Multiple sequence alignment - TraesCS7B01G484600

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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 TraesCS7B01G484600 chr7B 100.000 2495 0 0 1 2495 741620686 741618192 0.000000e+00 4608.0
1 TraesCS7B01G484600 chr7B 94.930 2071 66 6 458 2495 741548872 741550936 0.000000e+00 3206.0
2 TraesCS7B01G484600 chr7B 83.350 2060 236 51 455 2434 741588860 741586828 0.000000e+00 1805.0
3 TraesCS7B01G484600 chr7B 82.923 1827 195 49 455 2207 741558454 741560237 0.000000e+00 1537.0
4 TraesCS7B01G484600 chr7B 92.577 485 25 5 2016 2489 741554162 741554646 0.000000e+00 686.0
5 TraesCS7B01G484600 chr7D 92.199 2474 144 19 4 2446 634669054 634671509 0.000000e+00 3454.0
6 TraesCS7B01G484600 chr7D 85.054 2054 204 41 455 2432 634677541 634679567 0.000000e+00 1997.0
7 TraesCS7B01G484600 chr7D 86.065 1672 179 31 483 2111 634710113 634708453 0.000000e+00 1748.0
8 TraesCS7B01G484600 chr7D 97.619 42 1 0 2452 2493 634671562 634671603 3.440000e-09 73.1
9 TraesCS7B01G484600 chr7A 92.766 1963 108 15 501 2439 731389588 731387636 0.000000e+00 2808.0
10 TraesCS7B01G484600 chr7A 86.296 1671 173 29 484 2111 731252576 731254233 0.000000e+00 1766.0
11 TraesCS7B01G484600 chr7A 85.750 1607 165 31 862 2439 731236443 731238014 0.000000e+00 1640.0
12 TraesCS7B01G484600 chr7A 83.967 1553 159 38 455 1967 731017269 731018771 0.000000e+00 1406.0
13 TraesCS7B01G484600 chr7A 84.711 1452 154 33 474 1881 731501678 731500251 0.000000e+00 1389.0
14 TraesCS7B01G484600 chr7A 83.896 1037 112 21 455 1476 731421862 731420866 0.000000e+00 939.0
15 TraesCS7B01G484600 chr7A 85.588 791 97 9 666 1452 731345904 731345127 0.000000e+00 813.0
16 TraesCS7B01G484600 chr7A 92.357 471 32 4 3 473 731390047 731389581 0.000000e+00 667.0
17 TraesCS7B01G484600 chr7A 83.527 601 69 14 1868 2439 731385797 731385198 3.650000e-148 534.0
18 TraesCS7B01G484600 chr7A 87.371 388 47 1 2052 2439 731019029 731019414 6.330000e-121 444.0
19 TraesCS7B01G484600 chr7A 80.651 584 68 21 457 1011 731292445 731291878 6.420000e-111 411.0
20 TraesCS7B01G484600 chr7A 85.195 385 54 1 2055 2439 731499928 731499547 2.330000e-105 392.0
21 TraesCS7B01G484600 chr7A 86.397 272 32 2 3 270 731422130 731421860 2.430000e-75 292.0
22 TraesCS7B01G484600 chr7A 86.029 272 33 2 3 270 731017001 731017271 1.130000e-73 287.0
23 TraesCS7B01G484600 chr7A 83.500 200 26 4 453 650 731235716 731235910 1.970000e-41 180.0
24 TraesCS7B01G484600 chr7A 82.609 184 19 9 280 454 63333951 63333772 1.550000e-32 150.0
25 TraesCS7B01G484600 chr4B 86.054 1556 156 31 455 1971 625077765 625079298 0.000000e+00 1615.0
26 TraesCS7B01G484600 chr6D 85.475 179 20 5 277 453 5926868 5926694 5.480000e-42 182.0
27 TraesCS7B01G484600 chr6D 83.889 180 23 5 277 454 5926677 5926502 1.530000e-37 167.0
28 TraesCS7B01G484600 chr3B 76.410 195 29 14 270 455 2994294 2994480 3.420000e-14 89.8
29 TraesCS7B01G484600 chr6B 80.000 110 21 1 277 386 612269549 612269657 2.060000e-11 80.5
30 TraesCS7B01G484600 chr6B 87.500 64 7 1 336 399 706998373 706998435 3.440000e-09 73.1
31 TraesCS7B01G484600 chr2D 76.812 138 21 8 321 453 72575334 72575203 1.600000e-07 67.6


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 TraesCS7B01G484600 chr7B 741618192 741620686 2494 True 4608.000000 4608 100.000000 1 2495 1 chr7B.!!$R2 2494
1 TraesCS7B01G484600 chr7B 741548872 741560237 11365 False 1809.666667 3206 90.143333 455 2495 3 chr7B.!!$F1 2040
2 TraesCS7B01G484600 chr7B 741586828 741588860 2032 True 1805.000000 1805 83.350000 455 2434 1 chr7B.!!$R1 1979
3 TraesCS7B01G484600 chr7D 634677541 634679567 2026 False 1997.000000 1997 85.054000 455 2432 1 chr7D.!!$F1 1977
4 TraesCS7B01G484600 chr7D 634669054 634671603 2549 False 1763.550000 3454 94.909000 4 2493 2 chr7D.!!$F2 2489
5 TraesCS7B01G484600 chr7D 634708453 634710113 1660 True 1748.000000 1748 86.065000 483 2111 1 chr7D.!!$R1 1628
6 TraesCS7B01G484600 chr7A 731252576 731254233 1657 False 1766.000000 1766 86.296000 484 2111 1 chr7A.!!$F1 1627
7 TraesCS7B01G484600 chr7A 731385198 731390047 4849 True 1336.333333 2808 89.550000 3 2439 3 chr7A.!!$R4 2436
8 TraesCS7B01G484600 chr7A 731235716 731238014 2298 False 910.000000 1640 84.625000 453 2439 2 chr7A.!!$F3 1986
9 TraesCS7B01G484600 chr7A 731499547 731501678 2131 True 890.500000 1389 84.953000 474 2439 2 chr7A.!!$R6 1965
10 TraesCS7B01G484600 chr7A 731345127 731345904 777 True 813.000000 813 85.588000 666 1452 1 chr7A.!!$R3 786
11 TraesCS7B01G484600 chr7A 731017001 731019414 2413 False 712.333333 1406 85.789000 3 2439 3 chr7A.!!$F2 2436
12 TraesCS7B01G484600 chr7A 731420866 731422130 1264 True 615.500000 939 85.146500 3 1476 2 chr7A.!!$R5 1473
13 TraesCS7B01G484600 chr7A 731291878 731292445 567 True 411.000000 411 80.651000 457 1011 1 chr7A.!!$R2 554
14 TraesCS7B01G484600 chr4B 625077765 625079298 1533 False 1615.000000 1615 86.054000 455 1971 1 chr4B.!!$F1 1516

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
727 775 0.673985 CTCGCTCCCGTGATATTGGA 59.326 55.0 0.0 0.0 35.54 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2358 12605 0.315251 TGTTCTCCTGTGCGTCTCTG 59.685 55.0 0.0 0.0 0.0 3.35 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
133 138 9.565090 TGTTTATCTCATCTTATTCAATCCCAG 57.435 33.333 0.00 0.00 0.00 4.45
143 148 6.544931 TCTTATTCAATCCCAGCTGATCAAAG 59.455 38.462 17.39 6.23 0.00 2.77
274 279 2.151202 AGTTGGTGCAATAGGACAACG 58.849 47.619 0.00 0.00 37.91 4.10
275 280 1.877443 GTTGGTGCAATAGGACAACGT 59.123 47.619 0.00 0.00 37.91 3.99
279 284 1.535462 GTGCAATAGGACAACGTTGCT 59.465 47.619 27.61 19.11 42.32 3.91
327 334 6.238484 GCTTTTACATTGTCACTCTGAGTTGT 60.238 38.462 7.77 11.90 0.00 3.32
347 354 5.004361 TGTCAGGGGTTGATTGGATTAAA 57.996 39.130 0.00 0.00 38.29 1.52
352 359 3.310288 GGGGTTGATTGGATTAAAGGGGA 60.310 47.826 0.00 0.00 0.00 4.81
358 365 7.267857 GTTGATTGGATTAAAGGGGAAGATTG 58.732 38.462 0.00 0.00 0.00 2.67
396 406 2.270874 ATCAGGGGGCGCAGGTTTAG 62.271 60.000 10.83 0.00 0.00 1.85
414 424 1.852633 AGTTAAATGGAAGCAGCCCC 58.147 50.000 0.00 0.00 0.00 5.80
435 445 4.432712 CCATAAAAGCATGTAAACAGCCC 58.567 43.478 0.00 0.00 0.00 5.19
465 475 2.638855 AGCATTTTTGGGATTTGAGCCA 59.361 40.909 0.00 0.00 0.00 4.75
610 631 3.670377 GGCTTGTGTTCGGCCCAC 61.670 66.667 0.00 0.00 39.96 4.61
724 772 1.399714 TGTCTCGCTCCCGTGATATT 58.600 50.000 0.00 0.00 38.92 1.28
727 775 0.673985 CTCGCTCCCGTGATATTGGA 59.326 55.000 0.00 0.00 35.54 3.53
736 784 3.865745 CCCGTGATATTGGAAGCGATATC 59.134 47.826 0.00 0.00 36.33 1.63
737 785 3.547868 CCGTGATATTGGAAGCGATATCG 59.452 47.826 20.79 20.79 37.83 2.92
738 786 3.547868 CGTGATATTGGAAGCGATATCGG 59.452 47.826 25.51 8.53 37.83 4.18
739 787 3.865745 GTGATATTGGAAGCGATATCGGG 59.134 47.826 25.51 0.05 37.83 5.14
740 788 3.118775 TGATATTGGAAGCGATATCGGGG 60.119 47.826 25.51 0.00 37.83 5.73
1021 10998 2.338620 CTCGCAACGTGACCCTCA 59.661 61.111 0.00 0.00 0.00 3.86
1029 11006 3.615592 GCAACGTGACCCTCAAGTACATA 60.616 47.826 0.00 0.00 38.10 2.29
1149 11126 2.165998 GTACTGGTGTACGAAGAGGGT 58.834 52.381 0.00 0.00 39.49 4.34
1179 11156 1.562672 CGGAGGTGTTCCCTTCCCAT 61.563 60.000 0.00 0.00 46.51 4.00
1297 11274 0.115152 TGAGAAGCTCCAGGACCAGA 59.885 55.000 0.00 0.00 0.00 3.86
1334 11311 2.505118 GTGCGAGGACAGCGAGAC 60.505 66.667 0.00 0.00 37.44 3.36
1476 11453 3.686120 GCATGGCAAAAATCCATTCCCAT 60.686 43.478 0.00 0.00 42.11 4.00
1502 11501 1.447317 CCGGCAACATAGACATGGGC 61.447 60.000 0.00 0.00 36.39 5.36
1566 11569 2.104622 TGACTTGACATGGTGAGCTTCA 59.895 45.455 0.00 0.00 0.00 3.02
1633 11639 2.352651 GCTTCTGTTGCAGCGATATGAA 59.647 45.455 0.00 0.00 0.00 2.57
1763 11773 5.730550 TGGTGGTTAGTATGAGACATTCAC 58.269 41.667 0.00 0.00 38.99 3.18
1937 11957 4.914312 TGGTCGTAAATCTTTAGTTGCG 57.086 40.909 0.00 0.00 39.61 4.85
2042 12284 1.673033 GGTCGTGTGTTGGGAGATCTG 60.673 57.143 0.00 0.00 0.00 2.90
2111 12356 5.661458 TGGGATAGAAACGAGTTGAAGATC 58.339 41.667 0.00 0.00 0.00 2.75
2135 12380 5.221263 CCGTTCTCCTAGAGCAAGCTAAATA 60.221 44.000 0.00 0.00 0.00 1.40
2146 12391 7.229308 AGAGCAAGCTAAATATGATGGATGAA 58.771 34.615 0.00 0.00 0.00 2.57
2240 12485 3.501828 ACACGCAAACATCAGAAATAGCA 59.498 39.130 0.00 0.00 0.00 3.49
2302 12547 7.155442 TCTCTATTCTTCAGACCATCCTCTA 57.845 40.000 0.00 0.00 0.00 2.43
2358 12605 2.296471 TCTTCAGACTGTCCTTCGTTCC 59.704 50.000 3.76 0.00 0.00 3.62
2374 12628 0.539669 TTCCAGAGACGCACAGGAGA 60.540 55.000 0.00 0.00 0.00 3.71
2378 12632 1.067283 CAGAGACGCACAGGAGAACAT 60.067 52.381 0.00 0.00 0.00 2.71
2379 12633 2.164422 CAGAGACGCACAGGAGAACATA 59.836 50.000 0.00 0.00 0.00 2.29
2439 12694 0.038744 CAAGGAGACATGGTGGCCTT 59.961 55.000 3.32 1.60 39.42 4.35
2440 12695 0.329596 AAGGAGACATGGTGGCCTTC 59.670 55.000 3.32 0.00 33.94 3.46
2441 12696 0.842030 AGGAGACATGGTGGCCTTCA 60.842 55.000 3.32 2.11 0.00 3.02
2442 12697 0.257039 GGAGACATGGTGGCCTTCAT 59.743 55.000 3.32 4.81 0.00 2.57
2443 12698 1.386533 GAGACATGGTGGCCTTCATG 58.613 55.000 26.32 26.32 44.42 3.07
2444 12699 0.682209 AGACATGGTGGCCTTCATGC 60.682 55.000 27.24 21.63 43.12 4.06
2445 12700 0.682209 GACATGGTGGCCTTCATGCT 60.682 55.000 27.24 18.75 43.12 3.79
2447 12702 1.380785 ATGGTGGCCTTCATGCTGG 60.381 57.895 3.32 0.00 0.00 4.85
2448 12703 1.866483 ATGGTGGCCTTCATGCTGGA 61.866 55.000 3.32 0.00 0.00 3.86
2450 12705 0.183492 GGTGGCCTTCATGCTGGATA 59.817 55.000 3.32 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.466728 GCGAGATATCCAATAACACACACAT 59.533 40.000 0.00 0.00 0.00 3.21
11 12 8.367911 TGATAGTAAAAGTGCGAGATATCCAAT 58.632 33.333 0.00 0.00 0.00 3.16
65 70 2.376915 TTGTGCGCTACAAAAGAACG 57.623 45.000 18.68 0.00 45.86 3.95
123 128 4.305539 TCTTTGATCAGCTGGGATTGAA 57.694 40.909 15.13 1.29 0.00 2.69
130 135 4.015084 ACTTTCCATCTTTGATCAGCTGG 58.985 43.478 15.13 2.28 32.15 4.85
133 138 6.925165 TCAAAAACTTTCCATCTTTGATCAGC 59.075 34.615 0.00 0.00 32.54 4.26
258 263 1.401018 GCAACGTTGTCCTATTGCACC 60.401 52.381 27.78 4.40 45.38 5.01
274 279 0.727398 GAGCCCGTGAATGTAGCAAC 59.273 55.000 0.00 0.00 0.00 4.17
275 280 0.323302 TGAGCCCGTGAATGTAGCAA 59.677 50.000 0.00 0.00 0.00 3.91
279 284 2.482316 CCGTATTGAGCCCGTGAATGTA 60.482 50.000 0.00 0.00 0.00 2.29
327 334 4.571792 CCCTTTAATCCAATCAACCCCTGA 60.572 45.833 0.00 0.00 38.81 3.86
396 406 1.555967 TGGGGCTGCTTCCATTTAAC 58.444 50.000 10.30 0.00 0.00 2.01
414 424 4.104776 CGGGCTGTTTACATGCTTTTATG 58.895 43.478 0.00 0.00 0.00 1.90
575 596 1.115467 CCTTGCTCCTATCGGTCAGT 58.885 55.000 0.00 0.00 0.00 3.41
610 631 2.364324 CCCATCAAGCCATCCAAATGAG 59.636 50.000 0.00 0.00 34.61 2.90
724 772 0.761323 TTCCCCCGATATCGCTTCCA 60.761 55.000 19.78 0.17 38.18 3.53
727 775 1.366366 CGTTCCCCCGATATCGCTT 59.634 57.895 19.78 0.00 38.18 4.68
738 786 2.660258 ATAGCGCATGACCGTTCCCC 62.660 60.000 11.47 0.00 0.00 4.81
739 787 1.222115 GATAGCGCATGACCGTTCCC 61.222 60.000 11.47 0.00 0.00 3.97
740 788 1.548973 CGATAGCGCATGACCGTTCC 61.549 60.000 11.47 0.00 0.00 3.62
1021 10998 3.383825 GTCGAGTCATGGGGTATGTACTT 59.616 47.826 0.00 0.00 38.01 2.24
1029 11006 3.075005 CGGGTCGAGTCATGGGGT 61.075 66.667 0.00 0.00 0.00 4.95
1080 11057 2.636830 AGTTCATCCGCCTTCTTCATG 58.363 47.619 0.00 0.00 0.00 3.07
1232 11209 0.955428 GTTCATCGCCTCCTTGCACA 60.955 55.000 0.00 0.00 0.00 4.57
1314 11291 2.982744 CTCGCTGTCCTCGCACTCA 61.983 63.158 0.00 0.00 0.00 3.41
1502 11501 2.628178 TGCCAGATACAATACGGGAGAG 59.372 50.000 0.00 0.00 0.00 3.20
1618 11621 4.509230 TCTTCATCTTCATATCGCTGCAAC 59.491 41.667 0.00 0.00 0.00 4.17
1633 11639 7.228906 CCATATCAAAGAACTGCATCTTCATCT 59.771 37.037 3.10 0.00 38.69 2.90
1790 11800 3.183754 TGATTACAACGACGCACATAGG 58.816 45.455 0.00 0.00 0.00 2.57
2042 12284 3.161866 TGAAACTAAAGGCCCCAACATC 58.838 45.455 0.00 0.00 0.00 3.06
2111 12356 0.820871 AGCTTGCTCTAGGAGAACGG 59.179 55.000 0.00 0.00 0.00 4.44
2135 12380 9.262240 TCCATGCAAATATTATTCATCCATCAT 57.738 29.630 0.00 0.00 0.00 2.45
2240 12485 4.084287 ACAAGAGCACAATGTGGATCATT 58.916 39.130 15.78 0.00 46.32 2.57
2358 12605 0.315251 TGTTCTCCTGTGCGTCTCTG 59.685 55.000 0.00 0.00 0.00 3.35
2374 12628 4.688879 TCGTCTTGACGAGCAAATTATGTT 59.311 37.500 19.99 0.00 37.20 2.71
2378 12632 8.699749 CATAATATCGTCTTGACGAGCAAATTA 58.300 33.333 26.02 23.03 45.70 1.40
2379 12633 7.307396 CCATAATATCGTCTTGACGAGCAAATT 60.307 37.037 26.02 22.06 45.70 1.82


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

AutoCloner maintained by Alex Coulton.