Multiple sequence alignment - TraesCS1A01G343100

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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 TraesCS1A01G343100 chr1A 100.000 2294 0 0 1 2294 531840847 531838554 0.000000e+00 4237
1 TraesCS1A01G343100 chr1A 95.208 1565 72 3 731 2293 380400746 380402309 0.000000e+00 2471
2 TraesCS1A01G343100 chr7A 96.000 1500 57 3 797 2294 707844390 707845888 0.000000e+00 2435
3 TraesCS1A01G343100 chr7A 95.578 1515 64 3 782 2294 650324575 650323062 0.000000e+00 2423
4 TraesCS1A01G343100 chr7A 95.092 1528 72 3 768 2294 650260773 650259248 0.000000e+00 2403
5 TraesCS1A01G343100 chr7A 93.260 727 46 3 7 732 615540242 615539518 0.000000e+00 1068
6 TraesCS1A01G343100 chr2A 95.589 1519 58 5 783 2294 600113448 600111932 0.000000e+00 2425
7 TraesCS1A01G343100 chr2A 96.003 1476 57 2 820 2294 23796207 23797681 0.000000e+00 2398
8 TraesCS1A01G343100 chr2A 95.470 1435 60 5 862 2294 571019198 571020629 0.000000e+00 2285
9 TraesCS1A01G343100 chr1B 95.769 1489 61 2 807 2294 658504122 658502635 0.000000e+00 2399
10 TraesCS1A01G343100 chr4A 94.415 1486 78 5 811 2294 382145490 382146972 0.000000e+00 2279
11 TraesCS1A01G343100 chr4A 93.398 727 47 1 7 733 469887262 469886537 0.000000e+00 1075
12 TraesCS1A01G343100 chr7D 93.269 728 47 2 7 733 567632596 567631870 0.000000e+00 1072
13 TraesCS1A01G343100 chr3D 93.260 727 48 1 7 733 577325230 577325955 0.000000e+00 1070
14 TraesCS1A01G343100 chr2D 93.260 727 46 2 7 733 415153486 415154209 0.000000e+00 1068
15 TraesCS1A01G343100 chr6D 92.995 728 49 2 7 733 294699333 294698607 0.000000e+00 1061
16 TraesCS1A01G343100 chr3A 92.857 728 50 2 7 733 22387976 22387250 0.000000e+00 1055
17 TraesCS1A01G343100 chr6A 92.497 733 49 5 1 733 33175239 33174513 0.000000e+00 1044
18 TraesCS1A01G343100 chr6A 88.152 211 17 3 644 854 578665396 578665194 6.330000e-61 244
19 TraesCS1A01G343100 chrUn 88.109 841 93 6 7 846 79779776 79780610 0.000000e+00 992


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 TraesCS1A01G343100 chr1A 531838554 531840847 2293 True 4237 4237 100.000 1 2294 1 chr1A.!!$R1 2293
1 TraesCS1A01G343100 chr1A 380400746 380402309 1563 False 2471 2471 95.208 731 2293 1 chr1A.!!$F1 1562
2 TraesCS1A01G343100 chr7A 707844390 707845888 1498 False 2435 2435 96.000 797 2294 1 chr7A.!!$F1 1497
3 TraesCS1A01G343100 chr7A 650323062 650324575 1513 True 2423 2423 95.578 782 2294 1 chr7A.!!$R3 1512
4 TraesCS1A01G343100 chr7A 650259248 650260773 1525 True 2403 2403 95.092 768 2294 1 chr7A.!!$R2 1526
5 TraesCS1A01G343100 chr7A 615539518 615540242 724 True 1068 1068 93.260 7 732 1 chr7A.!!$R1 725
6 TraesCS1A01G343100 chr2A 600111932 600113448 1516 True 2425 2425 95.589 783 2294 1 chr2A.!!$R1 1511
7 TraesCS1A01G343100 chr2A 23796207 23797681 1474 False 2398 2398 96.003 820 2294 1 chr2A.!!$F1 1474
8 TraesCS1A01G343100 chr2A 571019198 571020629 1431 False 2285 2285 95.470 862 2294 1 chr2A.!!$F2 1432
9 TraesCS1A01G343100 chr1B 658502635 658504122 1487 True 2399 2399 95.769 807 2294 1 chr1B.!!$R1 1487
10 TraesCS1A01G343100 chr4A 382145490 382146972 1482 False 2279 2279 94.415 811 2294 1 chr4A.!!$F1 1483
11 TraesCS1A01G343100 chr4A 469886537 469887262 725 True 1075 1075 93.398 7 733 1 chr4A.!!$R1 726
12 TraesCS1A01G343100 chr7D 567631870 567632596 726 True 1072 1072 93.269 7 733 1 chr7D.!!$R1 726
13 TraesCS1A01G343100 chr3D 577325230 577325955 725 False 1070 1070 93.260 7 733 1 chr3D.!!$F1 726
14 TraesCS1A01G343100 chr2D 415153486 415154209 723 False 1068 1068 93.260 7 733 1 chr2D.!!$F1 726
15 TraesCS1A01G343100 chr6D 294698607 294699333 726 True 1061 1061 92.995 7 733 1 chr6D.!!$R1 726
16 TraesCS1A01G343100 chr3A 22387250 22387976 726 True 1055 1055 92.857 7 733 1 chr3A.!!$R1 726
17 TraesCS1A01G343100 chr6A 33174513 33175239 726 True 1044 1044 92.497 1 733 1 chr6A.!!$R1 732
18 TraesCS1A01G343100 chrUn 79779776 79780610 834 False 992 992 88.109 7 846 1 chrUn.!!$F1 839

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
969 973 0.248661 CTCGTCATCATCGTCGGCTT 60.249 55.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1787 1791 1.96593 GCCATGCGTGAACACAGGA 60.966 57.895 7.72 0.59 0.0 3.86 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
114 115 2.286365 TCAAATTTGACCCGCTTCCT 57.714 45.000 16.91 0.00 31.01 3.36
123 124 3.101437 TGACCCGCTTCCTACTAAATCA 58.899 45.455 0.00 0.00 0.00 2.57
141 142 6.769608 AAATCAGCGGAAATTTGTCTTTTC 57.230 33.333 0.00 0.00 33.31 2.29
167 168 5.215160 CGAGAGGTGGATCAAAAACTTTTG 58.785 41.667 8.35 8.35 46.70 2.44
201 202 7.244898 CCATTTGGTCAATTGTGCATTAAATG 58.755 34.615 5.13 13.16 34.50 2.32
359 361 6.486320 CCCTTAGGCAACATTGTTTGAAATTT 59.514 34.615 0.00 0.00 41.41 1.82
396 398 6.139048 TGTGCACAATATGAGATCATTTGG 57.861 37.500 19.28 0.00 37.76 3.28
454 456 7.046652 TCATTTTGAGCACTGAAAAATGGAAA 58.953 30.769 18.71 6.31 45.15 3.13
553 555 1.301637 CCATGGGCATATCACGCGA 60.302 57.895 15.93 0.00 0.00 5.87
568 570 4.953116 CGAATCACGCATCAACCG 57.047 55.556 0.00 0.00 34.51 4.44
681 684 4.325658 CCTCCATTCTTTCTCCCATTCCTT 60.326 45.833 0.00 0.00 0.00 3.36
710 713 1.167851 CCTGCATTCTTTCGCTCCAA 58.832 50.000 0.00 0.00 0.00 3.53
734 737 3.272042 CACCCACCCCAATCCCCA 61.272 66.667 0.00 0.00 0.00 4.96
790 793 4.562425 GATCCATTCCCGCCGCCA 62.562 66.667 0.00 0.00 0.00 5.69
899 902 3.295093 TCCAGAGCACAAATCCAAACAA 58.705 40.909 0.00 0.00 0.00 2.83
959 963 4.829518 CGCGCGACCTCGTCATCA 62.830 66.667 28.94 0.00 42.22 3.07
969 973 0.248661 CTCGTCATCATCGTCGGCTT 60.249 55.000 0.00 0.00 0.00 4.35
986 990 1.118838 CTTGGAGATCTCGCCTTCCT 58.881 55.000 16.46 0.00 36.72 3.36
1123 1127 2.996168 AAGACTCGCGCCTGCTTGTT 62.996 55.000 0.00 0.00 39.65 2.83
1215 1219 4.807039 CGGACGGCGATCGGGTTT 62.807 66.667 16.62 0.00 44.45 3.27
1234 1238 1.290955 GTCGTCATGGGGTTCGTCA 59.709 57.895 0.00 0.00 0.00 4.35
1313 1317 4.415332 GCGAACGCGTCTCCTCCA 62.415 66.667 14.44 0.00 40.36 3.86
1367 1371 3.864789 AGACTTGGGTCATGTTGTCTT 57.135 42.857 0.00 0.00 44.36 3.01
1483 1487 4.706476 TCCAAATAGACCTGCCAATTTCTG 59.294 41.667 0.00 0.00 0.00 3.02
1508 1512 4.672587 TGTTAGGAGAATTCGGATGAGG 57.327 45.455 0.00 0.00 0.00 3.86
1599 1603 1.809939 TTGGGGGCATAGGCTGGTTT 61.810 55.000 0.00 0.00 40.87 3.27
1809 1813 2.112928 TGTTCACGCATGGCCAGT 59.887 55.556 13.05 0.00 0.00 4.00
1989 1995 0.653636 GTCGCGTGTGACCTCAAAAA 59.346 50.000 5.77 0.00 32.61 1.94
2037 2043 9.965902 AAAATGAAGATGGTACTACTGATTCTT 57.034 29.630 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 1.271543 TGCAGCTGCCTCATAGTTTGT 60.272 47.619 34.64 0.00 41.18 2.83
114 115 7.681939 AAGACAAATTTCCGCTGATTTAGTA 57.318 32.000 0.00 0.00 0.00 1.82
123 124 4.041723 CGTTGAAAAGACAAATTTCCGCT 58.958 39.130 0.00 0.00 36.23 5.52
141 142 3.815401 AGTTTTTGATCCACCTCTCGTTG 59.185 43.478 0.00 0.00 0.00 4.10
222 223 6.343716 TGTTGCAAAATTGTACCAGATCAT 57.656 33.333 0.00 0.00 0.00 2.45
283 285 4.280677 TCATTTTCCATTTTTCGAGTGCCT 59.719 37.500 0.00 0.00 0.00 4.75
553 555 2.749865 CGGCGGTTGATGCGTGATT 61.750 57.895 0.00 0.00 0.00 2.57
598 600 0.947660 GTTTCGTCTCGGGTGGGTTC 60.948 60.000 0.00 0.00 0.00 3.62
650 652 2.520657 AAAGAATGGAGGCAGGGGGC 62.521 60.000 0.00 0.00 43.74 5.80
694 697 2.792542 CGGATTTGGAGCGAAAGAATGC 60.793 50.000 0.00 0.00 0.00 3.56
734 737 4.115199 GAAGGTGGGGGCAGCGAT 62.115 66.667 0.00 0.00 0.00 4.58
764 767 1.414158 GGGAATGGATCTCCTCGTCA 58.586 55.000 0.00 0.00 36.82 4.35
766 769 1.749334 GCGGGAATGGATCTCCTCGT 61.749 60.000 0.00 0.00 36.82 4.18
899 902 2.358247 GACGGGCGAATGGTGTGT 60.358 61.111 0.00 0.00 0.00 3.72
959 963 0.671251 GAGATCTCCAAGCCGACGAT 59.329 55.000 12.00 0.00 0.00 3.73
969 973 1.680522 GCAGGAAGGCGAGATCTCCA 61.681 60.000 17.13 0.00 0.00 3.86
1035 1039 1.301716 GCTGTCCTTGGCGAACTCA 60.302 57.895 0.00 0.00 0.00 3.41
1123 1127 1.621814 AGGAAAACGAACAGGATCCGA 59.378 47.619 5.98 0.00 32.22 4.55
1215 1219 1.290955 GACGAACCCCATGACGACA 59.709 57.895 0.00 0.00 0.00 4.35
1313 1317 3.879321 GCAAACAAGAGGGAGATGGGATT 60.879 47.826 0.00 0.00 0.00 3.01
1367 1371 0.036105 ATCCAACAGATCACAGCGCA 60.036 50.000 11.47 0.00 0.00 6.09
1483 1487 3.261981 TCCGAATTCTCCTAACAAGGC 57.738 47.619 3.52 0.00 0.00 4.35
1508 1512 1.098050 CCACAGCTGATTACCCTTGC 58.902 55.000 23.35 0.00 0.00 4.01
1599 1603 3.304911 TTCCCAAATTGTGTGGTGAGA 57.695 42.857 0.00 0.00 34.01 3.27
1787 1791 1.965930 GCCATGCGTGAACACAGGA 60.966 57.895 7.72 0.59 0.00 3.86
1844 1848 6.927936 TCTTATTTTACAAAAGCTTGCATGCA 59.072 30.769 24.65 18.46 35.84 3.96
1999 2005 7.779073 ACCATCTTCATTTTCAATCAGGATTC 58.221 34.615 0.00 0.00 0.00 2.52
2037 2043 4.104102 AGGAAACACAATGTTCCTGGTCTA 59.896 41.667 4.43 0.00 40.14 2.59
2148 2159 4.522722 AACAGCTAGAACAGACTGGTAC 57.477 45.455 7.51 0.00 34.56 3.34
2149 2160 4.587262 TGAAACAGCTAGAACAGACTGGTA 59.413 41.667 7.51 0.00 34.56 3.25


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

AutoCloner maintained by Alex Coulton.