Multiple sequence alignment - TraesCS4D01G349100

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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 TraesCS4D01G349100 chr4D 100.000 3281 0 0 1 3281 502413821 502410541 0.000000e+00 6059.0
1 TraesCS4D01G349100 chr4B 90.056 3218 218 61 5 3180 646660659 646657502 0.000000e+00 4076.0
2 TraesCS4D01G349100 chr4B 80.332 422 60 13 2147 2556 50251790 50252200 6.880000e-77 298.0
3 TraesCS4D01G349100 chr4B 93.103 58 4 0 3220 3277 50251370 50251313 5.830000e-13 86.1
4 TraesCS4D01G349100 chr5A 93.041 2443 121 26 1 2429 685539664 685537257 0.000000e+00 3524.0
5 TraesCS4D01G349100 chr5A 95.042 827 30 8 2457 3281 685537257 685536440 0.000000e+00 1290.0
6 TraesCS4D01G349100 chr2A 89.908 1417 138 4 984 2400 536623633 536625044 0.000000e+00 1820.0
7 TraesCS4D01G349100 chr2B 88.844 1479 145 16 984 2453 472898477 472899944 0.000000e+00 1799.0
8 TraesCS4D01G349100 chr2D 89.957 1394 129 8 1008 2400 398780042 398781425 0.000000e+00 1788.0
9 TraesCS4D01G349100 chr3D 91.379 58 5 0 3220 3277 93831804 93831861 2.710000e-11 80.5


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 TraesCS4D01G349100 chr4D 502410541 502413821 3280 True 6059 6059 100.0000 1 3281 1 chr4D.!!$R1 3280
1 TraesCS4D01G349100 chr4B 646657502 646660659 3157 True 4076 4076 90.0560 5 3180 1 chr4B.!!$R2 3175
2 TraesCS4D01G349100 chr5A 685536440 685539664 3224 True 2407 3524 94.0415 1 3281 2 chr5A.!!$R1 3280
3 TraesCS4D01G349100 chr2A 536623633 536625044 1411 False 1820 1820 89.9080 984 2400 1 chr2A.!!$F1 1416
4 TraesCS4D01G349100 chr2B 472898477 472899944 1467 False 1799 1799 88.8440 984 2453 1 chr2B.!!$F1 1469
5 TraesCS4D01G349100 chr2D 398780042 398781425 1383 False 1788 1788 89.9570 1008 2400 1 chr2D.!!$F1 1392

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
593 603 0.03213 ACGCTGTTGAGACACACGAT 59.968 50.0 0.0 0.0 35.39 3.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2510 2542 1.059657 CACAAAAGAATGTCGCGGCG 61.06 55.0 17.7 17.7 0.0 6.46 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
70 71 2.818274 CCGGCCTTTCAGGTACGC 60.818 66.667 0.00 0.00 37.80 4.42
98 99 1.676014 GCCATCCGCCGATTAGCTAAT 60.676 52.381 18.92 18.92 0.00 1.73
206 208 1.523934 CGTTGTTACTCCGCGAAAACT 59.476 47.619 8.23 0.00 0.00 2.66
225 227 1.299468 CGCTGCTGGATCGACCTAC 60.299 63.158 0.00 0.00 39.86 3.18
226 228 1.729470 CGCTGCTGGATCGACCTACT 61.729 60.000 0.00 0.00 39.86 2.57
247 250 1.016653 GTTCTGGAAGCCTGTCGAGC 61.017 60.000 0.00 0.00 0.00 5.03
266 270 2.947852 GCTTGTCAGCGTAGAGAGAAA 58.052 47.619 0.00 0.00 35.91 2.52
285 289 1.523258 CTGGATCTTGCTGAGGGCG 60.523 63.158 0.00 0.00 45.43 6.13
327 331 4.631234 TGTGTCTGTTTATCCCTATCCCT 58.369 43.478 0.00 0.00 0.00 4.20
368 372 3.953612 TCTGGTTATGGCAATTAGGCTTG 59.046 43.478 0.00 0.00 44.55 4.01
370 374 3.699038 TGGTTATGGCAATTAGGCTTGAC 59.301 43.478 0.00 0.00 44.55 3.18
374 378 1.003118 TGGCAATTAGGCTTGACGAGT 59.997 47.619 0.00 0.00 44.55 4.18
377 381 2.096013 GCAATTAGGCTTGACGAGTTCC 59.904 50.000 0.00 0.00 0.00 3.62
384 388 1.581934 CTTGACGAGTTCCTGTTGCA 58.418 50.000 0.00 0.00 0.00 4.08
432 436 5.041287 TCGATTCTACTGCCGATTTGTTAG 58.959 41.667 0.00 0.00 0.00 2.34
433 437 5.041287 CGATTCTACTGCCGATTTGTTAGA 58.959 41.667 0.00 0.00 0.00 2.10
477 483 7.913821 GGGTTTCACCGATTTAATTAGTTCATC 59.086 37.037 0.00 0.00 39.83 2.92
485 491 6.700081 CGATTTAATTAGTTCATCCTCCGACA 59.300 38.462 0.00 0.00 0.00 4.35
515 521 6.239204 CGTCTACCTGAATTGGACACCATATA 60.239 42.308 0.00 0.00 31.53 0.86
573 583 1.278985 CCTTGACAGTATGGTGCTGGA 59.721 52.381 0.41 0.00 43.62 3.86
587 597 0.880278 GCTGGAACGCTGTTGAGACA 60.880 55.000 0.00 0.00 0.00 3.41
592 602 0.179121 AACGCTGTTGAGACACACGA 60.179 50.000 0.00 0.00 35.39 4.35
593 603 0.032130 ACGCTGTTGAGACACACGAT 59.968 50.000 0.00 0.00 35.39 3.73
594 604 1.139989 CGCTGTTGAGACACACGATT 58.860 50.000 0.00 0.00 34.04 3.34
595 605 1.125021 CGCTGTTGAGACACACGATTC 59.875 52.381 0.00 0.00 34.04 2.52
596 606 2.408050 GCTGTTGAGACACACGATTCT 58.592 47.619 0.00 0.00 0.00 2.40
597 607 2.156504 GCTGTTGAGACACACGATTCTG 59.843 50.000 0.00 0.00 0.00 3.02
598 608 2.135139 TGTTGAGACACACGATTCTGC 58.865 47.619 0.00 0.00 0.00 4.26
599 609 1.461127 GTTGAGACACACGATTCTGCC 59.539 52.381 0.00 0.00 0.00 4.85
600 610 0.037326 TGAGACACACGATTCTGCCC 60.037 55.000 0.00 0.00 0.00 5.36
601 611 0.037326 GAGACACACGATTCTGCCCA 60.037 55.000 0.00 0.00 0.00 5.36
602 612 0.036952 AGACACACGATTCTGCCCAG 60.037 55.000 0.00 0.00 0.00 4.45
606 616 0.603707 ACACGATTCTGCCCAGTGTG 60.604 55.000 0.00 3.91 43.39 3.82
727 745 1.333619 GCGTGTGTGTTTCCTGACATT 59.666 47.619 0.00 0.00 0.00 2.71
755 774 4.202111 GGTATATGTGGGTTCATTTGCCAC 60.202 45.833 0.00 0.00 34.07 5.01
820 842 4.917415 GGTTAGTGTCGCTAAAGTAAACGA 59.083 41.667 7.43 0.00 40.94 3.85
880 903 6.431234 GTGTTCTTCATCTGTTAATTGGAGGT 59.569 38.462 0.00 0.00 0.00 3.85
925 948 6.828273 AGTTCACTTAGCATTATGTATTGGCA 59.172 34.615 0.00 0.00 0.00 4.92
933 956 7.528996 AGCATTATGTATTGGCATGTGTTAT 57.471 32.000 0.00 0.00 0.00 1.89
935 958 9.076781 AGCATTATGTATTGGCATGTGTTATTA 57.923 29.630 0.00 0.00 0.00 0.98
936 959 9.689976 GCATTATGTATTGGCATGTGTTATTAA 57.310 29.630 0.00 0.00 0.00 1.40
958 981 6.604735 AATTGATATTCTGTAACACCTCGC 57.395 37.500 0.00 0.00 0.00 5.03
1104 1127 3.621715 AGTCAATTTCGATCCTTTACCGC 59.378 43.478 0.00 0.00 0.00 5.68
1178 1201 4.453136 TGCGATTACCAACCTTACAAACTC 59.547 41.667 0.00 0.00 0.00 3.01
1554 1577 3.864160 GCAAACTCCACTTCTCTCTGAGG 60.864 52.174 4.59 0.00 0.00 3.86
1804 1827 3.654021 TGGTCAACCAGGCTGACA 58.346 55.556 22.10 7.90 44.16 3.58
2101 2124 3.322254 AGTTGACCATGTCGAGAAGAAGT 59.678 43.478 0.00 0.00 34.95 3.01
2187 2210 6.375455 TCATTATCTTTGAGGAGCAGAAAACC 59.625 38.462 0.00 0.00 0.00 3.27
2202 2225 2.536997 AAACCGAGGCCATCTTCCCG 62.537 60.000 5.01 0.00 0.00 5.14
2217 2240 1.890041 CCCGGCAACACTCGAAACA 60.890 57.895 0.00 0.00 0.00 2.83
2282 2305 1.952296 GGCGAAGATCATGGCTTGAAT 59.048 47.619 7.20 0.00 38.03 2.57
2289 2312 4.458397 AGATCATGGCTTGAATACTGGTG 58.542 43.478 7.20 0.00 38.03 4.17
2291 2314 2.025981 TCATGGCTTGAATACTGGTGCT 60.026 45.455 0.00 0.00 0.00 4.40
2314 2337 6.763135 GCTCACATGATAGTTTATCTGTTGGA 59.237 38.462 0.00 0.00 36.17 3.53
2332 2355 8.106462 TCTGTTGGATATGGTTTCATCTTGTTA 58.894 33.333 0.00 0.00 34.96 2.41
2333 2356 8.050778 TGTTGGATATGGTTTCATCTTGTTAC 57.949 34.615 0.00 0.00 34.96 2.50
2338 2361 5.964958 ATGGTTTCATCTTGTTACACAGG 57.035 39.130 0.00 0.00 0.00 4.00
2346 2369 6.822442 TCATCTTGTTACACAGGTCTGTTAA 58.178 36.000 0.20 2.26 42.83 2.01
2403 2427 5.772672 ACACTTTAATCTGCATGTTGGGTTA 59.227 36.000 0.00 0.00 0.00 2.85
2449 2479 5.001232 GCTCACAAACAGGATAGTTGGTTA 58.999 41.667 0.00 0.00 33.45 2.85
2453 2483 8.106247 TCACAAACAGGATAGTTGGTTATTTC 57.894 34.615 0.00 0.00 33.45 2.17
2473 2504 6.961359 TTTCTGTATGATTGAAGTGTACCG 57.039 37.500 0.00 0.00 0.00 4.02
2490 2521 5.467735 GTGTACCGTGAAAACTAGATGGTTT 59.532 40.000 0.00 0.00 40.59 3.27
2510 2542 6.273071 GGTTTAAGATGAACCATGTTATGCC 58.727 40.000 1.36 0.00 44.71 4.40
2629 2662 1.175983 TTTCTTTGGCATCGGCGGTT 61.176 50.000 7.21 0.00 42.47 4.44
2740 2778 7.499321 TTGAACCGATGTTTGTAGTTACAAT 57.501 32.000 5.62 0.00 44.72 2.71
2759 2797 5.316167 ACAATGCTCCTGTGTGATTTCTTA 58.684 37.500 0.00 0.00 0.00 2.10
2767 2815 5.045213 TCCTGTGTGATTTCTTAATGCCCTA 60.045 40.000 0.00 0.00 0.00 3.53
2991 3041 1.397692 GAGCTTGTCATCAGCTTGCTC 59.602 52.381 0.61 0.00 39.21 4.26
3002 3052 3.854666 TCAGCTTGCTCATTGTCTAGAC 58.145 45.455 16.32 16.32 0.00 2.59
3081 3137 0.183014 TCTTAGGTCTCGGATCCGCT 59.817 55.000 29.62 21.45 39.59 5.52
3224 3285 7.783090 AGTTCTCATGATATGTGAATGTGAC 57.217 36.000 0.00 0.00 42.50 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
206 208 1.453197 TAGGTCGATCCAGCAGCGA 60.453 57.895 0.00 0.00 39.02 4.93
225 227 0.734253 CGACAGGCTTCCAGAACGAG 60.734 60.000 0.00 0.00 0.00 4.18
226 228 1.176619 TCGACAGGCTTCCAGAACGA 61.177 55.000 0.00 0.00 0.00 3.85
247 250 3.917380 CAGTTTCTCTCTACGCTGACAAG 59.083 47.826 0.00 0.00 0.00 3.16
266 270 1.606531 GCCCTCAGCAAGATCCAGT 59.393 57.895 0.00 0.00 42.97 4.00
296 300 2.071778 AAACAGACACAAGGCATGGT 57.928 45.000 0.00 0.00 0.00 3.55
327 331 0.403750 AACCCCTGAACCCTAACCCA 60.404 55.000 0.00 0.00 0.00 4.51
368 372 1.569479 GGCTGCAACAGGAACTCGTC 61.569 60.000 0.50 0.00 34.60 4.20
370 374 0.037326 TAGGCTGCAACAGGAACTCG 60.037 55.000 0.50 0.00 34.60 4.18
374 378 0.401738 AAGCTAGGCTGCAACAGGAA 59.598 50.000 0.50 0.00 39.62 3.36
377 381 0.607489 ACCAAGCTAGGCTGCAACAG 60.607 55.000 0.50 0.00 39.62 3.16
384 388 1.994463 CCCTTCACCAAGCTAGGCT 59.006 57.895 0.00 0.00 42.56 4.58
477 483 1.668047 GGTAGACGTGTTTGTCGGAGG 60.668 57.143 0.00 0.00 43.70 4.30
485 491 4.062991 GTCCAATTCAGGTAGACGTGTTT 58.937 43.478 0.00 0.00 33.80 2.83
515 521 9.533253 GTGCTAAGTTGGCATAAATCAAAATAT 57.467 29.630 17.47 0.00 41.86 1.28
573 583 0.179121 TCGTGTGTCTCAACAGCGTT 60.179 50.000 0.00 0.00 35.64 4.84
587 597 0.603707 CACACTGGGCAGAATCGTGT 60.604 55.000 0.00 0.00 39.20 4.49
598 608 1.194781 ACCTAGAGTGCCACACTGGG 61.195 60.000 20.23 20.23 45.44 4.45
599 609 0.036952 CACCTAGAGTGCCACACTGG 60.037 60.000 4.71 1.73 45.44 4.00
600 610 3.521995 CACCTAGAGTGCCACACTG 57.478 57.895 4.71 0.00 45.44 3.66
619 629 6.036083 CACCGTTATTCAGATTTACAGGACAG 59.964 42.308 0.00 0.00 0.00 3.51
727 745 6.183360 GCAAATGAACCCACATATACCATGAA 60.183 38.462 0.00 0.00 0.00 2.57
755 774 3.818210 ACACTATCTGGAGTAGCTGATCG 59.182 47.826 0.00 0.00 0.00 3.69
820 842 0.252103 ACCCCGACCACTACAGATGT 60.252 55.000 0.00 0.00 0.00 3.06
880 903 4.331968 ACTTATGAATTTTCTCCACGGCA 58.668 39.130 0.00 0.00 0.00 5.69
933 956 7.766738 TGCGAGGTGTTACAGAATATCAATTAA 59.233 33.333 0.00 0.00 0.00 1.40
935 958 6.112734 TGCGAGGTGTTACAGAATATCAATT 58.887 36.000 0.00 0.00 0.00 2.32
936 959 5.670485 TGCGAGGTGTTACAGAATATCAAT 58.330 37.500 0.00 0.00 0.00 2.57
954 977 2.138596 AACAAATGCCAAGTTGCGAG 57.861 45.000 0.00 0.00 34.74 5.03
981 1004 1.367346 TGATCCCACCCTAAACTGCA 58.633 50.000 0.00 0.00 0.00 4.41
1104 1127 1.890894 AGACGGGTCTTGGATCACG 59.109 57.895 0.00 0.00 36.31 4.35
1178 1201 2.931320 GCACGGTTCTCTTTAGTGAGGG 60.931 54.545 0.00 0.00 35.03 4.30
1617 1640 4.421515 CCCTGCTGAGCTGGTGGG 62.422 72.222 25.60 17.43 44.45 4.61
1804 1827 8.985315 TTAGATGAGATTATTCCAGCAACATT 57.015 30.769 0.00 0.00 0.00 2.71
2101 2124 4.622260 TGTCAAGGATCATCTGTGACAA 57.378 40.909 16.87 5.79 44.06 3.18
2187 2210 4.918201 GCCGGGAAGATGGCCTCG 62.918 72.222 3.32 0.00 45.73 4.63
2202 2225 3.701241 TGAAATTGTTTCGAGTGTTGCC 58.299 40.909 0.00 0.00 42.55 4.52
2205 2228 5.395642 ACGTTTGAAATTGTTTCGAGTGTT 58.604 33.333 0.00 0.00 42.55 3.32
2217 2240 4.081365 ACAACCTTCCCAACGTTTGAAATT 60.081 37.500 0.00 0.00 0.00 1.82
2282 2305 5.420725 AAACTATCATGTGAGCACCAGTA 57.579 39.130 0.00 0.00 0.00 2.74
2289 2312 6.763135 TCCAACAGATAAACTATCATGTGAGC 59.237 38.462 0.00 0.00 37.65 4.26
2332 2355 5.680619 TGAAAGACATTAACAGACCTGTGT 58.319 37.500 3.13 0.00 44.13 3.72
2333 2356 6.483307 TCTTGAAAGACATTAACAGACCTGTG 59.517 38.462 3.13 0.00 44.13 3.66
2417 2441 2.224523 CCTGTTTGTGAGCAAGGGTAGA 60.225 50.000 0.00 0.00 35.82 2.59
2418 2442 2.154462 CCTGTTTGTGAGCAAGGGTAG 58.846 52.381 0.00 0.00 35.82 3.18
2419 2443 1.771854 TCCTGTTTGTGAGCAAGGGTA 59.228 47.619 0.00 0.00 35.82 3.69
2421 2445 1.915141 ATCCTGTTTGTGAGCAAGGG 58.085 50.000 0.00 0.00 35.82 3.95
2449 2479 7.064609 CACGGTACACTTCAATCATACAGAAAT 59.935 37.037 0.00 0.00 0.00 2.17
2453 2483 5.407502 TCACGGTACACTTCAATCATACAG 58.592 41.667 0.00 0.00 0.00 2.74
2464 2495 5.221581 ACCATCTAGTTTTCACGGTACACTT 60.222 40.000 0.00 0.00 0.00 3.16
2465 2496 4.282703 ACCATCTAGTTTTCACGGTACACT 59.717 41.667 0.00 0.00 0.00 3.55
2473 2504 9.827411 GTTCATCTTAAACCATCTAGTTTTCAC 57.173 33.333 0.00 0.00 40.38 3.18
2490 2521 3.563808 GCGGCATAACATGGTTCATCTTA 59.436 43.478 0.00 0.00 0.00 2.10
2510 2542 1.059657 CACAAAAGAATGTCGCGGCG 61.060 55.000 17.70 17.70 0.00 6.46
2572 2605 8.310122 TCTCAGCATGGTATATTCAGCATATA 57.690 34.615 0.00 0.00 34.96 0.86
2588 2621 1.945394 GCCATACAACCTCTCAGCATG 59.055 52.381 0.00 0.00 37.54 4.06
2629 2662 6.934048 TCCATGCACAAATTCGACATATTA 57.066 33.333 0.00 0.00 0.00 0.98
2656 2694 0.250209 CGCAGATGAGAATCCCAGGG 60.250 60.000 0.00 0.00 0.00 4.45
2694 2732 5.648178 AATATTCACAGCAGCATCAACAA 57.352 34.783 0.00 0.00 0.00 2.83
2708 2746 8.234546 ACTACAAACATCGGTTCAAATATTCAC 58.765 33.333 0.00 0.00 35.82 3.18
2740 2778 4.156556 GCATTAAGAAATCACACAGGAGCA 59.843 41.667 0.00 0.00 0.00 4.26
2767 2815 3.739519 GCTAGACAGAAATCACTGCCGAT 60.740 47.826 0.00 0.00 41.06 4.18
2991 3041 7.068103 ACACTTCTGATAGAGGTCTAGACAATG 59.932 40.741 23.91 2.65 31.70 2.82
3002 3052 6.867816 GCATAAGATGACACTTCTGATAGAGG 59.132 42.308 0.00 0.00 0.00 3.69
3081 3137 3.734463 TCAGATAAGTGCCAACGACAAA 58.266 40.909 0.00 0.00 0.00 2.83
3197 3258 8.917088 TCACATTCACATATCATGAGAACTAGA 58.083 33.333 0.09 0.00 41.43 2.43
3203 3264 7.558604 TCAAGTCACATTCACATATCATGAGA 58.441 34.615 0.09 0.00 0.00 3.27
3224 3285 8.558973 AGAAGTTCTTGTAGGAAATGATCAAG 57.441 34.615 0.00 0.00 37.44 3.02


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

AutoCloner maintained by Alex Coulton.