Multiple sequence alignment - TraesCS5D01G261300

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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 TraesCS5D01G261300 chr5D 100.000 3524 0 0 766 4289 367689515 367693038 0.000000e+00 6508.0
1 TraesCS5D01G261300 chr5D 100.000 485 0 0 1 485 367688750 367689234 0.000000e+00 896.0
2 TraesCS5D01G261300 chr5D 94.611 167 8 1 3725 3891 334801459 334801294 1.530000e-64 257.0
3 TraesCS5D01G261300 chr5D 90.625 64 4 2 3956 4017 41140030 41139967 2.750000e-12 84.2
4 TraesCS5D01G261300 chr5D 89.552 67 5 2 3950 4015 501776382 501776447 2.750000e-12 84.2
5 TraesCS5D01G261300 chr5A 94.535 3001 103 24 766 3729 469608309 469611285 0.000000e+00 4577.0
6 TraesCS5D01G261300 chr5A 88.822 501 20 20 1 485 469607801 469608281 2.220000e-162 582.0
7 TraesCS5D01G261300 chr5A 86.514 393 30 12 3899 4289 469611421 469611792 1.110000e-110 411.0
8 TraesCS5D01G261300 chr5B 93.519 1543 59 15 2209 3732 435157749 435159269 0.000000e+00 2257.0
9 TraesCS5D01G261300 chr5B 94.480 1413 58 7 766 2172 435156264 435157662 0.000000e+00 2159.0
10 TraesCS5D01G261300 chr5B 93.214 501 17 8 1 485 435155735 435156234 0.000000e+00 721.0
11 TraesCS5D01G261300 chr5B 82.759 203 20 9 4012 4213 435159387 435159575 2.650000e-37 167.0
12 TraesCS5D01G261300 chr1A 95.706 163 7 0 3729 3891 254348915 254349077 3.290000e-66 263.0
13 TraesCS5D01G261300 chr1A 93.023 172 10 2 3725 3896 580665928 580666097 2.560000e-62 250.0
14 TraesCS5D01G261300 chr1A 90.659 182 14 3 3728 3909 552407919 552408097 5.540000e-59 239.0
15 TraesCS5D01G261300 chr6B 94.578 166 9 0 3729 3894 286708620 286708455 1.530000e-64 257.0
16 TraesCS5D01G261300 chr4A 93.529 170 11 0 3725 3894 729701866 729702035 1.980000e-63 254.0
17 TraesCS5D01G261300 chr2B 94.048 168 9 1 3729 3895 616962791 616962958 1.980000e-63 254.0
18 TraesCS5D01G261300 chr2A 92.614 176 12 1 3727 3901 189021000 189020825 7.120000e-63 252.0
19 TraesCS5D01G261300 chr1B 94.012 167 9 1 3729 3895 136439995 136440160 7.120000e-63 252.0
20 TraesCS5D01G261300 chr1B 86.667 75 5 5 3942 4015 237010413 237010343 1.280000e-10 78.7
21 TraesCS5D01G261300 chr1D 89.706 68 4 3 3950 4016 22376938 22376873 2.750000e-12 84.2
22 TraesCS5D01G261300 chr7D 88.406 69 6 2 3948 4015 604972457 604972524 9.880000e-12 82.4
23 TraesCS5D01G261300 chr7B 89.394 66 3 4 3950 4014 376350595 376350657 3.560000e-11 80.5
24 TraesCS5D01G261300 chr6A 86.486 74 7 3 3946 4018 614534046 614533975 1.280000e-10 78.7
25 TraesCS5D01G261300 chr6A 86.486 74 4 4 3945 4016 104308560 104308491 4.600000e-10 76.8


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 TraesCS5D01G261300 chr5D 367688750 367693038 4288 False 3702.000000 6508 100.000 1 4289 2 chr5D.!!$F2 4288
1 TraesCS5D01G261300 chr5A 469607801 469611792 3991 False 1856.666667 4577 89.957 1 4289 3 chr5A.!!$F1 4288
2 TraesCS5D01G261300 chr5B 435155735 435159575 3840 False 1326.000000 2257 90.993 1 4213 4 chr5B.!!$F1 4212

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
483 513 0.178876 TGGTCTCATGGGGGTTCTCA 60.179 55.000 0.0 0.0 0.00 3.27 F
889 919 1.469703 CTGCTTCGGTGAATTGATGCA 59.530 47.619 0.0 0.0 41.28 3.96 F
2640 2735 0.736325 CGGACATCGTGAACCAGGTC 60.736 60.000 0.0 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1409 1446 1.067846 TCGGTGAAATCTCGACCACTG 60.068 52.381 0.0 0.0 37.28 3.66 R
2883 2978 1.474478 CTTGCCGAGAAGCTCACTAGA 59.526 52.381 0.0 0.0 0.00 2.43 R
3578 3682 0.179189 GCTGCATTGTCCGTTAGCAC 60.179 55.000 0.0 0.0 0.00 4.40 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
172 185 0.849540 TTCCTTCCTCCCCCTTTCCC 60.850 60.000 0.00 0.00 0.00 3.97
173 186 2.317378 CCTTCCTCCCCCTTTCCCC 61.317 68.421 0.00 0.00 0.00 4.81
175 188 0.851332 CTTCCTCCCCCTTTCCCCTT 60.851 60.000 0.00 0.00 0.00 3.95
264 282 0.455815 CGCCCTATTTTTGTGGGAGC 59.544 55.000 0.91 0.00 43.47 4.70
343 370 0.759060 GGCCCTCTCTCCTCTCTTCC 60.759 65.000 0.00 0.00 0.00 3.46
362 392 2.726351 CCTCCCTTCTCTGGCGTCC 61.726 68.421 0.00 0.00 0.00 4.79
448 478 0.514691 GTAGCAGCTTGTGTGTGAGC 59.485 55.000 0.00 0.00 39.17 4.26
478 508 0.995024 CTTCTTGGTCTCATGGGGGT 59.005 55.000 0.00 0.00 0.00 4.95
480 510 0.991920 TCTTGGTCTCATGGGGGTTC 59.008 55.000 0.00 0.00 0.00 3.62
481 511 0.995024 CTTGGTCTCATGGGGGTTCT 59.005 55.000 0.00 0.00 0.00 3.01
482 512 0.991920 TTGGTCTCATGGGGGTTCTC 59.008 55.000 0.00 0.00 0.00 2.87
483 513 0.178876 TGGTCTCATGGGGGTTCTCA 60.179 55.000 0.00 0.00 0.00 3.27
818 848 3.368495 CGGTTTAGGTTGTTGTTTCTGC 58.632 45.455 0.00 0.00 0.00 4.26
872 902 5.240403 GGAATATTTCTGATCCCTTGTCTGC 59.760 44.000 0.00 0.00 0.00 4.26
889 919 1.469703 CTGCTTCGGTGAATTGATGCA 59.530 47.619 0.00 0.00 41.28 3.96
900 930 4.211794 GTGAATTGATGCAAACAAACCCTG 59.788 41.667 12.36 0.00 30.45 4.45
1007 1044 3.314331 AGTGAGCACTGACCGGGG 61.314 66.667 6.32 0.00 40.75 5.73
1238 1275 3.017581 GGGGTCCTGGATGTGCCT 61.018 66.667 0.00 0.00 37.63 4.75
1271 1308 3.055963 AGGCAGAGTCTGATGAGTCAAAG 60.056 47.826 24.55 0.00 43.31 2.77
1316 1353 6.203723 CCAACGAGAATCAAGAAAAGAAGTCT 59.796 38.462 0.00 0.00 33.17 3.24
1409 1446 1.900486 ACCAGTGGTAGTGCTAAGACC 59.100 52.381 14.87 0.00 32.11 3.85
1415 1452 1.900486 GGTAGTGCTAAGACCAGTGGT 59.100 52.381 16.70 16.70 39.44 4.16
1589 1626 4.035102 AGGGAGGGCGTTCTTGGC 62.035 66.667 0.00 0.00 0.00 4.52
1667 1704 6.663523 TGTATCTCTCTGAATTGAGTGGTACA 59.336 38.462 13.09 13.09 44.66 2.90
1932 1969 6.232581 AGTATGCACTCTCTCTTGCTAATT 57.767 37.500 0.00 0.00 39.62 1.40
1933 1970 7.353414 AGTATGCACTCTCTCTTGCTAATTA 57.647 36.000 0.00 0.00 39.62 1.40
1934 1971 7.206687 AGTATGCACTCTCTCTTGCTAATTAC 58.793 38.462 0.00 0.00 39.62 1.89
1935 1972 4.759782 TGCACTCTCTCTTGCTAATTACC 58.240 43.478 0.00 0.00 39.62 2.85
1936 1973 4.123506 GCACTCTCTCTTGCTAATTACCC 58.876 47.826 0.00 0.00 35.74 3.69
1937 1974 4.698575 CACTCTCTCTTGCTAATTACCCC 58.301 47.826 0.00 0.00 0.00 4.95
1938 1975 3.385111 ACTCTCTCTTGCTAATTACCCCG 59.615 47.826 0.00 0.00 0.00 5.73
1956 1996 4.821805 ACCCCGTATTTCACATGAATGATC 59.178 41.667 0.00 0.00 33.54 2.92
2051 2091 2.357009 CCTGATAGCTTCATGTTGCCAC 59.643 50.000 0.00 0.00 32.72 5.01
2144 2188 5.181748 AGAATCAGAAAGGTGCAGTATGTC 58.818 41.667 0.00 0.00 39.31 3.06
2167 2211 5.046878 TCGTAGAAACTAATGTGTCCCATGT 60.047 40.000 0.00 0.00 32.82 3.21
2172 2216 5.902613 AACTAATGTGTCCCATGTTGATG 57.097 39.130 0.00 0.00 32.82 3.07
2264 2358 9.860898 AATGCTGACAAAGGATTTAACTTATTC 57.139 29.630 0.00 0.00 43.85 1.75
2550 2645 2.305928 CCATCCTGTGTTGTTCCAACA 58.694 47.619 5.73 5.73 37.08 3.33
2640 2735 0.736325 CGGACATCGTGAACCAGGTC 60.736 60.000 0.00 0.00 0.00 3.85
2883 2978 2.685380 CGCTTCCCAGAGTCCCCT 60.685 66.667 0.00 0.00 0.00 4.79
2994 3089 2.675658 TAAAGCAGCACCCCTTCTTT 57.324 45.000 0.00 0.00 39.72 2.52
3233 3328 0.321122 AGGCGCCACAGAAAGAGAAG 60.321 55.000 31.54 0.00 0.00 2.85
3234 3329 1.301677 GGCGCCACAGAAAGAGAAGG 61.302 60.000 24.80 0.00 0.00 3.46
3365 3462 1.812571 CCGCCATTGAACTTGTTAGCT 59.187 47.619 0.00 0.00 0.00 3.32
3372 3469 5.936956 CCATTGAACTTGTTAGCTCTCTCTT 59.063 40.000 0.00 0.00 0.00 2.85
3374 3471 7.604164 CCATTGAACTTGTTAGCTCTCTCTTTA 59.396 37.037 0.00 0.00 0.00 1.85
3375 3472 8.655092 CATTGAACTTGTTAGCTCTCTCTTTAG 58.345 37.037 0.00 0.00 0.00 1.85
3376 3473 7.291411 TGAACTTGTTAGCTCTCTCTTTAGT 57.709 36.000 0.00 0.00 0.00 2.24
3377 3474 7.371936 TGAACTTGTTAGCTCTCTCTTTAGTC 58.628 38.462 0.00 0.00 0.00 2.59
3378 3475 6.902771 ACTTGTTAGCTCTCTCTTTAGTCA 57.097 37.500 0.00 0.00 0.00 3.41
3382 3479 9.862371 CTTGTTAGCTCTCTCTTTAGTCAAATA 57.138 33.333 0.00 0.00 0.00 1.40
3459 3563 2.183858 GAACGGGTTTGAAGGAGCGC 62.184 60.000 0.00 0.00 0.00 5.92
3487 3591 1.446618 GGCCGTCGAATGTAACCGT 60.447 57.895 0.00 0.00 0.00 4.83
3522 3626 7.040478 CCTTGTAACTGATGTTTCTTCATCCAA 60.040 37.037 4.59 1.51 42.24 3.53
3523 3627 7.815840 TGTAACTGATGTTTCTTCATCCAAA 57.184 32.000 4.59 0.00 42.24 3.28
3532 3636 3.333029 TCTTCATCCAAACATCGCTCA 57.667 42.857 0.00 0.00 0.00 4.26
3619 3727 3.021695 TGTTACTATCTCACCAGGACCG 58.978 50.000 0.00 0.00 0.00 4.79
3622 3730 1.749334 CTATCTCACCAGGACCGGGC 61.749 65.000 11.05 0.21 0.00 6.13
3714 3842 6.549912 TTGATGTTGTGTGAGATGAAAGAG 57.450 37.500 0.00 0.00 0.00 2.85
3729 3857 8.840200 AGATGAAAGAGGAGTGGTTTATACTA 57.160 34.615 0.00 0.00 0.00 1.82
3738 3866 4.213513 AGTGGTTTATACTACTCCCTCCG 58.786 47.826 0.00 0.00 41.71 4.63
3740 3868 4.403752 GTGGTTTATACTACTCCCTCCGTT 59.596 45.833 0.00 0.00 33.36 4.44
3741 3869 5.025453 TGGTTTATACTACTCCCTCCGTTT 58.975 41.667 0.00 0.00 0.00 3.60
3742 3870 5.127682 TGGTTTATACTACTCCCTCCGTTTC 59.872 44.000 0.00 0.00 0.00 2.78
3743 3871 5.362143 GGTTTATACTACTCCCTCCGTTTCT 59.638 44.000 0.00 0.00 0.00 2.52
3744 3872 6.547510 GGTTTATACTACTCCCTCCGTTTCTA 59.452 42.308 0.00 0.00 0.00 2.10
3745 3873 7.068716 GGTTTATACTACTCCCTCCGTTTCTAA 59.931 40.741 0.00 0.00 0.00 2.10
3746 3874 8.470002 GTTTATACTACTCCCTCCGTTTCTAAA 58.530 37.037 0.00 0.00 0.00 1.85
3747 3875 8.773033 TTATACTACTCCCTCCGTTTCTAAAT 57.227 34.615 0.00 0.00 0.00 1.40
3748 3876 9.866655 TTATACTACTCCCTCCGTTTCTAAATA 57.133 33.333 0.00 0.00 0.00 1.40
3749 3877 8.953223 ATACTACTCCCTCCGTTTCTAAATAT 57.047 34.615 0.00 0.00 0.00 1.28
3751 3879 8.773033 ACTACTCCCTCCGTTTCTAAATATAA 57.227 34.615 0.00 0.00 0.00 0.98
3752 3880 8.858094 ACTACTCCCTCCGTTTCTAAATATAAG 58.142 37.037 0.00 0.00 0.00 1.73
3753 3881 7.672122 ACTCCCTCCGTTTCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
3754 3882 7.724287 ACTCCCTCCGTTTCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
3755 3883 7.564292 ACTCCCTCCGTTTCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
3756 3884 8.315220 TCCCTCCGTTTCTAAATATAAGTCTT 57.685 34.615 0.00 0.00 0.00 3.01
3757 3885 8.765517 TCCCTCCGTTTCTAAATATAAGTCTTT 58.234 33.333 0.00 0.00 0.00 2.52
3758 3886 8.827677 CCCTCCGTTTCTAAATATAAGTCTTTG 58.172 37.037 0.00 0.00 0.00 2.77
3759 3887 8.827677 CCTCCGTTTCTAAATATAAGTCTTTGG 58.172 37.037 0.00 0.00 0.00 3.28
3760 3888 9.595823 CTCCGTTTCTAAATATAAGTCTTTGGA 57.404 33.333 0.00 0.00 0.00 3.53
3761 3889 9.947433 TCCGTTTCTAAATATAAGTCTTTGGAA 57.053 29.630 0.00 0.00 32.27 3.53
3776 3904 8.477419 AGTCTTTGGAAAAATTTCACTATGGA 57.523 30.769 8.06 0.00 38.92 3.41
3777 3905 8.360390 AGTCTTTGGAAAAATTTCACTATGGAC 58.640 33.333 8.06 7.61 38.92 4.02
3778 3906 7.598869 GTCTTTGGAAAAATTTCACTATGGACC 59.401 37.037 8.06 0.00 38.92 4.46
3779 3907 6.985653 TTGGAAAAATTTCACTATGGACCA 57.014 33.333 0.00 0.00 38.92 4.02
3780 3908 6.339587 TGGAAAAATTTCACTATGGACCAC 57.660 37.500 0.00 0.00 38.92 4.16
3781 3909 5.835819 TGGAAAAATTTCACTATGGACCACA 59.164 36.000 0.00 0.00 38.92 4.17
3782 3910 6.496565 TGGAAAAATTTCACTATGGACCACAT 59.503 34.615 0.00 0.00 39.97 3.21
3783 3911 7.671819 TGGAAAAATTTCACTATGGACCACATA 59.328 33.333 0.00 0.00 38.67 2.29
3784 3912 8.527810 GGAAAAATTTCACTATGGACCACATAA 58.472 33.333 0.00 0.00 38.91 1.90
3785 3913 9.573133 GAAAAATTTCACTATGGACCACATAAG 57.427 33.333 0.00 0.00 38.03 1.73
3786 3914 7.645058 AAATTTCACTATGGACCACATAAGG 57.355 36.000 0.00 0.00 41.33 2.69
3787 3915 6.575244 ATTTCACTATGGACCACATAAGGA 57.425 37.500 0.00 0.00 41.33 3.36
3788 3916 5.614324 TTCACTATGGACCACATAAGGAG 57.386 43.478 0.00 0.00 41.33 3.69
3789 3917 3.388024 TCACTATGGACCACATAAGGAGC 59.612 47.826 0.00 0.00 41.33 4.70
3790 3918 3.134623 CACTATGGACCACATAAGGAGCA 59.865 47.826 0.00 0.00 41.33 4.26
3791 3919 3.780294 ACTATGGACCACATAAGGAGCAA 59.220 43.478 0.00 0.00 41.33 3.91
3792 3920 3.737559 ATGGACCACATAAGGAGCAAA 57.262 42.857 0.00 0.00 38.26 3.68
3796 3924 4.016444 GGACCACATAAGGAGCAAAATGA 58.984 43.478 0.00 0.00 0.00 2.57
3797 3925 4.096984 GGACCACATAAGGAGCAAAATGAG 59.903 45.833 0.00 0.00 0.00 2.90
3800 3928 4.701651 CCACATAAGGAGCAAAATGAGTGA 59.298 41.667 0.00 0.00 0.00 3.41
3802 3930 6.127535 CCACATAAGGAGCAAAATGAGTGAAT 60.128 38.462 0.00 0.00 0.00 2.57
3803 3931 7.318141 CACATAAGGAGCAAAATGAGTGAATT 58.682 34.615 0.00 0.00 0.00 2.17
3809 3937 8.814038 AGGAGCAAAATGAGTGAATTTATACT 57.186 30.769 0.00 0.00 0.00 2.12
3833 3961 8.031864 ACTCTAAAATGCATCTAGATACATCCG 58.968 37.037 17.09 7.74 0.00 4.18
3834 3962 7.323420 TCTAAAATGCATCTAGATACATCCGG 58.677 38.462 17.09 0.00 0.00 5.14
3837 3965 4.725790 TGCATCTAGATACATCCGGATG 57.274 45.455 37.23 37.23 44.15 3.51
3848 3976 3.475566 CATCCGGATGTGGTTCATAGT 57.524 47.619 32.39 0.00 36.83 2.12
3849 3977 2.979814 TCCGGATGTGGTTCATAGTG 57.020 50.000 0.00 0.00 36.83 2.74
3850 3978 2.462723 TCCGGATGTGGTTCATAGTGA 58.537 47.619 0.00 0.00 36.83 3.41
3851 3979 2.835156 TCCGGATGTGGTTCATAGTGAA 59.165 45.455 0.00 0.00 36.83 3.18
3852 3980 3.262151 TCCGGATGTGGTTCATAGTGAAA 59.738 43.478 0.00 0.00 38.22 2.69
3853 3981 4.080582 TCCGGATGTGGTTCATAGTGAAAT 60.081 41.667 0.00 0.00 38.22 2.17
3854 3982 4.273480 CCGGATGTGGTTCATAGTGAAATC 59.727 45.833 0.00 0.00 38.22 2.17
3855 3983 5.118990 CGGATGTGGTTCATAGTGAAATCT 58.881 41.667 0.00 0.00 38.22 2.40
3856 3984 5.235186 CGGATGTGGTTCATAGTGAAATCTC 59.765 44.000 0.00 0.00 38.22 2.75
3857 3985 6.352516 GGATGTGGTTCATAGTGAAATCTCT 58.647 40.000 0.00 0.00 38.22 3.10
3858 3986 7.500992 GGATGTGGTTCATAGTGAAATCTCTA 58.499 38.462 0.00 0.00 38.22 2.43
3859 3987 7.439655 GGATGTGGTTCATAGTGAAATCTCTAC 59.560 40.741 0.00 0.00 38.22 2.59
3864 3992 8.593679 TGGTTCATAGTGAAATCTCTACAAAGA 58.406 33.333 0.00 0.00 38.22 2.52
3866 3994 9.646427 GTTCATAGTGAAATCTCTACAAAGACT 57.354 33.333 0.00 0.00 38.22 3.24
3928 4121 1.532007 GTATGCTACTCCCTCGTCTCG 59.468 57.143 0.00 0.00 0.00 4.04
3935 4128 4.023021 GCTACTCCCTCGTCTCGAAATAAT 60.023 45.833 0.00 0.00 34.74 1.28
3937 4130 4.934515 ACTCCCTCGTCTCGAAATAATTC 58.065 43.478 0.00 0.00 34.74 2.17
3960 4153 8.690203 TTCTCTCTGATTTAGTATCTCCTCTG 57.310 38.462 0.00 0.00 0.00 3.35
3990 4183 9.906660 AGAAATATAAGAGCGTTTAGATCTCTG 57.093 33.333 0.00 0.00 46.24 3.35
4071 4265 1.047002 TTTTGCATGGGTCTTGGGTG 58.953 50.000 0.00 0.00 0.00 4.61
4072 4266 0.831288 TTTGCATGGGTCTTGGGTGG 60.831 55.000 0.00 0.00 0.00 4.61
4073 4267 2.362889 GCATGGGTCTTGGGTGGG 60.363 66.667 0.00 0.00 0.00 4.61
4074 4268 3.180282 CATGGGTCTTGGGTGGGT 58.820 61.111 0.00 0.00 0.00 4.51
4117 4311 4.322567 GCTGGAGATGAACTTTCAGAACT 58.677 43.478 0.00 0.00 41.08 3.01
4145 4339 1.533625 TATGCACCACCAGCACTTTC 58.466 50.000 0.00 0.00 45.95 2.62
4155 4349 2.016318 CCAGCACTTTCACAACTCACA 58.984 47.619 0.00 0.00 0.00 3.58
4156 4350 2.032550 CCAGCACTTTCACAACTCACAG 59.967 50.000 0.00 0.00 0.00 3.66
4177 4371 2.674380 CCTGTTGCCCACTCCAGC 60.674 66.667 0.00 0.00 0.00 4.85
4180 4374 2.203480 GTTGCCCACTCCAGCCAA 60.203 61.111 0.00 0.00 0.00 4.52
4199 4393 1.583556 ATTTGGGGATTTTGGAGGCC 58.416 50.000 0.00 0.00 0.00 5.19
4200 4394 0.192064 TTTGGGGATTTTGGAGGCCA 59.808 50.000 5.01 0.00 0.00 5.36
4203 4397 1.203415 TGGGGATTTTGGAGGCCATTT 60.203 47.619 5.01 0.00 31.53 2.32
4227 4421 1.959028 GCCTACCTAGGAACCGTGTCT 60.959 57.143 17.98 0.00 46.63 3.41
4228 4422 2.454538 CCTACCTAGGAACCGTGTCTT 58.545 52.381 17.98 0.00 46.63 3.01
4237 4431 1.264288 GAACCGTGTCTTTGCTGGAAG 59.736 52.381 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.673923 CGCGCCATGGATCATATGAGT 60.674 52.381 18.40 0.00 0.00 3.41
69 78 2.534272 CCCCCACCTTTCCCCTCA 60.534 66.667 0.00 0.00 0.00 3.86
172 185 4.410400 AAAGCGGCGAGGGGAAGG 62.410 66.667 12.98 0.00 0.00 3.46
173 186 3.127533 CAAAGCGGCGAGGGGAAG 61.128 66.667 12.98 0.00 0.00 3.46
312 339 0.985490 AGAGGGCCTGGCTAGAAAGG 60.985 60.000 12.95 6.75 36.58 3.11
343 370 2.685380 ACGCCAGAGAAGGGAGGG 60.685 66.667 0.00 0.00 0.00 4.30
362 392 3.825611 CCGCCGCATCCAAAAGGG 61.826 66.667 0.00 0.00 38.37 3.95
448 478 0.109342 ACCAAGAAGTCACCTGCAGG 59.891 55.000 31.60 31.60 42.17 4.85
799 829 3.065648 TCGGCAGAAACAACAACCTAAAC 59.934 43.478 0.00 0.00 0.00 2.01
872 902 3.899734 TGTTTGCATCAATTCACCGAAG 58.100 40.909 0.00 0.00 0.00 3.79
889 919 7.717436 CACCAATAAAATAACCAGGGTTTGTTT 59.283 33.333 9.30 11.77 39.31 2.83
900 930 6.910433 CGTATCAGCACACCAATAAAATAACC 59.090 38.462 0.00 0.00 0.00 2.85
1003 1040 1.269448 CAGAATCACAACAAACCCCCG 59.731 52.381 0.00 0.00 0.00 5.73
1007 1044 4.359706 GTTGACCAGAATCACAACAAACC 58.640 43.478 0.00 0.00 41.16 3.27
1256 1293 3.259374 TGGTCTCCTTTGACTCATCAGAC 59.741 47.826 0.00 0.00 35.83 3.51
1271 1308 2.418884 GGAATCGGAGTTCTTGGTCTCC 60.419 54.545 0.00 0.00 44.65 3.71
1316 1353 6.020971 TCACTGATACTACTCTTTTGCGAA 57.979 37.500 0.00 0.00 0.00 4.70
1409 1446 1.067846 TCGGTGAAATCTCGACCACTG 60.068 52.381 0.00 0.00 37.28 3.66
1562 1599 1.691219 GCCCTCCCTGGATTTGACA 59.309 57.895 0.00 0.00 38.35 3.58
1589 1626 2.450476 AGCAGCCTAAATTGGTTCAGG 58.550 47.619 0.00 0.00 0.00 3.86
1667 1704 4.646492 ACCTTCATTGCAAAGTGACTCTTT 59.354 37.500 1.71 0.00 45.96 2.52
1919 1956 3.821421 ACGGGGTAATTAGCAAGAGAG 57.179 47.619 16.07 3.60 0.00 3.20
1932 1969 5.360649 TCATTCATGTGAAATACGGGGTA 57.639 39.130 0.00 0.00 37.61 3.69
1933 1970 4.229304 TCATTCATGTGAAATACGGGGT 57.771 40.909 0.00 0.00 37.61 4.95
1934 1971 5.049198 CAGATCATTCATGTGAAATACGGGG 60.049 44.000 0.00 0.00 37.61 5.73
1935 1972 5.528690 ACAGATCATTCATGTGAAATACGGG 59.471 40.000 0.00 0.00 37.61 5.28
1936 1973 6.609237 ACAGATCATTCATGTGAAATACGG 57.391 37.500 0.00 0.00 37.61 4.02
2051 2091 5.363101 AGTATGTCATATGCAACCTGACTG 58.637 41.667 20.50 1.33 39.94 3.51
2172 2216 2.505447 GCAACGTGCAATTGACACC 58.495 52.632 20.15 8.42 44.26 4.16
2550 2645 2.496899 ATCGAGGACCAAAGCATGTT 57.503 45.000 0.00 0.00 0.00 2.71
2640 2735 4.564041 CGATCATCTCAGGGAATAGGTTG 58.436 47.826 0.00 0.00 0.00 3.77
2883 2978 1.474478 CTTGCCGAGAAGCTCACTAGA 59.526 52.381 0.00 0.00 0.00 2.43
2994 3089 4.329545 GCCCAGTTCACGCCCTCA 62.330 66.667 0.00 0.00 0.00 3.86
3036 3131 1.602237 CACGGGCTTGGGTATGTCT 59.398 57.895 0.00 0.00 0.00 3.41
3233 3328 1.052617 GGGGGAGCTCTACATCTTCC 58.947 60.000 14.64 3.12 0.00 3.46
3234 3329 1.967779 GAGGGGGAGCTCTACATCTTC 59.032 57.143 14.64 1.78 0.00 2.87
3321 3417 8.931775 CGGAAAAGAAAAAGGAAAGAAGAAAAA 58.068 29.630 0.00 0.00 0.00 1.94
3372 3469 8.918116 ACATGCATAGAGAGAGTATTTGACTAA 58.082 33.333 0.00 0.00 39.06 2.24
3374 3471 7.358770 ACATGCATAGAGAGAGTATTTGACT 57.641 36.000 0.00 0.00 42.90 3.41
3375 3472 9.534565 TTAACATGCATAGAGAGAGTATTTGAC 57.465 33.333 0.00 0.00 0.00 3.18
3382 3479 5.464722 CGCAATTAACATGCATAGAGAGAGT 59.535 40.000 13.66 0.00 44.01 3.24
3532 3636 1.269166 CAGAATAAGCGACGCGAAGT 58.731 50.000 15.93 5.60 0.00 3.01
3578 3682 0.179189 GCTGCATTGTCCGTTAGCAC 60.179 55.000 0.00 0.00 0.00 4.40
3586 3690 4.446371 AGATAGTAACAGCTGCATTGTCC 58.554 43.478 15.27 0.00 0.00 4.02
3619 3727 5.769662 TCATATTCATACAACAGGAATGCCC 59.230 40.000 0.00 0.00 38.12 5.36
3622 3730 8.354426 TGCAATCATATTCATACAACAGGAATG 58.646 33.333 0.00 0.00 38.12 2.67
3729 3857 7.564292 AGACTTATATTTAGAAACGGAGGGAGT 59.436 37.037 0.00 0.00 0.00 3.85
3731 3859 7.909485 AGACTTATATTTAGAAACGGAGGGA 57.091 36.000 0.00 0.00 0.00 4.20
3732 3860 8.827677 CAAAGACTTATATTTAGAAACGGAGGG 58.172 37.037 0.00 0.00 0.00 4.30
3733 3861 8.827677 CCAAAGACTTATATTTAGAAACGGAGG 58.172 37.037 0.00 0.00 0.00 4.30
3734 3862 9.595823 TCCAAAGACTTATATTTAGAAACGGAG 57.404 33.333 0.00 0.00 0.00 4.63
3750 3878 8.923270 TCCATAGTGAAATTTTTCCAAAGACTT 58.077 29.630 0.00 0.00 36.36 3.01
3751 3879 8.360390 GTCCATAGTGAAATTTTTCCAAAGACT 58.640 33.333 0.00 0.69 36.36 3.24
3752 3880 7.598869 GGTCCATAGTGAAATTTTTCCAAAGAC 59.401 37.037 0.00 0.00 36.36 3.01
3753 3881 7.288852 TGGTCCATAGTGAAATTTTTCCAAAGA 59.711 33.333 0.00 0.00 36.36 2.52
3754 3882 7.384932 GTGGTCCATAGTGAAATTTTTCCAAAG 59.615 37.037 0.00 0.00 36.36 2.77
3755 3883 7.147655 TGTGGTCCATAGTGAAATTTTTCCAAA 60.148 33.333 0.00 0.00 36.36 3.28
3756 3884 6.325028 TGTGGTCCATAGTGAAATTTTTCCAA 59.675 34.615 0.00 0.00 36.36 3.53
3757 3885 5.835819 TGTGGTCCATAGTGAAATTTTTCCA 59.164 36.000 0.00 0.00 36.36 3.53
3758 3886 6.339587 TGTGGTCCATAGTGAAATTTTTCC 57.660 37.500 0.00 0.00 36.36 3.13
3759 3887 9.573133 CTTATGTGGTCCATAGTGAAATTTTTC 57.427 33.333 0.00 0.00 37.34 2.29
3760 3888 8.531146 CCTTATGTGGTCCATAGTGAAATTTTT 58.469 33.333 0.00 0.00 37.34 1.94
3761 3889 7.893302 TCCTTATGTGGTCCATAGTGAAATTTT 59.107 33.333 0.00 0.00 37.34 1.82
3762 3890 7.410174 TCCTTATGTGGTCCATAGTGAAATTT 58.590 34.615 0.00 0.00 37.34 1.82
3763 3891 6.969043 TCCTTATGTGGTCCATAGTGAAATT 58.031 36.000 0.00 0.00 37.34 1.82
3764 3892 6.575244 TCCTTATGTGGTCCATAGTGAAAT 57.425 37.500 0.00 0.00 37.34 2.17
3765 3893 5.629133 GCTCCTTATGTGGTCCATAGTGAAA 60.629 44.000 0.00 0.00 37.34 2.69
3766 3894 4.141711 GCTCCTTATGTGGTCCATAGTGAA 60.142 45.833 0.00 0.00 37.34 3.18
3767 3895 3.388024 GCTCCTTATGTGGTCCATAGTGA 59.612 47.826 0.00 0.00 37.34 3.41
3768 3896 3.134623 TGCTCCTTATGTGGTCCATAGTG 59.865 47.826 0.00 0.00 37.34 2.74
3769 3897 3.384168 TGCTCCTTATGTGGTCCATAGT 58.616 45.455 0.00 0.00 37.34 2.12
3770 3898 4.422073 TTGCTCCTTATGTGGTCCATAG 57.578 45.455 0.00 0.00 37.34 2.23
3771 3899 4.853468 TTTGCTCCTTATGTGGTCCATA 57.147 40.909 0.00 0.00 34.86 2.74
3772 3900 3.737559 TTTGCTCCTTATGTGGTCCAT 57.262 42.857 0.00 0.00 37.58 3.41
3773 3901 3.517296 TTTTGCTCCTTATGTGGTCCA 57.483 42.857 0.00 0.00 0.00 4.02
3774 3902 4.016444 TCATTTTGCTCCTTATGTGGTCC 58.984 43.478 0.00 0.00 0.00 4.46
3775 3903 4.702131 ACTCATTTTGCTCCTTATGTGGTC 59.298 41.667 0.00 0.00 0.00 4.02
3776 3904 4.460382 CACTCATTTTGCTCCTTATGTGGT 59.540 41.667 0.00 0.00 0.00 4.16
3777 3905 4.701651 TCACTCATTTTGCTCCTTATGTGG 59.298 41.667 0.00 0.00 0.00 4.17
3778 3906 5.885230 TCACTCATTTTGCTCCTTATGTG 57.115 39.130 0.00 0.00 0.00 3.21
3779 3907 7.472334 AATTCACTCATTTTGCTCCTTATGT 57.528 32.000 0.00 0.00 0.00 2.29
3783 3911 9.247861 AGTATAAATTCACTCATTTTGCTCCTT 57.752 29.630 0.00 0.00 0.00 3.36
3784 3912 8.814038 AGTATAAATTCACTCATTTTGCTCCT 57.186 30.769 0.00 0.00 0.00 3.69
3785 3913 8.897752 AGAGTATAAATTCACTCATTTTGCTCC 58.102 33.333 13.99 0.00 42.99 4.70
3808 3936 7.490725 CCGGATGTATCTAGATGCATTTTAGAG 59.509 40.741 29.66 18.81 42.77 2.43
3809 3937 7.178451 TCCGGATGTATCTAGATGCATTTTAGA 59.822 37.037 29.66 21.90 42.77 2.10
3832 3960 5.118990 AGATTTCACTATGAACCACATCCG 58.881 41.667 0.00 0.00 35.89 4.18
3833 3961 6.352516 AGAGATTTCACTATGAACCACATCC 58.647 40.000 0.00 0.00 35.89 3.51
3834 3962 7.981789 TGTAGAGATTTCACTATGAACCACATC 59.018 37.037 0.00 0.00 35.89 3.06
3837 3965 8.547967 TTTGTAGAGATTTCACTATGAACCAC 57.452 34.615 0.00 0.00 35.89 4.16
3839 3967 8.874816 GTCTTTGTAGAGATTTCACTATGAACC 58.125 37.037 0.00 0.00 35.89 3.62
3858 3986 9.379791 CCTCCGTTTCTAAATATAAGTCTTTGT 57.620 33.333 0.00 0.00 0.00 2.83
3859 3987 8.827677 CCCTCCGTTTCTAAATATAAGTCTTTG 58.172 37.037 0.00 0.00 0.00 2.77
3864 3992 7.672122 ACTCCCTCCGTTTCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
3866 3994 8.537728 TGTACTCCCTCCGTTTCTAAATATAA 57.462 34.615 0.00 0.00 0.00 0.98
3868 3996 7.613551 ATGTACTCCCTCCGTTTCTAAATAT 57.386 36.000 0.00 0.00 0.00 1.28
3873 4001 5.121380 AGTATGTACTCCCTCCGTTTCTA 57.879 43.478 0.00 0.00 0.00 2.10
3874 4002 3.952967 GAGTATGTACTCCCTCCGTTTCT 59.047 47.826 8.65 0.00 45.33 2.52
3896 4024 5.468072 GGGAGTAGCATACATGATGTGAAAG 59.532 44.000 8.61 0.00 46.26 2.62
3935 4128 8.278639 ACAGAGGAGATACTAAATCAGAGAGAA 58.721 37.037 0.00 0.00 0.00 2.87
3937 4130 9.567776 TTACAGAGGAGATACTAAATCAGAGAG 57.432 37.037 0.00 0.00 0.00 3.20
3952 4145 8.353684 CGCTCTTATATTTCTTTACAGAGGAGA 58.646 37.037 0.00 0.00 0.00 3.71
3954 4147 8.008513 ACGCTCTTATATTTCTTTACAGAGGA 57.991 34.615 0.00 0.00 0.00 3.71
3987 4180 9.832445 ACTCTCACTGTAAAGAAATAAAACAGA 57.168 29.630 7.70 0.00 39.93 3.41
4005 4198 3.325135 CCTCCCAAAGTTGTACTCTCACT 59.675 47.826 0.00 0.00 0.00 3.41
4007 4200 2.637872 CCCTCCCAAAGTTGTACTCTCA 59.362 50.000 0.00 0.00 0.00 3.27
4009 4202 2.986050 TCCCTCCCAAAGTTGTACTCT 58.014 47.619 0.00 0.00 0.00 3.24
4117 4311 3.346315 CTGGTGGTGCATATTCAGTTCA 58.654 45.455 0.00 0.00 0.00 3.18
4122 4316 1.004628 AGTGCTGGTGGTGCATATTCA 59.995 47.619 0.00 0.00 42.69 2.57
4126 4320 1.202867 TGAAAGTGCTGGTGGTGCATA 60.203 47.619 0.00 0.00 42.69 3.14
4145 4339 2.924185 CAGGCCTCTGTGAGTTGTG 58.076 57.895 0.00 0.00 36.30 3.33
4174 4368 2.305343 TCCAAAATCCCCAAATTGGCTG 59.695 45.455 6.48 0.00 41.64 4.85
4177 4371 2.356022 GCCTCCAAAATCCCCAAATTGG 60.356 50.000 4.74 4.74 42.92 3.16
4180 4374 1.203415 TGGCCTCCAAAATCCCCAAAT 60.203 47.619 3.32 0.00 0.00 2.32
4212 4406 1.002087 AGCAAAGACACGGTTCCTAGG 59.998 52.381 0.82 0.82 0.00 3.02
4227 4421 4.680440 GCCAAAAGAAGAACTTCCAGCAAA 60.680 41.667 10.41 0.00 40.33 3.68
4228 4422 3.181476 GCCAAAAGAAGAACTTCCAGCAA 60.181 43.478 10.41 0.00 40.33 3.91
4237 4431 1.865340 ACTCGTCGCCAAAAGAAGAAC 59.135 47.619 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.