Multiple sequence alignment - TraesCS2D01G160400

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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 TraesCS2D01G160400 chr2D 100.000 4353 0 0 1 4353 103169111 103164759 0.000000e+00 8039.0
1 TraesCS2D01G160400 chr2D 93.007 143 10 0 4199 4341 106265610 106265468 4.410000e-50 209.0
2 TraesCS2D01G160400 chr2D 89.032 155 16 1 4188 4341 103147800 103147646 1.600000e-44 191.0
3 TraesCS2D01G160400 chr2D 92.537 67 5 0 4023 4089 648413070 648413136 3.580000e-16 97.1
4 TraesCS2D01G160400 chr2B 94.468 3091 122 22 514 3582 154722501 154719438 0.000000e+00 4715.0
5 TraesCS2D01G160400 chr2B 83.871 341 21 14 207 520 154722969 154722636 1.180000e-75 294.0
6 TraesCS2D01G160400 chr2B 96.429 168 6 0 1 168 154723132 154722965 1.190000e-70 278.0
7 TraesCS2D01G160400 chr2B 90.278 144 13 1 4199 4341 154907071 154906928 2.070000e-43 187.0
8 TraesCS2D01G160400 chr2B 88.652 141 16 0 4201 4341 154490558 154490698 5.790000e-39 172.0
9 TraesCS2D01G160400 chr2B 86.538 156 18 2 4189 4341 154491819 154491974 7.490000e-38 169.0
10 TraesCS2D01G160400 chr2B 88.112 143 16 1 4200 4341 154930225 154930083 7.490000e-38 169.0
11 TraesCS2D01G160400 chr2B 88.571 140 11 5 4204 4341 151108000 151107864 9.680000e-37 165.0
12 TraesCS2D01G160400 chr2A 95.309 2025 74 13 1597 3612 102328098 102326086 0.000000e+00 3193.0
13 TraesCS2D01G160400 chr2A 95.105 572 28 0 921 1492 102329096 102328525 0.000000e+00 902.0
14 TraesCS2D01G160400 chr2A 87.186 757 46 24 1 714 102330122 102329374 0.000000e+00 813.0
15 TraesCS2D01G160400 chr2A 97.203 143 4 0 4199 4341 102679379 102679237 4.350000e-60 243.0
16 TraesCS2D01G160400 chr2A 90.341 176 13 1 1491 1666 102328265 102328094 1.220000e-55 228.0
17 TraesCS2D01G160400 chr2A 90.395 177 9 2 716 892 102329266 102329098 4.380000e-55 226.0
18 TraesCS2D01G160400 chr2A 86.047 215 17 3 3777 3979 102325888 102325675 7.330000e-53 219.0
19 TraesCS2D01G160400 chr2A 85.629 167 21 3 4177 4341 102325502 102325337 5.790000e-39 172.0
20 TraesCS2D01G160400 chr4D 91.304 69 6 0 4021 4089 85730124 85730192 1.290000e-15 95.3
21 TraesCS2D01G160400 chr3D 91.304 69 6 0 4021 4089 363066650 363066718 1.290000e-15 95.3
22 TraesCS2D01G160400 chr3D 91.304 69 6 0 4021 4089 375238883 375238815 1.290000e-15 95.3
23 TraesCS2D01G160400 chr7B 91.045 67 6 0 4021 4087 552547181 552547247 1.670000e-14 91.6
24 TraesCS2D01G160400 chr7B 90.909 66 6 0 4021 4086 64969946 64970011 6.000000e-14 89.8
25 TraesCS2D01G160400 chr1D 91.045 67 6 0 4023 4089 267390330 267390264 1.670000e-14 91.6
26 TraesCS2D01G160400 chr1B 91.045 67 6 0 4021 4087 645733636 645733702 1.670000e-14 91.6
27 TraesCS2D01G160400 chr5B 89.855 69 7 0 4021 4089 485819720 485819652 6.000000e-14 89.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G160400 chr2D 103164759 103169111 4352 True 8039.000000 8039 100.000000 1 4353 1 chr2D.!!$R2 4352
1 TraesCS2D01G160400 chr2B 154719438 154723132 3694 True 1762.333333 4715 91.589333 1 3582 3 chr2B.!!$R4 3581
2 TraesCS2D01G160400 chr2A 102325337 102330122 4785 True 821.857143 3193 90.001714 1 4341 7 chr2A.!!$R2 4340

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
377 397 1.745320 AATAGCTGTCGGGGTAGCCG 61.745 60.0 4.56 0.51 40.76 5.52 F
1155 1446 0.389948 GTCGTGACTGCAGGTAAGGG 60.390 60.0 19.93 2.03 0.00 3.95 F
1788 2408 0.253160 TGGGGGATCAGCACTAACCT 60.253 55.0 0.00 0.00 0.00 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1411 1704 0.540365 CCCACATGGAAAGGCACAGT 60.540 55.000 0.0 0.0 37.39 3.55 R
2026 2647 1.066908 CGACCAAACTGTGCAAATGGT 59.933 47.619 0.0 0.0 46.63 3.55 R
3663 4302 0.471617 ACAGTTCCTTGCTCTGCTGT 59.528 50.000 0.0 0.0 33.12 4.40 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
183 185 2.159114 TGATTGACGATTCCGCTCATGA 60.159 45.455 0.00 0.00 39.95 3.07
250 263 3.927142 CAGATCTGTTGGTTCGTTAGACC 59.073 47.826 14.95 0.00 0.00 3.85
267 280 2.757894 ACCGTCTGGATAGGTCTGAT 57.242 50.000 0.00 0.00 39.21 2.90
268 281 2.588620 ACCGTCTGGATAGGTCTGATC 58.411 52.381 0.00 0.00 39.21 2.92
269 282 2.175931 ACCGTCTGGATAGGTCTGATCT 59.824 50.000 0.00 0.00 39.21 2.75
270 283 2.817258 CCGTCTGGATAGGTCTGATCTC 59.183 54.545 0.00 0.00 37.49 2.75
271 284 3.497763 CCGTCTGGATAGGTCTGATCTCT 60.498 52.174 0.00 0.00 37.49 3.10
272 285 3.501828 CGTCTGGATAGGTCTGATCTCTG 59.498 52.174 0.00 0.00 0.00 3.35
348 367 2.095059 GGTGCCAGTGTTCATGTTCATC 60.095 50.000 0.00 0.00 0.00 2.92
349 368 2.816087 GTGCCAGTGTTCATGTTCATCT 59.184 45.455 0.00 0.00 0.00 2.90
362 381 7.529880 TCATGTTCATCTATGCGCATAATAG 57.470 36.000 28.66 20.14 0.00 1.73
367 386 5.105063 TCATCTATGCGCATAATAGCTGTC 58.895 41.667 28.66 0.00 29.77 3.51
377 397 1.745320 AATAGCTGTCGGGGTAGCCG 61.745 60.000 4.56 0.51 40.76 5.52
392 412 3.189702 GGTAGCCGCTGTTTCATTGTAAA 59.810 43.478 2.16 0.00 0.00 2.01
426 446 4.456535 TCCCTTGTGTTGATTCGAGAAAA 58.543 39.130 0.00 0.00 0.00 2.29
427 447 4.274950 TCCCTTGTGTTGATTCGAGAAAAC 59.725 41.667 0.00 0.00 0.00 2.43
428 448 4.275936 CCCTTGTGTTGATTCGAGAAAACT 59.724 41.667 7.43 0.00 0.00 2.66
445 465 7.148722 CGAGAAAACTTTCTTGTGATCTCCTAC 60.149 40.741 6.18 0.00 46.84 3.18
446 466 7.740805 AGAAAACTTTCTTGTGATCTCCTACT 58.259 34.615 0.00 0.00 44.70 2.57
447 467 7.659390 AGAAAACTTTCTTGTGATCTCCTACTG 59.341 37.037 0.00 0.00 44.70 2.74
448 468 6.426646 AACTTTCTTGTGATCTCCTACTGT 57.573 37.500 0.00 0.00 0.00 3.55
454 496 5.778241 TCTTGTGATCTCCTACTGTTTGGTA 59.222 40.000 0.00 0.00 0.00 3.25
462 504 3.135994 CCTACTGTTTGGTAAACTGCGT 58.864 45.455 10.08 5.87 42.10 5.24
465 507 1.944024 CTGTTTGGTAAACTGCGTGGA 59.056 47.619 6.07 0.00 41.90 4.02
479 521 5.302360 ACTGCGTGGATACTTAAAAAGTCA 58.698 37.500 0.00 0.00 41.77 3.41
604 790 6.670027 ACTGAAATCTGTAGTGAACTATCCCT 59.330 38.462 0.00 0.00 0.00 4.20
606 792 6.440647 TGAAATCTGTAGTGAACTATCCCTGT 59.559 38.462 0.00 0.00 0.00 4.00
899 1190 4.570772 ACTTAATCTTCATTGCGCATACGT 59.429 37.500 12.75 0.00 42.83 3.57
1116 1407 1.414550 GGTAGAGATCTCCCAACCAGC 59.585 57.143 24.44 10.02 31.50 4.85
1155 1446 0.389948 GTCGTGACTGCAGGTAAGGG 60.390 60.000 19.93 2.03 0.00 3.95
1162 1453 1.774856 ACTGCAGGTAAGGGTTTCACT 59.225 47.619 19.93 0.00 0.00 3.41
1250 1541 7.254852 TCTTGGTGTTAAACATGTTCAGAAAC 58.745 34.615 12.39 13.68 35.85 2.78
1252 1543 6.559810 TGGTGTTAAACATGTTCAGAAACTG 58.440 36.000 12.39 0.00 36.30 3.16
1395 1688 6.374613 GCTTGGTGGTATAATAAGATAAGCCC 59.625 42.308 0.00 0.00 32.84 5.19
1411 1704 1.523154 GCCCATCTTCGGTTGTTGCA 61.523 55.000 0.00 0.00 0.00 4.08
1487 1780 3.243975 GCATCCAGGAATAGGCAATTTGG 60.244 47.826 0.00 0.00 29.76 3.28
1507 2061 6.677781 TTGGCATATGTGTTAGCTAAACTC 57.322 37.500 7.99 4.75 38.99 3.01
1527 2081 1.067821 CTCTCCTAGGCCAAACTAGCG 59.932 57.143 5.01 0.00 39.27 4.26
1537 2091 2.606795 GCCAAACTAGCGTGCATTTTCA 60.607 45.455 0.00 0.00 0.00 2.69
1542 2096 6.458751 CCAAACTAGCGTGCATTTTCATATCT 60.459 38.462 0.00 0.00 0.00 1.98
1644 2263 8.063200 TCTTTGACGTTCTATCCTCATTCTAA 57.937 34.615 0.00 0.00 0.00 2.10
1681 2300 8.995220 GTGTGTATTCATGTTCAACTAAGGTAA 58.005 33.333 0.00 0.00 0.00 2.85
1753 2373 1.349688 AGCCCATCTTCGGTTGTTACA 59.650 47.619 0.00 0.00 0.00 2.41
1754 2374 1.737793 GCCCATCTTCGGTTGTTACAG 59.262 52.381 0.00 0.00 0.00 2.74
1788 2408 0.253160 TGGGGGATCAGCACTAACCT 60.253 55.000 0.00 0.00 0.00 3.50
1805 2425 7.437748 CACTAACCTATAGGGATCAACTTCAG 58.562 42.308 22.91 6.40 40.27 3.02
1834 2454 6.514048 GCATCCTTGAATAGGCAATTAGTCAC 60.514 42.308 0.00 0.00 44.37 3.67
1852 2472 3.433615 GTCACATGTGTTACCTCTTGCTC 59.566 47.826 24.63 0.00 0.00 4.26
1873 2493 2.555757 CTCTGCTGCTTAACTGGCTTTT 59.444 45.455 0.00 0.00 0.00 2.27
1966 2587 8.180267 CCATGTAAGTGATGTGAATTTCTTCTC 58.820 37.037 0.00 0.00 32.29 2.87
2026 2647 2.892640 CCAGATGACCTTCGCCGA 59.107 61.111 0.00 0.00 0.00 5.54
2702 3329 7.548196 TCAGGACCATAAGCTTTTAATAACG 57.452 36.000 3.20 0.00 0.00 3.18
2704 3331 5.298527 AGGACCATAAGCTTTTAATAACGCC 59.701 40.000 3.20 0.00 0.00 5.68
2778 3405 0.761802 GGGGATTTGGGTTTGTGCAA 59.238 50.000 0.00 0.00 0.00 4.08
2986 3613 0.392461 GCCGGCCACTCAATTGACTA 60.392 55.000 18.11 0.00 0.00 2.59
3000 3627 7.927629 ACTCAATTGACTATTTGTTTGCACATT 59.072 29.630 3.38 0.00 31.06 2.71
3032 3659 2.397751 GGTCGGTCTTACGATCGGA 58.602 57.895 20.98 8.41 43.81 4.55
3430 4066 4.969816 TCTAAGTTTGCTATCGCTTTTGC 58.030 39.130 0.00 0.00 43.23 3.68
3471 4109 6.183360 TGGATTTATAGAGAAGATTGCCGTCA 60.183 38.462 0.00 0.00 0.00 4.35
3483 4122 2.330440 TGCCGTCATGTATCAGCAAT 57.670 45.000 0.00 0.00 0.00 3.56
3507 4146 5.103000 AGTATGTCAAACTATGTCTGCGAC 58.897 41.667 0.00 2.32 0.00 5.19
3508 4147 3.660501 TGTCAAACTATGTCTGCGACT 57.339 42.857 9.49 0.25 33.15 4.18
3545 4184 6.259829 TGCACTAGATTATTCAGCGCATAAAA 59.740 34.615 11.47 0.00 0.00 1.52
3577 4216 3.534554 TCTGCATTGCATATTCGTCACT 58.465 40.909 12.53 0.00 38.13 3.41
3587 4226 2.760634 ATTCGTCACTGGCATACACA 57.239 45.000 0.00 0.00 0.00 3.72
3612 4251 2.104963 CTGGGGTAAATGCTACTCCCTC 59.895 54.545 0.00 0.00 37.27 4.30
3613 4252 1.420514 GGGGTAAATGCTACTCCCTCC 59.579 57.143 0.00 0.00 38.31 4.30
3614 4253 2.124411 GGGTAAATGCTACTCCCTCCA 58.876 52.381 0.00 0.00 35.63 3.86
3615 4254 2.711547 GGGTAAATGCTACTCCCTCCAT 59.288 50.000 0.00 0.00 35.63 3.41
3617 4256 4.020128 GGGTAAATGCTACTCCCTCCATAG 60.020 50.000 0.00 0.00 35.63 2.23
3618 4257 4.838986 GGTAAATGCTACTCCCTCCATAGA 59.161 45.833 0.00 0.00 0.00 1.98
3619 4258 5.307196 GGTAAATGCTACTCCCTCCATAGAA 59.693 44.000 0.00 0.00 0.00 2.10
3620 4259 5.975988 AAATGCTACTCCCTCCATAGAAA 57.024 39.130 0.00 0.00 0.00 2.52
3622 4261 7.633018 AAATGCTACTCCCTCCATAGAAATA 57.367 36.000 0.00 0.00 0.00 1.40
3624 4263 8.917414 AATGCTACTCCCTCCATAGAAATATA 57.083 34.615 0.00 0.00 0.00 0.86
3626 4265 8.367660 TGCTACTCCCTCCATAGAAATATAAG 57.632 38.462 0.00 0.00 0.00 1.73
3628 4267 8.691797 GCTACTCCCTCCATAGAAATATAAGAG 58.308 40.741 0.00 0.00 0.00 2.85
3629 4268 7.489239 ACTCCCTCCATAGAAATATAAGAGC 57.511 40.000 0.00 0.00 0.00 4.09
3630 4269 6.153680 ACTCCCTCCATAGAAATATAAGAGCG 59.846 42.308 0.00 0.00 0.00 5.03
3631 4270 5.105310 TCCCTCCATAGAAATATAAGAGCGC 60.105 44.000 0.00 0.00 0.00 5.92
3632 4271 5.105146 CCCTCCATAGAAATATAAGAGCGCT 60.105 44.000 11.27 11.27 0.00 5.92
3633 4272 6.039616 CCTCCATAGAAATATAAGAGCGCTC 58.960 44.000 30.01 30.01 0.00 5.03
3634 4273 6.127479 CCTCCATAGAAATATAAGAGCGCTCT 60.127 42.308 33.83 33.83 42.75 4.09
3649 4288 7.278461 AGAGCGCTCTTATATCTCTTTTACA 57.722 36.000 33.83 0.00 36.31 2.41
3650 4289 7.367285 AGAGCGCTCTTATATCTCTTTTACAG 58.633 38.462 33.83 0.00 36.31 2.74
3691 4366 0.397941 CAAGGAACTGTCCCAGCTGA 59.602 55.000 17.39 0.00 46.30 4.26
3709 4384 6.770746 AGCTGAAATGCTGTCATCTTATTT 57.229 33.333 0.00 0.00 42.33 1.40
3710 4385 7.166691 AGCTGAAATGCTGTCATCTTATTTT 57.833 32.000 0.00 0.00 42.33 1.82
3711 4386 7.256286 AGCTGAAATGCTGTCATCTTATTTTC 58.744 34.615 0.00 0.00 42.33 2.29
3712 4387 7.031372 GCTGAAATGCTGTCATCTTATTTTCA 58.969 34.615 0.00 0.00 31.27 2.69
3713 4388 7.220300 GCTGAAATGCTGTCATCTTATTTTCAG 59.780 37.037 14.51 14.51 40.05 3.02
3714 4389 7.031372 TGAAATGCTGTCATCTTATTTTCAGC 58.969 34.615 7.83 7.83 45.39 4.26
3715 4390 6.770746 AATGCTGTCATCTTATTTTCAGCT 57.229 33.333 14.34 0.00 45.39 4.24
3716 4391 6.770746 ATGCTGTCATCTTATTTTCAGCTT 57.229 33.333 14.34 6.94 45.39 3.74
3742 4417 7.383029 TCTGAATTTTAAGCTCAATTTGTGCTG 59.617 33.333 22.56 9.89 45.23 4.41
3744 4419 7.710044 TGAATTTTAAGCTCAATTTGTGCTGAA 59.290 29.630 22.56 19.15 45.23 3.02
3745 4420 7.647907 ATTTTAAGCTCAATTTGTGCTGAAG 57.352 32.000 22.56 2.06 45.23 3.02
3746 4421 3.655276 AAGCTCAATTTGTGCTGAAGG 57.345 42.857 22.56 0.00 45.23 3.46
3747 4422 2.590821 AGCTCAATTTGTGCTGAAGGT 58.409 42.857 21.55 2.84 44.42 3.50
3748 4423 2.295349 AGCTCAATTTGTGCTGAAGGTG 59.705 45.455 21.55 0.00 44.42 4.00
3749 4424 2.294233 GCTCAATTTGTGCTGAAGGTGA 59.706 45.455 14.51 0.00 34.37 4.02
3750 4425 3.243501 GCTCAATTTGTGCTGAAGGTGAA 60.244 43.478 14.51 0.00 34.37 3.18
3752 4427 3.044986 CAATTTGTGCTGAAGGTGAACG 58.955 45.455 0.00 0.00 0.00 3.95
3753 4428 1.021202 TTTGTGCTGAAGGTGAACGG 58.979 50.000 0.00 0.00 0.00 4.44
3754 4429 1.444119 TTGTGCTGAAGGTGAACGGC 61.444 55.000 0.00 0.00 38.67 5.68
3756 4431 2.665185 GCTGAAGGTGAACGGCGT 60.665 61.111 6.77 6.77 0.00 5.68
3758 4433 0.947180 GCTGAAGGTGAACGGCGTAA 60.947 55.000 15.20 1.09 0.00 3.18
3759 4434 1.722011 CTGAAGGTGAACGGCGTAAT 58.278 50.000 15.20 0.00 0.00 1.89
3760 4435 2.073816 CTGAAGGTGAACGGCGTAATT 58.926 47.619 15.20 0.00 0.00 1.40
3761 4436 2.482721 CTGAAGGTGAACGGCGTAATTT 59.517 45.455 15.20 0.00 0.00 1.82
3762 4437 2.224549 TGAAGGTGAACGGCGTAATTTG 59.775 45.455 15.20 0.00 0.00 2.32
3763 4438 2.172851 AGGTGAACGGCGTAATTTGA 57.827 45.000 15.20 0.00 0.00 2.69
3764 4439 2.706890 AGGTGAACGGCGTAATTTGAT 58.293 42.857 15.20 0.00 0.00 2.57
3765 4440 3.864243 AGGTGAACGGCGTAATTTGATA 58.136 40.909 15.20 0.00 0.00 2.15
3766 4441 3.869246 AGGTGAACGGCGTAATTTGATAG 59.131 43.478 15.20 0.00 0.00 2.08
3767 4442 3.545426 GGTGAACGGCGTAATTTGATAGC 60.545 47.826 15.20 0.00 0.00 2.97
3768 4443 2.283086 TGAACGGCGTAATTTGATAGCG 59.717 45.455 15.20 0.00 0.00 4.26
3769 4444 2.212869 ACGGCGTAATTTGATAGCGA 57.787 45.000 12.58 0.00 0.00 4.93
3771 4446 2.475111 ACGGCGTAATTTGATAGCGATG 59.525 45.455 12.58 0.00 0.00 3.84
3773 4448 3.059868 CGGCGTAATTTGATAGCGATGTT 60.060 43.478 0.00 0.00 0.00 2.71
3774 4449 4.551990 CGGCGTAATTTGATAGCGATGTTT 60.552 41.667 0.00 0.00 0.00 2.83
3775 4450 5.332732 CGGCGTAATTTGATAGCGATGTTTA 60.333 40.000 0.00 0.00 0.00 2.01
3781 4477 5.712217 TTTGATAGCGATGTTTAGAACGG 57.288 39.130 0.00 0.00 0.00 4.44
3792 4488 5.441709 TGTTTAGAACGGTCCATTTTTCC 57.558 39.130 0.00 0.00 0.00 3.13
3800 4496 6.492087 AGAACGGTCCATTTTTCCTTGAATTA 59.508 34.615 0.00 0.00 0.00 1.40
3857 4553 6.805271 AGAATGTTTTCTTTCATGCAAGATCG 59.195 34.615 8.66 0.00 39.18 3.69
3867 4563 1.815421 GCAAGATCGGTGCATCGGT 60.815 57.895 21.08 13.84 41.80 4.69
3872 4568 0.652592 GATCGGTGCATCGGTTTCTG 59.347 55.000 21.08 0.00 0.00 3.02
3881 4577 1.464608 CATCGGTTTCTGCGTGAACAT 59.535 47.619 0.00 0.00 33.88 2.71
3883 4579 2.333926 TCGGTTTCTGCGTGAACATAG 58.666 47.619 0.00 0.00 33.88 2.23
3888 4596 0.735978 TCTGCGTGAACATAGGTGCG 60.736 55.000 0.00 0.00 0.00 5.34
3898 4606 2.356135 ACATAGGTGCGTCATTTCCAC 58.644 47.619 0.00 0.00 0.00 4.02
3923 4631 2.286833 CGGTGATCGTGAACACAAAAGT 59.713 45.455 11.60 0.00 38.57 2.66
3938 4646 4.919168 CACAAAAGTACACAATGCCAGATG 59.081 41.667 0.00 0.00 0.00 2.90
3948 4656 2.887568 GCCAGATGGACAGACGCG 60.888 66.667 3.53 3.53 37.39 6.01
3949 4657 2.202797 CCAGATGGACAGACGCGG 60.203 66.667 12.47 0.00 37.39 6.46
3957 4665 1.063006 GACAGACGCGGCGTACATA 59.937 57.895 29.49 0.00 41.37 2.29
3960 4668 1.205657 CAGACGCGGCGTACATAAAT 58.794 50.000 29.49 2.12 41.37 1.40
3962 4670 1.202203 GACGCGGCGTACATAAATGA 58.798 50.000 29.49 0.00 41.37 2.57
3963 4671 1.589320 GACGCGGCGTACATAAATGAA 59.411 47.619 29.49 0.00 41.37 2.57
3964 4672 1.591158 ACGCGGCGTACATAAATGAAG 59.409 47.619 28.37 0.00 38.73 3.02
3965 4673 1.855978 CGCGGCGTACATAAATGAAGA 59.144 47.619 15.36 0.00 0.00 2.87
3966 4674 2.097396 CGCGGCGTACATAAATGAAGAG 60.097 50.000 15.36 0.00 0.00 2.85
3967 4675 3.120792 GCGGCGTACATAAATGAAGAGA 58.879 45.455 9.37 0.00 0.00 3.10
3968 4676 3.182572 GCGGCGTACATAAATGAAGAGAG 59.817 47.826 9.37 0.00 0.00 3.20
3969 4677 4.360563 CGGCGTACATAAATGAAGAGAGT 58.639 43.478 0.00 0.00 0.00 3.24
3970 4678 4.804139 CGGCGTACATAAATGAAGAGAGTT 59.196 41.667 0.00 0.00 0.00 3.01
3971 4679 5.291128 CGGCGTACATAAATGAAGAGAGTTT 59.709 40.000 0.00 0.00 0.00 2.66
3972 4680 6.183360 CGGCGTACATAAATGAAGAGAGTTTT 60.183 38.462 0.00 0.00 0.00 2.43
3973 4681 7.009815 CGGCGTACATAAATGAAGAGAGTTTTA 59.990 37.037 0.00 0.00 0.00 1.52
3974 4682 8.827677 GGCGTACATAAATGAAGAGAGTTTTAT 58.172 33.333 0.00 0.00 0.00 1.40
4020 4728 1.928868 AAGCCAAATGAAGAGGTGGG 58.071 50.000 0.00 0.00 0.00 4.61
4021 4729 0.040204 AGCCAAATGAAGAGGTGGGG 59.960 55.000 0.00 0.00 0.00 4.96
4022 4730 0.972471 GCCAAATGAAGAGGTGGGGG 60.972 60.000 0.00 0.00 0.00 5.40
4023 4731 0.409484 CCAAATGAAGAGGTGGGGGT 59.591 55.000 0.00 0.00 0.00 4.95
4024 4732 1.549203 CAAATGAAGAGGTGGGGGTG 58.451 55.000 0.00 0.00 0.00 4.61
4025 4733 0.251787 AAATGAAGAGGTGGGGGTGC 60.252 55.000 0.00 0.00 0.00 5.01
4026 4734 2.484287 AATGAAGAGGTGGGGGTGCG 62.484 60.000 0.00 0.00 0.00 5.34
4030 4738 2.976494 AAGAGGTGGGGGTGCGTTTG 62.976 60.000 0.00 0.00 0.00 2.93
4031 4739 4.596585 AGGTGGGGGTGCGTTTGG 62.597 66.667 0.00 0.00 0.00 3.28
4032 4740 4.906537 GGTGGGGGTGCGTTTGGT 62.907 66.667 0.00 0.00 0.00 3.67
4035 4743 2.203437 GGGGGTGCGTTTGGTTCT 60.203 61.111 0.00 0.00 0.00 3.01
4036 4744 1.830847 GGGGGTGCGTTTGGTTCTT 60.831 57.895 0.00 0.00 0.00 2.52
4037 4745 1.396607 GGGGGTGCGTTTGGTTCTTT 61.397 55.000 0.00 0.00 0.00 2.52
4039 4747 0.741915 GGGTGCGTTTGGTTCTTTGA 59.258 50.000 0.00 0.00 0.00 2.69
4040 4748 1.535226 GGGTGCGTTTGGTTCTTTGAC 60.535 52.381 0.00 0.00 0.00 3.18
4041 4749 1.133407 GGTGCGTTTGGTTCTTTGACA 59.867 47.619 0.00 0.00 0.00 3.58
4044 4752 3.675698 GTGCGTTTGGTTCTTTGACAAAA 59.324 39.130 1.62 0.00 36.05 2.44
4045 4753 4.150804 GTGCGTTTGGTTCTTTGACAAAAA 59.849 37.500 1.62 0.00 36.05 1.94
4080 4788 2.877691 GGCTAGGCTTGCCGTTTG 59.122 61.111 23.60 0.00 41.03 2.93
4082 4790 1.971695 GCTAGGCTTGCCGTTTGGT 60.972 57.895 9.92 0.00 37.67 3.67
4084 4792 1.369625 CTAGGCTTGCCGTTTGGTAG 58.630 55.000 5.95 0.00 37.67 3.18
4085 4793 0.675522 TAGGCTTGCCGTTTGGTAGC 60.676 55.000 5.95 0.00 41.50 3.58
4086 4794 2.175811 GCTTGCCGTTTGGTAGCG 59.824 61.111 0.00 0.00 36.04 4.26
4089 4797 2.513065 CTTGCCGTTTGGTAGCGCAG 62.513 60.000 11.47 0.00 37.67 5.18
4090 4798 2.740826 GCCGTTTGGTAGCGCAGA 60.741 61.111 11.47 0.00 37.67 4.26
4091 4799 3.023591 GCCGTTTGGTAGCGCAGAC 62.024 63.158 11.47 7.11 37.67 3.51
4092 4800 2.388232 CCGTTTGGTAGCGCAGACC 61.388 63.158 21.24 21.24 37.49 3.85
4093 4801 1.666553 CGTTTGGTAGCGCAGACCA 60.667 57.895 25.42 25.42 45.38 4.02
4094 4802 1.019278 CGTTTGGTAGCGCAGACCAT 61.019 55.000 28.40 2.35 46.29 3.55
4095 4803 0.727398 GTTTGGTAGCGCAGACCATC 59.273 55.000 28.40 21.29 46.29 3.51
4096 4804 0.739462 TTTGGTAGCGCAGACCATCG 60.739 55.000 28.40 0.00 46.29 3.84
4098 4806 1.033202 TGGTAGCGCAGACCATCGTA 61.033 55.000 25.42 7.15 42.15 3.43
4099 4807 0.594284 GGTAGCGCAGACCATCGTAC 60.594 60.000 22.64 7.71 36.91 3.67
4100 4808 0.928908 GTAGCGCAGACCATCGTACG 60.929 60.000 11.47 9.53 0.00 3.67
4101 4809 1.091197 TAGCGCAGACCATCGTACGA 61.091 55.000 21.93 21.93 0.00 3.43
4102 4810 1.299165 GCGCAGACCATCGTACGAT 60.299 57.895 24.66 24.66 34.81 3.73
4103 4811 1.269444 GCGCAGACCATCGTACGATC 61.269 60.000 27.24 17.56 31.62 3.69
4114 4822 0.738412 CGTACGATCTTGGGCCGTTT 60.738 55.000 10.44 0.00 37.69 3.60
4120 4828 4.383602 CTTGGGCCGTTTGCGTCG 62.384 66.667 0.00 0.00 42.61 5.12
4126 4834 4.430423 CCGTTTGCGTCGCTGCTC 62.430 66.667 19.50 5.59 36.15 4.26
4127 4835 3.406361 CGTTTGCGTCGCTGCTCT 61.406 61.111 19.50 0.00 35.36 4.09
4138 4846 2.039405 GCTGCTCTTGGGCTGACAG 61.039 63.158 3.54 0.00 33.89 3.51
4139 4847 1.376942 CTGCTCTTGGGCTGACAGG 60.377 63.158 4.26 0.00 33.89 4.00
4140 4848 2.749441 GCTCTTGGGCTGACAGGC 60.749 66.667 20.32 20.32 40.51 4.85
4147 4855 2.825836 GGCTGACAGGCCGGAATG 60.826 66.667 17.97 4.95 42.82 2.67
4148 4856 3.512516 GCTGACAGGCCGGAATGC 61.513 66.667 10.86 6.45 0.00 3.56
4158 4866 4.096003 CGGAATGCCCAGACCCGT 62.096 66.667 0.00 0.00 35.83 5.28
4175 4883 2.429571 TCGTAACGTGCGTCTGGC 60.430 61.111 11.59 0.00 43.96 4.85
4201 4919 2.510613 CGGAGGGTGTACAAATGGTTT 58.489 47.619 0.00 0.00 0.00 3.27
4220 4938 2.430367 GTTTGGTCCCACCTCGCT 59.570 61.111 0.00 0.00 39.58 4.93
4222 4940 1.228124 TTTGGTCCCACCTCGCTTG 60.228 57.895 0.00 0.00 39.58 4.01
4230 4948 2.604686 ACCTCGCTTGGCTGAGGA 60.605 61.111 24.88 2.38 45.13 3.71
4238 4956 0.540923 CTTGGCTGAGGAAGAGAGGG 59.459 60.000 0.00 0.00 0.00 4.30
4242 4960 1.048160 GCTGAGGAAGAGAGGGGAGG 61.048 65.000 0.00 0.00 0.00 4.30
4246 4964 1.764454 GGAAGAGAGGGGAGGGAGC 60.764 68.421 0.00 0.00 0.00 4.70
4248 4966 0.759060 GAAGAGAGGGGAGGGAGCTC 60.759 65.000 4.71 4.71 0.00 4.09
4254 4972 2.203714 GGGAGGGAGCTCGGCTAT 60.204 66.667 7.83 0.00 39.88 2.97
4262 4980 2.691011 GGGAGCTCGGCTATATAAGAGG 59.309 54.545 7.83 0.00 39.88 3.69
4264 4982 3.622630 GAGCTCGGCTATATAAGAGGGA 58.377 50.000 0.00 0.00 39.88 4.20
4267 4985 4.227754 AGCTCGGCTATATAAGAGGGAGTA 59.772 45.833 9.96 0.00 36.99 2.59
4271 4989 4.641094 CGGCTATATAAGAGGGAGTAGTGG 59.359 50.000 0.00 0.00 0.00 4.00
4272 4990 4.957327 GGCTATATAAGAGGGAGTAGTGGG 59.043 50.000 0.00 0.00 0.00 4.61
4275 4993 2.456073 TAAGAGGGAGTAGTGGGAGC 57.544 55.000 0.00 0.00 0.00 4.70
4277 4995 2.042843 AGGGAGTAGTGGGAGCGG 60.043 66.667 0.00 0.00 0.00 5.52
4279 4997 2.722201 GGGAGTAGTGGGAGCGGTG 61.722 68.421 0.00 0.00 0.00 4.94
4280 4998 1.681327 GGAGTAGTGGGAGCGGTGA 60.681 63.158 0.00 0.00 0.00 4.02
4283 5001 0.608640 AGTAGTGGGAGCGGTGAAAG 59.391 55.000 0.00 0.00 0.00 2.62
4284 5002 0.391263 GTAGTGGGAGCGGTGAAAGG 60.391 60.000 0.00 0.00 0.00 3.11
4341 5059 9.756461 CTATTCTTTCGCCTTTTACTAAAGAAC 57.244 33.333 9.88 0.00 44.44 3.01
4342 5060 7.797038 TTCTTTCGCCTTTTACTAAAGAACT 57.203 32.000 0.00 0.00 42.78 3.01
4343 5061 8.891671 TTCTTTCGCCTTTTACTAAAGAACTA 57.108 30.769 0.00 0.00 42.78 2.24
4344 5062 8.530269 TCTTTCGCCTTTTACTAAAGAACTAG 57.470 34.615 0.00 0.00 42.78 2.57
4345 5063 8.362639 TCTTTCGCCTTTTACTAAAGAACTAGA 58.637 33.333 0.00 0.00 42.78 2.43
4346 5064 9.152595 CTTTCGCCTTTTACTAAAGAACTAGAT 57.847 33.333 0.00 0.00 42.78 1.98
4348 5066 9.798994 TTCGCCTTTTACTAAAGAACTAGATAG 57.201 33.333 0.00 0.00 42.78 2.08
4349 5067 8.411683 TCGCCTTTTACTAAAGAACTAGATAGG 58.588 37.037 0.00 0.00 42.78 2.57
4350 5068 8.411683 CGCCTTTTACTAAAGAACTAGATAGGA 58.588 37.037 0.00 0.00 42.78 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 1.114627 TCAGACGGATGATCACAGGG 58.885 55.000 0.00 0.00 0.00 4.45
183 185 7.862274 TCCATCATCCACTTACATCTTCTAT 57.138 36.000 0.00 0.00 0.00 1.98
250 263 3.501828 CAGAGATCAGACCTATCCAGACG 59.498 52.174 0.00 0.00 0.00 4.18
266 279 1.667724 CGCCGAATTTGCTTCAGAGAT 59.332 47.619 0.00 0.00 33.10 2.75
267 280 1.078709 CGCCGAATTTGCTTCAGAGA 58.921 50.000 0.00 0.00 33.10 3.10
268 281 0.522076 GCGCCGAATTTGCTTCAGAG 60.522 55.000 0.00 0.00 33.10 3.35
269 282 1.233950 TGCGCCGAATTTGCTTCAGA 61.234 50.000 4.18 0.00 33.10 3.27
270 283 0.795735 CTGCGCCGAATTTGCTTCAG 60.796 55.000 4.18 3.63 33.10 3.02
271 284 1.209898 CTGCGCCGAATTTGCTTCA 59.790 52.632 4.18 0.00 33.10 3.02
272 285 2.154569 GCTGCGCCGAATTTGCTTC 61.155 57.895 4.18 0.00 0.00 3.86
348 367 2.600420 CCGACAGCTATTATGCGCATAG 59.400 50.000 27.54 20.28 38.13 2.23
349 368 2.606108 CCGACAGCTATTATGCGCATA 58.394 47.619 25.78 25.78 38.13 3.14
377 397 6.529829 TGACAAACAGTTTACAATGAAACAGC 59.470 34.615 0.00 0.00 41.00 4.40
392 412 3.631250 ACACAAGGGAATGACAAACAGT 58.369 40.909 0.00 0.00 0.00 3.55
426 446 6.426646 AACAGTAGGAGATCACAAGAAAGT 57.573 37.500 0.00 0.00 0.00 2.66
427 447 6.148480 CCAAACAGTAGGAGATCACAAGAAAG 59.852 42.308 0.00 0.00 0.00 2.62
428 448 5.997746 CCAAACAGTAGGAGATCACAAGAAA 59.002 40.000 0.00 0.00 0.00 2.52
445 465 1.944024 TCCACGCAGTTTACCAAACAG 59.056 47.619 4.73 0.00 41.61 3.16
446 466 2.039818 TCCACGCAGTTTACCAAACA 57.960 45.000 4.73 0.00 41.61 2.83
447 467 3.749609 AGTATCCACGCAGTTTACCAAAC 59.250 43.478 0.00 0.00 41.61 2.93
448 468 4.010667 AGTATCCACGCAGTTTACCAAA 57.989 40.909 0.00 0.00 41.61 3.28
454 496 6.261381 TGACTTTTTAAGTATCCACGCAGTTT 59.739 34.615 0.00 0.00 40.26 2.66
462 504 6.128117 GGCGAACATGACTTTTTAAGTATCCA 60.128 38.462 0.00 0.00 43.03 3.41
465 507 5.944007 AGGGCGAACATGACTTTTTAAGTAT 59.056 36.000 0.00 0.00 43.03 2.12
479 521 0.609131 CAGGGTCAAAGGGCGAACAT 60.609 55.000 0.00 0.00 0.00 2.71
721 1012 9.198837 CATCATCACATGTTTTCTCATTCAAAA 57.801 29.630 0.00 0.00 0.00 2.44
725 1016 7.220300 GCTTCATCATCACATGTTTTCTCATTC 59.780 37.037 0.00 0.00 0.00 2.67
981 1272 9.099454 CTTCTCATATTGGTCTACAGTAAAACC 57.901 37.037 5.24 5.24 0.00 3.27
988 1279 5.304101 AGCCTCTTCTCATATTGGTCTACAG 59.696 44.000 0.00 0.00 0.00 2.74
1155 1446 1.609072 GCCTGGGAAGTTCAGTGAAAC 59.391 52.381 7.25 2.37 0.00 2.78
1162 1453 3.185880 AGTACTAGCCTGGGAAGTTCA 57.814 47.619 5.01 0.00 0.00 3.18
1250 1541 3.752747 TGTCACAGATGCATTTACCACAG 59.247 43.478 0.00 0.00 0.00 3.66
1252 1543 4.970662 ATGTCACAGATGCATTTACCAC 57.029 40.909 0.00 0.00 0.00 4.16
1387 1679 2.919228 ACAACCGAAGATGGGCTTATC 58.081 47.619 0.00 0.00 36.83 1.75
1395 1688 1.603802 ACAGTGCAACAACCGAAGATG 59.396 47.619 0.00 0.00 41.43 2.90
1411 1704 0.540365 CCCACATGGAAAGGCACAGT 60.540 55.000 0.00 0.00 37.39 3.55
1487 1780 6.422400 GGAGAGAGTTTAGCTAACACATATGC 59.578 42.308 5.45 1.40 39.30 3.14
1507 2061 1.067821 CGCTAGTTTGGCCTAGGAGAG 59.932 57.143 14.75 0.00 35.89 3.20
1616 2170 5.914898 TGAGGATAGAACGTCAAAGATGA 57.085 39.130 0.00 0.00 32.91 2.92
1644 2263 6.927416 ACATGAATACACACATGCTTCAAAT 58.073 32.000 0.00 0.00 45.03 2.32
1753 2373 0.974010 CCCACATGGAAAGGCATGCT 60.974 55.000 18.92 0.00 37.39 3.79
1754 2374 1.518774 CCCACATGGAAAGGCATGC 59.481 57.895 9.90 9.90 37.39 4.06
1788 2408 6.499106 TGCATTCTGAAGTTGATCCCTATA 57.501 37.500 0.00 0.00 0.00 1.31
1834 2454 3.931468 CAGAGAGCAAGAGGTAACACATG 59.069 47.826 0.00 0.00 41.41 3.21
1852 2472 1.818642 AAGCCAGTTAAGCAGCAGAG 58.181 50.000 0.00 0.00 0.00 3.35
1873 2493 2.255554 GAGAGACGCGCACAGACA 59.744 61.111 5.73 0.00 0.00 3.41
1966 2587 5.422214 TGAGTTAAAAAGGCTAGGAGGAG 57.578 43.478 0.00 0.00 0.00 3.69
2026 2647 1.066908 CGACCAAACTGTGCAAATGGT 59.933 47.619 0.00 0.00 46.63 3.55
2192 2815 1.303309 ATGACTAAAGCGGCATGAGC 58.697 50.000 1.45 0.25 41.10 4.26
2193 2816 3.062763 CCTATGACTAAAGCGGCATGAG 58.937 50.000 1.45 0.00 0.00 2.90
2194 2817 2.698274 TCCTATGACTAAAGCGGCATGA 59.302 45.455 1.45 0.00 0.00 3.07
2702 3329 8.414629 AAAGATCATATCCATCCTTAAAAGGC 57.585 34.615 3.73 0.00 46.06 4.35
2778 3405 2.872245 CGCATCGTTGGGATCAAAGTAT 59.128 45.455 4.63 0.00 38.00 2.12
2808 3435 6.613679 TGACCTGTCCATCCATGTAGTATTTA 59.386 38.462 0.00 0.00 0.00 1.40
3032 3659 1.151810 TTGGGGAAGGAGAGTGCCT 60.152 57.895 0.00 0.00 40.93 4.75
3143 3770 6.310197 GTGGAGAAAAAGATCAAGAATCGTG 58.690 40.000 0.00 0.00 39.55 4.35
3145 3772 5.645497 AGGTGGAGAAAAAGATCAAGAATCG 59.355 40.000 0.00 0.00 39.55 3.34
3271 3907 3.586961 CTCGCGCTCCTCGATCCA 61.587 66.667 5.56 0.00 41.67 3.41
3307 3943 1.533033 TCTTCGTGAGGACCTGCCA 60.533 57.895 0.00 0.00 40.02 4.92
3371 4007 3.836562 TCCACTACAGTTCTAGAAACCCC 59.163 47.826 6.78 0.00 0.00 4.95
3439 4075 9.929180 CAATCTTCTCTATAAATCCACGGATAA 57.071 33.333 0.00 0.00 33.97 1.75
3483 4122 6.445357 TCGCAGACATAGTTTGACATACTA 57.555 37.500 8.02 8.02 33.00 1.82
3507 4146 9.593134 AATAATCTAGTGCAAAAGTACAGAGAG 57.407 33.333 0.00 0.00 0.00 3.20
3508 4147 9.587772 GAATAATCTAGTGCAAAAGTACAGAGA 57.412 33.333 0.00 0.00 0.00 3.10
3545 4184 7.997773 ATATGCAATGCAGAGTCATCTTTAT 57.002 32.000 14.98 0.00 43.65 1.40
3577 4216 2.676608 CCAGCCCTGTGTATGCCA 59.323 61.111 0.00 0.00 0.00 4.92
3587 4226 0.551396 GTAGCATTTACCCCAGCCCT 59.449 55.000 0.00 0.00 0.00 5.19
3626 4265 7.364200 TCTGTAAAAGAGATATAAGAGCGCTC 58.636 38.462 30.01 30.01 0.00 5.03
3641 4280 7.522399 GCTGTCAACTACTCTCTCTGTAAAAGA 60.522 40.741 0.00 0.00 0.00 2.52
3642 4281 6.584563 GCTGTCAACTACTCTCTCTGTAAAAG 59.415 42.308 0.00 0.00 0.00 2.27
3643 4282 6.040504 TGCTGTCAACTACTCTCTCTGTAAAA 59.959 38.462 0.00 0.00 0.00 1.52
3644 4283 5.535030 TGCTGTCAACTACTCTCTCTGTAAA 59.465 40.000 0.00 0.00 0.00 2.01
3645 4284 5.070685 TGCTGTCAACTACTCTCTCTGTAA 58.929 41.667 0.00 0.00 0.00 2.41
3646 4285 4.652822 TGCTGTCAACTACTCTCTCTGTA 58.347 43.478 0.00 0.00 0.00 2.74
3647 4286 3.491342 TGCTGTCAACTACTCTCTCTGT 58.509 45.455 0.00 0.00 0.00 3.41
3648 4287 3.755905 TCTGCTGTCAACTACTCTCTCTG 59.244 47.826 0.00 0.00 0.00 3.35
3649 4288 4.009675 CTCTGCTGTCAACTACTCTCTCT 58.990 47.826 0.00 0.00 0.00 3.10
3650 4289 3.427503 GCTCTGCTGTCAACTACTCTCTC 60.428 52.174 0.00 0.00 0.00 3.20
3653 4292 2.242926 TGCTCTGCTGTCAACTACTCT 58.757 47.619 0.00 0.00 0.00 3.24
3663 4302 0.471617 ACAGTTCCTTGCTCTGCTGT 59.528 50.000 0.00 0.00 33.12 4.40
3713 4388 8.219105 CACAAATTGAGCTTAAAATTCAGAAGC 58.781 33.333 0.00 9.71 44.79 3.86
3714 4389 8.219105 GCACAAATTGAGCTTAAAATTCAGAAG 58.781 33.333 8.12 0.00 31.18 2.85
3715 4390 7.927629 AGCACAAATTGAGCTTAAAATTCAGAA 59.072 29.630 11.99 0.00 41.43 3.02
3716 4391 7.383029 CAGCACAAATTGAGCTTAAAATTCAGA 59.617 33.333 14.93 0.00 41.43 3.27
3733 4408 1.608590 CCGTTCACCTTCAGCACAAAT 59.391 47.619 0.00 0.00 0.00 2.32
3741 4416 2.172851 AATTACGCCGTTCACCTTCA 57.827 45.000 0.00 0.00 0.00 3.02
3742 4417 2.481185 TCAAATTACGCCGTTCACCTTC 59.519 45.455 0.00 0.00 0.00 3.46
3744 4419 2.172851 TCAAATTACGCCGTTCACCT 57.827 45.000 0.00 0.00 0.00 4.00
3745 4420 3.545426 GCTATCAAATTACGCCGTTCACC 60.545 47.826 0.00 0.00 0.00 4.02
3746 4421 3.604392 GCTATCAAATTACGCCGTTCAC 58.396 45.455 0.00 0.00 0.00 3.18
3747 4422 2.283086 CGCTATCAAATTACGCCGTTCA 59.717 45.455 0.00 0.00 0.00 3.18
3748 4423 2.536803 TCGCTATCAAATTACGCCGTTC 59.463 45.455 0.00 0.00 0.00 3.95
3749 4424 2.542597 TCGCTATCAAATTACGCCGTT 58.457 42.857 0.00 0.00 0.00 4.44
3750 4425 2.212869 TCGCTATCAAATTACGCCGT 57.787 45.000 0.00 0.00 0.00 5.68
3752 4427 4.468095 AACATCGCTATCAAATTACGCC 57.532 40.909 0.00 0.00 0.00 5.68
3753 4428 6.873656 TCTAAACATCGCTATCAAATTACGC 58.126 36.000 0.00 0.00 0.00 4.42
3754 4429 7.522884 CGTTCTAAACATCGCTATCAAATTACG 59.477 37.037 0.00 0.00 0.00 3.18
3756 4431 7.493320 ACCGTTCTAAACATCGCTATCAAATTA 59.507 33.333 0.00 0.00 0.00 1.40
3758 4433 5.815740 ACCGTTCTAAACATCGCTATCAAAT 59.184 36.000 0.00 0.00 0.00 2.32
3759 4434 5.172934 ACCGTTCTAAACATCGCTATCAAA 58.827 37.500 0.00 0.00 0.00 2.69
3760 4435 4.751060 ACCGTTCTAAACATCGCTATCAA 58.249 39.130 0.00 0.00 0.00 2.57
3761 4436 4.357142 GACCGTTCTAAACATCGCTATCA 58.643 43.478 0.00 0.00 0.00 2.15
3762 4437 3.734735 GGACCGTTCTAAACATCGCTATC 59.265 47.826 0.00 0.00 0.00 2.08
3763 4438 3.131577 TGGACCGTTCTAAACATCGCTAT 59.868 43.478 0.00 0.00 0.00 2.97
3764 4439 2.492881 TGGACCGTTCTAAACATCGCTA 59.507 45.455 0.00 0.00 0.00 4.26
3765 4440 1.274167 TGGACCGTTCTAAACATCGCT 59.726 47.619 0.00 0.00 0.00 4.93
3766 4441 1.717194 TGGACCGTTCTAAACATCGC 58.283 50.000 0.00 0.00 0.00 4.58
3767 4442 4.939509 AAATGGACCGTTCTAAACATCG 57.060 40.909 0.00 0.00 0.00 3.84
3768 4443 6.072119 AGGAAAAATGGACCGTTCTAAACATC 60.072 38.462 0.00 0.00 0.00 3.06
3769 4444 5.773176 AGGAAAAATGGACCGTTCTAAACAT 59.227 36.000 0.00 0.00 0.00 2.71
3771 4446 5.700722 AGGAAAAATGGACCGTTCTAAAC 57.299 39.130 0.00 0.00 0.00 2.01
3773 4448 5.378332 TCAAGGAAAAATGGACCGTTCTAA 58.622 37.500 0.00 0.00 0.00 2.10
3774 4449 4.975631 TCAAGGAAAAATGGACCGTTCTA 58.024 39.130 0.00 0.00 0.00 2.10
3775 4450 3.827722 TCAAGGAAAAATGGACCGTTCT 58.172 40.909 0.00 0.00 0.00 3.01
3800 4496 9.364302 AGGTATTCCCATCAAAAGGGTATATAT 57.636 33.333 0.00 0.00 46.82 0.86
3857 4553 2.325082 ACGCAGAAACCGATGCACC 61.325 57.895 0.00 0.00 42.68 5.01
3867 4563 1.804151 GCACCTATGTTCACGCAGAAA 59.196 47.619 0.00 0.00 38.13 2.52
3872 4568 1.011968 TGACGCACCTATGTTCACGC 61.012 55.000 0.00 0.00 0.00 5.34
3881 4577 0.390603 CCGTGGAAATGACGCACCTA 60.391 55.000 0.00 0.00 35.45 3.08
3883 4579 2.867472 CCGTGGAAATGACGCACC 59.133 61.111 0.00 0.00 35.45 5.01
3888 4596 2.359478 ACCGGCCGTGGAAATGAC 60.359 61.111 26.12 0.00 0.00 3.06
3898 4606 3.186047 GTTCACGATCACCGGCCG 61.186 66.667 21.04 21.04 43.93 6.13
3923 4631 2.571202 TCTGTCCATCTGGCATTGTGTA 59.429 45.455 0.00 0.00 34.44 2.90
3938 4646 2.327002 TATGTACGCCGCGTCTGTCC 62.327 60.000 23.94 7.06 41.54 4.02
3948 4656 6.663944 AAACTCTCTTCATTTATGTACGCC 57.336 37.500 0.00 0.00 0.00 5.68
4004 4712 0.409484 ACCCCCACCTCTTCATTTGG 59.591 55.000 0.00 0.00 0.00 3.28
4008 4716 2.971598 CGCACCCCCACCTCTTCAT 61.972 63.158 0.00 0.00 0.00 2.57
4020 4728 0.741915 TCAAAGAACCAAACGCACCC 59.258 50.000 0.00 0.00 0.00 4.61
4021 4729 1.133407 TGTCAAAGAACCAAACGCACC 59.867 47.619 0.00 0.00 0.00 5.01
4022 4730 2.553079 TGTCAAAGAACCAAACGCAC 57.447 45.000 0.00 0.00 0.00 5.34
4023 4731 3.577649 TTTGTCAAAGAACCAAACGCA 57.422 38.095 0.00 0.00 0.00 5.24
4024 4732 4.912528 TTTTTGTCAAAGAACCAAACGC 57.087 36.364 0.00 0.00 0.00 4.84
4056 4764 2.700329 GCAAGCCTAGCCTAGCAAG 58.300 57.895 0.00 0.00 0.00 4.01
4057 4765 4.963878 GCAAGCCTAGCCTAGCAA 57.036 55.556 0.00 0.00 0.00 3.91
4064 4772 0.675522 TACCAAACGGCAAGCCTAGC 60.676 55.000 9.73 0.00 0.00 3.42
4065 4773 1.369625 CTACCAAACGGCAAGCCTAG 58.630 55.000 9.73 0.00 0.00 3.02
4066 4774 0.675522 GCTACCAAACGGCAAGCCTA 60.676 55.000 9.73 0.00 32.26 3.93
4067 4775 1.971695 GCTACCAAACGGCAAGCCT 60.972 57.895 9.73 0.00 32.26 4.58
4068 4776 2.566529 GCTACCAAACGGCAAGCC 59.433 61.111 0.00 0.00 32.26 4.35
4069 4777 2.175811 CGCTACCAAACGGCAAGC 59.824 61.111 0.00 0.00 34.15 4.01
4070 4778 2.175811 GCGCTACCAAACGGCAAG 59.824 61.111 0.00 0.00 0.00 4.01
4071 4779 2.592001 TGCGCTACCAAACGGCAA 60.592 55.556 9.73 0.00 0.00 4.52
4072 4780 3.047280 CTGCGCTACCAAACGGCA 61.047 61.111 9.73 0.00 0.00 5.69
4080 4788 0.594284 GTACGATGGTCTGCGCTACC 60.594 60.000 21.27 21.27 37.53 3.18
4082 4790 1.091197 TCGTACGATGGTCTGCGCTA 61.091 55.000 15.28 0.00 0.00 4.26
4084 4792 1.269444 GATCGTACGATGGTCTGCGC 61.269 60.000 33.86 13.85 34.60 6.09
4085 4793 0.308068 AGATCGTACGATGGTCTGCG 59.692 55.000 33.86 0.00 34.60 5.18
4086 4794 2.120232 CAAGATCGTACGATGGTCTGC 58.880 52.381 33.86 18.35 34.60 4.26
4089 4797 1.868519 GCCCAAGATCGTACGATGGTC 60.869 57.143 33.86 20.89 34.60 4.02
4090 4798 0.104304 GCCCAAGATCGTACGATGGT 59.896 55.000 33.86 18.41 34.60 3.55
4091 4799 0.600255 GGCCCAAGATCGTACGATGG 60.600 60.000 33.86 28.07 34.60 3.51
4092 4800 0.939577 CGGCCCAAGATCGTACGATG 60.940 60.000 33.86 21.23 34.60 3.84
4093 4801 1.362717 CGGCCCAAGATCGTACGAT 59.637 57.895 29.79 29.79 37.59 3.73
4094 4802 1.597797 AACGGCCCAAGATCGTACGA 61.598 55.000 21.93 21.93 36.01 3.43
4095 4803 0.738412 AAACGGCCCAAGATCGTACG 60.738 55.000 9.53 9.53 36.01 3.67
4096 4804 0.725117 CAAACGGCCCAAGATCGTAC 59.275 55.000 0.00 0.00 36.01 3.67
4098 4806 2.332654 GCAAACGGCCCAAGATCGT 61.333 57.895 0.00 0.00 38.89 3.73
4099 4807 2.485122 GCAAACGGCCCAAGATCG 59.515 61.111 0.00 0.00 36.11 3.69
4100 4808 2.253414 GACGCAAACGGCCCAAGATC 62.253 60.000 0.00 0.00 43.48 2.75
4101 4809 2.282180 ACGCAAACGGCCCAAGAT 60.282 55.556 0.00 0.00 46.04 2.40
4102 4810 2.975799 GACGCAAACGGCCCAAGA 60.976 61.111 0.00 0.00 43.48 3.02
4120 4828 2.033141 TGTCAGCCCAAGAGCAGC 59.967 61.111 0.00 0.00 34.23 5.25
4140 4848 4.856801 CGGGTCTGGGCATTCCGG 62.857 72.222 0.00 0.00 43.43 5.14
4141 4849 4.096003 ACGGGTCTGGGCATTCCG 62.096 66.667 0.00 0.00 45.42 4.30
4142 4850 2.124695 GACGGGTCTGGGCATTCC 60.125 66.667 0.00 0.00 0.00 3.01
4143 4851 1.952102 TACGACGGGTCTGGGCATTC 61.952 60.000 0.00 0.00 0.00 2.67
4144 4852 1.546589 TTACGACGGGTCTGGGCATT 61.547 55.000 0.00 0.00 0.00 3.56
4145 4853 1.985662 TTACGACGGGTCTGGGCAT 60.986 57.895 0.00 0.00 0.00 4.40
4146 4854 2.601067 TTACGACGGGTCTGGGCA 60.601 61.111 0.00 0.00 0.00 5.36
4147 4855 2.125793 GTTACGACGGGTCTGGGC 60.126 66.667 0.00 0.00 0.00 5.36
4148 4856 2.180017 CGTTACGACGGGTCTGGG 59.820 66.667 0.00 0.00 45.32 4.45
4158 4866 2.429571 GCCAGACGCACGTTACGA 60.430 61.111 13.03 0.00 37.47 3.43
4175 4883 4.814294 GTACACCCTCCGCTGCCG 62.814 72.222 0.00 0.00 0.00 5.69
4177 4885 0.676782 ATTTGTACACCCTCCGCTGC 60.677 55.000 0.00 0.00 0.00 5.25
4178 4886 1.086696 CATTTGTACACCCTCCGCTG 58.913 55.000 0.00 0.00 0.00 5.18
4182 4900 2.486592 CGAAACCATTTGTACACCCTCC 59.513 50.000 0.00 0.00 0.00 4.30
4188 4906 4.202030 GGACCAAACGAAACCATTTGTACA 60.202 41.667 0.00 0.00 34.60 2.90
4191 4909 2.101750 GGGACCAAACGAAACCATTTGT 59.898 45.455 0.00 0.00 34.60 2.83
4201 4919 2.738480 CGAGGTGGGACCAAACGA 59.262 61.111 0.00 0.00 41.95 3.85
4220 4938 0.911525 CCCCTCTCTTCCTCAGCCAA 60.912 60.000 0.00 0.00 0.00 4.52
4222 4940 1.002274 TCCCCTCTCTTCCTCAGCC 59.998 63.158 0.00 0.00 0.00 4.85
4230 4948 1.313129 GAGCTCCCTCCCCTCTCTT 59.687 63.158 0.87 0.00 31.68 2.85
4238 4956 2.438800 TATATAGCCGAGCTCCCTCC 57.561 55.000 8.47 0.00 40.44 4.30
4242 4960 2.691011 CCCTCTTATATAGCCGAGCTCC 59.309 54.545 8.47 0.00 40.44 4.70
4246 4964 5.587043 CACTACTCCCTCTTATATAGCCGAG 59.413 48.000 0.00 0.00 0.00 4.63
4248 4966 4.641094 CCACTACTCCCTCTTATATAGCCG 59.359 50.000 0.00 0.00 0.00 5.52
4254 4972 3.498121 CGCTCCCACTACTCCCTCTTATA 60.498 52.174 0.00 0.00 0.00 0.98
4262 4980 1.255667 TTCACCGCTCCCACTACTCC 61.256 60.000 0.00 0.00 0.00 3.85
4264 4982 0.608640 CTTTCACCGCTCCCACTACT 59.391 55.000 0.00 0.00 0.00 2.57
4267 4985 2.750350 CCTTTCACCGCTCCCACT 59.250 61.111 0.00 0.00 0.00 4.00
4271 4989 3.423154 CGTGCCTTTCACCGCTCC 61.423 66.667 0.00 0.00 42.69 4.70
4272 4990 4.090057 GCGTGCCTTTCACCGCTC 62.090 66.667 0.00 0.00 42.69 5.03
4275 4993 4.389576 GCTGCGTGCCTTTCACCG 62.390 66.667 0.00 0.00 42.69 4.94
4277 4995 2.253452 CAGCTGCGTGCCTTTCAC 59.747 61.111 0.00 0.00 44.23 3.18


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

AutoCloner maintained by Alex Coulton.