Multiple sequence alignment - TraesCS4A01G485500

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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 TraesCS4A01G485500 chr4A 100.000 3931 0 0 1 3931 739078337 739082267 0.000000e+00 7260.0
1 TraesCS4A01G485500 chr4A 84.829 936 137 5 987 1919 739130015 739130948 0.000000e+00 937.0
2 TraesCS4A01G485500 chr4A 80.000 945 180 9 981 1919 739273616 739274557 0.000000e+00 689.0
3 TraesCS4A01G485500 chr4A 80.521 729 139 3 2207 2934 739153861 739154587 1.230000e-154 556.0
4 TraesCS4A01G485500 chr4A 78.407 653 131 10 2243 2890 738887535 738886888 2.190000e-112 416.0
5 TraesCS4A01G485500 chr4A 95.964 223 9 0 3534 3756 642447268 642447490 2.890000e-96 363.0
6 TraesCS4A01G485500 chr4A 74.318 880 196 14 991 1843 739311317 739312193 2.910000e-91 346.0
7 TraesCS4A01G485500 chr4A 93.590 78 5 0 718 795 739129614 739129691 2.480000e-22 117.0
8 TraesCS4A01G485500 chr4A 92.500 80 6 0 716 795 739310614 739310693 8.930000e-22 115.0
9 TraesCS4A01G485500 chr7A 90.226 1995 136 21 119 2082 4330726 4328760 0.000000e+00 2549.0
10 TraesCS4A01G485500 chr7A 92.604 1014 73 1 2082 3093 4328723 4327710 0.000000e+00 1456.0
11 TraesCS4A01G485500 chr7A 84.475 934 141 2 987 1919 4254338 4253408 0.000000e+00 918.0
12 TraesCS4A01G485500 chr7A 84.345 939 139 7 987 1919 29664668 29663732 0.000000e+00 913.0
13 TraesCS4A01G485500 chr7A 78.891 938 194 3 985 1919 4069967 4069031 1.990000e-177 632.0
14 TraesCS4A01G485500 chr7A 80.667 750 138 6 2167 2912 4207026 4206280 3.410000e-160 575.0
15 TraesCS4A01G485500 chr7A 91.971 274 20 2 891 1164 4394480 4394209 2.220000e-102 383.0
16 TraesCS4A01G485500 chr7A 92.500 80 6 0 716 795 4254738 4254659 8.930000e-22 115.0
17 TraesCS4A01G485500 chr7A 92.405 79 6 0 717 795 3986237 3986159 3.210000e-21 113.0
18 TraesCS4A01G485500 chr7A 86.275 102 11 2 697 795 4625649 4625750 1.490000e-19 108.0
19 TraesCS4A01G485500 chr7A 95.000 40 0 2 3079 3117 186527674 186527712 1.180000e-05 62.1
20 TraesCS4A01G485500 chr7D 90.278 1944 133 16 1 1915 4504399 4502483 0.000000e+00 2492.0
21 TraesCS4A01G485500 chr7D 92.951 993 67 1 2101 3093 4502299 4501310 0.000000e+00 1443.0
22 TraesCS4A01G485500 chr7D 84.615 936 139 5 987 1919 29404963 29404030 0.000000e+00 926.0
23 TraesCS4A01G485500 chr7D 83.833 934 147 2 987 1919 4425726 4424796 0.000000e+00 885.0
24 TraesCS4A01G485500 chr7D 80.064 943 181 7 981 1919 4291483 4290544 0.000000e+00 693.0
25 TraesCS4A01G485500 chr7D 79.597 794 153 7 2207 2999 4412902 4412117 9.540000e-156 560.0
26 TraesCS4A01G485500 chr7D 94.161 274 15 1 891 1164 4508617 4508345 2.190000e-112 416.0
27 TraesCS4A01G485500 chr7D 77.266 651 138 10 2245 2890 4796160 4796805 1.330000e-99 374.0
28 TraesCS4A01G485500 chr7D 91.241 137 11 1 1945 2081 4502483 4502348 6.710000e-43 185.0
29 TraesCS4A01G485500 chr7D 85.443 158 16 3 77 227 440256049 440255892 1.460000e-34 158.0
30 TraesCS4A01G485500 chr7D 85.106 141 8 6 232 369 4505100 4504970 8.860000e-27 132.0
31 TraesCS4A01G485500 chr7D 93.590 78 5 0 718 795 29405375 29405298 2.480000e-22 117.0
32 TraesCS4A01G485500 chr7D 85.437 103 12 2 696 795 4793109 4793211 1.930000e-18 104.0
33 TraesCS4A01G485500 chr7D 94.340 53 3 0 3854 3906 519971070 519971018 9.050000e-12 82.4
34 TraesCS4A01G485500 chr3A 91.814 452 30 5 3090 3536 741655043 741654594 1.200000e-174 623.0
35 TraesCS4A01G485500 chr3A 90.591 457 34 7 3079 3532 630877891 630878341 7.270000e-167 597.0
36 TraesCS4A01G485500 chr3A 90.991 444 33 5 3092 3532 715671399 715670960 3.380000e-165 592.0
37 TraesCS4A01G485500 chr3A 90.153 457 36 8 3079 3532 630838285 630838735 1.570000e-163 586.0
38 TraesCS4A01G485500 chr3A 90.385 156 14 1 3755 3909 741654592 741654437 1.850000e-48 204.0
39 TraesCS4A01G485500 chr3A 96.522 115 4 0 3792 3906 715670959 715670845 1.440000e-44 191.0
40 TraesCS4A01G485500 chr3A 93.913 115 7 0 3792 3906 630838736 630838850 1.450000e-39 174.0
41 TraesCS4A01G485500 chr3A 95.455 110 4 1 3792 3900 630878342 630878451 1.450000e-39 174.0
42 TraesCS4A01G485500 chr5A 91.216 444 32 5 3092 3532 688111243 688110804 7.270000e-167 597.0
43 TraesCS4A01G485500 chr5A 96.522 115 3 1 3792 3906 688072940 688072827 5.190000e-44 189.0
44 TraesCS4A01G485500 chr1A 89.677 465 42 5 3078 3537 525018241 525018704 4.380000e-164 588.0
45 TraesCS4A01G485500 chr1A 93.750 144 6 3 3765 3906 525018712 525018854 3.080000e-51 213.0
46 TraesCS4A01G485500 chr5B 96.522 230 6 2 3531 3758 711616811 711617040 2.870000e-101 379.0
47 TraesCS4A01G485500 chr7B 97.717 219 4 1 3536 3754 9687931 9688148 3.710000e-100 375.0
48 TraesCS4A01G485500 chr1B 97.285 221 6 0 3536 3756 654508628 654508408 3.710000e-100 375.0
49 TraesCS4A01G485500 chr3B 97.273 220 6 0 3535 3754 812801381 812801600 1.330000e-99 374.0
50 TraesCS4A01G485500 chr3B 96.396 222 8 0 3536 3757 550488079 550488300 2.230000e-97 366.0
51 TraesCS4A01G485500 chr3B 95.964 223 8 1 3532 3754 813188295 813188516 1.040000e-95 361.0
52 TraesCS4A01G485500 chr3B 79.339 121 16 4 119 232 647907055 647906937 4.210000e-10 76.8
53 TraesCS4A01G485500 chr4B 96.818 220 7 0 3535 3754 89052895 89053114 6.210000e-98 368.0
54 TraesCS4A01G485500 chr4B 87.500 72 4 3 98 164 564870726 564870797 1.170000e-10 78.7
55 TraesCS4A01G485500 chr2B 96.380 221 8 0 3536 3756 679055020 679054800 8.030000e-97 364.0
56 TraesCS4A01G485500 chr2B 79.091 110 19 3 84 192 568278394 568278288 5.450000e-09 73.1
57 TraesCS4A01G485500 chr3D 85.586 111 11 4 88 193 48801503 48801393 1.150000e-20 111.0
58 TraesCS4A01G485500 chr2D 84.685 111 15 2 84 193 8145783 8145892 4.150000e-20 110.0
59 TraesCS4A01G485500 chr1D 100.000 30 0 0 3090 3119 252477403 252477374 5.490000e-04 56.5


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 TraesCS4A01G485500 chr4A 739078337 739082267 3930 False 7260.0 7260 100.0000 1 3931 1 chr4A.!!$F2 3930
1 TraesCS4A01G485500 chr4A 739273616 739274557 941 False 689.0 689 80.0000 981 1919 1 chr4A.!!$F4 938
2 TraesCS4A01G485500 chr4A 739153861 739154587 726 False 556.0 556 80.5210 2207 2934 1 chr4A.!!$F3 727
3 TraesCS4A01G485500 chr4A 739129614 739130948 1334 False 527.0 937 89.2095 718 1919 2 chr4A.!!$F5 1201
4 TraesCS4A01G485500 chr4A 738886888 738887535 647 True 416.0 416 78.4070 2243 2890 1 chr4A.!!$R1 647
5 TraesCS4A01G485500 chr4A 739310614 739312193 1579 False 230.5 346 83.4090 716 1843 2 chr4A.!!$F6 1127
6 TraesCS4A01G485500 chr7A 4327710 4330726 3016 True 2002.5 2549 91.4150 119 3093 2 chr7A.!!$R7 2974
7 TraesCS4A01G485500 chr7A 29663732 29664668 936 True 913.0 913 84.3450 987 1919 1 chr7A.!!$R5 932
8 TraesCS4A01G485500 chr7A 4069031 4069967 936 True 632.0 632 78.8910 985 1919 1 chr7A.!!$R2 934
9 TraesCS4A01G485500 chr7A 4206280 4207026 746 True 575.0 575 80.6670 2167 2912 1 chr7A.!!$R3 745
10 TraesCS4A01G485500 chr7A 4253408 4254738 1330 True 516.5 918 88.4875 716 1919 2 chr7A.!!$R6 1203
11 TraesCS4A01G485500 chr7D 4501310 4508617 7307 True 933.6 2492 90.7474 1 3093 5 chr7D.!!$R6 3092
12 TraesCS4A01G485500 chr7D 4424796 4425726 930 True 885.0 885 83.8330 987 1919 1 chr7D.!!$R3 932
13 TraesCS4A01G485500 chr7D 4290544 4291483 939 True 693.0 693 80.0640 981 1919 1 chr7D.!!$R1 938
14 TraesCS4A01G485500 chr7D 4412117 4412902 785 True 560.0 560 79.5970 2207 2999 1 chr7D.!!$R2 792
15 TraesCS4A01G485500 chr7D 29404030 29405375 1345 True 521.5 926 89.1025 718 1919 2 chr7D.!!$R7 1201
16 TraesCS4A01G485500 chr7D 4793109 4796805 3696 False 239.0 374 81.3515 696 2890 2 chr7D.!!$F1 2194
17 TraesCS4A01G485500 chr3A 741654437 741655043 606 True 413.5 623 91.0995 3090 3909 2 chr3A.!!$R2 819
18 TraesCS4A01G485500 chr3A 715670845 715671399 554 True 391.5 592 93.7565 3092 3906 2 chr3A.!!$R1 814
19 TraesCS4A01G485500 chr3A 630877891 630878451 560 False 385.5 597 93.0230 3079 3900 2 chr3A.!!$F2 821
20 TraesCS4A01G485500 chr3A 630838285 630838850 565 False 380.0 586 92.0330 3079 3906 2 chr3A.!!$F1 827
21 TraesCS4A01G485500 chr1A 525018241 525018854 613 False 400.5 588 91.7135 3078 3906 2 chr1A.!!$F1 828

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
779 5010 0.111446 TCCATTTCCAGCCGGACAAA 59.889 50.0 5.05 0.0 42.67 2.83 F
940 5401 0.529337 CATCGATCACTTGCTCGCCT 60.529 55.0 0.00 0.0 34.12 5.52 F
2097 7856 0.179062 GTCCCCTATCTGCTGCTGTG 60.179 60.0 0.00 0.0 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2094 7853 0.035534 ACAATGGCTCGGCATACACA 60.036 50.0 6.38 0.00 0.0 3.72 R
2462 8615 0.673985 TGCAGTTGTAGCTCACGTCT 59.326 50.0 0.00 0.00 0.0 4.18 R
3577 9739 0.034756 GGGTGGTCAAATTGGCAACC 59.965 55.0 15.56 15.56 0.0 3.77 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
36 4255 8.907222 TGGATAATCTGATTCGATCATGAAAA 57.093 30.769 6.10 0.00 38.85 2.29
59 4278 3.643199 AGAAAGATCTTCCTCCAAGCC 57.357 47.619 8.78 0.00 29.15 4.35
60 4279 2.093235 AGAAAGATCTTCCTCCAAGCCG 60.093 50.000 8.78 0.00 29.15 5.52
63 4282 2.683768 AGATCTTCCTCCAAGCCGTAT 58.316 47.619 0.00 0.00 31.26 3.06
64 4283 2.366916 AGATCTTCCTCCAAGCCGTATG 59.633 50.000 0.00 0.00 31.26 2.39
93 4314 8.716674 ACGACTATTATTAAATACTCCCTCCA 57.283 34.615 0.00 0.00 0.00 3.86
269 4497 5.713792 TTTTAGGGCTAGATGAGATCGAG 57.286 43.478 0.00 0.00 35.44 4.04
310 4538 6.668541 TTTGATTTGGTTGATCTCTCGATC 57.331 37.500 0.00 0.00 45.09 3.69
318 4546 1.091537 GATCTCTCGATCGGCTAGGG 58.908 60.000 16.41 5.49 36.96 3.53
319 4547 0.963355 ATCTCTCGATCGGCTAGGGC 60.963 60.000 16.41 0.00 37.82 5.19
337 4565 1.762460 CCTAGGGGCATCGTGGAGT 60.762 63.158 0.00 0.00 0.00 3.85
358 4586 5.284079 AGTACGCGTTATCAATATTCGGTT 58.716 37.500 20.78 0.00 0.00 4.44
377 4605 3.131046 GGTTTGGTCAAATCTATGGGCAG 59.869 47.826 0.00 0.00 32.36 4.85
440 4668 1.251251 GAGCTGCCCAACACATTCTT 58.749 50.000 0.00 0.00 0.00 2.52
489 4717 7.740519 ACAAATTCTCTTTGTTCGAACTTTG 57.259 32.000 27.32 24.73 39.36 2.77
539 4767 2.416260 CCTTACCGGACTAGCGGC 59.584 66.667 9.46 0.00 33.16 6.53
779 5010 0.111446 TCCATTTCCAGCCGGACAAA 59.889 50.000 5.05 0.00 42.67 2.83
850 5197 1.085091 CTGTGGAGAAGCTGACATGC 58.915 55.000 0.00 0.00 0.00 4.06
854 5201 1.022735 GGAGAAGCTGACATGCATGG 58.977 55.000 29.41 13.76 34.99 3.66
940 5401 0.529337 CATCGATCACTTGCTCGCCT 60.529 55.000 0.00 0.00 34.12 5.52
968 5429 4.278669 TCTGTCTGTCTTCTGTGGAACTAC 59.721 45.833 0.00 0.00 38.04 2.73
970 5431 4.649674 TGTCTGTCTTCTGTGGAACTACTT 59.350 41.667 0.00 0.00 38.04 2.24
972 5433 4.649674 TCTGTCTTCTGTGGAACTACTTGT 59.350 41.667 0.00 0.00 38.04 3.16
974 5839 5.116180 TGTCTTCTGTGGAACTACTTGTTG 58.884 41.667 0.00 0.00 39.30 3.33
1190 6397 3.058160 CGCCACCTTGCTTCCCAG 61.058 66.667 0.00 0.00 0.00 4.45
1296 6503 2.997315 CTCCTCCGCACCTGGACA 60.997 66.667 0.00 0.00 33.48 4.02
1385 6592 5.957798 CATGACAGCATGGTTTGATAAGTT 58.042 37.500 0.00 0.00 46.45 2.66
1533 6743 3.249189 ACCGGCATGTGGGAGTGT 61.249 61.111 0.00 0.00 0.00 3.55
1581 6815 3.431486 GCAAGAACTCATCGGAGAAGGAT 60.431 47.826 0.00 0.00 44.26 3.24
1737 6971 2.817844 GGGAAAGTTATTTGCGTCCACT 59.182 45.455 0.00 0.00 37.60 4.00
1804 7038 1.524863 CGGTGAGACGGACTCCAACT 61.525 60.000 5.08 0.00 44.34 3.16
2013 7573 9.895138 TTGAGTATATCACTGCATGCATATATT 57.105 29.630 22.97 15.93 37.72 1.28
2094 7853 1.112315 CGAGTCCCCTATCTGCTGCT 61.112 60.000 0.00 0.00 0.00 4.24
2097 7856 0.179062 GTCCCCTATCTGCTGCTGTG 60.179 60.000 0.00 0.00 0.00 3.66
2105 7864 1.448365 CTGCTGCTGTGTATGCCGA 60.448 57.895 0.00 0.00 0.00 5.54
2198 7958 8.289618 GTGCATTCAAACTTGAGAACATACTTA 58.710 33.333 0.00 0.00 38.61 2.24
2199 7959 8.506437 TGCATTCAAACTTGAGAACATACTTAG 58.494 33.333 0.00 0.00 38.61 2.18
2223 8375 7.091443 AGTCAAAGAACTAACTAATGACTCGG 58.909 38.462 0.00 0.00 40.13 4.63
2235 8387 1.144716 GACTCGGGCATGATGAGCA 59.855 57.895 0.00 0.00 32.98 4.26
2281 8434 1.408822 GCTGGATGAAAAGACCCGGAT 60.409 52.381 0.73 0.00 0.00 4.18
2285 8438 3.053693 TGGATGAAAAGACCCGGATGAAT 60.054 43.478 0.73 0.00 0.00 2.57
2354 8507 1.346395 ACCAACTTCGGTAGCATCACA 59.654 47.619 0.00 0.00 37.57 3.58
2383 8536 2.037367 CTCTGTCGTCCCCCTCCA 59.963 66.667 0.00 0.00 0.00 3.86
2468 8621 1.734477 CCTGAACGAGGCAGACGTG 60.734 63.158 0.00 0.00 43.16 4.49
2738 8891 1.355381 AGGGTGCTTGTGGATCATTCA 59.645 47.619 0.00 0.00 0.00 2.57
2822 8975 1.302993 AATTAACGCGGCAGGTGGT 60.303 52.632 12.47 0.00 0.00 4.16
2935 9088 5.235516 TGTTGAAGGACGAGACTAAATTCC 58.764 41.667 0.00 0.00 0.00 3.01
3044 9199 9.396022 TCTCTCTTGAGTTTAGTGTCAAATTTT 57.604 29.630 0.00 0.00 40.98 1.82
3135 9292 1.606668 ACGTTGTCATCGTGGCAAAAT 59.393 42.857 8.12 0.00 44.23 1.82
3142 9299 4.217334 TGTCATCGTGGCAAAATAACATGT 59.783 37.500 0.00 0.00 0.00 3.21
3147 9304 3.440173 CGTGGCAAAATAACATGTCCTCT 59.560 43.478 0.00 0.00 0.00 3.69
3179 9338 3.237268 TGCCACCCAATGTTTACTTCT 57.763 42.857 0.00 0.00 0.00 2.85
3180 9339 2.890311 TGCCACCCAATGTTTACTTCTG 59.110 45.455 0.00 0.00 0.00 3.02
3372 9534 3.758023 TGTTGAAGCATATGAACACCAGG 59.242 43.478 6.97 0.00 0.00 4.45
3450 9612 7.833682 TGGTCTATTGACACATTTCCACATAAT 59.166 33.333 9.51 0.00 44.61 1.28
3542 9704 8.742125 TGACCATGAATATAAAGATACTCCCT 57.258 34.615 0.00 0.00 0.00 4.20
3543 9705 8.816894 TGACCATGAATATAAAGATACTCCCTC 58.183 37.037 0.00 0.00 0.00 4.30
3544 9706 8.152023 ACCATGAATATAAAGATACTCCCTCC 57.848 38.462 0.00 0.00 0.00 4.30
3545 9707 7.093289 ACCATGAATATAAAGATACTCCCTCCG 60.093 40.741 0.00 0.00 0.00 4.63
3546 9708 7.093289 CCATGAATATAAAGATACTCCCTCCGT 60.093 40.741 0.00 0.00 0.00 4.69
3547 9709 7.463961 TGAATATAAAGATACTCCCTCCGTC 57.536 40.000 0.00 0.00 0.00 4.79
3548 9710 7.239438 TGAATATAAAGATACTCCCTCCGTCT 58.761 38.462 0.00 0.00 0.00 4.18
3549 9711 7.393796 TGAATATAAAGATACTCCCTCCGTCTC 59.606 40.741 0.00 0.00 0.00 3.36
3550 9712 3.383698 AAAGATACTCCCTCCGTCTCA 57.616 47.619 0.00 0.00 0.00 3.27
3551 9713 2.649531 AGATACTCCCTCCGTCTCAG 57.350 55.000 0.00 0.00 0.00 3.35
3552 9714 1.847737 AGATACTCCCTCCGTCTCAGT 59.152 52.381 0.00 0.00 0.00 3.41
3553 9715 2.242708 AGATACTCCCTCCGTCTCAGTT 59.757 50.000 0.00 0.00 0.00 3.16
3554 9716 2.599408 TACTCCCTCCGTCTCAGTTT 57.401 50.000 0.00 0.00 0.00 2.66
3555 9717 2.599408 ACTCCCTCCGTCTCAGTTTA 57.401 50.000 0.00 0.00 0.00 2.01
3556 9718 2.169330 ACTCCCTCCGTCTCAGTTTAC 58.831 52.381 0.00 0.00 0.00 2.01
3557 9719 2.168496 CTCCCTCCGTCTCAGTTTACA 58.832 52.381 0.00 0.00 0.00 2.41
3558 9720 2.561419 CTCCCTCCGTCTCAGTTTACAA 59.439 50.000 0.00 0.00 0.00 2.41
3559 9721 2.561419 TCCCTCCGTCTCAGTTTACAAG 59.439 50.000 0.00 0.00 0.00 3.16
3560 9722 2.299297 CCCTCCGTCTCAGTTTACAAGT 59.701 50.000 0.00 0.00 0.00 3.16
3561 9723 3.576648 CCTCCGTCTCAGTTTACAAGTC 58.423 50.000 0.00 0.00 0.00 3.01
3562 9724 3.576648 CTCCGTCTCAGTTTACAAGTCC 58.423 50.000 0.00 0.00 0.00 3.85
3563 9725 3.228453 TCCGTCTCAGTTTACAAGTCCT 58.772 45.455 0.00 0.00 0.00 3.85
3564 9726 4.401022 TCCGTCTCAGTTTACAAGTCCTA 58.599 43.478 0.00 0.00 0.00 2.94
3565 9727 4.217118 TCCGTCTCAGTTTACAAGTCCTAC 59.783 45.833 0.00 0.00 0.00 3.18
3566 9728 4.156915 CGTCTCAGTTTACAAGTCCTACG 58.843 47.826 0.00 0.00 0.00 3.51
3567 9729 3.919197 GTCTCAGTTTACAAGTCCTACGC 59.081 47.826 0.00 0.00 0.00 4.42
3568 9730 2.915463 CTCAGTTTACAAGTCCTACGCG 59.085 50.000 3.53 3.53 0.00 6.01
3569 9731 2.294233 TCAGTTTACAAGTCCTACGCGT 59.706 45.455 19.17 19.17 0.00 6.01
3570 9732 3.501828 TCAGTTTACAAGTCCTACGCGTA 59.498 43.478 19.40 19.40 0.00 4.42
3571 9733 4.156556 TCAGTTTACAAGTCCTACGCGTAT 59.843 41.667 20.91 5.41 0.00 3.06
3572 9734 5.353956 TCAGTTTACAAGTCCTACGCGTATA 59.646 40.000 20.91 8.44 0.00 1.47
3573 9735 5.453587 CAGTTTACAAGTCCTACGCGTATAC 59.546 44.000 20.91 19.74 0.00 1.47
3574 9736 4.552166 TTACAAGTCCTACGCGTATACC 57.448 45.455 20.91 10.04 0.00 2.73
3575 9737 2.648059 ACAAGTCCTACGCGTATACCT 58.352 47.619 20.91 12.19 0.00 3.08
3576 9738 3.808728 ACAAGTCCTACGCGTATACCTA 58.191 45.455 20.91 0.00 0.00 3.08
3577 9739 3.812053 ACAAGTCCTACGCGTATACCTAG 59.188 47.826 20.91 8.56 0.00 3.02
3578 9740 3.051081 AGTCCTACGCGTATACCTAGG 57.949 52.381 20.91 18.03 0.00 3.02
3579 9741 2.370189 AGTCCTACGCGTATACCTAGGT 59.630 50.000 20.91 20.57 0.00 3.08
3580 9742 3.142174 GTCCTACGCGTATACCTAGGTT 58.858 50.000 22.11 10.62 0.00 3.50
3581 9743 3.058639 GTCCTACGCGTATACCTAGGTTG 60.059 52.174 22.11 9.15 0.00 3.77
3582 9744 2.351157 CCTACGCGTATACCTAGGTTGC 60.351 54.545 22.11 17.41 0.00 4.17
3583 9745 0.386838 ACGCGTATACCTAGGTTGCC 59.613 55.000 22.11 7.02 0.00 4.52
3584 9746 0.386476 CGCGTATACCTAGGTTGCCA 59.614 55.000 22.11 1.21 0.00 4.92
3585 9747 1.202440 CGCGTATACCTAGGTTGCCAA 60.202 52.381 22.11 0.75 0.00 4.52
3586 9748 2.547218 CGCGTATACCTAGGTTGCCAAT 60.547 50.000 22.11 9.64 0.00 3.16
3587 9749 3.473625 GCGTATACCTAGGTTGCCAATT 58.526 45.455 22.11 0.00 0.00 2.32
3588 9750 3.881089 GCGTATACCTAGGTTGCCAATTT 59.119 43.478 22.11 0.00 0.00 1.82
3589 9751 4.261031 GCGTATACCTAGGTTGCCAATTTG 60.261 45.833 22.11 4.31 0.00 2.32
3590 9752 5.120399 CGTATACCTAGGTTGCCAATTTGA 58.880 41.667 22.11 0.00 0.00 2.69
3591 9753 5.007332 CGTATACCTAGGTTGCCAATTTGAC 59.993 44.000 22.11 1.58 0.00 3.18
3592 9754 2.525368 ACCTAGGTTGCCAATTTGACC 58.475 47.619 9.21 0.00 0.00 4.02
3593 9755 2.158385 ACCTAGGTTGCCAATTTGACCA 60.158 45.455 9.21 0.00 34.60 4.02
3594 9756 2.231235 CCTAGGTTGCCAATTTGACCAC 59.769 50.000 0.00 0.00 34.60 4.16
3595 9757 1.047801 AGGTTGCCAATTTGACCACC 58.952 50.000 8.09 3.71 34.60 4.61
3596 9758 0.034756 GGTTGCCAATTTGACCACCC 59.965 55.000 0.00 0.00 32.41 4.61
3597 9759 1.047801 GTTGCCAATTTGACCACCCT 58.952 50.000 0.00 0.00 0.00 4.34
3598 9760 2.243810 GTTGCCAATTTGACCACCCTA 58.756 47.619 0.00 0.00 0.00 3.53
3599 9761 2.630580 GTTGCCAATTTGACCACCCTAA 59.369 45.455 0.00 0.00 0.00 2.69
3600 9762 3.182887 TGCCAATTTGACCACCCTAAT 57.817 42.857 0.00 0.00 0.00 1.73
3601 9763 4.323569 TGCCAATTTGACCACCCTAATA 57.676 40.909 0.00 0.00 0.00 0.98
3602 9764 4.877773 TGCCAATTTGACCACCCTAATAT 58.122 39.130 0.00 0.00 0.00 1.28
3603 9765 6.019656 TGCCAATTTGACCACCCTAATATA 57.980 37.500 0.00 0.00 0.00 0.86
3604 9766 6.436027 TGCCAATTTGACCACCCTAATATAA 58.564 36.000 0.00 0.00 0.00 0.98
3605 9767 6.897966 TGCCAATTTGACCACCCTAATATAAA 59.102 34.615 0.00 0.00 0.00 1.40
3606 9768 7.147811 TGCCAATTTGACCACCCTAATATAAAC 60.148 37.037 0.00 0.00 0.00 2.01
3607 9769 7.069455 GCCAATTTGACCACCCTAATATAAACT 59.931 37.037 0.00 0.00 0.00 2.66
3608 9770 9.635404 CCAATTTGACCACCCTAATATAAACTA 57.365 33.333 0.00 0.00 0.00 2.24
3703 9865 9.920946 ATATGACTTGTATTAGGTTGGTCAAAT 57.079 29.630 0.00 0.00 36.16 2.32
3705 9867 8.786826 TGACTTGTATTAGGTTGGTCAAATAG 57.213 34.615 0.00 0.00 30.81 1.73
3706 9868 8.598916 TGACTTGTATTAGGTTGGTCAAATAGA 58.401 33.333 0.00 0.00 30.81 1.98
3707 9869 8.788325 ACTTGTATTAGGTTGGTCAAATAGAC 57.212 34.615 0.00 0.00 46.83 2.59
3717 9879 3.729862 GTCAAATAGACGACCTAGGGG 57.270 52.381 14.81 7.16 37.53 4.79
3718 9880 3.029570 GTCAAATAGACGACCTAGGGGT 58.970 50.000 14.81 10.74 42.52 4.95
3719 9881 4.210331 GTCAAATAGACGACCTAGGGGTA 58.790 47.826 14.81 0.00 40.98 3.69
3720 9882 4.037327 GTCAAATAGACGACCTAGGGGTAC 59.963 50.000 14.81 1.97 40.98 3.34
3721 9883 7.215998 GTCAAATAGACGACCTAGGGGTACG 62.216 52.000 14.81 14.81 40.98 3.67
3734 9896 2.202824 GTACGCGCATGCCCTGTA 60.203 61.111 13.15 9.55 38.08 2.74
3735 9897 1.812093 GTACGCGCATGCCCTGTAA 60.812 57.895 13.15 0.00 38.08 2.41
3736 9898 1.079057 TACGCGCATGCCCTGTAAA 60.079 52.632 13.15 0.00 38.08 2.01
3737 9899 1.363145 TACGCGCATGCCCTGTAAAC 61.363 55.000 13.15 0.00 38.08 2.01
3738 9900 2.398554 CGCGCATGCCCTGTAAACT 61.399 57.895 13.15 0.00 38.08 2.66
3739 9901 1.137404 GCGCATGCCCTGTAAACTG 59.863 57.895 13.15 0.00 33.98 3.16
3740 9902 1.305219 GCGCATGCCCTGTAAACTGA 61.305 55.000 13.15 0.00 33.98 3.41
3741 9903 0.729116 CGCATGCCCTGTAAACTGAG 59.271 55.000 13.15 0.00 0.00 3.35
3742 9904 1.675714 CGCATGCCCTGTAAACTGAGA 60.676 52.381 13.15 0.00 0.00 3.27
3743 9905 2.012673 GCATGCCCTGTAAACTGAGAG 58.987 52.381 6.36 0.00 0.00 3.20
3744 9906 2.355108 GCATGCCCTGTAAACTGAGAGA 60.355 50.000 6.36 0.00 0.00 3.10
3745 9907 3.529533 CATGCCCTGTAAACTGAGAGAG 58.470 50.000 0.00 0.00 0.00 3.20
3746 9908 2.889512 TGCCCTGTAAACTGAGAGAGA 58.110 47.619 0.00 0.00 0.00 3.10
3747 9909 2.828520 TGCCCTGTAAACTGAGAGAGAG 59.171 50.000 0.00 0.00 0.00 3.20
3748 9910 2.167487 GCCCTGTAAACTGAGAGAGAGG 59.833 54.545 0.00 0.00 0.00 3.69
3749 9911 3.436243 CCCTGTAAACTGAGAGAGAGGT 58.564 50.000 0.00 0.00 0.00 3.85
3750 9912 4.601084 CCCTGTAAACTGAGAGAGAGGTA 58.399 47.826 0.00 0.00 0.00 3.08
3751 9913 4.642885 CCCTGTAAACTGAGAGAGAGGTAG 59.357 50.000 0.00 0.00 0.00 3.18
3752 9914 5.258051 CCTGTAAACTGAGAGAGAGGTAGT 58.742 45.833 0.00 0.00 0.00 2.73
3753 9915 6.416415 CCTGTAAACTGAGAGAGAGGTAGTA 58.584 44.000 0.00 0.00 0.00 1.82
3754 9916 6.540914 CCTGTAAACTGAGAGAGAGGTAGTAG 59.459 46.154 0.00 0.00 0.00 2.57
3755 9917 7.018487 TGTAAACTGAGAGAGAGGTAGTAGT 57.982 40.000 0.00 0.00 0.00 2.73
3756 9918 8.143673 TGTAAACTGAGAGAGAGGTAGTAGTA 57.856 38.462 0.00 0.00 0.00 1.82
3757 9919 8.259411 TGTAAACTGAGAGAGAGGTAGTAGTAG 58.741 40.741 0.00 0.00 0.00 2.57
3758 9920 7.499200 AAACTGAGAGAGAGGTAGTAGTAGA 57.501 40.000 0.00 0.00 0.00 2.59
3759 9921 7.499200 AACTGAGAGAGAGGTAGTAGTAGAA 57.501 40.000 0.00 0.00 0.00 2.10
3760 9922 7.499200 ACTGAGAGAGAGGTAGTAGTAGAAA 57.501 40.000 0.00 0.00 0.00 2.52
3761 9923 7.333323 ACTGAGAGAGAGGTAGTAGTAGAAAC 58.667 42.308 0.00 0.00 0.00 2.78
3762 9924 6.652053 TGAGAGAGAGGTAGTAGTAGAAACC 58.348 44.000 0.00 0.00 0.00 3.27
3763 9925 6.444493 TGAGAGAGAGGTAGTAGTAGAAACCT 59.556 42.308 0.00 0.00 45.02 3.50
3771 9936 7.289310 AGGTAGTAGTAGAAACCTCCTCATAC 58.711 42.308 0.00 0.00 37.87 2.39
3914 10081 8.189119 ACAGGGAGAAAAATAATGTTAAAGCA 57.811 30.769 0.00 0.00 0.00 3.91
3915 10082 8.306761 ACAGGGAGAAAAATAATGTTAAAGCAG 58.693 33.333 0.00 0.00 0.00 4.24
3916 10083 8.306761 CAGGGAGAAAAATAATGTTAAAGCAGT 58.693 33.333 0.00 0.00 0.00 4.40
3917 10084 9.528489 AGGGAGAAAAATAATGTTAAAGCAGTA 57.472 29.630 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 4244 9.875675 GGAAGATCTTTCTATTTTTCATGATCG 57.124 33.333 9.87 0.00 35.57 3.69
36 4255 5.686124 CGGCTTGGAGGAAGATCTTTCTATT 60.686 44.000 16.60 0.00 32.82 1.73
63 4282 9.865321 GGGAGTATTTAATAATAGTCGTATGCA 57.135 33.333 0.00 0.00 43.27 3.96
209 4437 4.041815 GGTTCTCCCTCCATTCCCTAATAC 59.958 50.000 0.00 0.00 0.00 1.89
255 4483 5.101628 GCCAATAAGCTCGATCTCATCTAG 58.898 45.833 0.00 0.00 0.00 2.43
256 4484 4.769488 AGCCAATAAGCTCGATCTCATCTA 59.231 41.667 0.00 0.00 39.48 1.98
257 4485 3.577848 AGCCAATAAGCTCGATCTCATCT 59.422 43.478 0.00 0.00 39.48 2.90
258 4486 3.924144 AGCCAATAAGCTCGATCTCATC 58.076 45.455 0.00 0.00 39.48 2.92
259 4487 4.322349 GGTAGCCAATAAGCTCGATCTCAT 60.322 45.833 0.00 0.00 43.67 2.90
260 4488 3.005897 GGTAGCCAATAAGCTCGATCTCA 59.994 47.826 0.00 0.00 43.67 3.27
261 4489 3.580731 GGTAGCCAATAAGCTCGATCTC 58.419 50.000 0.00 0.00 43.67 2.75
262 4490 2.300437 GGGTAGCCAATAAGCTCGATCT 59.700 50.000 5.96 0.00 43.67 2.75
263 4491 2.037251 TGGGTAGCCAATAAGCTCGATC 59.963 50.000 12.23 0.00 43.67 3.69
264 4492 2.037772 CTGGGTAGCCAATAAGCTCGAT 59.962 50.000 15.81 0.00 43.67 3.59
265 4493 1.412710 CTGGGTAGCCAATAAGCTCGA 59.587 52.381 15.81 0.00 43.67 4.04
266 4494 1.412710 TCTGGGTAGCCAATAAGCTCG 59.587 52.381 15.81 0.47 43.67 5.03
267 4495 3.778954 ATCTGGGTAGCCAATAAGCTC 57.221 47.619 15.81 0.00 43.67 4.09
269 4497 4.207165 TCAAATCTGGGTAGCCAATAAGC 58.793 43.478 15.81 0.00 0.00 3.09
270 4498 6.966534 AATCAAATCTGGGTAGCCAATAAG 57.033 37.500 15.81 3.20 0.00 1.73
271 4499 6.098124 CCAAATCAAATCTGGGTAGCCAATAA 59.902 38.462 15.81 3.97 0.00 1.40
272 4500 5.598005 CCAAATCAAATCTGGGTAGCCAATA 59.402 40.000 15.81 6.62 0.00 1.90
273 4501 4.406649 CCAAATCAAATCTGGGTAGCCAAT 59.593 41.667 15.81 8.74 0.00 3.16
319 4547 0.469331 TACTCCACGATGCCCCTAGG 60.469 60.000 0.06 0.06 0.00 3.02
320 4548 0.674534 GTACTCCACGATGCCCCTAG 59.325 60.000 0.00 0.00 0.00 3.02
321 4549 2.816746 GTACTCCACGATGCCCCTA 58.183 57.895 0.00 0.00 0.00 3.53
322 4550 3.630289 GTACTCCACGATGCCCCT 58.370 61.111 0.00 0.00 0.00 4.79
332 4560 4.913345 CGAATATTGATAACGCGTACTCCA 59.087 41.667 14.46 5.76 0.00 3.86
333 4561 4.322804 CCGAATATTGATAACGCGTACTCC 59.677 45.833 14.46 2.76 0.00 3.85
337 4565 5.050904 CCAAACCGAATATTGATAACGCGTA 60.051 40.000 14.46 0.72 0.00 4.42
358 4586 3.737559 ACTGCCCATAGATTTGACCAA 57.262 42.857 0.00 0.00 0.00 3.67
377 4605 1.407618 GGATTTGGGAACGGGCAATAC 59.592 52.381 0.00 0.00 0.00 1.89
388 4616 5.074515 GGAGGGATTTATAGTGGATTTGGGA 59.925 44.000 0.00 0.00 0.00 4.37
440 4668 2.224606 CTCTTGCTTCAGCTCAAACCA 58.775 47.619 0.00 0.00 42.66 3.67
487 4715 3.545124 ATCACGGCAGGCGAACCAA 62.545 57.895 25.17 3.44 39.06 3.67
489 4717 3.499737 CATCACGGCAGGCGAACC 61.500 66.667 25.17 0.00 0.00 3.62
633 4861 3.272334 GACATGATGCCCGTCGCC 61.272 66.667 0.00 0.00 36.24 5.54
654 4882 4.087892 CTCTGCCAGGACACGGGG 62.088 72.222 0.00 0.00 31.98 5.73
779 5010 0.963962 ACCGACCGTTCATGTAGTGT 59.036 50.000 0.00 0.00 0.00 3.55
833 5155 1.400846 CATGCATGTCAGCTTCTCCAC 59.599 52.381 18.91 0.00 34.99 4.02
850 5197 2.753966 CCGACGGAAAGCAGCCATG 61.754 63.158 8.64 0.00 0.00 3.66
863 5218 2.078914 GTATCGTATGCCGCCGACG 61.079 63.158 7.62 7.62 35.69 5.12
865 5220 1.577922 GAGTATCGTATGCCGCCGA 59.422 57.895 0.00 0.00 37.51 5.54
875 5230 1.359117 CATGTCGCCGGAGTATCGT 59.641 57.895 5.05 0.00 34.37 3.73
877 5232 2.016704 CGCATGTCGCCGGAGTATC 61.017 63.158 5.05 0.00 37.30 2.24
940 5401 3.068732 CCACAGAAGACAGACAGACAGAA 59.931 47.826 0.00 0.00 0.00 3.02
972 5433 5.416639 AGCTGCATGTTGTATTCTGAATCAA 59.583 36.000 6.10 8.34 0.00 2.57
974 5839 5.496133 AGCTGCATGTTGTATTCTGAATC 57.504 39.130 6.10 0.06 0.00 2.52
1296 6503 2.437449 GGGTTGCCCGGGTACTTT 59.563 61.111 24.63 0.00 32.13 2.66
1385 6592 2.089936 GTGCGCCACGTGTTATCGA 61.090 57.895 15.65 0.00 34.70 3.59
1454 6661 5.601662 AGTTGATGAAGTCTTTCGTCTTGA 58.398 37.500 9.98 0.00 45.54 3.02
1581 6815 2.076100 CTCGCCTTCAGCACATACAAA 58.924 47.619 0.00 0.00 44.04 2.83
1737 6971 3.493350 GCTTCGCAGGATCATAGAAGGAA 60.493 47.826 19.52 4.20 38.83 3.36
1794 7028 0.963962 TGTCGGTACAGTTGGAGTCC 59.036 55.000 0.73 0.73 0.00 3.85
1804 7038 1.216977 CCTTGGCGATGTCGGTACA 59.783 57.895 4.44 0.00 40.69 2.90
2013 7573 9.546428 AATTCACATGTACTGATTGATCGATTA 57.454 29.630 0.00 0.00 0.00 1.75
2035 7595 5.221322 GGAAGATGCCAAGGGTATTCAATTC 60.221 44.000 0.00 0.00 0.00 2.17
2094 7853 0.035534 ACAATGGCTCGGCATACACA 60.036 50.000 6.38 0.00 0.00 3.72
2097 7856 2.561569 AGTAACAATGGCTCGGCATAC 58.438 47.619 6.38 1.66 0.00 2.39
2198 7958 7.091443 CCGAGTCATTAGTTAGTTCTTTGACT 58.909 38.462 2.57 2.57 39.77 3.41
2199 7959 6.310711 CCCGAGTCATTAGTTAGTTCTTTGAC 59.689 42.308 0.00 0.00 33.53 3.18
2235 8387 1.922447 TGTCCTTGGAATGGCCTACAT 59.078 47.619 3.32 0.00 43.07 2.29
2281 8434 1.140852 CCGGCCATTGGAGTAGATTCA 59.859 52.381 6.95 0.00 0.00 2.57
2285 8438 1.622607 CCACCGGCCATTGGAGTAGA 61.623 60.000 13.56 0.00 34.46 2.59
2354 8507 2.683933 ACAGAGCCGGTCCCGATT 60.684 61.111 7.42 0.00 42.83 3.34
2373 8526 4.035102 GTGCAGGTGGAGGGGGAC 62.035 72.222 0.00 0.00 0.00 4.46
2405 8558 1.330655 GGAAGGAGGCCTCGATGTCA 61.331 60.000 26.36 0.00 30.89 3.58
2462 8615 0.673985 TGCAGTTGTAGCTCACGTCT 59.326 50.000 0.00 0.00 0.00 4.18
2468 8621 2.611518 CTGGTACTGCAGTTGTAGCTC 58.388 52.381 27.06 7.60 38.67 4.09
2510 8663 2.429930 CCAAAGGGTCCGAGCACA 59.570 61.111 0.00 0.00 0.00 4.57
2649 8802 2.650116 GCTTCACTGGCTCCTCGGA 61.650 63.158 0.00 0.00 0.00 4.55
2652 8805 2.125350 CCGCTTCACTGGCTCCTC 60.125 66.667 0.00 0.00 0.00 3.71
2660 8813 0.896940 TTCCGACTACCCGCTTCACT 60.897 55.000 0.00 0.00 0.00 3.41
2696 8849 1.543208 GCGGATAATGCCTCACCATGA 60.543 52.381 0.00 0.00 0.00 3.07
2738 8891 4.521146 CCATCACAAAGCTCTCCACTATT 58.479 43.478 0.00 0.00 0.00 1.73
2940 9093 9.628746 TTTGACAGTAAACTCAAAAGGTAAAAC 57.371 29.630 0.00 0.00 0.00 2.43
3135 9292 8.978472 GCATATATACCCTAAGAGGACATGTTA 58.022 37.037 0.00 0.00 37.67 2.41
3142 9299 5.278061 GGTGGCATATATACCCTAAGAGGA 58.722 45.833 0.00 0.00 37.67 3.71
3160 9317 2.890945 ACAGAAGTAAACATTGGGTGGC 59.109 45.455 0.00 0.00 0.00 5.01
3222 9382 3.667360 ACAATGAGCCCAAAATTCTTGC 58.333 40.909 0.00 0.00 0.00 4.01
3450 9612 4.343526 ACAATTATGTGTGTTGCCTGGAAA 59.656 37.500 0.00 0.00 38.69 3.13
3452 9614 3.495331 ACAATTATGTGTGTTGCCTGGA 58.505 40.909 0.00 0.00 38.69 3.86
3453 9615 3.940209 ACAATTATGTGTGTTGCCTGG 57.060 42.857 0.00 0.00 38.69 4.45
3537 9699 2.168496 TGTAAACTGAGACGGAGGGAG 58.832 52.381 0.00 0.00 0.00 4.30
3539 9701 2.299297 ACTTGTAAACTGAGACGGAGGG 59.701 50.000 0.00 0.00 0.00 4.30
3540 9702 3.576648 GACTTGTAAACTGAGACGGAGG 58.423 50.000 0.00 0.00 0.00 4.30
3541 9703 3.256136 AGGACTTGTAAACTGAGACGGAG 59.744 47.826 0.00 0.00 0.00 4.63
3542 9704 3.228453 AGGACTTGTAAACTGAGACGGA 58.772 45.455 0.00 0.00 0.00 4.69
3543 9705 3.662247 AGGACTTGTAAACTGAGACGG 57.338 47.619 0.00 0.00 0.00 4.79
3544 9706 4.156915 CGTAGGACTTGTAAACTGAGACG 58.843 47.826 0.00 0.00 0.00 4.18
3545 9707 3.919197 GCGTAGGACTTGTAAACTGAGAC 59.081 47.826 0.00 0.00 0.00 3.36
3546 9708 3.365666 CGCGTAGGACTTGTAAACTGAGA 60.366 47.826 0.00 0.00 0.00 3.27
3547 9709 2.915463 CGCGTAGGACTTGTAAACTGAG 59.085 50.000 0.00 0.00 0.00 3.35
3548 9710 2.294233 ACGCGTAGGACTTGTAAACTGA 59.706 45.455 11.67 0.00 0.00 3.41
3549 9711 2.669364 ACGCGTAGGACTTGTAAACTG 58.331 47.619 11.67 0.00 0.00 3.16
3550 9712 4.708726 ATACGCGTAGGACTTGTAAACT 57.291 40.909 24.78 0.00 0.00 2.66
3551 9713 4.735338 GGTATACGCGTAGGACTTGTAAAC 59.265 45.833 24.78 6.78 0.00 2.01
3552 9714 4.640201 AGGTATACGCGTAGGACTTGTAAA 59.360 41.667 24.78 0.00 0.00 2.01
3553 9715 4.199310 AGGTATACGCGTAGGACTTGTAA 58.801 43.478 24.78 0.00 0.00 2.41
3554 9716 3.808728 AGGTATACGCGTAGGACTTGTA 58.191 45.455 24.78 7.25 0.00 2.41
3555 9717 2.648059 AGGTATACGCGTAGGACTTGT 58.352 47.619 24.78 8.30 0.00 3.16
3556 9718 3.188048 CCTAGGTATACGCGTAGGACTTG 59.812 52.174 24.78 19.23 45.08 3.16
3557 9719 3.181450 ACCTAGGTATACGCGTAGGACTT 60.181 47.826 25.95 21.88 45.08 3.01
3558 9720 2.370189 ACCTAGGTATACGCGTAGGACT 59.630 50.000 25.95 22.11 45.08 3.85
3559 9721 2.772287 ACCTAGGTATACGCGTAGGAC 58.228 52.381 25.95 22.99 45.08 3.85
3560 9722 3.141398 CAACCTAGGTATACGCGTAGGA 58.859 50.000 25.95 14.03 45.08 2.94
3561 9723 2.351157 GCAACCTAGGTATACGCGTAGG 60.351 54.545 24.78 21.85 46.64 3.18
3562 9724 2.351157 GGCAACCTAGGTATACGCGTAG 60.351 54.545 24.78 11.28 0.00 3.51
3563 9725 1.608590 GGCAACCTAGGTATACGCGTA 59.391 52.381 22.94 22.94 0.00 4.42
3564 9726 0.386838 GGCAACCTAGGTATACGCGT 59.613 55.000 19.17 19.17 0.00 6.01
3565 9727 0.386476 TGGCAACCTAGGTATACGCG 59.614 55.000 16.67 3.53 0.00 6.01
3566 9728 2.607631 TTGGCAACCTAGGTATACGC 57.392 50.000 16.67 15.11 0.00 4.42
3567 9729 5.007332 GTCAAATTGGCAACCTAGGTATACG 59.993 44.000 16.67 5.52 0.00 3.06
3568 9730 5.298527 GGTCAAATTGGCAACCTAGGTATAC 59.701 44.000 16.67 8.74 0.00 1.47
3569 9731 5.044772 TGGTCAAATTGGCAACCTAGGTATA 60.045 40.000 16.67 0.00 32.82 1.47
3570 9732 4.264172 TGGTCAAATTGGCAACCTAGGTAT 60.264 41.667 16.67 0.83 32.82 2.73
3571 9733 3.074687 TGGTCAAATTGGCAACCTAGGTA 59.925 43.478 16.67 0.00 32.82 3.08
3572 9734 2.158385 TGGTCAAATTGGCAACCTAGGT 60.158 45.455 9.21 9.21 32.82 3.08
3573 9735 2.231235 GTGGTCAAATTGGCAACCTAGG 59.769 50.000 7.41 7.41 32.82 3.02
3574 9736 2.231235 GGTGGTCAAATTGGCAACCTAG 59.769 50.000 16.51 0.00 32.82 3.02
3575 9737 2.243810 GGTGGTCAAATTGGCAACCTA 58.756 47.619 16.51 0.00 32.82 3.08
3576 9738 1.047801 GGTGGTCAAATTGGCAACCT 58.952 50.000 16.51 0.00 32.82 3.50
3577 9739 0.034756 GGGTGGTCAAATTGGCAACC 59.965 55.000 15.56 15.56 0.00 3.77
3578 9740 1.047801 AGGGTGGTCAAATTGGCAAC 58.952 50.000 0.00 0.00 0.00 4.17
3579 9741 2.685106 TAGGGTGGTCAAATTGGCAA 57.315 45.000 0.68 0.68 0.00 4.52
3580 9742 2.685106 TTAGGGTGGTCAAATTGGCA 57.315 45.000 0.00 0.00 0.00 4.92
3581 9743 6.969993 TTATATTAGGGTGGTCAAATTGGC 57.030 37.500 0.00 0.00 0.00 4.52
3582 9744 8.533569 AGTTTATATTAGGGTGGTCAAATTGG 57.466 34.615 0.00 0.00 0.00 3.16
3677 9839 9.920946 ATTTGACCAACCTAATACAAGTCATAT 57.079 29.630 0.00 0.00 33.21 1.78
3679 9841 9.396022 CTATTTGACCAACCTAATACAAGTCAT 57.604 33.333 0.00 0.00 33.21 3.06
3680 9842 8.598916 TCTATTTGACCAACCTAATACAAGTCA 58.401 33.333 0.00 0.00 0.00 3.41
3681 9843 8.880750 GTCTATTTGACCAACCTAATACAAGTC 58.119 37.037 0.00 0.00 39.69 3.01
3682 9844 7.548075 CGTCTATTTGACCAACCTAATACAAGT 59.452 37.037 0.00 0.00 42.49 3.16
3683 9845 7.762615 TCGTCTATTTGACCAACCTAATACAAG 59.237 37.037 0.00 0.00 42.49 3.16
3684 9846 7.546667 GTCGTCTATTTGACCAACCTAATACAA 59.453 37.037 0.00 0.00 42.49 2.41
3685 9847 7.037438 GTCGTCTATTTGACCAACCTAATACA 58.963 38.462 0.00 0.00 42.49 2.29
3686 9848 7.460751 GTCGTCTATTTGACCAACCTAATAC 57.539 40.000 0.00 0.00 42.49 1.89
3696 9858 4.196345 ACCCCTAGGTCGTCTATTTGACC 61.196 52.174 8.29 3.22 46.45 4.02
3697 9859 3.029570 ACCCCTAGGTCGTCTATTTGAC 58.970 50.000 8.29 0.00 46.45 3.18
3698 9860 3.393426 ACCCCTAGGTCGTCTATTTGA 57.607 47.619 8.29 0.00 46.45 2.69
3699 9861 3.004106 CGTACCCCTAGGTCGTCTATTTG 59.996 52.174 8.29 0.00 46.45 2.32
3700 9862 3.217626 CGTACCCCTAGGTCGTCTATTT 58.782 50.000 8.29 0.00 46.45 1.40
3701 9863 2.856222 CGTACCCCTAGGTCGTCTATT 58.144 52.381 8.29 0.00 46.45 1.73
3702 9864 1.544314 GCGTACCCCTAGGTCGTCTAT 60.544 57.143 8.29 0.00 46.45 1.98
3703 9865 0.179045 GCGTACCCCTAGGTCGTCTA 60.179 60.000 8.29 0.00 46.45 2.59
3704 9866 1.452833 GCGTACCCCTAGGTCGTCT 60.453 63.158 8.29 0.00 46.45 4.18
3705 9867 2.828128 CGCGTACCCCTAGGTCGTC 61.828 68.421 8.29 3.46 46.45 4.20
3706 9868 2.825836 CGCGTACCCCTAGGTCGT 60.826 66.667 8.29 6.00 46.45 4.34
3707 9869 4.261781 GCGCGTACCCCTAGGTCG 62.262 72.222 8.43 8.12 46.45 4.79
3708 9870 2.496291 ATGCGCGTACCCCTAGGTC 61.496 63.158 8.43 0.00 46.45 3.85
3710 9872 2.029073 CATGCGCGTACCCCTAGG 59.971 66.667 8.43 0.06 40.04 3.02
3711 9873 2.661866 GCATGCGCGTACCCCTAG 60.662 66.667 8.43 0.00 0.00 3.02
3712 9874 4.230002 GGCATGCGCGTACCCCTA 62.230 66.667 12.44 0.00 39.92 3.53
3716 9878 3.726595 TACAGGGCATGCGCGTACC 62.727 63.158 26.71 10.65 39.92 3.34
3717 9879 1.363145 TTTACAGGGCATGCGCGTAC 61.363 55.000 26.71 5.72 39.92 3.67
3718 9880 1.079057 TTTACAGGGCATGCGCGTA 60.079 52.632 26.71 25.35 39.92 4.42
3719 9881 2.359354 TTTACAGGGCATGCGCGT 60.359 55.556 26.71 26.25 39.92 6.01
3720 9882 2.100216 GTTTACAGGGCATGCGCG 59.900 61.111 26.71 22.63 39.92 6.86
3721 9883 1.137404 CAGTTTACAGGGCATGCGC 59.863 57.895 26.04 26.04 37.44 6.09
3722 9884 0.729116 CTCAGTTTACAGGGCATGCG 59.271 55.000 12.44 0.00 0.00 4.73
3723 9885 2.012673 CTCTCAGTTTACAGGGCATGC 58.987 52.381 9.90 9.90 0.00 4.06
3724 9886 3.196469 TCTCTCTCAGTTTACAGGGCATG 59.804 47.826 0.00 0.00 0.00 4.06
3725 9887 3.445008 TCTCTCTCAGTTTACAGGGCAT 58.555 45.455 0.00 0.00 0.00 4.40
3726 9888 2.828520 CTCTCTCTCAGTTTACAGGGCA 59.171 50.000 0.00 0.00 0.00 5.36
3727 9889 2.167487 CCTCTCTCTCAGTTTACAGGGC 59.833 54.545 0.00 0.00 0.00 5.19
3728 9890 3.436243 ACCTCTCTCTCAGTTTACAGGG 58.564 50.000 0.00 0.00 0.00 4.45
3729 9891 5.258051 ACTACCTCTCTCTCAGTTTACAGG 58.742 45.833 0.00 0.00 0.00 4.00
3730 9892 7.107542 ACTACTACCTCTCTCTCAGTTTACAG 58.892 42.308 0.00 0.00 0.00 2.74
3731 9893 7.018487 ACTACTACCTCTCTCTCAGTTTACA 57.982 40.000 0.00 0.00 0.00 2.41
3732 9894 8.477256 TCTACTACTACCTCTCTCTCAGTTTAC 58.523 40.741 0.00 0.00 0.00 2.01
3733 9895 8.606754 TCTACTACTACCTCTCTCTCAGTTTA 57.393 38.462 0.00 0.00 0.00 2.01
3734 9896 7.499200 TCTACTACTACCTCTCTCTCAGTTT 57.501 40.000 0.00 0.00 0.00 2.66
3735 9897 7.499200 TTCTACTACTACCTCTCTCTCAGTT 57.501 40.000 0.00 0.00 0.00 3.16
3736 9898 7.333323 GTTTCTACTACTACCTCTCTCTCAGT 58.667 42.308 0.00 0.00 0.00 3.41
3737 9899 6.764560 GGTTTCTACTACTACCTCTCTCTCAG 59.235 46.154 0.00 0.00 0.00 3.35
3738 9900 6.444493 AGGTTTCTACTACTACCTCTCTCTCA 59.556 42.308 0.00 0.00 36.25 3.27
3739 9901 6.892485 AGGTTTCTACTACTACCTCTCTCTC 58.108 44.000 0.00 0.00 36.25 3.20
3740 9902 6.896452 AGGTTTCTACTACTACCTCTCTCT 57.104 41.667 0.00 0.00 36.25 3.10
3746 9908 5.793034 TGAGGAGGTTTCTACTACTACCT 57.207 43.478 0.00 0.00 43.48 3.08
3747 9909 7.059156 TGTATGAGGAGGTTTCTACTACTACC 58.941 42.308 0.00 0.00 33.42 3.18
3748 9910 8.517062 TTGTATGAGGAGGTTTCTACTACTAC 57.483 38.462 0.00 0.00 33.42 2.73
3749 9911 9.352191 GATTGTATGAGGAGGTTTCTACTACTA 57.648 37.037 0.00 0.00 33.42 1.82
3750 9912 7.839705 TGATTGTATGAGGAGGTTTCTACTACT 59.160 37.037 0.00 0.00 33.42 2.57
3751 9913 7.921745 GTGATTGTATGAGGAGGTTTCTACTAC 59.078 40.741 0.00 0.00 33.42 2.73
3752 9914 7.201794 CGTGATTGTATGAGGAGGTTTCTACTA 60.202 40.741 0.00 0.00 33.42 1.82
3753 9915 6.405953 CGTGATTGTATGAGGAGGTTTCTACT 60.406 42.308 0.00 0.00 36.74 2.57
3754 9916 5.749109 CGTGATTGTATGAGGAGGTTTCTAC 59.251 44.000 0.00 0.00 0.00 2.59
3755 9917 5.163447 CCGTGATTGTATGAGGAGGTTTCTA 60.163 44.000 0.00 0.00 0.00 2.10
3756 9918 4.383118 CCGTGATTGTATGAGGAGGTTTCT 60.383 45.833 0.00 0.00 0.00 2.52
3757 9919 3.871594 CCGTGATTGTATGAGGAGGTTTC 59.128 47.826 0.00 0.00 0.00 2.78
3758 9920 3.263425 ACCGTGATTGTATGAGGAGGTTT 59.737 43.478 0.00 0.00 0.00 3.27
3759 9921 2.838202 ACCGTGATTGTATGAGGAGGTT 59.162 45.455 0.00 0.00 0.00 3.50
3760 9922 2.168521 CACCGTGATTGTATGAGGAGGT 59.831 50.000 0.00 0.00 0.00 3.85
3761 9923 2.826428 CACCGTGATTGTATGAGGAGG 58.174 52.381 0.00 0.00 0.00 4.30
3762 9924 2.205074 GCACCGTGATTGTATGAGGAG 58.795 52.381 1.65 0.00 0.00 3.69
3763 9925 1.552792 TGCACCGTGATTGTATGAGGA 59.447 47.619 1.65 0.00 0.00 3.71
3771 9936 5.794687 TTAATTCTACTGCACCGTGATTG 57.205 39.130 1.65 0.00 0.00 2.67
3861 10027 9.720769 ATATTTAGTGATTATAGTGTTTCCCCG 57.279 33.333 0.00 0.00 0.00 5.73
3890 10056 8.306761 ACTGCTTTAACATTATTTTTCTCCCTG 58.693 33.333 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.