Multiple sequence alignment - TraesCS2B01G290100

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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 TraesCS2B01G290100 chr2B 100.000 4995 0 0 1 4995 402559343 402554349 0.000000e+00 9225.0
1 TraesCS2B01G290100 chr2D 98.121 2182 30 3 1469 3642 334265888 334263710 0.000000e+00 3792.0
2 TraesCS2B01G290100 chr2D 95.373 951 31 7 54 995 334266834 334265888 0.000000e+00 1500.0
3 TraesCS2B01G290100 chr2D 93.409 880 43 10 3641 4507 334263655 334262778 0.000000e+00 1290.0
4 TraesCS2B01G290100 chr2D 95.103 388 16 2 4610 4995 334262777 334262391 4.280000e-170 608.0
5 TraesCS2B01G290100 chr2A 95.406 2068 67 11 615 2671 445035215 445033165 0.000000e+00 3267.0
6 TraesCS2B01G290100 chr2A 97.172 990 20 1 2659 3640 445031990 445031001 0.000000e+00 1666.0
7 TraesCS2B01G290100 chr2A 92.319 690 37 7 3833 4507 445024145 445023457 0.000000e+00 966.0
8 TraesCS2B01G290100 chr2A 94.728 626 20 5 1 624 445035862 445035248 0.000000e+00 961.0
9 TraesCS2B01G290100 chr2A 91.811 403 16 7 4610 4995 445023456 445023054 3.400000e-151 545.0
10 TraesCS2B01G290100 chr2A 95.980 199 8 0 3641 3839 445030945 445030747 1.730000e-84 324.0
11 TraesCS2B01G290100 chr1A 77.539 2511 489 50 1043 3523 9129461 9126996 0.000000e+00 1443.0
12 TraesCS2B01G290100 chr1A 75.075 1669 322 63 1204 2830 9149630 9148014 0.000000e+00 691.0
13 TraesCS2B01G290100 chr1A 77.003 287 50 10 3872 4156 255850898 255851170 3.110000e-32 150.0
14 TraesCS2B01G290100 chr6B 78.414 2219 408 48 1325 3528 707007866 707010028 0.000000e+00 1378.0
15 TraesCS2B01G290100 chr6B 77.555 2290 425 56 1329 3603 706972968 706975183 0.000000e+00 1299.0
16 TraesCS2B01G290100 chr6A 78.688 2088 388 35 1325 3394 610268509 610270557 0.000000e+00 1338.0
17 TraesCS2B01G290100 chr6D 77.968 2215 414 51 1328 3528 463756567 463754413 0.000000e+00 1319.0
18 TraesCS2B01G290100 chr6D 80.927 1143 188 10 2279 3394 469604506 469605645 0.000000e+00 876.0
19 TraesCS2B01G290100 chr6D 91.176 68 2 4 4096 4161 62211777 62211842 6.890000e-14 89.8
20 TraesCS2B01G290100 chr5D 79.750 1600 291 24 1944 3522 510656962 510658549 0.000000e+00 1129.0
21 TraesCS2B01G290100 chr1D 78.734 1453 275 27 2096 3528 7050388 7051826 0.000000e+00 941.0
22 TraesCS2B01G290100 chr1D 76.923 624 124 16 1319 1935 7049737 7050347 2.230000e-88 337.0
23 TraesCS2B01G290100 chr5B 81.162 1136 200 11 2394 3522 641715048 641716176 0.000000e+00 900.0
24 TraesCS2B01G290100 chr5B 92.647 68 4 1 4094 4160 648966963 648967030 4.120000e-16 97.1
25 TraesCS2B01G290100 chr5B 91.045 67 5 1 4097 4162 535045960 535046026 6.890000e-14 89.8
26 TraesCS2B01G290100 chr3D 91.429 70 3 3 4097 4163 612690854 612690923 5.320000e-15 93.5
27 TraesCS2B01G290100 chr3A 93.548 62 3 1 4097 4157 12447911 12447850 1.910000e-14 91.6
28 TraesCS2B01G290100 chr7B 88.000 75 7 2 4096 4168 622618145 622618071 2.480000e-13 87.9


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 TraesCS2B01G290100 chr2B 402554349 402559343 4994 True 9225.0 9225 100.0000 1 4995 1 chr2B.!!$R1 4994
1 TraesCS2B01G290100 chr2D 334262391 334266834 4443 True 1797.5 3792 95.5015 54 4995 4 chr2D.!!$R1 4941
2 TraesCS2B01G290100 chr2A 445030747 445035862 5115 True 1554.5 3267 95.8215 1 3839 4 chr2A.!!$R2 3838
3 TraesCS2B01G290100 chr2A 445023054 445024145 1091 True 755.5 966 92.0650 3833 4995 2 chr2A.!!$R1 1162
4 TraesCS2B01G290100 chr1A 9126996 9129461 2465 True 1443.0 1443 77.5390 1043 3523 1 chr1A.!!$R1 2480
5 TraesCS2B01G290100 chr1A 9148014 9149630 1616 True 691.0 691 75.0750 1204 2830 1 chr1A.!!$R2 1626
6 TraesCS2B01G290100 chr6B 707007866 707010028 2162 False 1378.0 1378 78.4140 1325 3528 1 chr6B.!!$F2 2203
7 TraesCS2B01G290100 chr6B 706972968 706975183 2215 False 1299.0 1299 77.5550 1329 3603 1 chr6B.!!$F1 2274
8 TraesCS2B01G290100 chr6A 610268509 610270557 2048 False 1338.0 1338 78.6880 1325 3394 1 chr6A.!!$F1 2069
9 TraesCS2B01G290100 chr6D 463754413 463756567 2154 True 1319.0 1319 77.9680 1328 3528 1 chr6D.!!$R1 2200
10 TraesCS2B01G290100 chr6D 469604506 469605645 1139 False 876.0 876 80.9270 2279 3394 1 chr6D.!!$F2 1115
11 TraesCS2B01G290100 chr5D 510656962 510658549 1587 False 1129.0 1129 79.7500 1944 3522 1 chr5D.!!$F1 1578
12 TraesCS2B01G290100 chr1D 7049737 7051826 2089 False 639.0 941 77.8285 1319 3528 2 chr1D.!!$F1 2209
13 TraesCS2B01G290100 chr5B 641715048 641716176 1128 False 900.0 900 81.1620 2394 3522 1 chr5B.!!$F2 1128

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
25 26 0.250467 TGCCTGACTCTGAGTTTGCC 60.250 55.000 12.27 0.0 0.0 4.52 F
26 27 0.957888 GCCTGACTCTGAGTTTGCCC 60.958 60.000 12.27 0.0 0.0 5.36 F
1095 1156 1.012486 GTTTCGACTACCCCGCAGTG 61.012 60.000 0.00 0.0 0.0 3.66 F
1314 1375 1.097547 CCAAGATCACCATGCCGACC 61.098 60.000 0.00 0.0 0.0 4.79 F
1581 1643 1.194781 TCCCTGGGCAGTCACTTCTC 61.195 60.000 8.22 0.0 0.0 2.87 F
1747 1818 2.787994 AGACAGGAAAGGATGCAACAG 58.212 47.619 0.00 0.0 0.0 3.16 F
3844 5283 1.976045 GTGCTTCAATTGTTTACCGCG 59.024 47.619 5.13 0.0 0.0 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1252 1313 0.391597 AAGACGGCGAAGAGGAACAA 59.608 50.000 16.62 0.00 0.00 2.83 R
1581 1643 1.335142 GCTACGAGCCTCATACCTTCG 60.335 57.143 0.00 0.00 34.48 3.79 R
2084 2179 3.643320 ACAAGAGATTGGAGTCAGTGACA 59.357 43.478 24.73 4.73 34.60 3.58 R
3621 4949 8.638873 GGGTGCTATATTGCCTAAAAATTACTT 58.361 33.333 6.69 0.00 0.00 2.24 R
3689 5128 1.149101 TCTTCCTTCAAACTGCCCCT 58.851 50.000 0.00 0.00 0.00 4.79 R
3927 5366 1.659233 CAAACACCCGCAGCATTCA 59.341 52.632 0.00 0.00 0.00 2.57 R
4726 6180 3.391296 ACCAGTTGTTGAGCCTTCTAGAA 59.609 43.478 4.81 4.81 0.00 2.10 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
25 26 0.250467 TGCCTGACTCTGAGTTTGCC 60.250 55.000 12.27 0.00 0.00 4.52
26 27 0.957888 GCCTGACTCTGAGTTTGCCC 60.958 60.000 12.27 0.00 0.00 5.36
32 33 3.423154 CTGAGTTTGCCCGTCGCC 61.423 66.667 0.00 0.00 36.24 5.54
34 35 3.119096 GAGTTTGCCCGTCGCCTC 61.119 66.667 0.00 0.00 36.24 4.70
96 97 3.477530 ACGATCACGATATGGAGACTCA 58.522 45.455 4.53 0.00 42.66 3.41
98 99 3.120025 CGATCACGATATGGAGACTCAGG 60.120 52.174 4.53 0.00 42.66 3.86
128 129 5.201243 TGCTCTAACCATAGTAGCAAGAGA 58.799 41.667 0.00 0.00 38.34 3.10
179 182 2.589798 TTCCGAGTCAAGACGTGTTT 57.410 45.000 0.00 0.00 36.20 2.83
306 309 3.620488 GATCTTCACCTACCATGCCAAA 58.380 45.455 0.00 0.00 0.00 3.28
307 310 3.517296 TCTTCACCTACCATGCCAAAA 57.483 42.857 0.00 0.00 0.00 2.44
308 311 3.838565 TCTTCACCTACCATGCCAAAAA 58.161 40.909 0.00 0.00 0.00 1.94
309 312 4.415596 TCTTCACCTACCATGCCAAAAAT 58.584 39.130 0.00 0.00 0.00 1.82
310 313 4.220382 TCTTCACCTACCATGCCAAAAATG 59.780 41.667 0.00 0.00 0.00 2.32
413 420 5.525378 CCAAGAGAAATACAGCTGGTATGAC 59.475 44.000 19.93 10.48 41.87 3.06
557 564 5.339008 TTGCCTAAGTAATCATCGTGACT 57.661 39.130 0.00 0.00 0.00 3.41
601 608 3.604582 GAAAGTAGCAAGAGGACTGCAT 58.395 45.455 0.00 0.00 0.00 3.96
608 616 2.680339 GCAAGAGGACTGCATTTACTCC 59.320 50.000 4.40 0.00 0.00 3.85
942 995 3.124921 CGCACTAGCCCCCGTTTG 61.125 66.667 0.00 0.00 37.52 2.93
1022 1083 2.042843 CCCTGCCGGTCTCTACCT 60.043 66.667 1.90 0.00 44.35 3.08
1094 1155 1.291272 GTTTCGACTACCCCGCAGT 59.709 57.895 0.00 0.00 0.00 4.40
1095 1156 1.012486 GTTTCGACTACCCCGCAGTG 61.012 60.000 0.00 0.00 0.00 3.66
1104 1165 2.266055 CCCGCAGTGAACCTCTCC 59.734 66.667 0.00 0.00 0.00 3.71
1314 1375 1.097547 CCAAGATCACCATGCCGACC 61.098 60.000 0.00 0.00 0.00 4.79
1525 1587 7.280428 TGTTGTTTGATCAGAAAAATGCAACAT 59.720 29.630 11.46 0.00 37.92 2.71
1581 1643 1.194781 TCCCTGGGCAGTCACTTCTC 61.195 60.000 8.22 0.00 0.00 2.87
1741 1812 5.906073 ACAAAAACAAGACAGGAAAGGATG 58.094 37.500 0.00 0.00 0.00 3.51
1747 1818 2.787994 AGACAGGAAAGGATGCAACAG 58.212 47.619 0.00 0.00 0.00 3.16
2164 2259 3.120786 AGACGTTTCTTATTTTGACGCCG 60.121 43.478 0.00 0.00 37.24 6.46
3621 4949 9.116067 GTATGTTTTAAATGGCACCTAGATACA 57.884 33.333 0.00 0.00 0.00 2.29
3630 4958 8.823220 AATGGCACCTAGATACAAGTAATTTT 57.177 30.769 0.00 0.00 0.00 1.82
3689 5128 7.284074 TGAAACACCATAGAAAAGTGACCTAA 58.716 34.615 0.00 0.00 35.47 2.69
3713 5152 4.082190 GGGGCAGTTTGAAGGAAGAAATAC 60.082 45.833 0.00 0.00 0.00 1.89
3731 5170 8.934507 AGAAATACTCTAAGAGCACATGTAAC 57.065 34.615 0.00 0.00 32.04 2.50
3754 5193 4.908156 CGCAAAGTGCTTATAGATGAATGC 59.092 41.667 0.00 0.00 42.25 3.56
3844 5283 1.976045 GTGCTTCAATTGTTTACCGCG 59.024 47.619 5.13 0.00 0.00 6.46
3854 5293 2.945161 TTTACCGCGCAGGGTAGCA 61.945 57.895 19.73 7.15 46.96 3.49
3860 5299 2.828128 GCGCAGGGTAGCAGCAATC 61.828 63.158 0.30 0.00 35.30 2.67
3927 5366 3.009916 AGGATCTTCAGGCATGAACAACT 59.990 43.478 10.22 3.57 40.54 3.16
3937 5376 2.247637 CATGAACAACTGAATGCTGCG 58.752 47.619 0.00 0.00 0.00 5.18
3998 5437 0.971447 GGAGGCGTGGGAGTAGTCTT 60.971 60.000 0.00 0.00 0.00 3.01
4039 5478 3.572584 GCAGTTTGCATCTCTGGAAAAG 58.427 45.455 12.76 0.00 43.21 2.27
4042 5481 5.737063 GCAGTTTGCATCTCTGGAAAAGAAA 60.737 40.000 12.76 0.00 43.21 2.52
4044 5483 6.757947 CAGTTTGCATCTCTGGAAAAGAAAAA 59.242 34.615 0.00 0.00 43.21 1.94
4047 5486 7.718272 TTGCATCTCTGGAAAAGAAAAATTG 57.282 32.000 0.00 0.00 33.37 2.32
4049 5488 5.121298 GCATCTCTGGAAAAGAAAAATTGGC 59.879 40.000 0.00 0.00 33.37 4.52
4051 5490 5.846203 TCTCTGGAAAAGAAAAATTGGCTG 58.154 37.500 0.00 0.00 33.37 4.85
4057 5497 2.825861 AGAAAAATTGGCTGCTGGTG 57.174 45.000 0.00 0.00 0.00 4.17
4079 5519 3.254903 GTCTTTTTAGTTGCATTCCCGGT 59.745 43.478 0.00 0.00 0.00 5.28
4146 5587 1.001764 CAGAGCACCTGCCATTCCA 60.002 57.895 0.00 0.00 43.38 3.53
4320 5774 0.039256 TGACAGCAAAATGAAGCGCC 60.039 50.000 2.29 0.00 35.48 6.53
4332 5786 1.003233 AAGCGCCTCAAGGTTCCTC 60.003 57.895 2.29 0.00 37.57 3.71
4333 5787 1.768684 AAGCGCCTCAAGGTTCCTCA 61.769 55.000 2.29 0.00 37.57 3.86
4458 5912 1.237533 CAGCACACTGGCAATACACA 58.762 50.000 0.00 0.00 40.48 3.72
4466 5920 4.019792 ACTGGCAATACACAGTGATTGA 57.980 40.909 20.86 7.74 45.54 2.57
4477 5931 0.257039 AGTGATTGACTCCATGGGGC 59.743 55.000 13.00 5.18 0.00 5.80
4479 5933 0.034186 TGATTGACTCCATGGGGCAC 60.034 55.000 13.00 7.02 0.00 5.01
4507 5961 4.389374 TCGAAGATGAAGAGGCAAAGTTT 58.611 39.130 0.00 0.00 0.00 2.66
4508 5962 5.547465 TCGAAGATGAAGAGGCAAAGTTTA 58.453 37.500 0.00 0.00 0.00 2.01
4509 5963 5.408604 TCGAAGATGAAGAGGCAAAGTTTAC 59.591 40.000 0.00 0.00 0.00 2.01
4510 5964 5.179368 CGAAGATGAAGAGGCAAAGTTTACA 59.821 40.000 0.00 0.00 0.00 2.41
4511 5965 6.566197 AAGATGAAGAGGCAAAGTTTACAG 57.434 37.500 0.00 0.00 0.00 2.74
4512 5966 5.869579 AGATGAAGAGGCAAAGTTTACAGA 58.130 37.500 0.00 0.00 0.00 3.41
4513 5967 6.479884 AGATGAAGAGGCAAAGTTTACAGAT 58.520 36.000 0.00 0.00 0.00 2.90
4514 5968 7.624549 AGATGAAGAGGCAAAGTTTACAGATA 58.375 34.615 0.00 0.00 0.00 1.98
4515 5969 8.270744 AGATGAAGAGGCAAAGTTTACAGATAT 58.729 33.333 0.00 0.00 0.00 1.63
4516 5970 9.547753 GATGAAGAGGCAAAGTTTACAGATATA 57.452 33.333 0.00 0.00 0.00 0.86
4518 5972 9.330063 TGAAGAGGCAAAGTTTACAGATATATG 57.670 33.333 0.00 0.00 0.00 1.78
4519 5973 8.682936 AAGAGGCAAAGTTTACAGATATATGG 57.317 34.615 1.85 0.00 0.00 2.74
4520 5974 7.806180 AGAGGCAAAGTTTACAGATATATGGT 58.194 34.615 1.85 0.00 0.00 3.55
4521 5975 8.934697 AGAGGCAAAGTTTACAGATATATGGTA 58.065 33.333 1.85 0.00 0.00 3.25
4522 5976 8.904099 AGGCAAAGTTTACAGATATATGGTAC 57.096 34.615 1.85 0.00 0.00 3.34
4523 5977 8.714906 AGGCAAAGTTTACAGATATATGGTACT 58.285 33.333 1.85 0.00 0.00 2.73
4524 5978 8.989980 GGCAAAGTTTACAGATATATGGTACTC 58.010 37.037 1.85 0.00 0.00 2.59
4525 5979 8.700644 GCAAAGTTTACAGATATATGGTACTCG 58.299 37.037 1.85 0.00 0.00 4.18
4526 5980 9.745880 CAAAGTTTACAGATATATGGTACTCGT 57.254 33.333 1.85 0.00 0.00 4.18
4527 5981 9.962783 AAAGTTTACAGATATATGGTACTCGTC 57.037 33.333 1.85 0.00 0.00 4.20
4528 5982 7.804712 AGTTTACAGATATATGGTACTCGTCG 58.195 38.462 1.85 0.00 0.00 5.12
4529 5983 7.443575 AGTTTACAGATATATGGTACTCGTCGT 59.556 37.037 1.85 0.00 0.00 4.34
4530 5984 7.734924 TTACAGATATATGGTACTCGTCGTT 57.265 36.000 1.85 0.00 0.00 3.85
4531 5985 8.831715 TTACAGATATATGGTACTCGTCGTTA 57.168 34.615 1.85 0.00 0.00 3.18
4532 5986 7.734924 ACAGATATATGGTACTCGTCGTTAA 57.265 36.000 1.85 0.00 0.00 2.01
4533 5987 7.804712 ACAGATATATGGTACTCGTCGTTAAG 58.195 38.462 1.85 0.00 0.00 1.85
4534 5988 7.443575 ACAGATATATGGTACTCGTCGTTAAGT 59.556 37.037 1.85 0.00 0.00 2.24
4535 5989 8.288208 CAGATATATGGTACTCGTCGTTAAGTT 58.712 37.037 0.00 0.00 0.00 2.66
4536 5990 8.288208 AGATATATGGTACTCGTCGTTAAGTTG 58.712 37.037 0.00 0.00 0.00 3.16
4537 5991 3.988379 TGGTACTCGTCGTTAAGTTGT 57.012 42.857 0.00 0.00 0.00 3.32
4538 5992 4.305989 TGGTACTCGTCGTTAAGTTGTT 57.694 40.909 0.00 0.00 0.00 2.83
4539 5993 4.681744 TGGTACTCGTCGTTAAGTTGTTT 58.318 39.130 0.00 0.00 0.00 2.83
4540 5994 4.503734 TGGTACTCGTCGTTAAGTTGTTTG 59.496 41.667 0.00 0.00 0.00 2.93
4541 5995 4.739716 GGTACTCGTCGTTAAGTTGTTTGA 59.260 41.667 0.00 0.00 0.00 2.69
4542 5996 5.231991 GGTACTCGTCGTTAAGTTGTTTGAA 59.768 40.000 0.00 0.00 0.00 2.69
4543 5997 5.978934 ACTCGTCGTTAAGTTGTTTGAAT 57.021 34.783 0.00 0.00 0.00 2.57
4544 5998 7.114811 GGTACTCGTCGTTAAGTTGTTTGAATA 59.885 37.037 0.00 0.00 0.00 1.75
4545 5999 6.870517 ACTCGTCGTTAAGTTGTTTGAATAC 58.129 36.000 0.00 0.00 0.00 1.89
4546 6000 6.476380 ACTCGTCGTTAAGTTGTTTGAATACA 59.524 34.615 0.00 0.00 0.00 2.29
4547 6001 7.170320 ACTCGTCGTTAAGTTGTTTGAATACAT 59.830 33.333 0.00 0.00 0.00 2.29
4548 6002 8.518151 TCGTCGTTAAGTTGTTTGAATACATA 57.482 30.769 0.00 0.00 0.00 2.29
4549 6003 9.142515 TCGTCGTTAAGTTGTTTGAATACATAT 57.857 29.630 0.00 0.00 0.00 1.78
4550 6004 9.194716 CGTCGTTAAGTTGTTTGAATACATATG 57.805 33.333 0.00 0.00 0.00 1.78
4551 6005 9.485591 GTCGTTAAGTTGTTTGAATACATATGG 57.514 33.333 7.80 0.00 0.00 2.74
4552 6006 8.178964 TCGTTAAGTTGTTTGAATACATATGGC 58.821 33.333 7.80 0.00 0.00 4.40
4553 6007 8.181573 CGTTAAGTTGTTTGAATACATATGGCT 58.818 33.333 7.80 0.00 0.00 4.75
4554 6008 9.855021 GTTAAGTTGTTTGAATACATATGGCTT 57.145 29.630 7.80 0.00 0.00 4.35
4559 6013 9.301153 GTTGTTTGAATACATATGGCTTTTAGG 57.699 33.333 7.80 0.00 0.00 2.69
4560 6014 8.815565 TGTTTGAATACATATGGCTTTTAGGA 57.184 30.769 7.80 0.00 0.00 2.94
4561 6015 9.420118 TGTTTGAATACATATGGCTTTTAGGAT 57.580 29.630 7.80 0.00 0.00 3.24
4562 6016 9.683069 GTTTGAATACATATGGCTTTTAGGATG 57.317 33.333 7.80 0.00 0.00 3.51
4563 6017 9.639563 TTTGAATACATATGGCTTTTAGGATGA 57.360 29.630 7.80 0.00 0.00 2.92
4564 6018 9.639563 TTGAATACATATGGCTTTTAGGATGAA 57.360 29.630 7.80 0.00 0.00 2.57
4565 6019 9.066892 TGAATACATATGGCTTTTAGGATGAAC 57.933 33.333 7.80 0.00 0.00 3.18
4566 6020 9.289782 GAATACATATGGCTTTTAGGATGAACT 57.710 33.333 7.80 0.00 0.00 3.01
4567 6021 8.854614 ATACATATGGCTTTTAGGATGAACTC 57.145 34.615 7.80 0.00 0.00 3.01
4568 6022 6.662755 ACATATGGCTTTTAGGATGAACTCA 58.337 36.000 7.80 0.00 0.00 3.41
4569 6023 6.543831 ACATATGGCTTTTAGGATGAACTCAC 59.456 38.462 7.80 0.00 0.00 3.51
4570 6024 4.365514 TGGCTTTTAGGATGAACTCACA 57.634 40.909 0.00 0.00 0.00 3.58
4571 6025 4.724399 TGGCTTTTAGGATGAACTCACAA 58.276 39.130 0.00 0.00 0.00 3.33
4572 6026 4.761739 TGGCTTTTAGGATGAACTCACAAG 59.238 41.667 0.00 0.00 0.00 3.16
4573 6027 5.003804 GGCTTTTAGGATGAACTCACAAGA 58.996 41.667 0.00 0.00 0.00 3.02
4574 6028 5.649831 GGCTTTTAGGATGAACTCACAAGAT 59.350 40.000 0.00 0.00 0.00 2.40
4575 6029 6.404074 GGCTTTTAGGATGAACTCACAAGATG 60.404 42.308 0.00 0.00 0.00 2.90
4576 6030 6.404074 GCTTTTAGGATGAACTCACAAGATGG 60.404 42.308 0.00 0.00 0.00 3.51
4577 6031 5.762179 TTAGGATGAACTCACAAGATGGT 57.238 39.130 0.00 0.00 0.00 3.55
4578 6032 6.867519 TTAGGATGAACTCACAAGATGGTA 57.132 37.500 0.00 0.00 0.00 3.25
4579 6033 5.350504 AGGATGAACTCACAAGATGGTAG 57.649 43.478 0.00 0.00 0.00 3.18
4580 6034 4.780021 AGGATGAACTCACAAGATGGTAGT 59.220 41.667 0.00 0.00 0.00 2.73
4581 6035 5.958380 AGGATGAACTCACAAGATGGTAGTA 59.042 40.000 0.00 0.00 0.00 1.82
4582 6036 6.440647 AGGATGAACTCACAAGATGGTAGTAA 59.559 38.462 0.00 0.00 0.00 2.24
4583 6037 6.535508 GGATGAACTCACAAGATGGTAGTAAC 59.464 42.308 0.00 0.00 0.00 2.50
4584 6038 5.466819 TGAACTCACAAGATGGTAGTAACG 58.533 41.667 0.00 0.00 0.00 3.18
4585 6039 5.242171 TGAACTCACAAGATGGTAGTAACGA 59.758 40.000 0.00 0.00 0.00 3.85
4586 6040 5.056894 ACTCACAAGATGGTAGTAACGAC 57.943 43.478 0.00 0.00 0.00 4.34
4587 6041 4.765856 ACTCACAAGATGGTAGTAACGACT 59.234 41.667 0.00 0.00 39.92 4.18
4588 6042 5.243283 ACTCACAAGATGGTAGTAACGACTT 59.757 40.000 0.00 0.00 37.10 3.01
4589 6043 6.092955 TCACAAGATGGTAGTAACGACTTT 57.907 37.500 0.00 0.00 37.10 2.66
4590 6044 5.924254 TCACAAGATGGTAGTAACGACTTTG 59.076 40.000 0.00 0.00 37.10 2.77
4591 6045 4.689345 ACAAGATGGTAGTAACGACTTTGC 59.311 41.667 0.00 0.00 37.10 3.68
4592 6046 4.803098 AGATGGTAGTAACGACTTTGCT 57.197 40.909 0.00 0.00 37.10 3.91
4593 6047 5.909621 AGATGGTAGTAACGACTTTGCTA 57.090 39.130 0.00 0.00 37.10 3.49
4600 6054 7.214473 GTAGTAACGACTTTGCTACATAACC 57.786 40.000 12.91 0.00 46.99 2.85
4601 6055 5.786311 AGTAACGACTTTGCTACATAACCA 58.214 37.500 0.00 0.00 28.61 3.67
4602 6056 6.225318 AGTAACGACTTTGCTACATAACCAA 58.775 36.000 0.00 0.00 28.61 3.67
4603 6057 5.352643 AACGACTTTGCTACATAACCAAC 57.647 39.130 0.00 0.00 0.00 3.77
4604 6058 4.382291 ACGACTTTGCTACATAACCAACA 58.618 39.130 0.00 0.00 0.00 3.33
4605 6059 4.817464 ACGACTTTGCTACATAACCAACAA 59.183 37.500 0.00 0.00 0.00 2.83
4606 6060 5.297278 ACGACTTTGCTACATAACCAACAAA 59.703 36.000 0.00 0.00 0.00 2.83
4607 6061 6.183360 ACGACTTTGCTACATAACCAACAAAA 60.183 34.615 0.00 0.00 0.00 2.44
4608 6062 6.693545 CGACTTTGCTACATAACCAACAAAAA 59.306 34.615 0.00 0.00 0.00 1.94
4747 6216 3.685139 TCTAGAAGGCTCAACAACTGG 57.315 47.619 0.00 0.00 0.00 4.00
4784 6253 9.936759 TCTAAATAAAACAAATTAAGCAAGGGG 57.063 29.630 0.00 0.00 0.00 4.79
4795 6264 8.527810 CAAATTAAGCAAGGGGAAACAGTATAA 58.472 33.333 0.00 0.00 0.00 0.98
4858 6329 5.173131 GTGTTAGGCTCGTCAATTTTTGTTG 59.827 40.000 0.00 0.00 0.00 3.33
4864 6335 3.358775 TCGTCAATTTTTGTTGTCTGCG 58.641 40.909 0.00 0.00 0.00 5.18
4947 6418 4.498682 GCTTGCATGATTGGGAGTTACATC 60.499 45.833 3.33 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 0.671781 CGGGCAAACTCAGAGTCAGG 60.672 60.000 2.72 0.00 0.00 3.86
32 33 1.179174 TGGATATGGAGGTCGCCGAG 61.179 60.000 0.00 0.00 0.00 4.63
34 35 1.182667 TATGGATATGGAGGTCGCCG 58.817 55.000 0.00 0.00 0.00 6.46
96 97 5.520751 ACTATGGTTAGAGCAACTCTACCT 58.479 41.667 16.89 9.86 41.99 3.08
98 99 6.039493 TGCTACTATGGTTAGAGCAACTCTAC 59.961 42.308 2.94 1.00 41.99 2.59
128 129 2.289444 CGAAGTATATGGTCGGGGCATT 60.289 50.000 0.00 0.00 0.00 3.56
162 164 1.525619 GGAAAACACGTCTTGACTCGG 59.474 52.381 0.00 0.00 0.00 4.63
179 182 7.400339 CCCTGCTAGTATATGAATAGGAAGGAA 59.600 40.741 0.00 0.00 0.00 3.36
413 420 4.168291 GGGCTCGCCTTCCTCTGG 62.168 72.222 8.00 0.00 36.10 3.86
838 889 3.693578 GCTCCGTGGAAAGTACTACTAGT 59.306 47.826 0.00 0.00 0.00 2.57
942 995 5.309638 ACTTTAGGAGAGAAAAGGAGCAAC 58.690 41.667 0.00 0.00 37.09 4.17
1022 1083 2.224079 GCAAGCACGATGAACAAGAGAA 59.776 45.455 0.00 0.00 0.00 2.87
1094 1155 1.367471 CACAGCGTGGAGAGGTTCA 59.633 57.895 1.40 0.00 0.00 3.18
1095 1156 4.268687 CACAGCGTGGAGAGGTTC 57.731 61.111 1.40 0.00 0.00 3.62
1104 1165 0.943673 TGTTGTTGATCCACAGCGTG 59.056 50.000 8.84 2.27 30.82 5.34
1252 1313 0.391597 AAGACGGCGAAGAGGAACAA 59.608 50.000 16.62 0.00 0.00 2.83
1314 1375 1.372683 CACCTGTGGAGTCCCAGTG 59.627 63.158 20.04 15.54 44.55 3.66
1525 1587 1.337703 GTGAGCAAATGACTGCCACAA 59.662 47.619 10.38 0.00 43.73 3.33
1581 1643 1.335142 GCTACGAGCCTCATACCTTCG 60.335 57.143 0.00 0.00 34.48 3.79
1741 1812 3.674997 TCATGAAGGTAACCTCTGTTGC 58.325 45.455 0.00 0.00 35.87 4.17
1747 1818 3.620488 TGCCATTCATGAAGGTAACCTC 58.380 45.455 18.05 5.17 30.89 3.85
2084 2179 3.643320 ACAAGAGATTGGAGTCAGTGACA 59.357 43.478 24.73 4.73 34.60 3.58
3621 4949 8.638873 GGGTGCTATATTGCCTAAAAATTACTT 58.361 33.333 6.69 0.00 0.00 2.24
3630 4958 3.714280 TCACAGGGTGCTATATTGCCTAA 59.286 43.478 6.69 0.00 32.98 2.69
3689 5128 1.149101 TCTTCCTTCAAACTGCCCCT 58.851 50.000 0.00 0.00 0.00 4.79
3713 5152 3.511699 TGCGTTACATGTGCTCTTAGAG 58.488 45.455 9.11 4.63 0.00 2.43
3754 5193 9.094578 TGAATAGTAATAATCTCTCCCCTTGAG 57.905 37.037 0.00 0.00 42.90 3.02
3844 5283 2.158900 TCTTAGATTGCTGCTACCCTGC 60.159 50.000 0.00 0.00 38.72 4.85
3854 5293 3.620966 GCCACAGAAGGTCTTAGATTGCT 60.621 47.826 0.00 0.00 0.00 3.91
3860 5299 2.303022 TCCAAGCCACAGAAGGTCTTAG 59.697 50.000 0.00 0.00 0.00 2.18
3927 5366 1.659233 CAAACACCCGCAGCATTCA 59.341 52.632 0.00 0.00 0.00 2.57
3937 5376 3.149196 TCTGATCAAAGAGCAAACACCC 58.851 45.455 0.00 0.00 0.00 4.61
3998 5437 2.819608 GCATCCTGGCAGAAAAACTACA 59.180 45.455 17.94 0.00 0.00 2.74
4039 5478 2.036346 AGACACCAGCAGCCAATTTTTC 59.964 45.455 0.00 0.00 0.00 2.29
4042 5481 1.708341 AAGACACCAGCAGCCAATTT 58.292 45.000 0.00 0.00 0.00 1.82
4044 5483 1.708341 AAAAGACACCAGCAGCCAAT 58.292 45.000 0.00 0.00 0.00 3.16
4047 5486 2.230660 ACTAAAAAGACACCAGCAGCC 58.769 47.619 0.00 0.00 0.00 4.85
4049 5488 3.066621 TGCAACTAAAAAGACACCAGCAG 59.933 43.478 0.00 0.00 0.00 4.24
4051 5490 3.708563 TGCAACTAAAAAGACACCAGC 57.291 42.857 0.00 0.00 0.00 4.85
4057 5497 3.254903 ACCGGGAATGCAACTAAAAAGAC 59.745 43.478 6.32 0.00 0.00 3.01
4158 5599 6.647895 GCCACATGATTTGATCTTTGTTTTCT 59.352 34.615 0.00 0.00 0.00 2.52
4159 5600 6.647895 AGCCACATGATTTGATCTTTGTTTTC 59.352 34.615 0.00 0.00 0.00 2.29
4257 5711 0.976641 ACAGATTCGTCCTCTTGCCA 59.023 50.000 0.00 0.00 0.00 4.92
4262 5716 1.751924 GCACCTACAGATTCGTCCTCT 59.248 52.381 0.00 0.00 0.00 3.69
4320 5774 1.066286 CAGAGGCTGAGGAACCTTGAG 60.066 57.143 0.00 0.00 36.05 3.02
4458 5912 0.257039 GCCCCATGGAGTCAATCACT 59.743 55.000 15.22 0.00 38.45 3.41
4466 5920 4.722700 GCACGTGCCCCATGGAGT 62.723 66.667 30.12 2.05 34.31 3.85
4477 5931 2.328473 TCTTCATCTTCGAAGCACGTG 58.672 47.619 20.56 12.28 41.84 4.49
4479 5933 1.923204 CCTCTTCATCTTCGAAGCACG 59.077 52.381 20.56 10.67 41.84 5.34
4507 5961 8.831715 TTAACGACGAGTACCATATATCTGTA 57.168 34.615 0.00 0.00 0.00 2.74
4508 5962 7.443575 ACTTAACGACGAGTACCATATATCTGT 59.556 37.037 0.00 0.00 0.00 3.41
4509 5963 7.804712 ACTTAACGACGAGTACCATATATCTG 58.195 38.462 0.00 0.00 0.00 2.90
4510 5964 7.976135 ACTTAACGACGAGTACCATATATCT 57.024 36.000 0.00 0.00 0.00 1.98
4511 5965 8.072567 ACAACTTAACGACGAGTACCATATATC 58.927 37.037 0.00 0.00 0.00 1.63
4512 5966 7.934457 ACAACTTAACGACGAGTACCATATAT 58.066 34.615 0.00 0.00 0.00 0.86
4513 5967 7.320443 ACAACTTAACGACGAGTACCATATA 57.680 36.000 0.00 0.00 0.00 0.86
4514 5968 6.199937 ACAACTTAACGACGAGTACCATAT 57.800 37.500 0.00 0.00 0.00 1.78
4515 5969 5.627499 ACAACTTAACGACGAGTACCATA 57.373 39.130 0.00 0.00 0.00 2.74
4516 5970 4.510038 ACAACTTAACGACGAGTACCAT 57.490 40.909 0.00 0.00 0.00 3.55
4517 5971 3.988379 ACAACTTAACGACGAGTACCA 57.012 42.857 0.00 0.00 0.00 3.25
4518 5972 4.739716 TCAAACAACTTAACGACGAGTACC 59.260 41.667 0.00 0.00 0.00 3.34
4519 5973 5.871531 TCAAACAACTTAACGACGAGTAC 57.128 39.130 0.00 0.00 0.00 2.73
4520 5974 7.647318 TGTATTCAAACAACTTAACGACGAGTA 59.353 33.333 0.00 0.00 0.00 2.59
4521 5975 5.978934 ATTCAAACAACTTAACGACGAGT 57.021 34.783 0.00 0.00 0.00 4.18
4522 5976 6.869473 TGTATTCAAACAACTTAACGACGAG 58.131 36.000 0.00 0.00 0.00 4.18
4523 5977 6.825284 TGTATTCAAACAACTTAACGACGA 57.175 33.333 0.00 0.00 0.00 4.20
4524 5978 9.194716 CATATGTATTCAAACAACTTAACGACG 57.805 33.333 0.00 0.00 32.02 5.12
4525 5979 9.485591 CCATATGTATTCAAACAACTTAACGAC 57.514 33.333 1.24 0.00 32.02 4.34
4526 5980 8.178964 GCCATATGTATTCAAACAACTTAACGA 58.821 33.333 1.24 0.00 32.02 3.85
4527 5981 8.181573 AGCCATATGTATTCAAACAACTTAACG 58.818 33.333 1.24 0.00 32.02 3.18
4528 5982 9.855021 AAGCCATATGTATTCAAACAACTTAAC 57.145 29.630 1.24 0.00 32.02 2.01
4533 5987 9.301153 CCTAAAAGCCATATGTATTCAAACAAC 57.699 33.333 1.24 0.00 32.02 3.32
4534 5988 9.249053 TCCTAAAAGCCATATGTATTCAAACAA 57.751 29.630 1.24 0.00 32.02 2.83
4535 5989 8.815565 TCCTAAAAGCCATATGTATTCAAACA 57.184 30.769 1.24 0.00 0.00 2.83
4536 5990 9.683069 CATCCTAAAAGCCATATGTATTCAAAC 57.317 33.333 1.24 0.00 0.00 2.93
4537 5991 9.639563 TCATCCTAAAAGCCATATGTATTCAAA 57.360 29.630 1.24 0.00 0.00 2.69
4538 5992 9.639563 TTCATCCTAAAAGCCATATGTATTCAA 57.360 29.630 1.24 0.00 0.00 2.69
4539 5993 9.066892 GTTCATCCTAAAAGCCATATGTATTCA 57.933 33.333 1.24 0.00 0.00 2.57
4540 5994 9.289782 AGTTCATCCTAAAAGCCATATGTATTC 57.710 33.333 1.24 0.00 0.00 1.75
4541 5995 9.289782 GAGTTCATCCTAAAAGCCATATGTATT 57.710 33.333 1.24 0.00 0.00 1.89
4542 5996 8.439971 TGAGTTCATCCTAAAAGCCATATGTAT 58.560 33.333 1.24 0.00 0.00 2.29
4543 5997 7.715249 GTGAGTTCATCCTAAAAGCCATATGTA 59.285 37.037 1.24 0.00 0.00 2.29
4544 5998 6.543831 GTGAGTTCATCCTAAAAGCCATATGT 59.456 38.462 1.24 0.00 0.00 2.29
4545 5999 6.543465 TGTGAGTTCATCCTAAAAGCCATATG 59.457 38.462 0.00 0.00 0.00 1.78
4546 6000 6.662755 TGTGAGTTCATCCTAAAAGCCATAT 58.337 36.000 0.00 0.00 0.00 1.78
4547 6001 6.061022 TGTGAGTTCATCCTAAAAGCCATA 57.939 37.500 0.00 0.00 0.00 2.74
4548 6002 4.922206 TGTGAGTTCATCCTAAAAGCCAT 58.078 39.130 0.00 0.00 0.00 4.40
4549 6003 4.365514 TGTGAGTTCATCCTAAAAGCCA 57.634 40.909 0.00 0.00 0.00 4.75
4550 6004 5.003804 TCTTGTGAGTTCATCCTAAAAGCC 58.996 41.667 0.00 0.00 0.00 4.35
4551 6005 6.404074 CCATCTTGTGAGTTCATCCTAAAAGC 60.404 42.308 0.00 0.00 0.00 3.51
4552 6006 6.656693 ACCATCTTGTGAGTTCATCCTAAAAG 59.343 38.462 0.00 0.00 0.00 2.27
4553 6007 6.542821 ACCATCTTGTGAGTTCATCCTAAAA 58.457 36.000 0.00 0.00 0.00 1.52
4554 6008 6.126863 ACCATCTTGTGAGTTCATCCTAAA 57.873 37.500 0.00 0.00 0.00 1.85
4555 6009 5.762179 ACCATCTTGTGAGTTCATCCTAA 57.238 39.130 0.00 0.00 0.00 2.69
4556 6010 5.958380 ACTACCATCTTGTGAGTTCATCCTA 59.042 40.000 0.00 0.00 0.00 2.94
4557 6011 4.780021 ACTACCATCTTGTGAGTTCATCCT 59.220 41.667 0.00 0.00 0.00 3.24
4558 6012 5.091261 ACTACCATCTTGTGAGTTCATCC 57.909 43.478 0.00 0.00 0.00 3.51
4559 6013 6.253727 CGTTACTACCATCTTGTGAGTTCATC 59.746 42.308 0.00 0.00 0.00 2.92
4560 6014 6.071560 TCGTTACTACCATCTTGTGAGTTCAT 60.072 38.462 0.00 0.00 0.00 2.57
4561 6015 5.242171 TCGTTACTACCATCTTGTGAGTTCA 59.758 40.000 0.00 0.00 0.00 3.18
4562 6016 5.572126 GTCGTTACTACCATCTTGTGAGTTC 59.428 44.000 0.00 0.00 0.00 3.01
4563 6017 5.243283 AGTCGTTACTACCATCTTGTGAGTT 59.757 40.000 0.00 0.00 32.84 3.01
4564 6018 4.765856 AGTCGTTACTACCATCTTGTGAGT 59.234 41.667 0.00 0.00 32.84 3.41
4565 6019 5.312120 AGTCGTTACTACCATCTTGTGAG 57.688 43.478 0.00 0.00 32.84 3.51
4566 6020 5.717078 AAGTCGTTACTACCATCTTGTGA 57.283 39.130 0.00 0.00 33.75 3.58
4567 6021 5.389516 GCAAAGTCGTTACTACCATCTTGTG 60.390 44.000 0.00 0.00 33.75 3.33
4568 6022 4.689345 GCAAAGTCGTTACTACCATCTTGT 59.311 41.667 0.00 0.00 33.75 3.16
4569 6023 4.929808 AGCAAAGTCGTTACTACCATCTTG 59.070 41.667 0.00 0.00 33.75 3.02
4570 6024 5.148651 AGCAAAGTCGTTACTACCATCTT 57.851 39.130 0.00 0.00 33.75 2.40
4571 6025 4.803098 AGCAAAGTCGTTACTACCATCT 57.197 40.909 0.00 0.00 33.75 2.90
4572 6026 5.404946 TGTAGCAAAGTCGTTACTACCATC 58.595 41.667 6.48 0.00 33.75 3.51
4573 6027 5.395682 TGTAGCAAAGTCGTTACTACCAT 57.604 39.130 6.48 0.00 33.75 3.55
4574 6028 4.852134 TGTAGCAAAGTCGTTACTACCA 57.148 40.909 6.48 0.00 33.75 3.25
4575 6029 6.254373 GGTTATGTAGCAAAGTCGTTACTACC 59.746 42.308 6.48 0.00 33.75 3.18
4576 6030 6.808212 TGGTTATGTAGCAAAGTCGTTACTAC 59.192 38.462 2.84 2.84 33.75 2.73
4577 6031 6.923012 TGGTTATGTAGCAAAGTCGTTACTA 58.077 36.000 0.00 0.00 33.75 1.82
4578 6032 5.786311 TGGTTATGTAGCAAAGTCGTTACT 58.214 37.500 0.00 0.00 37.65 2.24
4579 6033 6.073657 TGTTGGTTATGTAGCAAAGTCGTTAC 60.074 38.462 0.00 0.00 45.10 2.50
4580 6034 5.990386 TGTTGGTTATGTAGCAAAGTCGTTA 59.010 36.000 0.00 0.00 45.10 3.18
4581 6035 4.817464 TGTTGGTTATGTAGCAAAGTCGTT 59.183 37.500 0.00 0.00 45.10 3.85
4582 6036 4.382291 TGTTGGTTATGTAGCAAAGTCGT 58.618 39.130 0.00 0.00 45.10 4.34
4583 6037 5.351233 TTGTTGGTTATGTAGCAAAGTCG 57.649 39.130 0.00 0.00 45.10 4.18
4584 6038 7.995463 TTTTTGTTGGTTATGTAGCAAAGTC 57.005 32.000 0.00 0.00 45.10 3.01
4608 6062 3.214328 AGTTGGTGCGACAGAGATTTTT 58.786 40.909 0.00 0.00 0.00 1.94
4618 6072 6.608610 ACAATAAAGATTTAGTTGGTGCGAC 58.391 36.000 0.00 0.00 0.00 5.19
4675 6129 4.702131 GGGAGCAAGATTTTGTATGTGACT 59.298 41.667 0.00 0.00 36.65 3.41
4726 6180 3.391296 ACCAGTTGTTGAGCCTTCTAGAA 59.609 43.478 4.81 4.81 0.00 2.10
4767 6236 5.130311 ACTGTTTCCCCTTGCTTAATTTGTT 59.870 36.000 0.00 0.00 0.00 2.83
4858 6329 3.664107 TGATAAGATAATGGGCGCAGAC 58.336 45.455 10.83 0.00 0.00 3.51
4864 6335 7.383300 GCAGTTTTTCATGATAAGATAATGGGC 59.617 37.037 0.00 0.00 0.00 5.36
4947 6418 8.122952 CGGAAAGCCAACTATGTAAAAGAATAG 58.877 37.037 0.00 0.00 33.42 1.73


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

AutoCloner maintained by Alex Coulton.