Multiple sequence alignment - TraesCS6D01G092500

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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 TraesCS6D01G092500 chr6D 100.000 3120 0 0 1 3120 57936630 57933511 0 5762
1 TraesCS6D01G092500 chr6B 96.139 3134 93 6 1 3120 596596285 596593166 0 5092
2 TraesCS6D01G092500 chr1D 96.107 3134 93 7 1 3120 212442287 212439169 0 5084
3 TraesCS6D01G092500 chrUn 95.819 3133 104 5 1 3120 171013859 171016977 0 5035
4 TraesCS6D01G092500 chrUn 96.675 2526 69 4 596 3120 267894005 267891494 0 4185
5 TraesCS6D01G092500 chrUn 96.595 2526 71 4 596 3120 209404303 209406814 0 4174
6 TraesCS6D01G092500 chr2B 95.787 3133 105 5 1 3120 391219671 391216553 0 5029
7 TraesCS6D01G092500 chr2B 95.531 3133 111 6 1 3120 391150375 391153491 0 4983
8 TraesCS6D01G092500 chr5B 95.595 3133 110 6 1 3120 567285544 567288661 0 4996
9 TraesCS6D01G092500 chr7B 95.465 3131 114 6 2 3118 54043608 54040492 0 4970
10 TraesCS6D01G092500 chr4B 95.408 3136 114 8 1 3120 495550528 495553649 0 4966
11 TraesCS6D01G092500 chr4B 95.716 2311 75 4 1 2298 495573521 495575820 0 3698
12 TraesCS6D01G092500 chr7D 96.477 2526 74 4 596 3120 579003592 579001081 0 4157
13 TraesCS6D01G092500 chr7D 94.801 654 21 2 1 641 382092231 382092884 0 1007
14 TraesCS6D01G092500 chr7D 94.648 654 22 2 1 641 626708763 626708110 0 1002
15 TraesCS6D01G092500 chr4D 95.942 2489 79 4 640 3120 123701771 123699297 0 4017
16 TraesCS6D01G092500 chr4D 94.487 653 23 2 1 640 123403948 123404600 0 994
17 TraesCS6D01G092500 chr1B 94.660 1573 60 4 1 1560 672546847 672548408 0 2418


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 TraesCS6D01G092500 chr6D 57933511 57936630 3119 True 5762 5762 100.000 1 3120 1 chr6D.!!$R1 3119
1 TraesCS6D01G092500 chr6B 596593166 596596285 3119 True 5092 5092 96.139 1 3120 1 chr6B.!!$R1 3119
2 TraesCS6D01G092500 chr1D 212439169 212442287 3118 True 5084 5084 96.107 1 3120 1 chr1D.!!$R1 3119
3 TraesCS6D01G092500 chrUn 171013859 171016977 3118 False 5035 5035 95.819 1 3120 1 chrUn.!!$F1 3119
4 TraesCS6D01G092500 chrUn 267891494 267894005 2511 True 4185 4185 96.675 596 3120 1 chrUn.!!$R1 2524
5 TraesCS6D01G092500 chrUn 209404303 209406814 2511 False 4174 4174 96.595 596 3120 1 chrUn.!!$F2 2524
6 TraesCS6D01G092500 chr2B 391216553 391219671 3118 True 5029 5029 95.787 1 3120 1 chr2B.!!$R1 3119
7 TraesCS6D01G092500 chr2B 391150375 391153491 3116 False 4983 4983 95.531 1 3120 1 chr2B.!!$F1 3119
8 TraesCS6D01G092500 chr5B 567285544 567288661 3117 False 4996 4996 95.595 1 3120 1 chr5B.!!$F1 3119
9 TraesCS6D01G092500 chr7B 54040492 54043608 3116 True 4970 4970 95.465 2 3118 1 chr7B.!!$R1 3116
10 TraesCS6D01G092500 chr4B 495550528 495553649 3121 False 4966 4966 95.408 1 3120 1 chr4B.!!$F1 3119
11 TraesCS6D01G092500 chr4B 495573521 495575820 2299 False 3698 3698 95.716 1 2298 1 chr4B.!!$F2 2297
12 TraesCS6D01G092500 chr7D 579001081 579003592 2511 True 4157 4157 96.477 596 3120 1 chr7D.!!$R1 2524
13 TraesCS6D01G092500 chr7D 382092231 382092884 653 False 1007 1007 94.801 1 641 1 chr7D.!!$F1 640
14 TraesCS6D01G092500 chr7D 626708110 626708763 653 True 1002 1002 94.648 1 641 1 chr7D.!!$R2 640
15 TraesCS6D01G092500 chr4D 123699297 123701771 2474 True 4017 4017 95.942 640 3120 1 chr4D.!!$R1 2480
16 TraesCS6D01G092500 chr4D 123403948 123404600 652 False 994 994 94.487 1 640 1 chr4D.!!$F1 639
17 TraesCS6D01G092500 chr1B 672546847 672548408 1561 False 2418 2418 94.660 1 1560 1 chr1B.!!$F1 1559

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
643 657 0.040204 CCTGCCCCTCATTGTCCTTT 59.960 55.0 0.0 0.0 0.00 3.11 F
1776 1800 0.036388 TGCTTAGGCAGTTCCTTCGG 60.036 55.0 0.0 0.0 44.75 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2083 2107 0.942884 GTCCGTTTCCGCTTCGAAGT 60.943 55.000 25.24 0.0 0.0 3.01 R
2701 2727 1.810755 CCAGTCACTCGTACTACAGCA 59.189 52.381 0.00 0.0 0.0 4.41 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
141 142 4.316025 TCTTTAGGGCATGGCTAGTTTT 57.684 40.909 19.78 1.26 0.00 2.43
143 144 3.730215 TTAGGGCATGGCTAGTTTTGA 57.270 42.857 19.78 0.00 0.00 2.69
253 254 2.310647 TGTGGACCCCTTCCCTTTAATC 59.689 50.000 0.00 0.00 45.17 1.75
257 258 4.228895 TGGACCCCTTCCCTTTAATCTAAC 59.771 45.833 0.00 0.00 45.17 2.34
274 275 7.800300 AATCTAACAAAGAGGTCTTCCTAGT 57.200 36.000 0.00 0.00 45.24 2.57
279 280 4.238514 CAAAGAGGTCTTCCTAGTTGACG 58.761 47.826 0.00 0.00 45.24 4.35
313 314 5.589192 TCTTCTTTCGAGTTTCGTTCTCTT 58.411 37.500 0.00 0.00 41.35 2.85
328 329 4.261155 CGTTCTCTTTGGCTTGTGAATTGA 60.261 41.667 0.00 0.00 0.00 2.57
333 334 6.660521 TCTCTTTGGCTTGTGAATTGATGTAT 59.339 34.615 0.00 0.00 0.00 2.29
364 365 5.458451 TCACTCTCTTCTAAGGGATCTCA 57.542 43.478 0.00 0.00 34.42 3.27
416 417 1.338020 GCATTTTCCATCTTAGGGCGG 59.662 52.381 0.00 0.00 0.00 6.13
427 428 3.244582 TCTTAGGGCGGGCAATATAAGA 58.755 45.455 3.27 8.45 0.00 2.10
535 540 2.833943 TGAGGTGCTTGCTAATCTCTCA 59.166 45.455 0.00 0.00 0.00 3.27
557 562 3.039405 GACGAGTCGATGTCAATAGCAG 58.961 50.000 21.50 0.00 35.20 4.24
643 657 0.040204 CCTGCCCCTCATTGTCCTTT 59.960 55.000 0.00 0.00 0.00 3.11
654 668 5.653769 CCTCATTGTCCTTTAATCATGGTGT 59.346 40.000 0.00 0.00 0.00 4.16
731 753 9.810545 TTCAAAGTGAAACGATTTTCCTTTTAT 57.189 25.926 0.00 0.00 45.86 1.40
816 838 0.816018 TTCCGCTCGCTTTCAACCAA 60.816 50.000 0.00 0.00 0.00 3.67
828 850 3.634568 TTCAACCAATGCCACTTTACG 57.365 42.857 0.00 0.00 0.00 3.18
954 977 3.774842 TGAATTAAGGGAGGGCCATTT 57.225 42.857 6.18 0.00 39.29 2.32
996 1019 6.101296 AGAGTTGGGTTCGATTCCCTTTATAT 59.899 38.462 21.52 7.01 44.84 0.86
1012 1035 4.884458 TTATATGCGATGTGGCGAAAAA 57.116 36.364 0.00 0.00 35.06 1.94
1053 1076 4.906065 TGACATGCCAGCATTAAGATTC 57.094 40.909 1.47 0.00 33.90 2.52
1072 1095 8.827177 AAGATTCAAAACATGTCGTCTACTTA 57.173 30.769 0.00 0.00 0.00 2.24
1092 1115 2.504367 ACAGGAAATGTTCGGAACAGG 58.496 47.619 25.74 14.03 45.95 4.00
1152 1175 3.708631 TGAGGAACAAGAGGAGATCCATC 59.291 47.826 0.92 0.00 38.89 3.51
1174 1197 7.094634 CCATCAAAAGAAATCTTTCTCGGAGAA 60.095 37.037 16.19 16.19 46.22 2.87
1260 1283 2.267174 CCATAAGGGAGATGCACAGG 57.733 55.000 0.00 0.00 40.01 4.00
1284 1307 7.728981 AGGGGAAGAGAACGAACTTCATATATA 59.271 37.037 0.00 0.00 42.67 0.86
1285 1308 8.532819 GGGGAAGAGAACGAACTTCATATATAT 58.467 37.037 0.00 0.00 42.67 0.86
1389 1412 1.440145 GCAAGGCAGCCGATAAGTCC 61.440 60.000 5.55 0.00 0.00 3.85
1560 1583 5.762179 ATCATAGGCAAATTCCTATCGGA 57.238 39.130 3.27 0.91 45.23 4.55
1662 1686 0.842030 ACAACTCAGAGGGGATGCCA 60.842 55.000 5.30 0.00 0.00 4.92
1690 1714 4.796038 ACTCAAATCCAAGGAATTGCAG 57.204 40.909 11.24 11.37 35.61 4.41
1776 1800 0.036388 TGCTTAGGCAGTTCCTTCGG 60.036 55.000 0.00 0.00 44.75 4.30
1960 1984 9.250624 CCGTTTACTAGGAAGATAAGAATCAAG 57.749 37.037 0.00 0.00 34.28 3.02
2083 2107 5.644188 AGATTGAAAGATCCAAACCTTCCA 58.356 37.500 0.00 0.00 0.00 3.53
2089 2113 2.637872 AGATCCAAACCTTCCACTTCGA 59.362 45.455 0.00 0.00 0.00 3.71
2285 2309 9.995003 AATATATGGAAAAACTGCACTTTTTGA 57.005 25.926 17.90 7.81 34.23 2.69
2286 2310 7.713764 ATATGGAAAAACTGCACTTTTTGAC 57.286 32.000 17.90 12.27 34.23 3.18
2287 2311 5.146010 TGGAAAAACTGCACTTTTTGACT 57.854 34.783 17.90 0.00 34.23 3.41
2496 2520 7.975616 CCAATTTCTCTTCTTTCTTTTCACACA 59.024 33.333 0.00 0.00 0.00 3.72
2519 2543 5.179182 CAGGCAACAATTGGGAATAAAACAC 59.821 40.000 10.83 0.00 41.41 3.32
2633 2659 2.294512 CTGTTTCTCTGAAAAGGTGGGC 59.705 50.000 0.00 0.00 0.00 5.36
2701 2727 0.106918 TTTGCCGGTGACCTTTGTCT 60.107 50.000 1.90 0.00 42.28 3.41
2829 2855 1.067635 CGCAAGGGGAAACAAGATTGG 60.068 52.381 0.00 0.00 0.00 3.16
2859 2885 8.660373 TGAATTAAAACACACCAAATGTTTCAC 58.340 29.630 3.76 0.00 46.88 3.18
2906 2932 5.650283 TCTGATACAAACCAGGGGAAAAAT 58.350 37.500 0.00 0.00 0.00 1.82
3062 3088 8.024865 AGGAAATTACTTACGCCAATAACAAAC 58.975 33.333 0.00 0.00 0.00 2.93
3081 3107 2.195922 ACACGAATACGAATTACGCCC 58.804 47.619 0.00 0.00 46.94 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.094078 TGGCCTTAGTAACGTAACGCAT 60.094 45.455 3.32 0.00 0.00 4.73
141 142 5.369833 TGGACGATGGTTTTAGAAAACTCA 58.630 37.500 15.48 12.37 45.70 3.41
143 144 5.826208 AGTTGGACGATGGTTTTAGAAAACT 59.174 36.000 15.48 0.00 45.70 2.66
161 162 5.926542 CGTGTCTGAATAAGAAAGAGTTGGA 59.073 40.000 0.00 0.00 36.40 3.53
253 254 6.869388 GTCAACTAGGAAGACCTCTTTGTTAG 59.131 42.308 0.00 0.00 46.43 2.34
257 258 4.238514 CGTCAACTAGGAAGACCTCTTTG 58.761 47.826 0.00 0.00 46.43 2.77
274 275 8.077991 TCGAAAGAAGATCTAGTTTTACGTCAA 58.922 33.333 0.00 0.00 37.03 3.18
313 314 5.170021 GCAATACATCAATTCACAAGCCAA 58.830 37.500 0.00 0.00 0.00 4.52
328 329 5.171339 AGAGAGTGAAACAGGCAATACAT 57.829 39.130 0.00 0.00 41.43 2.29
333 334 3.845781 AGAAGAGAGTGAAACAGGCAA 57.154 42.857 0.00 0.00 41.43 4.52
416 417 9.899226 GTTGATACCAGAATTTCTTATATTGCC 57.101 33.333 0.00 0.00 0.00 4.52
535 540 2.683362 TGCTATTGACATCGACTCGTCT 59.317 45.455 11.45 0.00 33.18 4.18
557 562 6.150140 AGGCACTAAAGATGTTTCATCAGAAC 59.850 38.462 11.47 0.00 36.02 3.01
828 850 3.238260 CTGCGTCACAGTGCTCAC 58.762 61.111 0.00 0.00 41.86 3.51
969 992 2.084546 GGGAATCGAACCCAACTCTTG 58.915 52.381 21.26 0.00 46.05 3.02
1012 1035 7.905604 TGTCATATTTCGTTGAATCAGTCTT 57.094 32.000 0.00 0.00 0.00 3.01
1034 1057 5.664294 TTTGAATCTTAATGCTGGCATGT 57.336 34.783 8.91 2.83 36.68 3.21
1053 1076 5.924254 TCCTGTAAGTAGACGACATGTTTTG 59.076 40.000 0.00 0.00 0.00 2.44
1072 1095 2.504367 CCTGTTCCGAACATTTCCTGT 58.496 47.619 14.29 0.00 41.26 4.00
1092 1115 3.374367 GGCGTTGGATTAGAGAAAGTTCC 59.626 47.826 0.00 0.00 0.00 3.62
1152 1175 8.856490 TTTTTCTCCGAGAAAGATTTCTTTTG 57.144 30.769 20.19 3.50 46.84 2.44
1186 1209 7.644490 TGTGTAGTTTGTGATTTGATGTTACC 58.356 34.615 0.00 0.00 0.00 2.85
1292 1315 8.772250 TGTTTCTTGATTGAGTAAGATAGGGAT 58.228 33.333 0.00 0.00 33.34 3.85
1293 1316 8.146053 TGTTTCTTGATTGAGTAAGATAGGGA 57.854 34.615 0.00 0.00 33.34 4.20
1298 1321 8.877779 CGATCTTGTTTCTTGATTGAGTAAGAT 58.122 33.333 0.00 0.00 35.69 2.40
1300 1323 7.331934 TCCGATCTTGTTTCTTGATTGAGTAAG 59.668 37.037 0.00 0.00 0.00 2.34
1341 1364 6.214412 AGGAAGAGTGTCACTAAAATGGAGAT 59.786 38.462 5.21 0.00 0.00 2.75
1389 1412 6.072175 TCCATTATTCAAACAAACCCTTCGAG 60.072 38.462 0.00 0.00 0.00 4.04
1427 1450 3.308530 CGTGGGAAACTTTCAAATGAGC 58.691 45.455 3.93 0.00 0.00 4.26
1519 1542 8.571336 CCTATGATTTTTCCAACTGATATGTCC 58.429 37.037 0.00 0.00 0.00 4.02
1560 1583 6.151817 GCCTCTTCTTTTTCCAACTGATATGT 59.848 38.462 0.00 0.00 0.00 2.29
1624 1648 2.037902 TGTGAGTAAGCGGAACCATTCA 59.962 45.455 0.00 0.00 0.00 2.57
1662 1686 7.121315 GCAATTCCTTGGATTTGAGTAGTAAGT 59.879 37.037 21.45 0.00 32.72 2.24
1690 1714 6.106877 TCTTGCATATAAGAACGCAACTTC 57.893 37.500 0.00 0.00 39.32 3.01
1776 1800 3.188048 CCTCTTCATTCTGTTGTGCTCAC 59.812 47.826 0.00 0.00 0.00 3.51
1960 1984 7.690952 ATAATGAGTAGGTAGTTCGATCCTC 57.309 40.000 0.00 0.00 33.34 3.71
2083 2107 0.942884 GTCCGTTTCCGCTTCGAAGT 60.943 55.000 25.24 0.00 0.00 3.01
2089 2113 2.663852 CCACGTCCGTTTCCGCTT 60.664 61.111 0.00 0.00 0.00 4.68
2273 2297 8.298140 AGTAGTAGTAGTAGTCAAAAAGTGCAG 58.702 37.037 0.00 0.00 0.00 4.41
2336 2360 2.105821 TCCGACCAATTCAGTCCAAACT 59.894 45.455 0.62 0.00 35.60 2.66
2337 2361 2.484264 CTCCGACCAATTCAGTCCAAAC 59.516 50.000 0.62 0.00 0.00 2.93
2448 2472 1.550524 CCATGTTTCCCGAGAGAGACA 59.449 52.381 0.00 0.00 0.00 3.41
2496 2520 5.163258 TGTGTTTTATTCCCAATTGTTGCCT 60.163 36.000 4.43 0.00 0.00 4.75
2519 2543 9.689976 TTACATTTTAAACTCATGTTCATGGTG 57.310 29.630 12.02 8.44 34.96 4.17
2701 2727 1.810755 CCAGTCACTCGTACTACAGCA 59.189 52.381 0.00 0.00 0.00 4.41
2829 2855 8.376889 ACATTTGGTGTGTTTTAATTCATTCC 57.623 30.769 0.00 0.00 40.28 3.01
2859 2885 6.352516 AGCTGACCACTGATAATAGGAAAAG 58.647 40.000 0.00 0.00 0.00 2.27
2906 2932 2.943036 AAAGAAGGCGTTCCAGGTTA 57.057 45.000 15.23 0.00 32.48 2.85
2969 2995 3.572682 AGTCCTCGTGTGTACATCTTTCA 59.427 43.478 0.00 0.00 0.00 2.69
2982 3008 4.832590 AATAGGAATCGTAGTCCTCGTG 57.167 45.455 7.06 0.00 42.02 4.35
3046 3072 4.808077 TTCGTGTTTGTTATTGGCGTAA 57.192 36.364 0.00 0.00 0.00 3.18
3062 3088 2.034339 GTGGGCGTAATTCGTATTCGTG 60.034 50.000 0.00 0.00 42.13 4.35


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

AutoCloner maintained by Alex Coulton.