Multiple sequence alignment - TraesCS1D01G078400

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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 TraesCS1D01G078400 chr1D 100.000 6723 0 0 1 6723 60225314 60218592 0.000000e+00 12416
1 TraesCS1D01G078400 chr1B 95.170 5072 144 21 1695 6723 96588865 96593878 0.000000e+00 7915
2 TraesCS1D01G078400 chr1B 93.505 1478 62 13 1 1462 96587268 96588727 0.000000e+00 2167
3 TraesCS1D01G078400 chr1B 96.269 134 4 1 1569 1701 626227008 626226875 1.140000e-52 219
4 TraesCS1D01G078400 chr1B 96.094 128 5 0 1446 1573 96588741 96588868 6.830000e-50 209
5 TraesCS1D01G078400 chr1A 97.690 3290 66 4 1697 4976 58907131 58903842 0.000000e+00 5646
6 TraesCS1D01G078400 chr1A 95.388 1713 62 8 4978 6677 58903734 58902026 0.000000e+00 2710
7 TraesCS1D01G078400 chr1A 95.277 1588 51 7 1 1573 58908708 58907130 0.000000e+00 2495
8 TraesCS1D01G078400 chr3A 96.269 134 5 0 1565 1698 648181592 648181459 3.160000e-53 220
9 TraesCS1D01G078400 chr3A 95.556 135 5 1 1569 1702 52198986 52198852 1.470000e-51 215
10 TraesCS1D01G078400 chr7D 97.638 127 3 0 1572 1698 333908200 333908074 1.140000e-52 219
11 TraesCS1D01G078400 chr7A 94.326 141 8 0 1561 1701 32293595 32293455 4.080000e-52 217
12 TraesCS1D01G078400 chr4A 96.212 132 5 0 1569 1700 530173876 530174007 4.080000e-52 217
13 TraesCS1D01G078400 chr4B 94.928 138 6 1 1562 1698 467275972 467276109 1.470000e-51 215
14 TraesCS1D01G078400 chr5A 96.154 130 5 0 1572 1701 583158511 583158640 5.280000e-51 213
15 TraesCS1D01G078400 chr5D 95.385 130 6 0 1570 1699 135659644 135659515 2.460000e-49 207


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 TraesCS1D01G078400 chr1D 60218592 60225314 6722 True 12416.000000 12416 100.000000 1 6723 1 chr1D.!!$R1 6722
1 TraesCS1D01G078400 chr1B 96587268 96593878 6610 False 3430.333333 7915 94.923000 1 6723 3 chr1B.!!$F1 6722
2 TraesCS1D01G078400 chr1A 58902026 58908708 6682 True 3617.000000 5646 96.118333 1 6677 3 chr1A.!!$R1 6676

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
634 660 0.461870 TTCGTGATGGATCCTTGCGG 60.462 55.0 14.23 0.00 0.00 5.69 F
1588 1651 0.038744 AGTACTCCCTCCGTCCGAAA 59.961 55.0 0.00 0.00 0.00 3.46 F
1694 1757 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.0 13.64 4.95 46.06 4.20 F
3498 3565 0.463474 GATGCCAGAAGAGGTGAGGC 60.463 60.0 0.00 0.00 45.41 4.70 F
3806 3873 0.395173 AACCTTTGCGTGGGAACTGT 60.395 50.0 0.00 0.00 0.00 3.55 F
4516 4591 1.275666 ATGACACGGAACCTGATCCA 58.724 50.0 0.00 0.00 39.61 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1675 1738 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.0 44.66 2.12 R
3008 3072 1.804748 GCAACCGAAAACTCCCTAGTG 59.195 52.381 0.00 0.0 35.62 2.74 R
3544 3611 2.031560 TGTGCATCACGAACAGTTGAAC 59.968 45.455 0.00 0.0 37.14 3.18 R
5117 5301 2.505405 TGGCGCAAAACCTAATGTGTA 58.495 42.857 10.83 0.0 0.00 2.90 R
5387 5571 2.620115 ACATTTTGATGCCCTCTATGCG 59.380 45.455 0.00 0.0 0.00 4.73 R
5893 6080 1.315257 GCATCCAAGGTCAACGGCAT 61.315 55.000 0.00 0.0 0.00 4.40 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
65 66 9.112725 TCATATAACACAGAACCAATTCATCAG 57.887 33.333 0.00 0.00 37.29 2.90
83 95 9.631257 ATTCATCAGTTCAACAATCCATACATA 57.369 29.630 0.00 0.00 0.00 2.29
84 96 8.667076 TCATCAGTTCAACAATCCATACATAG 57.333 34.615 0.00 0.00 0.00 2.23
86 98 8.554528 CATCAGTTCAACAATCCATACATAGAC 58.445 37.037 0.00 0.00 0.00 2.59
87 99 6.756542 TCAGTTCAACAATCCATACATAGACG 59.243 38.462 0.00 0.00 0.00 4.18
88 100 6.756542 CAGTTCAACAATCCATACATAGACGA 59.243 38.462 0.00 0.00 0.00 4.20
89 101 7.439356 CAGTTCAACAATCCATACATAGACGAT 59.561 37.037 0.00 0.00 0.00 3.73
90 102 8.638873 AGTTCAACAATCCATACATAGACGATA 58.361 33.333 0.00 0.00 0.00 2.92
91 103 8.700644 GTTCAACAATCCATACATAGACGATAC 58.299 37.037 0.00 0.00 0.00 2.24
92 104 7.947282 TCAACAATCCATACATAGACGATACA 58.053 34.615 0.00 0.00 0.00 2.29
93 105 7.865889 TCAACAATCCATACATAGACGATACAC 59.134 37.037 0.00 0.00 0.00 2.90
95 107 6.206048 ACAATCCATACATAGACGATACACGA 59.794 38.462 0.00 0.00 45.77 4.35
96 108 5.857822 TCCATACATAGACGATACACGAG 57.142 43.478 0.00 0.00 45.77 4.18
97 109 4.153655 TCCATACATAGACGATACACGAGC 59.846 45.833 0.00 0.00 45.77 5.03
180 195 5.569355 TCGGCAACATCATTGGGAATATAT 58.431 37.500 0.00 0.00 0.00 0.86
182 197 6.823182 TCGGCAACATCATTGGGAATATATAG 59.177 38.462 0.00 0.00 0.00 1.31
187 202 9.850628 CAACATCATTGGGAATATATAGCAAAG 57.149 33.333 0.00 0.00 0.00 2.77
472 498 0.751452 GCCTAACCCTAACTCTCCCG 59.249 60.000 0.00 0.00 0.00 5.14
536 562 4.547367 GCATCCCGTTCCCCTCCG 62.547 72.222 0.00 0.00 0.00 4.63
538 564 1.759299 CATCCCGTTCCCCTCCGTA 60.759 63.158 0.00 0.00 0.00 4.02
634 660 0.461870 TTCGTGATGGATCCTTGCGG 60.462 55.000 14.23 0.00 0.00 5.69
772 798 2.488836 AGGGGTTTTCATCGTAGGGAT 58.511 47.619 0.00 0.00 35.09 3.85
840 869 4.444876 CCCAGTCTCCGGATGAACATTTAT 60.445 45.833 3.57 0.00 0.00 1.40
877 906 8.364142 ACTAGAGAACATACTCCTCAAATATGC 58.636 37.037 0.00 0.00 37.60 3.14
936 965 4.918583 GCATCTCAGATAGGCGTAGTTTAC 59.081 45.833 0.00 0.00 0.00 2.01
1053 1082 1.154205 CCGTCGGCATCATCTTGTCC 61.154 60.000 0.00 0.00 0.00 4.02
1062 1091 3.275999 CATCATCTTGTCCATGCTGTCA 58.724 45.455 0.00 0.00 0.00 3.58
1156 1185 5.110814 TCCATTTGGATCGGTAAGTCATT 57.889 39.130 0.00 0.00 39.78 2.57
1209 1238 8.699283 TCAGATGCTGATATTTAGATTCATCG 57.301 34.615 0.00 0.00 35.39 3.84
1454 1487 1.336755 ACAGCGCAACCTACCTTTTTG 59.663 47.619 11.47 0.00 0.00 2.44
1547 1610 1.460255 CCTCCCCTGTTTTCTGGCA 59.540 57.895 0.00 0.00 37.55 4.92
1570 1633 5.359194 ACATTGTAATCACCACTCCCTAG 57.641 43.478 0.00 0.00 0.00 3.02
1571 1634 4.783227 ACATTGTAATCACCACTCCCTAGT 59.217 41.667 0.00 0.00 35.91 2.57
1572 1635 5.962031 ACATTGTAATCACCACTCCCTAGTA 59.038 40.000 0.00 0.00 33.48 1.82
1573 1636 5.927281 TTGTAATCACCACTCCCTAGTAC 57.073 43.478 0.00 0.00 33.48 2.73
1574 1637 5.202746 TGTAATCACCACTCCCTAGTACT 57.797 43.478 0.00 0.00 33.48 2.73
1575 1638 5.198965 TGTAATCACCACTCCCTAGTACTC 58.801 45.833 0.00 0.00 33.48 2.59
1576 1639 2.822707 TCACCACTCCCTAGTACTCC 57.177 55.000 0.00 0.00 33.48 3.85
1577 1640 1.287146 TCACCACTCCCTAGTACTCCC 59.713 57.143 0.00 0.00 33.48 4.30
1578 1641 1.288335 CACCACTCCCTAGTACTCCCT 59.712 57.143 0.00 0.00 33.48 4.20
1579 1642 1.570024 ACCACTCCCTAGTACTCCCTC 59.430 57.143 0.00 0.00 33.48 4.30
1580 1643 1.133419 CCACTCCCTAGTACTCCCTCC 60.133 61.905 0.00 0.00 33.48 4.30
1581 1644 0.845337 ACTCCCTAGTACTCCCTCCG 59.155 60.000 0.00 0.00 32.84 4.63
1582 1645 0.845337 CTCCCTAGTACTCCCTCCGT 59.155 60.000 0.00 0.00 0.00 4.69
1583 1646 0.842635 TCCCTAGTACTCCCTCCGTC 59.157 60.000 0.00 0.00 0.00 4.79
1584 1647 0.178995 CCCTAGTACTCCCTCCGTCC 60.179 65.000 0.00 0.00 0.00 4.79
1585 1648 0.534652 CCTAGTACTCCCTCCGTCCG 60.535 65.000 0.00 0.00 0.00 4.79
1586 1649 0.467384 CTAGTACTCCCTCCGTCCGA 59.533 60.000 0.00 0.00 0.00 4.55
1587 1650 0.911769 TAGTACTCCCTCCGTCCGAA 59.088 55.000 0.00 0.00 0.00 4.30
1588 1651 0.038744 AGTACTCCCTCCGTCCGAAA 59.961 55.000 0.00 0.00 0.00 3.46
1589 1652 0.890683 GTACTCCCTCCGTCCGAAAA 59.109 55.000 0.00 0.00 0.00 2.29
1590 1653 1.479730 GTACTCCCTCCGTCCGAAAAT 59.520 52.381 0.00 0.00 0.00 1.82
1591 1654 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
1592 1655 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
1593 1656 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
1594 1657 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
1595 1658 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
1596 1659 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
1597 1660 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
1598 1661 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
1599 1662 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
1600 1663 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
1601 1664 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
1602 1665 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
1603 1666 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
1604 1667 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
1605 1668 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
1606 1669 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
1607 1670 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
1608 1671 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
1609 1672 7.975616 CCGAAAATACTTGTCATCAAAATGGAT 59.024 33.333 0.00 0.00 33.42 3.41
1617 1680 8.096414 ACTTGTCATCAAAATGGATAAAAAGGG 58.904 33.333 0.00 0.00 33.42 3.95
1618 1681 7.789202 TGTCATCAAAATGGATAAAAAGGGA 57.211 32.000 0.00 0.00 33.42 4.20
1619 1682 8.378115 TGTCATCAAAATGGATAAAAAGGGAT 57.622 30.769 0.00 0.00 33.42 3.85
1620 1683 8.259411 TGTCATCAAAATGGATAAAAAGGGATG 58.741 33.333 0.00 0.00 33.42 3.51
1621 1684 8.260114 GTCATCAAAATGGATAAAAAGGGATGT 58.740 33.333 0.00 0.00 33.42 3.06
1622 1685 9.486123 TCATCAAAATGGATAAAAAGGGATGTA 57.514 29.630 0.00 0.00 33.42 2.29
1625 1688 9.713684 TCAAAATGGATAAAAAGGGATGTATCT 57.286 29.630 0.00 0.00 0.00 1.98
1631 1694 9.225682 TGGATAAAAAGGGATGTATCTAGAACT 57.774 33.333 0.00 0.00 0.00 3.01
1641 1704 9.384764 GGGATGTATCTAGAACTAAAATATGCC 57.615 37.037 0.00 0.00 0.00 4.40
1649 1712 9.650714 TCTAGAACTAAAATATGCCTAGGTACA 57.349 33.333 11.31 0.40 0.00 2.90
1652 1715 9.160412 AGAACTAAAATATGCCTAGGTACATCT 57.840 33.333 11.31 0.00 0.00 2.90
1653 1716 9.425577 GAACTAAAATATGCCTAGGTACATCTC 57.574 37.037 11.31 0.00 0.00 2.75
1654 1717 7.908453 ACTAAAATATGCCTAGGTACATCTCC 58.092 38.462 11.31 0.00 0.00 3.71
1655 1718 7.735321 ACTAAAATATGCCTAGGTACATCTCCT 59.265 37.037 11.31 0.00 38.91 3.69
1656 1719 7.394144 AAAATATGCCTAGGTACATCTCCTT 57.606 36.000 11.31 0.00 36.60 3.36
1657 1720 7.394144 AAATATGCCTAGGTACATCTCCTTT 57.606 36.000 11.31 2.94 36.60 3.11
1658 1721 7.394144 AATATGCCTAGGTACATCTCCTTTT 57.606 36.000 11.31 0.00 36.60 2.27
1659 1722 8.506196 AATATGCCTAGGTACATCTCCTTTTA 57.494 34.615 11.31 0.00 36.60 1.52
1660 1723 8.686739 ATATGCCTAGGTACATCTCCTTTTAT 57.313 34.615 11.31 0.00 36.60 1.40
1661 1724 6.420913 TGCCTAGGTACATCTCCTTTTATC 57.579 41.667 11.31 0.00 36.60 1.75
1662 1725 5.307196 TGCCTAGGTACATCTCCTTTTATCC 59.693 44.000 11.31 0.00 36.60 2.59
1663 1726 5.307196 GCCTAGGTACATCTCCTTTTATCCA 59.693 44.000 11.31 0.00 36.60 3.41
1664 1727 6.013293 GCCTAGGTACATCTCCTTTTATCCAT 60.013 42.308 11.31 0.00 36.60 3.41
1665 1728 7.474936 GCCTAGGTACATCTCCTTTTATCCATT 60.475 40.741 11.31 0.00 36.60 3.16
1666 1729 8.440771 CCTAGGTACATCTCCTTTTATCCATTT 58.559 37.037 0.00 0.00 36.60 2.32
1667 1730 9.853177 CTAGGTACATCTCCTTTTATCCATTTT 57.147 33.333 0.00 0.00 36.60 1.82
1668 1731 8.525290 AGGTACATCTCCTTTTATCCATTTTG 57.475 34.615 0.00 0.00 30.18 2.44
1669 1732 8.336235 AGGTACATCTCCTTTTATCCATTTTGA 58.664 33.333 0.00 0.00 30.18 2.69
1670 1733 9.136323 GGTACATCTCCTTTTATCCATTTTGAT 57.864 33.333 0.00 0.00 0.00 2.57
1671 1734 9.956720 GTACATCTCCTTTTATCCATTTTGATG 57.043 33.333 0.00 0.00 35.23 3.07
1672 1735 8.827832 ACATCTCCTTTTATCCATTTTGATGA 57.172 30.769 0.00 0.00 33.85 2.92
1673 1736 8.689972 ACATCTCCTTTTATCCATTTTGATGAC 58.310 33.333 0.00 0.00 33.85 3.06
1674 1737 8.689061 CATCTCCTTTTATCCATTTTGATGACA 58.311 33.333 0.00 0.00 32.05 3.58
1675 1738 8.648698 TCTCCTTTTATCCATTTTGATGACAA 57.351 30.769 0.00 0.00 0.00 3.18
1676 1739 8.742777 TCTCCTTTTATCCATTTTGATGACAAG 58.257 33.333 0.00 0.00 37.32 3.16
1677 1740 8.421249 TCCTTTTATCCATTTTGATGACAAGT 57.579 30.769 0.00 0.00 37.32 3.16
1678 1741 9.527157 TCCTTTTATCCATTTTGATGACAAGTA 57.473 29.630 0.00 0.00 37.32 2.24
1684 1747 6.851609 TCCATTTTGATGACAAGTATTTCCG 58.148 36.000 0.00 0.00 37.32 4.30
1685 1748 6.035843 CCATTTTGATGACAAGTATTTCCGG 58.964 40.000 0.00 0.00 37.32 5.14
1686 1749 6.127758 CCATTTTGATGACAAGTATTTCCGGA 60.128 38.462 0.00 0.00 37.32 5.14
1687 1750 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
1688 1751 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
1689 1752 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
1690 1753 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
1691 1754 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
1692 1755 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
1693 1756 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
1694 1757 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
1705 1768 3.190118 CGGACGGAGGGAGTATAATGTAC 59.810 52.174 0.00 0.00 0.00 2.90
1714 1777 8.091449 GGAGGGAGTATAATGTACTTGATCTTG 58.909 40.741 0.00 0.00 0.00 3.02
1937 2001 7.227049 TGAGTTATTTCTCCCAATTCAAACC 57.773 36.000 0.00 0.00 33.93 3.27
2283 2347 8.092521 TCTATTACCTGTACGCTGTCTTATAC 57.907 38.462 0.00 0.00 0.00 1.47
2406 2470 2.276201 CTTTCCGATGACGTGCCAATA 58.724 47.619 0.00 0.00 37.88 1.90
2632 2696 2.485903 TGTTTGTGGTACATCGTGGAC 58.514 47.619 0.00 0.00 44.52 4.02
2650 2714 7.426410 TCGTGGACTTAGAGTATGATGATTTC 58.574 38.462 0.00 0.00 0.00 2.17
2818 2882 2.290008 ACATGCTATGGTTCACCGTTCA 60.290 45.455 0.00 0.00 39.43 3.18
2820 2884 3.897141 TGCTATGGTTCACCGTTCATA 57.103 42.857 0.00 0.00 39.43 2.15
2874 2938 8.321353 CCTGAGCCAATATATATTGTCTGGTTA 58.679 37.037 26.36 15.84 41.04 2.85
3008 3072 8.770438 TTTTACATTCTGGAATATTTGGTTGC 57.230 30.769 0.00 0.00 0.00 4.17
3322 3389 7.872993 TGGACGGATTTCTGTTGAATATCTATC 59.127 37.037 0.00 0.00 35.19 2.08
3498 3565 0.463474 GATGCCAGAAGAGGTGAGGC 60.463 60.000 0.00 0.00 45.41 4.70
3502 3569 0.689623 CCAGAAGAGGTGAGGCTTGT 59.310 55.000 0.00 0.00 0.00 3.16
3529 3596 8.232913 TCTAATGGTTTGCTAAAGTCAACTTT 57.767 30.769 12.41 12.41 46.78 2.66
3544 3611 3.058293 TCAACTTTGTTGCTTATCTGGCG 60.058 43.478 5.65 0.00 0.00 5.69
3547 3614 3.058224 ACTTTGTTGCTTATCTGGCGTTC 60.058 43.478 0.00 0.00 0.00 3.95
3653 3720 7.534085 AGCTTGCAAAACATATCATTGATTG 57.466 32.000 4.14 5.99 0.00 2.67
3771 3838 6.451292 TGGTGACCTTAGGTTGGTTTTATA 57.549 37.500 4.99 0.00 38.03 0.98
3806 3873 0.395173 AACCTTTGCGTGGGAACTGT 60.395 50.000 0.00 0.00 0.00 3.55
3816 3883 2.875933 CGTGGGAACTGTAAAGCTCAAA 59.124 45.455 0.00 0.00 0.00 2.69
4051 4126 3.258123 ACAATTAGGATTGCGCCTTGTTT 59.742 39.130 4.18 0.00 45.25 2.83
4134 4209 3.181496 GCTTACTTCCAAGCTTATGGTGC 60.181 47.826 0.00 0.00 46.04 5.01
4216 4291 6.861065 ACAATAATATACTTGGCTGGTTCG 57.139 37.500 3.14 0.00 0.00 3.95
4516 4591 1.275666 ATGACACGGAACCTGATCCA 58.724 50.000 0.00 0.00 39.61 3.41
4972 5047 5.815233 ATGTCAGGATGTAGGTGGATAAG 57.185 43.478 0.00 0.00 37.40 1.73
5117 5301 6.518537 GCTTAATGTCGGGATGTAGGTAGATT 60.519 42.308 0.00 0.00 0.00 2.40
5215 5399 3.042887 GTGGTGTTCAAAAGCATCGTTC 58.957 45.455 0.00 0.00 0.00 3.95
5262 5446 8.831715 ATATGTAATTTCGCACATGATGACTA 57.168 30.769 0.00 0.00 36.13 2.59
5387 5571 3.686241 TCAGCATCTCAATAACAGTGCAC 59.314 43.478 9.40 9.40 35.17 4.57
5415 5599 3.019564 AGGGCATCAAAATGTCAGCTAC 58.980 45.455 0.00 0.00 39.36 3.58
5573 5757 4.947147 TGGTTCGCACCCTGGCAC 62.947 66.667 0.56 0.00 43.49 5.01
5653 5837 3.378512 AGATGATCCTAGCCAAGACACA 58.621 45.455 0.00 0.00 0.00 3.72
5665 5849 2.551721 CCAAGACACACAGCAGGAATCT 60.552 50.000 0.00 0.00 0.00 2.40
5680 5864 3.046390 GGAATCTGATAGAAGCGACACG 58.954 50.000 0.00 0.00 0.00 4.49
5755 5942 3.395607 AGATGGAGCTTACCCATTATGCA 59.604 43.478 6.86 0.00 43.96 3.96
5801 5988 2.736347 ACTACCAGCTCCAGATTACGT 58.264 47.619 0.00 0.00 0.00 3.57
5824 6011 2.604914 AGCAAGATCAGCGTACATTTCG 59.395 45.455 0.00 0.00 37.01 3.46
5856 6043 3.890527 CCAGAGGGCACTTGCTTAT 57.109 52.632 0.00 0.00 41.70 1.73
5893 6080 1.296392 CGTCCAGGCATGACAGGAA 59.704 57.895 15.35 0.00 32.91 3.36
6155 6349 1.065782 TGCATTGCGGTGTATGTAGGT 60.066 47.619 3.84 0.00 0.00 3.08
6159 6353 0.533491 TGCGGTGTATGTAGGTGGAC 59.467 55.000 0.00 0.00 0.00 4.02
6262 6459 5.226396 GTTATGTGTGCTTGTTTTGGCATA 58.774 37.500 0.00 0.00 40.66 3.14
6266 6463 2.692557 TGTGCTTGTTTTGGCATAGTGT 59.307 40.909 0.00 0.00 40.66 3.55
6360 6557 4.421365 GGCTCAGTTTGCCCATGA 57.579 55.556 0.00 0.00 44.32 3.07
6363 6560 0.179119 GCTCAGTTTGCCCATGATGC 60.179 55.000 0.00 0.00 0.00 3.91
6543 6750 0.111639 TCCAAGGCCTGTTGGTTACC 59.888 55.000 20.75 0.00 46.31 2.85
6544 6751 1.241315 CCAAGGCCTGTTGGTTACCG 61.241 60.000 14.58 0.00 41.96 4.02
6549 6756 0.250166 GCCTGTTGGTTACCGTCTGT 60.250 55.000 0.00 0.00 35.27 3.41
6550 6757 1.792006 CCTGTTGGTTACCGTCTGTC 58.208 55.000 0.00 0.00 0.00 3.51
6551 6758 1.343465 CCTGTTGGTTACCGTCTGTCT 59.657 52.381 0.00 0.00 0.00 3.41
6552 6759 2.559668 CCTGTTGGTTACCGTCTGTCTA 59.440 50.000 0.00 0.00 0.00 2.59
6658 6885 8.671028 GGTTACATAATGTTAGAACAACCGATT 58.329 33.333 0.00 0.00 43.03 3.34
6704 6931 1.153449 CTAAACTGCCCGGATCGCA 60.153 57.895 0.73 2.63 34.41 5.10
6708 6935 1.895020 AACTGCCCGGATCGCAACTA 61.895 55.000 0.73 0.00 35.40 2.24
6711 6938 0.032952 TGCCCGGATCGCAACTATAC 59.967 55.000 0.73 0.00 32.05 1.47
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 5.870978 GCTTGTATTTGCATGAAAATGAGGT 59.129 36.000 20.23 0.00 32.16 3.85
65 66 7.715265 ATCGTCTATGTATGGATTGTTGAAC 57.285 36.000 0.00 0.00 0.00 3.18
83 95 1.669265 TGATTCGCTCGTGTATCGTCT 59.331 47.619 0.00 0.00 40.80 4.18
84 96 2.101053 TGATTCGCTCGTGTATCGTC 57.899 50.000 0.00 0.00 40.80 4.20
86 98 4.196349 CAATTTGATTCGCTCGTGTATCG 58.804 43.478 0.00 0.00 41.41 2.92
87 99 5.005779 AGACAATTTGATTCGCTCGTGTATC 59.994 40.000 2.79 0.00 0.00 2.24
88 100 4.870426 AGACAATTTGATTCGCTCGTGTAT 59.130 37.500 2.79 0.00 0.00 2.29
89 101 4.242475 AGACAATTTGATTCGCTCGTGTA 58.758 39.130 2.79 0.00 0.00 2.90
90 102 3.067106 AGACAATTTGATTCGCTCGTGT 58.933 40.909 2.79 0.00 0.00 4.49
91 103 3.484229 GGAGACAATTTGATTCGCTCGTG 60.484 47.826 2.79 0.00 0.00 4.35
92 104 2.673368 GGAGACAATTTGATTCGCTCGT 59.327 45.455 2.79 0.00 0.00 4.18
93 105 2.030946 GGGAGACAATTTGATTCGCTCG 59.969 50.000 2.79 0.00 0.00 5.03
94 106 3.274288 AGGGAGACAATTTGATTCGCTC 58.726 45.455 2.79 2.31 0.00 5.03
95 107 3.356529 AGGGAGACAATTTGATTCGCT 57.643 42.857 2.79 10.20 0.00 4.93
96 108 3.191371 ACAAGGGAGACAATTTGATTCGC 59.809 43.478 2.79 8.28 0.00 4.70
97 109 5.376854 AACAAGGGAGACAATTTGATTCG 57.623 39.130 2.79 0.00 0.00 3.34
180 195 5.304357 CCTTCCTTTCTTTTTCCCTTTGCTA 59.696 40.000 0.00 0.00 0.00 3.49
182 197 4.100963 TCCTTCCTTTCTTTTTCCCTTTGC 59.899 41.667 0.00 0.00 0.00 3.68
187 202 5.716703 TCATCATCCTTCCTTTCTTTTTCCC 59.283 40.000 0.00 0.00 0.00 3.97
615 641 3.064079 CGCAAGGATCCATCACGAA 57.936 52.632 15.82 0.00 0.00 3.85
699 725 3.633116 CAACCCCCGTCTCCCGTT 61.633 66.667 0.00 0.00 33.66 4.44
799 825 2.637382 TGGGGCAGATCTTATCGCATAA 59.363 45.455 5.26 0.00 32.91 1.90
877 906 0.883833 AGAACCAGAAATGCAAGGCG 59.116 50.000 0.00 0.00 0.00 5.52
936 965 1.392589 ATATCAGCGTTTTGGGCAGG 58.607 50.000 0.00 0.00 0.00 4.85
1053 1082 4.391869 ACCAGCAGTGACAGCATG 57.608 55.556 2.10 0.00 46.00 4.06
1209 1238 9.010029 TCCAAAACAACTCTTTCCATAAGATAC 57.990 33.333 0.00 0.00 0.00 2.24
1398 1431 5.491982 ACAAACTGAATGACTAAGCTAGGG 58.508 41.667 0.00 0.00 0.00 3.53
1428 1461 0.110192 GTAGGTTGCGCTGTTTGCTC 60.110 55.000 9.73 0.00 40.11 4.26
1454 1487 6.051717 AGTATGTGTGCCTATTCAATGTCTC 58.948 40.000 0.00 0.00 0.00 3.36
1547 1610 4.657814 AGGGAGTGGTGATTACAATGTT 57.342 40.909 0.00 0.00 0.00 2.71
1570 1633 0.890683 TTTTCGGACGGAGGGAGTAC 59.109 55.000 0.00 0.00 0.00 2.73
1571 1634 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
1572 1635 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
1573 1636 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
1574 1637 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
1575 1638 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
1576 1639 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
1577 1640 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
1578 1641 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
1579 1642 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
1580 1643 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
1581 1644 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
1582 1645 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
1583 1646 7.312154 TCCATTTTGATGACAAGTATTTTCGG 58.688 34.615 0.00 0.00 37.32 4.30
1584 1647 8.915871 ATCCATTTTGATGACAAGTATTTTCG 57.084 30.769 0.00 0.00 37.32 3.46
1591 1654 8.096414 CCCTTTTTATCCATTTTGATGACAAGT 58.904 33.333 0.00 0.00 37.32 3.16
1592 1655 8.313292 TCCCTTTTTATCCATTTTGATGACAAG 58.687 33.333 0.00 0.00 37.32 3.16
1593 1656 8.200024 TCCCTTTTTATCCATTTTGATGACAA 57.800 30.769 0.00 0.00 0.00 3.18
1594 1657 7.789202 TCCCTTTTTATCCATTTTGATGACA 57.211 32.000 0.00 0.00 0.00 3.58
1595 1658 8.260114 ACATCCCTTTTTATCCATTTTGATGAC 58.740 33.333 0.00 0.00 32.39 3.06
1596 1659 8.378115 ACATCCCTTTTTATCCATTTTGATGA 57.622 30.769 0.00 0.00 32.39 2.92
1599 1662 9.713684 AGATACATCCCTTTTTATCCATTTTGA 57.286 29.630 0.00 0.00 0.00 2.69
1605 1668 9.225682 AGTTCTAGATACATCCCTTTTTATCCA 57.774 33.333 0.00 0.00 0.00 3.41
1615 1678 9.384764 GGCATATTTTAGTTCTAGATACATCCC 57.615 37.037 0.00 0.00 0.00 3.85
1623 1686 9.650714 TGTACCTAGGCATATTTTAGTTCTAGA 57.349 33.333 9.30 0.00 0.00 2.43
1626 1689 9.160412 AGATGTACCTAGGCATATTTTAGTTCT 57.840 33.333 9.30 0.00 0.00 3.01
1627 1690 9.425577 GAGATGTACCTAGGCATATTTTAGTTC 57.574 37.037 9.30 0.00 0.00 3.01
1628 1691 8.376270 GGAGATGTACCTAGGCATATTTTAGTT 58.624 37.037 9.30 0.00 0.00 2.24
1629 1692 7.735321 AGGAGATGTACCTAGGCATATTTTAGT 59.265 37.037 9.30 0.00 35.84 2.24
1630 1693 8.140112 AGGAGATGTACCTAGGCATATTTTAG 57.860 38.462 9.30 0.00 35.84 1.85
1631 1694 8.506196 AAGGAGATGTACCTAGGCATATTTTA 57.494 34.615 9.30 0.00 36.67 1.52
1632 1695 7.394144 AAGGAGATGTACCTAGGCATATTTT 57.606 36.000 9.30 0.00 36.67 1.82
1633 1696 7.394144 AAAGGAGATGTACCTAGGCATATTT 57.606 36.000 9.30 0.00 36.67 1.40
1634 1697 7.394144 AAAAGGAGATGTACCTAGGCATATT 57.606 36.000 9.30 0.00 36.67 1.28
1635 1698 8.686739 ATAAAAGGAGATGTACCTAGGCATAT 57.313 34.615 9.30 0.00 36.67 1.78
1636 1699 7.180408 GGATAAAAGGAGATGTACCTAGGCATA 59.820 40.741 9.30 0.00 36.67 3.14
1637 1700 6.013293 GGATAAAAGGAGATGTACCTAGGCAT 60.013 42.308 9.30 4.99 36.67 4.40
1638 1701 5.307196 GGATAAAAGGAGATGTACCTAGGCA 59.693 44.000 9.30 0.00 36.67 4.75
1639 1702 5.307196 TGGATAAAAGGAGATGTACCTAGGC 59.693 44.000 9.30 0.00 36.67 3.93
1640 1703 6.996180 TGGATAAAAGGAGATGTACCTAGG 57.004 41.667 7.41 7.41 36.67 3.02
1641 1704 9.853177 AAAATGGATAAAAGGAGATGTACCTAG 57.147 33.333 0.00 0.00 36.67 3.02
1642 1705 9.627123 CAAAATGGATAAAAGGAGATGTACCTA 57.373 33.333 0.00 0.00 36.67 3.08
1643 1706 8.336235 TCAAAATGGATAAAAGGAGATGTACCT 58.664 33.333 0.00 0.00 39.69 3.08
1644 1707 8.519799 TCAAAATGGATAAAAGGAGATGTACC 57.480 34.615 0.00 0.00 0.00 3.34
1645 1708 9.956720 CATCAAAATGGATAAAAGGAGATGTAC 57.043 33.333 0.00 0.00 0.00 2.90
1646 1709 9.919416 TCATCAAAATGGATAAAAGGAGATGTA 57.081 29.630 0.00 0.00 33.42 2.29
1647 1710 8.689972 GTCATCAAAATGGATAAAAGGAGATGT 58.310 33.333 0.00 0.00 33.42 3.06
1648 1711 8.689061 TGTCATCAAAATGGATAAAAGGAGATG 58.311 33.333 0.00 0.00 33.42 2.90
1649 1712 8.827832 TGTCATCAAAATGGATAAAAGGAGAT 57.172 30.769 0.00 0.00 33.42 2.75
1650 1713 8.648698 TTGTCATCAAAATGGATAAAAGGAGA 57.351 30.769 0.00 0.00 33.42 3.71
1651 1714 8.526147 ACTTGTCATCAAAATGGATAAAAGGAG 58.474 33.333 0.00 0.00 33.42 3.69
1652 1715 8.421249 ACTTGTCATCAAAATGGATAAAAGGA 57.579 30.769 0.00 0.00 33.42 3.36
1658 1721 8.620416 CGGAAATACTTGTCATCAAAATGGATA 58.380 33.333 0.00 0.00 33.42 2.59
1659 1722 7.416664 CCGGAAATACTTGTCATCAAAATGGAT 60.417 37.037 0.00 0.00 33.42 3.41
1660 1723 6.127758 CCGGAAATACTTGTCATCAAAATGGA 60.128 38.462 0.00 0.00 33.42 3.41
1661 1724 6.035843 CCGGAAATACTTGTCATCAAAATGG 58.964 40.000 0.00 0.00 33.42 3.16
1662 1725 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
1663 1726 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
1664 1727 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
1665 1728 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
1666 1729 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
1667 1730 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
1668 1731 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
1669 1732 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
1670 1733 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
1671 1734 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
1672 1735 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
1673 1736 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
1674 1737 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
1675 1738 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
1676 1739 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
1677 1740 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
1678 1741 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
1679 1742 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
1680 1743 0.846015 TATACTCCCTCCGTCCGGAA 59.154 55.000 5.23 0.00 44.66 4.30
1681 1744 0.846015 TTATACTCCCTCCGTCCGGA 59.154 55.000 0.00 0.00 42.90 5.14
1682 1745 1.544691 CATTATACTCCCTCCGTCCGG 59.455 57.143 0.00 0.00 0.00 5.14
1683 1746 2.236766 ACATTATACTCCCTCCGTCCG 58.763 52.381 0.00 0.00 0.00 4.79
1684 1747 4.405548 AGTACATTATACTCCCTCCGTCC 58.594 47.826 0.00 0.00 0.00 4.79
1685 1748 5.533903 TCAAGTACATTATACTCCCTCCGTC 59.466 44.000 0.00 0.00 0.00 4.79
1686 1749 5.452255 TCAAGTACATTATACTCCCTCCGT 58.548 41.667 0.00 0.00 0.00 4.69
1687 1750 6.434652 AGATCAAGTACATTATACTCCCTCCG 59.565 42.308 0.00 0.00 0.00 4.63
1688 1751 7.784470 AGATCAAGTACATTATACTCCCTCC 57.216 40.000 0.00 0.00 0.00 4.30
1689 1752 8.091449 CCAAGATCAAGTACATTATACTCCCTC 58.909 40.741 0.00 0.00 0.00 4.30
1690 1753 7.789831 TCCAAGATCAAGTACATTATACTCCCT 59.210 37.037 0.00 0.00 0.00 4.20
1691 1754 7.873505 GTCCAAGATCAAGTACATTATACTCCC 59.126 40.741 0.00 0.00 0.00 4.30
1692 1755 8.643324 AGTCCAAGATCAAGTACATTATACTCC 58.357 37.037 0.00 0.00 0.00 3.85
1693 1756 9.469807 CAGTCCAAGATCAAGTACATTATACTC 57.530 37.037 0.00 0.00 0.00 2.59
1694 1757 7.928706 GCAGTCCAAGATCAAGTACATTATACT 59.071 37.037 0.00 0.00 0.00 2.12
1705 1768 4.825422 TCAGTAAGCAGTCCAAGATCAAG 58.175 43.478 0.00 0.00 0.00 3.02
1714 1777 8.131731 GGAAAATCATTAATCAGTAAGCAGTCC 58.868 37.037 0.00 0.00 0.00 3.85
1937 2001 3.801050 CAGACTATTGATCAAGCGTGAGG 59.199 47.826 14.54 1.76 37.14 3.86
2283 2347 8.200792 AGAAGTAGAGCATTATTTAGTGGTCAG 58.799 37.037 12.75 0.00 41.17 3.51
2406 2470 2.443016 TTTGGCAAACCCCGCACT 60.443 55.556 8.93 0.00 33.59 4.40
2632 2696 6.920210 TGACTGCGAAATCATCATACTCTAAG 59.080 38.462 0.00 0.00 0.00 2.18
2650 2714 3.984292 GCAGGAAGAATTGACTGCG 57.016 52.632 0.00 0.00 42.93 5.18
2820 2884 8.246180 CACTGGCAACTACAGATAATTCAAAAT 58.754 33.333 0.00 0.00 39.24 1.82
2874 2938 5.392767 ACGATGAGAGTTACAGTCAATGT 57.607 39.130 0.00 0.00 46.45 2.71
2981 3045 9.927668 CAACCAAATATTCCAGAATGTAAAAGT 57.072 29.630 3.10 0.00 32.50 2.66
3008 3072 1.804748 GCAACCGAAAACTCCCTAGTG 59.195 52.381 0.00 0.00 35.62 2.74
3498 3565 8.134895 TGACTTTAGCAAACCATTAGAAACAAG 58.865 33.333 0.00 0.00 0.00 3.16
3502 3569 8.232913 AGTTGACTTTAGCAAACCATTAGAAA 57.767 30.769 0.00 0.00 0.00 2.52
3529 3596 2.177394 TGAACGCCAGATAAGCAACA 57.823 45.000 0.00 0.00 0.00 3.33
3544 3611 2.031560 TGTGCATCACGAACAGTTGAAC 59.968 45.455 0.00 0.00 37.14 3.18
3547 3614 2.975410 ATGTGCATCACGAACAGTTG 57.025 45.000 0.00 0.00 37.14 3.16
3653 3720 5.253330 TGACACCCTAAGATTTCCAATGTC 58.747 41.667 0.00 0.00 35.58 3.06
3722 3789 4.938832 TGTACATAAAACATGGGGAAGACG 59.061 41.667 0.00 0.00 0.00 4.18
3771 3838 6.861055 CGCAAAGGTTTAAACATGAAGTGTAT 59.139 34.615 19.57 0.00 41.14 2.29
4134 4209 8.287503 GTCCAACCTGTAAGTACAAATAGTTTG 58.712 37.037 0.00 1.15 45.95 2.93
4216 4291 2.169561 TCTTTGCCCACCAAAAGTTTCC 59.830 45.455 0.00 0.00 42.51 3.13
4516 4591 3.490348 CCTCCTAAATTCAATGGGCGAT 58.510 45.455 0.00 0.00 0.00 4.58
4735 4810 6.307318 AGTTATAAGCAAACTGTACGAAGTCG 59.693 38.462 0.00 0.00 37.63 4.18
4804 4879 4.031991 CACATATGCCAGCAATGTTTTTCG 59.968 41.667 13.92 4.14 31.60 3.46
5117 5301 2.505405 TGGCGCAAAACCTAATGTGTA 58.495 42.857 10.83 0.00 0.00 2.90
5215 5399 3.684305 TCAGTGAACAATCTACATTGGCG 59.316 43.478 0.00 0.00 43.47 5.69
5387 5571 2.620115 ACATTTTGATGCCCTCTATGCG 59.380 45.455 0.00 0.00 0.00 4.73
5415 5599 3.837213 AAGATGCAGGTTTTGACATCG 57.163 42.857 0.00 0.00 41.30 3.84
5573 5757 4.693283 TCATTATTCTTGGTAGGCACGAG 58.307 43.478 0.00 0.00 0.00 4.18
5579 5763 7.611855 ACTTTGAGGTTCATTATTCTTGGTAGG 59.388 37.037 0.00 0.00 0.00 3.18
5653 5837 3.492309 CGCTTCTATCAGATTCCTGCTGT 60.492 47.826 0.00 0.00 40.20 4.40
5665 5849 5.690409 GGATTTATTCGTGTCGCTTCTATCA 59.310 40.000 0.00 0.00 0.00 2.15
5680 5864 5.300752 TCCTCATCTTGCTCGGATTTATTC 58.699 41.667 0.00 0.00 0.00 1.75
5755 5942 5.050126 TCGACTAATCTGGACCTCATAGT 57.950 43.478 0.00 0.00 0.00 2.12
5801 5988 4.267690 CGAAATGTACGCTGATCTTGCTTA 59.732 41.667 9.02 2.61 0.00 3.09
5824 6011 2.038295 CCCTCTGGCCAAGTAGATCATC 59.962 54.545 7.01 0.00 0.00 2.92
5856 6043 2.233676 ACGCTTCCATGATGTGTCAGTA 59.766 45.455 0.00 0.00 37.87 2.74
5893 6080 1.315257 GCATCCAAGGTCAACGGCAT 61.315 55.000 0.00 0.00 0.00 4.40
5978 6165 7.467675 GCAAAAGAGCAAAAATGAAAGGAATGT 60.468 33.333 0.00 0.00 0.00 2.71
5989 6176 2.908688 ACCCGCAAAAGAGCAAAAAT 57.091 40.000 0.00 0.00 0.00 1.82
6155 6349 2.433970 TGTCATGAGTTGAGTGTGTCCA 59.566 45.455 0.00 0.00 34.17 4.02
6159 6353 2.804527 CCTGTGTCATGAGTTGAGTGTG 59.195 50.000 0.00 0.00 34.17 3.82
6231 6428 4.908736 ACAAGCACACATAACGCATAATC 58.091 39.130 0.00 0.00 0.00 1.75
6360 6557 6.212235 TGTTTTGATGTTTTCACATACGCAT 58.788 32.000 0.00 0.00 44.22 4.73
6363 6560 8.060020 ACATTGTTTTGATGTTTTCACATACG 57.940 30.769 0.00 0.00 44.22 3.06
6543 6750 6.876789 ACATCTCTAGGACATATAGACAGACG 59.123 42.308 0.00 0.00 0.00 4.18
6544 6751 8.630054 AACATCTCTAGGACATATAGACAGAC 57.370 38.462 0.00 0.00 0.00 3.51
6549 6756 7.178573 CCCAGAACATCTCTAGGACATATAGA 58.821 42.308 0.00 0.00 35.03 1.98
6550 6757 6.127479 GCCCAGAACATCTCTAGGACATATAG 60.127 46.154 0.00 0.00 35.03 1.31
6551 6758 5.717178 GCCCAGAACATCTCTAGGACATATA 59.283 44.000 0.00 0.00 35.03 0.86
6552 6759 4.530161 GCCCAGAACATCTCTAGGACATAT 59.470 45.833 0.00 0.00 35.03 1.78
6658 6885 3.849574 TCACATTCCAACCCAGGAGATTA 59.150 43.478 0.00 0.00 39.25 1.75


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

AutoCloner maintained by Alex Coulton.