Multiple sequence alignment - TraesCS2B01G342500

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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 TraesCS2B01G342500 chr2B 100.000 5245 0 0 1 5245 488646740 488641496 0.000000e+00 9686.0
1 TraesCS2B01G342500 chr2D 95.900 3244 83 21 656 3874 416762485 416759267 0.000000e+00 5208.0
2 TraesCS2B01G342500 chr2D 88.932 1274 67 26 3871 5138 416758419 416757214 0.000000e+00 1504.0
3 TraesCS2B01G342500 chr2A 95.577 3165 84 22 692 3826 573394287 573397425 0.000000e+00 5018.0
4 TraesCS2B01G342500 chr2A 88.462 1274 75 23 3871 5138 573398735 573399942 0.000000e+00 1472.0
5 TraesCS2B01G342500 chr2A 94.216 657 36 1 1 657 578391138 578390484 0.000000e+00 1002.0
6 TraesCS2B01G342500 chr2A 100.000 50 0 0 3825 3874 573397690 573397739 5.590000e-15 93.5
7 TraesCS2B01G342500 chr7D 94.064 657 37 1 1 657 548867283 548866629 0.000000e+00 996.0
8 TraesCS2B01G342500 chr7D 94.163 651 36 1 1 651 465339910 465340558 0.000000e+00 990.0
9 TraesCS2B01G342500 chr5A 94.308 650 34 2 1 650 222606932 222606286 0.000000e+00 992.0
10 TraesCS2B01G342500 chr5A 93.373 664 42 1 1 664 525482379 525481718 0.000000e+00 981.0
11 TraesCS2B01G342500 chr7A 94.163 651 36 1 1 651 118151410 118150762 0.000000e+00 990.0
12 TraesCS2B01G342500 chr7A 94.163 651 36 1 1 651 319591339 319591987 0.000000e+00 990.0
13 TraesCS2B01G342500 chr4D 94.163 651 36 1 1 651 242938310 242938958 0.000000e+00 990.0
14 TraesCS2B01G342500 chr3D 94.163 651 36 1 1 651 422742490 422743138 0.000000e+00 990.0
15 TraesCS2B01G342500 chr3D 100.000 30 0 0 5195 5224 34357580 34357609 7.340000e-04 56.5
16 TraesCS2B01G342500 chr4A 100.000 30 0 0 5195 5224 669582187 669582216 7.340000e-04 56.5
17 TraesCS2B01G342500 chr1D 100.000 29 0 0 5191 5219 175821758 175821786 3.000000e-03 54.7


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 TraesCS2B01G342500 chr2B 488641496 488646740 5244 True 9686.0 9686 100.000000 1 5245 1 chr2B.!!$R1 5244
1 TraesCS2B01G342500 chr2D 416757214 416762485 5271 True 3356.0 5208 92.416000 656 5138 2 chr2D.!!$R1 4482
2 TraesCS2B01G342500 chr2A 573394287 573399942 5655 False 2194.5 5018 94.679667 692 5138 3 chr2A.!!$F1 4446
3 TraesCS2B01G342500 chr2A 578390484 578391138 654 True 1002.0 1002 94.216000 1 657 1 chr2A.!!$R1 656
4 TraesCS2B01G342500 chr7D 548866629 548867283 654 True 996.0 996 94.064000 1 657 1 chr7D.!!$R1 656
5 TraesCS2B01G342500 chr7D 465339910 465340558 648 False 990.0 990 94.163000 1 651 1 chr7D.!!$F1 650
6 TraesCS2B01G342500 chr5A 222606286 222606932 646 True 992.0 992 94.308000 1 650 1 chr5A.!!$R1 649
7 TraesCS2B01G342500 chr5A 525481718 525482379 661 True 981.0 981 93.373000 1 664 1 chr5A.!!$R2 663
8 TraesCS2B01G342500 chr7A 118150762 118151410 648 True 990.0 990 94.163000 1 651 1 chr7A.!!$R1 650
9 TraesCS2B01G342500 chr7A 319591339 319591987 648 False 990.0 990 94.163000 1 651 1 chr7A.!!$F1 650
10 TraesCS2B01G342500 chr4D 242938310 242938958 648 False 990.0 990 94.163000 1 651 1 chr4D.!!$F1 650
11 TraesCS2B01G342500 chr3D 422742490 422743138 648 False 990.0 990 94.163000 1 651 1 chr3D.!!$F2 650

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
288 289 0.101399 CCACACGAGGAAGGATCGAG 59.899 60.0 1.94 0.0 42.76 4.04 F
1393 1412 0.035056 CTTCCGCCACTTCATCCCTT 60.035 55.0 0.00 0.0 0.00 3.95 F
2265 2284 0.037697 TTGTAGCGAGTGATGCGGTT 60.038 50.0 0.00 0.0 40.27 4.44 F
3159 3178 0.965439 ATAGCTCTAGCCCGCAGAAG 59.035 55.0 0.00 0.0 43.38 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1716 1735 1.346395 ACACCGAGTGCATTGACCTTA 59.654 47.619 0.00 0.00 36.98 2.69 R
3371 3408 1.285023 CTCACTTGCCAGCTGTTGC 59.715 57.895 13.81 10.56 40.05 4.17 R
3672 3712 0.321919 CAGGATGGGGTGATATGCCG 60.322 60.000 0.00 0.00 0.00 5.69 R
5090 7252 0.322816 CAGTGCAGGTATTGGCAGGT 60.323 55.000 0.00 0.00 41.35 4.00 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
157 158 6.709018 AAAGCTAAAAGGCAAGTTCTACAA 57.291 33.333 0.00 0.00 34.17 2.41
172 173 1.001048 CTACAAGACGGTGGTTCGACA 60.001 52.381 0.00 0.00 0.00 4.35
175 176 2.008268 AAGACGGTGGTTCGACACGT 62.008 55.000 0.62 0.00 42.23 4.49
233 234 3.002348 GGCGACATGTTCAATAGTTAGGC 59.998 47.826 0.00 0.00 0.00 3.93
246 247 2.355986 TTAGGCGTGGCGGAGATGT 61.356 57.895 0.00 0.00 0.00 3.06
259 260 4.262036 GGCGGAGATGTGTATGTTGAGATA 60.262 45.833 0.00 0.00 0.00 1.98
260 261 5.289595 GCGGAGATGTGTATGTTGAGATAA 58.710 41.667 0.00 0.00 0.00 1.75
287 288 1.945354 GCCACACGAGGAAGGATCGA 61.945 60.000 1.94 0.00 42.76 3.59
288 289 0.101399 CCACACGAGGAAGGATCGAG 59.899 60.000 1.94 0.00 42.76 4.04
317 318 7.773690 TCCGGAATGATGATATACGAGATAGAA 59.226 37.037 0.00 0.00 0.00 2.10
338 339 2.685106 TGGGGTAGCACCAATTGAAA 57.315 45.000 7.12 0.00 41.02 2.69
350 351 5.594926 CACCAATTGAAAAGAAGCTTGTCT 58.405 37.500 2.10 0.00 0.00 3.41
361 362 5.899120 AGAAGCTTGTCTAACATCGTCTA 57.101 39.130 2.10 0.00 0.00 2.59
363 364 6.688578 AGAAGCTTGTCTAACATCGTCTAAA 58.311 36.000 2.10 0.00 0.00 1.85
398 399 3.640407 AGCGCAGGCCTCCAGAAA 61.640 61.111 11.47 0.00 41.24 2.52
449 450 3.074412 GCGGAGAATGTCAAAAGAAGGA 58.926 45.455 0.00 0.00 0.00 3.36
472 473 3.606687 GGGTAGACCGAATTTGACATGT 58.393 45.455 0.00 0.00 36.71 3.21
487 488 3.322541 TGACATGTGAGGAGTCCGTTAAA 59.677 43.478 1.15 0.00 0.00 1.52
510 511 4.027437 AGAGACCTGAAGGATTGGAGTAC 58.973 47.826 2.62 0.00 38.94 2.73
563 564 2.025981 TGGAAGCTTGCTATCCATGTGT 60.026 45.455 19.34 0.00 38.30 3.72
568 569 3.136077 AGCTTGCTATCCATGTGTCAGAT 59.864 43.478 0.00 0.00 0.00 2.90
595 596 4.081697 TGAGTTGGTTGCGAGATCTTATGA 60.082 41.667 0.00 0.00 0.00 2.15
608 609 7.682261 GCGAGATCTTATGAGTTTCACCTCTAA 60.682 40.741 0.00 0.00 32.50 2.10
613 614 8.840200 TCTTATGAGTTTCACCTCTAACCTAT 57.160 34.615 0.00 0.00 32.50 2.57
616 617 5.590818 TGAGTTTCACCTCTAACCTATCCT 58.409 41.667 0.00 0.00 32.50 3.24
622 623 8.975295 GTTTCACCTCTAACCTATCCTAACTTA 58.025 37.037 0.00 0.00 0.00 2.24
651 652 6.478673 GGGATTAAAGACTTTGTTGTTGTTGG 59.521 38.462 10.80 0.00 0.00 3.77
654 655 3.866883 AGACTTTGTTGTTGTTGGTGG 57.133 42.857 0.00 0.00 0.00 4.61
660 661 2.093106 TGTTGTTGTTGGTGGTGGTAC 58.907 47.619 0.00 0.00 0.00 3.34
662 663 0.920438 TGTTGTTGGTGGTGGTACCT 59.080 50.000 14.36 0.00 41.43 3.08
668 669 4.805744 TGTTGGTGGTGGTACCTAAAATT 58.194 39.130 14.36 0.00 41.43 1.82
677 678 8.415553 GTGGTGGTACCTAAAATTGTTTTACTT 58.584 33.333 14.36 0.00 39.58 2.24
904 922 1.693640 CACTTTGGCCCAGGATCCT 59.306 57.895 9.02 9.02 0.00 3.24
907 925 0.554792 CTTTGGCCCAGGATCCTGAT 59.445 55.000 38.37 4.50 46.30 2.90
909 927 1.699054 TTGGCCCAGGATCCTGATCG 61.699 60.000 38.37 25.74 46.30 3.69
913 931 2.746359 CAGGATCCTGATCGGGGC 59.254 66.667 34.54 12.60 46.30 5.80
1143 1162 1.683011 CCATCCCAACATCGCTTCCTT 60.683 52.381 0.00 0.00 0.00 3.36
1365 1384 1.891150 TCCTCAGAGTTTCCCACGTAC 59.109 52.381 0.00 0.00 0.00 3.67
1393 1412 0.035056 CTTCCGCCACTTCATCCCTT 60.035 55.000 0.00 0.00 0.00 3.95
1485 1504 2.572284 GCCTTCGCCGAGTACTGT 59.428 61.111 0.00 0.00 0.00 3.55
1716 1735 1.273606 CTCGCCATGGAGGTATTCGAT 59.726 52.381 18.40 0.00 40.61 3.59
1966 1985 4.286032 ACCCTAGTGTGCTCAAGATTGTTA 59.714 41.667 0.00 0.00 0.00 2.41
2097 2116 0.998226 CTGGTGATTGCGTTGTTGCG 60.998 55.000 0.00 0.00 37.81 4.85
2265 2284 0.037697 TTGTAGCGAGTGATGCGGTT 60.038 50.000 0.00 0.00 40.27 4.44
2557 2576 2.136026 AGTTCCCCAACCTCACTTTCT 58.864 47.619 0.00 0.00 32.22 2.52
2724 2743 4.564821 GCGCCAGTTAATATAAGGGATCCA 60.565 45.833 15.23 0.00 0.00 3.41
2743 2762 4.415596 TCCAAAAGCCATGTACCATCTTT 58.584 39.130 0.00 0.00 0.00 2.52
2841 2860 2.369860 TGACACTGAACTGCTGGATCTT 59.630 45.455 0.00 0.00 0.00 2.40
3111 3130 4.884668 AGTTGGTTATGAAAGGACGAGA 57.115 40.909 0.00 0.00 0.00 4.04
3125 3144 3.194968 AGGACGAGATCGCTTCCTAAAAA 59.805 43.478 20.71 0.00 41.27 1.94
3156 3175 3.181485 GGTAATATAGCTCTAGCCCGCAG 60.181 52.174 0.00 0.00 43.38 5.18
3157 3176 2.516227 ATATAGCTCTAGCCCGCAGA 57.484 50.000 0.00 0.00 43.38 4.26
3158 3177 2.287977 TATAGCTCTAGCCCGCAGAA 57.712 50.000 0.00 0.00 43.38 3.02
3159 3178 0.965439 ATAGCTCTAGCCCGCAGAAG 59.035 55.000 0.00 0.00 43.38 2.85
3177 3212 6.092122 CGCAGAAGTTGTTTGTGGAGATAATA 59.908 38.462 0.00 0.00 31.02 0.98
3262 3297 6.758886 ACTTGTCTTTCTGATAAATAGAGGCG 59.241 38.462 0.00 0.00 0.00 5.52
3370 3407 7.994425 TGAGAACACTATGCTTTAATTCCAA 57.006 32.000 0.00 0.00 0.00 3.53
3371 3408 8.044060 TGAGAACACTATGCTTTAATTCCAAG 57.956 34.615 0.00 0.00 0.00 3.61
3412 3449 7.027874 AGTTTGTGAATTCTAGGTATTCCCA 57.972 36.000 7.05 7.43 34.66 4.37
3466 3506 9.829507 CCCAATGCCAACTTATAATAATTCAAA 57.170 29.630 0.00 0.00 0.00 2.69
3576 3616 7.008357 GCTTAAAACGTTAAATTGCTCCTGATC 59.992 37.037 0.00 0.00 0.00 2.92
3580 3620 5.730550 ACGTTAAATTGCTCCTGATCTGTA 58.269 37.500 0.00 0.00 0.00 2.74
3656 3696 5.468540 AAATCTTGGGTTGTTTCTTAGCC 57.531 39.130 0.00 0.00 0.00 3.93
3672 3712 0.668535 AGCCAACTTTCTTGTTCGCC 59.331 50.000 0.00 0.00 35.24 5.54
3684 3724 2.110213 TTCGCCGGCATATCACCC 59.890 61.111 28.98 0.00 0.00 4.61
3709 3749 3.969976 TCCTGATCCTGGTATCCTCTTTG 59.030 47.826 0.00 0.00 0.00 2.77
3739 3779 9.120538 GGATATTATTCTGGTTAGCTTTGTGAA 57.879 33.333 0.00 0.00 0.00 3.18
3744 3784 3.255642 TCTGGTTAGCTTTGTGAATTGCC 59.744 43.478 0.00 0.00 0.00 4.52
3912 6068 8.436200 GGTATGATTTATGTGACGCTATCTTTC 58.564 37.037 0.00 0.00 0.00 2.62
3957 6113 4.950050 AGAATTGAGTTACCGAGCCATAG 58.050 43.478 0.00 0.00 0.00 2.23
3962 6118 2.950309 GAGTTACCGAGCCATAGAGTCA 59.050 50.000 0.00 0.00 0.00 3.41
3983 6139 6.482641 AGTCAAGATTTGATATACTGCAGCAG 59.517 38.462 21.54 21.54 42.47 4.24
4051 6207 5.245531 ACATCGCCTGATCTTTTGAGTTAA 58.754 37.500 0.00 0.00 30.49 2.01
4126 6282 3.452474 TCGGGCATGTTTGAAAAGTTTG 58.548 40.909 0.00 0.00 0.00 2.93
4241 6397 3.864789 TCTTCTTTGAACCTTCTGGCT 57.135 42.857 0.00 0.00 36.63 4.75
4299 6455 2.173569 AGAAGAACCTGTTGAGCCAAGT 59.826 45.455 0.00 0.00 0.00 3.16
4317 6473 2.307309 TTGCGACGCCTCTTCAACG 61.307 57.895 18.69 0.00 0.00 4.10
4336 6492 0.817654 GCCCAAATCTGGTGCTTACC 59.182 55.000 0.00 0.00 41.72 2.85
4337 6493 1.616994 GCCCAAATCTGGTGCTTACCT 60.617 52.381 0.00 0.00 41.72 3.08
4338 6494 2.356741 GCCCAAATCTGGTGCTTACCTA 60.357 50.000 0.00 0.00 41.72 3.08
4339 6495 3.688414 GCCCAAATCTGGTGCTTACCTAT 60.688 47.826 0.00 0.00 41.72 2.57
4340 6496 4.445735 GCCCAAATCTGGTGCTTACCTATA 60.446 45.833 0.00 0.00 41.72 1.31
4341 6497 5.690865 CCCAAATCTGGTGCTTACCTATAA 58.309 41.667 0.00 0.00 41.72 0.98
4342 6498 6.306987 CCCAAATCTGGTGCTTACCTATAAT 58.693 40.000 0.00 0.00 41.72 1.28
4343 6499 7.458397 CCCAAATCTGGTGCTTACCTATAATA 58.542 38.462 0.00 0.00 41.72 0.98
4344 6500 7.607991 CCCAAATCTGGTGCTTACCTATAATAG 59.392 40.741 0.00 0.00 41.72 1.73
4345 6501 7.119846 CCAAATCTGGTGCTTACCTATAATAGC 59.880 40.741 0.00 0.00 38.00 2.97
4395 6551 3.309675 GCGTATGCCAGCTACGTG 58.690 61.111 16.97 0.00 42.92 4.49
4431 6587 2.121992 CTGAAGCCAGCCAGAGGTGT 62.122 60.000 0.00 0.00 39.97 4.16
4481 6637 5.221126 GCTATTTTATTGGCACCAGAAGAGG 60.221 44.000 0.00 0.00 0.00 3.69
4489 6645 0.107945 CACCAGAAGAGGTAGCTGCC 60.108 60.000 13.81 13.81 40.77 4.85
4519 6675 3.853831 TGTTGTGCAATGCTAGATTGG 57.146 42.857 6.82 0.00 0.00 3.16
4529 6685 2.554142 TGCTAGATTGGACGCTGAATG 58.446 47.619 0.00 0.00 0.00 2.67
4601 6757 2.806244 CCAGTATGCGGGTAATAAGCAC 59.194 50.000 0.00 0.00 44.12 4.40
4614 6770 5.813672 GGTAATAAGCACACGTGGAGATTTA 59.186 40.000 21.57 13.41 0.00 1.40
4620 6776 2.159627 CACACGTGGAGATTTACAAGGC 59.840 50.000 21.57 0.00 0.00 4.35
4624 6780 4.693566 CACGTGGAGATTTACAAGGCTTTA 59.306 41.667 7.95 0.00 0.00 1.85
4627 6783 6.433093 ACGTGGAGATTTACAAGGCTTTAATT 59.567 34.615 0.00 0.00 0.00 1.40
4632 6788 9.305925 GGAGATTTACAAGGCTTTAATTGATTG 57.694 33.333 0.00 0.00 0.00 2.67
4638 6794 6.691508 ACAAGGCTTTAATTGATTGTTCCTC 58.308 36.000 0.00 0.00 0.00 3.71
4639 6795 6.494835 ACAAGGCTTTAATTGATTGTTCCTCT 59.505 34.615 0.00 0.00 0.00 3.69
4640 6796 7.669722 ACAAGGCTTTAATTGATTGTTCCTCTA 59.330 33.333 0.00 0.00 0.00 2.43
4642 6798 8.286191 AGGCTTTAATTGATTGTTCCTCTAAG 57.714 34.615 0.00 0.00 0.00 2.18
4643 6799 7.890655 AGGCTTTAATTGATTGTTCCTCTAAGT 59.109 33.333 0.00 0.00 0.00 2.24
4740 6896 1.610624 GCCACTTTCGGGATGTTCTCA 60.611 52.381 0.00 0.00 0.00 3.27
4782 6939 3.721706 CTTTCTGGGCCCCGCTCT 61.722 66.667 22.27 0.00 0.00 4.09
4791 6948 2.202987 CCCCGCTCTGATGTCAGC 60.203 66.667 5.14 0.00 43.46 4.26
4795 6952 2.172372 CGCTCTGATGTCAGCTGCC 61.172 63.158 9.47 0.00 43.46 4.85
4816 6973 5.825679 TGCCAAGTAGACAAAATGTGTAACT 59.174 36.000 0.00 0.00 41.96 2.24
4835 6992 6.603997 TGTAACTTTATTTCCACAGTGGTTGT 59.396 34.615 19.65 8.75 41.94 3.32
4840 6997 0.537653 TTCCACAGTGGTTGTCGTGA 59.462 50.000 19.65 0.00 38.16 4.35
4871 7032 7.312154 TGTTTTGTTTATCTCGATTTGGGATG 58.688 34.615 0.00 0.00 0.00 3.51
4880 7041 0.652592 GATTTGGGATGCGAGTGACG 59.347 55.000 0.00 0.00 45.66 4.35
4893 7055 0.665835 AGTGACGCTCGATCAGATCC 59.334 55.000 4.73 0.00 0.00 3.36
4900 7062 2.288091 CGCTCGATCAGATCCATCTTGT 60.288 50.000 4.73 0.00 34.22 3.16
4946 7108 0.467384 AGCATTCTGATCCGTCCAGG 59.533 55.000 0.00 0.00 42.97 4.45
4956 7118 2.526888 TCCGTCCAGGATACAGAAGT 57.473 50.000 0.00 0.00 45.98 3.01
4957 7119 3.657398 TCCGTCCAGGATACAGAAGTA 57.343 47.619 0.00 0.00 45.98 2.24
4958 7120 3.552875 TCCGTCCAGGATACAGAAGTAG 58.447 50.000 0.00 0.00 45.98 2.57
4959 7121 3.201487 TCCGTCCAGGATACAGAAGTAGA 59.799 47.826 0.00 0.00 45.98 2.59
4960 7122 3.315749 CCGTCCAGGATACAGAAGTAGAC 59.684 52.174 0.00 0.00 45.00 2.59
4961 7123 3.002451 CGTCCAGGATACAGAAGTAGACG 59.998 52.174 0.00 0.00 37.47 4.18
4962 7124 4.197750 GTCCAGGATACAGAAGTAGACGA 58.802 47.826 0.00 0.00 41.41 4.20
4963 7125 4.273969 GTCCAGGATACAGAAGTAGACGAG 59.726 50.000 0.00 0.00 41.41 4.18
4964 7126 4.080469 TCCAGGATACAGAAGTAGACGAGT 60.080 45.833 0.00 0.00 41.41 4.18
4965 7127 4.035792 CCAGGATACAGAAGTAGACGAGTG 59.964 50.000 0.00 0.00 41.41 3.51
4966 7128 4.636648 CAGGATACAGAAGTAGACGAGTGT 59.363 45.833 0.00 0.00 41.41 3.55
4967 7129 5.124138 CAGGATACAGAAGTAGACGAGTGTT 59.876 44.000 0.00 0.00 41.41 3.32
4968 7130 5.711036 AGGATACAGAAGTAGACGAGTGTTT 59.289 40.000 0.00 0.00 41.41 2.83
4976 7138 5.258456 AGTAGACGAGTGTTTTCTTGACA 57.742 39.130 0.00 0.00 0.00 3.58
4980 7142 3.458189 ACGAGTGTTTTCTTGACAGAGG 58.542 45.455 0.00 0.00 0.00 3.69
4981 7143 2.221981 CGAGTGTTTTCTTGACAGAGGC 59.778 50.000 0.00 0.00 0.00 4.70
5014 7176 3.369576 GGGAGTACTGAGACATTTGGGAC 60.370 52.174 0.00 0.00 0.00 4.46
5028 7190 5.048294 ACATTTGGGACGAAGGAATTTACAC 60.048 40.000 0.00 0.00 0.00 2.90
5036 7198 6.146021 GGACGAAGGAATTTACACGAGTTTTA 59.854 38.462 0.00 0.00 0.00 1.52
5055 7217 7.649057 AGTTTTAAAGGATTCTCGTGGAAAAG 58.351 34.615 0.00 0.00 37.49 2.27
5075 7237 6.892310 AAAGTTCTTTTGTGTCTTGCATTC 57.108 33.333 0.00 0.00 0.00 2.67
5086 7248 3.565482 TGTCTTGCATTCAACACTCTTCC 59.435 43.478 0.00 0.00 0.00 3.46
5090 7252 6.003326 TCTTGCATTCAACACTCTTCCAATA 58.997 36.000 0.00 0.00 0.00 1.90
5091 7253 5.627499 TGCATTCAACACTCTTCCAATAC 57.373 39.130 0.00 0.00 0.00 1.89
5092 7254 4.458989 TGCATTCAACACTCTTCCAATACC 59.541 41.667 0.00 0.00 0.00 2.73
5093 7255 4.702131 GCATTCAACACTCTTCCAATACCT 59.298 41.667 0.00 0.00 0.00 3.08
5094 7256 5.392380 GCATTCAACACTCTTCCAATACCTG 60.392 44.000 0.00 0.00 0.00 4.00
5095 7257 3.674997 TCAACACTCTTCCAATACCTGC 58.325 45.455 0.00 0.00 0.00 4.85
5096 7258 2.749621 CAACACTCTTCCAATACCTGCC 59.250 50.000 0.00 0.00 0.00 4.85
5097 7259 1.985159 ACACTCTTCCAATACCTGCCA 59.015 47.619 0.00 0.00 0.00 4.92
5098 7260 2.375174 ACACTCTTCCAATACCTGCCAA 59.625 45.455 0.00 0.00 0.00 4.52
5099 7261 3.010584 ACACTCTTCCAATACCTGCCAAT 59.989 43.478 0.00 0.00 0.00 3.16
5100 7262 4.227300 ACACTCTTCCAATACCTGCCAATA 59.773 41.667 0.00 0.00 0.00 1.90
5113 7275 1.243342 GCCAATACCTGCACTGCACA 61.243 55.000 0.00 0.00 33.79 4.57
5143 7305 9.814899 ATATGAAGAAATCTAGTGTCACTGAAG 57.185 33.333 16.03 6.10 0.00 3.02
5144 7306 5.928839 TGAAGAAATCTAGTGTCACTGAAGC 59.071 40.000 16.03 5.47 0.00 3.86
5145 7307 5.474578 AGAAATCTAGTGTCACTGAAGCA 57.525 39.130 16.03 0.00 0.00 3.91
5146 7308 5.858381 AGAAATCTAGTGTCACTGAAGCAA 58.142 37.500 16.03 0.00 0.00 3.91
5147 7309 6.291377 AGAAATCTAGTGTCACTGAAGCAAA 58.709 36.000 16.03 0.00 0.00 3.68
5148 7310 6.939163 AGAAATCTAGTGTCACTGAAGCAAAT 59.061 34.615 16.03 0.00 0.00 2.32
5149 7311 6.492007 AATCTAGTGTCACTGAAGCAAATG 57.508 37.500 16.03 0.00 0.00 2.32
5150 7312 5.213891 TCTAGTGTCACTGAAGCAAATGA 57.786 39.130 16.03 0.00 0.00 2.57
5151 7313 5.233225 TCTAGTGTCACTGAAGCAAATGAG 58.767 41.667 16.03 0.97 0.00 2.90
5152 7314 4.077300 AGTGTCACTGAAGCAAATGAGA 57.923 40.909 4.21 0.00 0.00 3.27
5153 7315 4.649692 AGTGTCACTGAAGCAAATGAGAT 58.350 39.130 4.21 0.00 0.00 2.75
5154 7316 4.454847 AGTGTCACTGAAGCAAATGAGATG 59.545 41.667 4.21 0.00 0.00 2.90
5155 7317 3.754850 TGTCACTGAAGCAAATGAGATGG 59.245 43.478 0.00 0.00 0.00 3.51
5156 7318 3.755378 GTCACTGAAGCAAATGAGATGGT 59.245 43.478 0.00 0.00 0.00 3.55
5157 7319 4.217118 GTCACTGAAGCAAATGAGATGGTT 59.783 41.667 0.00 0.00 40.88 3.67
5158 7320 4.828939 TCACTGAAGCAAATGAGATGGTTT 59.171 37.500 0.00 0.00 38.51 3.27
5159 7321 4.921515 CACTGAAGCAAATGAGATGGTTTG 59.078 41.667 0.00 0.00 38.51 2.93
5160 7322 4.586001 ACTGAAGCAAATGAGATGGTTTGT 59.414 37.500 0.00 0.00 38.51 2.83
5161 7323 5.069516 ACTGAAGCAAATGAGATGGTTTGTT 59.930 36.000 0.00 0.00 38.51 2.83
5162 7324 5.291178 TGAAGCAAATGAGATGGTTTGTTG 58.709 37.500 0.00 0.00 38.51 3.33
5163 7325 4.942761 AGCAAATGAGATGGTTTGTTGT 57.057 36.364 0.00 0.00 37.57 3.32
5164 7326 6.040278 TGAAGCAAATGAGATGGTTTGTTGTA 59.960 34.615 0.00 0.00 38.51 2.41
5165 7327 6.017400 AGCAAATGAGATGGTTTGTTGTAG 57.983 37.500 0.00 0.00 37.57 2.74
5166 7328 5.769662 AGCAAATGAGATGGTTTGTTGTAGA 59.230 36.000 0.00 0.00 37.57 2.59
5167 7329 6.265196 AGCAAATGAGATGGTTTGTTGTAGAA 59.735 34.615 0.00 0.00 37.57 2.10
5168 7330 6.363357 GCAAATGAGATGGTTTGTTGTAGAAC 59.637 38.462 0.00 0.00 37.57 3.01
5169 7331 7.651808 CAAATGAGATGGTTTGTTGTAGAACT 58.348 34.615 4.21 0.00 32.79 3.01
5170 7332 6.808008 ATGAGATGGTTTGTTGTAGAACTG 57.192 37.500 4.21 0.00 32.79 3.16
5171 7333 5.924356 TGAGATGGTTTGTTGTAGAACTGA 58.076 37.500 4.21 0.00 32.79 3.41
5172 7334 6.353323 TGAGATGGTTTGTTGTAGAACTGAA 58.647 36.000 4.21 0.00 32.79 3.02
5173 7335 6.826231 TGAGATGGTTTGTTGTAGAACTGAAA 59.174 34.615 4.21 0.00 32.79 2.69
5174 7336 7.338196 TGAGATGGTTTGTTGTAGAACTGAAAA 59.662 33.333 4.21 0.00 32.79 2.29
5175 7337 8.062065 AGATGGTTTGTTGTAGAACTGAAAAA 57.938 30.769 4.21 0.00 32.79 1.94
5176 7338 8.695456 AGATGGTTTGTTGTAGAACTGAAAAAT 58.305 29.630 4.21 0.00 32.79 1.82
5177 7339 9.959749 GATGGTTTGTTGTAGAACTGAAAAATA 57.040 29.630 4.21 0.00 32.79 1.40
5178 7340 9.744468 ATGGTTTGTTGTAGAACTGAAAAATAC 57.256 29.630 4.21 0.00 32.79 1.89
5179 7341 8.962679 TGGTTTGTTGTAGAACTGAAAAATACT 58.037 29.630 4.21 0.00 32.79 2.12
5180 7342 9.447040 GGTTTGTTGTAGAACTGAAAAATACTC 57.553 33.333 4.21 0.00 32.79 2.59
5181 7343 9.447040 GTTTGTTGTAGAACTGAAAAATACTCC 57.553 33.333 4.21 0.00 32.79 3.85
5182 7344 7.739498 TGTTGTAGAACTGAAAAATACTCCC 57.261 36.000 4.21 0.00 32.79 4.30
5183 7345 7.514721 TGTTGTAGAACTGAAAAATACTCCCT 58.485 34.615 4.21 0.00 32.79 4.20
5184 7346 7.660208 TGTTGTAGAACTGAAAAATACTCCCTC 59.340 37.037 4.21 0.00 32.79 4.30
5185 7347 6.708285 TGTAGAACTGAAAAATACTCCCTCC 58.292 40.000 0.00 0.00 0.00 4.30
5186 7348 5.843019 AGAACTGAAAAATACTCCCTCCA 57.157 39.130 0.00 0.00 0.00 3.86
5187 7349 6.394345 AGAACTGAAAAATACTCCCTCCAT 57.606 37.500 0.00 0.00 0.00 3.41
5188 7350 6.418946 AGAACTGAAAAATACTCCCTCCATC 58.581 40.000 0.00 0.00 0.00 3.51
5189 7351 5.117406 ACTGAAAAATACTCCCTCCATCC 57.883 43.478 0.00 0.00 0.00 3.51
5190 7352 4.079730 ACTGAAAAATACTCCCTCCATCCC 60.080 45.833 0.00 0.00 0.00 3.85
5191 7353 3.855599 TGAAAAATACTCCCTCCATCCCA 59.144 43.478 0.00 0.00 0.00 4.37
5192 7354 4.482025 TGAAAAATACTCCCTCCATCCCAT 59.518 41.667 0.00 0.00 0.00 4.00
5193 7355 5.674496 TGAAAAATACTCCCTCCATCCCATA 59.326 40.000 0.00 0.00 0.00 2.74
5194 7356 6.335311 TGAAAAATACTCCCTCCATCCCATAT 59.665 38.462 0.00 0.00 0.00 1.78
5195 7357 7.519355 TGAAAAATACTCCCTCCATCCCATATA 59.481 37.037 0.00 0.00 0.00 0.86
5196 7358 7.516450 AAAATACTCCCTCCATCCCATATAG 57.484 40.000 0.00 0.00 0.00 1.31
5197 7359 5.840547 ATACTCCCTCCATCCCATATAGT 57.159 43.478 0.00 0.00 0.00 2.12
5198 7360 3.796111 ACTCCCTCCATCCCATATAGTG 58.204 50.000 0.00 0.00 0.00 2.74
5199 7361 3.144894 ACTCCCTCCATCCCATATAGTGT 59.855 47.826 0.00 0.00 0.00 3.55
5200 7362 3.772025 CTCCCTCCATCCCATATAGTGTC 59.228 52.174 0.00 0.00 0.00 3.67
5201 7363 3.143933 TCCCTCCATCCCATATAGTGTCA 59.856 47.826 0.00 0.00 0.00 3.58
5202 7364 3.909995 CCCTCCATCCCATATAGTGTCAA 59.090 47.826 0.00 0.00 0.00 3.18
5203 7365 4.350816 CCCTCCATCCCATATAGTGTCAAA 59.649 45.833 0.00 0.00 0.00 2.69
5204 7366 5.163099 CCCTCCATCCCATATAGTGTCAAAA 60.163 44.000 0.00 0.00 0.00 2.44
5205 7367 6.364701 CCTCCATCCCATATAGTGTCAAAAA 58.635 40.000 0.00 0.00 0.00 1.94
5206 7368 6.263168 CCTCCATCCCATATAGTGTCAAAAAC 59.737 42.308 0.00 0.00 0.00 2.43
5207 7369 5.820423 TCCATCCCATATAGTGTCAAAAACG 59.180 40.000 0.00 0.00 0.00 3.60
5208 7370 5.505654 CCATCCCATATAGTGTCAAAAACGC 60.506 44.000 0.00 0.00 38.74 4.84
5221 7383 8.545420 AGTGTCAAAAACGCTATTATATTACGG 58.455 33.333 0.00 0.00 46.85 4.02
5222 7384 7.795272 GTGTCAAAAACGCTATTATATTACGGG 59.205 37.037 0.00 0.00 35.42 5.28
5223 7385 7.710044 TGTCAAAAACGCTATTATATTACGGGA 59.290 33.333 0.00 0.00 0.00 5.14
5224 7386 8.550376 GTCAAAAACGCTATTATATTACGGGAA 58.450 33.333 0.00 0.00 0.00 3.97
5225 7387 8.767085 TCAAAAACGCTATTATATTACGGGAAG 58.233 33.333 0.00 0.00 0.00 3.46
5226 7388 8.553696 CAAAAACGCTATTATATTACGGGAAGT 58.446 33.333 0.00 0.00 0.00 3.01
5227 7389 7.647907 AAACGCTATTATATTACGGGAAGTG 57.352 36.000 0.00 0.00 0.00 3.16
5228 7390 5.717119 ACGCTATTATATTACGGGAAGTGG 58.283 41.667 0.00 0.00 0.00 4.00
5229 7391 5.477984 ACGCTATTATATTACGGGAAGTGGA 59.522 40.000 0.00 0.00 0.00 4.02
5230 7392 5.803967 CGCTATTATATTACGGGAAGTGGAC 59.196 44.000 0.00 0.00 0.00 4.02
5231 7393 6.570957 CGCTATTATATTACGGGAAGTGGACA 60.571 42.308 0.00 0.00 0.00 4.02
5232 7394 7.328737 GCTATTATATTACGGGAAGTGGACAT 58.671 38.462 0.00 0.00 0.00 3.06
5233 7395 7.822822 GCTATTATATTACGGGAAGTGGACATT 59.177 37.037 0.00 0.00 0.00 2.71
5234 7396 9.720769 CTATTATATTACGGGAAGTGGACATTT 57.279 33.333 0.00 0.00 0.00 2.32
5235 7397 8.617290 ATTATATTACGGGAAGTGGACATTTC 57.383 34.615 0.00 0.00 0.00 2.17
5236 7398 3.773418 TTACGGGAAGTGGACATTTCA 57.227 42.857 9.32 0.00 0.00 2.69
5237 7399 2.649531 ACGGGAAGTGGACATTTCAA 57.350 45.000 9.32 0.00 0.00 2.69
5238 7400 3.154827 ACGGGAAGTGGACATTTCAAT 57.845 42.857 9.32 0.00 0.00 2.57
5239 7401 3.081804 ACGGGAAGTGGACATTTCAATC 58.918 45.455 9.32 0.00 0.00 2.67
5240 7402 3.081061 CGGGAAGTGGACATTTCAATCA 58.919 45.455 9.32 0.00 0.00 2.57
5241 7403 3.505680 CGGGAAGTGGACATTTCAATCAA 59.494 43.478 9.32 0.00 0.00 2.57
5242 7404 4.158394 CGGGAAGTGGACATTTCAATCAAT 59.842 41.667 9.32 0.00 0.00 2.57
5243 7405 5.356751 CGGGAAGTGGACATTTCAATCAATA 59.643 40.000 9.32 0.00 0.00 1.90
5244 7406 6.564328 GGGAAGTGGACATTTCAATCAATAC 58.436 40.000 9.32 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
157 158 1.165907 TACGTGTCGAACCACCGTCT 61.166 55.000 0.00 0.00 31.47 4.18
172 173 1.663643 CAGCGCCATACAACATTACGT 59.336 47.619 2.29 0.00 0.00 3.57
175 176 2.935849 CACTCAGCGCCATACAACATTA 59.064 45.455 2.29 0.00 0.00 1.90
233 234 0.179111 ACATACACATCTCCGCCACG 60.179 55.000 0.00 0.00 0.00 4.94
246 247 5.356751 GGCCACACATTTATCTCAACATACA 59.643 40.000 0.00 0.00 0.00 2.29
287 288 5.254115 TCGTATATCATCATTCCGGACTCT 58.746 41.667 1.83 0.00 0.00 3.24
288 289 5.354513 TCTCGTATATCATCATTCCGGACTC 59.645 44.000 1.83 0.00 0.00 3.36
338 339 5.140747 AGACGATGTTAGACAAGCTTCTT 57.859 39.130 0.00 0.00 0.00 2.52
350 351 6.428465 TGCTCAAACCATTTTAGACGATGTTA 59.572 34.615 0.00 0.00 0.00 2.41
361 362 5.104374 CGCTGAATATGCTCAAACCATTTT 58.896 37.500 0.00 0.00 0.00 1.82
363 364 3.489738 GCGCTGAATATGCTCAAACCATT 60.490 43.478 0.00 0.00 0.00 3.16
398 399 1.517832 GTCCGCTATGCACTGGAGT 59.482 57.895 0.00 0.00 0.00 3.85
449 450 2.262637 TGTCAAATTCGGTCTACCCCT 58.737 47.619 0.00 0.00 0.00 4.79
472 473 3.257624 GGTCTCTTTTAACGGACTCCTCA 59.742 47.826 0.00 0.00 0.00 3.86
487 488 3.525862 ACTCCAATCCTTCAGGTCTCTT 58.474 45.455 0.00 0.00 36.34 2.85
510 511 2.435805 TCCATAGCTAGCTCTTTGGTGG 59.564 50.000 27.50 22.13 36.79 4.61
595 596 7.190501 AGTTAGGATAGGTTAGAGGTGAAACT 58.809 38.462 0.00 0.00 36.74 2.66
622 623 8.264347 ACAACAACAAAGTCTTTAATCCCAAAT 58.736 29.630 0.00 0.00 0.00 2.32
630 631 6.159988 CCACCAACAACAACAAAGTCTTTAA 58.840 36.000 0.00 0.00 0.00 1.52
636 637 2.028567 CCACCACCAACAACAACAAAGT 60.029 45.455 0.00 0.00 0.00 2.66
651 652 7.944061 AGTAAAACAATTTTAGGTACCACCAC 58.056 34.615 15.94 0.00 35.95 4.16
747 748 2.176364 AGCATCTACCGGTCTACCCTAA 59.824 50.000 12.40 0.00 0.00 2.69
748 749 1.779092 AGCATCTACCGGTCTACCCTA 59.221 52.381 12.40 0.00 0.00 3.53
749 750 0.556747 AGCATCTACCGGTCTACCCT 59.443 55.000 12.40 0.00 0.00 4.34
750 751 1.411041 AAGCATCTACCGGTCTACCC 58.589 55.000 12.40 0.00 0.00 3.69
751 752 2.694109 AGAAAGCATCTACCGGTCTACC 59.306 50.000 12.40 0.00 36.32 3.18
752 753 4.388378 AAGAAAGCATCTACCGGTCTAC 57.612 45.455 12.40 0.00 37.42 2.59
753 754 5.416271 AAAAGAAAGCATCTACCGGTCTA 57.584 39.130 12.40 0.00 37.42 2.59
754 755 3.983044 AAAGAAAGCATCTACCGGTCT 57.017 42.857 12.40 0.00 37.42 3.85
755 756 4.454504 TCAAAAAGAAAGCATCTACCGGTC 59.545 41.667 12.40 0.00 37.42 4.79
756 757 4.394729 TCAAAAAGAAAGCATCTACCGGT 58.605 39.130 13.98 13.98 37.42 5.28
757 758 4.672801 GCTCAAAAAGAAAGCATCTACCGG 60.673 45.833 0.00 0.00 37.42 5.28
758 759 4.083324 TGCTCAAAAAGAAAGCATCTACCG 60.083 41.667 0.00 0.00 40.91 4.02
763 764 7.880059 ATAACTTGCTCAAAAAGAAAGCATC 57.120 32.000 0.00 0.00 43.74 3.91
799 806 3.562973 GCGTGGAGAATGTGATGATTGAT 59.437 43.478 0.00 0.00 0.00 2.57
800 807 2.938451 GCGTGGAGAATGTGATGATTGA 59.062 45.455 0.00 0.00 0.00 2.57
935 954 0.253207 GGAAGAGGGGAAGAGGGGAA 60.253 60.000 0.00 0.00 0.00 3.97
1161 1180 1.900351 CAGCTTCCGATCAGGGTCA 59.100 57.895 0.00 0.00 41.52 4.02
1254 1273 3.998672 TCGTCCCACGTGGCCTTC 61.999 66.667 29.75 16.12 43.14 3.46
1325 1344 2.194212 GGGATGTAGAGCGCGAGGA 61.194 63.158 12.10 0.00 0.00 3.71
1393 1412 2.298158 GATTCTTGGGAGAGGCGCGA 62.298 60.000 12.10 0.00 32.44 5.87
1485 1504 2.101415 CTGATCCGCATGGTAGTTGAGA 59.899 50.000 0.00 0.00 36.30 3.27
1716 1735 1.346395 ACACCGAGTGCATTGACCTTA 59.654 47.619 0.00 0.00 36.98 2.69
1966 1985 2.099921 CAGTATCTGCGCAGACCTTACT 59.900 50.000 40.34 35.38 40.75 2.24
2743 2762 7.508687 TGGCTATAATGAGTAGCAAATCTCAA 58.491 34.615 7.36 0.00 44.92 3.02
2841 2860 1.666011 GACCTGGTGCTTCGTCTCA 59.334 57.895 2.82 0.00 0.00 3.27
2940 2959 4.387598 TGCCAAGCAAAACAGCAATATTT 58.612 34.783 0.00 0.00 34.76 1.40
3029 3048 2.614987 GCATTGCTGTCACTCTCCTCTT 60.615 50.000 0.16 0.00 0.00 2.85
3059 3078 5.650703 ACATTCTTTGCATCATCATCTGACA 59.349 36.000 0.00 0.00 36.48 3.58
3125 3144 8.103935 GGCTAGAGCTATATTACCTTGGAAATT 58.896 37.037 0.81 0.00 41.70 1.82
3262 3297 5.279156 GGTGGCATGGGATTCTTCATTATTC 60.279 44.000 0.00 0.00 0.00 1.75
3371 3408 1.285023 CTCACTTGCCAGCTGTTGC 59.715 57.895 13.81 10.56 40.05 4.17
3466 3506 5.551760 CTGGAAGTTGAGTTTGCGATTAT 57.448 39.130 0.00 0.00 0.00 1.28
3613 3653 6.783708 TTTACATGTTTGGAACTTCAGGTT 57.216 33.333 2.30 0.00 41.40 3.50
3626 3666 7.791029 AGAAACAACCCAAGATTTACATGTTT 58.209 30.769 2.30 0.00 41.06 2.83
3656 3696 0.660300 GCCGGCGAACAAGAAAGTTG 60.660 55.000 12.58 0.00 0.00 3.16
3672 3712 0.321919 CAGGATGGGGTGATATGCCG 60.322 60.000 0.00 0.00 0.00 5.69
3684 3724 2.836981 GAGGATACCAGGATCAGGATGG 59.163 54.545 10.14 7.11 40.10 3.51
3709 3749 5.810095 AGCTAACCAGAATAATATCCAGCC 58.190 41.667 0.00 0.00 0.00 4.85
3744 3784 5.885230 TGTTCAAGAAATACATGCTCCAG 57.115 39.130 0.00 0.00 0.00 3.86
3957 6113 6.481313 TGCTGCAGTATATCAAATCTTGACTC 59.519 38.462 16.64 0.00 43.48 3.36
3962 6118 5.068636 CCCTGCTGCAGTATATCAAATCTT 58.931 41.667 26.41 0.00 0.00 2.40
3983 6139 3.129988 CACTCATCCAAGATGAAAAGCCC 59.870 47.826 8.52 0.00 0.00 5.19
4032 6188 5.179368 TCTGTTTAACTCAAAAGATCAGGCG 59.821 40.000 0.00 0.00 0.00 5.52
4106 6262 2.032979 GCAAACTTTTCAAACATGCCCG 60.033 45.455 0.00 0.00 0.00 6.13
4241 6397 2.917713 ATAGCCAACCCCACAATCAA 57.082 45.000 0.00 0.00 0.00 2.57
4271 6427 4.241681 CTCAACAGGTTCTTCTCTAGCAC 58.758 47.826 0.00 0.00 0.00 4.40
4299 6455 2.307309 CGTTGAAGAGGCGTCGCAA 61.307 57.895 20.50 11.81 0.00 4.85
4342 6498 7.730084 AGAATAGAAATAGCTGTGACATGCTA 58.270 34.615 15.46 15.46 44.47 3.49
4343 6499 6.590068 AGAATAGAAATAGCTGTGACATGCT 58.410 36.000 12.69 12.69 42.67 3.79
4344 6500 6.857777 AGAATAGAAATAGCTGTGACATGC 57.142 37.500 0.00 0.00 0.00 4.06
4345 6501 7.496920 TGGAAGAATAGAAATAGCTGTGACATG 59.503 37.037 0.00 0.00 0.00 3.21
4360 6516 4.015872 ACGCCAAAACTGGAAGAATAGA 57.984 40.909 0.00 0.00 37.43 1.98
4392 6548 2.256158 CAACATGCCAGCACCACG 59.744 61.111 0.00 0.00 0.00 4.94
4431 6587 2.563620 AGTTGATGCAAATGTCATGGCA 59.436 40.909 0.60 0.60 41.00 4.92
4481 6637 3.099267 ACATCATTACTCGGCAGCTAC 57.901 47.619 0.00 0.00 0.00 3.58
4489 6645 3.787634 GCATTGCACAACATCATTACTCG 59.212 43.478 3.15 0.00 0.00 4.18
4519 6675 5.112686 ACTTAAAGATCCTCATTCAGCGTC 58.887 41.667 0.00 0.00 0.00 5.19
4558 6714 4.630069 GGTGTAGCATGTCAACGATAAACT 59.370 41.667 0.00 0.00 0.00 2.66
4563 6719 2.028112 ACTGGTGTAGCATGTCAACGAT 60.028 45.455 0.00 0.00 0.00 3.73
4565 6721 1.795768 ACTGGTGTAGCATGTCAACG 58.204 50.000 0.00 0.00 0.00 4.10
4567 6723 3.270027 GCATACTGGTGTAGCATGTCAA 58.730 45.455 0.00 0.00 33.46 3.18
4601 6757 2.699954 AGCCTTGTAAATCTCCACGTG 58.300 47.619 9.08 9.08 0.00 4.49
4614 6770 6.494835 AGAGGAACAATCAATTAAAGCCTTGT 59.505 34.615 0.00 0.00 0.00 3.16
4624 6780 8.697507 AAGACAACTTAGAGGAACAATCAATT 57.302 30.769 0.00 0.00 34.28 2.32
4640 6796 9.950496 ATCACACTAAATCATCTAAGACAACTT 57.050 29.630 0.00 0.00 39.81 2.66
4642 6798 9.979270 CAATCACACTAAATCATCTAAGACAAC 57.021 33.333 0.00 0.00 0.00 3.32
4643 6799 9.725019 ACAATCACACTAAATCATCTAAGACAA 57.275 29.630 0.00 0.00 0.00 3.18
4704 6860 7.604164 CCGAAAGTGGCATATAATACATCTCTT 59.396 37.037 0.00 0.00 0.00 2.85
4757 6913 1.325476 GGGCCCAGAAAGCTCCAATG 61.325 60.000 19.95 0.00 0.00 2.82
4779 6936 1.338864 ACTTGGCAGCTGACATCAGAG 60.339 52.381 26.07 20.25 46.59 3.35
4782 6939 1.901833 TCTACTTGGCAGCTGACATCA 59.098 47.619 26.07 8.73 30.06 3.07
4791 6948 4.836125 ACACATTTTGTCTACTTGGCAG 57.164 40.909 0.00 0.00 29.79 4.85
4816 6973 4.035792 CACGACAACCACTGTGGAAATAAA 59.964 41.667 32.30 0.00 40.96 1.40
4840 6997 7.596749 AATCGAGATAAACAAAACATCGACT 57.403 32.000 0.00 0.00 40.10 4.18
4850 7007 4.035091 CGCATCCCAAATCGAGATAAACAA 59.965 41.667 0.00 0.00 0.00 2.83
4851 7008 3.559655 CGCATCCCAAATCGAGATAAACA 59.440 43.478 0.00 0.00 0.00 2.83
4852 7009 3.807622 TCGCATCCCAAATCGAGATAAAC 59.192 43.478 0.00 0.00 0.00 2.01
4875 7036 0.382158 TGGATCTGATCGAGCGTCAC 59.618 55.000 11.28 0.00 0.00 3.67
4880 7041 3.383620 ACAAGATGGATCTGATCGAGC 57.616 47.619 9.51 9.51 37.19 5.03
4883 7044 6.276091 TCTACAAACAAGATGGATCTGATCG 58.724 40.000 11.28 0.00 37.19 3.69
4900 7062 4.487714 CCTAACAGGGCTCATCTACAAA 57.512 45.455 0.00 0.00 0.00 2.83
4946 7108 7.306953 AGAAAACACTCGTCTACTTCTGTATC 58.693 38.462 0.00 0.00 0.00 2.24
4947 7109 7.216973 AGAAAACACTCGTCTACTTCTGTAT 57.783 36.000 0.00 0.00 0.00 2.29
4948 7110 6.630444 AGAAAACACTCGTCTACTTCTGTA 57.370 37.500 0.00 0.00 0.00 2.74
4949 7111 5.517322 AGAAAACACTCGTCTACTTCTGT 57.483 39.130 0.00 0.00 0.00 3.41
4950 7112 5.977725 TCAAGAAAACACTCGTCTACTTCTG 59.022 40.000 0.00 0.00 0.00 3.02
4951 7113 5.978322 GTCAAGAAAACACTCGTCTACTTCT 59.022 40.000 0.00 0.00 0.00 2.85
4952 7114 5.747197 TGTCAAGAAAACACTCGTCTACTTC 59.253 40.000 0.00 0.00 0.00 3.01
4953 7115 5.657474 TGTCAAGAAAACACTCGTCTACTT 58.343 37.500 0.00 0.00 0.00 2.24
4954 7116 5.067413 TCTGTCAAGAAAACACTCGTCTACT 59.933 40.000 0.00 0.00 0.00 2.57
4955 7117 5.279384 TCTGTCAAGAAAACACTCGTCTAC 58.721 41.667 0.00 0.00 0.00 2.59
4956 7118 5.507482 CCTCTGTCAAGAAAACACTCGTCTA 60.507 44.000 0.00 0.00 30.03 2.59
4957 7119 4.363999 CTCTGTCAAGAAAACACTCGTCT 58.636 43.478 0.00 0.00 30.03 4.18
4958 7120 3.491267 CCTCTGTCAAGAAAACACTCGTC 59.509 47.826 0.00 0.00 30.03 4.20
4959 7121 3.458189 CCTCTGTCAAGAAAACACTCGT 58.542 45.455 0.00 0.00 30.03 4.18
4960 7122 2.221981 GCCTCTGTCAAGAAAACACTCG 59.778 50.000 0.00 0.00 30.03 4.18
4961 7123 3.206150 TGCCTCTGTCAAGAAAACACTC 58.794 45.455 0.00 0.00 30.03 3.51
4962 7124 3.281727 TGCCTCTGTCAAGAAAACACT 57.718 42.857 0.00 0.00 30.03 3.55
4963 7125 4.574599 ATTGCCTCTGTCAAGAAAACAC 57.425 40.909 0.00 0.00 30.03 3.32
4964 7126 5.376625 ACTATTGCCTCTGTCAAGAAAACA 58.623 37.500 0.00 0.00 30.03 2.83
4965 7127 5.948992 ACTATTGCCTCTGTCAAGAAAAC 57.051 39.130 0.00 0.00 30.03 2.43
4966 7128 6.650807 CAGTACTATTGCCTCTGTCAAGAAAA 59.349 38.462 0.00 0.00 30.03 2.29
4967 7129 6.166279 CAGTACTATTGCCTCTGTCAAGAAA 58.834 40.000 0.00 0.00 30.03 2.52
4968 7130 5.337571 CCAGTACTATTGCCTCTGTCAAGAA 60.338 44.000 0.00 0.00 30.03 2.52
4976 7138 2.022918 ACTCCCCAGTACTATTGCCTCT 60.023 50.000 0.00 0.00 0.00 3.69
5000 7162 1.974957 TCCTTCGTCCCAAATGTCTCA 59.025 47.619 0.00 0.00 0.00 3.27
5004 7166 5.048294 GTGTAAATTCCTTCGTCCCAAATGT 60.048 40.000 0.00 0.00 0.00 2.71
5014 7176 7.532884 CCTTTAAAACTCGTGTAAATTCCTTCG 59.467 37.037 0.00 0.00 0.00 3.79
5036 7198 5.377478 AGAACTTTTCCACGAGAATCCTTT 58.623 37.500 0.00 0.00 33.44 3.11
5055 7217 5.576384 TGTTGAATGCAAGACACAAAAGAAC 59.424 36.000 0.00 0.00 34.01 3.01
5075 7237 2.749621 GGCAGGTATTGGAAGAGTGTTG 59.250 50.000 0.00 0.00 0.00 3.33
5086 7248 2.358898 GTGCAGGTATTGGCAGGTATTG 59.641 50.000 0.00 0.00 41.35 1.90
5090 7252 0.322816 CAGTGCAGGTATTGGCAGGT 60.323 55.000 0.00 0.00 41.35 4.00
5091 7253 1.660560 GCAGTGCAGGTATTGGCAGG 61.661 60.000 11.09 0.00 41.35 4.85
5092 7254 0.961857 TGCAGTGCAGGTATTGGCAG 60.962 55.000 15.37 0.00 41.35 4.85
5093 7255 1.074599 TGCAGTGCAGGTATTGGCA 59.925 52.632 15.37 0.00 37.77 4.92
5094 7256 1.243342 TGTGCAGTGCAGGTATTGGC 61.243 55.000 20.42 4.45 40.08 4.52
5095 7257 1.402968 GATGTGCAGTGCAGGTATTGG 59.597 52.381 20.42 0.00 40.08 3.16
5096 7258 2.362736 AGATGTGCAGTGCAGGTATTG 58.637 47.619 20.42 0.00 40.08 1.90
5097 7259 2.795231 AGATGTGCAGTGCAGGTATT 57.205 45.000 20.42 1.15 40.08 1.89
5098 7260 5.246883 TCATATAGATGTGCAGTGCAGGTAT 59.753 40.000 20.42 13.40 40.08 2.73
5099 7261 4.588528 TCATATAGATGTGCAGTGCAGGTA 59.411 41.667 20.42 8.65 40.08 3.08
5100 7262 3.389002 TCATATAGATGTGCAGTGCAGGT 59.611 43.478 20.42 10.23 40.08 4.00
5138 7300 5.130292 ACAAACCATCTCATTTGCTTCAG 57.870 39.130 0.00 0.00 39.03 3.02
5139 7301 5.163426 ACAACAAACCATCTCATTTGCTTCA 60.163 36.000 0.00 0.00 39.03 3.02
5140 7302 5.291971 ACAACAAACCATCTCATTTGCTTC 58.708 37.500 0.00 0.00 39.03 3.86
5141 7303 5.280654 ACAACAAACCATCTCATTTGCTT 57.719 34.783 0.00 0.00 39.03 3.91
5142 7304 4.942761 ACAACAAACCATCTCATTTGCT 57.057 36.364 0.00 0.00 39.03 3.91
5143 7305 6.012658 TCTACAACAAACCATCTCATTTGC 57.987 37.500 0.00 0.00 39.03 3.68
5144 7306 7.592533 CAGTTCTACAACAAACCATCTCATTTG 59.407 37.037 0.00 0.00 40.83 2.32
5145 7307 7.502226 TCAGTTCTACAACAAACCATCTCATTT 59.498 33.333 0.00 0.00 34.60 2.32
5146 7308 6.998074 TCAGTTCTACAACAAACCATCTCATT 59.002 34.615 0.00 0.00 34.60 2.57
5147 7309 6.533730 TCAGTTCTACAACAAACCATCTCAT 58.466 36.000 0.00 0.00 34.60 2.90
5148 7310 5.924356 TCAGTTCTACAACAAACCATCTCA 58.076 37.500 0.00 0.00 34.60 3.27
5149 7311 6.861065 TTCAGTTCTACAACAAACCATCTC 57.139 37.500 0.00 0.00 34.60 2.75
5150 7312 7.639113 TTTTCAGTTCTACAACAAACCATCT 57.361 32.000 0.00 0.00 34.60 2.90
5151 7313 8.871686 ATTTTTCAGTTCTACAACAAACCATC 57.128 30.769 0.00 0.00 34.60 3.51
5152 7314 9.744468 GTATTTTTCAGTTCTACAACAAACCAT 57.256 29.630 0.00 0.00 34.60 3.55
5153 7315 8.962679 AGTATTTTTCAGTTCTACAACAAACCA 58.037 29.630 0.00 0.00 34.60 3.67
5154 7316 9.447040 GAGTATTTTTCAGTTCTACAACAAACC 57.553 33.333 0.00 0.00 34.60 3.27
5155 7317 9.447040 GGAGTATTTTTCAGTTCTACAACAAAC 57.553 33.333 0.00 0.00 34.60 2.93
5156 7318 8.626526 GGGAGTATTTTTCAGTTCTACAACAAA 58.373 33.333 0.00 0.00 34.60 2.83
5157 7319 7.996644 AGGGAGTATTTTTCAGTTCTACAACAA 59.003 33.333 0.00 0.00 34.60 2.83
5158 7320 7.514721 AGGGAGTATTTTTCAGTTCTACAACA 58.485 34.615 0.00 0.00 34.60 3.33
5159 7321 7.119407 GGAGGGAGTATTTTTCAGTTCTACAAC 59.881 40.741 0.00 0.00 0.00 3.32
5160 7322 7.166167 GGAGGGAGTATTTTTCAGTTCTACAA 58.834 38.462 0.00 0.00 0.00 2.41
5161 7323 6.271391 TGGAGGGAGTATTTTTCAGTTCTACA 59.729 38.462 0.00 0.00 0.00 2.74
5162 7324 6.708285 TGGAGGGAGTATTTTTCAGTTCTAC 58.292 40.000 0.00 0.00 0.00 2.59
5163 7325 6.945636 TGGAGGGAGTATTTTTCAGTTCTA 57.054 37.500 0.00 0.00 0.00 2.10
5164 7326 5.843019 TGGAGGGAGTATTTTTCAGTTCT 57.157 39.130 0.00 0.00 0.00 3.01
5165 7327 5.590663 GGATGGAGGGAGTATTTTTCAGTTC 59.409 44.000 0.00 0.00 0.00 3.01
5166 7328 5.510430 GGATGGAGGGAGTATTTTTCAGTT 58.490 41.667 0.00 0.00 0.00 3.16
5167 7329 4.079730 GGGATGGAGGGAGTATTTTTCAGT 60.080 45.833 0.00 0.00 0.00 3.41
5168 7330 4.079787 TGGGATGGAGGGAGTATTTTTCAG 60.080 45.833 0.00 0.00 0.00 3.02
5169 7331 3.855599 TGGGATGGAGGGAGTATTTTTCA 59.144 43.478 0.00 0.00 0.00 2.69
5170 7332 4.519906 TGGGATGGAGGGAGTATTTTTC 57.480 45.455 0.00 0.00 0.00 2.29
5171 7333 6.803587 ATATGGGATGGAGGGAGTATTTTT 57.196 37.500 0.00 0.00 0.00 1.94
5172 7334 7.031917 ACTATATGGGATGGAGGGAGTATTTT 58.968 38.462 0.00 0.00 0.00 1.82
5173 7335 6.445139 CACTATATGGGATGGAGGGAGTATTT 59.555 42.308 0.00 0.00 0.00 1.40
5174 7336 5.966935 CACTATATGGGATGGAGGGAGTATT 59.033 44.000 0.00 0.00 0.00 1.89
5175 7337 5.017866 ACACTATATGGGATGGAGGGAGTAT 59.982 44.000 0.00 0.00 0.00 2.12
5176 7338 4.360140 ACACTATATGGGATGGAGGGAGTA 59.640 45.833 0.00 0.00 0.00 2.59
5177 7339 3.144894 ACACTATATGGGATGGAGGGAGT 59.855 47.826 0.00 0.00 0.00 3.85
5178 7340 3.772025 GACACTATATGGGATGGAGGGAG 59.228 52.174 0.00 0.00 0.00 4.30
5179 7341 3.143933 TGACACTATATGGGATGGAGGGA 59.856 47.826 0.00 0.00 0.00 4.20
5180 7342 3.520696 TGACACTATATGGGATGGAGGG 58.479 50.000 0.00 0.00 0.00 4.30
5181 7343 5.567037 TTTGACACTATATGGGATGGAGG 57.433 43.478 0.00 0.00 0.00 4.30
5182 7344 6.017934 CGTTTTTGACACTATATGGGATGGAG 60.018 42.308 0.00 0.00 0.00 3.86
5183 7345 5.820423 CGTTTTTGACACTATATGGGATGGA 59.180 40.000 0.00 0.00 0.00 3.41
5184 7346 5.505654 GCGTTTTTGACACTATATGGGATGG 60.506 44.000 0.00 0.00 0.00 3.51
5185 7347 5.296780 AGCGTTTTTGACACTATATGGGATG 59.703 40.000 0.00 0.00 0.00 3.51
5186 7348 5.437060 AGCGTTTTTGACACTATATGGGAT 58.563 37.500 0.00 0.00 0.00 3.85
5187 7349 4.839121 AGCGTTTTTGACACTATATGGGA 58.161 39.130 0.00 0.00 0.00 4.37
5188 7350 6.861065 ATAGCGTTTTTGACACTATATGGG 57.139 37.500 0.00 0.00 33.07 4.00
5195 7357 8.545420 CCGTAATATAATAGCGTTTTTGACACT 58.455 33.333 0.00 0.00 0.00 3.55
5196 7358 7.795272 CCCGTAATATAATAGCGTTTTTGACAC 59.205 37.037 0.00 0.00 0.00 3.67
5197 7359 7.710044 TCCCGTAATATAATAGCGTTTTTGACA 59.290 33.333 0.00 0.00 0.00 3.58
5198 7360 8.075593 TCCCGTAATATAATAGCGTTTTTGAC 57.924 34.615 0.00 0.00 0.00 3.18
5199 7361 8.659925 TTCCCGTAATATAATAGCGTTTTTGA 57.340 30.769 0.00 0.00 0.00 2.69
5200 7362 8.553696 ACTTCCCGTAATATAATAGCGTTTTTG 58.446 33.333 0.00 0.00 0.00 2.44
5201 7363 8.553696 CACTTCCCGTAATATAATAGCGTTTTT 58.446 33.333 0.00 0.00 0.00 1.94
5202 7364 7.172019 CCACTTCCCGTAATATAATAGCGTTTT 59.828 37.037 0.00 0.00 0.00 2.43
5203 7365 6.647895 CCACTTCCCGTAATATAATAGCGTTT 59.352 38.462 0.00 0.00 0.00 3.60
5204 7366 6.015180 TCCACTTCCCGTAATATAATAGCGTT 60.015 38.462 0.00 0.00 0.00 4.84
5205 7367 5.477984 TCCACTTCCCGTAATATAATAGCGT 59.522 40.000 0.00 0.00 0.00 5.07
5206 7368 5.803967 GTCCACTTCCCGTAATATAATAGCG 59.196 44.000 0.00 0.00 0.00 4.26
5207 7369 6.694447 TGTCCACTTCCCGTAATATAATAGC 58.306 40.000 0.00 0.00 0.00 2.97
5208 7370 9.720769 AAATGTCCACTTCCCGTAATATAATAG 57.279 33.333 0.00 0.00 0.00 1.73
5209 7371 9.715121 GAAATGTCCACTTCCCGTAATATAATA 57.285 33.333 0.00 0.00 0.00 0.98
5210 7372 8.215050 TGAAATGTCCACTTCCCGTAATATAAT 58.785 33.333 0.00 0.00 0.00 1.28
5211 7373 7.566569 TGAAATGTCCACTTCCCGTAATATAA 58.433 34.615 0.00 0.00 0.00 0.98
5212 7374 7.127012 TGAAATGTCCACTTCCCGTAATATA 57.873 36.000 0.00 0.00 0.00 0.86
5213 7375 5.996644 TGAAATGTCCACTTCCCGTAATAT 58.003 37.500 0.00 0.00 0.00 1.28
5214 7376 5.423704 TGAAATGTCCACTTCCCGTAATA 57.576 39.130 0.00 0.00 0.00 0.98
5215 7377 4.295141 TGAAATGTCCACTTCCCGTAAT 57.705 40.909 0.00 0.00 0.00 1.89
5216 7378 3.773418 TGAAATGTCCACTTCCCGTAA 57.227 42.857 0.00 0.00 0.00 3.18
5217 7379 3.773418 TTGAAATGTCCACTTCCCGTA 57.227 42.857 0.00 0.00 0.00 4.02
5218 7380 2.649531 TTGAAATGTCCACTTCCCGT 57.350 45.000 0.00 0.00 0.00 5.28
5219 7381 3.081061 TGATTGAAATGTCCACTTCCCG 58.919 45.455 0.00 0.00 0.00 5.14
5220 7382 5.665916 ATTGATTGAAATGTCCACTTCCC 57.334 39.130 0.00 0.00 0.00 3.97


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

AutoCloner maintained by Alex Coulton.