Multiple sequence alignment - TraesCS7D01G227700

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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 TraesCS7D01G227700 chr7D 100.000 2779 0 0 1 2779 187916496 187913718 0.000000e+00 5132.0
1 TraesCS7D01G227700 chr7B 90.994 2787 233 13 1 2779 331659178 331656402 0.000000e+00 3740.0
2 TraesCS7D01G227700 chr7A 90.774 2699 202 26 119 2779 196141843 196144532 0.000000e+00 3561.0
3 TraesCS7D01G227700 chr5B 100.000 37 0 0 2248 2284 206440178 206440142 4.970000e-08 69.4
4 TraesCS7D01G227700 chr3A 100.000 37 0 0 2248 2284 560756453 560756417 4.970000e-08 69.4
5 TraesCS7D01G227700 chr3A 97.297 37 1 0 2248 2284 355927182 355927218 2.310000e-06 63.9
6 TraesCS7D01G227700 chr2B 86.154 65 7 2 2248 2312 435763338 435763276 4.970000e-08 69.4
7 TraesCS7D01G227700 chr4A 91.667 48 4 0 2248 2295 689398683 689398636 1.790000e-07 67.6
8 TraesCS7D01G227700 chr6B 97.297 37 1 0 2248 2284 165243094 165243130 2.310000e-06 63.9
9 TraesCS7D01G227700 chr6B 97.297 37 1 0 2248 2284 340156861 340156897 2.310000e-06 63.9


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 TraesCS7D01G227700 chr7D 187913718 187916496 2778 True 5132 5132 100.000 1 2779 1 chr7D.!!$R1 2778
1 TraesCS7D01G227700 chr7B 331656402 331659178 2776 True 3740 3740 90.994 1 2779 1 chr7B.!!$R1 2778
2 TraesCS7D01G227700 chr7A 196141843 196144532 2689 False 3561 3561 90.774 119 2779 1 chr7A.!!$F1 2660

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
332 333 0.322456 CCACCGGTCATGGACATGTT 60.322 55.0 2.59 0.0 39.87 2.71 F
625 627 0.461961 GTTGAGGAGGGAGGTGATCG 59.538 60.0 0.00 0.0 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1210 1239 0.464036 TCATATGTCCACCACGAGCC 59.536 55.000 1.9 0.0 0.0 4.70 R
1917 1950 1.136305 TCATCCGTTCAGTCGATTCCC 59.864 52.381 0.0 0.0 0.0 3.97 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
27 28 4.475016 AGTAGGGCTATTCCACTGTTTCAT 59.525 41.667 0.00 0.00 36.21 2.57
30 31 2.223340 GGCTATTCCACTGTTTCATGCG 60.223 50.000 0.00 0.00 34.01 4.73
38 39 3.114809 CACTGTTTCATGCGCAAGAAAA 58.885 40.909 34.27 24.16 43.02 2.29
41 42 3.715495 TGTTTCATGCGCAAGAAAATGT 58.285 36.364 34.27 6.20 43.02 2.71
42 43 3.490155 TGTTTCATGCGCAAGAAAATGTG 59.510 39.130 34.27 18.07 43.02 3.21
43 44 2.350899 TCATGCGCAAGAAAATGTGG 57.649 45.000 17.11 0.00 43.02 4.17
52 53 4.016444 GCAAGAAAATGTGGGATAGGACA 58.984 43.478 0.00 0.00 0.00 4.02
58 59 1.951209 TGTGGGATAGGACAGCTTCA 58.049 50.000 0.00 0.00 0.00 3.02
81 82 1.922821 CCCCGGGAAGACCAATGAT 59.077 57.895 26.32 0.00 40.22 2.45
92 93 2.437281 AGACCAATGATAGTGGCTCCAG 59.563 50.000 0.00 0.00 40.02 3.86
127 128 1.074926 AGCCATCATCGACCTCCCT 60.075 57.895 0.00 0.00 0.00 4.20
163 164 2.803479 GCGTCGTCCGGGTAGATT 59.197 61.111 0.00 0.00 36.94 2.40
190 191 2.514824 GCATCACCCCGAGAAGCC 60.515 66.667 0.00 0.00 0.00 4.35
248 249 2.278661 GCGTACTGGCTAGGTCGC 60.279 66.667 20.19 20.19 40.56 5.19
271 272 4.451150 CGTAAGGGCTCGCCTGCA 62.451 66.667 8.00 0.00 36.10 4.41
309 310 0.680921 CAATGACGTTGGCCCCAGAT 60.681 55.000 0.00 0.00 34.06 2.90
310 311 0.680921 AATGACGTTGGCCCCAGATG 60.681 55.000 0.00 0.00 0.00 2.90
332 333 0.322456 CCACCGGTCATGGACATGTT 60.322 55.000 2.59 0.00 39.87 2.71
377 378 1.139058 GCAGTTCATATGGTCCGGAGT 59.861 52.381 3.06 0.00 0.00 3.85
388 389 1.077805 TCCGGAGTGCTCCCAACTA 59.922 57.895 0.00 0.00 46.96 2.24
392 393 0.615850 GGAGTGCTCCCAACTAGCTT 59.384 55.000 6.98 0.00 43.94 3.74
396 397 1.815840 GCTCCCAACTAGCTTCCGC 60.816 63.158 0.00 0.00 37.01 5.54
399 400 2.264794 CCAACTAGCTTCCGCGGT 59.735 61.111 27.15 8.36 42.32 5.68
414 415 3.085208 CGGTAAGGCACTGCATGAT 57.915 52.632 2.82 0.00 40.86 2.45
418 419 3.555795 CGGTAAGGCACTGCATGATAGAT 60.556 47.826 2.82 0.00 40.86 1.98
419 420 3.750130 GGTAAGGCACTGCATGATAGATG 59.250 47.826 2.82 0.00 40.86 2.90
423 424 2.289882 GGCACTGCATGATAGATGGCTA 60.290 50.000 2.82 0.00 0.00 3.93
569 571 3.416156 AGTGAAGCACTTGGATTCTTCC 58.584 45.455 0.00 0.00 42.59 3.46
582 584 2.656947 TTCTTCCCAGGACACAAAGG 57.343 50.000 0.00 0.00 0.00 3.11
625 627 0.461961 GTTGAGGAGGGAGGTGATCG 59.538 60.000 0.00 0.00 0.00 3.69
644 646 2.961741 TCGAAGGGAGATTCCTCATCAG 59.038 50.000 0.00 0.00 41.20 2.90
647 649 2.048601 AGGGAGATTCCTCATCAGCAG 58.951 52.381 0.00 0.00 41.20 4.24
660 662 6.060136 CCTCATCAGCAGAATCCTTCAAATA 58.940 40.000 0.00 0.00 0.00 1.40
711 713 2.159421 GCAATGTTCAGAGTCATGCCAG 60.159 50.000 0.00 0.00 0.00 4.85
775 804 6.409234 GGACTCCCTGAATTGGTAATATCACA 60.409 42.308 0.00 0.00 0.00 3.58
891 920 9.406828 CTAATGTTATTTCGTCTATTCCATCGA 57.593 33.333 0.00 0.00 0.00 3.59
1035 1064 2.159142 ACTTGGCCTATACGTAGCACAC 60.159 50.000 3.32 0.00 0.00 3.82
1037 1066 1.826096 TGGCCTATACGTAGCACACAA 59.174 47.619 3.32 0.00 0.00 3.33
1070 1099 9.697990 AACCAACTTATAGTTAGTAGACTAGCT 57.302 33.333 10.42 10.42 41.76 3.32
1085 1114 4.528596 AGACTAGCTAGCAAAGGTCTTTCA 59.471 41.667 20.91 0.00 37.13 2.69
1117 1146 0.893270 TCAAGTTCATGGCAACCGGG 60.893 55.000 6.32 0.00 0.00 5.73
1118 1147 2.275380 AAGTTCATGGCAACCGGGC 61.275 57.895 6.32 0.00 43.73 6.13
1195 1224 0.689412 GCTCCTTCTGCCCTAGGACT 60.689 60.000 11.48 0.00 35.66 3.85
1210 1239 3.214696 AGGACTTTCACAAACCTCCAG 57.785 47.619 0.00 0.00 0.00 3.86
1283 1312 4.070716 GAGGAAGCATGAGGAATACATGG 58.929 47.826 0.00 0.00 43.39 3.66
1329 1358 2.647299 TGGACCCACTATCACCAAACAT 59.353 45.455 0.00 0.00 0.00 2.71
1514 1543 6.521162 GTGGAAGATAAGGAGAAAGGAGATC 58.479 44.000 0.00 0.00 0.00 2.75
1519 1548 7.360113 AGATAAGGAGAAAGGAGATCAAGAC 57.640 40.000 0.00 0.00 0.00 3.01
1543 1572 5.423015 GAGAACCTGAGCATTGATCTTACA 58.577 41.667 3.27 0.00 0.00 2.41
1579 1608 7.387673 TGATTTGATTCATCACTACGAGTTTGT 59.612 33.333 0.00 0.00 36.36 2.83
1580 1609 6.706055 TTGATTCATCACTACGAGTTTGTC 57.294 37.500 0.00 0.00 36.36 3.18
1766 1796 9.844790 TGTATGAAATGCTTCTTATCAACTTTG 57.155 29.630 0.00 0.00 32.33 2.77
1767 1797 9.294030 GTATGAAATGCTTCTTATCAACTTTGG 57.706 33.333 0.00 0.00 32.33 3.28
1810 1843 1.560860 GGTGAGTCTGTTCGCAGCAC 61.561 60.000 0.00 0.00 44.62 4.40
1816 1849 4.174009 GAGTCTGTTCGCAGCACTAAATA 58.826 43.478 0.00 0.00 44.62 1.40
1915 1948 7.287235 AGTTCGTTGTAGTAAATCTAGGCCTAT 59.713 37.037 14.30 0.02 0.00 2.57
1917 1950 8.332996 TCGTTGTAGTAAATCTAGGCCTATAG 57.667 38.462 14.30 4.22 0.00 1.31
2044 2077 9.161629 TGCATAATTACTCTCTTCAAATTCGAA 57.838 29.630 0.00 0.00 0.00 3.71
2084 2117 4.300189 TCCTTTCGGTGTTTCAAACATG 57.700 40.909 6.17 2.72 44.35 3.21
2283 2316 7.259290 AGGCGTGTAATATACCATTGAAAAG 57.741 36.000 0.00 0.00 0.00 2.27
2465 2499 3.253188 GCTGGAAATCTGCTACAAACACA 59.747 43.478 0.00 0.00 37.35 3.72
2474 2508 3.886505 CTGCTACAAACACACCCCTTTAA 59.113 43.478 0.00 0.00 0.00 1.52
2500 2534 7.931578 AACATTTCTCAAATTCCATACGGTA 57.068 32.000 0.00 0.00 0.00 4.02
2578 2615 9.598517 TTTGCTCTAATTTTGAAACATCTTGTT 57.401 25.926 0.00 0.00 43.41 2.83
2579 2616 8.578308 TGCTCTAATTTTGAAACATCTTGTTG 57.422 30.769 0.00 0.00 40.14 3.33
2689 2728 8.686334 GTTTAAATTGAAATATGAGAGCAGGGA 58.314 33.333 0.00 0.00 0.00 4.20
2696 2735 6.769822 TGAAATATGAGAGCAGGGAAATTCTC 59.230 38.462 0.00 0.00 37.24 2.87
2703 2742 5.008980 AGAGCAGGGAAATTCTCTTCAAAG 58.991 41.667 0.00 0.00 32.44 2.77
2705 2744 3.829026 GCAGGGAAATTCTCTTCAAAGGT 59.171 43.478 0.00 0.00 0.00 3.50
2734 2773 1.368374 AAAGGTTTCTCGGATGGGGA 58.632 50.000 0.00 0.00 0.00 4.81
2745 2784 6.696042 TCTCGGATGGGGAAAATGATATAA 57.304 37.500 0.00 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 2.431454 TGCGCATGAAACAGTGGAATA 58.569 42.857 5.66 0.00 0.00 1.75
13 14 1.246649 TGCGCATGAAACAGTGGAAT 58.753 45.000 5.66 0.00 0.00 3.01
14 15 1.001487 CTTGCGCATGAAACAGTGGAA 60.001 47.619 17.78 0.00 0.00 3.53
15 16 0.592637 CTTGCGCATGAAACAGTGGA 59.407 50.000 17.78 0.00 0.00 4.02
27 28 1.255882 ATCCCACATTTTCTTGCGCA 58.744 45.000 5.66 5.66 0.00 6.09
30 31 4.016444 TGTCCTATCCCACATTTTCTTGC 58.984 43.478 0.00 0.00 0.00 4.01
38 39 2.481441 TGAAGCTGTCCTATCCCACAT 58.519 47.619 0.00 0.00 0.00 3.21
41 42 1.210478 GCTTGAAGCTGTCCTATCCCA 59.790 52.381 10.44 0.00 38.45 4.37
42 43 1.808133 CGCTTGAAGCTGTCCTATCCC 60.808 57.143 15.92 0.00 39.60 3.85
43 44 1.576356 CGCTTGAAGCTGTCCTATCC 58.424 55.000 15.92 0.00 39.60 2.59
65 66 2.485479 CCACTATCATTGGTCTTCCCGG 60.485 54.545 0.00 0.00 35.15 5.73
69 70 3.118261 TGGAGCCACTATCATTGGTCTTC 60.118 47.826 0.00 0.00 36.40 2.87
110 111 1.070445 CAGGGAGGTCGATGATGGC 59.930 63.158 0.00 0.00 0.00 4.40
147 148 1.262683 GTCTAATCTACCCGGACGACG 59.737 57.143 0.73 0.00 43.80 5.12
149 150 2.569059 CAGTCTAATCTACCCGGACGA 58.431 52.381 0.73 0.00 32.86 4.20
158 159 3.004839 GGTGATGCGAGCAGTCTAATCTA 59.995 47.826 3.58 0.00 0.00 1.98
163 164 1.676678 GGGGTGATGCGAGCAGTCTA 61.677 60.000 3.58 0.00 0.00 2.59
255 256 2.046314 TTGCAGGCGAGCCCTTAC 60.046 61.111 10.95 0.00 43.06 2.34
271 272 1.147153 GGCGGCATTAGGAGCTCTT 59.853 57.895 14.64 8.96 0.00 2.85
277 278 0.465460 GTCATTGGGCGGCATTAGGA 60.465 55.000 12.47 0.00 0.00 2.94
306 307 0.761187 CCATGACCGGTGGATCATCT 59.239 55.000 14.63 0.00 39.12 2.90
309 310 0.907230 TGTCCATGACCGGTGGATCA 60.907 55.000 14.63 10.94 46.68 2.92
310 311 0.469917 ATGTCCATGACCGGTGGATC 59.530 55.000 14.63 8.40 46.68 3.36
377 378 1.596934 CGGAAGCTAGTTGGGAGCA 59.403 57.895 0.00 0.00 42.69 4.26
392 393 4.752879 GCAGTGCCTTACCGCGGA 62.753 66.667 35.90 13.31 0.00 5.54
396 397 2.138320 CTATCATGCAGTGCCTTACCG 58.862 52.381 13.72 0.00 0.00 4.02
399 400 3.808265 GCCATCTATCATGCAGTGCCTTA 60.808 47.826 13.72 0.00 0.00 2.69
414 415 2.041081 GAGAGAGCCTCCTAGCCATCTA 59.959 54.545 0.00 0.00 35.87 1.98
569 571 1.619654 TTCATGCCTTTGTGTCCTGG 58.380 50.000 0.00 0.00 0.00 4.45
582 584 8.937634 ACTCATCATTCCTTTAAAATTCATGC 57.062 30.769 0.00 0.00 0.00 4.06
625 627 2.437281 TGCTGATGAGGAATCTCCCTTC 59.563 50.000 0.00 0.00 37.19 3.46
647 649 8.645110 ATGGTTTCATGGATATTTGAAGGATTC 58.355 33.333 0.00 0.00 37.69 2.52
660 662 6.891361 TGTTTGTATCAGATGGTTTCATGGAT 59.109 34.615 0.00 0.00 32.98 3.41
711 713 5.691305 TGCAATGTAGCAGAAACATTCAAAC 59.309 36.000 0.00 0.00 43.84 2.93
783 812 5.789574 TTGGGAGTAGTAAATGGGTCAAT 57.210 39.130 0.00 0.00 0.00 2.57
891 920 8.451908 AACTACTGCACAAAAAGATAAAGAGT 57.548 30.769 0.00 0.00 0.00 3.24
1035 1064 9.367444 ACTAACTATAAGTTGGTTCGAGATTTG 57.633 33.333 3.29 0.00 45.78 2.32
1063 1092 4.822026 TGAAAGACCTTTGCTAGCTAGTC 58.178 43.478 21.62 15.81 32.11 2.59
1070 1099 5.072741 AGCTTCAATGAAAGACCTTTGCTA 58.927 37.500 0.00 0.00 32.11 3.49
1071 1100 3.893813 AGCTTCAATGAAAGACCTTTGCT 59.106 39.130 0.00 0.00 32.11 3.91
1072 1101 4.233005 GAGCTTCAATGAAAGACCTTTGC 58.767 43.478 0.00 0.00 32.11 3.68
1073 1102 4.470462 CGAGCTTCAATGAAAGACCTTTG 58.530 43.478 0.00 0.00 32.11 2.77
1085 1114 3.076621 TGAACTTGATGCGAGCTTCAAT 58.923 40.909 21.23 11.49 38.70 2.57
1195 1224 1.813862 CGAGCCTGGAGGTTTGTGAAA 60.814 52.381 0.00 0.00 37.57 2.69
1210 1239 0.464036 TCATATGTCCACCACGAGCC 59.536 55.000 1.90 0.00 0.00 4.70
1283 1312 2.959030 AGAACTCCTTGGACTTTTTGGC 59.041 45.455 0.00 0.00 0.00 4.52
1329 1358 3.494398 GCGATACCTTCTCCAATAAGCCA 60.494 47.826 0.00 0.00 0.00 4.75
1514 1543 2.376808 ATGCTCAGGTTCTCGTCTTG 57.623 50.000 0.00 0.00 0.00 3.02
1519 1548 3.176552 AGATCAATGCTCAGGTTCTCG 57.823 47.619 0.00 0.00 0.00 4.04
1571 1600 5.444983 CCTCACTAGATATCGACAAACTCG 58.555 45.833 0.00 0.00 44.44 4.18
1579 1608 6.056090 ACATAGAGCCTCACTAGATATCGA 57.944 41.667 0.00 0.00 0.00 3.59
1580 1609 6.183360 GGAACATAGAGCCTCACTAGATATCG 60.183 46.154 0.00 0.00 0.00 2.92
1744 1774 7.288810 ACCAAAGTTGATAAGAAGCATTTCA 57.711 32.000 0.00 0.00 35.70 2.69
1766 1796 7.860872 CCATTCTAATTTATTCGCCAAACTACC 59.139 37.037 0.00 0.00 0.00 3.18
1767 1797 8.403236 ACCATTCTAATTTATTCGCCAAACTAC 58.597 33.333 0.00 0.00 0.00 2.73
1893 1926 7.362747 CCCTATAGGCCTAGATTTACTACAACG 60.363 44.444 19.33 0.00 0.00 4.10
1915 1948 2.133281 TCCGTTCAGTCGATTCCCTA 57.867 50.000 0.00 0.00 0.00 3.53
1917 1950 1.136305 TCATCCGTTCAGTCGATTCCC 59.864 52.381 0.00 0.00 0.00 3.97
2070 2103 8.816640 AAGTATTTGATCATGTTTGAAACACC 57.183 30.769 13.56 4.07 45.50 4.16
2084 2117 9.474920 TTTGATGGTGTTTGAAAGTATTTGATC 57.525 29.630 0.00 0.00 39.27 2.92
2283 2316 8.553459 TGAGAATTTATCTTCTTGTCCTCAAC 57.447 34.615 0.00 0.00 38.96 3.18
2465 2499 9.337396 GAATTTGAGAAATGTTTTTAAAGGGGT 57.663 29.630 0.00 0.00 0.00 4.95
2474 2508 7.666623 ACCGTATGGAATTTGAGAAATGTTTT 58.333 30.769 8.33 0.00 39.21 2.43
2500 2534 6.284459 TCCACCGCTTTTCAAATTTGTTTAT 58.716 32.000 17.47 0.00 0.00 1.40
2505 2539 5.671742 AAATCCACCGCTTTTCAAATTTG 57.328 34.783 12.15 12.15 0.00 2.32
2672 2711 6.997476 AGAGAATTTCCCTGCTCTCATATTTC 59.003 38.462 0.00 0.00 37.39 2.17
2683 2722 3.829026 ACCTTTGAAGAGAATTTCCCTGC 59.171 43.478 0.00 0.00 0.00 4.85
2684 2723 4.219288 CCACCTTTGAAGAGAATTTCCCTG 59.781 45.833 0.00 0.00 0.00 4.45
2689 2728 5.791336 GGTTCCACCTTTGAAGAGAATTT 57.209 39.130 0.00 0.00 34.73 1.82
2726 2765 7.010160 TCCAACTTATATCATTTTCCCCATCC 58.990 38.462 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.