Multiple sequence alignment - TraesCS2B01G352700

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2B01G352700 chr2B 100.000 4866 0 0 999 5864 503750715 503755580 0.000000e+00 8986
1 TraesCS2B01G352700 chr2B 94.237 989 38 7 1819 2791 84216580 84217565 0.000000e+00 1493
2 TraesCS2B01G352700 chr2B 100.000 665 0 0 1 665 503749717 503750381 0.000000e+00 1229
3 TraesCS2B01G352700 chr2B 94.883 684 18 4 1819 2486 33564407 33565089 0.000000e+00 1053
4 TraesCS2B01G352700 chr2B 83.851 161 24 2 3114 3274 558295275 558295433 1.020000e-32 152
5 TraesCS2B01G352700 chr2D 95.061 2065 69 9 3077 5118 426928301 426930355 0.000000e+00 3217
6 TraesCS2B01G352700 chr2D 92.655 1307 57 12 999 2286 426926260 426927546 0.000000e+00 1845
7 TraesCS2B01G352700 chr2D 94.205 604 18 4 5256 5859 426930719 426931305 0.000000e+00 905
8 TraesCS2B01G352700 chr2D 96.656 299 9 1 368 665 426925536 426925834 4.080000e-136 496
9 TraesCS2B01G352700 chr2D 81.960 449 31 14 2488 2934 426927911 426928311 9.420000e-88 335
10 TraesCS2B01G352700 chr2D 79.514 288 30 4 1 287 426924866 426925125 1.680000e-40 178
11 TraesCS2B01G352700 chr2D 94.545 110 6 0 5116 5225 426930615 426930724 2.810000e-38 171
12 TraesCS2B01G352700 chr2D 85.350 157 20 3 3119 3274 476962731 476962885 6.080000e-35 159
13 TraesCS2B01G352700 chr2D 85.350 157 20 3 3119 3274 477072420 477072574 6.080000e-35 159
14 TraesCS2B01G352700 chr2D 95.181 83 4 0 287 369 426925155 426925237 1.330000e-26 132
15 TraesCS2B01G352700 chr2D 87.692 65 7 1 3210 3274 476984457 476984520 2.270000e-09 75
16 TraesCS2B01G352700 chr2A 92.988 2068 89 17 3080 5118 562099133 562097093 0.000000e+00 2964
17 TraesCS2B01G352700 chr2A 94.063 1297 55 8 999 2280 562101192 562099903 0.000000e+00 1949
18 TraesCS2B01G352700 chr2A 97.436 624 12 3 4162 4781 561848859 561848236 0.000000e+00 1061
19 TraesCS2B01G352700 chr2A 93.607 610 25 5 5256 5864 562096579 562095983 0.000000e+00 898
20 TraesCS2B01G352700 chr2A 97.097 310 7 2 356 665 562101610 562101303 6.730000e-144 521
21 TraesCS2B01G352700 chr2A 80.660 636 72 31 5247 5864 561847198 561846596 4.170000e-121 446
22 TraesCS2B01G352700 chr2A 81.718 454 33 9 2488 2939 562099526 562099121 3.390000e-87 333
23 TraesCS2B01G352700 chr2A 82.621 351 32 10 4789 5118 561847954 561847612 3.460000e-72 283
24 TraesCS2B01G352700 chr2A 85.714 259 19 8 5616 5864 561856094 561855844 2.100000e-64 257
25 TraesCS2B01G352700 chr2A 96.364 110 4 0 5116 5225 562096683 562096574 1.300000e-41 182
26 TraesCS2B01G352700 chr2A 87.261 157 17 3 3119 3274 619245735 619245889 6.040000e-40 176
27 TraesCS2B01G352700 chr2A 89.130 92 6 2 287 377 562101989 562101901 1.730000e-20 111
28 TraesCS2B01G352700 chr7B 95.297 978 29 5 1821 2784 627395139 627394165 0.000000e+00 1535
29 TraesCS2B01G352700 chr7B 92.395 618 29 7 1819 2420 724080028 724080643 0.000000e+00 865
30 TraesCS2B01G352700 chr7B 92.395 618 29 7 1819 2420 724133882 724134497 0.000000e+00 865
31 TraesCS2B01G352700 chr1B 94.242 990 38 7 1819 2791 31301101 31302088 0.000000e+00 1495
32 TraesCS2B01G352700 chr1B 97.241 145 2 2 2940 3082 440489514 440489658 1.630000e-60 244
33 TraesCS2B01G352700 chr1B 92.667 150 10 1 2928 3077 4039356 4039504 1.280000e-51 215
34 TraesCS2B01G352700 chr4B 94.168 926 36 6 1819 2728 650566666 650567589 0.000000e+00 1395
35 TraesCS2B01G352700 chr4B 99.275 138 1 0 2940 3077 212497256 212497119 3.510000e-62 250
36 TraesCS2B01G352700 chr6B 94.883 684 18 5 1819 2486 203235516 203236198 0.000000e+00 1053
37 TraesCS2B01G352700 chr6B 96.599 147 3 2 2940 3085 641890662 641890517 5.870000e-60 243
38 TraesCS2B01G352700 chr5B 95.525 648 28 1 2144 2791 698087428 698088074 0.000000e+00 1035
39 TraesCS2B01G352700 chr5B 91.343 335 15 2 1832 2152 698079622 698079956 4.170000e-121 446
40 TraesCS2B01G352700 chrUn 96.486 370 12 1 2422 2791 467114802 467114434 1.400000e-170 610
41 TraesCS2B01G352700 chr7A 98.551 138 2 0 2940 3077 105168855 105168992 1.630000e-60 244
42 TraesCS2B01G352700 chr7A 96.575 146 2 2 2940 3085 438151607 438151465 7.590000e-59 239
43 TraesCS2B01G352700 chr4D 95.425 153 7 0 2940 3092 478512321 478512169 1.630000e-60 244
44 TraesCS2B01G352700 chr4A 96.599 147 3 2 2940 3086 477497795 477497651 5.870000e-60 243
45 TraesCS2B01G352700 chr4A 94.268 157 5 3 2940 3094 359273931 359273777 2.730000e-58 237
46 TraesCS2B01G352700 chr4A 93.711 159 9 1 2940 3098 732486062 732485905 2.730000e-58 237


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 TraesCS2B01G352700 chr2B 503749717 503755580 5863 False 5107.500000 8986 100.000000 1 5864 2 chr2B.!!$F4 5863
1 TraesCS2B01G352700 chr2B 84216580 84217565 985 False 1493.000000 1493 94.237000 1819 2791 1 chr2B.!!$F2 972
2 TraesCS2B01G352700 chr2B 33564407 33565089 682 False 1053.000000 1053 94.883000 1819 2486 1 chr2B.!!$F1 667
3 TraesCS2B01G352700 chr2D 426924866 426931305 6439 False 909.875000 3217 91.222125 1 5859 8 chr2D.!!$F4 5858
4 TraesCS2B01G352700 chr2A 562095983 562101989 6006 True 994.000000 2964 92.138143 287 5864 7 chr2A.!!$R3 5577
5 TraesCS2B01G352700 chr2A 561846596 561848859 2263 True 596.666667 1061 86.905667 4162 5864 3 chr2A.!!$R2 1702
6 TraesCS2B01G352700 chr7B 627394165 627395139 974 True 1535.000000 1535 95.297000 1821 2784 1 chr7B.!!$R1 963
7 TraesCS2B01G352700 chr7B 724080028 724080643 615 False 865.000000 865 92.395000 1819 2420 1 chr7B.!!$F1 601
8 TraesCS2B01G352700 chr7B 724133882 724134497 615 False 865.000000 865 92.395000 1819 2420 1 chr7B.!!$F2 601
9 TraesCS2B01G352700 chr1B 31301101 31302088 987 False 1495.000000 1495 94.242000 1819 2791 1 chr1B.!!$F2 972
10 TraesCS2B01G352700 chr4B 650566666 650567589 923 False 1395.000000 1395 94.168000 1819 2728 1 chr4B.!!$F1 909
11 TraesCS2B01G352700 chr6B 203235516 203236198 682 False 1053.000000 1053 94.883000 1819 2486 1 chr6B.!!$F1 667
12 TraesCS2B01G352700 chr5B 698087428 698088074 646 False 1035.000000 1035 95.525000 2144 2791 1 chr5B.!!$F2 647

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
227 229 0.038067 TCCGCTTCGATCCAAACGAA 60.038 50.0 0.0 0.0 45.25 3.85 F
228 230 0.094730 CCGCTTCGATCCAAACGAAC 59.905 55.0 0.0 0.0 43.19 3.95 F
237 239 0.108281 TCCAAACGAACACACACGGA 60.108 50.0 0.0 0.0 0.00 4.69 F
1313 2048 0.108851 CTTTTTGGCGATTTCCCCCG 60.109 55.0 0.0 0.0 0.00 5.73 F
2962 3898 0.107831 CACGGGTTCAAGTCCTGGAA 59.892 55.0 0.0 0.0 35.79 3.53 F
3009 3945 0.177141 GGCTGCGTACAATAGACCCA 59.823 55.0 0.0 0.0 0.00 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1571 2306 0.247736 CCGTCCTCTTGAGTTCCCTG 59.752 60.000 0.00 0.0 0.00 4.45 R
1857 2592 3.637998 TCAACTACTCACGTCAGAACC 57.362 47.619 0.00 0.0 0.00 3.62 R
2326 3165 7.496346 AACTTGGTGTGAATAAGATCCTCTA 57.504 36.000 0.00 0.0 0.00 2.43 R
3090 4026 0.036732 TGCTGATGGAAAGAGCGGTT 59.963 50.000 0.00 0.0 35.36 4.44 R
3972 4910 0.391661 GGTTGCGGAGATTGCTCAGA 60.392 55.000 0.00 0.0 43.14 3.27 R
4997 6236 3.398954 TTTAACTCGCGCAAATGGATC 57.601 42.857 8.75 0.0 0.00 3.36 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 6.646653 CAGTACGTGGCTGTGATTAATATGAT 59.353 38.462 12.10 0.00 0.00 2.45
29 30 4.686091 CGTGGCTGTGATTAATATGATCGT 59.314 41.667 0.00 0.00 0.00 3.73
30 31 5.164051 CGTGGCTGTGATTAATATGATCGTC 60.164 44.000 0.00 0.00 0.00 4.20
34 35 5.164051 GCTGTGATTAATATGATCGTCGGTG 60.164 44.000 0.00 0.00 0.00 4.94
54 55 2.284276 TGGTTGGCCGGTCGACATA 61.284 57.895 27.34 13.25 37.67 2.29
63 64 2.665185 GTCGACATATGGGGCCGC 60.665 66.667 14.01 14.01 0.00 6.53
102 103 4.353437 GGCGTGTCCGTTCCTCGT 62.353 66.667 0.00 0.00 37.94 4.18
104 105 2.126580 CGTGTCCGTTCCTCGTCC 60.127 66.667 0.00 0.00 37.94 4.79
105 106 2.126580 GTGTCCGTTCCTCGTCCG 60.127 66.667 0.00 0.00 37.94 4.79
106 107 4.047059 TGTCCGTTCCTCGTCCGC 62.047 66.667 0.00 0.00 37.94 5.54
120 121 4.007940 CCGCGTGGACACAAACCG 62.008 66.667 10.20 0.03 37.49 4.44
144 145 4.330894 GGCTCAATTTTAGGCTTGAAATGC 59.669 41.667 0.00 0.00 36.63 3.56
145 146 4.032104 GCTCAATTTTAGGCTTGAAATGCG 59.968 41.667 0.00 0.00 37.98 4.73
146 147 5.132897 TCAATTTTAGGCTTGAAATGCGT 57.867 34.783 0.00 0.00 37.98 5.24
147 148 5.537188 TCAATTTTAGGCTTGAAATGCGTT 58.463 33.333 0.00 0.00 37.98 4.84
148 149 5.633182 TCAATTTTAGGCTTGAAATGCGTTC 59.367 36.000 0.00 0.00 37.98 3.95
149 150 4.576216 TTTTAGGCTTGAAATGCGTTCA 57.424 36.364 0.00 0.00 44.74 3.18
150 151 3.829886 TTAGGCTTGAAATGCGTTCAG 57.170 42.857 0.00 0.00 46.85 3.02
151 152 1.896220 AGGCTTGAAATGCGTTCAGA 58.104 45.000 0.00 0.00 46.85 3.27
152 153 1.537202 AGGCTTGAAATGCGTTCAGAC 59.463 47.619 0.00 0.00 46.85 3.51
153 154 1.266718 GGCTTGAAATGCGTTCAGACA 59.733 47.619 0.00 0.00 46.85 3.41
154 155 2.578495 GCTTGAAATGCGTTCAGACAG 58.422 47.619 0.00 0.00 46.85 3.51
155 156 2.224079 GCTTGAAATGCGTTCAGACAGA 59.776 45.455 0.00 0.00 46.85 3.41
156 157 3.803555 CTTGAAATGCGTTCAGACAGAC 58.196 45.455 0.00 0.00 46.85 3.51
162 163 0.596600 GCGTTCAGACAGACACCGAA 60.597 55.000 0.00 0.00 0.00 4.30
168 169 1.105167 AGACAGACACCGAACGGACA 61.105 55.000 20.14 0.00 38.96 4.02
183 184 1.878948 CGGACACGTTTTGGGTATGGT 60.879 52.381 0.00 0.00 34.81 3.55
184 185 1.808343 GGACACGTTTTGGGTATGGTC 59.192 52.381 0.00 0.00 0.00 4.02
185 186 2.496111 GACACGTTTTGGGTATGGTCA 58.504 47.619 0.00 0.00 0.00 4.02
226 228 0.734942 GTCCGCTTCGATCCAAACGA 60.735 55.000 0.00 0.00 37.99 3.85
227 229 0.038067 TCCGCTTCGATCCAAACGAA 60.038 50.000 0.00 0.00 45.25 3.85
228 230 0.094730 CCGCTTCGATCCAAACGAAC 59.905 55.000 0.00 0.00 43.19 3.95
229 231 0.787787 CGCTTCGATCCAAACGAACA 59.212 50.000 0.00 0.00 43.19 3.18
230 232 1.461888 CGCTTCGATCCAAACGAACAC 60.462 52.381 0.00 0.00 43.19 3.32
231 233 1.529438 GCTTCGATCCAAACGAACACA 59.471 47.619 0.00 0.00 43.19 3.72
232 234 2.661979 GCTTCGATCCAAACGAACACAC 60.662 50.000 0.00 0.00 43.19 3.82
233 235 2.226602 TCGATCCAAACGAACACACA 57.773 45.000 0.00 0.00 36.84 3.72
234 236 1.862201 TCGATCCAAACGAACACACAC 59.138 47.619 0.00 0.00 36.84 3.82
235 237 1.396690 CGATCCAAACGAACACACACG 60.397 52.381 0.00 0.00 0.00 4.49
236 238 0.941542 ATCCAAACGAACACACACGG 59.058 50.000 0.00 0.00 0.00 4.94
237 239 0.108281 TCCAAACGAACACACACGGA 60.108 50.000 0.00 0.00 0.00 4.69
238 240 0.941542 CCAAACGAACACACACGGAT 59.058 50.000 0.00 0.00 0.00 4.18
239 241 2.136728 CCAAACGAACACACACGGATA 58.863 47.619 0.00 0.00 0.00 2.59
270 272 2.364002 GGCTTGTTGAAGTTGCCCTAAA 59.636 45.455 0.00 0.00 37.81 1.85
279 281 2.973945 AGTTGCCCTAAACGAGATCAC 58.026 47.619 0.00 0.00 35.13 3.06
318 350 2.418197 CCGAGAGTCGCCCTTCAAATTA 60.418 50.000 0.00 0.00 38.82 1.40
326 358 4.338400 GTCGCCCTTCAAATTATAGCCTTT 59.662 41.667 0.00 0.00 0.00 3.11
342 374 3.254166 AGCCTTTATCTATGCGCATTTGG 59.746 43.478 30.42 18.38 0.00 3.28
349 381 5.924475 ATCTATGCGCATTTGGTTACTAC 57.076 39.130 30.42 0.00 0.00 2.73
499 1141 4.201851 CGAAAGAACGCATCCAAATCTCAT 60.202 41.667 0.00 0.00 0.00 2.90
572 1215 1.248101 CCATTCCCAAACACCGGACC 61.248 60.000 9.46 0.00 0.00 4.46
578 1221 1.074072 CAAACACCGGACCCATCCA 59.926 57.895 9.46 0.00 46.67 3.41
608 1251 1.067425 CCTCATACAAACGGACGGACA 60.067 52.381 0.00 0.00 0.00 4.02
1111 1846 5.246307 AGAAATCTCGGATTTCGTCCTTTT 58.754 37.500 22.51 9.62 45.46 2.27
1119 1854 2.668144 TTTCGTCCTTTTGTCCCCAT 57.332 45.000 0.00 0.00 0.00 4.00
1166 1901 3.564644 TGACGAGTTTCTTCGACTCTCTT 59.435 43.478 2.12 0.00 43.03 2.85
1169 1904 2.990514 GAGTTTCTTCGACTCTCTTGCC 59.009 50.000 0.00 0.00 40.24 4.52
1188 1923 1.482593 CCGCAGATCTGTTCTAGGGTT 59.517 52.381 23.38 0.00 31.77 4.11
1245 1980 1.261619 CAGGTAATGCGCGAGAAATCC 59.738 52.381 12.10 4.28 0.00 3.01
1299 2034 4.559153 CGCATCCATTTCTTGGTCTTTTT 58.441 39.130 0.00 0.00 46.52 1.94
1301 2036 4.692155 GCATCCATTTCTTGGTCTTTTTGG 59.308 41.667 0.00 0.00 46.52 3.28
1302 2037 4.335400 TCCATTTCTTGGTCTTTTTGGC 57.665 40.909 0.00 0.00 46.52 4.52
1303 2038 3.059166 CCATTTCTTGGTCTTTTTGGCG 58.941 45.455 0.00 0.00 40.99 5.69
1304 2039 3.243704 CCATTTCTTGGTCTTTTTGGCGA 60.244 43.478 0.00 0.00 40.99 5.54
1311 2046 1.067142 GGTCTTTTTGGCGATTTCCCC 60.067 52.381 0.00 0.00 0.00 4.81
1312 2047 1.067142 GTCTTTTTGGCGATTTCCCCC 60.067 52.381 0.00 0.00 0.00 5.40
1313 2048 0.108851 CTTTTTGGCGATTTCCCCCG 60.109 55.000 0.00 0.00 0.00 5.73
1361 2096 1.539776 CTTGGACGTTTTGCGCTTGC 61.540 55.000 9.73 0.00 46.11 4.01
1379 2114 2.998949 GGATTTCCGGGAGCAGGT 59.001 61.111 0.00 0.00 0.00 4.00
1485 2220 5.776173 TTTGAGTTTTCCGCCATTTCTTA 57.224 34.783 0.00 0.00 0.00 2.10
1504 2239 6.467723 TCTTACTCTTTTGATGCGTTTCTC 57.532 37.500 0.00 0.00 0.00 2.87
1857 2592 9.350357 CCAATTTTCTTCAGATCAAGTAATGTG 57.650 33.333 0.00 0.00 0.00 3.21
2251 3015 8.453238 TTTGTGCTACTTCTGTTATGGTTTTA 57.547 30.769 0.00 0.00 0.00 1.52
2592 3528 4.445385 GCTTTATGAACCACTGCTTTGTTG 59.555 41.667 0.00 0.00 0.00 3.33
2708 3644 7.360113 TGTTAGATGAATACTGTCATGCCTA 57.640 36.000 0.00 0.00 38.38 3.93
2787 3723 0.590195 CAATTGCCTATCGGAGCTGC 59.410 55.000 0.00 0.00 0.00 5.25
2806 3742 7.226720 GGAGCTGCTATTTGCTTAGTGTTTATA 59.773 37.037 0.15 0.00 43.37 0.98
2807 3743 8.682936 AGCTGCTATTTGCTTAGTGTTTATAT 57.317 30.769 0.00 0.00 43.37 0.86
2835 3771 3.708121 TGTACTGATGAGTGATGCCTGAT 59.292 43.478 0.00 0.00 33.21 2.90
2836 3772 3.928005 ACTGATGAGTGATGCCTGATT 57.072 42.857 0.00 0.00 0.00 2.57
2837 3773 4.232188 ACTGATGAGTGATGCCTGATTT 57.768 40.909 0.00 0.00 0.00 2.17
2838 3774 3.945921 ACTGATGAGTGATGCCTGATTTG 59.054 43.478 0.00 0.00 0.00 2.32
2839 3775 3.945921 CTGATGAGTGATGCCTGATTTGT 59.054 43.478 0.00 0.00 0.00 2.83
2840 3776 4.338012 TGATGAGTGATGCCTGATTTGTT 58.662 39.130 0.00 0.00 0.00 2.83
2841 3777 5.499313 TGATGAGTGATGCCTGATTTGTTA 58.501 37.500 0.00 0.00 0.00 2.41
2842 3778 5.355071 TGATGAGTGATGCCTGATTTGTTAC 59.645 40.000 0.00 0.00 0.00 2.50
2843 3779 4.650734 TGAGTGATGCCTGATTTGTTACA 58.349 39.130 0.00 0.00 0.00 2.41
2844 3780 5.255687 TGAGTGATGCCTGATTTGTTACAT 58.744 37.500 0.00 0.00 0.00 2.29
2845 3781 6.413892 TGAGTGATGCCTGATTTGTTACATA 58.586 36.000 0.00 0.00 0.00 2.29
2846 3782 7.056006 TGAGTGATGCCTGATTTGTTACATAT 58.944 34.615 0.00 0.00 0.00 1.78
2847 3783 7.012610 TGAGTGATGCCTGATTTGTTACATATG 59.987 37.037 0.00 0.00 0.00 1.78
2848 3784 6.830324 AGTGATGCCTGATTTGTTACATATGT 59.170 34.615 13.93 13.93 0.00 2.29
2849 3785 7.012704 AGTGATGCCTGATTTGTTACATATGTC 59.987 37.037 12.68 0.00 0.00 3.06
2850 3786 7.012704 GTGATGCCTGATTTGTTACATATGTCT 59.987 37.037 12.68 0.00 0.00 3.41
2851 3787 6.682423 TGCCTGATTTGTTACATATGTCTG 57.318 37.500 12.68 0.30 0.00 3.51
2852 3788 6.413892 TGCCTGATTTGTTACATATGTCTGA 58.586 36.000 12.68 0.00 0.00 3.27
2925 3861 9.095065 CACCAGTATTTATTTGTCTACCAGTAC 57.905 37.037 0.00 0.00 0.00 2.73
2935 3871 6.822667 TTGTCTACCAGTACTGTTTATCGA 57.177 37.500 21.18 6.33 0.00 3.59
2939 3875 8.143193 TGTCTACCAGTACTGTTTATCGAAAAA 58.857 33.333 21.18 0.00 0.00 1.94
2940 3876 8.645487 GTCTACCAGTACTGTTTATCGAAAAAG 58.355 37.037 21.18 4.00 36.15 2.27
2943 3879 6.426025 ACCAGTACTGTTTATCGAAAAAGGTC 59.574 38.462 21.18 0.00 34.57 3.85
2944 3880 6.425721 CCAGTACTGTTTATCGAAAAAGGTCA 59.574 38.462 21.18 0.00 34.57 4.02
2945 3881 7.288672 CAGTACTGTTTATCGAAAAAGGTCAC 58.711 38.462 15.06 0.00 34.57 3.67
2946 3882 5.338614 ACTGTTTATCGAAAAAGGTCACG 57.661 39.130 0.00 0.00 34.57 4.35
2947 3883 4.212636 ACTGTTTATCGAAAAAGGTCACGG 59.787 41.667 0.00 0.00 34.57 4.94
2948 3884 3.499157 TGTTTATCGAAAAAGGTCACGGG 59.501 43.478 0.00 0.00 0.00 5.28
2949 3885 3.405823 TTATCGAAAAAGGTCACGGGT 57.594 42.857 0.00 0.00 0.00 5.28
2950 3886 2.265589 ATCGAAAAAGGTCACGGGTT 57.734 45.000 0.00 0.00 0.00 4.11
2951 3887 1.585297 TCGAAAAAGGTCACGGGTTC 58.415 50.000 0.00 0.00 0.00 3.62
2952 3888 1.134461 TCGAAAAAGGTCACGGGTTCA 60.134 47.619 0.00 0.00 0.00 3.18
2953 3889 1.671845 CGAAAAAGGTCACGGGTTCAA 59.328 47.619 0.00 0.00 0.00 2.69
2954 3890 2.286772 CGAAAAAGGTCACGGGTTCAAG 60.287 50.000 0.00 0.00 0.00 3.02
2955 3891 2.430248 AAAAGGTCACGGGTTCAAGT 57.570 45.000 0.00 0.00 0.00 3.16
2956 3892 1.963172 AAAGGTCACGGGTTCAAGTC 58.037 50.000 0.00 0.00 0.00 3.01
2957 3893 0.108019 AAGGTCACGGGTTCAAGTCC 59.892 55.000 0.00 0.00 0.00 3.85
2958 3894 0.763223 AGGTCACGGGTTCAAGTCCT 60.763 55.000 0.00 0.00 0.00 3.85
2959 3895 0.602905 GGTCACGGGTTCAAGTCCTG 60.603 60.000 0.00 0.00 37.36 3.86
2960 3896 0.602905 GTCACGGGTTCAAGTCCTGG 60.603 60.000 0.00 0.00 35.79 4.45
2961 3897 0.761323 TCACGGGTTCAAGTCCTGGA 60.761 55.000 0.00 0.00 35.79 3.86
2962 3898 0.107831 CACGGGTTCAAGTCCTGGAA 59.892 55.000 0.00 0.00 35.79 3.53
2963 3899 0.841289 ACGGGTTCAAGTCCTGGAAA 59.159 50.000 0.00 0.00 35.79 3.13
2964 3900 1.235724 CGGGTTCAAGTCCTGGAAAC 58.764 55.000 0.00 0.00 0.00 2.78
2965 3901 1.476110 CGGGTTCAAGTCCTGGAAACA 60.476 52.381 0.00 0.00 32.36 2.83
2976 3912 3.025924 TGGAAACAGCCTCTTGCAG 57.974 52.632 0.00 0.00 44.83 4.41
2977 3913 0.473755 TGGAAACAGCCTCTTGCAGA 59.526 50.000 0.00 0.00 44.83 4.26
2978 3914 1.133823 TGGAAACAGCCTCTTGCAGAA 60.134 47.619 0.00 0.00 44.83 3.02
2979 3915 1.956477 GGAAACAGCCTCTTGCAGAAA 59.044 47.619 0.00 0.00 44.83 2.52
2980 3916 2.560105 GGAAACAGCCTCTTGCAGAAAT 59.440 45.455 0.00 0.00 44.83 2.17
2981 3917 3.572584 GAAACAGCCTCTTGCAGAAATG 58.427 45.455 0.00 0.00 44.83 2.32
2982 3918 2.283145 ACAGCCTCTTGCAGAAATGT 57.717 45.000 0.00 0.00 44.83 2.71
2983 3919 3.423539 ACAGCCTCTTGCAGAAATGTA 57.576 42.857 0.00 0.00 44.83 2.29
2984 3920 3.341823 ACAGCCTCTTGCAGAAATGTAG 58.658 45.455 0.00 0.00 44.83 2.74
2985 3921 2.681848 CAGCCTCTTGCAGAAATGTAGG 59.318 50.000 0.00 0.00 44.83 3.18
2986 3922 2.019984 GCCTCTTGCAGAAATGTAGGG 58.980 52.381 0.00 0.00 40.77 3.53
2987 3923 2.356125 GCCTCTTGCAGAAATGTAGGGA 60.356 50.000 0.00 0.00 40.77 4.20
2988 3924 3.873801 GCCTCTTGCAGAAATGTAGGGAA 60.874 47.826 0.00 0.00 40.77 3.97
2989 3925 4.335416 CCTCTTGCAGAAATGTAGGGAAA 58.665 43.478 0.00 0.00 0.00 3.13
2990 3926 4.397417 CCTCTTGCAGAAATGTAGGGAAAG 59.603 45.833 0.00 0.00 0.00 2.62
2991 3927 4.335416 TCTTGCAGAAATGTAGGGAAAGG 58.665 43.478 0.00 0.00 0.00 3.11
2992 3928 2.446435 TGCAGAAATGTAGGGAAAGGC 58.554 47.619 0.00 0.00 0.00 4.35
2993 3929 2.041620 TGCAGAAATGTAGGGAAAGGCT 59.958 45.455 0.00 0.00 0.00 4.58
2994 3930 2.424956 GCAGAAATGTAGGGAAAGGCTG 59.575 50.000 0.00 0.00 0.00 4.85
2995 3931 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
2996 3932 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
2997 3933 0.328258 AATGTAGGGAAAGGCTGCGT 59.672 50.000 0.00 0.00 0.00 5.24
2998 3934 1.200519 ATGTAGGGAAAGGCTGCGTA 58.799 50.000 0.00 0.00 0.00 4.42
2999 3935 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.000 0.00 0.00 37.28 3.67
3000 3936 0.248289 GTAGGGAAAGGCTGCGTACA 59.752 55.000 0.00 0.00 36.89 2.90
3001 3937 0.978151 TAGGGAAAGGCTGCGTACAA 59.022 50.000 0.00 0.00 0.00 2.41
3002 3938 0.328258 AGGGAAAGGCTGCGTACAAT 59.672 50.000 0.00 0.00 0.00 2.71
3003 3939 1.557832 AGGGAAAGGCTGCGTACAATA 59.442 47.619 0.00 0.00 0.00 1.90
3004 3940 1.940613 GGGAAAGGCTGCGTACAATAG 59.059 52.381 0.00 0.00 0.00 1.73
3005 3941 2.419574 GGGAAAGGCTGCGTACAATAGA 60.420 50.000 0.00 0.00 0.00 1.98
3006 3942 2.608090 GGAAAGGCTGCGTACAATAGAC 59.392 50.000 0.00 0.00 0.00 2.59
3007 3943 2.311124 AAGGCTGCGTACAATAGACC 57.689 50.000 0.00 0.00 0.00 3.85
3008 3944 0.464452 AGGCTGCGTACAATAGACCC 59.536 55.000 0.00 0.00 0.00 4.46
3009 3945 0.177141 GGCTGCGTACAATAGACCCA 59.823 55.000 0.00 0.00 0.00 4.51
3010 3946 1.406341 GGCTGCGTACAATAGACCCAA 60.406 52.381 0.00 0.00 0.00 4.12
3011 3947 2.352388 GCTGCGTACAATAGACCCAAA 58.648 47.619 0.00 0.00 0.00 3.28
3012 3948 2.351726 GCTGCGTACAATAGACCCAAAG 59.648 50.000 0.00 0.00 0.00 2.77
3013 3949 3.596214 CTGCGTACAATAGACCCAAAGT 58.404 45.455 0.00 0.00 0.00 2.66
3014 3950 3.331150 TGCGTACAATAGACCCAAAGTG 58.669 45.455 0.00 0.00 0.00 3.16
3015 3951 2.676342 GCGTACAATAGACCCAAAGTGG 59.324 50.000 0.00 0.00 37.25 4.00
3016 3952 3.867216 GCGTACAATAGACCCAAAGTGGT 60.867 47.826 0.00 0.00 42.79 4.16
3021 3957 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
3022 3958 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
3023 3959 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
3024 3960 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
3025 3961 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
3026 3962 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
3027 3963 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
3028 3964 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
3029 3965 3.714001 GTGGTCGGACCCTTCCCC 61.714 72.222 23.81 0.00 38.99 4.81
3036 3972 4.735599 GACCCTTCCCCGGACCCT 62.736 72.222 0.73 0.00 0.00 4.34
3063 3999 2.203070 GGAGCTACATGCACCGGG 60.203 66.667 6.32 0.00 42.21 5.73
3064 4000 2.203070 GAGCTACATGCACCGGGG 60.203 66.667 6.32 0.84 45.94 5.73
3065 4001 4.489771 AGCTACATGCACCGGGGC 62.490 66.667 25.59 25.59 45.94 5.80
3066 4002 4.489771 GCTACATGCACCGGGGCT 62.490 66.667 32.18 13.01 42.31 5.19
3067 4003 2.514592 CTACATGCACCGGGGCTG 60.515 66.667 32.18 26.08 34.04 4.85
3068 4004 4.794648 TACATGCACCGGGGCTGC 62.795 66.667 32.18 19.72 35.03 5.25
3074 4010 4.994756 CACCGGGGCTGCCCTTTT 62.995 66.667 34.99 17.53 44.66 2.27
3075 4011 4.233558 ACCGGGGCTGCCCTTTTT 62.234 61.111 34.99 15.74 44.66 1.94
3095 4031 6.973006 TTTTTACTGTTTATCGAAAACCGC 57.027 33.333 15.71 0.00 38.37 5.68
3102 4038 4.083696 TGTTTATCGAAAACCGCTCTTTCC 60.084 41.667 15.71 0.00 38.37 3.13
3107 4043 2.159653 CGAAAACCGCTCTTTCCATCAG 60.160 50.000 0.00 0.00 30.45 2.90
3246 4182 8.556213 TTGATATTACCTGACCAAGTGTAAAC 57.444 34.615 0.00 0.00 30.36 2.01
3337 4273 8.952278 GTAAAACCCACAATGTTGTCTATATGA 58.048 33.333 0.00 0.00 39.91 2.15
3374 4310 9.935241 CATATAGTTTGCATTATCCTCTAGTGT 57.065 33.333 0.00 0.00 0.00 3.55
3407 4343 8.156820 TGTACATTATGCATTATAGCTTGAGGT 58.843 33.333 3.54 0.00 34.99 3.85
3472 4408 4.754372 ATTGATACAATAGCATGCACCG 57.246 40.909 21.98 7.67 0.00 4.94
3488 4424 4.188462 TGCACCGGTTAGATGTCTATTTG 58.812 43.478 2.97 0.00 0.00 2.32
3489 4425 3.002348 GCACCGGTTAGATGTCTATTTGC 59.998 47.826 2.97 0.00 0.00 3.68
3546 4482 8.633075 AATGTTGCATATACAATTAACTGTGC 57.367 30.769 0.00 0.00 0.00 4.57
3631 4567 5.079643 AGCTGGAGTTATTTTGATTGGTGT 58.920 37.500 0.00 0.00 0.00 4.16
3727 4663 5.294552 GTGCTGTTACCACTGAATCCTAATC 59.705 44.000 0.00 0.00 0.00 1.75
3840 4776 4.451774 TCAAATGTTTATTTTGGCAGCAGC 59.548 37.500 0.00 0.00 34.34 5.25
3972 4910 2.331451 GGCAGCAAAGCGAAACGT 59.669 55.556 0.00 0.00 34.64 3.99
4128 5066 2.663075 CCTAGCCAGGCAGAGCACA 61.663 63.158 15.80 0.00 34.35 4.57
4199 5137 2.109799 CCCATCGATCCAGCGCTT 59.890 61.111 7.50 0.00 0.00 4.68
4504 5443 6.421485 AGCATGTTATGATAAGATGGGGATC 58.579 40.000 19.79 6.62 0.00 3.36
4845 6080 7.861176 TTAAGATTCATTTTTGTTGCCGTAC 57.139 32.000 0.00 0.00 0.00 3.67
4924 6159 4.698780 TCTGTTTCTCCATGATTTGAGCAG 59.301 41.667 0.00 0.00 0.00 4.24
4997 6236 4.074970 AGTTTGCCTGTCTTAATCAGTGG 58.925 43.478 0.00 0.00 0.00 4.00
5035 6275 6.633856 AGTTAAAATGCCAGCTCCAATAAAG 58.366 36.000 0.00 0.00 0.00 1.85
5045 6305 7.835682 TGCCAGCTCCAATAAAGCATATATAAT 59.164 33.333 0.00 0.00 42.35 1.28
5106 6366 4.389374 CAAAAGACCCTGAACTGCTTCTA 58.611 43.478 0.00 0.00 0.00 2.10
5124 6884 7.665690 TGCTTCTATTTTTCAAACTGGCATTA 58.334 30.769 0.00 0.00 0.00 1.90
5136 6896 7.754624 TCAAACTGGCATTATCCCTAATGATA 58.245 34.615 9.03 0.00 44.70 2.15
5137 6897 8.224025 TCAAACTGGCATTATCCCTAATGATAA 58.776 33.333 9.03 0.00 44.70 1.75
5173 6933 4.629634 CGTTGTTAGTAGGACATGATGCAA 59.370 41.667 0.00 0.00 0.00 4.08
5225 6985 9.666626 CTAGTAGTACAATCTATTCGTCAAAGG 57.333 37.037 2.52 0.00 0.00 3.11
5226 6986 7.490000 AGTAGTACAATCTATTCGTCAAAGGG 58.510 38.462 2.52 0.00 0.00 3.95
5227 6987 6.540438 AGTACAATCTATTCGTCAAAGGGA 57.460 37.500 0.00 0.00 0.00 4.20
5228 6988 6.574350 AGTACAATCTATTCGTCAAAGGGAG 58.426 40.000 0.00 0.00 0.00 4.30
5229 6989 4.192317 ACAATCTATTCGTCAAAGGGAGC 58.808 43.478 0.00 0.00 0.00 4.70
5230 6990 4.191544 CAATCTATTCGTCAAAGGGAGCA 58.808 43.478 0.00 0.00 0.00 4.26
5232 6992 3.596214 TCTATTCGTCAAAGGGAGCAAC 58.404 45.455 0.00 0.00 0.00 4.17
5233 6993 1.534729 ATTCGTCAAAGGGAGCAACC 58.465 50.000 0.00 0.00 38.08 3.77
5234 6994 0.181587 TTCGTCAAAGGGAGCAACCA 59.818 50.000 0.00 0.00 41.20 3.67
5235 6995 0.250295 TCGTCAAAGGGAGCAACCAG 60.250 55.000 0.00 0.00 41.20 4.00
5236 6996 0.250295 CGTCAAAGGGAGCAACCAGA 60.250 55.000 0.00 0.00 41.20 3.86
5237 6997 1.813862 CGTCAAAGGGAGCAACCAGAA 60.814 52.381 0.00 0.00 41.20 3.02
5238 6998 2.519013 GTCAAAGGGAGCAACCAGAAT 58.481 47.619 0.00 0.00 41.20 2.40
5239 6999 3.686016 GTCAAAGGGAGCAACCAGAATA 58.314 45.455 0.00 0.00 41.20 1.75
5240 7000 3.440522 GTCAAAGGGAGCAACCAGAATAC 59.559 47.826 0.00 0.00 41.20 1.89
5241 7001 2.755103 CAAAGGGAGCAACCAGAATACC 59.245 50.000 0.00 0.00 41.20 2.73
5242 7002 1.668826 AGGGAGCAACCAGAATACCA 58.331 50.000 0.00 0.00 41.20 3.25
5245 7009 2.173569 GGGAGCAACCAGAATACCAGAT 59.826 50.000 2.58 0.00 41.20 2.90
5251 7015 5.132648 AGCAACCAGAATACCAGATCCATAA 59.867 40.000 0.00 0.00 0.00 1.90
5254 7018 4.042187 ACCAGAATACCAGATCCATAAGGC 59.958 45.833 0.00 0.00 33.74 4.35
5258 7022 5.608437 AGAATACCAGATCCATAAGGCTCAA 59.392 40.000 0.00 0.00 32.35 3.02
5260 7024 4.162040 ACCAGATCCATAAGGCTCAAAG 57.838 45.455 0.00 0.00 32.35 2.77
5325 7095 4.785914 TGAGGGTCATTATACAAGTTCCCA 59.214 41.667 0.00 0.00 36.45 4.37
5349 7119 7.118825 CCATTGCAATTGACTCGATATACTCAT 59.881 37.037 9.83 0.00 0.00 2.90
5487 7257 3.973657 ACTTCACAAATGCTTCAAGCTG 58.026 40.909 11.57 3.05 42.97 4.24
5732 7509 2.094649 GGACTACAAGGTCAAGGACTCG 60.095 54.545 0.00 0.00 37.91 4.18
5744 7521 0.629596 AGGACTCGATACCACCTCCA 59.370 55.000 10.00 0.00 0.00 3.86
5745 7522 0.745468 GGACTCGATACCACCTCCAC 59.255 60.000 3.60 0.00 0.00 4.02
5746 7523 1.471119 GACTCGATACCACCTCCACA 58.529 55.000 0.00 0.00 0.00 4.17
5747 7524 1.405821 GACTCGATACCACCTCCACAG 59.594 57.143 0.00 0.00 0.00 3.66
5748 7525 1.272536 ACTCGATACCACCTCCACAGT 60.273 52.381 0.00 0.00 0.00 3.55
5749 7526 1.405821 CTCGATACCACCTCCACAGTC 59.594 57.143 0.00 0.00 0.00 3.51
5750 7527 0.460311 CGATACCACCTCCACAGTCC 59.540 60.000 0.00 0.00 0.00 3.85
5793 7571 0.322008 GTCCAGAGGTGGCCAAGAAG 60.322 60.000 7.24 0.00 44.60 2.85
5826 7605 1.134220 GGAGGGGCATCGTATCAACAA 60.134 52.381 0.00 0.00 0.00 2.83
5859 7638 2.804527 CCATGAGATATGTGTCCAAGCG 59.195 50.000 0.00 0.00 0.00 4.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 5.227152 CACCACCGACGATCATATTAATCA 58.773 41.667 0.00 0.00 0.00 2.57
15 16 4.625742 CCACCACCGACGATCATATTAATC 59.374 45.833 0.00 0.00 0.00 1.75
26 27 4.612412 GCCAACCACCACCGACGA 62.612 66.667 0.00 0.00 0.00 4.20
45 46 2.030562 CGGCCCCATATGTCGACC 59.969 66.667 14.12 0.00 0.00 4.79
46 47 2.665185 GCGGCCCCATATGTCGAC 60.665 66.667 9.11 9.11 0.00 4.20
47 48 4.293648 CGCGGCCCCATATGTCGA 62.294 66.667 0.00 0.00 0.00 4.20
102 103 2.589442 GGTTTGTGTCCACGCGGA 60.589 61.111 12.47 0.00 39.79 5.54
104 105 4.007940 CCGGTTTGTGTCCACGCG 62.008 66.667 3.53 3.53 0.00 6.01
105 106 3.656045 CCCGGTTTGTGTCCACGC 61.656 66.667 0.00 0.00 0.00 5.34
106 107 3.656045 GCCCGGTTTGTGTCCACG 61.656 66.667 0.00 0.00 0.00 4.94
107 108 2.203294 AGCCCGGTTTGTGTCCAC 60.203 61.111 0.00 0.00 0.00 4.02
108 109 2.112297 GAGCCCGGTTTGTGTCCA 59.888 61.111 0.00 0.00 0.00 4.02
109 110 0.893727 ATTGAGCCCGGTTTGTGTCC 60.894 55.000 0.00 0.00 0.00 4.02
113 114 2.560981 CCTAAAATTGAGCCCGGTTTGT 59.439 45.455 0.00 0.00 0.00 2.83
120 121 4.535526 TTTCAAGCCTAAAATTGAGCCC 57.464 40.909 0.00 0.00 36.81 5.19
144 145 1.129326 GTTCGGTGTCTGTCTGAACG 58.871 55.000 0.00 0.00 40.00 3.95
145 146 1.129326 CGTTCGGTGTCTGTCTGAAC 58.871 55.000 7.34 7.34 43.57 3.18
146 147 0.031585 CCGTTCGGTGTCTGTCTGAA 59.968 55.000 2.82 0.00 0.00 3.02
147 148 0.820482 TCCGTTCGGTGTCTGTCTGA 60.820 55.000 11.04 0.00 0.00 3.27
148 149 0.663568 GTCCGTTCGGTGTCTGTCTG 60.664 60.000 11.04 0.00 0.00 3.51
149 150 1.105167 TGTCCGTTCGGTGTCTGTCT 61.105 55.000 11.04 0.00 0.00 3.41
150 151 0.938168 GTGTCCGTTCGGTGTCTGTC 60.938 60.000 11.04 0.00 0.00 3.51
151 152 1.066918 GTGTCCGTTCGGTGTCTGT 59.933 57.895 11.04 0.00 0.00 3.41
152 153 2.014554 CGTGTCCGTTCGGTGTCTG 61.015 63.158 11.04 0.00 0.00 3.51
153 154 2.333938 CGTGTCCGTTCGGTGTCT 59.666 61.111 11.04 0.00 0.00 3.41
168 169 1.530323 GCTGACCATACCCAAAACGT 58.470 50.000 0.00 0.00 0.00 3.99
202 204 1.885560 TGGATCGAAGCGGACAAAAA 58.114 45.000 0.00 0.00 0.00 1.94
226 228 2.158726 ACCCAACTTATCCGTGTGTGTT 60.159 45.455 0.00 0.00 0.00 3.32
227 229 1.418637 ACCCAACTTATCCGTGTGTGT 59.581 47.619 0.00 0.00 0.00 3.72
228 230 2.073816 GACCCAACTTATCCGTGTGTG 58.926 52.381 0.00 0.00 0.00 3.82
229 231 1.337447 CGACCCAACTTATCCGTGTGT 60.337 52.381 0.00 0.00 0.00 3.72
230 232 1.355971 CGACCCAACTTATCCGTGTG 58.644 55.000 0.00 0.00 0.00 3.82
231 233 0.248289 CCGACCCAACTTATCCGTGT 59.752 55.000 0.00 0.00 0.00 4.49
232 234 1.087771 GCCGACCCAACTTATCCGTG 61.088 60.000 0.00 0.00 0.00 4.94
233 235 1.219935 GCCGACCCAACTTATCCGT 59.780 57.895 0.00 0.00 0.00 4.69
234 236 0.107848 AAGCCGACCCAACTTATCCG 60.108 55.000 0.00 0.00 0.00 4.18
235 237 1.339727 ACAAGCCGACCCAACTTATCC 60.340 52.381 0.00 0.00 0.00 2.59
236 238 2.109425 ACAAGCCGACCCAACTTATC 57.891 50.000 0.00 0.00 0.00 1.75
237 239 2.159382 CAACAAGCCGACCCAACTTAT 58.841 47.619 0.00 0.00 0.00 1.73
238 240 1.141254 TCAACAAGCCGACCCAACTTA 59.859 47.619 0.00 0.00 0.00 2.24
239 241 0.106918 TCAACAAGCCGACCCAACTT 60.107 50.000 0.00 0.00 0.00 2.66
270 272 1.374252 GGCAACCGTGTGATCTCGT 60.374 57.895 0.00 0.00 0.00 4.18
318 350 5.124457 CCAAATGCGCATAGATAAAGGCTAT 59.876 40.000 25.61 0.00 0.00 2.97
326 358 6.755206 AGTAGTAACCAAATGCGCATAGATA 58.245 36.000 25.61 11.62 0.00 1.98
472 1114 0.251916 TGGATGCGTTCTTTCGGGAT 59.748 50.000 0.00 0.00 0.00 3.85
572 1215 4.489771 GGTGGACGGGCTGGATGG 62.490 72.222 0.00 0.00 0.00 3.51
578 1221 0.907704 TTGTATGAGGTGGACGGGCT 60.908 55.000 0.00 0.00 0.00 5.19
608 1251 0.107993 CTGTGGACCATGTCGCATCT 60.108 55.000 0.00 0.00 32.65 2.90
1085 1820 4.045783 GGACGAAATCCGAGATTTCTCTC 58.954 47.826 24.33 19.84 43.86 3.20
1086 1821 4.048241 GGACGAAATCCGAGATTTCTCT 57.952 45.455 24.33 15.53 40.75 3.10
1098 1833 2.510613 TGGGGACAAAAGGACGAAATC 58.489 47.619 0.00 0.00 37.44 2.17
1166 1901 0.461548 CCTAGAACAGATCTGCGGCA 59.538 55.000 22.83 1.29 39.30 5.69
1169 1904 2.544685 CAACCCTAGAACAGATCTGCG 58.455 52.381 22.83 0.00 39.30 5.18
1245 1980 2.723273 GAAGACCACCAATAACCCCAG 58.277 52.381 0.00 0.00 0.00 4.45
1302 2037 0.823356 AATGGATGCGGGGGAAATCG 60.823 55.000 0.00 0.00 0.00 3.34
1303 2038 1.341209 GAAATGGATGCGGGGGAAATC 59.659 52.381 0.00 0.00 0.00 2.17
1304 2039 1.062962 AGAAATGGATGCGGGGGAAAT 60.063 47.619 0.00 0.00 0.00 2.17
1379 2114 3.071167 TCGTATCTCGAGATCCTTCCAGA 59.929 47.826 30.49 16.41 44.01 3.86
1410 2145 3.777522 TCTCTTCTTCCCTGGATCTTTCC 59.222 47.826 0.00 0.00 42.94 3.13
1485 2220 2.480419 CCGAGAAACGCATCAAAAGAGT 59.520 45.455 0.00 0.00 41.07 3.24
1571 2306 0.247736 CCGTCCTCTTGAGTTCCCTG 59.752 60.000 0.00 0.00 0.00 4.45
1857 2592 3.637998 TCAACTACTCACGTCAGAACC 57.362 47.619 0.00 0.00 0.00 3.62
2326 3165 7.496346 AACTTGGTGTGAATAAGATCCTCTA 57.504 36.000 0.00 0.00 0.00 2.43
2552 3488 2.399916 AGCACAAGAAGATCCTCTGC 57.600 50.000 0.00 0.00 0.00 4.26
2571 3507 5.105554 ACACAACAAAGCAGTGGTTCATAAA 60.106 36.000 8.24 0.00 37.58 1.40
2654 3590 6.038714 CACTTGATATAGGGAAGCAGGAAAAC 59.961 42.308 0.00 0.00 0.00 2.43
2708 3644 7.352739 CACTCGAAAATAACTGCACTTTAAGT 58.647 34.615 0.00 0.00 0.00 2.24
2749 3685 8.938906 GGCAATTGATATGTGTTTCTTTTGATT 58.061 29.630 10.34 0.00 0.00 2.57
2806 3742 5.587844 GCATCACTCATCAGTACAGGAAAAT 59.412 40.000 0.00 0.00 0.00 1.82
2807 3743 4.937620 GCATCACTCATCAGTACAGGAAAA 59.062 41.667 0.00 0.00 0.00 2.29
2837 3773 9.971922 CTGAATCATACTCAGACATATGTAACA 57.028 33.333 8.71 0.00 42.51 2.41
2838 3774 9.973450 ACTGAATCATACTCAGACATATGTAAC 57.027 33.333 8.71 0.00 42.51 2.50
2901 3837 9.314321 CAGTACTGGTAGACAAATAAATACTGG 57.686 37.037 15.49 0.00 34.69 4.00
2925 3861 4.378046 CCCGTGACCTTTTTCGATAAACAG 60.378 45.833 0.00 0.00 0.00 3.16
2935 3871 2.686405 GACTTGAACCCGTGACCTTTTT 59.314 45.455 0.00 0.00 0.00 1.94
2939 3875 0.763223 AGGACTTGAACCCGTGACCT 60.763 55.000 0.00 0.00 0.00 3.85
2940 3876 0.602905 CAGGACTTGAACCCGTGACC 60.603 60.000 0.00 0.00 0.00 4.02
2943 3879 0.107831 TTCCAGGACTTGAACCCGTG 59.892 55.000 0.00 0.00 0.00 4.94
2944 3880 0.841289 TTTCCAGGACTTGAACCCGT 59.159 50.000 0.00 0.00 0.00 5.28
2945 3881 1.235724 GTTTCCAGGACTTGAACCCG 58.764 55.000 0.00 0.00 0.00 5.28
2946 3882 2.230660 CTGTTTCCAGGACTTGAACCC 58.769 52.381 0.00 0.00 34.90 4.11
2947 3883 1.609072 GCTGTTTCCAGGACTTGAACC 59.391 52.381 0.00 0.00 39.22 3.62
2948 3884 1.609072 GGCTGTTTCCAGGACTTGAAC 59.391 52.381 0.00 0.00 39.22 3.18
2949 3885 1.494721 AGGCTGTTTCCAGGACTTGAA 59.505 47.619 0.00 0.00 39.22 2.69
2950 3886 1.072331 GAGGCTGTTTCCAGGACTTGA 59.928 52.381 0.00 0.00 39.22 3.02
2951 3887 1.072965 AGAGGCTGTTTCCAGGACTTG 59.927 52.381 0.00 0.00 39.22 3.16
2952 3888 1.439543 AGAGGCTGTTTCCAGGACTT 58.560 50.000 0.00 0.00 39.22 3.01
2953 3889 1.072965 CAAGAGGCTGTTTCCAGGACT 59.927 52.381 0.00 0.00 39.22 3.85
2954 3890 1.528129 CAAGAGGCTGTTTCCAGGAC 58.472 55.000 0.00 0.00 39.22 3.85
2955 3891 0.250901 GCAAGAGGCTGTTTCCAGGA 60.251 55.000 0.00 0.00 39.22 3.86
2956 3892 0.538057 TGCAAGAGGCTGTTTCCAGG 60.538 55.000 0.00 0.00 45.15 4.45
2957 3893 0.879765 CTGCAAGAGGCTGTTTCCAG 59.120 55.000 0.00 0.00 45.15 3.86
2958 3894 0.473755 TCTGCAAGAGGCTGTTTCCA 59.526 50.000 0.00 0.00 38.67 3.53
2959 3895 3.329300 TCTGCAAGAGGCTGTTTCC 57.671 52.632 0.00 0.00 38.67 3.13
2969 3905 4.335416 CCTTTCCCTACATTTCTGCAAGA 58.665 43.478 0.00 0.00 44.68 3.02
2970 3906 3.119352 GCCTTTCCCTACATTTCTGCAAG 60.119 47.826 0.00 0.00 0.00 4.01
2971 3907 2.825532 GCCTTTCCCTACATTTCTGCAA 59.174 45.455 0.00 0.00 0.00 4.08
2972 3908 2.041620 AGCCTTTCCCTACATTTCTGCA 59.958 45.455 0.00 0.00 0.00 4.41
2973 3909 2.424956 CAGCCTTTCCCTACATTTCTGC 59.575 50.000 0.00 0.00 0.00 4.26
2974 3910 2.424956 GCAGCCTTTCCCTACATTTCTG 59.575 50.000 0.00 0.00 0.00 3.02
2975 3911 2.728007 GCAGCCTTTCCCTACATTTCT 58.272 47.619 0.00 0.00 0.00 2.52
2976 3912 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
2977 3913 1.271926 ACGCAGCCTTTCCCTACATTT 60.272 47.619 0.00 0.00 0.00 2.32
2978 3914 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
2979 3915 1.134491 GTACGCAGCCTTTCCCTACAT 60.134 52.381 0.00 0.00 0.00 2.29
2980 3916 0.248289 GTACGCAGCCTTTCCCTACA 59.752 55.000 0.00 0.00 0.00 2.74
2981 3917 0.248289 TGTACGCAGCCTTTCCCTAC 59.752 55.000 0.00 0.00 0.00 3.18
2982 3918 0.978151 TTGTACGCAGCCTTTCCCTA 59.022 50.000 0.00 0.00 0.00 3.53
2983 3919 0.328258 ATTGTACGCAGCCTTTCCCT 59.672 50.000 0.00 0.00 0.00 4.20
2984 3920 1.940613 CTATTGTACGCAGCCTTTCCC 59.059 52.381 0.00 0.00 0.00 3.97
2985 3921 2.608090 GTCTATTGTACGCAGCCTTTCC 59.392 50.000 0.00 0.00 0.00 3.13
2986 3922 2.608090 GGTCTATTGTACGCAGCCTTTC 59.392 50.000 0.00 0.00 0.00 2.62
2987 3923 2.629051 GGTCTATTGTACGCAGCCTTT 58.371 47.619 0.00 0.00 0.00 3.11
2988 3924 1.134491 GGGTCTATTGTACGCAGCCTT 60.134 52.381 0.00 0.00 0.00 4.35
2989 3925 0.464452 GGGTCTATTGTACGCAGCCT 59.536 55.000 0.00 0.00 0.00 4.58
2990 3926 0.177141 TGGGTCTATTGTACGCAGCC 59.823 55.000 0.00 0.00 35.18 4.85
2991 3927 2.018542 TTGGGTCTATTGTACGCAGC 57.981 50.000 0.00 0.00 40.36 5.25
2992 3928 3.370978 CACTTTGGGTCTATTGTACGCAG 59.629 47.826 0.00 0.00 40.36 5.18
2993 3929 3.331150 CACTTTGGGTCTATTGTACGCA 58.669 45.455 0.00 0.00 37.94 5.24
2994 3930 2.676342 CCACTTTGGGTCTATTGTACGC 59.324 50.000 0.00 0.00 32.67 4.42
2995 3931 3.934068 ACCACTTTGGGTCTATTGTACG 58.066 45.455 0.00 0.00 43.37 3.67
3005 3941 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
3006 3942 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
3007 3943 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
3008 3944 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
3009 3945 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
3010 3946 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
3011 3947 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
3012 3948 3.714001 GGGGAAGGGTCCGACCAC 61.714 72.222 19.43 8.70 46.04 4.16
3019 3955 4.735599 AGGGTCCGGGGAAGGGTC 62.736 72.222 0.00 0.00 0.00 4.46
3035 3971 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
3038 3974 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
3039 3975 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
3040 3976 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
3041 3977 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
3047 3983 2.203070 CCCCGGTGCATGTAGCTC 60.203 66.667 11.25 0.00 45.94 4.09
3048 3984 4.489771 GCCCCGGTGCATGTAGCT 62.490 66.667 3.18 0.00 45.94 3.32
3049 3985 4.489771 AGCCCCGGTGCATGTAGC 62.490 66.667 12.68 2.56 45.96 3.58
3050 3986 2.514592 CAGCCCCGGTGCATGTAG 60.515 66.667 12.68 0.00 0.00 2.74
3072 4008 6.727215 AGCGGTTTTCGATAAACAGTAAAAA 58.273 32.000 18.39 0.00 42.43 1.94
3073 4009 6.203338 AGAGCGGTTTTCGATAAACAGTAAAA 59.797 34.615 18.39 0.00 42.43 1.52
3074 4010 5.697633 AGAGCGGTTTTCGATAAACAGTAAA 59.302 36.000 18.39 0.00 42.43 2.01
3075 4011 5.232463 AGAGCGGTTTTCGATAAACAGTAA 58.768 37.500 18.39 0.00 42.43 2.24
3076 4012 4.813027 AGAGCGGTTTTCGATAAACAGTA 58.187 39.130 18.39 0.00 42.43 2.74
3077 4013 3.660865 AGAGCGGTTTTCGATAAACAGT 58.339 40.909 18.39 9.71 42.43 3.55
3078 4014 4.663636 AAGAGCGGTTTTCGATAAACAG 57.336 40.909 18.39 16.28 42.43 3.16
3079 4015 4.083696 GGAAAGAGCGGTTTTCGATAAACA 60.084 41.667 18.39 0.00 42.43 2.83
3080 4016 4.083696 TGGAAAGAGCGGTTTTCGATAAAC 60.084 41.667 12.10 12.10 42.43 2.01
3081 4017 4.066490 TGGAAAGAGCGGTTTTCGATAAA 58.934 39.130 12.67 0.00 42.43 1.40
3082 4018 3.666274 TGGAAAGAGCGGTTTTCGATAA 58.334 40.909 12.67 0.00 42.43 1.75
3083 4019 3.322211 TGGAAAGAGCGGTTTTCGATA 57.678 42.857 12.67 0.00 42.43 2.92
3084 4020 2.178912 TGGAAAGAGCGGTTTTCGAT 57.821 45.000 12.67 0.00 42.43 3.59
3085 4021 2.073816 GATGGAAAGAGCGGTTTTCGA 58.926 47.619 12.67 10.62 42.43 3.71
3086 4022 1.804151 TGATGGAAAGAGCGGTTTTCG 59.196 47.619 12.67 0.00 42.76 3.46
3087 4023 2.414691 GCTGATGGAAAGAGCGGTTTTC 60.415 50.000 11.38 11.38 34.55 2.29
3088 4024 1.541588 GCTGATGGAAAGAGCGGTTTT 59.458 47.619 0.00 0.00 0.00 2.43
3089 4025 1.168714 GCTGATGGAAAGAGCGGTTT 58.831 50.000 0.00 0.00 0.00 3.27
3090 4026 0.036732 TGCTGATGGAAAGAGCGGTT 59.963 50.000 0.00 0.00 35.36 4.44
3091 4027 0.392193 CTGCTGATGGAAAGAGCGGT 60.392 55.000 0.00 0.00 34.87 5.68
3092 4028 0.392193 ACTGCTGATGGAAAGAGCGG 60.392 55.000 0.00 0.00 43.53 5.52
3093 4029 1.446907 AACTGCTGATGGAAAGAGCG 58.553 50.000 0.00 0.00 35.36 5.03
3094 4030 4.006319 AGTTAACTGCTGATGGAAAGAGC 58.994 43.478 7.48 0.00 0.00 4.09
3095 4031 5.121454 GTCAGTTAACTGCTGATGGAAAGAG 59.879 44.000 27.49 2.45 43.73 2.85
3102 4038 5.233225 TCTGAAGTCAGTTAACTGCTGATG 58.767 41.667 27.49 18.69 43.73 3.07
3146 4082 6.158598 GGTATGCTTGAACAAAACATCACAT 58.841 36.000 6.16 0.00 0.00 3.21
3148 4084 5.527951 TGGTATGCTTGAACAAAACATCAC 58.472 37.500 6.16 3.37 0.00 3.06
3180 4116 4.479158 AGGAAAATAGCCCAAAAGTGTGA 58.521 39.130 0.00 0.00 0.00 3.58
3370 4306 4.943093 TGCATAATGTACAGCATGAACACT 59.057 37.500 18.82 0.00 39.69 3.55
3374 4310 8.453320 GCTATAATGCATAATGTACAGCATGAA 58.547 33.333 17.93 10.83 46.10 2.57
3472 4408 8.568794 GGGATTTTAGCAAATAGACATCTAACC 58.431 37.037 0.00 0.00 32.35 2.85
3528 4464 8.777413 ACATGCTAGCACAGTTAATTGTATATG 58.223 33.333 22.07 10.78 0.00 1.78
3578 4514 3.581024 ATCATTTGAGCAACACGCAAT 57.419 38.095 0.00 0.00 46.13 3.56
3727 4663 7.118390 GCAGAGGTAGGCATATATGTTTTGTAG 59.882 40.741 14.14 0.00 0.00 2.74
3972 4910 0.391661 GGTTGCGGAGATTGCTCAGA 60.392 55.000 0.00 0.00 43.14 3.27
4128 5066 3.526534 GCGAAGAATAGACCTTGAAGCT 58.473 45.455 0.00 0.00 0.00 3.74
4199 5137 4.224594 AGTTTCTTCTCCATGAGATCAGCA 59.775 41.667 0.00 0.00 38.56 4.41
4768 5710 6.749118 GCCATAGCTAAACAGAAACATTTGAG 59.251 38.462 0.00 0.00 35.50 3.02
4924 6159 4.414337 AAGAATATGAGTGACCTCCAGC 57.586 45.455 0.00 0.00 36.86 4.85
4997 6236 3.398954 TTTAACTCGCGCAAATGGATC 57.601 42.857 8.75 0.00 0.00 3.36
5045 6305 5.362717 TCCTTCGAGCTATATCTTTGACCAA 59.637 40.000 0.00 0.00 0.00 3.67
5106 6366 6.625532 AGGGATAATGCCAGTTTGAAAAAT 57.374 33.333 0.00 0.00 0.00 1.82
5124 6884 6.950041 CCATGGTTCATGTTATCATTAGGGAT 59.050 38.462 2.57 0.00 39.94 3.85
5136 6896 1.327303 ACAACGCCATGGTTCATGTT 58.673 45.000 14.67 7.98 39.94 2.71
5137 6897 1.327303 AACAACGCCATGGTTCATGT 58.673 45.000 14.67 10.81 39.94 3.21
5225 6985 3.471680 GATCTGGTATTCTGGTTGCTCC 58.528 50.000 0.00 0.00 0.00 4.70
5226 6986 3.118261 TGGATCTGGTATTCTGGTTGCTC 60.118 47.826 0.00 0.00 0.00 4.26
5227 6987 2.846206 TGGATCTGGTATTCTGGTTGCT 59.154 45.455 0.00 0.00 0.00 3.91
5228 6988 3.281727 TGGATCTGGTATTCTGGTTGC 57.718 47.619 0.00 0.00 0.00 4.17
5229 6989 6.000219 CCTTATGGATCTGGTATTCTGGTTG 59.000 44.000 0.00 0.00 34.57 3.77
5230 6990 5.456763 GCCTTATGGATCTGGTATTCTGGTT 60.457 44.000 0.00 0.00 34.57 3.67
5232 6992 4.288105 AGCCTTATGGATCTGGTATTCTGG 59.712 45.833 0.00 0.00 34.57 3.86
5233 6993 5.486526 GAGCCTTATGGATCTGGTATTCTG 58.513 45.833 5.69 0.00 44.81 3.02
5234 6994 5.753721 GAGCCTTATGGATCTGGTATTCT 57.246 43.478 5.69 0.00 44.81 2.40
5245 7009 4.072131 GTCAACACTTTGAGCCTTATGGA 58.928 43.478 0.00 0.00 42.60 3.41
5251 7015 2.887152 GGAATGTCAACACTTTGAGCCT 59.113 45.455 0.00 0.00 42.60 4.58
5325 7095 8.093307 AGATGAGTATATCGAGTCAATTGCAAT 58.907 33.333 5.99 5.99 32.58 3.56
5501 7271 1.134521 TGCTGTTGTCGACTTGTCCTT 60.135 47.619 17.92 0.00 0.00 3.36
5503 7273 1.261619 CTTGCTGTTGTCGACTTGTCC 59.738 52.381 17.92 3.30 0.00 4.02
5535 7305 2.024176 TGTTACCAGCAAGAGGAGGA 57.976 50.000 0.00 0.00 0.00 3.71
5596 7373 4.072131 TCTTCTTTGGTTGTATGTGGCTC 58.928 43.478 0.00 0.00 0.00 4.70
5665 7442 1.418908 ATGGAAGGCGAGGGGTATGG 61.419 60.000 0.00 0.00 0.00 2.74
5732 7509 1.207329 GTGGACTGTGGAGGTGGTATC 59.793 57.143 0.00 0.00 0.00 2.24
5744 7521 0.178992 CCCAATGGTGTGTGGACTGT 60.179 55.000 0.00 0.00 37.03 3.55
5745 7522 0.110295 TCCCAATGGTGTGTGGACTG 59.890 55.000 0.00 0.00 37.03 3.51
5746 7523 0.401738 CTCCCAATGGTGTGTGGACT 59.598 55.000 0.00 0.00 37.03 3.85
5747 7524 1.244019 GCTCCCAATGGTGTGTGGAC 61.244 60.000 0.00 0.00 37.03 4.02
5748 7525 1.074775 GCTCCCAATGGTGTGTGGA 59.925 57.895 0.00 0.00 37.03 4.02
5749 7526 0.827089 TTGCTCCCAATGGTGTGTGG 60.827 55.000 0.00 0.00 34.44 4.17
5750 7527 1.259609 ATTGCTCCCAATGGTGTGTG 58.740 50.000 0.00 0.00 40.09 3.82
5826 7605 5.190528 ACATATCTCATGGTTCTGGACAACT 59.809 40.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.