Multiple sequence alignment - TraesCS5B01G128400

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 TraesCS5B01G128400 chr5B 100.000 5981 0 0 1 5981 234876055 234882035 0.000000e+00 11045.0
1 TraesCS5B01G128400 chr5B 94.702 755 32 6 5229 5981 709182452 709183200 0.000000e+00 1166.0
2 TraesCS5B01G128400 chr5D 91.034 2833 119 60 2422 5215 218188321 218191057 0.000000e+00 3699.0
3 TraesCS5B01G128400 chr5D 90.351 1824 72 45 652 2401 218186471 218188264 0.000000e+00 2298.0
4 TraesCS5B01G128400 chr5D 88.564 411 26 7 193 584 218185819 218186227 4.190000e-131 479.0
5 TraesCS5B01G128400 chr5D 87.234 141 18 0 4095 4235 454099269 454099129 1.730000e-35 161.0
6 TraesCS5B01G128400 chr5D 85.000 140 21 0 4092 4231 505215643 505215782 6.250000e-30 143.0
7 TraesCS5B01G128400 chr5D 95.294 85 4 0 41 125 218185275 218185359 1.050000e-27 135.0
8 TraesCS5B01G128400 chr5A 89.994 1769 64 36 708 2401 291129588 291131318 0.000000e+00 2182.0
9 TraesCS5B01G128400 chr5A 90.311 1641 77 28 3639 5225 291132864 291134476 0.000000e+00 2074.0
10 TraesCS5B01G128400 chr5A 85.087 751 37 26 2890 3610 291131862 291132567 0.000000e+00 697.0
11 TraesCS5B01G128400 chr5A 90.405 469 24 4 193 642 291129119 291129585 1.110000e-166 597.0
12 TraesCS5B01G128400 chr5A 93.600 125 7 1 1 125 291128657 291128780 1.020000e-42 185.0
13 TraesCS5B01G128400 chr5A 84.472 161 15 5 2420 2571 291131374 291131533 3.730000e-32 150.0
14 TraesCS5B01G128400 chr5A 85.507 138 20 0 4094 4231 632836475 632836612 1.740000e-30 145.0
15 TraesCS5B01G128400 chr5A 84.892 139 21 0 4097 4235 34262965 34263103 2.250000e-29 141.0
16 TraesCS5B01G128400 chr2B 96.676 752 15 7 5234 5981 68149609 68148864 0.000000e+00 1242.0
17 TraesCS5B01G128400 chr2B 94.555 753 35 4 5229 5981 454477541 454476795 0.000000e+00 1158.0
18 TraesCS5B01G128400 chr6B 96.026 755 23 5 5229 5981 26495033 26495782 0.000000e+00 1221.0
19 TraesCS5B01G128400 chr6B 95.856 748 26 3 5234 5981 679255906 679255164 0.000000e+00 1205.0
20 TraesCS5B01G128400 chr4B 95.509 757 27 5 5225 5979 310260479 310259728 0.000000e+00 1203.0
21 TraesCS5B01G128400 chr3B 94.960 754 32 4 5229 5981 420916728 420917476 0.000000e+00 1177.0
22 TraesCS5B01G128400 chr3B 94.954 753 30 5 5229 5981 558273997 558274741 0.000000e+00 1173.0
23 TraesCS5B01G128400 chr3B 88.079 151 18 0 4090 4240 137750703 137750853 4.760000e-41 180.0
24 TraesCS5B01G128400 chrUn 94.821 753 31 4 5229 5981 86411300 86410556 0.000000e+00 1168.0
25 TraesCS5B01G128400 chr3A 90.566 477 22 12 905 1365 725813806 725814275 1.430000e-170 610.0
26 TraesCS5B01G128400 chr3A 88.889 477 30 12 905 1365 120389618 120390087 3.130000e-157 566.0
27 TraesCS5B01G128400 chr3A 88.378 413 23 12 905 1300 59709381 59709785 1.950000e-129 473.0
28 TraesCS5B01G128400 chr3A 92.488 213 7 7 905 1114 519351537 519351743 4.530000e-76 296.0
29 TraesCS5B01G128400 chr3A 89.202 213 14 6 905 1114 190056591 190056385 2.140000e-64 257.0
30 TraesCS5B01G128400 chr3A 85.882 170 22 2 4090 4257 105112955 105112786 4.760000e-41 180.0
31 TraesCS5B01G128400 chr3A 100.000 34 0 0 1265 1298 519351790 519351823 5.000000e-06 63.9
32 TraesCS5B01G128400 chr3A 97.222 36 1 0 1265 1300 190056308 190056273 1.800000e-05 62.1
33 TraesCS5B01G128400 chr1A 90.049 412 17 13 905 1300 515807102 515807505 4.130000e-141 512.0
34 TraesCS5B01G128400 chr1A 88.720 328 25 4 1050 1365 421134308 421133981 2.020000e-104 390.0
35 TraesCS5B01G128400 chr1A 84.118 170 25 2 4467 4635 186213063 186213231 4.800000e-36 163.0
36 TraesCS5B01G128400 chr1A 74.505 404 86 14 4468 4861 387029202 387028806 6.200000e-35 159.0
37 TraesCS5B01G128400 chr3D 88.079 151 18 0 4090 4240 88352212 88352362 4.760000e-41 180.0
38 TraesCS5B01G128400 chr1D 84.706 170 24 2 4467 4635 127504596 127504764 1.030000e-37 169.0
39 TraesCS5B01G128400 chr1D 74.442 403 88 14 4468 4861 307832776 307832380 6.200000e-35 159.0
40 TraesCS5B01G128400 chr1B 74.690 403 87 14 4468 4861 416822571 416822175 1.330000e-36 165.0
41 TraesCS5B01G128400 chr1B 84.118 170 25 2 4467 4635 246454723 246454891 4.800000e-36 163.0


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 TraesCS5B01G128400 chr5B 234876055 234882035 5980 False 11045.000000 11045 100.000000 1 5981 1 chr5B.!!$F1 5980
1 TraesCS5B01G128400 chr5B 709182452 709183200 748 False 1166.000000 1166 94.702000 5229 5981 1 chr5B.!!$F2 752
2 TraesCS5B01G128400 chr5D 218185275 218191057 5782 False 1652.750000 3699 91.310750 41 5215 4 chr5D.!!$F2 5174
3 TraesCS5B01G128400 chr5A 291128657 291134476 5819 False 980.833333 2182 88.978167 1 5225 6 chr5A.!!$F3 5224
4 TraesCS5B01G128400 chr2B 68148864 68149609 745 True 1242.000000 1242 96.676000 5234 5981 1 chr2B.!!$R1 747
5 TraesCS5B01G128400 chr2B 454476795 454477541 746 True 1158.000000 1158 94.555000 5229 5981 1 chr2B.!!$R2 752
6 TraesCS5B01G128400 chr6B 26495033 26495782 749 False 1221.000000 1221 96.026000 5229 5981 1 chr6B.!!$F1 752
7 TraesCS5B01G128400 chr6B 679255164 679255906 742 True 1205.000000 1205 95.856000 5234 5981 1 chr6B.!!$R1 747
8 TraesCS5B01G128400 chr4B 310259728 310260479 751 True 1203.000000 1203 95.509000 5225 5979 1 chr4B.!!$R1 754
9 TraesCS5B01G128400 chr3B 420916728 420917476 748 False 1177.000000 1177 94.960000 5229 5981 1 chr3B.!!$F2 752
10 TraesCS5B01G128400 chr3B 558273997 558274741 744 False 1173.000000 1173 94.954000 5229 5981 1 chr3B.!!$F3 752
11 TraesCS5B01G128400 chrUn 86410556 86411300 744 True 1168.000000 1168 94.821000 5229 5981 1 chrUn.!!$R1 752

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
431 1116 0.179111 CGAGCCATCAAGACCGCTAA 60.179 55.0 0.0 0.0 0.00 3.09 F
862 1761 0.246635 CCGTCCGTCAACCAATCTCT 59.753 55.0 0.0 0.0 0.00 3.10 F
2130 3117 0.106015 ACAGCCTGCCCTGTTTCTTT 60.106 50.0 0.0 0.0 43.19 2.52 F
3619 5011 0.037326 GTCGAGATCAACACAGGGCA 60.037 55.0 0.0 0.0 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1965 2938 0.942962 GAAGGGCAGCAATCGATCTG 59.057 55.000 9.24 9.24 0.00 2.90 R
2808 4165 1.083015 GGCGCGTTACAAGTGTGTG 60.083 57.895 8.43 0.00 38.82 3.82 R
3665 5333 0.037046 AGCATCATGTGTGCACTCGA 60.037 50.000 19.41 8.59 44.87 4.04 R
5220 6952 1.132262 ACGAAATTTGGCCTATGCACG 59.868 47.619 3.32 6.34 40.13 5.34 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
26 27 1.375523 GTCGTTGGGTCCATTCGCT 60.376 57.895 9.15 0.00 0.00 4.93
40 41 2.951475 TTCGCTTGTCCCGGTTGCTT 62.951 55.000 0.00 0.00 0.00 3.91
95 96 2.824041 CCCGCCCATCCGTTTCAG 60.824 66.667 0.00 0.00 0.00 3.02
125 126 1.612395 GGCTCCCCTCTGTCAGTCAG 61.612 65.000 0.00 0.00 44.85 3.51
126 127 0.902516 GCTCCCCTCTGTCAGTCAGT 60.903 60.000 0.00 0.00 43.97 3.41
127 128 0.894141 CTCCCCTCTGTCAGTCAGTG 59.106 60.000 0.00 0.00 43.97 3.66
128 129 0.482887 TCCCCTCTGTCAGTCAGTGA 59.517 55.000 0.00 0.00 43.97 3.41
129 130 1.133167 TCCCCTCTGTCAGTCAGTGAA 60.133 52.381 0.00 0.00 43.97 3.18
130 131 1.905215 CCCCTCTGTCAGTCAGTGAAT 59.095 52.381 0.00 0.00 43.97 2.57
131 132 2.093764 CCCCTCTGTCAGTCAGTGAATC 60.094 54.545 0.00 0.00 43.97 2.52
132 133 2.564504 CCCTCTGTCAGTCAGTGAATCA 59.435 50.000 0.00 0.00 43.97 2.57
133 134 3.583806 CCTCTGTCAGTCAGTGAATCAC 58.416 50.000 5.02 5.02 43.97 3.06
134 135 3.583806 CTCTGTCAGTCAGTGAATCACC 58.416 50.000 10.12 0.00 43.97 4.02
149 150 1.220206 CACCTCACCTAGCTGCCTG 59.780 63.158 0.00 0.00 0.00 4.85
150 151 1.229336 ACCTCACCTAGCTGCCTGT 60.229 57.895 0.00 0.00 0.00 4.00
155 156 0.460987 CACCTAGCTGCCTGTACTGC 60.461 60.000 0.00 0.00 34.97 4.40
181 846 3.025176 GCGCGGCTCTCATACGAC 61.025 66.667 8.83 0.00 0.00 4.34
385 1069 1.981256 ATCAAGGAAGCAACAACGGT 58.019 45.000 0.00 0.00 0.00 4.83
431 1116 0.179111 CGAGCCATCAAGACCGCTAA 60.179 55.000 0.00 0.00 0.00 3.09
432 1117 1.576356 GAGCCATCAAGACCGCTAAG 58.424 55.000 0.00 0.00 0.00 2.18
477 1163 2.258726 GGTCAAACCCACTGACGCC 61.259 63.158 0.00 0.00 43.45 5.68
479 1165 1.227823 TCAAACCCACTGACGCCAG 60.228 57.895 0.00 0.00 45.76 4.85
503 1189 7.170489 CAGGAAAGCAATTCTTTTCTCTTTTCC 59.830 37.037 7.73 4.46 45.36 3.13
506 1192 5.523369 AGCAATTCTTTTCTCTTTTCCGTG 58.477 37.500 0.00 0.00 0.00 4.94
512 1198 0.812014 TTCTCTTTTCCGTGTGCGCA 60.812 50.000 5.66 5.66 36.67 6.09
516 1202 0.725784 CTTTTCCGTGTGCGCATCAC 60.726 55.000 24.18 24.18 45.82 3.06
539 1225 3.488778 AATGCAAGGAAAACAATGCCA 57.511 38.095 0.00 0.00 38.00 4.92
554 1263 2.695314 GCCAATCTTCTTCGGCGAT 58.305 52.632 11.76 0.00 34.26 4.58
557 1266 1.594862 CCAATCTTCTTCGGCGATGAC 59.405 52.381 22.95 0.00 0.00 3.06
648 1373 9.715119 TGGATGGATATTATATACTAGTGCTGT 57.285 33.333 5.39 0.00 0.00 4.40
649 1374 9.973450 GGATGGATATTATATACTAGTGCTGTG 57.027 37.037 5.39 0.00 0.00 3.66
650 1375 9.973450 GATGGATATTATATACTAGTGCTGTGG 57.027 37.037 5.39 0.00 0.00 4.17
652 1377 9.984590 TGGATATTATATACTAGTGCTGTGGTA 57.015 33.333 5.39 0.00 0.00 3.25
669 1561 7.124901 TGCTGTGGTAGTAGTAGTAGTAGTAGT 59.875 40.741 5.34 5.34 0.00 2.73
677 1569 8.156822 AGTAGTAGTAGTAGTAGTGGGAGTTT 57.843 38.462 3.00 0.00 0.00 2.66
729 1625 9.793259 TGAGAGTTCTTGTATAAAAGACCAAAT 57.207 29.630 4.75 0.00 35.92 2.32
786 1685 2.164624 CGGAGGTCCAAAGACTAGACAG 59.835 54.545 0.00 0.00 43.05 3.51
795 1694 7.155328 GTCCAAAGACTAGACAGAAAATCTCA 58.845 38.462 0.00 0.00 40.10 3.27
809 1708 1.743321 ATCTCACGCTAGCCTGGCTC 61.743 60.000 27.16 11.16 40.44 4.70
855 1754 2.125269 CATCCCCGTCCGTCAACC 60.125 66.667 0.00 0.00 0.00 3.77
858 1757 1.559065 ATCCCCGTCCGTCAACCAAT 61.559 55.000 0.00 0.00 0.00 3.16
862 1761 0.246635 CCGTCCGTCAACCAATCTCT 59.753 55.000 0.00 0.00 0.00 3.10
869 1768 1.210722 GTCAACCAATCTCTCCCCTCC 59.789 57.143 0.00 0.00 0.00 4.30
872 1771 0.327000 ACCAATCTCTCCCCTCCCTG 60.327 60.000 0.00 0.00 0.00 4.45
874 1773 1.385206 AATCTCTCCCCTCCCTGCC 60.385 63.158 0.00 0.00 0.00 4.85
875 1774 2.923852 AATCTCTCCCCTCCCTGCCC 62.924 65.000 0.00 0.00 0.00 5.36
967 1889 4.154347 GGAGCAGACCCGCCTCAG 62.154 72.222 0.00 0.00 0.00 3.35
971 1893 4.504916 CAGACCCGCCTCAGCTCG 62.505 72.222 0.00 0.00 36.60 5.03
979 1901 3.073735 CCTCAGCTCGCCTCACCT 61.074 66.667 0.00 0.00 0.00 4.00
980 1902 2.493973 CTCAGCTCGCCTCACCTC 59.506 66.667 0.00 0.00 0.00 3.85
981 1903 2.283173 TCAGCTCGCCTCACCTCA 60.283 61.111 0.00 0.00 0.00 3.86
982 1904 2.125753 CAGCTCGCCTCACCTCAC 60.126 66.667 0.00 0.00 0.00 3.51
983 1905 3.386237 AGCTCGCCTCACCTCACC 61.386 66.667 0.00 0.00 0.00 4.02
984 1906 3.695606 GCTCGCCTCACCTCACCA 61.696 66.667 0.00 0.00 0.00 4.17
985 1907 3.023949 GCTCGCCTCACCTCACCAT 62.024 63.158 0.00 0.00 0.00 3.55
986 1908 1.599047 CTCGCCTCACCTCACCATT 59.401 57.895 0.00 0.00 0.00 3.16
987 1909 0.460987 CTCGCCTCACCTCACCATTC 60.461 60.000 0.00 0.00 0.00 2.67
988 1910 1.191489 TCGCCTCACCTCACCATTCA 61.191 55.000 0.00 0.00 0.00 2.57
989 1911 1.021390 CGCCTCACCTCACCATTCAC 61.021 60.000 0.00 0.00 0.00 3.18
990 1912 0.678048 GCCTCACCTCACCATTCACC 60.678 60.000 0.00 0.00 0.00 4.02
991 1913 0.391661 CCTCACCTCACCATTCACCG 60.392 60.000 0.00 0.00 0.00 4.94
992 1914 1.003839 TCACCTCACCATTCACCGC 60.004 57.895 0.00 0.00 0.00 5.68
993 1915 1.302431 CACCTCACCATTCACCGCA 60.302 57.895 0.00 0.00 0.00 5.69
1136 2058 4.150454 CTCCTCCTCCTCGGGGCT 62.150 72.222 0.00 0.00 0.00 5.19
1341 2275 4.016706 CGGAACAAGGAGGGCCGT 62.017 66.667 0.00 0.00 39.96 5.68
1482 2416 4.056125 CACGTGCTCCGCCAGAGA 62.056 66.667 0.82 0.00 46.50 3.10
1540 2475 0.970937 CTACGCCACCTCCTCCTTCA 60.971 60.000 0.00 0.00 0.00 3.02
1541 2476 1.255667 TACGCCACCTCCTCCTTCAC 61.256 60.000 0.00 0.00 0.00 3.18
1542 2477 2.583441 CGCCACCTCCTCCTTCACA 61.583 63.158 0.00 0.00 0.00 3.58
1545 2480 1.059913 CCACCTCCTCCTTCACAACT 58.940 55.000 0.00 0.00 0.00 3.16
1548 2483 2.632996 CACCTCCTCCTTCACAACTACA 59.367 50.000 0.00 0.00 0.00 2.74
1551 2497 3.306364 CCTCCTCCTTCACAACTACACAG 60.306 52.174 0.00 0.00 0.00 3.66
1566 2512 7.277098 ACAACTACACAGGCACTTAATTATACG 59.723 37.037 0.00 0.00 34.60 3.06
1590 2536 7.219344 ACGTACCTCGAAAAATCAAACTTTTTG 59.781 33.333 0.00 0.00 38.19 2.44
1685 2640 4.650754 ACCAACGGTGAAGTAGCTATAG 57.349 45.455 0.00 0.00 32.98 1.31
1695 2650 7.119992 CGGTGAAGTAGCTATAGTAGTGATCAT 59.880 40.741 0.00 0.00 0.00 2.45
1848 2814 1.600916 GGACGCAAAGCCCAGTTCT 60.601 57.895 0.00 0.00 0.00 3.01
1921 2887 5.670149 CATTCATATGGAGTGCTTGTCTC 57.330 43.478 2.13 0.00 0.00 3.36
1922 2888 5.366460 CATTCATATGGAGTGCTTGTCTCT 58.634 41.667 2.13 0.00 33.06 3.10
1965 2938 9.683069 CCTGAAAACACAAGGCATAATAATATC 57.317 33.333 0.00 0.00 0.00 1.63
1982 2958 0.763652 ATCAGATCGATTGCTGCCCT 59.236 50.000 0.00 0.00 32.27 5.19
1984 2960 0.942962 CAGATCGATTGCTGCCCTTC 59.057 55.000 0.00 0.00 0.00 3.46
1997 2973 0.759436 GCCCTTCTGGACGGATCCTA 60.759 60.000 10.75 0.00 46.43 2.94
2114 3101 7.807433 TGAATGAAATAAACATCCAAACGACAG 59.193 33.333 0.00 0.00 0.00 3.51
2116 3103 4.434713 AATAAACATCCAAACGACAGCC 57.565 40.909 0.00 0.00 0.00 4.85
2130 3117 0.106015 ACAGCCTGCCCTGTTTCTTT 60.106 50.000 0.00 0.00 43.19 2.52
2132 3119 0.106015 AGCCTGCCCTGTTTCTTTGT 60.106 50.000 0.00 0.00 0.00 2.83
2133 3120 1.144913 AGCCTGCCCTGTTTCTTTGTA 59.855 47.619 0.00 0.00 0.00 2.41
2134 3121 2.171003 GCCTGCCCTGTTTCTTTGTAT 58.829 47.619 0.00 0.00 0.00 2.29
2135 3122 2.094545 GCCTGCCCTGTTTCTTTGTATG 60.095 50.000 0.00 0.00 0.00 2.39
2136 3123 3.157087 CCTGCCCTGTTTCTTTGTATGT 58.843 45.455 0.00 0.00 0.00 2.29
2241 3229 0.397564 TGGTTGCTGTCATGCTCTCA 59.602 50.000 0.00 0.00 0.00 3.27
2252 3240 1.207570 CATGCTCTCAGCTCTGAACCT 59.792 52.381 0.93 0.00 42.97 3.50
2260 3248 1.153269 GCTCTGAACCTAGCCAGCC 60.153 63.158 0.00 0.00 32.40 4.85
2261 3249 1.903877 GCTCTGAACCTAGCCAGCCA 61.904 60.000 0.00 0.00 32.40 4.75
2262 3250 0.177604 CTCTGAACCTAGCCAGCCAG 59.822 60.000 0.00 0.00 0.00 4.85
2263 3251 1.451028 CTGAACCTAGCCAGCCAGC 60.451 63.158 0.00 0.00 0.00 4.85
2342 3338 1.133823 AGTGTTTGCATGTGGAGACCA 60.134 47.619 0.00 0.00 0.00 4.02
2348 3344 2.104859 CATGTGGAGACCAGCAGCG 61.105 63.158 0.00 0.00 32.34 5.18
2349 3345 3.965539 ATGTGGAGACCAGCAGCGC 62.966 63.158 0.00 0.00 32.34 5.92
2467 3505 4.495422 ACGGACACTGATGTTACTTCATC 58.505 43.478 1.43 0.00 39.95 2.92
2505 3543 2.551912 GCATTATTCCCCGGCCGTG 61.552 63.158 26.12 13.81 0.00 4.94
2539 3580 3.548268 CGCTATGGACGAGAAGAAGAAAC 59.452 47.826 0.00 0.00 0.00 2.78
2600 3950 6.147821 TGCAGTAAAGATAAGAAACAGCACTC 59.852 38.462 0.00 0.00 29.20 3.51
2604 3954 6.707599 AAAGATAAGAAACAGCACTCGTAC 57.292 37.500 0.00 0.00 0.00 3.67
2649 3999 0.608130 ACAGCGTCATGTGGCTCTAA 59.392 50.000 9.73 0.00 37.41 2.10
2669 4019 1.826720 ACAATTTACCCGCTAGTCCGA 59.173 47.619 0.00 0.00 0.00 4.55
2704 4054 1.530013 GCTGGCCACTGCATTCACTT 61.530 55.000 11.92 0.00 40.80 3.16
2716 4066 3.182967 GCATTCACTTGTAGAGTCCTCG 58.817 50.000 0.00 0.00 36.10 4.63
2721 4071 3.252701 TCACTTGTAGAGTCCTCGTCAAC 59.747 47.826 0.00 0.00 36.10 3.18
2722 4072 3.004419 CACTTGTAGAGTCCTCGTCAACA 59.996 47.826 0.00 0.00 36.10 3.33
2855 4214 1.709147 CGTGGCAAGGCATCACTAGC 61.709 60.000 0.00 0.00 0.00 3.42
2875 4234 2.421248 GCCAGATGAAAGGGAGAAGGAG 60.421 54.545 0.00 0.00 0.00 3.69
2876 4235 3.110705 CCAGATGAAAGGGAGAAGGAGA 58.889 50.000 0.00 0.00 0.00 3.71
2942 4305 5.879237 TGTCTTTTGCTTAGACTTTGTGTG 58.121 37.500 12.42 0.00 41.99 3.82
2960 4326 4.487019 GTGTGGAAACAAACGAAAAGGAA 58.513 39.130 0.00 0.00 46.06 3.36
3005 4371 2.813908 ATGAACGAGCGGCCGAAC 60.814 61.111 33.48 20.43 0.00 3.95
3011 4377 0.039437 ACGAGCGGCCGAACATATAG 60.039 55.000 33.48 12.50 0.00 1.31
3012 4378 1.344942 CGAGCGGCCGAACATATAGC 61.345 60.000 33.48 7.47 0.00 2.97
3013 4379 0.319555 GAGCGGCCGAACATATAGCA 60.320 55.000 33.48 0.00 0.00 3.49
3015 4381 0.234884 GCGGCCGAACATATAGCAAC 59.765 55.000 33.48 1.16 0.00 4.17
3016 4382 1.577468 CGGCCGAACATATAGCAACA 58.423 50.000 24.07 0.00 0.00 3.33
3018 4384 2.286184 CGGCCGAACATATAGCAACAAC 60.286 50.000 24.07 0.00 0.00 3.32
3019 4385 2.680841 GGCCGAACATATAGCAACAACA 59.319 45.455 0.00 0.00 0.00 3.33
3021 4387 4.202010 GGCCGAACATATAGCAACAACAAT 60.202 41.667 0.00 0.00 0.00 2.71
3022 4388 5.008217 GGCCGAACATATAGCAACAACAATA 59.992 40.000 0.00 0.00 0.00 1.90
3023 4389 5.907391 GCCGAACATATAGCAACAACAATAC 59.093 40.000 0.00 0.00 0.00 1.89
3024 4390 6.238374 GCCGAACATATAGCAACAACAATACT 60.238 38.462 0.00 0.00 0.00 2.12
3025 4391 7.125755 CCGAACATATAGCAACAACAATACTG 58.874 38.462 0.00 0.00 0.00 2.74
3026 4392 7.201609 CCGAACATATAGCAACAACAATACTGT 60.202 37.037 0.00 0.00 37.39 3.55
3087 4453 2.620562 AAAAAGCCCACGTCGTACC 58.379 52.632 0.00 0.00 0.00 3.34
3180 4563 3.795561 CAGCACTAGTTGTTGCAGTAC 57.204 47.619 5.91 0.00 28.66 2.73
3181 4564 3.393800 CAGCACTAGTTGTTGCAGTACT 58.606 45.455 5.91 0.00 28.66 2.73
3182 4565 4.556233 CAGCACTAGTTGTTGCAGTACTA 58.444 43.478 0.00 0.00 28.66 1.82
3223 4606 2.039509 GCGGTAGGCAGTAGGTAGG 58.960 63.158 0.00 0.00 42.87 3.18
3226 4609 1.133853 CGGTAGGCAGTAGGTAGGAGT 60.134 57.143 0.00 0.00 0.00 3.85
3409 4795 3.439540 CCGGTTGCGGAACATGGG 61.440 66.667 21.74 14.65 33.27 4.00
3413 4799 1.249407 GGTTGCGGAACATGGGTTTA 58.751 50.000 21.74 0.00 37.36 2.01
3485 4871 1.978580 TCCTTCCTTGGTCAAGACTCC 59.021 52.381 11.87 0.00 40.79 3.85
3497 4883 2.158310 TCAAGACTCCACCCAAGAGAGA 60.158 50.000 0.00 0.00 35.27 3.10
3517 4904 4.600062 AGACAGCTTTTATTAACCCCCAG 58.400 43.478 0.00 0.00 0.00 4.45
3519 4906 4.341487 ACAGCTTTTATTAACCCCCAGTC 58.659 43.478 0.00 0.00 0.00 3.51
3520 4907 3.699538 CAGCTTTTATTAACCCCCAGTCC 59.300 47.826 0.00 0.00 0.00 3.85
3521 4908 3.028850 GCTTTTATTAACCCCCAGTCCC 58.971 50.000 0.00 0.00 0.00 4.46
3522 4909 3.638860 CTTTTATTAACCCCCAGTCCCC 58.361 50.000 0.00 0.00 0.00 4.81
3523 4910 1.610830 TTATTAACCCCCAGTCCCCC 58.389 55.000 0.00 0.00 0.00 5.40
3524 4911 0.426437 TATTAACCCCCAGTCCCCCA 59.574 55.000 0.00 0.00 0.00 4.96
3525 4912 1.219131 ATTAACCCCCAGTCCCCCAC 61.219 60.000 0.00 0.00 0.00 4.61
3526 4913 3.895253 TAACCCCCAGTCCCCCACC 62.895 68.421 0.00 0.00 0.00 4.61
3531 4918 2.941025 CCAGTCCCCCACCACCAT 60.941 66.667 0.00 0.00 0.00 3.55
3532 4919 2.356278 CAGTCCCCCACCACCATG 59.644 66.667 0.00 0.00 0.00 3.66
3533 4920 2.121506 AGTCCCCCACCACCATGT 60.122 61.111 0.00 0.00 0.00 3.21
3534 4921 2.035626 GTCCCCCACCACCATGTG 59.964 66.667 0.00 0.00 35.98 3.21
3535 4922 2.121735 TCCCCCACCACCATGTGA 60.122 61.111 0.00 0.00 38.55 3.58
3536 4923 1.543642 TCCCCCACCACCATGTGAT 60.544 57.895 0.00 0.00 38.55 3.06
3537 4924 1.145900 TCCCCCACCACCATGTGATT 61.146 55.000 0.00 0.00 38.55 2.57
3538 4925 0.252193 CCCCCACCACCATGTGATTT 60.252 55.000 0.00 0.00 38.55 2.17
3539 4926 0.896923 CCCCACCACCATGTGATTTG 59.103 55.000 0.00 0.00 38.55 2.32
3540 4927 0.247185 CCCACCACCATGTGATTTGC 59.753 55.000 0.00 0.00 38.55 3.68
3541 4928 1.259609 CCACCACCATGTGATTTGCT 58.740 50.000 0.00 0.00 38.55 3.91
3542 4929 2.445427 CCACCACCATGTGATTTGCTA 58.555 47.619 0.00 0.00 38.55 3.49
3543 4930 2.424601 CCACCACCATGTGATTTGCTAG 59.575 50.000 0.00 0.00 38.55 3.42
3544 4931 3.084039 CACCACCATGTGATTTGCTAGT 58.916 45.455 0.00 0.00 38.55 2.57
3605 4997 2.537560 GCCCATGAATGCGGTCGAG 61.538 63.158 0.00 0.00 0.00 4.04
3610 5002 2.204237 CATGAATGCGGTCGAGATCAA 58.796 47.619 0.00 0.00 0.00 2.57
3611 5003 1.640428 TGAATGCGGTCGAGATCAAC 58.360 50.000 0.00 0.00 0.00 3.18
3612 5004 1.067213 TGAATGCGGTCGAGATCAACA 60.067 47.619 0.00 0.00 0.00 3.33
3613 5005 1.324736 GAATGCGGTCGAGATCAACAC 59.675 52.381 0.00 0.00 0.00 3.32
3614 5006 0.246360 ATGCGGTCGAGATCAACACA 59.754 50.000 0.00 0.00 0.00 3.72
3615 5007 0.388520 TGCGGTCGAGATCAACACAG 60.389 55.000 0.00 0.00 0.00 3.66
3616 5008 1.078759 GCGGTCGAGATCAACACAGG 61.079 60.000 0.00 0.00 0.00 4.00
3617 5009 0.458543 CGGTCGAGATCAACACAGGG 60.459 60.000 0.00 0.00 0.00 4.45
3618 5010 0.741221 GGTCGAGATCAACACAGGGC 60.741 60.000 0.00 0.00 0.00 5.19
3619 5011 0.037326 GTCGAGATCAACACAGGGCA 60.037 55.000 0.00 0.00 0.00 5.36
3620 5012 0.904649 TCGAGATCAACACAGGGCAT 59.095 50.000 0.00 0.00 0.00 4.40
3621 5013 1.012086 CGAGATCAACACAGGGCATG 58.988 55.000 0.00 0.00 0.00 4.06
3655 5323 4.127907 GCTAATTAACCCGAGGAAGGAAG 58.872 47.826 0.00 0.00 0.00 3.46
3658 5326 5.354842 AATTAACCCGAGGAAGGAAGTAG 57.645 43.478 0.00 0.00 0.00 2.57
3659 5327 2.322339 AACCCGAGGAAGGAAGTAGT 57.678 50.000 0.00 0.00 0.00 2.73
3661 5329 3.684408 ACCCGAGGAAGGAAGTAGTAT 57.316 47.619 0.00 0.00 0.00 2.12
3662 5330 3.297736 ACCCGAGGAAGGAAGTAGTATG 58.702 50.000 0.00 0.00 0.00 2.39
3663 5331 3.053095 ACCCGAGGAAGGAAGTAGTATGA 60.053 47.826 0.00 0.00 0.00 2.15
3664 5332 3.958798 CCCGAGGAAGGAAGTAGTATGAA 59.041 47.826 0.00 0.00 0.00 2.57
3665 5333 4.589374 CCCGAGGAAGGAAGTAGTATGAAT 59.411 45.833 0.00 0.00 0.00 2.57
3666 5334 5.279056 CCCGAGGAAGGAAGTAGTATGAATC 60.279 48.000 0.00 0.00 0.00 2.52
3707 5381 2.561569 CCATTAAACTAGGCTCCACCG 58.438 52.381 0.00 0.00 46.52 4.94
3719 5393 3.882013 CCACCGCAACGTGCAACA 61.882 61.111 9.95 0.00 45.36 3.33
3770 5444 5.297569 AGTACTGTCTCTTGCCTTTCTTT 57.702 39.130 0.00 0.00 0.00 2.52
3900 5590 7.601073 TGCATGTGAATAAAGTCAAGAGTAG 57.399 36.000 0.00 0.00 0.00 2.57
3901 5591 7.161404 TGCATGTGAATAAAGTCAAGAGTAGT 58.839 34.615 0.00 0.00 0.00 2.73
3902 5592 7.118245 TGCATGTGAATAAAGTCAAGAGTAGTG 59.882 37.037 0.00 0.00 0.00 2.74
3903 5593 7.118390 GCATGTGAATAAAGTCAAGAGTAGTGT 59.882 37.037 0.00 0.00 0.00 3.55
3904 5594 9.639601 CATGTGAATAAAGTCAAGAGTAGTGTA 57.360 33.333 0.00 0.00 0.00 2.90
3989 5694 1.026718 GGGTCCATCGTTTCAGCCTG 61.027 60.000 0.00 0.00 0.00 4.85
3990 5695 1.648467 GGTCCATCGTTTCAGCCTGC 61.648 60.000 0.00 0.00 0.00 4.85
3991 5696 0.674895 GTCCATCGTTTCAGCCTGCT 60.675 55.000 0.00 0.00 0.00 4.24
3992 5697 0.674581 TCCATCGTTTCAGCCTGCTG 60.675 55.000 12.91 12.91 44.86 4.41
4077 5785 4.539726 AGTGGCAATGGTGAATGACATAT 58.460 39.130 0.00 0.00 36.84 1.78
4078 5786 5.693961 AGTGGCAATGGTGAATGACATATA 58.306 37.500 0.00 0.00 36.84 0.86
4134 5842 2.962253 GCCGCGCTGGAGTACATC 60.962 66.667 20.06 0.00 42.00 3.06
4279 5987 1.952102 GCACGTTATCTCCGACCCCA 61.952 60.000 0.00 0.00 0.00 4.96
4316 6024 2.579201 CTCCGCGTCATCCACCTT 59.421 61.111 4.92 0.00 0.00 3.50
4323 6031 2.545742 CGCGTCATCCACCTTCATCATA 60.546 50.000 0.00 0.00 0.00 2.15
4410 6118 2.262915 CGCAAGAAGGCCTCGAGT 59.737 61.111 5.23 0.00 43.02 4.18
4476 6193 1.289380 GCTCGACCTGGAGTTCGTT 59.711 57.895 0.00 0.00 36.41 3.85
4548 6265 4.222847 GCCCCGGAGATCGTGTCC 62.223 72.222 0.73 0.00 37.11 4.02
4704 6421 3.717294 CCCAAGGACCCCTCCGTG 61.717 72.222 0.00 0.00 43.69 4.94
4707 6424 2.995574 AAGGACCCCTCCGTGTCG 60.996 66.667 0.00 0.00 42.22 4.35
4710 6427 2.675772 GACCCCTCCGTGTCGTCT 60.676 66.667 0.00 0.00 0.00 4.18
4818 6535 2.325082 CCCCTTCTTCAACGGCGTG 61.325 63.158 15.70 8.32 0.00 5.34
5047 6777 0.242825 CAACAAGATGCTGCCACTGG 59.757 55.000 0.00 0.00 0.00 4.00
5081 6811 1.003718 AAGCTCGTACCACCCTTGC 60.004 57.895 0.00 0.00 0.00 4.01
5153 6883 1.072505 GAGGCGACCTTTGGTTGGA 59.927 57.895 6.17 0.00 37.56 3.53
5157 6887 1.172812 GCGACCTTTGGTTGGAAGCT 61.173 55.000 6.17 0.00 37.56 3.74
5208 6940 1.644786 GCGTCAAATAGTTGCCGGCT 61.645 55.000 29.70 10.43 36.64 5.52
5227 6959 3.185365 CGGCTTCGTGCGTGCATA 61.185 61.111 0.00 0.00 44.05 3.14
5273 7005 7.015779 ACCCTTTTTGAAAAGAAAATCGGGATA 59.984 33.333 15.79 0.00 46.39 2.59
5325 7057 2.700773 CCTTTTGCCTACCGCCAGC 61.701 63.158 0.00 0.00 36.24 4.85
5326 7058 1.971167 CTTTTGCCTACCGCCAGCA 60.971 57.895 0.00 0.00 36.24 4.41
5327 7059 1.926511 CTTTTGCCTACCGCCAGCAG 61.927 60.000 0.00 0.00 37.89 4.24
5328 7060 3.918253 TTTGCCTACCGCCAGCAGG 62.918 63.158 0.00 0.00 37.89 4.85
5351 7083 2.589540 CCTGGCGGTAGGATTGCA 59.410 61.111 0.00 0.00 40.42 4.08
5588 7325 1.536073 CCTCTCCACCGAGCTCAACA 61.536 60.000 15.40 0.00 35.94 3.33
5596 7334 2.286523 CGAGCTCAACACTCCCCCT 61.287 63.158 15.40 0.00 0.00 4.79
5602 7341 2.753168 GCTCAACACTCCCCCTTCTTTT 60.753 50.000 0.00 0.00 0.00 2.27
5680 7419 7.253422 GTGGATTCTTACCATTTTCATCACTG 58.747 38.462 0.00 0.00 39.69 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 0.953960 AAGCGAATGGACCCAACGAC 60.954 55.000 17.93 11.41 33.99 4.34
12 13 0.608035 GGACAAGCGAATGGACCCAA 60.608 55.000 0.00 0.00 0.00 4.12
26 27 1.733402 CTGCAAAGCAACCGGGACAA 61.733 55.000 6.32 0.00 38.41 3.18
40 41 1.003839 GTGATCCGTCCCACTGCAA 60.004 57.895 0.00 0.00 0.00 4.08
95 96 3.362262 GGGAGCCAAACCCGTTTC 58.638 61.111 0.00 0.00 37.85 2.78
132 133 0.041238 TACAGGCAGCTAGGTGAGGT 59.959 55.000 25.66 19.28 35.84 3.85
133 134 0.461961 GTACAGGCAGCTAGGTGAGG 59.538 60.000 25.66 14.85 0.00 3.86
134 135 1.135915 CAGTACAGGCAGCTAGGTGAG 59.864 57.143 25.66 15.48 0.00 3.51
181 846 0.033228 TTGGATTTGGGCGCAAACAG 59.967 50.000 28.62 0.00 0.00 3.16
274 950 2.096819 CAGACCAAGTAGTCTCTCTCGC 59.903 54.545 0.00 0.00 45.38 5.03
385 1069 2.170166 GATGGATGGTTTGCCTTGACA 58.830 47.619 0.00 0.00 35.27 3.58
431 1116 3.819337 TGAATAATCGCTACGCTAGACCT 59.181 43.478 0.00 0.00 0.00 3.85
432 1117 4.156664 TGAATAATCGCTACGCTAGACC 57.843 45.455 0.00 0.00 0.00 3.85
433 1118 4.159857 CCTGAATAATCGCTACGCTAGAC 58.840 47.826 0.00 0.00 0.00 2.59
477 1163 7.170489 GGAAAAGAGAAAAGAATTGCTTTCCTG 59.830 37.037 0.00 0.00 45.85 3.86
479 1165 6.144563 CGGAAAAGAGAAAAGAATTGCTTTCC 59.855 38.462 0.00 0.00 45.85 3.13
506 1192 4.268655 GCATTACGTGATGCGCAC 57.731 55.556 26.65 7.75 46.11 5.34
512 1198 5.446143 TTGTTTTCCTTGCATTACGTGAT 57.554 34.783 0.00 0.00 0.00 3.06
516 1202 3.367630 GGCATTGTTTTCCTTGCATTACG 59.632 43.478 0.00 0.00 36.82 3.18
539 1225 1.482593 AGGTCATCGCCGAAGAAGATT 59.517 47.619 0.00 0.00 0.00 2.40
554 1263 6.785337 TTAGAGGTTGATTCGATAAGGTCA 57.215 37.500 0.00 0.00 0.00 4.02
557 1266 7.217200 TCCAATTAGAGGTTGATTCGATAAGG 58.783 38.462 0.00 0.00 0.00 2.69
642 1367 6.112058 ACTACTACTACTACTACCACAGCAC 58.888 44.000 0.00 0.00 0.00 4.40
644 1369 7.437862 CACTACTACTACTACTACTACCACAGC 59.562 44.444 0.00 0.00 0.00 4.40
647 1372 7.070074 TCCCACTACTACTACTACTACTACCAC 59.930 44.444 0.00 0.00 0.00 4.16
648 1373 7.132805 TCCCACTACTACTACTACTACTACCA 58.867 42.308 0.00 0.00 0.00 3.25
649 1374 7.289084 ACTCCCACTACTACTACTACTACTACC 59.711 44.444 0.00 0.00 0.00 3.18
650 1375 8.245195 ACTCCCACTACTACTACTACTACTAC 57.755 42.308 0.00 0.00 0.00 2.73
652 1377 7.747809 AACTCCCACTACTACTACTACTACT 57.252 40.000 0.00 0.00 0.00 2.57
653 1378 8.800370 AAAACTCCCACTACTACTACTACTAC 57.200 38.462 0.00 0.00 0.00 2.73
689 1581 7.610305 ACAAGAACTCTCACTAAACCTCAAAAA 59.390 33.333 0.00 0.00 0.00 1.94
694 1586 9.924650 TTTATACAAGAACTCTCACTAAACCTC 57.075 33.333 0.00 0.00 0.00 3.85
699 1591 9.924650 GGTCTTTTATACAAGAACTCTCACTAA 57.075 33.333 9.06 0.00 37.49 2.24
701 1593 7.963532 TGGTCTTTTATACAAGAACTCTCACT 58.036 34.615 15.81 0.00 40.65 3.41
702 1594 8.603242 TTGGTCTTTTATACAAGAACTCTCAC 57.397 34.615 15.81 0.00 40.65 3.51
703 1595 9.793259 ATTTGGTCTTTTATACAAGAACTCTCA 57.207 29.630 15.81 3.27 40.65 3.27
724 1620 0.893270 TCCGGGTGCTGACAATTTGG 60.893 55.000 0.00 0.00 0.00 3.28
729 1625 1.070786 GTTCTCCGGGTGCTGACAA 59.929 57.895 0.00 0.00 0.00 3.18
770 1666 7.117092 GTGAGATTTTCTGTCTAGTCTTTGGAC 59.883 40.741 0.00 0.00 42.41 4.02
786 1685 1.936547 CCAGGCTAGCGTGAGATTTTC 59.063 52.381 33.15 5.63 34.13 2.29
795 1694 3.068691 TTCGAGCCAGGCTAGCGT 61.069 61.111 16.16 6.32 39.88 5.07
845 1744 1.405661 GGGAGAGATTGGTTGACGGAC 60.406 57.143 0.00 0.00 0.00 4.79
855 1754 1.704007 GGCAGGGAGGGGAGAGATTG 61.704 65.000 0.00 0.00 0.00 2.67
858 1757 4.095400 GGGCAGGGAGGGGAGAGA 62.095 72.222 0.00 0.00 0.00 3.10
862 1761 3.626596 AAGAGGGCAGGGAGGGGA 61.627 66.667 0.00 0.00 0.00 4.81
869 1768 5.237815 GGTTTTTAATTTGAAGAGGGCAGG 58.762 41.667 0.00 0.00 0.00 4.85
872 1771 4.994852 GTGGGTTTTTAATTTGAAGAGGGC 59.005 41.667 0.00 0.00 0.00 5.19
874 1773 4.684242 GCGTGGGTTTTTAATTTGAAGAGG 59.316 41.667 0.00 0.00 0.00 3.69
875 1774 5.174943 GTGCGTGGGTTTTTAATTTGAAGAG 59.825 40.000 0.00 0.00 0.00 2.85
967 1889 2.527951 AATGGTGAGGTGAGGCGAGC 62.528 60.000 0.00 0.00 0.00 5.03
971 1893 0.678048 GGTGAATGGTGAGGTGAGGC 60.678 60.000 0.00 0.00 0.00 4.70
974 1896 1.003839 GCGGTGAATGGTGAGGTGA 60.004 57.895 0.00 0.00 0.00 4.02
977 1899 2.401766 GCTGCGGTGAATGGTGAGG 61.402 63.158 0.00 0.00 0.00 3.86
979 1901 1.672030 CTGCTGCGGTGAATGGTGA 60.672 57.895 0.00 0.00 0.00 4.02
980 1902 2.872557 CTGCTGCGGTGAATGGTG 59.127 61.111 0.00 0.00 0.00 4.17
981 1903 3.058160 GCTGCTGCGGTGAATGGT 61.058 61.111 10.62 0.00 0.00 3.55
982 1904 1.940883 ATTGCTGCTGCGGTGAATGG 61.941 55.000 10.62 0.00 43.34 3.16
983 1905 0.800683 CATTGCTGCTGCGGTGAATG 60.801 55.000 10.62 13.96 43.34 2.67
984 1906 1.509463 CATTGCTGCTGCGGTGAAT 59.491 52.632 10.62 6.23 43.34 2.57
985 1907 2.956194 CATTGCTGCTGCGGTGAA 59.044 55.556 10.62 4.04 43.34 3.18
986 1908 3.740397 GCATTGCTGCTGCGGTGA 61.740 61.111 19.37 0.00 45.32 4.02
1320 2254 3.646715 CCCTCCTTGTTCCGGCCA 61.647 66.667 2.24 0.00 0.00 5.36
1540 2475 7.277098 CGTATAATTAAGTGCCTGTGTAGTTGT 59.723 37.037 0.00 0.00 0.00 3.32
1541 2476 7.277098 ACGTATAATTAAGTGCCTGTGTAGTTG 59.723 37.037 0.00 0.00 0.00 3.16
1542 2477 7.325694 ACGTATAATTAAGTGCCTGTGTAGTT 58.674 34.615 0.00 0.00 0.00 2.24
1545 2480 7.068593 AGGTACGTATAATTAAGTGCCTGTGTA 59.931 37.037 19.83 1.41 45.92 2.90
1548 2483 6.475596 AGGTACGTATAATTAAGTGCCTGT 57.524 37.500 19.83 5.58 45.92 4.00
1551 2497 5.762045 TCGAGGTACGTATAATTAAGTGCC 58.238 41.667 14.07 14.07 40.91 5.01
1566 2512 8.623310 TCAAAAAGTTTGATTTTTCGAGGTAC 57.377 30.769 0.00 0.00 39.69 3.34
1590 2536 5.184096 TCCACAGAGACAAACAGAGACTATC 59.816 44.000 0.00 0.00 0.00 2.08
1685 2640 5.185249 TCCGGAAAGGCTATATGATCACTAC 59.815 44.000 0.00 0.00 40.77 2.73
1695 2650 4.654262 ACATTCTTCTCCGGAAAGGCTATA 59.346 41.667 19.63 4.49 40.77 1.31
1921 2887 1.222936 GATGAGGGGCACTGTGGAG 59.777 63.158 10.21 0.00 0.00 3.86
1922 2888 2.300967 GGATGAGGGGCACTGTGGA 61.301 63.158 10.21 0.00 0.00 4.02
1965 2938 0.942962 GAAGGGCAGCAATCGATCTG 59.057 55.000 9.24 9.24 0.00 2.90
1967 2940 0.942962 CAGAAGGGCAGCAATCGATC 59.057 55.000 0.00 0.00 0.00 3.69
1984 2960 7.932510 CCATCTTGGTTTAGGATCCGTCCAG 62.933 52.000 5.98 7.95 38.78 3.86
1997 2973 1.187567 GGTGCCTGCCATCTTGGTTT 61.188 55.000 0.00 0.00 40.46 3.27
2114 3101 1.616159 TACAAAGAAACAGGGCAGGC 58.384 50.000 0.00 0.00 0.00 4.85
2116 3103 6.150976 TGAATACATACAAAGAAACAGGGCAG 59.849 38.462 0.00 0.00 0.00 4.85
2130 3117 4.032960 GGATGGCCCATGAATACATACA 57.967 45.455 0.00 0.00 35.09 2.29
2241 3229 1.621672 GGCTGGCTAGGTTCAGAGCT 61.622 60.000 0.00 0.00 38.79 4.09
2260 3248 4.332637 GCAACTGTGTGGCCGCTG 62.333 66.667 18.96 8.04 0.00 5.18
2261 3249 4.873810 TGCAACTGTGTGGCCGCT 62.874 61.111 18.96 0.00 30.14 5.52
2262 3250 4.629115 GTGCAACTGTGTGGCCGC 62.629 66.667 10.11 10.11 30.14 6.53
2263 3251 4.312231 CGTGCAACTGTGTGGCCG 62.312 66.667 0.00 0.00 30.14 6.13
2351 3347 4.986708 TTGGTTTCAGGGCGGGCC 62.987 66.667 13.58 13.58 0.00 5.80
2409 3424 1.733360 ACAAAATGATGCGGCAAATGC 59.267 42.857 6.82 0.00 41.14 3.56
2411 3426 1.733360 GCACAAAATGATGCGGCAAAT 59.267 42.857 6.82 0.61 30.97 2.32
2467 3505 7.745620 AATGCTATTTTAAGTCTATTCCGGG 57.254 36.000 0.00 0.00 0.00 5.73
2511 3549 3.747010 TCTTCTCGTCCATAGCGATAGAC 59.253 47.826 0.00 0.00 37.74 2.59
2600 3950 3.637998 ATCGTAGCCACCAATAGTACG 57.362 47.619 0.00 0.00 38.23 3.67
2604 3954 2.802816 GAGCAATCGTAGCCACCAATAG 59.197 50.000 0.00 0.00 0.00 1.73
2649 3999 1.826720 TCGGACTAGCGGGTAAATTGT 59.173 47.619 0.00 0.00 0.00 2.71
2704 4054 2.578786 TGTGTTGACGAGGACTCTACA 58.421 47.619 0.00 0.00 0.00 2.74
2716 4066 7.790000 ACGTTACTTATATGTGTTGTGTTGAC 58.210 34.615 1.63 0.00 0.00 3.18
2721 4071 7.496704 ACGTACGTTACTTATATGTGTTGTG 57.503 36.000 16.72 0.00 0.00 3.33
2722 4072 8.450964 ACTACGTACGTTACTTATATGTGTTGT 58.549 33.333 27.92 0.07 0.00 3.32
2768 4125 8.598041 AGAAACATGAAACTACTAGGAACATCT 58.402 33.333 0.00 0.00 0.00 2.90
2808 4165 1.083015 GGCGCGTTACAAGTGTGTG 60.083 57.895 8.43 0.00 38.82 3.82
2809 4166 2.248835 GGGCGCGTTACAAGTGTGT 61.249 57.895 8.43 0.00 42.09 3.72
2810 4167 2.554272 GGGCGCGTTACAAGTGTG 59.446 61.111 8.43 0.00 0.00 3.82
2816 4173 3.980989 ACTCACGGGCGCGTTACA 61.981 61.111 27.41 12.31 0.00 2.41
2855 4214 3.110705 TCTCCTTCTCCCTTTCATCTGG 58.889 50.000 0.00 0.00 0.00 3.86
2875 4234 2.290641 AGTTTGTTCCAACATCACGCTC 59.709 45.455 0.00 0.00 38.95 5.03
2876 4235 2.297701 AGTTTGTTCCAACATCACGCT 58.702 42.857 0.00 0.00 38.95 5.07
2926 4289 4.265893 TGTTTCCACACAAAGTCTAAGCA 58.734 39.130 0.00 0.00 0.00 3.91
2942 4305 6.954616 TTCTTTTCCTTTTCGTTTGTTTCC 57.045 33.333 0.00 0.00 0.00 3.13
2960 4326 3.988976 TGCTGCACTCTCCTATTCTTT 57.011 42.857 0.00 0.00 0.00 2.52
3011 4377 7.164171 CGAAAGCATATACAGTATTGTTGTTGC 59.836 37.037 0.00 3.91 38.76 4.17
3012 4378 7.639850 CCGAAAGCATATACAGTATTGTTGTTG 59.360 37.037 0.00 0.00 38.76 3.33
3013 4379 7.678690 GCCGAAAGCATATACAGTATTGTTGTT 60.679 37.037 0.00 0.00 42.97 2.83
3015 4381 6.136071 GCCGAAAGCATATACAGTATTGTTG 58.864 40.000 0.00 0.00 42.97 3.33
3016 4382 5.050363 CGCCGAAAGCATATACAGTATTGTT 60.050 40.000 0.00 0.00 44.04 2.83
3018 4384 4.143115 CCGCCGAAAGCATATACAGTATTG 60.143 45.833 0.00 0.00 44.04 1.90
3019 4385 3.994392 CCGCCGAAAGCATATACAGTATT 59.006 43.478 0.00 0.00 44.04 1.89
3021 4387 2.288579 CCCGCCGAAAGCATATACAGTA 60.289 50.000 0.00 0.00 44.04 2.74
3022 4388 1.540363 CCCGCCGAAAGCATATACAGT 60.540 52.381 0.00 0.00 44.04 3.55
3023 4389 1.148310 CCCGCCGAAAGCATATACAG 58.852 55.000 0.00 0.00 44.04 2.74
3024 4390 0.882927 GCCCGCCGAAAGCATATACA 60.883 55.000 0.00 0.00 44.04 2.29
3025 4391 1.866925 GCCCGCCGAAAGCATATAC 59.133 57.895 0.00 0.00 44.04 1.47
3026 4392 1.666553 CGCCCGCCGAAAGCATATA 60.667 57.895 0.00 0.00 44.04 0.86
3087 4453 2.029739 TGTATGTGTGTGGGAGTACGTG 60.030 50.000 0.00 0.00 0.00 4.49
3181 4564 2.871022 GCTACTGCTAGTGCTCGTACTA 59.129 50.000 0.00 0.00 40.48 1.82
3182 4565 1.671845 GCTACTGCTAGTGCTCGTACT 59.328 52.381 0.00 0.00 40.48 2.73
3219 4602 7.427214 CCTTGCATAGAAACTACTACTCCTAC 58.573 42.308 0.00 0.00 0.00 3.18
3220 4603 6.550108 CCCTTGCATAGAAACTACTACTCCTA 59.450 42.308 0.00 0.00 0.00 2.94
3221 4604 5.364157 CCCTTGCATAGAAACTACTACTCCT 59.636 44.000 0.00 0.00 0.00 3.69
3223 4606 5.051153 GCCCTTGCATAGAAACTACTACTC 58.949 45.833 0.00 0.00 37.47 2.59
3226 4609 3.449737 ACGCCCTTGCATAGAAACTACTA 59.550 43.478 0.00 0.00 37.32 1.82
3397 4783 4.608948 ATTTTTAAACCCATGTTCCGCA 57.391 36.364 0.00 0.00 32.15 5.69
3409 4795 5.824097 TGAGGGCGGGAGTATATTTTTAAAC 59.176 40.000 0.00 0.00 0.00 2.01
3413 4799 4.724279 ATGAGGGCGGGAGTATATTTTT 57.276 40.909 0.00 0.00 0.00 1.94
3485 4871 2.557920 AAAGCTGTCTCTCTTGGGTG 57.442 50.000 0.00 0.00 0.00 4.61
3497 4883 4.341487 GACTGGGGGTTAATAAAAGCTGT 58.659 43.478 0.00 0.00 0.00 4.40
3517 4904 1.863155 ATCACATGGTGGTGGGGGAC 61.863 60.000 0.00 0.00 39.27 4.46
3519 4906 0.252193 AAATCACATGGTGGTGGGGG 60.252 55.000 0.00 0.00 39.27 5.40
3520 4907 0.896923 CAAATCACATGGTGGTGGGG 59.103 55.000 0.00 0.00 39.27 4.96
3521 4908 0.247185 GCAAATCACATGGTGGTGGG 59.753 55.000 0.00 0.00 39.27 4.61
3522 4909 1.259609 AGCAAATCACATGGTGGTGG 58.740 50.000 0.00 0.00 39.27 4.61
3523 4910 3.084039 ACTAGCAAATCACATGGTGGTG 58.916 45.455 0.00 0.00 38.35 4.17
3524 4911 3.439857 ACTAGCAAATCACATGGTGGT 57.560 42.857 0.00 0.00 35.54 4.16
3525 4912 4.769688 TCTACTAGCAAATCACATGGTGG 58.230 43.478 0.00 0.00 33.87 4.61
3526 4913 6.539826 TGATTCTACTAGCAAATCACATGGTG 59.460 38.462 9.69 0.00 35.17 4.17
3527 4914 6.653020 TGATTCTACTAGCAAATCACATGGT 58.347 36.000 9.69 0.00 35.17 3.55
3533 4920 5.982356 AGCTGTGATTCTACTAGCAAATCA 58.018 37.500 9.69 9.69 37.14 2.57
3534 4921 6.200665 CAGAGCTGTGATTCTACTAGCAAATC 59.799 42.308 4.50 0.00 36.87 2.17
3535 4922 6.047870 CAGAGCTGTGATTCTACTAGCAAAT 58.952 40.000 4.50 0.00 36.87 2.32
3536 4923 5.185828 TCAGAGCTGTGATTCTACTAGCAAA 59.814 40.000 9.94 0.00 36.87 3.68
3537 4924 4.706962 TCAGAGCTGTGATTCTACTAGCAA 59.293 41.667 9.94 0.00 36.87 3.91
3538 4925 4.273318 TCAGAGCTGTGATTCTACTAGCA 58.727 43.478 9.94 0.00 36.87 3.49
3539 4926 4.909696 TCAGAGCTGTGATTCTACTAGC 57.090 45.455 9.94 0.00 34.71 3.42
3540 4927 6.529829 GTGTTTCAGAGCTGTGATTCTACTAG 59.470 42.308 15.15 0.00 0.00 2.57
3541 4928 6.015434 TGTGTTTCAGAGCTGTGATTCTACTA 60.015 38.462 15.15 0.00 0.00 1.82
3542 4929 5.221521 TGTGTTTCAGAGCTGTGATTCTACT 60.222 40.000 15.15 0.00 0.00 2.57
3543 4930 4.991056 TGTGTTTCAGAGCTGTGATTCTAC 59.009 41.667 15.15 11.68 0.00 2.59
3544 4931 4.991056 GTGTGTTTCAGAGCTGTGATTCTA 59.009 41.667 15.15 0.00 0.00 2.10
3612 5004 1.538047 GTGTTGATCACATGCCCTGT 58.462 50.000 0.00 0.00 45.51 4.00
3621 5013 5.447279 CGGGTTAATTAGCTGTGTTGATCAC 60.447 44.000 0.00 0.00 46.31 3.06
3623 5015 4.873827 TCGGGTTAATTAGCTGTGTTGATC 59.126 41.667 0.00 0.00 32.35 2.92
3624 5016 4.839121 TCGGGTTAATTAGCTGTGTTGAT 58.161 39.130 0.00 0.00 32.35 2.57
3625 5017 4.250464 CTCGGGTTAATTAGCTGTGTTGA 58.750 43.478 0.00 0.00 32.35 3.18
3626 5018 3.374058 CCTCGGGTTAATTAGCTGTGTTG 59.626 47.826 0.00 0.00 32.35 3.33
3627 5019 3.262405 TCCTCGGGTTAATTAGCTGTGTT 59.738 43.478 0.00 0.00 32.35 3.32
3628 5020 2.835764 TCCTCGGGTTAATTAGCTGTGT 59.164 45.455 0.00 0.00 32.35 3.72
3629 5021 3.536956 TCCTCGGGTTAATTAGCTGTG 57.463 47.619 0.00 0.00 32.35 3.66
3630 5022 3.118371 CCTTCCTCGGGTTAATTAGCTGT 60.118 47.826 0.00 0.00 32.35 4.40
3631 5023 3.134081 TCCTTCCTCGGGTTAATTAGCTG 59.866 47.826 0.00 0.00 0.00 4.24
3655 5323 4.421058 TGTGTGCACTCGATTCATACTAC 58.579 43.478 19.41 3.25 0.00 2.73
3658 5326 3.865164 TCATGTGTGCACTCGATTCATAC 59.135 43.478 19.41 4.78 0.00 2.39
3659 5327 4.122143 TCATGTGTGCACTCGATTCATA 57.878 40.909 19.41 0.00 0.00 2.15
3661 5329 2.453983 TCATGTGTGCACTCGATTCA 57.546 45.000 19.41 7.94 0.00 2.57
3662 5330 2.538333 GCATCATGTGTGCACTCGATTC 60.538 50.000 19.41 4.75 42.08 2.52
3663 5331 1.399440 GCATCATGTGTGCACTCGATT 59.601 47.619 19.41 0.71 42.08 3.34
3664 5332 1.012086 GCATCATGTGTGCACTCGAT 58.988 50.000 19.41 10.53 42.08 3.59
3665 5333 0.037046 AGCATCATGTGTGCACTCGA 60.037 50.000 19.41 8.59 44.87 4.04
3666 5334 0.372679 GAGCATCATGTGTGCACTCG 59.627 55.000 19.41 2.91 44.87 4.18
3707 5381 4.645921 GGGGCTGTTGCACGTTGC 62.646 66.667 0.00 3.44 45.19 4.17
3719 5393 1.529948 CATCATTGATGCCGGGGCT 60.530 57.895 13.43 0.00 42.51 5.19
3790 5467 1.002251 GCTCCAGTACTGCTACTAGCG 60.002 57.143 17.86 1.28 46.26 4.26
3900 5590 7.534085 TGCATAGCACAAAAGTATACTACAC 57.466 36.000 5.65 0.00 31.71 2.90
3901 5591 8.731275 ATTGCATAGCACAAAAGTATACTACA 57.269 30.769 5.65 0.00 38.71 2.74
3904 5594 9.396022 ACTAATTGCATAGCACAAAAGTATACT 57.604 29.630 0.00 0.00 38.71 2.12
3989 5694 2.610433 GAAATTTTACAGCCAGCCAGC 58.390 47.619 0.00 0.00 0.00 4.85
3990 5695 2.228822 ACGAAATTTTACAGCCAGCCAG 59.771 45.455 0.00 0.00 0.00 4.85
3991 5696 2.235016 ACGAAATTTTACAGCCAGCCA 58.765 42.857 0.00 0.00 0.00 4.75
3992 5697 2.986479 CAACGAAATTTTACAGCCAGCC 59.014 45.455 0.00 0.00 0.00 4.85
4077 5785 1.771565 ACCTGCCGCAGTACACTATA 58.228 50.000 18.98 0.00 0.00 1.31
4078 5786 0.902531 AACCTGCCGCAGTACACTAT 59.097 50.000 18.98 0.00 0.00 2.12
4308 6016 4.103785 CAGGAAGGTATGATGAAGGTGGAT 59.896 45.833 0.00 0.00 0.00 3.41
4316 6024 2.700371 ACGATGCAGGAAGGTATGATGA 59.300 45.455 0.00 0.00 0.00 2.92
4422 6130 3.114616 CTGCTGTTCACGCCTCCG 61.115 66.667 0.00 0.00 41.14 4.63
4425 6133 2.667536 CTGCTGCTGTTCACGCCT 60.668 61.111 0.00 0.00 0.00 5.52
4461 6178 2.372690 CGCAACGAACTCCAGGTCG 61.373 63.158 12.50 12.50 0.00 4.79
4569 6286 2.524394 AGCGTCCACCAGTCCACT 60.524 61.111 0.00 0.00 0.00 4.00
4797 6514 2.626780 GCCGTTGAAGAAGGGGTGC 61.627 63.158 0.00 0.00 37.55 5.01
4851 6568 2.033602 AAAGGCTGGGGCACGTAC 59.966 61.111 0.00 0.00 40.87 3.67
5215 6947 3.597675 TTGGCCTATGCACGCACGA 62.598 57.895 3.32 0.00 40.13 4.35
5219 6951 1.559831 GAAATTTGGCCTATGCACGC 58.440 50.000 3.32 0.00 40.13 5.34
5220 6952 1.132262 ACGAAATTTGGCCTATGCACG 59.868 47.619 3.32 6.34 40.13 5.34
5222 6954 2.166829 ACACGAAATTTGGCCTATGCA 58.833 42.857 3.32 0.00 40.13 3.96
5227 6959 3.453424 GTCAAAACACGAAATTTGGCCT 58.547 40.909 3.32 0.00 35.62 5.19
5330 7062 2.746375 AATCCTACCGCCAGGCCTG 61.746 63.158 26.87 26.87 42.76 4.85
5331 7063 2.366972 AATCCTACCGCCAGGCCT 60.367 61.111 5.63 0.00 42.76 5.19
5602 7341 1.956477 GGAGGCTCTTGTGCTTCAAAA 59.044 47.619 15.23 0.00 40.25 2.44
5680 7419 2.637947 GGAAATGAGAGAGCCACCTTC 58.362 52.381 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.