Multiple sequence alignment - TraesCS1B01G269800

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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 TraesCS1B01G269800 chr1B 100.000 5714 0 0 1 5714 474444027 474449740 0.000000e+00 10552.0
1 TraesCS1B01G269800 chr1D 95.888 3721 142 7 724 4441 352191130 352194842 0.000000e+00 6013.0
2 TraesCS1B01G269800 chr1D 85.852 728 87 10 1 720 36605418 36606137 0.000000e+00 760.0
3 TraesCS1B01G269800 chr1D 92.593 378 25 2 5339 5714 352232936 352233312 1.810000e-149 540.0
4 TraesCS1B01G269800 chr1D 95.918 245 8 2 4731 4975 352232585 352232827 4.150000e-106 396.0
5 TraesCS1B01G269800 chr1A 95.251 3727 139 8 724 4441 452753268 452756965 0.000000e+00 5867.0
6 TraesCS1B01G269800 chr1A 91.611 751 50 2 1046 1796 452743938 452744675 0.000000e+00 1026.0
7 TraesCS1B01G269800 chr1A 80.566 813 73 35 4600 5347 452757064 452757856 1.080000e-151 547.0
8 TraesCS1B01G269800 chr1A 93.051 331 20 2 5384 5712 452758732 452759061 1.110000e-131 481.0
9 TraesCS1B01G269800 chr1A 94.444 90 4 1 4517 4605 518662760 518662849 2.780000e-28 137.0
10 TraesCS1B01G269800 chr1A 94.937 79 3 1 871 949 452743845 452743922 7.770000e-24 122.0
11 TraesCS1B01G269800 chr4B 88.766 721 69 11 2 717 601941192 601941905 0.000000e+00 872.0
12 TraesCS1B01G269800 chr3B 87.466 726 78 9 1 720 684884604 684885322 0.000000e+00 824.0
13 TraesCS1B01G269800 chr3B 92.553 94 5 2 4517 4608 154213774 154213867 3.590000e-27 134.0
14 TraesCS1B01G269800 chr3B 91.579 95 6 2 4512 4605 802995971 802996064 4.650000e-26 130.0
15 TraesCS1B01G269800 chr3B 85.938 64 9 0 3058 3121 712571301 712571238 1.030000e-07 69.4
16 TraesCS1B01G269800 chr7B 86.915 726 81 8 2 720 512872560 512871842 0.000000e+00 802.0
17 TraesCS1B01G269800 chr7B 86.740 724 84 7 1 720 634870981 634871696 0.000000e+00 795.0
18 TraesCS1B01G269800 chr7D 85.165 728 91 11 2 720 383980731 383981450 0.000000e+00 730.0
19 TraesCS1B01G269800 chr7D 92.000 100 6 2 4516 4613 270505873 270505972 7.720000e-29 139.0
20 TraesCS1B01G269800 chr6A 85.048 729 92 11 1 720 523939964 523939244 0.000000e+00 726.0
21 TraesCS1B01G269800 chr6A 96.471 85 2 1 4518 4601 407093069 407093153 7.720000e-29 139.0
22 TraesCS1B01G269800 chr6A 89.216 102 8 3 4508 4608 405656231 405656132 2.160000e-24 124.0
23 TraesCS1B01G269800 chrUn 84.774 729 96 10 1 720 36559767 36560489 0.000000e+00 717.0
24 TraesCS1B01G269800 chr3D 84.499 729 95 12 1 720 174819051 174819770 0.000000e+00 704.0
25 TraesCS1B01G269800 chr3D 84.375 64 10 0 3058 3121 537916404 537916341 4.780000e-06 63.9
26 TraesCS1B01G269800 chr5A 91.584 404 25 5 4824 5221 6168514 6168114 3.010000e-152 549.0
27 TraesCS1B01G269800 chr2A 93.610 313 14 4 4913 5221 38316304 38315994 4.030000e-126 462.0
28 TraesCS1B01G269800 chr3A 92.473 93 7 0 4517 4609 45603268 45603360 3.590000e-27 134.0
29 TraesCS1B01G269800 chr3A 90.099 101 8 2 4509 4608 712187188 712187287 4.650000e-26 130.0
30 TraesCS1B01G269800 chr3A 85.965 57 8 0 3058 3114 673446552 673446496 1.720000e-05 62.1
31 TraesCS1B01G269800 chr6B 88.393 112 8 5 4498 4605 76149726 76149836 4.650000e-26 130.0


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 TraesCS1B01G269800 chr1B 474444027 474449740 5713 False 10552.000000 10552 100.000000 1 5714 1 chr1B.!!$F1 5713
1 TraesCS1B01G269800 chr1D 352191130 352194842 3712 False 6013.000000 6013 95.888000 724 4441 1 chr1D.!!$F2 3717
2 TraesCS1B01G269800 chr1D 36605418 36606137 719 False 760.000000 760 85.852000 1 720 1 chr1D.!!$F1 719
3 TraesCS1B01G269800 chr1D 352232585 352233312 727 False 468.000000 540 94.255500 4731 5714 2 chr1D.!!$F3 983
4 TraesCS1B01G269800 chr1A 452753268 452759061 5793 False 2298.333333 5867 89.622667 724 5712 3 chr1A.!!$F3 4988
5 TraesCS1B01G269800 chr1A 452743845 452744675 830 False 574.000000 1026 93.274000 871 1796 2 chr1A.!!$F2 925
6 TraesCS1B01G269800 chr4B 601941192 601941905 713 False 872.000000 872 88.766000 2 717 1 chr4B.!!$F1 715
7 TraesCS1B01G269800 chr3B 684884604 684885322 718 False 824.000000 824 87.466000 1 720 1 chr3B.!!$F2 719
8 TraesCS1B01G269800 chr7B 512871842 512872560 718 True 802.000000 802 86.915000 2 720 1 chr7B.!!$R1 718
9 TraesCS1B01G269800 chr7B 634870981 634871696 715 False 795.000000 795 86.740000 1 720 1 chr7B.!!$F1 719
10 TraesCS1B01G269800 chr7D 383980731 383981450 719 False 730.000000 730 85.165000 2 720 1 chr7D.!!$F2 718
11 TraesCS1B01G269800 chr6A 523939244 523939964 720 True 726.000000 726 85.048000 1 720 1 chr6A.!!$R2 719
12 TraesCS1B01G269800 chrUn 36559767 36560489 722 False 717.000000 717 84.774000 1 720 1 chrUn.!!$F1 719
13 TraesCS1B01G269800 chr3D 174819051 174819770 719 False 704.000000 704 84.499000 1 720 1 chr3D.!!$F1 719

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
311 315 0.673644 CAAGCGTCGGAGGTGGATTT 60.674 55.0 0.0 0.0 0.00 2.17 F
1731 1767 0.165944 CACGACGATTTGGTGAAGGC 59.834 55.0 0.0 0.0 33.58 4.35 F
2451 2493 0.106967 GGGGAGAAACTGGAGGATGC 60.107 60.0 0.0 0.0 0.00 3.91 F
2497 2539 0.110486 TGCAGGGTTCCTTCTTCCAC 59.890 55.0 0.0 0.0 0.00 4.02 F
3988 4030 0.242825 TGCGAGGTTTACGGTCTCTG 59.757 55.0 0.0 0.0 0.00 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1742 1778 0.179004 GGACACACCCACATCACCAA 60.179 55.0 0.00 0.0 0.00 3.67 R
3373 3415 0.398318 GGCACAGTGTCTTTCCCTCT 59.602 55.0 1.61 0.0 0.00 3.69 R
4445 4487 0.248907 ACACATCGCGTTAGATCCGG 60.249 55.0 5.77 0.0 0.00 5.14 R
4454 4496 0.166597 CTGAAATGCACACATCGCGT 59.833 50.0 5.77 0.0 34.62 6.01 R
5294 5429 0.321564 TTTGTCCCTGTGCATCCTCG 60.322 55.0 0.00 0.0 0.00 4.63 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
54 55 2.085320 AGAGTACGTGTCGCTGAGAAT 58.915 47.619 0.00 0.00 0.00 2.40
67 68 2.789893 GCTGAGAATAAAGCTACGTCCG 59.210 50.000 0.00 0.00 36.47 4.79
110 111 2.941064 AGATCATGACAATGAACCGCAG 59.059 45.455 0.00 0.00 45.81 5.18
212 215 2.380410 CGTGTTACAGTGCCGGAGC 61.380 63.158 5.05 0.00 40.48 4.70
231 235 2.360726 GGATTCGGTGCGGGGTTT 60.361 61.111 0.00 0.00 0.00 3.27
233 237 2.675075 ATTCGGTGCGGGGTTTGG 60.675 61.111 0.00 0.00 0.00 3.28
311 315 0.673644 CAAGCGTCGGAGGTGGATTT 60.674 55.000 0.00 0.00 0.00 2.17
334 338 2.103094 GTGGTTCCGATGATCTCCATGA 59.897 50.000 0.00 0.00 35.17 3.07
343 347 4.320788 CGATGATCTCCATGAACTCGATGA 60.321 45.833 0.00 0.00 35.17 2.92
428 437 4.214758 GCGTTTGTCCTACCAAAACTATGT 59.785 41.667 0.00 0.00 36.17 2.29
498 509 7.921786 TTTGTCGGAATCACTATCAAATTCT 57.078 32.000 0.00 0.00 31.53 2.40
503 515 9.314321 GTCGGAATCACTATCAAATTCTCTTAA 57.686 33.333 0.00 0.00 31.53 1.85
504 516 9.884636 TCGGAATCACTATCAAATTCTCTTAAA 57.115 29.630 0.00 0.00 31.53 1.52
552 565 2.363795 CTGCCCGAGTAGACCCCA 60.364 66.667 0.00 0.00 0.00 4.96
555 568 3.834799 CCCGAGTAGACCCCACGC 61.835 72.222 0.00 0.00 0.00 5.34
563 576 4.309950 GACCCCACGCAACCGACT 62.310 66.667 0.00 0.00 38.29 4.18
641 656 4.154347 GAGCCTGACCTCGCCTGG 62.154 72.222 0.00 0.00 0.00 4.45
722 737 1.336440 CAGGGTCTGCTAGAGATGACG 59.664 57.143 0.00 0.00 31.63 4.35
730 745 1.776662 CTAGAGATGACGGGGTCCAA 58.223 55.000 0.00 0.00 0.00 3.53
734 749 0.836400 AGATGACGGGGTCCAACAGT 60.836 55.000 0.00 0.00 0.00 3.55
755 770 1.207329 AGGAAATCTGTAGTGCCGTCC 59.793 52.381 0.00 0.00 0.00 4.79
799 814 3.512516 GGTAGTCCCGTCCGTCCG 61.513 72.222 0.00 0.00 0.00 4.79
923 940 1.698506 AATTTCCACGGCCTGACAAA 58.301 45.000 0.00 2.05 0.00 2.83
970 987 3.775654 GCTCCACCTAGCCGCTGT 61.776 66.667 2.16 0.00 36.45 4.40
977 994 3.541713 CTAGCCGCTGTCCCCTCC 61.542 72.222 2.16 0.00 0.00 4.30
1405 1441 1.727335 GAGTCGCTAAACAGGCTCAAC 59.273 52.381 0.00 0.00 38.82 3.18
1604 1640 1.911357 ACATGGTCTCTTGGCTGATCA 59.089 47.619 0.00 0.00 0.00 2.92
1731 1767 0.165944 CACGACGATTTGGTGAAGGC 59.834 55.000 0.00 0.00 33.58 4.35
1734 1770 0.721718 GACGATTTGGTGAAGGCGAG 59.278 55.000 0.00 0.00 0.00 5.03
1742 1778 3.071874 TGGTGAAGGCGAGATTCAATT 57.928 42.857 0.00 0.00 38.34 2.32
1763 1799 0.606401 GGTGATGTGGGTGTGTCCTG 60.606 60.000 0.00 0.00 36.25 3.86
1849 1885 4.022589 CCTGACAGCATGAACAACTTTGAT 60.023 41.667 0.00 0.00 39.69 2.57
1863 1899 2.373169 ACTTTGATTGTCTCCAGAGGCA 59.627 45.455 0.00 0.00 41.97 4.75
1926 1962 4.058124 CTCGACAATGTCTGGAACAAAGA 58.942 43.478 11.92 0.00 42.37 2.52
1957 1993 1.067821 GAGGATAACTGGAGCGAGGTG 59.932 57.143 0.00 0.00 0.00 4.00
1981 2017 1.210478 GCTCCTCTTAGATGTGGCCAA 59.790 52.381 7.24 0.00 0.00 4.52
2055 2091 3.793144 GGCGAGCAAGCTGGTTCG 61.793 66.667 21.77 21.77 43.21 3.95
2302 2338 1.080995 CCTCAACGCTAGAGCTGTGC 61.081 60.000 0.00 0.00 39.32 4.57
2451 2493 0.106967 GGGGAGAAACTGGAGGATGC 60.107 60.000 0.00 0.00 0.00 3.91
2485 2527 2.363306 TTGATCAACTTGTGCAGGGT 57.637 45.000 3.38 0.00 0.00 4.34
2497 2539 0.110486 TGCAGGGTTCCTTCTTCCAC 59.890 55.000 0.00 0.00 0.00 4.02
2506 2548 1.630244 CCTTCTTCCACGAGCGCAAG 61.630 60.000 11.47 5.17 43.44 4.01
2563 2605 1.818785 GCATGACCTGGCAGAGAGC 60.819 63.158 17.94 8.74 44.65 4.09
2659 2701 2.224257 TGTTACTGCTGATGCTGTCACA 60.224 45.455 9.72 9.72 46.06 3.58
2713 2755 5.284428 TGCGCACGTTCATAATTCTAAAA 57.716 34.783 5.66 0.00 0.00 1.52
2755 2797 5.011431 CAGTCAGTTGCCAGATGATATCCTA 59.989 44.000 0.00 0.00 0.00 2.94
2815 2857 3.721035 CTGCGATATGGTTGATCTGTCA 58.279 45.455 0.00 0.00 0.00 3.58
2818 2860 3.738282 GCGATATGGTTGATCTGTCAGAC 59.262 47.826 4.21 0.00 35.39 3.51
2914 2956 3.845781 AAGCTGTTCCTTCTTCAGACA 57.154 42.857 0.00 0.00 0.00 3.41
3025 3067 1.142474 GTACGTCGAAAGTTGTGGGG 58.858 55.000 0.00 0.00 0.00 4.96
3035 3077 0.863956 AGTTGTGGGGATTGGGGAAA 59.136 50.000 0.00 0.00 0.00 3.13
3075 3117 8.093927 GGGATCAATTGAGTTCCATGTTAAAAA 58.906 33.333 23.38 0.00 0.00 1.94
3082 3124 8.940768 TTGAGTTCCATGTTAAAAAGGAAAAG 57.059 30.769 3.90 0.00 41.42 2.27
3090 3132 8.539544 CCATGTTAAAAAGGAAAAGGGTCATAT 58.460 33.333 0.00 0.00 0.00 1.78
3217 3259 6.382919 AAGAAACAGGGTATTAAGGTGCTA 57.617 37.500 0.00 0.00 0.00 3.49
3332 3374 6.377429 GGTCCGTATCAGAAGATATCATGGTA 59.623 42.308 5.32 0.00 38.88 3.25
3336 3378 9.737427 CCGTATCAGAAGATATCATGGTAATAC 57.263 37.037 5.32 5.14 38.88 1.89
3343 3385 8.598041 AGAAGATATCATGGTAATACTTCACCC 58.402 37.037 21.58 6.54 36.15 4.61
3344 3386 6.936279 AGATATCATGGTAATACTTCACCCG 58.064 40.000 5.32 0.00 33.61 5.28
3373 3415 4.206375 TGGACATGAGCTTGAAGTTGAAA 58.794 39.130 0.00 0.00 0.00 2.69
3382 3424 4.582240 AGCTTGAAGTTGAAAGAGGGAAAG 59.418 41.667 0.00 0.00 0.00 2.62
3452 3494 2.285668 TCCTGCCTCCTCTTGGGG 60.286 66.667 0.00 0.00 35.33 4.96
3454 3496 1.925455 CCTGCCTCCTCTTGGGGAA 60.925 63.158 0.00 0.00 35.23 3.97
3513 3555 2.816087 GCTCACTGAGAAAGATTGGCAA 59.184 45.455 10.45 0.68 0.00 4.52
3517 3559 5.072055 TCACTGAGAAAGATTGGCAATGAA 58.928 37.500 19.07 0.00 0.00 2.57
3554 3596 4.525487 AGTTGATTGCATTTCCATGTCTGT 59.475 37.500 0.00 0.00 32.28 3.41
3686 3728 3.876309 TGGTTAAAGTGCCTCCTTTCT 57.124 42.857 0.00 0.00 36.18 2.52
3697 3739 3.034635 GCCTCCTTTCTCTCAGTCCATA 58.965 50.000 0.00 0.00 0.00 2.74
3901 3943 1.826385 ATTTTGAGGACCTTCAGGCG 58.174 50.000 0.00 0.00 39.32 5.52
3906 3948 3.435186 GGACCTTCAGGCGCTTGC 61.435 66.667 15.68 0.00 39.32 4.01
3982 4024 1.600485 ACTTGTTTGCGAGGTTTACGG 59.400 47.619 0.00 0.00 0.00 4.02
3985 4027 1.202557 TGTTTGCGAGGTTTACGGTCT 60.203 47.619 0.00 0.00 0.00 3.85
3988 4030 0.242825 TGCGAGGTTTACGGTCTCTG 59.757 55.000 0.00 0.00 0.00 3.35
4039 4081 6.549061 CAACATAACATCTCTTCCACATGTG 58.451 40.000 19.31 19.31 31.00 3.21
4261 4303 2.597217 CTGCCAAGCGGTTTCCCA 60.597 61.111 0.00 0.00 33.28 4.37
4405 4447 2.052237 GCTCGTTGTGTTGGTGCG 60.052 61.111 0.00 0.00 0.00 5.34
4441 4483 3.467119 CCAGTTCGTCGCCGTTCG 61.467 66.667 0.00 0.00 40.15 3.95
4442 4484 2.427905 CAGTTCGTCGCCGTTCGA 60.428 61.111 3.58 3.58 46.29 3.71
4454 4496 3.562639 CGTTCGATGCCGGATCTAA 57.437 52.632 5.05 1.06 36.24 2.10
4455 4497 1.129326 CGTTCGATGCCGGATCTAAC 58.871 55.000 5.05 12.52 34.73 2.34
4456 4498 1.129326 GTTCGATGCCGGATCTAACG 58.871 55.000 5.05 1.25 29.77 3.18
4457 4499 0.596600 TTCGATGCCGGATCTAACGC 60.597 55.000 5.05 0.00 36.24 4.84
4458 4500 2.365068 CGATGCCGGATCTAACGCG 61.365 63.158 5.05 3.53 0.00 6.01
4459 4501 1.007734 GATGCCGGATCTAACGCGA 60.008 57.895 15.93 0.00 0.00 5.87
4461 4503 0.667487 ATGCCGGATCTAACGCGATG 60.667 55.000 15.93 1.69 0.00 3.84
4477 4548 3.103738 GCGATGTGTGCATTTCAGATTC 58.896 45.455 0.00 0.00 35.07 2.52
4485 4556 5.355071 GTGTGCATTTCAGATTCCATAGTCA 59.645 40.000 0.00 0.00 0.00 3.41
4502 4573 2.029649 AGTCAATGTCTGCCATTTGTGC 60.030 45.455 0.00 0.00 41.93 4.57
4512 4583 2.035704 TGCCATTTGTGCGTGAAATTCT 59.964 40.909 0.00 0.00 0.00 2.40
4513 4584 3.254411 TGCCATTTGTGCGTGAAATTCTA 59.746 39.130 0.00 0.00 0.00 2.10
4514 4585 3.608073 GCCATTTGTGCGTGAAATTCTAC 59.392 43.478 0.00 0.00 0.00 2.59
4515 4586 4.615912 GCCATTTGTGCGTGAAATTCTACT 60.616 41.667 0.00 0.00 0.00 2.57
4516 4587 4.853196 CCATTTGTGCGTGAAATTCTACTG 59.147 41.667 0.00 0.00 0.00 2.74
4517 4588 5.451908 CATTTGTGCGTGAAATTCTACTGT 58.548 37.500 0.00 0.00 0.00 3.55
4518 4589 6.348132 CCATTTGTGCGTGAAATTCTACTGTA 60.348 38.462 0.00 0.00 0.00 2.74
4519 4590 5.585500 TTGTGCGTGAAATTCTACTGTAC 57.415 39.130 0.00 0.00 0.00 2.90
4520 4591 4.878439 TGTGCGTGAAATTCTACTGTACT 58.122 39.130 0.00 0.00 0.00 2.73
4521 4592 4.921515 TGTGCGTGAAATTCTACTGTACTC 59.078 41.667 0.00 0.00 0.00 2.59
4522 4593 4.326548 GTGCGTGAAATTCTACTGTACTCC 59.673 45.833 0.00 0.00 0.00 3.85
4523 4594 3.864003 GCGTGAAATTCTACTGTACTCCC 59.136 47.826 0.00 0.00 0.00 4.30
4524 4595 4.381718 GCGTGAAATTCTACTGTACTCCCT 60.382 45.833 0.00 0.00 0.00 4.20
4525 4596 5.341617 CGTGAAATTCTACTGTACTCCCTC 58.658 45.833 0.00 0.00 0.00 4.30
4526 4597 5.662456 GTGAAATTCTACTGTACTCCCTCC 58.338 45.833 0.00 0.00 0.00 4.30
4527 4598 4.401519 TGAAATTCTACTGTACTCCCTCCG 59.598 45.833 0.00 0.00 0.00 4.63
4528 4599 3.666345 ATTCTACTGTACTCCCTCCGT 57.334 47.619 0.00 0.00 0.00 4.69
4529 4600 4.785346 ATTCTACTGTACTCCCTCCGTA 57.215 45.455 0.00 0.00 0.00 4.02
4530 4601 4.574674 TTCTACTGTACTCCCTCCGTAA 57.425 45.455 0.00 0.00 0.00 3.18
4531 4602 4.574674 TCTACTGTACTCCCTCCGTAAA 57.425 45.455 0.00 0.00 0.00 2.01
4532 4603 4.521146 TCTACTGTACTCCCTCCGTAAAG 58.479 47.826 0.00 0.00 0.00 1.85
4533 4604 3.446442 ACTGTACTCCCTCCGTAAAGA 57.554 47.619 0.00 0.00 0.00 2.52
4534 4605 3.771216 ACTGTACTCCCTCCGTAAAGAA 58.229 45.455 0.00 0.00 0.00 2.52
4535 4606 4.154942 ACTGTACTCCCTCCGTAAAGAAA 58.845 43.478 0.00 0.00 0.00 2.52
4536 4607 4.776308 ACTGTACTCCCTCCGTAAAGAAAT 59.224 41.667 0.00 0.00 0.00 2.17
4537 4608 5.954150 ACTGTACTCCCTCCGTAAAGAAATA 59.046 40.000 0.00 0.00 0.00 1.40
4538 4609 6.610425 ACTGTACTCCCTCCGTAAAGAAATAT 59.390 38.462 0.00 0.00 0.00 1.28
4539 4610 7.781693 ACTGTACTCCCTCCGTAAAGAAATATA 59.218 37.037 0.00 0.00 0.00 0.86
4540 4611 8.537728 TGTACTCCCTCCGTAAAGAAATATAA 57.462 34.615 0.00 0.00 0.00 0.98
4541 4612 8.636213 TGTACTCCCTCCGTAAAGAAATATAAG 58.364 37.037 0.00 0.00 0.00 1.73
4542 4613 7.909485 ACTCCCTCCGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
4543 4614 7.953752 ACTCCCTCCGTAAAGAAATATAAGAG 58.046 38.462 0.00 0.00 0.00 2.85
4544 4615 6.756221 TCCCTCCGTAAAGAAATATAAGAGC 58.244 40.000 0.00 0.00 0.00 4.09
4545 4616 6.325545 TCCCTCCGTAAAGAAATATAAGAGCA 59.674 38.462 0.00 0.00 0.00 4.26
4546 4617 7.016268 TCCCTCCGTAAAGAAATATAAGAGCAT 59.984 37.037 0.00 0.00 0.00 3.79
4547 4618 7.661847 CCCTCCGTAAAGAAATATAAGAGCATT 59.338 37.037 0.00 0.00 0.00 3.56
4548 4619 9.057089 CCTCCGTAAAGAAATATAAGAGCATTT 57.943 33.333 0.00 0.00 0.00 2.32
4587 4658 9.654663 AGTTATCTAAACGCTCTTACATTTCTT 57.345 29.630 0.00 0.00 0.00 2.52
4595 4666 8.649973 AACGCTCTTACATTTCTTTATAGAGG 57.350 34.615 0.00 0.00 0.00 3.69
4596 4667 7.210873 ACGCTCTTACATTTCTTTATAGAGGG 58.789 38.462 0.00 0.00 43.02 4.30
4597 4668 7.069578 ACGCTCTTACATTTCTTTATAGAGGGA 59.930 37.037 16.73 0.00 41.16 4.20
4598 4669 7.596995 CGCTCTTACATTTCTTTATAGAGGGAG 59.403 40.741 0.00 0.00 41.16 4.30
4619 4690 6.661377 GGGAGTAGTATGCAAGATGAGAGATA 59.339 42.308 0.00 0.00 0.00 1.98
4622 4693 7.237982 AGTAGTATGCAAGATGAGAGATACCT 58.762 38.462 0.00 0.00 0.00 3.08
4661 4732 7.047891 CCCTTCTGTATGTATGTAATGTGTGT 58.952 38.462 0.00 0.00 0.00 3.72
4662 4733 7.011389 CCCTTCTGTATGTATGTAATGTGTGTG 59.989 40.741 0.00 0.00 0.00 3.82
4679 4750 8.858003 ATGTGTGTGAAATTCTAGTATACTCG 57.142 34.615 9.12 2.99 0.00 4.18
4696 4767 9.265901 AGTATACTCGTACGTTCTGTATGTAAT 57.734 33.333 16.05 3.64 40.36 1.89
4706 4778 6.037830 ACGTTCTGTATGTAATTAATGTGCCC 59.962 38.462 0.00 0.00 0.00 5.36
4850 4950 8.417106 TGATTGCAGTAAATAACAAAAGGTTGA 58.583 29.630 0.00 0.00 40.73 3.18
4874 4974 2.485426 AGATTTCAGTCCACAACGCATG 59.515 45.455 0.00 0.00 0.00 4.06
4934 5046 8.445275 TTTTGCTCTAGTCTGAAACATGTTTA 57.555 30.769 23.33 5.99 32.11 2.01
4977 5089 5.468072 CAGGATACATTGGATCAAGTGCTAC 59.532 44.000 11.00 0.00 41.41 3.58
4980 5092 6.239600 GGATACATTGGATCAAGTGCTACCTA 60.240 42.308 11.00 0.00 0.00 3.08
4982 5094 4.471386 ACATTGGATCAAGTGCTACCTAGT 59.529 41.667 0.00 0.00 0.00 2.57
4994 5106 4.020485 GTGCTACCTAGTTCCTCCTTTTCA 60.020 45.833 0.00 0.00 0.00 2.69
4996 5108 5.250774 TGCTACCTAGTTCCTCCTTTTCATT 59.749 40.000 0.00 0.00 0.00 2.57
5041 5153 6.974932 ACTACAGTTTTCTATCACAGCATG 57.025 37.500 0.00 0.00 46.00 4.06
5050 5162 4.941657 TCTATCACAGCATGCTACAGAAG 58.058 43.478 22.19 15.07 42.53 2.85
5122 5254 9.836076 ATGTTGATATTTTCATTCAGCATATCG 57.164 29.630 0.51 0.00 38.85 2.92
5133 5265 7.809665 TCATTCAGCATATCGTTTTCCATATG 58.190 34.615 0.00 0.00 36.45 1.78
5136 5268 7.601073 TCAGCATATCGTTTTCCATATGATC 57.399 36.000 3.65 0.00 35.70 2.92
5145 5277 8.105097 TCGTTTTCCATATGATCAAAGTTTCA 57.895 30.769 3.65 0.00 0.00 2.69
5151 5283 9.709495 TTCCATATGATCAAAGTTTCAAAAAGG 57.291 29.630 3.65 0.00 0.00 3.11
5157 5289 7.610865 TGATCAAAGTTTCAAAAAGGTTGAGT 58.389 30.769 0.00 0.00 0.00 3.41
5162 5294 5.351458 AGTTTCAAAAAGGTTGAGTGCATC 58.649 37.500 0.00 0.00 0.00 3.91
5184 5316 3.654414 GTCAGACGTCCACTTTTCTGAT 58.346 45.455 13.01 0.00 44.72 2.90
5187 5319 1.993370 GACGTCCACTTTTCTGATCGG 59.007 52.381 3.51 0.00 0.00 4.18
5199 5331 1.383109 TGATCGGAGGGAGCACCAT 60.383 57.895 1.58 0.00 43.89 3.55
5222 5354 7.362574 CCATAAGGTACCATTTCAAACATTCGT 60.363 37.037 15.94 0.00 0.00 3.85
5266 5401 7.924412 TCAATAAAGGACAATATACACTCGGTC 59.076 37.037 0.00 0.00 0.00 4.79
5270 5405 5.443283 AGGACAATATACACTCGGTCTGTA 58.557 41.667 0.00 0.00 0.00 2.74
5287 5422 6.866770 CGGTCTGTAAAATCAAGAACTAGTCA 59.133 38.462 0.00 0.00 0.00 3.41
5349 5504 8.560576 AAAGAGAAAACAAATAACATGACACG 57.439 30.769 0.00 0.00 0.00 4.49
5380 5535 3.680789 GCTACACGCATCAACATTAACC 58.319 45.455 0.00 0.00 38.92 2.85
5418 6392 5.470098 ACACATGCACTACAAAAAGAGGTAG 59.530 40.000 0.00 0.00 42.07 3.18
5494 6470 4.663120 AGGCTATATAATGGGTGTTCACCA 59.337 41.667 21.25 9.68 43.22 4.17
5499 6475 1.981256 AATGGGTGTTCACCACAGAC 58.019 50.000 21.25 6.33 46.44 3.51
5504 6480 1.092921 GTGTTCACCACAGACCGCAA 61.093 55.000 0.00 0.00 43.92 4.85
5570 6546 5.952347 ACTAACAGGTACCCCATTCTTAG 57.048 43.478 8.74 7.19 0.00 2.18
5645 6621 5.351740 GTGGATAAGAGAACCAAGCTACAAC 59.648 44.000 0.00 0.00 35.40 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 1.000060 AGCAACACGGACGTAGCTTTA 60.000 47.619 11.18 0.00 29.81 1.85
67 68 0.944311 TTCTCTTCGGCGAGCAACAC 60.944 55.000 10.46 0.00 0.00 3.32
110 111 0.389948 GGTGAGGTCGTCCATGTCAC 60.390 60.000 9.93 9.93 36.39 3.67
212 215 3.622060 AACCCCGCACCGAATCCAG 62.622 63.158 0.00 0.00 0.00 3.86
228 232 1.209127 CGGCGACATTGGTCCAAAC 59.791 57.895 8.75 2.81 41.13 2.93
231 235 1.449423 CATCGGCGACATTGGTCCA 60.449 57.895 13.76 0.00 41.13 4.02
233 237 2.709475 GCATCGGCGACATTGGTC 59.291 61.111 13.76 0.00 40.77 4.02
298 302 1.131303 ACCACCAAATCCACCTCCGA 61.131 55.000 0.00 0.00 0.00 4.55
311 315 0.830648 GGAGATCATCGGAACCACCA 59.169 55.000 0.00 0.00 38.90 4.17
334 338 1.154016 CACTCCGCGTCATCGAGTT 60.154 57.895 11.54 0.00 39.71 3.01
343 347 1.136984 GTCGATCTTCACTCCGCGT 59.863 57.895 4.92 0.00 0.00 6.01
433 442 3.791993 AAAACATAGTTCGCGCGTAAA 57.208 38.095 30.98 15.41 0.00 2.01
498 509 5.412286 CCGTAAACCGAAAATCCCTTTAAGA 59.588 40.000 0.00 0.00 39.56 2.10
503 515 2.224843 ACCCGTAAACCGAAAATCCCTT 60.225 45.455 0.00 0.00 39.56 3.95
504 516 1.352017 ACCCGTAAACCGAAAATCCCT 59.648 47.619 0.00 0.00 39.56 4.20
508 521 2.068519 GTCGACCCGTAAACCGAAAAT 58.931 47.619 3.51 0.00 39.56 1.82
544 557 2.601067 TCGGTTGCGTGGGGTCTA 60.601 61.111 0.00 0.00 0.00 2.59
552 565 1.569708 TTTTTACGAGTCGGTTGCGT 58.430 45.000 18.30 0.00 41.58 5.24
623 638 4.504916 CAGGCGAGGTCAGGCTCG 62.505 72.222 0.00 0.00 42.91 5.03
641 656 1.039233 AATATGTGTGCAGGCTGGCC 61.039 55.000 17.64 3.00 0.00 5.36
679 694 2.116827 AATCCGAACCCGCATAAACA 57.883 45.000 0.00 0.00 0.00 2.83
680 695 3.175929 CAAAATCCGAACCCGCATAAAC 58.824 45.455 0.00 0.00 0.00 2.01
720 735 0.472352 TTCCTACTGTTGGACCCCGT 60.472 55.000 10.53 0.00 32.65 5.28
721 736 0.688487 TTTCCTACTGTTGGACCCCG 59.312 55.000 10.53 0.00 32.65 5.73
722 737 2.576648 AGATTTCCTACTGTTGGACCCC 59.423 50.000 10.53 3.27 32.65 4.95
730 745 3.119101 CGGCACTACAGATTTCCTACTGT 60.119 47.826 0.00 0.00 46.81 3.55
734 749 2.429610 GGACGGCACTACAGATTTCCTA 59.570 50.000 0.00 0.00 0.00 2.94
755 770 1.478510 ACTGGCCACTCGAATCTACTG 59.521 52.381 0.00 0.00 0.00 2.74
859 876 1.810031 CGGGGCTATTTCTCGCATTGA 60.810 52.381 0.00 0.00 0.00 2.57
923 940 0.322187 CCGTTCGAGGGGTTTTGGAT 60.322 55.000 0.00 0.00 0.00 3.41
970 987 0.323542 GAGTTGACGAGAGGAGGGGA 60.324 60.000 0.00 0.00 0.00 4.81
977 994 1.257743 TTGGGAGGAGTTGACGAGAG 58.742 55.000 0.00 0.00 0.00 3.20
1405 1441 1.699656 CCAGCTTCTTGATGACGCCG 61.700 60.000 0.00 0.00 40.35 6.46
1580 1616 0.617413 AGCCAAGAGACCATGTCCTG 59.383 55.000 0.00 0.00 32.18 3.86
1731 1767 4.439153 CCCACATCACCAAATTGAATCTCG 60.439 45.833 0.00 0.00 0.00 4.04
1734 1770 4.021192 ACACCCACATCACCAAATTGAATC 60.021 41.667 0.00 0.00 0.00 2.52
1742 1778 0.179004 GGACACACCCACATCACCAA 60.179 55.000 0.00 0.00 0.00 3.67
1763 1799 2.690778 CCTTGTGGTAAGCGGCAGC 61.691 63.158 0.00 0.00 45.58 5.25
1849 1885 1.881903 CGAGCTGCCTCTGGAGACAA 61.882 60.000 0.00 0.00 42.06 3.18
1863 1899 1.253593 TGACACAGCATCCTCGAGCT 61.254 55.000 6.99 0.00 42.94 4.09
1876 1912 2.038952 CAGGAACCTCTTGGATGACACA 59.961 50.000 0.00 0.00 37.04 3.72
1926 1962 0.759346 GTTATCCTCGTCCATGCCCT 59.241 55.000 0.00 0.00 0.00 5.19
1957 1993 2.911484 CCACATCTAAGAGGAGCCAAC 58.089 52.381 0.00 0.00 0.00 3.77
1969 2005 2.994699 CCGGGTTGGCCACATCTA 59.005 61.111 3.88 0.00 36.17 1.98
1981 2017 1.452651 CATGATCTTGCTGCCGGGT 60.453 57.895 2.18 0.00 0.00 5.28
2002 2038 1.173913 CAATCCTTTTCCGGGTGGTC 58.826 55.000 0.00 0.00 36.30 4.02
2009 2045 4.766404 AGTTTGCTACAATCCTTTTCCG 57.234 40.909 0.00 0.00 0.00 4.30
2055 2091 3.819877 AACGCCAGTCCGTCCAACC 62.820 63.158 0.00 0.00 41.16 3.77
2203 2239 3.664025 CTTGAGCATCCCGCCGACA 62.664 63.158 0.00 0.00 44.04 4.35
2302 2338 1.517832 CTCCTGCAGGTTCCGGTAG 59.482 63.158 31.58 16.26 36.34 3.18
2435 2477 1.407989 CCCTGCATCCTCCAGTTTCTC 60.408 57.143 0.00 0.00 0.00 2.87
2436 2478 0.622665 CCCTGCATCCTCCAGTTTCT 59.377 55.000 0.00 0.00 0.00 2.52
2451 2493 4.826274 TGATCAAAGTACTCCTTCCCTG 57.174 45.455 0.00 0.00 31.27 4.45
2485 2527 1.374252 GCGCTCGTGGAAGAAGGAA 60.374 57.895 0.00 0.00 0.00 3.36
2506 2548 4.917906 ATAGTAATTCTGATGGCCCTCC 57.082 45.455 0.00 0.00 0.00 4.30
2563 2605 1.082038 ACAGTCAACTCGCGAGACG 60.082 57.895 40.58 28.66 45.62 4.18
2569 2611 0.510359 CTCTTGCACAGTCAACTCGC 59.490 55.000 0.00 0.00 0.00 5.03
2659 2701 2.281761 CACCGGCCTTTGAGCTGT 60.282 61.111 0.00 0.00 37.44 4.40
2713 2755 3.426615 ACTGAGAGAAGACGAGGAATGT 58.573 45.455 0.00 0.00 0.00 2.71
2755 2797 3.317993 CACGGACACCCTTCAATTCTTTT 59.682 43.478 0.00 0.00 0.00 2.27
2815 2857 3.755378 GCATCAGTTGACCAATTCTGTCT 59.245 43.478 6.28 0.00 33.83 3.41
2818 2860 3.366679 GGTGCATCAGTTGACCAATTCTG 60.367 47.826 0.00 0.00 0.00 3.02
2820 2862 2.821969 AGGTGCATCAGTTGACCAATTC 59.178 45.455 0.00 0.00 31.61 2.17
2896 2938 3.118905 AGTGTCTGAAGAAGGAACAGC 57.881 47.619 0.00 0.00 0.00 4.40
2914 2956 4.224762 GGCACCTCTTAGGGATACTTAGT 58.775 47.826 0.00 0.00 40.58 2.24
3025 3067 5.142639 TGGAGATGAATCATTTCCCCAATC 58.857 41.667 24.50 4.87 42.33 2.67
3035 3077 5.862422 ATTGATCCCTGGAGATGAATCAT 57.138 39.130 0.00 0.00 25.25 2.45
3075 3117 7.510675 TCTTCTAACATATGACCCTTTTCCT 57.489 36.000 10.38 0.00 0.00 3.36
3082 3124 9.778741 TCATACAAATCTTCTAACATATGACCC 57.221 33.333 10.38 0.00 0.00 4.46
3190 3232 6.246163 CACCTTAATACCCTGTTTCTTTCCT 58.754 40.000 0.00 0.00 0.00 3.36
3343 3385 0.606401 AGCTCATGTCCAACCAACCG 60.606 55.000 0.00 0.00 0.00 4.44
3344 3386 1.270550 CAAGCTCATGTCCAACCAACC 59.729 52.381 0.00 0.00 0.00 3.77
3373 3415 0.398318 GGCACAGTGTCTTTCCCTCT 59.602 55.000 1.61 0.00 0.00 3.69
3382 3424 6.803154 AAAGATTTAAGTAGGCACAGTGTC 57.197 37.500 0.00 0.00 0.00 3.67
3452 3494 0.402121 ACCTTCAGGCAGGGAAGTTC 59.598 55.000 11.07 0.00 40.06 3.01
3454 3496 0.853530 AAACCTTCAGGCAGGGAAGT 59.146 50.000 11.07 0.39 40.06 3.01
3513 3555 8.472413 CAATCAACTTGGTTCCATAGAATTCAT 58.528 33.333 8.44 0.00 33.67 2.57
3517 3559 5.716228 TGCAATCAACTTGGTTCCATAGAAT 59.284 36.000 0.00 0.00 35.25 2.40
3554 3596 7.339976 TGGCATATCATCAAATTCAAGTTCTGA 59.660 33.333 0.00 0.00 0.00 3.27
3686 3728 3.769844 GTGACCTTCCTTATGGACTGAGA 59.230 47.826 0.00 0.00 43.06 3.27
3697 3739 3.581332 TGTTTCGGATAGTGACCTTCCTT 59.419 43.478 0.73 0.00 0.00 3.36
3710 3752 0.958822 GCAAACCCTGTGTTTCGGAT 59.041 50.000 0.00 0.00 45.35 4.18
3877 3919 4.522789 GCCTGAAGGTCCTCAAAATTTACA 59.477 41.667 0.00 0.00 37.57 2.41
3901 3943 0.520847 GCTTCTTGAGTGAGGCAAGC 59.479 55.000 0.00 0.00 41.83 4.01
3906 3948 2.110901 ATGCAGCTTCTTGAGTGAGG 57.889 50.000 0.00 0.00 0.00 3.86
3913 3955 5.498393 AGATGGGATATATGCAGCTTCTTG 58.502 41.667 6.56 0.00 0.00 3.02
3982 4024 2.799126 TCTCCAGAGAGGTCAGAGAC 57.201 55.000 0.00 0.00 40.83 3.36
3985 4027 3.783082 TGTCTATCTCCAGAGAGGTCAGA 59.217 47.826 3.41 1.25 41.33 3.27
3988 4030 4.338118 CAGTTGTCTATCTCCAGAGAGGTC 59.662 50.000 3.41 0.00 41.33 3.85
4039 4081 2.461903 GTTAATCCGCTCGAACTCTCC 58.538 52.381 0.00 0.00 0.00 3.71
4255 4297 3.228188 ACTTGCAGTGAAGATGGGAAA 57.772 42.857 0.00 0.00 0.00 3.13
4261 4303 5.411977 CAGATCAAGAACTTGCAGTGAAGAT 59.588 40.000 9.38 0.00 40.24 2.40
4405 4447 1.798813 GGAATGATAACGGCATCGGAC 59.201 52.381 0.00 0.00 41.39 4.79
4441 4483 0.388649 ATCGCGTTAGATCCGGCATC 60.389 55.000 5.77 0.62 0.00 3.91
4442 4484 0.667487 CATCGCGTTAGATCCGGCAT 60.667 55.000 5.77 0.00 0.00 4.40
4443 4485 1.299850 CATCGCGTTAGATCCGGCA 60.300 57.895 5.77 0.00 0.00 5.69
4444 4486 1.299926 ACATCGCGTTAGATCCGGC 60.300 57.895 5.77 0.00 0.00 6.13
4445 4487 0.248907 ACACATCGCGTTAGATCCGG 60.249 55.000 5.77 0.00 0.00 5.14
4446 4488 0.846401 CACACATCGCGTTAGATCCG 59.154 55.000 5.77 0.00 0.00 4.18
4447 4489 0.577269 GCACACATCGCGTTAGATCC 59.423 55.000 5.77 0.00 0.00 3.36
4448 4490 1.277326 TGCACACATCGCGTTAGATC 58.723 50.000 5.77 0.00 0.00 2.75
4449 4491 1.939974 ATGCACACATCGCGTTAGAT 58.060 45.000 5.77 0.00 0.00 1.98
4450 4492 1.720805 AATGCACACATCGCGTTAGA 58.279 45.000 5.77 0.00 36.84 2.10
4452 4494 1.801178 TGAAATGCACACATCGCGTTA 59.199 42.857 5.77 0.00 37.62 3.18
4453 4495 0.590682 TGAAATGCACACATCGCGTT 59.409 45.000 5.77 0.00 40.26 4.84
4454 4496 0.166597 CTGAAATGCACACATCGCGT 59.833 50.000 5.77 0.00 34.62 6.01
4455 4497 0.443478 TCTGAAATGCACACATCGCG 59.557 50.000 0.00 0.00 34.62 5.87
4456 4498 2.838386 ATCTGAAATGCACACATCGC 57.162 45.000 0.00 0.00 34.62 4.58
4457 4499 3.127376 TGGAATCTGAAATGCACACATCG 59.873 43.478 0.00 0.00 34.62 3.84
4458 4500 4.707030 TGGAATCTGAAATGCACACATC 57.293 40.909 0.00 0.00 34.62 3.06
4459 4501 5.889853 ACTATGGAATCTGAAATGCACACAT 59.110 36.000 0.00 0.00 38.49 3.21
4461 4503 5.355071 TGACTATGGAATCTGAAATGCACAC 59.645 40.000 0.00 0.00 0.00 3.82
4502 4573 5.326200 AGGGAGTACAGTAGAATTTCACG 57.674 43.478 0.00 0.00 0.00 4.35
4512 4583 4.574674 TCTTTACGGAGGGAGTACAGTA 57.425 45.455 0.00 0.00 0.00 2.74
4513 4584 3.446442 TCTTTACGGAGGGAGTACAGT 57.554 47.619 0.00 0.00 0.00 3.55
4514 4585 4.796038 TTTCTTTACGGAGGGAGTACAG 57.204 45.455 0.00 0.00 0.00 2.74
4515 4586 8.537728 TTATATTTCTTTACGGAGGGAGTACA 57.462 34.615 0.00 0.00 0.00 2.90
4516 4587 8.854117 TCTTATATTTCTTTACGGAGGGAGTAC 58.146 37.037 0.00 0.00 0.00 2.73
4517 4588 9.075678 CTCTTATATTTCTTTACGGAGGGAGTA 57.924 37.037 0.00 0.00 0.00 2.59
4518 4589 7.471679 GCTCTTATATTTCTTTACGGAGGGAGT 60.472 40.741 0.00 0.00 0.00 3.85
4519 4590 6.869388 GCTCTTATATTTCTTTACGGAGGGAG 59.131 42.308 0.00 0.00 0.00 4.30
4520 4591 6.325545 TGCTCTTATATTTCTTTACGGAGGGA 59.674 38.462 0.00 0.00 0.00 4.20
4521 4592 6.522054 TGCTCTTATATTTCTTTACGGAGGG 58.478 40.000 0.00 0.00 0.00 4.30
4522 4593 8.608844 AATGCTCTTATATTTCTTTACGGAGG 57.391 34.615 0.00 0.00 0.00 4.30
4561 4632 9.654663 AAGAAATGTAAGAGCGTTTAGATAACT 57.345 29.630 0.00 0.00 0.00 2.24
4569 4640 9.099454 CCTCTATAAAGAAATGTAAGAGCGTTT 57.901 33.333 0.00 0.00 0.00 3.60
4570 4641 7.711339 CCCTCTATAAAGAAATGTAAGAGCGTT 59.289 37.037 0.00 0.00 0.00 4.84
4571 4642 7.069578 TCCCTCTATAAAGAAATGTAAGAGCGT 59.930 37.037 0.00 0.00 0.00 5.07
4572 4643 7.434492 TCCCTCTATAAAGAAATGTAAGAGCG 58.566 38.462 0.00 0.00 0.00 5.03
4573 4644 8.425703 ACTCCCTCTATAAAGAAATGTAAGAGC 58.574 37.037 0.00 0.00 0.00 4.09
4580 4651 9.646427 GCATACTACTCCCTCTATAAAGAAATG 57.354 37.037 0.00 0.00 0.00 2.32
4581 4652 9.381038 TGCATACTACTCCCTCTATAAAGAAAT 57.619 33.333 0.00 0.00 0.00 2.17
4582 4653 8.777578 TGCATACTACTCCCTCTATAAAGAAA 57.222 34.615 0.00 0.00 0.00 2.52
4583 4654 8.777578 TTGCATACTACTCCCTCTATAAAGAA 57.222 34.615 0.00 0.00 0.00 2.52
4584 4655 8.225416 TCTTGCATACTACTCCCTCTATAAAGA 58.775 37.037 0.00 0.00 0.00 2.52
4585 4656 8.410673 TCTTGCATACTACTCCCTCTATAAAG 57.589 38.462 0.00 0.00 0.00 1.85
4586 4657 8.807118 CATCTTGCATACTACTCCCTCTATAAA 58.193 37.037 0.00 0.00 0.00 1.40
4587 4658 8.170730 TCATCTTGCATACTACTCCCTCTATAA 58.829 37.037 0.00 0.00 0.00 0.98
4588 4659 7.699878 TCATCTTGCATACTACTCCCTCTATA 58.300 38.462 0.00 0.00 0.00 1.31
4589 4660 6.556639 TCATCTTGCATACTACTCCCTCTAT 58.443 40.000 0.00 0.00 0.00 1.98
4590 4661 5.953571 TCATCTTGCATACTACTCCCTCTA 58.046 41.667 0.00 0.00 0.00 2.43
4591 4662 4.809193 TCATCTTGCATACTACTCCCTCT 58.191 43.478 0.00 0.00 0.00 3.69
4592 4663 4.830046 TCTCATCTTGCATACTACTCCCTC 59.170 45.833 0.00 0.00 0.00 4.30
4593 4664 4.809193 TCTCATCTTGCATACTACTCCCT 58.191 43.478 0.00 0.00 0.00 4.20
4594 4665 4.830046 TCTCTCATCTTGCATACTACTCCC 59.170 45.833 0.00 0.00 0.00 4.30
4595 4666 6.588719 ATCTCTCATCTTGCATACTACTCC 57.411 41.667 0.00 0.00 0.00 3.85
4596 4667 7.393234 AGGTATCTCTCATCTTGCATACTACTC 59.607 40.741 0.00 0.00 0.00 2.59
4597 4668 7.176515 CAGGTATCTCTCATCTTGCATACTACT 59.823 40.741 0.00 0.00 0.00 2.57
4598 4669 7.175816 TCAGGTATCTCTCATCTTGCATACTAC 59.824 40.741 0.00 0.00 0.00 2.73
4640 4711 9.665719 ATTTCACACACATTACATACATACAGA 57.334 29.630 0.00 0.00 0.00 3.41
4661 4732 9.102757 AGAACGTACGAGTATACTAGAATTTCA 57.897 33.333 24.41 0.00 0.00 2.69
4662 4733 9.367717 CAGAACGTACGAGTATACTAGAATTTC 57.632 37.037 24.41 9.63 0.00 2.17
4679 4750 8.060090 GGCACATTAATTACATACAGAACGTAC 58.940 37.037 0.00 0.00 31.27 3.67
4706 4778 8.081633 TGTAATGAAAATGTACTTCAGCCAAAG 58.918 33.333 0.00 0.00 36.30 2.77
4724 4796 7.136119 CGGCTAAAAACAGAAAGTGTAATGAA 58.864 34.615 0.00 0.00 39.03 2.57
4763 4835 0.883153 TGTTCTGACATGCACATGCC 59.117 50.000 10.50 0.00 42.39 4.40
4850 4950 2.744202 GCGTTGTGGACTGAAATCTGAT 59.256 45.455 0.00 0.00 0.00 2.90
4874 4974 5.277683 CCTGATGATAAGTTACATGTGCTGC 60.278 44.000 9.11 0.00 0.00 5.25
4934 5046 1.134640 TGACGTAGGTGTTGTGTGCTT 60.135 47.619 0.00 0.00 0.00 3.91
4959 5071 4.471386 ACTAGGTAGCACTTGATCCAATGT 59.529 41.667 0.00 0.00 0.00 2.71
4960 5072 5.028549 ACTAGGTAGCACTTGATCCAATG 57.971 43.478 0.00 0.00 0.00 2.82
4961 5073 5.396884 GGAACTAGGTAGCACTTGATCCAAT 60.397 44.000 0.00 0.00 36.01 3.16
4977 5089 5.810095 AGACAATGAAAAGGAGGAACTAGG 58.190 41.667 0.00 0.00 41.55 3.02
4980 5092 7.234355 ATTGTAGACAATGAAAAGGAGGAACT 58.766 34.615 7.09 0.00 44.22 3.01
4982 5094 8.359642 CAAATTGTAGACAATGAAAAGGAGGAA 58.640 33.333 8.61 0.00 45.06 3.36
5019 5131 5.583854 AGCATGCTGTGATAGAAAACTGTAG 59.416 40.000 21.98 0.00 0.00 2.74
5022 5134 4.959596 AGCATGCTGTGATAGAAAACTG 57.040 40.909 21.98 0.00 0.00 3.16
5023 5135 5.491070 TGTAGCATGCTGTGATAGAAAACT 58.509 37.500 30.42 0.60 27.45 2.66
5024 5136 5.582269 TCTGTAGCATGCTGTGATAGAAAAC 59.418 40.000 30.42 15.88 27.45 2.43
5025 5137 5.733676 TCTGTAGCATGCTGTGATAGAAAA 58.266 37.500 30.42 2.54 27.45 2.29
5066 5198 9.930158 TTTTACCAGCCATAATTATTCCTAGTT 57.070 29.630 0.00 0.00 0.00 2.24
5068 5200 8.793592 GGTTTTACCAGCCATAATTATTCCTAG 58.206 37.037 0.00 0.00 38.42 3.02
5133 5265 7.464577 GCACTCAACCTTTTTGAAACTTTGATC 60.465 37.037 0.00 0.00 0.00 2.92
5136 5268 5.407995 TGCACTCAACCTTTTTGAAACTTTG 59.592 36.000 0.00 0.00 0.00 2.77
5145 5277 2.948979 TGACGATGCACTCAACCTTTTT 59.051 40.909 0.00 0.00 0.00 1.94
5151 5283 0.710567 CGTCTGACGATGCACTCAAC 59.289 55.000 24.86 0.00 46.05 3.18
5157 5289 1.080772 GTGGACGTCTGACGATGCA 60.081 57.895 33.99 24.57 46.05 3.96
5162 5294 3.857383 ATCAGAAAAGTGGACGTCTGACG 60.857 47.826 26.94 26.94 46.80 4.35
5184 5316 1.048724 CCTTATGGTGCTCCCTCCGA 61.049 60.000 1.59 0.00 0.00 4.55
5199 5331 6.487331 ACACGAATGTTTGAAATGGTACCTTA 59.513 34.615 14.36 0.00 34.46 2.69
5256 5391 6.335471 TCTTGATTTTACAGACCGAGTGTA 57.665 37.500 0.00 0.00 0.00 2.90
5266 5401 9.261180 TGTCTTGACTAGTTCTTGATTTTACAG 57.739 33.333 0.00 0.00 0.00 2.74
5270 5405 7.872993 TCGATGTCTTGACTAGTTCTTGATTTT 59.127 33.333 0.00 0.00 0.00 1.82
5287 5422 1.134580 CCTGTGCATCCTCGATGTCTT 60.135 52.381 0.00 0.00 41.60 3.01
5294 5429 0.321564 TTTGTCCCTGTGCATCCTCG 60.322 55.000 0.00 0.00 0.00 4.63
5331 5466 4.981674 CCTTGCGTGTCATGTTATTTGTTT 59.018 37.500 0.00 0.00 0.00 2.83
5349 5504 3.788766 CGTGTAGCGTGCCCTTGC 61.789 66.667 0.00 0.00 35.54 4.01
5380 5535 2.737359 GCATGTGTTGCCAAGGATGATG 60.737 50.000 0.00 0.00 46.15 3.07
5494 6470 2.799126 TATTGGGATTTGCGGTCTGT 57.201 45.000 0.00 0.00 0.00 3.41
5499 6475 1.039068 TGCCATATTGGGATTTGCGG 58.961 50.000 0.00 0.00 38.19 5.69
5570 6546 9.303537 GCGAGGATAATTTTCATACTACCTATC 57.696 37.037 0.00 0.00 0.00 2.08
5645 6621 7.095649 ACGCTGCACACAATGTATATATAGTTG 60.096 37.037 12.82 12.82 0.00 3.16


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

AutoCloner maintained by Alex Coulton.