Multiple sequence alignment - TraesCS1D01G386100

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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 TraesCS1D01G386100 chr1D 100.000 5588 0 0 1 5588 458882938 458877351 0.000000e+00 10320.0
1 TraesCS1D01G386100 chr1D 76.030 267 51 11 10 269 435296061 435295801 5.880000e-25 126.0
2 TraesCS1D01G386100 chr1B 94.527 3965 170 24 814 4753 630826502 630822560 0.000000e+00 6076.0
3 TraesCS1D01G386100 chr1B 90.476 588 54 2 4753 5339 630822515 630821929 0.000000e+00 774.0
4 TraesCS1D01G386100 chr1B 87.313 268 18 11 5324 5588 630821902 630821648 5.480000e-75 292.0
5 TraesCS1D01G386100 chr1B 81.509 265 33 4 9 257 630827501 630827237 2.640000e-48 204.0
6 TraesCS1D01G386100 chr1B 87.805 82 7 3 99 177 451069243 451069162 5.960000e-15 93.5
7 TraesCS1D01G386100 chr1A 92.894 3251 158 21 1524 4732 551317044 551313825 0.000000e+00 4656.0
8 TraesCS1D01G386100 chr1A 88.485 825 36 26 588 1389 551317989 551317201 0.000000e+00 942.0
9 TraesCS1D01G386100 chr1A 83.725 596 49 21 4753 5326 551313765 551313196 2.310000e-143 520.0
10 TraesCS1D01G386100 chr1A 80.623 578 74 21 2 544 551318810 551318236 4.030000e-111 412.0
11 TraesCS1D01G386100 chr1A 88.837 215 18 5 5375 5586 551313038 551312827 5.550000e-65 259.0
12 TraesCS1D01G386100 chr1A 83.333 102 12 5 121 219 474295448 474295547 7.710000e-14 89.8
13 TraesCS1D01G386100 chr2B 86.265 415 42 7 1537 1942 59916177 59916585 2.390000e-118 436.0
14 TraesCS1D01G386100 chr2B 77.255 255 32 11 835 1076 274990025 274990266 5.880000e-25 126.0
15 TraesCS1D01G386100 chr4A 81.905 210 24 9 1011 1218 609029047 609029244 1.250000e-36 165.0
16 TraesCS1D01G386100 chr2A 77.821 257 30 11 834 1076 675204086 675203843 3.510000e-27 134.0
17 TraesCS1D01G386100 chr7B 76.991 226 40 10 54 270 135889246 135889468 9.830000e-23 119.0
18 TraesCS1D01G386100 chr5A 76.892 251 32 11 834 1071 609688740 609688977 9.830000e-23 119.0
19 TraesCS1D01G386100 chr5A 88.889 81 7 2 99 177 435247666 435247746 1.280000e-16 99.0
20 TraesCS1D01G386100 chr6B 80.272 147 24 5 120 264 42409194 42409337 7.660000e-19 106.0
21 TraesCS1D01G386100 chr6B 82.569 109 12 4 5473 5578 718232538 718232434 7.710000e-14 89.8
22 TraesCS1D01G386100 chr5B 88.372 86 8 2 99 182 390135918 390136003 9.900000e-18 102.0
23 TraesCS1D01G386100 chr3B 90.769 65 6 0 1011 1075 406828781 406828717 2.770000e-13 87.9


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 TraesCS1D01G386100 chr1D 458877351 458882938 5587 True 10320.0 10320 100.00000 1 5588 1 chr1D.!!$R2 5587
1 TraesCS1D01G386100 chr1B 630821648 630827501 5853 True 1836.5 6076 88.45625 9 5588 4 chr1B.!!$R2 5579
2 TraesCS1D01G386100 chr1A 551312827 551318810 5983 True 1357.8 4656 86.91280 2 5586 5 chr1A.!!$R1 5584

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
294 312 0.448990 CATGTGGTTGATGCGAGGTG 59.551 55.000 0.00 0.00 0.00 4.00 F
364 390 0.731417 AAGCTCATGCAATCGACTGC 59.269 50.000 12.77 12.77 42.74 4.40 F
1650 2249 0.911769 TGCACCAGTTCTCCCATAGG 59.088 55.000 0.00 0.00 0.00 2.57 F
1653 2252 1.909302 CACCAGTTCTCCCATAGGTGT 59.091 52.381 0.00 0.00 41.11 4.16 F
1812 2411 3.181510 CGAGGCAGCTGTGTTTATTAACC 60.182 47.826 16.64 3.49 33.15 2.85 F
3040 3639 1.066430 GCATCGGGCGGAATAAGGATA 60.066 52.381 0.00 0.00 0.00 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1532 2119 0.177604 CAGATGGCTGTCCTGTCCTC 59.822 60.0 0.00 0.0 37.37 3.71 R
1981 2580 0.819582 TTAGTTCCTCCCGTAAGCCG 59.180 55.0 0.00 0.0 0.00 5.52 R
2564 3163 2.236395 GAGCTAACAGAGTTAAGGGCCA 59.764 50.0 6.18 0.0 0.00 5.36 R
2844 3443 2.346766 TTCAGTTGCTCAAGCCTCAA 57.653 45.0 0.00 0.0 41.18 3.02 R
3144 3743 5.221382 GGATCAATAGCACCTGCAATGAAAT 60.221 40.0 0.00 0.0 45.16 2.17 R
4963 5633 0.105246 TGGGGTTGAATTGTTGGCCT 60.105 50.0 3.32 0.0 0.00 5.19 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
35 36 8.166726 CCTATTTCTAATTATCTGGAAGGCCTT 58.833 37.037 20.65 20.65 34.31 4.35
182 200 7.903995 TTCATTAATGGCTTGATTTCCAAAC 57.096 32.000 15.36 0.00 35.75 2.93
184 202 8.359875 TCATTAATGGCTTGATTTCCAAACTA 57.640 30.769 15.36 0.00 35.75 2.24
187 205 9.822185 ATTAATGGCTTGATTTCCAAACTAATC 57.178 29.630 0.00 0.00 35.75 1.75
195 213 2.754946 TCCAAACTAATCCGACGCTT 57.245 45.000 0.00 0.00 0.00 4.68
202 220 5.622770 AACTAATCCGACGCTTGATTTTT 57.377 34.783 3.66 0.00 33.46 1.94
206 224 7.586747 ACTAATCCGACGCTTGATTTTTAAAA 58.413 30.769 0.00 0.00 33.46 1.52
214 232 7.261140 CGACGCTTGATTTTTAAAATGTTTTCG 59.739 33.333 7.72 7.22 0.00 3.46
245 263 4.798152 GTACGAACGACGACGACA 57.202 55.556 15.32 9.08 45.77 4.35
265 283 7.340256 ACGACATACACATTCCCCTTTAATAA 58.660 34.615 0.00 0.00 0.00 1.40
273 291 9.799106 ACACATTCCCCTTTAATAATAGAGATG 57.201 33.333 0.00 0.00 0.00 2.90
274 292 8.734386 CACATTCCCCTTTAATAATAGAGATGC 58.266 37.037 0.00 0.00 0.00 3.91
275 293 7.890655 ACATTCCCCTTTAATAATAGAGATGCC 59.109 37.037 0.00 0.00 0.00 4.40
284 302 6.889301 AATAATAGAGATGCCATGTGGTTG 57.111 37.500 0.35 0.00 37.57 3.77
287 305 2.651455 AGAGATGCCATGTGGTTGATG 58.349 47.619 0.35 0.00 37.57 3.07
288 306 1.066605 GAGATGCCATGTGGTTGATGC 59.933 52.381 0.35 0.00 37.57 3.91
291 309 1.307355 TGCCATGTGGTTGATGCGAG 61.307 55.000 0.35 0.00 37.57 5.03
294 312 0.448990 CATGTGGTTGATGCGAGGTG 59.551 55.000 0.00 0.00 0.00 4.00
302 320 5.405571 GTGGTTGATGCGAGGTGTATATAAG 59.594 44.000 0.00 0.00 0.00 1.73
304 322 5.864474 GGTTGATGCGAGGTGTATATAAGAG 59.136 44.000 0.00 0.00 0.00 2.85
340 358 4.463539 TGTGAATATTGGACAATGCAAGCT 59.536 37.500 7.76 0.00 29.36 3.74
341 359 5.039333 GTGAATATTGGACAATGCAAGCTC 58.961 41.667 7.76 0.00 29.36 4.09
360 386 1.001624 CGACAAGCTCATGCAATCGA 58.998 50.000 0.00 0.00 40.22 3.59
364 390 0.731417 AAGCTCATGCAATCGACTGC 59.269 50.000 12.77 12.77 42.74 4.40
379 405 3.067106 CGACTGCTTTGTATGGTGTTCT 58.933 45.455 0.00 0.00 0.00 3.01
484 533 6.911250 TGTCGTATACCATGAAGACCATAT 57.089 37.500 0.00 0.00 33.31 1.78
487 536 8.862085 TGTCGTATACCATGAAGACCATATAAA 58.138 33.333 0.00 0.00 33.31 1.40
488 537 9.701098 GTCGTATACCATGAAGACCATATAAAA 57.299 33.333 0.00 0.00 33.31 1.52
533 582 4.875536 GGCATGGTTTTTGAGTTCAGTTTT 59.124 37.500 0.00 0.00 0.00 2.43
544 593 8.715191 TTTGAGTTCAGTTTTAAAATGCACAT 57.285 26.923 10.02 0.00 0.00 3.21
545 594 8.715191 TTGAGTTCAGTTTTAAAATGCACATT 57.285 26.923 10.02 0.00 0.00 2.71
546 595 8.715191 TGAGTTCAGTTTTAAAATGCACATTT 57.285 26.923 10.02 2.77 42.35 2.32
547 596 8.816144 TGAGTTCAGTTTTAAAATGCACATTTC 58.184 29.630 10.02 1.11 39.88 2.17
548 597 8.141835 AGTTCAGTTTTAAAATGCACATTTCC 57.858 30.769 10.02 0.00 39.88 3.13
584 653 5.999600 TGAGAAAGAATGAGAATGCACAGAA 59.000 36.000 0.00 0.00 0.00 3.02
602 854 2.543067 AATGAGGAGGCGAGCCCAAC 62.543 60.000 10.95 1.34 36.58 3.77
606 859 4.785453 GAGGCGAGCCCAACCCAG 62.785 72.222 10.95 0.00 36.58 4.45
628 883 1.314730 GTTGCCTTCCCAACGAAAGA 58.685 50.000 0.00 0.00 36.16 2.52
629 884 1.679153 GTTGCCTTCCCAACGAAAGAA 59.321 47.619 0.00 0.00 36.16 2.52
630 885 2.060050 TGCCTTCCCAACGAAAGAAA 57.940 45.000 0.00 0.00 0.00 2.52
636 891 2.641305 TCCCAACGAAAGAAAAACGGA 58.359 42.857 0.00 0.00 0.00 4.69
644 899 1.328279 AAGAAAAACGGAAGGCCCAG 58.672 50.000 0.00 0.00 34.14 4.45
758 1017 4.918201 CCCGCAATCGCCTCCCTC 62.918 72.222 0.00 0.00 33.11 4.30
759 1018 4.918201 CCGCAATCGCCTCCCTCC 62.918 72.222 0.00 0.00 33.11 4.30
760 1019 4.918201 CGCAATCGCCTCCCTCCC 62.918 72.222 0.00 0.00 33.11 4.30
761 1020 4.570874 GCAATCGCCTCCCTCCCC 62.571 72.222 0.00 0.00 0.00 4.81
762 1021 3.089874 CAATCGCCTCCCTCCCCA 61.090 66.667 0.00 0.00 0.00 4.96
763 1022 2.039405 AATCGCCTCCCTCCCCAT 60.039 61.111 0.00 0.00 0.00 4.00
764 1023 1.697754 AATCGCCTCCCTCCCCATT 60.698 57.895 0.00 0.00 0.00 3.16
798 1057 1.961180 ATCAAACCTCTCCTCCGCCG 61.961 60.000 0.00 0.00 0.00 6.46
799 1058 2.603776 AAACCTCTCCTCCGCCGT 60.604 61.111 0.00 0.00 0.00 5.68
962 1458 1.005630 CTGATCCCCCTCGATTCGC 60.006 63.158 0.00 0.00 0.00 4.70
1099 1602 2.522638 GCCCCTTCGATTACGTGCG 61.523 63.158 0.00 0.00 40.69 5.34
1230 1752 2.512515 GGGACACGATGCTGCTCC 60.513 66.667 0.00 0.00 0.00 4.70
1468 2045 5.163447 CCCTACAATTCTGTTATCCAGTCGA 60.163 44.000 0.00 0.00 42.19 4.20
1502 2079 3.127425 AGGAACTTAACTCTGTGCCAC 57.873 47.619 0.00 0.00 34.32 5.01
1504 2081 1.798813 GAACTTAACTCTGTGCCACGG 59.201 52.381 0.00 0.00 0.00 4.94
1519 2106 2.261671 CGGCAGGTCAGCTACGTT 59.738 61.111 0.00 0.00 34.17 3.99
1529 2116 4.466726 AGGTCAGCTACGTTAGAAATTCCT 59.533 41.667 0.00 0.00 0.00 3.36
1532 2119 3.000322 CAGCTACGTTAGAAATTCCTGCG 60.000 47.826 0.00 0.00 0.00 5.18
1533 2120 3.119245 AGCTACGTTAGAAATTCCTGCGA 60.119 43.478 0.00 0.00 0.00 5.10
1534 2121 3.243177 GCTACGTTAGAAATTCCTGCGAG 59.757 47.826 0.00 3.34 0.00 5.03
1535 2122 2.618053 ACGTTAGAAATTCCTGCGAGG 58.382 47.619 7.45 0.00 36.46 4.63
1537 2124 2.603560 CGTTAGAAATTCCTGCGAGGAC 59.396 50.000 4.59 0.00 45.78 3.85
1538 2125 3.596214 GTTAGAAATTCCTGCGAGGACA 58.404 45.455 4.59 0.00 45.78 4.02
1539 2126 2.393271 AGAAATTCCTGCGAGGACAG 57.607 50.000 4.59 0.00 45.78 3.51
1545 2132 2.125753 CTGCGAGGACAGGACAGC 60.126 66.667 0.00 0.00 33.85 4.40
1546 2133 3.655810 CTGCGAGGACAGGACAGCC 62.656 68.421 0.00 0.00 33.85 4.85
1547 2134 3.695606 GCGAGGACAGGACAGCCA 61.696 66.667 0.00 0.00 36.29 4.75
1548 2135 3.023949 GCGAGGACAGGACAGCCAT 62.024 63.158 0.00 0.00 36.29 4.40
1549 2136 1.142748 CGAGGACAGGACAGCCATC 59.857 63.158 0.00 0.00 36.29 3.51
1550 2137 1.326213 CGAGGACAGGACAGCCATCT 61.326 60.000 0.00 0.00 36.29 2.90
1570 2157 6.912591 CCATCTGTTTTTGTTACTTCTGTCAC 59.087 38.462 0.00 0.00 0.00 3.67
1601 2188 8.198807 TCATCTGATGAGAAAGCAGGATATTA 57.801 34.615 16.06 0.00 42.82 0.98
1617 2204 8.113462 GCAGGATATTAAAATATGAACCCCCTA 58.887 37.037 0.00 0.00 31.96 3.53
1643 2242 9.807649 ATCAAATAAATAAATGCACCAGTTCTC 57.192 29.630 0.00 0.00 0.00 2.87
1650 2249 0.911769 TGCACCAGTTCTCCCATAGG 59.088 55.000 0.00 0.00 0.00 2.57
1653 2252 1.909302 CACCAGTTCTCCCATAGGTGT 59.091 52.381 0.00 0.00 41.11 4.16
1681 2280 7.975866 CAAGTATGCCTAATTGTCAACAATC 57.024 36.000 8.72 0.00 45.06 2.67
1726 2325 3.947834 GGTAGTGATTCCAACCAATCCAG 59.052 47.826 0.00 0.00 32.51 3.86
1812 2411 3.181510 CGAGGCAGCTGTGTTTATTAACC 60.182 47.826 16.64 3.49 33.15 2.85
1822 2421 7.175293 AGCTGTGTTTATTAACCGACCAATTTA 59.825 33.333 0.00 0.00 33.15 1.40
1886 2485 6.426633 TCGCTCCACACATATATTGTTAATGG 59.573 38.462 0.00 0.00 36.00 3.16
1981 2580 7.383102 TCTTCATTCTTAACAGAAAGGATGC 57.617 36.000 0.79 0.00 42.53 3.91
2018 2617 5.036117 ACTAAGTGCAATCGTCCCATATT 57.964 39.130 0.00 0.00 0.00 1.28
2043 2642 4.875536 GGAAGAGATGAAGAAGAGAAAGGC 59.124 45.833 0.00 0.00 0.00 4.35
2232 2831 7.067981 AGAGAAGGTTCATATTCATGCCTTTTC 59.932 37.037 0.00 0.00 35.77 2.29
2261 2860 7.447374 TTGTACCCACTGATTACATTTTCTG 57.553 36.000 0.00 0.00 0.00 3.02
2529 3128 3.521560 TGCAGAAGGTTAGCATCTTACG 58.478 45.455 0.00 0.00 32.55 3.18
2587 3186 3.526534 GCCCTTAACTCTGTTAGCTCTG 58.473 50.000 0.00 0.00 0.00 3.35
2777 3376 6.637483 TCAATGTGTTGTTTGCAGAACTTGC 61.637 40.000 11.34 0.00 43.32 4.01
2819 3418 8.141909 TGGTTAACTTAGTGGAGATGATATTCG 58.858 37.037 5.42 0.00 0.00 3.34
2844 3443 2.752030 TGCAGGTAGAAGCTGAGGTAT 58.248 47.619 10.13 0.00 45.98 2.73
2992 3591 1.383523 GAGGCCATTGAAGCAGGTAC 58.616 55.000 5.01 0.00 0.00 3.34
3040 3639 1.066430 GCATCGGGCGGAATAAGGATA 60.066 52.381 0.00 0.00 0.00 2.59
3136 3735 5.502153 TGTAACAACCAACGTAATTTGCT 57.498 34.783 0.00 0.00 0.00 3.91
3137 3736 5.892568 TGTAACAACCAACGTAATTTGCTT 58.107 33.333 0.00 0.00 0.00 3.91
3638 4253 7.585579 TTACTTACGATGGTGTATGTATCCA 57.414 36.000 0.00 0.00 35.89 3.41
3652 4267 8.285394 GTGTATGTATCCATAATTTCACTGCTG 58.715 37.037 0.00 0.00 35.37 4.41
3661 4276 4.989279 AATTTCACTGCTGTTCTTGTGT 57.011 36.364 0.00 0.00 0.00 3.72
3787 4402 4.713792 AAAGGAGCAGGAAAAGAAGAGA 57.286 40.909 0.00 0.00 0.00 3.10
3835 4451 6.305693 ACTTTTTCTGCACTTGTATCTGTC 57.694 37.500 0.00 0.00 0.00 3.51
3987 4603 2.716969 AGAAGCTTACCAGAAACCCCTT 59.283 45.455 0.00 0.00 0.00 3.95
4406 5022 1.662629 CAAGATACTCGCAGCACCAAG 59.337 52.381 0.00 0.00 0.00 3.61
4474 5090 2.357881 CTGCTCTGACTGCCGCAA 60.358 61.111 0.00 0.00 31.24 4.85
4476 5092 2.047844 GCTCTGACTGCCGCAAGA 60.048 61.111 0.00 0.00 43.02 3.02
4578 5194 2.356793 GCCTATCTCGCTGCGCAT 60.357 61.111 18.65 13.80 0.00 4.73
4594 5210 1.645455 CATGCCGCTTGAATCTCGG 59.355 57.895 0.00 5.18 45.46 4.63
4602 5218 2.018644 GCTTGAATCTCGGGGAATGCA 61.019 52.381 0.00 0.00 0.00 3.96
4643 5269 4.889112 ATCTGGCATGGCAGGGCG 62.889 66.667 39.38 21.85 0.00 6.13
4654 5280 2.665000 CAGGGCGTGTCCTGTGAT 59.335 61.111 12.38 0.00 46.89 3.06
4655 5281 1.742880 CAGGGCGTGTCCTGTGATG 60.743 63.158 12.38 0.00 46.89 3.07
4664 5290 0.037326 GTCCTGTGATGGACGCTTGA 60.037 55.000 0.00 0.00 45.69 3.02
4677 5303 3.546670 GGACGCTTGACTAAGTTGATACG 59.453 47.826 0.00 0.00 36.27 3.06
4722 5348 5.012239 AGTCACAGCCATATGTCATGTTTT 58.988 37.500 1.24 0.00 0.00 2.43
4732 5362 7.598493 GCCATATGTCATGTTTTTGTTAGTTGT 59.402 33.333 1.24 0.00 0.00 3.32
4733 5363 8.914654 CCATATGTCATGTTTTTGTTAGTTGTG 58.085 33.333 1.24 0.00 0.00 3.33
4734 5364 8.914654 CATATGTCATGTTTTTGTTAGTTGTGG 58.085 33.333 0.00 0.00 0.00 4.17
4735 5365 6.274157 TGTCATGTTTTTGTTAGTTGTGGT 57.726 33.333 0.00 0.00 0.00 4.16
4736 5366 6.692486 TGTCATGTTTTTGTTAGTTGTGGTT 58.308 32.000 0.00 0.00 0.00 3.67
4737 5367 6.587990 TGTCATGTTTTTGTTAGTTGTGGTTG 59.412 34.615 0.00 0.00 0.00 3.77
4739 5369 5.470047 TGTTTTTGTTAGTTGTGGTTGGT 57.530 34.783 0.00 0.00 0.00 3.67
4740 5370 6.585695 TGTTTTTGTTAGTTGTGGTTGGTA 57.414 33.333 0.00 0.00 0.00 3.25
4741 5371 6.989659 TGTTTTTGTTAGTTGTGGTTGGTAA 58.010 32.000 0.00 0.00 0.00 2.85
4742 5372 6.867293 TGTTTTTGTTAGTTGTGGTTGGTAAC 59.133 34.615 0.00 0.00 0.00 2.50
4850 5519 5.242615 TGGCAGCACTACATTTTTCATGTAA 59.757 36.000 0.00 0.00 34.50 2.41
4873 5542 0.036164 TGGCTGTGCGATAAACAGGT 59.964 50.000 5.78 0.00 44.29 4.00
4892 5561 2.166254 GGTAACATGTTGCCTGATTGGG 59.834 50.000 31.50 0.00 41.35 4.12
4950 5620 3.947834 ACCTATCCTGCACACTAATTTGC 59.052 43.478 0.00 0.00 39.33 3.68
4963 5633 8.871862 GCACACTAATTTGCAAAATGAATCATA 58.128 29.630 17.19 0.00 38.68 2.15
4971 5641 4.222366 TGCAAAATGAATCATAGGCCAACA 59.778 37.500 5.01 0.00 0.00 3.33
4990 5660 1.343789 CAATTCAACCCCACATGCACA 59.656 47.619 0.00 0.00 0.00 4.57
5016 5686 1.969208 TCAAAGCCATTGTGCCAATCA 59.031 42.857 0.34 0.00 40.11 2.57
5046 5716 1.144969 CAAGCGTCGAAAAGCACCTA 58.855 50.000 10.68 0.00 35.48 3.08
5076 5746 5.519206 CCTCAAGTTAGAGCATACGGTTTAC 59.481 44.000 0.00 0.00 34.26 2.01
5099 5769 4.142988 CGCCACACGTGTTCATATTTACTT 60.143 41.667 20.79 0.00 36.87 2.24
5124 5794 6.397272 TGATGATGAAAATTTACCAACAGGC 58.603 36.000 0.00 0.00 0.00 4.85
5125 5795 5.798125 TGATGAAAATTTACCAACAGGCA 57.202 34.783 0.00 0.00 0.00 4.75
5128 5798 5.195001 TGAAAATTTACCAACAGGCAGAC 57.805 39.130 0.00 0.00 0.00 3.51
5196 5866 0.869730 ACAATAACGTGTTCACCGCC 59.130 50.000 0.00 0.00 0.00 6.13
5212 5882 3.126171 CACCGCCAAATGTTTCGATTCTA 59.874 43.478 0.00 0.00 0.00 2.10
5251 5942 3.194755 TGTAACAGGATCGAAGCAGCTAA 59.805 43.478 0.00 0.00 0.00 3.09
5269 5960 6.581542 GCAGCTAAGATATCAATTGATTGCAC 59.418 38.462 25.26 13.90 37.68 4.57
5332 6023 2.247637 CTGTCTGCATTGCATTCAACG 58.752 47.619 12.53 0.00 38.13 4.10
5360 6151 0.110486 AAACAGGGGCACACCTACAG 59.890 55.000 0.00 0.00 39.34 2.74
5424 6225 0.959372 CCAGCCAAGGAGAACAGCAG 60.959 60.000 0.00 0.00 0.00 4.24
5440 6241 0.179034 GCAGAGCACCCAGGATAAGG 60.179 60.000 0.00 0.00 0.00 2.69
5444 6245 4.540153 CACCCAGGATAAGGTGCG 57.460 61.111 0.00 0.00 46.55 5.34
5467 6268 6.037172 GCGTACTGGATCAAGATTTACATGTT 59.963 38.462 2.30 0.00 0.00 2.71
5468 6269 7.414098 GCGTACTGGATCAAGATTTACATGTTT 60.414 37.037 2.30 0.00 0.00 2.83
5487 6291 8.043710 ACATGTTTTTGATAACCACTGGAAAAA 58.956 29.630 0.71 1.45 0.00 1.94
5488 6292 9.054922 CATGTTTTTGATAACCACTGGAAAAAT 57.945 29.630 0.71 0.00 0.00 1.82
5489 6293 8.430801 TGTTTTTGATAACCACTGGAAAAATG 57.569 30.769 0.71 0.00 0.00 2.32
5490 6294 8.260818 TGTTTTTGATAACCACTGGAAAAATGA 58.739 29.630 0.71 0.00 0.00 2.57
5491 6295 9.271828 GTTTTTGATAACCACTGGAAAAATGAT 57.728 29.630 0.71 0.00 0.00 2.45
5512 6316 6.074648 TGATTTTTAACATGACAGGGAAGGT 58.925 36.000 0.00 0.00 0.00 3.50
5530 6334 6.826741 GGGAAGGTAGACAGCAAACAATATAA 59.173 38.462 0.00 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 8.760980 ACAATTATTTAATTACTAGGCAGCCA 57.239 30.769 15.80 0.00 34.36 4.75
182 200 8.523464 CATTTTAAAAATCAAGCGTCGGATTAG 58.477 33.333 4.44 0.00 33.57 1.73
184 202 6.866248 ACATTTTAAAAATCAAGCGTCGGATT 59.134 30.769 4.44 0.00 35.34 3.01
187 205 6.446659 AACATTTTAAAAATCAAGCGTCGG 57.553 33.333 4.44 0.00 0.00 4.79
202 220 7.948137 GCAACTATCAATGCGAAAACATTTTA 58.052 30.769 0.00 0.00 38.19 1.52
214 232 3.594312 GTTCGTACGCAACTATCAATGC 58.406 45.455 11.24 0.00 39.17 3.56
265 283 4.395625 CATCAACCACATGGCATCTCTAT 58.604 43.478 0.00 0.00 39.32 1.98
272 290 1.303155 TCGCATCAACCACATGGCA 60.303 52.632 0.00 0.00 39.32 4.92
273 291 1.430632 CTCGCATCAACCACATGGC 59.569 57.895 0.00 0.00 39.32 4.40
274 292 0.677731 ACCTCGCATCAACCACATGG 60.678 55.000 0.00 0.00 42.17 3.66
275 293 0.448990 CACCTCGCATCAACCACATG 59.551 55.000 0.00 0.00 0.00 3.21
284 302 5.859114 CACACTCTTATATACACCTCGCATC 59.141 44.000 0.00 0.00 0.00 3.91
287 305 3.982058 GCACACTCTTATATACACCTCGC 59.018 47.826 0.00 0.00 0.00 5.03
288 306 5.440234 AGCACACTCTTATATACACCTCG 57.560 43.478 0.00 0.00 0.00 4.63
291 309 4.982916 CCGAAGCACACTCTTATATACACC 59.017 45.833 0.00 0.00 0.00 4.16
294 312 4.617959 TGCCGAAGCACACTCTTATATAC 58.382 43.478 0.00 0.00 46.52 1.47
316 334 5.128171 AGCTTGCATTGTCCAATATTCACAT 59.872 36.000 0.00 0.00 0.00 3.21
324 342 1.470098 GTCGAGCTTGCATTGTCCAAT 59.530 47.619 0.00 0.00 0.00 3.16
340 358 1.001624 CGATTGCATGAGCTTGTCGA 58.998 50.000 0.00 0.00 42.74 4.20
341 359 1.001624 TCGATTGCATGAGCTTGTCG 58.998 50.000 0.00 0.00 42.74 4.35
354 380 3.436704 ACACCATACAAAGCAGTCGATTG 59.563 43.478 3.12 3.12 0.00 2.67
355 381 3.674997 ACACCATACAAAGCAGTCGATT 58.325 40.909 0.00 0.00 0.00 3.34
360 386 4.202357 TGAGAGAACACCATACAAAGCAGT 60.202 41.667 0.00 0.00 0.00 4.40
364 390 7.496529 TTTCTTGAGAGAACACCATACAAAG 57.503 36.000 0.00 0.00 41.46 2.77
395 422 9.667107 AGAAGATGAATTGAATTAACCGAAGTA 57.333 29.630 0.00 0.00 0.00 2.24
397 424 7.912250 CCAGAAGATGAATTGAATTAACCGAAG 59.088 37.037 0.00 0.00 0.00 3.79
401 437 9.710900 AAAACCAGAAGATGAATTGAATTAACC 57.289 29.630 0.00 0.00 0.00 2.85
439 475 6.270064 ACATCGTTTTGAATTTCGGTTTCTT 58.730 32.000 0.00 0.00 0.00 2.52
441 477 5.164320 CGACATCGTTTTGAATTTCGGTTTC 60.164 40.000 0.00 0.00 34.11 2.78
487 536 5.163844 CCAAAAACAAATCGAACCGGTTTTT 60.164 36.000 23.22 15.28 46.56 1.94
488 537 4.330347 CCAAAAACAAATCGAACCGGTTTT 59.670 37.500 23.22 9.30 38.14 2.43
489 538 3.866327 CCAAAAACAAATCGAACCGGTTT 59.134 39.130 23.22 1.93 41.00 3.27
490 539 3.449632 CCAAAAACAAATCGAACCGGTT 58.550 40.909 22.50 22.50 0.00 4.44
491 540 2.800273 GCCAAAAACAAATCGAACCGGT 60.800 45.455 0.00 0.00 0.00 5.28
492 541 1.790043 GCCAAAAACAAATCGAACCGG 59.210 47.619 0.00 0.00 0.00 5.28
504 553 5.123027 TGAACTCAAAAACCATGCCAAAAAC 59.877 36.000 0.00 0.00 0.00 2.43
561 629 6.492007 TTCTGTGCATTCTCATTCTTTCTC 57.508 37.500 0.00 0.00 0.00 2.87
562 630 6.657966 TCATTCTGTGCATTCTCATTCTTTCT 59.342 34.615 0.00 0.00 0.00 2.52
563 631 6.849502 TCATTCTGTGCATTCTCATTCTTTC 58.150 36.000 0.00 0.00 0.00 2.62
564 632 6.127703 CCTCATTCTGTGCATTCTCATTCTTT 60.128 38.462 0.00 0.00 0.00 2.52
565 633 5.357314 CCTCATTCTGTGCATTCTCATTCTT 59.643 40.000 0.00 0.00 0.00 2.52
584 653 2.688666 TTGGGCTCGCCTCCTCAT 60.689 61.111 8.00 0.00 36.10 2.90
602 854 2.359975 GGGAAGGCAACGTCTGGG 60.360 66.667 0.00 0.00 45.21 4.45
606 859 2.943653 CGTTGGGAAGGCAACGTC 59.056 61.111 0.92 0.00 46.04 4.34
628 883 0.826256 GTCCTGGGCCTTCCGTTTTT 60.826 55.000 4.53 0.00 38.76 1.94
629 884 1.228459 GTCCTGGGCCTTCCGTTTT 60.228 57.895 4.53 0.00 38.76 2.43
630 885 2.434774 GTCCTGGGCCTTCCGTTT 59.565 61.111 4.53 0.00 38.76 3.60
636 891 3.090532 GGATCCGTCCTGGGCCTT 61.091 66.667 4.53 0.00 41.60 4.35
644 899 2.351336 ATTCGCGTCAGGATCCGTCC 62.351 60.000 5.77 0.00 45.45 4.79
650 905 1.659098 GTTTCGAATTCGCGTCAGGAT 59.341 47.619 22.90 0.00 39.60 3.24
683 938 1.021920 GGAGGAAGAAGGAACTGCGC 61.022 60.000 0.00 0.00 40.58 6.09
685 940 0.034960 GGGGAGGAAGAAGGAACTGC 60.035 60.000 0.00 0.00 40.86 4.40
686 941 0.250513 CGGGGAGGAAGAAGGAACTG 59.749 60.000 0.00 0.00 40.86 3.16
687 942 0.910088 CCGGGGAGGAAGAAGGAACT 60.910 60.000 0.00 0.00 45.00 3.01
689 944 4.147135 CCGGGGAGGAAGAAGGAA 57.853 61.111 0.00 0.00 45.00 3.36
744 1003 4.570874 GGGGAGGGAGGCGATTGC 62.571 72.222 0.00 0.00 41.71 3.56
745 1004 1.999634 AATGGGGAGGGAGGCGATTG 62.000 60.000 0.00 0.00 0.00 2.67
746 1005 1.697754 AATGGGGAGGGAGGCGATT 60.698 57.895 0.00 0.00 0.00 3.34
747 1006 2.039405 AATGGGGAGGGAGGCGAT 60.039 61.111 0.00 0.00 0.00 4.58
748 1007 2.768344 GAATGGGGAGGGAGGCGA 60.768 66.667 0.00 0.00 0.00 5.54
750 1009 2.316586 TTGGAATGGGGAGGGAGGC 61.317 63.158 0.00 0.00 0.00 4.70
751 1010 1.615262 GTTGGAATGGGGAGGGAGG 59.385 63.158 0.00 0.00 0.00 4.30
752 1011 1.615262 GGTTGGAATGGGGAGGGAG 59.385 63.158 0.00 0.00 0.00 4.30
753 1012 1.933812 GGGTTGGAATGGGGAGGGA 60.934 63.158 0.00 0.00 0.00 4.20
754 1013 1.593166 ATGGGTTGGAATGGGGAGGG 61.593 60.000 0.00 0.00 0.00 4.30
755 1014 0.339510 AATGGGTTGGAATGGGGAGG 59.660 55.000 0.00 0.00 0.00 4.30
756 1015 2.110578 GAAATGGGTTGGAATGGGGAG 58.889 52.381 0.00 0.00 0.00 4.30
757 1016 1.434773 TGAAATGGGTTGGAATGGGGA 59.565 47.619 0.00 0.00 0.00 4.81
758 1017 1.949799 TGAAATGGGTTGGAATGGGG 58.050 50.000 0.00 0.00 0.00 4.96
759 1018 4.019501 TGATTTGAAATGGGTTGGAATGGG 60.020 41.667 0.00 0.00 0.00 4.00
760 1019 5.163281 TGATTTGAAATGGGTTGGAATGG 57.837 39.130 0.00 0.00 0.00 3.16
761 1020 6.072563 GGTTTGATTTGAAATGGGTTGGAATG 60.073 38.462 0.00 0.00 0.00 2.67
762 1021 6.003326 GGTTTGATTTGAAATGGGTTGGAAT 58.997 36.000 0.00 0.00 0.00 3.01
763 1022 5.131809 AGGTTTGATTTGAAATGGGTTGGAA 59.868 36.000 0.00 0.00 0.00 3.53
764 1023 4.657969 AGGTTTGATTTGAAATGGGTTGGA 59.342 37.500 0.00 0.00 0.00 3.53
879 1374 4.969196 CTCACCAGTGTGCGGCGT 62.969 66.667 9.37 0.00 42.46 5.68
933 1429 1.709994 GGGGATCAGTTAGGGCCTGG 61.710 65.000 18.53 2.95 0.00 4.45
1013 1515 1.393746 TCCATCTGGAGGAGCTGGT 59.606 57.895 0.00 0.00 38.85 4.00
1400 1977 4.071423 TGTACACTGCACACAATTAGCAT 58.929 39.130 0.00 0.00 37.68 3.79
1468 2045 9.668497 GAGTTAAGTTCCTAACACAATTAGGAT 57.332 33.333 14.60 4.84 46.98 3.24
1502 2079 0.525668 CTAACGTAGCTGACCTGCCG 60.526 60.000 0.00 0.00 0.00 5.69
1504 2081 2.649331 TTCTAACGTAGCTGACCTGC 57.351 50.000 0.00 0.00 0.00 4.85
1509 2086 4.181578 GCAGGAATTTCTAACGTAGCTGA 58.818 43.478 0.00 0.00 0.00 4.26
1510 2087 3.000322 CGCAGGAATTTCTAACGTAGCTG 60.000 47.826 0.00 0.00 0.00 4.24
1511 2088 3.119245 TCGCAGGAATTTCTAACGTAGCT 60.119 43.478 7.91 0.00 0.00 3.32
1512 2089 3.184541 TCGCAGGAATTTCTAACGTAGC 58.815 45.455 7.91 0.00 0.00 3.58
1513 2090 3.797256 CCTCGCAGGAATTTCTAACGTAG 59.203 47.826 7.91 5.18 37.67 3.51
1529 2116 3.695606 GGCTGTCCTGTCCTCGCA 61.696 66.667 0.00 0.00 0.00 5.10
1532 2119 0.177604 CAGATGGCTGTCCTGTCCTC 59.822 60.000 0.00 0.00 37.37 3.71
1533 2120 2.294890 CAGATGGCTGTCCTGTCCT 58.705 57.895 0.00 0.00 37.37 3.85
1534 2121 4.950479 CAGATGGCTGTCCTGTCC 57.050 61.111 0.00 0.00 37.37 4.02
1543 2130 5.594317 ACAGAAGTAACAAAAACAGATGGCT 59.406 36.000 0.00 0.00 0.00 4.75
1544 2131 5.831997 ACAGAAGTAACAAAAACAGATGGC 58.168 37.500 0.00 0.00 0.00 4.40
1545 2132 6.912591 GTGACAGAAGTAACAAAAACAGATGG 59.087 38.462 0.00 0.00 0.00 3.51
1546 2133 7.697691 AGTGACAGAAGTAACAAAAACAGATG 58.302 34.615 0.00 0.00 30.87 2.90
1547 2134 7.865706 AGTGACAGAAGTAACAAAAACAGAT 57.134 32.000 0.00 0.00 30.87 2.90
1548 2135 7.389330 TGAAGTGACAGAAGTAACAAAAACAGA 59.611 33.333 0.00 0.00 30.87 3.41
1549 2136 7.526608 TGAAGTGACAGAAGTAACAAAAACAG 58.473 34.615 0.00 0.00 30.87 3.16
1550 2137 7.441890 TGAAGTGACAGAAGTAACAAAAACA 57.558 32.000 0.00 0.00 30.87 2.83
1570 2157 6.238511 CCTGCTTTCTCATCAGATGAATGAAG 60.239 42.308 14.25 16.42 39.11 3.02
1617 2204 9.807649 GAGAACTGGTGCATTTATTTATTTGAT 57.192 29.630 0.00 0.00 0.00 2.57
1643 2242 4.637483 CATACTTGCAAACACCTATGGG 57.363 45.455 0.00 0.00 38.88 4.00
1692 2291 5.013079 TGGAATCACTACCATTCTGAACACT 59.987 40.000 0.00 0.00 31.82 3.55
1694 2293 5.497464 TGGAATCACTACCATTCTGAACA 57.503 39.130 0.00 0.00 31.82 3.18
1700 2299 5.067805 GGATTGGTTGGAATCACTACCATTC 59.932 44.000 13.18 13.18 40.16 2.67
1726 2325 2.360844 GAGCCTTAGTTTTCCTCTGCC 58.639 52.381 0.00 0.00 0.00 4.85
1886 2485 4.326278 GCGCCAAGCCTTTAAAATTAGTTC 59.674 41.667 0.00 0.00 40.81 3.01
1967 2566 2.489938 AAGCCGCATCCTTTCTGTTA 57.510 45.000 0.00 0.00 0.00 2.41
1981 2580 0.819582 TTAGTTCCTCCCGTAAGCCG 59.180 55.000 0.00 0.00 0.00 5.52
2018 2617 6.471146 CCTTTCTCTTCTTCATCTCTTCCAA 58.529 40.000 0.00 0.00 0.00 3.53
2043 2642 5.819379 TCAAGAATCTGATTCCATCTTTCGG 59.181 40.000 23.12 3.83 40.13 4.30
2232 2831 2.899303 AATCAGTGGGTACAAAGGGG 57.101 50.000 0.00 0.00 0.00 4.79
2261 2860 5.355596 ACAGAGCTAGCATATGTGAGAAAC 58.644 41.667 18.83 0.00 0.00 2.78
2564 3163 2.236395 GAGCTAACAGAGTTAAGGGCCA 59.764 50.000 6.18 0.00 0.00 5.36
2587 3186 3.128589 AGACGAGAGATCTTGAAGCTGTC 59.871 47.826 0.00 0.00 30.65 3.51
2799 3398 7.348080 TCAACGAATATCATCTCCACTAAGT 57.652 36.000 0.00 0.00 0.00 2.24
2819 3418 2.935201 CTCAGCTTCTACCTGCATCAAC 59.065 50.000 0.00 0.00 0.00 3.18
2844 3443 2.346766 TTCAGTTGCTCAAGCCTCAA 57.653 45.000 0.00 0.00 41.18 3.02
2992 3591 7.323656 CCAAAGCATGTTAGAAAACTAGAAACG 59.676 37.037 0.00 0.00 36.51 3.60
3040 3639 7.498570 TGCAGCAAAGAAATTTACAGGAAAAAT 59.501 29.630 0.00 0.00 0.00 1.82
3141 3740 7.167924 TCAATAGCACCTGCAATGAAATAAA 57.832 32.000 0.00 0.00 45.16 1.40
3144 3743 5.221382 GGATCAATAGCACCTGCAATGAAAT 60.221 40.000 0.00 0.00 45.16 2.17
3561 4176 6.115450 AGAACTTTGTTTGTAAGAACGTCC 57.885 37.500 0.00 0.00 32.18 4.79
3638 4253 6.039717 ACACACAAGAACAGCAGTGAAATTAT 59.960 34.615 0.00 0.00 35.97 1.28
3673 4288 9.607988 TGAACTTTTGACAGTATAGAAACAGAA 57.392 29.630 0.00 0.00 0.00 3.02
3787 4402 9.869757 GTTAAGCAAAATATGAATACCCTTTGT 57.130 29.630 0.00 0.00 0.00 2.83
3987 4603 1.373435 CTCCGGTTTGTACCAGCCA 59.627 57.895 0.00 0.00 45.31 4.75
4406 5022 1.359475 GTCATCGGCGTCCTAGGAC 59.641 63.158 29.18 29.18 41.40 3.85
4474 5090 2.346739 GCAGACAGGTGCAGCTCT 59.653 61.111 17.16 8.77 43.41 4.09
4476 5092 3.873026 GACGCAGACAGGTGCAGCT 62.873 63.158 13.85 13.85 44.21 4.24
4578 5194 2.125147 CCCGAGATTCAAGCGGCA 60.125 61.111 1.45 0.00 43.52 5.69
4588 5204 1.414181 CTACACTGCATTCCCCGAGAT 59.586 52.381 0.00 0.00 0.00 2.75
4594 5210 1.486726 AGCTACCTACACTGCATTCCC 59.513 52.381 0.00 0.00 0.00 3.97
4602 5218 5.715279 TGACATACTTTCAGCTACCTACACT 59.285 40.000 0.00 0.00 0.00 3.55
4648 5274 2.654749 TAGTCAAGCGTCCATCACAG 57.345 50.000 0.00 0.00 0.00 3.66
4654 5280 3.678056 ATCAACTTAGTCAAGCGTCCA 57.322 42.857 0.00 0.00 34.94 4.02
4655 5281 3.546670 CGTATCAACTTAGTCAAGCGTCC 59.453 47.826 0.00 0.00 34.94 4.79
4664 5290 3.906720 ATGTGCCCGTATCAACTTAGT 57.093 42.857 0.00 0.00 0.00 2.24
4677 5303 5.066505 ACTTCGATCAGAAAAATATGTGCCC 59.933 40.000 0.00 0.00 38.57 5.36
4734 5364 5.117592 CCGTCGATATAATTCGGTTACCAAC 59.882 44.000 1.13 0.00 39.56 3.77
4735 5365 5.009510 TCCGTCGATATAATTCGGTTACCAA 59.990 40.000 1.13 0.00 41.58 3.67
4736 5366 4.518590 TCCGTCGATATAATTCGGTTACCA 59.481 41.667 1.13 0.00 41.58 3.25
4737 5367 5.046910 TCCGTCGATATAATTCGGTTACC 57.953 43.478 8.05 0.00 41.58 2.85
4739 5369 5.947228 ACTCCGTCGATATAATTCGGTTA 57.053 39.130 8.05 0.00 41.58 2.85
4740 5370 4.843220 ACTCCGTCGATATAATTCGGTT 57.157 40.909 8.05 0.00 41.58 4.44
4741 5371 4.543692 CAACTCCGTCGATATAATTCGGT 58.456 43.478 8.05 0.00 41.58 4.69
4742 5372 3.364023 GCAACTCCGTCGATATAATTCGG 59.636 47.826 2.21 2.21 39.56 4.30
4743 5373 3.057739 CGCAACTCCGTCGATATAATTCG 59.942 47.826 0.00 0.00 40.46 3.34
4744 5374 3.364023 CCGCAACTCCGTCGATATAATTC 59.636 47.826 0.00 0.00 0.00 2.17
4746 5376 2.555325 TCCGCAACTCCGTCGATATAAT 59.445 45.455 0.00 0.00 0.00 1.28
4748 5378 1.596603 TCCGCAACTCCGTCGATATA 58.403 50.000 0.00 0.00 0.00 0.86
4749 5379 0.742505 TTCCGCAACTCCGTCGATAT 59.257 50.000 0.00 0.00 0.00 1.63
4751 5381 1.445582 GTTCCGCAACTCCGTCGAT 60.446 57.895 0.00 0.00 0.00 3.59
4765 5434 6.026947 AGCAACACGGATATATAGAGTTCC 57.973 41.667 0.00 0.00 0.00 3.62
4766 5435 6.924060 ACAAGCAACACGGATATATAGAGTTC 59.076 38.462 0.00 0.00 0.00 3.01
4775 5444 8.342634 GTTTAATATCACAAGCAACACGGATAT 58.657 33.333 0.00 0.00 31.27 1.63
4782 5451 7.445707 TGTGTAGGTTTAATATCACAAGCAACA 59.554 33.333 0.00 0.00 33.81 3.33
4834 5503 5.092781 GCCACGGTTACATGAAAAATGTAG 58.907 41.667 0.00 0.00 36.09 2.74
4850 5519 1.004320 TTTATCGCACAGCCACGGT 60.004 52.632 0.00 0.00 0.00 4.83
4873 5542 3.355378 CTCCCAATCAGGCAACATGTTA 58.645 45.455 11.53 0.00 41.41 2.41
4892 5561 2.508526 ACTGGTTTCTGCATTCACCTC 58.491 47.619 9.16 0.00 0.00 3.85
4940 5610 8.545420 GCCTATGATTCATTTTGCAAATTAGTG 58.455 33.333 13.65 9.88 0.00 2.74
4950 5620 7.549842 TGAATTGTTGGCCTATGATTCATTTTG 59.450 33.333 17.65 0.00 30.93 2.44
4963 5633 0.105246 TGGGGTTGAATTGTTGGCCT 60.105 50.000 3.32 0.00 0.00 5.19
4971 5641 1.714541 TGTGCATGTGGGGTTGAATT 58.285 45.000 0.00 0.00 0.00 2.17
5046 5716 5.869888 CGTATGCTCTAACTTGAGGAAACTT 59.130 40.000 0.00 0.00 44.43 2.66
5080 5750 8.317891 TCATCAAAGTAAATATGAACACGTGT 57.682 30.769 17.22 17.22 0.00 4.49
5082 5752 9.161629 TCATCATCAAAGTAAATATGAACACGT 57.838 29.630 0.00 0.00 32.47 4.49
5099 5769 6.873076 GCCTGTTGGTAAATTTTCATCATCAA 59.127 34.615 0.00 0.00 35.27 2.57
5117 5787 3.340928 TGAATCATCAGTCTGCCTGTTG 58.659 45.455 0.00 0.00 42.19 3.33
5124 5794 5.870433 GCAGAGGATATGAATCATCAGTCTG 59.130 44.000 15.04 15.04 43.76 3.51
5125 5795 5.781306 AGCAGAGGATATGAATCATCAGTCT 59.219 40.000 0.00 0.00 43.76 3.24
5128 5798 6.935208 TGAAAGCAGAGGATATGAATCATCAG 59.065 38.462 0.00 0.00 43.76 2.90
5184 5854 0.030101 AACATTTGGCGGTGAACACG 59.970 50.000 0.00 0.00 0.00 4.49
5196 5866 6.912591 GCTGGGTATTAGAATCGAAACATTTG 59.087 38.462 0.00 0.00 0.00 2.32
5212 5882 5.329399 TGTTACAATTCCTTGCTGGGTATT 58.671 37.500 0.00 0.00 35.69 1.89
5251 5942 8.162085 AGATAGGTGTGCAATCAATTGATATCT 58.838 33.333 21.00 17.14 40.14 1.98
5307 5998 3.455469 GCAATGCAGACAGGGGCC 61.455 66.667 0.00 0.00 0.00 5.80
5332 6023 2.650778 CCCCTGTTTTGAAGCGCC 59.349 61.111 2.29 0.00 0.00 6.53
5360 6151 1.377536 GAGCTCCAGAAGTCCAATGC 58.622 55.000 0.87 0.00 0.00 3.56
5424 6225 3.788672 CACCTTATCCTGGGTGCTC 57.211 57.895 0.00 0.00 44.94 4.26
5440 6241 4.868171 TGTAAATCTTGATCCAGTACGCAC 59.132 41.667 0.00 0.00 0.00 5.34
5442 6243 5.523916 ACATGTAAATCTTGATCCAGTACGC 59.476 40.000 0.00 0.00 0.00 4.42
5467 6268 9.844257 AAATCATTTTTCCAGTGGTTATCAAAA 57.156 25.926 9.54 5.35 0.00 2.44
5468 6269 9.844257 AAAATCATTTTTCCAGTGGTTATCAAA 57.156 25.926 9.54 0.00 28.82 2.69
5487 6291 6.725834 ACCTTCCCTGTCATGTTAAAAATCAT 59.274 34.615 0.00 0.00 0.00 2.45
5488 6292 6.074648 ACCTTCCCTGTCATGTTAAAAATCA 58.925 36.000 0.00 0.00 0.00 2.57
5489 6293 6.590234 ACCTTCCCTGTCATGTTAAAAATC 57.410 37.500 0.00 0.00 0.00 2.17
5490 6294 7.393515 GTCTACCTTCCCTGTCATGTTAAAAAT 59.606 37.037 0.00 0.00 0.00 1.82
5491 6295 6.713450 GTCTACCTTCCCTGTCATGTTAAAAA 59.287 38.462 0.00 0.00 0.00 1.94
5512 6316 8.717821 GTTGTGTCTTATATTGTTTGCTGTCTA 58.282 33.333 0.00 0.00 0.00 2.59
5530 6334 4.607293 TCTCTGTGCATTAGTTGTGTCT 57.393 40.909 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.