Multiple sequence alignment - TraesCS5B01G242700

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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 TraesCS5B01G242700 chr5B 100.000 5727 0 0 1 5727 422520788 422526514 0.000000e+00 10576.0
1 TraesCS5B01G242700 chr5B 95.818 813 33 1 4915 5727 435817570 435816759 0.000000e+00 1312.0
2 TraesCS5B01G242700 chr5B 88.778 802 33 24 4914 5715 65167508 65168252 0.000000e+00 929.0
3 TraesCS5B01G242700 chr5B 84.045 539 48 17 792 1306 422218433 422218957 8.630000e-133 484.0
4 TraesCS5B01G242700 chr5B 84.038 520 53 21 1 509 422072751 422073251 1.870000e-129 473.0
5 TraesCS5B01G242700 chr5B 84.685 333 23 18 1 325 422185239 422185551 2.000000e-79 307.0
6 TraesCS5B01G242700 chr5B 96.040 101 4 0 655 755 422073678 422073778 1.280000e-36 165.0
7 TraesCS5B01G242700 chr5B 86.441 118 12 2 1242 1358 422104608 422104722 6.020000e-25 126.0
8 TraesCS5B01G242700 chr5B 87.805 82 8 1 1129 1208 422076975 422077056 1.700000e-15 95.3
9 TraesCS5B01G242700 chr5D 91.370 2978 133 47 516 3427 357505887 357508806 0.000000e+00 3962.0
10 TraesCS5B01G242700 chr5D 88.732 994 59 21 3902 4858 357509356 357510333 0.000000e+00 1166.0
11 TraesCS5B01G242700 chr5D 87.500 576 28 11 516 1087 357445934 357446469 4.870000e-175 625.0
12 TraesCS5B01G242700 chr5D 87.841 477 23 14 3439 3897 357508852 357509311 1.410000e-145 527.0
13 TraesCS5B01G242700 chr5D 87.013 308 27 11 40 342 357502495 357502794 9.190000e-88 335.0
14 TraesCS5B01G242700 chr5A 89.880 2757 153 57 686 3371 458667592 458670293 0.000000e+00 3430.0
15 TraesCS5B01G242700 chr5A 88.544 1257 58 29 3666 4858 458670564 458671798 0.000000e+00 1445.0
16 TraesCS5B01G242700 chr5A 91.631 466 31 6 625 1085 458604543 458605005 6.260000e-179 638.0
17 TraesCS5B01G242700 chr5A 86.719 128 11 3 516 637 458667458 458667585 2.780000e-28 137.0
18 TraesCS5B01G242700 chr5A 90.476 63 6 0 532 594 458604324 458604386 3.680000e-12 84.2
19 TraesCS5B01G242700 chr2B 95.572 813 30 1 4915 5727 90511052 90511858 0.000000e+00 1297.0
20 TraesCS5B01G242700 chr2B 94.363 816 32 4 4912 5727 648777550 648778351 0.000000e+00 1240.0
21 TraesCS5B01G242700 chr2B 89.401 802 28 21 4915 5715 534181429 534182174 0.000000e+00 957.0
22 TraesCS5B01G242700 chr2B 97.065 443 12 1 4915 5357 444597134 444596693 0.000000e+00 745.0
23 TraesCS5B01G242700 chr2B 95.690 232 10 0 5490 5721 444596616 444596385 1.950000e-99 374.0
24 TraesCS5B01G242700 chr1B 94.548 807 36 1 4915 5721 423941388 423940590 0.000000e+00 1240.0
25 TraesCS5B01G242700 chr1B 89.801 804 26 11 4912 5715 263526520 263527267 0.000000e+00 979.0
26 TraesCS5B01G242700 chr7B 89.614 828 23 16 4915 5727 713051061 713050282 0.000000e+00 994.0
27 TraesCS5B01G242700 chr7B 89.372 828 25 25 4915 5727 146805151 146805930 0.000000e+00 983.0


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 TraesCS5B01G242700 chr5B 422520788 422526514 5726 False 10576.000000 10576 100.000000 1 5727 1 chr5B.!!$F5 5726
1 TraesCS5B01G242700 chr5B 435816759 435817570 811 True 1312.000000 1312 95.818000 4915 5727 1 chr5B.!!$R1 812
2 TraesCS5B01G242700 chr5B 65167508 65168252 744 False 929.000000 929 88.778000 4914 5715 1 chr5B.!!$F1 801
3 TraesCS5B01G242700 chr5B 422218433 422218957 524 False 484.000000 484 84.045000 792 1306 1 chr5B.!!$F4 514
4 TraesCS5B01G242700 chr5B 422072751 422077056 4305 False 244.433333 473 89.294333 1 1208 3 chr5B.!!$F6 1207
5 TraesCS5B01G242700 chr5D 357502495 357510333 7838 False 1497.500000 3962 88.739000 40 4858 4 chr5D.!!$F2 4818
6 TraesCS5B01G242700 chr5D 357445934 357446469 535 False 625.000000 625 87.500000 516 1087 1 chr5D.!!$F1 571
7 TraesCS5B01G242700 chr5A 458667458 458671798 4340 False 1670.666667 3430 88.381000 516 4858 3 chr5A.!!$F2 4342
8 TraesCS5B01G242700 chr5A 458604324 458605005 681 False 361.100000 638 91.053500 532 1085 2 chr5A.!!$F1 553
9 TraesCS5B01G242700 chr2B 90511052 90511858 806 False 1297.000000 1297 95.572000 4915 5727 1 chr2B.!!$F1 812
10 TraesCS5B01G242700 chr2B 648777550 648778351 801 False 1240.000000 1240 94.363000 4912 5727 1 chr2B.!!$F3 815
11 TraesCS5B01G242700 chr2B 534181429 534182174 745 False 957.000000 957 89.401000 4915 5715 1 chr2B.!!$F2 800
12 TraesCS5B01G242700 chr2B 444596385 444597134 749 True 559.500000 745 96.377500 4915 5721 2 chr2B.!!$R1 806
13 TraesCS5B01G242700 chr1B 423940590 423941388 798 True 1240.000000 1240 94.548000 4915 5721 1 chr1B.!!$R1 806
14 TraesCS5B01G242700 chr1B 263526520 263527267 747 False 979.000000 979 89.801000 4912 5715 1 chr1B.!!$F1 803
15 TraesCS5B01G242700 chr7B 713050282 713051061 779 True 994.000000 994 89.614000 4915 5727 1 chr7B.!!$R1 812
16 TraesCS5B01G242700 chr7B 146805151 146805930 779 False 983.000000 983 89.372000 4915 5727 1 chr7B.!!$F1 812

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
670 3869 0.494095 AGGGAGGGAAGAGACCAACT 59.506 55.0 0.00 0.0 0.00 3.16 F
1757 7922 0.179129 CCCTGATGGCATTTTGCGAC 60.179 55.0 0.00 0.0 46.21 5.19 F
3327 9532 0.322816 GCTGGCCTTCTGGATCAACA 60.323 55.0 3.32 0.0 34.57 3.33 F
3612 9856 0.038526 GTGGTGGTTCTGACGACGAT 60.039 55.0 0.00 0.0 35.57 3.73 F
3613 9857 0.038618 TGGTGGTTCTGACGACGATG 60.039 55.0 0.00 0.0 35.57 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2116 8284 0.036732 TTGCCTCCGAAGCAGAATGT 59.963 50.0 0.00 0.0 42.17 2.71 R
3373 9578 0.261991 TAGGAGGAGGAGGACGCAAT 59.738 55.0 0.00 0.0 0.00 3.56 R
4370 10709 0.094901 CCGTCGTCGTCAGTACAGAG 59.905 60.0 0.71 0.0 35.01 3.35 R
4419 10761 0.392193 CCTCACCTGCACCATCAGAC 60.392 60.0 0.00 0.0 36.19 3.51 R
5409 11783 0.395311 ATGCGAAGGAGGACGAGGTA 60.395 55.0 0.00 0.0 0.00 3.08 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
31 32 9.677567 AATTCTTTTGTGAATACATACACACAC 57.322 29.630 0.00 0.00 44.81 3.82
34 35 5.583969 TTGTGAATACATACACACACGTG 57.416 39.130 15.48 15.48 44.81 4.49
114 117 7.961326 ACAAATATGTCTTTTCTAATGGGCT 57.039 32.000 0.00 0.00 33.41 5.19
115 118 7.775120 ACAAATATGTCTTTTCTAATGGGCTG 58.225 34.615 0.00 0.00 33.41 4.85
116 119 6.966534 AATATGTCTTTTCTAATGGGCTGG 57.033 37.500 0.00 0.00 0.00 4.85
117 120 2.446435 TGTCTTTTCTAATGGGCTGGC 58.554 47.619 0.00 0.00 0.00 4.85
118 121 2.041620 TGTCTTTTCTAATGGGCTGGCT 59.958 45.455 0.00 0.00 0.00 4.75
119 122 2.424956 GTCTTTTCTAATGGGCTGGCTG 59.575 50.000 0.00 0.00 0.00 4.85
171 174 1.151668 GTGCAGGCTACAACTCACAG 58.848 55.000 0.00 0.00 0.00 3.66
179 182 5.700832 CAGGCTACAACTCACAGTATTTTCA 59.299 40.000 0.00 0.00 0.00 2.69
183 186 7.414436 GCTACAACTCACAGTATTTTCAAACA 58.586 34.615 0.00 0.00 0.00 2.83
199 202 8.777865 TTTTCAAACACAATTTTACATGTCCA 57.222 26.923 0.00 0.00 0.00 4.02
295 300 1.115467 AATACCGAGCTCTGTGGAGG 58.885 55.000 19.81 10.91 39.80 4.30
318 323 1.108776 GCCTCCATACGTCCACACTA 58.891 55.000 0.00 0.00 0.00 2.74
319 324 1.202382 GCCTCCATACGTCCACACTAC 60.202 57.143 0.00 0.00 0.00 2.73
335 340 5.567534 CCACACTACGCATGTTGTTAATTTC 59.432 40.000 0.00 0.00 31.53 2.17
336 341 6.139435 CACACTACGCATGTTGTTAATTTCA 58.861 36.000 0.00 0.00 31.53 2.69
342 347 9.388346 CTACGCATGTTGTTAATTTCAGTTTTA 57.612 29.630 0.00 0.00 0.00 1.52
364 3221 9.943163 TTTTAAAAAGCCACTATTGAAAAATGC 57.057 25.926 0.00 0.00 0.00 3.56
406 3268 5.010282 AGACCTTATTGAAAACGCAGGAAT 58.990 37.500 0.00 0.00 0.00 3.01
466 3361 7.682055 CACACGTTTGAAAATAAATTAATGGCG 59.318 33.333 0.00 0.00 0.00 5.69
526 3456 8.619546 CAACTCATCCAAGGAAAATAGAGATTC 58.380 37.037 0.00 0.00 0.00 2.52
595 3535 4.099120 CAAGTGCGCAACTAGTACTAGAG 58.901 47.826 31.93 23.70 38.56 2.43
637 3835 2.654863 CAAGCTAAACCCGATTCCCAT 58.345 47.619 0.00 0.00 0.00 4.00
638 3836 3.023832 CAAGCTAAACCCGATTCCCATT 58.976 45.455 0.00 0.00 0.00 3.16
670 3869 0.494095 AGGGAGGGAAGAGACCAACT 59.506 55.000 0.00 0.00 0.00 3.16
944 5895 4.200283 CAGGCTCCTCGCTCCGTC 62.200 72.222 0.00 0.00 39.13 4.79
1087 6045 1.501654 AAGGCCTCTTCAACCCCTCC 61.502 60.000 5.23 0.00 0.00 4.30
1089 6047 2.985116 GCCTCTTCAACCCCTCCCC 61.985 68.421 0.00 0.00 0.00 4.81
1135 6118 3.602483 GCCACTTGCATTTGGATGATTT 58.398 40.909 16.51 0.00 40.77 2.17
1154 7291 3.552604 TTGAGTTAGAATTGCGCAACC 57.447 42.857 27.64 19.90 0.00 3.77
1181 7319 3.521796 GGAATTGAGCGCCCAGGC 61.522 66.667 2.29 0.00 37.85 4.85
1370 7529 0.447801 CGTGGTTGGTTAGCATCTGC 59.552 55.000 0.00 0.00 42.49 4.26
1397 7556 5.277779 CCATCTGAAGTTGTTTAGCGTTTCA 60.278 40.000 0.00 0.00 0.00 2.69
1479 7638 1.722011 AATGCGGAAGAGTACAACGG 58.278 50.000 0.00 0.00 0.00 4.44
1498 7657 1.137513 GCGAGCACTGTAGTTTCGTT 58.862 50.000 13.71 0.00 35.94 3.85
1499 7658 1.525619 GCGAGCACTGTAGTTTCGTTT 59.474 47.619 13.71 0.00 35.94 3.60
1501 7660 2.659291 CGAGCACTGTAGTTTCGTTTGC 60.659 50.000 7.26 0.00 31.73 3.68
1531 7690 2.815503 CAATGCCAAGCGATGATCCATA 59.184 45.455 0.00 0.00 0.00 2.74
1535 7694 0.792640 CAAGCGATGATCCATACGGC 59.207 55.000 0.00 0.00 0.00 5.68
1544 7703 2.660258 ATCCATACGGCCTGGTTCGC 62.660 60.000 9.23 0.00 35.19 4.70
1684 7843 1.256117 CTGTCGCTTTGCTTTTGTTGC 59.744 47.619 0.00 0.00 0.00 4.17
1756 7921 0.323269 TCCCTGATGGCATTTTGCGA 60.323 50.000 0.00 0.00 46.21 5.10
1757 7922 0.179129 CCCTGATGGCATTTTGCGAC 60.179 55.000 0.00 0.00 46.21 5.19
1758 7923 0.813184 CCTGATGGCATTTTGCGACT 59.187 50.000 0.00 0.00 46.21 4.18
1759 7924 2.016318 CCTGATGGCATTTTGCGACTA 58.984 47.619 0.00 0.00 46.21 2.59
1786 7953 2.190538 TGATGATGCAGAAGGACCAGA 58.809 47.619 0.00 0.00 0.00 3.86
1915 8082 7.592938 TGTGCGTGAATTCTATCTTGATTTTT 58.407 30.769 7.05 0.00 0.00 1.94
1929 8096 6.389091 TCTTGATTTTTGTTGAATCGATGGG 58.611 36.000 0.00 0.00 36.52 4.00
1939 8107 2.279451 TCGATGGGCTTCGATGCG 60.279 61.111 16.13 3.38 42.81 4.73
1974 8142 0.521735 GCTGACGGTGTTGGGAATTC 59.478 55.000 0.00 0.00 0.00 2.17
2108 8276 1.982395 CTGCCGTCCCAGGTCAGTA 60.982 63.158 0.00 0.00 33.66 2.74
2128 8296 1.081892 CCCACTCACATTCTGCTTCG 58.918 55.000 0.00 0.00 0.00 3.79
2131 8299 1.998315 CACTCACATTCTGCTTCGGAG 59.002 52.381 0.00 0.00 0.00 4.63
2134 8302 0.674581 CACATTCTGCTTCGGAGGCA 60.675 55.000 14.38 14.38 38.10 4.75
2139 8307 0.677731 TCTGCTTCGGAGGCAATTGG 60.678 55.000 15.88 4.64 39.30 3.16
2183 8351 3.373439 AGCAATTCGATTCTGAGCTGAAC 59.627 43.478 0.00 0.00 0.00 3.18
2210 8378 1.809209 GCAGACGCTGGCTCTTCTC 60.809 63.158 8.57 0.00 34.30 2.87
2327 8495 2.331451 GCCAAGAACGCGCACTTT 59.669 55.556 5.73 0.00 0.00 2.66
2332 8500 4.736631 GAACGCGCACTTTCCCGC 62.737 66.667 5.73 0.00 46.17 6.13
2435 8609 1.587613 GAACGGCAAGCAAACGCAA 60.588 52.632 0.00 0.00 0.00 4.85
2452 8626 1.000274 GCAAACACCAAGAAAGCCGAT 60.000 47.619 0.00 0.00 0.00 4.18
2453 8627 2.922335 GCAAACACCAAGAAAGCCGATC 60.922 50.000 0.00 0.00 0.00 3.69
2552 8726 4.090057 GCCAGAAACTGCCGCGTC 62.090 66.667 4.92 0.00 0.00 5.19
2693 8877 5.736207 GCCGAATTGTCCCCAAAATATTCTC 60.736 44.000 0.00 0.00 33.44 2.87
2699 8883 4.540099 TGTCCCCAAAATATTCTCCTCTGT 59.460 41.667 0.00 0.00 0.00 3.41
2700 8884 5.126779 GTCCCCAAAATATTCTCCTCTGTC 58.873 45.833 0.00 0.00 0.00 3.51
2764 8949 1.351430 TTTTCGACAGCAGGCGATCG 61.351 55.000 8.26 11.69 36.31 3.69
2910 9095 1.227497 CTTCTCGCAGATGGGCTCC 60.227 63.158 0.00 0.00 33.89 4.70
2955 9150 4.074526 GACGAGGAGCAGCAGCCA 62.075 66.667 0.00 0.00 43.56 4.75
2956 9151 3.382803 GACGAGGAGCAGCAGCCAT 62.383 63.158 0.00 0.00 43.56 4.40
3140 9335 1.304547 CCCGGAGACTGAGGTGAGT 60.305 63.158 0.73 0.00 0.00 3.41
3167 9368 1.176527 CACGGCCACCATCTTGATTT 58.823 50.000 2.24 0.00 0.00 2.17
3203 9407 3.081409 CCGGTGAGTAGGGGTGGG 61.081 72.222 0.00 0.00 0.00 4.61
3204 9408 2.284405 CGGTGAGTAGGGGTGGGT 60.284 66.667 0.00 0.00 0.00 4.51
3205 9409 2.656069 CGGTGAGTAGGGGTGGGTG 61.656 68.421 0.00 0.00 0.00 4.61
3206 9410 2.298661 GGTGAGTAGGGGTGGGTGG 61.299 68.421 0.00 0.00 0.00 4.61
3286 9491 2.172483 CTGTCCTCGGTTGACCTGGG 62.172 65.000 0.00 0.88 31.60 4.45
3327 9532 0.322816 GCTGGCCTTCTGGATCAACA 60.323 55.000 3.32 0.00 34.57 3.33
3373 9578 4.100084 CTCCGCTGGCACCCATCA 62.100 66.667 0.00 0.00 30.82 3.07
3374 9579 3.410628 TCCGCTGGCACCCATCAT 61.411 61.111 0.00 0.00 30.82 2.45
3377 9582 2.497770 GCTGGCACCCATCATTGC 59.502 61.111 0.00 0.00 38.06 3.56
3378 9583 2.802792 CTGGCACCCATCATTGCG 59.197 61.111 0.00 0.00 39.81 4.85
3380 9585 1.996786 CTGGCACCCATCATTGCGTC 61.997 60.000 0.00 0.00 39.81 5.19
3381 9586 2.774799 GGCACCCATCATTGCGTCC 61.775 63.158 0.00 0.00 39.81 4.79
3382 9587 1.750399 GCACCCATCATTGCGTCCT 60.750 57.895 0.00 0.00 0.00 3.85
3383 9588 1.718757 GCACCCATCATTGCGTCCTC 61.719 60.000 0.00 0.00 0.00 3.71
3385 9590 1.274703 ACCCATCATTGCGTCCTCCT 61.275 55.000 0.00 0.00 0.00 3.69
3386 9591 0.533755 CCCATCATTGCGTCCTCCTC 60.534 60.000 0.00 0.00 0.00 3.71
3387 9592 0.533755 CCATCATTGCGTCCTCCTCC 60.534 60.000 0.00 0.00 0.00 4.30
3388 9593 0.467384 CATCATTGCGTCCTCCTCCT 59.533 55.000 0.00 0.00 0.00 3.69
3389 9594 0.755686 ATCATTGCGTCCTCCTCCTC 59.244 55.000 0.00 0.00 0.00 3.71
3410 9620 7.574607 TCCTCCTAGTTTCCCTGAATTATTTC 58.425 38.462 0.00 0.00 0.00 2.17
3416 9626 7.651027 AGTTTCCCTGAATTATTTCCATCTG 57.349 36.000 0.00 0.00 0.00 2.90
3427 9637 9.282569 GAATTATTTCCATCTGCAGTCTATCTT 57.717 33.333 14.67 0.00 0.00 2.40
3435 9645 6.014755 CCATCTGCAGTCTATCTTATTGGAGA 60.015 42.308 14.67 0.00 39.87 3.71
3443 9687 4.832823 TCTATCTTATTGGAGATGGCGTGA 59.167 41.667 0.00 0.00 37.01 4.35
3504 9748 0.092519 GCGTCGCTTTTCGTAGAACC 59.907 55.000 10.68 0.00 45.90 3.62
3528 9772 2.298729 TGTTTGTATGCTGGGGCTTTTC 59.701 45.455 0.00 0.00 39.59 2.29
3546 9790 4.860802 TTTCTGGGAGGCTCATTCATAA 57.139 40.909 17.69 7.50 0.00 1.90
3548 9792 2.439507 TCTGGGAGGCTCATTCATAACC 59.560 50.000 17.69 6.04 0.00 2.85
3550 9794 2.173356 TGGGAGGCTCATTCATAACCAG 59.827 50.000 17.69 0.00 0.00 4.00
3553 9797 3.209410 GAGGCTCATTCATAACCAGTGG 58.791 50.000 10.25 7.91 0.00 4.00
3555 9799 2.684881 GGCTCATTCATAACCAGTGGTG 59.315 50.000 17.56 3.38 35.34 4.17
3556 9800 2.098117 GCTCATTCATAACCAGTGGTGC 59.902 50.000 17.56 7.69 35.34 5.01
3561 9805 1.674322 ATAACCAGTGGTGCGTGCC 60.674 57.895 17.56 0.00 35.34 5.01
3592 9836 2.529136 AGCCTGGGTGCTGTGGTA 60.529 61.111 0.00 0.00 40.90 3.25
3595 9839 1.003355 CCTGGGTGCTGTGGTAGTG 60.003 63.158 0.00 0.00 0.00 2.74
3608 9852 0.963962 GGTAGTGGTGGTTCTGACGA 59.036 55.000 0.00 0.00 0.00 4.20
3609 9853 1.336609 GGTAGTGGTGGTTCTGACGAC 60.337 57.143 0.00 0.00 34.16 4.34
3610 9854 0.594602 TAGTGGTGGTTCTGACGACG 59.405 55.000 0.00 0.00 35.57 5.12
3611 9855 1.105167 AGTGGTGGTTCTGACGACGA 61.105 55.000 0.00 0.00 35.57 4.20
3612 9856 0.038526 GTGGTGGTTCTGACGACGAT 60.039 55.000 0.00 0.00 35.57 3.73
3613 9857 0.038618 TGGTGGTTCTGACGACGATG 60.039 55.000 0.00 0.00 35.57 3.84
3614 9858 1.352156 GGTGGTTCTGACGACGATGC 61.352 60.000 0.00 0.00 35.57 3.91
3647 9891 8.178313 GCCTGCTTATTCTTTAGTAAGTTTGAG 58.822 37.037 0.00 0.00 31.98 3.02
3648 9892 8.669243 CCTGCTTATTCTTTAGTAAGTTTGAGG 58.331 37.037 0.00 0.00 31.98 3.86
3660 9904 4.353383 AAGTTTGAGGTAGACTGGGAAC 57.647 45.455 0.00 0.00 0.00 3.62
3661 9905 2.299297 AGTTTGAGGTAGACTGGGAACG 59.701 50.000 0.00 0.00 0.00 3.95
3664 9908 0.614134 GAGGTAGACTGGGAACGGGT 60.614 60.000 0.00 0.00 42.76 5.28
3666 9910 0.820226 GGTAGACTGGGAACGGGTAC 59.180 60.000 0.00 0.00 42.76 3.34
3667 9911 1.549203 GTAGACTGGGAACGGGTACA 58.451 55.000 0.00 0.00 42.76 2.90
3668 9912 2.105766 GTAGACTGGGAACGGGTACAT 58.894 52.381 0.00 0.00 42.76 2.29
3669 9913 1.652947 AGACTGGGAACGGGTACATT 58.347 50.000 0.00 0.00 42.76 2.71
3691 9941 0.039527 GTGGCATGTTGGTTCGTTCC 60.040 55.000 0.00 0.00 0.00 3.62
3798 10058 5.580691 TGCTGGATCTTGTGAGTTTAATACG 59.419 40.000 0.00 0.00 0.00 3.06
3799 10059 5.502544 GCTGGATCTTGTGAGTTTAATACGC 60.503 44.000 0.00 0.00 0.00 4.42
3800 10060 5.730550 TGGATCTTGTGAGTTTAATACGCT 58.269 37.500 0.00 0.00 0.00 5.07
3805 10065 8.773404 ATCTTGTGAGTTTAATACGCTTACTT 57.227 30.769 0.00 0.00 0.00 2.24
3806 10066 9.865321 ATCTTGTGAGTTTAATACGCTTACTTA 57.135 29.630 0.00 0.00 0.00 2.24
3928 10231 2.689691 GCCCTACCCCCTCAATGCA 61.690 63.158 0.00 0.00 0.00 3.96
3980 10286 0.179936 GCCTCTGCCTGCAGTAAGAT 59.820 55.000 17.96 0.00 43.96 2.40
3981 10287 1.407989 GCCTCTGCCTGCAGTAAGATT 60.408 52.381 17.96 0.00 43.96 2.40
3986 10292 5.065731 CCTCTGCCTGCAGTAAGATTTTAAG 59.934 44.000 17.96 4.90 43.96 1.85
4001 10307 3.328382 TTTAAGGATGGTGGTCTGACG 57.672 47.619 1.07 0.00 0.00 4.35
4117 10429 2.672714 GTCAAGCATGTACGTCTGTCA 58.327 47.619 0.00 0.00 0.00 3.58
4230 10553 2.125512 CCTGAGGGCGAAGGAACG 60.126 66.667 0.00 0.00 35.40 3.95
4236 10559 2.346365 GGCGAAGGAACGAAGGGT 59.654 61.111 0.00 0.00 35.09 4.34
4370 10709 2.186826 AGTGGCACGCAACAGTTCC 61.187 57.895 12.71 0.00 44.14 3.62
4504 10854 4.840005 GACTACCTGCAGGCGGCC 62.840 72.222 33.06 12.11 43.89 6.13
4561 10911 1.743252 GCTGCTGCACTGGTACCTC 60.743 63.158 14.36 0.39 39.41 3.85
4814 11180 7.663043 AAGGTTTATGGTTTGTGTTTTCCTA 57.337 32.000 0.00 0.00 0.00 2.94
4822 11188 6.702329 TGGTTTGTGTTTTCCTACAATTTGT 58.298 32.000 7.30 7.30 36.75 2.83
4827 11194 7.176589 TGTGTTTTCCTACAATTTGTCCTTT 57.823 32.000 5.07 0.00 0.00 3.11
4828 11195 8.294954 TGTGTTTTCCTACAATTTGTCCTTTA 57.705 30.769 5.07 0.00 0.00 1.85
4836 11203 7.614192 TCCTACAATTTGTCCTTTATTTCTCCC 59.386 37.037 5.07 0.00 0.00 4.30
4858 11225 5.304614 CCCGGTGAAGAGGAGAAGAAATATA 59.695 44.000 0.00 0.00 0.00 0.86
4859 11226 6.014156 CCCGGTGAAGAGGAGAAGAAATATAT 60.014 42.308 0.00 0.00 0.00 0.86
4860 11227 7.178628 CCCGGTGAAGAGGAGAAGAAATATATA 59.821 40.741 0.00 0.00 0.00 0.86
4861 11228 8.247562 CCGGTGAAGAGGAGAAGAAATATATAG 58.752 40.741 0.00 0.00 0.00 1.31
4862 11229 9.015367 CGGTGAAGAGGAGAAGAAATATATAGA 57.985 37.037 0.00 0.00 0.00 1.98
4884 11251 7.195839 AGAGTATGAGAAAGTTTTTCTGTGC 57.804 36.000 8.66 2.34 0.00 4.57
4885 11252 6.995091 AGAGTATGAGAAAGTTTTTCTGTGCT 59.005 34.615 8.66 6.39 0.00 4.40
4886 11253 7.172361 AGAGTATGAGAAAGTTTTTCTGTGCTC 59.828 37.037 8.66 13.12 0.00 4.26
4887 11254 6.995091 AGTATGAGAAAGTTTTTCTGTGCTCT 59.005 34.615 8.66 0.00 0.00 4.09
4888 11255 5.490139 TGAGAAAGTTTTTCTGTGCTCTG 57.510 39.130 8.66 0.00 0.00 3.35
4889 11256 4.336433 TGAGAAAGTTTTTCTGTGCTCTGG 59.664 41.667 8.66 0.00 0.00 3.86
4890 11257 4.273318 AGAAAGTTTTTCTGTGCTCTGGT 58.727 39.130 3.43 0.00 0.00 4.00
4891 11258 4.706962 AGAAAGTTTTTCTGTGCTCTGGTT 59.293 37.500 3.43 0.00 0.00 3.67
4892 11259 4.376340 AAGTTTTTCTGTGCTCTGGTTG 57.624 40.909 0.00 0.00 0.00 3.77
4893 11260 3.620488 AGTTTTTCTGTGCTCTGGTTGA 58.380 40.909 0.00 0.00 0.00 3.18
4894 11261 3.629398 AGTTTTTCTGTGCTCTGGTTGAG 59.371 43.478 0.00 0.00 45.33 3.02
4895 11262 3.558931 TTTTCTGTGCTCTGGTTGAGA 57.441 42.857 0.00 0.00 45.39 3.27
4896 11263 2.533266 TTCTGTGCTCTGGTTGAGAC 57.467 50.000 0.00 0.00 45.39 3.36
4897 11264 1.413118 TCTGTGCTCTGGTTGAGACA 58.587 50.000 0.00 0.00 45.39 3.41
4898 11265 1.762370 TCTGTGCTCTGGTTGAGACAA 59.238 47.619 0.00 0.00 45.39 3.18
4899 11266 1.869767 CTGTGCTCTGGTTGAGACAAC 59.130 52.381 6.13 6.13 45.39 3.32
4900 11267 1.230324 GTGCTCTGGTTGAGACAACC 58.770 55.000 21.96 21.96 45.39 3.77
4902 11269 1.230324 GCTCTGGTTGAGACAACCAC 58.770 55.000 25.87 16.06 44.74 4.16
4903 11270 1.884235 CTCTGGTTGAGACAACCACC 58.116 55.000 25.87 7.93 44.74 4.61
4904 11271 1.140852 CTCTGGTTGAGACAACCACCA 59.859 52.381 25.87 16.79 44.74 4.17
4905 11272 1.562008 TCTGGTTGAGACAACCACCAA 59.438 47.619 25.87 14.89 44.74 3.67
4906 11273 1.949525 CTGGTTGAGACAACCACCAAG 59.050 52.381 25.87 15.78 44.74 3.61
4907 11274 1.283613 TGGTTGAGACAACCACCAAGT 59.716 47.619 25.87 0.00 44.74 3.16
4908 11275 1.947456 GGTTGAGACAACCACCAAGTC 59.053 52.381 23.26 0.00 40.03 3.01
4909 11276 2.639065 GTTGAGACAACCACCAAGTCA 58.361 47.619 0.00 0.00 34.80 3.41
4910 11277 2.325583 TGAGACAACCACCAAGTCAC 57.674 50.000 0.00 0.00 34.80 3.67
4930 11297 5.296531 GTCACCACTCAAAATGGCAATTTTT 59.703 36.000 9.17 0.00 42.14 1.94
5409 11783 3.898627 CTCGCCTGCTCGTGACGTT 62.899 63.158 4.40 0.00 0.00 3.99
5410 11784 2.126618 CGCCTGCTCGTGACGTTA 60.127 61.111 4.40 0.00 0.00 3.18
5439 11813 1.741401 CTTCGCATCAAGGCACCGA 60.741 57.895 0.00 0.00 0.00 4.69
5443 11817 2.264480 CATCAAGGCACCGACCGA 59.736 61.111 0.00 0.00 33.69 4.69
5451 11825 3.359523 CACCGACCGACAGTCCGA 61.360 66.667 0.00 0.00 43.08 4.55
5480 11881 1.587613 GCTCATCTGGTCTCGTCGC 60.588 63.158 0.00 0.00 0.00 5.19
5633 12051 3.009115 CCATCCCAGGTGACCGGT 61.009 66.667 6.92 6.92 0.00 5.28
5688 12106 1.825622 GCCATCAGGGTAAGCAGCC 60.826 63.158 0.00 0.00 43.09 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 5.775852 CACATGCGTATTATACACGTGTGTG 60.776 44.000 30.83 19.81 46.10 3.82
31 32 8.541733 AAAATTTCACATGCGTATTATACACG 57.458 30.769 3.16 2.40 42.24 4.49
179 182 8.855110 TCAGTATGGACATGTAAAATTGTGTTT 58.145 29.630 0.00 0.00 36.16 2.83
264 268 7.065923 ACAGAGCTCGGTATTTAAAGAAATTCC 59.934 37.037 18.41 0.00 38.49 3.01
267 271 6.316390 CCACAGAGCTCGGTATTTAAAGAAAT 59.684 38.462 19.38 0.00 38.79 2.17
270 274 4.464951 TCCACAGAGCTCGGTATTTAAAGA 59.535 41.667 19.38 5.39 0.00 2.52
271 276 4.755411 TCCACAGAGCTCGGTATTTAAAG 58.245 43.478 19.38 5.31 0.00 1.85
295 300 2.416260 GGACGTATGGAGGCCGAC 59.584 66.667 0.00 0.00 0.00 4.79
318 323 8.635877 TTAAAACTGAAATTAACAACATGCGT 57.364 26.923 0.00 0.00 0.00 5.24
319 324 9.907576 TTTTAAAACTGAAATTAACAACATGCG 57.092 25.926 0.00 0.00 0.00 4.73
342 347 6.017192 GTGGCATTTTTCAATAGTGGCTTTTT 60.017 34.615 0.00 0.00 36.45 1.94
364 3221 8.888579 AAGGTCTCGAAAATATATAGTTGTGG 57.111 34.615 0.00 0.00 0.00 4.17
398 3260 1.811965 TCACCAACATCAATTCCTGCG 59.188 47.619 0.00 0.00 0.00 5.18
406 3268 9.913310 TTATAAATATCACCTCACCAACATCAA 57.087 29.630 0.00 0.00 0.00 2.57
478 3373 4.999311 TGTGACTCTCTGTGATTTGAATGG 59.001 41.667 0.00 0.00 0.00 3.16
509 3404 5.525378 CCTCCGTGAATCTCTATTTTCCTTG 59.475 44.000 0.00 0.00 0.00 3.61
514 3409 4.770795 CACCCTCCGTGAATCTCTATTTT 58.229 43.478 0.00 0.00 46.20 1.82
595 3535 4.099170 CTGCACAGCCAGCTTCGC 62.099 66.667 3.61 3.61 0.00 4.70
598 3538 4.281527 AGCCTGCACAGCCAGCTT 62.282 61.111 0.34 0.00 33.23 3.74
1087 6045 1.912371 GAGCTGGCGAAAGAAACGGG 61.912 60.000 0.00 0.00 0.00 5.28
1089 6047 0.164647 CAGAGCTGGCGAAAGAAACG 59.835 55.000 0.00 0.00 0.00 3.60
1135 6118 2.778299 AGGTTGCGCAATTCTAACTCA 58.222 42.857 27.79 0.00 0.00 3.41
1181 7319 1.083489 ATAACCGCACATTGTCACCG 58.917 50.000 0.00 0.00 0.00 4.94
1370 7529 3.181530 CGCTAAACAACTTCAGATGGACG 60.182 47.826 0.00 0.00 0.00 4.79
1419 7578 2.444624 CGACATGGACGGTGCGAAG 61.445 63.158 0.00 0.00 0.00 3.79
1479 7638 1.137513 AACGAAACTACAGTGCTCGC 58.862 50.000 11.85 0.00 37.57 5.03
1499 7658 1.732417 TTGGCATTGCACGAACAGCA 61.732 50.000 11.39 0.00 40.85 4.41
1501 7660 1.005294 GCTTGGCATTGCACGAACAG 61.005 55.000 11.39 0.00 0.00 3.16
1535 7694 4.760047 CCGTGGAGGCGAACCAGG 62.760 72.222 11.80 11.80 41.24 4.45
1544 7703 2.819595 CAACCGATGCCGTGGAGG 60.820 66.667 0.00 0.00 44.97 4.30
1611 7770 4.441495 CGGATTAAAGAGGGAAAATTGGGC 60.441 45.833 0.00 0.00 0.00 5.36
1684 7843 5.808030 GCTACCTAGCTGTCAAAGAAACTAG 59.192 44.000 0.00 0.00 45.62 2.57
1756 7921 5.280062 CCTTCTGCATCATCATCTGGATAGT 60.280 44.000 0.00 0.00 33.95 2.12
1757 7922 5.046520 TCCTTCTGCATCATCATCTGGATAG 60.047 44.000 0.00 0.00 33.95 2.08
1758 7923 4.842380 TCCTTCTGCATCATCATCTGGATA 59.158 41.667 0.00 0.00 33.95 2.59
1759 7924 3.651423 TCCTTCTGCATCATCATCTGGAT 59.349 43.478 0.00 0.00 36.39 3.41
1830 7997 2.811317 CTGTTCGCCACGCCTCTC 60.811 66.667 0.00 0.00 0.00 3.20
1915 8082 1.066502 TCGAAGCCCATCGATTCAACA 60.067 47.619 0.00 0.00 46.12 3.33
1926 8093 2.741985 CACACGCATCGAAGCCCA 60.742 61.111 7.11 0.00 0.00 5.36
1974 8142 1.446907 CTTGTCCACCTAGCAAGCAG 58.553 55.000 0.00 0.00 0.00 4.24
2098 8266 0.608640 GTGAGTGGGTACTGACCTGG 59.391 60.000 0.00 0.00 46.09 4.45
2108 8276 1.609061 CGAAGCAGAATGTGAGTGGGT 60.609 52.381 0.00 0.00 39.31 4.51
2114 8282 0.391661 GCCTCCGAAGCAGAATGTGA 60.392 55.000 0.00 0.00 39.31 3.58
2116 8284 0.036732 TTGCCTCCGAAGCAGAATGT 59.963 50.000 0.00 0.00 42.17 2.71
2128 8296 0.179103 CGAATTGCCCAATTGCCTCC 60.179 55.000 10.69 0.00 40.77 4.30
2131 8299 2.314323 AATCGAATTGCCCAATTGCC 57.686 45.000 10.69 0.00 40.77 4.52
2134 8302 4.806640 ACAGAAATCGAATTGCCCAATT 57.193 36.364 5.97 5.97 43.14 2.32
2139 8307 4.555262 TCCAAAACAGAAATCGAATTGCC 58.445 39.130 0.00 0.00 0.00 4.52
2222 8390 2.284995 ACCTCCTCCTCCAGCACC 60.285 66.667 0.00 0.00 0.00 5.01
2429 8603 1.470805 GGCTTTCTTGGTGTTTGCGTT 60.471 47.619 0.00 0.00 0.00 4.84
2435 8609 1.534729 GGATCGGCTTTCTTGGTGTT 58.465 50.000 0.00 0.00 0.00 3.32
2467 8641 3.374402 CGGAGTGCTCGTCCTGGT 61.374 66.667 0.00 0.00 31.14 4.00
2550 8724 2.876645 CTTCTGCGACGGCGAGAC 60.877 66.667 18.90 0.00 44.10 3.36
2552 8726 4.421479 ACCTTCTGCGACGGCGAG 62.421 66.667 18.90 9.67 44.10 5.03
2693 8877 1.379176 TCCCGCAGAGAGACAGAGG 60.379 63.158 0.00 0.00 0.00 3.69
2699 8883 1.289066 CAAACGTCCCGCAGAGAGA 59.711 57.895 0.00 0.00 0.00 3.10
2700 8884 2.383527 GCAAACGTCCCGCAGAGAG 61.384 63.158 0.00 0.00 0.00 3.20
2955 9150 2.660802 GACACCGACGGGGACAAT 59.339 61.111 26.07 0.00 39.97 2.71
2956 9151 3.618750 GGACACCGACGGGGACAA 61.619 66.667 26.07 0.00 39.97 3.18
3140 9335 4.980805 GGTGGCCGTGACAGCGAA 62.981 66.667 0.00 0.00 0.00 4.70
3167 9368 3.751175 CCGGACAGCAAAATCTAACTTGA 59.249 43.478 0.00 0.00 0.00 3.02
3203 9407 3.351416 GTCGGGTCAAACGGCCAC 61.351 66.667 2.24 0.00 0.00 5.01
3204 9408 4.973055 CGTCGGGTCAAACGGCCA 62.973 66.667 2.24 0.00 35.32 5.36
3270 9475 2.606519 CCCCAGGTCAACCGAGGA 60.607 66.667 13.30 0.00 42.08 3.71
3327 9532 5.363562 TTCATCATGCAGGAGTTGTAGAT 57.636 39.130 7.33 0.00 0.00 1.98
3371 9576 1.330655 GGAGGAGGAGGACGCAATGA 61.331 60.000 0.00 0.00 0.00 2.57
3373 9578 0.261991 TAGGAGGAGGAGGACGCAAT 59.738 55.000 0.00 0.00 0.00 3.56
3374 9579 0.395862 CTAGGAGGAGGAGGACGCAA 60.396 60.000 0.00 0.00 0.00 4.85
3377 9582 2.025898 GAAACTAGGAGGAGGAGGACG 58.974 57.143 0.00 0.00 0.00 4.79
3378 9583 2.390696 GGAAACTAGGAGGAGGAGGAC 58.609 57.143 0.00 0.00 0.00 3.85
3380 9585 1.292546 AGGGAAACTAGGAGGAGGAGG 59.707 57.143 0.00 0.00 0.00 4.30
3381 9586 2.023888 TCAGGGAAACTAGGAGGAGGAG 60.024 54.545 0.00 0.00 0.00 3.69
3382 9587 2.008400 TCAGGGAAACTAGGAGGAGGA 58.992 52.381 0.00 0.00 0.00 3.71
3383 9588 2.552093 TCAGGGAAACTAGGAGGAGG 57.448 55.000 0.00 0.00 0.00 4.30
3385 9590 7.366551 GGAAATAATTCAGGGAAACTAGGAGGA 60.367 40.741 0.00 0.00 37.29 3.71
3386 9591 6.773200 GGAAATAATTCAGGGAAACTAGGAGG 59.227 42.308 0.00 0.00 37.29 4.30
3387 9592 7.346471 TGGAAATAATTCAGGGAAACTAGGAG 58.654 38.462 0.00 0.00 37.29 3.69
3388 9593 7.278724 TGGAAATAATTCAGGGAAACTAGGA 57.721 36.000 0.00 0.00 37.29 2.94
3389 9594 8.001292 AGATGGAAATAATTCAGGGAAACTAGG 58.999 37.037 0.00 0.00 37.29 3.02
3410 9620 6.014755 TCTCCAATAAGATAGACTGCAGATGG 60.015 42.308 23.35 11.52 0.00 3.51
3416 9626 4.934602 GCCATCTCCAATAAGATAGACTGC 59.065 45.833 0.00 0.00 34.21 4.40
3427 9637 4.035091 CGAAATTTCACGCCATCTCCAATA 59.965 41.667 17.99 0.00 0.00 1.90
3428 9638 3.181497 CGAAATTTCACGCCATCTCCAAT 60.181 43.478 17.99 0.00 0.00 3.16
3435 9645 2.161609 GGAAGACGAAATTTCACGCCAT 59.838 45.455 17.99 0.00 0.00 4.40
3504 9748 0.527565 GCCCCAGCATACAAACAGTG 59.472 55.000 0.00 0.00 39.53 3.66
3528 9772 2.173356 TGGTTATGAATGAGCCTCCCAG 59.827 50.000 0.00 0.00 0.00 4.45
3546 9790 4.935495 CAGGCACGCACCACTGGT 62.935 66.667 0.00 0.00 35.62 4.00
3584 9828 0.396811 AGAACCACCACTACCACAGC 59.603 55.000 0.00 0.00 0.00 4.40
3588 9832 0.677288 CGTCAGAACCACCACTACCA 59.323 55.000 0.00 0.00 0.00 3.25
3589 9833 0.963962 TCGTCAGAACCACCACTACC 59.036 55.000 0.00 0.00 0.00 3.18
3590 9834 1.665161 CGTCGTCAGAACCACCACTAC 60.665 57.143 0.00 0.00 0.00 2.73
3591 9835 0.594602 CGTCGTCAGAACCACCACTA 59.405 55.000 0.00 0.00 0.00 2.74
3592 9836 1.105167 TCGTCGTCAGAACCACCACT 61.105 55.000 0.00 0.00 0.00 4.00
3595 9839 1.352156 GCATCGTCGTCAGAACCACC 61.352 60.000 0.00 0.00 0.00 4.61
3614 9858 3.795623 AAGAATAAGCAGGCAAGCATG 57.204 42.857 1.83 1.83 36.85 4.06
3623 9867 9.220767 ACCTCAAACTTACTAAAGAATAAGCAG 57.779 33.333 0.00 0.00 36.50 4.24
3647 9891 0.820226 GTACCCGTTCCCAGTCTACC 59.180 60.000 0.00 0.00 0.00 3.18
3648 9892 1.549203 TGTACCCGTTCCCAGTCTAC 58.451 55.000 0.00 0.00 0.00 2.59
3660 9904 1.077068 ATGCCACCCAATGTACCCG 60.077 57.895 0.00 0.00 0.00 5.28
3661 9905 0.324275 ACATGCCACCCAATGTACCC 60.324 55.000 0.00 0.00 0.00 3.69
3664 9908 1.203112 ACCAACATGCCACCCAATGTA 60.203 47.619 0.00 0.00 0.00 2.29
3666 9910 0.686224 AACCAACATGCCACCCAATG 59.314 50.000 0.00 0.00 0.00 2.82
3667 9911 0.975887 GAACCAACATGCCACCCAAT 59.024 50.000 0.00 0.00 0.00 3.16
3668 9912 1.459455 CGAACCAACATGCCACCCAA 61.459 55.000 0.00 0.00 0.00 4.12
3669 9913 1.900981 CGAACCAACATGCCACCCA 60.901 57.895 0.00 0.00 0.00 4.51
3798 10058 1.465856 GGCAAGCGCAAGTAAGTAAGC 60.466 52.381 11.47 0.00 41.24 3.09
3799 10059 2.076863 AGGCAAGCGCAAGTAAGTAAG 58.923 47.619 11.47 0.00 41.24 2.34
3800 10060 1.804151 CAGGCAAGCGCAAGTAAGTAA 59.196 47.619 11.47 0.00 41.24 2.24
3805 10065 3.055719 GGCAGGCAAGCGCAAGTA 61.056 61.111 11.47 0.00 41.24 2.24
3918 10221 2.046285 GTTCCCGGTGCATTGAGGG 61.046 63.158 0.00 11.16 45.10 4.30
3928 10231 0.540365 TTGAGTAGGTCGTTCCCGGT 60.540 55.000 0.00 0.00 36.75 5.28
3938 10241 1.676014 GCACGGCTCATTTGAGTAGGT 60.676 52.381 9.21 2.77 43.85 3.08
3980 10286 3.071892 ACGTCAGACCACCATCCTTAAAA 59.928 43.478 0.00 0.00 0.00 1.52
3981 10287 2.635915 ACGTCAGACCACCATCCTTAAA 59.364 45.455 0.00 0.00 0.00 1.52
3986 10292 1.079127 CCACGTCAGACCACCATCC 60.079 63.158 0.00 0.00 0.00 3.51
4105 10412 0.879839 TCGACGGTGACAGACGTACA 60.880 55.000 7.41 0.00 44.24 2.90
4133 10445 2.402640 ACTACATTCGCTAGCTACGC 57.597 50.000 13.93 7.68 0.00 4.42
4263 10586 2.893398 GGCCACTCCAGTCCGTAG 59.107 66.667 0.00 0.00 34.01 3.51
4370 10709 0.094901 CCGTCGTCGTCAGTACAGAG 59.905 60.000 0.71 0.00 35.01 3.35
4379 10721 3.735029 AGCTCCACCGTCGTCGTC 61.735 66.667 0.71 0.00 35.01 4.20
4380 10722 4.039357 CAGCTCCACCGTCGTCGT 62.039 66.667 0.71 0.00 35.01 4.34
4383 10725 1.323271 ATCATCAGCTCCACCGTCGT 61.323 55.000 0.00 0.00 0.00 4.34
4418 10760 0.738762 CTCACCTGCACCATCAGACG 60.739 60.000 0.00 0.00 36.19 4.18
4419 10761 0.392193 CCTCACCTGCACCATCAGAC 60.392 60.000 0.00 0.00 36.19 3.51
4421 10763 1.077930 CCCTCACCTGCACCATCAG 60.078 63.158 0.00 0.00 0.00 2.90
4480 10830 1.448540 CTGCAGGTAGTCCCGCTTG 60.449 63.158 5.57 0.00 38.74 4.01
4531 10881 4.809496 AGCAGCTTGGGGATGGCG 62.809 66.667 0.00 0.00 0.00 5.69
4684 11034 2.125961 CCGGAACTCGTAGGGGAGG 61.126 68.421 0.00 0.00 38.39 4.30
4745 11101 7.241663 TGTGTACAAAGCTAGTTACAAACAG 57.758 36.000 0.00 0.00 0.00 3.16
4811 11177 7.415206 CGGGAGAAATAAAGGACAAATTGTAGG 60.415 40.741 0.00 0.00 0.00 3.18
4814 11180 5.185056 CCGGGAGAAATAAAGGACAAATTGT 59.815 40.000 0.00 0.00 0.00 2.71
4822 11188 3.841845 TCTTCACCGGGAGAAATAAAGGA 59.158 43.478 6.32 0.00 0.00 3.36
4827 11194 3.031736 CTCCTCTTCACCGGGAGAAATA 58.968 50.000 6.32 0.23 46.82 1.40
4828 11195 1.834263 CTCCTCTTCACCGGGAGAAAT 59.166 52.381 6.32 0.00 46.82 2.17
4832 11199 0.820871 CTTCTCCTCTTCACCGGGAG 59.179 60.000 6.32 1.86 45.65 4.30
4833 11200 0.408309 TCTTCTCCTCTTCACCGGGA 59.592 55.000 6.32 0.00 0.00 5.14
4836 11203 9.015367 TCTATATATTTCTTCTCCTCTTCACCG 57.985 37.037 0.00 0.00 0.00 4.94
4858 11225 8.940952 GCACAGAAAAACTTTCTCATACTCTAT 58.059 33.333 0.00 0.00 0.00 1.98
4859 11226 8.150945 AGCACAGAAAAACTTTCTCATACTCTA 58.849 33.333 0.00 0.00 0.00 2.43
4860 11227 6.995091 AGCACAGAAAAACTTTCTCATACTCT 59.005 34.615 0.00 0.00 0.00 3.24
4861 11228 7.172361 AGAGCACAGAAAAACTTTCTCATACTC 59.828 37.037 0.00 4.88 0.00 2.59
4862 11229 6.995091 AGAGCACAGAAAAACTTTCTCATACT 59.005 34.615 0.00 0.00 0.00 2.12
4863 11230 7.074502 CAGAGCACAGAAAAACTTTCTCATAC 58.925 38.462 0.00 0.00 0.00 2.39
4864 11231 6.205464 CCAGAGCACAGAAAAACTTTCTCATA 59.795 38.462 0.00 0.00 0.00 2.15
4865 11232 5.009410 CCAGAGCACAGAAAAACTTTCTCAT 59.991 40.000 0.00 0.00 0.00 2.90
4866 11233 4.336433 CCAGAGCACAGAAAAACTTTCTCA 59.664 41.667 0.00 0.00 0.00 3.27
4867 11234 4.336713 ACCAGAGCACAGAAAAACTTTCTC 59.663 41.667 0.00 0.00 0.00 2.87
4868 11235 4.273318 ACCAGAGCACAGAAAAACTTTCT 58.727 39.130 0.00 0.00 0.00 2.52
4869 11236 4.639135 ACCAGAGCACAGAAAAACTTTC 57.361 40.909 0.00 0.00 0.00 2.62
4870 11237 4.462483 TCAACCAGAGCACAGAAAAACTTT 59.538 37.500 0.00 0.00 0.00 2.66
4871 11238 4.016444 TCAACCAGAGCACAGAAAAACTT 58.984 39.130 0.00 0.00 0.00 2.66
4872 11239 3.620488 TCAACCAGAGCACAGAAAAACT 58.380 40.909 0.00 0.00 0.00 2.66
4873 11240 3.627577 TCTCAACCAGAGCACAGAAAAAC 59.372 43.478 0.00 0.00 44.35 2.43
4874 11241 3.627577 GTCTCAACCAGAGCACAGAAAAA 59.372 43.478 0.00 0.00 44.35 1.94
4875 11242 3.206150 GTCTCAACCAGAGCACAGAAAA 58.794 45.455 0.00 0.00 44.35 2.29
4876 11243 2.170397 TGTCTCAACCAGAGCACAGAAA 59.830 45.455 0.00 0.00 44.35 2.52
4877 11244 1.762370 TGTCTCAACCAGAGCACAGAA 59.238 47.619 0.00 0.00 44.35 3.02
4878 11245 1.413118 TGTCTCAACCAGAGCACAGA 58.587 50.000 0.00 0.00 44.35 3.41
4879 11246 1.869767 GTTGTCTCAACCAGAGCACAG 59.130 52.381 1.70 0.00 44.35 3.66
4880 11247 1.475034 GGTTGTCTCAACCAGAGCACA 60.475 52.381 21.88 0.00 44.35 4.57
4881 11248 1.230324 GGTTGTCTCAACCAGAGCAC 58.770 55.000 21.88 0.00 44.35 4.40
4882 11249 0.836606 TGGTTGTCTCAACCAGAGCA 59.163 50.000 24.51 7.24 44.74 4.26
4883 11250 3.706055 TGGTTGTCTCAACCAGAGC 57.294 52.632 24.51 5.00 44.74 4.09
4888 11255 1.947456 GACTTGGTGGTTGTCTCAACC 59.053 52.381 20.55 20.55 40.67 3.77
4889 11256 2.354821 GTGACTTGGTGGTTGTCTCAAC 59.645 50.000 4.30 4.30 0.00 3.18
4890 11257 2.639065 GTGACTTGGTGGTTGTCTCAA 58.361 47.619 0.00 0.00 0.00 3.02
4891 11258 1.134220 GGTGACTTGGTGGTTGTCTCA 60.134 52.381 0.00 0.00 0.00 3.27
4892 11259 1.134220 TGGTGACTTGGTGGTTGTCTC 60.134 52.381 0.00 0.00 0.00 3.36
4893 11260 0.916086 TGGTGACTTGGTGGTTGTCT 59.084 50.000 0.00 0.00 0.00 3.41
4894 11261 1.021968 GTGGTGACTTGGTGGTTGTC 58.978 55.000 0.00 0.00 0.00 3.18
4895 11262 0.623723 AGTGGTGACTTGGTGGTTGT 59.376 50.000 0.00 0.00 0.00 3.32
4896 11263 1.308998 GAGTGGTGACTTGGTGGTTG 58.691 55.000 0.00 0.00 30.16 3.77
4897 11264 0.916086 TGAGTGGTGACTTGGTGGTT 59.084 50.000 0.00 0.00 30.16 3.67
4898 11265 0.916086 TTGAGTGGTGACTTGGTGGT 59.084 50.000 0.00 0.00 30.16 4.16
4899 11266 2.051334 TTTGAGTGGTGACTTGGTGG 57.949 50.000 0.00 0.00 30.16 4.61
4900 11267 3.243501 CCATTTTGAGTGGTGACTTGGTG 60.244 47.826 0.00 0.00 30.16 4.17
4901 11268 2.958355 CCATTTTGAGTGGTGACTTGGT 59.042 45.455 0.00 0.00 30.16 3.67
4902 11269 2.288395 GCCATTTTGAGTGGTGACTTGG 60.288 50.000 0.00 0.00 39.01 3.61
4903 11270 2.361757 TGCCATTTTGAGTGGTGACTTG 59.638 45.455 0.00 0.00 39.01 3.16
4904 11271 2.665165 TGCCATTTTGAGTGGTGACTT 58.335 42.857 0.00 0.00 39.01 3.01
4905 11272 2.363306 TGCCATTTTGAGTGGTGACT 57.637 45.000 0.00 0.00 39.01 3.41
4906 11273 3.665745 ATTGCCATTTTGAGTGGTGAC 57.334 42.857 0.00 0.00 39.01 3.67
4907 11274 4.686191 AAATTGCCATTTTGAGTGGTGA 57.314 36.364 0.00 0.00 39.01 4.02
4908 11275 5.277925 GGAAAAATTGCCATTTTGAGTGGTG 60.278 40.000 9.08 0.00 41.02 4.17
4909 11276 4.821260 GGAAAAATTGCCATTTTGAGTGGT 59.179 37.500 9.08 0.00 41.02 4.16
4910 11277 4.216042 GGGAAAAATTGCCATTTTGAGTGG 59.784 41.667 9.08 0.00 41.02 4.00
5055 11422 4.247380 GGAGCCTCCATGGAGCCG 62.247 72.222 32.97 22.26 40.69 5.52
5409 11783 0.395311 ATGCGAAGGAGGACGAGGTA 60.395 55.000 0.00 0.00 0.00 3.08
5410 11784 1.668101 GATGCGAAGGAGGACGAGGT 61.668 60.000 0.00 0.00 0.00 3.85
5439 11813 2.203451 AGGTGTCGGACTGTCGGT 60.203 61.111 13.99 0.00 0.00 4.69
5443 11817 0.891373 CTGATGAGGTGTCGGACTGT 59.109 55.000 9.88 0.00 0.00 3.55
5633 12051 2.123248 TTGGGTCGATGCAGAAGCCA 62.123 55.000 11.40 11.40 41.13 4.75
5688 12106 6.772078 ACAACTACAAGAACAGAAAGTTTCG 58.228 36.000 9.91 7.74 41.51 3.46


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

AutoCloner maintained by Alex Coulton.