Multiple sequence alignment - TraesCS2D01G005500

Loading Multiple Alignment...

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 TraesCS2D01G005500 chr2D 100.000 6354 0 0 1 6354 2889470 2895823 0.000000e+00 11734.0
1 TraesCS2D01G005500 chr2D 89.320 309 33 0 3599 3907 598718528 598718836 7.730000e-104 388.0
2 TraesCS2D01G005500 chr2B 92.932 3834 202 35 98 3907 8239233 8235445 0.000000e+00 5515.0
3 TraesCS2D01G005500 chr2B 92.510 3832 210 33 98 3907 8083756 8079980 0.000000e+00 5415.0
4 TraesCS2D01G005500 chr2B 92.410 3834 218 37 98 3907 7913990 7910206 0.000000e+00 5400.0
5 TraesCS2D01G005500 chr2B 92.598 2837 152 29 98 2923 7804643 7801854 0.000000e+00 4023.0
6 TraesCS2D01G005500 chr2B 93.732 2473 123 20 3905 6354 8235395 8232932 0.000000e+00 3679.0
7 TraesCS2D01G005500 chr2B 93.530 2473 128 20 3905 6354 8079930 8077467 0.000000e+00 3651.0
8 TraesCS2D01G005500 chr2B 92.473 1953 106 17 3905 5825 7800736 7798793 0.000000e+00 2754.0
9 TraesCS2D01G005500 chr2B 93.754 1633 76 10 4740 6354 7909357 7907733 0.000000e+00 2427.0
10 TraesCS2D01G005500 chr2B 95.251 1074 46 4 2836 3907 7801856 7800786 0.000000e+00 1696.0
11 TraesCS2D01G005500 chr2B 93.835 811 42 7 3905 4710 7910156 7909349 0.000000e+00 1214.0
12 TraesCS2D01G005500 chr2B 92.793 222 12 2 5901 6118 7798798 7798577 1.030000e-82 318.0
13 TraesCS2D01G005500 chr2B 87.571 177 17 4 326 502 41181016 41180845 3.880000e-47 200.0
14 TraesCS2D01G005500 chr5D 83.240 716 103 11 5644 6354 28949819 28950522 5.370000e-180 641.0
15 TraesCS2D01G005500 chr5D 85.574 305 35 8 5644 5943 48727341 48727641 1.720000e-80 311.0
16 TraesCS2D01G005500 chr6A 84.253 616 83 9 5740 6354 546622846 546623448 7.100000e-164 588.0
17 TraesCS2D01G005500 chr6A 87.151 179 20 1 319 497 143068141 143067966 3.880000e-47 200.0
18 TraesCS2D01G005500 chr5A 80.992 726 112 14 5644 6354 19682430 19683144 2.590000e-153 553.0
19 TraesCS2D01G005500 chr6B 81.168 685 99 15 5671 6354 32003792 32004447 2.030000e-144 523.0
20 TraesCS2D01G005500 chr2A 89.032 310 34 0 3598 3907 633949188 633948879 9.990000e-103 385.0
21 TraesCS2D01G005500 chr2A 84.639 332 45 3 6023 6354 3792037 3791712 6.140000e-85 326.0
22 TraesCS2D01G005500 chr2A 89.286 168 14 3 326 493 628342207 628342370 2.320000e-49 207.0
23 TraesCS2D01G005500 chr2A 88.439 173 15 4 321 493 26381743 26381576 3.000000e-48 204.0
24 TraesCS2D01G005500 chr3A 88.997 309 34 0 3599 3907 701221320 701221012 3.590000e-102 383.0
25 TraesCS2D01G005500 chr3A 79.949 389 73 3 1997 2381 52727928 52728315 1.350000e-71 281.0
26 TraesCS2D01G005500 chr3A 79.949 389 73 3 1997 2381 52774228 52774615 1.350000e-71 281.0
27 TraesCS2D01G005500 chr3A 79.692 389 74 3 1997 2381 52682073 52682460 6.270000e-70 276.0
28 TraesCS2D01G005500 chr3A 79.434 389 75 3 1997 2381 52589739 52590126 2.920000e-68 270.0
29 TraesCS2D01G005500 chr3A 79.434 389 75 3 1997 2381 52822120 52822507 2.920000e-68 270.0
30 TraesCS2D01G005500 chr3A 78.671 286 59 2 5033 5317 52685707 52685991 8.410000e-44 189.0
31 TraesCS2D01G005500 chr3A 78.596 285 61 0 5033 5317 52826010 52826294 8.410000e-44 189.0
32 TraesCS2D01G005500 chr3A 78.246 285 62 0 5033 5317 52593553 52593837 3.910000e-42 183.0
33 TraesCS2D01G005500 chr3A 78.246 285 62 0 5033 5317 52640087 52640371 3.910000e-42 183.0
34 TraesCS2D01G005500 chr3A 78.246 285 62 0 5033 5317 52778142 52778426 3.910000e-42 183.0
35 TraesCS2D01G005500 chr3A 84.375 160 25 0 2 161 59925885 59926044 2.370000e-34 158.0
36 TraesCS2D01G005500 chr3A 75.874 286 55 8 1252 1530 52589259 52589537 4.000000e-27 134.0
37 TraesCS2D01G005500 chr3A 75.874 286 55 8 1252 1530 52635602 52635880 4.000000e-27 134.0
38 TraesCS2D01G005500 chr3A 75.874 286 55 8 1252 1530 52681593 52681871 4.000000e-27 134.0
39 TraesCS2D01G005500 chr3A 75.874 286 55 7 1252 1530 52821640 52821918 4.000000e-27 134.0
40 TraesCS2D01G005500 chr3A 75.524 286 56 8 1252 1530 52727448 52727726 1.860000e-25 128.0
41 TraesCS2D01G005500 chr3B 88.050 318 34 3 3599 3915 663132081 663132395 2.160000e-99 374.0
42 TraesCS2D01G005500 chr1A 88.050 318 32 4 3592 3907 313906873 313906560 7.780000e-99 372.0
43 TraesCS2D01G005500 chr1A 81.319 91 16 1 5930 6020 578215836 578215925 8.840000e-09 73.1
44 TraesCS2D01G005500 chr7B 84.366 339 52 1 6017 6354 187595914 187596252 1.320000e-86 331.0
45 TraesCS2D01G005500 chr5B 83.784 296 42 5 5644 5937 51218483 51218774 6.270000e-70 276.0
46 TraesCS2D01G005500 chr4A 89.017 173 14 3 322 493 625818893 625819061 6.460000e-50 209.0
47 TraesCS2D01G005500 chr7A 100.000 32 0 0 5574 5605 135710253 135710222 6.880000e-05 60.2


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 TraesCS2D01G005500 chr2D 2889470 2895823 6353 False 11734.000000 11734 100.00000 1 6354 1 chr2D.!!$F1 6353
1 TraesCS2D01G005500 chr2B 8232932 8239233 6301 True 4597.000000 5515 93.33200 98 6354 2 chr2B.!!$R5 6256
2 TraesCS2D01G005500 chr2B 8077467 8083756 6289 True 4533.000000 5415 93.02000 98 6354 2 chr2B.!!$R4 6256
3 TraesCS2D01G005500 chr2B 7907733 7913990 6257 True 3013.666667 5400 93.33300 98 6354 3 chr2B.!!$R3 6256
4 TraesCS2D01G005500 chr2B 7798577 7804643 6066 True 2197.750000 4023 93.27875 98 6118 4 chr2B.!!$R2 6020
5 TraesCS2D01G005500 chr5D 28949819 28950522 703 False 641.000000 641 83.24000 5644 6354 1 chr5D.!!$F1 710
6 TraesCS2D01G005500 chr6A 546622846 546623448 602 False 588.000000 588 84.25300 5740 6354 1 chr6A.!!$F1 614
7 TraesCS2D01G005500 chr5A 19682430 19683144 714 False 553.000000 553 80.99200 5644 6354 1 chr5A.!!$F1 710
8 TraesCS2D01G005500 chr6B 32003792 32004447 655 False 523.000000 523 81.16800 5671 6354 1 chr6B.!!$F1 683
9 TraesCS2D01G005500 chr3A 52774228 52778426 4198 False 232.000000 281 79.09750 1997 5317 2 chr3A.!!$F7 3320
10 TraesCS2D01G005500 chr3A 52727448 52728315 867 False 204.500000 281 77.73650 1252 2381 2 chr3A.!!$F6 1129

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
778 779 0.036010 ACTTGGGAGGCAGACGATTG 60.036 55.000 0.00 0.00 0.00 2.67 F
899 900 0.106918 TTTTTCACAGACCCACGCCT 60.107 50.000 0.00 0.00 0.00 5.52 F
900 901 0.106918 TTTTCACAGACCCACGCCTT 60.107 50.000 0.00 0.00 0.00 4.35 F
1029 1034 0.249676 CCTCTCATGCTGCTGACACT 59.750 55.000 0.00 0.00 0.00 3.55 F
2249 2316 0.320697 GCGTGTAAGAGGGTGGAAGT 59.679 55.000 0.00 0.00 0.00 3.01 F
2986 3864 1.509463 ACGTATGACATCCGTGCGT 59.491 52.632 5.15 0.00 45.84 5.24 F
3714 5996 0.177604 TTGTGGCCCTTTTGCAACAG 59.822 50.000 5.59 5.59 45.50 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2622 3415 0.106519 ATGTGTGCTAATCCCAGCCC 60.107 55.000 0.0 0.0 41.04 5.19 R
2661 3454 4.828704 GCATTTGCATGATACAACATTGC 58.171 39.130 0.0 0.0 41.59 3.56 R
2686 3479 8.964476 AGACATATGGAGAAAATTATGTTCGT 57.036 30.769 7.8 0.0 0.00 3.85 R
2976 3854 0.319040 CCTCTATGGACGCACGGATG 60.319 60.000 0.0 0.0 38.35 3.51 R
3636 5913 0.740868 AATGACGGATGGCAGACACG 60.741 55.000 0.0 0.0 0.00 4.49 R
4341 6680 0.666913 CCATGCAGCCATCAGTAAGC 59.333 55.000 0.0 0.0 0.00 3.09 R
5572 7981 0.029834 GCAATGCATGGGCGTTCTAG 59.970 55.000 0.0 0.0 46.01 2.43 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
20 21 2.841442 AACAAGAGTAGGAGCACCAC 57.159 50.000 2.07 0.00 38.94 4.16
21 22 0.977395 ACAAGAGTAGGAGCACCACC 59.023 55.000 2.07 0.00 38.94 4.61
22 23 0.976641 CAAGAGTAGGAGCACCACCA 59.023 55.000 2.07 0.00 38.94 4.17
23 24 0.977395 AAGAGTAGGAGCACCACCAC 59.023 55.000 2.07 0.00 38.94 4.16
24 25 1.215647 GAGTAGGAGCACCACCACG 59.784 63.158 2.07 0.00 38.94 4.94
25 26 1.228769 AGTAGGAGCACCACCACGA 60.229 57.895 2.07 0.00 38.94 4.35
26 27 0.614979 AGTAGGAGCACCACCACGAT 60.615 55.000 2.07 0.00 38.94 3.73
27 28 0.179108 GTAGGAGCACCACCACGATC 60.179 60.000 2.07 0.00 38.94 3.69
28 29 0.324368 TAGGAGCACCACCACGATCT 60.324 55.000 2.07 0.00 38.94 2.75
29 30 1.448540 GGAGCACCACCACGATCTG 60.449 63.158 0.00 0.00 35.97 2.90
30 31 1.591703 GAGCACCACCACGATCTGA 59.408 57.895 0.00 0.00 0.00 3.27
31 32 0.037326 GAGCACCACCACGATCTGAA 60.037 55.000 0.00 0.00 0.00 3.02
32 33 0.396435 AGCACCACCACGATCTGAAA 59.604 50.000 0.00 0.00 0.00 2.69
33 34 0.517316 GCACCACCACGATCTGAAAC 59.483 55.000 0.00 0.00 0.00 2.78
34 35 1.156736 CACCACCACGATCTGAAACC 58.843 55.000 0.00 0.00 0.00 3.27
35 36 0.320421 ACCACCACGATCTGAAACCG 60.320 55.000 0.00 0.00 0.00 4.44
36 37 0.037697 CCACCACGATCTGAAACCGA 60.038 55.000 0.00 0.00 0.00 4.69
37 38 1.606994 CCACCACGATCTGAAACCGAA 60.607 52.381 0.00 0.00 0.00 4.30
38 39 1.459592 CACCACGATCTGAAACCGAAC 59.540 52.381 0.00 0.00 0.00 3.95
39 40 1.076332 CCACGATCTGAAACCGAACC 58.924 55.000 0.00 0.00 0.00 3.62
40 41 0.713883 CACGATCTGAAACCGAACCG 59.286 55.000 0.00 0.00 0.00 4.44
58 59 2.853731 CGGAGGTAGAGCTGTTGTAG 57.146 55.000 0.00 0.00 0.00 2.74
68 69 2.785868 CTGTTGTAGCATGGAGGCC 58.214 57.895 0.00 0.00 0.00 5.19
69 70 1.078497 TGTTGTAGCATGGAGGCCG 60.078 57.895 0.00 0.00 0.00 6.13
70 71 2.124736 TTGTAGCATGGAGGCCGC 60.125 61.111 0.00 0.00 0.00 6.53
71 72 3.697439 TTGTAGCATGGAGGCCGCC 62.697 63.158 20.28 20.28 0.00 6.13
72 73 4.175337 GTAGCATGGAGGCCGCCA 62.175 66.667 31.62 31.62 43.23 5.69
73 74 4.175337 TAGCATGGAGGCCGCCAC 62.175 66.667 32.15 19.21 41.56 5.01
75 76 4.175337 GCATGGAGGCCGCCACTA 62.175 66.667 32.15 8.72 41.56 2.74
76 77 2.203070 CATGGAGGCCGCCACTAC 60.203 66.667 32.15 0.75 41.56 2.73
77 78 3.480133 ATGGAGGCCGCCACTACC 61.480 66.667 32.15 10.50 41.56 3.18
78 79 4.715130 TGGAGGCCGCCACTACCT 62.715 66.667 26.11 0.00 36.19 3.08
79 80 4.162690 GGAGGCCGCCACTACCTG 62.163 72.222 22.24 0.00 32.67 4.00
80 81 4.840005 GAGGCCGCCACTACCTGC 62.840 72.222 13.15 0.00 32.67 4.85
125 126 3.310860 ATCCCAGCGGTCGTTGTCC 62.311 63.158 6.48 0.00 0.00 4.02
133 134 2.388232 GGTCGTTGTCCGCCATCAC 61.388 63.158 0.00 0.00 36.19 3.06
161 162 1.227973 GACCAAGATGGGATCCGCC 60.228 63.158 5.45 0.00 43.37 6.13
182 183 2.288091 CGCATCGATCTTGATCCTCTGT 60.288 50.000 0.00 0.00 0.00 3.41
197 198 1.270826 CTCTGTTGTGCGAGGAGAAGA 59.729 52.381 0.00 0.00 0.00 2.87
209 210 4.974438 AGAAGACCACCCCCGCCA 62.974 66.667 0.00 0.00 0.00 5.69
251 252 3.313524 TCTTCTCCGGCAGCTGCA 61.314 61.111 37.63 18.61 44.36 4.41
295 296 0.330604 AGGAGCGGTGTAGTCCTGTA 59.669 55.000 0.00 0.00 39.36 2.74
308 309 3.445008 AGTCCTGTAGTGTGATGGATGT 58.555 45.455 0.00 0.00 0.00 3.06
432 433 6.258230 TGTGGATCTACTCATTTTGCTTTG 57.742 37.500 10.82 0.00 0.00 2.77
501 502 4.651045 GGAACCGAGGGAGTAATAGGTAAA 59.349 45.833 0.00 0.00 0.00 2.01
519 520 3.634397 AAATCTGACCGACACATCCAT 57.366 42.857 0.00 0.00 0.00 3.41
532 533 5.409520 CGACACATCCATATACATTTGAGGG 59.590 44.000 0.00 0.00 0.00 4.30
543 544 1.681264 CATTTGAGGGGCCGGATTAAC 59.319 52.381 5.05 0.00 0.00 2.01
570 571 1.804372 GCTGTGGCTGTAGATTCCTCG 60.804 57.143 0.00 0.00 35.22 4.63
585 586 2.045045 TCGCAAAGGAGCCATGGG 60.045 61.111 15.13 0.00 0.00 4.00
600 601 2.125147 GGGCATGCAGCTCGTACA 60.125 61.111 21.36 0.00 44.79 2.90
603 604 1.645455 GCATGCAGCTCGTACATGG 59.355 57.895 14.21 1.55 41.17 3.66
645 646 3.005554 CGGGTAAGAGACGTACAGAAGA 58.994 50.000 0.00 0.00 0.00 2.87
687 688 1.078759 GGTCTCTCACGCATTCCACG 61.079 60.000 0.00 0.00 0.00 4.94
705 706 0.458025 CGAGTGGAAACTAGGGACGC 60.458 60.000 0.00 0.00 0.00 5.19
737 738 1.673665 CCAGCAGGCTTTCGCTCTT 60.674 57.895 0.00 0.00 35.96 2.85
774 775 0.955919 GGAAACTTGGGAGGCAGACG 60.956 60.000 0.00 0.00 0.00 4.18
778 779 0.036010 ACTTGGGAGGCAGACGATTG 60.036 55.000 0.00 0.00 0.00 2.67
785 786 1.003839 GGCAGACGATTGACACCCA 60.004 57.895 0.00 0.00 0.00 4.51
787 788 1.298859 GCAGACGATTGACACCCACC 61.299 60.000 0.00 0.00 0.00 4.61
848 849 5.069501 AGTCGAAAATACGCTAGACCTTT 57.930 39.130 0.00 0.00 0.00 3.11
849 850 5.476614 AGTCGAAAATACGCTAGACCTTTT 58.523 37.500 0.00 0.00 0.00 2.27
850 851 6.624423 AGTCGAAAATACGCTAGACCTTTTA 58.376 36.000 0.00 0.00 0.00 1.52
851 852 7.092716 AGTCGAAAATACGCTAGACCTTTTAA 58.907 34.615 0.00 0.00 0.00 1.52
852 853 7.599998 AGTCGAAAATACGCTAGACCTTTTAAA 59.400 33.333 0.00 0.00 0.00 1.52
897 898 2.793278 AATTTTTCACAGACCCACGC 57.207 45.000 0.00 0.00 0.00 5.34
898 899 0.958822 ATTTTTCACAGACCCACGCC 59.041 50.000 0.00 0.00 0.00 5.68
899 900 0.106918 TTTTTCACAGACCCACGCCT 60.107 50.000 0.00 0.00 0.00 5.52
900 901 0.106918 TTTTCACAGACCCACGCCTT 60.107 50.000 0.00 0.00 0.00 4.35
901 902 0.534203 TTTCACAGACCCACGCCTTC 60.534 55.000 0.00 0.00 0.00 3.46
902 903 1.407656 TTCACAGACCCACGCCTTCT 61.408 55.000 0.00 0.00 0.00 2.85
903 904 1.071471 CACAGACCCACGCCTTCTT 59.929 57.895 0.00 0.00 0.00 2.52
904 905 0.951040 CACAGACCCACGCCTTCTTC 60.951 60.000 0.00 0.00 0.00 2.87
905 906 1.738099 CAGACCCACGCCTTCTTCG 60.738 63.158 0.00 0.00 0.00 3.79
906 907 1.906824 AGACCCACGCCTTCTTCGA 60.907 57.895 0.00 0.00 0.00 3.71
907 908 1.737008 GACCCACGCCTTCTTCGAC 60.737 63.158 0.00 0.00 0.00 4.20
908 909 2.342279 CCCACGCCTTCTTCGACA 59.658 61.111 0.00 0.00 0.00 4.35
909 910 1.738099 CCCACGCCTTCTTCGACAG 60.738 63.158 0.00 0.00 0.00 3.51
910 911 2.383527 CCACGCCTTCTTCGACAGC 61.384 63.158 0.00 0.00 0.00 4.40
922 923 2.941891 TCGACAGCGACAAAACAATC 57.058 45.000 0.00 0.00 42.51 2.67
931 932 2.033577 CGACAAAACAATCCGTTCGACA 60.034 45.455 0.00 0.00 36.59 4.35
933 934 3.884169 ACAAAACAATCCGTTCGACATG 58.116 40.909 0.00 0.00 36.59 3.21
950 951 4.149922 CGACATGTATTTATAGGCCACACG 59.850 45.833 5.01 0.00 0.00 4.49
989 990 6.681777 TCCAAAAGCAAAATTAAGCTCTCTC 58.318 36.000 5.17 0.00 40.90 3.20
992 993 3.338249 AGCAAAATTAAGCTCTCTCGCA 58.662 40.909 0.00 0.00 36.00 5.10
1025 1030 1.206610 GTCTTCCTCTCATGCTGCTGA 59.793 52.381 0.00 1.50 0.00 4.26
1029 1034 0.249676 CCTCTCATGCTGCTGACACT 59.750 55.000 0.00 0.00 0.00 3.55
1121 1126 3.566742 CCGCCACCCAAGGTAATATAAAC 59.433 47.826 0.00 0.00 32.11 2.01
1126 1131 7.148306 CGCCACCCAAGGTAATATAAACATATC 60.148 40.741 0.00 0.00 32.11 1.63
1177 1184 2.159787 GCACTACGCACACAATCTTCTG 60.160 50.000 0.00 0.00 41.79 3.02
1199 1206 5.675970 TGTCTTCGCTTACAATTCTTTTCG 58.324 37.500 0.00 0.00 0.00 3.46
1222 1229 6.017687 TCGATTCATTAGTCAATGGATGCTTG 60.018 38.462 0.00 0.00 39.98 4.01
1224 1231 4.529897 TCATTAGTCAATGGATGCTTGCT 58.470 39.130 0.00 0.00 41.66 3.91
1227 1234 5.818136 TTAGTCAATGGATGCTTGCTTAC 57.182 39.130 0.00 0.00 0.00 2.34
1233 1240 7.886970 AGTCAATGGATGCTTGCTTACATATAT 59.113 33.333 6.63 0.00 0.00 0.86
1234 1241 9.166173 GTCAATGGATGCTTGCTTACATATATA 57.834 33.333 6.63 0.00 0.00 0.86
1235 1242 9.910267 TCAATGGATGCTTGCTTACATATATAT 57.090 29.630 6.63 0.00 0.00 0.86
1263 1272 3.641434 ATATATGCATGGCAGAGGTCC 57.359 47.619 10.16 0.00 43.65 4.46
1478 1487 0.820226 CTCCATGAGGTCGCTCTTCA 59.180 55.000 0.00 0.00 36.62 3.02
1602 1611 2.550855 GCCCGCAAATGATAGAGGATGA 60.551 50.000 0.00 0.00 0.00 2.92
1652 1661 5.500234 AGTTATCAAGCTTGGACTAATGCA 58.500 37.500 25.73 3.84 0.00 3.96
1674 1733 5.517770 GCACTTTTCATATTGAAGGACATGC 59.482 40.000 0.00 0.00 37.70 4.06
1790 1852 9.268255 TGATTTTACACTTATTATTTTCACGCG 57.732 29.630 3.53 3.53 0.00 6.01
1862 1925 4.021981 CGACAATGCTCTATCCTGATGGTA 60.022 45.833 0.00 0.00 34.23 3.25
1886 1949 3.117888 AGTTTCTGTGGACTGGATTGTGT 60.118 43.478 0.00 0.00 0.00 3.72
1921 1984 4.725556 TGTCACAAATTAAGTCGACTGC 57.274 40.909 20.85 2.25 0.00 4.40
1928 1991 9.974980 TCACAAATTAAGTCGACTGCATATATA 57.025 29.630 20.85 2.49 0.00 0.86
1932 1995 8.758633 AATTAAGTCGACTGCATATATACCAC 57.241 34.615 20.85 0.00 0.00 4.16
1933 1996 4.785511 AGTCGACTGCATATATACCACC 57.214 45.455 19.30 0.00 0.00 4.61
2007 2070 6.801539 TTTACTGATCTCGCAGATGTTTTT 57.198 33.333 0.00 0.00 34.53 1.94
2189 2255 2.254152 AGTCTGCAATCACCCCTAGA 57.746 50.000 0.00 0.00 0.00 2.43
2249 2316 0.320697 GCGTGTAAGAGGGTGGAAGT 59.679 55.000 0.00 0.00 0.00 3.01
2376 2443 8.719645 AGGAGCTCAAAGATATTACAGAGTAT 57.280 34.615 17.19 0.00 0.00 2.12
2438 2505 7.967908 AGATGAAAACTTTTCACCTCTCTAGA 58.032 34.615 17.33 0.00 0.00 2.43
2582 3375 7.444299 TGCACACAATCATCTATCATTAGCTA 58.556 34.615 0.00 0.00 0.00 3.32
2622 3415 3.127895 TGTGTTTCTTTCCTTTGTGGACG 59.872 43.478 0.00 0.00 46.14 4.79
2632 3425 2.075355 TTTGTGGACGGGCTGGGATT 62.075 55.000 0.00 0.00 0.00 3.01
2646 3439 4.455877 GGCTGGGATTAGCACACATATAAC 59.544 45.833 0.00 0.00 45.46 1.89
2755 3548 7.920682 AGCTACCTTTTTCTGTTTAACAACATG 59.079 33.333 0.00 0.00 42.21 3.21
2757 3550 6.402222 ACCTTTTTCTGTTTAACAACATGCA 58.598 32.000 0.00 0.00 42.21 3.96
2758 3551 7.047271 ACCTTTTTCTGTTTAACAACATGCAT 58.953 30.769 0.00 0.00 42.21 3.96
2759 3552 7.011295 ACCTTTTTCTGTTTAACAACATGCATG 59.989 33.333 25.09 25.09 42.21 4.06
2760 3553 7.224362 CCTTTTTCTGTTTAACAACATGCATGA 59.776 33.333 32.75 7.36 42.21 3.07
2976 3854 5.408356 ACCACTTTAGATGACACGTATGAC 58.592 41.667 0.00 0.00 0.00 3.06
2985 3863 1.917212 CACGTATGACATCCGTGCG 59.083 57.895 18.73 1.90 44.34 5.34
2986 3864 1.509463 ACGTATGACATCCGTGCGT 59.491 52.632 5.15 0.00 45.84 5.24
3033 3911 5.047802 ACATGAAGCCATACAAAGGTTTGAG 60.048 40.000 9.42 0.00 40.55 3.02
3063 3941 8.722342 TTTTTCTTTTAAACTTCCATCGATCG 57.278 30.769 9.36 9.36 0.00 3.69
3139 4018 5.207110 ACACTACTAGCTATGCATCCAAG 57.793 43.478 0.19 0.00 0.00 3.61
3241 5007 7.202526 ACTTTCAAAGTCATTGTTGTACCATG 58.797 34.615 0.00 0.00 37.02 3.66
3312 5200 5.856156 ACAATTTCCACAATGCTCAAATCA 58.144 33.333 0.00 0.00 0.00 2.57
3593 5870 7.466185 GCGGTAACTACATATATGTTTTGTGCA 60.466 37.037 22.90 3.07 41.97 4.57
3636 5913 1.871080 CCTCGGTTAGTGATGATGGC 58.129 55.000 0.00 0.00 0.00 4.40
3679 5956 9.941325 ATTTCTGACCATTAGATAAGCATCTAG 57.059 33.333 0.00 0.00 43.16 2.43
3714 5996 0.177604 TTGTGGCCCTTTTGCAACAG 59.822 50.000 5.59 5.59 45.50 3.16
3801 6083 3.561960 CCCTCACCTCATCAAAACATCCA 60.562 47.826 0.00 0.00 0.00 3.41
3877 6159 5.360714 TGAAAACAAGAGTGGCTTCTTTCAT 59.639 36.000 0.00 0.00 38.87 2.57
3942 6276 5.375354 TGTATCTTCCACAATGGGGGAATAT 59.625 40.000 3.63 5.72 42.02 1.28
4005 6339 8.691797 TCCTTTTGTTTGCTACTCTTTTGTATT 58.308 29.630 0.00 0.00 0.00 1.89
4007 6341 9.301153 CTTTTGTTTGCTACTCTTTTGTATTGT 57.699 29.630 0.00 0.00 0.00 2.71
4057 6391 5.890334 ACACTTTATTGTGACACCTTGTTG 58.110 37.500 2.45 0.00 40.12 3.33
4233 6569 8.638873 CAACACCTATACTATCCATGACTACAA 58.361 37.037 0.00 0.00 0.00 2.41
4419 6758 5.155161 AGATGATGGGGCAGTACATAACTA 58.845 41.667 0.00 0.00 35.76 2.24
4486 6826 1.202879 TCCAAGAAGCGGAATGGTGTT 60.203 47.619 0.00 0.00 34.50 3.32
4489 6829 3.074412 CAAGAAGCGGAATGGTGTTACT 58.926 45.455 0.00 0.00 0.00 2.24
4704 7086 7.567571 CAGCATTTGAGGTATGTAGTATTTCG 58.432 38.462 0.00 0.00 0.00 3.46
4705 7087 7.438160 CAGCATTTGAGGTATGTAGTATTTCGA 59.562 37.037 0.00 0.00 0.00 3.71
4706 7088 8.150945 AGCATTTGAGGTATGTAGTATTTCGAT 58.849 33.333 0.00 0.00 0.00 3.59
4707 7089 9.419297 GCATTTGAGGTATGTAGTATTTCGATA 57.581 33.333 0.00 0.00 0.00 2.92
4718 7100 7.614908 TGTAGTATTTCGATAAACATTCGTGC 58.385 34.615 0.00 0.00 37.82 5.34
4719 7101 6.656314 AGTATTTCGATAAACATTCGTGCA 57.344 33.333 0.00 0.00 37.82 4.57
4720 7102 7.246674 AGTATTTCGATAAACATTCGTGCAT 57.753 32.000 0.00 0.00 37.82 3.96
4721 7103 8.360325 AGTATTTCGATAAACATTCGTGCATA 57.640 30.769 0.00 0.00 37.82 3.14
4722 7104 8.273557 AGTATTTCGATAAACATTCGTGCATAC 58.726 33.333 0.00 0.00 37.82 2.39
4724 7106 5.383984 TCGATAAACATTCGTGCATACAC 57.616 39.130 0.00 0.00 43.76 2.90
4738 7120 5.920312 GTGCATACACATATCACATACTGC 58.080 41.667 0.00 0.00 46.61 4.40
4739 7121 5.466393 GTGCATACACATATCACATACTGCA 59.534 40.000 0.00 0.00 46.61 4.41
4740 7122 6.148315 GTGCATACACATATCACATACTGCAT 59.852 38.462 0.00 0.00 46.61 3.96
4749 7131 9.740239 ACATATCACATACTGCATTTGAAAATC 57.260 29.630 0.00 0.00 27.43 2.17
4789 7171 7.756272 TGCACATGTATCATGAAATCAAAGTTC 59.244 33.333 15.25 0.00 0.00 3.01
4815 7197 8.167985 CCACTGGCATTTAAACGAATAAAATTG 58.832 33.333 0.00 0.00 0.00 2.32
4860 7242 9.988350 GTGATACTTCCATATTGTTGTACAAAG 57.012 33.333 10.51 3.27 41.96 2.77
4903 7285 2.481289 TGTGTCCATGCGGTTATTCA 57.519 45.000 0.00 0.00 0.00 2.57
5107 7491 0.963856 ATGAGTACGGCGTCACAGGA 60.964 55.000 19.21 0.00 0.00 3.86
5172 7556 3.389329 TGGAGAACTCTGAACAAAGCTCT 59.611 43.478 1.86 0.00 0.00 4.09
5197 7581 0.333993 AAGACCATGCATTGCTCCCT 59.666 50.000 10.49 0.00 0.00 4.20
5526 7935 8.264347 TGCTCAATGTTTCTAACCACATATAGA 58.736 33.333 0.00 0.00 33.11 1.98
5572 7981 2.571206 GCGCACAACAGCTTTAACTAC 58.429 47.619 0.30 0.00 0.00 2.73
5583 7992 3.512724 AGCTTTAACTACTAGAACGCCCA 59.487 43.478 0.00 0.00 0.00 5.36
5603 8012 0.035915 TGCATTGCTACGGGCTACAA 60.036 50.000 10.49 0.00 42.39 2.41
5604 8013 1.308998 GCATTGCTACGGGCTACAAT 58.691 50.000 0.16 0.00 42.39 2.71
5605 8014 2.158885 TGCATTGCTACGGGCTACAATA 60.159 45.455 10.49 0.00 42.39 1.90
5606 8015 3.074412 GCATTGCTACGGGCTACAATAT 58.926 45.455 0.16 0.00 42.39 1.28
5704 8114 9.593134 AATGCACTCTTTGTTATTTTTGTTGTA 57.407 25.926 0.00 0.00 0.00 2.41
5799 8217 9.630098 TCAAGAATGATTGCTTTCATACTTTTC 57.370 29.630 2.94 0.00 35.29 2.29
5818 8236 3.558931 TCTGGAACTGTGTGTTGACAT 57.441 42.857 0.00 0.00 39.30 3.06
5888 8318 6.759356 TCTGAGAGTTTGTACAATTCGTGAAA 59.241 34.615 9.56 0.00 0.00 2.69
5916 8360 5.092781 GCGGGTAACATGTAATTGTGAAAG 58.907 41.667 0.00 0.00 39.74 2.62
5917 8361 5.106475 GCGGGTAACATGTAATTGTGAAAGA 60.106 40.000 0.00 0.00 39.74 2.52
5918 8362 6.568844 GCGGGTAACATGTAATTGTGAAAGAA 60.569 38.462 0.00 0.00 39.74 2.52
5982 8426 8.863049 CATAACTGGTATGTTGATTTCTTTTGC 58.137 33.333 4.52 0.00 35.72 3.68
5983 8427 6.655078 ACTGGTATGTTGATTTCTTTTGCT 57.345 33.333 0.00 0.00 0.00 3.91
6154 8601 6.146673 GCTTACGACAAACCTACAAAGTATGT 59.853 38.462 0.00 0.00 46.36 2.29
6281 8728 8.025445 AGCTTGACTTATGCTTTTGAACTAATG 58.975 33.333 0.00 0.00 36.47 1.90
6307 8754 5.104527 TCACTTTACCATCCTCCATAACCTG 60.105 44.000 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.565834 GGTGGTGCTCCTACTCTTGTTA 59.434 50.000 6.34 0.00 34.23 2.41
1 2 1.348036 GGTGGTGCTCCTACTCTTGTT 59.652 52.381 6.34 0.00 34.23 2.83
2 3 0.977395 GGTGGTGCTCCTACTCTTGT 59.023 55.000 6.34 0.00 34.23 3.16
3 4 0.976641 TGGTGGTGCTCCTACTCTTG 59.023 55.000 6.34 0.00 34.23 3.02
4 5 0.977395 GTGGTGGTGCTCCTACTCTT 59.023 55.000 6.34 0.00 34.23 2.85
5 6 1.251527 CGTGGTGGTGCTCCTACTCT 61.252 60.000 6.34 0.00 34.23 3.24
6 7 1.215647 CGTGGTGGTGCTCCTACTC 59.784 63.158 6.34 0.00 34.23 2.59
7 8 0.614979 ATCGTGGTGGTGCTCCTACT 60.615 55.000 6.34 0.00 34.23 2.57
8 9 0.179108 GATCGTGGTGGTGCTCCTAC 60.179 60.000 6.34 2.93 34.23 3.18
9 10 0.324368 AGATCGTGGTGGTGCTCCTA 60.324 55.000 6.34 0.00 34.23 2.94
10 11 1.610673 AGATCGTGGTGGTGCTCCT 60.611 57.895 6.34 0.00 34.23 3.69
11 12 1.448540 CAGATCGTGGTGGTGCTCC 60.449 63.158 0.00 0.00 0.00 4.70
12 13 0.037326 TTCAGATCGTGGTGGTGCTC 60.037 55.000 0.00 0.00 0.00 4.26
13 14 0.396435 TTTCAGATCGTGGTGGTGCT 59.604 50.000 0.00 0.00 0.00 4.40
14 15 0.517316 GTTTCAGATCGTGGTGGTGC 59.483 55.000 0.00 0.00 0.00 5.01
15 16 1.156736 GGTTTCAGATCGTGGTGGTG 58.843 55.000 0.00 0.00 0.00 4.17
16 17 0.320421 CGGTTTCAGATCGTGGTGGT 60.320 55.000 0.00 0.00 0.00 4.16
17 18 0.037697 TCGGTTTCAGATCGTGGTGG 60.038 55.000 0.00 0.00 0.00 4.61
18 19 1.459592 GTTCGGTTTCAGATCGTGGTG 59.540 52.381 0.00 0.00 0.00 4.17
19 20 1.607251 GGTTCGGTTTCAGATCGTGGT 60.607 52.381 0.00 0.00 0.00 4.16
20 21 1.076332 GGTTCGGTTTCAGATCGTGG 58.924 55.000 0.00 0.00 0.00 4.94
21 22 0.713883 CGGTTCGGTTTCAGATCGTG 59.286 55.000 0.00 0.00 0.00 4.35
22 23 0.389426 CCGGTTCGGTTTCAGATCGT 60.389 55.000 0.00 0.00 42.73 3.73
23 24 2.369870 CCGGTTCGGTTTCAGATCG 58.630 57.895 0.00 0.00 42.73 3.69
34 35 1.313812 ACAGCTCTACCTCCGGTTCG 61.314 60.000 0.00 0.00 37.09 3.95
35 36 0.896226 AACAGCTCTACCTCCGGTTC 59.104 55.000 0.00 0.00 37.09 3.62
36 37 0.608640 CAACAGCTCTACCTCCGGTT 59.391 55.000 0.00 0.00 37.09 4.44
37 38 0.542232 ACAACAGCTCTACCTCCGGT 60.542 55.000 0.00 0.00 40.16 5.28
38 39 1.405821 CTACAACAGCTCTACCTCCGG 59.594 57.143 0.00 0.00 0.00 5.14
39 40 2.853731 CTACAACAGCTCTACCTCCG 57.146 55.000 0.00 0.00 0.00 4.63
50 51 1.091771 CGGCCTCCATGCTACAACAG 61.092 60.000 0.00 0.00 0.00 3.16
51 52 1.078497 CGGCCTCCATGCTACAACA 60.078 57.895 0.00 0.00 0.00 3.33
52 53 2.472909 GCGGCCTCCATGCTACAAC 61.473 63.158 0.00 0.00 0.00 3.32
53 54 2.124736 GCGGCCTCCATGCTACAA 60.125 61.111 0.00 0.00 0.00 2.41
54 55 4.175337 GGCGGCCTCCATGCTACA 62.175 66.667 12.87 0.00 0.00 2.74
55 56 4.175337 TGGCGGCCTCCATGCTAC 62.175 66.667 21.46 0.00 0.00 3.58
56 57 4.175337 GTGGCGGCCTCCATGCTA 62.175 66.667 19.50 0.00 38.57 3.49
58 59 4.175337 TAGTGGCGGCCTCCATGC 62.175 66.667 19.50 5.94 38.57 4.06
59 60 2.203070 GTAGTGGCGGCCTCCATG 60.203 66.667 19.50 0.00 38.57 3.66
60 61 3.480133 GGTAGTGGCGGCCTCCAT 61.480 66.667 19.50 9.68 38.57 3.41
61 62 4.715130 AGGTAGTGGCGGCCTCCA 62.715 66.667 21.46 11.40 0.00 3.86
62 63 4.162690 CAGGTAGTGGCGGCCTCC 62.163 72.222 21.46 16.09 0.00 4.30
63 64 4.840005 GCAGGTAGTGGCGGCCTC 62.840 72.222 21.46 17.13 0.00 4.70
108 109 3.998672 GGACAACGACCGCTGGGA 61.999 66.667 0.00 0.00 36.97 4.37
133 134 0.179089 CATCTTGGTCTCCTCGGCAG 60.179 60.000 0.00 0.00 0.00 4.85
161 162 2.288091 ACAGAGGATCAAGATCGATGCG 60.288 50.000 0.54 0.00 38.64 4.73
182 183 0.033504 GTGGTCTTCTCCTCGCACAA 59.966 55.000 0.00 0.00 0.00 3.33
236 237 1.968017 CTTTGCAGCTGCCGGAGAA 60.968 57.895 34.64 19.58 41.18 2.87
245 246 1.079266 CGCTCTCCTCTTTGCAGCT 60.079 57.895 0.00 0.00 0.00 4.24
251 252 4.459089 GCCGCCGCTCTCCTCTTT 62.459 66.667 0.00 0.00 0.00 2.52
285 286 4.402793 ACATCCATCACACTACAGGACTAC 59.597 45.833 0.00 0.00 0.00 2.73
295 296 7.069986 ACTACCTATTCTACATCCATCACACT 58.930 38.462 0.00 0.00 0.00 3.55
406 407 7.472334 AAGCAAAATGAGTAGATCCACATTT 57.528 32.000 0.00 0.00 42.25 2.32
416 417 8.935844 TGACTACATACAAAGCAAAATGAGTAG 58.064 33.333 0.00 0.00 33.40 2.57
417 418 8.840833 TGACTACATACAAAGCAAAATGAGTA 57.159 30.769 0.00 0.00 0.00 2.59
465 466 7.681168 ACTCCCTCGGTTCCCATATAATATTTA 59.319 37.037 0.00 0.00 0.00 1.40
473 474 3.339713 TTACTCCCTCGGTTCCCATAT 57.660 47.619 0.00 0.00 0.00 1.78
474 475 2.852714 TTACTCCCTCGGTTCCCATA 57.147 50.000 0.00 0.00 0.00 2.74
475 476 2.191981 ATTACTCCCTCGGTTCCCAT 57.808 50.000 0.00 0.00 0.00 4.00
483 484 6.294620 GGTCAGATTTACCTATTACTCCCTCG 60.295 46.154 0.00 0.00 33.97 4.63
501 502 4.832823 TGTATATGGATGTGTCGGTCAGAT 59.167 41.667 0.00 0.00 32.56 2.90
519 520 1.809133 TCCGGCCCCTCAAATGTATA 58.191 50.000 0.00 0.00 0.00 1.47
532 533 2.290641 CAGCACATTAGTTAATCCGGCC 59.709 50.000 0.00 0.00 0.00 6.13
543 544 3.251479 TCTACAGCCACAGCACATTAG 57.749 47.619 0.00 0.00 43.56 1.73
581 582 1.524621 GTACGAGCTGCATGCCCAT 60.525 57.895 16.68 0.00 44.23 4.00
582 583 2.125147 GTACGAGCTGCATGCCCA 60.125 61.111 16.68 0.00 44.23 5.36
585 586 1.645455 CCATGTACGAGCTGCATGC 59.355 57.895 11.82 11.82 40.66 4.06
600 601 0.549950 CTGCTCCATCTTGTCCCCAT 59.450 55.000 0.00 0.00 0.00 4.00
603 604 0.615331 TCACTGCTCCATCTTGTCCC 59.385 55.000 0.00 0.00 0.00 4.46
667 668 0.741221 GTGGAATGCGTGAGAGACCC 60.741 60.000 0.00 0.00 0.00 4.46
687 688 0.606604 TGCGTCCCTAGTTTCCACTC 59.393 55.000 0.00 0.00 34.06 3.51
705 706 1.373497 GCTGGGTGTCAGTCGTCTG 60.373 63.158 3.03 3.03 45.08 3.51
759 760 0.036010 CAATCGTCTGCCTCCCAAGT 60.036 55.000 0.00 0.00 0.00 3.16
774 775 0.251341 AAGCCTGGTGGGTGTCAATC 60.251 55.000 0.00 0.00 44.35 2.67
778 779 1.966451 CGAAAGCCTGGTGGGTGTC 60.966 63.158 0.00 0.00 44.35 3.67
820 821 2.523015 AGCGTATTTTCGACTACACGG 58.477 47.619 9.85 0.00 0.00 4.94
875 876 4.321675 GGCGTGGGTCTGTGAAAAATTAAT 60.322 41.667 0.00 0.00 0.00 1.40
903 904 1.529438 GGATTGTTTTGTCGCTGTCGA 59.471 47.619 0.00 0.00 43.28 4.20
904 905 1.721489 CGGATTGTTTTGTCGCTGTCG 60.721 52.381 0.00 0.00 0.00 4.35
905 906 1.263217 ACGGATTGTTTTGTCGCTGTC 59.737 47.619 0.00 0.00 0.00 3.51
906 907 1.305201 ACGGATTGTTTTGTCGCTGT 58.695 45.000 0.00 0.00 0.00 4.40
907 908 2.307049 GAACGGATTGTTTTGTCGCTG 58.693 47.619 0.00 0.00 42.09 5.18
908 909 1.070175 CGAACGGATTGTTTTGTCGCT 60.070 47.619 0.00 0.00 42.09 4.93
909 910 1.070443 TCGAACGGATTGTTTTGTCGC 60.070 47.619 0.00 0.00 42.09 5.19
910 911 2.033577 TGTCGAACGGATTGTTTTGTCG 60.034 45.455 0.00 0.00 42.09 4.35
911 912 3.595709 TGTCGAACGGATTGTTTTGTC 57.404 42.857 0.00 0.00 42.09 3.18
914 915 5.873179 ATACATGTCGAACGGATTGTTTT 57.127 34.783 0.00 0.00 42.09 2.43
922 923 4.387862 GGCCTATAAATACATGTCGAACGG 59.612 45.833 0.00 0.00 0.00 4.44
931 932 3.813166 GCACGTGTGGCCTATAAATACAT 59.187 43.478 18.38 0.00 0.00 2.29
933 934 3.199677 TGCACGTGTGGCCTATAAATAC 58.800 45.455 18.38 0.00 0.00 1.89
950 951 1.538047 TTGGAAGCTCCTGAATGCAC 58.462 50.000 0.00 0.00 37.46 4.57
973 974 4.154918 AGGTTGCGAGAGAGCTTAATTTTG 59.845 41.667 0.00 0.00 38.13 2.44
992 993 0.250513 GGAAGACGCCATGAGAGGTT 59.749 55.000 0.00 0.00 0.00 3.50
1040 1045 0.809241 CTCAAAGCCTAGCTGCTCCG 60.809 60.000 4.91 0.00 41.80 4.63
1065 1070 3.696051 CGATGAAAAAGTCACCCCATGAT 59.304 43.478 0.00 0.00 39.72 2.45
1101 1106 7.888546 AGATATGTTTATATTACCTTGGGTGGC 59.111 37.037 0.00 0.00 31.70 5.01
1121 1126 9.535878 GAGAAGTTCTAAACCCAACTAGATATG 57.464 37.037 5.09 0.00 32.36 1.78
1126 1131 9.372369 CTTATGAGAAGTTCTAAACCCAACTAG 57.628 37.037 5.09 0.00 32.36 2.57
1167 1174 4.883083 TGTAAGCGAAGACAGAAGATTGT 58.117 39.130 0.00 0.00 0.00 2.71
1177 1184 5.912528 TCGAAAAGAATTGTAAGCGAAGAC 58.087 37.500 0.00 0.00 0.00 3.01
1199 1206 5.919141 GCAAGCATCCATTGACTAATGAATC 59.081 40.000 1.80 0.00 45.21 2.52
1234 1241 9.955102 CCTCTGCCATGCATATATATATGTAAT 57.045 33.333 26.27 19.37 41.63 1.89
1235 1242 8.937835 ACCTCTGCCATGCATATATATATGTAA 58.062 33.333 26.27 18.32 41.63 2.41
1236 1243 8.496534 ACCTCTGCCATGCATATATATATGTA 57.503 34.615 26.27 23.84 41.63 2.29
1237 1244 7.384524 ACCTCTGCCATGCATATATATATGT 57.615 36.000 26.27 11.02 41.63 2.29
1238 1245 6.877855 GGACCTCTGCCATGCATATATATATG 59.122 42.308 23.19 23.19 42.30 1.78
1239 1246 6.295518 CGGACCTCTGCCATGCATATATATAT 60.296 42.308 0.00 0.00 38.13 0.86
1240 1247 5.011023 CGGACCTCTGCCATGCATATATATA 59.989 44.000 0.00 0.00 38.13 0.86
1250 1259 1.617018 TTCCTCGGACCTCTGCCATG 61.617 60.000 0.00 0.00 0.00 3.66
1263 1272 1.572085 GCGCCATCATCCATTCCTCG 61.572 60.000 0.00 0.00 0.00 4.63
1340 1349 0.240945 CACCAAGAACATTCGTGCCC 59.759 55.000 2.41 0.00 35.72 5.36
1344 1353 4.000988 GTGTATCCACCAAGAACATTCGT 58.999 43.478 0.00 0.00 35.44 3.85
1478 1487 6.120220 CCATTCTCCCTAAGTAAACGGAATT 58.880 40.000 0.00 0.00 0.00 2.17
1616 1625 6.037098 AGCTTGATAACTCAACTAACTAGCG 58.963 40.000 0.00 0.00 36.46 4.26
1652 1661 5.716228 TGGCATGTCCTTCAATATGAAAAGT 59.284 36.000 0.00 0.00 35.73 2.66
1674 1733 8.335532 TGGAACTCTATAAGTGTCAAAAATGG 57.664 34.615 0.00 0.00 38.58 3.16
1767 1829 9.105206 GAACGCGTGAAAATAATAAGTGTAAAA 57.895 29.630 14.98 0.00 0.00 1.52
1862 1925 4.339247 CACAATCCAGTCCACAGAAACTTT 59.661 41.667 0.00 0.00 0.00 2.66
1886 1949 2.929641 TGTGACATTGCTTCAGGAACA 58.070 42.857 0.00 0.00 0.00 3.18
2007 2070 6.159575 TCCCATCTTCACCCTTGTATTTATCA 59.840 38.462 0.00 0.00 0.00 2.15
2189 2255 0.168128 GGCGCGTTTGACTTGCTTAT 59.832 50.000 8.43 0.00 0.00 1.73
2459 2713 9.865321 ATTTGATTTTCTGAATGGACACATAAG 57.135 29.630 0.00 0.00 35.94 1.73
2542 3335 4.905429 TGTGTGCATACTACCACTGAAAT 58.095 39.130 15.05 0.00 33.26 2.17
2547 3340 4.551702 TGATTGTGTGCATACTACCACT 57.448 40.909 15.05 0.00 33.26 4.00
2622 3415 0.106519 ATGTGTGCTAATCCCAGCCC 60.107 55.000 0.00 0.00 41.04 5.19
2632 3425 6.263617 TCCTATGTGTCGTTATATGTGTGCTA 59.736 38.462 0.00 0.00 0.00 3.49
2661 3454 4.828704 GCATTTGCATGATACAACATTGC 58.171 39.130 0.00 0.00 41.59 3.56
2686 3479 8.964476 AGACATATGGAGAAAATTATGTTCGT 57.036 30.769 7.80 0.00 0.00 3.85
2687 3480 9.045223 TGAGACATATGGAGAAAATTATGTTCG 57.955 33.333 7.80 0.00 0.00 3.95
2976 3854 0.319040 CCTCTATGGACGCACGGATG 60.319 60.000 0.00 0.00 38.35 3.51
2985 3863 2.910688 TTCGGCATTCCTCTATGGAC 57.089 50.000 0.00 0.00 46.14 4.02
2986 3864 2.485479 GCTTTCGGCATTCCTCTATGGA 60.485 50.000 0.00 0.00 41.29 3.41
3000 3878 1.737838 TGGCTTCATGTAGCTTTCGG 58.262 50.000 21.72 0.00 40.99 4.30
3033 3911 8.902735 CGATGGAAGTTTAAAAGAAAAAGCTAC 58.097 33.333 0.00 0.00 0.00 3.58
3063 3941 3.084039 TGGAACTCTGCAATGGTTGATC 58.916 45.455 3.82 0.00 0.00 2.92
3241 5007 3.187842 GGGAAACCGAACAACTACATGTC 59.812 47.826 0.00 0.00 43.64 3.06
3312 5200 8.600625 CACGCATGTGTAAGTTTATACAGTAAT 58.399 33.333 12.39 0.00 41.34 1.89
3617 5894 1.869754 CGCCATCATCACTAACCGAGG 60.870 57.143 0.00 0.00 0.00 4.63
3636 5913 0.740868 AATGACGGATGGCAGACACG 60.741 55.000 0.00 0.00 0.00 4.49
3679 5956 1.732259 CACAACTTACCTCATGGTCGC 59.268 52.381 0.00 0.00 44.78 5.19
3714 5996 6.098409 TGAATTGGAGTAGAGAAGTGGGATAC 59.902 42.308 0.00 0.00 0.00 2.24
3845 6127 7.944729 AGCCACTCTTGTTTTCATATACATT 57.055 32.000 0.00 0.00 0.00 2.71
4178 6514 9.679661 TGCTTGGAGAAAATATATGTAGTTCAA 57.320 29.630 0.00 0.00 0.00 2.69
4341 6680 0.666913 CCATGCAGCCATCAGTAAGC 59.333 55.000 0.00 0.00 0.00 3.09
4486 6826 2.168521 AGCTTGGCTTATGCTTCGAGTA 59.831 45.455 0.13 0.00 36.47 2.59
4489 6829 3.861341 AGCTTGGCTTATGCTTCGA 57.139 47.368 0.13 0.00 36.47 3.71
4714 7096 5.388786 GCAGTATGTGATATGTGTATGCACG 60.389 44.000 9.48 0.00 43.37 5.34
4715 7097 5.466393 TGCAGTATGTGATATGTGTATGCAC 59.534 40.000 7.03 7.03 41.78 4.57
4716 7098 5.609423 TGCAGTATGTGATATGTGTATGCA 58.391 37.500 0.00 0.00 39.31 3.96
4717 7099 6.732531 ATGCAGTATGTGATATGTGTATGC 57.267 37.500 0.00 0.00 39.31 3.14
4718 7100 8.776470 TCAAATGCAGTATGTGATATGTGTATG 58.224 33.333 0.00 0.00 39.31 2.39
4719 7101 8.907222 TCAAATGCAGTATGTGATATGTGTAT 57.093 30.769 0.00 0.00 39.31 2.29
4720 7102 8.729805 TTCAAATGCAGTATGTGATATGTGTA 57.270 30.769 0.00 0.00 39.31 2.90
4721 7103 7.628769 TTCAAATGCAGTATGTGATATGTGT 57.371 32.000 0.00 0.00 39.31 3.72
4722 7104 8.914328 TTTTCAAATGCAGTATGTGATATGTG 57.086 30.769 0.00 0.00 39.31 3.21
4724 7106 9.961265 AGATTTTCAAATGCAGTATGTGATATG 57.039 29.630 0.00 0.00 39.31 1.78
4763 7145 7.160547 ACTTTGATTTCATGATACATGTGCA 57.839 32.000 9.11 7.16 0.00 4.57
4764 7146 7.221452 GGAACTTTGATTTCATGATACATGTGC 59.779 37.037 9.11 0.69 0.00 4.57
4789 7171 7.826260 ATTTTATTCGTTTAAATGCCAGTGG 57.174 32.000 4.20 4.20 0.00 4.00
5036 7418 0.593128 CCCTTGCACTTTCGGTTCTG 59.407 55.000 0.00 0.00 0.00 3.02
5172 7556 3.159472 AGCAATGCATGGTCTTCAAAGA 58.841 40.909 8.35 0.00 33.56 2.52
5332 7716 9.851686 ATTTATTATTCATCTGTTGTGGCTAGA 57.148 29.630 0.00 0.00 0.00 2.43
5444 7828 9.710900 AGAGAAACAAAATCCAATATCCAAAAC 57.289 29.630 0.00 0.00 0.00 2.43
5491 7877 8.730680 GGTTAGAAACATTGAGCAGAAATCTTA 58.269 33.333 0.00 0.00 0.00 2.10
5494 7880 6.803807 GTGGTTAGAAACATTGAGCAGAAATC 59.196 38.462 0.00 0.00 0.00 2.17
5495 7881 6.265196 TGTGGTTAGAAACATTGAGCAGAAAT 59.735 34.615 0.00 0.00 0.00 2.17
5526 7935 1.137086 CTAGTGCCGAGCTACCACATT 59.863 52.381 11.87 0.00 32.09 2.71
5572 7981 0.029834 GCAATGCATGGGCGTTCTAG 59.970 55.000 0.00 0.00 46.01 2.43
5604 8013 9.439461 AGATGAGCCCTAAAGTATATGCATATA 57.561 33.333 20.25 20.25 0.00 0.86
5605 8014 8.329346 AGATGAGCCCTAAAGTATATGCATAT 57.671 34.615 22.31 22.31 0.00 1.78
5606 8015 7.621285 AGAGATGAGCCCTAAAGTATATGCATA 59.379 37.037 9.27 9.27 0.00 3.14
5747 8158 6.683974 ACAAGGTCATGCATGTCTAATTAC 57.316 37.500 25.43 14.26 0.00 1.89
5799 8217 4.126437 TGTATGTCAACACACAGTTCCAG 58.874 43.478 0.00 0.00 38.74 3.86
5818 8236 8.698973 TGTTCCTTTAGAAAAATGGACATGTA 57.301 30.769 0.00 0.00 35.85 2.29
5888 8318 5.295787 CACAATTACATGTTACCCGCATACT 59.704 40.000 2.30 0.00 0.00 2.12
6281 8728 5.998363 GGTTATGGAGGATGGTAAAGTGATC 59.002 44.000 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.