Multiple sequence alignment - TraesCS6A01G246600

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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 TraesCS6A01G246600 chr6A 100.000 3977 0 0 1 3977 457607877 457603901 0.000000e+00 7345
1 TraesCS6A01G246600 chr6A 98.008 3766 71 4 1 3764 457590474 457586711 0.000000e+00 6536
2 TraesCS6A01G246600 chr6A 96.460 226 8 0 6 231 457598258 457598033 1.350000e-99 374
3 TraesCS6A01G246600 chr6A 95.175 228 10 1 5 231 281758485 281758258 3.780000e-95 359
4 TraesCS6A01G246600 chr6A 95.175 228 10 1 5 231 603165648 603165421 3.780000e-95 359
5 TraesCS6A01G246600 chr6A 94.397 232 11 2 1 230 290768960 290768729 4.890000e-94 355
6 TraesCS6A01G246600 chr6A 86.100 259 27 8 5 257 262725735 262725480 1.820000e-68 270
7 TraesCS6A01G246600 chr1B 97.195 3494 90 7 271 3761 374331158 374334646 0.000000e+00 5903
8 TraesCS6A01G246600 chr1B 95.813 2508 97 7 1257 3761 53735521 53738023 0.000000e+00 4043
9 TraesCS6A01G246600 chr5A 96.922 3509 83 10 271 3760 704588933 704585431 0.000000e+00 5858
10 TraesCS6A01G246600 chr5A 93.671 237 13 2 1 235 42541752 42541516 1.760000e-93 353
11 TraesCS6A01G246600 chr5A 87.097 248 28 4 6 252 362097875 362097631 1.090000e-70 278
12 TraesCS6A01G246600 chr5A 79.592 196 31 1 3786 3972 607578616 607578421 8.970000e-27 132
13 TraesCS6A01G246600 chr3B 96.959 3453 86 9 324 3760 725369177 725372626 0.000000e+00 5777
14 TraesCS6A01G246600 chr2D 95.627 3339 128 8 438 3761 532131023 532134358 0.000000e+00 5341
15 TraesCS6A01G246600 chr2D 90.557 2478 205 15 1290 3762 203441432 203443885 0.000000e+00 3253
16 TraesCS6A01G246600 chr3D 95.424 2841 97 11 922 3760 194684651 194687460 0.000000e+00 4495
17 TraesCS6A01G246600 chr3D 93.262 564 32 5 271 830 194684096 194684657 0.000000e+00 826
18 TraesCS6A01G246600 chrUn 96.923 1950 59 1 317 2266 62697818 62695870 0.000000e+00 3267
19 TraesCS6A01G246600 chrUn 94.178 1666 74 14 343 1993 235724950 235726607 0.000000e+00 2518
20 TraesCS6A01G246600 chrUn 94.178 1666 74 14 343 1993 289922402 289924059 0.000000e+00 2518
21 TraesCS6A01G246600 chrUn 94.178 1666 74 14 343 1993 322256154 322257811 0.000000e+00 2518
22 TraesCS6A01G246600 chr5D 93.329 1664 79 12 271 1910 520750868 520752523 0.000000e+00 2429
23 TraesCS6A01G246600 chr5D 90.521 1171 65 19 271 1411 46342295 46341141 0.000000e+00 1506
24 TraesCS6A01G246600 chr4A 84.942 2258 314 22 1317 3557 697887526 697889774 0.000000e+00 2263
25 TraesCS6A01G246600 chr4A 89.764 254 17 7 1 248 329101604 329101854 2.310000e-82 316
26 TraesCS6A01G246600 chr4A 85.772 246 30 5 6 250 339782197 339781956 5.100000e-64 255
27 TraesCS6A01G246600 chr1A 89.782 734 47 9 271 983 45851137 45850411 0.000000e+00 915
28 TraesCS6A01G246600 chr6B 88.706 425 23 4 267 684 437149003 437148597 2.760000e-136 496
29 TraesCS6A01G246600 chr6B 93.392 227 6 1 3760 3977 503006013 503006239 1.070000e-85 327
30 TraesCS6A01G246600 chr7A 95.563 293 12 1 3469 3761 40877625 40877334 6.020000e-128 468
31 TraesCS6A01G246600 chr7A 88.142 253 26 4 1 250 368656083 368656334 8.360000e-77 298
32 TraesCS6A01G246600 chr7A 85.906 149 13 6 124 267 388528582 388528727 6.880000e-33 152
33 TraesCS6A01G246600 chr3A 94.850 233 10 2 1 231 198043671 198043903 2.920000e-96 363
34 TraesCS6A01G246600 chr2A 89.535 258 19 8 7 257 702929067 702929323 1.780000e-83 320
35 TraesCS6A01G246600 chr2A 90.123 243 21 2 7 248 342255587 342255347 2.980000e-81 313
36 TraesCS6A01G246600 chr6D 89.744 234 8 3 3760 3977 320071119 320070886 6.500000e-73 285
37 TraesCS6A01G246600 chr1D 81.773 203 24 8 3779 3970 402135706 402135906 1.480000e-34 158
38 TraesCS6A01G246600 chr2B 89.320 103 8 3 271 371 744182728 744182829 4.170000e-25 126


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 TraesCS6A01G246600 chr6A 457603901 457607877 3976 True 7345.0 7345 100.000 1 3977 1 chr6A.!!$R6 3976
1 TraesCS6A01G246600 chr6A 457586711 457590474 3763 True 6536.0 6536 98.008 1 3764 1 chr6A.!!$R4 3763
2 TraesCS6A01G246600 chr1B 374331158 374334646 3488 False 5903.0 5903 97.195 271 3761 1 chr1B.!!$F2 3490
3 TraesCS6A01G246600 chr1B 53735521 53738023 2502 False 4043.0 4043 95.813 1257 3761 1 chr1B.!!$F1 2504
4 TraesCS6A01G246600 chr5A 704585431 704588933 3502 True 5858.0 5858 96.922 271 3760 1 chr5A.!!$R4 3489
5 TraesCS6A01G246600 chr3B 725369177 725372626 3449 False 5777.0 5777 96.959 324 3760 1 chr3B.!!$F1 3436
6 TraesCS6A01G246600 chr2D 532131023 532134358 3335 False 5341.0 5341 95.627 438 3761 1 chr2D.!!$F2 3323
7 TraesCS6A01G246600 chr2D 203441432 203443885 2453 False 3253.0 3253 90.557 1290 3762 1 chr2D.!!$F1 2472
8 TraesCS6A01G246600 chr3D 194684096 194687460 3364 False 2660.5 4495 94.343 271 3760 2 chr3D.!!$F1 3489
9 TraesCS6A01G246600 chrUn 62695870 62697818 1948 True 3267.0 3267 96.923 317 2266 1 chrUn.!!$R1 1949
10 TraesCS6A01G246600 chrUn 235724950 235726607 1657 False 2518.0 2518 94.178 343 1993 1 chrUn.!!$F1 1650
11 TraesCS6A01G246600 chrUn 289922402 289924059 1657 False 2518.0 2518 94.178 343 1993 1 chrUn.!!$F2 1650
12 TraesCS6A01G246600 chrUn 322256154 322257811 1657 False 2518.0 2518 94.178 343 1993 1 chrUn.!!$F3 1650
13 TraesCS6A01G246600 chr5D 520750868 520752523 1655 False 2429.0 2429 93.329 271 1910 1 chr5D.!!$F1 1639
14 TraesCS6A01G246600 chr5D 46341141 46342295 1154 True 1506.0 1506 90.521 271 1411 1 chr5D.!!$R1 1140
15 TraesCS6A01G246600 chr4A 697887526 697889774 2248 False 2263.0 2263 84.942 1317 3557 1 chr4A.!!$F2 2240
16 TraesCS6A01G246600 chr1A 45850411 45851137 726 True 915.0 915 89.782 271 983 1 chr1A.!!$R1 712

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
214 216 1.003355 AAGACACCTGGCACATCGG 60.003 57.895 0.00 0.0 38.20 4.18 F
242 244 2.223340 GGCGTTACAAGGATGCAGATTG 60.223 50.000 0.00 0.0 0.00 2.67 F
1266 1351 0.886490 CGCAAGAGGTTGAGGTTGCT 60.886 55.000 4.56 0.0 42.55 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1182 1266 1.000955 ACAACCTCAACCTCTACTGCG 59.999 52.381 0.00 0.0 0.0 5.18 R
1748 1836 3.066621 TCGCTGAGCAACTTTGTCAATTT 59.933 39.130 4.88 0.0 0.0 1.82 R
3206 3322 6.541641 GCTCCATCAATATCTTTGTGTTCTCT 59.458 38.462 0.00 0.0 0.0 3.10 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
126 128 9.142515 GATGCAAGTTTTAAAACATGATGATGA 57.857 29.630 30.41 12.73 39.28 2.92
206 208 3.262420 CGAATAACTGGAAGACACCTGG 58.738 50.000 0.00 0.00 37.43 4.45
213 215 1.021390 GGAAGACACCTGGCACATCG 61.021 60.000 0.00 0.00 38.20 3.84
214 216 1.003355 AAGACACCTGGCACATCGG 60.003 57.895 0.00 0.00 38.20 4.18
224 226 4.873129 CACATCGGTCTCGGGGCG 62.873 72.222 0.00 0.00 36.95 6.13
242 244 2.223340 GGCGTTACAAGGATGCAGATTG 60.223 50.000 0.00 0.00 0.00 2.67
254 256 4.581824 GGATGCAGATTGATAGCCAAAGAA 59.418 41.667 0.00 0.00 38.43 2.52
262 264 6.894103 AGATTGATAGCCAAAGAAAATGGAGT 59.106 34.615 0.00 0.00 40.56 3.85
268 270 3.392882 CCAAAGAAAATGGAGTGCAACC 58.607 45.455 4.46 4.46 40.56 3.77
269 271 3.070015 CCAAAGAAAATGGAGTGCAACCT 59.930 43.478 11.60 0.00 40.56 3.50
719 794 4.678743 GGTGTGGTTGCCCTCCCC 62.679 72.222 0.00 0.00 0.00 4.81
1182 1266 6.791887 ATTGATGATGGTCACGATGATAAC 57.208 37.500 0.00 0.00 0.00 1.89
1266 1351 0.886490 CGCAAGAGGTTGAGGTTGCT 60.886 55.000 4.56 0.00 42.55 3.91
1748 1836 5.413833 GTCTCAGGATGCAGAAGAATCAAAA 59.586 40.000 0.00 0.00 34.76 2.44
2698 2810 2.629137 AGTGAAGCACAATCATTGGCAA 59.371 40.909 0.68 0.68 36.74 4.52
2890 3005 4.521146 TGGCTTTTCAAAAGCATTGGAAA 58.479 34.783 31.07 8.85 44.71 3.13
3206 3322 6.798427 ATCTTGAGGATGCACTTAAGAGTA 57.202 37.500 10.09 0.48 43.47 2.59
3394 3513 0.662619 CTGTTGCAACTGCGGAAAGA 59.337 50.000 28.61 5.75 45.83 2.52
3792 3915 3.741476 GGCGCCAACCTGCTGAAG 61.741 66.667 24.80 0.00 0.00 3.02
3793 3916 4.410743 GCGCCAACCTGCTGAAGC 62.411 66.667 0.00 0.00 42.50 3.86
3794 3917 3.741476 CGCCAACCTGCTGAAGCC 61.741 66.667 0.00 0.00 41.18 4.35
3795 3918 3.741476 GCCAACCTGCTGAAGCCG 61.741 66.667 0.00 0.00 41.18 5.52
3814 3937 2.266372 CATTGGCCCGTGGTCGTA 59.734 61.111 0.00 0.00 35.01 3.43
3815 3938 1.153249 CATTGGCCCGTGGTCGTAT 60.153 57.895 0.00 0.00 35.01 3.06
3816 3939 1.145377 ATTGGCCCGTGGTCGTATC 59.855 57.895 0.00 0.00 35.01 2.24
3817 3940 2.319890 ATTGGCCCGTGGTCGTATCC 62.320 60.000 0.00 0.00 35.01 2.59
3818 3941 4.580551 GGCCCGTGGTCGTATCCG 62.581 72.222 0.00 0.00 35.01 4.18
3819 3942 3.520862 GCCCGTGGTCGTATCCGA 61.521 66.667 0.00 0.00 41.73 4.55
3820 3943 2.853290 GCCCGTGGTCGTATCCGAT 61.853 63.158 0.00 0.00 46.30 4.18
3821 3944 1.007734 CCCGTGGTCGTATCCGATG 60.008 63.158 0.00 0.00 46.30 3.84
3822 3945 1.660575 CCGTGGTCGTATCCGATGC 60.661 63.158 0.00 0.00 46.30 3.91
3823 3946 2.009226 CGTGGTCGTATCCGATGCG 61.009 63.158 12.16 12.16 46.30 4.73
3824 3947 1.065273 GTGGTCGTATCCGATGCGT 59.935 57.895 16.93 0.00 46.30 5.24
3825 3948 1.065109 TGGTCGTATCCGATGCGTG 59.935 57.895 16.93 0.00 46.30 5.34
3826 3949 1.660575 GGTCGTATCCGATGCGTGG 60.661 63.158 16.93 0.00 46.30 4.94
3827 3950 1.660575 GTCGTATCCGATGCGTGGG 60.661 63.158 16.93 0.00 46.30 4.61
3828 3951 3.036084 CGTATCCGATGCGTGGGC 61.036 66.667 10.38 0.00 36.38 5.36
3829 3952 3.036084 GTATCCGATGCGTGGGCG 61.036 66.667 1.31 0.00 44.10 6.13
3843 3966 2.412112 GGCGCTACGACCTTCGAT 59.588 61.111 7.64 0.00 43.74 3.59
3844 3967 1.944676 GGCGCTACGACCTTCGATG 60.945 63.158 7.64 0.00 43.74 3.84
3845 3968 1.063649 GCGCTACGACCTTCGATGA 59.936 57.895 0.00 0.00 43.74 2.92
3846 3969 0.930742 GCGCTACGACCTTCGATGAG 60.931 60.000 0.00 0.00 43.74 2.90
3847 3970 0.377554 CGCTACGACCTTCGATGAGT 59.622 55.000 1.94 0.00 43.74 3.41
3848 3971 1.596260 CGCTACGACCTTCGATGAGTA 59.404 52.381 1.94 1.46 43.74 2.59
3849 3972 2.599377 CGCTACGACCTTCGATGAGTAC 60.599 54.545 1.94 0.00 43.74 2.73
3850 3973 2.286891 GCTACGACCTTCGATGAGTACC 60.287 54.545 1.94 0.00 43.74 3.34
3851 3974 0.731417 ACGACCTTCGATGAGTACCG 59.269 55.000 1.94 0.99 43.74 4.02
3852 3975 0.591741 CGACCTTCGATGAGTACCGC 60.592 60.000 0.00 0.00 43.74 5.68
3853 3976 0.454600 GACCTTCGATGAGTACCGCA 59.545 55.000 0.00 0.00 0.00 5.69
3854 3977 0.892755 ACCTTCGATGAGTACCGCAA 59.107 50.000 0.00 0.00 0.00 4.85
3855 3978 1.274167 ACCTTCGATGAGTACCGCAAA 59.726 47.619 0.00 0.00 0.00 3.68
3856 3979 2.093658 ACCTTCGATGAGTACCGCAAAT 60.094 45.455 0.00 0.00 0.00 2.32
3857 3980 3.131577 ACCTTCGATGAGTACCGCAAATA 59.868 43.478 0.00 0.00 0.00 1.40
3858 3981 3.489785 CCTTCGATGAGTACCGCAAATAC 59.510 47.826 0.00 0.00 0.00 1.89
3859 3982 3.786516 TCGATGAGTACCGCAAATACA 57.213 42.857 0.00 0.00 0.00 2.29
3860 3983 4.316205 TCGATGAGTACCGCAAATACAT 57.684 40.909 0.00 0.00 0.00 2.29
3861 3984 4.689071 TCGATGAGTACCGCAAATACATT 58.311 39.130 0.00 0.00 0.00 2.71
3862 3985 4.506288 TCGATGAGTACCGCAAATACATTG 59.494 41.667 0.00 0.00 42.21 2.82
3863 3986 4.506288 CGATGAGTACCGCAAATACATTGA 59.494 41.667 0.00 0.00 41.85 2.57
3864 3987 5.006261 CGATGAGTACCGCAAATACATTGAA 59.994 40.000 0.00 0.00 41.85 2.69
3865 3988 6.456315 CGATGAGTACCGCAAATACATTGAAA 60.456 38.462 0.00 0.00 41.85 2.69
3866 3989 6.561737 TGAGTACCGCAAATACATTGAAAA 57.438 33.333 0.00 0.00 41.85 2.29
3867 3990 6.971602 TGAGTACCGCAAATACATTGAAAAA 58.028 32.000 0.00 0.00 41.85 1.94
3868 3991 7.081349 TGAGTACCGCAAATACATTGAAAAAG 58.919 34.615 0.00 0.00 41.85 2.27
3869 3992 7.041030 TGAGTACCGCAAATACATTGAAAAAGA 60.041 33.333 0.00 0.00 41.85 2.52
3870 3993 7.081976 AGTACCGCAAATACATTGAAAAAGAC 58.918 34.615 0.00 0.00 41.85 3.01
3871 3994 4.915085 ACCGCAAATACATTGAAAAAGACG 59.085 37.500 0.00 0.00 41.85 4.18
3872 3995 4.201485 CCGCAAATACATTGAAAAAGACGC 60.201 41.667 0.00 0.00 41.85 5.19
3873 3996 4.201485 CGCAAATACATTGAAAAAGACGCC 60.201 41.667 0.00 0.00 41.85 5.68
3874 3997 4.201485 GCAAATACATTGAAAAAGACGCCG 60.201 41.667 0.00 0.00 41.85 6.46
3875 3998 2.604969 TACATTGAAAAAGACGCCGC 57.395 45.000 0.00 0.00 0.00 6.53
3876 3999 0.665835 ACATTGAAAAAGACGCCGCA 59.334 45.000 0.00 0.00 0.00 5.69
3877 4000 1.269448 ACATTGAAAAAGACGCCGCAT 59.731 42.857 0.00 0.00 0.00 4.73
3878 4001 2.288152 ACATTGAAAAAGACGCCGCATT 60.288 40.909 0.00 0.00 0.00 3.56
3879 4002 1.764851 TTGAAAAAGACGCCGCATTG 58.235 45.000 0.00 0.00 0.00 2.82
3880 4003 0.039617 TGAAAAAGACGCCGCATTGG 60.040 50.000 0.00 0.00 42.50 3.16
3881 4004 0.239879 GAAAAAGACGCCGCATTGGA 59.760 50.000 0.00 0.00 42.00 3.53
3882 4005 0.240945 AAAAAGACGCCGCATTGGAG 59.759 50.000 0.00 0.00 44.31 3.86
3883 4006 2.200170 AAAAGACGCCGCATTGGAGC 62.200 55.000 0.00 0.00 42.11 4.70
3891 4014 2.785258 GCATTGGAGCGACGGTTC 59.215 61.111 0.00 0.00 0.00 3.62
3892 4015 2.750888 GCATTGGAGCGACGGTTCC 61.751 63.158 2.28 5.80 43.36 3.62
3896 4019 2.654877 GGAGCGACGGTTCCAGAA 59.345 61.111 0.00 0.00 42.66 3.02
3897 4020 1.446272 GGAGCGACGGTTCCAGAAG 60.446 63.158 0.00 0.00 42.66 2.85
3898 4021 1.446272 GAGCGACGGTTCCAGAAGG 60.446 63.158 0.00 0.00 0.00 3.46
3899 4022 1.874345 GAGCGACGGTTCCAGAAGGA 61.874 60.000 0.00 0.00 43.93 3.36
3900 4023 1.446272 GCGACGGTTCCAGAAGGAG 60.446 63.158 0.00 0.00 46.74 3.69
3901 4024 1.215647 CGACGGTTCCAGAAGGAGG 59.784 63.158 0.00 0.00 46.74 4.30
3902 4025 1.248785 CGACGGTTCCAGAAGGAGGA 61.249 60.000 0.00 0.00 46.74 3.71
3903 4026 0.533032 GACGGTTCCAGAAGGAGGAG 59.467 60.000 0.00 0.00 46.74 3.69
3904 4027 1.219393 CGGTTCCAGAAGGAGGAGC 59.781 63.158 0.00 0.00 46.74 4.70
3906 4029 2.377136 GTTCCAGAAGGAGGAGCCA 58.623 57.895 0.00 0.00 46.74 4.75
3907 4030 0.693049 GTTCCAGAAGGAGGAGCCAA 59.307 55.000 0.00 0.00 46.74 4.52
3908 4031 0.987294 TTCCAGAAGGAGGAGCCAAG 59.013 55.000 0.00 0.00 46.74 3.61
3909 4032 1.077858 CCAGAAGGAGGAGCCAAGC 60.078 63.158 0.00 0.00 40.02 4.01
3910 4033 1.681666 CAGAAGGAGGAGCCAAGCA 59.318 57.895 0.00 0.00 40.02 3.91
3911 4034 0.676151 CAGAAGGAGGAGCCAAGCAC 60.676 60.000 0.00 0.00 40.02 4.40
3912 4035 1.743252 GAAGGAGGAGCCAAGCACG 60.743 63.158 0.00 0.00 40.02 5.34
3913 4036 3.909086 AAGGAGGAGCCAAGCACGC 62.909 63.158 0.00 0.00 40.02 5.34
3914 4037 4.704833 GGAGGAGCCAAGCACGCA 62.705 66.667 0.00 0.00 36.34 5.24
3915 4038 3.123620 GAGGAGCCAAGCACGCAG 61.124 66.667 0.00 0.00 0.00 5.18
3916 4039 4.711949 AGGAGCCAAGCACGCAGG 62.712 66.667 0.00 0.00 0.00 4.85
3921 4044 4.347453 CCAAGCACGCAGGCAACC 62.347 66.667 0.00 0.00 35.83 3.77
3922 4045 3.594775 CAAGCACGCAGGCAACCA 61.595 61.111 0.00 0.00 35.83 3.67
3923 4046 2.598394 AAGCACGCAGGCAACCAT 60.598 55.556 0.00 0.00 35.83 3.55
3924 4047 2.202395 AAGCACGCAGGCAACCATT 61.202 52.632 0.00 0.00 35.83 3.16
3925 4048 1.747325 AAGCACGCAGGCAACCATTT 61.747 50.000 0.00 0.00 35.83 2.32
3926 4049 2.023223 GCACGCAGGCAACCATTTG 61.023 57.895 0.00 0.00 35.62 2.32
3927 4050 1.363443 CACGCAGGCAACCATTTGT 59.637 52.632 0.00 0.00 34.90 2.83
3928 4051 0.595588 CACGCAGGCAACCATTTGTA 59.404 50.000 0.00 0.00 34.90 2.41
3929 4052 1.202114 CACGCAGGCAACCATTTGTAT 59.798 47.619 0.00 0.00 34.90 2.29
3930 4053 1.892474 ACGCAGGCAACCATTTGTATT 59.108 42.857 0.00 0.00 34.90 1.89
3931 4054 2.094752 ACGCAGGCAACCATTTGTATTC 60.095 45.455 0.00 0.00 34.90 1.75
3932 4055 2.164219 CGCAGGCAACCATTTGTATTCT 59.836 45.455 0.00 0.00 34.90 2.40
3933 4056 3.514645 GCAGGCAACCATTTGTATTCTG 58.485 45.455 0.00 0.00 34.90 3.02
3934 4057 3.514645 CAGGCAACCATTTGTATTCTGC 58.485 45.455 0.00 0.00 34.90 4.26
3935 4058 2.164219 AGGCAACCATTTGTATTCTGCG 59.836 45.455 0.00 0.00 34.90 5.18
3936 4059 2.529151 GCAACCATTTGTATTCTGCGG 58.471 47.619 0.00 0.00 34.90 5.69
3937 4060 2.735126 GCAACCATTTGTATTCTGCGGG 60.735 50.000 0.00 0.00 34.90 6.13
3938 4061 1.762708 ACCATTTGTATTCTGCGGGG 58.237 50.000 0.00 0.00 0.00 5.73
3939 4062 1.032014 CCATTTGTATTCTGCGGGGG 58.968 55.000 0.00 0.00 0.00 5.40
3940 4063 0.385390 CATTTGTATTCTGCGGGGGC 59.615 55.000 0.00 0.00 0.00 5.80
3941 4064 0.258774 ATTTGTATTCTGCGGGGGCT 59.741 50.000 0.00 0.00 0.00 5.19
3942 4065 0.913205 TTTGTATTCTGCGGGGGCTA 59.087 50.000 0.00 0.00 0.00 3.93
3943 4066 0.913205 TTGTATTCTGCGGGGGCTAA 59.087 50.000 0.00 0.00 0.00 3.09
3944 4067 0.913205 TGTATTCTGCGGGGGCTAAA 59.087 50.000 0.00 0.00 0.00 1.85
3945 4068 1.134220 TGTATTCTGCGGGGGCTAAAG 60.134 52.381 0.00 0.00 0.00 1.85
3946 4069 0.179029 TATTCTGCGGGGGCTAAAGC 60.179 55.000 0.00 0.00 41.14 3.51
3947 4070 2.210144 ATTCTGCGGGGGCTAAAGCA 62.210 55.000 4.07 0.00 44.36 3.91
3959 4082 2.550978 GCTAAAGCAGCGGTATGAAGA 58.449 47.619 0.00 0.00 41.37 2.87
3960 4083 2.541762 GCTAAAGCAGCGGTATGAAGAG 59.458 50.000 0.00 0.00 41.37 2.85
3961 4084 1.373570 AAAGCAGCGGTATGAAGAGC 58.626 50.000 0.00 0.00 0.00 4.09
3962 4085 0.250234 AAGCAGCGGTATGAAGAGCA 59.750 50.000 0.00 0.00 0.00 4.26
3963 4086 0.460987 AGCAGCGGTATGAAGAGCAC 60.461 55.000 0.00 0.00 0.00 4.40
3964 4087 1.432270 GCAGCGGTATGAAGAGCACC 61.432 60.000 0.00 0.00 0.00 5.01
3965 4088 0.108186 CAGCGGTATGAAGAGCACCA 60.108 55.000 0.00 0.00 32.32 4.17
3966 4089 0.833287 AGCGGTATGAAGAGCACCAT 59.167 50.000 0.00 0.00 32.32 3.55
3967 4090 0.940126 GCGGTATGAAGAGCACCATG 59.060 55.000 0.00 0.00 32.32 3.66
3968 4091 1.586422 CGGTATGAAGAGCACCATGG 58.414 55.000 11.19 11.19 32.32 3.66
3969 4092 1.312815 GGTATGAAGAGCACCATGGC 58.687 55.000 13.04 0.00 32.32 4.40
3970 4093 1.312815 GTATGAAGAGCACCATGGCC 58.687 55.000 13.04 2.82 0.00 5.36
3971 4094 1.133976 GTATGAAGAGCACCATGGCCT 60.134 52.381 13.04 8.63 0.00 5.19
3972 4095 0.333993 ATGAAGAGCACCATGGCCTT 59.666 50.000 13.04 10.19 0.00 4.35
3973 4096 0.991146 TGAAGAGCACCATGGCCTTA 59.009 50.000 13.04 0.00 0.00 2.69
3974 4097 1.354031 TGAAGAGCACCATGGCCTTAA 59.646 47.619 13.04 0.68 0.00 1.85
3975 4098 2.019984 GAAGAGCACCATGGCCTTAAG 58.980 52.381 13.04 0.00 0.00 1.85
3976 4099 1.289160 AGAGCACCATGGCCTTAAGA 58.711 50.000 13.04 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.836076 GTCCGAAATATTATTTTATAAGTGGCC 57.164 33.333 0.00 0.00 0.00 5.36
41 43 2.246397 CAGACACACTTGCACGCG 59.754 61.111 3.53 3.53 0.00 6.01
68 70 0.865769 CCAGTTTCTTCCGTTGTCCG 59.134 55.000 0.00 0.00 0.00 4.79
94 96 6.463995 TGTTTTAAAACTTGCATCTGTCCT 57.536 33.333 26.76 0.00 39.59 3.85
213 215 1.447314 CTTGTAACGCCCCGAGACC 60.447 63.158 0.00 0.00 0.00 3.85
214 216 1.447314 CCTTGTAACGCCCCGAGAC 60.447 63.158 0.00 0.00 0.00 3.36
224 226 5.049129 GGCTATCAATCTGCATCCTTGTAAC 60.049 44.000 0.00 0.00 0.00 2.50
242 244 4.158394 TGCACTCCATTTTCTTTGGCTATC 59.842 41.667 0.00 0.00 34.06 2.08
254 256 1.187567 GCCCAGGTTGCACTCCATTT 61.188 55.000 9.40 0.00 0.00 2.32
433 438 0.102300 ACGATCGATCAATCCACGCA 59.898 50.000 24.34 0.00 0.00 5.24
719 794 2.128507 GGGGAGAGTGTAGGGAGCG 61.129 68.421 0.00 0.00 0.00 5.03
920 1002 6.206243 GCTCACATGAAATATAGGCTTGTGAT 59.794 38.462 13.08 0.00 42.18 3.06
1182 1266 1.000955 ACAACCTCAACCTCTACTGCG 59.999 52.381 0.00 0.00 0.00 5.18
1266 1351 7.828717 TCATTACCTTCATCAATTTCTGTAGCA 59.171 33.333 0.00 0.00 0.00 3.49
1387 1472 8.970859 ATATCAATCTTTTTCGGATCAAGTCT 57.029 30.769 0.00 0.00 0.00 3.24
1748 1836 3.066621 TCGCTGAGCAACTTTGTCAATTT 59.933 39.130 4.88 0.00 0.00 1.82
2698 2810 7.936496 ATTCAAAACCACCAAGTTCATTTTT 57.064 28.000 0.00 0.00 0.00 1.94
3206 3322 6.541641 GCTCCATCAATATCTTTGTGTTCTCT 59.458 38.462 0.00 0.00 0.00 3.10
3394 3513 6.823689 TCAACAACTTGAGTTTAGAGAAGCTT 59.176 34.615 0.00 0.00 35.83 3.74
3708 3830 1.001974 GCGAAAAGAAAAATGGGGCCT 59.998 47.619 0.84 0.00 0.00 5.19
3775 3898 3.741476 CTTCAGCAGGTTGGCGCC 61.741 66.667 22.73 22.73 39.27 6.53
3776 3899 4.410743 GCTTCAGCAGGTTGGCGC 62.411 66.667 0.00 0.00 41.59 6.53
3777 3900 3.741476 GGCTTCAGCAGGTTGGCG 61.741 66.667 0.30 0.00 44.36 5.69
3778 3901 3.741476 CGGCTTCAGCAGGTTGGC 61.741 66.667 0.30 0.00 44.36 4.52
3784 3907 2.488355 CAATGCCGGCTTCAGCAG 59.512 61.111 29.70 6.60 43.38 4.24
3785 3908 3.063704 CCAATGCCGGCTTCAGCA 61.064 61.111 29.70 6.08 44.36 4.41
3796 3919 3.961838 TACGACCACGGGCCAATGC 62.962 63.158 4.39 0.00 44.46 3.56
3797 3920 1.153249 ATACGACCACGGGCCAATG 60.153 57.895 4.39 0.84 44.46 2.82
3798 3921 1.145377 GATACGACCACGGGCCAAT 59.855 57.895 4.39 0.00 44.46 3.16
3799 3922 2.580276 GATACGACCACGGGCCAA 59.420 61.111 4.39 0.00 44.46 4.52
3800 3923 3.463585 GGATACGACCACGGGCCA 61.464 66.667 4.39 0.00 44.46 5.36
3812 3935 3.036084 CGCCCACGCATCGGATAC 61.036 66.667 0.00 0.00 34.03 2.24
3822 3945 4.430765 AAGGTCGTAGCGCCCACG 62.431 66.667 22.17 22.17 44.07 4.94
3823 3946 2.508663 GAAGGTCGTAGCGCCCAC 60.509 66.667 2.29 0.73 0.00 4.61
3824 3947 4.124351 CGAAGGTCGTAGCGCCCA 62.124 66.667 2.29 0.00 34.72 5.36
3825 3948 3.135056 ATCGAAGGTCGTAGCGCCC 62.135 63.158 2.29 0.00 41.35 6.13
3826 3949 1.944676 CATCGAAGGTCGTAGCGCC 60.945 63.158 2.29 0.00 41.35 6.53
3827 3950 0.930742 CTCATCGAAGGTCGTAGCGC 60.931 60.000 0.00 0.00 41.35 5.92
3828 3951 0.377554 ACTCATCGAAGGTCGTAGCG 59.622 55.000 0.00 0.00 41.35 4.26
3829 3952 2.286891 GGTACTCATCGAAGGTCGTAGC 60.287 54.545 0.00 0.00 41.35 3.58
3830 3953 2.033065 CGGTACTCATCGAAGGTCGTAG 60.033 54.545 0.00 0.00 41.35 3.51
3831 3954 1.935873 CGGTACTCATCGAAGGTCGTA 59.064 52.381 0.00 0.00 41.35 3.43
3832 3955 0.731417 CGGTACTCATCGAAGGTCGT 59.269 55.000 0.00 0.00 41.35 4.34
3833 3956 0.591741 GCGGTACTCATCGAAGGTCG 60.592 60.000 0.00 0.00 42.10 4.79
3834 3957 0.454600 TGCGGTACTCATCGAAGGTC 59.545 55.000 0.00 0.00 0.00 3.85
3835 3958 0.892755 TTGCGGTACTCATCGAAGGT 59.107 50.000 0.00 0.00 0.00 3.50
3836 3959 2.004583 TTTGCGGTACTCATCGAAGG 57.995 50.000 0.00 0.00 0.00 3.46
3837 3960 4.109766 TGTATTTGCGGTACTCATCGAAG 58.890 43.478 0.00 0.00 0.00 3.79
3838 3961 4.112716 TGTATTTGCGGTACTCATCGAA 57.887 40.909 0.00 0.00 0.00 3.71
3839 3962 3.786516 TGTATTTGCGGTACTCATCGA 57.213 42.857 0.00 0.00 0.00 3.59
3840 3963 4.506288 TCAATGTATTTGCGGTACTCATCG 59.494 41.667 0.00 0.00 35.16 3.84
3841 3964 5.984233 TCAATGTATTTGCGGTACTCATC 57.016 39.130 0.00 0.00 35.16 2.92
3842 3965 6.751514 TTTCAATGTATTTGCGGTACTCAT 57.248 33.333 0.00 0.00 35.16 2.90
3843 3966 6.561737 TTTTCAATGTATTTGCGGTACTCA 57.438 33.333 0.00 0.00 35.16 3.41
3844 3967 7.270579 GTCTTTTTCAATGTATTTGCGGTACTC 59.729 37.037 0.00 0.00 35.16 2.59
3845 3968 7.081976 GTCTTTTTCAATGTATTTGCGGTACT 58.918 34.615 0.00 0.00 35.16 2.73
3846 3969 6.032042 CGTCTTTTTCAATGTATTTGCGGTAC 59.968 38.462 0.00 0.00 35.16 3.34
3847 3970 6.081049 CGTCTTTTTCAATGTATTTGCGGTA 58.919 36.000 0.00 0.00 35.16 4.02
3848 3971 4.915085 CGTCTTTTTCAATGTATTTGCGGT 59.085 37.500 0.00 0.00 35.16 5.68
3849 3972 4.201485 GCGTCTTTTTCAATGTATTTGCGG 60.201 41.667 0.00 0.00 35.16 5.69
3850 3973 4.201485 GGCGTCTTTTTCAATGTATTTGCG 60.201 41.667 0.00 0.00 35.16 4.85
3851 3974 4.201485 CGGCGTCTTTTTCAATGTATTTGC 60.201 41.667 0.00 0.00 35.16 3.68
3852 3975 4.201485 GCGGCGTCTTTTTCAATGTATTTG 60.201 41.667 9.37 0.00 36.61 2.32
3853 3976 3.917985 GCGGCGTCTTTTTCAATGTATTT 59.082 39.130 9.37 0.00 0.00 1.40
3854 3977 3.057876 TGCGGCGTCTTTTTCAATGTATT 60.058 39.130 9.37 0.00 0.00 1.89
3855 3978 2.486203 TGCGGCGTCTTTTTCAATGTAT 59.514 40.909 9.37 0.00 0.00 2.29
3856 3979 1.874231 TGCGGCGTCTTTTTCAATGTA 59.126 42.857 9.37 0.00 0.00 2.29
3857 3980 0.665835 TGCGGCGTCTTTTTCAATGT 59.334 45.000 9.37 0.00 0.00 2.71
3858 3981 1.981254 ATGCGGCGTCTTTTTCAATG 58.019 45.000 9.37 0.00 0.00 2.82
3859 3982 2.327568 CAATGCGGCGTCTTTTTCAAT 58.672 42.857 9.37 0.00 0.00 2.57
3860 3983 1.601663 CCAATGCGGCGTCTTTTTCAA 60.602 47.619 9.37 0.00 0.00 2.69
3861 3984 0.039617 CCAATGCGGCGTCTTTTTCA 60.040 50.000 9.37 0.00 0.00 2.69
3862 3985 0.239879 TCCAATGCGGCGTCTTTTTC 59.760 50.000 9.37 0.00 33.14 2.29
3863 3986 0.240945 CTCCAATGCGGCGTCTTTTT 59.759 50.000 9.37 0.00 33.14 1.94
3864 3987 1.875963 CTCCAATGCGGCGTCTTTT 59.124 52.632 9.37 0.00 33.14 2.27
3865 3988 2.690778 GCTCCAATGCGGCGTCTTT 61.691 57.895 9.37 2.73 33.14 2.52
3866 3989 3.127533 GCTCCAATGCGGCGTCTT 61.128 61.111 9.37 0.00 33.14 3.01
3874 3997 2.750888 GGAACCGTCGCTCCAATGC 61.751 63.158 6.70 0.00 0.00 3.56
3875 3998 1.361668 CTGGAACCGTCGCTCCAATG 61.362 60.000 13.43 2.44 41.20 2.82
3876 3999 1.079127 CTGGAACCGTCGCTCCAAT 60.079 57.895 13.43 0.00 41.20 3.16
3877 4000 1.750341 TTCTGGAACCGTCGCTCCAA 61.750 55.000 13.43 4.83 41.20 3.53
3878 4001 2.154798 CTTCTGGAACCGTCGCTCCA 62.155 60.000 12.26 12.26 39.47 3.86
3879 4002 1.446272 CTTCTGGAACCGTCGCTCC 60.446 63.158 4.97 4.97 0.00 4.70
3880 4003 1.446272 CCTTCTGGAACCGTCGCTC 60.446 63.158 0.00 0.00 34.57 5.03
3881 4004 1.878656 CTCCTTCTGGAACCGTCGCT 61.879 60.000 0.00 0.00 42.66 4.93
3882 4005 1.446272 CTCCTTCTGGAACCGTCGC 60.446 63.158 0.00 0.00 42.66 5.19
3883 4006 1.215647 CCTCCTTCTGGAACCGTCG 59.784 63.158 0.00 0.00 42.66 5.12
3884 4007 0.533032 CTCCTCCTTCTGGAACCGTC 59.467 60.000 0.00 0.00 42.66 4.79
3885 4008 1.545706 GCTCCTCCTTCTGGAACCGT 61.546 60.000 0.00 0.00 42.66 4.83
3886 4009 1.219393 GCTCCTCCTTCTGGAACCG 59.781 63.158 0.00 0.00 42.66 4.44
3887 4010 1.201429 TGGCTCCTCCTTCTGGAACC 61.201 60.000 0.00 0.00 42.66 3.62
3888 4011 0.693049 TTGGCTCCTCCTTCTGGAAC 59.307 55.000 0.00 0.00 42.66 3.62
3889 4012 0.987294 CTTGGCTCCTCCTTCTGGAA 59.013 55.000 0.00 0.00 42.66 3.53
3890 4013 1.557269 GCTTGGCTCCTCCTTCTGGA 61.557 60.000 0.00 0.00 40.69 3.86
3891 4014 1.077858 GCTTGGCTCCTCCTTCTGG 60.078 63.158 0.00 0.00 35.26 3.86
3892 4015 0.676151 GTGCTTGGCTCCTCCTTCTG 60.676 60.000 0.00 0.00 35.26 3.02
3893 4016 1.682257 GTGCTTGGCTCCTCCTTCT 59.318 57.895 0.00 0.00 35.26 2.85
3894 4017 1.743252 CGTGCTTGGCTCCTCCTTC 60.743 63.158 0.00 0.00 35.26 3.46
3895 4018 2.348998 CGTGCTTGGCTCCTCCTT 59.651 61.111 0.00 0.00 35.26 3.36
3896 4019 4.400961 GCGTGCTTGGCTCCTCCT 62.401 66.667 0.00 0.00 35.26 3.69
3897 4020 4.704833 TGCGTGCTTGGCTCCTCC 62.705 66.667 0.00 0.00 0.00 4.30
3898 4021 3.123620 CTGCGTGCTTGGCTCCTC 61.124 66.667 0.00 0.00 0.00 3.71
3899 4022 4.711949 CCTGCGTGCTTGGCTCCT 62.712 66.667 0.00 0.00 0.00 3.69
3904 4027 4.347453 GGTTGCCTGCGTGCTTGG 62.347 66.667 0.00 0.00 0.00 3.61
3905 4028 2.424705 AATGGTTGCCTGCGTGCTTG 62.425 55.000 0.00 0.00 0.00 4.01
3906 4029 1.747325 AAATGGTTGCCTGCGTGCTT 61.747 50.000 0.00 0.00 0.00 3.91
3907 4030 2.202395 AAATGGTTGCCTGCGTGCT 61.202 52.632 0.00 0.00 0.00 4.40
3908 4031 2.023223 CAAATGGTTGCCTGCGTGC 61.023 57.895 0.00 0.00 0.00 5.34
3909 4032 0.595588 TACAAATGGTTGCCTGCGTG 59.404 50.000 0.00 0.00 38.39 5.34
3910 4033 1.544724 ATACAAATGGTTGCCTGCGT 58.455 45.000 0.00 0.00 38.39 5.24
3911 4034 2.164219 AGAATACAAATGGTTGCCTGCG 59.836 45.455 0.00 0.00 38.39 5.18
3912 4035 3.514645 CAGAATACAAATGGTTGCCTGC 58.485 45.455 0.00 0.00 38.39 4.85
3913 4036 3.514645 GCAGAATACAAATGGTTGCCTG 58.485 45.455 0.00 0.00 38.39 4.85
3914 4037 2.164219 CGCAGAATACAAATGGTTGCCT 59.836 45.455 0.00 0.00 38.39 4.75
3915 4038 2.529151 CGCAGAATACAAATGGTTGCC 58.471 47.619 0.00 0.00 38.39 4.52
3916 4039 2.529151 CCGCAGAATACAAATGGTTGC 58.471 47.619 0.00 0.00 38.39 4.17
3917 4040 2.159254 CCCCGCAGAATACAAATGGTTG 60.159 50.000 0.00 0.00 40.84 3.77
3918 4041 2.099405 CCCCGCAGAATACAAATGGTT 58.901 47.619 0.00 0.00 0.00 3.67
3919 4042 1.684869 CCCCCGCAGAATACAAATGGT 60.685 52.381 0.00 0.00 0.00 3.55
3920 4043 1.032014 CCCCCGCAGAATACAAATGG 58.968 55.000 0.00 0.00 0.00 3.16
3921 4044 0.385390 GCCCCCGCAGAATACAAATG 59.615 55.000 0.00 0.00 34.03 2.32
3922 4045 0.258774 AGCCCCCGCAGAATACAAAT 59.741 50.000 0.00 0.00 37.52 2.32
3923 4046 0.913205 TAGCCCCCGCAGAATACAAA 59.087 50.000 0.00 0.00 37.52 2.83
3924 4047 0.913205 TTAGCCCCCGCAGAATACAA 59.087 50.000 0.00 0.00 37.52 2.41
3925 4048 0.913205 TTTAGCCCCCGCAGAATACA 59.087 50.000 0.00 0.00 37.52 2.29
3926 4049 1.594331 CTTTAGCCCCCGCAGAATAC 58.406 55.000 0.00 0.00 37.52 1.89
3927 4050 0.179029 GCTTTAGCCCCCGCAGAATA 60.179 55.000 0.00 0.00 37.52 1.75
3928 4051 1.453928 GCTTTAGCCCCCGCAGAAT 60.454 57.895 0.00 0.00 37.52 2.40
3929 4052 2.045340 GCTTTAGCCCCCGCAGAA 60.045 61.111 0.00 0.00 37.52 3.02
3930 4053 3.326578 TGCTTTAGCCCCCGCAGA 61.327 61.111 0.00 0.00 41.18 4.26
3931 4054 2.825836 CTGCTTTAGCCCCCGCAG 60.826 66.667 0.00 0.00 43.10 5.18
3940 4063 2.541762 GCTCTTCATACCGCTGCTTTAG 59.458 50.000 0.00 0.00 0.00 1.85
3941 4064 2.093711 TGCTCTTCATACCGCTGCTTTA 60.094 45.455 0.00 0.00 0.00 1.85
3942 4065 1.339055 TGCTCTTCATACCGCTGCTTT 60.339 47.619 0.00 0.00 0.00 3.51
3943 4066 0.250234 TGCTCTTCATACCGCTGCTT 59.750 50.000 0.00 0.00 0.00 3.91
3944 4067 0.460987 GTGCTCTTCATACCGCTGCT 60.461 55.000 0.00 0.00 0.00 4.24
3945 4068 1.432270 GGTGCTCTTCATACCGCTGC 61.432 60.000 0.00 0.00 0.00 5.25
3946 4069 0.108186 TGGTGCTCTTCATACCGCTG 60.108 55.000 0.00 0.00 37.29 5.18
3947 4070 0.833287 ATGGTGCTCTTCATACCGCT 59.167 50.000 0.00 0.00 37.29 5.52
3948 4071 0.940126 CATGGTGCTCTTCATACCGC 59.060 55.000 0.00 0.00 37.29 5.68
3949 4072 1.586422 CCATGGTGCTCTTCATACCG 58.414 55.000 2.57 0.00 37.29 4.02
3950 4073 1.312815 GCCATGGTGCTCTTCATACC 58.687 55.000 14.67 0.00 35.05 2.73
3951 4074 1.133976 AGGCCATGGTGCTCTTCATAC 60.134 52.381 14.67 0.00 0.00 2.39
3952 4075 1.216064 AGGCCATGGTGCTCTTCATA 58.784 50.000 14.67 0.00 0.00 2.15
3953 4076 0.333993 AAGGCCATGGTGCTCTTCAT 59.666 50.000 14.67 0.00 0.00 2.57
3954 4077 0.991146 TAAGGCCATGGTGCTCTTCA 59.009 50.000 14.67 0.58 0.00 3.02
3955 4078 2.019984 CTTAAGGCCATGGTGCTCTTC 58.980 52.381 14.67 0.00 0.00 2.87
3956 4079 1.635487 TCTTAAGGCCATGGTGCTCTT 59.365 47.619 14.67 13.84 0.00 2.85
3957 4080 1.289160 TCTTAAGGCCATGGTGCTCT 58.711 50.000 14.67 3.48 0.00 4.09
3958 4081 3.882131 TCTTAAGGCCATGGTGCTC 57.118 52.632 14.67 1.02 0.00 4.26


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

AutoCloner maintained by Alex Coulton.