Multiple sequence alignment - TraesCS4B01G181900

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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 TraesCS4B01G181900 chr4B 100.000 3957 0 0 1 3957 399034807 399038763 0.000000e+00 7308.0
1 TraesCS4B01G181900 chr4B 93.305 239 10 4 2340 2572 399037071 399037309 8.140000e-92 348.0
2 TraesCS4B01G181900 chr4B 93.305 239 10 4 2265 2503 399037146 399037378 8.140000e-92 348.0
3 TraesCS4B01G181900 chr4B 90.244 164 10 4 2415 2572 399037071 399037234 4.010000e-50 209.0
4 TraesCS4B01G181900 chr4B 90.244 164 10 4 2265 2428 399037221 399037378 4.010000e-50 209.0
5 TraesCS4B01G181900 chr4B 90.411 146 9 5 3815 3957 328009086 328009229 1.880000e-43 187.0
6 TraesCS4B01G181900 chr4A 93.108 1451 59 16 2339 3770 150659038 150660466 0.000000e+00 2087.0
7 TraesCS4B01G181900 chr4A 94.454 1172 49 11 1337 2503 150658111 150659271 0.000000e+00 1790.0
8 TraesCS4B01G181900 chr4A 86.842 570 38 24 794 1343 150657440 150657992 1.570000e-168 603.0
9 TraesCS4B01G181900 chr4A 95.082 305 11 3 1 302 150656257 150656560 9.950000e-131 477.0
10 TraesCS4B01G181900 chr4A 90.909 165 9 4 2414 2572 150659038 150659202 2.390000e-52 217.0
11 TraesCS4B01G181900 chr4A 87.805 164 14 4 2265 2428 150659114 150659271 1.880000e-43 187.0
12 TraesCS4B01G181900 chr4A 90.769 65 3 1 3765 3826 150660489 150660553 2.530000e-12 84.2
13 TraesCS4B01G181900 chr4D 89.119 1158 55 39 1368 2503 322227910 322226802 0.000000e+00 1375.0
14 TraesCS4B01G181900 chr4D 89.227 854 47 16 2133 2986 322227211 322226403 0.000000e+00 1026.0
15 TraesCS4B01G181900 chr4D 95.133 637 19 5 2985 3621 322221181 322220557 0.000000e+00 994.0
16 TraesCS4B01G181900 chr4D 91.209 273 14 6 1 267 322234519 322234251 2.910000e-96 363.0
17 TraesCS4B01G181900 chr4D 81.074 391 37 21 984 1352 322228267 322227892 1.080000e-70 278.0
18 TraesCS4B01G181900 chr4D 90.132 152 13 2 2414 2564 322227035 322226885 3.120000e-46 196.0
19 TraesCS4B01G181900 chr4D 89.552 67 3 1 794 856 322228413 322228347 9.110000e-12 82.4
20 TraesCS4B01G181900 chr6B 94.615 130 7 0 3828 3957 213152369 213152498 6.700000e-48 202.0
21 TraesCS4B01G181900 chr7D 93.382 136 6 3 3823 3957 118599053 118598920 8.670000e-47 198.0
22 TraesCS4B01G181900 chr3B 93.893 131 6 2 3827 3957 26771631 26771503 3.120000e-46 196.0
23 TraesCS4B01G181900 chr3B 91.367 139 10 2 3821 3957 606558338 606558476 5.220000e-44 189.0
24 TraesCS4B01G181900 chr3B 90.278 144 10 4 3815 3956 703068578 703068719 6.750000e-43 185.0
25 TraesCS4B01G181900 chr5D 91.096 146 8 5 3815 3957 248193331 248193474 4.040000e-45 193.0
26 TraesCS4B01G181900 chr5B 90.411 146 9 5 3815 3957 84580464 84580321 1.880000e-43 187.0
27 TraesCS4B01G181900 chr2B 91.367 139 9 3 3819 3957 649145266 649145131 1.880000e-43 187.0
28 TraesCS4B01G181900 chr1B 90.164 61 6 0 3378 3438 573391433 573391493 3.280000e-11 80.5
29 TraesCS4B01G181900 chr1D 82.222 90 14 2 3378 3466 423866116 423866204 4.240000e-10 76.8


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 TraesCS4B01G181900 chr4B 399034807 399038763 3956 False 1684.400000 7308 93.419600 1 3957 5 chr4B.!!$F2 3956
1 TraesCS4B01G181900 chr4A 150656257 150660553 4296 False 777.885714 2087 91.281286 1 3826 7 chr4A.!!$F1 3825
2 TraesCS4B01G181900 chr4D 322220557 322221181 624 True 994.000000 994 95.133000 2985 3621 1 chr4D.!!$R1 636
3 TraesCS4B01G181900 chr4D 322226403 322228413 2010 True 591.480000 1375 87.820800 794 2986 5 chr4D.!!$R3 2192

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
350 407 0.107410 AGTCCTCGTCGCTCTGAGAT 60.107 55.0 9.28 0.0 34.04 2.75 F
864 1291 0.178891 AGGGAGGAGAGTCTTGCCAA 60.179 55.0 5.30 0.0 36.42 4.52 F
1217 1695 0.535102 CTGAATGTATGACCCCGCCC 60.535 60.0 0.00 0.0 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1630 2254 0.035534 CCATCCCGTCAATCACACCA 60.036 55.0 0.0 0.0 0.0 4.17 R
2007 2637 0.978146 ACCCTCCTCTTCCATGACCG 60.978 60.0 0.0 0.0 0.0 4.79 R
3035 3669 0.036732 TCCCGTCACCGTGTAGTAGT 59.963 55.0 0.0 0.0 0.0 2.73 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
24 25 1.139734 CGTCGAGGTCCAGGACATG 59.860 63.158 21.75 10.00 33.68 3.21
95 99 3.188460 GTGTGATTTGTAGCGTGGTTGAT 59.812 43.478 0.00 0.00 0.00 2.57
102 106 1.075542 TAGCGTGGTTGATTGAAGCG 58.924 50.000 0.00 0.00 34.56 4.68
112 116 2.253414 GATTGAAGCGGCGTGGAACC 62.253 60.000 9.37 0.00 0.00 3.62
127 131 2.798148 GAACCGGCGGTTGATCTGGT 62.798 60.000 45.21 22.43 46.95 4.00
252 256 4.691685 TGTTCAGTTATTAACCGCGTTGAT 59.308 37.500 4.92 4.75 0.00 2.57
295 299 1.276415 TGCGTTTTGTTTCTTGCTGC 58.724 45.000 0.00 0.00 0.00 5.25
302 306 5.495502 GTTTTGTTTCTTGCTGCTTTGATG 58.504 37.500 0.00 0.00 0.00 3.07
305 309 4.801891 TGTTTCTTGCTGCTTTGATGATC 58.198 39.130 0.00 0.00 0.00 2.92
312 340 2.097142 GCTGCTTTGATGATCCTGACAC 59.903 50.000 0.00 0.00 0.00 3.67
313 341 2.681848 CTGCTTTGATGATCCTGACACC 59.318 50.000 0.00 0.00 0.00 4.16
329 357 2.193536 ACCGGTTGCTGGTTTGAGC 61.194 57.895 0.00 0.00 40.77 4.26
337 365 1.016653 GCTGGTTTGAGCGAGTCCTC 61.017 60.000 0.00 2.61 0.00 3.71
350 407 0.107410 AGTCCTCGTCGCTCTGAGAT 60.107 55.000 9.28 0.00 34.04 2.75
394 451 6.493189 AAAAAGTCCTCTCTCTCTCTTGTT 57.507 37.500 0.00 0.00 0.00 2.83
395 452 5.467035 AAAGTCCTCTCTCTCTCTTGTTG 57.533 43.478 0.00 0.00 0.00 3.33
396 453 2.825532 AGTCCTCTCTCTCTCTTGTTGC 59.174 50.000 0.00 0.00 0.00 4.17
397 454 1.815613 TCCTCTCTCTCTCTTGTTGCG 59.184 52.381 0.00 0.00 0.00 4.85
398 455 1.543802 CCTCTCTCTCTCTTGTTGCGT 59.456 52.381 0.00 0.00 0.00 5.24
399 456 2.415357 CCTCTCTCTCTCTTGTTGCGTC 60.415 54.545 0.00 0.00 0.00 5.19
403 460 3.993081 CTCTCTCTCTTGTTGCGTCAAAT 59.007 43.478 0.00 0.00 0.00 2.32
404 461 5.048013 TCTCTCTCTCTTGTTGCGTCAAATA 60.048 40.000 0.00 0.00 0.00 1.40
405 462 5.538118 TCTCTCTCTTGTTGCGTCAAATAA 58.462 37.500 0.00 0.00 0.00 1.40
406 463 5.635280 TCTCTCTCTTGTTGCGTCAAATAAG 59.365 40.000 9.48 9.48 0.00 1.73
407 464 5.538118 TCTCTCTTGTTGCGTCAAATAAGA 58.462 37.500 14.01 14.01 32.22 2.10
408 465 5.635280 TCTCTCTTGTTGCGTCAAATAAGAG 59.365 40.000 23.36 23.36 42.12 2.85
410 467 5.177511 TCTCTTGTTGCGTCAAATAAGAGTG 59.822 40.000 25.36 15.17 41.83 3.51
411 468 5.053811 TCTTGTTGCGTCAAATAAGAGTGA 58.946 37.500 12.23 0.00 30.74 3.41
412 469 5.525745 TCTTGTTGCGTCAAATAAGAGTGAA 59.474 36.000 12.23 0.00 30.74 3.18
413 470 5.090652 TGTTGCGTCAAATAAGAGTGAAC 57.909 39.130 0.00 0.00 0.00 3.18
418 756 4.326205 CGTCAAATAAGAGTGAACATGCG 58.674 43.478 0.00 0.00 0.00 4.73
422 760 2.672961 TAAGAGTGAACATGCGGAGG 57.327 50.000 0.00 0.00 0.00 4.30
425 763 1.078848 AGTGAACATGCGGAGGAGC 60.079 57.895 0.00 0.00 37.71 4.70
427 765 2.268920 GAACATGCGGAGGAGCCA 59.731 61.111 0.00 0.00 35.94 4.75
448 790 0.249699 TCGGCGAGCAAGAAGTGAAA 60.250 50.000 4.99 0.00 0.00 2.69
453 795 2.236690 CGAGCAAGAAGTGAAAATGCG 58.763 47.619 0.00 0.00 41.72 4.73
457 799 2.922335 GCAAGAAGTGAAAATGCGGACC 60.922 50.000 0.00 0.00 0.00 4.46
464 806 0.804989 GAAAATGCGGACCTGACCAG 59.195 55.000 0.00 0.00 0.00 4.00
471 813 2.009042 GCGGACCTGACCAGAATTCAG 61.009 57.143 8.44 0.00 40.30 3.02
477 819 3.201290 CCTGACCAGAATTCAGAATCCG 58.799 50.000 8.44 0.00 42.81 4.18
478 820 3.369892 CCTGACCAGAATTCAGAATCCGT 60.370 47.826 8.44 0.00 42.81 4.69
494 836 2.388735 TCCGTAGCCATCATCAGAAGT 58.611 47.619 0.00 0.00 0.00 3.01
527 869 2.844839 GGATGGGAGGGAGGGACG 60.845 72.222 0.00 0.00 0.00 4.79
544 886 1.734465 GACGCCTTTGATCAGTCTTGG 59.266 52.381 0.00 0.00 0.00 3.61
581 923 1.871772 CAAAGGCAGGCTCAACTCG 59.128 57.895 0.00 0.00 0.00 4.18
590 932 3.134458 CAGGCTCAACTCGACTTTCTTT 58.866 45.455 0.00 0.00 0.00 2.52
592 934 3.131396 GGCTCAACTCGACTTTCTTTCA 58.869 45.455 0.00 0.00 0.00 2.69
597 945 6.348050 GCTCAACTCGACTTTCTTTCAATGAT 60.348 38.462 0.00 0.00 0.00 2.45
658 1025 3.114616 CTTGTGCAGGCGACCGAG 61.115 66.667 0.00 0.00 0.00 4.63
688 1055 2.541588 CGAAAGCCTGTTCTGTTTGGTG 60.542 50.000 0.00 0.00 0.00 4.17
689 1056 1.402787 AAGCCTGTTCTGTTTGGTGG 58.597 50.000 0.00 0.00 0.00 4.61
693 1060 1.456705 TGTTCTGTTTGGTGGGGCC 60.457 57.895 0.00 0.00 37.90 5.80
694 1061 2.200092 TTCTGTTTGGTGGGGCCC 59.800 61.111 18.17 18.17 36.04 5.80
695 1062 3.460478 TTCTGTTTGGTGGGGCCCC 62.460 63.158 36.14 36.14 36.04 5.80
714 1087 1.795170 CGGAACAGCCCACCAACAAG 61.795 60.000 0.00 0.00 0.00 3.16
715 1088 0.467290 GGAACAGCCCACCAACAAGA 60.467 55.000 0.00 0.00 0.00 3.02
719 1092 0.468029 CAGCCCACCAACAAGAAGGT 60.468 55.000 0.00 0.00 39.10 3.50
738 1111 2.178580 GTGCCCCATTCAATTCCTTCA 58.821 47.619 0.00 0.00 0.00 3.02
745 1118 4.284178 CCATTCAATTCCTTCATCCCTGT 58.716 43.478 0.00 0.00 0.00 4.00
751 1124 0.252881 TCCTTCATCCCTGTCCTGCT 60.253 55.000 0.00 0.00 0.00 4.24
756 1129 2.729479 ATCCCTGTCCTGCTCTGCG 61.729 63.158 0.00 0.00 0.00 5.18
759 1132 2.508887 CTGTCCTGCTCTGCGCTC 60.509 66.667 9.73 0.00 40.11 5.03
760 1133 2.993840 TGTCCTGCTCTGCGCTCT 60.994 61.111 9.73 0.00 40.11 4.09
761 1134 2.508887 GTCCTGCTCTGCGCTCTG 60.509 66.667 9.73 0.00 40.11 3.35
762 1135 4.447989 TCCTGCTCTGCGCTCTGC 62.448 66.667 9.73 10.54 46.70 4.26
785 1165 2.298411 ACGTACGTCTCTCTCTCTCC 57.702 55.000 16.72 0.00 0.00 3.71
787 1167 1.574134 GTACGTCTCTCTCTCTCCCG 58.426 60.000 0.00 0.00 0.00 5.14
788 1168 0.464870 TACGTCTCTCTCTCTCCCGG 59.535 60.000 0.00 0.00 0.00 5.73
789 1169 1.525077 CGTCTCTCTCTCTCCCGGG 60.525 68.421 16.85 16.85 0.00 5.73
790 1170 1.152839 GTCTCTCTCTCTCCCGGGG 60.153 68.421 23.50 12.05 0.00 5.73
791 1171 2.520741 CTCTCTCTCTCCCGGGGC 60.521 72.222 23.50 0.00 0.00 5.80
792 1172 3.347590 TCTCTCTCTCCCGGGGCA 61.348 66.667 23.50 6.36 0.00 5.36
856 1273 2.686835 GCCAGCAGGGAGGAGAGT 60.687 66.667 0.00 0.00 40.01 3.24
864 1291 0.178891 AGGGAGGAGAGTCTTGCCAA 60.179 55.000 5.30 0.00 36.42 4.52
894 1321 1.529796 GAGAGGGCCGAGAGAGAGA 59.470 63.158 0.00 0.00 0.00 3.10
920 1361 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
921 1362 4.078922 AGAGAGAGAGAGAGAGAGAGAGGA 60.079 50.000 0.00 0.00 0.00 3.71
922 1363 4.222336 AGAGAGAGAGAGAGAGAGAGGAG 58.778 52.174 0.00 0.00 0.00 3.69
923 1364 3.964031 GAGAGAGAGAGAGAGAGAGGAGT 59.036 52.174 0.00 0.00 0.00 3.85
924 1365 4.366267 AGAGAGAGAGAGAGAGAGGAGTT 58.634 47.826 0.00 0.00 0.00 3.01
925 1366 4.163078 AGAGAGAGAGAGAGAGAGGAGTTG 59.837 50.000 0.00 0.00 0.00 3.16
929 1370 2.308570 AGAGAGAGAGAGGAGTTGAGCA 59.691 50.000 0.00 0.00 0.00 4.26
931 1372 1.134946 GAGAGAGAGGAGTTGAGCAGC 59.865 57.143 0.00 0.00 0.00 5.25
953 1398 1.812113 AAGGAGGACGGAGAAGGGGA 61.812 60.000 0.00 0.00 0.00 4.81
954 1399 1.758906 GGAGGACGGAGAAGGGGAG 60.759 68.421 0.00 0.00 0.00 4.30
955 1400 1.758906 GAGGACGGAGAAGGGGAGG 60.759 68.421 0.00 0.00 0.00 4.30
956 1401 2.226149 GAGGACGGAGAAGGGGAGGA 62.226 65.000 0.00 0.00 0.00 3.71
957 1402 1.758906 GGACGGAGAAGGGGAGGAG 60.759 68.421 0.00 0.00 0.00 3.69
958 1403 1.306970 GACGGAGAAGGGGAGGAGA 59.693 63.158 0.00 0.00 0.00 3.71
959 1404 0.753848 GACGGAGAAGGGGAGGAGAG 60.754 65.000 0.00 0.00 0.00 3.20
960 1405 1.456705 CGGAGAAGGGGAGGAGAGG 60.457 68.421 0.00 0.00 0.00 3.69
961 1406 1.074850 GGAGAAGGGGAGGAGAGGG 60.075 68.421 0.00 0.00 0.00 4.30
962 1407 1.764454 GAGAAGGGGAGGAGAGGGC 60.764 68.421 0.00 0.00 0.00 5.19
963 1408 2.041265 GAAGGGGAGGAGAGGGCA 59.959 66.667 0.00 0.00 0.00 5.36
964 1409 2.041928 AAGGGGAGGAGAGGGCAG 59.958 66.667 0.00 0.00 0.00 4.85
965 1410 3.649652 AAGGGGAGGAGAGGGCAGG 62.650 68.421 0.00 0.00 0.00 4.85
968 1413 4.095400 GGAGGAGAGGGCAGGGGA 62.095 72.222 0.00 0.00 0.00 4.81
969 1414 2.445654 GAGGAGAGGGCAGGGGAG 60.446 72.222 0.00 0.00 0.00 4.30
970 1415 4.101077 AGGAGAGGGCAGGGGAGG 62.101 72.222 0.00 0.00 0.00 4.30
978 1423 4.459089 GCAGGGGAGGCGTGAGTC 62.459 72.222 0.00 0.00 0.00 3.36
979 1424 4.135153 CAGGGGAGGCGTGAGTCG 62.135 72.222 0.00 0.00 43.49 4.18
982 1427 3.379445 GGGAGGCGTGAGTCGGAA 61.379 66.667 0.00 0.00 43.49 4.30
1149 1627 5.422970 ACTCTCAATCTCATCTGCTTCTCTT 59.577 40.000 0.00 0.00 0.00 2.85
1171 1649 3.129638 TGTTTTGGTTCCAACTTTCTCCG 59.870 43.478 3.56 0.00 0.00 4.63
1217 1695 0.535102 CTGAATGTATGACCCCGCCC 60.535 60.000 0.00 0.00 0.00 6.13
1226 1704 1.078356 GACCCCGCCCTTCTTCTTC 60.078 63.158 0.00 0.00 0.00 2.87
1231 1709 1.379642 CCGCCCTTCTTCTTCCATGC 61.380 60.000 0.00 0.00 0.00 4.06
1251 1729 6.703165 CCATGCATTTATTTCTCTTTTAGGGC 59.297 38.462 0.00 0.00 0.00 5.19
1254 1732 5.067283 GCATTTATTTCTCTTTTAGGGCGGA 59.933 40.000 0.00 0.00 0.00 5.54
1258 1736 8.810990 TTTATTTCTCTTTTAGGGCGGAATTA 57.189 30.769 0.00 0.00 0.00 1.40
1320 1803 5.105064 TGTTACTCCTATTCCCTTCTTTCGG 60.105 44.000 0.00 0.00 0.00 4.30
1623 2247 1.737355 TTTTGCTTTGCTCCGCTGCT 61.737 50.000 0.00 0.00 0.00 4.24
1625 2249 4.773117 GCTTTGCTCCGCTGCTGC 62.773 66.667 5.34 5.34 0.00 5.25
1626 2250 4.112341 CTTTGCTCCGCTGCTGCC 62.112 66.667 10.24 0.00 35.36 4.85
1627 2251 4.648626 TTTGCTCCGCTGCTGCCT 62.649 61.111 10.24 0.00 35.36 4.75
1733 2357 2.736995 GCTCAACGCTGCACGGTA 60.737 61.111 12.18 0.00 42.45 4.02
1968 2592 2.301738 GCACCTCCCCTTACCAGCT 61.302 63.158 0.00 0.00 0.00 4.24
2007 2637 1.301293 CCAAGGTGAAGGAGGAGGC 59.699 63.158 0.00 0.00 0.00 4.70
2260 2890 1.985116 GTTGGAGCCGACCCTCTCT 60.985 63.158 0.00 0.00 32.43 3.10
2263 2893 2.438795 GAGCCGACCCTCTCTCGT 60.439 66.667 0.00 0.00 0.00 4.18
2300 2930 4.776322 CGCCGGAACCATGCAGGA 62.776 66.667 5.05 0.00 41.22 3.86
2301 2931 2.825836 GCCGGAACCATGCAGGAG 60.826 66.667 5.05 0.00 41.22 3.69
2302 2932 2.825836 CCGGAACCATGCAGGAGC 60.826 66.667 0.00 0.00 41.22 4.70
2303 2933 2.825836 CGGAACCATGCAGGAGCC 60.826 66.667 0.00 4.30 41.22 4.70
2304 2934 2.825836 GGAACCATGCAGGAGCCG 60.826 66.667 0.00 0.00 41.22 5.52
2305 2935 2.825836 GAACCATGCAGGAGCCGG 60.826 66.667 0.00 0.00 41.22 6.13
2309 2939 3.865383 CATGCAGGAGCCGGCCTA 61.865 66.667 26.15 3.29 41.13 3.93
2310 2940 3.866582 ATGCAGGAGCCGGCCTAC 61.867 66.667 26.15 14.17 41.13 3.18
2331 2961 3.551407 GGAGCGGATCCTCCCCAC 61.551 72.222 10.75 0.00 45.64 4.61
2332 2962 2.764128 GAGCGGATCCTCCCCACA 60.764 66.667 10.75 0.00 31.13 4.17
2333 2963 3.083997 AGCGGATCCTCCCCACAC 61.084 66.667 10.75 0.00 31.13 3.82
2334 2964 4.176752 GCGGATCCTCCCCACACC 62.177 72.222 10.75 0.00 31.13 4.16
2335 2965 2.687200 CGGATCCTCCCCACACCA 60.687 66.667 10.75 0.00 31.13 4.17
2336 2966 2.998949 GGATCCTCCCCACACCAC 59.001 66.667 3.84 0.00 0.00 4.16
2337 2967 2.680370 GGATCCTCCCCACACCACC 61.680 68.421 3.84 0.00 0.00 4.61
2338 2968 1.923395 GATCCTCCCCACACCACCA 60.923 63.158 0.00 0.00 0.00 4.17
2339 2969 2.198304 GATCCTCCCCACACCACCAC 62.198 65.000 0.00 0.00 0.00 4.16
2340 2970 3.966543 CCTCCCCACACCACCACC 61.967 72.222 0.00 0.00 0.00 4.61
2341 2971 3.174987 CTCCCCACACCACCACCA 61.175 66.667 0.00 0.00 0.00 4.17
2342 2972 3.491598 CTCCCCACACCACCACCAC 62.492 68.421 0.00 0.00 0.00 4.16
2343 2973 4.596585 CCCCACACCACCACCACC 62.597 72.222 0.00 0.00 0.00 4.61
2344 2974 3.814906 CCCACACCACCACCACCA 61.815 66.667 0.00 0.00 0.00 4.17
2345 2975 2.203337 CCACACCACCACCACCAG 60.203 66.667 0.00 0.00 0.00 4.00
2346 2976 2.203337 CACACCACCACCACCAGG 60.203 66.667 0.00 0.00 42.21 4.45
2347 2977 4.204028 ACACCACCACCACCAGGC 62.204 66.667 0.00 0.00 39.06 4.85
2348 2978 3.889692 CACCACCACCACCAGGCT 61.890 66.667 0.00 0.00 39.06 4.58
2349 2979 3.103213 ACCACCACCACCAGGCTT 61.103 61.111 0.00 0.00 39.06 4.35
2350 2980 2.282462 CCACCACCACCAGGCTTC 60.282 66.667 0.00 0.00 39.06 3.86
2351 2981 2.669569 CACCACCACCAGGCTTCG 60.670 66.667 0.00 0.00 39.06 3.79
2352 2982 3.953775 ACCACCACCAGGCTTCGG 61.954 66.667 0.00 0.00 39.06 4.30
2971 3601 3.117813 ACTTCTAGGGACTGCTCTCGTAT 60.118 47.826 0.00 0.00 41.52 3.06
3034 3668 2.826725 ACGGTAGCTAAGCTTGAGAGTT 59.173 45.455 9.86 0.00 40.44 3.01
3035 3669 4.015084 ACGGTAGCTAAGCTTGAGAGTTA 58.985 43.478 9.86 0.00 40.44 2.24
3036 3670 4.142425 ACGGTAGCTAAGCTTGAGAGTTAC 60.142 45.833 9.86 10.79 40.44 2.50
3090 3724 6.759497 AGGTTATCAATTTACTGTTGGAGC 57.241 37.500 0.00 0.00 0.00 4.70
3146 3780 2.092484 TGCTAGTCTTGCCATGCCATTA 60.092 45.455 3.76 0.00 0.00 1.90
3218 3852 9.371136 CATGTCTCATGTTTACTTATGTACAGT 57.629 33.333 0.33 0.00 30.76 3.55
3265 3899 3.476024 GTCAAAGTTTTGTTCGCGTGTAC 59.524 43.478 5.77 3.82 39.18 2.90
3293 3927 8.407832 ACCACAACAAACCAGTTTTTATAGTAC 58.592 33.333 0.00 0.00 0.00 2.73
3295 3929 9.445786 CACAACAAACCAGTTTTTATAGTACTG 57.554 33.333 5.39 0.00 39.13 2.74
3296 3930 9.181061 ACAACAAACCAGTTTTTATAGTACTGT 57.819 29.630 5.39 0.39 38.04 3.55
3354 3988 5.163893 GCCAATTTCATCAAATCTGTTGCAG 60.164 40.000 0.00 0.00 30.37 4.41
3533 4173 2.392933 GAACAATCGTGCGAAAACCA 57.607 45.000 0.00 0.00 0.00 3.67
3542 4182 0.816018 TGCGAAAACCACGACCACAT 60.816 50.000 0.00 0.00 0.00 3.21
3653 4295 9.474920 TTTTGGATTAGTTTGAATTGCTAAGTG 57.525 29.630 0.00 0.00 0.00 3.16
3661 4303 8.401490 AGTTTGAATTGCTAAGTGAAGAAGAT 57.599 30.769 0.00 0.00 0.00 2.40
3662 4304 9.507329 AGTTTGAATTGCTAAGTGAAGAAGATA 57.493 29.630 0.00 0.00 0.00 1.98
3671 4321 6.708502 GCTAAGTGAAGAAGATATTCCTTCCC 59.291 42.308 0.00 0.00 42.58 3.97
3675 4325 6.619023 AGTGAAGAAGATATTCCTTCCCTCAT 59.381 38.462 0.00 0.00 42.58 2.90
3681 4331 6.838401 AGATATTCCTTCCCTCATGTCTTT 57.162 37.500 0.00 0.00 0.00 2.52
3729 4379 8.993121 ACATAATAATTGACGGCTGAGATTTAG 58.007 33.333 0.00 0.00 0.00 1.85
3733 4383 3.526931 TGACGGCTGAGATTTAGAAGG 57.473 47.619 0.00 0.00 0.00 3.46
3735 4385 3.706594 TGACGGCTGAGATTTAGAAGGAT 59.293 43.478 0.00 0.00 0.00 3.24
3737 4387 3.706594 ACGGCTGAGATTTAGAAGGATGA 59.293 43.478 0.00 0.00 0.00 2.92
3738 4388 4.202202 ACGGCTGAGATTTAGAAGGATGAG 60.202 45.833 0.00 0.00 0.00 2.90
3772 4450 1.065701 ACCTCACGGAAAGATCGATCG 59.934 52.381 19.33 9.36 0.00 3.69
3856 4537 6.509418 AAACAACAGTTTTGCTAGAACTCA 57.491 33.333 0.00 0.00 35.26 3.41
3857 4538 6.699575 AACAACAGTTTTGCTAGAACTCAT 57.300 33.333 0.00 0.00 35.26 2.90
3858 4539 6.305693 ACAACAGTTTTGCTAGAACTCATC 57.694 37.500 0.00 0.00 35.26 2.92
3859 4540 6.058183 ACAACAGTTTTGCTAGAACTCATCT 58.942 36.000 0.00 0.00 42.48 2.90
3860 4541 7.217200 ACAACAGTTTTGCTAGAACTCATCTA 58.783 34.615 0.00 0.00 39.71 1.98
3888 4569 8.908786 TGAGATATAATTTGGTCTCATTCACC 57.091 34.615 10.50 0.00 41.40 4.02
3889 4570 8.717717 TGAGATATAATTTGGTCTCATTCACCT 58.282 33.333 10.50 0.00 41.40 4.00
3890 4571 9.566432 GAGATATAATTTGGTCTCATTCACCTT 57.434 33.333 8.11 0.00 37.60 3.50
3891 4572 9.927081 AGATATAATTTGGTCTCATTCACCTTT 57.073 29.630 0.00 0.00 34.66 3.11
3897 4578 9.533831 AATTTGGTCTCATTCACCTTTTATAGT 57.466 29.630 0.00 0.00 34.66 2.12
3898 4579 8.561738 TTTGGTCTCATTCACCTTTTATAGTC 57.438 34.615 0.00 0.00 34.66 2.59
3899 4580 7.252612 TGGTCTCATTCACCTTTTATAGTCA 57.747 36.000 0.00 0.00 34.66 3.41
3900 4581 7.861629 TGGTCTCATTCACCTTTTATAGTCAT 58.138 34.615 0.00 0.00 34.66 3.06
3901 4582 8.328758 TGGTCTCATTCACCTTTTATAGTCATT 58.671 33.333 0.00 0.00 34.66 2.57
3902 4583 8.616076 GGTCTCATTCACCTTTTATAGTCATTG 58.384 37.037 0.00 0.00 0.00 2.82
3903 4584 8.616076 GTCTCATTCACCTTTTATAGTCATTGG 58.384 37.037 0.00 0.00 0.00 3.16
3904 4585 8.548025 TCTCATTCACCTTTTATAGTCATTGGA 58.452 33.333 0.00 0.00 0.00 3.53
3905 4586 9.347240 CTCATTCACCTTTTATAGTCATTGGAT 57.653 33.333 0.00 0.00 0.00 3.41
3906 4587 9.123902 TCATTCACCTTTTATAGTCATTGGATG 57.876 33.333 0.00 0.00 0.00 3.51
3907 4588 8.906867 CATTCACCTTTTATAGTCATTGGATGT 58.093 33.333 0.00 0.00 0.00 3.06
3908 4589 7.864108 TCACCTTTTATAGTCATTGGATGTG 57.136 36.000 0.00 0.00 0.00 3.21
3909 4590 7.629157 TCACCTTTTATAGTCATTGGATGTGA 58.371 34.615 0.00 0.00 0.00 3.58
3910 4591 8.274322 TCACCTTTTATAGTCATTGGATGTGAT 58.726 33.333 0.00 0.00 0.00 3.06
3911 4592 8.347771 CACCTTTTATAGTCATTGGATGTGATG 58.652 37.037 0.00 0.00 0.00 3.07
3912 4593 8.055181 ACCTTTTATAGTCATTGGATGTGATGT 58.945 33.333 0.00 0.00 0.00 3.06
3913 4594 8.906867 CCTTTTATAGTCATTGGATGTGATGTT 58.093 33.333 0.00 0.00 0.00 2.71
3921 4602 9.281371 AGTCATTGGATGTGATGTTATAAGATG 57.719 33.333 0.00 0.00 0.00 2.90
3922 4603 8.019669 GTCATTGGATGTGATGTTATAAGATGC 58.980 37.037 0.00 0.00 0.00 3.91
3923 4604 6.544038 TTGGATGTGATGTTATAAGATGCG 57.456 37.500 0.00 0.00 0.00 4.73
3924 4605 5.610398 TGGATGTGATGTTATAAGATGCGT 58.390 37.500 0.00 0.00 0.00 5.24
3925 4606 5.466393 TGGATGTGATGTTATAAGATGCGTG 59.534 40.000 0.00 0.00 0.00 5.34
3926 4607 5.466728 GGATGTGATGTTATAAGATGCGTGT 59.533 40.000 0.00 0.00 0.00 4.49
3927 4608 5.717038 TGTGATGTTATAAGATGCGTGTG 57.283 39.130 0.00 0.00 0.00 3.82
3928 4609 5.175127 TGTGATGTTATAAGATGCGTGTGT 58.825 37.500 0.00 0.00 0.00 3.72
3929 4610 5.063312 TGTGATGTTATAAGATGCGTGTGTG 59.937 40.000 0.00 0.00 0.00 3.82
3930 4611 4.033932 TGATGTTATAAGATGCGTGTGTGC 59.966 41.667 0.00 0.00 0.00 4.57
3931 4612 3.595173 TGTTATAAGATGCGTGTGTGCT 58.405 40.909 0.00 0.00 35.36 4.40
3932 4613 3.370672 TGTTATAAGATGCGTGTGTGCTG 59.629 43.478 0.00 0.00 35.36 4.41
3933 4614 2.385013 ATAAGATGCGTGTGTGCTGA 57.615 45.000 0.00 0.00 35.36 4.26
3934 4615 1.428448 TAAGATGCGTGTGTGCTGAC 58.572 50.000 0.00 0.00 35.36 3.51
3935 4616 1.560004 AAGATGCGTGTGTGCTGACG 61.560 55.000 0.00 0.00 38.63 4.35
3936 4617 2.280119 ATGCGTGTGTGCTGACGT 60.280 55.556 0.00 0.00 37.89 4.34
3937 4618 2.484631 GATGCGTGTGTGCTGACGTG 62.485 60.000 0.00 0.00 37.89 4.49
3938 4619 4.000557 GCGTGTGTGCTGACGTGG 62.001 66.667 0.00 0.00 37.89 4.94
3939 4620 3.337889 CGTGTGTGCTGACGTGGG 61.338 66.667 0.00 0.00 0.00 4.61
3940 4621 2.203015 GTGTGTGCTGACGTGGGT 60.203 61.111 0.00 0.00 0.00 4.51
3941 4622 1.817941 GTGTGTGCTGACGTGGGTT 60.818 57.895 0.00 0.00 0.00 4.11
3942 4623 1.817520 TGTGTGCTGACGTGGGTTG 60.818 57.895 0.00 0.00 0.00 3.77
3943 4624 1.817941 GTGTGCTGACGTGGGTTGT 60.818 57.895 0.00 0.00 0.00 3.32
3944 4625 0.531090 GTGTGCTGACGTGGGTTGTA 60.531 55.000 0.00 0.00 0.00 2.41
3945 4626 0.394938 TGTGCTGACGTGGGTTGTAT 59.605 50.000 0.00 0.00 0.00 2.29
3946 4627 1.619332 TGTGCTGACGTGGGTTGTATA 59.381 47.619 0.00 0.00 0.00 1.47
3947 4628 2.235155 TGTGCTGACGTGGGTTGTATAT 59.765 45.455 0.00 0.00 0.00 0.86
3948 4629 2.607635 GTGCTGACGTGGGTTGTATATG 59.392 50.000 0.00 0.00 0.00 1.78
3949 4630 1.597663 GCTGACGTGGGTTGTATATGC 59.402 52.381 0.00 0.00 0.00 3.14
3950 4631 2.741878 GCTGACGTGGGTTGTATATGCT 60.742 50.000 0.00 0.00 0.00 3.79
3951 4632 3.491964 GCTGACGTGGGTTGTATATGCTA 60.492 47.826 0.00 0.00 0.00 3.49
3952 4633 4.799586 GCTGACGTGGGTTGTATATGCTAT 60.800 45.833 0.00 0.00 0.00 2.97
3953 4634 5.284861 TGACGTGGGTTGTATATGCTATT 57.715 39.130 0.00 0.00 0.00 1.73
3954 4635 5.053811 TGACGTGGGTTGTATATGCTATTG 58.946 41.667 0.00 0.00 0.00 1.90
3955 4636 5.031066 ACGTGGGTTGTATATGCTATTGT 57.969 39.130 0.00 0.00 0.00 2.71
3956 4637 5.433526 ACGTGGGTTGTATATGCTATTGTT 58.566 37.500 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.153549 GCATGTCCTGGACCTCGAC 60.154 63.158 23.42 5.63 0.00 4.20
95 99 2.975799 GGTTCCACGCCGCTTCAA 60.976 61.111 0.00 0.00 0.00 2.69
112 116 2.047274 ACACCAGATCAACCGCCG 60.047 61.111 0.00 0.00 0.00 6.46
114 118 1.237285 AAGCACACCAGATCAACCGC 61.237 55.000 0.00 0.00 0.00 5.68
127 131 0.029300 GCAGCGAAGAACAAAGCACA 59.971 50.000 0.00 0.00 0.00 4.57
202 206 6.867816 GCAACATGGTTCTTCATCATTAACAA 59.132 34.615 0.00 0.00 0.00 2.83
214 218 2.624838 CTGAACAGGCAACATGGTTCTT 59.375 45.455 10.35 0.00 41.81 2.52
295 299 2.283298 CCGGTGTCAGGATCATCAAAG 58.717 52.381 0.00 0.00 0.00 2.77
302 306 1.021390 CAGCAACCGGTGTCAGGATC 61.021 60.000 8.52 0.00 35.85 3.36
305 309 2.669569 CCAGCAACCGGTGTCAGG 60.670 66.667 8.52 5.54 39.05 3.86
312 340 2.644992 GCTCAAACCAGCAACCGG 59.355 61.111 0.00 0.00 39.43 5.28
313 341 2.175184 CTCGCTCAAACCAGCAACCG 62.175 60.000 0.00 0.00 39.62 4.44
337 365 1.431036 TCTGCATCTCAGAGCGACG 59.569 57.895 0.00 0.00 46.34 5.12
371 428 6.287525 CAACAAGAGAGAGAGAGGACTTTTT 58.712 40.000 0.00 0.00 0.00 1.94
372 429 5.741673 GCAACAAGAGAGAGAGAGGACTTTT 60.742 44.000 0.00 0.00 0.00 2.27
373 430 4.262420 GCAACAAGAGAGAGAGAGGACTTT 60.262 45.833 0.00 0.00 0.00 2.66
387 444 5.177511 TCACTCTTATTTGACGCAACAAGAG 59.822 40.000 23.47 23.47 42.38 2.85
389 446 5.342806 TCACTCTTATTTGACGCAACAAG 57.657 39.130 0.00 0.00 0.00 3.16
390 447 5.065346 TGTTCACTCTTATTTGACGCAACAA 59.935 36.000 0.00 0.00 0.00 2.83
392 449 5.090652 TGTTCACTCTTATTTGACGCAAC 57.909 39.130 0.00 0.00 0.00 4.17
393 450 5.688823 CATGTTCACTCTTATTTGACGCAA 58.311 37.500 0.00 0.00 0.00 4.85
394 451 4.378356 GCATGTTCACTCTTATTTGACGCA 60.378 41.667 0.00 0.00 0.00 5.24
395 452 4.091424 GCATGTTCACTCTTATTTGACGC 58.909 43.478 0.00 0.00 0.00 5.19
396 453 4.326205 CGCATGTTCACTCTTATTTGACG 58.674 43.478 0.00 0.00 0.00 4.35
397 454 4.391830 TCCGCATGTTCACTCTTATTTGAC 59.608 41.667 0.00 0.00 0.00 3.18
398 455 4.574892 TCCGCATGTTCACTCTTATTTGA 58.425 39.130 0.00 0.00 0.00 2.69
399 456 4.201851 CCTCCGCATGTTCACTCTTATTTG 60.202 45.833 0.00 0.00 0.00 2.32
403 460 2.166459 CTCCTCCGCATGTTCACTCTTA 59.834 50.000 0.00 0.00 0.00 2.10
404 461 0.976641 TCCTCCGCATGTTCACTCTT 59.023 50.000 0.00 0.00 0.00 2.85
405 462 0.534412 CTCCTCCGCATGTTCACTCT 59.466 55.000 0.00 0.00 0.00 3.24
406 463 1.086634 GCTCCTCCGCATGTTCACTC 61.087 60.000 0.00 0.00 0.00 3.51
407 464 1.078848 GCTCCTCCGCATGTTCACT 60.079 57.895 0.00 0.00 0.00 3.41
408 465 2.109126 GGCTCCTCCGCATGTTCAC 61.109 63.158 0.00 0.00 0.00 3.18
410 467 2.109126 GTGGCTCCTCCGCATGTTC 61.109 63.158 0.00 0.00 44.77 3.18
411 468 2.045926 GTGGCTCCTCCGCATGTT 60.046 61.111 0.00 0.00 44.77 2.71
425 763 2.048222 TTCTTGCTCGCCGAGTGG 60.048 61.111 16.50 6.40 38.77 4.00
427 765 1.373497 CACTTCTTGCTCGCCGAGT 60.373 57.895 16.50 0.00 31.39 4.18
437 775 2.554032 AGGTCCGCATTTTCACTTCTTG 59.446 45.455 0.00 0.00 0.00 3.02
448 790 0.620556 ATTCTGGTCAGGTCCGCATT 59.379 50.000 0.00 0.00 0.00 3.56
453 795 3.703001 TTCTGAATTCTGGTCAGGTCC 57.297 47.619 11.89 0.00 42.37 4.46
457 799 3.866651 ACGGATTCTGAATTCTGGTCAG 58.133 45.455 11.89 12.44 43.28 3.51
464 806 4.380531 TGATGGCTACGGATTCTGAATTC 58.619 43.478 4.11 1.05 0.00 2.17
471 813 3.667497 TCTGATGATGGCTACGGATTC 57.333 47.619 0.00 0.00 0.00 2.52
477 819 5.016051 TCTCAACTTCTGATGATGGCTAC 57.984 43.478 0.00 0.00 32.14 3.58
478 820 5.423015 GTTCTCAACTTCTGATGATGGCTA 58.577 41.667 0.00 0.00 32.14 3.93
494 836 3.230134 CCATCCTTTGGTTGGTTCTCAA 58.770 45.455 5.72 0.00 40.99 3.02
505 847 1.649271 CCCTCCCTCCCATCCTTTGG 61.649 65.000 0.00 0.00 46.00 3.28
506 848 0.624500 TCCCTCCCTCCCATCCTTTG 60.625 60.000 0.00 0.00 0.00 2.77
507 849 0.624795 GTCCCTCCCTCCCATCCTTT 60.625 60.000 0.00 0.00 0.00 3.11
509 851 2.706071 GTCCCTCCCTCCCATCCT 59.294 66.667 0.00 0.00 0.00 3.24
510 852 2.844839 CGTCCCTCCCTCCCATCC 60.845 72.222 0.00 0.00 0.00 3.51
511 853 3.551407 GCGTCCCTCCCTCCCATC 61.551 72.222 0.00 0.00 0.00 3.51
515 857 3.009714 AAAGGCGTCCCTCCCTCC 61.010 66.667 0.00 0.00 41.90 4.30
516 858 1.627297 ATCAAAGGCGTCCCTCCCTC 61.627 60.000 0.00 0.00 41.90 4.30
517 859 1.616628 ATCAAAGGCGTCCCTCCCT 60.617 57.895 0.00 0.00 41.90 4.20
527 869 0.813821 GGCCAAGACTGATCAAAGGC 59.186 55.000 0.00 12.52 37.49 4.35
529 871 1.089920 CCGGCCAAGACTGATCAAAG 58.910 55.000 2.24 0.00 0.00 2.77
581 923 6.652481 TCAGGTCAGATCATTGAAAGAAAGTC 59.348 38.462 0.00 0.00 0.00 3.01
590 932 3.299503 TCCGATCAGGTCAGATCATTGA 58.700 45.455 0.00 0.00 43.61 2.57
592 934 3.899980 TCATCCGATCAGGTCAGATCATT 59.100 43.478 0.00 0.00 43.61 2.57
597 945 2.159043 GCTTTCATCCGATCAGGTCAGA 60.159 50.000 0.00 0.00 41.99 3.27
611 959 3.389002 ACCAAAGGCTCTTTTGCTTTCAT 59.611 39.130 0.00 0.00 36.86 2.57
655 1022 3.602317 CTTTCGCTCGCTCGCTCG 61.602 66.667 0.00 0.00 0.00 5.03
656 1023 3.907799 GCTTTCGCTCGCTCGCTC 61.908 66.667 0.00 0.00 0.00 5.03
659 1026 3.549150 CAGGCTTTCGCTCGCTCG 61.549 66.667 0.00 0.00 36.09 5.03
660 1027 1.960994 GAACAGGCTTTCGCTCGCTC 61.961 60.000 0.00 0.00 36.09 5.03
661 1028 2.029844 GAACAGGCTTTCGCTCGCT 61.030 57.895 0.00 0.00 36.09 4.93
667 1034 1.676006 ACCAAACAGAACAGGCTTTCG 59.324 47.619 0.00 0.00 0.00 3.46
693 1060 4.278513 TTGGTGGGCTGTTCCGGG 62.279 66.667 0.00 0.00 34.94 5.73
694 1061 2.983592 GTTGGTGGGCTGTTCCGG 60.984 66.667 0.00 0.00 34.94 5.14
695 1062 1.795170 CTTGTTGGTGGGCTGTTCCG 61.795 60.000 0.00 0.00 34.94 4.30
697 1070 1.338020 CTTCTTGTTGGTGGGCTGTTC 59.662 52.381 0.00 0.00 0.00 3.18
701 1074 1.930520 ACCTTCTTGTTGGTGGGCT 59.069 52.632 0.00 0.00 34.90 5.19
719 1092 2.619697 TGAAGGAATTGAATGGGGCA 57.380 45.000 0.00 0.00 0.00 5.36
738 1111 2.729479 CGCAGAGCAGGACAGGGAT 61.729 63.158 0.00 0.00 0.00 3.85
763 1136 3.551485 GGAGAGAGAGAGACGTACGTAAC 59.449 52.174 22.87 17.49 0.00 2.50
764 1137 3.430098 GGGAGAGAGAGAGACGTACGTAA 60.430 52.174 22.87 0.00 0.00 3.18
765 1138 2.100584 GGGAGAGAGAGAGACGTACGTA 59.899 54.545 22.87 0.00 0.00 3.57
766 1139 1.134729 GGGAGAGAGAGAGACGTACGT 60.135 57.143 23.04 23.04 0.00 3.57
767 1140 1.574134 GGGAGAGAGAGAGACGTACG 58.426 60.000 15.01 15.01 0.00 3.67
768 1141 1.574134 CGGGAGAGAGAGAGACGTAC 58.426 60.000 0.00 0.00 0.00 3.67
769 1142 0.464870 CCGGGAGAGAGAGAGACGTA 59.535 60.000 0.00 0.00 0.00 3.57
856 1273 1.228429 CCCCTTCCGTTTGGCAAGA 60.228 57.895 0.00 0.00 34.14 3.02
881 1308 0.468226 TCTCTCTCTCTCTCTCGGCC 59.532 60.000 0.00 0.00 0.00 6.13
883 1310 2.959030 TCTCTCTCTCTCTCTCTCTCGG 59.041 54.545 0.00 0.00 0.00 4.63
884 1311 3.885901 TCTCTCTCTCTCTCTCTCTCTCG 59.114 52.174 0.00 0.00 0.00 4.04
888 1315 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
894 1321 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
920 1361 0.739112 CTCCTTCCGCTGCTCAACTC 60.739 60.000 0.00 0.00 0.00 3.01
921 1362 1.294780 CTCCTTCCGCTGCTCAACT 59.705 57.895 0.00 0.00 0.00 3.16
922 1363 1.743252 CCTCCTTCCGCTGCTCAAC 60.743 63.158 0.00 0.00 0.00 3.18
923 1364 1.913262 TCCTCCTTCCGCTGCTCAA 60.913 57.895 0.00 0.00 0.00 3.02
924 1365 2.283894 TCCTCCTTCCGCTGCTCA 60.284 61.111 0.00 0.00 0.00 4.26
925 1366 2.185608 GTCCTCCTTCCGCTGCTC 59.814 66.667 0.00 0.00 0.00 4.26
929 1370 2.756283 CTCCGTCCTCCTTCCGCT 60.756 66.667 0.00 0.00 0.00 5.52
931 1372 1.668101 CCTTCTCCGTCCTCCTTCCG 61.668 65.000 0.00 0.00 0.00 4.30
953 1398 4.101077 CCTCCCCTGCCCTCTCCT 62.101 72.222 0.00 0.00 0.00 3.69
961 1406 4.459089 GACTCACGCCTCCCCTGC 62.459 72.222 0.00 0.00 0.00 4.85
962 1407 4.135153 CGACTCACGCCTCCCCTG 62.135 72.222 0.00 0.00 34.51 4.45
965 1410 3.358076 CTTCCGACTCACGCCTCCC 62.358 68.421 0.00 0.00 41.07 4.30
966 1411 2.182030 CTTCCGACTCACGCCTCC 59.818 66.667 0.00 0.00 41.07 4.30
967 1412 1.137825 CTCTTCCGACTCACGCCTC 59.862 63.158 0.00 0.00 41.07 4.70
968 1413 2.344203 CCTCTTCCGACTCACGCCT 61.344 63.158 0.00 0.00 41.07 5.52
969 1414 2.182030 CCTCTTCCGACTCACGCC 59.818 66.667 0.00 0.00 41.07 5.68
970 1415 1.137825 CTCCTCTTCCGACTCACGC 59.862 63.158 0.00 0.00 41.07 5.34
971 1416 0.730265 CTCTCCTCTTCCGACTCACG 59.270 60.000 0.00 0.00 42.18 4.35
972 1417 1.099689 CCTCTCCTCTTCCGACTCAC 58.900 60.000 0.00 0.00 0.00 3.51
973 1418 0.033991 CCCTCTCCTCTTCCGACTCA 60.034 60.000 0.00 0.00 0.00 3.41
974 1419 1.388837 GCCCTCTCCTCTTCCGACTC 61.389 65.000 0.00 0.00 0.00 3.36
975 1420 1.380650 GCCCTCTCCTCTTCCGACT 60.381 63.158 0.00 0.00 0.00 4.18
976 1421 2.776913 CGCCCTCTCCTCTTCCGAC 61.777 68.421 0.00 0.00 0.00 4.79
977 1422 2.440430 CGCCCTCTCCTCTTCCGA 60.440 66.667 0.00 0.00 0.00 4.55
978 1423 4.214327 GCGCCCTCTCCTCTTCCG 62.214 72.222 0.00 0.00 0.00 4.30
979 1424 4.214327 CGCGCCCTCTCCTCTTCC 62.214 72.222 0.00 0.00 0.00 3.46
980 1425 4.214327 CCGCGCCCTCTCCTCTTC 62.214 72.222 0.00 0.00 0.00 2.87
1149 1627 3.129638 CGGAGAAAGTTGGAACCAAAACA 59.870 43.478 7.89 0.00 37.70 2.83
1171 1649 2.271800 GAACATGGACACTCCGATCAC 58.728 52.381 0.00 0.00 40.17 3.06
1217 1695 8.684520 AGAGAAATAAATGCATGGAAGAAGAAG 58.315 33.333 0.00 0.00 0.00 2.85
1226 1704 6.703165 GCCCTAAAAGAGAAATAAATGCATGG 59.297 38.462 0.00 0.00 0.00 3.66
1231 1709 6.693315 TCCGCCCTAAAAGAGAAATAAATG 57.307 37.500 0.00 0.00 0.00 2.32
1251 1729 6.648725 AAGAGACACGAAAGATTAATTCCG 57.351 37.500 0.00 0.00 0.00 4.30
1254 1732 7.094334 GGGGAAAAGAGACACGAAAGATTAATT 60.094 37.037 0.00 0.00 0.00 1.40
1258 1736 4.072839 GGGGAAAAGAGACACGAAAGATT 58.927 43.478 0.00 0.00 0.00 2.40
1360 1971 8.480501 ACCTAGCGTAGTATTTAATTTCTCCAA 58.519 33.333 0.00 0.00 0.00 3.53
1361 1972 7.924412 CACCTAGCGTAGTATTTAATTTCTCCA 59.076 37.037 0.00 0.00 0.00 3.86
1363 1974 9.694137 ATCACCTAGCGTAGTATTTAATTTCTC 57.306 33.333 0.00 0.00 0.00 2.87
1372 1985 7.762588 ATTCAGTATCACCTAGCGTAGTATT 57.237 36.000 0.00 0.00 0.00 1.89
1491 2112 3.137459 CGCGCAGAGAGGAGAGGT 61.137 66.667 8.75 0.00 0.00 3.85
1623 2247 0.890542 GTCAATCACACCAGCAGGCA 60.891 55.000 0.00 0.00 39.06 4.75
1625 2249 1.300971 CCGTCAATCACACCAGCAGG 61.301 60.000 0.00 0.00 42.21 4.85
1626 2250 1.300971 CCCGTCAATCACACCAGCAG 61.301 60.000 0.00 0.00 0.00 4.24
1627 2251 1.302431 CCCGTCAATCACACCAGCA 60.302 57.895 0.00 0.00 0.00 4.41
1628 2252 0.392998 ATCCCGTCAATCACACCAGC 60.393 55.000 0.00 0.00 0.00 4.85
1629 2253 1.372582 CATCCCGTCAATCACACCAG 58.627 55.000 0.00 0.00 0.00 4.00
1630 2254 0.035534 CCATCCCGTCAATCACACCA 60.036 55.000 0.00 0.00 0.00 4.17
1933 2557 4.421479 CGCGTCCTCTTGGAGCGT 62.421 66.667 15.40 0.00 45.67 5.07
2007 2637 0.978146 ACCCTCCTCTTCCATGACCG 60.978 60.000 0.00 0.00 0.00 4.79
2260 2890 3.691342 CCGAAGCCTGGTGGACGA 61.691 66.667 0.00 0.00 34.57 4.20
2263 2893 3.706373 GAGCCGAAGCCTGGTGGA 61.706 66.667 0.00 0.00 41.25 4.02
2283 2913 4.776322 TCCTGCATGGTTCCGGCG 62.776 66.667 0.00 0.00 37.07 6.46
2284 2914 2.825836 CTCCTGCATGGTTCCGGC 60.826 66.667 0.00 0.00 37.07 6.13
2285 2915 2.825836 GCTCCTGCATGGTTCCGG 60.826 66.667 0.00 0.00 39.41 5.14
2286 2916 2.825836 GGCTCCTGCATGGTTCCG 60.826 66.667 0.00 0.00 41.91 4.30
2287 2917 2.825836 CGGCTCCTGCATGGTTCC 60.826 66.667 0.00 0.00 41.91 3.62
2288 2918 2.825836 CCGGCTCCTGCATGGTTC 60.826 66.667 0.00 0.00 41.91 3.62
2292 2922 3.865383 TAGGCCGGCTCCTGCATG 61.865 66.667 28.56 0.00 41.91 4.06
2293 2923 3.866582 GTAGGCCGGCTCCTGCAT 61.867 66.667 28.56 6.33 41.91 3.96
2320 2950 1.923395 TGGTGGTGTGGGGAGGATC 60.923 63.158 0.00 0.00 0.00 3.36
2321 2951 2.209809 TGGTGGTGTGGGGAGGAT 59.790 61.111 0.00 0.00 0.00 3.24
2322 2952 2.852075 GTGGTGGTGTGGGGAGGA 60.852 66.667 0.00 0.00 0.00 3.71
2323 2953 3.966543 GGTGGTGGTGTGGGGAGG 61.967 72.222 0.00 0.00 0.00 4.30
2324 2954 3.174987 TGGTGGTGGTGTGGGGAG 61.175 66.667 0.00 0.00 0.00 4.30
2325 2955 3.494254 GTGGTGGTGGTGTGGGGA 61.494 66.667 0.00 0.00 0.00 4.81
2326 2956 4.596585 GGTGGTGGTGGTGTGGGG 62.597 72.222 0.00 0.00 0.00 4.96
2327 2957 3.790416 CTGGTGGTGGTGGTGTGGG 62.790 68.421 0.00 0.00 0.00 4.61
2328 2958 2.203337 CTGGTGGTGGTGGTGTGG 60.203 66.667 0.00 0.00 0.00 4.17
2329 2959 2.203337 CCTGGTGGTGGTGGTGTG 60.203 66.667 0.00 0.00 0.00 3.82
2330 2960 4.204028 GCCTGGTGGTGGTGGTGT 62.204 66.667 0.00 0.00 35.27 4.16
2331 2961 3.435525 AAGCCTGGTGGTGGTGGTG 62.436 63.158 0.00 0.00 35.27 4.17
2332 2962 3.103213 AAGCCTGGTGGTGGTGGT 61.103 61.111 0.00 0.00 35.27 4.16
2333 2963 2.282462 GAAGCCTGGTGGTGGTGG 60.282 66.667 0.00 0.00 35.27 4.61
2334 2964 2.669569 CGAAGCCTGGTGGTGGTG 60.670 66.667 0.00 0.00 35.27 4.17
2335 2965 3.953775 CCGAAGCCTGGTGGTGGT 61.954 66.667 0.00 0.00 35.27 4.16
2404 3034 2.600731 CCTGGTGGTGGTGGTGTT 59.399 61.111 0.00 0.00 0.00 3.32
2479 3109 2.600731 CCTGGTGGTGGTGGTGTT 59.399 61.111 0.00 0.00 0.00 3.32
2881 3511 1.064621 CATCTCAAAATGCGGCGGG 59.935 57.895 9.78 0.00 0.00 6.13
3034 3668 1.277842 TCCCGTCACCGTGTAGTAGTA 59.722 52.381 0.00 0.00 0.00 1.82
3035 3669 0.036732 TCCCGTCACCGTGTAGTAGT 59.963 55.000 0.00 0.00 0.00 2.73
3036 3670 1.167851 TTCCCGTCACCGTGTAGTAG 58.832 55.000 0.00 0.00 0.00 2.57
3090 3724 2.378806 CAGAGCAAAAACAGTTCGCAG 58.621 47.619 5.40 0.00 0.00 5.18
3146 3780 2.291735 TGATCATGGTTCTGGGCACAAT 60.292 45.455 0.00 0.00 0.00 2.71
3218 3852 3.671008 TGCTAGTGCGGAAAGAAAGTA 57.329 42.857 0.00 0.00 43.34 2.24
3265 3899 2.931512 AAACTGGTTTGTTGTGGTCG 57.068 45.000 0.00 0.00 0.00 4.79
3293 3927 4.848562 TGGACGGAATAGCATACTACAG 57.151 45.455 0.00 0.00 0.00 2.74
3295 3929 4.982916 CACTTGGACGGAATAGCATACTAC 59.017 45.833 0.00 0.00 0.00 2.73
3296 3930 4.647853 ACACTTGGACGGAATAGCATACTA 59.352 41.667 0.00 0.00 0.00 1.82
3297 3931 3.451178 ACACTTGGACGGAATAGCATACT 59.549 43.478 0.00 0.00 0.00 2.12
3298 3932 3.555956 CACACTTGGACGGAATAGCATAC 59.444 47.826 0.00 0.00 0.00 2.39
3354 3988 3.581024 TCCAAAGCATTGTCAGCATTC 57.419 42.857 0.43 0.00 34.60 2.67
3474 4114 3.513680 AGTATGTGCGTTTGTATCGGA 57.486 42.857 0.00 0.00 0.00 4.55
3533 4173 4.080582 TCCCTTAATCAATCATGTGGTCGT 60.081 41.667 0.00 0.00 0.00 4.34
3542 4182 4.295141 ACGGTTGTCCCTTAATCAATCA 57.705 40.909 0.00 0.00 0.00 2.57
3653 4295 6.836242 ACATGAGGGAAGGAATATCTTCTTC 58.164 40.000 0.00 4.76 41.94 2.87
3661 4303 9.621239 AGATATAAAGACATGAGGGAAGGAATA 57.379 33.333 0.00 0.00 0.00 1.75
3662 4304 8.381636 CAGATATAAAGACATGAGGGAAGGAAT 58.618 37.037 0.00 0.00 0.00 3.01
3729 4379 7.834681 AGGTTACCTTTAAAATCCTCATCCTTC 59.165 37.037 0.00 0.00 0.00 3.46
3735 4385 5.935789 CGTGAGGTTACCTTTAAAATCCTCA 59.064 40.000 4.99 11.62 44.73 3.86
3772 4450 2.743636 TGTTCAGGAACGGATCAGTC 57.256 50.000 0.00 0.00 43.94 3.51
3830 4511 9.332502 TGAGTTCTAGCAAAACTGTTGTTTATA 57.667 29.630 0.32 0.00 44.70 0.98
3831 4512 8.220755 TGAGTTCTAGCAAAACTGTTGTTTAT 57.779 30.769 0.32 0.00 44.70 1.40
3832 4513 7.618502 TGAGTTCTAGCAAAACTGTTGTTTA 57.381 32.000 0.32 0.00 44.70 2.01
3833 4514 7.067494 AGATGAGTTCTAGCAAAACTGTTGTTT 59.933 33.333 0.32 0.00 39.38 2.83
3834 4515 6.543831 AGATGAGTTCTAGCAAAACTGTTGTT 59.456 34.615 0.32 0.00 37.10 2.83
3835 4516 6.058183 AGATGAGTTCTAGCAAAACTGTTGT 58.942 36.000 0.32 0.00 37.10 3.32
3836 4517 6.551385 AGATGAGTTCTAGCAAAACTGTTG 57.449 37.500 0.32 0.00 37.10 3.33
3837 4518 7.897575 CTAGATGAGTTCTAGCAAAACTGTT 57.102 36.000 0.32 0.00 45.63 3.16
3864 4545 9.566432 AAGGTGAATGAGACCAAATTATATCTC 57.434 33.333 0.00 6.03 38.46 2.75
3865 4546 9.927081 AAAGGTGAATGAGACCAAATTATATCT 57.073 29.630 0.00 0.00 35.76 1.98
3871 4552 9.533831 ACTATAAAAGGTGAATGAGACCAAATT 57.466 29.630 0.00 0.00 35.76 1.82
3872 4553 9.178758 GACTATAAAAGGTGAATGAGACCAAAT 57.821 33.333 0.00 0.00 35.76 2.32
3873 4554 8.160765 TGACTATAAAAGGTGAATGAGACCAAA 58.839 33.333 0.00 0.00 35.76 3.28
3874 4555 7.685481 TGACTATAAAAGGTGAATGAGACCAA 58.315 34.615 0.00 0.00 35.76 3.67
3875 4556 7.252612 TGACTATAAAAGGTGAATGAGACCA 57.747 36.000 0.00 0.00 35.76 4.02
3876 4557 8.616076 CAATGACTATAAAAGGTGAATGAGACC 58.384 37.037 0.00 0.00 0.00 3.85
3877 4558 8.616076 CCAATGACTATAAAAGGTGAATGAGAC 58.384 37.037 0.00 0.00 0.00 3.36
3878 4559 8.548025 TCCAATGACTATAAAAGGTGAATGAGA 58.452 33.333 0.00 0.00 0.00 3.27
3879 4560 8.737168 TCCAATGACTATAAAAGGTGAATGAG 57.263 34.615 0.00 0.00 0.00 2.90
3880 4561 9.123902 CATCCAATGACTATAAAAGGTGAATGA 57.876 33.333 0.00 0.00 0.00 2.57
3881 4562 8.906867 ACATCCAATGACTATAAAAGGTGAATG 58.093 33.333 0.00 0.00 0.00 2.67
3882 4563 8.906867 CACATCCAATGACTATAAAAGGTGAAT 58.093 33.333 0.00 0.00 0.00 2.57
3883 4564 8.106462 TCACATCCAATGACTATAAAAGGTGAA 58.894 33.333 0.00 0.00 0.00 3.18
3884 4565 7.629157 TCACATCCAATGACTATAAAAGGTGA 58.371 34.615 0.00 0.00 0.00 4.02
3885 4566 7.864108 TCACATCCAATGACTATAAAAGGTG 57.136 36.000 0.00 0.00 0.00 4.00
3886 4567 8.055181 ACATCACATCCAATGACTATAAAAGGT 58.945 33.333 0.00 0.00 0.00 3.50
3887 4568 8.455903 ACATCACATCCAATGACTATAAAAGG 57.544 34.615 0.00 0.00 0.00 3.11
3895 4576 9.281371 CATCTTATAACATCACATCCAATGACT 57.719 33.333 0.00 0.00 0.00 3.41
3896 4577 8.019669 GCATCTTATAACATCACATCCAATGAC 58.980 37.037 0.00 0.00 0.00 3.06
3897 4578 7.095102 CGCATCTTATAACATCACATCCAATGA 60.095 37.037 0.00 0.00 0.00 2.57
3898 4579 7.019418 CGCATCTTATAACATCACATCCAATG 58.981 38.462 0.00 0.00 0.00 2.82
3899 4580 6.712095 ACGCATCTTATAACATCACATCCAAT 59.288 34.615 0.00 0.00 0.00 3.16
3900 4581 6.018016 CACGCATCTTATAACATCACATCCAA 60.018 38.462 0.00 0.00 0.00 3.53
3901 4582 5.466393 CACGCATCTTATAACATCACATCCA 59.534 40.000 0.00 0.00 0.00 3.41
3902 4583 5.466728 ACACGCATCTTATAACATCACATCC 59.533 40.000 0.00 0.00 0.00 3.51
3903 4584 6.018751 ACACACGCATCTTATAACATCACATC 60.019 38.462 0.00 0.00 0.00 3.06
3904 4585 5.817296 ACACACGCATCTTATAACATCACAT 59.183 36.000 0.00 0.00 0.00 3.21
3905 4586 5.063312 CACACACGCATCTTATAACATCACA 59.937 40.000 0.00 0.00 0.00 3.58
3906 4587 5.492854 CACACACGCATCTTATAACATCAC 58.507 41.667 0.00 0.00 0.00 3.06
3907 4588 4.033932 GCACACACGCATCTTATAACATCA 59.966 41.667 0.00 0.00 0.00 3.07
3908 4589 4.271049 AGCACACACGCATCTTATAACATC 59.729 41.667 0.00 0.00 0.00 3.06
3909 4590 4.034394 CAGCACACACGCATCTTATAACAT 59.966 41.667 0.00 0.00 0.00 2.71
3910 4591 3.370672 CAGCACACACGCATCTTATAACA 59.629 43.478 0.00 0.00 0.00 2.41
3911 4592 3.616821 TCAGCACACACGCATCTTATAAC 59.383 43.478 0.00 0.00 0.00 1.89
3912 4593 3.616821 GTCAGCACACACGCATCTTATAA 59.383 43.478 0.00 0.00 0.00 0.98
3913 4594 3.186909 GTCAGCACACACGCATCTTATA 58.813 45.455 0.00 0.00 0.00 0.98
3914 4595 2.002586 GTCAGCACACACGCATCTTAT 58.997 47.619 0.00 0.00 0.00 1.73
3915 4596 1.428448 GTCAGCACACACGCATCTTA 58.572 50.000 0.00 0.00 0.00 2.10
3916 4597 1.560004 CGTCAGCACACACGCATCTT 61.560 55.000 0.00 0.00 0.00 2.40
3917 4598 2.023771 CGTCAGCACACACGCATCT 61.024 57.895 0.00 0.00 0.00 2.90
3918 4599 2.310233 ACGTCAGCACACACGCATC 61.310 57.895 0.00 0.00 39.73 3.91
3919 4600 2.280119 ACGTCAGCACACACGCAT 60.280 55.556 0.00 0.00 39.73 4.73
3920 4601 3.261216 CACGTCAGCACACACGCA 61.261 61.111 0.00 0.00 39.73 5.24
3921 4602 4.000557 CCACGTCAGCACACACGC 62.001 66.667 0.00 0.00 39.73 5.34
3922 4603 3.337889 CCCACGTCAGCACACACG 61.338 66.667 0.00 0.00 41.90 4.49
3923 4604 1.817941 AACCCACGTCAGCACACAC 60.818 57.895 0.00 0.00 0.00 3.82
3924 4605 1.817520 CAACCCACGTCAGCACACA 60.818 57.895 0.00 0.00 0.00 3.72
3925 4606 0.531090 TACAACCCACGTCAGCACAC 60.531 55.000 0.00 0.00 0.00 3.82
3926 4607 0.394938 ATACAACCCACGTCAGCACA 59.605 50.000 0.00 0.00 0.00 4.57
3927 4608 2.373540 TATACAACCCACGTCAGCAC 57.626 50.000 0.00 0.00 0.00 4.40
3928 4609 2.899976 CATATACAACCCACGTCAGCA 58.100 47.619 0.00 0.00 0.00 4.41
3929 4610 1.597663 GCATATACAACCCACGTCAGC 59.402 52.381 0.00 0.00 0.00 4.26
3930 4611 3.179443 AGCATATACAACCCACGTCAG 57.821 47.619 0.00 0.00 0.00 3.51
3931 4612 4.948341 ATAGCATATACAACCCACGTCA 57.052 40.909 0.00 0.00 0.00 4.35
3932 4613 5.054477 ACAATAGCATATACAACCCACGTC 58.946 41.667 0.00 0.00 0.00 4.34
3933 4614 5.031066 ACAATAGCATATACAACCCACGT 57.969 39.130 0.00 0.00 0.00 4.49


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

AutoCloner maintained by Alex Coulton.