Multiple sequence alignment - TraesCS7B01G475900

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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 TraesCS7B01G475900 chr7B 100.000 5528 0 0 1 5528 732191030 732196557 0.000000e+00 10209.0
1 TraesCS7B01G475900 chr7B 99.313 5531 34 2 1 5528 732149152 732154681 0.000000e+00 10000.0
2 TraesCS7B01G475900 chr7B 99.303 2294 16 0 1 2294 732142178 732144471 0.000000e+00 4148.0
3 TraesCS7B01G475900 chr7B 78.899 1308 227 38 3310 4587 732383315 732382027 0.000000e+00 841.0
4 TraesCS7B01G475900 chrUn 99.404 3354 17 2 100 3453 318739505 318736155 0.000000e+00 6080.0
5 TraesCS7B01G475900 chrUn 100.000 633 0 0 4004 4636 332435475 332436107 0.000000e+00 1170.0
6 TraesCS7B01G475900 chrUn 99.503 604 3 0 1 604 395795459 395796062 0.000000e+00 1099.0
7 TraesCS7B01G475900 chrUn 79.491 1258 211 37 3307 4533 88204211 88205452 0.000000e+00 850.0
8 TraesCS7B01G475900 chrUn 79.008 1310 225 40 3307 4584 234834703 234835994 0.000000e+00 850.0
9 TraesCS7B01G475900 chrUn 78.855 1310 228 39 3307 4584 224362575 224363867 0.000000e+00 839.0
10 TraesCS7B01G475900 chrUn 100.000 32 0 0 4565 4596 332436105 332436136 5.980000e-05 60.2
11 TraesCS7B01G475900 chr7D 92.711 2058 114 18 2664 4699 629330830 629328787 0.000000e+00 2937.0
12 TraesCS7B01G475900 chr7D 93.107 914 57 6 941 1852 629337803 629336894 0.000000e+00 1334.0
13 TraesCS7B01G475900 chr7D 80.393 1729 265 45 2962 4633 629422798 629421087 0.000000e+00 1247.0
14 TraesCS7B01G475900 chr7D 90.229 481 40 4 1882 2356 629331299 629330820 6.080000e-174 621.0
15 TraesCS7B01G475900 chr7D 83.514 461 74 2 1001 1461 629423594 629423136 3.960000e-116 429.0
16 TraesCS7B01G475900 chr7D 97.487 199 5 0 1 199 467527092 467527290 1.910000e-89 340.0
17 TraesCS7B01G475900 chr7D 96.517 201 7 0 1 201 593131707 593131507 3.190000e-87 333.0
18 TraesCS7B01G475900 chr7A 92.387 2049 118 15 2664 4689 725232174 725230141 0.000000e+00 2885.0
19 TraesCS7B01G475900 chr7A 91.099 1292 84 11 2662 3935 725312016 725310738 0.000000e+00 1720.0
20 TraesCS7B01G475900 chr7A 90.823 948 61 15 929 1867 725234360 725233430 0.000000e+00 1245.0
21 TraesCS7B01G475900 chr7A 84.538 595 54 16 972 1566 725326238 725325682 6.260000e-154 555.0
22 TraesCS7B01G475900 chr7A 87.692 455 46 8 1913 2362 725312573 725312124 6.350000e-144 521.0
23 TraesCS7B01G475900 chr7A 92.527 281 19 2 355 635 725245504 725245226 8.630000e-108 401.0
24 TraesCS7B01G475900 chr7A 90.301 299 17 6 1558 1854 725324394 725324106 1.120000e-101 381.0
25 TraesCS7B01G475900 chr7A 90.123 162 12 3 196 356 725250996 725250838 2.020000e-49 207.0
26 TraesCS7B01G475900 chr7A 86.010 193 16 7 1453 1643 725305944 725305761 4.370000e-46 196.0
27 TraesCS7B01G475900 chr7A 96.296 54 2 0 1808 1861 725305760 725305707 7.630000e-14 89.8
28 TraesCS7B01G475900 chr5D 87.222 540 67 1 4986 5525 414238730 414239267 1.020000e-171 614.0
29 TraesCS7B01G475900 chr5D 87.026 501 64 1 4987 5486 84825841 84826341 1.040000e-156 564.0
30 TraesCS7B01G475900 chr5D 87.417 302 36 2 2358 2658 497141459 497141759 4.100000e-91 346.0
31 TraesCS7B01G475900 chr5A 86.162 542 70 4 4986 5525 79207394 79207932 1.030000e-161 580.0
32 TraesCS7B01G475900 chr5A 88.591 298 34 0 2358 2655 647359555 647359852 4.070000e-96 363.0
33 TraesCS7B01G475900 chr1A 85.582 541 75 3 4986 5525 66703220 66703758 1.040000e-156 564.0
34 TraesCS7B01G475900 chr1A 75.594 631 125 15 3461 4087 104580388 104580993 9.060000e-73 285.0
35 TraesCS7B01G475900 chr2B 86.408 515 65 4 4982 5494 382936127 382936638 4.840000e-155 558.0
36 TraesCS7B01G475900 chr2B 74.839 1085 227 32 3475 4531 47542733 47541667 3.040000e-122 449.0
37 TraesCS7B01G475900 chr2B 83.519 449 69 5 1005 1450 47743871 47744317 1.110000e-111 414.0
38 TraesCS7B01G475900 chr2B 82.851 449 72 5 1005 1450 47773557 47774003 1.120000e-106 398.0
39 TraesCS7B01G475900 chr2B 87.500 304 35 3 2358 2659 769484480 769484178 1.140000e-91 348.0
40 TraesCS7B01G475900 chr2B 93.939 66 4 0 355 420 134500604 134500539 3.520000e-17 100.0
41 TraesCS7B01G475900 chr3B 85.343 539 77 2 4986 5523 622252988 622252451 1.740000e-154 556.0
42 TraesCS7B01G475900 chr3B 84.440 482 63 9 1882 2356 741604200 741604676 1.080000e-126 464.0
43 TraesCS7B01G475900 chr3B 91.772 158 9 2 2675 2829 800132139 800132295 3.350000e-52 217.0
44 TraesCS7B01G475900 chr5B 84.758 538 77 4 4988 5523 241192608 241192074 8.150000e-148 534.0
45 TraesCS7B01G475900 chr5B 87.459 303 36 2 2358 2658 594098011 594097709 1.140000e-91 348.0
46 TraesCS7B01G475900 chr6D 84.230 539 80 5 4986 5523 313184811 313185345 2.280000e-143 520.0
47 TraesCS7B01G475900 chr6D 75.188 266 44 18 196 448 455743197 455743453 7.570000e-19 106.0
48 TraesCS7B01G475900 chr4D 85.412 473 62 5 1888 2356 506411639 506412108 8.330000e-133 484.0
49 TraesCS7B01G475900 chr4D 91.379 116 10 0 2664 2779 506412098 506412213 5.730000e-35 159.0
50 TraesCS7B01G475900 chr4B 85.532 470 59 7 1893 2356 662757547 662757081 2.990000e-132 483.0
51 TraesCS7B01G475900 chr4B 85.593 472 55 11 1893 2356 663809426 663809892 2.990000e-132 483.0
52 TraesCS7B01G475900 chr4B 92.899 169 9 1 2664 2829 662757091 662756923 5.530000e-60 243.0
53 TraesCS7B01G475900 chr4B 92.308 169 10 1 2664 2829 663809882 663810050 2.570000e-58 237.0
54 TraesCS7B01G475900 chr2A 75.252 1091 211 42 3475 4531 31835144 31834079 1.080000e-126 464.0
55 TraesCS7B01G475900 chr2A 82.751 429 69 5 1005 1430 31896405 31896831 1.450000e-100 377.0
56 TraesCS7B01G475900 chr2A 87.213 305 37 2 2355 2658 590545011 590545314 4.100000e-91 346.0
57 TraesCS7B01G475900 chr2D 75.162 1083 217 37 3481 4531 29532106 29531044 3.900000e-126 462.0
58 TraesCS7B01G475900 chr6A 87.296 307 37 2 2355 2659 599872382 599872688 3.170000e-92 350.0
59 TraesCS7B01G475900 chr3D 87.296 307 37 2 2358 2662 528115388 528115694 3.170000e-92 350.0
60 TraesCS7B01G475900 chr3D 96.970 198 6 0 1 198 567893922 567894119 3.190000e-87 333.0
61 TraesCS7B01G475900 chr1D 96.098 205 7 1 1 204 396204474 396204678 3.190000e-87 333.0
62 TraesCS7B01G475900 chr1D 95.631 206 7 2 1 205 388305552 388305756 4.130000e-86 329.0
63 TraesCS7B01G475900 chr1D 82.632 190 28 3 3461 3646 100825630 100825442 4.430000e-36 163.0
64 TraesCS7B01G475900 chr1D 79.091 110 21 2 346 455 416405429 416405322 2.140000e-09 75.0
65 TraesCS7B01G475900 chr6B 78.061 392 78 7 4143 4531 689994262 689994648 1.990000e-59 241.0
66 TraesCS7B01G475900 chr1B 85.915 71 10 0 347 417 562749285 562749215 5.940000e-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 TraesCS7B01G475900 chr7B 732191030 732196557 5527 False 10209.0 10209 100.0000 1 5528 1 chr7B.!!$F3 5527
1 TraesCS7B01G475900 chr7B 732149152 732154681 5529 False 10000.0 10000 99.3130 1 5528 1 chr7B.!!$F2 5527
2 TraesCS7B01G475900 chr7B 732142178 732144471 2293 False 4148.0 4148 99.3030 1 2294 1 chr7B.!!$F1 2293
3 TraesCS7B01G475900 chr7B 732382027 732383315 1288 True 841.0 841 78.8990 3310 4587 1 chr7B.!!$R1 1277
4 TraesCS7B01G475900 chrUn 318736155 318739505 3350 True 6080.0 6080 99.4040 100 3453 1 chrUn.!!$R1 3353
5 TraesCS7B01G475900 chrUn 395795459 395796062 603 False 1099.0 1099 99.5030 1 604 1 chrUn.!!$F4 603
6 TraesCS7B01G475900 chrUn 88204211 88205452 1241 False 850.0 850 79.4910 3307 4533 1 chrUn.!!$F1 1226
7 TraesCS7B01G475900 chrUn 234834703 234835994 1291 False 850.0 850 79.0080 3307 4584 1 chrUn.!!$F3 1277
8 TraesCS7B01G475900 chrUn 224362575 224363867 1292 False 839.0 839 78.8550 3307 4584 1 chrUn.!!$F2 1277
9 TraesCS7B01G475900 chrUn 332435475 332436136 661 False 615.1 1170 100.0000 4004 4636 2 chrUn.!!$F5 632
10 TraesCS7B01G475900 chr7D 629328787 629331299 2512 True 1779.0 2937 91.4700 1882 4699 2 chr7D.!!$R3 2817
11 TraesCS7B01G475900 chr7D 629336894 629337803 909 True 1334.0 1334 93.1070 941 1852 1 chr7D.!!$R2 911
12 TraesCS7B01G475900 chr7D 629421087 629423594 2507 True 838.0 1247 81.9535 1001 4633 2 chr7D.!!$R4 3632
13 TraesCS7B01G475900 chr7A 725230141 725234360 4219 True 2065.0 2885 91.6050 929 4689 2 chr7A.!!$R3 3760
14 TraesCS7B01G475900 chr7A 725310738 725312573 1835 True 1120.5 1720 89.3955 1913 3935 2 chr7A.!!$R5 2022
15 TraesCS7B01G475900 chr7A 725324106 725326238 2132 True 468.0 555 87.4195 972 1854 2 chr7A.!!$R6 882
16 TraesCS7B01G475900 chr5D 414238730 414239267 537 False 614.0 614 87.2220 4986 5525 1 chr5D.!!$F2 539
17 TraesCS7B01G475900 chr5D 84825841 84826341 500 False 564.0 564 87.0260 4987 5486 1 chr5D.!!$F1 499
18 TraesCS7B01G475900 chr5A 79207394 79207932 538 False 580.0 580 86.1620 4986 5525 1 chr5A.!!$F1 539
19 TraesCS7B01G475900 chr1A 66703220 66703758 538 False 564.0 564 85.5820 4986 5525 1 chr1A.!!$F1 539
20 TraesCS7B01G475900 chr1A 104580388 104580993 605 False 285.0 285 75.5940 3461 4087 1 chr1A.!!$F2 626
21 TraesCS7B01G475900 chr2B 382936127 382936638 511 False 558.0 558 86.4080 4982 5494 1 chr2B.!!$F3 512
22 TraesCS7B01G475900 chr2B 47541667 47542733 1066 True 449.0 449 74.8390 3475 4531 1 chr2B.!!$R1 1056
23 TraesCS7B01G475900 chr3B 622252451 622252988 537 True 556.0 556 85.3430 4986 5523 1 chr3B.!!$R1 537
24 TraesCS7B01G475900 chr5B 241192074 241192608 534 True 534.0 534 84.7580 4988 5523 1 chr5B.!!$R1 535
25 TraesCS7B01G475900 chr6D 313184811 313185345 534 False 520.0 520 84.2300 4986 5523 1 chr6D.!!$F1 537
26 TraesCS7B01G475900 chr4D 506411639 506412213 574 False 321.5 484 88.3955 1888 2779 2 chr4D.!!$F1 891
27 TraesCS7B01G475900 chr4B 662756923 662757547 624 True 363.0 483 89.2155 1893 2829 2 chr4B.!!$R1 936
28 TraesCS7B01G475900 chr4B 663809426 663810050 624 False 360.0 483 88.9505 1893 2829 2 chr4B.!!$F1 936
29 TraesCS7B01G475900 chr2A 31834079 31835144 1065 True 464.0 464 75.2520 3475 4531 1 chr2A.!!$R1 1056
30 TraesCS7B01G475900 chr2D 29531044 29532106 1062 True 462.0 462 75.1620 3481 4531 1 chr2D.!!$R1 1050

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
605 606 7.645402 ACGATCTCTTTTTATTTGGAAAACGT 58.355 30.769 0.00 0.0 0.00 3.99 F
1776 3090 1.747924 CTCTCGAGAGTCAAGATGGCA 59.252 52.381 30.44 0.0 37.40 4.92 F
2397 4511 5.223382 AGACGCAAGCACTCATACATATAC 58.777 41.667 0.00 0.0 45.62 1.47 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2093 4201 0.325296 AATAGCCAGGTCGGACAGGA 60.325 55.000 19.27 3.6 36.56 3.86 R
3851 6214 2.696775 TCCTTGGGTGTAGTGGAAAGA 58.303 47.619 0.00 0.0 0.00 2.52 R
4977 7388 5.279356 CCAGCTGTAGATGCTCTGATAATGA 60.279 44.000 13.81 0.0 38.92 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
604 605 7.801315 TGACGATCTCTTTTTATTTGGAAAACG 59.199 33.333 0.00 0.0 0.00 3.60
605 606 7.645402 ACGATCTCTTTTTATTTGGAAAACGT 58.355 30.769 0.00 0.0 0.00 3.99
748 750 8.030106 ACCTCAACGTGTTTTCTTTATTTTTGA 58.970 29.630 0.00 0.0 0.00 2.69
1402 1410 4.717629 CGTTCGGCTCCAGCGACA 62.718 66.667 0.00 0.0 43.26 4.35
1776 3090 1.747924 CTCTCGAGAGTCAAGATGGCA 59.252 52.381 30.44 0.0 37.40 4.92
2042 3895 8.147704 TCCATCCAAAGTGTTTTATTTTCCTTC 58.852 33.333 0.00 0.0 0.00 3.46
2089 4195 7.942341 TGTTTCCATATGGAGTTTAACTGAACT 59.058 33.333 26.30 0.0 46.36 3.01
2397 4511 5.223382 AGACGCAAGCACTCATACATATAC 58.777 41.667 0.00 0.0 45.62 1.47
3851 6214 2.065799 GAGGGGATGGTGGGATGTATT 58.934 52.381 0.00 0.0 0.00 1.89
4750 7161 4.426416 CATGGATCAATGCACAATCGTTT 58.574 39.130 0.00 0.0 0.00 3.60
4977 7388 5.362717 AGGTCTTTTCCGGTCAATTTTCTTT 59.637 36.000 0.00 0.0 0.00 2.52
5290 7702 1.613630 GGCTCAGGGGACTCAAGGA 60.614 63.158 0.00 0.0 40.21 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
748 750 5.772393 TGATCAACCAGTATTACACCCTT 57.228 39.130 0.00 0.00 0.00 3.95
1529 1540 5.067936 TGACCACGAACAAACCAAATTGTAT 59.932 36.000 0.00 0.00 42.49 2.29
1776 3090 7.504238 TCGCCATCCAAACCAATATATAAAGTT 59.496 33.333 0.00 0.00 0.00 2.66
2089 4195 0.755698 GCCAGGTCGGACAGGATAGA 60.756 60.000 19.27 0.00 36.56 1.98
2093 4201 0.325296 AATAGCCAGGTCGGACAGGA 60.325 55.000 19.27 3.60 36.56 3.86
2231 4343 5.354234 CAGGTTGGTGTCGCTAGAATAATTT 59.646 40.000 0.00 0.00 0.00 1.82
2397 4511 1.686587 TCATAGGGGTGAGTGTATGCG 59.313 52.381 0.00 0.00 0.00 4.73
2493 4607 1.348696 TGATGAGGCGCATATGGTGAT 59.651 47.619 10.83 0.00 37.34 3.06
3851 6214 2.696775 TCCTTGGGTGTAGTGGAAAGA 58.303 47.619 0.00 0.00 0.00 2.52
4977 7388 5.279356 CCAGCTGTAGATGCTCTGATAATGA 60.279 44.000 13.81 0.00 38.92 2.57
5039 7450 0.391597 ATTCGGGAATGCGTACGGAT 59.608 50.000 17.18 17.18 0.00 4.18
5290 7702 4.195334 GCATGGGAGATGGCGGGT 62.195 66.667 0.00 0.00 0.00 5.28
5345 7757 1.692411 TCGATCTGACATCCACCGAT 58.308 50.000 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.