Multiple sequence alignment - TraesCS7B01G331200

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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 TraesCS7B01G331200 chr7B 100.000 2815 0 0 1 2815 586630196 586633010 0 5199
1 TraesCS7B01G331200 chr7D 95.127 2278 68 9 1 2249 543550079 543552342 0 3552
2 TraesCS7B01G331200 chr7D 93.509 570 20 8 2251 2815 543552529 543553086 0 832


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 TraesCS7B01G331200 chr7B 586630196 586633010 2814 False 5199 5199 100.000 1 2815 1 chr7B.!!$F1 2814
1 TraesCS7B01G331200 chr7D 543550079 543553086 3007 False 2192 3552 94.318 1 2815 2 chr7D.!!$F1 2814

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
475 501 0.324943 ATGTGAAGTTCCGACAGGGG 59.675 55.0 0.00 0.0 38.33 4.79 F
1047 1073 0.610232 GTCCAGAGCATTTGGGCAGT 60.610 55.0 1.42 0.0 40.09 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1618 1645 0.318441 CAAGTCTCGTTCCTGCCTCA 59.682 55.000 0.0 0.0 0.0 3.86 R
2507 2726 1.069204 ACACATCGCACTCAGACAACT 59.931 47.619 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
51 52 3.525800 AGTGTTGGGCATTTCTAAGGT 57.474 42.857 0.00 0.00 0.00 3.50
52 53 3.844640 AGTGTTGGGCATTTCTAAGGTT 58.155 40.909 0.00 0.00 0.00 3.50
53 54 4.993028 AGTGTTGGGCATTTCTAAGGTTA 58.007 39.130 0.00 0.00 0.00 2.85
133 135 3.133901 TCTTCTAATTGCTACCCGATGCA 59.866 43.478 0.00 0.00 37.42 3.96
138 140 3.492102 ATTGCTACCCGATGCAGTATT 57.508 42.857 0.00 0.00 40.46 1.89
148 150 5.071250 ACCCGATGCAGTATTGTCCTTATTA 59.929 40.000 0.00 0.00 0.00 0.98
172 174 9.535878 TTAAACACCAATTTAACTTGAACCATC 57.464 29.630 7.10 0.00 30.78 3.51
259 261 6.997655 TGCAATTAGGATAAGACGAGATCAT 58.002 36.000 0.00 0.00 0.00 2.45
278 280 7.932335 AGATCATTAGTTCACTAGTAAGGTCG 58.068 38.462 0.00 0.00 0.00 4.79
300 302 7.413767 GGTCGTTAACCTGAAAGATCATTAACC 60.414 40.741 0.00 0.00 45.45 2.85
302 304 7.881232 TCGTTAACCTGAAAGATCATTAACCTT 59.119 33.333 0.00 0.00 34.07 3.50
303 305 7.962918 CGTTAACCTGAAAGATCATTAACCTTG 59.037 37.037 0.00 0.00 34.07 3.61
347 370 6.100404 ACAAAACCATTGACATGTTAGCAT 57.900 33.333 0.00 0.00 35.32 3.79
377 403 4.957759 AACAACCGAGGCATGTAAATAC 57.042 40.909 0.00 0.00 0.00 1.89
416 442 2.693074 AGAACGTCCCAAACAAAAGCAT 59.307 40.909 0.00 0.00 0.00 3.79
467 493 2.301346 CCCAGCCATATGTGAAGTTCC 58.699 52.381 1.24 0.00 0.00 3.62
475 501 0.324943 ATGTGAAGTTCCGACAGGGG 59.675 55.000 0.00 0.00 38.33 4.79
496 522 3.580319 GGCAACAGTGGGGGTCCT 61.580 66.667 0.00 0.00 0.00 3.85
497 523 2.228480 GGCAACAGTGGGGGTCCTA 61.228 63.158 0.00 0.00 0.00 2.94
498 524 1.299976 GCAACAGTGGGGGTCCTAG 59.700 63.158 0.00 0.00 0.00 3.02
499 525 1.489560 GCAACAGTGGGGGTCCTAGT 61.490 60.000 0.00 0.00 0.00 2.57
500 526 0.324943 CAACAGTGGGGGTCCTAGTG 59.675 60.000 3.98 3.98 0.00 2.74
501 527 0.840722 AACAGTGGGGGTCCTAGTGG 60.841 60.000 9.41 0.00 0.00 4.00
502 528 1.229529 CAGTGGGGGTCCTAGTGGT 60.230 63.158 0.00 0.00 34.23 4.16
503 529 1.229529 AGTGGGGGTCCTAGTGGTG 60.230 63.158 0.00 0.00 34.23 4.17
619 645 0.999712 CCTGCCCCTCCTTTTCCTTA 59.000 55.000 0.00 0.00 0.00 2.69
656 682 1.077265 ATGGGCAGGGAGTTGTTGG 59.923 57.895 0.00 0.00 0.00 3.77
659 685 0.681243 GGGCAGGGAGTTGTTGGATC 60.681 60.000 0.00 0.00 0.00 3.36
718 744 4.268359 CTCTGCCTTTTCTCTTGGCTTAT 58.732 43.478 0.00 0.00 46.23 1.73
809 835 3.243068 CCTCTGTTGTGTTACTTGTTGGC 60.243 47.826 0.00 0.00 0.00 4.52
871 897 5.967088 GCGTAGTATTTAATTGTTTTCCCCG 59.033 40.000 0.00 0.00 0.00 5.73
921 947 7.452880 TTGTCTTTCCATCTTAGGATGTTTG 57.547 36.000 13.26 0.00 45.66 2.93
1013 1039 4.221703 ACTGAAGGAGATGTCTGTGGTTAG 59.778 45.833 0.00 0.00 0.00 2.34
1047 1073 0.610232 GTCCAGAGCATTTGGGCAGT 60.610 55.000 1.42 0.00 40.09 4.40
1121 1147 5.481473 ACCATGTTGTTAAATCAGCCTTCAT 59.519 36.000 0.00 0.00 0.00 2.57
1128 1154 7.716799 TGTTAAATCAGCCTTCATTAATGGT 57.283 32.000 15.36 0.00 0.00 3.55
1135 1161 6.899089 TCAGCCTTCATTAATGGTCTTATGA 58.101 36.000 15.36 9.95 0.00 2.15
1206 1232 1.747444 ATTTATCCGAGCCTGGGGAT 58.253 50.000 7.90 7.90 44.92 3.85
1212 1238 2.739996 CGAGCCTGGGGATCTTGCT 61.740 63.158 0.00 0.00 35.75 3.91
1225 1251 5.529060 GGGGATCTTGCTATACTTCAGTTTG 59.471 44.000 0.00 0.00 0.00 2.93
1237 1263 2.957402 TCAGTTTGATTGTGAGGGCT 57.043 45.000 0.00 0.00 0.00 5.19
1260 1286 5.886960 ATATGTTTGAACCTCTGCTGTTC 57.113 39.130 0.00 0.00 41.91 3.18
1280 1306 5.758296 TGTTCGCTGAAATATCTACCAATCC 59.242 40.000 0.00 0.00 0.00 3.01
1541 1567 6.071447 AAACTGGTGTTCATATGCTTTATGCA 60.071 34.615 0.00 0.00 45.39 3.96
1598 1624 7.317722 ACCAATTATTATGGGAGGTAGAGTC 57.682 40.000 0.00 0.00 42.48 3.36
1616 1643 2.158608 AGTCTTGGAGTCAACAAAGGGG 60.159 50.000 0.00 0.00 0.00 4.79
1618 1645 0.555769 TTGGAGTCAACAAAGGGGCT 59.444 50.000 0.00 0.00 0.00 5.19
1677 1706 2.481441 ACACCATGCTAGAGGATTGGA 58.519 47.619 0.00 0.00 0.00 3.53
1697 1726 4.281182 TGGACTGTAAGAGTTCCAGACTTC 59.719 45.833 0.00 0.00 39.19 3.01
1703 1732 6.110707 TGTAAGAGTTCCAGACTTCGTTTTT 58.889 36.000 0.00 0.00 39.19 1.94
1713 1742 5.861787 CCAGACTTCGTTTTTGTTGTTTTCT 59.138 36.000 0.00 0.00 0.00 2.52
1714 1743 7.024768 CCAGACTTCGTTTTTGTTGTTTTCTA 58.975 34.615 0.00 0.00 0.00 2.10
1715 1744 7.539366 CCAGACTTCGTTTTTGTTGTTTTCTAA 59.461 33.333 0.00 0.00 0.00 2.10
1800 1829 5.055642 TGAGATGCTTGAAATGCTTGAAG 57.944 39.130 0.00 0.00 37.94 3.02
1801 1830 4.763279 TGAGATGCTTGAAATGCTTGAAGA 59.237 37.500 0.00 0.00 37.94 2.87
1916 1945 6.599244 TCACTATGTCCAATTCACTCCATTTC 59.401 38.462 0.00 0.00 0.00 2.17
1921 1950 7.214467 TGTCCAATTCACTCCATTTCTTAAC 57.786 36.000 0.00 0.00 0.00 2.01
2005 2034 6.972901 GCTATATCTAAACAAAAACTGTGGGC 59.027 38.462 0.00 0.00 38.67 5.36
2038 2067 7.279981 TCTCAATTAGTATGTGTGTATGCCAAC 59.720 37.037 0.00 0.00 0.00 3.77
2043 2072 5.419542 AGTATGTGTGTATGCCAACAGTAG 58.580 41.667 0.00 0.00 0.00 2.57
2081 2110 3.842732 TCATCACACGTACTGTACCAG 57.157 47.619 12.08 7.43 37.52 4.00
2179 2208 5.432645 TCAGTCACAAACATAACTTCACCA 58.567 37.500 0.00 0.00 0.00 4.17
2249 2279 9.896645 ATGTACCTTGATATAATTAGCATGGAG 57.103 33.333 17.30 2.85 39.96 3.86
2280 2495 5.220381 TGAGTTTGTGAGTTCATAGTCGAC 58.780 41.667 7.70 7.70 0.00 4.20
2327 2542 8.408043 TTGAGGTCATAAATGTGTCTTTTGAT 57.592 30.769 0.00 0.00 0.00 2.57
2330 2545 6.435277 AGGTCATAAATGTGTCTTTTGATGCT 59.565 34.615 0.00 0.00 0.00 3.79
2331 2546 7.039504 AGGTCATAAATGTGTCTTTTGATGCTT 60.040 33.333 0.00 0.00 0.00 3.91
2332 2547 7.062605 GGTCATAAATGTGTCTTTTGATGCTTG 59.937 37.037 0.00 0.00 0.00 4.01
2333 2548 7.062605 GTCATAAATGTGTCTTTTGATGCTTGG 59.937 37.037 0.00 0.00 0.00 3.61
2334 2549 4.942761 AATGTGTCTTTTGATGCTTGGT 57.057 36.364 0.00 0.00 0.00 3.67
2335 2550 3.988379 TGTGTCTTTTGATGCTTGGTC 57.012 42.857 0.00 0.00 0.00 4.02
2336 2551 3.554934 TGTGTCTTTTGATGCTTGGTCT 58.445 40.909 0.00 0.00 0.00 3.85
2337 2552 4.713553 TGTGTCTTTTGATGCTTGGTCTA 58.286 39.130 0.00 0.00 0.00 2.59
2338 2553 5.316167 TGTGTCTTTTGATGCTTGGTCTAT 58.684 37.500 0.00 0.00 0.00 1.98
2339 2554 6.472016 TGTGTCTTTTGATGCTTGGTCTATA 58.528 36.000 0.00 0.00 0.00 1.31
2340 2555 7.112122 TGTGTCTTTTGATGCTTGGTCTATAT 58.888 34.615 0.00 0.00 0.00 0.86
2398 2614 5.850557 TTTTGTCAATTCTGAAGCCTTCA 57.149 34.783 7.00 7.00 38.17 3.02
2404 2620 6.091437 GTCAATTCTGAAGCCTTCAATGAAG 58.909 40.000 15.64 15.64 39.58 3.02
2449 2668 2.021068 GATACGCTGCTGGAGCCTCA 62.021 60.000 15.74 1.09 46.01 3.86
2480 2699 5.774690 AGTGAAAGATGGTTTATTGCTTCCA 59.225 36.000 0.00 0.00 0.00 3.53
2507 2726 5.686159 TTAAGCCGTCGTTTATTTTGGAA 57.314 34.783 0.00 0.00 0.00 3.53
2519 2738 6.632834 CGTTTATTTTGGAAGTTGTCTGAGTG 59.367 38.462 0.00 0.00 0.00 3.51
2539 2758 6.255670 TGAGTGCGATGTGTAATTTGTATCTC 59.744 38.462 0.00 0.00 0.00 2.75
2546 2765 9.062674 CGATGTGTAATTTGTATCTCTATACGG 57.937 37.037 0.00 0.00 40.84 4.02
2577 2796 7.647907 TTTAAGTTATTCTTGTCCGAGTGAC 57.352 36.000 0.00 0.00 44.72 3.67
2653 2872 7.125204 ACATAGGTTATTTGTGCCTGTAGAGTA 59.875 37.037 0.00 0.00 34.07 2.59
2696 2916 6.598503 TGGACTCCTGTCTATAAGATTCGTA 58.401 40.000 0.00 0.00 42.54 3.43
2722 2942 9.777297 AATGCTTGTTGGTGTATTTTTCTTTAT 57.223 25.926 0.00 0.00 0.00 1.40
2787 3007 3.334583 TGCTGACACCCAGATAGAAAC 57.665 47.619 0.00 0.00 45.78 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.054213 CCCTTGCATGAAAATCCCCAAAT 60.054 43.478 0.00 0.00 0.00 2.32
51 52 4.951094 CCCAAATCACCGAAACCCTAATAA 59.049 41.667 0.00 0.00 0.00 1.40
52 53 4.528920 CCCAAATCACCGAAACCCTAATA 58.471 43.478 0.00 0.00 0.00 0.98
53 54 3.361786 CCCAAATCACCGAAACCCTAAT 58.638 45.455 0.00 0.00 0.00 1.73
148 150 7.560368 TGATGGTTCAAGTTAAATTGGTGTTT 58.440 30.769 15.06 0.00 0.00 2.83
172 174 7.246674 AGCTACGGTTAATGTGATAATGTTG 57.753 36.000 0.00 0.00 0.00 3.33
259 261 7.593825 GGTTAACGACCTTACTAGTGAACTAA 58.406 38.462 5.39 0.00 45.55 2.24
278 280 9.010029 TCAAGGTTAATGATCTTTCAGGTTAAC 57.990 33.333 0.00 0.00 36.98 2.01
347 370 2.026729 TGCCTCGGTTGTTAATCATCCA 60.027 45.455 0.00 0.00 36.10 3.41
350 373 3.620488 ACATGCCTCGGTTGTTAATCAT 58.380 40.909 0.00 0.00 0.00 2.45
377 403 6.434596 ACGTTCTAATCTGAGATCAAGATCG 58.565 40.000 22.90 22.90 42.48 3.69
416 442 0.255890 GGGCAGCAAGGGACATCTAA 59.744 55.000 0.00 0.00 0.00 2.10
467 493 2.266055 GTTGCCTCTCCCCTGTCG 59.734 66.667 0.00 0.00 0.00 4.35
475 501 2.352805 CCCCCACTGTTGCCTCTC 59.647 66.667 0.00 0.00 0.00 3.20
526 552 1.561769 TACCACCACTGGCCATCCTG 61.562 60.000 5.51 1.53 42.08 3.86
606 632 5.758784 CGCCTAGTAATTAAGGAAAAGGAGG 59.241 44.000 7.30 0.00 34.58 4.30
619 645 1.200519 TGTCCCAGCGCCTAGTAATT 58.799 50.000 2.29 0.00 0.00 1.40
779 805 0.607489 ACACAACAGAGGAGGCATGC 60.607 55.000 9.90 9.90 0.00 4.06
871 897 9.915629 AATTAGACGAGTATCCATACTTCATTC 57.084 33.333 0.74 0.00 43.27 2.67
921 947 6.542735 GGAAATAAAGGTTGTCAGATAGGACC 59.457 42.308 0.00 0.00 36.97 4.46
1013 1039 2.038837 GGACTGCCGCCTTGTAACC 61.039 63.158 0.00 0.00 0.00 2.85
1108 1134 8.636213 CATAAGACCATTAATGAAGGCTGATTT 58.364 33.333 17.23 0.00 0.00 2.17
1128 1154 8.148351 CCAGGAAAGATAACCGTAATCATAAGA 58.852 37.037 0.00 0.00 0.00 2.10
1135 1161 4.472108 TCCACCAGGAAAGATAACCGTAAT 59.528 41.667 0.00 0.00 42.23 1.89
1206 1232 7.877612 TCACAATCAAACTGAAGTATAGCAAGA 59.122 33.333 0.00 0.00 0.00 3.02
1212 1238 5.880332 GCCCTCACAATCAAACTGAAGTATA 59.120 40.000 0.00 0.00 0.00 1.47
1225 1251 6.238759 GGTTCAAACATATAGCCCTCACAATC 60.239 42.308 0.00 0.00 0.00 2.67
1237 1263 5.580691 CGAACAGCAGAGGTTCAAACATATA 59.419 40.000 6.16 0.00 43.70 0.86
1260 1286 5.541845 TCAGGATTGGTAGATATTTCAGCG 58.458 41.667 0.00 0.00 0.00 5.18
1280 1306 5.835113 AACCGTCCATGGAAATAAATCAG 57.165 39.130 18.20 0.00 0.00 2.90
1390 1416 7.495279 TCAGCAAATGCACAAAAAGTAAGATTT 59.505 29.630 8.28 0.00 45.16 2.17
1446 1472 8.031864 CAGCAAATATGTATTTTAACCACCACA 58.968 33.333 0.00 0.00 33.88 4.17
1478 1504 6.374333 ACATACCGCTGAGATACAAACAAATT 59.626 34.615 0.00 0.00 0.00 1.82
1598 1624 0.961753 GCCCCTTTGTTGACTCCAAG 59.038 55.000 0.00 0.00 32.06 3.61
1616 1643 1.446966 GTCTCGTTCCTGCCTCAGC 60.447 63.158 0.00 0.00 40.48 4.26
1618 1645 0.318441 CAAGTCTCGTTCCTGCCTCA 59.682 55.000 0.00 0.00 0.00 3.86
1677 1706 3.890147 ACGAAGTCTGGAACTCTTACAGT 59.110 43.478 0.00 0.00 29.74 3.55
1697 1726 8.222984 AGACAGTTTAGAAAACAACAAAAACG 57.777 30.769 5.42 0.00 33.27 3.60
1703 1732 7.934665 TGCCTATAGACAGTTTAGAAAACAACA 59.065 33.333 0.00 0.00 0.00 3.33
1831 1860 6.432607 GGAAGTACCTTTAATACTTGGTGC 57.567 41.667 4.99 0.00 41.80 5.01
1916 1945 9.643693 ACAATTGGATATGCAAGAAAAGTTAAG 57.356 29.630 15.23 0.00 0.00 1.85
1921 1950 6.532657 GGACACAATTGGATATGCAAGAAAAG 59.467 38.462 15.23 6.71 0.00 2.27
2005 2034 6.697455 ACACACATACTAATTGAGATAGCACG 59.303 38.462 0.00 0.00 0.00 5.34
2081 2110 5.904362 ATTCCTTCCAAAGCATACAAGAC 57.096 39.130 0.00 0.00 0.00 3.01
2179 2208 7.126421 ACATTCTACAGGTAGGATTGAATGAGT 59.874 37.037 17.83 3.46 40.67 3.41
2223 2253 9.896645 CTCCATGCTAATTATATCAAGGTACAT 57.103 33.333 0.00 0.00 0.00 2.29
2280 2495 2.034053 ACACCACAAACATAAAGTGCGG 59.966 45.455 0.00 0.00 32.09 5.69
2404 2620 7.907214 AACATTCACTCCAAGTAACTGATAC 57.093 36.000 0.00 0.00 34.52 2.24
2423 2639 2.679837 CTCCAGCAGCGTATCAAACATT 59.320 45.455 0.00 0.00 0.00 2.71
2449 2668 1.747444 ACCATCTTTCACTCCACCCT 58.253 50.000 0.00 0.00 0.00 4.34
2480 2699 7.066043 TCCAAAATAAACGACGGCTTAATGTAT 59.934 33.333 0.00 0.00 0.00 2.29
2507 2726 1.069204 ACACATCGCACTCAGACAACT 59.931 47.619 0.00 0.00 0.00 3.16
2519 2738 8.576281 CGTATAGAGATACAAATTACACATCGC 58.424 37.037 0.00 0.00 38.30 4.58
2696 2916 9.777297 ATAAAGAAAAATACACCAACAAGCATT 57.223 25.926 0.00 0.00 0.00 3.56
2728 2948 9.463443 AGTTGCATTTTTCAGTAAGTATTTCAC 57.537 29.630 0.00 0.00 0.00 3.18
2739 2959 4.595762 ATCAGCAGTTGCATTTTTCAGT 57.404 36.364 6.90 0.00 45.16 3.41
2742 2962 6.327934 AGACATATCAGCAGTTGCATTTTTC 58.672 36.000 6.90 0.00 45.16 2.29
2787 3007 1.635663 CCAAAGCCTAACCGCAGACG 61.636 60.000 0.00 0.00 39.67 4.18


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

AutoCloner maintained by Alex Coulton.