Multiple sequence alignment - TraesCS2D01G589900

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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 TraesCS2D01G589900 chr2D 100.000 3182 0 0 1 3182 646053657 646056838 0.000000e+00 5877
1 TraesCS2D01G589900 chr2D 90.955 1791 99 28 530 2306 646085737 646083996 0.000000e+00 2351
2 TraesCS2D01G589900 chr2B 92.581 3208 152 49 21 3182 789406849 789403682 0.000000e+00 4527
3 TraesCS2D01G589900 chr2B 92.519 3208 156 46 21 3182 571964228 571961059 0.000000e+00 4518
4 TraesCS2D01G589900 chr2B 92.022 3234 166 58 1 3182 571851948 571848755 0.000000e+00 4458
5 TraesCS2D01G589900 chr2B 92.145 3221 152 50 21 3182 571994874 571991696 0.000000e+00 4453
6 TraesCS2D01G589900 chr2B 91.968 3237 156 52 1 3182 789358564 789355377 0.000000e+00 4442
7 TraesCS2D01G589900 chr2B 91.960 3234 159 50 1 3182 789375662 789372478 0.000000e+00 4438
8 TraesCS2D01G589900 chr2B 92.591 2659 131 33 565 3182 789296119 789293486 0.000000e+00 3759
9 TraesCS2D01G589900 chr2B 91.155 2702 148 48 21 2670 571877784 571875122 0.000000e+00 3581
10 TraesCS2D01G589900 chr2B 91.970 2553 122 37 671 3182 789326514 789324004 0.000000e+00 3502
11 TraesCS2D01G589900 chr2B 95.659 1912 68 7 1280 3182 571909339 571907434 0.000000e+00 3057
12 TraesCS2D01G589900 chr2B 89.273 1156 59 33 82 1206 789425171 789424050 0.000000e+00 1387
13 TraesCS2D01G589900 chr2B 88.322 1216 59 30 21 1204 571833859 571832695 0.000000e+00 1382
14 TraesCS2D01G589900 chr2B 93.603 469 23 7 21 485 789296886 789296421 0.000000e+00 693
15 TraesCS2D01G589900 chr2A 92.572 2208 138 21 995 3182 773380373 773378172 0.000000e+00 3145
16 TraesCS2D01G589900 chr2A 88.580 1296 103 16 1023 2306 773302605 773303867 0.000000e+00 1531
17 TraesCS2D01G589900 chr2A 91.918 730 25 11 18 740 773381075 773380373 0.000000e+00 990
18 TraesCS2D01G589900 chr2A 79.673 733 79 34 311 1015 773296342 773297032 6.220000e-127 464


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 TraesCS2D01G589900 chr2D 646053657 646056838 3181 False 5877.0 5877 100.000 1 3182 1 chr2D.!!$F1 3181
1 TraesCS2D01G589900 chr2D 646083996 646085737 1741 True 2351.0 2351 90.955 530 2306 1 chr2D.!!$R1 1776
2 TraesCS2D01G589900 chr2B 789403682 789406849 3167 True 4527.0 4527 92.581 21 3182 1 chr2B.!!$R10 3161
3 TraesCS2D01G589900 chr2B 571961059 571964228 3169 True 4518.0 4518 92.519 21 3182 1 chr2B.!!$R5 3161
4 TraesCS2D01G589900 chr2B 571848755 571851948 3193 True 4458.0 4458 92.022 1 3182 1 chr2B.!!$R2 3181
5 TraesCS2D01G589900 chr2B 571991696 571994874 3178 True 4453.0 4453 92.145 21 3182 1 chr2B.!!$R6 3161
6 TraesCS2D01G589900 chr2B 789355377 789358564 3187 True 4442.0 4442 91.968 1 3182 1 chr2B.!!$R8 3181
7 TraesCS2D01G589900 chr2B 789372478 789375662 3184 True 4438.0 4438 91.960 1 3182 1 chr2B.!!$R9 3181
8 TraesCS2D01G589900 chr2B 571875122 571877784 2662 True 3581.0 3581 91.155 21 2670 1 chr2B.!!$R3 2649
9 TraesCS2D01G589900 chr2B 789324004 789326514 2510 True 3502.0 3502 91.970 671 3182 1 chr2B.!!$R7 2511
10 TraesCS2D01G589900 chr2B 571907434 571909339 1905 True 3057.0 3057 95.659 1280 3182 1 chr2B.!!$R4 1902
11 TraesCS2D01G589900 chr2B 789293486 789296886 3400 True 2226.0 3759 93.097 21 3182 2 chr2B.!!$R12 3161
12 TraesCS2D01G589900 chr2B 789424050 789425171 1121 True 1387.0 1387 89.273 82 1206 1 chr2B.!!$R11 1124
13 TraesCS2D01G589900 chr2B 571832695 571833859 1164 True 1382.0 1382 88.322 21 1204 1 chr2B.!!$R1 1183
14 TraesCS2D01G589900 chr2A 773378172 773381075 2903 True 2067.5 3145 92.245 18 3182 2 chr2A.!!$R1 3164
15 TraesCS2D01G589900 chr2A 773302605 773303867 1262 False 1531.0 1531 88.580 1023 2306 1 chr2A.!!$F2 1283
16 TraesCS2D01G589900 chr2A 773296342 773297032 690 False 464.0 464 79.673 311 1015 1 chr2A.!!$F1 704

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
797 1067 0.532115 AATTCGCCCCAATGAACTGC 59.468 50.0 0.00 0.00 0.00 4.40 F
1626 2009 0.729116 GATGCCACTGACGACAATGG 59.271 55.0 11.01 11.01 44.97 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1800 2196 2.416547 CCTACTCTTGAAACGGCACATG 59.583 50.00 0.0 0.0 0.00 3.21 R
3030 3432 4.025360 TGAAGGCATTTCCACATAGCATT 58.975 39.13 0.0 0.0 37.29 3.56 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 38 3.514309 ACCTCTATGAACACACACCCTAC 59.486 47.826 0.00 0.00 0.00 3.18
105 114 3.842925 ATTGTGGGCGCCTCGTTGT 62.843 57.895 28.56 5.63 0.00 3.32
140 152 0.674581 CTCCCACTGAAAGCGCATCA 60.675 55.000 11.47 13.15 37.60 3.07
258 271 1.119684 GGTTGTTTGTTTGGGCCTCT 58.880 50.000 4.53 0.00 0.00 3.69
796 1066 1.736696 GCAATTCGCCCCAATGAACTG 60.737 52.381 0.00 0.00 32.94 3.16
797 1067 0.532115 AATTCGCCCCAATGAACTGC 59.468 50.000 0.00 0.00 0.00 4.40
799 1069 3.814268 CGCCCCAATGAACTGCGG 61.814 66.667 0.00 0.00 41.42 5.69
800 1070 2.361104 GCCCCAATGAACTGCGGA 60.361 61.111 0.00 0.00 0.00 5.54
801 1071 1.754234 GCCCCAATGAACTGCGGAT 60.754 57.895 0.00 0.00 0.00 4.18
930 1228 0.822164 TTTGTAGGCGACTAGGAGGC 59.178 55.000 0.00 5.35 45.49 4.70
1008 1306 1.063174 GCGGCAGATCACAGAATCAAC 59.937 52.381 0.00 0.00 0.00 3.18
1011 1309 3.678252 CGGCAGATCACAGAATCAACTCT 60.678 47.826 0.00 0.00 0.00 3.24
1119 1475 2.809601 CGCCGTCGACTTCCCTTG 60.810 66.667 14.70 0.00 38.10 3.61
1227 1597 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1229 1599 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1230 1600 4.219115 TCTCTCTCTCTCTCTCTCTCTCC 58.781 52.174 0.00 0.00 0.00 3.71
1231 1601 3.309296 TCTCTCTCTCTCTCTCTCTCCC 58.691 54.545 0.00 0.00 0.00 4.30
1233 1603 3.309296 TCTCTCTCTCTCTCTCTCCCTC 58.691 54.545 0.00 0.00 0.00 4.30
1235 1605 3.309296 TCTCTCTCTCTCTCTCCCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
1236 1606 3.051803 TCTCTCTCTCTCTCTCCCTCTCT 60.052 52.174 0.00 0.00 0.00 3.10
1239 1609 3.309296 TCTCTCTCTCTCCCTCTCTCTC 58.691 54.545 0.00 0.00 0.00 3.20
1240 1610 3.051803 TCTCTCTCTCTCCCTCTCTCTCT 60.052 52.174 0.00 0.00 0.00 3.10
1251 1621 3.070734 CCCTCTCTCTCTCTCTCTCTCTG 59.929 56.522 0.00 0.00 0.00 3.35
1492 1875 8.680001 TCACTAATACTATATGTTCGTGTGTGT 58.320 33.333 0.00 0.00 0.00 3.72
1626 2009 0.729116 GATGCCACTGACGACAATGG 59.271 55.000 11.01 11.01 44.97 3.16
1800 2196 2.030805 GTGACATGTGACAGAAAAGCCC 60.031 50.000 10.82 0.00 0.00 5.19
1992 2391 4.666655 CGAAGCACTATTTTGTCACCTTCG 60.667 45.833 0.00 0.00 35.02 3.79
2012 2411 4.450976 TCGGCTGTATATTGCTTGTTCAT 58.549 39.130 0.00 0.00 0.00 2.57
2142 2542 2.183679 GTATTGATGGGTTGGGCCAAA 58.816 47.619 22.82 5.97 39.65 3.28
2148 2548 1.302431 GGGTTGGGCCAAAATGTGC 60.302 57.895 22.82 7.18 39.65 4.57
2155 2555 0.820871 GGCCAAAATGTGCCCGATTA 59.179 50.000 0.00 0.00 41.97 1.75
2400 2802 4.764172 AGGATTCCTTCTTCTTGTCATCG 58.236 43.478 0.00 0.00 0.00 3.84
2910 3312 3.197116 TCATGATCAGTGATGTCAGCAGT 59.803 43.478 11.20 0.00 0.00 4.40
3030 3432 3.599343 GGAGCACATCAACACATGAGTA 58.401 45.455 0.00 0.00 42.53 2.59
3099 3501 6.036953 CAGATAAGCTTTGCAGTTTCTAGAGG 59.963 42.308 3.20 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.093128 GGGGTAGGGTGTGTGTTCATAG 60.093 54.545 0.00 0.00 0.00 2.23
29 38 0.894141 CTCGGAGATGCTCATAGGGG 59.106 60.000 0.00 0.00 33.89 4.79
105 114 0.815734 GGAGAGACATTCCCGTCGAA 59.184 55.000 0.00 0.00 40.98 3.71
161 174 1.409064 CTGGTGCTCGCATTACTCCTA 59.591 52.381 0.00 0.00 0.00 2.94
166 179 0.108138 AGTCCTGGTGCTCGCATTAC 60.108 55.000 0.00 0.00 0.00 1.89
258 271 1.408266 GGCGAGGAAAATAGCAAGGGA 60.408 52.381 0.00 0.00 0.00 4.20
796 1066 1.135939 GTTGGCAAACCGTATCCGC 59.864 57.895 0.00 0.00 39.70 5.54
797 1067 0.446222 CTGTTGGCAAACCGTATCCG 59.554 55.000 0.00 0.00 39.70 4.18
799 1069 5.751243 ATATTCTGTTGGCAAACCGTATC 57.249 39.130 0.00 0.00 39.70 2.24
800 1070 5.417580 ACAATATTCTGTTGGCAAACCGTAT 59.582 36.000 0.00 0.00 39.70 3.06
801 1071 4.762765 ACAATATTCTGTTGGCAAACCGTA 59.237 37.500 0.00 0.00 39.70 4.02
804 1074 5.092781 CGTACAATATTCTGTTGGCAAACC 58.907 41.667 0.00 0.00 35.25 3.27
806 1076 5.703592 AGACGTACAATATTCTGTTGGCAAA 59.296 36.000 0.00 0.00 0.00 3.68
807 1077 5.242434 AGACGTACAATATTCTGTTGGCAA 58.758 37.500 0.00 0.00 0.00 4.52
809 1079 5.796350 AAGACGTACAATATTCTGTTGGC 57.204 39.130 0.00 0.00 0.00 4.52
810 1080 7.129109 ACAAAGACGTACAATATTCTGTTGG 57.871 36.000 0.00 0.00 0.00 3.77
811 1081 8.380644 CCTACAAAGACGTACAATATTCTGTTG 58.619 37.037 0.00 0.00 0.00 3.33
812 1082 7.064253 GCCTACAAAGACGTACAATATTCTGTT 59.936 37.037 0.00 0.00 0.00 3.16
813 1083 6.534079 GCCTACAAAGACGTACAATATTCTGT 59.466 38.462 0.00 0.00 0.00 3.41
814 1084 6.533723 TGCCTACAAAGACGTACAATATTCTG 59.466 38.462 0.00 0.00 0.00 3.02
965 1263 7.396339 CCGCACAGCCCCTAATATATATATCTA 59.604 40.741 5.70 1.46 0.00 1.98
975 1273 2.324014 CTGCCGCACAGCCCCTAATA 62.324 60.000 0.00 0.00 40.19 0.98
976 1274 3.704231 CTGCCGCACAGCCCCTAAT 62.704 63.158 0.00 0.00 40.19 1.73
977 1275 4.408821 CTGCCGCACAGCCCCTAA 62.409 66.667 0.00 0.00 40.19 2.69
1008 1306 0.107654 ATTTTTCGAGGGGCGGAGAG 60.108 55.000 0.00 0.00 41.33 3.20
1011 1309 2.493414 TTTATTTTTCGAGGGGCGGA 57.507 45.000 0.00 0.00 41.33 5.54
1119 1475 2.226437 TGTTTTCTCTGGCGATCAAAGC 59.774 45.455 0.00 0.00 0.00 3.51
1227 1597 3.312890 AGAGAGAGAGAGAGAGAGGGAG 58.687 54.545 0.00 0.00 0.00 4.30
1229 1599 3.070734 CAGAGAGAGAGAGAGAGAGAGGG 59.929 56.522 0.00 0.00 0.00 4.30
1230 1600 3.708631 ACAGAGAGAGAGAGAGAGAGAGG 59.291 52.174 0.00 0.00 0.00 3.69
1231 1601 5.350504 AACAGAGAGAGAGAGAGAGAGAG 57.649 47.826 0.00 0.00 0.00 3.20
1233 1603 5.520288 CGTTAACAGAGAGAGAGAGAGAGAG 59.480 48.000 6.39 0.00 0.00 3.20
1235 1605 5.175859 ACGTTAACAGAGAGAGAGAGAGAG 58.824 45.833 6.39 0.00 0.00 3.20
1236 1606 5.155278 ACGTTAACAGAGAGAGAGAGAGA 57.845 43.478 6.39 0.00 0.00 3.10
1239 1609 8.973835 AAAAATACGTTAACAGAGAGAGAGAG 57.026 34.615 6.39 0.00 0.00 3.20
1240 1610 8.794553 AGAAAAATACGTTAACAGAGAGAGAGA 58.205 33.333 6.39 0.00 0.00 3.10
1251 1621 8.735837 TCTTCGCAAAAAGAAAAATACGTTAAC 58.264 29.630 0.00 0.00 32.42 2.01
1626 2009 3.054878 TCGGCGAAGAAGTACTTTTGTC 58.945 45.455 7.35 6.79 39.13 3.18
1800 2196 2.416547 CCTACTCTTGAAACGGCACATG 59.583 50.000 0.00 0.00 0.00 3.21
1992 2391 9.533253 AATAAAATGAACAAGCAATATACAGCC 57.467 29.630 0.00 0.00 0.00 4.85
2050 2450 8.488651 AAAAGTAATCCCGTAGTAACATCAAG 57.511 34.615 0.00 0.00 0.00 3.02
2064 2464 8.799367 AGTATACAACAACCAAAAAGTAATCCC 58.201 33.333 5.50 0.00 0.00 3.85
2142 2542 9.474313 AAACCATATATAATAATCGGGCACATT 57.526 29.630 0.00 0.00 0.00 2.71
2400 2802 4.144297 AGTCTAGCAGAGATGATGACTCC 58.856 47.826 0.00 0.00 36.29 3.85
3030 3432 4.025360 TGAAGGCATTTCCACATAGCATT 58.975 39.130 0.00 0.00 37.29 3.56


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

AutoCloner maintained by Alex Coulton.