Multiple sequence alignment - TraesCS6D01G226100

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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 TraesCS6D01G226100 chr6D 100.000 4590 0 0 1 4590 317855909 317851320 0.000000e+00 8477
1 TraesCS6D01G226100 chr6D 83.138 427 34 18 4192 4590 464578674 464578258 5.650000e-94 355
2 TraesCS6D01G226100 chr6B 95.006 3524 125 28 239 3745 506545023 506548512 0.000000e+00 5485
3 TraesCS6D01G226100 chr6B 93.048 374 21 4 3800 4173 506551131 506551499 4.040000e-150 542
4 TraesCS6D01G226100 chr6B 85.671 328 28 8 4196 4505 44244566 44244892 1.230000e-85 327
5 TraesCS6D01G226100 chr6B 87.554 233 11 7 3 228 506544523 506544744 2.120000e-63 254
6 TraesCS6D01G226100 chr6A 94.325 3401 121 29 495 3849 455317692 455314318 0.000000e+00 5145
7 TraesCS6D01G226100 chr6A 88.542 192 20 1 3984 4173 455313846 455313655 9.930000e-57 231
8 TraesCS6D01G226100 chr6A 96.721 122 3 1 3872 3993 455314328 455314208 7.790000e-48 202
9 TraesCS6D01G226100 chr4D 78.726 879 147 32 1490 2344 128168134 128167272 6.710000e-153 551
10 TraesCS6D01G226100 chr4D 84.247 292 37 7 4223 4505 557064 556773 4.520000e-70 276
11 TraesCS6D01G226100 chr4B 78.409 880 155 31 1490 2347 192059523 192058657 1.450000e-149 540
12 TraesCS6D01G226100 chr4A 78.458 882 151 32 1487 2344 440181010 440181876 1.450000e-149 540
13 TraesCS6D01G226100 chr4A 85.801 331 29 9 4193 4505 714425802 714426132 7.360000e-88 335
14 TraesCS6D01G226100 chr3B 82.232 439 38 18 4192 4590 814497473 814497911 4.400000e-90 342
15 TraesCS6D01G226100 chr3B 79.394 330 51 12 4192 4505 457570260 457569932 2.780000e-52 217
16 TraesCS6D01G226100 chr5B 82.367 414 43 13 4204 4590 532731553 532731963 2.650000e-87 333
17 TraesCS6D01G226100 chr2B 85.494 324 30 6 4199 4505 51080726 51080403 5.730000e-84 322
18 TraesCS6D01G226100 chr2B 80.503 318 35 14 4193 4505 784672287 784672582 7.730000e-53 219
19 TraesCS6D01G226100 chr2A 83.951 324 35 6 4199 4505 644223546 644223223 1.250000e-75 294
20 TraesCS6D01G226100 chr3A 79.602 402 40 21 4218 4579 510304536 510304935 2.740000e-62 250
21 TraesCS6D01G226100 chr7D 79.811 317 40 10 4206 4502 256222281 256221969 4.650000e-50 209


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 TraesCS6D01G226100 chr6D 317851320 317855909 4589 True 8477.000000 8477 100.000000 1 4590 1 chr6D.!!$R1 4589
1 TraesCS6D01G226100 chr6B 506544523 506551499 6976 False 2093.666667 5485 91.869333 3 4173 3 chr6B.!!$F2 4170
2 TraesCS6D01G226100 chr6A 455313655 455317692 4037 True 1859.333333 5145 93.196000 495 4173 3 chr6A.!!$R1 3678
3 TraesCS6D01G226100 chr4D 128167272 128168134 862 True 551.000000 551 78.726000 1490 2344 1 chr4D.!!$R2 854
4 TraesCS6D01G226100 chr4B 192058657 192059523 866 True 540.000000 540 78.409000 1490 2347 1 chr4B.!!$R1 857
5 TraesCS6D01G226100 chr4A 440181010 440181876 866 False 540.000000 540 78.458000 1487 2344 1 chr4A.!!$F1 857

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
431 707 0.037882 TTCTCTCCTGAGCTTGTGCG 60.038 55.0 0.00 0.00 45.42 5.34 F
1125 1417 0.106719 CCACCAATGGCCGGAACTAT 60.107 55.0 5.05 0.00 39.82 2.12 F
1188 1480 0.629058 AAATGGGTGGCTTCCGGTAT 59.371 50.0 0.00 0.00 0.00 2.73 F
2813 3121 0.328258 AGAACAACCCCAAGATCGGG 59.672 55.0 2.79 2.79 46.94 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2088 2395 0.038159 CGAAGGCGGTGAAGAAGTCT 60.038 55.0 0.00 0.00 0.00 3.24 R
2735 3043 0.837272 CCAGGATGATTGGGTACGGT 59.163 55.0 0.00 0.00 39.69 4.83 R
2944 3252 5.298026 TGACAATCCAAGAAACGTTTCATGA 59.702 36.0 35.30 28.09 37.92 3.07 R
4516 7773 0.039074 GGAGGGATCACATCGCGTAG 60.039 60.0 5.77 1.95 45.80 3.51 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
27 28 9.784680 TTGCAGTTTTAATACGACAAAAGTTTA 57.215 25.926 0.00 0.00 0.00 2.01
68 69 6.542821 TCTATATGTGGCCCTATTTTCTTGG 58.457 40.000 0.00 0.00 0.00 3.61
76 77 2.175715 CCCTATTTTCTTGGGGGAGAGG 59.824 54.545 0.00 0.00 39.42 3.69
81 82 1.584724 TTCTTGGGGGAGAGGATCAC 58.415 55.000 0.00 0.00 37.82 3.06
154 155 9.093970 GTTTATTTAACCCATTTGAATACCAGC 57.906 33.333 0.00 0.00 28.10 4.85
155 156 5.669164 TTTAACCCATTTGAATACCAGCC 57.331 39.130 0.00 0.00 0.00 4.85
156 157 3.473113 AACCCATTTGAATACCAGCCT 57.527 42.857 0.00 0.00 0.00 4.58
157 158 4.601406 AACCCATTTGAATACCAGCCTA 57.399 40.909 0.00 0.00 0.00 3.93
158 159 4.601406 ACCCATTTGAATACCAGCCTAA 57.399 40.909 0.00 0.00 0.00 2.69
159 160 4.941713 ACCCATTTGAATACCAGCCTAAA 58.058 39.130 0.00 0.00 0.00 1.85
160 161 5.528337 ACCCATTTGAATACCAGCCTAAAT 58.472 37.500 0.00 0.00 0.00 1.40
161 162 6.678547 ACCCATTTGAATACCAGCCTAAATA 58.321 36.000 0.00 0.00 0.00 1.40
162 163 6.777580 ACCCATTTGAATACCAGCCTAAATAG 59.222 38.462 0.00 0.00 0.00 1.73
183 184 1.350351 GATAGGTGATGCATGAGGCCT 59.650 52.381 3.86 3.86 43.89 5.19
184 185 0.761187 TAGGTGATGCATGAGGCCTC 59.239 55.000 26.78 26.78 43.89 4.70
185 186 1.225426 GGTGATGCATGAGGCCTCA 59.775 57.895 36.73 36.73 43.62 3.86
207 215 7.117241 TCATTTTATCTTGTTGTCAGTCGTC 57.883 36.000 0.00 0.00 0.00 4.20
219 227 4.329392 TGTCAGTCGTCTGTAATCCACTA 58.671 43.478 9.48 0.00 41.91 2.74
224 232 3.130693 GTCGTCTGTAATCCACTAAGGCT 59.869 47.826 0.00 0.00 37.29 4.58
228 236 5.519206 CGTCTGTAATCCACTAAGGCTTTAC 59.481 44.000 4.45 0.22 36.77 2.01
229 237 5.816258 GTCTGTAATCCACTAAGGCTTTACC 59.184 44.000 4.45 0.00 36.04 2.85
290 566 6.242396 TGCAGTAAGTAATTGGGTATTGTGT 58.758 36.000 0.00 0.00 0.00 3.72
295 571 6.603940 AAGTAATTGGGTATTGTGTGCATT 57.396 33.333 0.00 0.00 0.00 3.56
310 586 4.058124 TGTGCATTAATCGATGTAGAGGC 58.942 43.478 0.00 0.00 0.00 4.70
312 588 2.668457 GCATTAATCGATGTAGAGGCCG 59.332 50.000 0.00 0.00 0.00 6.13
341 617 8.951787 ATTTTAACCCTGTTTTTAACCTTGAC 57.048 30.769 0.00 0.00 0.00 3.18
344 620 4.862371 ACCCTGTTTTTAACCTTGACAGA 58.138 39.130 3.56 0.00 39.97 3.41
356 632 3.001414 CCTTGACAGATGACAAGCTGAG 58.999 50.000 16.30 3.19 42.67 3.35
386 662 4.580580 CCTCTGTTTCTTTTGTTGTAGGCT 59.419 41.667 0.00 0.00 0.00 4.58
397 673 6.966435 TTTGTTGTAGGCTAACGTATTACC 57.034 37.500 0.00 0.00 0.00 2.85
398 674 5.009854 TGTTGTAGGCTAACGTATTACCC 57.990 43.478 0.00 0.00 0.00 3.69
406 682 1.717194 AACGTATTACCCAGTGTGCG 58.283 50.000 0.00 0.00 0.00 5.34
431 707 0.037882 TTCTCTCCTGAGCTTGTGCG 60.038 55.000 0.00 0.00 45.42 5.34
437 713 0.723414 CCTGAGCTTGTGCGTGTATG 59.277 55.000 0.00 0.00 45.42 2.39
440 716 1.270041 TGAGCTTGTGCGTGTATGTCA 60.270 47.619 0.00 0.00 45.42 3.58
447 723 0.108851 TGCGTGTATGTCAGCGATGT 60.109 50.000 0.00 0.00 0.00 3.06
449 725 2.223711 TGCGTGTATGTCAGCGATGTAT 60.224 45.455 0.00 0.00 0.00 2.29
461 737 8.083462 TGTCAGCGATGTATAATCAATTAACC 57.917 34.615 0.00 0.00 0.00 2.85
466 742 7.063074 AGCGATGTATAATCAATTAACCGCTAC 59.937 37.037 0.00 2.93 44.88 3.58
483 759 4.025396 CCGCTACAATGATGATCTGTTGTC 60.025 45.833 16.09 6.52 36.34 3.18
490 766 2.639347 TGATGATCTGTTGTCCTGGTGT 59.361 45.455 0.00 0.00 0.00 4.16
492 768 3.576078 TGATCTGTTGTCCTGGTGTTT 57.424 42.857 0.00 0.00 0.00 2.83
539 815 6.135290 TCAGTGAGAACCAAGAAAAATGTG 57.865 37.500 0.00 0.00 0.00 3.21
559 843 3.064682 GTGTGTGCACAATACAGTCAACA 59.935 43.478 23.59 8.29 43.77 3.33
563 847 6.128309 TGTGTGCACAATACAGTCAACATATC 60.128 38.462 23.59 3.02 38.56 1.63
574 863 4.872124 CAGTCAACATATCAGTAGCTGCAA 59.128 41.667 4.12 0.00 0.00 4.08
601 890 3.845781 TCAGCAAGAAGTCAAGACCTT 57.154 42.857 0.00 0.00 0.00 3.50
642 931 6.326583 TGTCCCTAGATGGAAGTATAACTTGG 59.673 42.308 0.00 0.00 38.80 3.61
699 988 2.482326 GCACCTTCAGCCATACCAC 58.518 57.895 0.00 0.00 0.00 4.16
700 989 1.032114 GCACCTTCAGCCATACCACC 61.032 60.000 0.00 0.00 0.00 4.61
702 991 1.004745 CACCTTCAGCCATACCACCTT 59.995 52.381 0.00 0.00 0.00 3.50
704 993 3.117888 CACCTTCAGCCATACCACCTTAT 60.118 47.826 0.00 0.00 0.00 1.73
705 994 3.136626 ACCTTCAGCCATACCACCTTATC 59.863 47.826 0.00 0.00 0.00 1.75
706 995 3.136443 CCTTCAGCCATACCACCTTATCA 59.864 47.826 0.00 0.00 0.00 2.15
707 996 3.838244 TCAGCCATACCACCTTATCAC 57.162 47.619 0.00 0.00 0.00 3.06
708 997 2.102420 TCAGCCATACCACCTTATCACG 59.898 50.000 0.00 0.00 0.00 4.35
709 998 1.416401 AGCCATACCACCTTATCACGG 59.584 52.381 0.00 0.00 0.00 4.94
710 999 1.414919 GCCATACCACCTTATCACGGA 59.585 52.381 0.00 0.00 0.00 4.69
711 1000 2.158871 GCCATACCACCTTATCACGGAA 60.159 50.000 0.00 0.00 0.00 4.30
712 1001 3.683281 GCCATACCACCTTATCACGGAAA 60.683 47.826 0.00 0.00 0.00 3.13
713 1002 4.127171 CCATACCACCTTATCACGGAAAG 58.873 47.826 0.00 0.00 0.00 2.62
714 1003 2.781681 ACCACCTTATCACGGAAAGG 57.218 50.000 0.00 0.00 46.44 3.11
817 1107 1.163554 CCAGTTCTCCAGCTTTCAGC 58.836 55.000 0.00 0.00 42.84 4.26
843 1133 0.802494 CCTTTCCCGTGTTTGGATCG 59.198 55.000 0.00 0.00 0.00 3.69
846 1136 3.496131 CCCGTGTTTGGATCGGCG 61.496 66.667 0.00 0.00 42.48 6.46
944 1236 6.417044 CCTATATACACTGTTTCACTGTACGC 59.583 42.308 0.00 0.00 0.00 4.42
982 1274 1.294780 CCAAGAGCAGCGAGAGGTT 59.705 57.895 0.00 0.00 41.81 3.50
1038 1330 2.475371 ATTGCGTGCTCTTGGCCTCT 62.475 55.000 3.32 0.00 40.92 3.69
1044 1336 0.546267 TGCTCTTGGCCTCTCTCCTT 60.546 55.000 3.32 0.00 40.92 3.36
1047 1339 0.326264 TCTTGGCCTCTCTCCTTTGC 59.674 55.000 3.32 0.00 0.00 3.68
1125 1417 0.106719 CCACCAATGGCCGGAACTAT 60.107 55.000 5.05 0.00 39.82 2.12
1188 1480 0.629058 AAATGGGTGGCTTCCGGTAT 59.371 50.000 0.00 0.00 0.00 2.73
2403 2710 2.816360 CGCCACGGATGTCATGCTG 61.816 63.158 2.63 0.67 0.00 4.41
2684 2992 1.112113 GCAACGACAGGGAGGATCTA 58.888 55.000 0.00 0.00 33.73 1.98
2813 3121 0.328258 AGAACAACCCCAAGATCGGG 59.672 55.000 2.79 2.79 46.94 5.14
2820 3128 2.113986 CCAAGATCGGGGCCATCC 59.886 66.667 4.39 0.00 0.00 3.51
2896 3204 6.346096 TCTTCGGAAAATACAATCCAGGTAG 58.654 40.000 0.00 0.00 35.34 3.18
2897 3205 5.031066 TCGGAAAATACAATCCAGGTAGG 57.969 43.478 0.00 0.00 35.34 3.18
2940 3248 6.489675 CAGATCGATTCCTTGGTGTATTTTG 58.510 40.000 0.00 0.00 0.00 2.44
2943 3251 6.642707 TCGATTCCTTGGTGTATTTTGTTT 57.357 33.333 0.00 0.00 0.00 2.83
2944 3252 7.045126 TCGATTCCTTGGTGTATTTTGTTTT 57.955 32.000 0.00 0.00 0.00 2.43
2945 3253 7.142680 TCGATTCCTTGGTGTATTTTGTTTTC 58.857 34.615 0.00 0.00 0.00 2.29
3142 3450 2.094700 CGGTCTCAGCTACAGCAACTTA 60.095 50.000 3.70 0.00 45.16 2.24
3789 4135 8.157183 GCGCTAAAAATCGTTTTTGCTATTTAA 58.843 29.630 0.00 0.00 46.63 1.52
3831 6715 7.521871 ACTTGATTCTTTCTTGCTCTTCAAT 57.478 32.000 0.00 0.00 33.57 2.57
3972 6856 4.647564 AGAGAGATCTTGCCCTTCAAAA 57.352 40.909 0.00 0.00 33.65 2.44
4146 7403 1.137675 CGATCTCCATGAACTCCAGCA 59.862 52.381 0.00 0.00 0.00 4.41
4173 7430 2.169561 TGCGCAACATGTATCTTAGGGA 59.830 45.455 8.16 0.00 0.00 4.20
4174 7431 3.202906 GCGCAACATGTATCTTAGGGAA 58.797 45.455 0.30 0.00 0.00 3.97
4175 7432 3.248602 GCGCAACATGTATCTTAGGGAAG 59.751 47.826 0.30 0.00 0.00 3.46
4176 7433 3.248602 CGCAACATGTATCTTAGGGAAGC 59.751 47.826 0.00 0.00 32.21 3.86
4177 7434 4.199310 GCAACATGTATCTTAGGGAAGCA 58.801 43.478 0.00 0.00 32.21 3.91
4178 7435 4.035675 GCAACATGTATCTTAGGGAAGCAC 59.964 45.833 0.00 0.00 32.21 4.40
4179 7436 4.423625 ACATGTATCTTAGGGAAGCACC 57.576 45.455 0.00 0.00 38.08 5.01
4180 7437 4.040755 ACATGTATCTTAGGGAAGCACCT 58.959 43.478 0.00 0.24 44.75 4.00
4181 7438 4.141620 ACATGTATCTTAGGGAAGCACCTG 60.142 45.833 0.00 0.00 42.02 4.00
4182 7439 2.771943 TGTATCTTAGGGAAGCACCTGG 59.228 50.000 5.03 0.00 42.02 4.45
4183 7440 1.216990 ATCTTAGGGAAGCACCTGGG 58.783 55.000 0.00 0.00 42.02 4.45
4184 7441 0.118346 TCTTAGGGAAGCACCTGGGA 59.882 55.000 0.00 1.23 42.02 4.37
4185 7442 0.543749 CTTAGGGAAGCACCTGGGAG 59.456 60.000 0.00 0.00 42.02 4.30
4186 7443 0.914417 TTAGGGAAGCACCTGGGAGG 60.914 60.000 0.00 0.00 42.02 4.30
4187 7444 1.821966 TAGGGAAGCACCTGGGAGGA 61.822 60.000 0.00 0.00 42.02 3.71
4188 7445 2.003548 GGGAAGCACCTGGGAGGAT 61.004 63.158 0.00 0.00 37.67 3.24
4189 7446 1.529309 GGAAGCACCTGGGAGGATC 59.471 63.158 0.00 0.00 37.67 3.36
4190 7447 1.988982 GGAAGCACCTGGGAGGATCC 61.989 65.000 2.48 2.48 45.49 3.36
4257 7514 2.126914 CGAAACCCTAGATCGCAGAG 57.873 55.000 0.00 0.00 43.63 3.35
4276 7533 4.416601 CCCCCTTCCCGTCTCCCT 62.417 72.222 0.00 0.00 0.00 4.20
4277 7534 2.764547 CCCCTTCCCGTCTCCCTC 60.765 72.222 0.00 0.00 0.00 4.30
4278 7535 2.764547 CCCTTCCCGTCTCCCTCC 60.765 72.222 0.00 0.00 0.00 4.30
4279 7536 2.764547 CCTTCCCGTCTCCCTCCC 60.765 72.222 0.00 0.00 0.00 4.30
4280 7537 2.764547 CTTCCCGTCTCCCTCCCC 60.765 72.222 0.00 0.00 0.00 4.81
4281 7538 4.410033 TTCCCGTCTCCCTCCCCC 62.410 72.222 0.00 0.00 0.00 5.40
4313 7570 2.765356 GGCAAGCTTAGGGCGCTTC 61.765 63.158 9.23 0.00 45.27 3.86
4314 7571 2.765356 GCAAGCTTAGGGCGCTTCC 61.765 63.158 9.23 0.00 45.27 3.46
4315 7572 2.125106 AAGCTTAGGGCGCTTCCG 60.125 61.111 9.23 0.00 43.79 4.30
4316 7573 2.656069 AAGCTTAGGGCGCTTCCGA 61.656 57.895 9.23 0.00 43.79 4.55
4317 7574 2.579684 AAGCTTAGGGCGCTTCCGAG 62.580 60.000 9.23 6.09 43.79 4.63
4318 7575 2.107141 CTTAGGGCGCTTCCGAGG 59.893 66.667 9.23 0.00 36.29 4.63
4319 7576 2.363276 TTAGGGCGCTTCCGAGGA 60.363 61.111 9.23 0.00 36.29 3.71
4320 7577 1.956629 CTTAGGGCGCTTCCGAGGAA 61.957 60.000 9.23 4.34 36.29 3.36
4327 7584 2.125512 CTTCCGAGGAAGGTGGCG 60.126 66.667 21.08 0.00 45.60 5.69
4328 7585 3.665675 CTTCCGAGGAAGGTGGCGG 62.666 68.421 21.08 0.00 45.60 6.13
4344 7601 4.496336 GGCGGGGCTTCTGCTGAT 62.496 66.667 10.32 0.00 46.69 2.90
4345 7602 2.899339 GCGGGGCTTCTGCTGATC 60.899 66.667 0.00 0.00 44.20 2.92
4346 7603 2.906458 CGGGGCTTCTGCTGATCT 59.094 61.111 0.00 0.00 39.59 2.75
4347 7604 1.523258 CGGGGCTTCTGCTGATCTG 60.523 63.158 0.00 0.00 39.59 2.90
4348 7605 1.823041 GGGGCTTCTGCTGATCTGC 60.823 63.158 16.98 16.98 39.59 4.26
4349 7606 1.224039 GGGCTTCTGCTGATCTGCT 59.776 57.895 23.02 0.00 39.59 4.24
4350 7607 0.394080 GGGCTTCTGCTGATCTGCTT 60.394 55.000 23.02 0.00 39.59 3.91
4351 7608 1.461559 GGCTTCTGCTGATCTGCTTT 58.538 50.000 23.02 0.00 39.59 3.51
4352 7609 1.817447 GGCTTCTGCTGATCTGCTTTT 59.183 47.619 23.02 0.00 39.59 2.27
4353 7610 2.159407 GGCTTCTGCTGATCTGCTTTTC 60.159 50.000 23.02 9.95 39.59 2.29
4354 7611 2.475852 GCTTCTGCTGATCTGCTTTTCG 60.476 50.000 23.02 10.41 36.03 3.46
4355 7612 1.081892 TCTGCTGATCTGCTTTTCGC 58.918 50.000 23.02 1.13 39.77 4.70
4356 7613 0.098376 CTGCTGATCTGCTTTTCGCC 59.902 55.000 23.02 0.00 38.05 5.54
4357 7614 1.061570 GCTGATCTGCTTTTCGCCG 59.938 57.895 16.60 0.00 38.05 6.46
4358 7615 1.361668 GCTGATCTGCTTTTCGCCGA 61.362 55.000 16.60 0.00 38.05 5.54
4359 7616 0.649475 CTGATCTGCTTTTCGCCGAG 59.351 55.000 0.00 0.00 35.27 4.63
4360 7617 0.740868 TGATCTGCTTTTCGCCGAGG 60.741 55.000 0.00 0.00 35.27 4.63
4361 7618 1.432270 GATCTGCTTTTCGCCGAGGG 61.432 60.000 0.00 0.00 35.27 4.30
4362 7619 3.804193 CTGCTTTTCGCCGAGGGC 61.804 66.667 0.00 0.00 46.75 5.19
4393 7650 4.508128 GTGGCGGCCTCGATCGAA 62.508 66.667 19.92 0.00 39.00 3.71
4394 7651 4.207281 TGGCGGCCTCGATCGAAG 62.207 66.667 19.92 14.59 39.00 3.79
4395 7652 4.208686 GGCGGCCTCGATCGAAGT 62.209 66.667 19.92 0.00 39.00 3.01
4396 7653 2.956964 GCGGCCTCGATCGAAGTG 60.957 66.667 19.92 11.49 39.00 3.16
4397 7654 2.278857 CGGCCTCGATCGAAGTGG 60.279 66.667 19.92 17.49 39.00 4.00
4398 7655 2.586357 GGCCTCGATCGAAGTGGC 60.586 66.667 29.24 29.24 44.78 5.01
4399 7656 2.956964 GCCTCGATCGAAGTGGCG 60.957 66.667 25.33 11.17 38.29 5.69
4400 7657 2.956964 CCTCGATCGAAGTGGCGC 60.957 66.667 19.92 0.00 0.00 6.53
4401 7658 2.956964 CTCGATCGAAGTGGCGCC 60.957 66.667 22.73 22.73 0.00 6.53
4402 7659 3.699955 CTCGATCGAAGTGGCGCCA 62.700 63.158 29.03 29.03 0.00 5.69
4403 7660 3.554692 CGATCGAAGTGGCGCCAC 61.555 66.667 45.27 45.27 46.50 5.01
4416 7673 4.849329 GCCACCGGCTCTACGACG 62.849 72.222 0.00 0.00 46.69 5.12
4423 7680 2.277373 GCTCTACGACGAGCGGTG 60.277 66.667 13.18 0.00 45.91 4.94
4424 7681 2.403987 CTCTACGACGAGCGGTGG 59.596 66.667 0.00 0.00 46.49 4.61
4425 7682 3.736482 CTCTACGACGAGCGGTGGC 62.736 68.421 0.00 0.00 46.49 5.01
4444 7701 4.562425 CAGGCGTGGTGGTGGTGT 62.562 66.667 0.00 0.00 0.00 4.16
4445 7702 4.250305 AGGCGTGGTGGTGGTGTC 62.250 66.667 0.00 0.00 0.00 3.67
4448 7705 3.556306 CGTGGTGGTGGTGTCCCT 61.556 66.667 0.00 0.00 0.00 4.20
4449 7706 2.113139 GTGGTGGTGGTGTCCCTG 59.887 66.667 0.00 0.00 0.00 4.45
4450 7707 3.174987 TGGTGGTGGTGTCCCTGG 61.175 66.667 0.00 0.00 0.00 4.45
4451 7708 4.660938 GGTGGTGGTGTCCCTGGC 62.661 72.222 0.00 0.00 0.00 4.85
4452 7709 4.660938 GTGGTGGTGTCCCTGGCC 62.661 72.222 0.00 0.00 0.00 5.36
4457 7714 4.394712 GGTGTCCCTGGCCGTGAG 62.395 72.222 0.00 0.00 0.00 3.51
4470 7727 4.222847 GTGAGGACGGCGGGGATC 62.223 72.222 13.24 4.21 0.00 3.36
4481 7738 4.157120 GGGGATCCGGTGGACGTG 62.157 72.222 5.45 0.00 42.24 4.49
4482 7739 3.072468 GGGATCCGGTGGACGTGA 61.072 66.667 5.45 0.00 42.24 4.35
4483 7740 2.652095 GGGATCCGGTGGACGTGAA 61.652 63.158 5.45 0.00 42.24 3.18
4484 7741 1.447314 GGATCCGGTGGACGTGAAC 60.447 63.158 0.00 0.00 42.24 3.18
4485 7742 1.447314 GATCCGGTGGACGTGAACC 60.447 63.158 0.00 0.00 42.24 3.62
4486 7743 1.885163 GATCCGGTGGACGTGAACCT 61.885 60.000 12.99 0.00 42.24 3.50
4487 7744 0.612732 ATCCGGTGGACGTGAACCTA 60.613 55.000 12.99 3.51 42.24 3.08
4488 7745 1.214589 CCGGTGGACGTGAACCTAG 59.785 63.158 12.99 2.76 42.24 3.02
4489 7746 1.530013 CCGGTGGACGTGAACCTAGT 61.530 60.000 12.99 0.00 42.24 2.57
4490 7747 0.388134 CGGTGGACGTGAACCTAGTG 60.388 60.000 12.99 0.00 37.93 2.74
4491 7748 0.669625 GGTGGACGTGAACCTAGTGC 60.670 60.000 8.66 0.00 33.40 4.40
4492 7749 1.007336 GTGGACGTGAACCTAGTGCG 61.007 60.000 0.00 0.00 0.00 5.34
4493 7750 1.445582 GGACGTGAACCTAGTGCGG 60.446 63.158 0.00 0.00 0.00 5.69
4494 7751 1.288127 GACGTGAACCTAGTGCGGT 59.712 57.895 0.00 0.00 39.48 5.68
4495 7752 0.731855 GACGTGAACCTAGTGCGGTC 60.732 60.000 0.00 0.00 35.89 4.79
4496 7753 1.445582 CGTGAACCTAGTGCGGTCC 60.446 63.158 0.00 0.00 35.89 4.46
4497 7754 1.874345 CGTGAACCTAGTGCGGTCCT 61.874 60.000 0.00 0.00 35.89 3.85
4498 7755 0.389948 GTGAACCTAGTGCGGTCCTG 60.390 60.000 0.00 0.00 35.89 3.86
4499 7756 1.218316 GAACCTAGTGCGGTCCTGG 59.782 63.158 0.00 0.00 35.89 4.45
4500 7757 2.854187 GAACCTAGTGCGGTCCTGGC 62.854 65.000 0.00 0.00 35.89 4.85
4501 7758 4.514577 CCTAGTGCGGTCCTGGCG 62.515 72.222 0.00 0.00 0.00 5.69
4502 7759 4.514577 CTAGTGCGGTCCTGGCGG 62.515 72.222 0.00 0.00 0.00 6.13
4513 7770 4.803908 CTGGCGGCCCCTTCCTTC 62.804 72.222 17.97 0.00 0.00 3.46
4515 7772 4.048470 GGCGGCCCCTTCCTTCTT 62.048 66.667 8.12 0.00 0.00 2.52
4516 7773 2.438614 GCGGCCCCTTCCTTCTTC 60.439 66.667 0.00 0.00 0.00 2.87
4517 7774 2.972819 GCGGCCCCTTCCTTCTTCT 61.973 63.158 0.00 0.00 0.00 2.85
4518 7775 1.623542 GCGGCCCCTTCCTTCTTCTA 61.624 60.000 0.00 0.00 0.00 2.10
4519 7776 0.178301 CGGCCCCTTCCTTCTTCTAC 59.822 60.000 0.00 0.00 0.00 2.59
4520 7777 0.178301 GGCCCCTTCCTTCTTCTACG 59.822 60.000 0.00 0.00 0.00 3.51
4521 7778 0.462225 GCCCCTTCCTTCTTCTACGC 60.462 60.000 0.00 0.00 0.00 4.42
4522 7779 0.179108 CCCCTTCCTTCTTCTACGCG 60.179 60.000 3.53 3.53 0.00 6.01
4523 7780 0.815734 CCCTTCCTTCTTCTACGCGA 59.184 55.000 15.93 0.00 0.00 5.87
4524 7781 1.409427 CCCTTCCTTCTTCTACGCGAT 59.591 52.381 15.93 0.00 0.00 4.58
4525 7782 2.464865 CCTTCCTTCTTCTACGCGATG 58.535 52.381 15.93 4.70 0.00 3.84
4526 7783 2.159226 CCTTCCTTCTTCTACGCGATGT 60.159 50.000 15.93 0.00 0.00 3.06
4527 7784 2.561733 TCCTTCTTCTACGCGATGTG 57.438 50.000 15.93 0.00 0.00 3.21
4528 7785 2.089201 TCCTTCTTCTACGCGATGTGA 58.911 47.619 15.93 1.64 0.00 3.58
4529 7786 2.688446 TCCTTCTTCTACGCGATGTGAT 59.312 45.455 15.93 0.00 0.00 3.06
4530 7787 3.046390 CCTTCTTCTACGCGATGTGATC 58.954 50.000 15.93 0.00 0.00 2.92
4531 7788 2.776312 TCTTCTACGCGATGTGATCC 57.224 50.000 15.93 0.00 0.00 3.36
4532 7789 1.337071 TCTTCTACGCGATGTGATCCC 59.663 52.381 15.93 0.00 0.00 3.85
4533 7790 1.338337 CTTCTACGCGATGTGATCCCT 59.662 52.381 15.93 0.00 0.00 4.20
4534 7791 0.952280 TCTACGCGATGTGATCCCTC 59.048 55.000 15.93 0.00 0.00 4.30
4535 7792 0.039074 CTACGCGATGTGATCCCTCC 60.039 60.000 15.93 0.00 0.00 4.30
4536 7793 1.461091 TACGCGATGTGATCCCTCCC 61.461 60.000 15.93 0.00 0.00 4.30
4537 7794 2.427753 GCGATGTGATCCCTCCCC 59.572 66.667 0.00 0.00 0.00 4.81
4538 7795 2.143419 GCGATGTGATCCCTCCCCT 61.143 63.158 0.00 0.00 0.00 4.79
4539 7796 2.053618 CGATGTGATCCCTCCCCTC 58.946 63.158 0.00 0.00 0.00 4.30
4540 7797 1.476007 CGATGTGATCCCTCCCCTCC 61.476 65.000 0.00 0.00 0.00 4.30
4541 7798 1.460305 ATGTGATCCCTCCCCTCCG 60.460 63.158 0.00 0.00 0.00 4.63
4542 7799 2.844839 GTGATCCCTCCCCTCCGG 60.845 72.222 0.00 0.00 0.00 5.14
4560 7817 4.699522 GCCTGGGTCGGCGTTCTT 62.700 66.667 6.85 0.00 40.79 2.52
4561 7818 2.434359 CCTGGGTCGGCGTTCTTC 60.434 66.667 6.85 0.17 0.00 2.87
4562 7819 2.657237 CTGGGTCGGCGTTCTTCT 59.343 61.111 6.85 0.00 0.00 2.85
4563 7820 1.004918 CTGGGTCGGCGTTCTTCTT 60.005 57.895 6.85 0.00 0.00 2.52
4564 7821 0.602905 CTGGGTCGGCGTTCTTCTTT 60.603 55.000 6.85 0.00 0.00 2.52
4565 7822 0.882927 TGGGTCGGCGTTCTTCTTTG 60.883 55.000 6.85 0.00 0.00 2.77
4566 7823 0.601841 GGGTCGGCGTTCTTCTTTGA 60.602 55.000 6.85 0.00 0.00 2.69
4567 7824 1.439679 GGTCGGCGTTCTTCTTTGAT 58.560 50.000 6.85 0.00 0.00 2.57
4568 7825 1.393883 GGTCGGCGTTCTTCTTTGATC 59.606 52.381 6.85 0.00 0.00 2.92
4569 7826 2.338500 GTCGGCGTTCTTCTTTGATCT 58.662 47.619 6.85 0.00 0.00 2.75
4570 7827 2.737252 GTCGGCGTTCTTCTTTGATCTT 59.263 45.455 6.85 0.00 0.00 2.40
4571 7828 2.993899 TCGGCGTTCTTCTTTGATCTTC 59.006 45.455 6.85 0.00 0.00 2.87
4572 7829 2.736721 CGGCGTTCTTCTTTGATCTTCA 59.263 45.455 0.00 0.00 0.00 3.02
4573 7830 3.181526 CGGCGTTCTTCTTTGATCTTCAG 60.182 47.826 0.00 0.00 0.00 3.02
4574 7831 3.748568 GGCGTTCTTCTTTGATCTTCAGT 59.251 43.478 0.00 0.00 0.00 3.41
4575 7832 4.143009 GGCGTTCTTCTTTGATCTTCAGTC 60.143 45.833 0.00 0.00 0.00 3.51
4576 7833 4.688413 GCGTTCTTCTTTGATCTTCAGTCT 59.312 41.667 0.00 0.00 0.00 3.24
4577 7834 5.164002 GCGTTCTTCTTTGATCTTCAGTCTC 60.164 44.000 0.00 0.00 0.00 3.36
4578 7835 5.347364 CGTTCTTCTTTGATCTTCAGTCTCC 59.653 44.000 0.00 0.00 0.00 3.71
4579 7836 6.226787 GTTCTTCTTTGATCTTCAGTCTCCA 58.773 40.000 0.00 0.00 0.00 3.86
4580 7837 6.617782 TCTTCTTTGATCTTCAGTCTCCAT 57.382 37.500 0.00 0.00 0.00 3.41
4581 7838 6.404708 TCTTCTTTGATCTTCAGTCTCCATG 58.595 40.000 0.00 0.00 0.00 3.66
4582 7839 5.095145 TCTTTGATCTTCAGTCTCCATGG 57.905 43.478 4.97 4.97 0.00 3.66
4583 7840 4.533707 TCTTTGATCTTCAGTCTCCATGGT 59.466 41.667 12.58 0.00 0.00 3.55
4584 7841 3.900966 TGATCTTCAGTCTCCATGGTG 57.099 47.619 12.58 9.91 0.00 4.17
4585 7842 3.444029 TGATCTTCAGTCTCCATGGTGA 58.556 45.455 12.58 12.54 0.00 4.02
4586 7843 3.450096 TGATCTTCAGTCTCCATGGTGAG 59.550 47.826 16.73 5.40 0.00 3.51
4587 7844 2.182827 TCTTCAGTCTCCATGGTGAGG 58.817 52.381 16.73 10.83 33.04 3.86
4588 7845 1.209019 CTTCAGTCTCCATGGTGAGGG 59.791 57.143 16.73 11.67 33.04 4.30
4589 7846 0.117140 TCAGTCTCCATGGTGAGGGT 59.883 55.000 16.73 2.39 33.04 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.865590 AACTTTTGTCGTATTAAAACTGCAAT 57.134 26.923 0.00 0.00 0.00 3.56
1 2 8.690680 AAACTTTTGTCGTATTAAAACTGCAA 57.309 26.923 0.00 0.00 0.00 4.08
24 25 4.088634 AGATGGCATGCAAGAAAGGTAAA 58.911 39.130 21.36 0.00 0.00 2.01
27 28 2.226962 AGATGGCATGCAAGAAAGGT 57.773 45.000 21.36 0.00 0.00 3.50
55 56 2.175715 CCTCTCCCCCAAGAAAATAGGG 59.824 54.545 0.00 0.00 42.44 3.53
68 69 2.036089 GTGATTACGTGATCCTCTCCCC 59.964 54.545 16.77 0.00 0.00 4.81
81 82 7.852146 GTTGCATCCAAAGACCGTGATTACG 62.852 48.000 2.51 2.51 40.26 3.18
147 148 6.571624 TCACCTATCCTATTTAGGCTGGTAT 58.428 40.000 0.00 0.00 43.31 2.73
150 151 5.738909 CATCACCTATCCTATTTAGGCTGG 58.261 45.833 0.00 3.93 43.31 4.85
153 154 5.165961 TGCATCACCTATCCTATTTAGGC 57.834 43.478 0.00 0.00 43.31 3.93
154 155 6.950842 TCATGCATCACCTATCCTATTTAGG 58.049 40.000 0.00 0.00 45.02 2.69
155 156 7.046652 CCTCATGCATCACCTATCCTATTTAG 58.953 42.308 0.00 0.00 0.00 1.85
156 157 6.577039 GCCTCATGCATCACCTATCCTATTTA 60.577 42.308 0.00 0.00 40.77 1.40
157 158 5.805751 GCCTCATGCATCACCTATCCTATTT 60.806 44.000 0.00 0.00 40.77 1.40
158 159 4.324099 GCCTCATGCATCACCTATCCTATT 60.324 45.833 0.00 0.00 40.77 1.73
159 160 3.199508 GCCTCATGCATCACCTATCCTAT 59.800 47.826 0.00 0.00 40.77 2.57
160 161 2.568956 GCCTCATGCATCACCTATCCTA 59.431 50.000 0.00 0.00 40.77 2.94
161 162 1.350351 GCCTCATGCATCACCTATCCT 59.650 52.381 0.00 0.00 40.77 3.24
162 163 1.612726 GGCCTCATGCATCACCTATCC 60.613 57.143 0.00 0.00 43.89 2.59
183 184 6.929049 AGACGACTGACAACAAGATAAAATGA 59.071 34.615 0.00 0.00 0.00 2.57
184 185 7.011773 CAGACGACTGACAACAAGATAAAATG 58.988 38.462 9.38 0.00 46.03 2.32
185 186 6.706270 ACAGACGACTGACAACAAGATAAAAT 59.294 34.615 21.50 0.00 46.03 1.82
251 527 7.242914 ACTTACTGCAGTGTTTACAAGTTAC 57.757 36.000 29.57 0.00 0.00 2.50
259 535 6.300703 ACCCAATTACTTACTGCAGTGTTTA 58.699 36.000 29.57 13.56 0.00 2.01
290 566 3.664107 GGCCTCTACATCGATTAATGCA 58.336 45.455 0.00 0.00 0.00 3.96
295 571 1.254026 CCCGGCCTCTACATCGATTA 58.746 55.000 0.00 0.00 0.00 1.75
310 586 2.225382 AACAGGGTTAAAATCCCCGG 57.775 50.000 0.00 0.00 46.17 5.73
312 588 6.043474 AGGTTAAAAACAGGGTTAAAATCCCC 59.957 38.462 0.00 0.00 45.64 4.81
341 617 3.316071 ACTGTCTCAGCTTGTCATCTG 57.684 47.619 0.00 0.00 34.37 2.90
344 620 2.636893 AGGAACTGTCTCAGCTTGTCAT 59.363 45.455 0.00 0.00 37.18 3.06
386 662 2.417107 CCGCACACTGGGTAATACGTTA 60.417 50.000 0.00 0.00 0.00 3.18
397 673 2.673368 GAGAGAATTAACCGCACACTGG 59.327 50.000 0.00 0.00 0.00 4.00
398 674 2.673368 GGAGAGAATTAACCGCACACTG 59.327 50.000 0.00 0.00 0.00 3.66
406 682 4.633565 CACAAGCTCAGGAGAGAATTAACC 59.366 45.833 0.00 0.00 44.98 2.85
431 707 7.637709 TTGATTATACATCGCTGACATACAC 57.362 36.000 0.00 0.00 0.00 2.90
437 713 7.227461 CGGTTAATTGATTATACATCGCTGAC 58.773 38.462 0.00 0.00 0.00 3.51
440 716 5.932303 AGCGGTTAATTGATTATACATCGCT 59.068 36.000 7.78 7.78 42.87 4.93
449 725 8.669946 TCATCATTGTAGCGGTTAATTGATTA 57.330 30.769 0.00 0.00 0.00 1.75
461 737 4.025396 GGACAACAGATCATCATTGTAGCG 60.025 45.833 7.17 0.00 35.47 4.26
466 742 4.095932 CACCAGGACAACAGATCATCATTG 59.904 45.833 0.00 1.08 0.00 2.82
483 759 4.622260 AATTTTGATCCCAAACACCAGG 57.378 40.909 0.00 0.00 41.54 4.45
490 766 9.844257 AAATGAACACTAAATTTTGATCCCAAA 57.156 25.926 6.63 0.00 40.24 3.28
492 768 8.646004 TGAAATGAACACTAAATTTTGATCCCA 58.354 29.630 6.63 0.63 0.00 4.37
539 815 3.961477 TGTTGACTGTATTGTGCACAC 57.039 42.857 21.56 9.20 0.00 3.82
548 832 6.183360 TGCAGCTACTGATATGTTGACTGTAT 60.183 38.462 0.00 0.00 32.44 2.29
553 837 5.111989 TCTTGCAGCTACTGATATGTTGAC 58.888 41.667 0.00 0.00 32.44 3.18
555 839 5.352293 TGTTCTTGCAGCTACTGATATGTTG 59.648 40.000 0.00 0.00 32.44 3.33
559 843 6.351711 TGAATGTTCTTGCAGCTACTGATAT 58.648 36.000 0.00 0.00 32.44 1.63
563 847 4.337985 CTGAATGTTCTTGCAGCTACTG 57.662 45.455 0.00 0.00 34.12 2.74
574 863 5.238214 GTCTTGACTTCTTGCTGAATGTTCT 59.762 40.000 0.00 0.00 33.71 3.01
601 890 2.467880 GGACAACCCATCTCTCCTGTA 58.532 52.381 0.00 0.00 34.14 2.74
624 913 6.154706 ACGTTCTCCAAGTTATACTTCCATCT 59.845 38.462 0.00 0.00 36.03 2.90
633 922 4.773674 TCCTTCCACGTTCTCCAAGTTATA 59.226 41.667 0.00 0.00 0.00 0.98
642 931 3.452474 CTGATCATCCTTCCACGTTCTC 58.548 50.000 0.00 0.00 0.00 2.87
685 974 4.130118 GTGATAAGGTGGTATGGCTGAAG 58.870 47.826 0.00 0.00 0.00 3.02
698 987 2.829023 TCTCCCTTTCCGTGATAAGGT 58.171 47.619 0.00 0.00 39.43 3.50
699 988 3.451178 TCTTCTCCCTTTCCGTGATAAGG 59.549 47.826 0.00 0.00 40.50 2.69
700 989 4.737855 TCTTCTCCCTTTCCGTGATAAG 57.262 45.455 0.00 0.00 0.00 1.73
702 991 3.388024 CCATCTTCTCCCTTTCCGTGATA 59.612 47.826 0.00 0.00 0.00 2.15
704 993 1.555075 CCATCTTCTCCCTTTCCGTGA 59.445 52.381 0.00 0.00 0.00 4.35
705 994 1.555075 TCCATCTTCTCCCTTTCCGTG 59.445 52.381 0.00 0.00 0.00 4.94
706 995 1.555533 GTCCATCTTCTCCCTTTCCGT 59.444 52.381 0.00 0.00 0.00 4.69
707 996 1.471676 CGTCCATCTTCTCCCTTTCCG 60.472 57.143 0.00 0.00 0.00 4.30
708 997 1.831736 TCGTCCATCTTCTCCCTTTCC 59.168 52.381 0.00 0.00 0.00 3.13
709 998 2.233922 TGTCGTCCATCTTCTCCCTTTC 59.766 50.000 0.00 0.00 0.00 2.62
710 999 2.028020 GTGTCGTCCATCTTCTCCCTTT 60.028 50.000 0.00 0.00 0.00 3.11
711 1000 1.550976 GTGTCGTCCATCTTCTCCCTT 59.449 52.381 0.00 0.00 0.00 3.95
712 1001 1.187087 GTGTCGTCCATCTTCTCCCT 58.813 55.000 0.00 0.00 0.00 4.20
713 1002 0.175989 GGTGTCGTCCATCTTCTCCC 59.824 60.000 0.00 0.00 0.00 4.30
714 1003 0.895530 TGGTGTCGTCCATCTTCTCC 59.104 55.000 0.00 0.00 31.96 3.71
817 1107 0.537371 AACACGGGAAAGGCCAGAAG 60.537 55.000 5.01 0.00 38.95 2.85
982 1274 2.302260 CATTGCGACTAGAGAGGAGGA 58.698 52.381 0.00 0.00 0.00 3.71
1038 1330 1.964373 GGAAACGGCGCAAAGGAGA 60.964 57.895 10.83 0.00 0.00 3.71
2088 2395 0.038159 CGAAGGCGGTGAAGAAGTCT 60.038 55.000 0.00 0.00 0.00 3.24
2403 2710 5.741962 ACTTTTTACCTCTGTAGTCTCCC 57.258 43.478 0.00 0.00 0.00 4.30
2684 2992 0.904865 TCTGATTCCACGGCAGGAGT 60.905 55.000 0.00 0.00 39.25 3.85
2735 3043 0.837272 CCAGGATGATTGGGTACGGT 59.163 55.000 0.00 0.00 39.69 4.83
2896 3204 7.700234 CGATCTGCATTTCATCTATAGTACTCC 59.300 40.741 0.00 0.00 0.00 3.85
2897 3205 8.454894 TCGATCTGCATTTCATCTATAGTACTC 58.545 37.037 0.00 0.00 0.00 2.59
2898 3206 8.341892 TCGATCTGCATTTCATCTATAGTACT 57.658 34.615 0.00 0.00 0.00 2.73
2899 3207 9.579768 AATCGATCTGCATTTCATCTATAGTAC 57.420 33.333 0.00 0.00 0.00 2.73
2905 3213 6.106648 AGGAATCGATCTGCATTTCATCTA 57.893 37.500 0.00 0.00 0.00 1.98
2940 3248 7.010091 ACAATCCAAGAAACGTTTCATGAAAAC 59.990 33.333 35.30 14.19 43.22 2.43
2943 3251 6.142818 ACAATCCAAGAAACGTTTCATGAA 57.857 33.333 35.30 23.83 37.92 2.57
2944 3252 5.298026 TGACAATCCAAGAAACGTTTCATGA 59.702 36.000 35.30 28.09 37.92 3.07
2945 3253 5.518812 TGACAATCCAAGAAACGTTTCATG 58.481 37.500 35.29 32.48 39.61 3.07
3268 3576 2.847234 TCCTCTTGGCACCCGTGT 60.847 61.111 0.00 0.00 0.00 4.49
3344 3652 2.340809 CGGCACCGTGTAGACCAA 59.659 61.111 0.00 0.00 34.35 3.67
3493 3801 4.367023 GGCACGACGGTGTAGGCA 62.367 66.667 0.00 0.00 46.13 4.75
3547 3855 1.279271 ACGGGGAAAGAGAATGACAGG 59.721 52.381 0.00 0.00 0.00 4.00
3805 6689 7.426929 TGAAGAGCAAGAAAGAATCAAGTAC 57.573 36.000 0.00 0.00 0.00 2.73
3855 6739 3.242543 CGCGGAATGATCCTCAAAAAGAG 60.243 47.826 0.00 0.00 44.17 2.85
3856 6740 2.677836 CGCGGAATGATCCTCAAAAAGA 59.322 45.455 0.00 0.00 44.17 2.52
3857 6741 2.420022 ACGCGGAATGATCCTCAAAAAG 59.580 45.455 12.47 0.00 44.17 2.27
3858 6742 2.418628 GACGCGGAATGATCCTCAAAAA 59.581 45.455 12.47 0.00 44.17 1.94
3972 6856 7.382110 GGATGGTATATATAGATGCGCAAGAT 58.618 38.462 17.11 10.85 43.02 2.40
4032 7287 5.903198 AGGGGATTAGAAGGAGAGAATTG 57.097 43.478 0.00 0.00 0.00 2.32
4146 7403 1.472480 GATACATGTTGCGCAACCCTT 59.528 47.619 41.29 29.09 40.46 3.95
4173 7430 0.985490 GAGGATCCTCCCAGGTGCTT 60.985 60.000 28.84 0.00 37.19 3.91
4174 7431 1.383803 GAGGATCCTCCCAGGTGCT 60.384 63.158 28.84 0.00 37.19 4.40
4175 7432 3.235369 GAGGATCCTCCCAGGTGC 58.765 66.667 28.84 3.71 37.19 5.01
4238 7495 1.866063 GCTCTGCGATCTAGGGTTTCG 60.866 57.143 0.00 0.00 36.02 3.46
4239 7496 1.539280 GGCTCTGCGATCTAGGGTTTC 60.539 57.143 0.00 0.00 0.00 2.78
4240 7497 0.466124 GGCTCTGCGATCTAGGGTTT 59.534 55.000 0.00 0.00 0.00 3.27
4241 7498 1.403687 GGGCTCTGCGATCTAGGGTT 61.404 60.000 0.00 0.00 0.00 4.11
4242 7499 1.834822 GGGCTCTGCGATCTAGGGT 60.835 63.158 0.00 0.00 0.00 4.34
4243 7500 2.578714 GGGGCTCTGCGATCTAGGG 61.579 68.421 0.00 0.00 0.00 3.53
4244 7501 2.578714 GGGGGCTCTGCGATCTAGG 61.579 68.421 0.00 0.00 0.00 3.02
4245 7502 3.055580 GGGGGCTCTGCGATCTAG 58.944 66.667 0.00 0.00 0.00 2.43
4259 7516 4.416601 AGGGAGACGGGAAGGGGG 62.417 72.222 0.00 0.00 0.00 5.40
4260 7517 2.764547 GAGGGAGACGGGAAGGGG 60.765 72.222 0.00 0.00 0.00 4.79
4261 7518 2.764547 GGAGGGAGACGGGAAGGG 60.765 72.222 0.00 0.00 0.00 3.95
4262 7519 2.764547 GGGAGGGAGACGGGAAGG 60.765 72.222 0.00 0.00 0.00 3.46
4263 7520 2.764547 GGGGAGGGAGACGGGAAG 60.765 72.222 0.00 0.00 0.00 3.46
4264 7521 4.410033 GGGGGAGGGAGACGGGAA 62.410 72.222 0.00 0.00 0.00 3.97
4294 7551 4.803908 AGCGCCCTAAGCTTGCCC 62.804 66.667 9.86 0.00 43.24 5.36
4300 7557 2.586357 CTCGGAAGCGCCCTAAGC 60.586 66.667 2.29 0.00 38.52 3.09
4301 7558 1.956629 TTCCTCGGAAGCGCCCTAAG 61.957 60.000 2.29 0.00 0.00 2.18
4302 7559 1.956629 CTTCCTCGGAAGCGCCCTAA 61.957 60.000 12.39 0.00 43.95 2.69
4303 7560 2.363276 TTCCTCGGAAGCGCCCTA 60.363 61.111 2.29 0.00 0.00 3.53
4304 7561 3.775654 CTTCCTCGGAAGCGCCCT 61.776 66.667 12.39 0.00 43.95 5.19
4311 7568 3.702048 CCGCCACCTTCCTCGGAA 61.702 66.667 0.00 0.00 44.23 4.30
4327 7584 4.496336 ATCAGCAGAAGCCCCGCC 62.496 66.667 0.00 0.00 43.56 6.13
4328 7585 2.899339 GATCAGCAGAAGCCCCGC 60.899 66.667 0.00 0.00 43.56 6.13
4329 7586 1.523258 CAGATCAGCAGAAGCCCCG 60.523 63.158 0.00 0.00 43.56 5.73
4330 7587 1.823041 GCAGATCAGCAGAAGCCCC 60.823 63.158 5.05 0.00 43.56 5.80
4331 7588 0.394080 AAGCAGATCAGCAGAAGCCC 60.394 55.000 13.03 0.00 43.56 5.19
4332 7589 1.461559 AAAGCAGATCAGCAGAAGCC 58.538 50.000 13.03 0.00 43.56 4.35
4333 7590 2.475852 CGAAAAGCAGATCAGCAGAAGC 60.476 50.000 13.03 0.00 42.56 3.86
4334 7591 3.386613 CGAAAAGCAGATCAGCAGAAG 57.613 47.619 13.03 0.00 36.85 2.85
4376 7633 4.508128 TTCGATCGAGGCCGCCAC 62.508 66.667 18.54 4.11 35.37 5.01
4377 7634 4.207281 CTTCGATCGAGGCCGCCA 62.207 66.667 18.54 0.18 35.37 5.69
4378 7635 4.208686 ACTTCGATCGAGGCCGCC 62.209 66.667 25.25 0.00 35.37 6.13
4379 7636 2.956964 CACTTCGATCGAGGCCGC 60.957 66.667 25.25 0.00 35.37 6.53
4380 7637 2.278857 CCACTTCGATCGAGGCCG 60.279 66.667 25.25 16.80 37.07 6.13
4381 7638 2.586357 GCCACTTCGATCGAGGCC 60.586 66.667 27.75 14.22 39.42 5.19
4382 7639 2.956964 CGCCACTTCGATCGAGGC 60.957 66.667 28.03 28.03 41.86 4.70
4383 7640 2.956964 GCGCCACTTCGATCGAGG 60.957 66.667 23.94 23.94 0.00 4.63
4384 7641 2.956964 GGCGCCACTTCGATCGAG 60.957 66.667 24.80 14.40 0.00 4.04
4385 7642 3.754530 TGGCGCCACTTCGATCGA 61.755 61.111 29.03 15.15 0.00 3.59
4386 7643 3.554692 GTGGCGCCACTTCGATCG 61.555 66.667 44.62 9.36 43.12 3.69
4400 7657 3.109612 CTCGTCGTAGAGCCGGTGG 62.110 68.421 1.90 0.00 36.95 4.61
4401 7658 2.403987 CTCGTCGTAGAGCCGGTG 59.596 66.667 1.90 0.00 36.95 4.94
4407 7664 2.403987 CCACCGCTCGTCGTAGAG 59.596 66.667 5.72 5.72 36.95 2.43
4408 7665 3.807538 GCCACCGCTCGTCGTAGA 61.808 66.667 0.00 0.00 36.19 2.59
4427 7684 4.562425 ACACCACCACCACGCCTG 62.562 66.667 0.00 0.00 0.00 4.85
4428 7685 4.250305 GACACCACCACCACGCCT 62.250 66.667 0.00 0.00 0.00 5.52
4431 7688 3.556306 AGGGACACCACCACCACG 61.556 66.667 0.00 0.00 40.13 4.94
4432 7689 2.113139 CAGGGACACCACCACCAC 59.887 66.667 0.00 0.00 40.13 4.16
4433 7690 3.174987 CCAGGGACACCACCACCA 61.175 66.667 0.00 0.00 40.13 4.17
4434 7691 4.660938 GCCAGGGACACCACCACC 62.661 72.222 0.00 0.00 40.13 4.61
4435 7692 4.660938 GGCCAGGGACACCACCAC 62.661 72.222 0.00 0.00 40.13 4.16
4440 7697 4.394712 CTCACGGCCAGGGACACC 62.395 72.222 2.24 0.00 0.00 4.16
4441 7698 4.394712 CCTCACGGCCAGGGACAC 62.395 72.222 2.24 0.00 0.00 3.67
4442 7699 4.631740 TCCTCACGGCCAGGGACA 62.632 66.667 2.24 0.00 0.00 4.02
4443 7700 4.083862 GTCCTCACGGCCAGGGAC 62.084 72.222 14.67 14.67 40.86 4.46
4453 7710 4.222847 GATCCCCGCCGTCCTCAC 62.223 72.222 0.00 0.00 0.00 3.51
4464 7721 4.157120 CACGTCCACCGGATCCCC 62.157 72.222 9.46 0.00 42.24 4.81
4465 7722 2.652095 TTCACGTCCACCGGATCCC 61.652 63.158 9.46 0.00 42.24 3.85
4466 7723 1.447314 GTTCACGTCCACCGGATCC 60.447 63.158 9.46 0.00 42.24 3.36
4467 7724 1.447314 GGTTCACGTCCACCGGATC 60.447 63.158 9.46 0.00 42.24 3.36
4468 7725 0.612732 TAGGTTCACGTCCACCGGAT 60.613 55.000 9.46 0.00 42.24 4.18
4469 7726 1.228521 TAGGTTCACGTCCACCGGA 60.229 57.895 9.46 0.00 42.24 5.14
4470 7727 1.214589 CTAGGTTCACGTCCACCGG 59.785 63.158 0.00 0.00 42.24 5.28
4471 7728 0.388134 CACTAGGTTCACGTCCACCG 60.388 60.000 6.97 0.00 44.03 4.94
4472 7729 0.669625 GCACTAGGTTCACGTCCACC 60.670 60.000 4.70 4.70 0.00 4.61
4473 7730 1.007336 CGCACTAGGTTCACGTCCAC 61.007 60.000 0.00 0.00 0.00 4.02
4474 7731 1.287815 CGCACTAGGTTCACGTCCA 59.712 57.895 0.00 0.00 0.00 4.02
4475 7732 1.445582 CCGCACTAGGTTCACGTCC 60.446 63.158 0.00 0.00 0.00 4.79
4476 7733 0.731855 GACCGCACTAGGTTCACGTC 60.732 60.000 0.00 0.00 46.09 4.34
4477 7734 1.288127 GACCGCACTAGGTTCACGT 59.712 57.895 0.00 0.00 46.09 4.49
4478 7735 1.445582 GGACCGCACTAGGTTCACG 60.446 63.158 0.00 0.00 46.09 4.35
4479 7736 0.389948 CAGGACCGCACTAGGTTCAC 60.390 60.000 0.00 0.00 46.09 3.18
4480 7737 1.541310 CCAGGACCGCACTAGGTTCA 61.541 60.000 0.00 0.00 46.09 3.18
4481 7738 1.218316 CCAGGACCGCACTAGGTTC 59.782 63.158 0.00 0.00 46.09 3.62
4482 7739 2.955881 GCCAGGACCGCACTAGGTT 61.956 63.158 0.00 0.00 46.09 3.50
4484 7741 4.514577 CGCCAGGACCGCACTAGG 62.515 72.222 0.00 0.00 37.30 3.02
4485 7742 4.514577 CCGCCAGGACCGCACTAG 62.515 72.222 0.00 0.00 41.02 2.57
4496 7753 4.803908 GAAGGAAGGGGCCGCCAG 62.804 72.222 17.56 0.00 0.00 4.85
4498 7755 3.997400 GAAGAAGGAAGGGGCCGCC 62.997 68.421 17.56 9.34 0.00 6.13
4499 7756 1.623542 TAGAAGAAGGAAGGGGCCGC 61.624 60.000 12.88 12.88 0.00 6.53
4500 7757 0.178301 GTAGAAGAAGGAAGGGGCCG 59.822 60.000 0.00 0.00 0.00 6.13
4501 7758 0.178301 CGTAGAAGAAGGAAGGGGCC 59.822 60.000 0.00 0.00 0.00 5.80
4502 7759 0.462225 GCGTAGAAGAAGGAAGGGGC 60.462 60.000 0.00 0.00 0.00 5.80
4503 7760 0.179108 CGCGTAGAAGAAGGAAGGGG 60.179 60.000 0.00 0.00 0.00 4.79
4504 7761 0.815734 TCGCGTAGAAGAAGGAAGGG 59.184 55.000 5.77 0.00 0.00 3.95
4505 7762 2.159226 ACATCGCGTAGAAGAAGGAAGG 60.159 50.000 5.77 0.00 0.00 3.46
4506 7763 2.854777 CACATCGCGTAGAAGAAGGAAG 59.145 50.000 5.77 0.00 0.00 3.46
4507 7764 2.490509 TCACATCGCGTAGAAGAAGGAA 59.509 45.455 5.77 0.00 0.00 3.36
4508 7765 2.089201 TCACATCGCGTAGAAGAAGGA 58.911 47.619 5.77 0.00 0.00 3.36
4509 7766 2.561733 TCACATCGCGTAGAAGAAGG 57.438 50.000 5.77 0.00 0.00 3.46
4510 7767 3.046390 GGATCACATCGCGTAGAAGAAG 58.954 50.000 5.77 0.00 0.00 2.85
4511 7768 2.223735 GGGATCACATCGCGTAGAAGAA 60.224 50.000 5.77 0.00 32.41 2.52
4512 7769 1.337071 GGGATCACATCGCGTAGAAGA 59.663 52.381 5.77 4.66 32.41 2.87
4513 7770 1.338337 AGGGATCACATCGCGTAGAAG 59.662 52.381 5.77 0.00 45.80 2.85
4514 7771 1.337071 GAGGGATCACATCGCGTAGAA 59.663 52.381 5.77 0.00 45.80 2.10
4515 7772 0.952280 GAGGGATCACATCGCGTAGA 59.048 55.000 5.77 0.03 45.80 2.59
4516 7773 0.039074 GGAGGGATCACATCGCGTAG 60.039 60.000 5.77 1.95 45.80 3.51
4517 7774 1.461091 GGGAGGGATCACATCGCGTA 61.461 60.000 5.77 0.00 45.80 4.42
4518 7775 2.797278 GGGAGGGATCACATCGCGT 61.797 63.158 5.77 0.00 45.80 6.01
4519 7776 2.029666 GGGAGGGATCACATCGCG 59.970 66.667 0.00 0.00 45.80 5.87
4520 7777 2.105806 GAGGGGAGGGATCACATCGC 62.106 65.000 0.00 1.12 42.02 4.58
4521 7778 1.476007 GGAGGGGAGGGATCACATCG 61.476 65.000 0.00 0.00 0.00 3.84
4522 7779 1.476007 CGGAGGGGAGGGATCACATC 61.476 65.000 0.00 0.00 0.00 3.06
4523 7780 1.460305 CGGAGGGGAGGGATCACAT 60.460 63.158 0.00 0.00 0.00 3.21
4524 7781 2.041922 CGGAGGGGAGGGATCACA 60.042 66.667 0.00 0.00 0.00 3.58
4544 7801 2.434359 GAAGAACGCCGACCCAGG 60.434 66.667 0.00 0.00 0.00 4.45
4545 7802 0.602905 AAAGAAGAACGCCGACCCAG 60.603 55.000 0.00 0.00 0.00 4.45
4546 7803 0.882927 CAAAGAAGAACGCCGACCCA 60.883 55.000 0.00 0.00 0.00 4.51
4547 7804 0.601841 TCAAAGAAGAACGCCGACCC 60.602 55.000 0.00 0.00 0.00 4.46
4548 7805 1.393883 GATCAAAGAAGAACGCCGACC 59.606 52.381 0.00 0.00 0.00 4.79
4549 7806 2.338500 AGATCAAAGAAGAACGCCGAC 58.662 47.619 0.00 0.00 0.00 4.79
4550 7807 2.743636 AGATCAAAGAAGAACGCCGA 57.256 45.000 0.00 0.00 0.00 5.54
4551 7808 2.736721 TGAAGATCAAAGAAGAACGCCG 59.263 45.455 0.00 0.00 0.00 6.46
4552 7809 3.748568 ACTGAAGATCAAAGAAGAACGCC 59.251 43.478 0.00 0.00 0.00 5.68
4553 7810 4.688413 AGACTGAAGATCAAAGAAGAACGC 59.312 41.667 0.00 0.00 0.00 4.84
4554 7811 5.347364 GGAGACTGAAGATCAAAGAAGAACG 59.653 44.000 0.00 0.00 0.00 3.95
4555 7812 6.226787 TGGAGACTGAAGATCAAAGAAGAAC 58.773 40.000 0.00 0.00 0.00 3.01
4556 7813 6.425210 TGGAGACTGAAGATCAAAGAAGAA 57.575 37.500 0.00 0.00 0.00 2.52
4557 7814 6.404708 CATGGAGACTGAAGATCAAAGAAGA 58.595 40.000 0.00 0.00 0.00 2.87
4558 7815 5.585445 CCATGGAGACTGAAGATCAAAGAAG 59.415 44.000 5.56 0.00 0.00 2.85
4559 7816 5.013495 ACCATGGAGACTGAAGATCAAAGAA 59.987 40.000 21.47 0.00 0.00 2.52
4560 7817 4.533707 ACCATGGAGACTGAAGATCAAAGA 59.466 41.667 21.47 0.00 0.00 2.52
4561 7818 4.634883 CACCATGGAGACTGAAGATCAAAG 59.365 45.833 21.47 0.00 0.00 2.77
4562 7819 4.286808 TCACCATGGAGACTGAAGATCAAA 59.713 41.667 21.47 0.00 0.00 2.69
4563 7820 3.840078 TCACCATGGAGACTGAAGATCAA 59.160 43.478 21.47 0.00 0.00 2.57
4564 7821 3.444029 TCACCATGGAGACTGAAGATCA 58.556 45.455 21.47 0.00 0.00 2.92
4565 7822 3.181467 CCTCACCATGGAGACTGAAGATC 60.181 52.174 21.47 0.00 37.05 2.75
4566 7823 2.770802 CCTCACCATGGAGACTGAAGAT 59.229 50.000 21.47 0.00 37.05 2.40
4567 7824 2.182827 CCTCACCATGGAGACTGAAGA 58.817 52.381 21.47 2.14 37.05 2.87
4568 7825 1.209019 CCCTCACCATGGAGACTGAAG 59.791 57.143 21.47 5.20 37.05 3.02
4569 7826 1.279496 CCCTCACCATGGAGACTGAA 58.721 55.000 21.47 0.00 37.05 3.02
4570 7827 0.117140 ACCCTCACCATGGAGACTGA 59.883 55.000 21.47 10.81 37.05 3.41
4571 7828 2.689073 ACCCTCACCATGGAGACTG 58.311 57.895 21.47 10.04 37.05 3.51


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

AutoCloner maintained by Alex Coulton.