Multiple sequence alignment - TraesCS2B01G377600

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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 TraesCS2B01G377600 chr2B 100.000 2577 0 0 1 2577 540709377 540706801 0.000000e+00 4759.0
1 TraesCS2B01G377600 chr2D 94.178 1958 77 14 1 1944 459315557 459313623 0.000000e+00 2950.0
2 TraesCS2B01G377600 chr2D 96.231 451 15 2 1945 2394 459313566 459313117 0.000000e+00 737.0
3 TraesCS2B01G377600 chr2D 98.039 51 1 0 2527 2577 459312887 459312837 3.530000e-14 89.8
4 TraesCS2B01G377600 chr2A 91.393 1952 121 30 1 1920 602483152 602481216 0.000000e+00 2630.0
5 TraesCS2B01G377600 chr2A 80.930 430 30 17 2151 2573 602480568 602480184 2.510000e-75 292.0


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 TraesCS2B01G377600 chr2B 540706801 540709377 2576 True 4759.000000 4759 100.000000 1 2577 1 chr2B.!!$R1 2576
1 TraesCS2B01G377600 chr2D 459312837 459315557 2720 True 1258.933333 2950 96.149333 1 2577 3 chr2D.!!$R1 2576
2 TraesCS2B01G377600 chr2A 602480184 602483152 2968 True 1461.000000 2630 86.161500 1 2573 2 chr2A.!!$R1 2572

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
55 56 1.079503 CCAAGCACTTAACGAGCCTC 58.92 55.0 0.0 0.0 0.0 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1637 1678 0.669318 TCACCGTTAGCCGCAAAGAG 60.669 55.0 0.0 0.0 34.38 2.85 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
46 47 5.241403 TCCTTCTCAATTCCAAGCACTTA 57.759 39.130 0.00 0.00 0.00 2.24
55 56 1.079503 CCAAGCACTTAACGAGCCTC 58.920 55.000 0.00 0.00 0.00 4.70
434 435 4.477975 CGACCTCCACGAGACGGC 62.478 72.222 0.00 0.00 0.00 5.68
435 436 4.477975 GACCTCCACGAGACGGCG 62.478 72.222 4.80 4.80 37.29 6.46
698 700 4.259356 CAATGCTCTGAAGTCTGAATCCA 58.741 43.478 0.00 0.00 0.00 3.41
699 701 3.325293 TGCTCTGAAGTCTGAATCCAC 57.675 47.619 0.00 0.00 0.00 4.02
700 702 2.027745 TGCTCTGAAGTCTGAATCCACC 60.028 50.000 0.00 0.00 0.00 4.61
701 703 2.886081 CTCTGAAGTCTGAATCCACCG 58.114 52.381 0.00 0.00 0.00 4.94
702 704 2.493675 CTCTGAAGTCTGAATCCACCGA 59.506 50.000 0.00 0.00 0.00 4.69
747 749 2.755650 GCGACTTCCTTGTTCTTCTGA 58.244 47.619 0.00 0.00 0.00 3.27
824 835 6.348132 CGATTGTTTGTAAGTTGCCTGTCATA 60.348 38.462 0.00 0.00 0.00 2.15
881 892 3.612479 GCGTCCTACTTTTCCGTCAGTTA 60.612 47.826 0.00 0.00 0.00 2.24
1015 1027 2.182614 AAACAAACGCGCCGGATCAG 62.183 55.000 5.05 0.00 0.00 2.90
1051 1063 1.072505 GACCTTCCAAGTTCGGCCA 59.927 57.895 2.24 0.00 0.00 5.36
1126 1138 2.048222 CGAAGGTGCCAGCGAAGA 60.048 61.111 0.00 0.00 0.00 2.87
1134 1146 2.815647 CCAGCGAAGACGAAGGGC 60.816 66.667 0.00 0.00 42.66 5.19
1213 1225 3.845259 GCGGTATGCCCAGGTCGA 61.845 66.667 0.00 0.00 37.76 4.20
1309 1321 0.390866 ATCTCAGCAGCAGTTCACGG 60.391 55.000 0.00 0.00 0.00 4.94
1347 1359 0.035598 TTTTGAGATCGGCGTCCCAA 59.964 50.000 6.85 4.58 0.00 4.12
1400 1412 1.089481 TCGGCATCGTGGCAAGATTC 61.089 55.000 13.37 8.80 43.94 2.52
1408 1420 0.445436 GTGGCAAGATTCTGCTCACG 59.555 55.000 0.00 0.00 42.25 4.35
1413 1425 2.935201 GCAAGATTCTGCTCACGAGAAT 59.065 45.455 0.00 0.00 41.83 2.40
1417 1429 4.825422 AGATTCTGCTCACGAGAATTGAA 58.175 39.130 0.00 0.00 39.72 2.69
1528 1543 7.843490 TTTTGAAGCGCTAGATAGTTGTAAT 57.157 32.000 12.05 0.00 0.00 1.89
1536 1551 6.421202 GCGCTAGATAGTTGTAATTAGCACTT 59.579 38.462 0.00 0.00 34.64 3.16
1605 1646 5.645067 TGCTGAGATACACAGGAAAAATCTG 59.355 40.000 0.00 0.00 36.09 2.90
1637 1678 4.756084 CTGAACAACAGGATGGTTCTTC 57.244 45.455 0.00 0.00 43.62 2.87
1688 1729 5.228220 CGACAGAAATAACTACAAGCTCTCG 59.772 44.000 0.00 0.00 0.00 4.04
1706 1747 5.393243 GCTCTCGTCAAATACTCCACTACTT 60.393 44.000 0.00 0.00 0.00 2.24
1758 1799 2.035632 CTATCTCACCCTCTCCACCAC 58.964 57.143 0.00 0.00 0.00 4.16
1847 1892 2.412716 CGCTTGCAAACGAATGAAGCTA 60.413 45.455 16.99 0.00 37.48 3.32
1912 1959 8.988060 TGTATAAAACCTCTGGATTATCAGACA 58.012 33.333 0.00 0.00 38.70 3.41
1920 1967 4.943705 TCTGGATTATCAGACAAAACAGCC 59.056 41.667 0.00 0.00 38.70 4.85
2145 2263 5.477607 ACCTAGCCGTGTTGCATAATATA 57.522 39.130 0.00 0.00 0.00 0.86
2175 2648 4.546829 ACATTAACGAAAGCTACTGGGA 57.453 40.909 0.00 0.00 0.00 4.37
2222 2702 3.693085 ACACTTGCCTGATCAATCATCAC 59.307 43.478 0.00 0.00 36.51 3.06
2226 2706 3.483421 TGCCTGATCAATCATCACCATC 58.517 45.455 0.00 0.00 36.51 3.51
2401 2881 9.546428 ACATTTGCTAGATTTAAAAACAAAGCT 57.454 25.926 16.11 0.00 37.81 3.74
2406 2886 9.624697 TGCTAGATTTAAAAACAAAGCTATGTG 57.375 29.630 16.11 0.00 36.22 3.21
2407 2887 9.840427 GCTAGATTTAAAAACAAAGCTATGTGA 57.160 29.630 0.00 0.00 36.22 3.58
2415 2895 8.801715 AAAAACAAAGCTATGTGATGTACTTG 57.198 30.769 0.00 0.00 32.81 3.16
2416 2896 6.500684 AACAAAGCTATGTGATGTACTTGG 57.499 37.500 0.00 0.00 32.81 3.61
2417 2897 4.943705 ACAAAGCTATGTGATGTACTTGGG 59.056 41.667 0.00 0.00 30.82 4.12
2418 2898 3.199880 AGCTATGTGATGTACTTGGGC 57.800 47.619 0.00 0.00 0.00 5.36
2419 2899 2.158755 AGCTATGTGATGTACTTGGGCC 60.159 50.000 0.00 0.00 0.00 5.80
2420 2900 2.483876 CTATGTGATGTACTTGGGCCG 58.516 52.381 0.00 0.00 0.00 6.13
2421 2901 0.107214 ATGTGATGTACTTGGGCCGG 60.107 55.000 0.00 0.00 0.00 6.13
2422 2902 1.195442 TGTGATGTACTTGGGCCGGA 61.195 55.000 5.05 0.00 0.00 5.14
2423 2903 0.462047 GTGATGTACTTGGGCCGGAG 60.462 60.000 5.05 1.53 0.00 4.63
2448 2928 6.350445 GGGAGTATTCACCGTAGTCAGTTTAA 60.350 42.308 0.00 0.00 0.00 1.52
2487 2967 6.591448 TCGATGTGTATATTCTTGATGCCATC 59.409 38.462 0.00 0.00 0.00 3.51
2507 2987 9.669887 TGCCATCATAAAATTAATGAAAAGCTT 57.330 25.926 0.00 0.00 0.00 3.74
2547 3195 6.974932 AAGAGTATGCATGTAGTGTTTCTG 57.025 37.500 10.16 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.403814 CAGAGGGAATGGAGAGCGTA 58.596 55.000 0.00 0.00 0.00 4.42
46 47 0.326264 ATCTTGGCTTGAGGCTCGTT 59.674 50.000 10.42 0.00 41.69 3.85
55 56 0.455633 GCGCTGTTCATCTTGGCTTG 60.456 55.000 0.00 0.00 0.00 4.01
435 436 4.087892 TCCAGCTTCGCCCTGCTC 62.088 66.667 0.00 0.00 37.44 4.26
436 437 4.400961 GTCCAGCTTCGCCCTGCT 62.401 66.667 0.00 0.00 40.54 4.24
532 533 0.331278 AACCCAATGGCAGATTCGGA 59.669 50.000 0.00 0.00 33.59 4.55
698 700 2.541120 GATCGATCGGTCGGTCGGT 61.541 63.158 16.64 17.91 46.75 4.69
699 701 2.251667 GATCGATCGGTCGGTCGG 59.748 66.667 16.64 7.48 46.75 4.79
747 749 5.755375 ACGCTCGAACTCATCAATAATCAAT 59.245 36.000 0.00 0.00 0.00 2.57
824 835 8.822805 TGGAGAAACTTAACTGGTGATAGTTAT 58.177 33.333 0.00 0.00 41.37 1.89
1015 1027 1.421485 CGAATCTGTCGGCTGTTGC 59.579 57.895 0.00 0.00 46.45 4.17
1051 1063 3.593318 GGGACTCTCTCGCGTTCT 58.407 61.111 5.77 0.00 0.00 3.01
1077 1089 1.332997 GCGATCTTGGAAGCCATCTTG 59.667 52.381 0.00 0.00 31.53 3.02
1126 1138 2.045926 GATGCACTGGCCCTTCGT 60.046 61.111 0.00 0.00 40.13 3.85
1134 1146 3.200593 GGCGAGCAGATGCACTGG 61.201 66.667 15.16 0.06 45.82 4.00
1206 1218 1.226802 CTGGCACGAGATCGACCTG 60.227 63.158 9.58 9.77 43.02 4.00
1213 1225 1.446792 CGAACTGCTGGCACGAGAT 60.447 57.895 0.00 0.00 0.00 2.75
1281 1293 1.220206 CTGCTGAGATGCCGACCTT 59.780 57.895 0.00 0.00 0.00 3.50
1293 1305 2.666190 GCCGTGAACTGCTGCTGA 60.666 61.111 13.69 0.00 0.00 4.26
1367 1379 2.264480 CCGATCTTGGCACACCGA 59.736 61.111 0.00 0.00 39.29 4.69
1400 1412 4.214437 GTTTGTTCAATTCTCGTGAGCAG 58.786 43.478 0.00 0.00 37.49 4.24
1408 1420 5.278512 GGTTCAGGAGGTTTGTTCAATTCTC 60.279 44.000 6.93 6.93 0.00 2.87
1413 1425 3.287222 CTGGTTCAGGAGGTTTGTTCAA 58.713 45.455 0.00 0.00 0.00 2.69
1637 1678 0.669318 TCACCGTTAGCCGCAAAGAG 60.669 55.000 0.00 0.00 34.38 2.85
1688 1729 8.379457 AGTTTTCAAGTAGTGGAGTATTTGAC 57.621 34.615 0.29 0.00 30.75 3.18
1706 1747 6.492429 TGTAGTCTTCCTAGCACTAGTTTTCA 59.508 38.462 0.00 0.00 0.00 2.69
1758 1799 2.283617 CAGCTGCTATTGCTAAGTGTCG 59.716 50.000 0.00 0.00 38.92 4.35
1907 1954 3.820467 TCCACATTAGGCTGTTTTGTCTG 59.180 43.478 0.00 0.00 0.00 3.51
1912 1959 4.021192 CCACAATCCACATTAGGCTGTTTT 60.021 41.667 0.00 0.00 0.00 2.43
1920 1967 5.471456 GGCTAATCTCCACAATCCACATTAG 59.529 44.000 0.00 0.00 0.00 1.73
2162 2635 6.261158 GGTTGAAATATCTCCCAGTAGCTTTC 59.739 42.308 0.00 0.00 0.00 2.62
2166 2639 5.036117 TGGTTGAAATATCTCCCAGTAGC 57.964 43.478 0.00 0.00 0.00 3.58
2175 2648 9.553064 GTTCATAGTCTCATGGTTGAAATATCT 57.447 33.333 0.00 0.00 0.00 1.98
2222 2702 6.033966 GTCCCGCAAATAAAAAGTAAGATGG 58.966 40.000 0.00 0.00 0.00 3.51
2226 2706 5.182380 TGGAGTCCCGCAAATAAAAAGTAAG 59.818 40.000 6.74 0.00 34.29 2.34
2394 2874 4.943705 CCCAAGTACATCACATAGCTTTGT 59.056 41.667 3.73 3.73 0.00 2.83
2395 2875 4.201950 GCCCAAGTACATCACATAGCTTTG 60.202 45.833 2.27 2.27 0.00 2.77
2398 2878 2.158755 GGCCCAAGTACATCACATAGCT 60.159 50.000 0.00 0.00 0.00 3.32
2399 2879 2.222027 GGCCCAAGTACATCACATAGC 58.778 52.381 0.00 0.00 0.00 2.97
2400 2880 2.483876 CGGCCCAAGTACATCACATAG 58.516 52.381 0.00 0.00 0.00 2.23
2401 2881 1.140052 CCGGCCCAAGTACATCACATA 59.860 52.381 0.00 0.00 0.00 2.29
2402 2882 0.107214 CCGGCCCAAGTACATCACAT 60.107 55.000 0.00 0.00 0.00 3.21
2403 2883 1.195442 TCCGGCCCAAGTACATCACA 61.195 55.000 0.00 0.00 0.00 3.58
2404 2884 0.462047 CTCCGGCCCAAGTACATCAC 60.462 60.000 0.00 0.00 0.00 3.06
2405 2885 1.622607 CCTCCGGCCCAAGTACATCA 61.623 60.000 0.00 0.00 0.00 3.07
2406 2886 1.146263 CCTCCGGCCCAAGTACATC 59.854 63.158 0.00 0.00 0.00 3.06
2407 2887 2.375345 CCCTCCGGCCCAAGTACAT 61.375 63.158 0.00 0.00 0.00 2.29
2408 2888 3.006728 CCCTCCGGCCCAAGTACA 61.007 66.667 0.00 0.00 0.00 2.90
2409 2889 2.686106 TCCCTCCGGCCCAAGTAC 60.686 66.667 0.00 0.00 0.00 2.73
2410 2890 1.877672 TACTCCCTCCGGCCCAAGTA 61.878 60.000 0.00 0.00 0.00 2.24
2411 2891 2.547123 ATACTCCCTCCGGCCCAAGT 62.547 60.000 0.00 0.13 0.00 3.16
2412 2892 1.345715 AATACTCCCTCCGGCCCAAG 61.346 60.000 0.00 0.00 0.00 3.61
2414 2894 1.764854 GAATACTCCCTCCGGCCCA 60.765 63.158 0.00 0.00 0.00 5.36
2415 2895 1.764854 TGAATACTCCCTCCGGCCC 60.765 63.158 0.00 0.00 0.00 5.80
2416 2896 1.446366 GTGAATACTCCCTCCGGCC 59.554 63.158 0.00 0.00 0.00 6.13
2417 2897 1.446366 GGTGAATACTCCCTCCGGC 59.554 63.158 0.00 0.00 0.00 6.13
2418 2898 1.041447 ACGGTGAATACTCCCTCCGG 61.041 60.000 0.00 0.00 41.82 5.14
2419 2899 1.607628 CTACGGTGAATACTCCCTCCG 59.392 57.143 0.00 0.00 42.94 4.63
2420 2900 2.622470 GACTACGGTGAATACTCCCTCC 59.378 54.545 0.00 0.00 0.00 4.30
2421 2901 3.285484 TGACTACGGTGAATACTCCCTC 58.715 50.000 0.00 0.00 0.00 4.30
2422 2902 3.288964 CTGACTACGGTGAATACTCCCT 58.711 50.000 0.00 0.00 0.00 4.20
2423 2903 3.022406 ACTGACTACGGTGAATACTCCC 58.978 50.000 0.00 0.00 33.97 4.30
2424 2904 4.715527 AACTGACTACGGTGAATACTCC 57.284 45.455 0.00 0.00 35.61 3.85
2425 2905 9.793252 TTATTAAACTGACTACGGTGAATACTC 57.207 33.333 0.00 0.00 35.61 2.59
2462 2942 5.852827 TGGCATCAAGAATATACACATCGA 58.147 37.500 0.00 0.00 0.00 3.59
2463 2943 6.369615 TGATGGCATCAAGAATATACACATCG 59.630 38.462 27.03 0.00 36.11 3.84
2464 2944 7.677454 TGATGGCATCAAGAATATACACATC 57.323 36.000 27.03 0.00 36.11 3.06
2522 3002 7.573843 GCAGAAACACTACATGCATACTCTTTT 60.574 37.037 0.00 0.00 36.88 2.27
2523 3003 6.128172 GCAGAAACACTACATGCATACTCTTT 60.128 38.462 0.00 0.00 36.88 2.52
2524 3004 5.352569 GCAGAAACACTACATGCATACTCTT 59.647 40.000 0.00 0.00 36.88 2.85
2525 3005 4.872691 GCAGAAACACTACATGCATACTCT 59.127 41.667 0.00 0.00 36.88 3.24


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

AutoCloner maintained by Alex Coulton.