Multiple sequence alignment - TraesCS4B01G187300

Loading Multiple Alignment...

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 TraesCS4B01G187300 chr4B 100.000 4177 0 0 1 4177 407411588 407407412 0.000000e+00 7714
1 TraesCS4B01G187300 chr4D 94.178 3779 104 31 452 4177 327847820 327844105 0.000000e+00 5653
2 TraesCS4B01G187300 chr4D 87.086 302 24 7 170 467 327848127 327847837 1.120000e-85 327
3 TraesCS4B01G187300 chr4A 94.658 3557 102 23 1 3505 142795043 142798563 0.000000e+00 5435
4 TraesCS4B01G187300 chr4A 90.701 613 29 11 3568 4171 142798999 142799592 0.000000e+00 791
5 TraesCS4B01G187300 chr2A 75.558 806 172 16 1744 2532 46313833 46314630 1.420000e-99 374
6 TraesCS4B01G187300 chr2B 72.134 1317 318 30 1747 3023 68592775 68591468 1.850000e-93 353
7 TraesCS4B01G187300 chr2B 78.157 293 60 4 1276 1566 68593222 68592932 2.560000e-42 183
8 TraesCS4B01G187300 chr2D 72.000 1300 315 30 1747 3005 43899097 43897806 5.170000e-89 339
9 TraesCS4B01G187300 chr2D 77.816 293 61 4 1276 1566 43899544 43899254 1.190000e-40 178
10 TraesCS4B01G187300 chr1D 84.173 139 20 1 1044 1182 268087561 268087697 2.620000e-27 134


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 TraesCS4B01G187300 chr4B 407407412 407411588 4176 True 7714.0 7714 100.0000 1 4177 1 chr4B.!!$R1 4176
1 TraesCS4B01G187300 chr4D 327844105 327848127 4022 True 2990.0 5653 90.6320 170 4177 2 chr4D.!!$R1 4007
2 TraesCS4B01G187300 chr4A 142795043 142799592 4549 False 3113.0 5435 92.6795 1 4171 2 chr4A.!!$F1 4170
3 TraesCS4B01G187300 chr2A 46313833 46314630 797 False 374.0 374 75.5580 1744 2532 1 chr2A.!!$F1 788
4 TraesCS4B01G187300 chr2B 68591468 68593222 1754 True 268.0 353 75.1455 1276 3023 2 chr2B.!!$R1 1747
5 TraesCS4B01G187300 chr2D 43897806 43899544 1738 True 258.5 339 74.9080 1276 3005 2 chr2D.!!$R1 1729

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
703 780 0.168348 CGCACGTCACAGCTACTAGT 59.832 55.000 0.0 0.0 0.0 2.57 F
968 1053 1.075896 GTTCAAACCCACCACCCCA 60.076 57.895 0.0 0.0 0.0 4.96 F
1671 1778 1.492133 CCACCATCCTCACCACCTGT 61.492 60.000 0.0 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1609 1716 0.388134 CAGTTGTAGTCCGGGTCGTG 60.388 60.000 0.00 0.0 0.00 4.35 R
1939 2046 2.874086 CGCCATAGATGCAGTCATTGAA 59.126 45.455 0.00 0.0 31.96 2.69 R
3508 3653 0.468226 ACTGAAACTCCGGTGCAGAA 59.532 50.000 14.14 0.0 34.71 3.02 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
97 99 3.517296 TCAAAATGCACTTAGGGGTGA 57.483 42.857 0.00 0.00 39.34 4.02
113 115 2.352715 GGGTGAACATGCACTTTTAGCC 60.353 50.000 6.43 6.43 38.78 3.93
117 119 1.453155 ACATGCACTTTTAGCCCTCG 58.547 50.000 0.00 0.00 0.00 4.63
118 120 1.271379 ACATGCACTTTTAGCCCTCGT 60.271 47.619 0.00 0.00 0.00 4.18
165 167 2.552591 CCGATCTCGTCTACCCTACCAT 60.553 54.545 0.00 0.00 37.74 3.55
182 184 8.314751 ACCCTACCATAATTTGAGAGAATATCG 58.685 37.037 0.00 0.00 0.00 2.92
251 273 4.496341 GCGTTGGATCAAACCATACATGAG 60.496 45.833 7.41 0.00 39.82 2.90
360 384 1.489574 TACAAACGTGTTGCGACGAT 58.510 45.000 9.42 0.00 44.77 3.73
362 386 0.450482 CAAACGTGTTGCGACGATCC 60.450 55.000 9.42 0.00 44.77 3.36
365 389 2.769617 GTGTTGCGACGATCCGTG 59.230 61.111 0.00 0.00 41.37 4.94
402 426 6.867519 TCATCTGATTTCCTACCTTGTGTA 57.132 37.500 0.00 0.00 0.00 2.90
403 427 6.878317 TCATCTGATTTCCTACCTTGTGTAG 58.122 40.000 0.00 0.00 45.55 2.74
495 554 1.408683 CCGGAAGCATCCTGAAATCCA 60.409 52.381 6.39 0.00 44.17 3.41
502 561 2.659428 CATCCTGAAATCCAGTTCCCC 58.341 52.381 0.00 0.00 41.33 4.81
531 590 2.355481 GTTTCGACCGACCTGCGT 60.355 61.111 0.00 0.00 38.67 5.24
532 591 1.081242 GTTTCGACCGACCTGCGTA 60.081 57.895 0.00 0.00 38.67 4.42
533 592 0.664166 GTTTCGACCGACCTGCGTAA 60.664 55.000 0.00 0.00 38.67 3.18
534 593 0.244450 TTTCGACCGACCTGCGTAAT 59.756 50.000 0.00 0.00 38.67 1.89
608 674 0.991920 ACAGAACCCGACCATCCATT 59.008 50.000 0.00 0.00 0.00 3.16
612 678 1.211567 AACCCGACCATCCATTCCCA 61.212 55.000 0.00 0.00 0.00 4.37
703 780 0.168348 CGCACGTCACAGCTACTAGT 59.832 55.000 0.00 0.00 0.00 2.57
780 858 3.024217 GCTCCTCCCCTCTCCTCT 58.976 66.667 0.00 0.00 0.00 3.69
794 872 1.153127 CCTCTACCTCGTCTCGCCT 60.153 63.158 0.00 0.00 0.00 5.52
795 873 1.161563 CCTCTACCTCGTCTCGCCTC 61.162 65.000 0.00 0.00 0.00 4.70
796 874 1.153208 TCTACCTCGTCTCGCCTCC 60.153 63.158 0.00 0.00 0.00 4.30
871 949 1.617018 CCGTCCATCTCTGCCTTCCA 61.617 60.000 0.00 0.00 0.00 3.53
911 996 2.359967 GGACACGGAGGGAGGAAGG 61.360 68.421 0.00 0.00 0.00 3.46
968 1053 1.075896 GTTCAAACCCACCACCCCA 60.076 57.895 0.00 0.00 0.00 4.96
970 1055 1.875422 TTCAAACCCACCACCCCACA 61.875 55.000 0.00 0.00 0.00 4.17
971 1056 2.131067 CAAACCCACCACCCCACAC 61.131 63.158 0.00 0.00 0.00 3.82
972 1057 3.383031 AAACCCACCACCCCACACC 62.383 63.158 0.00 0.00 0.00 4.16
1671 1778 1.492133 CCACCATCCTCACCACCTGT 61.492 60.000 0.00 0.00 0.00 4.00
1939 2046 4.690153 ACCCATTGGAGGTGGACT 57.310 55.556 3.62 0.00 39.12 3.85
3069 3212 0.251033 TTGTCTTGCTCATGGCTGCT 60.251 50.000 0.00 0.00 42.39 4.24
3110 3253 7.008992 GCTTCAGCAATAATCTTGTTGATGTTC 59.991 37.037 14.46 4.99 43.27 3.18
3147 3290 1.352352 CCTTCAGGTGGTTCCATCAGT 59.648 52.381 4.86 0.00 39.02 3.41
3180 3323 2.971660 AACCTTTTTGTTTCCGGTGG 57.028 45.000 0.00 0.00 0.00 4.61
3186 3329 1.868469 TTTGTTTCCGGTGGTCTACG 58.132 50.000 0.00 0.00 0.00 3.51
3188 3331 1.259609 TGTTTCCGGTGGTCTACGAT 58.740 50.000 0.00 0.00 0.00 3.73
3271 3415 1.120795 AGATGCCAGGGAGCTAGCTC 61.121 60.000 32.65 32.65 42.04 4.09
3472 3616 5.802465 TCATTTCTGATTCTGAAGCTGTCT 58.198 37.500 7.22 0.00 0.00 3.41
3480 3624 2.603021 TCTGAAGCTGTCTTCTGAGGT 58.397 47.619 13.24 0.00 45.92 3.85
3508 3653 6.264292 TGTGCATACAGTGGAACAGTTAATTT 59.736 34.615 0.00 0.00 40.27 1.82
3533 4001 0.239347 ACCGGAGTTTCAGTCGTACG 59.761 55.000 9.46 9.53 0.00 3.67
3644 4166 6.944290 TCTACAATAGTATTAAGGCGCCTAGA 59.056 38.462 33.07 21.97 0.00 2.43
3700 4223 6.106877 TCGTTCCATTCAATTCGAAAGATC 57.893 37.500 0.00 0.00 41.60 2.75
3753 4276 1.628846 GGTCCACTTCAGTACCACCAT 59.371 52.381 0.00 0.00 32.04 3.55
3770 4293 2.093973 ACCATGTTTCAAACCGTTTGCA 60.094 40.909 17.62 11.16 40.43 4.08
3771 4294 2.932614 CCATGTTTCAAACCGTTTGCAA 59.067 40.909 17.62 11.45 40.43 4.08
3772 4295 3.242252 CCATGTTTCAAACCGTTTGCAAC 60.242 43.478 24.12 24.12 43.78 4.17
3773 4296 2.338500 TGTTTCAAACCGTTTGCAACC 58.662 42.857 26.32 14.85 43.17 3.77
3774 4297 2.028930 TGTTTCAAACCGTTTGCAACCT 60.029 40.909 26.32 0.00 43.17 3.50
3775 4298 2.285827 TTCAAACCGTTTGCAACCTG 57.714 45.000 17.62 0.00 40.43 4.00
3776 4299 0.179124 TCAAACCGTTTGCAACCTGC 60.179 50.000 17.62 0.00 45.29 4.85
3785 4308 2.732658 GCAACCTGCAAGCAAGCT 59.267 55.556 0.00 0.00 44.26 3.74
3786 4309 1.068585 GCAACCTGCAAGCAAGCTT 59.931 52.632 0.59 0.59 44.26 3.74
3838 4362 3.330701 AGGCTGAACAGATGGACCTTTTA 59.669 43.478 5.97 0.00 0.00 1.52
3871 4395 1.812686 AAGCCACTCGCGGTAGTTCA 61.813 55.000 6.13 0.00 44.76 3.18
3886 4410 6.055588 CGGTAGTTCATTGGTTGGATTAGAT 58.944 40.000 0.00 0.00 0.00 1.98
3903 4427 6.769822 GGATTAGATGAAACATCACATCCTGT 59.230 38.462 21.69 4.26 42.38 4.00
3904 4428 7.041508 GGATTAGATGAAACATCACATCCTGTC 60.042 40.741 21.69 0.00 42.38 3.51
4018 4545 0.674581 TCCATTTCGCAGCTGACTGG 60.675 55.000 20.43 14.96 44.63 4.00
4028 4555 1.555075 CAGCTGACTGGGCTAAGGTAA 59.445 52.381 8.42 0.00 40.48 2.85
4046 4573 0.874390 AACATAACTGGCACGCACAG 59.126 50.000 6.12 6.12 41.64 3.66
4065 4592 1.751924 AGCCGTTGGTTTGTTTAAGCA 59.248 42.857 0.00 0.00 42.19 3.91
4093 4620 2.062519 GACTTTGCTCGTCTGAGGTTC 58.937 52.381 0.00 0.00 42.79 3.62
4094 4621 1.270358 ACTTTGCTCGTCTGAGGTTCC 60.270 52.381 0.00 0.00 42.79 3.62
4142 4669 2.809696 GTTTTAGGTAGGCAGCGTTCAA 59.190 45.455 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 72 8.474025 CACCCCTAAGTGCATTTTGATAATTAA 58.526 33.333 0.00 0.00 0.00 1.40
87 89 2.496899 AGTGCATGTTCACCCCTAAG 57.503 50.000 0.00 0.00 37.68 2.18
97 99 1.812571 CGAGGGCTAAAAGTGCATGTT 59.187 47.619 0.00 0.00 0.00 2.71
113 115 0.514691 GCAAAACAGCAGAGACGAGG 59.485 55.000 0.00 0.00 0.00 4.63
117 119 0.235926 GTCGGCAAAACAGCAGAGAC 59.764 55.000 0.00 0.00 39.32 3.36
118 120 0.884704 GGTCGGCAAAACAGCAGAGA 60.885 55.000 0.00 0.00 39.32 3.10
165 167 6.174720 AGCACCCGATATTCTCTCAAATTA 57.825 37.500 0.00 0.00 0.00 1.40
198 200 1.001293 TCTCGTATCATGGAGCATGGC 59.999 52.381 0.00 0.00 41.66 4.40
199 201 2.956913 CTCTCGTATCATGGAGCATGG 58.043 52.381 0.00 0.00 41.66 3.66
251 273 2.626780 GCTTCCGGGTTCAAGTGCC 61.627 63.158 0.00 0.00 0.00 5.01
365 389 5.980698 ATCAGATGATTGATCGTGAACAC 57.019 39.130 0.00 0.00 36.04 3.32
414 438 8.388656 ACTGGAAAATAGGTAGGAAATCAGTA 57.611 34.615 0.00 0.00 0.00 2.74
495 554 1.333636 CCAGAGCTGATCGGGGAACT 61.334 60.000 4.07 0.00 39.43 3.01
502 561 1.272781 GTCGAAACCAGAGCTGATCG 58.727 55.000 0.00 6.53 34.62 3.69
531 590 7.848223 CATGTGTCTCATGTGAGGTTTATTA 57.152 36.000 9.94 0.00 46.18 0.98
532 591 6.748333 CATGTGTCTCATGTGAGGTTTATT 57.252 37.500 9.94 0.00 46.18 1.40
608 674 1.599518 GATTGTGGCGTGTGTGGGA 60.600 57.895 0.00 0.00 0.00 4.37
612 678 1.959226 GTCCGATTGTGGCGTGTGT 60.959 57.895 0.00 0.00 0.00 3.72
780 858 1.153208 GAGGAGGCGAGACGAGGTA 60.153 63.158 0.00 0.00 0.00 3.08
871 949 4.979815 CCGCGTTGTTTTATTTTCCTTTCT 59.020 37.500 4.92 0.00 0.00 2.52
911 996 3.319926 GACCGCAGCTTGCTTGCTC 62.320 63.158 12.46 4.23 42.25 4.26
968 1053 2.298661 GGGAAGACGATGGGGGTGT 61.299 63.158 0.00 0.00 0.00 4.16
970 1055 2.691252 GGGGAAGACGATGGGGGT 60.691 66.667 0.00 0.00 0.00 4.95
971 1056 1.984288 GAAGGGGAAGACGATGGGGG 61.984 65.000 0.00 0.00 0.00 5.40
972 1057 1.527370 GAAGGGGAAGACGATGGGG 59.473 63.158 0.00 0.00 0.00 4.96
973 1058 1.527370 GGAAGGGGAAGACGATGGG 59.473 63.158 0.00 0.00 0.00 4.00
974 1059 1.527370 GGGAAGGGGAAGACGATGG 59.473 63.158 0.00 0.00 0.00 3.51
975 1060 1.271840 TGGGGAAGGGGAAGACGATG 61.272 60.000 0.00 0.00 0.00 3.84
976 1061 0.983378 CTGGGGAAGGGGAAGACGAT 60.983 60.000 0.00 0.00 0.00 3.73
1509 1616 0.531532 CCTGGATCTGCGTGATGTCC 60.532 60.000 0.00 0.00 35.14 4.02
1609 1716 0.388134 CAGTTGTAGTCCGGGTCGTG 60.388 60.000 0.00 0.00 0.00 4.35
1671 1778 4.649705 TCGGGGGTGAGGAGGCAA 62.650 66.667 0.00 0.00 0.00 4.52
1939 2046 2.874086 CGCCATAGATGCAGTCATTGAA 59.126 45.455 0.00 0.00 31.96 2.69
3069 3212 1.795170 GAAGCAACAGCAAGGCCGAA 61.795 55.000 0.00 0.00 0.00 4.30
3105 3248 4.884164 GGAATCAAAGAATCGGAGGAACAT 59.116 41.667 0.00 0.00 0.00 2.71
3110 3253 4.517285 TGAAGGAATCAAAGAATCGGAGG 58.483 43.478 0.00 0.00 34.30 4.30
3147 3290 6.410540 ACAAAAAGGTTTCTTACAAATGGCA 58.589 32.000 0.00 0.00 32.01 4.92
3180 3323 7.588488 GCTACACAAGATCTTCTAATCGTAGAC 59.412 40.741 4.57 4.03 42.51 2.59
3186 3329 6.279882 AGCAGCTACACAAGATCTTCTAATC 58.720 40.000 4.57 0.00 0.00 1.75
3188 3331 5.667539 AGCAGCTACACAAGATCTTCTAA 57.332 39.130 4.57 0.00 0.00 2.10
3418 3562 1.198637 GATGAGCAGCCAAGTGAACAC 59.801 52.381 0.00 0.00 0.00 3.32
3472 3616 4.275689 CACTGTATGCACAAAACCTCAGAA 59.724 41.667 0.00 0.00 33.22 3.02
3480 3624 3.951037 ACTGTTCCACTGTATGCACAAAA 59.049 39.130 0.00 0.00 33.22 2.44
3508 3653 0.468226 ACTGAAACTCCGGTGCAGAA 59.532 50.000 14.14 0.00 34.71 3.02
3700 4223 2.137523 ACGTACACTTAACCGCCAAAG 58.862 47.619 0.00 0.00 0.00 2.77
3787 4310 2.095567 AGACATGAACGTTGCAGATTGC 60.096 45.455 5.00 0.00 45.29 3.56
3788 4311 3.485633 CAGACATGAACGTTGCAGATTG 58.514 45.455 5.00 2.27 0.00 2.67
3820 4343 6.601332 AGAAAGTAAAAGGTCCATCTGTTCA 58.399 36.000 0.00 0.00 0.00 3.18
3871 4395 7.396907 TGTGATGTTTCATCTAATCCAACCAAT 59.603 33.333 10.40 0.00 33.56 3.16
4018 4545 3.626217 GTGCCAGTTATGTTACCTTAGCC 59.374 47.826 0.00 0.00 0.00 3.93
4022 4549 2.081462 GCGTGCCAGTTATGTTACCTT 58.919 47.619 0.00 0.00 0.00 3.50
4028 4555 1.577328 GCTGTGCGTGCCAGTTATGT 61.577 55.000 10.57 0.00 32.41 2.29
4046 4573 2.124122 CTGCTTAAACAAACCAACGGC 58.876 47.619 0.00 0.00 0.00 5.68
4065 4592 2.564947 AGACGAGCAAAGTCTTCATCCT 59.435 45.455 3.38 0.00 45.74 3.24
4093 4620 1.165907 TGCTGTTCCACGCAAGAAGG 61.166 55.000 0.00 0.00 43.62 3.46
4094 4621 0.662619 TTGCTGTTCCACGCAAGAAG 59.337 50.000 0.00 0.00 40.84 2.85


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

AutoCloner maintained by Alex Coulton.