Multiple sequence alignment - TraesCS2B01G370500

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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 TraesCS2B01G370500 chr2B 100.000 3600 0 0 1 3600 528469517 528473116 0.000000e+00 6649.0
1 TraesCS2B01G370500 chr2B 94.418 1451 66 4 2151 3600 618309226 618307790 0.000000e+00 2217.0
2 TraesCS2B01G370500 chr2B 93.969 514 29 2 1 514 576041883 576041372 0.000000e+00 776.0
3 TraesCS2B01G370500 chr2B 93.385 514 33 1 1 514 545326743 545326231 0.000000e+00 760.0
4 TraesCS2B01G370500 chr7A 93.911 3022 144 17 593 3600 690713465 690716460 0.000000e+00 4525.0
5 TraesCS2B01G370500 chr7A 94.279 2255 116 6 593 2835 543306375 543304122 0.000000e+00 3437.0
6 TraesCS2B01G370500 chr3A 94.930 2505 106 9 512 3001 10028235 10025737 0.000000e+00 3903.0
7 TraesCS2B01G370500 chr3A 93.366 2035 91 23 593 2615 743896894 743894892 0.000000e+00 2970.0
8 TraesCS2B01G370500 chr3A 94.297 1701 65 11 1148 2835 243091544 243089863 0.000000e+00 2575.0
9 TraesCS2B01G370500 chr3A 97.181 603 16 1 2999 3600 10011692 10011090 0.000000e+00 1018.0
10 TraesCS2B01G370500 chr3A 95.525 514 23 0 1 514 10028777 10028264 0.000000e+00 822.0
11 TraesCS2B01G370500 chr3A 94.444 72 3 1 508 579 259334574 259334504 3.800000e-20 110.0
12 TraesCS2B01G370500 chr2D 96.183 1703 51 7 593 2282 152014903 152013202 0.000000e+00 2772.0
13 TraesCS2B01G370500 chr1B 95.373 1729 67 8 1846 3564 681772679 681774404 0.000000e+00 2737.0
14 TraesCS2B01G370500 chr1B 95.404 892 38 2 508 1397 681771797 681772687 0.000000e+00 1417.0
15 TraesCS2B01G370500 chr1B 94.757 515 26 1 1 514 681771257 681771771 0.000000e+00 800.0
16 TraesCS2B01G370500 chr6B 94.536 1281 59 6 593 1864 26548347 26549625 0.000000e+00 1967.0
17 TraesCS2B01G370500 chr6B 94.118 68 4 0 512 579 297413767 297413834 1.770000e-18 104.0
18 TraesCS2B01G370500 chr6B 91.667 72 6 0 508 579 375611196 375611125 2.290000e-17 100.0
19 TraesCS2B01G370500 chr4A 94.237 1180 59 4 1833 3003 678379622 678380801 0.000000e+00 1794.0
20 TraesCS2B01G370500 chr3B 91.568 1269 71 17 1745 3003 59963891 59962649 0.000000e+00 1718.0
21 TraesCS2B01G370500 chr3B 93.733 1101 58 9 593 1689 59965139 59964046 0.000000e+00 1640.0
22 TraesCS2B01G370500 chr3B 94.490 490 22 3 25 514 284560973 284560489 0.000000e+00 750.0
23 TraesCS2B01G370500 chr3B 93.056 72 4 1 508 579 284560463 284560393 1.770000e-18 104.0
24 TraesCS2B01G370500 chr3B 97.619 42 1 0 1707 1748 59964046 59964005 4.990000e-09 73.1
25 TraesCS2B01G370500 chr5A 95.813 1027 41 2 2576 3600 670326333 670327359 0.000000e+00 1657.0
26 TraesCS2B01G370500 chr5A 93.623 1035 52 5 1556 2580 670320544 670321574 0.000000e+00 1533.0
27 TraesCS2B01G370500 chr7B 93.642 1101 59 9 593 1689 161224769 161225862 0.000000e+00 1635.0
28 TraesCS2B01G370500 chr5B 93.814 582 32 2 1 579 206480151 206479571 0.000000e+00 872.0
29 TraesCS2B01G370500 chr5B 95.136 514 25 0 1 514 120533468 120532955 0.000000e+00 811.0
30 TraesCS2B01G370500 chr5B 94.358 514 26 2 1 514 392495758 392496268 0.000000e+00 785.0
31 TraesCS2B01G370500 chr5B 94.444 72 4 0 508 579 120532929 120532858 1.060000e-20 111.0
32 TraesCS2B01G370500 chr5B 93.056 72 4 1 508 579 170579504 170579574 1.770000e-18 104.0
33 TraesCS2B01G370500 chr4B 93.385 514 28 5 1 514 421854689 421854182 0.000000e+00 756.0


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 TraesCS2B01G370500 chr2B 528469517 528473116 3599 False 6649.000000 6649 100.000000 1 3600 1 chr2B.!!$F1 3599
1 TraesCS2B01G370500 chr2B 618307790 618309226 1436 True 2217.000000 2217 94.418000 2151 3600 1 chr2B.!!$R3 1449
2 TraesCS2B01G370500 chr2B 576041372 576041883 511 True 776.000000 776 93.969000 1 514 1 chr2B.!!$R2 513
3 TraesCS2B01G370500 chr2B 545326231 545326743 512 True 760.000000 760 93.385000 1 514 1 chr2B.!!$R1 513
4 TraesCS2B01G370500 chr7A 690713465 690716460 2995 False 4525.000000 4525 93.911000 593 3600 1 chr7A.!!$F1 3007
5 TraesCS2B01G370500 chr7A 543304122 543306375 2253 True 3437.000000 3437 94.279000 593 2835 1 chr7A.!!$R1 2242
6 TraesCS2B01G370500 chr3A 743894892 743896894 2002 True 2970.000000 2970 93.366000 593 2615 1 chr3A.!!$R4 2022
7 TraesCS2B01G370500 chr3A 243089863 243091544 1681 True 2575.000000 2575 94.297000 1148 2835 1 chr3A.!!$R2 1687
8 TraesCS2B01G370500 chr3A 10025737 10028777 3040 True 2362.500000 3903 95.227500 1 3001 2 chr3A.!!$R5 3000
9 TraesCS2B01G370500 chr3A 10011090 10011692 602 True 1018.000000 1018 97.181000 2999 3600 1 chr3A.!!$R1 601
10 TraesCS2B01G370500 chr2D 152013202 152014903 1701 True 2772.000000 2772 96.183000 593 2282 1 chr2D.!!$R1 1689
11 TraesCS2B01G370500 chr1B 681771257 681774404 3147 False 1651.333333 2737 95.178000 1 3564 3 chr1B.!!$F1 3563
12 TraesCS2B01G370500 chr6B 26548347 26549625 1278 False 1967.000000 1967 94.536000 593 1864 1 chr6B.!!$F1 1271
13 TraesCS2B01G370500 chr4A 678379622 678380801 1179 False 1794.000000 1794 94.237000 1833 3003 1 chr4A.!!$F1 1170
14 TraesCS2B01G370500 chr3B 59962649 59965139 2490 True 1143.700000 1718 94.306667 593 3003 3 chr3B.!!$R1 2410
15 TraesCS2B01G370500 chr3B 284560393 284560973 580 True 427.000000 750 93.773000 25 579 2 chr3B.!!$R2 554
16 TraesCS2B01G370500 chr5A 670326333 670327359 1026 False 1657.000000 1657 95.813000 2576 3600 1 chr5A.!!$F2 1024
17 TraesCS2B01G370500 chr5A 670320544 670321574 1030 False 1533.000000 1533 93.623000 1556 2580 1 chr5A.!!$F1 1024
18 TraesCS2B01G370500 chr7B 161224769 161225862 1093 False 1635.000000 1635 93.642000 593 1689 1 chr7B.!!$F1 1096
19 TraesCS2B01G370500 chr5B 206479571 206480151 580 True 872.000000 872 93.814000 1 579 1 chr5B.!!$R1 578
20 TraesCS2B01G370500 chr5B 392495758 392496268 510 False 785.000000 785 94.358000 1 514 1 chr5B.!!$F2 513
21 TraesCS2B01G370500 chr5B 120532858 120533468 610 True 461.000000 811 94.790000 1 579 2 chr5B.!!$R2 578
22 TraesCS2B01G370500 chr4B 421854182 421854689 507 True 756.000000 756 93.385000 1 514 1 chr4B.!!$R1 513

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
781 850 1.067071 ACTCGCCTACTGTTTAGTGGC 60.067 52.381 0.0 0.0 42.57 5.01 F
1371 1448 0.824182 GGGATCTCCGATCCTCGTGT 60.824 60.000 19.2 0.0 38.40 4.49 F
1442 1519 1.283613 TGTCCAACTGAACACAAGGGT 59.716 47.619 0.0 0.0 0.00 4.34 F
2427 2668 0.822532 AGGAACTCAGGACGACACGT 60.823 55.000 0.0 0.0 45.10 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2221 2461 0.320374 TTGCTTGTCTCCGTCGGATT 59.680 50.000 15.81 0.0 0.0 3.01 R
2407 2648 1.162698 CGTGTCGTCCTGAGTTCCTA 58.837 55.000 0.00 0.0 0.0 2.94 R
2586 2830 1.204704 TCACGGATCAACAGCGAGAAT 59.795 47.619 0.00 0.0 0.0 2.40 R
3545 3811 5.046159 TGGTACCCACTGACTACAATTAAGG 60.046 44.000 10.07 0.0 0.0 2.69 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
251 252 3.199946 AGTCATCGGGTTGTGGTATGAAT 59.800 43.478 0.00 0.00 0.00 2.57
256 257 3.078097 CGGGTTGTGGTATGAATTGACA 58.922 45.455 0.00 0.00 0.00 3.58
262 263 6.640907 GGTTGTGGTATGAATTGACAACTTTC 59.359 38.462 0.00 0.00 43.77 2.62
271 272 6.902341 TGAATTGACAACTTTCATAGTCAGC 58.098 36.000 0.97 0.00 41.46 4.26
277 278 5.865085 ACAACTTTCATAGTCAGCTTACCA 58.135 37.500 0.00 0.00 35.54 3.25
356 358 5.577945 CGCAGTAATTTTGGCAAAATGAGAT 59.422 36.000 32.24 21.33 40.05 2.75
646 710 4.055360 TGTCAGCGGGATGAATATTTACG 58.945 43.478 0.00 0.00 0.00 3.18
673 737 5.359194 TGATTATCTCCCAGGAAGACAAC 57.641 43.478 0.00 0.00 0.00 3.32
677 741 3.827817 TCTCCCAGGAAGACAACTAGA 57.172 47.619 0.00 0.00 0.00 2.43
687 751 7.332182 CCAGGAAGACAACTAGAAAGTATGTTC 59.668 40.741 0.00 0.00 33.75 3.18
777 846 3.909430 TGTTGACTCGCCTACTGTTTAG 58.091 45.455 0.00 0.00 0.00 1.85
781 850 1.067071 ACTCGCCTACTGTTTAGTGGC 60.067 52.381 0.00 0.00 42.57 5.01
922 991 4.385088 GGAGAAGCAATCCAAGGAGAAGAT 60.385 45.833 0.00 0.00 36.79 2.40
945 1014 2.032681 GTTCTGCGCCCAACCTCT 59.967 61.111 4.18 0.00 0.00 3.69
1049 1118 1.252904 GCAAGGCAGATGGGAAGCAA 61.253 55.000 0.00 0.00 0.00 3.91
1152 1222 1.663739 GAGCCGTGACACCAGTACA 59.336 57.895 0.00 0.00 0.00 2.90
1237 1311 6.811253 TTTGCGTAATTTAACTCCAGTGAT 57.189 33.333 0.00 0.00 0.00 3.06
1284 1360 9.638239 ATTTTGTTTATGTAGAAATTGATGCGT 57.362 25.926 0.00 0.00 0.00 5.24
1290 1366 5.697473 TGTAGAAATTGATGCGTTGGAAA 57.303 34.783 0.00 0.00 0.00 3.13
1361 1438 1.526917 GGGCAATGTGGGATCTCCG 60.527 63.158 0.00 0.00 38.76 4.63
1371 1448 0.824182 GGGATCTCCGATCCTCGTGT 60.824 60.000 19.20 0.00 38.40 4.49
1401 1478 5.239306 TGATTTCGCTTTGTTCATCTGACTT 59.761 36.000 0.00 0.00 0.00 3.01
1440 1517 3.213506 TCATGTCCAACTGAACACAAGG 58.786 45.455 0.00 0.00 0.00 3.61
1441 1518 2.051334 TGTCCAACTGAACACAAGGG 57.949 50.000 0.00 0.00 0.00 3.95
1442 1519 1.283613 TGTCCAACTGAACACAAGGGT 59.716 47.619 0.00 0.00 0.00 4.34
1560 1638 3.260632 GCTTTATTCATGGGTTGGGTTGT 59.739 43.478 0.00 0.00 0.00 3.32
1602 1680 1.393603 TGGGTTGCGATTGTTGTCAA 58.606 45.000 0.00 0.00 37.98 3.18
1605 1683 1.720852 GGTTGCGATTGTTGTCAATGC 59.279 47.619 0.00 4.08 43.33 3.56
1637 1715 4.943705 AGTACAAATCAATGATCCTGCGTT 59.056 37.500 0.00 0.00 0.00 4.84
1690 1800 4.930405 TGTACTCAACAAAACGTGAACTGA 59.070 37.500 0.00 0.00 34.29 3.41
1692 1802 3.749088 ACTCAACAAAACGTGAACTGACA 59.251 39.130 0.00 0.00 0.00 3.58
1719 1829 6.475504 CATGGTAGTATTATGATTCCTGGCA 58.524 40.000 0.00 0.00 0.00 4.92
1951 2182 1.672881 GATGACTGGCATGGTTAGTGC 59.327 52.381 0.00 0.00 41.78 4.40
2105 2344 2.093658 ACATGATGGTCGGTCCTGTTAC 60.094 50.000 0.00 0.00 37.07 2.50
2170 2410 4.644685 TGCTTTTCTATTGCTGGGTAATCC 59.355 41.667 0.00 0.00 0.00 3.01
2221 2461 1.632920 TGGTGCATGTATCTGGTCCAA 59.367 47.619 0.00 0.00 0.00 3.53
2350 2591 6.166279 TCACACACTTCATCTATCCTTGTTC 58.834 40.000 0.00 0.00 0.00 3.18
2379 2620 7.493743 AATTGTGCATGTTTTTGCTTCATTA 57.506 28.000 0.00 0.00 43.18 1.90
2396 2637 5.779241 TCATTAGTCCAGGAAAATCCAGT 57.221 39.130 0.00 0.00 39.61 4.00
2404 2645 4.959210 TCCAGGAAAATCCAGTTGAAAACA 59.041 37.500 0.00 0.00 42.75 2.83
2407 2648 6.767423 CCAGGAAAATCCAGTTGAAAACATTT 59.233 34.615 0.00 0.00 42.75 2.32
2427 2668 0.822532 AGGAACTCAGGACGACACGT 60.823 55.000 0.00 0.00 45.10 4.49
2586 2830 1.529010 CAACTTGTGAGGGCCTGCA 60.529 57.895 12.95 7.11 0.00 4.41
2614 2858 1.339920 TGTTGATCCGTGATGGCATGT 60.340 47.619 3.81 0.00 37.80 3.21
2661 2922 1.303236 TGATGGTTTGGGTCTGCCG 60.303 57.895 0.00 0.00 34.97 5.69
2742 3004 1.759562 GCTGTAGGAGTAGAGGGGCAT 60.760 57.143 0.00 0.00 0.00 4.40
2915 3177 0.030504 CACATTGGCACGCTGAAACA 59.969 50.000 0.00 0.00 0.00 2.83
2919 3181 1.661498 TTGGCACGCTGAAACAAGCA 61.661 50.000 0.00 0.00 43.73 3.91
2922 3184 0.318107 GCACGCTGAAACAAGCATGT 60.318 50.000 0.00 0.00 43.73 3.21
2976 3239 7.498900 TGCTAGTGGAGTGGATTATAACATTTG 59.501 37.037 0.00 0.00 0.00 2.32
3213 3477 6.169094 TGAAAAGGCTTGTCATAGAAGAGAG 58.831 40.000 16.14 0.00 0.00 3.20
3291 3555 6.075315 TCAAAGAATCTACGGGGATATGAGA 58.925 40.000 0.00 0.00 0.00 3.27
3530 3796 3.127721 GCTTCAGGCATGAGACTAAAACC 59.872 47.826 0.00 0.00 41.35 3.27
3537 3803 4.246458 GCATGAGACTAAAACCGTTCTCT 58.754 43.478 0.00 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
251 252 6.426937 GGTAAGCTGACTATGAAAGTTGTCAA 59.573 38.462 0.00 0.00 39.07 3.18
256 257 6.476378 ACATGGTAAGCTGACTATGAAAGTT 58.524 36.000 29.12 7.99 39.88 2.66
262 263 5.851720 AGATGACATGGTAAGCTGACTATG 58.148 41.667 22.66 22.66 42.35 2.23
322 324 4.466828 CAAAATTACTGCGTCAACCTGAG 58.533 43.478 0.00 0.00 0.00 3.35
333 335 6.973229 ATCTCATTTTGCCAAAATTACTGC 57.027 33.333 12.58 0.00 38.97 4.40
518 551 4.523173 GGTTCTCATATAGATGGACCGACA 59.477 45.833 0.00 0.00 33.05 4.35
631 695 7.745620 AATCAACCTCGTAAATATTCATCCC 57.254 36.000 0.00 0.00 0.00 3.85
646 710 4.656112 TCTTCCTGGGAGATAATCAACCTC 59.344 45.833 0.00 0.00 0.00 3.85
673 737 8.390354 TCATGAAATTGCGAACATACTTTCTAG 58.610 33.333 0.00 0.00 0.00 2.43
677 741 6.913170 AGTCATGAAATTGCGAACATACTTT 58.087 32.000 0.00 0.00 0.00 2.66
922 991 0.248289 GTTGGGCGCAGAACCTACTA 59.752 55.000 10.83 0.00 31.79 1.82
1077 1147 4.020751 ACCTCGATGCTGCTATCATGTATT 60.021 41.667 0.00 0.00 0.00 1.89
1152 1222 3.182152 AGTAGTATTGGAGGTTGTGGCT 58.818 45.455 0.00 0.00 0.00 4.75
1237 1311 9.650539 CAAAATTACCACATAATGAAATCCACA 57.349 29.630 0.00 0.00 33.53 4.17
1361 1438 4.669197 CGAAATCAAACCAACACGAGGATC 60.669 45.833 0.00 0.00 0.00 3.36
1371 1448 4.748892 TGAACAAAGCGAAATCAAACCAA 58.251 34.783 0.00 0.00 0.00 3.67
1509 1587 1.021202 CTGGAACGCAGGACAAACAA 58.979 50.000 0.00 0.00 0.00 2.83
1560 1638 6.760770 CCAAAAATTAAGTGGCTTGAAACTGA 59.239 34.615 0.00 0.00 0.00 3.41
1602 1680 8.959548 TCATTGATTTGTACTATTCAACAGCAT 58.040 29.630 14.06 0.16 31.45 3.79
1605 1683 9.941664 GGATCATTGATTTGTACTATTCAACAG 57.058 33.333 14.06 10.98 31.45 3.16
1690 1800 6.273260 AGGAATCATAATACTACCATGGCTGT 59.727 38.462 13.04 13.43 0.00 4.40
1692 1802 6.296662 CCAGGAATCATAATACTACCATGGCT 60.297 42.308 13.04 1.45 0.00 4.75
1719 1829 8.548880 ACACTACAGATAATACTACCATGGTT 57.451 34.615 25.38 8.75 0.00 3.67
2073 2307 5.652014 ACCGACCATCATGTAAATGAATTGT 59.348 36.000 0.00 0.00 33.83 2.71
2208 2448 2.159156 CGTCGGATTTGGACCAGATACA 60.159 50.000 7.94 0.00 0.00 2.29
2221 2461 0.320374 TTGCTTGTCTCCGTCGGATT 59.680 50.000 15.81 0.00 0.00 3.01
2350 2591 4.448005 GCAAAAACATGCACAATTTCTCG 58.552 39.130 0.00 0.00 45.70 4.04
2379 2620 4.453480 TTCAACTGGATTTTCCTGGACT 57.547 40.909 0.00 0.00 39.50 3.85
2396 2637 6.017440 CGTCCTGAGTTCCTAAATGTTTTCAA 60.017 38.462 0.00 0.00 0.00 2.69
2404 2645 3.367087 CGTGTCGTCCTGAGTTCCTAAAT 60.367 47.826 0.00 0.00 0.00 1.40
2407 2648 1.162698 CGTGTCGTCCTGAGTTCCTA 58.837 55.000 0.00 0.00 0.00 2.94
2586 2830 1.204704 TCACGGATCAACAGCGAGAAT 59.795 47.619 0.00 0.00 0.00 2.40
2638 2899 2.879756 GCAGACCCAAACCATCAGCTAA 60.880 50.000 0.00 0.00 0.00 3.09
2742 3004 2.891936 GCAGATCCATCACGCGCA 60.892 61.111 5.73 0.00 0.00 6.09
3159 3423 6.882140 TCGTTTAATCCCTACATCATTTGTGT 59.118 34.615 0.00 0.00 39.48 3.72
3213 3477 6.166984 TCCATTATGTTCTCTCTCACCATC 57.833 41.667 0.00 0.00 0.00 3.51
3545 3811 5.046159 TGGTACCCACTGACTACAATTAAGG 60.046 44.000 10.07 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.