Multiple sequence alignment - TraesCS6A01G206900

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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 TraesCS6A01G206900 chr6A 100.000 3747 0 0 1 3747 365564130 365560384 0.000000e+00 6920.0
1 TraesCS6A01G206900 chr6A 97.448 2508 62 2 992 3499 365555948 365553443 0.000000e+00 4276.0
2 TraesCS6A01G206900 chr6A 98.184 991 18 0 1 991 365577280 365576290 0.000000e+00 1731.0
3 TraesCS6A01G206900 chr6A 97.177 992 28 0 1 992 363418387 363419378 0.000000e+00 1677.0
4 TraesCS6A01G206900 chr6A 96.670 991 33 0 1 991 209485962 209484972 0.000000e+00 1648.0
5 TraesCS6A01G206900 chr6A 96.471 255 6 3 3496 3747 365553401 365553147 5.790000e-113 418.0
6 TraesCS6A01G206900 chr2A 97.087 2506 68 5 992 3496 667584075 667586576 0.000000e+00 4218.0
7 TraesCS6A01G206900 chr2A 96.825 252 8 0 3496 3747 667586615 667586866 4.470000e-114 422.0
8 TraesCS6A01G206900 chr4A 94.657 2508 127 5 992 3499 299912149 299909649 0.000000e+00 3882.0
9 TraesCS6A01G206900 chr4A 96.670 991 33 0 1 991 575149145 575148155 0.000000e+00 1648.0
10 TraesCS6A01G206900 chr4A 94.378 249 11 3 3496 3742 299909607 299909360 2.730000e-101 379.0
11 TraesCS6A01G206900 chr4A 83.193 238 35 4 3496 3730 238765934 238765699 2.930000e-51 213.0
12 TraesCS6A01G206900 chr1D 88.911 1533 104 31 1356 2837 457880532 457879015 0.000000e+00 1829.0
13 TraesCS6A01G206900 chr1D 91.433 677 48 9 2830 3499 237419976 237420649 0.000000e+00 920.0
14 TraesCS6A01G206900 chr1D 92.157 255 16 4 3496 3747 237424608 237424861 1.280000e-94 357.0
15 TraesCS6A01G206900 chr1D 90.909 253 21 2 3496 3747 237420691 237420942 4.640000e-89 339.0
16 TraesCS6A01G206900 chr1D 92.040 201 10 3 992 1187 457881070 457880871 1.020000e-70 278.0
17 TraesCS6A01G206900 chr5A 96.973 991 30 0 1 991 137470625 137469635 0.000000e+00 1664.0
18 TraesCS6A01G206900 chr5A 96.774 992 32 0 1 992 464138005 464137014 0.000000e+00 1655.0
19 TraesCS6A01G206900 chr5A 96.670 991 33 0 1 991 635758320 635757330 0.000000e+00 1648.0
20 TraesCS6A01G206900 chr5A 93.750 48 3 0 2894 2941 296728053 296728100 5.190000e-09 73.1
21 TraesCS6A01G206900 chr3A 96.872 991 31 0 1 991 462480122 462479132 0.000000e+00 1659.0
22 TraesCS6A01G206900 chr3A 93.750 48 3 0 2894 2941 6686666 6686619 5.190000e-09 73.1
23 TraesCS6A01G206900 chr1A 96.670 991 33 0 1 991 355204641 355203651 0.000000e+00 1648.0
24 TraesCS6A01G206900 chr1A 87.969 1438 108 35 1418 2837 550344274 550342884 0.000000e+00 1637.0
25 TraesCS6A01G206900 chr1A 93.307 254 15 1 3496 3747 232733848 232734101 1.270000e-99 374.0
26 TraesCS6A01G206900 chr1A 91.700 253 17 3 3247 3499 232733562 232733810 7.700000e-92 348.0
27 TraesCS6A01G206900 chr1A 96.154 78 3 0 1356 1433 550344380 550344303 1.090000e-25 128.0
28 TraesCS6A01G206900 chr1B 87.688 999 82 23 1359 2325 627947592 627946603 0.000000e+00 1125.0
29 TraesCS6A01G206900 chr1B 93.269 312 15 2 2526 2837 627946599 627946294 4.410000e-124 455.0
30 TraesCS6A01G206900 chr1B 91.054 313 18 6 992 1295 627948003 627947692 7.490000e-112 414.0
31 TraesCS6A01G206900 chr1B 93.478 46 3 0 2896 2941 376488375 376488420 6.720000e-08 69.4
32 TraesCS6A01G206900 chr3B 91.541 662 48 7 2840 3499 40047320 40047975 0.000000e+00 905.0
33 TraesCS6A01G206900 chr3B 90.772 661 56 5 2840 3499 42263496 42264152 0.000000e+00 878.0
34 TraesCS6A01G206900 chr3B 91.373 255 17 3 3496 3747 42264190 42264442 9.960000e-91 344.0
35 TraesCS6A01G206900 chr7A 92.520 254 16 3 3496 3747 60645298 60645046 9.890000e-96 361.0
36 TraesCS6A01G206900 chr7A 91.700 253 19 2 3247 3499 60645590 60645340 2.140000e-92 350.0
37 TraesCS6A01G206900 chr2B 93.966 116 7 0 1243 1358 425812009 425812124 3.850000e-40 176.0


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 TraesCS6A01G206900 chr6A 365560384 365564130 3746 True 6920.000000 6920 100.000000 1 3747 1 chr6A.!!$R2 3746
1 TraesCS6A01G206900 chr6A 365553147 365555948 2801 True 2347.000000 4276 96.959500 992 3747 2 chr6A.!!$R4 2755
2 TraesCS6A01G206900 chr6A 365576290 365577280 990 True 1731.000000 1731 98.184000 1 991 1 chr6A.!!$R3 990
3 TraesCS6A01G206900 chr6A 363418387 363419378 991 False 1677.000000 1677 97.177000 1 992 1 chr6A.!!$F1 991
4 TraesCS6A01G206900 chr6A 209484972 209485962 990 True 1648.000000 1648 96.670000 1 991 1 chr6A.!!$R1 990
5 TraesCS6A01G206900 chr2A 667584075 667586866 2791 False 2320.000000 4218 96.956000 992 3747 2 chr2A.!!$F1 2755
6 TraesCS6A01G206900 chr4A 299909360 299912149 2789 True 2130.500000 3882 94.517500 992 3742 2 chr4A.!!$R3 2750
7 TraesCS6A01G206900 chr4A 575148155 575149145 990 True 1648.000000 1648 96.670000 1 991 1 chr4A.!!$R2 990
8 TraesCS6A01G206900 chr1D 457879015 457881070 2055 True 1053.500000 1829 90.475500 992 2837 2 chr1D.!!$R1 1845
9 TraesCS6A01G206900 chr1D 237419976 237424861 4885 False 538.666667 920 91.499667 2830 3747 3 chr1D.!!$F1 917
10 TraesCS6A01G206900 chr5A 137469635 137470625 990 True 1664.000000 1664 96.973000 1 991 1 chr5A.!!$R1 990
11 TraesCS6A01G206900 chr5A 464137014 464138005 991 True 1655.000000 1655 96.774000 1 992 1 chr5A.!!$R2 991
12 TraesCS6A01G206900 chr5A 635757330 635758320 990 True 1648.000000 1648 96.670000 1 991 1 chr5A.!!$R3 990
13 TraesCS6A01G206900 chr3A 462479132 462480122 990 True 1659.000000 1659 96.872000 1 991 1 chr3A.!!$R2 990
14 TraesCS6A01G206900 chr1A 355203651 355204641 990 True 1648.000000 1648 96.670000 1 991 1 chr1A.!!$R1 990
15 TraesCS6A01G206900 chr1A 550342884 550344380 1496 True 882.500000 1637 92.061500 1356 2837 2 chr1A.!!$R2 1481
16 TraesCS6A01G206900 chr1A 232733562 232734101 539 False 361.000000 374 92.503500 3247 3747 2 chr1A.!!$F1 500
17 TraesCS6A01G206900 chr1B 627946294 627948003 1709 True 664.666667 1125 90.670333 992 2837 3 chr1B.!!$R1 1845
18 TraesCS6A01G206900 chr3B 40047320 40047975 655 False 905.000000 905 91.541000 2840 3499 1 chr3B.!!$F1 659
19 TraesCS6A01G206900 chr3B 42263496 42264442 946 False 611.000000 878 91.072500 2840 3747 2 chr3B.!!$F2 907
20 TraesCS6A01G206900 chr7A 60645046 60645590 544 True 355.500000 361 92.110000 3247 3747 2 chr7A.!!$R1 500

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
406 407 1.661341 GCGTTCTGAGCATCCAAGAT 58.339 50.000 0.0 0.0 34.19 2.40 F
533 534 1.908793 CGGTGAGGACTGGGTGTCT 60.909 63.158 0.0 0.0 44.74 3.41 F
1182 1187 2.031120 CTACCTCTCTCCAAGCTCCAG 58.969 57.143 0.0 0.0 0.00 3.86 F
1693 1983 1.494721 ACCCAAAGAGACCTGAAAGCA 59.505 47.619 0.0 0.0 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1323 1350 1.066002 CAAGCAATTACATGAGGGCGG 59.934 52.381 0.00 0.0 0.0 6.13 R
1693 1983 3.490078 CGGATCTTCGCTAGCTCTTCTTT 60.490 47.826 13.93 0.0 0.0 2.52 R
2704 3036 1.403647 CCAGCATTGTCGTCCGTTAGA 60.404 52.381 0.00 0.0 0.0 2.10 R
3125 3465 2.605837 TCACTGCCGAACAACAACTA 57.394 45.000 0.00 0.0 0.0 2.24 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
210 211 2.876091 CTGCTCGGATTGAAAGTACGA 58.124 47.619 0.00 0.00 0.00 3.43
406 407 1.661341 GCGTTCTGAGCATCCAAGAT 58.339 50.000 0.00 0.00 34.19 2.40
533 534 1.908793 CGGTGAGGACTGGGTGTCT 60.909 63.158 0.00 0.00 44.74 3.41
585 586 4.698780 GGGATTGTGTGTCCTAAGGTTTAC 59.301 45.833 0.00 0.00 36.00 2.01
604 605 3.309600 ACATACCTAGCCGTCCTAACT 57.690 47.619 0.00 0.00 0.00 2.24
606 607 4.796606 ACATACCTAGCCGTCCTAACTAA 58.203 43.478 0.00 0.00 0.00 2.24
1182 1187 2.031120 CTACCTCTCTCCAAGCTCCAG 58.969 57.143 0.00 0.00 0.00 3.86
1323 1350 4.992381 AGTCAACACTTTTAGATGACGC 57.008 40.909 0.00 0.00 43.85 5.19
1693 1983 1.494721 ACCCAAAGAGACCTGAAAGCA 59.505 47.619 0.00 0.00 0.00 3.91
2144 2453 5.689961 AGTGTTGTTGCGGTGATTATTTTTC 59.310 36.000 0.00 0.00 0.00 2.29
2276 2606 4.792704 GCAAGTCACAAAACGGATCAACAT 60.793 41.667 0.00 0.00 0.00 2.71
2483 2815 7.054124 TCATTTTCAGCCGGTAATTAGAGAAT 58.946 34.615 1.90 0.00 0.00 2.40
2641 2973 3.245803 TGAAGCTCTTCCTAGGAGAACCT 60.246 47.826 12.26 5.02 42.91 3.50
2883 3219 4.057428 GACGTCTCCGCTGCTGGT 62.057 66.667 8.70 0.00 37.70 4.00
2889 3225 1.080093 CTCCGCTGCTGGTAAACGA 60.080 57.895 9.66 0.00 0.00 3.85
3076 3416 5.071653 TGGGAATAGATGCAGTATGTTGCTA 59.928 40.000 0.00 0.00 44.38 3.49
3125 3465 8.761575 ATAGAAAATTTTGATGAAATGCACGT 57.238 26.923 8.47 0.00 37.98 4.49
3174 3514 5.242795 AGTCTTTGCAGTACCCAGTTAAT 57.757 39.130 0.00 0.00 0.00 1.40
3410 3754 8.511321 TGAAATAGTATGTCATTCGCAAAAACT 58.489 29.630 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
210 211 3.181500 GGTTGCTCTCAAACGACAAAAGT 60.181 43.478 0.00 0.00 33.37 2.66
406 407 1.003696 TCACCGGCAATCCACAATGTA 59.996 47.619 0.00 0.00 0.00 2.29
533 534 0.880278 GTCCTGAACACGCAGCTCAA 60.880 55.000 0.00 0.00 34.56 3.02
566 567 6.232692 GGTATGTAAACCTTAGGACACACAA 58.767 40.000 4.77 0.00 36.53 3.33
585 586 5.527033 GTTTAGTTAGGACGGCTAGGTATG 58.473 45.833 0.00 0.00 0.00 2.39
597 598 6.183360 TGTGACAACTGTACGTTTAGTTAGGA 60.183 38.462 14.32 2.36 35.50 2.94
604 605 3.783191 TGCTGTGACAACTGTACGTTTA 58.217 40.909 0.00 0.00 32.27 2.01
606 607 2.303163 TGCTGTGACAACTGTACGTT 57.697 45.000 0.00 0.00 35.88 3.99
1033 1038 6.985653 TCTCGATTCCTAAGAGAAATCCAT 57.014 37.500 0.00 0.00 38.00 3.41
1074 1079 5.413833 CCAAGATTAGGCGCAAATCAGATAT 59.586 40.000 26.73 10.81 36.09 1.63
1182 1187 1.202687 TGAGGATCATCATTCGCACCC 60.203 52.381 5.84 0.00 42.56 4.61
1323 1350 1.066002 CAAGCAATTACATGAGGGCGG 59.934 52.381 0.00 0.00 0.00 6.13
1693 1983 3.490078 CGGATCTTCGCTAGCTCTTCTTT 60.490 47.826 13.93 0.00 0.00 2.52
2122 2431 4.677378 CGAAAAATAATCACCGCAACAACA 59.323 37.500 0.00 0.00 0.00 3.33
2144 2453 7.592164 TCATATTTCTATGCAAAATGTGATGCG 59.408 33.333 14.28 0.00 45.47 4.73
2276 2606 7.448161 ACATGAAGAATTAGTTGTCAACCATCA 59.552 33.333 12.17 5.83 0.00 3.07
2483 2815 9.405587 GCTTATAGATTTTGTTTAACAGCACAA 57.594 29.630 0.00 0.00 0.00 3.33
2641 2973 2.124942 TTGTGCGCTGTCCACACA 60.125 55.556 9.73 0.00 42.39 3.72
2687 3019 6.885376 TCCGTTAGACTCTTCAGATACTCTTT 59.115 38.462 0.00 0.00 0.00 2.52
2696 3028 2.483106 TGTCGTCCGTTAGACTCTTCAG 59.517 50.000 3.69 0.00 43.91 3.02
2704 3036 1.403647 CCAGCATTGTCGTCCGTTAGA 60.404 52.381 0.00 0.00 0.00 2.10
3125 3465 2.605837 TCACTGCCGAACAACAACTA 57.394 45.000 0.00 0.00 0.00 2.24
3174 3514 8.912787 TTTTGCAGTATTAAACTTCGAAAACA 57.087 26.923 0.00 0.00 33.44 2.83
3238 3579 3.433274 CACCATATGATTCCGTCATTCCG 59.567 47.826 3.65 0.00 45.25 4.30
3243 3584 4.214986 ACAACACCATATGATTCCGTCA 57.785 40.909 3.65 0.00 42.06 4.35
3319 3660 6.463995 AGTTCATGCTTTTCCACTGTTTTA 57.536 33.333 0.00 0.00 0.00 1.52
3381 3724 6.603237 TGCGAATGACATACTATTTCAAGG 57.397 37.500 0.00 0.00 0.00 3.61
3410 3754 7.288852 TCACACTTTTTCATATTCTCCCCAAAA 59.711 33.333 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.