Multiple sequence alignment - TraesCS7D01G061900

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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 TraesCS7D01G061900 chr7D 100.000 2520 0 0 1 2520 33472335 33469816 0.000000e+00 4654.0
1 TraesCS7D01G061900 chr7D 89.944 537 39 13 993 1522 33217068 33216540 0.000000e+00 678.0
2 TraesCS7D01G061900 chr7D 88.783 526 42 14 998 1522 551737769 551738278 1.650000e-176 628.0
3 TraesCS7D01G061900 chr7A 91.522 1781 92 31 1 1758 34034341 34032597 0.000000e+00 2398.0
4 TraesCS7D01G061900 chr7A 83.125 1280 132 47 1170 2430 33977769 33976555 0.000000e+00 1090.0
5 TraesCS7D01G061900 chr7A 93.764 449 25 3 1849 2296 34032103 34031657 0.000000e+00 671.0
6 TraesCS7D01G061900 chr7A 87.037 540 46 17 998 1522 637297952 637298482 2.790000e-164 588.0
7 TraesCS7D01G061900 chr7A 96.552 174 6 0 2347 2520 34031211 34031038 3.170000e-74 289.0
8 TraesCS7D01G061900 chr7A 97.917 48 1 0 2288 2335 34031439 34031392 1.610000e-12 84.2
9 TraesCS7D01G061900 chr4A 87.040 2176 155 53 1 2144 692078333 692080413 0.000000e+00 2338.0
10 TraesCS7D01G061900 chr4A 90.019 531 31 13 998 1522 692358848 692359362 0.000000e+00 667.0
11 TraesCS7D01G061900 chr4A 89.642 531 33 13 998 1522 693596930 693596416 0.000000e+00 656.0
12 TraesCS7D01G061900 chrUn 91.412 524 32 7 997 1519 81832850 81833361 0.000000e+00 706.0
13 TraesCS7D01G061900 chr7B 87.947 531 42 18 999 1522 596606414 596606929 7.710000e-170 606.0
14 TraesCS7D01G061900 chr3B 83.307 629 70 23 9 614 592663327 592663943 4.740000e-152 547.0
15 TraesCS7D01G061900 chr6A 85.907 518 50 17 1001 1510 19167488 19167990 4.770000e-147 531.0
16 TraesCS7D01G061900 chr3D 82.547 636 67 27 9 614 450884661 450885282 1.030000e-143 520.0
17 TraesCS7D01G061900 chr3A 84.087 553 61 16 9 542 594031638 594032182 2.240000e-140 508.0


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 TraesCS7D01G061900 chr7D 33469816 33472335 2519 True 4654.00 4654 100.00000 1 2520 1 chr7D.!!$R2 2519
1 TraesCS7D01G061900 chr7D 33216540 33217068 528 True 678.00 678 89.94400 993 1522 1 chr7D.!!$R1 529
2 TraesCS7D01G061900 chr7D 551737769 551738278 509 False 628.00 628 88.78300 998 1522 1 chr7D.!!$F1 524
3 TraesCS7D01G061900 chr7A 33976555 33977769 1214 True 1090.00 1090 83.12500 1170 2430 1 chr7A.!!$R1 1260
4 TraesCS7D01G061900 chr7A 34031038 34034341 3303 True 860.55 2398 94.93875 1 2520 4 chr7A.!!$R2 2519
5 TraesCS7D01G061900 chr7A 637297952 637298482 530 False 588.00 588 87.03700 998 1522 1 chr7A.!!$F1 524
6 TraesCS7D01G061900 chr4A 692078333 692080413 2080 False 2338.00 2338 87.04000 1 2144 1 chr4A.!!$F1 2143
7 TraesCS7D01G061900 chr4A 692358848 692359362 514 False 667.00 667 90.01900 998 1522 1 chr4A.!!$F2 524
8 TraesCS7D01G061900 chr4A 693596416 693596930 514 True 656.00 656 89.64200 998 1522 1 chr4A.!!$R1 524
9 TraesCS7D01G061900 chrUn 81832850 81833361 511 False 706.00 706 91.41200 997 1519 1 chrUn.!!$F1 522
10 TraesCS7D01G061900 chr7B 596606414 596606929 515 False 606.00 606 87.94700 999 1522 1 chr7B.!!$F1 523
11 TraesCS7D01G061900 chr3B 592663327 592663943 616 False 547.00 547 83.30700 9 614 1 chr3B.!!$F1 605
12 TraesCS7D01G061900 chr6A 19167488 19167990 502 False 531.00 531 85.90700 1001 1510 1 chr6A.!!$F1 509
13 TraesCS7D01G061900 chr3D 450884661 450885282 621 False 520.00 520 82.54700 9 614 1 chr3D.!!$F1 605
14 TraesCS7D01G061900 chr3A 594031638 594032182 544 False 508.00 508 84.08700 9 542 1 chr3A.!!$F1 533

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
624 673 0.103572 CAGCCCAAATGCCACATAGC 59.896 55.0 0.0 0.0 0.0 2.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1539 1667 0.106369 TCATCCCGATCCACTACCGT 60.106 55.0 0.0 0.0 0.0 4.83 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
24 25 5.361285 TCCTAGGCTAAGCTAAGTTTCAGAG 59.639 44.000 2.96 0.0 0.00 3.35
31 32 6.200097 GCTAAGCTAAGTTTCAGAGATACAGC 59.800 42.308 0.00 0.0 0.00 4.40
36 37 3.589988 AGTTTCAGAGATACAGCAACCG 58.410 45.455 0.00 0.0 0.00 4.44
38 39 1.557099 TCAGAGATACAGCAACCGGT 58.443 50.000 0.00 0.0 0.00 5.28
178 196 0.176680 CCATCACTCAACCTCCCGAG 59.823 60.000 0.00 0.0 35.30 4.63
385 411 1.488705 ATGCCGTGGGGAGAACAGAA 61.489 55.000 0.00 0.0 34.06 3.02
573 613 0.739112 GCGAGACAGGCAGAAAGAGG 60.739 60.000 0.00 0.0 0.00 3.69
618 667 2.681064 GCCTCAGCCCAAATGCCA 60.681 61.111 0.00 0.0 0.00 4.92
619 668 3.010413 GCCTCAGCCCAAATGCCAC 62.010 63.158 0.00 0.0 0.00 5.01
620 669 1.607178 CCTCAGCCCAAATGCCACA 60.607 57.895 0.00 0.0 0.00 4.17
621 670 0.974010 CCTCAGCCCAAATGCCACAT 60.974 55.000 0.00 0.0 0.00 3.21
622 671 1.685803 CCTCAGCCCAAATGCCACATA 60.686 52.381 0.00 0.0 0.00 2.29
623 672 1.679680 CTCAGCCCAAATGCCACATAG 59.320 52.381 0.00 0.0 0.00 2.23
624 673 0.103572 CAGCCCAAATGCCACATAGC 59.896 55.000 0.00 0.0 0.00 2.97
625 674 1.044790 AGCCCAAATGCCACATAGCC 61.045 55.000 0.00 0.0 0.00 3.93
662 712 4.643387 ACCCGAACCAGCACAGCC 62.643 66.667 0.00 0.0 0.00 4.85
680 730 2.520458 CAGCCCAAACCAGACCCA 59.480 61.111 0.00 0.0 0.00 4.51
700 751 0.872388 CCTCCACGAAGAAAAACCCG 59.128 55.000 0.00 0.0 0.00 5.28
938 989 1.906105 TATTCGCCTTTCCGCACCCT 61.906 55.000 0.00 0.0 0.00 4.34
943 994 1.377333 CCTTTCCGCACCCTCTTCC 60.377 63.158 0.00 0.0 0.00 3.46
950 1001 4.796231 CACCCTCTTCCGTCGCCG 62.796 72.222 0.00 0.0 0.00 6.46
974 1026 1.068948 TTCGAACCTCCCCCAAATCA 58.931 50.000 0.00 0.0 0.00 2.57
987 1039 0.445436 CAAATCAGCAGCAGTCGACC 59.555 55.000 13.01 0.0 0.00 4.79
1082 1161 2.571216 CCACCAAGGTCCGTCTCGT 61.571 63.158 0.00 0.0 0.00 4.18
1090 1169 1.678300 GTCCGTCTCGTCCCCTCTT 60.678 63.158 0.00 0.0 0.00 2.85
1096 1175 2.044252 TCGTCCCCTCTTCCCTCG 60.044 66.667 0.00 0.0 0.00 4.63
1101 1180 3.532155 CCCTCTTCCCTCGCCTCG 61.532 72.222 0.00 0.0 0.00 4.63
1119 1219 4.378459 GCCTCGTTTGAATTCGATCTGTTT 60.378 41.667 0.04 0.0 35.57 2.83
1145 1262 4.154737 CCTTGTTGATTCGAGATTTGCTGA 59.845 41.667 0.00 0.0 0.00 4.26
1165 1287 5.064452 GCTGACTGACGATCTGATTTGAATT 59.936 40.000 0.00 0.0 0.00 2.17
1222 1350 1.301401 CACCGGCGGAGTGAAGAAA 60.301 57.895 35.78 0.0 37.42 2.52
1534 1662 0.457851 CCTAAGCTGTCCTCTCCGTG 59.542 60.000 0.00 0.0 0.00 4.94
1539 1667 1.863662 GCTGTCCTCTCCGTGAACGA 61.864 60.000 4.03 0.0 43.02 3.85
1554 1688 1.660560 AACGACGGTAGTGGATCGGG 61.661 60.000 0.00 0.0 38.88 5.14
1594 1728 6.952773 TGTAGTTTGTTCCTAATTGCTGTT 57.047 33.333 0.00 0.0 0.00 3.16
1603 1737 6.174049 GTTCCTAATTGCTGTTCTAGGTCTT 58.826 40.000 0.00 0.0 33.87 3.01
1604 1738 7.038587 TGTTCCTAATTGCTGTTCTAGGTCTTA 60.039 37.037 0.00 0.0 33.87 2.10
1605 1739 7.490657 TCCTAATTGCTGTTCTAGGTCTTAA 57.509 36.000 0.00 0.0 33.87 1.85
1653 1788 6.199937 TGTTAGGTATGAGTAAGACGAACC 57.800 41.667 0.00 0.0 0.00 3.62
1654 1789 5.711506 TGTTAGGTATGAGTAAGACGAACCA 59.288 40.000 0.00 0.0 0.00 3.67
1655 1790 6.209192 TGTTAGGTATGAGTAAGACGAACCAA 59.791 38.462 0.00 0.0 0.00 3.67
1656 1791 5.069501 AGGTATGAGTAAGACGAACCAAC 57.930 43.478 0.00 0.0 0.00 3.77
1658 1793 5.245526 AGGTATGAGTAAGACGAACCAACTT 59.754 40.000 0.00 0.0 0.00 2.66
1659 1794 5.347907 GGTATGAGTAAGACGAACCAACTTG 59.652 44.000 0.00 0.0 0.00 3.16
1660 1795 4.659111 TGAGTAAGACGAACCAACTTGA 57.341 40.909 0.00 0.0 0.00 3.02
1662 1797 6.335471 TGAGTAAGACGAACCAACTTGATA 57.665 37.500 0.00 0.0 0.00 2.15
1663 1798 6.931838 TGAGTAAGACGAACCAACTTGATAT 58.068 36.000 0.00 0.0 0.00 1.63
1664 1799 6.811665 TGAGTAAGACGAACCAACTTGATATG 59.188 38.462 0.00 0.0 0.00 1.78
1708 1843 5.232202 CGATGAAGCAAACGTATGTCTATGT 59.768 40.000 0.00 0.0 0.00 2.29
1734 1869 4.137543 AGACCTCAGAACCATTGTTGTTC 58.862 43.478 0.00 0.0 41.89 3.18
1737 1872 2.549754 CTCAGAACCATTGTTGTTCGCT 59.450 45.455 0.00 0.0 45.26 4.93
1758 1896 1.856014 GCAACTCTGTTGTTGTCGTGC 60.856 52.381 11.35 0.0 46.33 5.34
1780 1918 3.141398 CCTTGATCCCATCGTGGTATTG 58.859 50.000 0.00 0.0 35.17 1.90
1794 1932 7.302350 TCGTGGTATTGTATCTTGATTTGTG 57.698 36.000 0.00 0.0 0.00 3.33
1802 1940 2.254546 TCTTGATTTGTGGTGCGACT 57.745 45.000 0.00 0.0 0.00 4.18
1818 1956 5.334569 GGTGCGACTAATTGCTGTTTTTCTA 60.335 40.000 0.00 0.0 36.04 2.10
1861 2440 0.749818 TGTTGATGGTTGCCGTGTGT 60.750 50.000 0.00 0.0 0.00 3.72
1938 2518 1.574428 GACGCGTTGGTGATGCTTT 59.426 52.632 15.53 0.0 38.16 3.51
1939 2519 0.452784 GACGCGTTGGTGATGCTTTC 60.453 55.000 15.53 0.0 38.16 2.62
1945 2525 0.953471 TTGGTGATGCTTTCGGACGG 60.953 55.000 0.00 0.0 0.00 4.79
1946 2526 2.106683 GGTGATGCTTTCGGACGGG 61.107 63.158 0.00 0.0 0.00 5.28
2197 2780 3.731652 TTCAAAATGGCTCCACTGTTG 57.268 42.857 0.00 0.0 0.00 3.33
2201 2784 3.788227 AAATGGCTCCACTGTTGTCTA 57.212 42.857 0.00 0.0 0.00 2.59
2260 2844 8.404765 TGTTGAAATCGTGTATAATACCGACTA 58.595 33.333 0.00 0.0 35.39 2.59
2445 3429 8.739039 CCAAATGTAAGTCAATTACTCAATCCA 58.261 33.333 0.00 0.0 43.61 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.131396 CAGGAATACCGGTTGCTGTATC 58.869 50.000 15.04 0.78 41.09 2.24
31 32 3.543680 ATCTGTCAGGAATACCGGTTG 57.456 47.619 15.04 4.19 41.83 3.77
36 37 4.636206 GTGGTGAAATCTGTCAGGAATACC 59.364 45.833 0.00 4.03 0.00 2.73
38 39 5.497464 TGTGGTGAAATCTGTCAGGAATA 57.503 39.130 0.00 0.00 0.00 1.75
158 165 0.544357 TCGGGAGGTTGAGTGATGGT 60.544 55.000 0.00 0.00 0.00 3.55
335 360 2.034879 ATGAACCTGCTGAACGCGG 61.035 57.895 12.47 0.00 44.89 6.46
385 411 1.273896 CCCTCCTAAACCCCTCTCTGT 60.274 57.143 0.00 0.00 0.00 3.41
522 557 1.930908 GACATGGCCAGCAGCAACTC 61.931 60.000 13.05 0.00 46.50 3.01
573 613 3.723348 GGGCACAAACGACCTCGC 61.723 66.667 0.00 0.00 44.43 5.03
618 667 1.762460 CCTCTCGGGTGGGCTATGT 60.762 63.158 0.00 0.00 0.00 2.29
619 668 2.511452 CCCTCTCGGGTGGGCTATG 61.511 68.421 10.04 0.00 46.12 2.23
620 669 2.122813 CCCTCTCGGGTGGGCTAT 60.123 66.667 10.04 0.00 46.12 2.97
645 695 4.643387 GGCTGTGCTGGTTCGGGT 62.643 66.667 0.00 0.00 0.00 5.28
662 712 2.283173 GGGTCTGGTTTGGGCTGG 60.283 66.667 0.00 0.00 0.00 4.85
680 730 1.812708 CGGGTTTTTCTTCGTGGAGGT 60.813 52.381 0.00 0.00 0.00 3.85
758 809 1.710339 GAGAAAGCACACGATCCGC 59.290 57.895 0.00 0.00 0.00 5.54
909 960 3.498777 GGAAAGGCGAATAGTAGGATTGC 59.501 47.826 0.00 0.00 0.00 3.56
950 1001 1.143401 GGGGGAGGTTCGAATCGAC 59.857 63.158 4.25 0.56 34.89 4.20
974 1026 3.753434 CTCCGGTCGACTGCTGCT 61.753 66.667 19.31 0.00 0.00 4.24
1082 1161 3.680920 GAGGCGAGGGAAGAGGGGA 62.681 68.421 0.00 0.00 0.00 4.81
1090 1169 0.323629 AATTCAAACGAGGCGAGGGA 59.676 50.000 0.00 0.00 0.00 4.20
1096 1175 2.673368 ACAGATCGAATTCAAACGAGGC 59.327 45.455 6.22 0.00 41.63 4.70
1101 1180 6.002062 AGGACAAACAGATCGAATTCAAAC 57.998 37.500 6.22 0.00 0.00 2.93
1119 1219 4.083324 GCAAATCTCGAATCAACAAGGACA 60.083 41.667 0.00 0.00 0.00 4.02
1145 1262 4.940046 AGCAATTCAAATCAGATCGTCAGT 59.060 37.500 0.00 0.00 0.00 3.41
1165 1287 1.236616 CCGCCTGAAATCACACAGCA 61.237 55.000 0.00 0.00 33.40 4.41
1534 1662 0.248377 CCGATCCACTACCGTCGTTC 60.248 60.000 0.00 0.00 32.55 3.95
1539 1667 0.106369 TCATCCCGATCCACTACCGT 60.106 55.000 0.00 0.00 0.00 4.83
1542 1670 2.693591 TCAACTCATCCCGATCCACTAC 59.306 50.000 0.00 0.00 0.00 2.73
1554 1688 4.504858 ACTACAACCGGAATCAACTCATC 58.495 43.478 9.46 0.00 0.00 2.92
1594 1728 7.534723 TCTACACAAAAGCTTAAGACCTAGA 57.465 36.000 6.67 0.00 0.00 2.43
1603 1737 9.515226 ACCATATTTCTTCTACACAAAAGCTTA 57.485 29.630 0.00 0.00 0.00 3.09
1604 1738 8.409358 ACCATATTTCTTCTACACAAAAGCTT 57.591 30.769 0.00 0.00 0.00 3.74
1605 1739 8.299570 CAACCATATTTCTTCTACACAAAAGCT 58.700 33.333 0.00 0.00 0.00 3.74
1634 1769 4.771054 AGTTGGTTCGTCTTACTCATACCT 59.229 41.667 0.00 0.00 0.00 3.08
1653 1788 7.543172 CCAAAAGGAACATCACATATCAAGTTG 59.457 37.037 0.00 0.00 0.00 3.16
1654 1789 7.233348 ACCAAAAGGAACATCACATATCAAGTT 59.767 33.333 0.00 0.00 0.00 2.66
1655 1790 6.721208 ACCAAAAGGAACATCACATATCAAGT 59.279 34.615 0.00 0.00 0.00 3.16
1656 1791 7.161773 ACCAAAAGGAACATCACATATCAAG 57.838 36.000 0.00 0.00 0.00 3.02
1658 1793 7.377398 CAAACCAAAAGGAACATCACATATCA 58.623 34.615 0.00 0.00 0.00 2.15
1659 1794 6.311200 GCAAACCAAAAGGAACATCACATATC 59.689 38.462 0.00 0.00 0.00 1.63
1660 1795 6.165577 GCAAACCAAAAGGAACATCACATAT 58.834 36.000 0.00 0.00 0.00 1.78
1662 1797 4.379652 GCAAACCAAAAGGAACATCACAT 58.620 39.130 0.00 0.00 0.00 3.21
1663 1798 3.736433 CGCAAACCAAAAGGAACATCACA 60.736 43.478 0.00 0.00 0.00 3.58
1664 1799 2.794350 CGCAAACCAAAAGGAACATCAC 59.206 45.455 0.00 0.00 0.00 3.06
1708 1843 4.437682 ACAATGGTTCTGAGGTCTTCAA 57.562 40.909 0.00 0.00 34.81 2.69
1734 1869 3.153364 CAACAACAGAGTTGCAGCG 57.847 52.632 9.60 0.00 41.95 5.18
1758 1896 1.128200 TACCACGATGGGATCAAGGG 58.872 55.000 8.57 0.00 43.37 3.95
1780 1918 3.684788 AGTCGCACCACAAATCAAGATAC 59.315 43.478 0.00 0.00 0.00 2.24
1794 1932 2.989422 AAACAGCAATTAGTCGCACC 57.011 45.000 0.00 0.00 0.00 5.01
1802 1940 8.587950 CAAAACAACGTAGAAAAACAGCAATTA 58.412 29.630 0.00 0.00 0.00 1.40
1818 1956 1.135344 CGACCCAAACCAAAACAACGT 60.135 47.619 0.00 0.00 0.00 3.99
1861 2440 0.385098 CGACGACAGAACACGTAGCA 60.385 55.000 0.00 0.00 42.74 3.49
1923 2503 1.154225 CCGAAAGCATCACCAACGC 60.154 57.895 0.00 0.00 0.00 4.84
2426 3410 9.219603 CAAGAACTGGATTGAGTAATTGACTTA 57.780 33.333 0.00 0.00 39.06 2.24
2445 3429 6.585695 ATGATCAAATGCAAGTCAAGAACT 57.414 33.333 0.00 0.00 41.10 3.01


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

AutoCloner maintained by Alex Coulton.