Multiple sequence alignment - TraesCS5D01G505200

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 TraesCS5D01G505200 chr5D 100.000 6639 0 0 1 6639 531400766 531407404 0.000000e+00 12261.0
1 TraesCS5D01G505200 chr5D 86.261 1019 119 15 4631 5643 531390390 531391393 0.000000e+00 1086.0
2 TraesCS5D01G505200 chr5D 82.713 752 91 22 2999 3736 531388810 531389536 3.380000e-177 632.0
3 TraesCS5D01G505200 chr5D 86.217 341 39 5 4812 5146 26264862 26265200 4.890000e-96 363.0
4 TraesCS5D01G505200 chr5D 84.466 103 14 2 11 112 334261628 334261729 4.240000e-17 100.0
5 TraesCS5D01G505200 chr4A 92.373 4379 262 37 2298 6637 641011433 641007088 0.000000e+00 6170.0
6 TraesCS5D01G505200 chr4A 90.763 1743 149 7 567 2305 641013243 641011509 0.000000e+00 2316.0
7 TraesCS5D01G505200 chr4A 89.570 1745 170 7 567 2305 641070852 641069114 0.000000e+00 2204.0
8 TraesCS5D01G505200 chr4A 91.645 1544 104 8 2304 3834 641069032 641067501 0.000000e+00 2113.0
9 TraesCS5D01G505200 chr4A 85.061 1071 123 22 4596 5642 641251727 641250670 0.000000e+00 1057.0
10 TraesCS5D01G505200 chr4A 83.370 920 116 28 2836 3742 641253428 641252533 0.000000e+00 817.0
11 TraesCS5D01G505200 chr4A 81.028 253 32 11 322 567 641071133 641070890 3.160000e-43 187.0
12 TraesCS5D01G505200 chr4A 76.455 378 69 15 6191 6555 641249786 641249416 3.160000e-43 187.0
13 TraesCS5D01G505200 chr4A 80.000 90 11 5 211 297 196787411 196787326 7.190000e-05 60.2
14 TraesCS5D01G505200 chr5B 90.542 4409 313 54 2298 6639 670683394 670687765 0.000000e+00 5736.0
15 TraesCS5D01G505200 chr5B 87.816 1502 170 9 807 2302 670681821 670683315 0.000000e+00 1748.0
16 TraesCS5D01G505200 chr5B 85.533 1023 125 16 4631 5639 670536993 670538006 0.000000e+00 1048.0
17 TraesCS5D01G505200 chr5B 82.404 915 118 27 2836 3736 670535252 670536137 0.000000e+00 758.0
18 TraesCS5D01G505200 chr5B 85.252 278 35 5 1 274 670680952 670681227 1.410000e-71 281.0
19 TraesCS5D01G505200 chr5B 88.430 121 13 1 2186 2305 484881082 484881202 1.930000e-30 145.0
20 TraesCS5D01G505200 chr5B 94.872 39 2 0 335 373 507729459 507729497 2.000000e-05 62.1
21 TraesCS5D01G505200 chr5B 81.013 79 12 2 322 400 477905057 477904982 7.190000e-05 60.2
22 TraesCS5D01G505200 chr5B 85.714 56 6 1 318 373 230353139 230353086 2.590000e-04 58.4
23 TraesCS5D01G505200 chr5B 94.118 34 2 0 4299 4332 393755606 393755639 1.200000e-02 52.8
24 TraesCS5D01G505200 chr5A 78.988 257 36 13 25 276 674636257 674636500 6.890000e-35 159.0
25 TraesCS5D01G505200 chr5A 88.462 52 6 0 322 373 502977364 502977313 5.560000e-06 63.9
26 TraesCS5D01G505200 chr1B 90.351 114 11 0 2182 2295 601141816 601141703 4.150000e-32 150.0
27 TraesCS5D01G505200 chr1B 82.558 86 12 3 26 110 99142774 99142857 9.230000e-09 73.1
28 TraesCS5D01G505200 chr4D 89.655 116 12 0 2189 2304 7831207 7831322 1.490000e-31 148.0
29 TraesCS5D01G505200 chr4D 78.448 116 19 5 194 309 459315699 459315590 3.320000e-08 71.3
30 TraesCS5D01G505200 chr1D 90.909 110 10 0 2186 2295 416771146 416771037 1.490000e-31 148.0
31 TraesCS5D01G505200 chr1D 100.000 39 0 0 194 232 463499317 463499279 9.230000e-09 73.1
32 TraesCS5D01G505200 chrUn 90.179 112 11 0 2184 2295 27664986 27665097 5.360000e-31 147.0
33 TraesCS5D01G505200 chr7A 87.805 123 15 0 2183 2305 555660027 555660149 1.930000e-30 145.0
34 TraesCS5D01G505200 chr7A 81.915 94 14 3 1 93 230295472 230295381 7.140000e-10 76.8
35 TraesCS5D01G505200 chr2A 80.303 132 18 7 159 284 765178710 765178839 7.090000e-15 93.5
36 TraesCS5D01G505200 chr2D 83.178 107 11 6 6 110 180542920 180542819 2.550000e-14 91.6
37 TraesCS5D01G505200 chr2D 87.500 48 6 0 326 373 17428053 17428100 1.000000e-03 56.5
38 TraesCS5D01G505200 chr6D 85.714 84 9 2 162 244 264168503 264168422 1.190000e-12 86.1
39 TraesCS5D01G505200 chr3D 85.915 71 9 1 163 232 416137571 416137641 2.570000e-09 75.0
40 TraesCS5D01G505200 chr7B 93.617 47 2 1 6126 6171 449544890 449544936 1.190000e-07 69.4
41 TraesCS5D01G505200 chr4B 89.474 57 3 3 6126 6179 253670534 253670478 1.190000e-07 69.4
42 TraesCS5D01G505200 chr3B 88.235 51 6 0 323 373 696974262 696974312 2.000000e-05 62.1
43 TraesCS5D01G505200 chr3B 94.118 34 2 0 4299 4332 678722758 678722791 1.200000e-02 52.8
44 TraesCS5D01G505200 chr1A 94.872 39 2 0 335 373 32457994 32457956 2.000000e-05 62.1
45 TraesCS5D01G505200 chr1A 92.308 39 3 0 335 373 32465154 32465116 1.000000e-03 56.5
46 TraesCS5D01G505200 chr2B 81.690 71 9 3 162 230 588289585 588289517 1.000000e-03 56.5


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 TraesCS5D01G505200 chr5D 531400766 531407404 6638 False 12261.000000 12261 100.000000 1 6639 1 chr5D.!!$F3 6638
1 TraesCS5D01G505200 chr5D 531388810 531391393 2583 False 859.000000 1086 84.487000 2999 5643 2 chr5D.!!$F4 2644
2 TraesCS5D01G505200 chr4A 641007088 641013243 6155 True 4243.000000 6170 91.568000 567 6637 2 chr4A.!!$R2 6070
3 TraesCS5D01G505200 chr4A 641067501 641071133 3632 True 1501.333333 2204 87.414333 322 3834 3 chr4A.!!$R3 3512
4 TraesCS5D01G505200 chr4A 641249416 641253428 4012 True 687.000000 1057 81.628667 2836 6555 3 chr4A.!!$R4 3719
5 TraesCS5D01G505200 chr5B 670680952 670687765 6813 False 2588.333333 5736 87.870000 1 6639 3 chr5B.!!$F5 6638
6 TraesCS5D01G505200 chr5B 670535252 670538006 2754 False 903.000000 1048 83.968500 2836 5639 2 chr5B.!!$F4 2803

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
139 142 0.602905 ACCGGAAGAGCAAAACCGAG 60.603 55.000 9.46 6.65 46.94 4.63 F
1466 1644 0.107831 TTGTCCTACGCTGCTGGTTT 59.892 50.000 0.00 0.00 0.00 3.27 F
1580 1758 0.379669 GCCGCATCAGATTGTTCCTG 59.620 55.000 0.00 0.00 0.00 3.86 F
1752 1930 0.539986 GTAGGGTCTGATTTCGGGCA 59.460 55.000 0.00 0.00 0.00 5.36 F
1808 1986 0.830648 CGATTCAGGCCAGGAGGTTA 59.169 55.000 5.01 0.00 37.19 2.85 F
1814 1992 0.984995 AGGCCAGGAGGTTACTTCAC 59.015 55.000 5.01 0.00 37.19 3.18 F
2604 2868 1.265095 GATACATGAATGGTGCTGCGG 59.735 52.381 0.00 0.00 0.00 5.69 F
3592 3870 2.045536 GCCCTCCACCAGAAGCAG 60.046 66.667 0.00 0.00 0.00 4.24 F
3774 4123 3.475566 AACACAGAACTTGCAGCTCTA 57.524 42.857 0.00 0.00 0.00 2.43 F
3873 4222 3.651423 GGGTAGGCCTAGTTTATCCACAT 59.349 47.826 14.38 0.00 34.45 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1898 2076 0.101759 CACACTATTGCTGGGCATGC 59.898 55.000 9.90 9.9 38.76 4.06 R
2950 3220 0.250793 ATGCGTGGAAATACCCGACA 59.749 50.000 0.00 0.0 38.00 4.35 R
3172 3450 0.325296 ATCGCCTACCCAGGAGTTGA 60.325 55.000 0.00 0.0 45.91 3.18 R
3487 3765 0.744414 CCAGATCCGCGTCCAATGTT 60.744 55.000 4.92 0.0 0.00 2.71 R
3496 3774 1.002366 CTCTTTGTTCCAGATCCGCG 58.998 55.000 0.00 0.0 0.00 6.46 R
3592 3870 6.963049 ATTAATTACTCACGTCCAACAGAC 57.037 37.500 0.00 0.0 42.54 3.51 R
4021 4370 2.158519 CCAACACCTACCCAGTTTTCCT 60.159 50.000 0.00 0.0 0.00 3.36 R
4671 5111 0.464373 ACTTGGCATGGTCGCATAGG 60.464 55.000 5.31 0.0 0.00 2.57 R
4903 5356 2.736670 AGCATCCCCTAAAAAGCGAT 57.263 45.000 0.00 0.0 0.00 4.58 R
5639 6104 3.323243 TCGTACCTTTTACTGCAAGAGC 58.677 45.455 0.00 0.0 42.57 4.09 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
17 18 4.440145 AACCATGCGCCCAAATCT 57.560 50.000 4.18 0.00 0.00 2.40
23 24 2.466846 CATGCGCCCAAATCTTGAATC 58.533 47.619 4.18 0.00 0.00 2.52
24 25 1.543607 TGCGCCCAAATCTTGAATCA 58.456 45.000 4.18 0.00 0.00 2.57
39 40 4.497473 TGAATCATTTTCACCGTTGGAC 57.503 40.909 0.00 0.00 0.00 4.02
43 44 3.815809 TCATTTTCACCGTTGGACTTCT 58.184 40.909 0.00 0.00 0.00 2.85
45 46 1.860676 TTTCACCGTTGGACTTCTCG 58.139 50.000 0.00 0.00 0.00 4.04
46 47 0.748450 TTCACCGTTGGACTTCTCGT 59.252 50.000 0.00 0.00 0.00 4.18
92 95 7.589958 TCCTTTGTTAATAGGCTTTGACAAA 57.410 32.000 20.20 20.20 40.56 2.83
122 125 7.851387 TTTTCACAAAAATACTGGGAAAACC 57.149 32.000 8.50 0.00 46.25 3.27
123 126 5.189659 TCACAAAAATACTGGGAAAACCG 57.810 39.130 0.00 0.00 44.64 4.44
136 139 2.545113 GGAAAACCGGAAGAGCAAAACC 60.545 50.000 9.46 0.00 0.00 3.27
137 140 0.666374 AAACCGGAAGAGCAAAACCG 59.334 50.000 9.46 0.00 44.16 4.44
139 142 0.602905 ACCGGAAGAGCAAAACCGAG 60.603 55.000 9.46 6.65 46.94 4.63
142 145 1.497722 GAAGAGCAAAACCGAGCCG 59.502 57.895 0.00 0.00 0.00 5.52
219 223 0.961019 GAAGCAAACATGTGCCTCCA 59.039 50.000 0.00 0.00 46.14 3.86
234 238 2.617774 GCCTCCATGAGAAGCAAATCTC 59.382 50.000 0.00 7.11 44.96 2.75
244 248 1.153549 GCAAATCTCGGCCTCTCGT 60.154 57.895 0.00 0.00 0.00 4.18
246 250 1.866063 GCAAATCTCGGCCTCTCGTAG 60.866 57.143 0.00 0.00 0.00 3.51
265 269 6.576185 TCGTAGAGAAAAGTACACCTTGTTT 58.424 36.000 0.00 0.00 32.32 2.83
266 270 6.698766 TCGTAGAGAAAAGTACACCTTGTTTC 59.301 38.462 0.00 0.00 32.32 2.78
267 271 6.700520 CGTAGAGAAAAGTACACCTTGTTTCT 59.299 38.462 0.00 0.00 34.43 2.52
269 273 6.056236 AGAGAAAAGTACACCTTGTTTCTCC 58.944 40.000 16.73 4.30 42.71 3.71
270 274 5.131067 AGAAAAGTACACCTTGTTTCTCCC 58.869 41.667 0.00 0.00 28.42 4.30
273 277 4.790718 AGTACACCTTGTTTCTCCCTTT 57.209 40.909 0.00 0.00 0.00 3.11
275 279 5.131067 AGTACACCTTGTTTCTCCCTTTTC 58.869 41.667 0.00 0.00 0.00 2.29
280 319 3.748568 CCTTGTTTCTCCCTTTTCGAGAG 59.251 47.826 0.00 0.00 37.65 3.20
283 322 1.348064 TTCTCCCTTTTCGAGAGGCA 58.652 50.000 10.56 0.00 37.65 4.75
284 323 1.573108 TCTCCCTTTTCGAGAGGCAT 58.427 50.000 10.56 0.00 32.58 4.40
286 325 3.104512 TCTCCCTTTTCGAGAGGCATAA 58.895 45.455 10.56 0.00 32.58 1.90
287 326 3.711704 TCTCCCTTTTCGAGAGGCATAAT 59.288 43.478 10.56 0.00 32.58 1.28
299 338 3.833706 GCATAATTGTGCCTCTCGC 57.166 52.632 15.69 0.00 39.18 5.03
426 501 4.817874 TTTTTCCCTCCAAAACCTAGGA 57.182 40.909 17.98 0.00 31.64 2.94
431 506 5.348259 TCCCTCCAAAACCTAGGAAAAAT 57.652 39.130 17.98 0.00 32.57 1.82
433 508 5.542251 TCCCTCCAAAACCTAGGAAAAATTG 59.458 40.000 17.98 11.87 32.57 2.32
440 524 5.638530 AACCTAGGAAAAATTGGGCAAAA 57.361 34.783 17.98 0.00 0.00 2.44
519 617 1.899437 AAATCGAAGGAGCGCCCAGA 61.899 55.000 15.92 12.05 37.41 3.86
522 620 2.347490 GAAGGAGCGCCCAGAACA 59.653 61.111 15.92 0.00 37.41 3.18
530 628 3.712881 GCCCAGAACACGACACGC 61.713 66.667 0.00 0.00 0.00 5.34
584 721 3.837399 TTGGGTGCCCCTTATTAGTTT 57.163 42.857 11.10 0.00 45.70 2.66
619 756 5.511386 AGTGATCTCAGGGAAATTTCTGT 57.489 39.130 17.42 2.84 33.13 3.41
635 772 8.641498 AAATTTCTGTTGGATATATAGCCCTG 57.359 34.615 14.40 4.53 0.00 4.45
681 818 1.066143 AGTTACATGAGGCCCAACTCG 60.066 52.381 0.00 0.00 40.39 4.18
688 825 2.686106 GGCCCAACTCGTCCCCTA 60.686 66.667 0.00 0.00 0.00 3.53
697 834 3.956199 CAACTCGTCCCCTACCATTAGTA 59.044 47.826 0.00 0.00 0.00 1.82
763 900 7.499321 TTTCACCGTTAGATTACAAATGTGT 57.501 32.000 0.00 0.00 42.09 3.72
779 943 1.905894 TGTGTAGGCCTAGCATTGACA 59.094 47.619 14.38 5.28 0.00 3.58
780 944 2.505407 TGTGTAGGCCTAGCATTGACAT 59.495 45.455 14.38 0.00 0.00 3.06
781 945 2.874701 GTGTAGGCCTAGCATTGACATG 59.125 50.000 14.38 0.00 0.00 3.21
796 960 4.808414 TGACATGCCTATATACCTGAGC 57.192 45.455 0.00 0.00 0.00 4.26
797 961 3.515502 TGACATGCCTATATACCTGAGCC 59.484 47.826 0.00 0.00 0.00 4.70
798 962 2.840651 ACATGCCTATATACCTGAGCCC 59.159 50.000 0.00 0.00 0.00 5.19
799 963 1.952621 TGCCTATATACCTGAGCCCC 58.047 55.000 0.00 0.00 0.00 5.80
800 964 1.437149 TGCCTATATACCTGAGCCCCT 59.563 52.381 0.00 0.00 0.00 4.79
801 965 2.112190 GCCTATATACCTGAGCCCCTC 58.888 57.143 0.00 0.00 0.00 4.30
802 966 2.559931 GCCTATATACCTGAGCCCCTCA 60.560 54.545 0.00 0.00 38.25 3.86
803 967 3.887768 GCCTATATACCTGAGCCCCTCAT 60.888 52.174 0.00 0.00 39.92 2.90
804 968 3.964031 CCTATATACCTGAGCCCCTCATC 59.036 52.174 0.00 0.00 39.92 2.92
805 969 3.567375 ATATACCTGAGCCCCTCATCA 57.433 47.619 0.00 0.00 39.92 3.07
871 1035 4.445735 GGCCTACATAACCCTAAATGCTCA 60.446 45.833 0.00 0.00 0.00 4.26
889 1053 0.618981 CACACCCCCTACTCCTTTCC 59.381 60.000 0.00 0.00 0.00 3.13
894 1058 0.914417 CCCCTACTCCTTTCCTGCCA 60.914 60.000 0.00 0.00 0.00 4.92
895 1059 1.216990 CCCTACTCCTTTCCTGCCAT 58.783 55.000 0.00 0.00 0.00 4.40
896 1060 2.408565 CCCTACTCCTTTCCTGCCATA 58.591 52.381 0.00 0.00 0.00 2.74
897 1061 2.982488 CCCTACTCCTTTCCTGCCATAT 59.018 50.000 0.00 0.00 0.00 1.78
1037 1206 6.809630 AATTGTGTTTTTCTCCTCTCTAGC 57.190 37.500 0.00 0.00 0.00 3.42
1038 1207 4.955811 TGTGTTTTTCTCCTCTCTAGCA 57.044 40.909 0.00 0.00 0.00 3.49
1072 1241 2.202987 CTCCTGCGATCACCCTGC 60.203 66.667 0.00 0.00 0.00 4.85
1092 1261 1.349627 GACATGGTTGAGCATCGCG 59.650 57.895 0.00 0.00 38.61 5.87
1105 1274 3.233919 ATCGCGCCCCCTCCCTATA 62.234 63.158 0.00 0.00 0.00 1.31
1129 1298 4.517285 GTTGCATATTCTTGTCTCCCTCA 58.483 43.478 0.00 0.00 0.00 3.86
1134 1303 5.740224 GCATATTCTTGTCTCCCTCATCGAA 60.740 44.000 0.00 0.00 0.00 3.71
1139 1308 0.382515 GTCTCCCTCATCGAACTCGG 59.617 60.000 0.00 0.00 40.29 4.63
1143 1312 1.654954 CCCTCATCGAACTCGGTCGT 61.655 60.000 4.13 0.00 41.80 4.34
1149 1318 2.432628 GAACTCGGTCGTGGGCAG 60.433 66.667 0.00 0.00 0.00 4.85
1184 1353 1.667830 CGGCGAGTGAAAGAGGCAA 60.668 57.895 0.00 0.00 0.00 4.52
1447 1625 0.828022 TGCATCCGACGGAATACCTT 59.172 50.000 22.55 0.00 34.34 3.50
1449 1627 1.597663 GCATCCGACGGAATACCTTTG 59.402 52.381 22.55 13.66 34.34 2.77
1466 1644 0.107831 TTGTCCTACGCTGCTGGTTT 59.892 50.000 0.00 0.00 0.00 3.27
1518 1696 1.349067 ATCCACTATAACCGAGGCCC 58.651 55.000 0.00 0.00 0.00 5.80
1521 1699 1.457079 ACTATAACCGAGGCCCGCT 60.457 57.895 0.00 0.00 36.84 5.52
1542 1720 1.136147 CAGCATGGCTCGCTTGAAC 59.864 57.895 0.00 0.00 37.72 3.18
1580 1758 0.379669 GCCGCATCAGATTGTTCCTG 59.620 55.000 0.00 0.00 0.00 3.86
1638 1816 1.691976 AGGATTCCGTCGGATGCAATA 59.308 47.619 16.23 0.00 0.00 1.90
1665 1843 5.003804 GGACACATGTCACCAGATAAAAGT 58.996 41.667 13.77 0.00 46.47 2.66
1714 1892 2.281070 CTCCACAACACCGCTGCT 60.281 61.111 0.00 0.00 0.00 4.24
1752 1930 0.539986 GTAGGGTCTGATTTCGGGCA 59.460 55.000 0.00 0.00 0.00 5.36
1772 1950 3.243367 GCATGGTTTGTTAGTTGTCTGCA 60.243 43.478 0.00 0.00 0.00 4.41
1808 1986 0.830648 CGATTCAGGCCAGGAGGTTA 59.169 55.000 5.01 0.00 37.19 2.85
1814 1992 0.984995 AGGCCAGGAGGTTACTTCAC 59.015 55.000 5.01 0.00 37.19 3.18
1831 2009 4.574828 ACTTCACGTTGTAGTTCTTGCAAT 59.425 37.500 0.00 0.00 33.85 3.56
1881 2059 8.518430 TCCTGCATGATAATAGTTTTGCTTAA 57.482 30.769 0.00 0.00 0.00 1.85
1898 2076 2.270352 TAACTTGCAACAGGACCAGG 57.730 50.000 0.00 0.00 0.00 4.45
1987 2165 1.328680 CAGTGCAATGGCTATCGACAC 59.671 52.381 6.18 2.94 41.91 3.67
2031 2209 4.754114 CCTGTTTAGCTTCCATCTCTATGC 59.246 45.833 0.00 0.00 0.00 3.14
2041 2219 4.218312 TCCATCTCTATGCTAAGCACTCA 58.782 43.478 0.00 0.00 43.04 3.41
2112 2291 6.575411 TGCCTAGAGGGGATAAGAGAAATAT 58.425 40.000 0.00 0.00 35.18 1.28
2167 2346 6.931267 TTTGGCAATAAAAACCCAACGCAAG 61.931 40.000 0.00 0.00 37.10 4.01
2170 2349 4.372656 CAATAAAAACCCAACGCAAGGAA 58.627 39.130 0.00 0.00 46.39 3.36
2297 2476 4.783227 TCAAGCCTCACCTTAGGTAAGATT 59.217 41.667 2.45 0.00 39.02 2.40
2382 2644 3.458487 ACCTATAACCAAACAGCCCCTAG 59.542 47.826 0.00 0.00 0.00 3.02
2496 2758 2.548057 GTGAGGCGAAGTTCATTGAACA 59.452 45.455 26.73 5.35 44.11 3.18
2513 2775 9.362151 TCATTGAACAGGGAACTTTTATTTACT 57.638 29.630 0.00 0.00 40.21 2.24
2576 2840 1.331214 CTGCTTGGTTGTGGTGGAAT 58.669 50.000 0.00 0.00 0.00 3.01
2604 2868 1.265095 GATACATGAATGGTGCTGCGG 59.735 52.381 0.00 0.00 0.00 5.69
2697 2967 9.632807 CATCAACACTATCCTATTACTAAGCTC 57.367 37.037 0.00 0.00 0.00 4.09
2787 3057 6.202954 GGCACTATTAAGTATGCCAACTACTG 59.797 42.308 17.47 0.00 42.00 2.74
2802 3072 4.862641 ACTACTGATAATTGGCCAAGGT 57.137 40.909 24.94 16.44 0.00 3.50
2880 3150 3.667360 AGTGAAAATCAAGCATTTGCCC 58.333 40.909 0.00 0.00 43.38 5.36
2950 3220 8.254508 GGATATGAACAAGAGACAGAAAGTACT 58.745 37.037 0.00 0.00 0.00 2.73
3001 3272 9.927668 ACCATATTTTTCCTTGTTTAGAACATG 57.072 29.630 0.00 0.00 41.79 3.21
3089 3367 9.113876 GCAACTATGTTTACATACAACAGAAAC 57.886 33.333 0.00 0.00 37.55 2.78
3121 3399 3.837213 AAACAATGACCATCAGCTTCG 57.163 42.857 0.00 0.00 0.00 3.79
3139 3417 3.444703 TCGAGATCAGCCTAAAGAAGC 57.555 47.619 0.00 0.00 0.00 3.86
3140 3418 2.760650 TCGAGATCAGCCTAAAGAAGCA 59.239 45.455 0.00 0.00 0.00 3.91
3150 3428 2.678336 CCTAAAGAAGCAAAGGTAGCCG 59.322 50.000 0.00 0.00 0.00 5.52
3172 3450 5.163513 CGGTGCTGCAGATAAAAGAAAATT 58.836 37.500 20.43 0.00 0.00 1.82
3321 3599 8.597662 AATGATTATTATTGGCAAGCATTCAC 57.402 30.769 5.96 0.00 34.20 3.18
3487 3765 2.304470 TGTAAAGTGCCCACAGATGCTA 59.696 45.455 0.82 0.00 0.00 3.49
3496 3774 2.684881 CCCACAGATGCTAACATTGGAC 59.315 50.000 0.00 0.00 34.76 4.02
3592 3870 2.045536 GCCCTCCACCAGAAGCAG 60.046 66.667 0.00 0.00 0.00 4.24
3774 4123 3.475566 AACACAGAACTTGCAGCTCTA 57.524 42.857 0.00 0.00 0.00 2.43
3873 4222 3.651423 GGGTAGGCCTAGTTTATCCACAT 59.349 47.826 14.38 0.00 34.45 3.21
3979 4328 5.902613 ACAGTGTGGATGTATTTGGATTG 57.097 39.130 0.00 0.00 0.00 2.67
4021 4370 6.828502 CTTGCTTAGCAACGACTGATATTA 57.171 37.500 16.30 0.00 43.99 0.98
4089 4442 8.954350 AGATAACCTCAATCATTCTGTCTTTTG 58.046 33.333 0.00 0.00 0.00 2.44
4367 4723 7.754924 TGGATTTGATTATTCTTTCTTGCGAAC 59.245 33.333 0.00 0.00 0.00 3.95
4392 4748 9.998106 ACTAAGATTAACAAAAGCTACAAGAGA 57.002 29.630 0.00 0.00 0.00 3.10
4397 4753 7.875327 TTAACAAAAGCTACAAGAGAGGTTT 57.125 32.000 0.00 0.00 44.34 3.27
4491 4924 7.322664 TGAGAAATTGCCATTTTAGGATTCAC 58.677 34.615 0.00 0.00 32.35 3.18
4534 4967 4.058817 ACTAAGAGTGTTGTTAGTGCAGC 58.941 43.478 0.00 0.00 40.66 5.25
4671 5111 7.036829 GTCCTTGTGAACTCCTTACTCTATTC 58.963 42.308 0.00 0.00 0.00 1.75
4838 5285 5.711506 TGTTGTCCATTTTCTAGCATCACAT 59.288 36.000 0.00 0.00 0.00 3.21
4903 5356 3.691118 GCTTGTTATGCTCTGACATTCCA 59.309 43.478 0.00 0.00 0.00 3.53
4981 5434 5.067153 TGAATTTAAAGCATACCACCCATCG 59.933 40.000 0.00 0.00 0.00 3.84
5025 5478 2.246719 ATCGCCAAGAAGATGCCTAC 57.753 50.000 0.00 0.00 0.00 3.18
5107 5560 8.729805 AAATCTCTCCAGTTTATGAAGACATC 57.270 34.615 0.00 0.00 37.87 3.06
5485 5948 4.797800 TTGTTTTGCTTATATGCCTGCA 57.202 36.364 8.04 0.00 0.00 4.41
5513 5976 7.170320 ACAAAAATCAAATGCAGTGACTGATTC 59.830 33.333 18.18 0.00 36.07 2.52
5521 5986 7.516198 AATGCAGTGACTGATTCTTTTAGTT 57.484 32.000 18.18 0.00 32.44 2.24
5639 6104 4.631813 GGTTAGGTTCAGTTGCTACATGAG 59.368 45.833 0.00 0.00 0.00 2.90
5740 6245 6.161855 TGCTCTCTCTTTTCTGTTGTCTAA 57.838 37.500 0.00 0.00 0.00 2.10
5775 6302 3.860641 TCTCTCATGTTCGCTGCATTTA 58.139 40.909 0.00 0.00 0.00 1.40
5939 6734 3.876914 TGTGTAGCAGTGAGAACTTTTGG 59.123 43.478 0.00 0.00 0.00 3.28
5942 6737 5.177696 GTGTAGCAGTGAGAACTTTTGGTAG 59.822 44.000 0.00 0.00 0.00 3.18
5948 6749 7.338449 AGCAGTGAGAACTTTTGGTAGTTTTTA 59.662 33.333 0.00 0.00 38.43 1.52
6003 6804 9.657419 AAAAGAATAGCATGTTATTTTTCCCTG 57.343 29.630 15.00 0.00 28.76 4.45
6004 6805 6.809869 AGAATAGCATGTTATTTTTCCCTGC 58.190 36.000 15.00 1.76 0.00 4.85
6005 6806 6.608808 AGAATAGCATGTTATTTTTCCCTGCT 59.391 34.615 15.00 3.80 41.10 4.24
6006 6807 4.460948 AGCATGTTATTTTTCCCTGCTG 57.539 40.909 0.00 0.00 37.13 4.41
6007 6808 4.088634 AGCATGTTATTTTTCCCTGCTGA 58.911 39.130 0.00 0.00 37.13 4.26
6008 6809 4.082026 AGCATGTTATTTTTCCCTGCTGAC 60.082 41.667 0.00 0.00 37.13 3.51
6010 6811 3.482436 TGTTATTTTTCCCTGCTGACGT 58.518 40.909 0.00 0.00 0.00 4.34
6012 6813 4.226761 GTTATTTTTCCCTGCTGACGTTG 58.773 43.478 0.00 0.00 0.00 4.10
6013 6814 2.045561 TTTTTCCCTGCTGACGTTGA 57.954 45.000 0.00 0.00 0.00 3.18
6014 6815 1.305201 TTTTCCCTGCTGACGTTGAC 58.695 50.000 0.00 0.00 0.00 3.18
6017 6818 1.669115 CCCTGCTGACGTTGACTGG 60.669 63.158 0.00 0.00 0.00 4.00
6021 6822 0.317160 TGCTGACGTTGACTGGTAGG 59.683 55.000 0.00 0.00 0.00 3.18
6023 6824 1.270147 GCTGACGTTGACTGGTAGGTT 60.270 52.381 0.00 0.00 0.00 3.50
6039 6847 6.078664 TGGTAGGTTTATTCAATTGGGTGTT 58.921 36.000 5.42 0.00 0.00 3.32
6075 6885 7.811653 AGTTTAGAAAGTATTGCTCTTGCTTC 58.188 34.615 0.00 0.00 40.48 3.86
6078 6888 6.006759 AGAAAGTATTGCTCTTGCTTCAAC 57.993 37.500 0.00 0.00 40.48 3.18
6094 6904 1.428912 TCAACTTTCCCCAGCATCCTT 59.571 47.619 0.00 0.00 0.00 3.36
6261 7130 6.209986 AGCTTGAGAACCATTCATTCAATTGA 59.790 34.615 3.38 3.38 0.00 2.57
6333 7212 8.609478 TTTTAAGTTTAGACTTGCGAAAACTG 57.391 30.769 8.85 0.00 45.46 3.16
6335 7214 5.813080 AGTTTAGACTTGCGAAAACTGTT 57.187 34.783 1.45 0.00 39.89 3.16
6377 7259 4.288398 TCCAATTATGTGAACCATGCCAT 58.712 39.130 0.00 0.00 34.86 4.40
6443 7328 2.045561 TTCTAGAGACGGCTGAGGAG 57.954 55.000 0.00 0.00 0.00 3.69
6462 7347 6.071896 TGAGGAGTCTCCATTATATGTTAGCG 60.072 42.308 21.26 0.00 39.61 4.26
6487 7372 3.741344 GCTTACATTATGGTGTAGAGGCG 59.259 47.826 0.00 0.00 36.08 5.52
6489 7374 3.179443 ACATTATGGTGTAGAGGCGTG 57.821 47.619 0.00 0.00 0.00 5.34
6580 7467 0.529773 TTGTGGACTGTCGTGTCAGC 60.530 55.000 1.07 0.00 38.84 4.26
6600 7487 2.739292 CGTATGGGTCACTGTTATCCG 58.261 52.381 0.00 0.00 0.00 4.18
6620 7507 5.823353 TCCGTTTTGTTTGTCATCTTAACC 58.177 37.500 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.101783 TGATTCAAGATTTGGGCGCAT 58.898 42.857 10.83 0.00 0.00 4.73
11 12 7.359431 CCAACGGTGAAAATGATTCAAGATTTG 60.359 37.037 0.00 0.00 0.00 2.32
13 14 6.015519 TCCAACGGTGAAAATGATTCAAGATT 60.016 34.615 0.00 0.00 0.00 2.40
17 18 4.582656 AGTCCAACGGTGAAAATGATTCAA 59.417 37.500 0.00 0.00 0.00 2.69
23 24 3.363970 CGAGAAGTCCAACGGTGAAAATG 60.364 47.826 0.00 0.00 0.00 2.32
24 25 2.806244 CGAGAAGTCCAACGGTGAAAAT 59.194 45.455 0.00 0.00 0.00 1.82
43 44 6.617879 TCTAATTTCAAAGATCTCGACACGA 58.382 36.000 0.00 0.00 0.00 4.35
45 46 7.708752 AGGATCTAATTTCAAAGATCTCGACAC 59.291 37.037 13.22 0.20 44.94 3.67
46 47 7.786030 AGGATCTAATTTCAAAGATCTCGACA 58.214 34.615 13.22 0.00 44.94 4.35
62 65 9.920946 TCAAAGCCTATTAACAAAGGATCTAAT 57.079 29.630 4.85 0.00 34.58 1.73
63 66 9.174166 GTCAAAGCCTATTAACAAAGGATCTAA 57.826 33.333 4.85 0.00 34.58 2.10
113 116 0.183971 TTGCTCTTCCGGTTTTCCCA 59.816 50.000 0.00 0.00 36.42 4.37
114 117 1.324383 TTTGCTCTTCCGGTTTTCCC 58.676 50.000 0.00 0.00 36.42 3.97
115 118 2.545113 GGTTTTGCTCTTCCGGTTTTCC 60.545 50.000 0.00 0.00 0.00 3.13
121 124 1.912371 GCTCGGTTTTGCTCTTCCGG 61.912 60.000 0.00 0.00 42.71 5.14
122 125 1.497722 GCTCGGTTTTGCTCTTCCG 59.502 57.895 0.00 0.00 43.65 4.30
123 126 1.876664 GGCTCGGTTTTGCTCTTCC 59.123 57.895 0.00 0.00 0.00 3.46
127 130 0.110192 CTTTCGGCTCGGTTTTGCTC 60.110 55.000 0.00 0.00 0.00 4.26
128 131 1.949257 CTTTCGGCTCGGTTTTGCT 59.051 52.632 0.00 0.00 0.00 3.91
129 132 1.729484 GCTTTCGGCTCGGTTTTGC 60.729 57.895 0.00 0.00 38.06 3.68
136 139 0.307760 AAAACAGTGCTTTCGGCTCG 59.692 50.000 0.00 0.00 42.39 5.03
137 140 2.385315 GAAAAACAGTGCTTTCGGCTC 58.615 47.619 3.31 0.00 42.39 4.70
139 142 1.202359 TGGAAAAACAGTGCTTTCGGC 60.202 47.619 10.56 0.00 42.22 5.54
142 145 6.480524 AAAAAGTGGAAAAACAGTGCTTTC 57.519 33.333 8.97 8.97 0.00 2.62
191 195 3.684305 CACATGTTTGCTTCCGTGAGATA 59.316 43.478 0.00 0.00 0.00 1.98
219 223 1.211457 AGGCCGAGATTTGCTTCTCAT 59.789 47.619 0.00 0.00 41.89 2.90
234 238 1.473278 ACTTTTCTCTACGAGAGGCCG 59.527 52.381 0.00 0.00 42.54 6.13
235 239 3.442977 TGTACTTTTCTCTACGAGAGGCC 59.557 47.826 0.00 0.00 42.54 5.19
244 248 7.215085 GGAGAAACAAGGTGTACTTTTCTCTA 58.785 38.462 17.42 0.00 44.75 2.43
246 250 5.238868 GGGAGAAACAAGGTGTACTTTTCTC 59.761 44.000 12.05 12.05 44.70 2.87
248 252 5.131067 AGGGAGAAACAAGGTGTACTTTTC 58.869 41.667 0.00 0.00 37.29 2.29
254 258 4.131596 CGAAAAGGGAGAAACAAGGTGTA 58.868 43.478 0.00 0.00 0.00 2.90
257 261 3.135895 TCTCGAAAAGGGAGAAACAAGGT 59.864 43.478 0.00 0.00 37.59 3.50
267 271 4.199310 CAATTATGCCTCTCGAAAAGGGA 58.801 43.478 13.81 11.84 38.73 4.20
269 273 4.731773 GCACAATTATGCCTCTCGAAAAGG 60.732 45.833 0.00 8.80 39.86 3.11
270 274 4.346129 GCACAATTATGCCTCTCGAAAAG 58.654 43.478 0.00 0.00 39.86 2.27
312 351 9.931210 GGAGGTAAATATTTTCTTTCGTACATG 57.069 33.333 5.91 0.00 0.00 3.21
314 353 9.675464 ATGGAGGTAAATATTTTCTTTCGTACA 57.325 29.630 5.91 2.56 0.00 2.90
315 354 9.931210 CATGGAGGTAAATATTTTCTTTCGTAC 57.069 33.333 5.91 0.00 0.00 3.67
316 355 9.893634 TCATGGAGGTAAATATTTTCTTTCGTA 57.106 29.630 5.91 0.00 0.00 3.43
317 356 8.801882 TCATGGAGGTAAATATTTTCTTTCGT 57.198 30.769 5.91 0.00 0.00 3.85
318 357 9.109393 TCTCATGGAGGTAAATATTTTCTTTCG 57.891 33.333 5.91 0.00 0.00 3.46
405 480 4.817874 TCCTAGGTTTTGGAGGGAAAAA 57.182 40.909 9.08 0.00 0.00 1.94
413 488 4.041075 GCCCAATTTTTCCTAGGTTTTGGA 59.959 41.667 21.63 0.00 35.29 3.53
414 489 4.202409 TGCCCAATTTTTCCTAGGTTTTGG 60.202 41.667 9.08 14.31 33.54 3.28
415 490 4.967036 TGCCCAATTTTTCCTAGGTTTTG 58.033 39.130 9.08 6.77 0.00 2.44
519 617 3.640000 GCTGCTGCGTGTCGTGTT 61.640 61.111 0.00 0.00 0.00 3.32
584 721 8.007153 TCCCTGAGATCACTAATTAATGAGAGA 58.993 37.037 6.84 4.65 0.00 3.10
619 756 6.785466 TGTCAACTACAGGGCTATATATCCAA 59.215 38.462 5.04 0.00 33.01 3.53
635 772 4.022155 GCTATAGCCCTAGGTGTCAACTAC 60.022 50.000 14.13 0.00 34.31 2.73
660 797 2.167693 CGAGTTGGGCCTCATGTAACTA 59.832 50.000 4.53 0.00 32.23 2.24
668 805 3.319198 GGGACGAGTTGGGCCTCA 61.319 66.667 4.53 0.00 0.00 3.86
681 818 4.102681 AGCAACATACTAATGGTAGGGGAC 59.897 45.833 0.00 0.00 36.61 4.46
688 825 4.316025 ACCCAAGCAACATACTAATGGT 57.684 40.909 0.00 0.00 37.43 3.55
697 834 2.900547 GGCCATACCCAAGCAACAT 58.099 52.632 0.00 0.00 0.00 2.71
779 943 2.046447 AGGGGCTCAGGTATATAGGCAT 59.954 50.000 0.00 0.00 37.53 4.40
780 944 1.437149 AGGGGCTCAGGTATATAGGCA 59.563 52.381 0.00 0.00 37.53 4.75
781 945 2.112190 GAGGGGCTCAGGTATATAGGC 58.888 57.143 0.00 0.00 35.21 3.93
782 946 3.474798 TGAGGGGCTCAGGTATATAGG 57.525 52.381 0.00 0.00 35.39 2.57
783 947 4.614475 TGATGAGGGGCTCAGGTATATAG 58.386 47.826 0.00 0.00 44.08 1.31
784 948 4.692523 TGATGAGGGGCTCAGGTATATA 57.307 45.455 0.00 0.00 44.08 0.86
785 949 3.567375 TGATGAGGGGCTCAGGTATAT 57.433 47.619 0.00 0.00 44.08 0.86
786 950 3.344535 TTGATGAGGGGCTCAGGTATA 57.655 47.619 0.00 0.00 44.08 1.47
787 951 2.196742 TTGATGAGGGGCTCAGGTAT 57.803 50.000 0.00 0.00 44.08 2.73
788 952 1.965414 TTTGATGAGGGGCTCAGGTA 58.035 50.000 0.00 0.00 44.08 3.08
789 953 1.302907 ATTTGATGAGGGGCTCAGGT 58.697 50.000 0.00 0.00 44.08 4.00
790 954 2.429610 CAAATTTGATGAGGGGCTCAGG 59.570 50.000 13.08 0.00 44.08 3.86
791 955 2.429610 CCAAATTTGATGAGGGGCTCAG 59.570 50.000 19.86 0.00 44.08 3.35
792 956 2.459644 CCAAATTTGATGAGGGGCTCA 58.540 47.619 19.86 0.00 44.99 4.26
793 957 1.758862 CCCAAATTTGATGAGGGGCTC 59.241 52.381 19.86 0.00 35.83 4.70
794 958 1.870064 CCCAAATTTGATGAGGGGCT 58.130 50.000 19.86 0.00 35.83 5.19
796 960 0.832626 GGCCCAAATTTGATGAGGGG 59.167 55.000 19.86 11.80 39.96 4.79
797 961 0.832626 GGGCCCAAATTTGATGAGGG 59.167 55.000 19.95 12.52 42.55 4.30
798 962 0.832626 GGGGCCCAAATTTGATGAGG 59.167 55.000 26.86 12.60 0.00 3.86
799 963 0.461135 CGGGGCCCAAATTTGATGAG 59.539 55.000 26.86 6.45 0.00 2.90
800 964 0.975040 CCGGGGCCCAAATTTGATGA 60.975 55.000 26.86 0.00 0.00 2.92
801 965 1.521616 CCGGGGCCCAAATTTGATG 59.478 57.895 26.86 10.99 0.00 3.07
802 966 1.688884 CCCGGGGCCCAAATTTGAT 60.689 57.895 26.86 0.00 0.00 2.57
803 967 2.284258 CCCGGGGCCCAAATTTGA 60.284 61.111 26.86 0.00 0.00 2.69
804 968 3.398310 CCCCGGGGCCCAAATTTG 61.398 66.667 31.01 11.40 0.00 2.32
805 969 3.935265 ACCCCGGGGCCCAAATTT 61.935 61.111 40.67 15.28 39.32 1.82
847 1011 3.461831 AGCATTTAGGGTTATGTAGGCCA 59.538 43.478 5.01 0.00 0.00 5.36
871 1035 0.496841 AGGAAAGGAGTAGGGGGTGT 59.503 55.000 0.00 0.00 0.00 4.16
896 1060 8.896658 AGGAGACGAAGGAGGCTATATATATAT 58.103 37.037 10.10 10.10 0.00 0.86
897 1061 8.277720 AGGAGACGAAGGAGGCTATATATATA 57.722 38.462 2.49 2.49 0.00 0.86
991 1157 0.525761 TTCCTTACCATTTGCGCTGC 59.474 50.000 9.73 0.00 0.00 5.25
1022 1191 5.772004 AGGTCTATGCTAGAGAGGAGAAAA 58.228 41.667 0.00 0.00 35.04 2.29
1037 1206 1.770518 GGGGTGGGGGAGGTCTATG 60.771 68.421 0.00 0.00 0.00 2.23
1038 1207 1.952766 AGGGGTGGGGGAGGTCTAT 60.953 63.158 0.00 0.00 0.00 1.98
1072 1241 2.009108 CGATGCTCAACCATGTCCG 58.991 57.895 0.00 0.00 0.00 4.79
1092 1261 1.780107 GCAACCTATAGGGAGGGGGC 61.780 65.000 22.91 12.12 41.36 5.80
1105 1274 3.525199 AGGGAGACAAGAATATGCAACCT 59.475 43.478 0.00 0.00 0.00 3.50
1129 1298 2.882876 CCCACGACCGAGTTCGAT 59.117 61.111 2.59 0.00 41.78 3.59
1134 1303 2.282674 TACTGCCCACGACCGAGT 60.283 61.111 0.00 0.00 0.00 4.18
1139 1308 0.458716 GCTTCTCTACTGCCCACGAC 60.459 60.000 0.00 0.00 0.00 4.34
1149 1318 1.226717 CGCACGAGGGCTTCTCTAC 60.227 63.158 0.00 0.00 40.30 2.59
1184 1353 2.204090 TTCGCCTTCCCCTCCCTT 60.204 61.111 0.00 0.00 0.00 3.95
1351 1528 5.771469 CACACTGACTCCATGCAATTTTTA 58.229 37.500 0.00 0.00 0.00 1.52
1447 1625 0.107831 AAACCAGCAGCGTAGGACAA 59.892 50.000 8.37 0.00 0.00 3.18
1449 1627 1.019805 GGAAACCAGCAGCGTAGGAC 61.020 60.000 8.37 0.97 0.00 3.85
1466 1644 0.678950 TTGCGATATGAGCCGATGGA 59.321 50.000 0.00 0.00 0.00 3.41
1498 1676 1.697982 GGGCCTCGGTTATAGTGGATT 59.302 52.381 0.84 0.00 0.00 3.01
1499 1677 1.349067 GGGCCTCGGTTATAGTGGAT 58.651 55.000 0.84 0.00 0.00 3.41
1518 1696 2.963854 CGAGCCATGCTGGTAGCG 60.964 66.667 0.00 2.90 46.26 4.26
1521 1699 1.450134 CAAGCGAGCCATGCTGGTA 60.450 57.895 0.00 0.00 43.14 3.25
1528 1706 1.448540 CCGAGTTCAAGCGAGCCAT 60.449 57.895 0.00 0.00 0.00 4.40
1537 1715 2.370519 TCTTGTCATTCCCCGAGTTCAA 59.629 45.455 0.00 0.00 0.00 2.69
1538 1716 1.974957 TCTTGTCATTCCCCGAGTTCA 59.025 47.619 0.00 0.00 0.00 3.18
1542 1720 0.807667 CGCTCTTGTCATTCCCCGAG 60.808 60.000 0.00 0.00 0.00 4.63
1580 1758 3.515104 TGGCTTCCTTGATCCAAAATTCC 59.485 43.478 0.00 0.00 0.00 3.01
1638 1816 0.318441 CTGGTGACATGTGTCCGTCT 59.682 55.000 1.15 0.00 44.15 4.18
1665 1843 1.897423 CACCTCTCGTGCATACCCA 59.103 57.895 0.00 0.00 35.18 4.51
1725 1903 1.664321 ATCAGACCCTACCGTCGCAC 61.664 60.000 0.00 0.00 37.85 5.34
1726 1904 0.968901 AATCAGACCCTACCGTCGCA 60.969 55.000 0.00 0.00 37.85 5.10
1728 1906 1.533338 CGAAATCAGACCCTACCGTCG 60.533 57.143 0.00 0.00 37.85 5.12
1772 1950 5.556915 TGAATCGGGTTGAGATAAACAGTT 58.443 37.500 0.00 0.00 0.00 3.16
1808 1986 3.527533 TGCAAGAACTACAACGTGAAGT 58.472 40.909 0.00 0.00 0.00 3.01
1814 1992 6.183359 GCACAAATATTGCAAGAACTACAACG 60.183 38.462 4.94 0.00 39.93 4.10
1831 2009 2.942376 CAGAGCCATAACCGCACAAATA 59.058 45.455 0.00 0.00 0.00 1.40
1881 2059 1.529244 GCCTGGTCCTGTTGCAAGT 60.529 57.895 0.00 0.00 0.00 3.16
1888 2066 4.052518 GGGCATGCCTGGTCCTGT 62.053 66.667 34.70 0.00 36.10 4.00
1898 2076 0.101759 CACACTATTGCTGGGCATGC 59.898 55.000 9.90 9.90 38.76 4.06
1987 2165 4.163649 AGGGTTAAGAAAGAGGAATACCGG 59.836 45.833 0.00 0.00 41.83 5.28
2041 2219 8.441312 ACATGATGAAAAGAAGCACAATTTTT 57.559 26.923 0.00 0.00 0.00 1.94
2167 2346 8.370266 ACCCCTAAATTAATAGTTTTGGTTCC 57.630 34.615 7.63 0.00 32.06 3.62
2170 2349 8.730093 ACAACCCCTAAATTAATAGTTTTGGT 57.270 30.769 7.63 1.39 32.06 3.67
2382 2644 6.204495 GGATCATCTAGGAATGCTTTGAGTTC 59.796 42.308 0.00 0.00 0.00 3.01
2496 2758 9.862149 TTTGAGAGAAGTAAATAAAAGTTCCCT 57.138 29.630 0.00 0.00 0.00 4.20
2513 2775 4.536295 AAGGGGGAAAACTTTGAGAGAA 57.464 40.909 0.00 0.00 0.00 2.87
2576 2840 7.036829 CAGCACCATTCATGTATCATTTCAAA 58.963 34.615 0.00 0.00 0.00 2.69
2697 2967 3.713764 ACACCAAGATTAGGGAGGAGATG 59.286 47.826 0.00 0.00 0.00 2.90
2787 3057 4.690280 CACAACAAACCTTGGCCAATTATC 59.310 41.667 20.85 0.00 34.12 1.75
2880 3150 1.062440 TGCAATAGCGCATCGTTTCAG 59.938 47.619 11.47 0.00 46.23 3.02
2950 3220 0.250793 ATGCGTGGAAATACCCGACA 59.749 50.000 0.00 0.00 38.00 4.35
2954 3224 3.470645 ACTAGATGCGTGGAAATACCC 57.529 47.619 0.00 0.00 38.00 3.69
3057 3330 6.234920 TGTATGTAAACATAGTTGCACCTGT 58.765 36.000 3.06 0.00 39.29 4.00
3058 3331 6.735678 TGTATGTAAACATAGTTGCACCTG 57.264 37.500 3.06 0.00 39.29 4.00
3059 3332 6.712998 TGTTGTATGTAAACATAGTTGCACCT 59.287 34.615 3.06 0.00 39.29 4.00
3061 3334 7.802738 TCTGTTGTATGTAAACATAGTTGCAC 58.197 34.615 3.06 0.00 39.29 4.57
3062 3335 7.971183 TCTGTTGTATGTAAACATAGTTGCA 57.029 32.000 3.06 0.00 39.29 4.08
3063 3336 9.113876 GTTTCTGTTGTATGTAAACATAGTTGC 57.886 33.333 3.06 0.00 39.29 4.17
3064 3337 9.313323 CGTTTCTGTTGTATGTAAACATAGTTG 57.687 33.333 3.06 0.00 39.29 3.16
3066 3339 7.874016 TCCGTTTCTGTTGTATGTAAACATAGT 59.126 33.333 3.06 0.00 39.29 2.12
3072 3350 7.987649 ACTTTTCCGTTTCTGTTGTATGTAAA 58.012 30.769 0.00 0.00 0.00 2.01
3089 3367 7.436673 TGATGGTCATTGTTTTTAACTTTTCCG 59.563 33.333 0.00 0.00 0.00 4.30
3121 3399 4.335037 CCTTTGCTTCTTTAGGCTGATCTC 59.665 45.833 0.00 0.00 0.00 2.75
3150 3428 6.158598 TGAATTTTCTTTTATCTGCAGCACC 58.841 36.000 9.47 0.00 0.00 5.01
3172 3450 0.325296 ATCGCCTACCCAGGAGTTGA 60.325 55.000 0.00 0.00 45.91 3.18
3321 3599 9.778993 GAATAACAATATATGCATGCTAGGTTG 57.221 33.333 20.33 17.74 0.00 3.77
3368 3646 8.824159 AATTCAATCTGATGTAAGACCGATAG 57.176 34.615 0.00 0.00 0.00 2.08
3372 3650 7.278646 TCTGAAATTCAATCTGATGTAAGACCG 59.721 37.037 0.00 0.00 0.00 4.79
3426 3704 6.700960 TGTTAGCACTTCAAAAATGGATTGTG 59.299 34.615 0.00 0.00 0.00 3.33
3487 3765 0.744414 CCAGATCCGCGTCCAATGTT 60.744 55.000 4.92 0.00 0.00 2.71
3496 3774 1.002366 CTCTTTGTTCCAGATCCGCG 58.998 55.000 0.00 0.00 0.00 6.46
3592 3870 6.963049 ATTAATTACTCACGTCCAACAGAC 57.037 37.500 0.00 0.00 42.54 3.51
3645 3924 9.471702 AGTTGAAATGATCCATACTTTTGAGAT 57.528 29.630 0.00 0.00 0.00 2.75
3646 3925 8.868522 AGTTGAAATGATCCATACTTTTGAGA 57.131 30.769 0.00 0.00 0.00 3.27
3647 3926 9.350357 CAAGTTGAAATGATCCATACTTTTGAG 57.650 33.333 0.00 0.00 0.00 3.02
3979 4328 5.422650 AGCAAGCTAATATACCCTAGCCTAC 59.577 44.000 0.00 0.00 41.25 3.18
4013 4362 6.992715 CACCTACCCAGTTTTCCTAATATCAG 59.007 42.308 0.00 0.00 0.00 2.90
4021 4370 2.158519 CCAACACCTACCCAGTTTTCCT 60.159 50.000 0.00 0.00 0.00 3.36
4089 4442 4.287766 ACCTACCAGGAACAATCAGAAC 57.712 45.455 0.00 0.00 37.67 3.01
4273 4628 7.271511 TGCCAAGAAAGTATTTGTTTGTTCAT 58.728 30.769 0.00 0.00 38.53 2.57
4360 4715 6.966021 AGCTTTTGTTAATCTTAGTTCGCAA 58.034 32.000 0.00 0.00 0.00 4.85
4533 4966 4.530161 AGAAGGGATAGTGAGTGGATATGC 59.470 45.833 0.00 0.00 0.00 3.14
4534 4967 6.678568 AAGAAGGGATAGTGAGTGGATATG 57.321 41.667 0.00 0.00 0.00 1.78
4579 5012 6.128486 TGCATAAATGAGGGTGTTATGTGAT 58.872 36.000 0.00 0.00 37.48 3.06
4671 5111 0.464373 ACTTGGCATGGTCGCATAGG 60.464 55.000 5.31 0.00 0.00 2.57
4773 5213 7.268586 ACATGTTGATCATAAGAGACCAGTAC 58.731 38.462 0.00 0.00 34.67 2.73
4847 5294 9.685276 TGATTACATCTCAGACATACCAATTTT 57.315 29.630 0.00 0.00 0.00 1.82
4849 5296 8.489489 ACTGATTACATCTCAGACATACCAATT 58.511 33.333 7.28 0.00 42.22 2.32
4858 5309 7.432869 AGCTTATCACTGATTACATCTCAGAC 58.567 38.462 7.28 0.00 42.22 3.51
4881 5332 3.691118 TGGAATGTCAGAGCATAACAAGC 59.309 43.478 0.00 0.00 0.00 4.01
4903 5356 2.736670 AGCATCCCCTAAAAAGCGAT 57.263 45.000 0.00 0.00 0.00 4.58
4944 5397 8.954950 TGCTTTAAATTCACCAAGATTGAAAA 57.045 26.923 0.00 0.00 36.57 2.29
4981 5434 4.820894 ACAAACTCTGGGTGATACTACC 57.179 45.455 0.00 0.00 40.10 3.18
5107 5560 4.083324 TCAGCAGAGAAAAATAACAAGGCG 60.083 41.667 0.00 0.00 0.00 5.52
5168 5621 4.747540 TGCAGTCACACATAAACACATC 57.252 40.909 0.00 0.00 0.00 3.06
5407 5869 8.990163 ATTATGGGTGGTTCTATTTTTCGTAT 57.010 30.769 0.00 0.00 0.00 3.06
5485 5948 7.660112 TCAGTCACTGCATTTGATTTTTGTAT 58.340 30.769 0.00 0.00 0.00 2.29
5513 5976 9.341899 GGTATGAAATTAGCACACAACTAAAAG 57.658 33.333 0.00 0.00 33.54 2.27
5521 5986 5.260424 ACCATGGTATGAAATTAGCACACA 58.740 37.500 18.10 0.00 32.83 3.72
5639 6104 3.323243 TCGTACCTTTTACTGCAAGAGC 58.677 45.455 0.00 0.00 42.57 4.09
5821 6349 6.456795 GCTCACCCAGCTTAAAAAGATAAT 57.543 37.500 0.00 0.00 45.83 1.28
5909 6703 1.302832 ACTGCTACACAAGGCTGGC 60.303 57.895 0.00 0.00 0.00 4.85
5910 6704 0.035317 TCACTGCTACACAAGGCTGG 59.965 55.000 0.00 0.00 0.00 4.85
5995 6796 1.134220 AGTCAACGTCAGCAGGGAAAA 60.134 47.619 0.00 0.00 0.00 2.29
5997 6798 0.249868 CAGTCAACGTCAGCAGGGAA 60.250 55.000 0.00 0.00 0.00 3.97
5998 6799 1.367471 CAGTCAACGTCAGCAGGGA 59.633 57.895 0.00 0.00 0.00 4.20
6001 6802 1.670087 CCTACCAGTCAACGTCAGCAG 60.670 57.143 0.00 0.00 0.00 4.24
6002 6803 0.317160 CCTACCAGTCAACGTCAGCA 59.683 55.000 0.00 0.00 0.00 4.41
6003 6804 0.317479 ACCTACCAGTCAACGTCAGC 59.683 55.000 0.00 0.00 0.00 4.26
6004 6805 2.814280 AACCTACCAGTCAACGTCAG 57.186 50.000 0.00 0.00 0.00 3.51
6005 6806 4.877378 ATAAACCTACCAGTCAACGTCA 57.123 40.909 0.00 0.00 0.00 4.35
6006 6807 5.232463 TGAATAAACCTACCAGTCAACGTC 58.768 41.667 0.00 0.00 0.00 4.34
6007 6808 5.217978 TGAATAAACCTACCAGTCAACGT 57.782 39.130 0.00 0.00 0.00 3.99
6008 6809 6.737254 ATTGAATAAACCTACCAGTCAACG 57.263 37.500 0.00 0.00 0.00 4.10
6010 6811 6.435904 CCCAATTGAATAAACCTACCAGTCAA 59.564 38.462 7.12 0.00 0.00 3.18
6012 6813 5.949952 ACCCAATTGAATAAACCTACCAGTC 59.050 40.000 7.12 0.00 0.00 3.51
6013 6814 5.714806 CACCCAATTGAATAAACCTACCAGT 59.285 40.000 7.12 0.00 0.00 4.00
6014 6815 5.714806 ACACCCAATTGAATAAACCTACCAG 59.285 40.000 7.12 0.00 0.00 4.00
6017 6818 9.414295 GTTTAACACCCAATTGAATAAACCTAC 57.586 33.333 7.12 0.00 32.41 3.18
6075 6885 1.928868 AAGGATGCTGGGGAAAGTTG 58.071 50.000 0.00 0.00 0.00 3.16
6078 6888 5.187576 TCAAATTTAAGGATGCTGGGGAAAG 59.812 40.000 0.00 0.00 0.00 2.62
6129 6939 3.697166 GAGATCCTTTGGGGCAACTTAA 58.303 45.455 0.00 0.00 34.39 1.85
6131 6941 1.614317 CGAGATCCTTTGGGGCAACTT 60.614 52.381 0.00 0.00 34.39 2.66
6132 6942 0.035056 CGAGATCCTTTGGGGCAACT 60.035 55.000 0.00 0.00 34.39 3.16
6135 6945 0.918983 ATTCGAGATCCTTTGGGGCA 59.081 50.000 0.00 0.00 34.39 5.36
6322 7191 1.595976 GCACGCTAACAGTTTTCGCAA 60.596 47.619 0.00 0.00 0.00 4.85
6333 7212 3.058914 AGACAAATGAACTGCACGCTAAC 60.059 43.478 0.00 0.00 0.00 2.34
6335 7214 2.736721 GAGACAAATGAACTGCACGCTA 59.263 45.455 0.00 0.00 0.00 4.26
6443 7328 4.323868 GCGTCGCTAACATATAATGGAGAC 59.676 45.833 10.68 0.00 33.60 3.36
6462 7347 4.982916 CCTCTACACCATAATGTAAGCGTC 59.017 45.833 0.00 0.00 34.68 5.19
6487 7372 3.741388 CGAGTGGATCAACCTAATCCCAC 60.741 52.174 0.00 0.00 41.78 4.61
6489 7374 2.698797 TCGAGTGGATCAACCTAATCCC 59.301 50.000 0.00 0.00 41.78 3.85
6580 7467 2.100252 ACGGATAACAGTGACCCATACG 59.900 50.000 0.00 0.00 0.00 3.06
6600 7487 6.031471 ACACGGTTAAGATGACAAACAAAAC 58.969 36.000 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.