Multiple sequence alignment - TraesCS1B01G253200

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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 TraesCS1B01G253200 chr1B 100.000 3717 0 0 1 3717 446260107 446256391 0.000000e+00 6865.0
1 TraesCS1B01G253200 chr1D 93.693 2283 68 29 1 2230 332073386 332071127 0.000000e+00 3349.0
2 TraesCS1B01G253200 chr1D 95.549 719 15 10 2226 2937 332071088 332070380 0.000000e+00 1134.0
3 TraesCS1B01G253200 chr1D 98.099 263 5 0 3455 3717 332069743 332069481 3.380000e-125 459.0
4 TraesCS1B01G253200 chr1D 86.035 401 22 8 3004 3373 332070239 332069842 2.080000e-107 399.0
5 TraesCS1B01G253200 chr1D 96.491 57 2 0 3397 3453 332069844 332069788 1.100000e-15 95.3
6 TraesCS1B01G253200 chr1A 90.082 2319 87 60 1 2230 429004953 429002689 0.000000e+00 2876.0
7 TraesCS1B01G253200 chr1A 91.242 982 49 16 2226 3182 429002651 429001682 0.000000e+00 1303.0
8 TraesCS1B01G253200 chr1A 96.198 263 10 0 3455 3717 429001306 429001044 7.370000e-117 431.0
9 TraesCS1B01G253200 chr1A 84.013 319 19 16 3166 3453 429001671 429001354 1.020000e-70 278.0
10 TraesCS1B01G253200 chr5D 93.047 489 24 8 2226 2710 315913349 315912867 0.000000e+00 706.0
11 TraesCS1B01G253200 chr4D 91.992 487 30 6 2228 2710 1741927 1741446 0.000000e+00 675.0
12 TraesCS1B01G253200 chr4D 91.960 398 23 8 2317 2710 130857888 130858280 1.950000e-152 549.0
13 TraesCS1B01G253200 chr2D 92.231 399 21 8 2317 2710 52740477 52740870 1.170000e-154 556.0
14 TraesCS1B01G253200 chr2D 88.636 88 8 2 2136 2221 52740278 52740365 5.080000e-19 106.0
15 TraesCS1B01G253200 chr3B 84.746 59 8 1 873 931 786971054 786970997 1.440000e-04 58.4
16 TraesCS1B01G253200 chr3D 100.000 28 0 0 884 911 588489772 588489745 7.000000e-03 52.8


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 TraesCS1B01G253200 chr1B 446256391 446260107 3716 True 6865.00 6865 100.00000 1 3717 1 chr1B.!!$R1 3716
1 TraesCS1B01G253200 chr1D 332069481 332073386 3905 True 1087.26 3349 93.97340 1 3717 5 chr1D.!!$R1 3716
2 TraesCS1B01G253200 chr1A 429001044 429004953 3909 True 1222.00 2876 90.38375 1 3717 4 chr1A.!!$R1 3716
3 TraesCS1B01G253200 chr2D 52740278 52740870 592 False 331.00 556 90.43350 2136 2710 2 chr2D.!!$F1 574

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
633 716 0.121197 ATGGAGAGGAGGGGTTTCCA 59.879 55.0 0.00 0.0 41.75 3.53 F
979 1082 0.248743 CGCGCTCAACTACGGGATAA 60.249 55.0 5.56 0.0 44.04 1.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2137 2266 0.250727 TGGAAGTTAGCTGTGGCACC 60.251 55.000 16.26 0.0 41.7 5.01 R
2932 3171 1.679153 GCTCGGAAAAACACCTGGAAA 59.321 47.619 0.00 0.0 0.0 3.13 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
94 113 1.602888 CAGTGAAAGCTGCCAGGCT 60.603 57.895 14.15 0.00 45.30 4.58
189 218 3.559657 GAGATCCCGTGGCCGATCG 62.560 68.421 8.51 8.51 39.91 3.69
266 295 0.249489 AGACCTCACACACGCTGAAC 60.249 55.000 0.00 0.00 0.00 3.18
316 353 4.456535 TCTCCTTCTCTCCTATCTTCACG 58.543 47.826 0.00 0.00 0.00 4.35
360 406 0.469331 TCCCTCTCACGTTGTCCTGT 60.469 55.000 0.00 0.00 0.00 4.00
467 528 3.393278 GAGGAGAGAGAAGGCTACCTAGA 59.607 52.174 0.00 0.00 31.13 2.43
588 666 2.257409 GATGCCCCTTCCTTCGCTGA 62.257 60.000 0.00 0.00 0.00 4.26
633 716 0.121197 ATGGAGAGGAGGGGTTTCCA 59.879 55.000 0.00 0.00 41.75 3.53
709 802 0.250467 TCTGCTCTTGCGCCTTTTCT 60.250 50.000 4.18 0.00 43.34 2.52
800 903 3.015145 GGGAAGCTACTGCCCCCA 61.015 66.667 0.00 0.00 43.71 4.96
939 1042 4.986708 GCCAACGGCCTTTGGGGA 62.987 66.667 34.86 0.00 45.55 4.81
979 1082 0.248743 CGCGCTCAACTACGGGATAA 60.249 55.000 5.56 0.00 44.04 1.75
987 1093 1.041447 ACTACGGGATAACGGCTGCT 61.041 55.000 0.00 0.00 38.39 4.24
1308 1417 3.758172 GGCAACCAGGCGAAGAAA 58.242 55.556 0.00 0.00 33.57 2.52
1598 1715 1.735386 CACATCCCAAGTCTCAGCAG 58.265 55.000 0.00 0.00 0.00 4.24
1599 1716 1.002888 CACATCCCAAGTCTCAGCAGT 59.997 52.381 0.00 0.00 0.00 4.40
1600 1717 1.277557 ACATCCCAAGTCTCAGCAGTC 59.722 52.381 0.00 0.00 0.00 3.51
1601 1718 1.277273 CATCCCAAGTCTCAGCAGTCA 59.723 52.381 0.00 0.00 0.00 3.41
1602 1719 0.972134 TCCCAAGTCTCAGCAGTCAG 59.028 55.000 0.00 0.00 0.00 3.51
1603 1720 0.673022 CCCAAGTCTCAGCAGTCAGC 60.673 60.000 0.00 0.00 46.19 4.26
1625 1742 5.922544 AGCACACATAATTCAAGAAACTTGC 59.077 36.000 6.62 0.00 0.00 4.01
2081 2208 5.868454 TGTCACCTCATTTCTTTCATCTCA 58.132 37.500 0.00 0.00 0.00 3.27
2137 2266 4.771356 GCTGCATGCTGTGTGCCG 62.771 66.667 23.42 2.32 41.83 5.69
2169 2301 7.132863 CAGCTAACTTCCAAGTCTTTTGTTAC 58.867 38.462 0.00 0.00 38.57 2.50
2174 2306 8.664211 AACTTCCAAGTCTTTTGTTACTAGAG 57.336 34.615 0.00 0.00 38.57 2.43
2224 2356 7.176690 ACCAATCAGTATTTCCAAGGTAAACTG 59.823 37.037 11.09 11.09 0.00 3.16
2282 2459 4.020396 TGCATATGTTGGGAACTGCAAATT 60.020 37.500 4.29 0.00 37.22 1.82
2323 2540 2.696775 TGGTCTGTGGGTCCTTCTTTA 58.303 47.619 0.00 0.00 0.00 1.85
2391 2609 2.486191 CCATGGAGAGGTTGATGGTAGC 60.486 54.545 5.56 0.00 32.20 3.58
2546 2777 5.806502 AGCTAGTAGCACGTATACTCTATCG 59.193 44.000 23.77 3.73 45.56 2.92
2550 2781 4.407496 AGCACGTATACTCTATCGCTTC 57.593 45.455 0.56 0.00 0.00 3.86
2752 2991 5.107133 AGTAAATTACTTGGGTCACGATCG 58.893 41.667 14.88 14.88 34.86 3.69
2923 3162 5.543405 TCCCAAATCCAGAATGAAAACATGT 59.457 36.000 0.00 0.00 39.69 3.21
2932 3171 6.239572 CCAGAATGAAAACATGTACCCCTTTT 60.240 38.462 0.00 0.00 39.69 2.27
2960 3207 5.354234 CAGGTGTTTTTCCGAGCTAACATAT 59.646 40.000 1.09 0.00 33.57 1.78
2964 3211 7.061789 GGTGTTTTTCCGAGCTAACATATTTTG 59.938 37.037 1.09 0.00 33.57 2.44
3062 3376 1.961394 TCTGTCTCCGCAAGTACACTT 59.039 47.619 0.00 0.00 36.45 3.16
3091 3405 7.815068 AGAGATATATTTCCGACCAAGATTTCG 59.185 37.037 0.00 0.00 34.93 3.46
3155 3470 6.795098 TTGTTCTTAGCTGCGAGAAATAAA 57.205 33.333 18.44 12.52 34.00 1.40
3194 3537 9.778741 TTATGAGATTTGTTAGTTTCAGTCTGT 57.221 29.630 0.00 0.00 0.00 3.41
3195 3538 8.682936 ATGAGATTTGTTAGTTTCAGTCTGTT 57.317 30.769 0.00 0.00 0.00 3.16
3230 3575 2.901249 TCGTAAGCAGGCCAAGTTATC 58.099 47.619 5.01 0.00 37.18 1.75
3237 3582 2.493278 GCAGGCCAAGTTATCACACAAT 59.507 45.455 5.01 0.00 0.00 2.71
3262 3607 2.676839 GTCATCTTGTGCTGTGGATCTG 59.323 50.000 0.00 0.00 0.00 2.90
3265 3610 2.771089 TCTTGTGCTGTGGATCTGTTC 58.229 47.619 0.00 0.00 0.00 3.18
3266 3611 2.369860 TCTTGTGCTGTGGATCTGTTCT 59.630 45.455 0.00 0.00 0.00 3.01
3267 3612 3.578282 TCTTGTGCTGTGGATCTGTTCTA 59.422 43.478 0.00 0.00 0.00 2.10
3268 3613 3.319137 TGTGCTGTGGATCTGTTCTAC 57.681 47.619 0.00 0.00 36.42 2.59
3269 3614 2.632512 TGTGCTGTGGATCTGTTCTACA 59.367 45.455 5.07 5.07 42.86 2.74
3270 3615 3.070878 TGTGCTGTGGATCTGTTCTACAA 59.929 43.478 6.42 0.00 44.20 2.41
3271 3616 3.433615 GTGCTGTGGATCTGTTCTACAAC 59.566 47.826 6.42 3.33 44.20 3.32
3272 3617 3.324846 TGCTGTGGATCTGTTCTACAACT 59.675 43.478 6.42 0.00 44.20 3.16
3273 3618 4.202357 TGCTGTGGATCTGTTCTACAACTT 60.202 41.667 6.42 0.00 44.20 2.66
3274 3619 4.390297 GCTGTGGATCTGTTCTACAACTTC 59.610 45.833 6.42 0.00 44.20 3.01
3337 3712 6.435904 TGGTACACCTAATTTTTCTTCCATGG 59.564 38.462 4.97 4.97 36.82 3.66
3339 3714 4.777366 ACACCTAATTTTTCTTCCATGGGG 59.223 41.667 13.02 5.58 0.00 4.96
3400 3775 0.179045 ACCGAAGCACTGCTCTTTGT 60.179 50.000 3.40 0.00 38.25 2.83
3407 3782 5.334414 CGAAGCACTGCTCTTTGTAGATTTT 60.334 40.000 3.40 0.00 38.25 1.82
3411 3786 5.797434 GCACTGCTCTTTGTAGATTTTAAGC 59.203 40.000 0.00 0.00 32.51 3.09
3573 3994 4.142600 ACTTGAGGACGAAATTTATGCTGC 60.143 41.667 1.24 0.00 0.00 5.25
3601 4022 0.689055 GTCGAAGGGGTTGGGTAAGT 59.311 55.000 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
115 138 1.761174 GAGACTTCTTGTGGGGGCA 59.239 57.895 0.00 0.00 0.00 5.36
197 226 1.464608 CTGAAAAATTCCTCTGCGCGA 59.535 47.619 12.10 1.90 0.00 5.87
316 353 0.439985 CGTGTGTATGCTGTGTGCTC 59.560 55.000 0.00 0.00 43.37 4.26
360 406 6.271391 TGTGTTCTTTATCCCTCTACTTTCCA 59.729 38.462 0.00 0.00 0.00 3.53
419 465 3.842732 TGGAGTATCTGTGTGTGTACG 57.157 47.619 0.00 0.00 33.73 3.67
485 546 3.868619 AGTCTCTACAGCCTACCCTAG 57.131 52.381 0.00 0.00 0.00 3.02
486 547 4.564799 TCTAGTCTCTACAGCCTACCCTA 58.435 47.826 0.00 0.00 0.00 3.53
487 548 3.393278 CTCTAGTCTCTACAGCCTACCCT 59.607 52.174 0.00 0.00 0.00 4.34
488 549 3.391955 TCTCTAGTCTCTACAGCCTACCC 59.608 52.174 0.00 0.00 0.00 3.69
497 558 4.591924 AGCTACCCTCTCTCTAGTCTCTAC 59.408 50.000 0.00 0.00 0.00 2.59
633 716 1.751924 GAGTTGAGTGAGCCTACGGAT 59.248 52.381 0.00 0.00 0.00 4.18
925 1028 3.503839 TGGTCCCCAAAGGCCGTT 61.504 61.111 0.00 0.00 35.27 4.44
926 1029 3.966543 CTGGTCCCCAAAGGCCGT 61.967 66.667 0.00 0.00 35.27 5.68
979 1082 2.046892 GACATCACCAGCAGCCGT 60.047 61.111 0.00 0.00 0.00 5.68
987 1093 1.078497 GACCATGCCGACATCACCA 60.078 57.895 0.00 0.00 32.87 4.17
1155 1264 1.446792 CGAGTGCGACTGCCAGAAT 60.447 57.895 0.00 0.00 41.78 2.40
1283 1392 4.988598 CCTGGTTGCCGCAGTCGT 62.989 66.667 0.00 0.00 0.00 4.34
1598 1715 6.672147 AGTTTCTTGAATTATGTGTGCTGAC 58.328 36.000 0.00 0.00 0.00 3.51
1599 1716 6.882610 AGTTTCTTGAATTATGTGTGCTGA 57.117 33.333 0.00 0.00 0.00 4.26
1600 1717 6.129009 GCAAGTTTCTTGAATTATGTGTGCTG 60.129 38.462 12.77 0.00 0.00 4.41
1601 1718 5.922544 GCAAGTTTCTTGAATTATGTGTGCT 59.077 36.000 12.77 0.00 0.00 4.40
1602 1719 5.691305 TGCAAGTTTCTTGAATTATGTGTGC 59.309 36.000 12.77 0.00 0.00 4.57
1603 1720 6.696583 TGTGCAAGTTTCTTGAATTATGTGTG 59.303 34.615 12.77 0.00 0.00 3.82
1604 1721 6.697019 GTGTGCAAGTTTCTTGAATTATGTGT 59.303 34.615 12.77 0.00 0.00 3.72
1625 1742 6.820335 TGGGATAGAAGATGTGATTAGTGTG 58.180 40.000 0.00 0.00 0.00 3.82
2137 2266 0.250727 TGGAAGTTAGCTGTGGCACC 60.251 55.000 16.26 0.00 41.70 5.01
2169 2301 7.448469 TCCTTTCATTTTCTTTCCAACCTCTAG 59.552 37.037 0.00 0.00 0.00 2.43
2174 2306 7.201696 GGTTTTCCTTTCATTTTCTTTCCAACC 60.202 37.037 0.00 0.00 36.94 3.77
2250 2427 5.070770 TCCCAACATATGCAAACATGTTC 57.929 39.130 12.39 0.49 42.09 3.18
2305 2482 3.579151 ACTCTAAAGAAGGACCCACAGAC 59.421 47.826 0.00 0.00 0.00 3.51
2391 2609 5.953183 TCAGCTGCCAAATTAACAATAGTG 58.047 37.500 9.47 0.00 0.00 2.74
2932 3171 1.679153 GCTCGGAAAAACACCTGGAAA 59.321 47.619 0.00 0.00 0.00 3.13
2939 3186 7.410407 GCAAAATATGTTAGCTCGGAAAAACAC 60.410 37.037 0.00 0.00 34.89 3.32
2974 3221 3.448301 TCCGTCCCACAATATAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
2975 3222 3.025978 TCCGTCCCACAATATAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
2977 3224 5.209818 TCATCCGTCCCACAATATAAGAC 57.790 43.478 0.00 0.00 0.00 3.01
2987 3234 3.181478 CCTTAGTACTTCATCCGTCCCAC 60.181 52.174 0.00 0.00 0.00 4.61
2990 3237 3.952967 ACTCCTTAGTACTTCATCCGTCC 59.047 47.826 0.00 0.00 32.84 4.79
3081 3395 2.689471 TGGAATGGATGCGAAATCTTGG 59.311 45.455 0.00 0.00 0.00 3.61
3090 3404 5.749596 TTTACAAGTATGGAATGGATGCG 57.250 39.130 0.00 0.00 0.00 4.73
3091 3405 7.945134 AGATTTTACAAGTATGGAATGGATGC 58.055 34.615 0.00 0.00 0.00 3.91
3212 3557 3.127030 GTGTGATAACTTGGCCTGCTTAC 59.873 47.826 3.32 0.00 0.00 2.34
3237 3582 4.350368 TCCACAGCACAAGATGACTTTA 57.650 40.909 0.00 0.00 34.60 1.85
3262 3607 7.518529 GCACTCCTAAAACTGAAGTTGTAGAAC 60.519 40.741 18.22 0.00 44.70 3.01
3265 3610 5.758296 TGCACTCCTAAAACTGAAGTTGTAG 59.242 40.000 11.89 11.89 42.66 2.74
3266 3611 5.676552 TGCACTCCTAAAACTGAAGTTGTA 58.323 37.500 0.00 0.00 38.44 2.41
3267 3612 4.523083 TGCACTCCTAAAACTGAAGTTGT 58.477 39.130 0.00 0.00 38.44 3.32
3268 3613 5.499139 TTGCACTCCTAAAACTGAAGTTG 57.501 39.130 0.00 0.00 38.44 3.16
3269 3614 6.715347 ATTTGCACTCCTAAAACTGAAGTT 57.285 33.333 0.00 0.00 40.50 2.66
3270 3615 6.715347 AATTTGCACTCCTAAAACTGAAGT 57.285 33.333 0.00 0.00 0.00 3.01
3271 3616 7.648142 TGTAATTTGCACTCCTAAAACTGAAG 58.352 34.615 0.00 0.00 0.00 3.02
3272 3617 7.575414 TGTAATTTGCACTCCTAAAACTGAA 57.425 32.000 0.00 0.00 0.00 3.02
3273 3618 7.575414 TTGTAATTTGCACTCCTAAAACTGA 57.425 32.000 0.00 0.00 0.00 3.41
3274 3619 8.702438 CATTTGTAATTTGCACTCCTAAAACTG 58.298 33.333 0.00 0.00 0.00 3.16
3314 3687 6.127451 CCCCATGGAAGAAAAATTAGGTGTAC 60.127 42.308 15.22 0.00 0.00 2.90
3317 3692 5.022787 TCCCCATGGAAGAAAAATTAGGTG 58.977 41.667 15.22 0.00 37.86 4.00
3332 3707 0.323360 ACATCGTTGGTTCCCCATGG 60.323 55.000 4.14 4.14 41.49 3.66
3337 3712 4.332819 CAGATCTAAACATCGTTGGTTCCC 59.667 45.833 0.00 0.00 33.83 3.97
3339 3714 7.306051 CGATACAGATCTAAACATCGTTGGTTC 60.306 40.741 0.00 0.00 33.83 3.62
3407 3782 9.409918 ACATAGTAGACATTCTAGAAGTGCTTA 57.590 33.333 11.53 3.96 28.01 3.09
3573 3994 2.494918 CCCTTCGACCAGCTACCG 59.505 66.667 0.00 0.00 0.00 4.02
3601 4022 2.751259 GGCTTTGCTGATGACAAGATGA 59.249 45.455 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.