Multiple sequence alignment - TraesCS5B01G315200

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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 TraesCS5B01G315200 chr5B 100.000 2549 0 0 1 2549 497275599 497278147 0 4708
1 TraesCS5B01G315200 chr5B 95.665 1984 82 3 567 2549 643490988 643489008 0 3184
2 TraesCS5B01G315200 chr1B 96.175 1987 71 4 567 2549 581717561 581715576 0 3243
3 TraesCS5B01G315200 chr1B 95.766 1984 78 5 567 2549 520844119 520842141 0 3193
4 TraesCS5B01G315200 chr7B 95.974 1987 74 5 567 2549 677862790 677860806 0 3221
5 TraesCS5B01G315200 chr7B 95.921 1986 75 4 567 2549 720989190 720987208 0 3214
6 TraesCS5B01G315200 chr4A 95.840 1995 78 4 556 2549 705529262 705527272 0 3219
7 TraesCS5B01G315200 chr2B 95.785 1993 79 4 559 2549 692955888 692957877 0 3210
8 TraesCS5B01G315200 chr2B 95.541 1996 81 6 556 2549 458657413 458659402 0 3186
9 TraesCS5B01G315200 chr2B 95.580 1991 76 11 567 2549 492636665 492638651 0 3179
10 TraesCS5B01G315200 chr5D 90.510 569 51 2 1 566 537360598 537361166 0 749
11 TraesCS5B01G315200 chr5D 89.062 576 50 8 1 565 55773513 55774086 0 702
12 TraesCS5B01G315200 chr1D 89.565 575 48 7 1 566 283091536 283092107 0 719
13 TraesCS5B01G315200 chr1D 88.831 573 54 7 1 566 313377449 313378018 0 695
14 TraesCS5B01G315200 chr1D 88.792 571 53 8 4 566 316691026 316690459 0 689
15 TraesCS5B01G315200 chr2D 89.317 571 53 6 1 566 157860604 157861171 0 710
16 TraesCS5B01G315200 chr7D 89.005 573 51 7 4 566 268986908 268986338 0 699
17 TraesCS5B01G315200 chr4D 88.850 574 51 8 4 566 223602844 223602273 0 693
18 TraesCS5B01G315200 chr4D 88.869 566 58 4 4 566 410159864 410159301 0 691


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 TraesCS5B01G315200 chr5B 497275599 497278147 2548 False 4708 4708 100.000 1 2549 1 chr5B.!!$F1 2548
1 TraesCS5B01G315200 chr5B 643489008 643490988 1980 True 3184 3184 95.665 567 2549 1 chr5B.!!$R1 1982
2 TraesCS5B01G315200 chr1B 581715576 581717561 1985 True 3243 3243 96.175 567 2549 1 chr1B.!!$R2 1982
3 TraesCS5B01G315200 chr1B 520842141 520844119 1978 True 3193 3193 95.766 567 2549 1 chr1B.!!$R1 1982
4 TraesCS5B01G315200 chr7B 677860806 677862790 1984 True 3221 3221 95.974 567 2549 1 chr7B.!!$R1 1982
5 TraesCS5B01G315200 chr7B 720987208 720989190 1982 True 3214 3214 95.921 567 2549 1 chr7B.!!$R2 1982
6 TraesCS5B01G315200 chr4A 705527272 705529262 1990 True 3219 3219 95.840 556 2549 1 chr4A.!!$R1 1993
7 TraesCS5B01G315200 chr2B 692955888 692957877 1989 False 3210 3210 95.785 559 2549 1 chr2B.!!$F3 1990
8 TraesCS5B01G315200 chr2B 458657413 458659402 1989 False 3186 3186 95.541 556 2549 1 chr2B.!!$F1 1993
9 TraesCS5B01G315200 chr2B 492636665 492638651 1986 False 3179 3179 95.580 567 2549 1 chr2B.!!$F2 1982
10 TraesCS5B01G315200 chr5D 537360598 537361166 568 False 749 749 90.510 1 566 1 chr5D.!!$F2 565
11 TraesCS5B01G315200 chr5D 55773513 55774086 573 False 702 702 89.062 1 565 1 chr5D.!!$F1 564
12 TraesCS5B01G315200 chr1D 283091536 283092107 571 False 719 719 89.565 1 566 1 chr1D.!!$F1 565
13 TraesCS5B01G315200 chr1D 313377449 313378018 569 False 695 695 88.831 1 566 1 chr1D.!!$F2 565
14 TraesCS5B01G315200 chr1D 316690459 316691026 567 True 689 689 88.792 4 566 1 chr1D.!!$R1 562
15 TraesCS5B01G315200 chr2D 157860604 157861171 567 False 710 710 89.317 1 566 1 chr2D.!!$F1 565
16 TraesCS5B01G315200 chr7D 268986338 268986908 570 True 699 699 89.005 4 566 1 chr7D.!!$R1 562
17 TraesCS5B01G315200 chr4D 223602273 223602844 571 True 693 693 88.850 4 566 1 chr4D.!!$R1 562
18 TraesCS5B01G315200 chr4D 410159301 410159864 563 True 691 691 88.869 4 566 1 chr4D.!!$R2 562

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
424 432 0.325272 AAGCTTCGGGGGTCTCTTTC 59.675 55.0 0.0 0.0 0.0 2.62 F
1073 1083 0.171455 GAGATGCCTGTCTTCGTCGT 59.829 55.0 0.0 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1311 1321 1.213275 CAGCATGCGCAACCATTCA 59.787 52.632 17.11 0.0 42.27 2.57 R
2389 2409 2.027460 CCAAAACCACGTGGCAGC 59.973 61.111 34.26 0.0 39.32 5.25 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
29 30 9.639563 TTAACAAAGCCCATGATATATGAAGAA 57.360 29.630 0.00 0.00 0.00 2.52
56 63 3.631686 ACATCTCAAGATCACGAGAGAGG 59.368 47.826 16.40 14.74 41.39 3.69
61 68 3.634448 TCAAGATCACGAGAGAGGGATTC 59.366 47.826 0.00 0.00 0.00 2.52
150 157 1.595382 GGGACGATGAAGATGGCCG 60.595 63.158 0.00 0.00 0.00 6.13
200 207 3.198853 GTGCCAGAGAAGGGTCTAGATTT 59.801 47.826 0.00 0.00 32.80 2.17
329 336 2.238353 CCTCAAGGTGAGCACAACG 58.762 57.895 2.75 0.00 42.98 4.10
335 342 3.106552 GTGAGCACAACGCACCAA 58.893 55.556 0.00 0.00 46.13 3.67
340 347 3.041701 CACAACGCACCAAGGCAT 58.958 55.556 0.00 0.00 0.00 4.40
372 379 3.112709 GCACGCCTCGGTGTCTTC 61.113 66.667 0.00 0.00 40.08 2.87
382 389 1.005097 TCGGTGTCTTCTGCCCTACTA 59.995 52.381 0.00 0.00 0.00 1.82
383 390 1.405821 CGGTGTCTTCTGCCCTACTAG 59.594 57.143 0.00 0.00 0.00 2.57
424 432 0.325272 AAGCTTCGGGGGTCTCTTTC 59.675 55.000 0.00 0.00 0.00 2.62
545 555 3.427503 CGGGTTAGTTCCATGCAAATCAC 60.428 47.826 0.00 0.00 0.00 3.06
547 557 4.380867 GGGTTAGTTCCATGCAAATCACAG 60.381 45.833 0.00 0.00 0.00 3.66
660 670 4.514577 CCCCTAGTCCGTGCGCAG 62.515 72.222 12.22 4.91 0.00 5.18
760 770 6.264067 GCAGAGGTGGCTAATTTTATTCAGAT 59.736 38.462 0.00 0.00 0.00 2.90
845 855 2.074547 GCTATATTAGCGGGCGACAA 57.925 50.000 0.00 0.00 42.62 3.18
1072 1082 0.526524 GGAGATGCCTGTCTTCGTCG 60.527 60.000 0.00 0.00 0.00 5.12
1073 1083 0.171455 GAGATGCCTGTCTTCGTCGT 59.829 55.000 0.00 0.00 0.00 4.34
1132 1142 1.133915 ACACACCGAGGAACCACAATT 60.134 47.619 0.00 0.00 0.00 2.32
1140 1150 2.621526 GAGGAACCACAATTGTCCGTTT 59.378 45.455 17.44 6.89 0.00 3.60
1142 1152 3.120041 GGAACCACAATTGTCCGTTTTG 58.880 45.455 17.44 3.23 0.00 2.44
1144 1154 1.754226 ACCACAATTGTCCGTTTTGCT 59.246 42.857 8.48 0.00 0.00 3.91
1146 1156 2.794350 CCACAATTGTCCGTTTTGCTTC 59.206 45.455 8.48 0.00 0.00 3.86
1161 1171 1.442769 GCTTCTGCAACGAGAATGGA 58.557 50.000 0.00 0.00 39.41 3.41
1215 1225 1.480545 TCGGGATCTTTGAGCAATCGA 59.519 47.619 0.00 0.00 0.00 3.59
1237 1247 1.276138 TGATCTGCTCCGTGTTCATGT 59.724 47.619 0.00 0.00 0.00 3.21
1311 1321 3.682696 TGAACTGCAAGAAGAGCATGAT 58.317 40.909 0.00 0.00 41.82 2.45
1704 1718 9.755804 AAGAAATGAGGAATTCAGAAACTTTTC 57.244 29.630 7.93 11.63 39.68 2.29
1861 1875 3.229293 TGTCATGGAAAATGTGCCTCAA 58.771 40.909 0.00 0.00 0.00 3.02
2055 2070 1.538419 GGTAACCGCTAGGACAGATGC 60.538 57.143 0.00 0.00 41.02 3.91
2200 2218 1.569548 TGGGTTTGTGGTGTTTAGGGA 59.430 47.619 0.00 0.00 0.00 4.20
2327 2347 2.881266 TTTGCACACGCGTGAGAGC 61.881 57.895 42.94 36.65 46.80 4.09
2328 2348 4.583866 TGCACACGCGTGAGAGCA 62.584 61.111 42.94 38.42 46.80 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.066892 TCTTCATATATCATGGGCTTTGTTAAC 57.933 33.333 0.00 0.00 0.00 2.01
21 22 8.480501 TGATCTTGAGATGTCACATTCTTCATA 58.519 33.333 0.00 0.00 34.37 2.15
24 25 6.237781 CGTGATCTTGAGATGTCACATTCTTC 60.238 42.308 12.63 0.00 34.37 2.87
29 30 4.400567 TCTCGTGATCTTGAGATGTCACAT 59.599 41.667 11.83 0.00 36.36 3.21
45 46 2.231478 GTGTTGAATCCCTCTCTCGTGA 59.769 50.000 0.00 0.00 0.00 4.35
56 63 4.770795 ACCAGTAGCTATGTGTTGAATCC 58.229 43.478 0.00 0.00 0.00 3.01
61 68 5.121768 GGTTTGTACCAGTAGCTATGTGTTG 59.878 44.000 0.00 0.00 44.36 3.33
136 143 3.341043 CGGCGGCCATCTTCATCG 61.341 66.667 20.71 0.00 0.00 3.84
150 157 2.427753 GGGGAGATCATCACCGGC 59.572 66.667 0.00 0.00 43.24 6.13
186 193 6.371389 CACGAAAAACAAATCTAGACCCTTC 58.629 40.000 0.00 0.00 0.00 3.46
187 194 5.240844 CCACGAAAAACAAATCTAGACCCTT 59.759 40.000 0.00 0.00 0.00 3.95
200 207 2.223618 GCCTTTGTAGCCACGAAAAACA 60.224 45.455 0.00 0.00 0.00 2.83
329 336 3.305177 CTTGCCCATGCCTTGGTGC 62.305 63.158 2.44 5.88 44.83 5.01
362 369 0.251653 AGTAGGGCAGAAGACACCGA 60.252 55.000 0.00 0.00 0.00 4.69
372 379 2.428890 CAGAAGGTGACTAGTAGGGCAG 59.571 54.545 0.00 0.00 42.68 4.85
518 528 1.483415 GCATGGAACTAACCCGGACTA 59.517 52.381 0.73 0.00 0.00 2.59
545 555 6.413892 ACCCCAATTTTATATGGTTTTGCTG 58.586 36.000 0.00 0.00 34.79 4.41
547 557 8.794335 TTAACCCCAATTTTATATGGTTTTGC 57.206 30.769 0.00 0.00 37.31 3.68
660 670 3.354397 CAAAGTTCACAGAACAAGTCGC 58.646 45.455 11.92 0.00 0.00 5.19
666 676 1.668751 GACGCCAAAGTTCACAGAACA 59.331 47.619 11.92 0.00 0.00 3.18
742 752 7.922278 GTGCAATGATCTGAATAAAATTAGCCA 59.078 33.333 0.00 0.00 0.00 4.75
746 756 6.632434 CGCGTGCAATGATCTGAATAAAATTA 59.368 34.615 0.00 0.00 0.00 1.40
760 770 2.977456 AAGCCACGCGTGCAATGA 60.977 55.556 33.17 0.00 0.00 2.57
1048 1058 1.002430 GAAGACAGGCATCTCCACACA 59.998 52.381 0.00 0.00 37.29 3.72
1096 1106 1.697432 TGTGTGAGAAACCCTCCGATT 59.303 47.619 0.00 0.00 41.25 3.34
1142 1152 1.396301 CTCCATTCTCGTTGCAGAAGC 59.604 52.381 0.00 0.00 35.83 3.86
1144 1154 2.839486 ACTCCATTCTCGTTGCAGAA 57.161 45.000 0.00 0.00 36.82 3.02
1146 1156 3.849911 TCTTACTCCATTCTCGTTGCAG 58.150 45.455 0.00 0.00 0.00 4.41
1151 1161 3.068307 CCCGATTCTTACTCCATTCTCGT 59.932 47.826 0.00 0.00 0.00 4.18
1161 1171 2.024414 GCAATTGCCCCGATTCTTACT 58.976 47.619 20.06 0.00 34.31 2.24
1215 1225 2.768253 TGAACACGGAGCAGATCAAT 57.232 45.000 0.00 0.00 0.00 2.57
1224 1234 2.007049 GCCACCTACATGAACACGGAG 61.007 57.143 0.00 0.00 0.00 4.63
1237 1247 3.439857 AAGAAAGAAGCATGCCACCTA 57.560 42.857 15.66 0.00 0.00 3.08
1311 1321 1.213275 CAGCATGCGCAACCATTCA 59.787 52.632 17.11 0.00 42.27 2.57
1360 1370 1.781786 CCCTCCATCTCTTCTTCCGA 58.218 55.000 0.00 0.00 0.00 4.55
1420 1430 5.531287 GCTTCCTAACCTTCTTCTTCAACAA 59.469 40.000 0.00 0.00 0.00 2.83
1704 1718 7.946655 ATTCATTAGCTGCATTTCATTGATG 57.053 32.000 1.02 0.00 0.00 3.07
1861 1875 6.153000 CACTAGGTGTAAACATCTACCAGAGT 59.847 42.308 0.00 0.00 38.47 3.24
2055 2070 3.347216 CCTACCCATGTCAAACTCTTGG 58.653 50.000 0.00 0.00 33.01 3.61
2327 2347 6.959671 TTAGTGCAAAACAAAGGAAAACTG 57.040 33.333 0.00 0.00 0.00 3.16
2328 2348 7.971183 TTTTAGTGCAAAACAAAGGAAAACT 57.029 28.000 0.00 0.00 31.05 2.66
2389 2409 2.027460 CCAAAACCACGTGGCAGC 59.973 61.111 34.26 0.00 39.32 5.25


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

AutoCloner maintained by Alex Coulton.