Multiple sequence alignment - TraesCS4D01G185500

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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 TraesCS4D01G185500 chr4D 100.000 2504 0 0 1 2504 323373601 323371098 0.000000e+00 4625.0
1 TraesCS4D01G185500 chr4A 92.530 1593 65 15 268 1814 148546998 148548582 0.000000e+00 2233.0
2 TraesCS4D01G185500 chr4A 89.118 726 23 14 1798 2502 148548730 148549420 0.000000e+00 852.0
3 TraesCS4D01G185500 chr4A 97.458 236 6 0 1 236 148546526 148546761 1.080000e-108 403.0
4 TraesCS4D01G185500 chr4B 91.584 1509 81 19 942 2415 403674704 403673207 0.000000e+00 2041.0
5 TraesCS4D01G185500 chr4B 91.184 760 25 10 48 781 403675841 403675098 0.000000e+00 994.0
6 TraesCS4D01G185500 chr4B 97.959 49 1 0 2448 2496 403671853 403671805 4.440000e-13 86.1


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 TraesCS4D01G185500 chr4D 323371098 323373601 2503 True 4625.000000 4625 100.000000 1 2504 1 chr4D.!!$R1 2503
1 TraesCS4D01G185500 chr4A 148546526 148549420 2894 False 1162.666667 2233 93.035333 1 2502 3 chr4A.!!$F1 2501
2 TraesCS4D01G185500 chr4B 403671805 403675841 4036 True 1040.366667 2041 93.575667 48 2496 3 chr4B.!!$R1 2448

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
159 160 0.258774 ACCATACCTCCATTGGCCAC 59.741 55.0 3.88 0.0 33.66 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2013 2722 0.097325 TCGTTTGTGTGCAACGAACC 59.903 50.0 18.47 8.03 46.62 3.62 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
139 140 4.123276 TCGTGTGAATTTTCGTTAGCAC 57.877 40.909 0.00 0.00 0.00 4.40
159 160 0.258774 ACCATACCTCCATTGGCCAC 59.741 55.000 3.88 0.00 33.66 5.01
268 490 7.890515 TGCACCATTGTTTCATCAGTAATAAA 58.109 30.769 0.00 0.00 0.00 1.40
324 546 3.181454 ACAAAGGACACCTCGAATGAACT 60.181 43.478 3.45 0.00 30.89 3.01
414 660 1.418264 TGTCCGGTCATGGAAGTTTCA 59.582 47.619 0.00 0.00 40.44 2.69
475 721 2.259439 GCTGCAGCACTGACAGCTT 61.259 57.895 33.36 0.00 46.76 3.74
652 904 4.065088 TCGTTCCCAGAAGAAACATCAAG 58.935 43.478 0.00 0.00 0.00 3.02
856 1108 5.625568 AGTGGTAGTAGTGTGTTTCCTTT 57.374 39.130 0.00 0.00 0.00 3.11
857 1109 5.608449 AGTGGTAGTAGTGTGTTTCCTTTC 58.392 41.667 0.00 0.00 0.00 2.62
858 1110 4.753610 GTGGTAGTAGTGTGTTTCCTTTCC 59.246 45.833 0.00 0.00 0.00 3.13
859 1111 4.657039 TGGTAGTAGTGTGTTTCCTTTCCT 59.343 41.667 0.00 0.00 0.00 3.36
860 1112 5.131475 TGGTAGTAGTGTGTTTCCTTTCCTT 59.869 40.000 0.00 0.00 0.00 3.36
910 1162 0.798776 CTCCGGCTTGCAAGTAAGTG 59.201 55.000 26.55 12.48 0.00 3.16
965 1457 1.153449 TAGGAGCGGGAATTGCGTG 60.153 57.895 0.00 0.00 37.44 5.34
1125 1617 2.580867 GCGCAGAGATCTCGCGTT 60.581 61.111 37.35 16.70 46.16 4.84
1308 1800 0.106268 TCCAGCAGCAAAACTCCCAA 60.106 50.000 0.00 0.00 0.00 4.12
1315 1807 1.172812 GCAAAACTCCCAACTCCGCT 61.173 55.000 0.00 0.00 0.00 5.52
1583 2086 0.305922 GATGTGAGCTATGGCGTTGC 59.694 55.000 4.93 4.93 44.37 4.17
1586 2089 2.108514 TGAGCTATGGCGTTGCTGC 61.109 57.895 20.07 11.77 44.37 5.25
1617 2120 2.900716 TGCCCTACTTTTGTTTTGGC 57.099 45.000 0.00 0.00 38.66 4.52
1681 2190 5.655488 AGAGTGTGATGTGTTGCTCTATAC 58.345 41.667 0.00 0.00 32.32 1.47
1729 2238 2.254918 TGTGAAGTTGTGTTGTTGCG 57.745 45.000 0.00 0.00 0.00 4.85
1778 2292 6.847400 TCTAGCAGATCTCGCAAATATCTAC 58.153 40.000 16.20 0.00 0.00 2.59
1779 2293 5.459536 AGCAGATCTCGCAAATATCTACA 57.540 39.130 16.20 0.00 0.00 2.74
1793 2307 2.751166 TCTACAGAAAGCCAGTGAGC 57.249 50.000 0.00 0.00 0.00 4.26
1831 2509 2.799412 CCTTCGCTAGTGCATCATTCTC 59.201 50.000 0.00 0.00 39.64 2.87
1838 2518 4.202202 GCTAGTGCATCATTCTCCAGTAGT 60.202 45.833 0.00 0.00 39.41 2.73
1839 2519 4.833478 AGTGCATCATTCTCCAGTAGTT 57.167 40.909 0.00 0.00 0.00 2.24
1840 2520 5.939764 AGTGCATCATTCTCCAGTAGTTA 57.060 39.130 0.00 0.00 0.00 2.24
1993 2702 9.199982 GCATTCTCAAATCATGAAGAAGAAAAA 57.800 29.630 11.98 2.51 37.67 1.94
2046 2755 4.039032 CACAAACGAACAAATTAACGCCT 58.961 39.130 0.00 0.00 0.00 5.52
2176 2885 0.372679 GACTAGACGTCGATGCGTGA 59.627 55.000 10.46 0.00 45.79 4.35
2177 2886 0.374063 ACTAGACGTCGATGCGTGAG 59.626 55.000 10.46 5.82 45.79 3.51
2232 2941 1.112916 TCTCCTGGCTTGTCGTCACA 61.113 55.000 0.00 0.00 0.00 3.58
2496 4525 8.924511 AGTGTGGATTGGTAATTTCCTATATG 57.075 34.615 2.53 0.00 0.00 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 7.556275 ACCACAACACTCTTCTCAAGAAATAAA 59.444 33.333 0.00 0.00 37.02 1.40
139 140 0.258484 TGGCCAATGGAGGTATGGTG 59.742 55.000 0.61 0.00 36.57 4.17
268 490 5.959618 GGCACCTGTGTATTTTACTTCTT 57.040 39.130 0.00 0.00 0.00 2.52
378 624 4.261801 CCGGACAAATATGAAGGTTCTGT 58.738 43.478 0.00 0.00 0.00 3.41
491 737 0.803117 TTTGTTGTTGCGACGTTGGA 59.197 45.000 4.64 0.00 0.00 3.53
760 1012 0.106419 GGAGGAGGACGATGGAGAGT 60.106 60.000 0.00 0.00 0.00 3.24
818 1070 9.570468 CTACTACCACTACTATACTTTGGATGA 57.430 37.037 0.00 0.00 0.00 2.92
856 1108 3.068590 ACGGAAACAAGAACGTAGAAGGA 59.931 43.478 0.00 0.00 37.85 3.36
857 1109 3.387397 ACGGAAACAAGAACGTAGAAGG 58.613 45.455 0.00 0.00 37.85 3.46
858 1110 4.383948 GGTACGGAAACAAGAACGTAGAAG 59.616 45.833 0.00 0.00 41.71 2.85
859 1111 4.037923 AGGTACGGAAACAAGAACGTAGAA 59.962 41.667 0.00 0.00 41.71 2.10
860 1112 3.569701 AGGTACGGAAACAAGAACGTAGA 59.430 43.478 0.00 0.00 41.71 2.59
910 1162 1.516603 GAGCGGTGGAGAACGTAGC 60.517 63.158 0.00 0.00 0.00 3.58
965 1457 1.160329 ACGCAGAAACACACCAGAGC 61.160 55.000 0.00 0.00 0.00 4.09
1123 1615 2.787915 GCGCTGCTGCCTCTTAAC 59.212 61.111 10.24 0.00 35.36 2.01
1125 1617 3.706563 CTCGCGCTGCTGCCTCTTA 62.707 63.158 5.56 0.00 35.36 2.10
1163 1655 3.531207 CGATCGAGAGCTGGGCCA 61.531 66.667 10.26 5.85 0.00 5.36
1174 1666 1.663379 ATGGCCTCGTTGTCGATCGA 61.663 55.000 15.15 15.15 45.21 3.59
1175 1667 1.226974 ATGGCCTCGTTGTCGATCG 60.227 57.895 9.36 9.36 45.21 3.69
1416 1908 1.759459 GAATCTCCGGCGGGAAGGAT 61.759 60.000 27.98 19.90 43.27 3.24
1583 2086 1.571460 GGCAAGTCAACAGTCGCAG 59.429 57.895 0.00 0.00 0.00 5.18
1586 2089 1.000955 AGTAGGGCAAGTCAACAGTCG 59.999 52.381 0.00 0.00 0.00 4.18
1729 2238 5.615289 ACACATCTCAGTTATATTCCAGGC 58.385 41.667 0.00 0.00 0.00 4.85
1778 2292 3.257469 TGATAGCTCACTGGCTTTCTG 57.743 47.619 0.00 0.00 42.97 3.02
1779 2293 4.500499 AATGATAGCTCACTGGCTTTCT 57.500 40.909 0.00 0.00 42.97 2.52
1793 2307 5.406780 AGCGAAGGCGATTAAGAAATGATAG 59.593 40.000 0.00 0.00 46.35 2.08
1838 2518 9.174166 GCCTTCAAAAGATCCAAGTACTAATAA 57.826 33.333 0.00 0.00 0.00 1.40
1839 2519 8.548877 AGCCTTCAAAAGATCCAAGTACTAATA 58.451 33.333 0.00 0.00 0.00 0.98
1840 2520 7.406104 AGCCTTCAAAAGATCCAAGTACTAAT 58.594 34.615 0.00 0.00 0.00 1.73
2012 2721 0.179187 CGTTTGTGTGCAACGAACCA 60.179 50.000 18.47 0.00 46.62 3.67
2013 2722 0.097325 TCGTTTGTGTGCAACGAACC 59.903 50.000 18.47 8.03 46.62 3.62
2046 2755 3.321648 AGATGGCAGCGACCACCA 61.322 61.111 2.59 0.00 44.17 4.17
2210 2919 2.125912 CGACAAGCCAGGAGACGG 60.126 66.667 0.00 0.00 0.00 4.79
2402 3111 8.545420 CCATTATTTTGTGTAGTACGATGTACC 58.455 37.037 3.61 0.00 0.00 3.34
2403 3112 8.545420 CCCATTATTTTGTGTAGTACGATGTAC 58.455 37.037 0.00 0.00 0.00 2.90
2404 3113 8.259411 ACCCATTATTTTGTGTAGTACGATGTA 58.741 33.333 0.00 0.00 0.00 2.29
2405 3114 7.107542 ACCCATTATTTTGTGTAGTACGATGT 58.892 34.615 0.00 0.00 0.00 3.06
2406 3115 7.548196 ACCCATTATTTTGTGTAGTACGATG 57.452 36.000 0.00 0.00 0.00 3.84
2407 3116 8.480501 ACTACCCATTATTTTGTGTAGTACGAT 58.519 33.333 0.00 0.00 37.66 3.73
2408 3117 7.839907 ACTACCCATTATTTTGTGTAGTACGA 58.160 34.615 0.00 0.00 37.66 3.43
2409 3118 9.754382 ATACTACCCATTATTTTGTGTAGTACG 57.246 33.333 8.45 0.00 41.73 3.67


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

AutoCloner maintained by Alex Coulton.