Multiple sequence alignment - TraesCS7B01G355900

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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 TraesCS7B01G355900 chr7B 100.000 2420 0 0 1 2420 616408613 616406194 0.000000e+00 4470.0
1 TraesCS7B01G355900 chr7B 99.307 1443 10 0 978 2420 133704945 133706387 0.000000e+00 2610.0
2 TraesCS7B01G355900 chr7B 98.960 1443 15 0 978 2420 720550192 720551634 0.000000e+00 2582.0
3 TraesCS7B01G355900 chr7B 99.567 231 1 0 635 865 133703408 133703638 2.880000e-114 422.0
4 TraesCS7B01G355900 chr7B 100.000 75 0 0 865 939 133703943 133704017 3.240000e-29 139.0
5 TraesCS7B01G355900 chr7B 100.000 37 0 0 944 980 133704969 133705005 4.320000e-08 69.4
6 TraesCS7B01G355900 chr7B 100.000 37 0 0 944 980 616407612 616407576 4.320000e-08 69.4
7 TraesCS7B01G355900 chr7B 100.000 37 0 0 944 980 720550216 720550252 4.320000e-08 69.4
8 TraesCS7B01G355900 chr4B 99.307 1443 10 0 978 2420 668871498 668872940 0.000000e+00 2610.0
9 TraesCS7B01G355900 chr4B 100.000 37 0 0 944 980 668871522 668871558 4.320000e-08 69.4
10 TraesCS7B01G355900 chr3A 99.238 1443 11 0 978 2420 12635802 12637244 0.000000e+00 2604.0
11 TraesCS7B01G355900 chr3A 89.492 866 85 4 1 863 28723335 28722473 0.000000e+00 1090.0
12 TraesCS7B01G355900 chr3A 100.000 37 0 0 944 980 12635826 12635862 4.320000e-08 69.4
13 TraesCS7B01G355900 chr5A 99.238 1443 10 1 978 2420 513704776 513703335 0.000000e+00 2603.0
14 TraesCS7B01G355900 chr5A 99.168 1443 12 0 978 2420 335711289 335712731 0.000000e+00 2599.0
15 TraesCS7B01G355900 chr5A 99.161 715 4 2 153 865 335709167 335709881 0.000000e+00 1286.0
16 TraesCS7B01G355900 chr5A 100.000 75 0 0 865 939 335710353 335710427 3.240000e-29 139.0
17 TraesCS7B01G355900 chr5A 100.000 37 0 0 944 980 335711313 335711349 4.320000e-08 69.4
18 TraesCS7B01G355900 chr5A 100.000 37 0 0 944 980 513704752 513704716 4.320000e-08 69.4
19 TraesCS7B01G355900 chr6A 99.168 1443 12 0 978 2420 3634751 3636193 0.000000e+00 2599.0
20 TraesCS7B01G355900 chr6A 100.000 37 0 0 944 980 3634775 3634811 4.320000e-08 69.4
21 TraesCS7B01G355900 chr4A 99.099 1443 13 0 978 2420 741026773 741028215 0.000000e+00 2593.0
22 TraesCS7B01G355900 chr4A 94.545 55 3 0 885 939 17735043 17734989 4.290000e-13 86.1
23 TraesCS7B01G355900 chr4A 100.000 37 0 0 944 980 741026797 741026833 4.320000e-08 69.4
24 TraesCS7B01G355900 chr2A 99.168 1322 11 0 1099 2420 750960501 750961822 0.000000e+00 2381.0
25 TraesCS7B01G355900 chr2A 99.422 865 5 0 1 865 750959572 750960436 0.000000e+00 1570.0
26 TraesCS7B01G355900 chr5B 99.653 865 3 0 1 865 484823663 484824527 0.000000e+00 1581.0
27 TraesCS7B01G355900 chr5B 100.000 75 0 0 865 939 484824999 484825073 3.240000e-29 139.0
28 TraesCS7B01G355900 chr3B 89.803 863 82 4 1 860 802890929 802891788 0.000000e+00 1101.0
29 TraesCS7B01G355900 chr1A 89.687 863 83 4 1 860 576244155 576245014 0.000000e+00 1096.0
30 TraesCS7B01G355900 chr6B 89.571 863 84 4 1 860 480824172 480825031 0.000000e+00 1090.0
31 TraesCS7B01G355900 chrUn 90.698 688 55 5 1 681 315539578 315538893 0.000000e+00 907.0
32 TraesCS7B01G355900 chrUn 100.000 75 0 0 865 939 396392200 396392126 3.240000e-29 139.0
33 TraesCS7B01G355900 chrUn 100.000 75 0 0 865 939 476923536 476923462 3.240000e-29 139.0
34 TraesCS7B01G355900 chr1B 90.698 688 55 5 1 681 587491556 587490871 0.000000e+00 907.0
35 TraesCS7B01G355900 chr1D 88.710 62 7 0 876 937 26263827 26263766 2.580000e-10 76.8


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 TraesCS7B01G355900 chr7B 616406194 616408613 2419 True 2269.70 4470 100.00000 1 2420 2 chr7B.!!$R1 2419
1 TraesCS7B01G355900 chr7B 720550192 720551634 1442 False 1325.70 2582 99.48000 944 2420 2 chr7B.!!$F2 1476
2 TraesCS7B01G355900 chr7B 133703408 133706387 2979 False 810.10 2610 99.71850 635 2420 4 chr7B.!!$F1 1785
3 TraesCS7B01G355900 chr4B 668871498 668872940 1442 False 1339.70 2610 99.65350 944 2420 2 chr4B.!!$F1 1476
4 TraesCS7B01G355900 chr3A 12635802 12637244 1442 False 1336.70 2604 99.61900 944 2420 2 chr3A.!!$F1 1476
5 TraesCS7B01G355900 chr3A 28722473 28723335 862 True 1090.00 1090 89.49200 1 863 1 chr3A.!!$R1 862
6 TraesCS7B01G355900 chr5A 513703335 513704776 1441 True 1336.20 2603 99.61900 944 2420 2 chr5A.!!$R1 1476
7 TraesCS7B01G355900 chr5A 335709167 335712731 3564 False 1023.35 2599 99.58225 153 2420 4 chr5A.!!$F1 2267
8 TraesCS7B01G355900 chr6A 3634751 3636193 1442 False 1334.20 2599 99.58400 944 2420 2 chr6A.!!$F1 1476
9 TraesCS7B01G355900 chr4A 741026773 741028215 1442 False 1331.20 2593 99.54950 944 2420 2 chr4A.!!$F1 1476
10 TraesCS7B01G355900 chr2A 750959572 750961822 2250 False 1975.50 2381 99.29500 1 2420 2 chr2A.!!$F1 2419
11 TraesCS7B01G355900 chr5B 484823663 484825073 1410 False 860.00 1581 99.82650 1 939 2 chr5B.!!$F1 938
12 TraesCS7B01G355900 chr3B 802890929 802891788 859 False 1101.00 1101 89.80300 1 860 1 chr3B.!!$F1 859
13 TraesCS7B01G355900 chr1A 576244155 576245014 859 False 1096.00 1096 89.68700 1 860 1 chr1A.!!$F1 859
14 TraesCS7B01G355900 chr6B 480824172 480825031 859 False 1090.00 1090 89.57100 1 860 1 chr6B.!!$F1 859
15 TraesCS7B01G355900 chrUn 315538893 315539578 685 True 907.00 907 90.69800 1 681 1 chrUn.!!$R1 680
16 TraesCS7B01G355900 chr1B 587490871 587491556 685 True 907.00 907 90.69800 1 681 1 chr1B.!!$R1 680

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
956 1432 0.911769 TCCGATTGGAGTGGCTGAAT 59.088 50.0 0.0 0.0 40.17 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2367 3732 3.365969 GGCAAAATCTCGGACGAAATTGT 60.366 43.478 0.0 0.0 0.0 2.71 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
429 430 9.817809 ACTATGATGAAGCTAATTCGTTTCTTA 57.182 29.630 7.82 0.00 41.14 2.10
860 864 9.871238 TCTGTCCTATAGTTGTTTTATGTTCTC 57.129 33.333 0.00 0.00 0.00 2.87
939 1415 4.680975 GCACTAGAGTGGGTATTGAGTTCC 60.681 50.000 11.51 0.00 45.72 3.62
940 1416 3.700038 ACTAGAGTGGGTATTGAGTTCCG 59.300 47.826 0.00 0.00 0.00 4.30
941 1417 2.816411 AGAGTGGGTATTGAGTTCCGA 58.184 47.619 0.00 0.00 0.00 4.55
942 1418 3.375699 AGAGTGGGTATTGAGTTCCGAT 58.624 45.455 0.00 0.00 0.00 4.18
943 1419 3.775316 AGAGTGGGTATTGAGTTCCGATT 59.225 43.478 0.00 0.00 0.00 3.34
946 1422 2.841266 TGGGTATTGAGTTCCGATTGGA 59.159 45.455 0.00 0.00 44.61 3.53
954 1430 4.128580 TCCGATTGGAGTGGCTGA 57.871 55.556 0.00 0.00 40.17 4.26
956 1432 0.911769 TCCGATTGGAGTGGCTGAAT 59.088 50.000 0.00 0.00 40.17 2.57
958 1434 1.407299 CCGATTGGAGTGGCTGAATGA 60.407 52.381 0.00 0.00 37.49 2.57
959 1435 1.938577 CGATTGGAGTGGCTGAATGAG 59.061 52.381 0.00 0.00 0.00 2.90
960 1436 2.295885 GATTGGAGTGGCTGAATGAGG 58.704 52.381 0.00 0.00 0.00 3.86
964 1440 1.211457 GGAGTGGCTGAATGAGGATGT 59.789 52.381 0.00 0.00 0.00 3.06
965 1441 2.435805 GGAGTGGCTGAATGAGGATGTA 59.564 50.000 0.00 0.00 0.00 2.29
967 1443 3.378512 AGTGGCTGAATGAGGATGTAGA 58.621 45.455 0.00 0.00 0.00 2.59
968 1444 3.387374 AGTGGCTGAATGAGGATGTAGAG 59.613 47.826 0.00 0.00 0.00 2.43
969 1445 2.702478 TGGCTGAATGAGGATGTAGAGG 59.298 50.000 0.00 0.00 0.00 3.69
970 1446 2.968574 GGCTGAATGAGGATGTAGAGGA 59.031 50.000 0.00 0.00 0.00 3.71
971 1447 3.582208 GGCTGAATGAGGATGTAGAGGAT 59.418 47.826 0.00 0.00 0.00 3.24
972 1448 4.322650 GGCTGAATGAGGATGTAGAGGATC 60.323 50.000 0.00 0.00 0.00 3.36
973 1449 4.322650 GCTGAATGAGGATGTAGAGGATCC 60.323 50.000 2.48 2.48 39.94 3.36
974 1450 3.829026 TGAATGAGGATGTAGAGGATCCG 59.171 47.826 5.98 0.00 43.78 4.18
975 1451 3.816398 ATGAGGATGTAGAGGATCCGA 57.184 47.619 5.98 0.00 43.78 4.55
976 1452 3.816398 TGAGGATGTAGAGGATCCGAT 57.184 47.619 5.98 1.10 43.78 4.18
1082 2447 4.057432 GCTGTTTTTGAGCAAATAAGGCA 58.943 39.130 0.00 0.00 36.40 4.75
1297 2662 4.388485 TCAGCTAGAGACACAAATGCAAA 58.612 39.130 0.00 0.00 0.00 3.68
1556 2921 8.324163 TGCTTTCTTTAAGTAGGTTGATCTTC 57.676 34.615 0.00 0.00 36.19 2.87
2279 3644 5.199024 TGTTGTGCTGATATGTTTTGCTT 57.801 34.783 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
860 864 2.674747 GCAAACACATACCCAGGCATTG 60.675 50.000 0.00 0.00 0.00 2.82
939 1415 1.938577 CTCATTCAGCCACTCCAATCG 59.061 52.381 0.00 0.00 0.00 3.34
940 1416 2.092753 TCCTCATTCAGCCACTCCAATC 60.093 50.000 0.00 0.00 0.00 2.67
941 1417 1.918262 TCCTCATTCAGCCACTCCAAT 59.082 47.619 0.00 0.00 0.00 3.16
942 1418 1.361204 TCCTCATTCAGCCACTCCAA 58.639 50.000 0.00 0.00 0.00 3.53
943 1419 1.211212 CATCCTCATTCAGCCACTCCA 59.789 52.381 0.00 0.00 0.00 3.86
946 1422 3.378512 TCTACATCCTCATTCAGCCACT 58.621 45.455 0.00 0.00 0.00 4.00
947 1423 3.494048 CCTCTACATCCTCATTCAGCCAC 60.494 52.174 0.00 0.00 0.00 5.01
948 1424 2.702478 CCTCTACATCCTCATTCAGCCA 59.298 50.000 0.00 0.00 0.00 4.75
949 1425 2.968574 TCCTCTACATCCTCATTCAGCC 59.031 50.000 0.00 0.00 0.00 4.85
950 1426 4.322650 GGATCCTCTACATCCTCATTCAGC 60.323 50.000 3.84 0.00 37.44 4.26
951 1427 4.082300 CGGATCCTCTACATCCTCATTCAG 60.082 50.000 10.75 0.00 38.18 3.02
953 1429 4.082845 TCGGATCCTCTACATCCTCATTC 58.917 47.826 10.75 0.00 38.18 2.67
954 1430 4.119556 TCGGATCCTCTACATCCTCATT 57.880 45.455 10.75 0.00 38.18 2.57
956 1432 3.816398 ATCGGATCCTCTACATCCTCA 57.184 47.619 10.75 0.00 38.18 3.86
958 1434 3.850752 ACAATCGGATCCTCTACATCCT 58.149 45.455 10.75 0.00 38.18 3.24
959 1435 4.608948 AACAATCGGATCCTCTACATCC 57.391 45.455 10.75 0.00 37.10 3.51
960 1436 5.601662 TCAAACAATCGGATCCTCTACATC 58.398 41.667 10.75 0.00 0.00 3.06
964 1440 5.869649 TCATCAAACAATCGGATCCTCTA 57.130 39.130 10.75 0.00 0.00 2.43
965 1441 4.760530 TCATCAAACAATCGGATCCTCT 57.239 40.909 10.75 0.00 0.00 3.69
967 1443 5.567138 GTTTCATCAAACAATCGGATCCT 57.433 39.130 10.75 0.00 41.53 3.24
1082 2447 1.072965 CCTTCCTGCTTGAGTTGAGGT 59.927 52.381 0.00 0.00 0.00 3.85
1297 2662 7.275920 ACTTGTACTTGTGTCTCTTCTTCAAT 58.724 34.615 0.00 0.00 0.00 2.57
1556 2921 5.536554 ACATTAGAGCACGAGAACAATTG 57.463 39.130 3.24 3.24 0.00 2.32
2073 3438 5.714806 CCAACATAACCCTTAACAGTCCAAT 59.285 40.000 0.00 0.00 0.00 3.16
2367 3732 3.365969 GGCAAAATCTCGGACGAAATTGT 60.366 43.478 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.