Multiple sequence alignment - TraesCS3B01G245200

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 TraesCS3B01G245200 chr3B 100.000 4609 0 0 1 4609 389255283 389259891 0.000000e+00 8512.0
1 TraesCS3B01G245200 chr3B 87.755 147 14 3 4345 4488 478986781 478986926 7.930000e-38 169.0
2 TraesCS3B01G245200 chr3B 85.227 88 6 2 4202 4289 714048548 714048628 2.960000e-12 84.2
3 TraesCS3B01G245200 chr3B 85.227 88 6 2 4202 4289 714106423 714106503 2.960000e-12 84.2
4 TraesCS3B01G245200 chr3B 92.308 39 3 0 723 761 413835566 413835604 6.440000e-04 56.5
5 TraesCS3B01G245200 chr3D 95.819 3444 79 18 768 4198 295136926 295140317 0.000000e+00 5502.0
6 TraesCS3B01G245200 chr3D 92.026 765 51 6 1 756 295136031 295136794 0.000000e+00 1066.0
7 TraesCS3B01G245200 chr3D 89.189 148 10 5 4345 4488 595108431 595108576 3.660000e-41 180.0
8 TraesCS3B01G245200 chr3D 87.838 148 12 3 4344 4488 384654496 384654352 7.930000e-38 169.0
9 TraesCS3B01G245200 chr3D 92.661 109 8 0 1 109 275910731 275910839 1.720000e-34 158.0
10 TraesCS3B01G245200 chr3D 93.976 83 3 2 4527 4609 295140461 295140541 1.740000e-24 124.0
11 TraesCS3B01G245200 chr3D 98.182 55 1 0 4292 4346 295140406 295140460 3.800000e-16 97.1
12 TraesCS3B01G245200 chr3D 92.063 63 5 0 4224 4286 508385267 508385205 6.350000e-14 89.8
13 TraesCS3B01G245200 chr3D 85.882 85 6 3 4202 4286 228297098 228297176 8.220000e-13 86.1
14 TraesCS3B01G245200 chr3D 85.714 84 6 4 4202 4285 490039691 490039614 2.960000e-12 84.2
15 TraesCS3B01G245200 chr3A 96.729 1926 29 6 2089 3998 392779365 392781272 0.000000e+00 3177.0
16 TraesCS3B01G245200 chr3A 98.112 1324 25 0 770 2093 392777941 392779264 0.000000e+00 2307.0
17 TraesCS3B01G245200 chr3A 90.196 408 31 3 1 406 392777091 392777491 1.470000e-144 523.0
18 TraesCS3B01G245200 chr3A 92.562 121 8 1 3971 4090 392781272 392781392 6.130000e-39 172.0
19 TraesCS3B01G245200 chr3A 93.458 107 7 0 3 109 621697095 621696989 4.770000e-35 159.0
20 TraesCS3B01G245200 chrUn 92.424 132 9 1 4357 4488 57550167 57550037 2.190000e-43 187.0
21 TraesCS3B01G245200 chr7B 90.909 132 10 2 4357 4488 722225199 722225070 4.740000e-40 176.0
22 TraesCS3B01G245200 chr7B 86.486 74 10 0 4224 4297 618673663 618673590 1.060000e-11 82.4
23 TraesCS3B01G245200 chr7B 90.000 50 4 1 726 775 612297829 612297781 3.850000e-06 63.9
24 TraesCS3B01G245200 chr2A 90.909 132 10 2 4357 4488 279427797 279427926 4.740000e-40 176.0
25 TraesCS3B01G245200 chr2A 87.037 108 10 4 1111 1216 765080009 765080114 8.100000e-23 119.0
26 TraesCS3B01G245200 chr4B 88.514 148 11 5 4345 4488 152734084 152734229 1.700000e-39 174.0
27 TraesCS3B01G245200 chr4B 93.694 111 7 0 1 111 362185685 362185795 2.850000e-37 167.0
28 TraesCS3B01G245200 chr5A 93.860 114 7 0 1 114 353866095 353865982 6.130000e-39 172.0
29 TraesCS3B01G245200 chr2B 90.152 132 12 1 4357 4488 658489644 658489774 2.210000e-38 171.0
30 TraesCS3B01G245200 chr2B 86.486 74 10 0 4224 4297 215034855 215034782 1.060000e-11 82.4
31 TraesCS3B01G245200 chr7D 87.755 147 13 5 4345 4488 595719583 595719439 2.850000e-37 167.0
32 TraesCS3B01G245200 chr7D 92.793 111 8 0 1 111 367581851 367581741 1.330000e-35 161.0
33 TraesCS3B01G245200 chr7D 88.889 108 8 4 1111 1216 66071721 66071826 3.740000e-26 130.0
34 TraesCS3B01G245200 chr5D 92.793 111 8 0 1 111 373723238 373723348 1.330000e-35 161.0
35 TraesCS3B01G245200 chr5D 91.892 111 9 0 1 111 464136146 464136036 6.170000e-34 156.0
36 TraesCS3B01G245200 chr5D 100.000 34 0 0 731 764 6520739 6520772 3.850000e-06 63.9
37 TraesCS3B01G245200 chr1D 92.793 111 8 0 1 111 371542003 371542113 1.330000e-35 161.0
38 TraesCS3B01G245200 chr1D 94.444 36 1 1 725 760 4765995 4766029 2.000000e-03 54.7
39 TraesCS3B01G245200 chr6B 88.889 108 8 4 1111 1216 675803944 675804049 3.740000e-26 130.0
40 TraesCS3B01G245200 chr6B 93.103 87 5 1 1134 1219 713229621 713229535 4.840000e-25 126.0
41 TraesCS3B01G245200 chr6B 92.857 84 5 1 1134 1216 676793118 676793201 2.250000e-23 121.0
42 TraesCS3B01G245200 chr6B 89.231 65 7 0 4224 4288 246296646 246296710 1.060000e-11 82.4
43 TraesCS3B01G245200 chr5B 88.288 111 9 4 1111 1219 16405992 16405884 3.740000e-26 130.0
44 TraesCS3B01G245200 chr5B 95.000 40 0 2 726 764 26604266 26604304 1.380000e-05 62.1
45 TraesCS3B01G245200 chr5B 92.500 40 3 0 726 765 336209780 336209741 1.790000e-04 58.4
46 TraesCS3B01G245200 chr6A 92.857 84 5 1 1134 1216 463741342 463741425 2.250000e-23 121.0
47 TraesCS3B01G245200 chr6A 96.774 31 1 0 340 370 581103350 581103380 8.000000e-03 52.8
48 TraesCS3B01G245200 chr2D 86.047 86 6 4 4202 4287 206685573 206685652 2.280000e-13 87.9
49 TraesCS3B01G245200 chr7A 92.683 41 1 2 726 765 706446506 706446545 1.790000e-04 58.4
50 TraesCS3B01G245200 chr6D 92.500 40 3 0 726 765 427567840 427567801 1.790000e-04 58.4


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 TraesCS3B01G245200 chr3B 389255283 389259891 4608 False 8512.000 8512 100.00000 1 4609 1 chr3B.!!$F1 4608
1 TraesCS3B01G245200 chr3D 295136031 295140541 4510 False 1697.275 5502 95.00075 1 4609 4 chr3D.!!$F4 4608
2 TraesCS3B01G245200 chr3A 392777091 392781392 4301 False 1544.750 3177 94.39975 1 4090 4 chr3A.!!$F1 4089

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
413 416 0.107643 TCGTCCATGTTGTGAGGCAA 59.892 50.0 0.00 0.0 34.16 4.52 F
557 560 1.144969 GGTCGTTGCGATGTGAAGAA 58.855 50.0 0.00 0.0 38.42 2.52 F
1583 1716 1.364626 CTCATGAAGGACGGCTGCAC 61.365 60.0 0.50 0.0 0.00 4.57 F
2995 3261 0.524862 GTCAAGCTGGCACCAGAATG 59.475 55.0 20.92 16.4 46.30 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2377 2643 1.582968 CATGGCCTGCACAACAGTC 59.417 57.895 3.32 0.0 45.68 3.51 R
2495 2761 2.373224 GCAAGGAATTGAGGAAGGAGG 58.627 52.381 0.00 0.0 0.00 4.30 R
3001 3267 0.307760 GTTTGCCGAGTTGGTCAGTG 59.692 55.000 0.00 0.0 41.21 3.66 R
4176 4497 0.530744 GATCACGACAGCCACCTACA 59.469 55.000 0.00 0.0 0.00 2.74 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
144 145 7.496920 CCTGCAATGACAGAGTTAGATTTATCA 59.503 37.037 6.31 0.00 40.25 2.15
215 216 6.895782 TGTTCCTCTATCGTTTATCCCATTT 58.104 36.000 0.00 0.00 0.00 2.32
225 226 7.605410 TCGTTTATCCCATTTGAGTTAACTC 57.395 36.000 25.73 25.73 43.15 3.01
237 238 8.709646 CATTTGAGTTAACTCTGTAGTGTTACC 58.290 37.037 30.47 6.22 43.25 2.85
240 241 8.332996 TGAGTTAACTCTGTAGTGTTACCTAG 57.667 38.462 30.47 0.00 43.25 3.02
247 248 7.789026 ACTCTGTAGTGTTACCTAGTTGTTTT 58.211 34.615 0.00 0.00 33.57 2.43
337 338 8.344831 TGCATCTTCAAGATAATTTATTCCGTG 58.655 33.333 0.00 0.00 32.12 4.94
413 416 0.107643 TCGTCCATGTTGTGAGGCAA 59.892 50.000 0.00 0.00 34.16 4.52
418 421 3.989817 GTCCATGTTGTGAGGCAATTTTC 59.010 43.478 0.00 0.00 39.55 2.29
543 546 1.227853 GACTGCTTGTTGGGGTCGT 60.228 57.895 0.00 0.00 0.00 4.34
557 560 1.144969 GGTCGTTGCGATGTGAAGAA 58.855 50.000 0.00 0.00 38.42 2.52
605 608 5.105752 GCTGTTGTGTTGACCAATTTAACA 58.894 37.500 0.00 0.00 32.39 2.41
614 617 8.183104 TGTTGACCAATTTAACAACATATGGA 57.817 30.769 7.80 0.00 44.50 3.41
681 685 9.491675 ACATAATGCTCATCAAATTTTGACAAA 57.508 25.926 13.80 0.00 43.48 2.83
687 691 8.143193 TGCTCATCAAATTTTGACAAATGTAGT 58.857 29.630 13.80 0.00 43.48 2.73
737 747 4.205587 AGATATGACGTACTTCCTCCGTT 58.794 43.478 0.00 0.00 34.51 4.44
789 922 2.131972 TCGTTCTGTGATCCAAACACG 58.868 47.619 0.00 0.00 40.61 4.49
829 962 3.450457 GTCAGTGTGATCCCTTCTCATCT 59.550 47.826 0.00 0.00 31.03 2.90
878 1011 2.368439 CCCGAGCATTTTGGATCTTCA 58.632 47.619 0.00 0.00 31.06 3.02
882 1015 4.409570 CGAGCATTTTGGATCTTCACTTG 58.590 43.478 0.00 0.00 0.00 3.16
1583 1716 1.364626 CTCATGAAGGACGGCTGCAC 61.365 60.000 0.50 0.00 0.00 4.57
1584 1717 1.376424 CATGAAGGACGGCTGCACT 60.376 57.895 0.50 0.00 0.00 4.40
1781 1914 2.159057 CCATGCCCTTATTGTTCCTTGC 60.159 50.000 0.00 0.00 0.00 4.01
1944 2077 3.945285 CGTTGCAGGGAACATAAATACCT 59.055 43.478 4.58 0.00 0.00 3.08
1945 2078 5.104859 TCGTTGCAGGGAACATAAATACCTA 60.105 40.000 4.58 0.00 0.00 3.08
1946 2079 5.236478 CGTTGCAGGGAACATAAATACCTAG 59.764 44.000 4.58 0.00 0.00 3.02
1947 2080 5.304686 TGCAGGGAACATAAATACCTAGG 57.695 43.478 7.41 7.41 0.00 3.02
1948 2081 4.972568 TGCAGGGAACATAAATACCTAGGA 59.027 41.667 17.98 0.00 0.00 2.94
1949 2082 5.430417 TGCAGGGAACATAAATACCTAGGAA 59.570 40.000 17.98 0.00 0.00 3.36
1950 2083 6.102615 TGCAGGGAACATAAATACCTAGGAAT 59.897 38.462 17.98 0.00 0.00 3.01
1951 2084 7.293771 TGCAGGGAACATAAATACCTAGGAATA 59.706 37.037 17.98 0.00 0.00 1.75
1952 2085 7.824779 GCAGGGAACATAAATACCTAGGAATAG 59.175 40.741 17.98 0.85 0.00 1.73
1953 2086 7.824779 CAGGGAACATAAATACCTAGGAATAGC 59.175 40.741 17.98 0.00 0.00 2.97
1954 2087 7.037514 AGGGAACATAAATACCTAGGAATAGCC 60.038 40.741 17.98 3.25 0.00 3.93
1955 2088 7.256908 GGGAACATAAATACCTAGGAATAGCCA 60.257 40.741 17.98 0.00 40.02 4.75
1956 2089 8.329502 GGAACATAAATACCTAGGAATAGCCAT 58.670 37.037 17.98 0.00 40.02 4.40
1957 2090 9.167311 GAACATAAATACCTAGGAATAGCCATG 57.833 37.037 17.98 11.51 40.02 3.66
1958 2091 8.449423 ACATAAATACCTAGGAATAGCCATGA 57.551 34.615 17.98 0.00 40.02 3.07
1959 2092 8.543774 ACATAAATACCTAGGAATAGCCATGAG 58.456 37.037 17.98 0.00 40.02 2.90
1960 2093 5.428184 AATACCTAGGAATAGCCATGAGC 57.572 43.478 17.98 0.00 44.25 4.26
1978 2131 2.941480 AGCAAATAGGCTCATCCCTTG 58.059 47.619 0.00 0.00 41.05 3.61
1985 2138 7.417797 GCAAATAGGCTCATCCCTTGAATTAAA 60.418 37.037 0.00 0.00 36.41 1.52
2011 2164 2.359975 GGGCTGCTTAGGCGTTGT 60.360 61.111 0.00 0.00 42.25 3.32
2133 2391 3.052869 AGGGGTCTTTCTTGTGGAAACTT 60.053 43.478 0.00 0.00 38.81 2.66
2135 2393 3.699538 GGGTCTTTCTTGTGGAAACTTGT 59.300 43.478 0.00 0.00 38.81 3.16
2226 2492 3.802866 TGCATACCATCTTTGCGATGTA 58.197 40.909 0.00 0.00 46.56 2.29
2377 2643 9.010029 ACCATGTTTACTTATTTTAGACCACAG 57.990 33.333 0.00 0.00 0.00 3.66
2449 2715 6.304126 CAGCATTTTCATTTGTTTGCAGATC 58.696 36.000 0.00 0.00 32.66 2.75
2450 2716 5.410439 AGCATTTTCATTTGTTTGCAGATCC 59.590 36.000 0.00 0.00 32.66 3.36
2495 2761 9.119329 CAATACTTGTCTATCTTCGTATAGTGC 57.881 37.037 0.00 0.00 32.31 4.40
2598 2864 8.467963 TTGAGTTGTGATGATGGCATTATTAT 57.532 30.769 6.18 0.00 34.11 1.28
2990 3256 2.031012 CTCGTCAAGCTGGCACCA 59.969 61.111 0.00 0.00 0.00 4.17
2991 3257 2.031012 TCGTCAAGCTGGCACCAG 59.969 61.111 12.54 12.54 46.15 4.00
2992 3258 2.031012 CGTCAAGCTGGCACCAGA 59.969 61.111 20.92 0.00 46.30 3.86
2993 3259 1.597854 CGTCAAGCTGGCACCAGAA 60.598 57.895 20.92 0.00 46.30 3.02
2994 3260 0.957395 CGTCAAGCTGGCACCAGAAT 60.957 55.000 20.92 4.97 46.30 2.40
2995 3261 0.524862 GTCAAGCTGGCACCAGAATG 59.475 55.000 20.92 16.40 46.30 2.67
3100 3366 8.259049 TGTCGATTTTAAGTAACAATAGGTGG 57.741 34.615 0.00 0.00 0.00 4.61
3124 3390 8.151596 TGGTTGTTATTGTGTTGTATAGAGTCA 58.848 33.333 0.00 0.00 0.00 3.41
3173 3439 3.834813 TCACAGAGTGGCTTGTAGATCTT 59.165 43.478 0.00 0.00 33.87 2.40
3428 3694 1.635663 CCATGAAGGTGACGGCGAAC 61.636 60.000 16.62 11.65 0.00 3.95
3503 3769 4.623932 TGTGAAGTACAAGGCTGAAGAT 57.376 40.909 0.00 0.00 36.06 2.40
3526 3792 5.265350 AGCTCGGTTAAGGATTACTTCTC 57.735 43.478 0.00 0.00 40.64 2.87
3967 4241 6.814146 GTCATAGAAGAGTACCTTTCCTGTTG 59.186 42.308 3.95 0.00 34.68 3.33
4075 4378 2.496070 TGTCGTACCAGAGCTAGCAAAT 59.504 45.455 18.83 0.00 0.00 2.32
4140 4459 4.218200 TGGTTCAACAATCAACATAGGCAG 59.782 41.667 0.00 0.00 0.00 4.85
4148 4467 5.183904 ACAATCAACATAGGCAGTTTCCTTC 59.816 40.000 0.00 0.00 37.66 3.46
4173 4494 8.977505 TCTCTCTGAAAACAAAACAAAACTTTG 58.022 29.630 0.60 0.60 43.62 2.77
4176 4497 6.484977 TCTGAAAACAAAACAAAACTTTGCCT 59.515 30.769 2.07 0.00 41.79 4.75
4191 4512 2.943978 GCCTGTAGGTGGCTGTCGT 61.944 63.158 0.00 0.00 46.38 4.34
4198 4519 0.818296 AGGTGGCTGTCGTGATCTAC 59.182 55.000 0.00 0.00 0.00 2.59
4200 4521 1.202313 GGTGGCTGTCGTGATCTACTC 60.202 57.143 0.00 0.00 0.00 2.59
4202 4523 2.943690 GTGGCTGTCGTGATCTACTCTA 59.056 50.000 0.00 0.00 0.00 2.43
4203 4524 3.002862 GTGGCTGTCGTGATCTACTCTAG 59.997 52.174 0.00 0.00 0.00 2.43
4204 4525 3.118371 TGGCTGTCGTGATCTACTCTAGA 60.118 47.826 0.00 0.00 39.50 2.43
4206 4527 4.083537 GGCTGTCGTGATCTACTCTAGATG 60.084 50.000 0.00 0.00 45.16 2.90
4207 4528 4.752604 GCTGTCGTGATCTACTCTAGATGA 59.247 45.833 0.00 0.00 45.16 2.92
4208 4529 5.333798 GCTGTCGTGATCTACTCTAGATGAC 60.334 48.000 0.00 0.00 45.16 3.06
4210 4531 5.986741 TGTCGTGATCTACTCTAGATGACTC 59.013 44.000 0.00 2.58 44.11 3.36
4212 4533 6.480651 GTCGTGATCTACTCTAGATGACTCAA 59.519 42.308 0.00 0.00 44.11 3.02
4213 4534 6.480651 TCGTGATCTACTCTAGATGACTCAAC 59.519 42.308 0.00 0.00 44.11 3.18
4215 4536 7.011950 CGTGATCTACTCTAGATGACTCAACTT 59.988 40.741 0.00 0.00 44.11 2.66
4217 4538 8.681806 TGATCTACTCTAGATGACTCAACTTTG 58.318 37.037 0.00 0.00 45.16 2.77
4218 4539 8.588290 ATCTACTCTAGATGACTCAACTTTGT 57.412 34.615 0.00 0.00 43.59 2.83
4219 4540 9.688091 ATCTACTCTAGATGACTCAACTTTGTA 57.312 33.333 0.00 0.00 43.59 2.41
4220 4541 8.948145 TCTACTCTAGATGACTCAACTTTGTAC 58.052 37.037 0.00 0.00 0.00 2.90
4222 4543 8.865420 ACTCTAGATGACTCAACTTTGTACTA 57.135 34.615 0.00 0.00 0.00 1.82
4223 4544 8.952278 ACTCTAGATGACTCAACTTTGTACTAG 58.048 37.037 0.00 0.00 0.00 2.57
4225 4546 8.948145 TCTAGATGACTCAACTTTGTACTAGAC 58.052 37.037 0.00 0.00 31.38 2.59
4226 4547 7.768807 AGATGACTCAACTTTGTACTAGACT 57.231 36.000 0.00 0.00 0.00 3.24
4227 4548 7.822658 AGATGACTCAACTTTGTACTAGACTC 58.177 38.462 0.00 0.00 0.00 3.36
4228 4549 6.954487 TGACTCAACTTTGTACTAGACTCA 57.046 37.500 0.00 0.00 0.00 3.41
4229 4550 7.342769 TGACTCAACTTTGTACTAGACTCAA 57.657 36.000 0.00 0.00 0.00 3.02
4230 4551 7.201145 TGACTCAACTTTGTACTAGACTCAAC 58.799 38.462 0.00 0.00 0.00 3.18
4232 4553 7.783042 ACTCAACTTTGTACTAGACTCAACTT 58.217 34.615 0.00 0.00 0.00 2.66
4234 4555 8.420374 TCAACTTTGTACTAGACTCAACTTTG 57.580 34.615 0.00 5.16 0.00 2.77
4235 4556 8.038944 TCAACTTTGTACTAGACTCAACTTTGT 58.961 33.333 0.00 0.00 0.00 2.83
4236 4557 9.309516 CAACTTTGTACTAGACTCAACTTTGTA 57.690 33.333 0.00 0.00 0.00 2.41
4237 4558 8.868635 ACTTTGTACTAGACTCAACTTTGTAC 57.131 34.615 0.00 0.00 33.62 2.90
4238 4559 8.693625 ACTTTGTACTAGACTCAACTTTGTACT 58.306 33.333 0.00 0.00 33.87 2.73
4247 4568 8.747538 AGACTCAACTTTGTACTAAATTTGGT 57.252 30.769 12.16 12.16 0.00 3.67
4248 4569 9.841295 AGACTCAACTTTGTACTAAATTTGGTA 57.159 29.630 10.08 10.08 0.00 3.25
4249 4570 9.874215 GACTCAACTTTGTACTAAATTTGGTAC 57.126 33.333 28.40 28.40 43.06 3.34
4270 4591 8.783093 TGGTACAAAGTTGAGTCATCTATTTTG 58.217 33.333 4.14 8.00 40.82 2.44
4272 4593 7.823745 ACAAAGTTGAGTCATCTATTTTGGT 57.176 32.000 14.35 0.00 40.00 3.67
4273 4594 8.237811 ACAAAGTTGAGTCATCTATTTTGGTT 57.762 30.769 14.35 0.06 40.00 3.67
4274 4595 9.349713 ACAAAGTTGAGTCATCTATTTTGGTTA 57.650 29.630 14.35 0.00 40.00 2.85
4276 4597 8.567285 AAGTTGAGTCATCTATTTTGGTTAGG 57.433 34.615 4.14 0.00 0.00 2.69
4277 4598 7.112779 AGTTGAGTCATCTATTTTGGTTAGGG 58.887 38.462 1.70 0.00 0.00 3.53
4278 4599 6.001449 TGAGTCATCTATTTTGGTTAGGGG 57.999 41.667 0.00 0.00 0.00 4.79
4279 4600 5.104109 TGAGTCATCTATTTTGGTTAGGGGG 60.104 44.000 0.00 0.00 0.00 5.40
4346 4667 0.179073 ATGGTGCTGATGCCGTCTAC 60.179 55.000 0.00 0.00 38.71 2.59
4347 4668 1.257750 TGGTGCTGATGCCGTCTACT 61.258 55.000 0.00 0.00 38.71 2.57
4348 4669 0.528684 GGTGCTGATGCCGTCTACTC 60.529 60.000 0.00 0.00 38.71 2.59
4349 4670 0.528684 GTGCTGATGCCGTCTACTCC 60.529 60.000 0.00 0.00 38.71 3.85
4350 4671 1.068250 GCTGATGCCGTCTACTCCC 59.932 63.158 0.00 0.00 0.00 4.30
4351 4672 1.395826 GCTGATGCCGTCTACTCCCT 61.396 60.000 0.00 0.00 0.00 4.20
4352 4673 0.671251 CTGATGCCGTCTACTCCCTC 59.329 60.000 0.00 0.00 0.00 4.30
4353 4674 0.259065 TGATGCCGTCTACTCCCTCT 59.741 55.000 0.00 0.00 0.00 3.69
4354 4675 0.671251 GATGCCGTCTACTCCCTCTG 59.329 60.000 0.00 0.00 0.00 3.35
4355 4676 0.033011 ATGCCGTCTACTCCCTCTGT 60.033 55.000 0.00 0.00 0.00 3.41
4356 4677 0.251653 TGCCGTCTACTCCCTCTGTT 60.252 55.000 0.00 0.00 0.00 3.16
4357 4678 1.005097 TGCCGTCTACTCCCTCTGTTA 59.995 52.381 0.00 0.00 0.00 2.41
4358 4679 2.097825 GCCGTCTACTCCCTCTGTTAA 58.902 52.381 0.00 0.00 0.00 2.01
4359 4680 2.494870 GCCGTCTACTCCCTCTGTTAAA 59.505 50.000 0.00 0.00 0.00 1.52
4360 4681 3.132467 GCCGTCTACTCCCTCTGTTAAAT 59.868 47.826 0.00 0.00 0.00 1.40
4361 4682 4.340381 GCCGTCTACTCCCTCTGTTAAATA 59.660 45.833 0.00 0.00 0.00 1.40
4362 4683 5.010820 GCCGTCTACTCCCTCTGTTAAATAT 59.989 44.000 0.00 0.00 0.00 1.28
4363 4684 6.462628 GCCGTCTACTCCCTCTGTTAAATATT 60.463 42.308 0.00 0.00 0.00 1.28
4364 4685 7.498443 CCGTCTACTCCCTCTGTTAAATATTT 58.502 38.462 5.89 5.89 0.00 1.40
4365 4686 7.438459 CCGTCTACTCCCTCTGTTAAATATTTG 59.562 40.741 11.05 0.00 0.00 2.32
4366 4687 7.980099 CGTCTACTCCCTCTGTTAAATATTTGT 59.020 37.037 11.05 0.00 0.00 2.83
4367 4688 9.315525 GTCTACTCCCTCTGTTAAATATTTGTC 57.684 37.037 11.05 4.54 0.00 3.18
4368 4689 9.268282 TCTACTCCCTCTGTTAAATATTTGTCT 57.732 33.333 11.05 0.00 0.00 3.41
4369 4690 9.892130 CTACTCCCTCTGTTAAATATTTGTCTT 57.108 33.333 11.05 0.00 0.00 3.01
4371 4692 9.588096 ACTCCCTCTGTTAAATATTTGTCTTTT 57.412 29.630 11.05 0.00 0.00 2.27
4389 4710 9.965824 TTGTCTTTTTAGAGATTTTGAATGGAC 57.034 29.630 0.00 0.00 0.00 4.02
4390 4711 9.354673 TGTCTTTTTAGAGATTTTGAATGGACT 57.645 29.630 0.00 0.00 0.00 3.85
4396 4717 9.958180 TTTAGAGATTTTGAATGGACTATCACA 57.042 29.630 0.00 0.00 0.00 3.58
4399 4720 9.553064 AGAGATTTTGAATGGACTATCACATAC 57.447 33.333 0.00 0.00 0.00 2.39
4400 4721 8.370493 AGATTTTGAATGGACTATCACATACG 57.630 34.615 0.00 0.00 0.00 3.06
4401 4722 6.918892 TTTTGAATGGACTATCACATACGG 57.081 37.500 0.00 0.00 0.00 4.02
4402 4723 5.862678 TTGAATGGACTATCACATACGGA 57.137 39.130 0.00 0.00 0.00 4.69
4403 4724 6.419484 TTGAATGGACTATCACATACGGAT 57.581 37.500 0.00 0.00 0.00 4.18
4404 4725 6.419484 TGAATGGACTATCACATACGGATT 57.581 37.500 0.00 0.00 0.00 3.01
4405 4726 6.826668 TGAATGGACTATCACATACGGATTT 58.173 36.000 0.00 0.00 0.00 2.17
4406 4727 7.958088 TGAATGGACTATCACATACGGATTTA 58.042 34.615 0.00 0.00 0.00 1.40
4407 4728 8.593679 TGAATGGACTATCACATACGGATTTAT 58.406 33.333 0.00 0.00 0.00 1.40
4445 4766 9.638239 TTAAAGTGTAGATTCATCCATTTTTGC 57.362 29.630 0.00 0.00 0.00 3.68
4446 4767 5.883661 AGTGTAGATTCATCCATTTTTGCG 58.116 37.500 0.00 0.00 0.00 4.85
4447 4768 4.500477 GTGTAGATTCATCCATTTTTGCGC 59.500 41.667 0.00 0.00 0.00 6.09
4448 4769 4.398988 TGTAGATTCATCCATTTTTGCGCT 59.601 37.500 9.73 0.00 0.00 5.92
4449 4770 3.777478 AGATTCATCCATTTTTGCGCTG 58.223 40.909 9.73 0.00 0.00 5.18
4450 4771 3.194116 AGATTCATCCATTTTTGCGCTGT 59.806 39.130 9.73 0.00 0.00 4.40
4451 4772 4.398988 AGATTCATCCATTTTTGCGCTGTA 59.601 37.500 9.73 0.00 0.00 2.74
4452 4773 4.717233 TTCATCCATTTTTGCGCTGTAT 57.283 36.364 9.73 0.00 0.00 2.29
4453 4774 4.031418 TCATCCATTTTTGCGCTGTATG 57.969 40.909 9.73 7.14 0.00 2.39
4454 4775 3.443329 TCATCCATTTTTGCGCTGTATGT 59.557 39.130 9.73 0.00 0.00 2.29
4455 4776 4.637977 TCATCCATTTTTGCGCTGTATGTA 59.362 37.500 9.73 0.00 0.00 2.29
4456 4777 4.614555 TCCATTTTTGCGCTGTATGTAG 57.385 40.909 9.73 0.00 0.00 2.74
4457 4778 4.006989 TCCATTTTTGCGCTGTATGTAGT 58.993 39.130 9.73 0.00 0.00 2.73
4458 4779 4.094294 TCCATTTTTGCGCTGTATGTAGTC 59.906 41.667 9.73 0.00 0.00 2.59
4459 4780 4.142708 CCATTTTTGCGCTGTATGTAGTCA 60.143 41.667 9.73 0.00 0.00 3.41
4460 4781 4.398549 TTTTTGCGCTGTATGTAGTCAC 57.601 40.909 9.73 0.00 0.00 3.67
4461 4782 3.313012 TTTGCGCTGTATGTAGTCACT 57.687 42.857 9.73 0.00 0.00 3.41
4462 4783 3.313012 TTGCGCTGTATGTAGTCACTT 57.687 42.857 9.73 0.00 0.00 3.16
4463 4784 2.606108 TGCGCTGTATGTAGTCACTTG 58.394 47.619 9.73 0.00 0.00 3.16
4464 4785 2.029380 TGCGCTGTATGTAGTCACTTGT 60.029 45.455 9.73 0.00 0.00 3.16
4465 4786 2.993899 GCGCTGTATGTAGTCACTTGTT 59.006 45.455 0.00 0.00 0.00 2.83
4466 4787 3.181530 GCGCTGTATGTAGTCACTTGTTG 60.182 47.826 0.00 0.00 0.00 3.33
4467 4788 4.234574 CGCTGTATGTAGTCACTTGTTGA 58.765 43.478 0.00 0.00 0.00 3.18
4468 4789 4.684242 CGCTGTATGTAGTCACTTGTTGAA 59.316 41.667 0.00 0.00 35.39 2.69
4469 4790 5.176774 CGCTGTATGTAGTCACTTGTTGAAA 59.823 40.000 0.00 0.00 35.39 2.69
4470 4791 6.128553 CGCTGTATGTAGTCACTTGTTGAAAT 60.129 38.462 0.00 0.00 35.39 2.17
4471 4792 7.571244 CGCTGTATGTAGTCACTTGTTGAAATT 60.571 37.037 0.00 0.00 35.39 1.82
4472 4793 8.076178 GCTGTATGTAGTCACTTGTTGAAATTT 58.924 33.333 0.00 0.00 35.39 1.82
4473 4794 9.599322 CTGTATGTAGTCACTTGTTGAAATTTC 57.401 33.333 11.41 11.41 35.39 2.17
4474 4795 9.337396 TGTATGTAGTCACTTGTTGAAATTTCT 57.663 29.630 18.64 0.00 35.39 2.52
4521 4842 6.555463 AGACATATTTTAGGAACGAAGGGA 57.445 37.500 0.00 0.00 0.00 4.20
4522 4843 6.583562 AGACATATTTTAGGAACGAAGGGAG 58.416 40.000 0.00 0.00 0.00 4.30
4523 4844 6.156429 AGACATATTTTAGGAACGAAGGGAGT 59.844 38.462 0.00 0.00 0.00 3.85
4524 4845 7.343833 AGACATATTTTAGGAACGAAGGGAGTA 59.656 37.037 0.00 0.00 0.00 2.59
4525 4846 8.030913 ACATATTTTAGGAACGAAGGGAGTAT 57.969 34.615 0.00 0.00 0.00 2.12
4543 4864 7.228706 AGGGAGTATTTTTGTTTGTAGTGAGTG 59.771 37.037 0.00 0.00 0.00 3.51
4585 4906 0.251916 TACCCTTGGGTGAAGATGCG 59.748 55.000 20.78 0.00 32.82 4.73
4588 4909 0.606401 CCTTGGGTGAAGATGCGTGT 60.606 55.000 0.00 0.00 32.82 4.49
4589 4910 1.338674 CCTTGGGTGAAGATGCGTGTA 60.339 52.381 0.00 0.00 32.82 2.90
4597 4918 5.577164 GGGTGAAGATGCGTGTATATATGTC 59.423 44.000 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 6.670902 TGCCCTAGAGGTAATAGTAAAGTTGT 59.329 38.462 0.00 0.00 38.26 3.32
83 84 9.220767 GTTGAAAATATGCCCTAGAGGTAATAG 57.779 37.037 0.00 0.00 38.26 1.73
105 106 3.357919 GCAGGCAGCACATGTTGA 58.642 55.556 0.00 0.00 44.79 3.18
130 131 9.282247 CATGCAAACTTGTGATAAATCTAACTC 57.718 33.333 0.00 0.00 0.00 3.01
144 145 4.763793 AGACTAGAATGCATGCAAACTTGT 59.236 37.500 28.49 28.49 0.00 3.16
215 216 7.941238 ACTAGGTAACACTACAGAGTTAACTCA 59.059 37.037 31.80 14.64 42.62 3.41
225 226 8.205131 ACAAAAACAACTAGGTAACACTACAG 57.795 34.615 0.00 0.00 41.41 2.74
413 416 1.067635 GCAACATGGCCTCACGAAAAT 60.068 47.619 3.32 0.00 0.00 1.82
418 421 1.138036 CATGCAACATGGCCTCACG 59.862 57.895 3.32 0.00 0.00 4.35
543 546 2.223144 CGTTCCTTTCTTCACATCGCAA 59.777 45.455 0.00 0.00 0.00 4.85
557 560 1.137697 AGTGGTTCCCTTCGTTCCTT 58.862 50.000 0.00 0.00 0.00 3.36
578 581 2.121291 TGGTCAACACAACAGCAGAA 57.879 45.000 0.00 0.00 0.00 3.02
605 608 7.153985 CAGTTGTTTGATTGGTTCCATATGTT 58.846 34.615 1.24 0.00 0.00 2.71
614 617 4.081752 TGACTTGCAGTTGTTTGATTGGTT 60.082 37.500 0.00 0.00 0.00 3.67
709 719 7.468357 CGGAGGAAGTACGTCATATCTAAACTT 60.468 40.741 11.01 0.00 35.40 2.66
729 739 5.617252 AGACACTTATTTTGAAACGGAGGA 58.383 37.500 0.00 0.00 0.00 3.71
761 771 3.960755 TGGATCACAGAACGATGGAGTAT 59.039 43.478 0.00 0.00 0.00 2.12
765 775 3.244387 TGTTTGGATCACAGAACGATGGA 60.244 43.478 0.00 0.00 0.00 3.41
766 776 3.073678 TGTTTGGATCACAGAACGATGG 58.926 45.455 0.00 0.00 0.00 3.51
829 962 4.407365 GGGGGTTTGAAGAAGAAAGATGA 58.593 43.478 0.00 0.00 0.00 2.92
878 1011 3.284449 GTTCGGTTGCGGGCAAGT 61.284 61.111 6.30 0.00 36.52 3.16
1045 1178 2.664081 CGAGGCTGGGGAAGAAGCT 61.664 63.158 0.00 0.00 39.46 3.74
1583 1716 1.738099 CCGGCGAGGAAAGTGACAG 60.738 63.158 9.30 0.00 45.00 3.51
1584 1717 2.342279 CCGGCGAGGAAAGTGACA 59.658 61.111 9.30 0.00 45.00 3.58
1781 1914 3.244215 TGGAGTCACTAAACCTGAAGCTG 60.244 47.826 0.00 0.00 0.00 4.24
1944 2077 5.804446 GCCTATTTGCTCATGGCTATTCCTA 60.804 44.000 7.54 0.00 42.39 2.94
1945 2078 4.660168 CCTATTTGCTCATGGCTATTCCT 58.340 43.478 7.54 0.00 42.39 3.36
1946 2079 3.192212 GCCTATTTGCTCATGGCTATTCC 59.808 47.826 7.54 0.00 42.39 3.01
1947 2080 4.431661 GCCTATTTGCTCATGGCTATTC 57.568 45.455 7.54 0.00 42.39 1.75
1958 2091 2.511218 TCAAGGGATGAGCCTATTTGCT 59.489 45.455 0.00 0.00 46.37 3.91
1959 2092 2.936202 TCAAGGGATGAGCCTATTTGC 58.064 47.619 0.00 0.00 36.66 3.68
1960 2093 7.587037 TTAATTCAAGGGATGAGCCTATTTG 57.413 36.000 0.00 0.00 39.77 2.32
1961 2094 8.061304 TCTTTAATTCAAGGGATGAGCCTATTT 58.939 33.333 0.00 0.00 39.77 1.40
1962 2095 7.586349 TCTTTAATTCAAGGGATGAGCCTATT 58.414 34.615 0.00 0.00 39.77 1.73
1963 2096 7.154191 TCTTTAATTCAAGGGATGAGCCTAT 57.846 36.000 0.00 0.00 39.77 2.57
1978 2131 4.816925 AGCAGCCCTCGTATTCTTTAATTC 59.183 41.667 0.00 0.00 0.00 2.17
1985 2138 1.689273 CCTAAGCAGCCCTCGTATTCT 59.311 52.381 0.00 0.00 0.00 2.40
2051 2204 6.408869 TGCACAGTTCATATCTCATGAAAGA 58.591 36.000 0.00 0.00 39.43 2.52
2133 2391 4.043059 AGTCCTAGTACTGTTCTCCTCACA 59.957 45.833 5.39 0.00 0.00 3.58
2135 2393 4.931027 AGTCCTAGTACTGTTCTCCTCA 57.069 45.455 5.39 0.00 0.00 3.86
2226 2492 5.243981 CACAGATCAGACTTCATCCAGTTT 58.756 41.667 0.00 0.00 0.00 2.66
2377 2643 1.582968 CATGGCCTGCACAACAGTC 59.417 57.895 3.32 0.00 45.68 3.51
2397 2663 7.396540 AACTTAATTCATTAGCAAGGGACTG 57.603 36.000 0.00 0.00 40.86 3.51
2495 2761 2.373224 GCAAGGAATTGAGGAAGGAGG 58.627 52.381 0.00 0.00 0.00 4.30
2877 3143 4.982241 TCTCCTTTGGCCCTATTATCAG 57.018 45.455 0.00 0.00 0.00 2.90
2989 3255 1.310933 GGTCAGTGCCAGCCATTCTG 61.311 60.000 0.00 0.00 42.49 3.02
2990 3256 1.001641 GGTCAGTGCCAGCCATTCT 60.002 57.895 0.00 0.00 0.00 2.40
2991 3257 0.895100 TTGGTCAGTGCCAGCCATTC 60.895 55.000 6.43 0.00 40.01 2.67
2992 3258 1.153524 TTGGTCAGTGCCAGCCATT 59.846 52.632 6.43 0.00 40.01 3.16
2993 3259 1.604593 GTTGGTCAGTGCCAGCCAT 60.605 57.895 8.55 0.00 40.01 4.40
2994 3260 2.203337 GTTGGTCAGTGCCAGCCA 60.203 61.111 8.55 1.53 40.01 4.75
2995 3261 1.968540 GAGTTGGTCAGTGCCAGCC 60.969 63.158 13.89 6.90 40.08 4.85
2996 3262 2.320587 CGAGTTGGTCAGTGCCAGC 61.321 63.158 10.88 10.88 40.01 4.85
2997 3263 1.669115 CCGAGTTGGTCAGTGCCAG 60.669 63.158 6.43 0.00 40.01 4.85
2998 3264 2.425592 CCGAGTTGGTCAGTGCCA 59.574 61.111 2.57 2.57 36.62 4.92
2999 3265 3.050275 GCCGAGTTGGTCAGTGCC 61.050 66.667 0.00 0.00 41.21 5.01
3000 3266 1.444119 TTTGCCGAGTTGGTCAGTGC 61.444 55.000 0.00 0.00 41.21 4.40
3001 3267 0.307760 GTTTGCCGAGTTGGTCAGTG 59.692 55.000 0.00 0.00 41.21 3.66
3002 3268 0.818040 GGTTTGCCGAGTTGGTCAGT 60.818 55.000 0.00 0.00 41.21 3.41
3100 3366 9.204570 ACTGACTCTATACAACACAATAACAAC 57.795 33.333 0.00 0.00 0.00 3.32
3124 3390 3.492102 ACCATGTACAACTTCAGCACT 57.508 42.857 0.00 0.00 0.00 4.40
3173 3439 0.397941 CTGTGAGCCCCTTGTCTTCA 59.602 55.000 0.00 0.00 0.00 3.02
3292 3558 3.981211 TGCTTGTCAATGAAGAAAAGGC 58.019 40.909 0.00 0.00 34.15 4.35
3428 3694 2.999331 TCCTTCCTTTTCCTTATGCCG 58.001 47.619 0.00 0.00 0.00 5.69
3503 3769 5.008415 CGAGAAGTAATCCTTAACCGAGCTA 59.992 44.000 0.00 0.00 32.03 3.32
3526 3792 1.709147 GCCATTGGTAGCAGCAGACG 61.709 60.000 4.26 0.00 0.00 4.18
3967 4241 0.899720 TCAAGATGGTACCGTGGGAC 59.100 55.000 12.53 0.00 0.00 4.46
4127 4446 5.045286 AGAGAAGGAAACTGCCTATGTTGAT 60.045 40.000 0.00 0.00 42.68 2.57
4128 4447 4.287067 AGAGAAGGAAACTGCCTATGTTGA 59.713 41.667 0.00 0.00 42.68 3.18
4129 4448 4.583871 AGAGAAGGAAACTGCCTATGTTG 58.416 43.478 0.00 0.00 42.68 3.33
4130 4449 4.534103 AGAGAGAAGGAAACTGCCTATGTT 59.466 41.667 0.00 0.00 42.68 2.71
4131 4450 4.081198 CAGAGAGAAGGAAACTGCCTATGT 60.081 45.833 0.00 0.00 42.68 2.29
4132 4451 4.161189 TCAGAGAGAAGGAAACTGCCTATG 59.839 45.833 0.00 0.00 42.68 2.23
4133 4452 4.357325 TCAGAGAGAAGGAAACTGCCTAT 58.643 43.478 0.00 0.00 42.68 2.57
4140 4459 7.312899 TGTTTTGTTTTCAGAGAGAAGGAAAC 58.687 34.615 0.00 0.00 37.57 2.78
4148 4467 7.741652 GCAAAGTTTTGTTTTGTTTTCAGAGAG 59.258 33.333 6.48 0.00 40.24 3.20
4176 4497 0.530744 GATCACGACAGCCACCTACA 59.469 55.000 0.00 0.00 0.00 2.74
4191 4512 8.681806 CAAAGTTGAGTCATCTAGAGTAGATCA 58.318 37.037 4.14 0.00 43.41 2.92
4198 4519 9.168451 TCTAGTACAAAGTTGAGTCATCTAGAG 57.832 37.037 4.14 1.16 0.00 2.43
4200 4521 8.952278 AGTCTAGTACAAAGTTGAGTCATCTAG 58.048 37.037 4.14 3.67 0.00 2.43
4202 4523 7.448777 TGAGTCTAGTACAAAGTTGAGTCATCT 59.551 37.037 0.00 0.00 36.17 2.90
4203 4524 7.594714 TGAGTCTAGTACAAAGTTGAGTCATC 58.405 38.462 0.00 0.00 36.17 2.92
4204 4525 7.526142 TGAGTCTAGTACAAAGTTGAGTCAT 57.474 36.000 0.00 0.00 36.17 3.06
4205 4526 6.954487 TGAGTCTAGTACAAAGTTGAGTCA 57.046 37.500 0.00 0.00 37.68 3.41
4206 4527 7.427214 AGTTGAGTCTAGTACAAAGTTGAGTC 58.573 38.462 0.00 0.00 33.41 3.36
4207 4528 7.349412 AGTTGAGTCTAGTACAAAGTTGAGT 57.651 36.000 0.00 0.00 0.00 3.41
4208 4529 8.543774 CAAAGTTGAGTCTAGTACAAAGTTGAG 58.456 37.037 0.00 0.00 0.00 3.02
4210 4531 8.197988 ACAAAGTTGAGTCTAGTACAAAGTTG 57.802 34.615 0.00 0.00 0.00 3.16
4212 4533 8.693625 AGTACAAAGTTGAGTCTAGTACAAAGT 58.306 33.333 0.00 0.00 34.50 2.66
4222 4543 8.747538 ACCAAATTTAGTACAAAGTTGAGTCT 57.252 30.769 21.54 7.71 37.38 3.24
4223 4544 9.874215 GTACCAAATTTAGTACAAAGTTGAGTC 57.126 33.333 18.35 12.68 37.38 3.36
4234 4555 9.874215 GACTCAACTTTGTACCAAATTTAGTAC 57.126 33.333 16.96 16.96 39.44 2.73
4235 4556 9.616156 TGACTCAACTTTGTACCAAATTTAGTA 57.384 29.630 0.00 0.00 0.00 1.82
4236 4557 8.514330 TGACTCAACTTTGTACCAAATTTAGT 57.486 30.769 0.00 0.00 0.00 2.24
4237 4558 9.612620 GATGACTCAACTTTGTACCAAATTTAG 57.387 33.333 0.00 0.00 0.00 1.85
4238 4559 9.349713 AGATGACTCAACTTTGTACCAAATTTA 57.650 29.630 0.00 0.00 0.00 1.40
4239 4560 8.237811 AGATGACTCAACTTTGTACCAAATTT 57.762 30.769 0.00 0.00 0.00 1.82
4240 4561 7.823745 AGATGACTCAACTTTGTACCAAATT 57.176 32.000 0.00 0.00 0.00 1.82
4242 4563 8.918202 AATAGATGACTCAACTTTGTACCAAA 57.082 30.769 0.00 0.00 0.00 3.28
4243 4564 8.918202 AAATAGATGACTCAACTTTGTACCAA 57.082 30.769 0.00 0.00 0.00 3.67
4244 4565 8.783093 CAAAATAGATGACTCAACTTTGTACCA 58.217 33.333 0.00 0.00 0.00 3.25
4245 4566 8.237267 CCAAAATAGATGACTCAACTTTGTACC 58.763 37.037 0.00 0.00 0.00 3.34
4246 4567 8.784043 ACCAAAATAGATGACTCAACTTTGTAC 58.216 33.333 0.00 0.00 0.00 2.90
4247 4568 8.918202 ACCAAAATAGATGACTCAACTTTGTA 57.082 30.769 0.00 0.00 0.00 2.41
4248 4569 7.823745 ACCAAAATAGATGACTCAACTTTGT 57.176 32.000 0.00 0.00 0.00 2.83
4249 4570 9.831737 CTAACCAAAATAGATGACTCAACTTTG 57.168 33.333 0.00 0.00 0.00 2.77
4250 4571 9.014297 CCTAACCAAAATAGATGACTCAACTTT 57.986 33.333 0.00 0.00 0.00 2.66
4251 4572 7.611855 CCCTAACCAAAATAGATGACTCAACTT 59.388 37.037 0.00 0.00 0.00 2.66
4252 4573 7.112779 CCCTAACCAAAATAGATGACTCAACT 58.887 38.462 0.00 0.00 0.00 3.16
4254 4575 6.423182 CCCCTAACCAAAATAGATGACTCAA 58.577 40.000 0.00 0.00 0.00 3.02
4255 4576 5.104109 CCCCCTAACCAAAATAGATGACTCA 60.104 44.000 0.00 0.00 0.00 3.41
4256 4577 5.377478 CCCCCTAACCAAAATAGATGACTC 58.623 45.833 0.00 0.00 0.00 3.36
4257 4578 5.388599 CCCCCTAACCAAAATAGATGACT 57.611 43.478 0.00 0.00 0.00 3.41
4276 4597 5.778750 TGCATTACTTAGATACTACTCCCCC 59.221 44.000 0.00 0.00 0.00 5.40
4277 4598 6.912951 TGCATTACTTAGATACTACTCCCC 57.087 41.667 0.00 0.00 0.00 4.81
4278 4599 9.780186 AAAATGCATTACTTAGATACTACTCCC 57.220 33.333 13.39 0.00 0.00 4.30
4310 4631 4.451774 GCACCATGCAAAGCTATTTTTGAA 59.548 37.500 0.00 0.00 44.26 2.69
4363 4684 9.965824 GTCCATTCAAAATCTCTAAAAAGACAA 57.034 29.630 0.00 0.00 0.00 3.18
4364 4685 9.354673 AGTCCATTCAAAATCTCTAAAAAGACA 57.645 29.630 0.00 0.00 0.00 3.41
4370 4691 9.958180 TGTGATAGTCCATTCAAAATCTCTAAA 57.042 29.630 0.00 0.00 0.00 1.85
4373 4694 9.553064 GTATGTGATAGTCCATTCAAAATCTCT 57.447 33.333 0.00 0.00 0.00 3.10
4374 4695 8.491152 CGTATGTGATAGTCCATTCAAAATCTC 58.509 37.037 0.00 0.00 0.00 2.75
4375 4696 7.442364 CCGTATGTGATAGTCCATTCAAAATCT 59.558 37.037 0.00 0.00 0.00 2.40
4376 4697 7.441157 TCCGTATGTGATAGTCCATTCAAAATC 59.559 37.037 0.00 0.00 0.00 2.17
4377 4698 7.279615 TCCGTATGTGATAGTCCATTCAAAAT 58.720 34.615 0.00 0.00 0.00 1.82
4378 4699 6.645306 TCCGTATGTGATAGTCCATTCAAAA 58.355 36.000 0.00 0.00 0.00 2.44
4379 4700 6.228616 TCCGTATGTGATAGTCCATTCAAA 57.771 37.500 0.00 0.00 0.00 2.69
4380 4701 5.862678 TCCGTATGTGATAGTCCATTCAA 57.137 39.130 0.00 0.00 0.00 2.69
4381 4702 6.419484 AATCCGTATGTGATAGTCCATTCA 57.581 37.500 0.00 0.00 0.00 2.57
4419 4740 9.638239 GCAAAAATGGATGAATCTACACTTTAA 57.362 29.630 0.00 0.00 0.00 1.52
4420 4741 7.967854 CGCAAAAATGGATGAATCTACACTTTA 59.032 33.333 0.00 0.00 0.00 1.85
4421 4742 6.808212 CGCAAAAATGGATGAATCTACACTTT 59.192 34.615 0.00 0.00 0.00 2.66
4422 4743 6.324819 CGCAAAAATGGATGAATCTACACTT 58.675 36.000 0.00 0.00 0.00 3.16
4423 4744 5.677091 GCGCAAAAATGGATGAATCTACACT 60.677 40.000 0.30 0.00 0.00 3.55
4424 4745 4.500477 GCGCAAAAATGGATGAATCTACAC 59.500 41.667 0.30 0.00 0.00 2.90
4425 4746 4.398988 AGCGCAAAAATGGATGAATCTACA 59.601 37.500 11.47 0.00 0.00 2.74
4426 4747 4.736793 CAGCGCAAAAATGGATGAATCTAC 59.263 41.667 11.47 0.00 0.00 2.59
4427 4748 4.398988 ACAGCGCAAAAATGGATGAATCTA 59.601 37.500 11.47 0.00 0.00 1.98
4428 4749 3.194116 ACAGCGCAAAAATGGATGAATCT 59.806 39.130 11.47 0.00 0.00 2.40
4429 4750 3.514645 ACAGCGCAAAAATGGATGAATC 58.485 40.909 11.47 0.00 0.00 2.52
4430 4751 3.598019 ACAGCGCAAAAATGGATGAAT 57.402 38.095 11.47 0.00 0.00 2.57
4431 4752 4.082300 ACATACAGCGCAAAAATGGATGAA 60.082 37.500 21.72 0.00 37.44 2.57
4432 4753 3.443329 ACATACAGCGCAAAAATGGATGA 59.557 39.130 21.72 0.00 37.44 2.92
4433 4754 3.772932 ACATACAGCGCAAAAATGGATG 58.227 40.909 15.21 15.21 40.47 3.51
4434 4755 4.640201 ACTACATACAGCGCAAAAATGGAT 59.360 37.500 11.47 0.00 0.00 3.41
4435 4756 4.006989 ACTACATACAGCGCAAAAATGGA 58.993 39.130 11.47 3.36 0.00 3.41
4436 4757 4.142708 TGACTACATACAGCGCAAAAATGG 60.143 41.667 11.47 0.00 0.00 3.16
4437 4758 4.788100 GTGACTACATACAGCGCAAAAATG 59.212 41.667 11.47 10.25 0.00 2.32
4438 4759 4.695455 AGTGACTACATACAGCGCAAAAAT 59.305 37.500 11.47 0.00 0.00 1.82
4439 4760 4.062293 AGTGACTACATACAGCGCAAAAA 58.938 39.130 11.47 0.00 0.00 1.94
4440 4761 3.659786 AGTGACTACATACAGCGCAAAA 58.340 40.909 11.47 0.00 0.00 2.44
4441 4762 3.313012 AGTGACTACATACAGCGCAAA 57.687 42.857 11.47 0.00 0.00 3.68
4442 4763 2.993220 CAAGTGACTACATACAGCGCAA 59.007 45.455 11.47 0.00 0.00 4.85
4443 4764 2.029380 ACAAGTGACTACATACAGCGCA 60.029 45.455 11.47 0.00 0.00 6.09
4444 4765 2.607187 ACAAGTGACTACATACAGCGC 58.393 47.619 0.00 0.00 0.00 5.92
4445 4766 4.234574 TCAACAAGTGACTACATACAGCG 58.765 43.478 0.00 0.00 0.00 5.18
4446 4767 6.539649 TTTCAACAAGTGACTACATACAGC 57.460 37.500 0.00 0.00 35.39 4.40
4447 4768 9.599322 GAAATTTCAACAAGTGACTACATACAG 57.401 33.333 13.40 0.00 35.39 2.74
4448 4769 9.337396 AGAAATTTCAACAAGTGACTACATACA 57.663 29.630 19.99 0.00 35.39 2.29
4495 4816 9.370930 TCCCTTCGTTCCTAAAATATGTCTATA 57.629 33.333 0.00 0.00 0.00 1.31
4496 4817 8.258850 TCCCTTCGTTCCTAAAATATGTCTAT 57.741 34.615 0.00 0.00 0.00 1.98
4497 4818 7.343833 ACTCCCTTCGTTCCTAAAATATGTCTA 59.656 37.037 0.00 0.00 0.00 2.59
4498 4819 6.156429 ACTCCCTTCGTTCCTAAAATATGTCT 59.844 38.462 0.00 0.00 0.00 3.41
4499 4820 6.346896 ACTCCCTTCGTTCCTAAAATATGTC 58.653 40.000 0.00 0.00 0.00 3.06
4500 4821 6.309389 ACTCCCTTCGTTCCTAAAATATGT 57.691 37.500 0.00 0.00 0.00 2.29
4501 4822 8.904099 AATACTCCCTTCGTTCCTAAAATATG 57.096 34.615 0.00 0.00 0.00 1.78
4502 4823 9.916360 AAAATACTCCCTTCGTTCCTAAAATAT 57.084 29.630 0.00 0.00 0.00 1.28
4503 4824 9.743581 AAAAATACTCCCTTCGTTCCTAAAATA 57.256 29.630 0.00 0.00 0.00 1.40
4504 4825 8.520351 CAAAAATACTCCCTTCGTTCCTAAAAT 58.480 33.333 0.00 0.00 0.00 1.82
4505 4826 7.503230 ACAAAAATACTCCCTTCGTTCCTAAAA 59.497 33.333 0.00 0.00 0.00 1.52
4506 4827 6.999871 ACAAAAATACTCCCTTCGTTCCTAAA 59.000 34.615 0.00 0.00 0.00 1.85
4507 4828 6.536447 ACAAAAATACTCCCTTCGTTCCTAA 58.464 36.000 0.00 0.00 0.00 2.69
4508 4829 6.117975 ACAAAAATACTCCCTTCGTTCCTA 57.882 37.500 0.00 0.00 0.00 2.94
4509 4830 4.981812 ACAAAAATACTCCCTTCGTTCCT 58.018 39.130 0.00 0.00 0.00 3.36
4510 4831 5.700722 AACAAAAATACTCCCTTCGTTCC 57.299 39.130 0.00 0.00 0.00 3.62
4511 4832 6.500910 ACAAACAAAAATACTCCCTTCGTTC 58.499 36.000 0.00 0.00 0.00 3.95
4512 4833 6.459670 ACAAACAAAAATACTCCCTTCGTT 57.540 33.333 0.00 0.00 0.00 3.85
4513 4834 6.769341 ACTACAAACAAAAATACTCCCTTCGT 59.231 34.615 0.00 0.00 0.00 3.85
4514 4835 7.041644 TCACTACAAACAAAAATACTCCCTTCG 60.042 37.037 0.00 0.00 0.00 3.79
4515 4836 8.161699 TCACTACAAACAAAAATACTCCCTTC 57.838 34.615 0.00 0.00 0.00 3.46
4516 4837 7.778382 ACTCACTACAAACAAAAATACTCCCTT 59.222 33.333 0.00 0.00 0.00 3.95
4517 4838 7.228706 CACTCACTACAAACAAAAATACTCCCT 59.771 37.037 0.00 0.00 0.00 4.20
4518 4839 7.012989 ACACTCACTACAAACAAAAATACTCCC 59.987 37.037 0.00 0.00 0.00 4.30
4519 4840 7.927048 ACACTCACTACAAACAAAAATACTCC 58.073 34.615 0.00 0.00 0.00 3.85
4520 4841 9.434559 GAACACTCACTACAAACAAAAATACTC 57.565 33.333 0.00 0.00 0.00 2.59
4521 4842 8.120465 CGAACACTCACTACAAACAAAAATACT 58.880 33.333 0.00 0.00 0.00 2.12
4522 4843 7.906527 ACGAACACTCACTACAAACAAAAATAC 59.093 33.333 0.00 0.00 0.00 1.89
4523 4844 7.976826 ACGAACACTCACTACAAACAAAAATA 58.023 30.769 0.00 0.00 0.00 1.40
4524 4845 6.848451 ACGAACACTCACTACAAACAAAAAT 58.152 32.000 0.00 0.00 0.00 1.82
4525 4846 6.243811 ACGAACACTCACTACAAACAAAAA 57.756 33.333 0.00 0.00 0.00 1.94
4543 4864 7.218204 GGTAAACATAGCATCAAATCAACGAAC 59.782 37.037 0.00 0.00 0.00 3.95
4585 4906 5.470368 ACGGCACATGAGACATATATACAC 58.530 41.667 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.