Multiple sequence alignment - TraesCS7B01G135500

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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 TraesCS7B01G135500 chr7B 100.000 3986 0 0 1 3986 165533291 165529306 0.000000e+00 7361
1 TraesCS7B01G135500 chr7D 95.712 3661 91 27 40 3646 202059488 202055840 0.000000e+00 5830
2 TraesCS7B01G135500 chr7D 92.537 335 15 6 3662 3986 202055856 202055522 4.660000e-129 472
3 TraesCS7B01G135500 chr7D 94.686 207 8 1 3783 3986 201979084 201978878 6.430000e-83 318
4 TraesCS7B01G135500 chr7A 96.711 3497 79 10 21 3486 214436511 214433020 0.000000e+00 5788
5 TraesCS7B01G135500 chr7A 94.833 329 13 2 3662 3986 214432929 214432601 9.880000e-141 510
6 TraesCS7B01G135500 chr7A 92.568 148 8 2 3501 3646 214433059 214432913 4.040000e-50 209
7 TraesCS7B01G135500 chr6D 76.086 1865 385 50 1138 2979 375028608 375030434 0.000000e+00 917
8 TraesCS7B01G135500 chr6B 75.417 1920 413 46 1082 2979 561701016 561702898 0.000000e+00 876


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 TraesCS7B01G135500 chr7B 165529306 165533291 3985 True 7361 7361 100.0000 1 3986 1 chr7B.!!$R1 3985
1 TraesCS7B01G135500 chr7D 202055522 202059488 3966 True 3151 5830 94.1245 40 3986 2 chr7D.!!$R2 3946
2 TraesCS7B01G135500 chr7A 214432601 214436511 3910 True 2169 5788 94.7040 21 3986 3 chr7A.!!$R1 3965
3 TraesCS7B01G135500 chr6D 375028608 375030434 1826 False 917 917 76.0860 1138 2979 1 chr6D.!!$F1 1841
4 TraesCS7B01G135500 chr6B 561701016 561702898 1882 False 876 876 75.4170 1082 2979 1 chr6B.!!$F1 1897


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
298 305 0.173481 CCTTCTCGACGCTTCCATCA 59.827 55.000 0.0 0.0 0.00 3.07 F
1031 1063 1.595489 GCTGCACAGTTCTTGTTGTCG 60.595 52.381 0.0 0.0 38.16 4.35 F
2073 2105 2.092968 TGTGTTCAGAGAGCCAACTTGT 60.093 45.455 0.0 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2073 2105 5.245584 TCATGATGCATAATAGCTTGGGA 57.754 39.130 0.0 0.0 34.99 4.37 R
2499 2531 0.165944 GAATCTGGTTGGTGCGAACG 59.834 55.000 0.0 0.0 0.00 3.95 R
3759 3874 2.029844 GGTCACCAGAGCAGCGTTC 61.030 63.158 0.0 0.0 41.81 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
87 91 5.222130 GGCAGGAAATGGAAATCCTATCCTA 60.222 44.000 15.92 0.00 44.26 2.94
147 151 1.136828 CCCAAATATCTCGACCCCCA 58.863 55.000 0.00 0.00 0.00 4.96
298 305 0.173481 CCTTCTCGACGCTTCCATCA 59.827 55.000 0.00 0.00 0.00 3.07
378 385 1.930520 CCCGGATTTCATTCCCCCT 59.069 57.895 0.73 0.00 31.61 4.79
414 421 2.091555 AGATCTCCGAGTTCCTTAGGCT 60.092 50.000 0.00 0.00 0.00 4.58
422 429 4.177783 CGAGTTCCTTAGGCTCTTTTCTC 58.822 47.826 0.00 0.00 0.00 2.87
495 502 2.862536 CCTGCTCTGTAATCGATGTGTG 59.137 50.000 0.00 0.00 0.00 3.82
553 560 4.375706 CGATTTTAGGCGCGTAGGAAATAC 60.376 45.833 15.84 10.64 0.00 1.89
664 672 1.609072 GCCCTCTGTTTGTTGGAGAAC 59.391 52.381 0.00 0.00 0.00 3.01
740 753 9.339492 CGTTAGTTACTTCTTAAGGTAGTCAAG 57.661 37.037 12.53 6.22 0.00 3.02
775 788 6.585416 TCGGAGGGGAATTAATGTTTACTAC 58.415 40.000 0.00 0.00 0.00 2.73
873 904 4.526970 ACACCTTTCAGATGTTGTTGTCT 58.473 39.130 0.00 0.00 0.00 3.41
922 954 6.882610 ATGATGGATGTAATTTATGCGTGT 57.117 33.333 0.00 0.00 0.00 4.49
1024 1056 2.980233 GGGCGCTGCACAGTTCTT 60.980 61.111 7.64 0.00 0.00 2.52
1031 1063 1.595489 GCTGCACAGTTCTTGTTGTCG 60.595 52.381 0.00 0.00 38.16 4.35
2073 2105 2.092968 TGTGTTCAGAGAGCCAACTTGT 60.093 45.455 0.00 0.00 0.00 3.16
2337 2369 4.447138 TTTCCCTGGTGTCATGTTTACT 57.553 40.909 0.00 0.00 0.00 2.24
2499 2531 2.498885 AGCAGAGCAAATTGAATTCCCC 59.501 45.455 2.27 0.00 0.00 4.81
2778 2810 2.362077 GTGGAAGGCTTTCTTTGCTTCA 59.638 45.455 7.14 0.00 35.50 3.02
3119 3152 6.611381 TGTTTTTAGTAGATGTTGATGCAGC 58.389 36.000 0.00 0.00 0.00 5.25
3234 3268 5.371526 CAAGTCTGCAACCCATATCTACAT 58.628 41.667 0.00 0.00 0.00 2.29
3254 3288 6.630203 ACATAGTGTTAAGGGGTAATGACA 57.370 37.500 0.00 0.00 0.00 3.58
3413 3447 3.617284 AGTGTCGTTTTTCCTTCCAACT 58.383 40.909 0.00 0.00 0.00 3.16
3414 3448 3.377172 AGTGTCGTTTTTCCTTCCAACTG 59.623 43.478 0.00 0.00 0.00 3.16
3491 3605 4.787598 CAGAATGTCACTTTGTTAGCCAC 58.212 43.478 0.00 0.00 0.00 5.01
3492 3606 4.516698 CAGAATGTCACTTTGTTAGCCACT 59.483 41.667 0.00 0.00 0.00 4.00
3493 3607 5.009010 CAGAATGTCACTTTGTTAGCCACTT 59.991 40.000 0.00 0.00 0.00 3.16
3494 3608 5.239525 AGAATGTCACTTTGTTAGCCACTTC 59.760 40.000 0.00 0.00 0.00 3.01
3495 3609 4.150897 TGTCACTTTGTTAGCCACTTCT 57.849 40.909 0.00 0.00 0.00 2.85
3496 3610 5.284861 TGTCACTTTGTTAGCCACTTCTA 57.715 39.130 0.00 0.00 0.00 2.10
3497 3611 5.054477 TGTCACTTTGTTAGCCACTTCTAC 58.946 41.667 0.00 0.00 0.00 2.59
3498 3612 5.054477 GTCACTTTGTTAGCCACTTCTACA 58.946 41.667 0.00 0.00 0.00 2.74
3499 3613 5.526111 GTCACTTTGTTAGCCACTTCTACAA 59.474 40.000 0.00 0.00 0.00 2.41
3500 3614 5.758296 TCACTTTGTTAGCCACTTCTACAAG 59.242 40.000 0.00 0.00 35.50 3.16
3501 3615 5.758296 CACTTTGTTAGCCACTTCTACAAGA 59.242 40.000 0.00 0.00 33.34 3.02
3502 3616 6.260050 CACTTTGTTAGCCACTTCTACAAGAA 59.740 38.462 0.00 0.00 33.34 2.52
3503 3617 6.826741 ACTTTGTTAGCCACTTCTACAAGAAA 59.173 34.615 0.00 0.00 33.19 2.52
3504 3618 7.338449 ACTTTGTTAGCCACTTCTACAAGAAAA 59.662 33.333 0.00 0.00 33.19 2.29
3505 3619 7.817418 TTGTTAGCCACTTCTACAAGAAAAT 57.183 32.000 0.00 0.00 33.19 1.82
3506 3620 7.817418 TGTTAGCCACTTCTACAAGAAAATT 57.183 32.000 0.00 0.00 33.19 1.82
3507 3621 8.232913 TGTTAGCCACTTCTACAAGAAAATTT 57.767 30.769 0.00 0.00 33.19 1.82
3508 3622 8.349983 TGTTAGCCACTTCTACAAGAAAATTTC 58.650 33.333 0.00 0.00 33.19 2.17
3509 3623 8.568794 GTTAGCCACTTCTACAAGAAAATTTCT 58.431 33.333 1.80 1.80 43.15 2.52
3539 3653 9.337396 TGTTTCTTCTACATAATGTCACTTTGT 57.663 29.630 0.00 0.00 0.00 2.83
3597 3711 0.250295 CACTTCAGCGGTCCAGGAAA 60.250 55.000 0.00 0.00 0.00 3.13
3626 3740 1.073763 TGGCATGCTAGTGGTTCTGTT 59.926 47.619 18.92 0.00 0.00 3.16
3630 3744 1.882912 TGCTAGTGGTTCTGTTGCAG 58.117 50.000 0.00 0.00 0.00 4.41
3631 3745 1.140852 TGCTAGTGGTTCTGTTGCAGT 59.859 47.619 0.00 0.00 32.61 4.40
3632 3746 1.532868 GCTAGTGGTTCTGTTGCAGTG 59.467 52.381 0.00 0.00 32.61 3.66
3633 3747 2.806745 GCTAGTGGTTCTGTTGCAGTGA 60.807 50.000 0.00 0.00 32.61 3.41
3634 3748 1.668419 AGTGGTTCTGTTGCAGTGAC 58.332 50.000 0.00 0.00 32.61 3.67
3635 3749 1.065491 AGTGGTTCTGTTGCAGTGACA 60.065 47.619 0.00 0.00 32.61 3.58
3636 3750 1.949525 GTGGTTCTGTTGCAGTGACAT 59.050 47.619 0.00 0.00 32.61 3.06
3637 3751 1.948834 TGGTTCTGTTGCAGTGACATG 59.051 47.619 0.00 0.00 32.61 3.21
3638 3752 1.335324 GGTTCTGTTGCAGTGACATGC 60.335 52.381 0.00 1.00 46.68 4.06
3649 3763 5.752098 GCAGTGACATGCAAAAGTAATTC 57.248 39.130 0.00 0.00 45.77 2.17
3650 3764 4.321745 GCAGTGACATGCAAAAGTAATTCG 59.678 41.667 0.00 0.00 45.77 3.34
3651 3765 4.321745 CAGTGACATGCAAAAGTAATTCGC 59.678 41.667 0.00 0.00 0.00 4.70
3652 3766 4.023279 AGTGACATGCAAAAGTAATTCGCA 60.023 37.500 0.00 2.93 36.95 5.10
3653 3767 4.679197 GTGACATGCAAAAGTAATTCGCAA 59.321 37.500 4.38 0.00 35.98 4.85
3654 3768 5.174761 GTGACATGCAAAAGTAATTCGCAAA 59.825 36.000 4.38 0.00 35.98 3.68
3655 3769 5.750547 TGACATGCAAAAGTAATTCGCAAAA 59.249 32.000 4.38 0.00 35.98 2.44
3656 3770 6.256539 TGACATGCAAAAGTAATTCGCAAAAA 59.743 30.769 4.38 0.00 35.98 1.94
3704 3818 6.770785 AGAGTTTTTGTAGGCAGTTGAATACA 59.229 34.615 0.00 0.00 0.00 2.29
3759 3874 5.927030 TGCAGAAGCTGTTCTTTTATTACG 58.073 37.500 0.00 0.00 41.40 3.18
3812 3928 4.022589 TGAACAACAGAAGACGTAGGTAGG 60.023 45.833 0.00 0.00 0.00 3.18
3851 3975 0.379669 TCGATCTTAGTTCCGGCGAC 59.620 55.000 9.30 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.065474 CCCTACAAAACACGAACAAGAAAGA 59.935 40.000 0.00 0.0 0.00 2.52
1 2 5.270853 CCCTACAAAACACGAACAAGAAAG 58.729 41.667 0.00 0.0 0.00 2.62
2 3 4.096682 CCCCTACAAAACACGAACAAGAAA 59.903 41.667 0.00 0.0 0.00 2.52
3 4 3.628487 CCCCTACAAAACACGAACAAGAA 59.372 43.478 0.00 0.0 0.00 2.52
4 5 3.118334 TCCCCTACAAAACACGAACAAGA 60.118 43.478 0.00 0.0 0.00 3.02
5 6 3.207778 TCCCCTACAAAACACGAACAAG 58.792 45.455 0.00 0.0 0.00 3.16
6 7 3.207778 CTCCCCTACAAAACACGAACAA 58.792 45.455 0.00 0.0 0.00 2.83
7 8 2.171027 ACTCCCCTACAAAACACGAACA 59.829 45.455 0.00 0.0 0.00 3.18
8 9 2.842457 ACTCCCCTACAAAACACGAAC 58.158 47.619 0.00 0.0 0.00 3.95
9 10 3.564053 AACTCCCCTACAAAACACGAA 57.436 42.857 0.00 0.0 0.00 3.85
10 11 3.564053 AAACTCCCCTACAAAACACGA 57.436 42.857 0.00 0.0 0.00 4.35
11 12 4.337274 AGAAAAACTCCCCTACAAAACACG 59.663 41.667 0.00 0.0 0.00 4.49
12 13 5.847111 AGAAAAACTCCCCTACAAAACAC 57.153 39.130 0.00 0.0 0.00 3.32
13 14 6.192044 AGAAGAAAAACTCCCCTACAAAACA 58.808 36.000 0.00 0.0 0.00 2.83
14 15 6.710597 AGAAGAAAAACTCCCCTACAAAAC 57.289 37.500 0.00 0.0 0.00 2.43
15 16 6.038936 CGAAGAAGAAAAACTCCCCTACAAAA 59.961 38.462 0.00 0.0 0.00 2.44
16 17 5.529800 CGAAGAAGAAAAACTCCCCTACAAA 59.470 40.000 0.00 0.0 0.00 2.83
17 18 5.061179 CGAAGAAGAAAAACTCCCCTACAA 58.939 41.667 0.00 0.0 0.00 2.41
18 19 4.504340 CCGAAGAAGAAAAACTCCCCTACA 60.504 45.833 0.00 0.0 0.00 2.74
19 20 4.001652 CCGAAGAAGAAAAACTCCCCTAC 58.998 47.826 0.00 0.0 0.00 3.18
64 68 4.734266 AGGATAGGATTTCCATTTCCTGC 58.266 43.478 11.87 0.0 42.38 4.85
87 91 4.982701 GTTGGGCTGGGCTGCTGT 62.983 66.667 0.00 0.0 0.00 4.40
298 305 2.755103 GCGAATTGAAGGAGTGGGAATT 59.245 45.455 0.00 0.0 0.00 2.17
378 385 3.131933 GGAGATCTAGAGCAAGCAACTGA 59.868 47.826 11.20 0.0 0.00 3.41
414 421 2.695666 CCCCGCAGATCTAGAGAAAAGA 59.304 50.000 0.00 0.0 0.00 2.52
422 429 1.933853 CGAAAAACCCCGCAGATCTAG 59.066 52.381 0.00 0.0 0.00 2.43
483 490 5.405269 CACTTCACAGTTCACACATCGATTA 59.595 40.000 0.00 0.0 0.00 1.75
484 491 4.212004 CACTTCACAGTTCACACATCGATT 59.788 41.667 0.00 0.0 0.00 3.34
495 502 4.900635 ACCATGAAACACTTCACAGTTC 57.099 40.909 0.00 0.0 44.28 3.01
553 560 3.581755 TCTAACCAGACGAACAATTCCG 58.418 45.455 0.00 0.0 0.00 4.30
664 672 3.933155 ATAGAAGCGCGATGACAAAAG 57.067 42.857 12.10 0.0 0.00 2.27
740 753 6.954487 AATTCCCCTCCGATTAAACAATAC 57.046 37.500 0.00 0.0 0.00 1.89
775 788 5.512749 CCATCCATTCCCTCACAATCTAGAG 60.513 48.000 0.00 0.0 0.00 2.43
900 932 6.691754 AACACGCATAAATTACATCCATCA 57.308 33.333 0.00 0.0 0.00 3.07
1024 1056 2.224426 ACAATAACAGAGCCCGACAACA 60.224 45.455 0.00 0.0 0.00 3.33
1031 1063 1.474077 CAGCCAACAATAACAGAGCCC 59.526 52.381 0.00 0.0 0.00 5.19
2073 2105 5.245584 TCATGATGCATAATAGCTTGGGA 57.754 39.130 0.00 0.0 34.99 4.37
2337 2369 6.016610 GCACAAAGTTTAAGATGGTAAGGACA 60.017 38.462 0.00 0.0 0.00 4.02
2499 2531 0.165944 GAATCTGGTTGGTGCGAACG 59.834 55.000 0.00 0.0 0.00 3.95
2778 2810 1.216710 GTAGAGCGCAACAGAGCCT 59.783 57.895 11.47 0.0 0.00 4.58
3119 3152 6.036844 GCGGAACTACATTTACTAGGGAAAAG 59.963 42.308 0.00 0.0 0.00 2.27
3234 3268 7.260387 TCATTGTCATTACCCCTTAACACTA 57.740 36.000 0.00 0.0 0.00 2.74
3254 3288 5.220931 GCCACTCGCAGATTAGAATTTCATT 60.221 40.000 0.00 0.0 37.47 2.57
3336 3370 8.527810 AGTTTTGAAATTAGGTCAAGAAACACA 58.472 29.630 7.91 0.0 36.41 3.72
3374 3408 8.658499 ACGACACTATAAAAGAAACAGAAAGT 57.342 30.769 0.00 0.0 0.00 2.66
3391 3425 4.573201 CAGTTGGAAGGAAAAACGACACTA 59.427 41.667 0.00 0.0 0.00 2.74
3513 3627 9.337396 ACAAAGTGACATTATGTAGAAGAAACA 57.663 29.630 0.00 0.0 0.00 2.83
3516 3630 9.778741 AGAACAAAGTGACATTATGTAGAAGAA 57.221 29.630 0.00 0.0 0.00 2.52
3517 3631 9.778741 AAGAACAAAGTGACATTATGTAGAAGA 57.221 29.630 0.00 0.0 0.00 2.87
3519 3633 9.778741 AGAAGAACAAAGTGACATTATGTAGAA 57.221 29.630 0.00 0.0 0.00 2.10
3522 3636 9.990360 TGTAGAAGAACAAAGTGACATTATGTA 57.010 29.630 0.00 0.0 0.00 2.29
3523 3637 8.902540 TGTAGAAGAACAAAGTGACATTATGT 57.097 30.769 0.00 0.0 0.00 2.29
3524 3638 9.817365 CTTGTAGAAGAACAAAGTGACATTATG 57.183 33.333 0.00 0.0 38.81 1.90
3525 3639 9.778741 TCTTGTAGAAGAACAAAGTGACATTAT 57.221 29.630 0.00 0.0 38.81 1.28
3526 3640 9.607988 TTCTTGTAGAAGAACAAAGTGACATTA 57.392 29.630 10.82 0.0 42.23 1.90
3527 3641 8.506168 TTCTTGTAGAAGAACAAAGTGACATT 57.494 30.769 10.82 0.0 42.23 2.71
3540 3654 9.521503 CTGTTCGAATCATATTCTTGTAGAAGA 57.478 33.333 0.00 0.0 37.69 2.87
3630 3744 4.806056 GCGAATTACTTTTGCATGTCAC 57.194 40.909 0.00 0.0 43.26 3.67
3677 3791 3.315191 TCAACTGCCTACAAAAACTCTGC 59.685 43.478 0.00 0.0 0.00 4.26
3759 3874 2.029844 GGTCACCAGAGCAGCGTTC 61.030 63.158 0.00 0.0 41.81 3.95
3812 3928 9.426837 AGATCGATGTACTACTACTATCTGTTC 57.573 37.037 0.54 0.0 0.00 3.18



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

AutoCloner maintained by Alex Coulton.