Multiple sequence alignment - TraesCS7B01G484800

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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 TraesCS7B01G484800 chr7B 100.000 2809 0 0 1 2809 741642518 741639710 0.000000e+00 5188.0
1 TraesCS7B01G484800 chr7B 79.636 1154 201 25 1521 2658 741482663 741483798 0.000000e+00 798.0
2 TraesCS7B01G484800 chr7B 78.646 1241 222 28 1021 2249 703939511 703938302 0.000000e+00 784.0
3 TraesCS7B01G484800 chr7B 78.942 1002 204 4 1498 2494 741541906 741542905 0.000000e+00 675.0
4 TraesCS7B01G484800 chr7B 100.000 278 0 0 3064 3341 741639455 741639178 6.390000e-142 514.0
5 TraesCS7B01G484800 chr7D 94.699 2811 138 5 1 2802 634573878 634576686 0.000000e+00 4355.0
6 TraesCS7B01G484800 chr7D 79.919 1723 282 39 967 2646 583548572 583550273 0.000000e+00 1206.0
7 TraesCS7B01G484800 chr7D 79.643 1680 283 34 968 2608 634650679 634652338 0.000000e+00 1153.0
8 TraesCS7B01G484800 chr7D 80.421 1425 257 17 800 2218 630481362 630479954 0.000000e+00 1066.0
9 TraesCS7B01G484800 chr7D 78.750 880 169 10 1520 2383 634455257 634456134 1.040000e-159 573.0
10 TraesCS7B01G484800 chr7D 93.307 254 16 1 3088 3340 634576981 634577234 1.130000e-99 374.0
11 TraesCS7B01G484800 chr7D 90.551 254 23 1 3088 3340 634566515 634566768 5.340000e-88 335.0
12 TraesCS7B01G484800 chr7D 85.484 186 26 1 3088 3272 630478993 630478808 3.400000e-45 193.0
13 TraesCS7B01G484800 chr7A 93.320 2470 142 17 246 2704 731679912 731677455 0.000000e+00 3626.0
14 TraesCS7B01G484800 chr7A 84.070 1494 223 12 1020 2504 731743632 731742145 0.000000e+00 1426.0
15 TraesCS7B01G484800 chr7A 79.556 1893 317 47 952 2807 726431354 726429495 0.000000e+00 1288.0
16 TraesCS7B01G484800 chr7A 80.898 1581 256 28 968 2519 675021934 675023497 0.000000e+00 1205.0
17 TraesCS7B01G484800 chr7A 79.144 1683 289 36 968 2608 731571401 731569739 0.000000e+00 1107.0
18 TraesCS7B01G484800 chr7A 83.056 1204 178 19 1450 2639 731615962 731614771 0.000000e+00 1070.0
19 TraesCS7B01G484800 chr7A 77.890 1488 253 50 1032 2485 731186558 731188003 0.000000e+00 856.0
20 TraesCS7B01G484800 chr7A 83.764 696 95 10 667 1361 731616660 731615982 0.000000e+00 643.0
21 TraesCS7B01G484800 chr7A 78.825 902 181 8 1506 2401 731774379 731773482 1.720000e-167 599.0
22 TraesCS7B01G484800 chr7A 93.156 263 9 6 3088 3341 731674248 731673986 8.750000e-101 377.0
23 TraesCS7B01G484800 chr7A 96.804 219 7 0 1 219 731680128 731679910 1.890000e-97 366.0
24 TraesCS7B01G484800 chr7A 90.945 254 22 1 3088 3340 731686776 731686523 1.150000e-89 340.0
25 TraesCS7B01G484800 chr7A 89.370 254 26 1 3088 3340 731633114 731632861 5.380000e-83 318.0
26 TraesCS7B01G484800 chr7A 86.561 253 31 1 3088 3340 731613379 731613130 3.280000e-70 276.0
27 TraesCS7B01G484800 chr7A 84.946 186 27 1 3088 3272 726429351 726429166 1.580000e-43 187.0
28 TraesCS7B01G484800 chr7A 96.970 99 3 0 2709 2807 731674375 731674277 2.060000e-37 167.0
29 TraesCS7B01G484800 chr5D 79.563 641 112 16 1 633 432979548 432978919 1.100000e-119 440.0
30 TraesCS7B01G484800 chr2A 77.812 640 126 13 1 633 205497753 205497123 6.760000e-102 381.0
31 TraesCS7B01G484800 chr2A 76.461 633 131 16 9 633 257789508 257788886 8.940000e-86 327.0
32 TraesCS7B01G484800 chr2A 76.531 490 100 11 2 484 352435271 352435752 1.540000e-63 254.0
33 TraesCS7B01G484800 chr3B 77.535 641 125 16 1 633 485391436 485392065 5.270000e-98 368.0
34 TraesCS7B01G484800 chr5B 77.031 640 125 15 1 633 706408957 706409581 6.860000e-92 348.0
35 TraesCS7B01G484800 chr1B 76.255 518 104 16 46 556 512978441 512978946 1.190000e-64 257.0
36 TraesCS7B01G484800 chrUn 77.536 138 18 10 758 891 124524255 124524383 1.660000e-08 71.3
37 TraesCS7B01G484800 chr6B 80.682 88 15 2 809 895 217468610 217468524 2.150000e-07 67.6


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 TraesCS7B01G484800 chr7B 741639178 741642518 3340 True 2851.0 5188 100.000000 1 3341 2 chr7B.!!$R2 3340
1 TraesCS7B01G484800 chr7B 741482663 741483798 1135 False 798.0 798 79.636000 1521 2658 1 chr7B.!!$F1 1137
2 TraesCS7B01G484800 chr7B 703938302 703939511 1209 True 784.0 784 78.646000 1021 2249 1 chr7B.!!$R1 1228
3 TraesCS7B01G484800 chr7B 741541906 741542905 999 False 675.0 675 78.942000 1498 2494 1 chr7B.!!$F2 996
4 TraesCS7B01G484800 chr7D 634573878 634577234 3356 False 2364.5 4355 94.003000 1 3340 2 chr7D.!!$F5 3339
5 TraesCS7B01G484800 chr7D 583548572 583550273 1701 False 1206.0 1206 79.919000 967 2646 1 chr7D.!!$F1 1679
6 TraesCS7B01G484800 chr7D 634650679 634652338 1659 False 1153.0 1153 79.643000 968 2608 1 chr7D.!!$F4 1640
7 TraesCS7B01G484800 chr7D 630478808 630481362 2554 True 629.5 1066 82.952500 800 3272 2 chr7D.!!$R1 2472
8 TraesCS7B01G484800 chr7D 634455257 634456134 877 False 573.0 573 78.750000 1520 2383 1 chr7D.!!$F2 863
9 TraesCS7B01G484800 chr7A 731742145 731743632 1487 True 1426.0 1426 84.070000 1020 2504 1 chr7A.!!$R4 1484
10 TraesCS7B01G484800 chr7A 675021934 675023497 1563 False 1205.0 1205 80.898000 968 2519 1 chr7A.!!$F1 1551
11 TraesCS7B01G484800 chr7A 731673986 731680128 6142 True 1134.0 3626 95.062500 1 3341 4 chr7A.!!$R8 3340
12 TraesCS7B01G484800 chr7A 731569739 731571401 1662 True 1107.0 1107 79.144000 968 2608 1 chr7A.!!$R1 1640
13 TraesCS7B01G484800 chr7A 731186558 731188003 1445 False 856.0 856 77.890000 1032 2485 1 chr7A.!!$F2 1453
14 TraesCS7B01G484800 chr7A 726429166 726431354 2188 True 737.5 1288 82.251000 952 3272 2 chr7A.!!$R6 2320
15 TraesCS7B01G484800 chr7A 731613130 731616660 3530 True 663.0 1070 84.460333 667 3340 3 chr7A.!!$R7 2673
16 TraesCS7B01G484800 chr7A 731773482 731774379 897 True 599.0 599 78.825000 1506 2401 1 chr7A.!!$R5 895
17 TraesCS7B01G484800 chr5D 432978919 432979548 629 True 440.0 440 79.563000 1 633 1 chr5D.!!$R1 632
18 TraesCS7B01G484800 chr2A 205497123 205497753 630 True 381.0 381 77.812000 1 633 1 chr2A.!!$R1 632
19 TraesCS7B01G484800 chr2A 257788886 257789508 622 True 327.0 327 76.461000 9 633 1 chr2A.!!$R2 624
20 TraesCS7B01G484800 chr3B 485391436 485392065 629 False 368.0 368 77.535000 1 633 1 chr3B.!!$F1 632
21 TraesCS7B01G484800 chr5B 706408957 706409581 624 False 348.0 348 77.031000 1 633 1 chr5B.!!$F1 632
22 TraesCS7B01G484800 chr1B 512978441 512978946 505 False 257.0 257 76.255000 46 556 1 chr1B.!!$F1 510

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
281 287 0.393077 CTCGCCATTTATCCCGAGGT 59.607 55.000 0.00 0.0 42.37 3.85 F
402 408 0.542333 GGGGAGCCTCTCTACAAACC 59.458 60.000 0.00 0.0 0.00 3.27 F
1389 1436 1.268352 GTCCTCCTCGATTGGATCTCG 59.732 57.143 4.82 0.0 35.30 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1808 1874 0.305313 GCCGCGTACACAGTCAAAAA 59.695 50.000 4.92 0.0 0.00 1.94 R
2298 2577 3.073946 ACAGCCTTGGGAAGCTAAAGTAA 59.926 43.478 0.00 0.0 37.18 2.24 R
3174 7685 1.338674 TGTATGACCCAAGCAAGACCG 60.339 52.381 0.00 0.0 0.00 4.79 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
85 89 1.203001 TCCTTCCACCCGCTGATTTTT 60.203 47.619 0.00 0.00 0.00 1.94
146 150 2.028561 ATCCAAACCCACATTGGCTT 57.971 45.000 0.43 0.00 45.63 4.35
147 151 2.685106 TCCAAACCCACATTGGCTTA 57.315 45.000 0.43 0.00 45.63 3.09
218 223 3.243501 TGAGCAAATTTGTTCTCTGGTGC 60.244 43.478 28.14 9.45 38.92 5.01
265 271 2.058798 TGCTAGAGTTTTCAACGCTCG 58.941 47.619 0.00 0.00 40.79 5.03
281 287 0.393077 CTCGCCATTTATCCCGAGGT 59.607 55.000 0.00 0.00 42.37 3.85
295 301 2.742053 CCCGAGGTGACACAATACAAAG 59.258 50.000 8.08 0.00 0.00 2.77
297 303 2.805671 CGAGGTGACACAATACAAAGCA 59.194 45.455 8.08 0.00 0.00 3.91
300 306 3.815401 AGGTGACACAATACAAAGCAGAC 59.185 43.478 8.08 0.00 0.00 3.51
323 329 3.555527 TGATTTCAGAGCCTCCTCATG 57.444 47.619 0.00 0.00 40.68 3.07
334 340 1.630369 CCTCCTCATGGTGAAGGTTCA 59.370 52.381 0.00 0.00 34.20 3.18
402 408 0.542333 GGGGAGCCTCTCTACAAACC 59.458 60.000 0.00 0.00 0.00 3.27
474 480 7.719633 AGAGCAGTAAGATCCTTTGTACAAAAA 59.280 33.333 20.89 12.88 31.44 1.94
623 631 1.704628 TGCCCATCTCTCCTGAAAACA 59.295 47.619 0.00 0.00 0.00 2.83
653 661 5.952347 TCAAGACCTAAGCTAACATCTCTCA 59.048 40.000 0.00 0.00 0.00 3.27
747 756 7.998383 AGGGGCAAAATTGTCTTTTATTTTCTT 59.002 29.630 0.00 0.00 33.04 2.52
928 938 6.574465 GCTTTGTAAATCTCACTCTCCCACTA 60.574 42.308 0.00 0.00 0.00 2.74
963 973 3.490348 CCGCAGAAGATTTATCCCCAAT 58.510 45.455 0.00 0.00 0.00 3.16
1035 1051 2.372688 GTCTCCATCCCCCTCCCA 59.627 66.667 0.00 0.00 0.00 4.37
1122 1138 1.668294 CTGCACCTCCTTCTGTCGT 59.332 57.895 0.00 0.00 0.00 4.34
1389 1436 1.268352 GTCCTCCTCGATTGGATCTCG 59.732 57.143 4.82 0.00 35.30 4.04
1710 1764 4.392047 TCAAGGTGATATGCATAGCAAGG 58.608 43.478 25.18 14.69 43.62 3.61
1872 1939 6.968263 TGGTTTTGGAGTGACAATTTGATA 57.032 33.333 2.79 0.00 0.00 2.15
1905 1972 6.183360 ACACATGCACTTTGAGGTTTTCAATA 60.183 34.615 0.00 0.00 44.90 1.90
2075 2151 8.820831 CCATCATACCTCTCTACAGGATAATTT 58.179 37.037 0.00 0.00 36.96 1.82
2219 2498 8.902806 TGAGTTTCAGAATGTTGATTGTTACTT 58.097 29.630 0.00 0.00 37.40 2.24
2283 2562 4.860022 AGATGGGGAATTTCTTTGATCGT 58.140 39.130 0.00 0.00 0.00 3.73
2298 2577 2.277084 GATCGTAAACGTGCCATTCCT 58.723 47.619 2.02 0.00 40.80 3.36
2354 2633 6.150976 CCAACTATTTGATCAACTGGTAAGCA 59.849 38.462 13.87 0.00 34.24 3.91
2425 2713 6.042093 TCTCCTCACATGGTTATGAATAGACC 59.958 42.308 0.00 0.00 37.73 3.85
2447 2735 8.417884 AGACCTAGTCATTGTTCTATTAAGCTC 58.582 37.037 0.00 0.00 34.60 4.09
2772 6206 9.069078 CACTTGTTATGATCTGCAAATGTTTAG 57.931 33.333 0.00 0.00 0.00 1.85
2807 6241 4.931002 CCAAACTGCAATTAAATGGGTCTG 59.069 41.667 0.00 0.00 0.00 3.51
3174 7685 2.355717 ACTCGCTCTGTAGTTGCTTC 57.644 50.000 0.00 0.00 0.00 3.86
3230 7741 2.357009 GCGAATGATCAAGATGGTGCTT 59.643 45.455 0.00 0.00 0.00 3.91
3248 7759 6.765989 TGGTGCTTATGTAGTTTGATATGTCC 59.234 38.462 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
147 151 9.388506 CTCTCAATGACAAGTATTTTGGTCTAT 57.611 33.333 0.00 0.00 0.00 1.98
218 223 1.990799 TGTCCAAATACGAGACTGCG 58.009 50.000 0.00 0.00 37.29 5.18
252 258 1.766069 AAATGGCGAGCGTTGAAAAC 58.234 45.000 0.00 0.00 45.31 2.43
265 271 1.134220 TGTCACCTCGGGATAAATGGC 60.134 52.381 0.00 0.00 0.00 4.40
281 287 5.530543 TCAATGTCTGCTTTGTATTGTGTCA 59.469 36.000 0.00 0.00 33.21 3.58
295 301 3.015327 AGGCTCTGAAATCAATGTCTGC 58.985 45.455 0.00 0.00 0.00 4.26
297 303 3.522750 AGGAGGCTCTGAAATCAATGTCT 59.477 43.478 15.23 0.00 0.00 3.41
300 306 3.882444 TGAGGAGGCTCTGAAATCAATG 58.118 45.455 15.23 0.00 0.00 2.82
334 340 2.834549 ACTCGTGGATCCTCATGAAAGT 59.165 45.455 14.23 5.34 32.93 2.66
368 374 3.914435 GGCTCCCCCTATTACCAATCTTA 59.086 47.826 0.00 0.00 0.00 2.10
375 381 1.150347 AGAGAGGCTCCCCCTATTACC 59.850 57.143 11.71 0.00 46.60 2.85
477 483 8.223330 TCCTCTATACGTACCCTTATCTTTTCT 58.777 37.037 0.00 0.00 0.00 2.52
623 631 7.939588 AGATGTTAGCTTAGGTCTTGAAACTTT 59.060 33.333 0.00 0.00 0.00 2.66
708 716 1.631405 TGCCCCTCATGTTGAAAAGG 58.369 50.000 0.00 0.00 0.00 3.11
709 717 3.749665 TTTGCCCCTCATGTTGAAAAG 57.250 42.857 0.00 0.00 0.00 2.27
747 756 2.862541 ACTCACTAACAATGCCAAGCA 58.137 42.857 0.00 0.00 44.86 3.91
752 761 7.367285 TGTCAATTTTACTCACTAACAATGCC 58.633 34.615 0.00 0.00 0.00 4.40
753 762 8.795786 TTGTCAATTTTACTCACTAACAATGC 57.204 30.769 0.00 0.00 0.00 3.56
796 805 8.234546 CCTATTTGACACTAACGCTAAATTGTT 58.765 33.333 0.00 0.00 0.00 2.83
798 807 7.970384 TCCTATTTGACACTAACGCTAAATTG 58.030 34.615 0.00 0.00 0.00 2.32
839 848 0.396811 CTACCTCCCTATTTGGCCCG 59.603 60.000 0.00 0.00 0.00 6.13
913 923 4.623409 CGACTAGTTAGTGGGAGAGTGAGA 60.623 50.000 0.00 0.00 36.50 3.27
928 938 3.459063 GCGGGGGAGCGACTAGTT 61.459 66.667 0.00 0.00 0.00 2.24
963 973 3.052338 AGAAAGGGGATCTAGGGTTACGA 60.052 47.826 0.00 0.00 0.00 3.43
1011 1027 0.471211 GGGGGATGGAGACCGTCATA 60.471 60.000 11.36 0.00 41.05 2.15
1122 1138 3.430862 GCGCGCCCTTTGATGACA 61.431 61.111 23.24 0.00 0.00 3.58
1265 1282 1.753468 GACGAAGGAGAAATCCGCGC 61.753 60.000 0.00 0.00 36.44 6.86
1349 1385 4.891727 GACCATCGCGGGCGTCAT 62.892 66.667 13.21 0.00 40.22 3.06
1710 1764 4.390264 AGAGGACAAGCTTTTTCAGGTAC 58.610 43.478 0.00 0.00 30.90 3.34
1808 1874 0.305313 GCCGCGTACACAGTCAAAAA 59.695 50.000 4.92 0.00 0.00 1.94
2075 2151 3.076079 TCTCAAGCTTCCATTCATGCA 57.924 42.857 0.00 0.00 0.00 3.96
2283 2562 5.122711 GCTAAAGTAAGGAATGGCACGTTTA 59.877 40.000 0.00 0.00 0.00 2.01
2298 2577 3.073946 ACAGCCTTGGGAAGCTAAAGTAA 59.926 43.478 0.00 0.00 37.18 2.24
2383 2671 5.302568 TGAGGAGAACAAGAAAATTGTGCAT 59.697 36.000 1.78 0.00 30.28 3.96
2425 2713 9.469807 AATCGAGCTTAATAGAACAATGACTAG 57.530 33.333 0.00 0.00 0.00 2.57
2442 2730 1.896220 TTGACAAGGCAATCGAGCTT 58.104 45.000 0.00 0.00 34.17 3.74
2447 2735 2.744202 AGCTAGTTTGACAAGGCAATCG 59.256 45.455 0.00 0.00 0.00 3.34
2612 2922 3.838120 AGATGTACCATATGACGATGCG 58.162 45.455 3.65 0.00 0.00 4.73
2666 3004 8.567285 AAGAGCTTTTAACTTACATGCTATGT 57.433 30.769 0.00 6.93 46.92 2.29
2772 6206 4.981806 TGCAGTTTGGAAGCAATATACC 57.018 40.909 0.00 0.00 34.97 2.73
3069 6503 7.622893 ATCTTTCAGCAGAACCTTCTTATTC 57.377 36.000 0.00 0.00 34.74 1.75
3076 6510 3.181429 TGGGAATCTTTCAGCAGAACCTT 60.181 43.478 0.00 0.00 32.39 3.50
3079 6513 4.741342 CAATGGGAATCTTTCAGCAGAAC 58.259 43.478 0.00 0.00 32.39 3.01
3174 7685 1.338674 TGTATGACCCAAGCAAGACCG 60.339 52.381 0.00 0.00 0.00 4.79
3230 7741 9.908152 CTCATTACGGACATATCAAACTACATA 57.092 33.333 0.00 0.00 0.00 2.29
3248 7759 3.811514 AGATCATACGACGCTCATTACG 58.188 45.455 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.