Multiple sequence alignment - TraesCS4A01G469000

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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 TraesCS4A01G469000 chr4A 100.000 2330 0 0 1 2330 731021861 731019532 0.000000e+00 4303
1 TraesCS4A01G469000 chr4A 81.348 638 82 22 1459 2070 742763594 742764220 3.480000e-133 484
2 TraesCS4A01G469000 chr3B 97.374 1371 24 5 1 1361 64247473 64248841 0.000000e+00 2322
3 TraesCS4A01G469000 chr3B 90.307 815 63 8 560 1359 23474988 23474175 0.000000e+00 1053
4 TraesCS4A01G469000 chr3B 89.935 616 47 10 560 1160 23423533 23422918 0.000000e+00 780
5 TraesCS4A01G469000 chr7B 97.155 1371 28 5 1 1360 234904206 234905576 0.000000e+00 2305
6 TraesCS4A01G469000 chr7B 99.143 467 3 1 896 1361 392671144 392671610 0.000000e+00 839
7 TraesCS4A01G469000 chr2D 96.134 1371 41 7 1 1361 18898860 18900228 0.000000e+00 2228
8 TraesCS4A01G469000 chr2D 96.058 1370 41 8 1 1360 19003092 19004458 0.000000e+00 2218
9 TraesCS4A01G469000 chr5D 95.036 1370 57 6 1 1360 24877776 24879144 0.000000e+00 2143
10 TraesCS4A01G469000 chr2A 92.364 1375 80 15 2 1361 447991502 447992866 0.000000e+00 1934
11 TraesCS4A01G469000 chr7D 88.557 1372 118 19 1 1358 64477187 64478533 0.000000e+00 1628
12 TraesCS4A01G469000 chr7D 96.830 694 21 1 1 693 41769321 41770014 0.000000e+00 1158


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 TraesCS4A01G469000 chr4A 731019532 731021861 2329 True 4303 4303 100.000 1 2330 1 chr4A.!!$R1 2329
1 TraesCS4A01G469000 chr4A 742763594 742764220 626 False 484 484 81.348 1459 2070 1 chr4A.!!$F1 611
2 TraesCS4A01G469000 chr3B 64247473 64248841 1368 False 2322 2322 97.374 1 1361 1 chr3B.!!$F1 1360
3 TraesCS4A01G469000 chr3B 23474175 23474988 813 True 1053 1053 90.307 560 1359 1 chr3B.!!$R2 799
4 TraesCS4A01G469000 chr3B 23422918 23423533 615 True 780 780 89.935 560 1160 1 chr3B.!!$R1 600
5 TraesCS4A01G469000 chr7B 234904206 234905576 1370 False 2305 2305 97.155 1 1360 1 chr7B.!!$F1 1359
6 TraesCS4A01G469000 chr2D 18898860 18900228 1368 False 2228 2228 96.134 1 1361 1 chr2D.!!$F1 1360
7 TraesCS4A01G469000 chr2D 19003092 19004458 1366 False 2218 2218 96.058 1 1360 1 chr2D.!!$F2 1359
8 TraesCS4A01G469000 chr5D 24877776 24879144 1368 False 2143 2143 95.036 1 1360 1 chr5D.!!$F1 1359
9 TraesCS4A01G469000 chr2A 447991502 447992866 1364 False 1934 1934 92.364 2 1361 1 chr2A.!!$F1 1359
10 TraesCS4A01G469000 chr7D 64477187 64478533 1346 False 1628 1628 88.557 1 1358 1 chr7D.!!$F2 1357
11 TraesCS4A01G469000 chr7D 41769321 41770014 693 False 1158 1158 96.830 1 693 1 chr7D.!!$F1 692

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
70 73 1.093159 CAAGAGGCATCACCAGAAGC 58.907 55.0 0.0 0.0 43.14 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1394 1426 0.035317 TCATAGCTAGGCGCCAATGG 59.965 55.0 31.54 12.47 40.39 3.16 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
21 22 1.535015 GCGAGTCGGAGATGGAAGAAG 60.535 57.143 15.52 0.00 40.67 2.85
66 69 1.747709 CTTCCAAGAGGCATCACCAG 58.252 55.000 0.00 0.00 43.14 4.00
67 70 1.280133 CTTCCAAGAGGCATCACCAGA 59.720 52.381 0.00 0.00 43.14 3.86
70 73 1.093159 CAAGAGGCATCACCAGAAGC 58.907 55.000 0.00 0.00 43.14 3.86
131 134 4.819630 TGGCGGAACTTATTGATCCAATAC 59.180 41.667 0.00 0.00 36.26 1.89
694 711 3.389656 TGTGTATTCTGTTCTGGGTGTGA 59.610 43.478 0.00 0.00 0.00 3.58
721 738 4.240881 TGAGAGAAATAAGGCCAATGCT 57.759 40.909 5.01 0.00 37.74 3.79
874 891 7.201911 CCAAGTGGGATCCTCAAAATAAATACC 60.202 40.741 12.58 0.00 40.01 2.73
892 910 2.726821 ACCGATGGTGCTTTTCATGAT 58.273 42.857 0.00 0.00 32.98 2.45
893 911 3.884895 ACCGATGGTGCTTTTCATGATA 58.115 40.909 0.00 0.00 32.98 2.15
894 912 3.879295 ACCGATGGTGCTTTTCATGATAG 59.121 43.478 0.00 0.00 32.98 2.08
896 914 4.260907 CCGATGGTGCTTTTCATGATAGTG 60.261 45.833 0.00 0.00 0.00 2.74
897 915 4.260907 CGATGGTGCTTTTCATGATAGTGG 60.261 45.833 0.00 0.00 0.00 4.00
1083 1111 2.186160 CGTGGTGTTGAAGCAGGCA 61.186 57.895 0.00 0.00 36.83 4.75
1145 1173 6.645003 GCCGTGTTTCAGGAAATAAAATTTCT 59.355 34.615 11.11 0.00 32.36 2.52
1381 1413 5.622346 AAAAGACCTCAAGAGTCAAGAGT 57.378 39.130 9.98 0.91 0.00 3.24
1382 1414 4.599047 AAGACCTCAAGAGTCAAGAGTG 57.401 45.455 9.98 5.45 0.00 3.51
1383 1415 2.896685 AGACCTCAAGAGTCAAGAGTGG 59.103 50.000 9.98 1.43 0.00 4.00
1384 1416 2.894126 GACCTCAAGAGTCAAGAGTGGA 59.106 50.000 9.98 0.00 0.00 4.02
1385 1417 2.896685 ACCTCAAGAGTCAAGAGTGGAG 59.103 50.000 9.98 0.00 0.00 3.86
1386 1418 2.896685 CCTCAAGAGTCAAGAGTGGAGT 59.103 50.000 9.98 0.00 0.00 3.85
1387 1419 3.323403 CCTCAAGAGTCAAGAGTGGAGTT 59.677 47.826 9.98 0.00 0.00 3.01
1388 1420 4.202305 CCTCAAGAGTCAAGAGTGGAGTTT 60.202 45.833 9.98 0.00 0.00 2.66
1389 1421 4.950050 TCAAGAGTCAAGAGTGGAGTTTC 58.050 43.478 0.00 0.00 0.00 2.78
1390 1422 3.651803 AGAGTCAAGAGTGGAGTTTCG 57.348 47.619 0.00 0.00 0.00 3.46
1391 1423 3.223435 AGAGTCAAGAGTGGAGTTTCGA 58.777 45.455 0.00 0.00 0.00 3.71
1392 1424 3.254657 AGAGTCAAGAGTGGAGTTTCGAG 59.745 47.826 0.00 0.00 0.00 4.04
1393 1425 2.297597 AGTCAAGAGTGGAGTTTCGAGG 59.702 50.000 0.00 0.00 0.00 4.63
1394 1426 1.000955 TCAAGAGTGGAGTTTCGAGGC 59.999 52.381 0.00 0.00 0.00 4.70
1395 1427 0.321996 AAGAGTGGAGTTTCGAGGCC 59.678 55.000 0.00 0.00 0.00 5.19
1396 1428 0.832135 AGAGTGGAGTTTCGAGGCCA 60.832 55.000 5.01 0.00 0.00 5.36
1397 1429 0.250513 GAGTGGAGTTTCGAGGCCAT 59.749 55.000 5.01 0.00 32.26 4.40
1398 1430 0.693049 AGTGGAGTTTCGAGGCCATT 59.307 50.000 5.01 0.00 32.26 3.16
1399 1431 0.804989 GTGGAGTTTCGAGGCCATTG 59.195 55.000 5.01 0.00 32.26 2.82
1400 1432 0.322456 TGGAGTTTCGAGGCCATTGG 60.322 55.000 5.01 0.00 0.00 3.16
1419 1451 1.230324 GCGCCTAGCTATGAAAAGGG 58.770 55.000 0.00 0.00 44.04 3.95
1420 1452 1.230324 CGCCTAGCTATGAAAAGGGC 58.770 55.000 7.65 7.65 35.33 5.19
1421 1453 1.475034 CGCCTAGCTATGAAAAGGGCA 60.475 52.381 15.73 0.00 38.16 5.36
1422 1454 2.654863 GCCTAGCTATGAAAAGGGCAA 58.345 47.619 11.85 0.00 38.16 4.52
1423 1455 2.620585 GCCTAGCTATGAAAAGGGCAAG 59.379 50.000 11.85 0.00 38.16 4.01
1424 1456 3.685550 GCCTAGCTATGAAAAGGGCAAGA 60.686 47.826 11.85 0.00 38.16 3.02
1425 1457 4.526970 CCTAGCTATGAAAAGGGCAAGAA 58.473 43.478 0.00 0.00 0.00 2.52
1426 1458 4.949856 CCTAGCTATGAAAAGGGCAAGAAA 59.050 41.667 0.00 0.00 0.00 2.52
1427 1459 4.790765 AGCTATGAAAAGGGCAAGAAAC 57.209 40.909 0.00 0.00 0.00 2.78
1428 1460 4.151883 AGCTATGAAAAGGGCAAGAAACA 58.848 39.130 0.00 0.00 0.00 2.83
1429 1461 4.588528 AGCTATGAAAAGGGCAAGAAACAA 59.411 37.500 0.00 0.00 0.00 2.83
1430 1462 5.070313 AGCTATGAAAAGGGCAAGAAACAAA 59.930 36.000 0.00 0.00 0.00 2.83
1431 1463 5.177511 GCTATGAAAAGGGCAAGAAACAAAC 59.822 40.000 0.00 0.00 0.00 2.93
1432 1464 3.867857 TGAAAAGGGCAAGAAACAAACC 58.132 40.909 0.00 0.00 0.00 3.27
1433 1465 2.595124 AAAGGGCAAGAAACAAACCG 57.405 45.000 0.00 0.00 0.00 4.44
1434 1466 0.104120 AAGGGCAAGAAACAAACCGC 59.896 50.000 0.00 0.00 0.00 5.68
1435 1467 1.040339 AGGGCAAGAAACAAACCGCA 61.040 50.000 0.00 0.00 0.00 5.69
1436 1468 0.874175 GGGCAAGAAACAAACCGCAC 60.874 55.000 0.00 0.00 0.00 5.34
1437 1469 0.102300 GGCAAGAAACAAACCGCACT 59.898 50.000 0.00 0.00 0.00 4.40
1438 1470 1.199624 GCAAGAAACAAACCGCACTG 58.800 50.000 0.00 0.00 0.00 3.66
1439 1471 1.202245 GCAAGAAACAAACCGCACTGA 60.202 47.619 0.00 0.00 0.00 3.41
1440 1472 2.543653 GCAAGAAACAAACCGCACTGAT 60.544 45.455 0.00 0.00 0.00 2.90
1441 1473 3.044986 CAAGAAACAAACCGCACTGATG 58.955 45.455 0.00 0.00 0.00 3.07
1442 1474 1.608590 AGAAACAAACCGCACTGATGG 59.391 47.619 0.00 0.00 0.00 3.51
1443 1475 0.673437 AAACAAACCGCACTGATGGG 59.327 50.000 0.00 0.00 38.49 4.00
1444 1476 0.179004 AACAAACCGCACTGATGGGA 60.179 50.000 0.00 0.00 41.24 4.37
1445 1477 0.038166 ACAAACCGCACTGATGGGAT 59.962 50.000 0.00 0.00 41.24 3.85
1446 1478 1.280710 ACAAACCGCACTGATGGGATA 59.719 47.619 0.00 0.00 41.24 2.59
1447 1479 1.670811 CAAACCGCACTGATGGGATAC 59.329 52.381 0.00 0.00 41.24 2.24
1448 1480 0.908910 AACCGCACTGATGGGATACA 59.091 50.000 0.00 0.00 41.24 2.29
1449 1481 0.178068 ACCGCACTGATGGGATACAC 59.822 55.000 0.00 0.00 41.24 2.90
1450 1482 0.177836 CCGCACTGATGGGATACACA 59.822 55.000 0.00 0.00 41.24 3.72
1451 1483 1.202687 CCGCACTGATGGGATACACAT 60.203 52.381 0.00 0.00 41.24 3.21
1452 1484 1.869132 CGCACTGATGGGATACACATG 59.131 52.381 0.00 0.00 41.24 3.21
1453 1485 2.224606 GCACTGATGGGATACACATGG 58.775 52.381 0.00 0.00 39.74 3.66
1454 1486 2.224606 CACTGATGGGATACACATGGC 58.775 52.381 0.00 0.00 39.74 4.40
1455 1487 2.130193 ACTGATGGGATACACATGGCT 58.870 47.619 0.00 0.00 39.74 4.75
1456 1488 3.071457 CACTGATGGGATACACATGGCTA 59.929 47.826 0.00 0.00 39.74 3.93
1457 1489 3.326006 ACTGATGGGATACACATGGCTAG 59.674 47.826 0.00 0.00 39.74 3.42
1458 1490 2.639347 TGATGGGATACACATGGCTAGG 59.361 50.000 0.00 0.00 39.74 3.02
1459 1491 2.487746 TGGGATACACATGGCTAGGA 57.512 50.000 0.00 0.00 39.74 2.94
1460 1492 2.047061 TGGGATACACATGGCTAGGAC 58.953 52.381 0.00 0.00 39.74 3.85
1461 1493 1.348036 GGGATACACATGGCTAGGACC 59.652 57.143 0.00 0.00 39.74 4.46
1462 1494 1.348036 GGATACACATGGCTAGGACCC 59.652 57.143 0.00 0.00 0.00 4.46
1463 1495 1.348036 GATACACATGGCTAGGACCCC 59.652 57.143 0.00 0.00 0.00 4.95
1464 1496 1.046472 TACACATGGCTAGGACCCCG 61.046 60.000 0.00 0.00 0.00 5.73
1465 1497 2.040606 ACATGGCTAGGACCCCGT 59.959 61.111 0.00 0.00 0.00 5.28
1466 1498 1.046472 CACATGGCTAGGACCCCGTA 61.046 60.000 0.00 0.00 0.00 4.02
1467 1499 1.047034 ACATGGCTAGGACCCCGTAC 61.047 60.000 0.00 0.00 0.00 3.67
1493 1525 2.819595 CTCATGGGGTCCGTTGCG 60.820 66.667 0.00 0.00 0.00 4.85
1506 1538 1.305219 CGTTGCGACAACCATCCCAT 61.305 55.000 14.31 0.00 0.00 4.00
1510 1554 0.734889 GCGACAACCATCCCATCAAG 59.265 55.000 0.00 0.00 0.00 3.02
1512 1556 1.838112 GACAACCATCCCATCAAGCA 58.162 50.000 0.00 0.00 0.00 3.91
1521 1565 2.053865 CCATCAAGCAACCGCCCAT 61.054 57.895 0.00 0.00 39.83 4.00
1525 1569 0.611618 TCAAGCAACCGCCCATTCAT 60.612 50.000 0.00 0.00 39.83 2.57
1526 1570 0.458889 CAAGCAACCGCCCATTCATG 60.459 55.000 0.00 0.00 39.83 3.07
1527 1571 0.899717 AAGCAACCGCCCATTCATGT 60.900 50.000 0.00 0.00 39.83 3.21
1528 1572 1.139520 GCAACCGCCCATTCATGTC 59.860 57.895 0.00 0.00 0.00 3.06
1531 1575 2.148723 AACCGCCCATTCATGTCCCA 62.149 55.000 0.00 0.00 0.00 4.37
1532 1576 1.825191 CCGCCCATTCATGTCCCAG 60.825 63.158 0.00 0.00 0.00 4.45
1534 1578 1.614711 GCCCATTCATGTCCCAGGA 59.385 57.895 0.00 0.00 0.00 3.86
1536 1580 2.025863 GCCCATTCATGTCCCAGGAAG 61.026 57.143 0.00 0.00 37.57 3.46
1537 1581 1.396653 CCATTCATGTCCCAGGAAGC 58.603 55.000 0.00 0.00 37.57 3.86
1538 1582 1.341285 CCATTCATGTCCCAGGAAGCA 60.341 52.381 0.00 0.00 37.57 3.91
1539 1583 1.747355 CATTCATGTCCCAGGAAGCAC 59.253 52.381 0.00 0.00 37.57 4.40
1541 1585 1.133181 TCATGTCCCAGGAAGCACCA 61.133 55.000 0.00 0.00 42.04 4.17
1553 1598 2.420129 GGAAGCACCAGATACCGTCAAT 60.420 50.000 0.00 0.00 38.79 2.57
1573 1618 1.067142 TGCGACAAGATAAGCCGTCTT 60.067 47.619 0.00 0.00 36.40 3.01
1584 1629 2.674796 AGCCGTCTTGTCAAGGATAC 57.325 50.000 12.66 3.08 0.00 2.24
1587 1632 5.279809 TAAGCCGTCTTGTCAAGGATACTTT 60.280 40.000 12.66 4.18 43.42 2.66
1600 1645 2.812011 GGATACTTTGAACTGCACGGTT 59.188 45.455 0.00 0.00 0.00 4.44
1608 1653 3.006940 TGAACTGCACGGTTTATGGATC 58.993 45.455 0.00 0.00 0.00 3.36
1621 1667 9.621629 ACGGTTTATGGATCAAATTAAGATACA 57.378 29.630 7.86 7.86 40.42 2.29
1628 1674 9.872684 ATGGATCAAATTAAGATACACAGGAAT 57.127 29.630 7.64 0.00 39.05 3.01
1641 1687 9.886132 AGATACACAGGAATAATTCGTAGTTTT 57.114 29.630 0.00 0.00 0.00 2.43
1662 1708 3.579147 TCTTTGTGTTTGTTACGAGCG 57.421 42.857 0.00 0.00 0.00 5.03
1676 1722 1.140407 CGAGCGATGTCTTTCCGGTC 61.140 60.000 0.00 0.00 44.32 4.79
1677 1723 1.140407 GAGCGATGTCTTTCCGGTCG 61.140 60.000 0.00 2.09 40.19 4.79
1684 1730 1.270550 TGTCTTTCCGGTCGTAGGAAC 59.729 52.381 0.00 0.00 46.36 3.62
1685 1731 1.270550 GTCTTTCCGGTCGTAGGAACA 59.729 52.381 0.00 0.00 46.36 3.18
1690 1740 1.585006 CGGTCGTAGGAACACAGCT 59.415 57.895 0.81 0.00 0.00 4.24
1692 1742 1.467035 CGGTCGTAGGAACACAGCTAC 60.467 57.143 0.81 0.00 0.00 3.58
1696 1746 1.198408 CGTAGGAACACAGCTACGTCA 59.802 52.381 0.00 0.00 39.87 4.35
1718 1775 1.523758 CTGGTAACCTGTTGCTGGAC 58.476 55.000 0.00 0.00 0.00 4.02
1721 1778 1.071699 GGTAACCTGTTGCTGGACTCA 59.928 52.381 0.00 0.00 0.00 3.41
1722 1779 2.143925 GTAACCTGTTGCTGGACTCAC 58.856 52.381 0.00 0.00 0.00 3.51
1724 1781 1.669115 CCTGTTGCTGGACTCACGG 60.669 63.158 0.00 0.00 0.00 4.94
1726 1783 0.668706 CTGTTGCTGGACTCACGGAG 60.669 60.000 0.03 0.03 35.52 4.63
1728 1785 1.837051 TTGCTGGACTCACGGAGGT 60.837 57.895 5.98 0.00 33.35 3.85
1744 1801 4.894114 ACGGAGGTATGCAAGAAGTAGTAT 59.106 41.667 0.00 0.00 0.00 2.12
1745 1802 6.016527 CACGGAGGTATGCAAGAAGTAGTATA 60.017 42.308 0.00 0.00 0.00 1.47
1777 1837 5.677319 AAGACTAGTAAGTAGCAATGCCA 57.323 39.130 0.00 0.00 35.56 4.92
1801 1861 7.952671 CAATGATGATTGGATGAAAAGATCCT 58.047 34.615 0.00 0.00 42.36 3.24
1802 1862 7.762588 ATGATGATTGGATGAAAAGATCCTC 57.237 36.000 0.00 0.00 42.36 3.71
1803 1863 6.665695 TGATGATTGGATGAAAAGATCCTCA 58.334 36.000 0.00 0.00 42.36 3.86
1819 1879 8.641498 AAGATCCTCATAAAAATGTCACAACT 57.359 30.769 0.00 0.00 0.00 3.16
1824 1884 8.593679 TCCTCATAAAAATGTCACAACTCTAGA 58.406 33.333 0.00 0.00 0.00 2.43
1869 1929 9.371136 TCTAAATCATACACTAGAAACTTGCAG 57.629 33.333 0.00 0.00 0.00 4.41
1872 1932 5.237815 TCATACACTAGAAACTTGCAGTGG 58.762 41.667 0.00 0.00 42.13 4.00
1873 1933 2.851195 ACACTAGAAACTTGCAGTGGG 58.149 47.619 0.00 0.00 42.13 4.61
1877 1937 2.664402 AGAAACTTGCAGTGGGATGT 57.336 45.000 0.00 0.00 0.00 3.06
1911 1971 0.902531 GTTCCGGAGATCCCAACTGA 59.097 55.000 3.34 0.00 34.14 3.41
1996 2057 8.931385 ATAATGTTGGAAGCATGTCAAATTAC 57.069 30.769 0.00 0.00 0.00 1.89
1999 2060 7.701539 TGTTGGAAGCATGTCAAATTACTAT 57.298 32.000 0.00 0.00 0.00 2.12
2008 2069 9.979578 AGCATGTCAAATTACTATTTTTGAACA 57.020 25.926 0.00 2.70 41.90 3.18
2029 2090 6.677781 ACAATGGATGTTTCAACCGTATAG 57.322 37.500 0.00 0.00 40.06 1.31
2032 2093 7.392113 ACAATGGATGTTTCAACCGTATAGAAA 59.608 33.333 0.00 0.00 40.06 2.52
2063 2125 9.823647 TGCTAAACACAATTTCCTTTCATTAAA 57.176 25.926 0.00 0.00 0.00 1.52
2166 2228 9.456147 AAAAGTTTGGTATAAAATTTATGGGCC 57.544 29.630 8.39 0.00 28.94 5.80
2167 2229 7.131907 AGTTTGGTATAAAATTTATGGGCCC 57.868 36.000 17.59 17.59 0.00 5.80
2168 2230 6.100569 AGTTTGGTATAAAATTTATGGGCCCC 59.899 38.462 22.27 0.85 0.00 5.80
2169 2231 5.157770 TGGTATAAAATTTATGGGCCCCA 57.842 39.130 22.27 4.05 38.19 4.96
2170 2232 5.538877 TGGTATAAAATTTATGGGCCCCAA 58.461 37.500 22.27 11.02 36.95 4.12
2171 2233 5.970640 TGGTATAAAATTTATGGGCCCCAAA 59.029 36.000 22.27 19.85 36.95 3.28
2172 2234 6.447084 TGGTATAAAATTTATGGGCCCCAAAA 59.553 34.615 22.27 19.80 36.95 2.44
2173 2235 6.768861 GGTATAAAATTTATGGGCCCCAAAAC 59.231 38.462 22.27 12.54 36.95 2.43
2174 2236 6.650622 ATAAAATTTATGGGCCCCAAAACT 57.349 33.333 22.27 6.71 36.95 2.66
2175 2237 7.757242 ATAAAATTTATGGGCCCCAAAACTA 57.243 32.000 22.27 11.87 36.95 2.24
2176 2238 6.650622 AAAATTTATGGGCCCCAAAACTAT 57.349 33.333 22.27 6.53 36.95 2.12
2177 2239 5.628797 AATTTATGGGCCCCAAAACTATG 57.371 39.130 22.27 0.00 36.95 2.23
2178 2240 3.767309 TTATGGGCCCCAAAACTATGT 57.233 42.857 22.27 0.00 36.95 2.29
2179 2241 1.864669 ATGGGCCCCAAAACTATGTG 58.135 50.000 22.27 0.00 36.95 3.21
2180 2242 0.902516 TGGGCCCCAAAACTATGTGC 60.903 55.000 22.27 0.00 0.00 4.57
2181 2243 0.614697 GGGCCCCAAAACTATGTGCT 60.615 55.000 12.23 0.00 0.00 4.40
2182 2244 1.341581 GGGCCCCAAAACTATGTGCTA 60.342 52.381 12.23 0.00 0.00 3.49
2183 2245 2.452505 GGCCCCAAAACTATGTGCTAA 58.547 47.619 0.00 0.00 0.00 3.09
2184 2246 2.829120 GGCCCCAAAACTATGTGCTAAA 59.171 45.455 0.00 0.00 0.00 1.85
2185 2247 3.450817 GGCCCCAAAACTATGTGCTAAAT 59.549 43.478 0.00 0.00 0.00 1.40
2186 2248 4.647399 GGCCCCAAAACTATGTGCTAAATA 59.353 41.667 0.00 0.00 0.00 1.40
2187 2249 5.128008 GGCCCCAAAACTATGTGCTAAATAA 59.872 40.000 0.00 0.00 0.00 1.40
2188 2250 6.351456 GGCCCCAAAACTATGTGCTAAATAAA 60.351 38.462 0.00 0.00 0.00 1.40
2189 2251 7.272244 GCCCCAAAACTATGTGCTAAATAAAT 58.728 34.615 0.00 0.00 0.00 1.40
2190 2252 7.768582 GCCCCAAAACTATGTGCTAAATAAATT 59.231 33.333 0.00 0.00 0.00 1.82
2191 2253 9.665719 CCCCAAAACTATGTGCTAAATAAATTT 57.334 29.630 0.00 0.00 0.00 1.82
2243 2305 8.195165 AGTATCCATTCTAATTAGCTAGTGCA 57.805 34.615 7.67 0.00 42.74 4.57
2244 2306 8.820831 AGTATCCATTCTAATTAGCTAGTGCAT 58.179 33.333 7.67 0.00 42.74 3.96
2245 2307 7.918536 ATCCATTCTAATTAGCTAGTGCATG 57.081 36.000 7.67 0.00 42.74 4.06
2246 2308 5.702670 TCCATTCTAATTAGCTAGTGCATGC 59.297 40.000 11.82 11.82 42.74 4.06
2247 2309 5.471116 CCATTCTAATTAGCTAGTGCATGCA 59.529 40.000 18.46 18.46 42.74 3.96
2248 2310 5.991328 TTCTAATTAGCTAGTGCATGCAC 57.009 39.130 37.87 37.87 46.50 4.57
2256 2318 3.664495 GTGCATGCACAGTCAGCT 58.336 55.556 39.12 0.00 45.53 4.24
2257 2319 1.209383 GTGCATGCACAGTCAGCTG 59.791 57.895 39.12 7.63 45.53 4.24
2258 2320 2.178521 GCATGCACAGTCAGCTGC 59.821 61.111 14.21 4.26 46.30 5.25
2259 2321 2.875485 CATGCACAGTCAGCTGCC 59.125 61.111 9.47 0.00 46.30 4.85
2260 2322 1.969589 CATGCACAGTCAGCTGCCA 60.970 57.895 9.47 0.00 46.30 4.92
2261 2323 1.970114 ATGCACAGTCAGCTGCCAC 60.970 57.895 9.47 2.65 46.30 5.01
2262 2324 2.592574 GCACAGTCAGCTGCCACA 60.593 61.111 9.47 0.00 46.30 4.17
2263 2325 2.614446 GCACAGTCAGCTGCCACAG 61.614 63.158 9.47 2.39 46.30 3.66
2276 2338 1.963747 GCCACAGCAACGTTTACATC 58.036 50.000 0.00 0.00 39.53 3.06
2277 2339 1.265635 GCCACAGCAACGTTTACATCA 59.734 47.619 0.00 0.00 39.53 3.07
2278 2340 2.665519 GCCACAGCAACGTTTACATCAG 60.666 50.000 0.00 0.00 39.53 2.90
2279 2341 2.805671 CCACAGCAACGTTTACATCAGA 59.194 45.455 0.00 0.00 0.00 3.27
2280 2342 3.436704 CCACAGCAACGTTTACATCAGAT 59.563 43.478 0.00 0.00 0.00 2.90
2281 2343 4.629634 CCACAGCAACGTTTACATCAGATA 59.370 41.667 0.00 0.00 0.00 1.98
2282 2344 5.445939 CCACAGCAACGTTTACATCAGATAC 60.446 44.000 0.00 0.00 0.00 2.24
2283 2345 5.120053 CACAGCAACGTTTACATCAGATACA 59.880 40.000 0.00 0.00 0.00 2.29
2284 2346 5.699001 ACAGCAACGTTTACATCAGATACAA 59.301 36.000 0.00 0.00 0.00 2.41
2285 2347 6.128553 ACAGCAACGTTTACATCAGATACAAG 60.129 38.462 0.00 0.00 0.00 3.16
2286 2348 5.351465 AGCAACGTTTACATCAGATACAAGG 59.649 40.000 0.00 0.00 0.00 3.61
2287 2349 5.560148 CAACGTTTACATCAGATACAAGGC 58.440 41.667 0.00 0.00 0.00 4.35
2288 2350 5.086104 ACGTTTACATCAGATACAAGGCT 57.914 39.130 0.00 0.00 0.00 4.58
2289 2351 5.109903 ACGTTTACATCAGATACAAGGCTC 58.890 41.667 0.00 0.00 0.00 4.70
2290 2352 4.207224 CGTTTACATCAGATACAAGGCTCG 59.793 45.833 0.00 0.00 0.00 5.03
2291 2353 5.348986 GTTTACATCAGATACAAGGCTCGA 58.651 41.667 0.00 0.00 0.00 4.04
2292 2354 3.444703 ACATCAGATACAAGGCTCGAC 57.555 47.619 0.00 0.00 0.00 4.20
2293 2355 2.760650 ACATCAGATACAAGGCTCGACA 59.239 45.455 0.00 0.00 0.00 4.35
2294 2356 3.181482 ACATCAGATACAAGGCTCGACAG 60.181 47.826 0.00 0.00 0.00 3.51
2295 2357 1.135139 TCAGATACAAGGCTCGACAGC 59.865 52.381 0.00 0.00 46.06 4.40
2304 2366 3.389741 GCTCGACAGCCAAACAATG 57.610 52.632 0.00 0.00 40.14 2.82
2314 2376 2.906691 CCAAACAATGGCTTCCAACA 57.093 45.000 0.00 0.00 43.80 3.33
2315 2377 3.191078 CCAAACAATGGCTTCCAACAA 57.809 42.857 0.00 0.00 43.80 2.83
2316 2378 3.742385 CCAAACAATGGCTTCCAACAAT 58.258 40.909 0.00 0.00 43.80 2.71
2317 2379 3.499157 CCAAACAATGGCTTCCAACAATG 59.501 43.478 0.00 0.00 43.80 2.82
2318 2380 4.378774 CAAACAATGGCTTCCAACAATGA 58.621 39.130 0.00 0.00 36.95 2.57
2319 2381 4.895668 AACAATGGCTTCCAACAATGAT 57.104 36.364 0.00 0.00 36.95 2.45
2320 2382 4.895668 ACAATGGCTTCCAACAATGATT 57.104 36.364 0.00 0.00 36.95 2.57
2321 2383 5.231702 ACAATGGCTTCCAACAATGATTT 57.768 34.783 0.00 0.00 36.95 2.17
2322 2384 5.240121 ACAATGGCTTCCAACAATGATTTC 58.760 37.500 0.00 0.00 36.95 2.17
2323 2385 5.221682 ACAATGGCTTCCAACAATGATTTCA 60.222 36.000 0.00 0.00 36.95 2.69
2324 2386 4.255833 TGGCTTCCAACAATGATTTCAC 57.744 40.909 0.00 0.00 0.00 3.18
2325 2387 3.006752 TGGCTTCCAACAATGATTTCACC 59.993 43.478 0.00 0.00 0.00 4.02
2326 2388 3.006752 GGCTTCCAACAATGATTTCACCA 59.993 43.478 0.00 0.00 0.00 4.17
2327 2389 4.502950 GGCTTCCAACAATGATTTCACCAA 60.503 41.667 0.00 0.00 0.00 3.67
2328 2390 4.448732 GCTTCCAACAATGATTTCACCAAC 59.551 41.667 0.00 0.00 0.00 3.77
2329 2391 5.599732 CTTCCAACAATGATTTCACCAACA 58.400 37.500 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 7.255836 GCCAGGGGTCTTTCCAAATATTAATAC 60.256 40.741 0.00 0.00 38.11 1.89
66 69 0.941542 TTGCAGTGTGGTAACGCTTC 59.058 50.000 0.00 0.00 44.87 3.86
67 70 0.944386 CTTGCAGTGTGGTAACGCTT 59.056 50.000 0.00 0.00 44.87 4.68
70 73 0.865769 GTCCTTGCAGTGTGGTAACG 59.134 55.000 0.00 0.00 42.51 3.18
131 134 4.407365 AGGTCTTTGTCCAAACCATTAGG 58.593 43.478 4.25 0.00 42.21 2.69
141 144 1.071699 GGCACACTAGGTCTTTGTCCA 59.928 52.381 0.00 0.00 0.00 4.02
345 354 9.581289 TCCATTCAAAATTAGTTGTTTCTCCTA 57.419 29.630 0.00 0.00 0.00 2.94
438 447 8.437575 TCCTCAGTTTCATTCTTAAAGGTAAGT 58.562 33.333 0.00 0.00 38.33 2.24
694 711 3.117398 TGGCCTTATTTCTCTCATGCCAT 60.117 43.478 3.32 0.00 42.32 4.40
721 738 5.136105 TCGAGAGATTTCATCTGATCTCCA 58.864 41.667 9.14 0.00 46.01 3.86
874 891 4.260907 CCACTATCATGAAAAGCACCATCG 60.261 45.833 0.00 0.00 0.00 3.84
892 910 2.027007 CCGTAAAACCCCATCACCACTA 60.027 50.000 0.00 0.00 0.00 2.74
893 911 1.271707 CCGTAAAACCCCATCACCACT 60.272 52.381 0.00 0.00 0.00 4.00
894 912 1.170442 CCGTAAAACCCCATCACCAC 58.830 55.000 0.00 0.00 0.00 4.16
896 914 1.271488 TGACCGTAAAACCCCATCACC 60.271 52.381 0.00 0.00 0.00 4.02
897 915 2.081462 CTGACCGTAAAACCCCATCAC 58.919 52.381 0.00 0.00 0.00 3.06
1083 1111 3.957497 AGTCATACTCCTCGCTTGAGATT 59.043 43.478 0.00 0.00 42.66 2.40
1145 1173 4.933505 TCATCAAAAGCCACATTCAACA 57.066 36.364 0.00 0.00 0.00 3.33
1361 1393 3.323403 CCACTCTTGACTCTTGAGGTCTT 59.677 47.826 2.55 0.00 35.04 3.01
1362 1394 2.896685 CCACTCTTGACTCTTGAGGTCT 59.103 50.000 2.55 0.00 35.04 3.85
1363 1395 2.894126 TCCACTCTTGACTCTTGAGGTC 59.106 50.000 2.55 0.00 32.58 3.85
1364 1396 2.896685 CTCCACTCTTGACTCTTGAGGT 59.103 50.000 2.55 0.00 32.58 3.85
1365 1397 2.896685 ACTCCACTCTTGACTCTTGAGG 59.103 50.000 2.55 0.00 32.58 3.86
1366 1398 4.599047 AACTCCACTCTTGACTCTTGAG 57.401 45.455 0.00 0.00 0.00 3.02
1367 1399 4.499865 CGAAACTCCACTCTTGACTCTTGA 60.500 45.833 0.00 0.00 0.00 3.02
1368 1400 3.738282 CGAAACTCCACTCTTGACTCTTG 59.262 47.826 0.00 0.00 0.00 3.02
1369 1401 3.637229 TCGAAACTCCACTCTTGACTCTT 59.363 43.478 0.00 0.00 0.00 2.85
1370 1402 3.223435 TCGAAACTCCACTCTTGACTCT 58.777 45.455 0.00 0.00 0.00 3.24
1371 1403 3.570559 CTCGAAACTCCACTCTTGACTC 58.429 50.000 0.00 0.00 0.00 3.36
1372 1404 2.297597 CCTCGAAACTCCACTCTTGACT 59.702 50.000 0.00 0.00 0.00 3.41
1373 1405 2.678324 CCTCGAAACTCCACTCTTGAC 58.322 52.381 0.00 0.00 0.00 3.18
1374 1406 1.000955 GCCTCGAAACTCCACTCTTGA 59.999 52.381 0.00 0.00 0.00 3.02
1375 1407 1.433534 GCCTCGAAACTCCACTCTTG 58.566 55.000 0.00 0.00 0.00 3.02
1376 1408 0.321996 GGCCTCGAAACTCCACTCTT 59.678 55.000 0.00 0.00 0.00 2.85
1377 1409 0.832135 TGGCCTCGAAACTCCACTCT 60.832 55.000 3.32 0.00 0.00 3.24
1378 1410 0.250513 ATGGCCTCGAAACTCCACTC 59.749 55.000 3.32 0.00 0.00 3.51
1379 1411 0.693049 AATGGCCTCGAAACTCCACT 59.307 50.000 3.32 0.00 0.00 4.00
1380 1412 0.804989 CAATGGCCTCGAAACTCCAC 59.195 55.000 3.32 0.00 0.00 4.02
1381 1413 0.322456 CCAATGGCCTCGAAACTCCA 60.322 55.000 3.32 0.00 0.00 3.86
1382 1414 1.657751 GCCAATGGCCTCGAAACTCC 61.658 60.000 14.47 0.00 44.06 3.85
1383 1415 1.803289 GCCAATGGCCTCGAAACTC 59.197 57.895 14.47 0.00 44.06 3.01
1384 1416 4.002797 GCCAATGGCCTCGAAACT 57.997 55.556 14.47 0.00 44.06 2.66
1393 1425 1.302832 ATAGCTAGGCGCCAATGGC 60.303 57.895 31.54 22.57 46.75 4.40
1394 1426 0.035317 TCATAGCTAGGCGCCAATGG 59.965 55.000 31.54 12.47 40.39 3.16
1395 1427 1.882912 TTCATAGCTAGGCGCCAATG 58.117 50.000 31.54 21.60 40.39 2.82
1396 1428 2.638480 TTTCATAGCTAGGCGCCAAT 57.362 45.000 31.54 12.06 40.39 3.16
1397 1429 2.288666 CTTTTCATAGCTAGGCGCCAA 58.711 47.619 31.54 8.56 40.39 4.52
1398 1430 1.475034 CCTTTTCATAGCTAGGCGCCA 60.475 52.381 31.54 14.00 40.39 5.69
1399 1431 1.230324 CCTTTTCATAGCTAGGCGCC 58.770 55.000 21.89 21.89 40.39 6.53
1400 1432 1.230324 CCCTTTTCATAGCTAGGCGC 58.770 55.000 0.00 0.00 39.57 6.53
1401 1433 1.230324 GCCCTTTTCATAGCTAGGCG 58.770 55.000 0.00 0.00 0.00 5.52
1402 1434 2.348411 TGCCCTTTTCATAGCTAGGC 57.652 50.000 10.23 10.23 39.41 3.93
1403 1435 4.156455 TCTTGCCCTTTTCATAGCTAGG 57.844 45.455 0.00 0.00 0.00 3.02
1404 1436 5.415701 TGTTTCTTGCCCTTTTCATAGCTAG 59.584 40.000 0.00 0.00 0.00 3.42
1405 1437 5.321102 TGTTTCTTGCCCTTTTCATAGCTA 58.679 37.500 0.00 0.00 0.00 3.32
1406 1438 4.151883 TGTTTCTTGCCCTTTTCATAGCT 58.848 39.130 0.00 0.00 0.00 3.32
1407 1439 4.519540 TGTTTCTTGCCCTTTTCATAGC 57.480 40.909 0.00 0.00 0.00 2.97
1408 1440 5.696270 GGTTTGTTTCTTGCCCTTTTCATAG 59.304 40.000 0.00 0.00 0.00 2.23
1409 1441 5.606505 GGTTTGTTTCTTGCCCTTTTCATA 58.393 37.500 0.00 0.00 0.00 2.15
1410 1442 4.450976 GGTTTGTTTCTTGCCCTTTTCAT 58.549 39.130 0.00 0.00 0.00 2.57
1411 1443 3.677424 CGGTTTGTTTCTTGCCCTTTTCA 60.677 43.478 0.00 0.00 0.00 2.69
1412 1444 2.863740 CGGTTTGTTTCTTGCCCTTTTC 59.136 45.455 0.00 0.00 0.00 2.29
1413 1445 2.899976 CGGTTTGTTTCTTGCCCTTTT 58.100 42.857 0.00 0.00 0.00 2.27
1414 1446 1.472552 GCGGTTTGTTTCTTGCCCTTT 60.473 47.619 0.00 0.00 0.00 3.11
1415 1447 0.104120 GCGGTTTGTTTCTTGCCCTT 59.896 50.000 0.00 0.00 0.00 3.95
1416 1448 1.040339 TGCGGTTTGTTTCTTGCCCT 61.040 50.000 0.00 0.00 0.00 5.19
1417 1449 0.874175 GTGCGGTTTGTTTCTTGCCC 60.874 55.000 0.00 0.00 0.00 5.36
1418 1450 0.102300 AGTGCGGTTTGTTTCTTGCC 59.898 50.000 0.00 0.00 0.00 4.52
1419 1451 1.199624 CAGTGCGGTTTGTTTCTTGC 58.800 50.000 0.00 0.00 0.00 4.01
1420 1452 2.842208 TCAGTGCGGTTTGTTTCTTG 57.158 45.000 0.00 0.00 0.00 3.02
1421 1453 2.034558 CCATCAGTGCGGTTTGTTTCTT 59.965 45.455 0.00 0.00 0.00 2.52
1422 1454 1.608590 CCATCAGTGCGGTTTGTTTCT 59.391 47.619 0.00 0.00 0.00 2.52
1423 1455 1.335872 CCCATCAGTGCGGTTTGTTTC 60.336 52.381 0.00 0.00 0.00 2.78
1424 1456 0.673437 CCCATCAGTGCGGTTTGTTT 59.327 50.000 0.00 0.00 0.00 2.83
1425 1457 0.179004 TCCCATCAGTGCGGTTTGTT 60.179 50.000 0.00 0.00 0.00 2.83
1426 1458 0.038166 ATCCCATCAGTGCGGTTTGT 59.962 50.000 0.00 0.00 0.00 2.83
1427 1459 1.670811 GTATCCCATCAGTGCGGTTTG 59.329 52.381 0.00 0.00 0.00 2.93
1428 1460 1.280710 TGTATCCCATCAGTGCGGTTT 59.719 47.619 0.00 0.00 0.00 3.27
1429 1461 0.908910 TGTATCCCATCAGTGCGGTT 59.091 50.000 0.00 0.00 0.00 4.44
1430 1462 0.178068 GTGTATCCCATCAGTGCGGT 59.822 55.000 0.00 0.00 0.00 5.68
1431 1463 0.177836 TGTGTATCCCATCAGTGCGG 59.822 55.000 0.00 0.00 0.00 5.69
1432 1464 1.869132 CATGTGTATCCCATCAGTGCG 59.131 52.381 0.00 0.00 0.00 5.34
1433 1465 2.224606 CCATGTGTATCCCATCAGTGC 58.775 52.381 0.00 0.00 0.00 4.40
1434 1466 2.158711 AGCCATGTGTATCCCATCAGTG 60.159 50.000 0.00 0.00 0.00 3.66
1435 1467 2.130193 AGCCATGTGTATCCCATCAGT 58.870 47.619 0.00 0.00 0.00 3.41
1436 1468 2.945080 AGCCATGTGTATCCCATCAG 57.055 50.000 0.00 0.00 0.00 2.90
1437 1469 2.639347 CCTAGCCATGTGTATCCCATCA 59.361 50.000 0.00 0.00 0.00 3.07
1438 1470 2.906389 TCCTAGCCATGTGTATCCCATC 59.094 50.000 0.00 0.00 0.00 3.51
1439 1471 2.639839 GTCCTAGCCATGTGTATCCCAT 59.360 50.000 0.00 0.00 0.00 4.00
1440 1472 2.047061 GTCCTAGCCATGTGTATCCCA 58.953 52.381 0.00 0.00 0.00 4.37
1441 1473 1.348036 GGTCCTAGCCATGTGTATCCC 59.652 57.143 0.00 0.00 0.00 3.85
1442 1474 1.348036 GGGTCCTAGCCATGTGTATCC 59.652 57.143 0.00 0.00 35.40 2.59
1443 1475 1.348036 GGGGTCCTAGCCATGTGTATC 59.652 57.143 0.00 0.00 37.54 2.24
1444 1476 1.435256 GGGGTCCTAGCCATGTGTAT 58.565 55.000 0.00 0.00 37.54 2.29
1445 1477 1.046472 CGGGGTCCTAGCCATGTGTA 61.046 60.000 0.00 0.00 37.54 2.90
1446 1478 2.367202 CGGGGTCCTAGCCATGTGT 61.367 63.158 0.00 0.00 37.54 3.72
1447 1479 1.046472 TACGGGGTCCTAGCCATGTG 61.046 60.000 0.00 0.00 37.54 3.21
1448 1480 1.047034 GTACGGGGTCCTAGCCATGT 61.047 60.000 0.00 0.00 37.54 3.21
1449 1481 0.759436 AGTACGGGGTCCTAGCCATG 60.759 60.000 0.00 0.00 37.54 3.66
1450 1482 0.469518 GAGTACGGGGTCCTAGCCAT 60.470 60.000 0.00 0.00 37.54 4.40
1451 1483 1.076485 GAGTACGGGGTCCTAGCCA 60.076 63.158 0.00 0.00 37.54 4.75
1452 1484 1.108132 CAGAGTACGGGGTCCTAGCC 61.108 65.000 0.00 0.00 34.31 3.93
1453 1485 1.108132 CCAGAGTACGGGGTCCTAGC 61.108 65.000 0.00 0.00 0.00 3.42
1454 1486 0.258194 ACCAGAGTACGGGGTCCTAG 59.742 60.000 6.29 0.00 35.72 3.02
1455 1487 0.257039 GACCAGAGTACGGGGTCCTA 59.743 60.000 17.65 0.00 44.21 2.94
1456 1488 1.000107 GACCAGAGTACGGGGTCCT 60.000 63.158 17.65 0.00 44.21 3.85
1457 1489 3.613527 GACCAGAGTACGGGGTCC 58.386 66.667 17.65 5.40 44.21 4.46
1459 1491 2.038490 GGGACCAGAGTACGGGGT 59.962 66.667 5.94 5.94 37.70 4.95
1460 1492 1.757340 GAGGGACCAGAGTACGGGG 60.757 68.421 0.00 3.16 35.72 5.73
1461 1493 0.397254 ATGAGGGACCAGAGTACGGG 60.397 60.000 0.00 0.45 37.39 5.28
1462 1494 0.747255 CATGAGGGACCAGAGTACGG 59.253 60.000 0.00 0.00 0.00 4.02
1463 1495 0.747255 CCATGAGGGACCAGAGTACG 59.253 60.000 0.00 0.00 40.01 3.67
1486 1518 2.686816 GGGATGGTTGTCGCAACGG 61.687 63.158 13.85 0.00 0.00 4.44
1491 1523 0.734889 CTTGATGGGATGGTTGTCGC 59.265 55.000 0.00 0.00 0.00 5.19
1493 1525 1.838112 TGCTTGATGGGATGGTTGTC 58.162 50.000 0.00 0.00 0.00 3.18
1506 1538 0.611618 ATGAATGGGCGGTTGCTTGA 60.612 50.000 0.00 0.00 42.25 3.02
1510 1554 1.139520 GACATGAATGGGCGGTTGC 59.860 57.895 0.00 0.00 41.71 4.17
1512 1556 1.379843 GGGACATGAATGGGCGGTT 60.380 57.895 0.00 0.00 0.00 4.44
1521 1565 0.038166 GGTGCTTCCTGGGACATGAA 59.962 55.000 0.00 0.00 40.47 2.57
1525 1569 0.842030 ATCTGGTGCTTCCTGGGACA 60.842 55.000 0.00 0.00 36.08 4.02
1526 1570 1.134371 GTATCTGGTGCTTCCTGGGAC 60.134 57.143 0.00 0.00 36.08 4.46
1527 1571 1.204146 GTATCTGGTGCTTCCTGGGA 58.796 55.000 0.00 0.00 36.08 4.37
1528 1572 0.181350 GGTATCTGGTGCTTCCTGGG 59.819 60.000 0.00 0.00 36.08 4.45
1531 1575 0.824759 GACGGTATCTGGTGCTTCCT 59.175 55.000 0.00 0.00 37.07 3.36
1532 1576 0.535335 TGACGGTATCTGGTGCTTCC 59.465 55.000 0.00 0.00 0.00 3.46
1534 1578 2.632377 CATTGACGGTATCTGGTGCTT 58.368 47.619 0.00 0.00 0.00 3.91
1536 1580 0.657840 GCATTGACGGTATCTGGTGC 59.342 55.000 0.00 0.00 0.00 5.01
1537 1581 0.930310 CGCATTGACGGTATCTGGTG 59.070 55.000 0.00 0.00 0.00 4.17
1538 1582 0.821517 TCGCATTGACGGTATCTGGT 59.178 50.000 0.00 0.00 0.00 4.00
1539 1583 1.209128 GTCGCATTGACGGTATCTGG 58.791 55.000 0.00 0.00 37.96 3.86
1553 1598 0.530744 AGACGGCTTATCTTGTCGCA 59.469 50.000 0.00 0.00 35.80 5.10
1573 1618 4.515191 GTGCAGTTCAAAGTATCCTTGACA 59.485 41.667 0.00 0.00 0.00 3.58
1574 1619 4.377431 CGTGCAGTTCAAAGTATCCTTGAC 60.377 45.833 0.00 0.00 0.00 3.18
1575 1620 3.745975 CGTGCAGTTCAAAGTATCCTTGA 59.254 43.478 0.00 0.00 0.00 3.02
1584 1629 3.252215 TCCATAAACCGTGCAGTTCAAAG 59.748 43.478 0.00 0.00 0.00 2.77
1587 1632 2.552599 TCCATAAACCGTGCAGTTCA 57.447 45.000 0.00 0.00 0.00 3.18
1621 1667 9.893305 CAAAGAAAAACTACGAATTATTCCTGT 57.107 29.630 0.00 0.00 0.00 4.00
1623 1669 9.893305 CACAAAGAAAAACTACGAATTATTCCT 57.107 29.630 0.00 0.00 0.00 3.36
1624 1670 9.673454 ACACAAAGAAAAACTACGAATTATTCC 57.327 29.630 0.00 0.00 0.00 3.01
1628 1674 9.843334 ACAAACACAAAGAAAAACTACGAATTA 57.157 25.926 0.00 0.00 0.00 1.40
1629 1675 8.751302 ACAAACACAAAGAAAAACTACGAATT 57.249 26.923 0.00 0.00 0.00 2.17
1630 1676 8.751302 AACAAACACAAAGAAAAACTACGAAT 57.249 26.923 0.00 0.00 0.00 3.34
1631 1677 9.116054 GTAACAAACACAAAGAAAAACTACGAA 57.884 29.630 0.00 0.00 0.00 3.85
1632 1678 7.478044 CGTAACAAACACAAAGAAAAACTACGA 59.522 33.333 0.00 0.00 0.00 3.43
1633 1679 7.478044 TCGTAACAAACACAAAGAAAAACTACG 59.522 33.333 0.00 0.00 0.00 3.51
1634 1680 8.658171 TCGTAACAAACACAAAGAAAAACTAC 57.342 30.769 0.00 0.00 0.00 2.73
1635 1681 7.482428 GCTCGTAACAAACACAAAGAAAAACTA 59.518 33.333 0.00 0.00 0.00 2.24
1636 1682 6.307077 GCTCGTAACAAACACAAAGAAAAACT 59.693 34.615 0.00 0.00 0.00 2.66
1641 1687 3.617706 TCGCTCGTAACAAACACAAAGAA 59.382 39.130 0.00 0.00 0.00 2.52
1662 1708 1.747355 TCCTACGACCGGAAAGACATC 59.253 52.381 9.46 0.00 0.00 3.06
1677 1723 3.179830 CATGACGTAGCTGTGTTCCTAC 58.820 50.000 0.00 0.00 0.00 3.18
1690 1740 1.897133 ACAGGTTACCAGCATGACGTA 59.103 47.619 3.51 0.00 39.69 3.57
1692 1742 1.464608 CAACAGGTTACCAGCATGACG 59.535 52.381 3.51 0.00 39.69 4.35
1696 1746 1.538047 CAGCAACAGGTTACCAGCAT 58.462 50.000 3.51 0.00 0.00 3.79
1703 1753 1.270094 CGTGAGTCCAGCAACAGGTTA 60.270 52.381 0.00 0.00 0.00 2.85
1718 1775 2.093973 ACTTCTTGCATACCTCCGTGAG 60.094 50.000 0.00 0.00 0.00 3.51
1721 1778 3.097614 ACTACTTCTTGCATACCTCCGT 58.902 45.455 0.00 0.00 0.00 4.69
1722 1779 3.802948 ACTACTTCTTGCATACCTCCG 57.197 47.619 0.00 0.00 0.00 4.63
1724 1781 8.639761 TCCTTTATACTACTTCTTGCATACCTC 58.360 37.037 0.00 0.00 0.00 3.85
1726 1783 9.609346 TTTCCTTTATACTACTTCTTGCATACC 57.391 33.333 0.00 0.00 0.00 2.73
1756 1816 5.677319 TTGGCATTGCTACTTACTAGTCT 57.323 39.130 8.82 0.00 35.78 3.24
1757 1817 6.049149 TCATTGGCATTGCTACTTACTAGTC 58.951 40.000 8.82 0.00 35.78 2.59
1758 1818 5.989477 TCATTGGCATTGCTACTTACTAGT 58.011 37.500 8.82 0.00 38.44 2.57
1777 1837 7.783119 TGAGGATCTTTTCATCCAATCATCATT 59.217 33.333 2.39 0.00 44.57 2.57
1793 1853 9.082313 AGTTGTGACATTTTTATGAGGATCTTT 57.918 29.630 0.00 0.00 34.92 2.52
1885 1945 0.106894 GGATCTCCGGAACATGGGAC 59.893 60.000 5.23 0.00 0.00 4.46
1888 1948 0.546122 TTGGGATCTCCGGAACATGG 59.454 55.000 5.23 0.00 38.76 3.66
1892 1952 0.902531 TCAGTTGGGATCTCCGGAAC 59.097 55.000 5.23 0.00 38.76 3.62
2008 2069 7.931578 TTTCTATACGGTTGAAACATCCATT 57.068 32.000 0.00 0.00 28.75 3.16
2013 2074 7.360946 GCACTCTTTTCTATACGGTTGAAACAT 60.361 37.037 0.00 0.00 32.56 2.71
2140 2202 9.456147 GGCCCATAAATTTTATACCAAACTTTT 57.544 29.630 0.00 0.00 0.00 2.27
2141 2203 8.050325 GGGCCCATAAATTTTATACCAAACTTT 58.950 33.333 19.95 0.00 0.00 2.66
2142 2204 7.366101 GGGGCCCATAAATTTTATACCAAACTT 60.366 37.037 26.86 0.00 0.00 2.66
2143 2205 6.100569 GGGGCCCATAAATTTTATACCAAACT 59.899 38.462 26.86 0.00 0.00 2.66
2144 2206 6.126739 TGGGGCCCATAAATTTTATACCAAAC 60.127 38.462 24.76 0.00 0.00 2.93
2145 2207 5.970640 TGGGGCCCATAAATTTTATACCAAA 59.029 36.000 24.76 0.00 0.00 3.28
2146 2208 5.538877 TGGGGCCCATAAATTTTATACCAA 58.461 37.500 24.76 0.00 0.00 3.67
2147 2209 5.157770 TGGGGCCCATAAATTTTATACCA 57.842 39.130 24.76 3.44 0.00 3.25
2148 2210 6.502074 TTTGGGGCCCATAAATTTTATACC 57.498 37.500 29.34 0.22 31.53 2.73
2149 2211 7.570132 AGTTTTGGGGCCCATAAATTTTATAC 58.430 34.615 29.34 13.73 31.53 1.47
2150 2212 7.757242 AGTTTTGGGGCCCATAAATTTTATA 57.243 32.000 29.34 3.63 31.53 0.98
2151 2213 6.650622 AGTTTTGGGGCCCATAAATTTTAT 57.349 33.333 29.34 7.46 31.53 1.40
2152 2214 7.182930 ACATAGTTTTGGGGCCCATAAATTTTA 59.817 33.333 28.86 20.56 31.53 1.52
2153 2215 6.012069 ACATAGTTTTGGGGCCCATAAATTTT 60.012 34.615 28.86 18.21 31.53 1.82
2154 2216 5.490717 ACATAGTTTTGGGGCCCATAAATTT 59.509 36.000 28.86 20.31 31.53 1.82
2155 2217 5.036236 ACATAGTTTTGGGGCCCATAAATT 58.964 37.500 28.86 24.93 31.53 1.82
2156 2218 4.408596 CACATAGTTTTGGGGCCCATAAAT 59.591 41.667 29.34 28.11 31.53 1.40
2157 2219 3.772025 CACATAGTTTTGGGGCCCATAAA 59.228 43.478 29.34 24.35 31.53 1.40
2158 2220 3.370104 CACATAGTTTTGGGGCCCATAA 58.630 45.455 29.34 25.57 31.53 1.90
2159 2221 2.952702 GCACATAGTTTTGGGGCCCATA 60.953 50.000 29.34 20.45 31.53 2.74
2160 2222 1.864669 CACATAGTTTTGGGGCCCAT 58.135 50.000 29.34 14.65 31.53 4.00
2161 2223 0.902516 GCACATAGTTTTGGGGCCCA 60.903 55.000 24.76 24.76 0.00 5.36
2162 2224 0.614697 AGCACATAGTTTTGGGGCCC 60.615 55.000 18.17 18.17 0.00 5.80
2163 2225 2.137810 TAGCACATAGTTTTGGGGCC 57.862 50.000 0.00 0.00 0.00 5.80
2164 2226 4.736126 ATTTAGCACATAGTTTTGGGGC 57.264 40.909 0.00 0.00 0.00 5.80
2165 2227 9.665719 AAATTTATTTAGCACATAGTTTTGGGG 57.334 29.630 0.00 0.00 0.00 4.96
2217 2279 9.309224 TGCACTAGCTAATTAGAATGGATACTA 57.691 33.333 16.85 4.68 42.74 1.82
2218 2280 8.195165 TGCACTAGCTAATTAGAATGGATACT 57.805 34.615 16.85 3.75 42.74 2.12
2219 2281 8.877779 CATGCACTAGCTAATTAGAATGGATAC 58.122 37.037 16.85 0.00 42.74 2.24
2220 2282 7.550551 GCATGCACTAGCTAATTAGAATGGATA 59.449 37.037 16.85 0.00 42.74 2.59
2221 2283 6.373774 GCATGCACTAGCTAATTAGAATGGAT 59.626 38.462 16.85 10.73 42.74 3.41
2222 2284 5.702670 GCATGCACTAGCTAATTAGAATGGA 59.297 40.000 16.85 9.04 42.74 3.41
2223 2285 5.471116 TGCATGCACTAGCTAATTAGAATGG 59.529 40.000 18.46 8.09 42.74 3.16
2224 2286 6.017687 TGTGCATGCACTAGCTAATTAGAATG 60.018 38.462 41.43 8.61 46.30 2.67
2225 2287 6.057533 TGTGCATGCACTAGCTAATTAGAAT 58.942 36.000 41.43 6.29 46.30 2.40
2226 2288 5.427378 TGTGCATGCACTAGCTAATTAGAA 58.573 37.500 41.43 20.68 46.30 2.10
2227 2289 5.022282 TGTGCATGCACTAGCTAATTAGA 57.978 39.130 41.43 20.86 46.30 2.10
2228 2290 4.813161 ACTGTGCATGCACTAGCTAATTAG 59.187 41.667 41.43 30.64 46.30 1.73
2229 2291 4.769688 ACTGTGCATGCACTAGCTAATTA 58.230 39.130 41.43 22.92 46.30 1.40
2230 2292 3.614092 ACTGTGCATGCACTAGCTAATT 58.386 40.909 41.43 21.91 46.30 1.40
2231 2293 3.201290 GACTGTGCATGCACTAGCTAAT 58.799 45.455 41.43 24.06 46.30 1.73
2232 2294 2.028203 TGACTGTGCATGCACTAGCTAA 60.028 45.455 41.43 24.87 46.30 3.09
2233 2295 1.550072 TGACTGTGCATGCACTAGCTA 59.450 47.619 41.43 26.84 46.30 3.32
2234 2296 0.322648 TGACTGTGCATGCACTAGCT 59.677 50.000 41.43 27.10 46.30 3.32
2235 2297 0.725686 CTGACTGTGCATGCACTAGC 59.274 55.000 41.43 30.90 46.30 3.42
2236 2298 0.725686 GCTGACTGTGCATGCACTAG 59.274 55.000 41.43 35.71 46.30 2.57
2237 2299 0.322648 AGCTGACTGTGCATGCACTA 59.677 50.000 41.43 29.19 46.30 2.74
2238 2300 1.072678 AGCTGACTGTGCATGCACT 59.927 52.632 41.43 28.35 46.30 4.40
2239 2301 1.209383 CAGCTGACTGTGCATGCAC 59.791 57.895 38.00 38.00 46.33 4.57
2240 2302 2.622962 GCAGCTGACTGTGCATGCA 61.623 57.895 18.46 18.46 46.30 3.96
2241 2303 2.178521 GCAGCTGACTGTGCATGC 59.821 61.111 20.43 11.82 46.30 4.06
2242 2304 1.969589 TGGCAGCTGACTGTGCATG 60.970 57.895 22.80 0.00 46.30 4.06
2243 2305 1.970114 GTGGCAGCTGACTGTGCAT 60.970 57.895 22.80 0.00 46.30 3.96
2244 2306 2.592574 GTGGCAGCTGACTGTGCA 60.593 61.111 22.80 0.00 46.30 4.57
2245 2307 2.592574 TGTGGCAGCTGACTGTGC 60.593 61.111 22.80 8.99 46.30 4.57
2246 2308 3.651645 CTGTGGCAGCTGACTGTG 58.348 61.111 22.80 6.49 46.30 3.66
2257 2319 1.265635 TGATGTAAACGTTGCTGTGGC 59.734 47.619 0.00 0.00 39.26 5.01
2258 2320 2.805671 TCTGATGTAAACGTTGCTGTGG 59.194 45.455 0.00 0.00 0.00 4.17
2259 2321 4.668576 ATCTGATGTAAACGTTGCTGTG 57.331 40.909 0.00 0.00 0.00 3.66
2260 2322 5.234752 TGTATCTGATGTAAACGTTGCTGT 58.765 37.500 0.00 0.00 0.00 4.40
2261 2323 5.778161 TGTATCTGATGTAAACGTTGCTG 57.222 39.130 0.00 0.00 0.00 4.41
2262 2324 5.351465 CCTTGTATCTGATGTAAACGTTGCT 59.649 40.000 0.00 0.00 0.00 3.91
2263 2325 5.560148 CCTTGTATCTGATGTAAACGTTGC 58.440 41.667 0.00 0.00 0.00 4.17
2264 2326 5.351465 AGCCTTGTATCTGATGTAAACGTTG 59.649 40.000 0.00 0.00 0.00 4.10
2265 2327 5.488341 AGCCTTGTATCTGATGTAAACGTT 58.512 37.500 0.00 0.00 0.00 3.99
2266 2328 5.086104 AGCCTTGTATCTGATGTAAACGT 57.914 39.130 0.00 0.00 0.00 3.99
2267 2329 4.207224 CGAGCCTTGTATCTGATGTAAACG 59.793 45.833 0.00 0.00 0.00 3.60
2268 2330 5.232414 GTCGAGCCTTGTATCTGATGTAAAC 59.768 44.000 0.00 0.00 0.00 2.01
2269 2331 5.105513 TGTCGAGCCTTGTATCTGATGTAAA 60.106 40.000 0.00 0.00 0.00 2.01
2270 2332 4.401202 TGTCGAGCCTTGTATCTGATGTAA 59.599 41.667 0.00 0.00 0.00 2.41
2271 2333 3.951680 TGTCGAGCCTTGTATCTGATGTA 59.048 43.478 0.00 0.00 0.00 2.29
2272 2334 2.760650 TGTCGAGCCTTGTATCTGATGT 59.239 45.455 0.00 0.00 0.00 3.06
2273 2335 3.379240 CTGTCGAGCCTTGTATCTGATG 58.621 50.000 0.00 0.00 0.00 3.07
2274 2336 2.223923 GCTGTCGAGCCTTGTATCTGAT 60.224 50.000 0.00 0.00 39.57 2.90
2275 2337 1.135139 GCTGTCGAGCCTTGTATCTGA 59.865 52.381 0.00 0.00 39.57 3.27
2276 2338 1.565305 GCTGTCGAGCCTTGTATCTG 58.435 55.000 0.00 0.00 39.57 2.90
2286 2348 0.109597 CCATTGTTTGGCTGTCGAGC 60.110 55.000 0.00 0.00 45.40 5.03
2296 2358 4.378774 TCATTGTTGGAAGCCATTGTTTG 58.621 39.130 0.00 0.00 31.53 2.93
2297 2359 4.686191 TCATTGTTGGAAGCCATTGTTT 57.314 36.364 0.00 0.00 31.53 2.83
2298 2360 4.895668 ATCATTGTTGGAAGCCATTGTT 57.104 36.364 0.00 0.00 31.53 2.83
2299 2361 4.895668 AATCATTGTTGGAAGCCATTGT 57.104 36.364 0.00 0.00 31.53 2.71
2300 2362 5.121142 GTGAAATCATTGTTGGAAGCCATTG 59.879 40.000 0.00 0.00 31.53 2.82
2301 2363 5.240121 GTGAAATCATTGTTGGAAGCCATT 58.760 37.500 0.00 0.00 31.53 3.16
2302 2364 4.322953 GGTGAAATCATTGTTGGAAGCCAT 60.323 41.667 0.00 0.00 31.53 4.40
2303 2365 3.006752 GGTGAAATCATTGTTGGAAGCCA 59.993 43.478 0.00 0.00 0.00 4.75
2304 2366 3.006752 TGGTGAAATCATTGTTGGAAGCC 59.993 43.478 0.00 0.00 0.00 4.35
2305 2367 4.255833 TGGTGAAATCATTGTTGGAAGC 57.744 40.909 0.00 0.00 0.00 3.86
2306 2368 5.599732 TGTTGGTGAAATCATTGTTGGAAG 58.400 37.500 0.00 0.00 0.00 3.46
2307 2369 5.604758 TGTTGGTGAAATCATTGTTGGAA 57.395 34.783 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.