Multiple sequence alignment - TraesCS7B01G108100

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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 TraesCS7B01G108100 chr7B 100.000 2633 0 0 1 2633 124345688 124348320 0.000000e+00 4863.0
1 TraesCS7B01G108100 chr7B 85.085 590 55 18 1 563 10760969 10761552 2.940000e-159 571.0
2 TraesCS7B01G108100 chr6B 96.314 1031 35 3 1605 2633 518362881 518361852 0.000000e+00 1690.0
3 TraesCS7B01G108100 chr6B 94.622 595 32 0 1008 1602 286810522 286809928 0.000000e+00 922.0
4 TraesCS7B01G108100 chr6B 85.714 595 48 21 1 565 140357438 140356851 6.270000e-166 593.0
5 TraesCS7B01G108100 chr6B 87.019 416 49 3 592 1005 709508581 709508993 5.130000e-127 464.0
6 TraesCS7B01G108100 chr1B 95.745 1034 39 5 1598 2627 214385405 214386437 0.000000e+00 1661.0
7 TraesCS7B01G108100 chr1B 95.068 1034 46 5 1603 2633 500895246 500894215 0.000000e+00 1622.0
8 TraesCS7B01G108100 chr1B 88.038 418 43 5 592 1005 585897327 585896913 3.050000e-134 488.0
9 TraesCS7B01G108100 chr2B 95.362 1035 42 6 1603 2633 636050272 636049240 0.000000e+00 1640.0
10 TraesCS7B01G108100 chr2B 94.894 1038 48 5 1600 2633 594919349 594918313 0.000000e+00 1618.0
11 TraesCS7B01G108100 chr2B 85.320 579 51 15 1 574 699898702 699898153 3.800000e-158 568.0
12 TraesCS7B01G108100 chr2B 84.123 359 38 17 272 621 5099296 5098948 1.950000e-86 329.0
13 TraesCS7B01G108100 chr2B 90.071 141 12 2 592 731 699898019 699897880 5.790000e-42 182.0
14 TraesCS7B01G108100 chr4B 95.063 1033 44 4 1603 2633 546591518 546592545 0.000000e+00 1618.0
15 TraesCS7B01G108100 chr4B 95.063 1033 44 4 1603 2633 546615301 546616328 0.000000e+00 1618.0
16 TraesCS7B01G108100 chr4B 90.833 120 10 1 887 1005 8844657 8844538 2.710000e-35 159.0
17 TraesCS7B01G108100 chr3B 95.631 1007 40 4 1605 2609 186736694 186735690 0.000000e+00 1613.0
18 TraesCS7B01G108100 chr3B 95.229 1006 42 5 1 1005 22504377 22505377 0.000000e+00 1587.0
19 TraesCS7B01G108100 chr3B 94.327 1040 52 6 1599 2633 594327865 594328902 0.000000e+00 1587.0
20 TraesCS7B01G108100 chr2A 94.790 595 31 0 1008 1602 726541022 726540428 0.000000e+00 928.0
21 TraesCS7B01G108100 chr7A 94.454 595 33 0 1008 1602 182349787 182350381 0.000000e+00 917.0
22 TraesCS7B01G108100 chr7A 84.500 600 67 8 6 581 70311540 70310943 1.060000e-158 569.0
23 TraesCS7B01G108100 chr7A 84.199 443 38 18 150 563 90367331 90366892 4.080000e-108 401.0
24 TraesCS7B01G108100 chr1A 91.261 595 52 0 1008 1602 185081265 185080671 0.000000e+00 811.0
25 TraesCS7B01G108100 chr3D 95.112 491 21 3 1 490 33848280 33848768 0.000000e+00 771.0
26 TraesCS7B01G108100 chr3D 96.445 422 14 1 584 1005 33857832 33858252 0.000000e+00 695.0
27 TraesCS7B01G108100 chr7D 89.845 581 45 6 1 574 555229947 555230520 0.000000e+00 734.0
28 TraesCS7B01G108100 chr7D 86.248 589 51 16 1 563 65924806 65924222 1.730000e-171 612.0
29 TraesCS7B01G108100 chr7D 82.906 585 67 20 66 620 523083752 523084333 1.820000e-136 496.0
30 TraesCS7B01G108100 chr7D 91.349 289 22 2 584 869 555230618 555230906 2.460000e-105 392.0
31 TraesCS7B01G108100 chr7D 87.619 210 19 2 800 1005 555231051 555231257 1.220000e-58 237.0
32 TraesCS7B01G108100 chr7D 92.169 166 9 2 800 965 555230884 555231045 5.670000e-57 231.0
33 TraesCS7B01G108100 chr7D 80.682 88 10 6 787 869 555230988 555231073 7.870000e-06 62.1
34 TraesCS7B01G108100 chrUn 96.445 422 14 1 584 1005 240677973 240677553 0.000000e+00 695.0
35 TraesCS7B01G108100 chr6D 84.404 654 58 25 1 621 89332116 89332758 1.040000e-168 603.0
36 TraesCS7B01G108100 chr6D 85.500 600 51 20 1 570 65354694 65354101 6.270000e-166 593.0
37 TraesCS7B01G108100 chr6A 86.863 373 39 8 1 365 83464760 83465130 2.440000e-110 409.0
38 TraesCS7B01G108100 chr1D 79.685 571 69 30 41 574 116009615 116010175 4.140000e-98 368.0
39 TraesCS7B01G108100 chr4A 82.576 132 17 5 584 712 374571722 374571850 7.700000e-21 111.0
40 TraesCS7B01G108100 chr4A 80.303 132 20 5 584 712 626051689 626051817 7.760000e-16 95.3


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 TraesCS7B01G108100 chr7B 124345688 124348320 2632 False 4863.00 4863 100.0000 1 2633 1 chr7B.!!$F2 2632
1 TraesCS7B01G108100 chr7B 10760969 10761552 583 False 571.00 571 85.0850 1 563 1 chr7B.!!$F1 562
2 TraesCS7B01G108100 chr6B 518361852 518362881 1029 True 1690.00 1690 96.3140 1605 2633 1 chr6B.!!$R3 1028
3 TraesCS7B01G108100 chr6B 286809928 286810522 594 True 922.00 922 94.6220 1008 1602 1 chr6B.!!$R2 594
4 TraesCS7B01G108100 chr6B 140356851 140357438 587 True 593.00 593 85.7140 1 565 1 chr6B.!!$R1 564
5 TraesCS7B01G108100 chr1B 214385405 214386437 1032 False 1661.00 1661 95.7450 1598 2627 1 chr1B.!!$F1 1029
6 TraesCS7B01G108100 chr1B 500894215 500895246 1031 True 1622.00 1622 95.0680 1603 2633 1 chr1B.!!$R1 1030
7 TraesCS7B01G108100 chr2B 636049240 636050272 1032 True 1640.00 1640 95.3620 1603 2633 1 chr2B.!!$R3 1030
8 TraesCS7B01G108100 chr2B 594918313 594919349 1036 True 1618.00 1618 94.8940 1600 2633 1 chr2B.!!$R2 1033
9 TraesCS7B01G108100 chr2B 699897880 699898702 822 True 375.00 568 87.6955 1 731 2 chr2B.!!$R4 730
10 TraesCS7B01G108100 chr4B 546591518 546592545 1027 False 1618.00 1618 95.0630 1603 2633 1 chr4B.!!$F1 1030
11 TraesCS7B01G108100 chr4B 546615301 546616328 1027 False 1618.00 1618 95.0630 1603 2633 1 chr4B.!!$F2 1030
12 TraesCS7B01G108100 chr3B 186735690 186736694 1004 True 1613.00 1613 95.6310 1605 2609 1 chr3B.!!$R1 1004
13 TraesCS7B01G108100 chr3B 22504377 22505377 1000 False 1587.00 1587 95.2290 1 1005 1 chr3B.!!$F1 1004
14 TraesCS7B01G108100 chr3B 594327865 594328902 1037 False 1587.00 1587 94.3270 1599 2633 1 chr3B.!!$F2 1034
15 TraesCS7B01G108100 chr2A 726540428 726541022 594 True 928.00 928 94.7900 1008 1602 1 chr2A.!!$R1 594
16 TraesCS7B01G108100 chr7A 182349787 182350381 594 False 917.00 917 94.4540 1008 1602 1 chr7A.!!$F1 594
17 TraesCS7B01G108100 chr7A 70310943 70311540 597 True 569.00 569 84.5000 6 581 1 chr7A.!!$R1 575
18 TraesCS7B01G108100 chr1A 185080671 185081265 594 True 811.00 811 91.2610 1008 1602 1 chr1A.!!$R1 594
19 TraesCS7B01G108100 chr7D 65924222 65924806 584 True 612.00 612 86.2480 1 563 1 chr7D.!!$R1 562
20 TraesCS7B01G108100 chr7D 523083752 523084333 581 False 496.00 496 82.9060 66 620 1 chr7D.!!$F1 554
21 TraesCS7B01G108100 chr7D 555229947 555231257 1310 False 331.22 734 88.3328 1 1005 5 chr7D.!!$F2 1004
22 TraesCS7B01G108100 chr6D 89332116 89332758 642 False 603.00 603 84.4040 1 621 1 chr6D.!!$F1 620
23 TraesCS7B01G108100 chr6D 65354101 65354694 593 True 593.00 593 85.5000 1 570 1 chr6D.!!$R1 569
24 TraesCS7B01G108100 chr1D 116009615 116010175 560 False 368.00 368 79.6850 41 574 1 chr1D.!!$F1 533

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
538 612 2.549064 AAAATCCCACTTTTGGCTGC 57.451 45.0 0.0 0.0 42.35 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2097 2512 0.391597 GACCAAGACCAGTCCAACGA 59.608 55.0 0.0 0.0 0.0 3.85 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
101 106 5.461032 AAAAGGATTAAATGTTGCCACGA 57.539 34.783 0.00 0.00 0.00 4.35
233 240 9.628746 AAATTGCCATGCTTTTTGAAATAAATC 57.371 25.926 0.00 0.00 0.00 2.17
538 612 2.549064 AAAATCCCACTTTTGGCTGC 57.451 45.000 0.00 0.00 42.35 5.25
714 908 6.096001 ACAAGGATAGAGATGAAAATTGCCAC 59.904 38.462 0.00 0.00 0.00 5.01
727 921 2.593346 TTGCCACGAACTTTGCAAAT 57.407 40.000 13.23 0.00 40.46 2.32
985 1396 5.419760 AAAGAGTTTCTTCGGTTAGCAAC 57.580 39.130 0.00 0.00 35.27 4.17
986 1397 4.067972 AGAGTTTCTTCGGTTAGCAACA 57.932 40.909 0.00 0.00 0.00 3.33
1005 1416 5.122711 GCAACAAGCTAAAAATGCCATGATT 59.877 36.000 0.00 0.00 41.15 2.57
1006 1417 6.348704 GCAACAAGCTAAAAATGCCATGATTT 60.349 34.615 0.00 0.00 41.15 2.17
1027 1438 3.385384 CCTCCTCTGCCAGCGTCA 61.385 66.667 0.00 0.00 0.00 4.35
1175 1586 2.686835 GCTCCCTGGCTCCTCACT 60.687 66.667 0.00 0.00 0.00 3.41
1206 1617 1.264045 GGCTCCCTGACTCTTCTGCT 61.264 60.000 0.00 0.00 0.00 4.24
1264 1675 3.637273 GTCACCCTTCCCTGCGGT 61.637 66.667 0.00 0.00 0.00 5.68
1449 1860 1.990060 CTCTGTCCACCCCCGTCAT 60.990 63.158 0.00 0.00 0.00 3.06
1477 1888 2.091541 GATTTCTCATCCGGTTTGCCA 58.908 47.619 0.00 0.00 34.09 4.92
1531 1942 0.037326 TGTCAGCTCGCCTCGATTTT 60.037 50.000 0.00 0.00 34.61 1.82
1686 2097 2.838813 GCCTTCTACCTACCTGTTCCTT 59.161 50.000 0.00 0.00 0.00 3.36
1755 2166 3.308188 GCAGGGTTTATACTGGTTCAGGT 60.308 47.826 0.00 0.00 35.51 4.00
1848 2260 0.603707 CAAGGAAGAACAGCCTCGCA 60.604 55.000 0.00 0.00 32.07 5.10
1905 2319 1.685148 GGTTGATTCCAGATGCCCTC 58.315 55.000 0.00 0.00 0.00 4.30
2072 2487 3.583276 CTGTGGTGACGCCGGCTTA 62.583 63.158 26.68 7.53 41.24 3.09
2097 2512 1.229209 ACGGTGACCTCCATCCTGT 60.229 57.895 0.00 0.00 0.00 4.00
2165 2580 2.358756 GATGCTCTCGCTTGCGCTTC 62.359 60.000 9.73 0.00 36.97 3.86
2168 2583 1.739562 CTCTCGCTTGCGCTTCCTT 60.740 57.895 9.73 0.00 0.00 3.36
2303 2724 1.754621 CTCCTCGTGAGCCAGCCTA 60.755 63.158 0.00 0.00 33.47 3.93
2399 2820 0.327924 TTGATGAAGATGGGCCGTGT 59.672 50.000 1.02 0.00 0.00 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 5.687285 GCCATGGCAAAAATACTTCTATTCG 59.313 40.000 32.08 0.00 41.49 3.34
164 170 8.321005 GCAAATTTACATTTTTCGGAAGATAGC 58.679 33.333 0.00 0.00 32.76 2.97
538 612 6.238076 GGGCATGGCAAAAATACTTTTATTCG 60.238 38.462 22.06 0.00 32.85 3.34
727 921 5.448360 GCAATGTTTGTTTGGCTTAGCAAAA 60.448 36.000 6.53 4.26 33.43 2.44
985 1396 5.353123 AGCAAATCATGGCATTTTTAGCTTG 59.647 36.000 0.00 0.00 0.00 4.01
986 1397 5.493809 AGCAAATCATGGCATTTTTAGCTT 58.506 33.333 0.00 0.00 0.00 3.74
1005 1416 2.964310 GCTGGCAGAGGAGGAGCAA 61.964 63.158 20.86 0.00 0.00 3.91
1006 1417 3.397439 GCTGGCAGAGGAGGAGCA 61.397 66.667 20.86 0.00 0.00 4.26
1449 1860 1.424638 GGATGAGAAATCCCTCCGGA 58.575 55.000 2.93 2.93 44.33 5.14
1531 1942 0.907486 CAGGGATGGAGCAGAAGACA 59.093 55.000 0.00 0.00 0.00 3.41
1686 2097 5.068636 AGTTTAGATCCTAGCGATTCGGTA 58.931 41.667 16.27 16.27 38.83 4.02
1848 2260 2.290960 GCCACCACAAGAATAGACCCTT 60.291 50.000 0.00 0.00 0.00 3.95
1905 2319 6.919775 AAATAGGACTAGCCACCATAGTAG 57.080 41.667 6.07 0.00 40.02 2.57
2072 2487 2.997897 GAGGTCACCGTGGAGCCT 60.998 66.667 9.08 9.08 35.95 4.58
2097 2512 0.391597 GACCAAGACCAGTCCAACGA 59.608 55.000 0.00 0.00 0.00 3.85
2165 2580 1.251251 CTCTTTGGTGCAAGGGAAGG 58.749 55.000 0.00 0.00 0.00 3.46
2168 2583 0.850100 TTCCTCTTTGGTGCAAGGGA 59.150 50.000 0.10 0.00 37.07 4.20


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

AutoCloner maintained by Alex Coulton.