Multiple sequence alignment - TraesCS5D01G520100

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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 TraesCS5D01G520100 chr5D 100.000 3588 0 0 1 3588 541393678 541390091 0.000000e+00 6626.0
1 TraesCS5D01G520100 chr5D 91.081 1424 75 16 486 1888 540807199 540805807 0.000000e+00 1879.0
2 TraesCS5D01G520100 chr5D 84.901 1159 120 31 686 1829 541875483 541876601 0.000000e+00 1120.0
3 TraesCS5D01G520100 chr5D 94.199 724 37 3 2867 3588 541384110 541383390 0.000000e+00 1099.0
4 TraesCS5D01G520100 chr5D 84.102 1214 112 44 686 1887 541700809 541701953 0.000000e+00 1098.0
5 TraesCS5D01G520100 chr5D 90.856 689 38 4 2017 2705 540805065 540804402 0.000000e+00 900.0
6 TraesCS5D01G520100 chr5D 91.729 532 42 2 2180 2711 541876981 541877510 0.000000e+00 737.0
7 TraesCS5D01G520100 chr5D 98.123 373 7 0 1 373 540807645 540807273 0.000000e+00 651.0
8 TraesCS5D01G520100 chr5D 85.741 540 62 10 2132 2662 541702240 541702773 1.130000e-154 556.0
9 TraesCS5D01G520100 chr5D 79.447 253 26 17 178 408 541518974 541518726 4.800000e-34 156.0
10 TraesCS5D01G520100 chr5D 96.203 79 3 0 1889 1967 540805233 540805155 2.910000e-26 130.0
11 TraesCS5D01G520100 chr5D 95.833 48 2 0 1954 2001 540805097 540805050 1.070000e-10 78.7
12 TraesCS5D01G520100 chr4A 82.769 1271 128 49 592 1827 627499266 627498052 0.000000e+00 1050.0
13 TraesCS5D01G520100 chr4A 91.181 703 52 3 2017 2711 627497568 627496868 0.000000e+00 946.0
14 TraesCS5D01G520100 chr4A 93.976 83 2 1 434 513 627499349 627499267 4.860000e-24 122.0
15 TraesCS5D01G520100 chr4A 89.706 68 7 0 1894 1961 627497731 627497664 1.770000e-13 87.9
16 TraesCS5D01G520100 chr4A 100.000 36 0 0 1966 2001 627497588 627497553 2.310000e-07 67.6
17 TraesCS5D01G520100 chr5B 83.581 1145 116 28 686 1816 683595745 683596831 0.000000e+00 1007.0
18 TraesCS5D01G520100 chr5B 91.547 698 54 5 2017 2711 683596900 683597595 0.000000e+00 957.0
19 TraesCS5D01G520100 chr5B 88.000 100 8 4 425 522 683595455 683595552 8.140000e-22 115.0
20 TraesCS5D01G520100 chr2A 89.968 309 19 4 3263 3567 593759916 593760216 4.340000e-104 388.0
21 TraesCS5D01G520100 chr2A 88.685 327 23 6 3263 3585 593768079 593768395 1.560000e-103 387.0
22 TraesCS5D01G520100 chr2A 91.824 159 13 0 2708 2866 655879303 655879145 4.660000e-54 222.0
23 TraesCS5D01G520100 chr4D 89.933 298 23 5 3296 3588 376376986 376376691 9.400000e-101 377.0
24 TraesCS5D01G520100 chr4D 87.937 315 28 9 3258 3565 244100824 244100513 2.630000e-96 363.0
25 TraesCS5D01G520100 chr4D 80.826 339 59 6 2867 3201 206045110 206045446 9.880000e-66 261.0
26 TraesCS5D01G520100 chr3A 90.559 286 22 5 3285 3567 652170300 652170017 1.220000e-99 374.0
27 TraesCS5D01G520100 chr3A 90.559 286 22 5 3285 3567 652177806 652177523 1.220000e-99 374.0
28 TraesCS5D01G520100 chr3A 89.273 289 25 5 3285 3569 466706210 466705924 1.230000e-94 357.0
29 TraesCS5D01G520100 chr3A 92.258 155 12 0 2712 2866 471282865 471282711 1.680000e-53 220.0
30 TraesCS5D01G520100 chr3A 76.638 351 64 15 2882 3223 549656991 549657332 1.020000e-40 178.0
31 TraesCS5D01G520100 chr7A 87.692 325 25 7 3263 3583 499522328 499522015 7.320000e-97 364.0
32 TraesCS5D01G520100 chr7A 91.667 156 13 0 2711 2866 686326780 686326935 2.170000e-52 217.0
33 TraesCS5D01G520100 chr3D 96.795 156 5 0 2711 2866 436252394 436252239 9.880000e-66 261.0
34 TraesCS5D01G520100 chr3D 76.442 416 88 9 2867 3277 71983164 71982754 2.170000e-52 217.0
35 TraesCS5D01G520100 chr3D 76.019 417 88 11 2867 3277 70421277 70421687 4.700000e-49 206.0
36 TraesCS5D01G520100 chr3D 76.071 397 82 12 2887 3277 70455932 70456321 1.020000e-45 195.0
37 TraesCS5D01G520100 chr6B 83.142 261 41 3 2864 3123 646640643 646640385 5.990000e-58 235.0
38 TraesCS5D01G520100 chr7B 85.586 222 31 1 2866 3087 373198121 373198341 7.750000e-57 231.0
39 TraesCS5D01G520100 chr7D 76.329 414 92 6 2867 3277 239474466 239474876 2.170000e-52 217.0
40 TraesCS5D01G520100 chr7D 76.202 416 89 9 2867 3277 239420233 239420643 1.010000e-50 211.0
41 TraesCS5D01G520100 chr5A 91.026 156 14 0 2711 2866 17230052 17230207 1.010000e-50 211.0
42 TraesCS5D01G520100 chr6D 96.364 110 3 1 2711 2820 327362674 327362566 2.850000e-41 180.0
43 TraesCS5D01G520100 chr6D 100.000 28 0 0 2705 2732 8001991 8001964 6.000000e-03 52.8
44 TraesCS5D01G520100 chr1B 94.017 117 7 0 2750 2866 645352754 645352870 1.020000e-40 178.0
45 TraesCS5D01G520100 chr6A 76.136 352 70 12 2882 3226 550696149 550695805 4.760000e-39 172.0


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 TraesCS5D01G520100 chr5D 541390091 541393678 3587 True 6626.00 6626 100.000000 1 3588 1 chr5D.!!$R2 3587
1 TraesCS5D01G520100 chr5D 541383390 541384110 720 True 1099.00 1099 94.199000 2867 3588 1 chr5D.!!$R1 721
2 TraesCS5D01G520100 chr5D 541875483 541877510 2027 False 928.50 1120 88.315000 686 2711 2 chr5D.!!$F2 2025
3 TraesCS5D01G520100 chr5D 541700809 541702773 1964 False 827.00 1098 84.921500 686 2662 2 chr5D.!!$F1 1976
4 TraesCS5D01G520100 chr5D 540804402 540807645 3243 True 727.74 1879 94.419200 1 2705 5 chr5D.!!$R4 2704
5 TraesCS5D01G520100 chr4A 627496868 627499349 2481 True 454.70 1050 91.526400 434 2711 5 chr4A.!!$R1 2277
6 TraesCS5D01G520100 chr5B 683595455 683597595 2140 False 693.00 1007 87.709333 425 2711 3 chr5B.!!$F1 2286

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
789 867 0.099082 GTCTGTTAGACTCGGCCGAG 59.901 60.0 45.26 45.26 41.88 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2674 3564 0.322816 ATGGCAGCATCCGTCAAACT 60.323 50.0 0.0 0.0 0.0 2.66 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
179 180 1.133136 AGCGGGGAGTAGATACCATGT 60.133 52.381 0.00 0.00 30.50 3.21
284 285 3.319137 AGAGATACACAACACACGCAT 57.681 42.857 0.00 0.00 0.00 4.73
320 321 1.821332 CTGGAATTCTGGAGGCGCC 60.821 63.158 21.89 21.89 37.10 6.53
345 346 4.884257 GCCTTGCATGCGCCATGG 62.884 66.667 14.09 7.63 41.64 3.66
373 374 4.475135 GAGGAGGGGGCGCTTGAC 62.475 72.222 7.64 0.00 0.00 3.18
376 377 4.785453 GAGGGGGCGCTTGACCAG 62.785 72.222 7.64 0.00 45.79 4.00
394 395 1.497722 GCTCAAGCTGGTACGTTGC 59.502 57.895 0.00 0.00 38.21 4.17
409 410 1.965930 TTGCAGACCGACACATGGC 60.966 57.895 0.00 0.00 0.00 4.40
525 529 1.464608 CGTGTAGTGACAATGGCTTGG 59.535 52.381 0.00 0.00 37.31 3.61
774 852 6.641314 GGATCCAACACGTATATGTTAGTCTG 59.359 42.308 6.95 0.00 40.89 3.51
775 853 6.519679 TCCAACACGTATATGTTAGTCTGT 57.480 37.500 0.00 0.00 40.89 3.41
789 867 0.099082 GTCTGTTAGACTCGGCCGAG 59.901 60.000 45.26 45.26 41.88 4.63
848 926 0.522180 CGAGTCGGTCTGTACTTGCT 59.478 55.000 4.10 0.00 0.00 3.91
910 1025 6.944234 AAATAAGAACATAAGCCTACCAGC 57.056 37.500 0.00 0.00 0.00 4.85
912 1027 3.550437 AGAACATAAGCCTACCAGCTG 57.450 47.619 6.78 6.78 44.11 4.24
913 1028 1.943340 GAACATAAGCCTACCAGCTGC 59.057 52.381 8.66 0.00 44.11 5.25
914 1029 0.181350 ACATAAGCCTACCAGCTGCC 59.819 55.000 8.66 0.00 44.11 4.85
915 1030 0.471617 CATAAGCCTACCAGCTGCCT 59.528 55.000 8.66 0.00 44.11 4.75
916 1031 1.694150 CATAAGCCTACCAGCTGCCTA 59.306 52.381 8.66 0.00 44.11 3.93
917 1032 1.120530 TAAGCCTACCAGCTGCCTAC 58.879 55.000 8.66 0.00 44.11 3.18
918 1033 1.961180 AAGCCTACCAGCTGCCTACG 61.961 60.000 8.66 0.00 44.11 3.51
919 1034 2.722201 GCCTACCAGCTGCCTACGT 61.722 63.158 8.66 2.68 0.00 3.57
920 1035 1.389609 GCCTACCAGCTGCCTACGTA 61.390 60.000 8.66 3.85 0.00 3.57
921 1036 0.384669 CCTACCAGCTGCCTACGTAC 59.615 60.000 8.66 0.00 0.00 3.67
922 1037 1.100510 CTACCAGCTGCCTACGTACA 58.899 55.000 8.66 0.00 0.00 2.90
923 1038 0.813184 TACCAGCTGCCTACGTACAC 59.187 55.000 8.66 0.00 0.00 2.90
924 1039 1.516386 CCAGCTGCCTACGTACACG 60.516 63.158 8.66 0.00 46.33 4.49
1124 1248 1.143305 CTCCGCTTCAGTCAGTTGTG 58.857 55.000 0.00 0.00 0.00 3.33
1152 1291 4.789075 CGTACGGTCGCTGGGGTG 62.789 72.222 7.57 0.00 0.00 4.61
1153 1292 4.446413 GTACGGTCGCTGGGGTGG 62.446 72.222 0.00 0.00 0.00 4.61
1255 1394 0.105593 CATGGTCATCAGGTCTCCCG 59.894 60.000 0.00 0.00 35.12 5.14
1304 1443 4.561213 CCGTTTCACAAAGGACAAGAAAAC 59.439 41.667 0.00 0.00 33.52 2.43
1368 1508 3.507523 CGTTCGTGTACGCCGTATA 57.492 52.632 0.00 0.00 39.60 1.47
1374 1514 0.239347 GTGTACGCCGTATAGCCGAT 59.761 55.000 0.00 0.00 0.00 4.18
1378 1518 2.798976 ACGCCGTATAGCCGATAAAA 57.201 45.000 0.00 0.00 0.00 1.52
1398 1538 0.942410 TTATTCGCGCCACCTATCGC 60.942 55.000 0.00 0.00 46.98 4.58
1410 1550 2.894126 CACCTATCGCACTCTCCCTATT 59.106 50.000 0.00 0.00 0.00 1.73
1462 1602 4.569943 GAAGCCACAGACAAGTCATCTTA 58.430 43.478 2.72 0.00 32.07 2.10
1469 1609 4.256920 CAGACAAGTCATCTTAAGGGGTG 58.743 47.826 1.85 0.21 32.07 4.61
1501 1641 4.348168 AGGTGATACTTGTCAAAGACCACT 59.652 41.667 0.00 0.00 36.84 4.00
1504 1644 7.399191 AGGTGATACTTGTCAAAGACCACTATA 59.601 37.037 0.00 0.00 36.84 1.31
1538 1678 2.450992 CCCCTGGTGGCAAAATTGT 58.549 52.632 0.00 0.00 0.00 2.71
1738 1923 2.112928 ACATCGTTGCCAGGCACA 59.887 55.556 15.89 2.51 38.71 4.57
1861 2081 5.059343 CGCGCACACACACTATACTTATATC 59.941 44.000 8.75 0.00 0.00 1.63
1902 2713 2.743928 CTTCCTGCCACTCACCGC 60.744 66.667 0.00 0.00 0.00 5.68
2005 2887 8.784043 ACGGATGAAATTATACATCTTAAAGCC 58.216 33.333 15.00 0.00 41.50 4.35
2006 2888 8.783093 CGGATGAAATTATACATCTTAAAGCCA 58.217 33.333 15.00 0.00 41.50 4.75
2007 2889 9.899226 GGATGAAATTATACATCTTAAAGCCAC 57.101 33.333 15.00 0.00 41.50 5.01
2040 2922 7.952671 AGAAATTATACATCTTAGCTCGGTCA 58.047 34.615 0.00 0.00 0.00 4.02
2049 2931 5.084818 TCTTAGCTCGGTCAAATGATTGA 57.915 39.130 0.00 0.00 43.18 2.57
2061 2943 5.016173 TCAAATGATTGAACCCTGGGTTAG 58.984 41.667 30.31 11.80 46.95 2.34
2186 3076 7.648039 TTGGTTTCCTAAACTAACACATGTT 57.352 32.000 0.00 2.32 41.14 2.71
2206 3096 6.621316 TGTTTTGTTCTATAACTTTGCCGA 57.379 33.333 0.00 0.00 36.51 5.54
2207 3097 7.028926 TGTTTTGTTCTATAACTTTGCCGAA 57.971 32.000 0.00 0.00 36.51 4.30
2211 3101 4.941263 TGTTCTATAACTTTGCCGAATGCT 59.059 37.500 0.00 0.00 37.40 3.79
2381 3271 0.598680 GACGCCAGAAGATCCCATCG 60.599 60.000 0.00 0.00 0.00 3.84
2403 3293 5.105351 TCGCTCTTCATCCTTCACATAAGAA 60.105 40.000 0.00 0.00 0.00 2.52
2551 3441 3.382227 TGGGAGATGCATGCAAACTTATG 59.618 43.478 26.68 0.00 0.00 1.90
2582 3472 1.001633 TGAGACAAGTTCTTACGGGGC 59.998 52.381 0.00 0.00 33.22 5.80
2613 3503 4.952335 AGATTAGAATGCCCAAGTTGAAGG 59.048 41.667 3.87 0.00 0.00 3.46
2618 3508 0.555769 TGCCCAAGTTGAAGGAACCT 59.444 50.000 3.87 0.00 34.80 3.50
2625 3515 2.065799 AGTTGAAGGAACCTCCCACAT 58.934 47.619 0.00 0.00 37.19 3.21
2645 3535 1.069978 TCCACATCTTCAGCACGTTCA 59.930 47.619 0.00 0.00 0.00 3.18
2669 3559 0.742505 ATGAATGAACATGCAGGGCG 59.257 50.000 2.31 0.00 28.03 6.13
2674 3564 1.375908 GAACATGCAGGGCGAGTCA 60.376 57.895 2.31 0.00 0.00 3.41
2711 3601 9.066892 TGCTGCCATAACTATCCTAAAATTTAG 57.933 33.333 5.80 5.80 0.00 1.85
2712 3602 9.284968 GCTGCCATAACTATCCTAAAATTTAGA 57.715 33.333 13.87 1.58 0.00 2.10
2724 3614 8.782339 TCCTAAAATTTAGAGACCTTTTACGG 57.218 34.615 13.87 0.00 0.00 4.02
2725 3615 8.377799 TCCTAAAATTTAGAGACCTTTTACGGT 58.622 33.333 13.87 0.00 40.80 4.83
2726 3616 9.657419 CCTAAAATTTAGAGACCTTTTACGGTA 57.343 33.333 13.87 0.00 37.42 4.02
2728 3618 8.907222 AAAATTTAGAGACCTTTTACGGTACA 57.093 30.769 0.00 0.00 37.42 2.90
2729 3619 9.511272 AAAATTTAGAGACCTTTTACGGTACAT 57.489 29.630 0.00 0.00 37.42 2.29
2730 3620 8.713737 AATTTAGAGACCTTTTACGGTACATC 57.286 34.615 0.00 0.00 37.42 3.06
2731 3621 7.472334 TTTAGAGACCTTTTACGGTACATCT 57.528 36.000 0.00 0.00 37.42 2.90
2732 3622 5.326200 AGAGACCTTTTACGGTACATCTG 57.674 43.478 0.00 0.00 37.42 2.90
2733 3623 3.858247 AGACCTTTTACGGTACATCTGC 58.142 45.455 0.00 0.00 37.42 4.26
2734 3624 3.514309 AGACCTTTTACGGTACATCTGCT 59.486 43.478 0.00 0.00 37.42 4.24
2735 3625 3.858247 ACCTTTTACGGTACATCTGCTC 58.142 45.455 0.00 0.00 34.94 4.26
2736 3626 3.259876 ACCTTTTACGGTACATCTGCTCA 59.740 43.478 0.00 0.00 34.94 4.26
2737 3627 4.250464 CCTTTTACGGTACATCTGCTCAA 58.750 43.478 0.00 0.00 0.00 3.02
2738 3628 4.876107 CCTTTTACGGTACATCTGCTCAAT 59.124 41.667 0.00 0.00 0.00 2.57
2739 3629 6.046593 CCTTTTACGGTACATCTGCTCAATA 58.953 40.000 0.00 0.00 0.00 1.90
2740 3630 6.706270 CCTTTTACGGTACATCTGCTCAATAT 59.294 38.462 0.00 0.00 0.00 1.28
2741 3631 7.870954 CCTTTTACGGTACATCTGCTCAATATA 59.129 37.037 0.00 0.00 0.00 0.86
2742 3632 8.812147 TTTTACGGTACATCTGCTCAATATAG 57.188 34.615 0.00 0.00 0.00 1.31
2743 3633 7.754851 TTACGGTACATCTGCTCAATATAGA 57.245 36.000 0.00 0.00 0.00 1.98
2744 3634 6.015027 ACGGTACATCTGCTCAATATAGAC 57.985 41.667 0.00 0.00 0.00 2.59
2745 3635 5.047943 ACGGTACATCTGCTCAATATAGACC 60.048 44.000 0.00 0.00 0.00 3.85
2746 3636 5.403246 GGTACATCTGCTCAATATAGACCG 58.597 45.833 0.00 0.00 0.00 4.79
2747 3637 3.919216 ACATCTGCTCAATATAGACCGC 58.081 45.455 0.00 0.00 0.00 5.68
2748 3638 3.576118 ACATCTGCTCAATATAGACCGCT 59.424 43.478 0.00 0.00 0.00 5.52
2749 3639 4.039730 ACATCTGCTCAATATAGACCGCTT 59.960 41.667 0.00 0.00 0.00 4.68
2750 3640 5.243954 ACATCTGCTCAATATAGACCGCTTA 59.756 40.000 0.00 0.00 0.00 3.09
2751 3641 5.984695 TCTGCTCAATATAGACCGCTTAT 57.015 39.130 0.00 0.00 0.00 1.73
2752 3642 6.346477 TCTGCTCAATATAGACCGCTTATT 57.654 37.500 0.00 0.00 0.00 1.40
2753 3643 6.759272 TCTGCTCAATATAGACCGCTTATTT 58.241 36.000 0.00 0.00 0.00 1.40
2754 3644 6.868864 TCTGCTCAATATAGACCGCTTATTTC 59.131 38.462 0.00 0.00 0.00 2.17
2755 3645 6.759272 TGCTCAATATAGACCGCTTATTTCT 58.241 36.000 0.00 0.00 0.00 2.52
2756 3646 7.892609 TGCTCAATATAGACCGCTTATTTCTA 58.107 34.615 0.00 0.00 0.00 2.10
2757 3647 8.531982 TGCTCAATATAGACCGCTTATTTCTAT 58.468 33.333 0.00 0.00 36.67 1.98
2764 3654 6.630444 AGACCGCTTATTTCTATAGTTCGA 57.370 37.500 0.00 0.00 0.00 3.71
2765 3655 6.437094 AGACCGCTTATTTCTATAGTTCGAC 58.563 40.000 0.00 0.00 0.00 4.20
2766 3656 5.210715 ACCGCTTATTTCTATAGTTCGACG 58.789 41.667 0.00 0.00 0.00 5.12
2767 3657 4.615961 CCGCTTATTTCTATAGTTCGACGG 59.384 45.833 0.00 2.86 0.00 4.79
2768 3658 5.210715 CGCTTATTTCTATAGTTCGACGGT 58.789 41.667 0.00 0.00 0.00 4.83
2769 3659 5.339085 CGCTTATTTCTATAGTTCGACGGTC 59.661 44.000 0.00 0.00 0.00 4.79
2770 3660 5.628606 GCTTATTTCTATAGTTCGACGGTCC 59.371 44.000 1.91 0.00 0.00 4.46
2771 3661 6.698008 TTATTTCTATAGTTCGACGGTCCA 57.302 37.500 1.91 0.00 0.00 4.02
2772 3662 4.627611 TTTCTATAGTTCGACGGTCCAG 57.372 45.455 1.91 0.00 0.00 3.86
2773 3663 3.548745 TCTATAGTTCGACGGTCCAGA 57.451 47.619 1.91 0.00 0.00 3.86
2774 3664 4.082665 TCTATAGTTCGACGGTCCAGAT 57.917 45.455 1.91 0.00 0.00 2.90
2775 3665 3.813724 TCTATAGTTCGACGGTCCAGATG 59.186 47.826 1.91 0.00 0.00 2.90
2776 3666 2.118313 TAGTTCGACGGTCCAGATGA 57.882 50.000 1.91 0.00 0.00 2.92
2777 3667 1.475403 AGTTCGACGGTCCAGATGAT 58.525 50.000 1.91 0.00 0.00 2.45
2778 3668 2.651455 AGTTCGACGGTCCAGATGATA 58.349 47.619 1.91 0.00 0.00 2.15
2779 3669 2.358267 AGTTCGACGGTCCAGATGATAC 59.642 50.000 1.91 0.00 0.00 2.24
2780 3670 2.047002 TCGACGGTCCAGATGATACA 57.953 50.000 1.91 0.00 0.00 2.29
2781 3671 2.371306 TCGACGGTCCAGATGATACAA 58.629 47.619 1.91 0.00 0.00 2.41
2782 3672 2.956333 TCGACGGTCCAGATGATACAAT 59.044 45.455 1.91 0.00 0.00 2.71
2783 3673 4.139038 TCGACGGTCCAGATGATACAATA 58.861 43.478 1.91 0.00 0.00 1.90
2784 3674 4.023450 TCGACGGTCCAGATGATACAATAC 60.023 45.833 1.91 0.00 0.00 1.89
2785 3675 4.023107 CGACGGTCCAGATGATACAATACT 60.023 45.833 1.91 0.00 0.00 2.12
2786 3676 5.180680 CGACGGTCCAGATGATACAATACTA 59.819 44.000 1.91 0.00 0.00 1.82
2787 3677 6.328641 ACGGTCCAGATGATACAATACTAC 57.671 41.667 0.00 0.00 0.00 2.73
2788 3678 6.069331 ACGGTCCAGATGATACAATACTACT 58.931 40.000 0.00 0.00 0.00 2.57
2789 3679 6.207025 ACGGTCCAGATGATACAATACTACTC 59.793 42.308 0.00 0.00 0.00 2.59
2790 3680 6.431543 CGGTCCAGATGATACAATACTACTCT 59.568 42.308 0.00 0.00 0.00 3.24
2791 3681 7.606839 CGGTCCAGATGATACAATACTACTCTA 59.393 40.741 0.00 0.00 0.00 2.43
2792 3682 8.952278 GGTCCAGATGATACAATACTACTCTAG 58.048 40.741 0.00 0.00 0.00 2.43
2793 3683 9.727859 GTCCAGATGATACAATACTACTCTAGA 57.272 37.037 0.00 0.00 0.00 2.43
2804 3694 9.406113 ACAATACTACTCTAGATTTTCGGTAGT 57.594 33.333 18.68 18.68 41.41 2.73
2823 3713 8.143835 TCGGTAGTATATTAACTAAACAAGGGC 58.856 37.037 0.00 0.00 33.85 5.19
2824 3714 7.927629 CGGTAGTATATTAACTAAACAAGGGCA 59.072 37.037 0.00 0.00 33.85 5.36
2825 3715 9.788889 GGTAGTATATTAACTAAACAAGGGCAT 57.211 33.333 0.00 0.00 33.85 4.40
2831 3721 4.350368 AACTAAACAAGGGCATTTTGGG 57.650 40.909 0.00 0.00 0.00 4.12
2832 3722 3.313791 ACTAAACAAGGGCATTTTGGGT 58.686 40.909 0.00 0.00 0.00 4.51
2833 3723 4.484912 ACTAAACAAGGGCATTTTGGGTA 58.515 39.130 0.00 0.00 0.00 3.69
2834 3724 4.526650 ACTAAACAAGGGCATTTTGGGTAG 59.473 41.667 0.00 0.00 0.00 3.18
2835 3725 2.694616 ACAAGGGCATTTTGGGTAGT 57.305 45.000 0.00 0.00 0.00 2.73
2836 3726 3.818295 ACAAGGGCATTTTGGGTAGTA 57.182 42.857 0.00 0.00 0.00 1.82
2837 3727 3.427573 ACAAGGGCATTTTGGGTAGTAC 58.572 45.455 0.00 0.00 0.00 2.73
2838 3728 3.181427 ACAAGGGCATTTTGGGTAGTACA 60.181 43.478 2.06 0.00 0.00 2.90
2839 3729 3.081710 AGGGCATTTTGGGTAGTACAC 57.918 47.619 2.06 0.00 0.00 2.90
2840 3730 2.377193 AGGGCATTTTGGGTAGTACACA 59.623 45.455 0.00 0.00 0.00 3.72
2841 3731 3.011257 AGGGCATTTTGGGTAGTACACAT 59.989 43.478 5.96 0.00 27.78 3.21
2842 3732 3.767131 GGGCATTTTGGGTAGTACACATT 59.233 43.478 5.96 0.00 27.78 2.71
2843 3733 4.221924 GGGCATTTTGGGTAGTACACATTT 59.778 41.667 5.96 0.00 27.78 2.32
2844 3734 5.419471 GGGCATTTTGGGTAGTACACATTTA 59.581 40.000 5.96 0.00 27.78 1.40
2845 3735 6.097696 GGGCATTTTGGGTAGTACACATTTAT 59.902 38.462 5.96 0.00 27.78 1.40
2846 3736 7.200455 GGCATTTTGGGTAGTACACATTTATC 58.800 38.462 5.96 0.00 27.78 1.75
2847 3737 7.200455 GCATTTTGGGTAGTACACATTTATCC 58.800 38.462 5.96 0.00 27.78 2.59
2848 3738 7.147983 GCATTTTGGGTAGTACACATTTATCCA 60.148 37.037 5.96 0.00 27.78 3.41
2849 3739 8.912988 CATTTTGGGTAGTACACATTTATCCAT 58.087 33.333 5.96 0.00 27.78 3.41
2850 3740 8.514330 TTTTGGGTAGTACACATTTATCCATC 57.486 34.615 5.96 0.00 27.78 3.51
2851 3741 7.446106 TTGGGTAGTACACATTTATCCATCT 57.554 36.000 5.96 0.00 27.78 2.90
2852 3742 7.062749 TGGGTAGTACACATTTATCCATCTC 57.937 40.000 0.00 0.00 0.00 2.75
2853 3743 6.157211 GGGTAGTACACATTTATCCATCTCG 58.843 44.000 2.06 0.00 0.00 4.04
2854 3744 5.634020 GGTAGTACACATTTATCCATCTCGC 59.366 44.000 2.06 0.00 0.00 5.03
2855 3745 5.276461 AGTACACATTTATCCATCTCGCA 57.724 39.130 0.00 0.00 0.00 5.10
2856 3746 5.292765 AGTACACATTTATCCATCTCGCAG 58.707 41.667 0.00 0.00 0.00 5.18
2857 3747 3.470709 ACACATTTATCCATCTCGCAGG 58.529 45.455 0.00 0.00 0.00 4.85
2858 3748 2.225019 CACATTTATCCATCTCGCAGGC 59.775 50.000 0.00 0.00 0.00 4.85
2859 3749 2.158769 ACATTTATCCATCTCGCAGGCA 60.159 45.455 0.00 0.00 0.00 4.75
2860 3750 1.953559 TTTATCCATCTCGCAGGCAC 58.046 50.000 0.00 0.00 0.00 5.01
2861 3751 0.106708 TTATCCATCTCGCAGGCACC 59.893 55.000 0.00 0.00 0.00 5.01
2862 3752 0.760567 TATCCATCTCGCAGGCACCT 60.761 55.000 0.00 0.00 0.00 4.00
2863 3753 1.630126 ATCCATCTCGCAGGCACCTT 61.630 55.000 0.00 0.00 0.00 3.50
2864 3754 1.817099 CCATCTCGCAGGCACCTTC 60.817 63.158 0.00 0.00 0.00 3.46
2865 3755 1.817099 CATCTCGCAGGCACCTTCC 60.817 63.158 0.00 0.00 0.00 3.46
2879 3769 0.774908 CCTTCCTGTAACACCCCCAA 59.225 55.000 0.00 0.00 0.00 4.12
2897 3787 2.679837 CCAATGTCATGCTACAGTGACC 59.320 50.000 14.46 0.00 45.74 4.02
2921 3811 2.292267 CACTAATGGTGCCCTGTCATC 58.708 52.381 0.00 0.00 39.22 2.92
2964 3854 7.986889 AGTTGCCACTTGATAAAAATCAAAGTT 59.013 29.630 2.74 0.00 39.73 2.66
3077 3967 8.137437 CCATTGTCAAGTTGAAACTAACTTCAT 58.863 33.333 7.25 0.00 45.15 2.57
3187 4077 6.676237 TTTTTCAATTGGCCTCAAACTTTC 57.324 33.333 3.32 0.00 36.36 2.62
3197 4087 2.489802 CCTCAAACTTTCTGGGCCTCTT 60.490 50.000 4.53 0.00 0.00 2.85
3207 4097 3.955471 TCTGGGCCTCTTCAAGTTATTG 58.045 45.455 4.53 0.00 37.80 1.90
3220 4110 9.905713 TCTTCAAGTTATTGCCTAGTTTCATAT 57.094 29.630 0.00 0.00 36.30 1.78
3330 4222 0.902984 CCCCTTTTTACCTGGCCCAC 60.903 60.000 0.00 0.00 0.00 4.61
3336 4228 3.561120 TTACCTGGCCCACCTTGCG 62.561 63.158 0.00 0.00 36.63 4.85
3381 4273 1.604915 GGCCTTTCCCTCACCTCTC 59.395 63.158 0.00 0.00 0.00 3.20
3431 4323 4.129737 ACGAGCGACCGTCCATGG 62.130 66.667 4.97 4.97 38.56 3.66
3498 4390 1.152525 GAGCATCCTCGACCCCCTA 60.153 63.158 0.00 0.00 0.00 3.53
3514 4406 1.421480 CCTACTAACCCTAGTGCCCC 58.579 60.000 0.00 0.00 38.85 5.80
3536 4428 2.895426 TTCCCTCTCTCCCTCGCTCG 62.895 65.000 0.00 0.00 0.00 5.03
3539 4431 1.720694 CCTCTCTCCCTCGCTCGTTC 61.721 65.000 0.00 0.00 0.00 3.95
3552 4444 4.452733 CGTTCCCCTCGCTCCACC 62.453 72.222 0.00 0.00 0.00 4.61
3553 4445 3.319198 GTTCCCCTCGCTCCACCA 61.319 66.667 0.00 0.00 0.00 4.17
3554 4446 3.319198 TTCCCCTCGCTCCACCAC 61.319 66.667 0.00 0.00 0.00 4.16
3557 4449 3.314331 CCCTCGCTCCACCACACT 61.314 66.667 0.00 0.00 0.00 3.55
3573 4465 2.754552 CACACTCTCTCTCTCTCCCAAG 59.245 54.545 0.00 0.00 0.00 3.61
3574 4466 2.291540 ACACTCTCTCTCTCTCCCAAGG 60.292 54.545 0.00 0.00 0.00 3.61
3579 4471 1.713647 TCTCTCTCTCCCAAGGTCAGT 59.286 52.381 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 1.078567 CTGCAACCTCTCCTCTGCC 60.079 63.158 0.00 0.00 33.78 4.85
179 180 6.534475 TCGCAACCCTAGTTCTATTTCTAA 57.466 37.500 0.00 0.00 32.45 2.10
284 285 4.206375 TCCAGATGCTTGTTTCTGTTGAA 58.794 39.130 0.00 0.00 38.12 2.69
345 346 2.134933 CCCTCCTCTACCGCCCTTC 61.135 68.421 0.00 0.00 0.00 3.46
355 356 4.722535 TCAAGCGCCCCCTCCTCT 62.723 66.667 2.29 0.00 0.00 3.69
376 377 1.227999 TGCAACGTACCAGCTTGAGC 61.228 55.000 0.00 0.00 42.49 4.26
377 378 0.792640 CTGCAACGTACCAGCTTGAG 59.207 55.000 0.00 0.00 0.00 3.02
378 379 0.391228 TCTGCAACGTACCAGCTTGA 59.609 50.000 9.77 3.57 0.00 3.02
379 380 0.512952 GTCTGCAACGTACCAGCTTG 59.487 55.000 9.77 0.00 0.00 4.01
380 381 0.602905 GGTCTGCAACGTACCAGCTT 60.603 55.000 9.77 0.00 33.28 3.74
381 382 1.004918 GGTCTGCAACGTACCAGCT 60.005 57.895 9.77 0.00 33.28 4.24
382 383 2.380410 CGGTCTGCAACGTACCAGC 61.380 63.158 9.77 3.42 32.55 4.85
383 384 1.007336 GTCGGTCTGCAACGTACCAG 61.007 60.000 5.35 7.08 32.55 4.00
384 385 1.007038 GTCGGTCTGCAACGTACCA 60.007 57.895 5.35 0.00 32.55 3.25
385 386 1.007038 TGTCGGTCTGCAACGTACC 60.007 57.895 0.00 0.00 0.00 3.34
386 387 0.595567 TGTGTCGGTCTGCAACGTAC 60.596 55.000 0.00 6.65 0.00 3.67
387 388 0.315886 ATGTGTCGGTCTGCAACGTA 59.684 50.000 0.00 0.00 0.00 3.57
388 389 1.069090 ATGTGTCGGTCTGCAACGT 59.931 52.632 5.24 0.00 0.00 3.99
389 390 1.492873 CATGTGTCGGTCTGCAACG 59.507 57.895 0.00 0.00 0.00 4.10
390 391 1.868997 CCATGTGTCGGTCTGCAAC 59.131 57.895 0.00 0.00 0.00 4.17
391 392 1.965930 GCCATGTGTCGGTCTGCAA 60.966 57.895 0.00 0.00 0.00 4.08
392 393 2.358615 GCCATGTGTCGGTCTGCA 60.359 61.111 0.00 0.00 0.00 4.41
393 394 3.490759 CGCCATGTGTCGGTCTGC 61.491 66.667 0.00 0.00 0.00 4.26
394 395 2.815211 CCGCCATGTGTCGGTCTG 60.815 66.667 9.35 0.00 40.72 3.51
416 417 3.943479 TATCCACACCACACCGCGC 62.943 63.158 0.00 0.00 0.00 6.86
417 418 1.809619 CTATCCACACCACACCGCG 60.810 63.158 0.00 0.00 0.00 6.46
418 419 0.460284 CTCTATCCACACCACACCGC 60.460 60.000 0.00 0.00 0.00 5.68
421 422 5.791336 TGATATCTCTATCCACACCACAC 57.209 43.478 3.98 0.00 34.03 3.82
422 423 5.183904 CGATGATATCTCTATCCACACCACA 59.816 44.000 3.98 0.00 34.03 4.17
423 424 5.645624 CGATGATATCTCTATCCACACCAC 58.354 45.833 3.98 0.00 34.03 4.16
424 425 4.158579 GCGATGATATCTCTATCCACACCA 59.841 45.833 3.98 0.00 34.03 4.17
425 426 4.440802 GGCGATGATATCTCTATCCACACC 60.441 50.000 3.98 0.00 34.03 4.16
426 427 4.677584 GGCGATGATATCTCTATCCACAC 58.322 47.826 3.98 0.00 34.03 3.82
427 428 3.378427 CGGCGATGATATCTCTATCCACA 59.622 47.826 0.00 0.00 34.03 4.17
430 431 3.303461 CGACGGCGATGATATCTCTATCC 60.303 52.174 16.62 0.00 40.82 2.59
431 432 3.556365 TCGACGGCGATGATATCTCTATC 59.444 47.826 10.67 0.00 42.51 2.08
432 433 3.532542 TCGACGGCGATGATATCTCTAT 58.467 45.455 10.67 0.00 42.51 1.98
525 529 1.578206 GAAGCACGCTGGAGAAACCC 61.578 60.000 0.00 0.00 38.00 4.11
789 867 5.786401 ATGATTCTGCTTTAGACACGAAC 57.214 39.130 0.00 0.00 34.43 3.95
893 998 1.943340 GCAGCTGGTAGGCTTATGTTC 59.057 52.381 17.12 0.00 41.00 3.18
894 999 1.408822 GGCAGCTGGTAGGCTTATGTT 60.409 52.381 17.12 0.00 41.00 2.71
901 1016 1.389609 TACGTAGGCAGCTGGTAGGC 61.390 60.000 17.12 0.77 0.00 3.93
902 1017 0.384669 GTACGTAGGCAGCTGGTAGG 59.615 60.000 17.12 0.00 0.00 3.18
903 1018 1.100510 TGTACGTAGGCAGCTGGTAG 58.899 55.000 17.12 0.00 0.00 3.18
904 1019 0.813184 GTGTACGTAGGCAGCTGGTA 59.187 55.000 17.12 5.75 0.00 3.25
905 1020 1.590147 GTGTACGTAGGCAGCTGGT 59.410 57.895 17.12 6.83 0.00 4.00
906 1021 1.516386 CGTGTACGTAGGCAGCTGG 60.516 63.158 17.12 0.00 34.11 4.85
907 1022 2.158959 GCGTGTACGTAGGCAGCTG 61.159 63.158 10.11 10.11 42.22 4.24
908 1023 2.181021 GCGTGTACGTAGGCAGCT 59.819 61.111 6.27 0.00 42.22 4.24
909 1024 2.126228 TGCGTGTACGTAGGCAGC 60.126 61.111 10.77 8.14 42.22 5.25
910 1025 2.150218 CGTGCGTGTACGTAGGCAG 61.150 63.158 14.14 7.02 41.49 4.85
911 1026 2.126773 CGTGCGTGTACGTAGGCA 60.127 61.111 10.77 10.77 42.22 4.75
912 1027 2.877582 CCGTGCGTGTACGTAGGC 60.878 66.667 9.51 0.46 42.24 3.93
913 1028 1.512734 GACCGTGCGTGTACGTAGG 60.513 63.158 9.51 7.20 42.24 3.18
914 1029 1.512734 GGACCGTGCGTGTACGTAG 60.513 63.158 9.51 0.00 42.24 3.51
915 1030 1.585267 ATGGACCGTGCGTGTACGTA 61.585 55.000 9.51 0.00 42.24 3.57
916 1031 1.585267 TATGGACCGTGCGTGTACGT 61.585 55.000 9.51 0.00 42.24 3.57
917 1032 0.456482 TTATGGACCGTGCGTGTACG 60.456 55.000 3.41 3.41 43.35 3.67
918 1033 1.274596 CTTATGGACCGTGCGTGTAC 58.725 55.000 0.00 0.00 0.00 2.90
919 1034 0.458889 GCTTATGGACCGTGCGTGTA 60.459 55.000 0.00 0.00 0.00 2.90
920 1035 1.740296 GCTTATGGACCGTGCGTGT 60.740 57.895 0.00 0.00 0.00 4.49
921 1036 2.461110 GGCTTATGGACCGTGCGTG 61.461 63.158 0.00 0.00 0.00 5.34
922 1037 2.125269 GGCTTATGGACCGTGCGT 60.125 61.111 0.00 0.00 0.00 5.24
923 1038 2.895372 GGGCTTATGGACCGTGCG 60.895 66.667 0.00 0.00 30.75 5.34
1286 1425 3.699038 CCAGGTTTTCTTGTCCTTTGTGA 59.301 43.478 0.00 0.00 0.00 3.58
1304 1443 1.631405 TTGTGATTTGGAAGCCCAGG 58.369 50.000 0.00 0.00 44.60 4.45
1362 1502 6.408428 GCGAATAATTTTATCGGCTATACGG 58.592 40.000 8.61 0.00 0.00 4.02
1368 1508 2.095919 GGCGCGAATAATTTTATCGGCT 60.096 45.455 12.10 0.00 33.60 5.52
1374 1514 4.150980 CGATAGGTGGCGCGAATAATTTTA 59.849 41.667 12.10 0.00 0.00 1.52
1378 1518 1.710013 CGATAGGTGGCGCGAATAAT 58.290 50.000 12.10 0.00 0.00 1.28
1398 1538 3.462021 GCTGCTGTTAATAGGGAGAGTG 58.538 50.000 1.09 0.00 0.00 3.51
1401 1541 2.170607 GTGGCTGCTGTTAATAGGGAGA 59.829 50.000 0.00 0.00 0.00 3.71
1410 1550 4.615901 CCATCGTGGCTGCTGTTA 57.384 55.556 0.00 0.00 0.00 2.41
1462 1602 1.847968 CCTCCCACTCACACCCCTT 60.848 63.158 0.00 0.00 0.00 3.95
1469 1609 2.567615 ACAAGTATCACCTCCCACTCAC 59.432 50.000 0.00 0.00 0.00 3.51
1501 1641 1.013596 GCGCACATTGCACTGGTATA 58.986 50.000 9.06 0.00 45.36 1.47
1504 1644 3.673484 GGCGCACATTGCACTGGT 61.673 61.111 10.83 0.00 45.36 4.00
1538 1678 5.353400 CGGTCGAGCAATCCAGTATATACTA 59.647 44.000 15.03 1.43 34.13 1.82
1672 1850 7.386299 GGAGAGAACATTATGCACCTACATAAG 59.614 40.741 0.00 0.00 43.70 1.73
1738 1923 1.084289 GCGTACCAAATTTCCGAGCT 58.916 50.000 0.00 0.00 0.00 4.09
1870 2090 7.500559 AGTGGCAGGAAGACTAAATGATTTATC 59.499 37.037 0.00 0.00 0.00 1.75
1902 2713 4.375005 CGAATTTCCACAGCATATCGTACG 60.375 45.833 9.53 9.53 0.00 3.67
1963 2845 4.403432 TCATCCGTACCGAAGTAATTTCCT 59.597 41.667 0.00 0.00 31.82 3.36
2012 2894 9.614792 ACCGAGCTAAGATGTATAATTTCTTTT 57.385 29.630 0.00 0.00 32.28 2.27
2013 2895 9.262358 GACCGAGCTAAGATGTATAATTTCTTT 57.738 33.333 0.00 0.00 32.28 2.52
2014 2896 8.421784 TGACCGAGCTAAGATGTATAATTTCTT 58.578 33.333 0.00 0.00 34.29 2.52
2015 2897 7.952671 TGACCGAGCTAAGATGTATAATTTCT 58.047 34.615 0.00 0.00 0.00 2.52
2016 2898 8.589335 TTGACCGAGCTAAGATGTATAATTTC 57.411 34.615 0.00 0.00 0.00 2.17
2017 2899 8.958119 TTTGACCGAGCTAAGATGTATAATTT 57.042 30.769 0.00 0.00 0.00 1.82
2018 2900 8.993121 CATTTGACCGAGCTAAGATGTATAATT 58.007 33.333 0.00 0.00 0.00 1.40
2019 2901 8.367911 TCATTTGACCGAGCTAAGATGTATAAT 58.632 33.333 0.00 0.00 0.00 1.28
2020 2902 7.722363 TCATTTGACCGAGCTAAGATGTATAA 58.278 34.615 0.00 0.00 0.00 0.98
2021 2903 7.284919 TCATTTGACCGAGCTAAGATGTATA 57.715 36.000 0.00 0.00 0.00 1.47
2022 2904 6.161855 TCATTTGACCGAGCTAAGATGTAT 57.838 37.500 0.00 0.00 0.00 2.29
2023 2905 5.592104 TCATTTGACCGAGCTAAGATGTA 57.408 39.130 0.00 0.00 0.00 2.29
2024 2906 4.471904 TCATTTGACCGAGCTAAGATGT 57.528 40.909 0.00 0.00 0.00 3.06
2025 2907 5.525012 TCAATCATTTGACCGAGCTAAGATG 59.475 40.000 0.00 0.00 36.94 2.90
2026 2908 5.674525 TCAATCATTTGACCGAGCTAAGAT 58.325 37.500 0.00 0.00 36.94 2.40
2027 2909 5.084818 TCAATCATTTGACCGAGCTAAGA 57.915 39.130 0.00 0.00 36.94 2.10
2028 2910 5.447818 GGTTCAATCATTTGACCGAGCTAAG 60.448 44.000 0.00 0.00 41.50 2.18
2029 2911 4.394920 GGTTCAATCATTTGACCGAGCTAA 59.605 41.667 0.00 0.00 41.50 3.09
2030 2912 3.938963 GGTTCAATCATTTGACCGAGCTA 59.061 43.478 0.00 0.00 41.50 3.32
2031 2913 2.749621 GGTTCAATCATTTGACCGAGCT 59.250 45.455 0.00 0.00 41.50 4.09
2040 2922 5.010708 ACTAACCCAGGGTTCAATCATTT 57.989 39.130 28.49 2.65 43.05 2.32
2186 3076 6.090129 GCATTCGGCAAAGTTATAGAACAAA 58.910 36.000 2.62 0.00 43.97 2.83
2206 3096 6.769134 TTGATCATCAGAACATGAAGCATT 57.231 33.333 0.00 0.00 42.53 3.56
2207 3097 6.321435 ACATTGATCATCAGAACATGAAGCAT 59.679 34.615 0.00 0.00 42.53 3.79
2211 3101 6.327154 GCAACATTGATCATCAGAACATGAA 58.673 36.000 0.00 0.00 42.53 2.57
2381 3271 6.992063 TTTCTTATGTGAAGGATGAAGAGC 57.008 37.500 0.00 0.00 0.00 4.09
2403 3293 3.482436 TGATACAAACGCTCAACCCTTT 58.518 40.909 0.00 0.00 0.00 3.11
2551 3441 3.357166 ACTTGTCTCAGTCTTGTCGAC 57.643 47.619 9.11 9.11 43.17 4.20
2582 3472 4.129380 TGGGCATTCTAATCTGTTCATCG 58.871 43.478 0.00 0.00 0.00 3.84
2613 3503 1.561542 AGATGTGGATGTGGGAGGTTC 59.438 52.381 0.00 0.00 0.00 3.62
2618 3508 1.065199 GCTGAAGATGTGGATGTGGGA 60.065 52.381 0.00 0.00 0.00 4.37
2625 3515 1.069978 TGAACGTGCTGAAGATGTGGA 59.930 47.619 0.00 0.00 0.00 4.02
2645 3535 3.817084 CCCTGCATGTTCATTCATATCGT 59.183 43.478 0.00 0.00 0.00 3.73
2657 3547 1.376424 CTGACTCGCCCTGCATGTT 60.376 57.895 0.00 0.00 0.00 2.71
2669 3559 1.728971 CAGCATCCGTCAAACTGACTC 59.271 52.381 5.34 0.00 44.85 3.36
2674 3564 0.322816 ATGGCAGCATCCGTCAAACT 60.323 50.000 0.00 0.00 0.00 2.66
2711 3601 3.864003 GCAGATGTACCGTAAAAGGTCTC 59.136 47.826 0.00 0.00 44.68 3.36
2712 3602 3.514309 AGCAGATGTACCGTAAAAGGTCT 59.486 43.478 0.00 0.00 44.68 3.85
2713 3603 3.858247 AGCAGATGTACCGTAAAAGGTC 58.142 45.455 0.00 0.00 44.68 3.85
2715 3605 3.857052 TGAGCAGATGTACCGTAAAAGG 58.143 45.455 0.00 0.00 37.30 3.11
2716 3606 7.715265 ATATTGAGCAGATGTACCGTAAAAG 57.285 36.000 0.00 0.00 0.00 2.27
2717 3607 8.635328 TCTATATTGAGCAGATGTACCGTAAAA 58.365 33.333 0.00 0.00 0.00 1.52
2718 3608 8.080417 GTCTATATTGAGCAGATGTACCGTAAA 58.920 37.037 0.00 0.00 0.00 2.01
2719 3609 7.309012 GGTCTATATTGAGCAGATGTACCGTAA 60.309 40.741 10.83 0.00 34.88 3.18
2720 3610 6.150641 GGTCTATATTGAGCAGATGTACCGTA 59.849 42.308 10.83 0.00 34.88 4.02
2721 3611 5.047943 GGTCTATATTGAGCAGATGTACCGT 60.048 44.000 10.83 0.00 34.88 4.83
2722 3612 5.403246 GGTCTATATTGAGCAGATGTACCG 58.597 45.833 10.83 0.00 34.88 4.02
2723 3613 5.403246 CGGTCTATATTGAGCAGATGTACC 58.597 45.833 15.02 0.00 34.46 3.34
2724 3614 4.859798 GCGGTCTATATTGAGCAGATGTAC 59.140 45.833 15.02 0.00 34.46 2.90
2725 3615 4.767409 AGCGGTCTATATTGAGCAGATGTA 59.233 41.667 15.02 0.00 34.46 2.29
2726 3616 3.576118 AGCGGTCTATATTGAGCAGATGT 59.424 43.478 15.02 0.00 34.46 3.06
2727 3617 4.185467 AGCGGTCTATATTGAGCAGATG 57.815 45.455 15.02 2.00 34.46 2.90
2728 3618 4.881019 AAGCGGTCTATATTGAGCAGAT 57.119 40.909 15.02 5.49 34.46 2.90
2729 3619 5.984695 ATAAGCGGTCTATATTGAGCAGA 57.015 39.130 15.02 0.00 34.46 4.26
2730 3620 6.870965 AGAAATAAGCGGTCTATATTGAGCAG 59.129 38.462 15.02 9.46 34.46 4.24
2731 3621 6.759272 AGAAATAAGCGGTCTATATTGAGCA 58.241 36.000 15.02 0.00 34.46 4.26
2732 3622 8.934507 ATAGAAATAAGCGGTCTATATTGAGC 57.065 34.615 6.32 6.32 33.74 4.26
2738 3628 9.440773 TCGAACTATAGAAATAAGCGGTCTATA 57.559 33.333 6.78 0.00 36.31 1.31
2739 3629 8.235905 GTCGAACTATAGAAATAAGCGGTCTAT 58.764 37.037 6.78 0.00 38.04 1.98
2740 3630 7.570140 CGTCGAACTATAGAAATAAGCGGTCTA 60.570 40.741 6.78 0.00 0.00 2.59
2741 3631 6.437094 GTCGAACTATAGAAATAAGCGGTCT 58.563 40.000 6.78 0.00 0.00 3.85
2742 3632 5.339085 CGTCGAACTATAGAAATAAGCGGTC 59.661 44.000 6.78 0.00 0.00 4.79
2743 3633 5.210715 CGTCGAACTATAGAAATAAGCGGT 58.789 41.667 6.78 0.00 0.00 5.68
2744 3634 4.615961 CCGTCGAACTATAGAAATAAGCGG 59.384 45.833 6.78 7.49 0.00 5.52
2745 3635 5.210715 ACCGTCGAACTATAGAAATAAGCG 58.789 41.667 6.78 2.43 0.00 4.68
2746 3636 5.628606 GGACCGTCGAACTATAGAAATAAGC 59.371 44.000 6.78 0.00 0.00 3.09
2747 3637 6.732154 TGGACCGTCGAACTATAGAAATAAG 58.268 40.000 6.78 0.00 0.00 1.73
2748 3638 6.543465 TCTGGACCGTCGAACTATAGAAATAA 59.457 38.462 6.78 0.00 0.00 1.40
2749 3639 6.057533 TCTGGACCGTCGAACTATAGAAATA 58.942 40.000 6.78 0.00 0.00 1.40
2750 3640 4.885907 TCTGGACCGTCGAACTATAGAAAT 59.114 41.667 6.78 0.00 0.00 2.17
2751 3641 4.264253 TCTGGACCGTCGAACTATAGAAA 58.736 43.478 6.78 0.00 0.00 2.52
2752 3642 3.877559 TCTGGACCGTCGAACTATAGAA 58.122 45.455 6.78 0.00 0.00 2.10
2753 3643 3.548745 TCTGGACCGTCGAACTATAGA 57.451 47.619 6.78 0.00 0.00 1.98
2754 3644 3.813724 TCATCTGGACCGTCGAACTATAG 59.186 47.826 0.00 0.00 0.00 1.31
2755 3645 3.812262 TCATCTGGACCGTCGAACTATA 58.188 45.455 0.00 0.00 0.00 1.31
2756 3646 2.651455 TCATCTGGACCGTCGAACTAT 58.349 47.619 0.00 0.00 0.00 2.12
2757 3647 2.118313 TCATCTGGACCGTCGAACTA 57.882 50.000 0.00 0.00 0.00 2.24
2758 3648 1.475403 ATCATCTGGACCGTCGAACT 58.525 50.000 0.00 0.00 0.00 3.01
2759 3649 2.098607 TGTATCATCTGGACCGTCGAAC 59.901 50.000 0.00 0.00 0.00 3.95
2760 3650 2.371306 TGTATCATCTGGACCGTCGAA 58.629 47.619 0.00 0.00 0.00 3.71
2761 3651 2.047002 TGTATCATCTGGACCGTCGA 57.953 50.000 0.00 0.00 0.00 4.20
2762 3652 2.863401 TTGTATCATCTGGACCGTCG 57.137 50.000 0.00 0.00 0.00 5.12
2763 3653 5.455056 AGTATTGTATCATCTGGACCGTC 57.545 43.478 0.00 0.00 0.00 4.79
2764 3654 6.069331 AGTAGTATTGTATCATCTGGACCGT 58.931 40.000 0.00 0.00 0.00 4.83
2765 3655 6.431543 AGAGTAGTATTGTATCATCTGGACCG 59.568 42.308 0.00 0.00 0.00 4.79
2766 3656 7.768807 AGAGTAGTATTGTATCATCTGGACC 57.231 40.000 0.00 0.00 0.00 4.46
2767 3657 9.727859 TCTAGAGTAGTATTGTATCATCTGGAC 57.272 37.037 0.00 0.00 0.00 4.02
2778 3668 9.406113 ACTACCGAAAATCTAGAGTAGTATTGT 57.594 33.333 15.07 3.04 38.81 2.71
2797 3687 8.143835 GCCCTTGTTTAGTTAATATACTACCGA 58.856 37.037 0.00 0.00 30.62 4.69
2798 3688 7.927629 TGCCCTTGTTTAGTTAATATACTACCG 59.072 37.037 0.00 0.00 30.62 4.02
2799 3689 9.788889 ATGCCCTTGTTTAGTTAATATACTACC 57.211 33.333 0.00 0.00 30.62 3.18
2805 3695 8.264347 CCCAAAATGCCCTTGTTTAGTTAATAT 58.736 33.333 0.00 0.00 0.00 1.28
2806 3696 7.235812 ACCCAAAATGCCCTTGTTTAGTTAATA 59.764 33.333 0.00 0.00 0.00 0.98
2807 3697 6.043822 ACCCAAAATGCCCTTGTTTAGTTAAT 59.956 34.615 0.00 0.00 0.00 1.40
2808 3698 5.367060 ACCCAAAATGCCCTTGTTTAGTTAA 59.633 36.000 0.00 0.00 0.00 2.01
2809 3699 4.902448 ACCCAAAATGCCCTTGTTTAGTTA 59.098 37.500 0.00 0.00 0.00 2.24
2810 3700 3.714280 ACCCAAAATGCCCTTGTTTAGTT 59.286 39.130 0.00 0.00 0.00 2.24
2811 3701 3.313791 ACCCAAAATGCCCTTGTTTAGT 58.686 40.909 0.00 0.00 0.00 2.24
2812 3702 4.526650 ACTACCCAAAATGCCCTTGTTTAG 59.473 41.667 0.00 0.00 0.00 1.85
2813 3703 4.484912 ACTACCCAAAATGCCCTTGTTTA 58.515 39.130 0.00 0.00 0.00 2.01
2814 3704 3.313791 ACTACCCAAAATGCCCTTGTTT 58.686 40.909 0.00 0.00 0.00 2.83
2815 3705 2.970987 ACTACCCAAAATGCCCTTGTT 58.029 42.857 0.00 0.00 0.00 2.83
2816 3706 2.694616 ACTACCCAAAATGCCCTTGT 57.305 45.000 0.00 0.00 0.00 3.16
2817 3707 3.192633 GTGTACTACCCAAAATGCCCTTG 59.807 47.826 0.00 0.00 0.00 3.61
2818 3708 3.181427 TGTGTACTACCCAAAATGCCCTT 60.181 43.478 0.00 0.00 0.00 3.95
2819 3709 2.377193 TGTGTACTACCCAAAATGCCCT 59.623 45.455 0.00 0.00 0.00 5.19
2820 3710 2.797786 TGTGTACTACCCAAAATGCCC 58.202 47.619 0.00 0.00 0.00 5.36
2821 3711 5.400066 AAATGTGTACTACCCAAAATGCC 57.600 39.130 0.00 0.00 0.00 4.40
2822 3712 7.147983 TGGATAAATGTGTACTACCCAAAATGC 60.148 37.037 0.00 0.00 0.00 3.56
2823 3713 8.287439 TGGATAAATGTGTACTACCCAAAATG 57.713 34.615 0.00 0.00 0.00 2.32
2824 3714 9.131791 GATGGATAAATGTGTACTACCCAAAAT 57.868 33.333 0.00 0.00 0.00 1.82
2825 3715 8.333235 AGATGGATAAATGTGTACTACCCAAAA 58.667 33.333 0.00 0.00 0.00 2.44
2826 3716 7.867921 AGATGGATAAATGTGTACTACCCAAA 58.132 34.615 0.00 0.00 0.00 3.28
2827 3717 7.446106 AGATGGATAAATGTGTACTACCCAA 57.554 36.000 0.00 0.00 0.00 4.12
2828 3718 6.239204 CGAGATGGATAAATGTGTACTACCCA 60.239 42.308 0.00 0.00 0.00 4.51
2829 3719 6.157211 CGAGATGGATAAATGTGTACTACCC 58.843 44.000 0.00 0.00 0.00 3.69
2830 3720 5.634020 GCGAGATGGATAAATGTGTACTACC 59.366 44.000 0.00 0.00 0.00 3.18
2831 3721 6.213677 TGCGAGATGGATAAATGTGTACTAC 58.786 40.000 0.00 0.00 0.00 2.73
2832 3722 6.399639 TGCGAGATGGATAAATGTGTACTA 57.600 37.500 0.00 0.00 0.00 1.82
2833 3723 5.276461 TGCGAGATGGATAAATGTGTACT 57.724 39.130 0.00 0.00 0.00 2.73
2834 3724 4.449068 CCTGCGAGATGGATAAATGTGTAC 59.551 45.833 0.00 0.00 0.00 2.90
2835 3725 4.631131 CCTGCGAGATGGATAAATGTGTA 58.369 43.478 0.00 0.00 0.00 2.90
2836 3726 3.470709 CCTGCGAGATGGATAAATGTGT 58.529 45.455 0.00 0.00 0.00 3.72
2837 3727 2.225019 GCCTGCGAGATGGATAAATGTG 59.775 50.000 0.00 0.00 0.00 3.21
2838 3728 2.158769 TGCCTGCGAGATGGATAAATGT 60.159 45.455 0.00 0.00 0.00 2.71
2839 3729 2.225019 GTGCCTGCGAGATGGATAAATG 59.775 50.000 0.00 0.00 0.00 2.32
2840 3730 2.498167 GTGCCTGCGAGATGGATAAAT 58.502 47.619 0.00 0.00 0.00 1.40
2841 3731 1.475034 GGTGCCTGCGAGATGGATAAA 60.475 52.381 0.00 0.00 0.00 1.40
2842 3732 0.106708 GGTGCCTGCGAGATGGATAA 59.893 55.000 0.00 0.00 0.00 1.75
2843 3733 0.760567 AGGTGCCTGCGAGATGGATA 60.761 55.000 0.00 0.00 0.00 2.59
2844 3734 1.630126 AAGGTGCCTGCGAGATGGAT 61.630 55.000 0.00 0.00 0.00 3.41
2845 3735 2.244117 GAAGGTGCCTGCGAGATGGA 62.244 60.000 0.00 0.00 0.00 3.41
2846 3736 1.817099 GAAGGTGCCTGCGAGATGG 60.817 63.158 0.00 0.00 0.00 3.51
2847 3737 1.817099 GGAAGGTGCCTGCGAGATG 60.817 63.158 0.00 0.00 0.00 2.90
2848 3738 1.992277 AGGAAGGTGCCTGCGAGAT 60.992 57.895 0.00 0.00 36.76 2.75
2849 3739 2.604686 AGGAAGGTGCCTGCGAGA 60.605 61.111 0.00 0.00 36.76 4.04
2855 3745 0.400594 GGTGTTACAGGAAGGTGCCT 59.599 55.000 0.00 0.00 39.37 4.75
2856 3746 0.608308 GGGTGTTACAGGAAGGTGCC 60.608 60.000 0.00 0.00 0.00 5.01
2857 3747 0.608308 GGGGTGTTACAGGAAGGTGC 60.608 60.000 0.00 0.00 0.00 5.01
2858 3748 0.037734 GGGGGTGTTACAGGAAGGTG 59.962 60.000 0.00 0.00 0.00 4.00
2859 3749 0.402272 TGGGGGTGTTACAGGAAGGT 60.402 55.000 0.00 0.00 0.00 3.50
2860 3750 0.774908 TTGGGGGTGTTACAGGAAGG 59.225 55.000 0.00 0.00 0.00 3.46
2861 3751 2.225017 ACATTGGGGGTGTTACAGGAAG 60.225 50.000 0.00 0.00 0.00 3.46
2862 3752 1.783979 ACATTGGGGGTGTTACAGGAA 59.216 47.619 0.00 0.00 0.00 3.36
2863 3753 1.353022 GACATTGGGGGTGTTACAGGA 59.647 52.381 0.00 0.00 0.00 3.86
2864 3754 1.074727 TGACATTGGGGGTGTTACAGG 59.925 52.381 0.00 0.00 0.00 4.00
2865 3755 2.577606 TGACATTGGGGGTGTTACAG 57.422 50.000 0.00 0.00 0.00 2.74
2879 3769 2.833943 TGAGGTCACTGTAGCATGACAT 59.166 45.455 0.00 0.00 45.83 3.06
2914 3804 5.245531 TGGCTAAGTTAAACCTGATGACAG 58.754 41.667 3.87 0.00 43.12 3.51
3037 3927 4.236527 GACAATGGTCAGGGGAACTTAT 57.763 45.455 0.00 0.00 43.73 1.73
3077 3967 6.751157 TGTAGGAGTTCGATTGTGAGTAAAA 58.249 36.000 0.00 0.00 0.00 1.52
3167 4057 4.202243 CCAGAAAGTTTGAGGCCAATTGAA 60.202 41.667 5.01 0.00 31.46 2.69
3168 4058 3.321682 CCAGAAAGTTTGAGGCCAATTGA 59.678 43.478 5.01 0.00 31.46 2.57
3187 4077 2.424956 GCAATAACTTGAAGAGGCCCAG 59.575 50.000 0.00 0.00 34.04 4.45
3197 4087 7.013274 GGCATATGAAACTAGGCAATAACTTGA 59.987 37.037 6.97 0.00 34.04 3.02
3207 4097 6.572519 TGAAAATTGGCATATGAAACTAGGC 58.427 36.000 6.97 0.00 0.00 3.93
3220 4110 8.900983 ATTTTAGTTAGCTTTGAAAATTGGCA 57.099 26.923 0.00 0.00 0.00 4.92
3415 4307 4.873129 CCCATGGACGGTCGCTCG 62.873 72.222 15.22 0.00 0.00 5.03
3434 4326 0.179081 GGTCAACACGGGCTAGATCC 60.179 60.000 0.00 0.00 0.00 3.36
3439 4331 1.600107 GGATGGTCAACACGGGCTA 59.400 57.895 0.00 0.00 0.00 3.93
3449 4341 4.077184 GGCACCGACGGATGGTCA 62.077 66.667 23.38 0.00 46.42 4.02
3498 4390 2.055246 AAAGGGGCACTAGGGTTAGT 57.945 50.000 0.00 0.00 40.79 2.24
3514 4406 0.176910 GCGAGGGAGAGAGGGAAAAG 59.823 60.000 0.00 0.00 0.00 2.27
3536 4428 3.319198 TGGTGGAGCGAGGGGAAC 61.319 66.667 0.00 0.00 0.00 3.62
3539 4431 4.394712 GTGTGGTGGAGCGAGGGG 62.395 72.222 0.00 0.00 0.00 4.79
3552 4444 2.505650 TGGGAGAGAGAGAGAGTGTG 57.494 55.000 0.00 0.00 0.00 3.82
3553 4445 2.291540 CCTTGGGAGAGAGAGAGAGTGT 60.292 54.545 0.00 0.00 0.00 3.55
3554 4446 2.291540 ACCTTGGGAGAGAGAGAGAGTG 60.292 54.545 0.00 0.00 0.00 3.51
3557 4449 1.996291 TGACCTTGGGAGAGAGAGAGA 59.004 52.381 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.