Multiple sequence alignment - TraesCS2D01G520900

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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 TraesCS2D01G520900 chr2D 100.000 7541 0 0 1 7541 609781981 609774441 0.000000e+00 13926.0
1 TraesCS2D01G520900 chr2D 94.444 54 3 0 323 376 125468258 125468311 4.850000e-12 84.2
2 TraesCS2D01G520900 chr2D 83.516 91 11 4 297 386 67950575 67950488 1.740000e-11 82.4
3 TraesCS2D01G520900 chr2A 95.664 5327 162 29 1532 6832 742725398 742720115 0.000000e+00 8493.0
4 TraesCS2D01G520900 chr2A 84.153 1546 123 59 36 1519 742726929 742725444 0.000000e+00 1386.0
5 TraesCS2D01G520900 chr2A 93.431 685 19 11 6860 7541 742720059 742719398 0.000000e+00 992.0
6 TraesCS2D01G520900 chr2A 87.429 175 22 0 4627 4801 655039113 655039287 1.280000e-47 202.0
7 TraesCS2D01G520900 chr2A 80.392 204 19 6 582 782 307975927 307975742 1.320000e-27 135.0
8 TraesCS2D01G520900 chr2A 89.024 82 5 3 6 84 742727041 742726961 1.730000e-16 99.0
9 TraesCS2D01G520900 chr2B 92.782 4447 192 60 242 4656 744173354 744169005 0.000000e+00 6314.0
10 TraesCS2D01G520900 chr2B 95.567 2910 100 15 4652 7541 744168758 744165858 0.000000e+00 4632.0
11 TraesCS2D01G520900 chr2B 91.698 265 18 3 4205 4467 588234084 588234346 1.550000e-96 364.0
12 TraesCS2D01G520900 chr2B 83.420 193 8 12 1 192 744173761 744173592 2.820000e-34 158.0
13 TraesCS2D01G520900 chr4B 92.453 265 16 4 4205 4467 450022436 450022174 7.140000e-100 375.0
14 TraesCS2D01G520900 chr4B 89.606 279 27 2 4194 4471 64389774 64390051 3.350000e-93 353.0
15 TraesCS2D01G520900 chr4A 92.424 264 18 2 4205 4467 691994668 691994930 7.140000e-100 375.0
16 TraesCS2D01G520900 chr4A 91.720 157 13 0 4640 4796 150653466 150653310 1.270000e-52 219.0
17 TraesCS2D01G520900 chr1B 90.476 273 24 2 4197 4468 601141812 601141541 7.190000e-95 359.0
18 TraesCS2D01G520900 chr7D 89.716 282 25 4 4195 4473 133314916 133314636 2.590000e-94 357.0
19 TraesCS2D01G520900 chr7D 87.500 80 8 2 299 377 66303220 66303142 2.900000e-14 91.6
20 TraesCS2D01G520900 chr7D 86.585 82 9 2 297 377 564633087 564633007 1.040000e-13 89.8
21 TraesCS2D01G520900 chr7D 86.842 76 9 1 303 377 90567664 90567589 4.850000e-12 84.2
22 TraesCS2D01G520900 chr7B 90.299 268 24 2 4201 4467 110890042 110889776 4.330000e-92 350.0
23 TraesCS2D01G520900 chr7B 80.392 204 19 11 582 782 734092413 734092598 1.320000e-27 135.0
24 TraesCS2D01G520900 chr5D 92.258 155 12 0 4639 4793 461072756 461072602 3.540000e-53 220.0
25 TraesCS2D01G520900 chr5D 96.154 52 2 0 326 377 540479935 540479986 1.350000e-12 86.1
26 TraesCS2D01G520900 chr5D 86.842 76 9 1 303 377 544760083 544760008 4.850000e-12 84.2
27 TraesCS2D01G520900 chr6B 90.184 163 16 0 4631 4793 528091486 528091324 5.930000e-51 213.0
28 TraesCS2D01G520900 chr6B 82.412 199 14 6 587 782 653581988 653581808 3.640000e-33 154.0
29 TraesCS2D01G520900 chr6B 83.152 184 13 9 582 765 525982442 525982277 1.310000e-32 152.0
30 TraesCS2D01G520900 chr3D 91.613 155 11 1 4639 4793 539119784 539119632 5.930000e-51 213.0
31 TraesCS2D01G520900 chr3D 89.697 165 17 0 4629 4793 598889896 598889732 2.130000e-50 211.0
32 TraesCS2D01G520900 chr3D 93.333 45 3 0 332 376 261827043 261826999 4.880000e-07 67.6
33 TraesCS2D01G520900 chr5B 88.372 172 18 2 4623 4793 149590389 149590559 9.920000e-49 206.0
34 TraesCS2D01G520900 chr5B 82.743 226 27 5 6990 7209 61352857 61352638 2.780000e-44 191.0
35 TraesCS2D01G520900 chr3B 82.609 184 14 9 582 765 826120864 826121029 6.100000e-31 147.0
36 TraesCS2D01G520900 chr6D 80.882 204 18 11 582 782 199474774 199474589 2.840000e-29 141.0
37 TraesCS2D01G520900 chr6D 80.882 204 18 11 582 782 246427192 246427007 2.840000e-29 141.0
38 TraesCS2D01G520900 chr6D 88.158 76 7 2 303 377 467271239 467271313 1.040000e-13 89.8
39 TraesCS2D01G520900 chrUn 86.667 75 8 2 303 376 97860803 97860730 1.740000e-11 82.4


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 TraesCS2D01G520900 chr2D 609774441 609781981 7540 True 13926.000000 13926 100.000000 1 7541 1 chr2D.!!$R2 7540
1 TraesCS2D01G520900 chr2A 742719398 742727041 7643 True 2742.500000 8493 90.568000 6 7541 4 chr2A.!!$R2 7535
2 TraesCS2D01G520900 chr2B 744165858 744173761 7903 True 3701.333333 6314 90.589667 1 7541 3 chr2B.!!$R1 7540

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
881 1187 0.039527 CTGCGGGTTGCTTTTGGTAC 60.040 55.0 0.00 0.00 46.63 3.34 F
1318 1656 0.178068 CATGGTACCCCCTCGTCAAG 59.822 60.0 10.07 0.00 0.00 3.02 F
1337 1675 0.379669 GCACATGGCATCCTTTCTCG 59.620 55.0 0.00 0.00 43.97 4.04 F
1361 1699 0.379669 GCACATGGCATCCTTTCTCG 59.620 55.0 0.00 0.00 43.97 4.04 F
1363 1701 0.749454 ACATGGCATCCTTTCTCGCC 60.749 55.0 0.00 0.00 45.11 5.54 F
2502 2880 0.979709 AGCCTGGCTCTATGCACAGA 60.980 55.0 17.22 0.00 45.15 3.41 F
3433 3816 2.093075 AGAATCATGGTGGCAGTGAGAG 60.093 50.0 0.00 0.00 0.00 3.20 F
4289 4677 0.104120 GGTGGGTGTTTGGTTCAAGC 59.896 55.0 0.00 0.00 0.00 4.01 F
4320 4708 0.670546 CAAGTCACACTAGTGCCCCG 60.671 60.0 22.90 9.09 45.49 5.73 F
6192 6848 0.095417 GTGCCGACGAGCTGAAATTC 59.905 55.0 0.00 0.00 0.00 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1689 2060 1.067974 AGCCCACGGTTAAACAAAAGC 59.932 47.619 0.00 0.00 0.00 3.51 R
2487 2865 2.019249 GCAAATCTGTGCATAGAGCCA 58.981 47.619 18.52 0.00 44.29 4.75 R
2965 3348 2.290896 CCAGGTATGCAAGGAACCTCAA 60.291 50.000 9.68 0.00 41.75 3.02 R
3163 3546 5.907662 TGAGGAGAGAAGGATACCATCAAAT 59.092 40.000 0.00 0.00 37.17 2.32 R
3361 3744 1.471287 CATCTGTGGCATGACAGTTGG 59.529 52.381 0.00 0.00 43.38 3.77 R
4016 4401 0.240678 CACTAGCAATTTGGCGCACA 59.759 50.000 10.83 1.22 39.27 4.57 R
4314 4702 0.253327 TGTGTATGTAATGCGGGGCA 59.747 50.000 0.00 0.00 44.86 5.36 R
6192 6848 1.669115 CCTGAACTGACTGGCCACG 60.669 63.158 0.00 0.00 0.00 4.94 R
6363 7019 3.128188 CTGCTGCTGCTGCTCTGG 61.128 66.667 27.67 13.92 40.48 3.86 R
6999 7699 0.031857 CCGCAATCGAGCAGAGAGAT 59.968 55.000 0.00 0.00 38.10 2.75 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
26 27 3.001406 CCCCGTCCGTTTCCTCCT 61.001 66.667 0.00 0.00 0.00 3.69
27 28 2.590114 CCCCGTCCGTTTCCTCCTT 61.590 63.158 0.00 0.00 0.00 3.36
137 216 3.120191 CCTACCACCCTCCCTCCT 58.880 66.667 0.00 0.00 0.00 3.69
138 217 1.075151 CCTACCACCCTCCCTCCTC 60.075 68.421 0.00 0.00 0.00 3.71
139 218 1.455959 CTACCACCCTCCCTCCTCG 60.456 68.421 0.00 0.00 0.00 4.63
142 221 4.787280 CACCCTCCCTCCTCGCCT 62.787 72.222 0.00 0.00 0.00 5.52
143 222 4.012721 ACCCTCCCTCCTCGCCTT 62.013 66.667 0.00 0.00 0.00 4.35
187 266 3.342477 GCTGCTTCCCCTTCCCCT 61.342 66.667 0.00 0.00 0.00 4.79
194 273 4.712806 CCCCTTCCCCTCCCCCAA 62.713 72.222 0.00 0.00 0.00 4.12
196 275 2.204306 CCTTCCCCTCCCCCAACT 60.204 66.667 0.00 0.00 0.00 3.16
198 277 2.204244 TTCCCCTCCCCCAACTCC 60.204 66.667 0.00 0.00 0.00 3.85
202 286 2.792222 CCTCCCCCAACTCCCCTA 59.208 66.667 0.00 0.00 0.00 3.53
294 561 2.197324 CTCCTCCTCCTCCCTCGG 59.803 72.222 0.00 0.00 0.00 4.63
310 577 0.963856 TCGGTTCCTCGCTGCTCTTA 60.964 55.000 0.00 0.00 0.00 2.10
315 582 3.181506 GGTTCCTCGCTGCTCTTATTTTG 60.182 47.826 0.00 0.00 0.00 2.44
316 583 2.632377 TCCTCGCTGCTCTTATTTTGG 58.368 47.619 0.00 0.00 0.00 3.28
319 586 1.739466 TCGCTGCTCTTATTTTGGCTG 59.261 47.619 0.00 0.00 0.00 4.85
321 588 2.095059 CGCTGCTCTTATTTTGGCTGTT 60.095 45.455 0.00 0.00 0.00 3.16
324 592 2.892852 TGCTCTTATTTTGGCTGTTGCT 59.107 40.909 0.00 0.00 39.59 3.91
425 710 2.234143 CTCGTAGATCTGGATCAGCCA 58.766 52.381 5.18 0.00 39.90 4.75
497 789 1.551019 GGGGGTACTGCTTCCGTTCT 61.551 60.000 0.00 0.00 0.00 3.01
590 882 3.075998 CGCAGTACTTCAGCGCTG 58.924 61.111 31.53 31.53 44.08 5.18
618 917 8.621286 GCCTTTTTGCTTGCTAATAATAGTAGA 58.379 33.333 0.00 0.00 0.00 2.59
634 933 4.792521 AGTAGACTGCTCCACTTTACTG 57.207 45.455 0.00 0.00 0.00 2.74
635 934 4.153411 AGTAGACTGCTCCACTTTACTGT 58.847 43.478 0.00 0.00 0.00 3.55
636 935 5.322754 AGTAGACTGCTCCACTTTACTGTA 58.677 41.667 0.00 0.00 0.00 2.74
639 938 4.528596 AGACTGCTCCACTTTACTGTATGT 59.471 41.667 0.00 0.00 0.00 2.29
640 939 4.822026 ACTGCTCCACTTTACTGTATGTC 58.178 43.478 0.00 0.00 0.00 3.06
641 940 4.528596 ACTGCTCCACTTTACTGTATGTCT 59.471 41.667 0.00 0.00 0.00 3.41
642 941 4.820897 TGCTCCACTTTACTGTATGTCTG 58.179 43.478 0.00 0.00 0.00 3.51
643 942 4.283467 TGCTCCACTTTACTGTATGTCTGT 59.717 41.667 0.00 0.00 0.00 3.41
644 943 5.479027 TGCTCCACTTTACTGTATGTCTGTA 59.521 40.000 0.00 0.00 0.00 2.74
645 944 6.154534 TGCTCCACTTTACTGTATGTCTGTAT 59.845 38.462 0.00 0.00 32.17 2.29
648 947 9.517609 CTCCACTTTACTGTATGTCTGTATTAC 57.482 37.037 0.00 0.00 32.17 1.89
716 1016 1.133915 TGAGTGCTCCCGTTCCTTTTT 60.134 47.619 0.00 0.00 0.00 1.94
717 1017 1.266989 GAGTGCTCCCGTTCCTTTTTG 59.733 52.381 0.00 0.00 0.00 2.44
722 1022 1.607148 CTCCCGTTCCTTTTTGGTGTC 59.393 52.381 0.00 0.00 37.07 3.67
723 1023 1.213430 TCCCGTTCCTTTTTGGTGTCT 59.787 47.619 0.00 0.00 37.07 3.41
724 1024 1.607148 CCCGTTCCTTTTTGGTGTCTC 59.393 52.381 0.00 0.00 37.07 3.36
725 1025 2.294074 CCGTTCCTTTTTGGTGTCTCA 58.706 47.619 0.00 0.00 37.07 3.27
726 1026 2.032924 CCGTTCCTTTTTGGTGTCTCAC 59.967 50.000 0.00 0.00 37.07 3.51
727 1027 2.943033 CGTTCCTTTTTGGTGTCTCACT 59.057 45.455 0.06 0.00 37.07 3.41
728 1028 4.124238 CGTTCCTTTTTGGTGTCTCACTA 58.876 43.478 0.06 0.00 37.07 2.74
729 1029 4.211374 CGTTCCTTTTTGGTGTCTCACTAG 59.789 45.833 0.06 0.00 37.07 2.57
730 1030 5.123936 GTTCCTTTTTGGTGTCTCACTAGT 58.876 41.667 0.00 0.00 37.07 2.57
755 1055 5.122869 CACTACTGCATTTGTGCTACATCTT 59.877 40.000 5.77 0.00 35.49 2.40
790 1096 5.660460 CTTACCTTGCAACTTCCTTTTGTT 58.340 37.500 0.00 0.00 0.00 2.83
801 1107 3.619233 TCCTTTTGTTCTTACGCTTGC 57.381 42.857 0.00 0.00 0.00 4.01
817 1123 3.360956 CGCTTGCTTTTTGTGTTCATTCG 60.361 43.478 0.00 0.00 0.00 3.34
852 1158 4.778534 AACAGATCAGAGCATTTTGTGG 57.221 40.909 0.00 0.00 0.00 4.17
868 1174 4.452733 GGAAGGACGGACTGCGGG 62.453 72.222 0.00 0.00 0.00 6.13
869 1175 3.692406 GAAGGACGGACTGCGGGT 61.692 66.667 0.00 0.00 0.00 5.28
870 1176 3.236003 GAAGGACGGACTGCGGGTT 62.236 63.158 0.00 0.00 0.00 4.11
879 1185 1.734388 GACTGCGGGTTGCTTTTGGT 61.734 55.000 0.00 0.00 46.63 3.67
881 1187 0.039527 CTGCGGGTTGCTTTTGGTAC 60.040 55.000 0.00 0.00 46.63 3.34
901 1207 1.760613 CCATCAGCTAAAGGGTCGGTA 59.239 52.381 0.00 0.00 0.00 4.02
921 1227 4.520492 GGTAGATTGATGGCAGTTATTGGG 59.480 45.833 0.00 0.00 0.00 4.12
924 1230 0.396974 TGATGGCAGTTATTGGGGCC 60.397 55.000 0.00 0.00 46.58 5.80
1009 1315 5.999044 AGAAAGCTCAATACATGGACAGAT 58.001 37.500 0.00 0.00 0.00 2.90
1079 1385 3.242543 CCTGTCATGCGCTTTCATAACTC 60.243 47.826 9.73 0.00 0.00 3.01
1080 1386 3.599343 TGTCATGCGCTTTCATAACTCT 58.401 40.909 9.73 0.00 0.00 3.24
1154 1472 4.326826 TGACTGTCAATTCTTAAGCCTGG 58.673 43.478 8.27 0.00 0.00 4.45
1195 1532 1.827969 CTCTGGACACCTTCCTGTAGG 59.172 57.143 0.00 0.00 46.10 3.18
1196 1533 0.250513 CTGGACACCTTCCTGTAGGC 59.749 60.000 0.00 0.00 46.10 3.93
1197 1534 0.178903 TGGACACCTTCCTGTAGGCT 60.179 55.000 0.00 0.00 46.10 4.58
1198 1535 0.250513 GGACACCTTCCTGTAGGCTG 59.749 60.000 0.00 0.00 41.95 4.85
1199 1536 0.977395 GACACCTTCCTGTAGGCTGT 59.023 55.000 0.00 0.00 38.99 4.40
1200 1537 2.176889 GACACCTTCCTGTAGGCTGTA 58.823 52.381 0.00 0.00 38.99 2.74
1201 1538 2.166664 GACACCTTCCTGTAGGCTGTAG 59.833 54.545 0.00 0.00 38.99 2.74
1218 1555 0.467384 TAGCCTTGCATCTCTCCTGC 59.533 55.000 0.00 0.00 40.10 4.85
1232 1569 7.619050 CATCTCTCCTGCATATAGTGGTAATT 58.381 38.462 0.00 0.00 0.00 1.40
1239 1576 9.100197 TCCTGCATATAGTGGTAATTCTATTGA 57.900 33.333 0.00 0.00 0.00 2.57
1240 1577 9.725019 CCTGCATATAGTGGTAATTCTATTGAA 57.275 33.333 0.00 0.00 36.54 2.69
1277 1614 3.711190 TGCTGTATAGTCCATGTCCACAT 59.289 43.478 0.00 0.00 36.96 3.21
1288 1626 6.319658 AGTCCATGTCCACATCAAATATTCAC 59.680 38.462 0.00 0.00 33.61 3.18
1299 1637 6.316390 ACATCAAATATTCACGAGTTCTTCCC 59.684 38.462 0.00 0.00 0.00 3.97
1316 1654 1.687840 CCATGGTACCCCCTCGTCA 60.688 63.158 10.07 0.00 0.00 4.35
1317 1655 1.268992 CCATGGTACCCCCTCGTCAA 61.269 60.000 10.07 0.00 0.00 3.18
1318 1656 0.178068 CATGGTACCCCCTCGTCAAG 59.822 60.000 10.07 0.00 0.00 3.02
1322 1660 1.534476 TACCCCCTCGTCAAGCACA 60.534 57.895 0.00 0.00 0.00 4.57
1337 1675 0.379669 GCACATGGCATCCTTTCTCG 59.620 55.000 0.00 0.00 43.97 4.04
1338 1676 1.742761 CACATGGCATCCTTTCTCGT 58.257 50.000 0.00 0.00 0.00 4.18
1339 1677 1.667724 CACATGGCATCCTTTCTCGTC 59.332 52.381 0.00 0.00 0.00 4.20
1340 1678 1.278985 ACATGGCATCCTTTCTCGTCA 59.721 47.619 0.00 0.00 0.00 4.35
1341 1679 2.290260 ACATGGCATCCTTTCTCGTCAA 60.290 45.455 0.00 0.00 0.00 3.18
1342 1680 2.099141 TGGCATCCTTTCTCGTCAAG 57.901 50.000 0.00 0.00 0.00 3.02
1343 1681 0.729690 GGCATCCTTTCTCGTCAAGC 59.270 55.000 0.00 0.00 0.00 4.01
1344 1682 1.442769 GCATCCTTTCTCGTCAAGCA 58.557 50.000 0.00 0.00 0.00 3.91
1345 1683 1.129437 GCATCCTTTCTCGTCAAGCAC 59.871 52.381 0.00 0.00 0.00 4.40
1346 1684 2.416747 CATCCTTTCTCGTCAAGCACA 58.583 47.619 0.00 0.00 0.00 4.57
1347 1685 2.839486 TCCTTTCTCGTCAAGCACAT 57.161 45.000 0.00 0.00 0.00 3.21
1348 1686 2.416747 TCCTTTCTCGTCAAGCACATG 58.583 47.619 0.00 0.00 0.00 3.21
1349 1687 1.466167 CCTTTCTCGTCAAGCACATGG 59.534 52.381 0.00 0.00 0.00 3.66
1350 1688 0.874390 TTTCTCGTCAAGCACATGGC 59.126 50.000 0.00 0.00 45.30 4.40
1361 1699 0.379669 GCACATGGCATCCTTTCTCG 59.620 55.000 0.00 0.00 43.97 4.04
1363 1701 0.749454 ACATGGCATCCTTTCTCGCC 60.749 55.000 0.00 0.00 45.11 5.54
1370 1708 2.076863 CATCCTTTCTCGCCGTCTTTT 58.923 47.619 0.00 0.00 0.00 2.27
1371 1709 3.259064 CATCCTTTCTCGCCGTCTTTTA 58.741 45.455 0.00 0.00 0.00 1.52
1374 1712 5.075858 TCCTTTCTCGCCGTCTTTTATAA 57.924 39.130 0.00 0.00 0.00 0.98
1378 1716 6.532657 CCTTTCTCGCCGTCTTTTATAACTTA 59.467 38.462 0.00 0.00 0.00 2.24
1381 1719 7.887996 TCTCGCCGTCTTTTATAACTTAAAA 57.112 32.000 0.00 0.00 0.00 1.52
1382 1720 7.732664 TCTCGCCGTCTTTTATAACTTAAAAC 58.267 34.615 0.00 0.00 0.00 2.43
1440 1778 9.959721 ATTACCTGTAAGAGTTATGTCATGTTT 57.040 29.630 0.00 0.00 34.07 2.83
1555 1926 4.826274 AACAGAGAAGCAGCCAGTATTA 57.174 40.909 0.00 0.00 0.00 0.98
1662 2033 9.530129 GCGTTATATGATTTAACTTATCACTGC 57.470 33.333 4.68 0.00 35.03 4.40
1689 2060 7.844169 GCACTGTACGTACACATATTTATGTTG 59.156 37.037 24.10 11.96 43.99 3.33
1713 2091 1.765230 TGTTTAACCGTGGGCTGTTT 58.235 45.000 0.00 0.00 0.00 2.83
1714 2092 2.100989 TGTTTAACCGTGGGCTGTTTT 58.899 42.857 0.00 0.00 0.00 2.43
1715 2093 2.159226 TGTTTAACCGTGGGCTGTTTTG 60.159 45.455 0.00 0.00 0.00 2.44
1716 2094 2.054232 TTAACCGTGGGCTGTTTTGA 57.946 45.000 0.00 0.00 0.00 2.69
1717 2095 2.054232 TAACCGTGGGCTGTTTTGAA 57.946 45.000 0.00 0.00 0.00 2.69
1718 2096 1.408969 AACCGTGGGCTGTTTTGAAT 58.591 45.000 0.00 0.00 0.00 2.57
1719 2097 1.408969 ACCGTGGGCTGTTTTGAATT 58.591 45.000 0.00 0.00 0.00 2.17
2288 2666 7.045804 GCGATGCGTTACATTAAAAGTTACTTC 60.046 37.037 0.00 0.00 39.84 3.01
2397 2775 6.483307 TGTCACTTGGTCTTTATCTGAAACAG 59.517 38.462 0.00 0.00 0.00 3.16
2423 2801 5.956642 AGCCTTTTCTTTTACGTGAAAACA 58.043 33.333 6.96 0.00 37.28 2.83
2502 2880 0.979709 AGCCTGGCTCTATGCACAGA 60.980 55.000 17.22 0.00 45.15 3.41
2509 2887 3.118298 TGGCTCTATGCACAGATTTGCTA 60.118 43.478 0.00 0.00 43.41 3.49
2874 3254 9.166173 GCTATGCTATGTATTGTTTATCCATGA 57.834 33.333 0.00 0.00 0.00 3.07
2965 3348 7.492669 CCTCGAGTAGAAACATTGTTGATACAT 59.507 37.037 12.31 9.59 33.44 2.29
3000 3383 5.161358 GCATACCTGGTAGCTTTTCAAAAC 58.839 41.667 12.78 0.00 0.00 2.43
3163 3546 9.575868 TGGTTAGATGATTTTTGGTAGTTAACA 57.424 29.630 8.61 0.00 0.00 2.41
3179 3562 8.837389 GGTAGTTAACATTTGATGGTATCCTTC 58.163 37.037 8.61 0.00 31.48 3.46
3350 3733 3.032017 TCCATAGAGCGCAAAGATAGC 57.968 47.619 11.47 0.00 0.00 2.97
3431 3814 2.286872 GAGAATCATGGTGGCAGTGAG 58.713 52.381 0.00 0.00 33.17 3.51
3433 3816 2.093075 AGAATCATGGTGGCAGTGAGAG 60.093 50.000 0.00 0.00 0.00 3.20
3645 4028 7.556844 ACTCCGTACATCTGTTCATTATTCTT 58.443 34.615 0.00 0.00 0.00 2.52
3646 4029 7.707035 ACTCCGTACATCTGTTCATTATTCTTC 59.293 37.037 0.00 0.00 0.00 2.87
3647 4030 6.695713 TCCGTACATCTGTTCATTATTCTTCG 59.304 38.462 0.00 0.00 0.00 3.79
3648 4031 6.695713 CCGTACATCTGTTCATTATTCTTCGA 59.304 38.462 0.00 0.00 0.00 3.71
3649 4032 7.222031 CCGTACATCTGTTCATTATTCTTCGAA 59.778 37.037 0.00 0.00 0.00 3.71
3650 4033 8.262588 CGTACATCTGTTCATTATTCTTCGAAG 58.737 37.037 19.35 19.35 0.00 3.79
3651 4034 7.545362 ACATCTGTTCATTATTCTTCGAAGG 57.455 36.000 24.37 7.85 0.00 3.46
3722 4107 5.922544 CAGTTCCCACAAAATGAGTCATTTC 59.077 40.000 27.07 14.33 42.32 2.17
3749 4134 3.684788 CGAAACGGAATTTCTCTCATGGT 59.315 43.478 0.00 0.00 44.03 3.55
3756 4141 5.395768 CGGAATTTCTCTCATGGTAGGAGTT 60.396 44.000 0.00 0.00 34.04 3.01
3783 4168 2.982488 AGTCCATTTCACTCCCTGTCTT 59.018 45.455 0.00 0.00 0.00 3.01
3792 4177 5.165961 TCACTCCCTGTCTTGGAAAATAG 57.834 43.478 0.00 0.00 0.00 1.73
3994 4379 6.263168 AGAGCATGCCAGTTAATATTGGTTAC 59.737 38.462 15.66 0.00 36.81 2.50
4016 4401 5.079643 ACACTAATGGTCTGAAAAGCCAAT 58.920 37.500 0.00 0.00 35.74 3.16
4020 4405 1.340889 TGGTCTGAAAAGCCAATGTGC 59.659 47.619 0.00 0.00 0.00 4.57
4099 4484 6.886178 ATAACCTGGACTTACTGGTGTTAT 57.114 37.500 0.00 0.00 41.18 1.89
4199 4586 7.153217 GTTGCCCAACTTTCTAGCTATTTAA 57.847 36.000 3.99 0.00 38.25 1.52
4235 4622 3.882888 TGAGACTAAGTTTGCCAAAGGTG 59.117 43.478 0.00 0.00 0.00 4.00
4236 4623 3.883489 GAGACTAAGTTTGCCAAAGGTGT 59.117 43.478 0.00 0.00 0.00 4.16
4289 4677 0.104120 GGTGGGTGTTTGGTTCAAGC 59.896 55.000 0.00 0.00 0.00 4.01
4314 4702 3.006967 CACCTTAGGCAAGTCACACTAGT 59.993 47.826 0.00 0.00 0.00 2.57
4320 4708 0.670546 CAAGTCACACTAGTGCCCCG 60.671 60.000 22.90 9.09 45.49 5.73
4563 4951 2.384828 GGTTCTGGGTTTCCTGTTGTT 58.615 47.619 0.00 0.00 34.13 2.83
4573 4969 4.023963 GGTTTCCTGTTGTTCTAGCTCAAC 60.024 45.833 17.09 17.09 42.62 3.18
4635 5031 9.706691 GCCTTTAACAGAATGCATATACTACTA 57.293 33.333 0.00 0.00 42.53 1.82
4771 5422 7.189512 CGTATTGGAATCTCTAAAAAGGCTTG 58.810 38.462 0.00 0.00 0.00 4.01
4782 5433 9.227777 TCTCTAAAAAGGCTTGTATTTAGGAAC 57.772 33.333 21.19 0.00 36.48 3.62
4941 5592 5.191722 AGCTATTTTGTGAACCCTGATCCTA 59.808 40.000 0.00 0.00 0.00 2.94
5025 5676 3.770263 TGAGCAGCTATCATTGTTTGC 57.230 42.857 0.00 0.00 0.00 3.68
5033 5684 4.332819 AGCTATCATTGTTTGCGTACTTCC 59.667 41.667 0.00 0.00 0.00 3.46
5047 5698 4.045104 CGTACTTCCTCCGATTTCAGATG 58.955 47.826 0.00 0.00 0.00 2.90
5108 5760 8.554490 AAGACTAATGGACCTTCAGTGTATAT 57.446 34.615 0.00 0.00 0.00 0.86
5147 5799 5.062308 CAGCATGGAGTTCGTTTTACTAGAC 59.938 44.000 0.00 0.00 0.00 2.59
5161 5813 8.179615 CGTTTTACTAGACCTTTTGTGAGTTTT 58.820 33.333 0.00 0.00 0.00 2.43
5165 5817 9.895138 TTACTAGACCTTTTGTGAGTTTTACTT 57.105 29.630 0.00 0.00 0.00 2.24
5853 6509 3.366679 CCTGTTTTGCTGCTGAATAGGTG 60.367 47.826 16.91 1.36 29.95 4.00
6027 6683 2.190578 GATGGAGGCCGAAGTGGG 59.809 66.667 0.00 0.00 38.63 4.61
6096 6752 0.895100 TGCTCACTTGGGCATTGGAC 60.895 55.000 0.00 0.00 33.23 4.02
6192 6848 0.095417 GTGCCGACGAGCTGAAATTC 59.905 55.000 0.00 0.00 0.00 2.17
6380 7036 3.128188 CCAGAGCAGCAGCAGCAG 61.128 66.667 12.92 0.00 45.49 4.24
6501 7157 3.708220 GAGAGTGCCGAAGCCCTCG 62.708 68.421 0.00 0.00 46.92 4.63
6542 7198 1.862147 CCGACGACGCAGACTAACG 60.862 63.158 0.64 0.00 38.29 3.18
6557 7216 3.693085 GACTAACGACAGACCATACTGGA 59.307 47.826 0.00 0.00 40.96 3.86
6560 7219 3.314541 ACGACAGACCATACTGGAAAC 57.685 47.619 0.00 0.00 40.96 2.78
6752 7411 3.571401 CCTGAAACTTTTGATGCCTCTGT 59.429 43.478 0.00 0.00 0.00 3.41
6753 7412 4.543692 CTGAAACTTTTGATGCCTCTGTG 58.456 43.478 0.00 0.00 0.00 3.66
6754 7413 3.953612 TGAAACTTTTGATGCCTCTGTGT 59.046 39.130 0.00 0.00 0.00 3.72
6755 7414 3.996150 AACTTTTGATGCCTCTGTGTG 57.004 42.857 0.00 0.00 0.00 3.82
6778 7441 4.655963 ACCTAAAGTTGCACATCACTGAT 58.344 39.130 0.00 0.00 0.00 2.90
6780 7443 4.940046 CCTAAAGTTGCACATCACTGATCT 59.060 41.667 0.00 0.00 0.00 2.75
6782 7445 4.761235 AAGTTGCACATCACTGATCTTG 57.239 40.909 0.00 0.00 0.00 3.02
6783 7446 3.748083 AGTTGCACATCACTGATCTTGT 58.252 40.909 0.00 0.00 0.00 3.16
6790 7453 7.660112 TGCACATCACTGATCTTGTAAAAATT 58.340 30.769 0.00 0.00 0.00 1.82
6799 7462 4.662468 TCTTGTAAAAATTGCAGTGCCA 57.338 36.364 13.72 0.72 0.00 4.92
6826 7490 4.676546 TCTGCAAGACTTCATCTACATCG 58.323 43.478 0.00 0.00 38.67 3.84
6841 7505 3.773860 ACATCGAAATATTGCCGCAAA 57.226 38.095 10.42 0.21 0.00 3.68
6850 7514 6.019640 CGAAATATTGCCGCAAAGATGAAATT 60.020 34.615 10.42 0.00 0.00 1.82
6858 7550 5.230726 GCCGCAAAGATGAAATTGTTAGATG 59.769 40.000 0.00 0.00 0.00 2.90
6896 7588 7.881643 TGGAAATGTGGTTTGAATTTAATCG 57.118 32.000 0.00 0.00 0.00 3.34
6897 7589 7.661968 TGGAAATGTGGTTTGAATTTAATCGA 58.338 30.769 0.00 0.00 0.00 3.59
6910 7602 9.992910 TTGAATTTAATCGATTTGACTCAGATG 57.007 29.630 17.19 0.00 0.00 2.90
6941 7638 1.699634 TGGAGAAGTTTCAGGTCAGGG 59.300 52.381 0.00 0.00 0.00 4.45
6944 7641 1.202818 AGAAGTTTCAGGTCAGGGCAC 60.203 52.381 0.00 0.00 0.00 5.01
6954 7652 3.966543 CAGGGCACGGGGGAAAGT 61.967 66.667 0.00 0.00 0.00 2.66
6999 7699 2.280119 GCACTCGCACCACACTCA 60.280 61.111 0.00 0.00 38.36 3.41
7000 7700 1.669115 GCACTCGCACCACACTCAT 60.669 57.895 0.00 0.00 38.36 2.90
7001 7701 1.630244 GCACTCGCACCACACTCATC 61.630 60.000 0.00 0.00 38.36 2.92
7006 7706 0.529833 CGCACCACACTCATCTCTCT 59.470 55.000 0.00 0.00 0.00 3.10
7443 8146 1.613630 GCCTCCTTCCACCTCCTCA 60.614 63.158 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 2.931649 GGTCCGGGTGGGGAGAAA 60.932 66.667 0.00 0.00 36.58 2.52
137 216 2.605295 TTCGGGGAAGGAAGGCGA 60.605 61.111 0.00 0.00 0.00 5.54
138 217 2.436115 GTTCGGGGAAGGAAGGCG 60.436 66.667 0.00 0.00 0.00 5.52
139 218 2.045242 GGTTCGGGGAAGGAAGGC 60.045 66.667 0.00 0.00 0.00 4.35
142 221 2.527374 ACGGGTTCGGGGAAGGAA 60.527 61.111 0.00 0.00 41.39 3.36
143 222 3.315949 CACGGGTTCGGGGAAGGA 61.316 66.667 0.00 0.00 41.39 3.36
169 248 4.803908 GGGGAAGGGGAAGCAGCG 62.804 72.222 0.00 0.00 0.00 5.18
170 249 3.342477 AGGGGAAGGGGAAGCAGC 61.342 66.667 0.00 0.00 0.00 5.25
172 251 2.614013 GGAGGGGAAGGGGAAGCA 60.614 66.667 0.00 0.00 0.00 3.91
187 266 2.039951 CGTAGGGGAGTTGGGGGA 59.960 66.667 0.00 0.00 0.00 4.81
193 272 2.365237 GGGGAGCGTAGGGGAGTT 60.365 66.667 0.00 0.00 0.00 3.01
194 273 3.357082 AGGGGAGCGTAGGGGAGT 61.357 66.667 0.00 0.00 0.00 3.85
196 275 4.153330 GGAGGGGAGCGTAGGGGA 62.153 72.222 0.00 0.00 0.00 4.81
198 277 2.840102 CTGGAGGGGAGCGTAGGG 60.840 72.222 0.00 0.00 0.00 3.53
202 286 3.966930 GAGGTCTGGAGGGGAGCGT 62.967 68.421 0.00 0.00 36.47 5.07
294 561 3.181506 CCAAAATAAGAGCAGCGAGGAAC 60.182 47.826 0.00 0.00 0.00 3.62
310 577 0.601841 GCAGCAGCAACAGCCAAAAT 60.602 50.000 0.00 0.00 41.58 1.82
338 606 1.138266 GCCATGGCAGCATCAAATTCT 59.862 47.619 32.08 0.00 41.49 2.40
430 715 4.493747 CTTCGTCCCTCGCGTCCC 62.494 72.222 5.77 0.00 39.67 4.46
437 722 4.452733 CACCGGCCTTCGTCCCTC 62.453 72.222 0.00 0.00 37.11 4.30
440 725 4.754667 GTCCACCGGCCTTCGTCC 62.755 72.222 0.00 0.00 37.11 4.79
482 774 1.727335 GCAGAAGAACGGAAGCAGTAC 59.273 52.381 0.00 0.00 0.00 2.73
483 775 1.337823 GGCAGAAGAACGGAAGCAGTA 60.338 52.381 0.00 0.00 0.00 2.74
484 776 0.603975 GGCAGAAGAACGGAAGCAGT 60.604 55.000 0.00 0.00 0.00 4.40
486 778 0.603707 CTGGCAGAAGAACGGAAGCA 60.604 55.000 9.42 0.00 0.00 3.91
487 779 1.916697 GCTGGCAGAAGAACGGAAGC 61.917 60.000 20.86 0.00 0.00 3.86
497 789 1.879575 AGGGTACTATGCTGGCAGAA 58.120 50.000 20.86 8.68 0.00 3.02
578 870 0.321671 AAAGGCTCAGCGCTGAAGTA 59.678 50.000 37.16 18.26 39.39 2.24
579 871 0.536006 AAAAGGCTCAGCGCTGAAGT 60.536 50.000 37.16 22.97 39.39 3.01
580 872 0.595095 AAAAAGGCTCAGCGCTGAAG 59.405 50.000 37.16 29.67 39.39 3.02
590 882 7.484140 ACTATTATTAGCAAGCAAAAAGGCTC 58.516 34.615 0.00 0.00 45.07 4.70
618 917 4.528596 AGACATACAGTAAAGTGGAGCAGT 59.471 41.667 0.00 0.00 0.00 4.40
620 919 4.283467 ACAGACATACAGTAAAGTGGAGCA 59.717 41.667 0.00 0.00 0.00 4.26
635 934 9.750783 GGGTAGAATCCTAGTAATACAGACATA 57.249 37.037 0.00 0.00 0.00 2.29
636 935 8.457757 AGGGTAGAATCCTAGTAATACAGACAT 58.542 37.037 0.00 0.00 31.86 3.06
639 938 9.180282 AGTAGGGTAGAATCCTAGTAATACAGA 57.820 37.037 0.00 0.00 38.41 3.41
640 939 9.452287 GAGTAGGGTAGAATCCTAGTAATACAG 57.548 40.741 0.00 0.00 39.81 2.74
641 940 8.099537 CGAGTAGGGTAGAATCCTAGTAATACA 58.900 40.741 0.00 0.00 39.81 2.29
642 941 8.100164 ACGAGTAGGGTAGAATCCTAGTAATAC 58.900 40.741 0.00 0.00 39.81 1.89
643 942 8.212259 ACGAGTAGGGTAGAATCCTAGTAATA 57.788 38.462 0.00 0.00 39.81 0.98
644 943 7.089106 ACGAGTAGGGTAGAATCCTAGTAAT 57.911 40.000 0.00 0.00 39.81 1.89
645 944 6.506538 ACGAGTAGGGTAGAATCCTAGTAA 57.493 41.667 0.00 0.00 39.81 2.24
648 947 4.761227 GGAACGAGTAGGGTAGAATCCTAG 59.239 50.000 0.00 0.00 37.53 3.02
716 1016 4.072839 CAGTAGTGACTAGTGAGACACCA 58.927 47.826 20.09 0.00 45.86 4.17
717 1017 3.119779 GCAGTAGTGACTAGTGAGACACC 60.120 52.174 26.93 7.92 45.86 4.16
722 1022 5.347093 CACAAATGCAGTAGTGACTAGTGAG 59.653 44.000 26.93 14.17 39.10 3.51
723 1023 5.230182 CACAAATGCAGTAGTGACTAGTGA 58.770 41.667 26.93 14.42 39.10 3.41
724 1024 5.521516 CACAAATGCAGTAGTGACTAGTG 57.478 43.478 20.36 20.36 39.58 2.74
755 1055 2.739913 GCAAGGTAAGCGTCACACATAA 59.260 45.455 0.00 0.00 0.00 1.90
790 1096 4.142578 TGAACACAAAAAGCAAGCGTAAGA 60.143 37.500 0.00 0.00 43.02 2.10
801 1107 4.667262 TCACACCGAATGAACACAAAAAG 58.333 39.130 0.00 0.00 0.00 2.27
852 1158 3.236003 AACCCGCAGTCCGTCCTTC 62.236 63.158 0.00 0.00 34.38 3.46
868 1174 2.558359 AGCTGATGGTACCAAAAGCAAC 59.442 45.455 35.42 20.96 39.44 4.17
869 1175 2.875296 AGCTGATGGTACCAAAAGCAA 58.125 42.857 35.42 14.71 39.44 3.91
870 1176 2.584835 AGCTGATGGTACCAAAAGCA 57.415 45.000 35.42 23.47 39.44 3.91
879 1185 1.760613 CCGACCCTTTAGCTGATGGTA 59.239 52.381 9.26 0.00 0.00 3.25
881 1187 0.541863 ACCGACCCTTTAGCTGATGG 59.458 55.000 0.00 0.00 0.00 3.51
901 1207 3.569491 CCCCAATAACTGCCATCAATCT 58.431 45.455 0.00 0.00 0.00 2.40
921 1227 2.851071 CGAGAGATCCTCCACGGCC 61.851 68.421 0.00 0.00 38.71 6.13
924 1230 2.069465 CTGGCGAGAGATCCTCCACG 62.069 65.000 0.00 0.00 38.71 4.94
1009 1315 5.480772 CCAACCTCTTAAAGTCCTCTCTGTA 59.519 44.000 0.00 0.00 0.00 2.74
1061 1367 6.925610 AATAAGAGTTATGAAAGCGCATGA 57.074 33.333 11.47 0.00 0.00 3.07
1062 1368 9.162793 CTTTAATAAGAGTTATGAAAGCGCATG 57.837 33.333 11.47 0.00 37.30 4.06
1100 1406 6.183360 GCGAAAAGGAAAACATTGTCACTTTT 60.183 34.615 14.81 14.81 38.80 2.27
1154 1472 7.278868 CCAGAGAGAAATTGGTACTACAATGTC 59.721 40.741 6.83 6.83 42.72 3.06
1195 1532 1.580815 GAGAGATGCAAGGCTACAGC 58.419 55.000 0.00 0.00 41.14 4.40
1196 1533 1.761784 AGGAGAGATGCAAGGCTACAG 59.238 52.381 0.00 0.00 0.00 2.74
1197 1534 1.483827 CAGGAGAGATGCAAGGCTACA 59.516 52.381 0.00 0.00 0.00 2.74
1198 1535 1.809651 GCAGGAGAGATGCAAGGCTAC 60.810 57.143 0.00 0.00 43.31 3.58
1199 1536 0.467384 GCAGGAGAGATGCAAGGCTA 59.533 55.000 0.00 0.00 43.31 3.93
1200 1537 1.224039 GCAGGAGAGATGCAAGGCT 59.776 57.895 0.00 0.00 43.31 4.58
1201 1538 3.824810 GCAGGAGAGATGCAAGGC 58.175 61.111 0.00 0.00 43.31 4.35
1208 1545 7.677745 AGAATTACCACTATATGCAGGAGAGAT 59.322 37.037 0.00 0.00 0.00 2.75
1232 1569 6.255453 GCAAAAGTGTGTGCTTTTTCAATAGA 59.745 34.615 1.59 0.00 43.66 1.98
1244 1581 4.378459 GGACTATACAGCAAAAGTGTGTGC 60.378 45.833 0.00 0.00 41.22 4.57
1247 1584 5.412594 ACATGGACTATACAGCAAAAGTGTG 59.587 40.000 0.00 0.00 0.00 3.82
1277 1614 5.800296 TGGGAAGAACTCGTGAATATTTGA 58.200 37.500 0.00 0.00 0.00 2.69
1288 1626 2.311124 GGTACCATGGGAAGAACTCG 57.689 55.000 18.09 0.00 0.00 4.18
1316 1654 2.097825 GAGAAAGGATGCCATGTGCTT 58.902 47.619 7.54 1.84 42.00 3.91
1317 1655 1.760192 GAGAAAGGATGCCATGTGCT 58.240 50.000 7.54 0.00 42.00 4.40
1318 1656 0.379669 CGAGAAAGGATGCCATGTGC 59.620 55.000 0.00 0.00 41.77 4.57
1322 1660 2.636830 CTTGACGAGAAAGGATGCCAT 58.363 47.619 0.00 0.00 0.00 4.40
1329 1667 1.466167 CCATGTGCTTGACGAGAAAGG 59.534 52.381 0.00 0.00 0.00 3.11
1330 1668 1.135859 GCCATGTGCTTGACGAGAAAG 60.136 52.381 0.00 0.00 36.87 2.62
1331 1669 0.874390 GCCATGTGCTTGACGAGAAA 59.126 50.000 0.00 0.00 36.87 2.52
1332 1670 0.250252 TGCCATGTGCTTGACGAGAA 60.250 50.000 7.54 0.00 42.00 2.87
1333 1671 0.036105 ATGCCATGTGCTTGACGAGA 60.036 50.000 7.54 0.00 42.00 4.04
1334 1672 0.376152 GATGCCATGTGCTTGACGAG 59.624 55.000 7.54 0.00 42.00 4.18
1335 1673 1.026182 GGATGCCATGTGCTTGACGA 61.026 55.000 7.54 0.00 42.00 4.20
1336 1674 1.028330 AGGATGCCATGTGCTTGACG 61.028 55.000 7.54 0.00 42.00 4.35
1337 1675 1.180029 AAGGATGCCATGTGCTTGAC 58.820 50.000 7.54 0.00 42.00 3.18
1338 1676 1.820519 GAAAGGATGCCATGTGCTTGA 59.179 47.619 7.54 0.00 42.00 3.02
1339 1677 1.822990 AGAAAGGATGCCATGTGCTTG 59.177 47.619 7.54 0.00 42.00 4.01
1340 1678 2.097825 GAGAAAGGATGCCATGTGCTT 58.902 47.619 7.54 1.84 42.00 3.91
1341 1679 1.760192 GAGAAAGGATGCCATGTGCT 58.240 50.000 7.54 0.00 42.00 4.40
1342 1680 0.379669 CGAGAAAGGATGCCATGTGC 59.620 55.000 0.00 0.00 41.77 4.57
1343 1681 0.379669 GCGAGAAAGGATGCCATGTG 59.620 55.000 0.00 0.00 0.00 3.21
1344 1682 0.749454 GGCGAGAAAGGATGCCATGT 60.749 55.000 0.00 0.00 46.76 3.21
1345 1683 2.028130 GGCGAGAAAGGATGCCATG 58.972 57.895 0.00 0.00 46.76 3.66
1346 1684 4.567318 GGCGAGAAAGGATGCCAT 57.433 55.556 0.00 0.00 46.76 4.40
1348 1686 2.125106 ACGGCGAGAAAGGATGCC 60.125 61.111 16.62 0.00 44.09 4.40
1349 1687 0.741221 AAGACGGCGAGAAAGGATGC 60.741 55.000 16.62 0.00 0.00 3.91
1350 1688 1.726853 AAAGACGGCGAGAAAGGATG 58.273 50.000 16.62 0.00 0.00 3.51
1351 1689 2.474410 AAAAGACGGCGAGAAAGGAT 57.526 45.000 16.62 0.00 0.00 3.24
1352 1690 3.604875 ATAAAAGACGGCGAGAAAGGA 57.395 42.857 16.62 0.00 0.00 3.36
1353 1691 4.868734 AGTTATAAAAGACGGCGAGAAAGG 59.131 41.667 16.62 0.00 0.00 3.11
1361 1699 7.587629 ACCTGTTTTAAGTTATAAAAGACGGC 58.412 34.615 5.17 0.00 0.00 5.68
1370 1708 8.161425 AGAGCCAAAGACCTGTTTTAAGTTATA 58.839 33.333 0.00 0.00 0.00 0.98
1371 1709 7.004691 AGAGCCAAAGACCTGTTTTAAGTTAT 58.995 34.615 0.00 0.00 0.00 1.89
1374 1712 4.793201 AGAGCCAAAGACCTGTTTTAAGT 58.207 39.130 0.00 0.00 0.00 2.24
1378 1716 3.769300 ACAAAGAGCCAAAGACCTGTTTT 59.231 39.130 0.00 0.00 0.00 2.43
1381 1719 2.736670 ACAAAGAGCCAAAGACCTGT 57.263 45.000 0.00 0.00 0.00 4.00
1382 1720 3.381272 TCAAACAAAGAGCCAAAGACCTG 59.619 43.478 0.00 0.00 0.00 4.00
1440 1778 6.477360 GGCTTTGTCGTTTTCTTCCAAAAATA 59.523 34.615 0.00 0.00 31.29 1.40
1455 1793 2.297701 ACAAATGACTGGCTTTGTCGT 58.702 42.857 5.58 0.00 40.58 4.34
1555 1926 6.930722 CCAGCATGAAGGAAAATGTAAAAACT 59.069 34.615 0.00 0.00 39.69 2.66
1662 2033 6.197655 ACATAAATATGTGTACGTACAGTGCG 59.802 38.462 28.02 9.76 44.66 5.34
1689 2060 1.067974 AGCCCACGGTTAAACAAAAGC 59.932 47.619 0.00 0.00 0.00 3.51
1732 2110 5.543790 TCCAGCCTGCATAGAGTATTGATAA 59.456 40.000 0.00 0.00 0.00 1.75
2288 2666 4.074970 ACAGTGCAAAGAAGTCCATTAGG 58.925 43.478 0.00 0.00 0.00 2.69
2397 2775 7.485595 TGTTTTCACGTAAAAGAAAAGGCTTAC 59.514 33.333 10.70 0.00 42.43 2.34
2487 2865 2.019249 GCAAATCTGTGCATAGAGCCA 58.981 47.619 18.52 0.00 44.29 4.75
2540 2918 6.961360 TCATAGTTCAGGATAGTCGAATGT 57.039 37.500 0.00 0.00 0.00 2.71
2541 2919 9.347934 GTAATCATAGTTCAGGATAGTCGAATG 57.652 37.037 0.00 0.00 0.00 2.67
2874 3254 5.739647 GCTCTCTAGATGAAGATGCACATGT 60.740 44.000 0.00 0.00 0.00 3.21
2965 3348 2.290896 CCAGGTATGCAAGGAACCTCAA 60.291 50.000 9.68 0.00 41.75 3.02
3000 3383 7.271511 AGAGTTCAGATAGCAAAGATGGTAAG 58.728 38.462 0.00 0.00 42.37 2.34
3154 3537 9.614792 AGAAGGATACCATCAAATGTTAACTAC 57.385 33.333 7.22 0.00 37.17 2.73
3163 3546 5.907662 TGAGGAGAGAAGGATACCATCAAAT 59.092 40.000 0.00 0.00 37.17 2.32
3215 3598 8.887717 ACAAACTATGTTCAGAGAATTATGCTC 58.112 33.333 1.38 0.00 40.06 4.26
3361 3744 1.471287 CATCTGTGGCATGACAGTTGG 59.529 52.381 0.00 0.00 43.38 3.77
3421 3804 2.543777 TTTGTACCTCTCACTGCCAC 57.456 50.000 0.00 0.00 0.00 5.01
3423 3806 4.321230 CCAATTTTTGTACCTCTCACTGCC 60.321 45.833 0.00 0.00 0.00 4.85
3431 3814 5.930569 ACTCGTACTCCAATTTTTGTACCTC 59.069 40.000 0.00 0.00 33.73 3.85
3433 3816 6.091305 GGTACTCGTACTCCAATTTTTGTACC 59.909 42.308 7.12 0.00 39.20 3.34
3491 3874 9.412460 TGCTGATAGATACCAAAATTGAAAGAT 57.588 29.630 0.00 0.00 0.00 2.40
3645 4028 1.266718 GTGCACAATGAAAGCCTTCGA 59.733 47.619 13.17 0.00 33.94 3.71
3646 4029 1.001487 TGTGCACAATGAAAGCCTTCG 60.001 47.619 19.28 0.00 33.94 3.79
3647 4030 2.798976 TGTGCACAATGAAAGCCTTC 57.201 45.000 19.28 0.00 0.00 3.46
3648 4031 2.694628 TCTTGTGCACAATGAAAGCCTT 59.305 40.909 31.17 0.00 35.02 4.35
3649 4032 2.309613 TCTTGTGCACAATGAAAGCCT 58.690 42.857 31.17 0.00 35.02 4.58
3650 4033 2.798976 TCTTGTGCACAATGAAAGCC 57.201 45.000 31.17 0.00 35.02 4.35
3651 4034 5.662211 ATTTTCTTGTGCACAATGAAAGC 57.338 34.783 31.96 7.48 35.98 3.51
3749 4134 7.514721 AGTGAAATGGACTTTACAAACTCCTA 58.485 34.615 3.17 0.00 0.00 2.94
3756 4141 5.070001 CAGGGAGTGAAATGGACTTTACAA 58.930 41.667 0.00 0.00 0.00 2.41
3792 4177 8.213518 TGCAGATCCAAGTATCTAACAAAATC 57.786 34.615 0.00 0.00 34.40 2.17
3994 4379 5.047802 ACATTGGCTTTTCAGACCATTAGTG 60.048 40.000 0.00 0.00 32.39 2.74
4016 4401 0.240678 CACTAGCAATTTGGCGCACA 59.759 50.000 10.83 1.22 39.27 4.57
4020 4405 5.679734 ATATTCTCACTAGCAATTTGGCG 57.320 39.130 0.00 0.00 39.27 5.69
4199 4586 5.949952 ACTTAGTCTCAAACCAAACAAACCT 59.050 36.000 0.00 0.00 0.00 3.50
4289 4677 1.202758 TGTGACTTGCCTAAGGTGTGG 60.203 52.381 0.00 0.00 38.26 4.17
4305 4693 1.836999 AATGCGGGGCACTAGTGTGA 61.837 55.000 23.44 2.89 46.55 3.58
4314 4702 0.253327 TGTGTATGTAATGCGGGGCA 59.747 50.000 0.00 0.00 44.86 5.36
4563 4951 6.650807 CCTATTTTCAAGTGTGTTGAGCTAGA 59.349 38.462 0.00 0.00 0.00 2.43
4573 4969 4.340950 ACAACCACCCTATTTTCAAGTGTG 59.659 41.667 0.00 0.00 0.00 3.82
4635 5031 8.762481 AAGGGCTTATATTTAGAAACGGAAAT 57.238 30.769 0.00 0.00 0.00 2.17
4716 5367 0.603065 GGAGCAAAATGGGTGTGTCC 59.397 55.000 0.00 0.00 0.00 4.02
4719 5370 1.529226 TACGGAGCAAAATGGGTGTG 58.471 50.000 0.00 0.00 0.00 3.82
4720 5371 2.091541 CATACGGAGCAAAATGGGTGT 58.908 47.619 0.00 0.00 0.00 4.16
4724 5375 3.560068 GGACTACATACGGAGCAAAATGG 59.440 47.826 0.00 0.00 0.00 3.16
4771 5422 4.892345 AGTACTCCCTCCGTTCCTAAATAC 59.108 45.833 0.00 0.00 0.00 1.89
4782 5433 2.158652 TGGATGACTAGTACTCCCTCCG 60.159 54.545 16.75 0.00 0.00 4.63
5025 5676 3.777465 TCTGAAATCGGAGGAAGTACG 57.223 47.619 0.00 0.00 0.00 3.67
5033 5684 4.098654 AGGACACTACATCTGAAATCGGAG 59.901 45.833 0.00 0.00 34.27 4.63
5047 5698 5.887035 ACCAATACAGTCTCTAGGACACTAC 59.113 44.000 12.18 0.00 46.72 2.73
5108 5760 8.248904 ACTCCATGCTGCCAATATAAAAATTA 57.751 30.769 0.00 0.00 0.00 1.40
5132 5784 7.010830 ACTCACAAAAGGTCTAGTAAAACGAAC 59.989 37.037 0.00 0.00 0.00 3.95
5147 5799 7.038154 TCATGGAAGTAAAACTCACAAAAGG 57.962 36.000 0.00 0.00 0.00 3.11
5853 6509 6.455360 TCATCCATATTCTCAAACAAAGGC 57.545 37.500 0.00 0.00 0.00 4.35
6027 6683 2.576615 AGCTGGACCTTGTTGAAGAAC 58.423 47.619 0.00 0.00 0.00 3.01
6192 6848 1.669115 CCTGAACTGACTGGCCACG 60.669 63.158 0.00 0.00 0.00 4.94
6363 7019 3.128188 CTGCTGCTGCTGCTCTGG 61.128 66.667 27.67 13.92 40.48 3.86
6534 7190 4.966965 CAGTATGGTCTGTCGTTAGTCT 57.033 45.455 0.00 0.00 0.00 3.24
6557 7216 9.462606 AGCTTAATTAATTAGCACAGGTAGTTT 57.537 29.630 21.34 4.06 0.00 2.66
6560 7219 8.662781 TCAGCTTAATTAATTAGCACAGGTAG 57.337 34.615 21.34 11.20 0.00 3.18
6752 7411 3.563808 GTGATGTGCAACTTTAGGTCACA 59.436 43.478 0.00 0.00 37.17 3.58
6753 7412 3.815401 AGTGATGTGCAACTTTAGGTCAC 59.185 43.478 0.00 0.00 38.04 3.67
6754 7413 3.814842 CAGTGATGTGCAACTTTAGGTCA 59.185 43.478 0.00 0.00 38.04 4.02
6755 7414 4.065088 TCAGTGATGTGCAACTTTAGGTC 58.935 43.478 0.00 0.00 38.04 3.85
6778 7441 4.662468 TGGCACTGCAATTTTTACAAGA 57.338 36.364 2.82 0.00 0.00 3.02
6780 7443 6.500684 TTTTTGGCACTGCAATTTTTACAA 57.499 29.167 2.82 0.00 0.00 2.41
6782 7445 6.852345 CAGATTTTTGGCACTGCAATTTTTAC 59.148 34.615 2.82 0.00 0.00 2.01
6783 7446 6.957150 CAGATTTTTGGCACTGCAATTTTTA 58.043 32.000 2.82 0.00 0.00 1.52
6799 7462 7.750229 TGTAGATGAAGTCTTGCAGATTTTT 57.250 32.000 0.00 0.00 38.42 1.94
6815 7479 4.388773 GCGGCAATATTTCGATGTAGATGA 59.611 41.667 10.95 0.00 0.00 2.92
6817 7481 4.314961 TGCGGCAATATTTCGATGTAGAT 58.685 39.130 0.00 0.00 0.00 1.98
6818 7482 3.723260 TGCGGCAATATTTCGATGTAGA 58.277 40.909 0.00 0.00 0.00 2.59
6826 7490 6.833342 ATTTCATCTTTGCGGCAATATTTC 57.167 33.333 17.19 0.00 0.00 2.17
6834 7498 4.732784 TCTAACAATTTCATCTTTGCGGC 58.267 39.130 0.00 0.00 0.00 6.53
6850 7514 9.658799 TTCCAAATTTTCAACAAACATCTAACA 57.341 25.926 0.00 0.00 0.00 2.41
6858 7550 7.534282 ACCACATTTCCAAATTTTCAACAAAC 58.466 30.769 0.00 0.00 0.00 2.93
6896 7588 3.272574 TCAGCCCATCTGAGTCAAATC 57.727 47.619 0.00 0.00 46.34 2.17
6910 7602 2.797177 ACTTCTCCAAATCTCAGCCC 57.203 50.000 0.00 0.00 0.00 5.19
6941 7638 1.802337 GAAACCACTTTCCCCCGTGC 61.802 60.000 0.00 0.00 31.03 5.34
6944 7641 0.893727 CCTGAAACCACTTTCCCCCG 60.894 60.000 0.00 0.00 35.75 5.73
6954 7652 0.960364 GCGCCTGAATCCTGAAACCA 60.960 55.000 0.00 0.00 0.00 3.67
6999 7699 0.031857 CCGCAATCGAGCAGAGAGAT 59.968 55.000 0.00 0.00 38.10 2.75
7000 7700 1.435105 CCGCAATCGAGCAGAGAGA 59.565 57.895 0.00 0.00 38.10 3.10
7001 7701 1.591059 CCCGCAATCGAGCAGAGAG 60.591 63.158 0.00 0.00 38.10 3.20
7006 7706 2.896854 GCATCCCGCAATCGAGCA 60.897 61.111 0.00 0.00 41.79 4.26
7478 8181 4.990910 AGGCAGAGGTGGTGGGCT 62.991 66.667 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.