Multiple sequence alignment - TraesCS2D01G369700

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2D01G369700 chr2D 100.000 6854 0 0 1 6854 473720784 473713931 0.000000e+00 12658.0
1 TraesCS2D01G369700 chr2B 94.256 6058 184 55 297 6298 554459593 554453644 0.000000e+00 9108.0
2 TraesCS2D01G369700 chr2B 93.133 233 12 4 1 231 554459846 554459616 8.510000e-89 339.0
3 TraesCS2D01G369700 chr2B 81.234 389 51 13 6366 6744 554453487 554453111 1.870000e-75 294.0
4 TraesCS2D01G369700 chr2A 94.788 5871 181 51 616 6432 615743589 615737790 0.000000e+00 9031.0
5 TraesCS2D01G369700 chr2A 96.825 126 4 0 6579 6704 615737728 615737603 1.940000e-50 211.0
6 TraesCS2D01G369700 chr2A 97.619 42 1 0 6536 6577 615737794 615737753 9.540000e-09 73.1
7 TraesCS2D01G369700 chr6D 78.036 387 62 20 3945 4316 307881119 307881497 8.950000e-54 222.0
8 TraesCS2D01G369700 chr6A 77.922 385 66 18 3945 4316 445048202 445048580 8.950000e-54 222.0
9 TraesCS2D01G369700 chr6A 94.444 72 2 2 6757 6827 123958812 123958882 7.270000e-20 110.0
10 TraesCS2D01G369700 chr6B 77.320 388 63 24 3945 4316 475271358 475271736 9.010000e-49 206.0
11 TraesCS2D01G369700 chr5B 94.231 104 6 0 6744 6847 586872349 586872246 7.120000e-35 159.0
12 TraesCS2D01G369700 chr7B 94.231 104 5 1 6744 6847 705330962 705330860 2.560000e-34 158.0
13 TraesCS2D01G369700 chr5D 91.358 81 4 3 6755 6834 437126819 437126897 2.610000e-19 108.0
14 TraesCS2D01G369700 chr5A 93.182 44 2 1 6751 6794 536852365 536852323 5.740000e-06 63.9


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 TraesCS2D01G369700 chr2D 473713931 473720784 6853 True 12658.000000 12658 100.000000 1 6854 1 chr2D.!!$R1 6853
1 TraesCS2D01G369700 chr2B 554453111 554459846 6735 True 3247.000000 9108 89.541000 1 6744 3 chr2B.!!$R1 6743
2 TraesCS2D01G369700 chr2A 615737603 615743589 5986 True 3105.033333 9031 96.410667 616 6704 3 chr2A.!!$R1 6088

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
220 221 0.035343 CGTCTCCCTTTTCTTCCCCC 60.035 60.000 0.00 0.00 0.00 5.40 F
611 617 0.257905 GCCGGATTTTAACCTCCCCT 59.742 55.000 5.05 0.00 0.00 4.79 F
972 999 0.391263 GATTCCTCCTCGCGGTGTTT 60.391 55.000 6.13 0.00 0.00 2.83 F
1621 1657 0.667184 CCGCCAGAACATTGCAAACC 60.667 55.000 1.71 0.00 0.00 3.27 F
2190 2226 1.999735 GTCTCGCAATGTCGGAAATCA 59.000 47.619 0.00 0.00 0.00 2.57 F
2388 2424 3.689161 TGAGCACTCAATTTAATCCCACG 59.311 43.478 0.00 0.00 36.53 4.94 F
3361 3402 0.972471 CCCCTTTTAGGCCAAGCTGG 60.972 60.000 5.01 0.72 41.55 4.85 F
5225 5297 1.485066 TCCTTTTAGGACGGGATCTGC 59.515 52.381 0.00 0.00 40.06 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1446 1482 1.532238 GATTAGGCACCTGGGGTCC 59.468 63.158 0.0 0.00 31.02 4.46 R
2605 2641 1.537202 GCCTGTGTTTCTAAGCCACTG 59.463 52.381 0.0 0.00 0.00 3.66 R
2714 2754 2.093973 AGACAGATAGCGGGTTCAGTTG 60.094 50.000 0.0 0.00 0.00 3.16 R
3119 3159 4.214986 TCTTTCCGAACATCCAGCATAA 57.785 40.909 0.0 0.00 0.00 1.90 R
3361 3402 4.457466 TGACCTTCACTTAAACCCAGAAC 58.543 43.478 0.0 0.00 0.00 3.01 R
4208 4252 1.328680 CAGATGCGGACCTTTTCATCG 59.671 52.381 0.0 0.00 40.01 3.84 R
5343 5416 0.687354 ACACATGGGAGTTCTCGCTT 59.313 50.000 0.0 8.46 0.00 4.68 R
6759 7009 0.031010 AAGGCGGAGGAATAGAGGGT 60.031 55.000 0.0 0.00 0.00 4.34 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
17 18 4.530857 GGATGGGCTCGTGACGGG 62.531 72.222 4.70 1.40 0.00 5.28
64 65 2.561956 ATAGGATGCCCGACCGACG 61.562 63.158 0.00 0.00 42.18 5.12
97 98 1.479573 CGGGAGAGAGGAGCCTTGATA 60.480 57.143 0.00 0.00 0.00 2.15
98 99 2.247358 GGGAGAGAGGAGCCTTGATAG 58.753 57.143 0.00 0.00 0.00 2.08
176 177 2.475466 CGGCGCATGCATTCCTTCT 61.475 57.895 19.57 0.00 45.35 2.85
204 205 3.131478 CCCGGGTTTGGCATCGTC 61.131 66.667 14.18 0.00 0.00 4.20
211 212 1.534729 GTTTGGCATCGTCTCCCTTT 58.465 50.000 0.00 0.00 0.00 3.11
213 214 1.821216 TTGGCATCGTCTCCCTTTTC 58.179 50.000 0.00 0.00 0.00 2.29
216 217 2.010497 GGCATCGTCTCCCTTTTCTTC 58.990 52.381 0.00 0.00 0.00 2.87
218 219 2.633488 CATCGTCTCCCTTTTCTTCCC 58.367 52.381 0.00 0.00 0.00 3.97
220 221 0.035343 CGTCTCCCTTTTCTTCCCCC 60.035 60.000 0.00 0.00 0.00 5.40
247 248 8.556517 CGATTCATCGTGTAGTAAACATAGAA 57.443 34.615 0.80 0.00 44.74 2.10
248 249 8.469902 CGATTCATCGTGTAGTAAACATAGAAC 58.530 37.037 0.80 0.00 44.74 3.01
249 250 9.297586 GATTCATCGTGTAGTAAACATAGAACA 57.702 33.333 0.00 0.00 41.10 3.18
250 251 9.647797 ATTCATCGTGTAGTAAACATAGAACAA 57.352 29.630 0.00 0.00 41.10 2.83
251 252 9.478768 TTCATCGTGTAGTAAACATAGAACAAA 57.521 29.630 0.00 0.00 41.10 2.83
252 253 9.478768 TCATCGTGTAGTAAACATAGAACAAAA 57.521 29.630 0.00 0.00 41.10 2.44
253 254 9.741168 CATCGTGTAGTAAACATAGAACAAAAG 57.259 33.333 0.00 0.00 41.10 2.27
254 255 9.701098 ATCGTGTAGTAAACATAGAACAAAAGA 57.299 29.630 0.00 0.00 41.10 2.52
255 256 9.701098 TCGTGTAGTAAACATAGAACAAAAGAT 57.299 29.630 0.00 0.00 41.10 2.40
289 290 9.924650 ACTACCAGTAGTACAAGTTAGAAAATG 57.075 33.333 8.71 0.00 43.98 2.32
292 293 9.841295 ACCAGTAGTACAAGTTAGAAAATGAAA 57.159 29.630 2.52 0.00 0.00 2.69
321 322 2.202557 CACGATCGGTGTGCGCTA 60.203 61.111 20.98 0.00 41.89 4.26
331 332 0.387622 GTGTGCGCTAGTCAACGGTA 60.388 55.000 9.73 0.00 0.00 4.02
379 380 1.238439 CACCACTGCTGTAAACAGGG 58.762 55.000 11.86 6.87 43.94 4.45
388 389 2.774687 CTGTAAACAGGGGCGTAAACT 58.225 47.619 2.01 0.00 40.20 2.66
390 391 1.808343 GTAAACAGGGGCGTAAACTGG 59.192 52.381 0.00 0.00 36.57 4.00
398 399 2.048877 CGTAAACTGGACGGCCGT 60.049 61.111 34.89 34.89 36.66 5.68
421 422 1.002773 CCGGCCTCATCATCATCATCA 59.997 52.381 0.00 0.00 0.00 3.07
429 430 2.467566 TCATCATCATCATCGCCAGG 57.532 50.000 0.00 0.00 0.00 4.45
586 592 3.428664 GGGTCCCATCCCATGCCA 61.429 66.667 1.78 0.00 46.30 4.92
587 593 2.782417 GGGTCCCATCCCATGCCAT 61.782 63.158 1.78 0.00 46.30 4.40
588 594 1.532316 GGTCCCATCCCATGCCATG 60.532 63.158 0.00 0.00 0.00 3.66
606 612 1.751544 GGCGGCCGGATTTTAACCT 60.752 57.895 29.38 0.00 0.00 3.50
609 615 1.099295 CGGCCGGATTTTAACCTCCC 61.099 60.000 20.10 0.00 0.00 4.30
611 617 0.257905 GCCGGATTTTAACCTCCCCT 59.742 55.000 5.05 0.00 0.00 4.79
613 619 2.651455 CCGGATTTTAACCTCCCCTTC 58.349 52.381 0.00 0.00 0.00 3.46
756 773 2.631428 CATCGCCCCGCAATAACG 59.369 61.111 0.00 0.00 0.00 3.18
803 820 4.103103 CGAGGCAGACGCAGACGA 62.103 66.667 0.00 0.00 43.93 4.20
804 821 2.202544 GAGGCAGACGCAGACGAG 60.203 66.667 0.00 0.00 43.93 4.18
805 822 2.673341 AGGCAGACGCAGACGAGA 60.673 61.111 0.00 0.00 43.93 4.04
972 999 0.391263 GATTCCTCCTCGCGGTGTTT 60.391 55.000 6.13 0.00 0.00 2.83
1621 1657 0.667184 CCGCCAGAACATTGCAAACC 60.667 55.000 1.71 0.00 0.00 3.27
1777 1813 2.804368 AAGCAGCGACGAGAAGGACG 62.804 60.000 0.00 0.00 0.00 4.79
2190 2226 1.999735 GTCTCGCAATGTCGGAAATCA 59.000 47.619 0.00 0.00 0.00 2.57
2374 2410 4.058124 TGTTGACTACAATGTGAGCACTC 58.942 43.478 0.00 0.00 38.32 3.51
2388 2424 3.689161 TGAGCACTCAATTTAATCCCACG 59.311 43.478 0.00 0.00 36.53 4.94
2421 2457 8.691661 TTCTGCCTAATTTAGAAAACTCTGTT 57.308 30.769 4.96 0.00 0.00 3.16
2589 2625 6.524734 TGACTGTAAATGATGAACTGACAGT 58.475 36.000 1.07 1.07 46.41 3.55
2605 2641 6.421801 AACTGACAGTTAGCAAATCAAATTGC 59.578 34.615 19.28 3.92 42.30 3.56
2644 2680 4.338964 CAGGCCATATTGTATGCAAACTGA 59.661 41.667 5.01 0.00 38.21 3.41
2663 2699 5.389520 ACTGATATCCTGTAGCTCTAAGCA 58.610 41.667 0.00 0.00 45.56 3.91
2672 2712 5.065731 CCTGTAGCTCTAAGCAATTCTTTGG 59.934 44.000 0.00 0.00 45.56 3.28
2714 2754 8.474831 AGGAAGGTTGTAATAATGCATAAAACC 58.525 33.333 10.27 10.27 36.83 3.27
2759 2799 7.445402 TCTTAAAGAAAGGAATGTGTTCTCCAG 59.555 37.037 0.00 0.00 35.75 3.86
2876 2916 9.008965 ACATAAGCATTTCACACTGTAATGTTA 57.991 29.630 6.55 5.21 37.43 2.41
2929 2969 9.456797 GAAATTAACTAGATAACACGTGTTTCG 57.543 33.333 36.26 21.58 46.00 3.46
2976 3016 5.464030 TCCAAGAGTGTTAACTACTGGAC 57.536 43.478 13.23 0.39 40.15 4.02
3190 3230 7.136119 CGAAGTTAAGATTGTTGTGCCTAAAA 58.864 34.615 0.00 0.00 0.00 1.52
3361 3402 0.972471 CCCCTTTTAGGCCAAGCTGG 60.972 60.000 5.01 0.72 41.55 4.85
3366 3407 1.909700 TTTAGGCCAAGCTGGTTCTG 58.090 50.000 5.01 0.00 40.46 3.02
3455 3496 4.946160 TGATTAGGATGTCCCAGGTTTT 57.054 40.909 0.00 0.00 37.41 2.43
3456 3497 6.590656 ATGATTAGGATGTCCCAGGTTTTA 57.409 37.500 0.00 0.00 37.41 1.52
3457 3498 6.395780 TGATTAGGATGTCCCAGGTTTTAA 57.604 37.500 0.00 0.00 37.41 1.52
3458 3499 6.795590 TGATTAGGATGTCCCAGGTTTTAAA 58.204 36.000 0.00 0.00 37.41 1.52
3573 3614 4.442192 GGACGTCAGGAAATCTCTAGCATT 60.442 45.833 18.91 0.00 0.00 3.56
3844 3888 4.460382 ACAATTTGCAATAGTGACTCCAGG 59.540 41.667 0.00 0.00 0.00 4.45
3987 4031 3.251004 ACTTGCTTTCGTCTTCAATGGAC 59.749 43.478 0.00 0.00 0.00 4.02
3996 4040 5.361427 TCGTCTTCAATGGACAAAACAGTA 58.639 37.500 0.00 0.00 33.73 2.74
4329 4373 5.476614 GACAGGTTTGTATACTTTCGACCT 58.523 41.667 4.17 7.27 37.76 3.85
4477 4521 7.586664 CGCTCTGATGATTTATGACATTTTCAG 59.413 37.037 0.00 0.00 37.77 3.02
4644 4688 7.775053 TGGATTTCAGGTGCTTACTTTTAAT 57.225 32.000 0.00 0.00 0.00 1.40
4687 4736 4.352001 ACACCAGGCCATACAGATGATAAT 59.648 41.667 5.01 0.00 34.73 1.28
4734 4783 1.882623 CTTGAACAGTTCCTTCCAGGC 59.117 52.381 10.93 0.00 34.61 4.85
4889 4941 3.219281 TCTTCAAGGTTTGGCCAGTAAC 58.781 45.455 5.11 8.85 40.61 2.50
4920 4972 6.846283 CGAGACACTGTTGCTTTAAAGTTTAG 59.154 38.462 16.38 11.68 0.00 1.85
4921 4973 7.465513 CGAGACACTGTTGCTTTAAAGTTTAGT 60.466 37.037 16.38 12.22 0.00 2.24
4922 4974 8.051901 AGACACTGTTGCTTTAAAGTTTAGTT 57.948 30.769 16.38 7.40 0.00 2.24
4923 4975 7.968405 AGACACTGTTGCTTTAAAGTTTAGTTG 59.032 33.333 16.38 9.85 0.00 3.16
4924 4976 7.599171 ACACTGTTGCTTTAAAGTTTAGTTGT 58.401 30.769 16.38 10.40 0.00 3.32
4925 4977 8.732531 ACACTGTTGCTTTAAAGTTTAGTTGTA 58.267 29.630 16.38 0.00 0.00 2.41
4926 4978 9.221775 CACTGTTGCTTTAAAGTTTAGTTGTAG 57.778 33.333 16.38 6.06 0.00 2.74
4927 4979 8.953313 ACTGTTGCTTTAAAGTTTAGTTGTAGT 58.047 29.630 16.38 6.58 0.00 2.73
4928 4980 9.783256 CTGTTGCTTTAAAGTTTAGTTGTAGTT 57.217 29.630 16.38 0.00 0.00 2.24
4929 4981 9.777575 TGTTGCTTTAAAGTTTAGTTGTAGTTC 57.222 29.630 16.38 0.00 0.00 3.01
4930 4982 9.999009 GTTGCTTTAAAGTTTAGTTGTAGTTCT 57.001 29.630 16.38 0.00 0.00 3.01
4932 4984 9.997482 TGCTTTAAAGTTTAGTTGTAGTTCTTG 57.003 29.630 16.38 0.00 0.00 3.02
4933 4985 9.999009 GCTTTAAAGTTTAGTTGTAGTTCTTGT 57.001 29.630 16.38 0.00 0.00 3.16
4964 5030 6.602009 ACCTGTTTAACCTATTTGCCACTATC 59.398 38.462 0.00 0.00 0.00 2.08
5225 5297 1.485066 TCCTTTTAGGACGGGATCTGC 59.515 52.381 0.00 0.00 40.06 4.26
5252 5324 3.120338 CGTATGTTTTGTCGGTTGCTGAT 60.120 43.478 0.00 0.00 0.00 2.90
5316 5389 2.005451 CAAATCTCAGCTTGCTACGCT 58.995 47.619 0.00 0.00 38.49 5.07
5343 5416 1.067669 GGCAGATACGTGATCTCAGCA 59.932 52.381 0.00 0.00 43.52 4.41
5349 5422 0.457509 ACGTGATCTCAGCAAGCGAG 60.458 55.000 0.00 7.32 0.00 5.03
5383 5456 0.593008 CGTGTGGAGAAACGACGACA 60.593 55.000 0.00 0.00 42.32 4.35
5606 5688 3.129871 GAGATTCCTCTGATTTCCAGCG 58.870 50.000 0.00 0.00 42.62 5.18
5861 5946 2.226912 CCGTCAGAGTATAGTAGCAGCC 59.773 54.545 0.00 0.00 0.00 4.85
5862 5947 2.226912 CGTCAGAGTATAGTAGCAGCCC 59.773 54.545 0.00 0.00 0.00 5.19
5864 5949 3.254657 GTCAGAGTATAGTAGCAGCCCTG 59.745 52.174 0.00 0.00 0.00 4.45
5938 6032 2.415090 GCTGTTAGCGGTCTTCGAGTTA 60.415 50.000 0.00 0.00 42.43 2.24
6027 6125 1.145598 CGCCTGCATGAGAGTGGAT 59.854 57.895 0.00 0.00 0.00 3.41
6031 6129 0.108207 CTGCATGAGAGTGGATCCCC 59.892 60.000 9.90 0.00 0.00 4.81
6035 6133 1.693062 CATGAGAGTGGATCCCCAGAG 59.307 57.143 9.90 0.00 44.55 3.35
6083 6181 1.086696 CTCGCCACACCCATTTGTAG 58.913 55.000 0.00 0.00 0.00 2.74
6084 6182 0.398696 TCGCCACACCCATTTGTAGT 59.601 50.000 0.00 0.00 0.00 2.73
6085 6183 1.624312 TCGCCACACCCATTTGTAGTA 59.376 47.619 0.00 0.00 0.00 1.82
6086 6184 2.006888 CGCCACACCCATTTGTAGTAG 58.993 52.381 0.00 0.00 0.00 2.57
6087 6185 1.743394 GCCACACCCATTTGTAGTAGC 59.257 52.381 0.00 0.00 0.00 3.58
6088 6186 2.878117 GCCACACCCATTTGTAGTAGCA 60.878 50.000 0.00 0.00 0.00 3.49
6160 6258 1.135717 CCTTGTGTGTGTGTGTGTGTG 60.136 52.381 0.00 0.00 0.00 3.82
6162 6260 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
6164 6262 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
6167 6265 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
6168 6266 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
6169 6267 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
6170 6268 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
6171 6269 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
6172 6270 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
6173 6271 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
6174 6272 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
6175 6273 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
6184 6282 1.064952 GTGTGTGTGTGTTTACCCTGC 59.935 52.381 0.00 0.00 0.00 4.85
6213 6311 9.841880 GACATATTCTTGTAAGGAAAAGAAACC 57.158 33.333 2.31 0.00 43.57 3.27
6250 6348 8.942338 ACATACATACAGATAGAAAAGCGAAA 57.058 30.769 0.00 0.00 0.00 3.46
6251 6349 9.378551 ACATACATACAGATAGAAAAGCGAAAA 57.621 29.630 0.00 0.00 0.00 2.29
6317 6419 3.158676 GGTCTTCTCATACGGGAGCTAT 58.841 50.000 0.00 0.00 34.84 2.97
6354 6456 5.854431 AATCTCGAGTTCTGAAGCTTTTC 57.146 39.130 13.13 0.00 0.00 2.29
6362 6464 1.951510 TGAAGCTTTTCGGCTGCAG 59.048 52.632 10.11 10.11 42.39 4.41
6363 6465 1.211190 GAAGCTTTTCGGCTGCAGG 59.789 57.895 17.12 0.00 42.24 4.85
6364 6466 1.228245 AAGCTTTTCGGCTGCAGGA 60.228 52.632 17.12 1.62 42.24 3.86
6380 6601 5.039920 TGCAGGAATGTGTATGCTCTATT 57.960 39.130 0.00 0.00 39.42 1.73
6431 6657 2.710096 TCCCTGCTACTAATTGCACC 57.290 50.000 0.00 0.00 35.20 5.01
6440 6666 4.141914 GCTACTAATTGCACCTGTACCTCT 60.142 45.833 0.00 0.00 0.00 3.69
6452 6679 2.703798 TACCTCTACCGTGCCGTGC 61.704 63.158 0.00 0.00 0.00 5.34
6459 6686 2.376231 TACCGTGCCGTGCGTTTTTG 62.376 55.000 0.00 0.00 0.00 2.44
6466 6693 1.462791 CCGTGCGTTTTTGTTCACTC 58.537 50.000 0.00 0.00 0.00 3.51
6468 6695 2.285756 CCGTGCGTTTTTGTTCACTCTA 59.714 45.455 0.00 0.00 0.00 2.43
6469 6696 3.059188 CCGTGCGTTTTTGTTCACTCTAT 60.059 43.478 0.00 0.00 0.00 1.98
6470 6697 4.150980 CCGTGCGTTTTTGTTCACTCTATA 59.849 41.667 0.00 0.00 0.00 1.31
6471 6698 5.070862 CGTGCGTTTTTGTTCACTCTATAC 58.929 41.667 0.00 0.00 0.00 1.47
6472 6699 5.379827 GTGCGTTTTTGTTCACTCTATACC 58.620 41.667 0.00 0.00 0.00 2.73
6473 6700 4.453136 TGCGTTTTTGTTCACTCTATACCC 59.547 41.667 0.00 0.00 0.00 3.69
6474 6701 4.453136 GCGTTTTTGTTCACTCTATACCCA 59.547 41.667 0.00 0.00 0.00 4.51
6492 6719 0.038618 CACTCAACCATGACCGTCGA 60.039 55.000 0.00 0.00 0.00 4.20
6493 6720 0.243907 ACTCAACCATGACCGTCGAG 59.756 55.000 0.00 0.00 0.00 4.04
6494 6721 0.526211 CTCAACCATGACCGTCGAGA 59.474 55.000 0.00 0.00 0.00 4.04
6495 6722 0.963225 TCAACCATGACCGTCGAGAA 59.037 50.000 0.00 0.00 0.00 2.87
6496 6723 1.068474 CAACCATGACCGTCGAGAAC 58.932 55.000 0.00 0.00 0.00 3.01
6497 6724 0.966920 AACCATGACCGTCGAGAACT 59.033 50.000 0.00 0.00 0.00 3.01
6498 6725 0.243907 ACCATGACCGTCGAGAACTG 59.756 55.000 0.00 0.00 0.00 3.16
6499 6726 1.078759 CCATGACCGTCGAGAACTGC 61.079 60.000 0.00 0.00 0.00 4.40
6500 6727 0.388520 CATGACCGTCGAGAACTGCA 60.389 55.000 0.00 0.00 0.00 4.41
6503 6730 0.802607 GACCGTCGAGAACTGCATCC 60.803 60.000 0.00 0.00 0.00 3.51
6504 6731 1.874019 CCGTCGAGAACTGCATCCG 60.874 63.158 0.00 0.00 0.00 4.18
6505 6732 1.136774 CGTCGAGAACTGCATCCGA 59.863 57.895 0.00 0.00 0.00 4.55
6507 6734 1.482278 GTCGAGAACTGCATCCGATC 58.518 55.000 0.00 0.00 0.00 3.69
6508 6735 1.066303 GTCGAGAACTGCATCCGATCT 59.934 52.381 0.00 0.00 0.00 2.75
6511 6738 0.755686 AGAACTGCATCCGATCTCCC 59.244 55.000 0.00 0.00 0.00 4.30
6512 6739 0.755686 GAACTGCATCCGATCTCCCT 59.244 55.000 0.00 0.00 0.00 4.20
6514 6741 1.118356 ACTGCATCCGATCTCCCTCC 61.118 60.000 0.00 0.00 0.00 4.30
6515 6742 1.075301 TGCATCCGATCTCCCTCCA 60.075 57.895 0.00 0.00 0.00 3.86
6516 6743 1.117749 TGCATCCGATCTCCCTCCAG 61.118 60.000 0.00 0.00 0.00 3.86
6517 6744 1.118356 GCATCCGATCTCCCTCCAGT 61.118 60.000 0.00 0.00 0.00 4.00
6518 6745 0.965439 CATCCGATCTCCCTCCAGTC 59.035 60.000 0.00 0.00 0.00 3.51
6519 6746 0.178947 ATCCGATCTCCCTCCAGTCC 60.179 60.000 0.00 0.00 0.00 3.85
6520 6747 2.196925 CCGATCTCCCTCCAGTCCG 61.197 68.421 0.00 0.00 0.00 4.79
6521 6748 1.152943 CGATCTCCCTCCAGTCCGA 60.153 63.158 0.00 0.00 0.00 4.55
6522 6749 1.448922 CGATCTCCCTCCAGTCCGAC 61.449 65.000 0.00 0.00 0.00 4.79
6523 6750 1.448922 GATCTCCCTCCAGTCCGACG 61.449 65.000 0.00 0.00 0.00 5.12
6524 6751 2.912987 ATCTCCCTCCAGTCCGACGG 62.913 65.000 7.84 7.84 0.00 4.79
6525 6752 4.753662 TCCCTCCAGTCCGACGGG 62.754 72.222 15.25 11.21 34.60 5.28
6526 6753 4.753662 CCCTCCAGTCCGACGGGA 62.754 72.222 18.09 18.09 40.15 5.14
6577 6804 3.910914 AATGCGGCCACGGTAGCAA 62.911 57.895 2.24 0.00 43.19 3.91
6647 6897 2.210524 GAACGCATGGTCGTCACACG 62.211 60.000 0.00 0.00 42.46 4.49
6710 6960 3.320541 TGTGGCCAATCAAAACAGTTAGG 59.679 43.478 7.24 0.00 0.00 2.69
6724 6974 1.349688 AGTTAGGAATTGACGGTGCCA 59.650 47.619 0.00 0.00 0.00 4.92
6730 6980 0.958822 AATTGACGGTGCCACTTTCC 59.041 50.000 0.00 0.00 0.00 3.13
6744 6994 0.994995 CTTTCCAGATGCGTCGTCTG 59.005 55.000 17.11 17.11 44.45 3.51
6745 6995 0.317160 TTTCCAGATGCGTCGTCTGT 59.683 50.000 20.30 0.00 43.64 3.41
6746 6996 0.317160 TTCCAGATGCGTCGTCTGTT 59.683 50.000 20.30 0.00 43.64 3.16
6747 6997 1.170442 TCCAGATGCGTCGTCTGTTA 58.830 50.000 20.30 10.58 43.64 2.41
6748 6998 1.132453 TCCAGATGCGTCGTCTGTTAG 59.868 52.381 20.30 10.62 43.64 2.34
6749 6999 1.132453 CCAGATGCGTCGTCTGTTAGA 59.868 52.381 20.30 0.00 43.64 2.10
6750 7000 2.223595 CCAGATGCGTCGTCTGTTAGAT 60.224 50.000 20.30 0.00 43.64 1.98
6751 7001 3.439293 CAGATGCGTCGTCTGTTAGATT 58.561 45.455 16.28 0.00 41.17 2.40
6752 7002 3.859961 CAGATGCGTCGTCTGTTAGATTT 59.140 43.478 16.28 0.00 41.17 2.17
6753 7003 5.034797 CAGATGCGTCGTCTGTTAGATTTA 58.965 41.667 16.28 0.00 41.17 1.40
6754 7004 5.172232 CAGATGCGTCGTCTGTTAGATTTAG 59.828 44.000 16.28 0.00 41.17 1.85
6755 7005 3.766151 TGCGTCGTCTGTTAGATTTAGG 58.234 45.455 0.00 0.00 0.00 2.69
6756 7006 2.534757 GCGTCGTCTGTTAGATTTAGGC 59.465 50.000 0.00 0.00 0.00 3.93
6757 7007 3.114065 CGTCGTCTGTTAGATTTAGGCC 58.886 50.000 0.00 0.00 0.00 5.19
6758 7008 3.181489 CGTCGTCTGTTAGATTTAGGCCT 60.181 47.826 11.78 11.78 0.00 5.19
6759 7009 4.036027 CGTCGTCTGTTAGATTTAGGCCTA 59.964 45.833 8.91 8.91 0.00 3.93
6760 7010 5.280164 GTCGTCTGTTAGATTTAGGCCTAC 58.720 45.833 13.46 1.62 0.00 3.18
6761 7011 4.340381 TCGTCTGTTAGATTTAGGCCTACC 59.660 45.833 13.46 4.89 0.00 3.18
6762 7012 4.501058 CGTCTGTTAGATTTAGGCCTACCC 60.501 50.000 13.46 4.50 36.11 3.69
6764 7014 4.900054 TCTGTTAGATTTAGGCCTACCCTC 59.100 45.833 13.46 9.53 44.96 4.30
6765 7015 4.892198 TGTTAGATTTAGGCCTACCCTCT 58.108 43.478 13.46 16.18 44.96 3.69
6766 7016 6.034442 TGTTAGATTTAGGCCTACCCTCTA 57.966 41.667 13.46 15.20 44.96 2.43
6767 7017 6.631107 TGTTAGATTTAGGCCTACCCTCTAT 58.369 40.000 13.46 0.00 44.96 1.98
6768 7018 7.080353 TGTTAGATTTAGGCCTACCCTCTATT 58.920 38.462 13.46 0.00 44.96 1.73
6769 7019 7.234988 TGTTAGATTTAGGCCTACCCTCTATTC 59.765 40.741 13.46 13.69 44.96 1.75
6770 7020 5.095097 AGATTTAGGCCTACCCTCTATTCC 58.905 45.833 13.46 0.00 44.96 3.01
6771 7021 4.571366 TTTAGGCCTACCCTCTATTCCT 57.429 45.455 13.46 0.00 44.96 3.36
6772 7022 2.706112 AGGCCTACCCTCTATTCCTC 57.294 55.000 1.29 0.00 41.21 3.71
6773 7023 1.150347 AGGCCTACCCTCTATTCCTCC 59.850 57.143 1.29 0.00 41.21 4.30
6774 7024 1.258676 GCCTACCCTCTATTCCTCCG 58.741 60.000 0.00 0.00 0.00 4.63
6775 7025 1.258676 CCTACCCTCTATTCCTCCGC 58.741 60.000 0.00 0.00 0.00 5.54
6776 7026 1.258676 CTACCCTCTATTCCTCCGCC 58.741 60.000 0.00 0.00 0.00 6.13
6777 7027 0.858369 TACCCTCTATTCCTCCGCCT 59.142 55.000 0.00 0.00 0.00 5.52
6778 7028 0.031010 ACCCTCTATTCCTCCGCCTT 60.031 55.000 0.00 0.00 0.00 4.35
6779 7029 1.219724 ACCCTCTATTCCTCCGCCTTA 59.780 52.381 0.00 0.00 0.00 2.69
6780 7030 2.158143 ACCCTCTATTCCTCCGCCTTAT 60.158 50.000 0.00 0.00 0.00 1.73
6781 7031 2.498078 CCCTCTATTCCTCCGCCTTATC 59.502 54.545 0.00 0.00 0.00 1.75
6782 7032 2.164624 CCTCTATTCCTCCGCCTTATCG 59.835 54.545 0.00 0.00 0.00 2.92
6790 7040 2.895372 CGCCTTATCGGTGGTGCC 60.895 66.667 0.00 0.00 39.71 5.01
6799 7049 4.559502 GGTGGTGCCGCTCATAAT 57.440 55.556 1.58 0.00 0.00 1.28
6800 7050 2.024918 GGTGGTGCCGCTCATAATG 58.975 57.895 1.58 0.00 0.00 1.90
6801 7051 1.356624 GTGGTGCCGCTCATAATGC 59.643 57.895 0.00 0.00 0.00 3.56
6811 7061 1.127582 GCTCATAATGCGATTCGAGGC 59.872 52.381 10.88 0.00 0.00 4.70
6812 7062 2.681706 CTCATAATGCGATTCGAGGCT 58.318 47.619 10.88 0.00 0.00 4.58
6813 7063 3.838120 CTCATAATGCGATTCGAGGCTA 58.162 45.455 10.88 0.00 0.00 3.93
6814 7064 3.838120 TCATAATGCGATTCGAGGCTAG 58.162 45.455 10.88 0.00 0.00 3.42
6815 7065 3.506067 TCATAATGCGATTCGAGGCTAGA 59.494 43.478 10.88 0.00 0.00 2.43
6816 7066 2.430546 AATGCGATTCGAGGCTAGAG 57.569 50.000 10.88 0.00 0.00 2.43
6817 7067 0.600557 ATGCGATTCGAGGCTAGAGG 59.399 55.000 10.88 0.00 0.00 3.69
6818 7068 1.287503 GCGATTCGAGGCTAGAGGG 59.712 63.158 10.88 0.00 0.00 4.30
6819 7069 1.457009 GCGATTCGAGGCTAGAGGGT 61.457 60.000 10.88 0.00 0.00 4.34
6820 7070 0.312416 CGATTCGAGGCTAGAGGGTG 59.688 60.000 0.00 0.00 0.00 4.61
6821 7071 0.676736 GATTCGAGGCTAGAGGGTGG 59.323 60.000 0.00 0.00 0.00 4.61
6822 7072 0.760945 ATTCGAGGCTAGAGGGTGGG 60.761 60.000 0.00 0.00 0.00 4.61
6823 7073 1.870941 TTCGAGGCTAGAGGGTGGGA 61.871 60.000 0.00 0.00 0.00 4.37
6824 7074 2.128507 CGAGGCTAGAGGGTGGGAC 61.129 68.421 0.00 0.00 0.00 4.46
6825 7075 1.762858 GAGGCTAGAGGGTGGGACC 60.763 68.421 0.00 0.00 37.60 4.46
6826 7076 2.245143 GAGGCTAGAGGGTGGGACCT 62.245 65.000 0.00 0.00 45.57 3.85
6827 7077 0.929734 AGGCTAGAGGGTGGGACCTA 60.930 60.000 0.00 0.00 42.10 3.08
6828 7078 0.759812 GGCTAGAGGGTGGGACCTAC 60.760 65.000 0.00 0.00 42.10 3.18
6829 7079 0.262285 GCTAGAGGGTGGGACCTACT 59.738 60.000 8.03 0.00 42.10 2.57
6830 7080 1.343176 GCTAGAGGGTGGGACCTACTT 60.343 57.143 8.03 0.00 42.10 2.24
6831 7081 2.091444 GCTAGAGGGTGGGACCTACTTA 60.091 54.545 8.03 0.00 42.10 2.24
6832 7082 3.438225 GCTAGAGGGTGGGACCTACTTAT 60.438 52.174 8.03 0.00 42.10 1.73
6833 7083 4.202652 GCTAGAGGGTGGGACCTACTTATA 60.203 50.000 8.03 0.00 42.10 0.98
6834 7084 4.196118 AGAGGGTGGGACCTACTTATAC 57.804 50.000 8.03 0.00 42.10 1.47
6835 7085 3.798422 AGAGGGTGGGACCTACTTATACT 59.202 47.826 8.03 0.00 42.10 2.12
6836 7086 4.986900 AGAGGGTGGGACCTACTTATACTA 59.013 45.833 8.03 0.00 42.10 1.82
6837 7087 5.072129 AGGGTGGGACCTACTTATACTAC 57.928 47.826 8.03 0.00 39.65 2.73
6838 7088 4.736055 AGGGTGGGACCTACTTATACTACT 59.264 45.833 8.03 0.00 39.65 2.57
6839 7089 5.919469 AGGGTGGGACCTACTTATACTACTA 59.081 44.000 8.03 0.00 39.65 1.82
6840 7090 6.394039 AGGGTGGGACCTACTTATACTACTAA 59.606 42.308 8.03 0.00 39.65 2.24
6841 7091 7.076045 AGGGTGGGACCTACTTATACTACTAAT 59.924 40.741 8.03 0.00 39.65 1.73
6842 7092 7.732140 GGGTGGGACCTACTTATACTACTAATT 59.268 40.741 8.03 0.00 38.64 1.40
6843 7093 8.801299 GGTGGGACCTACTTATACTACTAATTC 58.199 40.741 8.03 0.00 34.73 2.17
6844 7094 8.801299 GTGGGACCTACTTATACTACTAATTCC 58.199 40.741 0.00 0.00 0.00 3.01
6845 7095 8.513658 TGGGACCTACTTATACTACTAATTCCA 58.486 37.037 0.00 0.00 0.00 3.53
6846 7096 9.022884 GGGACCTACTTATACTACTAATTCCAG 57.977 40.741 0.00 0.00 0.00 3.86
6847 7097 9.585369 GGACCTACTTATACTACTAATTCCAGT 57.415 37.037 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 1.071857 CTCTCCCGCTAATAAACCCCC 59.928 57.143 0.00 0.00 0.00 5.40
97 98 2.354422 CATCGCGCGCAGAGATCT 60.354 61.111 32.61 11.07 37.27 2.75
98 99 3.401411 CCATCGCGCGCAGAGATC 61.401 66.667 32.61 0.00 37.27 2.75
116 117 1.742880 CACATGCGGAGTGTCAGGG 60.743 63.158 0.00 0.00 32.44 4.45
154 155 2.051882 GAATGCATGCGCCGTAGC 60.052 61.111 14.09 4.00 37.32 3.58
223 224 9.297586 TGTTCTATGTTTACTACACGATGAATC 57.702 33.333 0.00 0.00 40.19 2.52
224 225 9.647797 TTGTTCTATGTTTACTACACGATGAAT 57.352 29.630 0.00 0.00 40.19 2.57
225 226 9.478768 TTTGTTCTATGTTTACTACACGATGAA 57.521 29.630 0.00 0.00 40.19 2.57
226 227 9.478768 TTTTGTTCTATGTTTACTACACGATGA 57.521 29.630 0.00 0.00 40.19 2.92
227 228 9.741168 CTTTTGTTCTATGTTTACTACACGATG 57.259 33.333 0.00 0.00 40.19 3.84
228 229 9.701098 TCTTTTGTTCTATGTTTACTACACGAT 57.299 29.630 0.00 0.00 40.19 3.73
229 230 9.701098 ATCTTTTGTTCTATGTTTACTACACGA 57.299 29.630 0.00 0.00 40.19 4.35
266 267 9.841295 TTTCATTTTCTAACTTGTACTACTGGT 57.159 29.630 0.00 0.00 0.00 4.00
291 292 5.212194 CACCGATCGTGTCATTTTCTTTTT 58.788 37.500 15.09 0.00 37.73 1.94
292 293 4.783242 CACCGATCGTGTCATTTTCTTTT 58.217 39.130 15.09 0.00 37.73 2.27
293 294 4.404507 CACCGATCGTGTCATTTTCTTT 57.595 40.909 15.09 0.00 37.73 2.52
331 332 2.359230 GCTCCTGCTCAAACGCCT 60.359 61.111 0.00 0.00 36.03 5.52
379 380 3.122971 GGCCGTCCAGTTTACGCC 61.123 66.667 0.00 0.00 39.00 5.68
398 399 1.462043 ATGATGATGAGGCCGGGGA 60.462 57.895 2.18 0.00 0.00 4.81
535 541 2.504244 GACACGAGTCGAAGGGCG 60.504 66.667 21.50 2.65 42.69 6.13
557 563 4.065281 GGACCCGTCTGTCACCCG 62.065 72.222 0.00 0.00 36.97 5.28
584 590 1.388065 TTAAAATCCGGCCGCCATGG 61.388 55.000 22.85 7.63 42.50 3.66
585 591 0.248866 GTTAAAATCCGGCCGCCATG 60.249 55.000 22.85 6.13 0.00 3.66
586 592 1.388837 GGTTAAAATCCGGCCGCCAT 61.389 55.000 22.85 11.23 0.00 4.40
587 593 2.047443 GGTTAAAATCCGGCCGCCA 61.047 57.895 22.85 8.89 0.00 5.69
588 594 1.721664 GAGGTTAAAATCCGGCCGCC 61.722 60.000 22.85 13.29 0.00 6.13
611 617 1.152139 CCCCCTTGGCCTTTTGGAA 60.152 57.895 3.32 0.00 44.07 3.53
613 619 1.610379 CTCCCCCTTGGCCTTTTGG 60.610 63.158 3.32 0.00 44.18 3.28
681 689 1.013596 TCGTTGCTGTCCTTGTTGTG 58.986 50.000 0.00 0.00 0.00 3.33
745 762 1.514657 TCGTCGTCGTTATTGCGGG 60.515 57.895 1.33 0.00 38.33 6.13
886 905 1.743321 CGAGGGGTCAGATCCAGCTC 61.743 65.000 0.94 0.00 0.00 4.09
887 906 1.760086 CGAGGGGTCAGATCCAGCT 60.760 63.158 0.94 0.00 0.00 4.24
944 964 3.483869 GGAGGAATCGCTGGGGCT 61.484 66.667 0.00 0.00 36.09 5.19
1446 1482 1.532238 GATTAGGCACCTGGGGTCC 59.468 63.158 0.00 0.00 31.02 4.46
1578 1614 3.746949 GAGCTCCTGCACGATGGGG 62.747 68.421 0.87 0.00 42.74 4.96
1777 1813 2.586357 GCCCTTCTCCGATGACGC 60.586 66.667 0.00 0.00 38.29 5.19
2190 2226 1.629043 TCAACCGGTCTGAGCTACTT 58.371 50.000 8.04 0.00 0.00 2.24
2247 2283 1.760029 TGCCCCTCAAAAGTTTTGACC 59.240 47.619 23.91 13.98 0.00 4.02
2337 2373 3.098636 GTCAACACGAAACAAGTTCAGC 58.901 45.455 0.00 0.00 35.83 4.26
2374 2410 5.337578 AATTGGGTCGTGGGATTAAATTG 57.662 39.130 0.00 0.00 0.00 2.32
2388 2424 7.404671 TTCTAAATTAGGCAGAAATTGGGTC 57.595 36.000 0.00 0.00 0.00 4.46
2461 2497 5.552870 TCAAGTTCTGCCTTTAAGAGACT 57.447 39.130 0.00 0.00 0.00 3.24
2462 2498 7.604545 ACTTATCAAGTTCTGCCTTTAAGAGAC 59.395 37.037 0.00 0.00 39.04 3.36
2463 2499 7.680730 ACTTATCAAGTTCTGCCTTTAAGAGA 58.319 34.615 0.00 0.00 39.04 3.10
2605 2641 1.537202 GCCTGTGTTTCTAAGCCACTG 59.463 52.381 0.00 0.00 0.00 3.66
2611 2647 7.642669 CATACAATATGGCCTGTGTTTCTAAG 58.357 38.462 3.32 0.00 0.00 2.18
2644 2680 7.552050 AGAATTGCTTAGAGCTACAGGATAT 57.448 36.000 1.29 0.00 42.97 1.63
2663 2699 9.538508 CTTTTGAAGAACAGATTCCAAAGAATT 57.461 29.630 6.46 0.00 42.93 2.17
2714 2754 2.093973 AGACAGATAGCGGGTTCAGTTG 60.094 50.000 0.00 0.00 0.00 3.16
2809 2849 5.920273 ACTTTACTGTTTGATTCAATTGCCG 59.080 36.000 0.00 0.00 0.00 5.69
2919 2959 5.853081 TCATATCACATTTCGAAACACGTG 58.147 37.500 21.94 21.94 43.13 4.49
3057 3097 9.282569 CATTTCTAAGATCTAATCCCTTTGGAG 57.717 37.037 0.00 0.00 46.08 3.86
3119 3159 4.214986 TCTTTCCGAACATCCAGCATAA 57.785 40.909 0.00 0.00 0.00 1.90
3361 3402 4.457466 TGACCTTCACTTAAACCCAGAAC 58.543 43.478 0.00 0.00 0.00 3.01
3366 3407 4.830600 TGGATTTGACCTTCACTTAAACCC 59.169 41.667 0.00 0.00 0.00 4.11
3489 3530 5.095490 GGGCAAGAACATTCGACAAATAAG 58.905 41.667 0.00 0.00 0.00 1.73
3542 3583 4.656112 AGATTTCCTGACGTCCCAAGATAT 59.344 41.667 14.12 5.16 0.00 1.63
3914 3958 7.584987 AGATAAGAAATTTTGTGAAGACACCG 58.415 34.615 0.00 0.00 45.40 4.94
3987 4031 7.657336 ACATGTCCCATAACTTTACTGTTTTG 58.343 34.615 0.00 0.00 0.00 2.44
3996 4040 5.385198 ACACTTGACATGTCCCATAACTTT 58.615 37.500 22.85 0.00 0.00 2.66
4208 4252 1.328680 CAGATGCGGACCTTTTCATCG 59.671 52.381 0.00 0.00 40.01 3.84
4329 4373 6.197364 ACTTAACAAACGGAACACATTTCA 57.803 33.333 0.00 0.00 0.00 2.69
4451 4495 7.412063 TGAAAATGTCATAAATCATCAGAGCG 58.588 34.615 0.00 0.00 0.00 5.03
4496 4540 9.171877 CAATTCTGAAGGAAAAGTAAGAGCTAT 57.828 33.333 0.00 0.00 37.49 2.97
4644 4688 5.227908 GTGTCAGAACAGATTCGGAAGTTA 58.772 41.667 0.00 0.00 40.18 2.24
4687 4736 8.830915 AACTATGATTCAGTAAGAGAGGAAGA 57.169 34.615 0.00 0.00 0.00 2.87
4734 4783 2.154854 TGAGCACCTTCGAAGAACTG 57.845 50.000 26.61 17.56 45.90 3.16
4889 4941 2.213499 AGCAACAGTGTCTCGAAAAGG 58.787 47.619 0.00 0.00 0.00 3.11
4920 4972 4.511826 CAGGTCAAGGACAAGAACTACAAC 59.488 45.833 0.00 0.00 33.68 3.32
4921 4973 4.163458 ACAGGTCAAGGACAAGAACTACAA 59.837 41.667 0.00 0.00 33.68 2.41
4922 4974 3.709653 ACAGGTCAAGGACAAGAACTACA 59.290 43.478 0.00 0.00 33.68 2.74
4923 4975 4.338379 ACAGGTCAAGGACAAGAACTAC 57.662 45.455 0.00 0.00 33.68 2.73
4924 4976 5.367945 AAACAGGTCAAGGACAAGAACTA 57.632 39.130 0.00 0.00 33.68 2.24
4925 4977 3.933861 AACAGGTCAAGGACAAGAACT 57.066 42.857 0.00 0.00 33.68 3.01
4926 4978 5.220989 GGTTAAACAGGTCAAGGACAAGAAC 60.221 44.000 0.00 0.00 33.68 3.01
4927 4979 4.885325 GGTTAAACAGGTCAAGGACAAGAA 59.115 41.667 0.00 0.00 33.68 2.52
4928 4980 4.165372 AGGTTAAACAGGTCAAGGACAAGA 59.835 41.667 0.00 0.00 33.68 3.02
4929 4981 4.461198 AGGTTAAACAGGTCAAGGACAAG 58.539 43.478 0.00 0.00 33.68 3.16
4930 4982 4.513406 AGGTTAAACAGGTCAAGGACAA 57.487 40.909 0.00 0.00 33.68 3.18
4931 4983 5.836024 ATAGGTTAAACAGGTCAAGGACA 57.164 39.130 0.00 0.00 33.68 4.02
4932 4984 6.569801 GCAAATAGGTTAAACAGGTCAAGGAC 60.570 42.308 0.00 0.00 0.00 3.85
4933 4985 5.475564 GCAAATAGGTTAAACAGGTCAAGGA 59.524 40.000 0.00 0.00 0.00 3.36
5225 5297 4.493545 GCAACCGACAAAACATACGGATAG 60.494 45.833 11.27 2.25 46.94 2.08
5252 5324 2.238521 GAAATGTGAAGGAACAGGGCA 58.761 47.619 0.00 0.00 32.52 5.36
5316 5389 6.519390 GAGATCACGTATCTGCCTCTTGCA 62.519 50.000 10.86 0.00 45.35 4.08
5319 5392 3.291584 TGAGATCACGTATCTGCCTCTT 58.708 45.455 10.86 0.00 45.35 2.85
5343 5416 0.687354 ACACATGGGAGTTCTCGCTT 59.313 50.000 0.00 8.46 0.00 4.68
5349 5422 2.066262 CACACGTACACATGGGAGTTC 58.934 52.381 0.00 0.00 0.00 3.01
5383 5456 0.608582 CTGCTTCTTTGCTCAGGGCT 60.609 55.000 0.00 0.00 42.39 5.19
5938 6032 2.749865 CCCAATCGCATTCGCACGT 61.750 57.895 0.00 0.00 38.40 4.49
6083 6181 5.239525 ACAAGAGTGGAAAAACAGATGCTAC 59.760 40.000 0.00 0.00 0.00 3.58
6084 6182 5.376625 ACAAGAGTGGAAAAACAGATGCTA 58.623 37.500 0.00 0.00 0.00 3.49
6085 6183 4.210331 ACAAGAGTGGAAAAACAGATGCT 58.790 39.130 0.00 0.00 0.00 3.79
6086 6184 4.540824 GACAAGAGTGGAAAAACAGATGC 58.459 43.478 0.00 0.00 0.00 3.91
6087 6185 4.319766 CGGACAAGAGTGGAAAAACAGATG 60.320 45.833 0.00 0.00 0.00 2.90
6088 6186 3.815401 CGGACAAGAGTGGAAAAACAGAT 59.185 43.478 0.00 0.00 0.00 2.90
6160 6258 2.159490 GGGTAAACACACACACACACAC 60.159 50.000 0.00 0.00 0.00 3.82
6162 6260 2.096819 CAGGGTAAACACACACACACAC 59.903 50.000 0.00 0.00 0.00 3.82
6164 6262 1.064952 GCAGGGTAAACACACACACAC 59.935 52.381 0.00 0.00 0.00 3.82
6167 6265 0.548989 AGGCAGGGTAAACACACACA 59.451 50.000 0.00 0.00 0.00 3.72
6168 6266 0.951558 CAGGCAGGGTAAACACACAC 59.048 55.000 0.00 0.00 0.00 3.82
6169 6267 0.840617 TCAGGCAGGGTAAACACACA 59.159 50.000 0.00 0.00 0.00 3.72
6170 6268 1.235724 GTCAGGCAGGGTAAACACAC 58.764 55.000 0.00 0.00 0.00 3.82
6171 6269 0.840617 TGTCAGGCAGGGTAAACACA 59.159 50.000 0.00 0.00 0.00 3.72
6172 6270 2.200373 ATGTCAGGCAGGGTAAACAC 57.800 50.000 0.00 0.00 0.00 3.32
6173 6271 4.227300 AGAATATGTCAGGCAGGGTAAACA 59.773 41.667 0.00 0.00 0.00 2.83
6174 6272 4.781934 AGAATATGTCAGGCAGGGTAAAC 58.218 43.478 0.00 0.00 0.00 2.01
6175 6273 5.192927 CAAGAATATGTCAGGCAGGGTAAA 58.807 41.667 0.00 0.00 0.00 2.01
6184 6282 8.792830 TCTTTTCCTTACAAGAATATGTCAGG 57.207 34.615 2.03 2.03 43.21 3.86
6208 6306 6.229936 TGTATGTATACACCTGAGGGTTTC 57.770 41.667 7.96 0.00 44.73 2.78
6212 6310 6.719829 TCTGTATGTATGTATACACCTGAGGG 59.280 42.308 7.96 0.00 45.11 4.30
6213 6311 7.761038 TCTGTATGTATGTATACACCTGAGG 57.239 40.000 7.96 0.00 45.11 3.86
6250 6348 5.454966 ACCCACCACTAAGAAAACTCATTT 58.545 37.500 0.00 0.00 0.00 2.32
6251 6349 5.061721 ACCCACCACTAAGAAAACTCATT 57.938 39.130 0.00 0.00 0.00 2.57
6253 6351 4.457466 GAACCCACCACTAAGAAAACTCA 58.543 43.478 0.00 0.00 0.00 3.41
6354 6456 0.659427 CATACACATTCCTGCAGCCG 59.341 55.000 8.66 0.00 0.00 5.52
6362 6464 5.822519 TGGAACAATAGAGCATACACATTCC 59.177 40.000 0.00 0.00 31.92 3.01
6363 6465 6.540189 AGTGGAACAATAGAGCATACACATTC 59.460 38.462 0.00 0.00 44.16 2.67
6364 6466 6.317140 CAGTGGAACAATAGAGCATACACATT 59.683 38.462 0.00 0.00 44.16 2.71
6380 6601 0.033601 AAGCAACCCACAGTGGAACA 60.034 50.000 22.37 0.00 40.96 3.18
6452 6679 5.699458 AGTGGGTATAGAGTGAACAAAAACG 59.301 40.000 0.00 0.00 0.00 3.60
6459 6686 4.222145 TGGTTGAGTGGGTATAGAGTGAAC 59.778 45.833 0.00 0.00 0.00 3.18
6466 6693 3.492656 CGGTCATGGTTGAGTGGGTATAG 60.493 52.174 0.00 0.00 30.85 1.31
6468 6695 1.209504 CGGTCATGGTTGAGTGGGTAT 59.790 52.381 0.00 0.00 30.85 2.73
6469 6696 0.611200 CGGTCATGGTTGAGTGGGTA 59.389 55.000 0.00 0.00 30.85 3.69
6470 6697 1.374947 CGGTCATGGTTGAGTGGGT 59.625 57.895 0.00 0.00 30.85 4.51
6471 6698 0.673644 GACGGTCATGGTTGAGTGGG 60.674 60.000 2.62 0.00 30.85 4.61
6472 6699 1.014044 CGACGGTCATGGTTGAGTGG 61.014 60.000 9.10 0.00 30.85 4.00
6473 6700 0.038618 TCGACGGTCATGGTTGAGTG 60.039 55.000 9.10 0.00 30.85 3.51
6474 6701 0.243907 CTCGACGGTCATGGTTGAGT 59.756 55.000 9.10 0.00 39.86 3.41
6492 6719 0.755686 GGGAGATCGGATGCAGTTCT 59.244 55.000 0.00 0.00 0.00 3.01
6493 6720 0.755686 AGGGAGATCGGATGCAGTTC 59.244 55.000 0.00 0.00 0.00 3.01
6494 6721 0.755686 GAGGGAGATCGGATGCAGTT 59.244 55.000 0.00 0.00 0.00 3.16
6495 6722 1.118356 GGAGGGAGATCGGATGCAGT 61.118 60.000 0.00 0.00 0.00 4.40
6496 6723 1.117749 TGGAGGGAGATCGGATGCAG 61.118 60.000 0.00 0.00 0.00 4.41
6497 6724 1.075301 TGGAGGGAGATCGGATGCA 60.075 57.895 0.00 0.00 0.00 3.96
6498 6725 1.118356 ACTGGAGGGAGATCGGATGC 61.118 60.000 0.00 0.00 0.00 3.91
6499 6726 0.965439 GACTGGAGGGAGATCGGATG 59.035 60.000 0.00 0.00 0.00 3.51
6500 6727 0.178947 GGACTGGAGGGAGATCGGAT 60.179 60.000 0.00 0.00 0.00 4.18
6503 6730 1.152943 TCGGACTGGAGGGAGATCG 60.153 63.158 0.00 0.00 0.00 3.69
6504 6731 1.448922 CGTCGGACTGGAGGGAGATC 61.449 65.000 6.57 0.00 0.00 2.75
6505 6732 1.454111 CGTCGGACTGGAGGGAGAT 60.454 63.158 6.57 0.00 0.00 2.75
6507 6734 3.141488 CCGTCGGACTGGAGGGAG 61.141 72.222 4.91 0.00 43.07 4.30
6508 6735 4.753662 CCCGTCGGACTGGAGGGA 62.754 72.222 14.39 0.00 44.70 4.20
6527 6754 4.415150 ATGTCGGTGCTGGCCCTG 62.415 66.667 0.00 0.00 0.00 4.45
6528 6755 4.101448 GATGTCGGTGCTGGCCCT 62.101 66.667 0.00 0.00 0.00 5.19
6577 6804 3.066900 GTCAGTAGTATCACATCGCAGGT 59.933 47.826 0.00 0.00 0.00 4.00
6710 6960 1.068541 GGAAAGTGGCACCGTCAATTC 60.069 52.381 15.27 9.24 0.00 2.17
6724 6974 0.603569 AGACGACGCATCTGGAAAGT 59.396 50.000 0.00 0.00 0.00 2.66
6744 6994 7.310547 GGAATAGAGGGTAGGCCTAAATCTAAC 60.311 44.444 23.53 20.22 34.45 2.34
6745 6995 6.729569 GGAATAGAGGGTAGGCCTAAATCTAA 59.270 42.308 23.53 13.36 34.45 2.10
6746 6996 6.048080 AGGAATAGAGGGTAGGCCTAAATCTA 59.952 42.308 22.61 22.61 34.45 1.98
6747 6997 5.095097 GGAATAGAGGGTAGGCCTAAATCT 58.905 45.833 15.83 18.92 34.45 2.40
6748 6998 5.095097 AGGAATAGAGGGTAGGCCTAAATC 58.905 45.833 15.83 12.67 34.45 2.17
6749 6999 5.095097 GAGGAATAGAGGGTAGGCCTAAAT 58.905 45.833 15.83 2.82 34.45 1.40
6750 7000 4.490706 GAGGAATAGAGGGTAGGCCTAAA 58.509 47.826 15.83 0.00 34.45 1.85
6751 7001 3.181409 GGAGGAATAGAGGGTAGGCCTAA 60.181 52.174 15.83 0.00 34.45 2.69
6752 7002 2.382649 GGAGGAATAGAGGGTAGGCCTA 59.617 54.545 8.91 8.91 34.45 3.93
6753 7003 1.150347 GGAGGAATAGAGGGTAGGCCT 59.850 57.143 11.78 11.78 34.45 5.19
6754 7004 1.646912 GGAGGAATAGAGGGTAGGCC 58.353 60.000 0.00 0.00 0.00 5.19
6755 7005 1.258676 CGGAGGAATAGAGGGTAGGC 58.741 60.000 0.00 0.00 0.00 3.93
6756 7006 1.258676 GCGGAGGAATAGAGGGTAGG 58.741 60.000 0.00 0.00 0.00 3.18
6757 7007 1.203075 AGGCGGAGGAATAGAGGGTAG 60.203 57.143 0.00 0.00 0.00 3.18
6758 7008 0.858369 AGGCGGAGGAATAGAGGGTA 59.142 55.000 0.00 0.00 0.00 3.69
6759 7009 0.031010 AAGGCGGAGGAATAGAGGGT 60.031 55.000 0.00 0.00 0.00 4.34
6760 7010 2.011122 TAAGGCGGAGGAATAGAGGG 57.989 55.000 0.00 0.00 0.00 4.30
6761 7011 2.164624 CGATAAGGCGGAGGAATAGAGG 59.835 54.545 0.00 0.00 0.00 3.69
6762 7012 3.495670 CGATAAGGCGGAGGAATAGAG 57.504 52.381 0.00 0.00 0.00 2.43
6773 7023 2.895372 GGCACCACCGATAAGGCG 60.895 66.667 0.00 0.00 46.52 5.52
6782 7032 2.024918 CATTATGAGCGGCACCACC 58.975 57.895 1.45 0.00 0.00 4.61
6783 7033 1.356624 GCATTATGAGCGGCACCAC 59.643 57.895 1.45 0.00 0.00 4.16
6784 7034 3.826221 GCATTATGAGCGGCACCA 58.174 55.556 1.45 0.00 0.00 4.17
6791 7041 1.127582 GCCTCGAATCGCATTATGAGC 59.872 52.381 0.00 0.00 0.00 4.26
6792 7042 2.681706 AGCCTCGAATCGCATTATGAG 58.318 47.619 0.00 0.00 0.00 2.90
6793 7043 2.820059 AGCCTCGAATCGCATTATGA 57.180 45.000 0.00 0.00 0.00 2.15
6794 7044 3.838120 TCTAGCCTCGAATCGCATTATG 58.162 45.455 0.00 0.00 0.00 1.90
6795 7045 3.119316 CCTCTAGCCTCGAATCGCATTAT 60.119 47.826 0.00 0.00 0.00 1.28
6796 7046 2.229062 CCTCTAGCCTCGAATCGCATTA 59.771 50.000 0.00 0.00 0.00 1.90
6797 7047 1.000283 CCTCTAGCCTCGAATCGCATT 60.000 52.381 0.00 0.00 0.00 3.56
6798 7048 0.600557 CCTCTAGCCTCGAATCGCAT 59.399 55.000 0.00 0.00 0.00 4.73
6799 7049 1.456196 CCCTCTAGCCTCGAATCGCA 61.456 60.000 0.00 0.00 0.00 5.10
6800 7050 1.287503 CCCTCTAGCCTCGAATCGC 59.712 63.158 0.00 0.00 0.00 4.58
6801 7051 0.312416 CACCCTCTAGCCTCGAATCG 59.688 60.000 0.00 0.00 0.00 3.34
6802 7052 0.676736 CCACCCTCTAGCCTCGAATC 59.323 60.000 0.00 0.00 0.00 2.52
6803 7053 0.760945 CCCACCCTCTAGCCTCGAAT 60.761 60.000 0.00 0.00 0.00 3.34
6804 7054 1.381327 CCCACCCTCTAGCCTCGAA 60.381 63.158 0.00 0.00 0.00 3.71
6805 7055 2.279073 CCCACCCTCTAGCCTCGA 59.721 66.667 0.00 0.00 0.00 4.04
6806 7056 2.128507 GTCCCACCCTCTAGCCTCG 61.129 68.421 0.00 0.00 0.00 4.63
6807 7057 1.762858 GGTCCCACCCTCTAGCCTC 60.763 68.421 0.00 0.00 30.04 4.70
6808 7058 0.929734 TAGGTCCCACCCTCTAGCCT 60.930 60.000 0.00 0.00 39.75 4.58
6809 7059 0.759812 GTAGGTCCCACCCTCTAGCC 60.760 65.000 0.00 0.00 39.75 3.93
6810 7060 0.262285 AGTAGGTCCCACCCTCTAGC 59.738 60.000 0.00 0.00 39.75 3.42
6811 7061 2.850695 AAGTAGGTCCCACCCTCTAG 57.149 55.000 0.00 0.00 39.75 2.43
6812 7062 4.986900 AGTATAAGTAGGTCCCACCCTCTA 59.013 45.833 0.00 0.00 39.75 2.43
6813 7063 3.798422 AGTATAAGTAGGTCCCACCCTCT 59.202 47.826 0.00 0.00 39.75 3.69
6814 7064 4.196118 AGTATAAGTAGGTCCCACCCTC 57.804 50.000 0.00 0.00 39.75 4.30
6815 7065 4.736055 AGTAGTATAAGTAGGTCCCACCCT 59.264 45.833 0.00 0.00 39.75 4.34
6816 7066 5.072129 AGTAGTATAAGTAGGTCCCACCC 57.928 47.826 0.00 0.00 39.75 4.61
6817 7067 8.718158 AATTAGTAGTATAAGTAGGTCCCACC 57.282 38.462 0.00 0.00 38.99 4.61
6818 7068 8.801299 GGAATTAGTAGTATAAGTAGGTCCCAC 58.199 40.741 0.00 0.00 0.00 4.61
6819 7069 8.513658 TGGAATTAGTAGTATAAGTAGGTCCCA 58.486 37.037 0.00 0.00 0.00 4.37
6820 7070 8.946797 TGGAATTAGTAGTATAAGTAGGTCCC 57.053 38.462 0.00 0.00 0.00 4.46
6821 7071 9.585369 ACTGGAATTAGTAGTATAAGTAGGTCC 57.415 37.037 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.