Multiple sequence alignment - TraesCS1A01G301500

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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 TraesCS1A01G301500 chr1A 100.000 2786 0 0 1 2786 495705423 495702638 0.000000e+00 5145.0
1 TraesCS1A01G301500 chr1B 95.465 1698 66 4 1099 2786 534667338 534665642 0.000000e+00 2699.0
2 TraesCS1A01G301500 chr1B 89.206 1121 67 30 1 1097 534668497 534667407 0.000000e+00 1351.0
3 TraesCS1A01G301500 chr1D 94.718 1704 72 6 1099 2786 398977645 398975944 0.000000e+00 2632.0
4 TraesCS1A01G301500 chr1D 91.995 762 37 12 357 1097 398978476 398977718 0.000000e+00 1048.0
5 TraesCS1A01G301500 chr1D 90.533 338 13 6 1 329 398978800 398978473 1.980000e-116 429.0
6 TraesCS1A01G301500 chr6D 89.286 84 9 0 685 768 58245373 58245456 3.800000e-19 106.0
7 TraesCS1A01G301500 chr6A 90.123 81 8 0 685 765 73561990 73562070 3.800000e-19 106.0
8 TraesCS1A01G301500 chr6A 85.542 83 12 0 686 768 101930664 101930582 1.370000e-13 87.9
9 TraesCS1A01G301500 chr6A 93.478 46 3 0 774 819 61420448 61420493 4.980000e-08 69.4
10 TraesCS1A01G301500 chr2B 90.000 80 8 0 689 768 632990261 632990182 1.360000e-18 104.0
11 TraesCS1A01G301500 chr2D 89.610 77 8 0 692 768 533167352 533167276 6.350000e-17 99.0
12 TraesCS1A01G301500 chr2D 97.619 42 1 0 775 816 554130051 554130010 3.850000e-09 73.1
13 TraesCS1A01G301500 chr4D 91.304 69 6 0 684 752 463465511 463465579 8.210000e-16 95.3
14 TraesCS1A01G301500 chr4D 97.561 41 1 0 775 815 47984337 47984297 1.380000e-08 71.3
15 TraesCS1A01G301500 chr3A 91.045 67 6 0 684 750 41365246 41365312 1.060000e-14 91.6
16 TraesCS1A01G301500 chr3A 93.617 47 2 1 774 820 420334708 420334663 4.980000e-08 69.4
17 TraesCS1A01G301500 chr6B 97.619 42 1 0 774 815 42421786 42421827 3.850000e-09 73.1
18 TraesCS1A01G301500 chr6B 90.566 53 4 1 764 815 485061234 485061286 4.980000e-08 69.4
19 TraesCS1A01G301500 chr5D 91.837 49 2 2 774 822 240087217 240087171 1.790000e-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 TraesCS1A01G301500 chr1A 495702638 495705423 2785 True 5145.000000 5145 100.000000 1 2786 1 chr1A.!!$R1 2785
1 TraesCS1A01G301500 chr1B 534665642 534668497 2855 True 2025.000000 2699 92.335500 1 2786 2 chr1B.!!$R1 2785
2 TraesCS1A01G301500 chr1D 398975944 398978800 2856 True 1369.666667 2632 92.415333 1 2786 3 chr1D.!!$R1 2785

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
170 175 0.106519 GGTCCTGCCAAGGTATGCAT 60.107 55.0 3.79 3.79 44.82 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1971 2092 0.744414 ATATGGACAGCGTGTGTGGC 60.744 55.0 0.0 0.0 40.56 5.01 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
101 102 0.463833 ATCCAACGCGGGGAAATCTC 60.464 55.000 22.90 0.00 38.09 2.75
109 110 1.599542 GCGGGGAAATCTCAATCTTCG 59.400 52.381 0.00 0.00 0.00 3.79
125 126 1.978455 TTCGGTTGGATCCCCCATCG 61.978 60.000 9.90 5.63 46.10 3.84
129 130 0.179045 GTTGGATCCCCCATCGTCAG 60.179 60.000 9.90 0.00 46.10 3.51
130 131 1.344953 TTGGATCCCCCATCGTCAGG 61.345 60.000 9.90 0.00 46.10 3.86
134 135 3.866582 CCCCCATCGTCAGGAGGC 61.867 72.222 0.00 0.00 0.00 4.70
169 174 1.302949 GGTCCTGCCAAGGTATGCA 59.697 57.895 0.00 0.00 44.82 3.96
170 175 0.106519 GGTCCTGCCAAGGTATGCAT 60.107 55.000 3.79 3.79 44.82 3.96
171 176 1.027357 GTCCTGCCAAGGTATGCATG 58.973 55.000 10.16 0.00 44.82 4.06
172 177 0.106569 TCCTGCCAAGGTATGCATGG 60.107 55.000 10.16 3.85 44.82 3.66
173 178 0.106569 CCTGCCAAGGTATGCATGGA 60.107 55.000 10.16 0.00 38.96 3.41
174 179 1.479942 CCTGCCAAGGTATGCATGGAT 60.480 52.381 10.16 4.68 38.96 3.41
175 180 2.313317 CTGCCAAGGTATGCATGGATT 58.687 47.619 10.16 0.00 36.79 3.01
176 181 2.033372 TGCCAAGGTATGCATGGATTG 58.967 47.619 10.16 10.59 36.27 2.67
180 185 3.257375 CCAAGGTATGCATGGATTGATGG 59.743 47.826 10.16 5.88 36.27 3.51
194 209 5.834204 TGGATTGATGGATATGTGCATTTCA 59.166 36.000 0.00 0.00 36.44 2.69
206 221 3.439129 TGTGCATTTCATTCTGCTCTCAG 59.561 43.478 0.00 0.00 41.67 3.35
360 381 7.881775 AGTAGGTCAACAAAAGTTCATTTCT 57.118 32.000 0.00 0.00 0.00 2.52
415 436 6.735556 AGGTCTCCTCCAATTTAATGAATGT 58.264 36.000 0.00 0.00 0.00 2.71
459 481 3.515502 TGACACCCTAGGATTGTCTGAAG 59.484 47.826 29.33 8.40 40.34 3.02
464 486 3.706594 CCCTAGGATTGTCTGAAGCTGTA 59.293 47.826 11.48 0.00 0.00 2.74
468 490 2.675348 GGATTGTCTGAAGCTGTAGCAC 59.325 50.000 6.65 0.83 45.16 4.40
496 518 5.465532 TTCAGGCAAATATGTTGAGCAAA 57.534 34.783 3.06 0.00 0.00 3.68
509 531 3.925688 TGAGCAAAATTCGCTATCGTC 57.074 42.857 2.51 0.00 40.63 4.20
510 532 2.281498 TGAGCAAAATTCGCTATCGTCG 59.719 45.455 2.51 0.00 40.63 5.12
524 546 4.384846 GCTATCGTCGAAACAAACTTCTCA 59.615 41.667 0.00 0.00 0.00 3.27
541 563 6.479884 ACTTCTCAGTTCTATTGGATTTGCT 58.520 36.000 0.00 0.00 0.00 3.91
606 630 9.440784 CTATCTAAAACAAACAGCACGTTTTTA 57.559 29.630 4.97 0.00 45.79 1.52
653 677 1.068055 GCAGTCTCTGGCCATTGTTTG 60.068 52.381 5.51 3.97 31.21 2.93
669 693 4.320608 TGTTTGGAAGAATTGAAGTGCC 57.679 40.909 0.00 0.00 0.00 5.01
709 733 8.612486 TGTACACCCTCTGTTCCTAAATATAA 57.388 34.615 0.00 0.00 33.91 0.98
744 768 8.168681 ACACTTCAATTTAAACTGTCAAAACG 57.831 30.769 0.00 0.00 0.00 3.60
952 997 2.841442 ACCTCTTTTTCCTCCTCGTG 57.159 50.000 0.00 0.00 0.00 4.35
1222 1338 6.407525 GCTCTGGGAATGTGACTCTTATAACT 60.408 42.308 0.00 0.00 0.00 2.24
1247 1363 7.922382 TGATCTAAAGAGTTGGGAGAAGAAAT 58.078 34.615 0.00 0.00 0.00 2.17
1332 1448 5.248640 ACACAAGGATATATAGGTGCATGC 58.751 41.667 11.82 11.82 0.00 4.06
1333 1449 5.221904 ACACAAGGATATATAGGTGCATGCA 60.222 40.000 18.46 18.46 0.00 3.96
1345 1462 4.004982 AGGTGCATGCAATTTCCAATTTC 58.995 39.130 24.58 4.87 0.00 2.17
1350 1467 5.063691 TGCATGCAATTTCCAATTTCGAATC 59.936 36.000 20.30 0.00 0.00 2.52
1354 1471 5.178061 GCAATTTCCAATTTCGAATCCCTT 58.822 37.500 0.00 0.00 0.00 3.95
1357 1474 6.603940 ATTTCCAATTTCGAATCCCTTCAA 57.396 33.333 0.00 0.00 0.00 2.69
1362 1479 5.414454 CCAATTTCGAATCCCTTCAACTGTA 59.586 40.000 0.00 0.00 0.00 2.74
1374 1491 6.657541 TCCCTTCAACTGTATTGATTAACCAC 59.342 38.462 0.00 0.00 0.00 4.16
1376 1493 6.148811 CCTTCAACTGTATTGATTAACCACGT 59.851 38.462 0.00 0.00 0.00 4.49
1379 1496 5.873179 ACTGTATTGATTAACCACGTTGG 57.127 39.130 2.92 2.92 45.02 3.77
1452 1569 0.249238 GTGTAGGATCGCTGCTCCTG 60.249 60.000 17.92 0.00 43.10 3.86
1499 1616 2.409975 TCCGATCTTGTTTTCGTGTCC 58.590 47.619 0.00 0.00 33.60 4.02
1539 1656 1.240256 GGTACACAAATGTTCCGCCA 58.760 50.000 0.00 0.00 40.48 5.69
1547 1664 3.995705 ACAAATGTTCCGCCAATTCATTG 59.004 39.130 0.00 0.00 37.52 2.82
1551 1668 2.163412 TGTTCCGCCAATTCATTGCTAC 59.837 45.455 0.00 0.00 36.48 3.58
1556 1673 4.095782 TCCGCCAATTCATTGCTACTTTAC 59.904 41.667 0.00 0.00 36.48 2.01
1571 1688 2.488153 ACTTTACCTTTGAGCGAATGCC 59.512 45.455 0.00 0.00 44.31 4.40
1668 1789 7.168972 CCGACATTCATCTTCTTGAGAGATAAC 59.831 40.741 0.00 0.00 37.93 1.89
1804 1925 2.743928 GTTCCTGCCTGCCAGTCG 60.744 66.667 0.00 0.00 40.06 4.18
1855 1976 4.237445 CTGGGAGCATCAGCAAGG 57.763 61.111 0.00 0.00 45.49 3.61
1971 2092 1.131126 CCCAGCATCTGTAACTTTGCG 59.869 52.381 0.00 0.00 40.00 4.85
2007 2128 3.845775 CCATATGAACTCGCACAAAAACG 59.154 43.478 3.65 0.00 0.00 3.60
2025 2146 8.514594 ACAAAAACGATGTACTGATTGATTGAT 58.485 29.630 0.00 0.00 0.00 2.57
2053 2174 3.071167 CCAGATGCCTTGAGATCTCATGA 59.929 47.826 30.48 16.32 39.64 3.07
2166 2295 4.536765 AGAAACTATATGCAGGGGTTTGG 58.463 43.478 12.32 0.00 31.51 3.28
2190 2319 2.666619 GCTTGTTCAATGAAGCCAGACG 60.667 50.000 0.00 0.00 38.96 4.18
2452 2584 1.801178 GAGTTGAAGTTCTTGAGGCCG 59.199 52.381 4.17 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 83 0.463833 GAGATTTCCCCGCGTTGGAT 60.464 55.000 14.50 1.97 42.00 3.41
101 102 1.680338 GGGGATCCAACCGAAGATTG 58.320 55.000 15.23 0.00 0.00 2.67
125 126 1.139095 CTACGTTCCGCCTCCTGAC 59.861 63.158 0.00 0.00 0.00 3.51
129 130 2.902759 GAAGCCTACGTTCCGCCTCC 62.903 65.000 0.00 0.00 0.00 4.30
130 131 1.518792 GAAGCCTACGTTCCGCCTC 60.519 63.158 0.00 0.00 0.00 4.70
134 135 0.037605 ACCAAGAAGCCTACGTTCCG 60.038 55.000 0.00 0.00 0.00 4.30
140 144 0.393132 GGCAGGACCAAGAAGCCTAC 60.393 60.000 0.00 0.00 42.01 3.18
169 174 6.495526 TGAAATGCACATATCCATCAATCCAT 59.504 34.615 0.00 0.00 0.00 3.41
170 175 5.834204 TGAAATGCACATATCCATCAATCCA 59.166 36.000 0.00 0.00 0.00 3.41
171 176 6.335471 TGAAATGCACATATCCATCAATCC 57.665 37.500 0.00 0.00 0.00 3.01
172 177 8.304596 AGAATGAAATGCACATATCCATCAATC 58.695 33.333 0.00 0.00 0.00 2.67
173 178 8.088365 CAGAATGAAATGCACATATCCATCAAT 58.912 33.333 0.00 0.00 39.69 2.57
174 179 7.430441 CAGAATGAAATGCACATATCCATCAA 58.570 34.615 0.00 0.00 39.69 2.57
175 180 6.516028 GCAGAATGAAATGCACATATCCATCA 60.516 38.462 0.00 0.00 42.11 3.07
176 181 5.862323 GCAGAATGAAATGCACATATCCATC 59.138 40.000 0.00 0.00 42.11 3.51
180 185 6.017357 TGAGAGCAGAATGAAATGCACATATC 60.017 38.462 0.00 0.00 45.01 1.63
206 221 4.555511 GCAGCCTGCTTATTACTACATTGC 60.556 45.833 10.04 0.00 40.96 3.56
221 241 4.891727 GCCATGCATGCAGCCTGC 62.892 66.667 26.69 19.89 44.83 4.85
337 358 8.807581 CAAAGAAATGAACTTTTGTTGACCTAC 58.192 33.333 0.00 0.00 43.66 3.18
346 367 5.290643 TGAACGCCAAAGAAATGAACTTTTG 59.709 36.000 0.00 0.00 35.74 2.44
451 473 0.667487 GCGTGCTACAGCTTCAGACA 60.667 55.000 2.44 0.00 42.66 3.41
459 481 1.756375 CTGAATCCGCGTGCTACAGC 61.756 60.000 4.92 0.00 42.50 4.40
464 486 3.899981 TTGCCTGAATCCGCGTGCT 62.900 57.895 4.92 0.00 0.00 4.40
468 490 1.603802 ACATATTTGCCTGAATCCGCG 59.396 47.619 0.00 0.00 0.00 6.46
509 531 7.042051 TCCAATAGAACTGAGAAGTTTGTTTCG 60.042 37.037 0.00 0.00 32.33 3.46
510 532 8.154649 TCCAATAGAACTGAGAAGTTTGTTTC 57.845 34.615 0.00 0.00 31.35 2.78
512 534 8.697507 AATCCAATAGAACTGAGAAGTTTGTT 57.302 30.769 0.00 0.00 31.35 2.83
524 546 4.666512 ACCACAGCAAATCCAATAGAACT 58.333 39.130 0.00 0.00 0.00 3.01
541 563 1.092921 GTCCGCAAGTCACAACCACA 61.093 55.000 0.00 0.00 0.00 4.17
606 630 5.690464 ATATGAACAAGAAGAGACCAGCT 57.310 39.130 0.00 0.00 0.00 4.24
653 677 4.488879 GTGAATGGCACTTCAATTCTTCC 58.511 43.478 11.97 0.00 44.27 3.46
669 693 5.652014 AGGGTGTACATACAAATGGTGAATG 59.348 40.000 0.00 0.00 38.04 2.67
719 743 7.810759 ACGTTTTGACAGTTTAAATTGAAGTGT 59.189 29.630 16.68 10.20 41.89 3.55
744 768 9.738832 GAGTACCTCTGTTCTTGAATATAAGAC 57.261 37.037 0.00 0.00 36.48 3.01
952 997 1.476477 GGACTCCTGGACTCTGGTAC 58.524 60.000 0.00 0.00 34.13 3.34
1091 1136 5.750067 TCGATAAACGGCTTCCTTACAATAC 59.250 40.000 0.00 0.00 42.82 1.89
1097 1142 4.460948 AACTCGATAAACGGCTTCCTTA 57.539 40.909 0.00 0.00 42.82 2.69
1137 1253 4.262420 GCAAAGGGAAGCATAACCAAAGAA 60.262 41.667 0.00 0.00 0.00 2.52
1222 1338 6.935240 TTCTTCTCCCAACTCTTTAGATCA 57.065 37.500 0.00 0.00 0.00 2.92
1247 1363 0.874390 GCGTCAGTTGCATCTTCCAA 59.126 50.000 0.00 0.00 0.00 3.53
1332 1448 6.397272 TGAAGGGATTCGAAATTGGAAATTG 58.603 36.000 0.00 0.00 0.00 2.32
1333 1449 6.603940 TGAAGGGATTCGAAATTGGAAATT 57.396 33.333 0.00 0.00 0.00 1.82
1345 1462 6.683974 AATCAATACAGTTGAAGGGATTCG 57.316 37.500 0.00 0.00 31.55 3.34
1350 1467 6.403200 CGTGGTTAATCAATACAGTTGAAGGG 60.403 42.308 0.00 0.00 31.55 3.95
1354 1471 6.072948 CCAACGTGGTTAATCAATACAGTTGA 60.073 38.462 16.72 0.00 37.88 3.18
1357 1474 4.155280 GCCAACGTGGTTAATCAATACAGT 59.845 41.667 0.00 0.00 40.46 3.55
1362 1479 4.799564 AATGCCAACGTGGTTAATCAAT 57.200 36.364 0.00 0.00 40.46 2.57
1452 1569 4.111375 TCAAAGAGAGTTCGGAGTATGC 57.889 45.455 0.00 0.00 0.00 3.14
1454 1571 4.220821 TGCTTCAAAGAGAGTTCGGAGTAT 59.779 41.667 0.00 0.00 0.00 2.12
1458 1575 3.685139 ATGCTTCAAAGAGAGTTCGGA 57.315 42.857 0.00 0.00 0.00 4.55
1499 1616 2.150797 GTAGTTCGTCTACGTCCACG 57.849 55.000 11.90 11.90 46.33 4.94
1539 1656 7.315890 GCTCAAAGGTAAAGTAGCAATGAATT 58.684 34.615 0.00 0.00 0.00 2.17
1547 1664 4.728021 GCATTCGCTCAAAGGTAAAGTAGC 60.728 45.833 0.00 0.00 34.30 3.58
1551 1668 2.159379 GGGCATTCGCTCAAAGGTAAAG 60.159 50.000 0.00 0.00 39.07 1.85
1598 1715 3.242739 CGTGACCAGTTCCTGACAAAAAG 60.243 47.826 0.00 0.00 32.44 2.27
1668 1789 1.066573 ACCAGCTTGTCGATCTCCTTG 60.067 52.381 0.00 0.00 0.00 3.61
1743 1864 4.227538 ACTGTTTACTCATGACTTCGTCG 58.772 43.478 0.00 0.00 34.95 5.12
1804 1925 1.678627 TGCTCGTCCTGAAGCTCTATC 59.321 52.381 0.00 0.00 0.00 2.08
1817 1938 3.665675 AATGGAGGCCGTGCTCGTC 62.666 63.158 7.47 0.00 35.01 4.20
1971 2092 0.744414 ATATGGACAGCGTGTGTGGC 60.744 55.000 0.00 0.00 40.56 5.01
2007 2128 6.148480 GGCTGGTATCAATCAATCAGTACATC 59.852 42.308 0.00 0.00 0.00 3.06
2053 2174 7.171337 GGCAATTTTGTTGTACAGTCATGATTT 59.829 33.333 0.00 0.00 0.00 2.17
2166 2295 1.266718 TGGCTTCATTGAACAAGCGAC 59.733 47.619 0.00 0.00 45.13 5.19
2190 2319 6.135290 TGCAGCTCACCAAATAATTGATAC 57.865 37.500 0.00 0.00 38.94 2.24
2242 2374 1.144057 CTATTTCCTGCTCGGCGGT 59.856 57.895 7.21 0.00 32.22 5.68
2338 2470 3.827898 GACCTCGACTCCGGCAGG 61.828 72.222 0.00 0.00 36.28 4.85
2658 2790 1.084370 GCGCATCGGCAAGAACTACT 61.084 55.000 0.30 0.00 41.24 2.57
2731 2863 1.376037 CAAGCCCTCCAACCTCGTC 60.376 63.158 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.