Multiple sequence alignment - TraesCS3D01G360500

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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 TraesCS3D01G360500 chr3D 100.000 3405 0 0 1 3405 474217831 474214427 0.000000e+00 6288.0
1 TraesCS3D01G360500 chr3D 85.882 170 12 6 1618 1781 23195785 23195622 1.620000e-38 171.0
2 TraesCS3D01G360500 chr3D 85.455 55 3 5 3230 3282 299684513 299684462 6.000000e-03 52.8
3 TraesCS3D01G360500 chr3B 92.561 2124 122 23 302 2412 630402797 630400697 0.000000e+00 3014.0
4 TraesCS3D01G360500 chr3B 90.123 729 34 19 2494 3212 630400578 630399878 0.000000e+00 913.0
5 TraesCS3D01G360500 chr3B 85.882 170 12 6 1618 1781 40908878 40908715 1.620000e-38 171.0
6 TraesCS3D01G360500 chr3B 97.222 36 1 0 1750 1785 766031802 766031767 1.020000e-05 62.1
7 TraesCS3D01G360500 chr3A 92.019 2155 123 20 1 2122 616494262 616492124 0.000000e+00 2981.0
8 TraesCS3D01G360500 chr3A 87.935 978 51 23 2151 3094 616492129 616491185 0.000000e+00 1090.0
9 TraesCS3D01G360500 chr3A 85.294 170 13 6 1618 1781 32385655 32385492 7.560000e-37 165.0
10 TraesCS3D01G360500 chr3A 86.822 129 17 0 1593 1721 624829956 624830084 9.850000e-31 145.0
11 TraesCS3D01G360500 chr3A 93.407 91 3 2 3140 3230 616491173 616491086 7.670000e-27 132.0
12 TraesCS3D01G360500 chr1A 93.689 206 10 1 1598 1803 474450729 474450527 4.270000e-79 305.0
13 TraesCS3D01G360500 chr1A 79.779 272 41 11 1877 2142 24394623 24394886 5.800000e-43 185.0
14 TraesCS3D01G360500 chr1B 93.532 201 10 1 1600 1800 499896494 499896691 2.570000e-76 296.0
15 TraesCS3D01G360500 chr1D 92.233 206 13 1 1598 1803 375646699 375646497 4.300000e-74 289.0
16 TraesCS3D01G360500 chr7D 91.429 175 9 5 3230 3402 500220626 500220456 5.680000e-58 235.0
17 TraesCS3D01G360500 chr7D 93.333 135 6 2 3270 3402 163535699 163535832 2.680000e-46 196.0
18 TraesCS3D01G360500 chr6D 88.398 181 11 4 3230 3402 413031402 413031580 3.440000e-50 209.0
19 TraesCS3D01G360500 chr6D 80.645 217 31 6 1931 2142 456114368 456114158 1.260000e-34 158.0
20 TraesCS3D01G360500 chr2D 88.043 184 12 4 3230 3405 268233782 268233601 3.440000e-50 209.0
21 TraesCS3D01G360500 chr2D 86.111 180 15 5 3230 3401 147116418 147116241 5.800000e-43 185.0
22 TraesCS3D01G360500 chr5A 87.845 181 11 6 3230 3401 307706220 307706398 5.760000e-48 202.0
23 TraesCS3D01G360500 chr4D 92.029 138 10 1 3264 3401 439740959 439741095 3.470000e-45 193.0
24 TraesCS3D01G360500 chr4D 81.481 216 30 5 1931 2142 295104243 295104034 5.840000e-38 169.0
25 TraesCS3D01G360500 chr4B 90.647 139 9 2 3265 3401 43770950 43770814 7.510000e-42 182.0
26 TraesCS3D01G360500 chr2A 85.714 182 12 9 3230 3402 588260793 588260969 2.700000e-41 180.0
27 TraesCS3D01G360500 chr2A 80.569 211 31 9 1877 2081 37742160 37742366 1.640000e-33 154.0
28 TraesCS3D01G360500 chr2A 84.615 78 6 4 3223 3299 724349517 724349445 4.710000e-09 73.1


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 TraesCS3D01G360500 chr3D 474214427 474217831 3404 True 6288.0 6288 100.000000 1 3405 1 chr3D.!!$R3 3404
1 TraesCS3D01G360500 chr3B 630399878 630402797 2919 True 1963.5 3014 91.342000 302 3212 2 chr3B.!!$R3 2910
2 TraesCS3D01G360500 chr3A 616491086 616494262 3176 True 1401.0 2981 91.120333 1 3230 3 chr3A.!!$R2 3229

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
650 680 0.317479 AAGCTCGCCTTGTAGTCGTT 59.683 50.0 0.0 0.0 30.99 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2573 2672 0.606673 GGTTTCAGGTGAGGTGAGCC 60.607 60.0 0.0 0.0 0.0 4.7 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
59 60 6.926280 TTTTTACTTTGCATTATGTCTGCG 57.074 33.333 0.00 0.00 42.62 5.18
176 177 9.915629 CACCTACATATCCTAGTTATGAAAGAC 57.084 37.037 13.90 0.00 32.53 3.01
218 219 4.170256 GTCTCTTCAAGGATCGACTCAAC 58.830 47.826 0.00 0.00 0.00 3.18
276 305 2.123769 GCCACTGCCCCATATGCA 60.124 61.111 0.00 0.00 37.17 3.96
278 307 2.019897 GCCACTGCCCCATATGCAAC 62.020 60.000 0.00 0.00 38.46 4.17
312 341 3.745975 TGACGACCTTCACATGTTCATTC 59.254 43.478 0.00 0.00 0.00 2.67
321 350 3.329225 TCACATGTTCATTCAGTACCCCA 59.671 43.478 0.00 0.00 0.00 4.96
325 354 4.771114 TGTTCATTCAGTACCCCATAGG 57.229 45.455 0.00 0.00 43.78 2.57
332 361 1.774254 CAGTACCCCATAGGCATCCAA 59.226 52.381 0.00 0.00 40.58 3.53
335 364 3.467103 AGTACCCCATAGGCATCCAAATT 59.533 43.478 0.00 0.00 40.58 1.82
354 383 2.212752 TTGGGATGCCCTATTCCTCT 57.787 50.000 0.00 0.00 45.70 3.69
355 384 2.212752 TGGGATGCCCTATTCCTCTT 57.787 50.000 0.00 0.00 45.70 2.85
387 416 2.972021 TCCATCGAGCTCATTTGGGATA 59.028 45.455 20.50 5.07 0.00 2.59
388 417 3.070018 CCATCGAGCTCATTTGGGATAC 58.930 50.000 15.40 0.00 0.00 2.24
402 431 0.834612 GGATACCCCCATGTTGTCGA 59.165 55.000 0.00 0.00 0.00 4.20
410 439 1.156736 CCATGTTGTCGAACCTCCAC 58.843 55.000 0.00 0.00 0.00 4.02
452 481 2.840038 TGCTCTCTCCTTGCTATGGAAA 59.160 45.455 0.00 0.00 32.61 3.13
483 512 7.436933 GGATTCCAGAAACATTCTTGTCTTTT 58.563 34.615 0.00 0.00 38.11 2.27
642 672 1.065358 CAATTGCAAAGCTCGCCTTG 58.935 50.000 1.71 0.00 33.01 3.61
650 680 0.317479 AAGCTCGCCTTGTAGTCGTT 59.683 50.000 0.00 0.00 30.99 3.85
668 698 4.029087 GTCGTTTTTGAGTAATGCATTCGC 59.971 41.667 16.86 10.38 39.24 4.70
796 828 7.335924 TGAATCTTGTTACCATTAGTTAGCACC 59.664 37.037 0.00 0.00 0.00 5.01
1034 1067 1.078214 CTTCCTCCATTGCTCGCCA 60.078 57.895 0.00 0.00 0.00 5.69
1035 1068 1.078214 TTCCTCCATTGCTCGCCAG 60.078 57.895 0.00 0.00 0.00 4.85
1036 1069 2.515523 CCTCCATTGCTCGCCAGG 60.516 66.667 0.00 0.00 0.00 4.45
1037 1070 3.207669 CTCCATTGCTCGCCAGGC 61.208 66.667 0.00 0.00 0.00 4.85
1038 1071 4.802051 TCCATTGCTCGCCAGGCC 62.802 66.667 5.63 0.00 0.00 5.19
1270 1303 1.227089 GAGATGGTCGCGCTGATGT 60.227 57.895 5.56 0.00 0.00 3.06
1413 1446 2.283966 ACTCTGGACTGGGACGGG 60.284 66.667 0.00 0.00 40.47 5.28
1558 1591 4.698780 TGATCTTCTTCTTGTGCTTGGATG 59.301 41.667 0.00 0.00 0.00 3.51
1586 1626 1.560923 CGGAAATCTGATCGCGTTCT 58.439 50.000 17.38 0.00 0.00 3.01
1977 2017 0.671781 GCACCAGAGCTCGTTCATGT 60.672 55.000 8.37 0.00 0.00 3.21
1978 2018 1.354040 CACCAGAGCTCGTTCATGTC 58.646 55.000 8.37 0.00 0.00 3.06
2127 2167 4.155733 CATCCACGGGCGCTACCA 62.156 66.667 7.64 0.00 42.05 3.25
2243 2284 1.539388 TGATGGAACGCAAGCGAAAAT 59.461 42.857 22.30 8.69 42.83 1.82
2317 2358 2.084546 GAAACCTCAAGAACCCATCGG 58.915 52.381 0.00 0.00 0.00 4.18
2485 2561 6.248839 CGAACGTTTCTCTGTCTATTGTACTC 59.751 42.308 0.46 0.00 0.00 2.59
2487 2563 5.475909 ACGTTTCTCTGTCTATTGTACTCCA 59.524 40.000 0.00 0.00 0.00 3.86
2489 2565 6.866770 CGTTTCTCTGTCTATTGTACTCCAAA 59.133 38.462 0.00 0.00 36.44 3.28
2491 2567 8.660373 GTTTCTCTGTCTATTGTACTCCAAATG 58.340 37.037 0.00 0.00 36.44 2.32
2509 2608 2.388310 TGAATCCGTCGCCATTGTTA 57.612 45.000 0.00 0.00 0.00 2.41
2510 2609 2.701107 TGAATCCGTCGCCATTGTTAA 58.299 42.857 0.00 0.00 0.00 2.01
2513 2612 2.172851 TCCGTCGCCATTGTTAAACT 57.827 45.000 0.00 0.00 0.00 2.66
2514 2613 2.496111 TCCGTCGCCATTGTTAAACTT 58.504 42.857 0.00 0.00 0.00 2.66
2515 2614 2.224549 TCCGTCGCCATTGTTAAACTTG 59.775 45.455 0.00 0.00 0.00 3.16
2517 2616 1.976045 GTCGCCATTGTTAAACTTGCG 59.024 47.619 0.00 0.00 41.68 4.85
2538 2637 3.465403 CCTGCCTCCCCGTGAGAG 61.465 72.222 1.04 0.00 44.42 3.20
2554 2653 3.253432 GTGAGAGGTTTCGATTTGGCTTT 59.747 43.478 0.00 0.00 0.00 3.51
2567 2666 2.164026 GGCTTTGCTCTCTCGCTCG 61.164 63.158 0.00 0.00 0.00 5.03
2568 2667 2.797462 GCTTTGCTCTCTCGCTCGC 61.797 63.158 0.00 0.00 0.00 5.03
2569 2668 1.153862 CTTTGCTCTCTCGCTCGCT 60.154 57.895 0.00 0.00 0.00 4.93
2570 2669 1.139226 CTTTGCTCTCTCGCTCGCTC 61.139 60.000 0.00 0.00 0.00 5.03
2571 2670 1.866853 TTTGCTCTCTCGCTCGCTCA 61.867 55.000 0.00 0.00 0.00 4.26
2572 2671 2.277884 GCTCTCTCGCTCGCTCAC 60.278 66.667 0.00 0.00 0.00 3.51
2573 2672 2.022623 CTCTCTCGCTCGCTCACG 59.977 66.667 0.00 0.00 42.01 4.35
2591 2690 0.951040 CGGCTCACCTCACCTGAAAC 60.951 60.000 0.00 0.00 0.00 2.78
2659 2767 3.902150 TCTCATTAATGCCGATCTCGTC 58.098 45.455 10.76 0.00 37.74 4.20
2741 2851 2.659016 CCTCGTGCTCCTTGCTCA 59.341 61.111 0.00 0.00 43.37 4.26
2838 2952 1.833934 CCCAGTTGGCCAGTTGCTT 60.834 57.895 5.11 0.00 40.92 3.91
2839 2953 1.364901 CCAGTTGGCCAGTTGCTTG 59.635 57.895 5.11 0.00 40.92 4.01
2840 2954 1.300388 CAGTTGGCCAGTTGCTTGC 60.300 57.895 5.11 0.00 40.92 4.01
2841 2955 2.029518 GTTGGCCAGTTGCTTGCC 59.970 61.111 5.11 4.51 41.89 4.52
2903 3018 2.126031 GTCGACGGGAAGTGCCTC 60.126 66.667 0.00 0.00 36.66 4.70
2960 3079 7.032580 GCAGCATCAATATACTGTAGGAGTAG 58.967 42.308 0.00 0.00 40.63 2.57
3095 3218 1.613520 CCCTTTTCGTCCCCTTCCTTC 60.614 57.143 0.00 0.00 0.00 3.46
3096 3219 1.613520 CCTTTTCGTCCCCTTCCTTCC 60.614 57.143 0.00 0.00 0.00 3.46
3097 3220 1.351350 CTTTTCGTCCCCTTCCTTCCT 59.649 52.381 0.00 0.00 0.00 3.36
3098 3221 0.981943 TTTCGTCCCCTTCCTTCCTC 59.018 55.000 0.00 0.00 0.00 3.71
3103 3226 2.003548 CCCCTTCCTTCCTCCCCAG 61.004 68.421 0.00 0.00 0.00 4.45
3121 3244 4.371786 CCCAGAGGAAAAGAAAAGCAAAC 58.628 43.478 0.00 0.00 33.47 2.93
3122 3245 4.100035 CCCAGAGGAAAAGAAAAGCAAACT 59.900 41.667 0.00 0.00 33.47 2.66
3123 3246 5.301805 CCCAGAGGAAAAGAAAAGCAAACTA 59.698 40.000 0.00 0.00 33.47 2.24
3124 3247 6.442112 CCAGAGGAAAAGAAAAGCAAACTAG 58.558 40.000 0.00 0.00 0.00 2.57
3126 3249 5.594317 AGAGGAAAAGAAAAGCAAACTAGCA 59.406 36.000 0.00 0.00 36.85 3.49
3127 3250 6.096846 AGAGGAAAAGAAAAGCAAACTAGCAA 59.903 34.615 0.00 0.00 36.85 3.91
3128 3251 6.639563 AGGAAAAGAAAAGCAAACTAGCAAA 58.360 32.000 0.00 0.00 36.85 3.68
3131 3254 3.982475 AGAAAAGCAAACTAGCAAAGCC 58.018 40.909 0.00 0.00 36.85 4.35
3132 3255 3.638627 AGAAAAGCAAACTAGCAAAGCCT 59.361 39.130 0.00 0.00 36.85 4.58
3168 3291 0.457853 TGTACGCTCGCACCATTCTC 60.458 55.000 0.00 0.00 0.00 2.87
3173 3296 1.493950 GCTCGCACCATTCTCCATCG 61.494 60.000 0.00 0.00 0.00 3.84
3230 3353 1.140589 CCGCAGTAGTGAGCCTCAG 59.859 63.158 0.42 0.00 0.00 3.35
3231 3354 1.315981 CCGCAGTAGTGAGCCTCAGA 61.316 60.000 0.42 0.00 0.00 3.27
3232 3355 0.100325 CGCAGTAGTGAGCCTCAGAG 59.900 60.000 0.42 0.00 0.00 3.35
3233 3356 0.179113 GCAGTAGTGAGCCTCAGAGC 60.179 60.000 0.42 0.00 0.00 4.09
3234 3357 1.180907 CAGTAGTGAGCCTCAGAGCA 58.819 55.000 0.00 0.00 34.23 4.26
3235 3358 1.547820 CAGTAGTGAGCCTCAGAGCAA 59.452 52.381 0.00 0.00 34.23 3.91
3236 3359 2.028658 CAGTAGTGAGCCTCAGAGCAAA 60.029 50.000 0.00 0.00 34.23 3.68
3237 3360 2.028567 AGTAGTGAGCCTCAGAGCAAAC 60.029 50.000 0.00 0.00 34.23 2.93
3238 3361 1.055040 AGTGAGCCTCAGAGCAAACT 58.945 50.000 0.00 0.00 34.23 2.66
3239 3362 1.001860 AGTGAGCCTCAGAGCAAACTC 59.998 52.381 0.00 0.00 43.82 3.01
3248 3371 2.467962 GAGCAAACTCTAACGGGCC 58.532 57.895 0.00 0.00 40.03 5.80
3249 3372 1.359459 GAGCAAACTCTAACGGGCCG 61.359 60.000 27.06 27.06 40.03 6.13
3250 3373 1.375013 GCAAACTCTAACGGGCCGA 60.375 57.895 35.78 10.64 0.00 5.54
3251 3374 1.632948 GCAAACTCTAACGGGCCGAC 61.633 60.000 35.78 4.33 0.00 4.79
3252 3375 1.017701 CAAACTCTAACGGGCCGACC 61.018 60.000 35.78 0.00 0.00 4.79
3265 3388 3.961729 CGACCCAAACGGAAGGTC 58.038 61.111 6.21 6.21 45.49 3.85
3266 3389 1.670083 CGACCCAAACGGAAGGTCC 60.670 63.158 9.65 0.00 46.08 4.46
3277 3400 0.596577 GGAAGGTCCGCTTTTTGTCC 59.403 55.000 0.00 0.00 0.00 4.02
3278 3401 0.237498 GAAGGTCCGCTTTTTGTCCG 59.763 55.000 0.00 0.00 0.00 4.79
3279 3402 0.464916 AAGGTCCGCTTTTTGTCCGT 60.465 50.000 0.00 0.00 0.00 4.69
3280 3403 0.464916 AGGTCCGCTTTTTGTCCGTT 60.465 50.000 0.00 0.00 0.00 4.44
3281 3404 0.382873 GGTCCGCTTTTTGTCCGTTT 59.617 50.000 0.00 0.00 0.00 3.60
3282 3405 1.472990 GTCCGCTTTTTGTCCGTTTG 58.527 50.000 0.00 0.00 0.00 2.93
3283 3406 0.382515 TCCGCTTTTTGTCCGTTTGG 59.617 50.000 0.00 0.00 0.00 3.28
3284 3407 0.596341 CCGCTTTTTGTCCGTTTGGG 60.596 55.000 0.00 0.00 35.24 4.12
3285 3408 0.101579 CGCTTTTTGTCCGTTTGGGT 59.898 50.000 0.00 0.00 37.00 4.51
3286 3409 1.847818 GCTTTTTGTCCGTTTGGGTC 58.152 50.000 0.00 0.00 37.00 4.46
3287 3410 1.862411 GCTTTTTGTCCGTTTGGGTCG 60.862 52.381 0.00 0.00 37.00 4.79
3289 3412 1.726533 TTTTGTCCGTTTGGGTCGGC 61.727 55.000 0.00 0.00 46.49 5.54
3290 3413 4.629523 TGTCCGTTTGGGTCGGCC 62.630 66.667 0.00 0.00 46.49 6.13
3291 3414 4.629523 GTCCGTTTGGGTCGGCCA 62.630 66.667 9.07 0.00 46.49 5.36
3292 3415 4.323477 TCCGTTTGGGTCGGCCAG 62.323 66.667 9.07 0.00 46.49 4.85
3306 3429 4.082523 CCAGGCGGACACGGATGT 62.083 66.667 0.00 0.00 43.71 3.06
3319 3442 3.857638 GGATGTCCGTTTTTGCGTT 57.142 47.368 0.00 0.00 0.00 4.84
3320 3443 2.128367 GGATGTCCGTTTTTGCGTTT 57.872 45.000 0.00 0.00 0.00 3.60
3321 3444 1.784283 GGATGTCCGTTTTTGCGTTTG 59.216 47.619 0.00 0.00 0.00 2.93
3322 3445 1.784283 GATGTCCGTTTTTGCGTTTGG 59.216 47.619 0.00 0.00 0.00 3.28
3323 3446 0.179134 TGTCCGTTTTTGCGTTTGGG 60.179 50.000 0.00 0.00 0.00 4.12
3324 3447 0.179132 GTCCGTTTTTGCGTTTGGGT 60.179 50.000 0.00 0.00 0.00 4.51
3325 3448 0.100861 TCCGTTTTTGCGTTTGGGTC 59.899 50.000 0.00 0.00 0.00 4.46
3326 3449 1.203600 CCGTTTTTGCGTTTGGGTCG 61.204 55.000 0.00 0.00 0.00 4.79
3327 3450 1.203600 CGTTTTTGCGTTTGGGTCGG 61.204 55.000 0.00 0.00 0.00 4.79
3328 3451 1.227002 TTTTTGCGTTTGGGTCGGC 60.227 52.632 0.00 0.00 0.00 5.54
3329 3452 2.938539 TTTTTGCGTTTGGGTCGGCG 62.939 55.000 0.00 0.00 0.00 6.46
3352 3475 3.426568 GCTCAACGCTGGCCTGAC 61.427 66.667 14.77 3.95 35.14 3.51
3353 3476 2.743928 CTCAACGCTGGCCTGACC 60.744 66.667 14.77 0.00 39.84 4.02
3354 3477 4.329545 TCAACGCTGGCCTGACCC 62.330 66.667 14.77 0.00 37.83 4.46
3355 3478 4.641645 CAACGCTGGCCTGACCCA 62.642 66.667 14.77 0.00 37.83 4.51
3356 3479 3.650950 AACGCTGGCCTGACCCAT 61.651 61.111 14.77 0.00 37.83 4.00
3357 3480 3.210012 AACGCTGGCCTGACCCATT 62.210 57.895 14.77 0.00 37.83 3.16
3358 3481 2.361610 CGCTGGCCTGACCCATTT 60.362 61.111 14.77 0.00 37.83 2.32
3359 3482 1.978617 CGCTGGCCTGACCCATTTT 60.979 57.895 14.77 0.00 37.83 1.82
3360 3483 1.593265 GCTGGCCTGACCCATTTTG 59.407 57.895 14.77 0.00 37.83 2.44
3361 3484 0.899717 GCTGGCCTGACCCATTTTGA 60.900 55.000 14.77 0.00 37.83 2.69
3362 3485 0.890683 CTGGCCTGACCCATTTTGAC 59.109 55.000 3.32 0.00 37.83 3.18
3363 3486 0.893270 TGGCCTGACCCATTTTGACG 60.893 55.000 3.32 0.00 37.83 4.35
3364 3487 1.595093 GGCCTGACCCATTTTGACGG 61.595 60.000 0.00 0.00 0.00 4.79
3365 3488 1.883021 CCTGACCCATTTTGACGGC 59.117 57.895 0.00 0.00 0.00 5.68
3366 3489 1.501741 CTGACCCATTTTGACGGCG 59.498 57.895 4.80 4.80 0.00 6.46
3367 3490 1.922135 CTGACCCATTTTGACGGCGG 61.922 60.000 13.24 0.00 0.00 6.13
3368 3491 1.969589 GACCCATTTTGACGGCGGT 60.970 57.895 13.24 0.00 0.00 5.68
3369 3492 0.674269 GACCCATTTTGACGGCGGTA 60.674 55.000 13.24 0.00 0.00 4.02
3370 3493 0.675522 ACCCATTTTGACGGCGGTAG 60.676 55.000 13.24 0.00 0.00 3.18
3371 3494 0.391927 CCCATTTTGACGGCGGTAGA 60.392 55.000 13.24 0.00 0.00 2.59
3372 3495 1.444836 CCATTTTGACGGCGGTAGAA 58.555 50.000 13.24 1.11 0.00 2.10
3373 3496 1.807742 CCATTTTGACGGCGGTAGAAA 59.192 47.619 13.24 7.14 0.00 2.52
3374 3497 2.226912 CCATTTTGACGGCGGTAGAAAA 59.773 45.455 13.24 10.59 0.00 2.29
3375 3498 3.304794 CCATTTTGACGGCGGTAGAAAAA 60.305 43.478 13.24 10.44 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
171 172 6.455646 CGAAATCGAAGGAATTGATCGTCTTT 60.456 38.462 0.00 0.00 43.02 2.52
174 175 4.267928 ACGAAATCGAAGGAATTGATCGTC 59.732 41.667 10.16 0.00 43.02 4.20
176 177 4.504461 AGACGAAATCGAAGGAATTGATCG 59.496 41.667 10.16 0.00 43.02 3.69
218 219 2.847327 TGAAGAGGTTGCTCTTGGAG 57.153 50.000 0.00 0.00 43.03 3.86
242 243 2.045340 CCGTTGGGGGTGATGGTC 60.045 66.667 0.00 0.00 0.00 4.02
267 293 0.464373 ACTGGAGCGTTGCATATGGG 60.464 55.000 4.56 0.00 0.00 4.00
268 294 1.064505 CAACTGGAGCGTTGCATATGG 59.935 52.381 4.56 0.00 37.98 2.74
270 296 2.401583 TCAACTGGAGCGTTGCATAT 57.598 45.000 0.00 0.00 42.98 1.78
271 297 2.009051 CATCAACTGGAGCGTTGCATA 58.991 47.619 0.00 0.00 42.98 3.14
276 305 0.317160 TCGTCATCAACTGGAGCGTT 59.683 50.000 0.00 0.00 0.00 4.84
278 307 1.078759 GGTCGTCATCAACTGGAGCG 61.079 60.000 0.00 0.00 0.00 5.03
312 341 1.434188 TGGATGCCTATGGGGTACTG 58.566 55.000 0.00 0.00 37.43 2.74
335 364 5.041460 CCAAGAGGAATAGGGCATCCCAA 62.041 52.174 4.51 0.00 41.67 4.12
348 377 4.344865 GGGCGGCACCAAGAGGAA 62.345 66.667 12.47 0.00 42.05 3.36
354 383 4.424711 GATGGAGGGCGGCACCAA 62.425 66.667 25.12 12.79 42.05 3.67
387 416 1.074248 GGTTCGACAACATGGGGGT 59.926 57.895 0.00 0.00 33.70 4.95
388 417 0.676782 GAGGTTCGACAACATGGGGG 60.677 60.000 0.00 0.00 33.70 5.40
394 423 1.068417 CCGTGGAGGTTCGACAACA 59.932 57.895 0.00 0.00 33.70 3.33
410 439 0.448990 TCGACGACCTAATGTCACCG 59.551 55.000 0.00 0.00 44.71 4.94
416 445 3.046390 GAGAGCAATCGACGACCTAATG 58.954 50.000 0.00 0.00 0.00 1.90
420 449 0.736053 GAGAGAGCAATCGACGACCT 59.264 55.000 0.00 0.00 0.00 3.85
452 481 6.940430 AGAATGTTTCTGGAATCCCAAATT 57.060 33.333 0.00 0.00 42.98 1.82
483 512 1.300620 CGGAGTGGAGTTCGTTGCA 60.301 57.895 0.00 0.00 0.00 4.08
642 672 6.461698 CGAATGCATTACTCAAAAACGACTAC 59.538 38.462 12.97 0.00 0.00 2.73
650 680 3.822594 ACGCGAATGCATTACTCAAAA 57.177 38.095 15.93 0.00 42.97 2.44
677 707 2.314852 TGACCAATCACTAGGGGAGAGA 59.685 50.000 0.00 0.00 0.00 3.10
758 790 7.433680 GGTAACAAGATTCAGTTTTGGTGAAT 58.566 34.615 0.00 0.00 45.37 2.57
759 791 6.801575 GGTAACAAGATTCAGTTTTGGTGAA 58.198 36.000 0.76 0.00 38.28 3.18
796 828 2.569404 AGCACAAGAGGTAAAGAGGAGG 59.431 50.000 0.00 0.00 0.00 4.30
924 957 2.178273 CGGGCGGCTACAAAAAGC 59.822 61.111 9.56 0.00 41.99 3.51
1035 1068 1.002502 AGTTGGCTTAAGGACGGCC 60.003 57.895 0.00 0.00 45.45 6.13
1036 1069 0.321298 TGAGTTGGCTTAAGGACGGC 60.321 55.000 4.29 0.00 0.00 5.68
1037 1070 1.676014 CCTGAGTTGGCTTAAGGACGG 60.676 57.143 4.29 0.00 33.24 4.79
1038 1071 1.002087 ACCTGAGTTGGCTTAAGGACG 59.998 52.381 4.29 0.00 34.66 4.79
1051 1084 2.757868 CTCTAGTTGCTGCTACCTGAGT 59.242 50.000 18.24 3.20 0.00 3.41
1270 1303 2.747686 GACCGTCTTCCTGGGCAA 59.252 61.111 0.00 0.00 31.69 4.52
1528 1561 4.083590 GCACAAGAAGAAGATCACCAAGAC 60.084 45.833 0.00 0.00 0.00 3.01
1533 1566 3.190118 CCAAGCACAAGAAGAAGATCACC 59.810 47.826 0.00 0.00 0.00 4.02
1558 1591 1.243902 TCAGATTTCCGCAACCAACC 58.756 50.000 0.00 0.00 0.00 3.77
1604 1644 2.867109 TCTTCAGCCCCTTCAAGAAG 57.133 50.000 2.83 2.83 37.60 2.85
1834 1874 2.834043 TGTCGACGGTGGTGACCA 60.834 61.111 11.62 0.00 43.33 4.02
1836 1876 2.666715 TTCGTGTCGACGGTGGTGAC 62.667 60.000 11.62 0.21 46.11 3.67
2097 2137 1.224075 GTGGATGCGATGATGGTGAG 58.776 55.000 0.00 0.00 0.00 3.51
2123 2163 1.608336 CCTCGTCCCTGGTGTGGTA 60.608 63.158 0.00 0.00 0.00 3.25
2124 2164 2.923035 CCTCGTCCCTGGTGTGGT 60.923 66.667 0.00 0.00 0.00 4.16
2127 2167 3.314331 CTGCCTCGTCCCTGGTGT 61.314 66.667 0.00 0.00 0.00 4.16
2243 2284 1.728069 GCCGTGTCGCTCTCAGATA 59.272 57.895 0.00 0.00 0.00 1.98
2377 2419 7.570324 GCTTCATCGAAGGCTTATTACAGATTC 60.570 40.741 0.00 0.00 39.76 2.52
2384 2427 5.294306 CACAAGCTTCATCGAAGGCTTATTA 59.706 40.000 6.19 0.00 39.76 0.98
2424 2485 1.007849 GCGCTAGCTAGCTCCTGAC 60.008 63.158 36.02 18.29 46.85 3.51
2485 2561 1.024271 ATGGCGACGGATTCATTTGG 58.976 50.000 0.00 0.00 0.00 3.28
2487 2563 2.091541 ACAATGGCGACGGATTCATTT 58.908 42.857 0.00 0.00 0.00 2.32
2489 2565 1.750193 AACAATGGCGACGGATTCAT 58.250 45.000 0.00 0.00 0.00 2.57
2491 2567 3.126343 AGTTTAACAATGGCGACGGATTC 59.874 43.478 0.00 0.00 0.00 2.52
2538 2637 2.029918 AGAGCAAAGCCAAATCGAAACC 60.030 45.455 0.00 0.00 0.00 3.27
2554 2653 2.747855 TGAGCGAGCGAGAGAGCA 60.748 61.111 0.00 0.00 40.15 4.26
2567 2666 2.433318 GTGAGGTGAGCCGTGAGC 60.433 66.667 0.00 0.00 44.25 4.26
2568 2667 2.262915 GGTGAGGTGAGCCGTGAG 59.737 66.667 0.00 0.00 40.50 3.51
2569 2668 2.203640 AGGTGAGGTGAGCCGTGA 60.204 61.111 0.00 0.00 40.50 4.35
2570 2669 2.047844 CAGGTGAGGTGAGCCGTG 60.048 66.667 0.00 0.00 40.50 4.94
2571 2670 1.407656 TTTCAGGTGAGGTGAGCCGT 61.408 55.000 0.00 0.00 40.50 5.68
2572 2671 0.951040 GTTTCAGGTGAGGTGAGCCG 60.951 60.000 0.00 0.00 40.50 5.52
2573 2672 0.606673 GGTTTCAGGTGAGGTGAGCC 60.607 60.000 0.00 0.00 0.00 4.70
2624 2728 4.856607 GAGAAGCCCGGTCGCTCG 62.857 72.222 5.63 0.00 38.44 5.03
2625 2729 2.579684 AATGAGAAGCCCGGTCGCTC 62.580 60.000 5.63 3.70 38.44 5.03
2626 2730 1.327690 TAATGAGAAGCCCGGTCGCT 61.328 55.000 0.00 0.00 42.22 4.93
2838 2952 1.271379 CCTTCTTTCTTTCTCCCGGCA 60.271 52.381 0.00 0.00 0.00 5.69
2839 2953 1.003233 TCCTTCTTTCTTTCTCCCGGC 59.997 52.381 0.00 0.00 0.00 6.13
2840 2954 2.567615 TCTCCTTCTTTCTTTCTCCCGG 59.432 50.000 0.00 0.00 0.00 5.73
2841 2955 3.259625 ACTCTCCTTCTTTCTTTCTCCCG 59.740 47.826 0.00 0.00 0.00 5.14
2903 3018 4.131376 CCACTATCAGGCAAGGCG 57.869 61.111 0.00 0.00 0.00 5.52
2960 3079 1.132500 CCAACTCATCCCCTCCCTAC 58.868 60.000 0.00 0.00 0.00 3.18
3096 3219 2.822561 GCTTTTCTTTTCCTCTGGGGAG 59.177 50.000 0.00 0.00 46.01 4.30
3097 3220 2.176798 TGCTTTTCTTTTCCTCTGGGGA 59.823 45.455 0.00 0.00 43.41 4.81
3098 3221 2.597455 TGCTTTTCTTTTCCTCTGGGG 58.403 47.619 0.00 0.00 0.00 4.96
3103 3226 5.831997 TGCTAGTTTGCTTTTCTTTTCCTC 58.168 37.500 0.00 0.00 0.00 3.71
3106 3229 6.414079 GCTTTGCTAGTTTGCTTTTCTTTTC 58.586 36.000 0.00 0.00 0.00 2.29
3112 3235 3.550842 CGAGGCTTTGCTAGTTTGCTTTT 60.551 43.478 0.00 0.00 0.00 2.27
3121 3244 3.567797 GCGCCGAGGCTTTGCTAG 61.568 66.667 12.70 0.00 39.32 3.42
3213 3336 0.100325 CTCTGAGGCTCACTACTGCG 59.900 60.000 14.43 1.89 0.00 5.18
3230 3353 1.359459 CGGCCCGTTAGAGTTTGCTC 61.359 60.000 0.00 0.00 41.94 4.26
3231 3354 1.375523 CGGCCCGTTAGAGTTTGCT 60.376 57.895 0.00 0.00 0.00 3.91
3232 3355 1.375013 TCGGCCCGTTAGAGTTTGC 60.375 57.895 1.63 0.00 0.00 3.68
3233 3356 1.017701 GGTCGGCCCGTTAGAGTTTG 61.018 60.000 1.63 0.00 0.00 2.93
3234 3357 1.294459 GGTCGGCCCGTTAGAGTTT 59.706 57.895 1.63 0.00 0.00 2.66
3235 3358 2.653087 GGGTCGGCCCGTTAGAGTT 61.653 63.158 10.71 0.00 46.51 3.01
3236 3359 3.073101 GGGTCGGCCCGTTAGAGT 61.073 66.667 10.71 0.00 46.51 3.24
3245 3368 3.053896 CTTCCGTTTGGGTCGGCC 61.054 66.667 0.00 0.00 46.49 6.13
3246 3369 3.053896 CCTTCCGTTTGGGTCGGC 61.054 66.667 0.00 0.00 46.49 5.54
3248 3371 3.961729 GACCTTCCGTTTGGGTCG 58.038 61.111 0.00 0.00 39.80 4.79
3249 3372 4.391869 GGACCTTCCGTTTGGGTC 57.608 61.111 0.00 0.00 46.14 4.46
3258 3381 0.596577 GGACAAAAAGCGGACCTTCC 59.403 55.000 0.00 0.00 31.99 3.46
3259 3382 0.237498 CGGACAAAAAGCGGACCTTC 59.763 55.000 0.00 0.00 31.99 3.46
3260 3383 0.464916 ACGGACAAAAAGCGGACCTT 60.465 50.000 0.00 0.00 34.51 3.50
3261 3384 0.464916 AACGGACAAAAAGCGGACCT 60.465 50.000 0.00 0.00 0.00 3.85
3262 3385 0.382873 AAACGGACAAAAAGCGGACC 59.617 50.000 0.00 0.00 0.00 4.46
3263 3386 1.472990 CAAACGGACAAAAAGCGGAC 58.527 50.000 0.00 0.00 0.00 4.79
3264 3387 0.382515 CCAAACGGACAAAAAGCGGA 59.617 50.000 0.00 0.00 0.00 5.54
3265 3388 0.596341 CCCAAACGGACAAAAAGCGG 60.596 55.000 0.00 0.00 0.00 5.52
3266 3389 0.101579 ACCCAAACGGACAAAAAGCG 59.898 50.000 0.00 0.00 34.64 4.68
3267 3390 1.847818 GACCCAAACGGACAAAAAGC 58.152 50.000 0.00 0.00 34.64 3.51
3268 3391 2.113910 CGACCCAAACGGACAAAAAG 57.886 50.000 0.00 0.00 34.64 2.27
3289 3412 4.082523 ACATCCGTGTCCGCCTGG 62.083 66.667 0.00 0.00 31.41 4.45
3301 3424 1.784283 CAAACGCAAAAACGGACATCC 59.216 47.619 0.00 0.00 37.37 3.51
3302 3425 1.784283 CCAAACGCAAAAACGGACATC 59.216 47.619 0.00 0.00 37.37 3.06
3303 3426 1.537135 CCCAAACGCAAAAACGGACAT 60.537 47.619 0.00 0.00 37.37 3.06
3304 3427 0.179134 CCCAAACGCAAAAACGGACA 60.179 50.000 0.00 0.00 37.37 4.02
3305 3428 0.179132 ACCCAAACGCAAAAACGGAC 60.179 50.000 0.00 0.00 37.37 4.79
3306 3429 0.100861 GACCCAAACGCAAAAACGGA 59.899 50.000 0.00 0.00 37.37 4.69
3307 3430 1.203600 CGACCCAAACGCAAAAACGG 61.204 55.000 0.00 0.00 37.37 4.44
3308 3431 1.203600 CCGACCCAAACGCAAAAACG 61.204 55.000 0.00 0.00 39.50 3.60
3309 3432 1.484227 GCCGACCCAAACGCAAAAAC 61.484 55.000 0.00 0.00 0.00 2.43
3310 3433 1.227002 GCCGACCCAAACGCAAAAA 60.227 52.632 0.00 0.00 0.00 1.94
3311 3434 2.413765 GCCGACCCAAACGCAAAA 59.586 55.556 0.00 0.00 0.00 2.44
3312 3435 3.955101 CGCCGACCCAAACGCAAA 61.955 61.111 0.00 0.00 0.00 3.68
3336 3459 2.743928 GGTCAGGCCAGCGTTGAG 60.744 66.667 5.01 0.00 37.17 3.02
3337 3460 4.329545 GGGTCAGGCCAGCGTTGA 62.330 66.667 5.01 0.00 39.65 3.18
3338 3461 3.925630 ATGGGTCAGGCCAGCGTTG 62.926 63.158 5.01 0.00 39.65 4.10
3339 3462 2.713531 AAATGGGTCAGGCCAGCGTT 62.714 55.000 5.01 0.00 39.65 4.84
3340 3463 2.713531 AAAATGGGTCAGGCCAGCGT 62.714 55.000 5.01 0.00 39.65 5.07
3341 3464 1.978617 AAAATGGGTCAGGCCAGCG 60.979 57.895 5.01 0.00 39.65 5.18
3342 3465 0.899717 TCAAAATGGGTCAGGCCAGC 60.900 55.000 5.01 0.00 39.65 4.85
3343 3466 0.890683 GTCAAAATGGGTCAGGCCAG 59.109 55.000 5.01 0.00 39.65 4.85
3344 3467 0.893270 CGTCAAAATGGGTCAGGCCA 60.893 55.000 5.01 0.00 39.65 5.36
3345 3468 1.595093 CCGTCAAAATGGGTCAGGCC 61.595 60.000 0.00 0.00 0.00 5.19
3346 3469 1.883021 CCGTCAAAATGGGTCAGGC 59.117 57.895 0.00 0.00 0.00 4.85
3347 3470 1.883021 GCCGTCAAAATGGGTCAGG 59.117 57.895 0.00 0.00 31.56 3.86
3348 3471 1.501741 CGCCGTCAAAATGGGTCAG 59.498 57.895 0.00 0.00 31.56 3.51
3349 3472 1.969064 CCGCCGTCAAAATGGGTCA 60.969 57.895 0.00 0.00 31.56 4.02
3350 3473 0.674269 TACCGCCGTCAAAATGGGTC 60.674 55.000 0.00 0.00 31.56 4.46
3351 3474 0.675522 CTACCGCCGTCAAAATGGGT 60.676 55.000 0.00 0.00 31.56 4.51
3352 3475 0.391927 TCTACCGCCGTCAAAATGGG 60.392 55.000 0.00 0.00 31.56 4.00
3353 3476 1.444836 TTCTACCGCCGTCAAAATGG 58.555 50.000 0.00 0.00 34.35 3.16
3354 3477 3.546002 TTTTCTACCGCCGTCAAAATG 57.454 42.857 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.