Multiple sequence alignment - TraesCS2A01G226100

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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 TraesCS2A01G226100 chr2A 100.000 2549 0 0 1 2549 233254674 233257222 0.000000e+00 4708
1 TraesCS2A01G226100 chr2A 96.097 1973 73 3 580 2549 611725144 611723173 0.000000e+00 3214
2 TraesCS2A01G226100 chr2A 94.801 1962 95 5 588 2546 674415062 674413105 0.000000e+00 3051
3 TraesCS2A01G226100 chr2A 94.932 592 25 3 1 587 103928691 103928100 0.000000e+00 922
4 TraesCS2A01G226100 chr2A 86.248 589 79 1 1 587 103876837 103877425 2.770000e-179 638
5 TraesCS2A01G226100 chr6A 96.846 1966 58 4 587 2549 57901158 57903122 0.000000e+00 3284
6 TraesCS2A01G226100 chr6A 96.496 1969 60 6 588 2549 203520912 203518946 0.000000e+00 3245
7 TraesCS2A01G226100 chr6B 96.416 1981 49 8 588 2549 660437743 660435766 0.000000e+00 3245
8 TraesCS2A01G226100 chr3A 96.216 1982 56 5 585 2549 617401020 617402999 0.000000e+00 3227
9 TraesCS2A01G226100 chr7B 96.169 1984 55 6 586 2549 552932145 552930163 0.000000e+00 3223
10 TraesCS2A01G226100 chr2D 95.015 1966 88 8 588 2549 498471644 498469685 0.000000e+00 3079
11 TraesCS2A01G226100 chr2D 94.255 1967 76 12 588 2549 547242743 547240809 0.000000e+00 2972
12 TraesCS2A01G226100 chr2D 97.183 355 9 1 588 942 16065486 16065839 1.310000e-167 599
13 TraesCS2A01G226100 chr7A 93.356 587 36 3 1 587 4847538 4848121 0.000000e+00 865
14 TraesCS2A01G226100 chr3B 91.414 594 43 5 1 587 299082094 299082686 0.000000e+00 808
15 TraesCS2A01G226100 chr3B 89.779 587 44 6 1 587 288033987 288034557 0.000000e+00 737
16 TraesCS2A01G226100 chr2B 90.764 563 47 5 1 560 163853378 163853938 0.000000e+00 747
17 TraesCS2A01G226100 chr4B 89.394 594 56 2 1 587 446151769 446152362 0.000000e+00 741
18 TraesCS2A01G226100 chr7D 88.927 587 60 3 2 587 424693375 424693957 0.000000e+00 719
19 TraesCS2A01G226100 chr5A 88.610 597 56 7 1 587 709462117 709462711 0.000000e+00 715
20 TraesCS2A01G226100 chr5A 95.518 357 14 2 588 944 689409578 689409224 1.020000e-158 569
21 TraesCS2A01G226100 chr1B 94.324 370 18 3 574 942 645321424 645321791 4.760000e-157 564


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 TraesCS2A01G226100 chr2A 233254674 233257222 2548 False 4708 4708 100.000 1 2549 1 chr2A.!!$F2 2548
1 TraesCS2A01G226100 chr2A 611723173 611725144 1971 True 3214 3214 96.097 580 2549 1 chr2A.!!$R2 1969
2 TraesCS2A01G226100 chr2A 674413105 674415062 1957 True 3051 3051 94.801 588 2546 1 chr2A.!!$R3 1958
3 TraesCS2A01G226100 chr2A 103928100 103928691 591 True 922 922 94.932 1 587 1 chr2A.!!$R1 586
4 TraesCS2A01G226100 chr2A 103876837 103877425 588 False 638 638 86.248 1 587 1 chr2A.!!$F1 586
5 TraesCS2A01G226100 chr6A 57901158 57903122 1964 False 3284 3284 96.846 587 2549 1 chr6A.!!$F1 1962
6 TraesCS2A01G226100 chr6A 203518946 203520912 1966 True 3245 3245 96.496 588 2549 1 chr6A.!!$R1 1961
7 TraesCS2A01G226100 chr6B 660435766 660437743 1977 True 3245 3245 96.416 588 2549 1 chr6B.!!$R1 1961
8 TraesCS2A01G226100 chr3A 617401020 617402999 1979 False 3227 3227 96.216 585 2549 1 chr3A.!!$F1 1964
9 TraesCS2A01G226100 chr7B 552930163 552932145 1982 True 3223 3223 96.169 586 2549 1 chr7B.!!$R1 1963
10 TraesCS2A01G226100 chr2D 498469685 498471644 1959 True 3079 3079 95.015 588 2549 1 chr2D.!!$R1 1961
11 TraesCS2A01G226100 chr2D 547240809 547242743 1934 True 2972 2972 94.255 588 2549 1 chr2D.!!$R2 1961
12 TraesCS2A01G226100 chr7A 4847538 4848121 583 False 865 865 93.356 1 587 1 chr7A.!!$F1 586
13 TraesCS2A01G226100 chr3B 299082094 299082686 592 False 808 808 91.414 1 587 1 chr3B.!!$F2 586
14 TraesCS2A01G226100 chr3B 288033987 288034557 570 False 737 737 89.779 1 587 1 chr3B.!!$F1 586
15 TraesCS2A01G226100 chr2B 163853378 163853938 560 False 747 747 90.764 1 560 1 chr2B.!!$F1 559
16 TraesCS2A01G226100 chr4B 446151769 446152362 593 False 741 741 89.394 1 587 1 chr4B.!!$F1 586
17 TraesCS2A01G226100 chr7D 424693375 424693957 582 False 719 719 88.927 2 587 1 chr7D.!!$F1 585
18 TraesCS2A01G226100 chr5A 709462117 709462711 594 False 715 715 88.610 1 587 1 chr5A.!!$F1 586

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
792 821 0.319986 TATTCAGACCGTTGCACGCA 60.32 50.0 0.0 0.0 40.91 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1749 1817 0.398381 TTGGCCCAAGAGCAACCTTT 60.398 50.0 0.0 0.0 0.0 3.11 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
216 241 5.179452 ACATGCTTCTATGGTTACCACTT 57.821 39.130 6.10 0.00 35.80 3.16
330 356 3.515502 TGGTAGAATGACTCAGGAACCTG 59.484 47.826 14.01 14.01 44.86 4.00
449 475 8.723942 ATTATAGAACTGTGCAAACTTCTAGG 57.276 34.615 10.57 0.00 30.63 3.02
453 479 4.373156 ACTGTGCAAACTTCTAGGGAAT 57.627 40.909 0.00 0.00 0.00 3.01
488 514 9.739276 GAACCACCTGATAATCCAAATGATATA 57.261 33.333 0.00 0.00 31.83 0.86
792 821 0.319986 TATTCAGACCGTTGCACGCA 60.320 50.000 0.00 0.00 40.91 5.24
880 939 1.959738 ACGACGACAGAGAGCACGA 60.960 57.895 0.00 0.00 0.00 4.35
958 1023 1.888436 CGGTGGGAAGCTAGCAGTGA 61.888 60.000 18.83 0.00 0.00 3.41
965 1030 1.831652 AAGCTAGCAGTGAAGGGCGT 61.832 55.000 18.83 0.00 34.54 5.68
1017 1082 2.500910 CTCCATGTCTTCCTCAAGCTCT 59.499 50.000 0.00 0.00 0.00 4.09
1079 1144 0.458370 CATGTCATCGTCTGTCCGCA 60.458 55.000 0.00 0.00 0.00 5.69
1151 1216 0.935831 CGTCCGTTCTACGTGTGCAA 60.936 55.000 0.00 0.00 40.58 4.08
1172 1237 3.028850 ACGAGAATGGGGTAAGAATCGA 58.971 45.455 0.00 0.00 33.43 3.59
1503 1568 7.971368 ATACTTTTGGGCATTTGTAGGTATT 57.029 32.000 0.00 0.00 0.00 1.89
2034 2102 7.537596 AGACCAAAATGTCATGGAAAATGTA 57.462 32.000 0.00 0.00 39.12 2.29
2040 2108 7.537596 AAATGTCATGGAAAATGTACCTCAA 57.462 32.000 0.00 0.00 0.00 3.02
2209 2279 2.489437 GGGTTTGTGGTGTTTAGGGCTA 60.489 50.000 0.00 0.00 0.00 3.93
2283 2353 6.773685 AGGAAGGTATACATAGTGAGACTGTC 59.226 42.308 5.01 0.00 0.00 3.51
2327 2400 1.064803 GACCGTGAATGTTTGCACACA 59.935 47.619 8.36 8.36 35.03 3.72
2329 2402 1.202234 CCGTGAATGTTTGCACACACA 60.202 47.619 8.06 0.00 35.03 3.72
2371 2444 6.644347 TGTTTTGCACTTAAATTTTGGAGGA 58.356 32.000 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
134 136 9.322776 CAAGCGTCTAATCATATAAGCATTTTC 57.677 33.333 0.00 0.00 0.00 2.29
216 241 8.413309 TGAGCCTTAAGTACTTGTTCTACTTA 57.587 34.615 18.56 2.62 36.18 2.24
330 356 0.107165 GGGTGGCCTTCAGGATACAC 60.107 60.000 3.32 2.43 37.39 2.90
426 452 6.439375 TCCCTAGAAGTTTGCACAGTTCTATA 59.561 38.462 23.78 13.54 37.82 1.31
449 475 3.629398 CAGGTGGTTCAGCAATAGATTCC 59.371 47.826 0.00 0.00 33.95 3.01
453 479 5.692115 TTATCAGGTGGTTCAGCAATAGA 57.308 39.130 0.00 0.00 33.95 1.98
488 514 9.217278 GATTATGTTTCAGCATCAGACATAGAT 57.783 33.333 0.00 0.00 35.39 1.98
792 821 2.765969 CTGGGTCCCACAAGCCAT 59.234 61.111 6.47 0.00 45.28 4.40
865 924 2.556792 CGTCGTGCTCTCTGTCGT 59.443 61.111 0.00 0.00 0.00 4.34
965 1030 4.467084 GGGATCTCAACGCCGCCA 62.467 66.667 0.00 0.00 0.00 5.69
1151 1216 3.028850 TCGATTCTTACCCCATTCTCGT 58.971 45.455 0.00 0.00 0.00 4.18
1172 1237 1.344114 ACGAAAATGGTGCAATTGCCT 59.656 42.857 26.94 7.00 41.18 4.75
1196 1261 1.358787 ACCCATTGCTCAAAGATCCCA 59.641 47.619 0.00 0.00 0.00 4.37
1503 1568 5.888691 ACATTACAACCAATGCGATTACA 57.111 34.783 0.00 0.00 39.13 2.41
1700 1766 5.867716 AGAGCTGCATTTCATTGATCAAAAC 59.132 36.000 13.09 0.00 0.00 2.43
1749 1817 0.398381 TTGGCCCAAGAGCAACCTTT 60.398 50.000 0.00 0.00 0.00 3.11
1838 1906 8.188139 AGAAAACAGAAAAATACGCAAGAGAAA 58.812 29.630 0.00 0.00 43.62 2.52
1995 2063 9.829507 ACATTTTGGTCTTTGATTTAAATCACA 57.170 25.926 26.69 20.43 44.54 3.58
2040 2108 1.823610 GGCGTAAACCTCTACCAGAGT 59.176 52.381 2.71 0.00 40.72 3.24
2209 2279 1.679977 TCCTAGCGGTTACCAGCGT 60.680 57.895 1.13 0.00 45.98 5.07
2327 2400 4.473444 ACAATGGAAAACCACTCTCATGT 58.527 39.130 0.00 0.00 0.00 3.21
2329 2402 6.282930 CAAAACAATGGAAAACCACTCTCAT 58.717 36.000 0.00 0.00 0.00 2.90
2371 2444 6.650390 GCAACATACATTTTCAACCTTCCAAT 59.350 34.615 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.