Multiple sequence alignment - TraesCS2D01G190700

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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 TraesCS2D01G190700 chr2D 100.000 3812 0 0 1 3812 134789880 134793691 0.000000e+00 7040
1 TraesCS2D01G190700 chr2B 95.647 3859 91 24 1 3812 191741220 191745048 0.000000e+00 6124
2 TraesCS2D01G190700 chr2A 96.042 3638 67 24 195 3812 142707146 142710726 0.000000e+00 5849
3 TraesCS2D01G190700 chr2A 83.500 200 6 8 1 198 142706679 142706853 1.100000e-35 161


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 TraesCS2D01G190700 chr2D 134789880 134793691 3811 False 7040 7040 100.000 1 3812 1 chr2D.!!$F1 3811
1 TraesCS2D01G190700 chr2B 191741220 191745048 3828 False 6124 6124 95.647 1 3812 1 chr2B.!!$F1 3811
2 TraesCS2D01G190700 chr2A 142706679 142710726 4047 False 3005 5849 89.771 1 3812 2 chr2A.!!$F1 3811

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
147 150 0.035056 CACCAACCTCCCCACTCATC 60.035 60.0 0.0 0.0 0.0 2.92 F
177 181 0.175989 GAGAACTTAGGGGAGCCACG 59.824 60.0 0.0 0.0 0.0 4.94 F
395 701 0.179089 CCATTGACCAGCGAGAGGAG 60.179 60.0 0.0 0.0 0.0 3.69 F
659 978 0.179113 GAGAGGAGAAAGAGGCAGCG 60.179 60.0 0.0 0.0 0.0 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2047 2405 0.039618 GCCATCCCCCTCTTTCACAA 59.960 55.000 0.00 0.00 0.00 3.33 R
2565 2923 2.557924 GTGGATGCATTCAAGAACCACA 59.442 45.455 20.72 0.85 43.59 4.17 R
2688 3046 1.006086 TATTCACATTCCACGCAGCG 58.994 50.000 14.82 14.82 0.00 5.18 R
2969 3327 4.728772 ACTGAGTATCTGGATCTCTCCTG 58.271 47.826 0.00 0.00 42.59 3.86 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
106 109 7.394872 GTTCATGTCAACGATATTCTTCTCAC 58.605 38.462 0.00 0.00 0.00 3.51
110 113 5.044558 GTCAACGATATTCTTCTCACCCTC 58.955 45.833 0.00 0.00 0.00 4.30
111 114 4.709886 TCAACGATATTCTTCTCACCCTCA 59.290 41.667 0.00 0.00 0.00 3.86
112 115 4.657436 ACGATATTCTTCTCACCCTCAC 57.343 45.455 0.00 0.00 0.00 3.51
113 116 3.385111 ACGATATTCTTCTCACCCTCACC 59.615 47.826 0.00 0.00 0.00 4.02
114 117 3.243907 CGATATTCTTCTCACCCTCACCC 60.244 52.174 0.00 0.00 0.00 4.61
115 118 2.350863 ATTCTTCTCACCCTCACCCT 57.649 50.000 0.00 0.00 0.00 4.34
116 119 1.645710 TTCTTCTCACCCTCACCCTC 58.354 55.000 0.00 0.00 0.00 4.30
117 120 0.487325 TCTTCTCACCCTCACCCTCA 59.513 55.000 0.00 0.00 0.00 3.86
118 121 0.610687 CTTCTCACCCTCACCCTCAC 59.389 60.000 0.00 0.00 0.00 3.51
119 122 0.105194 TTCTCACCCTCACCCTCACA 60.105 55.000 0.00 0.00 0.00 3.58
120 123 0.832135 TCTCACCCTCACCCTCACAC 60.832 60.000 0.00 0.00 0.00 3.82
147 150 0.035056 CACCAACCTCCCCACTCATC 60.035 60.000 0.00 0.00 0.00 2.92
148 151 0.475632 ACCAACCTCCCCACTCATCA 60.476 55.000 0.00 0.00 0.00 3.07
149 152 0.921896 CCAACCTCCCCACTCATCAT 59.078 55.000 0.00 0.00 0.00 2.45
159 162 2.371841 CCCACTCATCATTAATCCCCGA 59.628 50.000 0.00 0.00 0.00 5.14
177 181 0.175989 GAGAACTTAGGGGAGCCACG 59.824 60.000 0.00 0.00 0.00 4.94
363 669 1.908793 CACTGACACTCCGTCCCCT 60.909 63.158 0.00 0.00 44.71 4.79
366 672 2.283676 GACACTCCGTCCCCTCCA 60.284 66.667 0.00 0.00 38.85 3.86
379 685 3.736224 CTCCACAGCTGGCCCCAT 61.736 66.667 19.93 0.00 37.49 4.00
380 686 3.267233 TCCACAGCTGGCCCCATT 61.267 61.111 19.93 0.00 37.49 3.16
393 699 1.153289 CCCATTGACCAGCGAGAGG 60.153 63.158 0.00 0.00 0.00 3.69
395 701 0.179089 CCATTGACCAGCGAGAGGAG 60.179 60.000 0.00 0.00 0.00 3.69
397 703 1.333636 ATTGACCAGCGAGAGGAGGG 61.334 60.000 0.00 0.00 0.00 4.30
398 704 3.151022 GACCAGCGAGAGGAGGGG 61.151 72.222 0.00 0.00 0.00 4.79
543 852 3.143728 GCAGTAAAAACTCGGGAAGGAA 58.856 45.455 0.00 0.00 0.00 3.36
544 853 3.188667 GCAGTAAAAACTCGGGAAGGAAG 59.811 47.826 0.00 0.00 0.00 3.46
545 854 3.188667 CAGTAAAAACTCGGGAAGGAAGC 59.811 47.826 0.00 0.00 0.00 3.86
563 878 2.438614 AGTAGCTGCGGCGAGAGA 60.439 61.111 12.98 0.00 44.37 3.10
585 904 2.478831 GAAAGATTAGCAGCGAGAGGG 58.521 52.381 0.00 0.00 0.00 4.30
586 905 1.781786 AAGATTAGCAGCGAGAGGGA 58.218 50.000 0.00 0.00 0.00 4.20
587 906 1.327303 AGATTAGCAGCGAGAGGGAG 58.673 55.000 0.00 0.00 0.00 4.30
588 907 0.316841 GATTAGCAGCGAGAGGGAGG 59.683 60.000 0.00 0.00 0.00 4.30
659 978 0.179113 GAGAGGAGAAAGAGGCAGCG 60.179 60.000 0.00 0.00 0.00 5.18
1206 1563 5.086621 ACTGTTGCTTTCAGGGGATTTATT 58.913 37.500 7.87 0.00 37.25 1.40
1207 1564 6.252995 ACTGTTGCTTTCAGGGGATTTATTA 58.747 36.000 7.87 0.00 37.25 0.98
1208 1565 6.897413 ACTGTTGCTTTCAGGGGATTTATTAT 59.103 34.615 7.87 0.00 37.25 1.28
1209 1566 7.400052 ACTGTTGCTTTCAGGGGATTTATTATT 59.600 33.333 7.87 0.00 37.25 1.40
1495 1853 4.520111 TGCCTGCATTATTATGTCCACATC 59.480 41.667 0.00 0.00 37.76 3.06
1499 1857 6.713903 CCTGCATTATTATGTCCACATCTTCT 59.286 38.462 0.00 0.00 37.76 2.85
1584 1942 6.524101 AACCATGCGGATAAAATACTTTGT 57.476 33.333 0.00 0.00 35.59 2.83
1620 1978 5.805486 ACACGAACTTAGTACATATGCAGTG 59.195 40.000 1.58 0.00 0.00 3.66
1635 1993 2.369860 TGCAGTGTGAAGATGAGGTTCT 59.630 45.455 0.00 0.00 0.00 3.01
1638 1996 3.188048 CAGTGTGAAGATGAGGTTCTTGC 59.812 47.826 0.00 0.00 36.10 4.01
1650 2008 1.457346 GTTCTTGCTAGCATGCCAGT 58.543 50.000 20.13 0.00 0.00 4.00
1659 2017 2.338577 AGCATGCCAGTACTTGATCC 57.661 50.000 15.66 0.00 0.00 3.36
1951 2309 0.981183 ACCCACAGCAATACGAAGGA 59.019 50.000 0.00 0.00 0.00 3.36
2559 2917 0.380378 GTGCTTCTTGCCGTGTTCAA 59.620 50.000 0.00 0.00 42.00 2.69
2565 2923 1.347707 TCTTGCCGTGTTCAAGGAGAT 59.652 47.619 8.81 0.00 40.82 2.75
2688 3046 7.425577 TGGATTGAATCGTGATGATATTGAC 57.574 36.000 0.00 0.00 35.84 3.18
2757 3115 3.494045 GTGCTAAATTCACCTGCTTCC 57.506 47.619 0.00 0.00 0.00 3.46
2771 3129 2.163815 CTGCTTCCATGCCTTTCTTCAG 59.836 50.000 0.00 0.00 0.00 3.02
2858 3216 5.548056 ACTCTTTTCAGACCCTCATTCCTTA 59.452 40.000 0.00 0.00 0.00 2.69
3394 3752 2.156504 GCAGTGATGAAGTTCAGTGTCG 59.843 50.000 11.91 1.31 45.08 4.35
3419 3777 5.353956 CACAGGTGAATCCACGAAAATATCA 59.646 40.000 0.00 0.00 44.09 2.15
3430 3788 5.965334 CCACGAAAATATCAACATACACTGC 59.035 40.000 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.158534 TCTACTGCCAAAGGGAGCAAAA 60.159 45.455 4.35 0.00 45.32 2.44
16 17 5.222631 GTCAAATTGTTCTACTGCCAAAGG 58.777 41.667 0.00 0.00 0.00 3.11
17 18 5.221224 TGGTCAAATTGTTCTACTGCCAAAG 60.221 40.000 0.00 0.00 0.00 2.77
18 19 4.646945 TGGTCAAATTGTTCTACTGCCAAA 59.353 37.500 0.00 0.00 0.00 3.28
96 99 2.192263 GAGGGTGAGGGTGAGAAGAAT 58.808 52.381 0.00 0.00 0.00 2.40
106 109 2.146724 TGTGGTGTGAGGGTGAGGG 61.147 63.158 0.00 0.00 0.00 4.30
110 113 1.525995 GTGGTGTGGTGTGAGGGTG 60.526 63.158 0.00 0.00 0.00 4.61
111 114 1.998438 TGTGGTGTGGTGTGAGGGT 60.998 57.895 0.00 0.00 0.00 4.34
112 115 1.525995 GTGTGGTGTGGTGTGAGGG 60.526 63.158 0.00 0.00 0.00 4.30
113 116 1.525995 GGTGTGGTGTGGTGTGAGG 60.526 63.158 0.00 0.00 0.00 3.86
114 117 0.393673 TTGGTGTGGTGTGGTGTGAG 60.394 55.000 0.00 0.00 0.00 3.51
115 118 0.678366 GTTGGTGTGGTGTGGTGTGA 60.678 55.000 0.00 0.00 0.00 3.58
116 119 1.662438 GGTTGGTGTGGTGTGGTGTG 61.662 60.000 0.00 0.00 0.00 3.82
117 120 1.379309 GGTTGGTGTGGTGTGGTGT 60.379 57.895 0.00 0.00 0.00 4.16
118 121 1.077068 AGGTTGGTGTGGTGTGGTG 60.077 57.895 0.00 0.00 0.00 4.17
119 122 1.226262 GAGGTTGGTGTGGTGTGGT 59.774 57.895 0.00 0.00 0.00 4.16
120 123 1.528309 GGAGGTTGGTGTGGTGTGG 60.528 63.158 0.00 0.00 0.00 4.17
147 150 4.642429 CCCTAAGTTCTCGGGGATTAATG 58.358 47.826 0.00 0.00 41.25 1.90
148 151 4.976540 CCCTAAGTTCTCGGGGATTAAT 57.023 45.455 0.00 0.00 41.25 1.40
159 162 1.265454 CCGTGGCTCCCCTAAGTTCT 61.265 60.000 0.00 0.00 0.00 3.01
177 181 0.458669 TAGCCCGACGATTCTTCACC 59.541 55.000 0.00 0.00 0.00 4.02
366 672 2.036256 GTCAATGGGGCCAGCTGT 59.964 61.111 13.81 0.00 0.00 4.40
379 685 1.984570 CCCTCCTCTCGCTGGTCAA 60.985 63.158 0.00 0.00 0.00 3.18
380 686 2.363018 CCCTCCTCTCGCTGGTCA 60.363 66.667 0.00 0.00 0.00 4.02
545 854 2.278466 CTCTCGCCGCAGCTACTG 60.278 66.667 0.00 0.00 36.60 2.74
563 878 2.102252 CCTCTCGCTGCTAATCTTTCCT 59.898 50.000 0.00 0.00 0.00 3.36
585 904 1.208706 CTCCTCCCCCTTTCTTCCTC 58.791 60.000 0.00 0.00 0.00 3.71
586 905 0.253394 CCTCCTCCCCCTTTCTTCCT 60.253 60.000 0.00 0.00 0.00 3.36
587 906 0.253207 TCCTCCTCCCCCTTTCTTCC 60.253 60.000 0.00 0.00 0.00 3.46
588 907 1.208706 CTCCTCCTCCCCCTTTCTTC 58.791 60.000 0.00 0.00 0.00 2.87
659 978 3.371097 TACTACTGCTGCCGCTGCC 62.371 63.158 18.38 2.80 38.51 4.85
973 1304 1.550374 TCCTCTTCCTCCCCCTCCT 60.550 63.158 0.00 0.00 0.00 3.69
1206 1563 9.353431 TGAATTCCAGCTCAAATAATAGCAATA 57.647 29.630 2.27 0.00 41.32 1.90
1207 1564 8.241497 TGAATTCCAGCTCAAATAATAGCAAT 57.759 30.769 2.27 0.00 41.32 3.56
1208 1565 7.340232 ACTGAATTCCAGCTCAAATAATAGCAA 59.660 33.333 2.27 0.00 46.81 3.91
1209 1566 6.830324 ACTGAATTCCAGCTCAAATAATAGCA 59.170 34.615 2.27 0.00 46.81 3.49
1495 1853 0.322008 GGAGGGAGCACCAACAGAAG 60.322 60.000 1.58 0.00 43.89 2.85
1499 1857 1.360393 AAAGGGAGGGAGCACCAACA 61.360 55.000 1.58 0.00 43.89 3.33
1599 1957 6.033966 TCACACTGCATATGTACTAAGTTCG 58.966 40.000 4.29 0.00 0.00 3.95
1602 1960 7.170393 TCTTCACACTGCATATGTACTAAGT 57.830 36.000 4.29 0.00 0.00 2.24
1620 1978 3.620821 GCTAGCAAGAACCTCATCTTCAC 59.379 47.826 10.63 0.00 37.56 3.18
1635 1993 2.027285 TCAAGTACTGGCATGCTAGCAA 60.027 45.455 28.88 15.87 35.83 3.91
1638 1996 3.397482 GGATCAAGTACTGGCATGCTAG 58.603 50.000 27.56 27.56 0.00 3.42
1650 2008 6.001460 ACAAAAATGGAGAACGGATCAAGTA 58.999 36.000 0.00 0.00 0.00 2.24
1659 2017 7.653767 ACTAAGACTACAAAAATGGAGAACG 57.346 36.000 0.00 0.00 0.00 3.95
1951 2309 1.606531 GAGCTGAAGGAGTGGGCAT 59.393 57.895 0.00 0.00 0.00 4.40
2047 2405 0.039618 GCCATCCCCCTCTTTCACAA 59.960 55.000 0.00 0.00 0.00 3.33
2559 2917 3.245016 TGCATTCAAGAACCACATCTCCT 60.245 43.478 0.00 0.00 0.00 3.69
2565 2923 2.557924 GTGGATGCATTCAAGAACCACA 59.442 45.455 20.72 0.85 43.59 4.17
2688 3046 1.006086 TATTCACATTCCACGCAGCG 58.994 50.000 14.82 14.82 0.00 5.18
2757 3115 6.982724 AGAAAAGAAAACTGAAGAAAGGCATG 59.017 34.615 0.00 0.00 0.00 4.06
2771 3129 6.528072 CACAGGAGACAAACAGAAAAGAAAAC 59.472 38.462 0.00 0.00 0.00 2.43
2969 3327 4.728772 ACTGAGTATCTGGATCTCTCCTG 58.271 47.826 0.00 0.00 42.59 3.86
3394 3752 1.234821 TTTCGTGGATTCACCTGTGC 58.765 50.000 0.00 0.00 40.65 4.57
3419 3777 3.832490 TGTAGTCCAGAGCAGTGTATGTT 59.168 43.478 0.00 0.00 0.00 2.71
3430 3788 3.583806 CTGAAAGCAGTGTAGTCCAGAG 58.416 50.000 0.00 0.00 37.37 3.35


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

AutoCloner maintained by Alex Coulton.