Multiple sequence alignment - TraesCS7D01G224800

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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 TraesCS7D01G224800 chr7D 100.000 4972 0 0 1 4972 185004729 184999758 0.000000e+00 9182
1 TraesCS7D01G224800 chr7B 93.418 4421 180 35 1 4319 327146321 327141910 0.000000e+00 6449
2 TraesCS7D01G224800 chr7B 94.419 215 12 0 4713 4927 327141589 327141375 1.030000e-86 331
3 TraesCS7D01G224800 chr7B 82.927 287 37 8 4689 4969 722435686 722435406 1.070000e-61 248
4 TraesCS7D01G224800 chr7A 93.547 3580 177 14 794 4322 192448003 192444427 0.000000e+00 5282
5 TraesCS7D01G224800 chr7A 91.961 821 50 8 1 809 192448836 192448020 0.000000e+00 1136
6 TraesCS7D01G224800 chr7A 82.686 283 42 5 4689 4969 720206647 720206924 1.380000e-60 244
7 TraesCS7D01G224800 chr3D 86.713 286 31 4 4689 4968 503044287 503044003 1.340000e-80 311
8 TraesCS7D01G224800 chr3A 88.462 260 23 4 4689 4942 641871503 641871245 1.740000e-79 307
9 TraesCS7D01G224800 chr3A 83.630 281 39 5 4689 4968 83956375 83956649 1.780000e-64 257
10 TraesCS7D01G224800 chr2D 84.722 288 33 8 4689 4971 616432432 616432713 1.360000e-70 278
11 TraesCS7D01G224800 chr1B 84.155 284 39 5 4689 4969 484401260 484400980 2.280000e-68 270
12 TraesCS7D01G224800 chr1D 82.781 302 43 8 4675 4968 361938754 361938454 1.370000e-65 261
13 TraesCS7D01G224800 chr6A 77.636 313 44 15 4672 4971 337578205 337578504 3.080000e-37 167
14 TraesCS7D01G224800 chr6D 76.817 289 46 11 4689 4969 242226085 242225810 5.190000e-30 143


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 TraesCS7D01G224800 chr7D 184999758 185004729 4971 True 9182 9182 100.0000 1 4972 1 chr7D.!!$R1 4971
1 TraesCS7D01G224800 chr7B 327141375 327146321 4946 True 3390 6449 93.9185 1 4927 2 chr7B.!!$R2 4926
2 TraesCS7D01G224800 chr7A 192444427 192448836 4409 True 3209 5282 92.7540 1 4322 2 chr7A.!!$R1 4321

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
422 441 0.250858 TCCATCTGTGCCAAGGTGTG 60.251 55.000 0.00 0.00 0.00 3.82 F
426 445 0.254462 TCTGTGCCAAGGTGTGACAA 59.746 50.000 0.00 0.00 0.00 3.18 F
913 975 0.438830 GCGTTGATGTCGTCAGGTTC 59.561 55.000 0.00 0.00 38.29 3.62 F
1023 1085 2.828549 GGCGGCATTACCTGTGGG 60.829 66.667 3.07 0.00 35.61 4.61 F
2409 2506 3.304928 CCACACAAGAAAGGAGCATGTTC 60.305 47.826 0.04 0.04 0.00 3.18 F
3580 3729 0.548510 GCCTAGGGCTGATGTTTCCT 59.451 55.000 11.72 0.00 46.69 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1491 1570 0.687354 AGAATGACGTGGGAACTGCT 59.313 50.000 0.00 0.00 0.00 4.24 R
1503 1582 3.124297 CACAGCGAGAGGAAAAGAATGAC 59.876 47.826 0.00 0.00 0.00 3.06 R
2445 2542 0.108898 CTCCAGGAGCAGTGACTTCG 60.109 60.000 2.60 0.00 0.00 3.79 R
2674 2771 1.822371 TCTATTACTGTGTGAGCGCCA 59.178 47.619 2.29 0.00 0.00 5.69 R
3585 3734 0.183492 GGGGTCAAGAGCATATGCCA 59.817 55.000 23.96 0.52 43.38 4.92 R
4630 4820 0.038159 GCGGCTACACAGACAACTCT 60.038 55.000 0.00 0.00 0.00 3.24 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
92 104 0.749818 CTCTCGCCACTGCTCTCCTA 60.750 60.000 0.00 0.00 34.43 2.94
261 279 2.788807 TGCTATCTCTTCTCCTCCTCCT 59.211 50.000 0.00 0.00 0.00 3.69
403 422 0.842635 GGGGATCTCCACTTCATGCT 59.157 55.000 6.79 0.00 36.20 3.79
404 423 1.202746 GGGGATCTCCACTTCATGCTC 60.203 57.143 6.79 0.00 36.20 4.26
413 432 1.400846 CACTTCATGCTCCATCTGTGC 59.599 52.381 0.00 0.00 0.00 4.57
414 433 1.022735 CTTCATGCTCCATCTGTGCC 58.977 55.000 0.00 0.00 32.45 5.01
416 435 0.328926 TCATGCTCCATCTGTGCCAA 59.671 50.000 0.00 0.00 32.45 4.52
419 438 1.001641 GCTCCATCTGTGCCAAGGT 60.002 57.895 0.00 0.00 0.00 3.50
422 441 0.250858 TCCATCTGTGCCAAGGTGTG 60.251 55.000 0.00 0.00 0.00 3.82
423 442 0.250858 CCATCTGTGCCAAGGTGTGA 60.251 55.000 0.00 0.00 0.00 3.58
426 445 0.254462 TCTGTGCCAAGGTGTGACAA 59.746 50.000 0.00 0.00 0.00 3.18
552 571 2.357836 CTGCTTGGCCAGATGGGT 59.642 61.111 5.11 0.00 39.65 4.51
565 584 3.605749 ATGGGTCCGGTCAACTGCG 62.606 63.158 0.00 0.00 0.00 5.18
679 702 0.463833 GTGGGATCCCCTAGCGTTTG 60.464 60.000 28.58 0.00 45.70 2.93
681 704 1.632965 GGGATCCCCTAGCGTTTGGT 61.633 60.000 21.42 0.00 41.34 3.67
686 709 0.604511 CCCCTAGCGTTTGGTCGTTT 60.605 55.000 0.00 0.00 0.00 3.60
699 722 7.117454 CGTTTGGTCGTTTAGATGTCATTATC 58.883 38.462 0.00 0.00 0.00 1.75
783 812 3.897505 GGTGCTGCTAATTTGGGGATAAT 59.102 43.478 0.00 0.00 0.00 1.28
891 953 1.900016 GGGTGGGTTTGGTTCGACC 60.900 63.158 0.00 0.00 39.22 4.79
903 965 0.865769 GTTCGACCAAGCGTTGATGT 59.134 50.000 0.00 0.00 34.69 3.06
913 975 0.438830 GCGTTGATGTCGTCAGGTTC 59.561 55.000 0.00 0.00 38.29 3.62
927 989 3.817647 GTCAGGTTCAGAAGTGCATTTCT 59.182 43.478 17.94 17.94 37.90 2.52
957 1019 5.552178 AGAGTTCTAGTTTGGTAAGCAAGG 58.448 41.667 0.00 0.00 0.00 3.61
1023 1085 2.828549 GGCGGCATTACCTGTGGG 60.829 66.667 3.07 0.00 35.61 4.61
1051 1113 3.378112 GCTGCAGAAATTACAGGTATGCA 59.622 43.478 20.43 0.00 39.67 3.96
1055 1127 4.037208 GCAGAAATTACAGGTATGCAGCAT 59.963 41.667 13.73 13.73 32.58 3.79
1115 1194 6.015603 TGTCAACTTGGATTGTGCAATTGATA 60.016 34.615 10.34 0.00 0.00 2.15
1491 1570 5.758296 CGGCCTATGAAGCTTTTCTGTATTA 59.242 40.000 0.00 0.00 0.00 0.98
1503 1582 3.520290 TCTGTATTAGCAGTTCCCACG 57.480 47.619 0.00 0.00 37.70 4.94
1581 1660 6.775939 ATGATAACTCACTATGAATGCGTG 57.224 37.500 0.00 0.00 33.22 5.34
2409 2506 3.304928 CCACACAAGAAAGGAGCATGTTC 60.305 47.826 0.04 0.04 0.00 3.18
2674 2771 4.469227 ACTGAGTTGGAAGACATCTATGCT 59.531 41.667 0.00 0.00 0.00 3.79
2677 2774 2.615912 GTTGGAAGACATCTATGCTGGC 59.384 50.000 0.00 0.00 0.00 4.85
2698 2795 3.673594 GCGCTCACACAGTAATAGACACT 60.674 47.826 0.00 0.00 0.00 3.55
2786 2883 6.692849 TTGCAGATATGGAAGGTCAGATAT 57.307 37.500 0.00 0.00 0.00 1.63
2854 2951 5.534207 AAGTTGAAAAATGGATGTCTGCA 57.466 34.783 0.00 0.00 0.00 4.41
3239 3387 3.802685 GTCTGTCCTTTATGTATGACGGC 59.197 47.826 0.00 0.00 34.76 5.68
3471 3619 6.767524 TTGATTGTCTGGTTTGTACACTTT 57.232 33.333 0.00 0.00 0.00 2.66
3533 3682 4.219944 GGTAGGAAAAATGGAACTGGGAAC 59.780 45.833 0.00 0.00 0.00 3.62
3534 3683 3.922375 AGGAAAAATGGAACTGGGAACA 58.078 40.909 0.00 0.00 39.59 3.18
3579 3728 3.102090 GCCTAGGGCTGATGTTTCC 57.898 57.895 11.72 0.00 46.69 3.13
3580 3729 0.548510 GCCTAGGGCTGATGTTTCCT 59.451 55.000 11.72 0.00 46.69 3.36
3585 3734 4.141390 CCTAGGGCTGATGTTTCCTTATGT 60.141 45.833 0.00 0.00 0.00 2.29
3586 3735 3.624777 AGGGCTGATGTTTCCTTATGTG 58.375 45.455 0.00 0.00 0.00 3.21
3605 3754 0.183492 GGCATATGCTCTTGACCCCA 59.817 55.000 26.12 0.00 41.70 4.96
3611 3760 2.673775 TGCTCTTGACCCCAATTTCA 57.326 45.000 0.00 0.00 0.00 2.69
3612 3761 2.517959 TGCTCTTGACCCCAATTTCAG 58.482 47.619 0.00 0.00 0.00 3.02
3619 3768 5.476599 TCTTGACCCCAATTTCAGTAACATG 59.523 40.000 0.00 0.00 0.00 3.21
3622 3771 6.015918 TGACCCCAATTTCAGTAACATGAAT 58.984 36.000 0.00 0.00 38.90 2.57
3638 3787 5.786311 ACATGAATTCTCCATTTTGTGTGG 58.214 37.500 7.05 0.00 38.11 4.17
3689 3842 3.062763 CGAGCAGAAACTGAACACTGAT 58.937 45.455 2.81 0.00 32.44 2.90
3737 3890 2.363975 CCCTAACAGGCCGGCTACA 61.364 63.158 28.56 6.49 32.73 2.74
3761 3914 0.996583 AGAAGATACCCGGCCCAAAA 59.003 50.000 0.00 0.00 0.00 2.44
3767 3920 0.336737 TACCCGGCCCAAAATCCAAT 59.663 50.000 0.00 0.00 0.00 3.16
3806 3959 0.455410 CTCCTCCGAGCAGAAGACTG 59.545 60.000 0.00 0.00 45.91 3.51
3884 4037 4.814294 ACGAAGGCGGCGTCATCC 62.814 66.667 23.37 3.21 43.17 3.51
4097 4251 3.574396 AGGGAGTATATGTGACGTCCATG 59.426 47.826 22.20 0.00 0.00 3.66
4271 4425 7.090953 AGTCGTTGAAATAACCTTTTTGTGA 57.909 32.000 0.00 0.00 0.00 3.58
4278 4432 2.452600 AACCTTTTTGTGAGCCCTGA 57.547 45.000 0.00 0.00 0.00 3.86
4322 4477 6.813152 CCTATTAGCATGGTTTTTGTTTCCTG 59.187 38.462 1.12 0.00 0.00 3.86
4326 4481 2.977772 TGGTTTTTGTTTCCTGCCTG 57.022 45.000 0.00 0.00 0.00 4.85
4327 4482 1.484240 TGGTTTTTGTTTCCTGCCTGG 59.516 47.619 0.00 0.00 37.10 4.45
4328 4483 1.581934 GTTTTTGTTTCCTGCCTGGC 58.418 50.000 12.87 12.87 35.26 4.85
4329 4484 0.467804 TTTTTGTTTCCTGCCTGGCC 59.532 50.000 17.53 0.00 35.26 5.36
4330 4485 0.689080 TTTTGTTTCCTGCCTGGCCA 60.689 50.000 17.53 4.71 35.26 5.36
4331 4486 0.471591 TTTGTTTCCTGCCTGGCCAT 60.472 50.000 17.53 0.00 35.26 4.40
4332 4487 0.471591 TTGTTTCCTGCCTGGCCATT 60.472 50.000 17.53 0.00 35.26 3.16
4333 4488 1.186917 TGTTTCCTGCCTGGCCATTG 61.187 55.000 17.53 0.98 35.26 2.82
4334 4489 2.285024 TTTCCTGCCTGGCCATTGC 61.285 57.895 17.53 18.07 35.26 3.56
4345 4500 3.403936 GCCATTGCCTCGTAATCCT 57.596 52.632 0.00 0.00 0.00 3.24
4346 4501 2.543777 GCCATTGCCTCGTAATCCTA 57.456 50.000 0.00 0.00 0.00 2.94
4347 4502 3.059352 GCCATTGCCTCGTAATCCTAT 57.941 47.619 0.00 0.00 0.00 2.57
4348 4503 3.003480 GCCATTGCCTCGTAATCCTATC 58.997 50.000 0.00 0.00 0.00 2.08
4349 4504 3.557054 GCCATTGCCTCGTAATCCTATCA 60.557 47.826 0.00 0.00 0.00 2.15
4350 4505 4.248859 CCATTGCCTCGTAATCCTATCAG 58.751 47.826 0.00 0.00 0.00 2.90
4351 4506 3.386768 TTGCCTCGTAATCCTATCAGC 57.613 47.619 0.00 0.00 0.00 4.26
4352 4507 2.316108 TGCCTCGTAATCCTATCAGCA 58.684 47.619 0.00 0.00 0.00 4.41
4353 4508 2.899900 TGCCTCGTAATCCTATCAGCAT 59.100 45.455 0.00 0.00 0.00 3.79
4354 4509 3.257393 GCCTCGTAATCCTATCAGCATG 58.743 50.000 0.00 0.00 37.54 4.06
4355 4510 3.854666 CCTCGTAATCCTATCAGCATGG 58.145 50.000 0.00 0.00 36.16 3.66
4356 4511 3.259374 CCTCGTAATCCTATCAGCATGGT 59.741 47.826 0.00 0.00 36.16 3.55
4357 4512 4.262635 CCTCGTAATCCTATCAGCATGGTT 60.263 45.833 0.00 0.00 36.16 3.67
4358 4513 5.290493 TCGTAATCCTATCAGCATGGTTT 57.710 39.130 0.00 0.00 36.16 3.27
4359 4514 5.680619 TCGTAATCCTATCAGCATGGTTTT 58.319 37.500 0.00 0.00 36.16 2.43
4360 4515 6.119536 TCGTAATCCTATCAGCATGGTTTTT 58.880 36.000 0.00 0.00 36.16 1.94
4361 4516 6.038161 TCGTAATCCTATCAGCATGGTTTTTG 59.962 38.462 0.00 0.00 36.16 2.44
4362 4517 6.183360 CGTAATCCTATCAGCATGGTTTTTGT 60.183 38.462 0.00 0.00 36.16 2.83
4363 4518 6.610075 AATCCTATCAGCATGGTTTTTGTT 57.390 33.333 0.00 0.00 36.16 2.83
4364 4519 6.610075 ATCCTATCAGCATGGTTTTTGTTT 57.390 33.333 0.00 0.00 36.16 2.83
4365 4520 6.024552 TCCTATCAGCATGGTTTTTGTTTC 57.975 37.500 0.00 0.00 36.16 2.78
4366 4521 5.047377 TCCTATCAGCATGGTTTTTGTTTCC 60.047 40.000 0.00 0.00 36.16 3.13
4393 4548 0.950836 TCCCACGTTTGCTTGTGATG 59.049 50.000 0.00 0.00 38.36 3.07
4396 4551 1.269206 CCACGTTTGCTTGTGATGCTT 60.269 47.619 0.00 0.00 38.36 3.91
4405 4560 3.061322 GCTTGTGATGCTTTGATTTGCA 58.939 40.909 0.00 0.00 43.67 4.08
4411 4566 3.194755 TGATGCTTTGATTTGCAGCTGAT 59.805 39.130 20.43 1.01 44.67 2.90
4422 4577 3.682766 CAGCTGATGCCTGACCTAG 57.317 57.895 8.42 0.00 40.80 3.02
4424 4579 2.034878 CAGCTGATGCCTGACCTAGTA 58.965 52.381 8.42 0.00 40.80 1.82
4425 4580 2.035704 CAGCTGATGCCTGACCTAGTAG 59.964 54.545 8.42 0.00 40.80 2.57
4426 4581 2.091610 AGCTGATGCCTGACCTAGTAGA 60.092 50.000 0.00 0.00 40.80 2.59
4427 4582 2.295909 GCTGATGCCTGACCTAGTAGAG 59.704 54.545 0.00 0.00 0.00 2.43
4428 4583 3.826524 CTGATGCCTGACCTAGTAGAGA 58.173 50.000 0.00 0.00 0.00 3.10
4429 4584 3.820467 CTGATGCCTGACCTAGTAGAGAG 59.180 52.174 0.00 0.00 0.00 3.20
4431 4586 3.284793 TGCCTGACCTAGTAGAGAGTC 57.715 52.381 0.00 0.00 0.00 3.36
4432 4587 2.847449 TGCCTGACCTAGTAGAGAGTCT 59.153 50.000 0.00 0.00 0.00 3.24
4433 4588 3.118186 TGCCTGACCTAGTAGAGAGTCTC 60.118 52.174 12.54 12.54 0.00 3.36
4434 4589 3.135895 GCCTGACCTAGTAGAGAGTCTCT 59.864 52.174 25.51 25.51 43.83 3.10
4435 4590 4.345837 GCCTGACCTAGTAGAGAGTCTCTA 59.654 50.000 23.38 23.38 41.50 2.43
4444 4599 3.380471 AGAGAGTCTCTACATGTGGCT 57.620 47.619 21.42 0.00 39.28 4.75
4445 4600 3.023119 AGAGAGTCTCTACATGTGGCTG 58.977 50.000 21.42 2.16 39.28 4.85
4446 4601 3.020274 GAGAGTCTCTACATGTGGCTGA 58.980 50.000 13.17 4.67 0.00 4.26
4447 4602 3.636300 GAGAGTCTCTACATGTGGCTGAT 59.364 47.826 13.17 0.00 0.00 2.90
4448 4603 3.636300 AGAGTCTCTACATGTGGCTGATC 59.364 47.826 9.11 2.66 0.00 2.92
4449 4604 3.369175 AGTCTCTACATGTGGCTGATCA 58.631 45.455 9.11 0.00 0.00 2.92
4450 4605 3.131933 AGTCTCTACATGTGGCTGATCAC 59.868 47.826 9.11 2.36 38.09 3.06
4456 4611 2.144952 TGTGGCTGATCACACCAGT 58.855 52.632 12.10 0.00 42.05 4.00
4457 4612 1.347062 TGTGGCTGATCACACCAGTA 58.653 50.000 12.10 3.63 42.05 2.74
4458 4613 1.696884 TGTGGCTGATCACACCAGTAA 59.303 47.619 12.10 0.81 42.05 2.24
4459 4614 2.105649 TGTGGCTGATCACACCAGTAAA 59.894 45.455 12.10 0.00 42.05 2.01
4460 4615 3.146066 GTGGCTGATCACACCAGTAAAA 58.854 45.455 12.10 0.00 37.57 1.52
4461 4616 3.058224 GTGGCTGATCACACCAGTAAAAC 60.058 47.826 12.10 0.00 37.57 2.43
4462 4617 3.146066 GGCTGATCACACCAGTAAAACA 58.854 45.455 5.32 0.00 34.29 2.83
4463 4618 3.568007 GGCTGATCACACCAGTAAAACAA 59.432 43.478 5.32 0.00 34.29 2.83
4464 4619 4.537015 GCTGATCACACCAGTAAAACAAC 58.463 43.478 0.00 0.00 34.29 3.32
4465 4620 4.036262 GCTGATCACACCAGTAAAACAACA 59.964 41.667 0.00 0.00 34.29 3.33
4466 4621 5.493133 TGATCACACCAGTAAAACAACAC 57.507 39.130 0.00 0.00 0.00 3.32
4467 4622 5.189928 TGATCACACCAGTAAAACAACACT 58.810 37.500 0.00 0.00 0.00 3.55
4468 4623 6.350103 TGATCACACCAGTAAAACAACACTA 58.650 36.000 0.00 0.00 0.00 2.74
4469 4624 6.259167 TGATCACACCAGTAAAACAACACTAC 59.741 38.462 0.00 0.00 0.00 2.73
4470 4625 5.489249 TCACACCAGTAAAACAACACTACA 58.511 37.500 0.00 0.00 0.00 2.74
4471 4626 5.938710 TCACACCAGTAAAACAACACTACAA 59.061 36.000 0.00 0.00 0.00 2.41
4472 4627 6.600032 TCACACCAGTAAAACAACACTACAAT 59.400 34.615 0.00 0.00 0.00 2.71
4473 4628 6.910433 CACACCAGTAAAACAACACTACAATC 59.090 38.462 0.00 0.00 0.00 2.67
4474 4629 6.600032 ACACCAGTAAAACAACACTACAATCA 59.400 34.615 0.00 0.00 0.00 2.57
4475 4630 7.284489 ACACCAGTAAAACAACACTACAATCAT 59.716 33.333 0.00 0.00 0.00 2.45
4476 4631 7.591057 CACCAGTAAAACAACACTACAATCATG 59.409 37.037 0.00 0.00 0.00 3.07
4477 4632 7.500892 ACCAGTAAAACAACACTACAATCATGA 59.499 33.333 0.00 0.00 0.00 3.07
4478 4633 7.803189 CCAGTAAAACAACACTACAATCATGAC 59.197 37.037 0.00 0.00 0.00 3.06
4479 4634 7.530525 CAGTAAAACAACACTACAATCATGACG 59.469 37.037 0.00 0.00 0.00 4.35
4480 4635 6.612247 AAAACAACACTACAATCATGACGA 57.388 33.333 0.00 0.00 0.00 4.20
4481 4636 6.612247 AAACAACACTACAATCATGACGAA 57.388 33.333 0.00 0.00 0.00 3.85
4482 4637 5.591643 ACAACACTACAATCATGACGAAC 57.408 39.130 0.00 0.00 0.00 3.95
4483 4638 5.297547 ACAACACTACAATCATGACGAACT 58.702 37.500 0.00 0.00 0.00 3.01
4484 4639 6.452242 ACAACACTACAATCATGACGAACTA 58.548 36.000 0.00 0.00 0.00 2.24
4485 4640 7.097192 ACAACACTACAATCATGACGAACTAT 58.903 34.615 0.00 0.00 0.00 2.12
4486 4641 7.063426 ACAACACTACAATCATGACGAACTATG 59.937 37.037 0.00 0.00 0.00 2.23
4487 4642 5.520288 ACACTACAATCATGACGAACTATGC 59.480 40.000 0.00 0.00 0.00 3.14
4488 4643 4.740205 ACTACAATCATGACGAACTATGCG 59.260 41.667 0.00 0.00 0.00 4.73
4489 4644 3.780902 ACAATCATGACGAACTATGCGA 58.219 40.909 0.00 0.00 0.00 5.10
4490 4645 4.371786 ACAATCATGACGAACTATGCGAT 58.628 39.130 0.00 0.00 0.00 4.58
4491 4646 4.209911 ACAATCATGACGAACTATGCGATG 59.790 41.667 0.00 0.00 0.00 3.84
4492 4647 3.708563 TCATGACGAACTATGCGATGA 57.291 42.857 0.00 0.00 0.00 2.92
4493 4648 4.243007 TCATGACGAACTATGCGATGAT 57.757 40.909 0.00 0.00 0.00 2.45
4494 4649 3.983344 TCATGACGAACTATGCGATGATG 59.017 43.478 0.00 0.00 0.00 3.07
4499 4654 4.620982 ACGAACTATGCGATGATGATGAA 58.379 39.130 0.00 0.00 0.00 2.57
4503 4658 6.453922 CGAACTATGCGATGATGATGAAGATG 60.454 42.308 0.00 0.00 0.00 2.90
4549 4704 4.672899 AGGAGCCTTGCCTATTTTAACAA 58.327 39.130 0.00 0.00 32.92 2.83
4554 4709 4.805719 GCCTTGCCTATTTTAACAATGCTC 59.194 41.667 0.00 0.00 32.89 4.26
4556 4711 5.393027 CCTTGCCTATTTTAACAATGCTCGT 60.393 40.000 0.00 0.00 0.00 4.18
4560 4715 5.266242 CCTATTTTAACAATGCTCGTCTGC 58.734 41.667 0.00 0.00 0.00 4.26
4577 4732 2.260247 GCTTGAGCATGACCAAGCA 58.740 52.632 30.64 6.57 41.59 3.91
4578 4733 0.815734 GCTTGAGCATGACCAAGCAT 59.184 50.000 30.64 0.00 41.59 3.79
4579 4734 1.469251 GCTTGAGCATGACCAAGCATG 60.469 52.381 30.64 11.40 46.48 4.06
4580 4735 2.089201 CTTGAGCATGACCAAGCATGA 58.911 47.619 12.49 0.00 46.64 3.07
4581 4736 1.456296 TGAGCATGACCAAGCATGAC 58.544 50.000 8.40 2.74 46.64 3.06
4582 4737 0.737219 GAGCATGACCAAGCATGACC 59.263 55.000 8.40 0.00 46.64 4.02
4585 4740 1.135199 GCATGACCAAGCATGACCTTG 60.135 52.381 8.40 1.07 46.64 3.61
4593 4748 2.409948 AGCATGACCTTGGAGTAAGC 57.590 50.000 0.00 0.00 34.96 3.09
4597 4752 3.209410 CATGACCTTGGAGTAAGCATCC 58.791 50.000 0.00 0.00 34.96 3.51
4618 4773 5.194432 TCCTCTGCTACTTACCTAGTCTTG 58.806 45.833 0.00 0.00 38.33 3.02
4619 4774 4.202070 CCTCTGCTACTTACCTAGTCTTGC 60.202 50.000 0.00 0.00 38.33 4.01
4623 4813 3.447944 GCTACTTACCTAGTCTTGCACCT 59.552 47.826 0.00 0.00 38.33 4.00
4627 4817 5.306394 ACTTACCTAGTCTTGCACCTTTTC 58.694 41.667 0.00 0.00 28.23 2.29
4630 4820 4.532834 ACCTAGTCTTGCACCTTTTCAAA 58.467 39.130 0.00 0.00 0.00 2.69
4645 4835 6.316390 ACCTTTTCAAAGAGTTGTCTGTGTAG 59.684 38.462 0.56 0.00 38.96 2.74
4647 4837 3.728845 TCAAAGAGTTGTCTGTGTAGCC 58.271 45.455 0.00 0.00 38.96 3.93
4660 4850 0.391228 TGTAGCCGCTCACTTGTTCA 59.609 50.000 0.00 0.00 0.00 3.18
4661 4851 1.202592 TGTAGCCGCTCACTTGTTCAA 60.203 47.619 0.00 0.00 0.00 2.69
4662 4852 1.194772 GTAGCCGCTCACTTGTTCAAC 59.805 52.381 0.00 0.00 0.00 3.18
4663 4853 0.179045 AGCCGCTCACTTGTTCAACT 60.179 50.000 0.00 0.00 0.00 3.16
4664 4854 1.070134 AGCCGCTCACTTGTTCAACTA 59.930 47.619 0.00 0.00 0.00 2.24
4665 4855 1.194772 GCCGCTCACTTGTTCAACTAC 59.805 52.381 0.00 0.00 0.00 2.73
4666 4856 1.798813 CCGCTCACTTGTTCAACTACC 59.201 52.381 0.00 0.00 0.00 3.18
4667 4857 1.798813 CGCTCACTTGTTCAACTACCC 59.201 52.381 0.00 0.00 0.00 3.69
4669 4859 3.067833 GCTCACTTGTTCAACTACCCTC 58.932 50.000 0.00 0.00 0.00 4.30
4670 4860 3.665190 CTCACTTGTTCAACTACCCTCC 58.335 50.000 0.00 0.00 0.00 4.30
4671 4861 2.370849 TCACTTGTTCAACTACCCTCCC 59.629 50.000 0.00 0.00 0.00 4.30
4672 4862 1.703513 ACTTGTTCAACTACCCTCCCC 59.296 52.381 0.00 0.00 0.00 4.81
4694 4884 4.296056 CCCCCTCTGTATACTAACCACTT 58.704 47.826 4.17 0.00 0.00 3.16
4697 4887 5.302313 CCCCTCTGTATACTAACCACTTCTC 59.698 48.000 4.17 0.00 0.00 2.87
4698 4888 5.302313 CCCTCTGTATACTAACCACTTCTCC 59.698 48.000 4.17 0.00 0.00 3.71
4699 4889 6.130569 CCTCTGTATACTAACCACTTCTCCT 58.869 44.000 4.17 0.00 0.00 3.69
4701 4891 7.446013 CCTCTGTATACTAACCACTTCTCCTAG 59.554 44.444 4.17 0.00 0.00 3.02
4702 4892 6.771749 TCTGTATACTAACCACTTCTCCTAGC 59.228 42.308 4.17 0.00 0.00 3.42
4703 4893 6.429151 TGTATACTAACCACTTCTCCTAGCA 58.571 40.000 4.17 0.00 0.00 3.49
4704 4894 7.067421 TGTATACTAACCACTTCTCCTAGCAT 58.933 38.462 4.17 0.00 0.00 3.79
4705 4895 4.744795 ACTAACCACTTCTCCTAGCATG 57.255 45.455 0.00 0.00 0.00 4.06
4706 4896 4.353777 ACTAACCACTTCTCCTAGCATGA 58.646 43.478 0.00 0.00 0.00 3.07
4707 4897 4.965532 ACTAACCACTTCTCCTAGCATGAT 59.034 41.667 0.00 0.00 0.00 2.45
4708 4898 6.136857 ACTAACCACTTCTCCTAGCATGATA 58.863 40.000 0.00 0.00 0.00 2.15
4709 4899 5.543507 AACCACTTCTCCTAGCATGATAG 57.456 43.478 11.13 11.13 0.00 2.08
4726 4923 6.691818 GCATGATAGAAGAGCAACAATTCAAG 59.308 38.462 0.00 0.00 0.00 3.02
4729 4926 4.500603 AGAAGAGCAACAATTCAAGCAG 57.499 40.909 0.00 0.00 0.00 4.24
4805 5002 5.592054 TCATAAGGTAGAGCAAGTTCATCG 58.408 41.667 0.00 0.00 0.00 3.84
4836 5033 1.559682 GGTGTCATCCTACCACCACAT 59.440 52.381 3.28 0.00 46.33 3.21
4838 5035 2.236146 GTGTCATCCTACCACCACATCA 59.764 50.000 0.00 0.00 0.00 3.07
4847 5044 1.963515 ACCACCACATCAAAAAGAGGC 59.036 47.619 0.00 0.00 0.00 4.70
4854 5051 5.539955 ACCACATCAAAAAGAGGCTGTAATT 59.460 36.000 0.00 0.00 0.00 1.40
4855 5052 6.095377 CCACATCAAAAAGAGGCTGTAATTC 58.905 40.000 0.00 0.00 0.00 2.17
4869 5066 4.751060 CTGTAATTCTACCACCGCAACTA 58.249 43.478 0.00 0.00 0.00 2.24
4872 5069 3.906720 ATTCTACCACCGCAACTACAT 57.093 42.857 0.00 0.00 0.00 2.29
4897 5094 4.989277 TCAGCGTGAGGGGTTAGTATATA 58.011 43.478 0.00 0.00 0.00 0.86
4901 5098 4.321527 GCGTGAGGGGTTAGTATATACCAC 60.322 50.000 9.32 6.74 38.14 4.16
4927 5124 6.862209 TCATCAAAATATACAGGCCAACAAC 58.138 36.000 5.01 0.00 0.00 3.32
4928 5125 6.435591 TCATCAAAATATACAGGCCAACAACA 59.564 34.615 5.01 0.00 0.00 3.33
4929 5126 6.266168 TCAAAATATACAGGCCAACAACAG 57.734 37.500 5.01 0.00 0.00 3.16
4930 5127 5.772672 TCAAAATATACAGGCCAACAACAGT 59.227 36.000 5.01 0.00 0.00 3.55
4931 5128 6.266558 TCAAAATATACAGGCCAACAACAGTT 59.733 34.615 5.01 0.00 0.00 3.16
4932 5129 6.664428 AAATATACAGGCCAACAACAGTTT 57.336 33.333 5.01 0.00 0.00 2.66
4933 5130 6.664428 AATATACAGGCCAACAACAGTTTT 57.336 33.333 5.01 0.00 0.00 2.43
4934 5131 2.959507 ACAGGCCAACAACAGTTTTC 57.040 45.000 5.01 0.00 0.00 2.29
4935 5132 2.175202 ACAGGCCAACAACAGTTTTCA 58.825 42.857 5.01 0.00 0.00 2.69
4936 5133 2.564947 ACAGGCCAACAACAGTTTTCAA 59.435 40.909 5.01 0.00 0.00 2.69
4937 5134 3.189285 CAGGCCAACAACAGTTTTCAAG 58.811 45.455 5.01 0.00 0.00 3.02
4938 5135 1.933181 GGCCAACAACAGTTTTCAAGC 59.067 47.619 0.00 0.00 0.00 4.01
4939 5136 1.933181 GCCAACAACAGTTTTCAAGCC 59.067 47.619 0.00 0.00 0.00 4.35
4940 5137 2.549926 CCAACAACAGTTTTCAAGCCC 58.450 47.619 0.00 0.00 0.00 5.19
4941 5138 2.168313 CCAACAACAGTTTTCAAGCCCT 59.832 45.455 0.00 0.00 0.00 5.19
4942 5139 3.189285 CAACAACAGTTTTCAAGCCCTG 58.811 45.455 0.00 0.00 0.00 4.45
4943 5140 2.733956 ACAACAGTTTTCAAGCCCTGA 58.266 42.857 0.00 0.00 0.00 3.86
4944 5141 2.427095 ACAACAGTTTTCAAGCCCTGAC 59.573 45.455 0.00 0.00 32.21 3.51
4945 5142 2.689983 CAACAGTTTTCAAGCCCTGACT 59.310 45.455 0.00 0.00 32.21 3.41
4946 5143 3.857157 ACAGTTTTCAAGCCCTGACTA 57.143 42.857 0.00 0.00 32.21 2.59
4947 5144 3.477530 ACAGTTTTCAAGCCCTGACTAC 58.522 45.455 0.00 0.00 32.21 2.73
4948 5145 2.814336 CAGTTTTCAAGCCCTGACTACC 59.186 50.000 0.00 0.00 32.21 3.18
4949 5146 2.441750 AGTTTTCAAGCCCTGACTACCA 59.558 45.455 0.00 0.00 32.21 3.25
4950 5147 3.117663 AGTTTTCAAGCCCTGACTACCAA 60.118 43.478 0.00 0.00 32.21 3.67
4951 5148 3.586470 TTTCAAGCCCTGACTACCAAA 57.414 42.857 0.00 0.00 32.21 3.28
4952 5149 3.586470 TTCAAGCCCTGACTACCAAAA 57.414 42.857 0.00 0.00 32.21 2.44
4953 5150 3.586470 TCAAGCCCTGACTACCAAAAA 57.414 42.857 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 67 0.098728 GCGAGAGTGAGCTGAGACTC 59.901 60.000 0.00 0.00 39.18 3.36
261 279 1.398174 TACAACCCCACCGTGAACGA 61.398 55.000 4.03 0.00 43.02 3.85
403 422 0.250858 CACACCTTGGCACAGATGGA 60.251 55.000 0.00 0.00 42.39 3.41
404 423 0.250858 TCACACCTTGGCACAGATGG 60.251 55.000 0.00 0.00 42.39 3.51
413 432 2.276732 ACCAGATTGTCACACCTTGG 57.723 50.000 0.16 0.16 0.00 3.61
414 433 3.243501 CCAAACCAGATTGTCACACCTTG 60.244 47.826 0.00 0.00 0.00 3.61
416 435 2.586425 CCAAACCAGATTGTCACACCT 58.414 47.619 0.00 0.00 0.00 4.00
419 438 2.305928 CACCCAAACCAGATTGTCACA 58.694 47.619 0.00 0.00 0.00 3.58
422 441 2.955660 TCAACACCCAAACCAGATTGTC 59.044 45.455 0.00 0.00 0.00 3.18
423 442 2.958355 CTCAACACCCAAACCAGATTGT 59.042 45.455 0.00 0.00 0.00 2.71
426 445 2.443255 AGTCTCAACACCCAAACCAGAT 59.557 45.455 0.00 0.00 0.00 2.90
469 488 0.108615 ATCGAGCACCCAAGAGAACG 60.109 55.000 0.00 0.00 0.00 3.95
565 584 1.006688 AAAACATGGAAACCCGCGC 60.007 52.632 0.00 0.00 0.00 6.86
679 702 5.175126 CACCGATAATGACATCTAAACGACC 59.825 44.000 0.00 0.00 0.00 4.79
681 704 5.286438 CCACCGATAATGACATCTAAACGA 58.714 41.667 0.00 0.00 0.00 3.85
686 709 2.969262 TGGCCACCGATAATGACATCTA 59.031 45.455 0.00 0.00 0.00 1.98
699 722 4.127744 ACCCCATGATGGCCACCG 62.128 66.667 8.16 0.00 35.79 4.94
751 776 7.255312 CCCAAATTAGCAGCACCGTAATAATTA 60.255 37.037 0.00 0.00 0.00 1.40
760 789 0.679640 TCCCCAAATTAGCAGCACCG 60.680 55.000 0.00 0.00 0.00 4.94
783 812 9.998106 GAGCCCTATCACTAACTAATGATAAAA 57.002 33.333 0.00 0.00 37.36 1.52
891 953 0.439985 CCTGACGACATCAACGCTTG 59.560 55.000 0.00 0.00 36.69 4.01
903 965 0.750249 TGCACTTCTGAACCTGACGA 59.250 50.000 0.00 0.00 0.00 4.20
913 975 4.753610 TCTCAGACAAGAAATGCACTTCTG 59.246 41.667 11.77 8.29 35.79 3.02
927 989 5.871396 ACCAAACTAGAACTCTCAGACAA 57.129 39.130 0.00 0.00 0.00 3.18
957 1019 3.873952 AGGAGCATCGCTTGAGAATAAAC 59.126 43.478 0.00 0.00 39.88 2.01
1017 1079 1.970114 CTGCAGCAAGGACCCACAG 60.970 63.158 0.00 0.00 0.00 3.66
1023 1085 3.119708 CCTGTAATTTCTGCAGCAAGGAC 60.120 47.826 9.47 7.48 36.49 3.85
1115 1194 4.623932 TTCAGGTAAGAAGCATGTCACT 57.376 40.909 0.00 0.00 0.00 3.41
1469 1548 6.260936 TGCTAATACAGAAAAGCTTCATAGGC 59.739 38.462 0.00 0.00 35.95 3.93
1491 1570 0.687354 AGAATGACGTGGGAACTGCT 59.313 50.000 0.00 0.00 0.00 4.24
1503 1582 3.124297 CACAGCGAGAGGAAAAGAATGAC 59.876 47.826 0.00 0.00 0.00 3.06
2176 2273 8.345565 ACTGTCTTGTCAAGTTTTGATAATGTC 58.654 33.333 12.30 0.00 42.47 3.06
2276 2373 4.497473 TGTAATAAAATAGGGCATGCGC 57.503 40.909 26.04 26.04 37.44 6.09
2348 2445 5.009631 CCCAAAGATCATACAGTTGACCAA 58.990 41.667 0.00 0.00 0.00 3.67
2409 2506 3.261580 TCTGTTGCAGGTAACATGATCG 58.738 45.455 0.00 0.00 39.60 3.69
2445 2542 0.108898 CTCCAGGAGCAGTGACTTCG 60.109 60.000 2.60 0.00 0.00 3.79
2540 2637 3.367395 GGCCAAATAGAGCTGAACAAACC 60.367 47.826 0.00 0.00 0.00 3.27
2674 2771 1.822371 TCTATTACTGTGTGAGCGCCA 59.178 47.619 2.29 0.00 0.00 5.69
2677 2774 3.854240 CAGTGTCTATTACTGTGTGAGCG 59.146 47.826 0.00 0.00 40.43 5.03
2698 2795 2.076207 ATTTCATATGGGCAGCTGCA 57.924 45.000 37.63 20.97 44.36 4.41
2786 2883 4.942761 ATGCTTCTTCCTTTGCTTTTGA 57.057 36.364 0.00 0.00 0.00 2.69
2854 2951 3.151912 AGCCAGCTTTCTTCTTCACAT 57.848 42.857 0.00 0.00 0.00 3.21
2922 3019 2.760092 AGCAAGTTTCAAAACCAGCAGA 59.240 40.909 16.94 0.00 39.90 4.26
2935 3032 4.389890 TTTGTGCATCAGAAGCAAGTTT 57.610 36.364 0.90 0.00 44.64 2.66
3337 3485 4.946160 TCTAAACTGGGGAATGATTGGT 57.054 40.909 0.00 0.00 0.00 3.67
3438 3586 5.894298 ACCAGACAATCAATGCCTATCTA 57.106 39.130 0.00 0.00 0.00 1.98
3440 3588 5.126061 ACAAACCAGACAATCAATGCCTATC 59.874 40.000 0.00 0.00 0.00 2.08
3471 3619 5.827797 ACAGCATCCTAAAAACTGAACTCAA 59.172 36.000 0.00 0.00 32.67 3.02
3533 3682 7.194607 AGTGATGAATCAAGTAGTGTTTGTG 57.805 36.000 0.00 0.00 38.75 3.33
3534 3683 8.150945 ACTAGTGATGAATCAAGTAGTGTTTGT 58.849 33.333 12.56 0.00 37.41 2.83
3579 3728 4.214971 GGTCAAGAGCATATGCCACATAAG 59.785 45.833 23.96 8.19 43.38 1.73
3580 3729 4.136796 GGTCAAGAGCATATGCCACATAA 58.863 43.478 23.96 3.25 43.38 1.90
3585 3734 0.183492 GGGGTCAAGAGCATATGCCA 59.817 55.000 23.96 0.52 43.38 4.92
3586 3735 0.183492 TGGGGTCAAGAGCATATGCC 59.817 55.000 23.96 15.08 43.38 4.40
3611 3760 8.084073 CACACAAAATGGAGAATTCATGTTACT 58.916 33.333 8.44 0.00 31.86 2.24
3612 3761 7.329226 CCACACAAAATGGAGAATTCATGTTAC 59.671 37.037 8.44 0.00 31.86 2.50
3619 3768 3.989817 GCACCACACAAAATGGAGAATTC 59.010 43.478 0.00 0.00 39.87 2.17
3622 3771 2.382882 TGCACCACACAAAATGGAGAA 58.617 42.857 0.00 0.00 39.87 2.87
3638 3787 0.467290 TTTGTTCCTGGGGAGTGCAC 60.467 55.000 9.40 9.40 31.21 4.57
3643 3792 1.866853 GCGCTTTTGTTCCTGGGGAG 61.867 60.000 0.00 0.00 31.21 4.30
3645 3794 0.608035 TAGCGCTTTTGTTCCTGGGG 60.608 55.000 18.68 0.00 0.00 4.96
3689 3842 0.331278 ATCCAAACGGCCCTTCATGA 59.669 50.000 0.00 0.00 0.00 3.07
3722 3875 2.582436 GCTGTAGCCGGCCTGTTA 59.418 61.111 26.15 5.79 36.95 2.41
3737 3890 1.442148 GCCGGGTATCTTCTTCGCT 59.558 57.895 2.18 0.00 0.00 4.93
3806 3959 2.462456 TCTGCTGACCACTGATTGAC 57.538 50.000 0.00 0.00 0.00 3.18
3881 4034 3.178611 GCTCCATTCCCCGGGGAT 61.179 66.667 42.75 28.16 44.74 3.85
3884 4037 3.878667 GAGGCTCCATTCCCCGGG 61.879 72.222 15.80 15.80 0.00 5.73
4097 4251 3.204418 CGAACTACGGAGGGGTCC 58.796 66.667 0.00 0.00 38.46 4.46
4271 4425 1.076485 GGCAATGACCATCAGGGCT 60.076 57.895 0.00 0.00 46.30 5.19
4278 4432 3.059097 AGGATTAGGAGGCAATGACCAT 58.941 45.455 0.00 0.00 0.00 3.55
4327 4482 2.543777 TAGGATTACGAGGCAATGGC 57.456 50.000 0.00 0.00 40.13 4.40
4328 4483 4.248859 CTGATAGGATTACGAGGCAATGG 58.751 47.826 0.00 0.00 0.00 3.16
4329 4484 3.681897 GCTGATAGGATTACGAGGCAATG 59.318 47.826 0.00 0.00 0.00 2.82
4330 4485 3.324846 TGCTGATAGGATTACGAGGCAAT 59.675 43.478 0.00 0.00 0.00 3.56
4331 4486 2.698274 TGCTGATAGGATTACGAGGCAA 59.302 45.455 0.00 0.00 0.00 4.52
4332 4487 2.316108 TGCTGATAGGATTACGAGGCA 58.684 47.619 0.00 0.00 0.00 4.75
4333 4488 3.257393 CATGCTGATAGGATTACGAGGC 58.743 50.000 0.00 0.00 0.00 4.70
4334 4489 3.259374 ACCATGCTGATAGGATTACGAGG 59.741 47.826 0.00 0.00 0.00 4.63
4335 4490 4.527509 ACCATGCTGATAGGATTACGAG 57.472 45.455 0.00 0.00 0.00 4.18
4336 4491 4.955811 AACCATGCTGATAGGATTACGA 57.044 40.909 0.00 0.00 0.00 3.43
4337 4492 6.183360 ACAAAAACCATGCTGATAGGATTACG 60.183 38.462 0.00 0.00 0.00 3.18
4338 4493 7.100458 ACAAAAACCATGCTGATAGGATTAC 57.900 36.000 0.00 0.00 0.00 1.89
4339 4494 7.716799 AACAAAAACCATGCTGATAGGATTA 57.283 32.000 0.00 0.00 0.00 1.75
4340 4495 6.610075 AACAAAAACCATGCTGATAGGATT 57.390 33.333 0.00 0.00 0.00 3.01
4341 4496 6.351286 GGAAACAAAAACCATGCTGATAGGAT 60.351 38.462 0.00 0.00 0.00 3.24
4342 4497 5.047377 GGAAACAAAAACCATGCTGATAGGA 60.047 40.000 0.00 0.00 0.00 2.94
4343 4498 5.047092 AGGAAACAAAAACCATGCTGATAGG 60.047 40.000 0.00 0.00 0.00 2.57
4344 4499 6.029346 AGGAAACAAAAACCATGCTGATAG 57.971 37.500 0.00 0.00 0.00 2.08
4345 4500 6.418057 AAGGAAACAAAAACCATGCTGATA 57.582 33.333 0.00 0.00 0.00 2.15
4346 4501 4.961438 AGGAAACAAAAACCATGCTGAT 57.039 36.364 0.00 0.00 0.00 2.90
4347 4502 4.751767 AAGGAAACAAAAACCATGCTGA 57.248 36.364 0.00 0.00 0.00 4.26
4348 4503 4.635324 ACAAAGGAAACAAAAACCATGCTG 59.365 37.500 0.00 0.00 0.00 4.41
4349 4504 4.842574 ACAAAGGAAACAAAAACCATGCT 58.157 34.783 0.00 0.00 0.00 3.79
4350 4505 5.559427 AACAAAGGAAACAAAAACCATGC 57.441 34.783 0.00 0.00 0.00 4.06
4351 4506 7.026562 GGAAAACAAAGGAAACAAAAACCATG 58.973 34.615 0.00 0.00 0.00 3.66
4352 4507 6.151985 GGGAAAACAAAGGAAACAAAAACCAT 59.848 34.615 0.00 0.00 0.00 3.55
4353 4508 5.473846 GGGAAAACAAAGGAAACAAAAACCA 59.526 36.000 0.00 0.00 0.00 3.67
4354 4509 5.473846 TGGGAAAACAAAGGAAACAAAAACC 59.526 36.000 0.00 0.00 0.00 3.27
4355 4510 6.375377 GTGGGAAAACAAAGGAAACAAAAAC 58.625 36.000 0.00 0.00 0.00 2.43
4356 4511 5.179555 CGTGGGAAAACAAAGGAAACAAAAA 59.820 36.000 0.00 0.00 0.00 1.94
4357 4512 4.691216 CGTGGGAAAACAAAGGAAACAAAA 59.309 37.500 0.00 0.00 0.00 2.44
4358 4513 4.246458 CGTGGGAAAACAAAGGAAACAAA 58.754 39.130 0.00 0.00 0.00 2.83
4359 4514 3.258622 ACGTGGGAAAACAAAGGAAACAA 59.741 39.130 0.00 0.00 0.00 2.83
4360 4515 2.826725 ACGTGGGAAAACAAAGGAAACA 59.173 40.909 0.00 0.00 0.00 2.83
4361 4516 3.513680 ACGTGGGAAAACAAAGGAAAC 57.486 42.857 0.00 0.00 0.00 2.78
4362 4517 4.246458 CAAACGTGGGAAAACAAAGGAAA 58.754 39.130 0.00 0.00 0.00 3.13
4363 4518 3.851098 CAAACGTGGGAAAACAAAGGAA 58.149 40.909 0.00 0.00 0.00 3.36
4364 4519 2.417515 GCAAACGTGGGAAAACAAAGGA 60.418 45.455 0.00 0.00 0.00 3.36
4365 4520 1.930503 GCAAACGTGGGAAAACAAAGG 59.069 47.619 0.00 0.00 0.00 3.11
4366 4521 2.887337 AGCAAACGTGGGAAAACAAAG 58.113 42.857 0.00 0.00 0.00 2.77
4405 4560 2.091610 TCTACTAGGTCAGGCATCAGCT 60.092 50.000 0.00 0.00 41.70 4.24
4411 4566 2.847449 AGACTCTCTACTAGGTCAGGCA 59.153 50.000 0.00 0.00 31.45 4.75
4424 4579 3.023119 CAGCCACATGTAGAGACTCTCT 58.977 50.000 8.64 13.25 43.83 3.10
4425 4580 3.020274 TCAGCCACATGTAGAGACTCTC 58.980 50.000 8.64 0.00 0.00 3.20
4426 4581 3.093057 TCAGCCACATGTAGAGACTCT 57.907 47.619 10.47 10.47 0.00 3.24
4427 4582 3.382865 TGATCAGCCACATGTAGAGACTC 59.617 47.826 0.00 0.00 0.00 3.36
4428 4583 3.131933 GTGATCAGCCACATGTAGAGACT 59.868 47.826 0.00 0.00 37.04 3.24
4429 4584 3.118992 TGTGATCAGCCACATGTAGAGAC 60.119 47.826 0.00 0.00 41.63 3.36
4431 4586 3.531934 TGTGATCAGCCACATGTAGAG 57.468 47.619 0.00 0.00 41.63 2.43
4438 4593 1.347062 TACTGGTGTGATCAGCCACA 58.653 50.000 15.90 0.28 43.98 4.17
4439 4594 2.472695 TTACTGGTGTGATCAGCCAC 57.527 50.000 13.31 10.58 40.84 5.01
4440 4595 3.146066 GTTTTACTGGTGTGATCAGCCA 58.854 45.455 15.70 15.70 40.84 4.75
4441 4596 3.146066 TGTTTTACTGGTGTGATCAGCC 58.854 45.455 0.00 2.07 40.84 4.85
4442 4597 4.036262 TGTTGTTTTACTGGTGTGATCAGC 59.964 41.667 0.00 0.00 41.77 4.26
4443 4598 5.296780 AGTGTTGTTTTACTGGTGTGATCAG 59.703 40.000 0.00 0.00 38.16 2.90
4444 4599 5.189928 AGTGTTGTTTTACTGGTGTGATCA 58.810 37.500 0.00 0.00 0.00 2.92
4445 4600 5.751243 AGTGTTGTTTTACTGGTGTGATC 57.249 39.130 0.00 0.00 0.00 2.92
4446 4601 6.116806 TGTAGTGTTGTTTTACTGGTGTGAT 58.883 36.000 0.00 0.00 0.00 3.06
4447 4602 5.489249 TGTAGTGTTGTTTTACTGGTGTGA 58.511 37.500 0.00 0.00 0.00 3.58
4448 4603 5.804692 TGTAGTGTTGTTTTACTGGTGTG 57.195 39.130 0.00 0.00 0.00 3.82
4449 4604 6.600032 TGATTGTAGTGTTGTTTTACTGGTGT 59.400 34.615 0.00 0.00 0.00 4.16
4450 4605 7.022055 TGATTGTAGTGTTGTTTTACTGGTG 57.978 36.000 0.00 0.00 0.00 4.17
4451 4606 7.500892 TCATGATTGTAGTGTTGTTTTACTGGT 59.499 33.333 0.00 0.00 0.00 4.00
4452 4607 7.803189 GTCATGATTGTAGTGTTGTTTTACTGG 59.197 37.037 0.00 0.00 0.00 4.00
4453 4608 7.530525 CGTCATGATTGTAGTGTTGTTTTACTG 59.469 37.037 0.00 0.00 0.00 2.74
4454 4609 7.439955 TCGTCATGATTGTAGTGTTGTTTTACT 59.560 33.333 0.00 0.00 0.00 2.24
4455 4610 7.569297 TCGTCATGATTGTAGTGTTGTTTTAC 58.431 34.615 0.00 0.00 0.00 2.01
4456 4611 7.716768 TCGTCATGATTGTAGTGTTGTTTTA 57.283 32.000 0.00 0.00 0.00 1.52
4457 4612 6.612247 TCGTCATGATTGTAGTGTTGTTTT 57.388 33.333 0.00 0.00 0.00 2.43
4458 4613 6.260050 AGTTCGTCATGATTGTAGTGTTGTTT 59.740 34.615 0.00 0.00 0.00 2.83
4459 4614 5.758296 AGTTCGTCATGATTGTAGTGTTGTT 59.242 36.000 0.00 0.00 0.00 2.83
4460 4615 5.297547 AGTTCGTCATGATTGTAGTGTTGT 58.702 37.500 0.00 0.00 0.00 3.32
4461 4616 5.845985 AGTTCGTCATGATTGTAGTGTTG 57.154 39.130 0.00 0.00 0.00 3.33
4462 4617 6.036083 GCATAGTTCGTCATGATTGTAGTGTT 59.964 38.462 0.00 0.00 0.00 3.32
4463 4618 5.520288 GCATAGTTCGTCATGATTGTAGTGT 59.480 40.000 0.00 0.00 0.00 3.55
4464 4619 5.331830 CGCATAGTTCGTCATGATTGTAGTG 60.332 44.000 0.00 0.00 0.00 2.74
4465 4620 4.740205 CGCATAGTTCGTCATGATTGTAGT 59.260 41.667 0.00 0.00 0.00 2.73
4466 4621 4.976116 TCGCATAGTTCGTCATGATTGTAG 59.024 41.667 0.00 0.00 0.00 2.74
4467 4622 4.927422 TCGCATAGTTCGTCATGATTGTA 58.073 39.130 0.00 0.00 0.00 2.41
4468 4623 3.780902 TCGCATAGTTCGTCATGATTGT 58.219 40.909 0.00 0.00 0.00 2.71
4469 4624 4.445385 TCATCGCATAGTTCGTCATGATTG 59.555 41.667 0.00 0.00 0.00 2.67
4470 4625 4.620982 TCATCGCATAGTTCGTCATGATT 58.379 39.130 0.00 0.00 0.00 2.57
4471 4626 4.243007 TCATCGCATAGTTCGTCATGAT 57.757 40.909 0.00 0.00 0.00 2.45
4472 4627 3.708563 TCATCGCATAGTTCGTCATGA 57.291 42.857 0.00 0.00 0.00 3.07
4473 4628 3.983344 TCATCATCGCATAGTTCGTCATG 59.017 43.478 0.00 0.00 0.00 3.07
4474 4629 4.243007 TCATCATCGCATAGTTCGTCAT 57.757 40.909 0.00 0.00 0.00 3.06
4475 4630 3.708563 TCATCATCGCATAGTTCGTCA 57.291 42.857 0.00 0.00 0.00 4.35
4476 4631 4.229876 TCATCATCATCGCATAGTTCGTC 58.770 43.478 0.00 0.00 0.00 4.20
4477 4632 4.243007 TCATCATCATCGCATAGTTCGT 57.757 40.909 0.00 0.00 0.00 3.85
4478 4633 4.919754 TCTTCATCATCATCGCATAGTTCG 59.080 41.667 0.00 0.00 0.00 3.95
4479 4634 6.589139 TCATCTTCATCATCATCGCATAGTTC 59.411 38.462 0.00 0.00 0.00 3.01
4480 4635 6.461640 TCATCTTCATCATCATCGCATAGTT 58.538 36.000 0.00 0.00 0.00 2.24
4481 4636 6.034161 TCATCTTCATCATCATCGCATAGT 57.966 37.500 0.00 0.00 0.00 2.12
4482 4637 6.590677 ACTTCATCTTCATCATCATCGCATAG 59.409 38.462 0.00 0.00 0.00 2.23
4483 4638 6.461640 ACTTCATCTTCATCATCATCGCATA 58.538 36.000 0.00 0.00 0.00 3.14
4484 4639 5.306394 ACTTCATCTTCATCATCATCGCAT 58.694 37.500 0.00 0.00 0.00 4.73
4485 4640 4.700700 ACTTCATCTTCATCATCATCGCA 58.299 39.130 0.00 0.00 0.00 5.10
4486 4641 5.466058 AGAACTTCATCTTCATCATCATCGC 59.534 40.000 0.00 0.00 0.00 4.58
4487 4642 7.479897 AAGAACTTCATCTTCATCATCATCG 57.520 36.000 0.00 0.00 34.60 3.84
4503 4658 5.181245 TCGTCAATTTGGGATGAAGAACTTC 59.819 40.000 7.51 7.51 39.91 3.01
4516 4671 1.470098 CAAGGCTCCTCGTCAATTTGG 59.530 52.381 0.00 0.00 0.00 3.28
4521 4676 0.902984 TAGGCAAGGCTCCTCGTCAA 60.903 55.000 0.00 0.00 35.21 3.18
4560 4715 2.089201 TCATGCTTGGTCATGCTCAAG 58.911 47.619 17.78 17.78 42.58 3.02
4573 4728 2.040278 TGCTTACTCCAAGGTCATGCTT 59.960 45.455 0.00 0.00 34.56 3.91
4574 4729 1.630369 TGCTTACTCCAAGGTCATGCT 59.370 47.619 0.00 0.00 34.56 3.79
4575 4730 2.113860 TGCTTACTCCAAGGTCATGC 57.886 50.000 0.00 0.00 34.56 4.06
4576 4731 3.118112 AGGATGCTTACTCCAAGGTCATG 60.118 47.826 0.00 0.00 35.08 3.07
4577 4732 3.118531 AGGATGCTTACTCCAAGGTCAT 58.881 45.455 0.00 0.00 35.08 3.06
4578 4733 2.501723 GAGGATGCTTACTCCAAGGTCA 59.498 50.000 0.09 0.00 35.08 4.02
4579 4734 2.769095 AGAGGATGCTTACTCCAAGGTC 59.231 50.000 8.19 0.00 35.08 3.85
4580 4735 2.503356 CAGAGGATGCTTACTCCAAGGT 59.497 50.000 8.19 0.00 35.08 3.50
4581 4736 3.191078 CAGAGGATGCTTACTCCAAGG 57.809 52.381 8.19 0.00 35.08 3.61
4593 4748 5.381757 AGACTAGGTAAGTAGCAGAGGATG 58.618 45.833 0.00 0.00 39.07 3.51
4597 4752 4.399618 TGCAAGACTAGGTAAGTAGCAGAG 59.600 45.833 0.00 0.00 39.07 3.35
4603 4758 6.042322 TGAAAAGGTGCAAGACTAGGTAAGTA 59.958 38.462 0.00 0.00 39.07 2.24
4604 4759 4.976540 AAAGGTGCAAGACTAGGTAAGT 57.023 40.909 0.00 0.00 42.80 2.24
4608 4763 3.857157 TGAAAAGGTGCAAGACTAGGT 57.143 42.857 0.00 0.00 0.00 3.08
4612 4767 4.273318 ACTCTTTGAAAAGGTGCAAGACT 58.727 39.130 3.08 0.00 36.67 3.24
4618 4773 4.142381 ACAGACAACTCTTTGAAAAGGTGC 60.142 41.667 3.08 0.00 36.48 5.01
4619 4774 5.106157 ACACAGACAACTCTTTGAAAAGGTG 60.106 40.000 3.08 4.41 36.48 4.00
4623 4813 5.065988 GGCTACACAGACAACTCTTTGAAAA 59.934 40.000 0.00 0.00 36.48 2.29
4627 4817 2.476619 CGGCTACACAGACAACTCTTTG 59.523 50.000 0.00 0.00 38.83 2.77
4630 4820 0.038159 GCGGCTACACAGACAACTCT 60.038 55.000 0.00 0.00 0.00 3.24
4645 4835 1.194772 GTAGTTGAACAAGTGAGCGGC 59.805 52.381 0.00 0.00 0.00 6.53
4647 4837 1.798813 GGGTAGTTGAACAAGTGAGCG 59.201 52.381 0.00 0.00 0.00 5.03
4672 4862 3.924922 AGTGGTTAGTATACAGAGGGGG 58.075 50.000 5.50 0.00 0.00 5.40
4674 4864 5.302313 GGAGAAGTGGTTAGTATACAGAGGG 59.698 48.000 5.50 0.00 0.00 4.30
4675 4865 6.130569 AGGAGAAGTGGTTAGTATACAGAGG 58.869 44.000 5.50 0.00 0.00 3.69
4679 4869 6.429151 TGCTAGGAGAAGTGGTTAGTATACA 58.571 40.000 5.50 0.00 0.00 2.29
4680 4870 6.956202 TGCTAGGAGAAGTGGTTAGTATAC 57.044 41.667 0.00 0.00 0.00 1.47
4682 4872 6.136857 TCATGCTAGGAGAAGTGGTTAGTAT 58.863 40.000 0.00 0.00 0.00 2.12
4683 4873 5.516044 TCATGCTAGGAGAAGTGGTTAGTA 58.484 41.667 0.00 0.00 0.00 1.82
4684 4874 4.353777 TCATGCTAGGAGAAGTGGTTAGT 58.646 43.478 0.00 0.00 0.00 2.24
4685 4875 5.543507 ATCATGCTAGGAGAAGTGGTTAG 57.456 43.478 0.00 0.00 0.00 2.34
4686 4876 6.373759 TCTATCATGCTAGGAGAAGTGGTTA 58.626 40.000 3.84 0.00 0.00 2.85
4687 4877 5.211973 TCTATCATGCTAGGAGAAGTGGTT 58.788 41.667 3.84 0.00 0.00 3.67
4688 4878 4.809193 TCTATCATGCTAGGAGAAGTGGT 58.191 43.478 3.84 0.00 0.00 4.16
4689 4879 5.538053 TCTTCTATCATGCTAGGAGAAGTGG 59.462 44.000 11.45 0.00 42.39 4.00
4690 4880 6.647334 TCTTCTATCATGCTAGGAGAAGTG 57.353 41.667 11.45 0.00 42.39 3.16
4691 4881 5.243730 GCTCTTCTATCATGCTAGGAGAAGT 59.756 44.000 14.17 0.00 42.39 3.01
4692 4882 5.243507 TGCTCTTCTATCATGCTAGGAGAAG 59.756 44.000 14.17 13.02 42.89 2.85
4694 4884 4.734266 TGCTCTTCTATCATGCTAGGAGA 58.266 43.478 12.91 12.91 33.26 3.71
4697 4887 4.953667 TGTTGCTCTTCTATCATGCTAGG 58.046 43.478 3.84 0.00 0.00 3.02
4698 4888 7.226128 TGAATTGTTGCTCTTCTATCATGCTAG 59.774 37.037 0.00 0.00 0.00 3.42
4699 4889 7.049754 TGAATTGTTGCTCTTCTATCATGCTA 58.950 34.615 0.00 0.00 0.00 3.49
4701 4891 6.127810 TGAATTGTTGCTCTTCTATCATGC 57.872 37.500 0.00 0.00 0.00 4.06
4702 4892 6.691818 GCTTGAATTGTTGCTCTTCTATCATG 59.308 38.462 0.00 0.00 0.00 3.07
4703 4893 6.376299 TGCTTGAATTGTTGCTCTTCTATCAT 59.624 34.615 0.00 0.00 0.00 2.45
4704 4894 5.706833 TGCTTGAATTGTTGCTCTTCTATCA 59.293 36.000 0.00 0.00 0.00 2.15
4705 4895 6.187125 TGCTTGAATTGTTGCTCTTCTATC 57.813 37.500 0.00 0.00 0.00 2.08
4706 4896 5.392811 GCTGCTTGAATTGTTGCTCTTCTAT 60.393 40.000 0.00 0.00 0.00 1.98
4707 4897 4.083110 GCTGCTTGAATTGTTGCTCTTCTA 60.083 41.667 0.00 0.00 0.00 2.10
4708 4898 3.305199 GCTGCTTGAATTGTTGCTCTTCT 60.305 43.478 0.00 0.00 0.00 2.85
4709 4899 2.985139 GCTGCTTGAATTGTTGCTCTTC 59.015 45.455 0.00 0.00 0.00 2.87
4726 4923 1.372623 GTGCTCCTTTGCTTGCTGC 60.373 57.895 0.00 0.00 43.25 5.25
4729 4926 1.068954 GTAGTGTGCTCCTTTGCTTGC 60.069 52.381 0.00 0.00 0.00 4.01
4805 5002 7.871463 GTGGTAGGATGACACCATATTAGTTAC 59.129 40.741 0.00 0.00 46.15 2.50
4836 5033 6.430000 GTGGTAGAATTACAGCCTCTTTTTGA 59.570 38.462 0.00 0.00 0.00 2.69
4838 5035 5.710567 GGTGGTAGAATTACAGCCTCTTTTT 59.289 40.000 0.00 0.00 0.00 1.94
4847 5044 3.596214 AGTTGCGGTGGTAGAATTACAG 58.404 45.455 0.00 0.00 0.00 2.74
4854 5051 2.172679 TGATGTAGTTGCGGTGGTAGA 58.827 47.619 0.00 0.00 0.00 2.59
4855 5052 2.665649 TGATGTAGTTGCGGTGGTAG 57.334 50.000 0.00 0.00 0.00 3.18
4869 5066 1.267574 ACCCCTCACGCTGATGATGT 61.268 55.000 0.00 0.00 0.00 3.06
4872 5069 0.824109 CTAACCCCTCACGCTGATGA 59.176 55.000 0.00 0.00 0.00 2.92
4897 5094 5.133221 GCCTGTATATTTTGATGAGGTGGT 58.867 41.667 0.00 0.00 0.00 4.16
4901 5098 5.593909 TGTTGGCCTGTATATTTTGATGAGG 59.406 40.000 3.32 0.00 0.00 3.86
4927 5124 2.814336 GGTAGTCAGGGCTTGAAAACTG 59.186 50.000 0.00 0.00 37.61 3.16
4928 5125 2.441750 TGGTAGTCAGGGCTTGAAAACT 59.558 45.455 0.00 0.00 37.61 2.66
4929 5126 2.858745 TGGTAGTCAGGGCTTGAAAAC 58.141 47.619 0.00 2.48 37.61 2.43
4930 5127 3.586470 TTGGTAGTCAGGGCTTGAAAA 57.414 42.857 0.00 0.00 37.61 2.29
4931 5128 3.586470 TTTGGTAGTCAGGGCTTGAAA 57.414 42.857 0.00 0.00 37.61 2.69
4932 5129 3.586470 TTTTGGTAGTCAGGGCTTGAA 57.414 42.857 0.00 0.00 37.61 2.69
4933 5130 3.586470 TTTTTGGTAGTCAGGGCTTGA 57.414 42.857 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.