Multiple sequence alignment - TraesCS2D01G226400

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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 TraesCS2D01G226400 chr2D 100.000 5976 0 0 1 5976 194736444 194730469 0.000000e+00 11036.0
1 TraesCS2D01G226400 chr2D 90.777 206 16 3 3277 3482 604701751 604701549 7.630000e-69 272.0
2 TraesCS2D01G226400 chr2B 96.029 4004 131 14 1343 5338 250708053 250704070 0.000000e+00 6488.0
3 TraesCS2D01G226400 chr2B 92.493 1119 38 9 242 1355 250709151 250708074 0.000000e+00 1559.0
4 TraesCS2D01G226400 chr2B 90.226 399 17 6 5442 5839 250704072 250703695 8.940000e-138 501.0
5 TraesCS2D01G226400 chr2B 95.385 130 6 0 1 130 250709498 250709369 2.180000e-49 207.0
6 TraesCS2D01G226400 chr2B 88.415 164 4 4 5824 5972 250703637 250703474 3.680000e-42 183.0
7 TraesCS2D01G226400 chr2A 93.810 3554 159 25 1795 5338 209261091 209257589 0.000000e+00 5288.0
8 TraesCS2D01G226400 chr2A 85.887 1658 116 67 112 1705 209262784 209261181 0.000000e+00 1657.0
9 TraesCS2D01G226400 chr2A 88.462 520 25 8 5442 5946 209257591 209257092 3.990000e-166 595.0
10 TraesCS2D01G226400 chr2A 93.860 114 7 0 5331 5444 586908473 586908586 7.960000e-39 172.0
11 TraesCS2D01G226400 chr2A 89.286 56 4 2 1745 1798 209261193 209261138 1.070000e-07 69.4
12 TraesCS2D01G226400 chr7D 87.867 511 34 10 2999 3509 596669934 596669452 5.190000e-160 575.0
13 TraesCS2D01G226400 chr7D 90.708 226 16 4 2999 3222 598730110 598730332 4.530000e-76 296.0
14 TraesCS2D01G226400 chr7D 89.474 209 20 2 3274 3482 598730342 598730548 4.590000e-66 263.0
15 TraesCS2D01G226400 chr7D 96.429 112 4 0 5336 5447 83802021 83801910 1.020000e-42 185.0
16 TraesCS2D01G226400 chr7D 94.643 112 6 0 5334 5445 161297107 161297218 2.210000e-39 174.0
17 TraesCS2D01G226400 chr6D 90.708 226 16 5 2999 3222 231082980 231082758 4.530000e-76 296.0
18 TraesCS2D01G226400 chr6D 91.304 207 14 4 3277 3482 231082745 231082542 4.560000e-71 279.0
19 TraesCS2D01G226400 chr5D 90.708 226 16 4 2999 3222 35485915 35485693 4.530000e-76 296.0
20 TraesCS2D01G226400 chr5D 90.265 226 17 4 2999 3222 539780935 539780713 2.110000e-74 291.0
21 TraesCS2D01G226400 chr5D 91.220 205 16 2 3278 3482 35485679 35485477 1.640000e-70 278.0
22 TraesCS2D01G226400 chr5D 90.640 203 17 2 3280 3482 539780697 539780497 9.870000e-68 268.0
23 TraesCS2D01G226400 chr5B 89.655 232 19 4 2999 3230 673098957 673099183 2.110000e-74 291.0
24 TraesCS2D01G226400 chr5B 97.196 107 3 0 5337 5443 533892989 533893095 1.320000e-41 182.0
25 TraesCS2D01G226400 chr4B 91.163 215 15 3 3343 3555 456354310 456354098 7.580000e-74 289.0
26 TraesCS2D01G226400 chr1B 89.823 226 18 4 2999 3222 252371727 252371949 9.800000e-73 285.0
27 TraesCS2D01G226400 chr1B 94.444 36 2 0 3 38 655122516 655122481 8.370000e-04 56.5
28 TraesCS2D01G226400 chr1A 98.148 108 2 0 5337 5444 19894973 19894866 7.910000e-44 189.0
29 TraesCS2D01G226400 chr1D 97.248 109 3 0 5336 5444 475815099 475814991 1.020000e-42 185.0
30 TraesCS2D01G226400 chr6B 97.222 108 3 0 5337 5444 469780416 469780523 3.680000e-42 183.0
31 TraesCS2D01G226400 chrUn 96.330 109 4 0 5337 5445 74611566 74611458 4.760000e-41 180.0
32 TraesCS2D01G226400 chr3B 92.800 125 6 3 5321 5444 644018972 644019094 1.710000e-40 178.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G226400 chr2D 194730469 194736444 5975 True 11036.00 11036 100.00000 1 5976 1 chr2D.!!$R1 5975
1 TraesCS2D01G226400 chr2B 250703474 250709498 6024 True 1787.60 6488 92.50960 1 5972 5 chr2B.!!$R1 5971
2 TraesCS2D01G226400 chr2A 209257092 209262784 5692 True 1902.35 5288 89.36125 112 5946 4 chr2A.!!$R1 5834

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
933 1059 0.041135 GGCCGTCTAGATCGAGAACG 60.041 60.0 7.15 12.45 41.26 3.95 F
1269 1408 0.393820 ATTGCAGTGGCTTTGTTGGG 59.606 50.0 0.00 0.00 41.91 4.12 F
2761 3015 0.319641 ACCGTTCGAGCTTCAGTTCC 60.320 55.0 0.00 0.00 0.00 3.62 F
3557 3811 0.689623 CTGCCATAGGGGACATCTCC 59.310 60.0 0.00 0.00 40.01 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2611 2865 1.404391 GAAGCAACATGCCCAGATGAG 59.596 52.381 0.00 0.0 46.52 2.90 R
3153 3407 1.555075 TCTGACCAGGCCAGATAACAC 59.445 52.381 5.01 0.0 35.89 3.32 R
3873 4127 0.249676 AGGTGCAGAGCAGACATCAG 59.750 55.000 0.00 0.0 40.08 2.90 R
5427 5691 0.039911 AGCTACTCCCTCCGTTCACT 59.960 55.000 0.00 0.0 0.00 3.41 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
48 49 4.021456 ACACCGCCATGAATATCGATTAGA 60.021 41.667 1.71 0.00 0.00 2.10
49 50 4.929211 CACCGCCATGAATATCGATTAGAA 59.071 41.667 1.71 0.00 0.00 2.10
68 69 1.002366 ACTTCGTTCGATGCAGCATC 58.998 50.000 23.63 23.63 37.50 3.91
82 83 2.222678 GCAGCATCGACCATGTATGAAG 59.777 50.000 0.00 0.00 34.56 3.02
177 178 9.190317 GAATGTGAATATTTTAGAAAGGGGAGT 57.810 33.333 0.00 0.00 0.00 3.85
178 179 7.938140 TGTGAATATTTTAGAAAGGGGAGTG 57.062 36.000 0.00 0.00 0.00 3.51
180 181 7.829211 TGTGAATATTTTAGAAAGGGGAGTGAG 59.171 37.037 0.00 0.00 0.00 3.51
181 182 6.828785 TGAATATTTTAGAAAGGGGAGTGAGC 59.171 38.462 0.00 0.00 0.00 4.26
184 185 3.983044 TTAGAAAGGGGAGTGAGCTTC 57.017 47.619 0.00 0.00 0.00 3.86
185 186 0.610687 AGAAAGGGGAGTGAGCTTCG 59.389 55.000 0.00 0.00 0.00 3.79
187 188 1.208293 GAAAGGGGAGTGAGCTTCGAT 59.792 52.381 0.00 0.00 0.00 3.59
188 189 0.539051 AAGGGGAGTGAGCTTCGATG 59.461 55.000 0.00 0.00 0.00 3.84
189 190 0.324738 AGGGGAGTGAGCTTCGATGA 60.325 55.000 1.89 0.00 0.00 2.92
190 191 0.537188 GGGGAGTGAGCTTCGATGAA 59.463 55.000 1.89 0.00 0.00 2.57
192 193 2.275318 GGGAGTGAGCTTCGATGAAAG 58.725 52.381 1.89 0.00 0.00 2.62
298 414 5.534207 TGTCCAAACTGAATTTTGCTGAT 57.466 34.783 0.00 0.00 35.48 2.90
342 460 2.106683 CCGGGTGTCTCGCATTTCC 61.107 63.158 0.00 0.00 0.00 3.13
343 461 2.106683 CGGGTGTCTCGCATTTCCC 61.107 63.158 0.00 0.00 0.00 3.97
391 509 1.211190 GAGGGCAGCAAAGAAAGCG 59.789 57.895 0.00 0.00 37.01 4.68
488 607 0.179092 GGCAGGCAGGCATTTCATTC 60.179 55.000 0.00 0.00 43.51 2.67
494 613 4.407551 GGCATTTCATTCGCCAGC 57.592 55.556 0.00 0.00 45.52 4.85
554 673 2.203070 CATTTCCCTCCTCGGCCG 60.203 66.667 22.12 22.12 0.00 6.13
591 710 1.581447 GCCAAGAAACCAAGCGAGG 59.419 57.895 0.00 0.00 0.00 4.63
592 711 1.172812 GCCAAGAAACCAAGCGAGGT 61.173 55.000 0.00 0.00 45.91 3.85
620 739 2.435059 GGTGTTCTCGGCTGAGCC 60.435 66.667 18.28 14.89 46.75 4.70
680 805 1.876156 AGTCTTTTCTTCGGCAAGCAG 59.124 47.619 0.00 0.00 0.00 4.24
890 1016 0.102481 TGCGATCTCGGCCTCTAAAC 59.898 55.000 0.00 0.00 40.23 2.01
898 1024 2.100087 CTCGGCCTCTAAACTCCTTCTC 59.900 54.545 0.00 0.00 0.00 2.87
916 1042 0.110486 TCTTGGGTGGAAACAGAGGC 59.890 55.000 0.00 0.00 44.46 4.70
933 1059 0.041135 GGCCGTCTAGATCGAGAACG 60.041 60.000 7.15 12.45 41.26 3.95
1015 1154 1.906253 CAGATGGGCTCTGCTCACT 59.094 57.895 0.00 0.00 43.92 3.41
1157 1296 4.554036 GGTCATCGGGAGGGCAGC 62.554 72.222 0.00 0.00 0.00 5.25
1212 1351 2.315925 ATGCTGATCCAACCGTACTG 57.684 50.000 0.00 0.00 0.00 2.74
1225 1364 0.675522 CGTACTGCCCGGGACAAAAT 60.676 55.000 29.31 12.23 0.00 1.82
1269 1408 0.393820 ATTGCAGTGGCTTTGTTGGG 59.606 50.000 0.00 0.00 41.91 4.12
1288 1427 6.012858 TGTTGGGACTATTGAAGGTTCATACT 60.013 38.462 0.00 0.00 37.00 2.12
1506 1703 1.234821 CGCCAAGAAGGTGCAAAGTA 58.765 50.000 0.00 0.00 41.83 2.24
1525 1722 2.250939 CCTCGCTGCGACCAAAACA 61.251 57.895 22.24 0.00 0.00 2.83
1557 1754 6.734104 ACTTATGTAGAGAAGCAAGCAAAG 57.266 37.500 0.00 0.00 0.00 2.77
1576 1773 2.657143 AGTAAAGCCAAAACCGAACCA 58.343 42.857 0.00 0.00 0.00 3.67
1600 1797 9.906660 CCAAAACAAAACTGCTAGATATACAAA 57.093 29.630 0.00 0.00 0.00 2.83
1647 1844 2.906691 AGACATGAGTAGCAGATGGC 57.093 50.000 0.00 0.00 45.30 4.40
1668 1865 4.060900 GCGAAGATATTTGAGCCTGATCA 58.939 43.478 0.00 0.00 0.00 2.92
1691 1888 8.651391 TCATATTGAAATTAGCAATTTGCCAG 57.349 30.769 17.51 0.00 46.52 4.85
1705 1902 4.935352 TTTGCCAGTTTAATCTGCTTGT 57.065 36.364 7.87 0.00 34.47 3.16
1761 1958 3.767131 TCCCCTTTAACTAATTGCTTGGC 59.233 43.478 0.00 0.00 0.00 4.52
1793 1990 5.173131 CCTTGCACGTGTTGTATTTCTTTTC 59.827 40.000 18.38 0.00 0.00 2.29
1829 2076 1.468520 CAATCTTGGTAGCCAACACCG 59.531 52.381 0.00 0.00 38.75 4.94
1843 2090 4.165779 CCAACACCGTAATCAAATTCAGC 58.834 43.478 0.00 0.00 0.00 4.26
1939 2188 8.821894 GCAGATTTTAGTCCTACTGAGTATTTG 58.178 37.037 0.00 0.00 0.00 2.32
1949 2200 7.764443 GTCCTACTGAGTATTTGTTCTTATGCA 59.236 37.037 0.00 0.00 0.00 3.96
1950 2201 8.318412 TCCTACTGAGTATTTGTTCTTATGCAA 58.682 33.333 0.00 0.00 0.00 4.08
2073 2327 9.918630 AAATCTTGAAGAGTTTGATAACAATGG 57.081 29.630 1.56 0.00 36.70 3.16
2075 2329 8.463930 TCTTGAAGAGTTTGATAACAATGGTT 57.536 30.769 0.00 0.00 41.06 3.67
2110 2364 0.407139 AGCTTCTGGCCAAGGATGTT 59.593 50.000 7.01 0.00 43.05 2.71
2305 2559 7.572353 GCTGTAGCTAGTATCATCAGTCAGTAC 60.572 44.444 0.00 0.00 38.21 2.73
2371 2625 3.058160 GGCGGCATCACAGCACTT 61.058 61.111 3.07 0.00 41.85 3.16
2596 2850 1.208052 TGGATAGCAACAGACTGGCTC 59.792 52.381 9.20 0.00 39.01 4.70
2611 2865 1.753649 TGGCTCTCTGCAGTGATAGAC 59.246 52.381 18.19 10.87 45.15 2.59
2628 2882 0.737219 GACTCATCTGGGCATGTTGC 59.263 55.000 0.00 0.00 44.08 4.17
2664 2918 6.187682 CAGAAAACACTCAGGGGGTTATTAT 58.812 40.000 0.00 0.00 0.00 1.28
2670 2924 3.785887 ACTCAGGGGGTTATTATGCTTCA 59.214 43.478 0.00 0.00 0.00 3.02
2671 2925 4.416848 ACTCAGGGGGTTATTATGCTTCAT 59.583 41.667 0.00 0.00 0.00 2.57
2724 2978 0.746063 TTGCTGCCCAAACTGAACAG 59.254 50.000 0.00 0.00 0.00 3.16
2731 2985 2.917933 CCCAAACTGAACAGTCTGACA 58.082 47.619 10.88 5.67 41.58 3.58
2761 3015 0.319641 ACCGTTCGAGCTTCAGTTCC 60.320 55.000 0.00 0.00 0.00 3.62
2794 3048 3.792401 TGCTTATGACTCCGTATGGTTG 58.208 45.455 0.00 0.00 36.30 3.77
2903 3157 5.596772 AGTAGCCTTCAGTTAGATTCTCTCC 59.403 44.000 0.00 0.00 0.00 3.71
2927 3181 6.183360 CCGAGTTCTCAACAATGGAGATAAAC 60.183 42.308 0.00 0.00 40.82 2.01
3037 3291 2.224281 TGACATCCTGAATATCGGTGGC 60.224 50.000 0.00 0.00 0.00 5.01
3152 3406 7.078249 ACAACCAATGATATACAGCTCCATA 57.922 36.000 0.00 0.00 0.00 2.74
3153 3407 7.164122 ACAACCAATGATATACAGCTCCATAG 58.836 38.462 0.00 0.00 0.00 2.23
3205 3459 1.152839 CCGTGGTTGGGTGTTTCCT 60.153 57.895 0.00 0.00 36.25 3.36
3232 3486 2.242196 TGGGAAGCTTCTAAGGATTGGG 59.758 50.000 25.05 0.00 0.00 4.12
3301 3555 1.063942 CCTGATGGGGTAAAGGGGTTC 60.064 57.143 0.00 0.00 0.00 3.62
3316 3570 4.546674 AGGGGTTCTCAGTTGATGTTTTT 58.453 39.130 0.00 0.00 0.00 1.94
3385 3639 7.452880 TGTTTTATTTGGAGATGGACTGAAG 57.547 36.000 0.00 0.00 0.00 3.02
3557 3811 0.689623 CTGCCATAGGGGACATCTCC 59.310 60.000 0.00 0.00 40.01 3.71
3635 3889 4.061596 GTCTCATTATTGTAGCTCCAGCC 58.938 47.826 0.00 0.00 43.38 4.85
3853 4107 5.132897 TCTGTTTTTCAAAGTGTGCAAGT 57.867 34.783 0.00 0.00 0.00 3.16
4136 4390 5.276461 TCTCACAGTTCAAGAGCTAACAA 57.724 39.130 0.23 0.00 0.00 2.83
4186 4440 3.753272 TCTCTAGTTCAAGTGCAATTGGC 59.247 43.478 25.10 17.94 45.13 4.52
4739 4996 2.260154 TGTGGCCTTGCATGTGTCG 61.260 57.895 3.32 0.00 0.00 4.35
5179 5443 7.397892 TTTTCTCTGAAACATGTTACCAACA 57.602 32.000 12.39 6.80 46.94 3.33
5250 5514 7.182817 ACATACCACAATCTGAAGTAAGCTA 57.817 36.000 0.00 0.00 0.00 3.32
5339 5603 5.560966 CTTGTGTTCCAAGTTGTTGTACT 57.439 39.130 1.45 0.00 44.64 2.73
5340 5604 5.554822 TTGTGTTCCAAGTTGTTGTACTC 57.445 39.130 1.45 0.00 30.95 2.59
5341 5605 3.942748 TGTGTTCCAAGTTGTTGTACTCC 59.057 43.478 1.45 0.00 30.95 3.85
5342 5606 3.314357 GTGTTCCAAGTTGTTGTACTCCC 59.686 47.826 1.45 0.00 30.95 4.30
5343 5607 3.201266 TGTTCCAAGTTGTTGTACTCCCT 59.799 43.478 1.45 0.00 30.95 4.20
5344 5608 4.409574 TGTTCCAAGTTGTTGTACTCCCTA 59.590 41.667 1.45 0.00 30.95 3.53
5345 5609 5.072600 TGTTCCAAGTTGTTGTACTCCCTAT 59.927 40.000 1.45 0.00 30.95 2.57
5346 5610 5.160607 TCCAAGTTGTTGTACTCCCTATG 57.839 43.478 1.45 0.00 30.95 2.23
5347 5611 4.595781 TCCAAGTTGTTGTACTCCCTATGT 59.404 41.667 1.45 0.00 30.95 2.29
5348 5612 5.072600 TCCAAGTTGTTGTACTCCCTATGTT 59.927 40.000 1.45 0.00 30.95 2.71
5349 5613 5.411669 CCAAGTTGTTGTACTCCCTATGTTC 59.588 44.000 1.45 0.00 30.95 3.18
5350 5614 5.818678 AGTTGTTGTACTCCCTATGTTCA 57.181 39.130 0.00 0.00 0.00 3.18
5351 5615 5.548406 AGTTGTTGTACTCCCTATGTTCAC 58.452 41.667 0.00 0.00 0.00 3.18
5352 5616 5.307196 AGTTGTTGTACTCCCTATGTTCACT 59.693 40.000 0.00 0.00 0.00 3.41
5353 5617 5.818678 TGTTGTACTCCCTATGTTCACTT 57.181 39.130 0.00 0.00 0.00 3.16
5354 5618 6.182507 TGTTGTACTCCCTATGTTCACTTT 57.817 37.500 0.00 0.00 0.00 2.66
5355 5619 6.597562 TGTTGTACTCCCTATGTTCACTTTT 58.402 36.000 0.00 0.00 0.00 2.27
5356 5620 7.737869 TGTTGTACTCCCTATGTTCACTTTTA 58.262 34.615 0.00 0.00 0.00 1.52
5357 5621 8.380099 TGTTGTACTCCCTATGTTCACTTTTAT 58.620 33.333 0.00 0.00 0.00 1.40
5358 5622 9.880157 GTTGTACTCCCTATGTTCACTTTTATA 57.120 33.333 0.00 0.00 0.00 0.98
5363 5627 7.980099 ACTCCCTATGTTCACTTTTATAAGACG 59.020 37.037 0.00 0.00 35.30 4.18
5364 5628 7.844009 TCCCTATGTTCACTTTTATAAGACGT 58.156 34.615 0.00 0.00 35.30 4.34
5365 5629 8.316214 TCCCTATGTTCACTTTTATAAGACGTT 58.684 33.333 0.00 0.00 35.30 3.99
5366 5630 8.943002 CCCTATGTTCACTTTTATAAGACGTTT 58.057 33.333 0.00 0.00 35.30 3.60
5374 5638 8.706035 TCACTTTTATAAGACGTTTTAGACAGC 58.294 33.333 4.75 0.00 35.30 4.40
5375 5639 8.709646 CACTTTTATAAGACGTTTTAGACAGCT 58.290 33.333 4.75 0.00 35.30 4.24
5376 5640 8.709646 ACTTTTATAAGACGTTTTAGACAGCTG 58.290 33.333 13.48 13.48 35.30 4.24
5377 5641 8.821147 TTTTATAAGACGTTTTAGACAGCTGA 57.179 30.769 23.35 0.00 0.00 4.26
5378 5642 8.821147 TTTATAAGACGTTTTAGACAGCTGAA 57.179 30.769 23.35 0.48 0.00 3.02
5379 5643 8.821147 TTATAAGACGTTTTAGACAGCTGAAA 57.179 30.769 23.35 7.93 0.00 2.69
5380 5644 7.907214 ATAAGACGTTTTAGACAGCTGAAAT 57.093 32.000 23.35 8.03 33.03 2.17
5381 5645 6.619801 AAGACGTTTTAGACAGCTGAAATT 57.380 33.333 23.35 0.00 33.03 1.82
5382 5646 5.990408 AGACGTTTTAGACAGCTGAAATTG 58.010 37.500 23.35 9.51 33.03 2.32
5383 5647 5.758296 AGACGTTTTAGACAGCTGAAATTGA 59.242 36.000 23.35 0.00 33.03 2.57
5384 5648 6.260050 AGACGTTTTAGACAGCTGAAATTGAA 59.740 34.615 23.35 4.96 33.03 2.69
5385 5649 6.199393 ACGTTTTAGACAGCTGAAATTGAAC 58.801 36.000 23.35 15.30 33.03 3.18
5386 5650 6.038271 ACGTTTTAGACAGCTGAAATTGAACT 59.962 34.615 23.35 8.36 33.03 3.01
5387 5651 6.358030 CGTTTTAGACAGCTGAAATTGAACTG 59.642 38.462 23.35 9.82 33.03 3.16
5388 5652 6.942532 TTTAGACAGCTGAAATTGAACTGT 57.057 33.333 23.35 0.00 43.93 3.55
5389 5653 6.942532 TTAGACAGCTGAAATTGAACTGTT 57.057 33.333 23.35 0.00 41.45 3.16
5390 5654 5.841957 AGACAGCTGAAATTGAACTGTTT 57.158 34.783 23.35 0.00 41.45 2.83
5391 5655 6.212888 AGACAGCTGAAATTGAACTGTTTT 57.787 33.333 23.35 0.00 41.45 2.43
5392 5656 6.038356 AGACAGCTGAAATTGAACTGTTTTG 58.962 36.000 23.35 0.00 41.45 2.44
5393 5657 5.111293 ACAGCTGAAATTGAACTGTTTTGG 58.889 37.500 23.35 0.00 38.38 3.28
5394 5658 4.508861 CAGCTGAAATTGAACTGTTTTGGG 59.491 41.667 8.42 0.00 0.00 4.12
5395 5659 4.162131 AGCTGAAATTGAACTGTTTTGGGT 59.838 37.500 0.00 0.00 0.00 4.51
5396 5660 4.270808 GCTGAAATTGAACTGTTTTGGGTG 59.729 41.667 0.00 0.00 0.00 4.61
5397 5661 5.413309 TGAAATTGAACTGTTTTGGGTGT 57.587 34.783 0.00 0.00 0.00 4.16
5398 5662 5.799213 TGAAATTGAACTGTTTTGGGTGTT 58.201 33.333 0.00 0.00 0.00 3.32
5399 5663 5.641209 TGAAATTGAACTGTTTTGGGTGTTG 59.359 36.000 0.00 0.00 0.00 3.33
5400 5664 4.817318 ATTGAACTGTTTTGGGTGTTGT 57.183 36.364 0.00 0.00 0.00 3.32
5401 5665 3.859411 TGAACTGTTTTGGGTGTTGTC 57.141 42.857 0.00 0.00 0.00 3.18
5402 5666 3.426615 TGAACTGTTTTGGGTGTTGTCT 58.573 40.909 0.00 0.00 0.00 3.41
5403 5667 3.829601 TGAACTGTTTTGGGTGTTGTCTT 59.170 39.130 0.00 0.00 0.00 3.01
5404 5668 5.010933 TGAACTGTTTTGGGTGTTGTCTTA 58.989 37.500 0.00 0.00 0.00 2.10
5405 5669 5.477291 TGAACTGTTTTGGGTGTTGTCTTAA 59.523 36.000 0.00 0.00 0.00 1.85
5406 5670 5.986501 ACTGTTTTGGGTGTTGTCTTAAA 57.013 34.783 0.00 0.00 0.00 1.52
5407 5671 6.538945 ACTGTTTTGGGTGTTGTCTTAAAT 57.461 33.333 0.00 0.00 0.00 1.40
5408 5672 6.337356 ACTGTTTTGGGTGTTGTCTTAAATG 58.663 36.000 0.00 0.00 0.00 2.32
5409 5673 6.071051 ACTGTTTTGGGTGTTGTCTTAAATGT 60.071 34.615 0.00 0.00 0.00 2.71
5410 5674 6.334202 TGTTTTGGGTGTTGTCTTAAATGTC 58.666 36.000 0.00 0.00 0.00 3.06
5411 5675 6.153680 TGTTTTGGGTGTTGTCTTAAATGTCT 59.846 34.615 0.00 0.00 0.00 3.41
5412 5676 7.339721 TGTTTTGGGTGTTGTCTTAAATGTCTA 59.660 33.333 0.00 0.00 0.00 2.59
5413 5677 7.883391 TTTGGGTGTTGTCTTAAATGTCTAA 57.117 32.000 0.00 0.00 0.00 2.10
5414 5678 7.883391 TTGGGTGTTGTCTTAAATGTCTAAA 57.117 32.000 0.00 0.00 0.00 1.85
5415 5679 7.266922 TGGGTGTTGTCTTAAATGTCTAAAC 57.733 36.000 0.00 0.00 0.00 2.01
5416 5680 6.017770 TGGGTGTTGTCTTAAATGTCTAAACG 60.018 38.462 0.00 0.00 0.00 3.60
5417 5681 6.368213 GGTGTTGTCTTAAATGTCTAAACGG 58.632 40.000 0.00 0.00 0.00 4.44
5418 5682 6.017687 GGTGTTGTCTTAAATGTCTAAACGGT 60.018 38.462 0.00 0.00 0.00 4.83
5419 5683 7.067728 GTGTTGTCTTAAATGTCTAAACGGTC 58.932 38.462 0.00 0.00 0.00 4.79
5420 5684 6.987992 TGTTGTCTTAAATGTCTAAACGGTCT 59.012 34.615 0.00 0.00 0.00 3.85
5421 5685 7.496591 TGTTGTCTTAAATGTCTAAACGGTCTT 59.503 33.333 0.00 0.00 0.00 3.01
5422 5686 8.981647 GTTGTCTTAAATGTCTAAACGGTCTTA 58.018 33.333 0.00 0.00 0.00 2.10
5423 5687 8.524870 TGTCTTAAATGTCTAAACGGTCTTAC 57.475 34.615 0.00 0.00 0.00 2.34
5424 5688 8.143193 TGTCTTAAATGTCTAAACGGTCTTACA 58.857 33.333 0.00 0.00 0.00 2.41
5425 5689 8.981647 GTCTTAAATGTCTAAACGGTCTTACAA 58.018 33.333 0.00 0.00 0.00 2.41
5426 5690 9.545105 TCTTAAATGTCTAAACGGTCTTACAAA 57.455 29.630 0.00 0.00 0.00 2.83
5429 5693 7.797038 AATGTCTAAACGGTCTTACAAAAGT 57.203 32.000 0.00 0.00 34.13 2.66
5430 5694 6.592798 TGTCTAAACGGTCTTACAAAAGTG 57.407 37.500 0.00 0.00 34.13 3.16
5431 5695 6.339730 TGTCTAAACGGTCTTACAAAAGTGA 58.660 36.000 0.00 0.00 34.13 3.41
5432 5696 6.817641 TGTCTAAACGGTCTTACAAAAGTGAA 59.182 34.615 0.00 0.00 34.13 3.18
5433 5697 7.121911 GTCTAAACGGTCTTACAAAAGTGAAC 58.878 38.462 0.00 0.00 34.13 3.18
5434 5698 4.525411 AACGGTCTTACAAAAGTGAACG 57.475 40.909 0.00 0.00 34.13 3.95
5435 5699 2.867975 ACGGTCTTACAAAAGTGAACGG 59.132 45.455 0.00 0.00 34.13 4.44
5436 5700 3.125316 CGGTCTTACAAAAGTGAACGGA 58.875 45.455 0.00 0.00 34.13 4.69
5437 5701 3.183775 CGGTCTTACAAAAGTGAACGGAG 59.816 47.826 0.00 0.00 34.13 4.63
5438 5702 3.497262 GGTCTTACAAAAGTGAACGGAGG 59.503 47.826 0.00 0.00 34.13 4.30
5439 5703 3.497262 GTCTTACAAAAGTGAACGGAGGG 59.503 47.826 0.00 0.00 34.13 4.30
5440 5704 3.388676 TCTTACAAAAGTGAACGGAGGGA 59.611 43.478 0.00 0.00 34.13 4.20
5511 5775 0.179113 CCTTGTTTGGTGTGGTGTGC 60.179 55.000 0.00 0.00 0.00 4.57
5512 5776 0.179113 CTTGTTTGGTGTGGTGTGCC 60.179 55.000 0.00 0.00 0.00 5.01
5513 5777 0.900182 TTGTTTGGTGTGGTGTGCCA 60.900 50.000 0.00 0.00 43.73 4.92
5537 5801 2.299297 GTGTGCCTGGTACTCTAGTTGT 59.701 50.000 15.99 0.00 0.00 3.32
5558 5822 3.002791 TGCATTTCCTTTCGCTACTGAG 58.997 45.455 0.00 0.00 0.00 3.35
5559 5823 2.223135 GCATTTCCTTTCGCTACTGAGC 60.223 50.000 0.00 0.00 46.00 4.26
5587 5851 3.740832 TGTGCTGTGATGAAAGAGTAACG 59.259 43.478 0.00 0.00 0.00 3.18
5611 5875 3.515630 TGCATCTCTACTCTTTCGCTTG 58.484 45.455 0.00 0.00 0.00 4.01
5651 5915 1.411977 CATCCCAGCAGACTCGAATCT 59.588 52.381 0.00 0.00 0.00 2.40
5675 5939 9.249457 TCTACATCGAGCTTAATTAACATTCTG 57.751 33.333 0.00 0.00 0.00 3.02
5684 5948 7.555554 AGCTTAATTAACATTCTGCTCTGTGAT 59.444 33.333 0.00 0.00 29.91 3.06
5707 5971 4.597079 TGCAGAATTCACGTCTCAAAAAC 58.403 39.130 8.44 0.00 0.00 2.43
5754 6018 8.472683 AAAGAAATCTCTCTCTGATTACAACG 57.527 34.615 0.00 0.00 34.19 4.10
5755 6019 6.039616 AGAAATCTCTCTCTGATTACAACGC 58.960 40.000 0.00 0.00 34.19 4.84
5777 6041 1.305718 ACCTGTCCAGCTCTCCCTC 60.306 63.158 0.00 0.00 0.00 4.30
5778 6042 2.063378 CCTGTCCAGCTCTCCCTCC 61.063 68.421 0.00 0.00 0.00 4.30
5779 6043 2.039624 TGTCCAGCTCTCCCTCCC 59.960 66.667 0.00 0.00 0.00 4.30
5780 6044 2.366570 GTCCAGCTCTCCCTCCCT 59.633 66.667 0.00 0.00 0.00 4.20
5809 6073 1.066645 GCAAGGCAATGAAGGAAAGGG 60.067 52.381 0.00 0.00 0.00 3.95
5812 6076 3.023939 AGGCAATGAAGGAAAGGGATC 57.976 47.619 0.00 0.00 0.00 3.36
5930 6281 1.271102 TGTTTTAATTGCTGGTCCCGC 59.729 47.619 0.00 0.00 0.00 6.13
5955 6310 5.990120 AAGTTTGATTGCCTAATCTGCTT 57.010 34.783 0.00 0.00 42.56 3.91
5963 6318 5.420725 TTGCCTAATCTGCTTCTAACTGA 57.579 39.130 0.00 0.00 0.00 3.41
5965 6320 5.178797 TGCCTAATCTGCTTCTAACTGAAC 58.821 41.667 0.00 0.00 0.00 3.18
5966 6321 5.046304 TGCCTAATCTGCTTCTAACTGAACT 60.046 40.000 0.00 0.00 0.00 3.01
5967 6322 5.293079 GCCTAATCTGCTTCTAACTGAACTG 59.707 44.000 0.00 0.00 0.00 3.16
5968 6323 5.293079 CCTAATCTGCTTCTAACTGAACTGC 59.707 44.000 0.00 0.00 0.00 4.40
5969 6324 3.751479 TCTGCTTCTAACTGAACTGCA 57.249 42.857 0.00 0.00 35.48 4.41
5971 6326 3.809832 TCTGCTTCTAACTGAACTGCAAC 59.190 43.478 0.00 0.00 36.07 4.17
5973 6328 2.878406 GCTTCTAACTGAACTGCAACCA 59.122 45.455 0.00 0.00 0.00 3.67
5974 6329 3.315191 GCTTCTAACTGAACTGCAACCAA 59.685 43.478 0.00 0.00 0.00 3.67
5975 6330 4.202010 GCTTCTAACTGAACTGCAACCAAA 60.202 41.667 0.00 0.00 0.00 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 1.394917 GATGCTGCATCGAACGAAGTT 59.605 47.619 25.09 0.00 41.82 2.66
49 50 1.002366 GATGCTGCATCGAACGAAGT 58.998 50.000 25.09 0.00 34.40 3.01
68 69 2.604914 GCACTCACTTCATACATGGTCG 59.395 50.000 0.00 0.00 0.00 4.79
82 83 3.852536 GTCTATGAGTTGTACGCACTCAC 59.147 47.826 23.24 11.59 42.37 3.51
181 182 7.253817 GCAGTAGTACTAAAGCTTTCATCGAAG 60.254 40.741 16.57 8.91 0.00 3.79
184 185 6.020281 CAGCAGTAGTACTAAAGCTTTCATCG 60.020 42.308 21.45 5.63 0.00 3.84
185 186 6.256757 CCAGCAGTAGTACTAAAGCTTTCATC 59.743 42.308 21.45 5.32 0.00 2.92
187 188 5.245301 TCCAGCAGTAGTACTAAAGCTTTCA 59.755 40.000 21.45 10.12 0.00 2.69
188 189 5.721232 TCCAGCAGTAGTACTAAAGCTTTC 58.279 41.667 21.45 0.69 0.00 2.62
189 190 5.246429 ACTCCAGCAGTAGTACTAAAGCTTT 59.754 40.000 21.45 17.30 31.37 3.51
190 191 4.773149 ACTCCAGCAGTAGTACTAAAGCTT 59.227 41.667 21.45 9.58 31.37 3.74
192 193 4.722361 ACTCCAGCAGTAGTACTAAAGC 57.278 45.455 16.22 16.22 31.37 3.51
298 414 4.034258 GTGTCGCGGACGTCAGGA 62.034 66.667 18.91 10.06 37.99 3.86
342 460 4.513318 GGATTCCTTTCAGCGATAAAGAGG 59.487 45.833 9.25 0.00 36.27 3.69
343 461 5.118990 TGGATTCCTTTCAGCGATAAAGAG 58.881 41.667 3.95 2.19 36.27 2.85
494 613 4.082125 GGGGATATTTGTAGGCCATTCTG 58.918 47.826 5.01 0.00 0.00 3.02
530 649 3.521796 GGAGGGAAATGCTGCGGC 61.522 66.667 11.65 11.65 39.26 6.53
534 653 1.821332 GCCGAGGAGGGAAATGCTG 60.821 63.158 0.00 0.00 41.48 4.41
554 673 1.895707 CTTGCTGATGATCCCGGGC 60.896 63.158 18.49 2.59 0.00 6.13
620 739 1.355066 GACGGAAGCCAAAGAGCTCG 61.355 60.000 8.37 0.00 44.11 5.03
621 740 1.355066 CGACGGAAGCCAAAGAGCTC 61.355 60.000 5.27 5.27 44.11 4.09
623 742 2.391389 CCGACGGAAGCCAAAGAGC 61.391 63.158 8.64 0.00 0.00 4.09
624 743 0.245539 TACCGACGGAAGCCAAAGAG 59.754 55.000 23.38 0.00 0.00 2.85
806 932 0.990374 AATGAGTTCCTGCTCTGCCT 59.010 50.000 0.00 0.00 36.51 4.75
890 1016 2.106511 TGTTTCCACCCAAGAGAAGGAG 59.893 50.000 0.00 0.00 0.00 3.69
898 1024 0.895559 GGCCTCTGTTTCCACCCAAG 60.896 60.000 0.00 0.00 0.00 3.61
916 1042 2.608546 ACTTCGTTCTCGATCTAGACGG 59.391 50.000 14.51 1.12 45.65 4.79
933 1059 4.113354 CCAGAAGCTAACACGGATACTTC 58.887 47.826 0.00 0.00 35.00 3.01
1015 1154 1.271543 ACAGAGCAGTATGGCAGCAAA 60.272 47.619 0.00 0.00 35.86 3.68
1157 1296 2.731348 GCTCGATAGCCGGCTTCG 60.731 66.667 35.05 35.05 43.40 3.79
1212 1351 0.526211 GACTCAATTTTGTCCCGGGC 59.474 55.000 18.49 12.24 0.00 6.13
1225 1364 4.563580 GGTGTCCTGCATAAGAAGACTCAA 60.564 45.833 0.00 0.00 0.00 3.02
1269 1408 9.660180 AGAAAGAAGTATGAACCTTCAATAGTC 57.340 33.333 0.00 0.00 41.13 2.59
1323 1462 4.313282 TGCAGATATAGAATGCAGACAGC 58.687 43.478 5.45 0.00 44.56 4.40
1450 1631 3.846754 GCATTTTGGTGCGTGCTC 58.153 55.556 0.00 0.00 35.10 4.26
1506 1703 2.110213 TTTTGGTCGCAGCGAGGT 59.890 55.556 20.23 0.00 36.23 3.85
1525 1722 9.944376 TTGCTTCTCTACATAAGTTATGTTTCT 57.056 29.630 28.65 10.60 46.69 2.52
1557 1754 3.439895 TTGGTTCGGTTTTGGCTTTAC 57.560 42.857 0.00 0.00 0.00 2.01
1600 1797 5.731591 ACTAAGCGCAGTTAGAAACCTAAT 58.268 37.500 19.79 0.00 34.58 1.73
1647 1844 8.388853 CAATATGATCAGGCTCAAATATCTTCG 58.611 37.037 0.09 0.00 0.00 3.79
1668 1865 9.452287 AAACTGGCAAATTGCTAATTTCAATAT 57.548 25.926 18.04 0.00 44.28 1.28
1691 1888 6.564854 GATTGCATGACAAGCAGATTAAAC 57.435 37.500 5.40 0.00 44.25 2.01
1705 1902 6.724893 ATTCAGGAAATGATGATTGCATGA 57.275 33.333 0.00 0.00 36.35 3.07
1741 1938 5.405935 AAGCCAAGCAATTAGTTAAAGGG 57.594 39.130 0.00 0.00 0.00 3.95
1751 1948 4.383173 CAAGGAAAGAAAGCCAAGCAATT 58.617 39.130 0.00 0.00 0.00 2.32
1761 1958 3.108144 CAACACGTGCAAGGAAAGAAAG 58.892 45.455 17.22 0.00 0.00 2.62
1829 2076 7.849804 TTCCTCTGTAGCTGAATTTGATTAC 57.150 36.000 0.00 0.00 0.00 1.89
1843 2090 4.335416 TCCAAGCCAAATTTCCTCTGTAG 58.665 43.478 0.00 0.00 0.00 2.74
1909 2156 5.479306 TCAGTAGGACTAAAATCTGCACAC 58.521 41.667 0.00 0.00 0.00 3.82
1910 2157 5.246203 ACTCAGTAGGACTAAAATCTGCACA 59.754 40.000 0.00 0.00 0.00 4.57
1911 2158 5.725362 ACTCAGTAGGACTAAAATCTGCAC 58.275 41.667 0.00 0.00 0.00 4.57
1939 2188 8.747666 CGATCTACTTCTAGTTTGCATAAGAAC 58.252 37.037 0.00 0.00 0.00 3.01
2110 2364 5.303333 TGATTGTGGACCTAATACAGCGATA 59.697 40.000 0.00 0.00 0.00 2.92
2305 2559 2.208431 GCGATGACTTCTCTCCATTGG 58.792 52.381 0.00 0.00 0.00 3.16
2389 2643 5.537300 TGTAGGCTATCTTGGACATCTTC 57.463 43.478 0.00 0.00 0.00 2.87
2596 2850 4.261698 CCAGATGAGTCTATCACTGCAGAG 60.262 50.000 23.35 13.75 41.91 3.35
2611 2865 1.404391 GAAGCAACATGCCCAGATGAG 59.596 52.381 0.00 0.00 46.52 2.90
2670 2924 3.079578 CCAGAGTCAGCAACATGTTGAT 58.920 45.455 36.65 30.40 39.69 2.57
2671 2925 2.497138 CCAGAGTCAGCAACATGTTGA 58.503 47.619 36.65 17.74 42.93 3.18
2724 2978 2.548480 CGGTTTCCTTTCCTTGTCAGAC 59.452 50.000 0.00 0.00 0.00 3.51
2731 2985 2.490991 CTCGAACGGTTTCCTTTCCTT 58.509 47.619 0.00 0.00 29.40 3.36
2761 3015 4.186926 AGTCATAAGCATGTGCAGTGTAG 58.813 43.478 7.83 0.00 45.16 2.74
2827 3081 5.902613 CAGAAAAAGATACTGCATTCCCA 57.097 39.130 0.00 0.00 0.00 4.37
2903 3157 6.591834 AGTTTATCTCCATTGTTGAGAACTCG 59.408 38.462 0.00 0.00 41.87 4.18
2927 3181 3.070018 CCTGCAACACTTTCTCCAGTAG 58.930 50.000 0.00 0.00 0.00 2.57
3152 3406 1.556911 CTGACCAGGCCAGATAACACT 59.443 52.381 5.01 0.00 33.65 3.55
3153 3407 1.555075 TCTGACCAGGCCAGATAACAC 59.445 52.381 5.01 0.00 35.89 3.32
3205 3459 4.108570 TCCTTAGAAGCTTCCCATGGTAA 58.891 43.478 22.81 12.20 0.00 2.85
3232 3486 2.391389 GCTTGTACGCAGAGGCACC 61.391 63.158 0.00 0.00 41.24 5.01
3301 3555 8.578308 TTGCAGATTTAAAAACATCAACTGAG 57.422 30.769 0.00 0.00 0.00 3.35
3385 3639 1.751924 AGGTCACTGTAGCTCGGATTC 59.248 52.381 0.00 0.00 0.00 2.52
3557 3811 8.131100 ACAAGTCTTGTTCTATTTGTCACAATG 58.869 33.333 12.62 0.00 42.22 2.82
3635 3889 1.734465 GCGTTTGATTCAGTCTCCCTG 59.266 52.381 0.00 0.00 42.97 4.45
3873 4127 0.249676 AGGTGCAGAGCAGACATCAG 59.750 55.000 0.00 0.00 40.08 2.90
4136 4390 4.324331 GCTATCAAGACCTTTTACCCCTGT 60.324 45.833 0.00 0.00 0.00 4.00
4186 4440 3.689161 TGGCAAACGATCCAACTTGATAG 59.311 43.478 0.00 0.00 0.00 2.08
4526 4783 1.457267 TTGGAAAGGCCTGCAGCAA 60.457 52.632 5.69 2.11 46.50 3.91
4739 4996 4.155644 CCAGAAGAAAATCAGGAGAGCAAC 59.844 45.833 0.00 0.00 0.00 4.17
5038 5299 2.099141 TTCGGAATCTGCCACTTCAG 57.901 50.000 0.00 0.00 35.46 3.02
5179 5443 2.437281 CTGCTACTTCTCCCATCCACAT 59.563 50.000 0.00 0.00 0.00 3.21
5183 5447 0.833287 TGCTGCTACTTCTCCCATCC 59.167 55.000 0.00 0.00 0.00 3.51
5337 5601 7.980099 CGTCTTATAAAAGTGAACATAGGGAGT 59.020 37.037 0.00 0.00 34.13 3.85
5338 5602 7.980099 ACGTCTTATAAAAGTGAACATAGGGAG 59.020 37.037 0.00 0.00 34.13 4.30
5339 5603 7.844009 ACGTCTTATAAAAGTGAACATAGGGA 58.156 34.615 0.00 0.00 34.13 4.20
5340 5604 8.488651 AACGTCTTATAAAAGTGAACATAGGG 57.511 34.615 0.00 0.00 34.13 3.53
5348 5612 8.706035 GCTGTCTAAAACGTCTTATAAAAGTGA 58.294 33.333 0.00 0.00 34.13 3.41
5349 5613 8.709646 AGCTGTCTAAAACGTCTTATAAAAGTG 58.290 33.333 0.00 0.00 34.13 3.16
5350 5614 8.709646 CAGCTGTCTAAAACGTCTTATAAAAGT 58.290 33.333 5.25 0.00 34.13 2.66
5351 5615 8.922676 TCAGCTGTCTAAAACGTCTTATAAAAG 58.077 33.333 14.67 0.00 0.00 2.27
5352 5616 8.821147 TCAGCTGTCTAAAACGTCTTATAAAA 57.179 30.769 14.67 0.00 0.00 1.52
5353 5617 8.821147 TTCAGCTGTCTAAAACGTCTTATAAA 57.179 30.769 14.67 0.00 0.00 1.40
5354 5618 8.821147 TTTCAGCTGTCTAAAACGTCTTATAA 57.179 30.769 14.67 0.00 0.00 0.98
5355 5619 8.997621 ATTTCAGCTGTCTAAAACGTCTTATA 57.002 30.769 14.67 0.00 0.00 0.98
5356 5620 7.907214 ATTTCAGCTGTCTAAAACGTCTTAT 57.093 32.000 14.67 0.00 0.00 1.73
5357 5621 7.439955 TCAATTTCAGCTGTCTAAAACGTCTTA 59.560 33.333 14.67 0.00 0.00 2.10
5358 5622 6.260050 TCAATTTCAGCTGTCTAAAACGTCTT 59.740 34.615 14.67 0.00 0.00 3.01
5359 5623 5.758296 TCAATTTCAGCTGTCTAAAACGTCT 59.242 36.000 14.67 0.00 0.00 4.18
5360 5624 5.985781 TCAATTTCAGCTGTCTAAAACGTC 58.014 37.500 14.67 0.00 0.00 4.34
5361 5625 6.038271 AGTTCAATTTCAGCTGTCTAAAACGT 59.962 34.615 14.67 0.00 0.00 3.99
5362 5626 6.358030 CAGTTCAATTTCAGCTGTCTAAAACG 59.642 38.462 14.67 3.27 0.00 3.60
5363 5627 7.196331 ACAGTTCAATTTCAGCTGTCTAAAAC 58.804 34.615 14.67 11.99 35.78 2.43
5364 5628 7.333528 ACAGTTCAATTTCAGCTGTCTAAAA 57.666 32.000 14.67 7.20 35.78 1.52
5365 5629 6.942532 ACAGTTCAATTTCAGCTGTCTAAA 57.057 33.333 14.67 7.59 35.78 1.85
5366 5630 6.942532 AACAGTTCAATTTCAGCTGTCTAA 57.057 33.333 14.67 7.33 39.19 2.10
5367 5631 6.942532 AAACAGTTCAATTTCAGCTGTCTA 57.057 33.333 14.67 0.36 39.19 2.59
5368 5632 5.841957 AAACAGTTCAATTTCAGCTGTCT 57.158 34.783 14.67 0.00 39.19 3.41
5369 5633 5.232838 CCAAAACAGTTCAATTTCAGCTGTC 59.767 40.000 14.67 0.00 39.19 3.51
5370 5634 5.111293 CCAAAACAGTTCAATTTCAGCTGT 58.889 37.500 14.67 0.00 41.51 4.40
5371 5635 4.508861 CCCAAAACAGTTCAATTTCAGCTG 59.491 41.667 7.63 7.63 0.00 4.24
5372 5636 4.162131 ACCCAAAACAGTTCAATTTCAGCT 59.838 37.500 0.00 0.00 0.00 4.24
5373 5637 4.270808 CACCCAAAACAGTTCAATTTCAGC 59.729 41.667 0.00 0.00 0.00 4.26
5374 5638 5.418676 ACACCCAAAACAGTTCAATTTCAG 58.581 37.500 0.00 0.00 0.00 3.02
5375 5639 5.413309 ACACCCAAAACAGTTCAATTTCA 57.587 34.783 0.00 0.00 0.00 2.69
5376 5640 5.641636 ACAACACCCAAAACAGTTCAATTTC 59.358 36.000 0.00 0.00 0.00 2.17
5377 5641 5.555966 ACAACACCCAAAACAGTTCAATTT 58.444 33.333 0.00 0.00 0.00 1.82
5378 5642 5.046663 AGACAACACCCAAAACAGTTCAATT 60.047 36.000 0.00 0.00 0.00 2.32
5379 5643 4.466015 AGACAACACCCAAAACAGTTCAAT 59.534 37.500 0.00 0.00 0.00 2.57
5380 5644 3.829601 AGACAACACCCAAAACAGTTCAA 59.170 39.130 0.00 0.00 0.00 2.69
5381 5645 3.426615 AGACAACACCCAAAACAGTTCA 58.573 40.909 0.00 0.00 0.00 3.18
5382 5646 4.450082 AAGACAACACCCAAAACAGTTC 57.550 40.909 0.00 0.00 0.00 3.01
5383 5647 5.986501 TTAAGACAACACCCAAAACAGTT 57.013 34.783 0.00 0.00 0.00 3.16
5384 5648 5.986501 TTTAAGACAACACCCAAAACAGT 57.013 34.783 0.00 0.00 0.00 3.55
5385 5649 6.337356 ACATTTAAGACAACACCCAAAACAG 58.663 36.000 0.00 0.00 0.00 3.16
5386 5650 6.153680 AGACATTTAAGACAACACCCAAAACA 59.846 34.615 0.00 0.00 0.00 2.83
5387 5651 6.569780 AGACATTTAAGACAACACCCAAAAC 58.430 36.000 0.00 0.00 0.00 2.43
5388 5652 6.783708 AGACATTTAAGACAACACCCAAAA 57.216 33.333 0.00 0.00 0.00 2.44
5389 5653 7.883391 TTAGACATTTAAGACAACACCCAAA 57.117 32.000 0.00 0.00 0.00 3.28
5390 5654 7.467539 CGTTTAGACATTTAAGACAACACCCAA 60.468 37.037 0.00 0.00 0.00 4.12
5391 5655 6.017770 CGTTTAGACATTTAAGACAACACCCA 60.018 38.462 0.00 0.00 0.00 4.51
5392 5656 6.368213 CGTTTAGACATTTAAGACAACACCC 58.632 40.000 0.00 0.00 0.00 4.61
5393 5657 6.017687 ACCGTTTAGACATTTAAGACAACACC 60.018 38.462 0.00 0.00 0.00 4.16
5394 5658 6.951643 ACCGTTTAGACATTTAAGACAACAC 58.048 36.000 0.00 0.00 0.00 3.32
5395 5659 6.987992 AGACCGTTTAGACATTTAAGACAACA 59.012 34.615 0.00 0.00 0.00 3.33
5396 5660 7.417496 AGACCGTTTAGACATTTAAGACAAC 57.583 36.000 0.00 0.00 0.00 3.32
5397 5661 8.981647 GTAAGACCGTTTAGACATTTAAGACAA 58.018 33.333 0.00 0.00 0.00 3.18
5398 5662 8.143193 TGTAAGACCGTTTAGACATTTAAGACA 58.857 33.333 0.00 0.00 0.00 3.41
5399 5663 8.524870 TGTAAGACCGTTTAGACATTTAAGAC 57.475 34.615 0.00 0.00 0.00 3.01
5400 5664 9.545105 TTTGTAAGACCGTTTAGACATTTAAGA 57.455 29.630 0.00 0.00 0.00 2.10
5403 5667 9.328845 ACTTTTGTAAGACCGTTTAGACATTTA 57.671 29.630 0.00 0.00 35.30 1.40
5404 5668 8.126700 CACTTTTGTAAGACCGTTTAGACATTT 58.873 33.333 0.00 0.00 35.30 2.32
5405 5669 7.496591 TCACTTTTGTAAGACCGTTTAGACATT 59.503 33.333 0.00 0.00 35.30 2.71
5406 5670 6.987992 TCACTTTTGTAAGACCGTTTAGACAT 59.012 34.615 0.00 0.00 35.30 3.06
5407 5671 6.339730 TCACTTTTGTAAGACCGTTTAGACA 58.660 36.000 0.00 0.00 35.30 3.41
5408 5672 6.833342 TCACTTTTGTAAGACCGTTTAGAC 57.167 37.500 0.00 0.00 35.30 2.59
5409 5673 6.019640 CGTTCACTTTTGTAAGACCGTTTAGA 60.020 38.462 0.00 0.00 35.30 2.10
5410 5674 6.124759 CGTTCACTTTTGTAAGACCGTTTAG 58.875 40.000 0.00 0.00 35.30 1.85
5411 5675 5.006552 CCGTTCACTTTTGTAAGACCGTTTA 59.993 40.000 0.00 0.00 35.30 2.01
5412 5676 4.201841 CCGTTCACTTTTGTAAGACCGTTT 60.202 41.667 0.00 0.00 35.30 3.60
5413 5677 3.310501 CCGTTCACTTTTGTAAGACCGTT 59.689 43.478 0.00 0.00 35.30 4.44
5414 5678 2.867975 CCGTTCACTTTTGTAAGACCGT 59.132 45.455 0.00 0.00 35.30 4.83
5415 5679 3.125316 TCCGTTCACTTTTGTAAGACCG 58.875 45.455 0.00 0.00 35.30 4.79
5416 5680 3.497262 CCTCCGTTCACTTTTGTAAGACC 59.503 47.826 0.00 0.00 35.30 3.85
5417 5681 3.497262 CCCTCCGTTCACTTTTGTAAGAC 59.503 47.826 0.00 0.00 35.30 3.01
5418 5682 3.388676 TCCCTCCGTTCACTTTTGTAAGA 59.611 43.478 0.00 0.00 35.30 2.10
5419 5683 3.735591 TCCCTCCGTTCACTTTTGTAAG 58.264 45.455 0.00 0.00 37.40 2.34
5420 5684 3.135167 ACTCCCTCCGTTCACTTTTGTAA 59.865 43.478 0.00 0.00 0.00 2.41
5421 5685 2.701951 ACTCCCTCCGTTCACTTTTGTA 59.298 45.455 0.00 0.00 0.00 2.41
5422 5686 1.489230 ACTCCCTCCGTTCACTTTTGT 59.511 47.619 0.00 0.00 0.00 2.83
5423 5687 2.256117 ACTCCCTCCGTTCACTTTTG 57.744 50.000 0.00 0.00 0.00 2.44
5424 5688 2.289506 GCTACTCCCTCCGTTCACTTTT 60.290 50.000 0.00 0.00 0.00 2.27
5425 5689 1.275573 GCTACTCCCTCCGTTCACTTT 59.724 52.381 0.00 0.00 0.00 2.66
5426 5690 0.896226 GCTACTCCCTCCGTTCACTT 59.104 55.000 0.00 0.00 0.00 3.16
5427 5691 0.039911 AGCTACTCCCTCCGTTCACT 59.960 55.000 0.00 0.00 0.00 3.41
5428 5692 1.404748 GTAGCTACTCCCTCCGTTCAC 59.595 57.143 16.88 0.00 0.00 3.18
5429 5693 1.005097 TGTAGCTACTCCCTCCGTTCA 59.995 52.381 23.84 0.00 0.00 3.18
5430 5694 1.760192 TGTAGCTACTCCCTCCGTTC 58.240 55.000 23.84 0.00 0.00 3.95
5431 5695 2.226962 TTGTAGCTACTCCCTCCGTT 57.773 50.000 23.84 0.00 0.00 4.44
5432 5696 2.308690 GATTGTAGCTACTCCCTCCGT 58.691 52.381 23.84 2.20 0.00 4.69
5433 5697 2.307768 TGATTGTAGCTACTCCCTCCG 58.692 52.381 23.84 0.00 0.00 4.63
5434 5698 4.591072 AGATTGATTGTAGCTACTCCCTCC 59.409 45.833 23.84 8.55 0.00 4.30
5435 5699 5.303078 TCAGATTGATTGTAGCTACTCCCTC 59.697 44.000 23.84 14.65 0.00 4.30
5436 5700 5.211973 TCAGATTGATTGTAGCTACTCCCT 58.788 41.667 23.84 9.00 0.00 4.20
5437 5701 5.537300 TCAGATTGATTGTAGCTACTCCC 57.463 43.478 23.84 12.84 0.00 4.30
5438 5702 5.465056 GCTTCAGATTGATTGTAGCTACTCC 59.535 44.000 23.84 13.16 36.43 3.85
5439 5703 6.045318 TGCTTCAGATTGATTGTAGCTACTC 58.955 40.000 23.84 14.69 39.03 2.59
5440 5704 5.982356 TGCTTCAGATTGATTGTAGCTACT 58.018 37.500 23.84 5.34 39.03 2.57
5512 5776 0.681733 AGAGTACCAGGCACACACTG 59.318 55.000 0.00 0.00 35.74 3.66
5513 5777 2.171840 CTAGAGTACCAGGCACACACT 58.828 52.381 0.00 0.00 0.00 3.55
5514 5778 1.893801 ACTAGAGTACCAGGCACACAC 59.106 52.381 0.00 0.00 0.00 3.82
5515 5779 2.299013 CAACTAGAGTACCAGGCACACA 59.701 50.000 0.00 0.00 0.00 3.72
5516 5780 2.299297 ACAACTAGAGTACCAGGCACAC 59.701 50.000 0.00 0.00 0.00 3.82
5517 5781 2.299013 CACAACTAGAGTACCAGGCACA 59.701 50.000 0.00 0.00 0.00 4.57
5518 5782 2.931320 GCACAACTAGAGTACCAGGCAC 60.931 54.545 0.00 0.00 0.00 5.01
5537 5801 3.002791 CTCAGTAGCGAAAGGAAATGCA 58.997 45.455 0.00 0.00 0.00 3.96
5558 5822 1.209383 CATCACAGCACAGCACAGC 59.791 57.895 0.00 0.00 0.00 4.40
5559 5823 1.232119 TTCATCACAGCACAGCACAG 58.768 50.000 0.00 0.00 0.00 3.66
5560 5824 1.605232 CTTTCATCACAGCACAGCACA 59.395 47.619 0.00 0.00 0.00 4.57
5561 5825 1.875514 TCTTTCATCACAGCACAGCAC 59.124 47.619 0.00 0.00 0.00 4.40
5562 5826 2.148768 CTCTTTCATCACAGCACAGCA 58.851 47.619 0.00 0.00 0.00 4.41
5587 5851 4.865776 AGCGAAAGAGTAGAGATGCATAC 58.134 43.478 0.00 0.00 0.00 2.39
5611 5875 6.238130 GGGATGTACTAAAAGATTTCGCAGTC 60.238 42.308 0.00 0.00 0.00 3.51
5626 5890 2.092592 TCGAGTCTGCTGGGATGTACTA 60.093 50.000 0.00 0.00 0.00 1.82
5627 5891 1.107114 CGAGTCTGCTGGGATGTACT 58.893 55.000 0.00 0.00 0.00 2.73
5628 5892 1.103803 TCGAGTCTGCTGGGATGTAC 58.896 55.000 0.00 0.00 0.00 2.90
5651 5915 7.710907 AGCAGAATGTTAATTAAGCTCGATGTA 59.289 33.333 0.00 0.00 39.31 2.29
5675 5939 3.727079 CGTGAATTCTGCAATCACAGAGC 60.727 47.826 16.81 0.00 46.85 4.09
5684 5948 4.891627 TTTTGAGACGTGAATTCTGCAA 57.108 36.364 7.05 0.02 0.00 4.08
5725 5989 8.725148 TGTAATCAGAGAGAGATTTCTTTTTGC 58.275 33.333 0.00 0.00 37.02 3.68
5809 6073 5.049543 GCATGGAGAATCAGCAAGTAAGATC 60.050 44.000 0.00 0.00 36.25 2.75
5812 6076 3.002042 CGCATGGAGAATCAGCAAGTAAG 59.998 47.826 0.00 0.00 36.25 2.34
5930 6281 7.093322 AGCAGATTAGGCAATCAAACTTAAG 57.907 36.000 0.00 0.00 42.66 1.85


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

AutoCloner maintained by Alex Coulton.