Multiple sequence alignment - TraesCS4D01G288100

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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 TraesCS4D01G288100 chr4D 100.000 4670 0 0 1 4670 459318861 459323530 0.000000e+00 8624
1 TraesCS4D01G288100 chr4D 81.297 2144 341 39 1028 3156 478311014 478313112 0.000000e+00 1683
2 TraesCS4D01G288100 chr4D 81.075 2140 347 35 1031 3156 478320071 478322166 0.000000e+00 1655
3 TraesCS4D01G288100 chr4D 84.255 1664 213 23 1507 3162 478280152 478281774 0.000000e+00 1576
4 TraesCS4D01G288100 chr4D 83.975 1298 174 18 1734 3028 478431271 478432537 0.000000e+00 1214
5 TraesCS4D01G288100 chr4D 85.490 1144 138 17 2019 3156 478291726 478292847 0.000000e+00 1168
6 TraesCS4D01G288100 chr4D 79.753 889 121 34 3153 4022 478281805 478282653 1.450000e-164 590
7 TraesCS4D01G288100 chr4D 80.294 817 120 25 3194 3989 478313185 478313981 3.130000e-161 579
8 TraesCS4D01G288100 chr4D 79.618 314 42 12 3392 3701 478314021 478314316 6.130000e-49 206
9 TraesCS4D01G288100 chr4A 94.949 3999 169 19 678 4670 9451914 9447943 0.000000e+00 6235
10 TraesCS4D01G288100 chr4A 94.863 292 13 2 1 290 9452810 9452519 5.510000e-124 455
11 TraesCS4D01G288100 chr4A 88.142 253 11 4 454 687 9452349 9452097 2.750000e-72 283
12 TraesCS4D01G288100 chr4A 94.413 179 8 1 308 486 9452528 9452352 1.660000e-69 274
13 TraesCS4D01G288100 chr4B 90.857 4222 307 47 505 4670 574063142 574067340 0.000000e+00 5585
14 TraesCS4D01G288100 chr4B 82.317 1640 247 29 1523 3156 605005211 605006813 0.000000e+00 1382
15 TraesCS4D01G288100 chr4B 85.251 1356 161 18 1813 3162 604905240 604906562 0.000000e+00 1360
16 TraesCS4D01G288100 chr4B 85.435 1023 117 19 2034 3048 604943707 604944705 0.000000e+00 1035
17 TraesCS4D01G288100 chr4B 84.805 691 101 2 1977 2667 604957872 604958558 0.000000e+00 691
18 TraesCS4D01G288100 chr4B 80.024 841 121 23 3200 4022 604906632 604907443 3.130000e-161 579
19 TraesCS4D01G288100 chr4B 83.974 468 69 4 2692 3156 604969163 604969627 1.190000e-120 444
20 TraesCS4D01G288100 chr4B 94.313 211 9 3 314 522 574060782 574060991 2.100000e-83 320
21 TraesCS4D01G288100 chr4B 90.400 125 9 2 1 122 574060542 574060666 1.340000e-35 161


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 TraesCS4D01G288100 chr4D 459318861 459323530 4669 False 8624.000000 8624 100.000000 1 4670 1 chr4D.!!$F1 4669
1 TraesCS4D01G288100 chr4D 478320071 478322166 2095 False 1655.000000 1655 81.075000 1031 3156 1 chr4D.!!$F3 2125
2 TraesCS4D01G288100 chr4D 478431271 478432537 1266 False 1214.000000 1214 83.975000 1734 3028 1 chr4D.!!$F4 1294
3 TraesCS4D01G288100 chr4D 478291726 478292847 1121 False 1168.000000 1168 85.490000 2019 3156 1 chr4D.!!$F2 1137
4 TraesCS4D01G288100 chr4D 478280152 478282653 2501 False 1083.000000 1576 82.004000 1507 4022 2 chr4D.!!$F5 2515
5 TraesCS4D01G288100 chr4D 478311014 478314316 3302 False 822.666667 1683 80.403000 1028 3989 3 chr4D.!!$F6 2961
6 TraesCS4D01G288100 chr4A 9447943 9452810 4867 True 1811.750000 6235 93.091750 1 4670 4 chr4A.!!$R1 4669
7 TraesCS4D01G288100 chr4B 574060542 574067340 6798 False 2022.000000 5585 91.856667 1 4670 3 chr4B.!!$F5 4669
8 TraesCS4D01G288100 chr4B 605005211 605006813 1602 False 1382.000000 1382 82.317000 1523 3156 1 chr4B.!!$F4 1633
9 TraesCS4D01G288100 chr4B 604943707 604944705 998 False 1035.000000 1035 85.435000 2034 3048 1 chr4B.!!$F1 1014
10 TraesCS4D01G288100 chr4B 604905240 604907443 2203 False 969.500000 1360 82.637500 1813 4022 2 chr4B.!!$F6 2209
11 TraesCS4D01G288100 chr4B 604957872 604958558 686 False 691.000000 691 84.805000 1977 2667 1 chr4B.!!$F2 690


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
596 2813 0.035439 CTCGTACCCCAATGCCAACT 60.035 55.000 0.00 0.0 0.00 3.16 F
749 3167 0.176680 ATTGAGAGCGCAGGTGGTAG 59.823 55.000 11.47 0.0 39.88 3.18 F
1297 3719 1.139058 GTCCAGGTCAGTGTCTGTGTT 59.861 52.381 12.64 0.0 32.61 3.32 F
2202 4630 0.036577 CACCCTGTCCTGAGCTTGAG 60.037 60.000 0.00 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1836 4262 1.286354 GGACGATTTCGCGTTGTCCA 61.286 55.000 23.08 0.0 45.61 4.02 R
2050 4477 1.816961 GCCATGTATCCCTTGCTCCAG 60.817 57.143 0.00 0.0 0.00 3.86 R
3250 5742 2.778299 TCAGAGGGTCCAAAATCAACG 58.222 47.619 0.00 0.0 0.00 4.10 R
3868 6365 0.998928 TGGGGGTGCACATTGACTAT 59.001 50.000 20.43 0.0 0.00 2.12 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
34 35 7.989416 TTTGGTTAACTGGTCTTTGTATAGG 57.011 36.000 5.42 0.00 0.00 2.57
97 100 9.715121 AAAAACTTACTGTTGGTCGAAGATATA 57.285 29.630 0.00 0.00 37.75 0.86
107 111 5.466819 TGGTCGAAGATATATTAAGTGGCG 58.533 41.667 0.00 0.00 40.67 5.69
108 112 5.010314 TGGTCGAAGATATATTAAGTGGCGT 59.990 40.000 0.00 0.00 40.67 5.68
201 206 7.066284 ACAGATACAGTATCCTTTTGTGCATTC 59.934 37.037 15.87 0.00 35.79 2.67
226 231 3.861840 TCTCTTATGGCTCGTGGAAAAG 58.138 45.455 0.00 0.00 0.00 2.27
388 393 3.953612 AGTTGTTCTTGACTTGGCAATGA 59.046 39.130 0.00 0.00 0.00 2.57
397 402 6.885918 TCTTGACTTGGCAATGATGAATAAGA 59.114 34.615 0.00 0.76 0.00 2.10
452 457 5.903764 TCAATCGCAATTTTTGACAAAGG 57.096 34.783 0.10 0.00 0.00 3.11
460 465 5.702209 GCAATTTTTGACAAAGGATGATGGT 59.298 36.000 0.10 0.00 0.00 3.55
570 2779 4.382040 CCATCAATCTGAGGTTACAGTCGT 60.382 45.833 0.00 0.00 38.79 4.34
596 2813 0.035439 CTCGTACCCCAATGCCAACT 60.035 55.000 0.00 0.00 0.00 3.16
597 2814 0.322098 TCGTACCCCAATGCCAACTG 60.322 55.000 0.00 0.00 0.00 3.16
735 3153 5.584649 ACGTGTATGGTTATGGTGAATTGAG 59.415 40.000 0.00 0.00 0.00 3.02
749 3167 0.176680 ATTGAGAGCGCAGGTGGTAG 59.823 55.000 11.47 0.00 39.88 3.18
750 3168 1.185618 TTGAGAGCGCAGGTGGTAGT 61.186 55.000 11.47 0.00 39.88 2.73
1008 3429 1.528586 CCTCAGCACTCACAAGAAACG 59.471 52.381 0.00 0.00 0.00 3.60
1113 3535 1.267582 GCTCGATTTCGGCAGTAAAGC 60.268 52.381 0.00 0.00 40.29 3.51
1297 3719 1.139058 GTCCAGGTCAGTGTCTGTGTT 59.861 52.381 12.64 0.00 32.61 3.32
1888 4314 4.678509 TCGGAATGTTGCATACAGAAAC 57.321 40.909 7.58 0.00 40.83 2.78
2005 4431 5.083122 TGCTTGATGAACCCCAAAGAAATA 58.917 37.500 0.00 0.00 0.00 1.40
2050 4477 3.425162 AAGATGACTTCTTGGGACCAC 57.575 47.619 2.93 0.00 43.21 4.16
2064 4491 1.204146 GACCACTGGAGCAAGGGATA 58.796 55.000 0.71 0.00 0.00 2.59
2135 4563 0.321122 GTTGCCTGACCTGACTCTGG 60.321 60.000 0.44 0.44 33.43 3.86
2142 4570 1.048601 GACCTGACTCTGGGTGACAA 58.951 55.000 6.89 0.00 35.77 3.18
2202 4630 0.036577 CACCCTGTCCTGAGCTTGAG 60.037 60.000 0.00 0.00 0.00 3.02
2538 4971 7.388437 TGTTTTAGTGGTGTATCTCGGTTATT 58.612 34.615 0.00 0.00 0.00 1.40
2543 4976 5.041940 GTGGTGTATCTCGGTTATTCACTC 58.958 45.833 0.00 0.00 0.00 3.51
2958 5399 5.316158 AGAGGATATTACTGCAGCCAAAT 57.684 39.130 15.27 13.53 0.00 2.32
3174 5666 4.371624 TGATCTGGTTTGGTGATGAACT 57.628 40.909 0.00 0.00 0.00 3.01
3226 5718 6.560711 AGTTGTTATTTTCTGGTGTTGTGAC 58.439 36.000 0.00 0.00 0.00 3.67
3228 5720 4.636648 TGTTATTTTCTGGTGTTGTGACGT 59.363 37.500 0.00 0.00 0.00 4.34
3250 5742 8.193250 ACGTATAAGAAACAACATGACCATAC 57.807 34.615 0.00 0.00 0.00 2.39
3251 5743 7.009815 ACGTATAAGAAACAACATGACCATACG 59.990 37.037 0.00 0.00 41.75 3.06
3478 5973 2.035961 TCCGAAGAATCTGCTATTCCCG 59.964 50.000 8.26 10.97 0.00 5.14
3490 5986 4.951254 TGCTATTCCCGTTTATTCATCGA 58.049 39.130 0.00 0.00 0.00 3.59
3492 5988 5.995282 TGCTATTCCCGTTTATTCATCGAAT 59.005 36.000 0.00 0.00 36.20 3.34
3507 6003 4.975502 TCATCGAATTGTTCTGTGTTTTGC 59.024 37.500 0.00 0.00 0.00 3.68
3509 6005 5.743026 TCGAATTGTTCTGTGTTTTGCTA 57.257 34.783 0.00 0.00 0.00 3.49
3510 6006 6.125327 TCGAATTGTTCTGTGTTTTGCTAA 57.875 33.333 0.00 0.00 0.00 3.09
3511 6007 5.968848 TCGAATTGTTCTGTGTTTTGCTAAC 59.031 36.000 0.00 0.00 0.00 2.34
3512 6008 5.741510 CGAATTGTTCTGTGTTTTGCTAACA 59.258 36.000 1.54 1.54 0.00 2.41
3557 6053 9.914834 ACCATTCCAGTATTATTAGCTTAACAA 57.085 29.630 0.00 0.00 0.00 2.83
3585 6081 5.753921 GTGTAGTTCTATGGAGTATGTTGGC 59.246 44.000 0.00 0.00 0.00 4.52
3590 6086 1.696063 ATGGAGTATGTTGGCATGGC 58.304 50.000 13.29 13.29 36.58 4.40
3789 6285 8.637986 CCTTTCTACATGCTTCTCTCTTATAGT 58.362 37.037 0.00 0.00 0.00 2.12
3868 6365 2.360801 GCCAAGGCACAAAAAGACTACA 59.639 45.455 6.14 0.00 41.49 2.74
3922 6432 5.098211 GCTCTTAACTTGCCAATGATGAAC 58.902 41.667 0.00 0.00 0.00 3.18
3979 6509 8.897752 TGAAAATGAAAAGGGGTTAATTTTGTG 58.102 29.630 0.00 0.00 31.00 3.33
4262 6802 3.559238 AGGACACGATTCAATGTTTGC 57.441 42.857 0.00 0.00 0.00 3.68
4339 6880 8.021898 AGAACCCTCAATGAAAAATGAGAAAA 57.978 30.769 4.43 0.00 44.64 2.29
4360 6901 4.953940 ACTGGTTGTAATTGGCATTGTT 57.046 36.364 0.00 0.00 0.00 2.83
4366 6907 4.909696 TGTAATTGGCATTGTTATCGGG 57.090 40.909 0.00 0.00 0.00 5.14
4399 6940 6.248433 TCTTTTGTTTCCTGCCATAAGATCT 58.752 36.000 0.00 0.00 0.00 2.75
4451 7032 5.141182 TGGTTGGGTTTCTGTGCTATTTTA 58.859 37.500 0.00 0.00 0.00 1.52
4542 7124 1.134699 TGCTTATTCTGGCACTCCTCG 60.135 52.381 0.00 0.00 33.23 4.63
4578 7160 2.868583 CAGGCCATCTGATCTGTTTACG 59.131 50.000 5.01 0.00 46.18 3.18
4581 7164 2.030946 GCCATCTGATCTGTTTACGTGC 59.969 50.000 0.00 0.00 0.00 5.34
4640 7223 1.603455 CCAAAGACCCGTGCATGGT 60.603 57.895 23.39 16.86 39.32 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 3.181476 TGAGAGAAAGCAAACCAAAAGGC 60.181 43.478 0.00 0.00 0.00 4.35
97 100 7.391148 ACAGATTATTTTCACGCCACTTAAT 57.609 32.000 0.00 0.00 0.00 1.40
201 206 1.268794 CCACGAGCCATAAGAGAGACG 60.269 57.143 0.00 0.00 0.00 4.18
226 231 4.830826 AAGTTCATTCCCTTTTCGACAC 57.169 40.909 0.00 0.00 0.00 3.67
315 320 8.102676 CCTCCCAAATGAATAGGTGAAATTTTT 58.897 33.333 0.00 0.00 0.00 1.94
316 321 7.623630 CCTCCCAAATGAATAGGTGAAATTTT 58.376 34.615 0.00 0.00 0.00 1.82
317 322 6.352137 GCCTCCCAAATGAATAGGTGAAATTT 60.352 38.462 0.00 0.00 0.00 1.82
318 323 5.129320 GCCTCCCAAATGAATAGGTGAAATT 59.871 40.000 0.00 0.00 0.00 1.82
319 324 4.651045 GCCTCCCAAATGAATAGGTGAAAT 59.349 41.667 0.00 0.00 0.00 2.17
425 430 7.474398 TTGTCAAAAATTGCGATTGATTTCA 57.526 28.000 0.00 0.00 35.70 2.69
438 443 8.306761 GTCTACCATCATCCTTTGTCAAAAATT 58.693 33.333 0.00 0.00 0.00 1.82
527 2734 3.327757 TGGAGTCAGCACCTTTATCTTGT 59.672 43.478 0.00 0.00 0.00 3.16
570 2779 1.207089 CATTGGGGTACGAGAAGCAGA 59.793 52.381 0.00 0.00 0.00 4.26
689 3107 8.495949 CACGTATAAGAAAATCTCGCCAATATT 58.504 33.333 0.00 0.00 0.00 1.28
711 3129 5.492895 TCAATTCACCATAACCATACACGT 58.507 37.500 0.00 0.00 0.00 4.49
735 3153 1.153745 CTCACTACCACCTGCGCTC 60.154 63.158 9.73 0.00 0.00 5.03
749 3167 0.040603 GTTGCTGCAGCTTCACTCAC 60.041 55.000 36.61 18.13 42.66 3.51
750 3168 1.501337 CGTTGCTGCAGCTTCACTCA 61.501 55.000 36.61 14.44 42.66 3.41
842 3261 0.248458 GCCCATGAAATACAACGGCG 60.248 55.000 4.80 4.80 37.13 6.46
907 3326 1.334160 TGCTCCTTGTCGTGTTCCTA 58.666 50.000 0.00 0.00 0.00 2.94
970 3390 3.330720 AGAGGGGAGGCCGGTTTG 61.331 66.667 1.90 0.00 0.00 2.93
971 3391 3.009714 GAGAGGGGAGGCCGGTTT 61.010 66.667 1.90 0.00 0.00 3.27
1113 3535 0.813210 GAAGATCTTGCTCAGGGCGG 60.813 60.000 14.00 0.00 45.43 6.13
1118 3540 4.121317 GTCATGGAGAAGATCTTGCTCAG 58.879 47.826 24.12 17.27 0.00 3.35
1228 3650 2.110213 GTGGTGGCGTTCCTCACA 59.890 61.111 0.00 0.00 37.27 3.58
1287 3709 1.007336 CGGGTCGCTAACACAGACAC 61.007 60.000 0.00 0.00 36.68 3.67
1836 4262 1.286354 GGACGATTTCGCGTTGTCCA 61.286 55.000 23.08 0.00 45.61 4.02
1888 4314 4.421058 TCTCGACAAACTTGATCATACCG 58.579 43.478 0.00 0.00 0.00 4.02
2050 4477 1.816961 GCCATGTATCCCTTGCTCCAG 60.817 57.143 0.00 0.00 0.00 3.86
2064 4491 5.513233 AGATTTCCTTGTCATAAGCCATGT 58.487 37.500 0.00 0.00 35.96 3.21
2135 4563 6.586844 GTCAACTCTCTTACATAGTTGTCACC 59.413 42.308 12.61 0.00 46.49 4.02
2142 4570 8.037758 CCTTCAATGTCAACTCTCTTACATAGT 58.962 37.037 0.00 0.00 32.44 2.12
2202 4630 8.400947 AGTAAACAATATCATCACAATCACAGC 58.599 33.333 0.00 0.00 0.00 4.40
2538 4971 2.924302 TGAACCCTACCTAGAGGAGTGA 59.076 50.000 1.60 0.00 39.15 3.41
2543 4976 4.869451 AGTAAGTGAACCCTACCTAGAGG 58.131 47.826 0.00 0.00 42.17 3.69
2587 5020 9.559958 CTAGCTGAAGTTGTAACCAAATTTATG 57.440 33.333 0.00 0.00 38.84 1.90
3226 5718 7.009815 ACGTATGGTCATGTTGTTTCTTATACG 59.990 37.037 0.00 0.00 42.84 3.06
3228 5720 8.661257 CAACGTATGGTCATGTTGTTTCTTATA 58.339 33.333 0.00 0.00 39.52 0.98
3250 5742 2.778299 TCAGAGGGTCCAAAATCAACG 58.222 47.619 0.00 0.00 0.00 4.10
3251 5743 3.445096 CCATCAGAGGGTCCAAAATCAAC 59.555 47.826 0.00 0.00 0.00 3.18
3478 5973 8.728088 AACACAGAACAATTCGATGAATAAAC 57.272 30.769 0.00 0.00 31.46 2.01
3490 5986 7.981225 AGATTGTTAGCAAAACACAGAACAATT 59.019 29.630 10.98 1.67 43.75 2.32
3492 5988 6.862209 AGATTGTTAGCAAAACACAGAACAA 58.138 32.000 4.31 0.00 40.08 2.83
3507 6003 8.732531 GGTAGGTAGCTACTCATAGATTGTTAG 58.267 40.741 26.56 0.00 0.00 2.34
3509 6005 7.067421 TGGTAGGTAGCTACTCATAGATTGTT 58.933 38.462 26.56 0.00 0.00 2.83
3510 6006 6.611785 TGGTAGGTAGCTACTCATAGATTGT 58.388 40.000 26.56 0.00 0.00 2.71
3511 6007 7.710676 ATGGTAGGTAGCTACTCATAGATTG 57.289 40.000 26.56 0.00 0.00 2.67
3512 6008 7.397761 GGAATGGTAGGTAGCTACTCATAGATT 59.602 40.741 26.56 15.35 0.00 2.40
3585 6081 6.896021 AATTGGAGAGATCAATTAGCCATG 57.104 37.500 0.00 0.00 41.38 3.66
3752 6248 6.010219 AGCATGTAGAAAGGGTGTTGTATTT 58.990 36.000 0.00 0.00 0.00 1.40
3789 6285 6.127591 TGTTCCTTTTTCGACATTTTTGAGGA 60.128 34.615 0.00 0.00 0.00 3.71
3868 6365 0.998928 TGGGGGTGCACATTGACTAT 59.001 50.000 20.43 0.00 0.00 2.12
3922 6432 6.202570 CCACAACCATTTCCACAAAAGTATTG 59.797 38.462 0.00 0.00 0.00 1.90
3992 6528 2.980586 TGAAACAAAATCTGACGTGCG 58.019 42.857 0.00 0.00 0.00 5.34
3995 6531 6.189677 TCAACTTGAAACAAAATCTGACGT 57.810 33.333 0.00 0.00 0.00 4.34
4070 6606 2.880443 AGAGAGCATGCCAAAAAGGAA 58.120 42.857 15.66 0.00 41.22 3.36
4217 6757 7.499321 AGACATATCGGTAACTAAGAGTCTG 57.501 40.000 0.00 0.00 33.11 3.51
4305 6846 7.786178 TTTCATTGAGGGTTCTATGTAATCG 57.214 36.000 0.00 0.00 37.66 3.34
4339 6880 4.953940 AACAATGCCAATTACAACCAGT 57.046 36.364 0.00 0.00 0.00 4.00
4366 6907 4.441087 GCAGGAAACAAAAGAATGTCGAAC 59.559 41.667 0.00 0.00 31.81 3.95
4416 6957 3.328535 ACCCAACCAAGGACAGAAAAT 57.671 42.857 0.00 0.00 0.00 1.82
4451 7032 3.587061 TCACACATCAAGTTCCCCTATGT 59.413 43.478 0.00 0.00 0.00 2.29
4542 7124 1.269723 GGCCTGGTTGCTGAAACTAAC 59.730 52.381 0.00 0.00 38.92 2.34
4578 7160 7.989826 AGGAAACAAACATATGAGATTAGCAC 58.010 34.615 10.38 0.00 0.00 4.40
4581 7164 9.166173 TGTGAGGAAACAAACATATGAGATTAG 57.834 33.333 10.38 0.00 0.00 1.73



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

AutoCloner maintained by Alex Coulton.