Multiple sequence alignment - TraesCS5B01G412800

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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 TraesCS5B01G412800 chr5B 100.000 4366 0 0 1 4366 587785570 587789935 0.000000e+00 8063.0
1 TraesCS5B01G412800 chr5B 99.062 2132 15 5 1 2129 587761373 587763502 0.000000e+00 3821.0
2 TraesCS5B01G412800 chr5B 97.694 1431 7 2 2962 4366 587763499 587764929 0.000000e+00 2436.0
3 TraesCS5B01G412800 chr5B 85.083 181 26 1 2608 2787 685603661 685603481 2.680000e-42 183.0
4 TraesCS5B01G412800 chr5B 83.582 134 21 1 2605 2737 685438989 685439122 1.650000e-24 124.0
5 TraesCS5B01G412800 chr5D 91.816 1564 79 14 707 2266 480030646 480032164 0.000000e+00 2134.0
6 TraesCS5B01G412800 chr5D 96.151 1169 40 5 2403 3567 480032348 480033515 0.000000e+00 1905.0
7 TraesCS5B01G412800 chr5D 76.262 931 205 15 1242 2164 543835730 543836652 8.490000e-132 481.0
8 TraesCS5B01G412800 chr5D 93.210 324 22 0 3715 4038 480033711 480034034 1.100000e-130 477.0
9 TraesCS5B01G412800 chr5D 86.575 365 27 17 4022 4366 480034131 480034493 2.460000e-102 383.0
10 TraesCS5B01G412800 chr5D 83.598 189 30 1 2608 2795 543705847 543705659 4.490000e-40 176.0
11 TraesCS5B01G412800 chr5D 83.125 160 22 4 2608 2764 543836840 543836997 1.640000e-29 141.0
12 TraesCS5B01G412800 chr5D 82.237 152 12 11 3569 3716 480033544 480033684 2.760000e-22 117.0
13 TraesCS5B01G412800 chr5A 89.477 1454 82 26 2434 3831 598522060 598523498 0.000000e+00 1772.0
14 TraesCS5B01G412800 chr5A 91.185 1089 86 7 1182 2266 598520624 598521706 0.000000e+00 1471.0
15 TraesCS5B01G412800 chr5A 97.778 45 1 0 2403 2447 598521887 598521931 1.300000e-10 78.7
16 TraesCS5B01G412800 chrUn 100.000 387 0 0 3057 3443 480384961 480385347 0.000000e+00 715.0
17 TraesCS5B01G412800 chrUn 100.000 33 0 0 1143 1175 81901856 81901824 1.310000e-05 62.1
18 TraesCS5B01G412800 chr6D 85.978 271 28 4 3715 3980 87464312 87464047 9.240000e-72 281.0
19 TraesCS5B01G412800 chr6D 80.874 183 17 10 4166 4345 87466398 87466231 1.270000e-25 128.0
20 TraesCS5B01G412800 chr6D 100.000 34 0 0 3717 3750 87464417 87464384 3.650000e-06 63.9
21 TraesCS5B01G412800 chr6A 80.000 415 47 20 3715 4110 105589097 105588700 1.550000e-69 274.0
22 TraesCS5B01G412800 chr6A 79.459 185 16 14 4166 4345 105591831 105591664 1.280000e-20 111.0
23 TraesCS5B01G412800 chr4A 86.624 157 20 1 2608 2763 625396029 625396185 5.810000e-39 172.0
24 TraesCS5B01G412800 chr4A 80.791 177 33 1 2601 2776 624625811 624625987 2.120000e-28 137.0
25 TraesCS5B01G412800 chr1A 80.114 176 34 1 2602 2776 569457997 569457822 3.540000e-26 130.0
26 TraesCS5B01G412800 chr6B 81.081 111 7 7 4166 4273 166117763 166117664 4.680000e-10 76.8
27 TraesCS5B01G412800 chr6B 97.436 39 0 1 1143 1180 675251279 675251317 1.010000e-06 65.8
28 TraesCS5B01G412800 chr1B 97.059 34 1 0 1155 1188 392113795 392113762 1.700000e-04 58.4
29 TraesCS5B01G412800 chr2D 90.476 42 4 0 169 210 462185364 462185323 6.100000e-04 56.5
30 TraesCS5B01G412800 chr2B 100.000 30 0 0 169 198 741864031 741864060 6.100000e-04 56.5
31 TraesCS5B01G412800 chr4D 100.000 28 0 0 1155 1182 509837499 509837472 8.000000e-03 52.8
32 TraesCS5B01G412800 chr4B 100.000 28 0 0 1155 1182 654628560 654628587 8.000000e-03 52.8
33 TraesCS5B01G412800 chr4B 100.000 28 0 0 1155 1182 654745878 654745905 8.000000e-03 52.8
34 TraesCS5B01G412800 chr4B 100.000 28 0 0 1155 1182 654754621 654754648 8.000000e-03 52.8
35 TraesCS5B01G412800 chr1D 100.000 28 0 0 1155 1182 114157703 114157730 8.000000e-03 52.8


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 TraesCS5B01G412800 chr5B 587785570 587789935 4365 False 8063.000000 8063 100.000000 1 4366 1 chr5B.!!$F1 4365
1 TraesCS5B01G412800 chr5B 587761373 587764929 3556 False 3128.500000 3821 98.378000 1 4366 2 chr5B.!!$F3 4365
2 TraesCS5B01G412800 chr5D 480030646 480034493 3847 False 1003.200000 2134 89.997800 707 4366 5 chr5D.!!$F1 3659
3 TraesCS5B01G412800 chr5D 543835730 543836997 1267 False 311.000000 481 79.693500 1242 2764 2 chr5D.!!$F2 1522
4 TraesCS5B01G412800 chr5A 598520624 598523498 2874 False 1107.233333 1772 92.813333 1182 3831 3 chr5A.!!$F1 2649

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
628 631 1.286260 GCTGTCGAGTGTTCTCCGT 59.714 57.895 0.00 0.00 37.40 4.69 F
815 818 1.819288 CTGGCGACCTCTTCTAGTTCA 59.181 52.381 0.00 0.00 0.00 3.18 F
2288 2441 0.173029 CATAGGTTGGCAAATGCGCA 59.827 50.000 14.96 14.96 43.26 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2268 2421 0.173255 GCGCATTTGCCAACCTATGT 59.827 50.000 0.30 0.0 37.91 2.29 R
2766 3061 1.935933 ACGACACAACTCACCTGAAC 58.064 50.000 0.00 0.0 0.00 3.18 R
3443 3739 2.485426 GCAGCTACAGTGAGCATTCAAA 59.515 45.455 14.37 0.0 45.43 2.69 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
628 631 1.286260 GCTGTCGAGTGTTCTCCGT 59.714 57.895 0.00 0.00 37.40 4.69
815 818 1.819288 CTGGCGACCTCTTCTAGTTCA 59.181 52.381 0.00 0.00 0.00 3.18
998 1002 2.716217 CAGAAGACTCATTGGGTTCCC 58.284 52.381 0.12 0.12 0.00 3.97
2129 2137 3.305964 CACGGGCATACATACTCTAACG 58.694 50.000 0.00 0.00 0.00 3.18
2215 2247 8.155510 ACAGTTATCCTAGTGACATCGTAGATA 58.844 37.037 0.00 0.00 45.12 1.98
2227 2259 8.656849 GTGACATCGTAGATATGTTTCTTTGTT 58.343 33.333 0.00 0.00 45.12 2.83
2268 2421 3.068873 GCTGTGTTTGGTAATTCCCAACA 59.931 43.478 1.28 5.87 45.56 3.33
2287 2440 0.173255 ACATAGGTTGGCAAATGCGC 59.827 50.000 0.00 0.00 43.26 6.09
2288 2441 0.173029 CATAGGTTGGCAAATGCGCA 59.827 50.000 14.96 14.96 43.26 6.09
2326 2479 9.920946 TTTTAATGAAACCCTGCTCTATTCTAT 57.079 29.630 0.00 0.00 0.00 1.98
2327 2480 8.908786 TTAATGAAACCCTGCTCTATTCTATG 57.091 34.615 0.00 0.00 0.00 2.23
2328 2481 5.296151 TGAAACCCTGCTCTATTCTATGG 57.704 43.478 0.00 0.00 0.00 2.74
2330 2483 5.903010 TGAAACCCTGCTCTATTCTATGGTA 59.097 40.000 0.00 0.00 0.00 3.25
2331 2484 6.385759 TGAAACCCTGCTCTATTCTATGGTAA 59.614 38.462 0.00 0.00 0.00 2.85
2332 2485 6.824958 AACCCTGCTCTATTCTATGGTAAA 57.175 37.500 0.00 0.00 0.00 2.01
2334 2487 7.010339 ACCCTGCTCTATTCTATGGTAAATC 57.990 40.000 0.00 0.00 0.00 2.17
2335 2488 6.102663 CCCTGCTCTATTCTATGGTAAATCG 58.897 44.000 0.00 0.00 0.00 3.34
2336 2489 6.071334 CCCTGCTCTATTCTATGGTAAATCGA 60.071 42.308 0.00 0.00 0.00 3.59
2337 2490 6.809196 CCTGCTCTATTCTATGGTAAATCGAC 59.191 42.308 0.00 0.00 0.00 4.20
2338 2491 6.379386 TGCTCTATTCTATGGTAAATCGACG 58.621 40.000 0.00 0.00 0.00 5.12
2339 2492 6.016527 TGCTCTATTCTATGGTAAATCGACGT 60.017 38.462 0.00 0.00 0.00 4.34
2341 2494 7.268199 TCTATTCTATGGTAAATCGACGTGT 57.732 36.000 0.00 0.00 0.00 4.49
2343 2496 8.192774 TCTATTCTATGGTAAATCGACGTGTTT 58.807 33.333 0.00 0.66 0.00 2.83
2344 2497 7.605410 ATTCTATGGTAAATCGACGTGTTTT 57.395 32.000 0.00 0.00 0.00 2.43
2368 2521 7.943079 TTTTTGGTATGAGACACATCATCAT 57.057 32.000 0.00 0.00 40.40 2.45
2369 2522 6.930667 TTTGGTATGAGACACATCATCATG 57.069 37.500 0.00 0.00 40.40 3.07
2370 2523 5.619132 TGGTATGAGACACATCATCATGT 57.381 39.130 0.00 0.00 44.72 3.21
2371 2524 6.729690 TGGTATGAGACACATCATCATGTA 57.270 37.500 0.00 0.00 41.69 2.29
2372 2525 7.123355 TGGTATGAGACACATCATCATGTAA 57.877 36.000 0.00 0.00 41.69 2.41
2373 2526 7.563906 TGGTATGAGACACATCATCATGTAAA 58.436 34.615 0.00 0.00 41.69 2.01
2374 2527 8.046107 TGGTATGAGACACATCATCATGTAAAA 58.954 33.333 0.00 0.00 41.69 1.52
2375 2528 8.554528 GGTATGAGACACATCATCATGTAAAAG 58.445 37.037 0.00 0.00 41.69 2.27
2376 2529 9.102757 GTATGAGACACATCATCATGTAAAAGT 57.897 33.333 0.00 0.00 41.69 2.66
2377 2530 7.984422 TGAGACACATCATCATGTAAAAGTT 57.016 32.000 0.00 0.00 41.69 2.66
2378 2531 8.394971 TGAGACACATCATCATGTAAAAGTTT 57.605 30.769 0.00 0.00 41.69 2.66
2379 2532 9.500785 TGAGACACATCATCATGTAAAAGTTTA 57.499 29.630 0.00 0.00 41.69 2.01
2382 2535 9.722056 GACACATCATCATGTAAAAGTTTATCC 57.278 33.333 0.00 0.00 41.69 2.59
2383 2536 9.466497 ACACATCATCATGTAAAAGTTTATCCT 57.534 29.630 0.00 0.00 41.69 3.24
2494 2789 9.690913 TGATTCAATCATTTCTTAGAATGGAGT 57.309 29.630 0.00 0.00 37.56 3.85
2749 3044 0.251519 CTTCTTGAGGCAGCCCCTTT 60.252 55.000 8.22 0.00 46.60 3.11
2766 3061 7.331687 CAGCCCCTTTTGTTGAAATATTACAAG 59.668 37.037 3.25 0.00 33.74 3.16
2805 3100 5.894807 GTCGTTTCTGACTAAGAACGTTTTG 59.105 40.000 0.46 0.00 44.77 2.44
3055 3351 1.391157 CCTGAGAGAAGGAGCCCTCG 61.391 65.000 0.00 0.00 40.02 4.63
3516 3816 7.320324 CGATTGTTAATAAATGTATGCACGACC 59.680 37.037 0.00 0.00 0.00 4.79
4321 4829 0.731994 GAGGAGGTACGGACGAGAAC 59.268 60.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
612 615 1.679680 AGAAACGGAGAACACTCGACA 59.320 47.619 0.00 0.00 0.00 4.35
628 631 4.159879 GGATGGAAACCTAGACGAGAGAAA 59.840 45.833 0.00 0.00 0.00 2.52
815 818 0.693430 GGGGGTCCCTAATCCGACTT 60.693 60.000 8.15 0.00 41.34 3.01
998 1002 7.466455 GCGAATCATTATTATGTAGCTCCATGG 60.466 40.741 4.97 4.97 33.34 3.66
2230 2262 7.201848 CCAAACACAGCCATGTCATTATTATCT 60.202 37.037 0.00 0.00 37.65 1.98
2233 2265 5.714333 ACCAAACACAGCCATGTCATTATTA 59.286 36.000 0.00 0.00 37.65 0.98
2268 2421 0.173255 GCGCATTTGCCAACCTATGT 59.827 50.000 0.30 0.00 37.91 2.29
2287 2440 8.069574 GGGTTTCATTAAAATGTTGCTTTCTTG 58.930 33.333 2.80 0.00 37.65 3.02
2288 2441 7.992608 AGGGTTTCATTAAAATGTTGCTTTCTT 59.007 29.630 2.80 0.00 37.65 2.52
2344 2497 7.394077 ACATGATGATGTGTCTCATACCAAAAA 59.606 33.333 0.00 0.00 41.52 1.94
2346 2499 6.417258 ACATGATGATGTGTCTCATACCAAA 58.583 36.000 0.00 0.00 41.52 3.28
2347 2500 5.993055 ACATGATGATGTGTCTCATACCAA 58.007 37.500 0.00 0.00 41.52 3.67
2350 2503 9.102757 ACTTTTACATGATGATGTGTCTCATAC 57.897 33.333 8.17 0.00 43.03 2.39
2351 2504 9.671279 AACTTTTACATGATGATGTGTCTCATA 57.329 29.630 8.17 0.00 43.03 2.15
2352 2505 8.571461 AACTTTTACATGATGATGTGTCTCAT 57.429 30.769 8.17 0.00 43.03 2.90
2356 2509 9.722056 GGATAAACTTTTACATGATGATGTGTC 57.278 33.333 8.17 0.00 43.03 3.67
2357 2510 9.466497 AGGATAAACTTTTACATGATGATGTGT 57.534 29.630 8.17 0.00 43.03 3.72
2448 2743 7.656948 TGAATCAATTGGGACACATTCTTTTTC 59.343 33.333 5.42 0.00 39.29 2.29
2494 2789 4.518970 GGCAAAATGTACTTGGTGAGAGAA 59.481 41.667 0.00 0.00 0.00 2.87
2749 3044 9.126151 TCACCTGAACTTGTAATATTTCAACAA 57.874 29.630 3.61 3.29 0.00 2.83
2766 3061 1.935933 ACGACACAACTCACCTGAAC 58.064 50.000 0.00 0.00 0.00 3.18
2805 3100 4.446371 ACATACTCATTACTGAAGCTGGC 58.554 43.478 0.00 0.00 0.00 4.85
2917 3213 4.405116 AAATTTTCAGGTTCAGCAGCAA 57.595 36.364 0.00 0.00 0.00 3.91
3055 3351 2.592308 GGCAGTCCATCTCCCACC 59.408 66.667 0.00 0.00 0.00 4.61
3443 3739 2.485426 GCAGCTACAGTGAGCATTCAAA 59.515 45.455 14.37 0.00 45.43 2.69
3516 3816 2.653234 ATAGCAGAGGATTGGCTTGG 57.347 50.000 0.00 0.00 39.01 3.61


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

AutoCloner maintained by Alex Coulton.