Multiple sequence alignment - TraesCS7B01G099700

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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 TraesCS7B01G099700 chr7B 100.000 2528 0 0 1 2528 113920647 113923174 0.000000e+00 4669.0
1 TraesCS7B01G099700 chr7B 93.213 663 36 5 1871 2528 113802870 113802212 0.000000e+00 966.0
2 TraesCS7B01G099700 chr7B 88.889 765 78 4 1770 2528 113627115 113626352 0.000000e+00 935.0
3 TraesCS7B01G099700 chr7B 97.436 39 1 0 269 307 51591329 51591291 1.620000e-07 67.6
4 TraesCS7B01G099700 chr7A 94.675 1784 74 12 1 1775 579014446 579012675 0.000000e+00 2748.0
5 TraesCS7B01G099700 chr7A 89.844 768 59 9 1772 2528 151961686 151960927 0.000000e+00 968.0
6 TraesCS7B01G099700 chr5A 94.491 1779 77 12 1 1770 622373704 622375470 0.000000e+00 2723.0
7 TraesCS7B01G099700 chr5A 95.062 162 6 2 1609 1770 564983948 564983789 1.160000e-63 254.0
8 TraesCS7B01G099700 chr5D 87.528 1780 175 27 1 1747 87727724 87725959 0.000000e+00 2013.0
9 TraesCS7B01G099700 chr2A 95.411 1264 55 3 517 1779 667017392 667016131 0.000000e+00 2010.0
10 TraesCS7B01G099700 chr2A 94.175 515 18 6 1 505 667017951 667017439 0.000000e+00 774.0
11 TraesCS7B01G099700 chr3B 93.904 1214 69 5 547 1759 735244949 735246158 0.000000e+00 1827.0
12 TraesCS7B01G099700 chr3A 95.407 762 31 3 488 1248 40815061 40814303 0.000000e+00 1210.0
13 TraesCS7B01G099700 chr3A 93.494 538 32 3 1234 1771 40812003 40811469 0.000000e+00 797.0
14 TraesCS7B01G099700 chr1B 95.576 746 31 2 547 1291 633192737 633191993 0.000000e+00 1194.0
15 TraesCS7B01G099700 chr1B 85.597 611 40 21 120 725 169940000 169940567 4.650000e-167 597.0
16 TraesCS7B01G099700 chr1B 96.124 258 8 2 547 803 679309391 679309647 1.080000e-113 420.0
17 TraesCS7B01G099700 chr1B 81.179 526 59 19 717 1206 169943133 169943654 1.100000e-103 387.0
18 TraesCS7B01G099700 chr1B 91.770 243 18 2 1284 1526 633190252 633190012 1.120000e-88 337.0
19 TraesCS7B01G099700 chr1B 89.412 85 8 1 1686 1770 553900013 553899930 3.440000e-19 106.0
20 TraesCS7B01G099700 chr7D 93.570 762 36 6 1772 2528 151917098 151916345 0.000000e+00 1123.0
21 TraesCS7B01G099700 chr7D 93.421 760 39 4 1772 2528 151791582 151790831 0.000000e+00 1116.0
22 TraesCS7B01G099700 chrUn 88.889 765 78 4 1770 2528 85624322 85625085 0.000000e+00 935.0
23 TraesCS7B01G099700 chrUn 88.889 765 78 4 1770 2528 185555967 185555204 0.000000e+00 935.0
24 TraesCS7B01G099700 chrUn 91.027 691 56 3 1844 2528 85701014 85701704 0.000000e+00 928.0
25 TraesCS7B01G099700 chrUn 91.027 691 56 3 1844 2528 235702668 235701978 0.000000e+00 928.0
26 TraesCS7B01G099700 chrUn 76.758 327 52 11 269 582 392805875 392806190 7.240000e-36 161.0
27 TraesCS7B01G099700 chr6A 78.363 513 91 11 956 1452 143375524 143376032 5.250000e-82 315.0
28 TraesCS7B01G099700 chr6B 77.629 523 88 17 951 1452 204332091 204332605 8.850000e-75 291.0
29 TraesCS7B01G099700 chr3D 77.778 315 50 9 269 582 535746536 535746831 2.580000e-40 176.0
30 TraesCS7B01G099700 chr5B 80.995 221 38 4 323 541 550436207 550435989 3.340000e-39 172.0
31 TraesCS7B01G099700 chr1A 80.000 155 23 6 1631 1779 494813231 494813079 9.560000e-20 108.0
32 TraesCS7B01G099700 chr1A 92.000 50 1 3 269 315 537058238 537058189 1.620000e-07 67.6
33 TraesCS7B01G099700 chr2B 86.207 87 11 1 1684 1770 137438411 137438326 2.680000e-15 93.5
34 TraesCS7B01G099700 chr4A 92.000 50 1 2 269 315 615556904 615556855 1.620000e-07 67.6


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 TraesCS7B01G099700 chr7B 113920647 113923174 2527 False 4669.0 4669 100.0000 1 2528 1 chr7B.!!$F1 2527
1 TraesCS7B01G099700 chr7B 113802212 113802870 658 True 966.0 966 93.2130 1871 2528 1 chr7B.!!$R3 657
2 TraesCS7B01G099700 chr7B 113626352 113627115 763 True 935.0 935 88.8890 1770 2528 1 chr7B.!!$R2 758
3 TraesCS7B01G099700 chr7A 579012675 579014446 1771 True 2748.0 2748 94.6750 1 1775 1 chr7A.!!$R2 1774
4 TraesCS7B01G099700 chr7A 151960927 151961686 759 True 968.0 968 89.8440 1772 2528 1 chr7A.!!$R1 756
5 TraesCS7B01G099700 chr5A 622373704 622375470 1766 False 2723.0 2723 94.4910 1 1770 1 chr5A.!!$F1 1769
6 TraesCS7B01G099700 chr5D 87725959 87727724 1765 True 2013.0 2013 87.5280 1 1747 1 chr5D.!!$R1 1746
7 TraesCS7B01G099700 chr2A 667016131 667017951 1820 True 1392.0 2010 94.7930 1 1779 2 chr2A.!!$R1 1778
8 TraesCS7B01G099700 chr3B 735244949 735246158 1209 False 1827.0 1827 93.9040 547 1759 1 chr3B.!!$F1 1212
9 TraesCS7B01G099700 chr3A 40811469 40815061 3592 True 1003.5 1210 94.4505 488 1771 2 chr3A.!!$R1 1283
10 TraesCS7B01G099700 chr1B 633190012 633192737 2725 True 765.5 1194 93.6730 547 1526 2 chr1B.!!$R2 979
11 TraesCS7B01G099700 chr1B 169940000 169943654 3654 False 492.0 597 83.3880 120 1206 2 chr1B.!!$F2 1086
12 TraesCS7B01G099700 chr7D 151916345 151917098 753 True 1123.0 1123 93.5700 1772 2528 1 chr7D.!!$R2 756
13 TraesCS7B01G099700 chr7D 151790831 151791582 751 True 1116.0 1116 93.4210 1772 2528 1 chr7D.!!$R1 756
14 TraesCS7B01G099700 chrUn 85624322 85625085 763 False 935.0 935 88.8890 1770 2528 1 chrUn.!!$F1 758
15 TraesCS7B01G099700 chrUn 185555204 185555967 763 True 935.0 935 88.8890 1770 2528 1 chrUn.!!$R1 758
16 TraesCS7B01G099700 chrUn 85701014 85701704 690 False 928.0 928 91.0270 1844 2528 1 chrUn.!!$F2 684
17 TraesCS7B01G099700 chrUn 235701978 235702668 690 True 928.0 928 91.0270 1844 2528 1 chrUn.!!$R2 684
18 TraesCS7B01G099700 chr6A 143375524 143376032 508 False 315.0 315 78.3630 956 1452 1 chr6A.!!$F1 496
19 TraesCS7B01G099700 chr6B 204332091 204332605 514 False 291.0 291 77.6290 951 1452 1 chr6B.!!$F1 501

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
834 3472 0.17902 CAGTCCAACCAACTGCTCCA 60.179 55.0 0.0 0.0 37.88 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2019 8778 1.667154 CCTGGCGGACGATCTTCTCA 61.667 60.0 0.0 0.0 0.0 3.27 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
127 133 9.454859 TTTGGTTTTTGAATGTGATTTTAACCT 57.545 25.926 0.00 0.00 34.92 3.50
159 165 2.417924 CCTGTCACTCATCTGTACTGCC 60.418 54.545 0.00 0.00 0.00 4.85
394 412 3.403038 TGTTTAGAAGTCCAAGCAGCTC 58.597 45.455 0.00 0.00 0.00 4.09
536 588 7.556733 TTACGTAGGAATGACAACTGTTTTT 57.443 32.000 0.00 0.00 0.00 1.94
545 597 7.168135 GGAATGACAACTGTTTTTAGAAGCAAG 59.832 37.037 0.00 0.00 0.00 4.01
588 640 4.676109 ACCCTTGATGGATTGATGTTTGA 58.324 39.130 0.00 0.00 38.35 2.69
635 687 6.772716 AGAAGAACATGAAGCAGGTTTTCTAA 59.227 34.615 0.00 0.00 38.49 2.10
793 3420 7.891183 AAGTACAAGTTAGACTGTAGCATTG 57.109 36.000 0.00 0.00 0.00 2.82
794 3421 7.228314 AGTACAAGTTAGACTGTAGCATTGA 57.772 36.000 0.00 0.00 0.00 2.57
795 3422 7.841956 AGTACAAGTTAGACTGTAGCATTGAT 58.158 34.615 0.00 0.00 0.00 2.57
810 3444 4.519350 AGCATTGATCATTGCTATCCTGTG 59.481 41.667 33.03 1.27 43.63 3.66
834 3472 0.179020 CAGTCCAACCAACTGCTCCA 60.179 55.000 0.00 0.00 37.88 3.86
866 3504 2.713154 GACGTGCAAGTTGGCGTT 59.287 55.556 6.76 0.00 37.71 4.84
914 3566 1.558756 CTCTTCCAGAGCCACAAGGAT 59.441 52.381 0.00 0.00 35.30 3.24
1037 3707 2.665185 GAAGCGTGTCCGGCTGTT 60.665 61.111 0.00 0.00 41.39 3.16
1173 3843 3.766691 GCCTCCGTCAACGCCCTA 61.767 66.667 0.00 0.00 38.18 3.53
1241 6231 4.083324 AGCTCATCCAAATGTACGTGTTTG 60.083 41.667 0.00 7.09 35.60 2.93
1416 8156 2.375766 GCGTGCTCCTCTCGTTGTG 61.376 63.158 0.00 0.00 34.47 3.33
1422 8162 1.903877 CTCCTCTCGTTGTGGGCCAT 61.904 60.000 10.70 0.00 0.00 4.40
1625 8366 3.426292 GCATTTCCGCTGGTTTCTTCTAC 60.426 47.826 0.00 0.00 0.00 2.59
1818 8564 0.606096 TGTACACACCATCCGTCCAG 59.394 55.000 0.00 0.00 0.00 3.86
1837 8583 4.104261 TCCAGTTCCTCGACATAGATCCTA 59.896 45.833 0.00 0.00 0.00 2.94
1841 8587 6.148150 CAGTTCCTCGACATAGATCCTACTAC 59.852 46.154 0.00 0.00 0.00 2.73
1842 8588 5.163281 TCCTCGACATAGATCCTACTACC 57.837 47.826 0.00 0.00 0.00 3.18
1857 8603 7.074653 TCCTACTACCACTGAAACATTCTTT 57.925 36.000 0.00 0.00 0.00 2.52
1867 8613 5.241728 ACTGAAACATTCTTTTCTGTAGCCC 59.758 40.000 6.39 0.00 42.52 5.19
2019 8778 3.706373 AAGACATGCCCCGACGCT 61.706 61.111 0.00 0.00 0.00 5.07
2035 8794 1.590259 GCTGAGAAGATCGTCCGCC 60.590 63.158 4.93 0.00 0.00 6.13
2143 8907 7.096551 GGTACATAACTTACCCGTTCTTGTAA 58.903 38.462 0.00 0.00 33.98 2.41
2147 8911 7.335171 ACATAACTTACCCGTTCTTGTAATTCC 59.665 37.037 0.00 0.00 0.00 3.01
2328 9092 2.436109 GGGTGAAGGCCAAGCTCA 59.564 61.111 5.01 0.00 0.00 4.26
2405 9169 2.027073 CGCTGTCGTGCTGGCTAAA 61.027 57.895 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
127 133 0.473755 AGTGACAGGTCCATGTTGCA 59.526 50.000 0.00 0.00 32.25 4.08
321 339 9.090103 TCAGTAAAAAGAGTTCATCTAGAGGAA 57.910 33.333 15.55 15.55 37.23 3.36
536 588 5.995282 TCCGAATTCAAGTTTCTTGCTTCTA 59.005 36.000 6.22 7.23 0.00 2.10
545 597 5.161358 GGTTCCATTCCGAATTCAAGTTTC 58.839 41.667 6.22 0.00 0.00 2.78
557 609 1.064758 TCCATCAAGGGTTCCATTCCG 60.065 52.381 0.00 0.00 38.24 4.30
588 640 2.867624 TGCTGCAAGGACTTTCTTCAT 58.132 42.857 0.00 0.00 0.00 2.57
778 3405 6.609237 GCAATGATCAATGCTACAGTCTAA 57.391 37.500 25.28 0.00 39.46 2.10
789 3416 4.277423 TGCACAGGATAGCAATGATCAATG 59.723 41.667 6.39 6.39 37.90 2.82
791 3418 3.888583 TGCACAGGATAGCAATGATCAA 58.111 40.909 0.00 0.00 37.90 2.57
792 3419 3.564053 TGCACAGGATAGCAATGATCA 57.436 42.857 0.00 0.00 37.90 2.92
793 3420 4.999311 TGTATGCACAGGATAGCAATGATC 59.001 41.667 0.00 0.00 44.88 2.92
794 3421 4.976864 TGTATGCACAGGATAGCAATGAT 58.023 39.130 0.00 0.00 44.88 2.45
795 3422 4.420522 TGTATGCACAGGATAGCAATGA 57.579 40.909 0.00 0.00 44.88 2.57
810 3444 1.200020 GCAGTTGGTTGGACTGTATGC 59.800 52.381 6.18 0.00 44.88 3.14
834 3472 1.004918 CGTCGCCTTGGTTCCTCTT 60.005 57.895 0.00 0.00 0.00 2.85
866 3504 0.944386 GCTCCGACAAAGCTTCACAA 59.056 50.000 0.00 0.00 36.80 3.33
914 3566 3.516700 GTGGTACCCTGACTTTTAGGCTA 59.483 47.826 10.07 0.00 33.86 3.93
938 3603 8.806429 TGATTATACAAATTCTTGGAGAAGCA 57.194 30.769 0.00 0.00 39.91 3.91
1037 3707 2.739292 GTGCACACTTCTTCTCGTACA 58.261 47.619 13.17 0.00 0.00 2.90
1173 3843 2.722201 GGCGACGACCCTCTGGAAT 61.722 63.158 0.00 0.00 34.81 3.01
1241 6231 9.239002 GGATATCAATCGAGCACACTATAATAC 57.761 37.037 4.83 0.00 32.44 1.89
1358 8098 3.535561 GCTACATCACCTAGTGCATGTT 58.464 45.455 13.88 0.00 36.51 2.71
1367 8107 2.724977 GCTATGCGCTACATCACCTA 57.275 50.000 9.73 0.00 40.38 3.08
1391 8131 3.518998 GAGGAGCACGCTCGCCTA 61.519 66.667 12.65 0.00 43.59 3.93
1416 8156 1.153756 CCCTCCAACCATATGGCCC 59.846 63.158 22.18 0.00 40.46 5.80
1422 8162 1.140312 GATGCCTCCCTCCAACCATA 58.860 55.000 0.00 0.00 0.00 2.74
1585 8326 6.018098 GGAAATGCAACACATCTAGATCTCTG 60.018 42.308 1.03 1.37 38.34 3.35
1818 8564 5.412286 GGTAGTAGGATCTATGTCGAGGAAC 59.588 48.000 0.00 0.00 0.00 3.62
1837 8583 6.828785 ACAGAAAAGAATGTTTCAGTGGTAGT 59.171 34.615 0.97 0.00 39.52 2.73
1841 8587 6.145535 GCTACAGAAAAGAATGTTTCAGTGG 58.854 40.000 6.11 4.69 37.66 4.00
1842 8588 6.145535 GGCTACAGAAAAGAATGTTTCAGTG 58.854 40.000 6.11 0.00 37.66 3.66
2019 8778 1.667154 CCTGGCGGACGATCTTCTCA 61.667 60.000 0.00 0.00 0.00 3.27
2035 8794 2.780714 GATGATCTTGGCCATCTCCTG 58.219 52.381 6.09 0.00 36.97 3.86
2143 8907 3.079578 CCATGATCAATAGCAGCGGAAT 58.920 45.455 0.00 0.00 0.00 3.01
2147 8911 3.501062 ACATTCCATGATCAATAGCAGCG 59.499 43.478 0.00 0.00 0.00 5.18
2198 8962 5.395103 GGCATCACAACCCTGCAATTTAATA 60.395 40.000 0.00 0.00 37.64 0.98
2405 9169 4.658786 ACCGGCCAGAAGGGTCCT 62.659 66.667 0.00 0.00 38.37 3.85


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

AutoCloner maintained by Alex Coulton.