Multiple sequence alignment - TraesCS3D01G432100

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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 TraesCS3D01G432100 chr3D 100.000 3584 0 0 1 3584 545919351 545922934 0.000000e+00 6619.0
1 TraesCS3D01G432100 chr3A 93.002 3544 189 35 92 3584 682331383 682334918 0.000000e+00 5116.0
2 TraesCS3D01G432100 chr3B 92.130 3456 211 31 1 3424 722364177 722367603 0.000000e+00 4819.0
3 TraesCS3D01G432100 chr7D 76.398 161 28 8 1507 1663 452148841 452148995 1.070000e-10 78.7
4 TraesCS3D01G432100 chr4B 90.385 52 4 1 1588 1639 546677604 546677654 2.310000e-07 67.6
5 TraesCS3D01G432100 chrUn 95.122 41 2 0 1596 1636 260615026 260614986 8.310000e-07 65.8
6 TraesCS3D01G432100 chrUn 87.500 56 7 0 1581 1636 289331561 289331616 8.310000e-07 65.8


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 TraesCS3D01G432100 chr3D 545919351 545922934 3583 False 6619 6619 100.000 1 3584 1 chr3D.!!$F1 3583
1 TraesCS3D01G432100 chr3A 682331383 682334918 3535 False 5116 5116 93.002 92 3584 1 chr3A.!!$F1 3492
2 TraesCS3D01G432100 chr3B 722364177 722367603 3426 False 4819 4819 92.130 1 3424 1 chr3B.!!$F1 3423

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
254 266 1.115930 GCTTCCCTAGGCTCGATCCA 61.116 60.000 8.23 0.0 0.00 3.41 F
971 1005 1.138859 CTCATTGTCCCATACCAGCGA 59.861 52.381 0.00 0.0 0.00 4.93 F
1623 1657 0.250038 GTGAGCCAGACACAAGAGCA 60.250 55.000 0.00 0.0 38.05 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1169 1203 0.250234 CTCATCGGCTTCCACCTCAA 59.750 55.0 0.00 0.0 0.0 3.02 R
2372 2411 0.179015 TTGCCTTGGCTTTACGGACA 60.179 50.0 13.18 0.0 0.0 4.02 R
3501 3559 0.537143 AACCCGACAGCTGCATCAAA 60.537 50.0 15.27 0.0 0.0 2.69 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
29 30 3.689649 CCTACTTGTTGTTACAGGATGCC 59.310 47.826 0.00 0.00 42.53 4.40
56 57 3.370840 TGCCATAGCAGATCTTTTGGT 57.629 42.857 0.00 0.00 46.52 3.67
62 63 1.271656 AGCAGATCTTTTGGTTGCTGC 59.728 47.619 0.00 0.00 46.58 5.25
68 69 4.584325 AGATCTTTTGGTTGCTGCTTGTAA 59.416 37.500 0.00 0.00 0.00 2.41
73 74 2.494059 TGGTTGCTGCTTGTAACTCTC 58.506 47.619 0.00 0.00 40.41 3.20
151 153 9.880157 GCTTATGCATTTTGGATATATTTGGAT 57.120 29.630 3.54 0.00 39.41 3.41
179 191 2.566724 CAACACCTGCCCAACCAAATAT 59.433 45.455 0.00 0.00 0.00 1.28
182 194 3.260632 ACACCTGCCCAACCAAATATTTC 59.739 43.478 0.00 0.00 0.00 2.17
254 266 1.115930 GCTTCCCTAGGCTCGATCCA 61.116 60.000 8.23 0.00 0.00 3.41
268 280 3.605749 ATCCACGGTGGCGGTTCAG 62.606 63.158 22.42 0.00 37.47 3.02
429 457 4.214119 CCTGGCAACCATACATAATCTTCG 59.786 45.833 0.00 0.00 30.82 3.79
436 464 6.672266 ACCATACATAATCTTCGTGGAGAT 57.328 37.500 0.00 0.00 37.99 2.75
460 490 7.815840 TCATTCACTCTTAAAATGACAACCA 57.184 32.000 0.00 0.00 35.17 3.67
541 571 9.466497 TCAATATAAGATCTTGTTTTGAAGCCT 57.534 29.630 25.04 0.00 32.30 4.58
574 605 1.470051 TCATCGGTGAAGACGGATCA 58.530 50.000 0.00 0.00 39.46 2.92
796 828 2.910977 GTTAATCTATCCCCCGGTCCAT 59.089 50.000 0.00 0.00 0.00 3.41
838 870 2.143876 ATGCACCAGGAATAACCACC 57.856 50.000 0.00 0.00 42.04 4.61
949 981 2.657143 GGTATCCACTCTCGACCTCTT 58.343 52.381 0.00 0.00 0.00 2.85
968 1002 5.102953 TCTTTCTCATTGTCCCATACCAG 57.897 43.478 0.00 0.00 0.00 4.00
971 1005 1.138859 CTCATTGTCCCATACCAGCGA 59.861 52.381 0.00 0.00 0.00 4.93
988 1022 1.840630 CGAACGCACACCATCAAGCA 61.841 55.000 0.00 0.00 0.00 3.91
1035 1069 4.722535 TTGGCGAGGGAGGAGGCT 62.723 66.667 0.00 0.00 0.00 4.58
1116 1150 3.003763 AAGGCGGTGGAGGAGGAC 61.004 66.667 0.00 0.00 0.00 3.85
1170 1204 2.361610 CAGAAGGCCGCCCATGTT 60.362 61.111 5.55 0.00 0.00 2.71
1230 1264 3.640407 GCTGAGGCTGGGGTGTCA 61.640 66.667 0.00 0.00 35.22 3.58
1248 1282 3.274288 GTCAGCCAAGAAGAATCGGATT 58.726 45.455 2.19 2.19 0.00 3.01
1322 1356 7.919385 AGGTATGCCTTATCCAAATCAATTT 57.081 32.000 0.00 0.00 44.18 1.82
1474 1508 5.245977 TGAGAGAAATTGGATTCAAAACCCC 59.754 40.000 0.00 0.00 36.36 4.95
1475 1509 4.532126 AGAGAAATTGGATTCAAAACCCCC 59.468 41.667 0.00 0.00 36.36 5.40
1507 1541 5.998981 TCCTTTATGTAAGAAAAACCGAGCA 59.001 36.000 0.00 0.00 35.80 4.26
1623 1657 0.250038 GTGAGCCAGACACAAGAGCA 60.250 55.000 0.00 0.00 38.05 4.26
1665 1699 1.068055 GGCAACTCATGAGCAACCTTG 60.068 52.381 22.83 18.41 0.00 3.61
1683 1717 7.306749 GCAACCTTGTTTGATTCACATTAACAG 60.307 37.037 2.82 0.00 32.94 3.16
1717 1751 6.135290 TGCAGTCACATGCTTATATTTTCC 57.865 37.500 0.00 0.00 46.63 3.13
1792 1826 7.984002 TGAAATTGGTTAATATCATGCAACG 57.016 32.000 0.00 0.00 0.00 4.10
1960 1996 8.454859 TTCATGATTAATATTCTAGAGGGGCT 57.545 34.615 0.00 0.00 0.00 5.19
2107 2146 6.312399 ACTGCTTGATGTTTTCGTTAATCA 57.688 33.333 0.00 0.00 0.00 2.57
2108 2147 6.142817 ACTGCTTGATGTTTTCGTTAATCAC 58.857 36.000 0.00 0.00 0.00 3.06
2130 2169 8.800370 TCACTTCATTGTTGGCTATGTATTTA 57.200 30.769 0.00 0.00 0.00 1.40
2132 2171 9.454585 CACTTCATTGTTGGCTATGTATTTATG 57.545 33.333 0.00 0.00 0.00 1.90
2194 2233 6.570692 TGTATCGGAGATCCTAAAGAACAAC 58.429 40.000 0.00 0.00 45.12 3.32
2352 2391 4.202336 TGACATCAACAATTGGCACCAAAT 60.202 37.500 10.83 0.00 39.55 2.32
2372 2411 0.693049 ATGAGTCAAAGGGGCGACTT 59.307 50.000 0.00 0.00 42.48 3.01
2580 2619 3.588955 TGTTGACGATGAGATGAAGGTG 58.411 45.455 0.00 0.00 0.00 4.00
2777 2817 4.039488 TGTTCCAGCTCAAATCTGCAAAAT 59.961 37.500 0.00 0.00 0.00 1.82
2843 2883 5.584649 TGAAATGTACTTAGAATTCCTGCCG 59.415 40.000 0.65 0.00 0.00 5.69
2900 2941 7.690952 ACTTTTCAGTGTGTTGTACCTTTTA 57.309 32.000 0.00 0.00 0.00 1.52
2902 2943 8.745590 ACTTTTCAGTGTGTTGTACCTTTTATT 58.254 29.630 0.00 0.00 0.00 1.40
2920 2961 8.798153 CCTTTTATTCATGTAACGAAGCATTTC 58.202 33.333 0.00 0.00 0.00 2.17
2948 2989 6.544038 TGCAAATCGGTACTATGATCAATG 57.456 37.500 0.00 0.00 0.00 2.82
3013 3054 8.561738 TGATGGTTTTTCCTTACTTATCTGAC 57.438 34.615 0.00 0.00 37.07 3.51
3049 3090 3.642141 TCCTCCAGTCCAAAAGCTTTTT 58.358 40.909 21.70 4.83 0.00 1.94
3080 3121 4.368874 TGTTTTTATCATCCACCATGCG 57.631 40.909 0.00 0.00 31.70 4.73
3140 3182 3.084039 ACCATGGTCTTACATTGCAGTG 58.916 45.455 13.00 7.79 0.00 3.66
3234 3276 3.243636 CCACATGCATCTAAATCAAGGCC 60.244 47.826 0.00 0.00 0.00 5.19
3281 3323 4.202253 ACATTGGATTCTAGCTATGCACGA 60.202 41.667 0.00 0.00 0.00 4.35
3320 3362 5.713792 TGCTCTAGTATTAGCATCTCCAC 57.286 43.478 0.00 0.00 43.56 4.02
3350 3407 5.409826 GCATTCTCCCATATTAGTAGCACAC 59.590 44.000 0.00 0.00 0.00 3.82
3424 3481 1.000283 CTAGGTTGGCTCTCCTATGCG 60.000 57.143 4.11 0.00 36.00 4.73
3472 3530 7.812669 AGTTACTGCATTAACAAAGCAATTACC 59.187 33.333 23.89 0.00 37.89 2.85
3473 3531 5.160641 ACTGCATTAACAAAGCAATTACCG 58.839 37.500 0.00 0.00 37.89 4.02
3491 3549 9.529325 CAATTACCGAGTTATCTGATGAAGTTA 57.471 33.333 0.00 0.00 0.00 2.24
3498 3556 7.295952 AGTTATCTGATGAAGTTAGCAAACG 57.704 36.000 0.00 0.00 40.73 3.60
3499 3557 7.097192 AGTTATCTGATGAAGTTAGCAAACGA 58.903 34.615 0.00 0.00 40.73 3.85
3501 3559 6.992063 ATCTGATGAAGTTAGCAAACGATT 57.008 33.333 0.00 0.00 40.73 3.34
3511 3569 2.331194 AGCAAACGATTTTGATGCAGC 58.669 42.857 0.00 0.00 44.38 5.25
3536 3594 5.633182 TGTCGGGTTTTACGAATGTAGTTAC 59.367 40.000 0.00 0.00 42.55 2.50
3540 3598 4.329801 GGTTTTACGAATGTAGTTACCGGG 59.670 45.833 6.32 0.00 0.00 5.73
3541 3599 3.799281 TTACGAATGTAGTTACCGGGG 57.201 47.619 6.32 0.00 0.00 5.73
3545 3603 2.931969 CGAATGTAGTTACCGGGGTTTC 59.068 50.000 6.32 0.00 0.00 2.78
3547 3605 3.622166 ATGTAGTTACCGGGGTTTCTG 57.378 47.619 6.32 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.549037 GGGGGCATCCTGTAACAACAA 60.549 52.381 0.00 0.00 35.33 2.83
16 17 0.780637 TTTGGGGGCATCCTGTAACA 59.219 50.000 0.00 0.00 35.33 2.41
56 57 4.826274 ATAGGAGAGTTACAAGCAGCAA 57.174 40.909 0.00 0.00 0.00 3.91
125 127 9.880157 ATCCAAATATATCCAAAATGCATAAGC 57.120 29.630 0.00 0.00 42.57 3.09
179 191 1.018148 ACCACACAATCAACGCGAAA 58.982 45.000 15.93 0.00 0.00 3.46
182 194 0.657077 CACACCACACAATCAACGCG 60.657 55.000 3.53 3.53 0.00 6.01
229 241 1.408822 CGAGCCTAGGGAAGCCAATTT 60.409 52.381 11.72 0.00 0.00 1.82
230 242 0.181350 CGAGCCTAGGGAAGCCAATT 59.819 55.000 11.72 0.00 0.00 2.32
231 243 0.691078 TCGAGCCTAGGGAAGCCAAT 60.691 55.000 11.72 0.00 0.00 3.16
239 251 2.565645 CCGTGGATCGAGCCTAGGG 61.566 68.421 22.18 17.12 42.86 3.53
248 260 4.752879 AACCGCCACCGTGGATCG 62.753 66.667 22.37 15.32 42.83 3.69
254 266 0.179051 TAAAACTGAACCGCCACCGT 60.179 50.000 0.00 0.00 0.00 4.83
268 280 2.413634 CGCCGAGGAATTGGTGTAAAAC 60.414 50.000 0.00 0.00 0.00 2.43
332 360 2.100197 GTTTAGATTTGGCCTCCACCC 58.900 52.381 3.32 0.00 30.78 4.61
343 371 7.523873 GCAAAGTTAGAAGGGCTGTTTAGATTT 60.524 37.037 0.00 0.00 0.00 2.17
415 443 8.768957 AATGATCTCCACGAAGATTATGTATG 57.231 34.615 0.00 0.00 36.13 2.39
429 457 8.394121 GTCATTTTAAGAGTGAATGATCTCCAC 58.606 37.037 3.50 0.00 40.63 4.02
436 464 7.519809 CGTGGTTGTCATTTTAAGAGTGAATGA 60.520 37.037 0.00 0.00 37.43 2.57
460 490 1.810151 GTTGCCACATTATGTCACCGT 59.190 47.619 0.00 0.00 0.00 4.83
476 506 2.802719 TCTTTGGTCCCCATTAGTTGC 58.197 47.619 0.00 0.00 31.53 4.17
541 571 1.737236 CCGATGAATTTGCCTCGACAA 59.263 47.619 0.00 0.00 33.07 3.18
574 605 8.039603 TCTCACAAAGCATTAATACGATTTGT 57.960 30.769 13.43 13.43 40.45 2.83
621 652 7.432059 TGCTGATGTCAACACATTAATTTTCA 58.568 30.769 0.00 0.00 43.79 2.69
622 653 7.872163 TGCTGATGTCAACACATTAATTTTC 57.128 32.000 0.00 0.00 43.79 2.29
623 654 8.089597 TCATGCTGATGTCAACACATTAATTTT 58.910 29.630 0.00 0.00 43.79 1.82
651 683 0.994247 TGCATGGAGGAACCTCACAT 59.006 50.000 20.39 17.05 44.40 3.21
796 828 6.712179 TTTATGTGCATGCTTTCATCCATA 57.288 33.333 20.33 10.16 0.00 2.74
818 850 2.225242 TGGTGGTTATTCCTGGTGCATT 60.225 45.455 0.00 0.00 37.07 3.56
968 1002 1.154413 CTTGATGGTGTGCGTTCGC 60.154 57.895 10.34 10.34 0.00 4.70
971 1005 0.961019 AATGCTTGATGGTGTGCGTT 59.039 45.000 0.00 0.00 0.00 4.84
988 1022 1.396653 GCTTGCATGGTGGCTAGAAT 58.603 50.000 0.00 0.00 38.64 2.40
1035 1069 3.060000 GCATGCAGCTGCTCCACA 61.060 61.111 36.61 18.93 42.66 4.17
1116 1150 3.423162 CTCCTTCTCCTCAGGCGCG 62.423 68.421 0.00 0.00 0.00 6.86
1169 1203 0.250234 CTCATCGGCTTCCACCTCAA 59.750 55.000 0.00 0.00 0.00 3.02
1170 1204 0.614697 TCTCATCGGCTTCCACCTCA 60.615 55.000 0.00 0.00 0.00 3.86
1230 1264 3.539604 CTGAATCCGATTCTTCTTGGCT 58.460 45.455 19.51 0.00 39.96 4.75
1369 1403 6.766429 ACGAGGTTCCATAAAAACTTACTCT 58.234 36.000 0.00 0.00 0.00 3.24
1376 1410 3.120442 CCGTGACGAGGTTCCATAAAAAC 60.120 47.826 6.54 0.00 0.00 2.43
1507 1541 9.367444 TGTATTTCGTGTTTGTATTTGGTTTTT 57.633 25.926 0.00 0.00 0.00 1.94
1547 1581 2.698797 CGTCTTAATCCTAGCCCCAAGA 59.301 50.000 0.00 0.00 0.00 3.02
1623 1657 1.764454 GGTGGTTTTGGGCCTTGGT 60.764 57.895 4.53 0.00 0.00 3.67
1665 1699 4.165779 CCCGCTGTTAATGTGAATCAAAC 58.834 43.478 0.00 0.00 0.00 2.93
1683 1717 3.712881 GACTGCAACACGACCCGC 61.713 66.667 0.00 0.00 0.00 6.13
1717 1751 8.469200 TCATTGATTGGCCATTTTCTAAACTAG 58.531 33.333 6.09 0.00 0.00 2.57
1942 1976 8.322091 GCTAATTCAGCCCCTCTAGAATATTAA 58.678 37.037 0.00 0.00 45.23 1.40
1944 1978 6.716284 GCTAATTCAGCCCCTCTAGAATATT 58.284 40.000 0.00 0.00 45.23 1.28
1945 1979 6.306643 GCTAATTCAGCCCCTCTAGAATAT 57.693 41.667 0.00 0.00 45.23 1.28
1947 1981 4.632327 GCTAATTCAGCCCCTCTAGAAT 57.368 45.455 0.00 0.00 45.23 2.40
1960 1996 8.687292 AATGAGAGAAATAGCATGCTAATTCA 57.313 30.769 38.21 27.19 39.57 2.57
2107 2146 9.407380 TCATAAATACATAGCCAACAATGAAGT 57.593 29.630 0.00 0.00 0.00 3.01
2108 2147 9.888878 CTCATAAATACATAGCCAACAATGAAG 57.111 33.333 0.00 0.00 0.00 3.02
2130 2169 3.557686 GGCTGGAACAAAAATTGGCTCAT 60.558 43.478 0.00 0.00 38.70 2.90
2132 2171 2.224257 TGGCTGGAACAAAAATTGGCTC 60.224 45.455 0.00 0.00 38.70 4.70
2300 2339 1.271982 GGAGGGGGAGAGGAACAAAAC 60.272 57.143 0.00 0.00 0.00 2.43
2352 2391 1.568504 AGTCGCCCCTTTGACTCATA 58.431 50.000 0.00 0.00 41.46 2.15
2372 2411 0.179015 TTGCCTTGGCTTTACGGACA 60.179 50.000 13.18 0.00 0.00 4.02
2637 2676 7.262772 CCTAATTACTACTGAATCAACGTCCA 58.737 38.462 0.00 0.00 0.00 4.02
2639 2678 7.263496 ACCCTAATTACTACTGAATCAACGTC 58.737 38.462 0.00 0.00 0.00 4.34
2843 2883 7.176490 TCTTAGGAATACTATCTCCAGCCTAC 58.824 42.308 0.00 0.00 33.83 3.18
2920 2961 4.048504 TCATAGTACCGATTTGCATGTCG 58.951 43.478 12.71 12.71 37.58 4.35
2948 2989 8.920509 AGTACAACTTTGAAAACATTACAACC 57.079 30.769 0.00 0.00 0.00 3.77
3067 3108 6.707440 AAAATATTAACGCATGGTGGATGA 57.293 33.333 0.00 0.00 33.31 2.92
3099 3140 2.176546 GGCGTCGCACGTAGTACA 59.823 61.111 20.50 0.00 44.73 2.90
3132 3174 2.549064 TACAGAGTGTGCACTGCAAT 57.451 45.000 19.41 0.00 42.66 3.56
3140 3182 6.478344 CCTTTGAGAGAATATACAGAGTGTGC 59.522 42.308 0.00 0.00 0.00 4.57
3234 3276 2.357009 GAGTAGTTGGGAGCATGCATTG 59.643 50.000 21.98 0.00 0.00 2.82
3320 3362 5.862845 ACTAATATGGGAGAATGCACTCAG 58.137 41.667 0.00 0.00 38.51 3.35
3350 3407 9.459640 CAAAGAGGCATATTGATTGTAATTCTG 57.540 33.333 0.00 0.00 0.00 3.02
3472 3530 7.394872 GTTTGCTAACTTCATCAGATAACTCG 58.605 38.462 3.64 0.00 0.00 4.18
3473 3531 7.275779 TCGTTTGCTAACTTCATCAGATAACTC 59.724 37.037 9.32 0.00 31.89 3.01
3491 3549 2.029649 AGCTGCATCAAAATCGTTTGCT 60.030 40.909 1.02 0.00 43.30 3.91
3498 3556 1.202222 CCCGACAGCTGCATCAAAATC 60.202 52.381 15.27 0.00 0.00 2.17
3499 3557 0.813184 CCCGACAGCTGCATCAAAAT 59.187 50.000 15.27 0.00 0.00 1.82
3501 3559 0.537143 AACCCGACAGCTGCATCAAA 60.537 50.000 15.27 0.00 0.00 2.69
3511 3569 4.240096 ACTACATTCGTAAAACCCGACAG 58.760 43.478 0.00 0.00 33.41 3.51
3536 3594 1.553248 TGACTACATCAGAAACCCCGG 59.447 52.381 0.00 0.00 31.91 5.73
3540 3598 6.575162 AATTTGGTGACTACATCAGAAACC 57.425 37.500 0.00 0.00 38.43 3.27
3541 3599 8.324163 ACTAATTTGGTGACTACATCAGAAAC 57.676 34.615 0.00 0.00 38.43 2.78
3545 3603 7.604164 AGACAACTAATTTGGTGACTACATCAG 59.396 37.037 12.01 0.00 38.43 2.90
3547 3605 7.907214 AGACAACTAATTTGGTGACTACATC 57.093 36.000 12.01 0.00 39.84 3.06


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

AutoCloner maintained by Alex Coulton.