Multiple sequence alignment - TraesCS5A01G390300

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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 TraesCS5A01G390300 chr5A 100.000 6335 0 0 1 6335 585614729 585608395 0.000000e+00 11699.0
1 TraesCS5A01G390300 chr5A 100.000 86 0 0 2433 2518 585612211 585612126 6.570000e-35 159.0
2 TraesCS5A01G390300 chr5A 100.000 86 0 0 2519 2604 585612297 585612212 6.570000e-35 159.0
3 TraesCS5A01G390300 chr5D 97.502 3283 63 5 2519 5791 465368043 465364770 0.000000e+00 5590.0
4 TraesCS5A01G390300 chr5D 94.453 2506 86 19 19 2518 465370416 465367958 0.000000e+00 3808.0
5 TraesCS5A01G390300 chr5D 93.802 484 30 0 5852 6335 465364768 465364285 0.000000e+00 728.0
6 TraesCS5A01G390300 chr5D 88.406 69 7 1 4180 4248 382510510 382510443 1.460000e-11 82.4
7 TraesCS5A01G390300 chr5B 95.275 1672 65 8 2517 4177 572594168 572592500 0.000000e+00 2638.0
8 TraesCS5A01G390300 chr5B 95.542 1189 46 5 4692 5873 572592091 572590903 0.000000e+00 1895.0
9 TraesCS5A01G390300 chr5B 93.431 1096 39 5 1456 2518 572595176 572594081 0.000000e+00 1594.0
10 TraesCS5A01G390300 chr5B 92.233 515 26 4 941 1453 572595717 572595215 0.000000e+00 717.0
11 TraesCS5A01G390300 chr5B 94.808 443 18 3 5894 6335 572590461 572590023 0.000000e+00 686.0
12 TraesCS5A01G390300 chr5B 90.069 433 24 11 4221 4652 572592502 572592088 1.550000e-150 544.0
13 TraesCS5A01G390300 chr5B 96.429 252 9 0 610 861 572596205 572595954 3.530000e-112 416.0
14 TraesCS5A01G390300 chr7D 82.414 580 82 15 2893 3468 405105725 405105162 7.380000e-134 488.0
15 TraesCS5A01G390300 chr7D 82.080 452 58 12 3029 3468 405642757 405642317 1.300000e-96 364.0
16 TraesCS5A01G390300 chr7D 87.097 93 12 0 362 454 124028813 124028905 8.690000e-19 106.0
17 TraesCS5A01G390300 chr7D 82.051 117 20 1 356 472 43434126 43434241 1.450000e-16 99.0
18 TraesCS5A01G390300 chr7D 100.000 49 0 0 4179 4227 265172325 265172373 2.430000e-14 91.6
19 TraesCS5A01G390300 chr7B 81.784 538 81 10 2933 3468 373664573 373664051 9.750000e-118 435.0
20 TraesCS5A01G390300 chr7B 79.003 381 47 24 3818 4169 373663735 373663359 4.940000e-56 230.0
21 TraesCS5A01G390300 chr7B 83.966 237 30 4 3705 3941 5925370 5925142 2.970000e-53 220.0
22 TraesCS5A01G390300 chr7B 91.803 61 2 3 4166 4225 680211551 680211609 1.460000e-11 82.4
23 TraesCS5A01G390300 chr6A 85.319 361 40 8 3820 4175 4519683 4519331 1.680000e-95 361.0
24 TraesCS5A01G390300 chr6A 85.232 237 26 5 3705 3941 40915049 40914822 1.060000e-57 235.0
25 TraesCS5A01G390300 chr6A 92.537 67 3 1 3147 3211 326745119 326745053 1.880000e-15 95.3
26 TraesCS5A01G390300 chr4D 85.232 237 26 5 3705 3941 503516691 503516464 1.060000e-57 235.0
27 TraesCS5A01G390300 chr4D 84.946 93 13 1 362 454 16138337 16138428 6.760000e-15 93.5
28 TraesCS5A01G390300 chr3D 78.961 385 44 24 3818 4169 4507614 4507234 1.780000e-55 228.0
29 TraesCS5A01G390300 chr3D 85.714 133 8 5 3082 3211 408324527 408324403 5.150000e-26 130.0
30 TraesCS5A01G390300 chr3D 100.000 49 0 0 4180 4228 435451272 435451320 2.430000e-14 91.6
31 TraesCS5A01G390300 chr4A 83.966 237 30 4 3705 3941 641299364 641299592 2.970000e-53 220.0
32 TraesCS5A01G390300 chr1B 83.966 237 30 4 3705 3941 16458113 16457885 2.970000e-53 220.0
33 TraesCS5A01G390300 chr1B 94.545 55 3 0 4180 4234 303240412 303240466 1.130000e-12 86.1
34 TraesCS5A01G390300 chr3B 83.544 237 31 4 3705 3941 647902820 647903048 1.380000e-51 215.0
35 TraesCS5A01G390300 chr2B 83.544 237 31 4 3705 3941 587236824 587236596 1.380000e-51 215.0
36 TraesCS5A01G390300 chr2B 86.408 103 13 1 362 463 651737595 651737493 1.870000e-20 111.0
37 TraesCS5A01G390300 chr2B 79.021 143 25 4 331 472 363340192 363340330 6.760000e-15 93.5
38 TraesCS5A01G390300 chr2B 79.762 84 15 2 6231 6313 98579584 98579666 6.860000e-05 60.2
39 TraesCS5A01G390300 chr7A 80.090 221 33 7 2828 3039 444053661 444053879 3.060000e-33 154.0
40 TraesCS5A01G390300 chr7A 86.139 101 14 0 356 456 45677790 45677890 6.710000e-20 110.0
41 TraesCS5A01G390300 chr7A 81.148 122 19 3 356 475 43443290 43443409 1.880000e-15 95.3
42 TraesCS5A01G390300 chr7A 94.737 57 1 1 4166 4222 506285479 506285533 3.150000e-13 87.9
43 TraesCS5A01G390300 chr7A 92.063 63 3 2 4165 4225 663591531 663591593 3.150000e-13 87.9
44 TraesCS5A01G390300 chr7A 91.803 61 2 3 4166 4225 692919218 692919276 1.460000e-11 82.4
45 TraesCS5A01G390300 chr6B 86.735 98 12 1 357 454 474831205 474831109 2.420000e-19 108.0
46 TraesCS5A01G390300 chr4B 92.537 67 3 1 3147 3211 639443285 639443351 1.880000e-15 95.3
47 TraesCS5A01G390300 chr2D 92.537 67 3 1 3147 3211 47003676 47003610 1.880000e-15 95.3
48 TraesCS5A01G390300 chr2D 83.607 61 10 0 6230 6290 63390627 63390567 2.470000e-04 58.4
49 TraesCS5A01G390300 chr2D 96.970 33 1 0 6228 6260 63536094 63536126 8.870000e-04 56.5
50 TraesCS5A01G390300 chr1D 92.537 67 3 1 3147 3211 487146861 487146927 1.880000e-15 95.3
51 TraesCS5A01G390300 chrUn 84.375 96 11 4 343 435 263378342 263378248 2.430000e-14 91.6


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 TraesCS5A01G390300 chr5A 585608395 585614729 6334 True 4005.666667 11699 100.000000 1 6335 3 chr5A.!!$R1 6334
1 TraesCS5A01G390300 chr5D 465364285 465370416 6131 True 3375.333333 5590 95.252333 19 6335 3 chr5D.!!$R2 6316
2 TraesCS5A01G390300 chr5B 572590023 572596205 6182 True 1212.857143 2638 93.969571 610 6335 7 chr5B.!!$R1 5725
3 TraesCS5A01G390300 chr7D 405105162 405105725 563 True 488.000000 488 82.414000 2893 3468 1 chr7D.!!$R1 575
4 TraesCS5A01G390300 chr7B 373663359 373664573 1214 True 332.500000 435 80.393500 2933 4169 2 chr7B.!!$R2 1236

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
392 393 0.318762 GGATATGAGAGGTGCCGGTC 59.681 60.000 1.90 0.00 0.00 4.79 F
395 396 0.324368 TATGAGAGGTGCCGGTCAGT 60.324 55.000 1.90 0.00 0.00 3.41 F
1055 1214 0.390124 GACGACACCAACCACAGGTA 59.610 55.000 0.00 0.00 37.23 3.08 F
1161 1326 0.534203 TGTCCGTTCTTTGCAGGTCC 60.534 55.000 0.00 0.00 0.00 4.46 F
1946 2180 0.664166 GCCGTGTTTGTTGCATCCTG 60.664 55.000 0.00 0.00 0.00 3.86 F
2497 2731 0.817634 CGACACAAGCTGGGTTTGGA 60.818 55.000 0.00 0.00 31.64 3.53 F
2498 2732 1.620822 GACACAAGCTGGGTTTGGAT 58.379 50.000 0.00 0.00 31.64 3.41 F
2499 2733 1.963515 GACACAAGCTGGGTTTGGATT 59.036 47.619 0.00 0.00 31.64 3.01 F
2526 2760 2.092968 GGCTGACATATGTCTGGAACCA 60.093 50.000 31.73 15.11 44.99 3.67 F
4668 4981 2.705127 ACATTTTGCAGTCCCACCATTT 59.295 40.909 0.00 0.00 0.00 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2160 2394 0.108396 TGCACTGTGCCTTGCTCTTA 59.892 50.000 28.17 4.96 44.23 2.10 R
2273 2507 8.893219 TGAGGTAGCATTGAATTAAGTATCAG 57.107 34.615 0.00 0.00 0.00 2.90 R
2478 2712 0.817634 TCCAAACCCAGCTTGTGTCG 60.818 55.000 0.00 0.00 0.00 4.35 R
2564 2798 0.817634 TCCAAACCCAGCTTGTGTCG 60.818 55.000 0.00 0.00 0.00 4.35 R
2866 3101 1.234821 TGCACTTTTTAGCACCCTCG 58.765 50.000 0.00 0.00 35.51 4.63 R
4260 4565 2.378547 ACATGGTCTGTTGGGGTTATGT 59.621 45.455 0.00 0.00 32.90 2.29 R
4261 4566 3.016736 GACATGGTCTGTTGGGGTTATG 58.983 50.000 0.00 0.00 38.54 1.90 R
4318 4631 6.815089 ACTTAACTGGATGAGAAGCATAGAG 58.185 40.000 0.00 0.00 37.34 2.43 R
4920 5233 0.741927 GCCACCAGCATCCAAAATGC 60.742 55.000 1.80 1.80 44.85 3.56 R
5880 6200 0.676782 CTGGGTGTTTTAGGGGCGAG 60.677 60.000 0.00 0.00 0.00 5.03 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
62 63 2.187946 CGCATCCGCTTCCCTCTT 59.812 61.111 0.00 0.00 35.30 2.85
66 67 1.153349 ATCCGCTTCCCTCTTTCGC 60.153 57.895 0.00 0.00 0.00 4.70
71 72 0.320771 GCTTCCCTCTTTCGCTGTCA 60.321 55.000 0.00 0.00 0.00 3.58
77 78 2.357517 CTTTCGCTGTCACCGGCT 60.358 61.111 0.00 0.00 41.05 5.52
88 89 3.003763 ACCGGCTCTGGTTCCTCC 61.004 66.667 0.00 0.00 39.99 4.30
99 100 1.304134 GTTCCTCCGGGCCATGTTT 60.304 57.895 4.39 0.00 0.00 2.83
101 102 0.610785 TTCCTCCGGGCCATGTTTTC 60.611 55.000 4.39 0.00 0.00 2.29
103 104 1.304052 CTCCGGGCCATGTTTTCCA 60.304 57.895 4.39 0.00 0.00 3.53
126 127 1.144057 GCATGACGAACCCGAGGAT 59.856 57.895 0.00 0.00 39.50 3.24
154 155 2.280524 CGGACAAGGTGGACGCAA 60.281 61.111 0.00 0.00 0.00 4.85
160 161 4.533318 AGGTGGACGCAACCTCTA 57.467 55.556 0.55 0.00 45.13 2.43
171 172 2.009042 GCAACCTCTATCGCAGCAGTT 61.009 52.381 0.00 0.00 0.00 3.16
193 194 0.811616 GGGACATGCTGGACGACATC 60.812 60.000 0.00 0.00 0.00 3.06
202 203 2.125961 GGACGACATCTAGGGCGGT 61.126 63.158 0.00 0.00 0.00 5.68
227 228 2.036256 ATGGGGAGCAAGTGTGGC 59.964 61.111 0.00 0.00 0.00 5.01
240 241 4.309950 GTGGCGAACGGTGAGGGT 62.310 66.667 0.00 0.00 0.00 4.34
262 263 4.612412 ACGCGCGGAAGGTTGGAA 62.612 61.111 35.22 0.00 0.00 3.53
269 270 2.033194 GGAAGGTTGGAAGGACGCG 61.033 63.158 3.53 3.53 0.00 6.01
298 299 4.842531 GGGGGATGTTTTGATGGATTTT 57.157 40.909 0.00 0.00 0.00 1.82
299 300 5.178096 GGGGGATGTTTTGATGGATTTTT 57.822 39.130 0.00 0.00 0.00 1.94
300 301 4.943093 GGGGGATGTTTTGATGGATTTTTG 59.057 41.667 0.00 0.00 0.00 2.44
301 302 5.514659 GGGGGATGTTTTGATGGATTTTTGT 60.515 40.000 0.00 0.00 0.00 2.83
310 311 8.533153 GTTTTGATGGATTTTTGTTGCAATTTG 58.467 29.630 0.59 0.00 0.00 2.32
317 318 3.616956 TTTGTTGCAATTTGTGGTGGA 57.383 38.095 0.59 0.00 0.00 4.02
332 333 2.073716 TGGAGTTGGGTTGTCCGGT 61.074 57.895 0.00 0.00 38.76 5.28
334 335 1.302271 GAGTTGGGTTGTCCGGTCC 60.302 63.158 0.00 0.00 38.76 4.46
335 336 2.667199 GTTGGGTTGTCCGGTCCG 60.667 66.667 3.60 3.60 38.76 4.79
336 337 2.843411 TTGGGTTGTCCGGTCCGA 60.843 61.111 14.39 0.00 38.76 4.55
337 338 3.167822 TTGGGTTGTCCGGTCCGAC 62.168 63.158 14.39 9.76 38.76 4.79
338 339 4.729856 GGGTTGTCCGGTCCGACG 62.730 72.222 14.39 0.00 35.40 5.12
339 340 3.982241 GGTTGTCCGGTCCGACGT 61.982 66.667 14.39 0.00 35.40 4.34
340 341 2.732094 GTTGTCCGGTCCGACGTG 60.732 66.667 14.39 0.00 35.40 4.49
341 342 2.906388 TTGTCCGGTCCGACGTGA 60.906 61.111 14.39 0.00 35.40 4.35
342 343 3.198236 TTGTCCGGTCCGACGTGAC 62.198 63.158 14.39 11.98 35.40 3.67
343 344 4.748679 GTCCGGTCCGACGTGACG 62.749 72.222 14.39 2.24 36.07 4.35
371 372 1.217882 CGACCGTCTCATATTTGGGC 58.782 55.000 0.00 0.00 0.00 5.36
390 391 0.319728 CTGGATATGAGAGGTGCCGG 59.680 60.000 0.00 0.00 0.00 6.13
391 392 0.398522 TGGATATGAGAGGTGCCGGT 60.399 55.000 1.90 0.00 0.00 5.28
392 393 0.318762 GGATATGAGAGGTGCCGGTC 59.681 60.000 1.90 0.00 0.00 4.79
393 394 1.040646 GATATGAGAGGTGCCGGTCA 58.959 55.000 1.90 0.00 0.00 4.02
394 395 1.000283 GATATGAGAGGTGCCGGTCAG 60.000 57.143 1.90 0.00 0.00 3.51
395 396 0.324368 TATGAGAGGTGCCGGTCAGT 60.324 55.000 1.90 0.00 0.00 3.41
396 397 1.608717 ATGAGAGGTGCCGGTCAGTC 61.609 60.000 1.90 1.93 0.00 3.51
397 398 1.979693 GAGAGGTGCCGGTCAGTCT 60.980 63.158 1.90 6.84 0.00 3.24
398 399 2.219325 GAGAGGTGCCGGTCAGTCTG 62.219 65.000 1.90 0.00 0.00 3.51
399 400 3.302347 GAGGTGCCGGTCAGTCTGG 62.302 68.421 1.90 0.00 45.06 3.86
400 401 4.394712 GGTGCCGGTCAGTCTGGG 62.395 72.222 1.90 0.00 42.62 4.45
404 405 4.436998 CCGGTCAGTCTGGGCGTC 62.437 72.222 0.00 0.00 38.86 5.19
414 415 4.988716 TGGGCGTCTGAGTCCCGT 62.989 66.667 8.97 0.00 42.98 5.28
428 429 1.449070 CCCGTTTAAGGAGCCCGTC 60.449 63.158 0.00 0.00 0.00 4.79
466 467 1.100510 CCAGTCACTAATCGGGTCGA 58.899 55.000 0.00 0.00 41.13 4.20
503 505 0.812412 GGCGCCCGCTCTAATAACAA 60.812 55.000 18.11 0.00 41.60 2.83
507 509 2.676342 CGCCCGCTCTAATAACAAGTTT 59.324 45.455 0.00 0.00 0.00 2.66
508 510 3.126343 CGCCCGCTCTAATAACAAGTTTT 59.874 43.478 0.00 0.00 0.00 2.43
509 511 4.379082 CGCCCGCTCTAATAACAAGTTTTT 60.379 41.667 0.00 0.00 0.00 1.94
510 512 5.163834 CGCCCGCTCTAATAACAAGTTTTTA 60.164 40.000 0.00 0.00 0.00 1.52
511 513 6.457799 CGCCCGCTCTAATAACAAGTTTTTAT 60.458 38.462 0.00 0.00 0.00 1.40
512 514 7.255569 GCCCGCTCTAATAACAAGTTTTTATT 58.744 34.615 10.89 10.89 34.31 1.40
513 515 7.758076 GCCCGCTCTAATAACAAGTTTTTATTT 59.242 33.333 11.27 0.00 32.56 1.40
514 516 9.634163 CCCGCTCTAATAACAAGTTTTTATTTT 57.366 29.630 11.27 0.00 32.56 1.82
652 654 0.767375 GGCTGCAAGAGATATCCCCA 59.233 55.000 0.50 0.00 34.07 4.96
663 665 4.019860 AGAGATATCCCCATGATTTGTCCG 60.020 45.833 0.00 0.00 34.76 4.79
668 670 1.029408 CCCATGATTTGTCCGCGGAA 61.029 55.000 32.93 16.23 0.00 4.30
867 869 4.477119 GCCCCCGGTCCTCCTAGT 62.477 72.222 0.00 0.00 0.00 2.57
1055 1214 0.390124 GACGACACCAACCACAGGTA 59.610 55.000 0.00 0.00 37.23 3.08
1061 1220 0.832983 ACCAACCACAGGTACCGCTA 60.833 55.000 6.18 0.00 37.67 4.26
1151 1316 1.796459 GTGTAATGCGTTGTCCGTTCT 59.204 47.619 0.08 0.00 39.32 3.01
1161 1326 0.534203 TGTCCGTTCTTTGCAGGTCC 60.534 55.000 0.00 0.00 0.00 4.46
1176 1341 2.203938 TCCAAGCGGAGGAGGGTT 60.204 61.111 0.00 0.00 35.91 4.11
1260 1425 2.040544 GGCGCTGTACCACTGCAAT 61.041 57.895 7.64 0.00 42.26 3.56
1314 1479 1.228367 CAAGTGCTCCAAGTGCCCT 60.228 57.895 0.00 0.00 0.00 5.19
1624 1855 5.610398 GGAAACCCAAAAGATGAAATGTGT 58.390 37.500 0.00 0.00 0.00 3.72
1632 1863 5.695851 AAAGATGAAATGTGTCACTCCAC 57.304 39.130 4.27 0.00 35.86 4.02
1650 1882 1.227999 ACGCTGAATCAACCCACACG 61.228 55.000 0.00 0.00 0.00 4.49
1665 1897 2.555325 CCACACGACCACTGTCTTAGTA 59.445 50.000 0.00 0.00 37.60 1.82
1690 1922 1.747355 CCCATCACATTCAGGCTTCAC 59.253 52.381 0.00 0.00 0.00 3.18
1809 2041 5.683681 TCTTGATTGCAACTGGCTATATGA 58.316 37.500 0.00 0.00 45.15 2.15
1946 2180 0.664166 GCCGTGTTTGTTGCATCCTG 60.664 55.000 0.00 0.00 0.00 3.86
2048 2282 6.879400 TCCTTCTTCTAGAGGTATTTTCTGC 58.121 40.000 1.31 0.00 0.00 4.26
2444 2678 6.966534 ATCTATTTAGGCTGGAACCAAATG 57.033 37.500 0.00 0.00 0.00 2.32
2450 2684 3.157087 AGGCTGGAACCAAATGTTGTAG 58.843 45.455 0.00 0.00 37.29 2.74
2478 2712 9.651913 TTTTCTTGAATATTTGGTCTAATTGGC 57.348 29.630 0.00 0.00 0.00 4.52
2479 2713 7.026631 TCTTGAATATTTGGTCTAATTGGCG 57.973 36.000 0.00 0.00 0.00 5.69
2480 2714 6.826231 TCTTGAATATTTGGTCTAATTGGCGA 59.174 34.615 0.00 0.00 0.00 5.54
2481 2715 6.371809 TGAATATTTGGTCTAATTGGCGAC 57.628 37.500 0.00 0.00 0.00 5.19
2482 2716 5.883115 TGAATATTTGGTCTAATTGGCGACA 59.117 36.000 0.00 0.00 39.83 4.35
2483 2717 5.751243 ATATTTGGTCTAATTGGCGACAC 57.249 39.130 0.00 0.00 42.67 3.67
2484 2718 2.552599 TTGGTCTAATTGGCGACACA 57.447 45.000 0.00 0.00 42.67 3.72
2485 2719 2.552599 TGGTCTAATTGGCGACACAA 57.447 45.000 0.00 0.00 42.67 3.33
2486 2720 2.422597 TGGTCTAATTGGCGACACAAG 58.577 47.619 0.00 0.00 42.67 3.16
2487 2721 1.130561 GGTCTAATTGGCGACACAAGC 59.869 52.381 0.00 0.00 42.67 4.01
2488 2722 2.076863 GTCTAATTGGCGACACAAGCT 58.923 47.619 0.00 0.00 42.67 3.74
2489 2723 2.076100 TCTAATTGGCGACACAAGCTG 58.924 47.619 0.00 0.00 42.67 4.24
2490 2724 1.131126 CTAATTGGCGACACAAGCTGG 59.869 52.381 0.00 0.00 42.67 4.85
2491 2725 1.526575 AATTGGCGACACAAGCTGGG 61.527 55.000 0.00 0.00 42.67 4.45
2492 2726 2.697147 ATTGGCGACACAAGCTGGGT 62.697 55.000 0.00 0.00 42.67 4.51
2493 2727 2.594592 GGCGACACAAGCTGGGTT 60.595 61.111 0.00 0.00 31.64 4.11
2494 2728 2.193536 GGCGACACAAGCTGGGTTT 61.194 57.895 0.00 0.00 31.64 3.27
2495 2729 1.008538 GCGACACAAGCTGGGTTTG 60.009 57.895 0.00 0.00 31.64 2.93
2496 2730 1.654220 CGACACAAGCTGGGTTTGG 59.346 57.895 0.00 0.00 31.64 3.28
2497 2731 0.817634 CGACACAAGCTGGGTTTGGA 60.818 55.000 0.00 0.00 31.64 3.53
2498 2732 1.620822 GACACAAGCTGGGTTTGGAT 58.379 50.000 0.00 0.00 31.64 3.41
2499 2733 1.963515 GACACAAGCTGGGTTTGGATT 59.036 47.619 0.00 0.00 31.64 3.01
2500 2734 2.365293 GACACAAGCTGGGTTTGGATTT 59.635 45.455 0.00 0.00 31.64 2.17
2501 2735 2.771372 ACACAAGCTGGGTTTGGATTTT 59.229 40.909 0.00 0.00 21.35 1.82
2502 2736 3.132925 CACAAGCTGGGTTTGGATTTTG 58.867 45.455 0.00 0.00 0.00 2.44
2503 2737 3.037549 ACAAGCTGGGTTTGGATTTTGA 58.962 40.909 0.00 0.00 0.00 2.69
2504 2738 3.454082 ACAAGCTGGGTTTGGATTTTGAA 59.546 39.130 0.00 0.00 0.00 2.69
2505 2739 4.060205 CAAGCTGGGTTTGGATTTTGAAG 58.940 43.478 0.00 0.00 0.00 3.02
2506 2740 2.634453 AGCTGGGTTTGGATTTTGAAGG 59.366 45.455 0.00 0.00 0.00 3.46
2507 2741 2.871637 GCTGGGTTTGGATTTTGAAGGC 60.872 50.000 0.00 0.00 0.00 4.35
2508 2742 2.634453 CTGGGTTTGGATTTTGAAGGCT 59.366 45.455 0.00 0.00 0.00 4.58
2509 2743 2.368221 TGGGTTTGGATTTTGAAGGCTG 59.632 45.455 0.00 0.00 0.00 4.85
2510 2744 2.632512 GGGTTTGGATTTTGAAGGCTGA 59.367 45.455 0.00 0.00 0.00 4.26
2511 2745 3.554960 GGGTTTGGATTTTGAAGGCTGAC 60.555 47.826 0.00 0.00 0.00 3.51
2512 2746 3.069443 GGTTTGGATTTTGAAGGCTGACA 59.931 43.478 0.00 0.00 0.00 3.58
2513 2747 4.262592 GGTTTGGATTTTGAAGGCTGACAT 60.263 41.667 0.00 0.00 0.00 3.06
2514 2748 5.047377 GGTTTGGATTTTGAAGGCTGACATA 60.047 40.000 0.00 0.00 0.00 2.29
2515 2749 6.351286 GGTTTGGATTTTGAAGGCTGACATAT 60.351 38.462 0.00 0.00 0.00 1.78
2516 2750 5.840243 TGGATTTTGAAGGCTGACATATG 57.160 39.130 0.00 0.00 0.00 1.78
2517 2751 5.263599 TGGATTTTGAAGGCTGACATATGT 58.736 37.500 8.43 8.43 0.00 2.29
2518 2752 5.357878 TGGATTTTGAAGGCTGACATATGTC 59.642 40.000 25.95 25.95 44.97 3.06
2519 2753 5.591877 GGATTTTGAAGGCTGACATATGTCT 59.408 40.000 30.67 14.60 44.99 3.41
2520 2754 5.885230 TTTTGAAGGCTGACATATGTCTG 57.115 39.130 30.67 29.71 44.99 3.51
2521 2755 3.548745 TGAAGGCTGACATATGTCTGG 57.451 47.619 31.73 25.01 44.99 3.86
2522 2756 3.106827 TGAAGGCTGACATATGTCTGGA 58.893 45.455 31.73 16.39 44.99 3.86
2523 2757 3.519107 TGAAGGCTGACATATGTCTGGAA 59.481 43.478 31.73 16.09 44.99 3.53
2524 2758 3.550437 AGGCTGACATATGTCTGGAAC 57.450 47.619 31.73 20.52 44.99 3.62
2525 2759 2.171448 AGGCTGACATATGTCTGGAACC 59.829 50.000 31.73 25.91 44.99 3.62
2526 2760 2.092968 GGCTGACATATGTCTGGAACCA 60.093 50.000 31.73 15.11 44.99 3.67
2527 2761 3.609853 GCTGACATATGTCTGGAACCAA 58.390 45.455 31.73 14.01 44.99 3.67
2528 2762 4.009675 GCTGACATATGTCTGGAACCAAA 58.990 43.478 31.73 13.43 44.99 3.28
2529 2763 4.641989 GCTGACATATGTCTGGAACCAAAT 59.358 41.667 31.73 0.00 44.99 2.32
2530 2764 5.449588 GCTGACATATGTCTGGAACCAAATG 60.450 44.000 31.73 13.12 44.99 2.32
2531 2765 5.569355 TGACATATGTCTGGAACCAAATGT 58.431 37.500 30.67 0.00 44.99 2.71
2532 2766 6.009589 TGACATATGTCTGGAACCAAATGTT 58.990 36.000 30.67 0.00 44.99 2.71
2533 2767 6.072008 TGACATATGTCTGGAACCAAATGTTG 60.072 38.462 30.67 0.00 44.99 3.33
2534 2768 5.774690 ACATATGTCTGGAACCAAATGTTGT 59.225 36.000 1.41 0.00 37.29 3.32
2535 2769 6.945435 ACATATGTCTGGAACCAAATGTTGTA 59.055 34.615 1.41 0.00 37.29 2.41
2536 2770 5.964958 ATGTCTGGAACCAAATGTTGTAG 57.035 39.130 0.00 0.00 37.29 2.74
2537 2771 4.787551 TGTCTGGAACCAAATGTTGTAGT 58.212 39.130 0.00 0.00 37.29 2.73
2538 2772 5.197451 TGTCTGGAACCAAATGTTGTAGTT 58.803 37.500 0.00 0.00 37.29 2.24
2539 2773 5.654650 TGTCTGGAACCAAATGTTGTAGTTT 59.345 36.000 0.00 0.00 37.29 2.66
2540 2774 6.153680 TGTCTGGAACCAAATGTTGTAGTTTT 59.846 34.615 0.00 0.00 37.29 2.43
2541 2775 7.039270 GTCTGGAACCAAATGTTGTAGTTTTT 58.961 34.615 0.00 0.00 37.29 1.94
2542 2776 7.222031 GTCTGGAACCAAATGTTGTAGTTTTTC 59.778 37.037 0.00 0.00 37.29 2.29
2543 2777 7.123547 TCTGGAACCAAATGTTGTAGTTTTTCT 59.876 33.333 0.00 0.00 37.29 2.52
2544 2778 7.616313 TGGAACCAAATGTTGTAGTTTTTCTT 58.384 30.769 0.00 0.00 37.29 2.52
2545 2779 7.547370 TGGAACCAAATGTTGTAGTTTTTCTTG 59.453 33.333 0.00 0.00 37.29 3.02
2546 2780 7.762159 GGAACCAAATGTTGTAGTTTTTCTTGA 59.238 33.333 0.00 0.00 37.29 3.02
2547 2781 9.145865 GAACCAAATGTTGTAGTTTTTCTTGAA 57.854 29.630 0.00 0.00 37.29 2.69
2548 2782 9.665719 AACCAAATGTTGTAGTTTTTCTTGAAT 57.334 25.926 0.00 0.00 35.31 2.57
2564 2798 9.651913 TTTTCTTGAATATTTGGTCTAATTGGC 57.348 29.630 0.00 0.00 0.00 4.52
2866 3101 2.754552 TGTTGGTAATGGCTCTGAATGC 59.245 45.455 0.00 0.00 0.00 3.56
2991 3227 8.469309 TGATCTCATGTTTCCTTTCTTTTCTT 57.531 30.769 0.00 0.00 0.00 2.52
3138 3374 7.162082 GCAATAGGCTACTTACTGACCATTAT 58.838 38.462 0.00 0.00 40.25 1.28
3727 4005 9.064706 CAACTATATTTCTTCAGATTCCTGCAT 57.935 33.333 0.00 0.00 40.20 3.96
4108 4413 4.712051 AGATCATGGCAGCACCTTATTA 57.288 40.909 0.00 0.00 40.22 0.98
4253 4558 5.473162 TGCACAAATAGTTCTGCTTGTATGT 59.527 36.000 4.83 0.00 31.00 2.29
4260 4565 9.890629 AAATAGTTCTGCTTGTATGTCTTCATA 57.109 29.630 0.00 0.00 35.70 2.15
4668 4981 2.705127 ACATTTTGCAGTCCCACCATTT 59.295 40.909 0.00 0.00 0.00 2.32
4920 5233 3.955471 TGGATCTTAAGAAAGGCAGTGG 58.045 45.455 9.71 0.00 33.22 4.00
5075 5388 1.327303 TTCTTGATGCCGCCTTGTTT 58.673 45.000 0.00 0.00 0.00 2.83
5117 5432 4.215965 CAATAACGAAACAACCCGTCTTG 58.784 43.478 0.00 0.00 38.13 3.02
5277 5592 2.481276 CGATCCTGCCAAAGTCGATACA 60.481 50.000 0.00 0.00 34.46 2.29
5349 5664 3.118811 TGGTTTAGCTATGCAATTTGGGC 60.119 43.478 0.00 0.00 0.00 5.36
5583 5899 5.305585 TGCTGTTCGATTTTAAAGAGGAGT 58.694 37.500 0.00 0.00 0.00 3.85
5629 5945 7.785033 AGTGTACTGTGATGATGATGTGATAA 58.215 34.615 0.00 0.00 0.00 1.75
5740 6056 6.920758 TGTGCAACCATTCATTTTAAGTGTAC 59.079 34.615 0.00 0.00 34.36 2.90
5741 6057 6.364976 GTGCAACCATTCATTTTAAGTGTACC 59.635 38.462 0.00 0.00 0.00 3.34
5749 6065 6.266168 TCATTTTAAGTGTACCATTGCAGG 57.734 37.500 0.00 0.00 0.00 4.85
5796 6116 2.422276 GCCTTTGCGACTGTTGATTT 57.578 45.000 0.00 0.00 0.00 2.17
5800 6120 3.486841 CCTTTGCGACTGTTGATTTGTTG 59.513 43.478 0.00 0.00 0.00 3.33
5804 6124 3.623510 TGCGACTGTTGATTTGTTGTGTA 59.376 39.130 0.00 0.00 0.00 2.90
5806 6126 4.612614 GCGACTGTTGATTTGTTGTGTATG 59.387 41.667 0.00 0.00 0.00 2.39
5810 6130 5.163571 ACTGTTGATTTGTTGTGTATGTGCA 60.164 36.000 0.00 0.00 0.00 4.57
5838 6158 1.587946 GGTTTGAGCAAAAGCAACGTG 59.412 47.619 8.65 0.00 44.14 4.49
5880 6200 4.184079 ACAATCCTTGCATCAAAAGCTC 57.816 40.909 0.00 0.00 0.00 4.09
5883 6203 2.079158 TCCTTGCATCAAAAGCTCTCG 58.921 47.619 0.00 0.00 0.00 4.04
5914 6655 2.639347 CACCCAGTGGATATAGGCATCA 59.361 50.000 11.95 0.00 34.81 3.07
6040 6781 2.104451 AGGGCACTCTTCATCTGCATAG 59.896 50.000 0.00 0.00 32.20 2.23
6070 6811 2.357517 CTGGCGACGCAGAACCTT 60.358 61.111 23.09 0.00 0.00 3.50
6073 6814 2.357034 GCGACGCAGAACCTTCCA 60.357 61.111 16.42 0.00 0.00 3.53
6075 6816 1.970917 GCGACGCAGAACCTTCCATG 61.971 60.000 16.42 0.00 0.00 3.66
6094 6835 2.887568 CCGACATGCACGAGGAGC 60.888 66.667 13.20 0.00 0.00 4.70
6116 6857 4.106925 CCAGCAGCTCCCAGTCCC 62.107 72.222 0.00 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.280019 GTCCCCACCCACACACCC 62.280 72.222 0.00 0.00 0.00 4.61
11 12 3.063197 TTGTCCCCACCCACACACC 62.063 63.158 0.00 0.00 0.00 4.16
12 13 1.826487 GTTGTCCCCACCCACACAC 60.826 63.158 0.00 0.00 0.00 3.82
13 14 2.004120 AGTTGTCCCCACCCACACA 61.004 57.895 0.00 0.00 0.00 3.72
14 15 1.528309 CAGTTGTCCCCACCCACAC 60.528 63.158 0.00 0.00 0.00 3.82
15 16 2.923035 CAGTTGTCCCCACCCACA 59.077 61.111 0.00 0.00 0.00 4.17
16 17 2.597510 GCAGTTGTCCCCACCCAC 60.598 66.667 0.00 0.00 0.00 4.61
17 18 2.776526 AGCAGTTGTCCCCACCCA 60.777 61.111 0.00 0.00 0.00 4.51
33 34 1.482621 CGGATGCGGACATGAACGAG 61.483 60.000 15.76 2.48 36.35 4.18
62 63 3.303135 AGAGCCGGTGACAGCGAA 61.303 61.111 27.42 0.00 42.41 4.70
66 67 1.374758 GAACCAGAGCCGGTGACAG 60.375 63.158 1.90 0.00 39.95 3.51
71 72 3.003763 GGAGGAACCAGAGCCGGT 61.004 66.667 1.90 0.00 42.71 5.28
88 89 1.535204 AAGCTGGAAAACATGGCCCG 61.535 55.000 0.00 0.00 0.00 6.13
99 100 0.874390 GTTCGTCATGCAAGCTGGAA 59.126 50.000 0.00 0.00 0.00 3.53
101 102 1.503542 GGTTCGTCATGCAAGCTGG 59.496 57.895 0.00 0.00 0.00 4.85
103 104 2.034879 CGGGTTCGTCATGCAAGCT 61.035 57.895 0.00 0.00 0.00 3.74
129 130 4.353437 ACCTTGTCCGTCGGCGTC 62.353 66.667 9.28 0.00 36.15 5.19
154 155 0.176680 CCAACTGCTGCGATAGAGGT 59.823 55.000 0.00 0.00 39.76 3.85
160 161 3.329889 TCCCCCAACTGCTGCGAT 61.330 61.111 0.00 0.00 0.00 4.58
171 172 3.716195 CGTCCAGCATGTCCCCCA 61.716 66.667 0.00 0.00 0.00 4.96
193 194 1.276421 CCATCCTTATCACCGCCCTAG 59.724 57.143 0.00 0.00 0.00 3.02
202 203 2.173356 CACTTGCTCCCCATCCTTATCA 59.827 50.000 0.00 0.00 0.00 2.15
240 241 4.651008 ACCTTCCGCGCGTTCGAA 62.651 61.111 29.95 22.55 38.10 3.71
244 245 4.612412 TCCAACCTTCCGCGCGTT 62.612 61.111 29.95 13.32 0.00 4.84
252 253 2.033194 CCGCGTCCTTCCAACCTTC 61.033 63.158 4.92 0.00 0.00 3.46
281 282 6.957150 TGCAACAAAAATCCATCAAAACATC 58.043 32.000 0.00 0.00 0.00 3.06
283 284 6.748333 TTGCAACAAAAATCCATCAAAACA 57.252 29.167 0.00 0.00 0.00 2.83
292 293 5.272397 CACCACAAATTGCAACAAAAATCC 58.728 37.500 0.00 0.00 0.00 3.01
298 299 2.499289 ACTCCACCACAAATTGCAACAA 59.501 40.909 0.00 0.00 0.00 2.83
299 300 2.106566 ACTCCACCACAAATTGCAACA 58.893 42.857 0.00 0.00 0.00 3.33
300 301 2.865551 CAACTCCACCACAAATTGCAAC 59.134 45.455 0.00 0.00 0.00 4.17
301 302 2.158986 CCAACTCCACCACAAATTGCAA 60.159 45.455 0.00 0.00 0.00 4.08
310 311 0.822121 GGACAACCCAACTCCACCAC 60.822 60.000 0.00 0.00 34.14 4.16
317 318 2.833957 GGACCGGACAACCCAACT 59.166 61.111 9.46 0.00 34.14 3.16
347 348 2.694829 AATATGAGACGGTCGGGCGC 62.695 60.000 0.00 0.00 0.00 6.53
348 349 0.249322 AAATATGAGACGGTCGGGCG 60.249 55.000 1.89 0.00 0.00 6.13
349 350 1.217882 CAAATATGAGACGGTCGGGC 58.782 55.000 1.89 0.00 0.00 6.13
350 351 1.540363 CCCAAATATGAGACGGTCGGG 60.540 57.143 1.89 0.88 0.00 5.14
351 352 1.865865 CCCAAATATGAGACGGTCGG 58.134 55.000 1.89 0.00 0.00 4.79
352 353 1.202533 AGCCCAAATATGAGACGGTCG 60.203 52.381 1.89 0.00 0.00 4.79
353 354 2.213499 CAGCCCAAATATGAGACGGTC 58.787 52.381 0.00 0.00 0.00 4.79
354 355 1.134098 CCAGCCCAAATATGAGACGGT 60.134 52.381 0.00 0.00 0.00 4.83
355 356 1.140852 TCCAGCCCAAATATGAGACGG 59.859 52.381 0.00 0.00 0.00 4.79
356 357 2.620251 TCCAGCCCAAATATGAGACG 57.380 50.000 0.00 0.00 0.00 4.18
357 358 5.809001 TCATATCCAGCCCAAATATGAGAC 58.191 41.667 0.00 0.00 37.43 3.36
360 361 5.045359 CCTCTCATATCCAGCCCAAATATGA 60.045 44.000 0.00 0.00 39.09 2.15
371 372 0.319728 CCGGCACCTCTCATATCCAG 59.680 60.000 0.00 0.00 0.00 3.86
390 391 1.214062 CTCAGACGCCCAGACTGAC 59.786 63.158 3.32 0.00 44.35 3.51
391 392 1.228583 ACTCAGACGCCCAGACTGA 60.229 57.895 3.32 0.00 46.33 3.41
392 393 1.214062 GACTCAGACGCCCAGACTG 59.786 63.158 0.00 0.00 42.57 3.51
393 394 1.979693 GGACTCAGACGCCCAGACT 60.980 63.158 0.00 0.00 0.00 3.24
394 395 2.574399 GGACTCAGACGCCCAGAC 59.426 66.667 0.00 0.00 0.00 3.51
395 396 2.680352 GGGACTCAGACGCCCAGA 60.680 66.667 0.00 0.00 41.64 3.86
396 397 4.135153 CGGGACTCAGACGCCCAG 62.135 72.222 0.00 0.00 42.14 4.45
397 398 4.988716 ACGGGACTCAGACGCCCA 62.989 66.667 0.00 0.00 42.14 5.36
398 399 1.880819 TAAACGGGACTCAGACGCCC 61.881 60.000 0.00 0.00 38.53 6.13
399 400 0.037975 TTAAACGGGACTCAGACGCC 60.038 55.000 0.00 0.00 0.00 5.68
400 401 1.347320 CTTAAACGGGACTCAGACGC 58.653 55.000 0.00 0.00 0.00 5.19
401 402 1.542915 TCCTTAAACGGGACTCAGACG 59.457 52.381 0.00 0.00 0.00 4.18
402 403 2.674462 GCTCCTTAAACGGGACTCAGAC 60.674 54.545 0.00 0.00 0.00 3.51
403 404 1.549170 GCTCCTTAAACGGGACTCAGA 59.451 52.381 0.00 0.00 0.00 3.27
404 405 1.405661 GGCTCCTTAAACGGGACTCAG 60.406 57.143 0.00 0.00 0.00 3.35
414 415 1.549170 GACTCAGACGGGCTCCTTAAA 59.451 52.381 0.00 0.00 0.00 1.52
449 450 1.101331 GGTCGACCCGATTAGTGACT 58.899 55.000 24.75 0.00 38.42 3.41
522 524 7.148407 CGGTGCAGAACTTGTTATTAGAGAATT 60.148 37.037 0.00 0.00 0.00 2.17
652 654 0.251916 TCCTTCCGCGGACAAATCAT 59.748 50.000 31.19 0.00 0.00 2.45
683 685 1.070445 CCGTCCATCTGAGGCATCC 59.930 63.158 0.00 0.00 0.00 3.51
707 709 2.904676 TATACTGCCGGCGCGAGAG 61.905 63.158 23.90 15.87 38.08 3.20
711 713 1.442184 CTAGTATACTGCCGGCGCG 60.442 63.158 23.90 18.08 38.08 6.86
1151 1316 1.600636 CTCCGCTTGGACCTGCAAA 60.601 57.895 9.93 0.00 36.65 3.68
1161 1326 2.747855 GCAACCCTCCTCCGCTTG 60.748 66.667 0.00 0.00 0.00 4.01
1233 1398 1.295423 GTACAGCGCCTTCTTCCCA 59.705 57.895 2.29 0.00 0.00 4.37
1260 1425 2.486548 GGACAGGTCCTTGTTGCAGTAA 60.487 50.000 11.21 0.00 46.16 2.24
1314 1479 0.318699 CGACGCAGAGGTCAAAGTCA 60.319 55.000 0.00 0.00 36.73 3.41
1365 1530 4.265056 GGGTGGTTGCTCCGGTGT 62.265 66.667 0.00 0.00 39.52 4.16
1624 1855 1.608025 GGTTGATTCAGCGTGGAGTGA 60.608 52.381 0.00 0.00 0.00 3.41
1632 1863 0.948623 TCGTGTGGGTTGATTCAGCG 60.949 55.000 0.00 0.00 0.00 5.18
1650 1882 6.726490 TGGGAATATACTAAGACAGTGGTC 57.274 41.667 0.00 0.00 44.66 4.02
1665 1897 4.736611 AGCCTGAATGTGATGGGAATAT 57.263 40.909 0.00 0.00 0.00 1.28
1690 1922 8.842358 TGTAAGTGTATTCAAGTTAAGAAGGG 57.158 34.615 0.00 0.00 0.00 3.95
1809 2041 2.014128 GGGTGTGCATGTATTAAGCGT 58.986 47.619 0.00 0.00 0.00 5.07
1946 2180 7.306341 CCTGTTGCAAAATTTCGGTTAAGTTAC 60.306 37.037 0.00 0.00 0.00 2.50
2048 2282 5.704515 AGAAAGTGAACAGAACAGATGGATG 59.295 40.000 0.00 0.00 0.00 3.51
2160 2394 0.108396 TGCACTGTGCCTTGCTCTTA 59.892 50.000 28.17 4.96 44.23 2.10
2273 2507 8.893219 TGAGGTAGCATTGAATTAAGTATCAG 57.107 34.615 0.00 0.00 0.00 2.90
2478 2712 0.817634 TCCAAACCCAGCTTGTGTCG 60.818 55.000 0.00 0.00 0.00 4.35
2479 2713 1.620822 ATCCAAACCCAGCTTGTGTC 58.379 50.000 0.00 0.00 0.00 3.67
2480 2714 2.086610 AATCCAAACCCAGCTTGTGT 57.913 45.000 0.00 0.00 0.00 3.72
2481 2715 3.132925 CAAAATCCAAACCCAGCTTGTG 58.867 45.455 0.00 0.00 0.00 3.33
2482 2716 3.037549 TCAAAATCCAAACCCAGCTTGT 58.962 40.909 0.00 0.00 0.00 3.16
2483 2717 3.749665 TCAAAATCCAAACCCAGCTTG 57.250 42.857 0.00 0.00 0.00 4.01
2484 2718 3.071457 CCTTCAAAATCCAAACCCAGCTT 59.929 43.478 0.00 0.00 0.00 3.74
2485 2719 2.634453 CCTTCAAAATCCAAACCCAGCT 59.366 45.455 0.00 0.00 0.00 4.24
2486 2720 2.871637 GCCTTCAAAATCCAAACCCAGC 60.872 50.000 0.00 0.00 0.00 4.85
2487 2721 2.634453 AGCCTTCAAAATCCAAACCCAG 59.366 45.455 0.00 0.00 0.00 4.45
2488 2722 2.368221 CAGCCTTCAAAATCCAAACCCA 59.632 45.455 0.00 0.00 0.00 4.51
2489 2723 2.632512 TCAGCCTTCAAAATCCAAACCC 59.367 45.455 0.00 0.00 0.00 4.11
2490 2724 3.069443 TGTCAGCCTTCAAAATCCAAACC 59.931 43.478 0.00 0.00 0.00 3.27
2491 2725 4.320608 TGTCAGCCTTCAAAATCCAAAC 57.679 40.909 0.00 0.00 0.00 2.93
2492 2726 6.211184 ACATATGTCAGCCTTCAAAATCCAAA 59.789 34.615 1.41 0.00 0.00 3.28
2493 2727 5.716228 ACATATGTCAGCCTTCAAAATCCAA 59.284 36.000 1.41 0.00 0.00 3.53
2494 2728 5.263599 ACATATGTCAGCCTTCAAAATCCA 58.736 37.500 1.41 0.00 0.00 3.41
2495 2729 5.825507 GACATATGTCAGCCTTCAAAATCC 58.174 41.667 27.33 0.00 44.18 3.01
2506 2740 9.184403 AACATTTGGTTCCAGACATATGTCAGC 62.184 40.741 32.01 22.19 40.69 4.26
2507 2741 6.151648 AACATTTGGTTCCAGACATATGTCAG 59.848 38.462 32.01 25.43 40.69 3.51
2508 2742 6.009589 AACATTTGGTTCCAGACATATGTCA 58.990 36.000 32.01 13.51 40.69 3.58
2509 2743 6.071952 ACAACATTTGGTTCCAGACATATGTC 60.072 38.462 25.47 25.47 37.97 3.06
2510 2744 5.774690 ACAACATTTGGTTCCAGACATATGT 59.225 36.000 8.43 8.43 39.71 2.29
2511 2745 6.271488 ACAACATTTGGTTCCAGACATATG 57.729 37.500 0.00 0.00 37.72 1.78
2512 2746 7.175104 ACTACAACATTTGGTTCCAGACATAT 58.825 34.615 0.00 0.00 37.72 1.78
2513 2747 6.539173 ACTACAACATTTGGTTCCAGACATA 58.461 36.000 0.00 0.00 37.72 2.29
2514 2748 5.385198 ACTACAACATTTGGTTCCAGACAT 58.615 37.500 0.00 0.00 37.72 3.06
2515 2749 4.787551 ACTACAACATTTGGTTCCAGACA 58.212 39.130 0.00 0.00 37.72 3.41
2516 2750 5.767816 AACTACAACATTTGGTTCCAGAC 57.232 39.130 0.00 0.00 37.72 3.51
2517 2751 6.783708 AAAACTACAACATTTGGTTCCAGA 57.216 33.333 0.00 0.00 37.72 3.86
2518 2752 7.264947 AGAAAAACTACAACATTTGGTTCCAG 58.735 34.615 0.00 0.00 37.72 3.86
2519 2753 7.176589 AGAAAAACTACAACATTTGGTTCCA 57.823 32.000 0.00 0.00 37.72 3.53
2520 2754 7.762159 TCAAGAAAAACTACAACATTTGGTTCC 59.238 33.333 0.00 0.00 37.72 3.62
2521 2755 8.696410 TCAAGAAAAACTACAACATTTGGTTC 57.304 30.769 0.00 0.00 37.72 3.62
2522 2756 9.665719 ATTCAAGAAAAACTACAACATTTGGTT 57.334 25.926 0.00 0.00 41.47 3.67
2538 2772 9.651913 GCCAATTAGACCAAATATTCAAGAAAA 57.348 29.630 0.00 0.00 0.00 2.29
2539 2773 7.973388 CGCCAATTAGACCAAATATTCAAGAAA 59.027 33.333 0.00 0.00 0.00 2.52
2540 2774 7.338196 TCGCCAATTAGACCAAATATTCAAGAA 59.662 33.333 0.00 0.00 0.00 2.52
2541 2775 6.826231 TCGCCAATTAGACCAAATATTCAAGA 59.174 34.615 0.00 0.00 0.00 3.02
2542 2776 6.912591 GTCGCCAATTAGACCAAATATTCAAG 59.087 38.462 0.00 0.00 0.00 3.02
2543 2777 6.375736 TGTCGCCAATTAGACCAAATATTCAA 59.624 34.615 0.00 0.00 36.61 2.69
2544 2778 5.883115 TGTCGCCAATTAGACCAAATATTCA 59.117 36.000 0.00 0.00 36.61 2.57
2545 2779 6.183360 TGTGTCGCCAATTAGACCAAATATTC 60.183 38.462 0.00 0.00 36.61 1.75
2546 2780 5.650266 TGTGTCGCCAATTAGACCAAATATT 59.350 36.000 5.72 0.00 36.61 1.28
2547 2781 5.189928 TGTGTCGCCAATTAGACCAAATAT 58.810 37.500 5.72 0.00 36.61 1.28
2548 2782 4.580868 TGTGTCGCCAATTAGACCAAATA 58.419 39.130 5.72 0.00 36.61 1.40
2549 2783 3.417101 TGTGTCGCCAATTAGACCAAAT 58.583 40.909 5.72 0.00 36.61 2.32
2550 2784 2.852449 TGTGTCGCCAATTAGACCAAA 58.148 42.857 5.72 0.00 36.61 3.28
2551 2785 2.552599 TGTGTCGCCAATTAGACCAA 57.447 45.000 5.72 0.00 36.61 3.67
2552 2786 2.422597 CTTGTGTCGCCAATTAGACCA 58.577 47.619 5.72 2.19 36.61 4.02
2553 2787 1.130561 GCTTGTGTCGCCAATTAGACC 59.869 52.381 5.72 0.24 36.61 3.85
2554 2788 2.076863 AGCTTGTGTCGCCAATTAGAC 58.923 47.619 0.00 2.14 37.85 2.59
2555 2789 2.076100 CAGCTTGTGTCGCCAATTAGA 58.924 47.619 0.00 0.00 0.00 2.10
2556 2790 1.131126 CCAGCTTGTGTCGCCAATTAG 59.869 52.381 0.00 0.00 0.00 1.73
2557 2791 1.164411 CCAGCTTGTGTCGCCAATTA 58.836 50.000 0.00 0.00 0.00 1.40
2558 2792 1.526575 CCCAGCTTGTGTCGCCAATT 61.527 55.000 0.00 0.00 0.00 2.32
2559 2793 1.973281 CCCAGCTTGTGTCGCCAAT 60.973 57.895 0.00 0.00 0.00 3.16
2560 2794 2.594303 CCCAGCTTGTGTCGCCAA 60.594 61.111 0.00 0.00 0.00 4.52
2561 2795 2.902423 AAACCCAGCTTGTGTCGCCA 62.902 55.000 0.00 0.00 0.00 5.69
2562 2796 2.193536 AAACCCAGCTTGTGTCGCC 61.194 57.895 0.00 0.00 0.00 5.54
2563 2797 1.008538 CAAACCCAGCTTGTGTCGC 60.009 57.895 0.00 0.00 0.00 5.19
2564 2798 0.817634 TCCAAACCCAGCTTGTGTCG 60.818 55.000 0.00 0.00 0.00 4.35
2690 2925 3.482786 GCAGAAACAACGCTACTGAATG 58.517 45.455 0.00 0.00 0.00 2.67
2751 2986 3.701205 TGTCTGTGGTTCTGTGCATAT 57.299 42.857 0.00 0.00 0.00 1.78
2837 3072 4.460382 AGAGCCATTACCAACAGAACAATG 59.540 41.667 0.00 0.00 0.00 2.82
2866 3101 1.234821 TGCACTTTTTAGCACCCTCG 58.765 50.000 0.00 0.00 35.51 4.63
2991 3227 7.202093 CCCTGATAACAGTGGAATTCCTACATA 60.202 40.741 24.73 14.45 42.05 2.29
4253 4558 5.338871 GGTCTGTTGGGGTTATGTATGAAGA 60.339 44.000 0.00 0.00 0.00 2.87
4260 4565 2.378547 ACATGGTCTGTTGGGGTTATGT 59.621 45.455 0.00 0.00 32.90 2.29
4261 4566 3.016736 GACATGGTCTGTTGGGGTTATG 58.983 50.000 0.00 0.00 38.54 1.90
4318 4631 6.815089 ACTTAACTGGATGAGAAGCATAGAG 58.185 40.000 0.00 0.00 37.34 2.43
4920 5233 0.741927 GCCACCAGCATCCAAAATGC 60.742 55.000 1.80 1.80 44.85 3.56
5075 5388 6.952773 ATTGTAGCAAGAACCAAAAGTACA 57.047 33.333 0.00 0.00 0.00 2.90
5117 5432 6.858478 GCACAGAAGTTTTTCCTGAAATAGAC 59.142 38.462 0.00 0.00 33.64 2.59
5583 5899 2.177394 TCAGCAACAATGGCGTCTAA 57.823 45.000 0.00 0.00 36.08 2.10
5629 5945 4.086457 CCCTAAACCTACAACAAAGGCAT 58.914 43.478 0.00 0.00 37.67 4.40
5740 6056 2.159338 CGAACTCAAATCCCTGCAATGG 60.159 50.000 0.00 0.00 0.00 3.16
5741 6057 2.489329 ACGAACTCAAATCCCTGCAATG 59.511 45.455 0.00 0.00 0.00 2.82
5749 6065 2.365408 ACCTCGACGAACTCAAATCC 57.635 50.000 0.00 0.00 0.00 3.01
5791 6107 3.888323 AGGTGCACATACACAACAAATCA 59.112 39.130 20.43 0.00 42.55 2.57
5796 6116 2.629336 TCAGGTGCACATACACAACA 57.371 45.000 20.43 0.00 42.55 3.33
5838 6158 2.615869 TCAAGTTGCACTGGTTTTTGC 58.384 42.857 0.00 0.00 39.33 3.68
5847 6167 4.311816 CAAGGATTGTTCAAGTTGCACT 57.688 40.909 7.18 0.00 42.34 4.40
5880 6200 0.676782 CTGGGTGTTTTAGGGGCGAG 60.677 60.000 0.00 0.00 0.00 5.03
5883 6203 0.898326 CCACTGGGTGTTTTAGGGGC 60.898 60.000 0.00 0.00 0.00 5.80
5914 6655 5.729454 GCACAAATCCATACGCTACGAAATT 60.729 40.000 0.00 0.00 0.00 1.82
6040 6781 1.445582 CGCCAGGTTCTACCACGTC 60.446 63.158 0.00 0.00 41.95 4.34
6073 6814 2.512286 CTCGTGCATGTCGGCCAT 60.512 61.111 2.24 0.00 0.00 4.40
6075 6816 4.451150 TCCTCGTGCATGTCGGCC 62.451 66.667 5.68 0.00 0.00 6.13
6094 6835 3.368190 CTGGGAGCTGCTGGACTCG 62.368 68.421 7.01 0.00 33.55 4.18


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

AutoCloner maintained by Alex Coulton.