Multiple sequence alignment - TraesCS1D01G214000

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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 TraesCS1D01G214000 chr1D 100.000 2256 0 0 875 3130 299052899 299050644 0.000000e+00 4167
1 TraesCS1D01G214000 chr1D 100.000 578 0 0 1 578 299053773 299053196 0.000000e+00 1068
2 TraesCS1D01G214000 chr1B 92.634 2050 66 27 890 2895 403188756 403186748 0.000000e+00 2870
3 TraesCS1D01G214000 chr1B 90.510 569 37 11 21 578 403189336 403188774 0.000000e+00 736
4 TraesCS1D01G214000 chr1B 96.364 220 6 2 2912 3130 403186765 403186547 8.250000e-96 361
5 TraesCS1D01G214000 chr1A 93.431 1568 45 23 890 2441 373264275 373262750 0.000000e+00 2272
6 TraesCS1D01G214000 chr1A 89.018 601 42 15 1 577 373264894 373264294 0.000000e+00 723
7 TraesCS1D01G214000 chr1A 89.331 478 24 14 2439 2895 373262637 373262166 2.710000e-160 575
8 TraesCS1D01G214000 chr1A 94.186 86 4 1 3001 3086 373260337 373260253 2.530000e-26 130


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 TraesCS1D01G214000 chr1D 299050644 299053773 3129 True 2617.500000 4167 100.000000 1 3130 2 chr1D.!!$R1 3129
1 TraesCS1D01G214000 chr1B 403186547 403189336 2789 True 1322.333333 2870 93.169333 21 3130 3 chr1B.!!$R1 3109
2 TraesCS1D01G214000 chr1A 373260253 373264894 4641 True 925.000000 2272 91.491500 1 3086 4 chr1A.!!$R1 3085

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
570 595 0.625683 AATGGAGATGGGACTGGGCT 60.626 55.0 0.0 0.0 0.0 5.19 F
1967 2027 0.108851 CGCCAATTAACCAACCAGCC 60.109 55.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1972 2032 0.179140 TACGACGGGCGGTGATTAAC 60.179 55.0 8.66 0.0 46.49 2.01 R
2830 3042 0.174617 CCACCCACCAAACAACACAC 59.825 55.0 0.00 0.0 0.00 3.82 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
31 32 4.155709 TGCCCAGATAGATACCAGAAGAG 58.844 47.826 0.00 0.00 0.00 2.85
34 35 5.016173 CCCAGATAGATACCAGAAGAGGAG 58.984 50.000 0.00 0.00 0.00 3.69
85 96 5.163519 TGCCAAGAAAGAAGTGGAAAAAGAG 60.164 40.000 0.00 0.00 34.05 2.85
142 153 4.636206 AGCAAAAGAAGTGAACGAGAAAGT 59.364 37.500 0.00 0.00 0.00 2.66
361 384 4.497674 GCTACGTAGTACCTTGTCTCCATG 60.498 50.000 22.98 0.00 45.11 3.66
417 441 4.451774 TTCAAATGGAAAAGGTACGGTACG 59.548 41.667 11.86 0.00 46.39 3.67
458 482 0.829990 TGAGCTAATCATGTCGGGCA 59.170 50.000 0.00 0.00 31.12 5.36
465 489 2.202236 ATCATGTCGGGCAGCCAACT 62.202 55.000 15.19 0.00 0.00 3.16
466 490 2.045926 ATGTCGGGCAGCCAACTC 60.046 61.111 15.19 0.85 0.00 3.01
482 506 4.778415 TCGTTCGCCTCTCGCTGC 62.778 66.667 0.00 0.00 38.27 5.25
483 507 4.785512 CGTTCGCCTCTCGCTGCT 62.786 66.667 0.00 0.00 38.27 4.24
484 508 2.433318 GTTCGCCTCTCGCTGCTT 60.433 61.111 0.00 0.00 38.27 3.91
494 518 2.594303 CGCTGCTTTGTGGGTCCA 60.594 61.111 0.00 0.00 0.00 4.02
495 519 2.908073 CGCTGCTTTGTGGGTCCAC 61.908 63.158 12.89 12.89 46.33 4.02
499 523 1.903404 GCTTTGTGGGTCCACCTGG 60.903 63.158 16.57 7.97 45.63 4.45
530 555 2.069273 CACGTTTCAGTGAGGATGGAC 58.931 52.381 0.00 0.00 44.43 4.02
570 595 0.625683 AATGGAGATGGGACTGGGCT 60.626 55.000 0.00 0.00 0.00 5.19
1000 1025 2.049156 CAGCGAACCACGAGCTCA 60.049 61.111 15.40 0.00 45.77 4.26
1826 1886 4.070552 GACGACCCGCTGGCTCTT 62.071 66.667 0.00 0.00 33.59 2.85
1960 2020 4.468615 GCGCGCGCCAATTAACCA 62.469 61.111 42.83 0.00 34.56 3.67
1961 2021 2.177038 CGCGCGCCAATTAACCAA 59.823 55.556 27.72 0.00 0.00 3.67
1962 2022 2.149599 CGCGCGCCAATTAACCAAC 61.150 57.895 27.72 0.00 0.00 3.77
1963 2023 1.803922 GCGCGCCAATTAACCAACC 60.804 57.895 23.24 0.00 0.00 3.77
1964 2024 1.581954 CGCGCCAATTAACCAACCA 59.418 52.632 0.00 0.00 0.00 3.67
1965 2025 0.455972 CGCGCCAATTAACCAACCAG 60.456 55.000 0.00 0.00 0.00 4.00
1966 2026 0.735978 GCGCCAATTAACCAACCAGC 60.736 55.000 0.00 0.00 0.00 4.85
1967 2027 0.108851 CGCCAATTAACCAACCAGCC 60.109 55.000 0.00 0.00 0.00 4.85
1968 2028 0.972883 GCCAATTAACCAACCAGCCA 59.027 50.000 0.00 0.00 0.00 4.75
1969 2029 1.337728 GCCAATTAACCAACCAGCCAC 60.338 52.381 0.00 0.00 0.00 5.01
1970 2030 1.275010 CCAATTAACCAACCAGCCACC 59.725 52.381 0.00 0.00 0.00 4.61
1971 2031 1.275010 CAATTAACCAACCAGCCACCC 59.725 52.381 0.00 0.00 0.00 4.61
1972 2032 0.610785 ATTAACCAACCAGCCACCCG 60.611 55.000 0.00 0.00 0.00 5.28
1973 2033 1.997256 TTAACCAACCAGCCACCCGT 61.997 55.000 0.00 0.00 0.00 5.28
1974 2034 1.997256 TAACCAACCAGCCACCCGTT 61.997 55.000 0.00 0.00 0.00 4.44
1975 2035 1.997256 AACCAACCAGCCACCCGTTA 61.997 55.000 0.00 0.00 0.00 3.18
1976 2036 1.228306 CCAACCAGCCACCCGTTAA 60.228 57.895 0.00 0.00 0.00 2.01
1977 2037 0.610785 CCAACCAGCCACCCGTTAAT 60.611 55.000 0.00 0.00 0.00 1.40
1978 2038 0.808755 CAACCAGCCACCCGTTAATC 59.191 55.000 0.00 0.00 0.00 1.75
1986 2046 2.893404 CCCGTTAATCACCGCCCG 60.893 66.667 0.00 0.00 0.00 6.13
2116 2176 6.334202 CAAGCCCTTGTGTAAAACAGTAAAA 58.666 36.000 0.00 0.00 40.74 1.52
2217 2281 4.443913 TCACCGTCGATTCAAACATCTA 57.556 40.909 0.00 0.00 0.00 1.98
2247 2311 2.130395 CTCTGCATGCATGTACTACGG 58.870 52.381 26.79 14.88 0.00 4.02
2294 2358 1.691434 TGGCATCTTTTCCCGCTTTTT 59.309 42.857 0.00 0.00 0.00 1.94
2355 2419 1.372251 CGCACAGCTCTCTCGTGTT 60.372 57.895 3.40 0.00 33.13 3.32
2356 2420 0.941463 CGCACAGCTCTCTCGTGTTT 60.941 55.000 3.40 0.00 33.13 2.83
2357 2421 0.510359 GCACAGCTCTCTCGTGTTTG 59.490 55.000 3.40 0.00 33.13 2.93
2358 2422 0.510359 CACAGCTCTCTCGTGTTTGC 59.490 55.000 0.00 0.00 0.00 3.68
2507 2694 4.988716 TCGGGCTCGTGGTCTGGT 62.989 66.667 5.57 0.00 37.69 4.00
2512 2699 1.371558 GCTCGTGGTCTGGTCCTTT 59.628 57.895 0.00 0.00 0.00 3.11
2536 2723 0.320508 AAGAAAACGCCCGTCTCCTC 60.321 55.000 0.00 0.00 0.00 3.71
2654 2866 4.579869 TCTTCTTATGGTTGTCTTCAGGC 58.420 43.478 0.00 0.00 0.00 4.85
2708 2920 3.347958 TTCAGTGTCATTTTCGTTGCC 57.652 42.857 0.00 0.00 0.00 4.52
2746 2958 2.761304 GAAGCCCTGTTCAGCCAGCT 62.761 60.000 0.00 0.00 0.00 4.24
2794 3006 6.882678 GGTACCATAACCATACAATATCCACC 59.117 42.308 7.15 0.00 39.50 4.61
2830 3042 3.296322 ACGGTATTGCATTGTTTGGTG 57.704 42.857 0.00 0.00 0.00 4.17
2877 3089 4.150627 CGTCTATCTTTGTTCGGCCATATG 59.849 45.833 2.24 0.00 0.00 1.78
2878 3090 5.057149 GTCTATCTTTGTTCGGCCATATGT 58.943 41.667 2.24 0.00 0.00 2.29
2879 3091 5.177696 GTCTATCTTTGTTCGGCCATATGTC 59.822 44.000 2.24 0.00 0.00 3.06
2880 3092 2.276201 TCTTTGTTCGGCCATATGTCG 58.724 47.619 2.24 5.73 0.00 4.35
2881 3093 2.006888 CTTTGTTCGGCCATATGTCGT 58.993 47.619 2.24 0.00 0.00 4.34
2882 3094 1.647346 TTGTTCGGCCATATGTCGTC 58.353 50.000 2.24 9.49 0.00 4.20
2883 3095 0.821517 TGTTCGGCCATATGTCGTCT 59.178 50.000 2.24 0.00 0.00 4.18
2884 3096 1.202371 TGTTCGGCCATATGTCGTCTC 60.202 52.381 2.24 7.54 0.00 3.36
2885 3097 1.107945 TTCGGCCATATGTCGTCTCA 58.892 50.000 2.24 0.00 0.00 3.27
2886 3098 1.328279 TCGGCCATATGTCGTCTCAT 58.672 50.000 2.24 0.00 0.00 2.90
2887 3099 1.269723 TCGGCCATATGTCGTCTCATC 59.730 52.381 2.24 0.00 0.00 2.92
2888 3100 1.270826 CGGCCATATGTCGTCTCATCT 59.729 52.381 2.24 0.00 0.00 2.90
2889 3101 2.288457 CGGCCATATGTCGTCTCATCTT 60.288 50.000 2.24 0.00 0.00 2.40
2890 3102 3.733337 GGCCATATGTCGTCTCATCTTT 58.267 45.455 0.00 0.00 0.00 2.52
2891 3103 3.743396 GGCCATATGTCGTCTCATCTTTC 59.257 47.826 0.00 0.00 0.00 2.62
2892 3104 4.502259 GGCCATATGTCGTCTCATCTTTCT 60.502 45.833 0.00 0.00 0.00 2.52
2893 3105 5.053145 GCCATATGTCGTCTCATCTTTCTT 58.947 41.667 1.24 0.00 0.00 2.52
2894 3106 5.525378 GCCATATGTCGTCTCATCTTTCTTT 59.475 40.000 1.24 0.00 0.00 2.52
2895 3107 6.037610 GCCATATGTCGTCTCATCTTTCTTTT 59.962 38.462 1.24 0.00 0.00 2.27
2896 3108 7.414540 GCCATATGTCGTCTCATCTTTCTTTTT 60.415 37.037 1.24 0.00 0.00 1.94
2995 3207 2.462059 GCTTCTGGCTAGCATGTAGCG 61.462 57.143 18.24 5.05 42.81 4.26
3006 4975 0.673333 CATGTAGCGTTGGACCAGCA 60.673 55.000 9.20 0.00 0.00 4.41
3093 5063 0.392461 TGAGGGCGTGAGTTATTGGC 60.392 55.000 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.445008 TCTGGTATCTATCTGGGCATCC 58.555 50.000 0.00 0.00 0.00 3.51
12 13 5.016173 CCTCCTCTTCTGGTATCTATCTGG 58.984 50.000 0.00 0.00 0.00 3.86
55 56 3.235292 TTCTTTCTTGGCACGCGCG 62.235 57.895 30.96 30.96 39.92 6.86
142 153 4.428294 TTTGCATTTGGATTTTCCCACA 57.572 36.364 0.00 0.00 35.03 4.17
236 250 8.781067 TTTTATTTCGACTTGATTTGTGACAG 57.219 30.769 0.00 0.00 0.00 3.51
276 294 3.133003 TCGATTTGCTTTGGGTTTTTCCA 59.867 39.130 0.00 0.00 38.11 3.53
383 407 7.145323 CCTTTTCCATTTGAAATCAACGTACT 58.855 34.615 0.00 0.00 42.38 2.73
417 441 1.405661 GCTTAGTCCTGGCAGTGGTAC 60.406 57.143 14.43 6.12 0.00 3.34
421 445 1.065926 TCATGCTTAGTCCTGGCAGTG 60.066 52.381 14.43 5.19 39.38 3.66
458 482 2.048127 GAGGCGAACGAGTTGGCT 60.048 61.111 19.29 15.28 42.71 4.75
530 555 2.124983 CCACGCCACTCCCATCAG 60.125 66.667 0.00 0.00 0.00 2.90
1412 1466 1.222936 GATGAGCTCCACCACCTGG 59.777 63.158 12.15 0.00 42.29 4.45
1823 1883 3.760035 GAGGAGCGGTGCCGAAGA 61.760 66.667 15.45 0.00 42.83 2.87
1949 2009 0.972883 TGGCTGGTTGGTTAATTGGC 59.027 50.000 0.00 0.00 0.00 4.52
1950 2010 1.275010 GGTGGCTGGTTGGTTAATTGG 59.725 52.381 0.00 0.00 0.00 3.16
1951 2011 1.275010 GGGTGGCTGGTTGGTTAATTG 59.725 52.381 0.00 0.00 0.00 2.32
1953 2013 0.610785 CGGGTGGCTGGTTGGTTAAT 60.611 55.000 0.00 0.00 0.00 1.40
1955 2015 1.997256 AACGGGTGGCTGGTTGGTTA 61.997 55.000 0.00 0.00 0.00 2.85
1956 2016 1.997256 TAACGGGTGGCTGGTTGGTT 61.997 55.000 0.00 0.00 0.00 3.67
1957 2017 1.997256 TTAACGGGTGGCTGGTTGGT 61.997 55.000 0.00 0.00 0.00 3.67
1958 2018 0.610785 ATTAACGGGTGGCTGGTTGG 60.611 55.000 0.00 0.00 0.00 3.77
1959 2019 0.808755 GATTAACGGGTGGCTGGTTG 59.191 55.000 0.00 0.00 0.00 3.77
1960 2020 0.402504 TGATTAACGGGTGGCTGGTT 59.597 50.000 0.00 0.00 0.00 3.67
1961 2021 0.322187 GTGATTAACGGGTGGCTGGT 60.322 55.000 0.00 0.00 0.00 4.00
1962 2022 1.029947 GGTGATTAACGGGTGGCTGG 61.030 60.000 0.00 0.00 0.00 4.85
1963 2023 1.366111 CGGTGATTAACGGGTGGCTG 61.366 60.000 0.00 0.00 0.00 4.85
1964 2024 1.078708 CGGTGATTAACGGGTGGCT 60.079 57.895 0.00 0.00 0.00 4.75
1965 2025 2.757056 GCGGTGATTAACGGGTGGC 61.757 63.158 0.00 0.00 0.00 5.01
1966 2026 2.110352 GGCGGTGATTAACGGGTGG 61.110 63.158 0.00 0.00 0.00 4.61
1967 2027 2.110352 GGGCGGTGATTAACGGGTG 61.110 63.158 0.00 0.00 0.00 4.61
1968 2028 2.269883 GGGCGGTGATTAACGGGT 59.730 61.111 0.00 0.00 0.00 5.28
1969 2029 2.893404 CGGGCGGTGATTAACGGG 60.893 66.667 0.00 0.00 0.00 5.28
1970 2030 2.125431 ACGGGCGGTGATTAACGG 60.125 61.111 0.00 0.00 0.00 4.44
1971 2031 2.510594 CGACGGGCGGTGATTAACG 61.511 63.158 1.11 0.00 36.03 3.18
1972 2032 0.179140 TACGACGGGCGGTGATTAAC 60.179 55.000 8.66 0.00 46.49 2.01
1973 2033 0.179140 GTACGACGGGCGGTGATTAA 60.179 55.000 8.66 0.00 46.49 1.40
1974 2034 1.433064 GTACGACGGGCGGTGATTA 59.567 57.895 8.66 0.00 46.49 1.75
1975 2035 2.182537 GTACGACGGGCGGTGATT 59.817 61.111 8.66 0.00 46.49 2.57
1976 2036 3.830192 GGTACGACGGGCGGTGAT 61.830 66.667 8.66 0.00 46.49 3.06
1978 2038 3.862394 TTTGGTACGACGGGCGGTG 62.862 63.158 8.66 0.00 46.49 4.94
1986 2046 3.119352 AGAGGACGGTAATTTGGTACGAC 60.119 47.826 0.00 0.00 0.00 4.34
1994 2054 6.296803 AGAGACAAAAAGAGGACGGTAATTT 58.703 36.000 0.00 0.00 0.00 1.82
2058 2118 2.852413 CTGTCAATTCTACGTACTGGCG 59.148 50.000 0.00 0.00 37.94 5.69
2143 2207 7.713734 ACACCATTTCAAGATGAGATTCAAT 57.286 32.000 0.00 0.00 0.00 2.57
2217 2281 1.837789 CATGCAGAGAGGGAGCCAT 59.162 57.895 0.00 0.00 0.00 4.40
2247 2311 6.986904 AGGATAAAATTTCAGAACGGAGTC 57.013 37.500 0.00 0.00 45.00 3.36
2294 2358 3.969250 GACAAATCCCTGCGCCGGA 62.969 63.158 20.58 17.54 0.00 5.14
2355 2419 1.069049 GGCAAAAGGAGAAGCAAGCAA 59.931 47.619 0.00 0.00 0.00 3.91
2356 2420 0.675633 GGCAAAAGGAGAAGCAAGCA 59.324 50.000 0.00 0.00 0.00 3.91
2357 2421 0.675633 TGGCAAAAGGAGAAGCAAGC 59.324 50.000 0.00 0.00 0.00 4.01
2358 2422 3.323243 CAATGGCAAAAGGAGAAGCAAG 58.677 45.455 0.00 0.00 0.00 4.01
2426 2490 8.265055 CCTCTTATATCCTACCTGACAAAAACA 58.735 37.037 0.00 0.00 0.00 2.83
2507 2694 2.227194 GGCGTTTTCTTCCTCAAAGGA 58.773 47.619 0.00 0.00 44.10 3.36
2512 2699 0.601841 GACGGGCGTTTTCTTCCTCA 60.602 55.000 0.00 0.00 0.00 3.86
2536 2723 1.793820 AAGGGACCAAAGGCCTCCAG 61.794 60.000 5.23 0.00 0.00 3.86
2746 2958 0.401356 TGGAATCAGCCAGTTCAGCA 59.599 50.000 0.00 0.00 33.10 4.41
2794 3006 6.584942 GCAATACCGTAAAAGAAAAGGGAAAG 59.415 38.462 0.00 0.00 0.00 2.62
2830 3042 0.174617 CCACCCACCAAACAACACAC 59.825 55.000 0.00 0.00 0.00 3.82
2900 3112 1.872388 TGAGACGACCATCGCAAAAA 58.128 45.000 0.00 0.00 45.12 1.94
2901 3113 1.999735 GATGAGACGACCATCGCAAAA 59.000 47.619 0.00 0.00 45.12 2.44
2902 3114 1.204704 AGATGAGACGACCATCGCAAA 59.795 47.619 0.00 0.00 45.12 3.68
2903 3115 0.817654 AGATGAGACGACCATCGCAA 59.182 50.000 0.00 0.00 45.12 4.85
2904 3116 1.675552 TAGATGAGACGACCATCGCA 58.324 50.000 0.00 0.00 45.12 5.10
2905 3117 2.030717 ACATAGATGAGACGACCATCGC 60.031 50.000 0.00 0.00 45.12 4.58
2906 3118 3.906014 ACATAGATGAGACGACCATCG 57.094 47.619 0.00 0.00 46.93 3.84
2907 3119 7.115520 CACATAAACATAGATGAGACGACCATC 59.884 40.741 0.00 0.00 40.40 3.51
2908 3120 6.925718 CACATAAACATAGATGAGACGACCAT 59.074 38.462 0.00 0.00 0.00 3.55
2909 3121 6.273071 CACATAAACATAGATGAGACGACCA 58.727 40.000 0.00 0.00 0.00 4.02
2910 3122 5.175856 GCACATAAACATAGATGAGACGACC 59.824 44.000 0.00 0.00 0.00 4.79
3093 5063 1.153978 GACACCGCAACATGCCATG 60.154 57.895 2.40 2.40 41.12 3.66


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

AutoCloner maintained by Alex Coulton.