Multiple sequence alignment - TraesCS3B01G383000

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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 TraesCS3B01G383000 chr3B 100.000 2776 0 0 1 2776 602783674 602780899 0.000000e+00 5127
1 TraesCS3B01G383000 chr3D 94.408 1985 75 13 817 2776 456534045 456536018 0.000000e+00 3018
2 TraesCS3B01G383000 chr3A 94.753 1582 54 10 818 2380 599325773 599327344 0.000000e+00 2435
3 TraesCS3B01G383000 chr3A 95.291 361 17 0 2416 2776 599327342 599327702 8.620000e-160 573
4 TraesCS3B01G383000 chr3A 82.803 157 24 3 1253 1407 398879702 398879547 1.340000e-28 137
5 TraesCS3B01G383000 chr1D 96.463 820 27 2 1 818 479616029 479615210 0.000000e+00 1352
6 TraesCS3B01G383000 chr1D 95.859 821 31 3 1 818 464290451 464291271 0.000000e+00 1325
7 TraesCS3B01G383000 chrUn 96.229 822 29 2 1 820 94834306 94833485 0.000000e+00 1345
8 TraesCS3B01G383000 chr7B 96.328 817 29 1 1 816 537832961 537833777 0.000000e+00 1341
9 TraesCS3B01G383000 chr7D 96.762 803 24 2 1 802 389455977 389455176 0.000000e+00 1338
10 TraesCS3B01G383000 chr7D 95.971 819 31 2 1 818 563843301 563844118 0.000000e+00 1328
11 TraesCS3B01G383000 chr7D 95.732 820 33 2 1 818 80293621 80294440 0.000000e+00 1319
12 TraesCS3B01G383000 chr7D 82.424 165 26 3 1245 1407 243808148 243808311 1.040000e-29 141
13 TraesCS3B01G383000 chr6D 95.971 819 28 5 1 816 1556536 1555720 0.000000e+00 1325
14 TraesCS3B01G383000 chr5B 95.405 827 35 3 1 825 478923189 478922364 0.000000e+00 1314
15 TraesCS3B01G383000 chr5B 82.803 157 24 3 1253 1407 415127618 415127463 1.340000e-28 137
16 TraesCS3B01G383000 chr5A 83.439 157 23 3 1253 1407 453519597 453519752 2.880000e-30 143
17 TraesCS3B01G383000 chr7A 82.424 165 26 3 1245 1407 258824463 258824626 1.040000e-29 141
18 TraesCS3B01G383000 chr6A 82.803 157 24 3 1253 1407 116813117 116812962 1.340000e-28 137
19 TraesCS3B01G383000 chr5D 82.803 157 24 3 1253 1407 352454309 352454154 1.340000e-28 137


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 TraesCS3B01G383000 chr3B 602780899 602783674 2775 True 5127 5127 100.000 1 2776 1 chr3B.!!$R1 2775
1 TraesCS3B01G383000 chr3D 456534045 456536018 1973 False 3018 3018 94.408 817 2776 1 chr3D.!!$F1 1959
2 TraesCS3B01G383000 chr3A 599325773 599327702 1929 False 1504 2435 95.022 818 2776 2 chr3A.!!$F1 1958
3 TraesCS3B01G383000 chr1D 479615210 479616029 819 True 1352 1352 96.463 1 818 1 chr1D.!!$R1 817
4 TraesCS3B01G383000 chr1D 464290451 464291271 820 False 1325 1325 95.859 1 818 1 chr1D.!!$F1 817
5 TraesCS3B01G383000 chrUn 94833485 94834306 821 True 1345 1345 96.229 1 820 1 chrUn.!!$R1 819
6 TraesCS3B01G383000 chr7B 537832961 537833777 816 False 1341 1341 96.328 1 816 1 chr7B.!!$F1 815
7 TraesCS3B01G383000 chr7D 389455176 389455977 801 True 1338 1338 96.762 1 802 1 chr7D.!!$R1 801
8 TraesCS3B01G383000 chr7D 563843301 563844118 817 False 1328 1328 95.971 1 818 1 chr7D.!!$F3 817
9 TraesCS3B01G383000 chr7D 80293621 80294440 819 False 1319 1319 95.732 1 818 1 chr7D.!!$F1 817
10 TraesCS3B01G383000 chr6D 1555720 1556536 816 True 1325 1325 95.971 1 816 1 chr6D.!!$R1 815
11 TraesCS3B01G383000 chr5B 478922364 478923189 825 True 1314 1314 95.405 1 825 1 chr5B.!!$R2 824

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
554 556 0.957395 CTTCTGTTGCGAGGGTGCAT 60.957 55.0 0.00 0.0 45.78 3.96 F
1551 1566 0.385751 TGATGAGCTGCTACTACGCC 59.614 55.0 0.15 0.0 0.00 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1553 1568 0.809241 CTCTTCCACCTGATGCGCTC 60.809 60.000 9.73 4.27 0.00 5.03 R
2411 2454 1.403679 CCAAGTGGAGTTGCGTTTGAA 59.596 47.619 0.00 0.00 37.39 2.69 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
32 33 1.556911 AGGCTCAGTCCGTTGATGATT 59.443 47.619 0.00 0.00 0.00 2.57
159 160 1.754234 CCGGGATGCCTTCAAAGGG 60.754 63.158 10.70 0.00 46.56 3.95
228 230 2.917804 GGGGGAGTTCCTCGAAGAT 58.082 57.895 0.00 0.00 37.38 2.40
335 337 7.391016 CGTTTGGACAAGAAAAACAAAGATTC 58.609 34.615 0.00 0.00 34.23 2.52
554 556 0.957395 CTTCTGTTGCGAGGGTGCAT 60.957 55.000 0.00 0.00 45.78 3.96
725 728 1.942677 TCCCATATTAACCGTGCGTG 58.057 50.000 0.00 0.00 0.00 5.34
788 791 8.645110 CCATTTTCCCTCTTCTATAATGCAAAT 58.355 33.333 0.00 0.00 0.00 2.32
997 1004 4.640690 ACCCTCCACGGCTCCACT 62.641 66.667 0.00 0.00 0.00 4.00
1015 1027 2.930040 CACTCCAAACACATAGCTACCG 59.070 50.000 0.00 0.00 0.00 4.02
1064 1076 3.244422 TGGTTTAGACAACACCTAGCCAG 60.244 47.826 0.00 0.00 0.00 4.85
1126 1138 2.300967 ATCCATGACCCACACGGCT 61.301 57.895 0.00 0.00 31.22 5.52
1127 1139 0.980754 ATCCATGACCCACACGGCTA 60.981 55.000 0.00 0.00 31.22 3.93
1134 1149 1.302511 CCCACACGGCTACAGCTTT 60.303 57.895 0.54 0.00 41.70 3.51
1138 1153 2.100631 CACGGCTACAGCTTTCCCG 61.101 63.158 9.56 9.56 44.19 5.14
1144 1159 0.608640 CTACAGCTTTCCCGTCCACT 59.391 55.000 0.00 0.00 0.00 4.00
1293 1308 4.814294 GAGCGTCGGCACCGGATT 62.814 66.667 9.46 0.00 43.41 3.01
1299 1314 2.029073 CGGCACCGGATTAGCGAT 59.971 61.111 9.46 0.00 35.56 4.58
1540 1555 1.624479 CCTGCAGGAGGTGATGAGCT 61.624 60.000 29.88 0.00 37.02 4.09
1551 1566 0.385751 TGATGAGCTGCTACTACGCC 59.614 55.000 0.15 0.00 0.00 5.68
1553 1568 2.026301 GAGCTGCTACTACGCCGG 59.974 66.667 0.15 0.00 0.00 6.13
1741 1756 9.425577 CTTATTAGCCTAGTTATTTAGCCACTC 57.574 37.037 0.00 0.00 0.00 3.51
1767 1782 7.328493 CGCTATTAGTATTGCATGCAGTAGTAA 59.672 37.037 34.17 34.17 37.94 2.24
1806 1821 3.440173 CAGTTTGCCTACCCAAGTATGTG 59.560 47.826 0.00 0.00 0.00 3.21
1878 1893 2.354821 GCCTAATTAGGTCTTGCCGTTG 59.645 50.000 28.31 3.47 45.42 4.10
2049 2064 9.995003 ACTTTATCTTCATATTCTGATCCAGAC 57.005 33.333 0.00 0.00 40.46 3.51
2066 2081 6.452494 TCCAGACTAGTAGTATGTTTGCTC 57.548 41.667 20.55 0.00 35.78 4.26
2213 2248 1.134965 AGTTGCTGGCTCGAGTGTATC 60.135 52.381 15.13 4.21 0.00 2.24
2298 2333 4.946478 ACTCCATGGTAGAGTTATGCTC 57.054 45.455 12.58 0.00 41.87 4.26
2325 2360 5.428253 GGAAAGCTAATGTCTGGTGTATCA 58.572 41.667 0.00 0.00 0.00 2.15
2354 2389 3.070476 TGCAGTGGTTCAGATGCATAA 57.930 42.857 0.00 0.00 43.34 1.90
2453 2496 5.187967 TGGAAACTAGGAAGAGAACCAGATC 59.812 44.000 0.00 0.00 0.00 2.75
2457 2500 6.293004 ACTAGGAAGAGAACCAGATCTTTG 57.707 41.667 0.00 0.00 35.93 2.77
2542 2588 1.019673 CTTCATGCTCAACCCCATCG 58.980 55.000 0.00 0.00 0.00 3.84
2569 2615 4.691685 ACGAAAATATGTCTAACAACCGCA 59.308 37.500 0.00 0.00 0.00 5.69
2593 2639 3.055312 ACATGCATCTCCATATGATCGCT 60.055 43.478 3.65 0.00 0.00 4.93
2751 2797 6.393171 AGTTAACGGTCAATACACCTACTTC 58.607 40.000 0.00 0.00 33.77 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 1.603455 CCTTTTCCAAGGCAGGCGA 60.603 57.895 0.00 0.00 43.55 5.54
228 230 1.342496 CTGGACACAGTGAGAGCAAGA 59.658 52.381 7.81 0.00 39.92 3.02
335 337 1.656652 CTTGGCTACAGGAATGTCGG 58.343 55.000 0.00 0.00 0.00 4.79
554 556 1.106351 ACAATGGCAGCACACCGAAA 61.106 50.000 0.00 0.00 0.00 3.46
720 723 0.956410 CCCGAAAACCATACCACGCA 60.956 55.000 0.00 0.00 0.00 5.24
725 728 0.745486 CCGGACCCGAAAACCATACC 60.745 60.000 10.42 0.00 42.83 2.73
997 1004 2.018542 GCGGTAGCTATGTGTTTGGA 57.981 50.000 0.00 0.00 41.01 3.53
1064 1076 0.821301 GGCAAGCTAGGAAGGATGCC 60.821 60.000 6.06 6.06 45.54 4.40
1126 1138 0.606604 GAGTGGACGGGAAAGCTGTA 59.393 55.000 0.00 0.00 0.00 2.74
1127 1139 1.371558 GAGTGGACGGGAAAGCTGT 59.628 57.895 0.00 0.00 0.00 4.40
1411 1426 4.063967 CACGAGTGCGGCCTGGTA 62.064 66.667 0.00 0.00 43.17 3.25
1494 1509 4.537433 GCCGGAAGCTCCATCGCT 62.537 66.667 5.05 0.00 43.31 4.93
1551 1566 3.664025 TTCCACCTGATGCGCTCCG 62.664 63.158 9.73 0.00 0.00 4.63
1553 1568 0.809241 CTCTTCCACCTGATGCGCTC 60.809 60.000 9.73 4.27 0.00 5.03
1557 1572 1.093159 CAAGCTCTTCCACCTGATGC 58.907 55.000 0.00 0.00 0.00 3.91
1741 1756 4.997905 ACTGCATGCAATACTAATAGCG 57.002 40.909 22.88 7.71 0.00 4.26
1746 1761 9.559732 AATCATTACTACTGCATGCAATACTAA 57.440 29.630 22.88 15.00 0.00 2.24
1806 1821 1.132643 ACGGATCTAAGCGTCTGACAC 59.867 52.381 8.73 0.00 0.00 3.67
1878 1893 0.819582 AATTGCTGCCAGTGCCATAC 59.180 50.000 0.00 0.00 36.33 2.39
2047 2062 9.765795 AAATATGGAGCAAACATACTACTAGTC 57.234 33.333 0.00 0.00 33.98 2.59
2048 2063 9.765795 GAAATATGGAGCAAACATACTACTAGT 57.234 33.333 0.00 0.00 33.98 2.57
2049 2064 8.916654 CGAAATATGGAGCAAACATACTACTAG 58.083 37.037 0.00 0.00 33.98 2.57
2050 2065 8.418662 ACGAAATATGGAGCAAACATACTACTA 58.581 33.333 0.00 0.00 33.98 1.82
2051 2066 7.272978 ACGAAATATGGAGCAAACATACTACT 58.727 34.615 0.00 0.00 33.98 2.57
2052 2067 7.307219 GGACGAAATATGGAGCAAACATACTAC 60.307 40.741 0.00 0.00 33.98 2.73
2213 2248 5.509840 GCCTGTACATACATTCTACCTCCTG 60.510 48.000 0.00 0.00 35.36 3.86
2298 2333 2.009774 CCAGACATTAGCTTTCCCGTG 58.990 52.381 0.00 0.00 0.00 4.94
2411 2454 1.403679 CCAAGTGGAGTTGCGTTTGAA 59.596 47.619 0.00 0.00 37.39 2.69
2542 2588 7.171434 CGGTTGTTAGACATATTTTCGTTCTC 58.829 38.462 0.00 0.00 0.00 2.87
2569 2615 4.155462 GCGATCATATGGAGATGCATGTTT 59.845 41.667 2.46 0.00 0.00 2.83
2593 2639 2.287393 TAACTCTCAATAAGCGCGCA 57.713 45.000 35.10 14.88 0.00 6.09
2751 2797 5.996501 GGTAGAGCCAAGTGTCGACACAG 62.997 56.522 41.04 32.76 42.32 3.66


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

AutoCloner maintained by Alex Coulton.