Multiple sequence alignment - TraesCS7D01G258400

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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 TraesCS7D01G258400 chr7D 100.000 2511 0 0 1 2511 234139066 234141576 0.000000e+00 4638
1 TraesCS7D01G258400 chr7D 92.667 450 30 3 2064 2511 509425340 509425788 0.000000e+00 645
2 TraesCS7D01G258400 chr2B 96.894 1513 46 1 1 1513 733188637 733187126 0.000000e+00 2532
3 TraesCS7D01G258400 chr2B 95.770 1513 64 0 1 1513 198063354 198061842 0.000000e+00 2440
4 TraesCS7D01G258400 chr1B 94.980 1514 74 2 1 1514 526319869 526321380 0.000000e+00 2374
5 TraesCS7D01G258400 chr7A 94.250 1513 87 0 2 1514 194267722 194266210 0.000000e+00 2313
6 TraesCS7D01G258400 chr7A 96.327 599 21 1 1511 2108 247073910 247074508 0.000000e+00 983
7 TraesCS7D01G258400 chr7A 96.057 558 21 1 1511 2067 247156539 247157096 0.000000e+00 907
8 TraesCS7D01G258400 chr3D 85.210 1474 190 14 60 1512 160759481 160760947 0.000000e+00 1489
9 TraesCS7D01G258400 chr3D 92.617 447 28 5 2067 2511 417725278 417725721 2.720000e-179 638
10 TraesCS7D01G258400 chr3D 83.285 694 93 18 1683 2370 174788798 174789474 3.550000e-173 617
11 TraesCS7D01G258400 chr3D 84.651 645 70 21 1683 2312 346755807 346755177 1.280000e-172 616
12 TraesCS7D01G258400 chr3A 96.364 825 27 2 689 1513 589374739 589375560 0.000000e+00 1354
13 TraesCS7D01G258400 chr3A 85.690 580 62 14 1683 2258 551313867 551314429 2.150000e-165 592
14 TraesCS7D01G258400 chr3B 84.324 925 119 13 60 964 237555484 237556402 0.000000e+00 881
15 TraesCS7D01G258400 chr2D 83.412 844 106 24 1683 2511 53597627 53598451 0.000000e+00 752
16 TraesCS7D01G258400 chr2D 93.049 446 27 3 2067 2511 422861425 422860983 0.000000e+00 649
17 TraesCS7D01G258400 chr2D 93.049 446 27 3 2067 2511 422868410 422867968 0.000000e+00 649
18 TraesCS7D01G258400 chr2D 86.838 585 56 13 1683 2261 613301307 613300738 3.520000e-178 634
19 TraesCS7D01G258400 chr5D 92.857 448 27 5 2067 2511 34247342 34247787 0.000000e+00 645
20 TraesCS7D01G258400 chr5D 92.841 447 26 4 2066 2511 130607175 130606734 0.000000e+00 643
21 TraesCS7D01G258400 chr2A 85.860 587 64 13 1682 2261 485251586 485251012 7.680000e-170 606
22 TraesCS7D01G258400 chr2A 82.508 646 82 22 1682 2310 427853080 427852449 2.840000e-149 538
23 TraesCS7D01G258400 chr6D 83.978 181 20 7 1511 1683 53637998 53638177 5.560000e-37 165
24 TraesCS7D01G258400 chr6B 82.530 166 21 3 1511 1669 117977482 117977646 3.370000e-29 139
25 TraesCS7D01G258400 chr6A 82.390 159 21 5 1532 1683 61619482 61619324 5.640000e-27 132


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 TraesCS7D01G258400 chr7D 234139066 234141576 2510 False 4638 4638 100.000 1 2511 1 chr7D.!!$F1 2510
1 TraesCS7D01G258400 chr2B 733187126 733188637 1511 True 2532 2532 96.894 1 1513 1 chr2B.!!$R2 1512
2 TraesCS7D01G258400 chr2B 198061842 198063354 1512 True 2440 2440 95.770 1 1513 1 chr2B.!!$R1 1512
3 TraesCS7D01G258400 chr1B 526319869 526321380 1511 False 2374 2374 94.980 1 1514 1 chr1B.!!$F1 1513
4 TraesCS7D01G258400 chr7A 194266210 194267722 1512 True 2313 2313 94.250 2 1514 1 chr7A.!!$R1 1512
5 TraesCS7D01G258400 chr7A 247073910 247074508 598 False 983 983 96.327 1511 2108 1 chr7A.!!$F1 597
6 TraesCS7D01G258400 chr7A 247156539 247157096 557 False 907 907 96.057 1511 2067 1 chr7A.!!$F2 556
7 TraesCS7D01G258400 chr3D 160759481 160760947 1466 False 1489 1489 85.210 60 1512 1 chr3D.!!$F1 1452
8 TraesCS7D01G258400 chr3D 174788798 174789474 676 False 617 617 83.285 1683 2370 1 chr3D.!!$F2 687
9 TraesCS7D01G258400 chr3D 346755177 346755807 630 True 616 616 84.651 1683 2312 1 chr3D.!!$R1 629
10 TraesCS7D01G258400 chr3A 589374739 589375560 821 False 1354 1354 96.364 689 1513 1 chr3A.!!$F2 824
11 TraesCS7D01G258400 chr3A 551313867 551314429 562 False 592 592 85.690 1683 2258 1 chr3A.!!$F1 575
12 TraesCS7D01G258400 chr3B 237555484 237556402 918 False 881 881 84.324 60 964 1 chr3B.!!$F1 904
13 TraesCS7D01G258400 chr2D 53597627 53598451 824 False 752 752 83.412 1683 2511 1 chr2D.!!$F1 828
14 TraesCS7D01G258400 chr2D 613300738 613301307 569 True 634 634 86.838 1683 2261 1 chr2D.!!$R3 578
15 TraesCS7D01G258400 chr2A 485251012 485251586 574 True 606 606 85.860 1682 2261 1 chr2A.!!$R2 579
16 TraesCS7D01G258400 chr2A 427852449 427853080 631 True 538 538 82.508 1682 2310 1 chr2A.!!$R1 628

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
505 526 0.813821 GAACCTCAAATGGCCAGAGC 59.186 55.0 13.05 0.0 38.76 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2404 2456 0.260523 AGAGCTAGGTCAGGGGAGTC 59.739 60.0 23.18 0.0 0.0 3.36 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
316 337 6.136155 TGAGACATGGGATGATGAACTAGTA 58.864 40.000 0.00 0.00 0.00 1.82
505 526 0.813821 GAACCTCAAATGGCCAGAGC 59.186 55.000 13.05 0.00 38.76 4.09
538 559 1.417517 TGGCAGCATATCTGGACGATT 59.582 47.619 0.00 0.00 43.06 3.34
574 595 6.258947 GGAAAGTCTGTATGTTCTTATGGAGC 59.741 42.308 0.00 0.00 0.00 4.70
627 648 8.925161 ATGAATATAAAACGGAAACACATTGG 57.075 30.769 0.00 0.00 0.00 3.16
893 914 4.617298 CGGGTGACAAACAGAAAACAACTT 60.617 41.667 0.00 0.00 0.00 2.66
958 979 0.995024 ACTTGCAGACTAGGGGCAAT 59.005 50.000 15.34 6.47 45.43 3.56
971 992 1.185315 GGGCAATACACAAGGCATGT 58.815 50.000 0.00 0.00 45.34 3.21
1141 1163 4.459089 GTCCGGAGCCCTCTGCAC 62.459 72.222 3.06 0.00 44.83 4.57
1257 1279 4.035102 GCTCAAGGGCCGGGACTT 62.035 66.667 2.18 0.00 0.00 3.01
1302 1324 0.905357 TTCAGGGAAGCTAGGAGTGC 59.095 55.000 0.00 0.00 0.00 4.40
1341 1363 5.734720 TGGTTCCTATGAGTTCATGTTCTC 58.265 41.667 4.90 11.07 37.15 2.87
1365 1387 4.964262 TCGTAGGGAATGTAATAGGGTTGT 59.036 41.667 0.00 0.00 0.00 3.32
1547 1569 2.813754 TCGAGCTCCCATTTGAAACAAG 59.186 45.455 8.47 0.00 0.00 3.16
1548 1570 2.669391 CGAGCTCCCATTTGAAACAAGC 60.669 50.000 8.47 0.00 0.00 4.01
1552 1575 4.129380 GCTCCCATTTGAAACAAGCTTTT 58.871 39.130 0.00 0.00 0.00 2.27
1629 1652 3.197983 AGCTACTTGGTGTTCACCCTATC 59.802 47.826 17.78 4.36 0.00 2.08
1645 1668 2.300437 CCTATCTCGGTCCATCCTTTCC 59.700 54.545 0.00 0.00 0.00 3.13
1651 1674 2.107552 TCGGTCCATCCTTTCCTTTTGT 59.892 45.455 0.00 0.00 0.00 2.83
1977 2009 6.096673 TCCGTTAGCTTAGCATAATGATCA 57.903 37.500 7.07 0.00 0.00 2.92
2015 2048 8.965172 GCTATTGCTTTCTTCATGTCAAATATG 58.035 33.333 0.00 0.00 36.03 1.78
2207 2250 2.821437 AGAGCCTAGTGCCAGTTTCTA 58.179 47.619 0.21 0.00 42.71 2.10
2247 2293 3.935828 GAGCTTCGCAGAAAAGGAATACT 59.064 43.478 0.00 0.00 45.90 2.12
2258 2304 9.825109 GCAGAAAAGGAATACTAAATAGAGTCT 57.175 33.333 0.00 0.00 0.00 3.24
2280 2327 7.601508 AGTCTAAACGGAATAAAACTTCACGAT 59.398 33.333 0.00 0.00 0.00 3.73
2304 2351 5.299279 TGATTTTTCTTGGACCAGAAGACAC 59.701 40.000 0.00 0.00 34.22 3.67
2317 2364 0.401395 AAGACACCCAGGGGACTTGA 60.401 55.000 11.37 0.00 40.21 3.02
2321 2368 0.036875 CACCCAGGGGACTTGAAGTC 59.963 60.000 16.70 16.70 44.32 3.01
2336 2383 2.037772 TGAAGTCCAAGTCAGAAGAGCC 59.962 50.000 0.00 0.00 0.00 4.70
2403 2455 4.410400 GCCTTGTGGACCCCTCGG 62.410 72.222 0.00 0.00 34.57 4.63
2420 2472 3.957919 GGACTCCCCTGACCTAGC 58.042 66.667 0.00 0.00 0.00 3.42
2425 2477 1.342574 ACTCCCCTGACCTAGCTCTTC 60.343 57.143 0.00 0.00 0.00 2.87
2427 2479 0.031616 CCCCTGACCTAGCTCTTCCT 60.032 60.000 0.00 0.00 0.00 3.36
2437 2489 7.945278 TGACCTAGCTCTTCCTCCTATATATT 58.055 38.462 0.00 0.00 0.00 1.28
2439 2491 7.945278 ACCTAGCTCTTCCTCCTATATATTCA 58.055 38.462 0.00 0.00 0.00 2.57
2441 2493 7.836685 CCTAGCTCTTCCTCCTATATATTCACA 59.163 40.741 0.00 0.00 0.00 3.58
2459 2511 5.966853 TCACATATATTCCAGAACCACCA 57.033 39.130 0.00 0.00 0.00 4.17
2460 2512 5.928976 TCACATATATTCCAGAACCACCAG 58.071 41.667 0.00 0.00 0.00 4.00
2461 2513 5.665360 TCACATATATTCCAGAACCACCAGA 59.335 40.000 0.00 0.00 0.00 3.86
2462 2514 6.157820 TCACATATATTCCAGAACCACCAGAA 59.842 38.462 0.00 0.00 0.00 3.02
2463 2515 6.484643 CACATATATTCCAGAACCACCAGAAG 59.515 42.308 0.00 0.00 0.00 2.85
2464 2516 2.206576 ATTCCAGAACCACCAGAAGC 57.793 50.000 0.00 0.00 0.00 3.86
2466 2518 1.067295 TCCAGAACCACCAGAAGCAT 58.933 50.000 0.00 0.00 0.00 3.79
2470 2522 1.168714 GAACCACCAGAAGCATCCAC 58.831 55.000 0.00 0.00 0.00 4.02
2475 2527 1.879380 CACCAGAAGCATCCACGAAAA 59.121 47.619 0.00 0.00 0.00 2.29
2476 2528 2.489329 CACCAGAAGCATCCACGAAAAT 59.511 45.455 0.00 0.00 0.00 1.82
2485 2537 4.095610 GCATCCACGAAAATACTTTTCCG 58.904 43.478 6.74 5.24 44.73 4.30
2503 2555 2.978010 CCGCCGCAACCTTCTGTT 60.978 61.111 0.00 0.00 37.80 3.16
2507 2559 2.325082 CCGCAACCTTCTGTTCCCG 61.325 63.158 0.00 0.00 34.00 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 5.624738 CGCCTCCAGAATAGAACAGTTTAGT 60.625 44.000 0.00 0.00 0.00 2.24
60 61 4.382685 CCGCCTCCAGAATAGAACAGTTTA 60.383 45.833 0.00 0.00 0.00 2.01
316 337 2.823154 CTCCTCCGTGAAGAGTTCTCTT 59.177 50.000 13.91 13.91 31.53 2.85
509 530 2.440627 AGATATGCTGCCATTGGACTGA 59.559 45.455 6.95 0.00 32.85 3.41
538 559 2.852075 ACTTTCCCCGGCACCTCA 60.852 61.111 0.00 0.00 0.00 3.86
574 595 1.408822 GGAAGACTGTTATGGGCCAGG 60.409 57.143 13.78 2.03 32.90 4.45
893 914 2.642171 ATGACCCCACTCACTTCCTA 57.358 50.000 0.00 0.00 0.00 2.94
958 979 5.009210 GGACTGTTTTTACATGCCTTGTGTA 59.991 40.000 0.00 0.00 39.48 2.90
1106 1128 2.290323 GGACATACTGCAACTTCCCAGT 60.290 50.000 0.00 0.00 44.02 4.00
1234 1256 4.451150 CGGCCCTTGAGCGCACTA 62.451 66.667 11.47 0.00 0.00 2.74
1257 1279 1.367471 CCCAACTCTGCTGTGTCGA 59.633 57.895 0.00 0.00 0.00 4.20
1302 1324 2.684001 ACCAAATGAAGCATGGCATG 57.316 45.000 22.99 22.99 37.77 4.06
1341 1363 5.070047 ACAACCCTATTACATTCCCTACGAG 59.930 44.000 0.00 0.00 0.00 4.18
1519 1541 2.160721 AATGGGAGCTCGAGAAGGTA 57.839 50.000 18.75 0.00 35.33 3.08
1552 1575 5.946972 AGAGACGATAGAGTTGGAGAAGAAA 59.053 40.000 0.00 0.00 41.38 2.52
1629 1652 2.749621 CAAAAGGAAAGGATGGACCGAG 59.250 50.000 0.00 0.00 44.74 4.63
1645 1668 2.156891 GCTCATGTTGCATGCACAAAAG 59.843 45.455 22.58 20.32 0.00 2.27
1651 1674 0.963225 ACAAGCTCATGTTGCATGCA 59.037 45.000 18.46 18.46 33.12 3.96
1977 2009 9.578439 GAAGAAAGCAATAGCAATAAACTGAAT 57.422 29.630 0.00 0.00 45.49 2.57
2015 2048 6.975772 GCATAATCTCATAGTCGGAGGAATAC 59.024 42.308 0.00 0.00 33.18 1.89
2166 2208 7.435305 GCTCTAGGTTAATAGTTAGTCCCAAG 58.565 42.308 0.00 0.00 0.00 3.61
2258 2304 7.655236 TCATCGTGAAGTTTTATTCCGTTTA 57.345 32.000 0.00 0.00 0.00 2.01
2271 2318 5.048713 GGTCCAAGAAAAATCATCGTGAAGT 60.049 40.000 0.00 0.00 0.00 3.01
2276 2323 4.651778 TCTGGTCCAAGAAAAATCATCGT 58.348 39.130 0.00 0.00 0.00 3.73
2280 2327 5.299279 GTGTCTTCTGGTCCAAGAAAAATCA 59.701 40.000 0.00 0.00 35.79 2.57
2317 2364 2.050144 TGGCTCTTCTGACTTGGACTT 58.950 47.619 0.00 0.00 0.00 3.01
2321 2368 0.318441 TCGTGGCTCTTCTGACTTGG 59.682 55.000 0.00 0.00 0.00 3.61
2322 2369 1.671261 CCTCGTGGCTCTTCTGACTTG 60.671 57.143 0.00 0.00 0.00 3.16
2385 2437 3.636231 CGAGGGGTCCACAAGGCA 61.636 66.667 0.00 0.00 33.74 4.75
2386 2438 4.410400 CCGAGGGGTCCACAAGGC 62.410 72.222 0.00 0.00 33.74 4.35
2390 2442 3.899545 GAGTCCCGAGGGGTCCACA 62.900 68.421 8.53 0.00 44.74 4.17
2403 2455 0.757561 GAGCTAGGTCAGGGGAGTCC 60.758 65.000 16.98 0.00 0.00 3.85
2404 2456 0.260523 AGAGCTAGGTCAGGGGAGTC 59.739 60.000 23.18 0.00 0.00 3.36
2405 2457 0.713579 AAGAGCTAGGTCAGGGGAGT 59.286 55.000 23.18 0.00 0.00 3.85
2410 2462 1.063266 AGGAGGAAGAGCTAGGTCAGG 60.063 57.143 23.18 0.00 0.00 3.86
2412 2464 5.869540 ATATAGGAGGAAGAGCTAGGTCA 57.130 43.478 23.18 0.81 0.00 4.02
2437 2489 5.665360 TCTGGTGGTTCTGGAATATATGTGA 59.335 40.000 0.00 0.00 0.00 3.58
2439 2491 6.575244 TTCTGGTGGTTCTGGAATATATGT 57.425 37.500 0.00 0.00 0.00 2.29
2441 2493 5.132648 TGCTTCTGGTGGTTCTGGAATATAT 59.867 40.000 0.00 0.00 0.00 0.86
2446 2498 0.843309 TGCTTCTGGTGGTTCTGGAA 59.157 50.000 0.00 0.00 0.00 3.53
2447 2499 1.003580 GATGCTTCTGGTGGTTCTGGA 59.996 52.381 0.00 0.00 0.00 3.86
2449 2501 1.271543 TGGATGCTTCTGGTGGTTCTG 60.272 52.381 0.00 0.00 0.00 3.02
2450 2502 1.067295 TGGATGCTTCTGGTGGTTCT 58.933 50.000 0.00 0.00 0.00 3.01
2451 2503 1.168714 GTGGATGCTTCTGGTGGTTC 58.831 55.000 0.00 0.00 0.00 3.62
2454 2506 0.321564 TTCGTGGATGCTTCTGGTGG 60.322 55.000 0.00 0.00 0.00 4.61
2457 2509 3.941483 AGTATTTTCGTGGATGCTTCTGG 59.059 43.478 0.00 0.00 0.00 3.86
2475 2527 3.199891 GCGGCGGCGGAAAAGTAT 61.200 61.111 33.02 0.00 0.00 2.12
2476 2528 4.683721 TGCGGCGGCGGAAAAGTA 62.684 61.111 33.02 0.00 44.10 2.24


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

AutoCloner maintained by Alex Coulton.