Multiple sequence alignment - TraesCS2B01G195500

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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 TraesCS2B01G195500 chr2B 100.000 2309 0 0 1 2309 173187626 173189934 0.000000e+00 4265
1 TraesCS2B01G195500 chr2B 81.266 790 130 13 1 780 786784533 786785314 7.010000e-175 623
2 TraesCS2B01G195500 chr2B 83.283 329 48 3 1 323 34338425 34338752 1.730000e-76 296
3 TraesCS2B01G195500 chr7D 92.836 1689 101 10 1 1679 563697073 563698751 0.000000e+00 2431
4 TraesCS2B01G195500 chr7D 92.362 1689 104 13 1 1678 156075906 156077580 0.000000e+00 2381
5 TraesCS2B01G195500 chr7D 89.845 453 32 7 1232 1679 94792802 94793245 9.260000e-159 569
6 TraesCS2B01G195500 chr4A 92.367 1690 108 7 1 1679 566906493 566904814 0.000000e+00 2386
7 TraesCS2B01G195500 chr4A 80.197 1318 247 9 1 1309 617931660 617930348 0.000000e+00 976
8 TraesCS2B01G195500 chr4A 79.924 1320 250 10 1 1312 621424694 621423382 0.000000e+00 955
9 TraesCS2B01G195500 chr2A 92.235 1687 107 8 1 1678 25046464 25044793 0.000000e+00 2368
10 TraesCS2B01G195500 chr2A 89.748 634 55 6 1679 2309 275635595 275636221 0.000000e+00 802
11 TraesCS2B01G195500 chr7B 80.383 1305 239 12 1 1294 23302438 23303736 0.000000e+00 976
12 TraesCS2B01G195500 chr7B 79.635 1316 247 15 1 1304 37117085 37115779 0.000000e+00 926
13 TraesCS2B01G195500 chr7B 84.804 204 24 3 1 198 37115304 37115506 5.030000e-47 198
14 TraesCS2B01G195500 chr3B 90.506 632 57 3 1679 2309 97793753 97794382 0.000000e+00 832
15 TraesCS2B01G195500 chr5D 90.348 632 58 2 1679 2309 522477077 522476448 0.000000e+00 826
16 TraesCS2B01G195500 chr4D 90.348 632 53 4 1679 2309 216404515 216405139 0.000000e+00 822
17 TraesCS2B01G195500 chr4D 89.731 633 56 5 1679 2309 390296243 390296868 0.000000e+00 800
18 TraesCS2B01G195500 chr1B 90.205 633 59 3 1679 2309 433402859 433402228 0.000000e+00 822
19 TraesCS2B01G195500 chr1B 89.606 635 57 8 1679 2309 312621949 312622578 0.000000e+00 798
20 TraesCS2B01G195500 chr2D 89.873 632 57 3 1679 2309 513313578 513314203 0.000000e+00 806
21 TraesCS2B01G195500 chr5A 89.557 632 62 4 1679 2308 167058747 167058118 0.000000e+00 798
22 TraesCS2B01G195500 chr6A 87.611 226 22 2 1459 1678 46577587 46577362 8.190000e-65 257
23 TraesCS2B01G195500 chr4B 80.857 350 42 11 1349 1678 372357341 372357685 3.810000e-63 252
24 TraesCS2B01G195500 chr6D 81.703 317 37 5 1371 1681 171326520 171326219 6.370000e-61 244


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 TraesCS2B01G195500 chr2B 173187626 173189934 2308 False 4265 4265 100.000 1 2309 1 chr2B.!!$F2 2308
1 TraesCS2B01G195500 chr2B 786784533 786785314 781 False 623 623 81.266 1 780 1 chr2B.!!$F3 779
2 TraesCS2B01G195500 chr7D 563697073 563698751 1678 False 2431 2431 92.836 1 1679 1 chr7D.!!$F3 1678
3 TraesCS2B01G195500 chr7D 156075906 156077580 1674 False 2381 2381 92.362 1 1678 1 chr7D.!!$F2 1677
4 TraesCS2B01G195500 chr4A 566904814 566906493 1679 True 2386 2386 92.367 1 1679 1 chr4A.!!$R1 1678
5 TraesCS2B01G195500 chr4A 617930348 617931660 1312 True 976 976 80.197 1 1309 1 chr4A.!!$R2 1308
6 TraesCS2B01G195500 chr4A 621423382 621424694 1312 True 955 955 79.924 1 1312 1 chr4A.!!$R3 1311
7 TraesCS2B01G195500 chr2A 25044793 25046464 1671 True 2368 2368 92.235 1 1678 1 chr2A.!!$R1 1677
8 TraesCS2B01G195500 chr2A 275635595 275636221 626 False 802 802 89.748 1679 2309 1 chr2A.!!$F1 630
9 TraesCS2B01G195500 chr7B 23302438 23303736 1298 False 976 976 80.383 1 1294 1 chr7B.!!$F1 1293
10 TraesCS2B01G195500 chr7B 37115779 37117085 1306 True 926 926 79.635 1 1304 1 chr7B.!!$R1 1303
11 TraesCS2B01G195500 chr3B 97793753 97794382 629 False 832 832 90.506 1679 2309 1 chr3B.!!$F1 630
12 TraesCS2B01G195500 chr5D 522476448 522477077 629 True 826 826 90.348 1679 2309 1 chr5D.!!$R1 630
13 TraesCS2B01G195500 chr4D 216404515 216405139 624 False 822 822 90.348 1679 2309 1 chr4D.!!$F1 630
14 TraesCS2B01G195500 chr4D 390296243 390296868 625 False 800 800 89.731 1679 2309 1 chr4D.!!$F2 630
15 TraesCS2B01G195500 chr1B 433402228 433402859 631 True 822 822 90.205 1679 2309 1 chr1B.!!$R1 630
16 TraesCS2B01G195500 chr1B 312621949 312622578 629 False 798 798 89.606 1679 2309 1 chr1B.!!$F1 630
17 TraesCS2B01G195500 chr2D 513313578 513314203 625 False 806 806 89.873 1679 2309 1 chr2D.!!$F1 630
18 TraesCS2B01G195500 chr5A 167058118 167058747 629 True 798 798 89.557 1679 2308 1 chr5A.!!$R1 629

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
751 759 0.249031 AAAAGCACAAACAGCCGAGC 60.249 50.0 0.0 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2069 2094 0.318869 TGCGTTGATGCAAGCTTTGG 60.319 50.0 0.0 0.0 43.02 3.28 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
42 43 5.158141 AGAGGTCAAGGCTATGATAATGGA 58.842 41.667 0.00 0.00 0.00 3.41
326 332 6.657541 TCGGATAAAAAGTGTCCAAGCTATTT 59.342 34.615 0.00 0.00 32.23 1.40
376 382 6.701340 AGCTTTATTGGAATTGGAAAGAACC 58.299 36.000 0.00 0.00 30.29 3.62
388 394 6.627087 TTGGAAAGAACCTCTAGTGATGAT 57.373 37.500 0.00 0.00 0.00 2.45
469 476 3.091545 ACTTGGTATGGTCATTTGGCAG 58.908 45.455 0.00 0.00 0.00 4.85
559 566 3.244976 CCTTAAGCAAATTGAAGGTGCG 58.755 45.455 0.00 0.00 43.16 5.34
564 571 2.821969 AGCAAATTGAAGGTGCGATCTT 59.178 40.909 0.00 0.00 43.16 2.40
658 666 9.392506 TCTATGGATATTGAACCTAGATTTCCA 57.607 33.333 0.00 0.00 36.05 3.53
666 674 7.411486 TTGAACCTAGATTTCCAACAAAACA 57.589 32.000 0.00 0.00 0.00 2.83
700 708 8.026607 ACGAGAAAAAGACACTTTGATGAAAAA 58.973 29.630 0.00 0.00 0.00 1.94
751 759 0.249031 AAAAGCACAAACAGCCGAGC 60.249 50.000 0.00 0.00 0.00 5.03
758 769 0.886490 CAAACAGCCGAGCAGGAGTT 60.886 55.000 2.12 3.56 45.00 3.01
769 780 3.675698 CGAGCAGGAGTTGTTTAGAGTTC 59.324 47.826 0.00 0.00 0.00 3.01
1065 1077 5.972107 ATTTTGTTAGAGCTGCAGATTGT 57.028 34.783 20.43 5.35 0.00 2.71
1098 1110 4.024556 GTGTCCATTGCTTATCGAATCCTG 60.025 45.833 0.00 0.00 0.00 3.86
1115 1127 6.594159 CGAATCCTGTTAACTGTTCCTGTTAT 59.406 38.462 7.22 0.00 30.34 1.89
1145 1157 6.509039 GCATCTGCTGAAACAAGTTTTTCAAG 60.509 38.462 0.00 8.78 43.29 3.02
1152 1164 8.373256 GCTGAAACAAGTTTTTCAAGACTAAAC 58.627 33.333 0.00 0.00 43.29 2.01
1208 1220 4.263639 ACAAGAGAGATTGAATGGCTTGGA 60.264 41.667 0.00 0.00 36.49 3.53
1238 1250 6.543465 TGCTGTATTGAGAAAGATATGTTGGG 59.457 38.462 0.00 0.00 0.00 4.12
1243 1255 4.922206 TGAGAAAGATATGTTGGGCAACT 58.078 39.130 0.00 0.00 41.67 3.16
1305 1317 4.170723 CGAAGGTGTCGCTTCTCC 57.829 61.111 0.00 0.00 44.14 3.71
1325 1337 3.118261 TCCTGAGTATGCCATTCACTTCC 60.118 47.826 0.00 0.00 0.00 3.46
1336 1348 5.127845 TGCCATTCACTTCCTTTTTGTGTAA 59.872 36.000 0.00 0.00 33.82 2.41
1353 1365 6.129414 TGTGTAATTTTTAGGTGGCTCCTA 57.871 37.500 11.18 11.18 46.10 2.94
1367 1379 3.019564 GGCTCCTAATGTTTGCTGATGT 58.980 45.455 0.00 0.00 0.00 3.06
1369 1381 4.823989 GGCTCCTAATGTTTGCTGATGTAT 59.176 41.667 0.00 0.00 0.00 2.29
1376 1388 7.814107 CCTAATGTTTGCTGATGTATGTTTGTT 59.186 33.333 0.00 0.00 0.00 2.83
1386 1398 6.237154 TGATGTATGTTTGTTGATGGACTGA 58.763 36.000 0.00 0.00 0.00 3.41
1429 1441 5.063204 TCTGTCGTGTTGGATCAAGAATTT 58.937 37.500 0.00 0.00 0.00 1.82
1470 1483 5.258051 AGTTCAAACAAGACTTGTGGGTTA 58.742 37.500 21.24 4.28 44.59 2.85
1518 1531 8.593679 TGTAATCATTTGATATATCCGTGGACT 58.406 33.333 10.25 0.00 33.73 3.85
1528 1541 0.892755 TCCGTGGACTGTGGTGTATC 59.107 55.000 0.00 0.00 0.00 2.24
1535 1548 2.567615 GGACTGTGGTGTATCAAGACCT 59.432 50.000 0.00 0.00 39.80 3.85
1585 1601 9.767684 TTTTATAATGACTTTTCGCTGTACATG 57.232 29.630 0.00 0.00 0.00 3.21
1587 1603 7.792374 ATAATGACTTTTCGCTGTACATGAT 57.208 32.000 0.00 0.00 0.00 2.45
1588 1604 8.887036 ATAATGACTTTTCGCTGTACATGATA 57.113 30.769 0.00 0.00 0.00 2.15
1590 1606 5.109210 TGACTTTTCGCTGTACATGATAGG 58.891 41.667 0.00 0.00 0.00 2.57
1591 1607 3.871594 ACTTTTCGCTGTACATGATAGGC 59.128 43.478 0.00 0.00 0.00 3.93
1592 1608 3.819564 TTTCGCTGTACATGATAGGCT 57.180 42.857 0.00 0.00 0.00 4.58
1593 1609 3.819564 TTCGCTGTACATGATAGGCTT 57.180 42.857 0.00 0.00 0.00 4.35
1594 1610 3.097877 TCGCTGTACATGATAGGCTTG 57.902 47.619 0.00 0.00 0.00 4.01
1630 1651 7.844009 TGTCTATTATATAGTTTAAGGGCCCG 58.156 38.462 18.44 0.00 0.00 6.13
1662 1683 0.255890 GCACAAGGGCCTCTGGAATA 59.744 55.000 6.46 0.00 0.00 1.75
1666 1687 1.496429 CAAGGGCCTCTGGAATACCAT 59.504 52.381 6.46 0.00 45.87 3.55
1991 2015 6.930164 TGCAAATTTCTATGTCAACAATGCTT 59.070 30.769 0.00 0.00 0.00 3.91
2087 2112 1.620413 GCCAAAGCTTGCATCAACGC 61.620 55.000 0.00 0.00 35.50 4.84
2092 2117 1.007502 GCTTGCATCAACGCAACCA 60.008 52.632 0.00 0.00 46.61 3.67
2125 2151 6.407074 CGAACTCTTTATCACCTCCATAACCT 60.407 42.308 0.00 0.00 0.00 3.50
2149 2176 7.766738 CCTAGAAACATTTCCTTAGTCCTCTTC 59.233 40.741 0.68 0.00 37.92 2.87
2150 2177 7.079451 AGAAACATTTCCTTAGTCCTCTTCA 57.921 36.000 0.68 0.00 37.92 3.02
2154 2181 3.983044 TTCCTTAGTCCTCTTCAAGGC 57.017 47.619 0.00 0.00 45.78 4.35
2183 2210 6.494666 AGGATAATTTTGACCGATGTCCTA 57.505 37.500 0.00 0.00 41.01 2.94
2233 2261 2.517959 CCTTTCCAGACTCATGGCAAA 58.482 47.619 0.00 0.00 40.41 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 9.918630 CCTTGATGTTTTCTTTTCATGTTAGAT 57.081 29.630 0.00 0.00 0.00 1.98
222 228 7.280044 ACCAATACCTCCCAACTTTTAGTAT 57.720 36.000 0.00 0.00 0.00 2.12
326 332 5.604231 ACAATATCTGAGGAGCTTGATACCA 59.396 40.000 0.00 0.00 0.00 3.25
376 382 9.311916 CTCTTAGTTTTTGGATCATCACTAGAG 57.688 37.037 0.00 0.00 0.00 2.43
388 394 5.129634 TGTGCATCACTCTTAGTTTTTGGA 58.870 37.500 0.00 0.00 35.11 3.53
498 505 5.239525 ACAAACTTAGGCTGCAACTTCTTAG 59.760 40.000 0.50 0.00 0.00 2.18
632 640 9.392506 TGGAAATCTAGGTTCAATATCCATAGA 57.607 33.333 2.50 0.00 29.93 1.98
634 642 9.793259 GTTGGAAATCTAGGTTCAATATCCATA 57.207 33.333 6.88 0.00 34.65 2.74
658 666 8.918961 TTTTTCTCGTAACATGATGTTTTGTT 57.081 26.923 16.75 0.00 41.45 2.83
666 674 7.730364 AAGTGTCTTTTTCTCGTAACATGAT 57.270 32.000 0.00 0.00 0.00 2.45
733 741 1.360192 GCTCGGCTGTTTGTGCTTT 59.640 52.632 0.00 0.00 0.00 3.51
742 750 2.044806 AACAACTCCTGCTCGGCTGT 62.045 55.000 0.00 0.00 0.00 4.40
922 934 9.884465 GCTACCATGAGAATACATATTTGAAAC 57.116 33.333 0.00 0.00 0.00 2.78
932 944 5.422012 TCTGACAAGCTACCATGAGAATACA 59.578 40.000 0.00 0.00 0.00 2.29
970 982 7.671302 AGCACTCTTAGTTCAGAACAGAAATA 58.329 34.615 15.85 0.00 0.00 1.40
1042 1054 7.452880 AACAATCTGCAGCTCTAACAAAATA 57.547 32.000 9.47 0.00 0.00 1.40
1065 1077 7.914871 CGATAAGCAATGGACACATTTTGATAA 59.085 33.333 0.00 0.00 44.69 1.75
1098 1110 5.935789 TGCTACCATAACAGGAACAGTTAAC 59.064 40.000 0.00 0.00 43.20 2.01
1169 1181 5.884771 TCTCTTGTGACATAGTTGATCTCG 58.115 41.667 0.00 0.00 0.00 4.04
1208 1220 7.772292 ACATATCTTTCTCAATACAGCACATGT 59.228 33.333 0.00 0.00 46.45 3.21
1273 1285 4.253685 CACCTTCGAGCATTTTTAGAGGA 58.746 43.478 0.00 0.00 0.00 3.71
1305 1317 4.148128 AGGAAGTGAATGGCATACTCAG 57.852 45.455 0.00 0.00 0.00 3.35
1325 1337 7.170828 GGAGCCACCTAAAAATTACACAAAAAG 59.829 37.037 0.00 0.00 35.41 2.27
1353 1365 7.208777 TCAACAAACATACATCAGCAAACATT 58.791 30.769 0.00 0.00 0.00 2.71
1367 1379 6.763135 GCTCTATCAGTCCATCAACAAACATA 59.237 38.462 0.00 0.00 0.00 2.29
1369 1381 4.937620 GCTCTATCAGTCCATCAACAAACA 59.062 41.667 0.00 0.00 0.00 2.83
1376 1388 3.229293 CTCCAGCTCTATCAGTCCATCA 58.771 50.000 0.00 0.00 0.00 3.07
1453 1466 4.798882 TCCAATAACCCACAAGTCTTGTT 58.201 39.130 15.73 4.28 43.23 2.83
1470 1483 5.163301 ACAAGATTAGGATACACGCTCCAAT 60.163 40.000 0.00 0.00 41.41 3.16
1518 1531 9.173021 CATTAAATAAGGTCTTGATACACCACA 57.827 33.333 0.00 0.00 34.80 4.17
1553 1569 7.538678 CAGCGAAAAGTCATTATAAAAGCAAGT 59.461 33.333 0.00 0.00 0.00 3.16
1630 1651 2.287009 CCCTTGTGCGAACTGAGAAAAC 60.287 50.000 0.00 0.00 0.00 2.43
1734 1755 9.971922 AAGGTTTATTATTCATGCTAGAATTGC 57.028 29.630 9.01 0.00 38.97 3.56
1797 1818 6.182627 TGGAAATATGCCCTAGATGCAATAG 58.817 40.000 10.38 0.00 42.92 1.73
1804 1825 5.370880 AGACTGTTGGAAATATGCCCTAGAT 59.629 40.000 0.00 0.00 0.00 1.98
2069 2094 0.318869 TGCGTTGATGCAAGCTTTGG 60.319 50.000 0.00 0.00 43.02 3.28
2087 2112 4.985044 AAGAGTTCGTCGTAAATGGTTG 57.015 40.909 0.00 0.00 0.00 3.77
2092 2117 6.628185 AGGTGATAAAGAGTTCGTCGTAAAT 58.372 36.000 0.00 0.00 0.00 1.40
2125 2151 8.202461 TGAAGAGGACTAAGGAAATGTTTCTA 57.798 34.615 5.56 0.00 37.35 2.10
2149 2176 6.405842 GGTCAAAATTATCCTTAGGTGCCTTG 60.406 42.308 0.00 0.00 0.00 3.61
2150 2177 5.656859 GGTCAAAATTATCCTTAGGTGCCTT 59.343 40.000 0.00 0.00 0.00 4.35
2154 2181 6.542370 ACATCGGTCAAAATTATCCTTAGGTG 59.458 38.462 0.00 0.00 0.00 4.00
2207 2234 2.661176 TGAGTCTGGAAAGGGGGTAT 57.339 50.000 0.00 0.00 0.00 2.73
2233 2261 2.158682 TGTACCAAACCTGATGTGTGCT 60.159 45.455 0.00 0.00 30.06 4.40


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

AutoCloner maintained by Alex Coulton.