Multiple sequence alignment - TraesCS6D01G307800

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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 TraesCS6D01G307800 chr6D 100.000 2375 0 0 1 2375 418770965 418768591 0.000000e+00 4386.0
1 TraesCS6D01G307800 chr6D 92.748 786 36 10 937 1711 418732918 418733693 0.000000e+00 1116.0
2 TraesCS6D01G307800 chr6D 82.431 1127 82 59 252 1281 418883710 418882603 0.000000e+00 878.0
3 TraesCS6D01G307800 chr6D 84.113 812 62 31 589 1377 418893102 418892335 0.000000e+00 723.0
4 TraesCS6D01G307800 chr6D 84.854 548 43 13 252 762 418732252 418732796 1.260000e-142 516.0
5 TraesCS6D01G307800 chr6D 92.920 226 12 3 2152 2373 120666074 120665849 2.280000e-85 326.0
6 TraesCS6D01G307800 chr6D 93.750 48 1 1 1725 1770 418733727 418733774 1.180000e-08 71.3
7 TraesCS6D01G307800 chr6B 88.377 1497 85 42 248 1709 631192612 631194054 0.000000e+00 1718.0
8 TraesCS6D01G307800 chr6B 89.163 812 44 20 815 1600 631246256 631245463 0.000000e+00 972.0
9 TraesCS6D01G307800 chr6B 80.611 1310 137 63 252 1527 631741789 631740563 0.000000e+00 904.0
10 TraesCS6D01G307800 chr6B 81.521 1223 113 56 261 1402 631535623 631534433 0.000000e+00 902.0
11 TraesCS6D01G307800 chr6B 85.857 700 59 21 836 1529 631844072 631843407 0.000000e+00 708.0
12 TraesCS6D01G307800 chr6B 87.027 555 54 12 227 768 631247063 631246514 5.610000e-171 610.0
13 TraesCS6D01G307800 chr6B 92.793 222 12 3 2158 2375 693805971 693806192 3.810000e-83 318.0
14 TraesCS6D01G307800 chr6B 77.469 324 24 17 253 535 631846270 631845955 5.290000e-32 148.0
15 TraesCS6D01G307800 chr6B 86.364 66 6 3 1706 1770 631194215 631194278 4.240000e-08 69.4
16 TraesCS6D01G307800 chr6B 97.059 34 1 0 2113 2146 48072093 48072060 9.170000e-05 58.4
17 TraesCS6D01G307800 chr6A 87.011 1586 88 54 175 1671 562271145 562272701 0.000000e+00 1679.0
18 TraesCS6D01G307800 chr6A 87.453 1068 69 36 690 1708 562400791 562399740 0.000000e+00 1170.0
19 TraesCS6D01G307800 chr6A 81.220 1230 96 62 252 1402 562471253 562470080 0.000000e+00 867.0
20 TraesCS6D01G307800 chr6A 83.918 883 73 33 555 1402 562250432 562251280 0.000000e+00 780.0
21 TraesCS6D01G307800 chr6A 84.568 810 59 27 638 1406 562488261 562487477 0.000000e+00 743.0
22 TraesCS6D01G307800 chr6A 90.133 527 30 9 175 693 562402465 562401953 0.000000e+00 665.0
23 TraesCS6D01G307800 chr6A 91.813 171 6 2 1693 1855 562399725 562399555 5.110000e-57 231.0
24 TraesCS6D01G307800 chr6A 80.328 305 21 15 252 518 562249684 562249987 6.700000e-46 195.0
25 TraesCS6D01G307800 chr6A 92.593 108 3 2 1854 1960 562399344 562399241 1.470000e-32 150.0
26 TraesCS6D01G307800 chr6A 88.172 93 7 1 1960 2052 562397318 562397230 8.980000e-20 108.0
27 TraesCS6D01G307800 chr3D 94.273 227 9 4 2152 2375 460439955 460440180 6.280000e-91 344.0
28 TraesCS6D01G307800 chr3D 92.920 226 13 3 2153 2375 84888538 84888763 2.280000e-85 326.0
29 TraesCS6D01G307800 chr3D 87.671 73 9 0 2075 2147 47175658 47175586 4.210000e-13 86.1
30 TraesCS6D01G307800 chr1D 94.470 217 10 2 2158 2372 12412565 12412349 1.360000e-87 333.0
31 TraesCS6D01G307800 chr1D 93.119 218 12 3 2159 2375 66415985 66415770 1.370000e-82 316.0
32 TraesCS6D01G307800 chr2D 94.009 217 12 1 2158 2373 562351461 562351677 6.330000e-86 327.0
33 TraesCS6D01G307800 chr5D 93.243 222 10 4 2158 2375 122626686 122626906 2.940000e-84 322.0
34 TraesCS6D01G307800 chr5D 92.035 226 12 5 2154 2375 408295987 408295764 1.770000e-81 313.0
35 TraesCS6D01G307800 chr5D 81.818 132 22 2 37 167 343121105 343120975 2.500000e-20 110.0
36 TraesCS6D01G307800 chr1B 83.234 167 22 5 1 167 556971219 556971059 5.290000e-32 148.0
37 TraesCS6D01G307800 chr7A 82.249 169 25 3 1 169 639578825 639578988 8.850000e-30 141.0
38 TraesCS6D01G307800 chr7A 86.905 84 9 1 87 170 558108412 558108493 2.510000e-15 93.5
39 TraesCS6D01G307800 chr4A 95.181 83 4 0 2070 2152 137547118 137547200 5.330000e-27 132.0
40 TraesCS6D01G307800 chrUn 87.273 110 14 0 3 112 93831573 93831682 2.480000e-25 126.0
41 TraesCS6D01G307800 chrUn 97.500 40 1 0 2113 2152 97120259 97120298 4.240000e-08 69.4
42 TraesCS6D01G307800 chr5B 87.619 105 12 1 37 141 51970832 51970935 1.150000e-23 121.0
43 TraesCS6D01G307800 chr3B 86.585 82 9 2 87 167 804111805 804111725 3.250000e-14 89.8
44 TraesCS6D01G307800 chr3A 87.500 80 7 3 21 99 599581846 599581769 3.250000e-14 89.8
45 TraesCS6D01G307800 chr5A 94.444 54 3 0 114 167 444090345 444090292 1.510000e-12 84.2
46 TraesCS6D01G307800 chr7D 86.667 75 1 1 2076 2150 105286006 105286071 9.100000e-10 75.0
47 TraesCS6D01G307800 chr2A 97.143 35 1 0 2 36 649712818 649712852 2.550000e-05 60.2
48 TraesCS6D01G307800 chr2B 100.000 28 0 0 135 162 74025455 74025482 4.000000e-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 TraesCS6D01G307800 chr6D 418768591 418770965 2374 True 4386.000000 4386 100.000000 1 2375 1 chr6D.!!$R2 2374
1 TraesCS6D01G307800 chr6D 418882603 418883710 1107 True 878.000000 878 82.431000 252 1281 1 chr6D.!!$R3 1029
2 TraesCS6D01G307800 chr6D 418892335 418893102 767 True 723.000000 723 84.113000 589 1377 1 chr6D.!!$R4 788
3 TraesCS6D01G307800 chr6D 418732252 418733774 1522 False 567.766667 1116 90.450667 252 1770 3 chr6D.!!$F1 1518
4 TraesCS6D01G307800 chr6B 631740563 631741789 1226 True 904.000000 904 80.611000 252 1527 1 chr6B.!!$R3 1275
5 TraesCS6D01G307800 chr6B 631534433 631535623 1190 True 902.000000 902 81.521000 261 1402 1 chr6B.!!$R2 1141
6 TraesCS6D01G307800 chr6B 631192612 631194278 1666 False 893.700000 1718 87.370500 248 1770 2 chr6B.!!$F2 1522
7 TraesCS6D01G307800 chr6B 631245463 631247063 1600 True 791.000000 972 88.095000 227 1600 2 chr6B.!!$R4 1373
8 TraesCS6D01G307800 chr6B 631843407 631846270 2863 True 428.000000 708 81.663000 253 1529 2 chr6B.!!$R5 1276
9 TraesCS6D01G307800 chr6A 562271145 562272701 1556 False 1679.000000 1679 87.011000 175 1671 1 chr6A.!!$F1 1496
10 TraesCS6D01G307800 chr6A 562470080 562471253 1173 True 867.000000 867 81.220000 252 1402 1 chr6A.!!$R1 1150
11 TraesCS6D01G307800 chr6A 562487477 562488261 784 True 743.000000 743 84.568000 638 1406 1 chr6A.!!$R2 768
12 TraesCS6D01G307800 chr6A 562249684 562251280 1596 False 487.500000 780 82.123000 252 1402 2 chr6A.!!$F2 1150
13 TraesCS6D01G307800 chr6A 562397230 562402465 5235 True 464.800000 1170 90.032800 175 2052 5 chr6A.!!$R3 1877

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
687 2363 0.459899 AGCCACGCAGACGATCAATA 59.54 50.0 0.0 0.0 43.93 1.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2130 7879 0.031585 TCACGGAGTTGAGGTGTTCG 59.968 55.0 0.0 0.0 41.61 3.95 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
25 26 8.522178 CAGTCGACTAAGATTTAACAAAGTCT 57.478 34.615 19.57 0.00 32.96 3.24
26 27 8.640291 CAGTCGACTAAGATTTAACAAAGTCTC 58.360 37.037 19.57 0.00 32.96 3.36
27 28 8.358148 AGTCGACTAAGATTTAACAAAGTCTCA 58.642 33.333 18.46 0.00 32.96 3.27
28 29 8.640291 GTCGACTAAGATTTAACAAAGTCTCAG 58.360 37.037 8.70 0.00 32.96 3.35
29 30 8.358148 TCGACTAAGATTTAACAAAGTCTCAGT 58.642 33.333 0.00 0.00 32.96 3.41
30 31 8.640291 CGACTAAGATTTAACAAAGTCTCAGTC 58.360 37.037 4.62 4.62 32.96 3.51
31 32 8.522178 ACTAAGATTTAACAAAGTCTCAGTCG 57.478 34.615 0.00 0.00 0.00 4.18
32 33 8.358148 ACTAAGATTTAACAAAGTCTCAGTCGA 58.642 33.333 0.00 0.00 0.00 4.20
33 34 9.360093 CTAAGATTTAACAAAGTCTCAGTCGAT 57.640 33.333 0.00 0.00 0.00 3.59
34 35 7.588143 AGATTTAACAAAGTCTCAGTCGATG 57.412 36.000 0.00 0.00 0.00 3.84
35 36 7.155328 AGATTTAACAAAGTCTCAGTCGATGT 58.845 34.615 0.00 0.00 0.00 3.06
36 37 7.657761 AGATTTAACAAAGTCTCAGTCGATGTT 59.342 33.333 0.00 0.00 34.31 2.71
37 38 8.827177 ATTTAACAAAGTCTCAGTCGATGTTA 57.173 30.769 0.00 0.00 32.39 2.41
38 39 8.827177 TTTAACAAAGTCTCAGTCGATGTTAT 57.173 30.769 3.98 0.00 33.37 1.89
39 40 9.917129 TTTAACAAAGTCTCAGTCGATGTTATA 57.083 29.630 3.98 0.00 33.37 0.98
41 42 8.635877 AACAAAGTCTCAGTCGATGTTATATC 57.364 34.615 0.00 0.00 0.00 1.63
42 43 7.203910 ACAAAGTCTCAGTCGATGTTATATCC 58.796 38.462 0.00 0.00 0.00 2.59
43 44 5.614923 AGTCTCAGTCGATGTTATATCCG 57.385 43.478 0.00 0.00 0.00 4.18
44 45 5.064558 AGTCTCAGTCGATGTTATATCCGT 58.935 41.667 0.00 0.00 0.00 4.69
45 46 6.228995 AGTCTCAGTCGATGTTATATCCGTA 58.771 40.000 0.00 0.00 0.00 4.02
46 47 6.709397 AGTCTCAGTCGATGTTATATCCGTAA 59.291 38.462 0.00 0.00 0.00 3.18
47 48 7.016466 GTCTCAGTCGATGTTATATCCGTAAG 58.984 42.308 0.00 0.00 0.00 2.34
48 49 6.932960 TCTCAGTCGATGTTATATCCGTAAGA 59.067 38.462 0.00 0.00 43.02 2.10
49 50 7.606839 TCTCAGTCGATGTTATATCCGTAAGAT 59.393 37.037 0.00 0.00 43.02 2.40
50 51 8.782339 TCAGTCGATGTTATATCCGTAAGATA 57.218 34.615 0.00 0.00 41.73 1.98
66 67 9.017509 TCCGTAAGATATTACATTAAGATCCGT 57.982 33.333 10.64 0.00 37.15 4.69
67 68 9.073368 CCGTAAGATATTACATTAAGATCCGTG 57.927 37.037 10.64 0.00 37.15 4.94
68 69 9.622004 CGTAAGATATTACATTAAGATCCGTGT 57.378 33.333 10.64 0.00 37.15 4.49
116 117 9.671279 TCTTTTTCTCTCTTGCATGTTATATCA 57.329 29.630 0.00 0.00 0.00 2.15
117 118 9.713740 CTTTTTCTCTCTTGCATGTTATATCAC 57.286 33.333 0.00 0.00 0.00 3.06
118 119 9.453572 TTTTTCTCTCTTGCATGTTATATCACT 57.546 29.630 0.00 0.00 0.00 3.41
119 120 9.453572 TTTTCTCTCTTGCATGTTATATCACTT 57.546 29.630 0.00 0.00 0.00 3.16
120 121 8.429493 TTCTCTCTTGCATGTTATATCACTTG 57.571 34.615 0.00 0.00 0.00 3.16
121 122 7.785033 TCTCTCTTGCATGTTATATCACTTGA 58.215 34.615 7.02 0.00 0.00 3.02
122 123 7.708322 TCTCTCTTGCATGTTATATCACTTGAC 59.292 37.037 7.02 0.84 0.00 3.18
123 124 6.763135 TCTCTTGCATGTTATATCACTTGACC 59.237 38.462 7.02 0.00 0.00 4.02
124 125 5.523552 TCTTGCATGTTATATCACTTGACCG 59.476 40.000 7.02 0.00 0.00 4.79
125 126 5.017294 TGCATGTTATATCACTTGACCGA 57.983 39.130 7.02 0.00 0.00 4.69
126 127 5.049828 TGCATGTTATATCACTTGACCGAG 58.950 41.667 7.02 0.00 0.00 4.63
127 128 5.163457 TGCATGTTATATCACTTGACCGAGA 60.163 40.000 7.02 0.00 0.00 4.04
128 129 5.928839 GCATGTTATATCACTTGACCGAGAT 59.071 40.000 7.02 0.00 0.00 2.75
129 130 6.425114 GCATGTTATATCACTTGACCGAGATT 59.575 38.462 7.02 0.00 0.00 2.40
130 131 7.041780 GCATGTTATATCACTTGACCGAGATTT 60.042 37.037 7.02 0.00 0.00 2.17
131 132 7.770801 TGTTATATCACTTGACCGAGATTTG 57.229 36.000 0.00 0.00 0.00 2.32
132 133 6.761242 TGTTATATCACTTGACCGAGATTTGG 59.239 38.462 0.00 0.00 0.00 3.28
133 134 3.703001 ATCACTTGACCGAGATTTGGT 57.297 42.857 0.00 0.00 44.10 3.67
134 135 3.485463 TCACTTGACCGAGATTTGGTT 57.515 42.857 0.00 0.00 40.63 3.67
135 136 4.610605 TCACTTGACCGAGATTTGGTTA 57.389 40.909 0.00 0.00 40.63 2.85
136 137 4.963373 TCACTTGACCGAGATTTGGTTAA 58.037 39.130 0.00 0.00 40.63 2.01
137 138 5.369833 TCACTTGACCGAGATTTGGTTAAA 58.630 37.500 0.00 0.00 40.63 1.52
138 139 6.001460 TCACTTGACCGAGATTTGGTTAAAT 58.999 36.000 0.00 0.00 40.63 1.40
152 153 9.922305 GATTTGGTTAAATCTCAGTCGATTAAG 57.078 33.333 5.70 0.00 45.57 1.85
153 154 9.667107 ATTTGGTTAAATCTCAGTCGATTAAGA 57.333 29.630 0.00 0.00 33.47 2.10
154 155 8.475331 TTGGTTAAATCTCAGTCGATTAAGAC 57.525 34.615 0.00 0.00 41.23 3.01
155 156 7.039882 TGGTTAAATCTCAGTCGATTAAGACC 58.960 38.462 0.00 0.00 41.83 3.85
156 157 7.093465 TGGTTAAATCTCAGTCGATTAAGACCT 60.093 37.037 0.00 0.00 41.83 3.85
157 158 8.411683 GGTTAAATCTCAGTCGATTAAGACCTA 58.588 37.037 0.00 0.00 41.83 3.08
158 159 9.798994 GTTAAATCTCAGTCGATTAAGACCTAA 57.201 33.333 0.00 0.00 41.83 2.69
159 160 9.798994 TTAAATCTCAGTCGATTAAGACCTAAC 57.201 33.333 0.00 0.00 41.83 2.34
160 161 5.831702 TCTCAGTCGATTAAGACCTAACC 57.168 43.478 0.00 0.00 41.83 2.85
161 162 5.258841 TCTCAGTCGATTAAGACCTAACCA 58.741 41.667 0.00 0.00 41.83 3.67
162 163 5.125097 TCTCAGTCGATTAAGACCTAACCAC 59.875 44.000 0.00 0.00 41.83 4.16
163 164 4.768448 TCAGTCGATTAAGACCTAACCACA 59.232 41.667 0.00 0.00 41.83 4.17
164 165 4.863131 CAGTCGATTAAGACCTAACCACAC 59.137 45.833 0.00 0.00 41.83 3.82
165 166 4.081807 AGTCGATTAAGACCTAACCACACC 60.082 45.833 0.00 0.00 41.83 4.16
166 167 3.196254 TCGATTAAGACCTAACCACACCC 59.804 47.826 0.00 0.00 0.00 4.61
167 168 3.055675 CGATTAAGACCTAACCACACCCA 60.056 47.826 0.00 0.00 0.00 4.51
168 169 4.563993 CGATTAAGACCTAACCACACCCAA 60.564 45.833 0.00 0.00 0.00 4.12
169 170 2.651382 AAGACCTAACCACACCCAAC 57.349 50.000 0.00 0.00 0.00 3.77
170 171 0.769247 AGACCTAACCACACCCAACC 59.231 55.000 0.00 0.00 0.00 3.77
171 172 0.475044 GACCTAACCACACCCAACCA 59.525 55.000 0.00 0.00 0.00 3.67
172 173 1.074889 GACCTAACCACACCCAACCAT 59.925 52.381 0.00 0.00 0.00 3.55
173 174 1.203001 ACCTAACCACACCCAACCATG 60.203 52.381 0.00 0.00 0.00 3.66
403 449 3.242712 GCAACACACTCGGAAAACAATTG 59.757 43.478 3.24 3.24 0.00 2.32
641 2317 4.054825 GACCCCGACGCCGTAACA 62.055 66.667 0.00 0.00 0.00 2.41
650 2326 2.279659 CGACGCCGTAACACGATTATTT 59.720 45.455 0.00 0.00 46.05 1.40
684 2360 2.125952 CAGCCACGCAGACGATCA 60.126 61.111 0.00 0.00 43.93 2.92
687 2363 0.459899 AGCCACGCAGACGATCAATA 59.540 50.000 0.00 0.00 43.93 1.90
802 4066 5.408909 GCGGCTTAATCTTCTAACCTAATCC 59.591 44.000 0.00 0.00 0.00 3.01
831 4095 2.029288 CGCTCGAGCCAAGCAGAAA 61.029 57.895 30.66 0.00 39.81 2.52
885 4175 2.513666 CACCCACACACGCACACT 60.514 61.111 0.00 0.00 0.00 3.55
1607 5020 4.020573 TCGGCCTTGTTCTTCTGATTCTTA 60.021 41.667 0.00 0.00 0.00 2.10
1655 5080 9.924650 ATTAGTTAACAGACCCGATGTATAATC 57.075 33.333 8.61 0.00 0.00 1.75
1686 5113 2.566997 CGATCAGTCGTTACAGCCG 58.433 57.895 0.00 0.00 42.78 5.52
1736 5342 4.808895 GCTTCCCATCGTTTTTCTTTTTGT 59.191 37.500 0.00 0.00 0.00 2.83
1869 5694 0.257616 AGAAGGAGTCGAGGAGGAGG 59.742 60.000 0.00 0.00 0.00 4.30
1935 5761 4.264614 CGTGTTCTGTACGTATCATCAACC 59.735 45.833 0.00 0.88 36.83 3.77
1940 5766 4.860352 TCTGTACGTATCATCAACCGTTTG 59.140 41.667 0.00 0.00 34.95 2.93
2017 7766 3.069300 CGAGGAGTGATGTTCTGGATGAT 59.931 47.826 0.00 0.00 0.00 2.45
2018 7767 4.279420 CGAGGAGTGATGTTCTGGATGATA 59.721 45.833 0.00 0.00 0.00 2.15
2019 7768 5.047448 CGAGGAGTGATGTTCTGGATGATAT 60.047 44.000 0.00 0.00 0.00 1.63
2020 7769 6.518032 CGAGGAGTGATGTTCTGGATGATATT 60.518 42.308 0.00 0.00 0.00 1.28
2021 7770 7.146715 AGGAGTGATGTTCTGGATGATATTT 57.853 36.000 0.00 0.00 0.00 1.40
2036 7785 6.472163 GGATGATATTTTTGGCGTGTAGTTTG 59.528 38.462 0.00 0.00 0.00 2.93
2042 7791 1.218875 TGGCGTGTAGTTTGCAGACG 61.219 55.000 1.15 0.00 0.00 4.18
2045 7794 0.782384 CGTGTAGTTTGCAGACGACC 59.218 55.000 16.19 8.13 31.71 4.79
2049 7798 0.319211 TAGTTTGCAGACGACCCGTG 60.319 55.000 1.15 0.00 41.37 4.94
2052 7801 3.741830 TTGCAGACGACCCGTGCAA 62.742 57.895 11.50 11.50 42.99 4.08
2053 7802 3.712881 GCAGACGACCCGTGCAAC 61.713 66.667 0.00 0.00 41.37 4.17
2066 7815 2.174363 GTGCAACGGGGTAGTTTACT 57.826 50.000 0.00 0.00 30.96 2.24
2067 7816 2.071540 GTGCAACGGGGTAGTTTACTC 58.928 52.381 0.00 0.00 30.96 2.59
2068 7817 1.972795 TGCAACGGGGTAGTTTACTCT 59.027 47.619 0.00 0.00 30.96 3.24
2069 7818 2.369532 TGCAACGGGGTAGTTTACTCTT 59.630 45.455 0.00 0.00 30.96 2.85
2070 7819 3.577848 TGCAACGGGGTAGTTTACTCTTA 59.422 43.478 0.00 0.00 30.96 2.10
2071 7820 4.040217 TGCAACGGGGTAGTTTACTCTTAA 59.960 41.667 0.00 0.00 30.96 1.85
2072 7821 4.996758 GCAACGGGGTAGTTTACTCTTAAA 59.003 41.667 0.00 0.00 30.96 1.52
2073 7822 5.106948 GCAACGGGGTAGTTTACTCTTAAAC 60.107 44.000 0.00 0.00 45.22 2.01
2074 7823 5.152623 ACGGGGTAGTTTACTCTTAAACC 57.847 43.478 4.10 0.00 45.78 3.27
2075 7824 4.020218 ACGGGGTAGTTTACTCTTAAACCC 60.020 45.833 8.65 8.65 45.78 4.11
2076 7825 4.223700 CGGGGTAGTTTACTCTTAAACCCT 59.776 45.833 14.44 0.00 45.78 4.34
2077 7826 5.494724 GGGGTAGTTTACTCTTAAACCCTG 58.505 45.833 14.44 0.00 45.78 4.45
2078 7827 5.013495 GGGGTAGTTTACTCTTAAACCCTGT 59.987 44.000 14.44 0.00 45.78 4.00
2079 7828 6.466326 GGGGTAGTTTACTCTTAAACCCTGTT 60.466 42.308 14.44 0.00 45.78 3.16
2080 7829 6.652481 GGGTAGTTTACTCTTAAACCCTGTTC 59.348 42.308 9.57 0.00 45.78 3.18
2081 7830 6.367149 GGTAGTTTACTCTTAAACCCTGTTCG 59.633 42.308 4.10 0.00 45.78 3.95
2082 7831 5.303165 AGTTTACTCTTAAACCCTGTTCGG 58.697 41.667 4.10 0.00 45.78 4.30
2083 7832 2.180432 ACTCTTAAACCCTGTTCGGC 57.820 50.000 0.00 0.00 0.00 5.54
2084 7833 1.418637 ACTCTTAAACCCTGTTCGGCA 59.581 47.619 0.00 0.00 0.00 5.69
2085 7834 2.076863 CTCTTAAACCCTGTTCGGCAG 58.923 52.381 1.70 1.70 44.63 4.85
2086 7835 0.521735 CTTAAACCCTGTTCGGCAGC 59.478 55.000 2.96 0.00 43.71 5.25
2087 7836 0.891904 TTAAACCCTGTTCGGCAGCC 60.892 55.000 0.00 0.00 43.71 4.85
2088 7837 2.757980 TAAACCCTGTTCGGCAGCCC 62.758 60.000 5.63 0.00 43.71 5.19
2090 7839 4.785453 CCCTGTTCGGCAGCCCTC 62.785 72.222 5.63 0.00 43.71 4.30
2091 7840 4.785453 CCTGTTCGGCAGCCCTCC 62.785 72.222 5.63 0.00 43.71 4.30
2103 7852 4.821589 CCCTCCGCTCCGCAACTC 62.822 72.222 0.00 0.00 0.00 3.01
2104 7853 4.821589 CCTCCGCTCCGCAACTCC 62.822 72.222 0.00 0.00 0.00 3.85
2109 7858 3.491652 GCTCCGCAACTCCGCTTC 61.492 66.667 0.00 0.00 0.00 3.86
2110 7859 3.181967 CTCCGCAACTCCGCTTCG 61.182 66.667 0.00 0.00 0.00 3.79
2123 7872 4.521062 CTTCGGGAGCGGGCTGAG 62.521 72.222 0.00 0.00 0.00 3.35
2136 7885 3.414700 CTGAGCGGCACCGAACAC 61.415 66.667 14.43 1.04 42.83 3.32
2137 7886 4.980805 TGAGCGGCACCGAACACC 62.981 66.667 14.43 0.00 42.83 4.16
2138 7887 4.681978 GAGCGGCACCGAACACCT 62.682 66.667 14.43 0.00 42.83 4.00
2139 7888 4.681978 AGCGGCACCGAACACCTC 62.682 66.667 14.43 0.00 42.83 3.85
2140 7889 4.980805 GCGGCACCGAACACCTCA 62.981 66.667 14.43 0.00 42.83 3.86
2141 7890 2.280524 CGGCACCGAACACCTCAA 60.281 61.111 2.01 0.00 42.83 3.02
2142 7891 2.604174 CGGCACCGAACACCTCAAC 61.604 63.158 2.01 0.00 42.83 3.18
2143 7892 1.227853 GGCACCGAACACCTCAACT 60.228 57.895 0.00 0.00 0.00 3.16
2144 7893 1.228657 GGCACCGAACACCTCAACTC 61.229 60.000 0.00 0.00 0.00 3.01
2145 7894 1.228657 GCACCGAACACCTCAACTCC 61.229 60.000 0.00 0.00 0.00 3.85
2146 7895 0.944311 CACCGAACACCTCAACTCCG 60.944 60.000 0.00 0.00 0.00 4.63
2147 7896 1.366366 CCGAACACCTCAACTCCGT 59.634 57.895 0.00 0.00 0.00 4.69
2148 7897 0.944311 CCGAACACCTCAACTCCGTG 60.944 60.000 0.00 0.00 0.00 4.94
2149 7898 0.031585 CGAACACCTCAACTCCGTGA 59.968 55.000 0.00 0.00 0.00 4.35
2150 7899 1.537348 CGAACACCTCAACTCCGTGAA 60.537 52.381 0.00 0.00 0.00 3.18
2151 7900 2.767505 GAACACCTCAACTCCGTGAAT 58.232 47.619 0.00 0.00 0.00 2.57
2152 7901 2.930826 ACACCTCAACTCCGTGAATT 57.069 45.000 0.00 0.00 0.00 2.17
2153 7902 3.208747 ACACCTCAACTCCGTGAATTT 57.791 42.857 0.00 0.00 0.00 1.82
2154 7903 3.551846 ACACCTCAACTCCGTGAATTTT 58.448 40.909 0.00 0.00 0.00 1.82
2155 7904 3.951680 ACACCTCAACTCCGTGAATTTTT 59.048 39.130 0.00 0.00 0.00 1.94
2156 7905 5.127491 ACACCTCAACTCCGTGAATTTTTA 58.873 37.500 0.00 0.00 0.00 1.52
2157 7906 5.591067 ACACCTCAACTCCGTGAATTTTTAA 59.409 36.000 0.00 0.00 0.00 1.52
2158 7907 6.142817 CACCTCAACTCCGTGAATTTTTAAG 58.857 40.000 0.00 0.00 0.00 1.85
2159 7908 6.017440 CACCTCAACTCCGTGAATTTTTAAGA 60.017 38.462 0.00 0.00 0.00 2.10
2160 7909 6.204882 ACCTCAACTCCGTGAATTTTTAAGAG 59.795 38.462 0.00 0.00 0.00 2.85
2161 7910 5.997385 TCAACTCCGTGAATTTTTAAGAGC 58.003 37.500 0.00 0.00 0.00 4.09
2162 7911 5.529430 TCAACTCCGTGAATTTTTAAGAGCA 59.471 36.000 0.00 0.00 0.00 4.26
2163 7912 6.206634 TCAACTCCGTGAATTTTTAAGAGCAT 59.793 34.615 0.00 0.00 0.00 3.79
2164 7913 6.183309 ACTCCGTGAATTTTTAAGAGCATC 57.817 37.500 0.00 0.00 0.00 3.91
2176 7925 1.427020 GAGCATCTTCAACAGCCGC 59.573 57.895 0.00 0.00 0.00 6.53
2177 7926 2.099062 GCATCTTCAACAGCCGCG 59.901 61.111 0.00 0.00 0.00 6.46
2178 7927 2.099062 CATCTTCAACAGCCGCGC 59.901 61.111 0.00 0.00 0.00 6.86
2179 7928 2.358615 ATCTTCAACAGCCGCGCA 60.359 55.556 8.75 0.00 0.00 6.09
2180 7929 1.965930 ATCTTCAACAGCCGCGCAA 60.966 52.632 8.75 0.00 0.00 4.85
2181 7930 2.187599 ATCTTCAACAGCCGCGCAAC 62.188 55.000 8.75 0.00 0.00 4.17
2182 7931 4.306471 TTCAACAGCCGCGCAACG 62.306 61.111 8.75 0.00 43.15 4.10
2229 7978 4.383602 CGCCGTTCGCCTGGTTTG 62.384 66.667 0.00 0.00 0.00 2.93
2230 7979 4.038080 GCCGTTCGCCTGGTTTGG 62.038 66.667 0.00 0.00 0.00 3.28
2267 8016 4.617520 TCCAGCAGCCGCGTCAAA 62.618 61.111 4.92 0.00 45.49 2.69
2268 8017 3.659092 CCAGCAGCCGCGTCAAAA 61.659 61.111 4.92 0.00 45.49 2.44
2269 8018 2.562912 CAGCAGCCGCGTCAAAAT 59.437 55.556 4.92 0.00 45.49 1.82
2270 8019 1.081242 CAGCAGCCGCGTCAAAATT 60.081 52.632 4.92 0.00 45.49 1.82
2271 8020 1.081242 AGCAGCCGCGTCAAAATTG 60.081 52.632 4.92 0.00 45.49 2.32
2272 8021 1.081509 GCAGCCGCGTCAAAATTGA 60.082 52.632 4.92 0.00 34.20 2.57
2273 8022 1.067199 GCAGCCGCGTCAAAATTGAG 61.067 55.000 4.92 0.00 37.98 3.02
2274 8023 1.067199 CAGCCGCGTCAAAATTGAGC 61.067 55.000 4.92 0.00 37.98 4.26
2275 8024 2.145905 GCCGCGTCAAAATTGAGCG 61.146 57.895 21.88 21.88 45.45 5.03
2276 8025 2.145905 CCGCGTCAAAATTGAGCGC 61.146 57.895 22.71 22.28 45.01 5.92
2277 8026 3.352536 GCGTCAAAATTGAGCGCG 58.647 55.556 19.31 0.00 42.68 6.86
2278 8027 2.767919 GCGTCAAAATTGAGCGCGC 61.768 57.895 26.66 26.66 42.68 6.86
2279 8028 2.479782 CGTCAAAATTGAGCGCGCG 61.480 57.895 28.44 28.44 37.98 6.86
2280 8029 2.501650 TCAAAATTGAGCGCGCGC 60.502 55.556 45.10 45.10 42.33 6.86
2303 8052 4.683721 TCCACGGCCGCGCTAAAA 62.684 61.111 28.58 0.21 0.00 1.52
2304 8053 3.505184 CCACGGCCGCGCTAAAAT 61.505 61.111 28.58 0.00 0.00 1.82
2305 8054 2.277247 CACGGCCGCGCTAAAATG 60.277 61.111 28.58 9.73 0.00 2.32
2306 8055 4.174129 ACGGCCGCGCTAAAATGC 62.174 61.111 28.58 0.00 0.00 3.56
2307 8056 4.172772 CGGCCGCGCTAAAATGCA 62.173 61.111 14.67 0.00 0.00 3.96
2308 8057 2.278142 GGCCGCGCTAAAATGCAG 60.278 61.111 5.56 0.00 0.00 4.41
2309 8058 2.951227 GCCGCGCTAAAATGCAGC 60.951 61.111 5.56 0.00 35.61 5.25
2314 8063 3.307262 GCTAAAATGCAGCGCGCG 61.307 61.111 28.44 28.44 46.97 6.86
2315 8064 3.307262 CTAAAATGCAGCGCGCGC 61.307 61.111 45.10 45.10 46.97 6.86
2325 8074 3.597626 GCGCGCGCTAAACATTGC 61.598 61.111 44.38 18.46 38.26 3.56
2335 8084 5.739237 CGCTAAACATTGCGTACATTTTT 57.261 34.783 0.00 0.00 46.09 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.522178 AGACTTTGTTAAATCTTAGTCGACTG 57.478 34.615 28.12 12.46 37.62 3.51
1 2 8.358148 TGAGACTTTGTTAAATCTTAGTCGACT 58.642 33.333 23.66 23.66 37.62 4.18
2 3 8.516811 TGAGACTTTGTTAAATCTTAGTCGAC 57.483 34.615 7.70 7.70 37.62 4.20
3 4 8.358148 ACTGAGACTTTGTTAAATCTTAGTCGA 58.642 33.333 0.00 0.00 34.02 4.20
4 5 8.522178 ACTGAGACTTTGTTAAATCTTAGTCG 57.478 34.615 0.00 0.00 34.02 4.18
5 6 8.640291 CGACTGAGACTTTGTTAAATCTTAGTC 58.360 37.037 12.53 12.53 44.91 2.59
6 7 8.358148 TCGACTGAGACTTTGTTAAATCTTAGT 58.642 33.333 0.00 0.00 39.83 2.24
7 8 8.744008 TCGACTGAGACTTTGTTAAATCTTAG 57.256 34.615 0.00 0.00 32.56 2.18
8 9 9.140286 CATCGACTGAGACTTTGTTAAATCTTA 57.860 33.333 0.00 0.00 0.00 2.10
9 10 7.657761 ACATCGACTGAGACTTTGTTAAATCTT 59.342 33.333 0.00 0.00 0.00 2.40
10 11 7.155328 ACATCGACTGAGACTTTGTTAAATCT 58.845 34.615 0.00 0.00 0.00 2.40
11 12 7.352719 ACATCGACTGAGACTTTGTTAAATC 57.647 36.000 0.00 0.00 0.00 2.17
12 13 7.730364 AACATCGACTGAGACTTTGTTAAAT 57.270 32.000 0.00 0.00 0.00 1.40
13 14 8.827177 ATAACATCGACTGAGACTTTGTTAAA 57.173 30.769 6.56 0.00 33.37 1.52
15 16 9.731819 GATATAACATCGACTGAGACTTTGTTA 57.268 33.333 5.28 5.28 33.94 2.41
16 17 7.707035 GGATATAACATCGACTGAGACTTTGTT 59.293 37.037 0.00 0.00 0.00 2.83
17 18 7.203910 GGATATAACATCGACTGAGACTTTGT 58.796 38.462 0.00 0.00 0.00 2.83
18 19 6.360947 CGGATATAACATCGACTGAGACTTTG 59.639 42.308 0.00 0.00 0.00 2.77
19 20 6.039493 ACGGATATAACATCGACTGAGACTTT 59.961 38.462 0.00 0.00 0.00 2.66
20 21 5.531659 ACGGATATAACATCGACTGAGACTT 59.468 40.000 0.00 0.00 0.00 3.01
21 22 5.064558 ACGGATATAACATCGACTGAGACT 58.935 41.667 0.00 0.00 0.00 3.24
22 23 5.359716 ACGGATATAACATCGACTGAGAC 57.640 43.478 0.00 0.00 0.00 3.36
23 24 6.932960 TCTTACGGATATAACATCGACTGAGA 59.067 38.462 0.00 0.00 0.00 3.27
24 25 7.130303 TCTTACGGATATAACATCGACTGAG 57.870 40.000 0.00 0.00 0.00 3.35
25 26 7.683437 ATCTTACGGATATAACATCGACTGA 57.317 36.000 0.00 0.00 32.04 3.41
40 41 9.017509 ACGGATCTTAATGTAATATCTTACGGA 57.982 33.333 0.00 0.00 40.15 4.69
41 42 9.073368 CACGGATCTTAATGTAATATCTTACGG 57.927 37.037 0.00 0.00 40.15 4.02
42 43 9.622004 ACACGGATCTTAATGTAATATCTTACG 57.378 33.333 0.00 0.00 40.15 3.18
90 91 9.671279 TGATATAACATGCAAGAGAGAAAAAGA 57.329 29.630 0.00 0.00 0.00 2.52
91 92 9.713740 GTGATATAACATGCAAGAGAGAAAAAG 57.286 33.333 0.00 0.00 0.00 2.27
92 93 9.453572 AGTGATATAACATGCAAGAGAGAAAAA 57.546 29.630 0.00 0.00 0.00 1.94
93 94 9.453572 AAGTGATATAACATGCAAGAGAGAAAA 57.546 29.630 0.00 0.00 0.00 2.29
94 95 8.886719 CAAGTGATATAACATGCAAGAGAGAAA 58.113 33.333 0.00 0.00 0.00 2.52
95 96 8.260114 TCAAGTGATATAACATGCAAGAGAGAA 58.740 33.333 0.00 0.00 0.00 2.87
96 97 7.708322 GTCAAGTGATATAACATGCAAGAGAGA 59.292 37.037 0.00 0.00 0.00 3.10
97 98 7.042187 GGTCAAGTGATATAACATGCAAGAGAG 60.042 40.741 0.00 0.00 0.00 3.20
98 99 6.763135 GGTCAAGTGATATAACATGCAAGAGA 59.237 38.462 0.00 0.00 0.00 3.10
99 100 6.292542 CGGTCAAGTGATATAACATGCAAGAG 60.293 42.308 0.00 0.00 0.00 2.85
100 101 5.523552 CGGTCAAGTGATATAACATGCAAGA 59.476 40.000 0.00 0.00 0.00 3.02
101 102 5.523552 TCGGTCAAGTGATATAACATGCAAG 59.476 40.000 0.00 0.00 0.00 4.01
102 103 5.423886 TCGGTCAAGTGATATAACATGCAA 58.576 37.500 0.00 0.00 0.00 4.08
103 104 5.017294 TCGGTCAAGTGATATAACATGCA 57.983 39.130 0.00 0.00 0.00 3.96
104 105 5.289595 TCTCGGTCAAGTGATATAACATGC 58.710 41.667 0.00 0.00 0.00 4.06
105 106 7.953158 AATCTCGGTCAAGTGATATAACATG 57.047 36.000 0.00 0.00 0.00 3.21
106 107 7.442364 CCAAATCTCGGTCAAGTGATATAACAT 59.558 37.037 0.00 0.00 0.00 2.71
107 108 6.761242 CCAAATCTCGGTCAAGTGATATAACA 59.239 38.462 0.00 0.00 0.00 2.41
108 109 6.761714 ACCAAATCTCGGTCAAGTGATATAAC 59.238 38.462 0.00 0.00 27.30 1.89
109 110 6.884832 ACCAAATCTCGGTCAAGTGATATAA 58.115 36.000 0.00 0.00 27.30 0.98
110 111 6.479972 ACCAAATCTCGGTCAAGTGATATA 57.520 37.500 0.00 0.00 27.30 0.86
111 112 5.359194 ACCAAATCTCGGTCAAGTGATAT 57.641 39.130 0.00 0.00 27.30 1.63
112 113 4.819105 ACCAAATCTCGGTCAAGTGATA 57.181 40.909 0.00 0.00 27.30 2.15
113 114 3.703001 ACCAAATCTCGGTCAAGTGAT 57.297 42.857 0.00 0.00 27.30 3.06
114 115 3.485463 AACCAAATCTCGGTCAAGTGA 57.515 42.857 0.00 0.00 34.99 3.41
115 116 5.682943 TTTAACCAAATCTCGGTCAAGTG 57.317 39.130 0.00 0.00 34.99 3.16
116 117 6.496338 GATTTAACCAAATCTCGGTCAAGT 57.504 37.500 3.43 0.00 44.47 3.16
127 128 9.667107 TCTTAATCGACTGAGATTTAACCAAAT 57.333 29.630 7.99 0.00 40.83 2.32
128 129 8.932791 GTCTTAATCGACTGAGATTTAACCAAA 58.067 33.333 0.00 0.00 40.83 3.28
129 130 7.548075 GGTCTTAATCGACTGAGATTTAACCAA 59.452 37.037 0.00 0.00 40.83 3.67
130 131 7.039882 GGTCTTAATCGACTGAGATTTAACCA 58.960 38.462 0.00 0.00 40.83 3.67
131 132 7.266400 AGGTCTTAATCGACTGAGATTTAACC 58.734 38.462 0.00 11.36 40.83 2.85
132 133 9.798994 TTAGGTCTTAATCGACTGAGATTTAAC 57.201 33.333 0.00 5.48 40.83 2.01
133 134 9.798994 GTTAGGTCTTAATCGACTGAGATTTAA 57.201 33.333 0.00 0.00 40.83 1.52
134 135 8.411683 GGTTAGGTCTTAATCGACTGAGATTTA 58.588 37.037 0.00 0.00 40.83 1.40
135 136 7.093465 TGGTTAGGTCTTAATCGACTGAGATTT 60.093 37.037 0.00 0.00 40.83 2.17
136 137 6.380274 TGGTTAGGTCTTAATCGACTGAGATT 59.620 38.462 0.00 7.85 42.77 2.40
137 138 5.892119 TGGTTAGGTCTTAATCGACTGAGAT 59.108 40.000 0.00 0.00 34.38 2.75
138 139 5.125097 GTGGTTAGGTCTTAATCGACTGAGA 59.875 44.000 0.00 0.00 34.38 3.27
139 140 5.105877 TGTGGTTAGGTCTTAATCGACTGAG 60.106 44.000 0.00 0.00 34.38 3.35
140 141 4.768448 TGTGGTTAGGTCTTAATCGACTGA 59.232 41.667 0.00 0.00 34.38 3.41
141 142 4.863131 GTGTGGTTAGGTCTTAATCGACTG 59.137 45.833 0.00 0.00 34.38 3.51
142 143 4.081807 GGTGTGGTTAGGTCTTAATCGACT 60.082 45.833 0.00 0.00 34.38 4.18
143 144 4.179298 GGTGTGGTTAGGTCTTAATCGAC 58.821 47.826 0.00 0.00 0.00 4.20
144 145 3.196254 GGGTGTGGTTAGGTCTTAATCGA 59.804 47.826 0.00 0.00 0.00 3.59
145 146 3.055675 TGGGTGTGGTTAGGTCTTAATCG 60.056 47.826 0.00 0.00 0.00 3.34
146 147 4.563140 TGGGTGTGGTTAGGTCTTAATC 57.437 45.455 0.00 0.00 0.00 1.75
147 148 4.507869 GGTTGGGTGTGGTTAGGTCTTAAT 60.508 45.833 0.00 0.00 0.00 1.40
148 149 3.181441 GGTTGGGTGTGGTTAGGTCTTAA 60.181 47.826 0.00 0.00 0.00 1.85
149 150 2.372837 GGTTGGGTGTGGTTAGGTCTTA 59.627 50.000 0.00 0.00 0.00 2.10
150 151 1.144298 GGTTGGGTGTGGTTAGGTCTT 59.856 52.381 0.00 0.00 0.00 3.01
151 152 0.769247 GGTTGGGTGTGGTTAGGTCT 59.231 55.000 0.00 0.00 0.00 3.85
152 153 0.475044 TGGTTGGGTGTGGTTAGGTC 59.525 55.000 0.00 0.00 0.00 3.85
153 154 1.154430 ATGGTTGGGTGTGGTTAGGT 58.846 50.000 0.00 0.00 0.00 3.08
154 155 1.544724 CATGGTTGGGTGTGGTTAGG 58.455 55.000 0.00 0.00 0.00 2.69
155 156 0.887933 GCATGGTTGGGTGTGGTTAG 59.112 55.000 0.00 0.00 0.00 2.34
156 157 0.186143 TGCATGGTTGGGTGTGGTTA 59.814 50.000 0.00 0.00 0.00 2.85
157 158 0.471591 ATGCATGGTTGGGTGTGGTT 60.472 50.000 0.00 0.00 0.00 3.67
158 159 1.155859 ATGCATGGTTGGGTGTGGT 59.844 52.632 0.00 0.00 0.00 4.16
159 160 1.186917 ACATGCATGGTTGGGTGTGG 61.187 55.000 29.41 1.09 0.00 4.17
160 161 1.543607 TACATGCATGGTTGGGTGTG 58.456 50.000 29.41 3.23 0.00 3.82
161 162 2.101783 CATACATGCATGGTTGGGTGT 58.898 47.619 29.41 10.93 0.00 4.16
162 163 2.875087 CATACATGCATGGTTGGGTG 57.125 50.000 29.41 14.32 0.00 4.61
274 275 4.492570 CGAATTGTTGGATCGTAGCTGTTC 60.493 45.833 0.00 0.00 0.00 3.18
403 449 3.044305 GACTGGCGTGTCAGGTGC 61.044 66.667 6.41 0.00 38.98 5.01
509 579 2.043248 GGCTACGGTGAGGAGGGA 60.043 66.667 0.00 0.00 0.00 4.20
831 4095 3.340928 GCGGTGGTTTTTATAGGAGTGT 58.659 45.455 0.00 0.00 0.00 3.55
885 4175 2.482333 GCCTAGAGCCGAGCGAGAA 61.482 63.158 0.00 0.00 34.35 2.87
989 4303 1.430632 CCTTGCATGATGACGGCAC 59.569 57.895 0.00 0.00 37.26 5.01
994 4308 0.034186 TGGTCCCCTTGCATGATGAC 60.034 55.000 0.00 6.98 0.00 3.06
1467 4820 1.807165 CGTCTCCGGTGCACAGATG 60.807 63.158 20.43 14.19 0.00 2.90
1623 5036 6.446781 TCGGGTCTGTTAACTAATCTAGTG 57.553 41.667 7.22 0.00 39.39 2.74
1625 5038 7.040473 ACATCGGGTCTGTTAACTAATCTAG 57.960 40.000 7.22 0.00 0.00 2.43
1633 5055 7.493320 TGTTGATTATACATCGGGTCTGTTAAC 59.507 37.037 0.00 0.00 0.00 2.01
1642 5067 6.918892 TTCAACTGTTGATTATACATCGGG 57.081 37.500 22.60 0.00 39.84 5.14
1736 5342 6.707440 TGTTCAATTTGAGCTGGAAGTTTA 57.293 33.333 13.42 0.00 35.30 2.01
1869 5694 0.607489 ATGTCACTTGCAGTCAGGGC 60.607 55.000 0.00 0.00 0.00 5.19
1912 5738 4.264614 GGTTGATGATACGTACAGAACACG 59.735 45.833 0.00 0.00 44.80 4.49
1913 5739 4.264614 CGGTTGATGATACGTACAGAACAC 59.735 45.833 0.00 0.00 0.00 3.32
1914 5740 4.082625 ACGGTTGATGATACGTACAGAACA 60.083 41.667 0.00 0.00 37.85 3.18
1915 5741 4.418392 ACGGTTGATGATACGTACAGAAC 58.582 43.478 0.00 6.00 37.85 3.01
1962 7711 3.845860 TCCAGATCTATACCACCAGACC 58.154 50.000 0.00 0.00 0.00 3.85
1995 7744 2.428530 TCATCCAGAACATCACTCCTCG 59.571 50.000 0.00 0.00 0.00 4.63
2017 7766 4.276183 TCTGCAAACTACACGCCAAAAATA 59.724 37.500 0.00 0.00 0.00 1.40
2018 7767 3.067461 TCTGCAAACTACACGCCAAAAAT 59.933 39.130 0.00 0.00 0.00 1.82
2019 7768 2.423892 TCTGCAAACTACACGCCAAAAA 59.576 40.909 0.00 0.00 0.00 1.94
2020 7769 2.017782 TCTGCAAACTACACGCCAAAA 58.982 42.857 0.00 0.00 0.00 2.44
2021 7770 1.332375 GTCTGCAAACTACACGCCAAA 59.668 47.619 0.00 0.00 0.00 3.28
2036 7785 3.712881 GTTGCACGGGTCGTCTGC 61.713 66.667 0.00 0.00 38.32 4.26
2049 7798 2.756840 AGAGTAAACTACCCCGTTGC 57.243 50.000 0.00 0.00 0.00 4.17
2052 7801 4.020218 GGGTTTAAGAGTAAACTACCCCGT 60.020 45.833 6.75 0.00 45.69 5.28
2053 7802 4.223700 AGGGTTTAAGAGTAAACTACCCCG 59.776 45.833 12.48 0.00 45.69 5.73
2054 7803 5.013495 ACAGGGTTTAAGAGTAAACTACCCC 59.987 44.000 12.48 0.00 45.69 4.95
2055 7804 6.119240 ACAGGGTTTAAGAGTAAACTACCC 57.881 41.667 9.23 9.23 45.69 3.69
2056 7805 6.367149 CGAACAGGGTTTAAGAGTAAACTACC 59.633 42.308 8.73 3.85 45.69 3.18
2057 7806 6.367149 CCGAACAGGGTTTAAGAGTAAACTAC 59.633 42.308 8.73 3.92 45.69 2.73
2058 7807 6.458210 CCGAACAGGGTTTAAGAGTAAACTA 58.542 40.000 8.73 0.00 45.69 2.24
2059 7808 5.303165 CCGAACAGGGTTTAAGAGTAAACT 58.697 41.667 8.73 0.00 45.69 2.66
2060 7809 4.083643 GCCGAACAGGGTTTAAGAGTAAAC 60.084 45.833 1.54 1.54 45.68 2.01
2061 7810 4.067192 GCCGAACAGGGTTTAAGAGTAAA 58.933 43.478 0.00 0.00 41.48 2.01
2062 7811 3.071312 TGCCGAACAGGGTTTAAGAGTAA 59.929 43.478 0.00 0.00 41.48 2.24
2063 7812 2.633967 TGCCGAACAGGGTTTAAGAGTA 59.366 45.455 0.00 0.00 41.48 2.59
2064 7813 1.418637 TGCCGAACAGGGTTTAAGAGT 59.581 47.619 0.00 0.00 41.48 3.24
2065 7814 2.076863 CTGCCGAACAGGGTTTAAGAG 58.923 52.381 0.00 0.00 43.19 2.85
2066 7815 2.178912 CTGCCGAACAGGGTTTAAGA 57.821 50.000 0.00 0.00 43.19 2.10
2093 7842 3.181967 CGAAGCGGAGTTGCGGAG 61.182 66.667 0.00 0.00 40.67 4.63
2106 7855 4.521062 CTCAGCCCGCTCCCGAAG 62.521 72.222 0.00 0.00 36.29 3.79
2119 7868 3.414700 GTGTTCGGTGCCGCTCAG 61.415 66.667 5.64 0.00 39.59 3.35
2120 7869 4.980805 GGTGTTCGGTGCCGCTCA 62.981 66.667 5.64 4.80 39.59 4.26
2121 7870 4.681978 AGGTGTTCGGTGCCGCTC 62.682 66.667 5.64 2.24 39.59 5.03
2122 7871 4.681978 GAGGTGTTCGGTGCCGCT 62.682 66.667 5.64 0.00 39.59 5.52
2123 7872 4.980805 TGAGGTGTTCGGTGCCGC 62.981 66.667 5.64 0.00 39.59 6.53
2124 7873 2.280524 TTGAGGTGTTCGGTGCCG 60.281 61.111 3.94 3.94 41.35 5.69
2125 7874 1.227853 AGTTGAGGTGTTCGGTGCC 60.228 57.895 0.00 0.00 0.00 5.01
2126 7875 1.228657 GGAGTTGAGGTGTTCGGTGC 61.229 60.000 0.00 0.00 0.00 5.01
2127 7876 0.944311 CGGAGTTGAGGTGTTCGGTG 60.944 60.000 0.00 0.00 0.00 4.94
2128 7877 1.366366 CGGAGTTGAGGTGTTCGGT 59.634 57.895 0.00 0.00 0.00 4.69
2129 7878 0.944311 CACGGAGTTGAGGTGTTCGG 60.944 60.000 0.00 0.00 41.61 4.30
2130 7879 0.031585 TCACGGAGTTGAGGTGTTCG 59.968 55.000 0.00 0.00 41.61 3.95
2131 7880 2.234300 TTCACGGAGTTGAGGTGTTC 57.766 50.000 0.00 0.00 41.61 3.18
2132 7881 2.930826 ATTCACGGAGTTGAGGTGTT 57.069 45.000 0.00 0.00 41.61 3.32
2133 7882 2.930826 AATTCACGGAGTTGAGGTGT 57.069 45.000 0.00 0.00 41.61 4.16
2134 7883 4.568152 AAAAATTCACGGAGTTGAGGTG 57.432 40.909 0.00 0.00 41.61 4.00
2135 7884 6.059484 TCTTAAAAATTCACGGAGTTGAGGT 58.941 36.000 0.00 0.00 41.61 3.85
2136 7885 6.554334 TCTTAAAAATTCACGGAGTTGAGG 57.446 37.500 0.00 0.00 41.61 3.86
2137 7886 6.080406 GCTCTTAAAAATTCACGGAGTTGAG 58.920 40.000 0.00 0.00 41.61 3.02
2138 7887 5.529430 TGCTCTTAAAAATTCACGGAGTTGA 59.471 36.000 0.00 0.00 41.61 3.18
2139 7888 5.757886 TGCTCTTAAAAATTCACGGAGTTG 58.242 37.500 0.00 0.00 41.61 3.16
2140 7889 6.431234 AGATGCTCTTAAAAATTCACGGAGTT 59.569 34.615 0.00 0.00 41.61 3.01
2141 7890 6.431234 AAGATGCTCTTAAAAATTCACGGAGT 59.569 34.615 0.00 0.00 36.35 3.85
2142 7891 6.428385 AGATGCTCTTAAAAATTCACGGAG 57.572 37.500 0.00 0.00 0.00 4.63
2143 7892 6.429692 TGAAGATGCTCTTAAAAATTCACGGA 59.570 34.615 0.00 0.00 36.73 4.69
2144 7893 6.611381 TGAAGATGCTCTTAAAAATTCACGG 58.389 36.000 0.00 0.00 36.73 4.94
2145 7894 7.591057 TGTTGAAGATGCTCTTAAAAATTCACG 59.409 33.333 0.00 0.00 36.73 4.35
2146 7895 8.801715 TGTTGAAGATGCTCTTAAAAATTCAC 57.198 30.769 0.00 0.00 36.73 3.18
2147 7896 7.596248 GCTGTTGAAGATGCTCTTAAAAATTCA 59.404 33.333 0.00 0.00 36.73 2.57
2148 7897 7.062722 GGCTGTTGAAGATGCTCTTAAAAATTC 59.937 37.037 0.00 0.00 36.73 2.17
2149 7898 6.870439 GGCTGTTGAAGATGCTCTTAAAAATT 59.130 34.615 0.00 0.00 36.73 1.82
2150 7899 6.393171 GGCTGTTGAAGATGCTCTTAAAAAT 58.607 36.000 0.00 0.00 36.73 1.82
2151 7900 5.562696 CGGCTGTTGAAGATGCTCTTAAAAA 60.563 40.000 0.00 0.00 36.73 1.94
2152 7901 4.083324 CGGCTGTTGAAGATGCTCTTAAAA 60.083 41.667 0.00 0.00 36.73 1.52
2153 7902 3.436704 CGGCTGTTGAAGATGCTCTTAAA 59.563 43.478 0.00 0.00 36.73 1.52
2154 7903 3.002791 CGGCTGTTGAAGATGCTCTTAA 58.997 45.455 0.00 0.00 36.73 1.85
2155 7904 2.621338 CGGCTGTTGAAGATGCTCTTA 58.379 47.619 0.00 0.00 36.73 2.10
2156 7905 1.446907 CGGCTGTTGAAGATGCTCTT 58.553 50.000 0.00 0.00 39.87 2.85
2157 7906 1.023513 GCGGCTGTTGAAGATGCTCT 61.024 55.000 0.00 0.00 0.00 4.09
2158 7907 1.427020 GCGGCTGTTGAAGATGCTC 59.573 57.895 0.00 0.00 0.00 4.26
2159 7908 2.393768 CGCGGCTGTTGAAGATGCT 61.394 57.895 0.00 0.00 0.00 3.79
2160 7909 2.099062 CGCGGCTGTTGAAGATGC 59.901 61.111 0.00 0.00 0.00 3.91
2161 7910 2.099062 GCGCGGCTGTTGAAGATG 59.901 61.111 8.83 0.00 0.00 2.90
2162 7911 1.965930 TTGCGCGGCTGTTGAAGAT 60.966 52.632 8.83 0.00 0.00 2.40
2163 7912 2.590291 TTGCGCGGCTGTTGAAGA 60.590 55.556 8.83 0.00 0.00 2.87
2164 7913 2.427410 GTTGCGCGGCTGTTGAAG 60.427 61.111 8.83 0.00 0.00 3.02
2165 7914 4.306471 CGTTGCGCGGCTGTTGAA 62.306 61.111 8.83 0.00 36.85 2.69
2212 7961 4.383602 CAAACCAGGCGAACGGCG 62.384 66.667 4.80 4.80 44.92 6.46
2213 7962 4.038080 CCAAACCAGGCGAACGGC 62.038 66.667 12.58 12.58 42.51 5.68
2214 7963 4.038080 GCCAAACCAGGCGAACGG 62.038 66.667 0.00 0.00 46.12 4.44
2250 7999 4.617520 TTTGACGCGGCTGCTGGA 62.618 61.111 15.80 0.00 39.65 3.86
2251 8000 2.476534 AATTTTGACGCGGCTGCTGG 62.477 55.000 15.80 3.05 39.65 4.85
2252 8001 1.081242 AATTTTGACGCGGCTGCTG 60.081 52.632 15.80 11.74 39.65 4.41
2253 8002 1.081242 CAATTTTGACGCGGCTGCT 60.081 52.632 15.80 2.15 39.65 4.24
2254 8003 1.067199 CTCAATTTTGACGCGGCTGC 61.067 55.000 15.80 7.70 32.90 5.25
2255 8004 1.067199 GCTCAATTTTGACGCGGCTG 61.067 55.000 15.80 1.63 32.90 4.85
2256 8005 1.210155 GCTCAATTTTGACGCGGCT 59.790 52.632 15.80 0.00 32.90 5.52
2257 8006 2.145905 CGCTCAATTTTGACGCGGC 61.146 57.895 12.47 8.67 43.88 6.53
2258 8007 2.145905 GCGCTCAATTTTGACGCGG 61.146 57.895 24.51 14.32 45.69 6.46
2259 8008 3.352536 GCGCTCAATTTTGACGCG 58.647 55.556 21.73 21.73 46.93 6.01
2260 8009 2.767919 GCGCGCTCAATTTTGACGC 61.768 57.895 26.67 20.29 45.32 5.19
2261 8010 2.479782 CGCGCGCTCAATTTTGACG 61.480 57.895 30.48 4.48 35.96 4.35
2262 8011 2.767919 GCGCGCGCTCAATTTTGAC 61.768 57.895 44.38 13.88 38.26 3.18
2263 8012 2.501650 GCGCGCGCTCAATTTTGA 60.502 55.556 44.38 0.00 38.26 2.69
2264 8013 3.878384 CGCGCGCGCTCAATTTTG 61.878 61.111 45.97 27.76 39.32 2.44
2286 8035 3.961838 ATTTTAGCGCGGCCGTGGA 62.962 57.895 37.26 13.71 36.67 4.02
2287 8036 3.505184 ATTTTAGCGCGGCCGTGG 61.505 61.111 37.26 25.12 36.67 4.94
2288 8037 2.277247 CATTTTAGCGCGGCCGTG 60.277 61.111 33.75 33.75 36.67 4.94
2289 8038 4.174129 GCATTTTAGCGCGGCCGT 62.174 61.111 28.70 9.89 36.67 5.68
2290 8039 4.172772 TGCATTTTAGCGCGGCCG 62.173 61.111 24.05 24.05 37.31 6.13
2291 8040 2.278142 CTGCATTTTAGCGCGGCC 60.278 61.111 8.83 0.00 37.31 6.13
2297 8046 3.307262 CGCGCGCTGCATTTTAGC 61.307 61.111 30.48 6.56 46.97 3.09
2298 8047 3.307262 GCGCGCGCTGCATTTTAG 61.307 61.111 44.38 15.91 46.97 1.85
2308 8057 3.597626 GCAATGTTTAGCGCGCGC 61.598 61.111 45.10 45.10 42.33 6.86


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

AutoCloner maintained by Alex Coulton.