Multiple sequence alignment - TraesCS3A01G203200

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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 TraesCS3A01G203200 chr3A 100.000 2264 0 0 1 2264 349013698 349015961 0 4181
1 TraesCS3A01G203200 chr3A 96.207 580 20 2 1686 2264 581423813 581424391 0 948
2 TraesCS3A01G203200 chr5D 96.389 997 35 1 700 1695 348341943 348342939 0 1640
3 TraesCS3A01G203200 chr5D 96.398 583 17 4 1684 2264 433083176 433083756 0 957
4 TraesCS3A01G203200 chr5D 97.018 570 16 1 1696 2264 530120909 530121478 0 957
5 TraesCS3A01G203200 chr6D 96.012 1003 39 1 694 1695 377212899 377213901 0 1629
6 TraesCS3A01G203200 chr6D 95.214 1003 47 1 694 1695 62141934 62142936 0 1585
7 TraesCS3A01G203200 chr6D 96.857 700 20 1 1 700 62140154 62140851 0 1170
8 TraesCS3A01G203200 chr7D 95.509 1002 45 0 694 1695 131690088 131691089 0 1602
9 TraesCS3A01G203200 chr7D 95.214 1003 46 2 694 1695 528561881 528562882 0 1585
10 TraesCS3A01G203200 chr7D 97.286 700 19 0 1 700 460798800 460799499 0 1188
11 TraesCS3A01G203200 chr7D 96.718 579 18 1 1686 2263 83727393 83726815 0 963
12 TraesCS3A01G203200 chr7D 96.707 577 17 2 1689 2264 65959848 65960423 0 959
13 TraesCS3A01G203200 chr7D 96.690 574 17 2 1692 2264 234568356 234568928 0 953
14 TraesCS3A01G203200 chr7D 96.367 578 19 2 1687 2264 146025164 146024589 0 950
15 TraesCS3A01G203200 chr2D 95.513 1003 43 2 694 1695 619854325 619855326 0 1602
16 TraesCS3A01G203200 chr2D 97.143 700 20 0 1 700 619852543 619853242 0 1182
17 TraesCS3A01G203200 chr2D 97.004 701 19 2 1 700 152000123 152000822 0 1177
18 TraesCS3A01G203200 chr3D 95.414 1003 45 1 694 1695 446923118 446924120 0 1596
19 TraesCS3A01G203200 chr3D 97.000 700 21 0 1 700 446921336 446922035 0 1177
20 TraesCS3A01G203200 chr3D 97.018 570 15 2 1696 2264 94934754 94934186 0 957
21 TraesCS3A01G203200 chr4D 95.486 997 44 1 700 1695 470195938 470194942 0 1591
22 TraesCS3A01G203200 chr4D 96.571 700 23 1 1 700 450519145 450519843 0 1158
23 TraesCS3A01G203200 chr4D 96.286 700 26 0 1 700 470197726 470197027 0 1149
24 TraesCS3A01G203200 chrUn 95.309 1002 46 1 694 1695 10399867 10400867 0 1589
25 TraesCS3A01G203200 chr2B 96.429 700 24 1 1 700 546618116 546618814 0 1153
26 TraesCS3A01G203200 chr2B 96.418 698 25 0 1 698 465666286 465665589 0 1151
27 TraesCS3A01G203200 chr1D 96.864 574 15 3 1692 2264 255874153 255874724 0 957


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 TraesCS3A01G203200 chr3A 349013698 349015961 2263 False 4181.0 4181 100.0000 1 2264 1 chr3A.!!$F1 2263
1 TraesCS3A01G203200 chr3A 581423813 581424391 578 False 948.0 948 96.2070 1686 2264 1 chr3A.!!$F2 578
2 TraesCS3A01G203200 chr5D 348341943 348342939 996 False 1640.0 1640 96.3890 700 1695 1 chr5D.!!$F1 995
3 TraesCS3A01G203200 chr5D 433083176 433083756 580 False 957.0 957 96.3980 1684 2264 1 chr5D.!!$F2 580
4 TraesCS3A01G203200 chr5D 530120909 530121478 569 False 957.0 957 97.0180 1696 2264 1 chr5D.!!$F3 568
5 TraesCS3A01G203200 chr6D 377212899 377213901 1002 False 1629.0 1629 96.0120 694 1695 1 chr6D.!!$F1 1001
6 TraesCS3A01G203200 chr6D 62140154 62142936 2782 False 1377.5 1585 96.0355 1 1695 2 chr6D.!!$F2 1694
7 TraesCS3A01G203200 chr7D 131690088 131691089 1001 False 1602.0 1602 95.5090 694 1695 1 chr7D.!!$F2 1001
8 TraesCS3A01G203200 chr7D 528561881 528562882 1001 False 1585.0 1585 95.2140 694 1695 1 chr7D.!!$F5 1001
9 TraesCS3A01G203200 chr7D 460798800 460799499 699 False 1188.0 1188 97.2860 1 700 1 chr7D.!!$F4 699
10 TraesCS3A01G203200 chr7D 83726815 83727393 578 True 963.0 963 96.7180 1686 2263 1 chr7D.!!$R1 577
11 TraesCS3A01G203200 chr7D 65959848 65960423 575 False 959.0 959 96.7070 1689 2264 1 chr7D.!!$F1 575
12 TraesCS3A01G203200 chr7D 234568356 234568928 572 False 953.0 953 96.6900 1692 2264 1 chr7D.!!$F3 572
13 TraesCS3A01G203200 chr7D 146024589 146025164 575 True 950.0 950 96.3670 1687 2264 1 chr7D.!!$R2 577
14 TraesCS3A01G203200 chr2D 619852543 619855326 2783 False 1392.0 1602 96.3280 1 1695 2 chr2D.!!$F2 1694
15 TraesCS3A01G203200 chr2D 152000123 152000822 699 False 1177.0 1177 97.0040 1 700 1 chr2D.!!$F1 699
16 TraesCS3A01G203200 chr3D 446921336 446924120 2784 False 1386.5 1596 96.2070 1 1695 2 chr3D.!!$F1 1694
17 TraesCS3A01G203200 chr3D 94934186 94934754 568 True 957.0 957 97.0180 1696 2264 1 chr3D.!!$R1 568
18 TraesCS3A01G203200 chr4D 470194942 470197726 2784 True 1370.0 1591 95.8860 1 1695 2 chr4D.!!$R1 1694
19 TraesCS3A01G203200 chr4D 450519145 450519843 698 False 1158.0 1158 96.5710 1 700 1 chr4D.!!$F1 699
20 TraesCS3A01G203200 chrUn 10399867 10400867 1000 False 1589.0 1589 95.3090 694 1695 1 chrUn.!!$F1 1001
21 TraesCS3A01G203200 chr2B 546618116 546618814 698 False 1153.0 1153 96.4290 1 700 1 chr2B.!!$F1 699
22 TraesCS3A01G203200 chr2B 465665589 465666286 697 True 1151.0 1151 96.4180 1 698 1 chr2B.!!$R1 697
23 TraesCS3A01G203200 chr1D 255874153 255874724 571 False 957.0 957 96.8640 1692 2264 1 chr1D.!!$F1 572

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
311 312 0.174162 GCATGGATGGTGAAGGCAAC 59.826 55.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1805 2900 0.038159 ACTTCTACGACAGCACAGGC 60.038 55.0 0.0 0.0 41.61 4.85 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
176 177 0.311790 GGACACCGTCAACTCACGTA 59.688 55.000 0.00 0.00 38.14 3.57
311 312 0.174162 GCATGGATGGTGAAGGCAAC 59.826 55.000 0.00 0.00 0.00 4.17
449 450 3.585862 GAGTGTTTCATCGTGCCTTCTA 58.414 45.455 0.00 0.00 0.00 2.10
576 577 4.870636 TGGCCCACTCTTCAAATGATAAT 58.129 39.130 0.00 0.00 0.00 1.28
626 627 4.515191 GCCTTTGGAGCACGATGATAATTA 59.485 41.667 0.00 0.00 0.00 1.40
663 664 2.821969 GCATGTGAGAACCAAGGTGATT 59.178 45.455 0.00 0.00 0.00 2.57
698 1788 3.650281 ATGCATTATATCGGATGGCCA 57.350 42.857 8.56 8.56 0.00 5.36
702 1792 3.889815 CATTATATCGGATGGCCATGGT 58.110 45.455 26.56 8.75 0.00 3.55
825 1916 3.399181 GGCCGTGGATCTGGTGGA 61.399 66.667 0.00 0.00 0.00 4.02
877 1968 2.930040 CCTATCGACGTGTTGCTCAATT 59.070 45.455 0.00 0.00 0.00 2.32
883 1974 2.927477 GACGTGTTGCTCAATTCGGATA 59.073 45.455 0.00 0.00 0.00 2.59
963 2054 3.191162 TGCCTCTTTACATGTCAATGTGC 59.809 43.478 0.00 0.69 46.66 4.57
1034 2128 2.717044 CCATGACGAGGCCACCGTA 61.717 63.158 20.66 11.20 40.67 4.02
1074 2168 1.594293 ACACAAGTGGAAGGACGCG 60.594 57.895 3.53 3.53 34.19 6.01
1103 2197 4.006319 GACAAGGTGAAGGAGAAAGATGG 58.994 47.826 0.00 0.00 0.00 3.51
1112 2206 5.490357 TGAAGGAGAAAGATGGGAAGATTCT 59.510 40.000 0.00 0.00 33.28 2.40
1137 2231 3.011566 TGTTGGTGTGGAGATGTTTGT 57.988 42.857 0.00 0.00 0.00 2.83
1220 2314 3.146066 GCCCCAATTATGCTTACGATCA 58.854 45.455 0.00 0.00 0.00 2.92
1224 2318 4.456911 CCCAATTATGCTTACGATCATGCT 59.543 41.667 0.00 0.00 0.00 3.79
1236 2330 5.028549 ACGATCATGCTCTTCCAACTAAT 57.971 39.130 0.00 0.00 0.00 1.73
1343 2437 0.531532 CCGCCTCCTCTATGCAAGTG 60.532 60.000 0.00 0.00 0.00 3.16
1411 2505 7.182930 AGGACCAATTAGAAGATTGTCTTAGGT 59.817 37.037 0.00 0.00 36.73 3.08
1420 2514 1.476845 TTGTCTTAGGTGCCAGCGGA 61.477 55.000 0.00 0.00 0.00 5.54
1459 2553 2.037385 AAGAGGCTTGGAGGAAGAGT 57.963 50.000 0.00 0.00 32.82 3.24
1465 2559 1.270358 GCTTGGAGGAAGAGTGTCGTT 60.270 52.381 0.00 0.00 32.82 3.85
1492 2586 2.172293 GAGAGGATGGAGTGGAAGCAAT 59.828 50.000 0.00 0.00 0.00 3.56
1518 2612 4.704833 GAGAGGGCACGCCAAGCA 62.705 66.667 10.83 0.00 37.98 3.91
1596 2690 0.904865 AGGAGGATGAGGCACGTGAA 60.905 55.000 22.23 0.91 0.00 3.18
1599 2693 1.464997 GAGGATGAGGCACGTGAAAAC 59.535 52.381 22.23 5.78 0.00 2.43
1635 2729 4.503991 CCCCATATGACTCAGTAAAGCCTC 60.504 50.000 3.65 0.00 0.00 4.70
1747 2841 2.166870 ACGTGTTTGTCACAGTAGGTCA 59.833 45.455 0.00 0.00 46.44 4.02
1932 3027 2.048222 ACTGACACGTGGCATCCG 60.048 61.111 27.26 16.46 29.25 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
176 177 9.277783 GCAACAATTTGTATCCTAGATACTCAT 57.722 33.333 14.13 5.32 34.90 2.90
311 312 2.485426 CCATGCAACATCCTAATAGCGG 59.515 50.000 0.00 0.00 0.00 5.52
397 398 2.514592 CACCCGATGGCGCATTCT 60.515 61.111 10.83 0.00 35.83 2.40
449 450 3.159472 TCAATGCATTGTCCAAAGCTCT 58.841 40.909 32.67 0.00 38.84 4.09
524 525 4.081531 CCATCAATGTGCCCTTGTATTTGT 60.082 41.667 0.00 0.00 0.00 2.83
626 627 1.217057 ATGCCCCATGAACCACTCCT 61.217 55.000 0.00 0.00 0.00 3.69
663 664 1.153369 GCATACCTCTCGCTTGCCA 60.153 57.895 0.00 0.00 0.00 4.92
698 1788 2.670148 GCCCTTCCTCCACGACCAT 61.670 63.158 0.00 0.00 0.00 3.55
702 1792 2.058595 GCTAGCCCTTCCTCCACGA 61.059 63.158 2.29 0.00 0.00 4.35
771 1862 0.679002 TAGTCCTTCCTCCACGACCG 60.679 60.000 0.00 0.00 0.00 4.79
819 1910 1.471119 GACGTGTCCTAGATCCACCA 58.529 55.000 0.00 0.00 0.00 4.17
825 1916 0.815734 CAACCCGACGTGTCCTAGAT 59.184 55.000 0.00 0.00 0.00 1.98
877 1968 7.773224 ACCATTCACATTATTTCAACTATCCGA 59.227 33.333 0.00 0.00 0.00 4.55
883 1974 9.959721 AGTAGTACCATTCACATTATTTCAACT 57.040 29.630 0.00 0.00 0.00 3.16
1034 2128 2.089980 GCATGTCTTCTTGGTGAGCAT 58.910 47.619 0.00 0.00 0.00 3.79
1074 2168 3.142174 CTCCTTCACCTTGTCCAAAGAC 58.858 50.000 0.00 0.00 43.83 3.01
1103 2197 2.165030 CACCAACATGGCAGAATCTTCC 59.835 50.000 0.00 0.00 42.67 3.46
1112 2206 0.405198 ATCTCCACACCAACATGGCA 59.595 50.000 0.00 0.00 42.67 4.92
1198 2292 1.588674 TCGTAAGCATAATTGGGGCG 58.411 50.000 0.00 0.00 37.18 6.13
1220 2314 3.659183 AGGCATTAGTTGGAAGAGCAT 57.341 42.857 0.00 0.00 0.00 3.79
1224 2318 4.721776 AGGTCATAGGCATTAGTTGGAAGA 59.278 41.667 0.00 0.00 0.00 2.87
1236 2330 1.622607 CCGGTGGAAGGTCATAGGCA 61.623 60.000 0.00 0.00 0.00 4.75
1343 2437 4.268797 TCATGATCTATCCAGCTGAAGC 57.731 45.455 17.39 0.00 42.49 3.86
1411 2505 1.741401 CTTCGAACATCCGCTGGCA 60.741 57.895 0.00 0.00 0.00 4.92
1420 2514 6.238759 CCTCTTTGAAACCTTTCTTCGAACAT 60.239 38.462 0.00 0.00 38.02 2.71
1459 2553 4.341487 TCCATCCTCTCTTTCTAACGACA 58.659 43.478 0.00 0.00 0.00 4.35
1465 2559 4.609866 TCCACTCCATCCTCTCTTTCTA 57.390 45.455 0.00 0.00 0.00 2.10
1492 2586 4.382541 TGCCCTCTCCTCCTCGCA 62.383 66.667 0.00 0.00 0.00 5.10
1518 2612 0.321122 CCTCCTCACGAGCAAGCTTT 60.321 55.000 0.00 0.00 37.27 3.51
1596 2690 2.772102 GGGCCATTTCCCCTTGTTT 58.228 52.632 4.39 0.00 40.51 2.83
1805 2900 0.038159 ACTTCTACGACAGCACAGGC 60.038 55.000 0.00 0.00 41.61 4.85
1874 2969 0.643310 TGTGACGCGCGATTTATCAC 59.357 50.000 39.36 34.50 40.08 3.06


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

AutoCloner maintained by Alex Coulton.