Multiple sequence alignment - TraesCS2A01G320400

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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 TraesCS2A01G320400 chr2A 100.000 7155 0 0 1 7155 549972178 549965024 0.000000e+00 13213
1 TraesCS2A01G320400 chr2A 91.884 727 30 5 6405 7104 686196591 686195867 0.000000e+00 989
2 TraesCS2A01G320400 chr2A 91.586 725 34 4 6407 7104 421222852 421223576 0.000000e+00 976
3 TraesCS2A01G320400 chr2A 90.832 709 38 4 6404 7087 28465659 28466365 0.000000e+00 924
4 TraesCS2A01G320400 chr2A 97.024 168 5 0 3483 3650 746756987 746757154 4.230000e-72 283
5 TraesCS2A01G320400 chrUn 95.269 3509 102 29 21 3487 25909339 25905853 0.000000e+00 5502
6 TraesCS2A01G320400 chrUn 98.387 1922 25 6 3648 5568 25905855 25903939 0.000000e+00 3373
7 TraesCS2A01G320400 chrUn 97.758 803 15 1 5570 6369 464770144 464769342 0.000000e+00 1380
8 TraesCS2A01G320400 chrUn 91.803 732 31 5 6400 7104 81780849 81781578 0.000000e+00 992
9 TraesCS2A01G320400 chrUn 97.059 68 1 1 7089 7155 81781233 81781300 5.870000e-21 113
10 TraesCS2A01G320400 chrUn 97.059 68 1 1 7089 7155 274056976 274057043 5.870000e-21 113
11 TraesCS2A01G320400 chrUn 97.059 68 1 1 7089 7155 316506993 316507060 5.870000e-21 113
12 TraesCS2A01G320400 chr2B 90.070 3575 209 60 1 3483 516721029 516724549 0.000000e+00 4501
13 TraesCS2A01G320400 chr2B 91.725 1426 67 19 3650 5064 516724553 516725938 0.000000e+00 1932
14 TraesCS2A01G320400 chr2B 95.752 612 23 1 5797 6405 516726726 516727337 0.000000e+00 983
15 TraesCS2A01G320400 chr2B 90.463 713 38 18 5063 5752 516726019 516726724 0.000000e+00 913
16 TraesCS2A01G320400 chr2B 94.444 180 9 1 3476 3655 594833865 594834043 7.070000e-70 276
17 TraesCS2A01G320400 chr7A 92.011 726 30 11 6406 7104 130300859 130300135 0.000000e+00 994
18 TraesCS2A01G320400 chr7A 93.514 185 8 4 3486 3669 320981337 320981156 9.150000e-69 272
19 TraesCS2A01G320400 chr5A 92.011 726 30 11 6406 7104 426266462 426267186 0.000000e+00 994
20 TraesCS2A01G320400 chr5A 91.209 728 34 9 6404 7104 568331274 568331998 0.000000e+00 963
21 TraesCS2A01G320400 chr5A 96.471 170 5 1 3486 3655 382566802 382566634 5.470000e-71 279
22 TraesCS2A01G320400 chr1A 91.460 726 35 11 6406 7104 577832497 577831772 0.000000e+00 972
23 TraesCS2A01G320400 chr1A 90.646 727 38 13 6406 7104 361378758 361379482 0.000000e+00 939
24 TraesCS2A01G320400 chr1A 90.000 490 25 2 6405 6871 53994428 53994916 4.740000e-171 612
25 TraesCS2A01G320400 chr6A 91.120 732 36 6 6400 7104 60158546 60159275 0.000000e+00 965
26 TraesCS2A01G320400 chr6A 90.411 730 42 10 6402 7104 514048006 514048734 0.000000e+00 935
27 TraesCS2A01G320400 chr6A 91.394 581 27 4 6410 6967 67048258 67047678 0.000000e+00 774
28 TraesCS2A01G320400 chr6A 97.059 68 2 0 3169 3236 384730997 384730930 1.630000e-21 115
29 TraesCS2A01G320400 chr3A 91.059 727 37 12 6406 7104 738659529 738658803 0.000000e+00 957
30 TraesCS2A01G320400 chr5D 88.034 351 40 2 6401 6750 499690379 499690728 1.440000e-111 414
31 TraesCS2A01G320400 chr4D 95.954 173 7 0 3482 3654 477898791 477898963 1.520000e-71 281
32 TraesCS2A01G320400 chr4A 96.471 170 6 0 3481 3650 582530146 582529977 1.520000e-71 281
33 TraesCS2A01G320400 chr1D 95.954 173 6 1 3479 3651 178466476 178466305 5.470000e-71 279
34 TraesCS2A01G320400 chr2D 96.970 165 5 0 3486 3650 560959649 560959485 1.970000e-70 278
35 TraesCS2A01G320400 chr3D 94.382 178 8 2 3486 3662 7607558 7607382 9.150000e-69 272
36 TraesCS2A01G320400 chr6D 94.595 74 4 0 3160 3233 271295991 271296064 1.630000e-21 115
37 TraesCS2A01G320400 chr6B 94.595 74 4 0 3160 3233 432359463 432359536 1.630000e-21 115
38 TraesCS2A01G320400 chr4B 97.059 68 1 1 7089 7155 1739053 1738986 5.870000e-21 113
39 TraesCS2A01G320400 chr4B 97.059 68 1 1 7089 7155 11437873 11437806 5.870000e-21 113
40 TraesCS2A01G320400 chr4B 97.059 68 1 1 7089 7155 100930019 100930086 5.870000e-21 113
41 TraesCS2A01G320400 chr4B 97.059 68 1 1 7089 7155 366464350 366464283 5.870000e-21 113
42 TraesCS2A01G320400 chr4B 97.059 68 1 1 7089 7155 621753537 621753604 5.870000e-21 113
43 TraesCS2A01G320400 chr4B 97.059 68 1 1 7089 7155 662514043 662513976 5.870000e-21 113


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 TraesCS2A01G320400 chr2A 549965024 549972178 7154 True 13213.00 13213 100.0000 1 7155 1 chr2A.!!$R1 7154
1 TraesCS2A01G320400 chr2A 686195867 686196591 724 True 989.00 989 91.8840 6405 7104 1 chr2A.!!$R2 699
2 TraesCS2A01G320400 chr2A 421222852 421223576 724 False 976.00 976 91.5860 6407 7104 1 chr2A.!!$F2 697
3 TraesCS2A01G320400 chr2A 28465659 28466365 706 False 924.00 924 90.8320 6404 7087 1 chr2A.!!$F1 683
4 TraesCS2A01G320400 chrUn 25903939 25909339 5400 True 4437.50 5502 96.8280 21 5568 2 chrUn.!!$R2 5547
5 TraesCS2A01G320400 chrUn 464769342 464770144 802 True 1380.00 1380 97.7580 5570 6369 1 chrUn.!!$R1 799
6 TraesCS2A01G320400 chrUn 81780849 81781578 729 False 552.50 992 94.4310 6400 7155 2 chrUn.!!$F3 755
7 TraesCS2A01G320400 chr2B 516721029 516727337 6308 False 2082.25 4501 92.0025 1 6405 4 chr2B.!!$F2 6404
8 TraesCS2A01G320400 chr7A 130300135 130300859 724 True 994.00 994 92.0110 6406 7104 1 chr7A.!!$R1 698
9 TraesCS2A01G320400 chr5A 426266462 426267186 724 False 994.00 994 92.0110 6406 7104 1 chr5A.!!$F1 698
10 TraesCS2A01G320400 chr5A 568331274 568331998 724 False 963.00 963 91.2090 6404 7104 1 chr5A.!!$F2 700
11 TraesCS2A01G320400 chr1A 577831772 577832497 725 True 972.00 972 91.4600 6406 7104 1 chr1A.!!$R1 698
12 TraesCS2A01G320400 chr1A 361378758 361379482 724 False 939.00 939 90.6460 6406 7104 1 chr1A.!!$F2 698
13 TraesCS2A01G320400 chr6A 60158546 60159275 729 False 965.00 965 91.1200 6400 7104 1 chr6A.!!$F1 704
14 TraesCS2A01G320400 chr6A 514048006 514048734 728 False 935.00 935 90.4110 6402 7104 1 chr6A.!!$F2 702
15 TraesCS2A01G320400 chr6A 67047678 67048258 580 True 774.00 774 91.3940 6410 6967 1 chr6A.!!$R1 557
16 TraesCS2A01G320400 chr3A 738658803 738659529 726 True 957.00 957 91.0590 6406 7104 1 chr3A.!!$R1 698

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
123 126 1.299165 CCGGCGTTGGATCTCGTAG 60.299 63.158 6.01 0.00 0.00 3.51 F
176 179 1.561643 TGTCGCTCCCAGATTTCTCT 58.438 50.000 0.00 0.00 0.00 3.10 F
832 916 1.816224 TCGGATAAGCCAAACAAAGCC 59.184 47.619 0.00 0.00 35.94 4.35 F
2445 2562 2.928801 TTTAGCACTTCCAGCTGTGA 57.071 45.000 13.81 6.89 43.33 3.58 F
3499 3652 1.553704 ACATTGTACTCCCTCCGTTCC 59.446 52.381 0.00 0.00 0.00 3.62 F
3500 3653 1.831736 CATTGTACTCCCTCCGTTCCT 59.168 52.381 0.00 0.00 0.00 3.36 F
3605 3758 2.742348 ACATCCGTATGTGGTAGTCCA 58.258 47.619 0.00 0.00 44.79 4.02 F
3606 3759 3.305720 ACATCCGTATGTGGTAGTCCAT 58.694 45.455 0.00 0.00 44.79 3.41 F
3607 3760 3.709653 ACATCCGTATGTGGTAGTCCATT 59.290 43.478 0.00 0.00 44.79 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1622 1711 4.365514 TTCCAGCCATCAGAAACTTACA 57.634 40.909 0.00 0.00 0.00 2.41 R
2350 2467 7.070946 TCCTGATGAAGATAAAGCTTCTGAGAT 59.929 37.037 0.00 0.00 43.60 2.75 R
2576 2699 2.161486 CCAGCGCGAGAAGCTACAC 61.161 63.158 12.10 0.00 44.06 2.90 R
3634 3787 2.322339 AACTTACTCCCTCCGTTCCT 57.678 50.000 0.00 0.00 0.00 3.36 R
5530 5791 1.362224 TTAGGGGCTCTGTTCTGCTT 58.638 50.000 0.00 0.00 0.00 3.91 R
5678 5939 2.288666 GTATCCAAAATGAGGCGCTCA 58.711 47.619 7.64 9.80 44.99 4.26 R
5795 6062 6.478016 GTCCGAGTTACCATTATAAAGGACAC 59.522 42.308 13.56 8.84 42.66 3.67 R
5944 6211 3.469008 TGTCAGTGACAGAACGGAAAT 57.531 42.857 22.06 0.00 37.67 2.17 R
6179 6446 6.706716 ACTTTCACTCTTCCTAGCTAAACAAC 59.293 38.462 0.00 0.00 0.00 3.32 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
123 126 1.299165 CCGGCGTTGGATCTCGTAG 60.299 63.158 6.01 0.00 0.00 3.51
142 145 4.508128 CGTGATGCCTACCGCGGT 62.508 66.667 36.01 36.01 42.08 5.68
154 157 1.592669 CCGCGGTGATGGAGATGTC 60.593 63.158 19.50 0.00 0.00 3.06
176 179 1.561643 TGTCGCTCCCAGATTTCTCT 58.438 50.000 0.00 0.00 0.00 3.10
177 180 1.902508 TGTCGCTCCCAGATTTCTCTT 59.097 47.619 0.00 0.00 0.00 2.85
178 181 2.303022 TGTCGCTCCCAGATTTCTCTTT 59.697 45.455 0.00 0.00 0.00 2.52
179 182 2.933260 GTCGCTCCCAGATTTCTCTTTC 59.067 50.000 0.00 0.00 0.00 2.62
180 183 2.834549 TCGCTCCCAGATTTCTCTTTCT 59.165 45.455 0.00 0.00 0.00 2.52
181 184 3.118956 TCGCTCCCAGATTTCTCTTTCTC 60.119 47.826 0.00 0.00 0.00 2.87
203 206 5.336945 TCTTTCTCTTTGAGGATCTCTCCA 58.663 41.667 8.25 0.00 44.79 3.86
222 225 3.128589 TCCAATTAAATGGCGAGAGTTGC 59.871 43.478 4.54 0.00 40.46 4.17
282 285 7.655328 TCGCTCTGGAGTACTACTAGTATTTAC 59.345 40.741 6.66 8.15 32.65 2.01
388 407 4.142049 GGGAATGTTGTTTTGGTCTGTTCA 60.142 41.667 0.00 0.00 0.00 3.18
421 440 5.135508 TGTTTCAGTTCAGCTCTACTACC 57.864 43.478 0.00 0.00 0.00 3.18
428 447 4.647399 AGTTCAGCTCTACTACCAGAATCC 59.353 45.833 0.00 0.00 0.00 3.01
429 448 3.215151 TCAGCTCTACTACCAGAATCCG 58.785 50.000 0.00 0.00 0.00 4.18
447 487 5.649782 ATCCGAGTTTTGCAAGATCAAAT 57.350 34.783 0.00 0.00 36.04 2.32
450 490 5.009510 TCCGAGTTTTGCAAGATCAAATTCA 59.990 36.000 0.00 0.00 36.04 2.57
480 542 4.649088 GCACGGGCTTATTTTCCTTAAT 57.351 40.909 0.00 0.00 36.96 1.40
481 543 5.761165 GCACGGGCTTATTTTCCTTAATA 57.239 39.130 0.00 0.00 36.96 0.98
482 544 5.758924 GCACGGGCTTATTTTCCTTAATAG 58.241 41.667 0.00 0.00 36.96 1.73
483 545 5.758924 CACGGGCTTATTTTCCTTAATAGC 58.241 41.667 0.00 0.00 0.00 2.97
487 549 6.039382 CGGGCTTATTTTCCTTAATAGCTGTT 59.961 38.462 0.04 0.04 0.00 3.16
490 552 8.466798 GGCTTATTTTCCTTAATAGCTGTTCAA 58.533 33.333 0.00 0.00 0.00 2.69
491 553 9.855021 GCTTATTTTCCTTAATAGCTGTTCAAA 57.145 29.630 0.00 0.00 0.00 2.69
495 557 9.657419 ATTTTCCTTAATAGCTGTTCAAATTGG 57.343 29.630 0.00 0.00 0.00 3.16
496 558 8.415950 TTTCCTTAATAGCTGTTCAAATTGGA 57.584 30.769 0.00 0.00 0.00 3.53
497 559 8.415950 TTCCTTAATAGCTGTTCAAATTGGAA 57.584 30.769 0.00 3.71 0.00 3.53
498 560 8.593945 TCCTTAATAGCTGTTCAAATTGGAAT 57.406 30.769 0.00 0.00 0.00 3.01
499 561 9.034800 TCCTTAATAGCTGTTCAAATTGGAATT 57.965 29.630 0.00 0.00 0.00 2.17
500 562 9.090692 CCTTAATAGCTGTTCAAATTGGAATTG 57.909 33.333 0.00 0.00 0.00 2.32
501 563 9.859427 CTTAATAGCTGTTCAAATTGGAATTGA 57.141 29.630 0.00 0.00 35.11 2.57
502 564 9.859427 TTAATAGCTGTTCAAATTGGAATTGAG 57.141 29.630 0.00 0.00 38.01 3.02
503 565 5.796424 AGCTGTTCAAATTGGAATTGAGT 57.204 34.783 0.00 0.00 38.01 3.41
504 566 6.165700 AGCTGTTCAAATTGGAATTGAGTT 57.834 33.333 0.00 0.00 38.01 3.01
505 567 5.987347 AGCTGTTCAAATTGGAATTGAGTTG 59.013 36.000 0.00 0.00 38.01 3.16
506 568 5.754890 GCTGTTCAAATTGGAATTGAGTTGT 59.245 36.000 0.00 0.00 38.01 3.32
507 569 6.258507 GCTGTTCAAATTGGAATTGAGTTGTT 59.741 34.615 0.00 0.00 38.01 2.83
508 570 7.201635 GCTGTTCAAATTGGAATTGAGTTGTTT 60.202 33.333 0.00 0.00 38.01 2.83
520 582 7.326063 GGAATTGAGTTGTTTGTAGTTGTATGC 59.674 37.037 0.00 0.00 0.00 3.14
532 594 3.689347 AGTTGTATGCCTGATTTCAGCA 58.311 40.909 1.90 4.90 42.47 4.41
533 595 3.693085 AGTTGTATGCCTGATTTCAGCAG 59.307 43.478 1.90 0.00 42.47 4.24
536 598 3.691118 TGTATGCCTGATTTCAGCAGTTC 59.309 43.478 1.90 1.55 42.47 3.01
547 610 2.404215 TCAGCAGTTCTAAGTTGCGAC 58.596 47.619 0.00 0.00 42.47 5.19
548 611 2.035961 TCAGCAGTTCTAAGTTGCGACT 59.964 45.455 0.00 0.00 42.47 4.18
557 620 5.648178 TCTAAGTTGCGACTGGTGTAATA 57.352 39.130 7.56 0.00 35.91 0.98
567 630 5.006358 GCGACTGGTGTAATACTTAATGGTG 59.994 44.000 0.00 0.00 0.00 4.17
574 637 7.829706 TGGTGTAATACTTAATGGTGCATGTTA 59.170 33.333 0.00 0.00 0.00 2.41
583 653 9.243105 ACTTAATGGTGCATGTTAGTTTCTTAT 57.757 29.630 0.00 0.00 0.00 1.73
635 709 2.849942 TGATCTTGGATGCATAACGGG 58.150 47.619 0.00 0.00 0.00 5.28
653 734 2.741878 CGGGTTCAGTGTTCTTGACAGT 60.742 50.000 0.00 0.00 42.69 3.55
654 735 3.279434 GGGTTCAGTGTTCTTGACAGTT 58.721 45.455 0.00 0.00 39.94 3.16
655 736 3.065371 GGGTTCAGTGTTCTTGACAGTTG 59.935 47.826 0.00 0.00 39.94 3.16
656 737 3.065371 GGTTCAGTGTTCTTGACAGTTGG 59.935 47.826 0.00 0.00 39.94 3.77
657 738 3.904800 TCAGTGTTCTTGACAGTTGGA 57.095 42.857 0.00 0.00 39.94 3.53
658 739 3.797039 TCAGTGTTCTTGACAGTTGGAG 58.203 45.455 0.00 0.00 39.94 3.86
659 740 3.197766 TCAGTGTTCTTGACAGTTGGAGT 59.802 43.478 0.00 0.00 39.94 3.85
665 746 6.260050 GTGTTCTTGACAGTTGGAGTGATAAA 59.740 38.462 0.00 0.00 39.39 1.40
699 783 4.585955 TGTTGTCAGAAGAGTGAGGTAC 57.414 45.455 0.00 0.00 0.00 3.34
715 799 3.332034 AGGTACACCGAGCATTACAAAC 58.668 45.455 0.00 0.00 42.08 2.93
717 801 3.687698 GGTACACCGAGCATTACAAACAT 59.312 43.478 0.00 0.00 0.00 2.71
723 807 4.518970 ACCGAGCATTACAAACATTTCAGT 59.481 37.500 0.00 0.00 0.00 3.41
724 808 5.009610 ACCGAGCATTACAAACATTTCAGTT 59.990 36.000 0.00 0.00 0.00 3.16
725 809 5.920273 CCGAGCATTACAAACATTTCAGTTT 59.080 36.000 0.00 0.00 42.10 2.66
726 810 7.081349 CCGAGCATTACAAACATTTCAGTTTA 58.919 34.615 0.00 0.00 39.55 2.01
727 811 7.593273 CCGAGCATTACAAACATTTCAGTTTAA 59.407 33.333 0.00 0.00 39.55 1.52
728 812 8.963130 CGAGCATTACAAACATTTCAGTTTAAA 58.037 29.630 0.00 0.00 39.55 1.52
730 814 9.593134 AGCATTACAAACATTTCAGTTTAAACA 57.407 25.926 20.06 0.00 39.55 2.83
788 872 2.627699 TGTTTCCAGCTTTTAAGGGCAG 59.372 45.455 0.00 0.00 0.00 4.85
809 893 6.461509 GGCAGCAGTAGTATAAATTGGCAATT 60.462 38.462 19.39 19.39 0.00 2.32
832 916 1.816224 TCGGATAAGCCAAACAAAGCC 59.184 47.619 0.00 0.00 35.94 4.35
835 919 3.325870 GGATAAGCCAAACAAAGCCAAC 58.674 45.455 0.00 0.00 36.34 3.77
845 929 5.511202 CCAAACAAAGCCAACCATTCATACT 60.511 40.000 0.00 0.00 0.00 2.12
871 955 8.425577 TTCTGCTAGCTAATTTTGTCTGATAC 57.574 34.615 17.23 0.00 0.00 2.24
1622 1711 4.148825 GAGAGGGCGCATCCGTGT 62.149 66.667 10.83 0.00 36.67 4.49
2350 2467 9.216117 GTCCAAGTAAGTTTCTTTTCTATGCTA 57.784 33.333 0.00 0.00 0.00 3.49
2399 2516 6.204688 GGACCCTTTTCCTTTGCTTTATTTTG 59.795 38.462 0.00 0.00 32.24 2.44
2445 2562 2.928801 TTTAGCACTTCCAGCTGTGA 57.071 45.000 13.81 6.89 43.33 3.58
2526 2648 5.443185 AAACAGAACTACACGCTACTGTA 57.557 39.130 0.00 0.00 37.57 2.74
2576 2699 9.776451 CAATTTGATAAACATTAACGTTGTGTG 57.224 29.630 18.05 12.83 0.00 3.82
3494 3647 4.254492 GAGTTCAACATTGTACTCCCTCC 58.746 47.826 16.41 0.00 44.71 4.30
3495 3648 3.000727 GTTCAACATTGTACTCCCTCCG 58.999 50.000 0.00 0.00 0.00 4.63
3496 3649 2.253610 TCAACATTGTACTCCCTCCGT 58.746 47.619 0.00 0.00 0.00 4.69
3497 3650 2.635915 TCAACATTGTACTCCCTCCGTT 59.364 45.455 0.00 0.00 0.00 4.44
3498 3651 3.000727 CAACATTGTACTCCCTCCGTTC 58.999 50.000 0.00 0.00 0.00 3.95
3499 3652 1.553704 ACATTGTACTCCCTCCGTTCC 59.446 52.381 0.00 0.00 0.00 3.62
3500 3653 1.831736 CATTGTACTCCCTCCGTTCCT 59.168 52.381 0.00 0.00 0.00 3.36
3501 3654 2.905415 TTGTACTCCCTCCGTTCCTA 57.095 50.000 0.00 0.00 0.00 2.94
3502 3655 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
3503 3656 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
3504 3657 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
3505 3658 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
3506 3659 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
3507 3660 5.901276 TGTACTCCCTCCGTTCCTAAATATT 59.099 40.000 0.00 0.00 0.00 1.28
3508 3661 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
3509 3662 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
3510 3663 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
3511 3664 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
3512 3665 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
3513 3666 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
3514 3667 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
3515 3668 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
3516 3669 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
3517 3670 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
3518 3671 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
3519 3672 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
3532 3685 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
3533 3686 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
3534 3687 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
3535 3688 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
3536 3689 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
3537 3690 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
3543 3696 9.737427 AGAGATTTCAACAAGTGACTATATACG 57.263 33.333 0.00 0.00 35.39 3.06
3544 3697 8.873215 AGATTTCAACAAGTGACTATATACGG 57.127 34.615 0.00 0.00 35.39 4.02
3545 3698 8.692710 AGATTTCAACAAGTGACTATATACGGA 58.307 33.333 0.00 0.00 35.39 4.69
3546 3699 8.873215 ATTTCAACAAGTGACTATATACGGAG 57.127 34.615 0.00 0.00 35.39 4.63
3547 3700 5.828747 TCAACAAGTGACTATATACGGAGC 58.171 41.667 0.00 0.00 0.00 4.70
3548 3701 5.358725 TCAACAAGTGACTATATACGGAGCA 59.641 40.000 0.00 0.00 0.00 4.26
3549 3702 5.847111 ACAAGTGACTATATACGGAGCAA 57.153 39.130 0.00 0.00 0.00 3.91
3550 3703 6.216801 ACAAGTGACTATATACGGAGCAAA 57.783 37.500 0.00 0.00 0.00 3.68
3551 3704 6.636705 ACAAGTGACTATATACGGAGCAAAA 58.363 36.000 0.00 0.00 0.00 2.44
3552 3705 7.272978 ACAAGTGACTATATACGGAGCAAAAT 58.727 34.615 0.00 0.00 0.00 1.82
3553 3706 8.418662 ACAAGTGACTATATACGGAGCAAAATA 58.581 33.333 0.00 0.00 0.00 1.40
3554 3707 9.256477 CAAGTGACTATATACGGAGCAAAATAA 57.744 33.333 0.00 0.00 0.00 1.40
3555 3708 9.477484 AAGTGACTATATACGGAGCAAAATAAG 57.523 33.333 0.00 0.00 0.00 1.73
3556 3709 8.639761 AGTGACTATATACGGAGCAAAATAAGT 58.360 33.333 0.00 0.00 0.00 2.24
3557 3710 8.700644 GTGACTATATACGGAGCAAAATAAGTG 58.299 37.037 0.00 0.00 0.00 3.16
3558 3711 8.635328 TGACTATATACGGAGCAAAATAAGTGA 58.365 33.333 0.00 0.00 0.00 3.41
3559 3712 9.472361 GACTATATACGGAGCAAAATAAGTGAA 57.528 33.333 0.00 0.00 0.00 3.18
3560 3713 9.998106 ACTATATACGGAGCAAAATAAGTGAAT 57.002 29.630 0.00 0.00 0.00 2.57
3566 3719 8.366671 ACGGAGCAAAATAAGTGAATCTATAC 57.633 34.615 0.00 0.00 0.00 1.47
3567 3720 8.204836 ACGGAGCAAAATAAGTGAATCTATACT 58.795 33.333 0.00 0.00 0.00 2.12
3568 3721 8.704234 CGGAGCAAAATAAGTGAATCTATACTC 58.296 37.037 0.00 0.00 0.00 2.59
3569 3722 9.771534 GGAGCAAAATAAGTGAATCTATACTCT 57.228 33.333 0.00 0.00 0.00 3.24
3604 3757 4.806330 CATACATCCGTATGTGGTAGTCC 58.194 47.826 3.56 0.00 46.70 3.85
3605 3758 2.742348 ACATCCGTATGTGGTAGTCCA 58.258 47.619 0.00 0.00 44.79 4.02
3606 3759 3.305720 ACATCCGTATGTGGTAGTCCAT 58.694 45.455 0.00 0.00 44.79 3.41
3607 3760 3.709653 ACATCCGTATGTGGTAGTCCATT 59.290 43.478 0.00 0.00 44.79 3.16
3608 3761 4.163458 ACATCCGTATGTGGTAGTCCATTT 59.837 41.667 0.00 0.00 44.79 2.32
3609 3762 4.131649 TCCGTATGTGGTAGTCCATTTG 57.868 45.455 0.00 0.00 46.20 2.32
3610 3763 3.770388 TCCGTATGTGGTAGTCCATTTGA 59.230 43.478 0.00 0.00 46.20 2.69
3611 3764 4.223255 TCCGTATGTGGTAGTCCATTTGAA 59.777 41.667 0.00 0.00 46.20 2.69
3612 3765 4.938832 CCGTATGTGGTAGTCCATTTGAAA 59.061 41.667 0.00 0.00 46.20 2.69
3613 3766 5.588648 CCGTATGTGGTAGTCCATTTGAAAT 59.411 40.000 0.00 0.00 46.20 2.17
3614 3767 6.238374 CCGTATGTGGTAGTCCATTTGAAATC 60.238 42.308 0.00 0.00 46.20 2.17
3615 3768 6.538742 CGTATGTGGTAGTCCATTTGAAATCT 59.461 38.462 0.00 0.00 46.20 2.40
3616 3769 7.254455 CGTATGTGGTAGTCCATTTGAAATCTC 60.254 40.741 0.00 0.00 46.20 2.75
3617 3770 6.126863 TGTGGTAGTCCATTTGAAATCTCT 57.873 37.500 0.00 0.00 46.20 3.10
3618 3771 7.252612 TGTGGTAGTCCATTTGAAATCTCTA 57.747 36.000 0.00 0.00 46.20 2.43
3619 3772 7.685481 TGTGGTAGTCCATTTGAAATCTCTAA 58.315 34.615 0.00 0.00 46.20 2.10
3620 3773 7.824289 TGTGGTAGTCCATTTGAAATCTCTAAG 59.176 37.037 0.00 0.00 46.20 2.18
3621 3774 8.041323 GTGGTAGTCCATTTGAAATCTCTAAGA 58.959 37.037 0.00 0.00 46.20 2.10
3622 3775 8.602424 TGGTAGTCCATTTGAAATCTCTAAGAA 58.398 33.333 0.00 0.00 39.03 2.52
3623 3776 9.103861 GGTAGTCCATTTGAAATCTCTAAGAAG 57.896 37.037 0.00 0.00 0.00 2.85
3624 3777 9.877178 GTAGTCCATTTGAAATCTCTAAGAAGA 57.123 33.333 0.00 0.00 0.00 2.87
3625 3778 8.785329 AGTCCATTTGAAATCTCTAAGAAGAC 57.215 34.615 0.00 0.00 0.00 3.01
3626 3779 8.378565 AGTCCATTTGAAATCTCTAAGAAGACA 58.621 33.333 0.00 0.00 0.00 3.41
3627 3780 9.003658 GTCCATTTGAAATCTCTAAGAAGACAA 57.996 33.333 0.00 0.00 0.00 3.18
3628 3781 9.573166 TCCATTTGAAATCTCTAAGAAGACAAA 57.427 29.630 0.00 0.00 32.63 2.83
3641 3794 9.595823 TCTAAGAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
3642 3795 9.595823 CTAAGAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
3643 3796 8.494016 AAGAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
3644 3797 7.048512 AGAAGACAAATATTTAGGAACGGAGG 58.951 38.462 0.00 0.00 0.00 4.30
3645 3798 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
3646 3799 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
3647 3800 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
4019 4174 9.331282 CAGCTTATCCAACTAGCTTTTTACTAT 57.669 33.333 0.00 0.00 42.30 2.12
4234 4389 8.638873 GCCCACTAATAAATTATTGCTACCTTT 58.361 33.333 8.39 0.00 0.00 3.11
4408 4563 7.369803 AGCAGAGTACACATCTTATGTTTTG 57.630 36.000 0.00 0.00 42.70 2.44
4625 4780 6.826741 GGAAGGTATGTCTTTTAACCAGCATA 59.173 38.462 0.00 0.00 34.29 3.14
4876 5033 5.307196 ACAAAGTCACTACCTAATCCAGTGT 59.693 40.000 0.00 0.00 40.44 3.55
4953 5112 7.670559 AGACTAGGCAGTAGAAAACTAGAAGAA 59.329 37.037 0.00 0.00 35.76 2.52
5092 5336 5.971202 CACAACTGGATAAACAACACAAGAC 59.029 40.000 0.00 0.00 0.00 3.01
5267 5526 4.319261 CCACGTTTTAGGTTAGTGTCTTGC 60.319 45.833 0.00 0.00 0.00 4.01
5530 5791 8.845227 TCTGCAGTAAAATTTTCTGACATGTTA 58.155 29.630 23.21 0.00 0.00 2.41
5678 5939 6.371278 AGATGTCAAAATTCCAGAGGCATAT 58.629 36.000 0.00 0.00 0.00 1.78
5795 6062 6.480651 TGCATACATACAGTTTTACATACCCG 59.519 38.462 0.00 0.00 0.00 5.28
5944 6211 6.433847 TCTGGTTGAATGGAACTCTTCTAA 57.566 37.500 0.00 0.00 0.00 2.10
6347 6614 8.525316 TCAGTCATTGTTTATAAGACGGTTAGA 58.475 33.333 0.00 0.00 34.56 2.10
6349 6616 7.487189 AGTCATTGTTTATAAGACGGTTAGACG 59.513 37.037 0.00 0.00 40.31 4.18
6369 6636 0.400594 ACCTAAGTCAAGCACCACCC 59.599 55.000 0.00 0.00 0.00 4.61
6371 6638 0.034896 CTAAGTCAAGCACCACCCGT 59.965 55.000 0.00 0.00 0.00 5.28
6428 6698 1.335233 CGCCGATAAGTGCCATACGTA 60.335 52.381 0.00 0.00 0.00 3.57
6487 6757 4.705023 GTGTATAAAAGGAACAGCCCACAT 59.295 41.667 0.00 0.00 37.37 3.21
6516 6786 3.435671 GTGTGGACAAAACTATTAGCGCT 59.564 43.478 17.26 17.26 0.00 5.92
6580 6854 2.747446 GCGTGTGGGTGAAGTTGATAAT 59.253 45.455 0.00 0.00 0.00 1.28
6582 6856 3.751175 CGTGTGGGTGAAGTTGATAATGT 59.249 43.478 0.00 0.00 0.00 2.71
6606 6880 2.590092 GCCCGTATGTCAGGCCTT 59.410 61.111 0.00 0.00 41.00 4.35
6648 6945 2.345760 GCAGTTGCCATGGTCCAGG 61.346 63.158 14.67 0.00 34.31 4.45
6691 6988 1.792301 CAGTTGCCATGTCGCTGAG 59.208 57.895 0.00 0.00 0.00 3.35
6779 7076 7.016563 TGGTCTGATCTAATATAGTTGCCATGT 59.983 37.037 0.00 0.00 0.00 3.21
7104 7406 2.153645 CACACTAAGCAGTTGCCATGA 58.846 47.619 0.00 0.00 43.38 3.07
7105 7407 2.751259 CACACTAAGCAGTTGCCATGAT 59.249 45.455 0.00 0.00 43.38 2.45
7106 7408 3.192001 CACACTAAGCAGTTGCCATGATT 59.808 43.478 0.00 0.00 43.38 2.57
7107 7409 3.828451 ACACTAAGCAGTTGCCATGATTT 59.172 39.130 0.00 0.00 43.38 2.17
7108 7410 4.082571 ACACTAAGCAGTTGCCATGATTTC 60.083 41.667 0.00 0.00 43.38 2.17
7109 7411 4.081406 ACTAAGCAGTTGCCATGATTTCA 58.919 39.130 0.00 0.00 43.38 2.69
7110 7412 4.708421 ACTAAGCAGTTGCCATGATTTCAT 59.292 37.500 0.00 0.00 43.38 2.57
7111 7413 5.887598 ACTAAGCAGTTGCCATGATTTCATA 59.112 36.000 0.00 0.00 43.38 2.15
7112 7414 5.664294 AAGCAGTTGCCATGATTTCATAA 57.336 34.783 0.00 0.00 43.38 1.90
7113 7415 5.002464 AGCAGTTGCCATGATTTCATAAC 57.998 39.130 0.00 0.00 43.38 1.89
7114 7416 4.708421 AGCAGTTGCCATGATTTCATAACT 59.292 37.500 0.00 2.71 43.38 2.24
7115 7417 5.186409 AGCAGTTGCCATGATTTCATAACTT 59.814 36.000 0.00 0.00 43.38 2.66
7116 7418 5.870978 GCAGTTGCCATGATTTCATAACTTT 59.129 36.000 0.00 0.00 33.04 2.66
7117 7419 7.035004 GCAGTTGCCATGATTTCATAACTTTA 58.965 34.615 0.00 0.00 33.04 1.85
7118 7420 7.221452 GCAGTTGCCATGATTTCATAACTTTAG 59.779 37.037 0.00 0.00 33.04 1.85
7119 7421 7.703621 CAGTTGCCATGATTTCATAACTTTAGG 59.296 37.037 0.00 0.00 33.04 2.69
7120 7422 7.615365 AGTTGCCATGATTTCATAACTTTAGGA 59.385 33.333 0.00 0.00 31.98 2.94
7121 7423 7.572523 TGCCATGATTTCATAACTTTAGGAG 57.427 36.000 0.00 0.00 34.26 3.69
7122 7424 7.118723 TGCCATGATTTCATAACTTTAGGAGT 58.881 34.615 0.00 0.00 35.57 3.85
7133 7435 4.910458 ACTTTAGGAGTTGCCACATACT 57.090 40.909 0.00 0.00 40.02 2.12
7134 7436 6.368779 AACTTTAGGAGTTGCCACATACTA 57.631 37.500 0.00 0.00 46.66 1.82
7135 7437 6.368779 ACTTTAGGAGTTGCCACATACTAA 57.631 37.500 0.00 0.00 40.02 2.24
7136 7438 6.171213 ACTTTAGGAGTTGCCACATACTAAC 58.829 40.000 0.00 0.00 40.02 2.34
7137 7439 5.748670 TTAGGAGTTGCCACATACTAACA 57.251 39.130 0.00 0.00 40.02 2.41
7138 7440 3.939066 AGGAGTTGCCACATACTAACAC 58.061 45.455 0.00 0.00 40.02 3.32
7139 7441 3.583086 AGGAGTTGCCACATACTAACACT 59.417 43.478 0.00 0.00 40.02 3.55
7140 7442 4.775780 AGGAGTTGCCACATACTAACACTA 59.224 41.667 0.00 0.00 40.02 2.74
7141 7443 5.105310 AGGAGTTGCCACATACTAACACTAG 60.105 44.000 0.00 0.00 40.02 2.57
7142 7444 5.086104 AGTTGCCACATACTAACACTAGG 57.914 43.478 0.00 0.00 0.00 3.02
7143 7445 3.536956 TGCCACATACTAACACTAGGC 57.463 47.619 0.00 0.00 41.15 3.93
7144 7446 3.536956 GCCACATACTAACACTAGGCA 57.463 47.619 0.00 0.00 40.50 4.75
7145 7447 3.118775 TGCCACATACTAACACTAGGCAG 60.119 47.826 0.00 0.00 45.10 4.85
7146 7448 3.118738 GCCACATACTAACACTAGGCAGT 60.119 47.826 0.00 0.00 40.50 4.40
7147 7449 4.623171 GCCACATACTAACACTAGGCAGTT 60.623 45.833 0.00 0.00 40.50 3.16
7148 7450 4.870426 CCACATACTAACACTAGGCAGTTG 59.130 45.833 7.49 0.00 30.46 3.16
7149 7451 5.337250 CCACATACTAACACTAGGCAGTTGA 60.337 44.000 7.49 0.00 30.46 3.18
7150 7452 5.807520 CACATACTAACACTAGGCAGTTGAG 59.192 44.000 7.49 4.79 30.46 3.02
7151 7453 5.715279 ACATACTAACACTAGGCAGTTGAGA 59.285 40.000 7.49 0.00 30.46 3.27
7152 7454 4.792521 ACTAACACTAGGCAGTTGAGAG 57.207 45.455 7.49 1.59 30.46 3.20
7153 7455 4.408276 ACTAACACTAGGCAGTTGAGAGA 58.592 43.478 7.49 0.00 30.46 3.10
7154 7456 3.951775 AACACTAGGCAGTTGAGAGAG 57.048 47.619 0.00 0.00 30.46 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 107 1.299165 CTACGAGATCCAACGCCGG 60.299 63.158 0.00 0.00 0.00 6.13
123 126 2.954868 CGCGGTAGGCATCACGAC 60.955 66.667 0.00 0.00 43.84 4.34
142 145 1.134699 GCGACAAGGACATCTCCATCA 60.135 52.381 0.00 0.00 39.39 3.07
154 157 1.065854 AGAAATCTGGGAGCGACAAGG 60.066 52.381 0.00 0.00 0.00 3.61
176 179 7.310361 GGAGAGATCCTCAAAGAGAAAGAGAAA 60.310 40.741 11.73 0.00 43.76 2.52
177 180 6.154363 GGAGAGATCCTCAAAGAGAAAGAGAA 59.846 42.308 11.73 0.00 43.76 2.87
178 181 5.656416 GGAGAGATCCTCAAAGAGAAAGAGA 59.344 44.000 11.73 0.00 43.76 3.10
179 182 5.421693 TGGAGAGATCCTCAAAGAGAAAGAG 59.578 44.000 11.73 0.00 43.76 2.85
180 183 5.336945 TGGAGAGATCCTCAAAGAGAAAGA 58.663 41.667 11.73 0.00 43.76 2.52
181 184 5.674052 TGGAGAGATCCTCAAAGAGAAAG 57.326 43.478 11.73 0.00 43.76 2.62
203 206 2.097466 CCGCAACTCTCGCCATTTAATT 59.903 45.455 0.00 0.00 0.00 1.40
222 225 2.106683 CCGGGCTTAAGCTTGACCG 61.107 63.158 26.53 26.53 40.29 4.79
388 407 4.855340 TGAACTGAAACAGGAAAGGACTT 58.145 39.130 0.00 0.00 35.51 3.01
421 440 4.154737 TGATCTTGCAAAACTCGGATTCTG 59.845 41.667 0.00 0.00 0.00 3.02
428 447 5.344128 CCTGAATTTGATCTTGCAAAACTCG 59.656 40.000 0.00 0.00 40.72 4.18
429 448 6.449698 TCCTGAATTTGATCTTGCAAAACTC 58.550 36.000 0.00 0.00 40.72 3.01
447 487 0.960364 GCCCGTGCTTGAATCCTGAA 60.960 55.000 0.00 0.00 33.53 3.02
480 542 6.899393 ACTCAATTCCAATTTGAACAGCTA 57.101 33.333 0.00 0.00 0.00 3.32
481 543 5.796424 ACTCAATTCCAATTTGAACAGCT 57.204 34.783 0.00 0.00 0.00 4.24
482 544 5.754890 ACAACTCAATTCCAATTTGAACAGC 59.245 36.000 0.00 0.00 0.00 4.40
483 545 7.775397 AACAACTCAATTCCAATTTGAACAG 57.225 32.000 0.00 0.00 0.00 3.16
487 549 8.474025 ACTACAAACAACTCAATTCCAATTTGA 58.526 29.630 0.00 0.00 31.76 2.69
490 552 8.257306 ACAACTACAAACAACTCAATTCCAATT 58.743 29.630 0.00 0.00 0.00 2.32
491 553 7.781056 ACAACTACAAACAACTCAATTCCAAT 58.219 30.769 0.00 0.00 0.00 3.16
492 554 7.164230 ACAACTACAAACAACTCAATTCCAA 57.836 32.000 0.00 0.00 0.00 3.53
493 555 6.767524 ACAACTACAAACAACTCAATTCCA 57.232 33.333 0.00 0.00 0.00 3.53
494 556 7.326063 GCATACAACTACAAACAACTCAATTCC 59.674 37.037 0.00 0.00 0.00 3.01
495 557 7.326063 GGCATACAACTACAAACAACTCAATTC 59.674 37.037 0.00 0.00 0.00 2.17
496 558 7.014230 AGGCATACAACTACAAACAACTCAATT 59.986 33.333 0.00 0.00 0.00 2.32
497 559 6.490040 AGGCATACAACTACAAACAACTCAAT 59.510 34.615 0.00 0.00 0.00 2.57
498 560 5.825679 AGGCATACAACTACAAACAACTCAA 59.174 36.000 0.00 0.00 0.00 3.02
499 561 5.238432 CAGGCATACAACTACAAACAACTCA 59.762 40.000 0.00 0.00 0.00 3.41
500 562 5.468746 TCAGGCATACAACTACAAACAACTC 59.531 40.000 0.00 0.00 0.00 3.01
501 563 5.373222 TCAGGCATACAACTACAAACAACT 58.627 37.500 0.00 0.00 0.00 3.16
502 564 5.682943 TCAGGCATACAACTACAAACAAC 57.317 39.130 0.00 0.00 0.00 3.32
503 565 6.892658 AATCAGGCATACAACTACAAACAA 57.107 33.333 0.00 0.00 0.00 2.83
504 566 6.488344 TGAAATCAGGCATACAACTACAAACA 59.512 34.615 0.00 0.00 0.00 2.83
505 567 6.908825 TGAAATCAGGCATACAACTACAAAC 58.091 36.000 0.00 0.00 0.00 2.93
506 568 6.349280 GCTGAAATCAGGCATACAACTACAAA 60.349 38.462 12.09 0.00 43.94 2.83
507 569 5.123820 GCTGAAATCAGGCATACAACTACAA 59.876 40.000 12.09 0.00 43.94 2.41
508 570 4.635765 GCTGAAATCAGGCATACAACTACA 59.364 41.667 12.09 0.00 43.94 2.74
520 582 5.618640 GCAACTTAGAACTGCTGAAATCAGG 60.619 44.000 12.09 0.00 43.94 3.86
532 594 2.102588 ACACCAGTCGCAACTTAGAACT 59.897 45.455 0.00 0.00 31.71 3.01
533 595 2.480845 ACACCAGTCGCAACTTAGAAC 58.519 47.619 0.00 0.00 31.71 3.01
536 598 5.408356 AGTATTACACCAGTCGCAACTTAG 58.592 41.667 0.00 0.00 31.71 2.18
547 610 6.318648 ACATGCACCATTAAGTATTACACCAG 59.681 38.462 0.00 0.00 0.00 4.00
548 611 6.184068 ACATGCACCATTAAGTATTACACCA 58.816 36.000 0.00 0.00 0.00 4.17
557 620 7.524717 AAGAAACTAACATGCACCATTAAGT 57.475 32.000 0.00 0.00 0.00 2.24
574 637 9.968870 GACGACCTCATCTAAATATAAGAAACT 57.031 33.333 0.00 0.00 0.00 2.66
583 653 7.201609 GCAATGTTTGACGACCTCATCTAAATA 60.202 37.037 0.00 0.00 0.00 1.40
606 676 4.271661 TGCATCCAAGATCAACATAGCAA 58.728 39.130 0.00 0.00 0.00 3.91
635 709 3.938963 TCCAACTGTCAAGAACACTGAAC 59.061 43.478 0.00 0.00 33.24 3.18
659 740 7.714813 TGACAACAAAGTGATCTCAGTTTATCA 59.285 33.333 11.59 10.37 44.95 2.15
665 746 5.282055 TCTGACAACAAAGTGATCTCAGT 57.718 39.130 0.00 0.00 0.00 3.41
677 758 4.404394 TGTACCTCACTCTTCTGACAACAA 59.596 41.667 0.00 0.00 0.00 2.83
682 763 2.095161 CGGTGTACCTCACTCTTCTGAC 60.095 54.545 0.00 0.00 45.50 3.51
699 783 4.793071 TGAAATGTTTGTAATGCTCGGTG 58.207 39.130 0.00 0.00 0.00 4.94
715 799 9.840427 ATCGTATTTCCTGTTTAAACTGAAATG 57.160 29.630 32.28 24.70 39.30 2.32
723 807 9.849166 GATCCAAAATCGTATTTCCTGTTTAAA 57.151 29.630 0.00 0.00 0.00 1.52
724 808 9.238368 AGATCCAAAATCGTATTTCCTGTTTAA 57.762 29.630 0.00 0.00 0.00 1.52
725 809 8.801882 AGATCCAAAATCGTATTTCCTGTTTA 57.198 30.769 0.00 0.00 0.00 2.01
726 810 7.703058 AGATCCAAAATCGTATTTCCTGTTT 57.297 32.000 0.00 0.00 0.00 2.83
727 811 8.047310 ACTAGATCCAAAATCGTATTTCCTGTT 58.953 33.333 0.00 0.00 0.00 3.16
728 812 7.565680 ACTAGATCCAAAATCGTATTTCCTGT 58.434 34.615 0.00 0.00 0.00 4.00
729 813 7.710907 TGACTAGATCCAAAATCGTATTTCCTG 59.289 37.037 0.00 0.00 0.00 3.86
730 814 7.792032 TGACTAGATCCAAAATCGTATTTCCT 58.208 34.615 0.00 0.00 0.00 3.36
737 821 4.572389 GCACATGACTAGATCCAAAATCGT 59.428 41.667 0.00 0.00 0.00 3.73
788 872 7.535258 CGATGAATTGCCAATTTATACTACTGC 59.465 37.037 7.34 0.00 28.48 4.40
809 893 3.128589 GCTTTGTTTGGCTTATCCGATGA 59.871 43.478 0.00 0.00 37.80 2.92
832 916 5.587844 AGCTAGCAGAAAGTATGAATGGTTG 59.412 40.000 18.83 0.00 0.00 3.77
835 919 7.976135 ATTAGCTAGCAGAAAGTATGAATGG 57.024 36.000 18.83 0.00 0.00 3.16
845 929 7.928307 ATCAGACAAAATTAGCTAGCAGAAA 57.072 32.000 18.83 8.54 0.00 2.52
894 979 3.131046 ACTTAGCCTAACAATTGCCATGC 59.869 43.478 5.05 3.96 0.00 4.06
940 1025 5.221843 ACACCTAACCAAGTGAGCAAGATAA 60.222 40.000 0.00 0.00 37.43 1.75
1622 1711 4.365514 TTCCAGCCATCAGAAACTTACA 57.634 40.909 0.00 0.00 0.00 2.41
2350 2467 7.070946 TCCTGATGAAGATAAAGCTTCTGAGAT 59.929 37.037 0.00 0.00 43.60 2.75
2445 2562 6.547880 AGATGATCATGTCCTCGTTACTACTT 59.452 38.462 14.30 0.00 0.00 2.24
2526 2648 7.767261 TGACAAAAGTAACAGTGCAATTTAGT 58.233 30.769 0.00 0.00 0.00 2.24
2576 2699 2.161486 CCAGCGCGAGAAGCTACAC 61.161 63.158 12.10 0.00 44.06 2.90
2780 2903 5.242838 AGTTCAAAACGAATTAGCCCAATGA 59.757 36.000 0.00 0.00 35.63 2.57
3485 3638 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
3486 3639 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
3487 3640 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
3488 3641 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
3489 3642 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
3490 3643 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
3491 3644 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
3492 3645 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
3493 3646 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
3506 3659 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
3507 3660 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
3508 3661 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
3509 3662 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
3510 3663 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
3511 3664 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
3517 3670 9.737427 CGTATATAGTCACTTGTTGAAATCTCT 57.263 33.333 0.00 0.00 35.39 3.10
3518 3671 8.969267 CCGTATATAGTCACTTGTTGAAATCTC 58.031 37.037 0.00 0.00 35.39 2.75
3519 3672 8.692710 TCCGTATATAGTCACTTGTTGAAATCT 58.307 33.333 0.00 0.00 35.39 2.40
3520 3673 8.867112 TCCGTATATAGTCACTTGTTGAAATC 57.133 34.615 0.00 0.00 35.39 2.17
3521 3674 7.438459 GCTCCGTATATAGTCACTTGTTGAAAT 59.562 37.037 0.00 0.00 35.39 2.17
3522 3675 6.755141 GCTCCGTATATAGTCACTTGTTGAAA 59.245 38.462 0.00 0.00 35.39 2.69
3523 3676 6.127563 TGCTCCGTATATAGTCACTTGTTGAA 60.128 38.462 0.00 0.00 35.39 2.69
3524 3677 5.358725 TGCTCCGTATATAGTCACTTGTTGA 59.641 40.000 0.00 0.00 0.00 3.18
3525 3678 5.588240 TGCTCCGTATATAGTCACTTGTTG 58.412 41.667 0.00 0.00 0.00 3.33
3526 3679 5.847111 TGCTCCGTATATAGTCACTTGTT 57.153 39.130 0.00 0.00 0.00 2.83
3527 3680 5.847111 TTGCTCCGTATATAGTCACTTGT 57.153 39.130 0.00 0.00 0.00 3.16
3528 3681 7.715265 ATTTTGCTCCGTATATAGTCACTTG 57.285 36.000 0.00 0.00 0.00 3.16
3529 3682 9.477484 CTTATTTTGCTCCGTATATAGTCACTT 57.523 33.333 0.00 0.00 0.00 3.16
3530 3683 8.639761 ACTTATTTTGCTCCGTATATAGTCACT 58.360 33.333 0.00 0.00 0.00 3.41
3531 3684 8.700644 CACTTATTTTGCTCCGTATATAGTCAC 58.299 37.037 0.00 0.00 0.00 3.67
3532 3685 8.635328 TCACTTATTTTGCTCCGTATATAGTCA 58.365 33.333 0.00 0.00 0.00 3.41
3533 3686 9.472361 TTCACTTATTTTGCTCCGTATATAGTC 57.528 33.333 0.00 0.00 0.00 2.59
3534 3687 9.998106 ATTCACTTATTTTGCTCCGTATATAGT 57.002 29.630 0.00 0.00 0.00 2.12
3540 3693 9.472361 GTATAGATTCACTTATTTTGCTCCGTA 57.528 33.333 0.00 0.00 0.00 4.02
3541 3694 8.204836 AGTATAGATTCACTTATTTTGCTCCGT 58.795 33.333 0.00 0.00 0.00 4.69
3542 3695 8.594881 AGTATAGATTCACTTATTTTGCTCCG 57.405 34.615 0.00 0.00 0.00 4.63
3543 3696 9.771534 AGAGTATAGATTCACTTATTTTGCTCC 57.228 33.333 0.00 0.00 0.00 4.70
3583 3736 4.476297 TGGACTACCACATACGGATGTAT 58.524 43.478 14.23 7.46 44.82 2.29
3584 3737 3.900971 TGGACTACCACATACGGATGTA 58.099 45.455 14.23 0.00 44.82 2.29
3597 3750 9.103861 CTTCTTAGAGATTTCAAATGGACTACC 57.896 37.037 0.00 0.00 0.00 3.18
3598 3751 9.877178 TCTTCTTAGAGATTTCAAATGGACTAC 57.123 33.333 0.00 0.00 0.00 2.73
3599 3752 9.877178 GTCTTCTTAGAGATTTCAAATGGACTA 57.123 33.333 0.00 0.00 0.00 2.59
3600 3753 8.378565 TGTCTTCTTAGAGATTTCAAATGGACT 58.621 33.333 0.00 0.00 0.00 3.85
3601 3754 8.553459 TGTCTTCTTAGAGATTTCAAATGGAC 57.447 34.615 0.00 0.00 0.00 4.02
3602 3755 9.573166 TTTGTCTTCTTAGAGATTTCAAATGGA 57.427 29.630 0.00 0.00 0.00 3.41
3615 3768 9.595823 CCGTTCCTAAATATTTGTCTTCTTAGA 57.404 33.333 11.05 0.00 0.00 2.10
3616 3769 9.595823 TCCGTTCCTAAATATTTGTCTTCTTAG 57.404 33.333 11.05 0.00 0.00 2.18
3617 3770 9.595823 CTCCGTTCCTAAATATTTGTCTTCTTA 57.404 33.333 11.05 0.00 0.00 2.10
3618 3771 7.553044 CCTCCGTTCCTAAATATTTGTCTTCTT 59.447 37.037 11.05 0.00 0.00 2.52
3619 3772 7.048512 CCTCCGTTCCTAAATATTTGTCTTCT 58.951 38.462 11.05 0.00 0.00 2.85
3620 3773 6.260271 CCCTCCGTTCCTAAATATTTGTCTTC 59.740 42.308 11.05 0.00 0.00 2.87
3621 3774 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
3622 3775 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
3623 3776 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
3624 3777 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
3625 3778 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
3626 3779 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
3627 3780 6.614496 ACTTACTCCCTCCGTTCCTAAATATT 59.386 38.462 0.00 0.00 0.00 1.28
3628 3781 6.141790 ACTTACTCCCTCCGTTCCTAAATAT 58.858 40.000 0.00 0.00 0.00 1.28
3629 3782 5.522641 ACTTACTCCCTCCGTTCCTAAATA 58.477 41.667 0.00 0.00 0.00 1.40
3630 3783 4.359996 ACTTACTCCCTCCGTTCCTAAAT 58.640 43.478 0.00 0.00 0.00 1.40
3631 3784 3.782992 ACTTACTCCCTCCGTTCCTAAA 58.217 45.455 0.00 0.00 0.00 1.85
3632 3785 3.463048 ACTTACTCCCTCCGTTCCTAA 57.537 47.619 0.00 0.00 0.00 2.69
3633 3786 3.463048 AACTTACTCCCTCCGTTCCTA 57.537 47.619 0.00 0.00 0.00 2.94
3634 3787 2.322339 AACTTACTCCCTCCGTTCCT 57.678 50.000 0.00 0.00 0.00 3.36
3635 3788 4.750021 AATAACTTACTCCCTCCGTTCC 57.250 45.455 0.00 0.00 0.00 3.62
3636 3789 6.705863 TCTAATAACTTACTCCCTCCGTTC 57.294 41.667 0.00 0.00 0.00 3.95
3637 3790 7.672122 AATCTAATAACTTACTCCCTCCGTT 57.328 36.000 0.00 0.00 0.00 4.44
3638 3791 8.953223 ATAATCTAATAACTTACTCCCTCCGT 57.047 34.615 0.00 0.00 0.00 4.69
3671 3824 4.455533 CAGTAATGAGTGCTTTGGTTGCTA 59.544 41.667 0.00 0.00 0.00 3.49
4234 4389 3.971245 ACCAAACAGAAAACCTGCAAA 57.029 38.095 0.00 0.00 46.81 3.68
4408 4563 7.916914 TTTGGTTAGGACTAAACTAGAATGC 57.083 36.000 8.44 0.00 32.18 3.56
4625 4780 7.395489 ACAAAGGCATATCAAGTCAAAGAAGAT 59.605 33.333 0.00 0.00 0.00 2.40
4704 4859 6.877611 TTAAGAATGAAAGGAACACCTGTC 57.122 37.500 0.00 0.00 38.25 3.51
4892 5050 7.716799 TGTAGGGCACTTCATTCATATTTTT 57.283 32.000 0.00 0.00 0.00 1.94
4912 5071 5.712446 TGCCTAGTCTGCCTAGATAATGTAG 59.288 44.000 0.00 0.00 45.21 2.74
4953 5112 5.531287 GGAGGTGTCAAACTTATGAAAGTGT 59.469 40.000 0.00 0.00 45.37 3.55
4971 5130 3.743521 TCTTGTTTCAGATGTGGAGGTG 58.256 45.455 0.00 0.00 0.00 4.00
5010 5169 6.811954 TGACTATTTTGTGTACTGTCAGTGA 58.188 36.000 16.03 0.00 0.00 3.41
5021 5180 5.654650 TGGACCAGTTTTGACTATTTTGTGT 59.345 36.000 0.00 0.00 0.00 3.72
5022 5181 6.142818 TGGACCAGTTTTGACTATTTTGTG 57.857 37.500 0.00 0.00 0.00 3.33
5267 5526 2.775911 TCAACAGGAGAGGCATTCAG 57.224 50.000 0.00 0.00 0.00 3.02
5379 5640 4.534500 TCCCTGCTTCTTACCTTCAACATA 59.466 41.667 0.00 0.00 0.00 2.29
5530 5791 1.362224 TTAGGGGCTCTGTTCTGCTT 58.638 50.000 0.00 0.00 0.00 3.91
5678 5939 2.288666 GTATCCAAAATGAGGCGCTCA 58.711 47.619 7.64 9.80 44.99 4.26
5795 6062 6.478016 GTCCGAGTTACCATTATAAAGGACAC 59.522 42.308 13.56 8.84 42.66 3.67
5944 6211 3.469008 TGTCAGTGACAGAACGGAAAT 57.531 42.857 22.06 0.00 37.67 2.17
6179 6446 6.706716 ACTTTCACTCTTCCTAGCTAAACAAC 59.293 38.462 0.00 0.00 0.00 3.32
6324 6591 7.485913 TCGTCTAACCGTCTTATAAACAATGAC 59.514 37.037 0.00 0.00 0.00 3.06
6347 6614 1.045407 TGGTGCTTGACTTAGGTCGT 58.955 50.000 0.05 0.00 44.83 4.34
6349 6616 1.610886 GGGTGGTGCTTGACTTAGGTC 60.611 57.143 0.00 0.00 42.42 3.85
6394 6664 2.433868 TCGGCGTCCTAGAAATATGC 57.566 50.000 6.85 0.00 0.00 3.14
6428 6698 1.306654 TGGACTCCCTAACGCCCAT 60.307 57.895 0.00 0.00 0.00 4.00
6487 6757 9.542462 GCTAATAGTTTTGTCCACACATAGATA 57.458 33.333 0.00 0.00 30.55 1.98
6507 6777 1.688735 AGAGGCATGTGAGCGCTAATA 59.311 47.619 11.50 0.00 34.64 0.98
6516 6786 1.549950 GGGGGAAAAAGAGGCATGTGA 60.550 52.381 0.00 0.00 0.00 3.58
6568 6842 3.435327 GCGTGTGGACATTATCAACTTCA 59.565 43.478 0.00 0.00 31.64 3.02
6580 6854 2.263227 CATACGGGCGTGTGGACA 59.737 61.111 0.00 0.00 34.30 4.02
6582 6856 2.220615 CTGACATACGGGCGTGTGGA 62.221 60.000 0.00 0.00 40.75 4.02
6648 6945 0.953960 AAACGAACATGGACGAGGGC 60.954 55.000 17.79 0.00 0.00 5.19
6691 6988 2.461110 CCGACATGGCAACCGTAGC 61.461 63.158 0.00 0.00 0.00 3.58
6779 7076 6.547880 TGTGCCAACTCCTAAAGTTATGAAAA 59.452 34.615 0.00 0.00 46.69 2.29
6800 7097 4.124851 ACTGCCTAGTGTTAGTATGTGC 57.875 45.455 0.00 0.00 35.34 4.57
7104 7406 6.719370 TGTGGCAACTCCTAAAGTTATGAAAT 59.281 34.615 0.00 0.00 46.69 2.17
7105 7407 6.065374 TGTGGCAACTCCTAAAGTTATGAAA 58.935 36.000 0.00 0.00 46.69 2.69
7106 7408 5.626142 TGTGGCAACTCCTAAAGTTATGAA 58.374 37.500 0.00 0.00 46.69 2.57
7107 7409 5.235850 TGTGGCAACTCCTAAAGTTATGA 57.764 39.130 0.00 0.00 46.69 2.15
7108 7410 6.823689 AGTATGTGGCAACTCCTAAAGTTATG 59.176 38.462 0.00 0.00 46.69 1.90
7109 7411 6.958767 AGTATGTGGCAACTCCTAAAGTTAT 58.041 36.000 0.00 0.00 46.69 1.89
7110 7412 6.368779 AGTATGTGGCAACTCCTAAAGTTA 57.631 37.500 0.00 0.00 46.69 2.24
7112 7414 4.910458 AGTATGTGGCAACTCCTAAAGT 57.090 40.909 0.00 0.00 41.10 2.66
7113 7415 6.092259 GTGTTAGTATGTGGCAACTCCTAAAG 59.908 42.308 0.00 0.00 35.26 1.85
7114 7416 5.935789 GTGTTAGTATGTGGCAACTCCTAAA 59.064 40.000 0.00 0.00 35.26 1.85
7115 7417 5.247564 AGTGTTAGTATGTGGCAACTCCTAA 59.752 40.000 0.00 0.00 35.26 2.69
7116 7418 4.775780 AGTGTTAGTATGTGGCAACTCCTA 59.224 41.667 0.00 0.00 35.26 2.94
7117 7419 3.583086 AGTGTTAGTATGTGGCAACTCCT 59.417 43.478 0.00 0.00 35.26 3.69
7118 7420 3.939066 AGTGTTAGTATGTGGCAACTCC 58.061 45.455 0.00 0.00 37.61 3.85
7119 7421 5.109903 CCTAGTGTTAGTATGTGGCAACTC 58.890 45.833 0.00 0.00 37.61 3.01
7120 7422 4.623171 GCCTAGTGTTAGTATGTGGCAACT 60.623 45.833 0.00 0.00 38.99 3.16
7121 7423 3.621715 GCCTAGTGTTAGTATGTGGCAAC 59.378 47.826 0.00 0.00 38.99 4.17
7122 7424 3.262151 TGCCTAGTGTTAGTATGTGGCAA 59.738 43.478 0.00 0.00 44.86 4.52
7123 7425 2.835156 TGCCTAGTGTTAGTATGTGGCA 59.165 45.455 0.00 0.00 45.51 4.92
7124 7426 3.118738 ACTGCCTAGTGTTAGTATGTGGC 60.119 47.826 0.00 0.00 35.34 5.01
7125 7427 4.737855 ACTGCCTAGTGTTAGTATGTGG 57.262 45.455 0.00 0.00 35.34 4.17
7126 7428 5.720202 TCAACTGCCTAGTGTTAGTATGTG 58.280 41.667 0.00 0.00 37.19 3.21
7127 7429 5.715279 TCTCAACTGCCTAGTGTTAGTATGT 59.285 40.000 0.00 0.00 37.19 2.29
7128 7430 6.095580 TCTCTCAACTGCCTAGTGTTAGTATG 59.904 42.308 0.00 0.00 37.19 2.39
7129 7431 6.188407 TCTCTCAACTGCCTAGTGTTAGTAT 58.812 40.000 0.00 0.00 37.19 2.12
7130 7432 5.567430 TCTCTCAACTGCCTAGTGTTAGTA 58.433 41.667 0.00 0.00 37.19 1.82
7131 7433 4.408276 TCTCTCAACTGCCTAGTGTTAGT 58.592 43.478 0.00 0.00 37.19 2.24
7132 7434 4.992688 CTCTCTCAACTGCCTAGTGTTAG 58.007 47.826 0.00 0.00 37.19 2.34
7134 7436 3.951775 CTCTCTCAACTGCCTAGTGTT 57.048 47.619 0.00 0.00 37.19 3.32


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

AutoCloner maintained by Alex Coulton.