Multiple sequence alignment - TraesCS4A01G230800

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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 TraesCS4A01G230800 chr4A 100.000 4802 0 0 1 4802 540013447 540018248 0.000000e+00 8868.0
1 TraesCS4A01G230800 chr4A 95.718 1121 35 9 1909 3027 540081807 540082916 0.000000e+00 1792.0
2 TraesCS4A01G230800 chr4A 95.718 1121 35 9 1909 3027 540084030 540085139 0.000000e+00 1792.0
3 TraesCS4A01G230800 chr4A 95.629 1121 36 9 1909 3027 540086234 540087343 0.000000e+00 1786.0
4 TraesCS4A01G230800 chr4A 95.361 1121 38 10 1909 3027 540082919 540084027 0.000000e+00 1770.0
5 TraesCS4A01G230800 chr4A 93.756 1121 37 14 1909 3027 540085142 540086231 0.000000e+00 1652.0
6 TraesCS4A01G230800 chr4A 95.103 919 32 9 1909 2825 540080172 540081079 0.000000e+00 1435.0
7 TraesCS4A01G230800 chr4A 94.766 726 25 7 2304 3027 540081090 540081804 0.000000e+00 1118.0
8 TraesCS4A01G230800 chr4A 92.448 715 31 5 3265 3957 540087454 540088167 0.000000e+00 1000.0
9 TraesCS4A01G230800 chr4A 88.217 628 72 1 4173 4800 608142805 608143430 0.000000e+00 749.0
10 TraesCS4A01G230800 chr4A 94.357 319 16 2 2710 3027 540079852 540080169 5.590000e-134 488.0
11 TraesCS4A01G230800 chr4A 99.065 107 1 0 1909 2015 540087346 540087452 4.900000e-45 193.0
12 TraesCS4A01G230800 chr4A 84.483 58 6 3 1542 1598 297713259 297713204 2.000000e-03 54.7
13 TraesCS4A01G230800 chr4B 93.890 2504 111 18 1697 4172 85584301 85581812 0.000000e+00 3738.0
14 TraesCS4A01G230800 chr4B 90.495 1494 77 35 4 1466 85585869 85584410 0.000000e+00 1912.0
15 TraesCS4A01G230800 chr4B 100.000 40 0 0 1569 1608 85584347 85584308 1.850000e-09 75.0
16 TraesCS4A01G230800 chr4D 94.509 2422 99 14 1697 4098 56949139 56946732 0.000000e+00 3705.0
17 TraesCS4A01G230800 chr4D 90.192 1509 75 40 1 1466 56950721 56949243 0.000000e+00 1899.0
18 TraesCS4A01G230800 chr4D 100.000 40 0 0 1569 1608 56949185 56949146 1.850000e-09 75.0
19 TraesCS4A01G230800 chr6B 93.978 631 38 0 4172 4802 96628404 96629034 0.000000e+00 955.0
20 TraesCS4A01G230800 chr6B 92.880 632 44 1 4172 4802 77730903 77730272 0.000000e+00 917.0
21 TraesCS4A01G230800 chr3A 93.978 631 36 2 4172 4802 66403117 66403745 0.000000e+00 953.0
22 TraesCS4A01G230800 chr1A 91.223 638 49 1 4172 4802 47808855 47808218 0.000000e+00 861.0
23 TraesCS4A01G230800 chr7D 95.291 361 17 0 4172 4532 576742657 576742297 1.500000e-159 573.0
24 TraesCS4A01G230800 chr7D 93.015 272 19 0 4531 4802 576737295 576737024 9.680000e-107 398.0
25 TraesCS4A01G230800 chr7D 97.436 78 0 1 1497 1572 112833140 112833063 1.080000e-26 132.0
26 TraesCS4A01G230800 chr3D 97.468 79 0 2 1493 1569 508403128 508403206 3.020000e-27 134.0
27 TraesCS4A01G230800 chr6D 96.250 80 2 1 1496 1575 420732482 420732404 3.900000e-26 130.0
28 TraesCS4A01G230800 chr6D 98.630 73 0 1 1497 1569 29889977 29889906 1.400000e-25 128.0
29 TraesCS4A01G230800 chr3B 97.403 77 1 1 1494 1569 161590241 161590317 3.900000e-26 130.0
30 TraesCS4A01G230800 chr3B 91.209 91 6 2 1480 1569 219024486 219024397 6.530000e-24 122.0
31 TraesCS4A01G230800 chr2B 90.000 100 7 3 1472 1570 751187992 751188089 5.050000e-25 126.0
32 TraesCS4A01G230800 chr2A 93.902 82 4 1 1489 1570 675885091 675885171 6.530000e-24 122.0
33 TraesCS4A01G230800 chr6A 91.209 91 5 3 1480 1569 531408056 531407968 2.350000e-23 121.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G230800 chr4A 540013447 540018248 4801 False 8868.000000 8868 100.000000 1 4802 1 chr4A.!!$F1 4801
1 TraesCS4A01G230800 chr4A 540079852 540088167 8315 False 1302.600000 1792 95.192100 1909 3957 10 chr4A.!!$F3 2048
2 TraesCS4A01G230800 chr4A 608142805 608143430 625 False 749.000000 749 88.217000 4173 4800 1 chr4A.!!$F2 627
3 TraesCS4A01G230800 chr4B 85581812 85585869 4057 True 1908.333333 3738 94.795000 4 4172 3 chr4B.!!$R1 4168
4 TraesCS4A01G230800 chr4D 56946732 56950721 3989 True 1893.000000 3705 94.900333 1 4098 3 chr4D.!!$R1 4097
5 TraesCS4A01G230800 chr6B 96628404 96629034 630 False 955.000000 955 93.978000 4172 4802 1 chr6B.!!$F1 630
6 TraesCS4A01G230800 chr6B 77730272 77730903 631 True 917.000000 917 92.880000 4172 4802 1 chr6B.!!$R1 630
7 TraesCS4A01G230800 chr3A 66403117 66403745 628 False 953.000000 953 93.978000 4172 4802 1 chr3A.!!$F1 630
8 TraesCS4A01G230800 chr1A 47808218 47808855 637 True 861.000000 861 91.223000 4172 4802 1 chr1A.!!$R1 630

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
616 653 0.030101 ACACACGGGCGTTGAAAATG 59.970 50.000 0.00 0.0 35.44 2.32 F
762 800 0.107508 GAAGCTGACATGCCTAGCCA 60.108 55.000 11.46 0.0 38.18 4.75 F
1017 1061 1.153289 CATGGAACCGAGGAGGCTG 60.153 63.158 0.00 0.0 46.52 4.85 F
2220 2302 1.230635 GGAGAACAGCGCTTGAAGCA 61.231 55.000 18.22 0.0 42.58 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1864 1946 1.205417 AGGAAGCCCGCAAAAATGATG 59.795 47.619 0.00 0.0 37.58 3.07 R
2199 2281 1.301677 CTTCAAGCGCTGTTCTCCCC 61.302 60.000 12.58 0.0 0.00 4.81 R
2670 3858 2.383855 CCTCAGAGGTCTTCCCACTAG 58.616 57.143 8.54 0.0 34.66 2.57 R
3958 8357 1.138859 TGTGTATGGCTGGATTCTCCG 59.861 52.381 0.00 0.0 40.17 4.63 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
63 64 9.737427 TGAGTCGAATTTCTTCTCTGATATTAC 57.263 33.333 14.26 0.00 0.00 1.89
336 349 2.578495 GCACAATGCACTTTTCTCTCG 58.422 47.619 0.00 0.00 44.26 4.04
523 536 4.995124 TCTAGAAGAACGGTGCAGTAATC 58.005 43.478 0.00 0.00 0.00 1.75
579 601 4.209288 ACAATTTCGTCTGACTCAGAAACG 59.791 41.667 10.45 11.40 42.46 3.60
581 603 1.315690 TCGTCTGACTCAGAAACGGT 58.684 50.000 10.45 0.00 42.46 4.83
582 604 2.497138 TCGTCTGACTCAGAAACGGTA 58.503 47.619 10.45 0.00 42.46 4.02
586 608 5.181811 TCGTCTGACTCAGAAACGGTAATTA 59.818 40.000 10.45 0.00 42.46 1.40
588 610 6.530534 CGTCTGACTCAGAAACGGTAATTAAT 59.469 38.462 10.45 0.00 42.46 1.40
592 614 6.759827 TGACTCAGAAACGGTAATTAATAGGC 59.240 38.462 0.00 0.00 0.00 3.93
594 616 6.537660 ACTCAGAAACGGTAATTAATAGGCAC 59.462 38.462 0.00 0.00 0.00 5.01
595 617 6.408035 TCAGAAACGGTAATTAATAGGCACA 58.592 36.000 0.00 0.00 0.00 4.57
601 623 4.632251 CGGTAATTAATAGGCACACACACA 59.368 41.667 0.00 0.00 0.00 3.72
602 624 5.446741 CGGTAATTAATAGGCACACACACAC 60.447 44.000 0.00 0.00 0.00 3.82
603 625 4.678509 AATTAATAGGCACACACACACG 57.321 40.909 0.00 0.00 0.00 4.49
616 653 0.030101 ACACACGGGCGTTGAAAATG 59.970 50.000 0.00 0.00 35.44 2.32
670 708 1.014352 AAAGCAAGAAACTGACGCGT 58.986 45.000 13.85 13.85 0.00 6.01
714 752 0.441533 GCTGCACATTCTCGTGACTG 59.558 55.000 3.59 3.59 39.34 3.51
730 768 2.642311 TGACTGGACCAGAAATTAGGCA 59.358 45.455 28.56 3.49 35.18 4.75
732 770 2.644798 ACTGGACCAGAAATTAGGCAGT 59.355 45.455 28.56 0.00 35.18 4.40
738 776 2.648059 CAGAAATTAGGCAGTGGAGGG 58.352 52.381 0.00 0.00 0.00 4.30
762 800 0.107508 GAAGCTGACATGCCTAGCCA 60.108 55.000 11.46 0.00 38.18 4.75
781 819 4.017867 AGCCAGACTAGAAACTAGAGACCT 60.018 45.833 11.94 2.39 0.00 3.85
784 822 5.820947 CCAGACTAGAAACTAGAGACCTCTC 59.179 48.000 11.94 0.00 40.93 3.20
808 846 2.497138 TGACATGGAAAGCACTCACTG 58.503 47.619 0.00 0.00 0.00 3.66
833 874 2.487762 GGTTTGATCTGCGGATTGTCAA 59.512 45.455 9.98 7.72 31.46 3.18
1017 1061 1.153289 CATGGAACCGAGGAGGCTG 60.153 63.158 0.00 0.00 46.52 4.85
1019 1063 2.683933 GGAACCGAGGAGGCTGGA 60.684 66.667 0.00 0.00 46.52 3.86
1288 1342 1.589716 GCCTGTGTTGATCAGTGGGC 61.590 60.000 0.00 3.72 0.00 5.36
1400 1454 1.352352 AGGGAGGGTTCAACATCACAG 59.648 52.381 0.00 0.00 0.00 3.66
1435 1489 6.325286 ACTGGAGTGTAAGTTCTCTTCTTCTT 59.675 38.462 0.00 0.00 35.36 2.52
1437 1491 6.986817 TGGAGTGTAAGTTCTCTTCTTCTTTG 59.013 38.462 0.00 0.00 35.36 2.77
1485 1567 5.186198 ACACTTGCTGACAAAAGAACTACT 58.814 37.500 4.89 0.00 34.74 2.57
1486 1568 5.648092 ACACTTGCTGACAAAAGAACTACTT 59.352 36.000 4.89 0.00 40.98 2.24
1488 1570 6.688813 CACTTGCTGACAAAAGAACTACTTTC 59.311 38.462 4.89 0.00 46.55 2.62
1490 1572 6.363577 TGCTGACAAAAGAACTACTTTCTG 57.636 37.500 0.00 0.00 46.55 3.02
1504 1586 9.752961 GAACTACTTTCTGAATAATACTCCCTC 57.247 37.037 0.00 0.00 0.00 4.30
1506 1588 6.163135 ACTTTCTGAATAATACTCCCTCCG 57.837 41.667 0.00 0.00 0.00 4.63
1508 1590 6.156429 ACTTTCTGAATAATACTCCCTCCGTT 59.844 38.462 0.00 0.00 0.00 4.44
1509 1591 5.786264 TCTGAATAATACTCCCTCCGTTC 57.214 43.478 0.00 0.00 0.00 3.95
1510 1592 4.587684 TCTGAATAATACTCCCTCCGTTCC 59.412 45.833 0.00 0.00 0.00 3.62
1511 1593 4.291792 TGAATAATACTCCCTCCGTTCCA 58.708 43.478 0.00 0.00 0.00 3.53
1513 1595 5.190132 TGAATAATACTCCCTCCGTTCCAAA 59.810 40.000 0.00 0.00 0.00 3.28
1515 1597 4.586306 AATACTCCCTCCGTTCCAAATT 57.414 40.909 0.00 0.00 0.00 1.82
1516 1598 5.703730 AATACTCCCTCCGTTCCAAATTA 57.296 39.130 0.00 0.00 0.00 1.40
1517 1599 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
1518 1600 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
1519 1601 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
1521 1603 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
1522 1604 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
1523 1605 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
1524 1606 2.030007 TCCGTTCCAAATTACTCGTCGT 60.030 45.455 0.00 0.00 0.00 4.34
1526 1608 2.091588 CGTTCCAAATTACTCGTCGTGG 59.908 50.000 0.00 0.00 0.00 4.94
1527 1609 3.062042 GTTCCAAATTACTCGTCGTGGT 58.938 45.455 0.00 0.00 0.00 4.16
1528 1610 3.389925 TCCAAATTACTCGTCGTGGTT 57.610 42.857 0.00 0.00 0.00 3.67
1531 1613 5.295950 TCCAAATTACTCGTCGTGGTTTTA 58.704 37.500 0.00 0.00 0.00 1.52
1533 1615 5.178067 CCAAATTACTCGTCGTGGTTTTAGT 59.822 40.000 0.00 0.00 0.00 2.24
1534 1616 6.293027 CCAAATTACTCGTCGTGGTTTTAGTT 60.293 38.462 0.00 0.00 0.00 2.24
1535 1617 6.457851 AATTACTCGTCGTGGTTTTAGTTC 57.542 37.500 0.00 0.00 0.00 3.01
1536 1618 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
1537 1619 3.784338 ACTCGTCGTGGTTTTAGTTCAA 58.216 40.909 0.00 0.00 0.00 2.69
1538 1620 3.553105 ACTCGTCGTGGTTTTAGTTCAAC 59.447 43.478 0.00 0.00 0.00 3.18
1545 1627 3.243226 GGTTTTAGTTCAACCACGACG 57.757 47.619 0.00 0.00 43.00 5.12
1546 1628 2.865551 GGTTTTAGTTCAACCACGACGA 59.134 45.455 0.00 0.00 43.00 4.20
1550 1632 4.566545 TTAGTTCAACCACGACGAGTAA 57.433 40.909 0.00 0.00 0.00 2.24
1552 1634 3.986277 AGTTCAACCACGACGAGTAATT 58.014 40.909 0.00 0.00 0.00 1.40
1554 1636 4.210537 AGTTCAACCACGACGAGTAATTTG 59.789 41.667 0.00 0.00 0.00 2.32
1555 1637 3.061322 TCAACCACGACGAGTAATTTGG 58.939 45.455 0.00 0.00 0.00 3.28
1556 1638 3.061322 CAACCACGACGAGTAATTTGGA 58.939 45.455 0.00 0.00 0.00 3.53
1557 1639 3.389925 ACCACGACGAGTAATTTGGAA 57.610 42.857 0.00 0.00 0.00 3.53
1558 1640 3.062042 ACCACGACGAGTAATTTGGAAC 58.938 45.455 0.00 0.00 0.00 3.62
1559 1641 2.091588 CCACGACGAGTAATTTGGAACG 59.908 50.000 0.00 0.00 0.00 3.95
1561 1643 2.030007 ACGACGAGTAATTTGGAACGGA 60.030 45.455 0.00 0.00 0.00 4.69
1562 1644 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
1563 1645 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
1564 1646 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
1565 1647 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
1566 1648 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
1636 1718 9.716531 ATTACACTATACCATGTTCATGATCAG 57.283 33.333 13.51 2.71 0.00 2.90
1637 1719 6.528321 ACACTATACCATGTTCATGATCAGG 58.472 40.000 13.51 11.29 0.00 3.86
1638 1720 5.936372 CACTATACCATGTTCATGATCAGGG 59.064 44.000 27.72 27.72 40.68 4.45
1643 1725 6.514012 ACCATGTTCATGATCAGGGTATAA 57.486 37.500 31.63 0.00 44.96 0.98
1645 1727 7.529555 ACCATGTTCATGATCAGGGTATAAAT 58.470 34.615 31.63 13.60 44.96 1.40
1647 1729 6.882610 TGTTCATGATCAGGGTATAAATGC 57.117 37.500 7.64 0.00 0.00 3.56
1648 1730 6.363882 TGTTCATGATCAGGGTATAAATGCA 58.636 36.000 7.64 0.00 0.00 3.96
1649 1731 7.005902 TGTTCATGATCAGGGTATAAATGCAT 58.994 34.615 7.64 0.00 0.00 3.96
1651 1733 8.454106 GTTCATGATCAGGGTATAAATGCATAC 58.546 37.037 7.64 0.00 0.00 2.39
1653 1735 8.162746 TCATGATCAGGGTATAAATGCATACAA 58.837 33.333 7.64 0.00 33.77 2.41
1654 1736 7.984422 TGATCAGGGTATAAATGCATACAAG 57.016 36.000 0.00 0.00 33.77 3.16
1655 1737 7.744733 TGATCAGGGTATAAATGCATACAAGA 58.255 34.615 0.00 0.00 33.77 3.02
1656 1738 7.661437 TGATCAGGGTATAAATGCATACAAGAC 59.339 37.037 0.00 0.00 33.77 3.01
1657 1739 6.894682 TCAGGGTATAAATGCATACAAGACA 58.105 36.000 0.00 0.00 33.77 3.41
1658 1740 6.765989 TCAGGGTATAAATGCATACAAGACAC 59.234 38.462 0.00 0.00 33.77 3.67
1659 1741 6.017109 CAGGGTATAAATGCATACAAGACACC 60.017 42.308 0.00 1.51 33.77 4.16
1660 1742 6.062095 GGGTATAAATGCATACAAGACACCT 58.938 40.000 0.00 0.00 33.77 4.00
1661 1743 7.071950 AGGGTATAAATGCATACAAGACACCTA 59.928 37.037 0.00 0.00 33.77 3.08
1663 1745 9.284968 GGTATAAATGCATACAAGACACCTATT 57.715 33.333 0.00 0.00 33.77 1.73
1667 1749 6.867662 ATGCATACAAGACACCTATTTAGC 57.132 37.500 0.00 0.00 0.00 3.09
1670 1752 5.823045 GCATACAAGACACCTATTTAGCCTT 59.177 40.000 0.00 0.00 0.00 4.35
1671 1753 6.318900 GCATACAAGACACCTATTTAGCCTTT 59.681 38.462 0.00 0.00 0.00 3.11
1672 1754 7.148069 GCATACAAGACACCTATTTAGCCTTTT 60.148 37.037 0.00 0.00 0.00 2.27
1673 1755 8.739972 CATACAAGACACCTATTTAGCCTTTTT 58.260 33.333 0.00 0.00 0.00 1.94
1704 1786 7.812191 GTGCAAAAATGACCTTACACATTGATA 59.188 33.333 0.00 0.00 36.92 2.15
1787 1869 4.018779 TCCGGGATTAAAACTGATTGTCCT 60.019 41.667 0.00 0.00 0.00 3.85
1864 1946 2.364970 TGCATTATGGCTTATTGGTGGC 59.635 45.455 0.00 0.00 34.04 5.01
2199 2281 4.447054 GCAGAGTCCATCAAAGATATCGTG 59.553 45.833 0.00 0.15 0.00 4.35
2220 2302 1.230635 GGAGAACAGCGCTTGAAGCA 61.231 55.000 18.22 0.00 42.58 3.91
2226 2308 4.326766 GCGCTTGAAGCAACGGCA 62.327 61.111 18.22 0.00 42.58 5.69
2268 2350 2.175069 AGCCATTGAGAGGATGCAGAAT 59.825 45.455 0.00 0.00 0.00 2.40
2274 2356 7.566569 CCATTGAGAGGATGCAGAATATATCT 58.433 38.462 0.00 0.00 39.68 1.98
2417 2499 4.826733 AGGCATCAACACATTGTAAGAACA 59.173 37.500 0.00 0.00 37.11 3.18
2482 2566 6.206243 AGTTGTTGAATCTCATGAAACCTCAG 59.794 38.462 0.00 0.00 34.23 3.35
2486 2570 7.449395 TGTTGAATCTCATGAAACCTCAGAATT 59.551 33.333 0.00 0.00 34.23 2.17
2506 2590 9.224267 CAGAATTATCATGGGAACTAATACAGG 57.776 37.037 0.00 0.00 0.00 4.00
2610 2694 5.375773 TCATGGTGAAATGTTTCTCAGTGA 58.624 37.500 6.99 0.00 38.02 3.41
2622 2706 9.453572 AATGTTTCTCAGTGAGCATAAATTCTA 57.546 29.630 15.72 1.26 0.00 2.10
2623 2707 8.256611 TGTTTCTCAGTGAGCATAAATTCTAC 57.743 34.615 15.72 0.00 0.00 2.59
2624 2708 8.097038 TGTTTCTCAGTGAGCATAAATTCTACT 58.903 33.333 15.72 0.00 0.00 2.57
2625 2709 9.587772 GTTTCTCAGTGAGCATAAATTCTACTA 57.412 33.333 15.72 0.00 0.00 1.82
2708 3896 5.415077 TCTGAGGCTACAGAAGTTGTACTAC 59.585 44.000 12.32 0.00 42.79 2.73
2745 3933 4.019051 TCATTCACTTCAGACATCCACCAT 60.019 41.667 0.00 0.00 0.00 3.55
2757 3945 6.204301 CAGACATCCACCATAATAAGCTGAAG 59.796 42.308 0.00 0.00 0.00 3.02
3098 5414 5.190992 GCATGATGCATCCAGATTGTTTA 57.809 39.130 23.67 1.25 44.26 2.01
3140 5456 5.277601 ACAGGTGAATTCGAACATTTACG 57.722 39.130 0.00 0.00 0.00 3.18
3279 7656 3.408634 ACATCCCTCAGGTAAACAAACG 58.591 45.455 0.00 0.00 0.00 3.60
3721 8120 4.357947 TGAGGCACCTCACGTCGC 62.358 66.667 15.46 0.00 46.80 5.19
3838 8237 2.212869 TTTTGCTGTGCTCTTTGCTG 57.787 45.000 0.00 0.00 43.37 4.41
3857 8256 3.253188 GCTGTTTGCAGGTGATAGTTTGA 59.747 43.478 0.00 0.00 42.78 2.69
3863 8262 3.196469 TGCAGGTGATAGTTTGAGAGAGG 59.804 47.826 0.00 0.00 0.00 3.69
3947 8346 4.627900 ACGCGAAATGTTTGGTTTCTTTTT 59.372 33.333 15.93 0.00 34.28 1.94
3958 8357 2.190161 GTTTCTTTTTGTGCGTGGTCC 58.810 47.619 0.00 0.00 0.00 4.46
4030 8431 9.533831 AAGAAGAAATTGGTGTAATCCTGTATT 57.466 29.630 0.00 0.00 0.00 1.89
4114 8515 7.464830 TCTTACAAGAGACTTCTTTTTGTCG 57.535 36.000 11.25 6.79 41.71 4.35
4115 8516 7.262772 TCTTACAAGAGACTTCTTTTTGTCGA 58.737 34.615 11.25 8.28 41.71 4.20
4116 8517 7.762615 TCTTACAAGAGACTTCTTTTTGTCGAA 59.237 33.333 11.25 4.29 41.71 3.71
4117 8518 6.927294 ACAAGAGACTTCTTTTTGTCGAAT 57.073 33.333 0.00 0.00 41.71 3.34
4118 8519 6.949449 ACAAGAGACTTCTTTTTGTCGAATC 58.051 36.000 0.00 0.00 41.71 2.52
4119 8520 5.830900 AGAGACTTCTTTTTGTCGAATCG 57.169 39.130 0.00 0.00 38.16 3.34
4120 8521 4.150804 AGAGACTTCTTTTTGTCGAATCGC 59.849 41.667 0.00 0.00 38.16 4.58
4121 8522 3.807622 AGACTTCTTTTTGTCGAATCGCA 59.192 39.130 0.00 0.00 38.16 5.10
4122 8523 4.272504 AGACTTCTTTTTGTCGAATCGCAA 59.727 37.500 0.00 3.02 38.16 4.85
4123 8524 4.915704 ACTTCTTTTTGTCGAATCGCAAA 58.084 34.783 16.67 16.67 33.75 3.68
4125 8526 5.229260 ACTTCTTTTTGTCGAATCGCAAAAC 59.771 36.000 25.29 10.28 39.91 2.43
4126 8527 4.915704 TCTTTTTGTCGAATCGCAAAACT 58.084 34.783 25.29 0.00 39.91 2.66
4127 8528 5.336744 TCTTTTTGTCGAATCGCAAAACTT 58.663 33.333 25.29 0.00 39.91 2.66
4128 8529 5.229052 TCTTTTTGTCGAATCGCAAAACTTG 59.771 36.000 25.29 20.06 39.91 3.16
4166 8571 9.671279 TTGATAGAATAAAAGAGAATGAGTGCA 57.329 29.630 0.00 0.00 0.00 4.57
4181 8586 2.485814 GAGTGCAACAGAAAGTGGATCC 59.514 50.000 4.20 4.20 41.43 3.36
4272 8677 0.695462 ATGCCCTCCCACTCTATGCA 60.695 55.000 0.00 0.00 0.00 3.96
4324 8729 1.373497 CAGGCCATCGATAGTCGCC 60.373 63.158 5.01 14.09 40.21 5.54
4443 8848 1.606668 GGGTTTCTGTCGTTGCATCAA 59.393 47.619 0.00 0.00 0.00 2.57
4451 8856 2.241722 GTCGTTGCATCAATTCAACCG 58.758 47.619 0.00 0.00 39.36 4.44
4529 8934 3.721706 CCACCTGGCCTCCACCTC 61.722 72.222 3.32 0.00 0.00 3.85
4585 8990 5.051240 CCAACGCGTCTTAATACTGTTATCC 60.051 44.000 14.44 0.00 0.00 2.59
4653 9065 1.046472 TAATCCCTGGCGATGGTCGT 61.046 55.000 1.11 0.00 42.81 4.34
4756 9171 0.529378 TCTTAGACCGAACGCTTCCC 59.471 55.000 0.00 0.00 0.00 3.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 4.081309 TCCCACTTCAAGTAGGAAATACGG 60.081 45.833 1.62 0.00 33.07 4.02
87 88 4.654262 AGAACAGAGTAACTCCCACTTCAA 59.346 41.667 0.00 0.00 0.00 2.69
391 404 1.723870 GATGCCAATCACGGTGCTC 59.276 57.895 2.51 0.00 32.61 4.26
397 410 3.242284 ACGAATTTACGATGCCAATCACG 60.242 43.478 0.00 0.00 37.03 4.35
439 452 6.982141 ACATGCGAATATTGCAAATCAGAAAT 59.018 30.769 1.71 0.00 46.87 2.17
443 456 7.682593 TTTACATGCGAATATTGCAAATCAG 57.317 32.000 1.71 0.00 46.87 2.90
523 536 4.084537 GGACATGCCATTAATTCGAGTACG 60.085 45.833 0.00 0.00 37.47 3.67
554 573 4.322080 TCTGAGTCAGACGAAATTGTGT 57.678 40.909 19.10 0.00 35.39 3.72
579 601 5.446741 CGTGTGTGTGTGCCTATTAATTACC 60.447 44.000 0.00 0.00 0.00 2.85
581 603 4.632251 CCGTGTGTGTGTGCCTATTAATTA 59.368 41.667 0.00 0.00 0.00 1.40
582 604 3.438781 CCGTGTGTGTGTGCCTATTAATT 59.561 43.478 0.00 0.00 0.00 1.40
586 608 0.605319 CCCGTGTGTGTGTGCCTATT 60.605 55.000 0.00 0.00 0.00 1.73
588 610 2.423874 CCCGTGTGTGTGTGCCTA 59.576 61.111 0.00 0.00 0.00 3.93
592 614 3.199190 AACGCCCGTGTGTGTGTG 61.199 61.111 0.00 0.00 34.84 3.82
594 616 1.983196 TTTCAACGCCCGTGTGTGTG 61.983 55.000 0.00 0.00 34.84 3.82
595 617 1.306642 TTTTCAACGCCCGTGTGTGT 61.307 50.000 0.00 0.00 34.84 3.72
601 623 1.657556 CCACATTTTCAACGCCCGT 59.342 52.632 0.00 0.00 0.00 5.28
602 624 1.732683 GCCACATTTTCAACGCCCG 60.733 57.895 0.00 0.00 0.00 6.13
603 625 1.732683 CGCCACATTTTCAACGCCC 60.733 57.895 0.00 0.00 0.00 6.13
670 708 4.460731 CAGATATCTCATCTTCGGCCTGTA 59.539 45.833 1.03 0.00 0.00 2.74
714 752 2.026262 TCCACTGCCTAATTTCTGGTCC 60.026 50.000 0.00 0.00 0.00 4.46
730 768 1.203237 TCAGCTTCTTCTCCCTCCACT 60.203 52.381 0.00 0.00 0.00 4.00
732 770 1.270907 GTCAGCTTCTTCTCCCTCCA 58.729 55.000 0.00 0.00 0.00 3.86
738 776 2.399916 AGGCATGTCAGCTTCTTCTC 57.600 50.000 0.00 0.00 34.17 2.87
762 800 6.013206 TGTGAGAGGTCTCTAGTTTCTAGTCT 60.013 42.308 8.44 0.28 43.25 3.24
771 809 4.308526 TGTCATGTGAGAGGTCTCTAGT 57.691 45.455 8.44 0.00 43.25 2.57
773 811 3.956848 CCATGTCATGTGAGAGGTCTCTA 59.043 47.826 11.84 0.00 43.25 2.43
774 812 2.765135 CCATGTCATGTGAGAGGTCTCT 59.235 50.000 11.84 0.00 43.25 3.10
775 813 2.762887 TCCATGTCATGTGAGAGGTCTC 59.237 50.000 11.84 0.00 43.15 3.36
777 815 3.616956 TTCCATGTCATGTGAGAGGTC 57.383 47.619 11.84 0.00 0.00 3.85
778 816 3.871463 GCTTTCCATGTCATGTGAGAGGT 60.871 47.826 11.84 0.00 0.00 3.85
779 817 2.681848 GCTTTCCATGTCATGTGAGAGG 59.318 50.000 11.84 0.00 0.00 3.69
781 819 3.076621 GTGCTTTCCATGTCATGTGAGA 58.923 45.455 11.84 0.00 0.00 3.27
784 822 2.815503 TGAGTGCTTTCCATGTCATGTG 59.184 45.455 11.84 3.85 0.00 3.21
808 846 0.749454 ATCCGCAGATCAAACCTGGC 60.749 55.000 0.00 0.00 32.51 4.85
809 847 1.402968 CAATCCGCAGATCAAACCTGG 59.597 52.381 0.00 0.00 32.51 4.45
811 849 2.290260 TGACAATCCGCAGATCAAACCT 60.290 45.455 0.00 0.00 0.00 3.50
813 851 3.829886 TTGACAATCCGCAGATCAAAC 57.170 42.857 0.00 0.00 0.00 2.93
814 852 4.458642 TGATTTGACAATCCGCAGATCAAA 59.541 37.500 0.00 0.88 38.50 2.69
833 874 4.813161 CCGACTAGATTTCTGCATGTGATT 59.187 41.667 0.00 0.00 0.00 2.57
1017 1061 0.796927 GCAGAAACACTAACCGCTCC 59.203 55.000 0.00 0.00 0.00 4.70
1019 1063 1.344763 AGAGCAGAAACACTAACCGCT 59.655 47.619 0.00 0.00 0.00 5.52
1198 1247 5.064441 AGGCACACTTAATTTGCATCTTC 57.936 39.130 1.79 0.00 38.04 2.87
1201 1250 4.156556 TCAGAGGCACACTTAATTTGCATC 59.843 41.667 5.76 5.76 45.17 3.91
1240 1289 5.411361 CGATCAATTACCTCACAGGAAAACA 59.589 40.000 0.00 0.00 37.67 2.83
1245 1299 3.513912 ACACGATCAATTACCTCACAGGA 59.486 43.478 0.00 0.00 37.67 3.86
1288 1342 1.372997 CGTCTCCGACAACACCCTG 60.373 63.158 0.00 0.00 35.63 4.45
1400 1454 5.238583 ACTTACACTCCAGTAATGCTTGTC 58.761 41.667 0.00 0.00 33.82 3.18
1435 1489 5.877012 GGCTCTTCAGATTGTATTCAGACAA 59.123 40.000 0.00 0.00 43.23 3.18
1437 1491 5.423015 TGGCTCTTCAGATTGTATTCAGAC 58.577 41.667 0.00 0.00 0.00 3.51
1485 1567 6.407752 GGAACGGAGGGAGTATTATTCAGAAA 60.408 42.308 0.00 0.00 0.00 2.52
1486 1568 5.070047 GGAACGGAGGGAGTATTATTCAGAA 59.930 44.000 0.00 0.00 0.00 3.02
1487 1569 4.587684 GGAACGGAGGGAGTATTATTCAGA 59.412 45.833 0.00 0.00 0.00 3.27
1488 1570 4.344102 TGGAACGGAGGGAGTATTATTCAG 59.656 45.833 0.00 0.00 0.00 3.02
1490 1572 4.950205 TGGAACGGAGGGAGTATTATTC 57.050 45.455 0.00 0.00 0.00 1.75
1499 1581 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
1501 1583 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
1502 1584 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
1504 1586 2.091588 CACGACGAGTAATTTGGAACGG 59.908 50.000 0.00 0.00 0.00 4.44
1506 1588 3.062042 ACCACGACGAGTAATTTGGAAC 58.938 45.455 0.00 0.00 0.00 3.62
1508 1590 3.389925 AACCACGACGAGTAATTTGGA 57.610 42.857 0.00 0.00 0.00 3.53
1509 1591 4.477302 AAAACCACGACGAGTAATTTGG 57.523 40.909 0.00 0.00 0.00 3.28
1510 1592 6.219302 ACTAAAACCACGACGAGTAATTTG 57.781 37.500 0.00 2.39 0.00 2.32
1511 1593 6.479660 TGAACTAAAACCACGACGAGTAATTT 59.520 34.615 0.00 0.34 0.00 1.82
1513 1595 5.531634 TGAACTAAAACCACGACGAGTAAT 58.468 37.500 0.00 0.00 0.00 1.89
1515 1597 4.566545 TGAACTAAAACCACGACGAGTA 57.433 40.909 0.00 0.00 0.00 2.59
1516 1598 3.441496 TGAACTAAAACCACGACGAGT 57.559 42.857 0.00 0.00 0.00 4.18
1517 1599 3.060070 GGTTGAACTAAAACCACGACGAG 60.060 47.826 0.00 0.00 45.41 4.18
1518 1600 2.865551 GGTTGAACTAAAACCACGACGA 59.134 45.455 0.00 0.00 45.41 4.20
1519 1601 3.243226 GGTTGAACTAAAACCACGACG 57.757 47.619 0.00 0.00 45.41 5.12
1526 1608 3.553105 ACTCGTCGTGGTTGAACTAAAAC 59.447 43.478 0.00 0.00 0.00 2.43
1527 1609 3.784338 ACTCGTCGTGGTTGAACTAAAA 58.216 40.909 0.00 0.00 0.00 1.52
1528 1610 3.441496 ACTCGTCGTGGTTGAACTAAA 57.559 42.857 0.00 0.00 0.00 1.85
1531 1613 3.655276 ATTACTCGTCGTGGTTGAACT 57.345 42.857 0.00 0.00 0.00 3.01
1533 1615 3.495377 CCAAATTACTCGTCGTGGTTGAA 59.505 43.478 0.00 0.00 0.00 2.69
1534 1616 3.061322 CCAAATTACTCGTCGTGGTTGA 58.939 45.455 0.00 0.00 0.00 3.18
1535 1617 3.061322 TCCAAATTACTCGTCGTGGTTG 58.939 45.455 0.00 0.00 0.00 3.77
1536 1618 3.389925 TCCAAATTACTCGTCGTGGTT 57.610 42.857 0.00 0.00 0.00 3.67
1537 1619 3.062042 GTTCCAAATTACTCGTCGTGGT 58.938 45.455 0.00 0.00 0.00 4.16
1538 1620 2.091588 CGTTCCAAATTACTCGTCGTGG 59.908 50.000 0.00 0.00 0.00 4.94
1541 1623 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
1542 1624 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
1544 1626 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
1545 1627 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
1546 1628 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
1550 1632 2.829023 TCTACTCCCTCCGTTCCAAAT 58.171 47.619 0.00 0.00 0.00 2.32
1552 1634 2.314071 TTCTACTCCCTCCGTTCCAA 57.686 50.000 0.00 0.00 0.00 3.53
1554 1636 2.764572 TCATTTCTACTCCCTCCGTTCC 59.235 50.000 0.00 0.00 0.00 3.62
1555 1637 3.447944 AGTCATTTCTACTCCCTCCGTTC 59.552 47.826 0.00 0.00 0.00 3.95
1556 1638 3.195825 CAGTCATTTCTACTCCCTCCGTT 59.804 47.826 0.00 0.00 0.00 4.44
1557 1639 2.761208 CAGTCATTTCTACTCCCTCCGT 59.239 50.000 0.00 0.00 0.00 4.69
1558 1640 2.482142 GCAGTCATTTCTACTCCCTCCG 60.482 54.545 0.00 0.00 0.00 4.63
1559 1641 2.769095 AGCAGTCATTTCTACTCCCTCC 59.231 50.000 0.00 0.00 0.00 4.30
1561 1643 4.917906 AAAGCAGTCATTTCTACTCCCT 57.082 40.909 0.00 0.00 0.00 4.20
1562 1644 4.379918 GCAAAAGCAGTCATTTCTACTCCC 60.380 45.833 0.00 0.00 0.00 4.30
1563 1645 4.216257 TGCAAAAGCAGTCATTTCTACTCC 59.784 41.667 0.00 0.00 0.00 3.85
1564 1646 5.049129 ACTGCAAAAGCAGTCATTTCTACTC 60.049 40.000 16.62 0.00 46.65 2.59
1565 1647 4.823989 ACTGCAAAAGCAGTCATTTCTACT 59.176 37.500 16.62 0.00 46.65 2.57
1566 1648 5.113502 ACTGCAAAAGCAGTCATTTCTAC 57.886 39.130 16.62 0.00 46.65 2.59
1614 1696 5.936372 CCCTGATCATGAACATGGTATAGTG 59.064 44.000 16.15 0.00 39.24 2.74
1615 1697 5.608437 ACCCTGATCATGAACATGGTATAGT 59.392 40.000 24.85 11.05 39.24 2.12
1616 1698 6.119240 ACCCTGATCATGAACATGGTATAG 57.881 41.667 24.85 10.58 39.24 1.31
1618 1700 6.708885 ATACCCTGATCATGAACATGGTAT 57.291 37.500 30.40 30.40 40.46 2.73
1619 1701 7.625498 TTATACCCTGATCATGAACATGGTA 57.375 36.000 29.27 29.27 39.89 3.25
1620 1702 6.514012 TTATACCCTGATCATGAACATGGT 57.486 37.500 27.54 27.54 39.24 3.55
1621 1703 7.576287 GCATTTATACCCTGATCATGAACATGG 60.576 40.741 20.82 20.82 39.24 3.66
1622 1704 7.040271 TGCATTTATACCCTGATCATGAACATG 60.040 37.037 6.09 8.31 40.09 3.21
1623 1705 7.005902 TGCATTTATACCCTGATCATGAACAT 58.994 34.615 6.09 0.00 0.00 2.71
1624 1706 6.363882 TGCATTTATACCCTGATCATGAACA 58.636 36.000 5.47 5.47 0.00 3.18
1625 1707 6.882610 TGCATTTATACCCTGATCATGAAC 57.117 37.500 0.00 0.00 0.00 3.18
1626 1708 8.162746 TGTATGCATTTATACCCTGATCATGAA 58.837 33.333 3.54 0.00 33.56 2.57
1627 1709 7.688343 TGTATGCATTTATACCCTGATCATGA 58.312 34.615 3.54 0.00 33.56 3.07
1628 1710 7.926674 TGTATGCATTTATACCCTGATCATG 57.073 36.000 3.54 0.00 33.56 3.07
1629 1711 8.385491 TCTTGTATGCATTTATACCCTGATCAT 58.615 33.333 3.54 0.00 33.56 2.45
1631 1713 7.661437 TGTCTTGTATGCATTTATACCCTGATC 59.339 37.037 3.54 0.00 33.56 2.92
1632 1714 7.445402 GTGTCTTGTATGCATTTATACCCTGAT 59.555 37.037 3.54 0.00 33.56 2.90
1633 1715 6.765989 GTGTCTTGTATGCATTTATACCCTGA 59.234 38.462 3.54 0.00 33.56 3.86
1634 1716 6.017109 GGTGTCTTGTATGCATTTATACCCTG 60.017 42.308 3.54 0.00 33.56 4.45
1635 1717 6.062095 GGTGTCTTGTATGCATTTATACCCT 58.938 40.000 3.54 0.00 33.56 4.34
1636 1718 6.062095 AGGTGTCTTGTATGCATTTATACCC 58.938 40.000 3.54 2.19 33.56 3.69
1637 1719 8.848474 ATAGGTGTCTTGTATGCATTTATACC 57.152 34.615 3.54 5.35 33.56 2.73
1641 1723 8.836413 GCTAAATAGGTGTCTTGTATGCATTTA 58.164 33.333 3.54 0.00 0.00 1.40
1643 1725 6.263168 GGCTAAATAGGTGTCTTGTATGCATT 59.737 38.462 3.54 0.00 0.00 3.56
1645 1727 5.104527 AGGCTAAATAGGTGTCTTGTATGCA 60.105 40.000 0.00 0.00 0.00 3.96
1647 1729 7.865706 AAAGGCTAAATAGGTGTCTTGTATG 57.134 36.000 0.00 0.00 0.00 2.39
1648 1730 8.879427 AAAAAGGCTAAATAGGTGTCTTGTAT 57.121 30.769 0.00 0.00 0.00 2.29
1670 1752 9.383519 TGTAAGGTCATTTTTGCACATTAAAAA 57.616 25.926 0.00 0.00 40.17 1.94
1671 1753 8.821894 GTGTAAGGTCATTTTTGCACATTAAAA 58.178 29.630 0.00 0.00 38.99 1.52
1672 1754 7.981789 TGTGTAAGGTCATTTTTGCACATTAAA 59.018 29.630 4.43 0.00 42.33 1.52
1673 1755 7.492524 TGTGTAAGGTCATTTTTGCACATTAA 58.507 30.769 4.43 0.00 42.33 1.40
1674 1756 7.043961 TGTGTAAGGTCATTTTTGCACATTA 57.956 32.000 4.43 0.00 42.33 1.90
1675 1757 5.911752 TGTGTAAGGTCATTTTTGCACATT 58.088 33.333 4.43 0.00 42.33 2.71
1676 1758 5.528043 TGTGTAAGGTCATTTTTGCACAT 57.472 34.783 4.43 0.00 42.33 3.21
1677 1759 4.991153 TGTGTAAGGTCATTTTTGCACA 57.009 36.364 4.43 4.43 44.04 4.57
1678 1760 5.982516 TCAATGTGTAAGGTCATTTTTGCAC 59.017 36.000 0.00 0.00 39.41 4.57
1679 1761 6.154203 TCAATGTGTAAGGTCATTTTTGCA 57.846 33.333 0.00 0.00 32.85 4.08
1680 1762 8.931385 ATATCAATGTGTAAGGTCATTTTTGC 57.069 30.769 0.00 0.00 32.85 3.68
1721 1803 8.190784 CCGCCTCTCATTTTATTCAGTTAATTT 58.809 33.333 0.00 0.00 0.00 1.82
1723 1805 7.054124 TCCGCCTCTCATTTTATTCAGTTAAT 58.946 34.615 0.00 0.00 0.00 1.40
1726 1808 4.843728 TCCGCCTCTCATTTTATTCAGTT 58.156 39.130 0.00 0.00 0.00 3.16
1733 1815 3.066291 TGCTTTCCGCCTCTCATTTTA 57.934 42.857 0.00 0.00 38.05 1.52
1737 1819 2.775890 CATATGCTTTCCGCCTCTCAT 58.224 47.619 0.00 0.00 38.05 2.90
1787 1869 5.446206 CGGTCGACTGAAAAAGTAAACACAA 60.446 40.000 20.01 0.00 40.07 3.33
1864 1946 1.205417 AGGAAGCCCGCAAAAATGATG 59.795 47.619 0.00 0.00 37.58 3.07
2199 2281 1.301677 CTTCAAGCGCTGTTCTCCCC 61.302 60.000 12.58 0.00 0.00 4.81
2220 2302 3.251245 TGATGTTGTAAATCGTTGCCGTT 59.749 39.130 0.00 0.00 35.01 4.44
2226 2308 4.154195 GCTCCTGTGATGTTGTAAATCGTT 59.846 41.667 0.00 0.00 0.00 3.85
2274 2356 9.706691 GATTGGCTACTAATGTTGTATAGCTTA 57.293 33.333 0.00 0.00 38.63 3.09
2461 2545 6.808008 TTCTGAGGTTTCATGAGATTCAAC 57.192 37.500 0.00 0.00 31.68 3.18
2470 2554 6.774170 TCCCATGATAATTCTGAGGTTTCATG 59.226 38.462 0.00 12.18 38.96 3.07
2482 2566 9.003658 CACCTGTATTAGTTCCCATGATAATTC 57.996 37.037 0.00 0.00 0.00 2.17
2486 2570 7.872061 ATCACCTGTATTAGTTCCCATGATA 57.128 36.000 0.00 0.00 0.00 2.15
2506 2590 9.766277 GATGACAAGTTCTCTGAAAATTATCAC 57.234 33.333 0.00 0.00 24.40 3.06
2670 3858 2.383855 CCTCAGAGGTCTTCCCACTAG 58.616 57.143 8.54 0.00 34.66 2.57
2727 3915 6.017605 GCTTATTATGGTGGATGTCTGAAGTG 60.018 42.308 0.00 0.00 0.00 3.16
3098 5414 5.124457 CCTGTCGAAACCAAGATTGATTCAT 59.876 40.000 0.00 0.00 0.00 2.57
3140 5456 1.641577 GTGTACTCCGACTTGATGGC 58.358 55.000 0.00 0.00 0.00 4.40
3838 8237 4.997395 TCTCTCAAACTATCACCTGCAAAC 59.003 41.667 0.00 0.00 0.00 2.93
3857 8256 1.228490 CCGGCCGTATACCCTCTCT 60.228 63.158 26.12 0.00 0.00 3.10
3947 8346 2.501223 GATTCTCCGGACCACGCACA 62.501 60.000 0.00 0.00 42.52 4.57
3958 8357 1.138859 TGTGTATGGCTGGATTCTCCG 59.861 52.381 0.00 0.00 40.17 4.63
4030 8431 1.617850 AGCATCATTTTTGCCGGTCAA 59.382 42.857 1.90 5.14 41.06 3.18
4075 8476 9.988815 TCTCTTGTAAGATAATAAATCAGGCTC 57.011 33.333 0.00 0.00 33.93 4.70
4105 8506 5.414535 CAAGTTTTGCGATTCGACAAAAAG 58.585 37.500 27.02 20.29 40.84 2.27
4120 8521 9.512435 CTATCAATGAAAGATAGGCAAGTTTTG 57.488 33.333 0.00 0.00 40.66 2.44
4121 8522 9.466497 TCTATCAATGAAAGATAGGCAAGTTTT 57.534 29.630 9.56 0.00 43.21 2.43
4122 8523 9.466497 TTCTATCAATGAAAGATAGGCAAGTTT 57.534 29.630 9.56 0.00 43.21 2.66
4123 8524 9.638176 ATTCTATCAATGAAAGATAGGCAAGTT 57.362 29.630 9.56 0.00 43.21 2.66
4162 8567 1.197721 CGGATCCACTTTCTGTTGCAC 59.802 52.381 13.41 0.00 0.00 4.57
4164 8569 1.734465 CTCGGATCCACTTTCTGTTGC 59.266 52.381 13.41 0.00 0.00 4.17
4166 8571 2.900546 AGTCTCGGATCCACTTTCTGTT 59.099 45.455 13.41 0.00 0.00 3.16
4181 8586 2.811317 GCCAACCAGCGAGTCTCG 60.811 66.667 18.08 18.08 43.89 4.04
4253 8658 0.695462 TGCATAGAGTGGGAGGGCAT 60.695 55.000 0.00 0.00 0.00 4.40
4272 8677 2.305343 AGGAAGCAGAAGAGCAGACATT 59.695 45.455 0.00 0.00 36.85 2.71
4324 8729 1.741770 CCCAGAAGAAAGCCCGACG 60.742 63.158 0.00 0.00 0.00 5.12
4443 8848 1.978580 AGGAGAAGACACCGGTTGAAT 59.021 47.619 2.97 0.00 32.13 2.57
4451 8856 3.561725 CAGTTGTTTGAGGAGAAGACACC 59.438 47.826 0.00 0.00 0.00 4.16
4564 8969 4.285292 CGGATAACAGTATTAAGACGCGT 58.715 43.478 13.85 13.85 0.00 6.01
4573 8978 0.386476 TCGCGCCGGATAACAGTATT 59.614 50.000 5.05 0.00 0.00 1.89
4585 8990 4.817063 CTTTGCCATGTCGCGCCG 62.817 66.667 0.00 0.00 0.00 6.46
4653 9065 3.327757 AGTCTAGCCAGAATGTTGTGGAA 59.672 43.478 12.62 0.00 43.86 3.53
4659 9072 5.957771 TCCATAAGTCTAGCCAGAATGTT 57.042 39.130 0.00 0.00 30.85 2.71
4660 9073 5.012561 GGATCCATAAGTCTAGCCAGAATGT 59.987 44.000 6.95 0.00 30.85 2.71
4734 9149 2.421424 GGAAGCGTTCGGTCTAAGAGTA 59.579 50.000 0.00 0.00 0.00 2.59
4746 9161 2.563427 GCTGCAAGGGAAGCGTTC 59.437 61.111 0.00 0.00 35.53 3.95


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

AutoCloner maintained by Alex Coulton.