Multiple sequence alignment - TraesCS4B01G334300

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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 TraesCS4B01G334300 chr4B 100.000 3150 0 0 1 3150 625332987 625329838 0.000000e+00 5818.0
1 TraesCS4B01G334300 chr4B 94.943 1503 68 7 1356 2857 625336351 625337846 0.000000e+00 2348.0
2 TraesCS4B01G334300 chr4B 94.688 1280 54 6 1 1278 625335067 625336334 0.000000e+00 1975.0
3 TraesCS4B01G334300 chr4B 100.000 28 0 0 1309 1336 625331605 625331578 6.000000e-03 52.8
4 TraesCS4B01G334300 chr4B 100.000 28 0 0 1383 1410 625331679 625331652 6.000000e-03 52.8
5 TraesCS4B01G334300 chr4B 100.000 28 0 0 1309 1336 625336378 625336405 6.000000e-03 52.8
6 TraesCS4B01G334300 chr7D 91.493 1293 79 21 1 1277 521969915 521968638 0.000000e+00 1749.0
7 TraesCS4B01G334300 chr7D 92.441 807 52 9 1355 2159 521968621 521967822 0.000000e+00 1144.0
8 TraesCS4B01G334300 chr7D 85.242 393 31 19 2162 2535 521967781 521967397 2.290000e-101 379.0
9 TraesCS4B01G334300 chr7D 79.538 303 57 4 1852 2151 65630901 65631201 8.850000e-51 211.0
10 TraesCS4B01G334300 chr5D 93.284 819 48 6 1343 2159 499709974 499710787 0.000000e+00 1201.0
11 TraesCS4B01G334300 chr5D 91.059 425 28 7 858 1276 499709548 499709968 1.640000e-157 566.0
12 TraesCS4B01G334300 chr5D 85.901 383 34 15 2162 2535 499710829 499711200 1.060000e-104 390.0
13 TraesCS4B01G334300 chr5D 100.000 28 0 0 1309 1336 499710014 499710041 6.000000e-03 52.8
14 TraesCS4B01G334300 chr6B 87.241 580 49 14 2245 2822 555806789 555807345 3.430000e-179 638.0
15 TraesCS4B01G334300 chr6D 87.037 540 49 11 2245 2783 370690952 370691471 9.730000e-165 590.0
16 TraesCS4B01G334300 chr6A 86.604 321 25 9 2245 2564 511529769 511530072 3.890000e-89 339.0
17 TraesCS4B01G334300 chr6A 88.350 206 20 3 2619 2823 511530181 511530383 8.730000e-61 244.0
18 TraesCS4B01G334300 chr1B 88.583 254 29 0 1864 2117 557101935 557102188 3.050000e-80 309.0
19 TraesCS4B01G334300 chr1B 89.041 146 11 3 91 236 57102123 57101983 3.230000e-40 176.0
20 TraesCS4B01G334300 chr3A 88.298 188 16 5 2377 2560 735477686 735477501 1.470000e-53 220.0
21 TraesCS4B01G334300 chr3A 86.842 190 19 5 2377 2562 735480022 735479835 1.150000e-49 207.0
22 TraesCS4B01G334300 chr2B 81.034 232 43 1 1852 2082 795823959 795824190 1.930000e-42 183.0
23 TraesCS4B01G334300 chr4D 80.508 236 46 0 1859 2094 2997573 2997338 6.940000e-42 182.0
24 TraesCS4B01G334300 chr1A 80.342 234 46 0 1849 2082 97254754 97254987 8.980000e-41 178.0
25 TraesCS4B01G334300 chrUn 80.000 235 45 2 1850 2082 291162110 291162344 4.180000e-39 172.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G334300 chr4B 625329838 625332987 3149 True 1974.533333 5818 100.000000 1 3150 3 chr4B.!!$R1 3149
1 TraesCS4B01G334300 chr4B 625335067 625337846 2779 False 1458.600000 2348 96.543667 1 2857 3 chr4B.!!$F1 2856
2 TraesCS4B01G334300 chr7D 521967397 521969915 2518 True 1090.666667 1749 89.725333 1 2535 3 chr7D.!!$R1 2534
3 TraesCS4B01G334300 chr5D 499709548 499711200 1652 False 552.450000 1201 92.561000 858 2535 4 chr5D.!!$F1 1677
4 TraesCS4B01G334300 chr6B 555806789 555807345 556 False 638.000000 638 87.241000 2245 2822 1 chr6B.!!$F1 577
5 TraesCS4B01G334300 chr6D 370690952 370691471 519 False 590.000000 590 87.037000 2245 2783 1 chr6D.!!$F1 538
6 TraesCS4B01G334300 chr6A 511529769 511530383 614 False 291.500000 339 87.477000 2245 2823 2 chr6A.!!$F1 578
7 TraesCS4B01G334300 chr3A 735477501 735480022 2521 True 213.500000 220 87.570000 2377 2562 2 chr3A.!!$R1 185

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
609 615 1.474478 TGTGCATGTTTTCGGTGTGTT 59.526 42.857 0.0 0.0 0.0 3.32 F
1302 1326 0.341258 AGAGGGAGGAGCTGATTGGA 59.659 55.000 0.0 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1426 1450 0.265553 ATTACATTGCCCTGCCCCAT 59.734 50.0 0.00 0.00 0.0 4.00 R
3103 5191 0.039074 CTCAAGTTGCGAGTCGGACT 60.039 55.0 15.52 11.09 0.0 3.85 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
32 33 8.154649 TCAGTTCCTGTTTACTCTCATTTTTC 57.845 34.615 0.00 0.00 32.61 2.29
198 200 7.148641 TGTTCTCAAACTTTTAGTGCAAACAA 58.851 30.769 0.00 0.00 36.30 2.83
266 268 1.874739 CGTCTCCCCGTTGTTGCTTTA 60.875 52.381 0.00 0.00 0.00 1.85
296 299 5.105310 GGTGAGTAGCTTCCTGAATTACTGA 60.105 44.000 0.00 0.42 0.00 3.41
297 300 6.398918 GTGAGTAGCTTCCTGAATTACTGAA 58.601 40.000 0.00 0.00 0.00 3.02
298 301 7.044798 GTGAGTAGCTTCCTGAATTACTGAAT 58.955 38.462 0.00 0.00 0.00 2.57
299 302 7.550906 GTGAGTAGCTTCCTGAATTACTGAATT 59.449 37.037 0.00 0.00 38.00 2.17
300 303 8.758829 TGAGTAGCTTCCTGAATTACTGAATTA 58.241 33.333 0.00 0.00 35.33 1.40
301 304 8.950208 AGTAGCTTCCTGAATTACTGAATTAC 57.050 34.615 0.00 0.00 35.33 1.89
302 305 8.763601 AGTAGCTTCCTGAATTACTGAATTACT 58.236 33.333 0.00 0.00 35.33 2.24
303 306 7.856145 AGCTTCCTGAATTACTGAATTACTG 57.144 36.000 0.00 0.00 35.33 2.74
385 390 9.749490 CATTATTTTCACTGCAATTCATTGTTC 57.251 29.630 1.59 0.00 39.88 3.18
448 453 4.099881 TGAGGATTTTGCTGCTTCAGTTTT 59.900 37.500 0.00 0.00 33.43 2.43
461 466 8.504005 GCTGCTTCAGTTTTAGTAGTTTCATTA 58.496 33.333 0.00 0.00 33.43 1.90
513 518 8.504812 AACAAAGTGCCATTTTATTCAGTTTT 57.495 26.923 0.00 0.00 31.83 2.43
516 521 8.397148 CAAAGTGCCATTTTATTCAGTTTTGTT 58.603 29.630 0.00 0.00 31.83 2.83
575 581 4.456911 CGTCAGTAGTTCCACTGTTAGGTA 59.543 45.833 3.41 0.00 45.11 3.08
580 586 8.057011 TCAGTAGTTCCACTGTTAGGTATCATA 58.943 37.037 3.41 0.00 45.11 2.15
602 608 2.226200 TCCAGTCATGTGCATGTTTTCG 59.774 45.455 11.38 0.00 39.72 3.46
609 615 1.474478 TGTGCATGTTTTCGGTGTGTT 59.526 42.857 0.00 0.00 0.00 3.32
664 671 8.287503 GGTCGTGTAGTTGATTTACTCATTTTT 58.712 33.333 0.00 0.00 32.72 1.94
690 697 7.847096 TGTTTTGGCAGATAGTCTTCAGTATA 58.153 34.615 0.00 0.00 0.00 1.47
771 778 6.459670 TTCTAGTTTTGAACTGAAAACCCC 57.540 37.500 3.70 0.00 43.84 4.95
910 923 3.657634 TGTTTTTCTTTGTTGTGCTGCA 58.342 36.364 0.00 0.00 0.00 4.41
954 968 5.083122 ACATATCCGTCCTGATGATTCTCT 58.917 41.667 0.00 0.00 0.00 3.10
964 978 4.458295 CCTGATGATTCTCTTGCTTTGTGT 59.542 41.667 0.00 0.00 0.00 3.72
1249 1273 5.636123 TGCAAGGAATAGGTTTAACCAGAA 58.364 37.500 17.10 1.62 41.95 3.02
1278 1302 1.963190 GAACTTTAAGGCGGACGGCG 61.963 60.000 4.80 4.80 44.92 6.46
1279 1303 2.125832 CTTTAAGGCGGACGGCGA 60.126 61.111 16.62 2.35 44.92 5.54
1280 1304 1.738830 CTTTAAGGCGGACGGCGAA 60.739 57.895 16.62 8.37 44.92 4.70
1281 1305 1.693083 CTTTAAGGCGGACGGCGAAG 61.693 60.000 16.62 13.30 44.92 3.79
1282 1306 2.157305 TTTAAGGCGGACGGCGAAGA 62.157 55.000 16.62 0.00 44.92 2.87
1283 1307 2.157305 TTAAGGCGGACGGCGAAGAA 62.157 55.000 16.62 3.34 44.92 2.52
1284 1308 2.552585 TAAGGCGGACGGCGAAGAAG 62.553 60.000 16.62 0.69 44.92 2.85
1286 1310 2.881352 GCGGACGGCGAAGAAGAG 60.881 66.667 16.62 0.00 0.00 2.85
1288 1312 2.184579 GGACGGCGAAGAAGAGGG 59.815 66.667 16.62 0.00 0.00 4.30
1289 1313 2.348888 GGACGGCGAAGAAGAGGGA 61.349 63.158 16.62 0.00 0.00 4.20
1291 1315 2.286127 GACGGCGAAGAAGAGGGAGG 62.286 65.000 16.62 0.00 0.00 4.30
1292 1316 2.052690 CGGCGAAGAAGAGGGAGGA 61.053 63.158 0.00 0.00 0.00 3.71
1293 1317 1.819905 GGCGAAGAAGAGGGAGGAG 59.180 63.158 0.00 0.00 0.00 3.69
1294 1318 1.142965 GCGAAGAAGAGGGAGGAGC 59.857 63.158 0.00 0.00 0.00 4.70
1295 1319 1.326951 GCGAAGAAGAGGGAGGAGCT 61.327 60.000 0.00 0.00 0.00 4.09
1296 1320 0.459489 CGAAGAAGAGGGAGGAGCTG 59.541 60.000 0.00 0.00 0.00 4.24
1297 1321 1.859302 GAAGAAGAGGGAGGAGCTGA 58.141 55.000 0.00 0.00 0.00 4.26
1298 1322 2.397597 GAAGAAGAGGGAGGAGCTGAT 58.602 52.381 0.00 0.00 0.00 2.90
1299 1323 2.566708 AGAAGAGGGAGGAGCTGATT 57.433 50.000 0.00 0.00 0.00 2.57
1300 1324 2.117865 AGAAGAGGGAGGAGCTGATTG 58.882 52.381 0.00 0.00 0.00 2.67
1301 1325 1.140652 GAAGAGGGAGGAGCTGATTGG 59.859 57.143 0.00 0.00 0.00 3.16
1302 1326 0.341258 AGAGGGAGGAGCTGATTGGA 59.659 55.000 0.00 0.00 0.00 3.53
1303 1327 0.758123 GAGGGAGGAGCTGATTGGAG 59.242 60.000 0.00 0.00 0.00 3.86
1304 1328 0.693767 AGGGAGGAGCTGATTGGAGG 60.694 60.000 0.00 0.00 0.00 4.30
1305 1329 0.985490 GGGAGGAGCTGATTGGAGGT 60.985 60.000 0.00 0.00 0.00 3.85
1306 1330 1.692762 GGGAGGAGCTGATTGGAGGTA 60.693 57.143 0.00 0.00 0.00 3.08
1307 1331 2.119495 GGAGGAGCTGATTGGAGGTAA 58.881 52.381 0.00 0.00 0.00 2.85
1308 1332 2.708325 GGAGGAGCTGATTGGAGGTAAT 59.292 50.000 0.00 0.00 0.00 1.89
1309 1333 3.495806 GGAGGAGCTGATTGGAGGTAATG 60.496 52.174 0.00 0.00 0.00 1.90
1310 1334 3.387962 AGGAGCTGATTGGAGGTAATGA 58.612 45.455 0.00 0.00 0.00 2.57
1311 1335 3.979347 AGGAGCTGATTGGAGGTAATGAT 59.021 43.478 0.00 0.00 0.00 2.45
1312 1336 4.414846 AGGAGCTGATTGGAGGTAATGATT 59.585 41.667 0.00 0.00 0.00 2.57
1313 1337 4.518211 GGAGCTGATTGGAGGTAATGATTG 59.482 45.833 0.00 0.00 0.00 2.67
1314 1338 4.467769 AGCTGATTGGAGGTAATGATTGG 58.532 43.478 0.00 0.00 0.00 3.16
1315 1339 4.166725 AGCTGATTGGAGGTAATGATTGGA 59.833 41.667 0.00 0.00 0.00 3.53
1316 1340 4.518211 GCTGATTGGAGGTAATGATTGGAG 59.482 45.833 0.00 0.00 0.00 3.86
1317 1341 5.052693 TGATTGGAGGTAATGATTGGAGG 57.947 43.478 0.00 0.00 0.00 4.30
1318 1342 4.478317 TGATTGGAGGTAATGATTGGAGGT 59.522 41.667 0.00 0.00 0.00 3.85
1319 1343 3.931907 TGGAGGTAATGATTGGAGGTG 57.068 47.619 0.00 0.00 0.00 4.00
1320 1344 3.459828 TGGAGGTAATGATTGGAGGTGA 58.540 45.455 0.00 0.00 0.00 4.02
1321 1345 4.047166 TGGAGGTAATGATTGGAGGTGAT 58.953 43.478 0.00 0.00 0.00 3.06
1322 1346 4.141413 TGGAGGTAATGATTGGAGGTGATG 60.141 45.833 0.00 0.00 0.00 3.07
1323 1347 4.103153 GGAGGTAATGATTGGAGGTGATGA 59.897 45.833 0.00 0.00 0.00 2.92
1324 1348 5.222007 GGAGGTAATGATTGGAGGTGATGAT 60.222 44.000 0.00 0.00 0.00 2.45
1325 1349 6.271585 AGGTAATGATTGGAGGTGATGATT 57.728 37.500 0.00 0.00 0.00 2.57
1326 1350 6.066690 AGGTAATGATTGGAGGTGATGATTG 58.933 40.000 0.00 0.00 0.00 2.67
1327 1351 5.242393 GGTAATGATTGGAGGTGATGATTGG 59.758 44.000 0.00 0.00 0.00 3.16
1328 1352 4.801521 ATGATTGGAGGTGATGATTGGA 57.198 40.909 0.00 0.00 0.00 3.53
1329 1353 3.889815 TGATTGGAGGTGATGATTGGAC 58.110 45.455 0.00 0.00 0.00 4.02
1330 1354 2.806945 TTGGAGGTGATGATTGGACC 57.193 50.000 0.00 0.00 0.00 4.46
1331 1355 1.667595 TGGAGGTGATGATTGGACCA 58.332 50.000 0.00 0.00 31.61 4.02
1332 1356 1.991813 TGGAGGTGATGATTGGACCAA 59.008 47.619 9.92 9.92 31.61 3.67
1333 1357 2.025981 TGGAGGTGATGATTGGACCAAG 60.026 50.000 13.43 0.00 31.61 3.61
1334 1358 2.025887 GGAGGTGATGATTGGACCAAGT 60.026 50.000 13.43 1.11 31.61 3.16
1335 1359 3.562176 GGAGGTGATGATTGGACCAAGTT 60.562 47.826 13.43 0.00 31.61 2.66
1336 1360 3.424703 AGGTGATGATTGGACCAAGTTG 58.575 45.455 13.43 0.00 31.61 3.16
1337 1361 3.074390 AGGTGATGATTGGACCAAGTTGA 59.926 43.478 13.43 0.00 31.61 3.18
1338 1362 4.019174 GGTGATGATTGGACCAAGTTGAT 58.981 43.478 13.43 0.00 0.00 2.57
1339 1363 4.463891 GGTGATGATTGGACCAAGTTGATT 59.536 41.667 13.43 0.00 0.00 2.57
1340 1364 5.404946 GTGATGATTGGACCAAGTTGATTG 58.595 41.667 13.43 0.00 38.74 2.67
1352 1376 5.909621 CAAGTTGATTGGAGGTGATGATT 57.090 39.130 0.00 0.00 35.08 2.57
1353 1377 5.647589 CAAGTTGATTGGAGGTGATGATTG 58.352 41.667 0.00 0.00 35.08 2.67
1426 1450 0.303493 GTTCAAGCGCGACTTCAACA 59.697 50.000 19.19 2.53 39.05 3.33
1444 1468 0.687098 CATGGGGCAGGGCAATGTAA 60.687 55.000 0.00 0.00 0.00 2.41
1447 1471 1.203237 GGGGCAGGGCAATGTAATTT 58.797 50.000 0.00 0.00 31.22 1.82
1449 1473 2.631267 GGGCAGGGCAATGTAATTTTG 58.369 47.619 0.00 0.00 31.22 2.44
1455 1479 5.106987 GCAGGGCAATGTAATTTTGTTTGAG 60.107 40.000 0.00 0.00 31.22 3.02
1489 1513 5.583061 CGAACAACAAAGGTATATGTGGCTA 59.417 40.000 0.00 0.00 0.00 3.93
1536 1560 2.225019 AGCTGATGAAGAAGTTGTTGCG 59.775 45.455 0.00 0.00 0.00 4.85
1554 1578 2.237143 TGCGGTTGATGAAGAGGAAGAT 59.763 45.455 0.00 0.00 0.00 2.40
1572 1596 7.061054 AGGAAGATGTTGTCAATGATGATCAT 58.939 34.615 8.25 8.25 39.09 2.45
1647 1671 3.819368 TGGTGAATACGCAATGATGGAT 58.181 40.909 0.00 0.00 0.00 3.41
1697 1721 1.907807 GCCCACCCTTTGTGCATCA 60.908 57.895 0.00 0.00 44.01 3.07
1700 1724 0.452987 CCACCCTTTGTGCATCATCG 59.547 55.000 0.00 0.00 44.01 3.84
1855 1884 5.823312 TCTAACATTTACCCTCCCCTTTTC 58.177 41.667 0.00 0.00 0.00 2.29
2135 2165 1.001378 GCGTTGTCAATGCTTTGAGGT 60.001 47.619 20.35 0.00 42.41 3.85
2139 2169 1.202758 TGTCAATGCTTTGAGGTCGGT 60.203 47.619 14.79 0.00 42.41 4.69
2217 2286 5.416952 AGAAGCAAAATGTTAGCAGTGCTAT 59.583 36.000 24.99 9.38 41.01 2.97
2221 2290 5.863397 GCAAAATGTTAGCAGTGCTATTGAA 59.137 36.000 27.72 14.66 41.01 2.69
2289 2364 7.872113 ATTAGAGATGAATTGTGAAGTTCCC 57.128 36.000 0.00 0.00 0.00 3.97
2440 2535 6.713762 TTTTCTGTCCACATCATGAAACTT 57.286 33.333 0.00 0.00 0.00 2.66
2528 2628 7.281100 GCAGCTTTAGTTGTATTTGGTATCTCT 59.719 37.037 0.00 0.00 0.00 3.10
2539 2639 9.256477 TGTATTTGGTATCTCTTAATAAGCACG 57.744 33.333 0.00 0.00 0.00 5.34
2615 3214 6.305693 CTGGTTTAGCTTATATGCTCCAAC 57.694 41.667 15.80 17.44 42.97 3.77
2784 4658 3.194062 GCTGAGCAAAGATACTGACTCC 58.806 50.000 0.00 0.00 0.00 3.85
2857 4945 6.654161 CCACATAAATGGCCAATTCTTTTTGA 59.346 34.615 20.15 0.61 31.52 2.69
2859 4947 8.732531 CACATAAATGGCCAATTCTTTTTGATT 58.267 29.630 20.15 1.30 0.00 2.57
2861 4949 6.822667 AAATGGCCAATTCTTTTTGATTCC 57.177 33.333 10.96 0.00 0.00 3.01
2862 4950 4.284829 TGGCCAATTCTTTTTGATTCCC 57.715 40.909 0.61 0.00 0.00 3.97
2863 4951 3.008923 TGGCCAATTCTTTTTGATTCCCC 59.991 43.478 0.61 0.00 0.00 4.81
2864 4952 3.609853 GCCAATTCTTTTTGATTCCCCC 58.390 45.455 0.00 0.00 0.00 5.40
2865 4953 3.264193 GCCAATTCTTTTTGATTCCCCCT 59.736 43.478 0.00 0.00 0.00 4.79
2866 4954 4.263462 GCCAATTCTTTTTGATTCCCCCTT 60.263 41.667 0.00 0.00 0.00 3.95
2868 4956 6.306199 CCAATTCTTTTTGATTCCCCCTTTT 58.694 36.000 0.00 0.00 0.00 2.27
2870 4958 7.255555 CCAATTCTTTTTGATTCCCCCTTTTTG 60.256 37.037 0.00 0.00 0.00 2.44
2871 4959 4.713553 TCTTTTTGATTCCCCCTTTTTGC 58.286 39.130 0.00 0.00 0.00 3.68
2872 4960 4.164988 TCTTTTTGATTCCCCCTTTTTGCA 59.835 37.500 0.00 0.00 0.00 4.08
2873 4961 3.483808 TTTGATTCCCCCTTTTTGCAC 57.516 42.857 0.00 0.00 0.00 4.57
2874 4962 2.397044 TGATTCCCCCTTTTTGCACT 57.603 45.000 0.00 0.00 0.00 4.40
2875 4963 3.534357 TGATTCCCCCTTTTTGCACTA 57.466 42.857 0.00 0.00 0.00 2.74
2876 4964 3.430453 TGATTCCCCCTTTTTGCACTAG 58.570 45.455 0.00 0.00 0.00 2.57
2880 4968 2.962421 TCCCCCTTTTTGCACTAGTTTG 59.038 45.455 0.00 0.00 0.00 2.93
2881 4969 2.547855 CCCCCTTTTTGCACTAGTTTGC 60.548 50.000 0.00 0.00 43.31 3.68
2899 4987 2.486951 GCAAGATGCATGATGTGTCC 57.513 50.000 2.46 0.00 44.26 4.02
2900 4988 1.268386 GCAAGATGCATGATGTGTCCG 60.268 52.381 2.46 0.00 44.26 4.79
2901 4989 1.019673 AAGATGCATGATGTGTCCGC 58.980 50.000 2.46 0.00 0.00 5.54
2902 4990 0.107557 AGATGCATGATGTGTCCGCA 60.108 50.000 2.46 0.00 36.55 5.69
2904 4992 0.949397 ATGCATGATGTGTCCGCATC 59.051 50.000 12.71 12.71 43.97 3.91
2905 4993 1.277739 GCATGATGTGTCCGCATCG 59.722 57.895 14.22 4.45 45.98 3.84
2918 5006 4.227134 CATCGGGGGAGTCGCCAG 62.227 72.222 26.04 22.28 45.31 4.85
2922 5010 3.866582 GGGGGAGTCGCCAGGATG 61.867 72.222 26.04 0.00 44.52 3.51
2933 5021 2.264480 CAGGATGGTTGTCGGCGA 59.736 61.111 4.99 4.99 0.00 5.54
2934 5022 2.100631 CAGGATGGTTGTCGGCGAC 61.101 63.158 31.68 31.68 0.00 5.19
2950 5038 4.852609 GGCGACGGCGATTATTATTATT 57.147 40.909 18.90 0.00 41.24 1.40
2951 5039 5.212589 GGCGACGGCGATTATTATTATTT 57.787 39.130 18.90 0.00 41.24 1.40
2952 5040 5.624292 GGCGACGGCGATTATTATTATTTT 58.376 37.500 18.90 0.00 41.24 1.82
2953 5041 6.764094 GGCGACGGCGATTATTATTATTTTA 58.236 36.000 18.90 0.00 41.24 1.52
2954 5042 6.898189 GGCGACGGCGATTATTATTATTTTAG 59.102 38.462 18.90 0.00 41.24 1.85
2955 5043 7.412237 GGCGACGGCGATTATTATTATTTTAGT 60.412 37.037 18.90 0.00 41.24 2.24
2956 5044 7.953710 GCGACGGCGATTATTATTATTTTAGTT 59.046 33.333 18.90 0.00 40.82 2.24
2957 5045 9.456797 CGACGGCGATTATTATTATTTTAGTTC 57.543 33.333 16.62 0.00 40.82 3.01
2958 5046 9.456797 GACGGCGATTATTATTATTTTAGTTCG 57.543 33.333 16.62 0.00 0.00 3.95
2959 5047 8.437742 ACGGCGATTATTATTATTTTAGTTCGG 58.562 33.333 16.62 0.00 0.00 4.30
2960 5048 7.901377 CGGCGATTATTATTATTTTAGTTCGGG 59.099 37.037 0.00 0.00 0.00 5.14
2961 5049 8.179615 GGCGATTATTATTATTTTAGTTCGGGG 58.820 37.037 0.00 0.00 0.00 5.73
2962 5050 8.179615 GCGATTATTATTATTTTAGTTCGGGGG 58.820 37.037 0.00 0.00 0.00 5.40
2993 5081 2.927004 GTTGCCACGATGAGTTGGA 58.073 52.632 0.00 0.00 0.00 3.53
2994 5082 0.798776 GTTGCCACGATGAGTTGGAG 59.201 55.000 0.00 0.00 0.00 3.86
2995 5083 0.321564 TTGCCACGATGAGTTGGAGG 60.322 55.000 0.00 0.00 0.00 4.30
2996 5084 2.109126 GCCACGATGAGTTGGAGGC 61.109 63.158 0.00 0.00 0.00 4.70
2997 5085 1.296392 CCACGATGAGTTGGAGGCA 59.704 57.895 0.00 0.00 0.00 4.75
2998 5086 0.321564 CCACGATGAGTTGGAGGCAA 60.322 55.000 0.00 0.00 0.00 4.52
2999 5087 1.522668 CACGATGAGTTGGAGGCAAA 58.477 50.000 0.00 0.00 0.00 3.68
3000 5088 1.197721 CACGATGAGTTGGAGGCAAAC 59.802 52.381 0.00 0.00 0.00 2.93
3001 5089 0.443869 CGATGAGTTGGAGGCAAACG 59.556 55.000 0.00 0.00 32.65 3.60
3002 5090 0.169009 GATGAGTTGGAGGCAAACGC 59.831 55.000 0.00 0.00 32.65 4.84
3003 5091 0.537143 ATGAGTTGGAGGCAAACGCA 60.537 50.000 6.62 6.62 40.75 5.24
3004 5092 0.749818 TGAGTTGGAGGCAAACGCAA 60.750 50.000 2.64 0.00 34.93 4.85
3005 5093 0.317854 GAGTTGGAGGCAAACGCAAC 60.318 55.000 0.00 0.00 32.65 4.17
3006 5094 0.751643 AGTTGGAGGCAAACGCAACT 60.752 50.000 0.00 0.00 32.65 3.16
3007 5095 0.594796 GTTGGAGGCAAACGCAACTG 60.595 55.000 0.00 0.00 0.00 3.16
3008 5096 1.733402 TTGGAGGCAAACGCAACTGG 61.733 55.000 0.00 0.00 0.00 4.00
3009 5097 2.644992 GAGGCAAACGCAACTGGG 59.355 61.111 0.00 0.00 0.00 4.45
3010 5098 2.912025 AGGCAAACGCAACTGGGG 60.912 61.111 0.00 0.00 0.00 4.96
3011 5099 4.662961 GGCAAACGCAACTGGGGC 62.663 66.667 0.00 0.00 0.00 5.80
3040 5128 2.340078 GGCTATCGGCGCTGATGA 59.660 61.111 36.23 20.86 42.94 2.92
3041 5129 1.300931 GGCTATCGGCGCTGATGAA 60.301 57.895 36.23 19.97 42.94 2.57
3042 5130 0.880278 GGCTATCGGCGCTGATGAAA 60.880 55.000 36.23 19.27 42.94 2.69
3043 5131 1.151668 GCTATCGGCGCTGATGAAAT 58.848 50.000 36.23 17.40 0.00 2.17
3044 5132 2.337583 GCTATCGGCGCTGATGAAATA 58.662 47.619 36.23 18.56 0.00 1.40
3045 5133 2.346847 GCTATCGGCGCTGATGAAATAG 59.653 50.000 36.23 26.52 0.00 1.73
3046 5134 1.800805 ATCGGCGCTGATGAAATAGG 58.199 50.000 30.34 0.00 0.00 2.57
3047 5135 0.464036 TCGGCGCTGATGAAATAGGT 59.536 50.000 16.69 0.00 0.00 3.08
3048 5136 1.134521 TCGGCGCTGATGAAATAGGTT 60.135 47.619 16.69 0.00 0.00 3.50
3049 5137 1.261619 CGGCGCTGATGAAATAGGTTC 59.738 52.381 11.90 0.00 36.70 3.62
3050 5138 1.604278 GGCGCTGATGAAATAGGTTCC 59.396 52.381 7.64 0.00 35.12 3.62
3051 5139 2.288666 GCGCTGATGAAATAGGTTCCA 58.711 47.619 0.00 0.00 35.12 3.53
3052 5140 2.880890 GCGCTGATGAAATAGGTTCCAT 59.119 45.455 0.00 0.00 35.12 3.41
3053 5141 3.316308 GCGCTGATGAAATAGGTTCCATT 59.684 43.478 0.00 0.00 35.12 3.16
3054 5142 4.202050 GCGCTGATGAAATAGGTTCCATTT 60.202 41.667 0.00 0.00 35.12 2.32
3055 5143 5.679638 GCGCTGATGAAATAGGTTCCATTTT 60.680 40.000 0.00 0.00 35.12 1.82
3056 5144 6.332630 CGCTGATGAAATAGGTTCCATTTTT 58.667 36.000 0.00 0.00 35.12 1.94
3076 5164 5.883503 TTTTCGTTAGTGGTCTTTGTTGT 57.116 34.783 0.00 0.00 0.00 3.32
3077 5165 6.981762 TTTTCGTTAGTGGTCTTTGTTGTA 57.018 33.333 0.00 0.00 0.00 2.41
3078 5166 6.592798 TTTCGTTAGTGGTCTTTGTTGTAG 57.407 37.500 0.00 0.00 0.00 2.74
3079 5167 5.266733 TCGTTAGTGGTCTTTGTTGTAGT 57.733 39.130 0.00 0.00 0.00 2.73
3080 5168 5.663456 TCGTTAGTGGTCTTTGTTGTAGTT 58.337 37.500 0.00 0.00 0.00 2.24
3081 5169 6.108015 TCGTTAGTGGTCTTTGTTGTAGTTT 58.892 36.000 0.00 0.00 0.00 2.66
3082 5170 6.594937 TCGTTAGTGGTCTTTGTTGTAGTTTT 59.405 34.615 0.00 0.00 0.00 2.43
3083 5171 7.119553 TCGTTAGTGGTCTTTGTTGTAGTTTTT 59.880 33.333 0.00 0.00 0.00 1.94
3084 5172 7.217447 CGTTAGTGGTCTTTGTTGTAGTTTTTG 59.783 37.037 0.00 0.00 0.00 2.44
3085 5173 5.407502 AGTGGTCTTTGTTGTAGTTTTTGC 58.592 37.500 0.00 0.00 0.00 3.68
3086 5174 5.047660 AGTGGTCTTTGTTGTAGTTTTTGCA 60.048 36.000 0.00 0.00 0.00 4.08
3087 5175 5.635700 GTGGTCTTTGTTGTAGTTTTTGCAA 59.364 36.000 0.00 0.00 0.00 4.08
3088 5176 6.312672 GTGGTCTTTGTTGTAGTTTTTGCAAT 59.687 34.615 0.00 0.00 33.85 3.56
3089 5177 6.533367 TGGTCTTTGTTGTAGTTTTTGCAATC 59.467 34.615 0.00 0.00 33.85 2.67
3090 5178 6.533367 GGTCTTTGTTGTAGTTTTTGCAATCA 59.467 34.615 0.00 0.00 33.85 2.57
3091 5179 7.391016 GTCTTTGTTGTAGTTTTTGCAATCAC 58.609 34.615 0.00 0.00 33.85 3.06
3092 5180 6.533367 TCTTTGTTGTAGTTTTTGCAATCACC 59.467 34.615 0.00 0.00 33.85 4.02
3093 5181 4.688021 TGTTGTAGTTTTTGCAATCACCC 58.312 39.130 0.00 0.00 33.85 4.61
3094 5182 4.055360 GTTGTAGTTTTTGCAATCACCCC 58.945 43.478 0.00 0.00 33.85 4.95
3095 5183 3.300388 TGTAGTTTTTGCAATCACCCCA 58.700 40.909 0.00 0.00 0.00 4.96
3096 5184 3.320541 TGTAGTTTTTGCAATCACCCCAG 59.679 43.478 0.00 0.00 0.00 4.45
3097 5185 2.397597 AGTTTTTGCAATCACCCCAGT 58.602 42.857 0.00 0.00 0.00 4.00
3098 5186 2.771372 AGTTTTTGCAATCACCCCAGTT 59.229 40.909 0.00 0.00 0.00 3.16
3099 5187 3.199727 AGTTTTTGCAATCACCCCAGTTT 59.800 39.130 0.00 0.00 0.00 2.66
3100 5188 3.467374 TTTTGCAATCACCCCAGTTTC 57.533 42.857 0.00 0.00 0.00 2.78
3101 5189 1.337118 TTGCAATCACCCCAGTTTCC 58.663 50.000 0.00 0.00 0.00 3.13
3102 5190 0.187117 TGCAATCACCCCAGTTTCCA 59.813 50.000 0.00 0.00 0.00 3.53
3103 5191 1.337118 GCAATCACCCCAGTTTCCAA 58.663 50.000 0.00 0.00 0.00 3.53
3104 5192 1.273327 GCAATCACCCCAGTTTCCAAG 59.727 52.381 0.00 0.00 0.00 3.61
3105 5193 2.597455 CAATCACCCCAGTTTCCAAGT 58.403 47.619 0.00 0.00 0.00 3.16
3106 5194 2.558359 CAATCACCCCAGTTTCCAAGTC 59.442 50.000 0.00 0.00 0.00 3.01
3107 5195 0.476771 TCACCCCAGTTTCCAAGTCC 59.523 55.000 0.00 0.00 0.00 3.85
3108 5196 0.889186 CACCCCAGTTTCCAAGTCCG 60.889 60.000 0.00 0.00 0.00 4.79
3109 5197 1.057851 ACCCCAGTTTCCAAGTCCGA 61.058 55.000 0.00 0.00 0.00 4.55
3110 5198 0.605589 CCCCAGTTTCCAAGTCCGAC 60.606 60.000 0.00 0.00 0.00 4.79
3111 5199 0.396811 CCCAGTTTCCAAGTCCGACT 59.603 55.000 0.00 0.00 0.00 4.18
3112 5200 1.608283 CCCAGTTTCCAAGTCCGACTC 60.608 57.143 0.35 0.00 0.00 3.36
3113 5201 1.419374 CAGTTTCCAAGTCCGACTCG 58.581 55.000 0.35 0.00 0.00 4.18
3114 5202 0.319641 AGTTTCCAAGTCCGACTCGC 60.320 55.000 0.35 0.00 0.00 5.03
3115 5203 0.599204 GTTTCCAAGTCCGACTCGCA 60.599 55.000 0.35 0.00 0.00 5.10
3116 5204 0.105224 TTTCCAAGTCCGACTCGCAA 59.895 50.000 0.35 0.00 0.00 4.85
3117 5205 0.599204 TTCCAAGTCCGACTCGCAAC 60.599 55.000 0.35 0.00 0.00 4.17
3118 5206 1.006102 CCAAGTCCGACTCGCAACT 60.006 57.895 0.35 0.00 0.00 3.16
3119 5207 0.600255 CCAAGTCCGACTCGCAACTT 60.600 55.000 0.35 10.16 33.82 2.66
3120 5208 0.508641 CAAGTCCGACTCGCAACTTG 59.491 55.000 20.96 20.96 40.09 3.16
3121 5209 0.387929 AAGTCCGACTCGCAACTTGA 59.612 50.000 13.57 0.00 32.90 3.02
3122 5210 0.039074 AGTCCGACTCGCAACTTGAG 60.039 55.000 0.00 0.00 39.40 3.02
3123 5211 1.009389 GTCCGACTCGCAACTTGAGG 61.009 60.000 0.00 0.00 37.79 3.86
3124 5212 1.006102 CCGACTCGCAACTTGAGGT 60.006 57.895 0.00 0.00 37.79 3.85
3125 5213 0.600255 CCGACTCGCAACTTGAGGTT 60.600 55.000 0.00 0.00 37.79 3.50
3126 5214 1.217882 CGACTCGCAACTTGAGGTTT 58.782 50.000 0.00 0.00 37.79 3.27
3127 5215 1.597663 CGACTCGCAACTTGAGGTTTT 59.402 47.619 0.00 0.00 37.79 2.43
3128 5216 2.031683 CGACTCGCAACTTGAGGTTTTT 59.968 45.455 0.00 0.00 37.79 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
198 200 6.716628 TCTGTTTGGAGATGCTAAGAAATTGT 59.283 34.615 0.00 0.00 0.00 2.71
266 268 0.984995 GGAAGCTACTCACCCCAAGT 59.015 55.000 0.00 0.00 0.00 3.16
296 299 8.661752 AACTTCCTACTACACCTACAGTAATT 57.338 34.615 0.00 0.00 0.00 1.40
297 300 7.066766 CGAACTTCCTACTACACCTACAGTAAT 59.933 40.741 0.00 0.00 0.00 1.89
298 301 6.372659 CGAACTTCCTACTACACCTACAGTAA 59.627 42.308 0.00 0.00 0.00 2.24
299 302 5.877012 CGAACTTCCTACTACACCTACAGTA 59.123 44.000 0.00 0.00 0.00 2.74
300 303 4.699257 CGAACTTCCTACTACACCTACAGT 59.301 45.833 0.00 0.00 0.00 3.55
301 304 4.699257 ACGAACTTCCTACTACACCTACAG 59.301 45.833 0.00 0.00 0.00 2.74
302 305 4.655963 ACGAACTTCCTACTACACCTACA 58.344 43.478 0.00 0.00 0.00 2.74
303 306 5.635417 AACGAACTTCCTACTACACCTAC 57.365 43.478 0.00 0.00 0.00 3.18
461 466 9.593134 TTGCGAAATAATAAAATGGCACTTAAT 57.407 25.926 0.00 0.00 0.00 1.40
563 569 6.267699 TGACTGGATATGATACCTAACAGTGG 59.732 42.308 0.00 0.00 37.98 4.00
575 581 4.981812 ACATGCACATGACTGGATATGAT 58.018 39.130 17.19 0.00 41.20 2.45
580 586 3.119743 CGAAAACATGCACATGACTGGAT 60.120 43.478 17.19 0.00 41.20 3.41
602 608 4.870221 AACTACGAAGAAACAACACACC 57.130 40.909 0.00 0.00 0.00 4.16
609 615 6.103997 ACTCTCACAAAACTACGAAGAAACA 58.896 36.000 0.00 0.00 0.00 2.83
664 671 5.376625 ACTGAAGACTATCTGCCAAAACAA 58.623 37.500 0.00 0.00 0.00 2.83
785 792 1.408340 CAATGCCATATTGGAACGCCA 59.592 47.619 0.00 0.00 40.96 5.69
788 795 2.358582 TCTGCAATGCCATATTGGAACG 59.641 45.455 1.53 0.00 40.96 3.95
910 923 6.942532 TGTTTTCAGAGTAAGCAAACTGAT 57.057 33.333 0.00 0.00 38.79 2.90
954 968 1.818060 ACACAAGCTGACACAAAGCAA 59.182 42.857 0.00 0.00 43.37 3.91
1209 1233 1.180029 GCAGTGCATGGGATGTTCTT 58.820 50.000 11.09 0.00 0.00 2.52
1249 1273 3.487372 GCCTTAAAGTTCAACCCAGACT 58.513 45.455 0.00 0.00 0.00 3.24
1278 1302 1.859302 TCAGCTCCTCCCTCTTCTTC 58.141 55.000 0.00 0.00 0.00 2.87
1279 1303 2.504996 CAATCAGCTCCTCCCTCTTCTT 59.495 50.000 0.00 0.00 0.00 2.52
1280 1304 2.117865 CAATCAGCTCCTCCCTCTTCT 58.882 52.381 0.00 0.00 0.00 2.85
1281 1305 1.140652 CCAATCAGCTCCTCCCTCTTC 59.859 57.143 0.00 0.00 0.00 2.87
1282 1306 1.211456 CCAATCAGCTCCTCCCTCTT 58.789 55.000 0.00 0.00 0.00 2.85
1283 1307 0.341258 TCCAATCAGCTCCTCCCTCT 59.659 55.000 0.00 0.00 0.00 3.69
1284 1308 0.758123 CTCCAATCAGCTCCTCCCTC 59.242 60.000 0.00 0.00 0.00 4.30
1286 1310 0.985490 ACCTCCAATCAGCTCCTCCC 60.985 60.000 0.00 0.00 0.00 4.30
1288 1312 3.389329 TCATTACCTCCAATCAGCTCCTC 59.611 47.826 0.00 0.00 0.00 3.71
1289 1313 3.387962 TCATTACCTCCAATCAGCTCCT 58.612 45.455 0.00 0.00 0.00 3.69
1291 1315 4.518211 CCAATCATTACCTCCAATCAGCTC 59.482 45.833 0.00 0.00 0.00 4.09
1292 1316 4.166725 TCCAATCATTACCTCCAATCAGCT 59.833 41.667 0.00 0.00 0.00 4.24
1293 1317 4.464008 TCCAATCATTACCTCCAATCAGC 58.536 43.478 0.00 0.00 0.00 4.26
1294 1318 5.068636 CCTCCAATCATTACCTCCAATCAG 58.931 45.833 0.00 0.00 0.00 2.90
1295 1319 4.478317 ACCTCCAATCATTACCTCCAATCA 59.522 41.667 0.00 0.00 0.00 2.57
1296 1320 4.823989 CACCTCCAATCATTACCTCCAATC 59.176 45.833 0.00 0.00 0.00 2.67
1297 1321 4.478317 TCACCTCCAATCATTACCTCCAAT 59.522 41.667 0.00 0.00 0.00 3.16
1298 1322 3.849574 TCACCTCCAATCATTACCTCCAA 59.150 43.478 0.00 0.00 0.00 3.53
1299 1323 3.459828 TCACCTCCAATCATTACCTCCA 58.540 45.455 0.00 0.00 0.00 3.86
1300 1324 4.103153 TCATCACCTCCAATCATTACCTCC 59.897 45.833 0.00 0.00 0.00 4.30
1301 1325 5.296151 TCATCACCTCCAATCATTACCTC 57.704 43.478 0.00 0.00 0.00 3.85
1302 1326 5.919348 ATCATCACCTCCAATCATTACCT 57.081 39.130 0.00 0.00 0.00 3.08
1303 1327 5.242393 CCAATCATCACCTCCAATCATTACC 59.758 44.000 0.00 0.00 0.00 2.85
1304 1328 6.016777 GTCCAATCATCACCTCCAATCATTAC 60.017 42.308 0.00 0.00 0.00 1.89
1305 1329 6.064060 GTCCAATCATCACCTCCAATCATTA 58.936 40.000 0.00 0.00 0.00 1.90
1306 1330 4.891756 GTCCAATCATCACCTCCAATCATT 59.108 41.667 0.00 0.00 0.00 2.57
1307 1331 4.467769 GTCCAATCATCACCTCCAATCAT 58.532 43.478 0.00 0.00 0.00 2.45
1308 1332 3.371917 GGTCCAATCATCACCTCCAATCA 60.372 47.826 0.00 0.00 0.00 2.57
1309 1333 3.217626 GGTCCAATCATCACCTCCAATC 58.782 50.000 0.00 0.00 0.00 2.67
1310 1334 2.582172 TGGTCCAATCATCACCTCCAAT 59.418 45.455 0.00 0.00 0.00 3.16
1311 1335 1.991813 TGGTCCAATCATCACCTCCAA 59.008 47.619 0.00 0.00 0.00 3.53
1312 1336 1.667595 TGGTCCAATCATCACCTCCA 58.332 50.000 0.00 0.00 0.00 3.86
1313 1337 2.025887 ACTTGGTCCAATCATCACCTCC 60.026 50.000 4.34 0.00 0.00 4.30
1314 1338 3.356529 ACTTGGTCCAATCATCACCTC 57.643 47.619 4.34 0.00 0.00 3.85
1315 1339 3.074390 TCAACTTGGTCCAATCATCACCT 59.926 43.478 4.34 0.00 0.00 4.00
1316 1340 3.420893 TCAACTTGGTCCAATCATCACC 58.579 45.455 4.34 0.00 0.00 4.02
1317 1341 5.404946 CAATCAACTTGGTCCAATCATCAC 58.595 41.667 4.34 0.00 0.00 3.06
1318 1342 5.648178 CAATCAACTTGGTCCAATCATCA 57.352 39.130 4.34 0.00 0.00 3.07
1330 1354 5.393787 CCAATCATCACCTCCAATCAACTTG 60.394 44.000 0.00 0.00 34.42 3.16
1331 1355 4.708421 CCAATCATCACCTCCAATCAACTT 59.292 41.667 0.00 0.00 0.00 2.66
1332 1356 4.018141 TCCAATCATCACCTCCAATCAACT 60.018 41.667 0.00 0.00 0.00 3.16
1333 1357 4.272489 TCCAATCATCACCTCCAATCAAC 58.728 43.478 0.00 0.00 0.00 3.18
1334 1358 4.589647 TCCAATCATCACCTCCAATCAA 57.410 40.909 0.00 0.00 0.00 2.57
1335 1359 4.079615 ACATCCAATCATCACCTCCAATCA 60.080 41.667 0.00 0.00 0.00 2.57
1336 1360 4.277672 CACATCCAATCATCACCTCCAATC 59.722 45.833 0.00 0.00 0.00 2.67
1337 1361 4.212716 CACATCCAATCATCACCTCCAAT 58.787 43.478 0.00 0.00 0.00 3.16
1338 1362 3.010472 ACACATCCAATCATCACCTCCAA 59.990 43.478 0.00 0.00 0.00 3.53
1339 1363 2.577563 ACACATCCAATCATCACCTCCA 59.422 45.455 0.00 0.00 0.00 3.86
1340 1364 3.287867 ACACATCCAATCATCACCTCC 57.712 47.619 0.00 0.00 0.00 4.30
1341 1365 4.769688 TGTACACATCCAATCATCACCTC 58.230 43.478 0.00 0.00 0.00 3.85
1342 1366 4.384537 CCTGTACACATCCAATCATCACCT 60.385 45.833 0.00 0.00 0.00 4.00
1343 1367 3.879295 CCTGTACACATCCAATCATCACC 59.121 47.826 0.00 0.00 0.00 4.02
1344 1368 3.879295 CCCTGTACACATCCAATCATCAC 59.121 47.826 0.00 0.00 0.00 3.06
1345 1369 3.117926 CCCCTGTACACATCCAATCATCA 60.118 47.826 0.00 0.00 0.00 3.07
1346 1370 3.136443 TCCCCTGTACACATCCAATCATC 59.864 47.826 0.00 0.00 0.00 2.92
1347 1371 3.117888 GTCCCCTGTACACATCCAATCAT 60.118 47.826 0.00 0.00 0.00 2.45
1348 1372 2.238646 GTCCCCTGTACACATCCAATCA 59.761 50.000 0.00 0.00 0.00 2.57
1349 1373 2.238646 TGTCCCCTGTACACATCCAATC 59.761 50.000 0.00 0.00 0.00 2.67
1350 1374 2.026262 GTGTCCCCTGTACACATCCAAT 60.026 50.000 0.00 0.00 45.26 3.16
1351 1375 1.349688 GTGTCCCCTGTACACATCCAA 59.650 52.381 0.00 0.00 45.26 3.53
1352 1376 0.981183 GTGTCCCCTGTACACATCCA 59.019 55.000 0.00 0.00 45.26 3.41
1353 1377 0.108329 CGTGTCCCCTGTACACATCC 60.108 60.000 7.10 0.00 46.05 3.51
1426 1450 0.265553 ATTACATTGCCCTGCCCCAT 59.734 50.000 0.00 0.00 0.00 4.00
1444 1468 5.063204 TCGTCCAGTCATCTCAAACAAAAT 58.937 37.500 0.00 0.00 0.00 1.82
1447 1471 3.744238 TCGTCCAGTCATCTCAAACAA 57.256 42.857 0.00 0.00 0.00 2.83
1449 1473 3.390135 TGTTCGTCCAGTCATCTCAAAC 58.610 45.455 0.00 0.00 0.00 2.93
1455 1479 3.058914 CCTTTGTTGTTCGTCCAGTCATC 60.059 47.826 0.00 0.00 0.00 2.92
1489 1513 2.566724 CCTCTTCTTCAGCCTCAACTCT 59.433 50.000 0.00 0.00 0.00 3.24
1536 1560 5.006386 ACAACATCTTCCTCTTCATCAACC 58.994 41.667 0.00 0.00 0.00 3.77
1554 1578 3.382227 GCCCATGATCATCATTGACAACA 59.618 43.478 4.86 0.00 34.28 3.33
1572 1596 1.679944 GCTAGTGCATCTTCAAGCCCA 60.680 52.381 0.00 0.00 39.41 5.36
1700 1724 4.160635 CAATGTTCGCGGGCGTCC 62.161 66.667 13.21 0.00 40.74 4.79
1708 1732 2.090524 GCTTGCCTGCAATGTTCGC 61.091 57.895 4.84 1.28 35.20 4.70
1937 1967 1.004679 CACCCATGCAAAGGCCAAC 60.005 57.895 5.01 0.00 40.13 3.77
2135 2165 2.632996 CCCATCCTTATGCTTCTACCGA 59.367 50.000 0.00 0.00 0.00 4.69
2139 2169 3.360740 TCCCCCATCCTTATGCTTCTA 57.639 47.619 0.00 0.00 0.00 2.10
2238 2309 8.068892 ACCACCTCATAAACAACAAAAGTAAA 57.931 30.769 0.00 0.00 0.00 2.01
2289 2364 4.080919 TCCCAGTTCATAGTGGACAAGATG 60.081 45.833 0.59 0.00 46.20 2.90
2419 2513 6.713762 AAAAGTTTCATGATGTGGACAGAA 57.286 33.333 0.00 0.00 0.00 3.02
2520 2619 5.221382 TGGACCGTGCTTATTAAGAGATACC 60.221 44.000 7.63 4.04 0.00 2.73
2528 2628 4.020928 TCAACTCTGGACCGTGCTTATTAA 60.021 41.667 0.00 0.00 0.00 1.40
2539 2639 0.957888 GCAAGCCTCAACTCTGGACC 60.958 60.000 0.00 0.00 0.00 4.46
2615 3214 9.261180 ACCATTTGATTAGACTGTTATGTATCG 57.739 33.333 0.00 0.00 0.00 2.92
2763 4637 3.194062 GGAGTCAGTATCTTTGCTCAGC 58.806 50.000 0.00 0.00 0.00 4.26
2857 4945 3.542969 ACTAGTGCAAAAAGGGGGAAT 57.457 42.857 0.00 0.00 0.00 3.01
2859 4947 2.962421 CAAACTAGTGCAAAAAGGGGGA 59.038 45.455 0.00 0.00 0.00 4.81
2861 4949 2.754472 GCAAACTAGTGCAAAAAGGGG 58.246 47.619 0.00 0.00 44.29 4.79
2880 4968 1.268386 CGGACACATCATGCATCTTGC 60.268 52.381 0.00 0.00 45.29 4.01
2881 4969 1.268386 GCGGACACATCATGCATCTTG 60.268 52.381 0.00 0.00 0.00 3.02
2882 4970 1.019673 GCGGACACATCATGCATCTT 58.980 50.000 0.00 0.00 0.00 2.40
2883 4971 0.107557 TGCGGACACATCATGCATCT 60.108 50.000 0.00 0.00 34.07 2.90
2884 4972 0.949397 ATGCGGACACATCATGCATC 59.051 50.000 0.00 0.00 41.86 3.91
2885 4973 0.949397 GATGCGGACACATCATGCAT 59.051 50.000 0.00 0.00 45.74 3.96
2901 4989 4.227134 CTGGCGACTCCCCCGATG 62.227 72.222 0.00 0.00 0.00 3.84
2905 4993 3.866582 CATCCTGGCGACTCCCCC 61.867 72.222 0.00 0.00 0.00 5.40
2907 4995 2.670148 AACCATCCTGGCGACTCCC 61.670 63.158 0.00 0.00 42.67 4.30
2908 4996 1.450312 CAACCATCCTGGCGACTCC 60.450 63.158 0.00 0.00 42.67 3.85
2909 4997 0.741221 GACAACCATCCTGGCGACTC 60.741 60.000 0.00 0.00 42.67 3.36
2910 4998 1.296715 GACAACCATCCTGGCGACT 59.703 57.895 0.00 0.00 42.67 4.18
2911 4999 3.890674 GACAACCATCCTGGCGAC 58.109 61.111 0.00 0.00 42.67 5.19
2914 5002 3.134127 GCCGACAACCATCCTGGC 61.134 66.667 0.00 0.00 42.67 4.85
2915 5003 2.819595 CGCCGACAACCATCCTGG 60.820 66.667 0.00 0.00 45.02 4.45
2916 5004 2.100631 GTCGCCGACAACCATCCTG 61.101 63.158 13.23 0.00 32.09 3.86
2917 5005 2.264794 GTCGCCGACAACCATCCT 59.735 61.111 13.23 0.00 32.09 3.24
2918 5006 3.186047 CGTCGCCGACAACCATCC 61.186 66.667 18.40 0.00 35.63 3.51
2919 5007 3.186047 CCGTCGCCGACAACCATC 61.186 66.667 18.40 0.00 35.63 3.51
2924 5012 2.616786 ATAATCGCCGTCGCCGACAA 62.617 55.000 18.40 0.00 37.56 3.18
2925 5013 2.616786 AATAATCGCCGTCGCCGACA 62.617 55.000 18.40 0.00 37.56 4.35
2926 5014 0.661187 TAATAATCGCCGTCGCCGAC 60.661 55.000 7.29 7.29 37.56 4.79
2927 5015 0.241749 ATAATAATCGCCGTCGCCGA 59.758 50.000 0.00 0.00 39.24 5.54
2929 5017 4.852609 AATAATAATAATCGCCGTCGCC 57.147 40.909 0.00 0.00 35.26 5.54
2931 5019 9.456797 GAACTAAAATAATAATAATCGCCGTCG 57.543 33.333 0.00 0.00 0.00 5.12
2933 5021 8.437742 CCGAACTAAAATAATAATAATCGCCGT 58.562 33.333 0.00 0.00 0.00 5.68
2934 5022 7.901377 CCCGAACTAAAATAATAATAATCGCCG 59.099 37.037 0.00 0.00 0.00 6.46
2936 5024 8.179615 CCCCCGAACTAAAATAATAATAATCGC 58.820 37.037 0.00 0.00 0.00 4.58
2975 5063 0.798776 CTCCAACTCATCGTGGCAAC 59.201 55.000 0.00 0.00 0.00 4.17
2976 5064 0.321564 CCTCCAACTCATCGTGGCAA 60.322 55.000 0.00 0.00 0.00 4.52
2977 5065 1.296392 CCTCCAACTCATCGTGGCA 59.704 57.895 0.00 0.00 0.00 4.92
2978 5066 2.109126 GCCTCCAACTCATCGTGGC 61.109 63.158 0.00 0.00 0.00 5.01
2979 5067 0.321564 TTGCCTCCAACTCATCGTGG 60.322 55.000 0.00 0.00 0.00 4.94
2980 5068 1.197721 GTTTGCCTCCAACTCATCGTG 59.802 52.381 0.00 0.00 0.00 4.35
2981 5069 1.523758 GTTTGCCTCCAACTCATCGT 58.476 50.000 0.00 0.00 0.00 3.73
2982 5070 0.443869 CGTTTGCCTCCAACTCATCG 59.556 55.000 0.00 0.00 0.00 3.84
2983 5071 0.169009 GCGTTTGCCTCCAACTCATC 59.831 55.000 0.00 0.00 33.98 2.92
2984 5072 0.537143 TGCGTTTGCCTCCAACTCAT 60.537 50.000 0.00 0.00 41.78 2.90
2985 5073 0.749818 TTGCGTTTGCCTCCAACTCA 60.750 50.000 0.00 0.00 41.78 3.41
2986 5074 0.317854 GTTGCGTTTGCCTCCAACTC 60.318 55.000 0.00 0.00 41.78 3.01
2987 5075 0.751643 AGTTGCGTTTGCCTCCAACT 60.752 50.000 0.00 0.00 42.03 3.16
2988 5076 0.594796 CAGTTGCGTTTGCCTCCAAC 60.595 55.000 0.00 0.00 41.78 3.77
2989 5077 1.732917 CAGTTGCGTTTGCCTCCAA 59.267 52.632 0.00 0.00 41.78 3.53
2990 5078 2.192861 CCAGTTGCGTTTGCCTCCA 61.193 57.895 0.00 0.00 41.78 3.86
2991 5079 2.644992 CCAGTTGCGTTTGCCTCC 59.355 61.111 0.00 0.00 41.78 4.30
2992 5080 2.644992 CCCAGTTGCGTTTGCCTC 59.355 61.111 0.00 0.00 41.78 4.70
2993 5081 2.912025 CCCCAGTTGCGTTTGCCT 60.912 61.111 0.00 0.00 41.78 4.75
2994 5082 4.662961 GCCCCAGTTGCGTTTGCC 62.663 66.667 0.00 0.00 41.78 4.52
2995 5083 4.999939 CGCCCCAGTTGCGTTTGC 63.000 66.667 0.00 0.00 46.59 3.68
3019 5107 4.671569 CAGCGCCGATAGCCCTCC 62.672 72.222 2.29 0.00 38.78 4.30
3020 5108 2.936912 ATCAGCGCCGATAGCCCTC 61.937 63.158 3.79 0.00 38.78 4.30
3021 5109 2.919856 ATCAGCGCCGATAGCCCT 60.920 61.111 3.79 0.00 38.78 5.19
3022 5110 2.715532 TTCATCAGCGCCGATAGCCC 62.716 60.000 5.66 0.00 38.78 5.19
3023 5111 0.880278 TTTCATCAGCGCCGATAGCC 60.880 55.000 5.66 0.00 38.78 3.93
3024 5112 1.151668 ATTTCATCAGCGCCGATAGC 58.848 50.000 5.66 0.00 38.52 2.97
3025 5113 2.926200 CCTATTTCATCAGCGCCGATAG 59.074 50.000 5.66 0.00 0.00 2.08
3026 5114 2.299013 ACCTATTTCATCAGCGCCGATA 59.701 45.455 5.66 0.00 0.00 2.92
3027 5115 1.070758 ACCTATTTCATCAGCGCCGAT 59.929 47.619 2.29 0.33 0.00 4.18
3028 5116 0.464036 ACCTATTTCATCAGCGCCGA 59.536 50.000 2.29 0.00 0.00 5.54
3029 5117 1.261619 GAACCTATTTCATCAGCGCCG 59.738 52.381 2.29 0.00 33.94 6.46
3030 5118 1.604278 GGAACCTATTTCATCAGCGCC 59.396 52.381 2.29 0.00 35.70 6.53
3031 5119 2.288666 TGGAACCTATTTCATCAGCGC 58.711 47.619 0.00 0.00 35.70 5.92
3032 5120 5.505173 AAATGGAACCTATTTCATCAGCG 57.495 39.130 0.00 0.00 35.70 5.18
3053 5141 6.256912 ACAACAAAGACCACTAACGAAAAA 57.743 33.333 0.00 0.00 0.00 1.94
3054 5142 5.883503 ACAACAAAGACCACTAACGAAAA 57.116 34.783 0.00 0.00 0.00 2.29
3055 5143 6.108015 ACTACAACAAAGACCACTAACGAAA 58.892 36.000 0.00 0.00 0.00 3.46
3056 5144 5.663456 ACTACAACAAAGACCACTAACGAA 58.337 37.500 0.00 0.00 0.00 3.85
3057 5145 5.266733 ACTACAACAAAGACCACTAACGA 57.733 39.130 0.00 0.00 0.00 3.85
3058 5146 5.978934 AACTACAACAAAGACCACTAACG 57.021 39.130 0.00 0.00 0.00 3.18
3059 5147 7.008901 GCAAAAACTACAACAAAGACCACTAAC 59.991 37.037 0.00 0.00 0.00 2.34
3060 5148 7.030768 GCAAAAACTACAACAAAGACCACTAA 58.969 34.615 0.00 0.00 0.00 2.24
3061 5149 6.151312 TGCAAAAACTACAACAAAGACCACTA 59.849 34.615 0.00 0.00 0.00 2.74
3062 5150 5.047660 TGCAAAAACTACAACAAAGACCACT 60.048 36.000 0.00 0.00 0.00 4.00
3063 5151 5.164954 TGCAAAAACTACAACAAAGACCAC 58.835 37.500 0.00 0.00 0.00 4.16
3064 5152 5.392767 TGCAAAAACTACAACAAAGACCA 57.607 34.783 0.00 0.00 0.00 4.02
3065 5153 6.533367 TGATTGCAAAAACTACAACAAAGACC 59.467 34.615 1.71 0.00 0.00 3.85
3066 5154 7.391016 GTGATTGCAAAAACTACAACAAAGAC 58.609 34.615 1.71 0.00 0.00 3.01
3067 5155 6.533367 GGTGATTGCAAAAACTACAACAAAGA 59.467 34.615 1.71 0.00 0.00 2.52
3068 5156 6.238076 GGGTGATTGCAAAAACTACAACAAAG 60.238 38.462 1.71 0.00 0.00 2.77
3069 5157 5.582665 GGGTGATTGCAAAAACTACAACAAA 59.417 36.000 1.71 0.00 0.00 2.83
3070 5158 5.112686 GGGTGATTGCAAAAACTACAACAA 58.887 37.500 1.71 0.00 0.00 2.83
3071 5159 4.442192 GGGGTGATTGCAAAAACTACAACA 60.442 41.667 1.71 0.00 0.00 3.33
3072 5160 4.055360 GGGGTGATTGCAAAAACTACAAC 58.945 43.478 1.71 0.18 0.00 3.32
3073 5161 3.706594 TGGGGTGATTGCAAAAACTACAA 59.293 39.130 1.71 0.00 0.00 2.41
3074 5162 3.300388 TGGGGTGATTGCAAAAACTACA 58.700 40.909 1.71 5.71 0.00 2.74
3075 5163 3.320826 ACTGGGGTGATTGCAAAAACTAC 59.679 43.478 1.71 3.24 0.00 2.73
3076 5164 3.571590 ACTGGGGTGATTGCAAAAACTA 58.428 40.909 1.71 0.00 0.00 2.24
3077 5165 2.397597 ACTGGGGTGATTGCAAAAACT 58.602 42.857 1.71 0.00 0.00 2.66
3078 5166 2.908688 ACTGGGGTGATTGCAAAAAC 57.091 45.000 1.71 4.65 0.00 2.43
3079 5167 3.432890 GGAAACTGGGGTGATTGCAAAAA 60.433 43.478 1.71 0.00 0.00 1.94
3080 5168 2.103941 GGAAACTGGGGTGATTGCAAAA 59.896 45.455 1.71 0.00 0.00 2.44
3081 5169 1.691434 GGAAACTGGGGTGATTGCAAA 59.309 47.619 1.71 0.00 0.00 3.68
3082 5170 1.337118 GGAAACTGGGGTGATTGCAA 58.663 50.000 0.00 0.00 0.00 4.08
3083 5171 0.187117 TGGAAACTGGGGTGATTGCA 59.813 50.000 0.00 0.00 0.00 4.08
3084 5172 1.273327 CTTGGAAACTGGGGTGATTGC 59.727 52.381 0.00 0.00 0.00 3.56
3085 5173 2.558359 GACTTGGAAACTGGGGTGATTG 59.442 50.000 0.00 0.00 0.00 2.67
3086 5174 2.490902 GGACTTGGAAACTGGGGTGATT 60.491 50.000 0.00 0.00 0.00 2.57
3087 5175 1.075536 GGACTTGGAAACTGGGGTGAT 59.924 52.381 0.00 0.00 0.00 3.06
3088 5176 0.476771 GGACTTGGAAACTGGGGTGA 59.523 55.000 0.00 0.00 0.00 4.02
3089 5177 0.889186 CGGACTTGGAAACTGGGGTG 60.889 60.000 0.00 0.00 0.00 4.61
3090 5178 1.057851 TCGGACTTGGAAACTGGGGT 61.058 55.000 0.00 0.00 0.00 4.95
3091 5179 0.605589 GTCGGACTTGGAAACTGGGG 60.606 60.000 0.00 0.00 0.00 4.96
3092 5180 0.396811 AGTCGGACTTGGAAACTGGG 59.603 55.000 4.45 0.00 0.00 4.45
3093 5181 1.797025 GAGTCGGACTTGGAAACTGG 58.203 55.000 12.67 0.00 0.00 4.00
3094 5182 1.419374 CGAGTCGGACTTGGAAACTG 58.581 55.000 16.27 0.00 0.00 3.16
3095 5183 0.319641 GCGAGTCGGACTTGGAAACT 60.320 55.000 23.40 0.00 30.15 2.66
3096 5184 0.599204 TGCGAGTCGGACTTGGAAAC 60.599 55.000 23.40 9.86 30.15 2.78
3097 5185 0.105224 TTGCGAGTCGGACTTGGAAA 59.895 50.000 24.69 13.00 37.06 3.13
3098 5186 0.599204 GTTGCGAGTCGGACTTGGAA 60.599 55.000 23.55 23.55 37.56 3.53
3099 5187 1.006571 GTTGCGAGTCGGACTTGGA 60.007 57.895 23.40 19.41 30.15 3.53
3100 5188 0.600255 AAGTTGCGAGTCGGACTTGG 60.600 55.000 23.40 14.61 30.15 3.61
3101 5189 0.508641 CAAGTTGCGAGTCGGACTTG 59.491 55.000 23.50 23.50 33.55 3.16
3102 5190 0.387929 TCAAGTTGCGAGTCGGACTT 59.612 50.000 15.52 14.13 0.00 3.01
3103 5191 0.039074 CTCAAGTTGCGAGTCGGACT 60.039 55.000 15.52 11.09 0.00 3.85
3104 5192 1.009389 CCTCAAGTTGCGAGTCGGAC 61.009 60.000 15.52 6.59 0.00 4.79
3105 5193 1.289066 CCTCAAGTTGCGAGTCGGA 59.711 57.895 15.52 9.10 0.00 4.55
3106 5194 0.600255 AACCTCAAGTTGCGAGTCGG 60.600 55.000 15.52 0.00 37.29 4.79
3107 5195 1.217882 AAACCTCAAGTTGCGAGTCG 58.782 50.000 8.54 8.54 39.19 4.18
3108 5196 3.692791 AAAAACCTCAAGTTGCGAGTC 57.307 42.857 0.00 0.00 39.19 3.36


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

AutoCloner maintained by Alex Coulton.