Multiple sequence alignment - TraesCS3B01G151100

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 TraesCS3B01G151100 chr3B 100.000 4442 0 0 1 4442 142717787 142722228 0.000000e+00 8203.0
1 TraesCS3B01G151100 chr3B 95.082 122 5 1 2720 2841 637086446 637086326 1.630000e-44 191.0
2 TraesCS3B01G151100 chr3B 91.270 126 11 0 3107 3232 142720863 142720988 5.910000e-39 172.0
3 TraesCS3B01G151100 chr3B 91.270 126 11 0 3077 3202 142720893 142721018 5.910000e-39 172.0
4 TraesCS3B01G151100 chr3B 98.387 62 1 0 4046 4107 142721745 142721806 4.700000e-20 110.0
5 TraesCS3B01G151100 chr3B 98.387 62 1 0 3959 4020 142721832 142721893 4.700000e-20 110.0
6 TraesCS3B01G151100 chr3A 95.192 2392 88 19 344 2721 546568138 546570516 0.000000e+00 3755.0
7 TraesCS3B01G151100 chr3A 93.294 1372 62 17 3077 4442 546570880 546572227 0.000000e+00 1997.0
8 TraesCS3B01G151100 chr3A 94.242 330 18 1 2904 3232 546570676 546571005 1.840000e-138 503.0
9 TraesCS3B01G151100 chr3A 96.552 116 3 1 2720 2835 750495542 750495656 1.630000e-44 191.0
10 TraesCS3B01G151100 chr3A 91.270 126 11 0 3107 3232 546570850 546570975 5.910000e-39 172.0
11 TraesCS3B01G151100 chr3A 91.667 96 3 2 88 182 546567957 546568048 1.300000e-25 128.0
12 TraesCS3B01G151100 chr3A 98.305 59 1 0 3960 4018 546571832 546571890 2.190000e-18 104.0
13 TraesCS3B01G151100 chr3D 94.897 1548 45 17 1188 2723 93484755 93483230 0.000000e+00 2390.0
14 TraesCS3B01G151100 chr3D 93.304 1613 78 19 2837 4442 93483232 93481643 0.000000e+00 2353.0
15 TraesCS3B01G151100 chr3D 94.118 901 44 5 293 1189 93485728 93484833 0.000000e+00 1362.0
16 TraesCS3B01G151100 chr3D 88.889 126 14 0 3107 3232 93482988 93482863 5.950000e-34 156.0
17 TraesCS3B01G151100 chr3D 90.741 108 1 3 86 188 93488575 93488472 7.750000e-28 135.0
18 TraesCS3B01G151100 chr3D 98.387 62 1 0 3959 4020 93482039 93481978 4.700000e-20 110.0
19 TraesCS3B01G151100 chr5B 99.187 123 1 0 2719 2841 224621400 224621522 5.780000e-54 222.0
20 TraesCS3B01G151100 chr5B 90.141 71 7 0 3 73 489304436 489304506 4.730000e-15 93.5
21 TraesCS3B01G151100 chr5B 88.889 72 7 1 3 73 676171071 676171000 2.200000e-13 87.9
22 TraesCS3B01G151100 chr2B 96.694 121 4 0 2720 2840 135918316 135918436 7.530000e-48 202.0
23 TraesCS3B01G151100 chr6D 95.763 118 5 0 2721 2838 12017208 12017325 1.630000e-44 191.0
24 TraesCS3B01G151100 chr6D 93.651 126 7 1 2714 2839 108860772 108860648 2.110000e-43 187.0
25 TraesCS3B01G151100 chr4B 94.309 123 6 1 2719 2841 584118911 584118790 2.110000e-43 187.0
26 TraesCS3B01G151100 chr4A 93.600 125 7 1 2715 2839 658949237 658949114 7.590000e-43 185.0
27 TraesCS3B01G151100 chr1D 93.548 124 8 0 2720 2843 458700310 458700187 7.590000e-43 185.0
28 TraesCS3B01G151100 chr1D 84.507 71 9 2 3 73 336359904 336359836 7.970000e-08 69.4
29 TraesCS3B01G151100 chr1B 87.324 71 9 0 3 73 579943120 579943190 1.020000e-11 82.4
30 TraesCS3B01G151100 chr1A 89.062 64 5 2 11 73 16569831 16569769 1.320000e-10 78.7


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 TraesCS3B01G151100 chr3B 142717787 142722228 4441 False 1753.400000 8203 95.862800 1 4442 5 chr3B.!!$F1 4441
1 TraesCS3B01G151100 chr3A 546567957 546572227 4270 False 1109.833333 3755 93.995000 88 4442 6 chr3A.!!$F2 4354
2 TraesCS3B01G151100 chr3D 93481643 93488575 6932 True 1084.333333 2390 93.389333 86 4442 6 chr3D.!!$R1 4356

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
313 2994 0.030235 GCCTCGCGTCCTTTTGTTTT 59.970 50.0 5.77 0.00 0.00 2.43 F
951 3637 0.318869 TTCGCTGTTTGCTTGCATGG 60.319 50.0 1.34 0.00 40.11 3.66 F
2338 5113 0.237498 CCCGCGAGTTGTCTTTTTCC 59.763 55.0 8.23 0.00 0.00 3.13 F
2834 5616 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.0 13.64 4.95 46.06 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2283 5058 1.289160 TAGGGCTGTTCTGGCAATCT 58.711 50.0 5.75 0.0 0.00 2.40 R
2815 5597 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.0 5.23 0.0 44.66 2.12 R
3147 6062 0.684479 TCATAGGGCTGCGACTGTCT 60.684 55.0 6.21 0.0 0.00 3.41 R
3940 6857 1.173043 CTAAAACCGGCAGCATGGAA 58.827 50.0 0.00 0.0 35.86 3.53 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
42 43 4.988744 TTTTTCTGTCCGGGTGCA 57.011 50.000 0.00 0.00 0.00 4.57
43 44 2.714259 TTTTTCTGTCCGGGTGCAG 58.286 52.632 0.00 8.44 0.00 4.41
44 45 0.181587 TTTTTCTGTCCGGGTGCAGA 59.818 50.000 16.47 16.47 39.66 4.26
45 46 0.400213 TTTTCTGTCCGGGTGCAGAT 59.600 50.000 19.53 0.00 40.83 2.90
46 47 0.321564 TTTCTGTCCGGGTGCAGATG 60.322 55.000 19.53 0.83 40.83 2.90
47 48 1.191489 TTCTGTCCGGGTGCAGATGA 61.191 55.000 19.53 7.97 40.83 2.92
48 49 1.153489 CTGTCCGGGTGCAGATGAG 60.153 63.158 13.78 0.00 34.87 2.90
49 50 1.892819 CTGTCCGGGTGCAGATGAGT 61.893 60.000 13.78 0.00 34.87 3.41
50 51 1.153549 GTCCGGGTGCAGATGAGTC 60.154 63.158 0.00 0.00 0.00 3.36
51 52 1.305297 TCCGGGTGCAGATGAGTCT 60.305 57.895 0.00 0.00 34.14 3.24
52 53 0.033503 TCCGGGTGCAGATGAGTCTA 60.034 55.000 0.00 0.00 32.09 2.59
53 54 0.387202 CCGGGTGCAGATGAGTCTAG 59.613 60.000 0.00 0.00 32.09 2.43
54 55 0.387202 CGGGTGCAGATGAGTCTAGG 59.613 60.000 0.00 0.00 32.09 3.02
55 56 0.105778 GGGTGCAGATGAGTCTAGGC 59.894 60.000 0.00 0.00 32.09 3.93
56 57 0.826715 GGTGCAGATGAGTCTAGGCA 59.173 55.000 0.00 0.00 32.73 4.75
57 58 1.472376 GGTGCAGATGAGTCTAGGCAC 60.472 57.143 16.25 16.25 46.06 5.01
58 59 0.826715 TGCAGATGAGTCTAGGCACC 59.173 55.000 0.00 0.00 30.88 5.01
59 60 0.249238 GCAGATGAGTCTAGGCACCG 60.249 60.000 0.00 0.00 32.09 4.94
60 61 1.393603 CAGATGAGTCTAGGCACCGA 58.606 55.000 0.00 0.00 32.09 4.69
61 62 1.751351 CAGATGAGTCTAGGCACCGAA 59.249 52.381 0.00 0.00 32.09 4.30
62 63 2.166459 CAGATGAGTCTAGGCACCGAAA 59.834 50.000 0.00 0.00 32.09 3.46
63 64 3.034635 AGATGAGTCTAGGCACCGAAAT 58.965 45.455 0.00 0.00 31.36 2.17
64 65 2.672961 TGAGTCTAGGCACCGAAATG 57.327 50.000 0.00 0.00 0.00 2.32
65 66 1.291132 GAGTCTAGGCACCGAAATGC 58.709 55.000 0.00 0.00 45.34 3.56
71 72 3.737172 GCACCGAAATGCCGCACT 61.737 61.111 0.00 0.00 39.86 4.40
72 73 2.480555 CACCGAAATGCCGCACTC 59.519 61.111 0.00 0.00 0.00 3.51
73 74 2.034879 CACCGAAATGCCGCACTCT 61.035 57.895 0.00 0.00 0.00 3.24
74 75 1.302511 ACCGAAATGCCGCACTCTT 60.303 52.632 0.00 0.00 0.00 2.85
75 76 1.135315 CCGAAATGCCGCACTCTTG 59.865 57.895 0.00 0.00 0.00 3.02
76 77 1.577328 CCGAAATGCCGCACTCTTGT 61.577 55.000 0.00 0.00 0.00 3.16
77 78 0.238289 CGAAATGCCGCACTCTTGTT 59.762 50.000 0.00 0.00 0.00 2.83
78 79 1.334960 CGAAATGCCGCACTCTTGTTT 60.335 47.619 0.00 0.00 0.00 2.83
79 80 2.742774 GAAATGCCGCACTCTTGTTTT 58.257 42.857 0.00 0.00 0.00 2.43
80 81 2.888834 AATGCCGCACTCTTGTTTTT 57.111 40.000 0.00 0.00 0.00 1.94
185 191 1.688750 AGGGGTATTTGGGCCTAACA 58.311 50.000 0.00 0.00 0.00 2.41
186 192 1.569072 AGGGGTATTTGGGCCTAACAG 59.431 52.381 0.00 0.00 0.00 3.16
187 193 1.286849 GGGGTATTTGGGCCTAACAGT 59.713 52.381 0.00 0.00 0.00 3.55
189 195 3.437213 GGGTATTTGGGCCTAACAGTTT 58.563 45.455 0.00 0.00 0.00 2.66
190 196 3.835978 GGGTATTTGGGCCTAACAGTTTT 59.164 43.478 0.00 0.00 0.00 2.43
191 197 4.285003 GGGTATTTGGGCCTAACAGTTTTT 59.715 41.667 0.00 0.00 0.00 1.94
192 198 5.481122 GGGTATTTGGGCCTAACAGTTTTTA 59.519 40.000 0.00 0.00 0.00 1.52
193 199 6.155565 GGGTATTTGGGCCTAACAGTTTTTAT 59.844 38.462 0.00 0.00 0.00 1.40
194 200 7.310796 GGGTATTTGGGCCTAACAGTTTTTATT 60.311 37.037 0.00 0.00 0.00 1.40
195 201 8.751242 GGTATTTGGGCCTAACAGTTTTTATTA 58.249 33.333 0.00 0.00 0.00 0.98
196 202 9.797556 GTATTTGGGCCTAACAGTTTTTATTAG 57.202 33.333 0.00 0.00 0.00 1.73
198 204 8.937207 TTTGGGCCTAACAGTTTTTATTAGTA 57.063 30.769 0.00 0.00 0.00 1.82
199 205 9.536510 TTTGGGCCTAACAGTTTTTATTAGTAT 57.463 29.630 0.00 0.00 0.00 2.12
210 216 9.758651 CAGTTTTTATTAGTATAATTTGGGCCC 57.241 33.333 17.59 17.59 0.00 5.80
211 217 9.495382 AGTTTTTATTAGTATAATTTGGGCCCA 57.505 29.630 24.45 24.45 0.00 5.36
214 220 9.495382 TTTTATTAGTATAATTTGGGCCCAACT 57.505 29.630 37.33 29.93 35.46 3.16
233 2914 3.878778 ACTGGGTCTAAACATGCAGATC 58.121 45.455 0.00 0.00 0.00 2.75
239 2920 1.331756 CTAAACATGCAGATCGGCCAC 59.668 52.381 15.47 0.00 0.00 5.01
275 2956 4.379243 ACAGGCCTCGCGTCCTTG 62.379 66.667 0.00 5.03 0.00 3.61
277 2958 4.379243 AGGCCTCGCGTCCTTGTG 62.379 66.667 5.77 0.00 0.00 3.33
281 2962 1.300620 CCTCGCGTCCTTGTGTTCA 60.301 57.895 5.77 0.00 0.00 3.18
282 2963 0.878523 CCTCGCGTCCTTGTGTTCAA 60.879 55.000 5.77 0.00 0.00 2.69
283 2964 0.934496 CTCGCGTCCTTGTGTTCAAA 59.066 50.000 5.77 0.00 32.87 2.69
284 2965 1.329292 CTCGCGTCCTTGTGTTCAAAA 59.671 47.619 5.77 0.00 32.87 2.44
285 2966 1.738350 TCGCGTCCTTGTGTTCAAAAA 59.262 42.857 5.77 0.00 32.87 1.94
305 2986 2.430367 AAAAAGGCCTCGCGTCCT 59.570 55.556 5.23 8.80 0.00 3.85
306 2987 1.228154 AAAAAGGCCTCGCGTCCTT 60.228 52.632 5.23 18.97 44.07 3.36
307 2988 2.430367 AAAGGCCTCGCGTCCTTT 59.570 55.556 25.35 25.35 45.16 3.11
308 2989 2.430367 AAGGCCTCGCGTCCTTTT 59.570 55.556 5.23 3.83 39.53 2.27
309 2990 1.966451 AAGGCCTCGCGTCCTTTTG 60.966 57.895 5.23 0.00 39.53 2.44
310 2991 2.668550 GGCCTCGCGTCCTTTTGT 60.669 61.111 5.77 0.00 0.00 2.83
311 2992 2.258726 GGCCTCGCGTCCTTTTGTT 61.259 57.895 5.77 0.00 0.00 2.83
312 2993 1.652563 GCCTCGCGTCCTTTTGTTT 59.347 52.632 5.77 0.00 0.00 2.83
313 2994 0.030235 GCCTCGCGTCCTTTTGTTTT 59.970 50.000 5.77 0.00 0.00 2.43
314 2995 1.924629 GCCTCGCGTCCTTTTGTTTTC 60.925 52.381 5.77 0.00 0.00 2.29
340 3021 1.000955 TCTCTCGTCAAACAGGCCTTC 59.999 52.381 0.00 0.00 0.00 3.46
415 3096 4.222847 GTCGATGCCTCCCCCGAC 62.223 72.222 0.00 0.00 43.28 4.79
450 3131 0.386731 CAAACCAAATCGGGCGTGAC 60.387 55.000 0.00 0.00 40.22 3.67
569 3252 4.406173 CCCCGATCCGATCTCGCG 62.406 72.222 0.00 0.00 38.18 5.87
573 3256 4.726351 GATCCGATCTCGCGCCCC 62.726 72.222 0.00 0.00 38.18 5.80
669 3352 0.458889 TCGATTCGTCCGCGGAAATT 60.459 50.000 32.93 17.15 38.89 1.82
686 3369 2.530958 ATTCCGTCGGCCCGTGATTT 62.531 55.000 6.34 0.00 0.00 2.17
734 3417 3.259751 GGCGTGCCGTATCCGAAC 61.260 66.667 0.00 0.00 35.63 3.95
738 3421 0.659427 CGTGCCGTATCCGAACTAGA 59.341 55.000 0.00 0.00 35.63 2.43
778 3461 2.161609 GTGGCGGTGGTTTTCTAGATTG 59.838 50.000 0.00 0.00 0.00 2.67
791 3475 2.159382 CTAGATTGGTGCGGTTTTGGT 58.841 47.619 0.00 0.00 0.00 3.67
857 3543 2.117137 ACTGCGTAATAGATTGCGTCG 58.883 47.619 13.10 7.81 45.53 5.12
871 3557 1.367782 CGTCGCGAGATGTCCGTAG 60.368 63.158 10.24 0.00 45.19 3.51
891 3577 4.382345 AGGCTGCTCTAATTGAATTTGC 57.618 40.909 0.00 0.00 0.00 3.68
894 3580 3.111098 CTGCTCTAATTGAATTTGCGCC 58.889 45.455 4.18 0.00 0.00 6.53
934 3620 1.447945 GGAGGAGTTTGCTCTGCTTC 58.552 55.000 0.00 0.00 41.38 3.86
951 3637 0.318869 TTCGCTGTTTGCTTGCATGG 60.319 50.000 1.34 0.00 40.11 3.66
963 3649 1.682854 CTTGCATGGTGTCAGTGGTTT 59.317 47.619 0.00 0.00 0.00 3.27
964 3650 1.031235 TGCATGGTGTCAGTGGTTTG 58.969 50.000 0.00 0.00 0.00 2.93
966 3652 1.680735 GCATGGTGTCAGTGGTTTGAA 59.319 47.619 0.00 0.00 0.00 2.69
967 3653 2.543653 GCATGGTGTCAGTGGTTTGAAC 60.544 50.000 0.00 0.00 0.00 3.18
970 3656 3.013921 TGGTGTCAGTGGTTTGAACTTC 58.986 45.455 0.00 0.00 0.00 3.01
975 3661 3.001330 GTCAGTGGTTTGAACTTCTGACG 59.999 47.826 22.08 0.00 42.60 4.35
1221 3989 5.242434 TGTACAGCGGATGTATTTTGACTT 58.758 37.500 9.55 0.00 45.94 3.01
1279 4047 8.458843 TGTGATTTAGCTTTTAGTCAAATAGGC 58.541 33.333 0.00 0.00 0.00 3.93
1716 4487 5.069119 TCTGCGTGGTGATACATTTCTCTAT 59.931 40.000 0.00 0.00 0.00 1.98
1817 4588 5.662211 TTTGTTGTAAGTAACCGCTCTTC 57.338 39.130 0.00 0.00 0.00 2.87
1818 4589 3.656559 TGTTGTAAGTAACCGCTCTTCC 58.343 45.455 0.00 0.00 0.00 3.46
1821 4592 2.163010 TGTAAGTAACCGCTCTTCCTCG 59.837 50.000 0.00 0.00 0.00 4.63
1845 4616 5.920840 GCCTTGTTTTGACTTCTTAATCCAC 59.079 40.000 0.00 0.00 0.00 4.02
1999 4770 4.794334 TGTTGAGTTTGCTAAAGGGGTAA 58.206 39.130 0.00 0.00 0.00 2.85
2000 4771 5.390387 TGTTGAGTTTGCTAAAGGGGTAAT 58.610 37.500 0.00 0.00 0.00 1.89
2001 4772 5.836358 TGTTGAGTTTGCTAAAGGGGTAATT 59.164 36.000 0.00 0.00 0.00 1.40
2002 4773 7.005296 TGTTGAGTTTGCTAAAGGGGTAATTA 58.995 34.615 0.00 0.00 0.00 1.40
2283 5058 4.345257 GGAGATAGTGGCCACATAGAAAGA 59.655 45.833 36.39 11.76 0.00 2.52
2321 5096 2.808906 AAGAACCTCAAGTATGCCCC 57.191 50.000 0.00 0.00 0.00 5.80
2329 5104 1.449601 AAGTATGCCCCGCGAGTTG 60.450 57.895 8.23 0.00 0.00 3.16
2330 5105 2.125269 GTATGCCCCGCGAGTTGT 60.125 61.111 8.23 0.00 0.00 3.32
2331 5106 2.171725 GTATGCCCCGCGAGTTGTC 61.172 63.158 8.23 0.00 0.00 3.18
2332 5107 2.355986 TATGCCCCGCGAGTTGTCT 61.356 57.895 8.23 0.00 0.00 3.41
2338 5113 0.237498 CCCGCGAGTTGTCTTTTTCC 59.763 55.000 8.23 0.00 0.00 3.13
2481 5263 4.459685 CGCAGTAGGAGCTACAGGTATATT 59.540 45.833 0.00 0.00 39.22 1.28
2489 5271 8.507524 AGGAGCTACAGGTATATTTTGTTTTC 57.492 34.615 0.00 0.00 0.00 2.29
2720 5502 4.227300 TCTGTGGGCATAGGTTTACTTCAT 59.773 41.667 0.00 0.00 0.00 2.57
2721 5503 5.427157 TCTGTGGGCATAGGTTTACTTCATA 59.573 40.000 0.00 0.00 0.00 2.15
2722 5504 5.433526 TGTGGGCATAGGTTTACTTCATAC 58.566 41.667 0.00 0.00 0.00 2.39
2723 5505 5.190925 TGTGGGCATAGGTTTACTTCATACT 59.809 40.000 0.00 0.00 0.00 2.12
2724 5506 5.758784 GTGGGCATAGGTTTACTTCATACTC 59.241 44.000 0.00 0.00 0.00 2.59
2725 5507 5.163237 TGGGCATAGGTTTACTTCATACTCC 60.163 44.000 0.00 0.00 0.00 3.85
2726 5508 5.306394 GGCATAGGTTTACTTCATACTCCC 58.694 45.833 0.00 0.00 0.00 4.30
2727 5509 5.071923 GGCATAGGTTTACTTCATACTCCCT 59.928 44.000 0.00 0.00 0.00 4.20
2728 5510 6.224584 GCATAGGTTTACTTCATACTCCCTC 58.775 44.000 0.00 0.00 0.00 4.30
2729 5511 6.741801 GCATAGGTTTACTTCATACTCCCTCC 60.742 46.154 0.00 0.00 0.00 4.30
2730 5512 3.705072 AGGTTTACTTCATACTCCCTCCG 59.295 47.826 0.00 0.00 0.00 4.63
2731 5513 3.450096 GGTTTACTTCATACTCCCTCCGT 59.550 47.826 0.00 0.00 0.00 4.69
2732 5514 4.441217 GGTTTACTTCATACTCCCTCCGTC 60.441 50.000 0.00 0.00 0.00 4.79
2733 5515 1.777941 ACTTCATACTCCCTCCGTCC 58.222 55.000 0.00 0.00 0.00 4.79
2734 5516 0.669077 CTTCATACTCCCTCCGTCCG 59.331 60.000 0.00 0.00 0.00 4.79
2735 5517 0.256752 TTCATACTCCCTCCGTCCGA 59.743 55.000 0.00 0.00 0.00 4.55
2736 5518 0.256752 TCATACTCCCTCCGTCCGAA 59.743 55.000 0.00 0.00 0.00 4.30
2737 5519 1.108776 CATACTCCCTCCGTCCGAAA 58.891 55.000 0.00 0.00 0.00 3.46
2738 5520 1.479323 CATACTCCCTCCGTCCGAAAA 59.521 52.381 0.00 0.00 0.00 2.29
2739 5521 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
2740 5522 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
2741 5523 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
2742 5524 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
2743 5525 1.753073 TCCCTCCGTCCGAAAATACTC 59.247 52.381 0.00 0.00 0.00 2.59
2744 5526 1.535437 CCCTCCGTCCGAAAATACTCG 60.535 57.143 0.00 0.00 38.58 4.18
2745 5527 1.133790 CCTCCGTCCGAAAATACTCGT 59.866 52.381 0.00 0.00 37.11 4.18
2746 5528 2.448219 CTCCGTCCGAAAATACTCGTC 58.552 52.381 0.00 0.00 37.11 4.20
2747 5529 1.186030 CCGTCCGAAAATACTCGTCG 58.814 55.000 0.00 0.00 37.11 5.12
2755 5537 5.054780 CGAAAATACTCGTCGGAGAAATG 57.945 43.478 0.00 0.00 43.27 2.32
2756 5538 4.796830 CGAAAATACTCGTCGGAGAAATGA 59.203 41.667 0.00 0.00 43.27 2.57
2757 5539 5.287752 CGAAAATACTCGTCGGAGAAATGAA 59.712 40.000 0.00 0.00 43.27 2.57
2758 5540 6.404712 AAAATACTCGTCGGAGAAATGAAC 57.595 37.500 0.00 0.00 43.27 3.18
2759 5541 4.713824 ATACTCGTCGGAGAAATGAACA 57.286 40.909 0.00 0.00 43.27 3.18
2760 5542 3.380479 ACTCGTCGGAGAAATGAACAA 57.620 42.857 0.00 0.00 43.27 2.83
2761 5543 3.724374 ACTCGTCGGAGAAATGAACAAA 58.276 40.909 0.00 0.00 43.27 2.83
2762 5544 4.124238 ACTCGTCGGAGAAATGAACAAAA 58.876 39.130 0.00 0.00 43.27 2.44
2763 5545 4.573201 ACTCGTCGGAGAAATGAACAAAAA 59.427 37.500 0.00 0.00 43.27 1.94
2764 5546 5.238650 ACTCGTCGGAGAAATGAACAAAAAT 59.761 36.000 0.00 0.00 43.27 1.82
2765 5547 5.448438 TCGTCGGAGAAATGAACAAAAATG 58.552 37.500 0.00 0.00 39.69 2.32
2766 5548 4.616802 CGTCGGAGAAATGAACAAAAATGG 59.383 41.667 0.00 0.00 39.69 3.16
2767 5549 5.561919 CGTCGGAGAAATGAACAAAAATGGA 60.562 40.000 0.00 0.00 39.69 3.41
2768 5550 6.389906 GTCGGAGAAATGAACAAAAATGGAT 58.610 36.000 0.00 0.00 39.69 3.41
2769 5551 6.308766 GTCGGAGAAATGAACAAAAATGGATG 59.691 38.462 0.00 0.00 39.69 3.51
2770 5552 6.015519 TCGGAGAAATGAACAAAAATGGATGT 60.016 34.615 0.00 0.00 0.00 3.06
2771 5553 7.175816 TCGGAGAAATGAACAAAAATGGATGTA 59.824 33.333 0.00 0.00 0.00 2.29
2772 5554 7.975616 CGGAGAAATGAACAAAAATGGATGTAT 59.024 33.333 0.00 0.00 0.00 2.29
2773 5555 9.305925 GGAGAAATGAACAAAAATGGATGTATC 57.694 33.333 0.00 0.00 0.00 2.24
2811 5593 6.929625 ACATCTAGATACATTCATTCCTCCG 58.070 40.000 4.54 0.00 0.00 4.63
2812 5594 6.721668 ACATCTAGATACATTCATTCCTCCGA 59.278 38.462 4.54 0.00 0.00 4.55
2813 5595 6.576662 TCTAGATACATTCATTCCTCCGAC 57.423 41.667 0.00 0.00 0.00 4.79
2814 5596 6.068670 TCTAGATACATTCATTCCTCCGACA 58.931 40.000 0.00 0.00 0.00 4.35
2815 5597 5.614324 AGATACATTCATTCCTCCGACAA 57.386 39.130 0.00 0.00 0.00 3.18
2816 5598 5.605534 AGATACATTCATTCCTCCGACAAG 58.394 41.667 0.00 0.00 0.00 3.16
2817 5599 3.703001 ACATTCATTCCTCCGACAAGT 57.297 42.857 0.00 0.00 0.00 3.16
2818 5600 4.819105 ACATTCATTCCTCCGACAAGTA 57.181 40.909 0.00 0.00 0.00 2.24
2819 5601 5.359194 ACATTCATTCCTCCGACAAGTAT 57.641 39.130 0.00 0.00 0.00 2.12
2820 5602 5.745227 ACATTCATTCCTCCGACAAGTATT 58.255 37.500 0.00 0.00 0.00 1.89
2821 5603 6.180472 ACATTCATTCCTCCGACAAGTATTT 58.820 36.000 0.00 0.00 0.00 1.40
2822 5604 6.316390 ACATTCATTCCTCCGACAAGTATTTC 59.684 38.462 0.00 0.00 0.00 2.17
2823 5605 4.766375 TCATTCCTCCGACAAGTATTTCC 58.234 43.478 0.00 0.00 0.00 3.13
2824 5606 2.953466 TCCTCCGACAAGTATTTCCG 57.047 50.000 0.00 0.00 0.00 4.30
2825 5607 1.479323 TCCTCCGACAAGTATTTCCGG 59.521 52.381 0.00 0.00 41.36 5.14
2826 5608 1.479323 CCTCCGACAAGTATTTCCGGA 59.521 52.381 0.00 0.00 45.74 5.14
2827 5609 2.537401 CTCCGACAAGTATTTCCGGAC 58.463 52.381 1.83 0.00 43.47 4.79
2828 5610 1.135315 TCCGACAAGTATTTCCGGACG 60.135 52.381 1.83 0.00 43.47 4.79
2829 5611 1.274596 CGACAAGTATTTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
2830 5612 1.135315 CGACAAGTATTTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
2831 5613 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
2832 5614 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
2833 5615 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
2834 5616 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
2835 5617 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
2969 5853 5.623673 GCTTTTAAACATACTCGTGTTGTGG 59.376 40.000 0.00 0.00 41.22 4.17
3081 5966 2.420687 GGATGAAAGGCGATCAAGGAGT 60.421 50.000 0.00 0.00 0.00 3.85
3132 6047 4.662961 CGTGACAGTCGCAGCCCA 62.663 66.667 14.49 0.00 0.00 5.36
3242 6157 2.659610 GAGGAGCGCTTCACCTGT 59.340 61.111 19.98 0.00 35.81 4.00
3405 6320 1.805428 AAGACAATGGCAACCACCGC 61.805 55.000 0.00 0.00 35.80 5.68
3429 6344 1.757306 CAGTGGAAGTGCCTCACCT 59.243 57.895 0.00 0.00 37.63 4.00
3435 6350 1.768684 GAAGTGCCTCACCTGGTGGA 61.769 60.000 25.67 12.06 34.49 4.02
3452 6367 3.199946 GGTGGAGGTTGAGTTATGGATCA 59.800 47.826 0.00 0.00 0.00 2.92
3482 6397 1.140852 CAGTGTTCACCCAGTGGAAGA 59.859 52.381 11.95 4.96 33.87 2.87
3515 6430 2.158400 TGAGGGTCGAGAGATGGATCAT 60.158 50.000 0.00 0.00 45.19 2.45
3527 6442 7.121907 CGAGAGATGGATCATATTCTTCCTACA 59.878 40.741 0.00 0.00 0.00 2.74
3556 6471 5.417266 TGAAACTCTCCAAACATGTTGAACA 59.583 36.000 12.82 0.00 0.00 3.18
3610 6525 6.489675 TCGTGTACTCTATTTCGGTATTGAC 58.510 40.000 0.00 0.00 0.00 3.18
3671 6586 5.929992 CACATGGAATCATTTTGCAGTTTCT 59.070 36.000 0.00 0.00 0.00 2.52
3672 6587 7.092079 CACATGGAATCATTTTGCAGTTTCTA 58.908 34.615 0.00 0.00 0.00 2.10
3673 6588 7.062605 CACATGGAATCATTTTGCAGTTTCTAC 59.937 37.037 0.00 0.00 0.00 2.59
3674 6589 6.647334 TGGAATCATTTTGCAGTTTCTACA 57.353 33.333 0.00 0.00 0.00 2.74
3675 6590 7.230849 TGGAATCATTTTGCAGTTTCTACAT 57.769 32.000 0.00 0.00 0.00 2.29
3676 6591 7.669427 TGGAATCATTTTGCAGTTTCTACATT 58.331 30.769 0.00 0.00 0.00 2.71
3677 6592 7.814107 TGGAATCATTTTGCAGTTTCTACATTC 59.186 33.333 0.00 0.00 0.00 2.67
3678 6593 7.276438 GGAATCATTTTGCAGTTTCTACATTCC 59.724 37.037 0.00 0.00 0.00 3.01
3679 6594 6.647334 TCATTTTGCAGTTTCTACATTCCA 57.353 33.333 0.00 0.00 0.00 3.53
3680 6595 7.230849 TCATTTTGCAGTTTCTACATTCCAT 57.769 32.000 0.00 0.00 0.00 3.41
3681 6596 7.315142 TCATTTTGCAGTTTCTACATTCCATC 58.685 34.615 0.00 0.00 0.00 3.51
3697 6612 8.483307 ACATTCCATCAAATAATCTTTTGTGC 57.517 30.769 0.00 0.00 37.73 4.57
3698 6613 8.316214 ACATTCCATCAAATAATCTTTTGTGCT 58.684 29.630 0.00 0.00 37.73 4.40
3701 6616 9.859427 TTCCATCAAATAATCTTTTGTGCTTAG 57.141 29.630 0.00 0.00 37.73 2.18
3718 6633 8.256611 TGTGCTTAGTAATTTCTCATCTTCAC 57.743 34.615 0.00 0.00 0.00 3.18
3726 6641 4.471904 TTTCTCATCTTCACCGTGCTAT 57.528 40.909 0.00 0.00 0.00 2.97
3728 6643 4.569761 TCTCATCTTCACCGTGCTATAC 57.430 45.455 0.00 0.00 0.00 1.47
3729 6644 3.951680 TCTCATCTTCACCGTGCTATACA 59.048 43.478 0.00 0.00 0.00 2.29
3730 6645 4.584743 TCTCATCTTCACCGTGCTATACAT 59.415 41.667 0.00 0.00 0.00 2.29
3735 6650 3.620427 TCACCGTGCTATACATTGGTT 57.380 42.857 0.00 0.00 37.68 3.67
3737 6652 3.006940 CACCGTGCTATACATTGGTTGT 58.993 45.455 0.00 0.00 37.68 3.32
3745 6660 6.692681 GTGCTATACATTGGTTGTAAATGCTG 59.307 38.462 0.00 0.00 43.84 4.41
3766 6682 5.392057 GCTGGTAGTATTTGTCCTTGAAAGC 60.392 44.000 0.00 0.00 0.00 3.51
3774 6690 0.693049 GTCCTTGAAAGCTGGAGGGA 59.307 55.000 0.00 0.00 0.00 4.20
3782 6698 4.735369 TGAAAGCTGGAGGGAAAACAATA 58.265 39.130 0.00 0.00 0.00 1.90
3799 6715 6.610075 AACAATATTTTCCAGCATCCACTT 57.390 33.333 0.00 0.00 0.00 3.16
3806 6722 1.003580 TCCAGCATCCACTTTCCTCAC 59.996 52.381 0.00 0.00 0.00 3.51
3842 6758 7.581213 AAACACAACCATCTTCTCATACAAA 57.419 32.000 0.00 0.00 0.00 2.83
3845 6761 5.413833 CACAACCATCTTCTCATACAAAGCT 59.586 40.000 0.00 0.00 0.00 3.74
3848 6764 7.281774 ACAACCATCTTCTCATACAAAGCTATG 59.718 37.037 0.00 0.00 0.00 2.23
3883 6800 1.838112 GGACATTGACCATCTGCCAA 58.162 50.000 0.00 0.00 0.00 4.52
3923 6840 2.251040 CGTCTGTGAAATCGTCATCGT 58.749 47.619 0.00 0.00 38.90 3.73
3924 6841 2.276540 CGTCTGTGAAATCGTCATCGTC 59.723 50.000 0.00 0.00 38.90 4.20
3925 6842 2.276540 GTCTGTGAAATCGTCATCGTCG 59.723 50.000 0.00 0.00 38.90 5.12
3931 6848 0.736636 AATCGTCATCGTCGGCTACA 59.263 50.000 0.00 0.00 38.33 2.74
3945 6862 0.824759 GCTACACCGTCTCCTTCCAT 59.175 55.000 0.00 0.00 0.00 3.41
3957 6874 1.535204 CCTTCCATGCTGCCGGTTTT 61.535 55.000 1.90 0.00 0.00 2.43
4020 6937 4.373116 GAAGTCCAGGCCGTCGCA 62.373 66.667 0.00 0.00 36.38 5.10
4024 6941 4.812476 TCCAGGCCGTCGCAATCG 62.812 66.667 0.00 0.00 36.38 3.34
4210 7130 4.203076 GCCACCGTCTCGCCGTAT 62.203 66.667 0.00 0.00 0.00 3.06
4276 7196 1.733402 CGATCTTCTCCAGCTCGCCT 61.733 60.000 0.00 0.00 34.53 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 0.181587 TCTGCACCCGGACAGAAAAA 59.818 50.000 16.45 0.00 39.89 1.94
26 27 0.400213 ATCTGCACCCGGACAGAAAA 59.600 50.000 20.81 4.29 45.49 2.29
27 28 0.321564 CATCTGCACCCGGACAGAAA 60.322 55.000 20.81 4.88 45.49 2.52
28 29 1.191489 TCATCTGCACCCGGACAGAA 61.191 55.000 20.81 7.40 45.49 3.02
29 30 1.607801 CTCATCTGCACCCGGACAGA 61.608 60.000 19.70 19.70 46.34 3.41
30 31 1.153489 CTCATCTGCACCCGGACAG 60.153 63.158 0.73 8.00 35.15 3.51
31 32 1.888436 GACTCATCTGCACCCGGACA 61.888 60.000 0.73 0.00 0.00 4.02
32 33 1.153549 GACTCATCTGCACCCGGAC 60.154 63.158 0.73 0.00 0.00 4.79
33 34 0.033503 TAGACTCATCTGCACCCGGA 60.034 55.000 0.73 0.00 36.29 5.14
34 35 0.387202 CTAGACTCATCTGCACCCGG 59.613 60.000 0.00 0.00 36.29 5.73
35 36 0.387202 CCTAGACTCATCTGCACCCG 59.613 60.000 0.00 0.00 36.29 5.28
36 37 0.105778 GCCTAGACTCATCTGCACCC 59.894 60.000 0.00 0.00 36.29 4.61
37 38 0.826715 TGCCTAGACTCATCTGCACC 59.173 55.000 0.00 0.00 36.29 5.01
38 39 1.472376 GGTGCCTAGACTCATCTGCAC 60.472 57.143 9.95 9.95 46.67 4.57
39 40 0.826715 GGTGCCTAGACTCATCTGCA 59.173 55.000 0.00 0.00 36.29 4.41
40 41 0.249238 CGGTGCCTAGACTCATCTGC 60.249 60.000 0.00 0.00 36.29 4.26
41 42 1.393603 TCGGTGCCTAGACTCATCTG 58.606 55.000 0.00 0.00 36.29 2.90
42 43 2.145397 TTCGGTGCCTAGACTCATCT 57.855 50.000 0.00 0.00 39.15 2.90
43 44 2.961526 TTTCGGTGCCTAGACTCATC 57.038 50.000 0.00 0.00 0.00 2.92
44 45 2.743183 GCATTTCGGTGCCTAGACTCAT 60.743 50.000 0.00 0.00 39.18 2.90
45 46 1.405526 GCATTTCGGTGCCTAGACTCA 60.406 52.381 0.00 0.00 39.18 3.41
46 47 1.291132 GCATTTCGGTGCCTAGACTC 58.709 55.000 0.00 0.00 39.18 3.36
47 48 3.460648 GCATTTCGGTGCCTAGACT 57.539 52.632 0.00 0.00 39.18 3.24
54 55 3.667429 GAGTGCGGCATTTCGGTGC 62.667 63.158 5.72 0.61 44.31 5.01
55 56 1.577328 AAGAGTGCGGCATTTCGGTG 61.577 55.000 5.72 0.00 0.00 4.94
56 57 1.302511 AAGAGTGCGGCATTTCGGT 60.303 52.632 5.72 0.00 0.00 4.69
57 58 1.135315 CAAGAGTGCGGCATTTCGG 59.865 57.895 5.72 2.34 0.00 4.30
58 59 0.238289 AACAAGAGTGCGGCATTTCG 59.762 50.000 5.72 0.00 0.00 3.46
59 60 2.422276 AAACAAGAGTGCGGCATTTC 57.578 45.000 5.72 7.65 0.00 2.17
60 61 2.888834 AAAACAAGAGTGCGGCATTT 57.111 40.000 5.72 0.00 0.00 2.32
61 62 2.888834 AAAAACAAGAGTGCGGCATT 57.111 40.000 5.72 0.16 0.00 3.56
185 191 9.495382 TGGGCCCAAATTATACTAATAAAAACT 57.505 29.630 26.33 0.00 31.44 2.66
189 195 8.919145 CAGTTGGGCCCAAATTATACTAATAAA 58.081 33.333 38.70 8.35 37.70 1.40
190 196 7.507616 CCAGTTGGGCCCAAATTATACTAATAA 59.492 37.037 38.70 9.12 37.70 1.40
191 197 7.007723 CCAGTTGGGCCCAAATTATACTAATA 58.992 38.462 38.70 9.65 37.70 0.98
192 198 5.838521 CCAGTTGGGCCCAAATTATACTAAT 59.161 40.000 38.70 10.46 37.70 1.73
193 199 5.205056 CCAGTTGGGCCCAAATTATACTAA 58.795 41.667 38.70 10.51 37.70 2.24
194 200 4.798882 CCAGTTGGGCCCAAATTATACTA 58.201 43.478 38.70 11.39 37.70 1.82
195 201 3.642141 CCAGTTGGGCCCAAATTATACT 58.358 45.455 38.70 27.33 37.70 2.12
210 216 3.411446 TCTGCATGTTTAGACCCAGTTG 58.589 45.455 0.00 0.00 0.00 3.16
211 217 3.788227 TCTGCATGTTTAGACCCAGTT 57.212 42.857 0.00 0.00 0.00 3.16
212 218 3.679917 CGATCTGCATGTTTAGACCCAGT 60.680 47.826 0.00 0.00 0.00 4.00
213 219 2.868583 CGATCTGCATGTTTAGACCCAG 59.131 50.000 0.00 0.00 0.00 4.45
214 220 2.419990 CCGATCTGCATGTTTAGACCCA 60.420 50.000 0.00 0.00 0.00 4.51
239 2920 0.107703 TGATGGAAGGCGCCTAACAG 60.108 55.000 33.07 0.00 0.00 3.16
294 2975 0.030235 AAAACAAAAGGACGCGAGGC 59.970 50.000 15.93 0.62 39.70 4.70
295 2976 1.334689 GGAAAACAAAAGGACGCGAGG 60.335 52.381 15.93 0.00 0.00 4.63
296 2977 1.602377 AGGAAAACAAAAGGACGCGAG 59.398 47.619 15.93 0.00 0.00 5.03
297 2978 1.670791 AGGAAAACAAAAGGACGCGA 58.329 45.000 15.93 0.00 0.00 5.87
298 2979 2.485266 AAGGAAAACAAAAGGACGCG 57.515 45.000 3.53 3.53 0.00 6.01
299 2980 4.868171 AGAAAAAGGAAAACAAAAGGACGC 59.132 37.500 0.00 0.00 0.00 5.19
300 2981 6.330278 AGAGAAAAAGGAAAACAAAAGGACG 58.670 36.000 0.00 0.00 0.00 4.79
301 2982 6.472486 CGAGAGAAAAAGGAAAACAAAAGGAC 59.528 38.462 0.00 0.00 0.00 3.85
302 2983 6.152154 ACGAGAGAAAAAGGAAAACAAAAGGA 59.848 34.615 0.00 0.00 0.00 3.36
303 2984 6.330278 ACGAGAGAAAAAGGAAAACAAAAGG 58.670 36.000 0.00 0.00 0.00 3.11
304 2985 7.027161 TGACGAGAGAAAAAGGAAAACAAAAG 58.973 34.615 0.00 0.00 0.00 2.27
305 2986 6.915349 TGACGAGAGAAAAAGGAAAACAAAA 58.085 32.000 0.00 0.00 0.00 2.44
306 2987 6.503589 TGACGAGAGAAAAAGGAAAACAAA 57.496 33.333 0.00 0.00 0.00 2.83
307 2988 6.503589 TTGACGAGAGAAAAAGGAAAACAA 57.496 33.333 0.00 0.00 0.00 2.83
308 2989 6.072397 TGTTTGACGAGAGAAAAAGGAAAACA 60.072 34.615 0.00 0.00 32.96 2.83
309 2990 6.319399 TGTTTGACGAGAGAAAAAGGAAAAC 58.681 36.000 0.00 0.00 0.00 2.43
310 2991 6.404293 CCTGTTTGACGAGAGAAAAAGGAAAA 60.404 38.462 0.00 0.00 0.00 2.29
311 2992 5.065988 CCTGTTTGACGAGAGAAAAAGGAAA 59.934 40.000 0.00 0.00 0.00 3.13
312 2993 4.574828 CCTGTTTGACGAGAGAAAAAGGAA 59.425 41.667 0.00 0.00 0.00 3.36
313 2994 4.127171 CCTGTTTGACGAGAGAAAAAGGA 58.873 43.478 0.00 0.00 0.00 3.36
314 2995 3.304057 GCCTGTTTGACGAGAGAAAAAGG 60.304 47.826 0.00 0.00 0.00 3.11
450 3131 0.248743 TGACGGCGGCGAACTTATAG 60.249 55.000 38.93 5.69 0.00 1.31
573 3256 4.493747 GAGCGGAAGGACGGACGG 62.494 72.222 0.00 0.00 0.00 4.79
574 3257 4.831307 CGAGCGGAAGGACGGACG 62.831 72.222 0.00 0.00 0.00 4.79
575 3258 2.280823 AATCGAGCGGAAGGACGGAC 62.281 60.000 0.00 0.00 0.00 4.79
577 3260 1.589196 GAATCGAGCGGAAGGACGG 60.589 63.158 0.00 0.00 0.00 4.79
578 3261 1.589196 GGAATCGAGCGGAAGGACG 60.589 63.158 0.00 0.00 0.00 4.79
669 3352 3.697747 AAATCACGGGCCGACGGA 61.698 61.111 35.78 25.49 38.39 4.69
686 3369 3.492656 GGATCTATCCGTACAAGCAAGCA 60.493 47.826 0.00 0.00 37.19 3.91
738 3421 6.226787 CGCCACCTCTTCAGAATATCTAATT 58.773 40.000 0.00 0.00 0.00 1.40
778 3461 1.805428 ATCAGCACCAAAACCGCACC 61.805 55.000 0.00 0.00 0.00 5.01
791 3475 1.140852 CCCCCTTACGAATCATCAGCA 59.859 52.381 0.00 0.00 0.00 4.41
813 3497 2.418746 CCTAGCTGCGACCATACTGTTT 60.419 50.000 0.00 0.00 0.00 2.83
857 3543 1.299468 CAGCCTACGGACATCTCGC 60.299 63.158 0.00 0.00 0.00 5.03
871 3557 3.111098 CGCAAATTCAATTAGAGCAGCC 58.889 45.455 0.00 0.00 0.00 4.85
894 3580 2.481795 CCCATAAAAAGCAGCCAATCCG 60.482 50.000 0.00 0.00 0.00 4.18
951 3637 3.938963 TCAGAAGTTCAAACCACTGACAC 59.061 43.478 5.50 0.00 36.99 3.67
963 3649 2.223249 GCAGCAAAACGTCAGAAGTTCA 60.223 45.455 5.50 0.00 0.00 3.18
964 3650 2.032178 AGCAGCAAAACGTCAGAAGTTC 59.968 45.455 1.90 0.00 0.00 3.01
966 3652 1.668419 AGCAGCAAAACGTCAGAAGT 58.332 45.000 0.00 0.00 0.00 3.01
967 3653 2.223340 ACAAGCAGCAAAACGTCAGAAG 60.223 45.455 0.00 0.00 0.00 2.85
970 3656 2.193306 AACAAGCAGCAAAACGTCAG 57.807 45.000 0.00 0.00 0.00 3.51
975 3661 1.587946 CACCGAAACAAGCAGCAAAAC 59.412 47.619 0.00 0.00 0.00 2.43
1221 3989 3.220674 TGGGTGACATGACATGAAACA 57.779 42.857 22.19 14.57 0.00 2.83
1279 4047 1.534595 GACAAGAGAGCAAAGCACAGG 59.465 52.381 0.00 0.00 0.00 4.00
1310 4078 3.817647 GGTGTGTCTCAATTTCTGCTCTT 59.182 43.478 0.00 0.00 0.00 2.85
1400 4169 1.699634 GGTGCTGGCTTAGATATCCCA 59.300 52.381 0.00 0.00 0.00 4.37
1508 4279 4.501400 CCCCAAAACCTTCAACAAGATCAC 60.501 45.833 0.00 0.00 0.00 3.06
1716 4487 3.249799 CAGTAACACCATCAAGACGCAAA 59.750 43.478 0.00 0.00 0.00 3.68
1817 4588 2.222027 AGAAGTCAAAACAAGGCGAGG 58.778 47.619 0.00 0.00 0.00 4.63
1818 4589 3.971032 AAGAAGTCAAAACAAGGCGAG 57.029 42.857 0.00 0.00 0.00 5.03
1821 4592 5.920840 GTGGATTAAGAAGTCAAAACAAGGC 59.079 40.000 0.00 0.00 0.00 4.35
1845 4616 4.612614 GCATCAATGTGAACAGTACAAACG 59.387 41.667 0.00 0.00 0.00 3.60
1941 4712 2.766313 TCAAAGTCACGACCATCAAGG 58.234 47.619 0.00 0.00 45.67 3.61
2283 5058 1.289160 TAGGGCTGTTCTGGCAATCT 58.711 50.000 5.75 0.00 0.00 2.40
2321 5096 0.580104 ACGGAAAAAGACAACTCGCG 59.420 50.000 0.00 0.00 0.00 5.87
2329 5104 5.924825 TGCTCTACTTAGAACGGAAAAAGAC 59.075 40.000 0.00 0.00 0.00 3.01
2330 5105 6.092955 TGCTCTACTTAGAACGGAAAAAGA 57.907 37.500 0.00 0.00 0.00 2.52
2331 5106 6.969828 ATGCTCTACTTAGAACGGAAAAAG 57.030 37.500 0.00 0.00 0.00 2.27
2332 5107 8.475639 AGATATGCTCTACTTAGAACGGAAAAA 58.524 33.333 0.00 0.00 30.26 1.94
2338 5113 7.197071 AGTCAGATATGCTCTACTTAGAACG 57.803 40.000 0.00 0.00 31.13 3.95
2481 5263 4.142600 CGGTGCCCAAATTTTGAAAACAAA 60.143 37.500 10.72 0.00 0.00 2.83
2489 5271 2.543430 CAGAAACGGTGCCCAAATTTTG 59.457 45.455 1.99 1.99 0.00 2.44
2720 5502 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
2721 5503 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
2722 5504 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
2723 5505 1.753073 GAGTATTTTCGGACGGAGGGA 59.247 52.381 0.00 0.00 0.00 4.20
2724 5506 1.535437 CGAGTATTTTCGGACGGAGGG 60.535 57.143 0.00 0.00 36.95 4.30
2725 5507 1.133790 ACGAGTATTTTCGGACGGAGG 59.866 52.381 0.00 0.00 44.57 4.30
2726 5508 2.448219 GACGAGTATTTTCGGACGGAG 58.552 52.381 0.00 0.00 44.57 4.63
2727 5509 1.202065 CGACGAGTATTTTCGGACGGA 60.202 52.381 0.00 0.00 44.57 4.69
2728 5510 1.186030 CGACGAGTATTTTCGGACGG 58.814 55.000 0.00 0.00 44.57 4.79
2733 5515 4.796830 TCATTTCTCCGACGAGTATTTTCG 59.203 41.667 0.00 0.00 45.70 3.46
2734 5516 6.090358 TGTTCATTTCTCCGACGAGTATTTTC 59.910 38.462 0.00 0.00 37.40 2.29
2735 5517 5.929992 TGTTCATTTCTCCGACGAGTATTTT 59.070 36.000 0.00 0.00 37.40 1.82
2736 5518 5.475719 TGTTCATTTCTCCGACGAGTATTT 58.524 37.500 0.00 0.00 37.40 1.40
2737 5519 5.068234 TGTTCATTTCTCCGACGAGTATT 57.932 39.130 0.00 0.00 37.40 1.89
2738 5520 4.713824 TGTTCATTTCTCCGACGAGTAT 57.286 40.909 0.00 0.00 37.40 2.12
2739 5521 4.508461 TTGTTCATTTCTCCGACGAGTA 57.492 40.909 0.00 0.00 37.40 2.59
2740 5522 3.380479 TTGTTCATTTCTCCGACGAGT 57.620 42.857 0.00 0.00 37.40 4.18
2741 5523 4.725556 TTTTGTTCATTTCTCCGACGAG 57.274 40.909 0.00 0.00 37.48 4.18
2742 5524 5.448438 CATTTTTGTTCATTTCTCCGACGA 58.552 37.500 0.00 0.00 0.00 4.20
2743 5525 4.616802 CCATTTTTGTTCATTTCTCCGACG 59.383 41.667 0.00 0.00 0.00 5.12
2744 5526 5.768317 TCCATTTTTGTTCATTTCTCCGAC 58.232 37.500 0.00 0.00 0.00 4.79
2745 5527 6.015519 ACATCCATTTTTGTTCATTTCTCCGA 60.016 34.615 0.00 0.00 0.00 4.55
2746 5528 6.158598 ACATCCATTTTTGTTCATTTCTCCG 58.841 36.000 0.00 0.00 0.00 4.63
2747 5529 9.305925 GATACATCCATTTTTGTTCATTTCTCC 57.694 33.333 0.00 0.00 0.00 3.71
2785 5567 8.690884 CGGAGGAATGAATGTATCTAGATGTAT 58.309 37.037 15.79 6.61 0.00 2.29
2786 5568 7.888546 TCGGAGGAATGAATGTATCTAGATGTA 59.111 37.037 15.79 4.44 0.00 2.29
2787 5569 6.721668 TCGGAGGAATGAATGTATCTAGATGT 59.278 38.462 15.79 0.00 0.00 3.06
2788 5570 7.032580 GTCGGAGGAATGAATGTATCTAGATG 58.967 42.308 15.79 0.00 0.00 2.90
2789 5571 6.721668 TGTCGGAGGAATGAATGTATCTAGAT 59.278 38.462 10.73 10.73 0.00 1.98
2790 5572 6.068670 TGTCGGAGGAATGAATGTATCTAGA 58.931 40.000 0.00 0.00 0.00 2.43
2791 5573 6.332735 TGTCGGAGGAATGAATGTATCTAG 57.667 41.667 0.00 0.00 0.00 2.43
2792 5574 6.323996 ACTTGTCGGAGGAATGAATGTATCTA 59.676 38.462 0.00 0.00 0.00 1.98
2793 5575 5.129485 ACTTGTCGGAGGAATGAATGTATCT 59.871 40.000 0.00 0.00 0.00 1.98
2794 5576 5.360591 ACTTGTCGGAGGAATGAATGTATC 58.639 41.667 0.00 0.00 0.00 2.24
2795 5577 5.359194 ACTTGTCGGAGGAATGAATGTAT 57.641 39.130 0.00 0.00 0.00 2.29
2796 5578 4.819105 ACTTGTCGGAGGAATGAATGTA 57.181 40.909 0.00 0.00 0.00 2.29
2797 5579 3.703001 ACTTGTCGGAGGAATGAATGT 57.297 42.857 0.00 0.00 0.00 2.71
2798 5580 6.238484 GGAAATACTTGTCGGAGGAATGAATG 60.238 42.308 0.00 0.00 0.00 2.67
2799 5581 5.823045 GGAAATACTTGTCGGAGGAATGAAT 59.177 40.000 0.00 0.00 0.00 2.57
2800 5582 5.183228 GGAAATACTTGTCGGAGGAATGAA 58.817 41.667 0.00 0.00 0.00 2.57
2801 5583 4.679639 CGGAAATACTTGTCGGAGGAATGA 60.680 45.833 0.00 0.00 0.00 2.57
2802 5584 3.555956 CGGAAATACTTGTCGGAGGAATG 59.444 47.826 0.00 0.00 0.00 2.67
2803 5585 3.431766 CCGGAAATACTTGTCGGAGGAAT 60.432 47.826 0.00 0.00 42.94 3.01
2804 5586 2.093869 CCGGAAATACTTGTCGGAGGAA 60.094 50.000 0.00 0.00 42.94 3.36
2805 5587 1.479323 CCGGAAATACTTGTCGGAGGA 59.521 52.381 0.00 0.00 42.94 3.71
2806 5588 1.479323 TCCGGAAATACTTGTCGGAGG 59.521 52.381 0.00 0.00 43.84 4.30
2807 5589 2.953466 TCCGGAAATACTTGTCGGAG 57.047 50.000 0.00 0.00 43.84 4.63
2808 5590 1.135315 CGTCCGGAAATACTTGTCGGA 60.135 52.381 5.23 0.00 46.06 4.55
2809 5591 1.274596 CGTCCGGAAATACTTGTCGG 58.725 55.000 5.23 0.00 41.80 4.79
2810 5592 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
2811 5593 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
2812 5594 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
2813 5595 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
2814 5596 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
2815 5597 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
2816 5598 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
2817 5599 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
2818 5600 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
2819 5601 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
2820 5602 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
2821 5603 1.929860 ATGTACTCCCTCCGTCCGGA 61.930 60.000 0.00 0.00 42.90 5.14
2822 5604 1.041447 AATGTACTCCCTCCGTCCGG 61.041 60.000 0.00 0.00 0.00 5.14
2823 5605 0.822164 AAATGTACTCCCTCCGTCCG 59.178 55.000 0.00 0.00 0.00 4.79
2824 5606 3.450096 AGTAAAATGTACTCCCTCCGTCC 59.550 47.826 0.00 0.00 0.00 4.79
2825 5607 4.732672 AGTAAAATGTACTCCCTCCGTC 57.267 45.455 0.00 0.00 0.00 4.79
2826 5608 5.105187 GGTTAGTAAAATGTACTCCCTCCGT 60.105 44.000 0.00 0.00 0.00 4.69
2827 5609 5.128335 AGGTTAGTAAAATGTACTCCCTCCG 59.872 44.000 0.00 0.00 28.67 4.63
2828 5610 6.346896 CAGGTTAGTAAAATGTACTCCCTCC 58.653 44.000 0.00 0.00 30.96 4.30
2829 5611 5.816258 GCAGGTTAGTAAAATGTACTCCCTC 59.184 44.000 0.00 0.00 30.96 4.30
2830 5612 5.487845 AGCAGGTTAGTAAAATGTACTCCCT 59.512 40.000 0.00 0.00 32.52 4.20
2831 5613 5.585047 CAGCAGGTTAGTAAAATGTACTCCC 59.415 44.000 0.00 0.00 0.00 4.30
2832 5614 6.403878 TCAGCAGGTTAGTAAAATGTACTCC 58.596 40.000 0.00 0.00 0.00 3.85
2833 5615 7.900782 TTCAGCAGGTTAGTAAAATGTACTC 57.099 36.000 0.00 0.00 0.00 2.59
2834 5616 7.883311 ACATTCAGCAGGTTAGTAAAATGTACT 59.117 33.333 5.46 0.00 35.11 2.73
2835 5617 7.962918 CACATTCAGCAGGTTAGTAAAATGTAC 59.037 37.037 6.56 0.00 35.11 2.90
2890 5676 8.863086 ACTGGCATATATTCATTAGTTGCAAAT 58.137 29.630 4.23 4.23 0.00 2.32
3081 5966 3.680786 CTGCGACTGTCACGGGGA 61.681 66.667 8.73 0.00 0.00 4.81
3132 6047 3.684628 TCTCGGGGGCTCCTCCTT 61.685 66.667 0.52 0.00 34.39 3.36
3147 6062 0.684479 TCATAGGGCTGCGACTGTCT 60.684 55.000 6.21 0.00 0.00 3.41
3381 6296 1.327303 GGTTGCCATTGTCTTCACCA 58.673 50.000 0.00 0.00 0.00 4.17
3384 6299 1.327303 GGTGGTTGCCATTGTCTTCA 58.673 50.000 0.00 0.00 35.28 3.02
3405 6320 3.357079 GCACTTCCACTGGGTGCG 61.357 66.667 12.14 0.00 44.91 5.34
3429 6344 2.626785 TCCATAACTCAACCTCCACCA 58.373 47.619 0.00 0.00 0.00 4.17
3435 6350 6.735556 AGGATTTTGATCCATAACTCAACCT 58.264 36.000 8.06 0.00 43.14 3.50
3443 6358 6.493166 ACACTGGAAGGATTTTGATCCATAA 58.507 36.000 8.06 0.00 43.14 1.90
3444 6359 6.078456 ACACTGGAAGGATTTTGATCCATA 57.922 37.500 8.06 0.00 43.14 2.74
3452 6367 3.230976 GGGTGAACACTGGAAGGATTTT 58.769 45.455 4.96 0.00 39.30 1.82
3482 6397 1.539869 ACCCTCACCAGGTGATGCT 60.540 57.895 23.21 4.76 41.94 3.79
3556 6471 3.470645 ACTCGTACAGGCAAGTCTTTT 57.529 42.857 0.00 0.00 0.00 2.27
3610 6525 6.041409 ACAGATATTATGGTCTGACTGGAGTG 59.959 42.308 7.85 0.00 43.50 3.51
3671 6586 9.585099 GCACAAAAGATTATTTGATGGAATGTA 57.415 29.630 6.76 0.00 41.73 2.29
3672 6587 8.316214 AGCACAAAAGATTATTTGATGGAATGT 58.684 29.630 6.76 0.00 41.73 2.71
3673 6588 8.712285 AGCACAAAAGATTATTTGATGGAATG 57.288 30.769 6.76 0.00 41.73 2.67
3675 6590 9.859427 CTAAGCACAAAAGATTATTTGATGGAA 57.141 29.630 6.76 0.00 41.73 3.53
3676 6591 9.023962 ACTAAGCACAAAAGATTATTTGATGGA 57.976 29.630 6.76 0.00 41.73 3.41
3694 6609 7.464710 CGGTGAAGATGAGAAATTACTAAGCAC 60.465 40.741 0.00 0.00 0.00 4.40
3695 6610 6.535150 CGGTGAAGATGAGAAATTACTAAGCA 59.465 38.462 0.00 0.00 0.00 3.91
3696 6611 6.535508 ACGGTGAAGATGAGAAATTACTAAGC 59.464 38.462 0.00 0.00 0.00 3.09
3697 6612 7.464710 GCACGGTGAAGATGAGAAATTACTAAG 60.465 40.741 13.29 0.00 0.00 2.18
3698 6613 6.312918 GCACGGTGAAGATGAGAAATTACTAA 59.687 38.462 13.29 0.00 0.00 2.24
3700 6615 4.631813 GCACGGTGAAGATGAGAAATTACT 59.368 41.667 13.29 0.00 0.00 2.24
3701 6616 4.631813 AGCACGGTGAAGATGAGAAATTAC 59.368 41.667 13.29 0.00 0.00 1.89
3716 6631 3.006940 ACAACCAATGTATAGCACGGTG 58.993 45.455 3.15 3.15 41.63 4.94
3718 6633 5.804692 TTTACAACCAATGTATAGCACGG 57.195 39.130 0.00 0.00 43.84 4.94
3726 6641 6.242396 ACTACCAGCATTTACAACCAATGTA 58.758 36.000 0.00 0.00 43.63 2.29
3728 6643 5.643379 ACTACCAGCATTTACAACCAATG 57.357 39.130 0.00 0.00 35.12 2.82
3729 6644 7.954666 AATACTACCAGCATTTACAACCAAT 57.045 32.000 0.00 0.00 0.00 3.16
3730 6645 7.231722 ACAAATACTACCAGCATTTACAACCAA 59.768 33.333 0.00 0.00 0.00 3.67
3735 6650 6.717289 AGGACAAATACTACCAGCATTTACA 58.283 36.000 0.00 0.00 0.00 2.41
3737 6652 7.398829 TCAAGGACAAATACTACCAGCATTTA 58.601 34.615 0.00 0.00 0.00 1.40
3745 6660 5.123979 CCAGCTTTCAAGGACAAATACTACC 59.876 44.000 0.00 0.00 0.00 3.18
3774 6690 7.008021 AGTGGATGCTGGAAAATATTGTTTT 57.992 32.000 0.00 0.00 0.00 2.43
3782 6698 3.766051 GAGGAAAGTGGATGCTGGAAAAT 59.234 43.478 0.00 0.00 0.00 1.82
3824 6740 7.281774 CACATAGCTTTGTATGAGAAGATGGTT 59.718 37.037 9.60 0.00 34.88 3.67
3826 6742 6.204301 CCACATAGCTTTGTATGAGAAGATGG 59.796 42.308 9.60 0.00 34.88 3.51
3839 6755 3.693085 AGCAGATGAACCACATAGCTTTG 59.307 43.478 2.27 2.27 43.20 2.77
3842 6758 2.915349 CAGCAGATGAACCACATAGCT 58.085 47.619 0.00 0.00 45.08 3.32
3845 6761 1.655484 CGCAGCAGATGAACCACATA 58.345 50.000 0.00 0.00 39.56 2.29
3848 6764 1.375908 TCCGCAGCAGATGAACCAC 60.376 57.895 0.00 0.00 0.00 4.16
3883 6800 1.213926 GCATCCATGAGAGGGACCTTT 59.786 52.381 0.00 0.00 37.23 3.11
3925 6842 1.255667 TGGAAGGAGACGGTGTAGCC 61.256 60.000 0.00 0.00 0.00 3.93
3931 6848 1.599047 CAGCATGGAAGGAGACGGT 59.401 57.895 0.00 0.00 0.00 4.83
3940 6857 1.173043 CTAAAACCGGCAGCATGGAA 58.827 50.000 0.00 0.00 35.86 3.53
3957 6874 3.826754 CAGAGCTCACGCCGCCTA 61.827 66.667 17.77 0.00 36.60 3.93
4024 6941 2.876645 CGTCAGAGAAGCGCGGTC 60.877 66.667 12.91 5.38 0.00 4.79


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

AutoCloner maintained by Alex Coulton.