Multiple sequence alignment - TraesCS1D01G108400

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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 TraesCS1D01G108400 chr1D 100.000 3607 0 0 1 3607 101099407 101103013 0.000000e+00 6661.0
1 TraesCS1D01G108400 chr1A 94.959 1111 38 3 1978 3071 104242089 104240980 0.000000e+00 1725.0
2 TraesCS1D01G108400 chr1A 92.364 956 61 11 1 953 104243769 104242823 0.000000e+00 1351.0
3 TraesCS1D01G108400 chr1A 89.237 734 47 7 943 1662 104242806 104242091 0.000000e+00 889.0
4 TraesCS1D01G108400 chr1A 86.271 590 30 10 3063 3607 104240046 104239463 8.620000e-166 593.0
5 TraesCS1D01G108400 chr1B 93.010 1030 43 8 1971 2974 150546454 150545428 0.000000e+00 1476.0
6 TraesCS1D01G108400 chr1B 93.827 567 34 1 1097 1662 150547019 150546453 0.000000e+00 852.0
7 TraesCS1D01G108400 chr1B 81.975 871 105 24 59 918 150550075 150549246 0.000000e+00 691.0
8 TraesCS1D01G108400 chr1B 90.952 420 24 5 3196 3607 150545220 150544807 1.460000e-153 553.0
9 TraesCS1D01G108400 chr1B 96.250 160 6 0 3065 3224 150545394 150545235 2.760000e-66 263.0
10 TraesCS1D01G108400 chr1B 92.086 139 11 0 947 1085 150547268 150547130 2.840000e-46 196.0
11 TraesCS1D01G108400 chr1B 97.059 34 1 0 928 961 150547314 150547281 1.400000e-04 58.4
12 TraesCS1D01G108400 chr3D 81.106 217 31 7 12 227 564134613 564134406 8.010000e-37 165.0
13 TraesCS1D01G108400 chr3D 83.108 148 19 3 158 299 481579408 481579261 2.920000e-26 130.0
14 TraesCS1D01G108400 chr3A 79.583 240 37 5 59 292 694532643 694532410 1.040000e-35 161.0
15 TraesCS1D01G108400 chr3A 79.221 231 32 8 17 241 651420479 651420699 2.900000e-31 147.0
16 TraesCS1D01G108400 chr7A 83.735 166 25 2 3398 3563 7603469 7603306 4.820000e-34 156.0
17 TraesCS1D01G108400 chr4B 79.821 223 36 6 55 271 10586317 10586098 1.730000e-33 154.0
18 TraesCS1D01G108400 chr3B 79.911 224 33 8 1 222 751750404 751750191 1.730000e-33 154.0
19 TraesCS1D01G108400 chr6D 77.470 253 44 9 53 297 9373091 9373338 4.860000e-29 139.0
20 TraesCS1D01G108400 chr6D 80.620 129 13 9 2316 2438 767804 767926 4.960000e-14 89.8
21 TraesCS1D01G108400 chr2A 77.366 243 47 7 55 293 596151500 596151738 1.750000e-28 137.0
22 TraesCS1D01G108400 chr5A 85.981 107 9 2 3202 3308 510032151 510032251 3.810000e-20 110.0
23 TraesCS1D01G108400 chr7B 82.022 89 13 3 498 584 588246134 588246221 5.000000e-09 73.1
24 TraesCS1D01G108400 chr2D 100.000 29 0 0 498 526 628548907 628548935 2.000000e-03 54.7
25 TraesCS1D01G108400 chr2B 100.000 29 0 0 498 526 771787201 771787173 2.000000e-03 54.7
26 TraesCS1D01G108400 chr2B 100.000 28 0 0 4 31 716173883 716173856 7.000000e-03 52.8


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 TraesCS1D01G108400 chr1D 101099407 101103013 3606 False 6661.0 6661 100.000000 1 3607 1 chr1D.!!$F1 3606
1 TraesCS1D01G108400 chr1A 104239463 104243769 4306 True 1139.5 1725 90.707750 1 3607 4 chr1A.!!$R1 3606
2 TraesCS1D01G108400 chr1B 150544807 150550075 5268 True 584.2 1476 92.165571 59 3607 7 chr1B.!!$R1 3548

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
36 37 0.308684 CATGCGCACATACATCCACC 59.691 55.0 14.9 0.0 33.67 4.61 F
1706 3793 0.114364 TGAGCACCACTAGACCTCCA 59.886 55.0 0.0 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1943 4030 0.036732 GGTGGGAGCAGAATGTGTGA 59.963 55.0 0.00 0.0 39.31 3.58 R
3432 6533 0.107456 ATCCTGATGCGGCGAAGATT 59.893 50.0 12.98 0.0 0.00 2.40 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
32 33 3.424039 GCTCATACATGCGCACATACATC 60.424 47.826 14.90 0.00 38.33 3.06
35 36 1.016627 ACATGCGCACATACATCCAC 58.983 50.000 14.90 0.00 33.67 4.02
36 37 0.308684 CATGCGCACATACATCCACC 59.691 55.000 14.90 0.00 33.67 4.61
69 70 2.743538 ATGCACGCACGCACATCT 60.744 55.556 0.00 0.00 46.56 2.90
100 101 2.036475 TGAGCACCTTCAAGAGACTGAC 59.964 50.000 0.00 0.00 0.00 3.51
120 121 4.586421 TGACCTAGCACATTATCCTGAGAG 59.414 45.833 0.00 0.00 0.00 3.20
141 142 1.132588 GATGAAGTCGCCATAGACGC 58.867 55.000 0.00 0.00 45.26 5.19
157 158 2.756760 AGACGCCTTTATAGTCAACGGA 59.243 45.455 0.00 0.00 37.36 4.69
206 207 8.576442 ACATCACCGAAAAGTCTGAAATAAATT 58.424 29.630 0.00 0.00 0.00 1.82
222 223 6.892310 AATAAATTCAGAAAAATGCGAGCC 57.108 33.333 0.00 0.00 0.00 4.70
373 378 8.786826 TTGGTATCAGGAACAGTTTTATACAG 57.213 34.615 0.00 0.00 0.00 2.74
379 384 7.163441 TCAGGAACAGTTTTATACAGGGTTAC 58.837 38.462 0.00 0.00 0.00 2.50
488 497 6.198687 CGCATTCGACATTTTTGGTATACAT 58.801 36.000 5.01 0.00 38.10 2.29
490 499 7.192913 GCATTCGACATTTTTGGTATACATCA 58.807 34.615 5.01 0.00 0.00 3.07
494 503 7.279615 TCGACATTTTTGGTATACATCAGGAT 58.720 34.615 5.01 0.00 0.00 3.24
925 942 2.420022 TCTCTTGCGGCTTTTTATGCTC 59.580 45.455 0.00 0.00 0.00 4.26
1038 3011 0.846693 ATTTTCGGGAGGGGATGGAG 59.153 55.000 0.00 0.00 0.00 3.86
1077 3050 1.674441 CGTGAGGCGATTGAGGTACTA 59.326 52.381 0.00 0.00 41.30 1.82
1095 3167 2.959707 ACTAGACAAGGATAAGGCCGAG 59.040 50.000 0.00 0.00 0.00 4.63
1328 3400 1.485294 TTCAGTAAGCCCTTCCGCCA 61.485 55.000 0.00 0.00 0.00 5.69
1370 3442 0.966875 ACCGCCATTGATGCACATGT 60.967 50.000 0.00 0.00 0.00 3.21
1372 3444 1.273688 CGCCATTGATGCACATGTTG 58.726 50.000 0.00 0.00 0.00 3.33
1379 3451 5.290885 CCATTGATGCACATGTTGATCAAAG 59.709 40.000 23.59 20.36 36.34 2.77
1386 3458 4.074259 CACATGTTGATCAAAGTCCCTCA 58.926 43.478 10.35 2.28 0.00 3.86
1388 3460 4.703575 ACATGTTGATCAAAGTCCCTCATG 59.296 41.667 21.92 21.92 36.99 3.07
1402 3474 2.009051 CCTCATGTTTATGCGTGCAGA 58.991 47.619 0.00 0.00 34.21 4.26
1472 3544 1.899142 GCCTGGGAGGATGATACTCTC 59.101 57.143 4.40 0.06 37.67 3.20
1505 3577 4.222810 TCAATCGAAGTCATGGGAAGAGAA 59.777 41.667 0.00 0.00 0.00 2.87
1508 3580 3.323691 TCGAAGTCATGGGAAGAGAACAA 59.676 43.478 0.00 0.00 0.00 2.83
1538 3610 2.359850 TGGCCGCTGGATGTGTTC 60.360 61.111 0.00 0.00 0.00 3.18
1553 3625 1.295357 TGTTCGGTATGGTTGCTGCG 61.295 55.000 0.00 0.00 0.00 5.18
1608 3694 1.069513 TCAGTCGTGAACGGGACAATT 59.930 47.619 2.59 0.00 40.29 2.32
1658 3745 6.186420 ACTCCCACTTGGCAAATTTTAATT 57.814 33.333 0.00 0.00 0.00 1.40
1662 3749 9.230122 CTCCCACTTGGCAAATTTTAATTATTT 57.770 29.630 0.00 0.00 0.00 1.40
1663 3750 9.007901 TCCCACTTGGCAAATTTTAATTATTTG 57.992 29.630 14.58 14.58 42.88 2.32
1664 3751 8.242739 CCCACTTGGCAAATTTTAATTATTTGG 58.757 33.333 18.01 9.12 41.22 3.28
1670 3757 7.302350 GCAAATTTTAATTATTTGGCTCGGT 57.698 32.000 18.01 0.00 41.22 4.69
1671 3758 7.747888 GCAAATTTTAATTATTTGGCTCGGTT 58.252 30.769 18.01 0.00 41.22 4.44
1672 3759 7.902917 GCAAATTTTAATTATTTGGCTCGGTTC 59.097 33.333 18.01 3.61 41.22 3.62
1674 3761 9.719355 AAATTTTAATTATTTGGCTCGGTTCTT 57.281 25.926 0.00 0.00 0.00 2.52
1675 3762 8.926715 ATTTTAATTATTTGGCTCGGTTCTTC 57.073 30.769 0.00 0.00 0.00 2.87
1677 3764 8.795842 TTTAATTATTTGGCTCGGTTCTTCTA 57.204 30.769 0.00 0.00 0.00 2.10
1678 3765 8.974060 TTAATTATTTGGCTCGGTTCTTCTAT 57.026 30.769 0.00 0.00 0.00 1.98
1679 3766 6.867662 ATTATTTGGCTCGGTTCTTCTATG 57.132 37.500 0.00 0.00 0.00 2.23
1680 3767 2.024176 TTGGCTCGGTTCTTCTATGC 57.976 50.000 0.00 0.00 0.00 3.14
1681 3768 1.195115 TGGCTCGGTTCTTCTATGCT 58.805 50.000 0.00 0.00 0.00 3.79
1682 3769 1.555075 TGGCTCGGTTCTTCTATGCTT 59.445 47.619 0.00 0.00 0.00 3.91
1683 3770 2.027192 TGGCTCGGTTCTTCTATGCTTT 60.027 45.455 0.00 0.00 0.00 3.51
1684 3771 2.609916 GGCTCGGTTCTTCTATGCTTTC 59.390 50.000 0.00 0.00 0.00 2.62
1685 3772 3.262420 GCTCGGTTCTTCTATGCTTTCA 58.738 45.455 0.00 0.00 0.00 2.69
1686 3773 3.062774 GCTCGGTTCTTCTATGCTTTCAC 59.937 47.826 0.00 0.00 0.00 3.18
1687 3774 4.499183 CTCGGTTCTTCTATGCTTTCACT 58.501 43.478 0.00 0.00 0.00 3.41
1688 3775 4.245660 TCGGTTCTTCTATGCTTTCACTG 58.754 43.478 0.00 0.00 0.00 3.66
1689 3776 4.021456 TCGGTTCTTCTATGCTTTCACTGA 60.021 41.667 0.00 0.00 0.00 3.41
1690 3777 4.328440 CGGTTCTTCTATGCTTTCACTGAG 59.672 45.833 0.00 0.00 0.00 3.35
1691 3778 4.094146 GGTTCTTCTATGCTTTCACTGAGC 59.906 45.833 0.00 0.00 40.53 4.26
1696 3783 2.706636 TGCTTTCACTGAGCACCAC 58.293 52.632 0.00 0.00 44.63 4.16
1697 3784 0.181114 TGCTTTCACTGAGCACCACT 59.819 50.000 0.00 0.00 44.63 4.00
1698 3785 1.416030 TGCTTTCACTGAGCACCACTA 59.584 47.619 0.00 0.00 44.63 2.74
1699 3786 2.072298 GCTTTCACTGAGCACCACTAG 58.928 52.381 0.00 0.00 39.89 2.57
1700 3787 2.289072 GCTTTCACTGAGCACCACTAGA 60.289 50.000 0.00 0.00 39.89 2.43
1701 3788 3.321497 CTTTCACTGAGCACCACTAGAC 58.679 50.000 0.00 0.00 0.00 2.59
1702 3789 1.257743 TCACTGAGCACCACTAGACC 58.742 55.000 0.00 0.00 0.00 3.85
1703 3790 1.203063 TCACTGAGCACCACTAGACCT 60.203 52.381 0.00 0.00 0.00 3.85
1704 3791 1.203523 CACTGAGCACCACTAGACCTC 59.796 57.143 0.00 0.00 0.00 3.85
1705 3792 0.820871 CTGAGCACCACTAGACCTCC 59.179 60.000 0.00 0.00 0.00 4.30
1706 3793 0.114364 TGAGCACCACTAGACCTCCA 59.886 55.000 0.00 0.00 0.00 3.86
1707 3794 1.273267 TGAGCACCACTAGACCTCCAT 60.273 52.381 0.00 0.00 0.00 3.41
1708 3795 1.834263 GAGCACCACTAGACCTCCATT 59.166 52.381 0.00 0.00 0.00 3.16
1709 3796 3.031736 GAGCACCACTAGACCTCCATTA 58.968 50.000 0.00 0.00 0.00 1.90
1710 3797 3.450904 AGCACCACTAGACCTCCATTAA 58.549 45.455 0.00 0.00 0.00 1.40
1711 3798 3.452627 AGCACCACTAGACCTCCATTAAG 59.547 47.826 0.00 0.00 0.00 1.85
1712 3799 3.798202 CACCACTAGACCTCCATTAAGC 58.202 50.000 0.00 0.00 0.00 3.09
1713 3800 3.452627 CACCACTAGACCTCCATTAAGCT 59.547 47.826 0.00 0.00 0.00 3.74
1714 3801 3.452627 ACCACTAGACCTCCATTAAGCTG 59.547 47.826 0.00 0.00 0.00 4.24
1715 3802 3.706594 CCACTAGACCTCCATTAAGCTGA 59.293 47.826 0.00 0.00 0.00 4.26
1716 3803 4.346418 CCACTAGACCTCCATTAAGCTGAT 59.654 45.833 0.00 0.00 0.00 2.90
1717 3804 5.163258 CCACTAGACCTCCATTAAGCTGATT 60.163 44.000 0.00 0.00 0.00 2.57
1718 3805 6.352516 CACTAGACCTCCATTAAGCTGATTT 58.647 40.000 0.00 0.00 0.00 2.17
1719 3806 7.419057 CCACTAGACCTCCATTAAGCTGATTTA 60.419 40.741 0.00 0.00 0.00 1.40
1720 3807 7.987458 CACTAGACCTCCATTAAGCTGATTTAA 59.013 37.037 0.00 0.00 0.00 1.52
1721 3808 8.548877 ACTAGACCTCCATTAAGCTGATTTAAA 58.451 33.333 0.00 0.00 0.00 1.52
1722 3809 9.566432 CTAGACCTCCATTAAGCTGATTTAAAT 57.434 33.333 0.00 0.00 0.00 1.40
1723 3810 8.230472 AGACCTCCATTAAGCTGATTTAAATG 57.770 34.615 5.17 0.00 0.00 2.32
1724 3811 7.836183 AGACCTCCATTAAGCTGATTTAAATGT 59.164 33.333 5.17 0.00 0.00 2.71
1725 3812 7.775120 ACCTCCATTAAGCTGATTTAAATGTG 58.225 34.615 5.17 0.00 0.00 3.21
1726 3813 7.615365 ACCTCCATTAAGCTGATTTAAATGTGA 59.385 33.333 5.17 0.00 0.00 3.58
1727 3814 8.636213 CCTCCATTAAGCTGATTTAAATGTGAT 58.364 33.333 5.17 0.00 0.00 3.06
1758 3845 9.712305 AGTATACGATTTAATCAGGGATTTCAG 57.288 33.333 5.76 0.00 33.95 3.02
1759 3846 9.490379 GTATACGATTTAATCAGGGATTTCAGT 57.510 33.333 5.76 0.00 33.95 3.41
1760 3847 6.927294 ACGATTTAATCAGGGATTTCAGTC 57.073 37.500 5.76 0.00 33.95 3.51
1761 3848 5.823045 ACGATTTAATCAGGGATTTCAGTCC 59.177 40.000 5.76 0.00 33.95 3.85
1768 3855 2.083715 GGATTTCAGTCCCCACCCA 58.916 57.895 0.00 0.00 31.82 4.51
1769 3856 0.323451 GGATTTCAGTCCCCACCCAC 60.323 60.000 0.00 0.00 31.82 4.61
1770 3857 0.404040 GATTTCAGTCCCCACCCACA 59.596 55.000 0.00 0.00 0.00 4.17
1771 3858 0.856982 ATTTCAGTCCCCACCCACAA 59.143 50.000 0.00 0.00 0.00 3.33
1772 3859 0.184933 TTTCAGTCCCCACCCACAAG 59.815 55.000 0.00 0.00 0.00 3.16
1773 3860 0.696143 TTCAGTCCCCACCCACAAGA 60.696 55.000 0.00 0.00 0.00 3.02
1774 3861 0.696143 TCAGTCCCCACCCACAAGAA 60.696 55.000 0.00 0.00 0.00 2.52
1775 3862 0.537371 CAGTCCCCACCCACAAGAAC 60.537 60.000 0.00 0.00 0.00 3.01
1776 3863 0.991355 AGTCCCCACCCACAAGAACA 60.991 55.000 0.00 0.00 0.00 3.18
1777 3864 0.537371 GTCCCCACCCACAAGAACAG 60.537 60.000 0.00 0.00 0.00 3.16
1778 3865 0.696143 TCCCCACCCACAAGAACAGA 60.696 55.000 0.00 0.00 0.00 3.41
1779 3866 0.184933 CCCCACCCACAAGAACAGAA 59.815 55.000 0.00 0.00 0.00 3.02
1780 3867 1.203050 CCCCACCCACAAGAACAGAAT 60.203 52.381 0.00 0.00 0.00 2.40
1781 3868 1.888512 CCCACCCACAAGAACAGAATG 59.111 52.381 0.00 0.00 46.00 2.67
1818 3905 8.729805 ATTATAAGCTTGCTAGATCTTATGGC 57.270 34.615 9.86 1.67 34.62 4.40
1819 3906 4.428294 AAGCTTGCTAGATCTTATGGCA 57.572 40.909 0.00 4.44 0.00 4.92
1820 3907 3.737850 AGCTTGCTAGATCTTATGGCAC 58.262 45.455 0.00 0.00 32.47 5.01
1835 3922 2.653726 TGGCACAAATATGCTACCCTG 58.346 47.619 0.00 0.00 45.38 4.45
1836 3923 2.240921 TGGCACAAATATGCTACCCTGA 59.759 45.455 0.00 0.00 45.38 3.86
1837 3924 2.618709 GGCACAAATATGCTACCCTGAC 59.381 50.000 0.00 0.00 45.38 3.51
1838 3925 3.545703 GCACAAATATGCTACCCTGACT 58.454 45.455 0.00 0.00 42.62 3.41
1839 3926 4.444306 GGCACAAATATGCTACCCTGACTA 60.444 45.833 0.00 0.00 45.38 2.59
1840 3927 5.308825 GCACAAATATGCTACCCTGACTAT 58.691 41.667 0.00 0.00 42.62 2.12
1841 3928 5.765182 GCACAAATATGCTACCCTGACTATT 59.235 40.000 0.00 0.00 42.62 1.73
1842 3929 6.073003 GCACAAATATGCTACCCTGACTATTC 60.073 42.308 0.00 0.00 42.62 1.75
1843 3930 7.220030 CACAAATATGCTACCCTGACTATTCT 58.780 38.462 0.00 0.00 0.00 2.40
1844 3931 7.386299 CACAAATATGCTACCCTGACTATTCTC 59.614 40.741 0.00 0.00 0.00 2.87
1845 3932 6.613153 AATATGCTACCCTGACTATTCTCC 57.387 41.667 0.00 0.00 0.00 3.71
1846 3933 2.679082 TGCTACCCTGACTATTCTCCC 58.321 52.381 0.00 0.00 0.00 4.30
1847 3934 2.023404 TGCTACCCTGACTATTCTCCCA 60.023 50.000 0.00 0.00 0.00 4.37
1848 3935 3.243724 GCTACCCTGACTATTCTCCCAT 58.756 50.000 0.00 0.00 0.00 4.00
1849 3936 3.259625 GCTACCCTGACTATTCTCCCATC 59.740 52.174 0.00 0.00 0.00 3.51
1850 3937 2.320781 ACCCTGACTATTCTCCCATCG 58.679 52.381 0.00 0.00 0.00 3.84
1851 3938 2.320781 CCCTGACTATTCTCCCATCGT 58.679 52.381 0.00 0.00 0.00 3.73
1852 3939 2.036475 CCCTGACTATTCTCCCATCGTG 59.964 54.545 0.00 0.00 0.00 4.35
1853 3940 2.546795 CCTGACTATTCTCCCATCGTGC 60.547 54.545 0.00 0.00 0.00 5.34
1854 3941 2.363680 CTGACTATTCTCCCATCGTGCT 59.636 50.000 0.00 0.00 0.00 4.40
1855 3942 2.766263 TGACTATTCTCCCATCGTGCTT 59.234 45.455 0.00 0.00 0.00 3.91
1856 3943 3.126831 GACTATTCTCCCATCGTGCTTG 58.873 50.000 0.00 0.00 0.00 4.01
1857 3944 2.501723 ACTATTCTCCCATCGTGCTTGT 59.498 45.455 0.00 0.00 0.00 3.16
1858 3945 3.704566 ACTATTCTCCCATCGTGCTTGTA 59.295 43.478 0.00 0.00 0.00 2.41
1859 3946 3.627395 ATTCTCCCATCGTGCTTGTAA 57.373 42.857 0.00 0.00 0.00 2.41
1860 3947 3.627395 TTCTCCCATCGTGCTTGTAAT 57.373 42.857 0.00 0.00 0.00 1.89
1861 3948 2.905075 TCTCCCATCGTGCTTGTAATG 58.095 47.619 0.00 0.00 0.00 1.90
1862 3949 1.331756 CTCCCATCGTGCTTGTAATGC 59.668 52.381 0.00 0.00 37.54 3.56
1863 3950 1.093972 CCCATCGTGCTTGTAATGCA 58.906 50.000 0.00 0.00 45.42 3.96
1873 3960 4.779696 TGCTTGTAATGCACCTCATATCA 58.220 39.130 0.00 0.00 42.52 2.15
1874 3961 4.576053 TGCTTGTAATGCACCTCATATCAC 59.424 41.667 0.00 0.00 42.52 3.06
1875 3962 4.576053 GCTTGTAATGCACCTCATATCACA 59.424 41.667 0.00 0.00 36.91 3.58
1876 3963 5.504665 GCTTGTAATGCACCTCATATCACAC 60.505 44.000 0.00 0.00 36.91 3.82
1877 3964 5.096443 TGTAATGCACCTCATATCACACA 57.904 39.130 0.00 0.00 34.33 3.72
1878 3965 5.683681 TGTAATGCACCTCATATCACACAT 58.316 37.500 0.00 0.00 34.33 3.21
1879 3966 5.759763 TGTAATGCACCTCATATCACACATC 59.240 40.000 0.00 0.00 34.33 3.06
1880 3967 3.910568 TGCACCTCATATCACACATCA 57.089 42.857 0.00 0.00 0.00 3.07
1881 3968 4.426736 TGCACCTCATATCACACATCAT 57.573 40.909 0.00 0.00 0.00 2.45
1882 3969 4.784177 TGCACCTCATATCACACATCATT 58.216 39.130 0.00 0.00 0.00 2.57
1883 3970 5.195185 TGCACCTCATATCACACATCATTT 58.805 37.500 0.00 0.00 0.00 2.32
1884 3971 6.355747 TGCACCTCATATCACACATCATTTA 58.644 36.000 0.00 0.00 0.00 1.40
1885 3972 6.999871 TGCACCTCATATCACACATCATTTAT 59.000 34.615 0.00 0.00 0.00 1.40
1886 3973 7.040961 TGCACCTCATATCACACATCATTTATG 60.041 37.037 0.00 0.00 41.74 1.90
1899 3986 5.722263 CATCATTTATGTGCTTTGGGTTCA 58.278 37.500 0.00 0.00 0.00 3.18
1900 3987 5.389859 TCATTTATGTGCTTTGGGTTCAG 57.610 39.130 0.00 0.00 0.00 3.02
1901 3988 4.832266 TCATTTATGTGCTTTGGGTTCAGT 59.168 37.500 0.00 0.00 0.00 3.41
1902 3989 6.007076 TCATTTATGTGCTTTGGGTTCAGTA 58.993 36.000 0.00 0.00 0.00 2.74
1903 3990 6.491745 TCATTTATGTGCTTTGGGTTCAGTAA 59.508 34.615 0.00 0.00 0.00 2.24
1904 3991 5.957842 TTATGTGCTTTGGGTTCAGTAAG 57.042 39.130 0.00 0.00 0.00 2.34
1905 3992 3.569194 TGTGCTTTGGGTTCAGTAAGA 57.431 42.857 0.00 0.00 0.00 2.10
1906 3993 3.476552 TGTGCTTTGGGTTCAGTAAGAG 58.523 45.455 0.00 0.00 0.00 2.85
1907 3994 2.814336 GTGCTTTGGGTTCAGTAAGAGG 59.186 50.000 0.00 0.00 0.00 3.69
1908 3995 2.708861 TGCTTTGGGTTCAGTAAGAGGA 59.291 45.455 0.00 0.00 0.00 3.71
1909 3996 3.330701 TGCTTTGGGTTCAGTAAGAGGAT 59.669 43.478 0.00 0.00 0.00 3.24
1910 3997 4.202567 TGCTTTGGGTTCAGTAAGAGGATT 60.203 41.667 0.00 0.00 0.00 3.01
1911 3998 4.767409 GCTTTGGGTTCAGTAAGAGGATTT 59.233 41.667 0.00 0.00 0.00 2.17
1912 3999 5.243954 GCTTTGGGTTCAGTAAGAGGATTTT 59.756 40.000 0.00 0.00 0.00 1.82
1913 4000 6.648879 TTTGGGTTCAGTAAGAGGATTTTG 57.351 37.500 0.00 0.00 0.00 2.44
1914 4001 5.319043 TGGGTTCAGTAAGAGGATTTTGT 57.681 39.130 0.00 0.00 0.00 2.83
1915 4002 6.442541 TGGGTTCAGTAAGAGGATTTTGTA 57.557 37.500 0.00 0.00 0.00 2.41
1916 4003 6.843752 TGGGTTCAGTAAGAGGATTTTGTAA 58.156 36.000 0.00 0.00 0.00 2.41
1917 4004 7.466804 TGGGTTCAGTAAGAGGATTTTGTAAT 58.533 34.615 0.00 0.00 0.00 1.89
1918 4005 7.947890 TGGGTTCAGTAAGAGGATTTTGTAATT 59.052 33.333 0.00 0.00 0.00 1.40
1919 4006 8.803235 GGGTTCAGTAAGAGGATTTTGTAATTT 58.197 33.333 0.00 0.00 0.00 1.82
1920 4007 9.626045 GGTTCAGTAAGAGGATTTTGTAATTTG 57.374 33.333 0.00 0.00 0.00 2.32
1936 4023 9.474920 TTTGTAATTTGTTTCTCATTAAGCTGG 57.525 29.630 0.00 0.00 0.00 4.85
1937 4024 7.601856 TGTAATTTGTTTCTCATTAAGCTGGG 58.398 34.615 0.00 0.00 0.00 4.45
1938 4025 6.670695 AATTTGTTTCTCATTAAGCTGGGT 57.329 33.333 0.00 0.00 0.00 4.51
1939 4026 5.452078 TTTGTTTCTCATTAAGCTGGGTG 57.548 39.130 0.00 0.00 0.00 4.61
1940 4027 2.819608 TGTTTCTCATTAAGCTGGGTGC 59.180 45.455 0.00 0.00 43.29 5.01
1941 4028 2.128771 TTCTCATTAAGCTGGGTGCC 57.871 50.000 0.00 0.00 44.23 5.01
1942 4029 1.289160 TCTCATTAAGCTGGGTGCCT 58.711 50.000 0.00 0.00 44.23 4.75
1943 4030 1.635487 TCTCATTAAGCTGGGTGCCTT 59.365 47.619 0.00 0.00 44.23 4.35
1944 4031 2.019984 CTCATTAAGCTGGGTGCCTTC 58.980 52.381 0.00 0.00 44.23 3.46
1945 4032 1.354031 TCATTAAGCTGGGTGCCTTCA 59.646 47.619 0.00 0.00 44.23 3.02
1946 4033 1.474077 CATTAAGCTGGGTGCCTTCAC 59.526 52.381 0.00 0.00 44.23 3.18
1947 4034 0.476338 TTAAGCTGGGTGCCTTCACA 59.524 50.000 0.00 0.00 44.87 3.58
1948 4035 0.250727 TAAGCTGGGTGCCTTCACAC 60.251 55.000 0.00 0.00 46.66 3.82
1953 4040 3.346426 GGGTGCCTTCACACATTCT 57.654 52.632 0.00 0.00 45.79 2.40
1954 4041 0.883833 GGGTGCCTTCACACATTCTG 59.116 55.000 0.00 0.00 45.79 3.02
1955 4042 0.242017 GGTGCCTTCACACATTCTGC 59.758 55.000 0.00 0.00 44.87 4.26
1956 4043 1.242076 GTGCCTTCACACATTCTGCT 58.758 50.000 0.00 0.00 42.66 4.24
1957 4044 1.198637 GTGCCTTCACACATTCTGCTC 59.801 52.381 0.00 0.00 42.66 4.26
1958 4045 0.807496 GCCTTCACACATTCTGCTCC 59.193 55.000 0.00 0.00 0.00 4.70
1959 4046 1.457346 CCTTCACACATTCTGCTCCC 58.543 55.000 0.00 0.00 0.00 4.30
1960 4047 1.271543 CCTTCACACATTCTGCTCCCA 60.272 52.381 0.00 0.00 0.00 4.37
1961 4048 1.808945 CTTCACACATTCTGCTCCCAC 59.191 52.381 0.00 0.00 0.00 4.61
1962 4049 0.036732 TCACACATTCTGCTCCCACC 59.963 55.000 0.00 0.00 0.00 4.61
1963 4050 1.003355 ACACATTCTGCTCCCACCG 60.003 57.895 0.00 0.00 0.00 4.94
1964 4051 1.296392 CACATTCTGCTCCCACCGA 59.704 57.895 0.00 0.00 0.00 4.69
1965 4052 0.107508 CACATTCTGCTCCCACCGAT 60.108 55.000 0.00 0.00 0.00 4.18
1966 4053 1.138859 CACATTCTGCTCCCACCGATA 59.861 52.381 0.00 0.00 0.00 2.92
1967 4054 1.414181 ACATTCTGCTCCCACCGATAG 59.586 52.381 0.00 0.00 0.00 2.08
2006 4093 9.908152 AACATAATTAGTTAACTTCAGTTTGCC 57.092 29.630 14.49 0.00 39.31 4.52
2020 4107 8.028938 ACTTCAGTTTGCCATTATGTGATTTAC 58.971 33.333 0.00 0.00 0.00 2.01
2251 4347 1.951209 TGCTATTCCAGACCCACTCA 58.049 50.000 0.00 0.00 0.00 3.41
2284 4380 3.865011 TGAGAAGCTTGAGACTAGCAG 57.135 47.619 2.10 0.00 41.11 4.24
2376 4472 0.545171 CAGTGGATCATGGCCAGAGT 59.455 55.000 13.05 0.00 35.77 3.24
2430 4526 5.121105 CCAGCATAGATCACATGAAAGTCA 58.879 41.667 0.00 0.00 0.00 3.41
2486 4582 0.527113 CCGCTGATGGCAATGTTCAA 59.473 50.000 0.00 0.00 41.91 2.69
2525 4621 0.601046 CTGTCGAGCTTGCTGGTGAA 60.601 55.000 0.00 0.00 0.00 3.18
2628 4724 1.139058 AGCCATGGTATCCTCAACGTC 59.861 52.381 14.67 0.00 0.00 4.34
2748 4844 3.788227 TGGTTGTTGCTCACTTATCCT 57.212 42.857 0.00 0.00 0.00 3.24
2978 5090 6.563222 AAAATCAATGGCAATCAAAACTGG 57.437 33.333 0.00 0.00 0.00 4.00
2988 5100 4.933400 GCAATCAAAACTGGAGCATTCAAT 59.067 37.500 0.00 0.00 0.00 2.57
2989 5101 5.410439 GCAATCAAAACTGGAGCATTCAATT 59.590 36.000 0.00 0.00 0.00 2.32
2996 5108 5.998454 ACTGGAGCATTCAATTATCTTCG 57.002 39.130 0.00 0.00 0.00 3.79
2999 5111 6.480320 ACTGGAGCATTCAATTATCTTCGTAC 59.520 38.462 0.00 0.00 0.00 3.67
3050 5162 4.143115 GGTCACTGTCACATTTATCACACG 60.143 45.833 0.00 0.00 0.00 4.49
3095 6149 4.164796 ACTCATTATCCATCAGCAGGAACA 59.835 41.667 0.00 0.00 38.93 3.18
3212 6266 1.819632 GCAAATCGTCCGGCCTCAT 60.820 57.895 0.00 0.00 0.00 2.90
3224 6278 1.548719 CGGCCTCATCCGGATACATTA 59.451 52.381 18.63 0.00 45.38 1.90
3229 6322 6.177610 GGCCTCATCCGGATACATTAATTTA 58.822 40.000 18.63 0.00 0.00 1.40
3432 6533 3.208594 CTTGCATAGATGGCTTAGCACA 58.791 45.455 6.53 1.96 34.04 4.57
3589 6700 4.381718 CCGAGGTTAATCTTCTTCTCCGTT 60.382 45.833 0.00 0.00 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.016627 GTGGATGTATGTGCGCATGT 58.983 50.000 22.84 8.20 36.58 3.21
32 33 1.024579 GCGTGTGTTCATAGGGGTGG 61.025 60.000 0.00 0.00 0.00 4.61
35 36 1.016627 CATGCGTGTGTTCATAGGGG 58.983 55.000 0.00 0.00 0.00 4.79
36 37 0.378257 GCATGCGTGTGTTCATAGGG 59.622 55.000 0.00 0.00 0.00 3.53
62 63 3.070159 TGCTCATAGAGGGTAAGATGTGC 59.930 47.826 0.00 0.00 38.59 4.57
69 70 3.719871 TGAAGGTGCTCATAGAGGGTAA 58.280 45.455 0.00 0.00 0.00 2.85
100 101 4.586421 TCACTCTCAGGATAATGTGCTAGG 59.414 45.833 0.00 0.00 0.00 3.02
120 121 2.120232 CGTCTATGGCGACTTCATCAC 58.880 52.381 0.00 0.00 0.00 3.06
141 142 6.258068 GGAGACATTTCCGTTGACTATAAAGG 59.742 42.308 0.00 0.00 0.00 3.11
157 158 2.289694 CGTTCAGTGGGAGGAGACATTT 60.290 50.000 0.00 0.00 0.00 2.32
206 207 0.251121 TGGGGCTCGCATTTTTCTGA 60.251 50.000 0.00 0.00 0.00 3.27
222 223 1.340114 GGTTCAAGCCCTAGACTTGGG 60.340 57.143 16.93 16.93 43.79 4.12
463 472 1.696988 ACCAAAAATGTCGAATGCGC 58.303 45.000 0.00 0.00 37.46 6.09
1038 3011 2.034048 GAATCTCGCAGGGGAGGGTC 62.034 65.000 12.65 7.29 34.74 4.46
1044 3017 1.227089 CTCACGAATCTCGCAGGGG 60.227 63.158 0.00 0.00 45.12 4.79
1047 3020 3.698382 GCCTCACGAATCTCGCAG 58.302 61.111 0.00 0.00 45.12 5.18
1068 3041 4.894114 GCCTTATCCTTGTCTAGTACCTCA 59.106 45.833 0.00 0.00 0.00 3.86
1077 3050 0.466124 GCTCGGCCTTATCCTTGTCT 59.534 55.000 0.00 0.00 0.00 3.41
1095 3167 1.958205 CGCAATCTCCTGGATCCGC 60.958 63.158 7.39 0.28 32.76 5.54
1241 3313 2.481276 CGGCGACACCTATCTTCATCAA 60.481 50.000 0.00 0.00 35.61 2.57
1296 3368 4.876107 GGCTTACTGAAATCATCGAAGGAA 59.124 41.667 0.00 0.00 0.00 3.36
1328 3400 1.539388 TCATCGTTGCCAAGCGAATTT 59.461 42.857 6.29 0.00 40.61 1.82
1370 3442 6.127647 GCATAAACATGAGGGACTTTGATCAA 60.128 38.462 3.38 3.38 41.55 2.57
1372 3444 5.504665 CGCATAAACATGAGGGACTTTGATC 60.505 44.000 0.00 0.00 41.55 2.92
1379 3451 1.064060 GCACGCATAAACATGAGGGAC 59.936 52.381 0.00 0.00 0.00 4.46
1386 3458 2.977914 AGACTCTGCACGCATAAACAT 58.022 42.857 0.00 0.00 0.00 2.71
1388 3460 3.491267 GGATAGACTCTGCACGCATAAAC 59.509 47.826 0.00 0.00 0.00 2.01
1402 3474 1.050988 ACGCATGGCTGGGATAGACT 61.051 55.000 0.00 0.00 38.61 3.24
1472 3544 6.457934 CCATGACTTCGATTGAAAAGATCTGG 60.458 42.308 0.00 0.00 32.66 3.86
1505 3577 3.552068 GCGGCCACTCTAATTTTTGTTGT 60.552 43.478 2.24 0.00 0.00 3.32
1508 3580 2.228822 CAGCGGCCACTCTAATTTTTGT 59.771 45.455 2.24 0.00 0.00 2.83
1608 3694 2.174360 CTCCTCACTGATGGTCTGACA 58.826 52.381 10.38 0.00 0.00 3.58
1639 3725 7.754475 GCCAAATAATTAAAATTTGCCAAGTGG 59.246 33.333 15.93 0.00 41.11 4.00
1658 3745 4.127171 GCATAGAAGAACCGAGCCAAATA 58.873 43.478 0.00 0.00 0.00 1.40
1662 3749 1.195115 AGCATAGAAGAACCGAGCCA 58.805 50.000 0.00 0.00 0.00 4.75
1663 3750 2.317530 AAGCATAGAAGAACCGAGCC 57.682 50.000 0.00 0.00 0.00 4.70
1664 3751 3.062774 GTGAAAGCATAGAAGAACCGAGC 59.937 47.826 0.00 0.00 0.00 5.03
1665 3752 4.328440 CAGTGAAAGCATAGAAGAACCGAG 59.672 45.833 0.00 0.00 0.00 4.63
1666 3753 4.021456 TCAGTGAAAGCATAGAAGAACCGA 60.021 41.667 0.00 0.00 0.00 4.69
1667 3754 4.245660 TCAGTGAAAGCATAGAAGAACCG 58.754 43.478 0.00 0.00 0.00 4.44
1668 3755 4.094146 GCTCAGTGAAAGCATAGAAGAACC 59.906 45.833 0.00 0.00 39.61 3.62
1669 3756 4.692625 TGCTCAGTGAAAGCATAGAAGAAC 59.307 41.667 3.07 0.00 44.51 3.01
1670 3757 4.898320 TGCTCAGTGAAAGCATAGAAGAA 58.102 39.130 3.07 0.00 44.51 2.52
1671 3758 4.541973 TGCTCAGTGAAAGCATAGAAGA 57.458 40.909 3.07 0.00 44.51 2.87
1679 3766 2.072298 CTAGTGGTGCTCAGTGAAAGC 58.928 52.381 0.00 0.00 40.26 3.51
1680 3767 3.321497 GTCTAGTGGTGCTCAGTGAAAG 58.679 50.000 0.00 0.00 0.00 2.62
1681 3768 2.037251 GGTCTAGTGGTGCTCAGTGAAA 59.963 50.000 0.00 0.00 0.00 2.69
1682 3769 1.618837 GGTCTAGTGGTGCTCAGTGAA 59.381 52.381 0.00 0.00 0.00 3.18
1683 3770 1.203063 AGGTCTAGTGGTGCTCAGTGA 60.203 52.381 0.00 0.00 0.00 3.41
1684 3771 1.203523 GAGGTCTAGTGGTGCTCAGTG 59.796 57.143 0.00 0.00 0.00 3.66
1685 3772 1.551452 GAGGTCTAGTGGTGCTCAGT 58.449 55.000 0.00 0.00 0.00 3.41
1686 3773 0.820871 GGAGGTCTAGTGGTGCTCAG 59.179 60.000 0.00 0.00 0.00 3.35
1687 3774 0.114364 TGGAGGTCTAGTGGTGCTCA 59.886 55.000 0.00 0.00 0.00 4.26
1688 3775 1.490574 ATGGAGGTCTAGTGGTGCTC 58.509 55.000 0.00 0.00 0.00 4.26
1689 3776 1.958288 AATGGAGGTCTAGTGGTGCT 58.042 50.000 0.00 0.00 0.00 4.40
1690 3777 3.798202 CTTAATGGAGGTCTAGTGGTGC 58.202 50.000 0.00 0.00 0.00 5.01
1691 3778 3.452627 AGCTTAATGGAGGTCTAGTGGTG 59.547 47.826 0.00 0.00 0.00 4.17
1692 3779 3.452627 CAGCTTAATGGAGGTCTAGTGGT 59.547 47.826 0.00 0.00 0.00 4.16
1693 3780 3.706594 TCAGCTTAATGGAGGTCTAGTGG 59.293 47.826 0.00 0.00 0.00 4.00
1694 3781 5.543507 ATCAGCTTAATGGAGGTCTAGTG 57.456 43.478 0.00 0.00 0.00 2.74
1695 3782 6.567602 AAATCAGCTTAATGGAGGTCTAGT 57.432 37.500 0.00 0.00 0.00 2.57
1696 3783 8.964476 TTTAAATCAGCTTAATGGAGGTCTAG 57.036 34.615 0.00 0.00 0.00 2.43
1697 3784 9.342308 CATTTAAATCAGCTTAATGGAGGTCTA 57.658 33.333 0.00 0.00 0.00 2.59
1698 3785 7.836183 ACATTTAAATCAGCTTAATGGAGGTCT 59.164 33.333 0.00 0.00 0.00 3.85
1699 3786 7.917505 CACATTTAAATCAGCTTAATGGAGGTC 59.082 37.037 0.00 0.00 0.00 3.85
1700 3787 7.615365 TCACATTTAAATCAGCTTAATGGAGGT 59.385 33.333 0.00 0.00 0.00 3.85
1701 3788 7.999679 TCACATTTAAATCAGCTTAATGGAGG 58.000 34.615 0.00 0.00 0.00 4.30
1732 3819 9.712305 CTGAAATCCCTGATTAAATCGTATACT 57.288 33.333 0.56 0.00 31.46 2.12
1733 3820 9.490379 ACTGAAATCCCTGATTAAATCGTATAC 57.510 33.333 0.00 0.00 31.46 1.47
1734 3821 9.706691 GACTGAAATCCCTGATTAAATCGTATA 57.293 33.333 0.00 0.00 31.46 1.47
1735 3822 7.661847 GGACTGAAATCCCTGATTAAATCGTAT 59.338 37.037 0.00 0.00 31.46 3.06
1736 3823 6.990349 GGACTGAAATCCCTGATTAAATCGTA 59.010 38.462 0.00 0.00 31.46 3.43
1737 3824 5.823045 GGACTGAAATCCCTGATTAAATCGT 59.177 40.000 0.00 0.00 31.46 3.73
1738 3825 6.305693 GGACTGAAATCCCTGATTAAATCG 57.694 41.667 0.00 0.00 31.46 3.34
1750 3837 0.323451 GTGGGTGGGGACTGAAATCC 60.323 60.000 0.00 0.00 38.13 3.01
1751 3838 0.404040 TGTGGGTGGGGACTGAAATC 59.596 55.000 0.00 0.00 0.00 2.17
1752 3839 0.856982 TTGTGGGTGGGGACTGAAAT 59.143 50.000 0.00 0.00 0.00 2.17
1753 3840 0.184933 CTTGTGGGTGGGGACTGAAA 59.815 55.000 0.00 0.00 0.00 2.69
1754 3841 0.696143 TCTTGTGGGTGGGGACTGAA 60.696 55.000 0.00 0.00 0.00 3.02
1755 3842 0.696143 TTCTTGTGGGTGGGGACTGA 60.696 55.000 0.00 0.00 0.00 3.41
1756 3843 0.537371 GTTCTTGTGGGTGGGGACTG 60.537 60.000 0.00 0.00 0.00 3.51
1757 3844 0.991355 TGTTCTTGTGGGTGGGGACT 60.991 55.000 0.00 0.00 0.00 3.85
1758 3845 0.537371 CTGTTCTTGTGGGTGGGGAC 60.537 60.000 0.00 0.00 0.00 4.46
1759 3846 0.696143 TCTGTTCTTGTGGGTGGGGA 60.696 55.000 0.00 0.00 0.00 4.81
1760 3847 0.184933 TTCTGTTCTTGTGGGTGGGG 59.815 55.000 0.00 0.00 0.00 4.96
1761 3848 1.888512 CATTCTGTTCTTGTGGGTGGG 59.111 52.381 0.00 0.00 0.00 4.61
1762 3849 2.294233 CACATTCTGTTCTTGTGGGTGG 59.706 50.000 0.00 0.00 37.64 4.61
1763 3850 3.213506 TCACATTCTGTTCTTGTGGGTG 58.786 45.455 2.80 0.00 40.82 4.61
1764 3851 3.576078 TCACATTCTGTTCTTGTGGGT 57.424 42.857 2.80 0.00 40.82 4.51
1765 3852 5.458041 AAATCACATTCTGTTCTTGTGGG 57.542 39.130 2.80 0.00 40.82 4.61
1766 3853 6.506147 TGAAAATCACATTCTGTTCTTGTGG 58.494 36.000 2.80 0.00 40.82 4.17
1767 3854 7.916977 TCTTGAAAATCACATTCTGTTCTTGTG 59.083 33.333 0.00 0.00 41.60 3.33
1768 3855 7.999679 TCTTGAAAATCACATTCTGTTCTTGT 58.000 30.769 0.00 0.00 0.00 3.16
1769 3856 9.472361 AATCTTGAAAATCACATTCTGTTCTTG 57.528 29.630 0.00 0.00 0.00 3.02
1779 3866 9.525409 GCAAGCTTATAATCTTGAAAATCACAT 57.475 29.630 25.83 0.00 41.50 3.21
1780 3867 8.742777 AGCAAGCTTATAATCTTGAAAATCACA 58.257 29.630 25.83 0.00 41.50 3.58
1792 3879 8.825745 GCCATAAGATCTAGCAAGCTTATAATC 58.174 37.037 0.00 0.00 33.20 1.75
1793 3880 8.324306 TGCCATAAGATCTAGCAAGCTTATAAT 58.676 33.333 0.00 0.00 33.20 1.28
1794 3881 7.604164 GTGCCATAAGATCTAGCAAGCTTATAA 59.396 37.037 0.00 0.00 34.79 0.98
1795 3882 7.099764 GTGCCATAAGATCTAGCAAGCTTATA 58.900 38.462 0.00 0.00 34.79 0.98
1796 3883 5.936956 GTGCCATAAGATCTAGCAAGCTTAT 59.063 40.000 0.00 0.00 34.79 1.73
1797 3884 5.163311 TGTGCCATAAGATCTAGCAAGCTTA 60.163 40.000 0.00 0.00 34.79 3.09
1798 3885 4.133078 GTGCCATAAGATCTAGCAAGCTT 58.867 43.478 10.22 0.00 34.79 3.74
1799 3886 3.135348 TGTGCCATAAGATCTAGCAAGCT 59.865 43.478 10.22 0.00 34.79 3.74
1800 3887 3.470709 TGTGCCATAAGATCTAGCAAGC 58.529 45.455 10.22 4.90 34.79 4.01
1801 3888 6.630444 ATTTGTGCCATAAGATCTAGCAAG 57.370 37.500 10.22 0.00 34.79 4.01
1802 3889 7.308770 GCATATTTGTGCCATAAGATCTAGCAA 60.309 37.037 10.22 0.66 39.18 3.91
1803 3890 6.149973 GCATATTTGTGCCATAAGATCTAGCA 59.850 38.462 0.00 0.22 39.18 3.49
1804 3891 6.373774 AGCATATTTGTGCCATAAGATCTAGC 59.626 38.462 0.00 0.00 46.19 3.42
1805 3892 7.918536 AGCATATTTGTGCCATAAGATCTAG 57.081 36.000 0.00 0.00 46.19 2.43
1806 3893 7.824289 GGTAGCATATTTGTGCCATAAGATCTA 59.176 37.037 0.00 0.00 46.19 1.98
1807 3894 6.656693 GGTAGCATATTTGTGCCATAAGATCT 59.343 38.462 0.00 0.00 46.19 2.75
1808 3895 6.127897 GGGTAGCATATTTGTGCCATAAGATC 60.128 42.308 0.00 0.00 46.19 2.75
1809 3896 5.711976 GGGTAGCATATTTGTGCCATAAGAT 59.288 40.000 0.00 0.00 46.19 2.40
1810 3897 5.070001 GGGTAGCATATTTGTGCCATAAGA 58.930 41.667 0.00 0.00 46.19 2.10
1811 3898 5.048504 CAGGGTAGCATATTTGTGCCATAAG 60.049 44.000 0.00 0.00 46.19 1.73
1812 3899 4.826733 CAGGGTAGCATATTTGTGCCATAA 59.173 41.667 0.00 0.00 46.19 1.90
1813 3900 4.103943 TCAGGGTAGCATATTTGTGCCATA 59.896 41.667 0.00 0.00 46.19 2.74
1814 3901 3.117550 TCAGGGTAGCATATTTGTGCCAT 60.118 43.478 0.00 0.00 46.19 4.40
1815 3902 2.240921 TCAGGGTAGCATATTTGTGCCA 59.759 45.455 0.00 0.00 46.19 4.92
1816 3903 2.618709 GTCAGGGTAGCATATTTGTGCC 59.381 50.000 0.00 0.00 46.19 5.01
1817 3904 3.545703 AGTCAGGGTAGCATATTTGTGC 58.454 45.455 0.00 0.00 45.38 4.57
1818 3905 7.220030 AGAATAGTCAGGGTAGCATATTTGTG 58.780 38.462 0.00 0.00 0.00 3.33
1819 3906 7.380423 AGAATAGTCAGGGTAGCATATTTGT 57.620 36.000 0.00 0.00 0.00 2.83
1820 3907 6.876257 GGAGAATAGTCAGGGTAGCATATTTG 59.124 42.308 0.00 0.00 0.00 2.32
1821 3908 6.013293 GGGAGAATAGTCAGGGTAGCATATTT 60.013 42.308 0.00 0.00 0.00 1.40
1822 3909 5.485708 GGGAGAATAGTCAGGGTAGCATATT 59.514 44.000 0.00 0.00 0.00 1.28
1823 3910 5.026790 GGGAGAATAGTCAGGGTAGCATAT 58.973 45.833 0.00 0.00 0.00 1.78
1824 3911 4.140782 TGGGAGAATAGTCAGGGTAGCATA 60.141 45.833 0.00 0.00 0.00 3.14
1825 3912 3.243724 GGGAGAATAGTCAGGGTAGCAT 58.756 50.000 0.00 0.00 0.00 3.79
1826 3913 2.023404 TGGGAGAATAGTCAGGGTAGCA 60.023 50.000 0.00 0.00 0.00 3.49
1827 3914 2.679082 TGGGAGAATAGTCAGGGTAGC 58.321 52.381 0.00 0.00 0.00 3.58
1828 3915 3.508012 CGATGGGAGAATAGTCAGGGTAG 59.492 52.174 0.00 0.00 0.00 3.18
1829 3916 3.117246 ACGATGGGAGAATAGTCAGGGTA 60.117 47.826 0.00 0.00 0.00 3.69
1830 3917 2.320781 CGATGGGAGAATAGTCAGGGT 58.679 52.381 0.00 0.00 0.00 4.34
1831 3918 2.036475 CACGATGGGAGAATAGTCAGGG 59.964 54.545 0.00 0.00 0.00 4.45
1832 3919 2.546795 GCACGATGGGAGAATAGTCAGG 60.547 54.545 0.00 0.00 0.00 3.86
1833 3920 2.363680 AGCACGATGGGAGAATAGTCAG 59.636 50.000 0.00 0.00 0.00 3.51
1834 3921 2.388735 AGCACGATGGGAGAATAGTCA 58.611 47.619 0.00 0.00 0.00 3.41
1835 3922 3.126831 CAAGCACGATGGGAGAATAGTC 58.873 50.000 0.00 0.00 0.00 2.59
1836 3923 2.501723 ACAAGCACGATGGGAGAATAGT 59.498 45.455 0.00 0.00 0.00 2.12
1837 3924 3.185246 ACAAGCACGATGGGAGAATAG 57.815 47.619 0.00 0.00 0.00 1.73
1838 3925 4.746535 TTACAAGCACGATGGGAGAATA 57.253 40.909 0.00 0.00 0.00 1.75
1839 3926 3.627395 TTACAAGCACGATGGGAGAAT 57.373 42.857 0.00 0.00 0.00 2.40
1840 3927 3.270027 CATTACAAGCACGATGGGAGAA 58.730 45.455 0.00 0.00 0.00 2.87
1841 3928 2.905075 CATTACAAGCACGATGGGAGA 58.095 47.619 0.00 0.00 0.00 3.71
1842 3929 1.331756 GCATTACAAGCACGATGGGAG 59.668 52.381 0.00 0.00 0.00 4.30
1843 3930 1.339535 TGCATTACAAGCACGATGGGA 60.340 47.619 0.00 0.00 37.02 4.37
1844 3931 1.093972 TGCATTACAAGCACGATGGG 58.906 50.000 0.00 0.00 37.02 4.00
1851 3938 4.576053 GTGATATGAGGTGCATTACAAGCA 59.424 41.667 0.00 0.00 38.44 3.91
1852 3939 4.576053 TGTGATATGAGGTGCATTACAAGC 59.424 41.667 0.00 0.00 38.44 4.01
1853 3940 5.585844 TGTGTGATATGAGGTGCATTACAAG 59.414 40.000 0.00 0.00 38.44 3.16
1854 3941 5.495640 TGTGTGATATGAGGTGCATTACAA 58.504 37.500 0.00 0.00 38.44 2.41
1855 3942 5.096443 TGTGTGATATGAGGTGCATTACA 57.904 39.130 0.00 0.00 38.44 2.41
1856 3943 5.759763 TGATGTGTGATATGAGGTGCATTAC 59.240 40.000 0.00 0.00 38.44 1.89
1857 3944 5.927819 TGATGTGTGATATGAGGTGCATTA 58.072 37.500 0.00 0.00 38.44 1.90
1858 3945 4.784177 TGATGTGTGATATGAGGTGCATT 58.216 39.130 0.00 0.00 38.44 3.56
1859 3946 4.426736 TGATGTGTGATATGAGGTGCAT 57.573 40.909 0.00 0.00 41.08 3.96
1860 3947 3.910568 TGATGTGTGATATGAGGTGCA 57.089 42.857 0.00 0.00 0.00 4.57
1861 3948 5.762825 AAATGATGTGTGATATGAGGTGC 57.237 39.130 0.00 0.00 0.00 5.01
1876 3963 5.722263 TGAACCCAAAGCACATAAATGATG 58.278 37.500 0.00 0.00 41.79 3.07
1877 3964 5.481473 ACTGAACCCAAAGCACATAAATGAT 59.519 36.000 0.00 0.00 0.00 2.45
1878 3965 4.832266 ACTGAACCCAAAGCACATAAATGA 59.168 37.500 0.00 0.00 0.00 2.57
1879 3966 5.138125 ACTGAACCCAAAGCACATAAATG 57.862 39.130 0.00 0.00 0.00 2.32
1880 3967 6.719370 TCTTACTGAACCCAAAGCACATAAAT 59.281 34.615 0.00 0.00 0.00 1.40
1881 3968 6.065374 TCTTACTGAACCCAAAGCACATAAA 58.935 36.000 0.00 0.00 0.00 1.40
1882 3969 5.626142 TCTTACTGAACCCAAAGCACATAA 58.374 37.500 0.00 0.00 0.00 1.90
1883 3970 5.235850 TCTTACTGAACCCAAAGCACATA 57.764 39.130 0.00 0.00 0.00 2.29
1884 3971 4.074970 CTCTTACTGAACCCAAAGCACAT 58.925 43.478 0.00 0.00 0.00 3.21
1885 3972 3.476552 CTCTTACTGAACCCAAAGCACA 58.523 45.455 0.00 0.00 0.00 4.57
1886 3973 2.814336 CCTCTTACTGAACCCAAAGCAC 59.186 50.000 0.00 0.00 0.00 4.40
1887 3974 2.708861 TCCTCTTACTGAACCCAAAGCA 59.291 45.455 0.00 0.00 0.00 3.91
1888 3975 3.418684 TCCTCTTACTGAACCCAAAGC 57.581 47.619 0.00 0.00 0.00 3.51
1889 3976 6.265422 ACAAAATCCTCTTACTGAACCCAAAG 59.735 38.462 0.00 0.00 0.00 2.77
1890 3977 6.133356 ACAAAATCCTCTTACTGAACCCAAA 58.867 36.000 0.00 0.00 0.00 3.28
1891 3978 5.701224 ACAAAATCCTCTTACTGAACCCAA 58.299 37.500 0.00 0.00 0.00 4.12
1892 3979 5.319043 ACAAAATCCTCTTACTGAACCCA 57.681 39.130 0.00 0.00 0.00 4.51
1893 3980 7.939784 ATTACAAAATCCTCTTACTGAACCC 57.060 36.000 0.00 0.00 0.00 4.11
1894 3981 9.626045 CAAATTACAAAATCCTCTTACTGAACC 57.374 33.333 0.00 0.00 0.00 3.62
1910 3997 9.474920 CCAGCTTAATGAGAAACAAATTACAAA 57.525 29.630 0.00 0.00 0.00 2.83
1911 3998 8.087750 CCCAGCTTAATGAGAAACAAATTACAA 58.912 33.333 0.00 0.00 0.00 2.41
1912 3999 7.232534 ACCCAGCTTAATGAGAAACAAATTACA 59.767 33.333 0.00 0.00 0.00 2.41
1913 4000 7.542130 CACCCAGCTTAATGAGAAACAAATTAC 59.458 37.037 0.00 0.00 0.00 1.89
1914 4001 7.601856 CACCCAGCTTAATGAGAAACAAATTA 58.398 34.615 0.00 0.00 0.00 1.40
1915 4002 6.458210 CACCCAGCTTAATGAGAAACAAATT 58.542 36.000 0.00 0.00 0.00 1.82
1916 4003 5.567423 GCACCCAGCTTAATGAGAAACAAAT 60.567 40.000 0.00 0.00 41.15 2.32
1917 4004 4.261994 GCACCCAGCTTAATGAGAAACAAA 60.262 41.667 0.00 0.00 41.15 2.83
1918 4005 3.255642 GCACCCAGCTTAATGAGAAACAA 59.744 43.478 0.00 0.00 41.15 2.83
1919 4006 2.819608 GCACCCAGCTTAATGAGAAACA 59.180 45.455 0.00 0.00 41.15 2.83
1920 4007 2.164422 GGCACCCAGCTTAATGAGAAAC 59.836 50.000 0.00 0.00 44.79 2.78
1921 4008 2.041620 AGGCACCCAGCTTAATGAGAAA 59.958 45.455 0.00 0.00 44.79 2.52
1922 4009 1.635487 AGGCACCCAGCTTAATGAGAA 59.365 47.619 0.00 0.00 44.79 2.87
1923 4010 1.289160 AGGCACCCAGCTTAATGAGA 58.711 50.000 0.00 0.00 44.79 3.27
1924 4011 2.019984 GAAGGCACCCAGCTTAATGAG 58.980 52.381 0.00 0.00 44.79 2.90
1925 4012 1.354031 TGAAGGCACCCAGCTTAATGA 59.646 47.619 0.00 0.00 44.79 2.57
1926 4013 1.474077 GTGAAGGCACCCAGCTTAATG 59.526 52.381 0.00 0.00 44.79 1.90
1927 4014 1.075374 TGTGAAGGCACCCAGCTTAAT 59.925 47.619 0.00 0.00 44.51 1.40
1928 4015 0.476338 TGTGAAGGCACCCAGCTTAA 59.524 50.000 0.00 0.00 44.51 1.85
1929 4016 0.250727 GTGTGAAGGCACCCAGCTTA 60.251 55.000 0.00 0.00 44.51 3.09
1930 4017 1.529244 GTGTGAAGGCACCCAGCTT 60.529 57.895 0.00 0.00 44.51 3.74
1931 4018 2.072874 ATGTGTGAAGGCACCCAGCT 62.073 55.000 0.00 0.00 44.51 4.24
1932 4019 1.181098 AATGTGTGAAGGCACCCAGC 61.181 55.000 0.00 0.00 44.51 4.85
1933 4020 0.883833 GAATGTGTGAAGGCACCCAG 59.116 55.000 0.00 0.00 44.51 4.45
1934 4021 0.478072 AGAATGTGTGAAGGCACCCA 59.522 50.000 0.00 0.00 44.51 4.51
1935 4022 0.883833 CAGAATGTGTGAAGGCACCC 59.116 55.000 0.00 0.00 44.51 4.61
1936 4023 0.242017 GCAGAATGTGTGAAGGCACC 59.758 55.000 0.00 0.00 39.71 5.01
1937 4024 1.198637 GAGCAGAATGTGTGAAGGCAC 59.801 52.381 0.00 0.00 40.46 5.01
1938 4025 1.527034 GAGCAGAATGTGTGAAGGCA 58.473 50.000 0.00 0.00 39.31 4.75
1939 4026 0.807496 GGAGCAGAATGTGTGAAGGC 59.193 55.000 0.00 0.00 39.31 4.35
1940 4027 1.271543 TGGGAGCAGAATGTGTGAAGG 60.272 52.381 0.00 0.00 39.31 3.46
1941 4028 1.808945 GTGGGAGCAGAATGTGTGAAG 59.191 52.381 0.00 0.00 39.31 3.02
1942 4029 1.545428 GGTGGGAGCAGAATGTGTGAA 60.545 52.381 0.00 0.00 39.31 3.18
1943 4030 0.036732 GGTGGGAGCAGAATGTGTGA 59.963 55.000 0.00 0.00 39.31 3.58
1944 4031 1.300971 CGGTGGGAGCAGAATGTGTG 61.301 60.000 0.00 0.00 39.31 3.82
1945 4032 1.003355 CGGTGGGAGCAGAATGTGT 60.003 57.895 0.00 0.00 39.31 3.72
1946 4033 0.107508 ATCGGTGGGAGCAGAATGTG 60.108 55.000 0.00 0.00 39.31 3.21
1947 4034 1.414181 CTATCGGTGGGAGCAGAATGT 59.586 52.381 0.00 0.00 39.31 2.71
1948 4035 1.270518 CCTATCGGTGGGAGCAGAATG 60.271 57.143 0.00 0.00 40.87 2.67
1949 4036 1.051812 CCTATCGGTGGGAGCAGAAT 58.948 55.000 0.00 0.00 0.00 2.40
1950 4037 0.325296 ACCTATCGGTGGGAGCAGAA 60.325 55.000 4.49 0.00 43.51 3.02
1951 4038 0.325296 AACCTATCGGTGGGAGCAGA 60.325 55.000 4.49 0.00 44.73 4.26
1952 4039 0.541863 AAACCTATCGGTGGGAGCAG 59.458 55.000 4.49 0.00 44.73 4.24
1953 4040 1.483415 GTAAACCTATCGGTGGGAGCA 59.517 52.381 4.49 0.00 44.73 4.26
1954 4041 1.761198 AGTAAACCTATCGGTGGGAGC 59.239 52.381 4.49 0.00 44.73 4.70
1955 4042 4.587684 ACATAGTAAACCTATCGGTGGGAG 59.412 45.833 4.49 0.00 44.73 4.30
1956 4043 4.549668 ACATAGTAAACCTATCGGTGGGA 58.450 43.478 4.49 0.00 44.73 4.37
1957 4044 4.950205 ACATAGTAAACCTATCGGTGGG 57.050 45.455 0.00 0.00 44.73 4.61
1958 4045 7.267128 TGTTAACATAGTAAACCTATCGGTGG 58.733 38.462 3.59 0.00 44.73 4.61
1959 4046 8.882415 ATGTTAACATAGTAAACCTATCGGTG 57.118 34.615 19.51 0.00 38.04 4.94
1999 4086 7.895759 ACTTGTAAATCACATAATGGCAAACT 58.104 30.769 0.00 0.00 36.90 2.66
2052 4141 4.519540 AATGGGCAACAATGTACAGTTC 57.480 40.909 0.33 0.00 39.74 3.01
2251 4347 1.871080 CTTCTCAACCAAGCGTGAGT 58.129 50.000 0.00 0.00 0.00 3.41
2284 4380 0.947244 CAACTTGAGTGTGGTGAGCC 59.053 55.000 0.00 0.00 0.00 4.70
2376 4472 5.992829 TGGCAGTAAATAAACTTCGAGAACA 59.007 36.000 0.00 0.00 0.00 3.18
2480 4576 0.375454 CACGGCGTGAAAGTTGAACA 59.625 50.000 34.85 0.00 35.23 3.18
2486 4582 1.373590 AAGCAACACGGCGTGAAAGT 61.374 50.000 42.65 20.75 39.27 2.66
2525 4621 1.757682 CCTCAGCGGAGACTCTTAGT 58.242 55.000 16.02 0.00 44.26 2.24
2628 4724 3.190874 GACTTTCATCTTACAGGAGCCG 58.809 50.000 0.00 0.00 0.00 5.52
2748 4844 8.951787 AATTACCACTACGAGCATATTTAACA 57.048 30.769 0.00 0.00 0.00 2.41
2818 4914 5.651530 ACAGGACTACACAACGAGATAATG 58.348 41.667 0.00 0.00 0.00 1.90
2978 5090 8.804688 AGTAGTACGAAGATAATTGAATGCTC 57.195 34.615 0.00 0.00 0.00 4.26
2999 5111 9.429359 CTGGAGGTAAAATGCTATTGATAGTAG 57.571 37.037 0.44 0.00 32.96 2.57
3050 5162 7.981789 TGAGTCCATGTGAAGATAATTGTACTC 59.018 37.037 0.00 0.00 0.00 2.59
3086 6140 3.119316 CGACTCTTGTATCTGTTCCTGCT 60.119 47.826 0.00 0.00 0.00 4.24
3095 6149 2.457598 TGAAGGCCGACTCTTGTATCT 58.542 47.619 0.00 0.00 0.00 1.98
3212 6266 7.867305 TGCACTTTAAATTAATGTATCCGGA 57.133 32.000 6.61 6.61 0.00 5.14
3229 6322 8.252417 TGCTATTATGATCAACATTTGCACTTT 58.748 29.630 0.00 0.00 40.07 2.66
3311 6406 3.189606 ACAACCAGTCTGGGAATATCCA 58.810 45.455 23.06 0.00 43.37 3.41
3396 6497 1.881973 TGCAAGGATGTTGAAGCACTC 59.118 47.619 0.00 0.00 0.00 3.51
3432 6533 0.107456 ATCCTGATGCGGCGAAGATT 59.893 50.000 12.98 0.00 0.00 2.40
3589 6700 4.223800 GACATCTTCATGGCGGCA 57.776 55.556 16.34 16.34 33.82 5.69


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

AutoCloner maintained by Alex Coulton.