Multiple sequence alignment - TraesCS3D01G196900

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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 TraesCS3D01G196900 chr3D 100.000 5220 0 0 1511 6730 202496409 202501628 0.000000e+00 9640.0
1 TraesCS3D01G196900 chr3D 100.000 1173 0 0 1 1173 202494899 202496071 0.000000e+00 2167.0
2 TraesCS3D01G196900 chr3B 97.754 2093 41 4 3531 5620 289595092 289597181 0.000000e+00 3600.0
3 TraesCS3D01G196900 chr3B 97.300 926 18 5 1511 2432 289593111 289594033 0.000000e+00 1565.0
4 TraesCS3D01G196900 chr3B 92.263 685 40 3 5572 6245 289597167 289597849 0.000000e+00 959.0
5 TraesCS3D01G196900 chr3B 98.339 542 9 0 2546 3087 398842928 398842387 0.000000e+00 952.0
6 TraesCS3D01G196900 chr3B 91.727 689 42 7 5572 6249 289627323 289628007 0.000000e+00 942.0
7 TraesCS3D01G196900 chr3B 91.892 481 36 3 6247 6727 289628035 289628512 0.000000e+00 669.0
8 TraesCS3D01G196900 chr3B 96.259 294 5 1 877 1170 289592763 289593050 1.700000e-130 477.0
9 TraesCS3D01G196900 chr3B 94.382 89 5 0 6102 6190 289597794 289597706 3.270000e-28 137.0
10 TraesCS3D01G196900 chr3B 83.186 113 15 2 6378 6486 703120677 703120789 4.290000e-17 100.0
11 TraesCS3D01G196900 chr3B 96.429 56 2 0 5335 5390 289596948 289597003 7.190000e-15 93.5
12 TraesCS3D01G196900 chr3A 96.059 1624 39 6 4639 6249 256867011 256865400 0.000000e+00 2621.0
13 TraesCS3D01G196900 chr3A 97.786 1039 20 2 1511 2547 256869537 256868500 0.000000e+00 1788.0
14 TraesCS3D01G196900 chr3A 97.730 1013 21 2 3603 4615 256868015 256867005 0.000000e+00 1742.0
15 TraesCS3D01G196900 chr3A 96.715 487 8 2 3079 3558 256868508 256868023 0.000000e+00 804.0
16 TraesCS3D01G196900 chr3A 94.700 434 20 3 6295 6728 256863462 256863032 0.000000e+00 671.0
17 TraesCS3D01G196900 chr3A 97.619 294 6 1 880 1173 256869887 256869595 2.800000e-138 503.0
18 TraesCS3D01G196900 chr3A 96.429 56 2 0 5335 5390 256866262 256866207 7.190000e-15 93.5
19 TraesCS3D01G196900 chr3A 98.077 52 1 0 6247 6298 256865372 256865321 2.580000e-14 91.6
20 TraesCS3D01G196900 chr3A 94.595 37 2 0 3304 3340 719041676 719041712 2.620000e-04 58.4
21 TraesCS3D01G196900 chr7A 98.339 542 9 0 2546 3087 319591451 319591992 0.000000e+00 952.0
22 TraesCS3D01G196900 chr7A 85.106 94 8 3 6102 6191 42306430 42306339 2.580000e-14 91.6
23 TraesCS3D01G196900 chr2D 98.339 542 9 0 2546 3087 106332155 106332696 0.000000e+00 952.0
24 TraesCS3D01G196900 chr2D 98.339 542 9 0 2546 3087 285335649 285336190 0.000000e+00 952.0
25 TraesCS3D01G196900 chr2D 98.339 542 9 0 2546 3087 351053230 351053771 0.000000e+00 952.0
26 TraesCS3D01G196900 chr2D 79.221 154 9 13 3210 3340 272794477 272794324 1.200000e-12 86.1
27 TraesCS3D01G196900 chr2D 96.774 31 1 0 579 609 529540296 529540326 1.200000e-02 52.8
28 TraesCS3D01G196900 chr7D 98.336 541 9 0 2546 3086 465340022 465340562 0.000000e+00 950.0
29 TraesCS3D01G196900 chr7D 78.235 680 142 4 9 685 442786704 442787380 1.340000e-116 431.0
30 TraesCS3D01G196900 chr7D 90.588 85 4 2 714 798 54178173 54178253 7.140000e-20 110.0
31 TraesCS3D01G196900 chrUn 98.155 542 10 0 2546 3087 70286382 70285841 0.000000e+00 946.0
32 TraesCS3D01G196900 chrUn 88.550 131 11 3 6599 6727 295889747 295889619 9.040000e-34 156.0
33 TraesCS3D01G196900 chrUn 79.221 154 9 13 3210 3340 372772237 372772084 1.200000e-12 86.1
34 TraesCS3D01G196900 chr6D 98.155 542 10 0 2546 3087 242979444 242979985 0.000000e+00 946.0
35 TraesCS3D01G196900 chr6D 87.912 91 8 3 6102 6190 445778960 445778871 3.320000e-18 104.0
36 TraesCS3D01G196900 chr6D 86.022 93 9 3 6098 6190 334072726 334072638 5.560000e-16 97.1
37 TraesCS3D01G196900 chr4D 98.155 542 10 0 2546 3087 242938422 242938963 0.000000e+00 946.0
38 TraesCS3D01G196900 chr6B 78.537 629 128 7 91 715 492867256 492866631 2.260000e-109 407.0
39 TraesCS3D01G196900 chr4B 77.353 680 148 6 9 685 172512983 172513659 1.360000e-106 398.0
40 TraesCS3D01G196900 chr4B 78.571 154 10 13 3210 3340 365443590 365443437 5.590000e-11 80.5
41 TraesCS3D01G196900 chr5B 76.865 657 144 6 42 694 314946760 314946108 1.380000e-96 364.0
42 TraesCS3D01G196900 chr5B 90.435 115 7 1 6376 6486 355018942 355019056 1.510000e-31 148.0
43 TraesCS3D01G196900 chr5B 95.455 44 2 0 801 844 65195433 65195390 3.370000e-08 71.3
44 TraesCS3D01G196900 chr2B 76.436 679 156 4 9 685 92599850 92600526 1.380000e-96 364.0
45 TraesCS3D01G196900 chr2B 100.000 28 0 0 582 609 629027045 629027072 1.200000e-02 52.8
46 TraesCS3D01G196900 chr1D 86.842 114 11 2 6380 6489 488532390 488532277 2.550000e-24 124.0
47 TraesCS3D01G196900 chr5D 85.965 114 12 3 6377 6486 453820717 453820830 1.190000e-22 119.0
48 TraesCS3D01G196900 chr5D 86.667 90 8 3 6101 6190 346622830 346622915 5.560000e-16 97.1
49 TraesCS3D01G196900 chr5A 84.615 104 11 4 6102 6200 438354044 438353941 1.540000e-16 99.0
50 TraesCS3D01G196900 chr2A 86.813 91 8 3 6101 6191 324284711 324284797 1.540000e-16 99.0
51 TraesCS3D01G196900 chr2A 100.000 28 0 0 582 609 674042545 674042572 1.200000e-02 52.8
52 TraesCS3D01G196900 chr4A 95.556 45 2 0 6442 6486 501276874 501276830 9.360000e-09 73.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G196900 chr3D 202494899 202501628 6729 False 5903.5000 9640 100.000000 1 6730 2 chr3D.!!$F1 6729
1 TraesCS3D01G196900 chr3B 289592763 289597849 5086 False 1338.9000 3600 96.001000 877 6245 5 chr3B.!!$F2 5368
2 TraesCS3D01G196900 chr3B 398842387 398842928 541 True 952.0000 952 98.339000 2546 3087 1 chr3B.!!$R2 541
3 TraesCS3D01G196900 chr3B 289627323 289628512 1189 False 805.5000 942 91.809500 5572 6727 2 chr3B.!!$F3 1155
4 TraesCS3D01G196900 chr3A 256863032 256869887 6855 True 1039.2625 2621 96.889375 880 6728 8 chr3A.!!$R1 5848
5 TraesCS3D01G196900 chr7A 319591451 319591992 541 False 952.0000 952 98.339000 2546 3087 1 chr7A.!!$F1 541
6 TraesCS3D01G196900 chr2D 106332155 106332696 541 False 952.0000 952 98.339000 2546 3087 1 chr2D.!!$F1 541
7 TraesCS3D01G196900 chr2D 285335649 285336190 541 False 952.0000 952 98.339000 2546 3087 1 chr2D.!!$F2 541
8 TraesCS3D01G196900 chr2D 351053230 351053771 541 False 952.0000 952 98.339000 2546 3087 1 chr2D.!!$F3 541
9 TraesCS3D01G196900 chr7D 465340022 465340562 540 False 950.0000 950 98.336000 2546 3086 1 chr7D.!!$F3 540
10 TraesCS3D01G196900 chr7D 442786704 442787380 676 False 431.0000 431 78.235000 9 685 1 chr7D.!!$F2 676
11 TraesCS3D01G196900 chrUn 70285841 70286382 541 True 946.0000 946 98.155000 2546 3087 1 chrUn.!!$R1 541
12 TraesCS3D01G196900 chr6D 242979444 242979985 541 False 946.0000 946 98.155000 2546 3087 1 chr6D.!!$F1 541
13 TraesCS3D01G196900 chr4D 242938422 242938963 541 False 946.0000 946 98.155000 2546 3087 1 chr4D.!!$F1 541
14 TraesCS3D01G196900 chr6B 492866631 492867256 625 True 407.0000 407 78.537000 91 715 1 chr6B.!!$R1 624
15 TraesCS3D01G196900 chr4B 172512983 172513659 676 False 398.0000 398 77.353000 9 685 1 chr4B.!!$F1 676
16 TraesCS3D01G196900 chr5B 314946108 314946760 652 True 364.0000 364 76.865000 42 694 1 chr5B.!!$R2 652
17 TraesCS3D01G196900 chr2B 92599850 92600526 676 False 364.0000 364 76.436000 9 685 1 chr2B.!!$F1 676

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
840 842 0.040204 ATCCCCTCCTGCCAAACAAG 59.960 55.000 0.00 0.00 0.0 3.16 F
1170 1177 0.323542 ACATCCCCTCGTCGACTTCT 60.324 55.000 14.70 0.00 0.0 2.85 F
2678 2840 0.824759 AGTTAGGTGTGGCGGAGATC 59.175 55.000 0.00 0.00 0.0 2.75 F
3674 3985 1.850345 ACTGGAAAGTGGAAACTGGGA 59.150 47.619 0.00 0.00 0.0 4.37 F
3675 3986 2.243736 ACTGGAAAGTGGAAACTGGGAA 59.756 45.455 0.00 0.00 0.0 3.97 F
5135 5448 2.173356 TCAACCAGGCCAGATATCTTGG 59.827 50.000 16.48 16.48 0.0 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2382 2395 0.321996 AACGAAGAGCAACCTCCTCC 59.678 55.000 0.00 0.00 38.96 4.30 R
2709 2871 0.323999 TTCCGGACTCGATCCTTCCA 60.324 55.000 1.83 0.00 46.69 3.53 R
4602 4915 1.134610 GCCAGAAAATGCAATGAGGGG 60.135 52.381 0.00 0.00 0.00 4.79 R
5116 5429 2.441001 CTCCAAGATATCTGGCCTGGTT 59.559 50.000 17.10 0.67 0.00 3.67 R
5315 5628 3.632145 AGAAGTGTCATGAAGCCGTTTTT 59.368 39.130 0.00 0.00 0.00 1.94 R
6524 8791 0.320421 TTGTGCCTCAAGTAGACCGC 60.320 55.000 0.00 0.00 0.00 5.68 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
28 29 8.347035 GTGCTAGACTTACAAAAATTTGGTACA 58.653 33.333 10.38 0.00 42.34 2.90
29 30 9.073475 TGCTAGACTTACAAAAATTTGGTACAT 57.927 29.630 10.38 0.00 42.34 2.29
40 41 8.519526 CAAAAATTTGGTACATCACTAAGGCTA 58.480 33.333 0.00 0.00 39.30 3.93
73 74 4.512914 GCCTGGCAGGATCCACCC 62.513 72.222 37.07 13.52 37.67 4.61
79 80 3.849951 CAGGATCCACCCCGACCG 61.850 72.222 15.82 0.00 40.05 4.79
149 150 1.818060 CCATGGCAACCGAGATCAAAA 59.182 47.619 0.00 0.00 0.00 2.44
151 152 3.119029 CCATGGCAACCGAGATCAAAATT 60.119 43.478 0.00 0.00 0.00 1.82
160 161 2.006888 GAGATCAAAATTGGCGACGGA 58.993 47.619 0.00 0.00 0.00 4.69
166 168 0.885596 AAATTGGCGACGGACGGAAA 60.886 50.000 1.66 0.00 42.83 3.13
167 169 0.885596 AATTGGCGACGGACGGAAAA 60.886 50.000 1.66 0.00 42.83 2.29
172 174 1.300388 CGACGGACGGAAAACCAGT 60.300 57.895 0.00 0.00 38.46 4.00
187 189 0.379669 CCAGTTTCTGGCATGATCGC 59.620 55.000 0.00 0.00 45.13 4.58
193 195 2.203112 TGGCATGATCGCTGGCTC 60.203 61.111 18.41 2.74 39.72 4.70
194 196 3.344215 GGCATGATCGCTGGCTCG 61.344 66.667 12.65 0.00 36.34 5.03
212 214 1.883021 GACGGACAATGCCCCAAAG 59.117 57.895 0.00 0.00 0.00 2.77
214 216 0.402504 ACGGACAATGCCCCAAAGTA 59.597 50.000 0.00 0.00 0.00 2.24
217 219 1.818674 GGACAATGCCCCAAAGTACTG 59.181 52.381 0.00 0.00 0.00 2.74
218 220 2.554344 GGACAATGCCCCAAAGTACTGA 60.554 50.000 0.00 0.00 0.00 3.41
223 225 0.109723 GCCCCAAAGTACTGACACCA 59.890 55.000 0.00 0.00 0.00 4.17
224 226 1.271926 GCCCCAAAGTACTGACACCAT 60.272 52.381 0.00 0.00 0.00 3.55
229 231 3.338249 CAAAGTACTGACACCATCCCTG 58.662 50.000 0.00 0.00 0.00 4.45
232 234 2.567615 AGTACTGACACCATCCCTGTTC 59.432 50.000 0.00 0.00 0.00 3.18
236 238 2.350895 CACCATCCCTGTTCGCCA 59.649 61.111 0.00 0.00 0.00 5.69
244 246 0.962356 CCCTGTTCGCCATTTCAGCT 60.962 55.000 0.00 0.00 0.00 4.24
256 258 3.119495 CCATTTCAGCTAGGAAAAACCGG 60.119 47.826 0.00 0.00 44.74 5.28
259 261 1.975680 TCAGCTAGGAAAAACCGGACT 59.024 47.619 9.46 0.00 44.74 3.85
268 270 1.909700 AAAACCGGACTGTGCATGAT 58.090 45.000 9.46 0.00 0.00 2.45
270 272 0.677731 AACCGGACTGTGCATGATGG 60.678 55.000 9.46 0.00 0.00 3.51
272 274 0.179037 CCGGACTGTGCATGATGGAT 60.179 55.000 0.00 0.00 0.00 3.41
274 276 1.332686 CGGACTGTGCATGATGGATTG 59.667 52.381 0.00 0.00 0.00 2.67
276 278 2.617308 GGACTGTGCATGATGGATTGAG 59.383 50.000 0.00 0.00 0.00 3.02
279 281 1.285667 TGTGCATGATGGATTGAGGGT 59.714 47.619 0.00 0.00 0.00 4.34
284 286 3.220110 CATGATGGATTGAGGGTTCAGG 58.780 50.000 0.00 0.00 34.15 3.86
293 295 0.967380 GAGGGTTCAGGCATGGTTGG 60.967 60.000 0.00 0.00 0.00 3.77
305 307 1.546923 CATGGTTGGCTGATCTTGCAA 59.453 47.619 0.00 0.00 0.00 4.08
316 318 3.698040 CTGATCTTGCAAATGGGCTAACT 59.302 43.478 0.00 0.00 34.04 2.24
319 321 3.700538 TCTTGCAAATGGGCTAACTGAT 58.299 40.909 0.00 0.00 34.04 2.90
321 323 2.101783 TGCAAATGGGCTAACTGATGG 58.898 47.619 0.00 0.00 34.04 3.51
356 358 0.460311 TACTAGCCTTGCGGAGAAGC 59.540 55.000 0.00 0.00 37.71 3.86
364 366 0.884704 TTGCGGAGAAGCTGGACAAC 60.885 55.000 0.00 0.00 38.13 3.32
379 381 0.466543 ACAACGTGGTGCTACAGGAA 59.533 50.000 0.00 0.00 0.00 3.36
393 395 0.617413 CAGGAAGACCAGCCAGATGT 59.383 55.000 0.00 0.00 38.94 3.06
406 408 1.677576 CCAGATGTAATTGCATGGCGT 59.322 47.619 14.16 0.00 0.00 5.68
412 414 1.910819 GTAATTGCATGGCGTTTCACG 59.089 47.619 0.00 0.00 45.88 4.35
433 435 0.368907 CAAACCGTGAGTATTCCGCG 59.631 55.000 0.00 0.00 0.00 6.46
451 453 2.483583 CGAGATCCGCCTATATGCTC 57.516 55.000 0.00 0.00 0.00 4.26
468 470 1.432270 CTCCAATTCGAAGGCTCGGC 61.432 60.000 3.35 0.00 45.49 5.54
472 474 0.876342 AATTCGAAGGCTCGGCGATC 60.876 55.000 11.27 6.00 45.49 3.69
473 475 3.751401 TTCGAAGGCTCGGCGATCG 62.751 63.158 20.84 20.84 45.49 3.69
490 492 2.317609 CGCGGAAGGACACAACCTG 61.318 63.158 0.00 0.00 40.49 4.00
508 510 1.009997 TGATTTGGAAGGGATGGGCT 58.990 50.000 0.00 0.00 0.00 5.19
517 519 2.825836 GGATGGGCTCCACGCAAG 60.826 66.667 0.00 0.00 45.40 4.01
532 534 1.871772 CAAGTGCCGCTTCTTCCTG 59.128 57.895 0.00 0.00 34.69 3.86
539 541 1.006102 CGCTTCTTCCTGTGGACGT 60.006 57.895 0.00 0.00 0.00 4.34
550 552 3.569849 TGGACGTCCATGTTGGGT 58.430 55.556 33.23 0.00 42.01 4.51
556 558 3.508402 GGACGTCCATGTTGGGTAAAATT 59.492 43.478 29.75 0.00 38.32 1.82
562 564 7.149307 CGTCCATGTTGGGTAAAATTTTAACT 58.851 34.615 22.06 2.89 38.32 2.24
568 570 5.123805 TGGGTAAAATTTTAACTGCGGAC 57.876 39.130 22.06 7.99 31.13 4.79
569 571 4.583489 TGGGTAAAATTTTAACTGCGGACA 59.417 37.500 22.06 10.17 31.13 4.02
571 573 4.919168 GGTAAAATTTTAACTGCGGACACC 59.081 41.667 17.07 7.42 0.00 4.16
578 580 4.320456 CTGCGGACACCCTGCTGT 62.320 66.667 0.00 0.00 34.56 4.40
601 603 4.710375 TGTAGAGGATGGGAGAACAACTAC 59.290 45.833 0.00 0.00 0.00 2.73
613 615 5.512576 GGAGAACAACTACTTTTGCCCTCTA 60.513 44.000 0.00 0.00 32.79 2.43
649 651 2.250635 AAACCCCAACCCACCTGCTT 62.251 55.000 0.00 0.00 0.00 3.91
650 652 1.365105 AACCCCAACCCACCTGCTTA 61.365 55.000 0.00 0.00 0.00 3.09
661 663 0.698238 ACCTGCTTATTGAGTGCCCA 59.302 50.000 0.00 0.00 0.00 5.36
667 669 1.942657 CTTATTGAGTGCCCATGGTCG 59.057 52.381 11.73 0.00 0.00 4.79
685 687 1.223487 GCGGTATGCCTGGGAGAAA 59.777 57.895 0.00 0.00 37.76 2.52
688 690 2.654863 CGGTATGCCTGGGAGAAAATT 58.345 47.619 0.00 0.00 0.00 1.82
691 693 0.819582 ATGCCTGGGAGAAAATTGCG 59.180 50.000 0.00 0.00 0.00 4.85
694 696 0.109132 CCTGGGAGAAAATTGCGCAC 60.109 55.000 11.12 0.00 0.00 5.34
695 697 0.883833 CTGGGAGAAAATTGCGCACT 59.116 50.000 11.12 0.00 0.00 4.40
697 699 1.000385 TGGGAGAAAATTGCGCACTTG 60.000 47.619 11.12 0.00 0.00 3.16
699 701 2.545742 GGGAGAAAATTGCGCACTTGTT 60.546 45.455 11.12 8.54 0.00 2.83
700 702 2.472488 GGAGAAAATTGCGCACTTGTTG 59.528 45.455 11.12 0.00 0.00 3.33
710 712 4.041917 ACTTGTTGCGCATGCCGG 62.042 61.111 12.75 0.00 41.78 6.13
730 732 3.771160 CTCGCCTTGGGTACGCCT 61.771 66.667 7.55 0.00 34.45 5.52
731 733 4.077184 TCGCCTTGGGTACGCCTG 62.077 66.667 7.55 0.11 34.45 4.85
732 734 4.388499 CGCCTTGGGTACGCCTGT 62.388 66.667 7.55 0.00 34.45 4.00
733 735 2.983791 GCCTTGGGTACGCCTGTA 59.016 61.111 7.55 0.00 34.45 2.74
734 736 1.153429 GCCTTGGGTACGCCTGTAG 60.153 63.158 7.55 0.19 34.45 2.74
735 737 1.153429 CCTTGGGTACGCCTGTAGC 60.153 63.158 7.55 0.00 46.03 3.58
736 738 1.614241 CCTTGGGTACGCCTGTAGCT 61.614 60.000 7.55 0.00 46.01 3.32
737 739 0.179108 CTTGGGTACGCCTGTAGCTC 60.179 60.000 7.55 0.00 46.01 4.09
738 740 1.940883 TTGGGTACGCCTGTAGCTCG 61.941 60.000 7.55 0.00 46.01 5.03
739 741 2.117156 GGGTACGCCTGTAGCTCGA 61.117 63.158 0.00 0.00 46.01 4.04
740 742 1.063811 GGTACGCCTGTAGCTCGAC 59.936 63.158 0.00 0.00 43.95 4.20
741 743 1.375098 GGTACGCCTGTAGCTCGACT 61.375 60.000 0.00 0.00 43.95 4.18
742 744 0.450983 GTACGCCTGTAGCTCGACTT 59.549 55.000 0.00 0.00 40.39 3.01
743 745 1.135460 GTACGCCTGTAGCTCGACTTT 60.135 52.381 0.00 0.00 40.39 2.66
744 746 0.109226 ACGCCTGTAGCTCGACTTTC 60.109 55.000 0.00 0.00 40.39 2.62
745 747 0.171455 CGCCTGTAGCTCGACTTTCT 59.829 55.000 0.00 0.00 40.39 2.52
746 748 1.795889 CGCCTGTAGCTCGACTTTCTC 60.796 57.143 0.00 0.00 40.39 2.87
747 749 1.474879 GCCTGTAGCTCGACTTTCTCT 59.525 52.381 0.00 0.00 38.99 3.10
748 750 2.478879 GCCTGTAGCTCGACTTTCTCTC 60.479 54.545 0.00 0.00 38.99 3.20
749 751 2.098443 CCTGTAGCTCGACTTTCTCTCC 59.902 54.545 0.00 0.00 0.00 3.71
750 752 3.013921 CTGTAGCTCGACTTTCTCTCCT 58.986 50.000 0.00 0.00 0.00 3.69
751 753 3.422796 TGTAGCTCGACTTTCTCTCCTT 58.577 45.455 0.00 0.00 0.00 3.36
752 754 3.440872 TGTAGCTCGACTTTCTCTCCTTC 59.559 47.826 0.00 0.00 0.00 3.46
753 755 2.802719 AGCTCGACTTTCTCTCCTTCT 58.197 47.619 0.00 0.00 0.00 2.85
754 756 3.958018 AGCTCGACTTTCTCTCCTTCTA 58.042 45.455 0.00 0.00 0.00 2.10
755 757 4.337145 AGCTCGACTTTCTCTCCTTCTAA 58.663 43.478 0.00 0.00 0.00 2.10
756 758 4.953579 AGCTCGACTTTCTCTCCTTCTAAT 59.046 41.667 0.00 0.00 0.00 1.73
757 759 5.067283 AGCTCGACTTTCTCTCCTTCTAATC 59.933 44.000 0.00 0.00 0.00 1.75
758 760 5.163602 GCTCGACTTTCTCTCCTTCTAATCA 60.164 44.000 0.00 0.00 0.00 2.57
759 761 6.626181 GCTCGACTTTCTCTCCTTCTAATCAA 60.626 42.308 0.00 0.00 0.00 2.57
760 762 7.411486 TCGACTTTCTCTCCTTCTAATCAAT 57.589 36.000 0.00 0.00 0.00 2.57
761 763 7.261325 TCGACTTTCTCTCCTTCTAATCAATG 58.739 38.462 0.00 0.00 0.00 2.82
762 764 7.122799 TCGACTTTCTCTCCTTCTAATCAATGA 59.877 37.037 0.00 0.00 0.00 2.57
763 765 7.761704 CGACTTTCTCTCCTTCTAATCAATGAA 59.238 37.037 0.00 0.00 0.00 2.57
764 766 9.612066 GACTTTCTCTCCTTCTAATCAATGAAT 57.388 33.333 0.00 0.00 0.00 2.57
765 767 9.972106 ACTTTCTCTCCTTCTAATCAATGAATT 57.028 29.630 0.00 0.00 0.00 2.17
768 770 8.743085 TCTCTCCTTCTAATCAATGAATTTGG 57.257 34.615 0.00 0.00 35.92 3.28
769 771 8.331740 TCTCTCCTTCTAATCAATGAATTTGGT 58.668 33.333 0.00 0.00 35.92 3.67
770 772 9.618890 CTCTCCTTCTAATCAATGAATTTGGTA 57.381 33.333 0.00 0.00 35.92 3.25
771 773 9.618890 TCTCCTTCTAATCAATGAATTTGGTAG 57.381 33.333 0.00 0.00 35.92 3.18
772 774 9.618890 CTCCTTCTAATCAATGAATTTGGTAGA 57.381 33.333 0.00 0.00 35.92 2.59
773 775 9.973661 TCCTTCTAATCAATGAATTTGGTAGAA 57.026 29.630 0.00 9.78 38.56 2.10
781 783 9.807649 ATCAATGAATTTGGTAGAAAATGCTAC 57.192 29.630 0.00 0.00 39.97 3.58
793 795 8.810652 GTAGAAAATGCTACCAACATTCAAAA 57.189 30.769 0.00 0.00 36.74 2.44
794 796 9.255304 GTAGAAAATGCTACCAACATTCAAAAA 57.745 29.630 0.00 0.00 36.74 1.94
826 828 9.601810 AATCCCTTGTAATCTTAAATTATCCCC 57.398 33.333 0.00 0.00 0.00 4.81
827 829 8.358082 TCCCTTGTAATCTTAAATTATCCCCT 57.642 34.615 0.00 0.00 0.00 4.79
828 830 8.445588 TCCCTTGTAATCTTAAATTATCCCCTC 58.554 37.037 0.00 0.00 0.00 4.30
829 831 7.670140 CCCTTGTAATCTTAAATTATCCCCTCC 59.330 40.741 0.00 0.00 0.00 4.30
830 832 8.448816 CCTTGTAATCTTAAATTATCCCCTCCT 58.551 37.037 0.00 0.00 0.00 3.69
831 833 9.289782 CTTGTAATCTTAAATTATCCCCTCCTG 57.710 37.037 0.00 0.00 0.00 3.86
832 834 7.231467 TGTAATCTTAAATTATCCCCTCCTGC 58.769 38.462 0.00 0.00 0.00 4.85
833 835 4.724279 TCTTAAATTATCCCCTCCTGCC 57.276 45.455 0.00 0.00 0.00 4.85
834 836 4.051478 TCTTAAATTATCCCCTCCTGCCA 58.949 43.478 0.00 0.00 0.00 4.92
835 837 4.480537 TCTTAAATTATCCCCTCCTGCCAA 59.519 41.667 0.00 0.00 0.00 4.52
836 838 3.774842 AAATTATCCCCTCCTGCCAAA 57.225 42.857 0.00 0.00 0.00 3.28
837 839 2.755952 ATTATCCCCTCCTGCCAAAC 57.244 50.000 0.00 0.00 0.00 2.93
838 840 1.377690 TTATCCCCTCCTGCCAAACA 58.622 50.000 0.00 0.00 0.00 2.83
839 841 1.377690 TATCCCCTCCTGCCAAACAA 58.622 50.000 0.00 0.00 0.00 2.83
840 842 0.040204 ATCCCCTCCTGCCAAACAAG 59.960 55.000 0.00 0.00 0.00 3.16
841 843 1.607467 CCCCTCCTGCCAAACAAGG 60.607 63.158 0.00 0.00 0.00 3.61
883 885 3.357504 CGGTAGCTCCCGGTAAAAG 57.642 57.895 10.37 0.00 44.32 2.27
896 898 1.136500 GGTAAAAGCGACGGGATCTCT 59.864 52.381 0.00 0.00 0.00 3.10
959 966 2.286502 GGGGGAAGGAAGGGAGCT 60.287 66.667 0.00 0.00 0.00 4.09
960 967 2.379459 GGGGGAAGGAAGGGAGCTC 61.379 68.421 4.71 4.71 0.00 4.09
961 968 1.307430 GGGGAAGGAAGGGAGCTCT 60.307 63.158 14.64 0.00 0.00 4.09
962 969 1.341913 GGGGAAGGAAGGGAGCTCTC 61.342 65.000 14.64 10.30 0.00 3.20
1102 1109 1.074566 CCTCCAAGAAACCCAAGCTCT 59.925 52.381 0.00 0.00 0.00 4.09
1170 1177 0.323542 ACATCCCCTCGTCGACTTCT 60.324 55.000 14.70 0.00 0.00 2.85
1795 1802 3.352338 GGTCGCCGTCGATGACCTT 62.352 63.158 21.52 0.00 46.86 3.50
2037 2044 2.306341 AAGGTGCACTCTCGATCATG 57.694 50.000 17.98 0.00 0.00 3.07
2382 2395 1.838112 TAGGGCCTTGTGAAGCAATG 58.162 50.000 13.45 0.00 36.36 2.82
2678 2840 0.824759 AGTTAGGTGTGGCGGAGATC 59.175 55.000 0.00 0.00 0.00 2.75
2741 2903 4.106197 GAGTCCGGAATGATGATATACGC 58.894 47.826 10.26 0.00 0.00 4.42
3206 3508 5.572211 ACGTGACATATCATTTGTGCAATC 58.428 37.500 0.00 0.00 37.14 2.67
3512 3814 7.122138 AGTCTGCTGAGATCAATATTTCTCA 57.878 36.000 15.74 15.74 44.55 3.27
3674 3985 1.850345 ACTGGAAAGTGGAAACTGGGA 59.150 47.619 0.00 0.00 0.00 4.37
3675 3986 2.243736 ACTGGAAAGTGGAAACTGGGAA 59.756 45.455 0.00 0.00 0.00 3.97
4006 4317 4.763793 ACGTAGCACTGTCTAAAGTCCTTA 59.236 41.667 0.00 0.00 0.00 2.69
4007 4318 5.094134 CGTAGCACTGTCTAAAGTCCTTAC 58.906 45.833 0.00 0.00 0.00 2.34
4143 4454 4.616671 TCCCTCTGCTATATATGCTCCT 57.383 45.455 0.00 0.00 0.00 3.69
4335 4646 9.132923 TCTACAAGAAGGTCCACTACTATATTG 57.867 37.037 0.00 0.00 0.00 1.90
4712 5025 4.853924 AGTTTATGCCACCAGAACAAAG 57.146 40.909 0.00 0.00 0.00 2.77
4721 5034 4.451900 CCACCAGAACAAAGTAGTCAACT 58.548 43.478 0.00 0.00 41.49 3.16
4835 5148 5.354234 GGGTACAACCTAATTGACTGTGATG 59.646 44.000 0.00 0.00 41.23 3.07
5116 5429 7.339466 GGTCTAATTTTAGCATTTTCCTCCTCA 59.661 37.037 0.00 0.00 0.00 3.86
5135 5448 2.173356 TCAACCAGGCCAGATATCTTGG 59.827 50.000 16.48 16.48 0.00 3.61
5190 5503 5.988310 TTGATGTTCTTTCATGGAAGCAT 57.012 34.783 9.07 7.64 0.00 3.79
5273 5586 4.763793 AGTGCTATCATTGTTGTTCTGCTT 59.236 37.500 0.00 0.00 0.00 3.91
5315 5628 6.826741 GGTGGTGTAAATATTGAAGCCTCTTA 59.173 38.462 0.00 0.00 0.00 2.10
5333 5647 5.103290 TCTTAAAAACGGCTTCATGACAC 57.897 39.130 0.00 0.00 0.00 3.67
5658 6010 4.769345 ATGGTGTTTTGAATGGGTTGTT 57.231 36.364 0.00 0.00 0.00 2.83
5732 6084 3.638160 TGAATTTGAGGGCTGGATAATGC 59.362 43.478 0.00 0.00 0.00 3.56
5896 6251 5.825151 GCAAGGATCAAGCCTTAAGAATAGT 59.175 40.000 3.36 0.00 46.29 2.12
5920 6283 0.469705 AGGTGAATTGGCTGCCACAA 60.470 50.000 23.30 8.45 30.78 3.33
5989 6352 2.383298 AACTTGCAATCGTCGTGTTG 57.617 45.000 0.00 8.19 0.00 3.33
6013 6376 1.542030 CCGTCTGTTAGACTGCAGAGT 59.458 52.381 23.35 9.36 42.92 3.24
6160 6535 4.417506 AGTGTCAAAACCGCTGTAAAAAC 58.582 39.130 0.00 0.00 0.00 2.43
6161 6536 3.548668 GTGTCAAAACCGCTGTAAAAACC 59.451 43.478 0.00 0.00 0.00 3.27
6179 6554 9.227777 GTAAAAACCGCTCTTATATTATGGGAT 57.772 33.333 0.00 0.00 0.00 3.85
6252 6657 2.973224 CTGTGAGCGTTATGTTTTGTGC 59.027 45.455 0.00 0.00 0.00 4.57
6322 8589 8.150945 AGCTTGTAGAGAGAAGTTGAAAATACA 58.849 33.333 0.00 0.00 0.00 2.29
6432 8699 1.689984 TTGCAGTGATGGCAGTTCAA 58.310 45.000 0.00 0.00 43.05 2.69
6511 8778 2.307098 AGAAGGGGTCAAGTTCAGGATG 59.693 50.000 0.00 0.00 37.54 3.51
6524 8791 2.307768 TCAGGATGTAGTAGAAGGGCG 58.692 52.381 0.00 0.00 37.40 6.13
6568 8835 5.684550 AGTCGATTTACCACTGGTTTTTC 57.315 39.130 5.90 0.41 37.09 2.29
6728 8995 7.734924 TTGCAGTCTTCAACCATGATATATC 57.265 36.000 5.73 5.73 34.96 1.63
6729 8996 7.071069 TGCAGTCTTCAACCATGATATATCT 57.929 36.000 13.79 0.00 34.96 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 8.347035 TGTACCAAATTTTTGTAAGTCTAGCAC 58.653 33.333 2.63 0.00 36.45 4.40
3 4 8.453238 TGTACCAAATTTTTGTAAGTCTAGCA 57.547 30.769 2.63 0.00 36.45 3.49
4 5 9.556030 GATGTACCAAATTTTTGTAAGTCTAGC 57.444 33.333 2.63 0.00 36.45 3.42
7 8 9.131791 AGTGATGTACCAAATTTTTGTAAGTCT 57.868 29.630 2.63 0.00 36.45 3.24
15 16 7.539034 AGCCTTAGTGATGTACCAAATTTTT 57.461 32.000 0.00 0.00 0.00 1.94
16 17 8.644374 TTAGCCTTAGTGATGTACCAAATTTT 57.356 30.769 0.00 0.00 0.00 1.82
28 29 5.431765 CACAACCATCTTAGCCTTAGTGAT 58.568 41.667 0.00 0.00 0.00 3.06
29 30 4.323485 CCACAACCATCTTAGCCTTAGTGA 60.323 45.833 0.00 0.00 0.00 3.41
31 32 3.844211 TCCACAACCATCTTAGCCTTAGT 59.156 43.478 0.00 0.00 0.00 2.24
34 35 3.624777 CATCCACAACCATCTTAGCCTT 58.375 45.455 0.00 0.00 0.00 4.35
35 36 2.092212 CCATCCACAACCATCTTAGCCT 60.092 50.000 0.00 0.00 0.00 4.58
37 38 1.678101 GCCATCCACAACCATCTTAGC 59.322 52.381 0.00 0.00 0.00 3.09
40 41 0.706433 AGGCCATCCACAACCATCTT 59.294 50.000 5.01 0.00 33.74 2.40
89 90 2.124570 ATCGCATGGGAGTGGTGC 60.125 61.111 18.10 0.00 35.59 5.01
149 150 1.301874 TTTTCCGTCCGTCGCCAAT 60.302 52.632 0.00 0.00 38.35 3.16
151 152 2.662527 GTTTTCCGTCCGTCGCCA 60.663 61.111 0.00 0.00 38.35 5.69
172 174 1.378882 GCCAGCGATCATGCCAGAAA 61.379 55.000 0.00 0.00 34.65 2.52
187 189 2.456119 GCATTGTCCGTCGAGCCAG 61.456 63.158 0.00 0.00 0.00 4.85
193 195 1.922135 CTTTGGGGCATTGTCCGTCG 61.922 60.000 0.23 0.00 0.00 5.12
194 196 0.893727 ACTTTGGGGCATTGTCCGTC 60.894 55.000 0.23 0.00 0.00 4.79
212 214 2.674177 CGAACAGGGATGGTGTCAGTAC 60.674 54.545 0.00 0.00 0.00 2.73
214 216 0.321671 CGAACAGGGATGGTGTCAGT 59.678 55.000 0.00 0.00 0.00 3.41
217 219 1.745489 GGCGAACAGGGATGGTGTC 60.745 63.158 0.00 0.00 0.00 3.67
218 220 1.852157 ATGGCGAACAGGGATGGTGT 61.852 55.000 0.00 0.00 0.00 4.16
223 225 1.755179 CTGAAATGGCGAACAGGGAT 58.245 50.000 0.00 0.00 0.00 3.85
224 226 0.960364 GCTGAAATGGCGAACAGGGA 60.960 55.000 0.00 0.00 0.00 4.20
229 231 2.024176 TCCTAGCTGAAATGGCGAAC 57.976 50.000 0.00 0.00 34.52 3.95
232 234 3.501950 GTTTTTCCTAGCTGAAATGGCG 58.498 45.455 0.00 0.00 34.41 5.69
236 238 3.756963 GTCCGGTTTTTCCTAGCTGAAAT 59.243 43.478 0.00 0.00 34.41 2.17
244 246 1.141254 TGCACAGTCCGGTTTTTCCTA 59.859 47.619 0.00 0.00 0.00 2.94
256 258 2.617308 CCTCAATCCATCATGCACAGTC 59.383 50.000 0.00 0.00 0.00 3.51
259 261 1.285667 ACCCTCAATCCATCATGCACA 59.714 47.619 0.00 0.00 0.00 4.57
268 270 1.002069 ATGCCTGAACCCTCAATCCA 58.998 50.000 0.00 0.00 0.00 3.41
270 272 1.341383 ACCATGCCTGAACCCTCAATC 60.341 52.381 0.00 0.00 0.00 2.67
272 274 0.482446 AACCATGCCTGAACCCTCAA 59.518 50.000 0.00 0.00 0.00 3.02
274 276 0.967380 CCAACCATGCCTGAACCCTC 60.967 60.000 0.00 0.00 0.00 4.30
276 278 2.649129 GCCAACCATGCCTGAACCC 61.649 63.158 0.00 0.00 0.00 4.11
279 281 0.040058 ATCAGCCAACCATGCCTGAA 59.960 50.000 0.00 0.00 0.00 3.02
284 286 0.179119 GCAAGATCAGCCAACCATGC 60.179 55.000 0.00 0.00 0.00 4.06
293 295 0.822164 AGCCCATTTGCAAGATCAGC 59.178 50.000 0.00 0.00 0.00 4.26
294 296 3.698040 AGTTAGCCCATTTGCAAGATCAG 59.302 43.478 0.00 0.00 0.00 2.90
295 297 3.444742 CAGTTAGCCCATTTGCAAGATCA 59.555 43.478 0.00 0.00 0.00 2.92
298 300 3.153369 TCAGTTAGCCCATTTGCAAGA 57.847 42.857 0.00 0.00 0.00 3.02
305 307 2.313317 CATGCCATCAGTTAGCCCATT 58.687 47.619 0.00 0.00 0.00 3.16
356 358 0.249699 TGTAGCACCACGTTGTCCAG 60.250 55.000 0.00 0.00 0.00 3.86
364 366 0.389948 GGTCTTCCTGTAGCACCACG 60.390 60.000 0.00 0.00 0.00 4.94
379 381 2.025981 TGCAATTACATCTGGCTGGTCT 60.026 45.455 0.00 0.00 0.00 3.85
406 408 0.745128 ACTCACGGTTTGGCGTGAAA 60.745 50.000 0.44 0.00 43.25 2.69
412 414 0.725117 CGGAATACTCACGGTTTGGC 59.275 55.000 0.00 0.00 0.00 4.52
433 435 2.103373 TGGAGCATATAGGCGGATCTC 58.897 52.381 3.35 0.00 39.27 2.75
446 448 1.673168 GAGCCTTCGAATTGGAGCAT 58.327 50.000 7.59 0.00 0.00 3.79
468 470 1.445410 TTGTGTCCTTCCGCGATCG 60.445 57.895 11.69 11.69 0.00 3.69
472 474 2.030562 AGGTTGTGTCCTTCCGCG 59.969 61.111 0.00 0.00 33.52 6.46
473 475 0.321653 ATCAGGTTGTGTCCTTCCGC 60.322 55.000 0.00 0.00 35.37 5.54
478 480 3.490348 CTTCCAAATCAGGTTGTGTCCT 58.510 45.455 0.00 0.00 38.51 3.85
490 492 1.697284 GAGCCCATCCCTTCCAAATC 58.303 55.000 0.00 0.00 0.00 2.17
508 510 4.927782 AAGCGGCACTTGCGTGGA 62.928 61.111 1.45 0.00 43.26 4.02
517 519 2.328099 CCACAGGAAGAAGCGGCAC 61.328 63.158 1.45 0.00 0.00 5.01
539 541 6.931840 GCAGTTAAAATTTTACCCAACATGGA 59.068 34.615 10.18 0.00 40.96 3.41
550 552 4.828387 AGGGTGTCCGCAGTTAAAATTTTA 59.172 37.500 6.54 6.54 38.33 1.52
556 558 0.887387 GCAGGGTGTCCGCAGTTAAA 60.887 55.000 0.00 0.00 38.33 1.52
562 564 4.624364 CACAGCAGGGTGTCCGCA 62.624 66.667 0.38 0.00 38.33 5.69
568 570 1.134580 CATCCTCTACACAGCAGGGTG 60.135 57.143 0.00 0.00 44.35 4.61
569 571 1.198713 CATCCTCTACACAGCAGGGT 58.801 55.000 0.00 0.00 0.00 4.34
571 573 0.467384 CCCATCCTCTACACAGCAGG 59.533 60.000 0.00 0.00 0.00 4.85
578 580 3.791320 AGTTGTTCTCCCATCCTCTACA 58.209 45.455 0.00 0.00 0.00 2.74
581 583 4.067944 AGTAGTTGTTCTCCCATCCTCT 57.932 45.455 0.00 0.00 0.00 3.69
583 585 5.316987 CAAAAGTAGTTGTTCTCCCATCCT 58.683 41.667 0.00 0.00 0.00 3.24
601 603 2.208431 CTCTCGCATAGAGGGCAAAAG 58.792 52.381 5.36 0.00 46.98 2.27
625 627 1.602605 GTGGGTTGGGGTTTCGAGG 60.603 63.158 0.00 0.00 0.00 4.63
628 630 1.901464 CAGGTGGGTTGGGGTTTCG 60.901 63.158 0.00 0.00 0.00 3.46
649 651 0.463654 GCGACCATGGGCACTCAATA 60.464 55.000 20.22 0.00 0.00 1.90
650 652 1.750399 GCGACCATGGGCACTCAAT 60.750 57.895 20.22 0.00 0.00 2.57
661 663 2.108976 CAGGCATACCGCGACCAT 59.891 61.111 8.23 0.00 43.84 3.55
667 669 0.393808 TTTTCTCCCAGGCATACCGC 60.394 55.000 0.00 0.00 42.76 5.68
715 717 2.901051 CTACAGGCGTACCCAAGGCG 62.901 65.000 3.60 0.00 39.95 5.52
716 718 1.153429 CTACAGGCGTACCCAAGGC 60.153 63.158 3.60 0.00 38.28 4.35
717 719 1.153429 GCTACAGGCGTACCCAAGG 60.153 63.158 3.60 0.00 36.11 3.61
718 720 4.515404 GCTACAGGCGTACCCAAG 57.485 61.111 3.60 0.00 36.11 3.61
727 729 1.474879 AGAGAAAGTCGAGCTACAGGC 59.525 52.381 0.00 0.00 42.19 4.85
728 730 2.098443 GGAGAGAAAGTCGAGCTACAGG 59.902 54.545 0.00 0.00 0.00 4.00
729 731 3.013921 AGGAGAGAAAGTCGAGCTACAG 58.986 50.000 0.00 0.00 0.00 2.74
730 732 3.074675 AGGAGAGAAAGTCGAGCTACA 57.925 47.619 0.00 0.00 0.00 2.74
731 733 3.692593 AGAAGGAGAGAAAGTCGAGCTAC 59.307 47.826 0.00 0.00 0.00 3.58
732 734 3.958018 AGAAGGAGAGAAAGTCGAGCTA 58.042 45.455 0.00 0.00 0.00 3.32
733 735 2.802719 AGAAGGAGAGAAAGTCGAGCT 58.197 47.619 0.00 0.00 0.00 4.09
734 736 4.705337 TTAGAAGGAGAGAAAGTCGAGC 57.295 45.455 0.00 0.00 0.00 5.03
735 737 6.443934 TGATTAGAAGGAGAGAAAGTCGAG 57.556 41.667 0.00 0.00 0.00 4.04
736 738 6.835819 TTGATTAGAAGGAGAGAAAGTCGA 57.164 37.500 0.00 0.00 0.00 4.20
737 739 7.261325 TCATTGATTAGAAGGAGAGAAAGTCG 58.739 38.462 0.00 0.00 0.00 4.18
738 740 9.612066 ATTCATTGATTAGAAGGAGAGAAAGTC 57.388 33.333 0.00 0.00 0.00 3.01
739 741 9.972106 AATTCATTGATTAGAAGGAGAGAAAGT 57.028 29.630 0.00 0.00 0.00 2.66
742 744 9.182214 CCAAATTCATTGATTAGAAGGAGAGAA 57.818 33.333 0.00 0.00 41.85 2.87
743 745 8.331740 ACCAAATTCATTGATTAGAAGGAGAGA 58.668 33.333 0.00 0.00 41.85 3.10
744 746 8.517062 ACCAAATTCATTGATTAGAAGGAGAG 57.483 34.615 0.00 0.00 41.85 3.20
745 747 9.618890 CTACCAAATTCATTGATTAGAAGGAGA 57.381 33.333 0.00 0.00 41.85 3.71
746 748 9.618890 TCTACCAAATTCATTGATTAGAAGGAG 57.381 33.333 0.00 0.00 41.85 3.69
747 749 9.973661 TTCTACCAAATTCATTGATTAGAAGGA 57.026 29.630 0.00 0.00 41.85 3.36
755 757 9.807649 GTAGCATTTTCTACCAAATTCATTGAT 57.192 29.630 0.00 0.00 39.07 2.57
768 770 8.810652 TTTTGAATGTTGGTAGCATTTTCTAC 57.189 30.769 0.00 0.00 36.77 2.59
800 802 9.601810 GGGGATAATTTAAGATTACAAGGGATT 57.398 33.333 0.00 0.00 0.00 3.01
801 803 8.970813 AGGGGATAATTTAAGATTACAAGGGAT 58.029 33.333 0.00 0.00 0.00 3.85
802 804 8.358082 AGGGGATAATTTAAGATTACAAGGGA 57.642 34.615 0.00 0.00 0.00 4.20
803 805 7.670140 GGAGGGGATAATTTAAGATTACAAGGG 59.330 40.741 0.00 0.00 0.00 3.95
804 806 8.448816 AGGAGGGGATAATTTAAGATTACAAGG 58.551 37.037 0.00 0.00 0.00 3.61
805 807 9.289782 CAGGAGGGGATAATTTAAGATTACAAG 57.710 37.037 0.00 0.00 0.00 3.16
806 808 7.724061 GCAGGAGGGGATAATTTAAGATTACAA 59.276 37.037 0.00 0.00 0.00 2.41
807 809 7.231467 GCAGGAGGGGATAATTTAAGATTACA 58.769 38.462 0.00 0.00 0.00 2.41
808 810 6.659668 GGCAGGAGGGGATAATTTAAGATTAC 59.340 42.308 0.00 0.00 0.00 1.89
809 811 6.334237 TGGCAGGAGGGGATAATTTAAGATTA 59.666 38.462 0.00 0.00 0.00 1.75
810 812 5.136048 TGGCAGGAGGGGATAATTTAAGATT 59.864 40.000 0.00 0.00 0.00 2.40
811 813 4.669768 TGGCAGGAGGGGATAATTTAAGAT 59.330 41.667 0.00 0.00 0.00 2.40
812 814 4.051478 TGGCAGGAGGGGATAATTTAAGA 58.949 43.478 0.00 0.00 0.00 2.10
813 815 4.453480 TGGCAGGAGGGGATAATTTAAG 57.547 45.455 0.00 0.00 0.00 1.85
814 816 4.890499 TTGGCAGGAGGGGATAATTTAA 57.110 40.909 0.00 0.00 0.00 1.52
815 817 4.017037 TGTTTGGCAGGAGGGGATAATTTA 60.017 41.667 0.00 0.00 0.00 1.40
816 818 3.245948 TGTTTGGCAGGAGGGGATAATTT 60.246 43.478 0.00 0.00 0.00 1.82
817 819 2.314549 TGTTTGGCAGGAGGGGATAATT 59.685 45.455 0.00 0.00 0.00 1.40
818 820 1.929494 TGTTTGGCAGGAGGGGATAAT 59.071 47.619 0.00 0.00 0.00 1.28
819 821 1.377690 TGTTTGGCAGGAGGGGATAA 58.622 50.000 0.00 0.00 0.00 1.75
820 822 1.284785 CTTGTTTGGCAGGAGGGGATA 59.715 52.381 0.00 0.00 0.00 2.59
821 823 0.040204 CTTGTTTGGCAGGAGGGGAT 59.960 55.000 0.00 0.00 0.00 3.85
822 824 1.460255 CTTGTTTGGCAGGAGGGGA 59.540 57.895 0.00 0.00 0.00 4.81
823 825 1.607467 CCTTGTTTGGCAGGAGGGG 60.607 63.158 0.00 0.00 0.00 4.79
824 826 4.102113 CCTTGTTTGGCAGGAGGG 57.898 61.111 0.00 0.00 0.00 4.30
832 834 2.275380 CCCCTTCGGCCTTGTTTGG 61.275 63.158 0.00 0.00 0.00 3.28
833 835 2.275380 CCCCCTTCGGCCTTGTTTG 61.275 63.158 0.00 0.00 0.00 2.93
834 836 2.117423 CCCCCTTCGGCCTTGTTT 59.883 61.111 0.00 0.00 0.00 2.83
835 837 4.678743 GCCCCCTTCGGCCTTGTT 62.679 66.667 0.00 0.00 43.66 2.83
866 868 0.808847 CGCTTTTACCGGGAGCTACC 60.809 60.000 4.23 4.23 34.33 3.18
867 869 0.174162 TCGCTTTTACCGGGAGCTAC 59.826 55.000 6.32 0.00 34.33 3.58
868 870 0.174162 GTCGCTTTTACCGGGAGCTA 59.826 55.000 6.32 0.00 34.33 3.32
869 871 1.079336 GTCGCTTTTACCGGGAGCT 60.079 57.895 6.32 0.00 34.33 4.09
870 872 2.450345 CGTCGCTTTTACCGGGAGC 61.450 63.158 6.32 8.87 0.00 4.70
871 873 1.808390 CCGTCGCTTTTACCGGGAG 60.808 63.158 6.32 0.00 36.84 4.30
872 874 2.262292 CCGTCGCTTTTACCGGGA 59.738 61.111 6.32 0.00 36.84 5.14
874 876 1.149964 GATCCCGTCGCTTTTACCGG 61.150 60.000 0.00 0.00 40.12 5.28
875 877 0.179119 AGATCCCGTCGCTTTTACCG 60.179 55.000 0.00 0.00 0.00 4.02
876 878 1.136500 AGAGATCCCGTCGCTTTTACC 59.864 52.381 0.00 0.00 32.63 2.85
877 879 2.194271 CAGAGATCCCGTCGCTTTTAC 58.806 52.381 0.00 0.00 34.49 2.01
878 880 1.470979 GCAGAGATCCCGTCGCTTTTA 60.471 52.381 0.00 0.00 34.49 1.52
883 885 1.590259 GAAGCAGAGATCCCGTCGC 60.590 63.158 0.00 0.00 0.00 5.19
963 970 2.965716 CTAGCCAGGCGAATTGGGGG 62.966 65.000 5.55 0.00 36.19 5.40
964 971 1.526917 CTAGCCAGGCGAATTGGGG 60.527 63.158 5.55 0.00 36.19 4.96
1102 1109 2.204090 GGTGGGGAGAAGGGGTGA 60.204 66.667 0.00 0.00 0.00 4.02
1518 1525 4.813235 GGCGGCTATGGGGCAACA 62.813 66.667 0.00 0.00 40.90 3.33
1795 1802 4.893524 TCTTCGTCCTGCTTTATATCTCCA 59.106 41.667 0.00 0.00 0.00 3.86
2276 2289 7.145932 AGTGAACATAATTAGTTGCTTCCAC 57.854 36.000 5.41 0.00 0.00 4.02
2382 2395 0.321996 AACGAAGAGCAACCTCCTCC 59.678 55.000 0.00 0.00 38.96 4.30
2678 2840 3.557185 CACACATCCATCTCAACATACGG 59.443 47.826 0.00 0.00 0.00 4.02
2709 2871 0.323999 TTCCGGACTCGATCCTTCCA 60.324 55.000 1.83 0.00 46.69 3.53
2741 2903 1.068741 GGTGCTACCCCAACTCTATCG 59.931 57.143 0.00 0.00 30.04 2.92
3206 3508 0.390492 GGTCCGTTTAGTATCCCGGG 59.610 60.000 16.85 16.85 40.78 5.73
3305 3607 4.616802 CACGACCATGCATAACAAAGAAAC 59.383 41.667 0.00 0.00 0.00 2.78
3462 3764 5.388994 GCAAAAACACAAAACAGTTAACGCT 60.389 36.000 0.00 0.00 0.00 5.07
4143 4454 6.433847 TGGAGTCTGGAAAAAGAGAACATA 57.566 37.500 0.00 0.00 0.00 2.29
4335 4646 6.870965 TGCCACAATGGTGTAATAAAACATTC 59.129 34.615 0.00 0.00 43.71 2.67
4602 4915 1.134610 GCCAGAAAATGCAATGAGGGG 60.135 52.381 0.00 0.00 0.00 4.79
4835 5148 6.456795 AAGCTTGGAAATAGCATTTACCTC 57.543 37.500 0.00 0.00 41.11 3.85
5116 5429 2.441001 CTCCAAGATATCTGGCCTGGTT 59.559 50.000 17.10 0.67 0.00 3.67
5135 5448 6.183360 GCCATTCTTGTCTTTTACCTCATCTC 60.183 42.308 0.00 0.00 0.00 2.75
5315 5628 3.632145 AGAAGTGTCATGAAGCCGTTTTT 59.368 39.130 0.00 0.00 0.00 1.94
5333 5647 7.832503 AAAATTTTGTCTGACACCAAAGAAG 57.167 32.000 10.56 0.00 32.61 2.85
5415 5729 8.486210 AGAATATTGGTAGAGTAATGCTGTGAA 58.514 33.333 0.00 0.00 0.00 3.18
5658 6010 9.606631 AAAATAAGGCATGTGTTTCTACAAAAA 57.393 25.926 0.00 0.00 35.69 1.94
5732 6084 4.456280 TTATACCTATGATGCGCCTCTG 57.544 45.455 13.93 4.47 0.00 3.35
5811 6166 2.026262 GCATTTGGTACTCCAGGGAAGA 60.026 50.000 0.00 0.00 45.22 2.87
5870 6225 3.614092 TCTTAAGGCTTGATCCTTGCAG 58.386 45.455 10.69 2.26 45.51 4.41
5920 6283 0.035152 TCTGCGCCAAGAACATCCAT 60.035 50.000 4.18 0.00 0.00 3.41
5947 6310 2.872842 GCAACACCCTTTCCGTTAGCTA 60.873 50.000 0.00 0.00 0.00 3.32
5948 6311 1.892209 CAACACCCTTTCCGTTAGCT 58.108 50.000 0.00 0.00 0.00 3.32
5952 6315 1.134936 GTTTGCAACACCCTTTCCGTT 60.135 47.619 0.00 0.00 0.00 4.44
6013 6376 2.634940 CCCTCCTTTCAACTCTCAGTGA 59.365 50.000 0.00 0.00 0.00 3.41
6148 6523 0.872388 AAGAGCGGTTTTTACAGCGG 59.128 50.000 0.00 0.00 38.12 5.52
6160 6535 5.453903 CCTCCATCCCATAATATAAGAGCGG 60.454 48.000 0.00 0.00 0.00 5.52
6161 6536 5.453903 CCCTCCATCCCATAATATAAGAGCG 60.454 48.000 0.00 0.00 0.00 5.03
6179 6554 7.233962 TCGTGCTAAAATTATATACTCCCTCCA 59.766 37.037 0.00 0.00 0.00 3.86
6252 6657 6.034256 GGAAAAGAATGAGTTGATTTGCATCG 59.966 38.462 0.00 0.00 31.08 3.84
6322 8589 6.709018 AAGTAACACCATTTTTGTACTGCT 57.291 33.333 0.00 0.00 0.00 4.24
6363 8630 6.041523 ACTTGTTACACCCACATAAGCATTTT 59.958 34.615 0.00 0.00 0.00 1.82
6416 8683 2.082231 CCTCTTGAACTGCCATCACTG 58.918 52.381 0.00 0.00 0.00 3.66
6432 8699 0.610232 GAACCCACATGCTTGCCTCT 60.610 55.000 0.00 0.00 0.00 3.69
6511 8778 1.065436 GACCGCGCCCTTCTACTAC 59.935 63.158 0.00 0.00 0.00 2.73
6524 8791 0.320421 TTGTGCCTCAAGTAGACCGC 60.320 55.000 0.00 0.00 0.00 5.68
6607 8874 8.135529 GGGCATGTTTCCTAGTGAATAAATAAC 58.864 37.037 0.00 0.00 31.67 1.89


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

AutoCloner maintained by Alex Coulton.