Multiple sequence alignment - TraesCS2D01G191600

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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 TraesCS2D01G191600 chr2D 100.000 3028 0 0 1 3028 135600205 135603232 0.000000e+00 5592.0
1 TraesCS2D01G191600 chr2B 92.993 3097 110 41 1 3028 193389691 193392749 0.000000e+00 4418.0
2 TraesCS2D01G191600 chr2A 90.258 2556 108 48 1 2478 143722591 143725083 0.000000e+00 3210.0
3 TraesCS2D01G191600 chr2A 86.579 760 75 11 982 1731 143835490 143836232 0.000000e+00 813.0
4 TraesCS2D01G191600 chr2A 89.837 492 40 1 2544 3025 143725082 143725573 9.220000e-175 623.0
5 TraesCS2D01G191600 chr2A 96.552 58 2 0 2491 2548 161948620 161948677 2.480000e-16 97.1
6 TraesCS2D01G191600 chr2A 91.045 67 4 2 2491 2555 617636064 617636130 4.160000e-14 89.8
7 TraesCS2D01G191600 chr4A 96.552 58 2 0 2491 2548 548783071 548783014 2.480000e-16 97.1
8 TraesCS2D01G191600 chr6D 93.548 62 4 0 2494 2555 2956615 2956554 3.210000e-15 93.5
9 TraesCS2D01G191600 chr5A 94.915 59 3 0 2491 2549 382759465 382759523 3.210000e-15 93.5
10 TraesCS2D01G191600 chr5A 94.915 59 2 1 2491 2549 582386204 582386261 1.160000e-14 91.6
11 TraesCS2D01G191600 chr6B 92.188 64 5 0 2483 2546 543217446 543217509 1.160000e-14 91.6
12 TraesCS2D01G191600 chr4D 94.828 58 3 0 2491 2548 48595819 48595876 1.160000e-14 91.6


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 TraesCS2D01G191600 chr2D 135600205 135603232 3027 False 5592.0 5592 100.0000 1 3028 1 chr2D.!!$F1 3027
1 TraesCS2D01G191600 chr2B 193389691 193392749 3058 False 4418.0 4418 92.9930 1 3028 1 chr2B.!!$F1 3027
2 TraesCS2D01G191600 chr2A 143722591 143725573 2982 False 1916.5 3210 90.0475 1 3025 2 chr2A.!!$F4 3024
3 TraesCS2D01G191600 chr2A 143835490 143836232 742 False 813.0 813 86.5790 982 1731 1 chr2A.!!$F1 749

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
40 41 0.095935 CCAAGATTCTCTGCGTTGCG 59.904 55.0 0.0 0.0 0.0 4.85 F
639 667 0.386476 AACCGCTGACGTGACTACAA 59.614 50.0 0.0 0.0 37.7 2.41 F
963 1024 1.056660 CACTTGTCACCCTACCCTGT 58.943 55.0 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
1713 1795 0.811281 GCCTGTAACAGTCCAATGCC 59.189 55.000 0.0 0.0 0.00 4.40 R
1950 2033 2.499693 ACAACCCCCAAAAAGACAGTTG 59.500 45.455 0.0 0.0 39.14 3.16 R
2851 2987 1.071605 GCTAGAAGACCGCAGTGTTG 58.928 55.000 0.0 0.0 27.73 3.33 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
37 38 1.537202 GTTGCCAAGATTCTCTGCGTT 59.463 47.619 3.75 0.00 0.00 4.84
38 39 1.159285 TGCCAAGATTCTCTGCGTTG 58.841 50.000 3.75 0.00 0.00 4.10
39 40 0.179179 GCCAAGATTCTCTGCGTTGC 60.179 55.000 0.00 0.00 0.00 4.17
40 41 0.095935 CCAAGATTCTCTGCGTTGCG 59.904 55.000 0.00 0.00 0.00 4.85
41 42 0.792640 CAAGATTCTCTGCGTTGCGT 59.207 50.000 0.00 0.00 0.00 5.24
82 83 4.212004 CCTTTCAGTCATGCGGTATACATG 59.788 45.833 5.01 0.44 45.08 3.21
107 109 2.604046 ATGATTGTGTCCTCGTAGCC 57.396 50.000 0.00 0.00 0.00 3.93
119 121 3.787001 GTAGCCCCTGCCTCGCTT 61.787 66.667 0.00 0.00 38.69 4.68
120 122 2.042333 TAGCCCCTGCCTCGCTTA 60.042 61.111 0.00 0.00 38.69 3.09
121 123 2.134287 TAGCCCCTGCCTCGCTTAG 61.134 63.158 0.00 0.00 38.69 2.18
124 126 4.554036 CCCTGCCTCGCTTAGGGC 62.554 72.222 0.00 0.00 46.65 5.19
184 186 2.754658 TCGCTCTTCTCCCCGTCC 60.755 66.667 0.00 0.00 0.00 4.79
185 187 4.194720 CGCTCTTCTCCCCGTCCG 62.195 72.222 0.00 0.00 0.00 4.79
186 188 3.069318 GCTCTTCTCCCCGTCCGT 61.069 66.667 0.00 0.00 0.00 4.69
187 189 3.066233 GCTCTTCTCCCCGTCCGTC 62.066 68.421 0.00 0.00 0.00 4.79
212 214 1.373748 TGTTCTACGCCACTTCGCC 60.374 57.895 0.00 0.00 0.00 5.54
273 275 4.447989 GCAGCCGAGCAGAGCAGA 62.448 66.667 0.00 0.00 0.00 4.26
274 276 2.202770 CAGCCGAGCAGAGCAGAG 60.203 66.667 0.00 0.00 0.00 3.35
275 277 4.146075 AGCCGAGCAGAGCAGAGC 62.146 66.667 0.00 0.00 0.00 4.09
276 278 4.146075 GCCGAGCAGAGCAGAGCT 62.146 66.667 0.00 0.00 45.25 4.09
298 300 1.551452 AGTACACTGCCTCAGGAGAC 58.449 55.000 0.00 0.00 35.51 3.36
328 334 2.652079 CGTGCACAGTCACAGAGCG 61.652 63.158 18.64 0.00 36.80 5.03
447 460 4.168291 CGCCTTCCTCCTCCTGGC 62.168 72.222 0.00 0.00 40.14 4.85
634 662 2.594962 CCACAACCGCTGACGTGAC 61.595 63.158 0.00 0.00 37.70 3.67
639 667 0.386476 AACCGCTGACGTGACTACAA 59.614 50.000 0.00 0.00 37.70 2.41
648 691 1.554042 CGTGACTACAACACCGCCAC 61.554 60.000 0.00 0.00 35.17 5.01
665 708 2.187946 CCCGATTCTTGGCGCTCT 59.812 61.111 7.64 0.00 0.00 4.09
859 908 9.573166 TTCACATTTTCCTTCTTCTTAGATGAA 57.427 29.630 9.65 9.65 0.00 2.57
879 933 5.666462 TGAACTAAGTGCAGTTTACAGTGA 58.334 37.500 12.95 0.00 38.86 3.41
891 945 5.791974 CAGTTTACAGTGAGCAATTCGATTG 59.208 40.000 0.00 0.00 43.06 2.67
903 960 9.039870 TGAGCAATTCGATTGTATTTTGTTTTT 57.960 25.926 8.64 0.00 42.20 1.94
911 968 6.787043 CGATTGTATTTTGTTTTTGCTTCTGC 59.213 34.615 0.00 0.00 40.20 4.26
917 974 4.717233 TTGTTTTTGCTTCTGCTTCTGA 57.283 36.364 0.00 0.00 40.48 3.27
919 976 4.675510 TGTTTTTGCTTCTGCTTCTGAAG 58.324 39.130 13.02 13.02 40.67 3.02
953 1014 2.978010 CACGGGCCCACTTGTCAC 60.978 66.667 24.92 0.00 0.00 3.67
963 1024 1.056660 CACTTGTCACCCTACCCTGT 58.943 55.000 0.00 0.00 0.00 4.00
1426 1505 2.240162 CTCCCGCGCCTTACCTTTCT 62.240 60.000 0.00 0.00 0.00 2.52
1746 1829 4.020218 TGTTACAGGCTTACAGCTGAATCT 60.020 41.667 23.35 7.32 41.99 2.40
1951 2034 9.786105 CAGTAATGCACAATACATTTATGAACA 57.214 29.630 0.00 0.00 38.62 3.18
2002 2085 5.049680 TGTGCCGTTCTAAAAGACTGAATTC 60.050 40.000 0.00 0.00 0.00 2.17
2066 2149 4.040461 TGAGTGCTATATAGGCTTGGGAAC 59.960 45.833 11.72 0.00 0.00 3.62
2098 2181 4.648307 TGCAATGTTATGCCACATGGATTA 59.352 37.500 0.87 0.00 45.83 1.75
2185 2268 5.674933 ATCACCTTGTTTCTCTTTTCGAC 57.325 39.130 0.00 0.00 0.00 4.20
2192 2275 5.828299 TGTTTCTCTTTTCGACAAACCAT 57.172 34.783 0.00 0.00 31.77 3.55
2481 2591 9.973450 CTTGCATACTACAGTAATTGATACTCT 57.027 33.333 0.00 0.00 43.12 3.24
2558 2684 7.183460 ACAGAGGGAGTATATTCCAGTATACC 58.817 42.308 15.53 0.00 37.97 2.73
2652 2778 0.541863 ATTGGCTAGTTCCTGGACCG 59.458 55.000 0.00 0.00 0.00 4.79
2655 2781 1.448013 GCTAGTTCCTGGACCGCAC 60.448 63.158 0.00 0.00 0.00 5.34
2697 2823 6.994421 ACCTTTGGTTTATTTGGTGAGAAT 57.006 33.333 0.00 0.00 27.29 2.40
2718 2844 9.844257 GAGAATATGATGCCCTTAGCTTAATAT 57.156 33.333 0.00 0.00 44.23 1.28
2857 2993 7.624360 TCTAAACATTGAAGACAACAACACT 57.376 32.000 0.00 0.00 38.90 3.55
2861 2997 1.013596 TGAAGACAACAACACTGCGG 58.986 50.000 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 1.305219 TAGGAATGCTTGCCACACGC 61.305 55.000 0.00 0.00 38.31 5.34
39 40 0.447801 GTAGGAATGCTTGCCACACG 59.552 55.000 0.00 0.00 0.00 4.49
40 41 0.811281 GGTAGGAATGCTTGCCACAC 59.189 55.000 0.00 0.00 0.00 3.82
41 42 0.323360 GGGTAGGAATGCTTGCCACA 60.323 55.000 0.00 0.00 0.00 4.17
82 83 1.133025 CGAGGACACAATCATTTGGCC 59.867 52.381 0.00 0.00 37.15 5.36
119 121 0.390124 CTTTATACCGCCGTGCCCTA 59.610 55.000 0.00 0.00 0.00 3.53
120 122 1.145377 CTTTATACCGCCGTGCCCT 59.855 57.895 0.00 0.00 0.00 5.19
121 123 1.890510 CCTTTATACCGCCGTGCCC 60.891 63.158 0.00 0.00 0.00 5.36
122 124 1.890510 CCCTTTATACCGCCGTGCC 60.891 63.158 0.00 0.00 0.00 5.01
123 125 2.540228 GCCCTTTATACCGCCGTGC 61.540 63.158 0.00 0.00 0.00 5.34
124 126 0.463116 AAGCCCTTTATACCGCCGTG 60.463 55.000 0.00 0.00 0.00 4.94
172 174 0.034337 TTTTGACGGACGGGGAGAAG 59.966 55.000 0.00 0.00 0.00 2.85
212 214 3.486584 GAGAGAAAACTTCAGCGCATTG 58.513 45.455 11.47 0.00 0.00 2.82
271 273 2.096248 GAGGCAGTGTACTACAGCTCT 58.904 52.381 10.79 7.59 41.16 4.09
273 275 1.821753 CTGAGGCAGTGTACTACAGCT 59.178 52.381 10.79 0.00 41.16 4.24
274 276 1.134965 CCTGAGGCAGTGTACTACAGC 60.135 57.143 0.00 0.00 40.72 4.40
275 277 2.425312 CTCCTGAGGCAGTGTACTACAG 59.575 54.545 0.00 0.00 0.00 2.74
276 278 2.041216 TCTCCTGAGGCAGTGTACTACA 59.959 50.000 0.00 0.00 0.00 2.74
298 300 0.038801 TGTGCACGAGAGAAGCTGAG 60.039 55.000 13.13 0.00 36.80 3.35
328 334 4.426313 GGGCTGTGGTACCCTGCC 62.426 72.222 28.17 28.17 43.36 4.85
634 662 2.515996 ATCGGGTGGCGGTGTTGTAG 62.516 60.000 0.00 0.00 0.00 2.74
639 667 2.890766 AAGAATCGGGTGGCGGTGT 61.891 57.895 0.00 0.00 0.00 4.16
648 691 1.884926 GAGAGCGCCAAGAATCGGG 60.885 63.158 2.29 0.00 0.00 5.14
676 719 2.758089 GCCACGATCCAAGCAGCAG 61.758 63.158 0.00 0.00 0.00 4.24
717 764 3.838565 TCTTGGGCCTCTGATCTAGTAG 58.161 50.000 4.53 0.00 0.00 2.57
718 765 3.973472 TCTTGGGCCTCTGATCTAGTA 57.027 47.619 4.53 0.00 0.00 1.82
719 766 2.856760 TCTTGGGCCTCTGATCTAGT 57.143 50.000 4.53 0.00 0.00 2.57
859 908 4.058817 GCTCACTGTAAACTGCACTTAGT 58.941 43.478 0.00 0.00 0.00 2.24
874 928 6.803320 ACAAAATACAATCGAATTGCTCACTG 59.197 34.615 0.00 0.00 43.98 3.66
879 933 7.798052 GCAAAAACAAAATACAATCGAATTGCT 59.202 29.630 0.00 0.00 43.98 3.91
891 945 7.222611 TCAGAAGCAGAAGCAAAAACAAAATAC 59.777 33.333 0.00 0.00 45.49 1.89
903 960 3.567164 CCTTTTCTTCAGAAGCAGAAGCA 59.433 43.478 5.15 0.00 45.49 3.91
911 968 3.120060 CCGACATGCCTTTTCTTCAGAAG 60.120 47.826 3.45 3.45 35.21 2.85
917 974 1.250840 GGCCCGACATGCCTTTTCTT 61.251 55.000 0.00 0.00 45.70 2.52
919 976 2.885113 GGCCCGACATGCCTTTTC 59.115 61.111 0.00 0.00 45.70 2.29
941 1002 1.002502 GGTAGGGTGACAAGTGGGC 60.003 63.158 0.00 0.00 0.00 5.36
953 1014 2.499827 GCGAGGCTACAGGGTAGGG 61.500 68.421 5.63 0.00 0.00 3.53
1083 1154 4.814294 AGCGACGGACATTCGGGC 62.814 66.667 0.00 0.00 36.96 6.13
1084 1155 2.885644 CAGCGACGGACATTCGGG 60.886 66.667 0.00 0.00 36.96 5.14
1713 1795 0.811281 GCCTGTAACAGTCCAATGCC 59.189 55.000 0.00 0.00 0.00 4.40
1746 1829 2.897350 TCCCAGTAACCAAGAGCTACA 58.103 47.619 0.00 0.00 0.00 2.74
1801 1884 4.278170 CCAACTGATGCTTACACTGGAAAA 59.722 41.667 0.00 0.00 0.00 2.29
1950 2033 2.499693 ACAACCCCCAAAAAGACAGTTG 59.500 45.455 0.00 0.00 39.14 3.16
1951 2034 2.764010 GACAACCCCCAAAAAGACAGTT 59.236 45.455 0.00 0.00 0.00 3.16
2002 2085 6.732531 TGATCAGAACACTTCATTAAGCTG 57.267 37.500 0.00 0.00 36.05 4.24
2066 2149 2.801063 CATAACATTGCAGCGAAAGGG 58.199 47.619 0.00 0.00 0.00 3.95
2098 2181 9.845214 ACACCCTTTTCCTATCTCTATATACAT 57.155 33.333 0.00 0.00 0.00 2.29
2185 2268 7.658575 ACAATGAAAAAGAAGGATGATGGTTTG 59.341 33.333 0.00 0.00 0.00 2.93
2525 2651 9.225682 TGGAATATACTCCCTCTGTAAAGAAAT 57.774 33.333 0.00 0.00 34.22 2.17
2558 2684 8.741101 TGCAAAATTAACTATGCTTTACTGTG 57.259 30.769 8.95 0.00 39.49 3.66
2612 2738 7.775093 GCCAATCAGGTATATTAGCATCCATAA 59.225 37.037 0.00 0.00 40.61 1.90
2652 2778 3.318017 ACTCAGATACAGTGAAACGTGC 58.682 45.455 0.00 0.00 45.86 5.34
2655 2781 5.312120 AGGTACTCAGATACAGTGAAACG 57.688 43.478 0.00 0.00 45.86 3.60
2697 2823 8.382405 TCAACATATTAAGCTAAGGGCATCATA 58.618 33.333 0.00 0.00 44.79 2.15
2851 2987 1.071605 GCTAGAAGACCGCAGTGTTG 58.928 55.000 0.00 0.00 27.73 3.33
2857 2993 2.037251 ACTTCAAAGCTAGAAGACCGCA 59.963 45.455 26.61 0.00 44.00 5.69
2913 3049 7.021196 CACCTCGGTAAACTATTTTGATGTTG 58.979 38.462 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.