Multiple sequence alignment - TraesCS1A01G235900

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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 TraesCS1A01G235900 chr1A 100.000 7416 0 0 1 7416 418033259 418040674 0.000000e+00 13695.0
1 TraesCS1A01G235900 chr1D 95.945 4661 138 31 4 4628 325692020 325687375 0.000000e+00 7513.0
2 TraesCS1A01G235900 chr1D 93.465 2540 98 28 4887 7416 325687376 325684895 0.000000e+00 3709.0
3 TraesCS1A01G235900 chr1D 92.500 40 2 1 7260 7298 284300052 284300013 1.000000e-03 56.5
4 TraesCS1A01G235900 chr1B 93.560 4674 207 42 3 4628 438709824 438705197 0.000000e+00 6878.0
5 TraesCS1A01G235900 chr1B 93.606 2565 101 27 4887 7416 438705198 438702662 0.000000e+00 3770.0
6 TraesCS1A01G235900 chr5A 95.896 268 10 1 4627 4893 638636839 638637106 4.110000e-117 433.0
7 TraesCS1A01G235900 chr5A 95.455 264 11 1 4627 4889 490049347 490049084 3.200000e-113 420.0
8 TraesCS1A01G235900 chr5A 95.455 264 11 1 4627 4889 693552551 693552288 3.200000e-113 420.0
9 TraesCS1A01G235900 chr4A 96.198 263 9 1 4627 4888 45420101 45419839 5.320000e-116 429.0
10 TraesCS1A01G235900 chr7B 95.833 264 10 1 4627 4889 677299914 677300177 6.880000e-115 425.0
11 TraesCS1A01G235900 chr7B 88.462 260 27 2 3103 3360 107925850 107925592 2.010000e-80 311.0
12 TraesCS1A01G235900 chr3B 95.817 263 10 1 4627 4888 432599529 432599267 2.470000e-114 424.0
13 TraesCS1A01G235900 chr3A 95.489 266 11 1 4627 4891 333328052 333328317 2.470000e-114 424.0
14 TraesCS1A01G235900 chr3A 95.113 266 12 1 4627 4891 529744715 529744980 1.150000e-112 418.0
15 TraesCS1A01G235900 chr6B 95.455 264 11 1 4627 4889 712458222 712457959 3.200000e-113 420.0
16 TraesCS1A01G235900 chr4D 89.354 263 25 3 3098 3358 208560168 208560429 2.000000e-85 327.0
17 TraesCS1A01G235900 chr6D 88.168 262 29 2 3103 3362 103962485 103962224 2.010000e-80 311.0
18 TraesCS1A01G235900 chr7D 88.077 260 28 2 3103 3360 145766955 145766697 9.350000e-79 305.0
19 TraesCS1A01G235900 chr5B 87.109 256 31 1 3103 3356 324708382 324708127 9.410000e-74 289.0
20 TraesCS1A01G235900 chr5B 86.822 258 31 2 3102 3356 594870753 594870496 1.220000e-72 285.0
21 TraesCS1A01G235900 chr5B 86.154 260 31 4 3099 3356 317855564 317855820 7.330000e-70 276.0
22 TraesCS1A01G235900 chr2D 81.188 202 24 12 7206 7398 587108259 587108063 4.640000e-32 150.0
23 TraesCS1A01G235900 chr2B 80.864 162 22 8 7206 7361 708827481 708827323 1.310000e-22 119.0


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 TraesCS1A01G235900 chr1A 418033259 418040674 7415 False 13695 13695 100.000 1 7416 1 chr1A.!!$F1 7415
1 TraesCS1A01G235900 chr1D 325684895 325692020 7125 True 5611 7513 94.705 4 7416 2 chr1D.!!$R2 7412
2 TraesCS1A01G235900 chr1B 438702662 438709824 7162 True 5324 6878 93.583 3 7416 2 chr1B.!!$R1 7413

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
304 306 0.035439 ATGTTTGGTGCTACCGAGGG 60.035 55.000 0.00 0.0 42.58 4.30 F
619 622 0.602638 GGACGACACTTGTGGCATCA 60.603 55.000 5.06 0.0 0.00 3.07 F
1393 1415 0.676466 TTCGCGGGTGATTCAAGCAT 60.676 50.000 6.13 0.0 0.00 3.79 F
1587 1617 0.757188 AATGTCGGCCAAACCACCAA 60.757 50.000 2.24 0.0 39.03 3.67 F
2170 2207 2.215196 TCAGTGTAAGAAACGGCAACC 58.785 47.619 0.00 0.0 0.00 3.77 F
2885 2937 4.580580 GGTTCCTATATGCAAGAAAGGGTG 59.419 45.833 0.00 0.0 0.00 4.61 F
4651 4714 0.179145 CTCCGTCCGCGAATAAGTGT 60.179 55.000 8.23 0.0 41.33 3.55 F
5028 5091 0.178975 AAATGTTGGACGGGGAAGCA 60.179 50.000 0.00 0.0 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2170 2207 0.107017 ATCTCACCGGCCCATGAAAG 60.107 55.000 0.00 0.00 0.00 2.62 R
2404 2444 4.062991 ACCCGTCATTAAACTGTTGTCTC 58.937 43.478 0.00 0.00 0.00 3.36 R
3256 3311 3.333414 CACAACTGTGGCACTCCG 58.667 61.111 19.83 9.66 42.10 4.63 R
3540 3595 5.631096 GCAAAAAGAGGAGTACTTCAATTGC 59.369 40.000 3.42 8.45 35.95 3.56 R
3587 3642 3.558418 TCTGAAACCGTCTTTTGTAGCAC 59.442 43.478 0.00 0.00 0.00 4.40 R
4867 4930 0.033796 ACTCCCTCCGTCCACGAATA 60.034 55.000 0.00 0.00 43.02 1.75 R
6385 6458 1.403249 CCAGCCAGCAAACACAATAGC 60.403 52.381 0.00 0.00 0.00 2.97 R
6901 6993 0.482446 AACTGCCATCAGGGGTTTGA 59.518 50.000 0.00 0.00 44.54 2.69 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
20 21 3.947841 GCAACACGACGCAAGCCA 61.948 61.111 0.00 0.00 45.62 4.75
56 57 1.069090 GCACAACTGTCGTCCCTCA 59.931 57.895 0.00 0.00 0.00 3.86
79 80 0.909133 TAGTGGCATGGTGAGCTCCA 60.909 55.000 12.15 3.48 42.01 3.86
88 89 1.294780 GTGAGCTCCACTGACCAGG 59.705 63.158 12.15 0.00 42.44 4.45
202 204 1.133823 TGATATTCCCTGGTTGCGCAT 60.134 47.619 12.75 0.00 0.00 4.73
204 206 0.751277 TATTCCCTGGTTGCGCATGG 60.751 55.000 12.75 11.53 0.00 3.66
304 306 0.035439 ATGTTTGGTGCTACCGAGGG 60.035 55.000 0.00 0.00 42.58 4.30
349 351 1.202782 CCTGGGCCATCAGATTCTCAG 60.203 57.143 6.72 0.00 36.93 3.35
355 357 3.577667 GCCATCAGATTCTCAGATCGAG 58.422 50.000 7.88 7.88 43.80 4.04
392 394 5.876651 TGTTGTATCTGCTGGATCTATGT 57.123 39.130 0.00 0.00 35.98 2.29
416 418 7.976734 TGTTCAATTTTCGAACACCTAAAATGT 59.023 29.630 0.00 0.00 45.85 2.71
446 448 4.572985 CAAATGTTGCAGAGTTCTTGGA 57.427 40.909 0.00 0.00 0.00 3.53
454 456 2.617532 GCAGAGTTCTTGGAAGCCATCT 60.618 50.000 0.00 0.00 31.53 2.90
455 457 3.008330 CAGAGTTCTTGGAAGCCATCTG 58.992 50.000 0.00 0.00 31.53 2.90
460 462 4.718774 AGTTCTTGGAAGCCATCTGATCTA 59.281 41.667 0.00 0.00 31.53 1.98
470 472 4.220382 AGCCATCTGATCTAAGAATCCGAG 59.780 45.833 0.00 0.00 0.00 4.63
530 533 2.530701 AGCACCGGATATTCTCCTAGG 58.469 52.381 9.46 0.82 42.47 3.02
542 545 3.491766 TCTCCTAGGAATGAAGGTGGT 57.508 47.619 13.77 0.00 0.00 4.16
545 548 2.500098 TCCTAGGAATGAAGGTGGTTCG 59.500 50.000 9.71 0.00 38.09 3.95
551 554 3.370103 GGAATGAAGGTGGTTCGTGGATA 60.370 47.826 0.00 0.00 38.09 2.59
619 622 0.602638 GGACGACACTTGTGGCATCA 60.603 55.000 5.06 0.00 0.00 3.07
788 791 3.114616 CCTTGTCCTCGCACGCAG 61.115 66.667 0.00 0.00 0.00 5.18
789 792 3.782244 CTTGTCCTCGCACGCAGC 61.782 66.667 0.00 0.00 40.87 5.25
914 934 1.303317 ACAAGCCCAAACCCTAGCG 60.303 57.895 0.00 0.00 0.00 4.26
1380 1402 2.159226 ACTAGACTTTGGAGATTCGCGG 60.159 50.000 6.13 0.00 0.00 6.46
1393 1415 0.676466 TTCGCGGGTGATTCAAGCAT 60.676 50.000 6.13 0.00 0.00 3.79
1396 1418 1.668419 GCGGGTGATTCAAGCATAGT 58.332 50.000 5.49 0.00 0.00 2.12
1551 1581 5.600484 ACAGTTATCTAGGTGCTATCTTGCT 59.400 40.000 0.00 0.00 0.00 3.91
1587 1617 0.757188 AATGTCGGCCAAACCACCAA 60.757 50.000 2.24 0.00 39.03 3.67
1589 1619 0.757188 TGTCGGCCAAACCACCAAAT 60.757 50.000 2.24 0.00 39.03 2.32
1871 1903 5.916661 TTGTCTCTAGAACTATGGTGGAC 57.083 43.478 0.00 0.00 0.00 4.02
1884 1916 8.575649 AACTATGGTGGACGAAAAGAATAAAT 57.424 30.769 0.00 0.00 0.00 1.40
1941 1975 9.967451 TTTTTGTGTATTGAAGATCTGGGTATA 57.033 29.630 0.00 0.00 0.00 1.47
2155 2192 3.748048 ACATCCTGACACGATTTTCAGTG 59.252 43.478 0.00 0.00 43.46 3.66
2170 2207 2.215196 TCAGTGTAAGAAACGGCAACC 58.785 47.619 0.00 0.00 0.00 3.77
2843 2895 5.832539 TCAGGGAATCAGGGAAATAGATC 57.167 43.478 0.00 0.00 0.00 2.75
2866 2918 8.702163 ATCGAAACATTGAAATAATTGGGTTC 57.298 30.769 0.00 0.00 0.00 3.62
2885 2937 4.580580 GGTTCCTATATGCAAGAAAGGGTG 59.419 45.833 0.00 0.00 0.00 4.61
2903 2955 9.626045 GAAAGGGTGTTATCAGTTTTAAGAATG 57.374 33.333 0.00 0.00 0.00 2.67
3020 3073 7.771183 AGCTTTGATCACACAAAAGTAGAAAA 58.229 30.769 0.00 0.00 38.90 2.29
3471 3526 5.245301 TCCCATTTTGACTTCTCGAGAACTA 59.755 40.000 23.74 9.53 0.00 2.24
3540 3595 9.406828 CAGCATGACATTATTGAGAATATTTGG 57.593 33.333 0.00 0.00 39.69 3.28
3587 3642 3.881688 AGCTGATATAGTGGCAAGCTTTG 59.118 43.478 0.00 0.00 0.00 2.77
4186 4248 1.825090 CAATGAGGTTGGTGCTAGCA 58.175 50.000 14.93 14.93 34.06 3.49
4268 4330 5.721876 TTAGTTTTACACACTTGTCACCG 57.278 39.130 0.00 0.00 37.15 4.94
4365 4427 6.127196 TGCTTCTTGTTATTTGTCTTGGGTTT 60.127 34.615 0.00 0.00 0.00 3.27
4505 4567 5.949952 GGGACAAAGTACACCAGGAATATTT 59.050 40.000 0.00 0.00 0.00 1.40
4629 4692 8.856490 TTAAGAACGAAAAGAACGTACTTACT 57.144 30.769 0.00 0.00 43.16 2.24
4630 4693 6.983059 AGAACGAAAAGAACGTACTTACTC 57.017 37.500 0.00 0.00 43.16 2.59
4631 4694 5.917447 AGAACGAAAAGAACGTACTTACTCC 59.083 40.000 0.00 0.00 43.16 3.85
4632 4695 4.550422 ACGAAAAGAACGTACTTACTCCC 58.450 43.478 0.00 0.00 42.17 4.30
4633 4696 4.279420 ACGAAAAGAACGTACTTACTCCCT 59.721 41.667 0.00 0.00 42.17 4.20
4634 4697 4.855937 CGAAAAGAACGTACTTACTCCCTC 59.144 45.833 0.00 0.00 0.00 4.30
4635 4698 4.797800 AAAGAACGTACTTACTCCCTCC 57.202 45.455 0.00 0.00 0.00 4.30
4636 4699 2.363683 AGAACGTACTTACTCCCTCCG 58.636 52.381 0.00 0.00 0.00 4.63
4637 4700 2.087646 GAACGTACTTACTCCCTCCGT 58.912 52.381 0.00 0.00 0.00 4.69
4638 4701 1.743996 ACGTACTTACTCCCTCCGTC 58.256 55.000 0.00 0.00 0.00 4.79
4639 4702 1.020437 CGTACTTACTCCCTCCGTCC 58.980 60.000 0.00 0.00 0.00 4.79
4640 4703 1.020437 GTACTTACTCCCTCCGTCCG 58.980 60.000 0.00 0.00 0.00 4.79
4641 4704 0.749454 TACTTACTCCCTCCGTCCGC 60.749 60.000 0.00 0.00 0.00 5.54
4642 4705 3.122250 CTTACTCCCTCCGTCCGCG 62.122 68.421 0.00 0.00 37.95 6.46
4643 4706 3.626996 TTACTCCCTCCGTCCGCGA 62.627 63.158 8.23 0.00 41.33 5.87
4644 4707 3.626996 TACTCCCTCCGTCCGCGAA 62.627 63.158 8.23 0.00 41.33 4.70
4645 4708 2.898920 TACTCCCTCCGTCCGCGAAT 62.899 60.000 8.23 0.00 41.33 3.34
4646 4709 2.124193 TCCCTCCGTCCGCGAATA 60.124 61.111 8.23 0.00 41.33 1.75
4647 4710 1.731433 CTCCCTCCGTCCGCGAATAA 61.731 60.000 8.23 0.00 41.33 1.40
4648 4711 1.299926 CCCTCCGTCCGCGAATAAG 60.300 63.158 8.23 0.00 41.33 1.73
4649 4712 1.436336 CCTCCGTCCGCGAATAAGT 59.564 57.895 8.23 0.00 41.33 2.24
4650 4713 0.870307 CCTCCGTCCGCGAATAAGTG 60.870 60.000 8.23 0.00 41.33 3.16
4651 4714 0.179145 CTCCGTCCGCGAATAAGTGT 60.179 55.000 8.23 0.00 41.33 3.55
4652 4715 1.064505 CTCCGTCCGCGAATAAGTGTA 59.935 52.381 8.23 0.00 41.33 2.90
4653 4716 1.194495 CCGTCCGCGAATAAGTGTAC 58.806 55.000 8.23 0.00 41.33 2.90
4654 4717 1.467883 CCGTCCGCGAATAAGTGTACA 60.468 52.381 8.23 0.00 41.33 2.90
4655 4718 2.456989 CGTCCGCGAATAAGTGTACAT 58.543 47.619 8.23 0.00 41.33 2.29
4656 4719 2.466571 CGTCCGCGAATAAGTGTACATC 59.533 50.000 8.23 0.00 41.33 3.06
4657 4720 3.703420 GTCCGCGAATAAGTGTACATCT 58.297 45.455 8.23 0.00 0.00 2.90
4658 4721 4.553351 CGTCCGCGAATAAGTGTACATCTA 60.553 45.833 8.23 0.00 41.33 1.98
4659 4722 4.910456 GTCCGCGAATAAGTGTACATCTAG 59.090 45.833 8.23 0.00 0.00 2.43
4660 4723 3.669122 CCGCGAATAAGTGTACATCTAGC 59.331 47.826 8.23 0.00 0.00 3.42
4661 4724 4.537965 CGCGAATAAGTGTACATCTAGCT 58.462 43.478 0.00 0.00 0.00 3.32
4662 4725 4.976731 CGCGAATAAGTGTACATCTAGCTT 59.023 41.667 0.00 0.00 0.00 3.74
4663 4726 5.459107 CGCGAATAAGTGTACATCTAGCTTT 59.541 40.000 0.00 0.00 0.00 3.51
4664 4727 6.019801 CGCGAATAAGTGTACATCTAGCTTTT 60.020 38.462 0.00 0.00 0.00 2.27
4665 4728 7.119997 GCGAATAAGTGTACATCTAGCTTTTG 58.880 38.462 0.00 0.00 0.00 2.44
4666 4729 7.201530 GCGAATAAGTGTACATCTAGCTTTTGT 60.202 37.037 0.00 0.00 0.00 2.83
4667 4730 8.656849 CGAATAAGTGTACATCTAGCTTTTGTT 58.343 33.333 0.00 0.00 0.00 2.83
4668 4731 9.974750 GAATAAGTGTACATCTAGCTTTTGTTC 57.025 33.333 0.00 0.63 0.00 3.18
4669 4732 9.726438 AATAAGTGTACATCTAGCTTTTGTTCT 57.274 29.630 0.00 0.00 0.00 3.01
4672 4735 8.764524 AGTGTACATCTAGCTTTTGTTCTAAG 57.235 34.615 0.00 0.00 0.00 2.18
4673 4736 8.368668 AGTGTACATCTAGCTTTTGTTCTAAGT 58.631 33.333 0.00 0.00 0.00 2.24
4674 4737 8.648968 GTGTACATCTAGCTTTTGTTCTAAGTC 58.351 37.037 0.00 0.00 0.00 3.01
4675 4738 8.364894 TGTACATCTAGCTTTTGTTCTAAGTCA 58.635 33.333 0.00 0.00 0.00 3.41
4676 4739 9.204570 GTACATCTAGCTTTTGTTCTAAGTCAA 57.795 33.333 0.00 0.00 0.00 3.18
4677 4740 8.677148 ACATCTAGCTTTTGTTCTAAGTCAAA 57.323 30.769 0.00 0.00 32.75 2.69
4678 4741 8.778358 ACATCTAGCTTTTGTTCTAAGTCAAAG 58.222 33.333 0.00 0.00 35.47 2.77
4679 4742 8.778358 CATCTAGCTTTTGTTCTAAGTCAAAGT 58.222 33.333 0.00 0.00 35.47 2.66
4680 4743 8.732746 TCTAGCTTTTGTTCTAAGTCAAAGTT 57.267 30.769 0.00 0.00 35.47 2.66
4681 4744 9.174166 TCTAGCTTTTGTTCTAAGTCAAAGTTT 57.826 29.630 0.00 0.00 35.47 2.66
4682 4745 9.788960 CTAGCTTTTGTTCTAAGTCAAAGTTTT 57.211 29.630 0.00 0.00 35.47 2.43
4787 4850 8.894768 AGAATCTAGTGATACTAATTTGGTGC 57.105 34.615 0.00 0.00 29.00 5.01
4788 4851 7.934120 AGAATCTAGTGATACTAATTTGGTGCC 59.066 37.037 0.00 0.00 29.00 5.01
4789 4852 6.553953 TCTAGTGATACTAATTTGGTGCCA 57.446 37.500 0.00 0.00 29.00 4.92
4790 4853 7.136822 TCTAGTGATACTAATTTGGTGCCAT 57.863 36.000 0.00 0.00 29.00 4.40
4791 4854 8.257602 TCTAGTGATACTAATTTGGTGCCATA 57.742 34.615 0.00 0.00 29.00 2.74
4792 4855 8.710239 TCTAGTGATACTAATTTGGTGCCATAA 58.290 33.333 0.00 0.00 29.00 1.90
4793 4856 9.337396 CTAGTGATACTAATTTGGTGCCATAAA 57.663 33.333 0.00 0.00 29.00 1.40
4794 4857 8.766994 AGTGATACTAATTTGGTGCCATAAAT 57.233 30.769 0.00 0.00 0.00 1.40
4795 4858 8.632679 AGTGATACTAATTTGGTGCCATAAATG 58.367 33.333 0.00 0.00 0.00 2.32
4796 4859 7.382218 GTGATACTAATTTGGTGCCATAAATGC 59.618 37.037 0.00 0.00 0.00 3.56
4797 4860 5.937975 ACTAATTTGGTGCCATAAATGCT 57.062 34.783 0.00 0.00 0.00 3.79
4798 4861 6.298441 ACTAATTTGGTGCCATAAATGCTT 57.702 33.333 0.00 0.00 0.00 3.91
4799 4862 6.710278 ACTAATTTGGTGCCATAAATGCTTT 58.290 32.000 0.00 0.00 0.00 3.51
4800 4863 7.167535 ACTAATTTGGTGCCATAAATGCTTTT 58.832 30.769 2.86 2.86 0.00 2.27
4801 4864 8.317679 ACTAATTTGGTGCCATAAATGCTTTTA 58.682 29.630 7.20 7.20 0.00 1.52
4802 4865 6.983474 ATTTGGTGCCATAAATGCTTTTAC 57.017 33.333 6.92 0.00 30.33 2.01
4803 4866 5.736951 TTGGTGCCATAAATGCTTTTACT 57.263 34.783 6.92 0.00 30.33 2.24
4804 4867 5.736951 TGGTGCCATAAATGCTTTTACTT 57.263 34.783 6.92 0.00 30.33 2.24
4805 4868 6.107901 TGGTGCCATAAATGCTTTTACTTT 57.892 33.333 6.92 0.00 30.33 2.66
4806 4869 6.529220 TGGTGCCATAAATGCTTTTACTTTT 58.471 32.000 6.92 0.00 30.33 2.27
4807 4870 6.995091 TGGTGCCATAAATGCTTTTACTTTTT 59.005 30.769 6.92 0.00 30.33 1.94
4808 4871 7.172361 TGGTGCCATAAATGCTTTTACTTTTTC 59.828 33.333 6.92 0.00 30.33 2.29
4809 4872 7.360861 GGTGCCATAAATGCTTTTACTTTTTCC 60.361 37.037 6.92 3.64 30.33 3.13
4810 4873 7.387673 GTGCCATAAATGCTTTTACTTTTTCCT 59.612 33.333 6.92 0.00 30.33 3.36
4811 4874 8.589338 TGCCATAAATGCTTTTACTTTTTCCTA 58.411 29.630 6.92 0.00 30.33 2.94
4812 4875 9.087424 GCCATAAATGCTTTTACTTTTTCCTAG 57.913 33.333 6.92 0.00 30.33 3.02
4817 4880 9.764363 AAATGCTTTTACTTTTTCCTAGAAAGG 57.236 29.630 7.18 0.00 45.21 3.11
4818 4881 7.891498 TGCTTTTACTTTTTCCTAGAAAGGT 57.109 32.000 7.18 3.08 44.09 3.50
4819 4882 7.712797 TGCTTTTACTTTTTCCTAGAAAGGTG 58.287 34.615 7.18 0.00 44.09 4.00
4820 4883 7.145985 GCTTTTACTTTTTCCTAGAAAGGTGG 58.854 38.462 7.18 0.00 44.09 4.61
4821 4884 7.201884 GCTTTTACTTTTTCCTAGAAAGGTGGT 60.202 37.037 7.18 0.00 44.09 4.16
4822 4885 7.812690 TTTACTTTTTCCTAGAAAGGTGGTC 57.187 36.000 7.18 0.00 44.09 4.02
4823 4886 5.382664 ACTTTTTCCTAGAAAGGTGGTCA 57.617 39.130 7.18 0.00 44.09 4.02
4824 4887 5.762279 ACTTTTTCCTAGAAAGGTGGTCAA 58.238 37.500 7.18 0.00 44.09 3.18
4825 4888 6.192044 ACTTTTTCCTAGAAAGGTGGTCAAA 58.808 36.000 7.18 0.00 44.09 2.69
4826 4889 6.321435 ACTTTTTCCTAGAAAGGTGGTCAAAG 59.679 38.462 7.18 0.00 44.09 2.77
4827 4890 5.382664 TTTCCTAGAAAGGTGGTCAAAGT 57.617 39.130 0.00 0.00 44.09 2.66
4828 4891 5.382664 TTCCTAGAAAGGTGGTCAAAGTT 57.617 39.130 0.00 0.00 44.09 2.66
4829 4892 5.382664 TCCTAGAAAGGTGGTCAAAGTTT 57.617 39.130 0.00 0.00 44.09 2.66
4830 4893 5.762279 TCCTAGAAAGGTGGTCAAAGTTTT 58.238 37.500 0.00 0.00 44.09 2.43
4831 4894 6.902408 TCCTAGAAAGGTGGTCAAAGTTTTA 58.098 36.000 0.00 0.00 44.09 1.52
4832 4895 7.348033 TCCTAGAAAGGTGGTCAAAGTTTTAA 58.652 34.615 0.00 0.00 44.09 1.52
4833 4896 7.835181 TCCTAGAAAGGTGGTCAAAGTTTTAAA 59.165 33.333 0.00 0.00 44.09 1.52
4834 4897 8.471609 CCTAGAAAGGTGGTCAAAGTTTTAAAA 58.528 33.333 0.00 0.00 38.19 1.52
4835 4898 9.297586 CTAGAAAGGTGGTCAAAGTTTTAAAAC 57.702 33.333 21.06 21.06 39.17 2.43
4857 4920 9.788960 AAAACTTTGACTTAAGACAAAAGCTAG 57.211 29.630 25.68 18.71 38.68 3.42
4858 4921 8.732746 AACTTTGACTTAAGACAAAAGCTAGA 57.267 30.769 25.68 9.24 38.68 2.43
4859 4922 8.910351 ACTTTGACTTAAGACAAAAGCTAGAT 57.090 30.769 25.68 9.44 38.68 1.98
4860 4923 8.778358 ACTTTGACTTAAGACAAAAGCTAGATG 58.222 33.333 25.68 16.98 38.68 2.90
4861 4924 8.677148 TTTGACTTAAGACAAAAGCTAGATGT 57.323 30.769 24.34 0.00 36.92 3.06
4862 4925 9.772973 TTTGACTTAAGACAAAAGCTAGATGTA 57.227 29.630 24.34 4.07 36.92 2.29
4863 4926 8.758633 TGACTTAAGACAAAAGCTAGATGTAC 57.241 34.615 10.09 0.00 0.00 2.90
4864 4927 8.364894 TGACTTAAGACAAAAGCTAGATGTACA 58.635 33.333 10.09 0.00 0.00 2.90
4865 4928 8.535690 ACTTAAGACAAAAGCTAGATGTACAC 57.464 34.615 10.09 0.00 0.00 2.90
4866 4929 8.368668 ACTTAAGACAAAAGCTAGATGTACACT 58.631 33.333 10.09 0.13 0.00 3.55
4867 4930 9.209175 CTTAAGACAAAAGCTAGATGTACACTT 57.791 33.333 0.00 0.00 0.00 3.16
4870 4933 9.726438 AAGACAAAAGCTAGATGTACACTTATT 57.274 29.630 0.00 0.00 0.00 1.40
4871 4934 9.372369 AGACAAAAGCTAGATGTACACTTATTC 57.628 33.333 0.00 0.00 0.00 1.75
4872 4935 8.186178 ACAAAAGCTAGATGTACACTTATTCG 57.814 34.615 0.00 0.00 0.00 3.34
4873 4936 7.817962 ACAAAAGCTAGATGTACACTTATTCGT 59.182 33.333 0.00 0.00 0.00 3.85
4874 4937 7.757097 AAAGCTAGATGTACACTTATTCGTG 57.243 36.000 0.00 0.00 40.67 4.35
4875 4938 5.833082 AGCTAGATGTACACTTATTCGTGG 58.167 41.667 0.00 0.00 39.19 4.94
4876 4939 5.593095 AGCTAGATGTACACTTATTCGTGGA 59.407 40.000 0.00 0.00 39.19 4.02
4877 4940 5.686397 GCTAGATGTACACTTATTCGTGGAC 59.314 44.000 0.00 0.00 46.62 4.02
4880 4943 3.492421 GTACACTTATTCGTGGACGGA 57.508 47.619 0.00 0.00 38.82 4.69
4881 4944 2.649331 ACACTTATTCGTGGACGGAG 57.351 50.000 0.00 0.00 39.19 4.63
4882 4945 1.203994 ACACTTATTCGTGGACGGAGG 59.796 52.381 0.00 0.00 39.19 4.30
4883 4946 0.822164 ACTTATTCGTGGACGGAGGG 59.178 55.000 0.00 0.00 40.29 4.30
4884 4947 1.108776 CTTATTCGTGGACGGAGGGA 58.891 55.000 0.00 0.00 40.29 4.20
4885 4948 1.067212 CTTATTCGTGGACGGAGGGAG 59.933 57.143 0.00 0.00 40.29 4.30
5002 5065 7.669722 TGCCCTAAGACTCTTATTTTGTTGAAT 59.330 33.333 0.00 0.00 0.00 2.57
5028 5091 0.178975 AAATGTTGGACGGGGAAGCA 60.179 50.000 0.00 0.00 0.00 3.91
5119 5182 2.799017 TCACATGCTTTGCAGATCCTT 58.201 42.857 0.00 0.00 43.65 3.36
5404 5473 3.070590 TGACTCATGAAGATCATCGCCAT 59.929 43.478 0.00 0.00 34.28 4.40
5865 5934 3.070018 CTCCCAACACATGTGAGTCTTC 58.930 50.000 31.94 0.00 0.00 2.87
5869 5938 4.021104 CCCAACACATGTGAGTCTTCTCTA 60.021 45.833 31.94 0.00 40.98 2.43
5945 6014 3.356529 AGGCTTGGAGTTGGTAGATTG 57.643 47.619 0.00 0.00 0.00 2.67
5950 6019 5.488341 GCTTGGAGTTGGTAGATTGTTCTA 58.512 41.667 0.00 0.00 33.17 2.10
5951 6020 6.116126 GCTTGGAGTTGGTAGATTGTTCTAT 58.884 40.000 0.00 0.00 36.84 1.98
5952 6021 6.037610 GCTTGGAGTTGGTAGATTGTTCTATG 59.962 42.308 0.00 0.00 36.84 2.23
5953 6022 6.620877 TGGAGTTGGTAGATTGTTCTATGT 57.379 37.500 0.00 0.00 36.84 2.29
5997 6066 1.135139 GCAGACCTCAGCGATCAGTTA 59.865 52.381 0.00 0.00 0.00 2.24
6052 6121 9.562408 TTACTAAAATGATTTGGTGTACTGTGA 57.438 29.630 0.00 0.00 40.08 3.58
6053 6122 8.458573 ACTAAAATGATTTGGTGTACTGTGAA 57.541 30.769 0.00 0.00 38.62 3.18
6054 6123 9.077885 ACTAAAATGATTTGGTGTACTGTGAAT 57.922 29.630 0.00 0.00 38.62 2.57
6055 6124 9.912634 CTAAAATGATTTGGTGTACTGTGAATT 57.087 29.630 0.00 0.00 0.00 2.17
6066 6135 6.072728 GGTGTACTGTGAATTTGTGATGCTAA 60.073 38.462 0.00 0.00 0.00 3.09
6077 6146 3.521560 TGTGATGCTAAACGAGTCCATC 58.478 45.455 0.00 0.00 0.00 3.51
6120 6192 5.470437 CGGTGATACTGATGAGACTAGCTAA 59.530 44.000 0.00 0.00 0.00 3.09
6157 6230 7.510549 TGTCTCAAGGAATCCTTACAAAAAG 57.489 36.000 15.04 0.44 42.67 2.27
6182 6255 7.223582 AGACATGCTTAGTATCATCTTTGTTCG 59.776 37.037 0.00 0.00 0.00 3.95
6197 6270 8.702438 CATCTTTGTTCGCTGTTTCAATATTTT 58.298 29.630 0.00 0.00 0.00 1.82
6227 6300 6.664816 TCATGCTAGGAAATTTTTCATCCTGT 59.335 34.615 5.97 0.00 43.34 4.00
6242 6315 5.237815 TCATCCTGTTATCTGTGTTGTCAC 58.762 41.667 0.00 0.00 44.08 3.67
6248 6321 4.979815 TGTTATCTGTGTTGTCACGTGTAG 59.020 41.667 16.51 4.35 46.49 2.74
6312 6385 0.395686 GCAGCATATCCTCTCCTGCA 59.604 55.000 6.10 0.00 46.00 4.41
6385 6458 0.179156 GTCAATGGGCACTTGCGATG 60.179 55.000 0.00 0.00 43.26 3.84
6403 6476 1.619654 TGCTATTGTGTTTGCTGGCT 58.380 45.000 0.00 0.00 0.00 4.75
6426 6499 3.068873 GGTCTACCATGACAGAGCTAAGG 59.931 52.174 14.73 0.00 38.61 2.69
6456 6529 5.296748 GCTGAAGGCAGTCCAAAATAAAAA 58.703 37.500 0.00 0.00 44.17 1.94
6515 6595 3.282831 GCATTAGGCGTGAAAAACTGT 57.717 42.857 0.00 0.00 0.00 3.55
6575 6655 2.801077 ACTGGTGTTGGGGTATAAGC 57.199 50.000 0.00 0.00 0.00 3.09
6729 6813 0.931702 TACTGTTTGTTGTCCGCGTG 59.068 50.000 4.92 0.00 0.00 5.34
6784 6868 1.198867 TGAATTTTGCGTGGACCGATG 59.801 47.619 0.00 0.00 39.56 3.84
6788 6876 2.723586 TTTGCGTGGACCGATGCTCA 62.724 55.000 8.84 0.00 39.56 4.26
6799 6887 2.437281 ACCGATGCTCAATGATTCTCCT 59.563 45.455 0.00 0.00 0.00 3.69
6819 6907 5.918608 TCCTGAATAGTAAACCTGAGCATC 58.081 41.667 0.00 0.00 0.00 3.91
6964 7057 0.899717 TTTGGCTGGCTGGGATTCAC 60.900 55.000 2.00 0.00 0.00 3.18
7019 7112 7.370383 TCTAGGAAATTTGTGTCTGAAAATGC 58.630 34.615 0.00 0.00 0.00 3.56
7064 7161 1.616374 TCGGCAATAGCATATGGTCGA 59.384 47.619 11.40 10.85 44.61 4.20
7127 7224 3.192633 ACCAACTTTGTGAAACTGTGTCC 59.807 43.478 0.00 0.00 38.04 4.02
7184 7281 4.215399 CAGCCATTTTAAAGTCGACTGGAA 59.785 41.667 20.85 13.39 0.00 3.53
7242 7340 1.068250 GAGCTCCATGTAGGGCGAC 59.932 63.158 0.87 0.00 38.25 5.19
7246 7344 1.138266 GCTCCATGTAGGGCGACTTTA 59.862 52.381 0.00 0.00 38.24 1.85
7247 7345 2.419574 GCTCCATGTAGGGCGACTTTAA 60.420 50.000 0.00 0.00 38.24 1.52
7248 7346 3.869065 CTCCATGTAGGGCGACTTTAAA 58.131 45.455 0.00 0.00 38.24 1.52
7251 7349 5.258051 TCCATGTAGGGCGACTTTAAAAAT 58.742 37.500 0.00 0.00 38.24 1.82
7254 7352 8.212312 TCCATGTAGGGCGACTTTAAAAATATA 58.788 33.333 0.00 0.00 38.24 0.86
7255 7353 9.010029 CCATGTAGGGCGACTTTAAAAATATAT 57.990 33.333 0.00 0.00 0.00 0.86
7324 7423 7.987750 ACCAAACACATAATGTACACATGTA 57.012 32.000 19.37 3.07 42.31 2.29
7405 7507 3.686726 CCTTCTTAGCACATGAAGTCCAC 59.313 47.826 0.00 0.00 36.93 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.947841 TGGCTTGCGTCGTGTTGC 61.948 61.111 0.00 0.00 0.00 4.17
4 5 2.052237 GTGGCTTGCGTCGTGTTG 60.052 61.111 0.00 0.00 0.00 3.33
5 6 2.512745 TGTGGCTTGCGTCGTGTT 60.513 55.556 0.00 0.00 0.00 3.32
7 8 2.967076 ACTGTGGCTTGCGTCGTG 60.967 61.111 0.00 0.00 0.00 4.35
8 9 2.967076 CACTGTGGCTTGCGTCGT 60.967 61.111 0.00 0.00 0.00 4.34
20 21 0.740737 GCTGCAAGAACAACCACTGT 59.259 50.000 0.00 0.00 41.27 3.55
56 57 2.366916 GAGCTCACCATGCCACTACTAT 59.633 50.000 9.40 0.00 0.00 2.12
79 80 1.418908 CCCTTCCACACCTGGTCAGT 61.419 60.000 0.00 0.00 38.90 3.41
85 86 3.455910 TCTCATTATCCCTTCCACACCTG 59.544 47.826 0.00 0.00 0.00 4.00
88 89 5.359194 TCTTCTCATTATCCCTTCCACAC 57.641 43.478 0.00 0.00 0.00 3.82
176 178 1.874129 ACCAGGGAATATCACCACGA 58.126 50.000 0.00 0.00 0.00 4.35
202 204 2.837291 ACAAGCTTTTGGCCGCCA 60.837 55.556 8.43 8.43 43.05 5.69
204 206 2.356194 CCACAAGCTTTTGGCCGC 60.356 61.111 18.33 0.00 43.05 6.53
209 211 2.026014 ACGCGCCACAAGCTTTTG 59.974 55.556 5.73 5.59 40.39 2.44
241 243 2.822561 TCATCTATCACGATCAGGCTCC 59.177 50.000 0.00 0.00 0.00 4.70
248 250 4.322349 CCCTTTCCCTCATCTATCACGATC 60.322 50.000 0.00 0.00 0.00 3.69
304 306 1.802880 CGTATCACAGTAGCACCTGGC 60.803 57.143 7.45 0.00 45.30 4.85
349 351 1.066303 ACTTCCAGATGTCGCTCGATC 59.934 52.381 0.00 0.00 0.00 3.69
355 357 1.873591 ACAACAACTTCCAGATGTCGC 59.126 47.619 0.00 0.00 29.45 5.19
392 394 8.934507 AACATTTTAGGTGTTCGAAAATTGAA 57.065 26.923 0.00 0.00 38.17 2.69
446 448 4.590647 TCGGATTCTTAGATCAGATGGCTT 59.409 41.667 0.00 0.00 0.00 4.35
454 456 1.971357 GGCCCTCGGATTCTTAGATCA 59.029 52.381 0.00 0.00 0.00 2.92
455 457 1.971357 TGGCCCTCGGATTCTTAGATC 59.029 52.381 0.00 0.00 0.00 2.75
460 462 0.471617 CTCATGGCCCTCGGATTCTT 59.528 55.000 0.00 0.00 0.00 2.52
470 472 0.249911 GTGATACGGACTCATGGCCC 60.250 60.000 0.00 0.00 0.00 5.80
498 501 4.468689 GGTGCTACCGAGGGCCAC 62.469 72.222 6.18 0.00 0.00 5.01
530 533 2.178912 TCCACGAACCACCTTCATTC 57.821 50.000 0.00 0.00 0.00 2.67
542 545 1.484227 CGCGCCGAATTATCCACGAA 61.484 55.000 0.00 0.00 0.00 3.85
545 548 1.275657 CACGCGCCGAATTATCCAC 59.724 57.895 5.73 0.00 0.00 4.02
551 554 3.550992 CGTAGCACGCGCCGAATT 61.551 61.111 5.73 0.00 39.83 2.17
596 599 1.663702 CCACAAGTGTCGTCCGTCC 60.664 63.158 0.00 0.00 0.00 4.79
791 794 2.041405 GGTGGGAGAGAGAGGGGG 60.041 72.222 0.00 0.00 0.00 5.40
793 796 1.488393 GAAATGGTGGGAGAGAGAGGG 59.512 57.143 0.00 0.00 0.00 4.30
914 934 4.083862 GGGACCCACGTGAGGCTC 62.084 72.222 19.30 0.04 0.00 4.70
1062 1083 3.445987 TCCTCTTCTTCTTCCTTCTCCC 58.554 50.000 0.00 0.00 0.00 4.30
1156 1177 1.985116 AGAACAGGGCGGAGAGGAC 60.985 63.158 0.00 0.00 0.00 3.85
1343 1365 4.096682 AGTCTAGTCGCTGATTTAGTCACC 59.903 45.833 0.00 0.00 32.22 4.02
1380 1402 3.853671 CGCAAAACTATGCTTGAATCACC 59.146 43.478 0.00 0.00 44.21 4.02
1393 1415 1.618837 ACTCTCAGAGGCGCAAAACTA 59.381 47.619 10.83 0.00 33.35 2.24
1396 1418 2.831685 TTACTCTCAGAGGCGCAAAA 57.168 45.000 10.83 0.00 33.35 2.44
1470 1492 9.023967 GCAGAAGCTAATAAAAACATGTATTGG 57.976 33.333 0.00 0.00 37.91 3.16
1551 1581 5.820423 CCGACATTTCCTATCATGTTTACCA 59.180 40.000 0.00 0.00 33.62 3.25
1614 1644 2.293318 AACTCAGCGGCCATCCAGA 61.293 57.895 2.24 0.00 0.00 3.86
1697 1728 2.668632 CCCTAGAAGCGCCACCAA 59.331 61.111 2.29 0.00 0.00 3.67
1750 1782 3.071602 ACACATTGAGCTCCACAGTAACT 59.928 43.478 12.15 0.00 0.00 2.24
1756 1788 2.221169 GTTCACACATTGAGCTCCACA 58.779 47.619 12.15 0.00 34.94 4.17
1884 1916 3.625764 GCGGCATGTACTAAGAAAATGGA 59.374 43.478 0.00 0.00 0.00 3.41
1941 1975 2.354503 CCGCCAGCTCAAGCATATATCT 60.355 50.000 4.59 0.00 45.16 1.98
2155 2192 3.974871 TGAAAGGTTGCCGTTTCTTAC 57.025 42.857 8.80 0.00 42.90 2.34
2170 2207 0.107017 ATCTCACCGGCCCATGAAAG 60.107 55.000 0.00 0.00 0.00 2.62
2404 2444 4.062991 ACCCGTCATTAAACTGTTGTCTC 58.937 43.478 0.00 0.00 0.00 3.36
2647 2688 5.761234 GCTACCACCATTCCGTATATGAAAA 59.239 40.000 0.00 0.00 0.00 2.29
2648 2689 5.071250 AGCTACCACCATTCCGTATATGAAA 59.929 40.000 0.00 0.00 0.00 2.69
2843 2895 7.096551 AGGAACCCAATTATTTCAATGTTTCG 58.903 34.615 0.00 0.00 0.00 3.46
2866 2918 6.998074 TGATAACACCCTTTCTTGCATATAGG 59.002 38.462 0.00 0.00 0.00 2.57
2903 2955 7.544217 AGGTGTTCGTTTCATTTATAAATTGGC 59.456 33.333 8.01 0.00 0.00 4.52
3020 3073 5.255397 TGTAGAAGGACCATGTTCCATTT 57.745 39.130 12.37 0.00 38.25 2.32
3256 3311 3.333414 CACAACTGTGGCACTCCG 58.667 61.111 19.83 9.66 42.10 4.63
3471 3526 5.647658 TCAACAGAAAAGATCACAACACACT 59.352 36.000 0.00 0.00 0.00 3.55
3540 3595 5.631096 GCAAAAAGAGGAGTACTTCAATTGC 59.369 40.000 3.42 8.45 35.95 3.56
3587 3642 3.558418 TCTGAAACCGTCTTTTGTAGCAC 59.442 43.478 0.00 0.00 0.00 4.40
4268 4330 3.658757 TTGGTTCTACAGCAATTTGGC 57.341 42.857 0.00 0.00 37.98 4.52
4505 4567 6.151312 ACGGCCATACATGTATACAAAAACAA 59.849 34.615 17.86 0.00 0.00 2.83
4621 4684 1.020437 CGGACGGAGGGAGTAAGTAC 58.980 60.000 0.00 0.00 0.00 2.73
4626 4689 2.898920 ATTCGCGGACGGAGGGAGTA 62.899 60.000 6.13 0.00 40.63 2.59
4627 4690 2.898920 TATTCGCGGACGGAGGGAGT 62.899 60.000 6.13 0.00 40.63 3.85
4628 4691 1.731433 TTATTCGCGGACGGAGGGAG 61.731 60.000 6.13 0.00 40.63 4.30
4629 4692 1.731433 CTTATTCGCGGACGGAGGGA 61.731 60.000 6.13 0.00 40.63 4.20
4630 4693 1.299926 CTTATTCGCGGACGGAGGG 60.300 63.158 6.13 0.00 40.63 4.30
4631 4694 0.870307 CACTTATTCGCGGACGGAGG 60.870 60.000 6.13 0.00 40.63 4.30
4632 4695 0.179145 ACACTTATTCGCGGACGGAG 60.179 55.000 6.13 0.00 40.63 4.63
4633 4696 1.093972 TACACTTATTCGCGGACGGA 58.906 50.000 6.13 0.00 40.63 4.69
4634 4697 1.194495 GTACACTTATTCGCGGACGG 58.806 55.000 6.13 0.00 40.63 4.79
4635 4698 1.898938 TGTACACTTATTCGCGGACG 58.101 50.000 6.13 0.00 42.01 4.79
4636 4699 3.703420 AGATGTACACTTATTCGCGGAC 58.297 45.455 6.13 0.00 0.00 4.79
4637 4700 4.556104 GCTAGATGTACACTTATTCGCGGA 60.556 45.833 6.13 0.00 0.00 5.54
4638 4701 3.669122 GCTAGATGTACACTTATTCGCGG 59.331 47.826 6.13 0.00 0.00 6.46
4639 4702 4.537965 AGCTAGATGTACACTTATTCGCG 58.462 43.478 0.00 0.00 0.00 5.87
4640 4703 6.830114 AAAGCTAGATGTACACTTATTCGC 57.170 37.500 0.00 0.00 0.00 4.70
4641 4704 8.186178 ACAAAAGCTAGATGTACACTTATTCG 57.814 34.615 0.00 0.00 0.00 3.34
4642 4705 9.974750 GAACAAAAGCTAGATGTACACTTATTC 57.025 33.333 0.00 0.00 0.00 1.75
4643 4706 9.726438 AGAACAAAAGCTAGATGTACACTTATT 57.274 29.630 0.00 0.00 0.00 1.40
4646 4709 9.209175 CTTAGAACAAAAGCTAGATGTACACTT 57.791 33.333 0.00 0.00 0.00 3.16
4647 4710 8.368668 ACTTAGAACAAAAGCTAGATGTACACT 58.631 33.333 0.00 0.13 0.00 3.55
4648 4711 8.535690 ACTTAGAACAAAAGCTAGATGTACAC 57.464 34.615 0.00 0.00 0.00 2.90
4649 4712 8.364894 TGACTTAGAACAAAAGCTAGATGTACA 58.635 33.333 0.00 0.00 0.00 2.90
4650 4713 8.758633 TGACTTAGAACAAAAGCTAGATGTAC 57.241 34.615 0.00 0.00 0.00 2.90
4651 4714 9.772973 TTTGACTTAGAACAAAAGCTAGATGTA 57.227 29.630 0.00 0.00 33.90 2.29
4652 4715 8.677148 TTTGACTTAGAACAAAAGCTAGATGT 57.323 30.769 0.00 0.00 33.90 3.06
4653 4716 8.778358 ACTTTGACTTAGAACAAAAGCTAGATG 58.222 33.333 0.00 0.00 35.95 2.90
4654 4717 8.910351 ACTTTGACTTAGAACAAAAGCTAGAT 57.090 30.769 0.00 0.00 35.95 1.98
4655 4718 8.732746 AACTTTGACTTAGAACAAAAGCTAGA 57.267 30.769 0.00 0.00 35.95 2.43
4656 4719 9.788960 AAAACTTTGACTTAGAACAAAAGCTAG 57.211 29.630 0.00 0.00 35.95 3.42
4761 4824 9.331282 GCACCAAATTAGTATCACTAGATTCTT 57.669 33.333 0.00 0.00 34.29 2.52
4762 4825 7.934120 GGCACCAAATTAGTATCACTAGATTCT 59.066 37.037 0.00 0.00 36.14 2.40
4763 4826 7.715249 TGGCACCAAATTAGTATCACTAGATTC 59.285 37.037 0.00 0.00 35.67 2.52
4764 4827 7.573710 TGGCACCAAATTAGTATCACTAGATT 58.426 34.615 0.00 0.00 35.67 2.40
4765 4828 7.136822 TGGCACCAAATTAGTATCACTAGAT 57.863 36.000 0.00 0.00 38.29 1.98
4766 4829 6.553953 TGGCACCAAATTAGTATCACTAGA 57.446 37.500 0.00 0.00 31.47 2.43
4767 4830 8.902540 TTATGGCACCAAATTAGTATCACTAG 57.097 34.615 0.00 0.00 31.47 2.57
4768 4831 9.860650 ATTTATGGCACCAAATTAGTATCACTA 57.139 29.630 0.00 0.00 0.00 2.74
4769 4832 8.632679 CATTTATGGCACCAAATTAGTATCACT 58.367 33.333 6.24 0.00 0.00 3.41
4770 4833 7.382218 GCATTTATGGCACCAAATTAGTATCAC 59.618 37.037 6.24 0.00 0.00 3.06
4771 4834 7.287466 AGCATTTATGGCACCAAATTAGTATCA 59.713 33.333 6.24 0.00 0.00 2.15
4772 4835 7.661040 AGCATTTATGGCACCAAATTAGTATC 58.339 34.615 6.24 0.00 0.00 2.24
4773 4836 7.601705 AGCATTTATGGCACCAAATTAGTAT 57.398 32.000 6.24 0.00 0.00 2.12
4774 4837 7.416964 AAGCATTTATGGCACCAAATTAGTA 57.583 32.000 6.24 0.00 0.00 1.82
4775 4838 5.937975 AGCATTTATGGCACCAAATTAGT 57.062 34.783 6.24 0.00 0.00 2.24
4776 4839 7.614124 AAAAGCATTTATGGCACCAAATTAG 57.386 32.000 6.24 0.00 37.28 1.73
4777 4840 8.317679 AGTAAAAGCATTTATGGCACCAAATTA 58.682 29.630 6.24 0.00 37.28 1.40
4778 4841 7.167535 AGTAAAAGCATTTATGGCACCAAATT 58.832 30.769 6.24 0.00 37.28 1.82
4779 4842 6.710278 AGTAAAAGCATTTATGGCACCAAAT 58.290 32.000 0.00 0.00 37.28 2.32
4780 4843 6.107901 AGTAAAAGCATTTATGGCACCAAA 57.892 33.333 0.00 0.00 37.28 3.28
4781 4844 5.736951 AGTAAAAGCATTTATGGCACCAA 57.263 34.783 0.00 0.00 37.28 3.67
4782 4845 5.736951 AAGTAAAAGCATTTATGGCACCA 57.263 34.783 0.00 0.00 37.28 4.17
4783 4846 7.360861 GGAAAAAGTAAAAGCATTTATGGCACC 60.361 37.037 0.00 0.00 37.28 5.01
4784 4847 7.387673 AGGAAAAAGTAAAAGCATTTATGGCAC 59.612 33.333 0.00 0.00 37.28 5.01
4785 4848 7.449247 AGGAAAAAGTAAAAGCATTTATGGCA 58.551 30.769 0.00 0.00 37.28 4.92
4786 4849 7.905604 AGGAAAAAGTAAAAGCATTTATGGC 57.094 32.000 0.00 0.00 37.28 4.40
4791 4854 9.764363 CCTTTCTAGGAAAAAGTAAAAGCATTT 57.236 29.630 0.00 0.00 45.05 2.32
4792 4855 8.924303 ACCTTTCTAGGAAAAAGTAAAAGCATT 58.076 29.630 0.00 0.00 45.05 3.56
4793 4856 8.360390 CACCTTTCTAGGAAAAAGTAAAAGCAT 58.640 33.333 0.00 0.00 45.05 3.79
4794 4857 7.201875 CCACCTTTCTAGGAAAAAGTAAAAGCA 60.202 37.037 0.00 0.00 45.05 3.91
4795 4858 7.145985 CCACCTTTCTAGGAAAAAGTAAAAGC 58.854 38.462 0.00 0.00 45.05 3.51
4796 4859 8.234136 ACCACCTTTCTAGGAAAAAGTAAAAG 57.766 34.615 0.00 0.00 45.05 2.27
4797 4860 7.835181 TGACCACCTTTCTAGGAAAAAGTAAAA 59.165 33.333 0.00 0.00 45.05 1.52
4798 4861 7.348033 TGACCACCTTTCTAGGAAAAAGTAAA 58.652 34.615 0.00 0.00 45.05 2.01
4799 4862 6.902408 TGACCACCTTTCTAGGAAAAAGTAA 58.098 36.000 0.00 0.00 45.05 2.24
4800 4863 6.503560 TGACCACCTTTCTAGGAAAAAGTA 57.496 37.500 0.00 0.00 45.05 2.24
4801 4864 5.382664 TGACCACCTTTCTAGGAAAAAGT 57.617 39.130 0.00 0.00 45.05 2.66
4802 4865 6.321435 ACTTTGACCACCTTTCTAGGAAAAAG 59.679 38.462 0.00 0.00 45.05 2.27
4803 4866 6.192044 ACTTTGACCACCTTTCTAGGAAAAA 58.808 36.000 0.00 0.00 45.05 1.94
4804 4867 5.762279 ACTTTGACCACCTTTCTAGGAAAA 58.238 37.500 0.00 0.00 45.05 2.29
4805 4868 5.382664 ACTTTGACCACCTTTCTAGGAAA 57.617 39.130 0.00 0.00 45.05 3.13
4806 4869 5.382664 AACTTTGACCACCTTTCTAGGAA 57.617 39.130 0.00 0.00 45.05 3.36
4807 4870 5.382664 AAACTTTGACCACCTTTCTAGGA 57.617 39.130 0.00 0.00 45.05 2.94
4809 4872 9.297586 GTTTTAAAACTTTGACCACCTTTCTAG 57.702 33.333 21.27 0.00 36.03 2.43
4810 4873 9.027202 AGTTTTAAAACTTTGACCACCTTTCTA 57.973 29.630 24.66 0.00 46.52 2.10
4811 4874 7.903145 AGTTTTAAAACTTTGACCACCTTTCT 58.097 30.769 24.66 0.83 46.52 2.52
4831 4894 9.788960 CTAGCTTTTGTCTTAAGTCAAAGTTTT 57.211 29.630 21.47 13.93 35.29 2.43
4832 4895 9.174166 TCTAGCTTTTGTCTTAAGTCAAAGTTT 57.826 29.630 21.47 15.16 35.29 2.66
4833 4896 8.732746 TCTAGCTTTTGTCTTAAGTCAAAGTT 57.267 30.769 21.47 17.02 35.29 2.66
4834 4897 8.778358 CATCTAGCTTTTGTCTTAAGTCAAAGT 58.222 33.333 21.47 15.13 35.29 2.66
4835 4898 8.778358 ACATCTAGCTTTTGTCTTAAGTCAAAG 58.222 33.333 21.47 17.68 35.29 2.77
4836 4899 8.677148 ACATCTAGCTTTTGTCTTAAGTCAAA 57.323 30.769 19.60 19.60 32.81 2.69
4837 4900 9.204570 GTACATCTAGCTTTTGTCTTAAGTCAA 57.795 33.333 10.54 10.54 0.00 3.18
4838 4901 8.364894 TGTACATCTAGCTTTTGTCTTAAGTCA 58.635 33.333 1.63 0.00 0.00 3.41
4839 4902 8.648968 GTGTACATCTAGCTTTTGTCTTAAGTC 58.351 37.037 0.00 0.00 0.00 3.01
4840 4903 8.368668 AGTGTACATCTAGCTTTTGTCTTAAGT 58.631 33.333 0.00 0.00 0.00 2.24
4841 4904 8.764524 AGTGTACATCTAGCTTTTGTCTTAAG 57.235 34.615 0.00 0.00 0.00 1.85
4844 4907 9.726438 AATAAGTGTACATCTAGCTTTTGTCTT 57.274 29.630 0.00 0.00 0.00 3.01
4845 4908 9.372369 GAATAAGTGTACATCTAGCTTTTGTCT 57.628 33.333 0.00 0.00 0.00 3.41
4846 4909 8.321716 CGAATAAGTGTACATCTAGCTTTTGTC 58.678 37.037 0.00 0.00 0.00 3.18
4847 4910 7.817962 ACGAATAAGTGTACATCTAGCTTTTGT 59.182 33.333 0.00 0.00 0.00 2.83
4848 4911 8.110612 CACGAATAAGTGTACATCTAGCTTTTG 58.889 37.037 0.00 0.00 37.35 2.44
4849 4912 7.277981 CCACGAATAAGTGTACATCTAGCTTTT 59.722 37.037 0.00 0.00 40.33 2.27
4850 4913 6.757010 CCACGAATAAGTGTACATCTAGCTTT 59.243 38.462 0.00 0.00 40.33 3.51
4851 4914 6.096423 TCCACGAATAAGTGTACATCTAGCTT 59.904 38.462 0.00 0.00 40.33 3.74
4852 4915 5.593095 TCCACGAATAAGTGTACATCTAGCT 59.407 40.000 0.00 0.00 40.33 3.32
4853 4916 5.686397 GTCCACGAATAAGTGTACATCTAGC 59.314 44.000 0.00 0.00 40.33 3.42
4854 4917 5.907945 CGTCCACGAATAAGTGTACATCTAG 59.092 44.000 0.00 0.00 43.02 2.43
4855 4918 5.220912 CCGTCCACGAATAAGTGTACATCTA 60.221 44.000 0.00 0.00 43.02 1.98
4856 4919 4.439700 CCGTCCACGAATAAGTGTACATCT 60.440 45.833 0.00 0.00 43.02 2.90
4857 4920 3.795101 CCGTCCACGAATAAGTGTACATC 59.205 47.826 0.00 0.00 43.02 3.06
4858 4921 3.444742 TCCGTCCACGAATAAGTGTACAT 59.555 43.478 0.00 0.00 43.02 2.29
4859 4922 2.819019 TCCGTCCACGAATAAGTGTACA 59.181 45.455 0.00 0.00 43.02 2.90
4860 4923 3.432782 CTCCGTCCACGAATAAGTGTAC 58.567 50.000 0.00 0.00 43.02 2.90
4861 4924 2.424601 CCTCCGTCCACGAATAAGTGTA 59.575 50.000 0.00 0.00 43.02 2.90
4862 4925 1.203994 CCTCCGTCCACGAATAAGTGT 59.796 52.381 0.00 0.00 43.02 3.55
4863 4926 1.470979 CCCTCCGTCCACGAATAAGTG 60.471 57.143 0.00 0.00 43.02 3.16
4864 4927 0.822164 CCCTCCGTCCACGAATAAGT 59.178 55.000 0.00 0.00 43.02 2.24
4865 4928 1.067212 CTCCCTCCGTCCACGAATAAG 59.933 57.143 0.00 0.00 43.02 1.73
4866 4929 1.108776 CTCCCTCCGTCCACGAATAA 58.891 55.000 0.00 0.00 43.02 1.40
4867 4930 0.033796 ACTCCCTCCGTCCACGAATA 60.034 55.000 0.00 0.00 43.02 1.75
4868 4931 0.033796 TACTCCCTCCGTCCACGAAT 60.034 55.000 0.00 0.00 43.02 3.34
4869 4932 0.033796 ATACTCCCTCCGTCCACGAA 60.034 55.000 0.00 0.00 43.02 3.85
4870 4933 0.839277 TATACTCCCTCCGTCCACGA 59.161 55.000 0.00 0.00 43.02 4.35
4871 4934 1.540267 CATATACTCCCTCCGTCCACG 59.460 57.143 0.00 0.00 39.44 4.94
4872 4935 1.272769 GCATATACTCCCTCCGTCCAC 59.727 57.143 0.00 0.00 0.00 4.02
4873 4936 1.133294 TGCATATACTCCCTCCGTCCA 60.133 52.381 0.00 0.00 0.00 4.02
4874 4937 1.629043 TGCATATACTCCCTCCGTCC 58.371 55.000 0.00 0.00 0.00 4.79
4875 4938 3.963428 ATTGCATATACTCCCTCCGTC 57.037 47.619 0.00 0.00 0.00 4.79
4876 4939 7.490657 TTTATATTGCATATACTCCCTCCGT 57.509 36.000 0.00 0.00 0.00 4.69
4877 4940 8.204160 TCATTTATATTGCATATACTCCCTCCG 58.796 37.037 0.00 0.00 0.00 4.63
5248 5311 6.253746 CAAGTTTCCTGAAGATGAATTAGCG 58.746 40.000 0.00 0.00 0.00 4.26
5404 5473 1.914798 TGATGATGATGGTGGTGGTGA 59.085 47.619 0.00 0.00 0.00 4.02
5865 5934 6.822676 AGCTGTGGAAATGAGAAAAGATAGAG 59.177 38.462 0.00 0.00 0.00 2.43
5869 5938 4.082354 GCAGCTGTGGAAATGAGAAAAGAT 60.082 41.667 16.64 0.00 0.00 2.40
5950 6019 9.632638 ATGGAATAAAACTGCTATTCTGTACAT 57.367 29.630 0.00 0.00 36.44 2.29
5951 6020 8.892723 CATGGAATAAAACTGCTATTCTGTACA 58.107 33.333 0.00 0.00 36.44 2.90
5952 6021 7.857885 GCATGGAATAAAACTGCTATTCTGTAC 59.142 37.037 0.00 0.00 36.44 2.90
5953 6022 7.555914 TGCATGGAATAAAACTGCTATTCTGTA 59.444 33.333 0.00 0.00 36.44 2.74
6000 6069 7.662717 TCACTCAAATTGCAGTGACAAGCAC 62.663 44.000 17.78 0.00 43.31 4.40
6052 6121 4.759693 TGGACTCGTTTAGCATCACAAATT 59.240 37.500 0.00 0.00 0.00 1.82
6053 6122 4.323417 TGGACTCGTTTAGCATCACAAAT 58.677 39.130 0.00 0.00 0.00 2.32
6054 6123 3.734463 TGGACTCGTTTAGCATCACAAA 58.266 40.909 0.00 0.00 0.00 2.83
6055 6124 3.394674 TGGACTCGTTTAGCATCACAA 57.605 42.857 0.00 0.00 0.00 3.33
6066 6135 3.006967 AGTGCAGTTTAGATGGACTCGTT 59.993 43.478 0.00 0.00 44.91 3.85
6077 6146 2.604914 CCGACATAGCAGTGCAGTTTAG 59.395 50.000 19.20 4.31 0.00 1.85
6120 6192 5.933617 TCCTTGAGACATGCATTAAGCTAT 58.066 37.500 0.00 0.00 45.94 2.97
6157 6230 7.340699 CGAACAAAGATGATACTAAGCATGTC 58.659 38.462 0.00 0.00 30.10 3.06
6227 6300 5.009310 AGTCTACACGTGACAACACAGATAA 59.991 40.000 25.01 0.00 46.20 1.75
6242 6315 8.740906 AGGATGTATAATTGGATAGTCTACACG 58.259 37.037 0.00 0.00 0.00 4.49
6312 6385 3.219281 ACAAAACAGCGGATGGTAAGTT 58.781 40.909 0.00 0.00 0.00 2.66
6385 6458 1.403249 CCAGCCAGCAAACACAATAGC 60.403 52.381 0.00 0.00 0.00 2.97
6456 6529 3.146104 TGCTAGCTCTTGAAGGCTTTT 57.854 42.857 17.23 0.00 39.65 2.27
6784 6868 8.555361 GTTTACTATTCAGGAGAATCATTGAGC 58.445 37.037 0.00 0.00 43.26 4.26
6788 6876 8.772250 TCAGGTTTACTATTCAGGAGAATCATT 58.228 33.333 0.00 0.00 43.26 2.57
6799 6887 6.544928 TCTGATGCTCAGGTTTACTATTCA 57.455 37.500 11.63 0.00 44.39 2.57
6819 6907 1.730501 ACACATCATCACGCCTTCTG 58.269 50.000 0.00 0.00 0.00 3.02
6826 6914 4.847757 GTGTCATCAAAACACATCATCACG 59.152 41.667 1.72 0.00 45.05 4.35
6901 6993 0.482446 AACTGCCATCAGGGGTTTGA 59.518 50.000 0.00 0.00 44.54 2.69
6964 7057 4.687483 GTGAAATTTGGAAACATGCTCAGG 59.313 41.667 0.00 0.00 42.32 3.86
7043 7140 1.726791 CGACCATATGCTATTGCCGAC 59.273 52.381 0.00 0.00 38.71 4.79
7044 7141 1.616374 TCGACCATATGCTATTGCCGA 59.384 47.619 0.00 0.00 38.71 5.54
7064 7161 0.599558 ACAATCACGCTGCTTTGCAT 59.400 45.000 0.00 0.00 38.13 3.96
7127 7224 0.520404 GTCACAACTGCAGCTCCATG 59.480 55.000 15.27 7.99 0.00 3.66
7184 7281 2.568956 TCAGGCTGCTGAGTCATTTACT 59.431 45.455 10.34 0.00 42.80 2.24
7362 7461 5.178061 AGGCACAAAGTTTTTCCTTTTCTG 58.822 37.500 0.00 0.00 32.42 3.02
7363 7462 5.420725 AGGCACAAAGTTTTTCCTTTTCT 57.579 34.783 0.00 0.00 32.42 2.52
7364 7463 5.874810 AGAAGGCACAAAGTTTTTCCTTTTC 59.125 36.000 11.80 3.97 34.40 2.29
7369 7468 4.745125 GCTAAGAAGGCACAAAGTTTTTCC 59.255 41.667 0.00 0.00 0.00 3.13


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

AutoCloner maintained by Alex Coulton.