Multiple sequence alignment - TraesCS3D01G125200

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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 TraesCS3D01G125200 chr3D 100.000 5252 0 0 1 5252 83830161 83824910 0.000000e+00 9699.0
1 TraesCS3D01G125200 chr3D 87.009 662 67 14 4592 5251 607462858 607463502 0.000000e+00 728.0
2 TraesCS3D01G125200 chr3D 85.714 119 17 0 186 304 321947557 321947439 5.520000e-25 126.0
3 TraesCS3D01G125200 chr3D 94.286 70 4 0 4527 4596 386221396 386221327 2.000000e-19 108.0
4 TraesCS3D01G125200 chr3B 94.250 4191 190 20 302 4486 132719589 132723734 0.000000e+00 6357.0
5 TraesCS3D01G125200 chr3B 88.481 599 46 14 4598 5181 741504715 741505305 0.000000e+00 702.0
6 TraesCS3D01G125200 chr3B 85.662 272 38 1 32 303 132719273 132719543 8.610000e-73 285.0
7 TraesCS3D01G125200 chr3A 95.858 3935 124 10 480 4394 99626086 99622171 0.000000e+00 6327.0
8 TraesCS3D01G125200 chr3A 86.859 624 69 9 4609 5222 434042905 434042285 0.000000e+00 686.0
9 TraesCS3D01G125200 chr3A 87.145 599 57 15 4597 5180 30144441 30143848 0.000000e+00 662.0
10 TraesCS3D01G125200 chr3A 94.505 91 3 1 4422 4512 99620535 99620447 7.090000e-29 139.0
11 TraesCS3D01G125200 chr2D 94.019 535 30 2 4597 5130 43108887 43109420 0.000000e+00 809.0
12 TraesCS3D01G125200 chr5D 93.116 552 34 4 4597 5147 108353723 108353175 0.000000e+00 806.0
13 TraesCS3D01G125200 chr5D 88.832 591 55 11 4597 5180 15078388 15078974 0.000000e+00 715.0
14 TraesCS3D01G125200 chr5D 88.710 558 54 8 4597 5147 389930534 389929979 0.000000e+00 673.0
15 TraesCS3D01G125200 chr5D 88.636 396 38 7 4596 4987 84283051 84282659 4.760000e-130 475.0
16 TraesCS3D01G125200 chr5D 79.121 91 14 4 4039 4125 45259352 45259441 2.040000e-04 58.4
17 TraesCS3D01G125200 chr6A 88.290 649 58 13 4597 5234 74887555 74886914 0.000000e+00 761.0
18 TraesCS3D01G125200 chr1A 87.000 600 60 13 4595 5180 558464818 558464223 0.000000e+00 660.0
19 TraesCS3D01G125200 chr7A 86.894 557 64 8 4596 5147 62568427 62568979 2.690000e-172 616.0
20 TraesCS3D01G125200 chr7A 85.406 603 67 14 4593 5180 136799222 136798626 1.620000e-169 606.0
21 TraesCS3D01G125200 chr2A 89.558 249 22 4 4594 4838 720520159 720519911 3.950000e-81 313.0
22 TraesCS3D01G125200 chr4A 87.398 246 22 3 4594 4830 495064502 495064747 1.860000e-69 274.0
23 TraesCS3D01G125200 chr4A 95.588 68 3 0 4529 4596 280432979 280433046 5.560000e-20 110.0
24 TraesCS3D01G125200 chr6B 88.018 217 24 2 4596 4810 572541981 572541765 6.750000e-64 255.0
25 TraesCS3D01G125200 chr7D 94.286 70 4 0 4527 4596 393678475 393678544 2.000000e-19 108.0
26 TraesCS3D01G125200 chr7B 94.286 70 4 0 4527 4596 662417206 662417275 2.000000e-19 108.0
27 TraesCS3D01G125200 chr5B 94.286 70 4 0 4527 4596 657040142 657040211 2.000000e-19 108.0
28 TraesCS3D01G125200 chr4D 94.286 70 4 0 4527 4596 484999824 484999755 2.000000e-19 108.0
29 TraesCS3D01G125200 chr4B 94.286 70 4 0 4527 4596 313348774 313348705 2.000000e-19 108.0
30 TraesCS3D01G125200 chr4B 94.286 70 4 0 4527 4596 328482339 328482270 2.000000e-19 108.0
31 TraesCS3D01G125200 chr1B 94.286 70 4 0 4527 4596 295804982 295804913 2.000000e-19 108.0
32 TraesCS3D01G125200 chr1B 84.058 69 9 2 189 256 308340699 308340632 1.220000e-06 65.8
33 TraesCS3D01G125200 chrUn 100.000 33 0 0 4051 4083 380817035 380817003 1.580000e-05 62.1
34 TraesCS3D01G125200 chrUn 91.304 46 2 2 4039 4083 451705454 451705498 1.580000e-05 62.1
35 TraesCS3D01G125200 chr5A 100.000 33 0 0 4051 4083 36052803 36052771 1.580000e-05 62.1
36 TraesCS3D01G125200 chr5A 100.000 33 0 0 4051 4083 36079572 36079540 1.580000e-05 62.1
37 TraesCS3D01G125200 chr5A 100.000 33 0 0 4051 4083 36107520 36107488 1.580000e-05 62.1
38 TraesCS3D01G125200 chr5A 100.000 33 0 0 4051 4083 36136073 36136041 1.580000e-05 62.1
39 TraesCS3D01G125200 chr2B 82.432 74 10 3 219 291 160888143 160888214 1.580000e-05 62.1


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 TraesCS3D01G125200 chr3D 83824910 83830161 5251 True 9699 9699 100.0000 1 5252 1 chr3D.!!$R1 5251
1 TraesCS3D01G125200 chr3D 607462858 607463502 644 False 728 728 87.0090 4592 5251 1 chr3D.!!$F1 659
2 TraesCS3D01G125200 chr3B 132719273 132723734 4461 False 3321 6357 89.9560 32 4486 2 chr3B.!!$F2 4454
3 TraesCS3D01G125200 chr3B 741504715 741505305 590 False 702 702 88.4810 4598 5181 1 chr3B.!!$F1 583
4 TraesCS3D01G125200 chr3A 99620447 99626086 5639 True 3233 6327 95.1815 480 4512 2 chr3A.!!$R3 4032
5 TraesCS3D01G125200 chr3A 434042285 434042905 620 True 686 686 86.8590 4609 5222 1 chr3A.!!$R2 613
6 TraesCS3D01G125200 chr3A 30143848 30144441 593 True 662 662 87.1450 4597 5180 1 chr3A.!!$R1 583
7 TraesCS3D01G125200 chr2D 43108887 43109420 533 False 809 809 94.0190 4597 5130 1 chr2D.!!$F1 533
8 TraesCS3D01G125200 chr5D 108353175 108353723 548 True 806 806 93.1160 4597 5147 1 chr5D.!!$R2 550
9 TraesCS3D01G125200 chr5D 15078388 15078974 586 False 715 715 88.8320 4597 5180 1 chr5D.!!$F1 583
10 TraesCS3D01G125200 chr5D 389929979 389930534 555 True 673 673 88.7100 4597 5147 1 chr5D.!!$R3 550
11 TraesCS3D01G125200 chr6A 74886914 74887555 641 True 761 761 88.2900 4597 5234 1 chr6A.!!$R1 637
12 TraesCS3D01G125200 chr1A 558464223 558464818 595 True 660 660 87.0000 4595 5180 1 chr1A.!!$R1 585
13 TraesCS3D01G125200 chr7A 62568427 62568979 552 False 616 616 86.8940 4596 5147 1 chr7A.!!$F1 551
14 TraesCS3D01G125200 chr7A 136798626 136799222 596 True 606 606 85.4060 4593 5180 1 chr7A.!!$R1 587

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
975 1024 0.031857 CCAGATCGCTCTAGCTGTGG 59.968 60.0 0.0 0.0 39.32 4.17 F
1266 1317 0.035458 AGCTGTCTTTCGTGAAGGGG 59.965 55.0 0.0 0.0 35.98 4.79 F
1677 1728 1.027792 ACACCGACCGCAACAACTTT 61.028 50.0 0.0 0.0 0.00 2.66 F
2524 2575 0.315886 ACCGCTGAACATGACGTACA 59.684 50.0 0.0 0.0 0.00 2.90 F
2818 2869 1.177401 GGATGGACCTGGCAAAGAAC 58.823 55.0 0.0 0.0 35.41 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1894 1945 0.037975 ATGTCGTCGCGGTAAGGTTT 60.038 50.0 6.13 0.0 0.00 3.27 R
2524 2575 0.184933 TGCTTGGCCTTGGTGTAGTT 59.815 50.0 3.32 0.0 0.00 2.24 R
2848 2914 0.883814 ACGTTGAGGAGAGACGTCGT 60.884 55.0 10.46 0.0 45.82 4.34 R
4248 4314 0.028505 CGTCCGATCGGTCACGTTAT 59.971 55.0 29.96 0.0 41.85 1.89 R
4399 5227 0.379669 GAATGTGGCTGAGATTGGCG 59.620 55.0 0.00 0.0 0.00 5.69 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 2.888534 GTTCGCGCGCCCATCTAA 60.889 61.111 27.95 9.66 0.00 2.10
29 30 2.108157 TTCGCGCGCCCATCTAAT 59.892 55.556 27.95 0.00 0.00 1.73
30 31 1.522806 TTCGCGCGCCCATCTAATT 60.523 52.632 27.95 0.00 0.00 1.40
41 42 1.542547 CCATCTAATTTAGGCGCCCGT 60.543 52.381 26.15 8.44 0.00 5.28
45 46 0.538118 TAATTTAGGCGCCCGTGAGT 59.462 50.000 26.15 5.68 0.00 3.41
101 102 1.715019 CCCCTCTGTGGTGGGTTTGA 61.715 60.000 0.00 0.00 42.91 2.69
104 105 1.133792 CCTCTGTGGTGGGTTTGAGTT 60.134 52.381 0.00 0.00 0.00 3.01
107 108 2.506231 TCTGTGGTGGGTTTGAGTTACA 59.494 45.455 0.00 0.00 0.00 2.41
110 111 1.612676 GGTGGGTTTGAGTTACACCC 58.387 55.000 2.26 2.26 44.40 4.61
119 120 1.296056 GAGTTACACCCGCATGCGTT 61.296 55.000 35.55 21.26 37.81 4.84
121 122 0.797542 GTTACACCCGCATGCGTTTA 59.202 50.000 35.55 18.82 37.81 2.01
159 160 3.878519 CGAGAGGGCGAGACGGAC 61.879 72.222 0.00 0.00 0.00 4.79
161 162 4.361971 AGAGGGCGAGACGGACCA 62.362 66.667 0.00 0.00 0.00 4.02
165 166 4.131088 GGCGAGACGGACCAGACC 62.131 72.222 0.00 0.00 0.00 3.85
174 175 4.681978 GACCAGACCGCCAGCGTT 62.682 66.667 11.55 0.00 37.81 4.84
178 179 4.626081 AGACCGCCAGCGTTGCTT 62.626 61.111 11.55 0.00 36.40 3.91
196 197 2.046892 GCGAGCATGTGGAGTGGT 60.047 61.111 0.00 0.00 0.00 4.16
203 204 2.161855 GCATGTGGAGTGGTCATTCAA 58.838 47.619 0.00 0.00 0.00 2.69
217 218 4.919754 GGTCATTCAAAGTGTTGCAAGATC 59.080 41.667 0.00 0.00 34.50 2.75
224 225 2.699954 AGTGTTGCAAGATCGTTAGGG 58.300 47.619 0.00 0.00 0.00 3.53
233 234 4.873827 GCAAGATCGTTAGGGTATTGTTCA 59.126 41.667 0.00 0.00 0.00 3.18
251 252 3.564053 TCATGGAGCTGCAATGATGTA 57.436 42.857 13.45 0.00 0.00 2.29
253 254 2.336945 TGGAGCTGCAATGATGTAGG 57.663 50.000 5.01 0.00 39.43 3.18
256 257 3.117776 TGGAGCTGCAATGATGTAGGAAT 60.118 43.478 5.01 0.00 39.43 3.01
269 270 6.401394 TGATGTAGGAATCAGAGACTTTGTG 58.599 40.000 0.00 0.00 32.75 3.33
274 275 3.935828 GGAATCAGAGACTTTGTGGTAGC 59.064 47.826 0.00 0.00 0.00 3.58
278 279 3.641436 TCAGAGACTTTGTGGTAGCTGAA 59.359 43.478 0.00 0.00 31.37 3.02
279 280 4.284490 TCAGAGACTTTGTGGTAGCTGAAT 59.716 41.667 0.00 0.00 31.37 2.57
293 294 7.442364 GTGGTAGCTGAATACATATTGTGTCAT 59.558 37.037 0.00 0.00 42.29 3.06
298 299 9.793252 AGCTGAATACATATTGTGTCATTTTTC 57.207 29.630 0.00 0.00 42.29 2.29
299 300 9.571810 GCTGAATACATATTGTGTCATTTTTCA 57.428 29.630 0.00 0.00 42.29 2.69
346 390 9.819267 TTTAAGGTTTTAATACCAAAAGTGTGG 57.181 29.630 16.24 0.00 44.92 4.17
350 394 6.277605 GTTTTAATACCAAAAGTGTGGCTGT 58.722 36.000 0.00 0.00 43.00 4.40
351 395 5.699097 TTAATACCAAAAGTGTGGCTGTC 57.301 39.130 0.00 0.00 43.00 3.51
357 401 3.820467 CCAAAAGTGTGGCTGTCTAATCA 59.180 43.478 0.00 0.00 0.00 2.57
360 404 6.449698 CAAAAGTGTGGCTGTCTAATCAAAT 58.550 36.000 0.00 0.00 0.00 2.32
365 409 7.765307 AGTGTGGCTGTCTAATCAAATATTTG 58.235 34.615 20.13 20.13 39.48 2.32
377 421 4.823157 TCAAATATTTGAGGACCGTTCGA 58.177 39.130 23.86 0.86 41.88 3.71
378 422 5.424757 TCAAATATTTGAGGACCGTTCGAT 58.575 37.500 23.86 0.00 41.88 3.59
379 423 5.293324 TCAAATATTTGAGGACCGTTCGATG 59.707 40.000 23.86 0.00 41.88 3.84
380 424 1.369625 ATTTGAGGACCGTTCGATGC 58.630 50.000 0.00 0.00 0.00 3.91
381 425 1.011968 TTTGAGGACCGTTCGATGCG 61.012 55.000 3.33 3.33 0.00 4.73
382 426 2.149803 TTGAGGACCGTTCGATGCGT 62.150 55.000 8.67 0.00 0.00 5.24
383 427 1.872679 GAGGACCGTTCGATGCGTC 60.873 63.158 8.67 0.00 0.00 5.19
385 429 3.245315 GACCGTTCGATGCGTCCG 61.245 66.667 0.00 0.00 0.00 4.79
399 443 0.999406 CGTCCGCAAATGTCTAGGTG 59.001 55.000 0.00 0.00 0.00 4.00
400 444 1.671850 CGTCCGCAAATGTCTAGGTGT 60.672 52.381 0.00 0.00 0.00 4.16
401 445 2.423577 GTCCGCAAATGTCTAGGTGTT 58.576 47.619 0.00 0.00 0.00 3.32
402 446 3.592059 GTCCGCAAATGTCTAGGTGTTA 58.408 45.455 0.00 0.00 0.00 2.41
406 450 5.361571 TCCGCAAATGTCTAGGTGTTAGATA 59.638 40.000 0.00 0.00 40.42 1.98
410 454 7.224753 CGCAAATGTCTAGGTGTTAGATATGTT 59.775 37.037 0.00 0.00 38.75 2.71
420 464 5.756833 GGTGTTAGATATGTTAAAGTCCGGG 59.243 44.000 0.00 0.00 0.00 5.73
441 485 0.179215 GCCGATGCTCTGAAAACACG 60.179 55.000 0.00 0.00 33.53 4.49
442 486 1.428448 CCGATGCTCTGAAAACACGA 58.572 50.000 0.00 0.00 0.00 4.35
443 487 1.798223 CCGATGCTCTGAAAACACGAA 59.202 47.619 0.00 0.00 0.00 3.85
444 488 2.411547 CCGATGCTCTGAAAACACGAAC 60.412 50.000 0.00 0.00 0.00 3.95
448 492 2.284150 TGCTCTGAAAACACGAACGAAG 59.716 45.455 0.14 0.00 0.00 3.79
473 517 5.280215 CCAGAGTAAATTTCTCCACCTCAGT 60.280 44.000 0.00 0.00 32.93 3.41
482 526 2.357517 CACCTCAGTGGGCACGAC 60.358 66.667 0.00 0.00 40.55 4.34
816 865 7.609097 ATTCTTCTAGATCTGGCACATTCTA 57.391 36.000 5.18 0.00 38.20 2.10
904 953 2.485479 GCACTTCTTTCCTGGACACTCA 60.485 50.000 0.00 0.00 0.00 3.41
929 978 4.684134 GCTGGGCAAAGGGGCTGA 62.684 66.667 0.00 0.00 42.84 4.26
975 1024 0.031857 CCAGATCGCTCTAGCTGTGG 59.968 60.000 0.00 0.00 39.32 4.17
978 1027 1.133761 AGATCGCTCTAGCTGTGGGTA 60.134 52.381 0.00 0.00 39.32 3.69
986 1035 4.626042 CTCTAGCTGTGGGTATTAGCTTG 58.374 47.826 0.00 2.20 44.87 4.01
987 1036 2.044123 AGCTGTGGGTATTAGCTTGC 57.956 50.000 0.00 0.00 44.87 4.01
1036 1087 4.338539 AGTTCGTCGGCGCGTTCT 62.339 61.111 19.58 15.92 38.14 3.01
1254 1305 1.333636 CCCTCATTCCGGAGCTGTCT 61.334 60.000 3.34 0.00 33.47 3.41
1260 1311 0.319555 TTCCGGAGCTGTCTTTCGTG 60.320 55.000 3.34 0.00 0.00 4.35
1266 1317 0.035458 AGCTGTCTTTCGTGAAGGGG 59.965 55.000 0.00 0.00 35.98 4.79
1289 1340 2.504244 GAAGCAGGACGTCGACGG 60.504 66.667 37.89 22.86 44.95 4.79
1314 1365 2.586079 CCGCTGATGCCGTTCGAT 60.586 61.111 0.00 0.00 35.36 3.59
1503 1554 3.751246 CCCTACGTGTCGCCGGAA 61.751 66.667 5.05 0.00 0.00 4.30
1509 1560 1.952133 CGTGTCGCCGGAACTCAAA 60.952 57.895 5.05 0.00 0.00 2.69
1566 1617 2.503375 GGCGTGTACACCGAGACG 60.503 66.667 20.11 8.59 34.93 4.18
1677 1728 1.027792 ACACCGACCGCAACAACTTT 61.028 50.000 0.00 0.00 0.00 2.66
1696 1747 3.965258 AGCCGCCAATCACCCACA 61.965 61.111 0.00 0.00 0.00 4.17
1752 1803 4.778415 CTGACCCTGACGACGCGG 62.778 72.222 12.47 0.00 0.00 6.46
1863 1914 2.036733 CTCCAACTACAAGTTCGGGTCA 59.963 50.000 7.80 0.00 36.03 4.02
1996 2047 4.052229 CGGAGGACGTGTTCGCCT 62.052 66.667 0.00 0.00 42.68 5.52
2013 2064 1.237285 CCTTCGTGCCCAACTGGAAG 61.237 60.000 0.00 0.00 42.29 3.46
2487 2538 1.228154 GGAGCTGTGGAACCGGTTT 60.228 57.895 23.22 2.58 30.00 3.27
2524 2575 0.315886 ACCGCTGAACATGACGTACA 59.684 50.000 0.00 0.00 0.00 2.90
2622 2673 2.355599 CTGCTGAGCTATCCGCGG 60.356 66.667 22.12 22.12 45.59 6.46
2818 2869 1.177401 GGATGGACCTGGCAAAGAAC 58.823 55.000 0.00 0.00 35.41 3.01
2843 2909 2.636412 CCTCGGAAGTGCAGACGGA 61.636 63.158 0.00 0.00 0.00 4.69
2848 2914 1.251527 GGAAGTGCAGACGGAGAGGA 61.252 60.000 0.00 0.00 0.00 3.71
2902 2968 4.517934 TCTCCGGGAGCCCCTACG 62.518 72.222 19.48 0.00 42.67 3.51
3102 3168 2.438434 CTGATCAACCCCACCGCC 60.438 66.667 0.00 0.00 0.00 6.13
3210 3276 3.094062 GCAGCGGCAGGACATCCTA 62.094 63.158 3.18 0.00 46.65 2.94
3675 3741 4.195334 ATGGTGATCCTGGGCGCC 62.195 66.667 21.18 21.18 35.28 6.53
3795 3861 4.509737 GAGTACGTCGGGCTGGCC 62.510 72.222 10.75 10.75 0.00 5.36
4251 4317 2.792947 GGACGCCAGCCTCGGATAA 61.793 63.158 0.00 0.00 0.00 1.75
4252 4318 1.591863 GACGCCAGCCTCGGATAAC 60.592 63.158 0.00 0.00 0.00 1.89
4255 4321 1.883084 GCCAGCCTCGGATAACGTG 60.883 63.158 0.00 0.00 44.69 4.49
4258 4324 0.527817 CAGCCTCGGATAACGTGACC 60.528 60.000 0.00 0.00 44.69 4.02
4279 4345 2.015587 GATCGGACGGTTCTCTGTAGT 58.984 52.381 0.00 0.00 32.75 2.73
4280 4346 1.901591 TCGGACGGTTCTCTGTAGTT 58.098 50.000 0.00 0.00 32.75 2.24
4281 4347 2.233271 TCGGACGGTTCTCTGTAGTTT 58.767 47.619 0.00 0.00 32.75 2.66
4282 4348 2.227388 TCGGACGGTTCTCTGTAGTTTC 59.773 50.000 0.00 0.00 32.75 2.78
4283 4349 2.228343 CGGACGGTTCTCTGTAGTTTCT 59.772 50.000 0.00 0.00 32.75 2.52
4284 4350 3.305199 CGGACGGTTCTCTGTAGTTTCTT 60.305 47.826 0.00 0.00 32.75 2.52
4285 4351 4.629092 GGACGGTTCTCTGTAGTTTCTTT 58.371 43.478 0.00 0.00 32.75 2.52
4286 4352 5.055144 GGACGGTTCTCTGTAGTTTCTTTT 58.945 41.667 0.00 0.00 32.75 2.27
4292 4358 5.290493 TCTCTGTAGTTTCTTTTGCCTCA 57.710 39.130 0.00 0.00 0.00 3.86
4313 4380 4.021807 TCACGTAGGTTGACATGTATGTGT 60.022 41.667 13.44 0.00 41.95 3.72
4331 4399 9.787532 TGTATGTGTTTCTTCTTCTTCTTTTTG 57.212 29.630 0.00 0.00 0.00 2.44
4394 4462 3.997021 ACACATCTTTGAGCTTTACTCCG 59.003 43.478 0.00 0.00 45.61 4.63
4399 5227 3.250040 TCTTTGAGCTTTACTCCGTTTGC 59.750 43.478 0.00 0.00 45.61 3.68
4409 5237 1.298157 CTCCGTTTGCGCCAATCTCA 61.298 55.000 4.18 0.00 36.67 3.27
4418 5246 0.379669 CGCCAATCTCAGCCACATTC 59.620 55.000 0.00 0.00 0.00 2.67
4419 5247 1.760192 GCCAATCTCAGCCACATTCT 58.240 50.000 0.00 0.00 0.00 2.40
4420 5248 1.674962 GCCAATCTCAGCCACATTCTC 59.325 52.381 0.00 0.00 0.00 2.87
4438 6114 6.875726 ACATTCTCGAATTCTCTGAACATCAA 59.124 34.615 3.52 0.00 0.00 2.57
4492 6168 7.398024 AGAACTGTCCTAGTGCTGATTAATTT 58.602 34.615 0.00 0.00 44.04 1.82
4536 6212 3.621558 GCTATGGCTTCAAACTTAGGGT 58.378 45.455 0.00 0.00 35.22 4.34
4537 6213 3.628032 GCTATGGCTTCAAACTTAGGGTC 59.372 47.826 0.00 0.00 35.22 4.46
4538 6214 4.626529 GCTATGGCTTCAAACTTAGGGTCT 60.627 45.833 0.00 0.00 35.22 3.85
4539 6215 3.418684 TGGCTTCAAACTTAGGGTCTC 57.581 47.619 0.00 0.00 0.00 3.36
4540 6216 2.979678 TGGCTTCAAACTTAGGGTCTCT 59.020 45.455 0.00 0.00 0.00 3.10
4541 6217 3.394606 TGGCTTCAAACTTAGGGTCTCTT 59.605 43.478 0.00 0.00 0.00 2.85
4542 6218 4.141251 TGGCTTCAAACTTAGGGTCTCTTT 60.141 41.667 0.00 0.00 0.00 2.52
4543 6219 4.216472 GGCTTCAAACTTAGGGTCTCTTTG 59.784 45.833 0.00 0.00 0.00 2.77
4544 6220 5.063880 GCTTCAAACTTAGGGTCTCTTTGA 58.936 41.667 0.00 0.00 0.00 2.69
4545 6221 5.707764 GCTTCAAACTTAGGGTCTCTTTGAT 59.292 40.000 0.00 0.00 0.00 2.57
4546 6222 6.207614 GCTTCAAACTTAGGGTCTCTTTGATT 59.792 38.462 0.00 0.00 0.00 2.57
4547 6223 7.574030 GCTTCAAACTTAGGGTCTCTTTGATTC 60.574 40.741 0.00 0.00 0.00 2.52
4548 6224 5.932303 TCAAACTTAGGGTCTCTTTGATTCG 59.068 40.000 0.00 0.00 0.00 3.34
4549 6225 5.485209 AACTTAGGGTCTCTTTGATTCGT 57.515 39.130 0.00 0.00 0.00 3.85
4550 6226 6.600882 AACTTAGGGTCTCTTTGATTCGTA 57.399 37.500 0.00 0.00 0.00 3.43
4551 6227 5.963594 ACTTAGGGTCTCTTTGATTCGTAC 58.036 41.667 0.00 0.00 0.00 3.67
4552 6228 3.505464 AGGGTCTCTTTGATTCGTACG 57.495 47.619 9.53 9.53 0.00 3.67
4553 6229 3.087031 AGGGTCTCTTTGATTCGTACGA 58.913 45.455 15.28 15.28 0.00 3.43
4554 6230 3.700038 AGGGTCTCTTTGATTCGTACGAT 59.300 43.478 20.27 9.31 0.00 3.73
4555 6231 4.159879 AGGGTCTCTTTGATTCGTACGATT 59.840 41.667 20.27 15.90 0.00 3.34
4556 6232 4.868734 GGGTCTCTTTGATTCGTACGATTT 59.131 41.667 20.27 9.94 0.00 2.17
4557 6233 5.005490 GGGTCTCTTTGATTCGTACGATTTC 59.995 44.000 20.27 18.45 0.00 2.17
4558 6234 5.005490 GGTCTCTTTGATTCGTACGATTTCC 59.995 44.000 20.27 9.02 0.00 3.13
4559 6235 5.575606 GTCTCTTTGATTCGTACGATTTCCA 59.424 40.000 20.27 11.47 0.00 3.53
4560 6236 6.090358 GTCTCTTTGATTCGTACGATTTCCAA 59.910 38.462 20.27 16.31 0.00 3.53
4561 6237 6.647481 TCTCTTTGATTCGTACGATTTCCAAA 59.353 34.615 20.27 21.31 0.00 3.28
4562 6238 7.171848 TCTCTTTGATTCGTACGATTTCCAAAA 59.828 33.333 20.27 14.00 0.00 2.44
4563 6239 7.812648 TCTTTGATTCGTACGATTTCCAAAAT 58.187 30.769 20.27 6.66 0.00 1.82
4564 6240 7.748683 TCTTTGATTCGTACGATTTCCAAAATG 59.251 33.333 20.27 13.98 0.00 2.32
4565 6241 5.328691 TGATTCGTACGATTTCCAAAATGC 58.671 37.500 20.27 1.19 0.00 3.56
4566 6242 3.377434 TCGTACGATTTCCAAAATGCG 57.623 42.857 15.28 0.00 0.00 4.73
4567 6243 2.094575 TCGTACGATTTCCAAAATGCGG 59.905 45.455 15.28 0.00 0.00 5.69
4568 6244 2.789779 CGTACGATTTCCAAAATGCGGG 60.790 50.000 10.44 0.00 0.00 6.13
4569 6245 1.540267 ACGATTTCCAAAATGCGGGA 58.460 45.000 0.00 0.00 0.00 5.14
4570 6246 1.889829 ACGATTTCCAAAATGCGGGAA 59.110 42.857 0.00 0.00 41.27 3.97
4571 6247 2.495669 ACGATTTCCAAAATGCGGGAAT 59.504 40.909 0.00 0.00 42.44 3.01
4572 6248 3.697045 ACGATTTCCAAAATGCGGGAATA 59.303 39.130 0.00 0.00 42.44 1.75
4573 6249 4.202010 ACGATTTCCAAAATGCGGGAATAG 60.202 41.667 0.00 0.00 42.44 1.73
4574 6250 4.620982 GATTTCCAAAATGCGGGAATAGG 58.379 43.478 0.00 0.00 42.44 2.57
4575 6251 3.374042 TTCCAAAATGCGGGAATAGGA 57.626 42.857 0.00 0.00 38.23 2.94
4576 6252 3.374042 TCCAAAATGCGGGAATAGGAA 57.626 42.857 0.00 0.00 0.00 3.36
4577 6253 3.702792 TCCAAAATGCGGGAATAGGAAA 58.297 40.909 0.00 0.00 0.00 3.13
4578 6254 4.090090 TCCAAAATGCGGGAATAGGAAAA 58.910 39.130 0.00 0.00 0.00 2.29
4579 6255 4.528596 TCCAAAATGCGGGAATAGGAAAAA 59.471 37.500 0.00 0.00 0.00 1.94
4580 6256 4.629634 CCAAAATGCGGGAATAGGAAAAAC 59.370 41.667 0.00 0.00 0.00 2.43
4581 6257 5.233988 CAAAATGCGGGAATAGGAAAAACA 58.766 37.500 0.00 0.00 0.00 2.83
4582 6258 5.675684 AAATGCGGGAATAGGAAAAACAT 57.324 34.783 0.00 0.00 0.00 2.71
4583 6259 4.654091 ATGCGGGAATAGGAAAAACATG 57.346 40.909 0.00 0.00 0.00 3.21
4584 6260 3.691575 TGCGGGAATAGGAAAAACATGA 58.308 40.909 0.00 0.00 0.00 3.07
4585 6261 3.694072 TGCGGGAATAGGAAAAACATGAG 59.306 43.478 0.00 0.00 0.00 2.90
4586 6262 3.945285 GCGGGAATAGGAAAAACATGAGA 59.055 43.478 0.00 0.00 0.00 3.27
4587 6263 4.580580 GCGGGAATAGGAAAAACATGAGAT 59.419 41.667 0.00 0.00 0.00 2.75
4588 6264 5.067805 GCGGGAATAGGAAAAACATGAGATT 59.932 40.000 0.00 0.00 0.00 2.40
4589 6265 6.262273 GCGGGAATAGGAAAAACATGAGATTA 59.738 38.462 0.00 0.00 0.00 1.75
4590 6266 7.520614 GCGGGAATAGGAAAAACATGAGATTAG 60.521 40.741 0.00 0.00 0.00 1.73
4591 6267 7.715249 CGGGAATAGGAAAAACATGAGATTAGA 59.285 37.037 0.00 0.00 0.00 2.10
4592 6268 9.061435 GGGAATAGGAAAAACATGAGATTAGAG 57.939 37.037 0.00 0.00 0.00 2.43
4593 6269 9.620259 GGAATAGGAAAAACATGAGATTAGAGT 57.380 33.333 0.00 0.00 0.00 3.24
4644 6320 3.446442 ACACATCAAGGGCTGAGATTT 57.554 42.857 0.00 0.00 37.52 2.17
4838 6526 1.218047 GTCAGATGCAGGGCGTGTA 59.782 57.895 9.16 4.56 0.00 2.90
5002 6696 0.246635 CTGCTGTACTTGTAGGCCGT 59.753 55.000 0.00 0.00 0.00 5.68
5077 6771 3.121030 GCCAGCTGTTGACGCGAT 61.121 61.111 15.93 0.00 0.00 4.58
5167 6862 3.716006 CACGCCTTCACACGCCAG 61.716 66.667 0.00 0.00 0.00 4.85
5170 6865 4.030452 GCCTTCACACGCCAGCAC 62.030 66.667 0.00 0.00 0.00 4.40
5171 6866 2.281070 CCTTCACACGCCAGCACT 60.281 61.111 0.00 0.00 0.00 4.40
5172 6867 2.610694 CCTTCACACGCCAGCACTG 61.611 63.158 0.00 0.00 0.00 3.66
5173 6868 3.245948 CTTCACACGCCAGCACTGC 62.246 63.158 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.772063 AATTAGATGGGCGCGCGAAC 61.772 55.000 37.18 25.13 0.00 3.95
12 13 1.092921 AAATTAGATGGGCGCGCGAA 61.093 50.000 37.18 18.92 0.00 4.70
13 14 0.249531 TAAATTAGATGGGCGCGCGA 60.250 50.000 37.18 14.30 0.00 5.87
14 15 0.163788 CTAAATTAGATGGGCGCGCG 59.836 55.000 28.44 28.44 0.00 6.86
15 16 0.517316 CCTAAATTAGATGGGCGCGC 59.483 55.000 25.94 25.94 0.00 6.86
16 17 0.517316 GCCTAAATTAGATGGGCGCG 59.483 55.000 0.00 0.00 33.30 6.86
19 20 0.881796 GGCGCCTAAATTAGATGGGC 59.118 55.000 22.15 5.79 39.43 5.36
20 21 1.534729 GGGCGCCTAAATTAGATGGG 58.465 55.000 28.56 0.00 0.00 4.00
21 22 1.156736 CGGGCGCCTAAATTAGATGG 58.843 55.000 28.56 0.00 0.00 3.51
22 23 1.531149 CACGGGCGCCTAAATTAGATG 59.469 52.381 28.56 7.60 0.00 2.90
23 24 1.414919 TCACGGGCGCCTAAATTAGAT 59.585 47.619 28.56 0.00 0.00 1.98
24 25 0.825410 TCACGGGCGCCTAAATTAGA 59.175 50.000 28.56 11.91 0.00 2.10
25 26 1.217882 CTCACGGGCGCCTAAATTAG 58.782 55.000 28.56 12.63 0.00 1.73
26 27 0.538118 ACTCACGGGCGCCTAAATTA 59.462 50.000 28.56 6.48 0.00 1.40
27 28 1.024579 CACTCACGGGCGCCTAAATT 61.025 55.000 28.56 3.55 0.00 1.82
28 29 1.449601 CACTCACGGGCGCCTAAAT 60.450 57.895 28.56 6.41 0.00 1.40
29 30 2.047655 CACTCACGGGCGCCTAAA 60.048 61.111 28.56 8.79 0.00 1.85
30 31 3.291101 GACACTCACGGGCGCCTAA 62.291 63.158 28.56 8.41 0.00 2.69
41 42 1.080772 GACGCGTCATGGACACTCA 60.081 57.895 33.09 0.00 32.09 3.41
89 90 1.951602 GGTGTAACTCAAACCCACCAC 59.048 52.381 0.00 0.00 43.96 4.16
90 91 2.351706 GGTGTAACTCAAACCCACCA 57.648 50.000 0.00 0.00 43.96 4.17
101 102 0.887387 AAACGCATGCGGGTGTAACT 60.887 50.000 39.95 17.08 44.69 2.24
104 105 0.037139 AGTAAACGCATGCGGGTGTA 60.037 50.000 39.95 23.62 44.69 2.90
107 108 2.098233 CGAGTAAACGCATGCGGGT 61.098 57.895 39.95 29.32 44.69 5.28
137 138 4.212913 TCTCGCCCTCTCGCATGC 62.213 66.667 7.91 7.91 0.00 4.06
138 139 2.279120 GTCTCGCCCTCTCGCATG 60.279 66.667 0.00 0.00 0.00 4.06
139 140 3.893763 CGTCTCGCCCTCTCGCAT 61.894 66.667 0.00 0.00 0.00 4.73
142 143 3.878519 GTCCGTCTCGCCCTCTCG 61.879 72.222 0.00 0.00 0.00 4.04
161 162 4.626081 AAGCAACGCTGGCGGTCT 62.626 61.111 18.99 9.12 44.69 3.85
178 179 2.046988 CCACTCCACATGCTCGCA 60.047 61.111 0.00 0.00 0.00 5.10
181 182 2.012673 GAATGACCACTCCACATGCTC 58.987 52.381 0.00 0.00 0.00 4.26
184 185 3.822735 ACTTTGAATGACCACTCCACATG 59.177 43.478 0.00 0.00 0.00 3.21
196 197 4.275689 ACGATCTTGCAACACTTTGAATGA 59.724 37.500 0.00 0.00 34.24 2.57
203 204 3.074412 CCCTAACGATCTTGCAACACTT 58.926 45.455 0.00 0.00 0.00 3.16
217 218 3.560068 GCTCCATGAACAATACCCTAACG 59.440 47.826 0.00 0.00 0.00 3.18
224 225 4.096833 TCATTGCAGCTCCATGAACAATAC 59.903 41.667 0.00 0.00 0.00 1.89
233 234 2.440627 TCCTACATCATTGCAGCTCCAT 59.559 45.455 0.00 0.00 0.00 3.41
251 252 4.323104 GCTACCACAAAGTCTCTGATTCCT 60.323 45.833 0.00 0.00 0.00 3.36
253 254 4.629200 CAGCTACCACAAAGTCTCTGATTC 59.371 45.833 0.00 0.00 0.00 2.52
256 257 3.230976 TCAGCTACCACAAAGTCTCTGA 58.769 45.455 0.00 0.00 0.00 3.27
269 270 7.969536 ATGACACAATATGTATTCAGCTACC 57.030 36.000 0.00 0.00 43.56 3.18
321 322 7.927092 GCCACACTTTTGGTATTAAAACCTTAA 59.073 33.333 0.00 0.00 40.44 1.85
322 323 7.288158 AGCCACACTTTTGGTATTAAAACCTTA 59.712 33.333 0.00 0.00 40.44 2.69
323 324 6.099125 AGCCACACTTTTGGTATTAAAACCTT 59.901 34.615 0.00 0.00 40.44 3.50
324 325 5.600898 AGCCACACTTTTGGTATTAAAACCT 59.399 36.000 0.00 0.00 40.44 3.50
332 376 3.508845 AGACAGCCACACTTTTGGTAT 57.491 42.857 0.00 0.00 39.09 2.73
335 379 3.820467 TGATTAGACAGCCACACTTTTGG 59.180 43.478 0.00 0.00 39.98 3.28
336 380 5.437289 TTGATTAGACAGCCACACTTTTG 57.563 39.130 0.00 0.00 0.00 2.44
338 382 7.944729 ATATTTGATTAGACAGCCACACTTT 57.055 32.000 0.00 0.00 0.00 2.66
346 390 7.519008 CGGTCCTCAAATATTTGATTAGACAGC 60.519 40.741 31.62 23.09 45.26 4.40
350 394 7.223971 CGAACGGTCCTCAAATATTTGATTAGA 59.776 37.037 26.83 20.75 45.26 2.10
351 395 7.223971 TCGAACGGTCCTCAAATATTTGATTAG 59.776 37.037 26.83 19.18 45.26 1.73
357 401 4.035208 GCATCGAACGGTCCTCAAATATTT 59.965 41.667 0.00 0.00 0.00 1.40
360 404 2.546778 GCATCGAACGGTCCTCAAATA 58.453 47.619 0.00 0.00 0.00 1.40
365 409 1.872679 GACGCATCGAACGGTCCTC 60.873 63.158 14.62 1.02 34.00 3.71
379 423 0.739813 ACCTAGACATTTGCGGACGC 60.740 55.000 10.13 10.13 42.35 5.19
380 424 0.999406 CACCTAGACATTTGCGGACG 59.001 55.000 0.00 0.00 0.00 4.79
381 425 2.094762 ACACCTAGACATTTGCGGAC 57.905 50.000 0.00 0.00 0.00 4.79
382 426 2.851263 AACACCTAGACATTTGCGGA 57.149 45.000 0.00 0.00 0.00 5.54
383 427 3.857052 TCTAACACCTAGACATTTGCGG 58.143 45.455 0.00 0.00 31.28 5.69
385 429 8.438676 AACATATCTAACACCTAGACATTTGC 57.561 34.615 0.00 0.00 39.52 3.68
391 435 9.747293 GGACTTTAACATATCTAACACCTAGAC 57.253 37.037 0.00 0.00 39.52 2.59
393 437 7.866393 CCGGACTTTAACATATCTAACACCTAG 59.134 40.741 0.00 0.00 0.00 3.02
394 438 7.201938 CCCGGACTTTAACATATCTAACACCTA 60.202 40.741 0.73 0.00 0.00 3.08
395 439 6.407752 CCCGGACTTTAACATATCTAACACCT 60.408 42.308 0.73 0.00 0.00 4.00
399 443 5.235831 GCACCCGGACTTTAACATATCTAAC 59.764 44.000 0.73 0.00 0.00 2.34
400 444 5.362263 GCACCCGGACTTTAACATATCTAA 58.638 41.667 0.73 0.00 0.00 2.10
401 445 4.202284 GGCACCCGGACTTTAACATATCTA 60.202 45.833 0.73 0.00 0.00 1.98
402 446 3.433173 GGCACCCGGACTTTAACATATCT 60.433 47.826 0.73 0.00 0.00 1.98
406 450 0.675522 CGGCACCCGGACTTTAACAT 60.676 55.000 0.73 0.00 44.15 2.71
420 464 0.874390 TGTTTTCAGAGCATCGGCAC 59.126 50.000 0.00 0.00 44.61 5.01
441 485 5.163844 GGAGAAATTTACTCTGGCTTCGTTC 60.164 44.000 13.68 0.00 35.10 3.95
442 486 4.695928 GGAGAAATTTACTCTGGCTTCGTT 59.304 41.667 13.68 0.00 35.10 3.85
443 487 4.254492 GGAGAAATTTACTCTGGCTTCGT 58.746 43.478 13.68 0.00 35.10 3.85
444 488 4.093556 GTGGAGAAATTTACTCTGGCTTCG 59.906 45.833 13.68 0.00 35.10 3.79
448 492 3.942115 GAGGTGGAGAAATTTACTCTGGC 59.058 47.826 13.68 7.34 35.10 4.85
473 517 2.596338 TCTCGTGAGTCGTGCCCA 60.596 61.111 0.00 0.00 40.80 5.36
476 520 2.179517 CCCTCTCGTGAGTCGTGC 59.820 66.667 13.09 0.00 38.61 5.34
482 526 1.812922 GCATGTGCCCTCTCGTGAG 60.813 63.158 7.53 7.53 39.92 3.51
816 865 1.420514 CATGGGCATGGATCTCTGACT 59.579 52.381 0.00 0.00 35.24 3.41
904 953 4.269523 TTTGCCCAGCTCGCCAGT 62.270 61.111 0.00 0.00 0.00 4.00
925 974 7.094634 TGACCAGAACATAGAAATTTCTTCAGC 60.095 37.037 25.02 11.61 38.70 4.26
929 978 9.793259 TTACTGACCAGAACATAGAAATTTCTT 57.207 29.630 25.02 7.91 38.70 2.52
1200 1251 1.006571 GTCGAACTTGAGGTCGGCA 60.007 57.895 17.27 0.00 0.00 5.69
1233 1284 2.688666 AGCTCCGGAATGAGGGCA 60.689 61.111 5.23 0.00 32.81 5.36
1242 1293 1.176619 TCACGAAAGACAGCTCCGGA 61.177 55.000 2.93 2.93 0.00 5.14
1254 1305 0.765135 TCCAGTCCCCCTTCACGAAA 60.765 55.000 0.00 0.00 0.00 3.46
1260 1311 1.301293 CTGCTTCCAGTCCCCCTTC 59.699 63.158 0.00 0.00 34.31 3.46
1266 1317 1.079750 GACGTCCTGCTTCCAGTCC 60.080 63.158 3.51 0.00 37.38 3.85
1296 1347 3.076258 ATCGAACGGCATCAGCGGA 62.076 57.895 0.00 0.00 43.11 5.54
1503 1554 2.113139 CCGGGCCACACTTTGAGT 59.887 61.111 4.39 0.00 0.00 3.41
1677 1728 3.645660 TGGGTGATTGGCGGCTGA 61.646 61.111 11.43 0.00 0.00 4.26
1696 1747 2.146342 CACGAGCAGGATGTTCTTGTT 58.854 47.619 0.00 0.00 44.82 2.83
1894 1945 0.037975 ATGTCGTCGCGGTAAGGTTT 60.038 50.000 6.13 0.00 0.00 3.27
1896 1947 1.138247 GATGTCGTCGCGGTAAGGT 59.862 57.895 6.13 0.00 0.00 3.50
1996 2047 0.817634 CACTTCCAGTTGGGCACGAA 60.818 55.000 0.00 0.00 36.21 3.85
2013 2064 1.609840 GAGCGTCTGTCGAGTTGCAC 61.610 60.000 0.00 0.00 42.86 4.57
2082 2133 3.659089 ATCCTTGAACCCGCCGTCG 62.659 63.158 0.00 0.00 0.00 5.12
2394 2445 1.721487 GTCGATGCGGGTGATTTGG 59.279 57.895 0.00 0.00 0.00 3.28
2513 2564 4.304110 CTTGGTGTAGTTGTACGTCATGT 58.696 43.478 0.00 0.00 30.95 3.21
2518 2569 1.270465 GGCCTTGGTGTAGTTGTACGT 60.270 52.381 0.00 0.00 30.95 3.57
2524 2575 0.184933 TGCTTGGCCTTGGTGTAGTT 59.815 50.000 3.32 0.00 0.00 2.24
2833 2899 2.179517 CGTCCTCTCCGTCTGCAC 59.820 66.667 0.00 0.00 0.00 4.57
2843 2909 1.984817 AGGAGAGACGTCGTCCTCT 59.015 57.895 27.68 24.31 35.71 3.69
2848 2914 0.883814 ACGTTGAGGAGAGACGTCGT 60.884 55.000 10.46 0.00 45.82 4.34
2902 2968 3.041940 CAGGGCCGACACGTTCAC 61.042 66.667 0.00 0.00 0.00 3.18
3021 3087 3.303189 CAGTCCATGCCGTCCTCT 58.697 61.111 0.00 0.00 0.00 3.69
4248 4314 0.028505 CGTCCGATCGGTCACGTTAT 59.971 55.000 29.96 0.00 41.85 1.89
4251 4317 3.807538 CCGTCCGATCGGTCACGT 61.808 66.667 33.14 0.00 44.77 4.49
4258 4324 1.003759 CTACAGAGAACCGTCCGATCG 60.004 57.143 8.51 8.51 0.00 3.69
4292 4358 4.530710 ACACATACATGTCAACCTACGT 57.469 40.909 0.00 0.00 39.39 3.57
4394 4462 1.153958 GGCTGAGATTGGCGCAAAC 60.154 57.895 10.83 0.00 0.00 2.93
4399 5227 0.379669 GAATGTGGCTGAGATTGGCG 59.620 55.000 0.00 0.00 0.00 5.69
4409 5237 3.196469 TCAGAGAATTCGAGAATGTGGCT 59.804 43.478 0.00 0.00 0.00 4.75
4418 5246 6.312180 TGTCATTGATGTTCAGAGAATTCGAG 59.688 38.462 0.00 0.00 0.00 4.04
4419 5247 6.165577 TGTCATTGATGTTCAGAGAATTCGA 58.834 36.000 0.00 0.00 0.00 3.71
4420 5248 6.413018 TGTCATTGATGTTCAGAGAATTCG 57.587 37.500 0.00 0.00 0.00 3.34
4438 6114 6.638610 CCATCAGTTCTAGAGTTCTTGTCAT 58.361 40.000 0.00 0.00 0.00 3.06
4515 6191 3.621558 ACCCTAAGTTTGAAGCCATAGC 58.378 45.455 0.00 0.00 40.32 2.97
4516 6192 5.104259 AGACCCTAAGTTTGAAGCCATAG 57.896 43.478 0.00 0.00 0.00 2.23
4517 6193 4.783227 AGAGACCCTAAGTTTGAAGCCATA 59.217 41.667 0.00 0.00 0.00 2.74
4518 6194 3.589288 AGAGACCCTAAGTTTGAAGCCAT 59.411 43.478 0.00 0.00 0.00 4.40
4519 6195 2.979678 AGAGACCCTAAGTTTGAAGCCA 59.020 45.455 0.00 0.00 0.00 4.75
4520 6196 3.704800 AGAGACCCTAAGTTTGAAGCC 57.295 47.619 0.00 0.00 0.00 4.35
4521 6197 5.063880 TCAAAGAGACCCTAAGTTTGAAGC 58.936 41.667 0.00 0.00 34.91 3.86
4522 6198 7.360438 CGAATCAAAGAGACCCTAAGTTTGAAG 60.360 40.741 0.00 0.00 39.77 3.02
4523 6199 6.426937 CGAATCAAAGAGACCCTAAGTTTGAA 59.573 38.462 0.00 0.00 39.77 2.69
4524 6200 5.932303 CGAATCAAAGAGACCCTAAGTTTGA 59.068 40.000 0.00 0.00 40.42 2.69
4525 6201 5.701290 ACGAATCAAAGAGACCCTAAGTTTG 59.299 40.000 0.00 0.00 0.00 2.93
4526 6202 5.866207 ACGAATCAAAGAGACCCTAAGTTT 58.134 37.500 0.00 0.00 0.00 2.66
4527 6203 5.485209 ACGAATCAAAGAGACCCTAAGTT 57.515 39.130 0.00 0.00 0.00 2.66
4528 6204 5.392811 CGTACGAATCAAAGAGACCCTAAGT 60.393 44.000 10.44 0.00 0.00 2.24
4529 6205 5.035443 CGTACGAATCAAAGAGACCCTAAG 58.965 45.833 10.44 0.00 0.00 2.18
4530 6206 4.701651 TCGTACGAATCAAAGAGACCCTAA 59.298 41.667 17.11 0.00 0.00 2.69
4531 6207 4.264253 TCGTACGAATCAAAGAGACCCTA 58.736 43.478 17.11 0.00 0.00 3.53
4532 6208 3.087031 TCGTACGAATCAAAGAGACCCT 58.913 45.455 17.11 0.00 0.00 4.34
4533 6209 3.498927 TCGTACGAATCAAAGAGACCC 57.501 47.619 17.11 0.00 0.00 4.46
4534 6210 5.005490 GGAAATCGTACGAATCAAAGAGACC 59.995 44.000 23.56 9.87 0.00 3.85
4535 6211 5.575606 TGGAAATCGTACGAATCAAAGAGAC 59.424 40.000 23.56 9.25 0.00 3.36
4536 6212 5.716094 TGGAAATCGTACGAATCAAAGAGA 58.284 37.500 23.56 0.00 0.00 3.10
4537 6213 6.403333 TTGGAAATCGTACGAATCAAAGAG 57.597 37.500 23.56 0.00 0.00 2.85
4538 6214 6.788684 TTTGGAAATCGTACGAATCAAAGA 57.211 33.333 23.56 10.85 0.00 2.52
4539 6215 7.461416 GCATTTTGGAAATCGTACGAATCAAAG 60.461 37.037 23.56 16.92 0.00 2.77
4540 6216 6.306837 GCATTTTGGAAATCGTACGAATCAAA 59.693 34.615 23.56 22.83 0.00 2.69
4541 6217 5.797934 GCATTTTGGAAATCGTACGAATCAA 59.202 36.000 23.56 18.97 0.00 2.57
4542 6218 5.328691 GCATTTTGGAAATCGTACGAATCA 58.671 37.500 23.56 14.45 0.00 2.57
4543 6219 4.433304 CGCATTTTGGAAATCGTACGAATC 59.567 41.667 23.56 21.54 0.00 2.52
4544 6220 4.339429 CGCATTTTGGAAATCGTACGAAT 58.661 39.130 23.56 11.74 0.00 3.34
4545 6221 3.425094 CCGCATTTTGGAAATCGTACGAA 60.425 43.478 23.56 1.59 0.00 3.85
4546 6222 2.094575 CCGCATTTTGGAAATCGTACGA 59.905 45.455 21.93 21.93 0.00 3.43
4547 6223 2.436670 CCGCATTTTGGAAATCGTACG 58.563 47.619 9.53 9.53 0.00 3.67
4548 6224 2.420722 TCCCGCATTTTGGAAATCGTAC 59.579 45.455 0.00 0.00 0.00 3.67
4549 6225 2.712709 TCCCGCATTTTGGAAATCGTA 58.287 42.857 0.00 0.00 0.00 3.43
4550 6226 1.540267 TCCCGCATTTTGGAAATCGT 58.460 45.000 0.00 0.00 0.00 3.73
4551 6227 2.645730 TTCCCGCATTTTGGAAATCG 57.354 45.000 0.00 0.00 37.69 3.34
4552 6228 4.340950 TCCTATTCCCGCATTTTGGAAATC 59.659 41.667 0.00 0.00 43.50 2.17
4553 6229 4.285863 TCCTATTCCCGCATTTTGGAAAT 58.714 39.130 0.00 0.00 43.50 2.17
4554 6230 3.702792 TCCTATTCCCGCATTTTGGAAA 58.297 40.909 0.00 0.00 43.50 3.13
4555 6231 3.374042 TCCTATTCCCGCATTTTGGAA 57.626 42.857 0.00 0.00 44.34 3.53
4556 6232 3.374042 TTCCTATTCCCGCATTTTGGA 57.626 42.857 0.00 0.00 0.00 3.53
4557 6233 4.464069 TTTTCCTATTCCCGCATTTTGG 57.536 40.909 0.00 0.00 0.00 3.28
4558 6234 5.233988 TGTTTTTCCTATTCCCGCATTTTG 58.766 37.500 0.00 0.00 0.00 2.44
4559 6235 5.476091 TGTTTTTCCTATTCCCGCATTTT 57.524 34.783 0.00 0.00 0.00 1.82
4560 6236 5.186797 TCATGTTTTTCCTATTCCCGCATTT 59.813 36.000 0.00 0.00 0.00 2.32
4561 6237 4.709397 TCATGTTTTTCCTATTCCCGCATT 59.291 37.500 0.00 0.00 0.00 3.56
4562 6238 4.277476 TCATGTTTTTCCTATTCCCGCAT 58.723 39.130 0.00 0.00 0.00 4.73
4563 6239 3.691575 TCATGTTTTTCCTATTCCCGCA 58.308 40.909 0.00 0.00 0.00 5.69
4564 6240 3.945285 TCTCATGTTTTTCCTATTCCCGC 59.055 43.478 0.00 0.00 0.00 6.13
4565 6241 6.699575 AATCTCATGTTTTTCCTATTCCCG 57.300 37.500 0.00 0.00 0.00 5.14
4566 6242 8.980481 TCTAATCTCATGTTTTTCCTATTCCC 57.020 34.615 0.00 0.00 0.00 3.97
4567 6243 9.620259 ACTCTAATCTCATGTTTTTCCTATTCC 57.380 33.333 0.00 0.00 0.00 3.01
4569 6245 9.401058 CCACTCTAATCTCATGTTTTTCCTATT 57.599 33.333 0.00 0.00 0.00 1.73
4570 6246 7.500559 GCCACTCTAATCTCATGTTTTTCCTAT 59.499 37.037 0.00 0.00 0.00 2.57
4571 6247 6.823689 GCCACTCTAATCTCATGTTTTTCCTA 59.176 38.462 0.00 0.00 0.00 2.94
4572 6248 5.649831 GCCACTCTAATCTCATGTTTTTCCT 59.350 40.000 0.00 0.00 0.00 3.36
4573 6249 5.415701 TGCCACTCTAATCTCATGTTTTTCC 59.584 40.000 0.00 0.00 0.00 3.13
4574 6250 6.150140 AGTGCCACTCTAATCTCATGTTTTTC 59.850 38.462 0.00 0.00 0.00 2.29
4575 6251 6.006449 AGTGCCACTCTAATCTCATGTTTTT 58.994 36.000 0.00 0.00 0.00 1.94
4576 6252 5.564550 AGTGCCACTCTAATCTCATGTTTT 58.435 37.500 0.00 0.00 0.00 2.43
4577 6253 5.171339 AGTGCCACTCTAATCTCATGTTT 57.829 39.130 0.00 0.00 0.00 2.83
4578 6254 4.833478 AGTGCCACTCTAATCTCATGTT 57.167 40.909 0.00 0.00 0.00 2.71
4579 6255 4.469227 AGAAGTGCCACTCTAATCTCATGT 59.531 41.667 0.00 0.00 0.00 3.21
4580 6256 4.809958 CAGAAGTGCCACTCTAATCTCATG 59.190 45.833 0.00 0.00 0.00 3.07
4581 6257 4.682859 GCAGAAGTGCCACTCTAATCTCAT 60.683 45.833 0.00 0.00 44.72 2.90
4582 6258 3.368843 GCAGAAGTGCCACTCTAATCTCA 60.369 47.826 0.00 0.00 44.72 3.27
4583 6259 3.194062 GCAGAAGTGCCACTCTAATCTC 58.806 50.000 0.00 0.00 44.72 2.75
4584 6260 3.258971 GCAGAAGTGCCACTCTAATCT 57.741 47.619 0.00 0.00 44.72 2.40
4644 6320 2.690881 AGCGAAGGGGTATGGGCA 60.691 61.111 0.00 0.00 0.00 5.36
5053 6747 4.020617 CAACAGCTGGCCCGAGGA 62.021 66.667 19.93 0.00 0.00 3.71
5063 6757 3.181967 GCGATCGCGTCAACAGCT 61.182 61.111 26.12 0.00 40.36 4.24
5110 6805 4.704833 TGGCGTCTGAAGGCAGGC 62.705 66.667 15.25 0.00 43.31 4.85
5114 6809 3.665675 ATCGGTGGCGTCTGAAGGC 62.666 63.158 10.08 10.08 35.53 4.35
5150 6845 3.716006 CTGGCGTGTGAAGGCGTG 61.716 66.667 0.00 0.00 36.92 5.34
5153 6848 4.030452 GTGCTGGCGTGTGAAGGC 62.030 66.667 0.00 0.00 0.00 4.35
5154 6849 2.281070 AGTGCTGGCGTGTGAAGG 60.281 61.111 0.00 0.00 0.00 3.46
5155 6850 2.941333 CAGTGCTGGCGTGTGAAG 59.059 61.111 0.00 0.00 0.00 3.02
5156 6851 3.279116 GCAGTGCTGGCGTGTGAA 61.279 61.111 8.18 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.