Multiple sequence alignment - TraesCS6B01G126800

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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 TraesCS6B01G126800 chr6B 100.000 4638 0 0 1 4638 122289567 122294204 0.000000e+00 8565.0
1 TraesCS6B01G126800 chr6B 98.099 1946 34 2 1723 3665 121814398 121812453 0.000000e+00 3386.0
2 TraesCS6B01G126800 chr6B 89.286 448 25 12 1075 1505 121815167 121814726 1.470000e-149 540.0
3 TraesCS6B01G126800 chr6B 95.025 201 7 2 1500 1697 121814651 121814451 3.480000e-81 313.0
4 TraesCS6B01G126800 chr6D 93.650 3701 163 40 1 3671 48870485 48866827 0.000000e+00 5467.0
5 TraesCS6B01G126800 chr6D 96.186 1940 65 6 1720 3655 49219177 49221111 0.000000e+00 3164.0
6 TraesCS6B01G126800 chr6D 88.915 433 40 7 4210 4636 48859630 48859200 1.140000e-145 527.0
7 TraesCS6B01G126800 chr6D 85.408 466 56 10 1045 1505 49218390 49218848 1.510000e-129 473.0
8 TraesCS6B01G126800 chr6D 94.037 218 8 4 1500 1714 49218929 49219144 4.480000e-85 326.0
9 TraesCS6B01G126800 chr6D 96.610 59 2 0 3777 3835 48863431 48863373 1.060000e-16 99.0
10 TraesCS6B01G126800 chr6A 91.294 3331 188 58 374 3671 65797154 65800415 0.000000e+00 4451.0
11 TraesCS6B01G126800 chr6A 95.214 2194 84 10 1500 3673 65683920 65681728 0.000000e+00 3450.0
12 TraesCS6B01G126800 chr6A 90.000 420 21 10 1 406 65796736 65797148 1.480000e-144 523.0
13 TraesCS6B01G126800 chr6A 86.918 451 32 20 1075 1505 65684437 65683994 9.030000e-132 481.0
14 TraesCS6B01G126800 chr6A 96.000 50 2 0 512 561 65797329 65797378 1.070000e-11 82.4
15 TraesCS6B01G126800 chr5B 93.910 509 24 4 3170 3672 162833187 162833694 0.000000e+00 761.0


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 TraesCS6B01G126800 chr6B 122289567 122294204 4637 False 8565.000000 8565 100.000000 1 4638 1 chr6B.!!$F1 4637
1 TraesCS6B01G126800 chr6B 121812453 121815167 2714 True 1413.000000 3386 94.136667 1075 3665 3 chr6B.!!$R1 2590
2 TraesCS6B01G126800 chr6D 48859200 48870485 11285 True 2031.000000 5467 93.058333 1 4636 3 chr6D.!!$R1 4635
3 TraesCS6B01G126800 chr6D 49218390 49221111 2721 False 1321.000000 3164 91.877000 1045 3655 3 chr6D.!!$F1 2610
4 TraesCS6B01G126800 chr6A 65681728 65684437 2709 True 1965.500000 3450 91.066000 1075 3673 2 chr6A.!!$R1 2598
5 TraesCS6B01G126800 chr6A 65796736 65800415 3679 False 1685.466667 4451 92.431333 1 3671 3 chr6A.!!$F1 3670
6 TraesCS6B01G126800 chr5B 162833187 162833694 507 False 761.000000 761 93.910000 3170 3672 1 chr5B.!!$F1 502

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
630 678 0.030369 GGTCGGCCGTACATACAGAG 59.970 60.000 27.15 0.0 0.0 3.35 F
1247 1348 0.179215 CTGTTCGCGCAATGAGGTTC 60.179 55.000 8.75 0.0 0.0 3.62 F
1248 1349 1.134694 GTTCGCGCAATGAGGTTCC 59.865 57.895 8.75 0.0 0.0 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1706 1906 0.242825 TCGCGTCGTGGAAGAAGAAT 59.757 50.000 5.77 0.0 0.0 2.40 R
2375 2622 1.515954 CGAAGGGGAGCACGTACAT 59.484 57.895 0.00 0.0 0.0 2.29 R
3673 3934 6.927294 AATCTTCAAGACGGGAAACATATC 57.073 37.500 0.00 0.0 0.0 1.63 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
33 34 2.418976 CCAGTGCACAAGTGATCAGATG 59.581 50.000 21.04 3.40 0.00 2.90
36 37 3.007723 AGTGCACAAGTGATCAGATGAGT 59.992 43.478 21.04 0.00 0.00 3.41
104 105 2.941720 CAGTAGCCAGCTGAATTCCTTC 59.058 50.000 17.39 1.54 36.12 3.46
105 106 2.092699 AGTAGCCAGCTGAATTCCTTCC 60.093 50.000 17.39 0.00 0.00 3.46
106 107 0.998145 AGCCAGCTGAATTCCTTCCT 59.002 50.000 17.39 0.00 0.00 3.36
107 108 1.357079 AGCCAGCTGAATTCCTTCCTT 59.643 47.619 17.39 0.00 0.00 3.36
108 109 1.475682 GCCAGCTGAATTCCTTCCTTG 59.524 52.381 17.39 0.00 0.00 3.61
109 110 2.097825 CCAGCTGAATTCCTTCCTTGG 58.902 52.381 17.39 0.00 0.00 3.61
110 111 2.291153 CCAGCTGAATTCCTTCCTTGGA 60.291 50.000 17.39 0.00 31.70 3.53
306 315 4.380087 GCAGACAATATCGACACAGATACG 59.620 45.833 0.00 0.00 36.10 3.06
369 380 6.377080 TGAGATGGTTCTATACATCCACTCT 58.623 40.000 0.00 0.00 43.42 3.24
370 381 6.266330 TGAGATGGTTCTATACATCCACTCTG 59.734 42.308 0.00 0.00 43.42 3.35
383 394 2.846206 TCCACTCTGCACCATCCTATTT 59.154 45.455 0.00 0.00 0.00 1.40
390 401 4.411869 TCTGCACCATCCTATTTGTCCATA 59.588 41.667 0.00 0.00 0.00 2.74
391 402 4.460263 TGCACCATCCTATTTGTCCATAC 58.540 43.478 0.00 0.00 0.00 2.39
396 407 8.100791 GCACCATCCTATTTGTCCATACTAATA 58.899 37.037 0.00 0.00 33.83 0.98
562 610 7.601705 TTCCATGGAAAAGTTCTTCAGATTT 57.398 32.000 25.13 0.00 0.00 2.17
563 611 8.704849 TTCCATGGAAAAGTTCTTCAGATTTA 57.295 30.769 25.13 0.00 0.00 1.40
630 678 0.030369 GGTCGGCCGTACATACAGAG 59.970 60.000 27.15 0.00 0.00 3.35
641 689 6.618811 CCGTACATACAGAGTGAAAAGTACT 58.381 40.000 0.00 0.00 0.00 2.73
674 722 9.087424 TGAAATGTCAATTATGTAGAAGACGAG 57.913 33.333 0.00 0.00 0.00 4.18
711 759 9.533253 GGAATTATTTGATCCAGTTTACATTGG 57.467 33.333 0.00 0.00 35.74 3.16
724 772 1.238439 ACATTGGCAAACGACTGAGG 58.762 50.000 3.01 0.00 0.00 3.86
815 865 1.204146 ATAAGAGGTCGGCACCACAT 58.796 50.000 8.48 0.00 46.68 3.21
816 866 1.855295 TAAGAGGTCGGCACCACATA 58.145 50.000 8.48 0.00 46.68 2.29
817 867 0.981183 AAGAGGTCGGCACCACATAA 59.019 50.000 8.48 0.00 46.68 1.90
818 868 1.204146 AGAGGTCGGCACCACATAAT 58.796 50.000 8.48 0.00 46.68 1.28
819 869 1.139058 AGAGGTCGGCACCACATAATC 59.861 52.381 8.48 0.00 46.68 1.75
831 881 6.128282 GGCACCACATAATCATATAAGAACCG 60.128 42.308 0.00 0.00 0.00 4.44
850 900 5.182169 ACCGGGTTAAATTGATAAGGTCA 57.818 39.130 6.32 0.00 34.25 4.02
888 938 7.085116 CGGTAAAACGATAGCTCTAATGAGAT 58.915 38.462 0.00 0.00 40.49 2.75
1014 1081 0.907486 CAGGCATGGAGGAAGAGACA 59.093 55.000 0.00 0.00 0.00 3.41
1028 1095 1.533273 AGACACCTACCACGGCTGT 60.533 57.895 0.00 0.00 0.00 4.40
1114 1187 4.479993 ACGGCATCAGCTCCCTGC 62.480 66.667 3.60 3.60 41.70 4.85
1224 1297 0.250814 ACGAGTGAGTCTTCCGTCCT 60.251 55.000 0.00 0.00 0.00 3.85
1225 1298 0.448593 CGAGTGAGTCTTCCGTCCTC 59.551 60.000 0.00 0.00 0.00 3.71
1235 1336 1.874345 TTCCGTCCTCCTCTGTTCGC 61.874 60.000 0.00 0.00 0.00 4.70
1241 1342 1.699656 CCTCCTCTGTTCGCGCAATG 61.700 60.000 8.75 0.00 0.00 2.82
1247 1348 0.179215 CTGTTCGCGCAATGAGGTTC 60.179 55.000 8.75 0.00 0.00 3.62
1248 1349 1.134694 GTTCGCGCAATGAGGTTCC 59.865 57.895 8.75 0.00 0.00 3.62
1260 1361 3.222173 TGAGGTTCCTTGCTTGCTTAA 57.778 42.857 0.00 0.00 0.00 1.85
1267 1368 5.934043 GGTTCCTTGCTTGCTTAATGAATTT 59.066 36.000 0.00 0.00 0.00 1.82
1682 1882 2.076100 CGCAGCTCATTGTCAAGGTAA 58.924 47.619 0.00 0.00 0.00 2.85
1683 1883 2.679837 CGCAGCTCATTGTCAAGGTAAT 59.320 45.455 0.00 0.00 0.00 1.89
1684 1884 3.871006 CGCAGCTCATTGTCAAGGTAATA 59.129 43.478 0.00 0.00 0.00 0.98
1685 1885 4.332543 CGCAGCTCATTGTCAAGGTAATAA 59.667 41.667 0.00 0.00 0.00 1.40
1686 1886 5.008019 CGCAGCTCATTGTCAAGGTAATAAT 59.992 40.000 0.00 0.00 0.00 1.28
1687 1887 6.458751 CGCAGCTCATTGTCAAGGTAATAATT 60.459 38.462 0.00 0.00 0.00 1.40
1688 1888 7.254761 CGCAGCTCATTGTCAAGGTAATAATTA 60.255 37.037 0.00 0.00 0.00 1.40
1689 1889 8.405531 GCAGCTCATTGTCAAGGTAATAATTAA 58.594 33.333 0.00 0.00 0.00 1.40
1690 1890 9.941664 CAGCTCATTGTCAAGGTAATAATTAAG 57.058 33.333 0.00 0.00 0.00 1.85
1691 1891 8.624776 AGCTCATTGTCAAGGTAATAATTAAGC 58.375 33.333 0.00 0.00 0.00 3.09
1692 1892 7.862873 GCTCATTGTCAAGGTAATAATTAAGCC 59.137 37.037 0.00 0.00 0.00 4.35
1693 1893 9.125026 CTCATTGTCAAGGTAATAATTAAGCCT 57.875 33.333 0.00 0.00 0.00 4.58
1694 1894 9.474313 TCATTGTCAAGGTAATAATTAAGCCTT 57.526 29.630 10.80 10.80 39.86 4.35
1717 1917 8.308931 CCTTGATTTGATTTCATTCTTCTTCCA 58.691 33.333 0.00 0.00 0.00 3.53
1727 1966 1.371267 CTTCTTCCACGACGCGACA 60.371 57.895 15.93 0.00 0.00 4.35
1744 1983 1.193426 GACAACTCGAAGCTGCAAGAC 59.807 52.381 1.02 0.00 34.07 3.01
1761 2000 6.604171 TGCAAGACAGATATTAATGGATGGT 58.396 36.000 0.00 0.00 0.00 3.55
1764 2003 9.236006 GCAAGACAGATATTAATGGATGGTATT 57.764 33.333 0.00 0.00 0.00 1.89
1767 2006 9.950496 AGACAGATATTAATGGATGGTATTGTC 57.050 33.333 0.00 0.00 0.00 3.18
1775 2014 9.827198 ATTAATGGATGGTATTGTCATTGGTAT 57.173 29.630 0.00 0.00 31.55 2.73
2254 2501 4.814294 GTCATCGGCGGCGTCCTT 62.814 66.667 31.06 11.83 0.00 3.36
2323 2570 1.375396 CATCAACGACAAGGGCCGA 60.375 57.895 0.00 0.00 0.00 5.54
2509 2756 2.025418 GTACAACGACCTGGCCACG 61.025 63.158 12.30 12.30 0.00 4.94
3673 3934 3.684788 AGCTACTAGCACCATTTTTGTCG 59.315 43.478 10.73 0.00 45.56 4.35
3684 5605 5.804979 CACCATTTTTGTCGATATGTTTCCC 59.195 40.000 0.00 0.00 0.00 3.97
3694 5615 4.158949 TCGATATGTTTCCCGTCTTGAAGA 59.841 41.667 0.00 0.00 0.00 2.87
3695 5616 5.050490 CGATATGTTTCCCGTCTTGAAGAT 58.950 41.667 0.00 0.00 0.00 2.40
3697 5618 6.037172 CGATATGTTTCCCGTCTTGAAGATTT 59.963 38.462 0.00 0.00 0.00 2.17
3698 5619 4.829064 TGTTTCCCGTCTTGAAGATTTG 57.171 40.909 0.00 0.00 0.00 2.32
3699 5620 4.456535 TGTTTCCCGTCTTGAAGATTTGA 58.543 39.130 0.00 0.00 0.00 2.69
3700 5621 4.515191 TGTTTCCCGTCTTGAAGATTTGAG 59.485 41.667 0.00 0.00 0.00 3.02
3701 5622 2.699954 TCCCGTCTTGAAGATTTGAGC 58.300 47.619 0.00 0.00 0.00 4.26
3702 5623 2.038426 TCCCGTCTTGAAGATTTGAGCA 59.962 45.455 0.00 0.00 0.00 4.26
3703 5624 2.160417 CCCGTCTTGAAGATTTGAGCAC 59.840 50.000 0.00 0.00 0.00 4.40
3704 5625 2.807967 CCGTCTTGAAGATTTGAGCACA 59.192 45.455 0.00 0.00 0.00 4.57
3722 5643 3.062763 CACATGACTCACTTGTCTCACC 58.937 50.000 0.00 0.00 37.79 4.02
3723 5644 2.700371 ACATGACTCACTTGTCTCACCA 59.300 45.455 0.00 0.00 37.79 4.17
3724 5645 3.326006 ACATGACTCACTTGTCTCACCAT 59.674 43.478 0.00 0.00 37.79 3.55
3725 5646 4.202398 ACATGACTCACTTGTCTCACCATT 60.202 41.667 0.00 0.00 37.79 3.16
3726 5647 4.422073 TGACTCACTTGTCTCACCATTT 57.578 40.909 0.00 0.00 37.79 2.32
3728 5649 5.192927 TGACTCACTTGTCTCACCATTTTT 58.807 37.500 0.00 0.00 37.79 1.94
3832 7383 0.249531 ACACGCGTCCAATACACACA 60.250 50.000 9.86 0.00 0.00 3.72
3833 7384 0.162933 CACGCGTCCAATACACACAC 59.837 55.000 9.86 0.00 0.00 3.82
3834 7385 0.249531 ACGCGTCCAATACACACACA 60.250 50.000 5.58 0.00 0.00 3.72
3835 7386 0.162933 CGCGTCCAATACACACACAC 59.837 55.000 0.00 0.00 0.00 3.82
3836 7387 1.222300 GCGTCCAATACACACACACA 58.778 50.000 0.00 0.00 0.00 3.72
3837 7388 1.070175 GCGTCCAATACACACACACAC 60.070 52.381 0.00 0.00 0.00 3.82
3838 7389 2.205911 CGTCCAATACACACACACACA 58.794 47.619 0.00 0.00 0.00 3.72
3839 7390 2.033236 CGTCCAATACACACACACACAC 60.033 50.000 0.00 0.00 0.00 3.82
3840 7391 2.939756 GTCCAATACACACACACACACA 59.060 45.455 0.00 0.00 0.00 3.72
3841 7392 2.939756 TCCAATACACACACACACACAC 59.060 45.455 0.00 0.00 0.00 3.82
3842 7393 2.680339 CCAATACACACACACACACACA 59.320 45.455 0.00 0.00 0.00 3.72
3843 7394 3.486708 CCAATACACACACACACACACAC 60.487 47.826 0.00 0.00 0.00 3.82
3844 7395 2.457366 TACACACACACACACACACA 57.543 45.000 0.00 0.00 0.00 3.72
3845 7396 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3846 7397 1.155889 CACACACACACACACACACT 58.844 50.000 0.00 0.00 0.00 3.55
3847 7398 1.128507 CACACACACACACACACACTC 59.871 52.381 0.00 0.00 0.00 3.51
3848 7399 1.270571 ACACACACACACACACACTCA 60.271 47.619 0.00 0.00 0.00 3.41
3849 7400 2.009051 CACACACACACACACACTCAT 58.991 47.619 0.00 0.00 0.00 2.90
3850 7401 2.009051 ACACACACACACACACTCATG 58.991 47.619 0.00 0.00 0.00 3.07
3851 7402 2.278854 CACACACACACACACTCATGA 58.721 47.619 0.00 0.00 0.00 3.07
3852 7403 2.677337 CACACACACACACACTCATGAA 59.323 45.455 0.00 0.00 0.00 2.57
3853 7404 2.938451 ACACACACACACACTCATGAAG 59.062 45.455 0.00 0.00 0.00 3.02
3874 7425 7.161404 TGAAGTCATGATGCAGTAAGTAGTTT 58.839 34.615 0.00 0.00 0.00 2.66
3923 7479 1.429463 AAGCGAGATGTTCCAACGTC 58.571 50.000 3.79 3.79 43.60 4.34
3959 7515 4.864704 TTTTAATCTTTTTGGCGCCTCT 57.135 36.364 29.70 5.25 0.00 3.69
3961 7517 1.620822 AATCTTTTTGGCGCCTCTGT 58.379 45.000 29.70 4.12 0.00 3.41
3963 7519 1.207593 CTTTTTGGCGCCTCTGTCG 59.792 57.895 29.70 7.91 0.00 4.35
3964 7520 2.187599 CTTTTTGGCGCCTCTGTCGG 62.188 60.000 29.70 7.95 0.00 4.79
3965 7521 2.668185 TTTTTGGCGCCTCTGTCGGA 62.668 55.000 29.70 0.07 0.00 4.55
3967 7523 2.463589 TTTGGCGCCTCTGTCGGATT 62.464 55.000 29.70 0.00 0.00 3.01
3968 7524 2.125106 GGCGCCTCTGTCGGATTT 60.125 61.111 22.15 0.00 0.00 2.17
3969 7525 2.174319 GGCGCCTCTGTCGGATTTC 61.174 63.158 22.15 0.00 0.00 2.17
3970 7526 2.517450 GCGCCTCTGTCGGATTTCG 61.517 63.158 0.00 0.00 40.90 3.46
3972 7528 0.736325 CGCCTCTGTCGGATTTCGTT 60.736 55.000 0.00 0.00 40.32 3.85
3973 7529 0.721718 GCCTCTGTCGGATTTCGTTG 59.278 55.000 0.00 0.00 40.32 4.10
3974 7530 1.939838 GCCTCTGTCGGATTTCGTTGT 60.940 52.381 0.00 0.00 40.32 3.32
3975 7531 1.993370 CCTCTGTCGGATTTCGTTGTC 59.007 52.381 0.00 0.00 40.32 3.18
3977 7533 2.663602 CTCTGTCGGATTTCGTTGTCAG 59.336 50.000 0.00 0.00 40.32 3.51
3978 7534 1.126846 CTGTCGGATTTCGTTGTCAGC 59.873 52.381 0.00 0.00 40.32 4.26
3979 7535 1.144969 GTCGGATTTCGTTGTCAGCA 58.855 50.000 0.00 0.00 40.32 4.41
3980 7536 1.732259 GTCGGATTTCGTTGTCAGCAT 59.268 47.619 0.00 0.00 40.32 3.79
3982 7538 2.159430 TCGGATTTCGTTGTCAGCATTG 59.841 45.455 0.00 0.00 40.32 2.82
3984 7540 6.136747 TCGGATTTCGTTGTCAGCATTGAC 62.137 45.833 0.00 0.00 45.29 3.18
3991 7547 4.223800 TCAGCATTGACATCCGCC 57.776 55.556 0.00 0.00 0.00 6.13
3995 7551 0.530650 AGCATTGACATCCGCCTACG 60.531 55.000 0.00 0.00 39.67 3.51
3996 7552 0.529773 GCATTGACATCCGCCTACGA 60.530 55.000 0.00 0.00 43.93 3.43
3997 7553 1.934589 CATTGACATCCGCCTACGAA 58.065 50.000 0.00 0.00 43.93 3.85
3998 7554 1.593006 CATTGACATCCGCCTACGAAC 59.407 52.381 0.00 0.00 43.93 3.95
4000 7556 0.108992 TGACATCCGCCTACGAACAC 60.109 55.000 0.00 0.00 43.93 3.32
4001 7557 1.138047 GACATCCGCCTACGAACACG 61.138 60.000 0.00 0.00 43.93 4.49
4002 7558 2.202703 ATCCGCCTACGAACACGC 60.203 61.111 0.00 0.00 43.93 5.34
4003 7559 4.764336 TCCGCCTACGAACACGCG 62.764 66.667 3.53 3.53 43.93 6.01
4006 7562 3.296584 GCCTACGAACACGCGATC 58.703 61.111 15.93 7.21 34.83 3.69
4007 7563 1.515519 GCCTACGAACACGCGATCA 60.516 57.895 15.93 0.00 34.83 2.92
4008 7564 0.870307 GCCTACGAACACGCGATCAT 60.870 55.000 15.93 0.00 34.83 2.45
4009 7565 0.846401 CCTACGAACACGCGATCATG 59.154 55.000 15.93 2.09 34.83 3.07
4010 7566 0.227234 CTACGAACACGCGATCATGC 59.773 55.000 15.93 0.00 34.83 4.06
4030 7586 3.729356 TGCACACGCACAATTGTTT 57.271 42.105 8.77 0.00 45.36 2.83
4034 7590 2.097444 GCACACGCACAATTGTTTAAGC 60.097 45.455 8.77 8.45 38.36 3.09
4035 7591 3.371168 CACACGCACAATTGTTTAAGCT 58.629 40.909 8.77 0.00 0.00 3.74
4036 7592 3.180189 CACACGCACAATTGTTTAAGCTG 59.820 43.478 8.77 11.20 0.00 4.24
4037 7593 3.181491 ACACGCACAATTGTTTAAGCTGT 60.181 39.130 8.77 11.75 0.00 4.40
4038 7594 4.035792 ACACGCACAATTGTTTAAGCTGTA 59.964 37.500 8.77 0.00 0.00 2.74
4040 7596 6.072948 ACACGCACAATTGTTTAAGCTGTATA 60.073 34.615 8.77 0.00 0.00 1.47
4043 7599 6.075415 CGCACAATTGTTTAAGCTGTATATGC 60.075 38.462 8.77 3.18 0.00 3.14
4044 7600 6.974622 GCACAATTGTTTAAGCTGTATATGCT 59.025 34.615 8.77 0.00 43.32 3.79
4045 7601 8.128582 GCACAATTGTTTAAGCTGTATATGCTA 58.871 33.333 8.77 0.00 40.22 3.49
4046 7602 9.655769 CACAATTGTTTAAGCTGTATATGCTAG 57.344 33.333 8.77 0.00 40.22 3.42
4047 7603 9.613428 ACAATTGTTTAAGCTGTATATGCTAGA 57.387 29.630 4.92 0.00 40.22 2.43
4051 7607 9.884636 TTGTTTAAGCTGTATATGCTAGAAAGA 57.115 29.630 0.00 4.61 40.22 2.52
4052 7608 9.884636 TGTTTAAGCTGTATATGCTAGAAAGAA 57.115 29.630 0.00 0.00 40.22 2.52
4084 7640 5.712152 AAAGTTTTCGATCTTGCTTGGAT 57.288 34.783 0.00 0.00 0.00 3.41
4086 7642 4.326826 AGTTTTCGATCTTGCTTGGATCA 58.673 39.130 12.11 1.31 39.42 2.92
4087 7643 4.761739 AGTTTTCGATCTTGCTTGGATCAA 59.238 37.500 12.11 0.00 39.42 2.57
4088 7644 5.416952 AGTTTTCGATCTTGCTTGGATCAAT 59.583 36.000 12.11 0.00 39.42 2.57
4089 7645 4.888038 TTCGATCTTGCTTGGATCAATG 57.112 40.909 12.11 0.00 39.42 2.82
4090 7646 3.208594 TCGATCTTGCTTGGATCAATGG 58.791 45.455 12.11 0.00 39.42 3.16
4091 7647 3.118298 TCGATCTTGCTTGGATCAATGGA 60.118 43.478 12.11 0.00 39.42 3.41
4092 7648 3.250280 CGATCTTGCTTGGATCAATGGAG 59.750 47.826 12.11 0.00 39.42 3.86
4093 7649 3.726557 TCTTGCTTGGATCAATGGAGT 57.273 42.857 0.00 0.00 0.00 3.85
4094 7650 3.349927 TCTTGCTTGGATCAATGGAGTG 58.650 45.455 0.00 0.00 0.00 3.51
4095 7651 2.885135 TGCTTGGATCAATGGAGTGT 57.115 45.000 0.00 0.00 0.00 3.55
4096 7652 2.439409 TGCTTGGATCAATGGAGTGTG 58.561 47.619 0.00 0.00 0.00 3.82
4099 7655 3.276857 CTTGGATCAATGGAGTGTGGAG 58.723 50.000 0.00 0.00 0.00 3.86
4100 7656 2.269023 TGGATCAATGGAGTGTGGAGT 58.731 47.619 0.00 0.00 0.00 3.85
4101 7657 2.644299 TGGATCAATGGAGTGTGGAGTT 59.356 45.455 0.00 0.00 0.00 3.01
4102 7658 3.012518 GGATCAATGGAGTGTGGAGTTG 58.987 50.000 0.00 0.00 0.00 3.16
4103 7659 2.566833 TCAATGGAGTGTGGAGTTGG 57.433 50.000 0.00 0.00 0.00 3.77
4104 7660 1.774254 TCAATGGAGTGTGGAGTTGGT 59.226 47.619 0.00 0.00 0.00 3.67
4105 7661 2.174639 TCAATGGAGTGTGGAGTTGGTT 59.825 45.455 0.00 0.00 0.00 3.67
4106 7662 2.554032 CAATGGAGTGTGGAGTTGGTTC 59.446 50.000 0.00 0.00 0.00 3.62
4107 7663 0.472471 TGGAGTGTGGAGTTGGTTCC 59.528 55.000 0.00 0.00 37.77 3.62
4109 7665 0.472471 GAGTGTGGAGTTGGTTCCCA 59.528 55.000 0.00 0.00 36.35 4.37
4111 7667 4.494515 GTGGAGTTGGTTCCCACC 57.505 61.111 0.00 0.00 43.32 4.61
4112 7668 1.844130 GTGGAGTTGGTTCCCACCT 59.156 57.895 0.00 0.00 44.61 4.00
4114 7670 1.633945 GTGGAGTTGGTTCCCACCTAT 59.366 52.381 0.00 0.00 44.61 2.57
4116 7672 2.307686 TGGAGTTGGTTCCCACCTATTC 59.692 50.000 0.00 0.00 44.61 1.75
4117 7673 2.356844 GGAGTTGGTTCCCACCTATTCC 60.357 54.545 2.51 2.51 43.88 3.01
4118 7674 1.639108 AGTTGGTTCCCACCTATTCCC 59.361 52.381 0.00 0.00 44.61 3.97
4119 7675 1.356398 GTTGGTTCCCACCTATTCCCA 59.644 52.381 0.00 0.00 44.61 4.37
4120 7676 1.761711 TGGTTCCCACCTATTCCCAA 58.238 50.000 0.00 0.00 44.61 4.12
4121 7677 2.074579 TGGTTCCCACCTATTCCCAAA 58.925 47.619 0.00 0.00 44.61 3.28
4123 7679 3.859248 TGGTTCCCACCTATTCCCAAATA 59.141 43.478 0.00 0.00 44.61 1.40
4137 7693 6.969993 TTCCCAAATAGGTGGCATATAAAC 57.030 37.500 0.00 0.00 37.34 2.01
4139 7695 7.395525 TCCCAAATAGGTGGCATATAAACTA 57.604 36.000 0.00 0.00 37.34 2.24
4141 7697 7.942341 TCCCAAATAGGTGGCATATAAACTAAG 59.058 37.037 0.00 0.00 37.34 2.18
4142 7698 7.724061 CCCAAATAGGTGGCATATAAACTAAGT 59.276 37.037 0.00 0.00 37.34 2.24
4143 7699 9.131791 CCAAATAGGTGGCATATAAACTAAGTT 57.868 33.333 0.00 0.00 0.00 2.66
4144 7700 9.950680 CAAATAGGTGGCATATAAACTAAGTTG 57.049 33.333 0.00 0.00 0.00 3.16
4145 7701 9.914834 AAATAGGTGGCATATAAACTAAGTTGA 57.085 29.630 0.00 0.00 0.00 3.18
4146 7702 9.914834 AATAGGTGGCATATAAACTAAGTTGAA 57.085 29.630 0.00 0.00 0.00 2.69
4147 7703 9.914834 ATAGGTGGCATATAAACTAAGTTGAAA 57.085 29.630 0.00 0.00 0.00 2.69
4148 7704 8.644374 AGGTGGCATATAAACTAAGTTGAAAA 57.356 30.769 0.00 0.00 0.00 2.29
4149 7705 8.739972 AGGTGGCATATAAACTAAGTTGAAAAG 58.260 33.333 0.00 0.00 0.00 2.27
4150 7706 8.520351 GGTGGCATATAAACTAAGTTGAAAAGT 58.480 33.333 0.00 0.00 0.00 2.66
4151 7707 9.908152 GTGGCATATAAACTAAGTTGAAAAGTT 57.092 29.630 0.00 0.00 43.11 2.66
4204 8379 9.261180 TGAAGAAAGTATCAAGAACTTGTGTAG 57.739 33.333 13.15 0.00 41.16 2.74
4249 11194 1.343142 GAATTTGGTGTTGGTCCCCAC 59.657 52.381 1.05 1.05 30.78 4.61
4255 11200 4.612412 GTTGGTCCCCACGCGACA 62.612 66.667 15.93 0.00 30.78 4.35
4306 11251 0.735632 AGCTTCAAGAAGAGCGAGCG 60.736 55.000 13.70 0.00 40.79 5.03
4319 11264 2.874694 CGAGCGGTTGATGATGGCG 61.875 63.158 0.00 0.00 0.00 5.69
4321 11266 3.507924 GCGGTTGATGATGGCGCA 61.508 61.111 10.83 0.00 0.00 6.09
4334 11279 2.049063 GCGCAGTGGTCGTCTCTT 60.049 61.111 0.30 0.00 0.00 2.85
4335 11280 2.375766 GCGCAGTGGTCGTCTCTTG 61.376 63.158 0.30 0.00 0.00 3.02
4353 11298 3.318275 TCTTGTCGACTATATGGTGAGGC 59.682 47.826 17.92 0.00 0.00 4.70
4358 11303 3.944055 GACTATATGGTGAGGCGACAT 57.056 47.619 0.00 0.00 0.00 3.06
4366 11311 1.141665 TGAGGCGACATGATGACGG 59.858 57.895 17.78 1.67 36.16 4.79
4372 11317 2.610479 GGCGACATGATGACGGTGATAT 60.610 50.000 17.78 0.00 36.16 1.63
4396 11341 1.068417 GGGGTTGGCGTTGGTTTTC 59.932 57.895 0.00 0.00 0.00 2.29
4409 11354 2.279584 TTTTCGTCTGCGTCGCCA 60.280 55.556 15.88 1.83 39.49 5.69
4436 11381 0.249280 GGGGTTTCACTTTTGCCGTG 60.249 55.000 0.00 0.00 0.00 4.94
4474 11419 7.757941 TCAATGTCAGGTTTCAATTGTATCA 57.242 32.000 5.13 0.00 0.00 2.15
4478 11423 9.466497 AATGTCAGGTTTCAATTGTATCAGTAT 57.534 29.630 5.13 0.00 0.00 2.12
4515 11460 8.171196 CAGTTGTATCATATGACAAGTCACAAC 58.829 37.037 22.18 22.18 43.11 3.32
4517 11462 5.810074 TGTATCATATGACAAGTCACAACCG 59.190 40.000 7.78 0.00 43.11 4.44
4518 11463 4.529109 TCATATGACAAGTCACAACCGA 57.471 40.909 4.84 0.00 43.11 4.69
4520 11465 4.929211 TCATATGACAAGTCACAACCGAAG 59.071 41.667 4.84 0.00 43.11 3.79
4521 11466 1.295792 TGACAAGTCACAACCGAAGC 58.704 50.000 0.00 0.00 34.14 3.86
4573 11520 6.305877 CACTTTAGCTACTTGTAAGTCGTCTG 59.694 42.308 5.04 0.00 40.37 3.51
4574 11521 6.206243 ACTTTAGCTACTTGTAAGTCGTCTGA 59.794 38.462 0.00 0.00 40.37 3.27
4587 11534 8.885722 TGTAAGTCGTCTGAAAATAGTTTTTGT 58.114 29.630 0.00 0.00 35.20 2.83
4592 11539 7.373441 GTCGTCTGAAAATAGTTTTTGTGTCAG 59.627 37.037 0.00 0.00 35.20 3.51
4595 11542 7.644157 GTCTGAAAATAGTTTTTGTGTCAGTCC 59.356 37.037 0.00 0.00 35.20 3.85
4596 11543 6.491394 TGAAAATAGTTTTTGTGTCAGTCCG 58.509 36.000 0.00 0.00 35.20 4.79
4599 11547 3.536956 AGTTTTTGTGTCAGTCCGAGA 57.463 42.857 0.00 0.00 0.00 4.04
4610 11558 4.541213 TCCGAGAAGGAGCCACTT 57.459 55.556 0.00 0.00 45.98 3.16
4614 11562 0.108424 CGAGAAGGAGCCACTTGAGG 60.108 60.000 0.00 0.00 0.00 3.86
4618 11566 1.073923 GAAGGAGCCACTTGAGGGAAA 59.926 52.381 0.00 0.00 0.00 3.13
4636 11584 3.270877 GAAAGAAGAAGCTAATGCCGGA 58.729 45.455 5.05 0.00 40.80 5.14
4637 11585 3.567478 AAGAAGAAGCTAATGCCGGAT 57.433 42.857 5.05 0.00 40.80 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 2.359900 CAATGCCCAAGAGGTGTACTC 58.640 52.381 0.00 0.00 46.98 2.59
36 37 1.367346 TCCAATGCCCAAGAGGTGTA 58.633 50.000 0.00 0.00 38.26 2.90
112 113 8.876275 ATGTTAAATTACGTAAATCGCCTAGA 57.124 30.769 12.81 0.00 44.19 2.43
201 202 1.134640 TCCATGGCATCAGCAAATTGC 60.135 47.619 10.41 10.41 45.46 3.56
205 206 0.251698 TGGTCCATGGCATCAGCAAA 60.252 50.000 6.96 0.00 44.61 3.68
306 315 1.067354 CAAAAGGCATGGCTCTTGTCC 60.067 52.381 23.46 0.56 0.00 4.02
356 367 3.324846 GGATGGTGCAGAGTGGATGTATA 59.675 47.826 0.00 0.00 0.00 1.47
369 380 3.668141 ATGGACAAATAGGATGGTGCA 57.332 42.857 0.00 0.00 36.06 4.57
370 381 4.718961 AGTATGGACAAATAGGATGGTGC 58.281 43.478 0.00 0.00 0.00 5.01
396 407 7.014422 TCGGTATCCACTTGGTAAACAATTTTT 59.986 33.333 0.00 0.00 38.65 1.94
417 464 0.320050 TGCACACAGCTCATTCGGTA 59.680 50.000 0.00 0.00 45.94 4.02
535 583 6.364701 TCTGAAGAACTTTTCCATGGAAAGA 58.635 36.000 32.77 22.79 43.75 2.52
601 649 0.396139 ACGGCCGACCAATCCTACTA 60.396 55.000 35.90 0.00 34.57 1.82
606 654 0.390124 TATGTACGGCCGACCAATCC 59.610 55.000 35.90 11.04 34.57 3.01
649 697 9.302345 TCTCGTCTTCTACATAATTGACATTTC 57.698 33.333 0.00 0.00 0.00 2.17
705 753 1.202758 TCCTCAGTCGTTTGCCAATGT 60.203 47.619 0.00 0.00 0.00 2.71
711 759 4.223320 TGAAAATTCCTCAGTCGTTTGC 57.777 40.909 0.00 0.00 0.00 3.68
724 772 7.583230 TGTGGCTTTATTTTGCATGAAAATTC 58.417 30.769 16.00 7.75 40.73 2.17
772 820 3.627395 TGGACCTTATCAATGCGAACT 57.373 42.857 0.00 0.00 0.00 3.01
775 823 8.154203 TCTTATATTTGGACCTTATCAATGCGA 58.846 33.333 0.00 0.00 0.00 5.10
776 824 8.322906 TCTTATATTTGGACCTTATCAATGCG 57.677 34.615 0.00 0.00 0.00 4.73
816 866 9.635404 TCAATTTAACCCGGTTCTTATATGATT 57.365 29.630 5.94 0.00 0.00 2.57
817 867 9.807921 ATCAATTTAACCCGGTTCTTATATGAT 57.192 29.630 5.94 7.98 0.00 2.45
850 900 5.808403 TCGTTTTACCGCGCAATATATTTT 58.192 33.333 8.75 0.00 0.00 1.82
888 938 5.453339 GCGCTCTTATATAATGGCAGGGATA 60.453 44.000 0.00 0.00 0.00 2.59
895 945 4.795278 GCAAATGCGCTCTTATATAATGGC 59.205 41.667 9.73 3.17 0.00 4.40
1014 1081 3.066198 GGAACAGCCGTGGTAGGT 58.934 61.111 0.00 0.00 0.00 3.08
1215 1288 0.171455 CGAACAGAGGAGGACGGAAG 59.829 60.000 0.00 0.00 0.00 3.46
1224 1297 0.737367 CTCATTGCGCGAACAGAGGA 60.737 55.000 12.10 0.00 0.00 3.71
1225 1298 1.699656 CCTCATTGCGCGAACAGAGG 61.700 60.000 22.19 22.19 34.53 3.69
1241 1342 3.758554 TCATTAAGCAAGCAAGGAACCTC 59.241 43.478 0.00 0.00 0.00 3.85
1247 1348 6.255020 CAGCTAAATTCATTAAGCAAGCAAGG 59.745 38.462 0.00 0.00 0.00 3.61
1248 1349 7.031372 TCAGCTAAATTCATTAAGCAAGCAAG 58.969 34.615 0.00 0.00 0.00 4.01
1260 1361 3.008835 TGGCAGCTCAGCTAAATTCAT 57.991 42.857 0.00 0.00 36.40 2.57
1267 1368 1.476291 CCATTCATGGCAGCTCAGCTA 60.476 52.381 0.00 0.00 41.75 3.32
1293 1394 1.066152 CGTTCTCGATGATCCTGCAGA 59.934 52.381 17.39 1.21 39.71 4.26
1686 1886 9.643693 GAAGAATGAAATCAAATCAAGGCTTAA 57.356 29.630 0.00 0.00 0.00 1.85
1687 1887 9.028284 AGAAGAATGAAATCAAATCAAGGCTTA 57.972 29.630 0.00 0.00 0.00 3.09
1688 1888 7.904205 AGAAGAATGAAATCAAATCAAGGCTT 58.096 30.769 0.00 0.00 0.00 4.35
1689 1889 7.477945 AGAAGAATGAAATCAAATCAAGGCT 57.522 32.000 0.00 0.00 0.00 4.58
1690 1890 7.277319 GGAAGAAGAATGAAATCAAATCAAGGC 59.723 37.037 0.00 0.00 0.00 4.35
1691 1891 8.308931 TGGAAGAAGAATGAAATCAAATCAAGG 58.691 33.333 0.00 0.00 0.00 3.61
1692 1892 9.136952 GTGGAAGAAGAATGAAATCAAATCAAG 57.863 33.333 0.00 0.00 0.00 3.02
1693 1893 7.809331 CGTGGAAGAAGAATGAAATCAAATCAA 59.191 33.333 0.00 0.00 0.00 2.57
1694 1894 7.174772 TCGTGGAAGAAGAATGAAATCAAATCA 59.825 33.333 0.00 0.00 0.00 2.57
1695 1895 7.483059 GTCGTGGAAGAAGAATGAAATCAAATC 59.517 37.037 0.00 0.00 0.00 2.17
1696 1896 7.308435 GTCGTGGAAGAAGAATGAAATCAAAT 58.692 34.615 0.00 0.00 0.00 2.32
1706 1906 0.242825 TCGCGTCGTGGAAGAAGAAT 59.757 50.000 5.77 0.00 0.00 2.40
1717 1917 1.724929 CTTCGAGTTGTCGCGTCGT 60.725 57.895 14.46 0.00 46.39 4.34
1727 1966 1.069204 TCTGTCTTGCAGCTTCGAGTT 59.931 47.619 0.24 0.00 44.66 3.01
1761 2000 9.933723 CTATGATCTGACATACCAATGACAATA 57.066 33.333 0.00 0.00 37.33 1.90
1764 2003 6.742363 GCCTATGATCTGACATACCAATGACA 60.742 42.308 0.00 0.00 36.55 3.58
1765 2004 5.641209 GCCTATGATCTGACATACCAATGAC 59.359 44.000 0.00 0.00 36.54 3.06
1766 2005 5.307716 TGCCTATGATCTGACATACCAATGA 59.692 40.000 0.00 0.00 36.54 2.57
1767 2006 5.554070 TGCCTATGATCTGACATACCAATG 58.446 41.667 0.00 0.00 39.17 2.82
1771 2010 3.007290 TGCTGCCTATGATCTGACATACC 59.993 47.826 0.00 0.00 0.00 2.73
1772 2011 4.263018 TGCTGCCTATGATCTGACATAC 57.737 45.455 0.00 0.00 0.00 2.39
1774 2013 3.583526 AGATGCTGCCTATGATCTGACAT 59.416 43.478 0.00 0.00 0.00 3.06
1775 2014 2.970640 AGATGCTGCCTATGATCTGACA 59.029 45.455 0.00 0.00 0.00 3.58
2254 2501 3.997397 TGGTTGTAGAGCGCGCCA 61.997 61.111 30.33 16.33 0.00 5.69
2375 2622 1.515954 CGAAGGGGAGCACGTACAT 59.484 57.895 0.00 0.00 0.00 2.29
3673 3934 6.927294 AATCTTCAAGACGGGAAACATATC 57.073 37.500 0.00 0.00 0.00 1.63
3684 5605 4.152938 TCATGTGCTCAAATCTTCAAGACG 59.847 41.667 0.00 0.00 0.00 4.18
3694 5615 4.139786 ACAAGTGAGTCATGTGCTCAAAT 58.860 39.130 18.94 11.34 43.57 2.32
3695 5616 3.544684 ACAAGTGAGTCATGTGCTCAAA 58.455 40.909 18.94 1.76 43.57 2.69
3697 5618 2.366590 AGACAAGTGAGTCATGTGCTCA 59.633 45.455 15.21 15.21 40.98 4.26
3698 5619 2.992543 GAGACAAGTGAGTCATGTGCTC 59.007 50.000 4.10 11.33 40.98 4.26
3699 5620 2.366590 TGAGACAAGTGAGTCATGTGCT 59.633 45.455 4.10 4.06 40.98 4.40
3700 5621 2.478134 GTGAGACAAGTGAGTCATGTGC 59.522 50.000 4.10 0.00 40.98 4.57
3701 5622 3.062763 GGTGAGACAAGTGAGTCATGTG 58.937 50.000 4.10 4.51 40.98 3.21
3702 5623 2.700371 TGGTGAGACAAGTGAGTCATGT 59.300 45.455 0.00 0.00 40.98 3.21
3703 5624 3.391506 TGGTGAGACAAGTGAGTCATG 57.608 47.619 0.00 0.00 40.98 3.07
3704 5625 4.630644 AATGGTGAGACAAGTGAGTCAT 57.369 40.909 0.00 0.00 40.98 3.06
3725 5646 7.768240 AGAAGGAAGAAAAGAAAGCGTAAAAA 58.232 30.769 0.00 0.00 0.00 1.94
3726 5647 7.329588 AGAAGGAAGAAAAGAAAGCGTAAAA 57.670 32.000 0.00 0.00 0.00 1.52
3728 5649 6.937436 AAGAAGGAAGAAAAGAAAGCGTAA 57.063 33.333 0.00 0.00 0.00 3.18
3730 5651 5.836821 AAAGAAGGAAGAAAAGAAAGCGT 57.163 34.783 0.00 0.00 0.00 5.07
3731 5652 6.975197 AGAAAAAGAAGGAAGAAAAGAAAGCG 59.025 34.615 0.00 0.00 0.00 4.68
3760 5699 9.190858 GCAAACAAATCATGTACTCAAATGTTA 57.809 29.630 0.00 0.00 42.99 2.41
3761 5700 7.927629 AGCAAACAAATCATGTACTCAAATGTT 59.072 29.630 0.00 0.00 42.99 2.71
3763 5702 7.878477 AGCAAACAAATCATGTACTCAAATG 57.122 32.000 0.00 0.00 42.99 2.32
3765 5704 7.254387 GCAAAGCAAACAAATCATGTACTCAAA 60.254 33.333 0.00 0.00 42.99 2.69
3766 5705 6.200665 GCAAAGCAAACAAATCATGTACTCAA 59.799 34.615 0.00 0.00 42.99 3.02
3768 5707 5.922544 AGCAAAGCAAACAAATCATGTACTC 59.077 36.000 0.00 0.00 42.99 2.59
3769 5708 5.693104 CAGCAAAGCAAACAAATCATGTACT 59.307 36.000 0.00 0.00 42.99 2.73
3771 5710 4.448395 GCAGCAAAGCAAACAAATCATGTA 59.552 37.500 0.00 0.00 42.99 2.29
3772 5711 3.249080 GCAGCAAAGCAAACAAATCATGT 59.751 39.130 0.00 0.00 46.82 3.21
3775 5714 2.211806 GGCAGCAAAGCAAACAAATCA 58.788 42.857 0.00 0.00 35.83 2.57
3818 7369 2.033236 GTGTGTGTGTGTGTATTGGACG 60.033 50.000 0.00 0.00 0.00 4.79
3832 7383 2.689553 TCATGAGTGTGTGTGTGTGT 57.310 45.000 0.00 0.00 0.00 3.72
3833 7384 2.938451 ACTTCATGAGTGTGTGTGTGTG 59.062 45.455 0.00 0.00 37.17 3.82
3834 7385 3.198068 GACTTCATGAGTGTGTGTGTGT 58.802 45.455 7.95 0.00 39.19 3.72
3835 7386 3.197265 TGACTTCATGAGTGTGTGTGTG 58.803 45.455 7.95 0.00 39.19 3.82
3836 7387 3.541996 TGACTTCATGAGTGTGTGTGT 57.458 42.857 7.95 0.00 39.19 3.72
3848 7399 6.882656 ACTACTTACTGCATCATGACTTCAT 58.117 36.000 0.00 0.00 36.96 2.57
3849 7400 6.286240 ACTACTTACTGCATCATGACTTCA 57.714 37.500 0.00 0.00 0.00 3.02
3850 7401 7.602517 AAACTACTTACTGCATCATGACTTC 57.397 36.000 0.00 0.00 0.00 3.01
3851 7402 7.986085 AAAACTACTTACTGCATCATGACTT 57.014 32.000 0.00 0.00 0.00 3.01
3852 7403 7.986085 AAAAACTACTTACTGCATCATGACT 57.014 32.000 0.00 0.00 0.00 3.41
3893 7444 5.696270 GGAACATCTCGCTTTCCAAATTTTT 59.304 36.000 0.00 0.00 38.98 1.94
3896 7447 3.826157 TGGAACATCTCGCTTTCCAAATT 59.174 39.130 0.00 0.00 44.65 1.82
3897 7448 3.420893 TGGAACATCTCGCTTTCCAAAT 58.579 40.909 0.00 0.00 44.65 2.32
3898 7449 2.857483 TGGAACATCTCGCTTTCCAAA 58.143 42.857 0.00 0.00 44.65 3.28
3938 7494 4.038642 ACAGAGGCGCCAAAAAGATTAAAA 59.961 37.500 31.54 0.00 0.00 1.52
3940 7496 3.153919 ACAGAGGCGCCAAAAAGATTAA 58.846 40.909 31.54 0.00 0.00 1.40
3942 7498 1.541588 GACAGAGGCGCCAAAAAGATT 59.458 47.619 31.54 4.27 0.00 2.40
3949 7505 2.463589 AAATCCGACAGAGGCGCCAA 62.464 55.000 31.54 3.13 0.00 4.52
3950 7506 2.852495 GAAATCCGACAGAGGCGCCA 62.852 60.000 31.54 4.96 0.00 5.69
3951 7507 2.125106 AAATCCGACAGAGGCGCC 60.125 61.111 21.89 21.89 0.00 6.53
3953 7509 0.736325 AACGAAATCCGACAGAGGCG 60.736 55.000 0.00 0.00 41.76 5.52
3954 7510 0.721718 CAACGAAATCCGACAGAGGC 59.278 55.000 0.00 0.00 41.76 4.70
3955 7511 1.993370 GACAACGAAATCCGACAGAGG 59.007 52.381 0.00 0.00 41.76 3.69
3957 7513 2.672714 CTGACAACGAAATCCGACAGA 58.327 47.619 0.00 0.00 41.76 3.41
3958 7514 1.126846 GCTGACAACGAAATCCGACAG 59.873 52.381 0.00 0.00 41.76 3.51
3959 7515 1.144969 GCTGACAACGAAATCCGACA 58.855 50.000 0.00 0.00 41.76 4.35
3961 7517 2.093306 ATGCTGACAACGAAATCCGA 57.907 45.000 0.00 0.00 41.76 4.55
3963 7519 3.829886 TCAATGCTGACAACGAAATCC 57.170 42.857 0.00 0.00 0.00 3.01
3974 7530 0.829990 TAGGCGGATGTCAATGCTGA 59.170 50.000 0.00 0.00 0.00 4.26
3975 7531 0.940126 GTAGGCGGATGTCAATGCTG 59.060 55.000 0.00 0.00 0.00 4.41
3977 7533 0.529773 TCGTAGGCGGATGTCAATGC 60.530 55.000 0.00 0.00 38.89 3.56
3978 7534 1.593006 GTTCGTAGGCGGATGTCAATG 59.407 52.381 0.00 0.00 38.89 2.82
3979 7535 1.206132 TGTTCGTAGGCGGATGTCAAT 59.794 47.619 0.00 0.00 38.89 2.57
3980 7536 0.604073 TGTTCGTAGGCGGATGTCAA 59.396 50.000 0.00 0.00 38.89 3.18
3982 7538 1.138047 CGTGTTCGTAGGCGGATGTC 61.138 60.000 0.00 0.00 38.89 3.06
3984 7540 2.514013 GCGTGTTCGTAGGCGGATG 61.514 63.158 0.00 0.00 39.49 3.51
3989 7545 0.870307 ATGATCGCGTGTTCGTAGGC 60.870 55.000 5.77 0.00 39.49 3.93
3991 7547 0.227234 GCATGATCGCGTGTTCGTAG 59.773 55.000 5.77 0.98 39.49 3.51
4001 7557 2.276868 GTGTGCACGCATGATCGC 60.277 61.111 25.05 0.00 0.00 4.58
4013 7569 2.097444 GCTTAAACAATTGTGCGTGTGC 60.097 45.455 12.82 8.57 43.20 4.57
4014 7570 3.180189 CAGCTTAAACAATTGTGCGTGTG 59.820 43.478 12.82 2.29 0.00 3.82
4015 7571 3.181491 ACAGCTTAAACAATTGTGCGTGT 60.181 39.130 12.82 13.03 0.00 4.49
4016 7572 3.371168 ACAGCTTAAACAATTGTGCGTG 58.629 40.909 12.82 12.49 0.00 5.34
4017 7573 3.708563 ACAGCTTAAACAATTGTGCGT 57.291 38.095 12.82 10.29 0.00 5.24
4019 7575 6.974622 AGCATATACAGCTTAAACAATTGTGC 59.025 34.615 12.82 11.12 39.87 4.57
4020 7576 9.655769 CTAGCATATACAGCTTAAACAATTGTG 57.344 33.333 12.82 0.08 43.25 3.33
4021 7577 9.613428 TCTAGCATATACAGCTTAAACAATTGT 57.387 29.630 4.92 4.92 43.25 2.71
4026 7582 9.884636 TTCTTTCTAGCATATACAGCTTAAACA 57.115 29.630 6.81 0.00 43.25 2.83
4060 7616 5.901552 TCCAAGCAAGATCGAAAACTTTTT 58.098 33.333 0.00 0.00 0.00 1.94
4061 7617 5.514274 TCCAAGCAAGATCGAAAACTTTT 57.486 34.783 0.00 0.00 0.00 2.27
4062 7618 5.241506 TGATCCAAGCAAGATCGAAAACTTT 59.758 36.000 0.00 0.00 42.57 2.66
4063 7619 4.761739 TGATCCAAGCAAGATCGAAAACTT 59.238 37.500 0.00 0.00 42.57 2.66
4064 7620 4.326826 TGATCCAAGCAAGATCGAAAACT 58.673 39.130 0.00 0.00 42.57 2.66
4065 7621 4.685169 TGATCCAAGCAAGATCGAAAAC 57.315 40.909 0.00 0.00 42.57 2.43
4066 7622 5.393352 CCATTGATCCAAGCAAGATCGAAAA 60.393 40.000 0.00 0.00 42.57 2.29
4068 7624 3.628942 CCATTGATCCAAGCAAGATCGAA 59.371 43.478 0.00 2.96 42.57 3.71
4069 7625 3.118298 TCCATTGATCCAAGCAAGATCGA 60.118 43.478 0.00 0.00 42.57 3.59
4070 7626 3.208594 TCCATTGATCCAAGCAAGATCG 58.791 45.455 6.26 0.00 42.57 3.69
4071 7627 4.036498 CACTCCATTGATCCAAGCAAGATC 59.964 45.833 4.24 4.24 40.51 2.75
4072 7628 3.952323 CACTCCATTGATCCAAGCAAGAT 59.048 43.478 0.00 0.00 0.00 2.40
4073 7629 3.245016 ACACTCCATTGATCCAAGCAAGA 60.245 43.478 0.00 0.00 0.00 3.02
4074 7630 3.087031 ACACTCCATTGATCCAAGCAAG 58.913 45.455 0.00 0.00 0.00 4.01
4075 7631 2.821378 CACACTCCATTGATCCAAGCAA 59.179 45.455 0.00 0.00 0.00 3.91
4076 7632 2.439409 CACACTCCATTGATCCAAGCA 58.561 47.619 0.00 0.00 0.00 3.91
4079 7635 2.644299 ACTCCACACTCCATTGATCCAA 59.356 45.455 0.00 0.00 0.00 3.53
4081 7637 3.012518 CAACTCCACACTCCATTGATCC 58.987 50.000 0.00 0.00 0.00 3.36
4084 7640 1.774254 ACCAACTCCACACTCCATTGA 59.226 47.619 0.00 0.00 0.00 2.57
4086 7642 2.489073 GGAACCAACTCCACACTCCATT 60.489 50.000 0.00 0.00 35.36 3.16
4087 7643 1.073923 GGAACCAACTCCACACTCCAT 59.926 52.381 0.00 0.00 35.36 3.41
4088 7644 0.472471 GGAACCAACTCCACACTCCA 59.528 55.000 0.00 0.00 35.36 3.86
4089 7645 3.324207 GGAACCAACTCCACACTCC 57.676 57.895 0.00 0.00 35.36 3.85
4102 7658 4.470602 CTATTTGGGAATAGGTGGGAACC 58.529 47.826 0.00 0.00 44.09 3.62
4111 7667 8.739972 GTTTATATGCCACCTATTTGGGAATAG 58.260 37.037 0.00 0.31 40.88 1.73
4112 7668 8.452868 AGTTTATATGCCACCTATTTGGGAATA 58.547 33.333 0.00 0.00 40.88 1.75
4114 7670 6.678547 AGTTTATATGCCACCTATTTGGGAA 58.321 36.000 0.00 0.00 40.88 3.97
4116 7672 7.724061 ACTTAGTTTATATGCCACCTATTTGGG 59.276 37.037 0.00 0.00 41.11 4.12
4117 7673 8.691661 ACTTAGTTTATATGCCACCTATTTGG 57.308 34.615 0.00 0.00 42.93 3.28
4118 7674 9.950680 CAACTTAGTTTATATGCCACCTATTTG 57.049 33.333 0.00 0.00 0.00 2.32
4119 7675 9.914834 TCAACTTAGTTTATATGCCACCTATTT 57.085 29.630 0.00 0.00 0.00 1.40
4120 7676 9.914834 TTCAACTTAGTTTATATGCCACCTATT 57.085 29.630 0.00 0.00 0.00 1.73
4121 7677 9.914834 TTTCAACTTAGTTTATATGCCACCTAT 57.085 29.630 0.00 0.00 0.00 2.57
4123 7679 8.644374 TTTTCAACTTAGTTTATATGCCACCT 57.356 30.769 0.00 0.00 0.00 4.00
4125 7681 9.908152 AACTTTTCAACTTAGTTTATATGCCAC 57.092 29.630 0.00 0.00 0.00 5.01
4176 8351 9.125026 ACACAAGTTCTTGATACTTTCTTCATT 57.875 29.630 17.75 0.00 33.73 2.57
4211 8386 9.802039 ACCAAATTCTATTTTGTAGTCCTTGTA 57.198 29.630 0.00 0.00 35.30 2.41
4212 8387 8.576442 CACCAAATTCTATTTTGTAGTCCTTGT 58.424 33.333 0.00 0.00 35.30 3.16
4213 8388 8.576442 ACACCAAATTCTATTTTGTAGTCCTTG 58.424 33.333 0.00 0.00 35.30 3.61
4214 8389 8.706322 ACACCAAATTCTATTTTGTAGTCCTT 57.294 30.769 0.00 0.00 35.30 3.36
4215 8390 8.576442 CAACACCAAATTCTATTTTGTAGTCCT 58.424 33.333 0.00 0.00 35.30 3.85
4216 8391 7.812669 CCAACACCAAATTCTATTTTGTAGTCC 59.187 37.037 0.00 0.00 35.30 3.85
4217 8392 8.357402 ACCAACACCAAATTCTATTTTGTAGTC 58.643 33.333 0.00 0.00 35.30 2.59
4249 11194 3.386867 GAAGGGCAATGCTGTCGCG 62.387 63.158 4.82 0.00 39.65 5.87
4255 11200 2.345760 CGGCAAGAAGGGCAATGCT 61.346 57.895 4.82 0.00 38.79 3.79
4306 11251 1.430632 CACTGCGCCATCATCAACC 59.569 57.895 4.18 0.00 0.00 3.77
4319 11264 1.004277 CGACAAGAGACGACCACTGC 61.004 60.000 0.00 0.00 34.91 4.40
4321 11266 3.016997 TCGACAAGAGACGACCACT 57.983 52.632 0.00 0.00 37.04 4.00
4334 11279 1.607148 CGCCTCACCATATAGTCGACA 59.393 52.381 19.50 4.13 0.00 4.35
4335 11280 1.878088 TCGCCTCACCATATAGTCGAC 59.122 52.381 7.70 7.70 0.00 4.20
4353 11298 6.183360 CCATTTATATCACCGTCATCATGTCG 60.183 42.308 0.00 0.00 0.00 4.35
4358 11303 4.263287 CCCCCATTTATATCACCGTCATCA 60.263 45.833 0.00 0.00 0.00 3.07
4366 11311 2.556622 CGCCAACCCCCATTTATATCAC 59.443 50.000 0.00 0.00 0.00 3.06
4372 11317 0.900647 CCAACGCCAACCCCCATTTA 60.901 55.000 0.00 0.00 0.00 1.40
4411 11356 1.744320 AAAAGTGAAACCCCTGCGCC 61.744 55.000 4.18 0.00 37.80 6.53
4412 11357 0.597377 CAAAAGTGAAACCCCTGCGC 60.597 55.000 0.00 0.00 37.80 6.09
4414 11359 0.249868 GGCAAAAGTGAAACCCCTGC 60.250 55.000 0.00 0.00 37.80 4.85
4415 11360 0.031994 CGGCAAAAGTGAAACCCCTG 59.968 55.000 0.00 0.00 37.80 4.45
4416 11361 0.396556 ACGGCAAAAGTGAAACCCCT 60.397 50.000 0.00 0.00 37.80 4.79
4417 11362 0.249280 CACGGCAAAAGTGAAACCCC 60.249 55.000 0.00 0.00 41.83 4.95
4436 11381 1.065998 ACATTGATGGTTGCCATTGCC 60.066 47.619 1.88 0.00 45.26 4.52
4443 11388 3.005684 TGAAACCTGACATTGATGGTTGC 59.994 43.478 11.26 10.40 41.36 4.17
4447 11392 5.786311 ACAATTGAAACCTGACATTGATGG 58.214 37.500 13.59 0.00 0.00 3.51
4491 11436 7.464358 GGTTGTGACTTGTCATATGATACAAC 58.536 38.462 23.09 23.09 42.56 3.32
4497 11442 4.529109 TCGGTTGTGACTTGTCATATGA 57.471 40.909 0.00 0.00 0.00 2.15
4500 11445 3.064207 GCTTCGGTTGTGACTTGTCATA 58.936 45.455 6.74 1.35 0.00 2.15
4502 11447 1.295792 GCTTCGGTTGTGACTTGTCA 58.704 50.000 0.00 0.00 0.00 3.58
4550 11497 6.609533 TCAGACGACTTACAAGTAGCTAAAG 58.390 40.000 0.00 0.00 39.88 1.85
4573 11520 6.721321 TCGGACTGACACAAAAACTATTTTC 58.279 36.000 0.00 0.00 36.62 2.29
4574 11521 6.540914 TCTCGGACTGACACAAAAACTATTTT 59.459 34.615 0.00 0.00 39.30 1.82
4587 11534 1.251527 GGCTCCTTCTCGGACTGACA 61.252 60.000 0.00 0.00 36.69 3.58
4592 11539 0.390472 CAAGTGGCTCCTTCTCGGAC 60.390 60.000 0.00 0.00 36.69 4.79
4595 11542 0.108424 CCTCAAGTGGCTCCTTCTCG 60.108 60.000 0.00 0.00 0.00 4.04
4596 11543 0.251634 CCCTCAAGTGGCTCCTTCTC 59.748 60.000 0.00 0.00 0.00 2.87
4599 11547 1.074566 CTTTCCCTCAAGTGGCTCCTT 59.925 52.381 0.00 0.00 0.00 3.36
4607 11555 5.568620 TTAGCTTCTTCTTTCCCTCAAGT 57.431 39.130 0.00 0.00 0.00 3.16
4610 11558 4.265073 GCATTAGCTTCTTCTTTCCCTCA 58.735 43.478 0.00 0.00 37.91 3.86
4614 11562 2.356069 CCGGCATTAGCTTCTTCTTTCC 59.644 50.000 0.00 0.00 41.70 3.13


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

AutoCloner maintained by Alex Coulton.