Multiple sequence alignment - TraesCS7B01G225400

Loading Multiple Alignment...

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 TraesCS7B01G225400 chr7B 100.000 3142 0 0 1 3142 426100660 426103801 0.000000e+00 5803
1 TraesCS7B01G225400 chr7B 93.502 277 16 2 2630 2905 426110493 426110218 8.110000e-111 411
2 TraesCS7B01G225400 chr7D 94.244 2658 81 26 1 2633 411603535 411606145 0.000000e+00 3995
3 TraesCS7B01G225400 chr7A 93.698 2666 83 30 1 2633 472566213 472568826 0.000000e+00 3914
4 TraesCS7B01G225400 chr7A 98.225 507 6 1 2636 3142 52218516 52219019 0.000000e+00 883
5 TraesCS7B01G225400 chr4A 93.709 302 19 0 2636 2937 676316676 676316375 1.330000e-123 453
6 TraesCS7B01G225400 chr4A 93.092 304 19 2 2636 2937 676261687 676261990 8.000000e-121 444
7 TraesCS7B01G225400 chr6A 93.050 259 17 1 2883 3141 14150894 14151151 8.230000e-101 377
8 TraesCS7B01G225400 chr6A 94.737 209 11 0 2636 2844 14150433 14150641 3.020000e-85 326
9 TraesCS7B01G225400 chr6A 92.925 212 13 2 2636 2846 14157479 14157269 1.090000e-79 307
10 TraesCS7B01G225400 chr3A 83.843 229 36 1 2636 2864 357518483 357518256 1.900000e-52 217
11 TraesCS7B01G225400 chr3B 77.817 284 46 14 2626 2902 746692017 746691744 3.240000e-35 159
12 TraesCS7B01G225400 chr1B 77.419 279 46 14 2625 2895 484296296 484296027 1.950000e-32 150


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 TraesCS7B01G225400 chr7B 426100660 426103801 3141 False 5803.0 5803 100.0000 1 3142 1 chr7B.!!$F1 3141
1 TraesCS7B01G225400 chr7D 411603535 411606145 2610 False 3995.0 3995 94.2440 1 2633 1 chr7D.!!$F1 2632
2 TraesCS7B01G225400 chr7A 472566213 472568826 2613 False 3914.0 3914 93.6980 1 2633 1 chr7A.!!$F2 2632
3 TraesCS7B01G225400 chr7A 52218516 52219019 503 False 883.0 883 98.2250 2636 3142 1 chr7A.!!$F1 506
4 TraesCS7B01G225400 chr6A 14150433 14151151 718 False 351.5 377 93.8935 2636 3141 2 chr6A.!!$F1 505

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
491 516 0.179009 GGGCTGCTGCAGAATATGGA 60.179 55.0 32.3 0.0 41.91 3.41 F
1011 1050 0.106369 CATCTCCCATGCACCACCAT 60.106 55.0 0.0 0.0 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1476 1519 0.107703 GATGAGCCGATGGGTGTGAA 60.108 55.0 0.0 0.00 31.55 3.18 R
2158 2201 1.569708 GCTAGCTGCTGCAGAAGTAG 58.430 55.0 32.3 25.35 41.30 2.57 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
21 22 1.727062 ATCTCTCGGATTCCATGCCT 58.273 50.000 3.09 0.00 0.00 4.75
40 41 2.695147 CCTGCCTTTGAAACTTTGTCCT 59.305 45.455 0.00 0.00 0.00 3.85
41 42 3.243535 CCTGCCTTTGAAACTTTGTCCTC 60.244 47.826 0.00 0.00 0.00 3.71
42 43 2.693074 TGCCTTTGAAACTTTGTCCTCC 59.307 45.455 0.00 0.00 0.00 4.30
111 112 0.532862 GTGCATGCCAGGCGTACTAT 60.533 55.000 16.68 0.00 0.00 2.12
192 198 9.541143 ACACAGACAAAAGAAAAGAAAAGAAAA 57.459 25.926 0.00 0.00 0.00 2.29
203 209 9.836864 AGAAAAGAAAAGAAAATACAAGGCAAT 57.163 25.926 0.00 0.00 0.00 3.56
207 213 9.489084 AAGAAAAGAAAATACAAGGCAATTACC 57.511 29.630 0.00 0.00 0.00 2.85
208 214 7.812669 AGAAAAGAAAATACAAGGCAATTACCG 59.187 33.333 0.00 0.00 33.69 4.02
255 262 6.372659 GCTGCAACTGCCATATAGTATATGTT 59.627 38.462 22.83 11.71 41.18 2.71
297 304 1.655484 CAATGGCGAGTGATGCACTA 58.345 50.000 0.00 0.00 45.44 2.74
472 496 1.386525 CCACCCGGATTCAATGGCTG 61.387 60.000 0.73 0.00 0.00 4.85
491 516 0.179009 GGGCTGCTGCAGAATATGGA 60.179 55.000 32.30 0.00 41.91 3.41
492 517 1.683943 GGCTGCTGCAGAATATGGAA 58.316 50.000 32.30 0.00 41.91 3.53
519 544 3.379445 AGCAATGCCAGCTGCCAC 61.379 61.111 8.66 0.00 41.61 5.01
530 555 2.674380 CTGCCACCTCCAAGTGCC 60.674 66.667 0.00 0.00 36.38 5.01
618 643 1.078347 GGCAATGGTCCCCCTTGAA 59.922 57.895 2.91 0.00 0.00 2.69
668 696 3.343788 GACGGAGCGGAGTGGAGTG 62.344 68.421 0.00 0.00 0.00 3.51
669 697 3.062466 CGGAGCGGAGTGGAGTGA 61.062 66.667 0.00 0.00 0.00 3.41
670 698 2.888863 GGAGCGGAGTGGAGTGAG 59.111 66.667 0.00 0.00 0.00 3.51
671 699 1.679305 GGAGCGGAGTGGAGTGAGA 60.679 63.158 0.00 0.00 0.00 3.27
672 700 1.251527 GGAGCGGAGTGGAGTGAGAA 61.252 60.000 0.00 0.00 0.00 2.87
702 730 1.005748 GAAAACTGGCTTGGCTGGC 60.006 57.895 0.00 0.00 0.00 4.85
748 776 1.472480 ACGTTTTCCCATGCATGCTAC 59.528 47.619 21.69 11.84 0.00 3.58
749 777 1.531677 CGTTTTCCCATGCATGCTACG 60.532 52.381 21.69 18.58 0.00 3.51
750 778 0.455410 TTTTCCCATGCATGCTACGC 59.545 50.000 21.69 0.00 0.00 4.42
751 779 0.394216 TTTCCCATGCATGCTACGCT 60.394 50.000 21.69 0.00 0.00 5.07
752 780 0.467804 TTCCCATGCATGCTACGCTA 59.532 50.000 21.69 0.00 0.00 4.26
762 796 4.212847 TGCATGCTACGCTACTACTAGTAC 59.787 45.833 20.33 0.00 0.00 2.73
764 798 5.389725 GCATGCTACGCTACTACTAGTACTC 60.390 48.000 11.37 0.00 0.00 2.59
845 884 1.228644 AGCAGTCTTGGCAATGGCA 60.229 52.632 5.05 5.05 43.71 4.92
946 985 3.223589 GCCTCCTCTCCGCTCCTC 61.224 72.222 0.00 0.00 0.00 3.71
950 989 2.904866 CCTCTCCGCTCCTCTCCG 60.905 72.222 0.00 0.00 0.00 4.63
968 1007 6.177310 TCTCCGTCCTCTATATATAGGCTC 57.823 45.833 17.81 7.26 32.55 4.70
1011 1050 0.106369 CATCTCCCATGCACCACCAT 60.106 55.000 0.00 0.00 0.00 3.55
1037 1076 1.153939 CTCTGCTCTCACCGTTCCG 60.154 63.158 0.00 0.00 0.00 4.30
1048 1091 2.473760 CCGTTCCGGCAAACACACA 61.474 57.895 0.00 0.00 41.17 3.72
1053 1096 1.226547 CCGGCAAACACACACACAC 60.227 57.895 0.00 0.00 0.00 3.82
1054 1097 1.503994 CGGCAAACACACACACACA 59.496 52.632 0.00 0.00 0.00 3.72
1055 1098 0.796491 CGGCAAACACACACACACAC 60.796 55.000 0.00 0.00 0.00 3.82
1056 1099 0.242286 GGCAAACACACACACACACA 59.758 50.000 0.00 0.00 0.00 3.72
1057 1100 1.336332 GGCAAACACACACACACACAA 60.336 47.619 0.00 0.00 0.00 3.33
1058 1101 1.718711 GCAAACACACACACACACAAC 59.281 47.619 0.00 0.00 0.00 3.32
1191 1234 3.013932 CCCTTCCTCCAGCAGGCT 61.014 66.667 0.00 0.00 43.08 4.58
1242 1285 4.664677 GTCCACCTCGTGCAGCGT 62.665 66.667 8.22 0.00 42.13 5.07
1472 1515 1.645455 CCTATGCGTGCATGCTCAC 59.355 57.895 29.83 10.16 37.82 3.51
1476 1519 1.239296 ATGCGTGCATGCTCACTTGT 61.239 50.000 29.83 6.22 35.03 3.16
1481 1524 1.334556 GTGCATGCTCACTTGTTCACA 59.665 47.619 20.33 0.00 34.29 3.58
1487 1530 1.537202 GCTCACTTGTTCACACCCATC 59.463 52.381 0.00 0.00 0.00 3.51
1489 1532 0.874390 CACTTGTTCACACCCATCGG 59.126 55.000 0.00 0.00 0.00 4.18
1490 1533 0.889186 ACTTGTTCACACCCATCGGC 60.889 55.000 0.00 0.00 0.00 5.54
1491 1534 0.606401 CTTGTTCACACCCATCGGCT 60.606 55.000 0.00 0.00 0.00 5.52
1492 1535 0.605319 TTGTTCACACCCATCGGCTC 60.605 55.000 0.00 0.00 0.00 4.70
1493 1536 1.003839 GTTCACACCCATCGGCTCA 60.004 57.895 0.00 0.00 0.00 4.26
1494 1537 0.392998 GTTCACACCCATCGGCTCAT 60.393 55.000 0.00 0.00 0.00 2.90
1495 1538 0.107703 TTCACACCCATCGGCTCATC 60.108 55.000 0.00 0.00 0.00 2.92
1496 1539 1.884464 CACACCCATCGGCTCATCG 60.884 63.158 0.00 0.00 0.00 3.84
1497 1540 2.969238 CACCCATCGGCTCATCGC 60.969 66.667 0.00 0.00 38.13 4.58
1506 1549 2.517875 GCTCATCGCCCATTGCCT 60.518 61.111 0.00 0.00 36.24 4.75
1507 1550 2.123428 GCTCATCGCCCATTGCCTT 61.123 57.895 0.00 0.00 36.24 4.35
1508 1551 1.731700 CTCATCGCCCATTGCCTTG 59.268 57.895 0.00 0.00 36.24 3.61
1652 1695 4.406173 CTGCTGCTCGACGACCGT 62.406 66.667 0.00 0.00 39.75 4.83
1655 1698 2.254350 CTGCTCGACGACCGTTCA 59.746 61.111 0.00 0.00 39.75 3.18
1874 1917 2.818132 GAGGAGATGGAGGCGGTG 59.182 66.667 0.00 0.00 0.00 4.94
1925 1968 2.678934 TACGAGTTCCGGCAGGCT 60.679 61.111 0.00 0.00 43.93 4.58
2158 2201 2.613133 GCTGATCCAAGCTCACAATCTC 59.387 50.000 0.00 0.00 40.20 2.75
2236 2279 8.784043 AGTACAACAAGGCTAACAAATTAGAAG 58.216 33.333 0.00 0.00 40.38 2.85
2360 2405 3.151554 TGCACTGGAATATCATCATGCC 58.848 45.455 0.00 0.00 0.00 4.40
2439 2485 7.663493 GCTTAGGCCTATCTATTTGTCAGAATT 59.337 37.037 14.74 0.00 0.00 2.17
2497 2543 6.162079 GCATCGATCTTAGAGGATGAATTGA 58.838 40.000 22.12 0.93 38.80 2.57
2568 2614 1.543358 CAGCTCTTTGCCCTTTTCTCC 59.457 52.381 0.00 0.00 44.23 3.71
2608 2654 2.496828 GATGTGGGCAGCTTGTTGGC 62.497 60.000 2.63 2.63 42.44 4.52
2633 2679 7.819900 GCCAGAGACAAAAAGAGAGTTCTATAA 59.180 37.037 0.00 0.00 31.96 0.98
2634 2680 9.364989 CCAGAGACAAAAAGAGAGTTCTATAAG 57.635 37.037 0.00 0.00 31.96 1.73
2699 2745 3.088532 AGTTTGGTGCTGAAACTTGTGA 58.911 40.909 0.00 0.00 40.04 3.58
2778 2824 0.468226 TTGGATACGAGATGGGTGCC 59.532 55.000 0.00 0.00 42.51 5.01
2781 2827 0.603569 GATACGAGATGGGTGCCGAT 59.396 55.000 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.693074 GGAGGACAAAGTTTCAAAGGCA 59.307 45.455 0.00 0.00 0.00 4.75
40 41 3.036959 GGGGGAGGAGGAGGAGGA 61.037 72.222 0.00 0.00 0.00 3.71
41 42 3.039526 AGGGGGAGGAGGAGGAGG 61.040 72.222 0.00 0.00 0.00 4.30
42 43 2.018086 AGAGGGGGAGGAGGAGGAG 61.018 68.421 0.00 0.00 0.00 3.69
111 112 2.376808 GCTGCTGCTTCTTCTAGACA 57.623 50.000 8.53 0.00 36.03 3.41
191 197 7.732996 ACTAGTATCGGTAATTGCCTTGTATT 58.267 34.615 11.07 1.11 0.00 1.89
192 198 7.299246 ACTAGTATCGGTAATTGCCTTGTAT 57.701 36.000 11.07 2.12 0.00 2.29
193 199 6.720112 ACTAGTATCGGTAATTGCCTTGTA 57.280 37.500 11.07 0.00 0.00 2.41
195 201 6.746120 ACTACTAGTATCGGTAATTGCCTTG 58.254 40.000 11.07 0.00 0.00 3.61
197 203 8.647256 ATTACTACTAGTATCGGTAATTGCCT 57.353 34.615 15.31 0.00 31.62 4.75
198 204 9.780413 GTATTACTACTAGTATCGGTAATTGCC 57.220 37.037 21.65 1.83 35.55 4.52
207 213 9.343103 CAGCCAAATGTATTACTACTAGTATCG 57.657 37.037 2.33 0.00 29.64 2.92
208 214 9.141400 GCAGCCAAATGTATTACTACTAGTATC 57.859 37.037 2.33 0.00 29.64 2.24
255 262 3.766591 CACCCAGCCACCAAATTAATGTA 59.233 43.478 0.00 0.00 0.00 2.29
266 273 3.384532 CCATTGCACCCAGCCACC 61.385 66.667 0.00 0.00 44.83 4.61
472 496 0.179009 TCCATATTCTGCAGCAGCCC 60.179 55.000 18.43 0.00 41.13 5.19
519 544 0.108615 CAGTACTCGGCACTTGGAGG 60.109 60.000 0.00 0.00 34.58 4.30
530 555 2.882777 CGCCAGCAGCAGTACTCG 60.883 66.667 0.00 0.00 44.04 4.18
573 598 3.551846 CCCCAGGCGATTAATTACTTGT 58.448 45.455 0.00 0.00 0.00 3.16
618 643 4.342359 AGTTGTACGTACTCCTTCCAGAT 58.658 43.478 25.12 0.00 0.00 2.90
668 696 5.356470 CCAGTTTTCCCATGAATCTCTTCTC 59.644 44.000 0.00 0.00 32.29 2.87
669 697 5.259632 CCAGTTTTCCCATGAATCTCTTCT 58.740 41.667 0.00 0.00 32.29 2.85
670 698 4.142293 GCCAGTTTTCCCATGAATCTCTTC 60.142 45.833 0.00 0.00 0.00 2.87
671 699 3.766051 GCCAGTTTTCCCATGAATCTCTT 59.234 43.478 0.00 0.00 0.00 2.85
672 700 3.011032 AGCCAGTTTTCCCATGAATCTCT 59.989 43.478 0.00 0.00 0.00 3.10
748 776 4.281688 AGAGGAGGAGTACTAGTAGTAGCG 59.718 50.000 10.38 0.00 30.12 4.26
749 777 5.541484 AGAGAGGAGGAGTACTAGTAGTAGC 59.459 48.000 10.38 6.01 30.12 3.58
750 778 6.072286 CGAGAGAGGAGGAGTACTAGTAGTAG 60.072 50.000 10.38 2.87 30.12 2.57
751 779 5.769662 CGAGAGAGGAGGAGTACTAGTAGTA 59.230 48.000 10.28 5.90 0.00 1.82
752 780 4.586001 CGAGAGAGGAGGAGTACTAGTAGT 59.414 50.000 10.09 10.09 0.00 2.73
762 796 2.477176 CGCCACGAGAGAGGAGGAG 61.477 68.421 0.00 0.00 45.46 3.69
764 798 2.438614 TCGCCACGAGAGAGGAGG 60.439 66.667 0.00 0.00 45.46 4.30
945 984 5.666265 TGAGCCTATATATAGAGGACGGAGA 59.334 44.000 24.65 1.72 36.82 3.71
946 985 5.931294 TGAGCCTATATATAGAGGACGGAG 58.069 45.833 24.65 0.34 36.82 4.63
968 1007 0.105224 CTGAGCTGGAGCAGAGGATG 59.895 60.000 0.00 0.00 45.16 3.51
1011 1050 0.676184 GTGAGAGCAGAGTGTGGTGA 59.324 55.000 0.00 0.00 36.87 4.02
1037 1076 0.242286 TGTGTGTGTGTGTGTTTGCC 59.758 50.000 0.00 0.00 0.00 4.52
1048 1091 1.999735 CGACTCAAGTGTTGTGTGTGT 59.000 47.619 0.00 0.00 37.49 3.72
1053 1096 1.564622 CGCCGACTCAAGTGTTGTG 59.435 57.895 0.00 0.00 0.00 3.33
1054 1097 1.594293 CCGCCGACTCAAGTGTTGT 60.594 57.895 0.00 0.00 0.00 3.32
1055 1098 2.954753 GCCGCCGACTCAAGTGTTG 61.955 63.158 0.00 0.00 0.00 3.33
1056 1099 2.665185 GCCGCCGACTCAAGTGTT 60.665 61.111 0.00 0.00 0.00 3.32
1057 1100 3.865929 CTGCCGCCGACTCAAGTGT 62.866 63.158 0.00 0.00 0.00 3.55
1058 1101 3.114616 CTGCCGCCGACTCAAGTG 61.115 66.667 0.00 0.00 0.00 3.16
1472 1515 0.606401 AGCCGATGGGTGTGAACAAG 60.606 55.000 0.00 0.00 34.97 3.16
1476 1519 0.107703 GATGAGCCGATGGGTGTGAA 60.108 55.000 0.00 0.00 31.55 3.18
1489 1532 2.123428 AAGGCAATGGGCGATGAGC 61.123 57.895 0.00 0.00 46.16 4.26
1490 1533 1.033746 ACAAGGCAATGGGCGATGAG 61.034 55.000 9.06 0.00 46.16 2.90
1491 1534 0.611618 AACAAGGCAATGGGCGATGA 60.612 50.000 9.06 0.00 46.16 2.92
1492 1535 0.458889 CAACAAGGCAATGGGCGATG 60.459 55.000 1.66 1.66 46.16 3.84
1493 1536 1.606885 CCAACAAGGCAATGGGCGAT 61.607 55.000 0.00 0.00 46.16 4.58
1494 1537 2.274645 CCAACAAGGCAATGGGCGA 61.275 57.895 0.00 0.00 46.16 5.54
1495 1538 2.262292 CCAACAAGGCAATGGGCG 59.738 61.111 0.00 0.00 46.16 6.13
1504 1547 1.753073 GATCAATGGAGGCCAACAAGG 59.247 52.381 5.01 0.00 36.95 3.61
1505 1548 2.165030 GTGATCAATGGAGGCCAACAAG 59.835 50.000 5.01 0.78 36.95 3.16
1506 1549 2.170166 GTGATCAATGGAGGCCAACAA 58.830 47.619 5.01 0.00 36.95 2.83
1507 1550 1.075212 TGTGATCAATGGAGGCCAACA 59.925 47.619 5.01 3.03 36.95 3.33
1508 1551 1.474077 GTGTGATCAATGGAGGCCAAC 59.526 52.381 5.01 0.00 36.95 3.77
1610 1653 2.491022 CGGGTCGATCCTGGTCTCC 61.491 68.421 14.05 0.00 38.86 3.71
1652 1695 0.534203 GCTTGAACTCCACGGGTGAA 60.534 55.000 0.00 0.00 0.00 3.18
1655 1698 1.371558 GAGCTTGAACTCCACGGGT 59.628 57.895 0.00 0.00 0.00 5.28
1925 1968 3.106986 GCTCTCAATGCCGGCCCTA 62.107 63.158 26.77 5.45 0.00 3.53
1950 1993 4.580835 GACCCTGTCGAACTCTGC 57.419 61.111 0.00 0.00 0.00 4.26
2158 2201 1.569708 GCTAGCTGCTGCAGAAGTAG 58.430 55.000 32.30 25.35 41.30 2.57
2360 2405 5.016051 TGCTCTGCTTAGGAAGAATACAG 57.984 43.478 0.00 0.00 0.00 2.74
2459 2505 7.881775 AAGATCGATGCCCTAAAAATTACTT 57.118 32.000 0.54 0.00 0.00 2.24
2474 2520 8.033626 TCATCAATTCATCCTCTAAGATCGATG 58.966 37.037 0.54 0.00 34.66 3.84
2568 2614 4.199310 TCTCCACAGAACTTTTCCAGTTG 58.801 43.478 0.00 0.00 46.53 3.16
2608 2654 9.364989 CTTATAGAACTCTCTTTTTGTCTCTGG 57.635 37.037 0.00 0.00 32.70 3.86
2633 2679 2.979678 ACCTGTGGTGTAATTGACTCCT 59.020 45.455 0.00 0.00 41.53 3.69
2634 2680 3.418684 ACCTGTGGTGTAATTGACTCC 57.581 47.619 0.00 0.00 41.38 3.85


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

AutoCloner maintained by Alex Coulton.