Multiple sequence alignment - TraesCS4A01G169700

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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 TraesCS4A01G169700 chr4A 100.000 6156 0 0 1881 8036 428159321 428153166 0.000000e+00 11369.0
1 TraesCS4A01G169700 chr4A 100.000 1573 0 0 1 1573 428161201 428159629 0.000000e+00 2905.0
2 TraesCS4A01G169700 chr4A 94.340 53 3 0 7984 8036 428147470 428147418 1.860000e-11 82.4
3 TraesCS4A01G169700 chr4D 95.687 5008 138 22 3021 7983 133475408 133480382 0.000000e+00 7980.0
4 TraesCS4A01G169700 chr4D 96.856 1145 31 1 1881 3020 133474185 133475329 0.000000e+00 1910.0
5 TraesCS4A01G169700 chr4D 91.081 953 46 10 310 1232 133472820 133473763 0.000000e+00 1253.0
6 TraesCS4A01G169700 chr4D 94.643 280 11 2 1 276 133472540 133472819 1.600000e-116 431.0
7 TraesCS4A01G169700 chr4D 87.903 248 7 11 1312 1537 133473760 133474006 3.700000e-68 270.0
8 TraesCS4A01G169700 chr4D 92.188 64 4 1 7974 8036 168177692 168177629 1.110000e-13 89.8
9 TraesCS4A01G169700 chr4D 100.000 38 0 0 1536 1573 133474095 133474132 4.020000e-08 71.3
10 TraesCS4A01G169700 chr4B 97.104 4385 106 11 1881 6249 161557621 161553242 0.000000e+00 7374.0
11 TraesCS4A01G169700 chr4B 95.233 1741 67 6 6248 7983 161553160 161551431 0.000000e+00 2741.0
12 TraesCS4A01G169700 chr4B 92.010 1239 58 13 1 1227 161559173 161557964 0.000000e+00 1701.0
13 TraesCS4A01G169700 chr4B 87.847 288 7 2 1314 1573 161557960 161557673 6.050000e-81 313.0
14 TraesCS4A01G169700 chr4B 92.929 99 6 1 1226 1323 621712365 621712463 8.410000e-30 143.0
15 TraesCS4A01G169700 chr4B 92.157 51 4 0 7984 8034 8374231 8374281 1.120000e-08 73.1
16 TraesCS4A01G169700 chr6D 94.102 746 18 9 3361 4084 58841025 58840284 0.000000e+00 1110.0
17 TraesCS4A01G169700 chr6D 94.444 180 10 0 1 180 58841366 58841187 2.210000e-70 278.0
18 TraesCS4A01G169700 chr6D 96.226 53 2 0 1902 1954 411980998 411980946 4.000000e-13 87.9
19 TraesCS4A01G169700 chr6A 94.414 734 18 8 3371 4082 74823406 74822674 0.000000e+00 1107.0
20 TraesCS4A01G169700 chr6A 92.571 175 13 0 1 175 74887733 74887559 1.340000e-62 252.0
21 TraesCS4A01G169700 chr6A 92.157 51 3 1 7983 8032 10057856 10057906 4.020000e-08 71.3
22 TraesCS4A01G169700 chr6B 92.876 379 16 3 3706 4084 132412150 132411783 2.550000e-149 540.0
23 TraesCS4A01G169700 chr6B 92.790 319 5 5 3419 3719 132412736 132412418 5.720000e-121 446.0
24 TraesCS4A01G169700 chr6B 91.209 91 8 0 2080 2170 687209250 687209160 3.050000e-24 124.0
25 TraesCS4A01G169700 chr6B 94.000 50 3 0 7984 8033 655153798 655153749 8.650000e-10 76.8
26 TraesCS4A01G169700 chr7A 85.833 360 43 6 4529 4886 64130765 64130412 7.610000e-100 375.0
27 TraesCS4A01G169700 chr7A 91.837 98 8 0 5518 5615 64129346 64129249 3.910000e-28 137.0
28 TraesCS4A01G169700 chr5A 74.969 807 160 34 5039 5822 129113454 129112667 4.650000e-87 333.0
29 TraesCS4A01G169700 chr5A 95.745 94 3 1 1223 1315 526875407 526875314 5.020000e-32 150.0
30 TraesCS4A01G169700 chr5B 74.751 804 167 29 5039 5822 131320937 131320150 2.160000e-85 327.0
31 TraesCS4A01G169700 chr5B 93.069 101 5 2 1229 1329 52308847 52308749 6.500000e-31 147.0
32 TraesCS4A01G169700 chr5B 92.233 103 7 1 1228 1329 62940408 62940306 2.340000e-30 145.0
33 TraesCS4A01G169700 chr5D 76.789 517 106 9 5312 5822 119006726 119006218 2.210000e-70 278.0
34 TraesCS4A01G169700 chr5D 96.078 51 2 0 7984 8034 518965417 518965467 5.170000e-12 84.2
35 TraesCS4A01G169700 chr1A 91.503 153 9 3 2020 2169 281893616 281893767 2.940000e-49 207.0
36 TraesCS4A01G169700 chr1A 92.857 98 5 2 1218 1314 5651207 5651111 3.020000e-29 141.0
37 TraesCS4A01G169700 chr7D 89.610 154 12 3 2020 2170 24847967 24847815 8.230000e-45 193.0
38 TraesCS4A01G169700 chr7D 96.000 50 2 0 2351 2400 433731723 433731772 1.860000e-11 82.4
39 TraesCS4A01G169700 chr2A 83.957 187 26 2 5433 5615 38616925 38616739 8.290000e-40 176.0
40 TraesCS4A01G169700 chr2A 92.308 104 8 0 1213 1316 632953009 632952906 1.810000e-31 148.0
41 TraesCS4A01G169700 chr3D 90.769 130 12 0 2351 2480 85843161 85843290 2.980000e-39 174.0
42 TraesCS4A01G169700 chr3D 96.226 53 2 0 7982 8034 599485450 599485502 4.000000e-13 87.9
43 TraesCS4A01G169700 chr3B 90.769 130 12 0 2351 2480 136060937 136061066 2.980000e-39 174.0
44 TraesCS4A01G169700 chr3B 93.137 102 5 1 1230 1329 62308067 62307966 1.810000e-31 148.0
45 TraesCS4A01G169700 chr3B 92.308 91 7 0 2080 2170 657600116 657600026 6.540000e-26 130.0
46 TraesCS4A01G169700 chr3B 96.364 55 1 1 7673 7727 809597501 809597554 1.110000e-13 89.8
47 TraesCS4A01G169700 chr7B 93.069 101 5 2 1229 1329 107127399 107127497 6.500000e-31 147.0
48 TraesCS4A01G169700 chr2D 92.233 103 5 2 1229 1331 106348907 106348808 8.410000e-30 143.0
49 TraesCS4A01G169700 chr1D 94.340 53 3 0 1902 1954 380543517 380543465 1.860000e-11 82.4
50 TraesCS4A01G169700 chr1B 94.595 37 2 0 1902 1938 565679208 565679172 3.130000e-04 58.4


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 TraesCS4A01G169700 chr4A 428153166 428161201 8035 True 7137.000000 11369 100.000000 1 8036 2 chr4A.!!$R2 8035
1 TraesCS4A01G169700 chr4D 133472540 133480382 7842 False 1985.883333 7980 94.361667 1 7983 6 chr4D.!!$F1 7982
2 TraesCS4A01G169700 chr4B 161551431 161559173 7742 True 3032.250000 7374 93.048500 1 7983 4 chr4B.!!$R1 7982
3 TraesCS4A01G169700 chr6D 58840284 58841366 1082 True 694.000000 1110 94.273000 1 4084 2 chr6D.!!$R2 4083
4 TraesCS4A01G169700 chr6A 74822674 74823406 732 True 1107.000000 1107 94.414000 3371 4082 1 chr6A.!!$R1 711
5 TraesCS4A01G169700 chr6B 132411783 132412736 953 True 493.000000 540 92.833000 3419 4084 2 chr6B.!!$R3 665
6 TraesCS4A01G169700 chr7A 64129249 64130765 1516 True 256.000000 375 88.835000 4529 5615 2 chr7A.!!$R1 1086
7 TraesCS4A01G169700 chr5A 129112667 129113454 787 True 333.000000 333 74.969000 5039 5822 1 chr5A.!!$R1 783
8 TraesCS4A01G169700 chr5B 131320150 131320937 787 True 327.000000 327 74.751000 5039 5822 1 chr5B.!!$R3 783
9 TraesCS4A01G169700 chr5D 119006218 119006726 508 True 278.000000 278 76.789000 5312 5822 1 chr5D.!!$R1 510

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
779 785 1.143073 GGAGTCCACACCCTCAAAGTT 59.857 52.381 3.60 0.0 0.00 2.66 F
1435 1470 0.740149 TTGTGCTCAAACAGTGGCAG 59.260 50.000 0.00 0.0 35.09 4.85 F
2225 2383 0.602905 AGAACCTTGCCGAAGAACCG 60.603 55.000 0.00 0.0 0.00 4.44 F
2333 2491 1.200020 GTTGCATTCGTCCCCTTCAAG 59.800 52.381 0.00 0.0 0.00 3.02 F
3797 4336 0.973632 TGCTGGTGAACGGTGATAGT 59.026 50.000 0.00 0.0 0.00 2.12 F
4281 4821 0.898320 AGACTCATCCTTCGTGGTGG 59.102 55.000 0.00 0.0 37.07 4.61 F
4284 4824 1.909302 ACTCATCCTTCGTGGTGGAAT 59.091 47.619 0.00 0.0 35.81 3.01 F
5356 5969 2.505819 AGGGCGAGATTTAACATCAGGT 59.494 45.455 0.00 0.0 0.00 4.00 F
6662 7852 1.202463 AGGATTCAGATGACGGCGAAG 60.202 52.381 16.62 0.0 0.00 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2225 2383 0.466124 CCCGGAATTCCTCCTCAGAC 59.534 60.000 22.05 0.00 42.85 3.51 R
3083 3319 4.565166 TGAAGTAATCTACAACCGCGAATG 59.435 41.667 8.23 8.83 0.00 2.67 R
3775 4314 0.179032 ATCACCGTTCACCAGCACAA 60.179 50.000 0.00 0.00 0.00 3.33 R
4266 4806 1.678728 GCATTCCACCACGAAGGATGA 60.679 52.381 5.70 0.00 41.22 2.92 R
5356 5969 1.254975 TGCAGCCTCTTAGCACGGTA 61.255 55.000 0.00 0.00 32.55 4.02 R
6044 7148 1.963985 AGACATCCAGCTTCTTCCCT 58.036 50.000 0.00 0.00 0.00 4.20 R
6191 7295 4.114794 CACCAAACTTTCAGGCAAAGAAG 58.885 43.478 4.51 0.00 44.02 2.85 R
6744 7934 0.038801 GGCCTTCTTTGCAACTGAGC 60.039 55.000 0.00 1.70 0.00 4.26 R
7696 8887 0.529992 GTTTCGCAGCGCTATACCCT 60.530 55.000 10.99 0.00 0.00 4.34 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
108 109 3.712187 TGGAAAGAAAATTGCCACGTTC 58.288 40.909 0.00 0.00 0.00 3.95
162 167 2.484264 GGCACAACTCGTAGCAAAGATT 59.516 45.455 0.00 0.00 0.00 2.40
164 169 3.722082 GCACAACTCGTAGCAAAGATTCG 60.722 47.826 0.00 0.00 0.00 3.34
322 327 3.188254 CCGTGCATGACTTGTTTATGTCA 59.812 43.478 7.72 0.00 42.79 3.58
328 333 6.148645 TGCATGACTTGTTTATGTCACGTAAT 59.851 34.615 0.00 0.00 41.84 1.89
389 394 5.163468 ACAAAGATACACAACCAACATTGCA 60.163 36.000 0.00 0.00 32.47 4.08
397 402 6.572519 ACACAACCAACATTGCATATATTCC 58.427 36.000 0.00 0.00 32.47 3.01
399 404 5.592282 ACAACCAACATTGCATATATTCCGA 59.408 36.000 0.00 0.00 32.47 4.55
499 504 5.307196 ACACCTAGCCAAATCTCGGTAATAT 59.693 40.000 0.00 0.00 31.75 1.28
502 507 6.495872 ACCTAGCCAAATCTCGGTAATATACA 59.504 38.462 0.00 0.00 31.26 2.29
503 508 7.036220 CCTAGCCAAATCTCGGTAATATACAG 58.964 42.308 0.00 0.00 0.00 2.74
533 538 3.566523 CTGAAGTTTCGCTCGAGTTAGT 58.433 45.455 15.13 0.00 0.00 2.24
536 541 4.208460 TGAAGTTTCGCTCGAGTTAGTTTG 59.792 41.667 15.13 0.00 0.00 2.93
557 562 2.500504 GGAGTTCCCGTCTACCAATCTT 59.499 50.000 0.00 0.00 0.00 2.40
561 566 4.070009 GTTCCCGTCTACCAATCTTTGTT 58.930 43.478 0.00 0.00 0.00 2.83
603 608 4.285863 TCCCAAAATCTTTATTCCGGCAT 58.714 39.130 0.00 0.00 0.00 4.40
606 611 5.418676 CCAAAATCTTTATTCCGGCATTGT 58.581 37.500 0.00 0.00 0.00 2.71
612 617 5.649557 TCTTTATTCCGGCATTGTGAAATG 58.350 37.500 0.00 0.00 0.00 2.32
779 785 1.143073 GGAGTCCACACCCTCAAAGTT 59.857 52.381 3.60 0.00 0.00 2.66
876 888 1.348036 ACCGTTTGGAGGAGAAGGAAG 59.652 52.381 0.00 0.00 39.21 3.46
930 942 2.202878 CAATCCACCCGCGATCGT 60.203 61.111 17.81 0.00 0.00 3.73
1051 1081 1.888436 GACAGCCATCGTGGAGGACA 61.888 60.000 8.04 0.00 40.96 4.02
1072 1102 1.299648 CTGAGGATGCACGGGGAAA 59.700 57.895 0.00 0.00 0.00 3.13
1098 1128 2.768769 GGAGGAGGGGGTGTAGGC 60.769 72.222 0.00 0.00 0.00 3.93
1205 1240 6.887002 CCCTTCTTCATTAGGGGCTTATAATC 59.113 42.308 0.00 0.00 46.21 1.75
1235 1270 4.884668 TTCGTGAAATCTTGTACTCCCT 57.115 40.909 0.00 0.00 0.00 4.20
1236 1271 4.451629 TCGTGAAATCTTGTACTCCCTC 57.548 45.455 0.00 0.00 0.00 4.30
1237 1272 4.087182 TCGTGAAATCTTGTACTCCCTCT 58.913 43.478 0.00 0.00 0.00 3.69
1238 1273 4.082190 TCGTGAAATCTTGTACTCCCTCTG 60.082 45.833 0.00 0.00 0.00 3.35
1239 1274 4.322049 CGTGAAATCTTGTACTCCCTCTGT 60.322 45.833 0.00 0.00 0.00 3.41
1240 1275 5.105877 CGTGAAATCTTGTACTCCCTCTGTA 60.106 44.000 0.00 0.00 0.00 2.74
1241 1276 6.571731 CGTGAAATCTTGTACTCCCTCTGTAA 60.572 42.308 0.00 0.00 0.00 2.41
1242 1277 7.159372 GTGAAATCTTGTACTCCCTCTGTAAA 58.841 38.462 0.00 0.00 0.00 2.01
1243 1278 7.117956 GTGAAATCTTGTACTCCCTCTGTAAAC 59.882 40.741 0.00 0.00 0.00 2.01
1244 1279 6.681729 AATCTTGTACTCCCTCTGTAAACA 57.318 37.500 0.00 0.00 0.00 2.83
1245 1280 6.681729 ATCTTGTACTCCCTCTGTAAACAA 57.318 37.500 0.00 0.00 0.00 2.83
1246 1281 6.488769 TCTTGTACTCCCTCTGTAAACAAA 57.511 37.500 0.00 0.00 0.00 2.83
1247 1282 7.074653 TCTTGTACTCCCTCTGTAAACAAAT 57.925 36.000 0.00 0.00 0.00 2.32
1248 1283 8.197592 TCTTGTACTCCCTCTGTAAACAAATA 57.802 34.615 0.00 0.00 0.00 1.40
1249 1284 8.822805 TCTTGTACTCCCTCTGTAAACAAATAT 58.177 33.333 0.00 0.00 0.00 1.28
1255 1290 7.988028 ACTCCCTCTGTAAACAAATATAAGAGC 59.012 37.037 0.00 0.00 0.00 4.09
1256 1291 6.984474 TCCCTCTGTAAACAAATATAAGAGCG 59.016 38.462 0.00 0.00 0.00 5.03
1257 1292 6.761714 CCCTCTGTAAACAAATATAAGAGCGT 59.238 38.462 0.00 0.00 0.00 5.07
1258 1293 7.280205 CCCTCTGTAAACAAATATAAGAGCGTT 59.720 37.037 0.00 0.00 0.00 4.84
1259 1294 8.665685 CCTCTGTAAACAAATATAAGAGCGTTT 58.334 33.333 0.00 0.00 0.00 3.60
1267 1302 9.601217 AACAAATATAAGAGCGTTTAGATCACT 57.399 29.630 0.00 0.00 37.82 3.41
1274 1309 9.953697 ATAAGAGCGTTTAGATCACTAAAGTAG 57.046 33.333 0.00 0.00 45.42 2.57
1275 1310 7.393841 AGAGCGTTTAGATCACTAAAGTAGT 57.606 36.000 0.00 0.00 45.42 2.73
1289 1324 7.393841 ACTAAAGTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 37.69 4.09
1290 1325 7.828712 ACTAAAGTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 37.69 2.85
1291 1326 8.954350 ACTAAAGTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 37.69 2.10
1292 1327 9.953697 CTAAAGTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 0.00 1.73
1307 1342 8.608844 AACGCTCTTATATTTCTTTATGGAGG 57.391 34.615 0.00 0.00 0.00 4.30
1308 1343 7.162082 ACGCTCTTATATTTCTTTATGGAGGG 58.838 38.462 0.00 0.00 35.06 4.30
1309 1344 7.016268 ACGCTCTTATATTTCTTTATGGAGGGA 59.984 37.037 0.00 0.00 34.22 4.20
1310 1345 7.547370 CGCTCTTATATTTCTTTATGGAGGGAG 59.453 40.741 0.00 0.00 33.23 4.30
1338 1373 2.658285 TGATTGATGATGCTTGGACCC 58.342 47.619 0.00 0.00 0.00 4.46
1432 1467 4.614535 GCTTAGATTGTGCTCAAACAGTGG 60.615 45.833 5.15 0.00 37.11 4.00
1435 1470 0.740149 TTGTGCTCAAACAGTGGCAG 59.260 50.000 0.00 0.00 35.09 4.85
1505 1568 5.215160 GTTCAGCACAACGAATTCATCTTT 58.785 37.500 6.22 0.00 0.00 2.52
1954 2107 5.948758 TGATCTAGCTGTACCATCTATCCAG 59.051 44.000 0.00 0.00 0.00 3.86
2004 2157 6.092748 AGTCAACAAAGTGTTCAATGTGTTC 58.907 36.000 5.94 0.00 38.77 3.18
2087 2245 2.347697 TCTACAGCTAACGCAGTGTG 57.652 50.000 1.11 1.11 45.00 3.82
2097 2255 2.716828 CGCAGTGTGGTCGCTAACG 61.717 63.158 0.00 0.00 42.01 3.18
2225 2383 0.602905 AGAACCTTGCCGAAGAACCG 60.603 55.000 0.00 0.00 0.00 4.44
2333 2491 1.200020 GTTGCATTCGTCCCCTTCAAG 59.800 52.381 0.00 0.00 0.00 3.02
2706 2864 4.698276 CCACAGTGAACTTAACGAATTCG 58.302 43.478 25.64 25.64 46.33 3.34
2986 3144 1.878953 ACCCGCTGAAACAGTAAGTG 58.121 50.000 0.00 0.00 33.43 3.16
3003 3161 7.119846 ACAGTAAGTGCCTATTCATTCAAAGAC 59.880 37.037 0.00 0.00 0.00 3.01
3040 3276 7.228314 ACTCTATATATTTGCGGCTCTTACA 57.772 36.000 0.00 0.00 0.00 2.41
3091 3327 8.775220 TGAAATTATATTTGTTACATTCGCGG 57.225 30.769 6.13 0.00 0.00 6.46
3196 3432 8.613482 GTGAGCCTACTGGATAATTTACTTTTC 58.387 37.037 0.00 0.00 34.57 2.29
3341 3577 9.072375 TGTTTTGGTATGTTCACATATTTCAGA 57.928 29.630 3.00 0.00 40.53 3.27
3450 3690 7.701539 ATAGATCCTAATGACAGTAGCTCAG 57.298 40.000 4.37 0.00 0.00 3.35
3454 3694 6.641169 TCCTAATGACAGTAGCTCAGTATG 57.359 41.667 4.37 0.00 37.54 2.39
3533 3791 7.880160 TCATGGGAAGGTATCTATTTTGTTG 57.120 36.000 0.00 0.00 0.00 3.33
3775 4314 1.188219 ACGGGAGATGTCAGTGCTGT 61.188 55.000 0.00 0.00 0.00 4.40
3797 4336 0.973632 TGCTGGTGAACGGTGATAGT 59.026 50.000 0.00 0.00 0.00 2.12
3809 4348 2.159627 CGGTGATAGTGTGGCAAAAGAC 59.840 50.000 0.00 0.00 0.00 3.01
3820 4359 2.557924 TGGCAAAAGACATACAGGCAAG 59.442 45.455 0.00 0.00 0.00 4.01
3867 4407 8.934023 ACAAAAGAAACAGATCCAGGTATTTA 57.066 30.769 0.00 0.00 0.00 1.40
4266 4806 3.262660 TGAGGTCTTCATGATTGCAGACT 59.737 43.478 19.66 9.72 43.22 3.24
4281 4821 0.898320 AGACTCATCCTTCGTGGTGG 59.102 55.000 0.00 0.00 37.07 4.61
4284 4824 1.909302 ACTCATCCTTCGTGGTGGAAT 59.091 47.619 0.00 0.00 35.81 3.01
4295 4835 2.741553 CGTGGTGGAATGCTGCATACTA 60.742 50.000 16.58 5.77 0.00 1.82
4304 4844 6.707608 TGGAATGCTGCATACTAATACTTCAG 59.292 38.462 16.58 0.00 0.00 3.02
4385 4925 5.048846 TGGAAAAGTAAGTTCCTCAAGCT 57.951 39.130 4.92 0.00 44.24 3.74
4577 5117 3.327626 TGGCAATCAAAATGACATGCAC 58.672 40.909 16.79 9.86 41.56 4.57
4778 5320 7.436118 ACAATATTTTTGTGATGTTGCAGAGT 58.564 30.769 0.00 0.00 31.27 3.24
4968 5510 4.159135 ACAAGAAATATCCTTTGCTGCTGG 59.841 41.667 0.00 0.80 0.00 4.85
5176 5719 6.897706 TGTGGTTGATTTGATGAATCTTGA 57.102 33.333 1.09 0.00 43.74 3.02
5180 5723 7.487189 GTGGTTGATTTGATGAATCTTGATCAC 59.513 37.037 0.00 0.00 43.74 3.06
5240 5785 3.143211 AGTAGTCGCTCCCATAGGTAG 57.857 52.381 0.00 0.00 0.00 3.18
5253 5798 5.652014 TCCCATAGGTAGTGCTTGATTTTTG 59.348 40.000 0.00 0.00 0.00 2.44
5356 5969 2.505819 AGGGCGAGATTTAACATCAGGT 59.494 45.455 0.00 0.00 0.00 4.00
5359 5972 3.808174 GGCGAGATTTAACATCAGGTACC 59.192 47.826 2.73 2.73 0.00 3.34
5548 6648 4.901868 ACCGGAATAGCAAACTTACTCAA 58.098 39.130 9.46 0.00 0.00 3.02
5813 6917 4.244862 GAGGAGAAGTCAAAGAGCTCAAG 58.755 47.826 17.77 5.07 0.00 3.02
5845 6949 7.147602 GGTTAATTTAGTTACCAGCCTCCTCTA 60.148 40.741 0.00 0.00 0.00 2.43
6117 7221 8.412456 TCATAGCACAACTTTTTCTTGATCAAA 58.588 29.630 9.88 0.00 0.00 2.69
6118 7222 9.033481 CATAGCACAACTTTTTCTTGATCAAAA 57.967 29.630 9.88 4.50 0.00 2.44
6122 7226 9.002080 GCACAACTTTTTCTTGATCAAAATTTG 57.998 29.630 9.88 12.75 37.98 2.32
6169 7273 7.563924 AGTTCTAACTAGCCACAGATACCATTA 59.436 37.037 0.00 0.00 37.52 1.90
6191 7295 9.729023 CATTAGACTCATATACTCGGATGATTC 57.271 37.037 0.00 0.00 33.93 2.52
6424 7611 7.246674 TGTAATATGGAAGAATCGAAGCAAC 57.753 36.000 0.00 0.00 0.00 4.17
6662 7852 1.202463 AGGATTCAGATGACGGCGAAG 60.202 52.381 16.62 0.00 0.00 3.79
6924 8114 3.268330 GAAAAGGACATCTCCGTTACCC 58.732 50.000 0.00 0.00 42.22 3.69
7054 8244 6.115448 AGTAAGCAATACATATGGGAGGAC 57.885 41.667 7.80 0.00 36.94 3.85
7256 8446 6.485984 CCATTAGTGCAAATAGAGAAGATGCT 59.514 38.462 0.00 0.00 37.86 3.79
7289 8479 4.645762 TGAGGTCGAGAGAAATGATCAG 57.354 45.455 0.09 0.00 45.01 2.90
7416 8606 5.423015 ACTTGTAATCATGAGCGATGTTCT 58.577 37.500 0.09 0.00 33.29 3.01
7462 8652 4.479156 TGGGTATTTCAACCTTTTCCCT 57.521 40.909 0.00 0.00 39.65 4.20
7540 8731 3.385755 CCCCTGAGGCATTTGGAATTAAG 59.614 47.826 0.00 0.00 0.00 1.85
7542 8733 4.098501 CCCTGAGGCATTTGGAATTAAGAC 59.901 45.833 0.00 0.00 0.00 3.01
7608 8799 6.038271 GGAATCGGTGTATCTTTTTATGCACT 59.962 38.462 0.00 0.00 40.88 4.40
7652 8843 2.665165 TCACCAGCCACACTTGATTTT 58.335 42.857 0.00 0.00 0.00 1.82
7656 8847 2.624838 CCAGCCACACTTGATTTTCACT 59.375 45.455 0.00 0.00 0.00 3.41
7682 8873 1.156736 AAGAACAACGAATGGAGGCG 58.843 50.000 0.00 0.00 0.00 5.52
7696 8887 6.018588 CGAATGGAGGCGTGTATATTTTACAA 60.019 38.462 0.00 0.00 0.00 2.41
7727 8918 2.668279 GCTGCGAAACGACAATCCAATT 60.668 45.455 0.00 0.00 0.00 2.32
7728 8919 2.910482 CTGCGAAACGACAATCCAATTG 59.090 45.455 0.00 0.00 45.59 2.32
7812 9004 7.271511 ACAAAACAAGGCATACAATGAAGAAA 58.728 30.769 0.00 0.00 0.00 2.52
7872 9064 4.400251 CCATGCATACAAAACATCTCCAGT 59.600 41.667 0.00 0.00 0.00 4.00
7930 9122 4.142381 GGAGTTAGGCCATAAAAACTGCTG 60.142 45.833 5.01 0.00 37.33 4.41
7932 9124 0.527565 AGGCCATAAAAACTGCTGCG 59.472 50.000 5.01 0.00 0.00 5.18
7936 9128 2.584791 CCATAAAAACTGCTGCGACAC 58.415 47.619 0.00 0.00 0.00 3.67
7949 9141 1.965219 CGACACGTCCTCTTTCCCT 59.035 57.895 0.00 0.00 0.00 4.20
7983 9175 0.179089 GACGTCTGCAGATGATGGCT 60.179 55.000 36.58 17.96 35.16 4.75
7984 9176 0.461516 ACGTCTGCAGATGATGGCTG 60.462 55.000 36.58 14.20 35.16 4.85
7985 9177 0.461516 CGTCTGCAGATGATGGCTGT 60.462 55.000 28.61 0.00 35.81 4.40
7986 9178 1.202452 CGTCTGCAGATGATGGCTGTA 60.202 52.381 28.61 0.00 35.81 2.74
7987 9179 2.481854 GTCTGCAGATGATGGCTGTAG 58.518 52.381 21.47 0.00 44.30 2.74
7988 9180 2.904697 CTGCAGATGATGGCTGTAGA 57.095 50.000 8.42 0.00 45.31 2.59
7989 9181 2.970640 TCTGCAGATGATGGCTGTAGAT 59.029 45.455 13.74 0.00 45.79 1.98
7990 9182 4.154942 TCTGCAGATGATGGCTGTAGATA 58.845 43.478 13.74 0.00 45.79 1.98
7991 9183 4.220163 TCTGCAGATGATGGCTGTAGATAG 59.780 45.833 13.74 0.00 45.79 2.08
7992 9184 4.154942 TGCAGATGATGGCTGTAGATAGA 58.845 43.478 0.00 0.00 35.81 1.98
7993 9185 4.776308 TGCAGATGATGGCTGTAGATAGAT 59.224 41.667 0.00 0.00 35.81 1.98
7994 9186 5.954150 TGCAGATGATGGCTGTAGATAGATA 59.046 40.000 0.00 0.00 35.81 1.98
7995 9187 6.438425 TGCAGATGATGGCTGTAGATAGATAA 59.562 38.462 0.00 0.00 35.81 1.75
7996 9188 7.125356 TGCAGATGATGGCTGTAGATAGATAAT 59.875 37.037 0.00 0.00 35.81 1.28
7997 9189 7.986320 GCAGATGATGGCTGTAGATAGATAATT 59.014 37.037 0.00 0.00 35.81 1.40
7998 9190 9.887629 CAGATGATGGCTGTAGATAGATAATTT 57.112 33.333 0.00 0.00 0.00 1.82
7999 9191 9.887629 AGATGATGGCTGTAGATAGATAATTTG 57.112 33.333 0.00 0.00 0.00 2.32
8000 9192 7.912056 TGATGGCTGTAGATAGATAATTTGC 57.088 36.000 0.00 0.00 0.00 3.68
8001 9193 7.452562 TGATGGCTGTAGATAGATAATTTGCA 58.547 34.615 0.00 0.00 0.00 4.08
8002 9194 7.938490 TGATGGCTGTAGATAGATAATTTGCAA 59.062 33.333 0.00 0.00 0.00 4.08
8003 9195 8.874744 ATGGCTGTAGATAGATAATTTGCAAT 57.125 30.769 0.00 0.00 0.00 3.56
8004 9196 9.964354 ATGGCTGTAGATAGATAATTTGCAATA 57.036 29.630 0.00 0.00 0.00 1.90
8005 9197 9.219603 TGGCTGTAGATAGATAATTTGCAATAC 57.780 33.333 0.00 0.00 0.00 1.89
8006 9198 8.383619 GGCTGTAGATAGATAATTTGCAATACG 58.616 37.037 0.00 0.00 0.00 3.06
8007 9199 9.140286 GCTGTAGATAGATAATTTGCAATACGA 57.860 33.333 0.00 0.00 0.00 3.43
8022 9214 8.846943 TTGCAATACGATATATTGATTGAGGT 57.153 30.769 19.18 0.00 37.15 3.85
8023 9215 8.255394 TGCAATACGATATATTGATTGAGGTG 57.745 34.615 19.18 6.69 37.15 4.00
8024 9216 7.148423 TGCAATACGATATATTGATTGAGGTGC 60.148 37.037 19.18 13.06 37.15 5.01
8025 9217 7.065085 GCAATACGATATATTGATTGAGGTGCT 59.935 37.037 19.18 0.00 37.15 4.40
8026 9218 8.385858 CAATACGATATATTGATTGAGGTGCTG 58.614 37.037 6.98 0.00 37.15 4.41
8027 9219 5.240891 ACGATATATTGATTGAGGTGCTGG 58.759 41.667 6.98 0.00 0.00 4.85
8028 9220 5.221722 ACGATATATTGATTGAGGTGCTGGT 60.222 40.000 6.98 0.00 0.00 4.00
8029 9221 5.121298 CGATATATTGATTGAGGTGCTGGTG 59.879 44.000 0.00 0.00 0.00 4.17
8030 9222 1.180029 ATTGATTGAGGTGCTGGTGC 58.820 50.000 0.00 0.00 40.20 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
108 109 2.489938 TCGTTTGGATTGAGAAGGGG 57.510 50.000 0.00 0.00 0.00 4.79
162 167 8.585881 TCCCATCAAAAATAAAAATACCAACGA 58.414 29.630 0.00 0.00 0.00 3.85
184 189 1.002069 AGCACCAATGGATCTTCCCA 58.998 50.000 6.16 0.00 41.05 4.37
280 285 4.023707 ACGGAAAGAGCACAATGAAGAAAG 60.024 41.667 0.00 0.00 0.00 2.62
328 333 0.612732 ATGTGGTACCCCGAGAACGA 60.613 55.000 10.07 0.00 42.66 3.85
375 380 5.592282 TCGGAATATATGCAATGTTGGTTGT 59.408 36.000 0.00 0.00 0.00 3.32
414 419 4.876107 GTGTCCCGTGTCTCAAATGATATT 59.124 41.667 0.00 0.00 0.00 1.28
499 504 4.448210 GAAACTTCAGGGTGTGTTCTGTA 58.552 43.478 0.00 0.00 33.13 2.74
502 507 2.561569 CGAAACTTCAGGGTGTGTTCT 58.438 47.619 0.00 0.00 0.00 3.01
503 508 1.002792 GCGAAACTTCAGGGTGTGTTC 60.003 52.381 0.00 0.00 0.00 3.18
533 538 1.719529 TGGTAGACGGGAACTCCAAA 58.280 50.000 0.00 0.00 37.91 3.28
536 541 2.108970 AGATTGGTAGACGGGAACTCC 58.891 52.381 0.00 0.00 0.00 3.85
557 562 5.821516 AATGTGTGGACTTAAACGAACAA 57.178 34.783 0.00 0.00 0.00 2.83
561 566 4.276431 GGGAAAATGTGTGGACTTAAACGA 59.724 41.667 0.00 0.00 0.00 3.85
606 611 6.537660 TCAATCAAAATGTGTTGTGCATTTCA 59.462 30.769 0.00 0.00 43.30 2.69
612 617 6.528014 TGAATCAATCAAAATGTGTTGTGC 57.472 33.333 0.00 0.00 34.30 4.57
651 656 5.430007 TCGTTTGGGAAAACAAGAGTAGAA 58.570 37.500 2.62 0.00 33.08 2.10
779 785 2.310647 GGTGGGGAGTGGAAATAGGAAA 59.689 50.000 0.00 0.00 0.00 3.13
820 826 0.396556 AGCGGGTTGGTGTTTTCCTT 60.397 50.000 0.00 0.00 0.00 3.36
859 871 2.705730 GCTCTTCCTTCTCCTCCAAAC 58.294 52.381 0.00 0.00 0.00 2.93
876 888 2.762043 AAGAGGAGAGGGGCGCTC 60.762 66.667 22.73 22.73 0.00 5.03
913 925 2.202878 ACGATCGCGGGTGGATTG 60.203 61.111 16.60 0.00 43.17 2.67
1051 1081 2.191375 CCCGTGCATCCTCAGCAT 59.809 61.111 0.00 0.00 44.79 3.79
1072 1102 1.690148 CCCCCTCCTCCCCCTAATCT 61.690 65.000 0.00 0.00 0.00 2.40
1098 1128 1.746615 CCCCATCACCAGCACTTCG 60.747 63.158 0.00 0.00 0.00 3.79
1162 1192 1.339535 GGGAAGGAGCCAAGAGAACAG 60.340 57.143 0.00 0.00 0.00 3.16
1229 1264 7.988028 GCTCTTATATTTGTTTACAGAGGGAGT 59.012 37.037 0.00 0.00 0.00 3.85
1230 1265 7.169982 CGCTCTTATATTTGTTTACAGAGGGAG 59.830 40.741 4.76 0.00 36.40 4.30
1231 1266 6.984474 CGCTCTTATATTTGTTTACAGAGGGA 59.016 38.462 4.76 0.00 36.40 4.20
1232 1267 6.761714 ACGCTCTTATATTTGTTTACAGAGGG 59.238 38.462 8.36 8.36 38.95 4.30
1233 1268 7.772332 ACGCTCTTATATTTGTTTACAGAGG 57.228 36.000 0.00 0.00 0.00 3.69
1241 1276 9.601217 AGTGATCTAAACGCTCTTATATTTGTT 57.399 29.630 0.00 0.00 0.00 2.83
1248 1283 9.953697 CTACTTTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 40.05 1.73
1249 1284 8.954350 ACTACTTTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 40.05 2.10
1250 1285 7.828712 ACTACTTTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 40.05 2.85
1251 1286 7.393841 ACTACTTTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 40.05 4.09
1265 1300 7.393841 AGAGCGTTTAGATCACTACTTTAGT 57.606 36.000 0.00 0.00 37.82 2.24
1266 1301 9.953697 ATAAGAGCGTTTAGATCACTACTTTAG 57.046 33.333 0.00 0.00 37.82 1.85
1281 1316 9.057089 CCTCCATAAAGAAATATAAGAGCGTTT 57.943 33.333 0.00 0.00 0.00 3.60
1282 1317 7.661847 CCCTCCATAAAGAAATATAAGAGCGTT 59.338 37.037 0.00 0.00 0.00 4.84
1283 1318 7.016268 TCCCTCCATAAAGAAATATAAGAGCGT 59.984 37.037 0.00 0.00 0.00 5.07
1284 1319 7.386851 TCCCTCCATAAAGAAATATAAGAGCG 58.613 38.462 0.00 0.00 0.00 5.03
1285 1320 8.379331 ACTCCCTCCATAAAGAAATATAAGAGC 58.621 37.037 0.00 0.00 0.00 4.09
1291 1326 9.900112 ACTAGTACTCCCTCCATAAAGAAATAT 57.100 33.333 0.00 0.00 0.00 1.28
1292 1327 9.725206 AACTAGTACTCCCTCCATAAAGAAATA 57.275 33.333 0.00 0.00 0.00 1.40
1293 1328 8.487028 CAACTAGTACTCCCTCCATAAAGAAAT 58.513 37.037 0.00 0.00 0.00 2.17
1294 1329 7.676893 TCAACTAGTACTCCCTCCATAAAGAAA 59.323 37.037 0.00 0.00 0.00 2.52
1295 1330 7.186972 TCAACTAGTACTCCCTCCATAAAGAA 58.813 38.462 0.00 0.00 0.00 2.52
1296 1331 6.738635 TCAACTAGTACTCCCTCCATAAAGA 58.261 40.000 0.00 0.00 0.00 2.52
1297 1332 7.604657 ATCAACTAGTACTCCCTCCATAAAG 57.395 40.000 0.00 0.00 0.00 1.85
1298 1333 7.622081 TCAATCAACTAGTACTCCCTCCATAAA 59.378 37.037 0.00 0.00 0.00 1.40
1299 1334 7.130099 TCAATCAACTAGTACTCCCTCCATAA 58.870 38.462 0.00 0.00 0.00 1.90
1300 1335 6.679542 TCAATCAACTAGTACTCCCTCCATA 58.320 40.000 0.00 0.00 0.00 2.74
1301 1336 5.529289 TCAATCAACTAGTACTCCCTCCAT 58.471 41.667 0.00 0.00 0.00 3.41
1302 1337 4.942944 TCAATCAACTAGTACTCCCTCCA 58.057 43.478 0.00 0.00 0.00 3.86
1303 1338 5.598830 TCATCAATCAACTAGTACTCCCTCC 59.401 44.000 0.00 0.00 0.00 4.30
1304 1339 6.716934 TCATCAATCAACTAGTACTCCCTC 57.283 41.667 0.00 0.00 0.00 4.30
1305 1340 6.463614 GCATCATCAATCAACTAGTACTCCCT 60.464 42.308 0.00 0.00 0.00 4.20
1306 1341 5.698545 GCATCATCAATCAACTAGTACTCCC 59.301 44.000 0.00 0.00 0.00 4.30
1307 1342 6.520272 AGCATCATCAATCAACTAGTACTCC 58.480 40.000 0.00 0.00 0.00 3.85
1308 1343 7.042187 CCAAGCATCATCAATCAACTAGTACTC 60.042 40.741 0.00 0.00 0.00 2.59
1309 1344 6.765036 CCAAGCATCATCAATCAACTAGTACT 59.235 38.462 0.00 0.00 0.00 2.73
1310 1345 6.763135 TCCAAGCATCATCAATCAACTAGTAC 59.237 38.462 0.00 0.00 0.00 2.73
1338 1373 1.553248 TCCTTGGTTGAGATGTACCCG 59.447 52.381 0.00 0.00 33.34 5.28
1368 1403 5.370679 ACACTAAACGTATGGACCAAAAGT 58.629 37.500 0.00 0.00 0.00 2.66
1374 1409 6.549912 AAGAAAACACTAAACGTATGGACC 57.450 37.500 0.00 0.00 0.00 4.46
1432 1467 2.690778 CGGCTAAAGGTGTGGCTGC 61.691 63.158 0.00 0.00 0.00 5.25
1435 1470 0.676782 ATGTCGGCTAAAGGTGTGGC 60.677 55.000 0.00 0.00 0.00 5.01
1954 2107 9.820229 TTAATGAGATTACATTTTGTCGTCAAC 57.180 29.630 0.00 0.00 40.36 3.18
2087 2245 3.489785 CCAATTCAGATACGTTAGCGACC 59.510 47.826 5.81 0.00 42.00 4.79
2097 2255 7.599998 AGCACAATTTTCAACCAATTCAGATAC 59.400 33.333 0.00 0.00 0.00 2.24
2225 2383 0.466124 CCCGGAATTCCTCCTCAGAC 59.534 60.000 22.05 0.00 42.85 3.51
2706 2864 7.040494 GTCCACCCTATAGTTGAGTTTAAGAC 58.960 42.308 0.00 0.00 0.00 3.01
2986 3144 8.443953 ACTATTCTGTCTTTGAATGAATAGGC 57.556 34.615 18.87 0.00 44.99 3.93
3083 3319 4.565166 TGAAGTAATCTACAACCGCGAATG 59.435 41.667 8.23 8.83 0.00 2.67
3091 3327 7.548097 TGATGGAGTCTGAAGTAATCTACAAC 58.452 38.462 0.00 0.00 0.00 3.32
3341 3577 6.205464 CACAACTACAAGGTCATCAGAACAAT 59.795 38.462 0.00 0.00 32.39 2.71
3450 3690 7.598869 TGTGTCTGATGACTCTGTTTTACATAC 59.401 37.037 0.00 0.00 43.29 2.39
3454 3694 5.177696 GGTGTGTCTGATGACTCTGTTTTAC 59.822 44.000 0.00 0.00 43.29 2.01
3775 4314 0.179032 ATCACCGTTCACCAGCACAA 60.179 50.000 0.00 0.00 0.00 3.33
3797 4336 1.885887 GCCTGTATGTCTTTTGCCACA 59.114 47.619 0.00 0.00 0.00 4.17
3809 4348 2.936919 TATCTGCCCTTGCCTGTATG 57.063 50.000 0.00 0.00 36.33 2.39
3820 4359 5.997746 TGTAGCTCAAAATGTATATCTGCCC 59.002 40.000 0.00 0.00 0.00 5.36
4266 4806 1.678728 GCATTCCACCACGAAGGATGA 60.679 52.381 5.70 0.00 41.22 2.92
4281 4821 7.721286 ACTGAAGTATTAGTATGCAGCATTC 57.279 36.000 14.58 8.76 0.00 2.67
4284 4824 6.878923 ACAAACTGAAGTATTAGTATGCAGCA 59.121 34.615 0.00 0.00 0.00 4.41
4295 4835 6.039382 GGTGACAAAGGACAAACTGAAGTATT 59.961 38.462 0.00 0.00 0.00 1.89
4304 4844 1.681264 CCCTGGTGACAAAGGACAAAC 59.319 52.381 5.23 0.00 42.06 2.93
4369 4909 4.130118 CAACACAGCTTGAGGAACTTACT 58.870 43.478 3.37 0.00 41.55 2.24
4385 4925 2.857186 TCTTCTATGCCAGCAACACA 57.143 45.000 0.00 0.00 0.00 3.72
4577 5117 2.076100 TCCGCTGCAGTAATGAAAGTG 58.924 47.619 16.64 0.00 0.00 3.16
4778 5320 6.928348 TCTTCTGTCAGTATTTTAGGACCA 57.072 37.500 0.00 0.00 0.00 4.02
5040 5583 8.459911 TGTTAAGGAGATCAAGTATATCGTCA 57.540 34.615 0.00 0.00 0.00 4.35
5176 5719 1.967319 AACTGCACGGTTCTTGTGAT 58.033 45.000 0.00 0.00 39.73 3.06
5180 5723 2.872028 GCAAACTGCACGGTTCTTG 58.128 52.632 0.00 0.00 44.26 3.02
5240 5785 4.512571 AGGCAACATTCAAAAATCAAGCAC 59.487 37.500 0.00 0.00 41.41 4.40
5356 5969 1.254975 TGCAGCCTCTTAGCACGGTA 61.255 55.000 0.00 0.00 32.55 4.02
5359 5972 2.012237 CATGCAGCCTCTTAGCACG 58.988 57.895 0.00 0.00 41.60 5.34
5548 6648 3.177228 ACCAAGAGAGTCCTGCAGTAAT 58.823 45.455 13.81 0.00 0.00 1.89
5642 6746 4.440880 CTTGTCCTCCTGAGAATAGCAAG 58.559 47.826 0.00 0.00 0.00 4.01
5643 6747 3.369892 GCTTGTCCTCCTGAGAATAGCAA 60.370 47.826 0.00 0.00 0.00 3.91
5813 6917 6.127814 GGCTGGTAACTAAATTAACCTGTTCC 60.128 42.308 0.00 0.00 37.61 3.62
6044 7148 1.963985 AGACATCCAGCTTCTTCCCT 58.036 50.000 0.00 0.00 0.00 4.20
6117 7221 6.374565 TTTTGCAGCTTTGCATTACAAATT 57.625 29.167 0.98 0.00 46.90 1.82
6118 7222 6.374565 TTTTTGCAGCTTTGCATTACAAAT 57.625 29.167 0.98 0.00 46.90 2.32
6122 7226 6.710692 ACTATTTTTGCAGCTTTGCATTAC 57.289 33.333 0.98 0.00 44.94 1.89
6163 7267 7.175797 TCATCCGAGTATATGAGTCTAATGGT 58.824 38.462 0.00 0.00 0.00 3.55
6191 7295 4.114794 CACCAAACTTTCAGGCAAAGAAG 58.885 43.478 4.51 0.00 44.02 2.85
6409 7596 3.251571 AGTACCGTTGCTTCGATTCTTC 58.748 45.455 2.99 0.00 0.00 2.87
6413 7600 1.549170 AGGAGTACCGTTGCTTCGATT 59.451 47.619 2.99 0.00 41.83 3.34
6414 7601 1.183549 AGGAGTACCGTTGCTTCGAT 58.816 50.000 2.99 0.00 41.83 3.59
6415 7602 1.470098 GTAGGAGTACCGTTGCTTCGA 59.530 52.381 2.99 0.00 41.83 3.71
6424 7611 1.134560 GTCTGCCTTGTAGGAGTACCG 59.865 57.143 0.00 0.00 37.67 4.02
6637 7827 2.419297 GCCGTCATCTGAATCCTCTGTT 60.419 50.000 0.00 0.00 0.00 3.16
6662 7852 6.017934 TGTTCTGATGAGCAAGTAGTTTCAAC 60.018 38.462 0.00 0.00 30.53 3.18
6744 7934 0.038801 GGCCTTCTTTGCAACTGAGC 60.039 55.000 0.00 1.70 0.00 4.26
6893 8083 4.843728 AGATGTCCTTTTCGCAGGATTTA 58.156 39.130 1.67 0.00 45.14 1.40
6924 8114 2.231235 AGCCGTTCCATTAGCCTTTTTG 59.769 45.455 0.00 0.00 0.00 2.44
7054 8244 0.958091 TGGTCGCAACAAAATCCAGG 59.042 50.000 0.00 0.00 0.00 4.45
7208 8398 5.720041 GGAATGAATGAATGGATGGATGGAT 59.280 40.000 0.00 0.00 0.00 3.41
7209 8399 5.081728 GGAATGAATGAATGGATGGATGGA 58.918 41.667 0.00 0.00 0.00 3.41
7210 8400 4.836175 TGGAATGAATGAATGGATGGATGG 59.164 41.667 0.00 0.00 0.00 3.51
7211 8401 6.605471 ATGGAATGAATGAATGGATGGATG 57.395 37.500 0.00 0.00 0.00 3.51
7256 8446 3.826729 TCTCGACCTCATTGTTTCTCTGA 59.173 43.478 0.00 0.00 0.00 3.27
7310 8500 4.287067 ACCCAGCTTCCATAGGTATACATG 59.713 45.833 5.01 0.82 32.12 3.21
7416 8606 3.693578 TGATGTGCAACTCAAACAACTGA 59.306 39.130 0.00 0.00 38.04 3.41
7480 8670 7.816995 TGGTCAATTTTTAAATAAAGCGCAGAT 59.183 29.630 11.47 0.00 0.00 2.90
7481 8671 7.148641 TGGTCAATTTTTAAATAAAGCGCAGA 58.851 30.769 11.47 0.00 0.00 4.26
7482 8672 7.344910 TGGTCAATTTTTAAATAAAGCGCAG 57.655 32.000 11.47 0.00 0.00 5.18
7483 8673 7.224753 TGTTGGTCAATTTTTAAATAAAGCGCA 59.775 29.630 11.47 0.00 0.00 6.09
7484 8674 7.568433 TGTTGGTCAATTTTTAAATAAAGCGC 58.432 30.769 0.00 0.00 0.00 5.92
7485 8675 8.220434 CCTGTTGGTCAATTTTTAAATAAAGCG 58.780 33.333 0.00 0.00 0.00 4.68
7486 8676 8.503196 CCCTGTTGGTCAATTTTTAAATAAAGC 58.497 33.333 0.00 0.00 0.00 3.51
7540 8731 1.882623 CCTGGGTTGCTTCTTCTTGTC 59.117 52.381 0.00 0.00 0.00 3.18
7542 8733 0.600057 GCCTGGGTTGCTTCTTCTTG 59.400 55.000 0.00 0.00 0.00 3.02
7637 8828 3.068590 CCAAGTGAAAATCAAGTGTGGCT 59.931 43.478 0.00 0.00 0.00 4.75
7652 8843 5.630661 TTCGTTGTTCTTTTTCCAAGTGA 57.369 34.783 0.00 0.00 0.00 3.41
7656 8847 5.451242 CCTCCATTCGTTGTTCTTTTTCCAA 60.451 40.000 0.00 0.00 0.00 3.53
7682 8873 7.601508 AGCGCTATACCCTTGTAAAATATACAC 59.398 37.037 8.99 0.00 0.00 2.90
7696 8887 0.529992 GTTTCGCAGCGCTATACCCT 60.530 55.000 10.99 0.00 0.00 4.34
7727 8918 0.843309 TCTTTCTCACCAAGGCCACA 59.157 50.000 5.01 0.00 0.00 4.17
7728 8919 1.815003 CATCTTTCTCACCAAGGCCAC 59.185 52.381 5.01 0.00 0.00 5.01
7729 8920 1.425066 ACATCTTTCTCACCAAGGCCA 59.575 47.619 5.01 0.00 0.00 5.36
7733 8924 5.392380 GCCAACATACATCTTTCTCACCAAG 60.392 44.000 0.00 0.00 0.00 3.61
7812 9004 1.106351 TTTGCACATCAGCGTGGGTT 61.106 50.000 0.00 0.00 37.37 4.11
7862 9054 0.548682 AAGGGAGCCACTGGAGATGT 60.549 55.000 0.00 0.00 0.00 3.06
7872 9064 4.396357 TTTTATTGGAGAAAGGGAGCCA 57.604 40.909 0.00 0.00 0.00 4.75
7930 9122 1.737008 GGGAAAGAGGACGTGTCGC 60.737 63.158 0.00 0.00 0.00 5.19
7932 9124 3.889520 ATTAGGGAAAGAGGACGTGTC 57.110 47.619 0.00 0.00 0.00 3.67
7936 9128 7.415206 CCAACAATTTATTAGGGAAAGAGGACG 60.415 40.741 0.00 0.00 0.00 4.79
7949 9141 5.470437 TGCAGACGTCACCAACAATTTATTA 59.530 36.000 19.50 0.00 0.00 0.98
7996 9188 9.283768 ACCTCAATCAATATATCGTATTGCAAA 57.716 29.630 1.71 0.00 35.50 3.68
7997 9189 8.720562 CACCTCAATCAATATATCGTATTGCAA 58.279 33.333 0.00 0.00 35.50 4.08
7998 9190 7.148423 GCACCTCAATCAATATATCGTATTGCA 60.148 37.037 3.52 0.00 35.50 4.08
7999 9191 7.065085 AGCACCTCAATCAATATATCGTATTGC 59.935 37.037 3.52 0.00 35.50 3.56
8000 9192 8.385858 CAGCACCTCAATCAATATATCGTATTG 58.614 37.037 2.22 2.22 36.53 1.90
8001 9193 7.550551 CCAGCACCTCAATCAATATATCGTATT 59.449 37.037 0.00 0.00 0.00 1.89
8002 9194 7.044181 CCAGCACCTCAATCAATATATCGTAT 58.956 38.462 0.00 0.00 0.00 3.06
8003 9195 6.014584 ACCAGCACCTCAATCAATATATCGTA 60.015 38.462 0.00 0.00 0.00 3.43
8004 9196 5.221722 ACCAGCACCTCAATCAATATATCGT 60.222 40.000 0.00 0.00 0.00 3.73
8005 9197 5.121298 CACCAGCACCTCAATCAATATATCG 59.879 44.000 0.00 0.00 0.00 2.92
8006 9198 5.106396 GCACCAGCACCTCAATCAATATATC 60.106 44.000 0.00 0.00 41.58 1.63
8007 9199 4.763793 GCACCAGCACCTCAATCAATATAT 59.236 41.667 0.00 0.00 41.58 0.86
8008 9200 4.136796 GCACCAGCACCTCAATCAATATA 58.863 43.478 0.00 0.00 41.58 0.86
8009 9201 2.954318 GCACCAGCACCTCAATCAATAT 59.046 45.455 0.00 0.00 41.58 1.28
8010 9202 2.368439 GCACCAGCACCTCAATCAATA 58.632 47.619 0.00 0.00 41.58 1.90
8011 9203 1.180029 GCACCAGCACCTCAATCAAT 58.820 50.000 0.00 0.00 41.58 2.57
8012 9204 2.644887 GCACCAGCACCTCAATCAA 58.355 52.632 0.00 0.00 41.58 2.57
8013 9205 4.402851 GCACCAGCACCTCAATCA 57.597 55.556 0.00 0.00 41.58 2.57


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

AutoCloner maintained by Alex Coulton.