Multiple sequence alignment - TraesCS3A01G221500

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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 TraesCS3A01G221500 chr3A 100.000 2306 0 0 1 2306 411269195 411271500 0.000000e+00 4259.0
1 TraesCS3A01G221500 chr3A 94.165 497 21 1 1577 2073 193870392 193870880 0.000000e+00 750.0
2 TraesCS3A01G221500 chr6B 97.699 1521 31 3 558 2077 423094015 423092498 0.000000e+00 2612.0
3 TraesCS3A01G221500 chr6B 97.326 561 13 2 1 560 423094997 423094438 0.000000e+00 952.0
4 TraesCS3A01G221500 chr6B 89.825 570 11 11 1280 1821 255098479 255099029 0.000000e+00 688.0
5 TraesCS3A01G221500 chr6B 89.954 219 6 7 2101 2306 213156789 213157004 3.780000e-68 268.0
6 TraesCS3A01G221500 chr1A 97.546 1467 30 4 558 2022 508961586 508963048 0.000000e+00 2505.0
7 TraesCS3A01G221500 chr1A 97.861 561 3 2 1 560 508960608 508961160 0.000000e+00 961.0
8 TraesCS3A01G221500 chr1A 91.741 557 41 5 6 560 562931468 562932021 0.000000e+00 769.0
9 TraesCS3A01G221500 chr1A 89.136 359 15 5 1580 1922 232346816 232346466 2.120000e-115 425.0
10 TraesCS3A01G221500 chr1B 94.288 1593 56 7 558 2125 167564033 167562451 0.000000e+00 2405.0
11 TraesCS3A01G221500 chr1B 94.011 551 26 3 11 560 167565003 167564459 0.000000e+00 828.0
12 TraesCS3A01G221500 chr6A 96.349 1205 20 1 558 1738 26327740 26328944 0.000000e+00 1960.0
13 TraesCS3A01G221500 chr6A 98.039 561 9 2 1 560 26326756 26327315 0.000000e+00 974.0
14 TraesCS3A01G221500 chr6A 98.026 304 6 0 1776 2079 26328937 26329240 1.570000e-146 529.0
15 TraesCS3A01G221500 chr4B 95.593 885 25 9 1246 2125 494950351 494951226 0.000000e+00 1406.0
16 TraesCS3A01G221500 chr4B 94.286 700 39 1 581 1280 494949410 494950108 0.000000e+00 1070.0
17 TraesCS3A01G221500 chr4B 92.321 560 42 1 2 560 505155338 505154779 0.000000e+00 795.0
18 TraesCS3A01G221500 chr1D 96.728 764 22 2 558 1320 493749469 493748708 0.000000e+00 1269.0
19 TraesCS3A01G221500 chr1D 94.134 699 22 4 1064 1761 493748845 493748165 0.000000e+00 1046.0
20 TraesCS3A01G221500 chr1D 97.083 480 11 3 1827 2306 493748158 493747682 0.000000e+00 806.0
21 TraesCS3A01G221500 chr1D 91.979 561 43 2 1 560 399805518 399806077 0.000000e+00 785.0
22 TraesCS3A01G221500 chr6D 95.833 672 25 1 558 1229 79981137 79980469 0.000000e+00 1083.0
23 TraesCS3A01G221500 chr6D 91.712 555 28 6 1509 2050 79971005 79970456 0.000000e+00 754.0
24 TraesCS3A01G221500 chr6D 87.963 216 10 7 2101 2303 121092568 121092780 8.230000e-60 241.0
25 TraesCS3A01G221500 chr6D 89.130 92 8 1 2215 2306 104077327 104077416 1.870000e-21 113.0
26 TraesCS3A01G221500 chr2A 92.420 752 50 4 558 1308 355588243 355587498 0.000000e+00 1066.0
27 TraesCS3A01G221500 chr2A 95.017 301 14 1 1189 1488 467111708 467112008 2.680000e-129 472.0
28 TraesCS3A01G221500 chr5A 96.791 561 17 1 1 560 510201792 510201232 0.000000e+00 935.0
29 TraesCS3A01G221500 chr5A 87.732 807 81 11 558 1354 296676037 296675239 0.000000e+00 926.0
30 TraesCS3A01G221500 chr5A 93.271 535 27 2 1489 2022 510199558 510199032 0.000000e+00 780.0
31 TraesCS3A01G221500 chr5D 92.513 561 40 2 2 560 251070455 251071015 0.000000e+00 802.0
32 TraesCS3A01G221500 chr5B 90.426 564 30 5 1521 2068 397291813 397292368 0.000000e+00 721.0
33 TraesCS3A01G221500 chr7B 83.871 403 36 19 1919 2306 547962521 547962909 7.830000e-95 357.0
34 TraesCS3A01G221500 chr3D 93.839 211 4 4 2101 2306 168503121 168502915 2.230000e-80 309.0
35 TraesCS3A01G221500 chr2D 91.975 162 6 2 2150 2306 13209787 13209628 1.070000e-53 220.0
36 TraesCS3A01G221500 chr2D 90.435 115 9 1 2192 2306 33892895 33892783 1.430000e-32 150.0
37 TraesCS3A01G221500 chr2B 86.957 92 10 1 2215 2306 55991789 55991700 4.050000e-18 102.0
38 TraesCS3A01G221500 chr3B 96.078 51 0 2 1489 1539 158150122 158150074 5.280000e-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 TraesCS3A01G221500 chr3A 411269195 411271500 2305 False 4259.000000 4259 100.000000 1 2306 1 chr3A.!!$F2 2305
1 TraesCS3A01G221500 chr6B 423092498 423094997 2499 True 1782.000000 2612 97.512500 1 2077 2 chr6B.!!$R1 2076
2 TraesCS3A01G221500 chr6B 255098479 255099029 550 False 688.000000 688 89.825000 1280 1821 1 chr6B.!!$F2 541
3 TraesCS3A01G221500 chr1A 508960608 508963048 2440 False 1733.000000 2505 97.703500 1 2022 2 chr1A.!!$F2 2021
4 TraesCS3A01G221500 chr1A 562931468 562932021 553 False 769.000000 769 91.741000 6 560 1 chr1A.!!$F1 554
5 TraesCS3A01G221500 chr1B 167562451 167565003 2552 True 1616.500000 2405 94.149500 11 2125 2 chr1B.!!$R1 2114
6 TraesCS3A01G221500 chr6A 26326756 26329240 2484 False 1154.333333 1960 97.471333 1 2079 3 chr6A.!!$F1 2078
7 TraesCS3A01G221500 chr4B 494949410 494951226 1816 False 1238.000000 1406 94.939500 581 2125 2 chr4B.!!$F1 1544
8 TraesCS3A01G221500 chr4B 505154779 505155338 559 True 795.000000 795 92.321000 2 560 1 chr4B.!!$R1 558
9 TraesCS3A01G221500 chr1D 493747682 493749469 1787 True 1040.333333 1269 95.981667 558 2306 3 chr1D.!!$R1 1748
10 TraesCS3A01G221500 chr1D 399805518 399806077 559 False 785.000000 785 91.979000 1 560 1 chr1D.!!$F1 559
11 TraesCS3A01G221500 chr6D 79980469 79981137 668 True 1083.000000 1083 95.833000 558 1229 1 chr6D.!!$R2 671
12 TraesCS3A01G221500 chr6D 79970456 79971005 549 True 754.000000 754 91.712000 1509 2050 1 chr6D.!!$R1 541
13 TraesCS3A01G221500 chr2A 355587498 355588243 745 True 1066.000000 1066 92.420000 558 1308 1 chr2A.!!$R1 750
14 TraesCS3A01G221500 chr5A 296675239 296676037 798 True 926.000000 926 87.732000 558 1354 1 chr5A.!!$R1 796
15 TraesCS3A01G221500 chr5A 510199032 510201792 2760 True 857.500000 935 95.031000 1 2022 2 chr5A.!!$R2 2021
16 TraesCS3A01G221500 chr5D 251070455 251071015 560 False 802.000000 802 92.513000 2 560 1 chr5D.!!$F1 558
17 TraesCS3A01G221500 chr5B 397291813 397292368 555 False 721.000000 721 90.426000 1521 2068 1 chr5B.!!$F1 547

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
976 1408 0.695347 AGGAAAGGCTTGAGGGTCTG 59.305 55.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2230 3644 2.872245 TCTCTTCAGTGAACTTTTGGCG 59.128 45.455 0.08 0.0 0.0 5.69 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
681 1113 4.472833 AGATGACCAGGAATTTCTAGCAGT 59.527 41.667 0.0 0.0 0.00 4.40
759 1191 4.583907 TGATTTGAATGTGCTTGACCTTGA 59.416 37.500 0.0 0.0 0.00 3.02
976 1408 0.695347 AGGAAAGGCTTGAGGGTCTG 59.305 55.000 0.0 0.0 0.00 3.51
1117 1597 0.105593 TCGGATGCTTGAGATGAGGC 59.894 55.000 0.0 0.0 0.00 4.70
1124 1604 1.742268 GCTTGAGATGAGGCTTGTTCC 59.258 52.381 0.0 0.0 0.00 3.62
1136 1616 2.012673 GCTTGTTCCGATGCTTGAGAT 58.987 47.619 0.0 0.0 0.00 2.75
1137 1617 2.223203 GCTTGTTCCGATGCTTGAGATG 60.223 50.000 0.0 0.0 0.00 2.90
1556 2787 7.639378 AGAAGAGAGTAGTAGGAGACAAGATT 58.361 38.462 0.0 0.0 0.00 2.40
1735 3042 3.501349 AGAGAAGTCCTGCTGTAACTGA 58.499 45.455 0.0 0.0 0.00 3.41
1736 3043 3.898123 AGAGAAGTCCTGCTGTAACTGAA 59.102 43.478 0.0 0.0 0.00 3.02
1737 3044 4.345257 AGAGAAGTCCTGCTGTAACTGAAA 59.655 41.667 0.0 0.0 0.00 2.69
1738 3045 5.036117 AGAAGTCCTGCTGTAACTGAAAA 57.964 39.130 0.0 0.0 0.00 2.29
1739 3046 5.437060 AGAAGTCCTGCTGTAACTGAAAAA 58.563 37.500 0.0 0.0 0.00 1.94
1740 3047 5.529060 AGAAGTCCTGCTGTAACTGAAAAAG 59.471 40.000 0.0 0.0 0.00 2.27
1741 3048 4.781934 AGTCCTGCTGTAACTGAAAAAGT 58.218 39.130 0.0 0.0 42.60 2.66
1952 3344 9.653287 CTAATGTACCAAGTCAACAGAAGATTA 57.347 33.333 0.0 0.0 0.00 1.75
2144 3558 6.384305 ACCTGAACTGTATAGATAGCCACTTT 59.616 38.462 0.0 0.0 0.00 2.66
2234 3648 0.613260 ACTCACCTAGCATTTCGCCA 59.387 50.000 0.0 0.0 44.04 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
681 1113 2.750166 TCAAGTCCAGTTTTTGCGACAA 59.250 40.909 0.00 0.00 32.59 3.18
759 1191 3.715628 ATTGCAGCGAGTTGAAAAACT 57.284 38.095 0.00 0.00 35.34 2.66
976 1408 1.995626 TCTTGGAGGTAGCTGCCCC 60.996 63.158 18.24 17.89 0.00 5.80
1117 1597 3.264947 TCATCTCAAGCATCGGAACAAG 58.735 45.455 0.00 0.00 0.00 3.16
1124 1604 1.598132 CAAGCCTCATCTCAAGCATCG 59.402 52.381 0.00 0.00 0.00 3.84
1136 1616 0.036732 AAGCATCGGAACAAGCCTCA 59.963 50.000 0.00 0.00 0.00 3.86
1137 1617 0.449388 CAAGCATCGGAACAAGCCTC 59.551 55.000 0.00 0.00 0.00 4.70
1765 3072 9.616156 TGGTGTAAGTTTTAGTTCATTAACTGA 57.384 29.630 2.44 0.00 45.63 3.41
1774 3081 9.177304 GCAATAGTTTGGTGTAAGTTTTAGTTC 57.823 33.333 0.00 0.00 33.22 3.01
1775 3082 8.909923 AGCAATAGTTTGGTGTAAGTTTTAGTT 58.090 29.630 0.00 0.00 41.81 2.24
1776 3083 8.459911 AGCAATAGTTTGGTGTAAGTTTTAGT 57.540 30.769 0.00 0.00 41.81 2.24
1952 3344 7.148340 GCTTCTGCTACTGTTAATCTTGTCATT 60.148 37.037 0.00 0.00 36.03 2.57
1987 3401 4.771577 TGCCCATGAAGCTTCAGATTTTAA 59.228 37.500 31.14 12.80 41.08 1.52
2144 3558 3.240310 TGGGGGTCGTTTTATTTTCCA 57.760 42.857 0.00 0.00 0.00 3.53
2230 3644 2.872245 TCTCTTCAGTGAACTTTTGGCG 59.128 45.455 0.08 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.