Multiple sequence alignment - TraesCS4A01G134200

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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 TraesCS4A01G134200 chr4A 100.000 2339 0 0 1 2339 182183237 182185575 0.000000e+00 4320.0
1 TraesCS4A01G134200 chr4A 96.154 52 1 1 1361 1412 277104528 277104478 1.490000e-12 84.2
2 TraesCS4A01G134200 chr2A 96.405 1363 46 3 1 1362 593327565 593326205 0.000000e+00 2242.0
3 TraesCS4A01G134200 chr2A 95.745 1363 56 2 1 1362 766438957 766437596 0.000000e+00 2194.0
4 TraesCS4A01G134200 chr5A 95.235 1364 55 5 1 1362 306496897 306498252 0.000000e+00 2150.0
5 TraesCS4A01G134200 chr5A 91.142 1366 116 5 1 1362 26539411 26538047 0.000000e+00 1847.0
6 TraesCS4A01G134200 chr2D 94.644 1363 72 1 1 1362 75164028 75165390 0.000000e+00 2111.0
7 TraesCS4A01G134200 chr2D 94.355 1364 74 3 1 1363 104915585 104916946 0.000000e+00 2089.0
8 TraesCS4A01G134200 chr2D 93.690 1363 82 4 1 1362 89201359 89200000 0.000000e+00 2037.0
9 TraesCS4A01G134200 chr4B 93.764 1363 82 3 1 1362 161561580 161560220 0.000000e+00 2043.0
10 TraesCS4A01G134200 chr2B 93.250 1363 87 4 1 1362 206728241 206726883 0.000000e+00 2002.0
11 TraesCS4A01G134200 chr7D 95.309 938 42 2 1404 2339 161855162 161854225 0.000000e+00 1487.0
12 TraesCS4A01G134200 chr7D 95.096 938 45 1 1403 2339 509352498 509351561 0.000000e+00 1476.0
13 TraesCS4A01G134200 chr3D 95.309 938 43 1 1403 2339 357121561 357122498 0.000000e+00 1487.0
14 TraesCS4A01G134200 chr3D 96.296 54 1 1 1358 1411 610585129 610585181 1.150000e-13 87.9
15 TraesCS4A01G134200 chr4D 95.304 937 43 1 1404 2339 337177330 337178266 0.000000e+00 1485.0
16 TraesCS4A01G134200 chr4D 95.299 936 43 1 1404 2338 355939844 355940779 0.000000e+00 1483.0
17 TraesCS4A01G134200 chr4D 95.197 937 43 2 1404 2339 103872126 103873061 0.000000e+00 1480.0
18 TraesCS4A01G134200 chr4D 89.231 65 5 2 1358 1422 399736140 399736202 1.930000e-11 80.5
19 TraesCS4A01G134200 chr1D 95.203 938 44 1 1403 2339 153787367 153788304 0.000000e+00 1482.0
20 TraesCS4A01G134200 chr1D 95.096 938 44 2 1403 2339 52927300 52926364 0.000000e+00 1476.0
21 TraesCS4A01G134200 chr1D 98.039 51 0 1 1361 1411 236253129 236253080 1.150000e-13 87.9
22 TraesCS4A01G134200 chr1D 96.226 53 1 1 1359 1411 371397236 371397287 4.140000e-13 86.1
23 TraesCS4A01G134200 chr5D 95.101 939 44 2 1403 2339 384829268 384828330 0.000000e+00 1478.0
24 TraesCS4A01G134200 chr5D 90.323 62 4 2 1361 1422 281100968 281100909 1.930000e-11 80.5
25 TraesCS4A01G134200 chr6D 96.296 54 1 1 1358 1411 458754695 458754747 1.150000e-13 87.9
26 TraesCS4A01G134200 chr6B 96.296 54 1 1 1358 1411 697722870 697722922 1.150000e-13 87.9
27 TraesCS4A01G134200 chr6B 94.545 55 2 1 1358 1412 567622699 567622752 1.490000e-12 84.2


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 TraesCS4A01G134200 chr4A 182183237 182185575 2338 False 4320 4320 100.000 1 2339 1 chr4A.!!$F1 2338
1 TraesCS4A01G134200 chr2A 593326205 593327565 1360 True 2242 2242 96.405 1 1362 1 chr2A.!!$R1 1361
2 TraesCS4A01G134200 chr2A 766437596 766438957 1361 True 2194 2194 95.745 1 1362 1 chr2A.!!$R2 1361
3 TraesCS4A01G134200 chr5A 306496897 306498252 1355 False 2150 2150 95.235 1 1362 1 chr5A.!!$F1 1361
4 TraesCS4A01G134200 chr5A 26538047 26539411 1364 True 1847 1847 91.142 1 1362 1 chr5A.!!$R1 1361
5 TraesCS4A01G134200 chr2D 75164028 75165390 1362 False 2111 2111 94.644 1 1362 1 chr2D.!!$F1 1361
6 TraesCS4A01G134200 chr2D 104915585 104916946 1361 False 2089 2089 94.355 1 1363 1 chr2D.!!$F2 1362
7 TraesCS4A01G134200 chr2D 89200000 89201359 1359 True 2037 2037 93.690 1 1362 1 chr2D.!!$R1 1361
8 TraesCS4A01G134200 chr4B 161560220 161561580 1360 True 2043 2043 93.764 1 1362 1 chr4B.!!$R1 1361
9 TraesCS4A01G134200 chr2B 206726883 206728241 1358 True 2002 2002 93.250 1 1362 1 chr2B.!!$R1 1361
10 TraesCS4A01G134200 chr7D 161854225 161855162 937 True 1487 1487 95.309 1404 2339 1 chr7D.!!$R1 935
11 TraesCS4A01G134200 chr7D 509351561 509352498 937 True 1476 1476 95.096 1403 2339 1 chr7D.!!$R2 936
12 TraesCS4A01G134200 chr3D 357121561 357122498 937 False 1487 1487 95.309 1403 2339 1 chr3D.!!$F1 936
13 TraesCS4A01G134200 chr4D 337177330 337178266 936 False 1485 1485 95.304 1404 2339 1 chr4D.!!$F2 935
14 TraesCS4A01G134200 chr4D 355939844 355940779 935 False 1483 1483 95.299 1404 2338 1 chr4D.!!$F3 934
15 TraesCS4A01G134200 chr4D 103872126 103873061 935 False 1480 1480 95.197 1404 2339 1 chr4D.!!$F1 935
16 TraesCS4A01G134200 chr1D 153787367 153788304 937 False 1482 1482 95.203 1403 2339 1 chr1D.!!$F1 936
17 TraesCS4A01G134200 chr1D 52926364 52927300 936 True 1476 1476 95.096 1403 2339 1 chr1D.!!$R1 936
18 TraesCS4A01G134200 chr5D 384828330 384829268 938 True 1478 1478 95.101 1403 2339 1 chr5D.!!$R2 936

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
990 993 2.228582 CGGAAAGATCAACCATTGCACA 59.771 45.455 0.0 0.0 0.0 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1819 1827 0.039708 GCTGGAGCTTGCACACTTTC 60.04 55.0 0.0 0.0 38.21 2.62 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
385 387 6.493458 TCAGATATGGAAGTTATCATGTCCGA 59.507 38.462 9.99 5.25 33.74 4.55
509 511 4.353777 TGCTCTTAGGGTGTAGAAGACAT 58.646 43.478 0.00 0.00 41.14 3.06
745 747 3.886505 ACGGAAATTAGTGCACAAGGAAA 59.113 39.130 21.04 5.38 0.00 3.13
784 786 6.617538 ACTCAAATATCAATGGGGATCACAT 58.382 36.000 0.00 0.00 0.00 3.21
825 827 3.814005 AATGCATCATCTTCAAAGGCC 57.186 42.857 0.00 0.00 0.00 5.19
990 993 2.228582 CGGAAAGATCAACCATTGCACA 59.771 45.455 0.00 0.00 0.00 4.57
1271 1276 6.128391 CGATTTTCTTCAACTTCGGATTGGTA 60.128 38.462 0.00 0.00 0.00 3.25
1301 1306 8.686334 GGAGCCTCTAAATGAAATTGTAATGAA 58.314 33.333 0.00 0.00 36.10 2.57
1303 1308 8.184192 AGCCTCTAAATGAAATTGTAATGAACG 58.816 33.333 0.00 0.00 36.10 3.95
1312 1317 7.251281 TGAAATTGTAATGAACGTCACAAACA 58.749 30.769 0.00 0.00 34.79 2.83
1389 1394 5.192327 CATACAGATGGGCTTTTGGAATC 57.808 43.478 0.00 0.00 0.00 2.52
1390 1395 3.173953 ACAGATGGGCTTTTGGAATCA 57.826 42.857 0.00 0.00 0.00 2.57
1391 1396 2.827921 ACAGATGGGCTTTTGGAATCAC 59.172 45.455 0.00 0.00 0.00 3.06
1392 1397 3.094572 CAGATGGGCTTTTGGAATCACT 58.905 45.455 0.00 0.00 0.00 3.41
1393 1398 3.512724 CAGATGGGCTTTTGGAATCACTT 59.487 43.478 0.00 0.00 0.00 3.16
1394 1399 3.512724 AGATGGGCTTTTGGAATCACTTG 59.487 43.478 0.00 0.00 0.00 3.16
1395 1400 2.956132 TGGGCTTTTGGAATCACTTGA 58.044 42.857 0.00 0.00 0.00 3.02
1396 1401 3.509442 TGGGCTTTTGGAATCACTTGAT 58.491 40.909 0.00 0.00 36.07 2.57
1397 1402 3.258872 TGGGCTTTTGGAATCACTTGATG 59.741 43.478 0.00 0.00 34.49 3.07
1398 1403 3.256558 GGCTTTTGGAATCACTTGATGC 58.743 45.455 0.00 0.00 34.49 3.91
1399 1404 3.056322 GGCTTTTGGAATCACTTGATGCT 60.056 43.478 0.00 0.00 34.49 3.79
1400 1405 4.562143 GGCTTTTGGAATCACTTGATGCTT 60.562 41.667 0.00 0.00 34.49 3.91
1401 1406 4.387862 GCTTTTGGAATCACTTGATGCTTG 59.612 41.667 0.00 0.00 34.49 4.01
1407 1412 0.874390 TCACTTGATGCTTGCGAACC 59.126 50.000 0.00 0.00 0.00 3.62
1604 1611 7.458409 ACTATCTACAAAGGTCGACTTGTTA 57.542 36.000 23.18 14.72 39.96 2.41
1653 1660 4.767928 AGTTGACTACGATGAGACCTTCTT 59.232 41.667 0.00 0.00 0.00 2.52
1663 1670 2.097825 GAGACCTTCTTACCCGTAGCA 58.902 52.381 0.00 0.00 0.00 3.49
1701 1708 3.487376 CGAATCATGTTAGCAATTGCCGT 60.487 43.478 26.45 12.04 43.38 5.68
1753 1760 5.863935 GGATGTCAAAACTGCATTCCTTAAC 59.136 40.000 0.00 0.00 0.00 2.01
1754 1761 5.843673 TGTCAAAACTGCATTCCTTAACA 57.156 34.783 0.00 0.00 0.00 2.41
1819 1827 4.386867 TGTCGATCCTAAAGGTGCTAAG 57.613 45.455 0.00 0.00 36.34 2.18
1883 1891 4.421131 AGCCTCTCGGAGTTGGAATATAT 58.579 43.478 18.71 0.00 0.00 0.86
1949 1957 4.843728 TGGAGAAGCCTGTATTTACAAGG 58.156 43.478 0.00 0.00 35.50 3.61
2022 2030 8.777413 CATATTGTCGATTGGAAATGATGTAGT 58.223 33.333 0.00 0.00 0.00 2.73
2173 2181 9.906660 CAAAGCACATACCTTGATAAAGTTTTA 57.093 29.630 0.00 0.00 0.00 1.52
2279 2287 7.094975 CGATCACCGTAGAAGATAGAGAGAAAT 60.095 40.741 0.00 0.00 0.00 2.17
2313 2321 2.107204 CCTATGCCTCAGCCATAGGTTT 59.893 50.000 12.84 0.37 41.04 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
189 191 3.574284 TGTTGCGAAATTGGGATTGAG 57.426 42.857 0.00 0.00 0.00 3.02
385 387 7.494298 ACGCCAAATAAAATTTTTGACTTCTGT 59.506 29.630 9.06 0.00 36.40 3.41
509 511 8.165239 AGTACATAGAAAAAGCATGTGTTTCA 57.835 30.769 15.58 6.59 34.78 2.69
745 747 9.399797 TGATATTTGAGTTGCATTCTGAGTTAT 57.600 29.630 0.00 0.00 0.00 1.89
784 786 8.807118 TGCATTTACAAAATTGTATGTAAGGGA 58.193 29.630 6.82 0.18 42.66 4.20
1199 1204 9.495572 GTGCTACTTTATTTGCCTCTCTATTAT 57.504 33.333 0.00 0.00 0.00 1.28
1246 1251 5.088739 CCAATCCGAAGTTGAAGAAAATCG 58.911 41.667 0.00 0.00 32.13 3.34
1271 1276 6.430007 ACAATTTCATTTAGAGGCTCCTCAT 58.570 36.000 17.40 6.03 44.99 2.90
1301 1306 7.667043 ATAATCAGTACATTGTTTGTGACGT 57.333 32.000 0.00 0.00 39.48 4.34
1367 1372 4.646040 TGATTCCAAAAGCCCATCTGTATG 59.354 41.667 0.00 0.00 0.00 2.39
1368 1373 4.646492 GTGATTCCAAAAGCCCATCTGTAT 59.354 41.667 0.00 0.00 0.00 2.29
1369 1374 4.016444 GTGATTCCAAAAGCCCATCTGTA 58.984 43.478 0.00 0.00 0.00 2.74
1370 1375 2.827921 GTGATTCCAAAAGCCCATCTGT 59.172 45.455 0.00 0.00 0.00 3.41
1371 1376 3.094572 AGTGATTCCAAAAGCCCATCTG 58.905 45.455 0.00 0.00 0.00 2.90
1372 1377 3.463048 AGTGATTCCAAAAGCCCATCT 57.537 42.857 0.00 0.00 0.00 2.90
1373 1378 3.511146 TCAAGTGATTCCAAAAGCCCATC 59.489 43.478 0.00 0.00 0.00 3.51
1374 1379 3.509442 TCAAGTGATTCCAAAAGCCCAT 58.491 40.909 0.00 0.00 0.00 4.00
1375 1380 2.956132 TCAAGTGATTCCAAAAGCCCA 58.044 42.857 0.00 0.00 0.00 5.36
1376 1381 3.853475 CATCAAGTGATTCCAAAAGCCC 58.147 45.455 0.00 0.00 31.21 5.19
1377 1382 3.056322 AGCATCAAGTGATTCCAAAAGCC 60.056 43.478 0.00 0.00 31.21 4.35
1378 1383 4.184079 AGCATCAAGTGATTCCAAAAGC 57.816 40.909 0.00 0.00 31.21 3.51
1379 1384 4.387862 GCAAGCATCAAGTGATTCCAAAAG 59.612 41.667 0.00 0.00 33.33 2.27
1380 1385 4.309099 GCAAGCATCAAGTGATTCCAAAA 58.691 39.130 0.00 0.00 33.33 2.44
1381 1386 3.612241 CGCAAGCATCAAGTGATTCCAAA 60.612 43.478 0.00 0.00 33.33 3.28
1382 1387 2.095110 CGCAAGCATCAAGTGATTCCAA 60.095 45.455 0.00 0.00 33.33 3.53
1383 1388 1.469703 CGCAAGCATCAAGTGATTCCA 59.530 47.619 0.00 0.00 33.33 3.53
1384 1389 1.739466 TCGCAAGCATCAAGTGATTCC 59.261 47.619 0.00 0.00 33.33 3.01
1385 1390 3.166657 GTTCGCAAGCATCAAGTGATTC 58.833 45.455 0.00 0.00 33.33 2.52
1386 1391 2.095059 GGTTCGCAAGCATCAAGTGATT 60.095 45.455 0.00 0.00 36.76 2.57
1387 1392 1.470098 GGTTCGCAAGCATCAAGTGAT 59.530 47.619 0.00 0.00 34.56 3.06
1388 1393 0.874390 GGTTCGCAAGCATCAAGTGA 59.126 50.000 0.00 0.00 37.18 3.41
1389 1394 0.592637 TGGTTCGCAAGCATCAAGTG 59.407 50.000 0.00 0.00 33.29 3.16
1390 1395 1.200716 CATGGTTCGCAAGCATCAAGT 59.799 47.619 9.60 0.00 45.81 3.16
1391 1396 1.469703 TCATGGTTCGCAAGCATCAAG 59.530 47.619 9.60 2.36 45.81 3.02
1392 1397 1.469703 CTCATGGTTCGCAAGCATCAA 59.530 47.619 9.60 3.16 45.81 2.57
1393 1398 1.089112 CTCATGGTTCGCAAGCATCA 58.911 50.000 9.60 0.00 45.81 3.07
1394 1399 0.379669 CCTCATGGTTCGCAAGCATC 59.620 55.000 9.60 0.00 45.81 3.91
1396 1401 0.250684 TTCCTCATGGTTCGCAAGCA 60.251 50.000 0.00 3.82 43.83 3.91
1397 1402 0.449388 CTTCCTCATGGTTCGCAAGC 59.551 55.000 0.00 0.00 34.23 4.01
1398 1403 0.449388 GCTTCCTCATGGTTCGCAAG 59.551 55.000 0.00 0.00 34.23 4.01
1399 1404 0.250684 TGCTTCCTCATGGTTCGCAA 60.251 50.000 0.00 0.00 31.86 4.85
1400 1405 0.035152 ATGCTTCCTCATGGTTCGCA 60.035 50.000 0.00 0.00 36.18 5.10
1401 1406 0.379669 CATGCTTCCTCATGGTTCGC 59.620 55.000 0.00 0.00 39.98 4.70
1407 1412 1.880675 GGCTCATCATGCTTCCTCATG 59.119 52.381 0.00 0.00 43.84 3.07
1463 1469 5.370584 TGTTCTCATACATGGATCCCATCTT 59.629 40.000 9.90 0.00 43.15 2.40
1562 1569 9.712305 GTAGATAGTAACATTACCATCAGCATT 57.288 33.333 11.23 0.00 35.24 3.56
1593 1600 4.783959 AAACCTTTCGTAACAAGTCGAC 57.216 40.909 7.70 7.70 35.82 4.20
1604 1611 3.685756 TGAACTTGTCGAAAACCTTTCGT 59.314 39.130 18.05 1.57 42.09 3.85
1653 1660 3.449737 AGACTTAAGCATTGCTACGGGTA 59.550 43.478 12.39 0.00 38.25 3.69
1663 1670 4.832248 TGATTCGGACAGACTTAAGCATT 58.168 39.130 1.29 0.00 0.00 3.56
1819 1827 0.039708 GCTGGAGCTTGCACACTTTC 60.040 55.000 0.00 0.00 38.21 2.62
1921 1929 7.455058 TGTAAATACAGGCTTCTCCAAAAGTA 58.545 34.615 0.00 0.00 37.29 2.24
1949 1957 1.216710 CGGAGCTCCCACTCACTTC 59.783 63.158 27.20 0.00 38.50 3.01
2004 2012 8.285394 CCAGAAATACTACATCATTTCCAATCG 58.715 37.037 3.98 0.00 40.48 3.34
2018 2026 9.998106 TCCTTTTATGCTATCCAGAAATACTAC 57.002 33.333 0.00 0.00 34.87 2.73
2173 2181 5.656416 TGACTGGTCCATTTTGAACTTCTTT 59.344 36.000 0.00 0.00 0.00 2.52
2247 2255 0.387929 TTCTACGGTGATCGGGCATC 59.612 55.000 0.00 0.00 44.45 3.91
2256 2264 7.556635 TCAATTTCTCTCTATCTTCTACGGTGA 59.443 37.037 0.00 0.00 0.00 4.02
2260 2268 9.796120 ACTTTCAATTTCTCTCTATCTTCTACG 57.204 33.333 0.00 0.00 0.00 3.51
2313 2321 6.017192 GGTACACAGCATTGCATACATGATAA 60.017 38.462 11.91 0.00 0.00 1.75


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

AutoCloner maintained by Alex Coulton.