Multiple sequence alignment - TraesCS2A01G096600

Loading Multiple Alignment...

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 TraesCS2A01G096600 chr2A 100.000 6381 0 0 1 6381 50170047 50163667 0.000000e+00 11784.0
1 TraesCS2A01G096600 chr2B 94.364 5021 158 43 864 5801 74409404 74404426 0.000000e+00 7589.0
2 TraesCS2A01G096600 chr2B 82.055 769 99 22 1 755 74412286 74411543 2.530000e-173 619.0
3 TraesCS2A01G096600 chr2D 95.237 3149 111 15 871 4001 47015954 47012827 0.000000e+00 4948.0
4 TraesCS2A01G096600 chr2D 93.990 1198 35 18 4624 5800 47012228 47011047 0.000000e+00 1779.0
5 TraesCS2A01G096600 chr2D 96.918 584 13 2 4000 4582 47012799 47012220 0.000000e+00 974.0
6 TraesCS2A01G096600 chr5A 97.982 545 11 0 5837 6381 110510998 110511542 0.000000e+00 946.0
7 TraesCS2A01G096600 chr5A 97.615 545 13 0 5837 6381 238649747 238650291 0.000000e+00 935.0
8 TraesCS2A01G096600 chr5A 97.615 545 12 1 5837 6381 456429314 456428771 0.000000e+00 933.0
9 TraesCS2A01G096600 chr6A 97.798 545 12 0 5837 6381 779062 779606 0.000000e+00 941.0
10 TraesCS2A01G096600 chr6A 97.619 546 11 2 5836 6381 445576888 445577431 0.000000e+00 935.0
11 TraesCS2A01G096600 chr6A 97.441 547 14 0 5835 6381 140819989 140820535 0.000000e+00 933.0
12 TraesCS2A01G096600 chr3A 97.615 545 13 0 5837 6381 694838129 694838673 0.000000e+00 935.0
13 TraesCS2A01G096600 chr7A 97.263 548 15 0 5834 6381 726104421 726103874 0.000000e+00 929.0
14 TraesCS2A01G096600 chr4A 97.431 545 14 0 5837 6381 494124439 494124983 0.000000e+00 929.0
15 TraesCS2A01G096600 chr6B 94.872 39 1 1 186 224 62638822 62638785 6.910000e-05 60.2
16 TraesCS2A01G096600 chr7B 94.444 36 2 0 490 525 371734327 371734292 8.940000e-04 56.5


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 TraesCS2A01G096600 chr2A 50163667 50170047 6380 True 11784 11784 100.000000 1 6381 1 chr2A.!!$R1 6380
1 TraesCS2A01G096600 chr2B 74404426 74412286 7860 True 4104 7589 88.209500 1 5801 2 chr2B.!!$R1 5800
2 TraesCS2A01G096600 chr2D 47011047 47015954 4907 True 2567 4948 95.381667 871 5800 3 chr2D.!!$R1 4929
3 TraesCS2A01G096600 chr5A 110510998 110511542 544 False 946 946 97.982000 5837 6381 1 chr5A.!!$F1 544
4 TraesCS2A01G096600 chr5A 238649747 238650291 544 False 935 935 97.615000 5837 6381 1 chr5A.!!$F2 544
5 TraesCS2A01G096600 chr5A 456428771 456429314 543 True 933 933 97.615000 5837 6381 1 chr5A.!!$R1 544
6 TraesCS2A01G096600 chr6A 779062 779606 544 False 941 941 97.798000 5837 6381 1 chr6A.!!$F1 544
7 TraesCS2A01G096600 chr6A 445576888 445577431 543 False 935 935 97.619000 5836 6381 1 chr6A.!!$F3 545
8 TraesCS2A01G096600 chr6A 140819989 140820535 546 False 933 933 97.441000 5835 6381 1 chr6A.!!$F2 546
9 TraesCS2A01G096600 chr3A 694838129 694838673 544 False 935 935 97.615000 5837 6381 1 chr3A.!!$F1 544
10 TraesCS2A01G096600 chr7A 726103874 726104421 547 True 929 929 97.263000 5834 6381 1 chr7A.!!$R1 547
11 TraesCS2A01G096600 chr4A 494124439 494124983 544 False 929 929 97.431000 5837 6381 1 chr4A.!!$F1 544

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
591 609 0.116342 ATTTTGGGGAAGGGGGACAC 59.884 55.000 0.00 0.00 0.00 3.67 F
631 649 0.178767 TATCTCGGTCCTCGGACGAA 59.821 55.000 9.81 0.21 45.41 3.85 F
637 655 0.393537 GGTCCTCGGACGAAGGAGTA 60.394 60.000 9.81 0.00 45.41 2.59 F
639 657 0.617413 TCCTCGGACGAAGGAGTACT 59.383 55.000 0.00 0.00 0.00 2.73 F
640 658 1.004044 TCCTCGGACGAAGGAGTACTT 59.996 52.381 0.00 0.00 43.65 2.24 F
1523 3653 1.007963 AGGGGTTCGTCAGATAAGGGA 59.992 52.381 0.00 0.00 0.00 4.20 F
1767 3900 1.073964 CTCGCAGACTGGTTGACATG 58.926 55.000 4.26 0.00 0.00 3.21 F
2353 4496 1.404315 CGTCCTAACCTGTGCTCCTTC 60.404 57.143 0.00 0.00 0.00 3.46 F
2683 4827 2.034221 GGGTTGGGGCACAGAGTC 59.966 66.667 0.00 0.00 0.00 3.36 F
3760 5907 1.206132 CTACAACCGAGGTGCCATACA 59.794 52.381 0.00 0.00 0.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1523 3653 1.102978 GCCCGATTTGTAACCATGCT 58.897 50.000 0.0 0.0 0.00 3.79 R
2609 4753 0.689055 TTGCCATGAGACAGACAGCT 59.311 50.000 0.0 0.0 0.00 4.24 R
2757 4903 3.600448 AATGAATGGATGGGACCGATT 57.400 42.857 0.0 0.0 0.00 3.34 R
2764 4910 5.929992 GTGCATCAATAAATGAATGGATGGG 59.070 40.000 0.0 0.0 42.54 4.00 R
2791 4937 8.465273 AGTTTGGGCATTTAGGATAATAGTTC 57.535 34.615 0.0 0.0 0.00 3.01 R
3555 5702 2.417719 AGGGTTGAGTCCTGGTAGTT 57.582 50.000 0.0 0.0 32.53 2.24 R
3736 5883 0.535335 GGCACCTCGGTTGTAGATGA 59.465 55.000 0.0 0.0 0.00 2.92 R
3760 5907 0.839946 ACTTGTCCTTGTGGAGCTGT 59.160 50.000 0.0 0.0 44.16 4.40 R
3970 6117 1.060713 CTCGATCAGAAAACGTGCGT 58.939 50.000 0.0 0.0 0.00 5.24 R
5513 7711 0.106719 CACAACAAGGGGGACACTGT 60.107 55.000 0.0 0.0 0.00 3.55 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
26 27 6.231211 TCAAAAGGATCCAAACTCTAGACAC 58.769 40.000 15.82 0.00 0.00 3.67
36 37 4.401525 AACTCTAGACACACGAACGTAG 57.598 45.455 0.00 0.00 0.00 3.51
37 38 3.657634 ACTCTAGACACACGAACGTAGA 58.342 45.455 0.00 0.00 0.00 2.59
41 42 5.820131 TCTAGACACACGAACGTAGAAAAA 58.180 37.500 0.00 0.00 0.00 1.94
42 43 4.766969 AGACACACGAACGTAGAAAAAC 57.233 40.909 0.00 0.00 0.00 2.43
45 46 5.120519 AGACACACGAACGTAGAAAAACAAA 59.879 36.000 0.00 0.00 0.00 2.83
46 47 5.318349 ACACACGAACGTAGAAAAACAAAG 58.682 37.500 0.00 0.00 0.00 2.77
47 48 5.120519 ACACACGAACGTAGAAAAACAAAGA 59.879 36.000 0.00 0.00 0.00 2.52
48 49 5.446899 CACACGAACGTAGAAAAACAAAGAC 59.553 40.000 0.00 0.00 0.00 3.01
49 50 4.959757 CACGAACGTAGAAAAACAAAGACC 59.040 41.667 0.00 0.00 0.00 3.85
50 51 4.198584 CGAACGTAGAAAAACAAAGACCG 58.801 43.478 0.00 0.00 0.00 4.79
51 52 4.026640 CGAACGTAGAAAAACAAAGACCGA 60.027 41.667 0.00 0.00 0.00 4.69
52 53 5.500610 CGAACGTAGAAAAACAAAGACCGAA 60.501 40.000 0.00 0.00 0.00 4.30
53 54 5.996669 ACGTAGAAAAACAAAGACCGAAT 57.003 34.783 0.00 0.00 0.00 3.34
54 55 5.982324 ACGTAGAAAAACAAAGACCGAATC 58.018 37.500 0.00 0.00 0.00 2.52
55 56 5.049886 ACGTAGAAAAACAAAGACCGAATCC 60.050 40.000 0.00 0.00 0.00 3.01
56 57 5.049954 CGTAGAAAAACAAAGACCGAATCCA 60.050 40.000 0.00 0.00 0.00 3.41
57 58 5.845391 AGAAAAACAAAGACCGAATCCAA 57.155 34.783 0.00 0.00 0.00 3.53
58 59 5.588240 AGAAAAACAAAGACCGAATCCAAC 58.412 37.500 0.00 0.00 0.00 3.77
59 60 4.316205 AAAACAAAGACCGAATCCAACC 57.684 40.909 0.00 0.00 0.00 3.77
78 79 5.321516 CAACCGGATTTATCGAAGACAAAC 58.678 41.667 9.46 0.00 42.51 2.93
79 80 4.571919 ACCGGATTTATCGAAGACAAACA 58.428 39.130 9.46 0.00 42.51 2.83
95 96 0.539986 AACACCGAATGTATCCCGCT 59.460 50.000 0.00 0.00 42.31 5.52
101 102 2.755655 CCGAATGTATCCCGCTAGATCT 59.244 50.000 0.00 0.00 0.00 2.75
105 106 1.257743 GTATCCCGCTAGATCTGCCA 58.742 55.000 5.18 0.00 0.00 4.92
113 114 2.543445 CGCTAGATCTGCCAGAGACAAG 60.543 54.545 5.18 0.00 31.75 3.16
173 174 0.971447 GCTGGGGTTAGACGAGGAGT 60.971 60.000 0.00 0.00 0.00 3.85
191 194 6.356186 AGGAGTCGTATTCCATATTTACCC 57.644 41.667 5.64 0.00 37.18 3.69
200 203 7.201875 CGTATTCCATATTTACCCAAAAAGGCT 60.202 37.037 0.00 0.00 35.39 4.58
203 206 6.941857 TCCATATTTACCCAAAAAGGCTTTC 58.058 36.000 13.76 0.00 35.39 2.62
204 207 5.810074 CCATATTTACCCAAAAAGGCTTTCG 59.190 40.000 13.76 7.62 35.39 3.46
205 208 3.737032 TTTACCCAAAAAGGCTTTCGG 57.263 42.857 13.76 15.96 35.39 4.30
215 218 2.483745 GCTTTCGGCCCGCTTTAC 59.516 61.111 0.00 0.00 34.27 2.01
226 229 4.495184 CGGCCCGCTTTACATACTAAAAAG 60.495 45.833 0.00 0.00 34.14 2.27
255 258 1.981256 AAACAAAGTCATCCCGCAGT 58.019 45.000 0.00 0.00 0.00 4.40
267 270 0.469917 CCCGCAGTAAGGACCATGAT 59.530 55.000 0.00 0.00 0.00 2.45
275 278 2.588877 GGACCATGATCCACCGCG 60.589 66.667 0.00 0.00 38.77 6.46
280 283 4.241555 ATGATCCACCGCGCCTCC 62.242 66.667 0.00 0.00 0.00 4.30
282 285 4.241555 GATCCACCGCGCCTCCAT 62.242 66.667 0.00 0.00 0.00 3.41
283 286 2.842462 ATCCACCGCGCCTCCATA 60.842 61.111 0.00 0.00 0.00 2.74
284 287 2.377628 GATCCACCGCGCCTCCATAA 62.378 60.000 0.00 0.00 0.00 1.90
285 288 2.660258 ATCCACCGCGCCTCCATAAC 62.660 60.000 0.00 0.00 0.00 1.89
286 289 2.186903 CACCGCGCCTCCATAACT 59.813 61.111 0.00 0.00 0.00 2.24
287 290 1.883084 CACCGCGCCTCCATAACTC 60.883 63.158 0.00 0.00 0.00 3.01
288 291 2.058595 ACCGCGCCTCCATAACTCT 61.059 57.895 0.00 0.00 0.00 3.24
290 293 0.387929 CCGCGCCTCCATAACTCTAA 59.612 55.000 0.00 0.00 0.00 2.10
292 295 1.603172 CGCGCCTCCATAACTCTAAGG 60.603 57.143 0.00 0.00 0.00 2.69
293 296 1.413077 GCGCCTCCATAACTCTAAGGT 59.587 52.381 0.00 0.00 0.00 3.50
303 306 6.096987 TCCATAACTCTAAGGTCACATGAGAC 59.903 42.308 14.20 14.20 37.80 3.36
384 387 0.797249 GCGTCACGAGCGTATTGACT 60.797 55.000 0.00 0.00 37.99 3.41
394 397 2.301870 AGCGTATTGACTGGGAAACTCA 59.698 45.455 0.00 0.00 0.00 3.41
396 399 3.063997 GCGTATTGACTGGGAAACTCATG 59.936 47.826 0.00 0.00 0.00 3.07
401 404 2.029020 TGACTGGGAAACTCATGTCTCG 60.029 50.000 0.00 0.00 0.00 4.04
407 410 2.607282 GGAAACTCATGTCTCGTGTCGT 60.607 50.000 0.00 0.00 0.00 4.34
434 437 5.006746 CGTCAGCATTTTACCTATGAACTCC 59.993 44.000 0.00 0.00 0.00 3.85
445 448 4.647399 ACCTATGAACTCCTGCTAAGAGAC 59.353 45.833 5.41 1.20 35.27 3.36
501 505 9.654663 ACTAATATATTTTCTACTTCATCCGCC 57.345 33.333 2.68 0.00 0.00 6.13
517 521 8.547481 TTCATCCGCCCTATAATATAAGATCA 57.453 34.615 0.00 0.00 0.00 2.92
518 522 8.727100 TCATCCGCCCTATAATATAAGATCAT 57.273 34.615 0.00 0.00 0.00 2.45
540 544 0.616395 TGCATTGGGACGGAGGAGTA 60.616 55.000 0.00 0.00 0.00 2.59
558 562 6.151663 GGAGTACTCCTTAATTCAGTCCTC 57.848 45.833 31.12 2.05 46.16 3.71
559 563 5.069383 GGAGTACTCCTTAATTCAGTCCTCC 59.931 48.000 31.12 2.50 46.16 4.30
560 564 5.844601 AGTACTCCTTAATTCAGTCCTCCT 58.155 41.667 0.00 0.00 0.00 3.69
561 565 6.265304 AGTACTCCTTAATTCAGTCCTCCTT 58.735 40.000 0.00 0.00 0.00 3.36
577 581 5.523552 GTCCTCCTTGGTTGTTTTGATTTTG 59.476 40.000 0.00 0.00 37.07 2.44
585 589 4.133820 GTTGTTTTGATTTTGGGGAAGGG 58.866 43.478 0.00 0.00 0.00 3.95
587 605 2.037385 TTTGATTTTGGGGAAGGGGG 57.963 50.000 0.00 0.00 0.00 5.40
591 609 0.116342 ATTTTGGGGAAGGGGGACAC 59.884 55.000 0.00 0.00 0.00 3.67
596 614 2.603652 GGGAAGGGGGACACCTCAC 61.604 68.421 0.00 0.00 40.96 3.51
598 616 0.252558 GGAAGGGGGACACCTCACTA 60.253 60.000 0.00 0.00 40.96 2.74
602 620 0.252103 GGGGGACACCTCACTAGACA 60.252 60.000 0.00 0.00 37.13 3.41
603 621 1.187087 GGGGACACCTCACTAGACAG 58.813 60.000 0.00 0.00 36.80 3.51
604 622 1.550409 GGGGACACCTCACTAGACAGT 60.550 57.143 0.00 0.00 36.80 3.55
607 625 3.071167 GGGACACCTCACTAGACAGTTTT 59.929 47.826 0.00 0.00 30.46 2.43
614 632 7.670559 ACACCTCACTAGACAGTTTTCTACTAT 59.329 37.037 0.00 0.00 34.56 2.12
616 634 8.110908 ACCTCACTAGACAGTTTTCTACTATCT 58.889 37.037 0.00 0.00 43.06 1.98
617 635 8.617809 CCTCACTAGACAGTTTTCTACTATCTC 58.382 40.741 0.00 0.00 35.76 2.75
618 636 8.199176 TCACTAGACAGTTTTCTACTATCTCG 57.801 38.462 0.00 0.00 35.76 4.04
619 637 7.280428 TCACTAGACAGTTTTCTACTATCTCGG 59.720 40.741 0.00 0.00 35.76 4.63
624 642 5.357596 ACAGTTTTCTACTATCTCGGTCCTC 59.642 44.000 0.00 0.00 34.56 3.71
626 644 2.835580 TCTACTATCTCGGTCCTCGG 57.164 55.000 0.00 0.00 39.77 4.63
627 645 2.323599 TCTACTATCTCGGTCCTCGGA 58.676 52.381 0.00 0.00 39.77 4.55
628 646 2.036992 TCTACTATCTCGGTCCTCGGAC 59.963 54.545 7.57 7.57 43.87 4.79
629 647 0.532417 ACTATCTCGGTCCTCGGACG 60.532 60.000 9.81 5.93 45.41 4.79
630 648 0.249784 CTATCTCGGTCCTCGGACGA 60.250 60.000 9.81 9.47 45.41 4.20
631 649 0.178767 TATCTCGGTCCTCGGACGAA 59.821 55.000 9.81 0.21 45.41 3.85
632 650 1.096386 ATCTCGGTCCTCGGACGAAG 61.096 60.000 9.81 9.37 45.41 3.79
633 651 2.749044 TCGGTCCTCGGACGAAGG 60.749 66.667 9.81 0.29 45.41 3.46
634 652 2.749044 CGGTCCTCGGACGAAGGA 60.749 66.667 9.81 8.23 45.41 3.36
635 653 2.762234 CGGTCCTCGGACGAAGGAG 61.762 68.421 9.81 0.00 45.41 3.69
636 654 1.678300 GGTCCTCGGACGAAGGAGT 60.678 63.158 9.81 0.00 45.41 3.85
637 655 0.393537 GGTCCTCGGACGAAGGAGTA 60.394 60.000 9.81 0.00 45.41 2.59
638 656 0.731994 GTCCTCGGACGAAGGAGTAC 59.268 60.000 11.36 0.00 35.30 2.73
639 657 0.617413 TCCTCGGACGAAGGAGTACT 59.383 55.000 0.00 0.00 0.00 2.73
640 658 1.004044 TCCTCGGACGAAGGAGTACTT 59.996 52.381 0.00 0.00 43.65 2.24
653 671 5.632034 AGGAGTACTTCATAATTGGTCCC 57.368 43.478 3.42 0.00 0.00 4.46
664 682 9.586435 CTTCATAATTGGTCCCTTTTGTATTTC 57.414 33.333 0.00 0.00 0.00 2.17
670 688 6.463995 TGGTCCCTTTTGTATTTCATATGC 57.536 37.500 0.00 0.00 0.00 3.14
671 689 5.362430 TGGTCCCTTTTGTATTTCATATGCC 59.638 40.000 0.00 0.00 0.00 4.40
831 2958 8.665643 AAAATATAACACGAAATACGATGGGA 57.334 30.769 0.00 0.00 45.77 4.37
832 2959 8.665643 AAATATAACACGAAATACGATGGGAA 57.334 30.769 0.00 0.00 45.77 3.97
833 2960 5.978934 ATAACACGAAATACGATGGGAAC 57.021 39.130 0.00 0.00 45.77 3.62
834 2961 3.604875 ACACGAAATACGATGGGAACT 57.395 42.857 0.00 0.00 45.77 3.01
835 2962 4.724074 ACACGAAATACGATGGGAACTA 57.276 40.909 0.00 0.00 45.77 2.24
836 2963 4.679662 ACACGAAATACGATGGGAACTAG 58.320 43.478 0.00 0.00 45.77 2.57
837 2964 4.159135 ACACGAAATACGATGGGAACTAGT 59.841 41.667 0.00 0.00 45.77 2.57
838 2965 5.357878 ACACGAAATACGATGGGAACTAGTA 59.642 40.000 0.00 0.00 45.77 1.82
839 2966 5.913514 CACGAAATACGATGGGAACTAGTAG 59.086 44.000 0.00 0.00 45.77 2.57
840 2967 5.591877 ACGAAATACGATGGGAACTAGTAGT 59.408 40.000 0.00 0.00 45.77 2.73
841 2968 6.767902 ACGAAATACGATGGGAACTAGTAGTA 59.232 38.462 2.50 0.00 45.77 1.82
842 2969 7.283127 ACGAAATACGATGGGAACTAGTAGTAA 59.717 37.037 2.50 0.00 45.77 2.24
843 2970 8.131100 CGAAATACGATGGGAACTAGTAGTAAA 58.869 37.037 2.50 0.00 45.77 2.01
844 2971 9.978044 GAAATACGATGGGAACTAGTAGTAAAT 57.022 33.333 2.50 0.00 0.00 1.40
845 2972 9.978044 AAATACGATGGGAACTAGTAGTAAATC 57.022 33.333 2.50 4.24 0.00 2.17
846 2973 8.701908 ATACGATGGGAACTAGTAGTAAATCA 57.298 34.615 2.50 1.12 0.00 2.57
847 2974 7.040473 ACGATGGGAACTAGTAGTAAATCAG 57.960 40.000 2.50 4.71 0.00 2.90
848 2975 6.606395 ACGATGGGAACTAGTAGTAAATCAGT 59.394 38.462 2.50 5.20 0.00 3.41
849 2976 7.776969 ACGATGGGAACTAGTAGTAAATCAGTA 59.223 37.037 2.50 0.00 0.00 2.74
850 2977 8.627403 CGATGGGAACTAGTAGTAAATCAGTAA 58.373 37.037 2.50 0.00 0.00 2.24
853 2980 9.933723 TGGGAACTAGTAGTAAATCAGTAAAAC 57.066 33.333 2.50 0.00 0.00 2.43
854 2981 9.933723 GGGAACTAGTAGTAAATCAGTAAAACA 57.066 33.333 2.50 0.00 0.00 2.83
859 2986 9.804758 CTAGTAGTAAATCAGTAAAACAGGAGG 57.195 37.037 0.00 0.00 0.00 4.30
860 2987 7.104290 AGTAGTAAATCAGTAAAACAGGAGGC 58.896 38.462 0.00 0.00 0.00 4.70
861 2988 5.254115 AGTAAATCAGTAAAACAGGAGGCC 58.746 41.667 0.00 0.00 0.00 5.19
862 2989 2.403252 ATCAGTAAAACAGGAGGCCG 57.597 50.000 0.00 0.00 0.00 6.13
886 3013 3.056035 ACTCCGTAAACTCTTTGGCTAGG 60.056 47.826 0.00 0.00 0.00 3.02
942 3069 3.849953 GAACGCCACGGTGATCGC 61.850 66.667 10.28 3.67 43.89 4.58
943 3070 4.673298 AACGCCACGGTGATCGCA 62.673 61.111 10.28 0.00 43.89 5.10
1239 3366 1.228003 CAACCCGTACACCAGCCAA 60.228 57.895 0.00 0.00 0.00 4.52
1456 3583 3.865745 CACTGTCTCCGATTTGGTACATC 59.134 47.826 0.00 0.00 39.30 3.06
1523 3653 1.007963 AGGGGTTCGTCAGATAAGGGA 59.992 52.381 0.00 0.00 0.00 4.20
1534 3664 4.037222 TCAGATAAGGGAGCATGGTTACA 58.963 43.478 0.00 0.00 0.00 2.41
1550 3680 1.271856 TACAAATCGGGCCTCACTGA 58.728 50.000 0.84 0.00 0.00 3.41
1554 3687 2.514458 AATCGGGCCTCACTGATTTT 57.486 45.000 0.84 0.00 42.30 1.82
1557 3690 2.184533 TCGGGCCTCACTGATTTTCTA 58.815 47.619 0.84 0.00 0.00 2.10
1581 3714 5.056480 TCGAATCGATTGTTCTTGGCATAT 58.944 37.500 16.96 0.00 0.00 1.78
1667 3800 2.310647 TGGGTTCTAGGTTTGGGAATCC 59.689 50.000 0.00 0.00 39.81 3.01
1750 3883 1.666189 GCTCACCCGCATCTTAAACTC 59.334 52.381 0.00 0.00 0.00 3.01
1767 3900 1.073964 CTCGCAGACTGGTTGACATG 58.926 55.000 4.26 0.00 0.00 3.21
1828 3961 8.558973 AATCTTGACCATGAGAAGTTCTTTAG 57.441 34.615 6.88 0.00 0.00 1.85
2001 4134 7.106663 ACTGACGAAATAATAGAATAAGCGC 57.893 36.000 0.00 0.00 0.00 5.92
2108 4251 7.115378 GCAGATGTGAACTTTGGACATTTTTAG 59.885 37.037 0.00 0.00 30.39 1.85
2134 4277 7.584987 CCTAGTTGGAACTGTTGTATTTTCAG 58.415 38.462 0.00 0.00 40.07 3.02
2280 4423 7.994425 TTTCACCATTTTGACATAGCTTAGA 57.006 32.000 0.00 0.00 0.00 2.10
2353 4496 1.404315 CGTCCTAACCTGTGCTCCTTC 60.404 57.143 0.00 0.00 0.00 3.46
2478 4622 3.383162 GAGTGACCCTTCTCTCCCA 57.617 57.895 0.00 0.00 36.68 4.37
2495 4639 7.116736 TCTCTCCCATACTTGGTTAAAATTCC 58.883 38.462 0.00 0.00 41.91 3.01
2609 4753 5.540911 GTGATGGAAAATTGCCTTCAAAGA 58.459 37.500 9.87 0.00 40.10 2.52
2682 4826 3.580319 GGGGTTGGGGCACAGAGT 61.580 66.667 0.00 0.00 0.00 3.24
2683 4827 2.034221 GGGTTGGGGCACAGAGTC 59.966 66.667 0.00 0.00 0.00 3.36
2757 4903 3.105283 GTTCTTAGGCCTTAGGACCTGA 58.895 50.000 18.06 12.98 36.77 3.86
2791 4937 4.037803 TCCATTCATTTATTGATGCACGGG 59.962 41.667 0.00 0.00 33.34 5.28
2837 4983 7.834068 AACTCAATTGTAGTGCTAGTGTATG 57.166 36.000 5.13 0.00 0.00 2.39
2851 4997 8.883731 GTGCTAGTGTATGTATCTTGTTTCAAT 58.116 33.333 0.00 0.00 0.00 2.57
2863 5009 4.823442 TCTTGTTTCAATGTGAGCATCTGT 59.177 37.500 0.00 0.00 33.50 3.41
2945 5091 3.966543 CTCACCCCCGGCCACTTT 61.967 66.667 2.24 0.00 0.00 2.66
3008 5154 5.699097 TGTTCACACCTATTTTTGCCTAC 57.301 39.130 0.00 0.00 0.00 3.18
3053 5199 5.822519 ACTTGTTTCTGCTGAGAACATTGTA 59.177 36.000 16.12 6.47 37.97 2.41
3064 5210 4.523943 TGAGAACATTGTAGCCTGCAATTT 59.476 37.500 5.20 4.38 34.68 1.82
3083 5229 8.318412 TGCAATTTTCAGGTCTATTGAGTACTA 58.682 33.333 0.00 0.00 31.29 1.82
3154 5300 3.810941 ACTTGGCAGCATTCATTTGTTTG 59.189 39.130 0.00 0.00 0.00 2.93
3265 5411 4.898829 TGTCCTTGTCATGTCAAAACTG 57.101 40.909 6.82 0.00 0.00 3.16
3409 5556 6.547510 GTCCTATATTTGGATCAAGCAAAGGT 59.452 38.462 0.00 0.00 35.87 3.50
3493 5640 7.259290 TGACTGTTAATTCTTGAAAGACACC 57.741 36.000 0.00 0.00 34.13 4.16
3555 5702 8.171400 CCCAAAGGACTATATAGGAGAACTAGA 58.829 40.741 14.25 0.00 32.22 2.43
3736 5883 5.717078 AACATTGACTTCAACATGCATCT 57.283 34.783 0.00 0.00 38.86 2.90
3760 5907 1.206132 CTACAACCGAGGTGCCATACA 59.794 52.381 0.00 0.00 0.00 2.29
3812 5959 3.621268 GTGCGCCATAATACTTCACAAGA 59.379 43.478 4.18 0.00 0.00 3.02
3814 5961 3.871594 GCGCCATAATACTTCACAAGAGT 59.128 43.478 0.00 0.00 0.00 3.24
3898 6045 1.924731 ATCCTCAGTCGGTCTGTCAA 58.075 50.000 2.32 0.00 43.97 3.18
3970 6117 2.902705 ACGTTCAGTTAACTCCAGCA 57.097 45.000 4.77 0.00 35.81 4.41
3986 6133 0.512952 AGCACGCACGTTTTCTGATC 59.487 50.000 0.00 0.00 0.00 2.92
3998 6145 4.201628 CGTTTTCTGATCGAGTTTAGCCAG 60.202 45.833 0.00 0.00 0.00 4.85
4015 6191 2.421424 GCCAGGTTAGCAGAAACATCAG 59.579 50.000 0.00 0.00 0.00 2.90
4051 6227 9.447040 CATGCTATCTGAACTTCATTTTACATG 57.553 33.333 0.00 0.00 0.00 3.21
4176 6352 3.382865 TGTGCTTGGAGTGTAAATTTGCA 59.617 39.130 4.71 4.71 0.00 4.08
4192 6368 1.464734 TGCAGGTCTCGACTAAGAGG 58.535 55.000 0.00 0.00 38.71 3.69
4366 6543 3.969287 TGATACATAGCTGAGGGCATC 57.031 47.619 0.00 0.00 44.79 3.91
4539 6716 8.890472 AGACTGGGTGGCTATATATCAAATTTA 58.110 33.333 0.00 0.00 27.54 1.40
4558 6735 6.655078 ATTTAGTGCTGCCCCTAAAATATG 57.345 37.500 19.06 0.00 36.89 1.78
4579 6756 2.159198 GCTGGCCTCCATTTAATGTGTG 60.159 50.000 3.32 0.00 30.82 3.82
4580 6757 1.824230 TGGCCTCCATTTAATGTGTGC 59.176 47.619 3.32 3.25 0.00 4.57
4634 6811 5.898174 CATGGATTTCACATGTGCACTAAT 58.102 37.500 21.38 15.77 40.54 1.73
4713 6890 6.595326 TCAGTTCACCTTAATTGTATCTGCTG 59.405 38.462 0.00 0.00 0.00 4.41
5122 7301 1.968017 CGCCACTGCTGATGGTGTT 60.968 57.895 13.68 0.00 41.88 3.32
5319 7498 1.885887 GAAGCACAAGGCCAATGTACA 59.114 47.619 13.22 0.00 46.50 2.90
5385 7576 2.887568 GCATGTCGCCTGAGACGG 60.888 66.667 0.00 0.00 43.70 4.79
5468 7666 3.068560 CCAGCATTCAAAAACCCATGTG 58.931 45.455 0.00 0.00 0.00 3.21
5513 7711 4.873746 AGCTTAGTCTCTGTTGCAGTTA 57.126 40.909 0.00 0.00 32.61 2.24
5525 7723 0.766674 TGCAGTTACAGTGTCCCCCT 60.767 55.000 0.00 0.00 0.00 4.79
5544 7745 2.612212 CCTTGTTGTGCTGTAGAAACGT 59.388 45.455 0.00 0.00 0.00 3.99
5646 7847 5.181811 TCTGTTGATGAATGTTGTGGTGATC 59.818 40.000 0.00 0.00 0.00 2.92
5650 7851 5.315348 TGATGAATGTTGTGGTGATCTTGA 58.685 37.500 0.00 0.00 0.00 3.02
5703 7915 1.369839 TTCGCGCCGCATAAATGGAA 61.370 50.000 10.75 0.00 0.00 3.53
5820 8037 7.938140 TTTTTAGGGATTGTAGTCATCCTTG 57.062 36.000 0.00 0.00 34.95 3.61
5821 8038 5.630415 TTAGGGATTGTAGTCATCCTTGG 57.370 43.478 0.00 0.00 34.95 3.61
5822 8039 3.464828 AGGGATTGTAGTCATCCTTGGT 58.535 45.455 0.00 0.00 34.95 3.67
5823 8040 3.200825 AGGGATTGTAGTCATCCTTGGTG 59.799 47.826 0.00 0.00 34.95 4.17
5824 8041 3.054361 GGGATTGTAGTCATCCTTGGTGT 60.054 47.826 0.00 0.00 34.95 4.16
5825 8042 4.192317 GGATTGTAGTCATCCTTGGTGTC 58.808 47.826 0.00 0.00 0.00 3.67
5826 8043 3.313012 TTGTAGTCATCCTTGGTGTCG 57.687 47.619 0.00 0.00 0.00 4.35
5827 8044 1.067142 TGTAGTCATCCTTGGTGTCGC 60.067 52.381 0.00 0.00 0.00 5.19
5828 8045 1.067142 GTAGTCATCCTTGGTGTCGCA 60.067 52.381 0.00 0.00 0.00 5.10
5829 8046 0.615331 AGTCATCCTTGGTGTCGCAT 59.385 50.000 0.00 0.00 0.00 4.73
5830 8047 0.729116 GTCATCCTTGGTGTCGCATG 59.271 55.000 0.00 0.00 0.00 4.06
5831 8048 0.612744 TCATCCTTGGTGTCGCATGA 59.387 50.000 0.00 0.00 0.00 3.07
5832 8049 1.003003 TCATCCTTGGTGTCGCATGAA 59.997 47.619 0.00 0.00 0.00 2.57
5928 8145 0.811616 GAAGCATCCGCATCCGAACT 60.812 55.000 0.00 0.00 42.27 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 4.503767 TGTTTTTCTACGTTCGTGTGTC 57.496 40.909 8.14 0.00 0.00 3.67
26 27 4.959757 GGTCTTTGTTTTTCTACGTTCGTG 59.040 41.667 8.14 0.00 0.00 4.35
36 37 4.743151 GGTTGGATTCGGTCTTTGTTTTTC 59.257 41.667 0.00 0.00 0.00 2.29
37 38 4.689071 GGTTGGATTCGGTCTTTGTTTTT 58.311 39.130 0.00 0.00 0.00 1.94
41 42 1.519408 CGGTTGGATTCGGTCTTTGT 58.481 50.000 0.00 0.00 0.00 2.83
42 43 0.802494 CCGGTTGGATTCGGTCTTTG 59.198 55.000 0.00 0.00 41.23 2.77
45 46 4.123571 TCCGGTTGGATTCGGTCT 57.876 55.556 0.00 0.00 45.79 3.85
54 55 3.527533 TGTCTTCGATAAATCCGGTTGG 58.472 45.455 0.00 0.00 0.00 3.77
55 56 5.106869 TGTTTGTCTTCGATAAATCCGGTTG 60.107 40.000 0.00 0.00 0.00 3.77
56 57 4.998672 TGTTTGTCTTCGATAAATCCGGTT 59.001 37.500 0.00 0.00 0.00 4.44
57 58 4.390909 GTGTTTGTCTTCGATAAATCCGGT 59.609 41.667 0.00 0.00 0.00 5.28
58 59 4.201783 GGTGTTTGTCTTCGATAAATCCGG 60.202 45.833 0.00 0.00 0.00 5.14
59 60 4.491924 CGGTGTTTGTCTTCGATAAATCCG 60.492 45.833 13.19 13.19 37.05 4.18
67 68 2.828877 ACATTCGGTGTTTGTCTTCGA 58.171 42.857 0.00 0.00 38.01 3.71
68 69 4.201685 GGATACATTCGGTGTTTGTCTTCG 60.202 45.833 0.00 0.00 42.29 3.79
78 79 1.611977 TCTAGCGGGATACATTCGGTG 59.388 52.381 0.00 0.00 36.10 4.94
79 80 1.991121 TCTAGCGGGATACATTCGGT 58.009 50.000 0.00 0.00 38.23 4.69
95 96 1.759445 GGCTTGTCTCTGGCAGATCTA 59.241 52.381 19.11 10.18 32.08 1.98
101 102 1.842920 TGGAGGCTTGTCTCTGGCA 60.843 57.895 2.16 0.00 34.39 4.92
105 106 1.668294 CGTGTGGAGGCTTGTCTCT 59.332 57.895 2.16 0.00 34.39 3.10
113 114 3.075005 TAGAGGGCGTGTGGAGGC 61.075 66.667 0.00 0.00 0.00 4.70
129 130 4.768130 GATGGTACTTCTAGCATCGCTA 57.232 45.455 4.61 0.00 44.15 4.26
148 149 2.070650 GTCTAACCCCAGCCCCGAT 61.071 63.158 0.00 0.00 0.00 4.18
173 174 7.201839 GCCTTTTTGGGTAAATATGGAATACGA 60.202 37.037 0.00 0.00 36.00 3.43
174 175 6.921307 GCCTTTTTGGGTAAATATGGAATACG 59.079 38.462 0.00 0.00 36.00 3.06
175 176 8.018537 AGCCTTTTTGGGTAAATATGGAATAC 57.981 34.615 0.00 0.00 46.10 1.89
200 203 1.065998 AGTATGTAAAGCGGGCCGAAA 60.066 47.619 33.44 3.23 0.00 3.46
203 206 2.228138 TTAGTATGTAAAGCGGGCCG 57.772 50.000 24.35 24.35 0.00 6.13
204 207 4.397103 ACTTTTTAGTATGTAAAGCGGGCC 59.603 41.667 0.00 0.00 33.29 5.80
205 208 5.556355 ACTTTTTAGTATGTAAAGCGGGC 57.444 39.130 0.00 0.00 33.29 6.13
226 229 8.068380 GCGGGATGACTTTGTTTTTAGATATAC 58.932 37.037 0.00 0.00 0.00 1.47
239 242 2.009774 CCTTACTGCGGGATGACTTTG 58.990 52.381 0.00 0.00 0.00 2.77
240 243 1.906574 TCCTTACTGCGGGATGACTTT 59.093 47.619 0.00 0.00 0.00 2.66
243 246 0.179081 GGTCCTTACTGCGGGATGAC 60.179 60.000 0.00 0.00 33.89 3.06
244 247 0.616395 TGGTCCTTACTGCGGGATGA 60.616 55.000 0.00 0.00 33.89 2.92
255 258 0.468226 GCGGTGGATCATGGTCCTTA 59.532 55.000 25.35 3.52 39.12 2.69
267 270 3.078196 TTATGGAGGCGCGGTGGA 61.078 61.111 8.83 0.00 0.00 4.02
275 278 3.451178 TGTGACCTTAGAGTTATGGAGGC 59.549 47.826 0.00 0.00 0.00 4.70
280 283 5.974158 CGTCTCATGTGACCTTAGAGTTATG 59.026 44.000 19.41 0.72 33.70 1.90
281 284 5.886474 TCGTCTCATGTGACCTTAGAGTTAT 59.114 40.000 19.41 0.00 33.70 1.89
282 285 5.250982 TCGTCTCATGTGACCTTAGAGTTA 58.749 41.667 19.41 0.00 33.70 2.24
283 286 4.079970 TCGTCTCATGTGACCTTAGAGTT 58.920 43.478 19.41 0.00 33.70 3.01
284 287 3.687125 TCGTCTCATGTGACCTTAGAGT 58.313 45.455 19.41 0.00 33.70 3.24
285 288 3.066064 CCTCGTCTCATGTGACCTTAGAG 59.934 52.174 19.41 18.00 33.70 2.43
286 289 3.017442 CCTCGTCTCATGTGACCTTAGA 58.983 50.000 19.41 11.24 33.70 2.10
287 290 2.480416 GCCTCGTCTCATGTGACCTTAG 60.480 54.545 19.41 14.36 33.70 2.18
288 291 1.476891 GCCTCGTCTCATGTGACCTTA 59.523 52.381 19.41 7.08 33.70 2.69
290 293 0.900182 TGCCTCGTCTCATGTGACCT 60.900 55.000 19.41 0.00 33.70 3.85
292 295 0.528017 TCTGCCTCGTCTCATGTGAC 59.472 55.000 16.25 16.25 0.00 3.67
293 296 0.528017 GTCTGCCTCGTCTCATGTGA 59.472 55.000 0.00 0.00 0.00 3.58
384 387 1.691976 ACACGAGACATGAGTTTCCCA 59.308 47.619 0.00 0.00 0.00 4.37
394 397 2.202311 CGCGACGACACGAGACAT 60.202 61.111 0.00 0.00 35.31 3.06
396 399 2.864248 GACGCGACGACACGAGAC 60.864 66.667 15.93 0.00 36.92 3.36
401 404 1.886861 AAATGCTGACGCGACGACAC 61.887 55.000 15.93 0.00 39.65 3.67
407 410 2.658373 TAGGTAAAATGCTGACGCGA 57.342 45.000 15.93 0.00 39.65 5.87
493 497 8.727100 ATGATCTTATATTATAGGGCGGATGA 57.273 34.615 0.00 0.00 0.00 2.92
517 521 1.185315 CCTCCGTCCCAATGCAAAAT 58.815 50.000 0.00 0.00 0.00 1.82
518 522 0.111446 TCCTCCGTCCCAATGCAAAA 59.889 50.000 0.00 0.00 0.00 2.44
540 544 4.226168 CCAAGGAGGACTGAATTAAGGAGT 59.774 45.833 0.00 0.00 41.22 3.85
551 555 3.287222 TCAAAACAACCAAGGAGGACTG 58.713 45.455 0.00 0.00 41.22 3.51
558 562 3.882288 CCCCAAAATCAAAACAACCAAGG 59.118 43.478 0.00 0.00 0.00 3.61
559 563 4.775236 TCCCCAAAATCAAAACAACCAAG 58.225 39.130 0.00 0.00 0.00 3.61
560 564 4.844349 TCCCCAAAATCAAAACAACCAA 57.156 36.364 0.00 0.00 0.00 3.67
561 565 4.384647 CCTTCCCCAAAATCAAAACAACCA 60.385 41.667 0.00 0.00 0.00 3.67
577 581 3.015753 GAGGTGTCCCCCTTCCCC 61.016 72.222 0.00 0.00 34.03 4.81
585 589 1.926108 ACTGTCTAGTGAGGTGTCCC 58.074 55.000 0.00 0.00 35.34 4.46
587 605 5.203060 AGAAAACTGTCTAGTGAGGTGTC 57.797 43.478 0.00 0.00 37.19 3.67
602 620 4.575645 CGAGGACCGAGATAGTAGAAAACT 59.424 45.833 0.00 0.00 41.76 2.66
603 621 4.261114 CCGAGGACCGAGATAGTAGAAAAC 60.261 50.000 0.00 0.00 41.76 2.43
604 622 3.881688 CCGAGGACCGAGATAGTAGAAAA 59.118 47.826 0.00 0.00 41.76 2.29
607 625 2.036992 GTCCGAGGACCGAGATAGTAGA 59.963 54.545 11.07 0.00 41.76 2.59
614 632 1.744368 CTTCGTCCGAGGACCGAGA 60.744 63.158 15.88 5.59 41.76 4.04
616 634 2.749044 CCTTCGTCCGAGGACCGA 60.749 66.667 15.88 13.11 41.76 4.69
617 635 2.749044 TCCTTCGTCCGAGGACCG 60.749 66.667 15.88 11.20 41.76 4.79
618 636 0.393537 TACTCCTTCGTCCGAGGACC 60.394 60.000 15.88 0.00 41.76 4.46
619 637 0.731994 GTACTCCTTCGTCCGAGGAC 59.268 60.000 12.07 12.07 41.40 3.85
630 648 5.731678 AGGGACCAATTATGAAGTACTCCTT 59.268 40.000 0.00 0.00 35.59 3.36
631 649 5.289510 AGGGACCAATTATGAAGTACTCCT 58.710 41.667 0.00 0.00 0.00 3.69
632 650 5.632034 AGGGACCAATTATGAAGTACTCC 57.368 43.478 0.00 0.00 0.00 3.85
633 651 7.393515 ACAAAAGGGACCAATTATGAAGTACTC 59.606 37.037 0.00 0.00 0.00 2.59
634 652 7.238710 ACAAAAGGGACCAATTATGAAGTACT 58.761 34.615 0.00 0.00 0.00 2.73
635 653 7.462571 ACAAAAGGGACCAATTATGAAGTAC 57.537 36.000 0.00 0.00 0.00 2.73
636 654 9.762381 AATACAAAAGGGACCAATTATGAAGTA 57.238 29.630 0.00 0.00 0.00 2.24
637 655 8.664669 AATACAAAAGGGACCAATTATGAAGT 57.335 30.769 0.00 0.00 0.00 3.01
638 656 9.586435 GAAATACAAAAGGGACCAATTATGAAG 57.414 33.333 0.00 0.00 0.00 3.02
639 657 9.094578 TGAAATACAAAAGGGACCAATTATGAA 57.905 29.630 0.00 0.00 0.00 2.57
640 658 8.657387 TGAAATACAAAAGGGACCAATTATGA 57.343 30.769 0.00 0.00 0.00 2.15
644 662 7.986889 GCATATGAAATACAAAAGGGACCAATT 59.013 33.333 6.97 0.00 0.00 2.32
649 667 6.463995 TGGCATATGAAATACAAAAGGGAC 57.536 37.500 6.97 0.00 0.00 4.46
651 669 8.735692 AATTTGGCATATGAAATACAAAAGGG 57.264 30.769 6.97 0.00 29.75 3.95
669 687 7.938715 AGTCAGATCTATGATCAAAATTTGGC 58.061 34.615 5.83 1.21 0.00 4.52
805 2932 9.761504 TCCCATCGTATTTCGTGTTATATTTTA 57.238 29.630 0.00 0.00 40.80 1.52
806 2933 8.665643 TCCCATCGTATTTCGTGTTATATTTT 57.334 30.769 0.00 0.00 40.80 1.82
807 2934 8.553696 GTTCCCATCGTATTTCGTGTTATATTT 58.446 33.333 0.00 0.00 40.80 1.40
808 2935 7.929785 AGTTCCCATCGTATTTCGTGTTATATT 59.070 33.333 0.00 0.00 40.80 1.28
809 2936 7.439381 AGTTCCCATCGTATTTCGTGTTATAT 58.561 34.615 0.00 0.00 40.80 0.86
810 2937 6.808829 AGTTCCCATCGTATTTCGTGTTATA 58.191 36.000 0.00 0.00 40.80 0.98
811 2938 5.667466 AGTTCCCATCGTATTTCGTGTTAT 58.333 37.500 0.00 0.00 40.80 1.89
812 2939 5.075858 AGTTCCCATCGTATTTCGTGTTA 57.924 39.130 0.00 0.00 40.80 2.41
813 2940 3.934068 AGTTCCCATCGTATTTCGTGTT 58.066 40.909 0.00 0.00 40.80 3.32
814 2941 3.604875 AGTTCCCATCGTATTTCGTGT 57.395 42.857 0.00 0.00 40.80 4.49
815 2942 4.679662 ACTAGTTCCCATCGTATTTCGTG 58.320 43.478 0.00 0.00 40.80 4.35
816 2943 4.996788 ACTAGTTCCCATCGTATTTCGT 57.003 40.909 0.00 0.00 40.80 3.85
817 2944 6.069684 ACTACTAGTTCCCATCGTATTTCG 57.930 41.667 0.00 0.00 41.41 3.46
818 2945 9.978044 ATTTACTACTAGTTCCCATCGTATTTC 57.022 33.333 0.00 0.00 0.00 2.17
819 2946 9.978044 GATTTACTACTAGTTCCCATCGTATTT 57.022 33.333 0.00 0.00 0.00 1.40
820 2947 9.139734 TGATTTACTACTAGTTCCCATCGTATT 57.860 33.333 0.00 0.00 0.00 1.89
821 2948 8.701908 TGATTTACTACTAGTTCCCATCGTAT 57.298 34.615 0.00 0.00 0.00 3.06
822 2949 7.776969 ACTGATTTACTACTAGTTCCCATCGTA 59.223 37.037 0.00 0.00 0.00 3.43
823 2950 6.606395 ACTGATTTACTACTAGTTCCCATCGT 59.394 38.462 0.00 0.00 0.00 3.73
824 2951 7.040473 ACTGATTTACTACTAGTTCCCATCG 57.960 40.000 0.00 0.00 0.00 3.84
827 2954 9.933723 GTTTTACTGATTTACTACTAGTTCCCA 57.066 33.333 0.00 0.00 0.00 4.37
828 2955 9.933723 TGTTTTACTGATTTACTACTAGTTCCC 57.066 33.333 0.00 0.00 0.00 3.97
833 2960 9.804758 CCTCCTGTTTTACTGATTTACTACTAG 57.195 37.037 0.00 0.00 0.00 2.57
834 2961 8.255905 GCCTCCTGTTTTACTGATTTACTACTA 58.744 37.037 0.00 0.00 0.00 1.82
835 2962 7.104290 GCCTCCTGTTTTACTGATTTACTACT 58.896 38.462 0.00 0.00 0.00 2.57
836 2963 6.315642 GGCCTCCTGTTTTACTGATTTACTAC 59.684 42.308 0.00 0.00 0.00 2.73
837 2964 6.412214 GGCCTCCTGTTTTACTGATTTACTA 58.588 40.000 0.00 0.00 0.00 1.82
838 2965 5.254115 GGCCTCCTGTTTTACTGATTTACT 58.746 41.667 0.00 0.00 0.00 2.24
839 2966 4.094442 CGGCCTCCTGTTTTACTGATTTAC 59.906 45.833 0.00 0.00 0.00 2.01
840 2967 4.258543 CGGCCTCCTGTTTTACTGATTTA 58.741 43.478 0.00 0.00 0.00 1.40
841 2968 3.081804 CGGCCTCCTGTTTTACTGATTT 58.918 45.455 0.00 0.00 0.00 2.17
842 2969 2.039879 ACGGCCTCCTGTTTTACTGATT 59.960 45.455 0.00 0.00 0.00 2.57
843 2970 1.628846 ACGGCCTCCTGTTTTACTGAT 59.371 47.619 0.00 0.00 0.00 2.90
844 2971 1.053424 ACGGCCTCCTGTTTTACTGA 58.947 50.000 0.00 0.00 0.00 3.41
845 2972 2.028385 AGTACGGCCTCCTGTTTTACTG 60.028 50.000 0.00 0.00 0.00 2.74
846 2973 2.233186 GAGTACGGCCTCCTGTTTTACT 59.767 50.000 0.00 0.00 0.00 2.24
847 2974 2.614779 GAGTACGGCCTCCTGTTTTAC 58.385 52.381 0.00 0.00 0.00 2.01
848 2975 1.551883 GGAGTACGGCCTCCTGTTTTA 59.448 52.381 13.68 0.00 46.34 1.52
849 2976 0.323957 GGAGTACGGCCTCCTGTTTT 59.676 55.000 13.68 0.00 46.34 2.43
850 2977 1.980844 GGAGTACGGCCTCCTGTTT 59.019 57.895 13.68 0.00 46.34 2.83
851 2978 3.709567 GGAGTACGGCCTCCTGTT 58.290 61.111 13.68 0.00 46.34 3.16
852 2979 3.681302 TTACGGAGTACGGCCTCCTGT 62.681 57.143 17.39 17.30 45.76 4.00
853 2980 1.033746 TTACGGAGTACGGCCTCCTG 61.034 60.000 17.39 13.67 45.76 3.86
854 2981 0.323725 TTTACGGAGTACGGCCTCCT 60.324 55.000 17.39 9.30 45.76 3.69
855 2982 0.179127 GTTTACGGAGTACGGCCTCC 60.179 60.000 11.51 11.51 45.76 4.30
856 2983 0.813821 AGTTTACGGAGTACGGCCTC 59.186 55.000 0.00 0.00 45.76 4.70
857 2984 0.813821 GAGTTTACGGAGTACGGCCT 59.186 55.000 0.00 0.00 45.76 5.19
858 2985 0.813821 AGAGTTTACGGAGTACGGCC 59.186 55.000 0.00 0.00 45.76 6.13
859 2986 2.643933 AAGAGTTTACGGAGTACGGC 57.356 50.000 0.00 0.00 45.76 5.68
860 2987 3.248266 CCAAAGAGTTTACGGAGTACGG 58.752 50.000 0.00 0.00 45.76 4.02
861 2988 2.665052 GCCAAAGAGTTTACGGAGTACG 59.335 50.000 0.00 0.00 45.76 3.67
862 2989 3.922910 AGCCAAAGAGTTTACGGAGTAC 58.077 45.455 0.00 0.00 45.76 2.73
886 3013 1.008767 CGTATCGGGTTCTCTCGGC 60.009 63.158 0.00 0.00 0.00 5.54
942 3069 4.602259 AGGGTGCGACCGTGTGTG 62.602 66.667 0.00 0.00 39.83 3.82
943 3070 4.295119 GAGGGTGCGACCGTGTGT 62.295 66.667 5.45 0.00 39.83 3.72
1097 3224 0.397535 GGGATCGGGGTAGTGGTACA 60.398 60.000 0.00 0.00 0.00 2.90
1165 3292 3.378512 TGGAGTAGTAGTAGGAGGACGA 58.621 50.000 0.00 0.00 0.00 4.20
1239 3366 1.458639 GGGCGCCGTAGTAGTGGTAT 61.459 60.000 22.54 0.00 0.00 2.73
1440 3567 5.521735 CAGAGAAAGATGTACCAAATCGGAG 59.478 44.000 0.00 0.00 38.63 4.63
1523 3653 1.102978 GCCCGATTTGTAACCATGCT 58.897 50.000 0.00 0.00 0.00 3.79
1534 3664 2.514458 AAATCAGTGAGGCCCGATTT 57.486 45.000 0.00 4.03 34.16 2.17
1554 3687 4.745125 GCCAAGAACAATCGATTCGATAGA 59.255 41.667 21.00 0.00 46.30 1.98
1581 3714 9.430399 GGGCTACCTTCACCAACTATATATATA 57.570 37.037 2.49 2.49 0.00 0.86
1587 3720 3.726790 TGGGCTACCTTCACCAACTATA 58.273 45.455 0.00 0.00 37.76 1.31
1588 3721 2.557869 TGGGCTACCTTCACCAACTAT 58.442 47.619 0.00 0.00 37.76 2.12
1589 3722 2.032965 TGGGCTACCTTCACCAACTA 57.967 50.000 0.00 0.00 37.76 2.24
1590 3723 1.372501 ATGGGCTACCTTCACCAACT 58.627 50.000 0.00 0.00 36.44 3.16
1605 3738 6.758886 GCAATCGAGTTATCTAGGATTATGGG 59.241 42.308 0.00 0.00 30.78 4.00
1667 3800 5.741510 TGTTTTGTGATTTTTACAGTGCGAG 59.258 36.000 0.00 0.00 0.00 5.03
1714 3847 3.996363 GGTGAGCAATTTCCAAACCATTC 59.004 43.478 0.00 0.00 0.00 2.67
1750 3883 1.229975 TGCATGTCAACCAGTCTGCG 61.230 55.000 0.00 0.00 32.42 5.18
1767 3900 4.676546 GGAGTGATATCCTTTTTGCTTGC 58.323 43.478 0.00 0.00 36.35 4.01
1987 4120 5.190992 TCCAACTCGCGCTTATTCTATTA 57.809 39.130 5.56 0.00 0.00 0.98
2000 4133 2.922335 GCAAGGTTTCATTCCAACTCGC 60.922 50.000 0.00 0.00 0.00 5.03
2001 4134 2.554032 AGCAAGGTTTCATTCCAACTCG 59.446 45.455 0.00 0.00 0.00 4.18
2060 4203 4.789802 GCTGAGGTTAACTTTCAGTTGCAC 60.790 45.833 26.59 14.92 39.11 4.57
2108 4251 5.959618 AAATACAACAGTTCCAACTAGGC 57.040 39.130 0.00 0.00 37.08 3.93
2134 4277 6.803154 AATCTACAACAGTTCCAACTAAGC 57.197 37.500 0.00 0.00 37.08 3.09
2353 4496 3.826157 TGTGCTCTTTTCACCCAAATAGG 59.174 43.478 0.00 0.00 33.71 2.57
2478 4622 9.862149 ATTATCGGAGGAATTTTAACCAAGTAT 57.138 29.630 0.00 0.00 0.00 2.12
2563 4707 5.918576 ACGGCAATTTTAGCTCTACAAAAAC 59.081 36.000 0.00 0.00 0.00 2.43
2609 4753 0.689055 TTGCCATGAGACAGACAGCT 59.311 50.000 0.00 0.00 0.00 4.24
2757 4903 3.600448 AATGAATGGATGGGACCGATT 57.400 42.857 0.00 0.00 0.00 3.34
2764 4910 5.929992 GTGCATCAATAAATGAATGGATGGG 59.070 40.000 0.00 0.00 42.54 4.00
2791 4937 8.465273 AGTTTGGGCATTTAGGATAATAGTTC 57.535 34.615 0.00 0.00 0.00 3.01
2837 4983 6.965500 CAGATGCTCACATTGAAACAAGATAC 59.035 38.462 0.00 0.00 36.35 2.24
2851 4997 8.337532 CGAATTTTCAATATACAGATGCTCACA 58.662 33.333 0.00 0.00 0.00 3.58
2876 5022 7.061789 GGTGACCACTTTATTTCAATAAAAGCG 59.938 37.037 0.00 0.00 39.57 4.68
2910 5056 2.699954 GAGGAAAACTCGAGGATGCAA 58.300 47.619 18.41 0.00 36.29 4.08
2945 5091 2.432874 TCCACAGAGGAAGAACGAAACA 59.567 45.455 0.00 0.00 45.65 2.83
3064 5210 9.877222 TGGATATTAGTACTCAATAGACCTGAA 57.123 33.333 0.00 0.00 0.00 3.02
3083 5229 5.129320 GGAAGTGGGCAAAGAATTGGATATT 59.871 40.000 0.00 0.00 37.02 1.28
3326 5472 7.487822 TGAGCCAAAATGGGAAAATATGTTA 57.512 32.000 0.00 0.00 38.19 2.41
3409 5556 9.189156 CCAAACAAGGATATTCAAATTAGAGGA 57.811 33.333 0.00 0.00 0.00 3.71
3555 5702 2.417719 AGGGTTGAGTCCTGGTAGTT 57.582 50.000 0.00 0.00 32.53 2.24
3560 5707 4.200092 GCTTAAATAGGGTTGAGTCCTGG 58.800 47.826 0.00 0.00 35.92 4.45
3633 5780 8.187368 ACTGTAAGGGTAGCACTCAAGTGTAC 62.187 46.154 11.55 11.41 43.20 2.90
3683 5830 4.093556 GGATCAGATTCCTTGACGAAACAC 59.906 45.833 0.00 0.00 32.68 3.32
3736 5883 0.535335 GGCACCTCGGTTGTAGATGA 59.465 55.000 0.00 0.00 0.00 2.92
3760 5907 0.839946 ACTTGTCCTTGTGGAGCTGT 59.160 50.000 0.00 0.00 44.16 4.40
3812 5959 2.576191 ACCACTGCCCACAATGTATACT 59.424 45.455 4.17 0.00 0.00 2.12
3814 5961 3.730215 AACCACTGCCCACAATGTATA 57.270 42.857 0.00 0.00 0.00 1.47
3898 6045 3.070018 CTCAAAAACCTGAGACGAGCAT 58.930 45.455 0.00 0.00 44.82 3.79
3970 6117 1.060713 CTCGATCAGAAAACGTGCGT 58.939 50.000 0.00 0.00 0.00 5.24
3986 6133 2.094182 TCTGCTAACCTGGCTAAACTCG 60.094 50.000 0.00 0.00 0.00 4.18
3998 6145 6.072112 TGAAAACTGATGTTTCTGCTAACC 57.928 37.500 0.00 0.00 44.70 2.85
4015 6191 7.602517 AGTTCAGATAGCATGTACTGAAAAC 57.397 36.000 19.08 12.91 46.14 2.43
4051 6227 4.084900 CGAATTTGAACTTGGCAAGAAAGC 60.085 41.667 32.50 17.60 0.00 3.51
4136 6312 2.485426 CACAAGATGCGTCTGTGGAAAT 59.515 45.455 21.32 0.61 34.13 2.17
4176 6352 1.917568 AGGACCTCTTAGTCGAGACCT 59.082 52.381 0.00 0.00 37.66 3.85
4192 6368 4.771054 TCAGAGGTAAAGTTGGAGTAGGAC 59.229 45.833 0.00 0.00 0.00 3.85
4366 6543 2.212652 ACACCTGCGCATACACATATG 58.787 47.619 12.24 0.00 41.16 1.78
4495 6672 2.868583 GTCTGATGAATGGATGGTGACG 59.131 50.000 0.00 0.00 0.00 4.35
4539 6716 2.091665 AGCATATTTTAGGGGCAGCACT 60.092 45.455 0.00 0.00 0.00 4.40
4558 6735 2.102578 ACACATTAAATGGAGGCCAGC 58.897 47.619 5.01 0.00 36.75 4.85
4579 6756 5.572896 GTCAAGCATGGTTATACACAAAAGC 59.427 40.000 10.31 0.00 0.00 3.51
4580 6757 6.582295 GTGTCAAGCATGGTTATACACAAAAG 59.418 38.462 30.87 11.98 36.60 2.27
4659 6836 4.225042 AGATGTGCCATACAGTGAAGGTAA 59.775 41.667 0.00 0.00 43.80 2.85
4666 6843 3.603532 ACAGAAGATGTGCCATACAGTG 58.396 45.455 0.00 0.00 43.80 3.66
4915 7094 2.224621 ACAGAGTAATGGCTGCACAACT 60.225 45.455 0.50 0.00 35.57 3.16
5319 7498 2.745492 GCCGCTTCTGCTGCTTCT 60.745 61.111 0.00 0.00 44.32 2.85
5400 7598 5.310857 ACAGGAAATAAAGACAGGGAGAACT 59.689 40.000 0.00 0.00 0.00 3.01
5472 7670 2.351706 AGCCTACCAAACAACGGAAA 57.648 45.000 0.00 0.00 0.00 3.13
5513 7711 0.106719 CACAACAAGGGGGACACTGT 60.107 55.000 0.00 0.00 0.00 3.55
5525 7723 2.283086 CGACGTTTCTACAGCACAACAA 59.717 45.455 0.00 0.00 0.00 2.83
5544 7745 4.214119 CAGAAGTCTGAAGCAATTTTCCGA 59.786 41.667 1.88 0.00 46.59 4.55
5646 7847 9.814899 ACATTACAGAAGAACTCAGATATCAAG 57.185 33.333 5.32 4.63 0.00 3.02
5650 7851 9.761504 CATGACATTACAGAAGAACTCAGATAT 57.238 33.333 0.00 0.00 0.00 1.63
5750 7967 1.606480 CCATGATCACCGATTCCTCCG 60.606 57.143 0.00 0.00 0.00 4.63
5801 8018 3.200825 CACCAAGGATGACTACAATCCCT 59.799 47.826 0.00 0.00 35.11 4.20
5802 8019 3.054361 ACACCAAGGATGACTACAATCCC 60.054 47.826 0.00 0.00 35.11 3.85
5803 8020 4.192317 GACACCAAGGATGACTACAATCC 58.808 47.826 0.00 0.00 34.77 3.01
5804 8021 3.865745 CGACACCAAGGATGACTACAATC 59.134 47.826 0.00 0.00 0.00 2.67
5805 8022 3.861840 CGACACCAAGGATGACTACAAT 58.138 45.455 0.00 0.00 0.00 2.71
5806 8023 2.611971 GCGACACCAAGGATGACTACAA 60.612 50.000 0.00 0.00 0.00 2.41
5807 8024 1.067142 GCGACACCAAGGATGACTACA 60.067 52.381 0.00 0.00 0.00 2.74
5808 8025 1.067142 TGCGACACCAAGGATGACTAC 60.067 52.381 0.00 0.00 0.00 2.73
5809 8026 1.262417 TGCGACACCAAGGATGACTA 58.738 50.000 0.00 0.00 0.00 2.59
5810 8027 0.615331 ATGCGACACCAAGGATGACT 59.385 50.000 0.00 0.00 0.00 3.41
5811 8028 0.729116 CATGCGACACCAAGGATGAC 59.271 55.000 0.00 0.00 38.26 3.06
5812 8029 0.612744 TCATGCGACACCAAGGATGA 59.387 50.000 0.00 0.00 41.69 2.92
5813 8030 1.399440 CTTCATGCGACACCAAGGATG 59.601 52.381 0.00 0.00 37.51 3.51
5814 8031 1.278985 TCTTCATGCGACACCAAGGAT 59.721 47.619 0.00 0.00 0.00 3.24
5815 8032 0.684535 TCTTCATGCGACACCAAGGA 59.315 50.000 0.00 0.00 0.00 3.36
5816 8033 0.798776 GTCTTCATGCGACACCAAGG 59.201 55.000 9.30 0.00 0.00 3.61
5817 8034 1.800805 AGTCTTCATGCGACACCAAG 58.199 50.000 14.66 0.80 33.89 3.61
5818 8035 2.353704 CCTAGTCTTCATGCGACACCAA 60.354 50.000 14.66 0.00 33.89 3.67
5819 8036 1.204704 CCTAGTCTTCATGCGACACCA 59.795 52.381 14.66 2.51 33.89 4.17
5820 8037 1.471676 CCCTAGTCTTCATGCGACACC 60.472 57.143 14.66 0.00 33.89 4.16
5821 8038 1.471676 CCCCTAGTCTTCATGCGACAC 60.472 57.143 14.66 0.00 33.89 3.67
5822 8039 0.824109 CCCCTAGTCTTCATGCGACA 59.176 55.000 14.66 0.00 33.89 4.35
5823 8040 0.824759 ACCCCTAGTCTTCATGCGAC 59.175 55.000 6.82 6.82 0.00 5.19
5824 8041 0.824109 CACCCCTAGTCTTCATGCGA 59.176 55.000 0.00 0.00 0.00 5.10
5825 8042 0.179073 CCACCCCTAGTCTTCATGCG 60.179 60.000 0.00 0.00 0.00 4.73
5826 8043 1.204146 TCCACCCCTAGTCTTCATGC 58.796 55.000 0.00 0.00 0.00 4.06
5827 8044 4.510167 ATTTCCACCCCTAGTCTTCATG 57.490 45.455 0.00 0.00 0.00 3.07
5828 8045 4.325344 CCAATTTCCACCCCTAGTCTTCAT 60.325 45.833 0.00 0.00 0.00 2.57
5829 8046 3.010138 CCAATTTCCACCCCTAGTCTTCA 59.990 47.826 0.00 0.00 0.00 3.02
5830 8047 3.010250 ACCAATTTCCACCCCTAGTCTTC 59.990 47.826 0.00 0.00 0.00 2.87
5831 8048 2.993863 ACCAATTTCCACCCCTAGTCTT 59.006 45.455 0.00 0.00 0.00 3.01
5832 8049 2.644151 ACCAATTTCCACCCCTAGTCT 58.356 47.619 0.00 0.00 0.00 3.24
5912 8129 1.295792 TTTAGTTCGGATGCGGATGC 58.704 50.000 6.82 0.00 43.20 3.91


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

AutoCloner maintained by Alex Coulton.