Multiple sequence alignment - TraesCS2D01G214100

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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 TraesCS2D01G214100 chr2D 100.000 3512 0 0 1 3512 175330191 175333702 0.000000e+00 6486.0
1 TraesCS2D01G214100 chr2D 79.878 164 33 0 1072 1235 54317506 54317669 1.710000e-23 121.0
2 TraesCS2D01G214100 chr2D 100.000 28 0 0 3050 3077 175333142 175333169 6.000000e-03 52.8
3 TraesCS2D01G214100 chr2D 100.000 28 0 0 2952 2979 175333240 175333267 6.000000e-03 52.8
4 TraesCS2D01G214100 chr2B 95.243 2859 72 21 502 3329 223153623 223156448 0.000000e+00 4468.0
5 TraesCS2D01G214100 chr2B 81.132 159 30 0 1080 1238 85177920 85177762 1.020000e-25 128.0
6 TraesCS2D01G214100 chr2B 80.368 163 32 0 1073 1235 85074001 85074163 1.320000e-24 124.0
7 TraesCS2D01G214100 chr2B 95.946 74 2 1 430 503 223152395 223152467 6.160000e-23 119.0
8 TraesCS2D01G214100 chr2B 100.000 28 0 0 3050 3077 223156049 223156076 6.000000e-03 52.8
9 TraesCS2D01G214100 chr2A 96.111 2674 63 14 421 3078 175467039 175469687 0.000000e+00 4324.0
10 TraesCS2D01G214100 chr2A 93.091 275 18 1 3077 3351 175469903 175470176 5.460000e-108 401.0
11 TraesCS2D01G214100 chr2A 80.625 160 30 1 1072 1231 54882364 54882522 4.760000e-24 122.0
12 TraesCS2D01G214100 chr6D 86.055 2137 117 79 714 2745 60488234 60486174 0.000000e+00 2128.0
13 TraesCS2D01G214100 chr6D 89.809 157 10 4 512 663 60488390 60488235 2.770000e-46 196.0
14 TraesCS2D01G214100 chr6A 84.942 2145 120 84 714 2745 77100380 77098326 0.000000e+00 1984.0
15 TraesCS2D01G214100 chr6A 88.608 158 11 4 512 663 77100537 77100381 5.990000e-43 185.0
16 TraesCS2D01G214100 chr6B 83.993 2149 138 79 713 2745 134665082 134663024 0.000000e+00 1873.0
17 TraesCS2D01G214100 chr6B 89.172 157 11 4 512 663 134665234 134665079 1.290000e-44 191.0
18 TraesCS2D01G214100 chr6B 89.796 147 15 0 3366 3512 37105765 37105619 4.630000e-44 189.0
19 TraesCS2D01G214100 chr6B 85.455 110 6 3 2903 3011 134662973 134662873 4.790000e-19 106.0
20 TraesCS2D01G214100 chr3D 86.695 233 28 2 1451 1680 39325676 39325444 4.500000e-64 255.0
21 TraesCS2D01G214100 chr3D 90.476 147 14 0 3366 3512 382120476 382120330 9.950000e-46 195.0
22 TraesCS2D01G214100 chr3D 89.404 151 16 0 3362 3512 326275711 326275561 1.290000e-44 191.0
23 TraesCS2D01G214100 chr5A 85.597 243 30 4 1439 1680 317247919 317247681 2.090000e-62 250.0
24 TraesCS2D01G214100 chr7B 92.517 147 11 0 3366 3512 616291454 616291308 9.880000e-51 211.0
25 TraesCS2D01G214100 chr7B 91.156 147 13 0 3366 3512 378031894 378031748 2.140000e-47 200.0
26 TraesCS2D01G214100 chr7B 91.156 147 13 0 3366 3512 403790409 403790263 2.140000e-47 200.0
27 TraesCS2D01G214100 chr1B 90.728 151 14 0 3362 3512 26825799 26825949 5.940000e-48 202.0
28 TraesCS2D01G214100 chr5D 91.034 145 13 0 3368 3512 210601113 210601257 2.770000e-46 196.0
29 TraesCS2D01G214100 chr5B 90.476 147 14 0 3366 3512 576217729 576217583 9.950000e-46 195.0
30 TraesCS2D01G214100 chr5B 82.667 75 11 2 3186 3258 684062705 684062631 8.140000e-07 65.8
31 TraesCS2D01G214100 chr5B 97.297 37 1 0 3185 3221 105763707 105763743 2.930000e-06 63.9
32 TraesCS2D01G214100 chrUn 75.455 330 42 29 1 298 470980643 470980965 1.320000e-24 124.0
33 TraesCS2D01G214100 chr7A 83.333 78 9 3 3184 3258 247257068 247256992 6.290000e-08 69.4
34 TraesCS2D01G214100 chr4B 100.000 36 0 0 3186 3221 598457038 598457003 2.260000e-07 67.6
35 TraesCS2D01G214100 chr4A 100.000 36 0 0 3186 3221 681609125 681609160 2.260000e-07 67.6
36 TraesCS2D01G214100 chr3A 97.222 36 1 0 3186 3221 53027998 53028033 1.050000e-05 62.1
37 TraesCS2D01G214100 chr1D 97.222 36 1 0 3186 3221 10334902 10334867 1.050000e-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 TraesCS2D01G214100 chr2D 175330191 175333702 3511 False 2197.200000 6486 100.000000 1 3512 3 chr2D.!!$F2 3511
1 TraesCS2D01G214100 chr2B 223152395 223156448 4053 False 1546.600000 4468 97.063000 430 3329 3 chr2B.!!$F2 2899
2 TraesCS2D01G214100 chr2A 175467039 175470176 3137 False 2362.500000 4324 94.601000 421 3351 2 chr2A.!!$F2 2930
3 TraesCS2D01G214100 chr6D 60486174 60488390 2216 True 1162.000000 2128 87.932000 512 2745 2 chr6D.!!$R1 2233
4 TraesCS2D01G214100 chr6A 77098326 77100537 2211 True 1084.500000 1984 86.775000 512 2745 2 chr6A.!!$R1 2233
5 TraesCS2D01G214100 chr6B 134662873 134665234 2361 True 723.333333 1873 86.206667 512 3011 3 chr6B.!!$R2 2499

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
409 410 0.036388 GTCGTGCCTTGATTCCCTCA 60.036 55.0 0.0 0.0 0.00 3.86 F
410 411 0.690192 TCGTGCCTTGATTCCCTCAA 59.310 50.0 0.0 0.0 41.61 3.02 F
854 2033 1.022451 TCGCCGTAACAAATCCCAGC 61.022 55.0 0.0 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1807 3095 3.844211 TCAACCACAATACCCTAAGCTCT 59.156 43.478 0.00 0.0 0.00 4.09 R
2409 3717 2.202932 GCGCCGAGGATGACATGT 60.203 61.111 0.00 0.0 0.00 3.21 R
2799 4159 7.092489 TGGGGATTGTAATCAGCTGCATATATA 60.092 37.037 9.47 0.0 37.15 0.86 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
25 26 8.654230 TTTGAATTCGATGGACAAATTTTGAA 57.346 26.923 15.81 1.87 0.00 2.69
26 27 8.830201 TTGAATTCGATGGACAAATTTTGAAT 57.170 26.923 15.81 6.34 0.00 2.57
27 28 8.830201 TGAATTCGATGGACAAATTTTGAATT 57.170 26.923 15.81 8.77 37.47 2.17
28 29 9.270640 TGAATTCGATGGACAAATTTTGAATTT 57.729 25.926 15.81 0.00 35.59 1.82
29 30 9.532697 GAATTCGATGGACAAATTTTGAATTTG 57.467 29.630 19.22 19.22 42.81 2.32
30 31 8.830201 ATTCGATGGACAAATTTTGAATTTGA 57.170 26.923 24.79 9.63 40.42 2.69
31 32 8.830201 TTCGATGGACAAATTTTGAATTTGAT 57.170 26.923 24.79 12.95 40.42 2.57
32 33 8.242085 TCGATGGACAAATTTTGAATTTGATG 57.758 30.769 24.79 7.34 40.42 3.07
33 34 8.087136 TCGATGGACAAATTTTGAATTTGATGA 58.913 29.630 24.79 12.48 40.42 2.92
34 35 8.710551 CGATGGACAAATTTTGAATTTGATGAA 58.289 29.630 24.79 12.35 40.42 2.57
35 36 9.815936 GATGGACAAATTTTGAATTTGATGAAC 57.184 29.630 24.79 13.66 40.42 3.18
36 37 8.728337 TGGACAAATTTTGAATTTGATGAACA 57.272 26.923 24.79 15.28 40.42 3.18
37 38 9.339850 TGGACAAATTTTGAATTTGATGAACAT 57.660 25.926 24.79 7.62 40.42 2.71
65 66 9.713740 TTTTTGAAAATCAATGGACAAATTTCG 57.286 25.926 0.00 0.00 36.11 3.46
66 67 8.430801 TTTGAAAATCAATGGACAAATTTCGT 57.569 26.923 0.00 0.00 36.11 3.85
67 68 9.534565 TTTGAAAATCAATGGACAAATTTCGTA 57.465 25.926 0.00 0.00 36.11 3.43
68 69 9.703892 TTGAAAATCAATGGACAAATTTCGTAT 57.296 25.926 0.00 0.00 30.26 3.06
69 70 9.703892 TGAAAATCAATGGACAAATTTCGTATT 57.296 25.926 0.00 0.00 0.00 1.89
72 73 9.703892 AAATCAATGGACAAATTTCGTATTTGA 57.296 25.926 23.02 9.11 40.42 2.69
73 74 9.874205 AATCAATGGACAAATTTCGTATTTGAT 57.126 25.926 23.02 12.75 40.42 2.57
74 75 8.686397 TCAATGGACAAATTTCGTATTTGATG 57.314 30.769 23.02 15.61 40.42 3.07
75 76 7.275341 TCAATGGACAAATTTCGTATTTGATGC 59.725 33.333 23.02 15.77 40.42 3.91
76 77 6.018589 TGGACAAATTTCGTATTTGATGCA 57.981 33.333 23.02 17.27 40.42 3.96
77 78 5.861251 TGGACAAATTTCGTATTTGATGCAC 59.139 36.000 23.02 12.91 40.42 4.57
78 79 5.861251 GGACAAATTTCGTATTTGATGCACA 59.139 36.000 23.02 0.00 40.42 4.57
79 80 6.531240 GGACAAATTTCGTATTTGATGCACAT 59.469 34.615 23.02 7.28 40.42 3.21
80 81 7.063308 GGACAAATTTCGTATTTGATGCACATT 59.937 33.333 23.02 6.77 40.42 2.71
81 82 8.309163 ACAAATTTCGTATTTGATGCACATTT 57.691 26.923 23.02 4.43 40.42 2.32
82 83 8.772705 ACAAATTTCGTATTTGATGCACATTTT 58.227 25.926 23.02 3.92 40.42 1.82
83 84 9.596677 CAAATTTCGTATTTGATGCACATTTTT 57.403 25.926 15.79 0.00 40.42 1.94
199 200 5.574815 AAAAAGTTCGCGGATTTGAAATG 57.425 34.783 6.13 0.00 0.00 2.32
200 201 4.497473 AAAGTTCGCGGATTTGAAATGA 57.503 36.364 6.13 0.00 0.00 2.57
201 202 4.497473 AAGTTCGCGGATTTGAAATGAA 57.503 36.364 6.13 0.00 0.00 2.57
202 203 4.497473 AGTTCGCGGATTTGAAATGAAA 57.503 36.364 6.13 0.00 0.00 2.69
203 204 4.865776 AGTTCGCGGATTTGAAATGAAAA 58.134 34.783 6.13 0.00 0.00 2.29
204 205 5.469479 AGTTCGCGGATTTGAAATGAAAAT 58.531 33.333 6.13 0.00 0.00 1.82
205 206 5.925969 AGTTCGCGGATTTGAAATGAAAATT 59.074 32.000 6.13 0.00 0.00 1.82
206 207 6.089417 AGTTCGCGGATTTGAAATGAAAATTC 59.911 34.615 6.13 0.00 0.00 2.17
207 208 4.556912 TCGCGGATTTGAAATGAAAATTCG 59.443 37.500 6.13 5.43 44.99 3.34
209 210 5.760193 CGGATTTGAAATGAAAATTCGCA 57.240 34.783 0.00 0.00 38.70 5.10
210 211 6.150738 CGGATTTGAAATGAAAATTCGCAA 57.849 33.333 0.00 0.00 38.70 4.85
211 212 6.588552 CGGATTTGAAATGAAAATTCGCAAA 58.411 32.000 0.00 0.00 38.70 3.68
212 213 7.068341 CGGATTTGAAATGAAAATTCGCAAAA 58.932 30.769 0.00 0.00 38.70 2.44
213 214 7.585573 CGGATTTGAAATGAAAATTCGCAAAAA 59.414 29.630 0.00 0.00 38.70 1.94
272 273 9.625747 AAAAAGGCAATCAGGAAATAAAAAGAA 57.374 25.926 0.00 0.00 0.00 2.52
273 274 9.625747 AAAAGGCAATCAGGAAATAAAAAGAAA 57.374 25.926 0.00 0.00 0.00 2.52
274 275 9.625747 AAAGGCAATCAGGAAATAAAAAGAAAA 57.374 25.926 0.00 0.00 0.00 2.29
275 276 9.625747 AAGGCAATCAGGAAATAAAAAGAAAAA 57.374 25.926 0.00 0.00 0.00 1.94
331 332 6.902224 AAAACGAAAAAGACAGGAAAATGG 57.098 33.333 0.00 0.00 0.00 3.16
332 333 4.584327 ACGAAAAAGACAGGAAAATGGG 57.416 40.909 0.00 0.00 0.00 4.00
333 334 3.243737 ACGAAAAAGACAGGAAAATGGGC 60.244 43.478 0.00 0.00 0.00 5.36
334 335 3.664107 GAAAAAGACAGGAAAATGGGCC 58.336 45.455 0.00 0.00 0.00 5.80
335 336 1.256812 AAAGACAGGAAAATGGGCCG 58.743 50.000 0.00 0.00 0.00 6.13
336 337 0.611896 AAGACAGGAAAATGGGCCGG 60.612 55.000 0.00 0.00 0.00 6.13
337 338 1.304134 GACAGGAAAATGGGCCGGT 60.304 57.895 1.90 0.00 35.26 5.28
338 339 1.304134 ACAGGAAAATGGGCCGGTC 60.304 57.895 1.90 0.00 0.00 4.79
339 340 2.052104 CAGGAAAATGGGCCGGTCC 61.052 63.158 21.35 21.35 0.00 4.46
340 341 2.036572 GGAAAATGGGCCGGTCCA 59.963 61.111 33.79 33.79 41.60 4.02
342 343 0.106419 GGAAAATGGGCCGGTCCATA 60.106 55.000 39.78 15.47 46.05 2.74
343 344 1.029681 GAAAATGGGCCGGTCCATAC 58.970 55.000 39.78 27.84 46.05 2.39
344 345 0.333312 AAAATGGGCCGGTCCATACA 59.667 50.000 39.78 14.12 46.05 2.29
345 346 0.333312 AAATGGGCCGGTCCATACAA 59.667 50.000 39.78 13.66 46.05 2.41
346 347 0.395173 AATGGGCCGGTCCATACAAC 60.395 55.000 39.78 4.93 46.05 3.32
347 348 1.567208 ATGGGCCGGTCCATACAACA 61.567 55.000 39.10 10.74 45.03 3.33
348 349 1.747745 GGGCCGGTCCATACAACAC 60.748 63.158 23.50 0.00 36.21 3.32
349 350 1.747745 GGCCGGTCCATACAACACC 60.748 63.158 1.90 0.00 34.01 4.16
350 351 1.747745 GCCGGTCCATACAACACCC 60.748 63.158 1.90 0.00 0.00 4.61
351 352 1.448893 CCGGTCCATACAACACCCG 60.449 63.158 0.00 0.00 35.32 5.28
352 353 2.104253 CGGTCCATACAACACCCGC 61.104 63.158 0.00 0.00 0.00 6.13
353 354 2.104253 GGTCCATACAACACCCGCG 61.104 63.158 0.00 0.00 0.00 6.46
354 355 2.435234 TCCATACAACACCCGCGC 60.435 61.111 0.00 0.00 0.00 6.86
355 356 3.860125 CCATACAACACCCGCGCG 61.860 66.667 25.67 25.67 0.00 6.86
356 357 4.514569 CATACAACACCCGCGCGC 62.515 66.667 27.36 23.91 0.00 6.86
371 372 2.125512 CGCCAGTACAGGAGCCAC 60.126 66.667 8.77 0.00 0.00 5.01
372 373 2.269241 GCCAGTACAGGAGCCACC 59.731 66.667 8.77 0.00 39.35 4.61
373 374 2.579201 CCAGTACAGGAGCCACCG 59.421 66.667 0.00 0.00 44.74 4.94
374 375 2.579201 CAGTACAGGAGCCACCGG 59.421 66.667 0.00 0.00 44.74 5.28
375 376 1.982395 CAGTACAGGAGCCACCGGA 60.982 63.158 9.46 0.00 44.74 5.14
376 377 1.982938 AGTACAGGAGCCACCGGAC 60.983 63.158 9.46 0.00 44.74 4.79
377 378 3.066190 TACAGGAGCCACCGGACG 61.066 66.667 9.46 0.00 44.74 4.79
386 387 3.812019 CACCGGACGGACGAGGAG 61.812 72.222 18.80 0.00 38.96 3.69
389 390 4.180946 CGGACGGACGAGGAGCTG 62.181 72.222 0.00 0.00 35.47 4.24
390 391 3.827898 GGACGGACGAGGAGCTGG 61.828 72.222 0.00 0.00 0.00 4.85
391 392 3.063084 GACGGACGAGGAGCTGGT 61.063 66.667 0.00 0.00 0.00 4.00
392 393 3.053849 GACGGACGAGGAGCTGGTC 62.054 68.421 0.00 0.00 38.25 4.02
393 394 4.180946 CGGACGAGGAGCTGGTCG 62.181 72.222 11.80 11.80 39.53 4.79
397 398 4.803426 CGAGGAGCTGGTCGTGCC 62.803 72.222 6.80 0.00 37.90 5.01
398 399 3.386237 GAGGAGCTGGTCGTGCCT 61.386 66.667 6.80 0.00 38.35 4.75
399 400 2.925170 AGGAGCTGGTCGTGCCTT 60.925 61.111 0.00 0.00 38.35 4.35
400 401 2.743928 GGAGCTGGTCGTGCCTTG 60.744 66.667 0.00 0.00 38.35 3.61
401 402 2.343758 GAGCTGGTCGTGCCTTGA 59.656 61.111 0.00 0.00 38.35 3.02
402 403 1.078848 GAGCTGGTCGTGCCTTGAT 60.079 57.895 0.00 0.00 38.35 2.57
403 404 0.674895 GAGCTGGTCGTGCCTTGATT 60.675 55.000 0.00 0.00 38.35 2.57
404 405 0.674895 AGCTGGTCGTGCCTTGATTC 60.675 55.000 0.00 0.00 38.35 2.52
405 406 1.648467 GCTGGTCGTGCCTTGATTCC 61.648 60.000 1.06 0.00 38.35 3.01
406 407 1.002624 TGGTCGTGCCTTGATTCCC 60.003 57.895 1.06 0.00 38.35 3.97
407 408 1.299976 GGTCGTGCCTTGATTCCCT 59.700 57.895 0.00 0.00 0.00 4.20
408 409 0.744771 GGTCGTGCCTTGATTCCCTC 60.745 60.000 0.00 0.00 0.00 4.30
409 410 0.036388 GTCGTGCCTTGATTCCCTCA 60.036 55.000 0.00 0.00 0.00 3.86
410 411 0.690192 TCGTGCCTTGATTCCCTCAA 59.310 50.000 0.00 0.00 41.61 3.02
411 412 1.073125 TCGTGCCTTGATTCCCTCAAA 59.927 47.619 0.00 0.00 43.20 2.69
412 413 1.885887 CGTGCCTTGATTCCCTCAAAA 59.114 47.619 0.00 0.00 43.20 2.44
413 414 2.295909 CGTGCCTTGATTCCCTCAAAAA 59.704 45.455 0.00 0.00 43.20 1.94
497 498 5.122082 GCGTATAACTAGCGGAATACTCTCT 59.878 44.000 0.00 0.00 0.00 3.10
498 499 6.672836 GCGTATAACTAGCGGAATACTCTCTC 60.673 46.154 0.00 0.00 0.00 3.20
499 500 6.591062 CGTATAACTAGCGGAATACTCTCTCT 59.409 42.308 0.00 0.00 0.00 3.10
616 1782 2.125673 GCATACGTGTCCAGCGGT 60.126 61.111 0.00 0.00 0.00 5.68
743 1910 4.072088 CTCGCCACGGTTTCACGC 62.072 66.667 0.00 0.00 37.37 5.34
854 2033 1.022451 TCGCCGTAACAAATCCCAGC 61.022 55.000 0.00 0.00 0.00 4.85
858 2037 1.807226 GTAACAAATCCCAGCCCGC 59.193 57.895 0.00 0.00 0.00 6.13
918 2100 1.598130 GGCACCACAGTCCACAGAC 60.598 63.158 0.00 0.00 43.89 3.51
956 2138 5.043903 CGTGCATATATATACTCTGGTGGC 58.956 45.833 0.00 0.00 0.00 5.01
1038 2233 1.443828 GGACTCATCTTCCGGCTCC 59.556 63.158 0.00 0.00 0.00 4.70
1289 2518 4.735283 GCCGTAAATTTCCGGTGCAATTAT 60.735 41.667 21.41 0.26 45.91 1.28
1290 2519 5.344884 CCGTAAATTTCCGGTGCAATTATT 58.655 37.500 13.61 0.00 39.38 1.40
1291 2520 6.496571 CCGTAAATTTCCGGTGCAATTATTA 58.503 36.000 13.61 0.00 39.38 0.98
1299 2533 8.789881 TTTCCGGTGCAATTATTAAATAATCG 57.210 30.769 0.00 0.00 34.50 3.34
1301 2535 8.155821 TCCGGTGCAATTATTAAATAATCGAA 57.844 30.769 0.00 0.00 34.50 3.71
1558 2808 4.932789 GCACCGACAAGCCTATCA 57.067 55.556 0.00 0.00 0.00 2.15
1831 3127 4.781934 AGCTTAGGGTATTGTGGTTGATC 58.218 43.478 0.00 0.00 0.00 2.92
2181 3483 1.566018 CGGCTCCGACCAAACAGTTC 61.566 60.000 1.35 0.00 42.83 3.01
2409 3717 1.276989 GACGGGACCTACCATCAACAA 59.723 52.381 0.00 0.00 41.20 2.83
2530 3844 5.449041 CCCTGAACAAATGATATGAACACCG 60.449 44.000 0.00 0.00 0.00 4.94
2876 4239 6.146601 ACCTAGCTAGGAGTATTTTCGAAC 57.853 41.667 40.40 0.00 46.63 3.95
2993 4401 7.392766 TGATTACAATCCCCAGTCAGATATT 57.607 36.000 0.00 0.00 34.50 1.28
3117 4744 7.604549 CATGTAAATAGGGCATGCATGATAAA 58.395 34.615 30.64 12.33 35.58 1.40
3195 4822 9.883142 ATTAAGATTTCTGAGTTACTTCCTCTG 57.117 33.333 0.00 0.00 0.00 3.35
3355 5003 9.866655 TGTTTGGAAAATATGCTATTATCTCCT 57.133 29.630 0.00 0.00 0.00 3.69
3366 5014 8.894768 ATGCTATTATCTCCTTGAAGTTACAC 57.105 34.615 0.00 0.00 0.00 2.90
3367 5015 8.079211 TGCTATTATCTCCTTGAAGTTACACT 57.921 34.615 0.00 0.00 0.00 3.55
3368 5016 8.198109 TGCTATTATCTCCTTGAAGTTACACTC 58.802 37.037 0.00 0.00 0.00 3.51
3369 5017 7.654116 GCTATTATCTCCTTGAAGTTACACTCC 59.346 40.741 0.00 0.00 0.00 3.85
3370 5018 4.828072 ATCTCCTTGAAGTTACACTCCC 57.172 45.455 0.00 0.00 0.00 4.30
3371 5019 3.858135 TCTCCTTGAAGTTACACTCCCT 58.142 45.455 0.00 0.00 0.00 4.20
3372 5020 3.833070 TCTCCTTGAAGTTACACTCCCTC 59.167 47.826 0.00 0.00 0.00 4.30
3373 5021 3.835395 CTCCTTGAAGTTACACTCCCTCT 59.165 47.826 0.00 0.00 0.00 3.69
3374 5022 3.578716 TCCTTGAAGTTACACTCCCTCTG 59.421 47.826 0.00 0.00 0.00 3.35
3375 5023 3.325135 CCTTGAAGTTACACTCCCTCTGT 59.675 47.826 0.00 0.00 0.00 3.41
3376 5024 4.202367 CCTTGAAGTTACACTCCCTCTGTT 60.202 45.833 0.00 0.00 0.00 3.16
3377 5025 4.602340 TGAAGTTACACTCCCTCTGTTC 57.398 45.455 0.00 0.00 0.00 3.18
3378 5026 3.323979 TGAAGTTACACTCCCTCTGTTCC 59.676 47.826 0.00 0.00 0.00 3.62
3379 5027 3.261818 AGTTACACTCCCTCTGTTCCT 57.738 47.619 0.00 0.00 0.00 3.36
3380 5028 3.588569 AGTTACACTCCCTCTGTTCCTT 58.411 45.455 0.00 0.00 0.00 3.36
3381 5029 3.974642 AGTTACACTCCCTCTGTTCCTTT 59.025 43.478 0.00 0.00 0.00 3.11
3382 5030 5.152934 AGTTACACTCCCTCTGTTCCTTTA 58.847 41.667 0.00 0.00 0.00 1.85
3383 5031 5.785940 AGTTACACTCCCTCTGTTCCTTTAT 59.214 40.000 0.00 0.00 0.00 1.40
3384 5032 4.559862 ACACTCCCTCTGTTCCTTTATG 57.440 45.455 0.00 0.00 0.00 1.90
3385 5033 3.910627 ACACTCCCTCTGTTCCTTTATGT 59.089 43.478 0.00 0.00 0.00 2.29
3386 5034 5.091552 ACACTCCCTCTGTTCCTTTATGTA 58.908 41.667 0.00 0.00 0.00 2.29
3387 5035 5.546499 ACACTCCCTCTGTTCCTTTATGTAA 59.454 40.000 0.00 0.00 0.00 2.41
3388 5036 6.109359 CACTCCCTCTGTTCCTTTATGTAAG 58.891 44.000 0.00 0.00 0.00 2.34
3407 5055 6.613233 TGTAAGGTGTATTATTTTTGCCACG 58.387 36.000 0.00 0.00 0.00 4.94
3408 5056 4.712122 AGGTGTATTATTTTTGCCACGG 57.288 40.909 0.00 0.00 0.00 4.94
3409 5057 4.083565 AGGTGTATTATTTTTGCCACGGT 58.916 39.130 0.00 0.00 0.00 4.83
3410 5058 4.082463 AGGTGTATTATTTTTGCCACGGTG 60.082 41.667 0.00 0.00 0.00 4.94
3411 5059 4.082679 GGTGTATTATTTTTGCCACGGTGA 60.083 41.667 10.28 0.00 0.00 4.02
3412 5060 5.092781 GTGTATTATTTTTGCCACGGTGAG 58.907 41.667 10.28 0.83 0.00 3.51
3413 5061 2.715737 TTATTTTTGCCACGGTGAGC 57.284 45.000 10.28 11.77 0.00 4.26
3414 5062 1.610363 TATTTTTGCCACGGTGAGCA 58.390 45.000 16.76 16.76 37.18 4.26
3415 5063 0.749649 ATTTTTGCCACGGTGAGCAA 59.250 45.000 23.78 23.78 46.74 3.91
3417 5065 2.508436 TTGCCACGGTGAGCAAGA 59.492 55.556 23.78 10.69 43.74 3.02
3418 5066 1.891919 TTGCCACGGTGAGCAAGAC 60.892 57.895 23.78 3.00 43.74 3.01
3419 5067 2.280797 GCCACGGTGAGCAAGACA 60.281 61.111 10.28 0.00 0.00 3.41
3420 5068 2.607892 GCCACGGTGAGCAAGACAC 61.608 63.158 10.28 0.00 37.51 3.67
3421 5069 1.227527 CCACGGTGAGCAAGACACA 60.228 57.895 10.28 0.00 39.65 3.72
3422 5070 0.603707 CCACGGTGAGCAAGACACAT 60.604 55.000 10.28 0.00 39.65 3.21
3423 5071 1.337728 CCACGGTGAGCAAGACACATA 60.338 52.381 10.28 0.00 39.65 2.29
3424 5072 2.412870 CACGGTGAGCAAGACACATAA 58.587 47.619 0.74 0.00 39.65 1.90
3425 5073 3.002791 CACGGTGAGCAAGACACATAAT 58.997 45.455 0.74 0.00 39.65 1.28
3426 5074 3.436704 CACGGTGAGCAAGACACATAATT 59.563 43.478 0.74 0.00 39.65 1.40
3427 5075 4.629634 CACGGTGAGCAAGACACATAATTA 59.370 41.667 0.74 0.00 39.65 1.40
3428 5076 5.294306 CACGGTGAGCAAGACACATAATTAT 59.706 40.000 0.74 0.00 39.65 1.28
3429 5077 6.478673 CACGGTGAGCAAGACACATAATTATA 59.521 38.462 0.74 0.00 39.65 0.98
3430 5078 6.701841 ACGGTGAGCAAGACACATAATTATAG 59.298 38.462 0.00 0.00 39.65 1.31
3431 5079 6.923508 CGGTGAGCAAGACACATAATTATAGA 59.076 38.462 0.00 0.00 39.65 1.98
3432 5080 7.096023 CGGTGAGCAAGACACATAATTATAGAC 60.096 40.741 0.00 0.00 39.65 2.59
3433 5081 7.710907 GGTGAGCAAGACACATAATTATAGACA 59.289 37.037 0.00 0.00 39.65 3.41
3434 5082 9.098355 GTGAGCAAGACACATAATTATAGACAA 57.902 33.333 0.00 0.00 38.05 3.18
3435 5083 9.317936 TGAGCAAGACACATAATTATAGACAAG 57.682 33.333 0.00 0.00 0.00 3.16
3436 5084 9.319143 GAGCAAGACACATAATTATAGACAAGT 57.681 33.333 0.00 0.00 0.00 3.16
3437 5085 9.672673 AGCAAGACACATAATTATAGACAAGTT 57.327 29.630 0.00 0.00 0.00 2.66
3455 5103 9.442047 AGACAAGTTAGGATGAAATTACTCTTG 57.558 33.333 0.00 0.00 35.96 3.02
3456 5104 8.567285 ACAAGTTAGGATGAAATTACTCTTGG 57.433 34.615 0.00 0.00 34.73 3.61
3457 5105 7.121315 ACAAGTTAGGATGAAATTACTCTTGGC 59.879 37.037 0.00 0.00 34.73 4.52
3458 5106 6.721318 AGTTAGGATGAAATTACTCTTGGCA 58.279 36.000 0.00 0.00 0.00 4.92
3459 5107 7.175104 AGTTAGGATGAAATTACTCTTGGCAA 58.825 34.615 0.00 0.00 0.00 4.52
3460 5108 7.669722 AGTTAGGATGAAATTACTCTTGGCAAA 59.330 33.333 0.00 0.00 0.00 3.68
3461 5109 8.470002 GTTAGGATGAAATTACTCTTGGCAAAT 58.530 33.333 0.00 0.00 0.00 2.32
3462 5110 7.486407 AGGATGAAATTACTCTTGGCAAATT 57.514 32.000 0.00 0.00 0.00 1.82
3463 5111 7.910584 AGGATGAAATTACTCTTGGCAAATTT 58.089 30.769 0.00 3.92 34.98 1.82
3464 5112 7.820872 AGGATGAAATTACTCTTGGCAAATTTG 59.179 33.333 14.03 14.03 33.03 2.32
3465 5113 7.603784 GGATGAAATTACTCTTGGCAAATTTGT 59.396 33.333 19.03 5.69 33.03 2.83
3466 5114 8.907222 ATGAAATTACTCTTGGCAAATTTGTT 57.093 26.923 19.03 1.40 33.03 2.83
3467 5115 8.140677 TGAAATTACTCTTGGCAAATTTGTTG 57.859 30.769 19.03 7.57 33.03 3.33
3468 5116 7.226325 TGAAATTACTCTTGGCAAATTTGTTGG 59.774 33.333 19.03 7.86 33.03 3.77
3469 5117 5.606348 TTACTCTTGGCAAATTTGTTGGT 57.394 34.783 19.03 11.58 0.00 3.67
3470 5118 4.486125 ACTCTTGGCAAATTTGTTGGTT 57.514 36.364 19.03 0.00 0.00 3.67
3471 5119 5.606348 ACTCTTGGCAAATTTGTTGGTTA 57.394 34.783 19.03 1.42 0.00 2.85
3472 5120 5.600696 ACTCTTGGCAAATTTGTTGGTTAG 58.399 37.500 19.03 11.93 0.00 2.34
3473 5121 5.128663 ACTCTTGGCAAATTTGTTGGTTAGT 59.871 36.000 19.03 12.47 0.00 2.24
3474 5122 5.355596 TCTTGGCAAATTTGTTGGTTAGTG 58.644 37.500 19.03 1.98 0.00 2.74
3475 5123 4.744795 TGGCAAATTTGTTGGTTAGTGT 57.255 36.364 19.03 0.00 0.00 3.55
3476 5124 5.854010 TGGCAAATTTGTTGGTTAGTGTA 57.146 34.783 19.03 0.00 0.00 2.90
3477 5125 6.222038 TGGCAAATTTGTTGGTTAGTGTAA 57.778 33.333 19.03 0.00 0.00 2.41
3478 5126 6.640518 TGGCAAATTTGTTGGTTAGTGTAAA 58.359 32.000 19.03 0.00 0.00 2.01
3479 5127 6.758886 TGGCAAATTTGTTGGTTAGTGTAAAG 59.241 34.615 19.03 0.00 0.00 1.85
3480 5128 6.759356 GGCAAATTTGTTGGTTAGTGTAAAGT 59.241 34.615 19.03 0.00 0.00 2.66
3481 5129 7.921745 GGCAAATTTGTTGGTTAGTGTAAAGTA 59.078 33.333 19.03 0.00 0.00 2.24
3482 5130 9.303537 GCAAATTTGTTGGTTAGTGTAAAGTAA 57.696 29.630 19.03 0.00 0.00 2.24
3488 5136 8.967664 TGTTGGTTAGTGTAAAGTAAATCAGT 57.032 30.769 0.00 0.00 0.00 3.41
3489 5137 9.398538 TGTTGGTTAGTGTAAAGTAAATCAGTT 57.601 29.630 0.00 0.00 0.00 3.16
3508 5156 9.756571 AATCAGTTAGTCTAGGAAAGTAAGAGA 57.243 33.333 0.00 0.00 0.00 3.10
3509 5157 9.930158 ATCAGTTAGTCTAGGAAAGTAAGAGAT 57.070 33.333 0.00 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.654230 TTCAAAATTTGTCCATCGAATTCAAA 57.346 26.923 6.22 0.00 38.70 2.69
1 2 8.830201 ATTCAAAATTTGTCCATCGAATTCAA 57.170 26.923 6.22 0.00 38.70 2.69
2 3 8.830201 AATTCAAAATTTGTCCATCGAATTCA 57.170 26.923 6.22 0.00 38.70 2.57
3 4 9.532697 CAAATTCAAAATTTGTCCATCGAATTC 57.467 29.630 14.19 0.00 38.70 2.17
7 8 8.087136 TCATCAAATTCAAAATTTGTCCATCGA 58.913 29.630 19.22 0.00 39.36 3.59
8 9 8.242085 TCATCAAATTCAAAATTTGTCCATCG 57.758 30.769 19.22 7.76 39.36 3.84
10 11 9.339850 TGTTCATCAAATTCAAAATTTGTCCAT 57.660 25.926 19.22 7.94 39.36 3.41
39 40 9.713740 CGAAATTTGTCCATTGATTTTCAAAAA 57.286 25.926 0.00 0.00 40.12 1.94
40 41 8.887717 ACGAAATTTGTCCATTGATTTTCAAAA 58.112 25.926 0.00 0.00 40.12 2.44
41 42 8.430801 ACGAAATTTGTCCATTGATTTTCAAA 57.569 26.923 0.00 0.00 40.12 2.69
42 43 9.703892 ATACGAAATTTGTCCATTGATTTTCAA 57.296 25.926 0.00 0.00 41.09 2.69
43 44 9.703892 AATACGAAATTTGTCCATTGATTTTCA 57.296 25.926 0.00 0.00 0.00 2.69
46 47 9.703892 TCAAATACGAAATTTGTCCATTGATTT 57.296 25.926 19.84 0.00 39.36 2.17
47 48 9.874205 ATCAAATACGAAATTTGTCCATTGATT 57.126 25.926 19.84 0.00 39.36 2.57
48 49 9.304731 CATCAAATACGAAATTTGTCCATTGAT 57.695 29.630 19.84 11.91 39.36 2.57
49 50 7.275341 GCATCAAATACGAAATTTGTCCATTGA 59.725 33.333 19.84 1.86 39.36 2.57
50 51 7.063191 TGCATCAAATACGAAATTTGTCCATTG 59.937 33.333 19.84 14.11 39.36 2.82
51 52 7.063308 GTGCATCAAATACGAAATTTGTCCATT 59.937 33.333 19.84 0.00 39.36 3.16
52 53 6.531240 GTGCATCAAATACGAAATTTGTCCAT 59.469 34.615 19.84 9.61 39.36 3.41
53 54 5.861251 GTGCATCAAATACGAAATTTGTCCA 59.139 36.000 19.84 14.66 39.36 4.02
54 55 5.861251 TGTGCATCAAATACGAAATTTGTCC 59.139 36.000 19.84 13.14 39.36 4.02
55 56 6.926280 TGTGCATCAAATACGAAATTTGTC 57.074 33.333 19.84 13.77 39.36 3.18
56 57 7.887996 AATGTGCATCAAATACGAAATTTGT 57.112 28.000 19.84 0.00 39.36 2.83
57 58 9.596677 AAAAATGTGCATCAAATACGAAATTTG 57.403 25.926 16.66 16.66 39.61 2.32
177 178 5.285651 TCATTTCAAATCCGCGAACTTTTT 58.714 33.333 8.23 0.00 0.00 1.94
178 179 4.865776 TCATTTCAAATCCGCGAACTTTT 58.134 34.783 8.23 0.00 0.00 2.27
179 180 4.497473 TCATTTCAAATCCGCGAACTTT 57.503 36.364 8.23 0.59 0.00 2.66
180 181 4.497473 TTCATTTCAAATCCGCGAACTT 57.503 36.364 8.23 0.00 0.00 2.66
181 182 4.497473 TTTCATTTCAAATCCGCGAACT 57.503 36.364 8.23 0.00 0.00 3.01
182 183 5.761818 ATTTTCATTTCAAATCCGCGAAC 57.238 34.783 8.23 0.00 0.00 3.95
183 184 5.060323 CGAATTTTCATTTCAAATCCGCGAA 59.940 36.000 8.23 0.00 0.00 4.70
184 185 4.556912 CGAATTTTCATTTCAAATCCGCGA 59.443 37.500 8.23 0.00 0.00 5.87
185 186 4.775695 GCGAATTTTCATTTCAAATCCGCG 60.776 41.667 0.00 0.00 0.00 6.46
186 187 4.091220 TGCGAATTTTCATTTCAAATCCGC 59.909 37.500 2.50 2.50 0.00 5.54
187 188 5.760193 TGCGAATTTTCATTTCAAATCCG 57.240 34.783 0.00 0.00 0.00 4.18
188 189 8.779603 TTTTTGCGAATTTTCATTTCAAATCC 57.220 26.923 0.00 0.00 31.18 3.01
246 247 9.625747 TTCTTTTTATTTCCTGATTGCCTTTTT 57.374 25.926 0.00 0.00 0.00 1.94
247 248 9.625747 TTTCTTTTTATTTCCTGATTGCCTTTT 57.374 25.926 0.00 0.00 0.00 2.27
248 249 9.625747 TTTTCTTTTTATTTCCTGATTGCCTTT 57.374 25.926 0.00 0.00 0.00 3.11
249 250 9.625747 TTTTTCTTTTTATTTCCTGATTGCCTT 57.374 25.926 0.00 0.00 0.00 4.35
307 308 6.315144 CCCATTTTCCTGTCTTTTTCGTTTTT 59.685 34.615 0.00 0.00 0.00 1.94
308 309 5.815222 CCCATTTTCCTGTCTTTTTCGTTTT 59.185 36.000 0.00 0.00 0.00 2.43
309 310 5.356426 CCCATTTTCCTGTCTTTTTCGTTT 58.644 37.500 0.00 0.00 0.00 3.60
310 311 4.739436 GCCCATTTTCCTGTCTTTTTCGTT 60.739 41.667 0.00 0.00 0.00 3.85
311 312 3.243737 GCCCATTTTCCTGTCTTTTTCGT 60.244 43.478 0.00 0.00 0.00 3.85
312 313 3.317150 GCCCATTTTCCTGTCTTTTTCG 58.683 45.455 0.00 0.00 0.00 3.46
313 314 3.664107 GGCCCATTTTCCTGTCTTTTTC 58.336 45.455 0.00 0.00 0.00 2.29
314 315 2.037121 CGGCCCATTTTCCTGTCTTTTT 59.963 45.455 0.00 0.00 0.00 1.94
315 316 1.618343 CGGCCCATTTTCCTGTCTTTT 59.382 47.619 0.00 0.00 0.00 2.27
316 317 1.256812 CGGCCCATTTTCCTGTCTTT 58.743 50.000 0.00 0.00 0.00 2.52
317 318 0.611896 CCGGCCCATTTTCCTGTCTT 60.612 55.000 0.00 0.00 0.00 3.01
318 319 1.000896 CCGGCCCATTTTCCTGTCT 60.001 57.895 0.00 0.00 0.00 3.41
319 320 1.304134 ACCGGCCCATTTTCCTGTC 60.304 57.895 0.00 0.00 0.00 3.51
320 321 1.304134 GACCGGCCCATTTTCCTGT 60.304 57.895 0.00 0.00 0.00 4.00
321 322 2.052104 GGACCGGCCCATTTTCCTG 61.052 63.158 0.00 0.00 0.00 3.86
322 323 1.874299 ATGGACCGGCCCATTTTCCT 61.874 55.000 17.82 0.00 44.11 3.36
323 324 0.106419 TATGGACCGGCCCATTTTCC 60.106 55.000 28.46 12.95 44.11 3.13
324 325 1.029681 GTATGGACCGGCCCATTTTC 58.970 55.000 28.46 14.50 44.11 2.29
325 326 0.333312 TGTATGGACCGGCCCATTTT 59.667 50.000 28.46 7.17 44.11 1.82
326 327 0.333312 TTGTATGGACCGGCCCATTT 59.667 50.000 28.46 8.01 44.11 2.32
327 328 0.395173 GTTGTATGGACCGGCCCATT 60.395 55.000 28.46 11.97 44.11 3.16
329 330 2.224877 TGTTGTATGGACCGGCCCA 61.225 57.895 13.59 13.59 41.05 5.36
330 331 1.747745 GTGTTGTATGGACCGGCCC 60.748 63.158 0.00 0.00 34.97 5.80
331 332 1.747745 GGTGTTGTATGGACCGGCC 60.748 63.158 0.00 4.32 37.10 6.13
332 333 1.747745 GGGTGTTGTATGGACCGGC 60.748 63.158 0.00 0.00 0.00 6.13
333 334 1.448893 CGGGTGTTGTATGGACCGG 60.449 63.158 0.00 0.00 37.80 5.28
334 335 2.104253 GCGGGTGTTGTATGGACCG 61.104 63.158 0.00 0.00 43.81 4.79
335 336 2.104253 CGCGGGTGTTGTATGGACC 61.104 63.158 0.00 0.00 0.00 4.46
336 337 2.746803 GCGCGGGTGTTGTATGGAC 61.747 63.158 8.83 0.00 0.00 4.02
337 338 2.435234 GCGCGGGTGTTGTATGGA 60.435 61.111 8.83 0.00 0.00 3.41
338 339 3.860125 CGCGCGGGTGTTGTATGG 61.860 66.667 24.84 0.00 0.00 2.74
339 340 4.514569 GCGCGCGGGTGTTGTATG 62.515 66.667 33.06 0.00 0.00 2.39
353 354 4.082523 TGGCTCCTGTACTGGCGC 62.083 66.667 21.73 21.73 37.12 6.53
354 355 2.125512 GTGGCTCCTGTACTGGCG 60.126 66.667 13.72 9.07 0.00 5.69
355 356 2.269241 GGTGGCTCCTGTACTGGC 59.731 66.667 13.72 3.43 0.00 4.85
356 357 2.579201 CGGTGGCTCCTGTACTGG 59.421 66.667 12.42 12.42 0.00 4.00
357 358 1.982395 TCCGGTGGCTCCTGTACTG 60.982 63.158 0.00 0.00 0.00 2.74
358 359 1.982938 GTCCGGTGGCTCCTGTACT 60.983 63.158 0.00 0.00 0.00 2.73
359 360 2.577593 GTCCGGTGGCTCCTGTAC 59.422 66.667 0.00 0.00 0.00 2.90
360 361 3.066190 CGTCCGGTGGCTCCTGTA 61.066 66.667 0.00 0.00 0.00 2.74
369 370 3.812019 CTCCTCGTCCGTCCGGTG 61.812 72.222 0.00 0.00 36.47 4.94
372 373 4.180946 CAGCTCCTCGTCCGTCCG 62.181 72.222 0.00 0.00 0.00 4.79
373 374 3.827898 CCAGCTCCTCGTCCGTCC 61.828 72.222 0.00 0.00 0.00 4.79
374 375 3.053849 GACCAGCTCCTCGTCCGTC 62.054 68.421 0.00 0.00 0.00 4.79
375 376 3.063084 GACCAGCTCCTCGTCCGT 61.063 66.667 0.00 0.00 0.00 4.69
376 377 4.180946 CGACCAGCTCCTCGTCCG 62.181 72.222 1.98 0.00 0.00 4.79
377 378 3.063084 ACGACCAGCTCCTCGTCC 61.063 66.667 9.01 0.00 38.80 4.79
378 379 2.179517 CACGACCAGCTCCTCGTC 59.820 66.667 11.44 1.73 41.13 4.20
379 380 4.057428 GCACGACCAGCTCCTCGT 62.057 66.667 9.01 9.01 43.83 4.18
380 381 4.803426 GGCACGACCAGCTCCTCG 62.803 72.222 7.82 7.82 38.86 4.63
381 382 2.948720 AAGGCACGACCAGCTCCTC 61.949 63.158 0.00 0.00 43.14 3.71
382 383 2.925170 AAGGCACGACCAGCTCCT 60.925 61.111 0.00 0.00 43.14 3.69
383 384 2.527951 ATCAAGGCACGACCAGCTCC 62.528 60.000 0.00 0.00 43.14 4.70
384 385 0.674895 AATCAAGGCACGACCAGCTC 60.675 55.000 0.00 0.00 43.14 4.09
385 386 0.674895 GAATCAAGGCACGACCAGCT 60.675 55.000 0.00 0.00 43.14 4.24
386 387 1.648467 GGAATCAAGGCACGACCAGC 61.648 60.000 0.00 0.00 43.14 4.85
387 388 1.026718 GGGAATCAAGGCACGACCAG 61.027 60.000 0.00 0.00 43.14 4.00
388 389 1.002624 GGGAATCAAGGCACGACCA 60.003 57.895 0.00 0.00 43.14 4.02
389 390 0.744771 GAGGGAATCAAGGCACGACC 60.745 60.000 0.00 0.00 39.61 4.79
390 391 0.036388 TGAGGGAATCAAGGCACGAC 60.036 55.000 0.00 0.00 34.02 4.34
391 392 0.690192 TTGAGGGAATCAAGGCACGA 59.310 50.000 0.00 0.00 43.09 4.35
392 393 3.248043 TTGAGGGAATCAAGGCACG 57.752 52.632 0.00 0.00 43.09 5.34
415 416 1.676006 CTCAAGGCACGACCAGTTTTT 59.324 47.619 0.00 0.00 43.14 1.94
416 417 1.308998 CTCAAGGCACGACCAGTTTT 58.691 50.000 0.00 0.00 43.14 2.43
417 418 1.166531 GCTCAAGGCACGACCAGTTT 61.167 55.000 0.00 0.00 43.14 2.66
418 419 1.598130 GCTCAAGGCACGACCAGTT 60.598 57.895 0.00 0.00 43.14 3.16
419 420 2.031163 GCTCAAGGCACGACCAGT 59.969 61.111 0.00 0.00 43.14 4.00
478 479 7.642082 AAAAGAGAGAGTATTCCGCTAGTTA 57.358 36.000 0.00 0.00 0.00 2.24
770 1937 1.936547 GAGTGATCTGCGGTGGAAATC 59.063 52.381 0.00 0.00 0.00 2.17
854 2033 3.636231 TGGGTGTGAAGGAGCGGG 61.636 66.667 0.00 0.00 0.00 6.13
858 2037 1.302832 GCTGGTGGGTGTGAAGGAG 60.303 63.158 0.00 0.00 0.00 3.69
956 2138 3.318839 ACCAACAAACACACCAGATGATG 59.681 43.478 0.00 0.00 0.00 3.07
1289 2518 7.448161 AGCATGATGGATGGTTCGATTATTTAA 59.552 33.333 0.00 0.00 39.93 1.52
1290 2519 6.942005 AGCATGATGGATGGTTCGATTATTTA 59.058 34.615 0.00 0.00 39.93 1.40
1291 2520 5.771666 AGCATGATGGATGGTTCGATTATTT 59.228 36.000 0.00 0.00 39.93 1.40
1301 2535 6.270927 ACAGTAGTATAAGCATGATGGATGGT 59.729 38.462 0.00 0.00 44.97 3.55
1807 3095 3.844211 TCAACCACAATACCCTAAGCTCT 59.156 43.478 0.00 0.00 0.00 4.09
1831 3127 5.990162 CGACGACGTACACTAATTAACTTG 58.010 41.667 0.00 0.00 34.56 3.16
2181 3483 4.452733 GAAGACGACGGGGCCAGG 62.453 72.222 4.39 0.00 0.00 4.45
2409 3717 2.202932 GCGCCGAGGATGACATGT 60.203 61.111 0.00 0.00 0.00 3.21
2797 4157 9.347240 GGGATTGTAATCAGCTGCATATATATT 57.653 33.333 9.47 4.29 37.15 1.28
2798 4158 7.941238 GGGGATTGTAATCAGCTGCATATATAT 59.059 37.037 9.47 0.00 37.15 0.86
2799 4159 7.092489 TGGGGATTGTAATCAGCTGCATATATA 60.092 37.037 9.47 0.00 37.15 0.86
2993 4401 3.053544 TGGAATAGACCCGGCCAAAAATA 60.054 43.478 2.24 0.00 0.00 1.40
3092 4719 5.654603 ATCATGCATGCCCTATTTACATG 57.345 39.130 22.25 8.81 43.21 3.21
3117 4744 2.944349 TCAATCATACACGTGCATGCAT 59.056 40.909 25.64 10.48 0.00 3.96
3212 4839 6.183361 GGAGATCTGGTCCCTGAATCTAAAAT 60.183 42.308 0.00 0.00 0.00 1.82
3221 4848 1.362584 TCTTGGAGATCTGGTCCCTGA 59.637 52.381 0.00 0.00 32.49 3.86
3360 5008 4.353383 AAAGGAACAGAGGGAGTGTAAC 57.647 45.455 0.00 0.00 0.00 2.50
3361 5009 5.546499 ACATAAAGGAACAGAGGGAGTGTAA 59.454 40.000 0.00 0.00 0.00 2.41
3362 5010 5.091552 ACATAAAGGAACAGAGGGAGTGTA 58.908 41.667 0.00 0.00 0.00 2.90
3363 5011 3.910627 ACATAAAGGAACAGAGGGAGTGT 59.089 43.478 0.00 0.00 0.00 3.55
3364 5012 4.559862 ACATAAAGGAACAGAGGGAGTG 57.440 45.455 0.00 0.00 0.00 3.51
3365 5013 6.301169 CTTACATAAAGGAACAGAGGGAGT 57.699 41.667 0.00 0.00 0.00 3.85
3381 5029 8.399425 CGTGGCAAAAATAATACACCTTACATA 58.601 33.333 0.00 0.00 0.00 2.29
3382 5030 7.254852 CGTGGCAAAAATAATACACCTTACAT 58.745 34.615 0.00 0.00 0.00 2.29
3383 5031 6.349445 CCGTGGCAAAAATAATACACCTTACA 60.349 38.462 0.00 0.00 0.00 2.41
3384 5032 6.031471 CCGTGGCAAAAATAATACACCTTAC 58.969 40.000 0.00 0.00 0.00 2.34
3385 5033 5.711036 ACCGTGGCAAAAATAATACACCTTA 59.289 36.000 0.00 0.00 0.00 2.69
3386 5034 4.525100 ACCGTGGCAAAAATAATACACCTT 59.475 37.500 0.00 0.00 0.00 3.50
3387 5035 4.082463 CACCGTGGCAAAAATAATACACCT 60.082 41.667 0.00 0.00 0.00 4.00
3388 5036 4.082679 TCACCGTGGCAAAAATAATACACC 60.083 41.667 0.00 0.00 0.00 4.16
3389 5037 5.049398 TCACCGTGGCAAAAATAATACAC 57.951 39.130 0.00 0.00 0.00 2.90
3390 5038 4.380023 GCTCACCGTGGCAAAAATAATACA 60.380 41.667 0.00 0.00 0.00 2.29
3391 5039 4.102649 GCTCACCGTGGCAAAAATAATAC 58.897 43.478 0.00 0.00 0.00 1.89
3392 5040 3.759086 TGCTCACCGTGGCAAAAATAATA 59.241 39.130 10.99 0.00 35.40 0.98
3393 5041 2.560542 TGCTCACCGTGGCAAAAATAAT 59.439 40.909 10.99 0.00 35.40 1.28
3394 5042 1.957177 TGCTCACCGTGGCAAAAATAA 59.043 42.857 10.99 0.00 35.40 1.40
3395 5043 1.610363 TGCTCACCGTGGCAAAAATA 58.390 45.000 10.99 0.00 35.40 1.40
3396 5044 0.749649 TTGCTCACCGTGGCAAAAAT 59.250 45.000 19.06 0.00 44.01 1.82
3397 5045 0.102120 CTTGCTCACCGTGGCAAAAA 59.898 50.000 20.67 6.72 45.80 1.94
3398 5046 0.749818 TCTTGCTCACCGTGGCAAAA 60.750 50.000 20.67 10.94 45.80 2.44
3399 5047 1.153066 TCTTGCTCACCGTGGCAAA 60.153 52.632 20.67 12.92 45.80 3.68
3400 5048 1.891919 GTCTTGCTCACCGTGGCAA 60.892 57.895 19.72 19.72 44.64 4.52
3401 5049 2.280797 GTCTTGCTCACCGTGGCA 60.281 61.111 9.74 9.74 36.62 4.92
3402 5050 2.280797 TGTCTTGCTCACCGTGGC 60.281 61.111 0.00 2.02 0.00 5.01
3403 5051 0.603707 ATGTGTCTTGCTCACCGTGG 60.604 55.000 0.00 0.00 35.25 4.94
3404 5052 2.078849 TATGTGTCTTGCTCACCGTG 57.921 50.000 0.00 0.00 35.25 4.94
3405 5053 2.831685 TTATGTGTCTTGCTCACCGT 57.168 45.000 0.00 0.00 35.25 4.83
3406 5054 5.991328 ATAATTATGTGTCTTGCTCACCG 57.009 39.130 0.00 0.00 35.25 4.94
3407 5055 7.710907 TGTCTATAATTATGTGTCTTGCTCACC 59.289 37.037 8.28 0.00 35.25 4.02
3408 5056 8.648557 TGTCTATAATTATGTGTCTTGCTCAC 57.351 34.615 8.28 0.00 36.48 3.51
3409 5057 9.317936 CTTGTCTATAATTATGTGTCTTGCTCA 57.682 33.333 8.28 0.00 0.00 4.26
3410 5058 9.319143 ACTTGTCTATAATTATGTGTCTTGCTC 57.681 33.333 8.28 0.00 0.00 4.26
3411 5059 9.672673 AACTTGTCTATAATTATGTGTCTTGCT 57.327 29.630 8.28 0.00 0.00 3.91
3429 5077 9.442047 CAAGAGTAATTTCATCCTAACTTGTCT 57.558 33.333 0.00 0.00 0.00 3.41
3430 5078 8.669243 CCAAGAGTAATTTCATCCTAACTTGTC 58.331 37.037 0.00 0.00 32.20 3.18
3431 5079 7.121315 GCCAAGAGTAATTTCATCCTAACTTGT 59.879 37.037 0.00 0.00 32.20 3.16
3432 5080 7.121168 TGCCAAGAGTAATTTCATCCTAACTTG 59.879 37.037 0.00 0.00 0.00 3.16
3433 5081 7.175104 TGCCAAGAGTAATTTCATCCTAACTT 58.825 34.615 0.00 0.00 0.00 2.66
3434 5082 6.721318 TGCCAAGAGTAATTTCATCCTAACT 58.279 36.000 0.00 0.00 0.00 2.24
3435 5083 7.391148 TTGCCAAGAGTAATTTCATCCTAAC 57.609 36.000 0.00 0.00 0.00 2.34
3436 5084 8.593945 ATTTGCCAAGAGTAATTTCATCCTAA 57.406 30.769 0.00 0.00 0.00 2.69
3437 5085 8.593945 AATTTGCCAAGAGTAATTTCATCCTA 57.406 30.769 0.00 0.00 0.00 2.94
3438 5086 7.486407 AATTTGCCAAGAGTAATTTCATCCT 57.514 32.000 0.00 0.00 0.00 3.24
3439 5087 7.603784 ACAAATTTGCCAAGAGTAATTTCATCC 59.396 33.333 18.12 0.00 30.17 3.51
3440 5088 8.538409 ACAAATTTGCCAAGAGTAATTTCATC 57.462 30.769 18.12 0.00 30.17 2.92
3441 5089 8.776470 CAACAAATTTGCCAAGAGTAATTTCAT 58.224 29.630 18.12 0.00 30.17 2.57
3442 5090 7.226325 CCAACAAATTTGCCAAGAGTAATTTCA 59.774 33.333 18.12 0.00 30.17 2.69
3443 5091 7.226523 ACCAACAAATTTGCCAAGAGTAATTTC 59.773 33.333 18.12 0.00 30.17 2.17
3444 5092 7.053498 ACCAACAAATTTGCCAAGAGTAATTT 58.947 30.769 18.12 0.00 32.14 1.82
3445 5093 6.591001 ACCAACAAATTTGCCAAGAGTAATT 58.409 32.000 18.12 0.00 0.00 1.40
3446 5094 6.173427 ACCAACAAATTTGCCAAGAGTAAT 57.827 33.333 18.12 0.00 0.00 1.89
3447 5095 5.606348 ACCAACAAATTTGCCAAGAGTAA 57.394 34.783 18.12 0.00 0.00 2.24
3448 5096 5.606348 AACCAACAAATTTGCCAAGAGTA 57.394 34.783 18.12 0.00 0.00 2.59
3449 5097 4.486125 AACCAACAAATTTGCCAAGAGT 57.514 36.364 18.12 4.81 0.00 3.24
3450 5098 5.463061 CACTAACCAACAAATTTGCCAAGAG 59.537 40.000 18.12 10.69 0.00 2.85
3451 5099 5.105146 ACACTAACCAACAAATTTGCCAAGA 60.105 36.000 18.12 0.00 0.00 3.02
3452 5100 5.115480 ACACTAACCAACAAATTTGCCAAG 58.885 37.500 18.12 9.41 0.00 3.61
3453 5101 5.091261 ACACTAACCAACAAATTTGCCAA 57.909 34.783 18.12 0.00 0.00 4.52
3454 5102 4.744795 ACACTAACCAACAAATTTGCCA 57.255 36.364 18.12 0.00 0.00 4.92
3455 5103 6.759356 ACTTTACACTAACCAACAAATTTGCC 59.241 34.615 18.12 0.00 0.00 4.52
3456 5104 7.764695 ACTTTACACTAACCAACAAATTTGC 57.235 32.000 18.12 0.00 0.00 3.68
3462 5110 9.398538 ACTGATTTACTTTACACTAACCAACAA 57.601 29.630 0.00 0.00 0.00 2.83
3463 5111 8.967664 ACTGATTTACTTTACACTAACCAACA 57.032 30.769 0.00 0.00 0.00 3.33
3482 5130 9.756571 TCTCTTACTTTCCTAGACTAACTGATT 57.243 33.333 0.00 0.00 0.00 2.57
3483 5131 9.930158 ATCTCTTACTTTCCTAGACTAACTGAT 57.070 33.333 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.