Multiple sequence alignment - TraesCS4A01G351400

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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 TraesCS4A01G351400 chr4A 100.000 2567 0 0 1 2567 627303137 627300571 0.000000e+00 4741.0
1 TraesCS4A01G351400 chr4A 94.751 2515 105 8 1 2510 627291777 627289285 0.000000e+00 3888.0
2 TraesCS4A01G351400 chr4A 94.054 2506 116 10 1 2495 627168578 627166095 0.000000e+00 3771.0
3 TraesCS4A01G351400 chr4A 93.974 2506 118 10 1 2495 627088927 627086444 0.000000e+00 3760.0
4 TraesCS4A01G351400 chr4A 93.796 2176 104 10 1 2168 627005425 627003273 0.000000e+00 3241.0
5 TraesCS4A01G351400 chr4A 82.244 1346 186 30 952 2260 626990361 626989032 0.000000e+00 1112.0
6 TraesCS4A01G351400 chr4A 84.424 642 79 8 952 1574 627052538 627051899 1.690000e-171 612.0
7 TraesCS4A01G351400 chr4A 83.801 642 82 9 952 1574 627255854 627255216 7.910000e-165 590.0
8 TraesCS4A01G351400 chr4A 83.515 643 83 10 952 1574 627119473 627118834 1.710000e-161 579.0
9 TraesCS4A01G351400 chr4A 95.468 331 12 1 2168 2495 627000913 627000583 2.260000e-145 525.0
10 TraesCS4A01G351400 chr4A 98.684 76 1 0 2492 2567 627284046 627283971 4.460000e-28 135.0
11 TraesCS4A01G351400 chr4A 97.368 76 2 0 2492 2567 626995364 626995289 2.070000e-26 130.0
12 TraesCS4A01G351400 chr4A 97.368 76 2 0 2492 2567 627081225 627081150 2.070000e-26 130.0
13 TraesCS4A01G351400 chr4A 96.053 76 3 0 2492 2567 627160876 627160801 9.640000e-25 124.0
14 TraesCS4A01G351400 chr4A 82.857 105 9 3 2471 2566 626988840 626988736 4.550000e-13 86.1
15 TraesCS4A01G351400 chr5B 89.409 2606 208 35 1 2567 684031058 684033634 0.000000e+00 3221.0
16 TraesCS4A01G351400 chr5B 88.961 2618 209 40 1 2567 684038059 684040647 0.000000e+00 3160.0
17 TraesCS4A01G351400 chr5B 84.433 1349 169 22 935 2260 684049592 684050922 0.000000e+00 1290.0
18 TraesCS4A01G351400 chr5D 91.461 2272 143 27 1 2242 541989328 541991578 0.000000e+00 3073.0
19 TraesCS4A01G351400 chr5D 81.170 1248 189 29 1040 2260 542385284 542386512 0.000000e+00 961.0
20 TraesCS4A01G351400 chr5D 75.151 1159 231 34 1012 2143 542396510 542397638 2.290000e-135 492.0
21 TraesCS4A01G351400 chr5D 91.126 293 16 7 2277 2567 541991579 541991863 3.100000e-104 388.0
22 TraesCS4A01G351400 chr5D 77.632 304 51 14 1959 2258 542097422 542097712 4.390000e-38 169.0
23 TraesCS4A01G351400 chr5D 83.582 134 17 4 1959 2092 542316765 542316893 1.250000e-23 121.0
24 TraesCS4A01G351400 chr7B 72.909 550 114 29 1743 2284 87195526 87195004 9.510000e-35 158.0
25 TraesCS4A01G351400 chr7B 89.062 64 2 3 768 830 528407902 528407961 9.850000e-10 75.0


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 TraesCS4A01G351400 chr4A 627300571 627303137 2566 True 4741.00 4741 100.0000 1 2567 1 chr4A.!!$R11 2566
1 TraesCS4A01G351400 chr4A 627289285 627291777 2492 True 3888.00 3888 94.7510 1 2510 1 chr4A.!!$R10 2509
2 TraesCS4A01G351400 chr4A 627166095 627168578 2483 True 3771.00 3771 94.0540 1 2495 1 chr4A.!!$R7 2494
3 TraesCS4A01G351400 chr4A 627086444 627088927 2483 True 3760.00 3760 93.9740 1 2495 1 chr4A.!!$R4 2494
4 TraesCS4A01G351400 chr4A 627000583 627005425 4842 True 1883.00 3241 94.6320 1 2495 2 chr4A.!!$R13 2494
5 TraesCS4A01G351400 chr4A 627051899 627052538 639 True 612.00 612 84.4240 952 1574 1 chr4A.!!$R2 622
6 TraesCS4A01G351400 chr4A 626988736 626990361 1625 True 599.05 1112 82.5505 952 2566 2 chr4A.!!$R12 1614
7 TraesCS4A01G351400 chr4A 627255216 627255854 638 True 590.00 590 83.8010 952 1574 1 chr4A.!!$R8 622
8 TraesCS4A01G351400 chr4A 627118834 627119473 639 True 579.00 579 83.5150 952 1574 1 chr4A.!!$R5 622
9 TraesCS4A01G351400 chr5B 684031058 684033634 2576 False 3221.00 3221 89.4090 1 2567 1 chr5B.!!$F1 2566
10 TraesCS4A01G351400 chr5B 684038059 684040647 2588 False 3160.00 3160 88.9610 1 2567 1 chr5B.!!$F2 2566
11 TraesCS4A01G351400 chr5B 684049592 684050922 1330 False 1290.00 1290 84.4330 935 2260 1 chr5B.!!$F3 1325
12 TraesCS4A01G351400 chr5D 541989328 541991863 2535 False 1730.50 3073 91.2935 1 2567 2 chr5D.!!$F5 2566
13 TraesCS4A01G351400 chr5D 542385284 542386512 1228 False 961.00 961 81.1700 1040 2260 1 chr5D.!!$F3 1220
14 TraesCS4A01G351400 chr5D 542396510 542397638 1128 False 492.00 492 75.1510 1012 2143 1 chr5D.!!$F4 1131

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
215 218 0.639392 AGCCTGAGGTCCTAGGACAT 59.361 55.0 36.73 33.0 46.2 3.06 F
1352 1386 0.461961 GAGAGTTGCCGCACTAGGAT 59.538 55.0 0.00 0.0 0.0 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1356 1390 0.469331 TCACGAGGTCCCAGACAAGT 60.469 55.000 0.0 0.0 33.68 3.16 R
2425 4916 2.167487 GGGATGTGACTCTGGAACTCTC 59.833 54.545 0.0 0.0 0.00 3.20 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
80 81 9.970395 CATTGAATGTTGTATATGTAATTGGCT 57.030 29.630 0.00 0.00 0.00 4.75
98 99 3.758554 TGGCTTTTTCTTATGCTGACCTC 59.241 43.478 0.00 0.00 0.00 3.85
138 141 3.315191 TGAGTTTTCTTGCACTTAGCCAC 59.685 43.478 0.00 0.00 44.83 5.01
215 218 0.639392 AGCCTGAGGTCCTAGGACAT 59.361 55.000 36.73 33.00 46.20 3.06
276 279 9.687210 ACATTTTGCAAGCTATATGTCATATTG 57.313 29.630 10.59 9.84 0.00 1.90
371 375 7.824779 ACCTACCAATGTTGAGAGAAGATTAAC 59.175 37.037 0.00 0.00 0.00 2.01
547 552 4.426313 CGAAGGGTGGAAGGGGGC 62.426 72.222 0.00 0.00 0.00 5.80
572 581 1.880027 CTTAAGGGAAACGCTTGTGCT 59.120 47.619 10.48 0.00 37.24 4.40
679 689 6.070194 CCCACCTTATCTTGTTTCTTCCTCTA 60.070 42.308 0.00 0.00 0.00 2.43
680 690 6.819146 CCACCTTATCTTGTTTCTTCCTCTAC 59.181 42.308 0.00 0.00 0.00 2.59
681 691 6.819146 CACCTTATCTTGTTTCTTCCTCTACC 59.181 42.308 0.00 0.00 0.00 3.18
682 692 6.731448 ACCTTATCTTGTTTCTTCCTCTACCT 59.269 38.462 0.00 0.00 0.00 3.08
683 693 7.237887 ACCTTATCTTGTTTCTTCCTCTACCTT 59.762 37.037 0.00 0.00 0.00 3.50
684 694 7.766738 CCTTATCTTGTTTCTTCCTCTACCTTC 59.233 40.741 0.00 0.00 0.00 3.46
685 695 6.943899 ATCTTGTTTCTTCCTCTACCTTCT 57.056 37.500 0.00 0.00 0.00 2.85
686 696 6.749036 TCTTGTTTCTTCCTCTACCTTCTT 57.251 37.500 0.00 0.00 0.00 2.52
687 697 6.760291 TCTTGTTTCTTCCTCTACCTTCTTC 58.240 40.000 0.00 0.00 0.00 2.87
688 698 5.485209 TGTTTCTTCCTCTACCTTCTTCC 57.515 43.478 0.00 0.00 0.00 3.46
689 699 5.155905 TGTTTCTTCCTCTACCTTCTTCCT 58.844 41.667 0.00 0.00 0.00 3.36
690 700 5.012148 TGTTTCTTCCTCTACCTTCTTCCTG 59.988 44.000 0.00 0.00 0.00 3.86
691 701 4.405756 TCTTCCTCTACCTTCTTCCTGT 57.594 45.455 0.00 0.00 0.00 4.00
877 887 1.379044 CCTGGCCGCAGATTCCTTT 60.379 57.895 0.00 0.00 0.00 3.11
878 888 0.967380 CCTGGCCGCAGATTCCTTTT 60.967 55.000 0.00 0.00 0.00 2.27
929 939 5.359292 ACCTAGTACTCGCCCTAACTTAAAG 59.641 44.000 0.00 0.00 0.00 1.85
933 943 2.565834 ACTCGCCCTAACTTAAAGCAGA 59.434 45.455 0.00 0.00 0.00 4.26
972 982 0.773644 TCTCTCAAAGCCCAAAGCCT 59.226 50.000 0.00 0.00 45.47 4.58
1006 1036 2.690881 CCCCGAACCCCATGGAGA 60.691 66.667 15.22 0.00 34.81 3.71
1194 1225 3.053291 GATTTCCACGGCGGCACA 61.053 61.111 13.24 0.00 33.14 4.57
1246 1280 2.722201 CCTCCCTTCTTCGTCCCCG 61.722 68.421 0.00 0.00 0.00 5.73
1251 1285 2.283676 TTCTTCGTCCCCGCCTCT 60.284 61.111 0.00 0.00 0.00 3.69
1352 1386 0.461961 GAGAGTTGCCGCACTAGGAT 59.538 55.000 0.00 0.00 0.00 3.24
1356 1390 0.179084 GTTGCCGCACTAGGATGCTA 60.179 55.000 0.00 0.00 43.80 3.49
1417 1451 3.506059 CTCCCCGCGCAGGACTATG 62.506 68.421 12.38 0.00 45.00 2.23
1553 1596 1.154016 CATGCGTCTTCTCGTCCGT 60.154 57.895 0.00 0.00 0.00 4.69
1603 1646 8.669946 TTCGATTGTTATACCAGATGCATTAA 57.330 30.769 0.00 0.00 0.00 1.40
1664 1707 9.832445 GATCTACTTCCTGTTGGATAACAATAA 57.168 33.333 0.00 0.00 45.53 1.40
1671 1714 8.224389 TCCTGTTGGATAACAATAACATCATG 57.776 34.615 0.00 0.00 45.53 3.07
1678 1721 7.502226 TGGATAACAATAACATCATGGAGTTCC 59.498 37.037 6.91 0.00 0.00 3.62
1928 1989 4.080526 GTGTATGGTTGGAGGTATTGGAGT 60.081 45.833 0.00 0.00 0.00 3.85
2378 4869 8.865090 CACAACTAGAAGATGTATAGGAGGAAT 58.135 37.037 0.00 0.00 29.68 3.01
2408 4899 5.406175 GCATTGTTACTTGCATGTGTTTCAT 59.594 36.000 15.08 0.00 38.72 2.57
2425 4916 8.337532 TGTGTTTCATATATTTGCTCTTCATCG 58.662 33.333 0.00 0.00 0.00 3.84
2437 4928 3.489059 GCTCTTCATCGAGAGTTCCAGAG 60.489 52.174 4.08 0.00 44.03 3.35
2446 4937 2.167487 GAGAGTTCCAGAGTCACATCCC 59.833 54.545 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 9.241919 TCATAATTGAGGTCAGCATAAGAAAAA 57.758 29.630 0.00 0.0 0.00 1.94
215 218 4.767928 AGGCAAACAACCGGTTAATCATAA 59.232 37.500 21.79 0.0 39.29 1.90
352 356 7.162082 ACCTTCGTTAATCTTCTCTCAACATT 58.838 34.615 0.00 0.0 0.00 2.71
371 375 1.160137 CCTTTCCTCAGCAACCTTCG 58.840 55.000 0.00 0.0 0.00 3.79
547 552 4.070009 ACAAGCGTTTCCCTTAAGTTAGG 58.930 43.478 0.97 0.0 34.92 2.69
679 689 3.583526 GGAAGAAGGTACAGGAAGAAGGT 59.416 47.826 0.00 0.0 0.00 3.50
680 690 3.841255 AGGAAGAAGGTACAGGAAGAAGG 59.159 47.826 0.00 0.0 0.00 3.46
681 691 4.081365 GGAGGAAGAAGGTACAGGAAGAAG 60.081 50.000 0.00 0.0 0.00 2.85
682 692 3.838903 GGAGGAAGAAGGTACAGGAAGAA 59.161 47.826 0.00 0.0 0.00 2.52
683 693 3.181410 TGGAGGAAGAAGGTACAGGAAGA 60.181 47.826 0.00 0.0 0.00 2.87
684 694 3.173965 TGGAGGAAGAAGGTACAGGAAG 58.826 50.000 0.00 0.0 0.00 3.46
685 695 3.173965 CTGGAGGAAGAAGGTACAGGAA 58.826 50.000 0.00 0.0 0.00 3.36
686 696 2.382305 TCTGGAGGAAGAAGGTACAGGA 59.618 50.000 0.00 0.0 0.00 3.86
687 697 2.821437 TCTGGAGGAAGAAGGTACAGG 58.179 52.381 0.00 0.0 0.00 4.00
688 698 3.386402 GGATCTGGAGGAAGAAGGTACAG 59.614 52.174 0.00 0.0 0.00 2.74
689 699 3.375699 GGATCTGGAGGAAGAAGGTACA 58.624 50.000 0.00 0.0 0.00 2.90
690 700 2.701423 GGGATCTGGAGGAAGAAGGTAC 59.299 54.545 0.00 0.0 0.00 3.34
691 701 2.360423 GGGGATCTGGAGGAAGAAGGTA 60.360 54.545 0.00 0.0 0.00 3.08
842 852 2.032681 GGGCAGCGGAAGAAGTGT 59.967 61.111 0.00 0.0 0.00 3.55
893 903 4.217983 CGAGTACTAGGTGACTTCCAACTT 59.782 45.833 0.00 0.0 40.69 2.66
929 939 3.670627 CGAACAAAATAACTGGGCTCTGC 60.671 47.826 0.00 0.0 0.00 4.26
933 943 4.142038 AGAACGAACAAAATAACTGGGCT 58.858 39.130 0.00 0.0 0.00 5.19
972 982 0.475044 GGGGAAAGTGGGTGTGTGTA 59.525 55.000 0.00 0.0 0.00 2.90
1006 1036 1.301244 CTGGCGAGCTTGTCTGTGT 60.301 57.895 7.19 0.0 0.00 3.72
1010 1040 4.749310 CCGCTGGCGAGCTTGTCT 62.749 66.667 19.00 0.0 43.77 3.41
1352 1386 1.267121 GAGGTCCCAGACAAGTAGCA 58.733 55.000 0.00 0.0 33.68 3.49
1356 1390 0.469331 TCACGAGGTCCCAGACAAGT 60.469 55.000 0.00 0.0 33.68 3.16
1415 1449 1.372582 CACGCCATTGTACTGAGCAT 58.627 50.000 0.00 0.0 0.00 3.79
1417 1451 0.673644 ACCACGCCATTGTACTGAGC 60.674 55.000 0.00 0.0 0.00 4.26
1553 1596 3.000819 CACCCTAGGCACCGGTCA 61.001 66.667 2.59 0.0 0.00 4.02
1603 1646 2.040544 CCGTCGGCTTTGGCAGAAT 61.041 57.895 0.00 0.0 43.52 2.40
1638 1681 9.832445 TTATTGTTATCCAACAGGAAGTAGATC 57.168 33.333 0.00 0.0 45.17 2.75
1664 1707 4.387026 TCCAAAAGGAACTCCATGATGT 57.613 40.909 0.00 0.0 38.49 3.06
1671 1714 5.009110 GCTATGCTTATCCAAAAGGAACTCC 59.991 44.000 0.00 0.0 38.49 3.85
1928 1989 1.794151 CGCACAACCAACTGCATGGA 61.794 55.000 13.35 0.0 43.54 3.41
2378 4869 2.591923 TGCAAGTAACAATGCCAGGAA 58.408 42.857 0.00 0.0 41.87 3.36
2408 4899 7.148641 GGAACTCTCGATGAAGAGCAAATATA 58.851 38.462 0.92 0.0 45.56 0.86
2425 4916 2.167487 GGGATGTGACTCTGGAACTCTC 59.833 54.545 0.00 0.0 0.00 3.20
2437 4928 3.034569 GCAAATTGCGGGATGTGAC 57.965 52.632 0.90 0.0 31.71 3.67
2535 5066 2.191128 ACAAGCCCAAACTCTAGCAG 57.809 50.000 0.00 0.0 0.00 4.24


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

AutoCloner maintained by Alex Coulton.