Multiple sequence alignment - TraesCS1D01G235500

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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 TraesCS1D01G235500 chr1D 100.000 4711 0 0 1 4711 324703226 324698516 0.000000e+00 8700
1 TraesCS1D01G235500 chr1A 95.621 4727 156 18 1 4705 420064198 420068895 0.000000e+00 7535
2 TraesCS1D01G235500 chr1A 77.513 587 109 17 4134 4709 76471247 76471821 9.770000e-87 331
3 TraesCS1D01G235500 chr1A 78.210 514 87 19 4134 4635 76450352 76450852 5.920000e-79 305
4 TraesCS1D01G235500 chr1B 95.656 4121 126 22 1 4107 437188289 437184208 0.000000e+00 6569
5 TraesCS1D01G235500 chr1B 86.602 515 52 6 4211 4711 437184104 437183593 1.920000e-153 553
6 TraesCS1D01G235500 chr1B 75.753 598 119 21 4125 4707 405900439 405899853 1.290000e-70 278
7 TraesCS1D01G235500 chr5D 79.132 599 96 19 4126 4711 133852854 133852272 2.060000e-103 387
8 TraesCS1D01G235500 chr4B 78.428 598 104 18 4126 4706 403247843 403248432 2.680000e-97 366
9 TraesCS1D01G235500 chr2D 79.661 531 87 16 4144 4661 593876854 593876332 3.470000e-96 363
10 TraesCS1D01G235500 chr2D 74.897 486 86 28 4236 4706 12363841 12363377 6.220000e-44 189
11 TraesCS1D01G235500 chr2B 78.723 517 90 15 4146 4649 720886829 720887338 1.260000e-85 327
12 TraesCS1D01G235500 chr4D 79.522 293 43 11 4243 4528 94508628 94508910 4.810000e-45 193
13 TraesCS1D01G235500 chr2A 77.152 302 39 24 4135 4418 424965096 424964807 1.060000e-31 148
14 TraesCS1D01G235500 chr5A 76.744 301 41 23 4135 4418 292740252 292739964 1.770000e-29 141
15 TraesCS1D01G235500 chr7A 78.733 221 37 7 4323 4538 613031934 613032149 6.360000e-29 139


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 TraesCS1D01G235500 chr1D 324698516 324703226 4710 True 8700 8700 100.000 1 4711 1 chr1D.!!$R1 4710
1 TraesCS1D01G235500 chr1A 420064198 420068895 4697 False 7535 7535 95.621 1 4705 1 chr1A.!!$F3 4704
2 TraesCS1D01G235500 chr1A 76471247 76471821 574 False 331 331 77.513 4134 4709 1 chr1A.!!$F2 575
3 TraesCS1D01G235500 chr1A 76450352 76450852 500 False 305 305 78.210 4134 4635 1 chr1A.!!$F1 501
4 TraesCS1D01G235500 chr1B 437183593 437188289 4696 True 3561 6569 91.129 1 4711 2 chr1B.!!$R2 4710
5 TraesCS1D01G235500 chr1B 405899853 405900439 586 True 278 278 75.753 4125 4707 1 chr1B.!!$R1 582
6 TraesCS1D01G235500 chr5D 133852272 133852854 582 True 387 387 79.132 4126 4711 1 chr5D.!!$R1 585
7 TraesCS1D01G235500 chr4B 403247843 403248432 589 False 366 366 78.428 4126 4706 1 chr4B.!!$F1 580
8 TraesCS1D01G235500 chr2D 593876332 593876854 522 True 363 363 79.661 4144 4661 1 chr2D.!!$R2 517
9 TraesCS1D01G235500 chr2B 720886829 720887338 509 False 327 327 78.723 4146 4649 1 chr2B.!!$F1 503

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
860 883 1.275573 GGTAGGTGAGGACCAGTGTTC 59.724 57.143 0.0 0.0 45.98 3.18 F
1603 1628 0.321919 GCCATGCTTGTGACCAGAGA 60.322 55.000 0.0 0.0 0.00 3.10 F
2573 2601 1.878522 GTAGACTGCCATGTCGCCG 60.879 63.158 0.0 0.0 41.47 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2157 2182 2.486370 GGAGCCTTTCCCTGAATCTAGC 60.486 54.545 0.00 0.0 40.37 3.42 R
3152 3183 2.454055 GCAAAATCTACGCTCCATTGC 58.546 47.619 0.00 0.0 35.49 3.56 R
4120 4154 1.963515 GGCTTGAAACAATGTGTCCCT 59.036 47.619 0.46 0.0 0.00 4.20 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
97 99 7.040686 TCGGTGAAAATCTTCTAAAAAGAAGGG 60.041 37.037 13.61 0.00 43.89 3.95
105 107 7.713734 TCTTCTAAAAAGAAGGGATACTCGA 57.286 36.000 13.61 0.00 43.89 4.04
399 414 2.099405 AGCTTCTCTCTCTACACCAGC 58.901 52.381 0.00 0.00 0.00 4.85
645 660 1.974236 AGCTAGCACCCTATCCATCAC 59.026 52.381 18.83 0.00 0.00 3.06
860 883 1.275573 GGTAGGTGAGGACCAGTGTTC 59.724 57.143 0.00 0.00 45.98 3.18
914 937 3.243501 GCTTGACCATTTCTCAAGTGCAA 60.244 43.478 9.33 0.00 44.46 4.08
931 954 2.328099 AACGCTGCTGCTGCTTACC 61.328 57.895 25.43 1.13 40.48 2.85
1122 1145 1.153881 GCGTAACAGGACCTCCGAC 60.154 63.158 0.00 0.00 42.08 4.79
1183 1206 3.515316 CTGTTCCGTGCACCGTCCT 62.515 63.158 12.15 0.00 33.66 3.85
1194 1217 0.680921 CACCGTCCTTGGATGGCAAT 60.681 55.000 23.78 5.87 34.66 3.56
1195 1218 0.680921 ACCGTCCTTGGATGGCAATG 60.681 55.000 23.78 4.58 34.66 2.82
1196 1219 1.434696 CGTCCTTGGATGGCAATGC 59.565 57.895 0.00 0.00 0.00 3.56
1197 1220 1.033746 CGTCCTTGGATGGCAATGCT 61.034 55.000 4.82 0.00 0.00 3.79
1198 1221 0.458669 GTCCTTGGATGGCAATGCTG 59.541 55.000 4.82 0.00 0.00 4.41
1232 1257 2.028130 TGCTTTCTTTCTCCGGCAAAA 58.972 42.857 0.00 0.00 0.00 2.44
1236 1261 4.150627 GCTTTCTTTCTCCGGCAAAATTTC 59.849 41.667 0.00 0.00 0.00 2.17
1254 1279 0.534412 TCCAGCTCTGCTCTGCTAAC 59.466 55.000 0.00 0.00 36.40 2.34
1257 1282 2.512301 GCTCTGCTCTGCTAACGCG 61.512 63.158 3.53 3.53 39.65 6.01
1259 1284 1.136872 CTCTGCTCTGCTAACGCGAC 61.137 60.000 15.93 0.00 39.65 5.19
1603 1628 0.321919 GCCATGCTTGTGACCAGAGA 60.322 55.000 0.00 0.00 0.00 3.10
1679 1704 7.823745 AGTTTCTGGTTTTGATGTTCTATGT 57.176 32.000 0.00 0.00 0.00 2.29
1698 1723 7.785033 TCTATGTGATGCTGACTTGAGAATTA 58.215 34.615 0.00 0.00 0.00 1.40
1723 1748 7.539712 AGTGTCTTGAATTACATTGGATACG 57.460 36.000 0.00 0.00 42.51 3.06
1794 1819 7.506114 AGTGAACATTTTAGTGGAGTGACTTA 58.494 34.615 0.00 0.00 0.00 2.24
1940 1965 4.519540 TGGCATTCTTAACTTCTTTGGC 57.480 40.909 0.00 0.00 0.00 4.52
1978 2003 4.651503 CAGGTTAGGAGGCTTTCAGAGATA 59.348 45.833 0.00 0.00 0.00 1.98
2123 2148 5.351465 TCGTCAGAAATTAGATTGTGGCTTC 59.649 40.000 0.00 0.00 0.00 3.86
2127 2152 8.084684 GTCAGAAATTAGATTGTGGCTTCTTTT 58.915 33.333 0.00 0.00 0.00 2.27
2128 2153 8.641541 TCAGAAATTAGATTGTGGCTTCTTTTT 58.358 29.630 0.00 0.00 0.00 1.94
2157 2182 7.543756 TCTTTTCTGAAACCTTACACCTTTTG 58.456 34.615 1.58 0.00 0.00 2.44
2513 2541 3.499338 TCCCGAGTAAGTTCAAGTACCA 58.501 45.455 0.00 0.00 0.00 3.25
2561 2589 5.045578 AGACCAGGCAACAAATATGTAGACT 60.046 40.000 0.00 0.00 39.40 3.24
2570 2598 4.811024 ACAAATATGTAGACTGCCATGTCG 59.189 41.667 0.00 0.00 38.24 4.35
2573 2601 1.878522 GTAGACTGCCATGTCGCCG 60.879 63.158 0.00 0.00 41.47 6.46
2574 2602 2.049767 TAGACTGCCATGTCGCCGA 61.050 57.895 0.00 0.00 41.47 5.54
2828 2856 7.001674 TGTTTCTTTTGGAGCTAATTACTGGA 58.998 34.615 0.00 0.00 0.00 3.86
2934 2962 5.472820 GCTGCCTAGAGAAAATGCTATGAAT 59.527 40.000 0.00 0.00 0.00 2.57
2978 3006 3.633525 AGTCTTCAGCAAGCAAAATGACA 59.366 39.130 0.00 0.00 0.00 3.58
3001 3030 6.434028 ACAGCCTATGATTTTTAGCAAGTTGA 59.566 34.615 7.16 0.00 0.00 3.18
3013 3042 6.852420 TTAGCAAGTTGACAGACTACCTAT 57.148 37.500 7.16 0.00 0.00 2.57
3014 3043 5.078411 AGCAAGTTGACAGACTACCTATG 57.922 43.478 7.16 0.00 0.00 2.23
3015 3044 4.772624 AGCAAGTTGACAGACTACCTATGA 59.227 41.667 7.16 0.00 0.00 2.15
3016 3045 5.423610 AGCAAGTTGACAGACTACCTATGAT 59.576 40.000 7.16 0.00 0.00 2.45
3017 3046 6.070538 AGCAAGTTGACAGACTACCTATGATT 60.071 38.462 7.16 0.00 0.00 2.57
3018 3047 6.595716 GCAAGTTGACAGACTACCTATGATTT 59.404 38.462 7.16 0.00 0.00 2.17
3019 3048 7.764443 GCAAGTTGACAGACTACCTATGATTTA 59.236 37.037 7.16 0.00 0.00 1.40
3020 3049 9.823647 CAAGTTGACAGACTACCTATGATTTAT 57.176 33.333 0.00 0.00 0.00 1.40
3094 3124 7.528996 TCTTTGATTCACTGTTCCAATGATT 57.471 32.000 0.00 0.00 0.00 2.57
3152 3183 6.494893 TGTAACTATGTTGCCTTGCTAAAG 57.505 37.500 0.00 0.00 0.00 1.85
3228 3259 4.376340 AACAGTTTCACTCCTTTTGCTG 57.624 40.909 0.00 0.00 0.00 4.41
3237 3268 4.644234 TCACTCCTTTTGCTGTGATGAAAA 59.356 37.500 0.00 0.00 34.94 2.29
3317 3348 4.207891 AGTCCTTGACGTTTGATATGCT 57.792 40.909 0.00 0.00 37.67 3.79
3572 3606 1.512926 CTTTCCAGTGTCTGAACCCG 58.487 55.000 0.00 0.00 32.44 5.28
4017 4051 5.376625 TCAATTTGAGTTCCTGTGCTAAGT 58.623 37.500 0.00 0.00 0.00 2.24
4067 4101 1.328680 CAGCTACTGTAATTGCCAGCG 59.671 52.381 6.82 1.49 34.26 5.18
4076 4110 0.671163 AATTGCCAGCGGTTGCATTG 60.671 50.000 14.51 0.00 46.23 2.82
4119 4153 6.732896 TCCTAATCTTGGTTAGATCCTGAC 57.267 41.667 2.49 0.00 42.90 3.51
4120 4154 6.202331 TCCTAATCTTGGTTAGATCCTGACA 58.798 40.000 2.49 0.00 42.90 3.58
4124 4159 2.940514 TGGTTAGATCCTGACAGGGA 57.059 50.000 21.56 8.73 39.95 4.20
4226 4341 2.045131 GCTTGCTCAGCCCCTCTTG 61.045 63.158 0.00 0.00 43.65 3.02
4344 4472 1.280457 CTAAGGGTGGAAGGCTCAGT 58.720 55.000 0.00 0.00 0.00 3.41
4346 4474 0.768221 AAGGGTGGAAGGCTCAGTCA 60.768 55.000 0.00 0.00 0.00 3.41
4382 4511 0.476771 TTTCCACTCTGGTCAACCCC 59.523 55.000 0.00 0.00 39.03 4.95
4397 4526 5.059161 GTCAACCCCTAGTTTTCGTAGTTT 58.941 41.667 0.00 0.00 36.18 2.66
4650 4802 0.896479 GGAAACCGGGCTTGGCTAAA 60.896 55.000 6.32 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 3.998672 GCCTTGTCCACGGACCGA 61.999 66.667 23.38 0.00 43.97 4.69
60 61 4.715297 AGATTTTCACCGAGTATACCTGGT 59.285 41.667 4.05 4.05 34.29 4.00
92 94 4.679662 TCGTTTTCATCGAGTATCCCTTC 58.320 43.478 0.00 0.00 33.38 3.46
97 99 5.977725 TCTCCAATCGTTTTCATCGAGTATC 59.022 40.000 0.00 0.00 40.57 2.24
105 107 2.689983 GGCCATCTCCAATCGTTTTCAT 59.310 45.455 0.00 0.00 0.00 2.57
645 660 0.915364 CAAGAAGGGGAGGAAGAGGG 59.085 60.000 0.00 0.00 0.00 4.30
699 714 0.322906 GGGCAGGACCAAGAAGAAGG 60.323 60.000 0.00 0.00 42.05 3.46
860 883 1.400494 CCCAAATCTAAACCCGAAGCG 59.600 52.381 0.00 0.00 0.00 4.68
931 954 1.880027 CTTTTCCTTCCTTGTGTCGGG 59.120 52.381 0.00 0.00 0.00 5.14
1202 1225 0.314302 AAAGAAAGCAGCAGCAGCAG 59.686 50.000 12.92 0.00 45.49 4.24
1203 1226 0.313043 GAAAGAAAGCAGCAGCAGCA 59.687 50.000 12.92 0.00 45.49 4.41
1204 1227 0.597072 AGAAAGAAAGCAGCAGCAGC 59.403 50.000 3.17 0.46 45.49 5.25
1205 1228 1.199558 GGAGAAAGAAAGCAGCAGCAG 59.800 52.381 3.17 0.00 45.49 4.24
1232 1257 0.619505 AGCAGAGCAGAGCTGGAAAT 59.380 50.000 0.00 0.00 39.88 2.17
1236 1261 0.805322 CGTTAGCAGAGCAGAGCTGG 60.805 60.000 0.00 0.00 39.88 4.85
1254 1279 2.276123 GCAACACACAAACGTCGCG 61.276 57.895 0.00 0.00 0.00 5.87
1257 1282 0.450184 ACCAGCAACACACAAACGTC 59.550 50.000 0.00 0.00 0.00 4.34
1259 1284 0.525242 CCACCAGCAACACACAAACG 60.525 55.000 0.00 0.00 0.00 3.60
1262 1287 3.205395 GCCACCAGCAACACACAA 58.795 55.556 0.00 0.00 42.97 3.33
1376 1401 0.685097 AGTTGGCCTCGCTGAAGTTA 59.315 50.000 3.32 0.00 0.00 2.24
1603 1628 8.655935 ACATAAAATTCAGGAGACCAGATTTT 57.344 30.769 0.00 0.00 0.00 1.82
1679 1704 6.233434 ACACTTAATTCTCAAGTCAGCATCA 58.767 36.000 0.00 0.00 33.99 3.07
1698 1723 7.822334 TCGTATCCAATGTAATTCAAGACACTT 59.178 33.333 0.00 0.00 31.22 3.16
1723 1748 3.694889 GGCAATGCCGTTAACTGTC 57.305 52.632 9.14 0.00 39.62 3.51
1784 1809 3.434940 ACCCCACAAATAAGTCACTCC 57.565 47.619 0.00 0.00 0.00 3.85
1794 1819 4.810345 TCTTCCAAACTTACCCCACAAAT 58.190 39.130 0.00 0.00 0.00 2.32
1978 2003 4.098044 AGAGTTACGATGTTCCGATGACAT 59.902 41.667 0.00 0.00 40.27 3.06
2092 2117 8.664798 CACAATCTAATTTCTGACGATAACCAA 58.335 33.333 0.00 0.00 0.00 3.67
2128 2153 8.129496 AGGTGTAAGGTTTCAGAAAAGAAAAA 57.871 30.769 0.00 0.00 39.05 1.94
2129 2154 7.712204 AGGTGTAAGGTTTCAGAAAAGAAAA 57.288 32.000 0.00 0.00 39.05 2.29
2157 2182 2.486370 GGAGCCTTTCCCTGAATCTAGC 60.486 54.545 0.00 0.00 40.37 3.42
2544 2572 4.963276 TGGCAGTCTACATATTTGTTGC 57.037 40.909 0.00 0.00 35.88 4.17
2561 2589 3.738429 CTCCATCGGCGACATGGCA 62.738 63.158 21.67 11.52 45.16 4.92
2570 2598 3.369147 CGAACATATCAATCTCCATCGGC 59.631 47.826 0.00 0.00 0.00 5.54
2573 2601 7.041508 AGCTTTTCGAACATATCAATCTCCATC 60.042 37.037 0.00 0.00 0.00 3.51
2574 2602 6.769822 AGCTTTTCGAACATATCAATCTCCAT 59.230 34.615 0.00 0.00 0.00 3.41
2922 2950 8.071177 AGAGGCAGTAAAAATTCATAGCATTT 57.929 30.769 0.00 0.00 0.00 2.32
2934 2962 6.357367 ACTTCTTTCAGAGAGGCAGTAAAAA 58.643 36.000 0.00 0.00 34.98 1.94
2978 3006 6.434028 TGTCAACTTGCTAAAAATCATAGGCT 59.566 34.615 0.00 0.00 0.00 4.58
3013 3042 9.695526 CAGAAGGTTCACAAAATCAATAAATCA 57.304 29.630 0.00 0.00 0.00 2.57
3014 3043 8.650714 GCAGAAGGTTCACAAAATCAATAAATC 58.349 33.333 0.00 0.00 0.00 2.17
3015 3044 8.370182 AGCAGAAGGTTCACAAAATCAATAAAT 58.630 29.630 0.00 0.00 0.00 1.40
3016 3045 7.652909 CAGCAGAAGGTTCACAAAATCAATAAA 59.347 33.333 0.00 0.00 0.00 1.40
3017 3046 7.147312 CAGCAGAAGGTTCACAAAATCAATAA 58.853 34.615 0.00 0.00 0.00 1.40
3018 3047 6.680810 CAGCAGAAGGTTCACAAAATCAATA 58.319 36.000 0.00 0.00 0.00 1.90
3019 3048 5.535333 CAGCAGAAGGTTCACAAAATCAAT 58.465 37.500 0.00 0.00 0.00 2.57
3020 3049 4.737352 GCAGCAGAAGGTTCACAAAATCAA 60.737 41.667 0.00 0.00 0.00 2.57
3152 3183 2.454055 GCAAAATCTACGCTCCATTGC 58.546 47.619 0.00 0.00 35.49 3.56
3286 3317 8.524870 TCAAACGTCAAGGACTACTATTTAAC 57.475 34.615 0.00 0.00 0.00 2.01
3301 3332 7.624360 AGGAAAATAGCATATCAAACGTCAA 57.376 32.000 0.00 0.00 0.00 3.18
3370 3401 9.499585 CACAAGCAACATCAATTCTCTTTATAG 57.500 33.333 0.00 0.00 0.00 1.31
3918 3952 7.491372 ACATACAATTCGTCGAGTGACAAATAT 59.509 33.333 13.22 0.71 45.80 1.28
3957 3991 6.650390 GGGATTACAACATCAAAACAGCAAAT 59.350 34.615 0.00 0.00 0.00 2.32
4017 4051 9.719433 ACTAGTAGGAAGTTAATATGGTACCAA 57.281 33.333 20.76 8.96 0.00 3.67
4076 4110 4.878397 AGGAAAGTGCTACATTGTATGAGC 59.122 41.667 3.56 3.56 35.45 4.26
4119 4153 2.288395 GGCTTGAAACAATGTGTCCCTG 60.288 50.000 0.46 0.00 0.00 4.45
4120 4154 1.963515 GGCTTGAAACAATGTGTCCCT 59.036 47.619 0.46 0.00 0.00 4.20
4124 4159 1.963515 GGGAGGCTTGAAACAATGTGT 59.036 47.619 0.00 0.00 0.00 3.72
4382 4511 9.916397 CATAATAGCCAAAACTACGAAAACTAG 57.084 33.333 0.00 0.00 0.00 2.57
4397 4526 6.546772 TGCTCATCAATGAACATAATAGCCAA 59.453 34.615 0.00 0.00 36.18 4.52
4422 4551 1.992557 ACCCCACACATGGTAGAATGT 59.007 47.619 0.00 0.00 45.66 2.71
4650 4802 2.024414 GCCGGATGGAAAAGCTTACAT 58.976 47.619 5.05 5.09 38.94 2.29


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

AutoCloner maintained by Alex Coulton.