Multiple sequence alignment - TraesCS4B01G180400

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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 TraesCS4B01G180400 chr4B 100.000 4111 0 0 1 4111 394645580 394641470 0.000000e+00 7592.0
1 TraesCS4B01G180400 chr4B 100.000 2357 0 0 4284 6640 394641297 394638941 0.000000e+00 4353.0
2 TraesCS4B01G180400 chr4B 86.050 724 68 13 1 699 632335003 632335718 0.000000e+00 747.0
3 TraesCS4B01G180400 chr4B 98.354 243 4 0 5883 6125 394626001 394625759 1.710000e-115 427.0
4 TraesCS4B01G180400 chr4B 91.414 198 12 5 2115 2309 606650607 606650412 3.950000e-67 267.0
5 TraesCS4B01G180400 chr4A 97.823 1837 29 3 2284 4111 157204732 157206566 0.000000e+00 3160.0
6 TraesCS4B01G180400 chr4A 93.580 1620 50 22 4284 5882 157206797 157208383 0.000000e+00 2366.0
7 TraesCS4B01G180400 chr4A 97.312 1302 33 2 822 2123 157203434 157204733 0.000000e+00 2209.0
8 TraesCS4B01G180400 chr4A 86.780 469 45 10 232 684 592311721 592312188 2.140000e-139 507.0
9 TraesCS4B01G180400 chr4A 87.200 125 14 2 4317 4439 743670133 743670257 2.500000e-29 141.0
10 TraesCS4B01G180400 chr4A 86.719 128 13 3 4317 4442 528606330 528606205 8.980000e-29 139.0
11 TraesCS4B01G180400 chr4A 86.719 128 13 3 4317 4442 528646312 528646187 8.980000e-29 139.0
12 TraesCS4B01G180400 chr4D 91.359 1759 94 21 2381 4110 317604666 317602937 0.000000e+00 2353.0
13 TraesCS4B01G180400 chr4D 94.136 1296 50 13 831 2122 317606011 317604738 0.000000e+00 1949.0
14 TraesCS4B01G180400 chr4D 93.562 963 38 8 4929 5882 317601846 317600899 0.000000e+00 1413.0
15 TraesCS4B01G180400 chr4D 95.302 596 20 5 4295 4885 317602432 317601840 0.000000e+00 939.0
16 TraesCS4B01G180400 chr4D 85.446 852 84 20 1 820 69477421 69476578 0.000000e+00 850.0
17 TraesCS4B01G180400 chr4D 95.000 180 7 2 2115 2292 93338034 93338213 1.410000e-71 281.0
18 TraesCS4B01G180400 chr4D 94.944 178 7 2 2114 2289 322107464 322107287 1.820000e-70 278.0
19 TraesCS4B01G180400 chr4D 92.308 195 10 5 2115 2308 333771912 333771722 8.480000e-69 272.0
20 TraesCS4B01G180400 chr4D 95.385 65 3 0 2286 2350 317604736 317604672 3.280000e-18 104.0
21 TraesCS4B01G180400 chr4D 97.826 46 1 0 5325 5370 280308880 280308835 5.520000e-11 80.5
22 TraesCS4B01G180400 chr4D 97.826 46 1 0 5325 5370 294454534 294454579 5.520000e-11 80.5
23 TraesCS4B01G180400 chr2D 93.054 763 36 9 5883 6640 534289840 534289090 0.000000e+00 1099.0
24 TraesCS4B01G180400 chr2D 84.041 871 84 20 1 817 181246932 181247801 0.000000e+00 787.0
25 TraesCS4B01G180400 chr2D 83.673 882 80 33 1 823 55240657 55239781 0.000000e+00 773.0
26 TraesCS4B01G180400 chr2D 84.135 769 92 21 5878 6640 24865989 24866733 0.000000e+00 717.0
27 TraesCS4B01G180400 chr2D 93.833 227 8 4 5883 6107 534284835 534284613 2.970000e-88 337.0
28 TraesCS4B01G180400 chr2D 94.915 177 8 1 2122 2297 196347328 196347504 6.560000e-70 276.0
29 TraesCS4B01G180400 chr2D 95.745 47 2 0 5325 5371 19609756 19609802 7.140000e-10 76.8
30 TraesCS4B01G180400 chr2D 95.745 47 2 0 5325 5371 169966930 169966976 7.140000e-10 76.8
31 TraesCS4B01G180400 chr5A 90.458 765 55 9 5881 6640 638790166 638789415 0.000000e+00 992.0
32 TraesCS4B01G180400 chr5A 93.878 49 1 2 4816 4863 227929904 227929951 9.240000e-09 73.1
33 TraesCS4B01G180400 chr2A 90.183 764 56 12 5883 6640 9354118 9354868 0.000000e+00 977.0
34 TraesCS4B01G180400 chr2A 89.332 778 64 12 5869 6640 12254046 12254810 0.000000e+00 959.0
35 TraesCS4B01G180400 chr2A 82.584 890 94 29 1 850 738967964 738967096 0.000000e+00 728.0
36 TraesCS4B01G180400 chr2A 89.062 256 16 8 5883 6127 9361705 9361959 2.330000e-79 307.0
37 TraesCS4B01G180400 chr2A 88.987 227 22 3 5883 6107 12259046 12259271 1.820000e-70 278.0
38 TraesCS4B01G180400 chr2A 90.164 61 1 2 4794 4854 142713339 142713284 2.570000e-09 75.0
39 TraesCS4B01G180400 chr3A 90.132 760 61 7 5883 6640 596745069 596745816 0.000000e+00 976.0
40 TraesCS4B01G180400 chr3A 83.923 311 34 10 1 307 55712316 55712018 3.920000e-72 283.0
41 TraesCS4B01G180400 chr7B 86.698 857 64 23 3 817 517097274 517098122 0.000000e+00 905.0
42 TraesCS4B01G180400 chr3D 84.114 875 79 22 1 817 351131318 351132190 0.000000e+00 791.0
43 TraesCS4B01G180400 chr3D 90.058 513 43 3 6126 6638 355421808 355422312 0.000000e+00 658.0
44 TraesCS4B01G180400 chr1D 83.762 856 87 21 1 820 261091286 261090447 0.000000e+00 763.0
45 TraesCS4B01G180400 chr1D 90.179 112 10 1 4315 4426 48024731 48024621 1.930000e-30 145.0
46 TraesCS4B01G180400 chr6B 85.286 768 75 20 5877 6640 711497915 711498648 0.000000e+00 758.0
47 TraesCS4B01G180400 chr6B 85.283 761 77 18 5883 6640 56438653 56439381 0.000000e+00 752.0
48 TraesCS4B01G180400 chr6B 83.030 878 93 14 3 831 523889895 523889025 0.000000e+00 745.0
49 TraesCS4B01G180400 chr6B 83.995 756 62 26 1 699 515565751 515564998 0.000000e+00 671.0
50 TraesCS4B01G180400 chr6B 97.778 45 0 1 4812 4855 365708195 365708239 7.140000e-10 76.8
51 TraesCS4B01G180400 chr6B 95.745 47 2 0 5325 5371 710911453 710911499 7.140000e-10 76.8
52 TraesCS4B01G180400 chr1A 83.546 863 80 26 3 817 402275160 402276008 0.000000e+00 750.0
53 TraesCS4B01G180400 chr1A 84.183 765 89 23 5883 6640 12718457 12719196 0.000000e+00 713.0
54 TraesCS4B01G180400 chr1A 89.912 228 19 4 5883 6107 5150590 5150816 2.340000e-74 291.0
55 TraesCS4B01G180400 chr1A 80.216 278 43 8 555 823 28909476 28909202 1.460000e-46 198.0
56 TraesCS4B01G180400 chr1A 90.909 110 9 1 4317 4426 489400704 489400812 5.370000e-31 147.0
57 TraesCS4B01G180400 chr1A 100.000 30 0 0 4754 4783 473033753 473033782 1.000000e-03 56.5
58 TraesCS4B01G180400 chr1A 100.000 28 0 0 4757 4784 445501418 445501391 1.200000e-02 52.8
59 TraesCS4B01G180400 chr7D 84.896 768 83 22 5883 6640 52610156 52610900 0.000000e+00 745.0
60 TraesCS4B01G180400 chrUn 84.183 765 89 23 5883 6640 336792896 336793635 0.000000e+00 713.0
61 TraesCS4B01G180400 chr5B 84.115 768 86 26 5881 6640 411654480 411653741 0.000000e+00 710.0
62 TraesCS4B01G180400 chr5B 81.941 371 44 11 427 775 28226201 28226570 6.510000e-75 292.0
63 TraesCS4B01G180400 chr5B 92.593 189 12 2 2102 2289 554990352 554990539 3.050000e-68 270.0
64 TraesCS4B01G180400 chr5B 87.200 125 14 2 4317 4439 569341393 569341269 2.500000e-29 141.0
65 TraesCS4B01G180400 chr5B 92.157 51 4 0 5325 5375 127870281 127870231 9.240000e-09 73.1
66 TraesCS4B01G180400 chr5B 83.562 73 9 3 5298 5370 499167809 499167740 1.550000e-06 65.8
67 TraesCS4B01G180400 chr7A 84.252 762 77 14 4 724 412913486 412912727 0.000000e+00 702.0
68 TraesCS4B01G180400 chr7A 83.805 778 75 30 5883 6640 126179420 126180166 0.000000e+00 691.0
69 TraesCS4B01G180400 chr7A 85.304 313 31 11 1 305 21207828 21208133 6.470000e-80 309.0
70 TraesCS4B01G180400 chr7A 94.944 178 6 3 2114 2288 320981346 320981169 6.560000e-70 276.0
71 TraesCS4B01G180400 chr7A 93.443 183 10 2 2118 2300 541437987 541438167 3.050000e-68 270.0
72 TraesCS4B01G180400 chr5D 83.833 767 89 24 5883 6640 390710147 390710887 0.000000e+00 697.0
73 TraesCS4B01G180400 chr5D 80.742 862 86 34 1 817 70386281 70387107 3.430000e-167 599.0
74 TraesCS4B01G180400 chr1B 83.034 725 69 14 4 679 212437495 212436776 5.690000e-170 608.0
75 TraesCS4B01G180400 chr1B 89.565 115 10 2 4310 4424 576362082 576361970 1.930000e-30 145.0
76 TraesCS4B01G180400 chr2B 90.200 449 36 2 6192 6640 794454091 794453651 4.460000e-161 579.0
77 TraesCS4B01G180400 chr2B 97.727 44 0 1 4812 4854 373758737 373758694 2.570000e-09 75.0
78 TraesCS4B01G180400 chr6A 79.350 862 92 30 1 801 503244845 503245681 1.640000e-145 527.0
79 TraesCS4B01G180400 chr6A 97.727 44 0 1 4812 4854 262044765 262044722 2.570000e-09 75.0
80 TraesCS4B01G180400 chr6A 93.750 48 1 2 4815 4861 558616823 558616777 3.320000e-08 71.3
81 TraesCS4B01G180400 chr6D 79.107 627 84 27 227 817 54790335 54790950 8.070000e-104 388.0
82 TraesCS4B01G180400 chr6D 95.954 173 5 2 2119 2289 392896972 392897144 5.070000e-71 279.0
83 TraesCS4B01G180400 chr6D 97.727 44 0 1 4812 4854 221214302 221214259 2.570000e-09 75.0


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 TraesCS4B01G180400 chr4B 394638941 394645580 6639 True 5972.500000 7592 100.000000 1 6640 2 chr4B.!!$R3 6639
1 TraesCS4B01G180400 chr4B 632335003 632335718 715 False 747.000000 747 86.050000 1 699 1 chr4B.!!$F1 698
2 TraesCS4B01G180400 chr4A 157203434 157208383 4949 False 2578.333333 3160 96.238333 822 5882 3 chr4A.!!$F3 5060
3 TraesCS4B01G180400 chr4D 317600899 317606011 5112 True 1351.600000 2353 93.948800 831 5882 5 chr4D.!!$R5 5051
4 TraesCS4B01G180400 chr4D 69476578 69477421 843 True 850.000000 850 85.446000 1 820 1 chr4D.!!$R1 819
5 TraesCS4B01G180400 chr2D 534289090 534289840 750 True 1099.000000 1099 93.054000 5883 6640 1 chr2D.!!$R3 757
6 TraesCS4B01G180400 chr2D 181246932 181247801 869 False 787.000000 787 84.041000 1 817 1 chr2D.!!$F4 816
7 TraesCS4B01G180400 chr2D 55239781 55240657 876 True 773.000000 773 83.673000 1 823 1 chr2D.!!$R1 822
8 TraesCS4B01G180400 chr2D 24865989 24866733 744 False 717.000000 717 84.135000 5878 6640 1 chr2D.!!$F2 762
9 TraesCS4B01G180400 chr5A 638789415 638790166 751 True 992.000000 992 90.458000 5881 6640 1 chr5A.!!$R1 759
10 TraesCS4B01G180400 chr2A 9354118 9354868 750 False 977.000000 977 90.183000 5883 6640 1 chr2A.!!$F1 757
11 TraesCS4B01G180400 chr2A 12254046 12254810 764 False 959.000000 959 89.332000 5869 6640 1 chr2A.!!$F3 771
12 TraesCS4B01G180400 chr2A 738967096 738967964 868 True 728.000000 728 82.584000 1 850 1 chr2A.!!$R2 849
13 TraesCS4B01G180400 chr3A 596745069 596745816 747 False 976.000000 976 90.132000 5883 6640 1 chr3A.!!$F1 757
14 TraesCS4B01G180400 chr7B 517097274 517098122 848 False 905.000000 905 86.698000 3 817 1 chr7B.!!$F1 814
15 TraesCS4B01G180400 chr3D 351131318 351132190 872 False 791.000000 791 84.114000 1 817 1 chr3D.!!$F1 816
16 TraesCS4B01G180400 chr3D 355421808 355422312 504 False 658.000000 658 90.058000 6126 6638 1 chr3D.!!$F2 512
17 TraesCS4B01G180400 chr1D 261090447 261091286 839 True 763.000000 763 83.762000 1 820 1 chr1D.!!$R2 819
18 TraesCS4B01G180400 chr6B 711497915 711498648 733 False 758.000000 758 85.286000 5877 6640 1 chr6B.!!$F4 763
19 TraesCS4B01G180400 chr6B 56438653 56439381 728 False 752.000000 752 85.283000 5883 6640 1 chr6B.!!$F1 757
20 TraesCS4B01G180400 chr6B 523889025 523889895 870 True 745.000000 745 83.030000 3 831 1 chr6B.!!$R2 828
21 TraesCS4B01G180400 chr6B 515564998 515565751 753 True 671.000000 671 83.995000 1 699 1 chr6B.!!$R1 698
22 TraesCS4B01G180400 chr1A 402275160 402276008 848 False 750.000000 750 83.546000 3 817 1 chr1A.!!$F3 814
23 TraesCS4B01G180400 chr1A 12718457 12719196 739 False 713.000000 713 84.183000 5883 6640 1 chr1A.!!$F2 757
24 TraesCS4B01G180400 chr7D 52610156 52610900 744 False 745.000000 745 84.896000 5883 6640 1 chr7D.!!$F1 757
25 TraesCS4B01G180400 chrUn 336792896 336793635 739 False 713.000000 713 84.183000 5883 6640 1 chrUn.!!$F1 757
26 TraesCS4B01G180400 chr5B 411653741 411654480 739 True 710.000000 710 84.115000 5881 6640 1 chr5B.!!$R2 759
27 TraesCS4B01G180400 chr7A 412912727 412913486 759 True 702.000000 702 84.252000 4 724 1 chr7A.!!$R2 720
28 TraesCS4B01G180400 chr7A 126179420 126180166 746 False 691.000000 691 83.805000 5883 6640 1 chr7A.!!$F2 757
29 TraesCS4B01G180400 chr5D 390710147 390710887 740 False 697.000000 697 83.833000 5883 6640 1 chr5D.!!$F2 757
30 TraesCS4B01G180400 chr5D 70386281 70387107 826 False 599.000000 599 80.742000 1 817 1 chr5D.!!$F1 816
31 TraesCS4B01G180400 chr1B 212436776 212437495 719 True 608.000000 608 83.034000 4 679 1 chr1B.!!$R1 675
32 TraesCS4B01G180400 chr6A 503244845 503245681 836 False 527.000000 527 79.350000 1 801 1 chr6A.!!$F1 800
33 TraesCS4B01G180400 chr6D 54790335 54790950 615 False 388.000000 388 79.107000 227 817 1 chr6D.!!$F1 590

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
124 140 0.105555 CCTCCTCCTGCTCATCCTCT 60.106 60.000 0.00 0.0 0.00 3.69 F
982 1150 1.209747 CTCCTAGGGTTTTTAGCCGCT 59.790 52.381 9.46 0.0 0.00 5.52 F
1445 1613 0.167689 GCGTCTTAGTCGAGGTTCGT 59.832 55.000 2.72 0.0 41.35 3.85 F
1752 1920 0.320771 ACCATGACGTGAAGGCTGTC 60.321 55.000 0.00 0.0 0.00 3.51 F
1814 1984 2.352388 TGCAAAGGTATACGCTGGTTC 58.648 47.619 0.00 0.0 0.00 3.62 F
3300 3490 1.933853 GACTTGTGTCAGAACGCACTT 59.066 47.619 0.00 0.0 45.23 3.16 F
3721 3920 1.571919 ATCTTAGCGTGTCGAATGGC 58.428 50.000 0.00 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1242 1410 1.061131 CATCTGATCAACGAACGCACC 59.939 52.381 0.00 0.00 0.00 5.01 R
2269 2439 2.158295 AGCATATACTCCCTCCGTTCCT 60.158 50.000 0.00 0.00 0.00 3.36 R
2270 2440 2.249139 AGCATATACTCCCTCCGTTCC 58.751 52.381 0.00 0.00 0.00 3.62 R
3300 3490 3.642848 TGTCATAGGCTCATCATACTGCA 59.357 43.478 0.00 0.00 0.00 4.41 R
3320 3510 8.773404 AGAAATGTAATAGTTTAAGCGAGTGT 57.227 30.769 0.00 0.00 0.00 3.55 R
4956 5489 1.140652 ACCACAACCAATTGGGCAAAG 59.859 47.619 27.89 15.49 37.97 2.77 R
5678 6218 0.318360 ATTGTCGCTGTCGTTCGTCA 60.318 50.000 0.00 0.00 36.96 4.35 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
118 134 2.039624 GGGTCCTCCTCCTGCTCA 59.960 66.667 0.00 0.00 0.00 4.26
124 140 0.105555 CCTCCTCCTGCTCATCCTCT 60.106 60.000 0.00 0.00 0.00 3.69
154 170 3.755628 TCGCCGGCGCTCTTAAGT 61.756 61.111 42.78 0.00 39.59 2.24
166 182 2.870435 GCTCTTAAGTGTCAAGGCCGAA 60.870 50.000 1.63 0.00 0.00 4.30
307 405 1.227527 CAACGATGAGGCCGCCATA 60.228 57.895 13.15 0.00 0.00 2.74
349 447 3.209812 CGGACGGAGATGGAGCGA 61.210 66.667 0.00 0.00 0.00 4.93
640 785 4.081087 AGCTGTGAACCACCTAAATATCGT 60.081 41.667 0.00 0.00 32.73 3.73
642 787 5.408880 TGTGAACCACCTAAATATCGTCA 57.591 39.130 0.00 0.00 32.73 4.35
646 791 8.041919 TGTGAACCACCTAAATATCGTCAAATA 58.958 33.333 0.00 0.00 32.73 1.40
659 806 8.766000 ATATCGTCAAATATATGCCGTGTTTA 57.234 30.769 0.00 0.00 0.00 2.01
757 921 3.370104 TCGCCCCCACATCAAAAATATT 58.630 40.909 0.00 0.00 0.00 1.28
817 983 2.125512 GCGAACGGCTGGAGATGT 60.126 61.111 0.00 0.00 39.11 3.06
825 991 2.307768 CGGCTGGAGATGTTCCTACTA 58.692 52.381 0.00 0.00 46.92 1.82
831 997 5.360144 GCTGGAGATGTTCCTACTACTACAA 59.640 44.000 0.00 0.00 46.92 2.41
832 998 6.680872 GCTGGAGATGTTCCTACTACTACAAC 60.681 46.154 0.00 0.00 46.92 3.32
833 999 6.250711 TGGAGATGTTCCTACTACTACAACA 58.749 40.000 0.00 0.00 46.92 3.33
834 1000 6.152323 TGGAGATGTTCCTACTACTACAACAC 59.848 42.308 0.00 0.00 46.92 3.32
835 1001 6.152323 GGAGATGTTCCTACTACTACAACACA 59.848 42.308 0.00 0.00 43.16 3.72
836 1002 6.921914 AGATGTTCCTACTACTACAACACAC 58.078 40.000 0.00 0.00 30.04 3.82
840 1006 3.167485 CCTACTACTACAACACACCCCA 58.833 50.000 0.00 0.00 0.00 4.96
982 1150 1.209747 CTCCTAGGGTTTTTAGCCGCT 59.790 52.381 9.46 0.00 0.00 5.52
1166 1334 1.381872 CCAGGGATCTCGAGGTGGT 60.382 63.158 13.56 0.00 0.00 4.16
1242 1410 2.285834 GGTTGCTTATGAGATGCGTTCG 60.286 50.000 0.00 0.00 0.00 3.95
1445 1613 0.167689 GCGTCTTAGTCGAGGTTCGT 59.832 55.000 2.72 0.00 41.35 3.85
1471 1639 1.656652 GAATAGCATCCGCACTGTGT 58.343 50.000 9.86 0.00 42.27 3.72
1533 1701 1.156736 GTGTGGATCAGTTCGGTTGG 58.843 55.000 0.00 0.00 0.00 3.77
1653 1821 2.582498 CCGTTTAGCGAGGAGGCG 60.582 66.667 0.00 0.00 44.77 5.52
1752 1920 0.320771 ACCATGACGTGAAGGCTGTC 60.321 55.000 0.00 0.00 0.00 3.51
1814 1984 2.352388 TGCAAAGGTATACGCTGGTTC 58.648 47.619 0.00 0.00 0.00 3.62
2136 2306 8.855804 TCTTTATTAATACTCCCTCTGTTCCT 57.144 34.615 0.00 0.00 0.00 3.36
2137 2307 9.947189 TCTTTATTAATACTCCCTCTGTTCCTA 57.053 33.333 0.00 0.00 0.00 2.94
2145 2315 9.853177 AATACTCCCTCTGTTCCTAAATATTTG 57.147 33.333 11.05 1.40 0.00 2.32
2146 2316 7.272144 ACTCCCTCTGTTCCTAAATATTTGT 57.728 36.000 11.05 0.00 0.00 2.83
2147 2317 7.339482 ACTCCCTCTGTTCCTAAATATTTGTC 58.661 38.462 11.05 0.00 0.00 3.18
2148 2318 7.182930 ACTCCCTCTGTTCCTAAATATTTGTCT 59.817 37.037 11.05 0.00 0.00 3.41
2149 2319 7.928873 TCCCTCTGTTCCTAAATATTTGTCTT 58.071 34.615 11.05 0.00 0.00 3.01
2150 2320 8.390921 TCCCTCTGTTCCTAAATATTTGTCTTT 58.609 33.333 11.05 0.00 0.00 2.52
2151 2321 8.462016 CCCTCTGTTCCTAAATATTTGTCTTTG 58.538 37.037 11.05 0.00 0.00 2.77
2152 2322 9.014297 CCTCTGTTCCTAAATATTTGTCTTTGT 57.986 33.333 11.05 0.00 0.00 2.83
2167 2337 9.956720 ATTTGTCTTTGTAGAGATTTCAACAAG 57.043 29.630 0.00 0.00 33.70 3.16
2168 2338 8.506168 TTGTCTTTGTAGAGATTTCAACAAGT 57.494 30.769 0.00 0.00 33.70 3.16
2169 2339 7.919690 TGTCTTTGTAGAGATTTCAACAAGTG 58.080 34.615 0.00 0.00 33.70 3.16
2170 2340 7.768582 TGTCTTTGTAGAGATTTCAACAAGTGA 59.231 33.333 0.00 0.00 33.70 3.41
2171 2341 8.064814 GTCTTTGTAGAGATTTCAACAAGTGAC 58.935 37.037 0.00 0.00 35.39 3.67
2172 2342 7.987458 TCTTTGTAGAGATTTCAACAAGTGACT 59.013 33.333 0.00 0.00 35.39 3.41
2173 2343 9.261180 CTTTGTAGAGATTTCAACAAGTGACTA 57.739 33.333 0.00 0.00 35.39 2.59
2174 2344 8.589335 TTGTAGAGATTTCAACAAGTGACTAC 57.411 34.615 0.00 0.00 35.39 2.73
2175 2345 7.952671 TGTAGAGATTTCAACAAGTGACTACT 58.047 34.615 0.00 0.00 39.32 2.57
2177 2347 9.909644 GTAGAGATTTCAACAAGTGACTACTTA 57.090 33.333 0.00 0.00 45.12 2.24
2178 2348 8.819643 AGAGATTTCAACAAGTGACTACTTAC 57.180 34.615 0.00 0.00 45.12 2.34
2179 2349 7.595502 AGAGATTTCAACAAGTGACTACTTACG 59.404 37.037 0.00 0.00 45.12 3.18
2180 2350 6.645415 AGATTTCAACAAGTGACTACTTACGG 59.355 38.462 0.00 0.00 45.12 4.02
2181 2351 5.518848 TTCAACAAGTGACTACTTACGGA 57.481 39.130 0.00 0.00 45.12 4.69
2182 2352 5.117355 TCAACAAGTGACTACTTACGGAG 57.883 43.478 0.00 0.00 45.12 4.63
2183 2353 3.572604 ACAAGTGACTACTTACGGAGC 57.427 47.619 0.00 0.00 45.12 4.70
2184 2354 2.889045 ACAAGTGACTACTTACGGAGCA 59.111 45.455 0.00 0.00 45.12 4.26
2185 2355 3.319972 ACAAGTGACTACTTACGGAGCAA 59.680 43.478 0.00 0.00 45.12 3.91
2186 2356 4.202182 ACAAGTGACTACTTACGGAGCAAA 60.202 41.667 0.00 0.00 45.12 3.68
2187 2357 4.595762 AGTGACTACTTACGGAGCAAAA 57.404 40.909 0.00 0.00 31.66 2.44
2188 2358 5.148651 AGTGACTACTTACGGAGCAAAAT 57.851 39.130 0.00 0.00 31.66 1.82
2189 2359 4.929808 AGTGACTACTTACGGAGCAAAATG 59.070 41.667 0.00 0.00 31.66 2.32
2190 2360 4.927425 GTGACTACTTACGGAGCAAAATGA 59.073 41.667 0.00 0.00 0.00 2.57
2191 2361 5.062308 GTGACTACTTACGGAGCAAAATGAG 59.938 44.000 0.00 0.00 0.00 2.90
2192 2362 5.148651 ACTACTTACGGAGCAAAATGAGT 57.851 39.130 0.00 0.00 0.00 3.41
2193 2363 4.929808 ACTACTTACGGAGCAAAATGAGTG 59.070 41.667 0.00 0.00 0.00 3.51
2194 2364 4.002906 ACTTACGGAGCAAAATGAGTGA 57.997 40.909 0.00 0.00 0.00 3.41
2195 2365 4.385825 ACTTACGGAGCAAAATGAGTGAA 58.614 39.130 0.00 0.00 0.00 3.18
2196 2366 5.003804 ACTTACGGAGCAAAATGAGTGAAT 58.996 37.500 0.00 0.00 0.00 2.57
2197 2367 5.122396 ACTTACGGAGCAAAATGAGTGAATC 59.878 40.000 0.00 0.00 0.00 2.52
2198 2368 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
2199 2369 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
2200 2370 5.245531 ACGGAGCAAAATGAGTGAATCTAA 58.754 37.500 0.00 0.00 0.00 2.10
2201 2371 5.705441 ACGGAGCAAAATGAGTGAATCTAAA 59.295 36.000 0.00 0.00 0.00 1.85
2202 2372 6.024049 CGGAGCAAAATGAGTGAATCTAAAC 58.976 40.000 0.00 0.00 0.00 2.01
2203 2373 6.128172 CGGAGCAAAATGAGTGAATCTAAACT 60.128 38.462 0.00 0.00 0.00 2.66
2204 2374 7.247019 GGAGCAAAATGAGTGAATCTAAACTC 58.753 38.462 0.00 0.00 42.61 3.01
2205 2375 7.120432 GGAGCAAAATGAGTGAATCTAAACTCT 59.880 37.037 4.62 0.00 42.72 3.24
2206 2376 9.155975 GAGCAAAATGAGTGAATCTAAACTCTA 57.844 33.333 4.62 0.00 42.72 2.43
2207 2377 9.507329 AGCAAAATGAGTGAATCTAAACTCTAA 57.493 29.630 4.62 0.00 42.72 2.10
2240 2410 9.682465 TCTATATACATCTGTATGTGGTAGTCC 57.318 37.037 12.10 0.00 45.99 3.85
2241 2411 9.462606 CTATATACATCTGTATGTGGTAGTCCA 57.537 37.037 12.10 0.00 45.99 4.02
2242 2412 8.901472 ATATACATCTGTATGTGGTAGTCCAT 57.099 34.615 12.10 0.00 45.99 3.41
2243 2413 5.957771 ACATCTGTATGTGGTAGTCCATT 57.042 39.130 0.00 0.00 44.79 3.16
2244 2414 6.313519 ACATCTGTATGTGGTAGTCCATTT 57.686 37.500 0.00 0.00 44.79 2.32
2245 2415 6.115446 ACATCTGTATGTGGTAGTCCATTTG 58.885 40.000 0.00 0.00 44.79 2.32
2246 2416 6.070251 ACATCTGTATGTGGTAGTCCATTTGA 60.070 38.462 0.00 0.00 44.79 2.69
2247 2417 6.367374 TCTGTATGTGGTAGTCCATTTGAA 57.633 37.500 0.00 0.00 46.20 2.69
2248 2418 6.774673 TCTGTATGTGGTAGTCCATTTGAAA 58.225 36.000 0.00 0.00 46.20 2.69
2249 2419 7.402054 TCTGTATGTGGTAGTCCATTTGAAAT 58.598 34.615 0.00 0.00 46.20 2.17
2250 2420 7.552687 TCTGTATGTGGTAGTCCATTTGAAATC 59.447 37.037 0.00 0.00 46.20 2.17
2251 2421 7.402054 TGTATGTGGTAGTCCATTTGAAATCT 58.598 34.615 0.00 0.00 46.20 2.40
2252 2422 7.552687 TGTATGTGGTAGTCCATTTGAAATCTC 59.447 37.037 0.00 0.00 46.20 2.75
2253 2423 6.126863 TGTGGTAGTCCATTTGAAATCTCT 57.873 37.500 0.00 0.00 46.20 3.10
2254 2424 7.252612 TGTGGTAGTCCATTTGAAATCTCTA 57.747 36.000 0.00 0.00 46.20 2.43
2255 2425 7.685481 TGTGGTAGTCCATTTGAAATCTCTAA 58.315 34.615 0.00 0.00 46.20 2.10
2256 2426 8.160765 TGTGGTAGTCCATTTGAAATCTCTAAA 58.839 33.333 0.00 0.00 46.20 1.85
2257 2427 9.010029 GTGGTAGTCCATTTGAAATCTCTAAAA 57.990 33.333 0.00 0.00 46.20 1.52
2258 2428 9.231297 TGGTAGTCCATTTGAAATCTCTAAAAG 57.769 33.333 0.00 0.00 39.03 2.27
2259 2429 9.449719 GGTAGTCCATTTGAAATCTCTAAAAGA 57.550 33.333 0.00 0.00 38.72 2.52
2261 2431 8.924511 AGTCCATTTGAAATCTCTAAAAGACA 57.075 30.769 0.00 0.00 36.65 3.41
2262 2432 9.354673 AGTCCATTTGAAATCTCTAAAAGACAA 57.645 29.630 0.00 0.00 36.65 3.18
2263 2433 9.965824 GTCCATTTGAAATCTCTAAAAGACAAA 57.034 29.630 0.00 0.00 36.65 2.83
2277 2447 9.947433 TCTAAAAGACAAATATTTAGGAACGGA 57.053 29.630 0.00 0.00 37.29 4.69
2279 2449 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
2280 2450 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2281 2451 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
2282 2452 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
2301 2471 7.233389 AGGGAGTATATGCTTGTGTATGTAG 57.767 40.000 0.00 0.00 0.00 2.74
2452 2623 8.679100 TGTAACATGTGCTACAAAAACTTACTT 58.321 29.630 7.74 0.00 0.00 2.24
2544 2730 6.255020 GCATACAAAGAATGGAGCAAATTCAG 59.745 38.462 8.25 2.18 36.65 3.02
3300 3490 1.933853 GACTTGTGTCAGAACGCACTT 59.066 47.619 0.00 0.00 45.23 3.16
3320 3510 4.346127 ACTTGCAGTATGATGAGCCTATGA 59.654 41.667 0.00 0.00 39.69 2.15
3525 3724 9.649316 AGGTAAAGCTATGAAGAGTAGACTATT 57.351 33.333 0.00 0.00 0.00 1.73
3721 3920 1.571919 ATCTTAGCGTGTCGAATGGC 58.428 50.000 0.00 0.00 0.00 4.40
3732 3931 4.093703 CGTGTCGAATGGCCTTTTATGTAA 59.906 41.667 3.32 0.00 0.00 2.41
3860 4059 3.233507 GGATGTTGAATACCCATGCCAT 58.766 45.455 0.00 0.00 0.00 4.40
3919 4118 9.613428 TGAAGTATTGGTATCTTGAACTAATGG 57.387 33.333 0.00 0.00 31.47 3.16
4080 4279 3.008485 AGACTTGGTCCTTTTAGCTCCTG 59.992 47.826 0.00 0.00 32.18 3.86
4085 4284 5.552870 TGGTCCTTTTAGCTCCTGATATC 57.447 43.478 0.00 0.00 0.00 1.63
4308 4827 2.894126 ACTGGACGATTGCTCCCTATAG 59.106 50.000 0.00 0.00 0.00 1.31
4901 5434 6.888105 TGCAATTATCAGTAACCTCAGATGA 58.112 36.000 0.00 0.00 0.00 2.92
4919 5452 6.435591 TCAGATGACTAGGTTATATCTGCTGG 59.564 42.308 14.11 0.00 42.63 4.85
4920 5453 4.873746 TGACTAGGTTATATCTGCTGGC 57.126 45.455 0.00 0.00 0.00 4.85
4921 5454 4.483950 TGACTAGGTTATATCTGCTGGCT 58.516 43.478 0.00 0.00 0.00 4.75
4922 5455 4.524714 TGACTAGGTTATATCTGCTGGCTC 59.475 45.833 0.00 0.00 0.00 4.70
4923 5456 4.746466 ACTAGGTTATATCTGCTGGCTCT 58.254 43.478 0.00 0.00 0.00 4.09
4924 5457 5.151454 ACTAGGTTATATCTGCTGGCTCTT 58.849 41.667 0.00 0.00 0.00 2.85
4925 5458 5.604650 ACTAGGTTATATCTGCTGGCTCTTT 59.395 40.000 0.00 0.00 0.00 2.52
4926 5459 4.712476 AGGTTATATCTGCTGGCTCTTTG 58.288 43.478 0.00 0.00 0.00 2.77
4927 5460 3.817647 GGTTATATCTGCTGGCTCTTTGG 59.182 47.826 0.00 0.00 0.00 3.28
4939 5472 5.453762 GCTGGCTCTTTGGGCAATTAATTAT 60.454 40.000 0.00 0.00 41.12 1.28
4998 5531 3.876341 ACAGGTGAACAAAGTCCGTTTA 58.124 40.909 0.00 0.00 0.00 2.01
5130 5663 2.161855 TGCATGGAGTTTGTTAGGCTG 58.838 47.619 0.00 0.00 0.00 4.85
5177 5710 9.793259 TGGATCTTGATTTACTTTACTTTGTCT 57.207 29.630 0.00 0.00 0.00 3.41
5293 5831 2.951642 TCTCAAGTGGTCAAAGCCAAAG 59.048 45.455 0.00 0.00 40.68 2.77
5297 5835 1.410153 AGTGGTCAAAGCCAAAGCAAG 59.590 47.619 0.00 0.00 43.56 4.01
5381 5921 2.693762 GCTGCTGCGAGGCAAATCA 61.694 57.895 0.00 0.00 41.94 2.57
5390 5930 5.173854 GCTGCGAGGCAAATCATAATTTTAC 59.826 40.000 0.00 0.00 38.41 2.01
5398 5938 7.033185 GGCAAATCATAATTTTACCGTTGACT 58.967 34.615 0.00 0.00 32.69 3.41
5459 5999 6.317391 CCTATGAGAAACTGAAGGAAATGACC 59.683 42.308 0.00 0.00 0.00 4.02
5493 6033 0.727398 GACCAAAGACAGCATACGCC 59.273 55.000 0.00 0.00 39.83 5.68
5495 6035 1.164411 CCAAAGACAGCATACGCCAA 58.836 50.000 0.00 0.00 39.83 4.52
5648 6188 7.766278 GGATTTAAGATCAAGTGAGCTTCTACA 59.234 37.037 14.65 0.00 46.57 2.74
5662 6202 0.325296 TCTACACTGGCCCTGGGTAG 60.325 60.000 20.77 20.77 39.55 3.18
5844 6386 5.654603 TGTACCATCACTATTCGTTCTGT 57.345 39.130 0.00 0.00 0.00 3.41
5855 6397 1.596603 TCGTTCTGTCGTGTGGACTA 58.403 50.000 0.00 0.00 46.24 2.59
5856 6398 1.948834 TCGTTCTGTCGTGTGGACTAA 59.051 47.619 0.00 0.00 46.24 2.24
5862 6404 3.050619 CTGTCGTGTGGACTAACACTTC 58.949 50.000 5.97 0.40 46.73 3.01
5947 6491 4.023726 TGCGTGTTAAATAGAAGGGGTT 57.976 40.909 0.00 0.00 0.00 4.11
5948 6492 3.754323 TGCGTGTTAAATAGAAGGGGTTG 59.246 43.478 0.00 0.00 0.00 3.77
5949 6493 3.427098 GCGTGTTAAATAGAAGGGGTTGC 60.427 47.826 0.00 0.00 0.00 4.17
5950 6494 3.181514 CGTGTTAAATAGAAGGGGTTGCG 60.182 47.826 0.00 0.00 0.00 4.85
5951 6495 4.004982 GTGTTAAATAGAAGGGGTTGCGA 58.995 43.478 0.00 0.00 0.00 5.10
5952 6496 4.094442 GTGTTAAATAGAAGGGGTTGCGAG 59.906 45.833 0.00 0.00 0.00 5.03
5979 6535 5.662211 ATACGTGTACAGGTTGTTGAAAC 57.338 39.130 24.74 0.00 0.00 2.78
6110 6676 1.526887 CCTTGTACACGTCTGCAACTG 59.473 52.381 0.00 0.00 0.00 3.16
6111 6677 2.469826 CTTGTACACGTCTGCAACTGA 58.530 47.619 0.00 0.00 0.00 3.41
6113 6679 3.106242 TGTACACGTCTGCAACTGAAT 57.894 42.857 0.00 0.00 0.00 2.57
6116 6682 2.771089 ACACGTCTGCAACTGAATCAT 58.229 42.857 0.00 0.00 0.00 2.45
6118 6684 2.481568 CACGTCTGCAACTGAATCATGT 59.518 45.455 0.00 0.00 0.00 3.21
6120 6686 3.565482 ACGTCTGCAACTGAATCATGTTT 59.435 39.130 0.00 0.00 0.00 2.83
6121 6687 3.910170 CGTCTGCAACTGAATCATGTTTG 59.090 43.478 0.00 0.00 0.00 2.93
6123 6689 4.913924 GTCTGCAACTGAATCATGTTTGAC 59.086 41.667 0.00 5.90 33.85 3.18
6124 6690 4.579753 TCTGCAACTGAATCATGTTTGACA 59.420 37.500 0.00 0.00 33.85 3.58
6148 6733 4.463050 TGTTTGACACCCTCCCTTAATT 57.537 40.909 0.00 0.00 0.00 1.40
6209 6794 1.406205 GCTTCTTGTGGGTAGAGCCTC 60.406 57.143 0.00 0.00 37.43 4.70
6229 6814 2.641197 GTGAAACCATCCGCAACCT 58.359 52.632 0.00 0.00 0.00 3.50
6230 6815 0.240945 GTGAAACCATCCGCAACCTG 59.759 55.000 0.00 0.00 0.00 4.00
6231 6816 0.893270 TGAAACCATCCGCAACCTGG 60.893 55.000 0.00 0.00 36.09 4.45
6232 6817 0.893727 GAAACCATCCGCAACCTGGT 60.894 55.000 0.00 0.00 45.08 4.00
6233 6818 0.893727 AAACCATCCGCAACCTGGTC 60.894 55.000 0.00 0.00 42.38 4.02
6234 6819 1.779061 AACCATCCGCAACCTGGTCT 61.779 55.000 0.00 0.00 42.38 3.85
6235 6820 1.002134 CCATCCGCAACCTGGTCTT 60.002 57.895 0.00 0.00 0.00 3.01
6236 6821 1.026718 CCATCCGCAACCTGGTCTTC 61.027 60.000 0.00 0.00 0.00 2.87
6245 6830 1.807814 ACCTGGTCTTCTGGTCTTGT 58.192 50.000 0.00 0.00 43.08 3.16
6326 6912 9.424319 TGAAAGTCTATCTCAATGTGTTTAGTC 57.576 33.333 0.00 0.00 0.00 2.59
6380 6970 4.408182 GGTAGCACCTAGATTGTCACAT 57.592 45.455 0.00 0.00 34.73 3.21
6479 7073 4.505808 CATTGGCCAATGCTTTGTATTCA 58.494 39.130 38.33 5.96 41.27 2.57
6524 7119 1.882623 GTAGCTTGCTTCCTTGCACTT 59.117 47.619 0.00 0.00 43.20 3.16
6572 7167 0.031178 CTGCAAAGCCACCAGTTGAC 59.969 55.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
154 170 3.552384 ACGGGTTCGGCCTTGACA 61.552 61.111 0.00 0.00 41.39 3.58
166 182 4.344865 AGCGGCATTTCCACGGGT 62.345 61.111 1.45 0.00 34.01 5.28
508 627 1.592223 CGAAGTCGCCCTTCTCCTT 59.408 57.895 11.33 0.00 46.23 3.36
640 785 5.358090 TCGGTAAACACGGCATATATTTGA 58.642 37.500 0.00 0.00 0.00 2.69
642 787 6.680874 TTTCGGTAAACACGGCATATATTT 57.319 33.333 0.00 0.00 0.00 1.40
646 791 5.336744 CAAATTTCGGTAAACACGGCATAT 58.663 37.500 0.00 0.00 0.00 1.78
659 806 4.817318 ACATAATTGGGCAAATTTCGGT 57.183 36.364 4.94 0.00 39.29 4.69
728 892 4.796495 GTGGGGGCGATCGGCTTT 62.796 66.667 36.05 0.00 42.94 3.51
817 983 3.834231 GGGGTGTGTTGTAGTAGTAGGAA 59.166 47.826 0.00 0.00 0.00 3.36
825 991 0.534203 CGCTTGGGGTGTGTTGTAGT 60.534 55.000 0.00 0.00 0.00 2.73
831 997 2.426023 GAGACGCTTGGGGTGTGT 59.574 61.111 0.00 0.00 38.95 3.72
832 998 2.358737 GGAGACGCTTGGGGTGTG 60.359 66.667 0.00 0.00 38.95 3.82
833 999 1.990160 TTTGGAGACGCTTGGGGTGT 61.990 55.000 0.00 0.00 41.87 4.16
834 1000 1.228124 TTTGGAGACGCTTGGGGTG 60.228 57.895 0.00 0.00 0.00 4.61
835 1001 1.228154 GTTTGGAGACGCTTGGGGT 60.228 57.895 0.00 0.00 0.00 4.95
836 1002 1.971695 GGTTTGGAGACGCTTGGGG 60.972 63.158 0.00 0.00 0.00 4.96
840 1006 0.250770 GAAGGGGTTTGGAGACGCTT 60.251 55.000 0.00 0.00 39.64 4.68
1145 1313 1.456705 ACCTCGAGATCCCTGGCTC 60.457 63.158 15.71 0.00 0.00 4.70
1242 1410 1.061131 CATCTGATCAACGAACGCACC 59.939 52.381 0.00 0.00 0.00 5.01
1445 1613 1.681264 TGCGGATGCTATTCGAAGAGA 59.319 47.619 23.35 8.92 43.34 3.10
1495 1663 6.321435 TCCACACGAGTCAAGATTATACAGAT 59.679 38.462 0.00 0.00 0.00 2.90
1653 1821 3.317149 TGATTGCATCCAGAAATAGCTGC 59.683 43.478 0.00 0.00 34.56 5.25
1752 1920 5.174761 GCATTTCTGCTTCAGATAGTACTCG 59.825 44.000 0.00 0.00 45.32 4.18
1814 1984 5.775686 TCAACATCTGCCTTCAAAAATGAG 58.224 37.500 0.00 0.00 0.00 2.90
2121 2291 8.388656 ACAAATATTTAGGAACAGAGGGAGTA 57.611 34.615 0.00 0.00 0.00 2.59
2122 2292 7.182930 AGACAAATATTTAGGAACAGAGGGAGT 59.817 37.037 0.00 0.00 0.00 3.85
2123 2293 7.569240 AGACAAATATTTAGGAACAGAGGGAG 58.431 38.462 0.00 0.00 0.00 4.30
2124 2294 7.510675 AGACAAATATTTAGGAACAGAGGGA 57.489 36.000 0.00 0.00 0.00 4.20
2125 2295 8.462016 CAAAGACAAATATTTAGGAACAGAGGG 58.538 37.037 0.00 0.00 0.00 4.30
2126 2296 9.014297 ACAAAGACAAATATTTAGGAACAGAGG 57.986 33.333 0.00 0.00 0.00 3.69
2141 2311 9.956720 CTTGTTGAAATCTCTACAAAGACAAAT 57.043 29.630 0.00 0.00 43.56 2.32
2142 2312 8.956426 ACTTGTTGAAATCTCTACAAAGACAAA 58.044 29.630 0.00 0.00 43.56 2.83
2143 2313 8.397906 CACTTGTTGAAATCTCTACAAAGACAA 58.602 33.333 0.00 0.00 43.56 3.18
2144 2314 7.768582 TCACTTGTTGAAATCTCTACAAAGACA 59.231 33.333 0.00 0.00 43.56 3.41
2145 2315 8.064814 GTCACTTGTTGAAATCTCTACAAAGAC 58.935 37.037 10.49 10.49 43.56 3.01
2146 2316 7.987458 AGTCACTTGTTGAAATCTCTACAAAGA 59.013 33.333 0.00 0.00 43.56 2.52
2147 2317 8.147642 AGTCACTTGTTGAAATCTCTACAAAG 57.852 34.615 0.00 0.00 43.56 2.77
2148 2318 9.042008 GTAGTCACTTGTTGAAATCTCTACAAA 57.958 33.333 0.00 0.00 43.56 2.83
2149 2319 8.421784 AGTAGTCACTTGTTGAAATCTCTACAA 58.578 33.333 0.00 0.00 42.53 2.41
2150 2320 7.952671 AGTAGTCACTTGTTGAAATCTCTACA 58.047 34.615 0.00 0.00 35.39 2.74
2151 2321 8.819643 AAGTAGTCACTTGTTGAAATCTCTAC 57.180 34.615 0.00 0.00 43.50 2.59
2152 2322 9.909644 GTAAGTAGTCACTTGTTGAAATCTCTA 57.090 33.333 0.35 0.00 44.81 2.43
2153 2323 7.595502 CGTAAGTAGTCACTTGTTGAAATCTCT 59.404 37.037 0.35 0.00 44.81 3.10
2154 2324 7.148787 CCGTAAGTAGTCACTTGTTGAAATCTC 60.149 40.741 0.35 0.00 44.81 2.75
2155 2325 6.645415 CCGTAAGTAGTCACTTGTTGAAATCT 59.355 38.462 0.35 0.00 44.81 2.40
2156 2326 6.643770 TCCGTAAGTAGTCACTTGTTGAAATC 59.356 38.462 0.35 0.00 44.81 2.17
2157 2327 6.518493 TCCGTAAGTAGTCACTTGTTGAAAT 58.482 36.000 0.35 0.00 44.81 2.17
2158 2328 5.904941 TCCGTAAGTAGTCACTTGTTGAAA 58.095 37.500 0.35 0.00 44.81 2.69
2159 2329 5.518848 TCCGTAAGTAGTCACTTGTTGAA 57.481 39.130 0.35 0.00 44.81 2.69
2160 2330 4.558095 GCTCCGTAAGTAGTCACTTGTTGA 60.558 45.833 0.35 0.00 44.81 3.18
2161 2331 3.673809 GCTCCGTAAGTAGTCACTTGTTG 59.326 47.826 0.35 0.00 44.81 3.33
2162 2332 3.319972 TGCTCCGTAAGTAGTCACTTGTT 59.680 43.478 0.35 0.00 44.81 2.83
2163 2333 2.889045 TGCTCCGTAAGTAGTCACTTGT 59.111 45.455 0.35 0.00 44.81 3.16
2164 2334 3.570926 TGCTCCGTAAGTAGTCACTTG 57.429 47.619 0.35 0.00 44.81 3.16
2165 2335 4.595762 TTTGCTCCGTAAGTAGTCACTT 57.404 40.909 0.00 0.00 46.77 3.16
2166 2336 4.595762 TTTTGCTCCGTAAGTAGTCACT 57.404 40.909 0.00 0.00 36.19 3.41
2167 2337 4.927425 TCATTTTGCTCCGTAAGTAGTCAC 59.073 41.667 0.00 0.00 0.00 3.67
2168 2338 5.142061 TCATTTTGCTCCGTAAGTAGTCA 57.858 39.130 0.00 0.00 0.00 3.41
2169 2339 5.062308 CACTCATTTTGCTCCGTAAGTAGTC 59.938 44.000 0.00 0.00 0.00 2.59
2170 2340 4.929808 CACTCATTTTGCTCCGTAAGTAGT 59.070 41.667 0.00 0.00 0.00 2.73
2171 2341 5.168569 TCACTCATTTTGCTCCGTAAGTAG 58.831 41.667 0.00 0.00 0.00 2.57
2172 2342 5.142061 TCACTCATTTTGCTCCGTAAGTA 57.858 39.130 0.00 0.00 0.00 2.24
2173 2343 4.002906 TCACTCATTTTGCTCCGTAAGT 57.997 40.909 0.00 0.00 0.00 2.24
2174 2344 5.352569 AGATTCACTCATTTTGCTCCGTAAG 59.647 40.000 0.00 0.00 0.00 2.34
2175 2345 5.245531 AGATTCACTCATTTTGCTCCGTAA 58.754 37.500 0.00 0.00 0.00 3.18
2176 2346 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
2177 2347 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
2178 2348 5.801350 TTAGATTCACTCATTTTGCTCCG 57.199 39.130 0.00 0.00 0.00 4.63
2179 2349 7.120432 AGAGTTTAGATTCACTCATTTTGCTCC 59.880 37.037 2.36 0.00 41.77 4.70
2180 2350 8.038492 AGAGTTTAGATTCACTCATTTTGCTC 57.962 34.615 2.36 0.00 41.77 4.26
2181 2351 7.992754 AGAGTTTAGATTCACTCATTTTGCT 57.007 32.000 2.36 0.00 41.77 3.91
2214 2384 9.682465 GGACTACCACATACAGATGTATATAGA 57.318 37.037 5.21 0.00 44.82 1.98
2215 2385 9.462606 TGGACTACCACATACAGATGTATATAG 57.537 37.037 5.21 7.73 44.82 1.31
2233 2403 9.449719 TCTTTTAGAGATTTCAAATGGACTACC 57.550 33.333 0.00 0.00 0.00 3.18
2236 2406 8.924511 TGTCTTTTAGAGATTTCAAATGGACT 57.075 30.769 0.00 0.00 36.61 3.85
2237 2407 9.965824 TTTGTCTTTTAGAGATTTCAAATGGAC 57.034 29.630 0.00 0.00 36.61 4.02
2251 2421 9.947433 TCCGTTCCTAAATATTTGTCTTTTAGA 57.053 29.630 11.05 0.00 35.79 2.10
2253 2423 9.169592 CCTCCGTTCCTAAATATTTGTCTTTTA 57.830 33.333 11.05 0.00 0.00 1.52
2254 2424 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
2255 2425 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2256 2426 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
2257 2427 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
2258 2428 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2259 2429 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
2260 2430 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2261 2431 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2262 2432 8.759782 CATATACTCCCTCCGTTCCTAAATATT 58.240 37.037 0.00 0.00 0.00 1.28
2263 2433 7.147707 GCATATACTCCCTCCGTTCCTAAATAT 60.148 40.741 0.00 0.00 0.00 1.28
2264 2434 6.154021 GCATATACTCCCTCCGTTCCTAAATA 59.846 42.308 0.00 0.00 0.00 1.40
2265 2435 5.046520 GCATATACTCCCTCCGTTCCTAAAT 60.047 44.000 0.00 0.00 0.00 1.40
2266 2436 4.282703 GCATATACTCCCTCCGTTCCTAAA 59.717 45.833 0.00 0.00 0.00 1.85
2267 2437 3.830755 GCATATACTCCCTCCGTTCCTAA 59.169 47.826 0.00 0.00 0.00 2.69
2268 2438 3.075582 AGCATATACTCCCTCCGTTCCTA 59.924 47.826 0.00 0.00 0.00 2.94
2269 2439 2.158295 AGCATATACTCCCTCCGTTCCT 60.158 50.000 0.00 0.00 0.00 3.36
2270 2440 2.249139 AGCATATACTCCCTCCGTTCC 58.751 52.381 0.00 0.00 0.00 3.62
2271 2441 3.069729 ACAAGCATATACTCCCTCCGTTC 59.930 47.826 0.00 0.00 0.00 3.95
2272 2442 3.039011 ACAAGCATATACTCCCTCCGTT 58.961 45.455 0.00 0.00 0.00 4.44
2273 2443 2.365617 CACAAGCATATACTCCCTCCGT 59.634 50.000 0.00 0.00 0.00 4.69
2274 2444 2.365617 ACACAAGCATATACTCCCTCCG 59.634 50.000 0.00 0.00 0.00 4.63
2275 2445 5.012148 ACATACACAAGCATATACTCCCTCC 59.988 44.000 0.00 0.00 0.00 4.30
2276 2446 6.102897 ACATACACAAGCATATACTCCCTC 57.897 41.667 0.00 0.00 0.00 4.30
2277 2447 6.782988 ACTACATACACAAGCATATACTCCCT 59.217 38.462 0.00 0.00 0.00 4.20
2278 2448 6.994221 ACTACATACACAAGCATATACTCCC 58.006 40.000 0.00 0.00 0.00 4.30
2279 2449 8.794553 ACTACTACATACACAAGCATATACTCC 58.205 37.037 0.00 0.00 0.00 3.85
2280 2450 9.613957 CACTACTACATACACAAGCATATACTC 57.386 37.037 0.00 0.00 0.00 2.59
2281 2451 9.132923 ACACTACTACATACACAAGCATATACT 57.867 33.333 0.00 0.00 0.00 2.12
2282 2452 9.181805 CACACTACTACATACACAAGCATATAC 57.818 37.037 0.00 0.00 0.00 1.47
2452 2623 5.047448 TGGCAAGCAAATATAACAAAGCTCA 60.047 36.000 0.00 0.00 0.00 4.26
2544 2730 3.591023 GGAGTTAGGAACAGCAGACTTC 58.409 50.000 0.00 0.00 0.00 3.01
3216 3404 6.073276 CGTAAGGAACAATGAAGTGACAATGA 60.073 38.462 0.00 0.00 0.00 2.57
3300 3490 3.642848 TGTCATAGGCTCATCATACTGCA 59.357 43.478 0.00 0.00 0.00 4.41
3320 3510 8.773404 AGAAATGTAATAGTTTAAGCGAGTGT 57.227 30.769 0.00 0.00 0.00 3.55
3420 3619 9.743057 CAAGACAATGTTAAACTGGACAAATAA 57.257 29.630 0.00 0.00 0.00 1.40
3919 4118 3.003068 GTCATTGATGTAGCATGGCAGTC 59.997 47.826 0.00 0.00 0.00 3.51
4080 4279 8.239998 GGCTGAATGGCTACAAAATTAGATATC 58.760 37.037 0.00 0.00 38.32 1.63
4085 4284 4.646492 AGGGCTGAATGGCTACAAAATTAG 59.354 41.667 0.00 0.00 41.48 1.73
4308 4827 2.158885 GGGCAGAGGGAGTATTGAGTTC 60.159 54.545 0.00 0.00 0.00 3.01
4376 4895 4.340097 TGTCACGGAAATGGACGTATCTAT 59.660 41.667 0.00 0.00 42.04 1.98
4384 4903 5.391629 GGAATTACTTGTCACGGAAATGGAC 60.392 44.000 0.00 0.00 0.00 4.02
4552 5081 7.609760 TCATACATGTTGATGTCCTGTTAAC 57.390 36.000 2.30 0.00 42.14 2.01
4553 5082 8.806429 ATTCATACATGTTGATGTCCTGTTAA 57.194 30.769 2.30 0.00 42.14 2.01
4901 5434 4.746466 AGAGCCAGCAGATATAACCTAGT 58.254 43.478 0.00 0.00 0.00 2.57
4919 5452 6.698766 CAGTCATAATTAATTGCCCAAAGAGC 59.301 38.462 11.05 0.00 0.00 4.09
4920 5453 7.999679 TCAGTCATAATTAATTGCCCAAAGAG 58.000 34.615 11.05 0.00 0.00 2.85
4921 5454 7.953005 TCAGTCATAATTAATTGCCCAAAGA 57.047 32.000 11.05 0.00 0.00 2.52
4922 5455 9.252962 GAATCAGTCATAATTAATTGCCCAAAG 57.747 33.333 11.05 0.00 0.00 2.77
4923 5456 8.756927 TGAATCAGTCATAATTAATTGCCCAAA 58.243 29.630 11.05 0.00 0.00 3.28
4924 5457 8.303780 TGAATCAGTCATAATTAATTGCCCAA 57.696 30.769 11.05 0.00 0.00 4.12
4925 5458 7.894753 TGAATCAGTCATAATTAATTGCCCA 57.105 32.000 11.05 0.00 0.00 5.36
4939 5472 5.394443 GGGCAAAGCAATAATGAATCAGTCA 60.394 40.000 0.00 0.00 41.67 3.41
4956 5489 1.140652 ACCACAACCAATTGGGCAAAG 59.859 47.619 27.89 15.49 37.97 2.77
4998 5531 4.090761 TGTTTGCTCCAAGTCTTCATCT 57.909 40.909 0.00 0.00 0.00 2.90
5233 5766 7.759433 GCTTAAACAATAAACATAGTGGTGCAT 59.241 33.333 0.00 0.00 0.00 3.96
5234 5767 7.087639 GCTTAAACAATAAACATAGTGGTGCA 58.912 34.615 0.00 0.00 0.00 4.57
5235 5768 6.530181 GGCTTAAACAATAAACATAGTGGTGC 59.470 38.462 0.00 0.00 0.00 5.01
5293 5831 4.446051 GCCTCGAGTGAGAATAATACTTGC 59.554 45.833 12.31 0.00 45.57 4.01
5297 5835 6.701841 TGATTTGCCTCGAGTGAGAATAATAC 59.298 38.462 12.31 0.00 45.57 1.89
5381 5921 8.098912 ACCTACAGAAGTCAACGGTAAAATTAT 58.901 33.333 0.00 0.00 0.00 1.28
5390 5930 3.254060 CATCACCTACAGAAGTCAACGG 58.746 50.000 0.00 0.00 0.00 4.44
5398 5938 1.899814 ACCTTCGCATCACCTACAGAA 59.100 47.619 0.00 0.00 0.00 3.02
5459 5999 2.046507 GTCACAGCCTGGCCTCTG 60.047 66.667 16.57 10.10 36.45 3.35
5529 6069 6.095021 GGTGTTAACTTCAAAAGACTTGACCT 59.905 38.462 7.22 0.00 0.00 3.85
5530 6070 6.127842 TGGTGTTAACTTCAAAAGACTTGACC 60.128 38.462 7.22 1.42 0.00 4.02
5648 6188 1.613630 CAGACTACCCAGGGCCAGT 60.614 63.158 12.41 12.41 0.00 4.00
5678 6218 0.318360 ATTGTCGCTGTCGTTCGTCA 60.318 50.000 0.00 0.00 36.96 4.35
5679 6219 1.609932 TATTGTCGCTGTCGTTCGTC 58.390 50.000 0.00 0.00 36.96 4.20
5680 6220 1.717645 GTTATTGTCGCTGTCGTTCGT 59.282 47.619 0.00 0.00 36.96 3.85
5681 6221 1.717113 TGTTATTGTCGCTGTCGTTCG 59.283 47.619 0.00 0.00 36.96 3.95
5682 6222 3.539592 CGATGTTATTGTCGCTGTCGTTC 60.540 47.826 0.00 0.00 36.96 3.95
5683 6223 2.344441 CGATGTTATTGTCGCTGTCGTT 59.656 45.455 0.00 0.00 36.96 3.85
5810 6352 2.515290 GGTACAATTCCGCGGGGG 60.515 66.667 27.83 14.70 37.02 5.40
5811 6353 2.269562 TGGTACAATTCCGCGGGG 59.730 61.111 27.83 13.31 31.92 5.73
5855 6397 0.825010 CAAGCAGCCCTGGAAGTGTT 60.825 55.000 0.00 0.00 0.00 3.32
5856 6398 1.228367 CAAGCAGCCCTGGAAGTGT 60.228 57.895 0.00 0.00 0.00 3.55
5862 6404 2.793317 AATCCACCAAGCAGCCCTGG 62.793 60.000 9.24 9.24 0.00 4.45
5947 6491 0.458889 GTACACGTATTGGGCTCGCA 60.459 55.000 0.00 0.00 0.00 5.10
5948 6492 0.458889 TGTACACGTATTGGGCTCGC 60.459 55.000 0.00 0.00 0.00 5.03
5949 6493 1.556564 CTGTACACGTATTGGGCTCG 58.443 55.000 0.00 0.00 0.00 5.03
5950 6494 1.206371 ACCTGTACACGTATTGGGCTC 59.794 52.381 0.00 0.00 0.00 4.70
5951 6495 1.272807 ACCTGTACACGTATTGGGCT 58.727 50.000 0.00 0.00 0.00 5.19
5952 6496 1.735571 CAACCTGTACACGTATTGGGC 59.264 52.381 0.00 0.00 0.00 5.36
5955 6500 5.660629 TTCAACAACCTGTACACGTATTG 57.339 39.130 12.10 12.10 0.00 1.90
5979 6535 6.748333 TTCTTCCTTTGCAAGATGTATCTG 57.252 37.500 0.00 0.00 37.19 2.90
6116 6682 3.119316 GGGTGTCAAACATGTGTCAAACA 60.119 43.478 0.00 0.00 44.79 2.83
6118 6684 3.360867 AGGGTGTCAAACATGTGTCAAA 58.639 40.909 0.00 0.00 0.00 2.69
6120 6686 2.571212 GAGGGTGTCAAACATGTGTCA 58.429 47.619 0.00 0.00 0.00 3.58
6121 6687 1.880027 GGAGGGTGTCAAACATGTGTC 59.120 52.381 0.00 0.00 0.00 3.67
6123 6689 1.202927 AGGGAGGGTGTCAAACATGTG 60.203 52.381 0.00 0.00 0.00 3.21
6124 6690 1.149101 AGGGAGGGTGTCAAACATGT 58.851 50.000 0.00 0.00 0.00 3.21
6209 6794 1.209127 GTTGCGGATGGTTTCACCG 59.791 57.895 0.00 0.00 42.58 4.94
6229 6814 2.103094 CACTCACAAGACCAGAAGACCA 59.897 50.000 0.00 0.00 0.00 4.02
6230 6815 2.365617 TCACTCACAAGACCAGAAGACC 59.634 50.000 0.00 0.00 0.00 3.85
6231 6816 3.735237 TCACTCACAAGACCAGAAGAC 57.265 47.619 0.00 0.00 0.00 3.01
6232 6817 4.963318 ATTCACTCACAAGACCAGAAGA 57.037 40.909 0.00 0.00 0.00 2.87
6233 6818 6.073003 GGTTTATTCACTCACAAGACCAGAAG 60.073 42.308 0.00 0.00 0.00 2.85
6234 6819 5.763204 GGTTTATTCACTCACAAGACCAGAA 59.237 40.000 0.00 0.00 0.00 3.02
6235 6820 5.305585 GGTTTATTCACTCACAAGACCAGA 58.694 41.667 0.00 0.00 0.00 3.86
6236 6821 4.152402 CGGTTTATTCACTCACAAGACCAG 59.848 45.833 0.00 0.00 0.00 4.00
6245 6830 4.900684 TGGACATTCGGTTTATTCACTCA 58.099 39.130 0.00 0.00 0.00 3.41
6326 6912 4.866486 GCAAATCCAGTTTTTCATGCTAGG 59.134 41.667 0.00 0.00 0.00 3.02
6380 6970 4.406972 AGCACTAGAGCTCCATGTTTATGA 59.593 41.667 10.93 0.00 42.18 2.15
6433 7027 3.044156 ACAGCAGAGATCATATGGGTGT 58.956 45.455 2.13 4.77 32.75 4.16
6479 7073 5.012561 AGTTTCAAGATCCAGTACAGAAGCT 59.987 40.000 0.00 0.00 0.00 3.74
6591 7186 1.829849 CTCTGACTCAGATTGGGCTGA 59.170 52.381 9.26 0.00 39.92 4.26


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

AutoCloner maintained by Alex Coulton.