Multiple sequence alignment - TraesCS4D01G108700

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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 TraesCS4D01G108700 chr4D 100.000 3495 0 0 1 3495 87965773 87962279 0.000000e+00 6455.0
1 TraesCS4D01G108700 chr4A 93.070 3521 166 25 1 3488 500661046 500657571 0.000000e+00 5079.0
2 TraesCS4D01G108700 chr4A 77.844 167 25 7 1 164 593843543 593843386 3.710000e-15 93.5
3 TraesCS4D01G108700 chr4B 94.140 3191 140 18 310 3489 124564306 124561152 0.000000e+00 4813.0
4 TraesCS4D01G108700 chr4B 91.373 255 15 2 1 248 124565144 124564890 3.340000e-90 342.0


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 TraesCS4D01G108700 chr4D 87962279 87965773 3494 True 6455.0 6455 100.0000 1 3495 1 chr4D.!!$R1 3494
1 TraesCS4D01G108700 chr4A 500657571 500661046 3475 True 5079.0 5079 93.0700 1 3488 1 chr4A.!!$R1 3487
2 TraesCS4D01G108700 chr4B 124561152 124565144 3992 True 2577.5 4813 92.7565 1 3489 2 chr4B.!!$R1 3488

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
394 963 0.035820 GTCGCCATGTGAGGGGTTTA 60.036 55.0 0.00 0.0 41.92 2.01 F
2176 2763 0.315251 GGGCCTTCAGCTTGACAAAC 59.685 55.0 0.84 0.0 43.05 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2178 2765 0.719465 CCTGGCGATAACGAACACAC 59.281 55.0 0.00 0.0 42.66 3.82 R
2994 3594 0.254178 CAGCTGGGTGGTAGCATCTT 59.746 55.0 5.57 0.0 43.53 2.40 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
33 34 1.382522 CGCTACCATGCCACAGAAAT 58.617 50.000 0.00 0.00 0.00 2.17
34 35 1.331756 CGCTACCATGCCACAGAAATC 59.668 52.381 0.00 0.00 0.00 2.17
60 61 1.442769 CACAATGGTCTCAGGGTTCG 58.557 55.000 0.00 0.00 0.00 3.95
67 68 2.435586 CTCAGGGTTCGCCTGCAG 60.436 66.667 6.78 6.78 37.45 4.41
221 229 6.998074 ACAAATTCATATCCATGTCGGTGTAT 59.002 34.615 0.00 0.00 35.57 2.29
251 259 1.032014 GATCTTCCTCGCTGCTCTCT 58.968 55.000 0.00 0.00 0.00 3.10
278 838 0.461548 CTCTCCACGAAGGCATAGCA 59.538 55.000 0.00 0.00 37.29 3.49
294 862 3.120105 CATGGCGGCGACTAGAGA 58.880 61.111 16.45 0.00 0.00 3.10
382 951 1.077501 CCATCACCCTTGTCGCCAT 60.078 57.895 0.00 0.00 0.00 4.40
394 963 0.035820 GTCGCCATGTGAGGGGTTTA 60.036 55.000 0.00 0.00 41.92 2.01
396 965 0.322098 CGCCATGTGAGGGGTTTACA 60.322 55.000 0.00 0.00 36.89 2.41
407 976 4.141367 TGAGGGGTTTACAATGTCAGAACA 60.141 41.667 0.00 0.00 40.38 3.18
457 1028 7.915293 TTTGTCATAGTCAATTATTCCGTGT 57.085 32.000 0.00 0.00 0.00 4.49
469 1040 6.582677 ATTATTCCGTGTGGTGATTTTTGA 57.417 33.333 0.00 0.00 36.30 2.69
495 1066 6.140110 ACGAATTGTAAAGTGGTGATTTTCG 58.860 36.000 0.00 0.00 30.06 3.46
536 1110 2.699846 TGGCCTTTTGCATTTCACTCTT 59.300 40.909 3.32 0.00 43.89 2.85
552 1126 5.423015 TCACTCTTCTAAACCATGAGATGC 58.577 41.667 0.00 0.00 0.00 3.91
567 1141 6.921857 CCATGAGATGCACATTTATCCTTTTC 59.078 38.462 0.00 0.00 0.00 2.29
608 1182 5.335583 CGAGATCACATGACTATTCCCTCTC 60.336 48.000 0.00 0.00 0.00 3.20
744 1319 0.323360 GCATCTGCAACCCAACCCTA 60.323 55.000 0.00 0.00 41.59 3.53
933 1508 1.229984 CACCCCTTTCTCCCTCCCT 60.230 63.158 0.00 0.00 0.00 4.20
934 1509 1.083141 ACCCCTTTCTCCCTCCCTC 59.917 63.158 0.00 0.00 0.00 4.30
935 1510 1.694525 CCCCTTTCTCCCTCCCTCC 60.695 68.421 0.00 0.00 0.00 4.30
961 1536 4.640647 CCTCCCAACAAGGTTTAAGATAGC 59.359 45.833 0.00 0.00 34.66 2.97
976 1551 2.892852 AGATAGCTCTGCCTTCTAGCTG 59.107 50.000 6.33 0.00 45.83 4.24
1190 1768 1.871080 ACGAAAAGGAGTGTCAGCAG 58.129 50.000 0.00 0.00 0.00 4.24
1191 1769 0.514691 CGAAAAGGAGTGTCAGCAGC 59.485 55.000 0.00 0.00 0.00 5.25
1192 1770 1.597742 GAAAAGGAGTGTCAGCAGCA 58.402 50.000 0.00 0.00 0.00 4.41
1273 1860 1.379044 AGGGAAAGCTGCCGGAATG 60.379 57.895 5.05 0.00 38.32 2.67
1337 1924 2.813779 GACAATGACATCTTGTCCGC 57.186 50.000 9.79 0.00 46.40 5.54
1660 2247 2.687370 GCCATGCAGGTAACCAAAAAG 58.313 47.619 0.00 0.00 40.61 2.27
2154 2741 6.851222 TCAGAGTTCAGAGCTAAAGTTTTG 57.149 37.500 0.00 0.00 0.00 2.44
2176 2763 0.315251 GGGCCTTCAGCTTGACAAAC 59.685 55.000 0.84 0.00 43.05 2.93
2178 2765 1.000938 GGCCTTCAGCTTGACAAACTG 60.001 52.381 11.62 11.62 43.05 3.16
2220 2807 0.808755 GACGGCGATGGGAAAATTGT 59.191 50.000 16.62 0.00 0.00 2.71
2261 2848 2.856032 CTCACGACAAGGCGCAAG 59.144 61.111 10.83 0.00 43.44 4.01
2274 2861 3.123620 GCAAGCGCCTCTGTCCAG 61.124 66.667 2.29 0.00 0.00 3.86
2275 2862 3.123620 CAAGCGCCTCTGTCCAGC 61.124 66.667 2.29 0.00 0.00 4.85
2357 2944 1.466697 GGAGAGTGAAGAAGCTCGTCG 60.467 57.143 0.00 0.00 36.88 5.12
2425 3012 3.377485 CCTGCTCAGATTTGGATGAACTG 59.623 47.826 0.00 0.00 0.00 3.16
2427 3014 3.754850 TGCTCAGATTTGGATGAACTGTG 59.245 43.478 0.00 0.00 0.00 3.66
2431 3018 4.756642 TCAGATTTGGATGAACTGTGTGTC 59.243 41.667 0.00 0.00 0.00 3.67
2441 3028 2.799126 ACTGTGTGTCTTCAACCCAA 57.201 45.000 0.00 0.00 0.00 4.12
2563 3155 2.214347 GCTCCCTTAATTCGCTTCTCC 58.786 52.381 0.00 0.00 0.00 3.71
2629 3221 4.954875 TCAAATTTTCCGGTTGCAAATCT 58.045 34.783 0.00 0.00 0.00 2.40
2633 3225 5.671742 ATTTTCCGGTTGCAAATCTTTTG 57.328 34.783 0.00 0.00 0.00 2.44
2640 3232 4.207019 CGGTTGCAAATCTTTTGAAGTCAC 59.793 41.667 0.00 0.00 0.00 3.67
2641 3233 5.108517 GGTTGCAAATCTTTTGAAGTCACA 58.891 37.500 0.00 0.00 0.00 3.58
2646 3238 7.040494 TGCAAATCTTTTGAAGTCACATTTGA 58.960 30.769 12.75 0.00 0.00 2.69
2669 3261 6.494491 TGAAAATTTCACAGGATTCAGACCAT 59.506 34.615 4.03 0.00 34.08 3.55
2682 3274 4.498894 TCAGACCATGAAAGCATCTCAT 57.501 40.909 0.00 0.00 34.02 2.90
2683 3275 4.449131 TCAGACCATGAAAGCATCTCATC 58.551 43.478 0.00 0.00 34.02 2.92
2904 3499 0.887387 TTTTGGGTTCTTCCGCGGAG 60.887 55.000 29.20 21.49 37.00 4.63
2943 3538 7.201785 GGATTAAGAACAAACAGTCACTTTGGA 60.202 37.037 0.00 0.00 33.61 3.53
2960 3560 4.572985 TTGGAAGAAGCAATGAACTGTG 57.427 40.909 0.00 0.00 0.00 3.66
2994 3594 7.510675 ACTCAATCTCTTGTAATTCCCCTTA 57.489 36.000 0.00 0.00 33.87 2.69
3110 3710 4.938226 ACACAATGCTCTAGAAAACCTAGC 59.062 41.667 0.00 0.00 43.60 3.42
3116 3716 8.555361 CAATGCTCTAGAAAACCTAGCTTAATC 58.445 37.037 0.00 0.00 43.60 1.75
3186 3786 8.721133 ACCTGTATTTTAATTCAAAAGGAGGT 57.279 30.769 7.88 7.16 39.44 3.85
3275 3877 6.996106 CATTGTTAATTTAGCAATGCCTGTG 58.004 36.000 23.97 9.23 45.64 3.66
3276 3878 5.720371 TGTTAATTTAGCAATGCCTGTGT 57.280 34.783 0.00 0.00 0.00 3.72
3277 3879 6.095432 TGTTAATTTAGCAATGCCTGTGTT 57.905 33.333 0.00 0.00 0.00 3.32
3278 3880 7.220741 TGTTAATTTAGCAATGCCTGTGTTA 57.779 32.000 0.00 0.00 0.00 2.41
3392 3994 5.596361 TCCTCAAGTTGCTTGTTTTATTGGA 59.404 36.000 8.48 0.00 41.66 3.53
3465 4067 7.115947 GGATCAAGATTCAGCTTCAAAACAAAG 59.884 37.037 0.00 0.00 0.00 2.77
3473 4075 4.279169 CAGCTTCAAAACAAAGATGGGAGA 59.721 41.667 0.00 0.00 36.69 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 2.502947 CTGAGACCATTGTGGATCCAGA 59.497 50.000 16.81 12.14 40.96 3.86
34 35 2.421107 CCTGAGACCATTGTGGATCCAG 60.421 54.545 16.81 5.43 40.96 3.86
37 38 1.561542 ACCCTGAGACCATTGTGGATC 59.438 52.381 2.45 1.55 40.96 3.36
60 61 7.969536 TTATTTAGATTCTGATACTGCAGGC 57.030 36.000 19.93 7.61 36.55 4.85
251 259 2.103373 CCTTCGTGGAGAGATGGAGAA 58.897 52.381 0.00 0.00 38.35 2.87
278 838 2.196925 CCTCTCTAGTCGCCGCCAT 61.197 63.158 0.00 0.00 0.00 4.40
382 951 3.392947 TCTGACATTGTAAACCCCTCACA 59.607 43.478 0.00 0.00 0.00 3.58
394 963 5.493133 TTTTTAGCGTGTTCTGACATTGT 57.507 34.783 0.00 0.00 38.23 2.71
437 1008 5.815222 CACCACACGGAATAATTGACTATGA 59.185 40.000 0.00 0.00 35.59 2.15
449 1020 3.634448 TGTCAAAAATCACCACACGGAAT 59.366 39.130 0.00 0.00 35.59 3.01
457 1028 5.255710 ACAATTCGTGTCAAAAATCACCA 57.744 34.783 0.00 0.00 34.38 4.17
469 1040 6.385649 AAATCACCACTTTACAATTCGTGT 57.614 33.333 0.00 0.00 44.82 4.49
518 1092 6.642540 GGTTTAGAAGAGTGAAATGCAAAAGG 59.357 38.462 0.00 0.00 0.00 3.11
519 1093 7.202526 TGGTTTAGAAGAGTGAAATGCAAAAG 58.797 34.615 0.00 0.00 0.00 2.27
536 1110 7.229306 GGATAAATGTGCATCTCATGGTTTAGA 59.771 37.037 0.00 0.00 0.00 2.10
567 1141 8.017946 TGTGATCTCGATCTCAAGATTATAACG 58.982 37.037 8.69 0.00 38.08 3.18
639 1214 1.195115 TGTCTATCCCCTCTGTGTGC 58.805 55.000 0.00 0.00 0.00 4.57
744 1319 0.527565 GAATGGAAAGGCACGCACAT 59.472 50.000 0.00 0.00 0.00 3.21
933 1508 0.402861 AACCTTGTTGGGAGGGAGGA 60.403 55.000 0.00 0.00 41.11 3.71
934 1509 0.482887 AAACCTTGTTGGGAGGGAGG 59.517 55.000 0.00 0.00 41.11 4.30
935 1510 3.073946 TCTTAAACCTTGTTGGGAGGGAG 59.926 47.826 0.00 0.00 41.11 4.30
961 1536 1.481772 AGAAGCAGCTAGAAGGCAGAG 59.518 52.381 0.00 0.00 34.17 3.35
976 1551 0.034960 GTTGGGGAGGAAGGAGAAGC 60.035 60.000 0.00 0.00 0.00 3.86
1122 1697 2.615869 CTGCTGTTCTTGCTCTCTACC 58.384 52.381 0.00 0.00 0.00 3.18
1190 1768 1.035932 AGTCATGCTCCTGCCAATGC 61.036 55.000 0.00 0.00 38.71 3.56
1191 1769 1.134367 CAAGTCATGCTCCTGCCAATG 59.866 52.381 0.00 0.00 38.71 2.82
1192 1770 1.471119 CAAGTCATGCTCCTGCCAAT 58.529 50.000 0.00 0.00 38.71 3.16
1421 2008 3.978867 GACGACGACGACGAGCTGG 62.979 68.421 25.15 0.00 42.66 4.85
1933 2520 2.071262 CCTCCTGGCCAGCTCATCT 61.071 63.158 28.39 0.00 0.00 2.90
2154 2741 2.034687 TCAAGCTGAAGGCCCTGC 59.965 61.111 0.00 0.02 43.05 4.85
2176 2763 1.390123 CTGGCGATAACGAACACACAG 59.610 52.381 0.00 0.00 42.66 3.66
2178 2765 0.719465 CCTGGCGATAACGAACACAC 59.281 55.000 0.00 0.00 42.66 3.82
2220 2807 4.829518 CGCTCGTCGCCATCGTCA 62.830 66.667 0.00 0.00 36.96 4.35
2357 2944 2.419324 CCTCTGAAGAATTGCTGCTGTC 59.581 50.000 0.00 0.00 0.00 3.51
2425 3012 1.000274 GCCATTGGGTTGAAGACACAC 60.000 52.381 4.53 0.00 42.62 3.82
2427 3014 1.620822 AGCCATTGGGTTGAAGACAC 58.379 50.000 0.36 0.00 36.17 3.67
2431 3018 3.316308 GCAGTATAGCCATTGGGTTGAAG 59.684 47.826 13.49 1.65 34.28 3.02
2563 3155 2.427506 GGGAAACAGAGGTGCTACAAG 58.572 52.381 0.00 0.00 0.00 3.16
2633 3225 7.706179 TCCTGTGAAATTTTCAAATGTGACTTC 59.294 33.333 13.21 0.00 42.15 3.01
2640 3232 8.706035 GTCTGAATCCTGTGAAATTTTCAAATG 58.294 33.333 13.21 5.91 42.15 2.32
2641 3233 7.874528 GGTCTGAATCCTGTGAAATTTTCAAAT 59.125 33.333 13.21 3.30 42.15 2.32
2646 3238 6.494491 TCATGGTCTGAATCCTGTGAAATTTT 59.506 34.615 0.00 0.00 0.00 1.82
2669 3261 3.084039 GTTGTGGGATGAGATGCTTTCA 58.916 45.455 0.00 0.00 0.00 2.69
2682 3274 7.835682 AGATTTTGATGATCAATAGTTGTGGGA 59.164 33.333 8.90 0.00 36.11 4.37
2683 3275 7.919091 CAGATTTTGATGATCAATAGTTGTGGG 59.081 37.037 8.90 0.00 36.11 4.61
2904 3499 5.009610 TGTTCTTAATCCTTTGTCTGGTTGC 59.990 40.000 0.00 0.00 0.00 4.17
2907 3502 6.605594 TGTTTGTTCTTAATCCTTTGTCTGGT 59.394 34.615 0.00 0.00 0.00 4.00
2943 3538 2.035066 GTGGCACAGTTCATTGCTTCTT 59.965 45.455 13.86 0.00 41.80 2.52
2960 3560 5.181748 ACAAGAGATTGAGTAATCAGTGGC 58.818 41.667 0.00 0.00 44.14 5.01
2994 3594 0.254178 CAGCTGGGTGGTAGCATCTT 59.746 55.000 5.57 0.00 43.53 2.40
3086 3686 5.163814 GCTAGGTTTTCTAGAGCATTGTGTG 60.164 44.000 4.42 0.00 46.48 3.82
3110 3710 3.567478 ACTTGCTAGGGCCTGATTAAG 57.433 47.619 18.53 16.59 37.74 1.85
3116 3716 3.501349 TCTATCTACTTGCTAGGGCCTG 58.499 50.000 18.53 7.50 37.74 4.85
3176 3776 5.001874 GGTACCTGTCTAAACCTCCTTTTG 58.998 45.833 4.06 0.00 0.00 2.44
3186 3786 3.644265 TCAGCTTGTGGTACCTGTCTAAA 59.356 43.478 14.36 0.00 0.00 1.85
3274 3876 4.383010 CCATGTACAGAGCAGGTCATAACA 60.383 45.833 0.33 3.15 0.00 2.41
3275 3877 4.122776 CCATGTACAGAGCAGGTCATAAC 58.877 47.826 0.33 0.00 0.00 1.89
3276 3878 4.030216 TCCATGTACAGAGCAGGTCATAA 58.970 43.478 0.33 0.00 0.00 1.90
3277 3879 3.638627 CTCCATGTACAGAGCAGGTCATA 59.361 47.826 0.33 0.00 0.00 2.15
3278 3880 2.433604 CTCCATGTACAGAGCAGGTCAT 59.566 50.000 0.33 0.00 0.00 3.06
3392 3994 4.222124 ACGTAGCCTGAAGAATCCAAAT 57.778 40.909 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.