Multiple sequence alignment - TraesCS1D01G275400

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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 TraesCS1D01G275400 chr1D 100.000 2863 0 0 1 2863 371342928 371340066 0.000000e+00 5288
1 TraesCS1D01G275400 chr1B 91.967 2776 132 48 109 2862 495417254 495414548 0.000000e+00 3807
2 TraesCS1D01G275400 chr1B 93.636 110 7 0 1 110 495417456 495417347 6.350000e-37 165
3 TraesCS1D01G275400 chr1B 87.255 102 10 3 1 99 495418427 495418326 2.330000e-21 113
4 TraesCS1D01G275400 chr1A 95.067 2007 56 19 668 2643 470687092 470685098 0.000000e+00 3118
5 TraesCS1D01G275400 chr1A 94.073 523 28 3 1 522 470687696 470687176 0.000000e+00 791
6 TraesCS1D01G275400 chr1A 92.181 243 11 4 2629 2863 470685076 470684834 1.270000e-88 337
7 TraesCS1D01G275400 chr3A 89.947 189 16 2 1675 1863 624829963 624830148 1.020000e-59 241
8 TraesCS1D01G275400 chr3D 89.418 189 17 2 1675 1863 481702741 481702926 4.770000e-58 235
9 TraesCS1D01G275400 chr3B 89.418 189 17 2 1675 1863 643257326 643257511 4.770000e-58 235


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 TraesCS1D01G275400 chr1D 371340066 371342928 2862 True 5288.000000 5288 100.000000 1 2863 1 chr1D.!!$R1 2862
1 TraesCS1D01G275400 chr1B 495414548 495418427 3879 True 1361.666667 3807 90.952667 1 2862 3 chr1B.!!$R1 2861
2 TraesCS1D01G275400 chr1A 470684834 470687696 2862 True 1415.333333 3118 93.773667 1 2863 3 chr1A.!!$R1 2862

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
560 1630 2.025321 ACCCCAAGTGAACACAAACTCT 60.025 45.455 7.68 0.0 0.00 3.24 F
1535 2652 1.407721 TATTCGTCGGCGCGTTCTTG 61.408 55.000 19.58 0.0 38.14 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1712 2829 0.526524 GCGAGATGTTCCTCCAGTCG 60.527 60.000 0.0 0.0 0.0 4.18 R
2382 3515 1.961277 CGTCAGGCCGCTTTCAACT 60.961 57.895 0.0 0.0 0.0 3.16 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
38 1010 4.037446 TGGTTGCATCACAAAGAAAGGTAC 59.963 41.667 0.00 0.00 40.82 3.34
75 1047 8.759481 TGCATATACACAAGGGAAATGAATTA 57.241 30.769 0.00 0.00 0.00 1.40
187 1253 9.030301 CCAACAAATTAAACAAGTTTACAGAGG 57.970 33.333 4.97 0.00 35.05 3.69
192 1258 3.990318 AACAAGTTTACAGAGGCAAGC 57.010 42.857 0.00 0.00 0.00 4.01
238 1304 5.015178 ACCCTAAAAGAAGGAACATCATCCA 59.985 40.000 0.00 0.00 42.27 3.41
246 1312 8.421249 AAGAAGGAACATCATCCACAAAATAA 57.579 30.769 0.00 0.00 42.27 1.40
460 1526 8.843885 ATCAATAACCATATGAGATGTGACAG 57.156 34.615 3.65 0.00 0.00 3.51
470 1540 8.618677 CATATGAGATGTGACAGCAGTAAAAAT 58.381 33.333 2.86 0.00 0.00 1.82
541 1611 9.535878 TTTTACCAAAATGAGTTATTGTGAACC 57.464 29.630 0.00 0.00 36.28 3.62
560 1630 2.025321 ACCCCAAGTGAACACAAACTCT 60.025 45.455 7.68 0.00 0.00 3.24
563 1633 3.947834 CCCAAGTGAACACAAACTCTTCT 59.052 43.478 7.68 0.00 0.00 2.85
564 1634 5.123227 CCCAAGTGAACACAAACTCTTCTA 58.877 41.667 7.68 0.00 0.00 2.10
565 1635 5.237344 CCCAAGTGAACACAAACTCTTCTAG 59.763 44.000 7.68 0.00 0.00 2.43
566 1636 6.049149 CCAAGTGAACACAAACTCTTCTAGA 58.951 40.000 7.68 0.00 0.00 2.43
567 1637 6.708054 CCAAGTGAACACAAACTCTTCTAGAT 59.292 38.462 7.68 0.00 0.00 1.98
568 1638 7.227512 CCAAGTGAACACAAACTCTTCTAGATT 59.772 37.037 7.68 0.00 0.00 2.40
569 1639 7.954788 AGTGAACACAAACTCTTCTAGATTC 57.045 36.000 7.68 0.00 0.00 2.52
570 1640 6.931840 AGTGAACACAAACTCTTCTAGATTCC 59.068 38.462 7.68 0.00 0.00 3.01
571 1641 6.931840 GTGAACACAAACTCTTCTAGATTCCT 59.068 38.462 0.00 0.00 0.00 3.36
572 1642 7.442666 GTGAACACAAACTCTTCTAGATTCCTT 59.557 37.037 0.00 0.00 0.00 3.36
573 1643 8.647796 TGAACACAAACTCTTCTAGATTCCTTA 58.352 33.333 0.00 0.00 0.00 2.69
574 1644 8.834749 AACACAAACTCTTCTAGATTCCTTAC 57.165 34.615 0.00 0.00 0.00 2.34
575 1645 7.387643 ACACAAACTCTTCTAGATTCCTTACC 58.612 38.462 0.00 0.00 0.00 2.85
576 1646 6.819146 CACAAACTCTTCTAGATTCCTTACCC 59.181 42.308 0.00 0.00 0.00 3.69
577 1647 6.500751 ACAAACTCTTCTAGATTCCTTACCCA 59.499 38.462 0.00 0.00 0.00 4.51
578 1648 7.182930 ACAAACTCTTCTAGATTCCTTACCCAT 59.817 37.037 0.00 0.00 0.00 4.00
579 1649 6.987403 ACTCTTCTAGATTCCTTACCCATC 57.013 41.667 0.00 0.00 0.00 3.51
580 1650 6.688554 ACTCTTCTAGATTCCTTACCCATCT 58.311 40.000 0.00 0.00 0.00 2.90
581 1651 6.780522 ACTCTTCTAGATTCCTTACCCATCTC 59.219 42.308 0.00 0.00 0.00 2.75
582 1652 6.928202 TCTTCTAGATTCCTTACCCATCTCT 58.072 40.000 0.00 0.00 0.00 3.10
583 1653 7.366226 TCTTCTAGATTCCTTACCCATCTCTT 58.634 38.462 0.00 0.00 0.00 2.85
584 1654 7.846823 TCTTCTAGATTCCTTACCCATCTCTTT 59.153 37.037 0.00 0.00 0.00 2.52
585 1655 7.366847 TCTAGATTCCTTACCCATCTCTTTG 57.633 40.000 0.00 0.00 0.00 2.77
586 1656 7.132805 TCTAGATTCCTTACCCATCTCTTTGA 58.867 38.462 0.00 0.00 0.00 2.69
587 1657 6.838401 AGATTCCTTACCCATCTCTTTGAT 57.162 37.500 0.00 0.00 35.40 2.57
588 1658 7.937700 AGATTCCTTACCCATCTCTTTGATA 57.062 36.000 0.00 0.00 33.36 2.15
589 1659 7.740805 AGATTCCTTACCCATCTCTTTGATAC 58.259 38.462 0.00 0.00 33.36 2.24
590 1660 5.888982 TCCTTACCCATCTCTTTGATACC 57.111 43.478 0.00 0.00 33.36 2.73
591 1661 5.285401 TCCTTACCCATCTCTTTGATACCA 58.715 41.667 0.00 0.00 33.36 3.25
592 1662 5.911178 TCCTTACCCATCTCTTTGATACCAT 59.089 40.000 0.00 0.00 33.36 3.55
593 1663 6.389869 TCCTTACCCATCTCTTTGATACCATT 59.610 38.462 0.00 0.00 33.36 3.16
594 1664 7.570982 TCCTTACCCATCTCTTTGATACCATTA 59.429 37.037 0.00 0.00 33.36 1.90
595 1665 8.386264 CCTTACCCATCTCTTTGATACCATTAT 58.614 37.037 0.00 0.00 33.36 1.28
596 1666 9.224267 CTTACCCATCTCTTTGATACCATTATG 57.776 37.037 0.00 0.00 33.36 1.90
597 1667 7.392766 ACCCATCTCTTTGATACCATTATGA 57.607 36.000 0.00 0.00 33.36 2.15
598 1668 7.993416 ACCCATCTCTTTGATACCATTATGAT 58.007 34.615 0.00 0.00 33.36 2.45
638 1708 8.099364 TGTTTCTTCTTTGAACTATGTGATCC 57.901 34.615 0.00 0.00 0.00 3.36
658 1747 5.794687 TCCATAAACGTTCAACTATGCAG 57.205 39.130 0.00 0.00 0.00 4.41
666 1755 3.483574 CGTTCAACTATGCAGCGGTTTAG 60.484 47.826 0.00 0.00 0.00 1.85
690 1788 4.882671 CAACTAGTTGCACTTCACACTT 57.117 40.909 22.03 0.00 33.45 3.16
1036 2153 4.892965 GCGGCATGGGCATGGGTA 62.893 66.667 0.00 0.00 43.71 3.69
1037 2154 2.115910 CGGCATGGGCATGGGTAT 59.884 61.111 0.00 0.00 43.71 2.73
1038 2155 2.270257 CGGCATGGGCATGGGTATG 61.270 63.158 0.00 0.00 43.71 2.39
1039 2156 1.909781 GGCATGGGCATGGGTATGG 60.910 63.158 0.00 0.00 43.71 2.74
1444 2561 2.496070 GAGGAGCACAGGTATACACACA 59.504 50.000 5.01 0.00 0.00 3.72
1447 2564 1.974957 AGCACAGGTATACACACACCA 59.025 47.619 5.01 0.00 37.28 4.17
1535 2652 1.407721 TATTCGTCGGCGCGTTCTTG 61.408 55.000 19.58 0.00 38.14 3.02
1536 2653 3.976684 TATTCGTCGGCGCGTTCTTGT 62.977 52.381 19.58 6.91 38.14 3.16
1537 2654 4.117372 CGTCGGCGCGTTCTTGTC 62.117 66.667 8.43 0.00 0.00 3.18
1553 2670 5.113446 TCTTGTCGGTCCTAGATACTTCT 57.887 43.478 0.00 0.00 35.90 2.85
1618 2735 5.921408 TGCCACACGTAAATTTTTACCATTC 59.079 36.000 0.00 0.00 39.81 2.67
1638 2755 6.591448 CCATTCTTTGCTATGCGATCTATACA 59.409 38.462 0.00 0.00 0.00 2.29
1904 3021 2.106683 CACCAAGAATCCGGTCCGC 61.107 63.158 5.50 0.00 31.41 5.54
1988 3108 3.361977 GTCCGCCCGTGCAAATGT 61.362 61.111 0.00 0.00 37.32 2.71
1989 3109 2.036006 GTCCGCCCGTGCAAATGTA 61.036 57.895 0.00 0.00 37.32 2.29
1990 3110 1.078072 TCCGCCCGTGCAAATGTAT 60.078 52.632 0.00 0.00 37.32 2.29
1991 3111 1.063972 CCGCCCGTGCAAATGTATG 59.936 57.895 0.00 0.00 37.32 2.39
2043 3167 3.195661 GCGATTCGGAACCAGTAATCTT 58.804 45.455 8.34 0.00 0.00 2.40
2170 3300 1.202770 GGGTTATAGCAATCCACCGCT 60.203 52.381 0.00 0.00 42.34 5.52
2231 3364 3.026707 TCACATCCCGTTCTCATCCTA 57.973 47.619 0.00 0.00 0.00 2.94
2233 3366 4.736473 TCACATCCCGTTCTCATCCTATA 58.264 43.478 0.00 0.00 0.00 1.31
2234 3367 4.523173 TCACATCCCGTTCTCATCCTATAC 59.477 45.833 0.00 0.00 0.00 1.47
2289 3422 3.414700 CGGTGACCTGACAAGCGC 61.415 66.667 0.00 0.00 0.00 5.92
2317 3450 1.282875 GCTCCGTTTGTCAGGTTGC 59.717 57.895 0.00 0.00 0.00 4.17
2325 3458 0.874175 TTGTCAGGTTGCTCGTGTCG 60.874 55.000 0.00 0.00 34.10 4.35
2423 3556 1.947013 CGATGCAGATCATGGTGCC 59.053 57.895 11.54 0.00 39.04 5.01
2424 3557 0.534427 CGATGCAGATCATGGTGCCT 60.534 55.000 11.54 3.86 39.04 4.75
2425 3558 0.952280 GATGCAGATCATGGTGCCTG 59.048 55.000 11.54 2.38 39.04 4.85
2426 3559 3.117372 GCAGATCATGGTGCCTGC 58.883 61.111 4.08 4.08 44.00 4.85
2512 3645 9.665264 GAGCTGCAAAAACAATAGTAATATACC 57.335 33.333 1.02 0.00 0.00 2.73
2684 3867 3.677121 TCTCGTCTACTTCACTGTACGTC 59.323 47.826 0.00 0.00 0.00 4.34
2722 3907 5.187186 TGTTTTCTGGGTGTAGGTCTAGATC 59.813 44.000 0.00 0.00 0.00 2.75
2737 3928 6.884295 AGGTCTAGATCATAGATACTCTGTGC 59.116 42.308 5.64 0.00 35.84 4.57
2795 3992 0.323178 CACTCCAAAGCCTCAGCCAT 60.323 55.000 0.00 0.00 41.25 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 979 7.320443 TCTTTGTGATGCAACCATCTATTAC 57.680 36.000 0.00 0.00 46.43 1.89
98 1070 6.246163 ACTTTCCGTAAGATTGGAAGGAAAT 58.754 36.000 9.69 0.00 44.58 2.17
160 1226 8.413899 TCTGTAAACTTGTTTAATTTGTTGGC 57.586 30.769 7.43 0.00 0.00 4.52
187 1253 4.340381 AGGATGATGTTTCTTATGGCTTGC 59.660 41.667 0.00 0.00 0.00 4.01
192 1258 6.183360 GGGTTTGAGGATGATGTTTCTTATGG 60.183 42.308 0.00 0.00 0.00 2.74
246 1312 5.780958 AGGGCCTCTCTACTTTTGTAAAT 57.219 39.130 0.00 0.00 34.06 1.40
294 1360 8.787852 AGCAACAACCTTAAAATTTTCAACAAA 58.212 25.926 6.72 0.00 0.00 2.83
295 1361 8.329203 AGCAACAACCTTAAAATTTTCAACAA 57.671 26.923 6.72 0.00 0.00 2.83
452 1518 9.793252 GATGATTTATTTTTACTGCTGTCACAT 57.207 29.630 0.00 0.00 0.00 3.21
460 1526 9.076596 GGAGTGTTGATGATTTATTTTTACTGC 57.923 33.333 0.00 0.00 0.00 4.40
470 1540 6.611613 AGAGAGTGGAGTGTTGATGATTTA 57.388 37.500 0.00 0.00 0.00 1.40
526 1596 4.141287 CACTTGGGGTTCACAATAACTCA 58.859 43.478 0.00 0.00 31.01 3.41
533 1603 2.096248 GTGTTCACTTGGGGTTCACAA 58.904 47.619 0.00 0.00 0.00 3.33
541 1611 3.947834 AGAAGAGTTTGTGTTCACTTGGG 59.052 43.478 4.59 0.00 30.53 4.12
560 1630 7.623677 TCAAAGAGATGGGTAAGGAATCTAGAA 59.376 37.037 0.00 0.00 30.83 2.10
563 1633 7.937700 ATCAAAGAGATGGGTAAGGAATCTA 57.062 36.000 0.00 0.00 35.06 1.98
564 1634 6.838401 ATCAAAGAGATGGGTAAGGAATCT 57.162 37.500 0.00 0.00 35.06 2.40
565 1635 6.937465 GGTATCAAAGAGATGGGTAAGGAATC 59.063 42.308 0.00 0.00 37.57 2.52
566 1636 6.389869 TGGTATCAAAGAGATGGGTAAGGAAT 59.610 38.462 0.00 0.00 37.57 3.01
567 1637 5.729229 TGGTATCAAAGAGATGGGTAAGGAA 59.271 40.000 0.00 0.00 37.57 3.36
568 1638 5.285401 TGGTATCAAAGAGATGGGTAAGGA 58.715 41.667 0.00 0.00 37.57 3.36
569 1639 5.630415 TGGTATCAAAGAGATGGGTAAGG 57.370 43.478 0.00 0.00 37.57 2.69
570 1640 9.224267 CATAATGGTATCAAAGAGATGGGTAAG 57.776 37.037 0.00 0.00 37.57 2.34
571 1641 8.944138 TCATAATGGTATCAAAGAGATGGGTAA 58.056 33.333 0.00 0.00 37.57 2.85
572 1642 8.504811 TCATAATGGTATCAAAGAGATGGGTA 57.495 34.615 0.00 0.00 37.57 3.69
573 1643 7.392766 TCATAATGGTATCAAAGAGATGGGT 57.607 36.000 0.00 0.00 37.57 4.51
574 1644 8.105197 TCATCATAATGGTATCAAAGAGATGGG 58.895 37.037 10.19 0.00 34.50 4.00
575 1645 9.511272 TTCATCATAATGGTATCAAAGAGATGG 57.489 33.333 10.19 0.00 34.50 3.51
638 1708 4.021822 CGCTGCATAGTTGAACGTTTATG 58.978 43.478 0.46 7.77 0.00 1.90
658 1747 3.724295 CAACTAGTTGCTCTAAACCGC 57.276 47.619 22.03 0.00 33.45 5.68
1028 2145 1.909781 CCCATGCCCATACCCATGC 60.910 63.158 0.00 0.00 37.96 4.06
1029 2146 1.909781 GCCCATGCCCATACCCATG 60.910 63.158 0.00 0.00 38.78 3.66
1030 2147 1.742737 ATGCCCATGCCCATACCCAT 61.743 55.000 0.00 0.00 36.33 4.00
1031 2148 2.402173 ATGCCCATGCCCATACCCA 61.402 57.895 0.00 0.00 36.33 4.51
1032 2149 1.909781 CATGCCCATGCCCATACCC 60.910 63.158 0.00 0.00 36.33 3.69
1033 2150 1.909781 CCATGCCCATGCCCATACC 60.910 63.158 2.75 0.00 37.49 2.73
1034 2151 1.909781 CCCATGCCCATGCCCATAC 60.910 63.158 2.75 0.00 37.49 2.39
1035 2152 2.402173 ACCCATGCCCATGCCCATA 61.402 57.895 2.75 0.00 37.49 2.74
1036 2153 3.769617 ACCCATGCCCATGCCCAT 61.770 61.111 2.75 0.00 37.49 4.00
1037 2154 4.781616 CACCCATGCCCATGCCCA 62.782 66.667 2.75 0.00 37.49 5.36
1185 2302 4.612412 GCCACGAACACCCACCGA 62.612 66.667 0.00 0.00 0.00 4.69
1444 2561 0.953960 GAGATTTTGACGGCGGTGGT 60.954 55.000 13.24 0.00 0.00 4.16
1447 2564 2.028385 AGTTAGAGATTTTGACGGCGGT 60.028 45.455 13.24 0.00 0.00 5.68
1535 2652 2.807392 CGGAGAAGTATCTAGGACCGAC 59.193 54.545 0.00 0.00 40.14 4.79
1536 2653 2.224475 CCGGAGAAGTATCTAGGACCGA 60.224 54.545 0.00 0.00 40.14 4.69
1537 2654 2.152830 CCGGAGAAGTATCTAGGACCG 58.847 57.143 0.00 0.00 38.44 4.79
1618 2735 4.328440 GCCTGTATAGATCGCATAGCAAAG 59.672 45.833 0.00 0.00 0.00 2.77
1638 2755 0.606673 GGAGAAAAAGGTCAGCGCCT 60.607 55.000 2.29 0.00 41.41 5.52
1712 2829 0.526524 GCGAGATGTTCCTCCAGTCG 60.527 60.000 0.00 0.00 0.00 4.18
1904 3021 2.282958 TATCGGCTAGGCTCGGGG 60.283 66.667 15.11 0.00 0.00 5.73
1988 3108 0.834612 CCACGCCTTTCCCCTACATA 59.165 55.000 0.00 0.00 0.00 2.29
1989 3109 1.607612 CCACGCCTTTCCCCTACAT 59.392 57.895 0.00 0.00 0.00 2.29
1990 3110 3.074281 CCACGCCTTTCCCCTACA 58.926 61.111 0.00 0.00 0.00 2.74
1991 3111 2.437895 GCCACGCCTTTCCCCTAC 60.438 66.667 0.00 0.00 0.00 3.18
2043 3167 7.395190 TTCGACCATACAGCTAGTTTACTAA 57.605 36.000 0.00 0.00 0.00 2.24
2079 3207 1.040646 ACACACACGACAGAGGTGAT 58.959 50.000 0.00 0.00 38.73 3.06
2170 3300 3.025262 ACAGGAAAGCGGTAAAAACCAA 58.975 40.909 0.00 0.00 0.00 3.67
2289 3422 1.014352 CAAACGGAGCCGATAAAGGG 58.986 55.000 16.83 0.00 42.83 3.95
2325 3458 2.733593 GCACGGGTGACTCGACAC 60.734 66.667 13.67 0.00 39.70 3.67
2382 3515 1.961277 CGTCAGGCCGCTTTCAACT 60.961 57.895 0.00 0.00 0.00 3.16
2512 3645 2.433145 ACGCTGACGATGGTGCAG 60.433 61.111 0.00 0.00 43.93 4.41
2684 3867 4.094739 CCAGAAAACAAACTTGGCAAAAGG 59.905 41.667 0.00 0.00 0.00 3.11
2737 3928 7.176165 TCCTGTATACTAATGACACGGATAAGG 59.824 40.741 4.17 0.00 0.00 2.69
2795 3992 2.440517 TACCTACCTGCCGTGACATA 57.559 50.000 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.