Multiple sequence alignment - TraesCS7D01G324500

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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 TraesCS7D01G324500 chr7D 100.000 5046 0 0 1 5046 414376214 414371169 0.000000e+00 9319
1 TraesCS7D01G324500 chr7D 97.436 507 12 1 1 507 514084759 514085264 0.000000e+00 863
2 TraesCS7D01G324500 chr7D 96.844 507 15 1 1 507 603529399 603529904 0.000000e+00 846
3 TraesCS7D01G324500 chr7D 83.255 848 121 11 4125 4969 554878987 554879816 0.000000e+00 760
4 TraesCS7D01G324500 chr7A 94.733 2886 114 21 961 3818 476931947 476929072 0.000000e+00 4453
5 TraesCS7D01G324500 chr7A 93.405 925 58 1 4118 5042 730847583 730846662 0.000000e+00 1367
6 TraesCS7D01G324500 chr7A 86.455 347 29 7 3704 4047 476929126 476928795 1.030000e-96 364
7 TraesCS7D01G324500 chr7A 75.229 436 90 13 4555 4981 518691260 518691686 1.850000e-44 191
8 TraesCS7D01G324500 chr7A 92.857 112 6 2 3065 3175 94782444 94782334 1.450000e-35 161
9 TraesCS7D01G324500 chr7B 97.152 913 22 2 2008 2918 428838966 428838056 0.000000e+00 1539
10 TraesCS7D01G324500 chr7B 94.604 908 35 3 2911 3818 428837923 428837030 0.000000e+00 1393
11 TraesCS7D01G324500 chr7B 94.595 777 33 3 1235 2009 428839897 428839128 0.000000e+00 1194
12 TraesCS7D01G324500 chr7B 87.662 616 29 12 509 1124 428840758 428840190 0.000000e+00 673
13 TraesCS7D01G324500 chr7B 85.827 381 18 4 3723 4103 428837068 428836724 6.170000e-99 372
14 TraesCS7D01G324500 chr7B 95.327 107 5 0 3066 3172 357651484 357651590 2.420000e-38 171
15 TraesCS7D01G324500 chr1A 93.189 925 63 0 4118 5042 275770083 275769159 0.000000e+00 1360
16 TraesCS7D01G324500 chr1A 89.147 129 10 4 3066 3194 282548744 282548868 1.880000e-34 158
17 TraesCS7D01G324500 chr4B 93.182 924 61 2 4120 5042 573074923 573075845 0.000000e+00 1356
18 TraesCS7D01G324500 chr5B 92.633 923 68 0 4120 5042 612286322 612287244 0.000000e+00 1328
19 TraesCS7D01G324500 chr3B 91.441 923 58 10 4120 5042 745462015 745461114 0.000000e+00 1247
20 TraesCS7D01G324500 chr3B 79.656 349 48 8 4117 4463 27469688 27470015 3.930000e-56 230
21 TraesCS7D01G324500 chr3B 91.453 117 8 2 3063 3179 672778076 672778190 5.230000e-35 159
22 TraesCS7D01G324500 chr2A 91.694 915 52 5 4128 5042 732275198 732274308 0.000000e+00 1247
23 TraesCS7D01G324500 chr2D 93.034 646 43 2 4397 5042 186829009 186828366 0.000000e+00 942
24 TraesCS7D01G324500 chr2D 96.857 509 15 1 1 508 287019041 287018533 0.000000e+00 850
25 TraesCS7D01G324500 chr2D 96.660 509 17 0 1 509 636460061 636459553 0.000000e+00 846
26 TraesCS7D01G324500 chr5D 97.250 509 13 1 1 508 322689226 322688718 0.000000e+00 861
27 TraesCS7D01G324500 chr5D 97.047 508 14 1 1 507 461203951 461203444 0.000000e+00 854
28 TraesCS7D01G324500 chr5D 97.041 507 14 1 1 507 490722941 490722436 0.000000e+00 852
29 TraesCS7D01G324500 chr5D 96.863 510 13 2 1 508 177630184 177630692 0.000000e+00 850
30 TraesCS7D01G324500 chr5D 92.500 120 8 1 3057 3176 371860601 371860719 2.420000e-38 171
31 TraesCS7D01G324500 chr4D 96.654 508 17 0 1 508 144764550 144764043 0.000000e+00 845
32 TraesCS7D01G324500 chr6B 81.948 842 143 5 4128 4969 712105295 712106127 0.000000e+00 704
33 TraesCS7D01G324500 chr1B 83.860 285 46 0 4128 4412 10357809 10357525 6.440000e-69 272
34 TraesCS7D01G324500 chr2B 78.932 337 46 6 4128 4463 94812766 94813078 6.620000e-49 206
35 TraesCS7D01G324500 chr3D 93.636 110 7 0 3065 3174 477910558 477910667 1.120000e-36 165
36 TraesCS7D01G324500 chr1D 93.519 108 7 0 3065 3172 407673118 407673011 1.450000e-35 161


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 TraesCS7D01G324500 chr7D 414371169 414376214 5045 True 9319.0 9319 100.000 1 5046 1 chr7D.!!$R1 5045
1 TraesCS7D01G324500 chr7D 514084759 514085264 505 False 863.0 863 97.436 1 507 1 chr7D.!!$F1 506
2 TraesCS7D01G324500 chr7D 603529399 603529904 505 False 846.0 846 96.844 1 507 1 chr7D.!!$F3 506
3 TraesCS7D01G324500 chr7D 554878987 554879816 829 False 760.0 760 83.255 4125 4969 1 chr7D.!!$F2 844
4 TraesCS7D01G324500 chr7A 476928795 476931947 3152 True 2408.5 4453 90.594 961 4047 2 chr7A.!!$R3 3086
5 TraesCS7D01G324500 chr7A 730846662 730847583 921 True 1367.0 1367 93.405 4118 5042 1 chr7A.!!$R2 924
6 TraesCS7D01G324500 chr7B 428836724 428840758 4034 True 1034.2 1539 91.968 509 4103 5 chr7B.!!$R1 3594
7 TraesCS7D01G324500 chr1A 275769159 275770083 924 True 1360.0 1360 93.189 4118 5042 1 chr1A.!!$R1 924
8 TraesCS7D01G324500 chr4B 573074923 573075845 922 False 1356.0 1356 93.182 4120 5042 1 chr4B.!!$F1 922
9 TraesCS7D01G324500 chr5B 612286322 612287244 922 False 1328.0 1328 92.633 4120 5042 1 chr5B.!!$F1 922
10 TraesCS7D01G324500 chr3B 745461114 745462015 901 True 1247.0 1247 91.441 4120 5042 1 chr3B.!!$R1 922
11 TraesCS7D01G324500 chr2A 732274308 732275198 890 True 1247.0 1247 91.694 4128 5042 1 chr2A.!!$R1 914
12 TraesCS7D01G324500 chr2D 186828366 186829009 643 True 942.0 942 93.034 4397 5042 1 chr2D.!!$R1 645
13 TraesCS7D01G324500 chr2D 287018533 287019041 508 True 850.0 850 96.857 1 508 1 chr2D.!!$R2 507
14 TraesCS7D01G324500 chr2D 636459553 636460061 508 True 846.0 846 96.660 1 509 1 chr2D.!!$R3 508
15 TraesCS7D01G324500 chr5D 322688718 322689226 508 True 861.0 861 97.250 1 508 1 chr5D.!!$R1 507
16 TraesCS7D01G324500 chr5D 461203444 461203951 507 True 854.0 854 97.047 1 507 1 chr5D.!!$R2 506
17 TraesCS7D01G324500 chr5D 490722436 490722941 505 True 852.0 852 97.041 1 507 1 chr5D.!!$R3 506
18 TraesCS7D01G324500 chr5D 177630184 177630692 508 False 850.0 850 96.863 1 508 1 chr5D.!!$F1 507
19 TraesCS7D01G324500 chr4D 144764043 144764550 507 True 845.0 845 96.654 1 508 1 chr4D.!!$R1 507
20 TraesCS7D01G324500 chr6B 712105295 712106127 832 False 704.0 704 81.948 4128 4969 1 chr6B.!!$F1 841

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
956 959 0.108567 GCCACTCGTTCCTTCTCCTC 60.109 60.000 0.00 0.00 0.0 3.71 F
1223 1232 0.032615 AGGAGGAGGTCGAGCTTGAT 60.033 55.000 19.66 7.72 0.0 2.57 F
1435 1621 1.047801 GAGATCCCTCCTTCTGCTCC 58.952 60.000 0.00 0.00 33.3 4.70 F
2204 2568 1.339929 GTTCGTTGTGCCTTTCCCAAT 59.660 47.619 0.00 0.00 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2857 3227 1.532921 GCACTGTAAAAACACGCAGCA 60.533 47.619 0.00 0.0 32.65 4.41 R
2962 3480 3.106054 AGGCAATGCAATTTGTATGGGA 58.894 40.909 7.79 0.0 31.22 4.37 R
2963 3481 3.118702 TCAGGCAATGCAATTTGTATGGG 60.119 43.478 7.79 0.0 31.22 4.00 R
4114 4715 0.106521 GAGCCATGCTTCCTCTCCTC 59.893 60.000 0.00 0.0 39.88 3.71 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
97 98 3.577649 TGATGACGAGAGACCACTTTC 57.422 47.619 0.00 0.00 0.00 2.62
401 404 0.179073 GCAGTAGCATGGGACGACAT 60.179 55.000 0.00 0.00 41.58 3.06
466 469 0.240145 CGTCCCGCGCTATTGATAGA 59.760 55.000 5.56 0.00 32.05 1.98
513 516 4.715297 GGTTTTCCCTAGTAGTGAGATGGA 59.285 45.833 0.00 0.00 0.00 3.41
544 547 3.274288 GCTGACTAGGGACAAGGATTTG 58.726 50.000 0.00 0.00 40.24 2.32
545 548 3.055094 GCTGACTAGGGACAAGGATTTGA 60.055 47.826 0.00 0.00 37.73 2.69
550 553 3.721087 AGGGACAAGGATTTGAACGAT 57.279 42.857 0.00 0.00 37.73 3.73
553 556 3.127030 GGGACAAGGATTTGAACGATGAC 59.873 47.826 0.00 0.00 37.73 3.06
557 560 3.313012 AGGATTTGAACGATGACGACA 57.687 42.857 0.00 0.00 42.66 4.35
558 561 3.659786 AGGATTTGAACGATGACGACAA 58.340 40.909 0.00 0.00 42.66 3.18
560 563 2.914816 TTTGAACGATGACGACAACG 57.085 45.000 14.99 14.99 45.33 4.10
561 564 2.122563 TTGAACGATGACGACAACGA 57.877 45.000 22.16 0.00 43.20 3.85
562 565 1.401530 TGAACGATGACGACAACGAC 58.598 50.000 22.16 15.36 43.20 4.34
563 566 0.706729 GAACGATGACGACAACGACC 59.293 55.000 22.16 10.35 43.20 4.79
564 567 1.000233 AACGATGACGACAACGACCG 61.000 55.000 22.16 9.28 43.20 4.79
565 568 1.441515 CGATGACGACAACGACCGT 60.442 57.895 11.66 0.00 43.20 4.83
595 598 1.373497 CCTCATCGCCATCGCTACC 60.373 63.158 0.00 0.00 35.26 3.18
605 608 1.748122 ATCGCTACCACGACGTCCT 60.748 57.895 10.58 0.00 46.28 3.85
634 637 4.571176 GTGGATAAGAAGGAATGGAACGAC 59.429 45.833 0.00 0.00 0.00 4.34
710 713 9.814899 AGTGTCATGTCTAATCATCTTCTAAAG 57.185 33.333 0.00 0.00 0.00 1.85
728 731 9.528018 CTTCTAAAGCTACCTAAAATCAGAGAG 57.472 37.037 0.00 0.00 0.00 3.20
750 753 4.399303 AGTCAGAAACAAAACCACTCAAGG 59.601 41.667 0.00 0.00 0.00 3.61
791 794 4.521256 CCGGTTTTGAGAATTTTGGGTCTA 59.479 41.667 0.00 0.00 0.00 2.59
793 796 6.295067 CCGGTTTTGAGAATTTTGGGTCTAAT 60.295 38.462 0.00 0.00 0.00 1.73
795 798 8.301002 CGGTTTTGAGAATTTTGGGTCTAATAA 58.699 33.333 0.00 0.00 0.00 1.40
796 799 9.990360 GGTTTTGAGAATTTTGGGTCTAATAAA 57.010 29.630 0.00 0.00 0.00 1.40
804 807 9.599866 GAATTTTGGGTCTAATAAAGATTTGGG 57.400 33.333 0.00 0.00 36.36 4.12
805 808 7.489239 TTTTGGGTCTAATAAAGATTTGGGG 57.511 36.000 0.00 0.00 36.36 4.96
806 809 5.806955 TGGGTCTAATAAAGATTTGGGGT 57.193 39.130 0.00 0.00 36.36 4.95
807 810 5.762279 TGGGTCTAATAAAGATTTGGGGTC 58.238 41.667 0.00 0.00 36.36 4.46
808 811 5.494706 TGGGTCTAATAAAGATTTGGGGTCT 59.505 40.000 0.00 0.00 36.36 3.85
809 812 6.062749 GGGTCTAATAAAGATTTGGGGTCTC 58.937 44.000 0.00 0.00 36.36 3.36
810 813 6.062749 GGTCTAATAAAGATTTGGGGTCTCC 58.937 44.000 0.00 0.00 36.36 3.71
811 814 6.353602 GGTCTAATAAAGATTTGGGGTCTCCA 60.354 42.308 0.00 0.00 39.25 3.86
812 815 6.768381 GTCTAATAAAGATTTGGGGTCTCCAG 59.232 42.308 0.00 0.00 40.93 3.86
813 816 8.598609 GTCTAATAAAGATTTGGGGTCTCCAGC 61.599 44.444 0.00 0.00 40.93 4.85
818 821 0.850100 TTTGGGGTCTCCAGCTCAAA 59.150 50.000 0.00 0.00 46.14 2.69
819 822 1.202927 TTTGGGGTCTCCAGCTCAAAG 60.203 52.381 0.00 0.00 44.00 2.77
820 823 1.301293 GGGGTCTCCAGCTCAAAGG 59.699 63.158 0.00 0.00 35.00 3.11
821 824 1.201429 GGGGTCTCCAGCTCAAAGGA 61.201 60.000 0.00 0.00 35.00 3.36
825 828 3.425659 GGTCTCCAGCTCAAAGGAAAAT 58.574 45.455 0.00 0.00 32.57 1.82
844 847 9.547279 AGGAAAATAAAATGATTTAGGGTGTCT 57.453 29.630 0.00 0.00 34.62 3.41
851 854 2.378547 TGATTTAGGGTGTCTTTGGGCT 59.621 45.455 0.00 0.00 0.00 5.19
863 866 1.268899 CTTTGGGCTTGAAGTCTGCAG 59.731 52.381 7.63 7.63 0.00 4.41
864 867 0.183492 TTGGGCTTGAAGTCTGCAGT 59.817 50.000 14.67 0.00 0.00 4.40
865 868 0.535780 TGGGCTTGAAGTCTGCAGTG 60.536 55.000 14.67 0.00 0.00 3.66
898 901 0.185175 GGGCCGTCATTCCCCTAAAT 59.815 55.000 0.00 0.00 36.50 1.40
899 902 1.422402 GGGCCGTCATTCCCCTAAATA 59.578 52.381 0.00 0.00 36.50 1.40
900 903 2.158579 GGGCCGTCATTCCCCTAAATAA 60.159 50.000 0.00 0.00 36.50 1.40
901 904 3.558033 GGCCGTCATTCCCCTAAATAAA 58.442 45.455 0.00 0.00 0.00 1.40
919 922 1.731093 AAAAACACTTGGGCCGTCG 59.269 52.632 0.00 0.00 0.00 5.12
920 923 1.033202 AAAAACACTTGGGCCGTCGT 61.033 50.000 0.00 0.00 0.00 4.34
921 924 1.441732 AAAACACTTGGGCCGTCGTC 61.442 55.000 0.00 0.00 0.00 4.20
932 935 2.504244 CGTCGTCACTCTTCCGGC 60.504 66.667 0.00 0.00 0.00 6.13
934 937 3.744719 TCGTCACTCTTCCGGCCG 61.745 66.667 21.04 21.04 0.00 6.13
937 940 3.744719 TCACTCTTCCGGCCGTCG 61.745 66.667 26.12 10.11 38.88 5.12
949 952 4.052229 CCGTCGCCACTCGTTCCT 62.052 66.667 0.00 0.00 39.67 3.36
950 953 2.049433 CGTCGCCACTCGTTCCTT 60.049 61.111 0.00 0.00 39.67 3.36
951 954 2.087009 CGTCGCCACTCGTTCCTTC 61.087 63.158 0.00 0.00 39.67 3.46
954 957 1.446272 CGCCACTCGTTCCTTCTCC 60.446 63.158 0.00 0.00 0.00 3.71
955 958 1.878656 CGCCACTCGTTCCTTCTCCT 61.879 60.000 0.00 0.00 0.00 3.69
956 959 0.108567 GCCACTCGTTCCTTCTCCTC 60.109 60.000 0.00 0.00 0.00 3.71
957 960 0.533032 CCACTCGTTCCTTCTCCTCC 59.467 60.000 0.00 0.00 0.00 4.30
958 961 0.533032 CACTCGTTCCTTCTCCTCCC 59.467 60.000 0.00 0.00 0.00 4.30
959 962 0.410270 ACTCGTTCCTTCTCCTCCCT 59.590 55.000 0.00 0.00 0.00 4.20
960 963 1.203199 ACTCGTTCCTTCTCCTCCCTT 60.203 52.381 0.00 0.00 0.00 3.95
1126 1129 3.535962 CTCCCTGCTCCTCGCTCC 61.536 72.222 0.00 0.00 40.11 4.70
1143 1152 2.040779 CCCCTCCCCCTGTACCTC 60.041 72.222 0.00 0.00 0.00 3.85
1152 1161 1.574339 CCCCTGTACCTCTCTTCCCTA 59.426 57.143 0.00 0.00 0.00 3.53
1155 1164 3.309994 CCCTGTACCTCTCTTCCCTACTT 60.310 52.174 0.00 0.00 0.00 2.24
1169 1178 2.492484 CCCTACTTCTTACGCTGTCTGT 59.508 50.000 0.00 0.00 0.00 3.41
1174 1183 1.153823 CTTACGCTGTCTGTCCCCG 60.154 63.158 0.00 0.00 0.00 5.73
1178 1187 4.008933 GCTGTCTGTCCCCGCTGT 62.009 66.667 0.00 0.00 0.00 4.40
1200 1209 1.086696 GCGCAGAATAACCAAGCTCA 58.913 50.000 0.30 0.00 0.00 4.26
1202 1211 2.286654 GCGCAGAATAACCAAGCTCATC 60.287 50.000 0.30 0.00 0.00 2.92
1223 1232 0.032615 AGGAGGAGGTCGAGCTTGAT 60.033 55.000 19.66 7.72 0.00 2.57
1229 1238 1.522580 GGTCGAGCTTGATGAGGCC 60.523 63.158 7.00 0.00 0.00 5.19
1316 1501 8.999431 TCATCTTCATAAGTTGTTTACTGTTCC 58.001 33.333 0.00 0.00 37.12 3.62
1368 1554 5.356751 CGAGGAGGATGATAACTATCAGGAG 59.643 48.000 5.69 0.00 45.01 3.69
1435 1621 1.047801 GAGATCCCTCCTTCTGCTCC 58.952 60.000 0.00 0.00 33.30 4.70
1501 1696 3.884895 TGTTGGTCTTCTCTTTGCTCAA 58.115 40.909 0.00 0.00 0.00 3.02
1512 1707 9.696917 TCTTCTCTTTGCTCAAAATAATTTTCC 57.303 29.630 0.00 0.00 0.00 3.13
1603 1798 5.057149 AGTGAGAGGTAACACATGTTTCAC 58.943 41.667 14.48 14.48 39.33 3.18
1623 1818 3.367932 CACGTTAGCCCATAAGCATATCG 59.632 47.826 0.00 0.00 34.23 2.92
1812 2008 7.816995 GGATGATGAAGGTATAGATGACAAGAC 59.183 40.741 0.00 0.00 0.00 3.01
1814 2010 8.996651 TGATGAAGGTATAGATGACAAGACTA 57.003 34.615 0.00 0.00 0.00 2.59
1864 2060 4.227982 TCAGATGTTCCTGATGAATGGGAA 59.772 41.667 0.00 0.00 38.18 3.97
1867 2063 3.544684 TGTTCCTGATGAATGGGAATCG 58.455 45.455 0.00 0.00 40.58 3.34
1989 2186 3.391665 ATACAGCAGCCCTCCACGC 62.392 63.158 0.00 0.00 0.00 5.34
2025 2387 7.867921 TGGTTATTAGTATTCAGGGACAACAT 58.132 34.615 0.00 0.00 0.00 2.71
2046 2408 8.956426 CAACATAATCTTGTAGTACCCAACAAT 58.044 33.333 6.52 0.00 35.21 2.71
2204 2568 1.339929 GTTCGTTGTGCCTTTCCCAAT 59.660 47.619 0.00 0.00 0.00 3.16
2297 2661 1.710013 ATCTTGAACGTGTACTGGCG 58.290 50.000 0.00 0.00 0.00 5.69
2554 2918 4.296912 TCATTAATGGGGCATCATTTGGT 58.703 39.130 15.36 0.00 38.24 3.67
2737 3101 7.499563 TGCCAAGTATGTTTTCTGTACACTAAA 59.500 33.333 0.00 0.00 0.00 1.85
2797 3161 2.057922 TGAAGTTGGAGCTTCCTTCCT 58.942 47.619 8.15 0.00 42.98 3.36
2798 3162 2.039084 TGAAGTTGGAGCTTCCTTCCTC 59.961 50.000 8.15 0.00 42.98 3.71
2799 3163 2.037385 AGTTGGAGCTTCCTTCCTCT 57.963 50.000 0.00 0.00 37.46 3.69
2857 3227 9.539825 TTATGCACATGTTTCTGTTGTTTAATT 57.460 25.926 0.00 0.00 0.00 1.40
2957 3475 7.343057 AGAGAGTGTCAGATTATGTACAATCCA 59.657 37.037 0.00 0.00 36.02 3.41
2958 3476 7.851228 AGAGTGTCAGATTATGTACAATCCAA 58.149 34.615 0.00 0.00 36.02 3.53
2959 3477 7.766278 AGAGTGTCAGATTATGTACAATCCAAC 59.234 37.037 0.00 1.81 36.02 3.77
2960 3478 7.394016 AGTGTCAGATTATGTACAATCCAACA 58.606 34.615 0.00 4.34 35.85 3.33
2961 3479 7.882791 AGTGTCAGATTATGTACAATCCAACAA 59.117 33.333 0.00 0.00 35.85 2.83
2962 3480 8.677300 GTGTCAGATTATGTACAATCCAACAAT 58.323 33.333 0.00 0.00 35.85 2.71
2963 3481 8.892723 TGTCAGATTATGTACAATCCAACAATC 58.107 33.333 0.00 1.46 35.85 2.67
2964 3482 8.345565 GTCAGATTATGTACAATCCAACAATCC 58.654 37.037 0.00 0.00 35.85 3.01
3020 3538 3.941483 CACACCCTAGTTCTAGCAATTGG 59.059 47.826 7.72 0.75 0.00 3.16
3032 3550 6.299805 TCTAGCAATTGGTGTACTCTTCAT 57.700 37.500 20.13 0.00 0.00 2.57
3038 3556 7.066284 AGCAATTGGTGTACTCTTCATTGTATC 59.934 37.037 9.83 0.00 0.00 2.24
3072 3590 5.104652 TGAAATAGCAAAGGTAGTACTCCCC 60.105 44.000 0.00 0.28 0.00 4.81
3073 3591 2.644060 AGCAAAGGTAGTACTCCCCT 57.356 50.000 0.00 3.08 0.00 4.79
3074 3592 2.917205 AGCAAAGGTAGTACTCCCCTT 58.083 47.619 17.12 17.12 40.27 3.95
3158 3676 6.345298 TCCATTTGAGCGACAAGTAATATGA 58.655 36.000 0.00 0.00 39.77 2.15
3161 3679 7.800380 CCATTTGAGCGACAAGTAATATGAATC 59.200 37.037 0.00 0.00 39.77 2.52
3181 3699 3.437213 TCGGAGGGAGTACTTGATTCAA 58.563 45.455 0.00 0.00 0.00 2.69
3285 3804 7.770433 TCTCCATGGTTGTATTTGAAGTGATAG 59.230 37.037 12.58 0.00 0.00 2.08
3308 3828 7.997773 AGTCTTATTTGAGGTTTTACTTCCC 57.002 36.000 0.00 0.00 0.00 3.97
3398 3918 4.781934 AGAGGTACACTTTGTTGCTTTCT 58.218 39.130 0.00 0.00 0.00 2.52
3415 3935 6.405538 TGCTTTCTTTGGAACTGACATTTTT 58.594 32.000 0.00 0.00 0.00 1.94
3457 3977 7.048512 ACTCTTTAGTAAGTGAAACAGTGCTT 58.951 34.615 0.00 0.00 34.15 3.91
3478 3998 6.159988 GCTTAGTGTCTGAATGTAGACTTGT 58.840 40.000 10.05 0.00 45.70 3.16
3479 3999 6.090088 GCTTAGTGTCTGAATGTAGACTTGTG 59.910 42.308 10.05 1.13 45.70 3.33
3497 4017 7.661437 AGACTTGTGACATGCTAACATTTTCTA 59.339 33.333 0.00 0.00 32.87 2.10
3498 4018 8.340618 ACTTGTGACATGCTAACATTTTCTAT 57.659 30.769 0.00 0.00 32.87 1.98
3499 4019 8.239314 ACTTGTGACATGCTAACATTTTCTATG 58.761 33.333 0.00 0.00 32.87 2.23
3500 4020 7.087409 TGTGACATGCTAACATTTTCTATGG 57.913 36.000 0.00 0.00 32.87 2.74
3744 4264 2.738846 CTCTGACAGTGTGGTTGCATAC 59.261 50.000 0.00 0.00 0.00 2.39
3798 4373 4.182433 TCTGGTGGCGTGGTTGCA 62.182 61.111 0.00 0.00 36.28 4.08
3832 4407 7.766278 CCATGTTAGCATTAGAAACAGTAGAGT 59.234 37.037 0.00 0.00 36.62 3.24
3833 4408 8.598924 CATGTTAGCATTAGAAACAGTAGAGTG 58.401 37.037 0.00 0.00 36.62 3.51
3834 4409 7.892609 TGTTAGCATTAGAAACAGTAGAGTGA 58.107 34.615 0.00 0.00 0.00 3.41
3835 4410 7.813148 TGTTAGCATTAGAAACAGTAGAGTGAC 59.187 37.037 0.00 0.00 0.00 3.67
3836 4411 6.346477 AGCATTAGAAACAGTAGAGTGACA 57.654 37.500 0.00 0.00 0.00 3.58
3837 4412 6.159988 AGCATTAGAAACAGTAGAGTGACAC 58.840 40.000 0.00 0.00 0.00 3.67
3838 4413 5.926542 GCATTAGAAACAGTAGAGTGACACA 59.073 40.000 8.59 0.00 0.00 3.72
3839 4414 6.128795 GCATTAGAAACAGTAGAGTGACACAC 60.129 42.308 8.59 0.91 34.10 3.82
3928 4527 2.503331 TGTGTTAGGTGTGCTGGAATG 58.497 47.619 0.00 0.00 0.00 2.67
3935 4534 1.302431 TGTGCTGGAATGGTGGTCG 60.302 57.895 0.00 0.00 0.00 4.79
3942 4541 1.129058 GGAATGGTGGTCGTAGGGAT 58.871 55.000 0.00 0.00 0.00 3.85
4067 4668 4.859798 GTGGTTTTTGTTGACGACATTTGA 59.140 37.500 0.00 0.00 38.26 2.69
4069 4670 6.693545 GTGGTTTTTGTTGACGACATTTGATA 59.306 34.615 0.00 0.00 38.26 2.15
4103 4704 0.761802 GCAAGTATCCAGGGGAGAGG 59.238 60.000 0.00 0.00 34.05 3.69
4104 4705 1.692762 GCAAGTATCCAGGGGAGAGGA 60.693 57.143 0.00 0.00 34.05 3.71
4105 4706 2.324541 CAAGTATCCAGGGGAGAGGAG 58.675 57.143 0.00 0.00 37.34 3.69
4106 4707 1.626621 AGTATCCAGGGGAGAGGAGT 58.373 55.000 0.00 0.00 37.34 3.85
4107 4708 2.803215 AGTATCCAGGGGAGAGGAGTA 58.197 52.381 0.00 0.00 37.34 2.59
4108 4709 2.447811 AGTATCCAGGGGAGAGGAGTAC 59.552 54.545 0.00 0.00 37.34 2.73
4109 4710 0.186386 ATCCAGGGGAGAGGAGTACG 59.814 60.000 0.00 0.00 37.34 3.67
4110 4711 0.917821 TCCAGGGGAGAGGAGTACGA 60.918 60.000 0.00 0.00 0.00 3.43
4111 4712 0.752376 CCAGGGGAGAGGAGTACGAC 60.752 65.000 0.00 0.00 0.00 4.34
4112 4713 0.034380 CAGGGGAGAGGAGTACGACA 60.034 60.000 0.00 0.00 0.00 4.35
4113 4714 0.927767 AGGGGAGAGGAGTACGACAT 59.072 55.000 0.00 0.00 0.00 3.06
4114 4715 1.033574 GGGGAGAGGAGTACGACATG 58.966 60.000 0.00 0.00 0.00 3.21
4115 4716 1.409802 GGGGAGAGGAGTACGACATGA 60.410 57.143 0.00 0.00 0.00 3.07
4116 4717 1.950909 GGGAGAGGAGTACGACATGAG 59.049 57.143 0.00 0.00 0.00 2.90
4218 4819 2.203771 GCCGAGACCAGATCCGGAT 61.204 63.158 19.21 19.21 41.25 4.18
4337 4938 2.271497 GCCACCTCATCTGCTGCT 59.729 61.111 0.00 0.00 0.00 4.24
4489 5090 3.324671 CGGTGTCGACGCGTTGTT 61.325 61.111 25.12 0.00 39.00 2.83
4650 5251 2.681064 CAACCCCGACCCCGACTA 60.681 66.667 0.00 0.00 38.22 2.59
4849 5456 2.112297 GGCGTTGGGTCTGGACAA 59.888 61.111 3.10 0.00 0.00 3.18
4883 5490 3.333219 TGGAGCTCCCTTGCCCAG 61.333 66.667 29.95 0.00 35.38 4.45
4953 5560 1.677820 CGGCTACCAAATCCTCGGTTT 60.678 52.381 0.00 0.00 36.69 3.27
4974 5581 3.207669 CTACTCGGTCGGACGGGG 61.208 72.222 13.39 13.39 39.04 5.73
4991 5598 2.904866 GCGTGTGGAGGTTGGCAA 60.905 61.111 0.00 0.00 0.00 4.52
5043 5650 2.203806 GACTCACTAGTCCCTGCCC 58.796 63.158 0.00 0.00 45.50 5.36
5044 5651 0.324830 GACTCACTAGTCCCTGCCCT 60.325 60.000 0.00 0.00 45.50 5.19
5045 5652 0.616111 ACTCACTAGTCCCTGCCCTG 60.616 60.000 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 98 8.451748 GTCATCATCATAATCATCATCCAACAG 58.548 37.037 0.00 0.00 0.00 3.16
351 354 2.953669 GCAGTAGCGCGCTTTAGTA 58.046 52.632 41.04 19.08 0.00 1.82
459 462 7.919091 CAGTAGCGTAGGTATTTTGTCTATCAA 59.081 37.037 0.00 0.00 44.46 2.57
513 516 1.034838 CCTAGTCAGCCTGCTCGTCT 61.035 60.000 0.00 0.00 0.00 4.18
544 547 0.706729 GGTCGTTGTCGTCATCGTTC 59.293 55.000 11.74 7.42 37.80 3.95
545 548 1.000233 CGGTCGTTGTCGTCATCGTT 61.000 55.000 11.74 0.00 37.80 3.85
550 553 1.600164 CCTTAACGGTCGTTGTCGTCA 60.600 52.381 17.57 0.00 38.78 4.35
553 556 1.777199 GCCTTAACGGTCGTTGTCG 59.223 57.895 17.57 6.49 38.92 4.35
557 560 4.756630 AACGCCTTAACGGTCGTT 57.243 50.000 13.31 13.31 44.67 3.85
558 561 0.940991 GACAACGCCTTAACGGTCGT 60.941 55.000 0.00 0.00 43.83 4.34
560 563 0.320160 AGGACAACGCCTTAACGGTC 60.320 55.000 0.00 0.00 33.46 4.79
561 564 0.320160 GAGGACAACGCCTTAACGGT 60.320 55.000 0.00 0.00 38.73 4.83
562 565 0.320073 TGAGGACAACGCCTTAACGG 60.320 55.000 0.00 0.00 38.73 4.44
563 566 1.659098 GATGAGGACAACGCCTTAACG 59.341 52.381 0.00 0.00 38.73 3.18
564 567 1.659098 CGATGAGGACAACGCCTTAAC 59.341 52.381 0.00 0.00 38.73 2.01
565 568 2.004583 CGATGAGGACAACGCCTTAA 57.995 50.000 0.00 0.00 38.73 1.85
605 608 4.039245 CCATTCCTTCTTATCCACTAGCGA 59.961 45.833 0.00 0.00 0.00 4.93
634 637 1.826054 TTGCACCGGACCAAACCAG 60.826 57.895 9.46 0.00 0.00 4.00
663 666 0.321210 TTGACGTGGCATCGAACCAT 60.321 50.000 13.10 0.00 39.95 3.55
710 713 6.458232 TCTGACTCTCTGATTTTAGGTAGC 57.542 41.667 0.00 0.00 0.00 3.58
723 726 5.104259 AGTGGTTTTGTTTCTGACTCTCT 57.896 39.130 0.00 0.00 0.00 3.10
726 729 5.449177 CCTTGAGTGGTTTTGTTTCTGACTC 60.449 44.000 0.00 0.00 0.00 3.36
728 731 4.398044 TCCTTGAGTGGTTTTGTTTCTGAC 59.602 41.667 0.00 0.00 0.00 3.51
760 763 7.816995 CCAAAATTCTCAAAACCGGATAAATCA 59.183 33.333 9.46 0.00 0.00 2.57
761 764 7.277760 CCCAAAATTCTCAAAACCGGATAAATC 59.722 37.037 9.46 0.00 0.00 2.17
791 794 4.017130 AGCTGGAGACCCCAAATCTTTATT 60.017 41.667 0.00 0.00 46.07 1.40
793 796 2.919602 AGCTGGAGACCCCAAATCTTTA 59.080 45.455 0.00 0.00 46.07 1.85
795 798 1.283321 GAGCTGGAGACCCCAAATCTT 59.717 52.381 0.00 0.00 46.07 2.40
796 799 0.915364 GAGCTGGAGACCCCAAATCT 59.085 55.000 0.00 0.00 46.07 2.40
797 800 0.620556 TGAGCTGGAGACCCCAAATC 59.379 55.000 0.00 0.00 46.07 2.17
798 801 1.075601 TTGAGCTGGAGACCCCAAAT 58.924 50.000 0.00 0.00 46.07 2.32
799 802 0.850100 TTTGAGCTGGAGACCCCAAA 59.150 50.000 0.00 0.00 46.07 3.28
800 803 0.401738 CTTTGAGCTGGAGACCCCAA 59.598 55.000 0.00 0.00 46.07 4.12
801 804 1.492133 CCTTTGAGCTGGAGACCCCA 61.492 60.000 0.00 0.00 44.25 4.96
802 805 1.201429 TCCTTTGAGCTGGAGACCCC 61.201 60.000 0.00 0.00 0.00 4.95
803 806 0.693049 TTCCTTTGAGCTGGAGACCC 59.307 55.000 0.00 0.00 33.46 4.46
804 807 2.568623 TTTCCTTTGAGCTGGAGACC 57.431 50.000 0.00 0.00 33.46 3.85
805 808 6.575162 TTTATTTTCCTTTGAGCTGGAGAC 57.425 37.500 0.00 0.00 33.46 3.36
806 809 7.451255 TCATTTTATTTTCCTTTGAGCTGGAGA 59.549 33.333 0.00 0.00 33.46 3.71
807 810 7.605449 TCATTTTATTTTCCTTTGAGCTGGAG 58.395 34.615 0.00 0.00 33.46 3.86
808 811 7.537596 TCATTTTATTTTCCTTTGAGCTGGA 57.462 32.000 0.00 0.00 0.00 3.86
809 812 8.782339 AATCATTTTATTTTCCTTTGAGCTGG 57.218 30.769 0.00 0.00 0.00 4.85
818 821 9.547279 AGACACCCTAAATCATTTTATTTTCCT 57.453 29.630 0.00 0.00 31.63 3.36
825 828 6.071051 GCCCAAAGACACCCTAAATCATTTTA 60.071 38.462 0.00 0.00 0.00 1.52
839 842 2.291741 CAGACTTCAAGCCCAAAGACAC 59.708 50.000 0.00 0.00 0.00 3.67
844 847 1.321474 CTGCAGACTTCAAGCCCAAA 58.679 50.000 8.42 0.00 0.00 3.28
863 866 0.313987 GCCCAAGTGTAAGTTGCCAC 59.686 55.000 0.54 0.54 45.85 5.01
864 867 0.825840 GGCCCAAGTGTAAGTTGCCA 60.826 55.000 0.00 0.00 45.85 4.92
865 868 1.862602 CGGCCCAAGTGTAAGTTGCC 61.863 60.000 0.00 0.00 45.85 4.52
901 904 1.033202 ACGACGGCCCAAGTGTTTTT 61.033 50.000 0.00 0.00 0.00 1.94
919 922 2.126031 GACGGCCGGAAGAGTGAC 60.126 66.667 31.76 5.04 0.00 3.67
920 923 3.744719 CGACGGCCGGAAGAGTGA 61.745 66.667 31.76 0.00 33.91 3.41
932 935 3.569049 AAGGAACGAGTGGCGACGG 62.569 63.158 0.00 0.00 44.57 4.79
934 937 0.733223 GAGAAGGAACGAGTGGCGAC 60.733 60.000 0.00 0.00 44.57 5.19
937 940 0.108567 GAGGAGAAGGAACGAGTGGC 60.109 60.000 0.00 0.00 0.00 5.01
946 949 1.396594 GGGGAAGGGAGGAGAAGGA 59.603 63.158 0.00 0.00 0.00 3.36
947 950 0.550147 TTGGGGAAGGGAGGAGAAGG 60.550 60.000 0.00 0.00 0.00 3.46
949 952 1.596496 GATTGGGGAAGGGAGGAGAA 58.404 55.000 0.00 0.00 0.00 2.87
950 953 0.327576 GGATTGGGGAAGGGAGGAGA 60.328 60.000 0.00 0.00 0.00 3.71
951 954 1.356494 GGGATTGGGGAAGGGAGGAG 61.356 65.000 0.00 0.00 0.00 3.69
954 957 2.395353 GGGGGATTGGGGAAGGGAG 61.395 68.421 0.00 0.00 0.00 4.30
955 958 2.287661 GGGGGATTGGGGAAGGGA 60.288 66.667 0.00 0.00 0.00 4.20
956 959 2.620137 TGGGGGATTGGGGAAGGG 60.620 66.667 0.00 0.00 0.00 3.95
957 960 1.935931 AGTGGGGGATTGGGGAAGG 60.936 63.158 0.00 0.00 0.00 3.46
958 961 1.615262 GAGTGGGGGATTGGGGAAG 59.385 63.158 0.00 0.00 0.00 3.46
959 962 2.305607 CGAGTGGGGGATTGGGGAA 61.306 63.158 0.00 0.00 0.00 3.97
960 963 2.690881 CGAGTGGGGGATTGGGGA 60.691 66.667 0.00 0.00 0.00 4.81
1126 1129 2.040779 GAGGTACAGGGGGAGGGG 60.041 72.222 0.00 0.00 0.00 4.79
1137 1140 5.296531 CGTAAGAAGTAGGGAAGAGAGGTAC 59.703 48.000 0.00 0.00 43.02 3.34
1143 1152 3.444388 ACAGCGTAAGAAGTAGGGAAGAG 59.556 47.826 0.00 0.00 43.02 2.85
1152 1161 1.272769 GGGACAGACAGCGTAAGAAGT 59.727 52.381 0.00 0.00 43.02 3.01
1155 1164 1.592400 CGGGGACAGACAGCGTAAGA 61.592 60.000 0.00 0.00 43.02 2.10
1174 1183 1.068610 TGGTTATTCTGCGCAAACAGC 60.069 47.619 20.73 13.43 37.59 4.40
1178 1187 1.885887 AGCTTGGTTATTCTGCGCAAA 59.114 42.857 13.05 9.55 0.00 3.68
1187 1196 3.181461 CCTCCTCGATGAGCTTGGTTATT 60.181 47.826 11.83 0.00 0.00 1.40
1200 1209 1.527380 GCTCGACCTCCTCCTCGAT 60.527 63.158 0.00 0.00 38.22 3.59
1202 1211 1.751162 AAGCTCGACCTCCTCCTCG 60.751 63.158 0.00 0.00 0.00 4.63
1229 1238 1.680314 GGCTTCTTGGCCCCAGAAG 60.680 63.158 27.02 27.02 45.92 2.85
1316 1501 1.001406 AGAAAGGACGGAGCAGTTGAG 59.999 52.381 0.00 0.00 0.00 3.02
1465 1651 6.952773 AGACCAACAACAAAAGCTACAATA 57.047 33.333 0.00 0.00 0.00 1.90
1480 1666 3.558931 TGAGCAAAGAGAAGACCAACA 57.441 42.857 0.00 0.00 0.00 3.33
1501 1696 5.151297 CACAGGCAGTGGGAAAATTATTT 57.849 39.130 1.52 0.00 44.69 1.40
1569 1764 2.252714 ACCTCTCACTCACTTCCTTCC 58.747 52.381 0.00 0.00 0.00 3.46
1603 1798 2.930040 CCGATATGCTTATGGGCTAACG 59.070 50.000 7.57 0.00 28.42 3.18
1623 1818 2.168947 CAGTGCATGACTGTGCTCC 58.831 57.895 13.84 0.00 46.30 4.70
1812 2008 8.660373 GTTTGGATGAAGTTGTCTTATCAGTAG 58.340 37.037 0.00 0.00 33.64 2.57
1814 2010 6.998074 TGTTTGGATGAAGTTGTCTTATCAGT 59.002 34.615 0.00 0.00 33.64 3.41
1864 2060 3.887621 TTCCTGATCGTTTTCTCCGAT 57.112 42.857 0.00 0.00 46.91 4.18
1867 2063 5.392057 GGTTGATTTCCTGATCGTTTTCTCC 60.392 44.000 0.00 0.00 0.00 3.71
2046 2408 2.898612 TCAATCAGCCTGAAAATGCCAA 59.101 40.909 0.00 0.00 0.00 4.52
2088 2450 3.084039 CTCTTCTTAATTGGCTGGCACA 58.916 45.455 2.29 0.00 0.00 4.57
2089 2451 3.347216 TCTCTTCTTAATTGGCTGGCAC 58.653 45.455 2.29 0.00 0.00 5.01
2204 2568 3.266772 ACTGGCAGGTTCCATCTTTATCA 59.733 43.478 20.34 0.00 35.22 2.15
2297 2661 2.818751 TCTTCACCTCCTCCTCTCTC 57.181 55.000 0.00 0.00 0.00 3.20
2477 2841 5.257082 TCATAACTAGTAATCAGCACGCA 57.743 39.130 0.00 0.00 0.00 5.24
2554 2918 6.103997 AGTTGAAGTCGTACAAAGTTCAGAA 58.896 36.000 12.67 1.47 37.37 3.02
2737 3101 7.343833 AGGAACATGAATTAAGGAATGAGCAAT 59.656 33.333 0.00 0.00 0.00 3.56
2857 3227 1.532921 GCACTGTAAAAACACGCAGCA 60.533 47.619 0.00 0.00 32.65 4.41
2957 3475 5.354792 GCAATGCAATTTGTATGGGATTGTT 59.645 36.000 0.00 0.00 42.46 2.83
2958 3476 4.877251 GCAATGCAATTTGTATGGGATTGT 59.123 37.500 0.00 0.00 42.46 2.71
2959 3477 4.273969 GGCAATGCAATTTGTATGGGATTG 59.726 41.667 7.79 0.00 43.02 2.67
2960 3478 4.164604 AGGCAATGCAATTTGTATGGGATT 59.835 37.500 7.79 0.00 31.22 3.01
2961 3479 3.712733 AGGCAATGCAATTTGTATGGGAT 59.287 39.130 7.79 0.00 31.22 3.85
2962 3480 3.106054 AGGCAATGCAATTTGTATGGGA 58.894 40.909 7.79 0.00 31.22 4.37
2963 3481 3.118702 TCAGGCAATGCAATTTGTATGGG 60.119 43.478 7.79 0.00 31.22 4.00
2964 3482 4.126208 TCAGGCAATGCAATTTGTATGG 57.874 40.909 7.79 0.00 31.22 2.74
3020 3538 5.744345 CGACAGGATACAATGAAGAGTACAC 59.256 44.000 0.00 0.00 41.41 2.90
3032 3550 5.753438 GCTATTTCATCACGACAGGATACAA 59.247 40.000 0.00 0.00 41.41 2.41
3038 3556 4.201851 CCTTTGCTATTTCATCACGACAGG 60.202 45.833 0.00 0.00 0.00 4.00
3072 3590 5.985530 TGAGCGACAAGTAATATGGATCAAG 59.014 40.000 0.00 0.00 0.00 3.02
3073 3591 5.912892 TGAGCGACAAGTAATATGGATCAA 58.087 37.500 0.00 0.00 0.00 2.57
3074 3592 5.529581 TGAGCGACAAGTAATATGGATCA 57.470 39.130 0.00 0.00 0.00 2.92
3158 3676 4.030913 TGAATCAAGTACTCCCTCCGATT 58.969 43.478 0.00 0.00 0.00 3.34
3161 3679 3.887621 TTGAATCAAGTACTCCCTCCG 57.112 47.619 0.00 0.00 0.00 4.63
3181 3699 6.906157 AGGAGTGTGTTCATTTCAAATCAT 57.094 33.333 0.00 0.00 0.00 2.45
3198 3716 6.961360 TCAGGTGATACTAATGTAGGAGTG 57.039 41.667 0.00 0.00 31.51 3.51
3285 3804 7.447545 ACAGGGAAGTAAAACCTCAAATAAGAC 59.552 37.037 0.00 0.00 30.66 3.01
3308 3828 5.163550 TGTCTTTGGATCACGGTATCTACAG 60.164 44.000 0.00 0.00 0.00 2.74
3415 3935 4.519906 AGAGTTCCAACCCAGAAAGAAA 57.480 40.909 0.00 0.00 0.00 2.52
3416 3936 4.519906 AAGAGTTCCAACCCAGAAAGAA 57.480 40.909 0.00 0.00 0.00 2.52
3430 3950 7.224949 AGCACTGTTTCACTTACTAAAGAGTTC 59.775 37.037 0.00 0.00 37.16 3.01
3457 3977 6.264518 TGTCACAAGTCTACATTCAGACACTA 59.735 38.462 6.08 0.00 46.15 2.74
3478 3998 6.037062 CGTCCATAGAAAATGTTAGCATGTCA 59.963 38.462 0.00 0.00 35.15 3.58
3479 3999 6.422223 CGTCCATAGAAAATGTTAGCATGTC 58.578 40.000 0.00 0.00 35.15 3.06
3497 4017 0.960364 GAACACATGCACCCGTCCAT 60.960 55.000 0.00 0.00 0.00 3.41
3498 4018 1.599518 GAACACATGCACCCGTCCA 60.600 57.895 0.00 0.00 0.00 4.02
3499 4019 1.577328 CTGAACACATGCACCCGTCC 61.577 60.000 0.00 0.00 0.00 4.79
3500 4020 0.884704 ACTGAACACATGCACCCGTC 60.885 55.000 0.00 0.00 0.00 4.79
3832 4407 3.599343 GCATCAGGAACATAGTGTGTCA 58.401 45.455 0.00 0.00 41.14 3.58
3833 4408 2.939103 GGCATCAGGAACATAGTGTGTC 59.061 50.000 0.00 0.00 41.14 3.67
3834 4409 2.677902 CGGCATCAGGAACATAGTGTGT 60.678 50.000 0.00 0.00 44.84 3.72
3835 4410 1.935873 CGGCATCAGGAACATAGTGTG 59.064 52.381 0.00 0.00 0.00 3.82
3836 4411 1.743772 GCGGCATCAGGAACATAGTGT 60.744 52.381 0.00 0.00 0.00 3.55
3837 4412 0.940126 GCGGCATCAGGAACATAGTG 59.060 55.000 0.00 0.00 0.00 2.74
3838 4413 0.179045 GGCGGCATCAGGAACATAGT 60.179 55.000 3.07 0.00 0.00 2.12
3839 4414 1.224069 CGGCGGCATCAGGAACATAG 61.224 60.000 10.53 0.00 0.00 2.23
3840 4415 1.227527 CGGCGGCATCAGGAACATA 60.228 57.895 10.53 0.00 0.00 2.29
3899 4474 2.290641 CACACCTAACACAAGAAGCCAC 59.709 50.000 0.00 0.00 0.00 5.01
3928 4527 1.276989 TGAACAATCCCTACGACCACC 59.723 52.381 0.00 0.00 0.00 4.61
3935 4534 4.781934 AGGCTATGTTGAACAATCCCTAC 58.218 43.478 0.62 0.00 0.00 3.18
3942 4541 3.138884 TGCTGAGGCTATGTTGAACAA 57.861 42.857 0.62 0.00 39.59 2.83
4069 4670 7.892609 TGGATACTTGCAGATTATATGTACGT 58.107 34.615 0.00 0.00 37.61 3.57
4103 4704 2.920524 TCCTCTCCTCATGTCGTACTC 58.079 52.381 0.00 0.00 0.00 2.59
4104 4705 3.283751 CTTCCTCTCCTCATGTCGTACT 58.716 50.000 0.00 0.00 0.00 2.73
4105 4706 2.223618 GCTTCCTCTCCTCATGTCGTAC 60.224 54.545 0.00 0.00 0.00 3.67
4106 4707 2.025155 GCTTCCTCTCCTCATGTCGTA 58.975 52.381 0.00 0.00 0.00 3.43
4107 4708 0.820871 GCTTCCTCTCCTCATGTCGT 59.179 55.000 0.00 0.00 0.00 4.34
4108 4709 0.820226 TGCTTCCTCTCCTCATGTCG 59.180 55.000 0.00 0.00 0.00 4.35
4109 4710 2.485124 CCATGCTTCCTCTCCTCATGTC 60.485 54.545 0.00 0.00 34.36 3.06
4110 4711 1.489649 CCATGCTTCCTCTCCTCATGT 59.510 52.381 0.00 0.00 34.36 3.21
4111 4712 1.814634 GCCATGCTTCCTCTCCTCATG 60.815 57.143 0.00 0.00 35.55 3.07
4112 4713 0.473326 GCCATGCTTCCTCTCCTCAT 59.527 55.000 0.00 0.00 0.00 2.90
4113 4714 0.619832 AGCCATGCTTCCTCTCCTCA 60.620 55.000 0.00 0.00 33.89 3.86
4114 4715 0.106521 GAGCCATGCTTCCTCTCCTC 59.893 60.000 0.00 0.00 39.88 3.71
4115 4716 1.344191 GGAGCCATGCTTCCTCTCCT 61.344 60.000 6.49 0.00 39.88 3.69
4116 4717 1.148048 GGAGCCATGCTTCCTCTCC 59.852 63.158 6.49 0.00 39.88 3.71
4323 4924 2.271497 GGCAGCAGCAGATGAGGT 59.729 61.111 2.65 0.00 44.61 3.85
4475 5076 2.232296 GGTGAACAACGCGTCGACA 61.232 57.895 14.44 8.28 0.00 4.35
4489 5090 2.110213 GCGTTGTGTCCTGGGTGA 59.890 61.111 0.00 0.00 0.00 4.02
4849 5456 1.380403 CCACGAGACTGATCGCTCCT 61.380 60.000 0.00 0.00 46.60 3.69
4883 5490 5.230942 TCGTCATCCTTGTCTTCTTCTTTC 58.769 41.667 0.00 0.00 0.00 2.62
4932 5539 1.262640 ACCGAGGATTTGGTAGCCGT 61.263 55.000 0.00 0.00 39.45 5.68
4953 5560 2.821366 GTCCGACCGAGTAGCCGA 60.821 66.667 0.00 0.00 0.00 5.54
4974 5581 2.904866 TTGCCAACCTCCACACGC 60.905 61.111 0.00 0.00 0.00 5.34


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

AutoCloner maintained by Alex Coulton.