Multiple sequence alignment - TraesCS3B01G337900

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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 TraesCS3B01G337900 chr3B 100.000 5137 0 0 1 5137 544552309 544557445 0.000000e+00 9487
1 TraesCS3B01G337900 chr3B 90.811 185 15 2 1307 1490 263271172 263270989 3.970000e-61 246
2 TraesCS3B01G337900 chr3A 91.885 3093 149 45 2091 5137 532848973 532845937 0.000000e+00 4228
3 TraesCS3B01G337900 chr3A 92.290 1336 40 15 1 1316 532851283 532849991 0.000000e+00 1838
4 TraesCS3B01G337900 chr3A 91.905 630 27 5 1474 2102 532849994 532849388 0.000000e+00 859
5 TraesCS3B01G337900 chr3D 94.710 2382 69 23 1474 3814 418232660 418235025 0.000000e+00 3648
6 TraesCS3B01G337900 chr3D 92.337 1331 37 15 11 1316 418231371 418232661 0.000000e+00 1832
7 TraesCS3B01G337900 chr3D 95.375 800 32 3 3818 4612 418235088 418235887 0.000000e+00 1267
8 TraesCS3B01G337900 chr3D 85.749 407 11 5 4778 5137 418236248 418236654 2.240000e-103 387
9 TraesCS3B01G337900 chr3D 94.048 168 9 1 1315 1481 119413112 119413279 2.370000e-63 254
10 TraesCS3B01G337900 chr3D 90.104 192 13 5 1304 1492 211947744 211947556 1.430000e-60 244
11 TraesCS3B01G337900 chr3D 91.111 180 12 4 1298 1475 132930081 132929904 1.850000e-59 241
12 TraesCS3B01G337900 chr3D 92.254 142 7 3 4652 4790 418235886 418236026 1.130000e-46 198
13 TraesCS3B01G337900 chr5B 94.512 164 9 0 1312 1475 199658275 199658112 2.370000e-63 254
14 TraesCS3B01G337900 chr1D 93.567 171 9 2 1308 1476 249557347 249557177 2.370000e-63 254
15 TraesCS3B01G337900 chr1D 80.000 155 21 5 1482 1636 364494917 364495061 7.030000e-19 106
16 TraesCS3B01G337900 chr6D 93.064 173 10 2 1312 1483 406204731 406204902 8.540000e-63 252
17 TraesCS3B01G337900 chr4D 93.939 165 10 0 1315 1479 58643757 58643921 3.070000e-62 250
18 TraesCS3B01G337900 chr6B 91.620 179 13 2 1314 1491 601199433 601199610 3.970000e-61 246


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 TraesCS3B01G337900 chr3B 544552309 544557445 5136 False 9487.000000 9487 100.000000 1 5137 1 chr3B.!!$F1 5136
1 TraesCS3B01G337900 chr3A 532845937 532851283 5346 True 2308.333333 4228 92.026667 1 5137 3 chr3A.!!$R1 5136
2 TraesCS3B01G337900 chr3D 418231371 418236654 5283 False 1466.400000 3648 92.085000 11 5137 5 chr3D.!!$F2 5126

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
755 783 0.320073 TTCATGTGGTCGGGTTCGTC 60.320 55.0 0.00 0.0 37.69 4.20 F
1608 1645 0.243907 CATCCGATCCTAATCCGCGT 59.756 55.0 4.92 0.0 0.00 6.01 F
2437 2910 0.550914 TGGAACAACAGGTGAAGCCT 59.449 50.0 0.00 0.0 43.00 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2324 2797 1.413118 AGACCTGCAAACCAAAAGGG 58.587 50.000 0.00 0.00 44.81 3.95 R
3040 3539 1.557832 AGCAAATACCAGCGGAGGTTA 59.442 47.619 3.90 0.00 43.08 2.85 R
4408 4974 0.952280 TCTCAGTGTCAGTGGTCGAC 59.048 55.000 7.13 7.13 0.00 4.20 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
70 76 2.414691 GGCTGTTTCCTTTTGATCGCTC 60.415 50.000 0.00 0.00 0.00 5.03
158 164 2.420097 GCAACGTGCGGATGTTTTC 58.580 52.632 12.23 3.70 31.71 2.29
159 165 1.001745 GCAACGTGCGGATGTTTTCC 61.002 55.000 12.23 0.40 41.59 3.13
186 194 4.072088 GCGGTTTGAGTGACGCCG 62.072 66.667 0.00 0.00 45.70 6.46
288 304 8.931385 TTATTTAGTCAGGTTTATGGACGTAC 57.069 34.615 0.00 0.00 36.68 3.67
308 324 4.732672 ACCTTCTCCGTGTTACTTATCC 57.267 45.455 0.00 0.00 0.00 2.59
324 340 9.379811 GTTACTTATCCTCGAGTACTATTTTCG 57.620 37.037 12.31 0.00 35.76 3.46
569 597 2.106683 ATTGGCTTCGGCAGTACGC 61.107 57.895 1.72 1.72 43.96 4.42
611 639 7.782644 AGCTTCCAGTCTTTCAGTATAGAGTAT 59.217 37.037 0.00 0.00 0.00 2.12
612 640 9.069082 GCTTCCAGTCTTTCAGTATAGAGTATA 57.931 37.037 0.00 0.00 0.00 1.47
616 644 9.787435 CCAGTCTTTCAGTATAGAGTATAGAGT 57.213 37.037 0.00 0.00 0.00 3.24
749 777 1.026718 GGCTTCTTCATGTGGTCGGG 61.027 60.000 0.00 0.00 0.00 5.14
755 783 0.320073 TTCATGTGGTCGGGTTCGTC 60.320 55.000 0.00 0.00 37.69 4.20
877 911 1.148310 CGGTCAACTGGATGTCACAC 58.852 55.000 0.00 0.00 0.00 3.82
878 912 1.540146 CGGTCAACTGGATGTCACACA 60.540 52.381 0.00 0.00 0.00 3.72
959 993 8.908903 TCAAAATGTACCTTGTTATGTGACTTT 58.091 29.630 0.00 0.00 0.00 2.66
975 1009 5.059833 GTGACTTTGTCTCTTTCATCAGGT 58.940 41.667 0.00 0.00 33.15 4.00
1149 1184 6.321945 TGATGTGCAAGATGGTATTATTTGCT 59.678 34.615 8.68 0.00 43.29 3.91
1316 1353 9.403110 CTACCGAACACCATTTGTACTATATAC 57.597 37.037 0.00 0.00 37.51 1.47
1317 1354 8.015185 ACCGAACACCATTTGTACTATATACT 57.985 34.615 0.00 0.00 37.51 2.12
1318 1355 8.139989 ACCGAACACCATTTGTACTATATACTC 58.860 37.037 0.00 0.00 37.51 2.59
1319 1356 7.597743 CCGAACACCATTTGTACTATATACTCC 59.402 40.741 0.00 0.00 37.51 3.85
1320 1357 7.597743 CGAACACCATTTGTACTATATACTCCC 59.402 40.741 0.00 0.00 37.51 4.30
1321 1358 8.562949 AACACCATTTGTACTATATACTCCCT 57.437 34.615 0.00 0.00 37.51 4.20
1322 1359 8.191534 ACACCATTTGTACTATATACTCCCTC 57.808 38.462 0.00 0.00 36.32 4.30
1323 1360 7.234988 ACACCATTTGTACTATATACTCCCTCC 59.765 40.741 0.00 0.00 36.32 4.30
1324 1361 6.436532 ACCATTTGTACTATATACTCCCTCCG 59.563 42.308 0.00 0.00 0.00 4.63
1325 1362 6.436532 CCATTTGTACTATATACTCCCTCCGT 59.563 42.308 0.00 0.00 0.00 4.69
1326 1363 7.039223 CCATTTGTACTATATACTCCCTCCGTT 60.039 40.741 0.00 0.00 0.00 4.44
1327 1364 7.516198 TTTGTACTATATACTCCCTCCGTTC 57.484 40.000 0.00 0.00 0.00 3.95
1328 1365 5.564550 TGTACTATATACTCCCTCCGTTCC 58.435 45.833 0.00 0.00 0.00 3.62
1329 1366 5.311649 TGTACTATATACTCCCTCCGTTCCT 59.688 44.000 0.00 0.00 0.00 3.36
1330 1367 6.501805 TGTACTATATACTCCCTCCGTTCCTA 59.498 42.308 0.00 0.00 0.00 2.94
1331 1368 6.460103 ACTATATACTCCCTCCGTTCCTAA 57.540 41.667 0.00 0.00 0.00 2.69
1332 1369 6.856757 ACTATATACTCCCTCCGTTCCTAAA 58.143 40.000 0.00 0.00 0.00 1.85
1333 1370 7.477008 ACTATATACTCCCTCCGTTCCTAAAT 58.523 38.462 0.00 0.00 0.00 1.40
1334 1371 8.618385 ACTATATACTCCCTCCGTTCCTAAATA 58.382 37.037 0.00 0.00 0.00 1.40
1335 1372 9.643735 CTATATACTCCCTCCGTTCCTAAATAT 57.356 37.037 0.00 0.00 0.00 1.28
1338 1375 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
1339 1376 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
1340 1377 7.300658 ACTCCCTCCGTTCCTAAATATAAGTA 58.699 38.462 0.00 0.00 0.00 2.24
1341 1378 7.954620 ACTCCCTCCGTTCCTAAATATAAGTAT 59.045 37.037 0.00 0.00 0.00 2.12
1342 1379 8.731591 TCCCTCCGTTCCTAAATATAAGTATT 57.268 34.615 0.00 0.00 31.89 1.89
1343 1380 9.162733 TCCCTCCGTTCCTAAATATAAGTATTT 57.837 33.333 0.00 0.00 41.92 1.40
1344 1381 9.216117 CCCTCCGTTCCTAAATATAAGTATTTG 57.784 37.037 4.20 0.00 40.01 2.32
1345 1382 9.774413 CCTCCGTTCCTAAATATAAGTATTTGT 57.226 33.333 4.20 0.00 40.01 2.83
1361 1398 8.928270 AAGTATTTGTAGAGATTTCACTACGG 57.072 34.615 9.58 0.00 41.09 4.02
1362 1399 8.289939 AGTATTTGTAGAGATTTCACTACGGA 57.710 34.615 9.58 3.13 41.09 4.69
1363 1400 8.189460 AGTATTTGTAGAGATTTCACTACGGAC 58.811 37.037 9.58 5.93 41.09 4.79
1364 1401 6.585695 TTTGTAGAGATTTCACTACGGACT 57.414 37.500 9.58 0.00 41.09 3.85
1365 1402 7.692460 TTTGTAGAGATTTCACTACGGACTA 57.308 36.000 9.58 0.00 41.09 2.59
1366 1403 6.674694 TGTAGAGATTTCACTACGGACTAC 57.325 41.667 9.58 0.00 41.09 2.73
1367 1404 6.175471 TGTAGAGATTTCACTACGGACTACA 58.825 40.000 0.00 0.00 41.09 2.74
1368 1405 6.827251 TGTAGAGATTTCACTACGGACTACAT 59.173 38.462 0.00 0.00 41.09 2.29
1369 1406 7.989170 TGTAGAGATTTCACTACGGACTACATA 59.011 37.037 0.00 0.00 41.09 2.29
1370 1407 7.261829 AGAGATTTCACTACGGACTACATAC 57.738 40.000 0.00 0.00 0.00 2.39
1371 1408 6.018098 AGAGATTTCACTACGGACTACATACG 60.018 42.308 0.00 0.00 0.00 3.06
1372 1409 4.621068 TTTCACTACGGACTACATACGG 57.379 45.455 0.00 0.00 0.00 4.02
1373 1410 3.541996 TCACTACGGACTACATACGGA 57.458 47.619 0.00 0.00 0.00 4.69
1374 1411 3.461061 TCACTACGGACTACATACGGAG 58.539 50.000 0.00 0.00 43.89 4.63
1375 1412 2.032204 CACTACGGACTACATACGGAGC 60.032 54.545 0.00 0.00 42.12 4.70
1376 1413 2.216046 CTACGGACTACATACGGAGCA 58.784 52.381 0.00 0.00 31.15 4.26
1377 1414 1.466856 ACGGACTACATACGGAGCAA 58.533 50.000 0.00 0.00 0.00 3.91
1378 1415 1.820519 ACGGACTACATACGGAGCAAA 59.179 47.619 0.00 0.00 0.00 3.68
1379 1416 2.231964 ACGGACTACATACGGAGCAAAA 59.768 45.455 0.00 0.00 0.00 2.44
1380 1417 3.118884 ACGGACTACATACGGAGCAAAAT 60.119 43.478 0.00 0.00 0.00 1.82
1381 1418 3.245284 CGGACTACATACGGAGCAAAATG 59.755 47.826 0.00 0.00 0.00 2.32
1382 1419 4.439057 GGACTACATACGGAGCAAAATGA 58.561 43.478 0.00 0.00 0.00 2.57
1383 1420 4.508124 GGACTACATACGGAGCAAAATGAG 59.492 45.833 0.00 0.00 0.00 2.90
1384 1421 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
1385 1422 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
1386 1423 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
1387 1424 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
1388 1425 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
1389 1426 3.837213 ACGGAGCAAAATGAGTGAATG 57.163 42.857 0.00 0.00 0.00 2.67
1390 1427 3.149196 ACGGAGCAAAATGAGTGAATGT 58.851 40.909 0.00 0.00 0.00 2.71
1391 1428 4.323417 ACGGAGCAAAATGAGTGAATGTA 58.677 39.130 0.00 0.00 0.00 2.29
1392 1429 4.759693 ACGGAGCAAAATGAGTGAATGTAA 59.240 37.500 0.00 0.00 0.00 2.41
1393 1430 5.240623 ACGGAGCAAAATGAGTGAATGTAAA 59.759 36.000 0.00 0.00 0.00 2.01
1394 1431 5.569059 CGGAGCAAAATGAGTGAATGTAAAC 59.431 40.000 0.00 0.00 0.00 2.01
1395 1432 6.568462 CGGAGCAAAATGAGTGAATGTAAACT 60.568 38.462 0.00 0.00 0.00 2.66
1396 1433 7.147976 GGAGCAAAATGAGTGAATGTAAACTT 58.852 34.615 0.00 0.00 0.00 2.66
1397 1434 7.653311 GGAGCAAAATGAGTGAATGTAAACTTT 59.347 33.333 0.00 0.00 0.00 2.66
1398 1435 9.677567 GAGCAAAATGAGTGAATGTAAACTTTA 57.322 29.630 0.00 0.00 0.00 1.85
1404 1441 9.979578 AATGAGTGAATGTAAACTTTAAATGCA 57.020 25.926 0.00 0.00 0.00 3.96
1406 1443 9.624697 TGAGTGAATGTAAACTTTAAATGCATC 57.375 29.630 0.00 0.00 0.00 3.91
1407 1444 9.846248 GAGTGAATGTAAACTTTAAATGCATCT 57.154 29.630 0.00 0.00 0.00 2.90
1419 1456 9.944376 ACTTTAAATGCATCTATATACATCCGT 57.056 29.630 0.00 0.00 0.00 4.69
1424 1461 8.877808 AATGCATCTATATACATCCGTATGTG 57.122 34.615 3.56 0.00 45.99 3.21
1425 1462 6.273071 TGCATCTATATACATCCGTATGTGC 58.727 40.000 3.56 0.00 45.99 4.57
1426 1463 6.096846 TGCATCTATATACATCCGTATGTGCT 59.903 38.462 3.56 0.00 45.99 4.40
1427 1464 6.980978 GCATCTATATACATCCGTATGTGCTT 59.019 38.462 3.56 0.00 45.99 3.91
1428 1465 7.168302 GCATCTATATACATCCGTATGTGCTTC 59.832 40.741 3.56 0.00 45.99 3.86
1429 1466 7.696992 TCTATATACATCCGTATGTGCTTCA 57.303 36.000 3.56 0.00 45.99 3.02
1430 1467 8.293699 TCTATATACATCCGTATGTGCTTCAT 57.706 34.615 3.56 0.00 45.99 2.57
1431 1468 9.403583 TCTATATACATCCGTATGTGCTTCATA 57.596 33.333 3.56 0.00 45.99 2.15
1432 1469 9.670719 CTATATACATCCGTATGTGCTTCATAG 57.329 37.037 3.56 0.80 45.99 2.23
1433 1470 4.672587 ACATCCGTATGTGCTTCATAGT 57.327 40.909 0.00 0.00 44.79 2.12
1434 1471 4.371786 ACATCCGTATGTGCTTCATAGTG 58.628 43.478 0.00 3.93 44.79 2.74
1435 1472 3.452755 TCCGTATGTGCTTCATAGTGG 57.547 47.619 11.08 11.08 39.36 4.00
1436 1473 3.028130 TCCGTATGTGCTTCATAGTGGA 58.972 45.455 13.75 13.75 39.94 4.02
1437 1474 3.641436 TCCGTATGTGCTTCATAGTGGAT 59.359 43.478 13.75 0.00 38.61 3.41
1438 1475 4.100963 TCCGTATGTGCTTCATAGTGGATT 59.899 41.667 13.75 0.00 38.61 3.01
1439 1476 4.449068 CCGTATGTGCTTCATAGTGGATTC 59.551 45.833 11.53 0.00 39.36 2.52
1440 1477 5.292765 CGTATGTGCTTCATAGTGGATTCT 58.707 41.667 3.20 0.00 39.36 2.40
1441 1478 5.403766 CGTATGTGCTTCATAGTGGATTCTC 59.596 44.000 3.20 0.00 39.36 2.87
1442 1479 5.627182 ATGTGCTTCATAGTGGATTCTCT 57.373 39.130 0.00 0.00 34.67 3.10
1443 1480 6.737720 ATGTGCTTCATAGTGGATTCTCTA 57.262 37.500 0.00 0.00 34.67 2.43
1444 1481 5.907207 TGTGCTTCATAGTGGATTCTCTAC 58.093 41.667 0.00 0.00 0.00 2.59
1445 1482 5.422012 TGTGCTTCATAGTGGATTCTCTACA 59.578 40.000 0.00 0.00 29.47 2.74
1446 1483 6.070824 TGTGCTTCATAGTGGATTCTCTACAA 60.071 38.462 0.00 0.00 29.47 2.41
1447 1484 6.818644 GTGCTTCATAGTGGATTCTCTACAAA 59.181 38.462 0.00 0.00 29.47 2.83
1448 1485 7.010923 GTGCTTCATAGTGGATTCTCTACAAAG 59.989 40.741 0.00 3.49 29.47 2.77
1449 1486 7.093333 TGCTTCATAGTGGATTCTCTACAAAGA 60.093 37.037 9.13 0.00 29.47 2.52
1450 1487 7.223777 GCTTCATAGTGGATTCTCTACAAAGAC 59.776 40.741 9.13 0.00 29.47 3.01
1451 1488 7.962995 TCATAGTGGATTCTCTACAAAGACT 57.037 36.000 0.00 0.00 29.47 3.24
1452 1489 8.367660 TCATAGTGGATTCTCTACAAAGACTT 57.632 34.615 0.00 0.00 29.47 3.01
1453 1490 9.475620 TCATAGTGGATTCTCTACAAAGACTTA 57.524 33.333 0.00 0.00 29.47 2.24
1468 1505 8.943909 ACAAAGACTTATATTTAGGAACGGAG 57.056 34.615 0.00 0.00 0.00 4.63
1469 1506 7.985752 ACAAAGACTTATATTTAGGAACGGAGG 59.014 37.037 0.00 0.00 0.00 4.30
1470 1507 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
1471 1508 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
1472 1509 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
1473 1510 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
1474 1511 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
1482 1519 3.428532 GAACGGAGGGAGTATATGGCTA 58.571 50.000 0.00 0.00 0.00 3.93
1608 1645 0.243907 CATCCGATCCTAATCCGCGT 59.756 55.000 4.92 0.00 0.00 6.01
1623 1660 1.866601 CCGCGTATGCATCTGAAATCA 59.133 47.619 0.19 0.00 42.97 2.57
1767 1805 9.952188 GAGCAGTTAAGTTCTTCAGTAAAATTT 57.048 29.630 0.00 0.00 0.00 1.82
1807 1845 7.271511 AGATTTTCAAAACCAAGCATGTTACA 58.728 30.769 0.00 0.00 0.00 2.41
1899 1940 5.010922 CCATGGGAAACAGAAGTTGAATCAA 59.989 40.000 2.85 0.00 38.17 2.57
1950 1991 4.706842 ACAGGTTGACCTCAGTGTATTT 57.293 40.909 0.00 0.00 46.65 1.40
2003 2044 2.810439 TATTTGCCCTTTGTGTGTGC 57.190 45.000 0.00 0.00 0.00 4.57
2072 2116 5.680619 TCCTTTAGGCAATAGTGGTATGTG 58.319 41.667 0.00 0.00 34.44 3.21
2196 2669 0.839946 ACCCTTTGCACTCACTCACT 59.160 50.000 0.00 0.00 0.00 3.41
2214 2687 4.017126 TCACTCACACTACCACCTATGAG 58.983 47.826 0.00 0.00 39.56 2.90
2303 2776 5.244189 TCTCAGTGTACCAGAACTCTAGT 57.756 43.478 0.00 0.00 0.00 2.57
2324 2797 9.216117 TCTAGTTACTTTCTTGGCTACAAATTC 57.784 33.333 0.00 0.00 35.89 2.17
2437 2910 0.550914 TGGAACAACAGGTGAAGCCT 59.449 50.000 0.00 0.00 43.00 4.58
2492 2965 7.147479 ACCCTGTGCTTATTGACATATCTACTT 60.147 37.037 0.00 0.00 0.00 2.24
2659 3133 9.347240 TCTCTAATATTACACTAGCGGTAAAGT 57.653 33.333 10.55 0.00 34.67 2.66
3040 3539 2.176798 TGAAGGAACCACACCTGGAATT 59.823 45.455 0.00 0.00 40.55 2.17
3059 3558 2.032680 TAACCTCCGCTGGTATTTGC 57.967 50.000 0.00 0.00 39.83 3.68
3112 3611 7.711846 TGGGTCATTATTGTTATTTCATTCGG 58.288 34.615 0.00 0.00 0.00 4.30
3125 3624 3.165058 TCATTCGGTCTGATCTTTCCG 57.835 47.619 13.75 13.75 43.65 4.30
3335 3836 6.404954 CCTCAATGTGTGCATACATGAATGAA 60.405 38.462 27.09 12.08 40.24 2.57
3515 4016 8.911247 AGTCTTTTATTGTGTTTGTGTTCTTC 57.089 30.769 0.00 0.00 0.00 2.87
3527 4028 7.587757 GTGTTTGTGTTCTTCATAACTCACATC 59.412 37.037 0.00 0.00 36.08 3.06
3660 4161 0.392461 GTTTCTGTGCCGAGGCCATA 60.392 55.000 12.05 0.00 41.09 2.74
3678 4180 9.169592 GAGGCCATACTGTAATTTAGTTTAACA 57.830 33.333 5.01 0.00 0.00 2.41
3709 4211 4.903045 TCAGTAGGTTTTCCCTAGGTTG 57.097 45.455 8.29 0.00 46.75 3.77
3724 4226 3.801114 AGGTTGTTTGGCTTTGTCTTC 57.199 42.857 0.00 0.00 0.00 2.87
3730 4232 3.113322 GTTTGGCTTTGTCTTCGGTTTC 58.887 45.455 0.00 0.00 0.00 2.78
3757 4259 0.838554 TGCTAGGCCCTTGGTGTGTA 60.839 55.000 0.00 0.00 0.00 2.90
3758 4260 0.326927 GCTAGGCCCTTGGTGTGTAA 59.673 55.000 0.00 0.00 0.00 2.41
3773 4275 2.869801 TGTGTAACTGTTTCTGCTTCCG 59.130 45.455 0.00 0.00 38.04 4.30
3876 4441 2.769663 ACAGGTGGCACGGATAATTCTA 59.230 45.455 12.17 0.00 0.00 2.10
3932 4497 7.382488 CCACTATGATGACGTAATTCCTACTTG 59.618 40.741 0.00 0.00 0.00 3.16
3936 4501 5.867174 TGATGACGTAATTCCTACTTGTGTG 59.133 40.000 0.00 0.00 0.00 3.82
3937 4502 5.456548 TGACGTAATTCCTACTTGTGTGA 57.543 39.130 0.00 0.00 0.00 3.58
3943 4508 3.769739 TTCCTACTTGTGTGACAGCAT 57.230 42.857 0.00 0.00 0.00 3.79
3944 4509 3.044235 TCCTACTTGTGTGACAGCATG 57.956 47.619 0.00 0.00 46.00 4.06
4137 4702 3.018149 ACGCTAACTAAGAGGGAGTGAG 58.982 50.000 0.00 0.00 0.00 3.51
4170 4735 1.663379 GCAGATGCAAGCTCATGGCA 61.663 55.000 0.00 5.04 41.58 4.92
4214 4780 5.815581 TCCTGCCTTACAGTCACATAAAAT 58.184 37.500 0.00 0.00 45.68 1.82
4482 5048 3.428589 GGTTGAAATCTGGCATCTGCTTC 60.429 47.826 1.70 0.00 41.70 3.86
4513 5086 5.617087 CGACTTACGACTCTGAATGTGAAGA 60.617 44.000 0.00 0.00 45.77 2.87
4521 5094 5.411781 ACTCTGAATGTGAAGACGGTATTC 58.588 41.667 8.50 8.50 0.00 1.75
4556 5129 5.869344 TCAGAATCTGAATTGTAGTGGTTCG 59.131 40.000 10.99 0.00 37.57 3.95
4599 5172 1.238439 CCTGTTCAATCTTGGTGCGT 58.762 50.000 0.00 0.00 0.00 5.24
4600 5173 1.069022 CCTGTTCAATCTTGGTGCGTG 60.069 52.381 0.00 0.00 0.00 5.34
4641 5220 2.923655 GTGATCACTACCATGTGTGACG 59.076 50.000 18.83 0.00 44.52 4.35
4642 5221 1.927174 GATCACTACCATGTGTGACGC 59.073 52.381 13.23 0.00 44.52 5.19
4643 5222 0.676736 TCACTACCATGTGTGACGCA 59.323 50.000 0.00 0.00 38.15 5.24
4644 5223 2.930887 ATCACTACCATGTGTGACGCAC 60.931 50.000 12.29 12.29 44.52 5.34
4754 5335 1.846712 GAGAGCTGCTCCAGGGGTTT 61.847 60.000 25.09 4.73 37.69 3.27
4755 5336 0.547712 AGAGCTGCTCCAGGGGTTTA 60.548 55.000 25.09 0.00 31.21 2.01
4756 5337 0.548510 GAGCTGCTCCAGGGGTTTAT 59.451 55.000 18.80 0.00 31.21 1.40
4757 5338 0.257039 AGCTGCTCCAGGGGTTTATG 59.743 55.000 0.00 0.00 31.21 1.90
4761 5342 2.493278 CTGCTCCAGGGGTTTATGTTTG 59.507 50.000 0.00 0.00 0.00 2.93
4820 5636 8.900511 TGATTATTCTTTTCTTTTGCGATGAG 57.099 30.769 0.00 0.00 0.00 2.90
4854 5670 5.295431 TCTGCATACAAAGTGCACATAAC 57.705 39.130 21.04 0.28 46.76 1.89
4928 5770 0.859232 GTGTGTGTTACGTGAGGCTG 59.141 55.000 0.00 0.00 0.00 4.85
4937 5779 2.266055 GTGAGGCTGCGGCTAAGT 59.734 61.111 18.85 0.00 38.98 2.24
5033 5878 3.875134 GCACCACCACACCAATATAGTAC 59.125 47.826 0.00 0.00 0.00 2.73
5120 5983 1.648467 GGGATTGCCTGTGAGCGTTC 61.648 60.000 0.00 0.00 34.65 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 45 2.747686 GAAACAGCCCCGAGTCCA 59.252 61.111 0.00 0.00 0.00 4.02
70 76 1.852067 CGCCCGGAAGAAAACACCAG 61.852 60.000 0.73 0.00 0.00 4.00
94 100 3.047280 GGACGACAATGGCACGCA 61.047 61.111 0.00 0.00 0.00 5.24
288 304 4.497674 CGAGGATAAGTAACACGGAGAAGG 60.498 50.000 0.00 0.00 0.00 3.46
308 324 3.677601 TCGCACGAAAATAGTACTCGAG 58.322 45.455 11.84 11.84 36.45 4.04
500 528 7.770897 AGAGCCACAGTTTAAGTAAGATAATGG 59.229 37.037 0.00 0.00 0.00 3.16
501 529 8.723942 AGAGCCACAGTTTAAGTAAGATAATG 57.276 34.615 0.00 0.00 0.00 1.90
569 597 4.022935 TGGAAGCTGTGAATAAAGCAACAG 60.023 41.667 0.00 0.00 42.06 3.16
614 642 5.204292 TGCACCAGAGATTGAGTCTATACT 58.796 41.667 0.00 0.00 37.29 2.12
615 643 5.521906 TGCACCAGAGATTGAGTCTATAC 57.478 43.478 0.00 0.00 37.29 1.47
616 644 5.510349 GCATGCACCAGAGATTGAGTCTATA 60.510 44.000 14.21 0.00 37.29 1.31
617 645 4.743045 GCATGCACCAGAGATTGAGTCTAT 60.743 45.833 14.21 0.00 37.29 1.98
749 777 6.897259 TGCATAATGGTAAAGTAGACGAAC 57.103 37.500 0.00 0.00 0.00 3.95
755 783 8.892723 TCACTTGAATGCATAATGGTAAAGTAG 58.107 33.333 0.00 0.00 0.00 2.57
959 993 3.071457 TCAGCAACCTGATGAAAGAGACA 59.929 43.478 0.00 0.00 40.12 3.41
975 1009 7.795047 TCAATTCCTATATCTTGACTCAGCAA 58.205 34.615 0.00 0.00 0.00 3.91
1149 1184 8.112822 TCATAAATGTCAACAAATAAGAGGGGA 58.887 33.333 0.00 0.00 0.00 4.81
1316 1353 6.667558 ACTTATATTTAGGAACGGAGGGAG 57.332 41.667 0.00 0.00 0.00 4.30
1317 1354 8.731591 AATACTTATATTTAGGAACGGAGGGA 57.268 34.615 0.00 0.00 0.00 4.20
1318 1355 9.216117 CAAATACTTATATTTAGGAACGGAGGG 57.784 37.037 0.00 0.00 38.67 4.30
1319 1356 9.774413 ACAAATACTTATATTTAGGAACGGAGG 57.226 33.333 0.00 0.00 38.67 4.30
1336 1373 8.746530 TCCGTAGTGAAATCTCTACAAATACTT 58.253 33.333 17.80 0.00 40.85 2.24
1337 1374 8.189460 GTCCGTAGTGAAATCTCTACAAATACT 58.811 37.037 17.80 0.00 40.85 2.12
1338 1375 8.189460 AGTCCGTAGTGAAATCTCTACAAATAC 58.811 37.037 17.80 11.40 40.85 1.89
1339 1376 8.289939 AGTCCGTAGTGAAATCTCTACAAATA 57.710 34.615 17.80 3.02 40.85 1.40
1340 1377 7.171630 AGTCCGTAGTGAAATCTCTACAAAT 57.828 36.000 17.80 6.41 40.85 2.32
1341 1378 6.585695 AGTCCGTAGTGAAATCTCTACAAA 57.414 37.500 17.80 6.65 40.85 2.83
1342 1379 6.656270 TGTAGTCCGTAGTGAAATCTCTACAA 59.344 38.462 17.80 6.91 40.85 2.41
1343 1380 6.175471 TGTAGTCCGTAGTGAAATCTCTACA 58.825 40.000 17.80 0.00 40.85 2.74
1344 1381 6.674694 TGTAGTCCGTAGTGAAATCTCTAC 57.325 41.667 10.98 10.98 38.73 2.59
1345 1382 7.170489 CGTATGTAGTCCGTAGTGAAATCTCTA 59.830 40.741 0.00 0.00 0.00 2.43
1346 1383 6.018098 CGTATGTAGTCCGTAGTGAAATCTCT 60.018 42.308 0.00 0.00 0.00 3.10
1347 1384 6.134730 CGTATGTAGTCCGTAGTGAAATCTC 58.865 44.000 0.00 0.00 0.00 2.75
1348 1385 5.008415 CCGTATGTAGTCCGTAGTGAAATCT 59.992 44.000 0.00 0.00 0.00 2.40
1349 1386 5.008019 TCCGTATGTAGTCCGTAGTGAAATC 59.992 44.000 0.00 0.00 0.00 2.17
1350 1387 4.883585 TCCGTATGTAGTCCGTAGTGAAAT 59.116 41.667 0.00 0.00 0.00 2.17
1351 1388 4.260985 TCCGTATGTAGTCCGTAGTGAAA 58.739 43.478 0.00 0.00 0.00 2.69
1352 1389 3.872696 TCCGTATGTAGTCCGTAGTGAA 58.127 45.455 0.00 0.00 0.00 3.18
1353 1390 3.461061 CTCCGTATGTAGTCCGTAGTGA 58.539 50.000 0.00 0.00 0.00 3.41
1354 1391 2.032204 GCTCCGTATGTAGTCCGTAGTG 60.032 54.545 0.00 0.00 0.00 2.74
1355 1392 2.216898 GCTCCGTATGTAGTCCGTAGT 58.783 52.381 0.00 0.00 0.00 2.73
1356 1393 2.216046 TGCTCCGTATGTAGTCCGTAG 58.784 52.381 0.00 0.00 0.00 3.51
1357 1394 2.330440 TGCTCCGTATGTAGTCCGTA 57.670 50.000 0.00 0.00 0.00 4.02
1358 1395 1.466856 TTGCTCCGTATGTAGTCCGT 58.533 50.000 0.00 0.00 0.00 4.69
1359 1396 2.572191 TTTGCTCCGTATGTAGTCCG 57.428 50.000 0.00 0.00 0.00 4.79
1360 1397 4.439057 TCATTTTGCTCCGTATGTAGTCC 58.561 43.478 0.00 0.00 0.00 3.85
1361 1398 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
1362 1399 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
1363 1400 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
1364 1401 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
1365 1402 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
1366 1403 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
1367 1404 4.943705 ACATTCACTCATTTTGCTCCGTAT 59.056 37.500 0.00 0.00 0.00 3.06
1368 1405 4.323417 ACATTCACTCATTTTGCTCCGTA 58.677 39.130 0.00 0.00 0.00 4.02
1369 1406 3.149196 ACATTCACTCATTTTGCTCCGT 58.851 40.909 0.00 0.00 0.00 4.69
1370 1407 3.837213 ACATTCACTCATTTTGCTCCG 57.163 42.857 0.00 0.00 0.00 4.63
1371 1408 6.681777 AGTTTACATTCACTCATTTTGCTCC 58.318 36.000 0.00 0.00 0.00 4.70
1372 1409 8.579682 AAAGTTTACATTCACTCATTTTGCTC 57.420 30.769 0.00 0.00 0.00 4.26
1378 1415 9.979578 TGCATTTAAAGTTTACATTCACTCATT 57.020 25.926 0.00 0.00 0.00 2.57
1380 1417 9.624697 GATGCATTTAAAGTTTACATTCACTCA 57.375 29.630 0.00 0.00 0.00 3.41
1381 1418 9.846248 AGATGCATTTAAAGTTTACATTCACTC 57.154 29.630 0.00 0.00 0.00 3.51
1393 1430 9.944376 ACGGATGTATATAGATGCATTTAAAGT 57.056 29.630 11.19 0.00 38.38 2.66
1398 1435 9.317936 CACATACGGATGTATATAGATGCATTT 57.682 33.333 14.23 0.00 44.82 2.32
1399 1436 7.439356 GCACATACGGATGTATATAGATGCATT 59.561 37.037 14.23 1.23 44.82 3.56
1400 1437 6.925718 GCACATACGGATGTATATAGATGCAT 59.074 38.462 14.23 0.00 44.82 3.96
1401 1438 6.096846 AGCACATACGGATGTATATAGATGCA 59.903 38.462 14.23 0.00 44.82 3.96
1402 1439 6.507900 AGCACATACGGATGTATATAGATGC 58.492 40.000 14.23 10.17 44.82 3.91
1403 1440 8.190784 TGAAGCACATACGGATGTATATAGATG 58.809 37.037 14.23 0.00 44.82 2.90
1404 1441 8.293699 TGAAGCACATACGGATGTATATAGAT 57.706 34.615 14.23 0.00 44.82 1.98
1405 1442 7.696992 TGAAGCACATACGGATGTATATAGA 57.303 36.000 14.23 0.00 44.82 1.98
1406 1443 9.670719 CTATGAAGCACATACGGATGTATATAG 57.329 37.037 14.23 12.28 44.82 1.31
1407 1444 9.185680 ACTATGAAGCACATACGGATGTATATA 57.814 33.333 14.23 7.10 44.82 0.86
1408 1445 7.976175 CACTATGAAGCACATACGGATGTATAT 59.024 37.037 14.23 1.68 44.82 0.86
1409 1446 7.312899 CACTATGAAGCACATACGGATGTATA 58.687 38.462 14.23 6.48 44.82 1.47
1410 1447 6.159293 CACTATGAAGCACATACGGATGTAT 58.841 40.000 14.23 5.54 44.82 2.29
1411 1448 5.508994 CCACTATGAAGCACATACGGATGTA 60.509 44.000 14.23 0.00 44.82 2.29
1413 1450 3.742882 CCACTATGAAGCACATACGGATG 59.257 47.826 5.94 5.94 40.07 3.51
1414 1451 3.641436 TCCACTATGAAGCACATACGGAT 59.359 43.478 10.52 0.00 40.07 4.18
1415 1452 3.028130 TCCACTATGAAGCACATACGGA 58.972 45.455 10.52 10.52 40.07 4.69
1416 1453 3.452755 TCCACTATGAAGCACATACGG 57.547 47.619 0.00 0.00 40.07 4.02
1417 1454 5.292765 AGAATCCACTATGAAGCACATACG 58.707 41.667 0.00 0.00 40.07 3.06
1418 1455 6.520272 AGAGAATCCACTATGAAGCACATAC 58.480 40.000 0.00 0.00 36.68 2.39
1419 1456 6.737720 AGAGAATCCACTATGAAGCACATA 57.262 37.500 4.14 4.14 36.68 2.29
1420 1457 5.627182 AGAGAATCCACTATGAAGCACAT 57.373 39.130 2.31 2.31 38.35 3.21
1421 1458 5.422012 TGTAGAGAATCCACTATGAAGCACA 59.578 40.000 0.00 0.00 33.66 4.57
1422 1459 5.907207 TGTAGAGAATCCACTATGAAGCAC 58.093 41.667 0.00 0.00 33.66 4.40
1423 1460 6.544928 TTGTAGAGAATCCACTATGAAGCA 57.455 37.500 0.00 0.00 33.66 3.91
1424 1461 7.223777 GTCTTTGTAGAGAATCCACTATGAAGC 59.776 40.741 0.00 0.00 33.66 3.86
1425 1462 8.474025 AGTCTTTGTAGAGAATCCACTATGAAG 58.526 37.037 0.00 0.00 33.66 3.02
1426 1463 8.367660 AGTCTTTGTAGAGAATCCACTATGAA 57.632 34.615 0.00 0.00 33.66 2.57
1427 1464 7.962995 AGTCTTTGTAGAGAATCCACTATGA 57.037 36.000 0.00 0.00 33.66 2.15
1443 1480 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
1444 1481 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
1445 1482 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
1446 1483 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
1447 1484 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
1448 1485 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
1449 1486 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
1450 1487 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
1452 1489 9.417561 CATATACTCCCTCCGTTCCTAAATATA 57.582 37.037 0.00 0.00 0.00 0.86
1453 1490 7.344871 CCATATACTCCCTCCGTTCCTAAATAT 59.655 40.741 0.00 0.00 0.00 1.28
1454 1491 6.666546 CCATATACTCCCTCCGTTCCTAAATA 59.333 42.308 0.00 0.00 0.00 1.40
1455 1492 5.484290 CCATATACTCCCTCCGTTCCTAAAT 59.516 44.000 0.00 0.00 0.00 1.40
1456 1493 4.836736 CCATATACTCCCTCCGTTCCTAAA 59.163 45.833 0.00 0.00 0.00 1.85
1457 1494 4.413760 CCATATACTCCCTCCGTTCCTAA 58.586 47.826 0.00 0.00 0.00 2.69
1458 1495 3.816842 GCCATATACTCCCTCCGTTCCTA 60.817 52.174 0.00 0.00 0.00 2.94
1459 1496 2.890814 CCATATACTCCCTCCGTTCCT 58.109 52.381 0.00 0.00 0.00 3.36
1460 1497 1.275573 GCCATATACTCCCTCCGTTCC 59.724 57.143 0.00 0.00 0.00 3.62
1461 1498 2.249139 AGCCATATACTCCCTCCGTTC 58.751 52.381 0.00 0.00 0.00 3.95
1462 1499 2.400467 AGCCATATACTCCCTCCGTT 57.600 50.000 0.00 0.00 0.00 4.44
1463 1500 3.759815 ATAGCCATATACTCCCTCCGT 57.240 47.619 0.00 0.00 0.00 4.69
1464 1501 5.202004 ACTAATAGCCATATACTCCCTCCG 58.798 45.833 0.00 0.00 0.00 4.63
1465 1502 9.878737 TTATACTAATAGCCATATACTCCCTCC 57.121 37.037 0.00 0.00 0.00 4.30
1467 1504 9.369672 GCTTATACTAATAGCCATATACTCCCT 57.630 37.037 0.00 0.00 0.00 4.20
1468 1505 9.144298 TGCTTATACTAATAGCCATATACTCCC 57.856 37.037 0.00 0.00 0.00 4.30
1471 1508 9.716556 ACCTGCTTATACTAATAGCCATATACT 57.283 33.333 0.00 0.00 0.00 2.12
1474 1511 9.892130 GAAACCTGCTTATACTAATAGCCATAT 57.108 33.333 0.00 0.00 0.00 1.78
1548 1585 7.704472 CGACATATTCCTAATTAGATCTCAGCC 59.296 40.741 14.28 0.00 0.00 4.85
1549 1586 8.462811 TCGACATATTCCTAATTAGATCTCAGC 58.537 37.037 14.28 0.00 0.00 4.26
1552 1589 9.743057 CCATCGACATATTCCTAATTAGATCTC 57.257 37.037 14.28 0.00 0.00 2.75
1553 1590 8.200792 GCCATCGACATATTCCTAATTAGATCT 58.799 37.037 14.28 0.00 0.00 2.75
1554 1591 8.200792 AGCCATCGACATATTCCTAATTAGATC 58.799 37.037 14.28 0.00 0.00 2.75
1555 1592 8.083828 AGCCATCGACATATTCCTAATTAGAT 57.916 34.615 14.28 3.18 0.00 1.98
1608 1645 7.692460 AACTTCAACTGATTTCAGATGCATA 57.308 32.000 14.29 1.99 46.59 3.14
1700 1737 6.772770 AAACGTTACAAGCAAAACAAACTT 57.227 29.167 0.00 0.00 0.00 2.66
1856 1897 7.786943 TCCCATGGTAGCCAAATATTGATTAAA 59.213 33.333 11.73 0.00 36.95 1.52
1982 2023 3.462021 GCACACACAAAGGGCAAATAAA 58.538 40.909 0.00 0.00 0.00 1.40
2107 2580 4.774124 TCTGCATGCTGCTATCTACTTTT 58.226 39.130 20.33 0.00 45.31 2.27
2148 2621 7.545265 TGAAAAGTCAAACTCTGAAAACAATGG 59.455 33.333 0.00 0.00 35.22 3.16
2196 2669 5.084519 AGAAACTCATAGGTGGTAGTGTGA 58.915 41.667 0.00 0.00 0.00 3.58
2285 2758 7.724951 AGAAAGTAACTAGAGTTCTGGTACACT 59.275 37.037 0.00 3.49 36.63 3.55
2303 2776 6.311735 AGGGAATTTGTAGCCAAGAAAGTAA 58.688 36.000 0.00 0.00 0.00 2.24
2324 2797 1.413118 AGACCTGCAAACCAAAAGGG 58.587 50.000 0.00 0.00 44.81 3.95
2437 2910 6.647334 TGGACATAAATTTTGCAGACAGAA 57.353 33.333 0.00 0.00 0.00 3.02
2728 3202 8.511604 ACAGATACCTGGACAAATGAAATTAG 57.488 34.615 0.00 0.00 44.60 1.73
2885 3369 4.679197 TGAATACAAAAATGCAGCAACGAC 59.321 37.500 0.00 0.00 0.00 4.34
2888 3372 7.201461 CCATAGTGAATACAAAAATGCAGCAAC 60.201 37.037 0.00 0.00 0.00 4.17
3040 3539 1.557832 AGCAAATACCAGCGGAGGTTA 59.442 47.619 3.90 0.00 43.08 2.85
3112 3611 3.889520 AGGTAACCGGAAAGATCAGAC 57.110 47.619 9.46 0.00 37.17 3.51
3255 3754 1.795872 CAGTTGCGTGAAATACCGTGA 59.204 47.619 0.00 0.00 0.00 4.35
3335 3836 8.523915 TGATCTGGCTATACAATTTGAAATGT 57.476 30.769 2.79 0.00 0.00 2.71
3450 3951 3.118592 GCTTGAGGTATTCCACTAGCTGT 60.119 47.826 12.91 0.00 44.34 4.40
3515 4016 4.333649 AGCAAATGTCCGATGTGAGTTATG 59.666 41.667 0.00 0.00 0.00 1.90
3527 4028 2.607187 AGACGAGTTAGCAAATGTCCG 58.393 47.619 0.00 0.00 0.00 4.79
3678 4180 5.249420 GGAAAACCTACTGAAGAGAGCATT 58.751 41.667 0.00 0.00 0.00 3.56
3709 4211 2.863401 AACCGAAGACAAAGCCAAAC 57.137 45.000 0.00 0.00 0.00 2.93
3724 4226 2.095718 GCCTAGCAAGAAACAGAAACCG 60.096 50.000 0.00 0.00 0.00 4.44
3730 4232 1.815003 CAAGGGCCTAGCAAGAAACAG 59.185 52.381 6.41 0.00 0.00 3.16
3757 4259 4.450082 AAAAACGGAAGCAGAAACAGTT 57.550 36.364 0.00 0.00 0.00 3.16
3876 4441 8.083828 AGATGTGGTAGAACAAGTAGATGAAT 57.916 34.615 0.00 0.00 32.81 2.57
3932 4497 4.929211 TCACATAGTTACATGCTGTCACAC 59.071 41.667 0.00 0.00 27.41 3.82
3936 4501 6.480524 TTTGTCACATAGTTACATGCTGTC 57.519 37.500 0.00 0.00 0.00 3.51
3937 4502 8.737168 ATATTTGTCACATAGTTACATGCTGT 57.263 30.769 0.00 0.00 0.00 4.40
3955 4520 6.809869 TCAGAGTCATCGATGTGATATTTGT 58.190 36.000 24.09 0.91 34.83 2.83
4137 4702 3.070734 TGCATCTGCTATTCTTCTCCTCC 59.929 47.826 3.53 0.00 42.66 4.30
4170 4735 4.646492 GGATGATGTTTTTGTAGATGGGCT 59.354 41.667 0.00 0.00 0.00 5.19
4214 4780 7.902920 AGTTTTACTCGGGGAGTATATGTAA 57.097 36.000 6.34 0.00 43.45 2.41
4269 4835 5.310409 ACTTCTGGATTATGTACATGGGG 57.690 43.478 18.81 3.23 0.00 4.96
4408 4974 0.952280 TCTCAGTGTCAGTGGTCGAC 59.048 55.000 7.13 7.13 0.00 4.20
4482 5048 6.400579 TTCAGAGTCGTAAGTCGTAACTAG 57.599 41.667 0.00 0.00 40.80 2.57
4513 5086 6.097915 TCTGAAAGTCAAGAAGAATACCGT 57.902 37.500 0.00 0.00 33.76 4.83
4556 5129 7.121315 AGGGTTTACTTGCAATGATAAGAGAAC 59.879 37.037 0.00 0.00 0.00 3.01
4611 5190 3.402110 TGGTAGTGATCACAAGCAGTTG 58.598 45.455 27.02 0.00 39.82 3.16
4612 5191 3.769739 TGGTAGTGATCACAAGCAGTT 57.230 42.857 27.02 7.64 0.00 3.16
4617 5196 4.389992 GTCACACATGGTAGTGATCACAAG 59.610 45.833 27.02 11.99 45.46 3.16
4641 5220 1.106285 GATCAAAGGGGGTCATGTGC 58.894 55.000 0.00 0.00 0.00 4.57
4642 5221 2.291153 ACAGATCAAAGGGGGTCATGTG 60.291 50.000 0.00 0.00 0.00 3.21
4643 5222 1.995542 ACAGATCAAAGGGGGTCATGT 59.004 47.619 0.00 0.00 0.00 3.21
4644 5223 2.814805 ACAGATCAAAGGGGGTCATG 57.185 50.000 0.00 0.00 0.00 3.07
4645 5224 3.833559 AAACAGATCAAAGGGGGTCAT 57.166 42.857 0.00 0.00 0.00 3.06
4646 5225 3.496331 GAAAACAGATCAAAGGGGGTCA 58.504 45.455 0.00 0.00 0.00 4.02
4647 5226 2.826128 GGAAAACAGATCAAAGGGGGTC 59.174 50.000 0.00 0.00 0.00 4.46
4648 5227 2.178984 TGGAAAACAGATCAAAGGGGGT 59.821 45.455 0.00 0.00 0.00 4.95
4649 5228 2.888212 TGGAAAACAGATCAAAGGGGG 58.112 47.619 0.00 0.00 0.00 5.40
4722 5303 1.446966 GCTCTCCTGCGTTCCAGAC 60.447 63.158 0.00 0.00 44.64 3.51
4735 5316 1.846712 AAACCCCTGGAGCAGCTCTC 61.847 60.000 21.99 12.48 41.15 3.20
4750 5331 1.323791 GCACGCGTCAAACATAAACC 58.676 50.000 9.86 0.00 0.00 3.27
4751 5332 1.969256 CTGCACGCGTCAAACATAAAC 59.031 47.619 9.86 0.00 0.00 2.01
4754 5335 1.193650 GAACTGCACGCGTCAAACATA 59.806 47.619 9.86 0.00 0.00 2.29
4755 5336 0.041312 GAACTGCACGCGTCAAACAT 60.041 50.000 9.86 0.00 0.00 2.71
4756 5337 1.087202 AGAACTGCACGCGTCAAACA 61.087 50.000 9.86 4.53 0.00 2.83
4757 5338 0.027586 AAGAACTGCACGCGTCAAAC 59.972 50.000 9.86 0.00 0.00 2.93
4761 5342 1.000233 TACGAAGAACTGCACGCGTC 61.000 55.000 9.86 5.12 33.69 5.19
4854 5670 2.143008 TGCAATGCAGCAAGTGAAAG 57.857 45.000 2.72 0.00 42.46 2.62
4937 5779 2.402564 CTCCTCTCATTTCAGGGCCTA 58.597 52.381 5.28 0.00 0.00 3.93
5033 5878 4.655762 TTCGGATACAGATCTTGAGGTG 57.344 45.455 0.00 0.00 32.15 4.00


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

AutoCloner maintained by Alex Coulton.