Multiple sequence alignment - TraesCS4B01G106700

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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 TraesCS4B01G106700 chr4B 100.000 5549 0 0 1 5549 116217423 116211875 0.000000e+00 10248.0
1 TraesCS4B01G106700 chr4B 87.820 821 78 12 2223 3023 535249335 535248517 0.000000e+00 942.0
2 TraesCS4B01G106700 chr4B 88.586 771 70 12 3692 4454 535247763 535247003 0.000000e+00 920.0
3 TraesCS4B01G106700 chr4B 90.803 598 48 6 3092 3686 535248518 535247925 0.000000e+00 793.0
4 TraesCS4B01G106700 chr4B 88.124 421 36 7 898 1315 535251590 535251181 6.460000e-134 488.0
5 TraesCS4B01G106700 chr4B 91.489 282 11 9 4727 5000 535246580 535246304 5.250000e-100 375.0
6 TraesCS4B01G106700 chr4B 85.833 240 16 6 4727 4961 535237137 535236911 7.180000e-59 239.0
7 TraesCS4B01G106700 chr4B 80.115 347 35 16 575 916 535251924 535251607 1.560000e-55 228.0
8 TraesCS4B01G106700 chr4B 84.615 104 6 3 1465 1567 161664872 161664966 1.650000e-15 95.3
9 TraesCS4B01G106700 chr4B 87.838 74 9 0 2114 2187 535249481 535249408 2.750000e-13 87.9
10 TraesCS4B01G106700 chr4D 92.469 4714 215 66 1 4683 82296397 82291793 0.000000e+00 6610.0
11 TraesCS4B01G106700 chr4D 89.650 1343 109 19 3092 4419 435063943 435062616 0.000000e+00 1683.0
12 TraesCS4B01G106700 chr4D 94.325 881 25 9 4679 5549 82291668 82290803 0.000000e+00 1327.0
13 TraesCS4B01G106700 chr4D 87.277 786 82 14 2255 3023 435064726 435063942 0.000000e+00 881.0
14 TraesCS4B01G106700 chr4D 85.065 770 70 25 567 1324 435066116 435065380 0.000000e+00 743.0
15 TraesCS4B01G106700 chr4D 90.873 504 26 11 4727 5218 435062191 435061696 0.000000e+00 658.0
16 TraesCS4B01G106700 chr4D 88.696 230 15 6 1897 2116 435065392 435065164 2.550000e-68 270.0
17 TraesCS4B01G106700 chr4D 89.189 74 8 0 2114 2187 435064869 435064796 5.920000e-15 93.5
18 TraesCS4B01G106700 chr4A 96.893 1577 42 4 3110 4683 492532432 492530860 0.000000e+00 2634.0
19 TraesCS4B01G106700 chr4A 92.758 1229 43 12 1815 3031 492533623 492532429 0.000000e+00 1735.0
20 TraesCS4B01G106700 chr4A 88.484 1346 109 28 3092 4414 36413090 36411768 0.000000e+00 1585.0
21 TraesCS4B01G106700 chr4A 93.530 881 40 11 4679 5549 492530732 492529859 0.000000e+00 1295.0
22 TraesCS4B01G106700 chr4A 90.207 919 39 26 829 1739 492534776 492533901 0.000000e+00 1151.0
23 TraesCS4B01G106700 chr4A 86.951 843 86 15 2204 3023 36413930 36413089 0.000000e+00 926.0
24 TraesCS4B01G106700 chr4A 87.245 784 58 28 79 832 492536494 492535723 0.000000e+00 856.0
25 TraesCS4B01G106700 chr4A 89.815 432 31 7 898 1324 36414917 36414494 4.890000e-150 542.0
26 TraesCS4B01G106700 chr4A 90.566 159 9 4 4783 4939 36411304 36411150 7.290000e-49 206.0
27 TraesCS4B01G106700 chr4A 89.655 116 9 2 2001 2116 36414446 36414334 1.610000e-30 145.0
28 TraesCS4B01G106700 chr4A 92.473 93 6 1 3027 3118 556767954 556768046 1.250000e-26 132.0
29 TraesCS4B01G106700 chr2B 94.624 93 4 1 3027 3118 17023935 17024027 5.790000e-30 143.0
30 TraesCS4B01G106700 chr7A 92.632 95 6 1 3020 3113 136806098 136806192 9.700000e-28 135.0
31 TraesCS4B01G106700 chr3D 89.815 108 8 3 3011 3117 303788441 303788546 9.700000e-28 135.0
32 TraesCS4B01G106700 chr2D 93.478 92 5 1 3028 3118 53145811 53145720 9.700000e-28 135.0
33 TraesCS4B01G106700 chr6A 90.196 102 7 3 3012 3111 525997945 525997845 4.510000e-26 130.0
34 TraesCS4B01G106700 chr1D 90.000 100 8 2 3021 3118 295954208 295954307 1.620000e-25 128.0
35 TraesCS4B01G106700 chr6D 88.462 104 9 3 3011 3111 309072485 309072588 7.550000e-24 122.0


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 TraesCS4B01G106700 chr4B 116211875 116217423 5548 True 10248.000000 10248 100.000000 1 5549 1 chr4B.!!$R1 5548
1 TraesCS4B01G106700 chr4B 535246304 535251924 5620 True 547.700000 942 87.825000 575 5000 7 chr4B.!!$R3 4425
2 TraesCS4B01G106700 chr4D 82290803 82296397 5594 True 3968.500000 6610 93.397000 1 5549 2 chr4D.!!$R1 5548
3 TraesCS4B01G106700 chr4D 435061696 435066116 4420 True 721.416667 1683 88.458333 567 5218 6 chr4D.!!$R2 4651
4 TraesCS4B01G106700 chr4A 492529859 492536494 6635 True 1534.200000 2634 92.126600 79 5549 5 chr4A.!!$R2 5470
5 TraesCS4B01G106700 chr4A 36411150 36414917 3767 True 680.800000 1585 89.094200 898 4939 5 chr4A.!!$R1 4041

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
414 428 0.250901 AAACAGCAACCAGATCGGCT 60.251 50.000 3.85 0.00 39.03 5.52 F
1004 2044 0.174617 CACCTCTCCGGCTCTCTTTC 59.825 60.000 0.00 0.00 35.61 2.62 F
1330 2381 0.179089 CCTACTGGCTACTGCTGCTG 60.179 60.000 4.89 4.89 39.59 4.41 F
1877 3165 1.021390 GTGGCCTGATGACTGGAACG 61.021 60.000 3.32 0.00 37.31 3.95 F
2320 5192 1.150827 GCTGCAAAATTTCACTGGCC 58.849 50.000 0.00 0.00 0.00 5.36 F
2898 5796 1.264288 GCTAACGATAATGCAGGGCAC 59.736 52.381 0.00 0.00 43.04 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1526 2577 0.391661 GTTGCTCCTCGAATCCAGCA 60.392 55.000 3.76 3.76 40.13 4.41 R
2862 5760 0.306840 TAGCGTAGAATCACTCGCCG 59.693 55.000 11.43 0.00 41.92 6.46 R
3090 6014 0.767060 ACCCCCTCCGTCCCATAATC 60.767 60.000 0.00 0.00 0.00 1.75 R
3469 6397 2.095567 CAGCAATCAAAGGTTCTGACGG 60.096 50.000 0.00 0.00 0.00 4.79 R
3674 6606 3.255642 ACCAACATGTGTATTTGGCAGAC 59.744 43.478 12.50 0.00 43.18 3.51 R
4661 7820 2.477825 GTGTGGACCGATGAGATGATG 58.522 52.381 0.00 0.00 0.00 3.07 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
23 24 2.112198 GGCGATTGAATGGCGACCA 61.112 57.895 6.09 1.01 38.19 4.02
36 37 0.958382 GCGACCAACCCAACTGCATA 60.958 55.000 0.00 0.00 0.00 3.14
138 142 1.205655 TCGCTATGCTGCTCTTCTTGT 59.794 47.619 0.00 0.00 0.00 3.16
151 155 0.550914 TTCTTGTGCTGGTGACCCTT 59.449 50.000 0.00 0.00 0.00 3.95
173 177 5.873179 TTTCCATGTCGACATAGGAAAAC 57.127 39.130 38.48 12.48 42.89 2.43
185 189 6.128661 CGACATAGGAAAACGAACAAGATCAA 60.129 38.462 0.00 0.00 0.00 2.57
194 198 3.255149 ACGAACAAGATCAACTAGGACGT 59.745 43.478 0.00 0.00 0.00 4.34
199 203 4.521639 ACAAGATCAACTAGGACGTGTGTA 59.478 41.667 0.00 0.00 0.00 2.90
200 204 4.966965 AGATCAACTAGGACGTGTGTAG 57.033 45.455 0.00 0.00 0.00 2.74
202 206 3.909776 TCAACTAGGACGTGTGTAGTG 57.090 47.619 0.00 0.00 0.00 2.74
203 207 2.030540 TCAACTAGGACGTGTGTAGTGC 60.031 50.000 0.00 0.00 0.00 4.40
204 208 1.906990 ACTAGGACGTGTGTAGTGCT 58.093 50.000 0.00 0.00 42.78 4.40
205 209 3.063510 ACTAGGACGTGTGTAGTGCTA 57.936 47.619 0.00 0.00 40.68 3.49
206 210 3.618351 ACTAGGACGTGTGTAGTGCTAT 58.382 45.455 0.00 0.00 40.73 2.97
208 212 3.955650 AGGACGTGTGTAGTGCTATTT 57.044 42.857 0.00 0.00 38.51 1.40
209 213 3.585862 AGGACGTGTGTAGTGCTATTTG 58.414 45.455 0.00 0.00 38.51 2.32
210 214 3.006537 AGGACGTGTGTAGTGCTATTTGT 59.993 43.478 0.00 0.00 38.51 2.83
211 215 3.367025 GGACGTGTGTAGTGCTATTTGTC 59.633 47.826 0.00 0.00 0.00 3.18
214 218 4.210537 ACGTGTGTAGTGCTATTTGTCAAC 59.789 41.667 0.00 0.00 0.00 3.18
215 219 4.377022 CGTGTGTAGTGCTATTTGTCAACC 60.377 45.833 0.00 0.00 0.00 3.77
216 220 3.743911 TGTGTAGTGCTATTTGTCAACCG 59.256 43.478 0.00 0.00 0.00 4.44
219 223 5.406175 GTGTAGTGCTATTTGTCAACCGTAA 59.594 40.000 0.00 0.00 0.00 3.18
228 241 7.437267 GCTATTTGTCAACCGTAATAAGCTAGA 59.563 37.037 0.00 0.00 0.00 2.43
232 245 5.098211 GTCAACCGTAATAAGCTAGAACGT 58.902 41.667 0.00 0.00 31.87 3.99
235 248 3.445096 ACCGTAATAAGCTAGAACGTGGT 59.555 43.478 0.00 0.59 31.87 4.16
261 274 8.045507 TCTAGATCAACTTCTAAGTAACCTCGA 58.954 37.037 0.00 0.00 38.57 4.04
263 276 5.382618 TCAACTTCTAAGTAACCTCGACC 57.617 43.478 0.00 0.00 38.57 4.79
281 294 1.002134 CGTTTCTGGTCCCATGGCT 60.002 57.895 6.09 0.00 0.00 4.75
348 361 2.201022 CCCCGTCGGTCCCTCTATG 61.201 68.421 11.06 0.00 0.00 2.23
409 422 3.826729 GGTTAGGAAAACAGCAACCAGAT 59.173 43.478 0.00 0.00 38.79 2.90
414 428 0.250901 AAACAGCAACCAGATCGGCT 60.251 50.000 3.85 0.00 39.03 5.52
472 488 5.796350 GGATACTATTGTTTTGACGTGCT 57.204 39.130 0.00 0.00 0.00 4.40
488 504 2.352814 CGTGCTAGAAGAATATCCCCCG 60.353 54.545 0.00 0.00 0.00 5.73
501 517 1.750399 CCCCCGCTGGATGTTTGAG 60.750 63.158 0.00 0.00 35.39 3.02
538 559 6.178607 AGTCTTGATTGCTTTGGGAAAAAT 57.821 33.333 0.00 0.00 0.00 1.82
567 592 4.579869 AGTGTTGACGCATCCTAAAAGAT 58.420 39.130 0.00 0.00 0.00 2.40
568 593 5.003804 AGTGTTGACGCATCCTAAAAGATT 58.996 37.500 0.00 0.00 0.00 2.40
613 639 3.627123 TCACTCCATGCCATAACGAAATG 59.373 43.478 0.00 0.00 0.00 2.32
615 641 2.294233 CTCCATGCCATAACGAAATGGG 59.706 50.000 18.19 5.94 45.63 4.00
619 645 3.289407 TGCCATAACGAAATGGGATCA 57.711 42.857 18.19 8.44 45.63 2.92
677 705 3.605634 TGTCCCAACATTTACGATGAGG 58.394 45.455 0.00 0.00 0.00 3.86
684 713 4.965119 ACATTTACGATGAGGCTTTTCC 57.035 40.909 0.00 0.00 0.00 3.13
721 753 6.096705 AGTCTAGATTCATCACCTTCTCACAG 59.903 42.308 0.00 0.00 0.00 3.66
742 778 5.423015 CAGCATGTACCATATACATCCTCC 58.577 45.833 0.00 0.00 36.13 4.30
743 779 5.046376 CAGCATGTACCATATACATCCTCCA 60.046 44.000 0.00 0.00 36.13 3.86
744 780 5.547666 AGCATGTACCATATACATCCTCCAA 59.452 40.000 0.00 0.00 36.13 3.53
745 781 6.044287 AGCATGTACCATATACATCCTCCAAA 59.956 38.462 0.00 0.00 36.13 3.28
805 854 7.880160 AATATTAGTACAGCATTTTCCAGCA 57.120 32.000 0.00 0.00 0.00 4.41
809 858 1.412079 ACAGCATTTTCCAGCAACCA 58.588 45.000 0.00 0.00 0.00 3.67
990 2030 0.539669 CCAAGAACCCAACCCACCTC 60.540 60.000 0.00 0.00 0.00 3.85
991 2031 0.478507 CAAGAACCCAACCCACCTCT 59.521 55.000 0.00 0.00 0.00 3.69
992 2032 0.771755 AAGAACCCAACCCACCTCTC 59.228 55.000 0.00 0.00 0.00 3.20
993 2033 1.134438 AGAACCCAACCCACCTCTCC 61.134 60.000 0.00 0.00 0.00 3.71
994 2034 2.465055 GAACCCAACCCACCTCTCCG 62.465 65.000 0.00 0.00 0.00 4.63
995 2035 3.717294 CCCAACCCACCTCTCCGG 61.717 72.222 0.00 0.00 39.35 5.14
996 2036 4.410400 CCAACCCACCTCTCCGGC 62.410 72.222 0.00 0.00 35.61 6.13
997 2037 3.322466 CAACCCACCTCTCCGGCT 61.322 66.667 0.00 0.00 35.61 5.52
998 2038 3.003763 AACCCACCTCTCCGGCTC 61.004 66.667 0.00 0.00 35.61 4.70
999 2039 3.547787 AACCCACCTCTCCGGCTCT 62.548 63.158 0.00 0.00 35.61 4.09
1000 2040 3.151022 CCCACCTCTCCGGCTCTC 61.151 72.222 0.00 0.00 35.61 3.20
1001 2041 2.043450 CCACCTCTCCGGCTCTCT 60.043 66.667 0.00 0.00 35.61 3.10
1002 2042 1.684049 CCACCTCTCCGGCTCTCTT 60.684 63.158 0.00 0.00 35.61 2.85
1003 2043 1.261238 CCACCTCTCCGGCTCTCTTT 61.261 60.000 0.00 0.00 35.61 2.52
1004 2044 0.174617 CACCTCTCCGGCTCTCTTTC 59.825 60.000 0.00 0.00 35.61 2.62
1026 2074 2.837291 CCTCCTCCCTCGCCTCTG 60.837 72.222 0.00 0.00 0.00 3.35
1049 2097 2.579684 ATTCCGGTTGCTCTCGAGGC 62.580 60.000 13.56 15.15 0.00 4.70
1105 2153 2.823593 TGGCGGTGGCGATGATTG 60.824 61.111 0.00 0.00 41.24 2.67
1106 2154 4.256090 GGCGGTGGCGATGATTGC 62.256 66.667 0.00 0.00 41.24 3.56
1113 2161 0.254462 TGGCGATGATTGCTTGGGTA 59.746 50.000 4.42 0.00 0.00 3.69
1326 2377 2.830651 AGTACCTACTGGCTACTGCT 57.169 50.000 0.00 0.00 39.59 4.24
1327 2378 2.379972 AGTACCTACTGGCTACTGCTG 58.620 52.381 0.00 0.00 39.59 4.41
1328 2379 1.112113 TACCTACTGGCTACTGCTGC 58.888 55.000 0.00 0.00 39.59 5.25
1329 2380 0.616111 ACCTACTGGCTACTGCTGCT 60.616 55.000 0.00 0.00 39.59 4.24
1330 2381 0.179089 CCTACTGGCTACTGCTGCTG 60.179 60.000 4.89 4.89 39.59 4.41
1377 2428 4.761058 TCTCTTCTCCGCGGCCCT 62.761 66.667 23.51 0.00 0.00 5.19
1499 2550 8.330302 CCTTGTTTTGTTTTGCTTCAGAATTAG 58.670 33.333 0.00 0.00 0.00 1.73
1500 2551 7.769272 TGTTTTGTTTTGCTTCAGAATTAGG 57.231 32.000 0.00 0.00 0.00 2.69
1501 2552 6.760770 TGTTTTGTTTTGCTTCAGAATTAGGG 59.239 34.615 0.00 0.00 0.00 3.53
1502 2553 6.723298 TTTGTTTTGCTTCAGAATTAGGGA 57.277 33.333 0.00 0.00 0.00 4.20
1503 2554 6.723298 TTGTTTTGCTTCAGAATTAGGGAA 57.277 33.333 0.00 0.00 0.00 3.97
1504 2555 6.916360 TGTTTTGCTTCAGAATTAGGGAAT 57.084 33.333 0.00 0.00 0.00 3.01
1505 2556 8.415950 TTGTTTTGCTTCAGAATTAGGGAATA 57.584 30.769 0.00 0.00 0.00 1.75
1526 2577 7.917505 GGAATATGTTCGCATCTGAATTTTCTT 59.082 33.333 0.00 0.00 38.94 2.52
1539 2590 4.156556 TGAATTTTCTTGCTGGATTCGAGG 59.843 41.667 0.00 0.00 31.15 4.63
1540 2591 3.417069 TTTTCTTGCTGGATTCGAGGA 57.583 42.857 0.00 0.00 0.00 3.71
1676 2730 5.191722 AGGAATTTCTACCTGGTCTGCATTA 59.808 40.000 0.63 0.00 34.99 1.90
1740 2795 3.020274 CTGGATCTCGAGAGTTTCTGGA 58.980 50.000 21.52 0.00 30.50 3.86
1743 2798 4.467795 TGGATCTCGAGAGTTTCTGGAAAT 59.532 41.667 21.52 0.00 30.88 2.17
1744 2799 5.047188 GGATCTCGAGAGTTTCTGGAAATC 58.953 45.833 21.52 8.36 30.77 2.17
1756 2811 7.795047 AGTTTCTGGAAATCATTTTGGTTTCT 58.205 30.769 11.75 0.00 44.61 2.52
1758 2813 6.975196 TCTGGAAATCATTTTGGTTTCTCA 57.025 33.333 11.75 8.08 44.61 3.27
1769 2824 8.716909 TCATTTTGGTTTCTCAAAACAGTTTTC 58.283 29.630 8.40 0.00 45.58 2.29
1870 3158 2.945668 GTTCCATTAGTGGCCTGATGAC 59.054 50.000 3.32 0.00 45.63 3.06
1875 3163 1.951209 TAGTGGCCTGATGACTGGAA 58.049 50.000 3.32 0.00 37.31 3.53
1877 3165 1.021390 GTGGCCTGATGACTGGAACG 61.021 60.000 3.32 0.00 37.31 3.95
1878 3166 1.450312 GGCCTGATGACTGGAACGG 60.450 63.158 0.00 0.00 42.99 4.44
1893 3181 4.501071 TGGAACGGTGAAGTTAATCTAGC 58.499 43.478 0.00 0.00 34.00 3.42
1894 3182 4.020928 TGGAACGGTGAAGTTAATCTAGCA 60.021 41.667 0.00 0.00 34.00 3.49
1895 3183 5.116882 GGAACGGTGAAGTTAATCTAGCAT 58.883 41.667 0.00 0.00 34.00 3.79
1896 3184 5.234543 GGAACGGTGAAGTTAATCTAGCATC 59.765 44.000 0.00 0.00 34.00 3.91
1897 3185 4.694339 ACGGTGAAGTTAATCTAGCATCC 58.306 43.478 0.00 0.00 0.00 3.51
1898 3186 4.406003 ACGGTGAAGTTAATCTAGCATCCT 59.594 41.667 0.00 0.00 0.00 3.24
1899 3187 5.597182 ACGGTGAAGTTAATCTAGCATCCTA 59.403 40.000 0.00 0.00 0.00 2.94
1900 3188 6.267928 ACGGTGAAGTTAATCTAGCATCCTAT 59.732 38.462 0.00 0.00 0.00 2.57
1901 3189 7.450634 ACGGTGAAGTTAATCTAGCATCCTATA 59.549 37.037 0.00 0.00 0.00 1.31
1917 3205 6.876257 GCATCCTATACTACTCATTTCCTTGG 59.124 42.308 0.00 0.00 0.00 3.61
1918 3206 7.473511 GCATCCTATACTACTCATTTCCTTGGT 60.474 40.741 0.00 0.00 0.00 3.67
1919 3207 9.090103 CATCCTATACTACTCATTTCCTTGGTA 57.910 37.037 0.00 0.00 0.00 3.25
1921 3209 7.508296 TCCTATACTACTCATTTCCTTGGTACC 59.492 40.741 4.43 4.43 0.00 3.34
2055 3361 1.781429 CGTTAATCGTCATCTGCTCCG 59.219 52.381 0.00 0.00 34.52 4.63
2158 4951 1.745232 TGTGTGTTGTGGTCCTTGAC 58.255 50.000 0.00 0.00 0.00 3.18
2167 4960 5.008217 TGTTGTGGTCCTTGACGATTTTTAG 59.992 40.000 0.00 0.00 32.65 1.85
2172 4965 4.435651 GGTCCTTGACGATTTTTAGAAGCG 60.436 45.833 0.00 0.00 32.65 4.68
2295 5167 4.439305 TGGAAATGTGATTGCTAACTGC 57.561 40.909 0.00 0.00 43.25 4.40
2320 5192 1.150827 GCTGCAAAATTTCACTGGCC 58.849 50.000 0.00 0.00 0.00 5.36
2594 5479 2.684943 TGGTCCTACTCCAACACTTCA 58.315 47.619 0.00 0.00 31.50 3.02
2700 5589 8.116753 CACATCAATCTAACCGTATGTTTCTTC 58.883 37.037 0.00 0.00 38.42 2.87
2712 5607 6.257423 CGTATGTTTCTTCAATTATGCAGCA 58.743 36.000 0.00 0.00 0.00 4.41
2845 5740 6.879458 AGTTCTACTTCAGGAATATGCGTTTT 59.121 34.615 0.00 0.00 0.00 2.43
2862 5760 4.436183 GCGTTTTGATTGCCTCTCTTCTAC 60.436 45.833 0.00 0.00 0.00 2.59
2876 5774 3.538591 TCTTCTACGGCGAGTGATTCTA 58.461 45.455 16.62 0.00 0.00 2.10
2898 5796 1.264288 GCTAACGATAATGCAGGGCAC 59.736 52.381 0.00 0.00 43.04 5.01
3032 5956 8.470805 TCTCTTGAATCAACTATGTTCTACTCC 58.529 37.037 0.00 0.00 0.00 3.85
3033 5957 7.556844 TCTTGAATCAACTATGTTCTACTCCC 58.443 38.462 0.00 0.00 0.00 4.30
3034 5958 7.400339 TCTTGAATCAACTATGTTCTACTCCCT 59.600 37.037 0.00 0.00 0.00 4.20
3035 5959 7.113658 TGAATCAACTATGTTCTACTCCCTC 57.886 40.000 0.00 0.00 0.00 4.30
3036 5960 6.098409 TGAATCAACTATGTTCTACTCCCTCC 59.902 42.308 0.00 0.00 0.00 4.30
3037 5961 3.952323 TCAACTATGTTCTACTCCCTCCG 59.048 47.826 0.00 0.00 0.00 4.63
3038 5962 3.666345 ACTATGTTCTACTCCCTCCGT 57.334 47.619 0.00 0.00 0.00 4.69
3039 5963 3.553904 ACTATGTTCTACTCCCTCCGTC 58.446 50.000 0.00 0.00 0.00 4.79
3055 5979 4.466370 CCTCCGTCCCATAATATAAGAGCA 59.534 45.833 0.00 0.00 0.00 4.26
3056 5980 5.401531 TCCGTCCCATAATATAAGAGCAC 57.598 43.478 0.00 0.00 0.00 4.40
3057 5981 5.084519 TCCGTCCCATAATATAAGAGCACT 58.915 41.667 0.00 0.00 0.00 4.40
3070 5994 8.709386 ATATAAGAGCACTTTTGACACTAGTG 57.291 34.615 21.44 21.44 41.64 2.74
3071 5995 4.770795 AAGAGCACTTTTGACACTAGTGT 58.229 39.130 28.27 28.27 40.99 3.55
3072 5996 5.531122 AGAGCACTTTTGACACTAGTGTA 57.469 39.130 27.98 11.50 45.05 2.90
3075 5999 8.372600 AAGAGCACTTTTGACACTAGTGTAGTG 61.373 40.741 33.25 33.25 46.06 2.74
3090 6014 9.640963 ACTAGTGTAGTGTAAAAATGCTCTTAG 57.359 33.333 0.00 0.00 37.69 2.18
3107 6031 2.320681 TAGATTATGGGACGGAGGGG 57.679 55.000 0.00 0.00 0.00 4.79
3442 6366 3.002656 ACTGCGCAAATATGTATGCTCAC 59.997 43.478 13.05 0.00 40.39 3.51
3471 6399 6.172630 TCATGGATGGTACATGATATTTCCG 58.827 40.000 0.00 0.00 46.99 4.30
3674 6606 5.230306 GTGAGTAAGTGCTTCTATTGCTACG 59.770 44.000 0.00 0.00 0.00 3.51
3688 6776 2.343101 TGCTACGTCTGCCAAATACAC 58.657 47.619 10.33 0.00 0.00 2.90
3924 7021 9.220906 ACTTACCTTTTCATACTCCCATATACA 57.779 33.333 0.00 0.00 0.00 2.29
3938 7043 9.469097 ACTCCCATATACAAGTCTGAGTATATC 57.531 37.037 12.17 0.00 40.24 1.63
4201 7314 7.686438 AACATGAATGTAACATCTGTTGCTA 57.314 32.000 11.53 0.81 40.80 3.49
4385 7500 1.208535 CCACCCATTGGCGACTAAGTA 59.791 52.381 0.00 0.00 39.07 2.24
4525 7670 7.816031 CAGAAAGAATGGAAAAGTAATGCATGT 59.184 33.333 0.00 0.00 0.00 3.21
4544 7696 7.919690 TGCATGTTAGCAAGTATGATCTTTAC 58.080 34.615 0.00 0.00 42.46 2.01
4568 7720 6.183361 ACCAGGATTATTAGATTGCATCCCTT 60.183 38.462 0.00 0.00 34.94 3.95
4661 7820 4.455877 ACTTGCAAATGTAACTCTGCCTAC 59.544 41.667 0.00 0.00 33.78 3.18
4816 8139 5.445964 TCCTTGCCTTAATCAGGGTTATTC 58.554 41.667 6.10 0.00 44.16 1.75
4875 8199 3.686916 AGGTCCAGAAAGTAGAACTGC 57.313 47.619 0.00 0.00 0.00 4.40
4876 8200 2.972713 AGGTCCAGAAAGTAGAACTGCA 59.027 45.455 0.00 0.00 0.00 4.41
4877 8201 3.584848 AGGTCCAGAAAGTAGAACTGCAT 59.415 43.478 0.00 0.00 0.00 3.96
4961 8290 4.753610 GGTAGTTTAAGACCTGGAACACAC 59.246 45.833 0.00 0.00 32.58 3.82
5113 8448 5.596772 TCATGAAGTGAATCTGGACGGTATA 59.403 40.000 0.00 0.00 32.78 1.47
5190 8525 5.183228 AGGGTGACAAAGTATTACCATTCG 58.817 41.667 0.00 0.00 33.10 3.34
5244 8580 4.597507 AGAGTTGTATCTTCCTTTGGACCA 59.402 41.667 0.00 0.00 0.00 4.02
5316 8652 3.821033 AGTGTGTAGCCAAACTGGATTTC 59.179 43.478 0.00 0.00 40.96 2.17
5321 8657 5.241728 GTGTAGCCAAACTGGATTTCTCTTT 59.758 40.000 0.00 0.00 40.96 2.52
5322 8658 5.833131 TGTAGCCAAACTGGATTTCTCTTTT 59.167 36.000 0.00 0.00 40.96 2.27
5382 8726 1.143813 ATGAATCCCTACCCTGCTGG 58.856 55.000 1.89 1.89 41.37 4.85
5383 8727 1.149401 GAATCCCTACCCTGCTGGC 59.851 63.158 3.63 0.00 37.83 4.85
5384 8728 1.619363 AATCCCTACCCTGCTGGCA 60.619 57.895 3.63 0.00 37.83 4.92
5385 8729 1.214305 AATCCCTACCCTGCTGGCAA 61.214 55.000 3.63 0.00 37.83 4.52
5386 8730 1.214305 ATCCCTACCCTGCTGGCAAA 61.214 55.000 3.63 0.00 37.83 3.68
5387 8731 1.214305 TCCCTACCCTGCTGGCAAAT 61.214 55.000 3.63 0.00 37.83 2.32
5388 8732 0.550914 CCCTACCCTGCTGGCAAATA 59.449 55.000 3.63 0.00 37.83 1.40
5389 8733 1.064017 CCCTACCCTGCTGGCAAATAA 60.064 52.381 3.63 0.00 37.83 1.40
5390 8734 2.301346 CCTACCCTGCTGGCAAATAAG 58.699 52.381 3.63 0.00 37.83 1.73
5447 8794 2.702270 AGAAGAAAGCCACCCCAAAT 57.298 45.000 0.00 0.00 0.00 2.32
5498 8845 7.560262 AGCAGTACCTTAATACTCATACTGACA 59.440 37.037 12.21 0.00 41.21 3.58
5534 8881 5.188948 AGCCAACATAGTGACTACAACCATA 59.811 40.000 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.112198 GGTCGCCATTCAATCGCCA 61.112 57.895 0.00 0.00 0.00 5.69
7 8 0.098728 GGTTGGTCGCCATTCAATCG 59.901 55.000 0.00 0.00 31.53 3.34
23 24 4.650972 TTTACTCCTATGCAGTTGGGTT 57.349 40.909 0.00 0.00 0.00 4.11
36 37 5.430089 AGGTGATAAGAAGCCATTTACTCCT 59.570 40.000 0.00 0.00 0.00 3.69
138 142 0.482446 ATGGAAAAGGGTCACCAGCA 59.518 50.000 0.00 0.00 40.13 4.41
151 155 4.390603 CGTTTTCCTATGTCGACATGGAAA 59.609 41.667 37.83 37.83 43.42 3.13
173 177 3.608506 CACGTCCTAGTTGATCTTGTTCG 59.391 47.826 0.00 0.00 0.00 3.95
185 189 1.906990 AGCACTACACACGTCCTAGT 58.093 50.000 0.00 0.00 0.00 2.57
194 198 3.743911 CGGTTGACAAATAGCACTACACA 59.256 43.478 0.00 0.00 0.00 3.72
199 203 6.183360 GCTTATTACGGTTGACAAATAGCACT 60.183 38.462 0.00 0.00 0.00 4.40
200 204 5.963586 GCTTATTACGGTTGACAAATAGCAC 59.036 40.000 0.00 0.00 0.00 4.40
202 206 6.359480 AGCTTATTACGGTTGACAAATAGC 57.641 37.500 0.00 0.00 0.00 2.97
203 207 8.867112 TCTAGCTTATTACGGTTGACAAATAG 57.133 34.615 0.00 0.00 0.00 1.73
204 208 9.090692 GTTCTAGCTTATTACGGTTGACAAATA 57.909 33.333 0.00 0.00 0.00 1.40
205 209 7.201496 CGTTCTAGCTTATTACGGTTGACAAAT 60.201 37.037 0.00 0.00 0.00 2.32
206 210 6.089820 CGTTCTAGCTTATTACGGTTGACAAA 59.910 38.462 0.00 0.00 0.00 2.83
208 212 5.097529 CGTTCTAGCTTATTACGGTTGACA 58.902 41.667 0.00 0.00 0.00 3.58
209 213 5.004156 CACGTTCTAGCTTATTACGGTTGAC 59.996 44.000 12.69 0.00 36.60 3.18
210 214 5.097529 CACGTTCTAGCTTATTACGGTTGA 58.902 41.667 12.69 0.00 36.60 3.18
211 215 4.266976 CCACGTTCTAGCTTATTACGGTTG 59.733 45.833 12.69 5.28 36.60 3.77
214 218 4.037858 ACCACGTTCTAGCTTATTACGG 57.962 45.455 12.69 1.09 36.60 4.02
215 219 4.918037 AGACCACGTTCTAGCTTATTACG 58.082 43.478 0.00 0.00 38.14 3.18
216 220 7.256756 TCTAGACCACGTTCTAGCTTATTAC 57.743 40.000 16.31 0.00 43.40 1.89
219 223 6.062749 TGATCTAGACCACGTTCTAGCTTAT 58.937 40.000 16.31 7.67 43.40 1.73
228 241 6.208994 ACTTAGAAGTTGATCTAGACCACGTT 59.791 38.462 0.00 0.00 35.21 3.99
232 245 7.894364 AGGTTACTTAGAAGTTGATCTAGACCA 59.106 37.037 0.00 0.00 40.37 4.02
235 248 8.045507 TCGAGGTTACTTAGAAGTTGATCTAGA 58.954 37.037 0.00 0.00 40.37 2.43
261 274 1.378762 CCATGGGACCAGAAACGGT 59.621 57.895 2.85 0.00 43.91 4.83
263 276 1.002134 AGCCATGGGACCAGAAACG 60.002 57.895 15.13 0.00 0.00 3.60
281 294 2.507484 CAGCATGAGAAACCACTTCCA 58.493 47.619 0.00 0.00 39.69 3.53
409 422 1.673920 GGTGACTTGTTTTTCAGCCGA 59.326 47.619 0.00 0.00 34.76 5.54
414 428 7.703328 GTCAAGAATAGGTGACTTGTTTTTCA 58.297 34.615 0.00 0.00 43.67 2.69
472 488 2.158219 TCCAGCGGGGGATATTCTTCTA 60.158 50.000 2.05 0.00 37.22 2.10
488 504 1.668047 GCTTGCACTCAAACATCCAGC 60.668 52.381 0.00 0.00 0.00 4.85
501 517 6.253746 CAATCAAGACTATTACAGCTTGCAC 58.746 40.000 0.00 0.00 37.85 4.57
538 559 0.179004 ATGCGTCAACACTTTCCCCA 60.179 50.000 0.00 0.00 0.00 4.96
613 639 1.985473 TGCCAATGCATAGTGATCCC 58.015 50.000 0.00 0.00 44.23 3.85
677 705 6.809630 AGACTATCTTTTGAGTGGAAAAGC 57.190 37.500 0.00 0.00 41.05 3.51
740 776 7.017056 ACCCTTATTTGTGATTTTGGATTTGGA 59.983 33.333 0.00 0.00 0.00 3.53
741 777 7.167535 ACCCTTATTTGTGATTTTGGATTTGG 58.832 34.615 0.00 0.00 0.00 3.28
742 778 8.620116 AACCCTTATTTGTGATTTTGGATTTG 57.380 30.769 0.00 0.00 0.00 2.32
743 779 8.435982 TGAACCCTTATTTGTGATTTTGGATTT 58.564 29.630 0.00 0.00 0.00 2.17
744 780 7.972301 TGAACCCTTATTTGTGATTTTGGATT 58.028 30.769 0.00 0.00 0.00 3.01
745 781 7.552050 TGAACCCTTATTTGTGATTTTGGAT 57.448 32.000 0.00 0.00 0.00 3.41
800 849 2.830923 TGATAAATTGGGTGGTTGCTGG 59.169 45.455 0.00 0.00 0.00 4.85
802 851 4.613437 AGATGATAAATTGGGTGGTTGCT 58.387 39.130 0.00 0.00 0.00 3.91
803 852 5.127682 AGAAGATGATAAATTGGGTGGTTGC 59.872 40.000 0.00 0.00 0.00 4.17
804 853 6.604795 AGAGAAGATGATAAATTGGGTGGTTG 59.395 38.462 0.00 0.00 0.00 3.77
805 854 6.735556 AGAGAAGATGATAAATTGGGTGGTT 58.264 36.000 0.00 0.00 0.00 3.67
809 858 9.401058 CAGTTAAGAGAAGATGATAAATTGGGT 57.599 33.333 0.00 0.00 0.00 4.51
990 2030 1.681486 GGAGGGAAAGAGAGCCGGAG 61.681 65.000 5.05 0.00 0.00 4.63
991 2031 1.686110 GGAGGGAAAGAGAGCCGGA 60.686 63.158 5.05 0.00 0.00 5.14
992 2032 2.736826 GGGAGGGAAAGAGAGCCGG 61.737 68.421 0.00 0.00 0.00 6.13
993 2033 1.681486 GAGGGAGGGAAAGAGAGCCG 61.681 65.000 0.00 0.00 0.00 5.52
994 2034 1.341913 GGAGGGAGGGAAAGAGAGCC 61.342 65.000 0.00 0.00 0.00 4.70
995 2035 0.326143 AGGAGGGAGGGAAAGAGAGC 60.326 60.000 0.00 0.00 0.00 4.09
996 2036 1.691163 GGAGGAGGGAGGGAAAGAGAG 60.691 61.905 0.00 0.00 0.00 3.20
997 2037 0.340208 GGAGGAGGGAGGGAAAGAGA 59.660 60.000 0.00 0.00 0.00 3.10
998 2038 0.692756 GGGAGGAGGGAGGGAAAGAG 60.693 65.000 0.00 0.00 0.00 2.85
999 2039 1.162951 AGGGAGGAGGGAGGGAAAGA 61.163 60.000 0.00 0.00 0.00 2.52
1000 2040 0.692756 GAGGGAGGAGGGAGGGAAAG 60.693 65.000 0.00 0.00 0.00 2.62
1001 2041 1.396594 GAGGGAGGAGGGAGGGAAA 59.603 63.158 0.00 0.00 0.00 3.13
1002 2042 3.010226 CGAGGGAGGAGGGAGGGAA 62.010 68.421 0.00 0.00 0.00 3.97
1003 2043 3.430497 CGAGGGAGGAGGGAGGGA 61.430 72.222 0.00 0.00 0.00 4.20
1026 2074 1.803289 GAGAGCAACCGGAATTGGC 59.197 57.895 9.46 3.73 0.00 4.52
1325 2376 4.099170 GAAGCAGCACCGCAGCAG 62.099 66.667 6.13 0.00 43.44 4.24
1328 2379 3.123620 GAGGAAGCAGCACCGCAG 61.124 66.667 0.00 0.00 0.00 5.18
1333 2384 1.016653 GGAAGACGAGGAAGCAGCAC 61.017 60.000 0.00 0.00 0.00 4.40
1335 2386 0.818296 TAGGAAGACGAGGAAGCAGC 59.182 55.000 0.00 0.00 0.00 5.25
1377 2428 0.833409 TGACAGCCCAAGAGCAGAGA 60.833 55.000 0.00 0.00 34.23 3.10
1499 2550 5.695851 AATTCAGATGCGAACATATTCCC 57.304 39.130 0.00 0.00 36.35 3.97
1500 2551 7.420800 AGAAAATTCAGATGCGAACATATTCC 58.579 34.615 0.00 0.00 36.35 3.01
1501 2552 8.740369 CAAGAAAATTCAGATGCGAACATATTC 58.260 33.333 0.00 0.00 36.35 1.75
1502 2553 7.221452 GCAAGAAAATTCAGATGCGAACATATT 59.779 33.333 0.00 0.00 36.35 1.28
1503 2554 6.694411 GCAAGAAAATTCAGATGCGAACATAT 59.306 34.615 0.00 0.00 36.35 1.78
1504 2555 6.029607 GCAAGAAAATTCAGATGCGAACATA 58.970 36.000 0.00 0.00 36.35 2.29
1505 2556 4.860907 GCAAGAAAATTCAGATGCGAACAT 59.139 37.500 0.00 0.00 39.98 2.71
1526 2577 0.391661 GTTGCTCCTCGAATCCAGCA 60.392 55.000 3.76 3.76 40.13 4.41
1539 2590 1.080974 GTGCATGCCACTGTTGCTC 60.081 57.895 16.68 0.00 41.35 4.26
1540 2591 3.045142 GTGCATGCCACTGTTGCT 58.955 55.556 16.68 0.00 41.35 3.91
1601 2655 2.555199 GAGAGCTAATCAACCGTGCAT 58.445 47.619 0.00 0.00 0.00 3.96
1676 2730 5.178797 GTGAAGGCTGTATGTGTAAGATGT 58.821 41.667 0.00 0.00 0.00 3.06
1740 2795 8.791327 ACTGTTTTGAGAAACCAAAATGATTT 57.209 26.923 0.00 0.00 44.63 2.17
1743 2798 8.614469 AAAACTGTTTTGAGAAACCAAAATGA 57.386 26.923 17.06 0.00 44.63 2.57
1744 2799 8.502387 TGAAAACTGTTTTGAGAAACCAAAATG 58.498 29.630 22.06 0.00 44.63 2.32
1796 2851 9.218440 CAGCACCATGGTATTTTTATTTTCTTT 57.782 29.630 19.28 0.00 0.00 2.52
1799 2854 7.327214 TCCAGCACCATGGTATTTTTATTTTC 58.673 34.615 19.28 0.00 41.43 2.29
1806 2861 4.531732 ACAATTCCAGCACCATGGTATTTT 59.468 37.500 19.28 2.77 38.01 1.82
1807 2862 4.095946 ACAATTCCAGCACCATGGTATTT 58.904 39.130 19.28 2.81 38.01 1.40
1811 2866 1.203038 TGACAATTCCAGCACCATGGT 60.203 47.619 13.00 13.00 41.43 3.55
1820 3108 7.533426 GCTATTATTAGCCATGACAATTCCAG 58.467 38.462 5.49 0.00 44.29 3.86
1870 3158 4.567159 GCTAGATTAACTTCACCGTTCCAG 59.433 45.833 0.00 0.00 0.00 3.86
1875 3163 4.406003 AGGATGCTAGATTAACTTCACCGT 59.594 41.667 0.00 0.00 0.00 4.83
1877 3165 8.808092 AGTATAGGATGCTAGATTAACTTCACC 58.192 37.037 0.00 0.00 0.00 4.02
1888 3176 8.394822 AGGAAATGAGTAGTATAGGATGCTAGA 58.605 37.037 0.00 0.00 0.00 2.43
1889 3177 8.588290 AGGAAATGAGTAGTATAGGATGCTAG 57.412 38.462 0.00 0.00 0.00 3.42
1890 3178 8.807118 CAAGGAAATGAGTAGTATAGGATGCTA 58.193 37.037 0.00 0.00 0.00 3.49
1892 3180 6.876257 CCAAGGAAATGAGTAGTATAGGATGC 59.124 42.308 0.00 0.00 0.00 3.91
1893 3181 7.967908 ACCAAGGAAATGAGTAGTATAGGATG 58.032 38.462 0.00 0.00 0.00 3.51
1894 3182 9.091220 GTACCAAGGAAATGAGTAGTATAGGAT 57.909 37.037 0.00 0.00 0.00 3.24
1895 3183 7.508296 GGTACCAAGGAAATGAGTAGTATAGGA 59.492 40.741 7.15 0.00 0.00 2.94
1896 3184 7.509659 AGGTACCAAGGAAATGAGTAGTATAGG 59.490 40.741 15.94 0.00 0.00 2.57
1897 3185 8.480133 AGGTACCAAGGAAATGAGTAGTATAG 57.520 38.462 15.94 0.00 0.00 1.31
1898 3186 8.849543 AAGGTACCAAGGAAATGAGTAGTATA 57.150 34.615 15.94 0.00 0.00 1.47
1899 3187 7.750947 AAGGTACCAAGGAAATGAGTAGTAT 57.249 36.000 15.94 0.00 0.00 2.12
1900 3188 7.310858 GGAAAGGTACCAAGGAAATGAGTAGTA 60.311 40.741 15.94 0.00 0.00 1.82
1901 3189 6.449830 AAAGGTACCAAGGAAATGAGTAGT 57.550 37.500 15.94 0.00 0.00 2.73
1917 3205 2.258109 ACAGTGGAGGAGGAAAGGTAC 58.742 52.381 0.00 0.00 0.00 3.34
1918 3206 2.715763 ACAGTGGAGGAGGAAAGGTA 57.284 50.000 0.00 0.00 0.00 3.08
1919 3207 2.258109 GTACAGTGGAGGAGGAAAGGT 58.742 52.381 0.00 0.00 0.00 3.50
1921 3209 2.541466 AGGTACAGTGGAGGAGGAAAG 58.459 52.381 0.00 0.00 0.00 2.62
2158 4951 2.223044 GCCTCACCGCTTCTAAAAATCG 60.223 50.000 0.00 0.00 0.00 3.34
2167 4960 1.098050 AAATGATGCCTCACCGCTTC 58.902 50.000 0.00 0.00 33.22 3.86
2172 4965 4.799564 TTTTACCAAATGATGCCTCACC 57.200 40.909 0.00 0.00 33.22 4.02
2295 5167 4.319190 CCAGTGAAATTTTGCAGCAACATG 60.319 41.667 7.54 3.41 0.00 3.21
2320 5192 0.689623 AGAACAGCCAGGACCTGAAG 59.310 55.000 23.77 13.75 32.44 3.02
2408 5280 8.347035 CCTTTATTCCACGACTTCTTGTTTAAA 58.653 33.333 0.00 0.00 0.00 1.52
2524 5409 6.899393 ATAGAAGATTGGACACTGCAAAAA 57.101 33.333 0.00 0.00 29.75 1.94
2594 5479 5.278709 CGCATCTCCTGTATTGTAGTCTGAT 60.279 44.000 0.00 0.00 0.00 2.90
2656 5542 2.303600 TGTGTTCAGGCTAACCGGTATT 59.696 45.455 8.00 0.00 42.76 1.89
2700 5589 9.465985 TTGTACATATCATTTGCTGCATAATTG 57.534 29.630 1.84 4.71 0.00 2.32
2712 5607 9.874205 CCCAACAGAAATTTGTACATATCATTT 57.126 29.630 0.00 0.00 0.00 2.32
2862 5760 0.306840 TAGCGTAGAATCACTCGCCG 59.693 55.000 11.43 0.00 41.92 6.46
2876 5774 1.865865 CCCTGCATTATCGTTAGCGT 58.134 50.000 0.00 0.00 39.49 5.07
2883 5781 5.050490 GGTATATAGTGCCCTGCATTATCG 58.950 45.833 7.28 0.00 39.89 2.92
2898 5796 3.909776 TCGGTGAGTTGCGGTATATAG 57.090 47.619 0.00 0.00 0.00 1.31
3031 5955 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
3032 5956 4.466370 TGCTCTTATATTATGGGACGGAGG 59.534 45.833 0.00 0.00 0.00 4.30
3033 5957 5.186021 AGTGCTCTTATATTATGGGACGGAG 59.814 44.000 0.00 0.00 0.00 4.63
3034 5958 5.084519 AGTGCTCTTATATTATGGGACGGA 58.915 41.667 0.00 0.00 0.00 4.69
3035 5959 5.407407 AGTGCTCTTATATTATGGGACGG 57.593 43.478 0.00 0.00 0.00 4.79
3036 5960 7.441157 TCAAAAGTGCTCTTATATTATGGGACG 59.559 37.037 0.66 0.00 33.09 4.79
3037 5961 8.560374 GTCAAAAGTGCTCTTATATTATGGGAC 58.440 37.037 0.66 0.00 33.09 4.46
3038 5962 8.271458 TGTCAAAAGTGCTCTTATATTATGGGA 58.729 33.333 0.66 0.00 33.09 4.37
3039 5963 8.345565 GTGTCAAAAGTGCTCTTATATTATGGG 58.654 37.037 0.66 0.00 33.09 4.00
3072 5996 9.125026 CCCATAATCTAAGAGCATTTTTACACT 57.875 33.333 0.00 0.00 0.00 3.55
3075 5999 8.283291 CGTCCCATAATCTAAGAGCATTTTTAC 58.717 37.037 0.00 0.00 0.00 2.01
3076 6000 7.444183 CCGTCCCATAATCTAAGAGCATTTTTA 59.556 37.037 0.00 0.00 0.00 1.52
3077 6001 6.263168 CCGTCCCATAATCTAAGAGCATTTTT 59.737 38.462 0.00 0.00 0.00 1.94
3078 6002 5.765182 CCGTCCCATAATCTAAGAGCATTTT 59.235 40.000 0.00 0.00 0.00 1.82
3082 6006 3.572642 TCCGTCCCATAATCTAAGAGCA 58.427 45.455 0.00 0.00 0.00 4.26
3090 6014 0.767060 ACCCCCTCCGTCCCATAATC 60.767 60.000 0.00 0.00 0.00 1.75
3387 6311 3.565482 GCATCACAATCGATGGGTAACAT 59.435 43.478 4.46 0.00 42.58 2.71
3442 6366 2.105306 TCATGTACCATCCATGAGGCAG 59.895 50.000 0.00 0.00 42.73 4.85
3469 6397 2.095567 CAGCAATCAAAGGTTCTGACGG 60.096 50.000 0.00 0.00 0.00 4.79
3471 6399 4.202050 ACAACAGCAATCAAAGGTTCTGAC 60.202 41.667 0.00 0.00 0.00 3.51
3516 6447 5.783360 TCCTAAACTGATCTTGGTCACCTAA 59.217 40.000 0.00 0.00 0.00 2.69
3674 6606 3.255642 ACCAACATGTGTATTTGGCAGAC 59.744 43.478 12.50 0.00 43.18 3.51
3688 6776 8.055279 ACATATTTACTGAAAGGACCAACATG 57.945 34.615 0.00 0.00 39.30 3.21
3909 7006 7.531857 ACTCAGACTTGTATATGGGAGTATG 57.468 40.000 0.00 0.00 33.01 2.39
3912 7009 9.469097 GATATACTCAGACTTGTATATGGGAGT 57.531 37.037 16.54 0.00 40.40 3.85
3913 7010 9.693739 AGATATACTCAGACTTGTATATGGGAG 57.306 37.037 16.54 0.00 40.40 4.30
4201 7314 4.594491 AGCCTCCAACCTTGAAAATCAAAT 59.406 37.500 0.00 0.00 35.73 2.32
4238 7353 4.365514 TGCAAAGGTCAGAAGATTACCA 57.634 40.909 0.00 0.00 35.64 3.25
4385 7500 4.510167 ATCCAGCTGCTTTTGTAGGTAT 57.490 40.909 8.66 0.00 40.76 2.73
4499 7644 7.816031 ACATGCATTACTTTTCCATTCTTTCTG 59.184 33.333 0.00 0.00 0.00 3.02
4525 7670 7.432148 TCCTGGTAAAGATCATACTTGCTAA 57.568 36.000 0.00 0.00 0.00 3.09
4544 7696 5.824421 AGGGATGCAATCTAATAATCCTGG 58.176 41.667 0.00 0.00 44.71 4.45
4568 7720 3.078837 GGAATCTGCGTTCCAGGTTTTA 58.921 45.455 9.66 0.00 44.80 1.52
4661 7820 2.477825 GTGTGGACCGATGAGATGATG 58.522 52.381 0.00 0.00 0.00 3.07
4816 8139 3.318839 TGGTCAAGCAGAATTTGTTCAGG 59.681 43.478 0.00 0.00 0.00 3.86
4855 8179 2.972713 TGCAGTTCTACTTTCTGGACCT 59.027 45.455 0.00 0.00 0.00 3.85
4961 8290 1.975407 CCAACTGGGGCAGCTTCTG 60.975 63.158 0.00 0.00 34.37 3.02
5051 8386 7.172342 ACTGCCCAAGAACAACAAATATAGTA 58.828 34.615 0.00 0.00 0.00 1.82
5113 8448 3.131396 GTGATCACTTGTCACCTCGTTT 58.869 45.455 18.83 0.00 39.99 3.60
5190 8525 6.817765 TCCATCCAAGTTAACATTGTTCTC 57.182 37.500 8.61 0.90 0.00 2.87
5284 8620 6.763135 AGTTTGGCTACACACTGATATGTATG 59.237 38.462 0.00 0.00 36.33 2.39
5294 8630 3.508845 AATCCAGTTTGGCTACACACT 57.491 42.857 0.00 0.00 38.11 3.55
5382 8726 7.736447 AGTATAGCACTGGAATCTTATTTGC 57.264 36.000 0.00 0.00 35.62 3.68
5447 8794 9.263538 CTGTATACTTTGTAAAGTTGTGTACCA 57.736 33.333 14.47 0.00 46.52 3.25


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

AutoCloner maintained by Alex Coulton.