Multiple sequence alignment - TraesCS5A01G254500

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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 TraesCS5A01G254500 chr5A 100.000 4330 0 0 1 4330 470183272 470187601 0.000000e+00 7997.0
1 TraesCS5A01G254500 chr5A 83.159 2684 300 64 745 3327 470174808 470177440 0.000000e+00 2313.0
2 TraesCS5A01G254500 chr5D 92.477 2765 140 22 741 3479 368299221 368301943 0.000000e+00 3892.0
3 TraesCS5A01G254500 chr5D 83.911 2511 291 60 744 3190 368290331 368292792 0.000000e+00 2294.0
4 TraesCS5A01G254500 chr5D 88.651 793 50 18 3476 4236 368302076 368302860 0.000000e+00 929.0
5 TraesCS5A01G254500 chr5D 88.095 504 26 9 257 744 368298653 368299138 6.280000e-158 568.0
6 TraesCS5A01G254500 chr5D 82.410 415 37 19 296 685 368289898 368290301 3.230000e-86 329.0
7 TraesCS5A01G254500 chr5D 95.556 90 4 0 4239 4328 368324408 368324497 1.250000e-30 145.0
8 TraesCS5A01G254500 chr5B 92.056 2442 132 20 762 3161 436244268 436246689 0.000000e+00 3378.0
9 TraesCS5A01G254500 chr5B 83.358 2686 288 74 744 3327 436213614 436216242 0.000000e+00 2337.0
10 TraesCS5A01G254500 chr5B 86.444 509 27 20 3756 4236 436247220 436247714 1.780000e-143 520.0
11 TraesCS5A01G254500 chr5B 85.337 416 21 9 257 656 436243748 436244139 1.130000e-105 394.0
12 TraesCS5A01G254500 chr5B 88.843 242 15 7 1 236 436243527 436243762 1.970000e-73 287.0
13 TraesCS5A01G254500 chr5B 91.444 187 12 3 3145 3327 436246704 436246890 2.000000e-63 254.0
14 TraesCS5A01G254500 chr5B 83.219 292 14 8 326 591 436213229 436213511 7.240000e-58 235.0
15 TraesCS5A01G254500 chr6D 88.095 84 10 0 3628 3711 2625191 2625274 2.760000e-17 100.0
16 TraesCS5A01G254500 chr3A 98.214 56 1 0 689 744 671629484 671629429 9.910000e-17 99.0
17 TraesCS5A01G254500 chr2A 98.214 56 1 0 689 744 469895047 469894992 9.910000e-17 99.0
18 TraesCS5A01G254500 chr2A 92.647 68 5 0 677 744 628673034 628673101 9.910000e-17 99.0
19 TraesCS5A01G254500 chr6B 96.491 57 2 0 688 744 617675164 617675220 1.280000e-15 95.3
20 TraesCS5A01G254500 chr6B 96.429 56 1 1 689 744 377934344 377934398 1.660000e-14 91.6
21 TraesCS5A01G254500 chr7D 96.429 56 2 0 689 744 452449644 452449699 4.610000e-15 93.5
22 TraesCS5A01G254500 chr7D 94.643 56 3 0 689 744 115052305 115052250 2.150000e-13 87.9
23 TraesCS5A01G254500 chr2B 96.429 56 2 0 689 744 8493854 8493799 4.610000e-15 93.5


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 TraesCS5A01G254500 chr5A 470183272 470187601 4329 False 7997.000000 7997 100.0000 1 4330 1 chr5A.!!$F2 4329
1 TraesCS5A01G254500 chr5A 470174808 470177440 2632 False 2313.000000 2313 83.1590 745 3327 1 chr5A.!!$F1 2582
2 TraesCS5A01G254500 chr5D 368298653 368302860 4207 False 1796.333333 3892 89.7410 257 4236 3 chr5D.!!$F3 3979
3 TraesCS5A01G254500 chr5D 368289898 368292792 2894 False 1311.500000 2294 83.1605 296 3190 2 chr5D.!!$F2 2894
4 TraesCS5A01G254500 chr5B 436213229 436216242 3013 False 1286.000000 2337 83.2885 326 3327 2 chr5B.!!$F1 3001
5 TraesCS5A01G254500 chr5B 436243527 436247714 4187 False 966.600000 3378 88.8248 1 4236 5 chr5B.!!$F2 4235

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
232 239 0.034863 GGTTGGGGATTGAAGCCGTA 60.035 55.0 0.00 0.0 0.0 4.02 F
285 292 0.174845 TATCCGTTCCGAACCTGCTG 59.825 55.0 5.67 0.0 0.0 4.41 F
989 1149 0.179078 GGATCTGGCAGCACTCTCAG 60.179 60.0 10.34 0.0 0.0 3.35 F
1482 1646 0.249447 GTTTCAGCCCAGCCACAAAC 60.249 55.0 0.00 0.0 0.0 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1113 1274 0.031178 CCCACTGCTTGCAGACAAAC 59.969 55.0 26.71 0.00 34.74 2.93 R
1114 1275 0.106769 TCCCACTGCTTGCAGACAAA 60.107 50.0 26.71 8.59 34.74 2.83 R
2372 2557 0.037046 GCCATTTCCTGCCAACAAGG 60.037 55.0 0.00 0.00 41.84 3.61 R
3329 3655 0.034863 ATTAACCGGGCACGTGGATT 60.035 50.0 18.88 0.00 38.78 3.01 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
60 62 8.669946 TTGGGAATTTGAAATAAAAGTTCACC 57.330 30.769 0.00 0.00 34.78 4.02
145 147 2.203280 CCACAGGAAACCGCCACA 60.203 61.111 0.00 0.00 0.00 4.17
172 174 2.586357 GCGGGAAGCGGATCAGAC 60.586 66.667 0.00 0.00 35.41 3.51
173 175 2.892640 CGGGAAGCGGATCAGACA 59.107 61.111 0.00 0.00 0.00 3.41
188 195 7.379529 GCGGATCAGACAAAAATAACAATATGG 59.620 37.037 0.00 0.00 0.00 2.74
192 199 7.546358 TCAGACAAAAATAACAATATGGCCAG 58.454 34.615 13.05 0.00 0.00 4.85
202 209 1.959042 ATATGGCCAGCGCTATATGC 58.041 50.000 10.99 10.86 44.77 3.14
223 230 3.474083 CACAAAGGGGTTGGGGATT 57.526 52.632 0.00 0.00 41.97 3.01
224 231 0.975887 CACAAAGGGGTTGGGGATTG 59.024 55.000 0.00 0.00 41.97 2.67
225 232 0.863956 ACAAAGGGGTTGGGGATTGA 59.136 50.000 0.00 0.00 41.97 2.57
226 233 1.221781 ACAAAGGGGTTGGGGATTGAA 59.778 47.619 0.00 0.00 41.97 2.69
227 234 1.901833 CAAAGGGGTTGGGGATTGAAG 59.098 52.381 0.00 0.00 33.18 3.02
228 235 0.252239 AAGGGGTTGGGGATTGAAGC 60.252 55.000 0.00 0.00 0.00 3.86
229 236 1.685765 GGGGTTGGGGATTGAAGCC 60.686 63.158 0.00 0.00 38.73 4.35
230 237 2.052104 GGGTTGGGGATTGAAGCCG 61.052 63.158 0.00 0.00 30.49 5.52
231 238 1.304134 GGTTGGGGATTGAAGCCGT 60.304 57.895 0.00 0.00 0.00 5.68
232 239 0.034863 GGTTGGGGATTGAAGCCGTA 60.035 55.000 0.00 0.00 0.00 4.02
233 240 1.409661 GGTTGGGGATTGAAGCCGTAT 60.410 52.381 0.00 0.00 0.00 3.06
234 241 1.947456 GTTGGGGATTGAAGCCGTATC 59.053 52.381 0.00 0.00 0.00 2.24
235 242 0.472471 TGGGGATTGAAGCCGTATCC 59.528 55.000 0.00 0.00 37.66 2.59
236 243 0.765510 GGGGATTGAAGCCGTATCCT 59.234 55.000 0.00 0.00 38.30 3.24
237 244 1.143073 GGGGATTGAAGCCGTATCCTT 59.857 52.381 0.00 0.00 38.30 3.36
238 245 2.422945 GGGGATTGAAGCCGTATCCTTT 60.423 50.000 0.00 0.00 38.30 3.11
239 246 3.288092 GGGATTGAAGCCGTATCCTTTT 58.712 45.455 0.00 0.00 38.30 2.27
240 247 3.699538 GGGATTGAAGCCGTATCCTTTTT 59.300 43.478 0.00 0.00 38.30 1.94
283 290 1.143969 CGTATCCGTTCCGAACCTGC 61.144 60.000 5.67 0.00 0.00 4.85
284 291 0.175073 GTATCCGTTCCGAACCTGCT 59.825 55.000 5.67 0.00 0.00 4.24
285 292 0.174845 TATCCGTTCCGAACCTGCTG 59.825 55.000 5.67 0.00 0.00 4.41
292 299 3.052082 CGAACCTGCTGGCCACTG 61.052 66.667 0.00 3.18 36.63 3.66
353 365 2.413310 CCCACAGGCGGTTAAATACT 57.587 50.000 0.00 0.00 0.00 2.12
354 366 2.285977 CCCACAGGCGGTTAAATACTC 58.714 52.381 0.00 0.00 0.00 2.59
382 394 2.881827 CGATGAAACGGCGGCGTA 60.882 61.111 37.59 22.89 0.00 4.42
476 504 2.360980 CGTGAGTCTCCCCTCCCT 59.639 66.667 0.00 0.00 0.00 4.20
477 505 1.305381 CGTGAGTCTCCCCTCCCTT 60.305 63.158 0.00 0.00 0.00 3.95
478 506 1.324005 CGTGAGTCTCCCCTCCCTTC 61.324 65.000 0.00 0.00 0.00 3.46
479 507 0.978667 GTGAGTCTCCCCTCCCTTCC 60.979 65.000 0.00 0.00 0.00 3.46
480 508 1.383386 GAGTCTCCCCTCCCTTCCC 60.383 68.421 0.00 0.00 0.00 3.97
486 514 1.696674 CCCCTCCCTTCCCCTAACC 60.697 68.421 0.00 0.00 0.00 2.85
528 556 3.311106 CTCTACGTTTTCTGTAACCGCA 58.689 45.455 0.00 0.00 0.00 5.69
529 557 3.311106 TCTACGTTTTCTGTAACCGCAG 58.689 45.455 0.00 0.00 37.81 5.18
605 650 2.291190 GGGAAAAACGTTCAATCCGTCA 59.709 45.455 16.24 0.00 37.61 4.35
705 760 0.251742 TTTACTCCCTCCGTCCGGAA 60.252 55.000 5.23 0.00 44.66 4.30
709 764 1.534717 TCCCTCCGTCCGGAAAAGT 60.535 57.895 5.23 0.00 44.66 2.66
827 982 2.242043 GGGGATAATGTTGAGGGCATG 58.758 52.381 0.00 0.00 0.00 4.06
828 985 2.424812 GGGGATAATGTTGAGGGCATGT 60.425 50.000 0.00 0.00 0.00 3.21
838 995 3.071874 TGAGGGCATGTCGATTTCTTT 57.928 42.857 0.00 0.00 0.00 2.52
839 996 2.749076 TGAGGGCATGTCGATTTCTTTG 59.251 45.455 0.00 0.00 0.00 2.77
846 1006 2.699954 TGTCGATTTCTTTGGCTCCTC 58.300 47.619 0.00 0.00 0.00 3.71
854 1014 6.571150 CGATTTCTTTGGCTCCTCTTTTGATT 60.571 38.462 0.00 0.00 0.00 2.57
887 1047 1.160137 AAACTGCGCTGAATGACCTC 58.840 50.000 21.92 0.00 0.00 3.85
899 1059 4.769688 TGAATGACCTCGCTTTCATGTAT 58.230 39.130 0.00 0.00 32.63 2.29
937 1097 2.066262 TCAGTCTCCGAATTCGTTTGC 58.934 47.619 25.10 13.01 37.74 3.68
962 1122 1.867233 CCAGTCCGTCAAACTGTTGAG 59.133 52.381 0.00 0.00 44.44 3.02
989 1149 0.179078 GGATCTGGCAGCACTCTCAG 60.179 60.000 10.34 0.00 0.00 3.35
1037 1198 2.760092 TGCAGCCAACAAAGAAGAAACT 59.240 40.909 0.00 0.00 0.00 2.66
1078 1239 9.254133 CACAAGATATCATCGAACTGATACTTT 57.746 33.333 10.20 6.13 40.08 2.66
1198 1359 4.821589 CGCAGCCTCGACCCCTTC 62.822 72.222 0.00 0.00 0.00 3.46
1217 1378 1.735571 TCTATTTTTCCAACGAGGCGC 59.264 47.619 0.00 0.00 37.29 6.53
1224 1385 2.442188 CCAACGAGGCGCGACTTAC 61.442 63.158 19.64 2.24 44.57 2.34
1482 1646 0.249447 GTTTCAGCCCAGCCACAAAC 60.249 55.000 0.00 0.00 0.00 2.93
1873 2040 2.594592 GGCTTGCACGGAGGTTGT 60.595 61.111 0.00 0.00 0.00 3.32
1936 2106 7.816995 GGATCCAGAAGCATAGTATTGAGTTAG 59.183 40.741 6.95 0.00 0.00 2.34
1938 2108 6.325028 TCCAGAAGCATAGTATTGAGTTAGCT 59.675 38.462 0.00 0.00 0.00 3.32
1947 2117 5.738909 AGTATTGAGTTAGCTGCACTTGAT 58.261 37.500 1.02 0.03 0.00 2.57
1955 2125 8.206867 TGAGTTAGCTGCACTTGATATTCTAAT 58.793 33.333 1.02 0.00 0.00 1.73
1956 2126 8.375608 AGTTAGCTGCACTTGATATTCTAATG 57.624 34.615 1.02 0.00 0.00 1.90
2163 2336 1.392589 CATACAAGAAGGCCGGCATT 58.607 50.000 28.81 28.81 0.00 3.56
2238 2411 1.261619 GAACACAAACGCTCTGAGGTG 59.738 52.381 6.83 7.98 0.00 4.00
2371 2556 5.338614 GTGTGACACACTGTAATAACCAC 57.661 43.478 27.73 0.18 45.27 4.16
2372 2557 4.212636 GTGTGACACACTGTAATAACCACC 59.787 45.833 27.73 0.00 45.27 4.61
2400 2585 1.064060 GCAGGAAATGGCACGTATGAC 59.936 52.381 0.00 0.00 0.00 3.06
2460 2645 6.352565 CCAGATCAGGTAAACTTCATCCTTCT 60.353 42.308 0.00 0.00 0.00 2.85
2520 2706 7.535139 TCGGATCAACATTTCCTTACAATTTC 58.465 34.615 0.00 0.00 0.00 2.17
2600 2790 2.356125 GCTTAATTGGGTGGAGCAGAGA 60.356 50.000 0.00 0.00 33.68 3.10
2608 2798 2.997897 GGAGCAGAGACGGGTGGT 60.998 66.667 0.00 0.00 0.00 4.16
2625 2815 3.256631 GGTGGTGAACATGCTGAAATCTT 59.743 43.478 0.00 0.00 0.00 2.40
2682 2880 6.475504 TGGTCTTCTTTGAGCAGAATCATTA 58.524 36.000 0.00 0.00 39.20 1.90
2683 2881 6.942005 TGGTCTTCTTTGAGCAGAATCATTAA 59.058 34.615 0.00 0.00 39.20 1.40
2684 2882 7.613022 TGGTCTTCTTTGAGCAGAATCATTAAT 59.387 33.333 0.00 0.00 39.20 1.40
2685 2883 8.465201 GGTCTTCTTTGAGCAGAATCATTAATT 58.535 33.333 0.00 0.00 32.21 1.40
2686 2884 9.852091 GTCTTCTTTGAGCAGAATCATTAATTT 57.148 29.630 0.00 0.00 32.21 1.82
2693 2891 6.308524 TGAGCAGAATCATTAATTTTGTTGCG 59.691 34.615 0.00 0.00 33.16 4.85
2719 2917 6.698008 TGTCTCTGTGATGTTGTGAATTTT 57.302 33.333 0.00 0.00 0.00 1.82
2752 2950 7.791029 TGACATGTTATTTCTAGGTCATAGCA 58.209 34.615 0.00 0.00 0.00 3.49
2765 2963 2.659063 ATAGCACAGGCAGCGGACA 61.659 57.895 0.00 0.00 44.61 4.02
2874 3076 5.496556 CCTCCCTGTTCATGTTACATGTTA 58.503 41.667 22.58 11.07 0.00 2.41
2910 3117 5.279456 CCATTTCCCTTAAACAAGGAAGGTG 60.279 44.000 4.97 1.59 42.62 4.00
2930 3137 3.041211 TGATGACTTGCTGCTAGGGTAT 58.959 45.455 15.18 6.42 0.00 2.73
2959 3166 6.968904 CAGTATGATGGTATTCACTTTTGCAC 59.031 38.462 0.00 0.00 39.69 4.57
3002 3238 8.402798 TCATTTATTCAAAGCACTGGTAGAAA 57.597 30.769 0.00 0.00 0.00 2.52
3068 3324 4.370364 AGACGCACACAAAAGTTGAAAT 57.630 36.364 0.00 0.00 0.00 2.17
3083 3342 5.242434 AGTTGAAATTCTGCACCATACGTA 58.758 37.500 0.00 0.00 0.00 3.57
3084 3343 5.121768 AGTTGAAATTCTGCACCATACGTAC 59.878 40.000 0.00 0.00 0.00 3.67
3085 3344 3.615056 TGAAATTCTGCACCATACGTACG 59.385 43.478 15.01 15.01 0.00 3.67
3086 3345 2.953466 ATTCTGCACCATACGTACGT 57.047 45.000 25.98 25.98 0.00 3.57
3087 3346 1.985334 TTCTGCACCATACGTACGTG 58.015 50.000 30.25 16.37 0.00 4.49
3088 3347 0.883153 TCTGCACCATACGTACGTGT 59.117 50.000 30.25 21.74 0.00 4.49
3089 3348 1.270274 TCTGCACCATACGTACGTGTT 59.730 47.619 30.25 15.00 0.00 3.32
3090 3349 2.063266 CTGCACCATACGTACGTGTTT 58.937 47.619 30.25 12.43 0.00 2.83
3091 3350 3.057666 TCTGCACCATACGTACGTGTTTA 60.058 43.478 30.25 11.31 0.00 2.01
3092 3351 3.646946 TGCACCATACGTACGTGTTTAA 58.353 40.909 30.25 10.89 0.00 1.52
3176 3471 3.374988 TCATTTTGCAAGGCTGTAGATCG 59.625 43.478 0.00 0.00 0.00 3.69
3224 3547 2.409975 CATCCTTTGTTTTGCAGCAGG 58.590 47.619 0.00 0.00 33.09 4.85
3281 3607 1.003355 CGAAAGAGGAAGCCCAGCA 60.003 57.895 0.00 0.00 33.88 4.41
3286 3612 3.635268 GAGGAAGCCCAGCACCAGG 62.635 68.421 5.82 0.00 33.88 4.45
3329 3655 2.815211 GATTCTGCAGCGCCGTGA 60.815 61.111 9.47 0.00 0.00 4.35
3332 3658 1.709147 ATTCTGCAGCGCCGTGAATC 61.709 55.000 9.47 0.00 0.00 2.52
3333 3659 3.869272 CTGCAGCGCCGTGAATCC 61.869 66.667 2.29 0.00 0.00 3.01
3334 3660 4.695993 TGCAGCGCCGTGAATCCA 62.696 61.111 2.29 0.00 0.00 3.41
3444 3770 1.977854 ACTGTATGGTGCCAAGACTCA 59.022 47.619 0.00 0.00 0.00 3.41
3469 3795 1.061546 AAGCCGTGGTCCCTTTTAGA 58.938 50.000 0.00 0.00 0.00 2.10
3470 3796 0.323957 AGCCGTGGTCCCTTTTAGAC 59.676 55.000 0.00 0.00 0.00 2.59
3471 3797 0.323957 GCCGTGGTCCCTTTTAGACT 59.676 55.000 0.00 0.00 34.56 3.24
3472 3798 1.675116 GCCGTGGTCCCTTTTAGACTC 60.675 57.143 0.00 0.00 34.56 3.36
3473 3799 1.621814 CCGTGGTCCCTTTTAGACTCA 59.378 52.381 0.00 0.00 34.56 3.41
3483 3949 4.153655 CCCTTTTAGACTCAAAAGCGTACC 59.846 45.833 3.37 0.00 41.93 3.34
3506 3972 3.570926 TCTTCAGTAGGCGTTGTGTAG 57.429 47.619 0.00 0.00 0.00 2.74
3508 3974 3.057736 TCTTCAGTAGGCGTTGTGTAGAC 60.058 47.826 0.00 0.00 0.00 2.59
3553 4019 7.940178 ATCGGTGTTTATCAAAAAGGAAAAC 57.060 32.000 0.00 0.00 0.00 2.43
3556 4022 7.650104 TCGGTGTTTATCAAAAAGGAAAACATC 59.350 33.333 2.68 1.58 40.82 3.06
3615 4088 3.490759 GATGCCGCGTCACCACTG 61.491 66.667 4.92 0.00 0.00 3.66
3630 4103 3.947834 CACCACTGGAATTTCCTCATACC 59.052 47.826 16.25 0.00 37.46 2.73
3641 4114 1.443407 CTCATACCCCGAGTGCCTG 59.557 63.158 0.00 0.00 0.00 4.85
3648 4121 2.348998 CCGAGTGCCTGGCTCTTT 59.651 61.111 22.78 3.48 32.35 2.52
3665 4138 3.037549 TCTTTGCCAAGAACCAAACCAT 58.962 40.909 0.00 0.00 35.99 3.55
3715 4205 4.574599 GAGGAAAACTCAGCAAACACAT 57.425 40.909 0.00 0.00 45.85 3.21
3716 4206 4.540824 GAGGAAAACTCAGCAAACACATC 58.459 43.478 0.00 0.00 45.85 3.06
3725 4215 4.406456 TCAGCAAACACATCCATTTACCT 58.594 39.130 0.00 0.00 0.00 3.08
3778 4278 1.927174 CCGTTGTTCCTCGATCATCAC 59.073 52.381 0.00 0.00 0.00 3.06
3894 4401 4.141846 GGTGACATGACATGACCAGTCTAT 60.142 45.833 22.19 0.00 36.94 1.98
3895 4402 5.069119 GGTGACATGACATGACCAGTCTATA 59.931 44.000 22.19 0.00 36.94 1.31
3924 4431 1.522355 AGTTCCTGCATCGATGGCG 60.522 57.895 26.00 13.60 39.35 5.69
4224 4749 1.751927 GGCACAATCAGGGAGCAGG 60.752 63.158 0.00 0.00 0.00 4.85
4239 4764 4.658786 AGGGAGGAGGGTGCCGTT 62.659 66.667 0.00 0.00 31.91 4.44
4240 4765 2.686106 GGGAGGAGGGTGCCGTTA 60.686 66.667 0.00 0.00 0.00 3.18
4241 4766 2.732619 GGGAGGAGGGTGCCGTTAG 61.733 68.421 0.00 0.00 0.00 2.34
4242 4767 1.988406 GGAGGAGGGTGCCGTTAGT 60.988 63.158 0.00 0.00 0.00 2.24
4243 4768 1.551019 GGAGGAGGGTGCCGTTAGTT 61.551 60.000 0.00 0.00 0.00 2.24
4244 4769 0.108281 GAGGAGGGTGCCGTTAGTTC 60.108 60.000 0.00 0.00 0.00 3.01
4245 4770 1.447314 GGAGGGTGCCGTTAGTTCG 60.447 63.158 0.00 0.00 0.00 3.95
4246 4771 1.588082 GAGGGTGCCGTTAGTTCGA 59.412 57.895 0.00 0.00 0.00 3.71
4247 4772 0.458025 GAGGGTGCCGTTAGTTCGAG 60.458 60.000 0.00 0.00 0.00 4.04
4248 4773 0.896940 AGGGTGCCGTTAGTTCGAGA 60.897 55.000 0.00 0.00 0.00 4.04
4249 4774 0.458025 GGGTGCCGTTAGTTCGAGAG 60.458 60.000 0.00 0.00 0.00 3.20
4250 4775 0.458025 GGTGCCGTTAGTTCGAGAGG 60.458 60.000 0.00 0.00 0.00 3.69
4251 4776 0.458025 GTGCCGTTAGTTCGAGAGGG 60.458 60.000 0.00 0.00 0.00 4.30
4252 4777 0.609957 TGCCGTTAGTTCGAGAGGGA 60.610 55.000 0.00 0.00 0.00 4.20
4253 4778 0.179142 GCCGTTAGTTCGAGAGGGAC 60.179 60.000 0.00 0.00 0.00 4.46
4254 4779 0.098376 CCGTTAGTTCGAGAGGGACG 59.902 60.000 0.00 0.00 0.00 4.79
4255 4780 1.081892 CGTTAGTTCGAGAGGGACGA 58.918 55.000 0.00 0.00 37.99 4.20
4256 4781 1.202009 CGTTAGTTCGAGAGGGACGAC 60.202 57.143 0.00 0.00 39.46 4.34
4257 4782 2.083002 GTTAGTTCGAGAGGGACGACT 58.917 52.381 0.00 0.00 39.46 4.18
4258 4783 3.265791 GTTAGTTCGAGAGGGACGACTA 58.734 50.000 0.00 0.00 39.46 2.59
4259 4784 2.713863 AGTTCGAGAGGGACGACTAT 57.286 50.000 0.00 0.00 39.46 2.12
4260 4785 2.290464 AGTTCGAGAGGGACGACTATG 58.710 52.381 0.00 0.00 39.46 2.23
4261 4786 1.334243 GTTCGAGAGGGACGACTATGG 59.666 57.143 0.00 0.00 39.46 2.74
4262 4787 0.179026 TCGAGAGGGACGACTATGGG 60.179 60.000 0.00 0.00 34.85 4.00
4263 4788 1.797211 CGAGAGGGACGACTATGGGC 61.797 65.000 0.00 0.00 0.00 5.36
4264 4789 1.457831 AGAGGGACGACTATGGGCC 60.458 63.158 0.00 0.00 0.00 5.80
4265 4790 1.457831 GAGGGACGACTATGGGCCT 60.458 63.158 4.53 0.00 0.00 5.19
4266 4791 1.749334 GAGGGACGACTATGGGCCTG 61.749 65.000 4.53 0.00 0.00 4.85
4267 4792 2.064581 GGGACGACTATGGGCCTGT 61.065 63.158 4.53 0.41 0.00 4.00
4268 4793 1.623542 GGGACGACTATGGGCCTGTT 61.624 60.000 4.53 0.00 0.00 3.16
4269 4794 0.252197 GGACGACTATGGGCCTGTTT 59.748 55.000 4.53 0.00 0.00 2.83
4270 4795 1.369625 GACGACTATGGGCCTGTTTG 58.630 55.000 4.53 1.41 0.00 2.93
4271 4796 0.690762 ACGACTATGGGCCTGTTTGT 59.309 50.000 4.53 0.00 0.00 2.83
4272 4797 1.903860 ACGACTATGGGCCTGTTTGTA 59.096 47.619 4.53 0.00 0.00 2.41
4273 4798 2.093658 ACGACTATGGGCCTGTTTGTAG 60.094 50.000 4.53 0.42 0.00 2.74
4274 4799 2.741878 CGACTATGGGCCTGTTTGTAGG 60.742 54.545 4.53 0.00 40.95 3.18
4275 4800 2.504175 GACTATGGGCCTGTTTGTAGGA 59.496 50.000 4.53 0.00 40.42 2.94
4276 4801 2.916934 ACTATGGGCCTGTTTGTAGGAA 59.083 45.455 4.53 0.00 40.42 3.36
4277 4802 3.527665 ACTATGGGCCTGTTTGTAGGAAT 59.472 43.478 4.53 0.00 40.42 3.01
4278 4803 2.990740 TGGGCCTGTTTGTAGGAATT 57.009 45.000 4.53 0.00 40.42 2.17
4279 4804 3.252554 TGGGCCTGTTTGTAGGAATTT 57.747 42.857 4.53 0.00 40.42 1.82
4280 4805 3.582164 TGGGCCTGTTTGTAGGAATTTT 58.418 40.909 4.53 0.00 40.42 1.82
4281 4806 3.323403 TGGGCCTGTTTGTAGGAATTTTG 59.677 43.478 4.53 0.00 40.42 2.44
4282 4807 3.306710 GGGCCTGTTTGTAGGAATTTTGG 60.307 47.826 0.84 0.00 40.42 3.28
4283 4808 3.576550 GGCCTGTTTGTAGGAATTTTGGA 59.423 43.478 0.00 0.00 40.42 3.53
4284 4809 4.039852 GGCCTGTTTGTAGGAATTTTGGAA 59.960 41.667 0.00 0.00 40.42 3.53
4285 4810 5.230182 GCCTGTTTGTAGGAATTTTGGAAG 58.770 41.667 0.00 0.00 40.42 3.46
4286 4811 5.783111 CCTGTTTGTAGGAATTTTGGAAGG 58.217 41.667 0.00 0.00 40.42 3.46
4287 4812 5.538433 CCTGTTTGTAGGAATTTTGGAAGGA 59.462 40.000 0.00 0.00 40.42 3.36
4288 4813 6.211384 CCTGTTTGTAGGAATTTTGGAAGGAT 59.789 38.462 0.00 0.00 40.42 3.24
4289 4814 7.256296 CCTGTTTGTAGGAATTTTGGAAGGATT 60.256 37.037 0.00 0.00 40.42 3.01
4290 4815 8.028652 TGTTTGTAGGAATTTTGGAAGGATTT 57.971 30.769 0.00 0.00 0.00 2.17
4291 4816 9.148879 TGTTTGTAGGAATTTTGGAAGGATTTA 57.851 29.630 0.00 0.00 0.00 1.40
4292 4817 9.990360 GTTTGTAGGAATTTTGGAAGGATTTAA 57.010 29.630 0.00 0.00 0.00 1.52
4293 4818 9.990360 TTTGTAGGAATTTTGGAAGGATTTAAC 57.010 29.630 0.00 0.00 0.00 2.01
4294 4819 7.822658 TGTAGGAATTTTGGAAGGATTTAACG 58.177 34.615 0.00 0.00 0.00 3.18
4295 4820 7.666388 TGTAGGAATTTTGGAAGGATTTAACGA 59.334 33.333 0.00 0.00 0.00 3.85
4296 4821 7.158099 AGGAATTTTGGAAGGATTTAACGAG 57.842 36.000 0.00 0.00 0.00 4.18
4297 4822 6.152831 AGGAATTTTGGAAGGATTTAACGAGG 59.847 38.462 0.00 0.00 0.00 4.63
4298 4823 6.152154 GGAATTTTGGAAGGATTTAACGAGGA 59.848 38.462 0.00 0.00 0.00 3.71
4299 4824 6.759497 ATTTTGGAAGGATTTAACGAGGAG 57.241 37.500 0.00 0.00 0.00 3.69
4300 4825 4.903045 TTGGAAGGATTTAACGAGGAGT 57.097 40.909 0.00 0.00 0.00 3.85
4301 4826 4.202245 TGGAAGGATTTAACGAGGAGTG 57.798 45.455 0.00 0.00 0.00 3.51
4302 4827 3.835978 TGGAAGGATTTAACGAGGAGTGA 59.164 43.478 0.00 0.00 0.00 3.41
4303 4828 4.081642 TGGAAGGATTTAACGAGGAGTGAG 60.082 45.833 0.00 0.00 0.00 3.51
4304 4829 4.159879 GGAAGGATTTAACGAGGAGTGAGA 59.840 45.833 0.00 0.00 0.00 3.27
4305 4830 5.163395 GGAAGGATTTAACGAGGAGTGAGAT 60.163 44.000 0.00 0.00 0.00 2.75
4306 4831 5.269505 AGGATTTAACGAGGAGTGAGATG 57.730 43.478 0.00 0.00 0.00 2.90
4307 4832 3.804873 GGATTTAACGAGGAGTGAGATGC 59.195 47.826 0.00 0.00 0.00 3.91
4308 4833 3.953712 TTTAACGAGGAGTGAGATGCA 57.046 42.857 0.00 0.00 0.00 3.96
4309 4834 4.471904 TTTAACGAGGAGTGAGATGCAT 57.528 40.909 0.00 0.00 0.00 3.96
4310 4835 2.306341 AACGAGGAGTGAGATGCATG 57.694 50.000 2.46 0.00 0.00 4.06
4311 4836 0.463204 ACGAGGAGTGAGATGCATGG 59.537 55.000 2.46 0.00 0.00 3.66
4312 4837 0.249784 CGAGGAGTGAGATGCATGGG 60.250 60.000 2.46 0.00 0.00 4.00
4313 4838 1.126488 GAGGAGTGAGATGCATGGGA 58.874 55.000 2.46 0.00 0.00 4.37
4314 4839 1.698532 GAGGAGTGAGATGCATGGGAT 59.301 52.381 2.46 0.00 0.00 3.85
4315 4840 1.420514 AGGAGTGAGATGCATGGGATG 59.579 52.381 2.46 0.00 0.00 3.51
4316 4841 1.142465 GGAGTGAGATGCATGGGATGT 59.858 52.381 2.46 0.00 0.00 3.06
4317 4842 2.492012 GAGTGAGATGCATGGGATGTC 58.508 52.381 2.46 0.00 0.00 3.06
4318 4843 1.841919 AGTGAGATGCATGGGATGTCA 59.158 47.619 2.46 0.00 0.00 3.58
4319 4844 2.442126 AGTGAGATGCATGGGATGTCAT 59.558 45.455 2.46 0.00 32.43 3.06
4320 4845 3.649502 AGTGAGATGCATGGGATGTCATA 59.350 43.478 2.46 0.00 30.80 2.15
4321 4846 4.103627 AGTGAGATGCATGGGATGTCATAA 59.896 41.667 2.46 0.00 30.80 1.90
4322 4847 5.008331 GTGAGATGCATGGGATGTCATAAT 58.992 41.667 2.46 0.00 30.80 1.28
4323 4848 6.013119 AGTGAGATGCATGGGATGTCATAATA 60.013 38.462 2.46 0.00 30.80 0.98
4324 4849 6.093219 GTGAGATGCATGGGATGTCATAATAC 59.907 42.308 2.46 0.00 30.80 1.89
4325 4850 6.013119 TGAGATGCATGGGATGTCATAATACT 60.013 38.462 2.46 0.00 30.80 2.12
4326 4851 7.180766 TGAGATGCATGGGATGTCATAATACTA 59.819 37.037 2.46 0.00 30.80 1.82
4327 4852 8.098963 AGATGCATGGGATGTCATAATACTAT 57.901 34.615 2.46 0.00 30.80 2.12
4328 4853 8.209584 AGATGCATGGGATGTCATAATACTATC 58.790 37.037 2.46 0.00 30.80 2.08
4329 4854 7.500629 TGCATGGGATGTCATAATACTATCT 57.499 36.000 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 37 7.439655 CGGTGAACTTTTATTTCAAATTCCCAA 59.560 33.333 0.00 0.00 34.78 4.12
156 158 0.391130 TTTGTCTGATCCGCTTCCCG 60.391 55.000 0.00 0.00 0.00 5.14
166 168 8.076910 TGGCCATATTGTTATTTTTGTCTGAT 57.923 30.769 0.00 0.00 0.00 2.90
168 170 6.256321 GCTGGCCATATTGTTATTTTTGTCTG 59.744 38.462 5.51 0.00 0.00 3.51
170 172 5.231991 CGCTGGCCATATTGTTATTTTTGTC 59.768 40.000 5.51 0.00 0.00 3.18
171 173 5.108517 CGCTGGCCATATTGTTATTTTTGT 58.891 37.500 5.51 0.00 0.00 2.83
172 174 4.025813 GCGCTGGCCATATTGTTATTTTTG 60.026 41.667 5.51 0.00 0.00 2.44
173 175 4.119136 GCGCTGGCCATATTGTTATTTTT 58.881 39.130 5.51 0.00 0.00 1.94
200 207 3.222855 CAACCCCTTTGTGGCGCA 61.223 61.111 10.83 0.00 0.00 6.09
202 209 3.302344 CCCAACCCCTTTGTGGCG 61.302 66.667 0.00 0.00 32.71 5.69
244 251 3.122297 CGGCTTCAATGTTGCTCAAAAA 58.878 40.909 0.00 0.00 0.00 1.94
245 252 2.100584 ACGGCTTCAATGTTGCTCAAAA 59.899 40.909 0.00 0.00 0.00 2.44
246 253 1.680735 ACGGCTTCAATGTTGCTCAAA 59.319 42.857 0.00 0.00 0.00 2.69
247 254 1.317613 ACGGCTTCAATGTTGCTCAA 58.682 45.000 0.00 0.00 0.00 3.02
248 255 2.177394 TACGGCTTCAATGTTGCTCA 57.823 45.000 0.00 0.00 0.00 4.26
249 256 2.032178 GGATACGGCTTCAATGTTGCTC 59.968 50.000 0.00 0.00 0.00 4.26
250 257 2.017049 GGATACGGCTTCAATGTTGCT 58.983 47.619 0.00 0.00 0.00 3.91
251 258 2.475200 GGATACGGCTTCAATGTTGC 57.525 50.000 0.00 0.00 0.00 4.17
353 365 0.683179 TTTCATCGAGAGGGAGCGGA 60.683 55.000 0.00 0.00 0.00 5.54
354 366 0.528684 GTTTCATCGAGAGGGAGCGG 60.529 60.000 0.00 0.00 0.00 5.52
430 443 1.227002 GATGAACTCCTCCGCCGAC 60.227 63.158 0.00 0.00 0.00 4.79
431 444 1.379977 AGATGAACTCCTCCGCCGA 60.380 57.895 0.00 0.00 0.00 5.54
432 445 1.227089 CAGATGAACTCCTCCGCCG 60.227 63.158 0.00 0.00 0.00 6.46
433 446 0.537188 TTCAGATGAACTCCTCCGCC 59.463 55.000 0.00 0.00 0.00 6.13
476 504 0.399519 GAGATCCGGGGTTAGGGGAA 60.400 60.000 0.00 0.00 32.71 3.97
477 505 1.235112 GAGATCCGGGGTTAGGGGA 59.765 63.158 0.00 0.00 0.00 4.81
478 506 2.207924 CGAGATCCGGGGTTAGGGG 61.208 68.421 0.00 0.00 33.91 4.79
479 507 1.047034 AACGAGATCCGGGGTTAGGG 61.047 60.000 0.00 0.00 43.93 3.53
480 508 0.828677 AAACGAGATCCGGGGTTAGG 59.171 55.000 0.00 0.00 43.93 2.69
486 514 0.739813 AAGCGAAAACGAGATCCGGG 60.740 55.000 0.00 0.00 43.93 5.73
529 557 4.235762 TAGGGGATCAAGGCGCGC 62.236 66.667 25.94 25.94 0.00 6.86
618 671 8.108837 TCGTACTCGCCTGAATTTCATAATTCA 61.109 37.037 11.51 11.51 44.61 2.57
619 672 6.200286 TCGTACTCGCCTGAATTTCATAATTC 59.800 38.462 0.00 0.00 41.81 2.17
620 673 6.046593 TCGTACTCGCCTGAATTTCATAATT 58.953 36.000 0.00 0.00 35.49 1.40
621 674 5.597806 TCGTACTCGCCTGAATTTCATAAT 58.402 37.500 0.00 0.00 36.96 1.28
622 675 5.001237 TCGTACTCGCCTGAATTTCATAA 57.999 39.130 0.00 0.00 36.96 1.90
705 760 3.502123 TCCATTCGAGGGACAAACTTT 57.498 42.857 3.95 0.00 0.00 2.66
709 764 4.408921 AGATACATCCATTCGAGGGACAAA 59.591 41.667 9.77 0.20 37.23 2.83
770 914 2.504367 CCCAAGAGGTTCGTCAAACAT 58.496 47.619 0.00 0.00 39.81 2.71
806 960 0.555769 TGCCCTCAACATTATCCCCC 59.444 55.000 0.00 0.00 0.00 5.40
810 964 3.466836 TCGACATGCCCTCAACATTATC 58.533 45.455 0.00 0.00 0.00 1.75
827 982 2.979240 AGAGGAGCCAAAGAAATCGAC 58.021 47.619 0.00 0.00 0.00 4.20
828 985 3.703001 AAGAGGAGCCAAAGAAATCGA 57.297 42.857 0.00 0.00 0.00 3.59
838 995 3.010472 TCATGGAATCAAAAGAGGAGCCA 59.990 43.478 0.00 0.00 0.00 4.75
839 996 3.624777 TCATGGAATCAAAAGAGGAGCC 58.375 45.455 0.00 0.00 0.00 4.70
854 1014 4.022416 AGCGCAGTTTTTAAACATCATGGA 60.022 37.500 11.47 0.00 41.30 3.41
887 1047 5.393124 TCTGCAGAAAAATACATGAAAGCG 58.607 37.500 15.67 0.00 0.00 4.68
899 1059 7.041098 GGAGACTGAATAAACTCTGCAGAAAAA 60.041 37.037 18.85 4.04 0.00 1.94
937 1097 0.535102 AGTTTGACGGACTGGCAAGG 60.535 55.000 2.07 0.00 0.00 3.61
962 1122 1.375098 GCTGCCAGATCCTTCTGCAC 61.375 60.000 0.00 0.00 46.76 4.57
982 1142 1.067283 CATCGAAGCCACACTGAGAGT 60.067 52.381 0.00 0.00 0.00 3.24
1053 1214 9.823647 AAAAGTATCAGTTCGATGATATCTTGT 57.176 29.630 10.98 8.92 42.54 3.16
1078 1239 2.050836 TTGCTCACCGGAAGCCTCAA 62.051 55.000 24.17 13.32 0.00 3.02
1113 1274 0.031178 CCCACTGCTTGCAGACAAAC 59.969 55.000 26.71 0.00 34.74 2.93
1114 1275 0.106769 TCCCACTGCTTGCAGACAAA 60.107 50.000 26.71 8.59 34.74 2.83
1191 1352 4.332828 CTCGTTGGAAAAATAGAAGGGGT 58.667 43.478 0.00 0.00 0.00 4.95
1198 1359 1.529010 CGCGCCTCGTTGGAAAAATAG 60.529 52.381 0.00 0.00 38.35 1.73
1482 1646 6.414408 AGAAAGTGCAAGATCTTGTATTCG 57.586 37.500 30.88 10.12 42.31 3.34
1870 2037 5.416013 TGTTGTCAAGTGTCCAAACATACAA 59.584 36.000 0.00 0.00 37.81 2.41
1873 2040 5.067153 CCTTGTTGTCAAGTGTCCAAACATA 59.933 40.000 7.11 0.00 46.70 2.29
1898 2065 1.632409 TCTGGATCCAGCTTTGCTTCT 59.368 47.619 33.39 0.00 43.31 2.85
1936 2106 4.612259 CGGCATTAGAATATCAAGTGCAGC 60.612 45.833 0.00 0.00 33.05 5.25
1938 2108 3.250762 GCGGCATTAGAATATCAAGTGCA 59.749 43.478 0.00 0.00 33.05 4.57
1947 2117 6.090763 CGTAGATGAAATGCGGCATTAGAATA 59.909 38.462 26.87 13.99 32.43 1.75
1955 2125 0.813610 CCCGTAGATGAAATGCGGCA 60.814 55.000 4.58 4.58 40.94 5.69
1956 2126 1.507141 CCCCGTAGATGAAATGCGGC 61.507 60.000 0.00 0.00 40.94 6.53
2180 2353 5.705400 TCTTCAATCTCCAACCCTCTTTTT 58.295 37.500 0.00 0.00 0.00 1.94
2224 2397 0.832135 TCCTCCACCTCAGAGCGTTT 60.832 55.000 0.00 0.00 0.00 3.60
2238 2411 2.730524 GGCTCTCCACAGCTCCTCC 61.731 68.421 0.00 0.00 39.58 4.30
2329 2514 5.050091 CACACTCAACATCTTCAACAGTACC 60.050 44.000 0.00 0.00 0.00 3.34
2330 2515 5.753438 TCACACTCAACATCTTCAACAGTAC 59.247 40.000 0.00 0.00 0.00 2.73
2370 2555 1.341080 CATTTCCTGCCAACAAGGGT 58.659 50.000 0.00 0.00 38.09 4.34
2371 2556 0.609662 CCATTTCCTGCCAACAAGGG 59.390 55.000 0.00 0.00 38.09 3.95
2372 2557 0.037046 GCCATTTCCTGCCAACAAGG 60.037 55.000 0.00 0.00 41.84 3.61
2460 2645 2.289382 TGGTAGCTTTCAGTTCGATGCA 60.289 45.455 0.00 0.00 0.00 3.96
2520 2706 5.238583 ACACTTCTAAAAATCCTCACTCCG 58.761 41.667 0.00 0.00 0.00 4.63
2600 2790 1.600636 CAGCATGTTCACCACCCGT 60.601 57.895 0.00 0.00 0.00 5.28
2608 2798 7.066645 CCTCAAGATAAGATTTCAGCATGTTCA 59.933 37.037 0.00 0.00 37.40 3.18
2625 2815 4.156455 GAGCATCCAAACCCTCAAGATA 57.844 45.455 0.00 0.00 0.00 1.98
2649 2839 2.094390 TCAAAGAAGACCATACCGTCCG 60.094 50.000 0.00 0.00 32.91 4.79
2682 2880 3.181487 ACAGAGACAAGCGCAACAAAATT 60.181 39.130 11.47 0.00 0.00 1.82
2683 2881 2.358898 ACAGAGACAAGCGCAACAAAAT 59.641 40.909 11.47 0.00 0.00 1.82
2684 2882 1.742831 ACAGAGACAAGCGCAACAAAA 59.257 42.857 11.47 0.00 0.00 2.44
2685 2883 1.063912 CACAGAGACAAGCGCAACAAA 59.936 47.619 11.47 0.00 0.00 2.83
2686 2884 0.657312 CACAGAGACAAGCGCAACAA 59.343 50.000 11.47 0.00 0.00 2.83
2687 2885 0.179086 TCACAGAGACAAGCGCAACA 60.179 50.000 11.47 0.00 0.00 3.33
2688 2886 1.136141 CATCACAGAGACAAGCGCAAC 60.136 52.381 11.47 0.00 0.00 4.17
2693 2891 3.133691 TCACAACATCACAGAGACAAGC 58.866 45.455 0.00 0.00 0.00 4.01
2719 2917 9.787435 ACCTAGAAATAACATGTCAACTTTGTA 57.213 29.630 0.00 0.00 0.00 2.41
2765 2963 0.472471 TTTTTCTCACCAGAGGCCGT 59.528 50.000 0.00 0.00 42.34 5.68
2772 2970 4.457257 GGGTCATCTTCTTTTTCTCACCAG 59.543 45.833 0.00 0.00 0.00 4.00
2874 3076 3.681311 AGGGAAATGGGGCTAGATAAGT 58.319 45.455 0.00 0.00 0.00 2.24
2910 3117 3.760580 ATACCCTAGCAGCAAGTCATC 57.239 47.619 0.00 0.00 0.00 2.92
3018 3254 8.767478 ATTTCAATGTTTCCAAGATGAATCAC 57.233 30.769 0.00 0.00 29.42 3.06
3038 3274 6.326375 ACTTTTGTGTGCGTCTTTAATTTCA 58.674 32.000 0.00 0.00 0.00 2.69
3068 3324 1.270274 ACACGTACGTATGGTGCAGAA 59.730 47.619 22.34 0.00 35.11 3.02
3083 3342 7.307811 GCTCTTTTCTGACCTAATTAAACACGT 60.308 37.037 0.00 0.00 0.00 4.49
3084 3343 7.015877 GCTCTTTTCTGACCTAATTAAACACG 58.984 38.462 0.00 0.00 0.00 4.49
3085 3344 7.871853 TGCTCTTTTCTGACCTAATTAAACAC 58.128 34.615 0.00 0.00 0.00 3.32
3086 3345 7.174946 CCTGCTCTTTTCTGACCTAATTAAACA 59.825 37.037 0.00 0.00 0.00 2.83
3087 3346 7.362142 CCCTGCTCTTTTCTGACCTAATTAAAC 60.362 40.741 0.00 0.00 0.00 2.01
3088 3347 6.659242 CCCTGCTCTTTTCTGACCTAATTAAA 59.341 38.462 0.00 0.00 0.00 1.52
3089 3348 6.180472 CCCTGCTCTTTTCTGACCTAATTAA 58.820 40.000 0.00 0.00 0.00 1.40
3090 3349 5.339200 CCCCTGCTCTTTTCTGACCTAATTA 60.339 44.000 0.00 0.00 0.00 1.40
3091 3350 4.568592 CCCCTGCTCTTTTCTGACCTAATT 60.569 45.833 0.00 0.00 0.00 1.40
3092 3351 3.054065 CCCCTGCTCTTTTCTGACCTAAT 60.054 47.826 0.00 0.00 0.00 1.73
3176 3471 6.412362 TCTAAGAGAAAGGATACAGATGCC 57.588 41.667 0.00 0.00 41.41 4.40
3224 3547 1.528309 CCTCGCTCTCCTCTCCTCC 60.528 68.421 0.00 0.00 0.00 4.30
3329 3655 0.034863 ATTAACCGGGCACGTGGATT 60.035 50.000 18.88 0.00 38.78 3.01
3332 3658 2.403378 CCATTAACCGGGCACGTGG 61.403 63.158 18.88 3.57 38.78 4.94
3333 3659 1.366111 CTCCATTAACCGGGCACGTG 61.366 60.000 12.28 12.28 38.78 4.49
3334 3660 1.078708 CTCCATTAACCGGGCACGT 60.079 57.895 7.97 0.00 38.78 4.49
3337 3663 0.916086 ATGTCTCCATTAACCGGGCA 59.084 50.000 6.32 0.00 0.00 5.36
3338 3664 1.308998 CATGTCTCCATTAACCGGGC 58.691 55.000 6.32 0.00 0.00 6.13
3444 3770 2.032681 GGACCACGGCTTGCTCTT 59.967 61.111 0.00 0.00 0.00 2.85
3461 3787 5.278964 GGTACGCTTTTGAGTCTAAAAGG 57.721 43.478 20.01 15.12 44.12 3.11
3483 3949 1.920574 CACAACGCCTACTGAAGATCG 59.079 52.381 0.00 0.00 0.00 3.69
3520 3986 5.518529 TGATAAACACCGATTACAACACG 57.481 39.130 0.00 0.00 0.00 4.49
3521 3987 8.563289 TTTTTGATAAACACCGATTACAACAC 57.437 30.769 0.00 0.00 0.00 3.32
3577 4049 6.461788 GCATCTTCTCGAAACTTAGATAGGGT 60.462 42.308 0.00 0.00 0.00 4.34
3578 4050 5.923684 GCATCTTCTCGAAACTTAGATAGGG 59.076 44.000 0.00 0.00 0.00 3.53
3582 4054 4.363999 CGGCATCTTCTCGAAACTTAGAT 58.636 43.478 0.00 0.00 0.00 1.98
3584 4056 2.282820 GCGGCATCTTCTCGAAACTTAG 59.717 50.000 0.00 0.00 0.00 2.18
3586 4058 1.079503 GCGGCATCTTCTCGAAACTT 58.920 50.000 0.00 0.00 0.00 2.66
3615 4088 2.438392 ACTCGGGGTATGAGGAAATTCC 59.562 50.000 3.29 3.29 37.79 3.01
3630 4103 3.259633 AAAGAGCCAGGCACTCGGG 62.260 63.158 15.80 0.00 39.23 5.14
3648 4121 1.047002 CCATGGTTTGGTTCTTGGCA 58.953 50.000 2.57 0.00 40.99 4.92
3652 4125 1.047801 GTGCCCATGGTTTGGTTCTT 58.952 50.000 11.73 0.00 44.83 2.52
3668 4141 1.289109 TACTTCGCTTTGCCGAGTGC 61.289 55.000 0.00 0.00 38.60 4.40
3682 4155 3.927758 GAGTTTTCCTCTCGGCTTACTTC 59.072 47.826 0.00 0.00 37.22 3.01
3705 4178 6.546034 GGTATAGGTAAATGGATGTGTTTGCT 59.454 38.462 0.00 0.00 0.00 3.91
3714 4204 6.199557 TGCACATGGTATAGGTAAATGGAT 57.800 37.500 0.00 0.00 0.00 3.41
3715 4205 5.638530 TGCACATGGTATAGGTAAATGGA 57.361 39.130 0.00 0.00 0.00 3.41
3716 4206 6.707440 TTTGCACATGGTATAGGTAAATGG 57.293 37.500 0.00 0.00 0.00 3.16
3746 4236 2.729360 GGAACAACGGCAAGCATTTTAC 59.271 45.455 0.00 0.00 0.00 2.01
3747 4237 2.625790 AGGAACAACGGCAAGCATTTTA 59.374 40.909 0.00 0.00 0.00 1.52
3778 4278 1.741732 CGGTTTCTGAGCAGATGGAGG 60.742 57.143 0.37 0.00 37.29 4.30
3924 4431 4.410400 CGGCAACCTGGGACCTCC 62.410 72.222 0.00 0.00 0.00 4.30
4066 4577 4.451150 ATCCGCATGCACGTCCGT 62.451 61.111 19.57 0.00 0.00 4.69
4224 4749 1.551019 AACTAACGGCACCCTCCTCC 61.551 60.000 0.00 0.00 0.00 4.30
4236 4761 1.081892 TCGTCCCTCTCGAACTAACG 58.918 55.000 0.00 0.00 34.36 3.18
4237 4762 2.083002 AGTCGTCCCTCTCGAACTAAC 58.917 52.381 0.00 0.00 39.01 2.34
4238 4763 2.486472 AGTCGTCCCTCTCGAACTAA 57.514 50.000 0.00 0.00 39.01 2.24
4239 4764 3.464907 CATAGTCGTCCCTCTCGAACTA 58.535 50.000 0.00 0.00 39.01 2.24
4240 4765 2.290464 CATAGTCGTCCCTCTCGAACT 58.710 52.381 0.00 0.00 39.01 3.01
4241 4766 1.334243 CCATAGTCGTCCCTCTCGAAC 59.666 57.143 0.00 0.00 39.01 3.95
4242 4767 1.676746 CCATAGTCGTCCCTCTCGAA 58.323 55.000 0.00 0.00 39.01 3.71
4243 4768 0.179026 CCCATAGTCGTCCCTCTCGA 60.179 60.000 0.00 0.00 34.91 4.04
4244 4769 1.797211 GCCCATAGTCGTCCCTCTCG 61.797 65.000 0.00 0.00 0.00 4.04
4245 4770 1.465200 GGCCCATAGTCGTCCCTCTC 61.465 65.000 0.00 0.00 0.00 3.20
4246 4771 1.457831 GGCCCATAGTCGTCCCTCT 60.458 63.158 0.00 0.00 0.00 3.69
4247 4772 1.457831 AGGCCCATAGTCGTCCCTC 60.458 63.158 0.00 0.00 0.00 4.30
4248 4773 1.762460 CAGGCCCATAGTCGTCCCT 60.762 63.158 0.00 0.00 0.00 4.20
4249 4774 1.623542 AACAGGCCCATAGTCGTCCC 61.624 60.000 0.00 0.00 0.00 4.46
4250 4775 0.252197 AAACAGGCCCATAGTCGTCC 59.748 55.000 0.00 0.00 0.00 4.79
4251 4776 1.338769 ACAAACAGGCCCATAGTCGTC 60.339 52.381 0.00 0.00 0.00 4.20
4252 4777 0.690762 ACAAACAGGCCCATAGTCGT 59.309 50.000 0.00 0.00 0.00 4.34
4253 4778 2.550978 CTACAAACAGGCCCATAGTCG 58.449 52.381 0.00 0.00 0.00 4.18
4254 4779 2.504175 TCCTACAAACAGGCCCATAGTC 59.496 50.000 0.00 0.00 35.49 2.59
4255 4780 2.557869 TCCTACAAACAGGCCCATAGT 58.442 47.619 0.00 0.00 35.49 2.12
4256 4781 3.644966 TTCCTACAAACAGGCCCATAG 57.355 47.619 0.00 0.00 35.49 2.23
4257 4782 4.601406 AATTCCTACAAACAGGCCCATA 57.399 40.909 0.00 0.00 35.49 2.74
4258 4783 3.473113 AATTCCTACAAACAGGCCCAT 57.527 42.857 0.00 0.00 35.49 4.00
4259 4784 2.990740 AATTCCTACAAACAGGCCCA 57.009 45.000 0.00 0.00 35.49 5.36
4260 4785 3.306710 CCAAAATTCCTACAAACAGGCCC 60.307 47.826 0.00 0.00 35.49 5.80
4261 4786 3.576550 TCCAAAATTCCTACAAACAGGCC 59.423 43.478 0.00 0.00 35.49 5.19
4262 4787 4.864704 TCCAAAATTCCTACAAACAGGC 57.135 40.909 0.00 0.00 35.49 4.85
4263 4788 5.538433 TCCTTCCAAAATTCCTACAAACAGG 59.462 40.000 0.00 0.00 37.00 4.00
4264 4789 6.648879 TCCTTCCAAAATTCCTACAAACAG 57.351 37.500 0.00 0.00 0.00 3.16
4265 4790 7.610580 AATCCTTCCAAAATTCCTACAAACA 57.389 32.000 0.00 0.00 0.00 2.83
4266 4791 9.990360 TTAAATCCTTCCAAAATTCCTACAAAC 57.010 29.630 0.00 0.00 0.00 2.93
4267 4792 9.990360 GTTAAATCCTTCCAAAATTCCTACAAA 57.010 29.630 0.00 0.00 0.00 2.83
4268 4793 8.301002 CGTTAAATCCTTCCAAAATTCCTACAA 58.699 33.333 0.00 0.00 0.00 2.41
4269 4794 7.666388 TCGTTAAATCCTTCCAAAATTCCTACA 59.334 33.333 0.00 0.00 0.00 2.74
4270 4795 8.047413 TCGTTAAATCCTTCCAAAATTCCTAC 57.953 34.615 0.00 0.00 0.00 3.18
4271 4796 7.338449 CCTCGTTAAATCCTTCCAAAATTCCTA 59.662 37.037 0.00 0.00 0.00 2.94
4272 4797 6.152831 CCTCGTTAAATCCTTCCAAAATTCCT 59.847 38.462 0.00 0.00 0.00 3.36
4273 4798 6.152154 TCCTCGTTAAATCCTTCCAAAATTCC 59.848 38.462 0.00 0.00 0.00 3.01
4274 4799 7.094334 ACTCCTCGTTAAATCCTTCCAAAATTC 60.094 37.037 0.00 0.00 0.00 2.17
4275 4800 6.719829 ACTCCTCGTTAAATCCTTCCAAAATT 59.280 34.615 0.00 0.00 0.00 1.82
4276 4801 6.151144 CACTCCTCGTTAAATCCTTCCAAAAT 59.849 38.462 0.00 0.00 0.00 1.82
4277 4802 5.472137 CACTCCTCGTTAAATCCTTCCAAAA 59.528 40.000 0.00 0.00 0.00 2.44
4278 4803 5.001232 CACTCCTCGTTAAATCCTTCCAAA 58.999 41.667 0.00 0.00 0.00 3.28
4279 4804 4.285003 TCACTCCTCGTTAAATCCTTCCAA 59.715 41.667 0.00 0.00 0.00 3.53
4280 4805 3.835978 TCACTCCTCGTTAAATCCTTCCA 59.164 43.478 0.00 0.00 0.00 3.53
4281 4806 4.159879 TCTCACTCCTCGTTAAATCCTTCC 59.840 45.833 0.00 0.00 0.00 3.46
4282 4807 5.326200 TCTCACTCCTCGTTAAATCCTTC 57.674 43.478 0.00 0.00 0.00 3.46
4283 4808 5.665459 CATCTCACTCCTCGTTAAATCCTT 58.335 41.667 0.00 0.00 0.00 3.36
4284 4809 4.442192 GCATCTCACTCCTCGTTAAATCCT 60.442 45.833 0.00 0.00 0.00 3.24
4285 4810 3.804873 GCATCTCACTCCTCGTTAAATCC 59.195 47.826 0.00 0.00 0.00 3.01
4286 4811 4.433615 TGCATCTCACTCCTCGTTAAATC 58.566 43.478 0.00 0.00 0.00 2.17
4287 4812 4.471904 TGCATCTCACTCCTCGTTAAAT 57.528 40.909 0.00 0.00 0.00 1.40
4288 4813 3.953712 TGCATCTCACTCCTCGTTAAA 57.046 42.857 0.00 0.00 0.00 1.52
4289 4814 3.430790 CCATGCATCTCACTCCTCGTTAA 60.431 47.826 0.00 0.00 0.00 2.01
4290 4815 2.101415 CCATGCATCTCACTCCTCGTTA 59.899 50.000 0.00 0.00 0.00 3.18
4291 4816 1.134580 CCATGCATCTCACTCCTCGTT 60.135 52.381 0.00 0.00 0.00 3.85
4292 4817 0.463204 CCATGCATCTCACTCCTCGT 59.537 55.000 0.00 0.00 0.00 4.18
4293 4818 0.249784 CCCATGCATCTCACTCCTCG 60.250 60.000 0.00 0.00 0.00 4.63
4294 4819 1.126488 TCCCATGCATCTCACTCCTC 58.874 55.000 0.00 0.00 0.00 3.71
4295 4820 1.420514 CATCCCATGCATCTCACTCCT 59.579 52.381 0.00 0.00 0.00 3.69
4296 4821 1.142465 ACATCCCATGCATCTCACTCC 59.858 52.381 0.00 0.00 0.00 3.85
4297 4822 2.158856 TGACATCCCATGCATCTCACTC 60.159 50.000 0.00 0.00 0.00 3.51
4298 4823 1.841919 TGACATCCCATGCATCTCACT 59.158 47.619 0.00 0.00 0.00 3.41
4299 4824 2.336945 TGACATCCCATGCATCTCAC 57.663 50.000 0.00 0.00 0.00 3.51
4300 4825 4.710313 TTATGACATCCCATGCATCTCA 57.290 40.909 0.00 0.00 32.25 3.27
4301 4826 6.413052 AGTATTATGACATCCCATGCATCTC 58.587 40.000 0.00 0.00 32.25 2.75
4302 4827 6.384342 AGTATTATGACATCCCATGCATCT 57.616 37.500 0.00 0.00 32.25 2.90
4303 4828 8.209584 AGATAGTATTATGACATCCCATGCATC 58.790 37.037 0.00 0.00 32.25 3.91
4304 4829 8.098963 AGATAGTATTATGACATCCCATGCAT 57.901 34.615 0.00 0.00 33.67 3.96
4305 4830 7.500629 AGATAGTATTATGACATCCCATGCA 57.499 36.000 0.00 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.