Multiple sequence alignment - TraesCS7A01G005900

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 TraesCS7A01G005900 chr7A 100.000 3846 0 0 1 3846 2858965 2862810 0.000000e+00 7103.0
1 TraesCS7A01G005900 chr7A 88.403 1121 113 11 859 1976 2570510 2571616 0.000000e+00 1334.0
2 TraesCS7A01G005900 chr7A 87.978 890 93 8 2711 3595 3009841 3010721 0.000000e+00 1038.0
3 TraesCS7A01G005900 chr7A 87.865 890 91 10 2711 3595 3629531 3628654 0.000000e+00 1029.0
4 TraesCS7A01G005900 chr7A 86.507 919 99 12 2711 3614 3322728 3321820 0.000000e+00 987.0
5 TraesCS7A01G005900 chr7A 82.828 990 135 23 943 1919 3324707 3323740 0.000000e+00 854.0
6 TraesCS7A01G005900 chr7A 87.453 534 61 3 3063 3596 2579847 2580374 9.130000e-171 610.0
7 TraesCS7A01G005900 chr7A 85.118 551 43 21 1962 2482 2572057 2572598 9.460000e-146 527.0
8 TraesCS7A01G005900 chr7A 84.630 527 64 10 2711 3226 3572610 3572090 3.430000e-140 508.0
9 TraesCS7A01G005900 chr7A 79.198 524 97 11 31 549 71975528 71976044 1.700000e-93 353.0
10 TraesCS7A01G005900 chr7A 81.455 426 66 8 2711 3130 2579565 2579983 1.710000e-88 337.0
11 TraesCS7A01G005900 chr7A 89.076 238 14 4 550 775 2570258 2570495 6.290000e-73 285.0
12 TraesCS7A01G005900 chr7A 87.273 220 21 5 3629 3846 3321838 3321624 1.070000e-60 244.0
13 TraesCS7A01G005900 chr7A 89.916 119 8 1 2481 2595 2572781 2572899 2.390000e-32 150.0
14 TraesCS7A01G005900 chr7A 90.179 112 11 0 2597 2708 130224613 130224724 3.100000e-31 147.0
15 TraesCS7A01G005900 chr4A 84.729 1552 160 41 968 2479 740872962 740874476 0.000000e+00 1482.0
16 TraesCS7A01G005900 chr4A 84.766 1326 153 28 971 2264 739802768 739801460 0.000000e+00 1284.0
17 TraesCS7A01G005900 chr4A 80.299 1670 223 71 838 2476 739828981 739827387 0.000000e+00 1164.0
18 TraesCS7A01G005900 chr4A 80.519 1504 197 56 989 2476 733931398 733932821 0.000000e+00 1066.0
19 TraesCS7A01G005900 chr4A 86.378 925 92 16 2711 3614 739817527 739816616 0.000000e+00 979.0
20 TraesCS7A01G005900 chr4A 84.375 1024 127 20 989 1987 740065755 740066770 0.000000e+00 974.0
21 TraesCS7A01G005900 chr4A 85.082 972 109 19 968 1919 741971352 741972307 0.000000e+00 959.0
22 TraesCS7A01G005900 chr4A 85.545 927 112 13 989 1912 742274014 742274921 0.000000e+00 950.0
23 TraesCS7A01G005900 chr4A 81.818 880 134 13 2711 3586 733961573 733962430 0.000000e+00 715.0
24 TraesCS7A01G005900 chr4A 86.139 606 51 13 2711 3314 742275919 742276493 1.170000e-174 623.0
25 TraesCS7A01G005900 chr4A 84.058 207 29 2 3641 3843 740893100 740893306 3.030000e-46 196.0
26 TraesCS7A01G005900 chr4A 89.256 121 12 1 2589 2709 599359803 599359684 2.390000e-32 150.0
27 TraesCS7A01G005900 chr7D 88.209 1111 109 10 859 1967 3740464 3741554 0.000000e+00 1306.0
28 TraesCS7A01G005900 chr7D 86.703 910 98 10 2711 3606 3755310 3756210 0.000000e+00 989.0
29 TraesCS7A01G005900 chr7D 83.090 1029 142 16 971 1992 3435071 3434068 0.000000e+00 907.0
30 TraesCS7A01G005900 chr7D 84.452 894 96 20 2711 3598 3769760 3768904 0.000000e+00 841.0
31 TraesCS7A01G005900 chr7D 84.597 422 34 14 2085 2482 3742120 3742534 1.300000e-104 390.0
32 TraesCS7A01G005900 chr7D 87.815 238 17 4 550 775 3740212 3740449 6.330000e-68 268.0
33 TraesCS7A01G005900 chr7D 90.756 119 7 1 2481 2595 3742722 3742840 5.140000e-34 156.0
34 TraesCS7A01G005900 chr7D 90.991 111 10 0 2599 2709 173608828 173608718 2.390000e-32 150.0
35 TraesCS7A01G005900 chr3A 96.903 549 14 1 1 549 733287037 733287582 0.000000e+00 917.0
36 TraesCS7A01G005900 chr3A 88.544 515 42 6 14 527 10345745 10346243 3.290000e-170 608.0
37 TraesCS7A01G005900 chrUn 83.754 911 135 7 975 1879 23779951 23780854 0.000000e+00 850.0
38 TraesCS7A01G005900 chrUn 83.754 911 135 7 975 1879 291094408 291095311 0.000000e+00 850.0
39 TraesCS7A01G005900 chrUn 80.217 460 72 11 2711 3158 23781865 23782317 1.030000e-85 327.0
40 TraesCS7A01G005900 chrUn 80.217 460 72 11 2711 3158 291096322 291096774 1.030000e-85 327.0
41 TraesCS7A01G005900 chrUn 91.150 113 10 0 2597 2709 76192484 76192596 1.850000e-33 154.0
42 TraesCS7A01G005900 chrUn 77.863 131 27 2 3653 3782 90512000 90511871 3.190000e-11 80.5
43 TraesCS7A01G005900 chrUn 80.233 86 15 2 3653 3737 368737092 368737008 3.210000e-06 63.9
44 TraesCS7A01G005900 chr7B 81.785 549 86 11 4 549 604776785 604777322 7.580000e-122 448.0
45 TraesCS7A01G005900 chr7B 80.072 552 95 14 3 549 623569046 623569587 2.780000e-106 396.0
46 TraesCS7A01G005900 chr7B 89.686 223 17 6 213 433 747804087 747804305 2.930000e-71 279.0
47 TraesCS7A01G005900 chr7B 89.381 113 12 0 2597 2709 173991599 173991711 4.010000e-30 143.0
48 TraesCS7A01G005900 chr2B 79.891 552 96 14 3 549 717580840 717581381 1.300000e-104 390.0
49 TraesCS7A01G005900 chr5D 80.350 514 88 12 41 549 426779219 426778714 1.010000e-100 377.0
50 TraesCS7A01G005900 chr3D 78.662 553 104 13 3 550 585931765 585932308 4.730000e-94 355.0
51 TraesCS7A01G005900 chr2A 93.651 126 6 2 426 550 778633002 778632878 1.820000e-43 187.0
52 TraesCS7A01G005900 chr4B 82.096 229 19 16 342 561 429680303 429680088 3.950000e-40 176.0
53 TraesCS7A01G005900 chr4B 89.381 113 12 0 2597 2709 117779875 117779987 4.010000e-30 143.0
54 TraesCS7A01G005900 chr2D 93.805 113 6 1 2597 2709 188519258 188519369 6.610000e-38 169.0
55 TraesCS7A01G005900 chr2D 90.265 113 11 0 2597 2709 405409164 405409276 8.610000e-32 148.0
56 TraesCS7A01G005900 chr5B 91.892 111 9 0 2599 2709 382911260 382911150 5.140000e-34 156.0


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 TraesCS7A01G005900 chr7A 2858965 2862810 3845 False 7103.0 7103 100.00000 1 3846 1 chr7A.!!$F1 3845
1 TraesCS7A01G005900 chr7A 3009841 3010721 880 False 1038.0 1038 87.97800 2711 3595 1 chr7A.!!$F2 884
2 TraesCS7A01G005900 chr7A 3628654 3629531 877 True 1029.0 1029 87.86500 2711 3595 1 chr7A.!!$R2 884
3 TraesCS7A01G005900 chr7A 3321624 3324707 3083 True 695.0 987 85.53600 943 3846 3 chr7A.!!$R3 2903
4 TraesCS7A01G005900 chr7A 2570258 2572899 2641 False 574.0 1334 88.12825 550 2595 4 chr7A.!!$F5 2045
5 TraesCS7A01G005900 chr7A 3572090 3572610 520 True 508.0 508 84.63000 2711 3226 1 chr7A.!!$R1 515
6 TraesCS7A01G005900 chr7A 2579565 2580374 809 False 473.5 610 84.45400 2711 3596 2 chr7A.!!$F6 885
7 TraesCS7A01G005900 chr7A 71975528 71976044 516 False 353.0 353 79.19800 31 549 1 chr7A.!!$F3 518
8 TraesCS7A01G005900 chr4A 740872962 740874476 1514 False 1482.0 1482 84.72900 968 2479 1 chr4A.!!$F4 1511
9 TraesCS7A01G005900 chr4A 739801460 739802768 1308 True 1284.0 1284 84.76600 971 2264 1 chr4A.!!$R2 1293
10 TraesCS7A01G005900 chr4A 739827387 739828981 1594 True 1164.0 1164 80.29900 838 2476 1 chr4A.!!$R4 1638
11 TraesCS7A01G005900 chr4A 733931398 733932821 1423 False 1066.0 1066 80.51900 989 2476 1 chr4A.!!$F1 1487
12 TraesCS7A01G005900 chr4A 739816616 739817527 911 True 979.0 979 86.37800 2711 3614 1 chr4A.!!$R3 903
13 TraesCS7A01G005900 chr4A 740065755 740066770 1015 False 974.0 974 84.37500 989 1987 1 chr4A.!!$F3 998
14 TraesCS7A01G005900 chr4A 741971352 741972307 955 False 959.0 959 85.08200 968 1919 1 chr4A.!!$F6 951
15 TraesCS7A01G005900 chr4A 742274014 742276493 2479 False 786.5 950 85.84200 989 3314 2 chr4A.!!$F7 2325
16 TraesCS7A01G005900 chr4A 733961573 733962430 857 False 715.0 715 81.81800 2711 3586 1 chr4A.!!$F2 875
17 TraesCS7A01G005900 chr7D 3755310 3756210 900 False 989.0 989 86.70300 2711 3606 1 chr7D.!!$F1 895
18 TraesCS7A01G005900 chr7D 3434068 3435071 1003 True 907.0 907 83.09000 971 1992 1 chr7D.!!$R1 1021
19 TraesCS7A01G005900 chr7D 3768904 3769760 856 True 841.0 841 84.45200 2711 3598 1 chr7D.!!$R2 887
20 TraesCS7A01G005900 chr7D 3740212 3742840 2628 False 530.0 1306 87.84425 550 2595 4 chr7D.!!$F2 2045
21 TraesCS7A01G005900 chr3A 733287037 733287582 545 False 917.0 917 96.90300 1 549 1 chr3A.!!$F2 548
22 TraesCS7A01G005900 chrUn 23779951 23782317 2366 False 588.5 850 81.98550 975 3158 2 chrUn.!!$F2 2183
23 TraesCS7A01G005900 chrUn 291094408 291096774 2366 False 588.5 850 81.98550 975 3158 2 chrUn.!!$F3 2183
24 TraesCS7A01G005900 chr7B 604776785 604777322 537 False 448.0 448 81.78500 4 549 1 chr7B.!!$F2 545
25 TraesCS7A01G005900 chr7B 623569046 623569587 541 False 396.0 396 80.07200 3 549 1 chr7B.!!$F3 546
26 TraesCS7A01G005900 chr2B 717580840 717581381 541 False 390.0 390 79.89100 3 549 1 chr2B.!!$F1 546
27 TraesCS7A01G005900 chr5D 426778714 426779219 505 True 377.0 377 80.35000 41 549 1 chr5D.!!$R1 508
28 TraesCS7A01G005900 chr3D 585931765 585932308 543 False 355.0 355 78.66200 3 550 1 chr3D.!!$F1 547

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
970 1001 0.104487 GTAGCTAGGCCCGTTCCTTC 59.896 60.0 0.00 0.0 37.66 3.46 F
1590 1672 0.622136 TCAGAATGGTGCAGCCTCAT 59.378 50.0 14.36 0.0 38.35 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2706 4045 1.066787 GGGACATATCTCTTAGCCCGC 60.067 57.143 0.0 0.0 0.00 6.13 R
3383 4927 0.179094 TTCGCCACCCGTGTATCATC 60.179 55.000 0.0 0.0 38.35 2.92 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
253 255 2.433318 GTCGCCTTCGCTGCTTCT 60.433 61.111 0.00 0.00 35.26 2.85
254 256 2.029844 GTCGCCTTCGCTGCTTCTT 61.030 57.895 0.00 0.00 35.26 2.52
335 339 0.767998 CCCCTTCTGATTAGAGCCCC 59.232 60.000 0.00 0.00 33.70 5.80
562 567 2.659063 CCTGACATCCACCTGCCGA 61.659 63.158 0.00 0.00 0.00 5.54
585 590 3.322254 CCGGCACTCTATTCTTGGAGTAT 59.678 47.826 0.00 0.00 41.31 2.12
619 624 7.987750 AAGGAGAAAAGAATAGTCTTGTTCC 57.012 36.000 16.64 16.64 43.59 3.62
645 650 7.523293 TTTACTCAAGGAAATGAAAGCATCA 57.477 32.000 0.00 0.00 43.67 3.07
668 673 3.766591 TGTTCCTTGTCCTTGCTTTTTCA 59.233 39.130 0.00 0.00 0.00 2.69
694 708 8.595362 AAAGGAAAAGGAAAAGAAGAAGAAGA 57.405 30.769 0.00 0.00 0.00 2.87
696 710 8.175925 AGGAAAAGGAAAAGAAGAAGAAGATG 57.824 34.615 0.00 0.00 0.00 2.90
697 711 7.782168 AGGAAAAGGAAAAGAAGAAGAAGATGT 59.218 33.333 0.00 0.00 0.00 3.06
708 722 5.948992 AGAAGAAGATGTTAAGCAACCAC 57.051 39.130 0.00 0.00 33.41 4.16
710 724 3.421844 AGAAGATGTTAAGCAACCACCC 58.578 45.455 0.00 0.00 33.41 4.61
711 725 2.215942 AGATGTTAAGCAACCACCCC 57.784 50.000 0.00 0.00 33.41 4.95
712 726 1.710809 AGATGTTAAGCAACCACCCCT 59.289 47.619 0.00 0.00 33.41 4.79
713 727 1.818674 GATGTTAAGCAACCACCCCTG 59.181 52.381 0.00 0.00 33.41 4.45
714 728 0.825840 TGTTAAGCAACCACCCCTGC 60.826 55.000 0.00 0.00 38.91 4.85
777 794 4.817987 GCACGTGGCACTATATATAACG 57.182 45.455 18.88 10.80 43.97 3.18
778 795 4.478699 GCACGTGGCACTATATATAACGA 58.521 43.478 18.88 0.00 43.97 3.85
780 797 4.855388 CACGTGGCACTATATATAACGACC 59.145 45.833 16.72 7.16 33.96 4.79
781 798 4.520111 ACGTGGCACTATATATAACGACCA 59.480 41.667 16.72 9.15 33.96 4.02
782 799 5.184479 ACGTGGCACTATATATAACGACCAT 59.816 40.000 16.72 0.00 33.96 3.55
783 800 6.097356 CGTGGCACTATATATAACGACCATT 58.903 40.000 16.72 0.00 0.00 3.16
784 801 6.252869 CGTGGCACTATATATAACGACCATTC 59.747 42.308 16.72 0.00 0.00 2.67
785 802 7.321153 GTGGCACTATATATAACGACCATTCT 58.679 38.462 11.13 0.00 0.00 2.40
786 803 7.817962 GTGGCACTATATATAACGACCATTCTT 59.182 37.037 11.13 0.00 0.00 2.52
787 804 8.033038 TGGCACTATATATAACGACCATTCTTC 58.967 37.037 0.00 0.00 0.00 2.87
788 805 8.251721 GGCACTATATATAACGACCATTCTTCT 58.748 37.037 0.00 0.00 0.00 2.85
789 806 9.291664 GCACTATATATAACGACCATTCTTCTC 57.708 37.037 0.00 0.00 0.00 2.87
807 824 2.102420 TCTCTGTCCGCTTTCAAGACAA 59.898 45.455 0.00 0.00 39.86 3.18
810 827 2.872245 CTGTCCGCTTTCAAGACAAAGA 59.128 45.455 0.00 0.00 39.86 2.52
811 828 3.275143 TGTCCGCTTTCAAGACAAAGAA 58.725 40.909 0.00 0.00 37.58 2.52
813 830 2.616842 TCCGCTTTCAAGACAAAGAACC 59.383 45.455 0.00 0.00 35.67 3.62
814 831 2.287608 CCGCTTTCAAGACAAAGAACCC 60.288 50.000 0.00 0.00 35.67 4.11
815 832 2.618709 CGCTTTCAAGACAAAGAACCCT 59.381 45.455 0.00 0.00 35.67 4.34
816 833 3.066760 CGCTTTCAAGACAAAGAACCCTT 59.933 43.478 0.00 0.00 35.67 3.95
817 834 4.440112 CGCTTTCAAGACAAAGAACCCTTT 60.440 41.667 0.00 0.00 42.98 3.11
818 835 5.419542 GCTTTCAAGACAAAGAACCCTTTT 58.580 37.500 0.00 0.00 40.42 2.27
819 836 6.569780 GCTTTCAAGACAAAGAACCCTTTTA 58.430 36.000 0.00 0.00 40.42 1.52
820 837 7.210174 GCTTTCAAGACAAAGAACCCTTTTAT 58.790 34.615 0.00 0.00 40.42 1.40
821 838 7.382488 GCTTTCAAGACAAAGAACCCTTTTATC 59.618 37.037 0.00 0.00 40.42 1.75
822 839 8.533569 TTTCAAGACAAAGAACCCTTTTATCT 57.466 30.769 0.00 0.00 40.42 1.98
823 840 7.745620 TCAAGACAAAGAACCCTTTTATCTC 57.254 36.000 0.00 0.00 40.42 2.75
824 841 7.287061 TCAAGACAAAGAACCCTTTTATCTCA 58.713 34.615 0.00 0.00 40.42 3.27
825 842 7.944554 TCAAGACAAAGAACCCTTTTATCTCAT 59.055 33.333 0.00 0.00 40.42 2.90
826 843 7.693969 AGACAAAGAACCCTTTTATCTCATG 57.306 36.000 0.00 0.00 40.42 3.07
827 844 6.660949 AGACAAAGAACCCTTTTATCTCATGG 59.339 38.462 0.00 0.00 40.42 3.66
828 845 5.185828 ACAAAGAACCCTTTTATCTCATGGC 59.814 40.000 0.00 0.00 40.42 4.40
829 846 4.870021 AGAACCCTTTTATCTCATGGCT 57.130 40.909 0.00 0.00 0.00 4.75
830 847 4.530875 AGAACCCTTTTATCTCATGGCTG 58.469 43.478 0.00 0.00 0.00 4.85
831 848 3.303351 ACCCTTTTATCTCATGGCTGG 57.697 47.619 0.00 0.00 0.00 4.85
832 849 2.852449 ACCCTTTTATCTCATGGCTGGA 59.148 45.455 0.00 0.00 0.00 3.86
833 850 3.117738 ACCCTTTTATCTCATGGCTGGAG 60.118 47.826 0.00 0.35 0.00 3.86
834 851 3.117738 CCCTTTTATCTCATGGCTGGAGT 60.118 47.826 0.00 0.00 34.04 3.85
835 852 4.133078 CCTTTTATCTCATGGCTGGAGTC 58.867 47.826 0.00 0.00 34.04 3.36
836 853 3.845781 TTTATCTCATGGCTGGAGTCC 57.154 47.619 0.73 0.73 34.04 3.85
852 869 4.899433 GAGTCCATCTCCACGTTCCACG 62.899 59.091 0.00 0.00 41.23 4.94
865 882 2.683968 GTTCCACGCAGATAGACACAA 58.316 47.619 0.00 0.00 0.00 3.33
867 884 3.610040 TCCACGCAGATAGACACAATT 57.390 42.857 0.00 0.00 0.00 2.32
868 885 3.521560 TCCACGCAGATAGACACAATTC 58.478 45.455 0.00 0.00 0.00 2.17
934 965 0.179192 CACACACACACACACACAGC 60.179 55.000 0.00 0.00 0.00 4.40
941 972 2.120282 CACACACACAGCAGGCCAA 61.120 57.895 5.01 0.00 0.00 4.52
967 998 2.416260 CGTAGCTAGGCCCGTTCC 59.584 66.667 0.00 0.00 0.00 3.62
969 1000 1.673808 CGTAGCTAGGCCCGTTCCTT 61.674 60.000 0.00 0.00 37.66 3.36
970 1001 0.104487 GTAGCTAGGCCCGTTCCTTC 59.896 60.000 0.00 0.00 37.66 3.46
972 1003 1.153349 GCTAGGCCCGTTCCTTCAG 60.153 63.158 0.00 0.00 37.66 3.02
973 1004 1.153349 CTAGGCCCGTTCCTTCAGC 60.153 63.158 0.00 0.00 37.66 4.26
1086 1128 2.047655 CTGGGCGGCGACTACAAA 60.048 61.111 14.66 0.00 0.00 2.83
1094 1136 2.524300 GCGACTACAAACTTCGGCA 58.476 52.632 0.00 0.00 33.28 5.69
1236 1278 2.359214 GCTGGATCTCGCCGATGATATA 59.641 50.000 0.00 0.00 30.84 0.86
1287 1329 2.439156 GAGCCCAGCCGCAGAAAT 60.439 61.111 0.00 0.00 0.00 2.17
1346 1394 4.013050 CCCTTCCAAGATTTCAGGAGAAC 58.987 47.826 0.00 0.00 32.39 3.01
1353 1401 5.872070 CCAAGATTTCAGGAGAACAGTAGAC 59.128 44.000 0.00 0.00 32.39 2.59
1356 1404 4.768130 TTTCAGGAGAACAGTAGACGAG 57.232 45.455 0.00 0.00 32.39 4.18
1445 1497 5.607119 TTATTCTCAAGAAAGAACGCCAC 57.393 39.130 0.00 0.00 38.06 5.01
1448 1500 4.265904 TCTCAAGAAAGAACGCCACATA 57.734 40.909 0.00 0.00 0.00 2.29
1452 1504 3.678056 AGAAAGAACGCCACATACAGA 57.322 42.857 0.00 0.00 0.00 3.41
1562 1629 4.346418 CCTCATCAAATACCTGCTAGGAGT 59.654 45.833 10.65 1.38 37.67 3.85
1566 1636 6.265649 TCATCAAATACCTGCTAGGAGTAGAC 59.734 42.308 10.65 0.00 37.67 2.59
1571 1647 2.440253 ACCTGCTAGGAGTAGACGAGAT 59.560 50.000 10.65 0.00 37.67 2.75
1587 1669 0.917533 AGATCAGAATGGTGCAGCCT 59.082 50.000 14.36 0.00 38.35 4.58
1590 1672 0.622136 TCAGAATGGTGCAGCCTCAT 59.378 50.000 14.36 0.00 38.35 2.90
1684 1778 6.020121 GCATGAGGACATTCAAAATCATTTCG 60.020 38.462 0.00 0.00 34.15 3.46
1746 1840 5.407407 TGAAGGAGGTTCTCACAAGTATC 57.593 43.478 0.00 0.00 35.99 2.24
1806 1900 5.070981 CCAAGCAAGGACAGAGGAAGATATA 59.929 44.000 0.00 0.00 0.00 0.86
1862 1956 5.400066 AGGTGCGCAAATTTATAAAAGGT 57.600 34.783 14.00 0.00 0.00 3.50
1913 2040 1.074566 CCTATGAGGGCCAGGATTTCC 59.925 57.143 6.18 0.00 0.00 3.13
1962 2092 8.623310 TTTGAAAAACTAATTCGGTCAAGTTC 57.377 30.769 0.00 0.00 31.15 3.01
2019 2838 6.454795 TGTGGATTTTGGCAAATAAGAAGTC 58.545 36.000 14.29 0.00 32.35 3.01
2044 2869 1.977854 TCTATATGAAGCCGGCCATGT 59.022 47.619 26.15 20.30 0.00 3.21
2127 2955 6.613271 ACTCCAGGTAGTTATCAATCTGATGT 59.387 38.462 0.00 0.00 37.70 3.06
2128 2956 7.785028 ACTCCAGGTAGTTATCAATCTGATGTA 59.215 37.037 0.00 0.00 37.70 2.29
2129 2957 8.547481 TCCAGGTAGTTATCAATCTGATGTAA 57.453 34.615 0.00 0.00 37.70 2.41
2130 2958 9.159254 TCCAGGTAGTTATCAATCTGATGTAAT 57.841 33.333 0.00 0.00 37.70 1.89
2154 2982 2.303175 AGATCCGAACTCTAGGCTCAC 58.697 52.381 0.00 0.00 0.00 3.51
2164 3009 5.234466 ACTCTAGGCTCACAGACAAAAAT 57.766 39.130 0.00 0.00 0.00 1.82
2200 3045 9.243637 TGCAGCAGTAACTATTTTAACTTTTTG 57.756 29.630 0.00 0.00 0.00 2.44
2221 3066 6.647334 TTGGCACATTTTCTGTTTGAGATA 57.353 33.333 0.00 0.00 39.30 1.98
2250 3095 6.878923 TCAGATAACCAAATCTCACGTTCATT 59.121 34.615 0.00 0.00 33.87 2.57
2430 3386 7.237209 AGCAAAGAAAAGGCTTCAGATTTAT 57.763 32.000 0.00 0.00 33.21 1.40
2499 3834 4.324267 CCGGAATAGGAAGAACAACAACT 58.676 43.478 0.00 0.00 0.00 3.16
2501 3836 4.994852 CGGAATAGGAAGAACAACAACTCA 59.005 41.667 0.00 0.00 0.00 3.41
2562 3901 6.759497 AATAACTTCAGCTTGGTGTATTCC 57.241 37.500 0.00 0.00 0.00 3.01
2564 3903 3.679389 ACTTCAGCTTGGTGTATTCCAG 58.321 45.455 0.00 0.00 38.80 3.86
2599 3938 8.766994 AATGTATAAGCACATGAAAATAGGGT 57.233 30.769 0.00 0.00 39.10 4.34
2600 3939 7.566760 TGTATAAGCACATGAAAATAGGGTG 57.433 36.000 0.00 0.00 0.00 4.61
2601 3940 7.342581 TGTATAAGCACATGAAAATAGGGTGA 58.657 34.615 0.00 0.00 0.00 4.02
2602 3941 6.949352 ATAAGCACATGAAAATAGGGTGAG 57.051 37.500 0.00 0.00 0.00 3.51
2603 3942 3.624777 AGCACATGAAAATAGGGTGAGG 58.375 45.455 0.00 0.00 0.00 3.86
2604 3943 2.689983 GCACATGAAAATAGGGTGAGGG 59.310 50.000 0.00 0.00 0.00 4.30
2605 3944 2.689983 CACATGAAAATAGGGTGAGGGC 59.310 50.000 0.00 0.00 0.00 5.19
2606 3945 2.582636 ACATGAAAATAGGGTGAGGGCT 59.417 45.455 0.00 0.00 0.00 5.19
2607 3946 3.011708 ACATGAAAATAGGGTGAGGGCTT 59.988 43.478 0.00 0.00 0.00 4.35
2608 3947 3.825908 TGAAAATAGGGTGAGGGCTTT 57.174 42.857 0.00 0.00 0.00 3.51
2609 3948 4.126520 TGAAAATAGGGTGAGGGCTTTT 57.873 40.909 0.00 0.00 0.00 2.27
2610 3949 3.831911 TGAAAATAGGGTGAGGGCTTTTG 59.168 43.478 0.00 0.00 0.00 2.44
2611 3950 2.532250 AATAGGGTGAGGGCTTTTGG 57.468 50.000 0.00 0.00 0.00 3.28
2612 3951 1.681229 ATAGGGTGAGGGCTTTTGGA 58.319 50.000 0.00 0.00 0.00 3.53
2613 3952 0.991920 TAGGGTGAGGGCTTTTGGAG 59.008 55.000 0.00 0.00 0.00 3.86
2614 3953 1.304464 GGGTGAGGGCTTTTGGAGG 60.304 63.158 0.00 0.00 0.00 4.30
2620 3959 3.443925 GGCTTTTGGAGGCCGAGC 61.444 66.667 0.00 1.32 44.81 5.03
2621 3960 2.360475 GCTTTTGGAGGCCGAGCT 60.360 61.111 0.00 0.00 0.00 4.09
2622 3961 2.402572 GCTTTTGGAGGCCGAGCTC 61.403 63.158 2.73 2.73 0.00 4.09
2623 3962 1.746991 CTTTTGGAGGCCGAGCTCC 60.747 63.158 8.47 0.00 40.05 4.70
2624 3963 2.469465 CTTTTGGAGGCCGAGCTCCA 62.469 60.000 8.47 7.35 46.84 3.86
2639 3978 2.099141 CTCCACGGAGCTCATTTTGA 57.901 50.000 17.19 4.16 35.31 2.69
2640 3979 2.426522 CTCCACGGAGCTCATTTTGAA 58.573 47.619 17.19 0.00 35.31 2.69
2641 3980 2.813754 CTCCACGGAGCTCATTTTGAAA 59.186 45.455 17.19 0.00 35.31 2.69
2642 3981 3.218453 TCCACGGAGCTCATTTTGAAAA 58.782 40.909 17.19 0.00 0.00 2.29
2643 3982 3.826157 TCCACGGAGCTCATTTTGAAAAT 59.174 39.130 17.19 0.00 0.00 1.82
2644 3983 5.007034 TCCACGGAGCTCATTTTGAAAATA 58.993 37.500 17.19 0.00 0.00 1.40
2645 3984 5.095490 CCACGGAGCTCATTTTGAAAATAC 58.905 41.667 17.19 0.00 0.00 1.89
2646 3985 5.335583 CCACGGAGCTCATTTTGAAAATACA 60.336 40.000 17.19 0.00 0.00 2.29
2647 3986 6.148948 CACGGAGCTCATTTTGAAAATACAA 58.851 36.000 17.19 0.00 0.00 2.41
2648 3987 6.640499 CACGGAGCTCATTTTGAAAATACAAA 59.360 34.615 17.19 0.00 37.87 2.83
2649 3988 7.329226 CACGGAGCTCATTTTGAAAATACAAAT 59.671 33.333 17.19 0.00 39.09 2.32
2650 3989 7.872483 ACGGAGCTCATTTTGAAAATACAAATT 59.128 29.630 17.19 0.00 39.09 1.82
2651 3990 8.711457 CGGAGCTCATTTTGAAAATACAAATTT 58.289 29.630 17.19 0.00 39.09 1.82
2654 3993 9.558396 AGCTCATTTTGAAAATACAAATTTCCA 57.442 25.926 2.42 0.00 39.09 3.53
2655 3994 9.597999 GCTCATTTTGAAAATACAAATTTCCAC 57.402 29.630 2.42 0.00 39.09 4.02
2702 4041 8.445275 TTTTGTATACACTTTCAGACATGTGT 57.555 30.769 1.15 0.00 44.46 3.72
2703 4042 9.549078 TTTTGTATACACTTTCAGACATGTGTA 57.451 29.630 1.15 7.18 45.77 2.90
2707 4046 5.362556 ACACTTTCAGACATGTGTATTGC 57.637 39.130 1.15 0.00 41.17 3.56
2709 4048 3.436704 ACTTTCAGACATGTGTATTGCGG 59.563 43.478 1.15 0.00 0.00 5.69
2743 4221 4.803452 TGTCCCTTTTGAGAAGTTGGAAT 58.197 39.130 0.00 0.00 0.00 3.01
2775 4253 5.066505 GGTGTTGGATCTTCAATATCACCAC 59.933 44.000 13.46 5.72 39.28 4.16
2781 4259 5.704515 GGATCTTCAATATCACCACCATCAG 59.295 44.000 0.00 0.00 0.00 2.90
2797 4275 4.992951 ACCATCAGCTTGAATTCAAAAAGC 59.007 37.500 20.82 19.71 45.30 3.51
2803 4281 4.129380 GCTTGAATTCAAAAAGCCTGGTT 58.871 39.130 20.82 0.00 40.32 3.67
2805 4283 4.070630 TGAATTCAAAAAGCCTGGTTGG 57.929 40.909 5.45 0.00 39.35 3.77
2806 4284 3.708631 TGAATTCAAAAAGCCTGGTTGGA 59.291 39.130 5.45 0.00 38.35 3.53
2808 4286 4.769345 ATTCAAAAAGCCTGGTTGGAAA 57.231 36.364 0.00 0.00 38.35 3.13
2838 4367 0.695924 TCGAGGCCCTTGGAAATCAA 59.304 50.000 0.00 0.00 0.00 2.57
2857 4386 9.888878 GAAATCAACATGTGAAGGATATATGTG 57.111 33.333 0.00 0.00 40.50 3.21
2858 4387 7.991084 ATCAACATGTGAAGGATATATGTGG 57.009 36.000 0.00 0.00 40.50 4.17
2859 4388 6.899089 TCAACATGTGAAGGATATATGTGGT 58.101 36.000 0.00 0.00 31.49 4.16
2890 4419 1.264749 TGTGAGGCACCTATTCGGCT 61.265 55.000 0.00 0.00 41.35 5.52
2953 4484 2.574006 TGCAGCATCTGGAGACTTTT 57.426 45.000 0.00 0.00 31.21 2.27
3101 4632 3.431486 GCATTTAGAGACTCTGGACCTGG 60.431 52.174 15.55 0.00 0.00 4.45
3120 4657 1.340991 GGGCTTTAGCACCAGGATCAA 60.341 52.381 3.88 0.00 44.36 2.57
3189 4730 1.436600 CTGCAGTACACCAAGCTCAG 58.563 55.000 5.25 0.00 0.00 3.35
3251 4795 2.933287 TGGAGGTGGGTTCGGCAT 60.933 61.111 0.00 0.00 0.00 4.40
3263 4807 0.327924 TTCGGCATGGATCACAAGGT 59.672 50.000 0.00 0.00 0.00 3.50
3299 4843 1.065126 GGGACCTGCAGCATTTAGAGT 60.065 52.381 8.66 0.00 0.00 3.24
3306 4850 2.019984 GCAGCATTTAGAGTCCTTGGG 58.980 52.381 0.00 0.00 0.00 4.12
3314 4858 1.197430 AGAGTCCTTGGGCCTGAGTG 61.197 60.000 4.53 0.00 0.00 3.51
3315 4859 2.190488 GAGTCCTTGGGCCTGAGTGG 62.190 65.000 4.53 0.00 39.35 4.00
3325 4869 3.116091 CCTGAGTGGCAACTTTGGT 57.884 52.632 0.00 0.00 36.52 3.67
3474 5018 0.657840 GATACCATCGTTGCACTGGC 59.342 55.000 0.00 0.00 41.68 4.85
3497 5041 1.997874 CCCTGGGAAGCTAGCCAGT 60.998 63.158 12.13 0.00 0.00 4.00
3502 5046 0.905357 GGGAAGCTAGCCAGTTCTCA 59.095 55.000 12.13 0.00 0.00 3.27
3505 5049 3.006247 GGAAGCTAGCCAGTTCTCAAAG 58.994 50.000 12.13 0.00 0.00 2.77
3587 5134 2.066999 GCCGGGGAGATCTTGTCCT 61.067 63.158 2.18 0.00 34.16 3.85
3608 5155 1.523032 CGACTGGTTAATCGGGCCC 60.523 63.158 13.57 13.57 34.67 5.80
3609 5156 1.153025 GACTGGTTAATCGGGCCCC 60.153 63.158 18.66 0.00 0.00 5.80
3615 5162 1.411074 GGTTAATCGGGCCCCTGATTT 60.411 52.381 24.69 11.24 46.44 2.17
3616 5163 2.384828 GTTAATCGGGCCCCTGATTTT 58.615 47.619 24.69 9.73 46.44 1.82
3617 5164 2.764010 GTTAATCGGGCCCCTGATTTTT 59.236 45.455 24.69 9.11 46.44 1.94
3618 5165 1.485124 AATCGGGCCCCTGATTTTTC 58.515 50.000 18.66 0.00 46.44 2.29
3619 5166 0.397114 ATCGGGCCCCTGATTTTTCC 60.397 55.000 18.66 0.00 38.80 3.13
3620 5167 2.414785 CGGGCCCCTGATTTTTCCG 61.415 63.158 18.66 0.00 0.00 4.30
3621 5168 1.000145 GGGCCCCTGATTTTTCCGA 60.000 57.895 12.23 0.00 0.00 4.55
3622 5169 0.613572 GGGCCCCTGATTTTTCCGAA 60.614 55.000 12.23 0.00 0.00 4.30
3623 5170 1.262417 GGCCCCTGATTTTTCCGAAA 58.738 50.000 0.00 0.00 0.00 3.46
3624 5171 1.621317 GGCCCCTGATTTTTCCGAAAA 59.379 47.619 2.01 2.01 38.96 2.29
3625 5172 2.353704 GGCCCCTGATTTTTCCGAAAAG 60.354 50.000 6.41 0.00 38.09 2.27
3626 5173 2.930887 GCCCCTGATTTTTCCGAAAAGC 60.931 50.000 6.41 4.50 40.59 3.51
3627 5174 2.595386 CCCTGATTTTTCCGAAAAGCG 58.405 47.619 6.41 0.00 42.51 4.68
3637 5184 3.889780 CGAAAAGCGGGTTAATCGG 57.110 52.632 15.83 0.00 36.03 4.18
3638 5185 0.375803 CGAAAAGCGGGTTAATCGGG 59.624 55.000 15.83 0.00 36.03 5.14
3679 5226 4.320608 AATCGTTGGCAGAAAACACATT 57.679 36.364 0.00 0.00 0.00 2.71
3719 5266 5.005740 TCAAGGATCACTTCAATGACCTTG 58.994 41.667 17.09 17.09 46.22 3.61
3720 5267 3.350833 AGGATCACTTCAATGACCTTGC 58.649 45.455 0.00 0.00 34.66 4.01
3721 5268 2.424956 GGATCACTTCAATGACCTTGCC 59.575 50.000 0.00 0.00 34.66 4.52
3723 5270 4.517285 GATCACTTCAATGACCTTGCCTA 58.483 43.478 0.00 0.00 34.66 3.93
3725 5272 2.749621 CACTTCAATGACCTTGCCTACC 59.250 50.000 0.00 0.00 34.66 3.18
3751 5298 2.099141 TCAGGATTCGCAAACTGGAG 57.901 50.000 0.00 0.00 0.00 3.86
3760 5307 1.604378 CAAACTGGAGGAGCGGGAT 59.396 57.895 0.00 0.00 0.00 3.85
3764 5311 2.519541 TGGAGGAGCGGGATCTCG 60.520 66.667 11.62 11.62 33.98 4.04
3774 5321 0.670706 CGGGATCTCGAGATTCTGCA 59.329 55.000 28.66 1.82 34.37 4.41
3793 5340 1.535685 GGAGATGCCTTGGCTGGAT 59.464 57.895 13.18 0.00 0.00 3.41
3794 5341 0.106318 GGAGATGCCTTGGCTGGATT 60.106 55.000 13.18 0.00 0.00 3.01
3795 5342 1.143684 GGAGATGCCTTGGCTGGATTA 59.856 52.381 13.18 0.00 0.00 1.75
3796 5343 2.224967 GGAGATGCCTTGGCTGGATTAT 60.225 50.000 13.18 0.00 0.00 1.28
3816 5363 2.413837 TCTCACGCTAAGGTTTGAAGC 58.586 47.619 0.00 0.00 0.00 3.86
3818 5365 1.202710 TCACGCTAAGGTTTGAAGCCA 60.203 47.619 0.00 0.00 32.50 4.75
3827 5374 1.821136 GGTTTGAAGCCATCCCAAGAG 59.179 52.381 0.00 0.00 0.00 2.85
3832 5379 2.203126 GCCATCCCAAGAGAGCCG 60.203 66.667 0.00 0.00 0.00 5.52
3843 5390 1.709578 AGAGAGCCGATAGCCATCAA 58.290 50.000 0.00 0.00 45.47 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
437 442 3.243053 TCGCGGTCCCCTTTTCCA 61.243 61.111 6.13 0.00 0.00 3.53
562 567 1.482593 CTCCAAGAATAGAGTGCCGGT 59.517 52.381 1.90 0.00 0.00 5.28
597 602 7.987750 AAGGAACAAGACTATTCTTTTCTCC 57.012 36.000 12.75 9.91 40.34 3.71
619 624 8.084073 TGATGCTTTCATTTCCTTGAGTAAAAG 58.916 33.333 0.00 0.00 31.96 2.27
645 650 4.405358 TGAAAAAGCAAGGACAAGGAACAT 59.595 37.500 0.00 0.00 0.00 2.71
668 673 9.035890 TCTTCTTCTTCTTTTCCTTTTCCTTTT 57.964 29.630 0.00 0.00 0.00 2.27
694 708 1.923356 CAGGGGTGGTTGCTTAACAT 58.077 50.000 0.00 0.00 0.00 2.71
696 710 1.964448 GCAGGGGTGGTTGCTTAAC 59.036 57.895 0.00 0.00 37.35 2.01
697 711 4.511838 GCAGGGGTGGTTGCTTAA 57.488 55.556 0.00 0.00 37.35 1.85
708 722 0.468029 AACTGACAAACCAGCAGGGG 60.468 55.000 0.00 0.00 42.91 4.79
710 724 1.067516 CCAAACTGACAAACCAGCAGG 59.932 52.381 0.00 0.00 37.68 4.85
711 725 1.750778 ACCAAACTGACAAACCAGCAG 59.249 47.619 0.00 0.00 37.68 4.24
712 726 1.476085 CACCAAACTGACAAACCAGCA 59.524 47.619 0.00 0.00 37.68 4.41
713 727 1.802508 GCACCAAACTGACAAACCAGC 60.803 52.381 0.00 0.00 37.68 4.85
714 728 1.750778 AGCACCAAACTGACAAACCAG 59.249 47.619 0.00 0.00 39.93 4.00
775 792 1.202582 CGGACAGAGAAGAATGGTCGT 59.797 52.381 0.00 0.00 0.00 4.34
777 794 1.205893 AGCGGACAGAGAAGAATGGTC 59.794 52.381 0.00 0.00 0.00 4.02
778 795 1.270907 AGCGGACAGAGAAGAATGGT 58.729 50.000 0.00 0.00 0.00 3.55
780 797 3.329386 TGAAAGCGGACAGAGAAGAATG 58.671 45.455 0.00 0.00 0.00 2.67
781 798 3.685139 TGAAAGCGGACAGAGAAGAAT 57.315 42.857 0.00 0.00 0.00 2.40
782 799 3.069586 TCTTGAAAGCGGACAGAGAAGAA 59.930 43.478 0.00 0.00 0.00 2.52
783 800 2.628178 TCTTGAAAGCGGACAGAGAAGA 59.372 45.455 0.00 0.00 0.00 2.87
784 801 2.734079 GTCTTGAAAGCGGACAGAGAAG 59.266 50.000 0.00 0.00 0.00 2.85
785 802 2.102420 TGTCTTGAAAGCGGACAGAGAA 59.898 45.455 0.00 0.00 35.44 2.87
786 803 1.686587 TGTCTTGAAAGCGGACAGAGA 59.313 47.619 0.00 0.00 35.44 3.10
787 804 2.154854 TGTCTTGAAAGCGGACAGAG 57.845 50.000 0.00 0.00 35.44 3.35
788 805 2.613026 TTGTCTTGAAAGCGGACAGA 57.387 45.000 0.00 0.00 40.38 3.41
789 806 2.872245 TCTTTGTCTTGAAAGCGGACAG 59.128 45.455 0.00 0.00 40.38 3.51
790 807 2.912771 TCTTTGTCTTGAAAGCGGACA 58.087 42.857 0.00 0.00 38.07 4.02
791 808 3.548214 GGTTCTTTGTCTTGAAAGCGGAC 60.548 47.826 0.00 0.00 33.63 4.79
792 809 2.616842 GGTTCTTTGTCTTGAAAGCGGA 59.383 45.455 0.00 0.00 33.63 5.54
807 824 4.952335 CAGCCATGAGATAAAAGGGTTCTT 59.048 41.667 0.00 0.00 34.07 2.52
810 827 3.269381 TCCAGCCATGAGATAAAAGGGTT 59.731 43.478 0.00 0.00 0.00 4.11
811 828 2.852449 TCCAGCCATGAGATAAAAGGGT 59.148 45.455 0.00 0.00 0.00 4.34
813 830 4.133078 GACTCCAGCCATGAGATAAAAGG 58.867 47.826 0.00 0.00 33.95 3.11
814 831 4.133078 GGACTCCAGCCATGAGATAAAAG 58.867 47.826 0.00 0.00 33.95 2.27
815 832 3.523157 TGGACTCCAGCCATGAGATAAAA 59.477 43.478 0.00 0.00 33.95 1.52
816 833 3.114606 TGGACTCCAGCCATGAGATAAA 58.885 45.455 0.00 0.00 33.95 1.40
817 834 2.763039 TGGACTCCAGCCATGAGATAA 58.237 47.619 0.00 0.00 33.95 1.75
818 835 2.477104 TGGACTCCAGCCATGAGATA 57.523 50.000 0.00 0.00 33.95 1.98
819 836 1.698532 GATGGACTCCAGCCATGAGAT 59.301 52.381 1.44 0.00 45.81 2.75
820 837 1.126488 GATGGACTCCAGCCATGAGA 58.874 55.000 1.44 0.00 45.81 3.27
821 838 1.070445 GAGATGGACTCCAGCCATGAG 59.930 57.143 9.82 0.00 45.81 2.90
822 839 1.126488 GAGATGGACTCCAGCCATGA 58.874 55.000 9.82 0.00 45.81 3.07
823 840 3.702147 GAGATGGACTCCAGCCATG 57.298 57.895 9.82 0.00 45.81 3.66
831 848 0.895530 TGGAACGTGGAGATGGACTC 59.104 55.000 0.00 0.00 44.24 3.36
832 849 0.608640 GTGGAACGTGGAGATGGACT 59.391 55.000 0.00 0.00 0.00 3.85
833 850 3.139029 GTGGAACGTGGAGATGGAC 57.861 57.895 0.00 0.00 0.00 4.02
852 869 3.190079 TGCGAGAATTGTGTCTATCTGC 58.810 45.455 0.00 0.00 0.00 4.26
911 928 1.136085 GTGTGTGTGTGTGTGTGTGTC 60.136 52.381 0.00 0.00 0.00 3.67
934 965 1.899437 TACGGCTCCTTCTTGGCCTG 61.899 60.000 3.32 0.00 43.29 4.85
962 993 1.294659 GCACTGGAGCTGAAGGAACG 61.295 60.000 0.00 0.00 0.00 3.95
967 998 2.687700 AGTATGCACTGGAGCTGAAG 57.312 50.000 0.00 0.00 32.25 3.02
1075 1117 0.947180 TGCCGAAGTTTGTAGTCGCC 60.947 55.000 0.00 0.00 33.46 5.54
1086 1128 4.052229 CGAGTCCGGTGCCGAAGT 62.052 66.667 12.71 0.00 42.83 3.01
1094 1136 4.052229 CGTCCTTGCGAGTCCGGT 62.052 66.667 0.00 0.00 36.06 5.28
1236 1278 1.443872 GTCGTCGATGGCGTCTTGT 60.444 57.895 4.48 0.00 38.98 3.16
1346 1394 0.171455 GCCTGACACCTCGTCTACTG 59.829 60.000 0.00 0.00 45.60 2.74
1353 1401 2.047844 CACTGGCCTGACACCTCG 60.048 66.667 17.64 0.00 0.00 4.63
1445 1497 0.034186 TTTGCTGGGGGCTCTGTATG 60.034 55.000 0.00 0.00 42.39 2.39
1448 1500 2.116125 GTTTGCTGGGGGCTCTGT 59.884 61.111 0.00 0.00 42.39 3.41
1562 1629 3.023832 TGCACCATTCTGATCTCGTCTA 58.976 45.455 0.00 0.00 0.00 2.59
1566 1636 0.935898 GCTGCACCATTCTGATCTCG 59.064 55.000 0.00 0.00 0.00 4.04
1571 1647 0.622136 ATGAGGCTGCACCATTCTGA 59.378 50.000 0.50 0.00 43.14 3.27
1684 1778 1.228154 ACACAAAAGCCCGGGACTC 60.228 57.895 29.31 6.57 0.00 3.36
1806 1900 4.895297 AGGAAATTTGATATGGCGTGGATT 59.105 37.500 0.00 0.00 0.00 3.01
1893 2014 1.074566 GGAAATCCTGGCCCTCATAGG 59.925 57.143 0.00 0.00 34.30 2.57
2011 2830 7.808381 CGGCTTCATATAGAATTCGACTTCTTA 59.192 37.037 21.29 13.88 36.82 2.10
2019 2838 2.673368 GGCCGGCTTCATATAGAATTCG 59.327 50.000 28.56 0.00 35.25 3.34
2071 2898 9.927081 ATTTGAAGGAAATATAGATGGAACAGT 57.073 29.630 0.00 0.00 35.12 3.55
2127 2955 7.287005 TGAGCCTAGAGTTCGGATCTTTAATTA 59.713 37.037 0.00 0.00 36.68 1.40
2128 2956 6.098409 TGAGCCTAGAGTTCGGATCTTTAATT 59.902 38.462 0.00 0.00 36.68 1.40
2129 2957 5.598830 TGAGCCTAGAGTTCGGATCTTTAAT 59.401 40.000 0.00 0.00 36.68 1.40
2130 2958 4.954202 TGAGCCTAGAGTTCGGATCTTTAA 59.046 41.667 0.00 0.00 36.68 1.52
2154 2982 7.273164 TGCTGCATCGTATTTAATTTTTGTCTG 59.727 33.333 0.00 0.00 0.00 3.51
2164 3009 8.657074 AATAGTTACTGCTGCATCGTATTTAA 57.343 30.769 1.31 0.00 0.00 1.52
2200 3045 7.989826 ACTATATCTCAAACAGAAAATGTGCC 58.010 34.615 0.00 0.00 43.00 5.01
2221 3066 7.113658 ACGTGAGATTTGGTTATCTGACTAT 57.886 36.000 0.00 0.00 36.84 2.12
2459 3510 4.839121 TCCGGCTTTCTGCTTCTAAATTA 58.161 39.130 0.00 0.00 42.39 1.40
2478 3553 4.994852 TGAGTTGTTGTTCTTCCTATTCCG 59.005 41.667 0.00 0.00 0.00 4.30
2484 3819 5.192927 TGTTGATGAGTTGTTGTTCTTCCT 58.807 37.500 0.00 0.00 0.00 3.36
2548 3883 2.571653 TGTAGCTGGAATACACCAAGCT 59.428 45.455 0.00 0.00 42.38 3.74
2562 3901 8.593492 TGTGCTTATACATTATCTTGTAGCTG 57.407 34.615 0.00 0.00 35.65 4.24
2564 3903 9.208022 TCATGTGCTTATACATTATCTTGTAGC 57.792 33.333 0.00 0.00 39.17 3.58
2595 3934 1.770324 CTCCAAAAGCCCTCACCCT 59.230 57.895 0.00 0.00 0.00 4.34
2596 3935 1.304464 CCTCCAAAAGCCCTCACCC 60.304 63.158 0.00 0.00 0.00 4.61
2597 3936 1.979155 GCCTCCAAAAGCCCTCACC 60.979 63.158 0.00 0.00 0.00 4.02
2598 3937 1.979155 GGCCTCCAAAAGCCCTCAC 60.979 63.158 0.00 0.00 43.76 3.51
2599 3938 2.440599 GGCCTCCAAAAGCCCTCA 59.559 61.111 0.00 0.00 43.76 3.86
2603 3942 3.443925 GCTCGGCCTCCAAAAGCC 61.444 66.667 0.00 0.00 46.17 4.35
2604 3943 2.360475 AGCTCGGCCTCCAAAAGC 60.360 61.111 0.00 0.00 0.00 3.51
2605 3944 3.896479 GAGCTCGGCCTCCAAAAG 58.104 61.111 0.00 0.00 0.00 2.27
2620 3959 2.099141 TCAAAATGAGCTCCGTGGAG 57.901 50.000 12.15 11.67 44.56 3.86
2621 3960 2.559698 TTCAAAATGAGCTCCGTGGA 57.440 45.000 12.15 0.00 0.00 4.02
2622 3961 3.641437 TTTTCAAAATGAGCTCCGTGG 57.359 42.857 12.15 0.00 0.00 4.94
2623 3962 5.698832 TGTATTTTCAAAATGAGCTCCGTG 58.301 37.500 12.15 4.03 0.00 4.94
2624 3963 5.957842 TGTATTTTCAAAATGAGCTCCGT 57.042 34.783 12.15 0.00 0.00 4.69
2625 3964 7.816945 ATTTGTATTTTCAAAATGAGCTCCG 57.183 32.000 12.15 0.00 40.05 4.63
2628 3967 9.558396 TGGAAATTTGTATTTTCAAAATGAGCT 57.442 25.926 5.56 0.00 36.51 4.09
2629 3968 9.597999 GTGGAAATTTGTATTTTCAAAATGAGC 57.402 29.630 5.56 0.00 40.17 4.26
2677 4016 8.445275 ACACATGTCTGAAAGTGTATACAAAA 57.555 30.769 7.25 0.00 42.84 2.44
2686 4025 4.397382 CGCAATACACATGTCTGAAAGTG 58.603 43.478 0.00 0.00 37.95 3.16
2688 4027 3.181507 CCCGCAATACACATGTCTGAAAG 60.182 47.826 0.00 0.00 0.00 2.62
2694 4033 1.948104 TAGCCCGCAATACACATGTC 58.052 50.000 0.00 0.00 0.00 3.06
2695 4034 2.093181 TCTTAGCCCGCAATACACATGT 60.093 45.455 0.00 0.00 0.00 3.21
2696 4035 2.545526 CTCTTAGCCCGCAATACACATG 59.454 50.000 0.00 0.00 0.00 3.21
2697 4036 2.434336 TCTCTTAGCCCGCAATACACAT 59.566 45.455 0.00 0.00 0.00 3.21
2699 4038 2.596904 TCTCTTAGCCCGCAATACAC 57.403 50.000 0.00 0.00 0.00 2.90
2700 4039 4.283467 ACATATCTCTTAGCCCGCAATACA 59.717 41.667 0.00 0.00 0.00 2.29
2701 4040 4.822026 ACATATCTCTTAGCCCGCAATAC 58.178 43.478 0.00 0.00 0.00 1.89
2702 4041 4.081642 GGACATATCTCTTAGCCCGCAATA 60.082 45.833 0.00 0.00 0.00 1.90
2703 4042 3.307059 GGACATATCTCTTAGCCCGCAAT 60.307 47.826 0.00 0.00 0.00 3.56
2706 4045 1.066787 GGGACATATCTCTTAGCCCGC 60.067 57.143 0.00 0.00 0.00 6.13
2707 4046 2.530701 AGGGACATATCTCTTAGCCCG 58.469 52.381 0.00 0.00 39.09 6.13
2709 4048 5.930135 TCAAAAGGGACATATCTCTTAGCC 58.070 41.667 0.00 0.00 45.54 3.93
2743 4221 1.599518 GATCCAACACCCGCACACA 60.600 57.895 0.00 0.00 0.00 3.72
2775 4253 4.390909 GGCTTTTTGAATTCAAGCTGATGG 59.609 41.667 23.24 12.04 42.24 3.51
2781 4259 3.732212 ACCAGGCTTTTTGAATTCAAGC 58.268 40.909 19.64 18.95 41.93 4.01
2797 4275 7.319646 TCGAATTCAAAATATTTCCAACCAGG 58.680 34.615 6.22 0.00 39.47 4.45
2803 4281 5.163457 GGGCCTCGAATTCAAAATATTTCCA 60.163 40.000 0.84 0.00 0.00 3.53
2805 4283 6.149129 AGGGCCTCGAATTCAAAATATTTC 57.851 37.500 0.00 0.00 0.00 2.17
2806 4284 6.340522 CAAGGGCCTCGAATTCAAAATATTT 58.659 36.000 6.46 0.00 0.00 1.40
2808 4286 4.342092 CCAAGGGCCTCGAATTCAAAATAT 59.658 41.667 6.46 0.00 0.00 1.28
2838 4367 5.369404 TCCACCACATATATCCTTCACATGT 59.631 40.000 0.00 0.00 0.00 3.21
2857 4386 2.357517 CACACGGAGCAGTCCACC 60.358 66.667 0.00 0.00 44.18 4.61
2858 4387 1.373497 CTCACACGGAGCAGTCCAC 60.373 63.158 0.00 0.00 44.18 4.02
2859 4388 2.574018 CCTCACACGGAGCAGTCCA 61.574 63.158 0.00 0.00 44.18 4.02
2890 4419 4.425772 TCACTGATTCCTGTCCCTTCTAA 58.574 43.478 0.00 0.00 0.00 2.10
2953 4484 5.189539 TGTGATCCATGTGAATCTTACCTGA 59.810 40.000 0.00 0.00 0.00 3.86
3004 4535 2.161211 GTCCAGAGTCTTCAATTGCTGC 59.839 50.000 0.00 0.00 0.00 5.25
3101 4632 2.019984 CTTGATCCTGGTGCTAAAGCC 58.980 52.381 0.00 0.00 41.18 4.35
3120 4657 0.469070 GATCTCATGTGGCAGCTCCT 59.531 55.000 0.00 0.00 35.26 3.69
3263 4807 1.279846 GTCCCCGATTTCACTGGGTAA 59.720 52.381 0.00 0.00 41.63 2.85
3314 4858 1.334869 CTGTGTGAGACCAAAGTTGCC 59.665 52.381 0.00 0.00 0.00 4.52
3315 4859 1.268743 GCTGTGTGAGACCAAAGTTGC 60.269 52.381 0.00 0.00 0.00 4.17
3322 4866 2.104572 GAGGCAGCTGTGTGAGACCA 62.105 60.000 16.64 0.00 0.00 4.02
3325 4869 2.203082 ACGAGGCAGCTGTGTGAGA 61.203 57.895 16.64 0.00 0.00 3.27
3383 4927 0.179094 TTCGCCACCCGTGTATCATC 60.179 55.000 0.00 0.00 38.35 2.92
3473 5017 2.883267 CTAGCTTCCCAGGGCAGTGC 62.883 65.000 6.55 6.55 0.00 4.40
3474 5018 1.222936 CTAGCTTCCCAGGGCAGTG 59.777 63.158 7.04 0.00 0.00 3.66
3475 5019 2.674220 GCTAGCTTCCCAGGGCAGT 61.674 63.158 7.70 0.00 0.00 4.40
3478 5022 3.411517 TGGCTAGCTTCCCAGGGC 61.412 66.667 15.72 0.00 0.00 5.19
3497 5041 2.487265 GCACTCCCTCCAACTTTGAGAA 60.487 50.000 0.00 0.00 0.00 2.87
3587 5134 1.676615 GGCCCGATTAACCAGTCGAAA 60.677 52.381 0.00 0.00 40.11 3.46
3619 5166 0.375803 CCCGATTAACCCGCTTTTCG 59.624 55.000 0.00 0.00 38.08 3.46
3620 5167 0.099968 GCCCGATTAACCCGCTTTTC 59.900 55.000 0.00 0.00 0.00 2.29
3621 5168 1.317431 GGCCCGATTAACCCGCTTTT 61.317 55.000 0.00 0.00 0.00 2.27
3622 5169 1.751544 GGCCCGATTAACCCGCTTT 60.752 57.895 0.00 0.00 0.00 3.51
3623 5170 2.124445 GGCCCGATTAACCCGCTT 60.124 61.111 0.00 0.00 0.00 4.68
3624 5171 3.404438 TGGCCCGATTAACCCGCT 61.404 61.111 0.00 0.00 0.00 5.52
3625 5172 3.206957 GTGGCCCGATTAACCCGC 61.207 66.667 0.00 0.00 0.00 6.13
3626 5173 1.817941 CAGTGGCCCGATTAACCCG 60.818 63.158 0.00 0.00 0.00 5.28
3627 5174 0.182775 ATCAGTGGCCCGATTAACCC 59.817 55.000 0.00 0.00 0.00 4.11
3628 5175 2.767505 CTATCAGTGGCCCGATTAACC 58.232 52.381 0.00 0.00 0.00 2.85
3629 5176 2.143925 GCTATCAGTGGCCCGATTAAC 58.856 52.381 0.00 0.00 0.00 2.01
3630 5177 1.270094 CGCTATCAGTGGCCCGATTAA 60.270 52.381 0.00 0.00 0.00 1.40
3631 5178 0.317160 CGCTATCAGTGGCCCGATTA 59.683 55.000 0.00 0.00 0.00 1.75
3632 5179 1.069765 CGCTATCAGTGGCCCGATT 59.930 57.895 0.00 0.00 0.00 3.34
3633 5180 2.737180 CGCTATCAGTGGCCCGAT 59.263 61.111 0.00 2.05 0.00 4.18
3634 5181 3.536917 CCGCTATCAGTGGCCCGA 61.537 66.667 0.00 0.00 39.28 5.14
3635 5182 4.609018 CCCGCTATCAGTGGCCCG 62.609 72.222 0.00 0.00 44.40 6.13
3636 5183 4.256180 CCCCGCTATCAGTGGCCC 62.256 72.222 0.00 0.00 44.40 5.80
3637 5184 4.256180 CCCCCGCTATCAGTGGCC 62.256 72.222 0.00 0.00 44.40 5.36
3638 5185 4.937431 GCCCCCGCTATCAGTGGC 62.937 72.222 0.01 0.00 44.40 5.01
3694 5241 5.435291 AGGTCATTGAAGTGATCCTTGATC 58.565 41.667 1.70 0.00 39.31 2.92
3725 5272 4.212847 CAGTTTGCGAATCCTGATATCCAG 59.787 45.833 0.00 0.00 42.55 3.86
3740 5287 3.121030 CCGCTCCTCCAGTTTGCG 61.121 66.667 0.00 0.00 45.22 4.85
3751 5298 0.242555 GAATCTCGAGATCCCGCTCC 59.757 60.000 27.43 8.03 32.75 4.70
3760 5307 2.426842 TCTCCTGCAGAATCTCGAGA 57.573 50.000 19.19 19.19 0.00 4.04
3782 5329 2.487934 CGTGAGATAATCCAGCCAAGG 58.512 52.381 0.00 0.00 0.00 3.61
3783 5330 1.869767 GCGTGAGATAATCCAGCCAAG 59.130 52.381 0.00 0.00 0.00 3.61
3784 5331 1.486310 AGCGTGAGATAATCCAGCCAA 59.514 47.619 0.00 0.00 31.83 4.52
3785 5332 1.123077 AGCGTGAGATAATCCAGCCA 58.877 50.000 0.00 0.00 31.83 4.75
3786 5333 3.321497 CTTAGCGTGAGATAATCCAGCC 58.679 50.000 0.00 0.00 41.61 4.85
3788 5335 4.592485 ACCTTAGCGTGAGATAATCCAG 57.408 45.455 0.00 0.00 41.61 3.86
3789 5336 5.105106 TCAAACCTTAGCGTGAGATAATCCA 60.105 40.000 0.00 0.00 41.61 3.41
3790 5337 5.357257 TCAAACCTTAGCGTGAGATAATCC 58.643 41.667 0.00 0.00 41.61 3.01
3793 5340 4.630069 GCTTCAAACCTTAGCGTGAGATAA 59.370 41.667 0.00 0.00 40.03 1.75
3794 5341 4.181578 GCTTCAAACCTTAGCGTGAGATA 58.818 43.478 0.00 0.00 0.00 1.98
3795 5342 3.003480 GCTTCAAACCTTAGCGTGAGAT 58.997 45.455 0.00 0.00 0.00 2.75
3796 5343 2.413837 GCTTCAAACCTTAGCGTGAGA 58.586 47.619 0.00 0.00 0.00 3.27
3816 5363 1.274728 CTATCGGCTCTCTTGGGATGG 59.725 57.143 0.00 0.00 0.00 3.51
3818 5365 0.972883 GCTATCGGCTCTCTTGGGAT 59.027 55.000 0.00 0.00 38.06 3.85
3827 5374 2.522060 CGTTGATGGCTATCGGCTC 58.478 57.895 5.52 0.00 41.46 4.70


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

AutoCloner maintained by Alex Coulton.