Multiple sequence alignment - TraesCS7D01G216800

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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 TraesCS7D01G216800 chr7D 100.000 3028 0 0 1 3028 176580237 176577210 0.000000e+00 5592.0
1 TraesCS7D01G216800 chr7D 84.670 1559 122 48 764 2252 176444390 176442879 0.000000e+00 1447.0
2 TraesCS7D01G216800 chr7D 88.848 825 53 18 1 794 176471622 176470806 0.000000e+00 977.0
3 TraesCS7D01G216800 chr7D 83.495 412 34 18 2297 2694 176442765 176442374 1.340000e-93 353.0
4 TraesCS7D01G216800 chr7B 90.901 2209 112 33 123 2271 142867690 142865511 0.000000e+00 2883.0
5 TraesCS7D01G216800 chr7B 90.263 1561 70 29 123 1626 143056735 143055200 0.000000e+00 1965.0
6 TraesCS7D01G216800 chr7B 86.612 1464 109 35 1553 2977 142779680 142778265 0.000000e+00 1537.0
7 TraesCS7D01G216800 chr7B 86.526 1425 112 35 764 2117 142284418 142283003 0.000000e+00 1495.0
8 TraesCS7D01G216800 chr7B 91.631 693 49 5 1584 2271 143055293 143054605 0.000000e+00 950.0
9 TraesCS7D01G216800 chr7B 87.945 730 49 19 340 1042 142781432 142780715 0.000000e+00 824.0
10 TraesCS7D01G216800 chr7B 83.521 534 52 18 1 506 142284943 142284418 1.640000e-127 466.0
11 TraesCS7D01G216800 chr7B 87.179 390 34 8 1 384 142781723 142781344 2.160000e-116 429.0
12 TraesCS7D01G216800 chr7B 88.184 347 33 4 2690 3028 142283333 142282987 1.010000e-109 407.0
13 TraesCS7D01G216800 chr7B 86.792 318 35 4 2696 3006 143055085 143054768 6.210000e-92 348.0
14 TraesCS7D01G216800 chr7B 86.164 318 36 5 2696 3006 142865990 142865674 1.340000e-88 337.0
15 TraesCS7D01G216800 chr7B 94.309 123 7 0 1 123 143059968 143059846 3.990000e-44 189.0
16 TraesCS7D01G216800 chr7B 93.496 123 8 0 1 123 142870923 142870801 1.850000e-42 183.0
17 TraesCS7D01G216800 chr7B 92.537 67 5 0 2962 3028 142865677 142865611 2.480000e-16 97.1
18 TraesCS7D01G216800 chr7A 90.285 2213 169 20 856 3027 179602946 179600739 0.000000e+00 2854.0
19 TraesCS7D01G216800 chr7A 92.051 1648 85 18 1 1626 180170131 180168508 0.000000e+00 2276.0
20 TraesCS7D01G216800 chr7A 93.059 1556 81 6 1 1533 180380172 180378621 0.000000e+00 2250.0
21 TraesCS7D01G216800 chr7A 91.486 1656 82 19 1 1626 179910560 179908934 0.000000e+00 2222.0
22 TraesCS7D01G216800 chr7A 87.846 1555 116 32 1527 3026 180375214 180373678 0.000000e+00 1757.0
23 TraesCS7D01G216800 chr7A 87.659 1491 131 29 1584 3028 180168601 180167118 0.000000e+00 1685.0
24 TraesCS7D01G216800 chr7A 84.778 1419 143 34 764 2117 178913865 178912455 0.000000e+00 1356.0
25 TraesCS7D01G216800 chr7A 83.803 1420 140 41 764 2117 178905269 178903874 0.000000e+00 1266.0
26 TraesCS7D01G216800 chr7A 85.875 1246 106 34 1603 2807 179909005 179907789 0.000000e+00 1262.0
27 TraesCS7D01G216800 chr7A 90.111 809 41 12 1 788 179603784 179602994 0.000000e+00 1014.0
28 TraesCS7D01G216800 chr7A 79.221 616 72 33 2117 2697 178912492 178911898 7.920000e-101 377.0
29 TraesCS7D01G216800 chr7A 78.947 627 72 32 2117 2707 178903911 178903309 3.690000e-99 372.0
30 TraesCS7D01G216800 chr7A 95.385 65 3 0 2962 3026 180168079 180168015 1.480000e-18 104.0
31 TraesCS7D01G216800 chr7A 93.846 65 4 0 2962 3026 180374642 180374578 6.910000e-17 99.0
32 TraesCS7D01G216800 chr2B 94.624 93 5 0 674 766 121646690 121646598 8.750000e-31 145.0


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 TraesCS7D01G216800 chr7D 176577210 176580237 3027 True 5592.000000 5592 100.000000 1 3028 1 chr7D.!!$R2 3027
1 TraesCS7D01G216800 chr7D 176470806 176471622 816 True 977.000000 977 88.848000 1 794 1 chr7D.!!$R1 793
2 TraesCS7D01G216800 chr7D 176442374 176444390 2016 True 900.000000 1447 84.082500 764 2694 2 chr7D.!!$R3 1930
3 TraesCS7D01G216800 chr7B 142865511 142867690 2179 True 1105.700000 2883 89.867333 123 3028 3 chr7B.!!$R4 2905
4 TraesCS7D01G216800 chr7B 142778265 142781723 3458 True 930.000000 1537 87.245333 1 2977 3 chr7B.!!$R3 2976
5 TraesCS7D01G216800 chr7B 143054605 143059968 5363 True 863.000000 1965 90.748750 1 3006 4 chr7B.!!$R5 3005
6 TraesCS7D01G216800 chr7B 142282987 142284943 1956 True 789.333333 1495 86.077000 1 3028 3 chr7B.!!$R2 3027
7 TraesCS7D01G216800 chr7A 179600739 179603784 3045 True 1934.000000 2854 90.198000 1 3027 2 chr7A.!!$R3 3026
8 TraesCS7D01G216800 chr7A 179907789 179910560 2771 True 1742.000000 2222 88.680500 1 2807 2 chr7A.!!$R4 2806
9 TraesCS7D01G216800 chr7A 180373678 180380172 6494 True 1368.666667 2250 91.583667 1 3026 3 chr7A.!!$R6 3025
10 TraesCS7D01G216800 chr7A 180167118 180170131 3013 True 1355.000000 2276 91.698333 1 3028 3 chr7A.!!$R5 3027
11 TraesCS7D01G216800 chr7A 178911898 178913865 1967 True 866.500000 1356 81.999500 764 2697 2 chr7A.!!$R2 1933
12 TraesCS7D01G216800 chr7A 178903309 178905269 1960 True 819.000000 1266 81.375000 764 2707 2 chr7A.!!$R1 1943

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
837 4046 0.112412 AGAAAAACCACGGCCCTCAT 59.888 50.0 0.0 0.0 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2633 10050 0.106268 TGCTGAAAGGGAAGTTGGCA 60.106 50.0 0.0 0.0 0.0 4.92 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
567 3718 1.308069 GCCACGTAGACTCGGGTGTA 61.308 60.000 0.00 0.00 34.94 2.90
572 3723 1.669779 CGTAGACTCGGGTGTAAGAGG 59.330 57.143 0.00 0.00 38.72 3.69
586 3737 2.347490 GAGGCGGTGGCTTCTCAA 59.653 61.111 0.00 0.00 41.68 3.02
588 3739 2.281484 GGCGGTGGCTTCTCAACA 60.281 61.111 0.00 0.00 39.81 3.33
648 3826 1.271379 CGAAAAGGAAGGGAAGCCTGA 60.271 52.381 0.00 0.00 34.00 3.86
826 4035 9.755804 AGATCATGAGAAAAGAAAAGAAAAACC 57.244 29.630 0.09 0.00 0.00 3.27
837 4046 0.112412 AGAAAAACCACGGCCCTCAT 59.888 50.000 0.00 0.00 0.00 2.90
860 4069 7.988028 TCATCACCAACGGTTATAATCACATTA 59.012 33.333 0.00 0.00 31.02 1.90
865 4074 9.787435 ACCAACGGTTATAATCACATTATACAT 57.213 29.630 0.00 0.00 37.41 2.29
997 4238 3.055747 GCCAGCACCTAATACCTATCTCC 60.056 52.174 0.00 0.00 0.00 3.71
1084 4417 2.080336 TTGCACCTTGGCTAGCCCTT 62.080 55.000 30.81 9.46 34.56 3.95
1683 8980 1.377612 TGCAGGTTCAGATGCAGCT 59.622 52.632 0.00 0.00 46.97 4.24
1774 9071 1.072505 CGGGCAGTACCAGGTGTTT 59.927 57.895 0.76 0.00 42.05 2.83
1986 9295 2.190313 CCAATCTGGCTAGCCGCA 59.810 61.111 28.28 17.63 41.67 5.69
2010 9321 2.740714 GGCGTGCGTTAGCTTCTGG 61.741 63.158 0.00 0.00 45.42 3.86
2018 9329 0.324943 GTTAGCTTCTGGGTCCTGCA 59.675 55.000 0.00 0.00 0.00 4.41
2019 9330 1.065126 GTTAGCTTCTGGGTCCTGCAT 60.065 52.381 0.00 0.00 0.00 3.96
2026 9337 0.904649 CTGGGTCCTGCATGTACTGA 59.095 55.000 0.00 0.00 0.00 3.41
2083 9394 4.158209 TGTGTGCGTACTGCTTACCTAATA 59.842 41.667 4.97 0.00 46.63 0.98
2088 9399 4.262335 GCGTACTGCTTACCTAATATGGGT 60.262 45.833 6.01 6.01 41.73 4.51
2093 9404 6.490492 ACTGCTTACCTAATATGGGTTTGTT 58.510 36.000 6.03 0.00 38.19 2.83
2152 9467 8.453238 TGTCCTCTAGTAATTCATGTACTCTC 57.547 38.462 0.00 0.00 33.80 3.20
2187 9502 7.364970 AGTTATCGTCGCTTAATTTGGTTTTT 58.635 30.769 0.00 0.00 0.00 1.94
2219 9534 4.277423 TGGCTACTCGTAATTGATGATCGA 59.723 41.667 0.00 0.00 0.00 3.59
2236 9552 3.701532 TCGAGTGAAAAACCGCATTTT 57.298 38.095 0.00 0.00 42.55 1.82
2295 9637 4.314740 TTGCGTTGCAAATTAGACCTTT 57.685 36.364 0.00 0.00 45.96 3.11
2358 9747 5.700722 TCTCTCACGCTTAAACAGAAGTA 57.299 39.130 0.00 0.00 0.00 2.24
2427 9836 0.604243 ATCTCTCGCTCCGTCGCTAT 60.604 55.000 0.00 0.00 0.00 2.97
2522 9933 1.745489 GGCCGGTGGTGACATCTTC 60.745 63.158 1.90 0.00 46.14 2.87
2530 9941 0.376152 GGTGACATCTTCTGCGCATG 59.624 55.000 12.24 8.77 0.00 4.06
2531 9942 0.247974 GTGACATCTTCTGCGCATGC 60.248 55.000 12.24 7.91 43.20 4.06
2546 9961 2.286872 GCATGCATAGCTGAGTGTCTT 58.713 47.619 14.21 0.00 0.00 3.01
2547 9962 2.031807 GCATGCATAGCTGAGTGTCTTG 59.968 50.000 14.21 0.36 0.00 3.02
2633 10050 2.874701 GCGGCATGATTGATAGACTTGT 59.125 45.455 0.00 0.00 0.00 3.16
2711 10136 1.151777 CCGTGGCCAGCAATACTACG 61.152 60.000 5.11 1.88 0.00 3.51
2762 10187 0.898320 GGTAGCAGCAACAGAGGAGA 59.102 55.000 0.00 0.00 0.00 3.71
2773 10198 1.228583 AGAGGAGACTGTGCCGACA 60.229 57.895 0.00 0.00 44.43 4.35
2810 10235 4.465512 CGTGCCAGTGCCGAATGC 62.466 66.667 0.00 0.00 41.77 3.56
2856 10281 2.366533 CCAGCAGCAGAAGAATCACAT 58.633 47.619 0.00 0.00 0.00 3.21
2881 10306 1.972660 GCCCGTCCAATCTGGCTAGT 61.973 60.000 0.00 0.00 40.77 2.57
2885 10310 0.175760 GTCCAATCTGGCTAGTCGCA 59.824 55.000 0.00 0.00 41.67 5.10
2907 10332 3.078560 CGAGGCGCGTTAGTTTCC 58.921 61.111 8.43 0.00 34.64 3.13
2934 10359 3.538003 CGTGTGTGCTGTAATAATTTGCG 59.462 43.478 0.00 0.00 0.00 4.85
2961 10388 2.199652 CCGGCCATGGTTTGTGTGT 61.200 57.895 14.67 0.00 0.00 3.72
2980 10407 6.015265 TGTGTGTGTACTGCTTACCTAATGTA 60.015 38.462 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 6.665992 ATTATATCGTGCCTAGGAGACAAA 57.334 37.500 14.75 4.50 0.00 2.83
567 3718 1.768684 TTGAGAAGCCACCGCCTCTT 61.769 55.000 0.00 0.00 35.86 2.85
572 3723 0.109597 CATTGTTGAGAAGCCACCGC 60.110 55.000 0.00 0.00 0.00 5.68
583 3734 3.561310 GCAGACAACTCTGACATTGTTGA 59.439 43.478 20.43 0.00 46.32 3.18
586 3737 3.136763 CTGCAGACAACTCTGACATTGT 58.863 45.455 8.42 2.94 46.32 2.71
588 3739 3.758755 TCTGCAGACAACTCTGACATT 57.241 42.857 13.74 0.00 46.32 2.71
648 3826 3.827876 TGTTCATCCACTCATGCAACAAT 59.172 39.130 0.00 0.00 0.00 2.71
695 3874 4.161565 TCCACATAGGATTGTACTGGTGAC 59.838 45.833 0.00 0.00 43.07 3.67
750 3937 2.880443 CACATTAAGGGCATGGGCTAT 58.120 47.619 0.00 0.00 40.87 2.97
826 4035 2.040544 GTTGGTGATGAGGGCCGTG 61.041 63.158 0.65 0.00 0.00 4.94
837 4046 9.263538 GTATAATGTGATTATAACCGTTGGTGA 57.736 33.333 0.00 0.00 38.89 4.02
997 4238 3.435327 TGCTTCAGTGTGTTAAATAGGCG 59.565 43.478 0.00 0.00 0.00 5.52
1084 4417 2.264480 CCGTCGTTCTCCATGGCA 59.736 61.111 6.96 0.00 0.00 4.92
1593 8890 4.937431 GAGCCGGGGCAGCATACC 62.937 72.222 12.97 0.00 44.88 2.73
1617 8914 0.325933 CTGCACCTGATTCTGACCCA 59.674 55.000 0.00 0.00 0.00 4.51
1620 8917 1.364626 CCGCTGCACCTGATTCTGAC 61.365 60.000 0.00 0.00 0.00 3.51
1774 9071 1.153309 CATGACATGCTCTCCGCCA 60.153 57.895 1.71 0.00 38.05 5.69
1863 9172 0.458543 GCTCTCTTCGTCGCCAATGA 60.459 55.000 0.00 0.00 0.00 2.57
1876 9185 1.604023 ACCGTTGGACGAGCTCTCT 60.604 57.895 12.85 0.00 46.05 3.10
1906 9215 4.133373 TCCTCCGTACCCTCCCCG 62.133 72.222 0.00 0.00 0.00 5.73
1915 9224 2.442272 GGCTCTGGCTCCTCCGTA 60.442 66.667 0.00 0.00 37.80 4.02
2010 9321 6.699575 AATTATTTCAGTACATGCAGGACC 57.300 37.500 4.84 0.00 0.00 4.46
2018 9329 6.509418 ACACGGCAAATTATTTCAGTACAT 57.491 33.333 0.00 0.00 0.00 2.29
2019 9330 5.390040 CGACACGGCAAATTATTTCAGTACA 60.390 40.000 0.00 0.00 0.00 2.90
2026 9337 3.242608 CGGATCGACACGGCAAATTATTT 60.243 43.478 2.88 0.00 0.00 1.40
2083 9394 8.109634 ACATGAATTACTAGAGAACAAACCCAT 58.890 33.333 0.00 0.00 0.00 4.00
2088 9399 9.871238 GGAGTACATGAATTACTAGAGAACAAA 57.129 33.333 0.00 0.00 29.58 2.83
2113 9424 2.025887 AGAGGACAAGCCCACATTAAGG 60.026 50.000 0.00 0.00 37.37 2.69
2152 9467 3.428870 AGCGACGATAACTTCAACAACAG 59.571 43.478 0.00 0.00 0.00 3.16
2187 9502 8.780846 TCAATTACGAGTAGCCAAATTAAGAA 57.219 30.769 0.00 0.00 0.00 2.52
2241 9557 2.959030 GCAGGAGTCTGAAACCCTTTTT 59.041 45.455 0.00 0.00 43.49 1.94
2253 9569 5.163581 GCAAAATACAATGATGCAGGAGTCT 60.164 40.000 0.00 0.00 37.00 3.24
2258 9574 3.772932 ACGCAAAATACAATGATGCAGG 58.227 40.909 0.00 0.00 36.84 4.85
2295 9637 4.815269 TGACATGTTCGTGACATCATACA 58.185 39.130 0.00 0.00 45.88 2.29
2530 9941 0.649475 CGCAAGACACTCAGCTATGC 59.351 55.000 0.00 0.00 43.02 3.14
2531 9942 2.001812 ACGCAAGACACTCAGCTATG 57.998 50.000 0.00 0.00 43.62 2.23
2532 9943 2.341257 CAACGCAAGACACTCAGCTAT 58.659 47.619 0.00 0.00 43.62 2.97
2536 9947 0.583438 CACCAACGCAAGACACTCAG 59.417 55.000 0.00 0.00 43.62 3.35
2537 9948 0.107897 ACACCAACGCAAGACACTCA 60.108 50.000 0.00 0.00 43.62 3.41
2538 9949 1.525619 GTACACCAACGCAAGACACTC 59.474 52.381 0.00 0.00 43.62 3.51
2546 9961 0.321210 CCCATCAGTACACCAACGCA 60.321 55.000 0.00 0.00 0.00 5.24
2547 9962 1.024579 CCCCATCAGTACACCAACGC 61.025 60.000 0.00 0.00 0.00 4.84
2633 10050 0.106268 TGCTGAAAGGGAAGTTGGCA 60.106 50.000 0.00 0.00 0.00 4.92
2762 10187 1.668294 CTCTCCTTGTCGGCACAGT 59.332 57.895 0.00 0.00 32.71 3.55
2773 10198 1.587054 CGTTGGACGAGCTCTCCTT 59.413 57.895 23.96 4.24 46.05 3.36
2856 10281 0.321564 CAGATTGGACGGGCTTGTCA 60.322 55.000 11.44 0.00 40.72 3.58
2892 10317 3.116531 GCGGAAACTAACGCGCCT 61.117 61.111 5.73 0.00 46.58 5.52
2910 10335 5.331902 GCAAATTATTACAGCACACACGAT 58.668 37.500 0.00 0.00 0.00 3.73
2980 10407 6.476378 ACATGAATTACTAGACAACAAGCCT 58.524 36.000 0.00 0.00 0.00 4.58


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

AutoCloner maintained by Alex Coulton.