39.130 0.00 0.00 0.00 1.73
247 249 4.821589 CCCTTGACGCCTCTCCGC 62.822 72.222 0.00 0.00 0.00 5.54
380 392 2.237392 CCAGGGGGTTTTGTGAAAAACA 59.763 45.455 14.12 0.00 42.73 2.83
389 401 2.270275 TGTGAAAAACAACACGCAGG 57.730 45.000 0.00 0.00 39.52 4.85
393 405 1.658686 AAAAACAACACGCAGGCGGA 61.659 50.000 18.63 0.00 44.69 5.54
424 437 3.803082 CTGGCGCGGTGAATGGTG 61.803 66.667 8.83 0.00 0.00 4.17
430 443 1.502990 CGCGGTGAATGGTGAACACA 61.503 55.000 0.00 0.00 36.42 3.72
493 508 4.295870 TGACCGTATAATCATCTTGTCGC 58.704 43.478 0.00 0.00 0.00 5.19
541 567 0.034337 GGGTGCGGTGACTAAAGTGA 59.966 55.000 0.00 0.00 0.00 3.41
572 872 1.798813 CAAGTTAAGTGACTGGCGGTC 59.201 52.381 19.61 19.61 44.70 4.79
669 970 3.010472 TGACAATCATCACCAATCAGGGT 59.990 43.478 0.00 0.00 43.89 4.34
971 1292 2.358003 ACGACCAGCAGCAAGAGC 60.358 61.111 0.00 0.00 42.56 4.09
1189 1512 3.745975 TGCGTCATCAAACCTTCTTACTG 59.254 43.478 0.00 0.00 0.00 2.74
1269 1592 1.916697 GCCCAAGACTGCTCGCTTTC 61.917 60.000 0.00 0.00 0.00 2.62
1372 1696 1.753073 AGTTGCCCTGCTTCATTATGC 59.247 47.619 0.00 0.00 0.00 3.14
1395 1719 5.349543 GCGAAATTTCTGATTTGGCAAAGAT 59.650 36.000 18.61 1.92 40.72 2.40
1474 1798 8.815565 TCCAATTTGCATGAATTAAGTACCTA 57.184 30.769 0.00 0.00 0.00 3.08
1516 1840 2.281761 CCTGGCAAGCAAGTCCGT 60.282 61.111 0.00 0.00 0.00 4.69
1595 1919 5.044030 ACACTTCTCTCCCTCCACTAATCTA 60.044 44.000 0.00 0.00 0.00 1.98
1633 1957 9.026170 AGGGGATAAATTAATTAAGTCCTTCCT 57.974 33.333 18.38 15.57 0.00 3.36
1634 1958 9.656323 GGGGATAAATTAATTAAGTCCTTCCTT 57.344 33.333 18.38 0.00 0.00 3.36
1713 2298 5.930569 CCTTGTAGTACTAGGTTGGTTTGAC 59.069 44.000 19.29 0.00 36.55 3.18
1869 2454 4.082026 ACAGGTAATGCAAAGCTGATTTCC 60.082 41.667 28.22 9.38 43.52 3.13
1906 2491 5.607939 TTTCTTTGTTTTTCTTCCCCTCC 57.392 39.130 0.00 0.00 0.00 4.30
1910 2495 5.362717 TCTTTGTTTTTCTTCCCCTCCTTTC 59.637 40.000 0.00 0.00 0.00 2.62
1921 2506 3.009473 TCCCCTCCTTTCTCATTGTTCAG 59.991 47.826 0.00 0.00 0.00 3.02
2114 2699 9.000486 GCCTAAAGTCTTATTGTTGTAGTTTCT 58.000 33.333 0.00 0.00 0.00 2.52
2289 2911 3.416119 TTCGCTCCGAGTACAATACAG 57.584 47.619 0.00 0.00 37.14 2.74
2424 3046 1.190643 AGCCTCCAGAAGACACTAGC 58.809 55.000 0.00 0.00 0.00 3.42
2454 3076 1.963515 GTTGGTGAAGGGCTTGTGATT 59.036 47.619 0.00 0.00 0.00 2.57
2602 3263 6.942976 TGAAGAGGTTGATTCGGTATAAACT 58.057 36.000 0.00 0.00 29.50 2.66
2607 3268 5.360714 AGGTTGATTCGGTATAAACTCGGTA 59.639 40.000 0.00 0.00 29.50 4.02
2608 3269 6.041296 AGGTTGATTCGGTATAAACTCGGTAT 59.959 38.462 0.00 0.00 29.50 2.73
2610 3271 5.692814 TGATTCGGTATAAACTCGGTATCG 58.307 41.667 0.00 0.00 37.82 2.92
2882 3543 5.009010 TCTGAAAAATCACTCTTCAAGGTGC 59.991 40.000 2.09 0.00 33.91 5.01
3003 3664 4.689612 TCCGGGGAATCTTTCTCTAATG 57.310 45.455 0.00 0.00 0.00 1.90
3112 3781 0.969894 AACTGACAGGTCTTCGAGGG 59.030 55.000 7.51 0.00 0.00 4.30
3152 3821 5.728471 CTCAGCATCTGGTTCTTCTCTTTA 58.272 41.667 0.00 0.00 31.51 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 54 6.331845 TGCAATATTTCGTTTCAGCATCAAT 58.668 32.000 0.00 0.00 0.00 2.57
60 62 9.123709 GTTGTTAATCTGCAATATTTCGTTTCA 57.876 29.630 0.00 0.00 0.00 2.69
125 127 2.670251 CGCCGCCCCAAACTACAA 60.670 61.111 0.00 0.00 0.00 2.41
176 178 3.792736 GGGGGTGCATAGGCGTGA 61.793 66.667 0.00 0.00 45.35 4.35
267 269 1.668101 GAGAGGAAGGTGATCGCCGT 61.668 60.000 19.45 16.80 0.00 5.68
350 352 4.018195 ACCCCCTGGTGTCATTGT 57.982 55.556 0.00 0.00 45.58 2.71
424 437 1.599419 GCCGTTGTTGACCATGTGTTC 60.599 52.381 0.00 0.00 0.00 3.18
430 443 3.722295 CGCGCCGTTGTTGACCAT 61.722 61.111 0.00 0.00 0.00 3.55
493 508 3.882888 ACATCCATTACGGCCACTAAATG 59.117 43.478 2.24 6.47 33.14 2.32
541 567 2.607635 CACTTAACTTGTGTCGTGTGCT 59.392 45.455 0.00 0.00 0.00 4.40
572 872 7.545615 GCCATGGTAGTTAAAAGAGAAAAATGG 59.454 37.037 14.67 0.00 33.15 3.16
669 970 2.444033 TTAACCCTCCTTCCCTTCCA 57.556 50.000 0.00 0.00 0.00 3.53
844 1165 4.986708 GGGGCGCCTTGGTTGGAA 62.987 66.667 28.56 0.00 0.00 3.53
888 1209 2.648102 GGATCGTCGCTCGTCGTG 60.648 66.667 8.50 0.00 40.80 4.35
1171 1494 7.509546 AGAAGAACAGTAAGAAGGTTTGATGA 58.490 34.615 0.00 0.00 0.00 2.92
1189 1512 1.567357 AGCAGAGGAGGGAGAAGAAC 58.433 55.000 0.00 0.00 0.00 3.01
1269 1592 1.478510 ACGTAGCAGGAGAGATGGTTG 59.521 52.381 0.00 0.00 0.00 3.77
1372 1696 6.956299 ATCTTTGCCAAATCAGAAATTTCG 57.044 33.333 12.42 7.92 0.00 3.46
1474 1798 5.250200 TCATCTGCACGGTTAAAAGGTATT 58.750 37.500 0.00 0.00 0.00 1.89
1516 1840 1.035385 TCTTGATCCTCACCGCGCTA 61.035 55.000 5.56 0.00 0.00 4.26
1635 1959 9.533253 GGTCAAGTTATGGGATTTAATTCATTG 57.467 33.333 0.20 0.00 0.00 2.82
1695 2280 5.068987 TGTTACGTCAAACCAACCTAGTACT 59.931 40.000 0.00 0.00 0.00 2.73
1696 2281 5.288804 TGTTACGTCAAACCAACCTAGTAC 58.711 41.667 0.00 0.00 0.00 2.73
1869 2454 5.051816 ACAAAGAAATGCACATCAAAGGTG 58.948 37.500 0.00 0.00 39.25 4.00
1906 2491 5.381174 TGAATGGCTGAACAATGAGAAAG 57.619 39.130 0.00 0.00 0.00 2.62
1910 2495 3.863424 GCATTGAATGGCTGAACAATGAG 59.137 43.478 21.29 6.10 46.81 2.90
2141 2757 5.734503 GCTCATCGAACTGTGACATATGAGA 60.735 44.000 10.38 4.23 40.69 3.27
2142 2758 4.443725 GCTCATCGAACTGTGACATATGAG 59.556 45.833 10.38 13.18 41.01 2.90
2143 2759 4.142182 TGCTCATCGAACTGTGACATATGA 60.142 41.667 10.38 0.00 0.00 2.15
2144 2760 4.114794 TGCTCATCGAACTGTGACATATG 58.885 43.478 0.00 0.00 0.00 1.78
2145 2761 4.098501 TCTGCTCATCGAACTGTGACATAT 59.901 41.667 0.00 0.00 0.00 1.78
2146 2762 3.443681 TCTGCTCATCGAACTGTGACATA 59.556 43.478 0.00 0.00 0.00 2.29
2289 2911 1.203287 GAATTTGCTGCTCCCCAGAAC 59.797 52.381 0.00 0.00 44.64 3.01
2454 3076 4.164796 AGCACTGATCTTACCCATTCATCA 59.835 41.667 0.00 0.00 0.00 3.07
2528 3189 6.381420 TCTCTTCGTTCCTTCTGAAATAGGAT 59.619 38.462 0.00 0.00 40.15 3.24
2602 3263 3.306917 TTGCAGAGTTTTCGATACCGA 57.693 42.857 0.00 0.00 43.96 4.69
2607 3268 3.548014 CGGTGTTTTGCAGAGTTTTCGAT 60.548 43.478 0.00 0.00 0.00 3.59
2608 3269 2.223157 CGGTGTTTTGCAGAGTTTTCGA 60.223 45.455 0.00 0.00 0.00 3.71
2610 3271 2.159296 ACCGGTGTTTTGCAGAGTTTTC 60.159 45.455 6.12 0.00 0.00 2.29
2882 3543 5.879223 ACATGAGCAGAGAACTTCCATTAAG 59.121 40.000 0.00 0.00 41.33 1.85
3003 3664 9.016438 TCTACTATTTTGTTGGGGAAAACATAC 57.984 33.333 0.00 0.00 39.68 2.39
3108 3777 0.240945 CCACAACGTTTCATGCCCTC 59.759 55.000 0.00 0.00 0.00 4.30
3112 3781 0.387239 GAGCCCACAACGTTTCATGC 60.387 55.000 0.00 0.00 0.00 4.06
3376 4048 5.296151 TCTGGCTATGAAGTGGAAATAGG 57.704 43.478 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.