Multiple sequence alignment - TraesCS4B01G261300

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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 TraesCS4B01G261300 chr4B 100.000 3167 0 0 1 3167 530208702 530205536 0 5849
1 TraesCS4B01G261300 chr4A 90.635 3278 133 74 1 3167 33647101 33643887 0 4193
2 TraesCS4B01G261300 chr4D 93.311 1764 61 23 1425 3167 432428148 432426421 0 2551
3 TraesCS4B01G261300 chr4D 98.021 960 15 2 1 956 432429614 432428655 0 1664
4 TraesCS4B01G261300 chr4D 98.241 398 7 0 948 1345 432428631 432428234 0 697


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 TraesCS4B01G261300 chr4B 530205536 530208702 3166 True 5849.000000 5849 100.000000 1 3167 1 chr4B.!!$R1 3166
1 TraesCS4B01G261300 chr4A 33643887 33647101 3214 True 4193.000000 4193 90.635000 1 3167 1 chr4A.!!$R1 3166
2 TraesCS4B01G261300 chr4D 432426421 432429614 3193 True 1637.333333 2551 96.524333 1 3167 3 chr4D.!!$R1 3166

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
674 705 0.307760 GGCATTATGGCGTGTACAGC 59.692 55.0 2.34 2.02 31.79 4.40 F
1317 1388 0.105658 CCTCCCTCCCCGTCTTCATA 60.106 60.0 0.00 0.00 0.00 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1942 2091 0.795085 CTTCTCTTTGTCGCTGCTGG 59.205 55.0 0.0 0.0 0.00 4.85 R
2762 2951 0.459934 CGCCCTCTTCTTGCTCAGAG 60.460 60.0 0.0 0.0 36.96 3.35 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
674 705 0.307760 GGCATTATGGCGTGTACAGC 59.692 55.000 2.34 2.02 31.79 4.40
959 1030 7.180229 TCAGTTCCACACACATATATATAGGGG 59.820 40.741 5.11 5.11 0.00 4.79
1306 1377 1.268283 CCAAGTGAGTCCCTCCCTCC 61.268 65.000 0.00 0.00 0.00 4.30
1317 1388 0.105658 CCTCCCTCCCCGTCTTCATA 60.106 60.000 0.00 0.00 0.00 2.15
1384 1508 4.069304 TGGGTACAACTCATTTCTTTCCG 58.931 43.478 0.00 0.00 0.00 4.30
1403 1527 5.056894 TCCGTAGCTCTCTCAACTAAAAC 57.943 43.478 0.00 0.00 0.00 2.43
1404 1528 4.521639 TCCGTAGCTCTCTCAACTAAAACA 59.478 41.667 0.00 0.00 0.00 2.83
1405 1529 5.010314 TCCGTAGCTCTCTCAACTAAAACAA 59.990 40.000 0.00 0.00 0.00 2.83
1406 1530 5.694910 CCGTAGCTCTCTCAACTAAAACAAA 59.305 40.000 0.00 0.00 0.00 2.83
1407 1531 6.202188 CCGTAGCTCTCTCAACTAAAACAAAA 59.798 38.462 0.00 0.00 0.00 2.44
1408 1532 7.095187 CCGTAGCTCTCTCAACTAAAACAAAAT 60.095 37.037 0.00 0.00 0.00 1.82
1409 1533 7.952637 CGTAGCTCTCTCAACTAAAACAAAATC 59.047 37.037 0.00 0.00 0.00 2.17
1410 1534 7.807977 AGCTCTCTCAACTAAAACAAAATCA 57.192 32.000 0.00 0.00 0.00 2.57
1411 1535 8.401490 AGCTCTCTCAACTAAAACAAAATCAT 57.599 30.769 0.00 0.00 0.00 2.45
1412 1536 8.854117 AGCTCTCTCAACTAAAACAAAATCATT 58.146 29.630 0.00 0.00 0.00 2.57
1413 1537 9.468532 GCTCTCTCAACTAAAACAAAATCATTT 57.531 29.630 0.00 0.00 0.00 2.32
1469 1593 2.169327 GCGCCGACACGTGTTAAC 59.831 61.111 24.26 13.61 34.88 2.01
1490 1618 3.504520 ACAGCCGGTAAAGTTAATTGTGG 59.495 43.478 1.90 0.00 0.00 4.17
1514 1642 0.310854 AAAGCTATTTATGGCGCGGC 59.689 50.000 27.61 27.61 39.47 6.53
1578 1707 2.634815 TTGGTGGCAAAAATGCATGT 57.365 40.000 0.00 0.00 36.33 3.21
1642 1773 2.755655 CCCTACTATCTATGACGCCCAG 59.244 54.545 0.00 0.00 0.00 4.45
1691 1833 6.708054 ACATTGCCTAGAAGATGCAAGTATAC 59.292 38.462 8.88 0.00 46.90 1.47
1942 2091 1.205893 CTGCTCCTACCCTCTCACAAC 59.794 57.143 0.00 0.00 0.00 3.32
2276 2447 7.517320 ACTATGCATGTATGTTAATCAAGGGA 58.483 34.615 10.16 0.00 0.00 4.20
2648 2837 2.125512 CCTCCTCCTTCGGTTGCG 60.126 66.667 0.00 0.00 0.00 4.85
2748 2937 9.331282 GAACAAACAATAACCTGAGATAGCTAT 57.669 33.333 5.76 5.76 0.00 2.97
2750 2939 9.765795 ACAAACAATAACCTGAGATAGCTATAC 57.234 33.333 6.13 4.91 0.00 1.47
2754 2943 9.019656 ACAATAACCTGAGATAGCTATACAGAG 57.980 37.037 27.60 21.94 0.00 3.35
2755 2944 5.975693 AACCTGAGATAGCTATACAGAGC 57.024 43.478 27.60 9.83 43.19 4.09
2786 2975 2.660064 GCAAGAAGAGGGCGAGGGA 61.660 63.158 0.00 0.00 0.00 4.20
2847 3046 3.259064 ACACGACACCTATACATGCAAC 58.741 45.455 0.00 0.00 0.00 4.17
2855 3054 2.481568 CCTATACATGCAACGCAGGATG 59.518 50.000 7.71 7.49 43.36 3.51
2867 3069 1.521010 CAGGATGCAGCTCCACTCG 60.521 63.158 9.02 0.00 37.81 4.18
2906 3108 0.025513 GCTAATGAGCGTGCACTTCG 59.974 55.000 16.19 2.60 39.39 3.79
2912 3114 3.649986 GCGTGCACTTCGCCACTT 61.650 61.111 16.19 0.00 46.61 3.16
2913 3115 2.551270 CGTGCACTTCGCCACTTC 59.449 61.111 16.19 0.00 41.33 3.01
2914 3116 2.946762 GTGCACTTCGCCACTTCC 59.053 61.111 10.32 0.00 41.33 3.46
2915 3117 1.598130 GTGCACTTCGCCACTTCCT 60.598 57.895 10.32 0.00 41.33 3.36
2944 3146 2.540515 CAAGGCGTCGAATCTACATGT 58.459 47.619 2.69 2.69 0.00 3.21
2945 3147 2.209838 AGGCGTCGAATCTACATGTG 57.790 50.000 9.11 0.00 0.00 3.21
2946 3148 0.577269 GGCGTCGAATCTACATGTGC 59.423 55.000 9.11 0.00 0.00 4.57
2984 3190 2.671070 CCAGGAATCAGGCGTGGT 59.329 61.111 6.56 0.00 36.73 4.16
2997 3203 1.578206 GCGTGGTTCTGCTCTTTCCC 61.578 60.000 0.00 0.00 0.00 3.97
3024 3230 1.716503 ACTTGGCCCTAGGTTGGAAAT 59.283 47.619 8.29 0.00 0.00 2.17
3092 3299 0.822164 GCCTCGGCCTAACTTGTCTA 59.178 55.000 0.00 0.00 34.56 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
619 650 4.518970 GGAGAGCAACACCACAAAATCTAA 59.481 41.667 0.00 0.00 0.00 2.10
674 705 3.506059 CTCGCTCTACATGCCCGGG 62.506 68.421 19.09 19.09 0.00 5.73
959 1030 0.396435 TGATGACAGACACCACCACC 59.604 55.000 0.00 0.00 0.00 4.61
1306 1377 9.141400 GAATAATTAGCTACTTATGAAGACGGG 57.859 37.037 14.95 0.00 0.00 5.28
1346 1456 5.851720 TGTACCCAACGTAGAACATACAAA 58.148 37.500 0.00 0.00 0.00 2.83
1380 1504 5.010314 TGTTTTAGTTGAGAGAGCTACGGAA 59.990 40.000 0.00 0.00 0.00 4.30
1384 1508 8.774586 TGATTTTGTTTTAGTTGAGAGAGCTAC 58.225 33.333 0.00 0.00 0.00 3.58
1406 1530 9.720667 GCTTTAGTTTTCTTTTTGCAAATGATT 57.279 25.926 13.65 4.40 0.00 2.57
1407 1531 8.891720 TGCTTTAGTTTTCTTTTTGCAAATGAT 58.108 25.926 13.65 2.83 0.00 2.45
1408 1532 8.261492 TGCTTTAGTTTTCTTTTTGCAAATGA 57.739 26.923 13.65 11.58 0.00 2.57
1409 1533 8.892887 TTGCTTTAGTTTTCTTTTTGCAAATG 57.107 26.923 13.65 9.36 35.42 2.32
1410 1534 9.905171 TTTTGCTTTAGTTTTCTTTTTGCAAAT 57.095 22.222 13.65 0.00 43.88 2.32
1411 1535 9.905171 ATTTTGCTTTAGTTTTCTTTTTGCAAA 57.095 22.222 8.05 8.05 43.16 3.68
1412 1536 9.553418 GATTTTGCTTTAGTTTTCTTTTTGCAA 57.447 25.926 0.00 0.00 36.35 4.08
1413 1537 7.902403 CGATTTTGCTTTAGTTTTCTTTTTGCA 59.098 29.630 0.00 0.00 0.00 4.08
1414 1538 8.113675 TCGATTTTGCTTTAGTTTTCTTTTTGC 58.886 29.630 0.00 0.00 0.00 3.68
1415 1539 9.623687 CTCGATTTTGCTTTAGTTTTCTTTTTG 57.376 29.630 0.00 0.00 0.00 2.44
1416 1540 8.328146 GCTCGATTTTGCTTTAGTTTTCTTTTT 58.672 29.630 0.00 0.00 0.00 1.94
1417 1541 7.491048 TGCTCGATTTTGCTTTAGTTTTCTTTT 59.509 29.630 0.00 0.00 0.00 2.27
1418 1542 6.978080 TGCTCGATTTTGCTTTAGTTTTCTTT 59.022 30.769 0.00 0.00 0.00 2.52
1419 1543 6.503524 TGCTCGATTTTGCTTTAGTTTTCTT 58.496 32.000 0.00 0.00 0.00 2.52
1420 1544 6.072112 TGCTCGATTTTGCTTTAGTTTTCT 57.928 33.333 0.00 0.00 0.00 2.52
1421 1545 6.363357 ACATGCTCGATTTTGCTTTAGTTTTC 59.637 34.615 0.00 0.00 0.00 2.29
1422 1546 6.215845 ACATGCTCGATTTTGCTTTAGTTTT 58.784 32.000 0.00 0.00 0.00 2.43
1423 1547 5.772521 ACATGCTCGATTTTGCTTTAGTTT 58.227 33.333 0.00 0.00 0.00 2.66
1424 1548 5.182001 AGACATGCTCGATTTTGCTTTAGTT 59.818 36.000 0.00 0.00 0.00 2.24
1425 1549 4.697352 AGACATGCTCGATTTTGCTTTAGT 59.303 37.500 0.00 0.00 0.00 2.24
1426 1550 5.227238 AGACATGCTCGATTTTGCTTTAG 57.773 39.130 0.00 0.00 0.00 1.85
1427 1551 5.220397 CGTAGACATGCTCGATTTTGCTTTA 60.220 40.000 0.00 0.00 0.00 1.85
1428 1552 4.436050 CGTAGACATGCTCGATTTTGCTTT 60.436 41.667 0.00 0.00 0.00 3.51
1429 1553 3.062639 CGTAGACATGCTCGATTTTGCTT 59.937 43.478 0.00 0.00 0.00 3.91
1430 1554 2.604914 CGTAGACATGCTCGATTTTGCT 59.395 45.455 0.00 0.00 0.00 3.91
1431 1555 2.285834 CCGTAGACATGCTCGATTTTGC 60.286 50.000 0.00 0.00 0.00 3.68
1469 1593 3.754323 TCCACAATTAACTTTACCGGCTG 59.246 43.478 0.00 0.00 0.00 4.85
1490 1618 3.482110 CGCGCCATAAATAGCTTTTGTTC 59.518 43.478 0.00 0.00 0.00 3.18
1544 1672 2.101249 CCACCAATAACCATGTCCATGC 59.899 50.000 1.64 0.00 37.49 4.06
1582 1711 1.401931 GCTTTCTGCATGCACGTTCAT 60.402 47.619 18.46 0.00 42.31 2.57
1642 1773 3.521947 ACTACGTACAAAGATGCCTCC 57.478 47.619 0.00 0.00 0.00 4.30
1691 1833 4.441217 CCATGCTGGATACTCCTATCGATG 60.441 50.000 8.54 0.00 40.96 3.84
1942 2091 0.795085 CTTCTCTTTGTCGCTGCTGG 59.205 55.000 0.00 0.00 0.00 4.85
2246 2417 6.989759 TGATTAACATACATGCATAGTCGGTT 59.010 34.615 0.00 10.28 0.00 4.44
2276 2447 8.322091 AGTACAAGATTTACTTACTTGCTCCAT 58.678 33.333 0.00 0.00 42.93 3.41
2400 2577 1.170290 GGGGCAACAGTGTGTGTACC 61.170 60.000 0.00 4.98 39.03 3.34
2648 2837 1.026718 CACGGAAGGGAATGGAGTGC 61.027 60.000 0.00 0.00 35.60 4.40
2755 2944 2.227626 TCTTCTTGCTCAGAGTGTCGAG 59.772 50.000 0.00 0.00 31.12 4.04
2757 2946 2.594321 CTCTTCTTGCTCAGAGTGTCG 58.406 52.381 0.00 0.00 33.13 4.35
2759 2948 1.622811 CCCTCTTCTTGCTCAGAGTGT 59.377 52.381 0.00 0.00 35.64 3.55
2760 2949 1.675415 GCCCTCTTCTTGCTCAGAGTG 60.675 57.143 0.00 0.00 35.64 3.51
2761 2950 0.612744 GCCCTCTTCTTGCTCAGAGT 59.387 55.000 0.00 0.00 35.64 3.24
2762 2951 0.459934 CGCCCTCTTCTTGCTCAGAG 60.460 60.000 0.00 0.00 36.96 3.35
2786 2975 3.149196 CACAGTTTGCACAACCTAGGAT 58.851 45.455 17.98 0.00 0.00 3.24
2855 3054 4.479993 ATGGGCGAGTGGAGCTGC 62.480 66.667 0.00 0.00 34.52 5.25
2856 3055 2.513204 CATGGGCGAGTGGAGCTG 60.513 66.667 0.00 0.00 34.52 4.24
2876 3078 0.601558 CTCATTAGCATGGGCATGGC 59.398 55.000 11.56 11.56 44.61 4.40
2906 3108 3.414700 CGTGCGTGAGGAAGTGGC 61.415 66.667 0.00 0.00 0.00 5.01
2908 3110 2.162921 CTTGCGTGCGTGAGGAAGTG 62.163 60.000 0.00 0.00 32.78 3.16
2909 3111 1.956170 CTTGCGTGCGTGAGGAAGT 60.956 57.895 0.00 0.00 32.78 3.01
2910 3112 2.671177 CCTTGCGTGCGTGAGGAAG 61.671 63.158 8.84 1.79 35.89 3.46
2911 3113 2.664851 CCTTGCGTGCGTGAGGAA 60.665 61.111 8.84 0.00 0.00 3.36
2944 3146 1.219393 CAATGGCCACATGCATGCA 59.781 52.632 26.53 25.04 43.89 3.96
2945 3147 2.177580 GCAATGGCCACATGCATGC 61.178 57.895 30.70 20.09 43.89 4.06
2946 3148 4.118480 GCAATGGCCACATGCATG 57.882 55.556 30.70 25.09 43.89 4.06
3024 3230 1.699083 TGACCAAGGAACAGAGCATGA 59.301 47.619 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.