Multiple sequence alignment - TraesCS7B01G492300

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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 TraesCS7B01G492300 chr7B 100.000 4379 0 0 1 4379 744459641 744464019 0.000000e+00 8087
1 TraesCS7B01G492300 chr7B 97.700 3521 64 6 837 4341 744482199 744485718 0.000000e+00 6037
2 TraesCS7B01G492300 chr7B 97.582 3516 72 5 837 4341 744504699 744508212 0.000000e+00 6010
3 TraesCS7B01G492300 chr7B 97.574 2061 41 1 2290 4341 744494560 744496620 0.000000e+00 3520
4 TraesCS7B01G492300 chr7B 97.974 1876 37 1 837 2711 744443793 744445668 0.000000e+00 3253
5 TraesCS7B01G492300 chr7B 96.406 1419 29 4 2934 4341 744445677 744447084 0.000000e+00 2318
6 TraesCS7B01G492300 chr7B 98.101 1106 19 2 839 1943 744493444 744494548 0.000000e+00 1925
7 TraesCS7B01G492300 chr7B 97.616 839 19 1 1 838 744490687 744491525 0.000000e+00 1437
8 TraesCS7B01G492300 chr7B 97.020 839 22 2 1 838 744502364 744503200 0.000000e+00 1408
9 TraesCS7B01G492300 chr7B 94.302 860 27 2 1 838 744524651 744525510 0.000000e+00 1297
10 TraesCS7B01G492300 chr7B 97.652 511 12 0 1 511 744411988 744412498 0.000000e+00 878
11 TraesCS7B01G492300 chr7B 82.609 759 83 22 27 770 154817701 154816977 3.720000e-175 625
12 TraesCS7B01G492300 chr7B 96.375 331 11 1 509 838 744421120 744421450 1.070000e-150 544
13 TraesCS7B01G492300 chr7B 87.799 418 47 3 3926 4341 317894042 317893627 1.830000e-133 486
14 TraesCS7B01G492300 chr7D 92.782 3117 188 19 837 3928 632352336 632355440 0.000000e+00 4475
15 TraesCS7B01G492300 chr7D 92.409 3122 190 26 837 3928 632360726 632363830 0.000000e+00 4409
16 TraesCS7B01G492300 chr7D 91.557 758 55 9 17 770 632339506 632340258 0.000000e+00 1037
17 TraesCS7B01G492300 chr7D 88.834 403 43 2 3940 4341 443965461 443965060 1.090000e-135 494
18 TraesCS7B01G492300 chr7D 88.452 407 45 2 3926 4331 361777781 361777376 1.420000e-134 490
19 TraesCS7B01G492300 chr7A 97.914 2061 42 1 837 2896 735396016 735393956 0.000000e+00 3567
20 TraesCS7B01G492300 chr7A 97.817 2061 44 1 837 2896 735377949 735375889 0.000000e+00 3555
21 TraesCS7B01G492300 chr7A 97.816 2015 43 1 839 2852 735359721 735357707 0.000000e+00 3476
22 TraesCS7B01G492300 chr7A 97.057 1393 29 3 2961 4341 735375889 735374497 0.000000e+00 2335
23 TraesCS7B01G492300 chr7A 96.981 1391 32 2 2961 4341 735393956 735392566 0.000000e+00 2327
24 TraesCS7B01G492300 chr7A 96.163 1251 37 3 3101 4341 735343035 735341786 0.000000e+00 2034
25 TraesCS7B01G492300 chr7A 90.326 827 59 6 17 824 735362103 735361279 0.000000e+00 1064
26 TraesCS7B01G492300 chr7A 89.976 828 60 8 17 824 735380334 735379510 0.000000e+00 1048
27 TraesCS7B01G492300 chr7A 89.568 834 59 9 17 824 735398408 735397577 0.000000e+00 1033
28 TraesCS7B01G492300 chr7A 99.306 144 1 0 2961 3104 735357645 735357502 1.210000e-65 261
29 TraesCS7B01G492300 chr7A 100.000 40 0 0 2857 2896 735357684 735357645 1.690000e-09 75
30 TraesCS7B01G492300 chr3D 83.897 739 100 13 21 746 270156016 270156748 0.000000e+00 688
31 TraesCS7B01G492300 chr5B 89.423 416 42 2 3927 4341 148676401 148676815 1.400000e-144 523
32 TraesCS7B01G492300 chr5B 88.783 419 43 4 3926 4341 198172654 198172237 1.090000e-140 510
33 TraesCS7B01G492300 chr5B 75.163 769 150 34 17 764 115325700 115324952 1.520000e-84 324
34 TraesCS7B01G492300 chr4D 88.969 417 43 3 3926 4341 383766199 383766613 3.020000e-141 512
35 TraesCS7B01G492300 chr3B 88.780 410 42 3 3933 4340 334302780 334302373 2.350000e-137 499
36 TraesCS7B01G492300 chr6B 86.353 425 44 5 3928 4341 363159989 363160410 6.680000e-123 451
37 TraesCS7B01G492300 chr5A 86.158 419 50 5 3925 4341 208741994 208742406 3.110000e-121 446
38 TraesCS7B01G492300 chr4A 75.868 547 99 24 2855 3382 732780171 732780703 9.400000e-62 248


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 TraesCS7B01G492300 chr7B 744459641 744464019 4378 False 8087.000000 8087 100.000000 1 4379 1 chr7B.!!$F3 4378
1 TraesCS7B01G492300 chr7B 744482199 744485718 3519 False 6037.000000 6037 97.700000 837 4341 1 chr7B.!!$F4 3504
2 TraesCS7B01G492300 chr7B 744502364 744508212 5848 False 3709.000000 6010 97.301000 1 4341 2 chr7B.!!$F8 4340
3 TraesCS7B01G492300 chr7B 744443793 744447084 3291 False 2785.500000 3253 97.190000 837 4341 2 chr7B.!!$F6 3504
4 TraesCS7B01G492300 chr7B 744490687 744496620 5933 False 2294.000000 3520 97.763667 1 4341 3 chr7B.!!$F7 4340
5 TraesCS7B01G492300 chr7B 744524651 744525510 859 False 1297.000000 1297 94.302000 1 838 1 chr7B.!!$F5 837
6 TraesCS7B01G492300 chr7B 744411988 744412498 510 False 878.000000 878 97.652000 1 511 1 chr7B.!!$F1 510
7 TraesCS7B01G492300 chr7B 154816977 154817701 724 True 625.000000 625 82.609000 27 770 1 chr7B.!!$R1 743
8 TraesCS7B01G492300 chr7D 632352336 632355440 3104 False 4475.000000 4475 92.782000 837 3928 1 chr7D.!!$F2 3091
9 TraesCS7B01G492300 chr7D 632360726 632363830 3104 False 4409.000000 4409 92.409000 837 3928 1 chr7D.!!$F3 3091
10 TraesCS7B01G492300 chr7D 632339506 632340258 752 False 1037.000000 1037 91.557000 17 770 1 chr7D.!!$F1 753
11 TraesCS7B01G492300 chr7A 735374497 735380334 5837 True 2312.666667 3555 94.950000 17 4341 3 chr7A.!!$R3 4324
12 TraesCS7B01G492300 chr7A 735392566 735398408 5842 True 2309.000000 3567 94.821000 17 4341 3 chr7A.!!$R4 4324
13 TraesCS7B01G492300 chr7A 735341786 735343035 1249 True 2034.000000 2034 96.163000 3101 4341 1 chr7A.!!$R1 1240
14 TraesCS7B01G492300 chr7A 735357502 735362103 4601 True 1219.000000 3476 96.862000 17 3104 4 chr7A.!!$R2 3087
15 TraesCS7B01G492300 chr3D 270156016 270156748 732 False 688.000000 688 83.897000 21 746 1 chr3D.!!$F1 725
16 TraesCS7B01G492300 chr5B 115324952 115325700 748 True 324.000000 324 75.163000 17 764 1 chr5B.!!$R1 747
17 TraesCS7B01G492300 chr4A 732780171 732780703 532 False 248.000000 248 75.868000 2855 3382 1 chr4A.!!$F1 527

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
472 492 0.108138 CTCAAGTACTCCCGGCCAAG 60.108 60.000 2.24 0.0 0.00 3.61 F
631 654 0.178891 AGAAGCCAACCTCTCCCAGA 60.179 55.000 0.00 0.0 0.00 3.86 F
1147 3180 1.952296 CTGACAAAGGCTTGTTGCTCT 59.048 47.619 0.00 0.0 45.98 4.09 F
1656 3690 2.300437 AGCTAGGTTCGGGCATTATCTC 59.700 50.000 0.00 0.0 0.00 2.75 F
3168 5343 1.016130 ACCAATGCTTCGCTCTGACG 61.016 55.000 0.00 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2001 4047 1.660167 AGGATGACACATGCGACATG 58.340 50.000 15.34 15.34 0.00 3.21 R
2460 4530 1.886542 GGGAAGTCATGTGTGGTTTCC 59.113 52.381 0.00 0.00 37.44 3.13 R
2804 4879 4.019771 TGGCTAGTACACCACAATCATCAA 60.020 41.667 0.00 0.00 0.00 2.57 R
3241 5417 1.300620 CGACGGTCTGGCAAGTCAA 60.301 57.895 6.57 0.00 33.56 3.18 R
4351 6546 0.681733 ATATAGCCTGTGCGTCCCAG 59.318 55.000 0.00 0.00 44.33 4.45 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
67 76 2.235016 CCTCTTCTCTCCTATCGGGTG 58.765 57.143 0.00 0.00 36.25 4.61
99 108 6.094742 TGTTTTCACAAGAGTAATGCACTGAA 59.905 34.615 0.00 0.00 37.72 3.02
472 492 0.108138 CTCAAGTACTCCCGGCCAAG 60.108 60.000 2.24 0.00 0.00 3.61
507 527 4.558226 ATCTTGCAGAACCTGTACATGA 57.442 40.909 0.00 0.00 33.43 3.07
631 654 0.178891 AGAAGCCAACCTCTCCCAGA 60.179 55.000 0.00 0.00 0.00 3.86
805 871 2.819984 ATTCAACGCCGGAGCATGGT 62.820 55.000 5.05 0.00 39.83 3.55
830 917 2.214376 TTGAGCCCCTAAATGTGGTG 57.786 50.000 0.00 0.00 0.00 4.17
1134 3167 4.256110 TCGAGGACGACTATACTGACAAA 58.744 43.478 0.00 0.00 43.81 2.83
1147 3180 1.952296 CTGACAAAGGCTTGTTGCTCT 59.048 47.619 0.00 0.00 45.98 4.09
1488 3522 5.368256 ACTTGTGTCTGATTGAGATTTGC 57.632 39.130 0.00 0.00 31.63 3.68
1656 3690 2.300437 AGCTAGGTTCGGGCATTATCTC 59.700 50.000 0.00 0.00 0.00 2.75
1670 3704 6.451393 GGCATTATCTCGGGAGCTATATTAG 58.549 44.000 0.00 0.00 0.00 1.73
2001 4047 5.499004 TGGTTTATCATAGATAGGGTGGC 57.501 43.478 0.00 0.00 0.00 5.01
2345 4411 6.999272 TCTACGAATGCCTTCTTCTATCTAGT 59.001 38.462 0.13 0.00 0.00 2.57
2460 4530 3.762779 GATGCTTTCCATCGTTTGAAGG 58.237 45.455 0.00 0.00 40.84 3.46
2498 4568 5.103515 ACTTCCCATGGCCACTATAAAATCT 60.104 40.000 8.16 0.00 0.00 2.40
2505 4575 7.884877 CCATGGCCACTATAAAATCTTGATCTA 59.115 37.037 8.16 0.00 0.00 1.98
2804 4879 6.600427 TGTTCATCTGTGTATCATTGCTTGAT 59.400 34.615 7.67 7.67 46.86 2.57
3160 5333 5.957910 TGTTTTTGTAAACCAATGCTTCG 57.042 34.783 0.00 0.00 42.39 3.79
3168 5343 1.016130 ACCAATGCTTCGCTCTGACG 61.016 55.000 0.00 0.00 0.00 4.35
3241 5417 0.105246 CATCAGGGGGCTCCTAGACT 60.105 60.000 5.06 0.00 46.12 3.24
3396 5572 0.687757 AGAGGAACATCTAGGCCGCA 60.688 55.000 0.00 0.00 0.00 5.69
3529 5708 6.654793 TTCAGTGGTTATGTTTGCAAAAAC 57.345 33.333 14.67 14.39 0.00 2.43
4099 6294 0.865769 GCGTGGTCAACAAACGAGAT 59.134 50.000 10.60 0.00 39.64 2.75
4159 6354 2.257409 GACGCACCAGGTCCATGGAT 62.257 60.000 19.62 0.00 43.57 3.41
4181 6376 2.032681 ACTGCAACCGCCTCCTTC 59.967 61.111 0.00 0.00 37.32 3.46
4341 6536 6.152831 AGTGACTCCTTATTATGGGCAAAAAC 59.847 38.462 0.00 0.00 0.00 2.43
4342 6537 5.420739 TGACTCCTTATTATGGGCAAAAACC 59.579 40.000 0.00 0.00 0.00 3.27
4343 6538 5.589831 ACTCCTTATTATGGGCAAAAACCT 58.410 37.500 0.00 0.00 0.00 3.50
4344 6539 5.656859 ACTCCTTATTATGGGCAAAAACCTC 59.343 40.000 0.00 0.00 0.00 3.85
4345 6540 5.837829 TCCTTATTATGGGCAAAAACCTCT 58.162 37.500 0.00 0.00 0.00 3.69
4346 6541 5.656416 TCCTTATTATGGGCAAAAACCTCTG 59.344 40.000 0.00 0.00 0.00 3.35
4347 6542 5.656416 CCTTATTATGGGCAAAAACCTCTGA 59.344 40.000 0.00 0.00 0.00 3.27
4348 6543 6.405842 CCTTATTATGGGCAAAAACCTCTGAC 60.406 42.308 0.00 0.00 0.00 3.51
4349 6544 1.632589 ATGGGCAAAAACCTCTGACC 58.367 50.000 0.00 0.00 41.60 4.02
4350 6545 3.125520 GGGCAAAAACCTCTGACCA 57.874 52.632 0.00 0.00 40.83 4.02
4351 6546 0.673985 GGGCAAAAACCTCTGACCAC 59.326 55.000 0.00 0.00 40.83 4.16
4352 6547 1.692411 GGCAAAAACCTCTGACCACT 58.308 50.000 0.00 0.00 0.00 4.00
4353 6548 1.338020 GGCAAAAACCTCTGACCACTG 59.662 52.381 0.00 0.00 0.00 3.66
4354 6549 1.338020 GCAAAAACCTCTGACCACTGG 59.662 52.381 0.00 0.00 0.00 4.00
4355 6550 1.956477 CAAAAACCTCTGACCACTGGG 59.044 52.381 0.00 0.00 41.29 4.45
4356 6551 1.518367 AAAACCTCTGACCACTGGGA 58.482 50.000 0.00 0.00 38.05 4.37
4357 6552 0.765510 AAACCTCTGACCACTGGGAC 59.234 55.000 0.00 0.00 38.05 4.46
4358 6553 1.472662 AACCTCTGACCACTGGGACG 61.473 60.000 0.00 0.00 38.05 4.79
4359 6554 2.262915 CTCTGACCACTGGGACGC 59.737 66.667 0.00 0.00 38.05 5.19
4360 6555 2.523168 TCTGACCACTGGGACGCA 60.523 61.111 0.00 0.00 38.05 5.24
4361 6556 2.357517 CTGACCACTGGGACGCAC 60.358 66.667 0.00 0.00 38.05 5.34
4362 6557 3.157949 TGACCACTGGGACGCACA 61.158 61.111 0.00 0.00 38.05 4.57
4363 6558 2.357517 GACCACTGGGACGCACAG 60.358 66.667 7.44 7.44 41.64 3.66
4364 6559 3.883744 GACCACTGGGACGCACAGG 62.884 68.421 12.63 4.46 40.23 4.00
4366 6561 4.320456 CACTGGGACGCACAGGCT 62.320 66.667 12.63 0.00 40.23 4.58
4367 6562 2.603473 ACTGGGACGCACAGGCTA 60.603 61.111 12.63 0.00 40.23 3.93
4368 6563 1.990060 ACTGGGACGCACAGGCTAT 60.990 57.895 12.63 0.00 40.23 2.97
4369 6564 0.686441 ACTGGGACGCACAGGCTATA 60.686 55.000 12.63 0.00 40.23 1.31
4370 6565 0.681733 CTGGGACGCACAGGCTATAT 59.318 55.000 1.66 0.00 38.10 0.86
4371 6566 1.893137 CTGGGACGCACAGGCTATATA 59.107 52.381 1.66 0.00 38.10 0.86
4372 6567 2.497675 CTGGGACGCACAGGCTATATAT 59.502 50.000 1.66 0.00 38.10 0.86
4373 6568 2.903784 TGGGACGCACAGGCTATATATT 59.096 45.455 0.00 0.00 38.10 1.28
4374 6569 3.056107 TGGGACGCACAGGCTATATATTC 60.056 47.826 0.00 0.00 38.10 1.75
4375 6570 3.522553 GGACGCACAGGCTATATATTCC 58.477 50.000 0.00 0.00 38.10 3.01
4376 6571 3.056107 GGACGCACAGGCTATATATTCCA 60.056 47.826 0.00 0.00 38.10 3.53
4377 6572 3.926616 ACGCACAGGCTATATATTCCAC 58.073 45.455 0.00 0.00 38.10 4.02
4378 6573 3.262420 CGCACAGGCTATATATTCCACC 58.738 50.000 0.00 0.00 38.10 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 76 4.918810 ACTCTTGTGAAAACAATCCCAC 57.081 40.909 0.00 0.00 0.00 4.61
472 492 2.421073 TGCAAGATTGTGCTAGTGATGC 59.579 45.455 0.00 0.00 45.17 3.91
631 654 0.107456 CATATGCAAGGAGGACGCCT 59.893 55.000 0.00 0.00 40.93 5.52
770 836 3.377346 TGAATCGCAATAGAGAGAGCC 57.623 47.619 0.00 0.00 0.00 4.70
805 871 2.771943 ACATTTAGGGGCTCAATCTCGA 59.228 45.455 0.00 0.00 0.00 4.04
830 917 1.273887 CGATTGAGCAACGCCGATC 59.726 57.895 0.00 0.00 0.00 3.69
1134 3167 4.585070 TTGCAGAGCAACAAGCCT 57.415 50.000 0.00 0.00 43.99 4.58
1147 3180 4.401022 AGGATCTTTGAGTTGACATTGCA 58.599 39.130 0.00 0.00 0.00 4.08
1656 3690 6.867293 GGAACTGTAAACTAATATAGCTCCCG 59.133 42.308 0.00 0.00 28.40 5.14
1670 3704 5.473504 ACCAGATGAACATGGAACTGTAAAC 59.526 40.000 0.00 0.00 39.02 2.01
2001 4047 1.660167 AGGATGACACATGCGACATG 58.340 50.000 15.34 15.34 0.00 3.21
2345 4411 9.747898 AGAACCACAATTAATACTCAACCAATA 57.252 29.630 0.00 0.00 0.00 1.90
2460 4530 1.886542 GGGAAGTCATGTGTGGTTTCC 59.113 52.381 0.00 0.00 37.44 3.13
2498 4568 6.710295 TGCTAAACTCTTGCAAACTAGATCAA 59.290 34.615 0.00 0.00 33.48 2.57
2505 4575 6.884280 AATAGTGCTAAACTCTTGCAAACT 57.116 33.333 0.00 0.00 40.56 2.66
2804 4879 4.019771 TGGCTAGTACACCACAATCATCAA 60.020 41.667 0.00 0.00 0.00 2.57
3160 5333 1.599542 GGAATAATGGTGCGTCAGAGC 59.400 52.381 0.00 0.00 37.71 4.09
3168 5343 4.725790 AGAGCAAAAGGAATAATGGTGC 57.274 40.909 0.00 0.00 0.00 5.01
3241 5417 1.300620 CGACGGTCTGGCAAGTCAA 60.301 57.895 6.57 0.00 33.56 3.18
4099 6294 6.496911 TCCATGTATAATCCTCTTCCGATGAA 59.503 38.462 0.00 0.00 0.00 2.57
4120 6315 1.270414 CCCACTGTCAGCCTCTCCAT 61.270 60.000 0.00 0.00 0.00 3.41
4224 6419 1.137513 GCGAAGATATACGTGGTGGC 58.862 55.000 0.00 0.00 0.00 5.01
4341 6536 2.973899 CGTCCCAGTGGTCAGAGG 59.026 66.667 8.74 0.26 0.00 3.69
4342 6537 2.262915 GCGTCCCAGTGGTCAGAG 59.737 66.667 8.74 0.00 0.00 3.35
4343 6538 2.523168 TGCGTCCCAGTGGTCAGA 60.523 61.111 8.74 0.00 0.00 3.27
4344 6539 2.357517 GTGCGTCCCAGTGGTCAG 60.358 66.667 8.74 0.00 0.00 3.51
4345 6540 3.157949 TGTGCGTCCCAGTGGTCA 61.158 61.111 8.74 0.00 0.00 4.02
4346 6541 2.357517 CTGTGCGTCCCAGTGGTC 60.358 66.667 8.74 0.00 0.00 4.02
4347 6542 3.941188 CCTGTGCGTCCCAGTGGT 61.941 66.667 8.74 0.00 0.00 4.16
4349 6544 2.244117 ATAGCCTGTGCGTCCCAGTG 62.244 60.000 0.00 0.00 44.33 3.66
4350 6545 0.686441 TATAGCCTGTGCGTCCCAGT 60.686 55.000 0.00 0.00 44.33 4.00
4351 6546 0.681733 ATATAGCCTGTGCGTCCCAG 59.318 55.000 0.00 0.00 44.33 4.45
4352 6547 2.003937 TATATAGCCTGTGCGTCCCA 57.996 50.000 0.00 0.00 44.33 4.37
4353 6548 3.522553 GAATATATAGCCTGTGCGTCCC 58.477 50.000 0.00 0.00 44.33 4.46
4354 6549 3.056107 TGGAATATATAGCCTGTGCGTCC 60.056 47.826 6.22 0.00 44.33 4.79
4355 6550 3.927142 GTGGAATATATAGCCTGTGCGTC 59.073 47.826 6.22 0.00 44.33 5.19
4356 6551 3.306780 GGTGGAATATATAGCCTGTGCGT 60.307 47.826 6.22 0.00 44.33 5.24
4357 6552 3.262420 GGTGGAATATATAGCCTGTGCG 58.738 50.000 6.22 0.00 44.33 5.34


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

AutoCloner maintained by Alex Coulton.