Multiple sequence alignment - TraesCS1A01G042400

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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 TraesCS1A01G042400 chr1A 100.000 2621 0 0 1 2621 23125368 23127988 0.000000e+00 4841
1 TraesCS1A01G042400 chr1A 83.482 1120 139 21 677 1784 23117308 23118393 0.000000e+00 1002
2 TraesCS1A01G042400 chr1A 91.444 187 16 0 61 247 23116388 23116574 9.310000e-65 257
3 TraesCS1A01G042400 chr1A 88.500 200 13 7 252 446 23116613 23116807 1.570000e-57 233
4 TraesCS1A01G042400 chr1B 92.125 1638 112 7 995 2621 36273719 36272088 0.000000e+00 2294
5 TraesCS1A01G042400 chr1B 88.846 260 19 7 677 934 36273999 36273748 7.040000e-81 311
6 TraesCS1A01G042400 chr1B 90.795 239 11 5 1 235 36277254 36277023 2.530000e-80 309
7 TraesCS1A01G042400 chr1D 95.643 987 36 4 677 1657 21824477 21825462 0.000000e+00 1578
8 TraesCS1A01G042400 chr1D 94.304 632 31 2 1742 2373 21825467 21826093 0.000000e+00 963
9 TraesCS1A01G042400 chr1D 92.540 563 16 9 1 558 21823650 21824191 0.000000e+00 784
10 TraesCS1A01G042400 chr1D 93.578 109 7 0 2513 2621 21826153 21826261 2.090000e-36 163
11 TraesCS1A01G042400 chr5B 94.466 759 34 3 1597 2348 567383522 567382765 0.000000e+00 1162
12 TraesCS1A01G042400 chr5B 90.547 201 16 2 2424 2621 473796921 473797121 2.000000e-66 263
13 TraesCS1A01G042400 chr4B 94.466 759 34 3 1597 2348 528246370 528245613 0.000000e+00 1162
14 TraesCS1A01G042400 chr4B 94.466 759 33 4 1597 2348 276892289 276891533 0.000000e+00 1160
15 TraesCS1A01G042400 chr4B 94.466 759 32 5 1597 2348 483688238 483687483 0.000000e+00 1160
16 TraesCS1A01G042400 chr4B 94.226 762 36 3 1594 2348 463530318 463531078 0.000000e+00 1157
17 TraesCS1A01G042400 chr2B 94.335 759 35 3 1597 2348 123329247 123328490 0.000000e+00 1157
18 TraesCS1A01G042400 chr2B 94.226 762 36 3 1594 2348 463994795 463995555 0.000000e+00 1157
19 TraesCS1A01G042400 chr2B 94.335 759 35 3 1597 2348 480431709 480430952 0.000000e+00 1157
20 TraesCS1A01G042400 chr6B 87.758 678 37 14 1976 2621 218964390 218965053 0.000000e+00 750
21 TraesCS1A01G042400 chrUn 73.817 634 129 26 997 1598 60928703 60929331 1.580000e-52 217


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 TraesCS1A01G042400 chr1A 23125368 23127988 2620 False 4841.000000 4841 100.000000 1 2621 1 chr1A.!!$F1 2620
1 TraesCS1A01G042400 chr1A 23116388 23118393 2005 False 497.333333 1002 87.808667 61 1784 3 chr1A.!!$F2 1723
2 TraesCS1A01G042400 chr1B 36272088 36277254 5166 True 971.333333 2294 90.588667 1 2621 3 chr1B.!!$R1 2620
3 TraesCS1A01G042400 chr1D 21823650 21826261 2611 False 872.000000 1578 94.016250 1 2621 4 chr1D.!!$F1 2620
4 TraesCS1A01G042400 chr5B 567382765 567383522 757 True 1162.000000 1162 94.466000 1597 2348 1 chr5B.!!$R1 751
5 TraesCS1A01G042400 chr4B 528245613 528246370 757 True 1162.000000 1162 94.466000 1597 2348 1 chr4B.!!$R3 751
6 TraesCS1A01G042400 chr4B 276891533 276892289 756 True 1160.000000 1160 94.466000 1597 2348 1 chr4B.!!$R1 751
7 TraesCS1A01G042400 chr4B 483687483 483688238 755 True 1160.000000 1160 94.466000 1597 2348 1 chr4B.!!$R2 751
8 TraesCS1A01G042400 chr4B 463530318 463531078 760 False 1157.000000 1157 94.226000 1594 2348 1 chr4B.!!$F1 754
9 TraesCS1A01G042400 chr2B 123328490 123329247 757 True 1157.000000 1157 94.335000 1597 2348 1 chr2B.!!$R1 751
10 TraesCS1A01G042400 chr2B 463994795 463995555 760 False 1157.000000 1157 94.226000 1594 2348 1 chr2B.!!$F1 754
11 TraesCS1A01G042400 chr2B 480430952 480431709 757 True 1157.000000 1157 94.335000 1597 2348 1 chr2B.!!$R2 751
12 TraesCS1A01G042400 chr6B 218964390 218965053 663 False 750.000000 750 87.758000 1976 2621 1 chr6B.!!$F1 645
13 TraesCS1A01G042400 chrUn 60928703 60929331 628 False 217.000000 217 73.817000 997 1598 1 chrUn.!!$F1 601

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
848 3664 0.610785 TTGGTTTCTCCGGCAATCCC 60.611 55.0 0.0 0.0 39.52 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1890 4752 0.318441 GACCTGCTTTTCTTTGGCCC 59.682 55.0 0.0 0.0 0.0 5.8 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
55 56 3.914426 AAAGGGCGTGATTACTGAGAT 57.086 42.857 0.00 0.00 0.00 2.75
56 57 5.353394 AAAAGGGCGTGATTACTGAGATA 57.647 39.130 0.00 0.00 0.00 1.98
57 58 4.323553 AAGGGCGTGATTACTGAGATAC 57.676 45.455 0.00 0.00 0.00 2.24
58 59 3.567397 AGGGCGTGATTACTGAGATACT 58.433 45.455 0.00 0.00 0.00 2.12
59 60 3.570550 AGGGCGTGATTACTGAGATACTC 59.429 47.826 0.00 0.00 0.00 2.59
267 1786 4.665009 AGAGATGTGGATTGCCCCTTATTA 59.335 41.667 0.00 0.00 0.00 0.98
293 1813 3.895041 TCAAGGTGTTTGATCTTTTCCCC 59.105 43.478 0.00 0.00 40.82 4.81
350 1870 0.620556 TCATCTCCCTTTGACTGGGC 59.379 55.000 0.00 0.00 44.23 5.36
399 1921 1.923204 CGGAGCAGATCAAACTCGAAG 59.077 52.381 0.00 0.00 0.00 3.79
412 1934 5.472137 TCAAACTCGAAGGGGAAAATAACAG 59.528 40.000 0.00 0.00 0.00 3.16
438 1960 6.258947 ACAGTTAACTGAAGAAAGAACAGAGC 59.741 38.462 36.14 0.00 46.59 4.09
447 1969 4.517285 AGAAAGAACAGAGCACTCACAAA 58.483 39.130 0.00 0.00 0.00 2.83
448 1970 5.128919 AGAAAGAACAGAGCACTCACAAAT 58.871 37.500 0.00 0.00 0.00 2.32
449 1971 6.291377 AGAAAGAACAGAGCACTCACAAATA 58.709 36.000 0.00 0.00 0.00 1.40
450 1972 6.767902 AGAAAGAACAGAGCACTCACAAATAA 59.232 34.615 0.00 0.00 0.00 1.40
451 1973 6.551385 AAGAACAGAGCACTCACAAATAAG 57.449 37.500 0.00 0.00 0.00 1.73
452 1974 5.615289 AGAACAGAGCACTCACAAATAAGT 58.385 37.500 0.00 0.00 0.00 2.24
454 1976 7.217200 AGAACAGAGCACTCACAAATAAGTTA 58.783 34.615 0.00 0.00 0.00 2.24
455 1977 7.880195 AGAACAGAGCACTCACAAATAAGTTAT 59.120 33.333 0.00 0.00 0.00 1.89
456 1978 7.602517 ACAGAGCACTCACAAATAAGTTATC 57.397 36.000 0.00 0.00 0.00 1.75
458 1980 8.531982 ACAGAGCACTCACAAATAAGTTATCTA 58.468 33.333 0.00 0.00 0.00 1.98
472 2043 9.901172 AATAAGTTATCTATTTTTCGGAGTGGT 57.099 29.630 0.00 0.00 0.00 4.16
515 3008 3.627577 GCTCTTTCTCAACCTGTTGACAA 59.372 43.478 8.58 2.88 43.90 3.18
575 3068 1.284785 CACCCATTGACCCATACCACT 59.715 52.381 0.00 0.00 0.00 4.00
578 3071 2.025416 CCCATTGACCCATACCACTCAA 60.025 50.000 0.00 0.00 0.00 3.02
605 3098 2.415090 GCTACAACTTTGCTGATGGCTG 60.415 50.000 0.00 0.00 42.39 4.85
610 3103 0.877071 CTTTGCTGATGGCTGACGTT 59.123 50.000 0.00 0.00 42.39 3.99
707 3518 2.806244 ACCAAGAAACCTGTCGAATTCG 59.194 45.455 21.78 21.78 41.45 3.34
730 3541 5.278907 CGGGATAGGCAATTTATTTGATGCA 60.279 40.000 0.00 0.00 40.51 3.96
848 3664 0.610785 TTGGTTTCTCCGGCAATCCC 60.611 55.000 0.00 0.00 39.52 3.85
853 3670 3.878667 CTCCGGCAATCCCTCCCC 61.879 72.222 0.00 0.00 0.00 4.81
859 3676 0.972471 GGCAATCCCTCCCCAACAAG 60.972 60.000 0.00 0.00 0.00 3.16
885 3705 9.724839 GGTAAGCTGTTTAATTATAAATTGCGA 57.275 29.630 0.00 0.00 37.26 5.10
895 3715 2.004583 TAAATTGCGAGTCCTCACCG 57.995 50.000 0.00 0.00 0.00 4.94
978 3798 3.181493 GCTAGCACCCAAACATCATCAAG 60.181 47.826 10.63 0.00 0.00 3.02
985 3805 4.219288 ACCCAAACATCATCAAGAAGCTTC 59.781 41.667 19.11 19.11 0.00 3.86
1233 4081 2.852075 TTCCCAGCCCTGAACGGT 60.852 61.111 0.00 0.00 0.00 4.83
1622 4470 1.235724 GCTTTCCGGTGCTGTTAACT 58.764 50.000 7.22 0.00 0.00 2.24
1663 4519 2.620115 ACCATGCTGTGTTCTGAGTTTG 59.380 45.455 0.00 0.00 0.00 2.93
1664 4520 2.030540 CCATGCTGTGTTCTGAGTTTGG 60.031 50.000 0.00 0.00 0.00 3.28
1740 4598 2.683211 AAGGCAAAGTGGGTGATCTT 57.317 45.000 0.00 0.00 0.00 2.40
1890 4752 8.984891 TTGGACTTTAGAAATACAATTGCATG 57.015 30.769 5.05 0.00 0.00 4.06
1930 4793 5.297527 GGTCACCTCTTTTAACCGAAGAAAA 59.702 40.000 0.00 0.00 33.10 2.29
1972 4835 3.020984 ACGAAACTTCCAAAGGCTTTGA 58.979 40.909 35.18 20.86 43.26 2.69
2037 4900 6.605594 AGAAAGATTTCCAAACCAGTGTGTTA 59.394 34.615 1.73 0.00 37.92 2.41
2076 4939 4.221041 GGTAACCCATATAGCAGAGGAGAC 59.779 50.000 0.00 0.00 0.00 3.36
2341 5240 9.507280 CAGTATACAGATTTGTAAAATGCAAGG 57.493 33.333 5.50 0.00 42.72 3.61
2376 5296 3.828875 AGTAAAGCATCTGAGCCCTAC 57.171 47.619 0.00 0.00 34.23 3.18
2443 5363 9.180551 GAAACTAATTCTGTGGTGCCTATTGCA 62.181 40.741 0.00 0.00 40.47 4.08
2581 5504 3.662247 ACTATATTACGCACCCTCTGC 57.338 47.619 0.00 0.00 43.21 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 8.991783 TGCCTAACTTCTTATTAGCTAGAGTA 57.008 34.615 0.00 0.00 0.00 2.59
56 57 7.899648 TGCCTAACTTCTTATTAGCTAGAGT 57.100 36.000 0.00 0.00 0.00 3.24
289 1809 1.478503 TCCACATTGGAGGAGGGGA 59.521 57.895 0.00 0.00 42.67 4.81
308 1828 6.375455 TGAATGAGACCCTAAAGCTTGAAATC 59.625 38.462 0.00 0.00 0.00 2.17
309 1829 6.248433 TGAATGAGACCCTAAAGCTTGAAAT 58.752 36.000 0.00 0.00 0.00 2.17
399 1921 6.713450 TCAGTTAACTGTCTGTTATTTTCCCC 59.287 38.462 29.83 0.00 44.12 4.81
412 1934 7.517575 GCTCTGTTCTTTCTTCAGTTAACTGTC 60.518 40.741 29.83 13.30 44.12 3.51
447 1969 9.901172 AACCACTCCGAAAAATAGATAACTTAT 57.099 29.630 0.00 0.00 0.00 1.73
448 1970 9.729281 AAACCACTCCGAAAAATAGATAACTTA 57.271 29.630 0.00 0.00 0.00 2.24
449 1971 8.512138 CAAACCACTCCGAAAAATAGATAACTT 58.488 33.333 0.00 0.00 0.00 2.66
450 1972 7.120726 CCAAACCACTCCGAAAAATAGATAACT 59.879 37.037 0.00 0.00 0.00 2.24
451 1973 7.248437 CCAAACCACTCCGAAAAATAGATAAC 58.752 38.462 0.00 0.00 0.00 1.89
452 1974 6.127842 GCCAAACCACTCCGAAAAATAGATAA 60.128 38.462 0.00 0.00 0.00 1.75
454 1976 4.157840 GCCAAACCACTCCGAAAAATAGAT 59.842 41.667 0.00 0.00 0.00 1.98
455 1977 3.504520 GCCAAACCACTCCGAAAAATAGA 59.495 43.478 0.00 0.00 0.00 1.98
456 1978 3.506067 AGCCAAACCACTCCGAAAAATAG 59.494 43.478 0.00 0.00 0.00 1.73
458 1980 2.316108 AGCCAAACCACTCCGAAAAAT 58.684 42.857 0.00 0.00 0.00 1.82
515 3008 1.133823 TGTCCTGTGGAACTGTTGCAT 60.134 47.619 17.67 0.00 38.04 3.96
548 3041 0.037590 GGGTCAATGGGTGTGCACTA 59.962 55.000 19.41 1.23 0.00 2.74
558 3051 3.016736 GTTGAGTGGTATGGGTCAATGG 58.983 50.000 0.00 0.00 31.84 3.16
559 3052 3.684908 TGTTGAGTGGTATGGGTCAATG 58.315 45.455 0.00 0.00 31.84 2.82
560 3053 4.526970 GATGTTGAGTGGTATGGGTCAAT 58.473 43.478 0.00 0.00 31.84 2.57
561 3054 3.618752 CGATGTTGAGTGGTATGGGTCAA 60.619 47.826 0.00 0.00 0.00 3.18
562 3055 2.093711 CGATGTTGAGTGGTATGGGTCA 60.094 50.000 0.00 0.00 0.00 4.02
563 3056 2.550978 CGATGTTGAGTGGTATGGGTC 58.449 52.381 0.00 0.00 0.00 4.46
575 3068 2.225491 GCAAAGTTGTAGCCGATGTTGA 59.775 45.455 0.00 0.00 0.00 3.18
578 3071 1.806542 CAGCAAAGTTGTAGCCGATGT 59.193 47.619 0.00 0.00 0.00 3.06
605 3098 5.567138 ATCCATTTCATTCCTCAAACGTC 57.433 39.130 0.00 0.00 0.00 4.34
610 3103 5.393068 AGGCTATCCATTTCATTCCTCAA 57.607 39.130 0.00 0.00 33.74 3.02
653 3150 9.674824 GACAAAACATGATTTCCTGATATGATC 57.325 33.333 0.00 0.00 0.00 2.92
707 3518 5.928264 GTGCATCAAATAAATTGCCTATCCC 59.072 40.000 0.00 0.00 38.98 3.85
730 3541 2.101917 GCCTGCTTTTGGATGCATATGT 59.898 45.455 0.00 0.00 38.59 2.29
848 3664 1.073923 ACAGCTTACCTTGTTGGGGAG 59.926 52.381 0.00 0.00 41.11 4.30
859 3676 9.724839 TCGCAATTTATAATTAAACAGCTTACC 57.275 29.630 0.00 0.00 32.44 2.85
883 3703 2.567049 GTGACCGGTGAGGACTCG 59.433 66.667 14.63 0.00 45.00 4.18
885 3705 2.200370 TGGTGACCGGTGAGGACT 59.800 61.111 14.63 0.00 45.00 3.85
895 3715 0.400213 TTGTCATGGAGGTGGTGACC 59.600 55.000 0.00 0.00 41.09 4.02
978 3798 1.390463 GAATCGGTGTCGTGAAGCTTC 59.610 52.381 19.89 19.89 37.69 3.86
985 3805 0.096976 GCCATTGAATCGGTGTCGTG 59.903 55.000 0.00 0.00 37.69 4.35
1622 4470 3.006537 GGTAGGCAGGTATCAAGCGATTA 59.993 47.826 0.00 0.00 32.73 1.75
1663 4519 7.119387 CAGGGGTCTGGAATTATATAAATCCC 58.881 42.308 21.76 13.07 34.96 3.85
1664 4520 6.603599 GCAGGGGTCTGGAATTATATAAATCC 59.396 42.308 19.02 19.02 41.19 3.01
1724 4582 3.674997 TCAGTAAGATCACCCACTTTGC 58.325 45.455 0.00 0.00 0.00 3.68
1771 4632 7.746526 GTACTACAGTACTAAATCGGTTTGG 57.253 40.000 3.29 2.92 45.47 3.28
1890 4752 0.318441 GACCTGCTTTTCTTTGGCCC 59.682 55.000 0.00 0.00 0.00 5.80
1930 4793 7.050970 TCGTCAGCTTATAATGAACTGGTAT 57.949 36.000 0.00 0.00 0.00 2.73
1972 4835 6.882610 TGAAAATTGCAGTTACTGTCAGAT 57.117 33.333 14.23 6.48 33.43 2.90
2058 4921 3.306641 GCTTGTCTCCTCTGCTATATGGG 60.307 52.174 0.00 0.00 0.00 4.00
2076 4939 4.491676 CAGATCCTTGATGGTTTTGCTTG 58.508 43.478 0.00 0.00 37.07 4.01
2165 5029 7.068716 ACCTATCTGCATTTTTCCCAATAGTTC 59.931 37.037 0.00 0.00 0.00 3.01
2172 5036 4.207165 GCTACCTATCTGCATTTTTCCCA 58.793 43.478 0.00 0.00 0.00 4.37
2341 5240 5.491982 TGCTTTACTTCTCAGAGAAATCCC 58.508 41.667 14.01 2.21 33.19 3.85
2376 5296 5.375417 TTTACCACATGATGCAACTTCTG 57.625 39.130 0.00 0.00 0.00 3.02
2443 5363 3.336122 CAAGAGTCTTGCCTTGCCT 57.664 52.632 19.55 0.00 34.20 4.75
2541 5464 5.852282 AGTACCAAATCTGTTTGCTTTGT 57.148 34.783 0.00 0.00 42.66 2.83


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

AutoCloner maintained by Alex Coulton.