Multiple sequence alignment - TraesCS1D01G187600

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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 TraesCS1D01G187600 chr1D 100.000 5417 0 0 1 5417 258985339 258979923 0.000000e+00 10004.0
1 TraesCS1D01G187600 chr1D 98.438 64 1 0 2026 2089 258983251 258983188 4.430000e-21 113.0
2 TraesCS1D01G187600 chr1D 98.438 64 1 0 2089 2152 258983314 258983251 4.430000e-21 113.0
3 TraesCS1D01G187600 chr1A 91.711 2606 86 31 2089 4614 341869260 341871815 0.000000e+00 3496.0
4 TraesCS1D01G187600 chr1A 94.973 1691 67 16 1 1681 341867008 341868690 0.000000e+00 2636.0
5 TraesCS1D01G187600 chr1A 93.360 738 29 10 4687 5415 341871822 341872548 0.000000e+00 1074.0
6 TraesCS1D01G187600 chr1A 88.998 409 34 8 1681 2089 341868926 341869323 3.770000e-136 496.0
7 TraesCS1D01G187600 chr1A 82.716 81 10 4 4607 4685 581268514 581268436 9.740000e-08 69.4
8 TraesCS1D01G187600 chr1B 89.731 2600 125 50 2089 4614 353943092 353945623 0.000000e+00 3192.0
9 TraesCS1D01G187600 chr1B 93.579 1386 67 14 705 2090 353941793 353943156 0.000000e+00 2047.0
10 TraesCS1D01G187600 chr1B 93.103 754 34 9 4679 5415 353945619 353946371 0.000000e+00 1088.0
11 TraesCS1D01G187600 chr4D 80.488 328 54 9 890 1212 502571394 502571716 5.420000e-60 243.0
12 TraesCS1D01G187600 chr5A 80.635 315 53 7 890 1200 685988676 685988986 2.520000e-58 237.0
13 TraesCS1D01G187600 chr5A 96.078 51 2 0 4601 4651 578056653 578056703 3.480000e-12 84.2
14 TraesCS1D01G187600 chr4B 80.573 314 53 7 891 1200 646968311 646968620 9.070000e-58 235.0
15 TraesCS1D01G187600 chr7B 84.286 140 18 1 2308 2447 652931761 652931626 3.400000e-27 134.0
16 TraesCS1D01G187600 chr7B 94.444 54 2 1 4601 4654 138750094 138750042 1.250000e-11 82.4
17 TraesCS1D01G187600 chr2B 90.667 75 4 3 4609 4681 676586528 676586455 4.470000e-16 97.1
18 TraesCS1D01G187600 chr7D 97.917 48 1 0 4607 4654 168580859 168580906 3.480000e-12 84.2
19 TraesCS1D01G187600 chr7D 97.917 48 1 0 4607 4654 423587102 423587149 3.480000e-12 84.2
20 TraesCS1D01G187600 chr3B 96.154 52 1 1 4603 4654 65214147 65214097 3.480000e-12 84.2
21 TraesCS1D01G187600 chr3B 83.721 86 12 2 4607 4690 677724740 677724655 4.500000e-11 80.5
22 TraesCS1D01G187600 chr2A 96.078 51 2 0 4604 4654 572054208 572054258 3.480000e-12 84.2
23 TraesCS1D01G187600 chr5D 74.146 205 34 18 67 265 199731911 199732102 3.500000e-07 67.6


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 TraesCS1D01G187600 chr1D 258979923 258985339 5416 True 3410.0 10004 98.958667 1 5417 3 chr1D.!!$R1 5416
1 TraesCS1D01G187600 chr1A 341867008 341872548 5540 False 1925.5 3496 92.260500 1 5415 4 chr1A.!!$F1 5414
2 TraesCS1D01G187600 chr1B 353941793 353946371 4578 False 2109.0 3192 92.137667 705 5415 3 chr1B.!!$F1 4710

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
561 567 0.532196 GGTATGTTCTACGGGCCTGC 60.532 60.000 12.89 0.00 0.00 4.85 F
1728 1974 1.001706 CAGGGATTCATGAAGCATGCG 60.002 52.381 23.99 6.64 41.18 4.73 F
2076 2322 1.410153 CTTTGGGCTGGACATAATGCC 59.590 52.381 0.00 0.00 44.22 4.40 F
3635 3906 0.240411 CAGTTGCTCTCCTTGCTTGC 59.760 55.000 0.00 0.00 0.00 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2551 2810 0.393132 GCTCCCTTACTTCAGGCACC 60.393 60.000 0.00 0.00 31.69 5.01 R
3635 3906 2.621338 ACATCGTATCAGTGCAAGTGG 58.379 47.619 0.00 0.00 38.01 4.00 R
3920 4218 4.072131 CCATAGCGGCTGGTATTAATTGT 58.928 43.478 14.57 0.00 36.67 2.71 R
5040 5400 0.035152 CTTCCACCTGCATGTGCCTA 60.035 55.000 15.87 1.88 41.18 3.93 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
87 90 7.375230 TCAAAATCGATGAACGTTTTTCAAG 57.625 32.000 0.46 0.00 45.66 3.02
91 94 6.969669 ATCGATGAACGTTTTTCAAGTTTC 57.030 33.333 0.46 0.00 43.13 2.78
96 99 7.044380 CGATGAACGTTTTTCAAGTTTCATGAA 60.044 33.333 3.38 3.38 34.80 2.57
129 132 8.330302 CAAAATTTTGAACTGTTGTGAGATTCC 58.670 33.333 23.72 0.00 40.55 3.01
138 141 6.773638 ACTGTTGTGAGATTCCTGAACTTAT 58.226 36.000 0.00 0.00 0.00 1.73
231 234 7.434897 CCGTGAAGTTTTCTTTGAATTCATGAA 59.565 33.333 11.26 11.26 40.61 2.57
232 235 8.806634 CGTGAAGTTTTCTTTGAATTCATGAAA 58.193 29.630 22.40 22.40 40.61 2.69
275 278 6.473397 TGTTTTTGAAATTCACGCAACTTT 57.527 29.167 0.00 0.00 0.00 2.66
315 319 4.545823 TTCAGATTCGCGAACTGTTTTT 57.454 36.364 31.50 16.68 33.93 1.94
319 323 5.905181 TCAGATTCGCGAACTGTTTTTAAAC 59.095 36.000 31.50 9.37 39.33 2.01
326 330 5.053286 CGCGAACTGTTTTTAAACTCACAAG 60.053 40.000 0.00 0.00 39.59 3.16
327 331 5.798434 GCGAACTGTTTTTAAACTCACAAGT 59.202 36.000 6.87 0.00 39.59 3.16
352 356 2.100087 ACTTTAAAACACTGGCAACCGG 59.900 45.455 0.00 0.00 35.68 5.28
382 386 2.027926 GTGAACAACGCAGCACAAAAAG 59.972 45.455 0.00 0.00 0.00 2.27
419 424 6.976636 AAAAGCGAACCAATGAAAAGAAAA 57.023 29.167 0.00 0.00 0.00 2.29
454 460 2.076622 CTGGGACACGGGCGAGATAG 62.077 65.000 0.00 0.00 0.00 2.08
543 549 2.550978 CTACAGGCGTCAAATAGGTGG 58.449 52.381 0.00 0.00 0.00 4.61
561 567 0.532196 GGTATGTTCTACGGGCCTGC 60.532 60.000 12.89 0.00 0.00 4.85
587 593 1.338484 TGCTCTGCCACACTCTTCATC 60.338 52.381 0.00 0.00 0.00 2.92
602 608 3.055819 TCTTCATCTGGGCCGATATAAGC 60.056 47.826 17.73 0.00 0.00 3.09
622 628 1.215647 CTAGCGAGAAGGTGGCGTT 59.784 57.895 0.00 0.00 34.44 4.84
626 632 3.423154 GAGAAGGTGGCGTTGGCG 61.423 66.667 0.00 0.00 41.24 5.69
666 672 2.009051 TGCCTGTGCGACAAATAGATG 58.991 47.619 0.00 0.00 41.78 2.90
696 702 1.541233 CGTCTCCCAAACAGTTCTGCT 60.541 52.381 0.00 0.00 0.00 4.24
776 783 1.153208 ACCTCTATCTCGCCGTCGT 60.153 57.895 0.00 0.00 36.96 4.34
978 985 2.279784 CGGCTCCTCTTCATCGCC 60.280 66.667 0.00 0.00 37.40 5.54
1188 1195 1.495069 GCTTGACAGCGAGCTCAAC 59.505 57.895 15.40 4.97 46.18 3.18
1299 1309 1.664016 GCATTGGCGTGTGTTCTGAAG 60.664 52.381 0.00 0.00 0.00 3.02
1310 1320 4.691216 GTGTGTTCTGAAGTCATTCTACCC 59.309 45.833 0.00 0.00 36.33 3.69
1342 1352 4.537751 TCTGATCAAAGAGAGTATCCGGT 58.462 43.478 0.00 0.00 33.66 5.28
1548 1558 2.574399 GAGCAGACCCCAGACGAC 59.426 66.667 0.00 0.00 0.00 4.34
1665 1675 6.311690 GTGCACTAGAATCTCCTTTACTTGTC 59.688 42.308 10.32 0.00 0.00 3.18
1682 1928 8.718102 TTACTTGTCATTGTTTCTATCCTAGC 57.282 34.615 0.00 0.00 0.00 3.42
1688 1934 7.828717 TGTCATTGTTTCTATCCTAGCATTTCA 59.171 33.333 0.00 0.00 0.00 2.69
1700 1946 5.887598 TCCTAGCATTTCATGTTGCTACATT 59.112 36.000 11.24 0.00 46.92 2.71
1701 1947 7.053498 TCCTAGCATTTCATGTTGCTACATTA 58.947 34.615 11.24 0.77 46.92 1.90
1703 1949 7.227314 CCTAGCATTTCATGTTGCTACATTAGA 59.773 37.037 11.24 4.28 46.92 2.10
1728 1974 1.001706 CAGGGATTCATGAAGCATGCG 60.002 52.381 23.99 6.64 41.18 4.73
1751 1997 5.920273 CGCATTTAATCTGTTGGAACTTTGT 59.080 36.000 0.00 0.00 0.00 2.83
1753 1999 7.271223 CGCATTTAATCTGTTGGAACTTTGTAG 59.729 37.037 0.00 0.00 0.00 2.74
1759 2005 5.741011 TCTGTTGGAACTTTGTAGTGTTCT 58.259 37.500 0.00 0.00 41.42 3.01
1760 2006 6.880484 TCTGTTGGAACTTTGTAGTGTTCTA 58.120 36.000 0.00 0.00 41.42 2.10
1761 2007 6.759827 TCTGTTGGAACTTTGTAGTGTTCTAC 59.240 38.462 0.00 0.00 44.72 2.59
1762 2008 6.646267 TGTTGGAACTTTGTAGTGTTCTACT 58.354 36.000 0.00 0.00 44.74 2.57
1802 2048 5.459110 AGCTGATGCATTTTAAAATTGCG 57.541 34.783 20.43 10.02 42.74 4.85
1828 2074 2.917933 TGTGCTATTGGAGATTTCGGG 58.082 47.619 0.00 0.00 0.00 5.14
1838 2084 4.960938 TGGAGATTTCGGGAGTGATATTG 58.039 43.478 0.00 0.00 0.00 1.90
1869 2115 7.621796 ACCTGTGGTTTATTAGAAGTAAGGAG 58.378 38.462 0.00 0.00 27.29 3.69
1906 2152 4.919793 GGGATCCCCTAACTTTATTAGCC 58.080 47.826 21.42 0.00 41.34 3.93
1945 2191 7.255139 GCTATGTTTGTCAGTTTGTTTACTCCT 60.255 37.037 0.00 0.00 0.00 3.69
2016 2262 5.373812 TGTATTCCCTCATCCTTTTCTCC 57.626 43.478 0.00 0.00 0.00 3.71
2017 2263 5.039645 TGTATTCCCTCATCCTTTTCTCCT 58.960 41.667 0.00 0.00 0.00 3.69
2021 2267 2.573462 CCCTCATCCTTTTCTCCTGACA 59.427 50.000 0.00 0.00 0.00 3.58
2064 2310 8.773033 AGATATATCAATTTCAACTTTGGGCT 57.227 30.769 15.08 0.00 0.00 5.19
2065 2311 8.636213 AGATATATCAATTTCAACTTTGGGCTG 58.364 33.333 15.08 0.00 0.00 4.85
2066 2312 3.749665 TCAATTTCAACTTTGGGCTGG 57.250 42.857 0.00 0.00 0.00 4.85
2067 2313 3.303938 TCAATTTCAACTTTGGGCTGGA 58.696 40.909 0.00 0.00 0.00 3.86
2068 2314 3.069443 TCAATTTCAACTTTGGGCTGGAC 59.931 43.478 0.00 0.00 0.00 4.02
2069 2315 2.151502 TTTCAACTTTGGGCTGGACA 57.848 45.000 0.00 0.00 0.00 4.02
2070 2316 2.380064 TTCAACTTTGGGCTGGACAT 57.620 45.000 0.00 0.00 0.00 3.06
2071 2317 3.517296 TTCAACTTTGGGCTGGACATA 57.483 42.857 0.00 0.00 0.00 2.29
2072 2318 3.517296 TCAACTTTGGGCTGGACATAA 57.483 42.857 0.00 0.00 0.00 1.90
2073 2319 4.046286 TCAACTTTGGGCTGGACATAAT 57.954 40.909 0.00 0.00 0.00 1.28
2074 2320 3.763360 TCAACTTTGGGCTGGACATAATG 59.237 43.478 0.00 0.00 0.00 1.90
2075 2321 2.102578 ACTTTGGGCTGGACATAATGC 58.897 47.619 0.00 0.00 0.00 3.56
2076 2322 1.410153 CTTTGGGCTGGACATAATGCC 59.590 52.381 0.00 0.00 44.22 4.40
2079 2325 3.205815 GGCTGGACATAATGCCCAA 57.794 52.632 0.00 0.00 39.49 4.12
2080 2326 1.708341 GGCTGGACATAATGCCCAAT 58.292 50.000 0.00 0.00 39.49 3.16
2081 2327 2.875296 GGCTGGACATAATGCCCAATA 58.125 47.619 0.00 0.00 39.49 1.90
2082 2328 3.230134 GGCTGGACATAATGCCCAATAA 58.770 45.455 0.00 0.00 39.49 1.40
2083 2329 3.834231 GGCTGGACATAATGCCCAATAAT 59.166 43.478 0.00 0.00 39.49 1.28
2084 2330 4.284234 GGCTGGACATAATGCCCAATAATT 59.716 41.667 0.00 0.00 39.49 1.40
2085 2331 5.232463 GCTGGACATAATGCCCAATAATTG 58.768 41.667 0.00 0.00 26.63 2.32
2136 2382 5.450818 TTCTACTTTGGGCTGGACATAAT 57.549 39.130 0.00 0.00 0.00 1.28
2243 2489 3.349488 CGTACTCACGCTTATGATGGA 57.651 47.619 0.00 0.00 42.05 3.41
2244 2490 3.043586 CGTACTCACGCTTATGATGGAC 58.956 50.000 0.00 0.00 42.05 4.02
2245 2491 2.209838 ACTCACGCTTATGATGGACG 57.790 50.000 0.00 0.00 0.00 4.79
2246 2492 1.749063 ACTCACGCTTATGATGGACGA 59.251 47.619 0.00 0.00 0.00 4.20
2306 2552 3.322191 TTAAAAGTGTGCCCCCTTCTT 57.678 42.857 0.00 0.00 0.00 2.52
2318 2564 6.012333 TGTGCCCCCTTCTTAAGTTTATAGAA 60.012 38.462 1.63 0.00 0.00 2.10
2333 2579 7.271511 AGTTTATAGAAACAGGATCAGAGCTG 58.728 38.462 14.93 0.00 46.30 4.24
2454 2713 4.095483 GTCTTTGCCTGAACTACATGGATG 59.905 45.833 0.00 0.00 0.00 3.51
2613 2875 5.608798 AGGTACTAGGAATCTAGGATGCT 57.391 43.478 0.00 0.00 45.50 3.79
2722 2984 9.982651 GTCCTATAGCAAAGAGTATTATGAACA 57.017 33.333 0.00 0.00 0.00 3.18
2950 3212 5.076873 TCCAAATTTACTCCCAGTTCCTTG 58.923 41.667 0.00 0.00 0.00 3.61
3349 3618 7.716560 TGTCATCCTATCATTTGTAAGTGATGG 59.283 37.037 11.45 8.94 36.53 3.51
3354 3623 7.707104 CCTATCATTTGTAAGTGATGGGTTTC 58.293 38.462 18.25 0.00 44.11 2.78
3374 3645 8.248253 GGGTTTCTTTAACTTGAAAGAGAACAA 58.752 33.333 16.55 0.00 44.22 2.83
3435 3706 3.511699 TGATTTTCGGTGAGACATCTCG 58.488 45.455 4.49 0.00 45.72 4.04
3579 3850 9.813446 GGCAGAATTATGAATTTGAAAAGAGAT 57.187 29.630 3.77 0.00 0.00 2.75
3598 3869 6.243900 AGAGATGTCATGTTGTCATTCCTTT 58.756 36.000 0.00 0.00 31.15 3.11
3606 3877 5.947228 TGTTGTCATTCCTTTCACATCTC 57.053 39.130 0.00 0.00 0.00 2.75
3635 3906 0.240411 CAGTTGCTCTCCTTGCTTGC 59.760 55.000 0.00 0.00 0.00 4.01
3656 3927 3.780902 CCACTTGCACTGATACGATGTA 58.219 45.455 0.00 0.00 0.00 2.29
3677 3948 6.406370 TGTAGTCATTGACTGGTGGATAAAG 58.594 40.000 26.01 0.00 43.30 1.85
3707 3978 3.119637 ACTGAACCAACAAAAACCTGTCG 60.120 43.478 0.00 0.00 0.00 4.35
3738 4036 8.226819 TGGTTGTTGTTGTCTATTTATTCACA 57.773 30.769 0.00 0.00 0.00 3.58
3770 4068 9.851686 TCTCACATTGTAGCTGGATTTATTATT 57.148 29.630 0.00 0.00 0.00 1.40
4053 4351 2.267426 TCGACACAAAGCCATCATACG 58.733 47.619 0.00 0.00 0.00 3.06
4225 4532 1.075374 ACACCTGCAGGGCTAATTTGA 59.925 47.619 35.42 0.00 40.27 2.69
4226 4533 2.170166 CACCTGCAGGGCTAATTTGAA 58.830 47.619 35.42 0.00 40.27 2.69
4227 4534 2.094545 CACCTGCAGGGCTAATTTGAAC 60.095 50.000 35.42 0.00 40.27 3.18
4266 4593 2.159920 CGACTCGCACAACAAGATTCTG 60.160 50.000 0.00 0.00 0.00 3.02
4295 4622 4.084888 CGCCGACCAAAGGAACGC 62.085 66.667 0.00 0.00 0.00 4.84
4383 4710 1.714794 CGAACCTTCTCAAGCACGAT 58.285 50.000 0.00 0.00 0.00 3.73
4428 4756 5.016831 AGGAAGGTGTGAAAACAAGTTTCT 58.983 37.500 0.00 0.00 45.14 2.52
4437 4765 5.859648 GTGAAAACAAGTTTCTTTGGTTCGA 59.140 36.000 0.00 0.00 45.14 3.71
4481 4809 7.663081 AGATTTTAGTGATGATTCGTGCCATAT 59.337 33.333 0.00 0.00 0.00 1.78
4483 4811 6.544038 TTAGTGATGATTCGTGCCATATTG 57.456 37.500 0.00 0.00 0.00 1.90
4490 4819 4.332543 TGATTCGTGCCATATTGAGTGTTC 59.667 41.667 0.00 0.00 0.00 3.18
4550 4879 9.478019 CTAGATTTAAGTATGTTTTTGAGCACG 57.522 33.333 0.00 0.00 0.00 5.34
4551 4880 8.094798 AGATTTAAGTATGTTTTTGAGCACGA 57.905 30.769 0.00 0.00 0.00 4.35
4576 4905 9.289782 GAAAAGATAATATAACTCCTGCCATGT 57.710 33.333 0.00 0.00 0.00 3.21
4616 4945 5.961272 CCATGTGGTTAATTTTGTACTCCC 58.039 41.667 0.00 0.00 0.00 4.30
4617 4946 5.714806 CCATGTGGTTAATTTTGTACTCCCT 59.285 40.000 0.00 0.00 0.00 4.20
4618 4947 6.127730 CCATGTGGTTAATTTTGTACTCCCTC 60.128 42.308 0.00 0.00 0.00 4.30
4619 4948 5.318630 TGTGGTTAATTTTGTACTCCCTCC 58.681 41.667 0.00 0.00 0.00 4.30
4620 4949 4.393990 GTGGTTAATTTTGTACTCCCTCCG 59.606 45.833 0.00 0.00 0.00 4.63
4621 4950 4.041938 TGGTTAATTTTGTACTCCCTCCGT 59.958 41.667 0.00 0.00 0.00 4.69
4622 4951 5.248020 TGGTTAATTTTGTACTCCCTCCGTA 59.752 40.000 0.00 0.00 0.00 4.02
4623 4952 6.172630 GGTTAATTTTGTACTCCCTCCGTAA 58.827 40.000 0.00 0.00 0.00 3.18
4624 4953 6.654582 GGTTAATTTTGTACTCCCTCCGTAAA 59.345 38.462 0.00 0.00 0.00 2.01
4625 4954 7.148356 GGTTAATTTTGTACTCCCTCCGTAAAG 60.148 40.741 0.00 0.00 0.00 1.85
4626 4955 5.750352 ATTTTGTACTCCCTCCGTAAAGA 57.250 39.130 0.00 0.00 0.00 2.52
4627 4956 5.549742 TTTTGTACTCCCTCCGTAAAGAA 57.450 39.130 0.00 0.00 0.00 2.52
4628 4957 5.549742 TTTGTACTCCCTCCGTAAAGAAA 57.450 39.130 0.00 0.00 0.00 2.52
4629 4958 5.750352 TTGTACTCCCTCCGTAAAGAAAT 57.250 39.130 0.00 0.00 0.00 2.17
4630 4959 6.855763 TTGTACTCCCTCCGTAAAGAAATA 57.144 37.500 0.00 0.00 0.00 1.40
4631 4960 7.427989 TTGTACTCCCTCCGTAAAGAAATAT 57.572 36.000 0.00 0.00 0.00 1.28
4632 4961 8.537728 TTGTACTCCCTCCGTAAAGAAATATA 57.462 34.615 0.00 0.00 0.00 0.86
4633 4962 8.537728 TGTACTCCCTCCGTAAAGAAATATAA 57.462 34.615 0.00 0.00 0.00 0.98
4634 4963 9.151177 TGTACTCCCTCCGTAAAGAAATATAAT 57.849 33.333 0.00 0.00 0.00 1.28
4637 4966 8.312564 ACTCCCTCCGTAAAGAAATATAATAGC 58.687 37.037 0.00 0.00 0.00 2.97
4638 4967 7.318141 TCCCTCCGTAAAGAAATATAATAGCG 58.682 38.462 0.00 0.00 0.00 4.26
4639 4968 7.039504 TCCCTCCGTAAAGAAATATAATAGCGT 60.040 37.037 0.00 0.00 0.00 5.07
4640 4969 7.601508 CCCTCCGTAAAGAAATATAATAGCGTT 59.398 37.037 0.00 0.00 0.00 4.84
4641 4970 8.985805 CCTCCGTAAAGAAATATAATAGCGTTT 58.014 33.333 0.00 0.00 0.00 3.60
4656 4985 6.830114 ATAGCGTTTAGATCACTAAAGCAC 57.170 37.500 17.18 7.25 45.42 4.40
4657 4986 4.822026 AGCGTTTAGATCACTAAAGCACT 58.178 39.130 17.18 8.64 45.42 4.40
4658 4987 4.865365 AGCGTTTAGATCACTAAAGCACTC 59.135 41.667 17.18 3.83 45.42 3.51
4659 4988 4.625742 GCGTTTAGATCACTAAAGCACTCA 59.374 41.667 0.00 0.00 45.42 3.41
4660 4989 5.292101 GCGTTTAGATCACTAAAGCACTCAT 59.708 40.000 0.00 0.00 45.42 2.90
4661 4990 6.475727 GCGTTTAGATCACTAAAGCACTCATA 59.524 38.462 0.00 0.00 45.42 2.15
4662 4991 7.169982 GCGTTTAGATCACTAAAGCACTCATAT 59.830 37.037 0.00 0.00 45.42 1.78
4663 4992 9.035607 CGTTTAGATCACTAAAGCACTCATATT 57.964 33.333 0.00 0.00 45.42 1.28
4666 4995 9.890629 TTAGATCACTAAAGCACTCATATTTGT 57.109 29.630 0.00 0.00 35.92 2.83
4667 4996 8.798859 AGATCACTAAAGCACTCATATTTGTT 57.201 30.769 0.00 0.00 0.00 2.83
4668 4997 9.236006 AGATCACTAAAGCACTCATATTTGTTT 57.764 29.630 0.00 0.00 0.00 2.83
4672 5001 9.559958 CACTAAAGCACTCATATTTGTTTAAGG 57.440 33.333 0.00 0.00 0.00 2.69
4673 5002 9.515226 ACTAAAGCACTCATATTTGTTTAAGGA 57.485 29.630 0.00 0.00 0.00 3.36
4674 5003 9.994432 CTAAAGCACTCATATTTGTTTAAGGAG 57.006 33.333 0.00 0.00 0.00 3.69
4675 5004 7.396540 AAGCACTCATATTTGTTTAAGGAGG 57.603 36.000 0.00 0.00 0.00 4.30
4676 5005 6.721318 AGCACTCATATTTGTTTAAGGAGGA 58.279 36.000 0.00 0.00 0.00 3.71
4677 5006 7.175104 AGCACTCATATTTGTTTAAGGAGGAA 58.825 34.615 0.00 0.00 0.00 3.36
4678 5007 7.337942 AGCACTCATATTTGTTTAAGGAGGAAG 59.662 37.037 0.00 0.00 0.00 3.46
4679 5008 7.121315 GCACTCATATTTGTTTAAGGAGGAAGT 59.879 37.037 0.00 0.00 0.00 3.01
4680 5009 9.667107 CACTCATATTTGTTTAAGGAGGAAGTA 57.333 33.333 0.00 0.00 0.00 2.24
4681 5010 9.668497 ACTCATATTTGTTTAAGGAGGAAGTAC 57.332 33.333 0.00 0.00 0.00 2.73
4682 5011 9.892130 CTCATATTTGTTTAAGGAGGAAGTACT 57.108 33.333 0.00 0.00 0.00 2.73
4774 5106 4.152625 CTACAGCCGCGCTTGCAC 62.153 66.667 19.03 0.00 36.40 4.57
4818 5171 7.443272 TGCTGATAATATGTTCTGACTGGAATG 59.557 37.037 0.00 0.00 0.00 2.67
4819 5172 7.572724 GCTGATAATATGTTCTGACTGGAATGC 60.573 40.741 0.00 0.00 0.00 3.56
4821 5174 1.742761 ATGTTCTGACTGGAATGCCG 58.257 50.000 0.00 0.00 36.79 5.69
4822 5175 0.684535 TGTTCTGACTGGAATGCCGA 59.315 50.000 0.00 0.00 36.79 5.54
4823 5176 1.278985 TGTTCTGACTGGAATGCCGAT 59.721 47.619 0.00 0.00 36.79 4.18
4824 5177 1.936547 GTTCTGACTGGAATGCCGATC 59.063 52.381 0.00 0.00 36.79 3.69
4825 5178 1.194218 TCTGACTGGAATGCCGATCA 58.806 50.000 0.00 0.00 36.79 2.92
4826 5179 1.764723 TCTGACTGGAATGCCGATCAT 59.235 47.619 0.00 0.00 36.79 2.45
4827 5180 2.141517 CTGACTGGAATGCCGATCATC 58.858 52.381 0.00 0.00 36.79 2.92
4828 5181 1.485895 TGACTGGAATGCCGATCATCA 59.514 47.619 0.00 0.00 36.79 3.07
4873 5229 0.030101 CTTGCTTTCGGTGCGGAAAA 59.970 50.000 6.43 0.00 35.64 2.29
4928 5284 2.093306 TAATCTGCACCGACCAGTTG 57.907 50.000 0.00 0.00 0.00 3.16
5073 5433 6.060788 GCAGGTGGAAGATTCAAGATATTCT 58.939 40.000 0.00 0.00 0.00 2.40
5263 5628 3.094062 GCAGCTCCATCTGGCGGTA 62.094 63.158 0.00 0.00 34.74 4.02
5405 5770 0.984995 AAGTCCAGAGCCCACCTAAC 59.015 55.000 0.00 0.00 0.00 2.34
5408 5773 0.714180 TCCAGAGCCCACCTAACCTA 59.286 55.000 0.00 0.00 0.00 3.08
5415 5780 2.305052 AGCCCACCTAACCTAAACTCAC 59.695 50.000 0.00 0.00 0.00 3.51
5416 5781 2.933928 GCCCACCTAACCTAAACTCACG 60.934 54.545 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
108 111 5.885352 TCAGGAATCTCACAACAGTTCAAAA 59.115 36.000 0.00 0.00 0.00 2.44
109 112 5.436175 TCAGGAATCTCACAACAGTTCAAA 58.564 37.500 0.00 0.00 0.00 2.69
115 118 7.678947 AATAAGTTCAGGAATCTCACAACAG 57.321 36.000 0.00 0.00 0.00 3.16
195 198 8.439286 CAAAGAAAACTTCACGGATTTGAAAAA 58.561 29.630 0.00 0.00 35.07 1.94
196 199 7.815068 TCAAAGAAAACTTCACGGATTTGAAAA 59.185 29.630 0.00 0.00 35.07 2.29
246 249 6.473521 TGCGTGAATTTCAAAAACAAATCAC 58.526 32.000 0.00 0.00 0.00 3.06
287 290 4.970003 CAGTTCGCGAATCTGAAAAAGTTT 59.030 37.500 30.58 6.27 0.00 2.66
296 299 5.907391 AGTTTAAAAACAGTTCGCGAATCTG 59.093 36.000 31.51 31.51 41.30 2.90
319 323 9.878599 CCAGTGTTTTAAAGTATTACTTGTGAG 57.121 33.333 9.78 0.00 38.66 3.51
326 330 6.579666 CGGTTGCCAGTGTTTTAAAGTATTAC 59.420 38.462 0.00 0.00 0.00 1.89
327 331 6.294065 CCGGTTGCCAGTGTTTTAAAGTATTA 60.294 38.462 0.00 0.00 0.00 0.98
419 424 0.890996 CCAGCCTCGCTTGTCCTTTT 60.891 55.000 0.00 0.00 36.40 2.27
445 451 1.442857 CGATGGTCGCTATCTCGCC 60.443 63.158 2.79 0.00 31.14 5.54
451 457 2.134287 ACAGGCCGATGGTCGCTAT 61.134 57.895 0.00 0.00 38.82 2.97
454 460 4.760047 ACACAGGCCGATGGTCGC 62.760 66.667 13.17 0.00 38.82 5.19
507 513 0.804933 GTAGCGCCACTTACCTTCCG 60.805 60.000 2.29 0.00 0.00 4.30
543 549 0.464452 AGCAGGCCCGTAGAACATAC 59.536 55.000 0.00 0.00 0.00 2.39
561 567 0.250640 AGTGTGGCAGAGCAGGAAAG 60.251 55.000 0.00 0.00 0.00 2.62
587 593 2.159170 GCTAGAGCTTATATCGGCCCAG 60.159 54.545 0.00 0.00 38.21 4.45
602 608 1.064946 CGCCACCTTCTCGCTAGAG 59.935 63.158 0.00 0.00 45.69 2.43
700 706 1.813753 TCTGTAAATCCGCGCTGGC 60.814 57.895 5.56 0.00 37.80 4.85
701 707 1.429148 GGTCTGTAAATCCGCGCTGG 61.429 60.000 5.56 9.07 40.09 4.85
703 709 0.036765 TTGGTCTGTAAATCCGCGCT 60.037 50.000 5.56 0.00 0.00 5.92
776 783 2.185310 GAAGCAAAGGAGCGGGGAGA 62.185 60.000 0.00 0.00 40.15 3.71
978 985 3.685214 CTCCGACCCGCACTTCTCG 62.685 68.421 0.00 0.00 0.00 4.04
1059 1066 3.429141 GAGACGTCGCGGTGGAGA 61.429 66.667 10.46 0.00 0.00 3.71
1188 1195 1.135286 GGTTTCGGTACCCTGTAGACG 60.135 57.143 6.25 0.00 31.71 4.18
1299 1309 0.535335 TGGTCTGCGGGTAGAATGAC 59.465 55.000 0.00 0.00 0.00 3.06
1342 1352 1.427368 ACCAAGGTCATTGTAGCCCAA 59.573 47.619 0.00 0.00 37.17 4.12
1509 1519 4.576053 TCCGCCTTGATGACATAATTTGAG 59.424 41.667 0.00 0.00 0.00 3.02
1548 1558 2.350522 GCGGCAGTAATAGGATCCATG 58.649 52.381 15.82 3.80 0.00 3.66
1700 1946 7.320384 TGCTTCATGAATCCCTGATAATCTA 57.680 36.000 8.96 0.00 0.00 1.98
1701 1947 6.196918 TGCTTCATGAATCCCTGATAATCT 57.803 37.500 8.96 0.00 0.00 2.40
1703 1949 5.185249 GCATGCTTCATGAATCCCTGATAAT 59.815 40.000 11.37 0.00 43.81 1.28
1728 1974 8.082242 ACTACAAAGTTCCAACAGATTAAATGC 58.918 33.333 0.00 0.00 29.00 3.56
1751 1997 9.636789 TCAAGCCAATATAGTAGTAGAACACTA 57.363 33.333 0.00 0.00 38.80 2.74
1753 1999 9.765795 ATTCAAGCCAATATAGTAGTAGAACAC 57.234 33.333 0.00 0.00 0.00 3.32
1775 2021 8.605746 GCAATTTTAAAATGCATCAGCTATTCA 58.394 29.630 14.04 0.00 42.74 2.57
1785 2031 6.202570 ACAACTGTCGCAATTTTAAAATGCAT 59.797 30.769 23.11 0.00 0.00 3.96
1788 2034 5.840267 GCACAACTGTCGCAATTTTAAAATG 59.160 36.000 14.04 9.43 0.00 2.32
1789 2035 5.752955 AGCACAACTGTCGCAATTTTAAAAT 59.247 32.000 7.64 7.64 0.00 1.82
1802 2048 5.446473 CGAAATCTCCAATAGCACAACTGTC 60.446 44.000 0.00 0.00 0.00 3.51
1828 2074 5.938125 ACCACAGGTTACAACAATATCACTC 59.062 40.000 0.00 0.00 27.29 3.51
1838 2084 8.387190 ACTTCTAATAAACCACAGGTTACAAC 57.613 34.615 1.26 0.00 46.20 3.32
1869 2115 6.161855 GGGGATCCCTTTATTTGTTTCATC 57.838 41.667 30.08 3.72 41.34 2.92
1905 2151 5.163301 ACAAACATAGCAGATGTACCCTAGG 60.163 44.000 0.06 0.06 0.00 3.02
1906 2152 5.918608 ACAAACATAGCAGATGTACCCTAG 58.081 41.667 4.84 0.00 0.00 3.02
2005 2251 6.129179 TGAGTTTTTGTCAGGAGAAAAGGAT 58.871 36.000 4.80 0.00 35.45 3.24
2054 2300 2.497273 GCATTATGTCCAGCCCAAAGTT 59.503 45.455 0.00 0.00 0.00 2.66
2055 2301 2.102578 GCATTATGTCCAGCCCAAAGT 58.897 47.619 0.00 0.00 0.00 2.66
2056 2302 1.410153 GGCATTATGTCCAGCCCAAAG 59.590 52.381 0.00 0.00 41.25 2.77
2057 2303 1.484038 GGCATTATGTCCAGCCCAAA 58.516 50.000 0.00 0.00 41.25 3.28
2058 2304 3.205815 GGCATTATGTCCAGCCCAA 57.794 52.632 0.00 0.00 41.25 4.12
2102 2348 9.512588 CAGCCCAAAGTAGAAATTGATATATCT 57.487 33.333 13.79 0.00 0.00 1.98
2103 2349 8.734386 CCAGCCCAAAGTAGAAATTGATATATC 58.266 37.037 5.73 5.73 0.00 1.63
2104 2350 8.448008 TCCAGCCCAAAGTAGAAATTGATATAT 58.552 33.333 0.00 0.00 0.00 0.86
2105 2351 7.719633 GTCCAGCCCAAAGTAGAAATTGATATA 59.280 37.037 0.00 0.00 0.00 0.86
2106 2352 6.547510 GTCCAGCCCAAAGTAGAAATTGATAT 59.452 38.462 0.00 0.00 0.00 1.63
2107 2353 5.885912 GTCCAGCCCAAAGTAGAAATTGATA 59.114 40.000 0.00 0.00 0.00 2.15
2108 2354 4.706962 GTCCAGCCCAAAGTAGAAATTGAT 59.293 41.667 0.00 0.00 0.00 2.57
2109 2355 4.079253 GTCCAGCCCAAAGTAGAAATTGA 58.921 43.478 0.00 0.00 0.00 2.57
2110 2356 3.826157 TGTCCAGCCCAAAGTAGAAATTG 59.174 43.478 0.00 0.00 0.00 2.32
2111 2357 4.112634 TGTCCAGCCCAAAGTAGAAATT 57.887 40.909 0.00 0.00 0.00 1.82
2112 2358 3.806949 TGTCCAGCCCAAAGTAGAAAT 57.193 42.857 0.00 0.00 0.00 2.17
2113 2359 3.806949 ATGTCCAGCCCAAAGTAGAAA 57.193 42.857 0.00 0.00 0.00 2.52
2114 2360 4.919774 TTATGTCCAGCCCAAAGTAGAA 57.080 40.909 0.00 0.00 0.00 2.10
2115 2361 4.780815 CATTATGTCCAGCCCAAAGTAGA 58.219 43.478 0.00 0.00 0.00 2.59
2116 2362 3.316308 GCATTATGTCCAGCCCAAAGTAG 59.684 47.826 0.00 0.00 0.00 2.57
2119 2365 1.410153 GGCATTATGTCCAGCCCAAAG 59.590 52.381 0.00 0.00 41.25 2.77
2224 2470 3.043586 CGTCCATCATAAGCGTGAGTAC 58.956 50.000 0.00 0.00 0.00 2.73
2232 2478 8.709386 ACTATTATCAATCGTCCATCATAAGC 57.291 34.615 0.00 0.00 0.00 3.09
2270 2516 5.348724 CACTTTTAATTCTCGCAGTCAGCTA 59.651 40.000 0.00 0.00 42.61 3.32
2273 2519 5.377358 CACACTTTTAATTCTCGCAGTCAG 58.623 41.667 0.00 0.00 0.00 3.51
2282 2528 3.542969 AGGGGGCACACTTTTAATTCT 57.457 42.857 0.00 0.00 0.00 2.40
2306 2552 8.982723 AGCTCTGATCCTGTTTCTATAAACTTA 58.017 33.333 5.45 0.00 44.44 2.24
2318 2564 2.109774 CTCCTCAGCTCTGATCCTGTT 58.890 52.381 0.00 0.00 39.13 3.16
2333 2579 7.383843 GCTATAACTTCAGAATAGTTGCTCCTC 59.616 40.741 0.00 0.00 36.56 3.71
2551 2810 0.393132 GCTCCCTTACTTCAGGCACC 60.393 60.000 0.00 0.00 31.69 5.01
2613 2875 5.951747 AGGGAGAAAATTAATTGCAGCACTA 59.048 36.000 0.39 0.00 0.00 2.74
2649 2911 6.189677 TCCCGCAGAAAAATATACAGTTTG 57.810 37.500 0.00 0.00 0.00 2.93
2650 2912 6.601613 TCATCCCGCAGAAAAATATACAGTTT 59.398 34.615 0.00 0.00 0.00 2.66
2692 2954 9.209175 CATAATACTCTTTGCTATAGGACCAAC 57.791 37.037 1.04 0.00 0.00 3.77
2722 2984 6.206042 AGAAGACCAGAACTCCTACCATATT 58.794 40.000 0.00 0.00 0.00 1.28
2735 2997 6.127054 CCCATCTGTTATGTAGAAGACCAGAA 60.127 42.308 0.00 0.00 29.78 3.02
2950 3212 4.158579 CCTTCAAATCTTTCAGGGCCTAAC 59.841 45.833 5.28 0.00 0.00 2.34
3349 3618 9.634163 TTTGTTCTCTTTCAAGTTAAAGAAACC 57.366 29.630 14.51 3.80 43.13 3.27
3354 3623 9.840427 TGAAGTTTGTTCTCTTTCAAGTTAAAG 57.160 29.630 0.00 0.00 37.73 1.85
3374 3645 6.357367 ACCTGACTAATGAACAACTGAAGTT 58.643 36.000 0.00 0.00 39.12 2.66
3435 3706 3.056328 GCCCAGAACGTGGCCTTC 61.056 66.667 3.32 0.00 46.45 3.46
3579 3850 4.886489 TGTGAAAGGAATGACAACATGACA 59.114 37.500 0.00 0.00 36.79 3.58
3586 3857 8.102676 TCTTATGAGATGTGAAAGGAATGACAA 58.897 33.333 0.00 0.00 0.00 3.18
3598 3869 5.173664 CAACTGCTGTCTTATGAGATGTGA 58.826 41.667 0.00 0.00 33.70 3.58
3635 3906 2.621338 ACATCGTATCAGTGCAAGTGG 58.379 47.619 0.00 0.00 38.01 4.00
3656 3927 5.505181 ACTTTATCCACCAGTCAATGACT 57.495 39.130 10.56 10.56 44.44 3.41
3677 3948 7.977293 AGGTTTTTGTTGGTTCAGTTGTTATAC 59.023 33.333 0.00 0.00 0.00 1.47
3707 3978 6.843069 AATAGACAACAACAACCAAAATGC 57.157 33.333 0.00 0.00 0.00 3.56
3738 4036 4.164796 TCCAGCTACAATGTGAGAATCCAT 59.835 41.667 0.00 0.00 0.00 3.41
3770 4068 5.778241 TCTGGTAGAAGGTTCAACACATCTA 59.222 40.000 0.00 0.00 0.00 1.98
3920 4218 4.072131 CCATAGCGGCTGGTATTAATTGT 58.928 43.478 14.57 0.00 36.67 2.71
4053 4351 6.357367 ACAGATATGAATGGGAAAGTGTACC 58.643 40.000 0.00 0.00 0.00 3.34
4225 4532 2.487934 GATACGAGCCTGCATGATGTT 58.512 47.619 0.00 0.00 0.00 2.71
4226 4533 1.603931 CGATACGAGCCTGCATGATGT 60.604 52.381 0.00 0.00 0.00 3.06
4227 4534 1.066136 CGATACGAGCCTGCATGATG 58.934 55.000 0.00 0.00 0.00 3.07
4266 4593 2.429571 TCGGCGTGACTTGCGTAC 60.430 61.111 6.85 0.00 0.00 3.67
4275 4602 1.595929 GTTCCTTTGGTCGGCGTGA 60.596 57.895 6.85 0.00 0.00 4.35
4295 4622 0.317269 CAGTGCACGCTGGAAAGTTG 60.317 55.000 12.01 0.00 33.11 3.16
4428 4756 0.250295 CACCTCTGGCTCGAACCAAA 60.250 55.000 9.21 0.00 39.86 3.28
4437 4765 0.252479 CTCTCAATGCACCTCTGGCT 59.748 55.000 0.00 0.00 0.00 4.75
4490 4819 7.575155 GCTTGAATATGGAAGATCATGACATGG 60.575 40.741 15.37 0.00 0.00 3.66
4543 4872 8.421784 AGGAGTTATATTATCTTTTCGTGCTCA 58.578 33.333 0.00 0.00 0.00 4.26
4550 4879 9.289782 ACATGGCAGGAGTTATATTATCTTTTC 57.710 33.333 5.99 0.00 0.00 2.29
4576 4905 0.675083 TGGTCTCCGCAAAAGACGTA 59.325 50.000 0.00 0.00 43.33 3.57
4614 4943 7.095270 ACGCTATTATATTTCTTTACGGAGGG 58.905 38.462 0.00 0.00 0.00 4.30
4615 4944 8.530269 AACGCTATTATATTTCTTTACGGAGG 57.470 34.615 0.00 0.00 0.00 4.30
4630 4959 8.979574 GTGCTTTAGTGATCTAAACGCTATTAT 58.020 33.333 15.47 0.00 40.05 1.28
4631 4960 8.195436 AGTGCTTTAGTGATCTAAACGCTATTA 58.805 33.333 15.47 0.00 40.05 0.98
4632 4961 7.042335 AGTGCTTTAGTGATCTAAACGCTATT 58.958 34.615 15.47 0.00 40.05 1.73
4633 4962 6.574350 AGTGCTTTAGTGATCTAAACGCTAT 58.426 36.000 15.47 7.74 40.05 2.97
4634 4963 5.962433 AGTGCTTTAGTGATCTAAACGCTA 58.038 37.500 15.47 0.00 40.05 4.26
4635 4964 4.822026 AGTGCTTTAGTGATCTAAACGCT 58.178 39.130 15.47 12.22 40.05 5.07
4636 4965 4.625742 TGAGTGCTTTAGTGATCTAAACGC 59.374 41.667 0.00 0.00 40.05 4.84
4637 4966 6.893958 ATGAGTGCTTTAGTGATCTAAACG 57.106 37.500 0.00 0.00 40.05 3.60
4640 4969 9.890629 ACAAATATGAGTGCTTTAGTGATCTAA 57.109 29.630 0.00 0.00 34.76 2.10
4641 4970 9.890629 AACAAATATGAGTGCTTTAGTGATCTA 57.109 29.630 0.00 0.00 0.00 1.98
4642 4971 8.798859 AACAAATATGAGTGCTTTAGTGATCT 57.201 30.769 0.00 0.00 0.00 2.75
4646 4975 9.559958 CCTTAAACAAATATGAGTGCTTTAGTG 57.440 33.333 0.00 0.00 0.00 2.74
4647 4976 9.515226 TCCTTAAACAAATATGAGTGCTTTAGT 57.485 29.630 0.00 0.00 0.00 2.24
4648 4977 9.994432 CTCCTTAAACAAATATGAGTGCTTTAG 57.006 33.333 0.00 0.00 0.00 1.85
4649 4978 8.956426 CCTCCTTAAACAAATATGAGTGCTTTA 58.044 33.333 0.00 0.00 0.00 1.85
4650 4979 7.669722 TCCTCCTTAAACAAATATGAGTGCTTT 59.330 33.333 0.00 0.00 0.00 3.51
4651 4980 7.175104 TCCTCCTTAAACAAATATGAGTGCTT 58.825 34.615 0.00 0.00 0.00 3.91
4652 4981 6.721318 TCCTCCTTAAACAAATATGAGTGCT 58.279 36.000 0.00 0.00 0.00 4.40
4653 4982 7.121315 ACTTCCTCCTTAAACAAATATGAGTGC 59.879 37.037 0.00 0.00 0.00 4.40
4654 4983 8.567285 ACTTCCTCCTTAAACAAATATGAGTG 57.433 34.615 0.00 0.00 0.00 3.51
4655 4984 9.668497 GTACTTCCTCCTTAAACAAATATGAGT 57.332 33.333 0.00 0.00 0.00 3.41
4656 4985 9.892130 AGTACTTCCTCCTTAAACAAATATGAG 57.108 33.333 0.00 0.00 0.00 2.90
4659 4988 9.813446 CGTAGTACTTCCTCCTTAAACAAATAT 57.187 33.333 0.00 0.00 0.00 1.28
4660 4989 8.806146 ACGTAGTACTTCCTCCTTAAACAAATA 58.194 33.333 0.00 0.00 41.94 1.40
4661 4990 7.674120 ACGTAGTACTTCCTCCTTAAACAAAT 58.326 34.615 0.00 0.00 41.94 2.32
4662 4991 7.054491 ACGTAGTACTTCCTCCTTAAACAAA 57.946 36.000 0.00 0.00 41.94 2.83
4663 4992 6.655078 ACGTAGTACTTCCTCCTTAAACAA 57.345 37.500 0.00 0.00 41.94 2.83
4679 5008 5.583061 CCAAAATGAATGCCAGTACGTAGTA 59.417 40.000 1.81 0.00 45.11 1.82
4681 5010 4.634004 TCCAAAATGAATGCCAGTACGTAG 59.366 41.667 0.00 0.00 0.00 3.51
4682 5011 4.580868 TCCAAAATGAATGCCAGTACGTA 58.419 39.130 0.00 0.00 0.00 3.57
4737 5069 6.506147 TGTAGTAGACTGTTAAAAGCGACAA 58.494 36.000 0.00 0.00 0.00 3.18
4800 5132 3.134623 TCGGCATTCCAGTCAGAACATAT 59.865 43.478 0.00 0.00 0.00 1.78
4818 5171 2.016318 TCACAACCAATGATGATCGGC 58.984 47.619 0.00 0.00 0.00 5.54
4819 5172 4.700268 TTTCACAACCAATGATGATCGG 57.300 40.909 0.00 0.00 0.00 4.18
4821 5174 7.977293 TGAATGATTTCACAACCAATGATGATC 59.023 33.333 0.00 0.00 36.94 2.92
4822 5175 7.842982 TGAATGATTTCACAACCAATGATGAT 58.157 30.769 0.00 0.00 36.94 2.45
4823 5176 7.229581 TGAATGATTTCACAACCAATGATGA 57.770 32.000 0.00 0.00 36.94 2.92
4824 5177 8.487313 AATGAATGATTTCACAACCAATGATG 57.513 30.769 0.00 0.00 44.36 3.07
4826 5179 9.421806 GTTAATGAATGATTTCACAACCAATGA 57.578 29.630 0.00 0.00 44.36 2.57
4827 5180 9.205719 TGTTAATGAATGATTTCACAACCAATG 57.794 29.630 10.24 0.00 44.36 2.82
4828 5181 9.206870 GTGTTAATGAATGATTTCACAACCAAT 57.793 29.630 10.24 0.00 44.36 3.16
4851 5204 2.542907 CCGCACCGAAAGCAAGTGT 61.543 57.895 0.00 0.00 33.96 3.55
4878 5234 6.672593 TGGCTTCAGGTAGGAAATGATTTAT 58.327 36.000 0.00 0.00 0.00 1.40
4883 5239 4.591321 AATGGCTTCAGGTAGGAAATGA 57.409 40.909 0.00 0.00 0.00 2.57
4894 5250 6.293845 GGTGCAGATTATAGAAATGGCTTCAG 60.294 42.308 0.00 0.00 36.40 3.02
4928 5284 3.319122 AGATTCCACAAAGCCAAGACAAC 59.681 43.478 0.00 0.00 0.00 3.32
5040 5400 0.035152 CTTCCACCTGCATGTGCCTA 60.035 55.000 15.87 1.88 41.18 3.93
5073 5433 5.105310 TCGGTTGTTTGATTTGAAAAAGGGA 60.105 36.000 0.00 0.00 0.00 4.20
5263 5628 2.997315 TACCTCAGCTGCGTGCCT 60.997 61.111 9.47 0.00 44.23 4.75


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

AutoCloner maintained by Alex Coulton.