Multiple sequence alignment - TraesCS3D01G135900

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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 TraesCS3D01G135900 chr3D 100.000 4342 0 0 1 4342 94722597 94718256 0.000000e+00 8019.0
1 TraesCS3D01G135900 chr3D 89.182 379 30 4 3964 4342 94760788 94761155 3.060000e-126 462.0
2 TraesCS3D01G135900 chr3D 76.644 441 81 14 354 785 23214516 23214089 1.570000e-54 224.0
3 TraesCS3D01G135900 chr3D 83.544 237 27 10 1126 1356 457406359 457406129 1.220000e-50 211.0
4 TraesCS3D01G135900 chr3B 90.487 3984 268 59 1 3895 145361362 145365323 0.000000e+00 5155.0
5 TraesCS3D01G135900 chr3B 89.737 380 27 5 3964 4342 145367866 145368234 3.930000e-130 475.0
6 TraesCS3D01G135900 chr3B 80.645 279 39 12 1087 1356 605017357 605017085 7.360000e-48 202.0
7 TraesCS3D01G135900 chr3B 82.609 230 23 13 3620 3838 145367437 145367660 2.060000e-43 187.0
8 TraesCS3D01G135900 chr3A 91.314 3235 180 48 770 3913 549264718 549267942 0.000000e+00 4324.0
9 TraesCS3D01G135900 chr3A 89.489 333 25 4 4008 4340 549267953 549268275 3.120000e-111 412.0
10 TraesCS3D01G135900 chr3A 82.143 280 33 14 1087 1356 600319820 600319548 1.570000e-54 224.0
11 TraesCS3D01G135900 chr3A 96.875 32 1 0 176 207 549264689 549264720 2.000000e-03 54.7
12 TraesCS3D01G135900 chr4D 78.897 417 65 10 354 751 99207179 99207591 1.200000e-65 261.0
13 TraesCS3D01G135900 chr5D 82.333 300 43 8 474 766 371279049 371278753 7.210000e-63 252.0
14 TraesCS3D01G135900 chr5D 81.098 328 48 8 460 777 530488042 530487719 2.590000e-62 250.0
15 TraesCS3D01G135900 chr7D 84.861 251 35 3 516 766 153076076 153075829 2.590000e-62 250.0
16 TraesCS3D01G135900 chr4A 84.064 251 38 2 516 766 578768073 578767825 1.560000e-59 241.0
17 TraesCS3D01G135900 chr2B 84.127 252 36 4 516 766 683031991 683032239 1.560000e-59 241.0
18 TraesCS3D01G135900 chr4B 81.884 276 48 2 503 778 605949411 605949138 9.390000e-57 231.0
19 TraesCS3D01G135900 chr1D 77.113 284 50 15 1085 1362 72906897 72906623 2.700000e-32 150.0
20 TraesCS3D01G135900 chr1D 76.699 206 43 5 1100 1304 73054361 73054160 4.590000e-20 110.0
21 TraesCS3D01G135900 chr5A 77.953 254 40 14 1084 1329 458525106 458524861 1.260000e-30 145.0
22 TraesCS3D01G135900 chr5B 75.197 254 47 14 1084 1329 422040660 422040415 5.940000e-19 106.0
23 TraesCS3D01G135900 chr2A 100.000 35 0 0 295 329 768683133 768683099 1.010000e-06 65.8


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 TraesCS3D01G135900 chr3D 94718256 94722597 4341 True 8019.0 8019 100.000000 1 4342 1 chr3D.!!$R2 4341
1 TraesCS3D01G135900 chr3B 145361362 145368234 6872 False 1939.0 5155 87.611000 1 4342 3 chr3B.!!$F1 4341
2 TraesCS3D01G135900 chr3A 549264689 549268275 3586 False 1596.9 4324 92.559333 176 4340 3 chr3A.!!$F1 4164

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
371 374 0.036022 GTCCCTGCATAGCCTCCATC 59.964 60.0 0.00 0.00 0.00 3.51 F
428 431 0.102300 CGTGTGTATCCGCTGGATCA 59.898 55.0 12.43 8.68 42.11 2.92 F
615 625 0.314935 ACAAGTTTTGCATGGCTCCG 59.685 50.0 0.00 0.00 0.00 4.63 F
1385 1419 0.320421 CTCTCCCTTTTCGCCGTTCA 60.320 55.0 0.00 0.00 0.00 3.18 F
2565 2644 0.316937 TGCAGAAAGCTTTTCGTGCG 60.317 50.0 24.96 10.15 45.94 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1365 1399 0.037605 GAACGGCGAAAAGGGAGAGA 60.038 55.0 16.62 0.00 0.00 3.10 R
1579 1619 0.098376 GCAAGTGCAGCACTAGCATC 59.902 55.0 28.48 11.73 44.62 3.91 R
2039 2079 0.108520 TGACCGCATTTCCGACCTAC 60.109 55.0 0.00 0.00 0.00 3.18 R
2596 2675 0.471617 AGTTGAACAGACCTGCAGCT 59.528 50.0 8.66 0.00 0.00 4.24 R
4053 6670 0.100325 CGTTGGCTGCTGTTTGTCAA 59.900 50.0 0.00 0.00 0.00 3.18 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
66 67 7.615582 TCACACAAGTCATAAATCCATTCTC 57.384 36.000 0.00 0.00 0.00 2.87
111 113 5.163744 TGCTTCATCGACTAGTCTGTACTTC 60.164 44.000 20.34 6.03 37.15 3.01
112 114 5.731126 GCTTCATCGACTAGTCTGTACTTCC 60.731 48.000 20.34 0.03 37.15 3.46
115 117 4.232188 TCGACTAGTCTGTACTTCCCAT 57.768 45.455 20.34 0.00 37.15 4.00
117 119 5.748402 TCGACTAGTCTGTACTTCCCATTA 58.252 41.667 20.34 0.00 37.15 1.90
130 132 9.337396 TGTACTTCCCATTAGCTATTGTAAATG 57.663 33.333 13.19 6.33 0.00 2.32
134 136 8.677148 TTCCCATTAGCTATTGTAAATGACTC 57.323 34.615 13.19 0.00 32.29 3.36
156 158 9.880064 GACTCTTTAGCAACTTAAAAAGGTAAG 57.120 33.333 0.00 0.00 37.16 2.34
160 162 9.447040 CTTTAGCAACTTAAAAAGGTAAGTGAC 57.553 33.333 0.00 0.00 42.25 3.67
207 209 3.733443 TTTCTTCTCTTTTGGGCAAGC 57.267 42.857 0.00 0.00 0.00 4.01
209 211 0.954452 CTTCTCTTTTGGGCAAGCGT 59.046 50.000 0.00 0.00 0.00 5.07
210 212 0.667993 TTCTCTTTTGGGCAAGCGTG 59.332 50.000 0.00 0.00 0.00 5.34
233 235 0.535335 ACGGCTTATCTTTCGCCTCA 59.465 50.000 0.00 0.00 41.61 3.86
238 240 2.418746 GCTTATCTTTCGCCTCACCTCA 60.419 50.000 0.00 0.00 0.00 3.86
240 242 2.393271 ATCTTTCGCCTCACCTCAAG 57.607 50.000 0.00 0.00 0.00 3.02
241 243 0.320771 TCTTTCGCCTCACCTCAAGC 60.321 55.000 0.00 0.00 0.00 4.01
242 244 0.603707 CTTTCGCCTCACCTCAAGCA 60.604 55.000 0.00 0.00 0.00 3.91
243 245 0.179032 TTTCGCCTCACCTCAAGCAA 60.179 50.000 0.00 0.00 0.00 3.91
254 257 2.192608 CTCAAGCAAACAGGCGGCTC 62.193 60.000 9.32 0.00 36.76 4.70
267 270 2.665603 GGCTCGGGCTTCTGTCTT 59.334 61.111 7.48 0.00 38.73 3.01
275 278 1.289380 GCTTCTGTCTTCCGTCGGT 59.711 57.895 11.88 0.00 0.00 4.69
277 280 0.314302 CTTCTGTCTTCCGTCGGTGT 59.686 55.000 11.88 0.00 0.00 4.16
286 289 3.103911 CGTCGGTGTCGCCTGTTC 61.104 66.667 0.00 0.00 36.13 3.18
301 304 4.559704 CGCCTGTTCTTCTATAGCCTTAGG 60.560 50.000 0.00 0.00 0.00 2.69
303 306 4.902448 CCTGTTCTTCTATAGCCTTAGGGT 59.098 45.833 8.42 8.42 37.19 4.34
309 312 4.759793 TCTATAGCCTTAGGGTCATGGA 57.240 45.455 6.12 4.32 34.28 3.41
324 327 0.695803 ATGGAGGTGAGGTGGATCCC 60.696 60.000 9.90 0.00 36.75 3.85
326 329 1.381327 GAGGTGAGGTGGATCCCGA 60.381 63.158 9.90 0.00 36.75 5.14
328 331 2.732619 GGTGAGGTGGATCCCGACC 61.733 68.421 9.90 11.39 36.75 4.79
356 359 1.935873 GGCTCCGTTTTTATACGTCCC 59.064 52.381 0.00 0.00 39.81 4.46
363 366 4.210537 CCGTTTTTATACGTCCCTGCATAG 59.789 45.833 0.00 0.00 39.81 2.23
368 371 1.113517 TACGTCCCTGCATAGCCTCC 61.114 60.000 0.00 0.00 0.00 4.30
371 374 0.036022 GTCCCTGCATAGCCTCCATC 59.964 60.000 0.00 0.00 0.00 3.51
373 376 1.377994 CCTGCATAGCCTCCATCCC 59.622 63.158 0.00 0.00 0.00 3.85
374 377 1.004080 CTGCATAGCCTCCATCCCG 60.004 63.158 0.00 0.00 0.00 5.14
421 424 1.080366 TGTGGACGTGTGTATCCGC 60.080 57.895 0.00 0.00 44.37 5.54
428 431 0.102300 CGTGTGTATCCGCTGGATCA 59.898 55.000 12.43 8.68 42.11 2.92
433 436 1.607148 TGTATCCGCTGGATCACGTAG 59.393 52.381 12.43 0.00 42.11 3.51
444 447 2.287668 GGATCACGTAGGATTCAGTCGG 60.288 54.545 0.00 0.00 0.00 4.79
450 453 2.618053 GTAGGATTCAGTCGGTGGTTG 58.382 52.381 0.00 0.00 0.00 3.77
462 465 4.007659 GTCGGTGGTTGTCTTTAATGGAT 58.992 43.478 0.00 0.00 0.00 3.41
466 469 3.377172 GTGGTTGTCTTTAATGGATCCGG 59.623 47.826 7.39 0.00 0.00 5.14
472 475 5.183228 TGTCTTTAATGGATCCGGTCTTTC 58.817 41.667 7.39 0.00 0.00 2.62
476 479 2.604046 ATGGATCCGGTCTTTCTTCG 57.396 50.000 7.39 0.00 0.00 3.79
481 484 3.488890 GGATCCGGTCTTTCTTCGTCTAC 60.489 52.174 0.00 0.00 0.00 2.59
486 489 3.842984 CGGTCTTTCTTCGTCTACGTTAC 59.157 47.826 0.00 0.00 40.80 2.50
495 498 4.818534 TCGTCTACGTTACTGTGTCTTT 57.181 40.909 0.00 0.00 40.80 2.52
502 505 7.433425 GTCTACGTTACTGTGTCTTTAAGTTGT 59.567 37.037 0.00 0.00 0.00 3.32
503 506 6.579491 ACGTTACTGTGTCTTTAAGTTGTC 57.421 37.500 0.00 0.00 0.00 3.18
548 558 1.729149 GCGGTTGCTATTCTGTTGTGC 60.729 52.381 0.00 0.00 38.39 4.57
557 567 5.363868 TGCTATTCTGTTGTGCTAGTCCTAT 59.636 40.000 0.00 0.00 0.00 2.57
558 568 5.694006 GCTATTCTGTTGTGCTAGTCCTATG 59.306 44.000 0.00 0.00 0.00 2.23
579 589 0.714439 GGCTTTAGCACGACGACTTC 59.286 55.000 0.00 0.00 44.36 3.01
580 590 0.714439 GCTTTAGCACGACGACTTCC 59.286 55.000 0.00 0.00 41.59 3.46
583 593 1.236616 TTAGCACGACGACTTCCCGA 61.237 55.000 0.00 0.00 0.00 5.14
591 601 1.808945 GACGACTTCCCGACTGTCTAA 59.191 52.381 6.21 0.00 0.00 2.10
597 607 6.141462 CGACTTCCCGACTGTCTAATATAAC 58.859 44.000 6.21 0.00 0.00 1.89
607 617 8.440059 CGACTGTCTAATATAACAAGTTTTGCA 58.560 33.333 6.21 0.00 0.00 4.08
610 620 9.507280 CTGTCTAATATAACAAGTTTTGCATGG 57.493 33.333 0.00 0.00 0.00 3.66
613 623 8.405531 TCTAATATAACAAGTTTTGCATGGCTC 58.594 33.333 0.00 0.00 0.00 4.70
614 624 2.531522 AACAAGTTTTGCATGGCTCC 57.468 45.000 0.00 0.00 0.00 4.70
615 625 0.314935 ACAAGTTTTGCATGGCTCCG 59.685 50.000 0.00 0.00 0.00 4.63
616 626 0.597568 CAAGTTTTGCATGGCTCCGA 59.402 50.000 0.00 0.00 0.00 4.55
617 627 0.598065 AAGTTTTGCATGGCTCCGAC 59.402 50.000 0.00 0.00 0.00 4.79
620 630 0.886938 TTTTGCATGGCTCCGACGAA 60.887 50.000 0.00 0.00 0.00 3.85
637 647 2.595009 GAAGGAGGGGTGATGACGGC 62.595 65.000 0.00 0.00 0.00 5.68
644 654 3.788766 GTGATGACGGCGGTGTGC 61.789 66.667 13.24 0.00 45.38 4.57
671 681 1.168407 TCACTTGAGTGCTTGCAGCC 61.168 55.000 6.27 0.00 45.25 4.85
672 682 1.900498 ACTTGAGTGCTTGCAGCCC 60.900 57.895 0.00 0.00 41.51 5.19
675 685 3.123620 GAGTGCTTGCAGCCCTCG 61.124 66.667 0.00 0.00 41.51 4.63
680 690 2.190313 CTTGCAGCCCTCGCCATA 59.810 61.111 0.00 0.00 34.57 2.74
688 698 2.027745 CAGCCCTCGCCATATTGTCTAT 60.028 50.000 0.00 0.00 34.57 1.98
689 699 2.027745 AGCCCTCGCCATATTGTCTATG 60.028 50.000 0.00 0.00 34.57 2.23
694 704 4.323028 CCTCGCCATATTGTCTATGGATGT 60.323 45.833 14.05 0.00 45.57 3.06
695 705 5.227569 TCGCCATATTGTCTATGGATGTT 57.772 39.130 14.05 0.00 45.57 2.71
735 749 4.801891 TCTGATGTTCGTTGTACTACCAC 58.198 43.478 1.76 0.47 0.00 4.16
744 758 4.156373 TCGTTGTACTACCACGATTGATGA 59.844 41.667 10.61 0.00 0.00 2.92
745 759 5.041287 CGTTGTACTACCACGATTGATGAT 58.959 41.667 6.94 0.00 0.00 2.45
751 765 7.865889 TGTACTACCACGATTGATGATGAATAC 59.134 37.037 0.00 0.00 0.00 1.89
828 850 1.044231 TGGCCCATGGACAATGATGC 61.044 55.000 15.22 4.92 38.06 3.91
831 853 1.361271 CCATGGACAATGATGCGCC 59.639 57.895 5.56 0.00 38.72 6.53
841 866 1.490693 ATGATGCGCCGACGAATGAC 61.491 55.000 4.18 0.00 37.81 3.06
1191 1225 1.142748 CGCCCTCTTCTACTGGCTG 59.857 63.158 0.00 0.00 41.80 4.85
1198 1232 1.178276 CTTCTACTGGCTGGTCGAGT 58.822 55.000 0.00 0.00 37.51 4.18
1361 1395 4.243270 CCGTACTCCTGGAACAAAAGTAG 58.757 47.826 0.00 0.00 38.70 2.57
1365 1399 6.649557 CGTACTCCTGGAACAAAAGTAGATTT 59.350 38.462 0.00 0.00 38.70 2.17
1371 1405 6.372937 CCTGGAACAAAAGTAGATTTCTCTCC 59.627 42.308 0.00 0.00 38.70 3.71
1373 1407 6.044404 TGGAACAAAAGTAGATTTCTCTCCCT 59.956 38.462 0.00 0.00 31.92 4.20
1385 1419 0.320421 CTCTCCCTTTTCGCCGTTCA 60.320 55.000 0.00 0.00 0.00 3.18
1579 1619 3.957497 AGATCAGACTACCTACTTGCCTG 59.043 47.826 0.00 0.00 0.00 4.85
1693 1733 1.075601 ATTGGCTGGAGAGGTTTCCA 58.924 50.000 0.00 0.00 44.84 3.53
1811 1851 9.494271 TCTGAATTTAGCAGGAATCATATGTAC 57.506 33.333 1.90 0.00 34.20 2.90
1901 1941 4.021104 CACTATGTCCCTCAGTTGTCTCAA 60.021 45.833 0.00 0.00 0.00 3.02
1904 1944 2.103094 TGTCCCTCAGTTGTCTCAACTG 59.897 50.000 26.65 26.65 46.67 3.16
2039 2079 9.987272 TCTTGTTCTTACATATGGTCTGATATG 57.013 33.333 7.80 0.00 40.69 1.78
2108 2148 0.963856 TCGAGTACTGGTGGACGCAT 60.964 55.000 0.00 0.00 0.00 4.73
2159 2199 2.804212 GCTGCAGTTGGCTTGTGAATTT 60.804 45.455 16.64 0.00 45.15 1.82
2357 2402 7.411486 AGTTCTGCTGATAACTAAGCTAAGA 57.589 36.000 0.00 0.00 40.21 2.10
2358 2403 7.262048 AGTTCTGCTGATAACTAAGCTAAGAC 58.738 38.462 0.00 0.00 40.21 3.01
2371 2416 4.974368 AGCTAAGACTACTGTAGCAGTG 57.026 45.455 14.55 3.49 45.01 3.66
2403 2482 3.775202 ACTATGCAGCTGTTTAGACTCG 58.225 45.455 23.49 6.10 0.00 4.18
2407 2486 1.989165 GCAGCTGTTTAGACTCGTCTG 59.011 52.381 16.64 0.00 40.71 3.51
2408 2487 2.351835 GCAGCTGTTTAGACTCGTCTGA 60.352 50.000 16.64 0.00 40.71 3.27
2416 2495 5.477291 TGTTTAGACTCGTCTGAGATTCCTT 59.523 40.000 9.73 0.00 45.57 3.36
2432 2511 9.177608 TGAGATTCCTTTGGAACATAATAACAG 57.822 33.333 0.71 0.00 45.07 3.16
2450 2529 2.644798 ACAGTTCCTATGTTGCCTCCTT 59.355 45.455 0.00 0.00 0.00 3.36
2452 2531 4.475016 ACAGTTCCTATGTTGCCTCCTTAT 59.525 41.667 0.00 0.00 0.00 1.73
2454 2533 6.183361 ACAGTTCCTATGTTGCCTCCTTATAG 60.183 42.308 0.00 0.00 0.00 1.31
2461 2540 9.220767 CCTATGTTGCCTCCTTATAGTATTTTC 57.779 37.037 0.00 0.00 0.00 2.29
2565 2644 0.316937 TGCAGAAAGCTTTTCGTGCG 60.317 50.000 24.96 10.15 45.94 5.34
2595 2674 1.692519 GGAATACCGTATGCCTGGACT 59.307 52.381 8.22 0.00 30.53 3.85
2596 2675 2.895404 GGAATACCGTATGCCTGGACTA 59.105 50.000 8.22 0.00 30.53 2.59
2649 2728 6.578020 TGTTTTACTCACAACTAGTTCACG 57.422 37.500 4.77 0.00 0.00 4.35
2653 2732 2.691526 ACTCACAACTAGTTCACGGTGA 59.308 45.455 19.61 19.61 34.46 4.02
2669 2748 2.615493 CGGTGACTGACCATAAAGCCTT 60.615 50.000 0.00 0.00 46.55 4.35
2681 2760 7.615365 TGACCATAAAGCCTTCTTGTTAATGAT 59.385 33.333 0.00 0.00 31.78 2.45
2689 2768 5.739161 GCCTTCTTGTTAATGATAGTTTGCG 59.261 40.000 0.00 0.00 0.00 4.85
2769 2848 3.785887 AGGTCCATGCTTCCTATTTACCA 59.214 43.478 0.00 0.00 0.00 3.25
2773 2852 5.471456 GTCCATGCTTCCTATTTACCATGAG 59.529 44.000 0.00 0.00 33.71 2.90
2812 2891 7.398024 GCATAAGAATATGGGTCTTCAGGTAT 58.602 38.462 0.00 0.00 39.49 2.73
2813 2892 7.335422 GCATAAGAATATGGGTCTTCAGGTATG 59.665 40.741 0.00 0.00 39.49 2.39
2824 2903 6.461509 GGGTCTTCAGGTATGCCAAATTTATG 60.462 42.308 1.54 0.00 37.19 1.90
2850 2929 8.408043 TTGAAAACATGATTTACACAGGATCT 57.592 30.769 0.00 0.00 0.00 2.75
2926 3007 3.181478 GCTCACAGTATTAAGTAGCCCGT 60.181 47.826 0.00 0.00 0.00 5.28
2929 3010 5.439721 TCACAGTATTAAGTAGCCCGTCTA 58.560 41.667 0.00 0.00 0.00 2.59
2937 3019 1.005687 AGTAGCCCGTCTACCTTCTGT 59.994 52.381 8.05 0.00 46.98 3.41
2994 3077 1.612463 GATGCCGATTCCGTAGTACCT 59.388 52.381 0.00 0.00 0.00 3.08
3039 3122 4.521130 TGATGCACTATATCTTCCGACC 57.479 45.455 0.00 0.00 0.00 4.79
3098 3181 8.921205 AGAGGTTAGTCAGAAACAGTACTAAAA 58.079 33.333 0.00 0.00 36.48 1.52
3105 3188 7.822822 AGTCAGAAACAGTACTAAAACAACACT 59.177 33.333 0.00 0.00 0.00 3.55
3107 3190 7.065324 TCAGAAACAGTACTAAAACAACACTGG 59.935 37.037 0.00 0.00 40.69 4.00
3122 3206 3.844640 ACACTGGCAGTTTTATTCCCTT 58.155 40.909 19.43 0.00 0.00 3.95
3127 3211 5.543790 ACTGGCAGTTTTATTCCCTTTTCAT 59.456 36.000 15.88 0.00 0.00 2.57
3150 3234 9.287373 TCATTTTGCTACATATATGCTCATCAA 57.713 29.630 12.79 7.34 0.00 2.57
3151 3235 9.902196 CATTTTGCTACATATATGCTCATCAAA 57.098 29.630 12.79 12.07 0.00 2.69
3165 3249 4.697352 GCTCATCAAACTCTAATGGTGTGT 59.303 41.667 0.00 0.00 0.00 3.72
3206 3290 0.313987 GGTGCCAAGTGTACAAAGGC 59.686 55.000 21.36 21.36 45.41 4.35
3329 3413 0.315568 CTCGGCCTGTACCTAGCATC 59.684 60.000 0.00 0.00 0.00 3.91
3335 3419 1.338337 CCTGTACCTAGCATCCAGTCG 59.662 57.143 0.00 0.00 0.00 4.18
3347 3431 6.183309 AGCATCCAGTCGTTTTAGAATTTC 57.817 37.500 0.00 0.00 0.00 2.17
3373 3457 4.949856 TCCACTTAAAATGGAAGATCAGCC 59.050 41.667 5.78 0.00 43.43 4.85
3402 3486 5.772521 AGCCATGTTGTACAATTTCAAGTC 58.227 37.500 12.26 0.00 0.00 3.01
3406 3490 3.003897 TGTTGTACAATTTCAAGTCCGGC 59.996 43.478 12.26 0.00 0.00 6.13
3408 3492 4.274602 TGTACAATTTCAAGTCCGGCTA 57.725 40.909 0.00 0.00 0.00 3.93
3412 3496 2.403252 ATTTCAAGTCCGGCTACCAG 57.597 50.000 0.00 0.00 0.00 4.00
3425 3509 3.372206 CGGCTACCAGATTTTCAGTTGAG 59.628 47.826 0.00 0.00 0.00 3.02
3433 3517 6.091437 CCAGATTTTCAGTTGAGCAGATTTC 58.909 40.000 0.00 0.00 0.00 2.17
3450 3534 6.034591 CAGATTTCCTCTGTTCATTTGATGC 58.965 40.000 0.00 0.00 45.42 3.91
3453 3537 2.027285 TCCTCTGTTCATTTGATGCCGA 60.027 45.455 0.00 0.00 0.00 5.54
3463 3547 5.584442 TCATTTGATGCCGATTGAGAAATG 58.416 37.500 0.00 0.00 32.88 2.32
3507 3591 6.098266 AGTGGGACAATTAGAGCTTTGTTTTT 59.902 34.615 3.15 0.00 44.16 1.94
3529 3613 1.815003 GTTTTCATGAGCTCTGGGGTG 59.185 52.381 16.19 6.32 0.00 4.61
3530 3614 0.329261 TTTCATGAGCTCTGGGGTGG 59.671 55.000 16.19 0.00 0.00 4.61
3600 3684 8.511321 GTGACCATGTCATTGTTATCTGTTAAA 58.489 33.333 0.00 0.00 44.63 1.52
3602 3686 7.526608 ACCATGTCATTGTTATCTGTTAAACG 58.473 34.615 0.00 0.00 0.00 3.60
3615 3706 5.849510 TCTGTTAAACGACTCCTTGATCAA 58.150 37.500 8.12 8.12 0.00 2.57
3639 3732 5.013599 AGTTAGGCTTGAATTCTCCTTGACT 59.986 40.000 15.95 15.91 0.00 3.41
3658 3751 2.303890 ACTCTGTTGCTGACATGATCCA 59.696 45.455 0.00 0.00 37.69 3.41
3663 3756 3.692593 TGTTGCTGACATGATCCAATCAG 59.307 43.478 0.00 11.12 43.53 2.90
3665 3758 4.758773 TGCTGACATGATCCAATCAGTA 57.241 40.909 14.96 10.06 43.53 2.74
3669 3779 5.355071 GCTGACATGATCCAATCAGTAAACA 59.645 40.000 14.96 0.00 43.53 2.83
3684 3794 9.893305 AATCAGTAAACATGTTAAGCTTGTAAC 57.107 29.630 12.39 7.21 34.84 2.50
3752 3863 1.813786 AGTTGTCCTCTGTAGCGACTC 59.186 52.381 0.00 0.00 0.00 3.36
3767 3878 8.723777 TGTAGCGACTCGTATTTAGATAAATG 57.276 34.615 7.87 0.00 36.62 2.32
3771 3882 9.740239 AGCGACTCGTATTTAGATAAATGTTAA 57.260 29.630 7.87 0.00 36.62 2.01
3794 3905 7.597288 AAGAGTAATTTTTGGTAAGCTTGGT 57.403 32.000 9.86 0.00 0.00 3.67
3809 3920 9.169592 GGTAAGCTTGGTATATGTTACAGAAAA 57.830 33.333 9.86 0.00 0.00 2.29
3870 3984 9.490379 CTTTTTGTAGTCAGATAACCAGTACTT 57.510 33.333 0.00 0.00 0.00 2.24
3873 3987 9.524496 TTTGTAGTCAGATAACCAGTACTTAGA 57.476 33.333 0.00 0.00 0.00 2.10
3904 6521 3.760684 GCAACCAAGGAAAGTGATCTCAT 59.239 43.478 0.00 0.00 0.00 2.90
3940 6557 8.000285 GTGCAACTTCTTGAAGACATAATTTG 58.000 34.615 16.21 9.44 0.00 2.32
3941 6558 6.642131 TGCAACTTCTTGAAGACATAATTTGC 59.358 34.615 16.21 17.13 37.80 3.68
3942 6559 6.642131 GCAACTTCTTGAAGACATAATTTGCA 59.358 34.615 16.21 0.00 37.57 4.08
3943 6560 7.169645 GCAACTTCTTGAAGACATAATTTGCAA 59.830 33.333 16.21 0.00 37.57 4.08
3944 6561 9.033481 CAACTTCTTGAAGACATAATTTGCAAA 57.967 29.630 15.44 15.44 0.00 3.68
3945 6562 9.598517 AACTTCTTGAAGACATAATTTGCAAAA 57.401 25.926 17.19 0.11 0.00 2.44
3946 6563 9.768662 ACTTCTTGAAGACATAATTTGCAAAAT 57.231 25.926 17.19 10.81 0.00 1.82
3984 6601 8.514594 TGACCACATAAAATTCATTCAGAACTC 58.485 33.333 0.00 0.00 39.49 3.01
4038 6655 4.277672 CCCATGCATCAAACTGATCTTAGG 59.722 45.833 0.00 0.00 34.28 2.69
4040 6657 3.889815 TGCATCAAACTGATCTTAGGGG 58.110 45.455 0.00 0.00 34.28 4.79
4041 6658 3.217626 GCATCAAACTGATCTTAGGGGG 58.782 50.000 0.00 0.00 34.28 5.40
4063 6680 1.537202 GCTAGGGCAGTTGACAAACAG 59.463 52.381 0.00 0.00 38.88 3.16
4099 6716 2.685897 TGGTAACAGAACACAACCAAGC 59.314 45.455 0.00 0.00 46.17 4.01
4167 6784 0.679002 CTTCCACTGCCCACCATCAG 60.679 60.000 0.00 0.00 36.45 2.90
4174 6791 0.994247 TGCCCACCATCAGACTCAAT 59.006 50.000 0.00 0.00 0.00 2.57
4205 6822 1.918467 CTGCCTCTCCATTCTGCCCA 61.918 60.000 0.00 0.00 0.00 5.36
4246 6863 1.673665 CCTTGACCTGCAGCCACTC 60.674 63.158 8.66 0.03 0.00 3.51
4264 6881 3.415087 CCCCCTGGGCTTCTCCTG 61.415 72.222 7.39 0.00 35.35 3.86
4292 6909 1.364626 CCTTGTGCTGCTGGATCGTC 61.365 60.000 0.00 0.00 0.00 4.20
4315 6932 2.754375 GGGGAACTTGAGCCGGAA 59.246 61.111 5.05 0.00 0.00 4.30
4334 6951 4.651008 TTCACCGGCGTCGACCAC 62.651 66.667 12.93 1.93 39.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 8.408043 AGAATGGATTTATGACTTGTGTGAAA 57.592 30.769 0.00 0.00 0.00 2.69
66 67 8.822652 AAGCAGTCCTTAATTTCATTTTCTTG 57.177 30.769 0.00 0.00 30.18 3.02
111 113 8.682936 AAGAGTCATTTACAATAGCTAATGGG 57.317 34.615 13.30 0.00 0.00 4.00
115 117 9.884636 TGCTAAAGAGTCATTTACAATAGCTAA 57.115 29.630 0.00 0.00 0.00 3.09
117 119 8.669243 GTTGCTAAAGAGTCATTTACAATAGCT 58.331 33.333 0.00 0.00 0.00 3.32
130 132 9.880064 CTTACCTTTTTAAGTTGCTAAAGAGTC 57.120 33.333 0.00 0.00 30.97 3.36
134 136 9.447040 GTCACTTACCTTTTTAAGTTGCTAAAG 57.553 33.333 0.00 0.00 39.77 1.85
210 212 0.301987 GCGAAAGATAAGCCGTGAGC 59.698 55.000 0.00 0.00 44.25 4.26
233 235 1.898574 CCGCCTGTTTGCTTGAGGT 60.899 57.895 0.00 0.00 0.00 3.85
238 240 3.357079 CGAGCCGCCTGTTTGCTT 61.357 61.111 0.00 0.00 34.99 3.91
254 257 1.446272 GACGGAAGACAGAAGCCCG 60.446 63.158 0.00 0.00 45.09 6.13
275 278 2.100916 GGCTATAGAAGAACAGGCGACA 59.899 50.000 3.21 0.00 0.00 4.35
277 280 2.667470 AGGCTATAGAAGAACAGGCGA 58.333 47.619 3.21 0.00 38.51 5.54
286 289 5.087323 TCCATGACCCTAAGGCTATAGAAG 58.913 45.833 3.21 0.00 36.11 2.85
301 304 0.909610 TCCACCTCACCTCCATGACC 60.910 60.000 0.00 0.00 0.00 4.02
303 306 1.500474 GATCCACCTCACCTCCATGA 58.500 55.000 0.00 0.00 0.00 3.07
309 312 1.686110 GTCGGGATCCACCTCACCT 60.686 63.158 15.23 0.00 38.98 4.00
324 327 3.217743 GGAGCCCTCCTACGGTCG 61.218 72.222 7.08 0.00 46.16 4.79
349 352 1.113517 GGAGGCTATGCAGGGACGTA 61.114 60.000 0.00 0.00 0.00 3.57
351 354 1.762522 ATGGAGGCTATGCAGGGACG 61.763 60.000 0.00 0.00 30.11 4.79
356 359 1.004080 CGGGATGGAGGCTATGCAG 60.004 63.158 0.00 0.00 30.11 4.41
368 371 0.250038 CTAGATGCACCACCGGGATG 60.250 60.000 6.32 1.28 38.05 3.51
371 374 2.203070 GCTAGATGCACCACCGGG 60.203 66.667 6.32 0.00 42.31 5.73
392 395 2.351276 GTCCACACGCCCTTGGAT 59.649 61.111 0.00 0.00 43.85 3.41
414 417 1.068472 CCTACGTGATCCAGCGGATAC 60.068 57.143 9.60 7.97 43.27 2.24
415 418 1.202842 TCCTACGTGATCCAGCGGATA 60.203 52.381 9.60 0.00 43.27 2.59
421 424 3.549019 CGACTGAATCCTACGTGATCCAG 60.549 52.174 0.00 0.00 0.00 3.86
428 431 0.815734 CCACCGACTGAATCCTACGT 59.184 55.000 0.00 0.00 0.00 3.57
433 436 1.002087 AGACAACCACCGACTGAATCC 59.998 52.381 0.00 0.00 0.00 3.01
440 443 3.404899 TCCATTAAAGACAACCACCGAC 58.595 45.455 0.00 0.00 0.00 4.79
444 447 3.377172 CCGGATCCATTAAAGACAACCAC 59.623 47.826 13.41 0.00 0.00 4.16
450 453 5.429130 AGAAAGACCGGATCCATTAAAGAC 58.571 41.667 9.46 0.00 0.00 3.01
462 465 1.466167 CGTAGACGAAGAAAGACCGGA 59.534 52.381 9.46 0.00 43.02 5.14
466 469 5.339085 CACAGTAACGTAGACGAAGAAAGAC 59.661 44.000 9.41 0.00 43.02 3.01
472 475 4.401525 AGACACAGTAACGTAGACGAAG 57.598 45.455 9.41 0.00 43.02 3.79
476 479 7.433425 ACAACTTAAAGACACAGTAACGTAGAC 59.567 37.037 0.00 0.00 0.00 2.59
481 484 5.456497 TCGACAACTTAAAGACACAGTAACG 59.544 40.000 0.00 0.00 0.00 3.18
486 489 9.011407 GTATAGATCGACAACTTAAAGACACAG 57.989 37.037 0.00 0.00 0.00 3.66
502 505 6.150318 GCCGATGAAGAAAAGTATAGATCGA 58.850 40.000 0.00 0.00 34.75 3.59
503 506 5.059832 CGCCGATGAAGAAAAGTATAGATCG 59.940 44.000 0.00 0.00 33.06 3.69
535 545 6.219473 CCATAGGACTAGCACAACAGAATAG 58.781 44.000 0.00 0.00 0.00 1.73
548 558 2.972713 TGCTAAAGCCCCATAGGACTAG 59.027 50.000 0.00 0.00 41.18 2.57
557 567 2.047655 CGTCGTGCTAAAGCCCCA 60.048 61.111 0.00 0.00 41.18 4.96
558 568 2.098831 GTCGTCGTGCTAAAGCCCC 61.099 63.158 0.00 0.00 41.18 5.80
563 573 0.387622 CGGGAAGTCGTCGTGCTAAA 60.388 55.000 0.00 0.00 0.00 1.85
573 583 4.832590 ATATTAGACAGTCGGGAAGTCG 57.167 45.455 0.00 0.00 37.36 4.18
579 589 8.388103 CAAAACTTGTTATATTAGACAGTCGGG 58.612 37.037 0.00 0.00 0.00 5.14
580 590 7.903431 GCAAAACTTGTTATATTAGACAGTCGG 59.097 37.037 0.00 0.00 0.00 4.79
591 601 5.450412 CGGAGCCATGCAAAACTTGTTATAT 60.450 40.000 0.00 0.00 0.00 0.86
597 607 0.597568 TCGGAGCCATGCAAAACTTG 59.402 50.000 0.00 0.00 0.00 3.16
607 617 3.211288 CTCCTTCGTCGGAGCCAT 58.789 61.111 9.24 0.00 43.69 4.40
613 623 2.058595 ATCACCCCTCCTTCGTCGG 61.059 63.158 0.00 0.00 0.00 4.79
614 624 1.141881 CATCACCCCTCCTTCGTCG 59.858 63.158 0.00 0.00 0.00 5.12
615 625 0.175989 GTCATCACCCCTCCTTCGTC 59.824 60.000 0.00 0.00 0.00 4.20
616 626 1.605058 CGTCATCACCCCTCCTTCGT 61.605 60.000 0.00 0.00 0.00 3.85
617 627 1.141881 CGTCATCACCCCTCCTTCG 59.858 63.158 0.00 0.00 0.00 3.79
620 630 3.083997 GCCGTCATCACCCCTCCT 61.084 66.667 0.00 0.00 0.00 3.69
671 681 3.961480 TCCATAGACAATATGGCGAGG 57.039 47.619 8.72 0.00 43.12 4.63
672 682 4.825422 ACATCCATAGACAATATGGCGAG 58.175 43.478 8.72 4.48 43.12 5.03
675 685 8.340618 ACATTAACATCCATAGACAATATGGC 57.659 34.615 8.72 0.00 43.12 4.40
708 722 8.089597 TGGTAGTACAACGAACATCAGAAATAA 58.910 33.333 2.06 0.00 0.00 1.40
714 728 3.606777 CGTGGTAGTACAACGAACATCAG 59.393 47.826 23.22 0.00 0.00 2.90
716 730 3.825308 TCGTGGTAGTACAACGAACATC 58.175 45.455 26.80 0.00 0.00 3.06
717 731 3.921119 TCGTGGTAGTACAACGAACAT 57.079 42.857 26.80 0.00 0.00 2.71
722 736 4.417506 TCATCAATCGTGGTAGTACAACG 58.582 43.478 21.91 21.91 0.00 4.10
731 745 8.096414 TCATATGTATTCATCATCAATCGTGGT 58.904 33.333 1.90 0.00 35.70 4.16
732 746 8.483307 TCATATGTATTCATCATCAATCGTGG 57.517 34.615 1.90 0.00 35.70 4.94
765 779 9.912634 CACCAGCAATAGAGATTTTTCTTTTTA 57.087 29.630 0.00 0.00 0.00 1.52
767 781 7.233348 TCCACCAGCAATAGAGATTTTTCTTTT 59.767 33.333 0.00 0.00 0.00 2.27
770 784 5.819991 TCCACCAGCAATAGAGATTTTTCT 58.180 37.500 0.00 0.00 0.00 2.52
771 785 6.515272 TTCCACCAGCAATAGAGATTTTTC 57.485 37.500 0.00 0.00 0.00 2.29
828 850 3.902063 CTGCGTCATTCGTCGGCG 61.902 66.667 1.15 1.15 42.13 6.46
831 853 0.179275 CACAACTGCGTCATTCGTCG 60.179 55.000 0.00 0.00 42.13 5.12
850 875 2.478894 CTGTTTGGATCGTGTGGTGTAC 59.521 50.000 0.00 0.00 0.00 2.90
854 879 0.762418 TCCTGTTTGGATCGTGTGGT 59.238 50.000 0.00 0.00 40.56 4.16
887 912 2.551912 CGTGGAGTGGTGGTTTGGC 61.552 63.158 0.00 0.00 0.00 4.52
1341 1375 7.878644 AGAAATCTACTTTTGTTCCAGGAGTAC 59.121 37.037 0.00 0.00 0.00 2.73
1361 1395 1.666189 CGGCGAAAAGGGAGAGAAATC 59.334 52.381 0.00 0.00 0.00 2.17
1365 1399 0.037605 GAACGGCGAAAAGGGAGAGA 60.038 55.000 16.62 0.00 0.00 3.10
1371 1405 0.793104 GCGATTGAACGGCGAAAAGG 60.793 55.000 16.62 2.84 0.00 3.11
1373 1407 4.830708 GCGATTGAACGGCGAAAA 57.169 50.000 16.62 4.87 0.00 2.29
1385 1419 4.280494 CGATCGGACGGGGCGATT 62.280 66.667 7.38 0.00 0.00 3.34
1579 1619 0.098376 GCAAGTGCAGCACTAGCATC 59.902 55.000 28.48 11.73 44.62 3.91
1693 1733 3.057033 AGAAATCGCGGTACTTGTACTGT 60.057 43.478 17.71 1.71 0.00 3.55
1771 1811 3.557228 ATTCAGAACTGAGCCTCCATC 57.443 47.619 4.72 0.00 41.13 3.51
1811 1851 5.822519 ACTGTGGCACATAAACCATATACAG 59.177 40.000 22.35 6.49 44.52 2.74
1901 1941 3.945285 CCTTGTTGTTTCTGTACACCAGT 59.055 43.478 0.00 0.00 42.19 4.00
1904 1944 3.547746 TCCCTTGTTGTTTCTGTACACC 58.452 45.455 0.00 0.00 0.00 4.16
1913 1953 3.555966 CTTCCTCACTCCCTTGTTGTTT 58.444 45.455 0.00 0.00 0.00 2.83
2039 2079 0.108520 TGACCGCATTTCCGACCTAC 60.109 55.000 0.00 0.00 0.00 3.18
2096 2136 4.415150 AGCCCATGCGTCCACCAG 62.415 66.667 0.00 0.00 44.33 4.00
2108 2148 1.483827 GTGTCATCAGAGATCAGCCCA 59.516 52.381 0.00 0.00 0.00 5.36
2159 2199 3.002791 GGAAGCGTGTTCAGATGAATCA 58.997 45.455 0.00 0.00 36.33 2.57
2171 2211 2.434884 CATGCCTCGGAAGCGTGT 60.435 61.111 11.75 0.00 41.39 4.49
2355 2400 2.877866 ACCACACTGCTACAGTAGTCT 58.122 47.619 9.42 0.00 43.43 3.24
2356 2401 4.985538 ATACCACACTGCTACAGTAGTC 57.014 45.455 9.42 2.71 43.43 2.59
2357 2402 7.419711 AATTATACCACACTGCTACAGTAGT 57.580 36.000 9.42 1.85 43.43 2.73
2358 2403 8.630917 AGTAATTATACCACACTGCTACAGTAG 58.369 37.037 2.85 2.85 36.24 2.57
2370 2415 6.826668 ACAGCTGCATAGTAATTATACCACA 58.173 36.000 15.27 0.00 32.08 4.17
2371 2416 7.730364 AACAGCTGCATAGTAATTATACCAC 57.270 36.000 15.27 0.00 32.08 4.16
2403 2482 7.872113 ATTATGTTCCAAAGGAATCTCAGAC 57.128 36.000 1.30 0.00 44.04 3.51
2407 2486 9.178758 ACTGTTATTATGTTCCAAAGGAATCTC 57.821 33.333 1.30 0.00 44.04 2.75
2408 2487 9.533831 AACTGTTATTATGTTCCAAAGGAATCT 57.466 29.630 1.30 0.00 44.04 2.40
2432 2511 6.176014 ACTATAAGGAGGCAACATAGGAAC 57.824 41.667 0.00 0.00 41.41 3.62
2440 2519 8.507524 AACAGAAAATACTATAAGGAGGCAAC 57.492 34.615 0.00 0.00 0.00 4.17
2452 2531 8.032451 GGGCTGCATTTTAAACAGAAAATACTA 58.968 33.333 0.50 0.00 36.99 1.82
2454 2533 6.873605 AGGGCTGCATTTTAAACAGAAAATAC 59.126 34.615 0.50 0.00 36.99 1.89
2461 2540 2.299867 ACCAGGGCTGCATTTTAAACAG 59.700 45.455 0.50 1.00 34.48 3.16
2473 2552 1.975407 CTCTTGGCAACCAGGGCTG 60.975 63.158 0.00 0.00 33.81 4.85
2565 2644 4.211374 GCATACGGTATTCCAGTGACATTC 59.789 45.833 0.00 0.00 0.00 2.67
2595 2674 1.694150 AGTTGAACAGACCTGCAGCTA 59.306 47.619 8.66 0.00 0.00 3.32
2596 2675 0.471617 AGTTGAACAGACCTGCAGCT 59.528 50.000 8.66 0.00 0.00 4.24
2649 2728 6.827642 CAAGAAGGCTTTATGGTCAGTCACC 61.828 48.000 0.00 0.00 37.76 4.02
2653 2732 4.373156 ACAAGAAGGCTTTATGGTCAGT 57.627 40.909 14.97 0.00 30.14 3.41
2669 2748 7.603963 TTAGCGCAAACTATCATTAACAAGA 57.396 32.000 11.47 0.00 0.00 3.02
2689 2768 7.913297 TCACTGTGAAATACAAACAAGTTTAGC 59.087 33.333 8.27 0.00 39.20 3.09
2698 2777 7.417612 ACAAGACATCACTGTGAAATACAAAC 58.582 34.615 15.31 1.63 39.20 2.93
2700 2779 7.566760 AACAAGACATCACTGTGAAATACAA 57.433 32.000 15.31 0.00 39.20 2.41
2701 2780 7.281999 TCAAACAAGACATCACTGTGAAATACA 59.718 33.333 15.31 0.00 35.14 2.29
2702 2781 7.639039 TCAAACAAGACATCACTGTGAAATAC 58.361 34.615 15.31 7.00 35.14 1.89
2746 2825 4.229582 TGGTAAATAGGAAGCATGGACCTT 59.770 41.667 0.00 0.00 35.52 3.50
2824 2903 8.299570 AGATCCTGTGTAAATCATGTTTTCAAC 58.700 33.333 5.03 6.25 0.00 3.18
2850 2929 6.672266 TTGGCACCATTGTTAAGGATTTAA 57.328 33.333 0.00 0.00 0.00 1.52
2926 3007 8.528044 AAACAATTAAAACCACAGAAGGTAGA 57.472 30.769 0.00 0.00 42.25 2.59
2994 3077 4.930696 TGGAGTATCTTGTACCAGTGAGA 58.069 43.478 0.00 0.00 33.73 3.27
3039 3122 3.120792 CCACGGATACCAATTAGTGACG 58.879 50.000 0.00 0.00 0.00 4.35
3098 3181 3.320826 GGGAATAAAACTGCCAGTGTTGT 59.679 43.478 10.61 0.39 26.94 3.32
3105 3188 6.432403 AATGAAAAGGGAATAAAACTGCCA 57.568 33.333 0.00 0.00 0.00 4.92
3107 3190 7.041167 AGCAAAATGAAAAGGGAATAAAACTGC 60.041 33.333 0.00 0.00 0.00 4.40
3127 3211 9.123902 AGTTTGATGAGCATATATGTAGCAAAA 57.876 29.630 20.79 11.52 31.35 2.44
3138 3222 7.228108 CACACCATTAGAGTTTGATGAGCATAT 59.772 37.037 0.00 0.00 0.00 1.78
3147 3231 6.371548 GCAAGATACACACCATTAGAGTTTGA 59.628 38.462 0.00 0.00 0.00 2.69
3150 3234 6.054860 AGCAAGATACACACCATTAGAGTT 57.945 37.500 0.00 0.00 0.00 3.01
3151 3235 5.683876 AGCAAGATACACACCATTAGAGT 57.316 39.130 0.00 0.00 0.00 3.24
3165 3249 4.009675 CAACCAGCAACCTAAGCAAGATA 58.990 43.478 0.00 0.00 0.00 1.98
3206 3290 1.194547 CGGATTGTCACCAACGTCAAG 59.805 52.381 0.00 0.00 32.26 3.02
3329 3413 5.472137 TGGAAGGAAATTCTAAAACGACTGG 59.528 40.000 0.00 0.00 38.07 4.00
3402 3486 2.403252 ACTGAAAATCTGGTAGCCGG 57.597 50.000 0.00 0.00 0.00 6.13
3406 3490 5.240891 TCTGCTCAACTGAAAATCTGGTAG 58.759 41.667 0.00 0.00 0.00 3.18
3408 3492 4.090761 TCTGCTCAACTGAAAATCTGGT 57.909 40.909 0.00 0.00 0.00 4.00
3412 3496 6.150809 AGAGGAAATCTGCTCAACTGAAAATC 59.849 38.462 0.00 0.00 42.28 2.17
3433 3517 2.358957 TCGGCATCAAATGAACAGAGG 58.641 47.619 0.00 0.00 0.00 3.69
3449 3533 2.091541 TGTTCCCATTTCTCAATCGGC 58.908 47.619 0.00 0.00 0.00 5.54
3450 3534 3.609853 TCTGTTCCCATTTCTCAATCGG 58.390 45.455 0.00 0.00 0.00 4.18
3483 3567 5.453567 AAACAAAGCTCTAATTGTCCCAC 57.546 39.130 2.11 0.00 38.75 4.61
3507 3591 2.158475 ACCCCAGAGCTCATGAAAACAA 60.158 45.455 17.77 0.00 0.00 2.83
3508 3592 1.425066 ACCCCAGAGCTCATGAAAACA 59.575 47.619 17.77 0.00 0.00 2.83
3510 3594 1.272092 CCACCCCAGAGCTCATGAAAA 60.272 52.381 17.77 0.00 0.00 2.29
3525 3609 5.083533 TGATTCAAATTACATTGCCACCC 57.916 39.130 0.00 0.00 0.00 4.61
3529 3613 7.707893 AGCAAGTATGATTCAAATTACATTGCC 59.292 33.333 17.69 9.16 29.75 4.52
3530 3614 8.638685 AGCAAGTATGATTCAAATTACATTGC 57.361 30.769 15.79 15.79 0.00 3.56
3583 3667 7.383687 AGGAGTCGTTTAACAGATAACAATGA 58.616 34.615 0.00 0.00 0.00 2.57
3586 3670 7.211573 TCAAGGAGTCGTTTAACAGATAACAA 58.788 34.615 0.00 0.00 0.00 2.83
3600 3684 3.368531 GCCTAACTTGATCAAGGAGTCGT 60.369 47.826 33.11 14.03 42.53 4.34
3602 3686 4.479786 AGCCTAACTTGATCAAGGAGTC 57.520 45.455 33.11 21.54 42.53 3.36
3615 3706 5.013599 AGTCAAGGAGAATTCAAGCCTAACT 59.986 40.000 8.44 13.63 0.00 2.24
3639 3732 3.421919 TTGGATCATGTCAGCAACAGA 57.578 42.857 0.00 0.00 42.37 3.41
3658 3751 9.893305 GTTACAAGCTTAACATGTTTACTGATT 57.107 29.630 17.78 6.91 32.95 2.57
3663 3756 7.127686 ACACGTTACAAGCTTAACATGTTTAC 58.872 34.615 17.78 6.73 35.41 2.01
3665 3758 6.126568 ACACGTTACAAGCTTAACATGTTT 57.873 33.333 17.78 0.00 35.41 2.83
3669 3779 6.484308 AGGTTAACACGTTACAAGCTTAACAT 59.516 34.615 8.10 0.00 32.32 2.71
3684 3794 2.029290 ACCACTCAGCTAGGTTAACACG 60.029 50.000 8.10 0.00 29.58 4.49
3767 3878 9.406828 CCAAGCTTACCAAAAATTACTCTTAAC 57.593 33.333 0.00 0.00 0.00 2.01
3770 3881 7.597288 ACCAAGCTTACCAAAAATTACTCTT 57.403 32.000 0.00 0.00 0.00 2.85
3771 3882 8.879427 ATACCAAGCTTACCAAAAATTACTCT 57.121 30.769 0.00 0.00 0.00 3.24
3809 3920 4.399303 AGTGCTGCACTAACTTCTGTTTTT 59.601 37.500 32.18 4.53 43.46 1.94
3810 3921 3.947834 AGTGCTGCACTAACTTCTGTTTT 59.052 39.130 32.18 4.99 43.46 2.43
3811 3922 3.313526 CAGTGCTGCACTAACTTCTGTTT 59.686 43.478 32.51 5.96 43.43 2.83
3859 3973 8.827832 TGCTATAAACCTCTAAGTACTGGTTA 57.172 34.615 13.99 3.44 41.36 2.85
3882 3996 3.149196 TGAGATCACTTTCCTTGGTTGC 58.851 45.455 0.00 0.00 0.00 4.17
3904 6521 8.902540 TTCAAGAAGTTGCACTAGAAAGAATA 57.097 30.769 0.00 0.00 33.23 1.75
3956 6573 9.643693 GTTCTGAATGAATTTTATGTGGTCATT 57.356 29.630 0.00 0.00 40.65 2.57
3957 6574 9.028284 AGTTCTGAATGAATTTTATGTGGTCAT 57.972 29.630 0.00 0.00 36.99 3.06
3958 6575 8.408043 AGTTCTGAATGAATTTTATGTGGTCA 57.592 30.769 0.00 0.00 36.99 4.02
3959 6576 8.734386 AGAGTTCTGAATGAATTTTATGTGGTC 58.266 33.333 0.00 0.00 36.99 4.02
3960 6577 8.641498 AGAGTTCTGAATGAATTTTATGTGGT 57.359 30.769 0.00 0.00 36.99 4.16
3961 6578 9.350357 CAAGAGTTCTGAATGAATTTTATGTGG 57.650 33.333 0.00 0.00 36.99 4.17
3998 6615 7.894753 TGCATGGGAATAATATTTTCAGTGA 57.105 32.000 0.00 0.00 0.00 3.41
4001 6618 9.767228 TTTGATGCATGGGAATAATATTTTCAG 57.233 29.630 2.46 0.00 0.00 3.02
4040 6657 2.137177 TTGTCAACTGCCCTAGCCCC 62.137 60.000 0.00 0.00 38.69 5.80
4041 6658 0.251165 TTTGTCAACTGCCCTAGCCC 60.251 55.000 0.00 0.00 38.69 5.19
4043 6660 1.537202 CTGTTTGTCAACTGCCCTAGC 59.463 52.381 0.00 0.00 40.48 3.42
4045 6662 1.604604 GCTGTTTGTCAACTGCCCTA 58.395 50.000 5.85 0.00 46.80 3.53
4046 6663 2.419057 GCTGTTTGTCAACTGCCCT 58.581 52.632 5.85 0.00 46.80 5.19
4050 6667 0.740149 TGGCTGCTGTTTGTCAACTG 59.260 50.000 0.00 0.00 35.47 3.16
4051 6668 1.134946 GTTGGCTGCTGTTTGTCAACT 59.865 47.619 0.00 0.00 33.77 3.16
4052 6669 1.559831 GTTGGCTGCTGTTTGTCAAC 58.440 50.000 0.00 0.00 0.00 3.18
4053 6670 0.100325 CGTTGGCTGCTGTTTGTCAA 59.900 50.000 0.00 0.00 0.00 3.18
4054 6671 0.746204 TCGTTGGCTGCTGTTTGTCA 60.746 50.000 0.00 0.00 0.00 3.58
4086 6703 3.665745 ATGAATGGCTTGGTTGTGTTC 57.334 42.857 0.00 0.00 0.00 3.18
4097 6714 4.355549 TCATCCCAAAAGAATGAATGGCT 58.644 39.130 0.00 0.00 0.00 4.75
4098 6715 4.741321 TCATCCCAAAAGAATGAATGGC 57.259 40.909 0.00 0.00 0.00 4.40
4099 6716 6.726490 AGATCATCCCAAAAGAATGAATGG 57.274 37.500 0.00 0.00 0.00 3.16
4167 6784 4.309099 GCAGAGATCTCCATGATTGAGTC 58.691 47.826 19.30 0.00 35.14 3.36
4174 6791 2.596346 GAGAGGCAGAGATCTCCATGA 58.404 52.381 19.30 0.00 36.72 3.07
4205 6822 1.272480 GGGGAGGTTAAGCCACACAAT 60.272 52.381 0.00 0.00 40.61 2.71
4315 6932 4.353437 GGTCGACGCCGGTGAACT 62.353 66.667 24.59 0.00 36.24 3.01


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

AutoCloner maintained by Alex Coulton.