Multiple sequence alignment - TraesCS5A01G368500

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 TraesCS5A01G368500 chr5A 100.000 4240 0 0 1 4240 569150700 569154939 0.000000e+00 7830.0
1 TraesCS5A01G368500 chr5A 89.963 2451 179 36 912 3328 569224767 569222350 0.000000e+00 3101.0
2 TraesCS5A01G368500 chr5A 86.647 2651 237 54 912 3508 569183973 569181386 0.000000e+00 2826.0
3 TraesCS5A01G368500 chr5A 87.251 2408 222 46 993 3350 569219786 569217414 0.000000e+00 2667.0
4 TraesCS5A01G368500 chr5A 80.571 700 62 30 152 812 569225431 569224767 4.960000e-129 472.0
5 TraesCS5A01G368500 chr5A 85.349 430 40 10 3745 4160 569175003 569174583 1.410000e-114 424.0
6 TraesCS5A01G368500 chr5A 82.940 381 33 20 3357 3709 569217370 569216994 8.850000e-82 315.0
7 TraesCS5A01G368500 chr5A 100.000 34 0 0 4207 4240 578943291 578943258 3.540000e-06 63.9
8 TraesCS5A01G368500 chr5D 90.722 2479 184 22 907 3350 449941004 449938537 0.000000e+00 3262.0
9 TraesCS5A01G368500 chr5D 89.701 2476 203 28 907 3350 449983307 449980852 0.000000e+00 3112.0
10 TraesCS5A01G368500 chr5D 85.795 2478 263 53 916 3350 449936227 449933796 0.000000e+00 2543.0
11 TraesCS5A01G368500 chr5D 94.395 1231 38 7 1913 3132 449886406 449887616 0.000000e+00 1862.0
12 TraesCS5A01G368500 chr5D 94.358 1028 33 8 907 1924 449883685 449884697 0.000000e+00 1554.0
13 TraesCS5A01G368500 chr5D 82.336 702 62 26 152 812 449941679 449940999 1.720000e-153 553.0
14 TraesCS5A01G368500 chr5D 92.898 352 18 5 3814 4160 449887712 449888061 4.890000e-139 505.0
15 TraesCS5A01G368500 chr5D 88.167 431 27 10 3745 4160 449912962 449912541 3.810000e-135 492.0
16 TraesCS5A01G368500 chr5D 82.578 574 48 15 5 562 449882888 449883425 3.860000e-125 459.0
17 TraesCS5A01G368500 chr5D 88.608 158 11 3 3493 3643 449933651 449933494 7.240000e-43 185.0
18 TraesCS5A01G368500 chr5D 97.087 103 3 0 3153 3255 449887607 449887709 1.570000e-39 174.0
19 TraesCS5A01G368500 chr5D 88.462 130 1 3 554 670 449883466 449883594 1.230000e-30 145.0
20 TraesCS5A01G368500 chr5D 90.909 99 9 0 709 807 449883587 449883685 2.660000e-27 134.0
21 TraesCS5A01G368500 chr5D 84.348 115 14 1 700 810 449983421 449983307 4.480000e-20 110.0
22 TraesCS5A01G368500 chr5D 90.909 66 6 0 47 112 94046022 94046087 5.840000e-14 89.8
23 TraesCS5A01G368500 chr5D 88.000 50 3 1 808 857 361576959 361576913 5.920000e-04 56.5
24 TraesCS5A01G368500 chr5B 86.060 2518 243 47 907 3350 549949274 549946791 0.000000e+00 2606.0
25 TraesCS5A01G368500 chr5B 89.366 1420 109 21 1943 3347 549953067 549951675 0.000000e+00 1748.0
26 TraesCS5A01G368500 chr5B 90.077 1300 89 24 729 1997 549710914 549712204 0.000000e+00 1650.0
27 TraesCS5A01G368500 chr5B 90.751 1211 47 16 2161 3354 549712195 549713357 0.000000e+00 1555.0
28 TraesCS5A01G368500 chr5B 93.103 1044 67 2 908 1946 549954222 549953179 0.000000e+00 1524.0
29 TraesCS5A01G368500 chr5B 86.912 489 42 9 207 677 549710426 549710910 2.900000e-146 529.0
30 TraesCS5A01G368500 chr5B 90.244 246 16 5 3796 4037 549713594 549713835 8.850000e-82 315.0
31 TraesCS5A01G368500 chr5B 87.838 222 12 9 3357 3577 549713391 549713598 3.270000e-61 246.0
32 TraesCS5A01G368500 chr5B 79.876 323 33 10 508 812 549954526 549954218 1.550000e-49 207.0
33 TraesCS5A01G368500 chr5B 91.000 100 7 2 4062 4160 549945584 549945486 2.660000e-27 134.0
34 TraesCS5A01G368500 chr5B 94.366 71 2 2 4092 4160 549768705 549768775 1.610000e-19 108.0
35 TraesCS5A01G368500 chr2D 86.845 1756 172 27 914 2621 347807276 347809020 0.000000e+00 1908.0
36 TraesCS5A01G368500 chr2D 87.597 129 15 1 198 326 296850135 296850262 9.500000e-32 148.0
37 TraesCS5A01G368500 chr2A 86.821 1343 121 24 908 2219 461414808 461416125 0.000000e+00 1448.0
38 TraesCS5A01G368500 chr2A 80.189 318 50 10 505 812 461414484 461414798 4.270000e-55 226.0
39 TraesCS5A01G368500 chr2A 91.429 70 6 0 47 116 42185454 42185523 3.490000e-16 97.1
40 TraesCS5A01G368500 chr3B 83.256 430 46 16 3745 4160 818311519 818311936 5.180000e-99 372.0
41 TraesCS5A01G368500 chr3D 82.641 409 42 17 3773 4160 608586671 608586271 6.790000e-88 335.0
42 TraesCS5A01G368500 chr3D 86.250 80 10 1 43 122 393011366 393011444 7.550000e-13 86.1
43 TraesCS5A01G368500 chr3D 91.803 61 5 0 62 122 400039659 400039599 7.550000e-13 86.1
44 TraesCS5A01G368500 chr3D 97.059 34 1 0 4207 4240 608920479 608920512 1.650000e-04 58.4
45 TraesCS5A01G368500 chr4D 89.286 140 14 1 198 337 258907550 258907412 1.570000e-39 174.0
46 TraesCS5A01G368500 chr4A 89.286 140 14 1 198 337 242899529 242899391 1.570000e-39 174.0
47 TraesCS5A01G368500 chr4B 87.857 140 15 2 198 337 235395172 235395035 3.390000e-36 163.0
48 TraesCS5A01G368500 chr6D 85.616 146 18 2 198 343 397355365 397355223 2.640000e-32 150.0
49 TraesCS5A01G368500 chr6B 85.315 143 18 2 198 340 594010417 594010278 1.230000e-30 145.0
50 TraesCS5A01G368500 chr6B 88.158 76 8 1 47 122 462124751 462124677 5.840000e-14 89.8
51 TraesCS5A01G368500 chr2B 91.803 61 5 0 62 122 217797354 217797414 7.550000e-13 86.1
52 TraesCS5A01G368500 chr1B 90.164 61 3 2 62 122 253082257 253082314 4.550000e-10 76.8
53 TraesCS5A01G368500 chr3A 96.970 33 0 1 90 122 102837925 102837956 2.000000e-03 54.7


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 TraesCS5A01G368500 chr5A 569150700 569154939 4239 False 7830.000000 7830 100.000000 1 4240 1 chr5A.!!$F1 4239
1 TraesCS5A01G368500 chr5A 569181386 569183973 2587 True 2826.000000 2826 86.647000 912 3508 1 chr5A.!!$R2 2596
2 TraesCS5A01G368500 chr5A 569216994 569225431 8437 True 1638.750000 3101 85.181250 152 3709 4 chr5A.!!$R4 3557
3 TraesCS5A01G368500 chr5D 449933494 449941679 8185 True 1635.750000 3262 86.865250 152 3643 4 chr5D.!!$R3 3491
4 TraesCS5A01G368500 chr5D 449980852 449983421 2569 True 1611.000000 3112 87.024500 700 3350 2 chr5D.!!$R4 2650
5 TraesCS5A01G368500 chr5D 449882888 449888061 5173 False 690.428571 1862 91.526714 5 4160 7 chr5D.!!$F2 4155
6 TraesCS5A01G368500 chr5B 549945486 549954526 9040 True 1243.800000 2606 87.881000 508 4160 5 chr5B.!!$R1 3652
7 TraesCS5A01G368500 chr5B 549710426 549713835 3409 False 859.000000 1650 89.164400 207 4037 5 chr5B.!!$F2 3830
8 TraesCS5A01G368500 chr2D 347807276 347809020 1744 False 1908.000000 1908 86.845000 914 2621 1 chr2D.!!$F2 1707
9 TraesCS5A01G368500 chr2A 461414484 461416125 1641 False 837.000000 1448 83.505000 505 2219 2 chr2A.!!$F2 1714

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
60 68 0.610232 CCCAAGCCTTCTGAAGTGGG 60.610 60.0 22.72 22.72 36.39 4.61 F
1399 1685 0.249031 GCTTGGAAACACTGTGTGGC 60.249 55.0 15.11 9.29 42.67 5.01 F
3046 5277 0.752743 TGCTGCTGGCCATTACCATC 60.753 55.0 5.51 0.00 39.54 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1415 1701 0.103208 CCGAGCAGATGGTACTGTCC 59.897 60.000 0.0 0.0 39.73 4.02 R
3144 10297 1.065199 TGGAAGATGATGAGCCACACC 60.065 52.381 0.0 0.0 0.00 4.16 R
4218 17197 0.109132 GGCCAGAGCGTGATTTTTGG 60.109 55.000 0.0 0.0 41.24 3.28 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
33 34 4.079253 AGCTTTTTACACCGGATCACATT 58.921 39.130 9.46 0.00 0.00 2.71
36 37 5.106475 GCTTTTTACACCGGATCACATTGTA 60.106 40.000 9.46 0.66 0.00 2.41
44 45 3.951037 CCGGATCACATTGTATTTTCCCA 59.049 43.478 0.00 0.00 0.00 4.37
46 47 5.450412 CCGGATCACATTGTATTTTCCCAAG 60.450 44.000 0.00 0.00 0.00 3.61
50 58 4.837860 TCACATTGTATTTTCCCAAGCCTT 59.162 37.500 0.00 0.00 0.00 4.35
60 68 0.610232 CCCAAGCCTTCTGAAGTGGG 60.610 60.000 22.72 22.72 36.39 4.61
64 72 1.002011 GCCTTCTGAAGTGGGTCCC 60.002 63.158 15.72 0.00 0.00 4.46
65 73 1.296715 CCTTCTGAAGTGGGTCCCG 59.703 63.158 15.72 0.00 0.00 5.14
76 84 2.506472 GGTCCCGCTTCTCCATCC 59.494 66.667 0.00 0.00 0.00 3.51
102 110 4.282195 ACCTATTTCTCCTGACATCCGATC 59.718 45.833 0.00 0.00 0.00 3.69
109 117 2.893489 TCCTGACATCCGATCCTACATG 59.107 50.000 0.00 0.00 0.00 3.21
114 122 2.289882 ACATCCGATCCTACATGGCATG 60.290 50.000 25.31 25.31 35.26 4.06
124 141 3.665515 CATGGCATGTGGGGCAGGA 62.666 63.158 19.32 0.00 46.49 3.86
144 161 0.846015 TATGCACTAGCCATGCCCTT 59.154 50.000 6.72 0.00 42.69 3.95
148 165 1.542108 GCACTAGCCATGCCCTTAGAG 60.542 57.143 0.00 0.00 37.08 2.43
149 166 0.761802 ACTAGCCATGCCCTTAGAGC 59.238 55.000 0.00 0.00 0.00 4.09
150 167 1.055040 CTAGCCATGCCCTTAGAGCT 58.945 55.000 0.00 0.00 0.00 4.09
178 195 5.827797 TCTGTTTGTTTCTACAATTGGCTCT 59.172 36.000 10.83 0.00 43.43 4.09
194 211 1.728971 GCTCTGAATCACTTGTGGACG 59.271 52.381 0.64 0.00 0.00 4.79
230 250 6.258230 TCAGTCAATTGCACTGAAAATAGG 57.742 37.500 25.42 8.64 45.84 2.57
233 253 3.831333 TCAATTGCACTGAAAATAGGCCA 59.169 39.130 5.01 0.00 0.00 5.36
267 287 2.288640 GCTTCACTGGCAAAGCTGATTT 60.289 45.455 13.71 0.00 43.57 2.17
296 316 4.588528 AGCTATTGGGTTTCAGCTTTTGAA 59.411 37.500 0.00 0.00 41.50 2.69
376 398 2.635714 GGTGGTTAACCGATACCTTGG 58.364 52.381 20.39 0.00 39.81 3.61
412 434 8.770010 TCTTAGGAAATTCCCTTTTGTTTGTA 57.230 30.769 8.66 0.00 37.19 2.41
461 488 3.181490 CGTCCGAGGTTCAGATATGACAA 60.181 47.826 0.00 0.00 0.00 3.18
466 493 5.464722 CCGAGGTTCAGATATGACAAATGAG 59.535 44.000 0.00 0.00 0.00 2.90
524 580 4.720530 TCGTTAACTTTCGAGCCTTTTC 57.279 40.909 3.71 0.00 0.00 2.29
681 811 2.425592 CACTTGACCCAGGCACGA 59.574 61.111 0.00 0.00 0.00 4.35
698 828 3.736213 CACGATGAAATTGACTGGTTCG 58.264 45.455 0.00 0.00 0.00 3.95
706 836 2.432628 GACTGGTTCGGAGGCACG 60.433 66.667 0.00 0.00 0.00 5.34
707 837 4.681978 ACTGGTTCGGAGGCACGC 62.682 66.667 0.00 0.00 0.00 5.34
711 841 4.070552 GTTCGGAGGCACGCTCCT 62.071 66.667 6.02 1.03 38.78 3.69
806 943 6.964807 ATGCAGCATTGATAAGGTTGATTA 57.035 33.333 0.52 0.00 0.00 1.75
807 944 6.772360 TGCAGCATTGATAAGGTTGATTAA 57.228 33.333 0.00 0.00 0.00 1.40
808 945 7.350744 TGCAGCATTGATAAGGTTGATTAAT 57.649 32.000 0.00 0.00 0.00 1.40
809 946 8.462589 TGCAGCATTGATAAGGTTGATTAATA 57.537 30.769 0.00 0.00 0.00 0.98
810 947 8.352201 TGCAGCATTGATAAGGTTGATTAATAC 58.648 33.333 0.00 0.00 0.00 1.89
811 948 8.571336 GCAGCATTGATAAGGTTGATTAATACT 58.429 33.333 0.00 0.00 0.00 2.12
813 950 9.289782 AGCATTGATAAGGTTGATTAATACTCC 57.710 33.333 0.00 0.00 0.00 3.85
814 951 8.515414 GCATTGATAAGGTTGATTAATACTCCC 58.485 37.037 0.00 0.00 0.00 4.30
815 952 9.799106 CATTGATAAGGTTGATTAATACTCCCT 57.201 33.333 0.00 0.00 0.00 4.20
816 953 9.799106 ATTGATAAGGTTGATTAATACTCCCTG 57.201 33.333 0.00 0.00 0.00 4.45
817 954 8.331931 TGATAAGGTTGATTAATACTCCCTGT 57.668 34.615 0.00 0.00 0.00 4.00
818 955 8.210946 TGATAAGGTTGATTAATACTCCCTGTG 58.789 37.037 0.00 0.00 0.00 3.66
819 956 6.388619 AAGGTTGATTAATACTCCCTGTGT 57.611 37.500 0.00 0.00 0.00 3.72
820 957 7.504926 AAGGTTGATTAATACTCCCTGTGTA 57.495 36.000 0.00 0.00 0.00 2.90
821 958 7.504926 AGGTTGATTAATACTCCCTGTGTAA 57.495 36.000 0.00 0.00 0.00 2.41
822 959 7.924541 AGGTTGATTAATACTCCCTGTGTAAA 58.075 34.615 0.00 0.00 0.00 2.01
823 960 7.827729 AGGTTGATTAATACTCCCTGTGTAAAC 59.172 37.037 0.00 0.00 0.00 2.01
824 961 7.827729 GGTTGATTAATACTCCCTGTGTAAACT 59.172 37.037 0.00 0.00 0.00 2.66
825 962 9.880157 GTTGATTAATACTCCCTGTGTAAACTA 57.120 33.333 0.00 0.00 0.00 2.24
827 964 9.263446 TGATTAATACTCCCTGTGTAAACTAGT 57.737 33.333 0.00 0.00 0.00 2.57
838 975 9.694137 CCCTGTGTAAACTAGTAATATAAGAGC 57.306 37.037 0.00 0.00 0.00 4.09
877 1014 9.817809 TCTAAATACTCACTAATGTTGTGATCC 57.182 33.333 0.00 0.00 42.57 3.36
878 1015 9.599866 CTAAATACTCACTAATGTTGTGATCCA 57.400 33.333 0.00 0.00 42.57 3.41
879 1016 8.862325 AAATACTCACTAATGTTGTGATCCAA 57.138 30.769 0.00 0.00 42.57 3.53
880 1017 8.862325 AATACTCACTAATGTTGTGATCCAAA 57.138 30.769 0.00 0.00 42.57 3.28
881 1018 6.560253 ACTCACTAATGTTGTGATCCAAAC 57.440 37.500 0.00 0.00 42.57 2.93
882 1019 5.179368 ACTCACTAATGTTGTGATCCAAACG 59.821 40.000 0.00 0.00 42.57 3.60
883 1020 4.083537 TCACTAATGTTGTGATCCAAACGC 60.084 41.667 0.00 0.00 39.23 4.84
884 1021 4.072131 ACTAATGTTGTGATCCAAACGCT 58.928 39.130 0.00 0.00 34.07 5.07
885 1022 4.518970 ACTAATGTTGTGATCCAAACGCTT 59.481 37.500 0.00 0.00 34.07 4.68
886 1023 4.320608 AATGTTGTGATCCAAACGCTTT 57.679 36.364 0.00 0.00 34.07 3.51
887 1024 3.791973 TGTTGTGATCCAAACGCTTTT 57.208 38.095 0.00 0.00 34.07 2.27
888 1025 4.902443 TGTTGTGATCCAAACGCTTTTA 57.098 36.364 0.00 0.00 34.07 1.52
889 1026 5.446143 TGTTGTGATCCAAACGCTTTTAT 57.554 34.783 0.00 0.00 34.07 1.40
890 1027 5.218885 TGTTGTGATCCAAACGCTTTTATG 58.781 37.500 0.00 0.00 34.07 1.90
891 1028 5.219633 GTTGTGATCCAAACGCTTTTATGT 58.780 37.500 0.00 0.00 34.07 2.29
892 1029 5.446143 TGTGATCCAAACGCTTTTATGTT 57.554 34.783 0.00 0.00 0.00 2.71
893 1030 6.561737 TGTGATCCAAACGCTTTTATGTTA 57.438 33.333 0.00 0.00 0.00 2.41
894 1031 6.607689 TGTGATCCAAACGCTTTTATGTTAG 58.392 36.000 0.00 0.00 0.00 2.34
895 1032 6.205853 TGTGATCCAAACGCTTTTATGTTAGT 59.794 34.615 0.00 0.00 0.00 2.24
896 1033 7.081976 GTGATCCAAACGCTTTTATGTTAGTT 58.918 34.615 0.00 0.00 0.00 2.24
897 1034 7.593644 GTGATCCAAACGCTTTTATGTTAGTTT 59.406 33.333 0.00 0.00 32.82 2.66
898 1035 8.784994 TGATCCAAACGCTTTTATGTTAGTTTA 58.215 29.630 0.00 0.00 31.63 2.01
899 1036 8.959734 ATCCAAACGCTTTTATGTTAGTTTAC 57.040 30.769 0.00 0.00 31.63 2.01
900 1037 8.156994 TCCAAACGCTTTTATGTTAGTTTACT 57.843 30.769 0.00 0.00 31.63 2.24
901 1038 8.071368 TCCAAACGCTTTTATGTTAGTTTACTG 58.929 33.333 0.00 0.00 31.63 2.74
902 1039 8.071368 CCAAACGCTTTTATGTTAGTTTACTGA 58.929 33.333 0.00 0.00 31.63 3.41
903 1040 8.889000 CAAACGCTTTTATGTTAGTTTACTGAC 58.111 33.333 0.00 0.00 33.59 3.51
904 1041 6.814343 ACGCTTTTATGTTAGTTTACTGACG 58.186 36.000 1.13 0.00 35.49 4.35
905 1042 6.642131 ACGCTTTTATGTTAGTTTACTGACGA 59.358 34.615 0.00 0.00 35.49 4.20
951 1195 9.487442 ACAAACATGATAAATATACCCCACTTT 57.513 29.630 0.00 0.00 0.00 2.66
964 1212 3.460712 ACCCCACTTTACCTGTTAACACT 59.539 43.478 3.59 0.00 0.00 3.55
975 1223 3.741344 CCTGTTAACACTCACCTTCTTCG 59.259 47.826 3.59 0.00 0.00 3.79
982 1237 1.070289 ACTCACCTTCTTCGGAACCAC 59.930 52.381 0.00 0.00 0.00 4.16
1106 1379 2.771089 TGAGGTTAAGAAGCAGCTGTG 58.229 47.619 16.64 0.00 0.00 3.66
1299 1574 6.749139 TCACCTCTCCTACATATTTTGATCG 58.251 40.000 0.00 0.00 0.00 3.69
1379 1665 0.329261 TTAGTCTGGCATGGCAAGCT 59.671 50.000 23.47 22.87 28.00 3.74
1399 1685 0.249031 GCTTGGAAACACTGTGTGGC 60.249 55.000 15.11 9.29 42.67 5.01
1450 1736 1.474330 TCGGCATCTACAAGCAGAGA 58.526 50.000 0.00 0.00 31.52 3.10
1522 1808 2.041265 ACCGGGCAGATCCTCCTT 59.959 61.111 6.32 0.00 34.39 3.36
1654 1940 1.901085 GCAGAACATCGTCCTCCCT 59.099 57.895 0.00 0.00 0.00 4.20
1716 2002 2.120282 TGTGCTGGTTGCTGGTGTG 61.120 57.895 0.00 0.00 43.37 3.82
1721 2007 2.519302 GGTTGCTGGTGTGCAGGT 60.519 61.111 0.00 0.00 44.27 4.00
1816 2102 1.407936 ACATCAGGGTCTCTCCATCG 58.592 55.000 0.00 0.00 38.11 3.84
1945 4080 2.019156 GCCCCTCAGATTTGCAGGTAC 61.019 57.143 0.00 0.00 0.00 3.34
2124 4266 6.653020 TGGAGTATTTCACATTCTGTATGCT 58.347 36.000 0.00 0.00 37.81 3.79
2491 4668 1.753930 ACATTGCGAGAATGATGCCA 58.246 45.000 12.94 0.00 0.00 4.92
2560 4737 4.716784 TCAGGTAAATGTAGAGGATGCACT 59.283 41.667 0.00 0.00 0.00 4.40
2587 4764 9.855021 AAATAACTCAAATTCCAAGTATTTCCG 57.145 29.630 0.00 0.00 0.00 4.30
2621 4808 8.690884 TCCTGAATTTCAACTCTAGTCTATCTG 58.309 37.037 0.01 0.00 0.00 2.90
2656 4862 1.476891 GCACCCGTCTATCTTGTCTCA 59.523 52.381 0.00 0.00 0.00 3.27
2787 5011 2.673326 GCTTGCAAAGGATTGGAGCTTC 60.673 50.000 0.00 0.00 46.35 3.86
2913 5142 3.424703 ACCATGCATACAGAAAGTTGCT 58.575 40.909 0.00 0.00 36.14 3.91
3046 5277 0.752743 TGCTGCTGGCCATTACCATC 60.753 55.000 5.51 0.00 39.54 3.51
3099 10252 2.492881 CAAAACCTCTGCCATGCATACA 59.507 45.455 0.00 0.00 38.13 2.29
3123 10276 1.094785 ATTCCATCGGTCGGCTTTTG 58.905 50.000 0.00 0.00 0.00 2.44
3126 10279 2.750237 ATCGGTCGGCTTTTGGGC 60.750 61.111 0.00 0.00 37.12 5.36
3144 10297 9.090692 CTTTTGGGCATCTTGAATTATTGTAAG 57.909 33.333 0.00 0.00 0.00 2.34
3165 10318 2.422519 GGTGTGGCTCATCATCTTCCAT 60.423 50.000 0.00 0.00 0.00 3.41
3271 10425 3.428532 AGATGCACAAATTCTCTTGGCT 58.571 40.909 0.00 0.00 0.00 4.75
3337 15591 6.481954 ACTCGTGAAGAATTAATTGGTCAC 57.518 37.500 20.92 20.92 33.62 3.67
3354 15616 2.047655 CCGCTTAGTCACCGGCAA 60.048 61.111 0.00 0.00 35.14 4.52
3355 15617 1.669760 CCGCTTAGTCACCGGCAAA 60.670 57.895 0.00 0.00 35.14 3.68
3386 15679 6.105333 TCTGTTTTGGTGATTTTTGTCCAAG 58.895 36.000 0.00 0.00 40.34 3.61
3403 15713 8.496534 TTGTCCAAGATGAGATAGAATGGATA 57.503 34.615 0.00 0.00 37.76 2.59
3458 15775 5.247507 TGCGGGAATGAATCAATAAAGTG 57.752 39.130 0.00 0.00 0.00 3.16
3523 15840 6.530120 TGCAACATTTTCCTTCTGAGTACTA 58.470 36.000 0.00 0.00 0.00 1.82
3577 15901 1.066752 GTTGTTTTGTCCCGGTGGC 59.933 57.895 0.00 0.00 0.00 5.01
3579 15903 2.519780 GTTTTGTCCCGGTGGCCA 60.520 61.111 0.00 0.00 0.00 5.36
3635 15959 1.806542 CGACAAGGAAGTGGTGGAATG 59.193 52.381 0.00 0.00 0.00 2.67
3643 15967 1.198759 AGTGGTGGAATGTACCGGCT 61.199 55.000 0.00 0.00 41.18 5.52
3646 15975 1.202952 TGGTGGAATGTACCGGCTTTT 60.203 47.619 0.00 0.00 41.18 2.27
3655 15984 1.659098 GTACCGGCTTTTCATCGTCTG 59.341 52.381 0.00 0.00 0.00 3.51
3656 15985 0.034896 ACCGGCTTTTCATCGTCTGT 59.965 50.000 0.00 0.00 0.00 3.41
3663 15992 4.142600 GGCTTTTCATCGTCTGTATTTGCT 60.143 41.667 0.00 0.00 0.00 3.91
3670 16002 3.521560 TCGTCTGTATTTGCTGATCACC 58.478 45.455 0.00 0.00 0.00 4.02
3699 16034 8.339344 TCAAGTACATGATGAATTTGTGACAT 57.661 30.769 0.00 0.00 0.00 3.06
3709 16044 3.767902 ATTTGTGACATGTTTTGGGGG 57.232 42.857 0.00 0.00 0.00 5.40
3711 16046 2.692709 TGTGACATGTTTTGGGGGAT 57.307 45.000 0.00 0.00 0.00 3.85
3712 16047 3.816398 TGTGACATGTTTTGGGGGATA 57.184 42.857 0.00 0.00 0.00 2.59
3713 16048 4.329638 TGTGACATGTTTTGGGGGATAT 57.670 40.909 0.00 0.00 0.00 1.63
3769 16738 7.385778 ACAAAGAGGATCGAGCTATATAGTC 57.614 40.000 11.38 6.88 42.67 2.59
3770 16739 6.376018 ACAAAGAGGATCGAGCTATATAGTCC 59.624 42.308 11.38 9.42 42.67 3.85
3772 16741 6.260700 AGAGGATCGAGCTATATAGTCCAT 57.739 41.667 15.24 5.92 42.67 3.41
3773 16742 7.381789 AGAGGATCGAGCTATATAGTCCATA 57.618 40.000 15.24 0.00 42.67 2.74
3774 16743 7.984475 AGAGGATCGAGCTATATAGTCCATAT 58.016 38.462 15.24 3.81 42.67 1.78
3775 16744 7.882791 AGAGGATCGAGCTATATAGTCCATATG 59.117 40.741 15.24 0.00 42.67 1.78
3804 16773 3.873952 GCTATGCTACTTTGGTGGAAGAG 59.126 47.826 0.00 0.00 0.00 2.85
3812 16783 2.514824 GGTGGAAGAGATGGCCGC 60.515 66.667 0.00 0.00 0.00 6.53
3817 16788 3.371097 GAAGAGATGGCCGCCGTCA 62.371 63.158 29.36 2.14 41.68 4.35
3858 16829 3.586470 ACCTCGAGTCTACATCCATCT 57.414 47.619 12.31 0.00 0.00 2.90
3901 16873 6.488006 GCATCTAAAGCATCTTCCTTATTGGA 59.512 38.462 0.00 0.00 44.51 3.53
3939 16914 1.671054 GCCTTGTGAGCGCTTGGTA 60.671 57.895 13.26 0.00 0.00 3.25
3945 16920 3.552604 TGTGAGCGCTTGGTATTTTTC 57.447 42.857 13.26 0.00 0.00 2.29
3975 16950 2.430244 CGGCGCTAGACACGTTGT 60.430 61.111 7.64 0.00 0.00 3.32
3986 16961 1.798223 GACACGTTGTCATGCTTGCTA 59.202 47.619 11.62 0.00 46.22 3.49
3989 16964 3.228749 CACGTTGTCATGCTTGCTAAAG 58.771 45.455 0.00 0.00 36.41 1.85
4032 17007 2.695359 TCACGGTGAGAGGCAAATTAC 58.305 47.619 6.76 0.00 0.00 1.89
4038 17013 1.337354 TGAGAGGCAAATTACGCACGA 60.337 47.619 0.00 0.00 0.00 4.35
4053 17028 2.419667 GCACGAAGCACCCTAAAACTA 58.580 47.619 0.00 0.00 44.79 2.24
4059 17034 1.095600 GCACCCTAAAACTAGGCTGC 58.904 55.000 0.00 3.38 40.40 5.25
4106 17082 5.953548 TGTGTGTTGGCCTATAACTAGAGTA 59.046 40.000 3.32 0.00 0.00 2.59
4160 17139 3.433314 CCCTCTCATTGAGTTCCTGATGG 60.433 52.174 13.23 4.79 41.11 3.51
4161 17140 3.433314 CCTCTCATTGAGTTCCTGATGGG 60.433 52.174 13.23 1.01 41.11 4.00
4162 17141 2.507058 TCTCATTGAGTTCCTGATGGGG 59.493 50.000 13.23 0.00 35.33 4.96
4163 17142 1.565759 TCATTGAGTTCCTGATGGGGG 59.434 52.381 0.00 0.00 35.33 5.40
4164 17143 0.259938 ATTGAGTTCCTGATGGGGGC 59.740 55.000 0.00 0.00 35.33 5.80
4165 17144 1.139498 TTGAGTTCCTGATGGGGGCA 61.139 55.000 0.00 0.00 35.33 5.36
4166 17145 1.139498 TGAGTTCCTGATGGGGGCAA 61.139 55.000 0.00 0.00 35.33 4.52
4167 17146 0.039618 GAGTTCCTGATGGGGGCAAA 59.960 55.000 0.00 0.00 35.33 3.68
4168 17147 0.251787 AGTTCCTGATGGGGGCAAAC 60.252 55.000 0.00 0.00 35.33 2.93
4169 17148 1.078347 TTCCTGATGGGGGCAAACC 59.922 57.895 0.00 0.00 39.11 3.27
4170 17149 1.734420 TTCCTGATGGGGGCAAACCA 61.734 55.000 0.00 0.00 42.91 3.67
4174 17153 4.032653 ATGGGGGCAAACCATTCG 57.967 55.556 2.24 0.00 46.25 3.34
4175 17154 1.078347 ATGGGGGCAAACCATTCGT 59.922 52.632 2.24 0.00 46.25 3.85
4176 17155 1.257055 ATGGGGGCAAACCATTCGTG 61.257 55.000 2.24 0.00 46.25 4.35
4177 17156 1.605165 GGGGGCAAACCATTCGTGA 60.605 57.895 0.00 0.00 42.91 4.35
4178 17157 1.595093 GGGGGCAAACCATTCGTGAG 61.595 60.000 0.00 0.00 42.91 3.51
4179 17158 1.212751 GGGCAAACCATTCGTGAGC 59.787 57.895 0.00 0.00 39.85 4.26
4180 17159 1.244019 GGGCAAACCATTCGTGAGCT 61.244 55.000 0.00 0.00 39.85 4.09
4181 17160 0.598065 GGCAAACCATTCGTGAGCTT 59.402 50.000 0.00 0.00 35.26 3.74
4182 17161 1.000274 GGCAAACCATTCGTGAGCTTT 60.000 47.619 0.00 0.00 35.26 3.51
4183 17162 2.053627 GCAAACCATTCGTGAGCTTTG 58.946 47.619 0.00 0.00 0.00 2.77
4184 17163 2.287547 GCAAACCATTCGTGAGCTTTGA 60.288 45.455 0.00 0.00 0.00 2.69
4185 17164 3.612479 GCAAACCATTCGTGAGCTTTGAT 60.612 43.478 0.00 0.00 0.00 2.57
4186 17165 4.549458 CAAACCATTCGTGAGCTTTGATT 58.451 39.130 0.00 0.00 0.00 2.57
4187 17166 4.853924 AACCATTCGTGAGCTTTGATTT 57.146 36.364 0.00 0.00 0.00 2.17
4188 17167 4.853924 ACCATTCGTGAGCTTTGATTTT 57.146 36.364 0.00 0.00 0.00 1.82
4189 17168 5.200368 ACCATTCGTGAGCTTTGATTTTT 57.800 34.783 0.00 0.00 0.00 1.94
4210 17189 6.981762 TTTTTGACTTCTGTAACCGTAACA 57.018 33.333 0.00 0.00 0.00 2.41
4211 17190 6.981762 TTTTGACTTCTGTAACCGTAACAA 57.018 33.333 0.00 0.00 0.00 2.83
4212 17191 6.981762 TTTGACTTCTGTAACCGTAACAAA 57.018 33.333 0.00 0.00 0.00 2.83
4213 17192 5.971895 TGACTTCTGTAACCGTAACAAAC 57.028 39.130 0.00 0.00 0.00 2.93
4214 17193 4.810491 TGACTTCTGTAACCGTAACAAACC 59.190 41.667 0.00 0.00 0.00 3.27
4215 17194 5.027293 ACTTCTGTAACCGTAACAAACCT 57.973 39.130 0.00 0.00 0.00 3.50
4216 17195 5.052481 ACTTCTGTAACCGTAACAAACCTC 58.948 41.667 0.00 0.00 0.00 3.85
4217 17196 4.942761 TCTGTAACCGTAACAAACCTCT 57.057 40.909 0.00 0.00 0.00 3.69
4218 17197 4.874970 TCTGTAACCGTAACAAACCTCTC 58.125 43.478 0.00 0.00 0.00 3.20
4219 17198 3.992427 CTGTAACCGTAACAAACCTCTCC 59.008 47.826 0.00 0.00 0.00 3.71
4220 17199 3.387374 TGTAACCGTAACAAACCTCTCCA 59.613 43.478 0.00 0.00 0.00 3.86
4221 17200 3.564053 AACCGTAACAAACCTCTCCAA 57.436 42.857 0.00 0.00 0.00 3.53
4222 17201 3.564053 ACCGTAACAAACCTCTCCAAA 57.436 42.857 0.00 0.00 0.00 3.28
4223 17202 3.888583 ACCGTAACAAACCTCTCCAAAA 58.111 40.909 0.00 0.00 0.00 2.44
4224 17203 4.271661 ACCGTAACAAACCTCTCCAAAAA 58.728 39.130 0.00 0.00 0.00 1.94
4225 17204 4.891168 ACCGTAACAAACCTCTCCAAAAAT 59.109 37.500 0.00 0.00 0.00 1.82
4226 17205 5.009310 ACCGTAACAAACCTCTCCAAAAATC 59.991 40.000 0.00 0.00 0.00 2.17
4227 17206 5.009210 CCGTAACAAACCTCTCCAAAAATCA 59.991 40.000 0.00 0.00 0.00 2.57
4228 17207 5.912955 CGTAACAAACCTCTCCAAAAATCAC 59.087 40.000 0.00 0.00 0.00 3.06
4229 17208 4.568152 ACAAACCTCTCCAAAAATCACG 57.432 40.909 0.00 0.00 0.00 4.35
4230 17209 3.243401 ACAAACCTCTCCAAAAATCACGC 60.243 43.478 0.00 0.00 0.00 5.34
4231 17210 2.568623 ACCTCTCCAAAAATCACGCT 57.431 45.000 0.00 0.00 0.00 5.07
4232 17211 2.427506 ACCTCTCCAAAAATCACGCTC 58.572 47.619 0.00 0.00 0.00 5.03
4233 17212 2.039084 ACCTCTCCAAAAATCACGCTCT 59.961 45.455 0.00 0.00 0.00 4.09
4234 17213 2.417933 CCTCTCCAAAAATCACGCTCTG 59.582 50.000 0.00 0.00 0.00 3.35
4235 17214 2.417933 CTCTCCAAAAATCACGCTCTGG 59.582 50.000 0.00 0.00 0.00 3.86
4236 17215 0.881118 TCCAAAAATCACGCTCTGGC 59.119 50.000 0.00 0.00 0.00 4.85
4237 17216 0.109132 CCAAAAATCACGCTCTGGCC 60.109 55.000 0.00 0.00 34.44 5.36
4238 17217 0.109132 CAAAAATCACGCTCTGGCCC 60.109 55.000 0.00 0.00 34.44 5.80
4239 17218 1.250840 AAAAATCACGCTCTGGCCCC 61.251 55.000 0.00 0.00 34.44 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.278413 GTAAAAAGCTCCTCCCTCCGT 59.722 52.381 0.00 0.00 0.00 4.69
1 2 1.278127 TGTAAAAAGCTCCTCCCTCCG 59.722 52.381 0.00 0.00 0.00 4.63
2 3 2.618302 GGTGTAAAAAGCTCCTCCCTCC 60.618 54.545 0.00 0.00 0.00 4.30
10 11 3.071479 TGTGATCCGGTGTAAAAAGCTC 58.929 45.455 0.00 0.00 0.00 4.09
33 34 4.380843 TCAGAAGGCTTGGGAAAATACA 57.619 40.909 3.46 0.00 0.00 2.29
36 37 3.575687 CACTTCAGAAGGCTTGGGAAAAT 59.424 43.478 14.90 0.00 0.00 1.82
44 45 0.402121 GGACCCACTTCAGAAGGCTT 59.598 55.000 14.90 0.00 0.00 4.35
46 47 1.002011 GGGACCCACTTCAGAAGGC 60.002 63.158 14.90 0.00 0.00 4.35
50 58 1.827399 GAAGCGGGACCCACTTCAGA 61.827 60.000 29.03 0.00 39.66 3.27
60 68 1.956629 TTCGGATGGAGAAGCGGGAC 61.957 60.000 0.00 0.00 0.00 4.46
64 72 0.744874 TAGGTTCGGATGGAGAAGCG 59.255 55.000 3.08 0.00 46.89 4.68
65 73 3.477210 AATAGGTTCGGATGGAGAAGC 57.523 47.619 0.51 0.51 43.92 3.86
76 84 4.372656 GGATGTCAGGAGAAATAGGTTCG 58.627 47.826 0.00 0.00 41.52 3.95
102 110 1.829533 GCCCCACATGCCATGTAGG 60.830 63.158 14.53 14.53 42.70 3.18
109 117 0.896940 CATATCCTGCCCCACATGCC 60.897 60.000 0.00 0.00 0.00 4.40
124 141 1.070604 AGGGCATGGCTAGTGCATAT 58.929 50.000 19.78 0.00 44.25 1.78
133 150 1.530771 CAGCTCTAAGGGCATGGCT 59.469 57.895 19.78 2.39 0.00 4.75
144 161 8.143157 TGTAGAAACAAACAGAGCCAGCTCTA 62.143 42.308 21.19 0.00 41.04 2.43
148 165 2.878406 TGTAGAAACAAACAGAGCCAGC 59.122 45.455 0.00 0.00 30.91 4.85
178 195 1.872952 CAAGCGTCCACAAGTGATTCA 59.127 47.619 0.94 0.00 0.00 2.57
194 211 0.880278 TGACTGAAGCACGTCCAAGC 60.880 55.000 0.00 0.00 0.00 4.01
230 250 4.880696 AGTGAAGCTGAATCTAGATTTGGC 59.119 41.667 23.98 23.98 0.00 4.52
267 287 5.509498 AGCTGAAACCCAATAGCTATTTGA 58.491 37.500 16.46 0.00 44.10 2.69
296 316 4.826183 GGCAGCAGATTCTCATAGGAAAAT 59.174 41.667 0.00 0.00 0.00 1.82
376 398 2.113860 TTCCTAAGATGCACTGCCAC 57.886 50.000 0.00 0.00 0.00 5.01
412 434 3.318275 ACGACCTACTTCATGACGCATAT 59.682 43.478 0.00 0.00 0.00 1.78
443 470 5.464722 CCTCATTTGTCATATCTGAACCTCG 59.535 44.000 0.00 0.00 31.85 4.63
445 472 6.352516 GTCCTCATTTGTCATATCTGAACCT 58.647 40.000 0.00 0.00 31.85 3.50
461 488 0.820871 GAGCCACTCTCGTCCTCATT 59.179 55.000 0.00 0.00 31.20 2.57
466 493 3.827898 CCGGAGCCACTCTCGTCC 61.828 72.222 0.00 0.00 42.82 4.79
524 580 3.183775 GCCCGTTTGCACTATTATAGTCG 59.816 47.826 1.33 3.04 36.76 4.18
563 669 3.066621 GCAAGATTGGATGGAATGCGTTA 59.933 43.478 0.00 0.00 37.56 3.18
564 670 2.159198 GCAAGATTGGATGGAATGCGTT 60.159 45.455 0.00 0.00 37.56 4.84
565 671 1.406539 GCAAGATTGGATGGAATGCGT 59.593 47.619 0.00 0.00 37.56 5.24
566 672 1.679680 AGCAAGATTGGATGGAATGCG 59.320 47.619 0.00 0.00 37.56 4.73
567 673 2.287427 CGAGCAAGATTGGATGGAATGC 60.287 50.000 0.00 0.00 33.97 3.56
681 811 3.347216 CCTCCGAACCAGTCAATTTCAT 58.653 45.455 0.00 0.00 0.00 2.57
706 836 2.034687 TTGGCAGCCAAGAGGAGC 59.965 61.111 23.88 0.00 38.75 4.70
812 949 9.694137 GCTCTTATATTACTAGTTTACACAGGG 57.306 37.037 0.00 0.00 0.00 4.45
861 998 4.083324 AGCGTTTGGATCACAACATTAGTG 60.083 41.667 0.00 0.00 39.19 2.74
862 999 4.072131 AGCGTTTGGATCACAACATTAGT 58.928 39.130 0.00 0.00 39.19 2.24
863 1000 4.685169 AGCGTTTGGATCACAACATTAG 57.315 40.909 0.00 0.00 39.19 1.73
864 1001 5.446143 AAAGCGTTTGGATCACAACATTA 57.554 34.783 0.00 0.00 39.19 1.90
865 1002 4.320608 AAAGCGTTTGGATCACAACATT 57.679 36.364 0.00 0.00 39.19 2.71
866 1003 4.320608 AAAAGCGTTTGGATCACAACAT 57.679 36.364 0.00 0.00 39.19 2.71
867 1004 3.791973 AAAAGCGTTTGGATCACAACA 57.208 38.095 0.00 0.00 39.19 3.33
868 1005 5.219633 ACATAAAAGCGTTTGGATCACAAC 58.780 37.500 7.95 0.00 39.19 3.32
869 1006 5.446143 ACATAAAAGCGTTTGGATCACAA 57.554 34.783 7.95 0.00 37.28 3.33
870 1007 5.446143 AACATAAAAGCGTTTGGATCACA 57.554 34.783 7.95 0.00 0.00 3.58
871 1008 6.608610 ACTAACATAAAAGCGTTTGGATCAC 58.391 36.000 7.95 0.00 0.00 3.06
872 1009 6.811253 ACTAACATAAAAGCGTTTGGATCA 57.189 33.333 7.95 0.00 0.00 2.92
873 1010 9.058424 GTAAACTAACATAAAAGCGTTTGGATC 57.942 33.333 7.95 0.00 0.00 3.36
874 1011 8.789762 AGTAAACTAACATAAAAGCGTTTGGAT 58.210 29.630 7.95 0.00 0.00 3.41
875 1012 8.071368 CAGTAAACTAACATAAAAGCGTTTGGA 58.929 33.333 7.95 0.00 0.00 3.53
876 1013 8.071368 TCAGTAAACTAACATAAAAGCGTTTGG 58.929 33.333 7.95 2.80 0.00 3.28
877 1014 8.889000 GTCAGTAAACTAACATAAAAGCGTTTG 58.111 33.333 7.95 0.00 0.00 2.93
878 1015 7.795272 CGTCAGTAAACTAACATAAAAGCGTTT 59.205 33.333 2.53 2.53 0.00 3.60
879 1016 7.169645 TCGTCAGTAAACTAACATAAAAGCGTT 59.830 33.333 0.00 0.00 0.00 4.84
880 1017 6.642131 TCGTCAGTAAACTAACATAAAAGCGT 59.358 34.615 0.00 0.00 0.00 5.07
881 1018 7.041187 TCGTCAGTAAACTAACATAAAAGCG 57.959 36.000 0.00 0.00 0.00 4.68
882 1019 8.493547 ACTTCGTCAGTAAACTAACATAAAAGC 58.506 33.333 0.00 0.00 31.97 3.51
951 1195 5.508489 CGAAGAAGGTGAGTGTTAACAGGTA 60.508 44.000 8.98 0.00 0.00 3.08
964 1212 0.032952 CGTGGTTCCGAAGAAGGTGA 59.967 55.000 0.00 0.00 30.91 4.02
975 1223 0.953960 AAATCTCACGCCGTGGTTCC 60.954 55.000 18.32 0.00 33.87 3.62
982 1237 0.729116 ATGCTTGAAATCTCACGCCG 59.271 50.000 0.00 0.00 44.22 6.46
1299 1574 7.538678 GGTTGATGTTAGTTGTTCATTCATGAC 59.461 37.037 0.00 0.00 36.36 3.06
1379 1665 1.102154 CCACACAGTGTTTCCAAGCA 58.898 50.000 2.45 0.00 0.00 3.91
1415 1701 0.103208 CCGAGCAGATGGTACTGTCC 59.897 60.000 0.00 0.00 39.73 4.02
1539 1825 2.199535 CCCCCATGGCAATCTCCC 59.800 66.667 6.09 0.00 0.00 4.30
1654 1940 1.375908 GCCTGAACTCGCCATCACA 60.376 57.895 0.00 0.00 0.00 3.58
1721 2007 2.139484 CCTTGTTGCCCAGCCCAAA 61.139 57.895 0.00 0.00 0.00 3.28
2124 4266 3.330405 TCCACATTTCCCATCAGAACAGA 59.670 43.478 0.00 0.00 0.00 3.41
2396 4573 5.520649 CCGAGAGCATAAGAAGTCCTAAAAC 59.479 44.000 0.00 0.00 0.00 2.43
2397 4574 5.187186 ACCGAGAGCATAAGAAGTCCTAAAA 59.813 40.000 0.00 0.00 0.00 1.52
2491 4668 3.594603 ATGATCGACACGGAAAGAAGT 57.405 42.857 0.00 0.00 0.00 3.01
2787 5011 3.223423 AGTACGCACTGAGATTGACAG 57.777 47.619 0.00 0.00 40.68 3.51
2913 5142 9.288576 AGATGAGAATGAAATACAAGTGAAACA 57.711 29.630 0.00 0.00 41.43 2.83
3046 5277 1.795170 CTTTGTCCCAGTTGGTGCGG 61.795 60.000 0.00 0.00 34.77 5.69
3099 10252 1.416401 AGCCGACCGATGGAATAATGT 59.584 47.619 0.00 0.00 0.00 2.71
3123 10276 6.096846 ACACCTTACAATAATTCAAGATGCCC 59.903 38.462 0.00 0.00 0.00 5.36
3126 10279 6.974622 GCCACACCTTACAATAATTCAAGATG 59.025 38.462 0.00 0.00 0.00 2.90
3144 10297 1.065199 TGGAAGATGATGAGCCACACC 60.065 52.381 0.00 0.00 0.00 4.16
3271 10425 2.043248 GTCCTGCTCCCGGTCCTA 60.043 66.667 0.00 0.00 0.00 2.94
3354 15616 9.048446 CAAAAATCACCAAAACAGATCATTCTT 57.952 29.630 0.00 0.00 0.00 2.52
3355 15617 8.206189 ACAAAAATCACCAAAACAGATCATTCT 58.794 29.630 0.00 0.00 0.00 2.40
3403 15713 2.289819 CCATGCCTTTGCCTGTGAAAAT 60.290 45.455 0.00 0.00 36.33 1.82
3428 15738 0.249120 TTCATTCCCGCATCGACTGT 59.751 50.000 0.00 0.00 0.00 3.55
3437 15747 5.499139 TCACTTTATTGATTCATTCCCGC 57.501 39.130 0.00 0.00 0.00 6.13
3465 15782 4.694037 GGATTTTCTAGTAAACGCACCACT 59.306 41.667 0.00 0.00 0.00 4.00
3466 15783 4.435121 CGGATTTTCTAGTAAACGCACCAC 60.435 45.833 0.00 0.00 0.00 4.16
3468 15785 3.484721 GCGGATTTTCTAGTAAACGCACC 60.485 47.826 18.48 10.10 44.52 5.01
3469 15786 3.667050 GCGGATTTTCTAGTAAACGCAC 58.333 45.455 18.48 4.34 44.52 5.34
3472 15789 6.292168 CCATACTGCGGATTTTCTAGTAAACG 60.292 42.308 0.00 0.00 0.00 3.60
3553 15877 4.295051 CACCGGGACAAAACAACTTAATG 58.705 43.478 6.32 0.00 0.00 1.90
3558 15882 1.388837 GCCACCGGGACAAAACAACT 61.389 55.000 6.32 0.00 35.59 3.16
3579 15903 7.823745 AGTAATTCAGTTTTTCCACATCAGT 57.176 32.000 0.00 0.00 0.00 3.41
3635 15959 1.659098 CAGACGATGAAAAGCCGGTAC 59.341 52.381 1.90 0.00 0.00 3.34
3643 15967 6.371271 TGATCAGCAAATACAGACGATGAAAA 59.629 34.615 0.00 0.00 0.00 2.29
3646 15975 4.805719 GTGATCAGCAAATACAGACGATGA 59.194 41.667 0.00 0.00 0.00 2.92
3670 16002 8.671028 TCACAAATTCATCATGTACTTGATCAG 58.329 33.333 18.63 10.75 34.09 2.90
3699 16034 9.945904 GTTTAATTTGTTATATCCCCCAAAACA 57.054 29.630 0.00 0.00 31.30 2.83
3735 16070 8.207545 AGCTCGATCCTCTTTGTTATTCTAAAT 58.792 33.333 0.00 0.00 0.00 1.40
3743 16078 8.865420 ACTATATAGCTCGATCCTCTTTGTTA 57.135 34.615 9.78 0.00 0.00 2.41
3786 16755 3.307691 CCATCTCTTCCACCAAAGTAGCA 60.308 47.826 0.00 0.00 0.00 3.49
3796 16765 2.514824 GGCGGCCATCTCTTCCAC 60.515 66.667 15.62 0.00 0.00 4.02
3812 16783 2.032071 GTGGGAAGGTGGTGACGG 59.968 66.667 0.00 0.00 0.00 4.79
3817 16788 1.152546 GCTTTGGTGGGAAGGTGGT 60.153 57.895 0.00 0.00 0.00 4.16
3858 16829 9.719355 TTTAGATGCTCTGAACACACTATTTTA 57.281 29.630 0.00 0.00 0.00 1.52
3901 16873 2.223249 GCAACATTATCGACGGCACATT 60.223 45.455 0.00 0.00 0.00 2.71
3939 16914 5.282510 CGCCGAGTGATCTACTAGAAAAAT 58.717 41.667 0.00 0.00 40.53 1.82
3945 16920 1.231221 AGCGCCGAGTGATCTACTAG 58.769 55.000 2.29 0.00 40.53 2.57
3975 16950 5.065914 ACAACTCTTCTTTAGCAAGCATGA 58.934 37.500 0.00 0.00 0.00 3.07
3977 16952 6.234177 ACTACAACTCTTCTTTAGCAAGCAT 58.766 36.000 0.00 0.00 0.00 3.79
3980 16955 7.224753 TCACAACTACAACTCTTCTTTAGCAAG 59.775 37.037 0.00 0.00 0.00 4.01
3986 16961 7.331791 AGAACTCACAACTACAACTCTTCTTT 58.668 34.615 0.00 0.00 0.00 2.52
3989 16964 6.757010 TGAAGAACTCACAACTACAACTCTTC 59.243 38.462 0.00 0.00 37.72 2.87
4032 17007 0.110373 GTTTTAGGGTGCTTCGTGCG 60.110 55.000 0.00 0.00 46.63 5.34
4053 17028 1.912043 ACCAAGAGACATTAGCAGCCT 59.088 47.619 0.00 0.00 0.00 4.58
4059 17034 2.926200 CGCTCACACCAAGAGACATTAG 59.074 50.000 0.00 0.00 35.09 1.73
4160 17139 1.883021 CTCACGAATGGTTTGCCCC 59.117 57.895 0.00 0.00 0.00 5.80
4161 17140 1.212751 GCTCACGAATGGTTTGCCC 59.787 57.895 0.00 0.00 0.00 5.36
4162 17141 0.598065 AAGCTCACGAATGGTTTGCC 59.402 50.000 0.00 0.00 0.00 4.52
4163 17142 2.053627 CAAAGCTCACGAATGGTTTGC 58.946 47.619 13.93 0.00 42.12 3.68
4164 17143 3.624326 TCAAAGCTCACGAATGGTTTG 57.376 42.857 17.51 17.51 46.57 2.93
4165 17144 4.853924 AATCAAAGCTCACGAATGGTTT 57.146 36.364 0.00 0.00 34.74 3.27
4166 17145 4.853924 AAATCAAAGCTCACGAATGGTT 57.146 36.364 0.00 0.00 0.00 3.67
4167 17146 4.853924 AAAATCAAAGCTCACGAATGGT 57.146 36.364 0.00 0.00 0.00 3.55
4187 17166 6.981762 TGTTACGGTTACAGAAGTCAAAAA 57.018 33.333 0.00 0.00 0.00 1.94
4188 17167 6.981762 TTGTTACGGTTACAGAAGTCAAAA 57.018 33.333 0.00 0.00 0.00 2.44
4189 17168 6.183360 GGTTTGTTACGGTTACAGAAGTCAAA 60.183 38.462 0.00 0.00 0.00 2.69
4190 17169 5.294060 GGTTTGTTACGGTTACAGAAGTCAA 59.706 40.000 0.00 0.00 0.00 3.18
4191 17170 4.810491 GGTTTGTTACGGTTACAGAAGTCA 59.190 41.667 0.00 0.00 0.00 3.41
4192 17171 5.052481 AGGTTTGTTACGGTTACAGAAGTC 58.948 41.667 0.00 0.00 0.00 3.01
4193 17172 5.027293 AGGTTTGTTACGGTTACAGAAGT 57.973 39.130 0.00 0.00 0.00 3.01
4194 17173 5.295152 AGAGGTTTGTTACGGTTACAGAAG 58.705 41.667 0.00 0.00 0.00 2.85
4195 17174 5.280654 AGAGGTTTGTTACGGTTACAGAA 57.719 39.130 0.00 0.00 0.00 3.02
4196 17175 4.262164 GGAGAGGTTTGTTACGGTTACAGA 60.262 45.833 0.00 0.00 0.00 3.41
4197 17176 3.992427 GGAGAGGTTTGTTACGGTTACAG 59.008 47.826 0.00 0.00 0.00 2.74
4198 17177 3.387374 TGGAGAGGTTTGTTACGGTTACA 59.613 43.478 0.00 0.00 0.00 2.41
4199 17178 3.993920 TGGAGAGGTTTGTTACGGTTAC 58.006 45.455 0.00 0.00 0.00 2.50
4200 17179 4.686191 TTGGAGAGGTTTGTTACGGTTA 57.314 40.909 0.00 0.00 0.00 2.85
4201 17180 3.564053 TTGGAGAGGTTTGTTACGGTT 57.436 42.857 0.00 0.00 0.00 4.44
4202 17181 3.564053 TTTGGAGAGGTTTGTTACGGT 57.436 42.857 0.00 0.00 0.00 4.83
4203 17182 4.904253 TTTTTGGAGAGGTTTGTTACGG 57.096 40.909 0.00 0.00 0.00 4.02
4204 17183 5.912955 GTGATTTTTGGAGAGGTTTGTTACG 59.087 40.000 0.00 0.00 0.00 3.18
4205 17184 5.912955 CGTGATTTTTGGAGAGGTTTGTTAC 59.087 40.000 0.00 0.00 0.00 2.50
4206 17185 5.506649 GCGTGATTTTTGGAGAGGTTTGTTA 60.507 40.000 0.00 0.00 0.00 2.41
4207 17186 4.736464 GCGTGATTTTTGGAGAGGTTTGTT 60.736 41.667 0.00 0.00 0.00 2.83
4208 17187 3.243401 GCGTGATTTTTGGAGAGGTTTGT 60.243 43.478 0.00 0.00 0.00 2.83
4209 17188 3.004734 AGCGTGATTTTTGGAGAGGTTTG 59.995 43.478 0.00 0.00 0.00 2.93
4210 17189 3.222603 AGCGTGATTTTTGGAGAGGTTT 58.777 40.909 0.00 0.00 0.00 3.27
4211 17190 2.814336 GAGCGTGATTTTTGGAGAGGTT 59.186 45.455 0.00 0.00 0.00 3.50
4212 17191 2.039084 AGAGCGTGATTTTTGGAGAGGT 59.961 45.455 0.00 0.00 0.00 3.85
4213 17192 2.417933 CAGAGCGTGATTTTTGGAGAGG 59.582 50.000 0.00 0.00 0.00 3.69
4214 17193 2.417933 CCAGAGCGTGATTTTTGGAGAG 59.582 50.000 0.00 0.00 0.00 3.20
4215 17194 2.426522 CCAGAGCGTGATTTTTGGAGA 58.573 47.619 0.00 0.00 0.00 3.71
4216 17195 1.135575 GCCAGAGCGTGATTTTTGGAG 60.136 52.381 0.00 0.00 0.00 3.86
4217 17196 0.881118 GCCAGAGCGTGATTTTTGGA 59.119 50.000 0.00 0.00 0.00 3.53
4218 17197 0.109132 GGCCAGAGCGTGATTTTTGG 60.109 55.000 0.00 0.00 41.24 3.28
4219 17198 0.109132 GGGCCAGAGCGTGATTTTTG 60.109 55.000 4.39 0.00 41.24 2.44
4220 17199 1.250840 GGGGCCAGAGCGTGATTTTT 61.251 55.000 4.39 0.00 41.24 1.94
4221 17200 1.678970 GGGGCCAGAGCGTGATTTT 60.679 57.895 4.39 0.00 41.24 1.82
4222 17201 2.044946 GGGGCCAGAGCGTGATTT 60.045 61.111 4.39 0.00 41.24 2.17


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

AutoCloner maintained by Alex Coulton.