Multiple sequence alignment - TraesCS5D01G086600

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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 TraesCS5D01G086600 chr5D 100.000 3316 0 0 1 3316 91864956 91868271 0.000000e+00 6124.0
1 TraesCS5D01G086600 chr5D 95.015 983 25 1 1 983 435482790 435481832 0.000000e+00 1522.0
2 TraesCS5D01G086600 chr5D 97.285 884 20 2 2436 3316 91652589 91653471 0.000000e+00 1496.0
3 TraesCS5D01G086600 chr5D 89.354 1146 95 11 1038 2176 91616670 91617795 0.000000e+00 1415.0
4 TraesCS5D01G086600 chr5D 99.258 539 4 0 1801 2339 91652017 91652555 0.000000e+00 974.0
5 TraesCS5D01G086600 chr5D 96.095 461 13 1 1351 1806 91637287 91637747 0.000000e+00 747.0
6 TraesCS5D01G086600 chr5D 91.815 281 12 6 1043 1323 91634199 91634468 6.710000e-102 381.0
7 TraesCS5D01G086600 chr5D 89.175 194 19 2 791 983 91865038 91864846 1.190000e-59 241.0
8 TraesCS5D01G086600 chr5D 85.141 249 18 5 791 1037 435482708 435482939 1.540000e-58 237.0
9 TraesCS5D01G086600 chr5D 100.000 49 0 0 2361 2409 91652556 91652604 1.270000e-14 91.6
10 TraesCS5D01G086600 chr5D 97.826 46 1 0 987 1032 435481843 435481798 2.740000e-11 80.5
11 TraesCS5D01G086600 chr5B 90.278 2016 140 20 1034 3043 96906127 96908092 0.000000e+00 2586.0
12 TraesCS5D01G086600 chr5B 90.072 695 31 8 304 983 542054574 542055245 0.000000e+00 867.0
13 TraesCS5D01G086600 chr5B 90.144 416 33 7 1047 1462 96903955 96904362 4.870000e-148 534.0
14 TraesCS5D01G086600 chr5B 91.367 278 19 3 3041 3316 96908132 96908406 3.120000e-100 375.0
15 TraesCS5D01G086600 chr5B 80.750 400 70 3 1093 1489 684066549 684066944 4.160000e-79 305.0
16 TraesCS5D01G086600 chr6D 97.355 983 24 1 1 983 417352432 417353412 0.000000e+00 1670.0
17 TraesCS5D01G086600 chr6D 88.718 195 18 4 791 983 417352514 417352322 5.530000e-58 235.0
18 TraesCS5D01G086600 chr6D 97.826 46 1 0 987 1032 417353401 417353446 2.740000e-11 80.5
19 TraesCS5D01G086600 chr7D 96.541 983 32 1 1 983 214337423 214338403 0.000000e+00 1626.0
20 TraesCS5D01G086600 chr7D 88.205 195 19 4 791 983 214337505 214337313 2.570000e-56 230.0
21 TraesCS5D01G086600 chr7D 97.826 46 1 0 987 1032 214338392 214338437 2.740000e-11 80.5
22 TraesCS5D01G086600 chr7A 95.176 995 36 8 1 983 10093432 10092438 0.000000e+00 1561.0
23 TraesCS5D01G086600 chr1B 94.795 999 29 7 1 983 585940065 585941056 0.000000e+00 1535.0
24 TraesCS5D01G086600 chr5A 89.125 1223 104 13 1041 2256 85266842 85268042 0.000000e+00 1495.0
25 TraesCS5D01G086600 chr5A 90.132 608 51 6 1065 1672 85352734 85353332 0.000000e+00 782.0
26 TraesCS5D01G086600 chr5A 89.967 608 34 9 2436 3043 85354078 85354658 0.000000e+00 760.0
27 TraesCS5D01G086600 chr5A 95.703 256 8 1 3041 3296 85354698 85354950 3.080000e-110 409.0
28 TraesCS5D01G086600 chr5A 92.797 236 16 1 2175 2409 85353858 85354093 1.140000e-89 340.0
29 TraesCS5D01G086600 chr5A 93.919 148 7 2 837 983 645758183 645758037 4.310000e-54 222.0
30 TraesCS5D01G086600 chr5A 98.438 64 1 0 2731 2794 85353330 85353393 2.700000e-21 113.0
31 TraesCS5D01G086600 chr1A 93.373 1011 41 9 1 985 534256742 534257752 0.000000e+00 1472.0
32 TraesCS5D01G086600 chr4A 93.089 984 39 3 1 983 539150230 539151185 0.000000e+00 1413.0
33 TraesCS5D01G086600 chr2D 85.586 1117 153 4 1118 2230 559229317 559228205 0.000000e+00 1164.0
34 TraesCS5D01G086600 chr2A 84.802 1033 147 5 1221 2246 699818426 699817397 0.000000e+00 1029.0
35 TraesCS5D01G086600 chr2B 95.382 628 29 0 1 628 448698256 448698883 0.000000e+00 1000.0
36 TraesCS5D01G086600 chr6A 94.876 605 31 0 1 605 434802321 434802925 0.000000e+00 946.0
37 TraesCS5D01G086600 chr6A 85.279 197 12 3 837 1032 523821882 523822062 1.570000e-43 187.0
38 TraesCS5D01G086600 chrUn 100.000 401 0 0 1870 2270 478636223 478636623 0.000000e+00 741.0
39 TraesCS5D01G086600 chr3D 83.302 527 78 4 1 527 7091897 7091381 8.320000e-131 477.0
40 TraesCS5D01G086600 chr3D 85.169 445 63 3 528 971 7091306 7090864 1.400000e-123 453.0


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 TraesCS5D01G086600 chr5D 91864956 91868271 3315 False 6124.000000 6124 100.000000 1 3316 1 chr5D.!!$F2 3315
1 TraesCS5D01G086600 chr5D 91616670 91617795 1125 False 1415.000000 1415 89.354000 1038 2176 1 chr5D.!!$F1 1138
2 TraesCS5D01G086600 chr5D 91652017 91653471 1454 False 853.866667 1496 98.847667 1801 3316 3 chr5D.!!$F5 1515
3 TraesCS5D01G086600 chr5D 435481798 435482790 992 True 801.250000 1522 96.420500 1 1032 2 chr5D.!!$R2 1031
4 TraesCS5D01G086600 chr5D 91634199 91637747 3548 False 564.000000 747 93.955000 1043 1806 2 chr5D.!!$F4 763
5 TraesCS5D01G086600 chr5B 96903955 96908406 4451 False 1165.000000 2586 90.596333 1034 3316 3 chr5B.!!$F3 2282
6 TraesCS5D01G086600 chr5B 542054574 542055245 671 False 867.000000 867 90.072000 304 983 1 chr5B.!!$F1 679
7 TraesCS5D01G086600 chr6D 417352432 417353446 1014 False 875.250000 1670 97.590500 1 1032 2 chr6D.!!$F1 1031
8 TraesCS5D01G086600 chr7D 214337423 214338437 1014 False 853.250000 1626 97.183500 1 1032 2 chr7D.!!$F1 1031
9 TraesCS5D01G086600 chr7A 10092438 10093432 994 True 1561.000000 1561 95.176000 1 983 1 chr7A.!!$R1 982
10 TraesCS5D01G086600 chr1B 585940065 585941056 991 False 1535.000000 1535 94.795000 1 983 1 chr1B.!!$F1 982
11 TraesCS5D01G086600 chr5A 85266842 85268042 1200 False 1495.000000 1495 89.125000 1041 2256 1 chr5A.!!$F1 1215
12 TraesCS5D01G086600 chr5A 85352734 85354950 2216 False 480.800000 782 93.407400 1065 3296 5 chr5A.!!$F2 2231
13 TraesCS5D01G086600 chr1A 534256742 534257752 1010 False 1472.000000 1472 93.373000 1 985 1 chr1A.!!$F1 984
14 TraesCS5D01G086600 chr4A 539150230 539151185 955 False 1413.000000 1413 93.089000 1 983 1 chr4A.!!$F1 982
15 TraesCS5D01G086600 chr2D 559228205 559229317 1112 True 1164.000000 1164 85.586000 1118 2230 1 chr2D.!!$R1 1112
16 TraesCS5D01G086600 chr2A 699817397 699818426 1029 True 1029.000000 1029 84.802000 1221 2246 1 chr2A.!!$R1 1025
17 TraesCS5D01G086600 chr2B 448698256 448698883 627 False 1000.000000 1000 95.382000 1 628 1 chr2B.!!$F1 627
18 TraesCS5D01G086600 chr6A 434802321 434802925 604 False 946.000000 946 94.876000 1 605 1 chr6A.!!$F1 604
19 TraesCS5D01G086600 chr3D 7090864 7091897 1033 True 465.000000 477 84.235500 1 971 2 chr3D.!!$R1 970

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
669 764 0.255033 GGATTTTAGGTCGCTGGGGT 59.745 55.0 0.0 0.0 0.0 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2467 6833 1.331756 CGTCTGCAATGAACTATGGCC 59.668 52.381 0.0 0.0 34.6 5.36 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
229 231 2.282887 GGTGCATTGGGAACGGGT 60.283 61.111 0.00 0.00 0.00 5.28
669 764 0.255033 GGATTTTAGGTCGCTGGGGT 59.745 55.000 0.00 0.00 0.00 4.95
844 939 2.032634 CACATAGGCACGCCACGTT 61.033 57.895 11.35 0.00 38.32 3.99
845 940 1.740296 ACATAGGCACGCCACGTTC 60.740 57.895 11.35 0.00 38.32 3.95
988 1084 2.706636 CCGACCGGTTACCTATCGA 58.293 57.895 20.69 0.00 32.66 3.59
989 1085 0.308993 CCGACCGGTTACCTATCGAC 59.691 60.000 20.69 0.00 32.66 4.20
990 1086 0.308993 CGACCGGTTACCTATCGACC 59.691 60.000 9.42 0.00 32.66 4.79
1015 1111 1.767692 CCTAGCCCCAAGTGTGGTT 59.232 57.895 0.00 0.00 44.30 3.67
1124 2264 1.475403 CTCCGCCTCTTACTCTTCCA 58.525 55.000 0.00 0.00 0.00 3.53
1137 2277 0.684535 TCTTCCACTTCCGCATGACA 59.315 50.000 0.00 0.00 0.00 3.58
1659 5598 1.426816 CGCCTGCGTCTACTCGTCTA 61.427 60.000 2.83 0.00 34.35 2.59
1868 5807 2.514592 ATTGTCCTCATGCCGGCG 60.515 61.111 23.90 8.74 0.00 6.46
2410 6776 8.607441 TGCAAATTGTATATGTCTCCTACATC 57.393 34.615 0.00 0.00 46.15 3.06
2411 6777 7.661437 TGCAAATTGTATATGTCTCCTACATCC 59.339 37.037 0.00 0.00 46.15 3.51
2457 6823 8.959548 TCAAGTATATGTCTCCTACACGTTTTA 58.040 33.333 0.00 0.00 42.09 1.52
2467 6833 4.981674 TCCTACACGTTTTAAAGTGTACGG 59.018 41.667 14.52 17.13 46.95 4.02
2468 6834 4.150451 CCTACACGTTTTAAAGTGTACGGG 59.850 45.833 14.52 11.97 46.95 5.28
2516 6882 6.039941 AGTCTCATTAACTGACTTCCTATCCG 59.960 42.308 0.00 0.00 37.76 4.18
2688 7057 8.871629 AATAACCACCATACAAGTGAAACATA 57.128 30.769 0.00 0.00 41.43 2.29
2723 7093 4.701171 TGTTGTTCTTCTTTACCGGTGTTT 59.299 37.500 19.93 0.00 0.00 2.83
2808 7178 1.125633 GGAATGGGCCTGCATTCAAT 58.874 50.000 26.40 1.46 39.01 2.57
2811 7181 0.325860 ATGGGCCTGCATTCAATGGT 60.326 50.000 4.53 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
505 508 1.865788 GCGGCAAACCAGAAGCATCA 61.866 55.000 0.00 0.00 34.57 3.07
992 1088 0.989602 ACACTTGGGGCTAGGGTAAC 59.010 55.000 0.00 0.00 0.00 2.50
993 1089 0.988832 CACACTTGGGGCTAGGGTAA 59.011 55.000 0.00 0.00 0.00 2.85
994 1090 0.912487 CCACACTTGGGGCTAGGGTA 60.912 60.000 0.00 0.00 39.57 3.69
995 1091 2.231380 CCACACTTGGGGCTAGGGT 61.231 63.158 0.00 0.00 39.57 4.34
1124 2264 0.321653 GGAGGTTGTCATGCGGAAGT 60.322 55.000 0.00 0.00 0.00 3.01
1868 5807 2.123982 CCAAGGCCTCCATGCTCC 60.124 66.667 5.23 0.00 0.00 4.70
2270 6624 4.114794 CAGGCAAAGTAAATTATGCAGCC 58.885 43.478 0.00 0.00 40.51 4.85
2349 6714 2.564062 CCTTCAGGCAACATGGTTCAAT 59.436 45.455 0.00 0.00 41.41 2.57
2411 6777 3.437395 TGACCGGATACAAAATTTGACCG 59.563 43.478 23.65 23.65 41.09 4.79
2457 6823 2.303600 TGAACTATGGCCCGTACACTTT 59.696 45.455 0.00 0.00 0.00 2.66
2467 6833 1.331756 CGTCTGCAATGAACTATGGCC 59.668 52.381 0.00 0.00 34.60 5.36
2468 6834 2.279741 TCGTCTGCAATGAACTATGGC 58.720 47.619 0.00 0.00 36.18 4.40
2534 6900 3.740832 TGATACAAGAACTTGAGTGCACG 59.259 43.478 19.35 0.00 42.93 5.34
2653 7019 4.584638 ATGGTGGTTATTTCCTAGCACA 57.415 40.909 0.00 0.00 42.82 4.57
2688 7057 5.930135 AGAAGAACAACAGAACACACCTAT 58.070 37.500 0.00 0.00 0.00 2.57
2723 7093 7.717436 GGTCTGGACGATGATATAGATATCTGA 59.283 40.741 15.79 3.60 39.82 3.27
2808 7178 8.707796 TGTTTGTAAATCCCTGTTTATAACCA 57.292 30.769 0.00 0.00 28.58 3.67
2902 7272 3.782046 TGCTCTCGGTAAATACAAGCTC 58.218 45.455 0.00 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.