Multiple sequence alignment - TraesCS1A01G407300

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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 TraesCS1A01G407300 chr1A 100.000 2375 0 0 1 2375 569764321 569761947 0.000000e+00 4386.0
1 TraesCS1A01G407300 chr1A 99.017 407 2 2 1629 2035 569757715 569757311 0.000000e+00 728.0
2 TraesCS1A01G407300 chr1A 88.028 142 15 2 1431 1570 180413813 180413954 1.460000e-37 167.0
3 TraesCS1A01G407300 chr4A 97.534 892 22 0 738 1629 623723889 623722998 0.000000e+00 1526.0
4 TraesCS1A01G407300 chr4A 96.637 892 17 1 738 1629 623680607 623679729 0.000000e+00 1469.0
5 TraesCS1A01G407300 chr4A 98.014 705 8 2 39 741 623681503 623680803 0.000000e+00 1219.0
6 TraesCS1A01G407300 chr4A 97.730 705 10 2 39 741 623724787 623724087 0.000000e+00 1208.0
7 TraesCS1A01G407300 chr4A 96.929 521 8 5 1856 2375 706461230 706461743 0.000000e+00 867.0
8 TraesCS1A01G407300 chr4A 87.020 547 61 7 198 741 623690086 623689547 2.020000e-170 608.0
9 TraesCS1A01G407300 chr4A 87.020 547 61 7 198 741 623749892 623749353 2.020000e-170 608.0
10 TraesCS1A01G407300 chr4A 83.516 637 82 9 739 1365 623749155 623748532 7.360000e-160 573.0
11 TraesCS1A01G407300 chr4A 83.046 637 85 10 739 1365 623741209 623740586 7.420000e-155 556.0
12 TraesCS1A01G407300 chr4A 85.556 450 50 4 919 1365 623689011 623688574 7.740000e-125 457.0
13 TraesCS1A01G407300 chr4A 84.848 231 13 6 48 256 623743643 623743413 1.850000e-51 213.0
14 TraesCS1A01G407300 chr4A 88.750 160 16 2 1413 1570 29299425 29299584 6.700000e-46 195.0
15 TraesCS1A01G407300 chr4A 86.517 178 23 1 1402 1579 697738466 697738642 6.700000e-46 195.0
16 TraesCS1A01G407300 chr4A 81.250 176 25 5 739 910 623689349 623689178 4.120000e-28 135.0
17 TraesCS1A01G407300 chr4A 100.000 48 0 0 1 48 559949089 559949042 3.250000e-14 89.8
18 TraesCS1A01G407300 chr4A 85.897 78 4 7 1 77 585383373 585383302 2.530000e-10 76.8
19 TraesCS1A01G407300 chr4A 93.750 48 3 0 48 95 623690185 623690138 3.270000e-09 73.1
20 TraesCS1A01G407300 chr4A 93.750 48 3 0 48 95 623749991 623749944 3.270000e-09 73.1
21 TraesCS1A01G407300 chr2A 99.331 747 4 1 1629 2375 21310048 21310793 0.000000e+00 1351.0
22 TraesCS1A01G407300 chr2A 99.331 747 4 1 1629 2375 21354796 21355541 0.000000e+00 1351.0
23 TraesCS1A01G407300 chr2A 99.248 399 3 0 1629 2027 21359773 21360171 0.000000e+00 721.0
24 TraesCS1A01G407300 chr1B 99.198 748 5 1 1628 2375 121516257 121517003 0.000000e+00 1347.0
25 TraesCS1A01G407300 chr1B 99.244 397 3 0 1629 2025 121527375 121527771 0.000000e+00 717.0
26 TraesCS1A01G407300 chr4B 99.196 746 5 1 1630 2375 2422264 2423008 0.000000e+00 1343.0
27 TraesCS1A01G407300 chr4B 97.132 523 7 6 1856 2375 421575761 421575244 0.000000e+00 876.0
28 TraesCS1A01G407300 chr4B 88.095 168 19 1 1412 1579 656830314 656830480 5.180000e-47 198.0
29 TraesCS1A01G407300 chrUn 98.929 747 6 2 1630 2375 47705092 47705837 0.000000e+00 1334.0
30 TraesCS1A01G407300 chr5B 98.394 747 8 2 1630 2375 535037975 535038718 0.000000e+00 1310.0
31 TraesCS1A01G407300 chr5B 94.811 713 17 6 37 741 688840885 688841585 0.000000e+00 1094.0
32 TraesCS1A01G407300 chr5B 95.970 670 27 0 738 1407 688841782 688842451 0.000000e+00 1088.0
33 TraesCS1A01G407300 chr5B 89.136 718 48 9 49 741 688719876 688720588 0.000000e+00 867.0
34 TraesCS1A01G407300 chr5B 89.021 674 65 5 739 1403 688927593 688928266 0.000000e+00 826.0
35 TraesCS1A01G407300 chr5B 89.021 674 64 5 739 1403 689027506 689028178 0.000000e+00 826.0
36 TraesCS1A01G407300 chr5B 88.177 609 59 7 132 738 688926795 688927392 0.000000e+00 713.0
37 TraesCS1A01G407300 chr5B 87.702 618 57 9 132 741 689026702 689027308 0.000000e+00 702.0
38 TraesCS1A01G407300 chr5B 76.246 602 113 15 742 1337 689070195 689069618 2.310000e-75 292.0
39 TraesCS1A01G407300 chr5B 94.340 53 3 0 1 53 558560201 558560253 5.440000e-12 82.4
40 TraesCS1A01G407300 chr5D 97.147 666 19 0 738 1403 545922362 545923027 0.000000e+00 1125.0
41 TraesCS1A01G407300 chr5D 93.575 716 20 7 48 741 545921454 545922165 0.000000e+00 1044.0
42 TraesCS1A01G407300 chr5D 92.518 548 26 10 1832 2375 35095066 35094530 0.000000e+00 771.0
43 TraesCS1A01G407300 chr2B 91.477 176 15 0 1412 1587 12285448 12285623 2.360000e-60 243.0
44 TraesCS1A01G407300 chr2B 87.324 71 4 4 1 67 738257686 738257617 2.530000e-10 76.8
45 TraesCS1A01G407300 chr2B 100.000 28 0 0 1588 1615 12285638 12285665 4.000000e-03 52.8
46 TraesCS1A01G407300 chr6B 88.750 160 16 2 1413 1570 614434745 614434904 6.700000e-46 195.0
47 TraesCS1A01G407300 chr7B 86.957 161 18 3 1413 1570 587440661 587440501 6.750000e-41 178.0
48 TraesCS1A01G407300 chr7A 96.154 52 2 0 1 52 122027957 122028008 4.210000e-13 86.1
49 TraesCS1A01G407300 chr5A 96.154 52 2 0 1 52 547789116 547789167 4.210000e-13 86.1
50 TraesCS1A01G407300 chr3B 93.220 59 2 2 1 58 22525334 22525277 4.210000e-13 86.1
51 TraesCS1A01G407300 chr2D 93.103 58 3 1 1 58 492514495 492514439 1.510000e-12 84.2
52 TraesCS1A01G407300 chr6A 87.879 66 6 2 1 66 550743553 550743490 2.530000e-10 76.8


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 TraesCS1A01G407300 chr1A 569761947 569764321 2374 True 4386.000000 4386 100.000000 1 2375 1 chr1A.!!$R2 2374
1 TraesCS1A01G407300 chr4A 623722998 623724787 1789 True 1367.000000 1526 97.632000 39 1629 2 chr4A.!!$R5 1590
2 TraesCS1A01G407300 chr4A 623679729 623681503 1774 True 1344.000000 1469 97.325500 39 1629 2 chr4A.!!$R3 1590
3 TraesCS1A01G407300 chr4A 706461230 706461743 513 False 867.000000 867 96.929000 1856 2375 1 chr4A.!!$F3 519
4 TraesCS1A01G407300 chr4A 623748532 623749991 1459 True 418.033333 608 88.095333 48 1365 3 chr4A.!!$R7 1317
5 TraesCS1A01G407300 chr4A 623740586 623743643 3057 True 384.500000 556 83.947000 48 1365 2 chr4A.!!$R6 1317
6 TraesCS1A01G407300 chr4A 623688574 623690185 1611 True 318.275000 608 86.894000 48 1365 4 chr4A.!!$R4 1317
7 TraesCS1A01G407300 chr2A 21310048 21310793 745 False 1351.000000 1351 99.331000 1629 2375 1 chr2A.!!$F1 746
8 TraesCS1A01G407300 chr2A 21354796 21355541 745 False 1351.000000 1351 99.331000 1629 2375 1 chr2A.!!$F2 746
9 TraesCS1A01G407300 chr1B 121516257 121517003 746 False 1347.000000 1347 99.198000 1628 2375 1 chr1B.!!$F1 747
10 TraesCS1A01G407300 chr4B 2422264 2423008 744 False 1343.000000 1343 99.196000 1630 2375 1 chr4B.!!$F1 745
11 TraesCS1A01G407300 chr4B 421575244 421575761 517 True 876.000000 876 97.132000 1856 2375 1 chr4B.!!$R1 519
12 TraesCS1A01G407300 chrUn 47705092 47705837 745 False 1334.000000 1334 98.929000 1630 2375 1 chrUn.!!$F1 745
13 TraesCS1A01G407300 chr5B 535037975 535038718 743 False 1310.000000 1310 98.394000 1630 2375 1 chr5B.!!$F1 745
14 TraesCS1A01G407300 chr5B 688840885 688842451 1566 False 1091.000000 1094 95.390500 37 1407 2 chr5B.!!$F4 1370
15 TraesCS1A01G407300 chr5B 688719876 688720588 712 False 867.000000 867 89.136000 49 741 1 chr5B.!!$F3 692
16 TraesCS1A01G407300 chr5B 688926795 688928266 1471 False 769.500000 826 88.599000 132 1403 2 chr5B.!!$F5 1271
17 TraesCS1A01G407300 chr5B 689026702 689028178 1476 False 764.000000 826 88.361500 132 1403 2 chr5B.!!$F6 1271
18 TraesCS1A01G407300 chr5B 689069618 689070195 577 True 292.000000 292 76.246000 742 1337 1 chr5B.!!$R1 595
19 TraesCS1A01G407300 chr5D 545921454 545923027 1573 False 1084.500000 1125 95.361000 48 1403 2 chr5D.!!$F1 1355
20 TraesCS1A01G407300 chr5D 35094530 35095066 536 True 771.000000 771 92.518000 1832 2375 1 chr5D.!!$R1 543

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
394 1946 1.294659 GCTTCCTGCACCTCAACGAG 61.295 60.0 0.0 0.0 42.31 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1553 3486 1.283613 ACGTTGGATGGGGCTAATCAA 59.716 47.619 0.0 0.0 0.0 2.57 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
31 32 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.0 0.00 4.44
32 33 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.0 0.00 4.69
33 34 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.0 0.00 4.63
34 35 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.0 0.00 4.30
35 36 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.0 0.00 4.30
36 37 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.0 0.00 4.20
37 38 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.0 0.00 4.30
393 1945 1.301716 GCTTCCTGCACCTCAACGA 60.302 57.895 0.00 0.0 42.31 3.85
394 1946 1.294659 GCTTCCTGCACCTCAACGAG 61.295 60.000 0.00 0.0 42.31 4.18
395 1947 1.294659 CTTCCTGCACCTCAACGAGC 61.295 60.000 0.00 0.0 0.00 5.03
396 1948 3.114616 CCTGCACCTCAACGAGCG 61.115 66.667 0.00 0.0 0.00 5.03
879 2642 3.279183 CTCCTCGGAGTCAGCGTT 58.721 61.111 4.02 0.0 37.47 4.84
1274 3207 0.811219 CACATGACCATCATCGGCGT 60.811 55.000 6.85 0.0 34.28 5.68
1311 3244 0.500178 CGCGCTTCGTCTATGACATG 59.500 55.000 5.56 0.0 32.09 3.21
1553 3486 3.591254 GAGTCAACGCGCTTCCCCT 62.591 63.158 5.73 0.0 0.00 4.79
1570 3503 1.217689 CCCTTGATTAGCCCCATCCAA 59.782 52.381 0.00 0.0 0.00 3.53
1579 3512 0.679960 GCCCCATCCAACGTAGCTTT 60.680 55.000 0.00 0.0 0.00 3.51
1827 3760 1.932156 GCCGATCGATTAACCCCGTAC 60.932 57.143 18.66 0.0 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
9 10 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
11 12 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
12 13 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
13 14 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
14 15 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
15 16 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
16 17 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
17 18 6.141790 ACTACTCCCTCCGTTCCTAAATATT 58.858 40.000 0.00 0.00 0.00 1.28
18 19 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
19 20 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
20 21 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
21 22 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
22 23 3.525199 ACTACTACTCCCTCCGTTCCTAA 59.475 47.826 0.00 0.00 0.00 2.69
23 24 3.118531 ACTACTACTCCCTCCGTTCCTA 58.881 50.000 0.00 0.00 0.00 2.94
24 25 1.921748 ACTACTACTCCCTCCGTTCCT 59.078 52.381 0.00 0.00 0.00 3.36
25 26 2.433662 ACTACTACTCCCTCCGTTCC 57.566 55.000 0.00 0.00 0.00 3.62
26 27 6.107901 TCTATACTACTACTCCCTCCGTTC 57.892 45.833 0.00 0.00 0.00 3.95
27 28 6.700845 ATCTATACTACTACTCCCTCCGTT 57.299 41.667 0.00 0.00 0.00 4.44
28 29 7.635529 GCATATCTATACTACTACTCCCTCCGT 60.636 44.444 0.00 0.00 0.00 4.69
29 30 6.707161 GCATATCTATACTACTACTCCCTCCG 59.293 46.154 0.00 0.00 0.00 4.63
30 31 7.499895 GTGCATATCTATACTACTACTCCCTCC 59.500 44.444 0.00 0.00 0.00 4.30
31 32 8.047911 TGTGCATATCTATACTACTACTCCCTC 58.952 40.741 0.00 0.00 0.00 4.30
32 33 7.929959 TGTGCATATCTATACTACTACTCCCT 58.070 38.462 0.00 0.00 0.00 4.20
33 34 8.754991 ATGTGCATATCTATACTACTACTCCC 57.245 38.462 0.00 0.00 0.00 4.30
352 1904 3.179265 CCGTCGACGTGCATGGTC 61.179 66.667 33.49 10.58 37.74 4.02
396 1948 4.341783 AGTGGTGGCTGCCTGCTC 62.342 66.667 21.03 8.17 42.39 4.26
550 2108 2.112198 GGGAACGGATGCGCAATCA 61.112 57.895 17.11 0.00 36.98 2.57
992 2919 1.687494 GAGCTGCGTCATTGTCGTCC 61.687 60.000 0.00 0.00 0.00 4.79
1274 3207 1.302752 GTGTCCACCTGCTGCATCA 60.303 57.895 1.31 0.00 0.00 3.07
1311 3244 2.109126 GTGGATCTTGCCGGCTGTC 61.109 63.158 29.70 18.63 0.00 3.51
1553 3486 1.283613 ACGTTGGATGGGGCTAATCAA 59.716 47.619 0.00 0.00 0.00 2.57
1570 3503 2.452813 CGATGCCGCAAAGCTACGT 61.453 57.895 0.00 0.00 0.00 3.57
1827 3760 2.022129 GGCGTGTTGTCTCGTGAGG 61.022 63.158 0.00 0.00 33.82 3.86


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

AutoCloner maintained by Alex Coulton.