Multiple sequence alignment - TraesCS4D01G206700

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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 TraesCS4D01G206700 chr4D 100.000 3611 0 0 1 3611 354147625 354144015 0.000000e+00 6669
1 TraesCS4D01G206700 chr4A 95.217 3136 96 22 511 3611 110378632 110381748 0.000000e+00 4911
2 TraesCS4D01G206700 chr4A 95.385 325 7 3 197 521 110378072 110378388 8.940000e-141 510
3 TraesCS4D01G206700 chr4B 95.784 2965 77 17 518 3448 438227883 438224933 0.000000e+00 4739
4 TraesCS4D01G206700 chr4B 96.154 520 3 5 1 509 438228790 438228277 0.000000e+00 833
5 TraesCS4D01G206700 chr4B 94.737 76 4 0 3500 3575 438224932 438224857 6.330000e-23 119
6 TraesCS4D01G206700 chr3B 79.695 394 76 4 1538 1929 59186335 59186726 7.630000e-72 281
7 TraesCS4D01G206700 chr3B 77.949 390 80 6 1542 1929 616182900 616183285 4.660000e-59 239
8 TraesCS4D01G206700 chr3A 77.662 385 82 4 1547 1929 606425501 606425883 7.800000e-57 231
9 TraesCS4D01G206700 chr3D 77.403 385 83 4 1547 1929 463082335 463081953 3.630000e-55 226


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 TraesCS4D01G206700 chr4D 354144015 354147625 3610 True 6669.0 6669 100.000000 1 3611 1 chr4D.!!$R1 3610
1 TraesCS4D01G206700 chr4A 110378072 110381748 3676 False 2710.5 4911 95.301000 197 3611 2 chr4A.!!$F1 3414
2 TraesCS4D01G206700 chr4B 438224857 438228790 3933 True 1897.0 4739 95.558333 1 3575 3 chr4B.!!$R1 3574

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
727 1138 0.248621 GATTTGGGCTTCGAATGCGG 60.249 55.000 0.00 0.00 38.28 5.69 F
1266 1686 1.061131 GAATCCAACGTCGACATGCTG 59.939 52.381 17.16 6.30 0.00 4.41 F
1536 1956 2.849943 TGGGAATGGTAATAGTGCCACT 59.150 45.455 0.92 1.54 42.96 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2187 2607 0.606130 AAGCATGACGCATCACACCA 60.606 50.0 0.00 0.00 46.13 4.17 R
2388 2808 0.949105 CCGTCAACTTGAAGGTCCGG 60.949 60.0 13.93 8.93 40.46 5.14 R
3448 3892 1.151777 ACAAGGTGTTGCGTGAGACG 61.152 55.0 0.00 0.00 45.88 4.18 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
335 341 2.897350 GCGAGCCAATCCTTCCCG 60.897 66.667 0.00 0.00 0.00 5.14
557 954 6.412943 CGATTTGATTTCGACTGATTGATTGG 59.587 38.462 0.00 0.00 38.88 3.16
697 1108 0.597637 CGGATCTCGAATTCGTGGGG 60.598 60.000 25.93 14.86 42.43 4.96
716 1127 2.422479 GGGTTTCTCGTTAGATTTGGGC 59.578 50.000 0.00 0.00 0.00 5.36
727 1138 0.248621 GATTTGGGCTTCGAATGCGG 60.249 55.000 0.00 0.00 38.28 5.69
742 1153 2.416680 TGCGGGATTGATTGATGTGA 57.583 45.000 0.00 0.00 0.00 3.58
748 1168 5.232838 GCGGGATTGATTGATGTGATTTTTC 59.767 40.000 0.00 0.00 0.00 2.29
762 1182 3.891977 TGATTTTTCCCCGTGTGATTTGA 59.108 39.130 0.00 0.00 0.00 2.69
763 1183 4.526262 TGATTTTTCCCCGTGTGATTTGAT 59.474 37.500 0.00 0.00 0.00 2.57
764 1184 4.946478 TTTTTCCCCGTGTGATTTGATT 57.054 36.364 0.00 0.00 0.00 2.57
765 1185 4.946478 TTTTCCCCGTGTGATTTGATTT 57.054 36.364 0.00 0.00 0.00 2.17
767 1187 1.543802 TCCCCGTGTGATTTGATTTGC 59.456 47.619 0.00 0.00 0.00 3.68
768 1188 1.271934 CCCCGTGTGATTTGATTTGCA 59.728 47.619 0.00 0.00 0.00 4.08
769 1189 2.598589 CCCGTGTGATTTGATTTGCAG 58.401 47.619 0.00 0.00 0.00 4.41
770 1190 2.598589 CCGTGTGATTTGATTTGCAGG 58.401 47.619 0.00 0.00 0.00 4.85
771 1191 2.598589 CGTGTGATTTGATTTGCAGGG 58.401 47.619 0.00 0.00 0.00 4.45
772 1192 2.228582 CGTGTGATTTGATTTGCAGGGA 59.771 45.455 0.00 0.00 0.00 4.20
1238 1658 2.283101 GGCCATGCAGACCACCAA 60.283 61.111 0.00 0.00 0.00 3.67
1266 1686 1.061131 GAATCCAACGTCGACATGCTG 59.939 52.381 17.16 6.30 0.00 4.41
1536 1956 2.849943 TGGGAATGGTAATAGTGCCACT 59.150 45.455 0.92 1.54 42.96 4.00
1596 2016 4.391155 TGTACATGTGGGTGTTTAAGGAC 58.609 43.478 9.11 0.00 33.62 3.85
1856 2276 3.011032 ACTGGGAGAGATGCCAATTTCTT 59.989 43.478 0.00 0.00 27.67 2.52
2187 2607 3.961480 TCATGGACGAATGACTTCACT 57.039 42.857 0.00 0.00 31.58 3.41
2331 2751 4.039973 TGGAAGAACACTCTTACGAATGGT 59.960 41.667 0.00 0.00 44.57 3.55
2388 2808 2.476854 GCCATTCTTGAAGCGACATGAC 60.477 50.000 0.00 0.00 0.00 3.06
2660 3080 7.997773 TGTTCATGTAGTAGTTAGAGTGTCT 57.002 36.000 0.00 0.00 0.00 3.41
2873 3293 2.496899 ACAGGCCACAAGGAACATAG 57.503 50.000 5.01 0.00 36.89 2.23
2926 3360 8.044908 GGGAGTACCTTGTGTATTATCTTTTGA 58.955 37.037 0.00 0.00 35.85 2.69
3062 3502 2.565841 GTGAGAAGTCTGCTTTGTGGT 58.434 47.619 0.00 0.00 34.61 4.16
3064 3504 2.170397 TGAGAAGTCTGCTTTGTGGTCA 59.830 45.455 0.00 0.00 34.61 4.02
3068 3508 3.498774 AGTCTGCTTTGTGGTCATTCT 57.501 42.857 0.00 0.00 0.00 2.40
3093 3533 5.047092 TGGAAATTTCATCCAAGAAAGGAGC 60.047 40.000 19.49 0.00 43.84 4.70
3108 3548 1.884579 AGGAGCTCATGCAAGTGTTTG 59.115 47.619 17.19 0.00 42.74 2.93
3130 3570 6.325919 TGTAGGATTTGTCCATGTTTTGTC 57.674 37.500 0.00 0.00 0.00 3.18
3148 3590 9.881529 TGTTTTGTCGGTACTATTGTTTTTATC 57.118 29.630 0.00 0.00 0.00 1.75
3156 3598 7.582679 CGGTACTATTGTTTTTATCAGCATTCG 59.417 37.037 0.00 0.00 0.00 3.34
3209 3651 4.404073 AGTGCAATTGTTTGAAGGTACCAA 59.596 37.500 15.94 0.00 34.60 3.67
3328 3770 0.182775 AGTTCAACTTCAACCCCGCT 59.817 50.000 0.00 0.00 0.00 5.52
3337 3780 0.400213 TCAACCCCGCTGAAGTGATT 59.600 50.000 0.00 0.00 0.00 2.57
3386 3829 5.663456 TCTGCATTTTTCTTTTGCTGAAGT 58.337 33.333 0.00 0.00 40.08 3.01
3448 3892 7.440198 GGTATTTACCTATTCTGGTGTCCTAC 58.560 42.308 0.00 0.00 43.10 3.18
3470 3914 2.221055 GTCTCACGCAACACCTTGTTAG 59.779 50.000 0.00 0.00 38.77 2.34
3482 3926 4.074970 CACCTTGTTAGCAACCAGAGAAT 58.925 43.478 0.00 0.00 0.00 2.40
3561 4006 2.045634 GCTGCTCACCCTGCATCA 60.046 61.111 0.00 0.00 39.86 3.07
3578 4023 6.409524 TGCATCATCTTTTGAGAACCTTTT 57.590 33.333 0.00 0.00 37.89 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
697 1108 4.435651 CGAAGCCCAAATCTAACGAGAAAC 60.436 45.833 0.00 0.00 34.61 2.78
716 1127 2.613595 TCAATCAATCCCGCATTCGAAG 59.386 45.455 3.35 0.00 38.10 3.79
727 1138 6.051074 GGGGAAAAATCACATCAATCAATCC 58.949 40.000 0.00 0.00 0.00 3.01
742 1153 5.482163 AATCAAATCACACGGGGAAAAAT 57.518 34.783 0.00 0.00 0.00 1.82
748 1168 1.271934 TGCAAATCAAATCACACGGGG 59.728 47.619 0.00 0.00 0.00 5.73
893 1313 2.847234 TGGTGCCCAACTCTCCGT 60.847 61.111 0.00 0.00 0.00 4.69
1225 1645 1.380302 GGAGGTTGGTGGTCTGCAT 59.620 57.895 0.00 0.00 0.00 3.96
1238 1658 1.405526 CGACGTTGGATTCATGGAGGT 60.406 52.381 0.00 0.00 0.00 3.85
1266 1686 2.825836 CAGCCGAGGCCAACATCC 60.826 66.667 10.95 0.00 43.17 3.51
2187 2607 0.606130 AAGCATGACGCATCACACCA 60.606 50.000 0.00 0.00 46.13 4.17
2331 2751 6.918022 CACTAGTGCATGATATCTTAACGACA 59.082 38.462 10.54 0.00 0.00 4.35
2388 2808 0.949105 CCGTCAACTTGAAGGTCCGG 60.949 60.000 13.93 8.93 40.46 5.14
2660 3080 5.814188 CAGTCAAGAGCAGCTGACAATAATA 59.186 40.000 20.43 0.00 34.06 0.98
2873 3293 1.263217 CGATACCAAAACATAGGGCGC 59.737 52.381 0.00 0.00 0.00 6.53
2941 3376 6.143278 CAGGCGACAAACCTTTTAATACAAAC 59.857 38.462 0.00 0.00 34.42 2.93
2949 3384 1.877443 GAGCAGGCGACAAACCTTTTA 59.123 47.619 0.00 0.00 34.42 1.52
3084 3524 2.224719 ACACTTGCATGAGCTCCTTTCT 60.225 45.455 12.15 0.00 42.74 2.52
3093 3533 5.633830 AATCCTACAAACACTTGCATGAG 57.366 39.130 6.60 0.66 35.84 2.90
3108 3548 5.390613 CGACAAAACATGGACAAATCCTAC 58.609 41.667 0.00 0.00 46.43 3.18
3130 3570 7.582679 CGAATGCTGATAAAAACAATAGTACCG 59.417 37.037 0.00 0.00 0.00 4.02
3156 3598 2.029918 AGCAATTTCCTGGAAAGCGTTC 60.030 45.455 24.65 12.77 34.92 3.95
3328 3770 1.264020 GCGAACACTGCAATCACTTCA 59.736 47.619 0.00 0.00 0.00 3.02
3337 3780 2.894879 AGCGTTGCGAACACTGCA 60.895 55.556 0.00 0.00 41.38 4.41
3354 3797 7.169645 GCAAAAGAAAAATGCAGATACAACTCA 59.830 33.333 0.00 0.00 39.81 3.41
3386 3829 6.753913 AATCCTATCCTTGCAGATACTTCA 57.246 37.500 0.00 0.00 0.00 3.02
3448 3892 1.151777 ACAAGGTGTTGCGTGAGACG 61.152 55.000 0.00 0.00 45.88 4.18
3482 3926 6.756074 CAGTTGCCACTTTGTTATGAGAAAAA 59.244 34.615 0.00 0.00 0.00 1.94
3584 4029 0.038618 CACATCGTGAGTGGTTCGGA 60.039 55.000 0.00 0.00 35.23 4.55
3585 4030 2.445274 CACATCGTGAGTGGTTCGG 58.555 57.895 0.00 0.00 35.23 4.30


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

AutoCloner maintained by Alex Coulton.