Multiple sequence alignment - TraesCS4A01G436300

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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 TraesCS4A01G436300 chr4A 100.000 3361 0 0 1 3361 705957557 705960917 0.000000e+00 6207.0
1 TraesCS4A01G436300 chr4A 97.048 3388 64 17 1 3361 706093863 706097241 0.000000e+00 5670.0
2 TraesCS4A01G436300 chr4A 97.069 1160 30 2 2206 3361 705906864 705908023 0.000000e+00 1951.0
3 TraesCS4A01G436300 chr4A 92.562 1210 70 5 1020 2209 707478317 707477108 0.000000e+00 1718.0
4 TraesCS4A01G436300 chr4A 93.385 1164 62 9 2206 3361 707477045 707475889 0.000000e+00 1709.0
5 TraesCS4A01G436300 chr4A 91.369 1205 74 4 1020 2209 707177788 707178977 0.000000e+00 1622.0
6 TraesCS4A01G436300 chr4A 91.369 1205 74 4 1020 2209 707201313 707202502 0.000000e+00 1622.0
7 TraesCS4A01G436300 chr4A 91.429 1190 87 3 1020 2194 707402862 707404051 0.000000e+00 1618.0
8 TraesCS4A01G436300 chr4A 91.008 1190 92 3 1020 2194 705889390 705890579 0.000000e+00 1591.0
9 TraesCS4A01G436300 chr4A 88.653 1084 91 18 898 1958 705903619 705904693 0.000000e+00 1291.0
10 TraesCS4A01G436300 chr4A 95.842 505 21 0 1014 1518 707646587 707646083 0.000000e+00 817.0
11 TraesCS4A01G436300 chr4A 93.600 375 16 5 2410 2782 707645625 707645257 1.360000e-153 553.0
12 TraesCS4A01G436300 chr4A 92.857 224 16 0 2773 2996 707643443 707643220 3.230000e-85 326.0
13 TraesCS4A01G436300 chr4A 95.789 95 3 1 2316 2409 707645840 707645746 5.810000e-33 152.0
14 TraesCS4A01G436300 chr4A 84.211 95 9 5 869 959 707484619 707484527 1.660000e-13 87.9
15 TraesCS4A01G436300 chr4A 85.057 87 8 3 2565 2651 707301288 707301369 2.150000e-12 84.2
16 TraesCS4A01G436300 chrUn 96.665 1829 27 15 554 2356 220054487 220056307 0.000000e+00 3009.0
17 TraesCS4A01G436300 chrUn 99.615 1038 4 0 1628 2665 447800388 447801425 0.000000e+00 1895.0
18 TraesCS4A01G436300 chrUn 98.417 695 11 0 2667 3361 343476104 343476798 0.000000e+00 1223.0
19 TraesCS4A01G436300 chrUn 92.105 38 3 0 2653 2690 368050301 368050338 2.000000e-03 54.7
20 TraesCS4A01G436300 chr7D 92.016 1215 75 7 1010 2203 24157222 24156009 0.000000e+00 1687.0
21 TraesCS4A01G436300 chr7D 91.646 1209 74 7 1010 2194 24032588 24033793 0.000000e+00 1648.0
22 TraesCS4A01G436300 chr7D 91.583 1093 77 3 1010 2087 24144809 24145901 0.000000e+00 1495.0
23 TraesCS4A01G436300 chr7D 87.167 413 43 5 2500 2903 24155530 24155119 8.500000e-126 460.0
24 TraesCS4A01G436300 chr7D 84.689 209 20 9 2206 2408 24033892 24034094 7.360000e-47 198.0
25 TraesCS4A01G436300 chr7D 89.583 48 5 0 951 998 93126852 93126805 1.010000e-05 62.1
26 TraesCS4A01G436300 chr6B 93.316 748 44 4 1 743 168071516 168072262 0.000000e+00 1099.0
27 TraesCS4A01G436300 chr6B 92.838 754 45 5 1 746 204593085 204593837 0.000000e+00 1085.0
28 TraesCS4A01G436300 chr6B 95.349 43 2 0 956 998 692236061 692236019 6.020000e-08 69.4
29 TraesCS4A01G436300 chr1B 93.076 751 46 4 1 746 109247240 109246491 0.000000e+00 1094.0
30 TraesCS4A01G436300 chr1B 92.790 749 46 6 1 744 2351398 2350653 0.000000e+00 1077.0
31 TraesCS4A01G436300 chr1B 97.500 40 1 0 956 995 315353859 315353898 6.020000e-08 69.4
32 TraesCS4A01G436300 chr5B 93.057 749 46 4 1 744 142232267 142233014 0.000000e+00 1090.0
33 TraesCS4A01G436300 chr5B 92.686 752 47 7 1 746 706849602 706848853 0.000000e+00 1077.0
34 TraesCS4A01G436300 chr5B 88.722 133 13 1 743 873 250927264 250927396 9.650000e-36 161.0
35 TraesCS4A01G436300 chr5B 95.349 43 2 0 956 998 381026298 381026256 6.020000e-08 69.4
36 TraesCS4A01G436300 chr5B 95.349 43 2 0 956 998 665971390 665971348 6.020000e-08 69.4
37 TraesCS4A01G436300 chr5B 95.122 41 2 0 958 998 471313465 471313425 7.780000e-07 65.8
38 TraesCS4A01G436300 chr2D 92.829 753 47 5 1 746 81455121 81455873 0.000000e+00 1085.0
39 TraesCS4A01G436300 chr2D 94.737 38 2 0 2653 2690 251023839 251023876 3.620000e-05 60.2
40 TraesCS4A01G436300 chr6D 92.914 748 45 6 1 742 168299040 168298295 0.000000e+00 1081.0
41 TraesCS4A01G436300 chr6D 91.200 125 9 1 749 871 456946171 456946047 5.770000e-38 169.0
42 TraesCS4A01G436300 chr6D 93.333 45 1 2 948 991 202977428 202977471 7.780000e-07 65.8
43 TraesCS4A01G436300 chr5D 90.840 131 10 1 743 871 157169892 157170022 1.240000e-39 174.0
44 TraesCS4A01G436300 chr7A 89.630 135 12 1 743 875 96936456 96936322 1.600000e-38 171.0
45 TraesCS4A01G436300 chr3A 90.076 131 11 2 743 871 702207517 702207387 5.770000e-38 169.0
46 TraesCS4A01G436300 chr3A 100.000 42 0 0 950 991 145617232 145617191 1.000000e-10 78.7
47 TraesCS4A01G436300 chr1D 88.722 133 13 1 743 873 397751173 397751041 9.650000e-36 161.0
48 TraesCS4A01G436300 chr4B 87.681 138 15 1 743 878 154548128 154548265 3.470000e-35 159.0
49 TraesCS4A01G436300 chr4B 95.122 41 2 0 958 998 40785768 40785728 7.780000e-07 65.8
50 TraesCS4A01G436300 chr4D 79.186 221 46 0 3141 3361 359843236 359843016 1.610000e-33 154.0
51 TraesCS4A01G436300 chr4D 100.000 29 0 0 2662 2690 20241357 20241329 2.000000e-03 54.7


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 TraesCS4A01G436300 chr4A 705957557 705960917 3360 False 6207.0 6207 100.0000 1 3361 1 chr4A.!!$F2 3360
1 TraesCS4A01G436300 chr4A 706093863 706097241 3378 False 5670.0 5670 97.0480 1 3361 1 chr4A.!!$F3 3360
2 TraesCS4A01G436300 chr4A 707475889 707478317 2428 True 1713.5 1718 92.9735 1020 3361 2 chr4A.!!$R2 2341
3 TraesCS4A01G436300 chr4A 707177788 707178977 1189 False 1622.0 1622 91.3690 1020 2209 1 chr4A.!!$F4 1189
4 TraesCS4A01G436300 chr4A 707201313 707202502 1189 False 1622.0 1622 91.3690 1020 2209 1 chr4A.!!$F5 1189
5 TraesCS4A01G436300 chr4A 705903619 705908023 4404 False 1621.0 1951 92.8610 898 3361 2 chr4A.!!$F8 2463
6 TraesCS4A01G436300 chr4A 707402862 707404051 1189 False 1618.0 1618 91.4290 1020 2194 1 chr4A.!!$F7 1174
7 TraesCS4A01G436300 chr4A 705889390 705890579 1189 False 1591.0 1591 91.0080 1020 2194 1 chr4A.!!$F1 1174
8 TraesCS4A01G436300 chr4A 707643220 707646587 3367 True 462.0 817 94.5220 1014 2996 4 chr4A.!!$R3 1982
9 TraesCS4A01G436300 chrUn 220054487 220056307 1820 False 3009.0 3009 96.6650 554 2356 1 chrUn.!!$F1 1802
10 TraesCS4A01G436300 chrUn 447800388 447801425 1037 False 1895.0 1895 99.6150 1628 2665 1 chrUn.!!$F4 1037
11 TraesCS4A01G436300 chrUn 343476104 343476798 694 False 1223.0 1223 98.4170 2667 3361 1 chrUn.!!$F2 694
12 TraesCS4A01G436300 chr7D 24144809 24145901 1092 False 1495.0 1495 91.5830 1010 2087 1 chr7D.!!$F1 1077
13 TraesCS4A01G436300 chr7D 24155119 24157222 2103 True 1073.5 1687 89.5915 1010 2903 2 chr7D.!!$R2 1893
14 TraesCS4A01G436300 chr7D 24032588 24034094 1506 False 923.0 1648 88.1675 1010 2408 2 chr7D.!!$F2 1398
15 TraesCS4A01G436300 chr6B 168071516 168072262 746 False 1099.0 1099 93.3160 1 743 1 chr6B.!!$F1 742
16 TraesCS4A01G436300 chr6B 204593085 204593837 752 False 1085.0 1085 92.8380 1 746 1 chr6B.!!$F2 745
17 TraesCS4A01G436300 chr1B 109246491 109247240 749 True 1094.0 1094 93.0760 1 746 1 chr1B.!!$R2 745
18 TraesCS4A01G436300 chr1B 2350653 2351398 745 True 1077.0 1077 92.7900 1 744 1 chr1B.!!$R1 743
19 TraesCS4A01G436300 chr5B 142232267 142233014 747 False 1090.0 1090 93.0570 1 744 1 chr5B.!!$F1 743
20 TraesCS4A01G436300 chr5B 706848853 706849602 749 True 1077.0 1077 92.6860 1 746 1 chr5B.!!$R4 745
21 TraesCS4A01G436300 chr2D 81455121 81455873 752 False 1085.0 1085 92.8290 1 746 1 chr2D.!!$F1 745
22 TraesCS4A01G436300 chr6D 168298295 168299040 745 True 1081.0 1081 92.9140 1 742 1 chr6D.!!$R1 741

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
550 556 0.108186 TTAGGTCTGGCTGCGATGTG 60.108 55.000 0.00 0.0 0.00 3.21 F
978 992 1.479730 ACTCCCTCCGTTCGGAAATAC 59.520 52.381 14.79 0.0 33.41 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1587 1650 0.533308 GGACTGCCGTGTGGTAAACA 60.533 55.000 0.0 0.0 37.67 2.83 R
2991 7042 2.512056 TCCCCAAGAGGAGAAAAACACA 59.488 45.455 0.0 0.0 38.24 3.72 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
74 76 2.355716 CCGTTCCCTTCTTGAAGGCATA 60.356 50.000 20.71 8.14 38.63 3.14
76 78 3.619979 CGTTCCCTTCTTGAAGGCATAGT 60.620 47.826 20.71 0.00 38.63 2.12
220 226 2.603776 AGGGACCAGTGGACGACC 60.604 66.667 18.40 11.79 0.00 4.79
403 409 2.752903 TCGATGCAGCAGTACAACTCTA 59.247 45.455 1.53 0.00 0.00 2.43
550 556 0.108186 TTAGGTCTGGCTGCGATGTG 60.108 55.000 0.00 0.00 0.00 3.21
665 675 8.426489 ACTGTTGTATGACTTTGTAAGGTCTTA 58.574 33.333 8.11 4.09 34.01 2.10
831 845 4.870363 ACATTCACATGGTTAACTTGCAC 58.130 39.130 5.42 0.00 34.27 4.57
837 851 3.381908 ACATGGTTAACTTGCACGGAAAA 59.618 39.130 5.42 0.00 0.00 2.29
857 871 9.730420 CGGAAAACAATAAACCTTATATTCTGG 57.270 33.333 0.00 0.00 0.00 3.86
968 982 9.322769 ACTGATATTATTAATTACTCCCTCCGT 57.677 33.333 0.00 0.00 0.00 4.69
971 985 9.298774 GATATTATTAATTACTCCCTCCGTTCG 57.701 37.037 0.00 0.00 0.00 3.95
972 986 3.806625 TTAATTACTCCCTCCGTTCGG 57.193 47.619 4.74 4.74 0.00 4.30
973 987 1.856629 AATTACTCCCTCCGTTCGGA 58.143 50.000 13.34 13.34 0.00 4.55
974 988 1.856629 ATTACTCCCTCCGTTCGGAA 58.143 50.000 14.79 0.04 33.41 4.30
975 989 1.631405 TTACTCCCTCCGTTCGGAAA 58.369 50.000 14.79 2.93 33.41 3.13
976 990 1.856629 TACTCCCTCCGTTCGGAAAT 58.143 50.000 14.79 2.39 33.41 2.17
977 991 1.856629 ACTCCCTCCGTTCGGAAATA 58.143 50.000 14.79 2.82 33.41 1.40
978 992 1.479730 ACTCCCTCCGTTCGGAAATAC 59.520 52.381 14.79 0.00 33.41 1.89
979 993 1.755380 CTCCCTCCGTTCGGAAATACT 59.245 52.381 14.79 0.00 33.41 2.12
980 994 2.167900 CTCCCTCCGTTCGGAAATACTT 59.832 50.000 14.79 0.00 33.41 2.24
981 995 2.093869 TCCCTCCGTTCGGAAATACTTG 60.094 50.000 14.79 1.97 33.41 3.16
982 996 2.354403 CCCTCCGTTCGGAAATACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
983 997 2.928116 CCTCCGTTCGGAAATACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
984 998 3.581755 CTCCGTTCGGAAATACTTGTCA 58.418 45.455 14.79 0.00 33.41 3.58
985 999 4.181578 CTCCGTTCGGAAATACTTGTCAT 58.818 43.478 14.79 0.00 33.41 3.06
986 1000 4.571919 TCCGTTCGGAAATACTTGTCATT 58.428 39.130 11.66 0.00 0.00 2.57
987 1001 4.390603 TCCGTTCGGAAATACTTGTCATTG 59.609 41.667 11.66 0.00 0.00 2.82
1008 1022 2.511600 GGGACGTGCCGATGAAGG 60.512 66.667 11.44 0.00 37.63 3.46
2356 4434 8.299990 TCTCCTATAGTCCTACGTATACTACC 57.700 42.308 16.08 0.00 0.00 3.18
2991 7042 7.820386 TGAATTATGCATGAACTCAAAAAGCAT 59.180 29.630 10.16 13.22 42.98 3.79
3344 7395 0.178975 AGTCGGGGCCAATTTGTTCA 60.179 50.000 4.39 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 76 6.781943 AGTAGTCTACAACTTCTCCACTACT 58.218 40.000 12.54 3.53 40.01 2.57
76 78 8.770322 AGATAGTAGTCTACAACTTCTCCACTA 58.230 37.037 12.54 0.00 39.55 2.74
220 226 2.328099 GCACCGCTCCACCAAAGAG 61.328 63.158 0.00 0.00 0.00 2.85
403 409 2.564062 CACTTGCCACCAATCCATCTTT 59.436 45.455 0.00 0.00 0.00 2.52
550 556 2.375146 CCTGGGCCTAATACCAAACAC 58.625 52.381 4.53 0.00 36.09 3.32
831 845 9.730420 CCAGAATATAAGGTTTATTGTTTTCCG 57.270 33.333 0.00 0.00 0.00 4.30
857 871 8.652290 AGGTTGTCTTATATACTCCCTCAATTC 58.348 37.037 0.00 0.00 0.00 2.17
959 973 1.755380 AGTATTTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
961 975 2.277084 CAAGTATTTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
962 976 2.928116 GACAAGTATTTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
963 977 3.581755 TGACAAGTATTTCCGAACGGAG 58.418 45.455 15.34 5.60 46.06 4.63
964 978 3.663995 TGACAAGTATTTCCGAACGGA 57.336 42.857 12.04 12.04 43.52 4.69
965 979 4.390603 TCAATGACAAGTATTTCCGAACGG 59.609 41.667 6.94 6.94 0.00 4.44
966 980 5.524511 TCAATGACAAGTATTTCCGAACG 57.475 39.130 0.00 0.00 0.00 3.95
967 981 6.801862 CCTTTCAATGACAAGTATTTCCGAAC 59.198 38.462 0.00 0.00 0.00 3.95
968 982 6.072175 CCCTTTCAATGACAAGTATTTCCGAA 60.072 38.462 0.00 0.00 0.00 4.30
969 983 5.414454 CCCTTTCAATGACAAGTATTTCCGA 59.586 40.000 0.00 0.00 0.00 4.55
970 984 5.414454 TCCCTTTCAATGACAAGTATTTCCG 59.586 40.000 0.00 0.00 0.00 4.30
971 985 6.621613 GTCCCTTTCAATGACAAGTATTTCC 58.378 40.000 0.00 0.00 0.00 3.13
972 986 6.072673 ACGTCCCTTTCAATGACAAGTATTTC 60.073 38.462 0.00 0.00 0.00 2.17
973 987 5.768164 ACGTCCCTTTCAATGACAAGTATTT 59.232 36.000 0.00 0.00 0.00 1.40
974 988 5.181245 CACGTCCCTTTCAATGACAAGTATT 59.819 40.000 0.00 0.00 0.00 1.89
975 989 4.695455 CACGTCCCTTTCAATGACAAGTAT 59.305 41.667 0.00 0.00 0.00 2.12
976 990 4.062293 CACGTCCCTTTCAATGACAAGTA 58.938 43.478 0.00 0.00 0.00 2.24
977 991 2.878406 CACGTCCCTTTCAATGACAAGT 59.122 45.455 0.00 0.00 0.00 3.16
978 992 2.350772 GCACGTCCCTTTCAATGACAAG 60.351 50.000 0.00 0.00 0.00 3.16
979 993 1.606668 GCACGTCCCTTTCAATGACAA 59.393 47.619 0.00 0.00 0.00 3.18
980 994 1.234821 GCACGTCCCTTTCAATGACA 58.765 50.000 0.00 0.00 0.00 3.58
981 995 0.521735 GGCACGTCCCTTTCAATGAC 59.478 55.000 0.00 0.00 0.00 3.06
982 996 2.941210 GGCACGTCCCTTTCAATGA 58.059 52.632 0.00 0.00 0.00 2.57
1587 1650 0.533308 GGACTGCCGTGTGGTAAACA 60.533 55.000 0.00 0.00 37.67 2.83
2991 7042 2.512056 TCCCCAAGAGGAGAAAAACACA 59.488 45.455 0.00 0.00 38.24 3.72


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

AutoCloner maintained by Alex Coulton.