Multiple sequence alignment - TraesCS2B01G434100

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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 TraesCS2B01G434100 chr2B 100.000 2645 0 0 1 2645 623871076 623868432 0.000000e+00 4885
1 TraesCS2B01G434100 chr2B 87.119 295 31 5 1082 1371 624287334 624287042 7.060000e-86 327
2 TraesCS2B01G434100 chr2D 93.975 2191 73 23 462 2644 527004844 527002705 0.000000e+00 3260
3 TraesCS2B01G434100 chr2D 94.105 475 24 4 1 475 527005335 527004865 0.000000e+00 719
4 TraesCS2B01G434100 chr2D 87.713 293 33 2 1082 1371 527272592 527272300 3.260000e-89 339
5 TraesCS2B01G434100 chr2D 86.475 244 33 0 1117 1360 527293783 527293540 4.340000e-68 268
6 TraesCS2B01G434100 chr2A 89.639 2355 127 47 276 2593 672235671 672233397 0.000000e+00 2889
7 TraesCS2B01G434100 chr2A 87.119 295 31 6 1082 1371 672265710 672265418 7.060000e-86 327
8 TraesCS2B01G434100 chr2A 83.893 298 35 7 1 288 672236810 672236516 3.350000e-69 272
9 TraesCS2B01G434100 chr6A 80.623 578 79 20 1090 1643 465389760 465390328 1.460000e-112 416
10 TraesCS2B01G434100 chr6D 80.316 569 85 21 1090 1643 326760684 326761240 3.170000e-109 405
11 TraesCS2B01G434100 chr6B 79.863 586 81 20 1090 1643 495543800 495543220 6.860000e-106 394
12 TraesCS2B01G434100 chr5A 81.915 94 11 3 1338 1431 8111600 8111513 1.020000e-09 75


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 TraesCS2B01G434100 chr2B 623868432 623871076 2644 True 4885.0 4885 100.000 1 2645 1 chr2B.!!$R1 2644
1 TraesCS2B01G434100 chr2D 527002705 527005335 2630 True 1989.5 3260 94.040 1 2644 2 chr2D.!!$R3 2643
2 TraesCS2B01G434100 chr2A 672233397 672236810 3413 True 1580.5 2889 86.766 1 2593 2 chr2A.!!$R2 2592
3 TraesCS2B01G434100 chr6A 465389760 465390328 568 False 416.0 416 80.623 1090 1643 1 chr6A.!!$F1 553
4 TraesCS2B01G434100 chr6D 326760684 326761240 556 False 405.0 405 80.316 1090 1643 1 chr6D.!!$F1 553
5 TraesCS2B01G434100 chr6B 495543220 495543800 580 True 394.0 394 79.863 1090 1643 1 chr6B.!!$R1 553

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
809 1716 0.249238 CGGGCGAGAGATCTTTCCTG 60.249 60.0 7.63 3.41 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2237 3213 0.1078 TGGTTTTCGGTGTTCGTGGA 60.108 50.0 0.0 0.0 40.32 4.02 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
107 108 1.597663 CGGGTCATTTATGCGAGGTTC 59.402 52.381 0.00 0.00 0.00 3.62
116 117 1.148310 ATGCGAGGTTCTGTGAAACG 58.852 50.000 0.00 0.00 42.39 3.60
205 215 5.825679 TGTTCTTTTGAGAGATTTCGGGAAA 59.174 36.000 0.00 0.00 34.46 3.13
209 219 4.701956 TTGAGAGATTTCGGGAAATTGC 57.298 40.909 7.97 4.22 40.77 3.56
447 1317 8.408601 CAAATGGATACTAGGTTCAAGGAATTG 58.591 37.037 0.00 0.00 37.61 2.32
505 1409 7.547370 CCTAGCAGGCATTTGATACTCTTATAC 59.453 40.741 0.00 0.00 0.00 1.47
506 1410 7.072263 AGCAGGCATTTGATACTCTTATACT 57.928 36.000 0.00 0.00 0.00 2.12
507 1411 8.195165 AGCAGGCATTTGATACTCTTATACTA 57.805 34.615 0.00 0.00 0.00 1.82
572 1479 0.600557 ACTGAGCTGGACTGAACTCG 59.399 55.000 0.00 0.00 31.64 4.18
590 1497 4.678622 ACTCGTCGCATTTCACATACATA 58.321 39.130 0.00 0.00 0.00 2.29
633 1540 6.946340 AGTATCACATACATGAACAGTTCCA 58.054 36.000 10.93 0.00 38.21 3.53
671 1578 1.679153 CATGGGCCGGGTGTAAATAAC 59.321 52.381 2.18 0.00 0.00 1.89
809 1716 0.249238 CGGGCGAGAGATCTTTCCTG 60.249 60.000 7.63 3.41 0.00 3.86
953 1863 3.775654 CGACCACTCTCCCCTGCC 61.776 72.222 0.00 0.00 0.00 4.85
955 1865 3.933542 GACCACTCTCCCCTGCCCT 62.934 68.421 0.00 0.00 0.00 5.19
1050 1965 4.974438 TCCCCAACGGCCACCTCT 62.974 66.667 2.24 0.00 0.00 3.69
1071 1986 0.727970 CCTCGTCTTCATCGTCGTCT 59.272 55.000 0.00 0.00 0.00 4.18
1080 1995 1.397343 TCATCGTCGTCTTCTTCCTCG 59.603 52.381 0.00 0.00 0.00 4.63
1137 2052 3.133464 CCGACCTACCACGGCGTA 61.133 66.667 14.22 0.00 42.55 4.42
1194 2109 2.436824 GAGCCCCGCAAGAAGTCC 60.437 66.667 0.00 0.00 43.02 3.85
1670 2626 1.670406 CGCTGCAGCAGAAGGTTCT 60.670 57.895 36.03 0.00 42.21 3.01
1671 2627 1.233285 CGCTGCAGCAGAAGGTTCTT 61.233 55.000 36.03 0.00 42.21 2.52
1672 2628 0.240411 GCTGCAGCAGAAGGTTCTTG 59.760 55.000 33.36 0.00 41.59 3.02
1673 2629 0.879765 CTGCAGCAGAAGGTTCTTGG 59.120 55.000 18.42 0.00 34.74 3.61
1674 2630 0.473755 TGCAGCAGAAGGTTCTTGGA 59.526 50.000 0.00 0.00 34.74 3.53
1675 2631 0.877743 GCAGCAGAAGGTTCTTGGAC 59.122 55.000 0.00 0.00 34.74 4.02
1676 2632 1.151668 CAGCAGAAGGTTCTTGGACG 58.848 55.000 0.00 0.00 34.74 4.79
1677 2633 0.035458 AGCAGAAGGTTCTTGGACGG 59.965 55.000 0.00 0.00 34.74 4.79
1678 2634 1.578206 GCAGAAGGTTCTTGGACGGC 61.578 60.000 0.00 0.00 34.74 5.68
1679 2635 1.004918 AGAAGGTTCTTGGACGGCG 60.005 57.895 4.80 4.80 32.55 6.46
1703 2659 1.219522 CGTTCCCGTCACTTCACACC 61.220 60.000 0.00 0.00 0.00 4.16
1759 2715 2.228822 GACATGGAAATGCACCTCGTTT 59.771 45.455 0.00 0.00 36.65 3.60
1763 2719 1.265905 GGAAATGCACCTCGTTTCGTT 59.734 47.619 0.00 0.00 46.62 3.85
1777 2733 8.411683 ACCTCGTTTCGTTAATCATCTTACTAT 58.588 33.333 0.00 0.00 0.00 2.12
1865 2823 7.819415 CCTTTCTTCTTTTCCAAGTTCTGTTTT 59.181 33.333 0.00 0.00 0.00 2.43
2025 2989 7.283329 AGCATCTTATCTTACCTTACCCTTTG 58.717 38.462 0.00 0.00 0.00 2.77
2123 3099 5.470098 GCATACTTTTCCTGACTTGACAAGA 59.530 40.000 21.95 0.00 0.00 3.02
2237 3213 4.996434 GCACGCAGCTCCACAGGT 62.996 66.667 0.00 0.00 41.15 4.00
2239 3215 4.008933 ACGCAGCTCCACAGGTCC 62.009 66.667 0.00 0.00 0.00 4.46
2244 3220 1.837051 AGCTCCACAGGTCCACGAA 60.837 57.895 0.00 0.00 0.00 3.85
2402 3378 1.624813 TCCCGGGTTACTGTAACAAGG 59.375 52.381 26.67 25.45 40.39 3.61
2443 3424 0.673644 AATGCCCGGTCTCGTCAAAG 60.674 55.000 0.00 0.00 33.95 2.77
2607 3589 3.844090 GAGAGCCAGCGGAGGGAC 61.844 72.222 0.00 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
107 108 3.039134 GGCCCAACCGTTTCACAG 58.961 61.111 0.00 0.00 0.00 3.66
189 199 3.691118 CAGCAATTTCCCGAAATCTCTCA 59.309 43.478 3.25 0.00 39.88 3.27
226 236 8.863049 AGCAAATGATTTTACTCGCTTAAAATG 58.137 29.630 14.79 6.56 40.28 2.32
228 238 8.810652 AAGCAAATGATTTTACTCGCTTAAAA 57.189 26.923 9.73 4.21 36.74 1.52
458 1328 6.723471 AGGTGTTTAATTCCTAACCCCTAA 57.277 37.500 0.00 0.00 31.55 2.69
467 1371 3.010138 TGCCTGCTAGGTGTTTAATTCCT 59.990 43.478 4.45 0.00 37.80 3.36
482 1386 7.072263 AGTATAAGAGTATCAAATGCCTGCT 57.928 36.000 0.00 0.00 37.82 4.24
529 1433 5.592688 TGTGGATGAGATTCATGTACTACGA 59.407 40.000 0.00 0.00 37.20 3.43
628 1535 9.669353 CATGAAAAATATATGCAGTACTGGAAC 57.331 33.333 21.59 6.60 33.77 3.62
633 1540 6.209391 GGCCCATGAAAAATATATGCAGTACT 59.791 38.462 0.00 0.00 0.00 2.73
644 1551 1.272760 ACACCCGGCCCATGAAAAATA 60.273 47.619 0.00 0.00 0.00 1.40
645 1552 0.544120 ACACCCGGCCCATGAAAAAT 60.544 50.000 0.00 0.00 0.00 1.82
646 1553 0.112606 TACACCCGGCCCATGAAAAA 59.887 50.000 0.00 0.00 0.00 1.94
690 1597 0.834261 TGAACCGGATCACACAGGGA 60.834 55.000 10.84 0.00 0.00 4.20
696 1603 2.073056 CGTTCATTGAACCGGATCACA 58.927 47.619 20.87 6.49 39.14 3.58
809 1716 3.006752 TGCTGAAATTTGAACCATGGGTC 59.993 43.478 23.74 23.74 33.12 4.46
891 1801 3.284617 GAATAGCGGGGTTTTATGGTGT 58.715 45.455 0.00 0.00 0.00 4.16
953 1863 4.823732 TAGGCAGGGCAGGGGAGG 62.824 72.222 0.00 0.00 0.00 4.30
1050 1965 1.129998 GACGACGATGAAGACGAGGAA 59.870 52.381 0.00 0.00 33.85 3.36
1254 2169 1.522580 GCCCTTGATGGCGAGAGTC 60.523 63.158 0.00 0.00 42.54 3.36
1646 2602 1.750572 CTTCTGCTGCAGCGACGATC 61.751 60.000 32.11 6.25 45.83 3.69
1690 2646 0.946221 GAGCCAGGTGTGAAGTGACG 60.946 60.000 0.00 0.00 0.00 4.35
1694 2650 2.330216 AGTAAGAGCCAGGTGTGAAGT 58.670 47.619 0.00 0.00 0.00 3.01
1703 2659 2.376109 TCCCGAAGTAGTAAGAGCCAG 58.624 52.381 0.00 0.00 0.00 4.85
1957 2919 0.686224 CCCCAAATCAAGCAAGGCAA 59.314 50.000 0.00 0.00 0.00 4.52
1958 2920 1.193462 CCCCCAAATCAAGCAAGGCA 61.193 55.000 0.00 0.00 0.00 4.75
2025 2989 7.677309 ACCGCTAAACAAACAAAATAAAACAC 58.323 30.769 0.00 0.00 0.00 3.32
2067 3031 5.647658 TCGCTGTCAATTTGGTTCATATCTT 59.352 36.000 0.00 0.00 0.00 2.40
2123 3099 3.334583 TTGCTTAAATGTCGCTCTCCT 57.665 42.857 0.00 0.00 0.00 3.69
2237 3213 0.107800 TGGTTTTCGGTGTTCGTGGA 60.108 50.000 0.00 0.00 40.32 4.02
2239 3215 2.032302 TCAATGGTTTTCGGTGTTCGTG 59.968 45.455 0.00 0.00 40.32 4.35
2244 3220 5.467035 AATCAATCAATGGTTTTCGGTGT 57.533 34.783 0.00 0.00 0.00 4.16
2359 3335 1.587613 GCTTTTTCACGCGGCAACA 60.588 52.632 12.47 0.00 0.00 3.33
2414 3390 4.025145 CGAGACCGGGCATTAATAAAACTC 60.025 45.833 11.69 0.00 0.00 3.01
2416 3392 3.624410 ACGAGACCGGGCATTAATAAAAC 59.376 43.478 11.69 0.00 40.78 2.43
2417 3393 3.872771 GACGAGACCGGGCATTAATAAAA 59.127 43.478 11.69 0.00 40.78 1.52
2418 3394 3.118702 TGACGAGACCGGGCATTAATAAA 60.119 43.478 11.69 0.00 40.78 1.40
2424 3400 0.673644 CTTTGACGAGACCGGGCATT 60.674 55.000 11.69 0.00 40.78 3.56


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

AutoCloner maintained by Alex Coulton.