Multiple sequence alignment - TraesCS2B01G478600

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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 TraesCS2B01G478600 chr2B 100.000 3691 0 0 1 3691 675968200 675964510 0 6817
1 TraesCS2B01G478600 chr2B 92.608 3720 231 21 1 3691 260628256 260631960 0 5306
2 TraesCS2B01G478600 chr2B 90.254 2760 229 22 6 2739 249627562 249630307 0 3570
3 TraesCS2B01G478600 chr2B 92.408 2384 140 13 1 2353 67196764 67194391 0 3362
4 TraesCS2B01G478600 chr2B 90.901 2385 170 16 1 2353 687305090 687302721 0 3158
5 TraesCS2B01G478600 chr2B 91.730 1983 136 19 1710 3691 504863211 504865166 0 2728
6 TraesCS2B01G478600 chr6B 90.929 3737 252 49 1 3691 169045528 169049223 0 4942
7 TraesCS2B01G478600 chr6B 91.334 2631 180 27 1 2602 677467986 677470597 0 3552
8 TraesCS2B01G478600 chr6B 91.643 1783 117 24 1913 3691 593274840 593273086 0 2438
9 TraesCS2B01G478600 chr7B 90.342 3717 311 36 1 3691 54291686 54287992 0 4831
10 TraesCS2B01G478600 chr7B 91.044 3506 264 32 211 3691 331002081 330998601 0 4689
11 TraesCS2B01G478600 chr7B 91.522 2595 156 30 1 2542 655035987 655033404 0 3515
12 TraesCS2B01G478600 chr7B 92.653 2382 136 11 1 2353 16171985 16169614 0 3393
13 TraesCS2B01G478600 chr1B 89.510 3718 324 37 1 3691 117925548 117929226 0 4645
14 TraesCS2B01G478600 chr1B 92.614 2383 133 19 1 2353 547571325 547568956 0 3386
15 TraesCS2B01G478600 chr3B 88.606 3730 340 56 1 3691 543862331 543858648 0 4455
16 TraesCS2B01G478600 chr3B 89.522 2806 242 32 1 2778 725450344 725447563 0 3506
17 TraesCS2B01G478600 chr3B 92.401 2382 139 12 1 2353 46768146 46770514 0 3358
18 TraesCS2B01G478600 chr5B 92.065 2382 148 15 1 2351 541106378 541108749 0 3314
19 TraesCS2B01G478600 chr4B 93.700 1857 108 9 1838 3691 409315886 409317736 0 2772


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 TraesCS2B01G478600 chr2B 675964510 675968200 3690 True 6817 6817 100.000 1 3691 1 chr2B.!!$R2 3690
1 TraesCS2B01G478600 chr2B 260628256 260631960 3704 False 5306 5306 92.608 1 3691 1 chr2B.!!$F2 3690
2 TraesCS2B01G478600 chr2B 249627562 249630307 2745 False 3570 3570 90.254 6 2739 1 chr2B.!!$F1 2733
3 TraesCS2B01G478600 chr2B 67194391 67196764 2373 True 3362 3362 92.408 1 2353 1 chr2B.!!$R1 2352
4 TraesCS2B01G478600 chr2B 687302721 687305090 2369 True 3158 3158 90.901 1 2353 1 chr2B.!!$R3 2352
5 TraesCS2B01G478600 chr2B 504863211 504865166 1955 False 2728 2728 91.730 1710 3691 1 chr2B.!!$F3 1981
6 TraesCS2B01G478600 chr6B 169045528 169049223 3695 False 4942 4942 90.929 1 3691 1 chr6B.!!$F1 3690
7 TraesCS2B01G478600 chr6B 677467986 677470597 2611 False 3552 3552 91.334 1 2602 1 chr6B.!!$F2 2601
8 TraesCS2B01G478600 chr6B 593273086 593274840 1754 True 2438 2438 91.643 1913 3691 1 chr6B.!!$R1 1778
9 TraesCS2B01G478600 chr7B 54287992 54291686 3694 True 4831 4831 90.342 1 3691 1 chr7B.!!$R2 3690
10 TraesCS2B01G478600 chr7B 330998601 331002081 3480 True 4689 4689 91.044 211 3691 1 chr7B.!!$R3 3480
11 TraesCS2B01G478600 chr7B 655033404 655035987 2583 True 3515 3515 91.522 1 2542 1 chr7B.!!$R4 2541
12 TraesCS2B01G478600 chr7B 16169614 16171985 2371 True 3393 3393 92.653 1 2353 1 chr7B.!!$R1 2352
13 TraesCS2B01G478600 chr1B 117925548 117929226 3678 False 4645 4645 89.510 1 3691 1 chr1B.!!$F1 3690
14 TraesCS2B01G478600 chr1B 547568956 547571325 2369 True 3386 3386 92.614 1 2353 1 chr1B.!!$R1 2352
15 TraesCS2B01G478600 chr3B 543858648 543862331 3683 True 4455 4455 88.606 1 3691 1 chr3B.!!$R1 3690
16 TraesCS2B01G478600 chr3B 725447563 725450344 2781 True 3506 3506 89.522 1 2778 1 chr3B.!!$R2 2777
17 TraesCS2B01G478600 chr3B 46768146 46770514 2368 False 3358 3358 92.401 1 2353 1 chr3B.!!$F1 2352
18 TraesCS2B01G478600 chr5B 541106378 541108749 2371 False 3314 3314 92.065 1 2351 1 chr5B.!!$F1 2350
19 TraesCS2B01G478600 chr4B 409315886 409317736 1850 False 2772 2772 93.700 1838 3691 1 chr4B.!!$F1 1853


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
574 615 0.037975 GCATGGCAACTCTTTGGTGG 60.038 55.0 0.0 0.0 33.01 4.61 F
1026 1127 0.545171 ATGCTACTGTGAGCCATGCT 59.455 50.0 0.0 0.0 42.11 3.79 F
1744 1849 0.394762 GCATGAGAGGCACCCAATGA 60.395 55.0 0.0 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1522 1626 0.112995 ATTGGGAGCTTGGAAGTGCA 59.887 50.0 0.00 0.0 0.0 4.57 R
1854 1959 0.478072 TGACCTCAACCATTGGCTGT 59.522 50.0 1.54 0.0 0.0 4.40 R
3512 3673 0.392998 CTCCTGGAACATGGGGAACG 60.393 60.0 0.00 0.0 38.2 3.95 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
29 32 2.545106 GACAATTGCCACCTTTTTGCAG 59.455 45.455 5.05 0.00 36.21 4.41
338 366 3.657610 TCTATCATCAGTCCCACATGGT 58.342 45.455 0.00 0.00 34.77 3.55
367 399 5.449725 GCTGCTTTAAAATGATCTCACTCCC 60.450 44.000 0.00 0.00 0.00 4.30
441 480 3.113322 GGCCAAACGACAACTCTTTTTC 58.887 45.455 0.00 0.00 0.00 2.29
506 546 6.567891 GCTCACCACATACCTAGTTTTCAAAC 60.568 42.308 0.00 0.00 39.17 2.93
518 558 3.560068 AGTTTTCAAACTGCACTACTCGG 59.440 43.478 4.08 0.00 46.80 4.63
571 612 1.133790 GCTAGCATGGCAACTCTTTGG 59.866 52.381 10.63 0.00 44.73 3.28
572 613 2.440409 CTAGCATGGCAACTCTTTGGT 58.560 47.619 0.00 0.00 32.81 3.67
574 615 0.037975 GCATGGCAACTCTTTGGTGG 60.038 55.000 0.00 0.00 33.01 4.61
575 616 1.619654 CATGGCAACTCTTTGGTGGA 58.380 50.000 0.00 0.00 33.01 4.02
576 617 2.173519 CATGGCAACTCTTTGGTGGAT 58.826 47.619 0.00 0.00 33.01 3.41
785 885 2.224209 ACCCACTCGAACGTCTTCATTT 60.224 45.455 0.00 0.00 0.00 2.32
855 955 2.916527 AAACTGCTGCTGCACCACCT 62.917 55.000 14.93 0.00 45.31 4.00
886 986 0.607489 AAACTCTGATGCAAGCGGCT 60.607 50.000 0.00 0.00 45.15 5.52
899 999 2.579201 CGGCTGACCATCTCCGTT 59.421 61.111 0.00 0.00 37.33 4.44
1026 1127 0.545171 ATGCTACTGTGAGCCATGCT 59.455 50.000 0.00 0.00 42.11 3.79
1060 1162 1.498264 CATTGAATTGGATGCCCCCA 58.502 50.000 0.00 0.00 0.00 4.96
1285 1387 1.380785 CCTAGGTGTCGTAGCCCCA 60.381 63.158 0.00 0.00 0.00 4.96
1369 1473 1.746322 TTACGTCCCTGCGTCCACAA 61.746 55.000 0.00 0.00 44.55 3.33
1441 1545 2.872557 CAACTGATGCAGGTGCCG 59.127 61.111 0.00 0.00 42.40 5.69
1522 1626 4.264352 TGGAAATCCCCAGCTTAAATCTGT 60.264 41.667 0.00 0.00 34.29 3.41
1562 1666 1.209504 CAACATCGGTGTCCCCTACAT 59.790 52.381 0.00 0.00 41.10 2.29
1592 1696 8.517878 CAACAAGAGGATTGTCAACAAATCTAT 58.482 33.333 0.00 0.00 39.55 1.98
1595 1699 8.733458 CAAGAGGATTGTCAACAAATCTATGAA 58.267 33.333 0.00 0.00 39.55 2.57
1612 1716 4.664677 ACGTCACCGCTGACAGCC 62.665 66.667 21.55 6.23 46.47 4.85
1672 1776 5.007626 GCGGCTGATTCAGATATGTTTGTTA 59.992 40.000 17.87 0.00 32.44 2.41
1695 1799 4.038271 TCTTTCACCATTGGATTCTGCT 57.962 40.909 10.37 0.00 0.00 4.24
1696 1800 4.410099 TCTTTCACCATTGGATTCTGCTT 58.590 39.130 10.37 0.00 0.00 3.91
1744 1849 0.394762 GCATGAGAGGCACCCAATGA 60.395 55.000 0.00 0.00 0.00 2.57
1823 1928 1.075374 TCCTATGCCAGTTGCCTTTGT 59.925 47.619 0.00 0.00 40.16 2.83
1871 1976 1.181098 GCACAGCCAATGGTTGAGGT 61.181 55.000 22.86 0.00 37.36 3.85
2079 2207 3.252215 TCTCACCTACATTTTTGTTGCCG 59.748 43.478 0.00 0.00 0.00 5.69
2290 2425 2.034432 CACAACATGGCAACTGCAGTTA 59.966 45.455 30.67 16.98 44.36 2.24
2295 2430 3.384467 ACATGGCAACTGCAGTTACTTTT 59.616 39.130 30.67 14.85 44.36 2.27
2330 2465 1.200020 GTGCAATACACCTGGCAACTC 59.800 52.381 0.00 0.00 44.02 3.01
2435 2571 8.929487 TGTTTTGTTTTTCCAGGTATCCTAAAT 58.071 29.630 0.00 0.00 29.64 1.40
2442 2578 8.519799 TTTTCCAGGTATCCTAAATCACATTC 57.480 34.615 0.00 0.00 29.64 2.67
2466 2602 3.177884 TTGCAGCCACCCCTGAGT 61.178 61.111 0.00 0.00 34.77 3.41
2467 2603 2.703675 CTTGCAGCCACCCCTGAGTT 62.704 60.000 0.00 0.00 34.77 3.01
2568 2704 3.193267 GCAATCAAGTTCCAACATGCCTA 59.807 43.478 0.00 0.00 0.00 3.93
2664 2800 2.110967 CCCGCGGAAGACTACGAGA 61.111 63.158 30.73 0.00 31.48 4.04
2687 2823 0.555769 AGGTCAAGGCCACAAAGGAA 59.444 50.000 5.01 0.00 41.22 3.36
2688 2824 1.147817 AGGTCAAGGCCACAAAGGAAT 59.852 47.619 5.01 0.00 41.22 3.01
2854 2995 7.526142 ACTTTCTAGATATGATCCGCTTACA 57.474 36.000 0.00 0.00 0.00 2.41
3115 3259 3.758023 CAGTGTGACCTGCAAAATATGGA 59.242 43.478 0.00 0.00 0.00 3.41
3208 3352 7.180229 TGAAGAAATATGTGAGTACTCCTTCCA 59.820 37.037 20.11 11.43 0.00 3.53
3222 3367 4.162131 ACTCCTTCCATGTTTGCACTTTTT 59.838 37.500 0.00 0.00 0.00 1.94
3331 3485 1.626686 TTTGATTTGCATCCCCGTGT 58.373 45.000 0.00 0.00 0.00 4.49
3402 3560 5.169836 ACATGGACGACAACTTTCTTTTC 57.830 39.130 0.00 0.00 0.00 2.29
3404 3562 5.124776 ACATGGACGACAACTTTCTTTTCAA 59.875 36.000 0.00 0.00 0.00 2.69
3406 3564 6.202516 TGGACGACAACTTTCTTTTCAATT 57.797 33.333 0.00 0.00 0.00 2.32
3407 3565 7.323049 TGGACGACAACTTTCTTTTCAATTA 57.677 32.000 0.00 0.00 0.00 1.40
3408 3566 7.190871 TGGACGACAACTTTCTTTTCAATTAC 58.809 34.615 0.00 0.00 0.00 1.89
3489 3648 4.934001 TCATGTGAACTCTGCTTCTCATTC 59.066 41.667 0.00 0.00 33.91 2.67
3512 3673 3.193479 CCTTCATTTTACTTGCAGGTCCC 59.807 47.826 4.04 0.00 0.00 4.46
3598 3759 4.321601 CGATCTGTCTTGACCTGAAGAACT 60.322 45.833 0.00 0.00 33.73 3.01
3630 3791 2.351641 GGTGCTTGATTCAATGCGTTCA 60.352 45.455 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 32 3.179830 CTCACTACACGTGTAAGATGGC 58.820 50.000 27.16 0.00 44.16 4.40
65 68 3.306166 CCTGTTTATTCGTAACTGCTCGG 59.694 47.826 0.00 0.00 0.00 4.63
338 366 7.391554 AGTGAGATCATTTTAAAGCAGCAGTTA 59.608 33.333 0.00 0.00 0.00 2.24
367 399 5.630680 CAGTAGTTGCCATGCAGTTAAAAAG 59.369 40.000 0.00 0.00 40.61 2.27
441 480 0.529378 GGAAGTTGCCATGCAGGAAG 59.471 55.000 0.00 0.00 40.61 3.46
506 546 0.453793 CTGGTCTCCGAGTAGTGCAG 59.546 60.000 0.00 0.00 0.00 4.41
569 610 1.054231 TTGCCATGCAAAATCCACCA 58.946 45.000 0.00 0.00 45.96 4.17
617 681 2.200373 AGTTGCCATGTAGGTGGAAC 57.800 50.000 0.00 0.00 42.02 3.62
670 740 6.463995 TTATTGGCCATGGTAGAAAATGTC 57.536 37.500 14.67 0.00 0.00 3.06
747 823 2.856231 TGGGTCCCTAATGGTATGCTTT 59.144 45.455 10.00 0.00 34.77 3.51
785 885 3.006112 TGCCACCTGTTGACAACTTTA 57.994 42.857 18.73 0.00 0.00 1.85
855 955 4.511454 GCATCAGAGTTTGTGTGAACAGTA 59.489 41.667 0.00 0.00 30.90 2.74
886 986 1.234821 GCAACAAACGGAGATGGTCA 58.765 50.000 0.00 0.00 0.00 4.02
1026 1127 1.284491 TCAATGCTTGCTGATGGGGTA 59.716 47.619 0.00 0.00 0.00 3.69
1048 1149 1.734420 TTGGTCTTGGGGGCATCCAA 61.734 55.000 10.42 10.42 43.82 3.53
1060 1162 3.394606 TCTTCCTTGCTTAGGTTGGTCTT 59.605 43.478 5.52 0.00 45.03 3.01
1285 1387 1.597742 ACGTCTGTTGATTGCTTGCT 58.402 45.000 0.00 0.00 0.00 3.91
1324 1428 2.694628 ACTCATCTCTGCTGCTCCTAAG 59.305 50.000 0.00 0.00 0.00 2.18
1325 1429 2.692557 GACTCATCTCTGCTGCTCCTAA 59.307 50.000 0.00 0.00 0.00 2.69
1369 1473 0.402504 TTGGTAGTTGGCGGGAACAT 59.597 50.000 0.00 0.00 0.00 2.71
1441 1545 4.148825 ATCACTCGTGCCCGGCTC 62.149 66.667 11.61 6.14 33.95 4.70
1522 1626 0.112995 ATTGGGAGCTTGGAAGTGCA 59.887 50.000 0.00 0.00 0.00 4.57
1562 1666 2.061848 TGACAATCCTCTTGTTGGGGA 58.938 47.619 0.00 0.00 31.96 4.81
1612 1716 4.929707 GTTCATAGGGCGGGGCGG 62.930 72.222 0.00 0.00 0.00 6.13
1672 1776 5.021458 AGCAGAATCCAATGGTGAAAGATT 58.979 37.500 0.00 0.00 0.00 2.40
1695 1799 0.303493 GACTGCGAACAACTTGCGAA 59.697 50.000 0.00 0.00 0.00 4.70
1696 1800 1.495584 GGACTGCGAACAACTTGCGA 61.496 55.000 0.00 0.00 0.00 5.10
1744 1849 3.637273 GCTCGGTGGGGTGAAGGT 61.637 66.667 0.00 0.00 0.00 3.50
1823 1928 0.904394 GGGCATGCCTCCCAGAAAAA 60.904 55.000 34.70 0.00 43.37 1.94
1854 1959 0.478072 TGACCTCAACCATTGGCTGT 59.522 50.000 1.54 0.00 0.00 4.40
1871 1976 1.270305 CGAACTTGACAGCCTTCCTGA 60.270 52.381 0.00 0.00 44.64 3.86
1937 2046 5.420739 TCATACTGCACAGGTGTATACAAGA 59.579 40.000 7.25 0.00 0.00 3.02
2079 2207 2.095415 GCCCGAATGGAAACTACAACAC 60.095 50.000 0.00 0.00 37.49 3.32
2204 2336 2.364970 TGGAAACAGAAAATGCAGGTGG 59.635 45.455 0.00 0.00 35.01 4.61
2290 2425 7.403312 TGCACTATAATTGCCATGTAAAAGT 57.597 32.000 4.03 0.00 39.39 2.66
2295 2430 7.040755 GGTGTATTGCACTATAATTGCCATGTA 60.041 37.037 4.86 0.00 46.86 2.29
2435 2571 2.362736 GCTGCAAGGATCAGAATGTGA 58.637 47.619 0.00 0.00 40.38 3.58
2442 2578 1.751927 GGGTGGCTGCAAGGATCAG 60.752 63.158 0.50 0.00 34.79 2.90
2466 2602 4.893608 TCATCAAGAGACGGTGAAATCAA 58.106 39.130 0.00 0.00 0.00 2.57
2467 2603 4.535526 TCATCAAGAGACGGTGAAATCA 57.464 40.909 0.00 0.00 0.00 2.57
2664 2800 1.990160 TTTGTGGCCTTGACCTCGGT 61.990 55.000 3.32 0.00 0.00 4.69
2687 2823 6.876789 TGACAATGTCGTACAATTGGTTCTAT 59.123 34.615 10.83 0.00 34.95 1.98
2688 2824 6.224584 TGACAATGTCGTACAATTGGTTCTA 58.775 36.000 10.83 0.00 34.95 2.10
3006 3150 4.549599 GCAACTACATTCGTCGACATTTTG 59.450 41.667 17.16 9.51 0.00 2.44
3132 3276 5.714806 AGCAAAATTCTTCCTCGGGATTTTA 59.285 36.000 0.00 0.00 0.00 1.52
3331 3485 6.952773 ACTTTGAAGTTGCCACATAGTTTA 57.047 33.333 0.00 0.00 35.21 2.01
3406 3564 8.632679 CGTAGAATGTTTAGTTATAGTGGGGTA 58.367 37.037 0.00 0.00 0.00 3.69
3407 3565 7.124750 ACGTAGAATGTTTAGTTATAGTGGGGT 59.875 37.037 0.00 0.00 0.00 4.95
3408 3566 7.437267 CACGTAGAATGTTTAGTTATAGTGGGG 59.563 40.741 0.00 0.00 0.00 4.96
3451 3610 4.971939 TCACATGAAGAACAACAGATGGA 58.028 39.130 0.00 0.00 0.00 3.41
3489 3648 3.193479 GGACCTGCAAGTAAAATGAAGGG 59.807 47.826 5.57 0.00 46.50 3.95
3512 3673 0.392998 CTCCTGGAACATGGGGAACG 60.393 60.000 0.00 0.00 38.20 3.95
3598 3759 5.129634 TGAATCAAGCACCTCAAAGTGTTA 58.870 37.500 0.00 0.00 40.04 2.41



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

AutoCloner maintained by Alex Coulton.