Multiple sequence alignment - TraesCS3D01G233500

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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 TraesCS3D01G233500 chr3D 100.000 3443 0 0 1 3443 321992838 321996280 0 6359
1 TraesCS3D01G233500 chr3D 85.706 3309 465 8 139 3442 450450877 450447572 0 3483
2 TraesCS3D01G233500 chr3D 93.015 859 56 4 1 858 295208266 295207411 0 1251
3 TraesCS3D01G233500 chr3D 91.977 860 68 1 1 859 113525829 113526688 0 1205
4 TraesCS3D01G233500 chr1D 90.972 3445 306 5 1 3442 86596049 86599491 0 4634
5 TraesCS3D01G233500 chr1D 91.075 3070 265 7 376 3442 70713633 70710570 0 4143
6 TraesCS3D01G233500 chr1D 85.536 3443 471 22 16 3442 234078794 234082225 0 3574
7 TraesCS3D01G233500 chr5D 90.859 3446 305 8 1 3442 166873206 166869767 0 4610
8 TraesCS3D01G233500 chr5D 90.298 3453 320 10 1 3442 179982394 179985842 0 4506
9 TraesCS3D01G233500 chr4D 90.191 3456 315 11 1 3442 194817311 194820756 0 4482
10 TraesCS3D01G233500 chr4D 90.118 3461 318 13 1 3442 233318100 233314645 0 4475
11 TraesCS3D01G233500 chr7D 88.680 3463 363 16 2 3439 257274772 257278230 0 4196


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 TraesCS3D01G233500 chr3D 321992838 321996280 3442 False 6359 6359 100.000 1 3443 1 chr3D.!!$F2 3442
1 TraesCS3D01G233500 chr3D 450447572 450450877 3305 True 3483 3483 85.706 139 3442 1 chr3D.!!$R2 3303
2 TraesCS3D01G233500 chr3D 295207411 295208266 855 True 1251 1251 93.015 1 858 1 chr3D.!!$R1 857
3 TraesCS3D01G233500 chr3D 113525829 113526688 859 False 1205 1205 91.977 1 859 1 chr3D.!!$F1 858
4 TraesCS3D01G233500 chr1D 86596049 86599491 3442 False 4634 4634 90.972 1 3442 1 chr1D.!!$F1 3441
5 TraesCS3D01G233500 chr1D 70710570 70713633 3063 True 4143 4143 91.075 376 3442 1 chr1D.!!$R1 3066
6 TraesCS3D01G233500 chr1D 234078794 234082225 3431 False 3574 3574 85.536 16 3442 1 chr1D.!!$F2 3426
7 TraesCS3D01G233500 chr5D 166869767 166873206 3439 True 4610 4610 90.859 1 3442 1 chr5D.!!$R1 3441
8 TraesCS3D01G233500 chr5D 179982394 179985842 3448 False 4506 4506 90.298 1 3442 1 chr5D.!!$F1 3441
9 TraesCS3D01G233500 chr4D 194817311 194820756 3445 False 4482 4482 90.191 1 3442 1 chr4D.!!$F1 3441
10 TraesCS3D01G233500 chr4D 233314645 233318100 3455 True 4475 4475 90.118 1 3442 1 chr4D.!!$R1 3441
11 TraesCS3D01G233500 chr7D 257274772 257278230 3458 False 4196 4196 88.680 2 3439 1 chr7D.!!$F1 3437

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
639 684 0.61782 AAGATGGGACGTACCAGGCT 60.618 55.0 26.6 21.24 45.2 4.58 F
1045 1090 0.03496 GAAGAAGAAGCCCCAGTCCC 60.035 60.0 0.0 0.00 0.0 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1799 1845 0.105778 CTCAAGAGGAAGCCCGGATC 59.894 60.0 0.73 0.00 37.58 3.36 R
2501 2550 0.108138 CCACCTTAGCAGAAGGGACG 60.108 60.0 18.67 8.77 41.71 4.79 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
27 28 2.949644 GGTGTGGTGGATTGCCTTATAC 59.050 50.000 0.00 0.00 34.31 1.47
70 71 1.210722 GGAAGAACAGCCTCCTAAGGG 59.789 57.143 0.00 0.00 43.58 3.95
213 226 2.478335 GAAGGGATCCCACAACGGCA 62.478 60.000 32.69 0.00 38.92 5.69
222 236 2.134346 CCCACAACGGCAAATTTGAAG 58.866 47.619 22.31 15.59 0.00 3.02
315 338 4.162690 GGGCTCCGCGATGACCTT 62.163 66.667 8.23 0.00 0.00 3.50
316 339 2.125106 GGCTCCGCGATGACCTTT 60.125 61.111 8.23 0.00 0.00 3.11
404 427 3.602513 CTTCGCCTGTGCCTGCTCT 62.603 63.158 0.00 0.00 0.00 4.09
570 615 1.341531 CTGAGGAGGTCTTGTGTCGTT 59.658 52.381 0.00 0.00 0.00 3.85
639 684 0.617820 AAGATGGGACGTACCAGGCT 60.618 55.000 26.60 21.24 45.20 4.58
900 945 2.177580 ACCGCGACCAACACAGTTG 61.178 57.895 8.23 3.00 0.00 3.16
986 1031 1.134461 CCAATCTGACCTGAGCTCTGG 60.134 57.143 31.73 31.73 40.37 3.86
1045 1090 0.034960 GAAGAAGAAGCCCCAGTCCC 60.035 60.000 0.00 0.00 0.00 4.46
1116 1161 1.002069 TCAACCAGGAAGCCATGGAT 58.998 50.000 18.40 6.18 39.02 3.41
1152 1197 2.813908 GCCGCCGACTTCAACGAT 60.814 61.111 0.00 0.00 0.00 3.73
1217 1262 1.976112 GGACAGTCACTGAGGTCCC 59.024 63.158 13.14 0.66 43.14 4.46
1417 1463 0.246360 TCGCCATTTCTTCTCGCTGA 59.754 50.000 0.00 0.00 0.00 4.26
1452 1498 3.036429 GCAGTCCTCGGGATGCCTT 62.036 63.158 0.28 0.00 33.43 4.35
1497 1543 1.682451 CCGGCTCGGGGATTGACTTA 61.682 60.000 5.79 0.00 44.15 2.24
1507 1553 2.032620 GGATTGACTTAGAGCTCCCGA 58.967 52.381 10.93 0.00 0.00 5.14
1527 1573 2.989253 TCTGCGAGCAGGTTCCGA 60.989 61.111 22.93 2.01 43.75 4.55
1582 1628 4.567385 CTCTGCTCTCGCTCCCGC 62.567 72.222 0.00 0.00 36.97 6.13
1679 1725 2.026822 GGTTGAAGAGGCTGAAGGATCA 60.027 50.000 0.00 0.00 0.00 2.92
1799 1845 3.197790 CCGCATGAGGCTTCACGG 61.198 66.667 12.45 12.45 41.67 4.94
1800 1846 2.125552 CGCATGAGGCTTCACGGA 60.126 61.111 0.00 0.00 41.67 4.69
1855 1901 2.043852 AGATCCTGACGGGCGACT 60.044 61.111 0.00 0.00 34.39 4.18
1856 1902 2.105128 GATCCTGACGGGCGACTG 59.895 66.667 0.00 0.00 44.60 3.51
1897 1943 0.391263 GGAGGGTTGCCTCTTGTACG 60.391 60.000 0.00 0.00 37.05 3.67
2147 2193 0.965866 CACGGCTACCTGGAGAGTCA 60.966 60.000 0.00 0.00 0.00 3.41
2160 2206 2.106566 GAGAGTCATCCTGAGGAAGCA 58.893 52.381 4.76 0.00 34.34 3.91
2255 2302 1.310933 GCCAAGGTCTCCATGCAGTG 61.311 60.000 0.00 0.00 0.00 3.66
2382 2431 0.494095 AGAGGAAGGGGTCTCCAAGT 59.506 55.000 0.00 0.00 38.24 3.16
2464 2513 8.867097 AGTGAGTACCTTATCTTTGTAGTTTCA 58.133 33.333 0.00 0.00 0.00 2.69
2501 2550 1.079266 CTGACTGTGGCTCCTCAGC 60.079 63.158 15.60 10.23 46.06 4.26
2518 2567 0.905337 AGCGTCCCTTCTGCTAAGGT 60.905 55.000 14.80 0.00 37.15 3.50
2563 2612 1.920325 CTCCTGCCTCAAGTCCCCA 60.920 63.158 0.00 0.00 0.00 4.96
2665 2715 3.747976 GCCCGCGTTCTTGCCATT 61.748 61.111 4.92 0.00 0.00 3.16
2712 2762 4.368003 CAGGCATGCCAAGGGATT 57.632 55.556 37.18 13.31 38.92 3.01
3007 3066 1.503542 GGAAGAACTCGCCGACGTA 59.496 57.895 0.00 0.00 41.18 3.57
3125 3184 2.203056 CGAAGGCCGATGCATCCA 60.203 61.111 20.87 0.00 41.76 3.41
3319 3379 0.719015 TGAGGGGGAGATCTTGAGGT 59.281 55.000 0.00 0.00 0.00 3.85
3329 3389 1.205893 GATCTTGAGGTGCGAGGAAGT 59.794 52.381 0.00 0.00 0.00 3.01
3423 3483 3.129502 GAAGATGCTGCCAGCGCA 61.130 61.111 12.80 10.60 46.26 6.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 2.959516 TGTACTTGTTCATCCTCAGCG 58.040 47.619 0.00 0.00 0.00 5.18
70 71 0.390472 CCGAGCTCAAGAACACCTCC 60.390 60.000 15.40 0.00 0.00 4.30
315 338 3.241530 AGCAGGACGGCAGGACAA 61.242 61.111 0.00 0.00 35.83 3.18
316 339 4.007644 CAGCAGGACGGCAGGACA 62.008 66.667 0.00 0.00 35.83 4.02
404 427 4.282496 TGGTTTCCTCTTTGGTGCTAAAA 58.718 39.130 0.00 0.00 37.07 1.52
461 506 0.458543 GTGACGTGAGCCATGACGAT 60.459 55.000 11.17 0.00 38.94 3.73
593 638 0.468226 AAACACTCAAGACCCTCGCA 59.532 50.000 0.00 0.00 0.00 5.10
665 710 1.676967 CCCCAGACTTGCCTGCTTC 60.677 63.158 0.00 0.00 32.97 3.86
667 712 2.530151 TCCCCAGACTTGCCTGCT 60.530 61.111 0.00 0.00 32.97 4.24
723 768 4.492160 CAAGTCCGAGCGCGCCTA 62.492 66.667 30.33 7.96 35.83 3.93
852 897 1.278127 GCCAGGCGGATATTAAGGCTA 59.722 52.381 0.00 0.00 38.79 3.93
900 945 3.267860 CGCCAGCGATGAAGGAGC 61.268 66.667 6.06 0.00 42.83 4.70
986 1031 4.899239 CCATGGCGACGGAGAGGC 62.899 72.222 0.00 0.00 35.41 4.70
1009 1054 2.436115 CCCCTTCTTCGTTCGGCC 60.436 66.667 0.00 0.00 0.00 6.13
1152 1197 2.770130 GCCACCATCTTCCCCCAA 59.230 61.111 0.00 0.00 0.00 4.12
1217 1262 3.418995 CATAGGGCATCAAGGAGAATGG 58.581 50.000 0.00 0.00 0.00 3.16
1439 1485 0.250081 GAAGCTAAGGCATCCCGAGG 60.250 60.000 0.00 0.00 41.70 4.63
1452 1498 4.096003 GCCACGGCCTGGAAGCTA 62.096 66.667 21.37 0.00 43.95 3.32
1497 1543 3.444805 GCAGACGTCGGGAGCTCT 61.445 66.667 17.45 0.00 0.00 4.09
1507 1553 2.049063 GAACCTGCTCGCAGACGT 60.049 61.111 19.78 7.64 46.30 4.34
1527 1573 1.079405 CACGAATACCCACCGCTGT 60.079 57.895 0.00 0.00 0.00 4.40
1742 1788 1.065491 TCCACATTGGTCGAGAATGGG 60.065 52.381 17.32 14.32 39.03 4.00
1774 1820 2.825836 CCTCATGCGGTCCTTGCC 60.826 66.667 0.00 0.00 0.00 4.52
1799 1845 0.105778 CTCAAGAGGAAGCCCGGATC 59.894 60.000 0.73 0.00 37.58 3.36
1800 1846 2.216148 CTCAAGAGGAAGCCCGGAT 58.784 57.895 0.73 0.00 37.58 4.18
1855 1901 2.672651 CATGTTGGCTGGCGACCA 60.673 61.111 17.87 7.51 34.65 4.02
1856 1902 4.120331 GCATGTTGGCTGGCGACC 62.120 66.667 17.87 0.29 0.00 4.79
1897 1943 2.328099 CCACCTTGTTCGAGCAGCC 61.328 63.158 1.23 0.00 0.00 4.85
1967 2013 2.187946 CGCGAGGCCCTTCAAGAT 59.812 61.111 0.00 0.00 0.00 2.40
2135 2181 1.342874 CCTCAGGATGACTCTCCAGGT 60.343 57.143 0.00 0.00 42.56 4.00
2147 2193 0.324738 TCCGACTGCTTCCTCAGGAT 60.325 55.000 0.00 0.00 38.36 3.24
2232 2279 1.919600 GCATGGAGACCTTGGCCTCT 61.920 60.000 3.32 0.00 0.00 3.69
2382 2431 2.282391 AAGGCATCACCGCTGCAA 60.282 55.556 0.00 0.00 46.52 4.08
2464 2513 2.925170 AGGGGAAGCAGCACTCGT 60.925 61.111 0.00 0.00 0.00 4.18
2501 2550 0.108138 CCACCTTAGCAGAAGGGACG 60.108 60.000 18.67 8.77 41.71 4.79
2665 2715 0.185901 AGCAAGGCCACAAAGGAGAA 59.814 50.000 5.01 0.00 41.22 2.87
2867 2926 0.790814 CCGAAAGTCGTTGAAGAGGC 59.209 55.000 0.00 0.00 38.40 4.70
2942 3001 4.069232 CCGGAAGAGCTCGTGGCA 62.069 66.667 6.97 0.00 44.79 4.92
3007 3066 3.178540 AACTTCAAGGCGGGCGTCT 62.179 57.895 0.00 0.00 0.00 4.18
3101 3160 4.388499 ATCGGCCTTCGCGTTGGT 62.388 61.111 18.01 0.05 39.05 3.67
3319 3379 0.035317 AACATCAGCACTTCCTCGCA 59.965 50.000 0.00 0.00 0.00 5.10
3329 3389 0.108186 CGTAGCCTCCAACATCAGCA 60.108 55.000 0.00 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.