Multiple sequence alignment - TraesCS5B01G334200

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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 TraesCS5B01G334200 chr5B 100.000 5425 0 0 1 5425 517693392 517698816 0.000000e+00 10019.0
1 TraesCS5B01G334200 chr5B 83.237 3621 534 49 997 4577 517774909 517778496 0.000000e+00 3256.0
2 TraesCS5B01G334200 chr5B 83.785 3466 504 40 1107 4550 517797829 517801258 0.000000e+00 3234.0
3 TraesCS5B01G334200 chr5B 95.623 1028 38 5 3559 4585 517706538 517707559 0.000000e+00 1642.0
4 TraesCS5B01G334200 chr5B 90.529 359 19 11 4974 5326 163263458 163263807 1.380000e-125 460.0
5 TraesCS5B01G334200 chr5B 87.432 366 29 5 4592 4941 517707606 517707970 6.540000e-109 405.0
6 TraesCS5B01G334200 chr5B 91.000 100 9 0 5326 5425 163263881 163263980 9.480000e-28 135.0
7 TraesCS5B01G334200 chr5B 88.462 52 1 4 4923 4971 163263245 163263294 2.110000e-04 58.4
8 TraesCS5B01G334200 chr5D 84.730 3975 510 40 646 4574 428565179 428569102 0.000000e+00 3888.0
9 TraesCS5B01G334200 chr5D 85.670 3573 456 35 1038 4585 428512257 428515798 0.000000e+00 3711.0
10 TraesCS5B01G334200 chr5D 84.050 3467 495 34 1107 4554 428670771 428674198 0.000000e+00 3286.0
11 TraesCS5B01G334200 chr5D 83.511 3566 518 46 997 4537 428593008 428596528 0.000000e+00 3264.0
12 TraesCS5B01G334200 chr5D 87.387 666 52 23 1 649 428564461 428565111 0.000000e+00 736.0
13 TraesCS5B01G334200 chr5D 87.278 338 12 5 4586 4910 428569150 428569469 1.860000e-94 357.0
14 TraesCS5B01G334200 chr5D 92.347 196 15 0 4739 4934 428517562 428517757 4.140000e-71 279.0
15 TraesCS5B01G334200 chr5D 85.549 173 13 10 4592 4753 428515845 428516016 2.600000e-38 171.0
16 TraesCS5B01G334200 chr5A 84.928 3324 448 36 1118 4418 544453043 544456336 0.000000e+00 3314.0
17 TraesCS5B01G334200 chr5A 82.519 3358 512 51 1118 4425 544502488 544505820 0.000000e+00 2880.0
18 TraesCS5B01G334200 chr5A 89.049 1799 183 8 2801 4587 544163678 544165474 0.000000e+00 2218.0
19 TraesCS5B01G334200 chr5A 85.104 2108 282 18 2376 4472 544246346 544248432 0.000000e+00 2124.0
20 TraesCS5B01G334200 chr5A 83.048 1870 281 20 948 2793 544158500 544160357 0.000000e+00 1664.0
21 TraesCS5B01G334200 chr5A 83.539 1622 242 16 1118 2719 544461753 544463369 0.000000e+00 1493.0
22 TraesCS5B01G334200 chr5A 80.579 1416 231 33 997 2381 544244129 544245531 0.000000e+00 1051.0
23 TraesCS5B01G334200 chr5A 90.244 328 28 3 4618 4942 544165552 544165878 5.020000e-115 425.0
24 TraesCS5B01G334200 chr2B 92.437 357 23 2 4973 5326 707591362 707591717 1.740000e-139 507.0
25 TraesCS5B01G334200 chr2B 97.000 100 3 0 5326 5425 707591792 707591891 9.350000e-38 169.0
26 TraesCS5B01G334200 chr4B 91.620 358 27 2 4972 5326 569760194 569759837 4.880000e-135 492.0
27 TraesCS5B01G334200 chr4B 91.092 348 29 2 4972 5318 100687607 100687953 2.290000e-128 470.0
28 TraesCS5B01G334200 chr4B 92.500 40 3 0 4932 4971 100687400 100687439 2.110000e-04 58.4
29 TraesCS5B01G334200 chr4B 94.737 38 1 1 4934 4971 534719076 534719040 2.110000e-04 58.4
30 TraesCS5B01G334200 chr4B 100.000 29 0 0 4943 4971 411177861 411177889 3.000000e-03 54.7
31 TraesCS5B01G334200 chr6D 89.972 359 21 8 4973 5326 159861458 159861110 2.980000e-122 449.0
32 TraesCS5B01G334200 chr3A 85.165 364 31 13 4972 5326 17000679 17000330 8.650000e-93 351.0
33 TraesCS5B01G334200 chr3A 90.000 100 10 0 5326 5425 17000258 17000159 4.410000e-26 130.0
34 TraesCS5B01G334200 chr3A 100.000 31 0 0 4941 4971 17000877 17000847 2.110000e-04 58.4
35 TraesCS5B01G334200 chr3A 100.000 31 0 0 4941 4971 17061453 17061423 2.110000e-04 58.4
36 TraesCS5B01G334200 chr7A 85.271 258 22 11 5072 5326 602994535 602994291 9.020000e-63 252.0
37 TraesCS5B01G334200 chr7A 100.000 31 0 0 4941 4971 602995217 602995187 2.110000e-04 58.4
38 TraesCS5B01G334200 chr2A 89.189 185 15 4 5146 5326 479824036 479823853 5.470000e-55 226.0
39 TraesCS5B01G334200 chr2A 94.737 38 1 1 4934 4971 479824370 479824334 2.110000e-04 58.4
40 TraesCS5B01G334200 chr2A 100.000 31 0 0 4941 4971 719359353 719359323 2.110000e-04 58.4
41 TraesCS5B01G334200 chr3B 84.252 127 16 4 133 258 414160569 414160446 2.650000e-23 121.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G334200 chr5B 517693392 517698816 5424 False 10019.000000 10019 100.000000 1 5425 1 chr5B.!!$F1 5424
1 TraesCS5B01G334200 chr5B 517774909 517778496 3587 False 3256.000000 3256 83.237000 997 4577 1 chr5B.!!$F2 3580
2 TraesCS5B01G334200 chr5B 517797829 517801258 3429 False 3234.000000 3234 83.785000 1107 4550 1 chr5B.!!$F3 3443
3 TraesCS5B01G334200 chr5B 517706538 517707970 1432 False 1023.500000 1642 91.527500 3559 4941 2 chr5B.!!$F5 1382
4 TraesCS5B01G334200 chr5B 163263245 163263980 735 False 217.800000 460 89.997000 4923 5425 3 chr5B.!!$F4 502
5 TraesCS5B01G334200 chr5D 428670771 428674198 3427 False 3286.000000 3286 84.050000 1107 4554 1 chr5D.!!$F2 3447
6 TraesCS5B01G334200 chr5D 428593008 428596528 3520 False 3264.000000 3264 83.511000 997 4537 1 chr5D.!!$F1 3540
7 TraesCS5B01G334200 chr5D 428564461 428569469 5008 False 1660.333333 3888 86.465000 1 4910 3 chr5D.!!$F4 4909
8 TraesCS5B01G334200 chr5D 428512257 428517757 5500 False 1387.000000 3711 87.855333 1038 4934 3 chr5D.!!$F3 3896
9 TraesCS5B01G334200 chr5A 544453043 544456336 3293 False 3314.000000 3314 84.928000 1118 4418 1 chr5A.!!$F1 3300
10 TraesCS5B01G334200 chr5A 544502488 544505820 3332 False 2880.000000 2880 82.519000 1118 4425 1 chr5A.!!$F3 3307
11 TraesCS5B01G334200 chr5A 544244129 544248432 4303 False 1587.500000 2124 82.841500 997 4472 2 chr5A.!!$F5 3475
12 TraesCS5B01G334200 chr5A 544461753 544463369 1616 False 1493.000000 1493 83.539000 1118 2719 1 chr5A.!!$F2 1601
13 TraesCS5B01G334200 chr5A 544158500 544165878 7378 False 1435.666667 2218 87.447000 948 4942 3 chr5A.!!$F4 3994
14 TraesCS5B01G334200 chr2B 707591362 707591891 529 False 338.000000 507 94.718500 4973 5425 2 chr2B.!!$F1 452
15 TraesCS5B01G334200 chr4B 100687400 100687953 553 False 264.200000 470 91.796000 4932 5318 2 chr4B.!!$F2 386

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
831 940 0.100325 CGCAAACACACCAAGCAGAA 59.900 50.0 0.0 0.0 0.00 3.02 F
1450 1620 0.178944 TTCCACCCTCGACTTCTCCA 60.179 55.0 0.0 0.0 0.00 3.86 F
2160 2333 0.321671 ACATGTCTTCACTCACCCGG 59.678 55.0 0.0 0.0 0.00 5.73 F
2495 3488 0.178935 CCCCTCCCAAAAGGCTTGAA 60.179 55.0 0.0 0.0 34.88 2.69 F
3421 7738 0.107897 TTGCCGCACGAAGGTATCAT 60.108 50.0 0.0 0.0 0.00 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1837 2010 0.034896 GTGAGGTTTCCAAGCGAGGA 59.965 55.000 0.00 0.0 35.41 3.71 R
2289 2462 0.109643 GCATTTCTGTCATGCGTGCA 60.110 50.000 0.00 0.0 37.88 4.57 R
3299 7613 1.336332 GCTCTCGTGTATGATCCGCAT 60.336 52.381 0.00 0.0 41.08 4.73 R
4307 8638 1.421268 TCTTTTGCCTCCTCAGCTTCA 59.579 47.619 0.00 0.0 0.00 3.02 R
5362 11592 0.618458 TATTGGTCGGCCTGCTTTCT 59.382 50.000 7.97 0.0 35.27 2.52 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
42 44 5.615544 GCACAACTGCATGAACACTTACTAG 60.616 44.000 0.00 0.00 43.62 2.57
43 45 4.452455 ACAACTGCATGAACACTTACTAGC 59.548 41.667 0.00 0.00 0.00 3.42
49 51 4.832248 CATGAACACTTACTAGCCAAGGA 58.168 43.478 8.97 0.00 0.00 3.36
50 52 4.967084 TGAACACTTACTAGCCAAGGAA 57.033 40.909 8.97 0.00 0.00 3.36
347 355 5.730550 AGGAAAAAGGAACCAAAACAGAAC 58.269 37.500 0.00 0.00 0.00 3.01
362 381 6.575162 AAACAGAACAAAACACTGAGAACT 57.425 33.333 0.00 0.00 35.85 3.01
374 393 2.945668 ACTGAGAACTGGACAAAACAGC 59.054 45.455 0.00 0.00 39.55 4.40
379 400 3.442273 AGAACTGGACAAAACAGCGAAAA 59.558 39.130 0.00 0.00 39.55 2.29
418 439 9.509855 AAACCACAAAAGAAAAACAAAGAAAAC 57.490 25.926 0.00 0.00 0.00 2.43
421 442 9.676195 CCACAAAAGAAAAACAAAGAAAACAAT 57.324 25.926 0.00 0.00 0.00 2.71
427 448 6.538381 AGAAAAACAAAGAAAACAATCCGCAT 59.462 30.769 0.00 0.00 0.00 4.73
435 456 4.984161 AGAAAACAATCCGCATGAAACAAG 59.016 37.500 0.00 0.00 0.00 3.16
448 469 5.330792 GCATGAAACAAGAACGAACGAAAAG 60.331 40.000 0.00 0.00 0.00 2.27
454 475 5.738370 ACAAGAACGAACGAAAAGAATCAG 58.262 37.500 0.14 0.00 0.00 2.90
467 488 4.713792 AAGAATCAGGTGGATCCATACC 57.286 45.455 19.62 15.63 39.02 2.73
471 492 3.264477 AGGTGGATCCATACCTGGG 57.736 57.895 20.49 0.00 45.30 4.45
562 583 9.976511 CCATTAGTTTTGGTCGAATATAGACTA 57.023 33.333 10.03 3.09 38.58 2.59
573 594 7.116519 GGTCGAATATAGACTAGAATTTGTGCC 59.883 40.741 0.00 7.31 38.58 5.01
574 595 7.652105 GTCGAATATAGACTAGAATTTGTGCCA 59.348 37.037 0.00 0.00 35.84 4.92
600 621 2.968675 AGACCTTAAATGTTCGTCCCG 58.031 47.619 0.00 0.00 0.00 5.14
626 651 3.963129 AGTTTAATTTCTGGATCCGCCA 58.037 40.909 7.39 0.00 46.96 5.69
640 665 3.791539 GCCACTGCGAGTCATGAG 58.208 61.111 0.00 0.00 0.00 2.90
644 669 0.987715 CACTGCGAGTCATGAGAACG 59.012 55.000 0.00 3.65 0.00 3.95
659 752 4.719369 ACGACCGGCGCAGAAGAC 62.719 66.667 10.83 0.00 46.04 3.01
687 780 0.680061 GTCTTGGTCGGAGTCAAGGT 59.320 55.000 16.20 0.00 39.09 3.50
695 788 6.340962 TGGTCGGAGTCAAGGTATATATTG 57.659 41.667 0.00 0.00 0.00 1.90
699 792 5.542635 TCGGAGTCAAGGTATATATTGGCTT 59.457 40.000 5.01 0.00 41.25 4.35
742 835 0.476338 TGGGTGAGGCTGCTTTACAA 59.524 50.000 8.82 0.00 0.00 2.41
746 839 2.222027 GTGAGGCTGCTTTACAAGTGT 58.778 47.619 0.00 0.00 0.00 3.55
764 857 3.707611 AGTGTTTTTAAACCCCTGAACCC 59.292 43.478 3.13 0.00 38.11 4.11
766 859 3.962063 TGTTTTTAAACCCCTGAACCCTC 59.038 43.478 3.13 0.00 38.11 4.30
767 860 3.962063 GTTTTTAAACCCCTGAACCCTCA 59.038 43.478 0.00 0.00 32.82 3.86
768 861 2.963599 TTAAACCCCTGAACCCTCAC 57.036 50.000 0.00 0.00 0.00 3.51
769 862 1.069775 TAAACCCCTGAACCCTCACC 58.930 55.000 0.00 0.00 0.00 4.02
770 863 0.701310 AAACCCCTGAACCCTCACCT 60.701 55.000 0.00 0.00 0.00 4.00
771 864 1.134438 AACCCCTGAACCCTCACCTC 61.134 60.000 0.00 0.00 0.00 3.85
772 865 2.660064 CCCCTGAACCCTCACCTCG 61.660 68.421 0.00 0.00 0.00 4.63
773 866 2.266055 CCTGAACCCTCACCTCGC 59.734 66.667 0.00 0.00 0.00 5.03
774 867 2.583441 CCTGAACCCTCACCTCGCA 61.583 63.158 0.00 0.00 0.00 5.10
778 877 2.820767 GAACCCTCACCTCGCACTCG 62.821 65.000 0.00 0.00 0.00 4.18
784 883 2.986413 ACCTCGCACTCGCACTCT 60.986 61.111 0.00 0.00 38.40 3.24
810 909 2.088674 GAGCTCACACACGGACACCT 62.089 60.000 9.40 0.00 0.00 4.00
829 938 1.299316 CCGCAAACACACCAAGCAG 60.299 57.895 0.00 0.00 0.00 4.24
830 939 1.723608 CCGCAAACACACCAAGCAGA 61.724 55.000 0.00 0.00 0.00 4.26
831 940 0.100325 CGCAAACACACCAAGCAGAA 59.900 50.000 0.00 0.00 0.00 3.02
832 941 1.843992 GCAAACACACCAAGCAGAAG 58.156 50.000 0.00 0.00 0.00 2.85
853 962 2.102553 GTACGTCTGCTCTCCGGC 59.897 66.667 0.00 0.00 0.00 6.13
870 989 4.383861 CCGGACAGCTGCTGCAGA 62.384 66.667 32.30 1.36 42.74 4.26
884 1003 2.047465 CAGAGGTGCGCTGCTCTT 60.047 61.111 9.73 0.00 0.00 2.85
885 1004 1.670406 CAGAGGTGCGCTGCTCTTT 60.670 57.895 9.73 0.00 0.00 2.52
886 1005 1.375268 AGAGGTGCGCTGCTCTTTC 60.375 57.895 9.73 0.00 0.00 2.62
887 1006 2.359230 AGGTGCGCTGCTCTTTCC 60.359 61.111 9.73 0.00 0.00 3.13
927 1048 4.354212 CGTCTTGCCGTGTGTGCG 62.354 66.667 0.00 0.00 0.00 5.34
944 1065 1.593933 TGCGTCCTTGTTTTACACGAC 59.406 47.619 0.00 0.00 0.00 4.34
965 1086 3.707611 ACCATTTTCCATATGCATGCAGT 59.292 39.130 26.69 14.39 0.00 4.40
966 1087 4.894705 ACCATTTTCCATATGCATGCAGTA 59.105 37.500 26.69 17.52 0.00 2.74
969 1090 6.932400 CCATTTTCCATATGCATGCAGTAATT 59.068 34.615 26.69 11.35 0.00 1.40
986 1107 6.763355 CAGTAATTGCTCCATAGTCCATACT 58.237 40.000 0.00 0.00 39.91 2.12
1052 1174 2.750637 TCGCCTGGTCCTCTCGTC 60.751 66.667 0.00 0.00 0.00 4.20
1085 1207 1.206849 GCTGCTGCTTCTCCTTAGTCT 59.793 52.381 8.53 0.00 36.03 3.24
1245 1388 1.003355 CAACTGGACCGGCATCACT 60.003 57.895 0.00 0.00 0.00 3.41
1278 1440 1.765597 GAGGGACCACGGTGAAGGTT 61.766 60.000 10.28 0.00 38.50 3.50
1341 1511 1.671379 GGACGCCCTGAGTTTCCAC 60.671 63.158 0.00 0.00 0.00 4.02
1366 1536 1.203087 TCCCTTACCTCGTCAACCTCA 60.203 52.381 0.00 0.00 0.00 3.86
1428 1598 1.070758 GGCATCGGCTCTCTTTCCATA 59.929 52.381 0.00 0.00 40.87 2.74
1441 1611 3.055385 TCTTTCCATACTTTCCACCCTCG 60.055 47.826 0.00 0.00 0.00 4.63
1450 1620 0.178944 TTCCACCCTCGACTTCTCCA 60.179 55.000 0.00 0.00 0.00 3.86
1515 1685 1.153289 GAGGCTCACGCACATGGAT 60.153 57.895 10.25 0.00 38.10 3.41
1516 1686 0.745845 GAGGCTCACGCACATGGATT 60.746 55.000 10.25 0.00 38.10 3.01
1592 1762 7.275920 TCAAGACTTGCTTTTCTTTCTCTACT 58.724 34.615 10.50 0.00 33.60 2.57
1602 1772 7.414651 GCTTTTCTTTCTCTACTTGGGAATAGC 60.415 40.741 0.00 0.00 32.65 2.97
1617 1787 3.326297 GGAATAGCCTCTCAGGTAGCATT 59.674 47.826 0.00 0.00 37.80 3.56
1657 1827 1.527844 GGGGACATGAGGCAGATGC 60.528 63.158 0.00 0.00 41.14 3.91
1675 1845 3.317455 TGCATTTGGGCTGGAATATCT 57.683 42.857 0.00 0.00 34.04 1.98
1696 1866 3.534357 TTTCTGGCCAAATACCTTCCA 57.466 42.857 7.01 0.00 0.00 3.53
1701 1871 1.685180 GGCCAAATACCTTCCACCCTC 60.685 57.143 0.00 0.00 0.00 4.30
1739 1909 2.362077 TCAACTTTCTTGGCCTTTCTGC 59.638 45.455 3.32 0.00 0.00 4.26
1756 1926 3.291584 TCTGCTAATCGTCTGTCAGGAT 58.708 45.455 0.00 0.00 0.00 3.24
1815 1988 7.406799 GCAAAAACTATACTTGCACAACAAT 57.593 32.000 1.34 0.00 43.89 2.71
1842 2015 3.173540 TGGCACAATTCCATCCTCG 57.826 52.632 0.00 0.00 31.92 4.63
1875 2048 2.111384 ACGATGCTCAGGTTCCTGTAT 58.889 47.619 17.00 10.84 35.70 2.29
2013 2186 8.515414 GTTGCTGGAAATCTTACTTCATTAGTT 58.485 33.333 0.00 0.00 38.33 2.24
2031 2204 8.241367 TCATTAGTTTATTTTTCTCTTTCGGGC 58.759 33.333 0.00 0.00 0.00 6.13
2055 2228 6.306199 CAACAATATAACTGGATCCATCCCA 58.694 40.000 16.63 1.17 46.59 4.37
2080 2253 7.654520 CACATGAGTTTGGAAATCTTGTGAATT 59.345 33.333 21.94 0.00 45.10 2.17
2098 2271 6.475076 TGTGAATTTGGAAACACTTGATTTCG 59.525 34.615 0.00 0.00 42.67 3.46
2118 2291 3.689161 TCGCAGTCAATTTCATAGTTGGG 59.311 43.478 0.00 0.00 0.00 4.12
2156 2329 3.126001 TGGGAACATGTCTTCACTCAC 57.874 47.619 0.00 0.00 33.40 3.51
2160 2333 0.321671 ACATGTCTTCACTCACCCGG 59.678 55.000 0.00 0.00 0.00 5.73
2163 2336 0.608130 TGTCTTCACTCACCCGGATG 59.392 55.000 0.73 0.00 0.00 3.51
2164 2337 0.608640 GTCTTCACTCACCCGGATGT 59.391 55.000 0.73 0.00 0.00 3.06
2169 2342 2.184533 TCACTCACCCGGATGTACATT 58.815 47.619 10.30 0.00 0.00 2.71
2170 2343 2.569853 TCACTCACCCGGATGTACATTT 59.430 45.455 10.30 0.00 0.00 2.32
2171 2344 2.936498 CACTCACCCGGATGTACATTTC 59.064 50.000 10.30 5.04 0.00 2.17
2190 2363 7.800092 ACATTTCTAGCAATAATCTCTCTGGT 58.200 34.615 0.00 0.00 0.00 4.00
2223 2396 3.494251 CCGAGTTTGGAAATTTGGCAAAG 59.506 43.478 18.61 0.00 0.00 2.77
2253 2426 4.034285 ACTTGATTCCTCCGAAAACCAT 57.966 40.909 0.00 0.00 0.00 3.55
2289 2462 8.052141 TCAATCCCTCAAAGTTTTGGAAAATTT 58.948 29.630 4.89 0.00 38.66 1.82
2292 2465 5.356470 CCCTCAAAGTTTTGGAAAATTTGCA 59.644 36.000 16.81 0.00 38.66 4.08
2293 2466 6.257423 CCTCAAAGTTTTGGAAAATTTGCAC 58.743 36.000 16.81 0.00 38.66 4.57
2319 2492 4.102649 TGACAGAAATGCGACTATACACG 58.897 43.478 0.00 0.00 0.00 4.49
2335 2508 0.247460 CACGAATCACCTCTCTGGCA 59.753 55.000 0.00 0.00 40.22 4.92
2367 2540 2.180276 TCTCTCTCCAACCTTACCAGC 58.820 52.381 0.00 0.00 0.00 4.85
2382 3375 1.457346 CCAGCTTGGTCCTCATTGAC 58.543 55.000 0.00 0.00 31.35 3.18
2390 3383 2.990066 GTCCTCATTGACCTAGGTGG 57.010 55.000 22.10 13.46 42.93 4.61
2416 3409 1.227823 CTGACGGGACACTTGCCAA 60.228 57.895 0.00 0.00 30.80 4.52
2421 3414 1.760029 ACGGGACACTTGCCAAATTTT 59.240 42.857 0.00 0.00 30.80 1.82
2436 3429 5.235401 GCCAAATTTTTGCCGAAGTAAAAGA 59.765 36.000 0.00 0.00 38.55 2.52
2440 3433 9.026074 CAAATTTTTGCCGAAGTAAAAGACTAA 57.974 29.630 0.00 0.00 38.55 2.24
2448 3441 8.626526 TGCCGAAGTAAAAGACTAAAGATTTTT 58.373 29.630 0.00 0.00 37.44 1.94
2449 3442 8.902735 GCCGAAGTAAAAGACTAAAGATTTTTG 58.097 33.333 0.00 0.00 37.44 2.44
2478 3471 3.138283 TGGATAACAATCTGGATGGTCCC 59.862 47.826 0.00 0.00 35.03 4.46
2479 3472 3.498661 GGATAACAATCTGGATGGTCCCC 60.499 52.174 0.00 0.00 35.03 4.81
2495 3488 0.178935 CCCCTCCCAAAAGGCTTGAA 60.179 55.000 0.00 0.00 34.88 2.69
2504 3497 3.062042 CAAAAGGCTTGAAGGATTGCAC 58.938 45.455 0.00 0.00 0.00 4.57
2524 3517 4.003648 CACTTCACTAACATCCCTTGGAC 58.996 47.826 0.00 0.00 32.98 4.02
2529 3522 4.536090 TCACTAACATCCCTTGGACTTGAT 59.464 41.667 0.00 0.00 32.98 2.57
2577 3570 4.230502 ACTGAATCATTTGGGGTGTATCCT 59.769 41.667 0.00 0.00 36.25 3.24
2649 3642 1.479323 CCAAATTGGGGCTCATGTCAG 59.521 52.381 3.60 0.00 32.67 3.51
2739 3732 1.767759 AAAATCTTGGATGGCTCGGG 58.232 50.000 0.00 0.00 0.00 5.14
2757 3750 2.678336 CGGGCTCAGTTTCAATAGGTTC 59.322 50.000 0.00 0.00 0.00 3.62
2774 3767 7.914427 ATAGGTTCAATAGTGAGATACCACA 57.086 36.000 13.42 3.26 35.43 4.17
2786 3779 4.701651 TGAGATACCACAAGAAATTGGCAG 59.298 41.667 0.00 0.00 36.20 4.85
2797 7103 6.549736 ACAAGAAATTGGCAGGTTAAGTAACT 59.450 34.615 1.48 0.00 36.47 2.24
2856 7162 2.961062 CCAGATCCCTAAGCAAATTGGG 59.039 50.000 0.00 0.00 39.23 4.12
2863 7169 3.588955 CCTAAGCAAATTGGGCAACTTC 58.411 45.455 5.30 0.00 32.09 3.01
2871 7177 0.881118 TTGGGCAACTTCGCAATCTC 59.119 50.000 0.00 0.00 34.58 2.75
2876 7182 1.726791 GCAACTTCGCAATCTCGAGAA 59.273 47.619 20.91 0.00 39.82 2.87
2877 7183 2.473049 GCAACTTCGCAATCTCGAGAAC 60.473 50.000 20.91 11.09 39.82 3.01
2909 7215 6.966021 TCTCAAGCAACTTTTTATGTGGTAC 58.034 36.000 0.00 0.00 0.00 3.34
2939 7245 5.886960 AAGGAGATCGGAAATTGTTTGAG 57.113 39.130 0.00 0.00 0.00 3.02
3058 7372 1.412710 TGAACAGTCTCAGTGGACCAC 59.587 52.381 17.43 17.43 36.95 4.16
3072 7386 0.321653 GACCACTGCCATCGGAACTT 60.322 55.000 0.00 0.00 0.00 2.66
3074 7388 1.349688 ACCACTGCCATCGGAACTTAA 59.650 47.619 0.00 0.00 0.00 1.85
3077 7391 2.416547 CACTGCCATCGGAACTTAACAG 59.583 50.000 0.00 0.00 0.00 3.16
3095 7409 8.247562 ACTTAACAGACTAGAGATGTTGATGTC 58.752 37.037 16.71 0.00 37.69 3.06
3098 7412 5.042593 CAGACTAGAGATGTTGATGTCTGC 58.957 45.833 0.00 0.00 41.80 4.26
3102 7416 6.413052 ACTAGAGATGTTGATGTCTGCAAAT 58.587 36.000 0.00 0.00 33.28 2.32
3138 7452 0.546507 TCAGTGGTGCCATCCCTGTA 60.547 55.000 7.06 0.00 32.02 2.74
3147 7461 1.432514 CCATCCCTGTATCGATTGCG 58.567 55.000 1.71 0.00 39.35 4.85
3198 7512 6.253758 TCTGTCATACAACTTCCTAGAAGGA 58.746 40.000 9.05 0.00 44.10 3.36
3204 7518 7.400339 TCATACAACTTCCTAGAAGGATCTGTT 59.600 37.037 9.05 1.03 45.34 3.16
3280 7594 0.251297 TGGAGACCTTGTTGGCATGG 60.251 55.000 0.00 0.00 43.34 3.66
3288 7602 1.818959 TTGTTGGCATGGCTCCTTGC 61.819 55.000 21.08 15.90 43.56 4.01
3299 7613 1.899142 GGCTCCTTGCAATTTACCCAA 59.101 47.619 0.00 0.00 45.15 4.12
3311 7625 5.460646 CAATTTACCCAATGCGGATCATAC 58.539 41.667 0.00 0.00 36.56 2.39
3316 7630 1.794701 CCAATGCGGATCATACACGAG 59.205 52.381 0.00 0.00 36.56 4.18
3414 7731 4.843147 TCATATTTATTTGCCGCACGAAG 58.157 39.130 0.00 0.00 0.00 3.79
3420 7737 0.320858 TTTGCCGCACGAAGGTATCA 60.321 50.000 0.00 0.00 0.00 2.15
3421 7738 0.107897 TTGCCGCACGAAGGTATCAT 60.108 50.000 0.00 0.00 0.00 2.45
3422 7739 0.529773 TGCCGCACGAAGGTATCATC 60.530 55.000 0.00 0.00 0.00 2.92
3466 7783 5.832539 AAGGGATGTATTCTCTGTATGGG 57.167 43.478 0.00 0.00 34.48 4.00
3485 7802 3.785887 TGGGGCTTTGATGGTAGAATAGT 59.214 43.478 0.00 0.00 0.00 2.12
3490 7807 7.175119 GGGGCTTTGATGGTAGAATAGTATTTC 59.825 40.741 0.00 0.00 0.00 2.17
3510 7827 9.846248 GTATTTCAGGATATTATCAATGCAACC 57.154 33.333 6.04 0.00 0.00 3.77
3534 7851 6.642131 CCGACAATTTTGATGAGAAACATTGT 59.358 34.615 0.00 1.49 39.56 2.71
3546 7863 4.860022 AGAAACATTGTATTGGAGAGGGG 58.140 43.478 0.00 0.00 0.00 4.79
3786 8104 6.917217 AATGTAGCTTCTATCTTGAGCAAC 57.083 37.500 0.00 0.00 0.00 4.17
4307 8638 2.758423 GGACAAACAACTTCCACAACCT 59.242 45.455 0.00 0.00 0.00 3.50
4402 8736 1.467920 AGGCCAACTATGCAGAAAGC 58.532 50.000 5.01 0.00 45.96 3.51
4425 8759 5.863397 GCTTATCGAGATCTTTCCATCTGAG 59.137 44.000 0.00 0.00 32.94 3.35
4426 8760 6.516527 GCTTATCGAGATCTTTCCATCTGAGT 60.517 42.308 0.00 0.00 32.94 3.41
4428 8762 5.003692 TCGAGATCTTTCCATCTGAGTTG 57.996 43.478 0.00 0.00 32.94 3.16
4429 8763 4.464244 TCGAGATCTTTCCATCTGAGTTGT 59.536 41.667 0.00 0.00 32.94 3.32
4432 8766 6.254589 CGAGATCTTTCCATCTGAGTTGTTAC 59.745 42.308 0.00 0.00 32.94 2.50
4433 8767 7.251321 AGATCTTTCCATCTGAGTTGTTACT 57.749 36.000 0.00 0.00 37.31 2.24
4472 8815 6.963805 GCTTGCAGATGTACATTTTAGTCTTC 59.036 38.462 10.30 0.00 0.00 2.87
4689 9105 1.947456 CCTTTATCTTTAGCACCGCCC 59.053 52.381 0.00 0.00 0.00 6.13
4732 9151 8.627208 ATTTAGTCGGAAATTCTATGATGCAT 57.373 30.769 0.00 0.00 0.00 3.96
4823 10805 4.294232 CTCAAGATAGGCAGACACGTATG 58.706 47.826 0.00 0.00 0.00 2.39
4971 10953 1.615392 GTTGATATTGAGGGCCATGGC 59.385 52.381 29.47 29.47 41.06 4.40
4995 11144 7.864379 GGCAGGATGAACATTGTATAGAAATTG 59.136 37.037 0.00 0.00 39.69 2.32
5024 11175 7.625682 AGAGATTAAGATTCTAGGGTTTCCTGT 59.374 37.037 0.00 0.00 44.61 4.00
5036 11187 2.153898 TTTCCTGTGATGGGGGCCTG 62.154 60.000 0.84 0.00 0.00 4.85
5154 11305 2.749682 TGCTTGTGCATCGGAGGT 59.250 55.556 0.00 0.00 45.31 3.85
5207 11359 2.252072 GAGGTGCCTGTGCGGGAATA 62.252 60.000 0.39 0.00 41.78 1.75
5346 11576 0.179070 GGAGCCTCTGATTTCGGGAC 60.179 60.000 0.00 0.00 0.00 4.46
5362 11592 1.348696 GGGACAGTAGAAACGGGGAAA 59.651 52.381 0.00 0.00 0.00 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 85 8.248253 TGATACGCATTAGTATATGGTACAAGG 58.752 37.037 0.00 0.00 38.66 3.61
310 318 9.383519 GTTCCTTTTTCCTTTTCTGAATTTTCT 57.616 29.630 0.00 0.00 0.00 2.52
314 322 7.194112 TGGTTCCTTTTTCCTTTTCTGAATT 57.806 32.000 0.00 0.00 0.00 2.17
315 323 6.806668 TGGTTCCTTTTTCCTTTTCTGAAT 57.193 33.333 0.00 0.00 0.00 2.57
316 324 6.613153 TTGGTTCCTTTTTCCTTTTCTGAA 57.387 33.333 0.00 0.00 0.00 3.02
317 325 6.613153 TTTGGTTCCTTTTTCCTTTTCTGA 57.387 33.333 0.00 0.00 0.00 3.27
318 326 6.652900 TGTTTTGGTTCCTTTTTCCTTTTCTG 59.347 34.615 0.00 0.00 0.00 3.02
319 327 6.774673 TGTTTTGGTTCCTTTTTCCTTTTCT 58.225 32.000 0.00 0.00 0.00 2.52
320 328 6.876789 TCTGTTTTGGTTCCTTTTTCCTTTTC 59.123 34.615 0.00 0.00 0.00 2.29
321 329 6.774673 TCTGTTTTGGTTCCTTTTTCCTTTT 58.225 32.000 0.00 0.00 0.00 2.27
322 330 6.367374 TCTGTTTTGGTTCCTTTTTCCTTT 57.633 33.333 0.00 0.00 0.00 3.11
323 331 6.170506 GTTCTGTTTTGGTTCCTTTTTCCTT 58.829 36.000 0.00 0.00 0.00 3.36
324 332 5.247337 TGTTCTGTTTTGGTTCCTTTTTCCT 59.753 36.000 0.00 0.00 0.00 3.36
325 333 5.483811 TGTTCTGTTTTGGTTCCTTTTTCC 58.516 37.500 0.00 0.00 0.00 3.13
326 334 7.428282 TTTGTTCTGTTTTGGTTCCTTTTTC 57.572 32.000 0.00 0.00 0.00 2.29
347 355 4.963276 TTGTCCAGTTCTCAGTGTTTTG 57.037 40.909 0.00 0.00 0.00 2.44
400 421 7.095017 TGCGGATTGTTTTCTTTGTTTTTCTTT 60.095 29.630 0.00 0.00 0.00 2.52
410 431 5.355596 TGTTTCATGCGGATTGTTTTCTTT 58.644 33.333 0.00 0.00 0.00 2.52
412 433 4.582701 TGTTTCATGCGGATTGTTTTCT 57.417 36.364 0.00 0.00 0.00 2.52
413 434 4.981674 TCTTGTTTCATGCGGATTGTTTTC 59.018 37.500 0.00 0.00 0.00 2.29
418 439 2.910482 CGTTCTTGTTTCATGCGGATTG 59.090 45.455 0.00 0.00 0.00 2.67
421 442 1.872388 TCGTTCTTGTTTCATGCGGA 58.128 45.000 0.00 0.00 0.00 5.54
427 448 5.533533 TCTTTTCGTTCGTTCTTGTTTCA 57.466 34.783 0.00 0.00 0.00 2.69
435 456 4.455124 CACCTGATTCTTTTCGTTCGTTC 58.545 43.478 0.00 0.00 0.00 3.95
467 488 1.975407 CTCCAGTTGGCAAGCCCAG 60.975 63.158 8.89 0.00 46.39 4.45
491 512 6.092670 CGAAAATAGTCATGGCTTCTCTGAAA 59.907 38.462 4.49 0.00 0.00 2.69
596 617 3.257127 CCAGAAATTAAACTTTGCCGGGA 59.743 43.478 2.18 0.00 0.00 5.14
600 621 5.102313 CGGATCCAGAAATTAAACTTTGCC 58.898 41.667 13.41 0.00 0.00 4.52
626 651 0.881796 TCGTTCTCATGACTCGCAGT 59.118 50.000 0.00 0.00 0.00 4.40
631 656 0.802607 GCCGGTCGTTCTCATGACTC 60.803 60.000 1.90 0.00 38.78 3.36
632 657 1.215647 GCCGGTCGTTCTCATGACT 59.784 57.895 1.90 0.00 38.78 3.41
633 658 2.158959 CGCCGGTCGTTCTCATGAC 61.159 63.158 1.90 0.00 38.12 3.06
635 660 3.554692 GCGCCGGTCGTTCTCATG 61.555 66.667 17.38 0.00 41.07 3.07
637 662 4.717629 CTGCGCCGGTCGTTCTCA 62.718 66.667 17.38 7.78 41.07 3.27
638 663 3.909258 TTCTGCGCCGGTCGTTCTC 62.909 63.158 17.38 4.05 41.07 2.87
640 665 3.479269 CTTCTGCGCCGGTCGTTC 61.479 66.667 17.38 4.95 41.07 3.95
651 744 2.743928 CACAGGCCGGTCTTCTGC 60.744 66.667 5.38 0.00 32.19 4.26
659 752 2.358737 GACCAAGACACAGGCCGG 60.359 66.667 0.00 0.00 0.00 6.13
660 753 2.738521 CGACCAAGACACAGGCCG 60.739 66.667 0.00 0.00 0.00 6.13
661 754 2.358737 CCGACCAAGACACAGGCC 60.359 66.667 0.00 0.00 0.00 5.19
662 755 1.374758 CTCCGACCAAGACACAGGC 60.375 63.158 0.00 0.00 0.00 4.85
687 780 6.419710 CGTTTCTCGTGTGAAGCCAATATATA 59.580 38.462 0.00 0.00 34.52 0.86
695 788 1.204312 GCGTTTCTCGTGTGAAGCC 59.796 57.895 0.00 0.00 42.13 4.35
729 822 8.321920 GGTTTAAAAACACTTGTAAAGCAGCCT 61.322 37.037 7.80 0.00 40.32 4.58
735 828 7.548967 TCAGGGGTTTAAAAACACTTGTAAAG 58.451 34.615 16.55 0.00 46.05 1.85
742 835 3.707611 GGGTTCAGGGGTTTAAAAACACT 59.292 43.478 7.70 0.00 41.95 3.55
746 839 3.962063 GTGAGGGTTCAGGGGTTTAAAAA 59.038 43.478 0.00 0.00 32.98 1.94
772 865 1.805134 GAGCTGAGAGTGCGAGTGC 60.805 63.158 0.00 0.00 43.20 4.40
773 866 1.513800 CGAGCTGAGAGTGCGAGTG 60.514 63.158 0.00 0.00 35.28 3.51
774 867 1.672682 TCGAGCTGAGAGTGCGAGT 60.673 57.895 0.00 0.00 35.28 4.18
810 909 1.723608 CTGCTTGGTGTGTTTGCGGA 61.724 55.000 0.00 0.00 32.29 5.54
829 938 2.159352 GGAGAGCAGACGTACCTTCTTC 60.159 54.545 0.00 0.00 0.00 2.87
830 939 1.819903 GGAGAGCAGACGTACCTTCTT 59.180 52.381 0.00 0.00 0.00 2.52
831 940 1.465794 GGAGAGCAGACGTACCTTCT 58.534 55.000 0.00 0.00 0.00 2.85
832 941 0.099082 CGGAGAGCAGACGTACCTTC 59.901 60.000 0.00 0.00 0.00 3.46
853 962 4.383861 TCTGCAGCAGCTGTCCGG 62.384 66.667 23.60 12.78 42.74 5.14
867 976 1.633852 GAAAGAGCAGCGCACCTCTG 61.634 60.000 24.47 9.61 38.38 3.35
870 989 2.359230 GGAAAGAGCAGCGCACCT 60.359 61.111 11.47 4.50 0.00 4.00
879 998 7.770897 TGTTGAAGGAGATAATAAGGAAAGAGC 59.229 37.037 0.00 0.00 0.00 4.09
884 1003 9.396022 GTGATTGTTGAAGGAGATAATAAGGAA 57.604 33.333 0.00 0.00 0.00 3.36
885 1004 7.710907 CGTGATTGTTGAAGGAGATAATAAGGA 59.289 37.037 0.00 0.00 0.00 3.36
886 1005 7.495934 ACGTGATTGTTGAAGGAGATAATAAGG 59.504 37.037 0.00 0.00 0.00 2.69
887 1006 8.425577 ACGTGATTGTTGAAGGAGATAATAAG 57.574 34.615 0.00 0.00 0.00 1.73
927 1048 4.823790 AATGGTCGTGTAAAACAAGGAC 57.176 40.909 4.70 4.70 34.79 3.85
944 1065 4.330944 ACTGCATGCATATGGAAAATGG 57.669 40.909 22.97 7.24 34.03 3.16
965 1086 7.728532 TCACTAGTATGGACTATGGAGCAATTA 59.271 37.037 0.00 0.00 37.53 1.40
966 1087 6.554982 TCACTAGTATGGACTATGGAGCAATT 59.445 38.462 0.00 0.00 37.53 2.32
969 1090 5.061721 TCACTAGTATGGACTATGGAGCA 57.938 43.478 0.00 0.00 37.53 4.26
971 1092 5.636123 ACCTCACTAGTATGGACTATGGAG 58.364 45.833 17.17 6.48 37.53 3.86
972 1093 5.632118 GACCTCACTAGTATGGACTATGGA 58.368 45.833 17.17 0.00 37.53 3.41
974 1095 5.306394 TCGACCTCACTAGTATGGACTATG 58.694 45.833 17.17 2.99 37.53 2.23
975 1096 5.563876 TCGACCTCACTAGTATGGACTAT 57.436 43.478 17.17 0.00 37.53 2.12
976 1097 5.071384 TGATCGACCTCACTAGTATGGACTA 59.929 44.000 17.17 6.45 37.10 2.59
977 1098 3.928005 TCGACCTCACTAGTATGGACT 57.072 47.619 17.17 0.00 39.92 3.85
978 1099 4.135306 TGATCGACCTCACTAGTATGGAC 58.865 47.826 17.17 11.38 0.00 4.02
980 1101 4.082517 CCATGATCGACCTCACTAGTATGG 60.083 50.000 10.70 10.70 0.00 2.74
981 1102 4.617067 GCCATGATCGACCTCACTAGTATG 60.617 50.000 0.00 0.00 0.00 2.39
982 1103 3.508012 GCCATGATCGACCTCACTAGTAT 59.492 47.826 0.00 0.00 0.00 2.12
983 1104 2.885266 GCCATGATCGACCTCACTAGTA 59.115 50.000 0.00 0.00 0.00 1.82
984 1105 1.683917 GCCATGATCGACCTCACTAGT 59.316 52.381 0.00 0.00 0.00 2.57
985 1106 1.335415 CGCCATGATCGACCTCACTAG 60.335 57.143 0.00 0.00 0.00 2.57
986 1107 0.668535 CGCCATGATCGACCTCACTA 59.331 55.000 0.00 0.00 0.00 2.74
1114 1251 4.168291 CCTCAGCGAAGGGCCTCC 62.168 72.222 6.46 0.00 45.17 4.30
1245 1388 2.342279 CCTCTTCGTGACCCGCAA 59.658 61.111 0.00 0.00 36.19 4.85
1257 1416 1.481056 CCTTCACCGTGGTCCCTCTT 61.481 60.000 0.00 0.00 0.00 2.85
1263 1425 2.232941 TCTGATAACCTTCACCGTGGTC 59.767 50.000 0.00 0.00 35.17 4.02
1278 1440 3.433598 CGCCAAGGGAAATTCCTCTGATA 60.434 47.826 12.28 0.00 36.57 2.15
1341 1511 1.835494 TGACGAGGTAAGGGAGTGAG 58.165 55.000 0.00 0.00 0.00 3.51
1366 1536 1.140252 ACGGTAGTTGTTGCTGAGGTT 59.860 47.619 0.00 0.00 0.00 3.50
1428 1598 1.619332 GAGAAGTCGAGGGTGGAAAGT 59.381 52.381 0.00 0.00 0.00 2.66
1441 1611 3.056250 TCAAGCTGATCACTGGAGAAGTC 60.056 47.826 0.00 0.00 36.83 3.01
1450 1620 0.035317 TTGCCGTCAAGCTGATCACT 59.965 50.000 0.00 0.00 0.00 3.41
1515 1685 3.563808 CGGTGAGATTGTTGTTGGAGAAA 59.436 43.478 0.00 0.00 0.00 2.52
1516 1686 3.138304 CGGTGAGATTGTTGTTGGAGAA 58.862 45.455 0.00 0.00 0.00 2.87
1592 1762 2.270434 ACCTGAGAGGCTATTCCCAA 57.730 50.000 0.00 0.00 39.63 4.12
1602 1772 2.224475 CCATGGAATGCTACCTGAGAGG 60.224 54.545 5.56 0.00 44.97 3.69
1617 1787 3.002583 TGTCCGAGCTGCCATGGA 61.003 61.111 18.40 0.00 0.00 3.41
1642 1812 2.223735 CCAAATGCATCTGCCTCATGTC 60.224 50.000 0.00 0.00 41.18 3.06
1657 1827 6.278363 CAGAAAAGATATTCCAGCCCAAATG 58.722 40.000 0.00 0.00 0.00 2.32
1675 1845 3.576550 GTGGAAGGTATTTGGCCAGAAAA 59.423 43.478 5.11 0.00 0.00 2.29
1696 1866 2.030562 CGTCAGGTTTGCGAGGGT 59.969 61.111 0.00 0.00 0.00 4.34
1701 1871 0.878523 TGAGGTTCGTCAGGTTTGCG 60.879 55.000 0.00 0.00 0.00 4.85
1739 1909 4.862902 ATGGATCCTGACAGACGATTAG 57.137 45.455 14.23 0.00 0.00 1.73
1756 1926 3.052869 TGTCCTAGCTCTTCAGGTATGGA 60.053 47.826 0.00 0.00 32.08 3.41
1836 2009 0.984230 TGAGGTTTCCAAGCGAGGAT 59.016 50.000 0.86 0.00 37.56 3.24
1837 2010 0.034896 GTGAGGTTTCCAAGCGAGGA 59.965 55.000 0.00 0.00 35.41 3.71
1842 2015 0.169009 GCATCGTGAGGTTTCCAAGC 59.831 55.000 0.00 0.00 0.00 4.01
1900 2073 1.107538 CCAAGCTCTACCGGGATCGA 61.108 60.000 6.32 0.00 39.00 3.59
2013 2186 5.776173 TGTTGCCCGAAAGAGAAAAATAA 57.224 34.783 0.00 0.00 0.00 1.40
2055 2228 6.713762 TTCACAAGATTTCCAAACTCATGT 57.286 33.333 0.00 0.00 0.00 3.21
2080 2253 3.380004 ACTGCGAAATCAAGTGTTTCCAA 59.620 39.130 0.00 0.00 33.15 3.53
2098 2271 4.437390 CGACCCAACTATGAAATTGACTGC 60.437 45.833 0.00 0.00 0.00 4.40
2118 2291 2.325082 AATGCTTGACGGCACCGAC 61.325 57.895 17.40 10.61 45.36 4.79
2133 2306 4.074259 TGAGTGAAGACATGTTCCCAATG 58.926 43.478 0.00 0.00 0.00 2.82
2156 2329 3.469008 TGCTAGAAATGTACATCCGGG 57.531 47.619 9.23 4.47 0.00 5.73
2163 2336 9.202273 CCAGAGAGATTATTGCTAGAAATGTAC 57.798 37.037 6.17 0.00 0.00 2.90
2164 2337 8.928448 ACCAGAGAGATTATTGCTAGAAATGTA 58.072 33.333 6.17 0.00 0.00 2.29
2169 2342 5.828328 TCGACCAGAGAGATTATTGCTAGAA 59.172 40.000 0.00 0.00 0.00 2.10
2170 2343 5.377478 TCGACCAGAGAGATTATTGCTAGA 58.623 41.667 0.00 0.00 0.00 2.43
2171 2344 5.697473 TCGACCAGAGAGATTATTGCTAG 57.303 43.478 0.00 0.00 0.00 3.42
2190 2363 3.599285 AAACTCGGCCGGCAATCGA 62.599 57.895 30.85 25.82 42.43 3.59
2223 2396 4.277423 TCGGAGGAATCAAGTTTTTCCAAC 59.723 41.667 14.08 8.87 43.21 3.77
2253 2426 1.704628 TGAGGGATTGAGCCAGACAAA 59.295 47.619 0.00 0.00 0.00 2.83
2289 2462 0.109643 GCATTTCTGTCATGCGTGCA 60.110 50.000 0.00 0.00 37.88 4.57
2315 2488 0.247736 GCCAGAGAGGTGATTCGTGT 59.752 55.000 0.00 0.00 40.61 4.49
2319 2492 2.746362 CAAAGTGCCAGAGAGGTGATTC 59.254 50.000 0.00 0.00 40.61 2.52
2335 2508 1.205893 GGAGAGAGATGACGGCAAAGT 59.794 52.381 0.00 0.00 0.00 2.66
2343 2516 3.769844 TGGTAAGGTTGGAGAGAGATGAC 59.230 47.826 0.00 0.00 0.00 3.06
2349 2522 2.327325 AGCTGGTAAGGTTGGAGAGA 57.673 50.000 0.00 0.00 0.00 3.10
2382 3375 1.377725 CAGCTGGTTGCCACCTAGG 60.378 63.158 7.41 7.41 44.61 3.02
2390 3383 3.050275 GTCCCGTCAGCTGGTTGC 61.050 66.667 15.13 1.23 43.29 4.17
2403 3396 2.290367 GCAAAAATTTGGCAAGTGTCCC 59.710 45.455 0.00 0.00 38.57 4.46
2416 3409 9.244799 CTTTAGTCTTTTACTTCGGCAAAAATT 57.755 29.630 0.00 0.00 39.80 1.82
2421 3414 7.739498 AATCTTTAGTCTTTTACTTCGGCAA 57.261 32.000 0.00 0.00 39.80 4.52
2451 3444 7.908862 GGACCATCCAGATTGTTATCCATAACA 60.909 40.741 7.88 7.88 42.27 2.41
2455 3448 4.202609 GGGACCATCCAGATTGTTATCCAT 60.203 45.833 0.00 0.00 38.64 3.41
2457 3450 3.756117 GGGACCATCCAGATTGTTATCC 58.244 50.000 0.00 0.00 38.64 2.59
2478 3471 1.203050 TCCTTCAAGCCTTTTGGGAGG 60.203 52.381 0.00 0.00 40.82 4.30
2479 3472 2.292828 TCCTTCAAGCCTTTTGGGAG 57.707 50.000 0.00 0.00 40.82 4.30
2495 3488 4.265073 GGATGTTAGTGAAGTGCAATCCT 58.735 43.478 0.00 0.00 0.00 3.24
2504 3497 4.559862 AGTCCAAGGGATGTTAGTGAAG 57.440 45.455 0.00 0.00 32.73 3.02
2524 3517 9.434420 GTCTCCCTCAATCTGATTATTATCAAG 57.566 37.037 1.98 0.00 40.17 3.02
2671 3664 5.994250 ACTGCCTTCTATCATGTTATGTGT 58.006 37.500 0.00 0.00 0.00 3.72
2676 3669 8.492415 AAGGTATACTGCCTTCTATCATGTTA 57.508 34.615 2.25 0.00 42.19 2.41
2738 3731 5.904362 ATTGAACCTATTGAAACTGAGCC 57.096 39.130 0.00 0.00 0.00 4.70
2739 3732 7.334421 TCACTATTGAACCTATTGAAACTGAGC 59.666 37.037 0.00 0.00 0.00 4.26
2757 3750 8.400947 CCAATTTCTTGTGGTATCTCACTATTG 58.599 37.037 0.00 0.00 38.40 1.90
2774 3767 7.069455 ACAAGTTACTTAACCTGCCAATTTCTT 59.931 33.333 0.00 0.00 36.88 2.52
2786 3779 8.747538 ATCCATCCAATACAAGTTACTTAACC 57.252 34.615 0.00 0.00 36.88 2.85
2856 7162 1.350193 TCTCGAGATTGCGAAGTTGC 58.650 50.000 12.08 0.00 40.13 4.17
2863 7169 1.996292 TCAAGGTTCTCGAGATTGCG 58.004 50.000 17.44 4.58 0.00 4.85
2876 7182 5.859205 AAAGTTGCTTGAGAAATCAAGGT 57.141 34.783 17.18 0.00 45.19 3.50
2877 7183 8.706035 CATAAAAAGTTGCTTGAGAAATCAAGG 58.294 33.333 17.18 2.71 45.19 3.61
2909 7215 6.095440 ACAATTTCCGATCTCCTTTGGTATTG 59.905 38.462 0.00 0.00 33.84 1.90
2917 7223 5.412904 GTCTCAAACAATTTCCGATCTCCTT 59.587 40.000 0.00 0.00 0.00 3.36
2919 7225 4.938226 AGTCTCAAACAATTTCCGATCTCC 59.062 41.667 0.00 0.00 0.00 3.71
2999 7313 6.412362 TGCTTTGCAGGGAAGTTAAATTAA 57.588 33.333 0.00 0.00 33.32 1.40
3058 7372 2.673368 GTCTGTTAAGTTCCGATGGCAG 59.327 50.000 0.00 0.00 0.00 4.85
3060 7374 2.973945 AGTCTGTTAAGTTCCGATGGC 58.026 47.619 0.00 0.00 0.00 4.40
3072 7386 7.766283 CAGACATCAACATCTCTAGTCTGTTA 58.234 38.462 10.56 0.21 43.77 2.41
3074 7388 6.206395 CAGACATCAACATCTCTAGTCTGT 57.794 41.667 10.56 0.00 43.77 3.41
3077 7391 5.003692 TGCAGACATCAACATCTCTAGTC 57.996 43.478 0.00 0.00 0.00 2.59
3095 7409 7.170151 TGAATTGATTGTGTGAGAAATTTGCAG 59.830 33.333 0.00 0.00 0.00 4.41
3098 7412 8.484799 CACTGAATTGATTGTGTGAGAAATTTG 58.515 33.333 0.00 0.00 0.00 2.32
3102 7416 5.593909 ACCACTGAATTGATTGTGTGAGAAA 59.406 36.000 0.00 0.00 0.00 2.52
3138 7452 2.396700 TTGCATGCTCGCAATCGAT 58.603 47.368 20.33 0.00 46.61 3.59
3147 7461 5.640189 ATATTGATAGGCTTTGCATGCTC 57.360 39.130 20.33 5.79 0.00 4.26
3175 7489 6.531503 TCCTTCTAGGAAGTTGTATGACAG 57.468 41.667 6.55 0.00 42.51 3.51
3280 7594 3.524541 CATTGGGTAAATTGCAAGGAGC 58.475 45.455 4.94 1.96 45.96 4.70
3288 7602 4.589216 ATGATCCGCATTGGGTAAATTG 57.411 40.909 0.00 0.00 38.76 2.32
3299 7613 1.336332 GCTCTCGTGTATGATCCGCAT 60.336 52.381 0.00 0.00 41.08 4.73
3311 7625 4.675190 ACAATCTTTTGATGCTCTCGTG 57.325 40.909 0.00 0.00 39.48 4.35
3316 7630 8.430801 ACTGATAGTACAATCTTTTGATGCTC 57.569 34.615 0.00 0.00 39.48 4.26
3349 7663 4.037089 TGAAATAGTAGCGGCGAACATAGA 59.963 41.667 12.98 0.00 0.00 1.98
3385 7702 8.698854 CGTGCGGCAAATAAATATGAAAATTAT 58.301 29.630 3.23 0.00 0.00 1.28
3391 7708 4.884458 TCGTGCGGCAAATAAATATGAA 57.116 36.364 3.23 0.00 0.00 2.57
3392 7709 4.260990 CCTTCGTGCGGCAAATAAATATGA 60.261 41.667 3.23 0.00 0.00 2.15
3394 7711 3.630312 ACCTTCGTGCGGCAAATAAATAT 59.370 39.130 3.23 0.00 0.00 1.28
3396 7713 1.816224 ACCTTCGTGCGGCAAATAAAT 59.184 42.857 3.23 0.00 0.00 1.40
3421 7738 5.771153 TTGCTCACATCATCAGTTTTTGA 57.229 34.783 0.00 0.00 40.85 2.69
3422 7739 6.073980 CCTTTTGCTCACATCATCAGTTTTTG 60.074 38.462 0.00 0.00 0.00 2.44
3466 7783 8.677148 TGAAATACTATTCTACCATCAAAGCC 57.323 34.615 0.00 0.00 0.00 4.35
3485 7802 8.729756 CGGTTGCATTGATAATATCCTGAAATA 58.270 33.333 0.00 0.00 0.00 1.40
3490 7807 5.469760 TGTCGGTTGCATTGATAATATCCTG 59.530 40.000 0.00 0.00 0.00 3.86
3510 7827 7.627585 ACAATGTTTCTCATCAAAATTGTCG 57.372 32.000 0.00 0.00 35.48 4.35
3534 7851 1.683943 CGTACGACCCCTCTCCAATA 58.316 55.000 10.44 0.00 0.00 1.90
3546 7863 4.735338 GCCTTATAAACACTACCGTACGAC 59.265 45.833 18.76 0.00 0.00 4.34
4179 8507 2.035832 GCACCACAACACCAAAGCTATT 59.964 45.455 0.00 0.00 0.00 1.73
4278 8609 6.148480 TGTGGAAGTTGTTTGTCCAAAATTTG 59.852 34.615 0.00 0.00 42.97 2.32
4307 8638 1.421268 TCTTTTGCCTCCTCAGCTTCA 59.579 47.619 0.00 0.00 0.00 3.02
4402 8736 6.980593 ACTCAGATGGAAAGATCTCGATAAG 58.019 40.000 0.00 0.00 29.72 1.73
4425 8759 8.953990 CAAGCATTTAACAAGTACAGTAACAAC 58.046 33.333 0.00 0.00 0.00 3.32
4426 8760 7.646130 GCAAGCATTTAACAAGTACAGTAACAA 59.354 33.333 0.00 0.00 0.00 2.83
4428 8762 7.136119 TGCAAGCATTTAACAAGTACAGTAAC 58.864 34.615 0.00 0.00 0.00 2.50
4429 8763 7.227711 TCTGCAAGCATTTAACAAGTACAGTAA 59.772 33.333 0.00 0.00 0.00 2.24
4432 8766 6.000891 TCTGCAAGCATTTAACAAGTACAG 57.999 37.500 0.00 0.00 0.00 2.74
4433 8767 6.016360 ACATCTGCAAGCATTTAACAAGTACA 60.016 34.615 0.00 0.00 0.00 2.90
4472 8815 3.625764 TCCAAGTTTGTTCTGAACCGAAG 59.374 43.478 17.26 3.55 0.00 3.79
4605 9001 2.093447 ACAACTATCAAGCCTCCTTCCG 60.093 50.000 0.00 0.00 0.00 4.30
4689 9105 7.589954 CGACTAAATTTTAAAGAACCCACAGTG 59.410 37.037 0.00 0.00 0.00 3.66
4710 9129 7.041167 CCAAATGCATCATAGAATTTCCGACTA 60.041 37.037 0.00 0.00 0.00 2.59
4725 9144 8.747471 TGATTTTCTTACATACCAAATGCATCA 58.253 29.630 0.00 0.00 0.00 3.07
4732 9151 6.348950 CCGTGCTGATTTTCTTACATACCAAA 60.349 38.462 0.00 0.00 0.00 3.28
4823 10805 1.747355 CCACTCATTTGCAGTCCATCC 59.253 52.381 0.00 0.00 0.00 3.51
4971 10953 9.123902 TCCAATTTCTATACAATGTTCATCCTG 57.876 33.333 0.00 0.00 0.00 3.86
4995 11144 7.934665 GGAAACCCTAGAATCTTAATCTCTTCC 59.065 40.741 0.00 0.00 0.00 3.46
5000 11149 7.403231 TCACAGGAAACCCTAGAATCTTAATCT 59.597 37.037 0.00 0.00 31.47 2.40
5036 11187 1.774217 TCCATGGGCACTATCCCCC 60.774 63.158 13.02 0.00 45.97 5.40
5207 11359 1.003233 GTGCCTCTCCGCCTTTCTT 60.003 57.895 0.00 0.00 0.00 2.52
5267 11419 1.375396 CGCACATCGAACTCCCCAA 60.375 57.895 0.00 0.00 41.67 4.12
5346 11576 3.188667 GCTTTCTTTCCCCGTTTCTACTG 59.811 47.826 0.00 0.00 0.00 2.74
5362 11592 0.618458 TATTGGTCGGCCTGCTTTCT 59.382 50.000 7.97 0.00 35.27 2.52
5396 11626 0.749454 GGCCATGGAATTGACGCTCT 60.749 55.000 18.40 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.