Multiple sequence alignment - TraesCS5B01G424000

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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 TraesCS5B01G424000 chr5B 100.000 1736 0 0 1 1736 600303343 600301608 0.000000e+00 3206
1 TraesCS5B01G424000 chr5B 100.000 304 0 0 1954 2257 600301390 600301087 1.510000e-156 562
2 TraesCS5B01G424000 chr4B 90.085 1301 113 3 2 1286 617428481 617427181 0.000000e+00 1674
3 TraesCS5B01G424000 chr4B 91.003 289 26 0 1954 2242 644327659 644327371 7.560000e-105 390
4 TraesCS5B01G424000 chr2B 88.942 1248 125 10 5 1248 180552494 180553732 0.000000e+00 1528
5 TraesCS5B01G424000 chr6B 88.212 1247 139 8 7 1248 256006680 256005437 0.000000e+00 1482
6 TraesCS5B01G424000 chr6B 94.406 286 16 0 1954 2239 337730573 337730858 7.400000e-120 440
7 TraesCS5B01G424000 chr6A 87.610 1251 151 4 1 1248 539629266 539628017 0.000000e+00 1448
8 TraesCS5B01G424000 chr3A 89.170 1145 117 6 103 1244 653317997 653316857 0.000000e+00 1421
9 TraesCS5B01G424000 chr6D 87.071 1253 154 8 1 1248 451924204 451922955 0.000000e+00 1410
10 TraesCS5B01G424000 chr1B 85.955 1246 166 9 2 1244 642128219 642129458 0.000000e+00 1323
11 TraesCS5B01G424000 chr1B 93.007 286 20 0 1954 2239 30036068 30036353 3.470000e-113 418
12 TraesCS5B01G424000 chr1B 90.391 281 27 0 1956 2236 49111859 49112139 9.850000e-99 370
13 TraesCS5B01G424000 chr1B 91.770 243 20 0 1997 2239 565941530 565941288 2.780000e-89 339
14 TraesCS5B01G424000 chr7B 85.612 1258 163 17 1 1248 640380441 640381690 0.000000e+00 1304
15 TraesCS5B01G424000 chr7B 90.942 276 25 0 1964 2239 673588815 673588540 2.740000e-99 372
16 TraesCS5B01G424000 chr7A 85.542 1245 176 4 1 1243 491246013 491244771 0.000000e+00 1299
17 TraesCS5B01G424000 chr3B 90.845 284 25 1 1954 2236 734988302 734988585 1.640000e-101 379
18 TraesCS5B01G424000 chr3B 91.538 260 20 2 1981 2239 144279849 144279591 7.670000e-95 357
19 TraesCS5B01G424000 chr5D 93.089 246 10 4 1288 1527 487745993 487745749 9.920000e-94 353
20 TraesCS5B01G424000 chr3D 87.018 285 34 3 1954 2236 319046022 319046305 3.620000e-83 318


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 TraesCS5B01G424000 chr5B 600301087 600303343 2256 True 1884 3206 100.000 1 2257 2 chr5B.!!$R1 2256
1 TraesCS5B01G424000 chr4B 617427181 617428481 1300 True 1674 1674 90.085 2 1286 1 chr4B.!!$R1 1284
2 TraesCS5B01G424000 chr2B 180552494 180553732 1238 False 1528 1528 88.942 5 1248 1 chr2B.!!$F1 1243
3 TraesCS5B01G424000 chr6B 256005437 256006680 1243 True 1482 1482 88.212 7 1248 1 chr6B.!!$R1 1241
4 TraesCS5B01G424000 chr6A 539628017 539629266 1249 True 1448 1448 87.610 1 1248 1 chr6A.!!$R1 1247
5 TraesCS5B01G424000 chr3A 653316857 653317997 1140 True 1421 1421 89.170 103 1244 1 chr3A.!!$R1 1141
6 TraesCS5B01G424000 chr6D 451922955 451924204 1249 True 1410 1410 87.071 1 1248 1 chr6D.!!$R1 1247
7 TraesCS5B01G424000 chr1B 642128219 642129458 1239 False 1323 1323 85.955 2 1244 1 chr1B.!!$F3 1242
8 TraesCS5B01G424000 chr7B 640380441 640381690 1249 False 1304 1304 85.612 1 1248 1 chr7B.!!$F1 1247
9 TraesCS5B01G424000 chr7A 491244771 491246013 1242 True 1299 1299 85.542 1 1243 1 chr7A.!!$R1 1242

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
529 537 0.321671 CTGGGAAGAAGCGAGGTTGA 59.678 55.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2217 2241 0.03601 ACCAAAGCCAGATCCAGACG 60.036 55.0 0.0 0.0 0.0 4.18 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
24 25 4.658786 ACGGCTCCCAGAACCCCT 62.659 66.667 0.00 0.00 0.00 4.79
77 78 4.219115 AGGGTCAGTGATCTTATCGACAT 58.781 43.478 2.82 0.00 0.00 3.06
84 85 8.240682 GTCAGTGATCTTATCGACATAGCTAAT 58.759 37.037 0.00 0.00 0.00 1.73
128 129 6.068010 TGGTTCAGGAAACATTTATCACACT 58.932 36.000 0.00 0.00 39.81 3.55
428 436 5.921962 TTGCACTACAGACATATCAGAGT 57.078 39.130 0.00 0.00 0.00 3.24
529 537 0.321671 CTGGGAAGAAGCGAGGTTGA 59.678 55.000 0.00 0.00 0.00 3.18
696 704 3.821421 GGAGTGAAGTATGATCCGGTT 57.179 47.619 0.00 0.00 0.00 4.44
741 749 1.376543 CTCTGGCCTTACTCGACGTA 58.623 55.000 3.32 0.00 0.00 3.57
1045 1053 3.585862 GTTAATCTCTGGAACACTCGCA 58.414 45.455 0.00 0.00 0.00 5.10
1055 1063 2.135139 GAACACTCGCATCAACAGTCA 58.865 47.619 0.00 0.00 0.00 3.41
1100 1108 1.808945 CGAAATTGAGGAGCTTGCTGT 59.191 47.619 0.00 0.00 0.00 4.40
1145 1154 6.416631 TCTCATGTAAGCAGATCAGCTAAT 57.583 37.500 13.54 5.18 45.89 1.73
1152 1161 2.507058 AGCAGATCAGCTAATGGTCCAA 59.493 45.455 11.39 0.00 44.50 3.53
1163 1172 2.795231 ATGGTCCAACACATCTCTGG 57.205 50.000 0.00 0.00 0.00 3.86
1173 1182 3.390521 ATCTCTGGGCGCAACGGA 61.391 61.111 10.83 11.34 0.00 4.69
1183 1192 1.225637 CGCAACGGACATGTAACGC 60.226 57.895 18.90 8.31 0.00 4.84
1199 1208 1.233285 ACGCGTCTGTAACCGAGAGT 61.233 55.000 5.58 0.00 0.00 3.24
1261 1285 7.432252 CCTCATGGCGACTTTTATTTGAATAAC 59.568 37.037 0.00 0.00 31.03 1.89
1301 1325 0.519961 AAAAAGTGACGCGCATACCC 59.480 50.000 5.73 0.00 0.00 3.69
1302 1326 1.303091 AAAAGTGACGCGCATACCCC 61.303 55.000 5.73 0.00 0.00 4.95
1303 1327 4.508128 AGTGACGCGCATACCCCG 62.508 66.667 5.73 0.00 0.00 5.73
1366 1390 3.912907 GACGCGTCCGGATCCCAT 61.913 66.667 28.61 0.00 39.22 4.00
1367 1391 4.221422 ACGCGTCCGGATCCCATG 62.221 66.667 7.81 0.00 39.22 3.66
1368 1392 4.221422 CGCGTCCGGATCCCATGT 62.221 66.667 7.81 0.00 0.00 3.21
1369 1393 2.852180 CGCGTCCGGATCCCATGTA 61.852 63.158 7.81 0.00 0.00 2.29
1370 1394 1.300697 GCGTCCGGATCCCATGTAC 60.301 63.158 7.81 0.00 0.00 2.90
1371 1395 1.745320 GCGTCCGGATCCCATGTACT 61.745 60.000 7.81 0.00 0.00 2.73
1372 1396 1.612676 CGTCCGGATCCCATGTACTA 58.387 55.000 7.81 0.00 0.00 1.82
1373 1397 1.268899 CGTCCGGATCCCATGTACTAC 59.731 57.143 7.81 0.00 0.00 2.73
1374 1398 2.595238 GTCCGGATCCCATGTACTACT 58.405 52.381 7.81 0.00 0.00 2.57
1375 1399 3.759581 GTCCGGATCCCATGTACTACTA 58.240 50.000 7.81 0.00 0.00 1.82
1376 1400 3.505293 GTCCGGATCCCATGTACTACTAC 59.495 52.174 7.81 0.00 0.00 2.73
1377 1401 2.486982 CCGGATCCCATGTACTACTACG 59.513 54.545 6.06 0.00 0.00 3.51
1378 1402 3.144506 CGGATCCCATGTACTACTACGT 58.855 50.000 6.06 0.00 0.00 3.57
1379 1403 4.318332 CGGATCCCATGTACTACTACGTA 58.682 47.826 6.06 0.00 0.00 3.57
1380 1404 4.153117 CGGATCCCATGTACTACTACGTAC 59.847 50.000 6.06 0.00 40.06 3.67
1381 1405 4.153117 GGATCCCATGTACTACTACGTACG 59.847 50.000 15.01 15.01 42.00 3.67
1382 1406 3.466836 TCCCATGTACTACTACGTACGG 58.533 50.000 21.06 5.00 42.00 4.02
1383 1407 2.031682 CCCATGTACTACTACGTACGGC 60.032 54.545 21.06 0.00 42.00 5.68
1384 1408 2.874701 CCATGTACTACTACGTACGGCT 59.125 50.000 21.06 1.34 42.00 5.52
1385 1409 3.313526 CCATGTACTACTACGTACGGCTT 59.686 47.826 21.06 5.11 42.00 4.35
1386 1410 4.521943 CATGTACTACTACGTACGGCTTC 58.478 47.826 21.06 2.37 42.00 3.86
1387 1411 2.603110 TGTACTACTACGTACGGCTTCG 59.397 50.000 21.06 7.36 42.00 3.79
1388 1412 1.009829 ACTACTACGTACGGCTTCGG 58.990 55.000 21.06 7.45 38.38 4.30
1389 1413 0.316524 CTACTACGTACGGCTTCGGC 60.317 60.000 21.06 0.00 38.38 5.54
1390 1414 1.024046 TACTACGTACGGCTTCGGCA 61.024 55.000 21.06 0.00 43.96 5.69
1391 1415 1.585521 CTACGTACGGCTTCGGCAG 60.586 63.158 21.06 0.00 43.96 4.85
1392 1416 2.931713 CTACGTACGGCTTCGGCAGG 62.932 65.000 21.06 0.00 43.96 4.85
1438 1462 2.894387 GCACGAGCCAGCTGATCC 60.894 66.667 17.39 2.86 33.58 3.36
1439 1463 2.898738 CACGAGCCAGCTGATCCT 59.101 61.111 17.39 8.30 0.00 3.24
1440 1464 2.021068 GCACGAGCCAGCTGATCCTA 62.021 60.000 17.39 0.00 33.58 2.94
1441 1465 0.678395 CACGAGCCAGCTGATCCTAT 59.322 55.000 17.39 0.00 0.00 2.57
1442 1466 1.889170 CACGAGCCAGCTGATCCTATA 59.111 52.381 17.39 0.00 0.00 1.31
1443 1467 1.889829 ACGAGCCAGCTGATCCTATAC 59.110 52.381 17.39 0.00 0.00 1.47
1444 1468 1.203523 CGAGCCAGCTGATCCTATACC 59.796 57.143 17.39 0.00 0.00 2.73
1445 1469 1.552792 GAGCCAGCTGATCCTATACCC 59.447 57.143 17.39 0.00 0.00 3.69
1446 1470 0.615850 GCCAGCTGATCCTATACCCC 59.384 60.000 17.39 0.00 0.00 4.95
1447 1471 2.030027 CCAGCTGATCCTATACCCCA 57.970 55.000 17.39 0.00 0.00 4.96
1448 1472 1.625818 CCAGCTGATCCTATACCCCAC 59.374 57.143 17.39 0.00 0.00 4.61
1449 1473 1.625818 CAGCTGATCCTATACCCCACC 59.374 57.143 8.42 0.00 0.00 4.61
1450 1474 0.984995 GCTGATCCTATACCCCACCC 59.015 60.000 0.00 0.00 0.00 4.61
1451 1475 1.657804 CTGATCCTATACCCCACCCC 58.342 60.000 0.00 0.00 0.00 4.95
1452 1476 0.178915 TGATCCTATACCCCACCCCG 60.179 60.000 0.00 0.00 0.00 5.73
1453 1477 0.178912 GATCCTATACCCCACCCCGT 60.179 60.000 0.00 0.00 0.00 5.28
1454 1478 0.178912 ATCCTATACCCCACCCCGTC 60.179 60.000 0.00 0.00 0.00 4.79
1455 1479 1.235112 CCTATACCCCACCCCGTCT 59.765 63.158 0.00 0.00 0.00 4.18
1456 1480 0.484212 CCTATACCCCACCCCGTCTA 59.516 60.000 0.00 0.00 0.00 2.59
1457 1481 1.625511 CTATACCCCACCCCGTCTAC 58.374 60.000 0.00 0.00 0.00 2.59
1458 1482 0.178992 TATACCCCACCCCGTCTACG 60.179 60.000 0.00 0.00 39.44 3.51
1459 1483 1.936767 ATACCCCACCCCGTCTACGA 61.937 60.000 3.65 0.00 43.02 3.43
1460 1484 1.936767 TACCCCACCCCGTCTACGAT 61.937 60.000 3.65 0.00 43.02 3.73
1461 1485 2.496291 CCCCACCCCGTCTACGATC 61.496 68.421 3.65 0.00 43.02 3.69
1462 1486 1.755395 CCCACCCCGTCTACGATCA 60.755 63.158 3.65 0.00 43.02 2.92
1463 1487 1.734137 CCACCCCGTCTACGATCAG 59.266 63.158 3.65 0.00 43.02 2.90
1464 1488 1.065928 CACCCCGTCTACGATCAGC 59.934 63.158 3.65 0.00 43.02 4.26
1465 1489 2.125961 ACCCCGTCTACGATCAGCC 61.126 63.158 3.65 0.00 43.02 4.85
1466 1490 2.728817 CCCGTCTACGATCAGCCC 59.271 66.667 3.65 0.00 43.02 5.19
1467 1491 2.331805 CCGTCTACGATCAGCCCG 59.668 66.667 3.65 0.00 43.02 6.13
1468 1492 2.478890 CCGTCTACGATCAGCCCGT 61.479 63.158 3.65 0.00 43.02 5.28
1469 1493 1.298413 CGTCTACGATCAGCCCGTG 60.298 63.158 0.00 0.00 43.02 4.94
1470 1494 1.807886 GTCTACGATCAGCCCGTGT 59.192 57.895 0.00 0.00 40.76 4.49
1471 1495 0.525668 GTCTACGATCAGCCCGTGTG 60.526 60.000 0.00 0.00 40.76 3.82
1472 1496 1.878522 CTACGATCAGCCCGTGTGC 60.879 63.158 0.00 0.00 40.76 4.57
1473 1497 3.365291 TACGATCAGCCCGTGTGCC 62.365 63.158 0.00 0.00 40.76 5.01
1474 1498 4.457496 CGATCAGCCCGTGTGCCT 62.457 66.667 0.00 0.00 0.00 4.75
1475 1499 2.512515 GATCAGCCCGTGTGCCTC 60.513 66.667 0.00 0.00 0.00 4.70
1476 1500 3.315142 GATCAGCCCGTGTGCCTCA 62.315 63.158 0.00 0.00 0.00 3.86
1477 1501 2.599645 GATCAGCCCGTGTGCCTCAT 62.600 60.000 0.00 0.00 0.00 2.90
1478 1502 2.202236 ATCAGCCCGTGTGCCTCATT 62.202 55.000 0.00 0.00 0.00 2.57
1479 1503 2.045926 AGCCCGTGTGCCTCATTC 60.046 61.111 0.00 0.00 0.00 2.67
1480 1504 3.499737 GCCCGTGTGCCTCATTCG 61.500 66.667 0.00 0.00 0.00 3.34
1481 1505 3.499737 CCCGTGTGCCTCATTCGC 61.500 66.667 0.00 0.00 0.00 4.70
1482 1506 2.741985 CCGTGTGCCTCATTCGCA 60.742 61.111 0.00 0.00 0.00 5.10
1487 1511 2.741985 TGCCTCATTCGCACACCG 60.742 61.111 0.00 0.00 38.61 4.94
1488 1512 2.742372 GCCTCATTCGCACACCGT 60.742 61.111 0.00 0.00 38.35 4.83
1489 1513 2.740714 GCCTCATTCGCACACCGTC 61.741 63.158 0.00 0.00 38.35 4.79
1490 1514 1.374125 CCTCATTCGCACACCGTCA 60.374 57.895 0.00 0.00 38.35 4.35
1491 1515 1.626654 CCTCATTCGCACACCGTCAC 61.627 60.000 0.00 0.00 38.35 3.67
1492 1516 1.626654 CTCATTCGCACACCGTCACC 61.627 60.000 0.00 0.00 38.35 4.02
1493 1517 2.736995 ATTCGCACACCGTCACCG 60.737 61.111 0.00 0.00 38.35 4.94
1504 1528 4.162690 GTCACCGGCAGGCCCTAG 62.163 72.222 0.00 0.00 42.76 3.02
1512 1536 4.880537 CAGGCCCTAGCGAGCGTG 62.881 72.222 0.00 6.11 41.24 5.34
1514 1538 4.874977 GGCCCTAGCGAGCGTGAC 62.875 72.222 0.00 0.00 41.24 3.67
1516 1540 3.812019 CCCTAGCGAGCGTGACGT 61.812 66.667 6.91 0.00 0.00 4.34
1517 1541 2.277373 CCTAGCGAGCGTGACGTC 60.277 66.667 9.11 9.11 0.00 4.34
1518 1542 2.751913 CCTAGCGAGCGTGACGTCT 61.752 63.158 17.92 4.05 0.00 4.18
1519 1543 1.426816 CCTAGCGAGCGTGACGTCTA 61.427 60.000 17.92 0.00 0.00 2.59
1520 1544 0.042880 CTAGCGAGCGTGACGTCTAG 60.043 60.000 17.92 11.52 34.37 2.43
1521 1545 2.033328 TAGCGAGCGTGACGTCTAGC 62.033 60.000 22.13 22.13 34.37 3.42
1522 1546 2.785921 CGAGCGTGACGTCTAGCT 59.214 61.111 28.84 28.84 43.33 3.32
1523 1547 2.004445 CGAGCGTGACGTCTAGCTA 58.996 57.895 28.63 3.54 40.39 3.32
1524 1548 0.582482 CGAGCGTGACGTCTAGCTAT 59.418 55.000 28.63 14.91 40.39 2.97
1525 1549 1.791204 CGAGCGTGACGTCTAGCTATA 59.209 52.381 28.63 2.12 40.39 1.31
1526 1550 2.220363 CGAGCGTGACGTCTAGCTATAA 59.780 50.000 28.63 1.41 40.39 0.98
1527 1551 3.543670 GAGCGTGACGTCTAGCTATAAC 58.456 50.000 28.63 17.38 40.39 1.89
1528 1552 2.033065 AGCGTGACGTCTAGCTATAACG 60.033 50.000 27.89 21.36 41.93 3.18
1529 1553 2.296563 CGTGACGTCTAGCTATAACGC 58.703 52.381 21.92 16.60 39.93 4.84
1530 1554 2.033065 CGTGACGTCTAGCTATAACGCT 60.033 50.000 21.92 12.97 43.83 5.07
1531 1555 3.289911 GTGACGTCTAGCTATAACGCTG 58.710 50.000 21.92 0.00 41.12 5.18
1532 1556 2.286831 TGACGTCTAGCTATAACGCTGC 60.287 50.000 21.92 14.74 41.12 5.25
1533 1557 1.948145 ACGTCTAGCTATAACGCTGCT 59.052 47.619 21.92 6.36 41.12 4.24
1534 1558 2.358267 ACGTCTAGCTATAACGCTGCTT 59.642 45.455 21.92 6.08 41.12 3.91
1535 1559 3.181489 ACGTCTAGCTATAACGCTGCTTT 60.181 43.478 21.92 0.00 41.12 3.51
1536 1560 3.797256 CGTCTAGCTATAACGCTGCTTTT 59.203 43.478 13.74 0.00 41.12 2.27
1537 1561 4.267928 CGTCTAGCTATAACGCTGCTTTTT 59.732 41.667 13.74 0.00 41.12 1.94
1565 1589 3.380479 GGTTGAAACCTACCAAAAGGC 57.620 47.619 4.92 0.00 45.75 4.35
1566 1590 2.696187 GGTTGAAACCTACCAAAAGGCA 59.304 45.455 4.92 0.00 45.75 4.75
1567 1591 3.243737 GGTTGAAACCTACCAAAAGGCAG 60.244 47.826 4.92 0.00 45.75 4.85
1568 1592 3.306472 TGAAACCTACCAAAAGGCAGT 57.694 42.857 0.00 0.00 40.62 4.40
1569 1593 3.219281 TGAAACCTACCAAAAGGCAGTC 58.781 45.455 0.00 0.00 40.62 3.51
1570 1594 2.287977 AACCTACCAAAAGGCAGTCC 57.712 50.000 0.00 0.00 40.62 3.85
1571 1595 0.404426 ACCTACCAAAAGGCAGTCCC 59.596 55.000 0.00 0.00 40.62 4.46
1572 1596 0.323451 CCTACCAAAAGGCAGTCCCC 60.323 60.000 0.00 0.00 0.00 4.81
1573 1597 0.323451 CTACCAAAAGGCAGTCCCCC 60.323 60.000 0.00 0.00 0.00 5.40
1587 1611 4.098235 CCCCCGTTCCCCTCCCTA 62.098 72.222 0.00 0.00 0.00 3.53
1588 1612 2.446036 CCCCGTTCCCCTCCCTAG 60.446 72.222 0.00 0.00 0.00 3.02
1589 1613 2.446036 CCCGTTCCCCTCCCTAGG 60.446 72.222 0.06 0.06 43.25 3.02
1668 1692 4.416601 CCGTTCCCCTCCCCCTCT 62.417 72.222 0.00 0.00 0.00 3.69
1669 1693 2.764547 CGTTCCCCTCCCCCTCTC 60.765 72.222 0.00 0.00 0.00 3.20
1670 1694 2.367107 GTTCCCCTCCCCCTCTCC 60.367 72.222 0.00 0.00 0.00 3.71
1671 1695 2.543637 TTCCCCTCCCCCTCTCCT 60.544 66.667 0.00 0.00 0.00 3.69
1672 1696 2.647949 TTCCCCTCCCCCTCTCCTC 61.648 68.421 0.00 0.00 0.00 3.71
1673 1697 3.039526 CCCCTCCCCCTCTCCTCT 61.040 72.222 0.00 0.00 0.00 3.69
1674 1698 2.652113 CCCCTCCCCCTCTCCTCTT 61.652 68.421 0.00 0.00 0.00 2.85
1675 1699 1.074850 CCCTCCCCCTCTCCTCTTC 60.075 68.421 0.00 0.00 0.00 2.87
1676 1700 1.074850 CCTCCCCCTCTCCTCTTCC 60.075 68.421 0.00 0.00 0.00 3.46
1677 1701 1.074850 CTCCCCCTCTCCTCTTCCC 60.075 68.421 0.00 0.00 0.00 3.97
1678 1702 2.040359 CCCCCTCTCCTCTTCCCC 60.040 72.222 0.00 0.00 0.00 4.81
1679 1703 2.040359 CCCCTCTCCTCTTCCCCC 60.040 72.222 0.00 0.00 0.00 5.40
1680 1704 2.652113 CCCCTCTCCTCTTCCCCCT 61.652 68.421 0.00 0.00 0.00 4.79
1681 1705 1.074850 CCCTCTCCTCTTCCCCCTC 60.075 68.421 0.00 0.00 0.00 4.30
1682 1706 1.074850 CCTCTCCTCTTCCCCCTCC 60.075 68.421 0.00 0.00 0.00 4.30
1683 1707 1.074850 CTCTCCTCTTCCCCCTCCC 60.075 68.421 0.00 0.00 0.00 4.30
1684 1708 2.040359 CTCCTCTTCCCCCTCCCC 60.040 72.222 0.00 0.00 0.00 4.81
1685 1709 2.543637 TCCTCTTCCCCCTCCCCT 60.544 66.667 0.00 0.00 0.00 4.79
1686 1710 2.040359 CCTCTTCCCCCTCCCCTC 60.040 72.222 0.00 0.00 0.00 4.30
1687 1711 2.040359 CTCTTCCCCCTCCCCTCC 60.040 72.222 0.00 0.00 0.00 4.30
1688 1712 3.707189 TCTTCCCCCTCCCCTCCC 61.707 72.222 0.00 0.00 0.00 4.30
1689 1713 4.845307 CTTCCCCCTCCCCTCCCC 62.845 77.778 0.00 0.00 0.00 4.81
1696 1720 4.179599 CTCCCCTCCCCTCCCCTC 62.180 77.778 0.00 0.00 0.00 4.30
2008 2032 4.570874 GCGATGGGGCCCTCCTTC 62.571 72.222 25.93 12.52 35.33 3.46
2009 2033 3.878667 CGATGGGGCCCTCCTTCC 61.879 72.222 25.93 3.69 35.33 3.46
2010 2034 3.502875 GATGGGGCCCTCCTTCCC 61.503 72.222 25.93 2.81 41.87 3.97
2011 2035 4.058505 ATGGGGCCCTCCTTCCCT 62.059 66.667 25.93 0.00 42.25 4.20
2014 2038 3.412408 GGGCCCTCCTTCCCTGTC 61.412 72.222 17.04 0.00 39.46 3.51
2015 2039 3.412408 GGCCCTCCTTCCCTGTCC 61.412 72.222 0.00 0.00 0.00 4.02
2016 2040 3.787001 GCCCTCCTTCCCTGTCCG 61.787 72.222 0.00 0.00 0.00 4.79
2017 2041 3.787001 CCCTCCTTCCCTGTCCGC 61.787 72.222 0.00 0.00 0.00 5.54
2018 2042 2.685380 CCTCCTTCCCTGTCCGCT 60.685 66.667 0.00 0.00 0.00 5.52
2019 2043 2.294078 CCTCCTTCCCTGTCCGCTT 61.294 63.158 0.00 0.00 0.00 4.68
2020 2044 1.078848 CTCCTTCCCTGTCCGCTTG 60.079 63.158 0.00 0.00 0.00 4.01
2021 2045 1.535444 TCCTTCCCTGTCCGCTTGA 60.535 57.895 0.00 0.00 0.00 3.02
2022 2046 1.078848 CCTTCCCTGTCCGCTTGAG 60.079 63.158 0.00 0.00 0.00 3.02
2023 2047 1.078848 CTTCCCTGTCCGCTTGAGG 60.079 63.158 0.00 0.00 0.00 3.86
2025 2049 4.785453 CCCTGTCCGCTTGAGGGC 62.785 72.222 0.00 0.00 40.22 5.19
2054 2078 4.090057 GCGGCTCCTTTGTGCGAC 62.090 66.667 0.00 0.00 31.76 5.19
2055 2079 3.777925 CGGCTCCTTTGTGCGACG 61.778 66.667 0.00 0.00 31.76 5.12
2056 2080 2.357034 GGCTCCTTTGTGCGACGA 60.357 61.111 0.00 0.00 31.76 4.20
2057 2081 1.741770 GGCTCCTTTGTGCGACGAT 60.742 57.895 0.00 0.00 31.76 3.73
2058 2082 1.421485 GCTCCTTTGTGCGACGATG 59.579 57.895 0.00 0.00 0.00 3.84
2059 2083 1.421485 CTCCTTTGTGCGACGATGC 59.579 57.895 0.00 0.00 0.00 3.91
2060 2084 1.005037 TCCTTTGTGCGACGATGCT 60.005 52.632 0.00 0.00 35.36 3.79
2061 2085 1.133253 CCTTTGTGCGACGATGCTG 59.867 57.895 0.00 0.00 35.36 4.41
2062 2086 1.133253 CTTTGTGCGACGATGCTGG 59.867 57.895 0.00 0.00 35.36 4.85
2063 2087 1.291184 CTTTGTGCGACGATGCTGGA 61.291 55.000 0.00 0.00 35.36 3.86
2064 2088 0.673333 TTTGTGCGACGATGCTGGAT 60.673 50.000 0.00 0.00 35.36 3.41
2065 2089 1.360931 TTGTGCGACGATGCTGGATG 61.361 55.000 0.00 0.00 35.36 3.51
2066 2090 2.891936 TGCGACGATGCTGGATGC 60.892 61.111 0.00 0.00 43.25 3.91
2067 2091 3.643978 GCGACGATGCTGGATGCC 61.644 66.667 0.00 0.00 42.00 4.40
2068 2092 2.969238 CGACGATGCTGGATGCCC 60.969 66.667 0.00 0.00 42.00 5.36
2069 2093 2.969238 GACGATGCTGGATGCCCG 60.969 66.667 0.00 0.00 42.00 6.13
2076 2100 2.974698 CTGGATGCCCGCGGAATC 60.975 66.667 30.73 26.85 34.29 2.52
2077 2101 4.562425 TGGATGCCCGCGGAATCC 62.562 66.667 35.09 35.09 40.34 3.01
2078 2102 4.256180 GGATGCCCGCGGAATCCT 62.256 66.667 34.73 17.18 37.48 3.24
2079 2103 2.974698 GATGCCCGCGGAATCCTG 60.975 66.667 30.73 10.02 0.00 3.86
2232 2256 4.461119 TCCGTCTGGATCTGGCTT 57.539 55.556 0.00 0.00 40.17 4.35
2233 2257 2.683916 TCCGTCTGGATCTGGCTTT 58.316 52.632 0.00 0.00 40.17 3.51
2234 2258 0.250234 TCCGTCTGGATCTGGCTTTG 59.750 55.000 0.00 0.00 40.17 2.77
2235 2259 0.745845 CCGTCTGGATCTGGCTTTGG 60.746 60.000 0.00 0.00 37.49 3.28
2236 2260 0.036010 CGTCTGGATCTGGCTTTGGT 60.036 55.000 0.00 0.00 0.00 3.67
2237 2261 1.457346 GTCTGGATCTGGCTTTGGTG 58.543 55.000 0.00 0.00 0.00 4.17
2238 2262 0.329261 TCTGGATCTGGCTTTGGTGG 59.671 55.000 0.00 0.00 0.00 4.61
2239 2263 0.038744 CTGGATCTGGCTTTGGTGGT 59.961 55.000 0.00 0.00 0.00 4.16
2240 2264 0.038166 TGGATCTGGCTTTGGTGGTC 59.962 55.000 0.00 0.00 0.00 4.02
2241 2265 0.038166 GGATCTGGCTTTGGTGGTCA 59.962 55.000 0.00 0.00 0.00 4.02
2242 2266 1.341383 GGATCTGGCTTTGGTGGTCAT 60.341 52.381 0.00 0.00 0.00 3.06
2243 2267 1.747355 GATCTGGCTTTGGTGGTCATG 59.253 52.381 0.00 0.00 0.00 3.07
2244 2268 0.478072 TCTGGCTTTGGTGGTCATGT 59.522 50.000 0.00 0.00 0.00 3.21
2245 2269 1.133513 TCTGGCTTTGGTGGTCATGTT 60.134 47.619 0.00 0.00 0.00 2.71
2246 2270 1.000060 CTGGCTTTGGTGGTCATGTTG 60.000 52.381 0.00 0.00 0.00 3.33
2247 2271 0.318120 GGCTTTGGTGGTCATGTTGG 59.682 55.000 0.00 0.00 0.00 3.77
2248 2272 0.318120 GCTTTGGTGGTCATGTTGGG 59.682 55.000 0.00 0.00 0.00 4.12
2249 2273 0.968405 CTTTGGTGGTCATGTTGGGG 59.032 55.000 0.00 0.00 0.00 4.96
2250 2274 0.558220 TTTGGTGGTCATGTTGGGGA 59.442 50.000 0.00 0.00 0.00 4.81
2251 2275 0.558220 TTGGTGGTCATGTTGGGGAA 59.442 50.000 0.00 0.00 0.00 3.97
2252 2276 0.178975 TGGTGGTCATGTTGGGGAAC 60.179 55.000 0.00 0.00 0.00 3.62
2253 2277 1.241315 GGTGGTCATGTTGGGGAACG 61.241 60.000 0.00 0.00 0.00 3.95
2254 2278 0.536460 GTGGTCATGTTGGGGAACGT 60.536 55.000 0.00 0.00 0.00 3.99
2255 2279 1.057471 TGGTCATGTTGGGGAACGTA 58.943 50.000 0.00 0.00 0.00 3.57
2256 2280 1.002659 TGGTCATGTTGGGGAACGTAG 59.997 52.381 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 8.599792 ACAGTAGTATTAGGAGGTTTTAGCAAA 58.400 33.333 0.00 0.00 0.00 3.68
77 78 4.325030 CCCTTTTCCAGGTCCAATTAGCTA 60.325 45.833 0.00 0.00 42.02 3.32
84 85 1.529744 ACTCCCTTTTCCAGGTCCAA 58.470 50.000 0.00 0.00 42.02 3.53
128 129 0.179111 CAGGATTGCTTCGGCGTCTA 60.179 55.000 6.85 0.00 45.37 2.59
198 199 5.233050 CACACTATAGTTGCCTGATTTCTCG 59.767 44.000 1.56 0.00 0.00 4.04
428 436 8.840833 TTGACATACTTTACATAAGCTGACAA 57.159 30.769 0.00 0.00 0.00 3.18
529 537 4.467769 CTTGGCAGTTTGATATCCAGGAT 58.532 43.478 7.27 7.27 0.00 3.24
696 704 7.284074 CCTCTCTGGTGAGTCTAATAGAAGTA 58.716 42.308 0.00 0.00 40.98 2.24
741 749 4.785453 GCCGCCTGCTGCTTAGGT 62.785 66.667 7.73 0.00 37.64 3.08
756 764 4.850347 ACTGTGTCTCGGTAATATAGCC 57.150 45.455 0.00 0.00 33.34 3.93
769 777 1.451936 GTGGCCTCCAACTGTGTCT 59.548 57.895 3.32 0.00 34.18 3.41
1145 1154 0.692476 CCCAGAGATGTGTTGGACCA 59.308 55.000 0.00 0.00 33.76 4.02
1152 1161 1.672356 GTTGCGCCCAGAGATGTGT 60.672 57.895 4.18 0.00 0.00 3.72
1163 1172 1.133869 GTTACATGTCCGTTGCGCC 59.866 57.895 4.18 0.00 0.00 6.53
1173 1182 2.331194 GGTTACAGACGCGTTACATGT 58.669 47.619 15.53 18.07 0.00 3.21
1183 1192 1.538512 TCCAACTCTCGGTTACAGACG 59.461 52.381 0.00 0.00 36.23 4.18
1199 1208 4.982241 ACTTGGAGTTTCAGAGATCCAA 57.018 40.909 10.89 10.89 46.80 3.53
1244 1253 9.394477 ACTTTGAGCGTTATTCAAATAAAAGTC 57.606 29.630 1.40 0.00 41.98 3.01
1261 1285 3.338818 TTTTGCAGAGAACTTTGAGCG 57.661 42.857 0.00 0.00 0.00 5.03
1286 1310 4.508128 CGGGGTATGCGCGTCACT 62.508 66.667 4.79 0.00 0.00 3.41
1349 1373 3.912907 ATGGGATCCGGACGCGTC 61.913 66.667 30.67 30.67 0.00 5.19
1350 1374 4.221422 CATGGGATCCGGACGCGT 62.221 66.667 13.85 13.85 0.00 6.01
1351 1375 2.852180 TACATGGGATCCGGACGCG 61.852 63.158 6.12 3.53 0.00 6.01
1352 1376 1.300697 GTACATGGGATCCGGACGC 60.301 63.158 6.12 10.24 0.00 5.19
1353 1377 1.268899 GTAGTACATGGGATCCGGACG 59.731 57.143 6.12 0.00 0.00 4.79
1354 1378 2.595238 AGTAGTACATGGGATCCGGAC 58.405 52.381 6.12 0.00 0.00 4.79
1355 1379 3.759581 GTAGTAGTACATGGGATCCGGA 58.240 50.000 6.61 6.61 0.00 5.14
1356 1380 2.486982 CGTAGTAGTACATGGGATCCGG 59.513 54.545 5.45 0.00 0.00 5.14
1357 1381 3.144506 ACGTAGTAGTACATGGGATCCG 58.855 50.000 5.45 0.00 41.94 4.18
1370 1394 2.928676 TGCCGAAGCCGTACGTAGTAG 61.929 57.143 15.21 0.00 40.93 2.57
1371 1395 1.024046 TGCCGAAGCCGTACGTAGTA 61.024 55.000 15.21 0.00 39.68 1.82
1372 1396 2.262471 CTGCCGAAGCCGTACGTAGT 62.262 60.000 15.21 0.00 41.81 2.73
1373 1397 1.585521 CTGCCGAAGCCGTACGTAG 60.586 63.158 15.21 0.29 38.69 3.51
1374 1398 2.486504 CTGCCGAAGCCGTACGTA 59.513 61.111 15.21 0.00 38.69 3.57
1375 1399 4.430765 CCTGCCGAAGCCGTACGT 62.431 66.667 15.21 0.00 38.69 3.57
1421 1445 2.021068 TAGGATCAGCTGGCTCGTGC 62.021 60.000 15.13 0.00 38.76 5.34
1422 1446 0.678395 ATAGGATCAGCTGGCTCGTG 59.322 55.000 15.13 0.00 0.00 4.35
1423 1447 1.889829 GTATAGGATCAGCTGGCTCGT 59.110 52.381 15.13 14.47 0.00 4.18
1424 1448 1.203523 GGTATAGGATCAGCTGGCTCG 59.796 57.143 15.13 0.00 0.00 5.03
1425 1449 1.552792 GGGTATAGGATCAGCTGGCTC 59.447 57.143 15.13 11.06 0.00 4.70
1426 1450 1.650528 GGGTATAGGATCAGCTGGCT 58.349 55.000 15.13 0.98 0.00 4.75
1427 1451 0.615850 GGGGTATAGGATCAGCTGGC 59.384 60.000 15.13 6.41 0.00 4.85
1428 1452 1.625818 GTGGGGTATAGGATCAGCTGG 59.374 57.143 15.13 0.00 0.00 4.85
1429 1453 1.625818 GGTGGGGTATAGGATCAGCTG 59.374 57.143 7.63 7.63 0.00 4.24
1430 1454 1.485210 GGGTGGGGTATAGGATCAGCT 60.485 57.143 0.00 0.00 0.00 4.24
1431 1455 0.984995 GGGTGGGGTATAGGATCAGC 59.015 60.000 0.00 0.00 0.00 4.26
1432 1456 1.657804 GGGGTGGGGTATAGGATCAG 58.342 60.000 0.00 0.00 0.00 2.90
1433 1457 0.178915 CGGGGTGGGGTATAGGATCA 60.179 60.000 0.00 0.00 0.00 2.92
1434 1458 0.178912 ACGGGGTGGGGTATAGGATC 60.179 60.000 0.00 0.00 0.00 3.36
1435 1459 0.178912 GACGGGGTGGGGTATAGGAT 60.179 60.000 0.00 0.00 0.00 3.24
1436 1460 1.233949 GACGGGGTGGGGTATAGGA 59.766 63.158 0.00 0.00 0.00 2.94
1437 1461 0.484212 TAGACGGGGTGGGGTATAGG 59.516 60.000 0.00 0.00 0.00 2.57
1438 1462 1.625511 GTAGACGGGGTGGGGTATAG 58.374 60.000 0.00 0.00 0.00 1.31
1439 1463 0.178992 CGTAGACGGGGTGGGGTATA 60.179 60.000 0.00 0.00 35.37 1.47
1440 1464 1.456331 CGTAGACGGGGTGGGGTAT 60.456 63.158 0.00 0.00 35.37 2.73
1441 1465 1.936767 ATCGTAGACGGGGTGGGGTA 61.937 60.000 1.67 0.00 42.51 3.69
1442 1466 3.307089 ATCGTAGACGGGGTGGGGT 62.307 63.158 1.67 0.00 42.51 4.95
1443 1467 2.443390 ATCGTAGACGGGGTGGGG 60.443 66.667 1.67 0.00 42.51 4.96
1444 1468 1.735376 CTGATCGTAGACGGGGTGGG 61.735 65.000 1.67 0.00 42.51 4.61
1445 1469 1.734137 CTGATCGTAGACGGGGTGG 59.266 63.158 1.67 0.00 42.51 4.61
1446 1470 1.065928 GCTGATCGTAGACGGGGTG 59.934 63.158 1.67 0.00 42.51 4.61
1447 1471 2.125961 GGCTGATCGTAGACGGGGT 61.126 63.158 1.67 0.00 42.51 4.95
1448 1472 2.728817 GGCTGATCGTAGACGGGG 59.271 66.667 1.67 0.00 42.51 5.73
1449 1473 2.728817 GGGCTGATCGTAGACGGG 59.271 66.667 1.67 0.00 42.51 5.28
1450 1474 2.331805 CGGGCTGATCGTAGACGG 59.668 66.667 1.67 0.00 42.51 4.79
1451 1475 1.298413 CACGGGCTGATCGTAGACG 60.298 63.158 0.00 0.00 42.51 4.18
1452 1476 0.525668 CACACGGGCTGATCGTAGAC 60.526 60.000 0.00 0.00 42.51 2.59
1453 1477 1.807226 CACACGGGCTGATCGTAGA 59.193 57.895 0.00 0.00 45.75 2.59
1454 1478 1.878522 GCACACGGGCTGATCGTAG 60.879 63.158 0.00 0.00 38.94 3.51
1455 1479 2.183300 GCACACGGGCTGATCGTA 59.817 61.111 0.00 0.00 38.94 3.43
1456 1480 4.760047 GGCACACGGGCTGATCGT 62.760 66.667 0.00 0.00 41.93 3.73
1463 1487 3.499737 CGAATGAGGCACACGGGC 61.500 66.667 0.00 0.00 43.80 6.13
1464 1488 3.499737 GCGAATGAGGCACACGGG 61.500 66.667 0.00 0.00 0.00 5.28
1465 1489 2.741985 TGCGAATGAGGCACACGG 60.742 61.111 0.00 0.00 35.04 4.94
1470 1494 2.741985 CGGTGTGCGAATGAGGCA 60.742 61.111 0.00 0.00 38.25 4.75
1471 1495 2.740714 GACGGTGTGCGAATGAGGC 61.741 63.158 0.00 0.00 0.00 4.70
1472 1496 1.374125 TGACGGTGTGCGAATGAGG 60.374 57.895 0.00 0.00 0.00 3.86
1473 1497 1.626654 GGTGACGGTGTGCGAATGAG 61.627 60.000 0.00 0.00 0.00 2.90
1474 1498 1.666553 GGTGACGGTGTGCGAATGA 60.667 57.895 0.00 0.00 0.00 2.57
1475 1499 2.860293 GGTGACGGTGTGCGAATG 59.140 61.111 0.00 0.00 0.00 2.67
1487 1511 4.162690 CTAGGGCCTGCCGGTGAC 62.163 72.222 18.53 0.00 36.85 3.67
1495 1519 4.880537 CACGCTCGCTAGGGCCTG 62.881 72.222 18.53 7.50 42.00 4.85
1497 1521 4.874977 GTCACGCTCGCTAGGGCC 62.875 72.222 1.02 0.00 42.00 5.80
1499 1523 3.736482 GACGTCACGCTCGCTAGGG 62.736 68.421 11.55 0.00 41.33 3.53
1500 1524 1.426816 TAGACGTCACGCTCGCTAGG 61.427 60.000 19.50 0.00 0.00 3.02
1501 1525 0.042880 CTAGACGTCACGCTCGCTAG 60.043 60.000 19.50 4.09 33.16 3.42
1502 1526 2.004445 CTAGACGTCACGCTCGCTA 58.996 57.895 19.50 0.00 0.00 4.26
1503 1527 2.785921 CTAGACGTCACGCTCGCT 59.214 61.111 19.50 0.00 0.00 4.93
1504 1528 2.033328 TAGCTAGACGTCACGCTCGC 62.033 60.000 27.56 15.67 34.14 5.03
1505 1529 0.582482 ATAGCTAGACGTCACGCTCG 59.418 55.000 27.56 7.83 34.14 5.03
1506 1530 3.543670 GTTATAGCTAGACGTCACGCTC 58.456 50.000 27.56 14.40 34.14 5.03
1507 1531 2.033065 CGTTATAGCTAGACGTCACGCT 60.033 50.000 27.09 27.09 36.56 5.07
1508 1532 2.296563 CGTTATAGCTAGACGTCACGC 58.703 52.381 19.50 18.61 32.52 5.34
1509 1533 2.296563 GCGTTATAGCTAGACGTCACG 58.703 52.381 24.49 16.41 38.90 4.35
1541 1565 6.799241 CCTTTTGGTAGGTTTCAACCACGC 62.799 50.000 11.36 0.85 45.31 5.34
1542 1566 3.243267 CCTTTTGGTAGGTTTCAACCACG 60.243 47.826 11.36 0.00 45.31 4.94
1543 1567 3.491964 GCCTTTTGGTAGGTTTCAACCAC 60.492 47.826 11.36 7.03 45.31 4.16
1544 1568 2.696187 GCCTTTTGGTAGGTTTCAACCA 59.304 45.455 11.36 0.00 46.30 3.67
1545 1569 2.696187 TGCCTTTTGGTAGGTTTCAACC 59.304 45.455 0.00 0.00 45.16 3.77
1546 1570 3.977427 CTGCCTTTTGGTAGGTTTCAAC 58.023 45.455 0.00 0.00 46.76 3.18
1555 1579 1.771646 GGGGGACTGCCTTTTGGTA 59.228 57.895 0.00 0.00 42.99 3.25
1556 1580 2.526110 GGGGGACTGCCTTTTGGT 59.474 61.111 0.00 0.00 42.99 3.67
1570 1594 4.098235 TAGGGAGGGGAACGGGGG 62.098 72.222 0.00 0.00 0.00 5.40
1571 1595 2.446036 CTAGGGAGGGGAACGGGG 60.446 72.222 0.00 0.00 0.00 5.73
1572 1596 2.446036 CCTAGGGAGGGGAACGGG 60.446 72.222 0.00 0.00 39.48 5.28
1651 1675 4.416601 AGAGGGGGAGGGGAACGG 62.417 72.222 0.00 0.00 0.00 4.44
1652 1676 2.764547 GAGAGGGGGAGGGGAACG 60.765 72.222 0.00 0.00 0.00 3.95
1653 1677 2.367107 GGAGAGGGGGAGGGGAAC 60.367 72.222 0.00 0.00 0.00 3.62
1654 1678 2.543637 AGGAGAGGGGGAGGGGAA 60.544 66.667 0.00 0.00 0.00 3.97
1655 1679 3.036959 GAGGAGAGGGGGAGGGGA 61.037 72.222 0.00 0.00 0.00 4.81
1656 1680 2.613576 GAAGAGGAGAGGGGGAGGGG 62.614 70.000 0.00 0.00 0.00 4.79
1657 1681 1.074850 GAAGAGGAGAGGGGGAGGG 60.075 68.421 0.00 0.00 0.00 4.30
1658 1682 1.074850 GGAAGAGGAGAGGGGGAGG 60.075 68.421 0.00 0.00 0.00 4.30
1659 1683 1.074850 GGGAAGAGGAGAGGGGGAG 60.075 68.421 0.00 0.00 0.00 4.30
1660 1684 2.647949 GGGGAAGAGGAGAGGGGGA 61.648 68.421 0.00 0.00 0.00 4.81
1661 1685 2.040359 GGGGAAGAGGAGAGGGGG 60.040 72.222 0.00 0.00 0.00 5.40
1662 1686 2.040359 GGGGGAAGAGGAGAGGGG 60.040 72.222 0.00 0.00 0.00 4.79
1663 1687 1.074850 GAGGGGGAAGAGGAGAGGG 60.075 68.421 0.00 0.00 0.00 4.30
1664 1688 1.074850 GGAGGGGGAAGAGGAGAGG 60.075 68.421 0.00 0.00 0.00 3.69
1665 1689 1.074850 GGGAGGGGGAAGAGGAGAG 60.075 68.421 0.00 0.00 0.00 3.20
1666 1690 2.647949 GGGGAGGGGGAAGAGGAGA 61.648 68.421 0.00 0.00 0.00 3.71
1667 1691 2.040359 GGGGAGGGGGAAGAGGAG 60.040 72.222 0.00 0.00 0.00 3.69
1668 1692 2.543637 AGGGGAGGGGGAAGAGGA 60.544 66.667 0.00 0.00 0.00 3.71
1669 1693 2.040359 GAGGGGAGGGGGAAGAGG 60.040 72.222 0.00 0.00 0.00 3.69
1670 1694 2.040359 GGAGGGGAGGGGGAAGAG 60.040 72.222 0.00 0.00 0.00 2.85
1671 1695 3.707189 GGGAGGGGAGGGGGAAGA 61.707 72.222 0.00 0.00 0.00 2.87
1672 1696 4.845307 GGGGAGGGGAGGGGGAAG 62.845 77.778 0.00 0.00 0.00 3.46
1679 1703 4.179599 GAGGGGAGGGGAGGGGAG 62.180 77.778 0.00 0.00 0.00 4.30
1991 2015 4.570874 GAAGGAGGGCCCCATCGC 62.571 72.222 21.43 1.15 34.66 4.58
1992 2016 3.878667 GGAAGGAGGGCCCCATCG 61.879 72.222 21.43 0.00 34.66 3.84
1993 2017 3.502875 GGGAAGGAGGGCCCCATC 61.503 72.222 21.43 10.92 39.89 3.51
1994 2018 4.058505 AGGGAAGGAGGGCCCCAT 62.059 66.667 21.43 4.56 45.89 4.00
1997 2021 3.412408 GACAGGGAAGGAGGGCCC 61.412 72.222 16.46 16.46 45.04 5.80
1998 2022 3.412408 GGACAGGGAAGGAGGGCC 61.412 72.222 0.00 0.00 0.00 5.80
1999 2023 3.787001 CGGACAGGGAAGGAGGGC 61.787 72.222 0.00 0.00 0.00 5.19
2000 2024 3.787001 GCGGACAGGGAAGGAGGG 61.787 72.222 0.00 0.00 0.00 4.30
2001 2025 2.294078 AAGCGGACAGGGAAGGAGG 61.294 63.158 0.00 0.00 0.00 4.30
2002 2026 1.078848 CAAGCGGACAGGGAAGGAG 60.079 63.158 0.00 0.00 0.00 3.69
2003 2027 1.535444 TCAAGCGGACAGGGAAGGA 60.535 57.895 0.00 0.00 0.00 3.36
2004 2028 1.078848 CTCAAGCGGACAGGGAAGG 60.079 63.158 0.00 0.00 0.00 3.46
2005 2029 1.078848 CCTCAAGCGGACAGGGAAG 60.079 63.158 0.00 0.00 0.00 3.46
2006 2030 3.068881 CCTCAAGCGGACAGGGAA 58.931 61.111 0.00 0.00 0.00 3.97
2037 2061 4.090057 GTCGCACAAAGGAGCCGC 62.090 66.667 0.00 0.00 0.00 6.53
2038 2062 3.777925 CGTCGCACAAAGGAGCCG 61.778 66.667 0.00 0.00 0.00 5.52
2039 2063 1.741770 ATCGTCGCACAAAGGAGCC 60.742 57.895 0.00 0.00 0.00 4.70
2040 2064 1.421485 CATCGTCGCACAAAGGAGC 59.579 57.895 0.00 0.00 0.00 4.70
2041 2065 1.016130 AGCATCGTCGCACAAAGGAG 61.016 55.000 1.90 0.00 0.00 3.69
2042 2066 1.005037 AGCATCGTCGCACAAAGGA 60.005 52.632 1.90 0.00 0.00 3.36
2043 2067 1.133253 CAGCATCGTCGCACAAAGG 59.867 57.895 1.90 0.00 0.00 3.11
2044 2068 1.133253 CCAGCATCGTCGCACAAAG 59.867 57.895 1.90 0.00 0.00 2.77
2045 2069 0.673333 ATCCAGCATCGTCGCACAAA 60.673 50.000 1.90 0.00 0.00 2.83
2046 2070 1.079197 ATCCAGCATCGTCGCACAA 60.079 52.632 1.90 0.00 0.00 3.33
2047 2071 1.810853 CATCCAGCATCGTCGCACA 60.811 57.895 1.90 0.00 0.00 4.57
2048 2072 3.009140 CATCCAGCATCGTCGCAC 58.991 61.111 1.90 0.00 0.00 5.34
2049 2073 2.891936 GCATCCAGCATCGTCGCA 60.892 61.111 1.90 0.00 44.79 5.10
2059 2083 2.974698 GATTCCGCGGGCATCCAG 60.975 66.667 27.83 0.00 0.00 3.86
2060 2084 4.562425 GGATTCCGCGGGCATCCA 62.562 66.667 34.77 14.01 37.10 3.41
2061 2085 4.256180 AGGATTCCGCGGGCATCC 62.256 66.667 33.70 33.70 37.36 3.51
2062 2086 2.974698 CAGGATTCCGCGGGCATC 60.975 66.667 27.83 24.89 0.00 3.91
2216 2240 0.745845 CCAAAGCCAGATCCAGACGG 60.746 60.000 0.00 0.00 0.00 4.79
2217 2241 0.036010 ACCAAAGCCAGATCCAGACG 60.036 55.000 0.00 0.00 0.00 4.18
2218 2242 1.457346 CACCAAAGCCAGATCCAGAC 58.543 55.000 0.00 0.00 0.00 3.51
2219 2243 0.329261 CCACCAAAGCCAGATCCAGA 59.671 55.000 0.00 0.00 0.00 3.86
2220 2244 0.038744 ACCACCAAAGCCAGATCCAG 59.961 55.000 0.00 0.00 0.00 3.86
2221 2245 0.038166 GACCACCAAAGCCAGATCCA 59.962 55.000 0.00 0.00 0.00 3.41
2222 2246 0.038166 TGACCACCAAAGCCAGATCC 59.962 55.000 0.00 0.00 0.00 3.36
2223 2247 1.747355 CATGACCACCAAAGCCAGATC 59.253 52.381 0.00 0.00 0.00 2.75
2224 2248 1.076024 ACATGACCACCAAAGCCAGAT 59.924 47.619 0.00 0.00 0.00 2.90
2225 2249 0.478072 ACATGACCACCAAAGCCAGA 59.522 50.000 0.00 0.00 0.00 3.86
2226 2250 1.000060 CAACATGACCACCAAAGCCAG 60.000 52.381 0.00 0.00 0.00 4.85
2227 2251 1.039068 CAACATGACCACCAAAGCCA 58.961 50.000 0.00 0.00 0.00 4.75
2228 2252 0.318120 CCAACATGACCACCAAAGCC 59.682 55.000 0.00 0.00 0.00 4.35
2229 2253 0.318120 CCCAACATGACCACCAAAGC 59.682 55.000 0.00 0.00 0.00 3.51
2230 2254 0.968405 CCCCAACATGACCACCAAAG 59.032 55.000 0.00 0.00 0.00 2.77
2231 2255 0.558220 TCCCCAACATGACCACCAAA 59.442 50.000 0.00 0.00 0.00 3.28
2232 2256 0.558220 TTCCCCAACATGACCACCAA 59.442 50.000 0.00 0.00 0.00 3.67
2233 2257 0.178975 GTTCCCCAACATGACCACCA 60.179 55.000 0.00 0.00 32.14 4.17
2234 2258 1.241315 CGTTCCCCAACATGACCACC 61.241 60.000 0.00 0.00 32.14 4.61
2235 2259 0.536460 ACGTTCCCCAACATGACCAC 60.536 55.000 0.00 0.00 32.14 4.16
2236 2260 1.002659 CTACGTTCCCCAACATGACCA 59.997 52.381 0.00 0.00 32.14 4.02
2237 2261 1.734163 CTACGTTCCCCAACATGACC 58.266 55.000 0.00 0.00 32.14 4.02


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

AutoCloner maintained by Alex Coulton.