Multiple sequence alignment - TraesCS4D01G106300

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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 TraesCS4D01G106300 chr4D 100.000 4835 0 0 353 5187 84780040 84775206 0.000000e+00 8929.0
1 TraesCS4D01G106300 chr4D 100.000 100 0 0 1 100 84780392 84780293 8.870000e-43 185.0
2 TraesCS4D01G106300 chr4B 95.805 3480 82 24 933 4383 121590269 121593713 0.000000e+00 5559.0
3 TraesCS4D01G106300 chr4B 94.779 249 6 4 682 930 121576166 121576407 1.050000e-101 381.0
4 TraesCS4D01G106300 chr4B 86.667 225 11 8 4370 4580 121593730 121593949 1.120000e-56 231.0
5 TraesCS4D01G106300 chr4B 84.343 198 15 8 465 657 121575898 121576084 4.130000e-41 180.0
6 TraesCS4D01G106300 chr4B 90.000 60 4 2 1816 1875 121591068 121591125 5.570000e-10 76.8
7 TraesCS4D01G106300 chr4A 93.918 1529 64 11 2040 3551 497908107 497906591 0.000000e+00 2281.0
8 TraesCS4D01G106300 chr4A 91.003 1167 52 28 656 1804 497909740 497908609 0.000000e+00 1524.0
9 TraesCS4D01G106300 chr4A 90.256 1016 45 15 3614 4580 497906590 497905580 0.000000e+00 1279.0
10 TraesCS4D01G106300 chr4A 91.311 633 22 9 4580 5187 497905538 497904914 0.000000e+00 833.0
11 TraesCS4D01G106300 chr4A 88.632 519 31 13 1457 1967 497908600 497908102 1.600000e-169 606.0
12 TraesCS4D01G106300 chr4A 85.938 64 6 2 1816 1878 497908678 497908617 1.210000e-06 65.8
13 TraesCS4D01G106300 chr7B 84.235 647 76 16 3214 3856 407940587 407939963 1.600000e-169 606.0
14 TraesCS4D01G106300 chr7B 84.235 647 75 16 3214 3856 403563933 403563310 5.750000e-169 604.0
15 TraesCS4D01G106300 chr7B 84.235 647 75 16 3214 3856 403729784 403729161 5.750000e-169 604.0
16 TraesCS4D01G106300 chr7B 84.080 647 74 19 3214 3856 408111523 408110902 9.610000e-167 597.0
17 TraesCS4D01G106300 chr7B 80.127 629 97 21 3211 3833 383503355 383503961 1.330000e-120 444.0
18 TraesCS4D01G106300 chr7B 80.784 255 45 3 1020 1272 403732347 403732095 4.100000e-46 196.0
19 TraesCS4D01G106300 chr7B 75.161 467 78 25 997 1447 403566526 403566082 8.870000e-43 185.0
20 TraesCS4D01G106300 chr7B 79.004 281 52 5 997 1272 407943216 407942938 8.870000e-43 185.0
21 TraesCS4D01G106300 chr7B 93.671 79 5 0 1371 1449 383502749 383502827 9.120000e-23 119.0
22 TraesCS4D01G106300 chr7A 80.257 623 101 19 3217 3833 438169573 438170179 2.850000e-122 449.0
23 TraesCS4D01G106300 chr7A 93.590 78 5 0 1372 1449 438168963 438169040 3.280000e-22 117.0
24 TraesCS4D01G106300 chr5A 84.194 310 25 11 4902 5187 114679153 114678844 3.960000e-71 279.0
25 TraesCS4D01G106300 chr3D 83.849 291 34 8 4129 4407 96589091 96589380 1.110000e-66 265.0
26 TraesCS4D01G106300 chr7D 93.671 79 5 0 1371 1449 388022243 388022321 9.120000e-23 119.0
27 TraesCS4D01G106300 chr3B 74.839 155 30 4 4925 5072 706742413 706742565 1.560000e-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 TraesCS4D01G106300 chr4D 84775206 84780392 5186 True 4557.000000 8929 100.000000 1 5187 2 chr4D.!!$R1 5186
1 TraesCS4D01G106300 chr4B 121590269 121593949 3680 False 1955.600000 5559 90.824000 933 4580 3 chr4B.!!$F2 3647
2 TraesCS4D01G106300 chr4B 121575898 121576407 509 False 280.500000 381 89.561000 465 930 2 chr4B.!!$F1 465
3 TraesCS4D01G106300 chr4A 497904914 497909740 4826 True 1098.133333 2281 90.176333 656 5187 6 chr4A.!!$R1 4531
4 TraesCS4D01G106300 chr7B 408110902 408111523 621 True 597.000000 597 84.080000 3214 3856 1 chr7B.!!$R1 642
5 TraesCS4D01G106300 chr7B 403729161 403732347 3186 True 400.000000 604 82.509500 1020 3856 2 chr7B.!!$R3 2836
6 TraesCS4D01G106300 chr7B 407939963 407943216 3253 True 395.500000 606 81.619500 997 3856 2 chr7B.!!$R4 2859
7 TraesCS4D01G106300 chr7B 403563310 403566526 3216 True 394.500000 604 79.698000 997 3856 2 chr7B.!!$R2 2859
8 TraesCS4D01G106300 chr7B 383502749 383503961 1212 False 281.500000 444 86.899000 1371 3833 2 chr7B.!!$F1 2462
9 TraesCS4D01G106300 chr7A 438168963 438170179 1216 False 283.000000 449 86.923500 1372 3833 2 chr7A.!!$F1 2461

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
411 412 0.031857 CTCGGTGCCTCTGAGCTATG 59.968 60.000 0.00 0.0 41.81 2.23 F
413 414 0.249238 CGGTGCCTCTGAGCTATGAC 60.249 60.000 0.00 0.0 0.00 3.06 F
764 827 0.674581 CCCATTGCAGAGCAGACGAA 60.675 55.000 0.00 0.0 40.61 3.85 F
1519 1602 0.039256 TTGATTGCTGCCGACTTTGC 60.039 50.000 0.00 0.0 0.00 3.68 F
1769 1874 3.609853 TGAGATCAGGTGGTTATTGTGC 58.390 45.455 0.00 0.0 0.00 4.57 F
1987 2474 4.961551 CGTTGTTAACACAAAGTAGCACAG 59.038 41.667 8.07 0.0 44.72 3.66 F
3366 4786 2.058798 CTTGTCTGATAACACGCACGT 58.941 47.619 0.00 0.0 0.00 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1467 1550 0.178981 ACAGAACAAGGGCATGCAGT 60.179 50.000 21.36 9.22 0.00 4.40 R
1468 1551 0.242825 CACAGAACAAGGGCATGCAG 59.757 55.000 21.36 8.54 0.00 4.41 R
1921 2396 5.733620 TCCGTTTTACTACTGAACCATCT 57.266 39.130 0.00 0.00 0.00 2.90 R
2967 4347 0.680280 TCTCCCGACTCTACTGCACC 60.680 60.000 0.00 0.00 0.00 5.01 R
3361 4781 1.195448 CATCAGGAGAACACAACGTGC 59.805 52.381 0.00 0.00 36.98 5.34 R
3475 4900 1.946156 CACATGGGCGACGATCTCG 60.946 63.158 0.00 9.37 45.97 4.04 R
4390 5875 0.321122 CAGACTGGAGGTGAGTTGCC 60.321 60.000 0.00 0.00 0.00 4.52 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
23 24 6.791887 TTTAGCTCAATGTTCAGAGAACAG 57.208 37.500 16.47 5.92 33.74 3.16
24 25 3.672808 AGCTCAATGTTCAGAGAACAGG 58.327 45.455 16.47 11.68 33.74 4.00
25 26 2.746362 GCTCAATGTTCAGAGAACAGGG 59.254 50.000 16.47 11.39 33.74 4.45
26 27 3.808618 GCTCAATGTTCAGAGAACAGGGT 60.809 47.826 16.47 3.88 33.74 4.34
27 28 3.743521 TCAATGTTCAGAGAACAGGGTG 58.256 45.455 16.47 13.72 33.18 4.61
28 29 2.816087 CAATGTTCAGAGAACAGGGTGG 59.184 50.000 16.47 2.86 33.18 4.61
29 30 1.801242 TGTTCAGAGAACAGGGTGGA 58.199 50.000 8.39 0.00 0.00 4.02
30 31 1.694150 TGTTCAGAGAACAGGGTGGAG 59.306 52.381 8.39 0.00 0.00 3.86
31 32 0.687354 TTCAGAGAACAGGGTGGAGC 59.313 55.000 0.00 0.00 0.00 4.70
32 33 1.079543 CAGAGAACAGGGTGGAGCG 60.080 63.158 0.00 0.00 0.00 5.03
33 34 1.228894 AGAGAACAGGGTGGAGCGA 60.229 57.895 0.00 0.00 0.00 4.93
34 35 1.216710 GAGAACAGGGTGGAGCGAG 59.783 63.158 0.00 0.00 0.00 5.03
35 36 2.435059 GAACAGGGTGGAGCGAGC 60.435 66.667 0.00 0.00 0.00 5.03
36 37 2.925170 AACAGGGTGGAGCGAGCT 60.925 61.111 0.00 0.00 0.00 4.09
37 38 1.605058 GAACAGGGTGGAGCGAGCTA 61.605 60.000 0.00 0.00 0.00 3.32
38 39 1.608717 AACAGGGTGGAGCGAGCTAG 61.609 60.000 0.00 0.00 0.00 3.42
39 40 3.151022 AGGGTGGAGCGAGCTAGC 61.151 66.667 11.29 11.29 37.41 3.42
40 41 4.228567 GGGTGGAGCGAGCTAGCC 62.229 72.222 15.76 6.96 38.01 3.93
41 42 4.228567 GGTGGAGCGAGCTAGCCC 62.229 72.222 15.76 15.88 38.01 5.19
42 43 3.461773 GTGGAGCGAGCTAGCCCA 61.462 66.667 19.80 19.80 38.01 5.36
43 44 3.461773 TGGAGCGAGCTAGCCCAC 61.462 66.667 19.80 10.41 38.01 4.61
44 45 4.228567 GGAGCGAGCTAGCCCACC 62.229 72.222 15.76 12.58 38.01 4.61
45 46 3.151022 GAGCGAGCTAGCCCACCT 61.151 66.667 15.76 2.60 38.01 4.00
46 47 1.828660 GAGCGAGCTAGCCCACCTA 60.829 63.158 15.76 0.00 38.01 3.08
47 48 1.801309 GAGCGAGCTAGCCCACCTAG 61.801 65.000 15.76 0.00 45.26 3.02
48 49 2.862223 GCGAGCTAGCCCACCTAGG 61.862 68.421 12.13 7.41 43.15 3.02
56 57 3.527641 CCCACCTAGGCTCGAGTC 58.472 66.667 9.58 9.58 35.39 3.36
57 58 2.482333 CCCACCTAGGCTCGAGTCG 61.482 68.421 15.13 6.09 35.39 4.18
58 59 1.451567 CCACCTAGGCTCGAGTCGA 60.452 63.158 15.64 15.64 0.00 4.20
59 60 0.820074 CCACCTAGGCTCGAGTCGAT 60.820 60.000 16.94 3.82 34.61 3.59
60 61 1.025812 CACCTAGGCTCGAGTCGATT 58.974 55.000 16.94 7.58 34.61 3.34
61 62 1.405821 CACCTAGGCTCGAGTCGATTT 59.594 52.381 16.94 7.21 34.61 2.17
62 63 1.405821 ACCTAGGCTCGAGTCGATTTG 59.594 52.381 16.94 5.76 34.61 2.32
63 64 1.676529 CCTAGGCTCGAGTCGATTTGA 59.323 52.381 16.94 1.55 34.61 2.69
64 65 2.287308 CCTAGGCTCGAGTCGATTTGAG 60.287 54.545 16.94 18.42 34.61 3.02
65 66 1.178276 AGGCTCGAGTCGATTTGAGT 58.822 50.000 22.16 5.05 34.61 3.41
66 67 1.546476 AGGCTCGAGTCGATTTGAGTT 59.454 47.619 22.16 11.26 34.61 3.01
67 68 2.028930 AGGCTCGAGTCGATTTGAGTTT 60.029 45.455 22.16 10.97 34.61 2.66
68 69 2.737252 GGCTCGAGTCGATTTGAGTTTT 59.263 45.455 22.16 0.00 34.61 2.43
69 70 3.186613 GGCTCGAGTCGATTTGAGTTTTT 59.813 43.478 22.16 0.00 34.61 1.94
372 373 3.710326 TGGCTCACAGTATATGTCGAC 57.290 47.619 9.11 9.11 41.41 4.20
373 374 3.288092 TGGCTCACAGTATATGTCGACT 58.712 45.455 17.92 4.95 41.41 4.18
374 375 4.457466 TGGCTCACAGTATATGTCGACTA 58.543 43.478 17.92 7.13 41.41 2.59
375 376 4.275196 TGGCTCACAGTATATGTCGACTAC 59.725 45.833 17.92 10.98 41.41 2.73
376 377 4.515944 GGCTCACAGTATATGTCGACTACT 59.484 45.833 17.92 13.13 41.41 2.57
377 378 5.008811 GGCTCACAGTATATGTCGACTACTT 59.991 44.000 17.92 5.07 41.41 2.24
378 379 6.459848 GGCTCACAGTATATGTCGACTACTTT 60.460 42.308 17.92 6.70 41.41 2.66
379 380 6.633634 GCTCACAGTATATGTCGACTACTTTC 59.366 42.308 17.92 3.39 41.41 2.62
380 381 6.712549 TCACAGTATATGTCGACTACTTTCG 58.287 40.000 17.92 7.29 41.41 3.46
381 382 5.395778 CACAGTATATGTCGACTACTTTCGC 59.604 44.000 17.92 0.00 41.41 4.70
382 383 4.910456 CAGTATATGTCGACTACTTTCGCC 59.090 45.833 17.92 0.00 38.95 5.54
383 384 2.463553 TATGTCGACTACTTTCGCCG 57.536 50.000 17.92 0.00 38.95 6.46
384 385 0.806868 ATGTCGACTACTTTCGCCGA 59.193 50.000 17.92 0.00 38.95 5.54
385 386 0.592637 TGTCGACTACTTTCGCCGAA 59.407 50.000 17.92 0.00 38.95 4.30
386 387 1.200716 TGTCGACTACTTTCGCCGAAT 59.799 47.619 17.92 0.00 38.95 3.34
387 388 1.844962 GTCGACTACTTTCGCCGAATC 59.155 52.381 8.70 0.00 38.95 2.52
388 389 1.741706 TCGACTACTTTCGCCGAATCT 59.258 47.619 0.00 0.00 38.95 2.40
389 390 2.163010 TCGACTACTTTCGCCGAATCTT 59.837 45.455 0.00 0.00 38.95 2.40
390 391 2.921754 CGACTACTTTCGCCGAATCTTT 59.078 45.455 0.00 0.00 31.03 2.52
391 392 3.241678 CGACTACTTTCGCCGAATCTTTG 60.242 47.826 0.00 0.00 31.03 2.77
392 393 2.415512 ACTACTTTCGCCGAATCTTTGC 59.584 45.455 0.00 0.00 0.00 3.68
393 394 1.523758 ACTTTCGCCGAATCTTTGCT 58.476 45.000 0.00 0.00 0.00 3.91
394 395 1.464997 ACTTTCGCCGAATCTTTGCTC 59.535 47.619 0.00 0.00 0.00 4.26
395 396 0.442310 TTTCGCCGAATCTTTGCTCG 59.558 50.000 0.00 0.00 34.83 5.03
400 401 1.425428 CGAATCTTTGCTCGGTGCC 59.575 57.895 0.00 0.00 42.00 5.01
401 402 1.021390 CGAATCTTTGCTCGGTGCCT 61.021 55.000 0.00 0.00 42.00 4.75
402 403 0.729690 GAATCTTTGCTCGGTGCCTC 59.270 55.000 0.00 0.00 42.00 4.70
403 404 0.326264 AATCTTTGCTCGGTGCCTCT 59.674 50.000 0.00 0.00 42.00 3.69
404 405 0.392193 ATCTTTGCTCGGTGCCTCTG 60.392 55.000 0.00 0.00 42.00 3.35
405 406 1.004560 CTTTGCTCGGTGCCTCTGA 60.005 57.895 0.00 0.00 42.00 3.27
409 410 3.926003 CTCGGTGCCTCTGAGCTA 58.074 61.111 0.00 0.00 41.81 3.32
410 411 2.424474 CTCGGTGCCTCTGAGCTAT 58.576 57.895 0.00 0.00 41.81 2.97
411 412 0.031857 CTCGGTGCCTCTGAGCTATG 59.968 60.000 0.00 0.00 41.81 2.23
412 413 0.395724 TCGGTGCCTCTGAGCTATGA 60.396 55.000 0.00 0.00 0.00 2.15
413 414 0.249238 CGGTGCCTCTGAGCTATGAC 60.249 60.000 0.00 0.00 0.00 3.06
414 415 1.118838 GGTGCCTCTGAGCTATGACT 58.881 55.000 0.00 0.00 0.00 3.41
415 416 1.484240 GGTGCCTCTGAGCTATGACTT 59.516 52.381 0.00 0.00 0.00 3.01
416 417 2.093235 GGTGCCTCTGAGCTATGACTTT 60.093 50.000 0.00 0.00 0.00 2.66
417 418 2.935201 GTGCCTCTGAGCTATGACTTTG 59.065 50.000 0.00 0.00 0.00 2.77
418 419 2.568956 TGCCTCTGAGCTATGACTTTGT 59.431 45.455 0.00 0.00 0.00 2.83
419 420 3.194062 GCCTCTGAGCTATGACTTTGTC 58.806 50.000 0.00 0.00 0.00 3.18
420 421 3.118811 GCCTCTGAGCTATGACTTTGTCT 60.119 47.826 0.00 0.00 33.15 3.41
421 422 4.622695 GCCTCTGAGCTATGACTTTGTCTT 60.623 45.833 0.00 0.00 33.15 3.01
422 423 5.486526 CCTCTGAGCTATGACTTTGTCTTT 58.513 41.667 0.00 0.00 33.15 2.52
423 424 5.936956 CCTCTGAGCTATGACTTTGTCTTTT 59.063 40.000 0.00 0.00 33.15 2.27
424 425 6.429385 CCTCTGAGCTATGACTTTGTCTTTTT 59.571 38.462 0.00 0.00 33.15 1.94
468 469 9.001542 AGAGTTATGTCTATACTATCGACCAAC 57.998 37.037 0.00 3.94 0.00 3.77
471 472 8.781196 GTTATGTCTATACTATCGACCAACTCA 58.219 37.037 0.00 0.00 0.00 3.41
476 477 8.569641 GTCTATACTATCGACCAACTCAATTCT 58.430 37.037 0.00 0.00 0.00 2.40
478 479 4.673441 ACTATCGACCAACTCAATTCTCG 58.327 43.478 0.00 0.00 0.00 4.04
485 486 3.815401 ACCAACTCAATTCTCGTGGAAAG 59.185 43.478 0.00 0.00 37.49 2.62
486 487 3.365364 CCAACTCAATTCTCGTGGAAAGC 60.365 47.826 0.00 0.00 37.49 3.51
487 488 2.069273 ACTCAATTCTCGTGGAAAGCG 58.931 47.619 0.00 0.00 37.49 4.68
488 489 0.796312 TCAATTCTCGTGGAAAGCGC 59.204 50.000 0.00 0.00 37.49 5.92
523 525 3.358118 TCGGAACCACCACTTTCTTTTT 58.642 40.909 0.00 0.00 38.90 1.94
524 526 4.525024 TCGGAACCACCACTTTCTTTTTA 58.475 39.130 0.00 0.00 38.90 1.52
525 527 5.134661 TCGGAACCACCACTTTCTTTTTAT 58.865 37.500 0.00 0.00 38.90 1.40
528 530 5.279306 GGAACCACCACTTTCTTTTTATCCC 60.279 44.000 0.00 0.00 38.79 3.85
551 556 7.558444 TCCCAATACTTTTGAGTACTGTGTTTT 59.442 33.333 0.00 0.00 0.00 2.43
575 580 2.618241 GTGTCTGGTTTCTGAACATGCA 59.382 45.455 0.00 0.00 37.51 3.96
594 599 9.800433 AACATGCATTGATCGTTGAAATATTTA 57.200 25.926 0.00 0.00 0.00 1.40
595 600 9.970395 ACATGCATTGATCGTTGAAATATTTAT 57.030 25.926 0.00 0.00 0.00 1.40
626 631 6.458206 CGTGTTTGAAAGTTCTGAAGATTCCA 60.458 38.462 10.75 0.78 0.00 3.53
764 827 0.674581 CCCATTGCAGAGCAGACGAA 60.675 55.000 0.00 0.00 40.61 3.85
765 828 0.725686 CCATTGCAGAGCAGACGAAG 59.274 55.000 0.00 0.00 40.61 3.79
766 829 1.673923 CCATTGCAGAGCAGACGAAGA 60.674 52.381 0.00 0.00 40.61 2.87
779 842 2.559231 AGACGAAGAAGAGTCCAGAACC 59.441 50.000 0.00 0.00 38.08 3.62
907 974 1.673329 GCCTCAAGACGTCCTCTTTCC 60.673 57.143 13.01 0.00 37.08 3.13
908 975 1.896465 CCTCAAGACGTCCTCTTTCCT 59.104 52.381 13.01 0.00 37.08 3.36
909 976 2.094442 CCTCAAGACGTCCTCTTTCCTC 60.094 54.545 13.01 0.00 37.08 3.71
910 977 1.893801 TCAAGACGTCCTCTTTCCTCC 59.106 52.381 13.01 0.00 37.08 4.30
1230 1305 4.070552 GAGAGGTCGGGCAACGCT 62.071 66.667 0.00 0.00 43.86 5.07
1275 1350 2.690734 CCAAGTAAGCCCCTCCCCC 61.691 68.421 0.00 0.00 0.00 5.40
1276 1351 1.619669 CAAGTAAGCCCCTCCCCCT 60.620 63.158 0.00 0.00 0.00 4.79
1340 1421 1.464997 AGGATTCGTTTTCTCAAGCGC 59.535 47.619 0.00 0.00 36.62 5.92
1449 1532 2.028385 AGGTCGCCAAGTACAAGGTAAG 60.028 50.000 0.00 0.00 0.00 2.34
1451 1534 3.555586 GGTCGCCAAGTACAAGGTAAGAA 60.556 47.826 0.00 0.00 0.00 2.52
1452 1535 3.431233 GTCGCCAAGTACAAGGTAAGAAC 59.569 47.826 0.00 0.00 0.00 3.01
1453 1536 3.322828 TCGCCAAGTACAAGGTAAGAACT 59.677 43.478 0.00 0.00 0.00 3.01
1456 1539 5.873164 CGCCAAGTACAAGGTAAGAACTATT 59.127 40.000 0.00 0.00 0.00 1.73
1457 1540 6.183360 CGCCAAGTACAAGGTAAGAACTATTG 60.183 42.308 0.00 0.00 0.00 1.90
1461 1544 9.052759 CAAGTACAAGGTAAGAACTATTGTGTT 57.947 33.333 0.00 0.00 36.67 3.32
1462 1545 8.603242 AGTACAAGGTAAGAACTATTGTGTTG 57.397 34.615 0.00 0.00 36.67 3.33
1464 1547 5.049680 ACAAGGTAAGAACTATTGTGTTGCG 60.050 40.000 0.00 0.00 35.54 4.85
1465 1548 3.435671 AGGTAAGAACTATTGTGTTGCGC 59.564 43.478 0.00 0.00 0.00 6.09
1467 1550 1.890876 AGAACTATTGTGTTGCGCCA 58.109 45.000 4.18 0.00 0.00 5.69
1468 1551 1.535462 AGAACTATTGTGTTGCGCCAC 59.465 47.619 4.18 4.28 35.86 5.01
1472 1555 1.169034 TATTGTGTTGCGCCACTGCA 61.169 50.000 13.27 8.98 44.61 4.41
1486 1569 0.178981 ACTGCATGCCCTTGTTCTGT 60.179 50.000 16.68 0.00 0.00 3.41
1496 1579 2.213499 CCTTGTTCTGTGAGCGAGTTT 58.787 47.619 0.00 0.00 0.00 2.66
1519 1602 0.039256 TTGATTGCTGCCGACTTTGC 60.039 50.000 0.00 0.00 0.00 3.68
1523 1606 4.410743 GCTGCCGACTTTGCCTGC 62.411 66.667 0.00 0.00 0.00 4.85
1564 1647 4.042311 TGTGGTTGCTAGTTATGGAAAGGA 59.958 41.667 0.00 0.00 0.00 3.36
1565 1648 5.193679 GTGGTTGCTAGTTATGGAAAGGAT 58.806 41.667 0.00 0.00 0.00 3.24
1566 1649 5.652452 GTGGTTGCTAGTTATGGAAAGGATT 59.348 40.000 0.00 0.00 0.00 3.01
1567 1650 6.826741 GTGGTTGCTAGTTATGGAAAGGATTA 59.173 38.462 0.00 0.00 0.00 1.75
1693 1796 8.613034 AGATCTAGATCATTTATGGCAGGAAAT 58.387 33.333 29.83 4.70 40.22 2.17
1769 1874 3.609853 TGAGATCAGGTGGTTATTGTGC 58.390 45.455 0.00 0.00 0.00 4.57
1921 2396 6.108015 GCTTAAATGCCTCCATGAATTTGAA 58.892 36.000 0.00 0.00 0.00 2.69
1987 2474 4.961551 CGTTGTTAACACAAAGTAGCACAG 59.038 41.667 8.07 0.00 44.72 3.66
2465 3530 6.935771 CCAGATCTTCATTTATGGGAGAGAAG 59.064 42.308 0.00 0.00 35.13 2.85
3019 4399 7.759489 TGAAAATAGTGAATTGTGCCTACTT 57.241 32.000 0.00 0.00 0.00 2.24
3068 4452 8.852671 AATTTGGGGGAATGATATTGAAGTTA 57.147 30.769 0.00 0.00 0.00 2.24
3361 4781 7.170998 AGGTAAAAACTCTTGTCTGATAACACG 59.829 37.037 0.00 0.00 0.00 4.49
3366 4786 2.058798 CTTGTCTGATAACACGCACGT 58.941 47.619 0.00 0.00 0.00 4.49
3475 4900 3.191371 CCAAGATTAACAAGGGCAGTGTC 59.809 47.826 0.00 0.00 0.00 3.67
3600 5025 3.245518 TGTGATCACCAATGTCTACGG 57.754 47.619 22.85 0.00 0.00 4.02
3775 5200 3.016474 GAACGTGCTTGCTCTCGCC 62.016 63.158 0.00 0.00 34.43 5.54
3918 5358 0.179026 CTGTATGCCTGCCATCTGCT 60.179 55.000 0.00 0.00 42.00 4.24
3932 5372 4.619863 GCCATCTGCTTCATGATTGTTGTT 60.620 41.667 0.00 0.00 36.87 2.83
3933 5373 5.393352 GCCATCTGCTTCATGATTGTTGTTA 60.393 40.000 0.00 0.00 36.87 2.41
3937 5377 9.608617 CATCTGCTTCATGATTGTTGTTATATC 57.391 33.333 0.00 0.00 0.00 1.63
3944 5384 9.685276 TTCATGATTGTTGTTATATCTGTTCCT 57.315 29.630 0.00 0.00 0.00 3.36
3952 5392 9.878667 TGTTGTTATATCTGTTCCTATTTCGAA 57.121 29.630 0.00 0.00 0.00 3.71
4068 5523 1.666209 AAGTTTGCTGTTGCTGCCGT 61.666 50.000 0.00 0.00 40.48 5.68
4385 5840 5.241506 TCATGACCTGCTTTCCTTTTAACTG 59.758 40.000 0.00 0.00 0.00 3.16
4386 5841 3.888930 TGACCTGCTTTCCTTTTAACTGG 59.111 43.478 0.00 0.00 0.00 4.00
4390 5875 4.537015 CTGCTTTCCTTTTAACTGGAACG 58.463 43.478 7.61 7.51 41.47 3.95
4661 6210 3.490348 CTTCATGGGAGTTTGAGGTTGT 58.510 45.455 0.00 0.00 0.00 3.32
4667 6216 2.135933 GGAGTTTGAGGTTGTGAGACG 58.864 52.381 0.00 0.00 0.00 4.18
4668 6217 1.527311 GAGTTTGAGGTTGTGAGACGC 59.473 52.381 0.00 0.00 0.00 5.19
4669 6218 0.232303 GTTTGAGGTTGTGAGACGCG 59.768 55.000 3.53 3.53 0.00 6.01
4684 6234 2.190841 CGCGGGGTTTTGTTGTCCT 61.191 57.895 0.00 0.00 0.00 3.85
4714 6269 2.366533 TCGCTGACCGAGAGTTAGATT 58.633 47.619 0.00 0.00 41.89 2.40
4728 6283 6.514063 AGAGTTAGATTATAGTTGTTCGCCC 58.486 40.000 0.00 0.00 0.00 6.13
4732 6287 4.307432 AGATTATAGTTGTTCGCCCGATG 58.693 43.478 0.00 0.00 0.00 3.84
4738 6293 2.358247 GTTCGCCCGATGTGGTGT 60.358 61.111 0.00 0.00 37.20 4.16
4761 6316 3.787394 TCGGAGACCCACTTGGAC 58.213 61.111 0.00 0.00 37.39 4.02
4773 6328 0.108329 ACTTGGACAGTTATCCCGCG 60.108 55.000 0.00 0.00 38.06 6.46
4878 6450 7.385267 AGAATCCAAAGATTAGATCTGGATCG 58.615 38.462 5.18 0.00 42.93 3.69
4986 6558 5.378230 ACATGGGATCATATGTGTCAACT 57.622 39.130 11.82 0.00 36.26 3.16
4987 6559 5.371526 ACATGGGATCATATGTGTCAACTC 58.628 41.667 11.82 0.00 36.26 3.01
4988 6560 4.422073 TGGGATCATATGTGTCAACTCC 57.578 45.455 1.90 0.99 0.00 3.85
4989 6561 3.779738 TGGGATCATATGTGTCAACTCCA 59.220 43.478 1.90 3.30 0.00 3.86
4990 6562 4.413189 TGGGATCATATGTGTCAACTCCAT 59.587 41.667 1.90 0.00 0.00 3.41
4991 6563 4.999950 GGGATCATATGTGTCAACTCCATC 59.000 45.833 1.90 0.00 0.00 3.51
4992 6564 5.455183 GGGATCATATGTGTCAACTCCATCA 60.455 44.000 1.90 0.00 0.00 3.07
5005 6577 8.708378 TGTCAACTCCATCATAATCATACTCTT 58.292 33.333 0.00 0.00 0.00 2.85
5078 6650 1.541620 GGAGGAAACCCCAGACCCT 60.542 63.158 0.00 0.00 37.41 4.34
5088 6660 1.281925 CCCAGACCCTAACAGGCCAT 61.282 60.000 5.01 0.00 32.73 4.40
5098 6670 2.885135 AACAGGCCATTGATGACTGA 57.115 45.000 5.01 0.00 36.64 3.41
5100 6672 1.022735 CAGGCCATTGATGACTGAGC 58.977 55.000 5.01 0.00 35.81 4.26
5115 6689 2.109774 CTGAGCTCAGAGACTTGGGAT 58.890 52.381 35.69 0.00 46.59 3.85
5124 6698 3.131933 CAGAGACTTGGGATACAGAGGTG 59.868 52.174 0.00 0.00 39.74 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.702670 CCTGTTCTCTGAACATTGAGCTAAA 59.297 40.000 12.63 0.00 0.00 1.85
1 2 5.240891 CCTGTTCTCTGAACATTGAGCTAA 58.759 41.667 12.63 0.00 0.00 3.09
2 3 4.323028 CCCTGTTCTCTGAACATTGAGCTA 60.323 45.833 12.63 0.00 0.00 3.32
3 4 3.558746 CCCTGTTCTCTGAACATTGAGCT 60.559 47.826 12.63 0.00 0.00 4.09
4 5 2.746362 CCCTGTTCTCTGAACATTGAGC 59.254 50.000 12.63 0.00 0.00 4.26
5 6 3.750130 CACCCTGTTCTCTGAACATTGAG 59.250 47.826 12.63 2.88 0.00 3.02
6 7 3.496692 CCACCCTGTTCTCTGAACATTGA 60.497 47.826 12.63 0.00 0.00 2.57
7 8 2.816087 CCACCCTGTTCTCTGAACATTG 59.184 50.000 12.63 10.24 0.00 2.82
8 9 2.711009 TCCACCCTGTTCTCTGAACATT 59.289 45.455 12.63 0.05 0.00 2.71
9 10 2.304180 CTCCACCCTGTTCTCTGAACAT 59.696 50.000 12.63 0.00 0.00 2.71
10 11 1.694150 CTCCACCCTGTTCTCTGAACA 59.306 52.381 11.83 11.83 0.00 3.18
11 12 1.609320 GCTCCACCCTGTTCTCTGAAC 60.609 57.143 3.74 3.74 0.00 3.18
12 13 0.687354 GCTCCACCCTGTTCTCTGAA 59.313 55.000 0.00 0.00 0.00 3.02
13 14 1.536073 CGCTCCACCCTGTTCTCTGA 61.536 60.000 0.00 0.00 0.00 3.27
14 15 1.079543 CGCTCCACCCTGTTCTCTG 60.080 63.158 0.00 0.00 0.00 3.35
15 16 1.228894 TCGCTCCACCCTGTTCTCT 60.229 57.895 0.00 0.00 0.00 3.10
16 17 1.216710 CTCGCTCCACCCTGTTCTC 59.783 63.158 0.00 0.00 0.00 2.87
17 18 2.948720 GCTCGCTCCACCCTGTTCT 61.949 63.158 0.00 0.00 0.00 3.01
18 19 1.605058 TAGCTCGCTCCACCCTGTTC 61.605 60.000 0.00 0.00 0.00 3.18
19 20 1.608717 CTAGCTCGCTCCACCCTGTT 61.609 60.000 0.00 0.00 0.00 3.16
20 21 2.037367 TAGCTCGCTCCACCCTGT 59.963 61.111 0.00 0.00 0.00 4.00
21 22 2.811101 CTAGCTCGCTCCACCCTG 59.189 66.667 0.00 0.00 0.00 4.45
22 23 3.151022 GCTAGCTCGCTCCACCCT 61.151 66.667 7.70 0.00 0.00 4.34
23 24 4.228567 GGCTAGCTCGCTCCACCC 62.229 72.222 15.72 0.00 0.00 4.61
24 25 4.228567 GGGCTAGCTCGCTCCACC 62.229 72.222 15.72 0.13 0.00 4.61
25 26 3.461773 TGGGCTAGCTCGCTCCAC 61.462 66.667 15.72 0.00 0.00 4.02
26 27 3.461773 GTGGGCTAGCTCGCTCCA 61.462 66.667 21.08 13.02 0.00 3.86
27 28 4.228567 GGTGGGCTAGCTCGCTCC 62.229 72.222 26.51 16.43 0.00 4.70
28 29 1.801309 CTAGGTGGGCTAGCTCGCTC 61.801 65.000 26.51 16.75 38.31 5.03
29 30 1.830408 CTAGGTGGGCTAGCTCGCT 60.830 63.158 26.51 15.24 38.31 4.93
30 31 2.731374 CTAGGTGGGCTAGCTCGC 59.269 66.667 20.24 20.24 38.31 5.03
31 32 3.449349 CCTAGGTGGGCTAGCTCG 58.551 66.667 15.72 0.00 38.31 5.03
39 40 2.482333 CGACTCGAGCCTAGGTGGG 61.482 68.421 13.61 3.30 36.00 4.61
40 41 0.820074 ATCGACTCGAGCCTAGGTGG 60.820 60.000 13.61 0.00 39.91 4.61
41 42 1.025812 AATCGACTCGAGCCTAGGTG 58.974 55.000 13.61 0.80 39.91 4.00
42 43 1.405821 CAAATCGACTCGAGCCTAGGT 59.594 52.381 13.61 0.00 39.91 3.08
43 44 1.676529 TCAAATCGACTCGAGCCTAGG 59.323 52.381 13.61 3.67 39.91 3.02
44 45 2.356382 ACTCAAATCGACTCGAGCCTAG 59.644 50.000 13.61 1.30 39.91 3.02
45 46 2.366533 ACTCAAATCGACTCGAGCCTA 58.633 47.619 13.61 0.00 39.91 3.93
46 47 1.178276 ACTCAAATCGACTCGAGCCT 58.822 50.000 13.61 0.00 39.91 4.58
47 48 1.997669 AACTCAAATCGACTCGAGCC 58.002 50.000 13.61 0.00 39.91 4.70
48 49 4.391140 AAAAACTCAAATCGACTCGAGC 57.609 40.909 13.61 4.47 39.91 5.03
352 353 3.288092 AGTCGACATATACTGTGAGCCA 58.712 45.455 19.50 0.00 38.54 4.75
353 354 3.992260 AGTCGACATATACTGTGAGCC 57.008 47.619 19.50 0.00 38.54 4.70
354 355 5.676532 AGTAGTCGACATATACTGTGAGC 57.323 43.478 19.50 0.00 38.54 4.26
355 356 6.846786 CGAAAGTAGTCGACATATACTGTGAG 59.153 42.308 19.50 5.12 43.86 3.51
356 357 6.712549 CGAAAGTAGTCGACATATACTGTGA 58.287 40.000 19.50 0.00 43.86 3.58
357 358 5.395778 GCGAAAGTAGTCGACATATACTGTG 59.604 44.000 19.50 10.75 43.86 3.66
358 359 5.508872 GCGAAAGTAGTCGACATATACTGT 58.491 41.667 19.50 11.81 43.86 3.55
367 368 1.844962 GATTCGGCGAAAGTAGTCGAC 59.155 52.381 27.40 7.70 45.94 4.20
368 369 1.741706 AGATTCGGCGAAAGTAGTCGA 59.258 47.619 27.40 0.00 43.86 4.20
369 370 2.190325 AGATTCGGCGAAAGTAGTCG 57.810 50.000 27.40 0.00 43.98 4.18
370 371 3.483738 GCAAAGATTCGGCGAAAGTAGTC 60.484 47.826 27.40 18.38 0.00 2.59
371 372 2.415512 GCAAAGATTCGGCGAAAGTAGT 59.584 45.455 27.40 9.68 0.00 2.73
372 373 2.673368 AGCAAAGATTCGGCGAAAGTAG 59.327 45.455 27.40 15.81 0.00 2.57
373 374 2.671396 GAGCAAAGATTCGGCGAAAGTA 59.329 45.455 27.40 3.43 0.00 2.24
374 375 1.464997 GAGCAAAGATTCGGCGAAAGT 59.535 47.619 27.40 11.38 0.00 2.66
375 376 1.527793 CGAGCAAAGATTCGGCGAAAG 60.528 52.381 27.40 14.45 33.39 2.62
376 377 0.442310 CGAGCAAAGATTCGGCGAAA 59.558 50.000 27.40 10.32 33.39 3.46
377 378 2.078226 CGAGCAAAGATTCGGCGAA 58.922 52.632 25.88 25.88 33.39 4.70
378 379 3.780693 CGAGCAAAGATTCGGCGA 58.219 55.556 4.99 4.99 33.39 5.54
392 393 0.031857 CATAGCTCAGAGGCACCGAG 59.968 60.000 0.00 0.00 34.17 4.63
393 394 0.395724 TCATAGCTCAGAGGCACCGA 60.396 55.000 0.00 0.00 34.17 4.69
394 395 0.249238 GTCATAGCTCAGAGGCACCG 60.249 60.000 0.00 0.00 34.17 4.94
395 396 1.118838 AGTCATAGCTCAGAGGCACC 58.881 55.000 0.00 0.00 34.17 5.01
396 397 2.935201 CAAAGTCATAGCTCAGAGGCAC 59.065 50.000 0.00 0.00 34.17 5.01
397 398 2.568956 ACAAAGTCATAGCTCAGAGGCA 59.431 45.455 0.00 0.00 34.17 4.75
398 399 3.118811 AGACAAAGTCATAGCTCAGAGGC 60.119 47.826 0.00 0.00 34.60 4.70
399 400 4.734398 AGACAAAGTCATAGCTCAGAGG 57.266 45.455 0.00 0.00 34.60 3.69
400 401 7.432350 AAAAAGACAAAGTCATAGCTCAGAG 57.568 36.000 0.00 0.00 34.60 3.35
441 442 9.570468 TTGGTCGATAGTATAGACATAACTCTT 57.430 33.333 20.69 0.00 36.74 2.85
442 443 9.001542 GTTGGTCGATAGTATAGACATAACTCT 57.998 37.037 20.69 0.00 36.74 3.24
443 444 9.001542 AGTTGGTCGATAGTATAGACATAACTC 57.998 37.037 23.79 11.03 38.31 3.01
444 445 8.921353 AGTTGGTCGATAGTATAGACATAACT 57.079 34.615 23.79 23.79 38.12 2.24
445 446 8.781196 TGAGTTGGTCGATAGTATAGACATAAC 58.219 37.037 20.69 21.22 36.74 1.89
446 447 8.913487 TGAGTTGGTCGATAGTATAGACATAA 57.087 34.615 20.69 13.78 36.74 1.90
447 448 8.913487 TTGAGTTGGTCGATAGTATAGACATA 57.087 34.615 20.69 9.58 36.74 2.29
448 449 7.818997 TTGAGTTGGTCGATAGTATAGACAT 57.181 36.000 20.69 7.30 36.74 3.06
449 450 7.818997 ATTGAGTTGGTCGATAGTATAGACA 57.181 36.000 20.69 8.06 36.74 3.41
450 451 8.569641 AGAATTGAGTTGGTCGATAGTATAGAC 58.430 37.037 13.37 13.37 34.64 2.59
451 452 8.693120 AGAATTGAGTTGGTCGATAGTATAGA 57.307 34.615 0.00 0.00 37.40 1.98
452 453 7.746916 CGAGAATTGAGTTGGTCGATAGTATAG 59.253 40.741 0.00 0.00 37.40 1.31
453 454 7.228108 ACGAGAATTGAGTTGGTCGATAGTATA 59.772 37.037 0.00 0.00 37.40 1.47
454 455 6.039493 ACGAGAATTGAGTTGGTCGATAGTAT 59.961 38.462 0.00 0.00 37.40 2.12
455 456 5.356190 ACGAGAATTGAGTTGGTCGATAGTA 59.644 40.000 0.00 0.00 37.40 1.82
456 457 4.158025 ACGAGAATTGAGTTGGTCGATAGT 59.842 41.667 0.00 0.00 37.40 2.12
457 458 4.500837 CACGAGAATTGAGTTGGTCGATAG 59.499 45.833 0.00 0.00 30.88 2.08
458 459 4.421058 CACGAGAATTGAGTTGGTCGATA 58.579 43.478 0.00 0.00 30.88 2.92
459 460 3.254060 CACGAGAATTGAGTTGGTCGAT 58.746 45.455 0.00 0.00 30.88 3.59
460 461 2.609491 CCACGAGAATTGAGTTGGTCGA 60.609 50.000 0.00 0.00 30.88 4.20
461 462 1.726791 CCACGAGAATTGAGTTGGTCG 59.273 52.381 0.00 0.00 0.00 4.79
462 463 3.040147 TCCACGAGAATTGAGTTGGTC 57.960 47.619 0.00 0.00 0.00 4.02
463 464 3.485463 TTCCACGAGAATTGAGTTGGT 57.515 42.857 0.00 0.00 0.00 3.67
468 469 1.201965 GCGCTTTCCACGAGAATTGAG 60.202 52.381 0.00 0.00 33.44 3.02
471 472 0.605319 TGGCGCTTTCCACGAGAATT 60.605 50.000 7.64 0.00 33.44 2.17
485 486 1.734117 GAACAGCAAATGGTGGCGC 60.734 57.895 16.12 0.00 46.90 6.53
486 487 1.442520 CGAACAGCAAATGGTGGCG 60.443 57.895 16.12 14.36 46.90 5.69
487 488 1.080569 CCGAACAGCAAATGGTGGC 60.081 57.895 16.12 7.42 46.90 5.01
488 489 0.958091 TTCCGAACAGCAAATGGTGG 59.042 50.000 16.12 0.00 46.90 4.61
493 495 0.958822 GGTGGTTCCGAACAGCAAAT 59.041 50.000 13.23 0.00 35.33 2.32
523 525 7.913789 ACACAGTACTCAAAAGTATTGGGATA 58.086 34.615 14.79 0.00 46.65 2.59
524 526 6.779860 ACACAGTACTCAAAAGTATTGGGAT 58.220 36.000 14.79 0.57 46.65 3.85
525 527 6.182507 ACACAGTACTCAAAAGTATTGGGA 57.817 37.500 14.79 0.00 46.65 4.37
551 556 4.439974 GCATGTTCAGAAACCAGACACAAA 60.440 41.667 0.00 0.00 34.28 2.83
553 558 2.618241 GCATGTTCAGAAACCAGACACA 59.382 45.455 0.00 0.00 34.28 3.72
554 559 2.618241 TGCATGTTCAGAAACCAGACAC 59.382 45.455 0.00 0.00 34.28 3.67
555 560 2.929641 TGCATGTTCAGAAACCAGACA 58.070 42.857 0.00 0.00 34.28 3.41
556 561 4.022935 TCAATGCATGTTCAGAAACCAGAC 60.023 41.667 0.00 0.00 34.28 3.51
557 562 4.143543 TCAATGCATGTTCAGAAACCAGA 58.856 39.130 0.00 0.00 34.28 3.86
558 563 4.508461 TCAATGCATGTTCAGAAACCAG 57.492 40.909 0.00 0.00 34.28 4.00
594 599 8.973835 TTCAGAACTTTCAAACACGTTTAAAT 57.026 26.923 0.00 0.00 0.00 1.40
595 600 8.291032 TCTTCAGAACTTTCAAACACGTTTAAA 58.709 29.630 0.00 0.00 0.00 1.52
596 601 7.808672 TCTTCAGAACTTTCAAACACGTTTAA 58.191 30.769 0.00 0.00 0.00 1.52
597 602 7.367159 TCTTCAGAACTTTCAAACACGTTTA 57.633 32.000 0.00 0.00 0.00 2.01
598 603 6.249035 TCTTCAGAACTTTCAAACACGTTT 57.751 33.333 0.00 0.00 0.00 3.60
601 606 5.909610 GGAATCTTCAGAACTTTCAAACACG 59.090 40.000 3.76 0.00 0.00 4.49
610 615 5.310409 TGGAAGTGGAATCTTCAGAACTT 57.690 39.130 8.36 5.22 43.72 2.66
626 631 2.026262 ACATGCCCGAAGTATTGGAAGT 60.026 45.455 0.00 0.00 0.00 3.01
681 744 0.322546 GTCAGTCCGGCCCAAATTCT 60.323 55.000 0.00 0.00 0.00 2.40
682 745 1.644786 CGTCAGTCCGGCCCAAATTC 61.645 60.000 0.00 0.00 0.00 2.17
683 746 1.674322 CGTCAGTCCGGCCCAAATT 60.674 57.895 0.00 0.00 0.00 1.82
764 827 2.448453 CTACCGGTTCTGGACTCTTCT 58.552 52.381 15.04 0.00 0.00 2.85
765 828 1.477295 CCTACCGGTTCTGGACTCTTC 59.523 57.143 15.04 0.00 0.00 2.87
766 829 1.558233 CCTACCGGTTCTGGACTCTT 58.442 55.000 15.04 0.00 0.00 2.85
779 842 1.067071 GTCTTTCCACACTCCCTACCG 60.067 57.143 0.00 0.00 0.00 4.02
907 974 1.528309 GCGAGAGGAGGAGGAGGAG 60.528 68.421 0.00 0.00 0.00 3.69
908 975 2.598467 GCGAGAGGAGGAGGAGGA 59.402 66.667 0.00 0.00 0.00 3.71
909 976 2.520741 GGCGAGAGGAGGAGGAGG 60.521 72.222 0.00 0.00 0.00 4.30
910 977 2.124693 GTGGCGAGAGGAGGAGGAG 61.125 68.421 0.00 0.00 0.00 3.69
1230 1305 0.535335 GTATGAGGGCCTTGACGTCA 59.465 55.000 15.76 15.76 39.82 4.35
1449 1532 1.535462 AGTGGCGCAACACAATAGTTC 59.465 47.619 19.06 0.00 43.72 3.01
1451 1534 0.874390 CAGTGGCGCAACACAATAGT 59.126 50.000 19.06 0.00 43.72 2.12
1452 1535 0.454957 GCAGTGGCGCAACACAATAG 60.455 55.000 19.06 6.04 43.72 1.73
1453 1536 1.169034 TGCAGTGGCGCAACACAATA 61.169 50.000 19.06 0.61 45.35 1.90
1456 1539 2.906388 ATGCAGTGGCGCAACACA 60.906 55.556 19.06 15.36 46.87 3.72
1457 1540 2.429571 CATGCAGTGGCGCAACAC 60.430 61.111 19.06 13.32 46.87 3.32
1465 1548 0.896940 AGAACAAGGGCATGCAGTGG 60.897 55.000 21.36 5.64 0.00 4.00
1467 1550 0.178981 ACAGAACAAGGGCATGCAGT 60.179 50.000 21.36 9.22 0.00 4.40
1468 1551 0.242825 CACAGAACAAGGGCATGCAG 59.757 55.000 21.36 8.54 0.00 4.41
1472 1555 0.957395 CGCTCACAGAACAAGGGCAT 60.957 55.000 0.00 0.00 0.00 4.40
1486 1569 2.286950 GCAATCAACACAAACTCGCTCA 60.287 45.455 0.00 0.00 0.00 4.26
1496 1579 0.534877 AGTCGGCAGCAATCAACACA 60.535 50.000 0.00 0.00 0.00 3.72
1519 1602 3.254166 ACAATTAGCACACTTCAAGCAGG 59.746 43.478 0.00 0.00 0.00 4.85
1523 1606 4.036734 ACCACACAATTAGCACACTTCAAG 59.963 41.667 0.00 0.00 0.00 3.02
1564 1647 7.377696 ACATCCATGCAACCCAATAATTAAT 57.622 32.000 0.00 0.00 0.00 1.40
1565 1648 6.805016 ACATCCATGCAACCCAATAATTAA 57.195 33.333 0.00 0.00 0.00 1.40
1566 1649 7.904558 TTACATCCATGCAACCCAATAATTA 57.095 32.000 0.00 0.00 0.00 1.40
1567 1650 6.805016 TTACATCCATGCAACCCAATAATT 57.195 33.333 0.00 0.00 0.00 1.40
1616 1708 6.744112 AGATGAAGTAGTAGTAGCATGCTTC 58.256 40.000 28.02 21.48 29.76 3.86
1630 1722 9.941664 CCAAATAATTACAGCAAGATGAAGTAG 57.058 33.333 0.00 0.00 0.00 2.57
1631 1723 9.679661 TCCAAATAATTACAGCAAGATGAAGTA 57.320 29.630 0.00 0.00 0.00 2.24
1632 1724 8.579850 TCCAAATAATTACAGCAAGATGAAGT 57.420 30.769 0.00 0.00 0.00 3.01
1921 2396 5.733620 TCCGTTTTACTACTGAACCATCT 57.266 39.130 0.00 0.00 0.00 2.90
1987 2474 5.880332 ACCATATATACGACAATTGATGGCC 59.120 40.000 13.59 0.00 36.81 5.36
2465 3530 5.755861 ACTGAGAAGCTTTGTCTGAACTAAC 59.244 40.000 17.91 0.00 0.00 2.34
2967 4347 0.680280 TCTCCCGACTCTACTGCACC 60.680 60.000 0.00 0.00 0.00 5.01
3068 4452 5.118990 GGTACAACATCATGCATAGACTGT 58.881 41.667 0.00 2.46 0.00 3.55
3361 4781 1.195448 CATCAGGAGAACACAACGTGC 59.805 52.381 0.00 0.00 36.98 5.34
3366 4786 4.072131 GCTTAACCATCAGGAGAACACAA 58.928 43.478 0.00 0.00 38.69 3.33
3475 4900 1.946156 CACATGGGCGACGATCTCG 60.946 63.158 0.00 9.37 45.97 4.04
3775 5200 3.427243 GAACGAGTAATCTGTCTCCACG 58.573 50.000 0.00 0.00 0.00 4.94
3918 5358 9.685276 AGGAACAGATATAACAACAATCATGAA 57.315 29.630 0.00 0.00 0.00 2.57
3937 5377 9.314321 ACATATGTAACTTCGAAATAGGAACAG 57.686 33.333 6.56 0.00 0.00 3.16
3944 5384 9.438228 TCAAACCACATATGTAACTTCGAAATA 57.562 29.630 8.32 0.00 0.00 1.40
3947 5387 7.731882 TTCAAACCACATATGTAACTTCGAA 57.268 32.000 8.32 0.00 0.00 3.71
3952 5392 7.446931 TCACACATTCAAACCACATATGTAACT 59.553 33.333 8.32 0.00 0.00 2.24
3960 5400 4.998671 TGTTCACACATTCAAACCACAT 57.001 36.364 0.00 0.00 0.00 3.21
4068 5523 4.248842 CACCACCACCAGACGGCA 62.249 66.667 0.00 0.00 34.57 5.69
4150 5605 1.883678 TCATGAATCCCTCCTCAGCA 58.116 50.000 0.00 0.00 0.00 4.41
4385 5840 1.671379 GGAGGTGAGTTGCCGTTCC 60.671 63.158 0.00 0.00 0.00 3.62
4386 5841 0.951040 CTGGAGGTGAGTTGCCGTTC 60.951 60.000 0.00 0.00 0.00 3.95
4390 5875 0.321122 CAGACTGGAGGTGAGTTGCC 60.321 60.000 0.00 0.00 0.00 4.52
4429 5914 1.407258 TGTGCTTTAGGTGTGTTTGGC 59.593 47.619 0.00 0.00 0.00 4.52
4487 5993 1.472878 AGTGAAGATCGCGTCTAAGCA 59.527 47.619 5.77 5.54 35.67 3.91
4488 5994 2.196295 AGTGAAGATCGCGTCTAAGC 57.804 50.000 5.77 3.13 35.67 3.09
4661 6210 1.153127 AACAAAACCCCGCGTCTCA 60.153 52.632 4.92 0.00 0.00 3.27
4667 6216 1.658114 GAGGACAACAAAACCCCGC 59.342 57.895 0.00 0.00 0.00 6.13
4668 6217 1.512156 CGGAGGACAACAAAACCCCG 61.512 60.000 0.00 0.00 33.80 5.73
4669 6218 2.337361 CGGAGGACAACAAAACCCC 58.663 57.895 0.00 0.00 0.00 4.95
4697 6247 7.932335 ACAACTATAATCTAACTCTCGGTCAG 58.068 38.462 0.00 0.00 0.00 3.51
4698 6248 7.876936 ACAACTATAATCTAACTCTCGGTCA 57.123 36.000 0.00 0.00 0.00 4.02
4699 6249 7.587028 CGAACAACTATAATCTAACTCTCGGTC 59.413 40.741 0.00 0.00 0.00 4.79
4714 6269 2.482316 CCACATCGGGCGAACAACTATA 60.482 50.000 0.00 0.00 0.00 1.31
4728 6283 1.600013 TCCGACAAAAACACCACATCG 59.400 47.619 0.00 0.00 0.00 3.84
4732 6287 1.332686 GGTCTCCGACAAAAACACCAC 59.667 52.381 0.00 0.00 33.68 4.16
4738 6293 2.294074 CAAGTGGGTCTCCGACAAAAA 58.706 47.619 4.02 0.00 33.68 1.94
4761 6316 1.663695 AACATTCCGCGGGATAACTG 58.336 50.000 27.83 14.85 0.00 3.16
4773 6328 7.661040 TCTTCATCCTTTTTCTCAAACATTCC 58.339 34.615 0.00 0.00 0.00 3.01
4867 6439 7.615757 TCCACAATATACATACGATCCAGATCT 59.384 37.037 6.12 0.00 35.72 2.75
4878 6450 9.719355 TGTTACCATCATCCACAATATACATAC 57.281 33.333 0.00 0.00 0.00 2.39
4885 6457 9.693739 AAGTTATTGTTACCATCATCCACAATA 57.306 29.630 0.00 0.00 38.64 1.90
4979 6551 8.255111 AGAGTATGATTATGATGGAGTTGACA 57.745 34.615 0.00 0.00 0.00 3.58
4980 6552 9.202273 GAAGAGTATGATTATGATGGAGTTGAC 57.798 37.037 0.00 0.00 0.00 3.18
4986 6558 7.238305 ACCATGGAAGAGTATGATTATGATGGA 59.762 37.037 21.47 0.00 31.75 3.41
4987 6559 7.400439 ACCATGGAAGAGTATGATTATGATGG 58.600 38.462 21.47 0.00 33.22 3.51
4988 6560 8.727910 CAACCATGGAAGAGTATGATTATGATG 58.272 37.037 21.47 0.00 0.00 3.07
4989 6561 8.443176 ACAACCATGGAAGAGTATGATTATGAT 58.557 33.333 21.47 0.00 0.00 2.45
4990 6562 7.805163 ACAACCATGGAAGAGTATGATTATGA 58.195 34.615 21.47 0.00 0.00 2.15
4991 6563 8.347771 CAACAACCATGGAAGAGTATGATTATG 58.652 37.037 21.47 1.02 0.00 1.90
4992 6564 8.274322 TCAACAACCATGGAAGAGTATGATTAT 58.726 33.333 21.47 0.00 0.00 1.28
5005 6577 1.430853 TCCCCAATCAACAACCATGGA 59.569 47.619 21.47 0.00 32.82 3.41
5056 6628 1.229853 TCTGGGGTTTCCTCCCTCC 60.230 63.158 1.72 0.00 46.27 4.30
5078 6650 3.877559 CTCAGTCATCAATGGCCTGTTA 58.122 45.455 3.32 0.00 31.37 2.41
5088 6660 3.429492 AGTCTCTGAGCTCAGTCATCAA 58.571 45.455 36.32 19.53 44.12 2.57
5098 6670 3.030291 CTGTATCCCAAGTCTCTGAGCT 58.970 50.000 0.00 0.00 0.00 4.09
5100 6672 3.636300 CCTCTGTATCCCAAGTCTCTGAG 59.364 52.174 0.00 0.00 0.00 3.35
5124 6698 1.005340 CTCTGCCAAGTGAAGCGATC 58.995 55.000 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.