Multiple sequence alignment - TraesCS7B01G049600

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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 TraesCS7B01G049600 chr7B 100.000 2219 0 0 1 2219 49612493 49610275 0.000000e+00 4098.0
1 TraesCS7B01G049600 chr7B 93.374 1811 103 6 1 1798 49361678 49363484 0.000000e+00 2663.0
2 TraesCS7B01G049600 chr7B 92.882 1447 101 2 1 1446 49587797 49589242 0.000000e+00 2100.0
3 TraesCS7B01G049600 chr7B 93.057 1253 62 11 982 2215 49549784 49548538 0.000000e+00 1808.0
4 TraesCS7B01G049600 chr7B 91.058 794 46 10 1446 2219 49607632 49608420 0.000000e+00 1050.0
5 TraesCS7B01G049600 chr7B 92.162 421 24 5 1798 2212 49368586 49369003 8.830000e-164 586.0
6 TraesCS7B01G049600 chr7B 87.259 259 30 3 1 258 50681320 50681064 2.160000e-75 292.0
7 TraesCS7B01G049600 chr7D 85.671 1326 178 8 1 1320 95834871 95833552 0.000000e+00 1386.0
8 TraesCS7B01G049600 chr7D 85.381 1327 165 18 1 1320 96031677 96030373 0.000000e+00 1349.0
9 TraesCS7B01G049600 chr7D 85.061 1312 188 4 1 1308 95990262 95988955 0.000000e+00 1330.0
10 TraesCS7B01G049600 chr7D 84.725 1329 196 5 1 1324 96017130 96015804 0.000000e+00 1323.0
11 TraesCS7B01G049600 chr7D 84.679 1325 187 9 1 1318 95964250 95962935 0.000000e+00 1308.0
12 TraesCS7B01G049600 chr7D 84.063 1324 189 8 1 1320 95970317 95969012 0.000000e+00 1256.0
13 TraesCS7B01G049600 chr7D 84.933 1188 164 8 144 1320 95976277 95975094 0.000000e+00 1188.0
14 TraesCS7B01G049600 chr7D 88.525 61 5 2 1788 1847 95147017 95146958 3.060000e-09 73.1
15 TraesCS7B01G049600 chr7D 100.000 30 0 0 1962 1991 96079254 96079225 3.080000e-04 56.5
16 TraesCS7B01G049600 chr7A 85.774 949 73 29 1250 2166 98888142 98887224 0.000000e+00 948.0
17 TraesCS7B01G049600 chr7A 80.484 579 111 2 1 578 98730167 98730744 2.020000e-120 442.0
18 TraesCS7B01G049600 chr7A 82.927 246 25 13 1615 1848 99141854 99141614 2.890000e-49 206.0
19 TraesCS7B01G049600 chr5B 96.296 54 2 0 2166 2219 400104819 400104766 3.030000e-14 89.8


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 TraesCS7B01G049600 chr7B 49610275 49612493 2218 True 4098 4098 100.000 1 2219 1 chr7B.!!$R2 2218
1 TraesCS7B01G049600 chr7B 49361678 49363484 1806 False 2663 2663 93.374 1 1798 1 chr7B.!!$F1 1797
2 TraesCS7B01G049600 chr7B 49587797 49589242 1445 False 2100 2100 92.882 1 1446 1 chr7B.!!$F3 1445
3 TraesCS7B01G049600 chr7B 49548538 49549784 1246 True 1808 1808 93.057 982 2215 1 chr7B.!!$R1 1233
4 TraesCS7B01G049600 chr7B 49607632 49608420 788 False 1050 1050 91.058 1446 2219 1 chr7B.!!$F4 773
5 TraesCS7B01G049600 chr7D 95833552 95834871 1319 True 1386 1386 85.671 1 1320 1 chr7D.!!$R2 1319
6 TraesCS7B01G049600 chr7D 96030373 96031677 1304 True 1349 1349 85.381 1 1320 1 chr7D.!!$R8 1319
7 TraesCS7B01G049600 chr7D 95988955 95990262 1307 True 1330 1330 85.061 1 1308 1 chr7D.!!$R6 1307
8 TraesCS7B01G049600 chr7D 96015804 96017130 1326 True 1323 1323 84.725 1 1324 1 chr7D.!!$R7 1323
9 TraesCS7B01G049600 chr7D 95962935 95964250 1315 True 1308 1308 84.679 1 1318 1 chr7D.!!$R3 1317
10 TraesCS7B01G049600 chr7D 95969012 95970317 1305 True 1256 1256 84.063 1 1320 1 chr7D.!!$R4 1319
11 TraesCS7B01G049600 chr7D 95975094 95976277 1183 True 1188 1188 84.933 144 1320 1 chr7D.!!$R5 1176
12 TraesCS7B01G049600 chr7A 98887224 98888142 918 True 948 948 85.774 1250 2166 1 chr7A.!!$R1 916
13 TraesCS7B01G049600 chr7A 98730167 98730744 577 False 442 442 80.484 1 578 1 chr7A.!!$F1 577

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
606 611 0.17904 TTTCGGTCACCTTCACCCAC 60.179 55.0 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2181 2227 0.114364 TCCAGTGAGCAGGTGGTCTA 59.886 55.0 10.35 0.0 42.6 2.59 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
53 54 0.459237 GACACTGCATCCTCCTCGTG 60.459 60.000 0.00 0.00 0.00 4.35
129 130 3.002583 TCTGGCCCATCTCGTGCA 61.003 61.111 0.00 0.00 0.00 4.57
196 197 2.651361 CTCGTCGTCAAGGCCACT 59.349 61.111 5.01 0.00 0.00 4.00
348 349 0.680280 CCATGCCTTCAGCTTGCTCT 60.680 55.000 0.00 0.00 43.55 4.09
354 355 2.613977 GCCTTCAGCTTGCTCTTAGTCA 60.614 50.000 0.00 0.00 38.99 3.41
360 361 2.493675 AGCTTGCTCTTAGTCATCGACA 59.506 45.455 0.00 0.00 34.60 4.35
370 371 0.382158 GTCATCGACATCTCCGCTGA 59.618 55.000 0.00 0.00 32.09 4.26
451 452 0.401356 TGCAAGGTCATCTGCCTGAA 59.599 50.000 0.00 0.00 36.30 3.02
470 475 0.419459 AGGACATGAAGACCCCCTCT 59.581 55.000 0.00 0.00 31.96 3.69
473 478 1.208293 GACATGAAGACCCCCTCTGAC 59.792 57.143 0.00 0.00 0.00 3.51
484 489 3.831651 CCTCTGACGACCTAGGGAT 57.168 57.895 14.81 0.00 0.00 3.85
500 505 2.572104 AGGGATGTTTAAAGAGGCGAGT 59.428 45.455 0.00 0.00 0.00 4.18
513 518 2.811317 CGAGTTGCTGCGACCTCC 60.811 66.667 16.22 5.64 0.00 4.30
516 521 2.031163 GTTGCTGCGACCTCCAGT 59.969 61.111 8.91 0.00 32.93 4.00
519 524 2.031163 GCTGCGACCTCCAGTTGT 59.969 61.111 0.00 0.00 32.93 3.32
584 589 0.337773 TGAGAGACCTCCAGGCATCT 59.662 55.000 0.74 0.74 38.66 2.90
592 597 0.179062 CTCCAGGCATCTCCTTTCGG 60.179 60.000 0.00 0.00 44.75 4.30
606 611 0.179040 TTTCGGTCACCTTCACCCAC 60.179 55.000 0.00 0.00 0.00 4.61
628 633 3.088941 AATTCGAGATGCGGGCGGA 62.089 57.895 0.00 0.00 41.33 5.54
716 721 3.650950 GGCAAGCCACTGGAGGGA 61.651 66.667 6.14 0.00 35.81 4.20
731 736 4.107051 GGAATGCGCGTGCTGCTT 62.107 61.111 23.16 12.67 43.27 3.91
785 790 1.661341 GGCAGATGTTGAGCGATCTT 58.339 50.000 0.90 0.00 0.00 2.40
800 805 0.400213 ATCTTGGAGCAACCGTGGAA 59.600 50.000 0.00 0.00 42.61 3.53
945 952 8.391106 CCAAACATCGGTTAATTTGTTTCAAAA 58.609 29.630 1.60 0.00 39.55 2.44
1098 1106 1.825090 TTGCACTGATGGCGAATTCT 58.175 45.000 3.52 0.00 0.00 2.40
1130 1138 1.964608 CTGCAGGAGGCCATCGAAGA 61.965 60.000 5.01 0.00 43.89 2.87
1186 1194 1.412710 AGCCGAAGATCGCAAGGATTA 59.587 47.619 4.20 0.00 38.82 1.75
1207 1215 3.698029 TTCTTGAGCTCTGCAAACAAC 57.302 42.857 16.19 0.00 0.00 3.32
1210 1218 0.657312 TGAGCTCTGCAAACAACACG 59.343 50.000 16.19 0.00 0.00 4.49
1493 1507 3.069443 CCAAAAATTCCATACCCCATCCG 59.931 47.826 0.00 0.00 0.00 4.18
1517 1531 1.803519 GCGAACTGAGTGAGCTCCG 60.804 63.158 12.15 5.81 40.95 4.63
1576 1590 3.751175 CGCACAGAGAAAGGTTAAATCCA 59.249 43.478 0.00 0.00 0.00 3.41
1583 1597 7.675619 ACAGAGAAAGGTTAAATCCAATTCCAT 59.324 33.333 0.00 0.00 0.00 3.41
1595 1609 5.705397 TCCAATTCCATGTCAGAAGAGAT 57.295 39.130 0.00 0.00 0.00 2.75
1677 1704 7.595502 TCGTATGTCTCTCTTCTTTCTTTCAAC 59.404 37.037 0.00 0.00 0.00 3.18
1752 1779 9.950496 ATCTCTTGTTTCTAGAGCAAATAGAAA 57.050 29.630 17.65 11.70 43.52 2.52
1786 1823 9.719355 TTTGAAGTATATCTAGTTGCAAGAACA 57.281 29.630 0.00 0.00 0.00 3.18
1822 1859 3.936902 TGAACTCTTGTTTGCGTGTAC 57.063 42.857 0.00 0.00 36.39 2.90
2132 2177 1.196104 AGTTAAGGGCCGTGCTACCA 61.196 55.000 0.90 0.00 0.00 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
183 184 1.532604 ATCGACAGTGGCCTTGACGA 61.533 55.000 26.36 26.36 44.07 4.20
232 233 3.126831 CGATCTATGGTGTCTTCCAAGC 58.873 50.000 0.00 0.00 41.09 4.01
348 349 2.033424 CAGCGGAGATGTCGATGACTAA 59.967 50.000 0.00 0.00 45.36 2.24
405 406 2.586792 GAGCTTGGTCCTCGCCAT 59.413 61.111 0.00 0.00 38.48 4.40
430 431 1.001641 AGGCAGATGACCTTGCACC 60.002 57.895 0.00 0.00 31.87 5.01
436 437 0.908198 GTCCTTCAGGCAGATGACCT 59.092 55.000 0.00 0.00 38.35 3.85
451 452 0.419459 AGAGGGGGTCTTCATGTCCT 59.581 55.000 0.00 0.00 27.07 3.85
470 475 4.773674 TCTTTAAACATCCCTAGGTCGTCA 59.226 41.667 8.29 0.00 0.00 4.35
473 478 4.694339 CCTCTTTAAACATCCCTAGGTCG 58.306 47.826 8.29 0.00 0.00 4.79
484 489 2.548057 CAGCAACTCGCCTCTTTAAACA 59.452 45.455 0.00 0.00 44.04 2.83
500 505 1.597854 CAACTGGAGGTCGCAGCAA 60.598 57.895 0.00 0.00 0.00 3.91
513 518 1.180456 TGGATGGGCTTGCACAACTG 61.180 55.000 0.37 0.00 0.00 3.16
516 521 2.267351 CGTGGATGGGCTTGCACAA 61.267 57.895 0.37 0.00 37.77 3.33
592 597 2.270352 TTGATGTGGGTGAAGGTGAC 57.730 50.000 0.00 0.00 0.00 3.67
606 611 0.236711 GCCCGCATCTCGAATTGATG 59.763 55.000 8.40 8.40 42.86 3.07
731 736 0.602638 GAAGCATGGTGTCGTCCACA 60.603 55.000 0.00 0.00 46.44 4.17
785 790 0.958091 CAATTTCCACGGTTGCTCCA 59.042 50.000 0.00 0.00 35.57 3.86
800 805 2.123428 GGAGCCATCGCCTGCAATT 61.123 57.895 0.00 0.00 34.57 2.32
923 930 8.977505 CATCTTTTGAAACAAATTAACCGATGT 58.022 29.630 0.00 0.00 0.00 3.06
964 971 0.040514 CGAATTGCCAGCAACGTCAA 60.041 50.000 7.31 0.00 38.88 3.18
1098 1106 1.267574 CCTGCAGCCCTTCCTCTACA 61.268 60.000 8.66 0.00 0.00 2.74
1130 1138 2.441001 GTCAGGTGAAGATCCATCCCAT 59.559 50.000 0.00 0.00 0.00 4.00
1186 1194 3.633525 TGTTGTTTGCAGAGCTCAAGAAT 59.366 39.130 17.77 0.00 0.00 2.40
1207 1215 5.344066 AGTATAACAGCATCAGTTCTCGTG 58.656 41.667 0.00 0.00 0.00 4.35
1210 1218 5.912396 CGAGAGTATAACAGCATCAGTTCTC 59.088 44.000 0.00 0.00 0.00 2.87
1493 1507 0.784778 CTCACTCAGTTCGCGTTTCC 59.215 55.000 5.77 0.00 0.00 3.13
1517 1531 6.785488 TGTTGTCAGTTCAACTATGTGATC 57.215 37.500 10.18 0.00 45.26 2.92
1576 1590 5.705397 TGGATCTCTTCTGACATGGAATT 57.295 39.130 0.00 0.00 0.00 2.17
1583 1597 4.035814 ACCATCATGGATCTCTTCTGACA 58.964 43.478 11.90 0.00 40.96 3.58
1677 1704 7.755582 AAACCTCAACGAAGATTTTGAAAAG 57.244 32.000 0.00 0.00 31.41 2.27
1991 2028 5.007626 TGCTCACATACGAAATAGAAATGGC 59.992 40.000 0.00 0.00 0.00 4.40
2132 2177 4.599241 ACATTACTCTATATGGGCCAGCTT 59.401 41.667 13.78 0.00 0.00 3.74
2181 2227 0.114364 TCCAGTGAGCAGGTGGTCTA 59.886 55.000 10.35 0.00 42.60 2.59


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

AutoCloner maintained by Alex Coulton.