Multiple sequence alignment - TraesCS7B01G319600

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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 TraesCS7B01G319600 chr7B 100.000 2827 0 0 1 2827 569482499 569479673 0.000000e+00 5221.0
1 TraesCS7B01G319600 chr7B 89.363 2087 122 43 793 2827 591057006 591054968 0.000000e+00 2532.0
2 TraesCS7B01G319600 chr7B 94.851 1340 30 15 692 2010 569439949 569438628 0.000000e+00 2056.0
3 TraesCS7B01G319600 chr7B 84.621 1398 121 51 681 2032 591565943 591567292 0.000000e+00 1304.0
4 TraesCS7B01G319600 chr7B 85.096 1201 95 45 793 1955 591684290 591685444 0.000000e+00 1149.0
5 TraesCS7B01G319600 chr7B 85.222 1015 89 37 843 1814 633001104 633002100 0.000000e+00 987.0
6 TraesCS7B01G319600 chr7B 90.186 591 20 13 1 561 569440739 569440157 0.000000e+00 736.0
7 TraesCS7B01G319600 chr7B 85.747 435 48 3 1 431 591683801 591684225 5.560000e-122 448.0
8 TraesCS7B01G319600 chr7B 89.706 272 17 5 2562 2822 569437085 569436814 1.250000e-88 337.0
9 TraesCS7B01G319600 chr7B 86.264 182 13 3 1 178 591599321 591599494 1.340000e-43 187.0
10 TraesCS7B01G319600 chr7B 95.122 41 2 0 2473 2513 591070986 591070946 6.540000e-07 65.8
11 TraesCS7B01G319600 chr7A 82.299 2079 165 79 1 1955 630670769 630672768 0.000000e+00 1613.0
12 TraesCS7B01G319600 chr7A 83.299 1473 135 62 636 2032 632265569 632267006 0.000000e+00 1254.0
13 TraesCS7B01G319600 chr7A 84.344 1303 106 32 592 1838 617552176 617550916 0.000000e+00 1186.0
14 TraesCS7B01G319600 chr7A 83.847 1331 114 48 560 1827 631652729 631651437 0.000000e+00 1173.0
15 TraesCS7B01G319600 chr7A 86.377 991 75 30 783 1724 632187995 632188974 0.000000e+00 1027.0
16 TraesCS7B01G319600 chr7A 90.328 610 43 9 845 1449 631872502 631871904 0.000000e+00 785.0
17 TraesCS7B01G319600 chr7A 90.816 490 25 10 2053 2539 630672962 630673434 3.070000e-179 638.0
18 TraesCS7B01G319600 chr7A 85.918 561 54 5 9 552 625641577 625642129 2.440000e-160 575.0
19 TraesCS7B01G319600 chr7A 85.614 570 55 9 9 561 631653316 631652757 8.780000e-160 573.0
20 TraesCS7B01G319600 chr7A 85.766 555 54 8 15 552 625674356 625674902 5.290000e-157 564.0
21 TraesCS7B01G319600 chr7A 78.846 832 87 31 5 783 632187167 632187962 1.970000e-131 479.0
22 TraesCS7B01G319600 chr7A 85.867 467 27 12 1584 2028 631849533 631849084 7.140000e-126 460.0
23 TraesCS7B01G319600 chr7A 90.831 349 20 7 2052 2389 631848993 631848646 9.230000e-125 457.0
24 TraesCS7B01G319600 chr7A 92.216 167 12 1 592 757 625674990 625675156 4.710000e-58 235.0
25 TraesCS7B01G319600 chr7A 90.361 166 15 1 592 756 625642208 625642373 1.710000e-52 217.0
26 TraesCS7B01G319600 chr7A 85.955 178 8 7 1869 2032 631651429 631651255 1.040000e-39 174.0
27 TraesCS7B01G319600 chr7A 90.385 104 10 0 680 783 631878015 631877912 1.370000e-28 137.0
28 TraesCS7B01G319600 chr7A 83.333 150 21 3 2682 2827 630673446 630673595 4.910000e-28 135.0
29 TraesCS7B01G319600 chr7A 91.089 101 8 1 670 769 631878026 631877926 4.910000e-28 135.0
30 TraesCS7B01G319600 chr7A 93.902 82 5 0 2372 2453 630622991 630623072 1.060000e-24 124.0
31 TraesCS7B01G319600 chr7A 92.683 82 5 1 2372 2453 617549844 617549764 1.780000e-22 117.0
32 TraesCS7B01G319600 chr7A 93.443 61 4 0 593 653 663574673 663574733 1.080000e-14 91.6
33 TraesCS7B01G319600 chr4A 83.253 1875 177 48 49 1847 141909601 141907788 0.000000e+00 1596.0
34 TraesCS7B01G319600 chr7D 93.581 1075 54 7 785 1847 530430789 530429718 0.000000e+00 1589.0
35 TraesCS7B01G319600 chr7D 87.305 1347 83 44 716 2032 530361750 530360462 0.000000e+00 1459.0
36 TraesCS7B01G319600 chr7D 84.729 1290 83 57 811 2028 548324917 548326164 0.000000e+00 1186.0
37 TraesCS7B01G319600 chr7D 86.580 1073 67 38 783 1796 548560698 548561752 0.000000e+00 1112.0
38 TraesCS7B01G319600 chr7D 85.546 1017 82 32 842 1814 573969167 573970162 0.000000e+00 1003.0
39 TraesCS7B01G319600 chr7D 81.112 1313 112 66 793 2031 548066914 548065664 0.000000e+00 926.0
40 TraesCS7B01G319600 chr7D 88.946 579 28 10 1 561 530431623 530431063 0.000000e+00 682.0
41 TraesCS7B01G319600 chr7D 91.042 480 22 9 2064 2537 548065574 548065110 1.850000e-176 628.0
42 TraesCS7B01G319600 chr7D 85.027 561 59 9 9 552 543730810 543731362 5.320000e-152 547.0
43 TraesCS7B01G319600 chr7D 84.220 564 62 8 6 552 548550345 548550898 8.970000e-145 523.0
44 TraesCS7B01G319600 chr7D 89.607 356 22 7 2052 2404 595751385 595751042 3.340000e-119 438.0
45 TraesCS7B01G319600 chr7D 89.326 356 23 6 2052 2404 588776415 588776758 1.560000e-117 433.0
46 TraesCS7B01G319600 chr7D 82.396 551 35 24 19 552 548067529 548067024 9.360000e-115 424.0
47 TraesCS7B01G319600 chr7D 90.406 271 21 3 2562 2827 530429257 530428987 4.480000e-93 351.0
48 TraesCS7B01G319600 chr7D 84.722 360 29 8 1 343 548324164 548324514 1.250000e-88 337.0
49 TraesCS7B01G319600 chr7D 91.566 166 13 1 592 756 543731447 543731612 7.880000e-56 228.0
50 TraesCS7B01G319600 chr7D 93.548 124 5 2 2416 2539 548326551 548326671 6.220000e-42 182.0
51 TraesCS7B01G319600 chr7D 95.181 83 4 0 2372 2454 530358299 530358217 6.350000e-27 132.0
52 TraesCS7B01G319600 chr7D 93.478 46 2 1 2468 2513 548087730 548087686 1.820000e-07 67.6
53 TraesCS7B01G319600 chr7D 81.928 83 9 3 2374 2450 573970741 573970823 6.540000e-07 65.8
54 TraesCS7B01G319600 chr7D 81.928 83 9 3 2374 2450 574248369 574248451 6.540000e-07 65.8
55 TraesCS7B01G319600 chr7D 91.304 46 3 1 2468 2513 548093235 548093191 8.460000e-06 62.1
56 TraesCS7B01G319600 chrUn 84.934 1281 105 47 687 1923 355335469 355334233 0.000000e+00 1216.0
57 TraesCS7B01G319600 chrUn 84.329 1289 106 52 793 2032 337590886 337589645 0.000000e+00 1173.0
58 TraesCS7B01G319600 chrUn 90.196 357 19 9 2052 2404 70734926 70735270 4.290000e-123 451.0
59 TraesCS7B01G319600 chrUn 85.747 435 48 3 1 431 337591375 337590951 5.560000e-122 448.0
60 TraesCS7B01G319600 chr1D 85.205 561 58 4 9 552 110904567 110905119 1.140000e-153 553.0
61 TraesCS7B01G319600 chr1D 91.124 169 14 1 592 759 110905207 110905375 7.880000e-56 228.0
62 TraesCS7B01G319600 chr6B 84.520 562 60 8 9 552 694680372 694680924 5.360000e-147 531.0
63 TraesCS7B01G319600 chr6B 90.980 255 19 3 2052 2304 241431622 241431874 9.700000e-90 340.0
64 TraesCS7B01G319600 chr6B 89.286 168 13 4 592 756 694681003 694681168 3.690000e-49 206.0
65 TraesCS7B01G319600 chr1B 84.314 561 63 4 9 552 169024351 169024903 2.490000e-145 525.0
66 TraesCS7B01G319600 chr2B 81.335 659 78 16 73 697 671010536 671009889 7.040000e-136 494.0
67 TraesCS7B01G319600 chr5D 90.169 356 18 9 2052 2404 86777764 86777423 5.560000e-122 448.0
68 TraesCS7B01G319600 chr3D 88.764 356 25 6 2052 2404 220218941 220218598 3.370000e-114 422.0
69 TraesCS7B01G319600 chr4B 88.732 355 24 6 2052 2404 158048972 158048632 1.210000e-113 420.0
70 TraesCS7B01G319600 chr4B 76.259 139 18 9 1885 2010 158049159 158049023 3.040000e-05 60.2
71 TraesCS7B01G319600 chr6A 88.483 356 26 6 2052 2404 455872682 455872339 1.570000e-112 416.0
72 TraesCS7B01G319600 chr2A 89.349 169 14 4 592 758 701783095 701782929 2.850000e-50 209.0


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 TraesCS7B01G319600 chr7B 569479673 569482499 2826 True 5221.000000 5221 100.000000 1 2827 1 chr7B.!!$R1 2826
1 TraesCS7B01G319600 chr7B 591054968 591057006 2038 True 2532.000000 2532 89.363000 793 2827 1 chr7B.!!$R2 2034
2 TraesCS7B01G319600 chr7B 591565943 591567292 1349 False 1304.000000 1304 84.621000 681 2032 1 chr7B.!!$F1 1351
3 TraesCS7B01G319600 chr7B 569436814 569440739 3925 True 1043.000000 2056 91.581000 1 2822 3 chr7B.!!$R4 2821
4 TraesCS7B01G319600 chr7B 633001104 633002100 996 False 987.000000 987 85.222000 843 1814 1 chr7B.!!$F3 971
5 TraesCS7B01G319600 chr7B 591683801 591685444 1643 False 798.500000 1149 85.421500 1 1955 2 chr7B.!!$F4 1954
6 TraesCS7B01G319600 chr7A 632265569 632267006 1437 False 1254.000000 1254 83.299000 636 2032 1 chr7A.!!$F2 1396
7 TraesCS7B01G319600 chr7A 630670769 630673595 2826 False 795.333333 1613 85.482667 1 2827 3 chr7A.!!$F6 2826
8 TraesCS7B01G319600 chr7A 631871904 631872502 598 True 785.000000 785 90.328000 845 1449 1 chr7A.!!$R1 604
9 TraesCS7B01G319600 chr7A 632187167 632188974 1807 False 753.000000 1027 82.611500 5 1724 2 chr7A.!!$F7 1719
10 TraesCS7B01G319600 chr7A 617549764 617552176 2412 True 651.500000 1186 88.513500 592 2453 2 chr7A.!!$R2 1861
11 TraesCS7B01G319600 chr7A 631651255 631653316 2061 True 640.000000 1173 85.138667 9 2032 3 chr7A.!!$R3 2023
12 TraesCS7B01G319600 chr7A 631848646 631849533 887 True 458.500000 460 88.349000 1584 2389 2 chr7A.!!$R4 805
13 TraesCS7B01G319600 chr7A 625674356 625675156 800 False 399.500000 564 88.991000 15 757 2 chr7A.!!$F5 742
14 TraesCS7B01G319600 chr7A 625641577 625642373 796 False 396.000000 575 88.139500 9 756 2 chr7A.!!$F4 747
15 TraesCS7B01G319600 chr4A 141907788 141909601 1813 True 1596.000000 1596 83.253000 49 1847 1 chr4A.!!$R1 1798
16 TraesCS7B01G319600 chr7D 548560698 548561752 1054 False 1112.000000 1112 86.580000 783 1796 1 chr7D.!!$F2 1013
17 TraesCS7B01G319600 chr7D 530428987 530431623 2636 True 874.000000 1589 90.977667 1 2827 3 chr7D.!!$R5 2826
18 TraesCS7B01G319600 chr7D 530358217 530361750 3533 True 795.500000 1459 91.243000 716 2454 2 chr7D.!!$R4 1738
19 TraesCS7B01G319600 chr7D 548065110 548067529 2419 True 659.333333 926 84.850000 19 2537 3 chr7D.!!$R6 2518
20 TraesCS7B01G319600 chr7D 548324164 548326671 2507 False 568.333333 1186 87.666333 1 2539 3 chr7D.!!$F6 2538
21 TraesCS7B01G319600 chr7D 573969167 573970823 1656 False 534.400000 1003 83.737000 842 2450 2 chr7D.!!$F7 1608
22 TraesCS7B01G319600 chr7D 548550345 548550898 553 False 523.000000 523 84.220000 6 552 1 chr7D.!!$F1 546
23 TraesCS7B01G319600 chr7D 543730810 543731612 802 False 387.500000 547 88.296500 9 756 2 chr7D.!!$F5 747
24 TraesCS7B01G319600 chrUn 355334233 355335469 1236 True 1216.000000 1216 84.934000 687 1923 1 chrUn.!!$R1 1236
25 TraesCS7B01G319600 chrUn 337589645 337591375 1730 True 810.500000 1173 85.038000 1 2032 2 chrUn.!!$R2 2031
26 TraesCS7B01G319600 chr1D 110904567 110905375 808 False 390.500000 553 88.164500 9 759 2 chr1D.!!$F1 750
27 TraesCS7B01G319600 chr6B 694680372 694681168 796 False 368.500000 531 86.903000 9 756 2 chr6B.!!$F2 747
28 TraesCS7B01G319600 chr1B 169024351 169024903 552 False 525.000000 525 84.314000 9 552 1 chr1B.!!$F1 543
29 TraesCS7B01G319600 chr2B 671009889 671010536 647 True 494.000000 494 81.335000 73 697 1 chr2B.!!$R1 624
30 TraesCS7B01G319600 chr4B 158048632 158049159 527 True 240.100000 420 82.495500 1885 2404 2 chr4B.!!$R1 519

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
71 76 1.250154 GCTGTGGCCAGGCAACAATA 61.250 55.000 22.8 0.0 42.32 1.90 F
582 697 1.675641 GCGGGTGAGGCATTTGAGT 60.676 57.895 0.0 0.0 0.00 3.41 F
1731 2164 1.214673 AGATGATGCAGCCAATCAGGT 59.785 47.619 0.0 0.0 40.61 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1418 1764 1.369692 CGTGGCTGGTGTGACCTTA 59.630 57.895 0.0 0.0 39.58 2.69 R
1595 2001 2.604686 TCCGAGCAGAACCCAGCT 60.605 61.111 0.0 0.0 45.25 4.24 R
2602 6510 1.165907 TGAAAGGCACCACGAGCTTG 61.166 55.000 0.0 0.0 0.00 4.01 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
71 76 1.250154 GCTGTGGCCAGGCAACAATA 61.250 55.000 22.80 0.00 42.32 1.90
122 127 4.717629 CGAGCGACCAAGCGTCCA 62.718 66.667 0.00 0.00 43.00 4.02
123 128 3.112709 GAGCGACCAAGCGTCCAC 61.113 66.667 0.00 0.00 43.00 4.02
126 131 2.805353 CGACCAAGCGTCCACGAG 60.805 66.667 2.58 0.00 43.02 4.18
127 132 3.112709 GACCAAGCGTCCACGAGC 61.113 66.667 2.58 0.00 43.02 5.03
128 133 3.858868 GACCAAGCGTCCACGAGCA 62.859 63.158 2.58 0.00 43.02 4.26
129 134 3.114616 CCAAGCGTCCACGAGCAG 61.115 66.667 2.58 0.00 43.02 4.24
247 291 4.382040 CCCGAGATCGCATATCTTTACCAT 60.382 45.833 0.00 0.00 38.18 3.55
568 683 3.760035 AGTAGCACGGTGAGCGGG 61.760 66.667 13.29 5.14 37.01 6.13
582 697 1.675641 GCGGGTGAGGCATTTGAGT 60.676 57.895 0.00 0.00 0.00 3.41
1731 2164 1.214673 AGATGATGCAGCCAATCAGGT 59.785 47.619 0.00 0.00 40.61 4.00
1960 2490 2.801111 CTCGTAGCTCGTATGCTCTGTA 59.199 50.000 0.00 0.00 42.97 2.74
2061 2698 9.546428 AATTATATAATTCTGCCCTTTTGCAAC 57.454 29.630 13.85 0.00 41.51 4.17
2108 2823 2.045536 GCAGAGGCTGGGGTCTTG 60.046 66.667 0.00 0.00 36.96 3.02
2120 2835 3.030415 GGTCTTGCCCCTTTTCGAA 57.970 52.632 0.00 0.00 0.00 3.71
2123 2839 2.288213 GGTCTTGCCCCTTTTCGAAAAG 60.288 50.000 33.84 33.84 43.82 2.27
2126 2842 3.895041 TCTTGCCCCTTTTCGAAAAGAAT 59.105 39.130 39.33 0.00 46.39 2.40
2130 2846 3.987868 GCCCCTTTTCGAAAAGAATGTTC 59.012 43.478 39.33 22.55 46.39 3.18
2132 2848 5.222631 CCCCTTTTCGAAAAGAATGTTCAG 58.777 41.667 39.33 24.50 46.39 3.02
2277 2998 4.704540 TCTTTTCTGAGGTTTGCAAGTTGA 59.295 37.500 7.16 0.00 0.00 3.18
2594 6502 8.908903 TCAAAGAAAAGGCTATGTTACAAAGAA 58.091 29.630 0.00 0.00 0.00 2.52
2602 6510 5.511729 GGCTATGTTACAAAGAACGAAATGC 59.488 40.000 0.00 0.00 31.59 3.56
2609 6517 2.601481 AAGAACGAAATGCAAGCTCG 57.399 45.000 12.31 12.31 38.53 5.03
2666 6574 5.385198 ACAGGTGTACATGATTTCCACTTT 58.615 37.500 0.00 0.00 0.00 2.66
2696 6604 3.117888 ACCCTGATTCGGTTCATATGCTT 60.118 43.478 0.00 0.00 0.00 3.91
2795 6710 4.703897 TCCTTTCTATCGCCAAATGGTAG 58.296 43.478 0.71 0.00 37.57 3.18
2822 6737 8.439286 GCAATAACTGAACTTCAAACTAGAGAG 58.561 37.037 0.00 0.00 0.00 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 69 2.709475 GCCGGCGAGCTATTGTTG 59.291 61.111 12.58 0.00 0.00 3.33
115 120 4.406173 CGTCTGCTCGTGGACGCT 62.406 66.667 2.72 0.00 46.23 5.07
262 306 1.923395 AAGCCCGGGAACATCCTCA 60.923 57.895 29.31 0.00 36.57 3.86
568 683 0.166814 GTCGCACTCAAATGCCTCAC 59.833 55.000 0.00 0.00 42.99 3.51
634 772 1.722677 GAGGACTACGAGCTGACGG 59.277 63.158 0.00 0.00 37.61 4.79
737 919 4.758251 CATGGCCACCGTCTCGCA 62.758 66.667 8.16 0.00 0.00 5.10
1418 1764 1.369692 CGTGGCTGGTGTGACCTTA 59.630 57.895 0.00 0.00 39.58 2.69
1595 2001 2.604686 TCCGAGCAGAACCCAGCT 60.605 61.111 0.00 0.00 45.25 4.24
1770 2203 3.470567 GTGAAGCTGCGTCGTCCG 61.471 66.667 10.83 0.00 40.40 4.79
2061 2698 5.471116 TGAACATGGACATGAGAACTCAAAG 59.529 40.000 18.38 7.22 43.58 2.77
2108 2823 3.660501 ACATTCTTTTCGAAAAGGGGC 57.339 42.857 37.27 0.00 44.22 5.80
2183 2899 7.175104 AGTTTTATATCAAGAACAGCAAGGGA 58.825 34.615 0.00 0.00 0.00 4.20
2277 2998 6.579666 ATGCAATCTGTGTTGAGTACAATT 57.420 33.333 0.00 0.00 38.80 2.32
2471 6379 9.787435 GGGAATCATGTACACCTGTAAATATTA 57.213 33.333 0.00 0.00 31.52 0.98
2602 6510 1.165907 TGAAAGGCACCACGAGCTTG 61.166 55.000 0.00 0.00 0.00 4.01
2609 6517 5.472137 TGTACTTCTAAATGAAAGGCACCAC 59.528 40.000 0.00 0.00 33.79 4.16
2696 6604 1.610673 GACTGGCTCTCCTGGTCCA 60.611 63.158 0.00 0.00 35.80 4.02
2795 6710 7.387948 TCTCTAGTTTGAAGTTCAGTTATTGCC 59.612 37.037 5.56 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.