Multiple sequence alignment - TraesCS6A01G357700

Loading Multiple Alignment...

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 TraesCS6A01G357700 chr6A 100.000 4586 0 0 1 4586 587889682 587894267 0.000000e+00 8469.0
1 TraesCS6A01G357700 chr6A 89.254 3071 241 35 607 3643 587972181 587969166 0.000000e+00 3760.0
2 TraesCS6A01G357700 chr6A 81.538 1690 234 36 624 2290 775006 773372 0.000000e+00 1321.0
3 TraesCS6A01G357700 chr6A 90.619 533 33 2 4058 4581 587968791 587968267 0.000000e+00 691.0
4 TraesCS6A01G357700 chr6A 97.561 41 1 0 4002 4042 144488377 144488337 2.290000e-08 71.3
5 TraesCS6A01G357700 chr6A 97.500 40 1 0 406 445 587972219 587972180 8.230000e-08 69.4
6 TraesCS6A01G357700 chr6D 97.664 2868 59 7 1 2865 439615447 439618309 0.000000e+00 4918.0
7 TraesCS6A01G357700 chr6D 90.504 3054 249 21 607 3644 439662514 439659486 0.000000e+00 3995.0
8 TraesCS6A01G357700 chr6D 80.180 2558 365 72 624 3125 2133978 2136449 0.000000e+00 1784.0
9 TraesCS6A01G357700 chr6D 93.672 806 37 9 2865 3657 439618351 439619155 0.000000e+00 1194.0
10 TraesCS6A01G357700 chr6D 89.184 527 43 5 4058 4580 439656781 439656265 0.000000e+00 645.0
11 TraesCS6A01G357700 chr6D 92.784 388 28 0 4046 4433 439619490 439619877 3.100000e-156 562.0
12 TraesCS6A01G357700 chr6D 79.161 763 99 27 1540 2290 4209039 4209753 1.490000e-129 473.0
13 TraesCS6A01G357700 chr6D 90.406 271 17 4 3657 3923 439619189 439619454 9.440000e-92 348.0
14 TraesCS6A01G357700 chr6D 79.235 366 37 15 3482 3836 439615139 439615476 7.730000e-53 219.0
15 TraesCS6A01G357700 chr6D 88.506 87 8 1 25 111 439619447 439619531 2.260000e-18 104.0
16 TraesCS6A01G357700 chr6D 95.349 43 2 0 4000 4042 94272817 94272859 8.230000e-08 69.4
17 TraesCS6A01G357700 chr6D 97.500 40 1 0 406 445 439662552 439662513 8.230000e-08 69.4
18 TraesCS6A01G357700 chr6B 96.764 2627 71 4 1 2624 664476702 664479317 0.000000e+00 4368.0
19 TraesCS6A01G357700 chr6B 92.871 1529 83 7 607 2134 664525173 664523670 0.000000e+00 2196.0
20 TraesCS6A01G357700 chr6B 80.590 2169 324 49 624 2753 3799635 3801745 0.000000e+00 1583.0
21 TraesCS6A01G357700 chr6B 86.474 1486 147 29 2173 3636 664523577 664522124 0.000000e+00 1581.0
22 TraesCS6A01G357700 chr6B 80.461 2037 320 39 1098 3097 664506677 664504682 0.000000e+00 1485.0
23 TraesCS6A01G357700 chr6B 93.511 786 39 6 2865 3644 664479711 664480490 0.000000e+00 1158.0
24 TraesCS6A01G357700 chr6B 89.264 503 45 6 4060 4558 664501719 664501222 5.040000e-174 621.0
25 TraesCS6A01G357700 chr6B 89.080 522 28 7 4058 4567 664521791 664521287 5.040000e-174 621.0
26 TraesCS6A01G357700 chr6B 97.458 354 9 0 2512 2865 664479316 664479669 5.080000e-169 604.0
27 TraesCS6A01G357700 chr6B 92.884 267 19 0 3657 3923 664492331 664492597 5.560000e-104 388.0
28 TraesCS6A01G357700 chr6B 89.535 172 17 1 438 608 465147944 465148115 2.780000e-52 217.0
29 TraesCS6A01G357700 chr6B 95.455 88 4 0 971 1058 664507916 664508003 1.720000e-29 141.0
30 TraesCS6A01G357700 chr6B 97.333 75 2 0 1725 1799 664508049 664508123 1.340000e-25 128.0
31 TraesCS6A01G357700 chr6B 85.057 87 11 2 298 382 664525301 664525215 2.270000e-13 87.9
32 TraesCS6A01G357700 chr3D 92.727 165 12 0 444 608 409892008 409891844 5.930000e-59 239.0
33 TraesCS6A01G357700 chr3D 97.561 41 1 0 4002 4042 295303241 295303201 2.290000e-08 71.3
34 TraesCS6A01G357700 chr3D 97.561 41 1 0 4002 4042 313051116 313051076 2.290000e-08 71.3
35 TraesCS6A01G357700 chr2D 92.727 165 12 0 444 608 47658453 47658289 5.930000e-59 239.0
36 TraesCS6A01G357700 chr4A 90.643 171 15 1 444 614 665604122 665604291 4.620000e-55 226.0
37 TraesCS6A01G357700 chr4B 89.326 178 18 1 432 608 9545111 9545288 5.970000e-54 222.0
38 TraesCS6A01G357700 chr4B 85.333 75 11 0 3659 3733 93286610 93286536 1.370000e-10 78.7
39 TraesCS6A01G357700 chr4B 85.135 74 11 0 3660 3733 28618470 28618543 4.920000e-10 76.8
40 TraesCS6A01G357700 chr4B 97.561 41 1 0 4002 4042 600515074 600515034 2.290000e-08 71.3
41 TraesCS6A01G357700 chr5D 88.889 180 17 2 430 608 513980313 513980490 7.730000e-53 219.0
42 TraesCS6A01G357700 chr5D 95.349 43 2 0 4000 4042 377106179 377106221 8.230000e-08 69.4
43 TraesCS6A01G357700 chr7B 89.143 175 18 1 444 618 537844463 537844290 2.780000e-52 217.0
44 TraesCS6A01G357700 chr1A 88.889 90 6 2 113 198 131517611 131517700 1.740000e-19 108.0
45 TraesCS6A01G357700 chr2B 86.364 88 8 4 3658 3742 721137152 721137238 4.890000e-15 93.5
46 TraesCS6A01G357700 chr2B 87.013 77 7 3 3659 3733 472909630 472909705 2.940000e-12 84.2
47 TraesCS6A01G357700 chr2B 85.333 75 11 0 3659 3733 560893394 560893468 1.370000e-10 78.7
48 TraesCS6A01G357700 chrUn 85.526 76 10 1 3659 3733 86970836 86970761 1.370000e-10 78.7
49 TraesCS6A01G357700 chr3A 86.111 72 10 0 3659 3730 420335000 420334929 1.370000e-10 78.7
50 TraesCS6A01G357700 chr3A 97.674 43 1 0 4000 4042 103020924 103020966 1.770000e-09 75.0
51 TraesCS6A01G357700 chr3A 97.561 41 1 0 4002 4042 383415774 383415734 2.290000e-08 71.3
52 TraesCS6A01G357700 chr3B 97.561 41 1 0 4002 4042 452766420 452766380 2.290000e-08 71.3


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 TraesCS6A01G357700 chr6A 587889682 587894267 4585 False 8469.000000 8469 100.000000 1 4586 1 chr6A.!!$F1 4585
1 TraesCS6A01G357700 chr6A 587968267 587972219 3952 True 1506.800000 3760 92.457667 406 4581 3 chr6A.!!$R3 4175
2 TraesCS6A01G357700 chr6A 773372 775006 1634 True 1321.000000 1321 81.538000 624 2290 1 chr6A.!!$R1 1666
3 TraesCS6A01G357700 chr6D 2133978 2136449 2471 False 1784.000000 1784 80.180000 624 3125 1 chr6D.!!$F1 2501
4 TraesCS6A01G357700 chr6D 439656265 439662552 6287 True 1569.800000 3995 92.396000 406 4580 3 chr6D.!!$R1 4174
5 TraesCS6A01G357700 chr6D 439615139 439619877 4738 False 1224.166667 4918 90.377833 1 4433 6 chr6D.!!$F4 4432
6 TraesCS6A01G357700 chr6D 4209039 4209753 714 False 473.000000 473 79.161000 1540 2290 1 chr6D.!!$F2 750
7 TraesCS6A01G357700 chr6B 664476702 664480490 3788 False 2043.333333 4368 95.911000 1 3644 3 chr6B.!!$F4 3643
8 TraesCS6A01G357700 chr6B 3799635 3801745 2110 False 1583.000000 1583 80.590000 624 2753 1 chr6B.!!$F1 2129
9 TraesCS6A01G357700 chr6B 664521287 664525301 4014 True 1121.475000 2196 88.370500 298 4567 4 chr6B.!!$R2 4269
10 TraesCS6A01G357700 chr6B 664501222 664506677 5455 True 1053.000000 1485 84.862500 1098 4558 2 chr6B.!!$R1 3460

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
59 368 1.487976 ACCGAGTACTGATAGACCGGA 59.512 52.381 20.07 0.0 38.86 5.14 F
1113 1457 3.772025 AGGAAGACAGTACCCAGATTCTG 59.228 47.826 6.70 6.7 0.00 3.02 F
2160 2568 6.758416 GGAATGATTTTTGTGCCCTTAGATTC 59.242 38.462 0.00 0.0 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1243 1587 4.035091 GGTTGCTTATACACATCGATGCAA 59.965 41.667 25.11 16.93 36.93 4.08 R
3012 3659 2.644299 TCTTGATCCAGGACCAATGTGT 59.356 45.455 0.00 0.00 0.00 3.72 R
4092 9248 0.247460 CACAGCCAATCTCGTCTCCA 59.753 55.000 0.00 0.00 0.00 3.86 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
51 360 6.096423 TGAGCAAAACTATACCGAGTACTGAT 59.904 38.462 0.00 0.00 0.00 2.90
59 368 1.487976 ACCGAGTACTGATAGACCGGA 59.512 52.381 20.07 0.00 38.86 5.14
453 763 8.660435 CCTTCTCATTTATATTTACTCCCTCCA 58.340 37.037 0.00 0.00 0.00 3.86
622 932 6.042093 CAGAGGGAGTAGCATATCTTTTGGTA 59.958 42.308 0.00 0.00 0.00 3.25
938 1282 4.276183 TGCAACATTAAATGTGTGGTACGT 59.724 37.500 0.00 0.00 44.07 3.57
944 1288 6.483974 ACATTAAATGTGTGGTACGTTCAGAA 59.516 34.615 0.00 0.00 43.01 3.02
979 1323 5.893500 TGGTGGTATAGGAATTCCAAAACA 58.106 37.500 26.22 15.98 34.65 2.83
1035 1379 4.899352 AGCCATTAGTGTGACTCTTCTT 57.101 40.909 0.00 0.00 0.00 2.52
1113 1457 3.772025 AGGAAGACAGTACCCAGATTCTG 59.228 47.826 6.70 6.70 0.00 3.02
1304 1648 7.016072 ACCCATTGTTGAAAGACCATAAAATCA 59.984 33.333 0.00 0.00 0.00 2.57
1441 1787 7.741027 TTCATCAATCTTTCTGGATATGCTC 57.259 36.000 0.00 0.00 0.00 4.26
1449 1795 9.638176 AATCTTTCTGGATATGCTCTTTTACAT 57.362 29.630 0.00 0.00 0.00 2.29
1450 1796 9.638176 ATCTTTCTGGATATGCTCTTTTACATT 57.362 29.630 0.00 0.00 0.00 2.71
2055 2423 8.405531 CAATAATGAACGGTTTAGATTCACCAT 58.594 33.333 0.00 0.00 35.28 3.55
2160 2568 6.758416 GGAATGATTTTTGTGCCCTTAGATTC 59.242 38.462 0.00 0.00 0.00 2.52
3012 3659 1.064758 GGATATGTGCAAGTCCACCCA 60.065 52.381 0.00 0.00 34.85 4.51
3077 3724 1.341482 TGGAGACCAGAGAGTAGCAGG 60.341 57.143 0.00 0.00 0.00 4.85
3097 3744 5.979517 GCAGGCATTCAAATATTCAAGGTAC 59.020 40.000 0.00 0.00 0.00 3.34
3361 4389 2.415491 CCGACAGCGTCATCAAAGTCTA 60.415 50.000 8.91 0.00 35.23 2.59
3462 4490 1.228154 GGTCAAGTTTGCGACCCCT 60.228 57.895 0.00 0.00 45.03 4.79
3479 4507 3.077695 ACCCCTGATAGATACCTAGTGGG 59.922 52.174 0.00 0.00 41.89 4.61
3510 4538 1.480954 AGCGATCCGTCCAAATACACT 59.519 47.619 0.00 0.00 0.00 3.55
3640 4700 9.209175 CTAGACAAAGCTAATAAAACAGTCACT 57.791 33.333 0.00 0.00 0.00 3.41
3655 4715 6.567687 ACAGTCACTATAGGATCGAATGAG 57.432 41.667 14.14 0.00 0.00 2.90
3704 4802 7.200434 AGAGATTTCAATACGGGCCATATAT 57.800 36.000 4.39 0.00 0.00 0.86
3705 4803 8.319057 AGAGATTTCAATACGGGCCATATATA 57.681 34.615 4.39 0.00 0.00 0.86
3741 4839 7.069986 AGTGAATGTACCCTCTACATCTGTAT 58.930 38.462 0.00 0.00 37.18 2.29
3744 4842 7.344612 TGAATGTACCCTCTACATCTGTATGTT 59.655 37.037 0.00 0.00 44.07 2.71
3746 4844 5.955959 TGTACCCTCTACATCTGTATGTTGT 59.044 40.000 0.00 0.00 44.07 3.32
3752 4850 7.255312 CCCTCTACATCTGTATGTTGTCTCTAC 60.255 44.444 0.00 0.00 44.07 2.59
3753 4851 7.255312 CCTCTACATCTGTATGTTGTCTCTACC 60.255 44.444 0.00 0.00 44.07 3.18
3758 4856 5.190677 TCTGTATGTTGTCTCTACCGATGA 58.809 41.667 0.00 0.00 0.00 2.92
3762 4860 6.978659 TGTATGTTGTCTCTACCGATGAAATC 59.021 38.462 0.00 0.00 40.89 2.17
3768 4866 7.640597 TGTCTCTACCGATGAAATCTCTAAA 57.359 36.000 0.00 0.00 42.58 1.85
3791 4889 8.553459 AAAAGGCTTATATATCATGGAGTTCG 57.447 34.615 0.00 0.00 0.00 3.95
3895 5032 1.407575 GGAGGGAGTAGAAAAGCCAGC 60.408 57.143 0.00 0.00 0.00 4.85
3897 5034 0.328258 GGGAGTAGAAAAGCCAGCCA 59.672 55.000 0.00 0.00 0.00 4.75
3898 5035 1.064389 GGGAGTAGAAAAGCCAGCCAT 60.064 52.381 0.00 0.00 0.00 4.40
3899 5036 2.019984 GGAGTAGAAAAGCCAGCCATG 58.980 52.381 0.00 0.00 0.00 3.66
3947 8584 4.675029 CTCCGCGGTCCGTTGGTT 62.675 66.667 27.15 0.00 34.38 3.67
3948 8585 4.668118 TCCGCGGTCCGTTGGTTC 62.668 66.667 27.15 0.12 34.38 3.62
3949 8586 4.675029 CCGCGGTCCGTTGGTTCT 62.675 66.667 19.50 0.00 34.38 3.01
3950 8587 2.259204 CGCGGTCCGTTGGTTCTA 59.741 61.111 13.94 0.00 0.00 2.10
3951 8588 2.090524 CGCGGTCCGTTGGTTCTAC 61.091 63.158 13.94 0.00 0.00 2.59
3952 8589 1.291272 GCGGTCCGTTGGTTCTACT 59.709 57.895 13.94 0.00 0.00 2.57
3953 8590 0.320160 GCGGTCCGTTGGTTCTACTT 60.320 55.000 13.94 0.00 0.00 2.24
3954 8591 1.875157 GCGGTCCGTTGGTTCTACTTT 60.875 52.381 13.94 0.00 0.00 2.66
3955 8592 2.486918 CGGTCCGTTGGTTCTACTTTT 58.513 47.619 2.08 0.00 0.00 2.27
3956 8593 3.652274 CGGTCCGTTGGTTCTACTTTTA 58.348 45.455 2.08 0.00 0.00 1.52
3957 8594 4.248058 CGGTCCGTTGGTTCTACTTTTAT 58.752 43.478 2.08 0.00 0.00 1.40
3958 8595 4.328169 CGGTCCGTTGGTTCTACTTTTATC 59.672 45.833 2.08 0.00 0.00 1.75
3959 8596 5.485620 GGTCCGTTGGTTCTACTTTTATCT 58.514 41.667 0.00 0.00 0.00 1.98
3960 8597 5.350640 GGTCCGTTGGTTCTACTTTTATCTG 59.649 44.000 0.00 0.00 0.00 2.90
3961 8598 6.161381 GTCCGTTGGTTCTACTTTTATCTGA 58.839 40.000 0.00 0.00 0.00 3.27
3962 8599 6.310711 GTCCGTTGGTTCTACTTTTATCTGAG 59.689 42.308 0.00 0.00 0.00 3.35
3963 8600 5.063564 CCGTTGGTTCTACTTTTATCTGAGC 59.936 44.000 0.00 0.00 0.00 4.26
3964 8601 5.637810 CGTTGGTTCTACTTTTATCTGAGCA 59.362 40.000 0.00 0.00 0.00 4.26
3965 8602 6.313905 CGTTGGTTCTACTTTTATCTGAGCAT 59.686 38.462 0.00 0.00 0.00 3.79
3966 8603 7.467623 GTTGGTTCTACTTTTATCTGAGCATG 58.532 38.462 0.00 0.00 0.00 4.06
3967 8604 6.115446 TGGTTCTACTTTTATCTGAGCATGG 58.885 40.000 0.00 0.00 0.00 3.66
3968 8605 6.116126 GGTTCTACTTTTATCTGAGCATGGT 58.884 40.000 0.00 0.00 0.00 3.55
3969 8606 6.037610 GGTTCTACTTTTATCTGAGCATGGTG 59.962 42.308 0.00 0.00 0.00 4.17
3970 8607 6.544928 TCTACTTTTATCTGAGCATGGTGA 57.455 37.500 0.00 0.00 0.00 4.02
3971 8608 6.341316 TCTACTTTTATCTGAGCATGGTGAC 58.659 40.000 0.00 0.00 0.00 3.67
3972 8609 4.265073 ACTTTTATCTGAGCATGGTGACC 58.735 43.478 0.00 0.00 0.00 4.02
3973 8610 3.281727 TTTATCTGAGCATGGTGACCC 57.718 47.619 0.00 0.00 0.00 4.46
3974 8611 0.752658 TATCTGAGCATGGTGACCCG 59.247 55.000 0.00 0.00 0.00 5.28
3975 8612 1.267574 ATCTGAGCATGGTGACCCGT 61.268 55.000 0.00 0.00 0.00 5.28
3976 8613 1.003355 CTGAGCATGGTGACCCGTT 60.003 57.895 0.00 0.00 0.00 4.44
3977 8614 1.300971 CTGAGCATGGTGACCCGTTG 61.301 60.000 0.00 0.00 0.00 4.10
3978 8615 2.034066 AGCATGGTGACCCGTTGG 59.966 61.111 0.00 0.00 37.80 3.77
3992 8629 4.248058 ACCCGTTGGTTCTACTTTTATCG 58.752 43.478 0.00 0.00 44.75 2.92
3993 8630 4.021192 ACCCGTTGGTTCTACTTTTATCGA 60.021 41.667 0.00 0.00 44.75 3.59
3994 8631 4.328169 CCCGTTGGTTCTACTTTTATCGAC 59.672 45.833 0.00 0.00 0.00 4.20
3998 8635 5.733620 TGGTTCTACTTTTATCGACAGGT 57.266 39.130 0.00 0.00 0.00 4.00
4007 8644 7.611213 ACTTTTATCGACAGGTTTAGATTGG 57.389 36.000 0.00 0.00 0.00 3.16
4011 8648 5.670792 ATCGACAGGTTTAGATTGGTACA 57.329 39.130 0.00 0.00 0.00 2.90
4012 8649 5.670792 TCGACAGGTTTAGATTGGTACAT 57.329 39.130 0.00 0.00 39.30 2.29
4013 8650 5.416083 TCGACAGGTTTAGATTGGTACATG 58.584 41.667 0.00 0.00 39.30 3.21
4014 8651 5.046878 TCGACAGGTTTAGATTGGTACATGT 60.047 40.000 2.69 2.69 39.30 3.21
4016 8653 5.253330 ACAGGTTTAGATTGGTACATGTGG 58.747 41.667 9.11 0.00 39.30 4.17
4018 8655 4.291249 AGGTTTAGATTGGTACATGTGGGT 59.709 41.667 9.11 0.00 39.30 4.51
4019 8656 5.014202 GGTTTAGATTGGTACATGTGGGTT 58.986 41.667 9.11 0.00 39.30 4.11
4020 8657 5.105917 GGTTTAGATTGGTACATGTGGGTTG 60.106 44.000 9.11 0.00 39.30 3.77
4021 8658 2.446435 AGATTGGTACATGTGGGTTGC 58.554 47.619 9.11 0.00 39.30 4.17
4023 8660 3.265737 AGATTGGTACATGTGGGTTGCTA 59.734 43.478 9.11 0.00 39.30 3.49
4024 8661 2.779755 TGGTACATGTGGGTTGCTAG 57.220 50.000 9.11 0.00 0.00 3.42
4025 8662 1.982226 TGGTACATGTGGGTTGCTAGT 59.018 47.619 9.11 0.00 0.00 2.57
4027 8664 3.196901 TGGTACATGTGGGTTGCTAGTAG 59.803 47.826 9.11 0.00 0.00 2.57
4028 8665 3.197116 GGTACATGTGGGTTGCTAGTAGT 59.803 47.826 9.11 0.00 0.00 2.73
4029 8666 3.334583 ACATGTGGGTTGCTAGTAGTG 57.665 47.619 0.00 0.00 0.00 2.74
4030 8667 2.637872 ACATGTGGGTTGCTAGTAGTGT 59.362 45.455 0.00 0.00 0.00 3.55
4033 8670 4.959560 TGTGGGTTGCTAGTAGTGTTAA 57.040 40.909 0.00 0.00 0.00 2.01
4034 8671 5.492855 TGTGGGTTGCTAGTAGTGTTAAT 57.507 39.130 0.00 0.00 0.00 1.40
4035 8672 5.871834 TGTGGGTTGCTAGTAGTGTTAATT 58.128 37.500 0.00 0.00 0.00 1.40
4036 8673 7.006865 TGTGGGTTGCTAGTAGTGTTAATTA 57.993 36.000 0.00 0.00 0.00 1.40
4037 8674 7.626390 TGTGGGTTGCTAGTAGTGTTAATTAT 58.374 34.615 0.00 0.00 0.00 1.28
4038 8675 8.760735 TGTGGGTTGCTAGTAGTGTTAATTATA 58.239 33.333 0.00 0.00 0.00 0.98
4039 8676 9.774413 GTGGGTTGCTAGTAGTGTTAATTATAT 57.226 33.333 0.00 0.00 0.00 0.86
4040 8677 9.991906 TGGGTTGCTAGTAGTGTTAATTATATC 57.008 33.333 0.00 0.00 0.00 1.63
4074 9230 1.270625 CCGTTGGTTCTACCTGAGCAA 60.271 52.381 0.00 0.00 39.58 3.91
4081 9237 1.905637 TCTACCTGAGCAACGACTCA 58.094 50.000 7.21 7.21 44.32 3.41
4092 9248 2.494059 CAACGACTCATCCTTGTGGTT 58.506 47.619 0.00 0.00 35.96 3.67
4102 9258 0.679505 CCTTGTGGTTGGAGACGAGA 59.320 55.000 0.00 0.00 0.00 4.04
4108 9264 0.250513 GGTTGGAGACGAGATTGGCT 59.749 55.000 0.00 0.00 0.00 4.75
4282 9438 4.681421 CACGCCTTGCTCTCTTCA 57.319 55.556 0.00 0.00 0.00 3.02
4454 9622 5.927281 AATCAATGGGAATTCAGTTCAGG 57.073 39.130 7.93 0.00 38.64 3.86
4533 9713 1.303888 TGGACGGTACCTCGAGCTT 60.304 57.895 10.90 0.00 0.00 3.74
4573 9753 0.598680 CGCATTCCTCCTCATCGTCC 60.599 60.000 0.00 0.00 0.00 4.79
4581 9761 0.034380 TCCTCATCGTCCTCCTCGTT 60.034 55.000 0.00 0.00 0.00 3.85
4582 9762 0.101399 CCTCATCGTCCTCCTCGTTG 59.899 60.000 0.00 0.00 0.00 4.10
4583 9763 0.811915 CTCATCGTCCTCCTCGTTGT 59.188 55.000 0.00 0.00 32.27 3.32
4584 9764 0.809385 TCATCGTCCTCCTCGTTGTC 59.191 55.000 0.00 0.00 32.27 3.18
4585 9765 0.811915 CATCGTCCTCCTCGTTGTCT 59.188 55.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 325 7.064134 CGGTATAGTTTTGCTCAGTGTGATTTA 59.936 37.037 0.00 0.00 0.00 1.40
38 347 2.700371 TCCGGTCTATCAGTACTCGGTA 59.300 50.000 14.39 2.08 37.54 4.02
39 348 1.487976 TCCGGTCTATCAGTACTCGGT 59.512 52.381 14.39 1.08 37.54 4.69
75 384 2.028748 GCTTAGGTAGAACCAACGGACA 60.029 50.000 0.00 0.00 41.95 4.02
231 540 0.324645 ATCCAAAGCGAAGGGCCAAT 60.325 50.000 6.18 0.00 45.17 3.16
491 801 5.926542 GTCTATGTGCATCCGTATGTTGTAT 59.073 40.000 0.00 0.00 35.38 2.29
593 903 6.567602 AAGATATGCTACTCCCTCTGTTTT 57.432 37.500 0.00 0.00 0.00 2.43
594 904 6.567602 AAAGATATGCTACTCCCTCTGTTT 57.432 37.500 0.00 0.00 0.00 2.83
979 1323 7.595819 TCATTGTTAGAACCTGGAATTGTTT 57.404 32.000 0.00 0.00 0.00 2.83
1035 1379 5.810587 GGTCGCTAGAACAAGAAATGACATA 59.189 40.000 0.00 0.00 33.32 2.29
1243 1587 4.035091 GGTTGCTTATACACATCGATGCAA 59.965 41.667 25.11 16.93 36.93 4.08
1472 1834 7.122055 TGTCAAAAGGTTGTCACTTTAGTTCAT 59.878 33.333 0.00 0.00 37.18 2.57
2618 3187 3.385384 TGAGTCCTGCCCTCTGCG 61.385 66.667 0.00 0.00 45.60 5.18
2942 3589 4.870426 TCTTTGAATAGCCATCGAACTGTC 59.130 41.667 0.00 0.00 0.00 3.51
3012 3659 2.644299 TCTTGATCCAGGACCAATGTGT 59.356 45.455 0.00 0.00 0.00 3.72
3127 3774 8.229253 TGTACATGGTACGTACTTGAGATATT 57.771 34.615 24.07 8.68 39.96 1.28
3130 3777 6.519679 TTGTACATGGTACGTACTTGAGAT 57.480 37.500 24.07 9.85 39.96 2.75
3131 3778 5.963176 TTGTACATGGTACGTACTTGAGA 57.037 39.130 24.07 12.76 39.96 3.27
3200 4223 7.930217 TGATTTCGGCTCCTAAAATAATTCAG 58.070 34.615 0.00 0.00 0.00 3.02
3380 4408 3.005367 TCCAAATCCTTCCGAAGCAAAAC 59.995 43.478 2.27 0.00 0.00 2.43
3479 4507 1.227002 GGATCGCTCGACCCTTGAC 60.227 63.158 0.00 0.00 0.00 3.18
3480 4508 2.771639 CGGATCGCTCGACCCTTGA 61.772 63.158 0.74 0.00 0.00 3.02
3483 4511 3.210528 GACGGATCGCTCGACCCT 61.211 66.667 0.74 0.00 0.00 4.34
3510 4538 4.590918 TGCTAATTTCAAATCCACCCGTA 58.409 39.130 0.00 0.00 0.00 4.02
3644 4704 8.879759 TGTATTTAGAAACAACTCATTCGATCC 58.120 33.333 0.00 0.00 0.00 3.36
3647 4707 9.268268 ACTTGTATTTAGAAACAACTCATTCGA 57.732 29.630 0.00 0.00 32.43 3.71
3691 4789 7.681679 TCATTTTGTTCTATATATGGCCCGTA 58.318 34.615 0.00 0.00 0.00 4.02
3692 4790 6.539173 TCATTTTGTTCTATATATGGCCCGT 58.461 36.000 0.00 0.00 0.00 5.28
3704 4802 7.458397 AGGGTACATTCACTCATTTTGTTCTA 58.542 34.615 0.00 0.00 0.00 2.10
3705 4803 6.306987 AGGGTACATTCACTCATTTTGTTCT 58.693 36.000 0.00 0.00 0.00 3.01
3727 4825 6.707440 AGAGACAACATACAGATGTAGAGG 57.293 41.667 0.00 0.00 45.93 3.69
3741 4839 5.419155 AGAGATTTCATCGGTAGAGACAACA 59.581 40.000 0.00 0.00 0.00 3.33
3744 4842 7.640597 TTTAGAGATTTCATCGGTAGAGACA 57.359 36.000 0.00 0.00 0.00 3.41
3746 4844 7.684670 GCCTTTTAGAGATTTCATCGGTAGAGA 60.685 40.741 0.00 0.00 0.00 3.10
3752 4850 7.736447 ATAAGCCTTTTAGAGATTTCATCGG 57.264 36.000 0.00 0.00 0.00 4.18
3768 4866 6.213600 ACCGAACTCCATGATATATAAGCCTT 59.786 38.462 0.00 0.00 0.00 4.35
3791 4889 1.797046 CTCGCTATCATCATGCACACC 59.203 52.381 0.00 0.00 0.00 4.16
3895 5032 0.961019 CGCAACCATTATCCCCATGG 59.039 55.000 4.14 4.14 46.07 3.66
3897 5034 1.813862 CGTCGCAACCATTATCCCCAT 60.814 52.381 0.00 0.00 0.00 4.00
3898 5035 0.462937 CGTCGCAACCATTATCCCCA 60.463 55.000 0.00 0.00 0.00 4.96
3899 5036 1.164041 CCGTCGCAACCATTATCCCC 61.164 60.000 0.00 0.00 0.00 4.81
3932 8569 3.285523 TAGAACCAACGGACCGCGG 62.286 63.158 26.86 26.86 0.00 6.46
3933 8570 2.090524 GTAGAACCAACGGACCGCG 61.091 63.158 15.39 5.23 0.00 6.46
3934 8571 0.320160 AAGTAGAACCAACGGACCGC 60.320 55.000 15.39 0.00 0.00 5.68
3935 8572 2.159327 AAAGTAGAACCAACGGACCG 57.841 50.000 13.61 13.61 0.00 4.79
3936 8573 5.350640 CAGATAAAAGTAGAACCAACGGACC 59.649 44.000 0.00 0.00 0.00 4.46
3937 8574 6.161381 TCAGATAAAAGTAGAACCAACGGAC 58.839 40.000 0.00 0.00 0.00 4.79
3938 8575 6.349243 TCAGATAAAAGTAGAACCAACGGA 57.651 37.500 0.00 0.00 0.00 4.69
3940 8577 5.637810 TGCTCAGATAAAAGTAGAACCAACG 59.362 40.000 0.00 0.00 0.00 4.10
3941 8578 7.414540 CCATGCTCAGATAAAAGTAGAACCAAC 60.415 40.741 0.00 0.00 0.00 3.77
3942 8579 6.599244 CCATGCTCAGATAAAAGTAGAACCAA 59.401 38.462 0.00 0.00 0.00 3.67
3943 8580 6.115446 CCATGCTCAGATAAAAGTAGAACCA 58.885 40.000 0.00 0.00 0.00 3.67
3944 8581 6.037610 CACCATGCTCAGATAAAAGTAGAACC 59.962 42.308 0.00 0.00 0.00 3.62
3945 8582 6.818644 TCACCATGCTCAGATAAAAGTAGAAC 59.181 38.462 0.00 0.00 0.00 3.01
3946 8583 6.818644 GTCACCATGCTCAGATAAAAGTAGAA 59.181 38.462 0.00 0.00 0.00 2.10
3947 8584 6.341316 GTCACCATGCTCAGATAAAAGTAGA 58.659 40.000 0.00 0.00 0.00 2.59
3948 8585 5.525378 GGTCACCATGCTCAGATAAAAGTAG 59.475 44.000 0.00 0.00 0.00 2.57
3949 8586 5.428253 GGTCACCATGCTCAGATAAAAGTA 58.572 41.667 0.00 0.00 0.00 2.24
3950 8587 4.265073 GGTCACCATGCTCAGATAAAAGT 58.735 43.478 0.00 0.00 0.00 2.66
3951 8588 3.629398 GGGTCACCATGCTCAGATAAAAG 59.371 47.826 0.00 0.00 36.50 2.27
3952 8589 3.620488 GGGTCACCATGCTCAGATAAAA 58.380 45.455 0.00 0.00 36.50 1.52
3953 8590 2.419990 CGGGTCACCATGCTCAGATAAA 60.420 50.000 0.00 0.00 36.13 1.40
3954 8591 1.138859 CGGGTCACCATGCTCAGATAA 59.861 52.381 0.00 0.00 36.13 1.75
3955 8592 0.752658 CGGGTCACCATGCTCAGATA 59.247 55.000 0.00 0.00 36.13 1.98
3956 8593 1.267574 ACGGGTCACCATGCTCAGAT 61.268 55.000 0.00 0.00 36.13 2.90
3957 8594 1.480212 AACGGGTCACCATGCTCAGA 61.480 55.000 0.00 0.00 36.13 3.27
3958 8595 1.003355 AACGGGTCACCATGCTCAG 60.003 57.895 0.00 0.00 36.13 3.35
3959 8596 1.302431 CAACGGGTCACCATGCTCA 60.302 57.895 0.00 0.00 36.13 4.26
3960 8597 2.040544 CCAACGGGTCACCATGCTC 61.041 63.158 0.00 0.00 36.13 4.26
3961 8598 2.034066 CCAACGGGTCACCATGCT 59.966 61.111 0.00 0.00 36.13 3.79
3971 8608 4.328169 GTCGATAAAAGTAGAACCAACGGG 59.672 45.833 0.00 0.00 41.29 5.28
3972 8609 4.925054 TGTCGATAAAAGTAGAACCAACGG 59.075 41.667 0.00 0.00 0.00 4.44
3973 8610 5.061808 CCTGTCGATAAAAGTAGAACCAACG 59.938 44.000 0.00 0.00 0.00 4.10
3974 8611 5.930569 ACCTGTCGATAAAAGTAGAACCAAC 59.069 40.000 0.00 0.00 0.00 3.77
3975 8612 6.105397 ACCTGTCGATAAAAGTAGAACCAA 57.895 37.500 0.00 0.00 0.00 3.67
3976 8613 5.733620 ACCTGTCGATAAAAGTAGAACCA 57.266 39.130 0.00 0.00 0.00 3.67
3977 8614 8.031277 TCTAAACCTGTCGATAAAAGTAGAACC 58.969 37.037 0.00 0.00 0.00 3.62
3978 8615 8.976986 TCTAAACCTGTCGATAAAAGTAGAAC 57.023 34.615 0.00 0.00 0.00 3.01
3980 8617 9.582431 CAATCTAAACCTGTCGATAAAAGTAGA 57.418 33.333 0.00 0.00 0.00 2.59
3981 8618 8.818057 CCAATCTAAACCTGTCGATAAAAGTAG 58.182 37.037 0.00 0.00 0.00 2.57
3982 8619 8.316214 ACCAATCTAAACCTGTCGATAAAAGTA 58.684 33.333 0.00 0.00 0.00 2.24
3983 8620 7.166167 ACCAATCTAAACCTGTCGATAAAAGT 58.834 34.615 0.00 0.00 0.00 2.66
3984 8621 7.611213 ACCAATCTAAACCTGTCGATAAAAG 57.389 36.000 0.00 0.00 0.00 2.27
3985 8622 8.095792 TGTACCAATCTAAACCTGTCGATAAAA 58.904 33.333 0.00 0.00 0.00 1.52
3986 8623 7.613585 TGTACCAATCTAAACCTGTCGATAAA 58.386 34.615 0.00 0.00 0.00 1.40
3987 8624 7.172868 TGTACCAATCTAAACCTGTCGATAA 57.827 36.000 0.00 0.00 0.00 1.75
3988 8625 6.778834 TGTACCAATCTAAACCTGTCGATA 57.221 37.500 0.00 0.00 0.00 2.92
3989 8626 5.670792 TGTACCAATCTAAACCTGTCGAT 57.329 39.130 0.00 0.00 0.00 3.59
3990 8627 5.046878 ACATGTACCAATCTAAACCTGTCGA 60.047 40.000 0.00 0.00 0.00 4.20
3991 8628 5.063438 CACATGTACCAATCTAAACCTGTCG 59.937 44.000 0.00 0.00 0.00 4.35
3992 8629 5.354234 CCACATGTACCAATCTAAACCTGTC 59.646 44.000 0.00 0.00 0.00 3.51
3993 8630 5.253330 CCACATGTACCAATCTAAACCTGT 58.747 41.667 0.00 0.00 0.00 4.00
3994 8631 4.640201 CCCACATGTACCAATCTAAACCTG 59.360 45.833 0.00 0.00 0.00 4.00
3998 8635 4.461081 GCAACCCACATGTACCAATCTAAA 59.539 41.667 0.00 0.00 0.00 1.85
4007 8644 4.181578 CACTACTAGCAACCCACATGTAC 58.818 47.826 0.00 0.00 0.00 2.90
4011 8648 5.492855 TTAACACTACTAGCAACCCACAT 57.507 39.130 0.00 0.00 0.00 3.21
4012 8649 4.959560 TTAACACTACTAGCAACCCACA 57.040 40.909 0.00 0.00 0.00 4.17
4013 8650 9.774413 ATATAATTAACACTACTAGCAACCCAC 57.226 33.333 0.00 0.00 0.00 4.61
4014 8651 9.991906 GATATAATTAACACTACTAGCAACCCA 57.008 33.333 0.00 0.00 0.00 4.51
4025 8662 9.556030 CGCGAAGATGAGATATAATTAACACTA 57.444 33.333 0.00 0.00 0.00 2.74
4027 8664 7.328737 ACCGCGAAGATGAGATATAATTAACAC 59.671 37.037 8.23 0.00 0.00 3.32
4028 8665 7.375834 ACCGCGAAGATGAGATATAATTAACA 58.624 34.615 8.23 0.00 0.00 2.41
4029 8666 7.009357 GGACCGCGAAGATGAGATATAATTAAC 59.991 40.741 8.23 0.00 0.00 2.01
4030 8667 7.033791 GGACCGCGAAGATGAGATATAATTAA 58.966 38.462 8.23 0.00 0.00 1.40
4033 8670 4.438880 CGGACCGCGAAGATGAGATATAAT 60.439 45.833 8.23 0.00 0.00 1.28
4034 8671 3.119955 CGGACCGCGAAGATGAGATATAA 60.120 47.826 8.23 0.00 0.00 0.98
4035 8672 2.418976 CGGACCGCGAAGATGAGATATA 59.581 50.000 8.23 0.00 0.00 0.86
4036 8673 1.200252 CGGACCGCGAAGATGAGATAT 59.800 52.381 8.23 0.00 0.00 1.63
4037 8674 0.591659 CGGACCGCGAAGATGAGATA 59.408 55.000 8.23 0.00 0.00 1.98
4038 8675 1.360551 CGGACCGCGAAGATGAGAT 59.639 57.895 8.23 0.00 0.00 2.75
4039 8676 1.592400 AACGGACCGCGAAGATGAGA 61.592 55.000 15.39 0.00 0.00 3.27
4040 8677 1.153823 AACGGACCGCGAAGATGAG 60.154 57.895 15.39 0.00 0.00 2.90
4041 8678 1.445410 CAACGGACCGCGAAGATGA 60.445 57.895 15.39 0.00 0.00 2.92
4042 8679 2.452813 CCAACGGACCGCGAAGATG 61.453 63.158 15.39 3.74 0.00 2.90
4044 8681 3.154584 AACCAACGGACCGCGAAGA 62.155 57.895 15.39 0.00 0.00 2.87
4045 8682 2.663852 AACCAACGGACCGCGAAG 60.664 61.111 15.39 2.82 0.00 3.79
4046 8683 1.804396 TAGAACCAACGGACCGCGAA 61.804 55.000 15.39 0.00 0.00 4.70
4047 8684 2.267351 TAGAACCAACGGACCGCGA 61.267 57.895 15.39 0.00 0.00 5.87
4049 8686 1.739196 GGTAGAACCAACGGACCGC 60.739 63.158 15.39 0.00 38.42 5.68
4050 8687 0.389426 CAGGTAGAACCAACGGACCG 60.389 60.000 13.61 13.61 41.95 4.79
4074 9230 1.270839 CCAACCACAAGGATGAGTCGT 60.271 52.381 0.00 0.00 39.92 4.34
4081 9237 1.276421 CTCGTCTCCAACCACAAGGAT 59.724 52.381 0.00 0.00 38.69 3.24
4092 9248 0.247460 CACAGCCAATCTCGTCTCCA 59.753 55.000 0.00 0.00 0.00 3.86
4123 9279 2.992114 AAGGAGCGCGAGGTGTCT 60.992 61.111 12.10 0.00 45.11 3.41
4282 9438 1.683629 GGAGACACTGACGAGGAGGAT 60.684 57.143 0.00 0.00 0.00 3.24
4454 9622 0.310543 TGTGCCAATTTGACGCTGTC 59.689 50.000 0.00 2.32 0.00 3.51
4517 9697 0.456312 CACAAGCTCGAGGTACCGTC 60.456 60.000 18.94 3.83 0.00 4.79
4533 9713 4.492160 GACCGCGGCGAGATCACA 62.492 66.667 28.58 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.