Multiple sequence alignment - TraesCS4B01G188200
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 | TraesCS4B01G188200 | chr4B | 100.000 | 6763 | 0 | 0 | 1 | 6763 | 408985351 | 408978589 | 0.000000e+00 | 12490.0 |
1 | TraesCS4B01G188200 | chr4B | 92.934 | 1670 | 97 | 9 | 2966 | 4619 | 147075653 | 147073989 | 0.000000e+00 | 2410.0 |
2 | TraesCS4B01G188200 | chr4B | 94.957 | 1170 | 42 | 6 | 2964 | 4130 | 182238966 | 182237811 | 0.000000e+00 | 1818.0 |
3 | TraesCS4B01G188200 | chr4B | 93.622 | 1176 | 68 | 4 | 2962 | 4130 | 471722459 | 471721284 | 0.000000e+00 | 1749.0 |
4 | TraesCS4B01G188200 | chr4D | 95.703 | 2211 | 49 | 14 | 797 | 2965 | 329140607 | 329138401 | 0.000000e+00 | 3515.0 |
5 | TraesCS4B01G188200 | chr4D | 97.372 | 1408 | 37 | 0 | 4620 | 6027 | 329138405 | 329136998 | 0.000000e+00 | 2396.0 |
6 | TraesCS4B01G188200 | chr4D | 88.778 | 401 | 19 | 13 | 6277 | 6659 | 329136845 | 329136453 | 1.030000e-127 | 468.0 |
7 | TraesCS4B01G188200 | chr4D | 93.277 | 119 | 5 | 2 | 6022 | 6140 | 329136967 | 329136852 | 9.020000e-39 | 172.0 |
8 | TraesCS4B01G188200 | chr6B | 98.225 | 1690 | 7 | 6 | 2953 | 4621 | 346318345 | 346316658 | 0.000000e+00 | 2933.0 |
9 | TraesCS4B01G188200 | chr6B | 93.487 | 1689 | 75 | 9 | 2966 | 4620 | 552131979 | 552133666 | 0.000000e+00 | 2477.0 |
10 | TraesCS4B01G188200 | chr6B | 96.764 | 989 | 18 | 3 | 3645 | 4620 | 124082530 | 124083517 | 0.000000e+00 | 1637.0 |
11 | TraesCS4B01G188200 | chr6B | 95.648 | 988 | 28 | 4 | 3646 | 4620 | 113651066 | 113652051 | 0.000000e+00 | 1572.0 |
12 | TraesCS4B01G188200 | chr7A | 98.140 | 1667 | 21 | 1 | 2966 | 4622 | 692307686 | 692306020 | 0.000000e+00 | 2898.0 |
13 | TraesCS4B01G188200 | chr7A | 85.008 | 1294 | 147 | 30 | 4620 | 5897 | 661594039 | 661595301 | 0.000000e+00 | 1271.0 |
14 | TraesCS4B01G188200 | chr7A | 85.314 | 606 | 69 | 12 | 1140 | 1735 | 661589392 | 661589987 | 5.800000e-170 | 608.0 |
15 | TraesCS4B01G188200 | chr7A | 83.427 | 356 | 44 | 9 | 2398 | 2747 | 661590777 | 661591123 | 3.940000e-82 | 316.0 |
16 | TraesCS4B01G188200 | chr7A | 85.477 | 241 | 27 | 5 | 1766 | 2006 | 661590247 | 661590479 | 1.880000e-60 | 244.0 |
17 | TraesCS4B01G188200 | chr3B | 93.954 | 1687 | 77 | 8 | 2966 | 4628 | 276489240 | 276490925 | 0.000000e+00 | 2527.0 |
18 | TraesCS4B01G188200 | chr3B | 93.493 | 1168 | 71 | 3 | 2966 | 4130 | 104382382 | 104381217 | 0.000000e+00 | 1731.0 |
19 | TraesCS4B01G188200 | chr3B | 84.091 | 88 | 10 | 2 | 6188 | 6274 | 727790667 | 727790751 | 1.560000e-11 | 82.4 |
20 | TraesCS4B01G188200 | chr2B | 93.321 | 1677 | 94 | 7 | 2963 | 4625 | 197585326 | 197586998 | 0.000000e+00 | 2460.0 |
21 | TraesCS4B01G188200 | chr2B | 94.383 | 997 | 32 | 7 | 3651 | 4624 | 463928426 | 463927431 | 0.000000e+00 | 1509.0 |
22 | TraesCS4B01G188200 | chr2B | 75.500 | 200 | 37 | 9 | 529 | 717 | 781578584 | 781578386 | 3.360000e-13 | 87.9 |
23 | TraesCS4B01G188200 | chr7B | 92.857 | 1680 | 95 | 10 | 2963 | 4625 | 234647197 | 234645526 | 0.000000e+00 | 2414.0 |
24 | TraesCS4B01G188200 | chr7B | 94.128 | 1141 | 64 | 1 | 2993 | 4130 | 457412591 | 457411451 | 0.000000e+00 | 1733.0 |
25 | TraesCS4B01G188200 | chr7B | 87.050 | 1112 | 117 | 18 | 4671 | 5767 | 629580846 | 629579747 | 0.000000e+00 | 1230.0 |
26 | TraesCS4B01G188200 | chr7B | 83.759 | 665 | 79 | 20 | 1092 | 1735 | 629582717 | 629582061 | 2.700000e-168 | 603.0 |
27 | TraesCS4B01G188200 | chr7B | 87.409 | 413 | 44 | 5 | 2548 | 2956 | 629581295 | 629580887 | 1.030000e-127 | 468.0 |
28 | TraesCS4B01G188200 | chr7B | 93.333 | 120 | 8 | 0 | 1890 | 2009 | 629581576 | 629581457 | 1.940000e-40 | 178.0 |
29 | TraesCS4B01G188200 | chr4A | 93.135 | 1646 | 96 | 6 | 2987 | 4619 | 661533954 | 661535595 | 0.000000e+00 | 2398.0 |
30 | TraesCS4B01G188200 | chr4A | 96.449 | 1408 | 49 | 1 | 4620 | 6027 | 140978531 | 140979937 | 0.000000e+00 | 2322.0 |
31 | TraesCS4B01G188200 | chr4A | 95.128 | 862 | 33 | 6 | 793 | 1653 | 140975853 | 140976706 | 0.000000e+00 | 1351.0 |
32 | TraesCS4B01G188200 | chr4A | 91.371 | 591 | 45 | 5 | 210 | 799 | 140974603 | 140975188 | 0.000000e+00 | 804.0 |
33 | TraesCS4B01G188200 | chr4A | 93.750 | 496 | 17 | 9 | 2469 | 2963 | 140978051 | 140978533 | 0.000000e+00 | 732.0 |
34 | TraesCS4B01G188200 | chr4A | 94.866 | 448 | 22 | 1 | 4620 | 5067 | 253273794 | 253274240 | 0.000000e+00 | 699.0 |
35 | TraesCS4B01G188200 | chr4A | 94.231 | 364 | 18 | 2 | 1655 | 2016 | 140976975 | 140977337 | 2.760000e-153 | 553.0 |
36 | TraesCS4B01G188200 | chr4A | 87.683 | 479 | 30 | 15 | 2017 | 2483 | 140977469 | 140977930 | 1.290000e-146 | 531.0 |
37 | TraesCS4B01G188200 | chr4A | 84.980 | 506 | 36 | 17 | 6272 | 6763 | 140980148 | 140980627 | 1.710000e-130 | 477.0 |
38 | TraesCS4B01G188200 | chr4A | 96.491 | 114 | 3 | 1 | 6027 | 6140 | 140980035 | 140980147 | 3.220000e-43 | 187.0 |
39 | TraesCS4B01G188200 | chr4A | 90.000 | 70 | 7 | 0 | 1 | 70 | 140797734 | 140797803 | 2.600000e-14 | 91.6 |
40 | TraesCS4B01G188200 | chr4A | 88.000 | 75 | 7 | 2 | 6202 | 6274 | 743374387 | 743374461 | 3.360000e-13 | 87.9 |
41 | TraesCS4B01G188200 | chr4A | 100.000 | 28 | 0 | 0 | 6202 | 6229 | 70811589 | 70811562 | 1.200000e-02 | 52.8 |
42 | TraesCS4B01G188200 | chr1B | 96.233 | 1407 | 51 | 2 | 4620 | 6025 | 135816366 | 135817771 | 0.000000e+00 | 2303.0 |
43 | TraesCS4B01G188200 | chr1B | 93.782 | 1351 | 61 | 6 | 3295 | 4622 | 141118536 | 141119886 | 0.000000e+00 | 2008.0 |
44 | TraesCS4B01G188200 | chr1B | 93.545 | 1100 | 34 | 9 | 925 | 2016 | 135814266 | 135815336 | 0.000000e+00 | 1604.0 |
45 | TraesCS4B01G188200 | chr1B | 91.104 | 978 | 51 | 19 | 2018 | 2965 | 135815399 | 135816370 | 0.000000e+00 | 1291.0 |
46 | TraesCS4B01G188200 | chr1B | 85.057 | 87 | 10 | 3 | 6188 | 6273 | 549520470 | 549520554 | 1.210000e-12 | 86.1 |
47 | TraesCS4B01G188200 | chr5B | 95.467 | 1103 | 35 | 4 | 3531 | 4619 | 216657113 | 216658214 | 0.000000e+00 | 1746.0 |
48 | TraesCS4B01G188200 | chr7D | 85.714 | 1225 | 140 | 20 | 4682 | 5897 | 572553697 | 572554895 | 0.000000e+00 | 1260.0 |
49 | TraesCS4B01G188200 | chr7D | 83.387 | 939 | 115 | 28 | 1083 | 2006 | 572549022 | 572549934 | 0.000000e+00 | 832.0 |
50 | TraesCS4B01G188200 | chr7D | 95.556 | 45 | 2 | 0 | 6188 | 6232 | 632891066 | 632891110 | 9.410000e-09 | 73.1 |
51 | TraesCS4B01G188200 | chr2D | 78.283 | 198 | 31 | 6 | 530 | 716 | 553759049 | 553759245 | 4.290000e-22 | 117.0 |
52 | TraesCS4B01G188200 | chr2D | 79.231 | 130 | 26 | 1 | 505 | 633 | 377120569 | 377120698 | 9.340000e-14 | 89.8 |
53 | TraesCS4B01G188200 | chr2D | 87.931 | 58 | 3 | 2 | 6197 | 6253 | 348194639 | 348194693 | 1.570000e-06 | 65.8 |
54 | TraesCS4B01G188200 | chr6D | 81.818 | 88 | 11 | 2 | 6188 | 6273 | 453809351 | 453809435 | 1.220000e-07 | 69.4 |
55 | TraesCS4B01G188200 | chr3D | 88.525 | 61 | 2 | 3 | 6202 | 6261 | 105124434 | 105124490 | 1.220000e-07 | 69.4 |
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 | TraesCS4B01G188200 | chr4B | 408978589 | 408985351 | 6762 | True | 12490.000000 | 12490 | 100.000000 | 1 | 6763 | 1 | chr4B.!!$R3 | 6762 |
1 | TraesCS4B01G188200 | chr4B | 147073989 | 147075653 | 1664 | True | 2410.000000 | 2410 | 92.934000 | 2966 | 4619 | 1 | chr4B.!!$R1 | 1653 |
2 | TraesCS4B01G188200 | chr4B | 182237811 | 182238966 | 1155 | True | 1818.000000 | 1818 | 94.957000 | 2964 | 4130 | 1 | chr4B.!!$R2 | 1166 |
3 | TraesCS4B01G188200 | chr4B | 471721284 | 471722459 | 1175 | True | 1749.000000 | 1749 | 93.622000 | 2962 | 4130 | 1 | chr4B.!!$R4 | 1168 |
4 | TraesCS4B01G188200 | chr4D | 329136453 | 329140607 | 4154 | True | 1637.750000 | 3515 | 93.782500 | 797 | 6659 | 4 | chr4D.!!$R1 | 5862 |
5 | TraesCS4B01G188200 | chr6B | 346316658 | 346318345 | 1687 | True | 2933.000000 | 2933 | 98.225000 | 2953 | 4621 | 1 | chr6B.!!$R1 | 1668 |
6 | TraesCS4B01G188200 | chr6B | 552131979 | 552133666 | 1687 | False | 2477.000000 | 2477 | 93.487000 | 2966 | 4620 | 1 | chr6B.!!$F3 | 1654 |
7 | TraesCS4B01G188200 | chr6B | 124082530 | 124083517 | 987 | False | 1637.000000 | 1637 | 96.764000 | 3645 | 4620 | 1 | chr6B.!!$F2 | 975 |
8 | TraesCS4B01G188200 | chr6B | 113651066 | 113652051 | 985 | False | 1572.000000 | 1572 | 95.648000 | 3646 | 4620 | 1 | chr6B.!!$F1 | 974 |
9 | TraesCS4B01G188200 | chr7A | 692306020 | 692307686 | 1666 | True | 2898.000000 | 2898 | 98.140000 | 2966 | 4622 | 1 | chr7A.!!$R1 | 1656 |
10 | TraesCS4B01G188200 | chr7A | 661589392 | 661595301 | 5909 | False | 609.750000 | 1271 | 84.806500 | 1140 | 5897 | 4 | chr7A.!!$F1 | 4757 |
11 | TraesCS4B01G188200 | chr3B | 276489240 | 276490925 | 1685 | False | 2527.000000 | 2527 | 93.954000 | 2966 | 4628 | 1 | chr3B.!!$F1 | 1662 |
12 | TraesCS4B01G188200 | chr3B | 104381217 | 104382382 | 1165 | True | 1731.000000 | 1731 | 93.493000 | 2966 | 4130 | 1 | chr3B.!!$R1 | 1164 |
13 | TraesCS4B01G188200 | chr2B | 197585326 | 197586998 | 1672 | False | 2460.000000 | 2460 | 93.321000 | 2963 | 4625 | 1 | chr2B.!!$F1 | 1662 |
14 | TraesCS4B01G188200 | chr2B | 463927431 | 463928426 | 995 | True | 1509.000000 | 1509 | 94.383000 | 3651 | 4624 | 1 | chr2B.!!$R1 | 973 |
15 | TraesCS4B01G188200 | chr7B | 234645526 | 234647197 | 1671 | True | 2414.000000 | 2414 | 92.857000 | 2963 | 4625 | 1 | chr7B.!!$R1 | 1662 |
16 | TraesCS4B01G188200 | chr7B | 457411451 | 457412591 | 1140 | True | 1733.000000 | 1733 | 94.128000 | 2993 | 4130 | 1 | chr7B.!!$R2 | 1137 |
17 | TraesCS4B01G188200 | chr7B | 629579747 | 629582717 | 2970 | True | 619.750000 | 1230 | 87.887750 | 1092 | 5767 | 4 | chr7B.!!$R3 | 4675 |
18 | TraesCS4B01G188200 | chr4A | 661533954 | 661535595 | 1641 | False | 2398.000000 | 2398 | 93.135000 | 2987 | 4619 | 1 | chr4A.!!$F3 | 1632 |
19 | TraesCS4B01G188200 | chr4A | 140974603 | 140980627 | 6024 | False | 869.625000 | 2322 | 92.510375 | 210 | 6763 | 8 | chr4A.!!$F5 | 6553 |
20 | TraesCS4B01G188200 | chr1B | 141118536 | 141119886 | 1350 | False | 2008.000000 | 2008 | 93.782000 | 3295 | 4622 | 1 | chr1B.!!$F1 | 1327 |
21 | TraesCS4B01G188200 | chr1B | 135814266 | 135817771 | 3505 | False | 1732.666667 | 2303 | 93.627333 | 925 | 6025 | 3 | chr1B.!!$F3 | 5100 |
22 | TraesCS4B01G188200 | chr5B | 216657113 | 216658214 | 1101 | False | 1746.000000 | 1746 | 95.467000 | 3531 | 4619 | 1 | chr5B.!!$F1 | 1088 |
23 | TraesCS4B01G188200 | chr7D | 572549022 | 572554895 | 5873 | False | 1046.000000 | 1260 | 84.550500 | 1083 | 5897 | 2 | chr7D.!!$F2 | 4814 |
AutoCloner calculated primer pairsThese primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible. |
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Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
46 | 47 | 0.096976 | CGCTACAGTGCATTTTCCGG | 59.903 | 55.000 | 0.00 | 0.00 | 0.00 | 5.14 | F |
139 | 140 | 0.105039 | CGTCACATAAGAGCTCCCCC | 59.895 | 60.000 | 10.93 | 0.00 | 0.00 | 5.40 | F |
360 | 361 | 0.171231 | CTCGCGTCTCTCACATGGAA | 59.829 | 55.000 | 5.77 | 0.00 | 0.00 | 3.53 | F |
1011 | 1687 | 0.179171 | CGACGACGATGGCAACTACT | 60.179 | 55.000 | 0.00 | 0.00 | 42.66 | 2.57 | F |
1138 | 1814 | 1.022451 | AGCTCGACGAGTCACTCTCC | 61.022 | 60.000 | 24.80 | 6.73 | 39.84 | 3.71 | F |
1586 | 2274 | 1.134670 | GGTGACACTACTGAGCCCATC | 60.135 | 57.143 | 5.39 | 0.00 | 0.00 | 3.51 | F |
2740 | 4359 | 3.055240 | CAGGTTCAGAATGCCTCTTCTCT | 60.055 | 47.826 | 0.00 | 0.00 | 33.18 | 3.10 | F |
4801 | 11337 | 4.758773 | TGAATACATGAGATGCAGTCCA | 57.241 | 40.909 | 0.00 | 0.00 | 0.00 | 4.02 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1345 | 2032 | 0.321741 | TGGCATTCCGCGAAACCTTA | 60.322 | 50.000 | 8.23 | 0.00 | 43.84 | 2.69 | R |
1586 | 2274 | 1.676006 | GCATTTGTTATGACCTCCGGG | 59.324 | 52.381 | 0.00 | 0.00 | 38.88 | 5.73 | R |
1808 | 2997 | 2.411547 | GCAAAGATGTGTACTGTGTCGC | 60.412 | 50.000 | 0.00 | 0.00 | 0.00 | 5.19 | R |
2612 | 4231 | 1.247567 | TTGCTGCCCTTAGTTTCTGC | 58.752 | 50.000 | 0.00 | 0.00 | 0.00 | 4.26 | R |
2740 | 4359 | 6.681729 | AACATGAACAGTAGACTAAAGGGA | 57.318 | 37.500 | 0.00 | 0.00 | 0.00 | 4.20 | R |
3265 | 6928 | 3.621805 | TGACCGGCAGCGGAAGAA | 61.622 | 61.111 | 8.49 | 0.00 | 0.00 | 2.52 | R |
4700 | 11236 | 6.015180 | ACACTTGAATCAACATATGCCTGTTT | 60.015 | 34.615 | 1.58 | 2.34 | 37.25 | 2.83 | R |
6158 | 12803 | 0.031449 | GGCTCTCTCCAGTGTATCGC | 59.969 | 60.000 | 0.00 | 0.00 | 0.00 | 4.58 | R |
All possible primersListed 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. |
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Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.