Multiple sequence alignment - TraesCS7A01G343100

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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 TraesCS7A01G343100 chr7A 100.000 2216 0 0 1 2216 503325563 503327778 0.000000e+00 4093
1 TraesCS7A01G343100 chr5A 97.157 2216 58 1 1 2216 302990139 302987929 0.000000e+00 3738
2 TraesCS7A01G343100 chr5A 90.462 650 42 4 1 630 475608062 475607413 0.000000e+00 839
3 TraesCS7A01G343100 chr5A 89.062 192 11 9 886 1073 489933001 489933186 1.710000e-56 230
4 TraesCS7A01G343100 chr5A 88.125 160 18 1 2058 2216 256233698 256233857 2.900000e-44 189
5 TraesCS7A01G343100 chr4A 96.872 1886 55 1 1 1886 142904452 142902571 0.000000e+00 3153
6 TraesCS7A01G343100 chr2A 92.937 1076 71 4 1 1072 239932576 239933650 0.000000e+00 1561
7 TraesCS7A01G343100 chr2A 90.239 1004 66 11 1069 2052 684122149 684121158 0.000000e+00 1282
8 TraesCS7A01G343100 chr2A 94.521 292 16 0 339 630 165026526 165026817 3.360000e-123 451
9 TraesCS7A01G343100 chr6B 92.044 1081 76 5 1 1072 389762716 389763795 0.000000e+00 1511
10 TraesCS7A01G343100 chr2B 90.319 1002 74 8 1069 2052 646019654 646018658 0.000000e+00 1291
11 TraesCS7A01G343100 chr2B 91.264 538 40 5 544 1079 391878011 391877479 0.000000e+00 726
12 TraesCS7A01G343100 chr2D 90.081 988 82 8 1069 2044 540639351 540638368 0.000000e+00 1267
13 TraesCS7A01G343100 chr6D 92.719 467 33 1 1 467 162249250 162248785 0.000000e+00 673
14 TraesCS7A01G343100 chr6D 95.417 240 10 1 673 911 162248482 162248243 4.470000e-102 381
15 TraesCS7A01G343100 chr6D 94.012 167 10 0 464 630 162248647 162248481 1.020000e-63 254
16 TraesCS7A01G343100 chr6D 88.043 184 9 8 907 1079 162246656 162246475 2.880000e-49 206
17 TraesCS7A01G343100 chr1B 92.961 412 27 2 84 494 51329209 51329619 1.130000e-167 599
18 TraesCS7A01G343100 chr7B 92.233 412 29 3 84 494 720100904 720100495 4.100000e-162 580
19 TraesCS7A01G343100 chr7B 91.837 245 18 2 645 888 204337716 204337473 7.580000e-90 340
20 TraesCS7A01G343100 chr5B 91.748 412 31 3 84 494 142835899 142836308 8.880000e-159 569
21 TraesCS7A01G343100 chr4B 91.463 246 19 2 645 888 429610675 429610920 9.800000e-89 337
22 TraesCS7A01G343100 chr4B 87.500 192 22 2 436 627 349791502 349791691 1.030000e-53 220
23 TraesCS7A01G343100 chr3A 91.020 245 19 2 645 888 199618473 199618715 5.900000e-86 327
24 TraesCS7A01G343100 chr5D 87.302 189 12 8 886 1073 387250152 387250329 2.880000e-49 206
25 TraesCS7A01G343100 chr3D 88.312 154 17 1 2061 2213 239098004 239097851 1.350000e-42 183


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 TraesCS7A01G343100 chr7A 503325563 503327778 2215 False 4093.0 4093 100.00000 1 2216 1 chr7A.!!$F1 2215
1 TraesCS7A01G343100 chr5A 302987929 302990139 2210 True 3738.0 3738 97.15700 1 2216 1 chr5A.!!$R1 2215
2 TraesCS7A01G343100 chr5A 475607413 475608062 649 True 839.0 839 90.46200 1 630 1 chr5A.!!$R2 629
3 TraesCS7A01G343100 chr4A 142902571 142904452 1881 True 3153.0 3153 96.87200 1 1886 1 chr4A.!!$R1 1885
4 TraesCS7A01G343100 chr2A 239932576 239933650 1074 False 1561.0 1561 92.93700 1 1072 1 chr2A.!!$F2 1071
5 TraesCS7A01G343100 chr2A 684121158 684122149 991 True 1282.0 1282 90.23900 1069 2052 1 chr2A.!!$R1 983
6 TraesCS7A01G343100 chr6B 389762716 389763795 1079 False 1511.0 1511 92.04400 1 1072 1 chr6B.!!$F1 1071
7 TraesCS7A01G343100 chr2B 646018658 646019654 996 True 1291.0 1291 90.31900 1069 2052 1 chr2B.!!$R2 983
8 TraesCS7A01G343100 chr2B 391877479 391878011 532 True 726.0 726 91.26400 544 1079 1 chr2B.!!$R1 535
9 TraesCS7A01G343100 chr2D 540638368 540639351 983 True 1267.0 1267 90.08100 1069 2044 1 chr2D.!!$R1 975
10 TraesCS7A01G343100 chr6D 162246475 162249250 2775 True 378.5 673 92.54775 1 1079 4 chr6D.!!$R1 1078

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
146 148 0.250234 CCATCCTCTTCTGCGACCAA 59.75 55.0 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1509 3307 1.341531 CTCAACCAACACTCGTCCTCT 59.658 52.381 0.0 0.0 0.0 3.69 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
142 144 0.904865 ACACCCATCCTCTTCTGCGA 60.905 55.000 0.00 0.00 0.00 5.10
146 148 0.250234 CCATCCTCTTCTGCGACCAA 59.750 55.000 0.00 0.00 0.00 3.67
330 332 5.456548 TCAATTACAGGTCACTAACGACA 57.543 39.130 0.00 0.00 37.66 4.35
377 379 4.042809 TGGCCCTCTAGAAGTTCAATTTGA 59.957 41.667 0.00 0.00 0.00 2.69
526 671 3.697045 CACTCCTCTAACTAGTCCTGTGG 59.303 52.174 0.00 0.48 0.00 4.17
560 725 1.002087 ACTCCTAGGTTCGGCACAAAG 59.998 52.381 9.08 0.00 0.00 2.77
562 727 2.232941 CTCCTAGGTTCGGCACAAAGTA 59.767 50.000 9.08 0.00 0.00 2.24
655 820 4.770010 GGAATTGGTCAATGTTGTTCCCTA 59.230 41.667 0.00 0.00 0.00 3.53
700 866 7.361127 TCAATCGTCGATTCCTATTCTCTAAC 58.639 38.462 17.43 0.00 28.87 2.34
869 1035 3.246226 CGAAGACGAGGGATGCTATTTTG 59.754 47.826 0.00 0.00 42.66 2.44
943 2700 2.164624 GCAGTACGTGTCTCTCTCCATT 59.835 50.000 0.00 0.00 0.00 3.16
958 2715 6.256819 TCTCTCCATTGTCCTTCTCTCTTTA 58.743 40.000 0.00 0.00 0.00 1.85
1095 2871 2.396700 TCGTCGCCATAACGAGCTA 58.603 52.632 0.00 0.00 43.65 3.32
1237 3022 0.107508 CCGTTGGTGCTCAGGATCAT 60.108 55.000 0.00 0.00 0.00 2.45
1509 3307 5.007034 TGTCAGAGTGTTTCACAAAAAGGA 58.993 37.500 2.80 0.00 36.74 3.36
1799 3619 6.426937 CCAAAGAAACCTAAATCGAAGTCTCA 59.573 38.462 0.00 0.00 0.00 3.27
1846 3667 7.237471 ACCACATGATGAATCCACATATACCTA 59.763 37.037 0.00 0.00 0.00 3.08
1886 3707 1.663695 CGAACCAATACGGAAGCCAT 58.336 50.000 0.00 0.00 38.63 4.40
2028 3851 1.915141 CTTGTCTTTGCACCCCAGAT 58.085 50.000 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
323 325 6.152932 ACCTTTCTCTTTGTAGTGTCGTTA 57.847 37.500 0.00 0.00 0.00 3.18
330 332 4.689612 TGCTGACCTTTCTCTTTGTAGT 57.310 40.909 0.00 0.00 0.00 2.73
526 671 0.106419 AGGAGTCGAGGAGATCACCC 60.106 60.000 5.46 0.61 0.00 4.61
560 725 8.485976 ACTCAGAAGATGCTTACAATTCTTAC 57.514 34.615 0.00 0.00 35.07 2.34
562 727 7.992754 AACTCAGAAGATGCTTACAATTCTT 57.007 32.000 0.00 0.00 35.07 2.52
700 866 7.590322 CAGTTGAACTTCAGACATCAAAATCAG 59.410 37.037 0.00 0.00 33.93 2.90
869 1035 2.802247 GCTGATTCACAAAAGCAAACCC 59.198 45.455 0.00 0.00 35.69 4.11
943 2700 6.957020 AGAGAAAGGATAAAGAGAGAAGGACA 59.043 38.462 0.00 0.00 0.00 4.02
958 2715 4.949856 GTGAGAGAGTGAGAGAGAAAGGAT 59.050 45.833 0.00 0.00 0.00 3.24
1095 2871 3.808618 GCCTGTCAAGTCTGTTTGGAGAT 60.809 47.826 0.00 0.00 0.00 2.75
1237 3022 3.007074 TGCATGGTTGAACTACCGAAGTA 59.993 43.478 0.00 0.00 41.28 2.24
1509 3307 1.341531 CTCAACCAACACTCGTCCTCT 59.658 52.381 0.00 0.00 0.00 3.69
1799 3619 5.480073 TGGTATGGAACTTTATGCAGCTTTT 59.520 36.000 0.00 0.00 0.00 2.27
1846 3667 1.660607 CATCGCGCTCTGTACATTGTT 59.339 47.619 5.56 0.00 0.00 2.83
1886 3707 4.098349 GCTCATTTTCAGGTTCATGGCATA 59.902 41.667 0.00 0.00 0.00 3.14
2028 3851 8.579850 AAATGCTTCATGTTCAGGATAAACTA 57.420 30.769 0.00 0.00 0.00 2.24
2169 3992 7.119116 ACCATTGGACTTTTTGTTTTGTTCTTC 59.881 33.333 10.37 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.