Multiple sequence alignment - TraesCS3A01G414600

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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 TraesCS3A01G414600 chr3A 100.000 2972 0 0 1 2972 658185863 658188834 0.000000e+00 5489.0
1 TraesCS3A01G414600 chr3A 96.392 2993 62 13 1 2972 655937617 655934650 0.000000e+00 4887.0
2 TraesCS3A01G414600 chr3A 92.586 1160 80 3 961 2120 655994968 655993815 0.000000e+00 1661.0
3 TraesCS3A01G414600 chr3A 90.244 738 37 14 2259 2970 651484577 651483849 0.000000e+00 931.0
4 TraesCS3A01G414600 chr3B 93.345 2269 111 23 11 2260 685876167 685873920 0.000000e+00 3317.0
5 TraesCS3A01G414600 chr3B 95.326 1455 67 1 807 2260 685763763 685762309 0.000000e+00 2309.0
6 TraesCS3A01G414600 chr3B 88.874 1528 105 31 626 2120 685910500 685909005 0.000000e+00 1820.0
7 TraesCS3A01G414600 chr3B 85.642 1588 166 25 626 2169 685941996 685940427 0.000000e+00 1613.0
8 TraesCS3A01G414600 chr3B 86.546 1494 155 21 626 2092 685980452 685978978 0.000000e+00 1604.0
9 TraesCS3A01G414600 chr3B 89.959 737 45 9 2260 2972 330590611 330589880 0.000000e+00 924.0
10 TraesCS3A01G414600 chr3B 91.158 622 43 7 1 615 685764414 685763798 0.000000e+00 833.0
11 TraesCS3A01G414600 chr3B 85.116 215 23 3 317 529 686045881 686045674 8.350000e-51 211.0
12 TraesCS3A01G414600 chr3B 86.719 128 15 1 819 944 685883081 685882954 1.110000e-29 141.0
13 TraesCS3A01G414600 chr3D 95.404 1262 57 1 1000 2260 520641870 520640609 0.000000e+00 2008.0
14 TraesCS3A01G414600 chr3D 89.325 1527 101 28 626 2120 520678584 520677088 0.000000e+00 1860.0
15 TraesCS3A01G414600 chr3D 87.105 1489 150 17 712 2169 520684429 520682952 0.000000e+00 1648.0
16 TraesCS3A01G414600 chr3D 86.676 1501 142 24 626 2092 520703905 520702429 0.000000e+00 1611.0
17 TraesCS3A01G414600 chr3D 92.237 979 57 10 3 965 520642847 520641872 0.000000e+00 1369.0
18 TraesCS3A01G414600 chr3D 86.312 1147 127 22 1119 2260 520640133 520639012 0.000000e+00 1221.0
19 TraesCS3A01G414600 chr3D 82.132 985 138 20 1119 2092 520638536 520637579 0.000000e+00 809.0
20 TraesCS3A01G414600 chr3D 83.232 328 38 8 264 582 520704240 520703921 4.850000e-73 285.0
21 TraesCS3A01G414600 chr3D 86.207 145 18 1 819 961 520656991 520656847 3.970000e-34 156.0
22 TraesCS3A01G414600 chr3D 81.343 134 16 8 20 150 38005006 38004879 1.880000e-17 100.0
23 TraesCS3A01G414600 chr3D 79.845 129 14 4 443 568 520676674 520676555 1.900000e-12 84.2
24 TraesCS3A01G414600 chr7A 90.617 746 40 12 2250 2972 171639659 171638921 0.000000e+00 963.0
25 TraesCS3A01G414600 chr7A 88.584 473 28 8 2523 2972 476230396 476229927 4.330000e-153 551.0
26 TraesCS3A01G414600 chr7A 87.975 474 30 8 2522 2972 476228170 476227701 4.360000e-148 534.0
27 TraesCS3A01G414600 chr1A 90.604 745 42 11 2251 2972 292538188 292538927 0.000000e+00 963.0
28 TraesCS3A01G414600 chr1A 77.536 138 31 0 18 155 414910704 414910841 1.900000e-12 84.2
29 TraesCS3A01G414600 chr7D 90.146 751 41 14 2250 2972 498917355 498916610 0.000000e+00 946.0
30 TraesCS3A01G414600 chr7D 84.615 65 6 3 18 80 538488731 538488669 8.890000e-06 62.1
31 TraesCS3A01G414600 chrUn 90.283 741 38 12 2260 2972 97102136 97101402 0.000000e+00 939.0
32 TraesCS3A01G414600 chr4D 89.826 747 46 11 2252 2972 246415973 246416715 0.000000e+00 931.0
33 TraesCS3A01G414600 chr4D 89.782 734 49 10 2260 2972 335737917 335737189 0.000000e+00 917.0
34 TraesCS3A01G414600 chr5A 89.637 743 46 16 2251 2972 220937290 220938022 0.000000e+00 917.0
35 TraesCS3A01G414600 chr5A 90.281 463 17 8 2531 2972 480389299 480388844 5.520000e-162 580.0
36 TraesCS3A01G414600 chr7B 87.450 757 41 17 2238 2972 639272751 639272027 0.000000e+00 822.0
37 TraesCS3A01G414600 chr7B 88.027 735 34 11 2259 2972 594767358 594768059 0.000000e+00 821.0
38 TraesCS3A01G414600 chr6B 87.045 741 40 28 2260 2972 574523626 574522914 0.000000e+00 785.0
39 TraesCS3A01G414600 chr6B 85.938 64 8 1 17 79 141696000 141695937 1.910000e-07 67.6
40 TraesCS3A01G414600 chr4B 86.395 735 49 25 2259 2972 283350599 283351303 0.000000e+00 756.0
41 TraesCS3A01G414600 chr2A 90.287 453 26 3 2537 2972 291781849 291782300 7.140000e-161 577.0
42 TraesCS3A01G414600 chr1B 89.500 400 18 4 2594 2972 415722494 415722890 4.450000e-133 484.0
43 TraesCS3A01G414600 chr2B 97.368 38 0 1 20 57 786004344 786004380 2.470000e-06 63.9


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 TraesCS3A01G414600 chr3A 658185863 658188834 2971 False 5489.00 5489 100.00000 1 2972 1 chr3A.!!$F1 2971
1 TraesCS3A01G414600 chr3A 655934650 655937617 2967 True 4887.00 4887 96.39200 1 2972 1 chr3A.!!$R2 2971
2 TraesCS3A01G414600 chr3A 655993815 655994968 1153 True 1661.00 1661 92.58600 961 2120 1 chr3A.!!$R3 1159
3 TraesCS3A01G414600 chr3A 651483849 651484577 728 True 931.00 931 90.24400 2259 2970 1 chr3A.!!$R1 711
4 TraesCS3A01G414600 chr3B 685873920 685876167 2247 True 3317.00 3317 93.34500 11 2260 1 chr3B.!!$R2 2249
5 TraesCS3A01G414600 chr3B 685909005 685910500 1495 True 1820.00 1820 88.87400 626 2120 1 chr3B.!!$R4 1494
6 TraesCS3A01G414600 chr3B 685940427 685941996 1569 True 1613.00 1613 85.64200 626 2169 1 chr3B.!!$R5 1543
7 TraesCS3A01G414600 chr3B 685978978 685980452 1474 True 1604.00 1604 86.54600 626 2092 1 chr3B.!!$R6 1466
8 TraesCS3A01G414600 chr3B 685762309 685764414 2105 True 1571.00 2309 93.24200 1 2260 2 chr3B.!!$R8 2259
9 TraesCS3A01G414600 chr3B 330589880 330590611 731 True 924.00 924 89.95900 2260 2972 1 chr3B.!!$R1 712
10 TraesCS3A01G414600 chr3D 520682952 520684429 1477 True 1648.00 1648 87.10500 712 2169 1 chr3D.!!$R3 1457
11 TraesCS3A01G414600 chr3D 520637579 520642847 5268 True 1351.75 2008 89.02125 3 2260 4 chr3D.!!$R4 2257
12 TraesCS3A01G414600 chr3D 520676555 520678584 2029 True 972.10 1860 84.58500 443 2120 2 chr3D.!!$R5 1677
13 TraesCS3A01G414600 chr3D 520702429 520704240 1811 True 948.00 1611 84.95400 264 2092 2 chr3D.!!$R6 1828
14 TraesCS3A01G414600 chr7A 171638921 171639659 738 True 963.00 963 90.61700 2250 2972 1 chr7A.!!$R1 722
15 TraesCS3A01G414600 chr7A 476227701 476230396 2695 True 542.50 551 88.27950 2522 2972 2 chr7A.!!$R2 450
16 TraesCS3A01G414600 chr1A 292538188 292538927 739 False 963.00 963 90.60400 2251 2972 1 chr1A.!!$F1 721
17 TraesCS3A01G414600 chr7D 498916610 498917355 745 True 946.00 946 90.14600 2250 2972 1 chr7D.!!$R1 722
18 TraesCS3A01G414600 chrUn 97101402 97102136 734 True 939.00 939 90.28300 2260 2972 1 chrUn.!!$R1 712
19 TraesCS3A01G414600 chr4D 246415973 246416715 742 False 931.00 931 89.82600 2252 2972 1 chr4D.!!$F1 720
20 TraesCS3A01G414600 chr4D 335737189 335737917 728 True 917.00 917 89.78200 2260 2972 1 chr4D.!!$R1 712
21 TraesCS3A01G414600 chr5A 220937290 220938022 732 False 917.00 917 89.63700 2251 2972 1 chr5A.!!$F1 721
22 TraesCS3A01G414600 chr7B 639272027 639272751 724 True 822.00 822 87.45000 2238 2972 1 chr7B.!!$R1 734
23 TraesCS3A01G414600 chr7B 594767358 594768059 701 False 821.00 821 88.02700 2259 2972 1 chr7B.!!$F1 713
24 TraesCS3A01G414600 chr6B 574522914 574523626 712 True 785.00 785 87.04500 2260 2972 1 chr6B.!!$R2 712
25 TraesCS3A01G414600 chr4B 283350599 283351303 704 False 756.00 756 86.39500 2259 2972 1 chr4B.!!$F1 713

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
136 137 1.315690 AACCGAACACTCTCAGACGA 58.684 50.000 0.0 0.0 0.00 4.20 F
1377 1452 2.778679 GACGACATCAAGCGTGCC 59.221 61.111 0.0 0.0 41.34 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1505 1580 1.014044 GTTGGCGCTCTCGATGTTGA 61.014 55.0 7.64 0.0 38.1 3.18 R
2378 4265 2.808543 GGAGGATAAGCGGCAACATAAG 59.191 50.0 1.45 0.0 0.0 1.73 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
39 40 4.834496 AGAAAAGGATGAAACTTGGCATGA 59.166 37.500 7.45 0.0 0.00 3.07
131 132 3.450578 GTGTACAAACCGAACACTCTCA 58.549 45.455 0.00 0.0 40.25 3.27
136 137 1.315690 AACCGAACACTCTCAGACGA 58.684 50.000 0.00 0.0 0.00 4.20
158 159 5.238650 CGAAGTATCAGGGTTTCAAACAGTT 59.761 40.000 1.93 0.0 0.00 3.16
159 160 6.391227 AAGTATCAGGGTTTCAAACAGTTG 57.609 37.500 1.93 0.0 35.95 3.16
945 986 6.519213 GCGATATTCCTTCATTCCCTTCTAGT 60.519 42.308 0.00 0.0 0.00 2.57
1187 1262 4.592192 CCGGCGCGTCATCCAGAT 62.592 66.667 12.89 0.0 0.00 2.90
1377 1452 2.778679 GACGACATCAAGCGTGCC 59.221 61.111 0.00 0.0 41.34 5.01
2182 2386 4.083537 CGCTTTACCACTGCTACAAAATGA 60.084 41.667 0.00 0.0 0.00 2.57
2335 4222 8.918202 TCTTAACTCAACAACCATCACTTAAT 57.082 30.769 0.00 0.0 0.00 1.40
2378 4265 5.687285 CCTTTATTTTTGCGAGGCATCATAC 59.313 40.000 0.00 0.0 38.76 2.39
2631 6798 5.677091 GCGACATTTTTCAGAGGTATGCATT 60.677 40.000 3.54 0.0 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 7.062255 GCCAAGTTTCATCCTTTTCTAAAATCG 59.938 37.037 0.00 0.00 0.00 3.34
82 83 7.653647 AGTGCATTCGGTTTTTCTTGTAATAA 58.346 30.769 0.00 0.00 0.00 1.40
131 132 4.884668 TTGAAACCCTGATACTTCGTCT 57.115 40.909 0.00 0.00 0.00 4.18
136 137 5.301805 CCAACTGTTTGAAACCCTGATACTT 59.698 40.000 5.50 0.00 34.24 2.24
158 159 6.716284 TGTGTTCTATATCAATTCCACACCA 58.284 36.000 0.00 0.00 33.78 4.17
159 160 7.624360 TTGTGTTCTATATCAATTCCACACC 57.376 36.000 0.00 0.00 33.78 4.16
281 287 1.963515 GTGGGAAAAGGAAGCATGTGT 59.036 47.619 0.00 0.00 0.00 3.72
433 442 6.599445 ACATTTCTTCTATCCTTCTCCCATG 58.401 40.000 0.00 0.00 0.00 3.66
610 631 0.389948 CTGTACTCCAGCCGTTCCAC 60.390 60.000 0.00 0.00 33.59 4.02
903 942 1.144716 GCAGCGATGGATGTGAGGA 59.855 57.895 1.46 0.00 0.00 3.71
945 986 7.865707 GCTAGAATTAATTTGCAAGCTAGCTA 58.134 34.615 19.70 1.28 43.62 3.32
1324 1399 2.738521 CGCTGACCTGTCGTTGGG 60.739 66.667 0.00 0.00 0.00 4.12
1377 1452 2.825836 GGGCATGCGTTCTCCAGG 60.826 66.667 12.44 0.00 0.00 4.45
1505 1580 1.014044 GTTGGCGCTCTCGATGTTGA 61.014 55.000 7.64 0.00 38.10 3.18
1697 1772 1.179814 AGGGGTGACTGTGTCGAGAC 61.180 60.000 5.61 5.61 34.95 3.36
1927 2002 5.395768 CCCTCCTACAGTTGTTCCTAATCTG 60.396 48.000 0.00 0.00 0.00 2.90
2182 2386 9.720874 ACATAGATATATAGTCCCATGACATGT 57.279 33.333 14.26 0.00 44.33 3.21
2289 4176 3.219281 AGCGTGTGTTATGTTTTCCCTT 58.781 40.909 0.00 0.00 0.00 3.95
2335 4222 9.629649 AATAAAGGAGATGGACCTATTATGGTA 57.370 33.333 0.00 0.00 41.00 3.25
2378 4265 2.808543 GGAGGATAAGCGGCAACATAAG 59.191 50.000 1.45 0.00 0.00 1.73


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

AutoCloner maintained by Alex Coulton.