Multiple sequence alignment - TraesCS7D01G469900

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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 TraesCS7D01G469900 chr7D 100.000 2485 0 0 1 2485 583039424 583036940 0.000000e+00 4590.0
1 TraesCS7D01G469900 chr7D 91.064 940 70 11 1541 2476 582661662 582660733 0.000000e+00 1258.0
2 TraesCS7D01G469900 chr7D 90.532 940 75 10 1541 2476 582556487 582555558 0.000000e+00 1230.0
3 TraesCS7D01G469900 chr7D 92.951 837 40 3 720 1540 582748231 582747398 0.000000e+00 1201.0
4 TraesCS7D01G469900 chr7D 87.273 825 87 14 720 1540 582557330 582556520 0.000000e+00 926.0
5 TraesCS7D01G469900 chr7D 86.909 825 90 14 720 1540 582662505 582661695 0.000000e+00 909.0
6 TraesCS7D01G469900 chr7D 92.471 611 41 4 1541 2150 582747364 582746758 0.000000e+00 869.0
7 TraesCS7D01G469900 chr7D 90.265 339 30 3 2148 2485 582746665 582746329 8.160000e-120 440.0
8 TraesCS7D01G469900 chr7D 78.919 185 25 12 1869 2045 537877969 537878147 2.020000e-21 113.0
9 TraesCS7D01G469900 chr7A 92.806 834 47 1 720 1540 674506507 674505674 0.000000e+00 1195.0
10 TraesCS7D01G469900 chr7A 88.057 988 71 18 723 1663 674738108 674737121 0.000000e+00 1127.0
11 TraesCS7D01G469900 chr7A 88.057 988 71 18 723 1663 674752842 674751855 0.000000e+00 1127.0
12 TraesCS7D01G469900 chr7A 90.959 730 48 9 1 719 28167233 28167955 0.000000e+00 966.0
13 TraesCS7D01G469900 chr7A 92.436 661 49 1 881 1540 674521287 674520627 0.000000e+00 942.0
14 TraesCS7D01G469900 chr7A 90.013 741 51 10 1 729 636128753 636128024 0.000000e+00 937.0
15 TraesCS7D01G469900 chr7A 92.157 612 42 5 1541 2150 674796302 674795695 0.000000e+00 859.0
16 TraesCS7D01G469900 chr7A 89.344 610 41 9 1541 2148 674520594 674520007 0.000000e+00 745.0
17 TraesCS7D01G469900 chr7A 89.052 612 47 9 1541 2150 674607942 674607349 0.000000e+00 741.0
18 TraesCS7D01G469900 chr7A 90.619 501 39 6 1651 2150 674751444 674750951 0.000000e+00 658.0
19 TraesCS7D01G469900 chr7A 90.400 500 38 5 1651 2149 674736709 674736219 0.000000e+00 649.0
20 TraesCS7D01G469900 chr7A 89.941 338 32 2 2148 2485 674736136 674735801 3.800000e-118 435.0
21 TraesCS7D01G469900 chr7A 89.941 338 32 2 2148 2485 674750869 674750534 3.800000e-118 435.0
22 TraesCS7D01G469900 chr7A 89.941 338 28 3 2148 2485 674519923 674519592 4.910000e-117 431.0
23 TraesCS7D01G469900 chr7A 89.844 256 26 0 2218 2473 674786169 674785914 1.840000e-86 329.0
24 TraesCS7D01G469900 chr7A 95.181 166 7 1 720 885 674522758 674522594 6.820000e-66 261.0
25 TraesCS7D01G469900 chr7A 93.103 174 9 2 2148 2321 674556181 674556011 4.100000e-63 252.0
26 TraesCS7D01G469900 chr7A 93.976 166 8 2 720 885 674527027 674526864 1.480000e-62 250.0
27 TraesCS7D01G469900 chr7A 92.593 162 12 0 2319 2480 674533845 674533684 1.490000e-57 233.0
28 TraesCS7D01G469900 chr7A 98.630 73 1 0 2148 2220 674795602 674795530 2.010000e-26 130.0
29 TraesCS7D01G469900 chr3D 95.417 720 22 6 1 719 526943424 526944133 0.000000e+00 1136.0
30 TraesCS7D01G469900 chr3D 83.942 137 14 8 1740 1872 189263440 189263308 9.330000e-25 124.0
31 TraesCS7D01G469900 chr1D 94.766 726 28 7 1 723 8353670 8354388 0.000000e+00 1122.0
32 TraesCS7D01G469900 chr7B 94.207 725 31 7 1 721 65821165 65821882 0.000000e+00 1096.0
33 TraesCS7D01G469900 chr7B 90.095 838 60 10 723 1540 650455978 650455144 0.000000e+00 1066.0
34 TraesCS7D01G469900 chr7B 89.737 838 64 10 723 1540 650362239 650361404 0.000000e+00 1051.0
35 TraesCS7D01G469900 chr7B 89.492 847 57 18 723 1540 650295048 650294205 0.000000e+00 1042.0
36 TraesCS7D01G469900 chr7B 89.492 847 57 18 723 1540 650301195 650300352 0.000000e+00 1042.0
37 TraesCS7D01G469900 chr7B 89.499 838 65 13 723 1540 650409222 650408388 0.000000e+00 1038.0
38 TraesCS7D01G469900 chr7B 89.811 265 22 3 2226 2485 650342619 650342355 3.960000e-88 335.0
39 TraesCS7D01G469900 chr7B 95.200 125 5 1 1541 1664 650455111 650454987 1.950000e-46 196.0
40 TraesCS7D01G469900 chr6B 92.424 726 47 7 1 721 34510357 34509635 0.000000e+00 1029.0
41 TraesCS7D01G469900 chr6B 87.912 91 8 3 2004 2094 414192207 414192294 1.220000e-18 104.0
42 TraesCS7D01G469900 chr4B 92.265 724 35 8 1 720 661569344 661568638 0.000000e+00 1007.0
43 TraesCS7D01G469900 chr4B 84.116 277 42 1 1234 1508 654719902 654719626 1.470000e-67 267.0
44 TraesCS7D01G469900 chr4B 90.667 75 4 3 1055 1128 655059157 655059085 2.030000e-16 97.1
45 TraesCS7D01G469900 chr6A 90.872 734 50 9 1 724 573034093 573034819 0.000000e+00 968.0
46 TraesCS7D01G469900 chr3A 90.959 730 46 9 1 719 24596843 24597563 0.000000e+00 965.0
47 TraesCS7D01G469900 chrUn 92.969 128 8 1 1538 1664 388900273 388900400 4.220000e-43 185.0
48 TraesCS7D01G469900 chr3B 83.453 139 15 8 1739 1873 412547623 412547757 3.360000e-24 122.0
49 TraesCS7D01G469900 chr5D 79.839 124 16 7 1672 1791 565911974 565911856 5.700000e-12 82.4


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 TraesCS7D01G469900 chr7D 583036940 583039424 2484 True 4590.000000 4590 100.000000 1 2485 1 chr7D.!!$R1 2484
1 TraesCS7D01G469900 chr7D 582660733 582662505 1772 True 1083.500000 1258 88.986500 720 2476 2 chr7D.!!$R3 1756
2 TraesCS7D01G469900 chr7D 582555558 582557330 1772 True 1078.000000 1230 88.902500 720 2476 2 chr7D.!!$R2 1756
3 TraesCS7D01G469900 chr7D 582746329 582748231 1902 True 836.666667 1201 91.895667 720 2485 3 chr7D.!!$R4 1765
4 TraesCS7D01G469900 chr7A 674505674 674506507 833 True 1195.000000 1195 92.806000 720 1540 1 chr7A.!!$R2 820
5 TraesCS7D01G469900 chr7A 28167233 28167955 722 False 966.000000 966 90.959000 1 719 1 chr7A.!!$F1 718
6 TraesCS7D01G469900 chr7A 636128024 636128753 729 True 937.000000 937 90.013000 1 729 1 chr7A.!!$R1 728
7 TraesCS7D01G469900 chr7A 674607349 674607942 593 True 741.000000 741 89.052000 1541 2150 1 chr7A.!!$R6 609
8 TraesCS7D01G469900 chr7A 674750534 674752842 2308 True 740.000000 1127 89.539000 723 2485 3 chr7A.!!$R10 1762
9 TraesCS7D01G469900 chr7A 674735801 674738108 2307 True 737.000000 1127 89.466000 723 2485 3 chr7A.!!$R9 1762
10 TraesCS7D01G469900 chr7A 674519592 674522758 3166 True 594.750000 942 91.725500 720 2485 4 chr7A.!!$R8 1765
11 TraesCS7D01G469900 chr7A 674795530 674796302 772 True 494.500000 859 95.393500 1541 2220 2 chr7A.!!$R11 679
12 TraesCS7D01G469900 chr3D 526943424 526944133 709 False 1136.000000 1136 95.417000 1 719 1 chr3D.!!$F1 718
13 TraesCS7D01G469900 chr1D 8353670 8354388 718 False 1122.000000 1122 94.766000 1 723 1 chr1D.!!$F1 722
14 TraesCS7D01G469900 chr7B 65821165 65821882 717 False 1096.000000 1096 94.207000 1 721 1 chr7B.!!$F1 720
15 TraesCS7D01G469900 chr7B 650361404 650362239 835 True 1051.000000 1051 89.737000 723 1540 1 chr7B.!!$R4 817
16 TraesCS7D01G469900 chr7B 650294205 650295048 843 True 1042.000000 1042 89.492000 723 1540 1 chr7B.!!$R1 817
17 TraesCS7D01G469900 chr7B 650300352 650301195 843 True 1042.000000 1042 89.492000 723 1540 1 chr7B.!!$R2 817
18 TraesCS7D01G469900 chr7B 650408388 650409222 834 True 1038.000000 1038 89.499000 723 1540 1 chr7B.!!$R5 817
19 TraesCS7D01G469900 chr7B 650454987 650455978 991 True 631.000000 1066 92.647500 723 1664 2 chr7B.!!$R6 941
20 TraesCS7D01G469900 chr6B 34509635 34510357 722 True 1029.000000 1029 92.424000 1 721 1 chr6B.!!$R1 720
21 TraesCS7D01G469900 chr4B 661568638 661569344 706 True 1007.000000 1007 92.265000 1 720 1 chr4B.!!$R3 719
22 TraesCS7D01G469900 chr6A 573034093 573034819 726 False 968.000000 968 90.872000 1 724 1 chr6A.!!$F1 723
23 TraesCS7D01G469900 chr3A 24596843 24597563 720 False 965.000000 965 90.959000 1 719 1 chr3A.!!$F1 718

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
575 599 2.669569 GGCTGAGCTTTGCCGACA 60.670 61.111 13.84 0.0 39.71 4.35 F
1111 2461 0.247736 CTGAACCTCGTCCTCCTTGG 59.752 60.000 0.00 0.0 37.10 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1420 2776 1.535444 TCGGAGGGGCACTTCTTGA 60.535 57.895 0.0 0.0 0.00 3.02 R
2427 4448 2.032681 GCCTTGTGGGACGAGCTT 59.967 61.111 0.0 0.0 37.23 3.74 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
575 599 2.669569 GGCTGAGCTTTGCCGACA 60.670 61.111 13.84 0.0 39.71 4.35
740 764 8.469309 AGTGAACCCATCAAATCTTTATATGG 57.531 34.615 0.00 0.0 40.50 2.74
1100 2450 1.219393 CTTCCTCGCCCTGAACCTC 59.781 63.158 0.00 0.0 0.00 3.85
1111 2461 0.247736 CTGAACCTCGTCCTCCTTGG 59.752 60.000 0.00 0.0 37.10 3.61
1166 2516 3.159347 GTCCCTACCCCGCCGATT 61.159 66.667 0.00 0.0 0.00 3.34
1216 2572 2.760092 GGGGCAGCTTATCAATCAACAA 59.240 45.455 0.00 0.0 0.00 2.83
1224 2580 5.947443 GCTTATCAATCAACAAGCTGAAGT 58.053 37.500 0.00 0.0 40.16 3.01
1231 2587 0.465460 AACAAGCTGAAGTTGGGCGA 60.465 50.000 0.00 0.0 0.00 5.54
1420 2776 1.821061 CTCCTCCTCAACCAGTGCGT 61.821 60.000 0.00 0.0 0.00 5.24
1445 2801 2.525629 TGCCCCTCCGACTTCACA 60.526 61.111 0.00 0.0 0.00 3.58
1468 2826 2.684630 GCCACATCTGATCCATCCAACA 60.685 50.000 0.00 0.0 0.00 3.33
1770 3589 9.567776 TGTGTGGATGAAGTTTTTAAGATCTAA 57.432 29.630 0.00 0.0 0.00 2.10
1848 3669 2.702261 CCAAGGCATCCCAAACAAATG 58.298 47.619 0.00 0.0 0.00 2.32
1854 3675 3.498018 GGCATCCCAAACAAATGTTCAAC 59.502 43.478 0.00 0.0 37.25 3.18
1866 3687 4.574599 AATGTTCAACAAGTCTCAAGCC 57.425 40.909 0.00 0.0 0.00 4.35
1994 3816 5.344743 TTTCATAGGGAGAGACACACATC 57.655 43.478 0.00 0.0 0.00 3.06
1995 3817 3.981212 TCATAGGGAGAGACACACATCA 58.019 45.455 0.00 0.0 0.00 3.07
2273 4293 2.447429 ACTGGAGAGGGGATCGAAGATA 59.553 50.000 0.00 0.0 45.12 1.98
2396 4417 4.038162 AGCGGATCTTGTAAACCTAGCTAG 59.962 45.833 14.20 14.2 0.00 3.42
2404 4425 8.307582 TCTTGTAAACCTAGCTAGCTTAATCT 57.692 34.615 24.88 8.0 0.00 2.40
2452 4473 1.992834 TCCCACAAGGCTCGCCATA 60.993 57.895 11.02 0.0 38.92 2.74
2453 4474 1.149174 CCCACAAGGCTCGCCATAT 59.851 57.895 11.02 0.0 38.92 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
490 514 1.138036 CCGTCGGCATAGAACGTGA 59.862 57.895 0.00 0.00 0.00 4.35
591 615 1.884579 AGTCGTCGGCGTATATCCATT 59.115 47.619 10.18 0.00 39.49 3.16
740 764 1.080974 GCATGTTGTCTGCTGTGCC 60.081 57.895 0.00 0.00 36.68 5.01
901 2238 5.499334 CGAGCTAATTAGTTTGACTCTTGCG 60.499 44.000 13.91 1.37 0.00 4.85
1128 2478 3.717294 CGGTGGGCAGTAGGGCTT 61.717 66.667 0.00 0.00 42.84 4.35
1193 2549 0.925558 TGATTGATAAGCTGCCCCCA 59.074 50.000 0.00 0.00 0.00 4.96
1204 2560 5.183713 CCCAACTTCAGCTTGTTGATTGATA 59.816 40.000 19.53 0.00 44.29 2.15
1205 2561 4.021719 CCCAACTTCAGCTTGTTGATTGAT 60.022 41.667 19.53 0.00 44.29 2.57
1216 2572 1.302033 CACTCGCCCAACTTCAGCT 60.302 57.895 0.00 0.00 0.00 4.24
1231 2587 1.898094 TTCAGCATGTTGGCGCACT 60.898 52.632 10.83 0.00 39.27 4.40
1242 2598 0.037877 AGCTTCAGCAGGTTCAGCAT 59.962 50.000 0.75 0.00 45.16 3.79
1420 2776 1.535444 TCGGAGGGGCACTTCTTGA 60.535 57.895 0.00 0.00 0.00 3.02
1445 2801 1.778484 TGGATGGATCAGATGTGGCAT 59.222 47.619 0.00 0.00 0.00 4.40
1593 2987 5.729974 ACACTGATCATTGATCAATCACG 57.270 39.130 25.29 17.26 46.51 4.35
1731 3550 8.137437 ACTTCATCCACACAAAACTTCATAAAG 58.863 33.333 0.00 0.00 38.54 1.85
1843 3664 4.741676 GGCTTGAGACTTGTTGAACATTTG 59.258 41.667 0.00 0.00 0.00 2.32
1848 3669 3.471680 AGAGGCTTGAGACTTGTTGAAC 58.528 45.455 0.00 0.00 30.09 3.18
1965 3787 6.070021 TGTGTCTCTCCCTATGAAATGTGATT 60.070 38.462 0.00 0.00 0.00 2.57
2113 3941 9.995003 AGCAAGAGTTATCATCCTTTCTATAAG 57.005 33.333 0.00 0.00 0.00 1.73
2217 4236 8.246615 CCCCACCTTATACTACCCCATATATAT 58.753 40.741 0.00 0.00 0.00 0.86
2218 4237 7.415695 TCCCCACCTTATACTACCCCATATATA 59.584 40.741 0.00 0.00 0.00 0.86
2273 4293 2.434884 CGTGCCGTGCCTTGATCT 60.435 61.111 0.00 0.00 0.00 2.75
2299 4319 8.308851 GAACTAGGGTTCTAAGATAAGAGGTT 57.691 38.462 0.00 0.00 45.90 3.50
2396 4417 5.912396 CGACATGAGTCTCACTAGATTAAGC 59.088 44.000 4.21 0.00 42.73 3.09
2404 4425 2.437413 AGCACGACATGAGTCTCACTA 58.563 47.619 4.21 0.00 42.73 2.74
2427 4448 2.032681 GCCTTGTGGGACGAGCTT 59.967 61.111 0.00 0.00 37.23 3.74
2452 4473 2.040043 AGGCCAGGGAGCTGCTAT 60.040 61.111 5.01 0.00 0.00 2.97
2453 4474 2.765807 GAGGCCAGGGAGCTGCTA 60.766 66.667 5.01 0.00 0.00 3.49


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

AutoCloner maintained by Alex Coulton.