Multiple sequence alignment - TraesCS7A01G064600

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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 TraesCS7A01G064600 chr7A 100.000 2811 0 0 1 2811 32297087 32294277 0.000000e+00 5192.0
1 TraesCS7A01G064600 chr7A 97.399 2768 44 9 65 2811 32038719 32035959 0.000000e+00 4687.0
2 TraesCS7A01G064600 chr7A 90.323 1240 92 13 256 1476 32063362 32062132 0.000000e+00 1600.0
3 TraesCS7A01G064600 chr7A 85.879 694 55 21 1776 2441 32129255 32128577 0.000000e+00 699.0
4 TraesCS7A01G064600 chr7A 82.180 578 65 20 655 1215 32130178 32129622 1.970000e-126 462.0
5 TraesCS7A01G064600 chr7A 82.075 318 39 9 147 457 32158498 32158192 3.590000e-64 255.0
6 TraesCS7A01G064600 chr7A 97.727 44 1 0 133 176 32063562 32063519 3.000000e-10 76.8
7 TraesCS7A01G064600 chr7D 94.259 2839 103 19 1 2811 31962340 31959534 0.000000e+00 4285.0
8 TraesCS7A01G064600 chr7D 92.676 1065 44 12 1487 2545 32004569 32003533 0.000000e+00 1504.0
9 TraesCS7A01G064600 chr7D 84.507 426 51 11 1651 2072 31943093 31943507 9.370000e-110 407.0
10 TraesCS7A01G064600 chr7D 84.053 301 40 6 141 438 32005969 32005674 1.650000e-72 283.0
11 TraesCS7A01G064600 chr7D 80.417 240 31 9 655 881 32005449 32005213 4.820000e-38 169.0
12 TraesCS7A01G064600 chrUn 90.403 1365 91 17 1475 2811 298011982 298010630 0.000000e+00 1759.0
13 TraesCS7A01G064600 chrUn 88.839 1344 107 18 1493 2811 238523559 238522234 0.000000e+00 1611.0
14 TraesCS7A01G064600 chrUn 88.839 1344 107 18 1493 2811 238537668 238536343 0.000000e+00 1611.0
15 TraesCS7A01G064600 chrUn 88.839 1344 107 18 1493 2811 271022440 271021115 0.000000e+00 1611.0
16 TraesCS7A01G064600 chrUn 88.790 1347 108 18 1490 2811 278812437 278813765 0.000000e+00 1611.0
17 TraesCS7A01G064600 chrUn 88.108 1295 108 20 1545 2811 176753947 176755223 0.000000e+00 1496.0
18 TraesCS7A01G064600 chrUn 82.992 976 122 20 530 1476 238524687 238523727 0.000000e+00 843.0
19 TraesCS7A01G064600 chrUn 82.992 976 122 20 530 1476 238538796 238537836 0.000000e+00 843.0
20 TraesCS7A01G064600 chrUn 82.992 976 122 20 530 1476 271023568 271022608 0.000000e+00 843.0
21 TraesCS7A01G064600 chrUn 82.992 976 122 20 530 1476 278811312 278812272 0.000000e+00 843.0
22 TraesCS7A01G064600 chrUn 82.684 976 124 21 530 1476 176718584 176719543 0.000000e+00 824.0
23 TraesCS7A01G064600 chrUn 84.421 751 95 11 742 1476 359476483 359477227 0.000000e+00 719.0
24 TraesCS7A01G064600 chrUn 84.492 748 94 11 745 1476 386554396 386553655 0.000000e+00 719.0
25 TraesCS7A01G064600 chrUn 85.746 456 47 8 1036 1476 355020106 355020558 1.520000e-127 466.0
26 TraesCS7A01G064600 chr3B 88.726 1295 100 16 1545 2811 713874002 713872726 0.000000e+00 1541.0
27 TraesCS7A01G064600 chr3B 82.992 976 121 21 530 1476 713771906 713770947 0.000000e+00 841.0
28 TraesCS7A01G064600 chr3B 82.992 976 121 21 530 1476 713807089 713806130 0.000000e+00 841.0
29 TraesCS7A01G064600 chr3B 82.787 976 123 21 530 1476 713841045 713840086 0.000000e+00 830.0
30 TraesCS7A01G064600 chr2D 79.904 1463 202 54 65 1476 91377694 91379115 0.000000e+00 989.0
31 TraesCS7A01G064600 chr2D 76.879 865 122 48 83 915 91446597 91447415 4.330000e-113 418.0
32 TraesCS7A01G064600 chr2D 82.704 318 40 10 144 457 91461865 91462171 4.620000e-68 268.0
33 TraesCS7A01G064600 chr2D 87.681 138 11 5 288 422 91472606 91472740 3.750000e-34 156.0
34 TraesCS7A01G064600 chr4A 83.529 425 56 11 1653 2072 696010992 696010577 4.390000e-103 385.0


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 TraesCS7A01G064600 chr7A 32294277 32297087 2810 True 5192.0 5192 100.000000 1 2811 1 chr7A.!!$R3 2810
1 TraesCS7A01G064600 chr7A 32035959 32038719 2760 True 4687.0 4687 97.399000 65 2811 1 chr7A.!!$R1 2746
2 TraesCS7A01G064600 chr7A 32062132 32063562 1430 True 838.4 1600 94.025000 133 1476 2 chr7A.!!$R4 1343
3 TraesCS7A01G064600 chr7A 32128577 32130178 1601 True 580.5 699 84.029500 655 2441 2 chr7A.!!$R5 1786
4 TraesCS7A01G064600 chr7D 31959534 31962340 2806 True 4285.0 4285 94.259000 1 2811 1 chr7D.!!$R1 2810
5 TraesCS7A01G064600 chr7D 32003533 32005969 2436 True 652.0 1504 85.715333 141 2545 3 chr7D.!!$R2 2404
6 TraesCS7A01G064600 chrUn 298010630 298011982 1352 True 1759.0 1759 90.403000 1475 2811 1 chrUn.!!$R1 1336
7 TraesCS7A01G064600 chrUn 176753947 176755223 1276 False 1496.0 1496 88.108000 1545 2811 1 chrUn.!!$F2 1266
8 TraesCS7A01G064600 chrUn 238522234 238524687 2453 True 1227.0 1611 85.915500 530 2811 2 chrUn.!!$R3 2281
9 TraesCS7A01G064600 chrUn 238536343 238538796 2453 True 1227.0 1611 85.915500 530 2811 2 chrUn.!!$R4 2281
10 TraesCS7A01G064600 chrUn 271021115 271023568 2453 True 1227.0 1611 85.915500 530 2811 2 chrUn.!!$R5 2281
11 TraesCS7A01G064600 chrUn 278811312 278813765 2453 False 1227.0 1611 85.891000 530 2811 2 chrUn.!!$F5 2281
12 TraesCS7A01G064600 chrUn 176718584 176719543 959 False 824.0 824 82.684000 530 1476 1 chrUn.!!$F1 946
13 TraesCS7A01G064600 chrUn 359476483 359477227 744 False 719.0 719 84.421000 742 1476 1 chrUn.!!$F4 734
14 TraesCS7A01G064600 chrUn 386553655 386554396 741 True 719.0 719 84.492000 745 1476 1 chrUn.!!$R2 731
15 TraesCS7A01G064600 chr3B 713872726 713874002 1276 True 1541.0 1541 88.726000 1545 2811 1 chr3B.!!$R4 1266
16 TraesCS7A01G064600 chr3B 713770947 713771906 959 True 841.0 841 82.992000 530 1476 1 chr3B.!!$R1 946
17 TraesCS7A01G064600 chr3B 713806130 713807089 959 True 841.0 841 82.992000 530 1476 1 chr3B.!!$R2 946
18 TraesCS7A01G064600 chr3B 713840086 713841045 959 True 830.0 830 82.787000 530 1476 1 chr3B.!!$R3 946
19 TraesCS7A01G064600 chr2D 91377694 91379115 1421 False 989.0 989 79.904000 65 1476 1 chr2D.!!$F1 1411
20 TraesCS7A01G064600 chr2D 91446597 91447415 818 False 418.0 418 76.879000 83 915 1 chr2D.!!$F2 832

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
55 56 0.729116 CAGGACATTAGCAAGCACGG 59.271 55.000 0.0 0.0 0.0 4.94 F
1137 1354 1.077005 AGAGAGTTCACCCAGAGAGCT 59.923 52.381 0.0 0.0 0.0 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1202 1419 1.398041 GCGCATACTTCACATGCTCAA 59.602 47.619 0.30 0.00 45.32 3.02 R
2682 3115 1.009829 CGGGTTCTTACAGAGCATGC 58.990 55.000 10.51 10.51 0.00 4.06 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
44 45 4.530875 GGAATTGGAGACATCAGGACATT 58.469 43.478 0.00 0.00 42.32 2.71
55 56 0.729116 CAGGACATTAGCAAGCACGG 59.271 55.000 0.00 0.00 0.00 4.94
270 399 3.278574 TGGCCTAGCACATGAATACAAC 58.721 45.455 3.32 0.00 0.00 3.32
271 400 3.054434 TGGCCTAGCACATGAATACAACT 60.054 43.478 3.32 0.00 0.00 3.16
552 685 1.191489 TGTACTGGCCAGCACAGCTA 61.191 55.000 31.16 13.99 36.40 3.32
734 923 7.648142 TGCATAAAGTCTTACCAAACTCAAAG 58.352 34.615 0.00 0.00 0.00 2.77
1137 1354 1.077005 AGAGAGTTCACCCAGAGAGCT 59.923 52.381 0.00 0.00 0.00 4.09
1144 1361 1.193323 CACCCAGAGAGCTCATGACT 58.807 55.000 17.77 6.71 0.00 3.41
1202 1419 5.584649 TCAACAACTTTGACAAGATCTTCGT 59.415 36.000 4.57 7.58 33.72 3.85
1517 1916 6.910536 ATTTAGAGAGTAAACTGAATGCCG 57.089 37.500 0.00 0.00 0.00 5.69
1810 2213 8.574251 ACAGAATTACCATAAACATGCAGTAA 57.426 30.769 0.00 0.00 0.00 2.24
2326 2758 8.178313 ACTATCGGTATGTTGATATGTTCTGA 57.822 34.615 0.00 0.00 0.00 3.27
2682 3115 6.318900 GGAAATACCCTTACATGGTTCTTCTG 59.681 42.308 0.00 0.00 37.31 3.02
2752 3185 3.776969 TCAGAGAATATGTTGAGTGGGCT 59.223 43.478 0.00 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 2.745281 GTGGAATTAACCGTGCTTGCTA 59.255 45.455 0.00 0.00 0.00 3.49
270 399 7.224362 GCATACATAGCAGCTGGATTTATCTAG 59.776 40.741 17.12 0.00 38.31 2.43
271 400 7.044181 GCATACATAGCAGCTGGATTTATCTA 58.956 38.462 17.12 6.64 0.00 1.98
1137 1354 1.549243 TAAGCGGTGGCCAGTCATGA 61.549 55.000 5.11 0.00 41.24 3.07
1202 1419 1.398041 GCGCATACTTCACATGCTCAA 59.602 47.619 0.30 0.00 45.32 3.02
1291 1508 1.634702 GTCTTGAGGACATGCTCGAC 58.365 55.000 0.00 0.00 43.94 4.20
1318 1539 5.354842 AGAACTACCCTGCTGTATTTACC 57.645 43.478 0.00 0.00 0.00 2.85
1517 1916 7.381408 GTCTTCTACTTTTTGTAAATTGCCACC 59.619 37.037 0.00 0.00 0.00 4.61
2326 2758 7.661847 CCCGATATAAGATACCTTTTCAGCTTT 59.338 37.037 0.00 0.00 33.94 3.51
2682 3115 1.009829 CGGGTTCTTACAGAGCATGC 58.990 55.000 10.51 10.51 0.00 4.06
2752 3185 4.842531 TTCCATGCTGGTATCTTCTTGA 57.157 40.909 2.68 0.00 39.03 3.02


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

AutoCloner maintained by Alex Coulton.