Multiple sequence alignment - TraesCS5D01G217800

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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 TraesCS5D01G217800 chr5D 100.000 3001 0 0 3072 6072 326743359 326740359 0.000000e+00 5542.0
1 TraesCS5D01G217800 chr5D 100.000 2459 0 0 1 2459 326746430 326743972 0.000000e+00 4542.0
2 TraesCS5D01G217800 chr5D 92.989 271 14 2 3162 3427 294578116 294578386 2.050000e-104 390.0
3 TraesCS5D01G217800 chr5D 100.000 48 0 0 1 48 267803506 267803459 8.380000e-14 89.8
4 TraesCS5D01G217800 chr5D 100.000 48 0 0 2 49 335936047 335936000 8.380000e-14 89.8
5 TraesCS5D01G217800 chr5B 92.412 1476 51 15 45 1507 379449889 379448462 0.000000e+00 2049.0
6 TraesCS5D01G217800 chr5B 91.517 1061 69 8 3433 4487 379448460 379447415 0.000000e+00 1441.0
7 TraesCS5D01G217800 chr5B 93.348 932 50 9 4485 5406 379447333 379446404 0.000000e+00 1367.0
8 TraesCS5D01G217800 chr5B 89.408 321 19 5 3112 3424 697575140 697574827 2.050000e-104 390.0
9 TraesCS5D01G217800 chr5B 92.683 205 7 4 5870 6072 379446292 379446094 7.700000e-74 289.0
10 TraesCS5D01G217800 chr5A 88.435 1444 119 15 3433 4856 429749019 429750434 0.000000e+00 1698.0
11 TraesCS5D01G217800 chr5A 93.548 961 50 7 1505 2458 569541357 569542312 0.000000e+00 1421.0
12 TraesCS5D01G217800 chr5A 93.191 749 26 6 82 820 429733850 429734583 0.000000e+00 1077.0
13 TraesCS5D01G217800 chr5A 92.088 771 36 10 4859 5609 429750520 429751285 0.000000e+00 1062.0
14 TraesCS5D01G217800 chr5A 92.599 581 27 9 933 1504 429748443 429749016 0.000000e+00 821.0
15 TraesCS5D01G217800 chr5A 93.379 438 16 4 5606 6038 429751540 429751969 2.390000e-178 636.0
16 TraesCS5D01G217800 chr5A 86.792 106 4 1 817 922 429748370 429748465 6.430000e-20 110.0
17 TraesCS5D01G217800 chr5A 95.000 40 0 1 6035 6072 429752134 429752173 1.830000e-05 62.1
18 TraesCS5D01G217800 chrUn 96.747 953 30 1 1507 2459 79925139 79926090 0.000000e+00 1587.0
19 TraesCS5D01G217800 chrUn 95.945 937 32 3 1507 2437 108948174 108949110 0.000000e+00 1515.0
20 TraesCS5D01G217800 chr3D 95.421 961 32 5 1507 2455 526481146 526482106 0.000000e+00 1520.0
21 TraesCS5D01G217800 chr3D 90.909 66 2 3 2 65 67534015 67533952 1.080000e-12 86.1
22 TraesCS5D01G217800 chr6D 94.933 967 34 6 1505 2459 18022264 18023227 0.000000e+00 1500.0
23 TraesCS5D01G217800 chr6D 92.780 277 15 2 3152 3424 18023812 18024087 4.410000e-106 396.0
24 TraesCS5D01G217800 chr6D 100.000 47 0 0 1 47 468637807 468637761 3.010000e-13 87.9
25 TraesCS5D01G217800 chr2D 95.861 918 35 1 1502 2419 54889121 54890035 0.000000e+00 1482.0
26 TraesCS5D01G217800 chr2D 89.489 333 24 4 3096 3424 109401452 109401127 1.580000e-110 411.0
27 TraesCS5D01G217800 chr2D 100.000 48 0 0 1 48 635109753 635109800 8.380000e-14 89.8
28 TraesCS5D01G217800 chr2D 96.296 54 1 1 1 54 486349225 486349173 3.010000e-13 87.9
29 TraesCS5D01G217800 chr2D 98.000 50 1 0 2 51 572049750 572049701 3.010000e-13 87.9
30 TraesCS5D01G217800 chr4D 96.811 878 26 1 1504 2381 145624377 145625252 0.000000e+00 1465.0
31 TraesCS5D01G217800 chr4D 89.888 356 23 6 3074 3424 314522824 314523171 4.320000e-121 446.0
32 TraesCS5D01G217800 chr4D 94.444 54 2 1 2 55 440274722 440274774 1.400000e-11 82.4
33 TraesCS5D01G217800 chr2A 94.692 942 38 3 1505 2437 760760053 760759115 0.000000e+00 1452.0
34 TraesCS5D01G217800 chr6A 93.388 968 48 6 1503 2456 146538776 146537811 0.000000e+00 1419.0
35 TraesCS5D01G217800 chr6A 90.030 331 22 4 3098 3424 9522466 9522143 9.410000e-113 418.0
36 TraesCS5D01G217800 chr7B 81.193 553 87 14 3598 4144 640936532 640935991 4.350000e-116 429.0
37 TraesCS5D01G217800 chr1D 90.060 332 21 6 3098 3424 441580392 441580068 2.620000e-113 420.0
38 TraesCS5D01G217800 chr1D 90.000 60 5 1 2 61 462983777 462983835 6.530000e-10 76.8
39 TraesCS5D01G217800 chr3A 89.790 333 23 6 3097 3424 9515776 9515450 3.390000e-112 416.0
40 TraesCS5D01G217800 chr1A 80.866 554 85 15 3599 4144 74095116 74094576 3.390000e-112 416.0
41 TraesCS5D01G217800 chr4A 80.431 557 86 19 3598 4144 628890440 628889897 2.640000e-108 403.0
42 TraesCS5D01G217800 chr7D 93.141 277 14 2 3152 3424 376528091 376527816 9.480000e-108 401.0
43 TraesCS5D01G217800 chr7D 100.000 48 0 0 1 48 387370854 387370901 8.380000e-14 89.8
44 TraesCS5D01G217800 chr7A 78.843 553 91 18 3598 4144 644529631 644530163 3.480000e-92 350.0
45 TraesCS5D01G217800 chr7A 85.890 163 14 7 3738 3892 211219332 211219171 1.350000e-36 165.0
46 TraesCS5D01G217800 chr7A 84.431 167 18 6 3738 3896 261401363 261401529 2.270000e-34 158.0
47 TraesCS5D01G217800 chr1B 83.939 330 45 5 3598 3922 4553351 4553025 5.910000e-80 309.0
48 TraesCS5D01G217800 chr4B 81.944 288 33 10 3741 4011 606307720 606307435 6.120000e-55 226.0
49 TraesCS5D01G217800 chr2B 89.394 66 5 2 1 65 383334764 383334828 1.400000e-11 82.4


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 TraesCS5D01G217800 chr5D 326740359 326746430 6071 True 5042.000000 5542 100.000000 1 6072 2 chr5D.!!$R3 6071
1 TraesCS5D01G217800 chr5B 379446094 379449889 3795 True 1286.500000 2049 92.490000 45 6072 4 chr5B.!!$R2 6027
2 TraesCS5D01G217800 chr5A 569541357 569542312 955 False 1421.000000 1421 93.548000 1505 2458 1 chr5A.!!$F2 953
3 TraesCS5D01G217800 chr5A 429733850 429734583 733 False 1077.000000 1077 93.191000 82 820 1 chr5A.!!$F1 738
4 TraesCS5D01G217800 chr5A 429748370 429752173 3803 False 731.516667 1698 91.382167 817 6072 6 chr5A.!!$F3 5255
5 TraesCS5D01G217800 chrUn 79925139 79926090 951 False 1587.000000 1587 96.747000 1507 2459 1 chrUn.!!$F1 952
6 TraesCS5D01G217800 chrUn 108948174 108949110 936 False 1515.000000 1515 95.945000 1507 2437 1 chrUn.!!$F2 930
7 TraesCS5D01G217800 chr3D 526481146 526482106 960 False 1520.000000 1520 95.421000 1507 2455 1 chr3D.!!$F1 948
8 TraesCS5D01G217800 chr6D 18022264 18024087 1823 False 948.000000 1500 93.856500 1505 3424 2 chr6D.!!$F1 1919
9 TraesCS5D01G217800 chr2D 54889121 54890035 914 False 1482.000000 1482 95.861000 1502 2419 1 chr2D.!!$F1 917
10 TraesCS5D01G217800 chr4D 145624377 145625252 875 False 1465.000000 1465 96.811000 1504 2381 1 chr4D.!!$F1 877
11 TraesCS5D01G217800 chr2A 760759115 760760053 938 True 1452.000000 1452 94.692000 1505 2437 1 chr2A.!!$R1 932
12 TraesCS5D01G217800 chr6A 146537811 146538776 965 True 1419.000000 1419 93.388000 1503 2456 1 chr6A.!!$R2 953
13 TraesCS5D01G217800 chr7B 640935991 640936532 541 True 429.000000 429 81.193000 3598 4144 1 chr7B.!!$R1 546
14 TraesCS5D01G217800 chr1A 74094576 74095116 540 True 416.000000 416 80.866000 3599 4144 1 chr1A.!!$R1 545
15 TraesCS5D01G217800 chr4A 628889897 628890440 543 True 403.000000 403 80.431000 3598 4144 1 chr4A.!!$R1 546
16 TraesCS5D01G217800 chr7A 644529631 644530163 532 False 350.000000 350 78.843000 3598 4144 1 chr7A.!!$F2 546

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
28 29 0.038526 AACGCGGACTACCAACTGAG 60.039 55.000 12.47 0.0 35.59 3.35 F
30 31 0.456312 CGCGGACTACCAACTGAGAC 60.456 60.000 0.00 0.0 35.59 3.36 F
31 32 0.601558 GCGGACTACCAACTGAGACA 59.398 55.000 0.00 0.0 35.59 3.41 F
1383 1396 0.247458 GCAAAGCTCGCATCGTTCTC 60.247 55.000 3.31 0.0 0.00 2.87 F
1865 1893 2.041405 CACCCCTCCTCCTCCTCC 60.041 72.222 0.00 0.0 0.00 4.30 F
3368 3433 0.535335 TATGGACCGTCTGTTGGAGC 59.465 55.000 0.00 0.0 0.00 4.70 F
3569 3639 0.461548 CACCTGCTAAGCATCTCCGA 59.538 55.000 0.00 0.0 38.13 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1098 1108 2.024918 GGCGTTACCGACCGAGATA 58.975 57.895 0.00 0.00 35.50 1.98 R
1383 1396 2.228822 GGGACAACAACACAAGCTATGG 59.771 50.000 3.17 0.00 0.00 2.74 R
1865 1893 2.492090 CGGGCAGACTTCTCGGAG 59.508 66.667 0.00 0.00 0.00 4.63 R
3137 3202 0.250338 CCCGCCTAAGATTAGCACCC 60.250 60.000 0.00 0.00 0.00 4.61 R
3428 3497 0.320683 GGTGAAACAGCCATTTGCCC 60.321 55.000 0.00 0.00 42.71 5.36 R
4897 5211 1.340405 CCCAACCTCTCCAATCCACAG 60.340 57.143 0.00 0.00 0.00 3.66 R
5377 5709 1.135344 TGTACATCGTCAAATCGGCGA 60.135 47.619 13.87 13.87 39.02 5.54 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
24 25 3.866356 GGAACGCGGACTACCAAC 58.134 61.111 12.47 0.00 35.59 3.77
25 26 1.291272 GGAACGCGGACTACCAACT 59.709 57.895 12.47 0.00 35.59 3.16
26 27 1.012486 GGAACGCGGACTACCAACTG 61.012 60.000 12.47 0.00 35.59 3.16
27 28 0.038892 GAACGCGGACTACCAACTGA 60.039 55.000 12.47 0.00 35.59 3.41
28 29 0.038526 AACGCGGACTACCAACTGAG 60.039 55.000 12.47 0.00 35.59 3.35
29 30 0.892358 ACGCGGACTACCAACTGAGA 60.892 55.000 12.47 0.00 35.59 3.27
30 31 0.456312 CGCGGACTACCAACTGAGAC 60.456 60.000 0.00 0.00 35.59 3.36
31 32 0.601558 GCGGACTACCAACTGAGACA 59.398 55.000 0.00 0.00 35.59 3.41
32 33 1.204941 GCGGACTACCAACTGAGACAT 59.795 52.381 0.00 0.00 35.59 3.06
33 34 2.353803 GCGGACTACCAACTGAGACATT 60.354 50.000 0.00 0.00 35.59 2.71
34 35 3.119245 GCGGACTACCAACTGAGACATTA 60.119 47.826 0.00 0.00 35.59 1.90
35 36 4.673441 CGGACTACCAACTGAGACATTAG 58.327 47.826 0.00 0.00 35.59 1.73
36 37 4.440250 CGGACTACCAACTGAGACATTAGG 60.440 50.000 0.00 0.00 35.59 2.69
37 38 4.710375 GGACTACCAACTGAGACATTAGGA 59.290 45.833 0.00 0.00 35.97 2.94
38 39 5.163499 GGACTACCAACTGAGACATTAGGAG 60.163 48.000 0.00 0.00 35.97 3.69
39 40 5.334421 ACTACCAACTGAGACATTAGGAGT 58.666 41.667 0.00 0.00 0.00 3.85
40 41 6.491383 ACTACCAACTGAGACATTAGGAGTA 58.509 40.000 0.00 0.00 0.00 2.59
41 42 5.923733 ACCAACTGAGACATTAGGAGTAG 57.076 43.478 0.00 0.00 0.00 2.57
42 43 5.580998 ACCAACTGAGACATTAGGAGTAGA 58.419 41.667 0.00 0.00 0.00 2.59
43 44 5.654650 ACCAACTGAGACATTAGGAGTAGAG 59.345 44.000 0.00 0.00 0.00 2.43
52 53 9.391006 GAGACATTAGGAGTAGAGATATAGGTG 57.609 40.741 0.00 0.00 0.00 4.00
58 59 5.074115 GGAGTAGAGATATAGGTGTGCACT 58.926 45.833 19.41 0.00 0.00 4.40
437 446 4.619863 CGAGATTACTGAAACCGGAAAGGA 60.620 45.833 9.46 0.00 45.00 3.36
453 462 1.079750 GGAGCCGTGTCTTGAGACC 60.080 63.158 8.56 0.19 44.15 3.85
454 463 1.444553 GAGCCGTGTCTTGAGACCG 60.445 63.158 8.56 10.69 44.15 4.79
771 780 3.151022 CCTCGGAGCCCCTCTGTC 61.151 72.222 0.00 0.00 38.01 3.51
851 861 2.226912 CTCGAAAAATAACGTGGCCCAA 59.773 45.455 0.00 0.00 0.00 4.12
852 862 2.030981 TCGAAAAATAACGTGGCCCAAC 60.031 45.455 0.00 0.00 0.00 3.77
853 863 2.030628 CGAAAAATAACGTGGCCCAACT 60.031 45.455 0.00 0.00 0.00 3.16
854 864 3.313690 GAAAAATAACGTGGCCCAACTG 58.686 45.455 0.00 0.00 0.00 3.16
855 865 1.989706 AAATAACGTGGCCCAACTGT 58.010 45.000 0.00 0.00 0.00 3.55
856 866 2.863132 AATAACGTGGCCCAACTGTA 57.137 45.000 0.00 0.00 0.00 2.74
857 867 2.863132 ATAACGTGGCCCAACTGTAA 57.137 45.000 0.00 0.00 0.00 2.41
858 868 2.172851 TAACGTGGCCCAACTGTAAG 57.827 50.000 0.00 0.00 42.29 2.34
906 916 2.124695 GGGTCATCCAAGACGGGC 60.125 66.667 0.00 0.00 39.42 6.13
930 940 4.614475 AGAGACAGAGAGAGAGAGAGAGA 58.386 47.826 0.00 0.00 0.00 3.10
932 942 4.614475 AGACAGAGAGAGAGAGAGAGAGA 58.386 47.826 0.00 0.00 0.00 3.10
933 943 4.648762 AGACAGAGAGAGAGAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
934 944 4.614475 ACAGAGAGAGAGAGAGAGAGAGA 58.386 47.826 0.00 0.00 0.00 3.10
935 945 4.648762 ACAGAGAGAGAGAGAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
936 946 4.892345 CAGAGAGAGAGAGAGAGAGAGAGA 59.108 50.000 0.00 0.00 0.00 3.10
937 947 5.009911 CAGAGAGAGAGAGAGAGAGAGAGAG 59.990 52.000 0.00 0.00 0.00 3.20
938 948 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
939 949 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
940 950 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
941 951 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
942 952 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
943 953 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
944 954 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
945 955 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
946 956 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
947 957 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
948 958 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
949 959 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
950 960 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
951 961 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
952 962 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
953 963 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
954 964 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
955 965 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
956 966 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
957 967 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
958 968 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
959 969 4.078922 AGAGAGAGAGAGAGAGAGAGAGGA 60.079 50.000 0.00 0.00 0.00 3.71
1383 1396 0.247458 GCAAAGCTCGCATCGTTCTC 60.247 55.000 3.31 0.00 0.00 2.87
1402 1415 4.065088 TCTCCATAGCTTGTGTTGTTGTC 58.935 43.478 0.00 0.00 0.00 3.18
1449 1466 3.485711 CGATTGTTGGTGATGTTCATCCG 60.486 47.826 9.83 0.60 0.00 4.18
1471 1488 5.065859 CCGCTTTTGGAATCACATACATACA 59.934 40.000 0.00 0.00 0.00 2.29
1483 1500 9.511272 AATCACATACATACATCTTATGTGCAT 57.489 29.630 13.66 7.59 46.79 3.96
1865 1893 2.041405 CACCCCTCCTCCTCCTCC 60.041 72.222 0.00 0.00 0.00 4.30
1882 1916 2.492090 CTCCGAGAAGTCTGCCCG 59.508 66.667 0.00 0.00 0.00 6.13
2058 2093 2.436292 CCTCCTCGTCGGTCTCGT 60.436 66.667 0.00 0.00 37.69 4.18
3088 3153 4.025401 GTGGCGGCGTGGAAACAG 62.025 66.667 9.37 0.00 44.46 3.16
3091 3156 4.389576 GCGGCGTGGAAACAGCAG 62.390 66.667 9.37 0.00 44.46 4.24
3092 3157 4.389576 CGGCGTGGAAACAGCAGC 62.390 66.667 0.00 0.00 44.46 5.25
3093 3158 4.389576 GGCGTGGAAACAGCAGCG 62.390 66.667 0.00 0.00 44.46 5.18
3094 3159 4.389576 GCGTGGAAACAGCAGCGG 62.390 66.667 0.00 0.00 44.46 5.52
3095 3160 3.726517 CGTGGAAACAGCAGCGGG 61.727 66.667 0.00 0.00 44.46 6.13
3096 3161 3.365265 GTGGAAACAGCAGCGGGG 61.365 66.667 0.00 0.00 44.46 5.73
3097 3162 4.659172 TGGAAACAGCAGCGGGGG 62.659 66.667 0.00 0.00 35.01 5.40
3121 3186 2.281345 CGGGGCAGGATCTGATGC 60.281 66.667 0.29 0.29 41.80 3.91
3122 3187 2.281345 GGGGCAGGATCTGATGCG 60.281 66.667 3.41 0.74 43.49 4.73
3124 3189 2.281345 GGCAGGATCTGATGCGGG 60.281 66.667 10.82 5.65 43.49 6.13
3125 3190 2.976903 GCAGGATCTGATGCGGGC 60.977 66.667 10.82 11.19 32.44 6.13
3148 3213 4.547367 GCGGCGGGGTGCTAATCT 62.547 66.667 9.78 0.00 45.43 2.40
3149 3214 2.189521 CGGCGGGGTGCTAATCTT 59.810 61.111 0.00 0.00 45.43 2.40
3150 3215 1.444250 CGGCGGGGTGCTAATCTTA 59.556 57.895 0.00 0.00 45.43 2.10
3330 3395 2.292794 TTACATCACGAGGAGGCCGC 62.293 60.000 0.00 0.00 0.00 6.53
3365 3430 2.691409 ACATATGGACCGTCTGTTGG 57.309 50.000 7.80 0.00 0.00 3.77
3368 3433 0.535335 TATGGACCGTCTGTTGGAGC 59.465 55.000 0.00 0.00 0.00 4.70
3401 3466 4.652822 ACCTCAGATGGTCCAAAAGTTAC 58.347 43.478 0.00 0.00 34.86 2.50
3419 3488 9.758651 AAAAGTTACTTTTACATTTGGACCATC 57.241 29.630 19.94 0.00 41.17 3.51
3429 3498 8.746052 TTACATTTGGACCATCTATTAAGTGG 57.254 34.615 0.00 0.00 38.96 4.00
3430 3499 6.129179 ACATTTGGACCATCTATTAAGTGGG 58.871 40.000 0.00 0.00 37.33 4.61
3431 3500 3.857157 TGGACCATCTATTAAGTGGGC 57.143 47.619 0.00 0.00 40.45 5.36
3457 3526 3.630312 TGGCTGTTTCACCAAGTTCTTAC 59.370 43.478 0.00 0.00 31.46 2.34
3499 3568 9.491675 TCTCTTGTGGACGTTTATTTATGTTTA 57.508 29.630 0.00 0.00 0.00 2.01
3530 3600 8.893219 TTGTGATTTCTGTAGATAGCCTTATG 57.107 34.615 0.00 0.00 0.00 1.90
3569 3639 0.461548 CACCTGCTAAGCATCTCCGA 59.538 55.000 0.00 0.00 38.13 4.55
3571 3641 1.035923 CCTGCTAAGCATCTCCGAGA 58.964 55.000 0.00 0.00 38.13 4.04
3593 3663 6.100668 AGATGATGATGATGATGATGACGAC 58.899 40.000 0.00 0.00 0.00 4.34
3594 3664 4.232221 TGATGATGATGATGATGACGACG 58.768 43.478 0.00 0.00 0.00 5.12
3595 3665 3.988379 TGATGATGATGATGACGACGA 57.012 42.857 0.00 0.00 0.00 4.20
3596 3666 3.632189 TGATGATGATGATGACGACGAC 58.368 45.455 0.00 0.00 0.00 4.34
3608 3678 0.727970 ACGACGACGAGGATGAAGAG 59.272 55.000 15.32 0.00 42.66 2.85
3668 3738 6.795144 ATTGTATTTTCAATCCATGCTCCA 57.205 33.333 0.00 0.00 33.43 3.86
3672 3742 7.888424 TGTATTTTCAATCCATGCTCCATATG 58.112 34.615 0.00 0.00 0.00 1.78
3680 3750 5.628797 TCCATGCTCCATATGACAGTTAA 57.371 39.130 3.65 0.00 0.00 2.01
3698 3770 6.012858 ACAGTTAATGGTCCATCCTGTAGAAA 60.013 38.462 21.48 1.48 37.07 2.52
3722 3797 9.665719 AAATTCAAAATACCTCAAACAACAACT 57.334 25.926 0.00 0.00 0.00 3.16
3733 3810 4.157656 TCAAACAACAACTTGGTGGAAGAG 59.842 41.667 11.54 0.00 39.97 2.85
3809 3887 7.266922 TGACACACCCTTATTTTCTGTAAAC 57.733 36.000 0.00 0.00 0.00 2.01
3814 3892 6.264518 ACACCCTTATTTTCTGTAAACTGGTG 59.735 38.462 0.00 0.00 38.22 4.17
3833 3911 2.035704 GTGGTGCAAATGACCAATGTGA 59.964 45.455 0.00 0.00 45.17 3.58
3835 3913 3.056678 TGGTGCAAATGACCAATGTGATC 60.057 43.478 0.00 0.00 40.65 2.92
3838 3916 3.193903 TGCAAATGACCAATGTGATCTGG 59.806 43.478 0.00 0.00 38.77 3.86
3841 3919 5.735354 GCAAATGACCAATGTGATCTGGATC 60.735 44.000 5.76 3.83 36.49 3.36
3846 3924 2.216046 CAATGTGATCTGGATCCCACG 58.784 52.381 9.90 0.00 37.02 4.94
3876 3954 7.572724 GCAGATATCTTGTTGATGGCACTATTC 60.573 40.741 1.33 0.00 36.65 1.75
3978 4056 7.873505 GGACCTTTATATGTAAGTAGCTCCTTG 59.126 40.741 1.10 0.00 0.00 3.61
4034 4119 4.701663 CCGTGCTCTTCATGGTGT 57.298 55.556 0.00 0.00 45.01 4.16
4072 4196 5.163581 GCATTGTCAAAACATATCTGGAGCT 60.164 40.000 0.00 0.00 34.73 4.09
4131 4267 4.957954 AGACACGGGAATAATACCTGTACA 59.042 41.667 0.00 0.00 44.09 2.90
4145 4281 3.320826 ACCTGTACATTGCTTGGAAAACC 59.679 43.478 0.00 0.00 0.00 3.27
4152 4288 2.452600 TGCTTGGAAAACCAGAACCT 57.547 45.000 0.00 0.00 0.00 3.50
4201 4337 6.605594 TGGTTTTCAATTCTATGTATGGTCCC 59.394 38.462 0.00 0.00 0.00 4.46
4220 4356 2.874701 CCCTTAATTCATGACTCAGCCG 59.125 50.000 0.00 0.00 0.00 5.52
4246 4382 6.797454 AGAAGTCGAGTACATGTAATCCTTC 58.203 40.000 27.21 27.21 33.14 3.46
4294 4430 2.104792 ACTCTGTGTGTAGCAATGGTGT 59.895 45.455 0.00 0.00 0.00 4.16
4306 4442 3.317993 AGCAATGGTGTTACAGTTTCCAC 59.682 43.478 0.00 0.00 0.00 4.02
4323 4459 7.867403 CAGTTTCCACAGTAATTAGCAATGTTT 59.133 33.333 0.00 0.00 0.00 2.83
4350 4486 9.860898 GATTTGGTGCTAGATTTCAGTTTATTT 57.139 29.630 0.00 0.00 0.00 1.40
4418 4554 9.965902 ACAGGTTTCTTGATCATACTTCTTAAT 57.034 29.630 0.00 0.00 0.00 1.40
4480 4618 0.807496 GCCCTTCAGTCTGATGTTGC 59.193 55.000 2.68 7.42 0.00 4.17
4506 4728 7.332557 TGTGTAGTTTAGAGTGAAAAGTTGGA 58.667 34.615 0.00 0.00 0.00 3.53
4547 4774 2.315925 AGCGACATAATGGTGGTCTG 57.684 50.000 0.00 0.00 0.00 3.51
4553 4780 2.224992 ACATAATGGTGGTCTGTGCCAA 60.225 45.455 0.00 0.00 40.68 4.52
4629 4857 5.827797 TCACTTGTTGGATAAAAGTTCTGCT 59.172 36.000 0.00 0.00 31.88 4.24
4630 4858 6.995686 TCACTTGTTGGATAAAAGTTCTGCTA 59.004 34.615 0.00 0.00 31.88 3.49
4636 4864 7.387948 TGTTGGATAAAAGTTCTGCTAGAGTTC 59.612 37.037 0.00 0.00 0.00 3.01
4660 4888 7.801104 TCCATTACATAGGCTGTGAAGAATAA 58.199 34.615 18.69 6.04 38.92 1.40
4687 4915 6.408858 AATGCTTCGTCAACATTAGTAGTG 57.591 37.500 0.00 0.00 32.42 2.74
4719 4950 4.884164 GCTGCCTGGACTATTAAAATCTGT 59.116 41.667 0.00 0.00 0.00 3.41
4725 4956 7.201741 GCCTGGACTATTAAAATCTGTTCCTTC 60.202 40.741 0.00 0.00 0.00 3.46
4908 5222 5.875224 TGATAAACAGAACTGTGGATTGGA 58.125 37.500 8.25 0.00 44.13 3.53
4909 5223 5.939883 TGATAAACAGAACTGTGGATTGGAG 59.060 40.000 8.25 0.00 44.13 3.86
4911 5225 3.692257 ACAGAACTGTGGATTGGAGAG 57.308 47.619 6.67 0.00 43.11 3.20
5074 5392 2.159382 CGGGCAGGTCAATTGTAAGTT 58.841 47.619 5.13 0.00 0.00 2.66
5229 5554 2.051423 GCAACTGCTTTAGCCGTTTTC 58.949 47.619 8.54 1.85 44.15 2.29
5233 5558 0.663688 TGCTTTAGCCGTTTTCGCAA 59.336 45.000 0.00 0.00 42.58 4.85
5338 5669 2.495669 TGATGTGCGTCAGATCTACCAA 59.504 45.455 14.63 0.00 35.54 3.67
5473 5805 7.270779 TGAGAGCTACATTCGTACTACTAAGA 58.729 38.462 0.00 0.00 0.00 2.10
5479 5811 6.770746 ACATTCGTACTACTAAGACCATGT 57.229 37.500 0.00 0.00 0.00 3.21
5481 5813 7.928103 ACATTCGTACTACTAAGACCATGTAG 58.072 38.462 0.00 0.00 39.43 2.74
5482 5814 7.555554 ACATTCGTACTACTAAGACCATGTAGT 59.444 37.037 9.47 9.47 45.72 2.73
5489 5821 8.591114 ACTACTAAGACCATGTAGTACAATGT 57.409 34.615 7.16 7.39 43.20 2.71
5490 5822 8.467598 ACTACTAAGACCATGTAGTACAATGTG 58.532 37.037 7.16 1.17 43.20 3.21
5491 5823 6.640518 ACTAAGACCATGTAGTACAATGTGG 58.359 40.000 16.57 16.57 33.24 4.17
5589 5924 3.609853 CGAACATTCCATTCCTTCCTGA 58.390 45.455 0.00 0.00 0.00 3.86
5594 5929 6.139679 ACATTCCATTCCTTCCTGAGTTAA 57.860 37.500 0.00 0.00 0.00 2.01
5604 5939 5.245526 TCCTTCCTGAGTTAACACTTACTCC 59.754 44.000 8.61 0.00 40.00 3.85
5613 6206 7.038302 TGAGTTAACACTTACTCCAAGATGGAT 60.038 37.037 8.61 0.00 38.65 3.41
5644 6237 7.501225 AGTTAGCAGCTGGTTAAAAACTTCTTA 59.499 33.333 25.47 0.00 0.00 2.10
5668 6261 7.750229 AATGATGGATACGAATTTAGCATGT 57.250 32.000 0.00 0.00 42.51 3.21
5669 6262 8.846943 AATGATGGATACGAATTTAGCATGTA 57.153 30.769 0.00 0.00 42.51 2.29
5730 6323 2.662866 CGTCCTCTAATACAGTCCCCA 58.337 52.381 0.00 0.00 0.00 4.96
5782 6375 1.279496 TAGTGCTTCAGCCATCAGGT 58.721 50.000 0.00 0.00 41.18 4.00
5837 6435 6.928348 ATGAAACTATGGACGGATACCATA 57.072 37.500 0.00 0.00 44.96 2.74
5840 6438 5.934402 AACTATGGACGGATACCATATCC 57.066 43.478 0.00 4.98 45.47 2.59
6018 6616 2.036256 AGCTCCACCCATGGCAAC 59.964 61.111 6.09 0.00 46.80 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.090524 GTTGGTAGTCCGCGTTCCG 61.091 63.158 4.92 0.00 36.30 4.30
7 8 1.012486 CAGTTGGTAGTCCGCGTTCC 61.012 60.000 4.92 0.18 36.30 3.62
8 9 0.038892 TCAGTTGGTAGTCCGCGTTC 60.039 55.000 4.92 0.00 36.30 3.95
9 10 0.038526 CTCAGTTGGTAGTCCGCGTT 60.039 55.000 4.92 0.00 36.30 4.84
10 11 0.892358 TCTCAGTTGGTAGTCCGCGT 60.892 55.000 4.92 0.00 36.30 6.01
11 12 0.456312 GTCTCAGTTGGTAGTCCGCG 60.456 60.000 0.00 0.00 36.30 6.46
12 13 0.601558 TGTCTCAGTTGGTAGTCCGC 59.398 55.000 0.00 0.00 36.30 5.54
13 14 3.594603 AATGTCTCAGTTGGTAGTCCG 57.405 47.619 0.00 0.00 36.30 4.79
14 15 4.710375 TCCTAATGTCTCAGTTGGTAGTCC 59.290 45.833 0.00 0.00 0.00 3.85
15 16 5.419471 ACTCCTAATGTCTCAGTTGGTAGTC 59.581 44.000 0.00 0.00 0.00 2.59
16 17 5.334421 ACTCCTAATGTCTCAGTTGGTAGT 58.666 41.667 0.00 0.00 0.00 2.73
17 18 5.923733 ACTCCTAATGTCTCAGTTGGTAG 57.076 43.478 0.00 0.00 0.00 3.18
18 19 6.728411 TCTACTCCTAATGTCTCAGTTGGTA 58.272 40.000 0.00 0.00 0.00 3.25
19 20 5.580998 TCTACTCCTAATGTCTCAGTTGGT 58.419 41.667 0.00 0.00 0.00 3.67
20 21 5.888724 TCTCTACTCCTAATGTCTCAGTTGG 59.111 44.000 0.00 0.00 0.00 3.77
21 22 7.581213 ATCTCTACTCCTAATGTCTCAGTTG 57.419 40.000 0.00 0.00 0.00 3.16
24 25 9.613428 CCTATATCTCTACTCCTAATGTCTCAG 57.387 40.741 0.00 0.00 0.00 3.35
25 26 9.118367 ACCTATATCTCTACTCCTAATGTCTCA 57.882 37.037 0.00 0.00 0.00 3.27
26 27 9.391006 CACCTATATCTCTACTCCTAATGTCTC 57.609 40.741 0.00 0.00 0.00 3.36
27 28 8.896658 ACACCTATATCTCTACTCCTAATGTCT 58.103 37.037 0.00 0.00 0.00 3.41
28 29 8.952278 CACACCTATATCTCTACTCCTAATGTC 58.048 40.741 0.00 0.00 0.00 3.06
29 30 7.394923 GCACACCTATATCTCTACTCCTAATGT 59.605 40.741 0.00 0.00 0.00 2.71
30 31 7.394641 TGCACACCTATATCTCTACTCCTAATG 59.605 40.741 0.00 0.00 0.00 1.90
31 32 7.394923 GTGCACACCTATATCTCTACTCCTAAT 59.605 40.741 13.17 0.00 0.00 1.73
32 33 6.715718 GTGCACACCTATATCTCTACTCCTAA 59.284 42.308 13.17 0.00 0.00 2.69
33 34 6.044520 AGTGCACACCTATATCTCTACTCCTA 59.955 42.308 21.04 0.00 0.00 2.94
34 35 5.074115 GTGCACACCTATATCTCTACTCCT 58.926 45.833 13.17 0.00 0.00 3.69
35 36 5.048364 CAGTGCACACCTATATCTCTACTCC 60.048 48.000 21.04 0.00 0.00 3.85
36 37 5.048364 CCAGTGCACACCTATATCTCTACTC 60.048 48.000 21.04 0.00 0.00 2.59
37 38 4.830046 CCAGTGCACACCTATATCTCTACT 59.170 45.833 21.04 0.00 0.00 2.57
38 39 4.827835 TCCAGTGCACACCTATATCTCTAC 59.172 45.833 21.04 0.00 0.00 2.59
39 40 5.061721 TCCAGTGCACACCTATATCTCTA 57.938 43.478 21.04 0.00 0.00 2.43
40 41 3.916035 TCCAGTGCACACCTATATCTCT 58.084 45.455 21.04 0.00 0.00 3.10
41 42 4.564041 CATCCAGTGCACACCTATATCTC 58.436 47.826 21.04 0.00 0.00 2.75
42 43 4.613925 CATCCAGTGCACACCTATATCT 57.386 45.455 21.04 0.00 0.00 1.98
58 59 0.821517 CGTGGTACCTACAGCATCCA 59.178 55.000 14.36 0.00 0.00 3.41
66 67 2.103537 AAATGTGGCGTGGTACCTAC 57.896 50.000 14.36 8.80 0.00 3.18
70 75 4.957759 AGAATAAAATGTGGCGTGGTAC 57.042 40.909 0.00 0.00 0.00 3.34
437 446 2.651361 CGGTCTCAAGACACGGCT 59.349 61.111 11.99 0.00 46.47 5.52
453 462 0.251698 GAGGTACCCTATCTCCCCCG 60.252 65.000 8.74 0.00 31.76 5.73
454 463 1.168853 AGAGGTACCCTATCTCCCCC 58.831 60.000 8.74 0.00 36.57 5.40
503 512 2.325166 GAGCTCTACTCCGCGTCG 59.675 66.667 6.43 0.00 39.75 5.12
555 564 2.692741 CCCCTTCCTCCTCCCCAC 60.693 72.222 0.00 0.00 0.00 4.61
556 565 2.879490 TCCCCTTCCTCCTCCCCA 60.879 66.667 0.00 0.00 0.00 4.96
661 670 3.785122 AAGCGCGGGTTTCCCAACT 62.785 57.895 8.83 0.00 45.83 3.16
851 861 6.398918 CAAACAGGCTATCTACACTTACAGT 58.601 40.000 0.00 0.00 0.00 3.55
852 862 5.812642 CCAAACAGGCTATCTACACTTACAG 59.187 44.000 0.00 0.00 0.00 2.74
853 863 5.338056 CCCAAACAGGCTATCTACACTTACA 60.338 44.000 0.00 0.00 35.39 2.41
854 864 5.116882 CCCAAACAGGCTATCTACACTTAC 58.883 45.833 0.00 0.00 35.39 2.34
855 865 5.353394 CCCAAACAGGCTATCTACACTTA 57.647 43.478 0.00 0.00 35.39 2.24
856 866 4.222124 CCCAAACAGGCTATCTACACTT 57.778 45.455 0.00 0.00 35.39 3.16
857 867 3.914426 CCCAAACAGGCTATCTACACT 57.086 47.619 0.00 0.00 35.39 3.55
892 902 0.250234 CTCTTGCCCGTCTTGGATGA 59.750 55.000 0.00 0.00 42.00 2.92
906 916 5.089970 TCTCTCTCTCTCTCTGTCTCTTG 57.910 47.826 0.00 0.00 0.00 3.02
930 940 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
932 942 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
933 943 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
934 944 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
935 945 4.280677 CCTCTCTCTCTCTCTCTCTCTCTC 59.719 54.167 0.00 0.00 0.00 3.20
936 946 4.078922 TCCTCTCTCTCTCTCTCTCTCTCT 60.079 50.000 0.00 0.00 0.00 3.10
937 947 4.219115 TCCTCTCTCTCTCTCTCTCTCTC 58.781 52.174 0.00 0.00 0.00 3.20
938 948 4.271807 TCCTCTCTCTCTCTCTCTCTCT 57.728 50.000 0.00 0.00 0.00 3.10
939 949 5.359194 TTTCCTCTCTCTCTCTCTCTCTC 57.641 47.826 0.00 0.00 0.00 3.20
940 950 5.779241 TTTTCCTCTCTCTCTCTCTCTCT 57.221 43.478 0.00 0.00 0.00 3.10
1098 1108 2.024918 GGCGTTACCGACCGAGATA 58.975 57.895 0.00 0.00 35.50 1.98
1133 1143 3.583383 CGGAGCAAGGCAAGAAGG 58.417 61.111 0.00 0.00 0.00 3.46
1383 1396 2.228822 GGGACAACAACACAAGCTATGG 59.771 50.000 3.17 0.00 0.00 2.74
1402 1415 7.217906 GTGGAAAGTATGAAATAGTCCTAGGG 58.782 42.308 9.46 0.00 29.22 3.53
1449 1466 7.934457 AGATGTATGTATGTGATTCCAAAAGC 58.066 34.615 0.00 0.00 0.00 3.51
1471 1488 6.795144 TGGGAAATTTCATGCACATAAGAT 57.205 33.333 19.49 0.00 0.00 2.40
1865 1893 2.492090 CGGGCAGACTTCTCGGAG 59.508 66.667 0.00 0.00 0.00 4.63
2058 2093 2.028484 GGTTGTCGTCAGTGCCGA 59.972 61.111 0.00 0.00 0.00 5.54
2303 2341 1.527370 GCAGAAGCCCTCCGGTAAT 59.473 57.895 0.00 0.00 33.58 1.89
3071 3136 4.025401 CTGTTTCCACGCCGCCAC 62.025 66.667 0.00 0.00 0.00 5.01
3074 3139 4.389576 CTGCTGTTTCCACGCCGC 62.390 66.667 0.00 0.00 0.00 6.53
3075 3140 4.389576 GCTGCTGTTTCCACGCCG 62.390 66.667 0.00 0.00 0.00 6.46
3076 3141 4.389576 CGCTGCTGTTTCCACGCC 62.390 66.667 0.00 0.00 0.00 5.68
3077 3142 4.389576 CCGCTGCTGTTTCCACGC 62.390 66.667 0.00 0.00 0.00 5.34
3078 3143 3.726517 CCCGCTGCTGTTTCCACG 61.727 66.667 0.00 0.00 0.00 4.94
3079 3144 3.365265 CCCCGCTGCTGTTTCCAC 61.365 66.667 0.00 0.00 0.00 4.02
3080 3145 4.659172 CCCCCGCTGCTGTTTCCA 62.659 66.667 0.00 0.00 0.00 3.53
3102 3167 3.564218 ATCAGATCCTGCCCCGCC 61.564 66.667 0.00 0.00 0.00 6.13
3103 3168 2.281345 CATCAGATCCTGCCCCGC 60.281 66.667 0.00 0.00 0.00 6.13
3107 3172 2.281345 CCCGCATCAGATCCTGCC 60.281 66.667 6.87 0.00 34.89 4.85
3109 3174 2.664185 CGCCCGCATCAGATCCTG 60.664 66.667 0.00 0.00 0.00 3.86
3131 3196 2.653953 TAAGATTAGCACCCCGCCGC 62.654 60.000 0.00 0.00 44.04 6.53
3132 3197 0.600255 CTAAGATTAGCACCCCGCCG 60.600 60.000 0.00 0.00 44.04 6.46
3135 3200 0.600255 CGCCTAAGATTAGCACCCCG 60.600 60.000 0.00 0.00 0.00 5.73
3137 3202 0.250338 CCCGCCTAAGATTAGCACCC 60.250 60.000 0.00 0.00 0.00 4.61
3140 3205 0.468226 CACCCCGCCTAAGATTAGCA 59.532 55.000 0.00 0.00 0.00 3.49
3142 3207 1.202651 CCACACCCCGCCTAAGATTAG 60.203 57.143 0.00 0.00 0.00 1.73
3144 3209 0.912487 TCCACACCCCGCCTAAGATT 60.912 55.000 0.00 0.00 0.00 2.40
3145 3210 1.306654 TCCACACCCCGCCTAAGAT 60.307 57.895 0.00 0.00 0.00 2.40
3147 3212 2.584608 CTCCACACCCCGCCTAAG 59.415 66.667 0.00 0.00 0.00 2.18
3148 3213 3.006728 CCTCCACACCCCGCCTAA 61.007 66.667 0.00 0.00 0.00 2.69
3378 3443 4.993705 AACTTTTGGACCATCTGAGGTA 57.006 40.909 0.00 0.00 43.38 3.08
3379 3444 3.884037 AACTTTTGGACCATCTGAGGT 57.116 42.857 0.00 0.00 46.82 3.85
3380 3445 4.911390 AGTAACTTTTGGACCATCTGAGG 58.089 43.478 0.00 0.00 0.00 3.86
3383 3448 7.936584 TGTAAAAGTAACTTTTGGACCATCTG 58.063 34.615 0.00 0.00 42.61 2.90
3387 3452 8.934507 CAAATGTAAAAGTAACTTTTGGACCA 57.065 30.769 0.00 0.00 42.61 4.02
3392 3457 8.934507 TGGTCCAAATGTAAAAGTAACTTTTG 57.065 30.769 0.00 9.90 42.61 2.44
3419 3488 3.701040 ACAGCCATTTGCCCACTTAATAG 59.299 43.478 0.00 0.00 42.71 1.73
3424 3493 1.070601 GAAACAGCCATTTGCCCACTT 59.929 47.619 0.00 0.00 42.71 3.16
3425 3494 0.681175 GAAACAGCCATTTGCCCACT 59.319 50.000 0.00 0.00 42.71 4.00
3426 3495 0.392336 TGAAACAGCCATTTGCCCAC 59.608 50.000 0.00 0.00 42.71 4.61
3427 3496 0.392336 GTGAAACAGCCATTTGCCCA 59.608 50.000 0.00 0.00 42.71 5.36
3428 3497 0.320683 GGTGAAACAGCCATTTGCCC 60.321 55.000 0.00 0.00 42.71 5.36
3429 3498 0.392336 TGGTGAAACAGCCATTTGCC 59.608 50.000 0.00 0.00 42.71 4.52
3430 3499 2.137523 CTTGGTGAAACAGCCATTTGC 58.862 47.619 0.00 0.00 39.98 3.68
3431 3500 3.457610 ACTTGGTGAAACAGCCATTTG 57.542 42.857 0.00 0.00 39.98 2.32
3457 3526 6.183360 CCACAAGAGATATTAAGTGCACCAAG 60.183 42.308 14.63 0.00 0.00 3.61
3460 3529 5.294552 GTCCACAAGAGATATTAAGTGCACC 59.705 44.000 14.63 0.00 0.00 5.01
3499 3568 9.277783 GGCTATCTACAGAAATCACAATGTAAT 57.722 33.333 0.00 0.00 0.00 1.89
3506 3576 7.071196 ACCATAAGGCTATCTACAGAAATCACA 59.929 37.037 0.00 0.00 39.06 3.58
3530 3600 3.853698 TTTAGGTGCCACGGCCACC 62.854 63.158 17.09 17.09 40.24 4.61
3569 3639 6.100668 GTCGTCATCATCATCATCATCATCT 58.899 40.000 0.00 0.00 0.00 2.90
3571 3641 4.863131 CGTCGTCATCATCATCATCATCAT 59.137 41.667 0.00 0.00 0.00 2.45
3593 3663 1.746220 AGTTCCTCTTCATCCTCGTCG 59.254 52.381 0.00 0.00 0.00 5.12
3594 3664 2.159170 CCAGTTCCTCTTCATCCTCGTC 60.159 54.545 0.00 0.00 0.00 4.20
3595 3665 1.827969 CCAGTTCCTCTTCATCCTCGT 59.172 52.381 0.00 0.00 0.00 4.18
3596 3666 1.827969 ACCAGTTCCTCTTCATCCTCG 59.172 52.381 0.00 0.00 0.00 4.63
3608 3678 4.618920 TTGAGAAGACCTTACCAGTTCC 57.381 45.455 0.00 0.00 0.00 3.62
3668 3738 6.101734 ACAGGATGGACCATTAACTGTCATAT 59.898 38.462 23.75 9.95 43.62 1.78
3672 3742 4.222124 ACAGGATGGACCATTAACTGTC 57.778 45.455 23.75 7.33 43.62 3.51
3680 3750 5.715439 TGAATTTCTACAGGATGGACCAT 57.285 39.130 6.71 6.71 43.62 3.55
3698 3770 9.097257 CAAGTTGTTGTTTGAGGTATTTTGAAT 57.903 29.630 0.00 0.00 0.00 2.57
3722 3797 8.884124 ATATGAAAATTCTTCTCTTCCACCAA 57.116 30.769 0.00 0.00 0.00 3.67
3761 3838 8.531982 TCATATACATTACCAGGTAATCTCAGC 58.468 37.037 20.53 0.00 36.70 4.26
3809 3887 1.039068 TTGGTCATTTGCACCACCAG 58.961 50.000 5.61 0.00 43.93 4.00
3814 3892 3.194116 AGATCACATTGGTCATTTGCACC 59.806 43.478 0.00 0.00 27.47 5.01
3833 3911 0.977627 TGCAGACGTGGGATCCAGAT 60.978 55.000 15.23 0.00 32.34 2.90
3835 3913 1.153489 CTGCAGACGTGGGATCCAG 60.153 63.158 15.23 6.83 32.34 3.86
3838 3916 2.560542 AGATATCTGCAGACGTGGGATC 59.439 50.000 20.97 14.05 0.00 3.36
3841 3919 2.159043 ACAAGATATCTGCAGACGTGGG 60.159 50.000 20.97 9.90 0.00 4.61
3846 3924 4.024218 GCCATCAACAAGATATCTGCAGAC 60.024 45.833 20.97 6.64 34.43 3.51
3876 3954 4.763073 TCCATGCTTTCATAGTGACAGAG 58.237 43.478 0.00 0.00 0.00 3.35
3971 4049 2.440409 TGGAGAAGCAAATCAAGGAGC 58.560 47.619 0.00 0.00 0.00 4.70
4002 4080 5.186198 AGAGCACGGAAACTGCTAATAATT 58.814 37.500 0.00 0.00 42.34 1.40
4015 4093 0.396435 ACACCATGAAGAGCACGGAA 59.604 50.000 0.00 0.00 32.36 4.30
4020 4098 1.421268 ACCTCAACACCATGAAGAGCA 59.579 47.619 0.00 0.00 0.00 4.26
4034 4119 5.159273 TGACAATGCTACATGTACCTCAA 57.841 39.130 0.08 0.00 0.00 3.02
4100 4227 7.043565 GGTATTATTCCCGTGTCTTGAACTAA 58.956 38.462 0.00 0.00 0.00 2.24
4113 4240 5.305585 AGCAATGTACAGGTATTATTCCCG 58.694 41.667 0.33 0.00 0.00 5.14
4145 4281 5.941555 AAGATAGTAACTCCCAGGTTCTG 57.058 43.478 0.00 0.00 0.00 3.02
4152 4288 7.093465 CCACTTGAAGTAAGATAGTAACTCCCA 60.093 40.741 0.00 0.00 39.76 4.37
4164 4300 8.519799 AGAATTGAAAACCACTTGAAGTAAGA 57.480 30.769 0.00 0.00 39.76 2.10
4196 4332 3.879892 GCTGAGTCATGAATTAAGGGACC 59.120 47.826 0.00 0.00 0.00 4.46
4201 4337 5.592054 TCTACGGCTGAGTCATGAATTAAG 58.408 41.667 0.00 0.00 0.00 1.85
4220 4356 7.261829 AGGATTACATGTACTCGACTTCTAC 57.738 40.000 14.85 1.81 0.00 2.59
4274 4410 2.771089 ACACCATTGCTACACACAGAG 58.229 47.619 0.00 0.00 0.00 3.35
4294 4430 8.511321 CATTGCTAATTACTGTGGAAACTGTAA 58.489 33.333 9.73 9.73 38.03 2.41
4306 4442 8.649841 CACCAAATCAAACATTGCTAATTACTG 58.350 33.333 0.00 0.00 0.00 2.74
4323 4459 6.899393 AAACTGAAATCTAGCACCAAATCA 57.101 33.333 0.00 0.00 0.00 2.57
4356 4492 5.883673 GGGCAGACACCAAACAGTAATAATA 59.116 40.000 0.00 0.00 0.00 0.98
4357 4493 4.705023 GGGCAGACACCAAACAGTAATAAT 59.295 41.667 0.00 0.00 0.00 1.28
4358 4494 4.076394 GGGCAGACACCAAACAGTAATAA 58.924 43.478 0.00 0.00 0.00 1.40
4371 4507 1.373570 GCAAGTATCTGGGCAGACAC 58.626 55.000 0.00 0.00 40.75 3.67
4418 4554 2.169769 ACCTTGTTGTCGTCTTCCAAGA 59.830 45.455 0.00 0.00 35.64 3.02
4480 4618 7.494625 TCCAACTTTTCACTCTAAACTACACAG 59.505 37.037 0.00 0.00 0.00 3.66
4547 4774 7.010460 GCAAGAATAAAACTATTCCATTGGCAC 59.990 37.037 0.00 0.00 37.20 5.01
4588 4815 5.067283 ACAAGTGAAACCACAGAATACCAAC 59.933 40.000 0.00 0.00 37.80 3.77
4600 4827 6.783708 ACTTTTATCCAACAAGTGAAACCA 57.216 33.333 0.00 0.00 37.80 3.67
4629 4857 5.897250 TCACAGCCTATGTAATGGAACTCTA 59.103 40.000 0.00 0.00 41.41 2.43
4630 4858 4.716784 TCACAGCCTATGTAATGGAACTCT 59.283 41.667 0.00 0.00 41.41 3.24
4636 4864 8.450578 TTTATTCTTCACAGCCTATGTAATGG 57.549 34.615 0.00 0.00 41.41 3.16
4660 4888 9.162764 ACTACTAATGTTGACGAAGCATTTATT 57.837 29.630 9.35 0.00 34.97 1.40
4687 4915 2.239400 AGTCCAGGCAGCTTTTAAACC 58.761 47.619 0.00 0.00 0.00 3.27
4719 4950 3.319122 GCTTCTGCCAAAAAGAGAAGGAA 59.681 43.478 0.00 0.00 41.99 3.36
4763 4994 8.603242 AACACGACTGTAGTTTGAGAAATAAT 57.397 30.769 0.00 0.00 0.00 1.28
4765 4996 8.332464 CAAAACACGACTGTAGTTTGAGAAATA 58.668 33.333 0.00 0.00 35.79 1.40
4779 5010 2.536761 TCCTACCCAAAACACGACTG 57.463 50.000 0.00 0.00 0.00 3.51
4851 5082 5.297776 CCGCAAGATTTAGATGGTCATTTCT 59.702 40.000 0.00 0.00 43.02 2.52
4860 5174 3.461061 TGAGCTCCGCAAGATTTAGATG 58.539 45.455 12.15 0.00 43.02 2.90
4863 5177 2.032204 GCATGAGCTCCGCAAGATTTAG 60.032 50.000 17.76 0.00 37.37 1.85
4894 5208 3.077359 CAACCTCTCCAATCCACAGTTC 58.923 50.000 0.00 0.00 0.00 3.01
4897 5211 1.340405 CCCAACCTCTCCAATCCACAG 60.340 57.143 0.00 0.00 0.00 3.66
4905 5219 2.637872 CTGTAACTTCCCAACCTCTCCA 59.362 50.000 0.00 0.00 0.00 3.86
4906 5220 2.638363 ACTGTAACTTCCCAACCTCTCC 59.362 50.000 0.00 0.00 0.00 3.71
4908 5222 3.714798 TGAACTGTAACTTCCCAACCTCT 59.285 43.478 0.00 0.00 0.00 3.69
4909 5223 4.081322 TGAACTGTAACTTCCCAACCTC 57.919 45.455 0.00 0.00 0.00 3.85
4911 5225 5.070685 AGAATGAACTGTAACTTCCCAACC 58.929 41.667 0.00 0.00 0.00 3.77
4993 5311 7.211897 TGGAATCTCCCTGAAATCTTCATTA 57.788 36.000 0.00 0.00 35.07 1.90
5002 5320 2.986019 TGTTCCTGGAATCTCCCTGAAA 59.014 45.455 13.07 0.00 35.03 2.69
5074 5392 4.081642 GCAGTCCTGGTAACACAGATAAGA 60.082 45.833 0.00 0.00 46.17 2.10
5249 5575 3.041211 CAGGAGATGACAATCAGGGGTA 58.959 50.000 0.00 0.00 35.03 3.69
5377 5709 1.135344 TGTACATCGTCAAATCGGCGA 60.135 47.619 13.87 13.87 39.02 5.54
5378 5710 1.273688 TGTACATCGTCAAATCGGCG 58.726 50.000 0.00 0.00 0.00 6.46
5473 5805 5.755409 TCTTCCACATTGTACTACATGGT 57.245 39.130 0.00 0.00 30.05 3.55
5479 5811 7.093509 TGTCTAAGCATCTTCCACATTGTACTA 60.094 37.037 0.00 0.00 0.00 1.82
5481 5813 5.874810 TGTCTAAGCATCTTCCACATTGTAC 59.125 40.000 0.00 0.00 0.00 2.90
5482 5814 6.048732 TGTCTAAGCATCTTCCACATTGTA 57.951 37.500 0.00 0.00 0.00 2.41
5484 5816 4.334759 CCTGTCTAAGCATCTTCCACATTG 59.665 45.833 0.00 0.00 0.00 2.82
5485 5817 4.018960 ACCTGTCTAAGCATCTTCCACATT 60.019 41.667 0.00 0.00 0.00 2.71
5486 5818 3.521126 ACCTGTCTAAGCATCTTCCACAT 59.479 43.478 0.00 0.00 0.00 3.21
5487 5819 2.906389 ACCTGTCTAAGCATCTTCCACA 59.094 45.455 0.00 0.00 0.00 4.17
5488 5820 3.265791 CACCTGTCTAAGCATCTTCCAC 58.734 50.000 0.00 0.00 0.00 4.02
5489 5821 2.355108 GCACCTGTCTAAGCATCTTCCA 60.355 50.000 0.00 0.00 0.00 3.53
5490 5822 2.093235 AGCACCTGTCTAAGCATCTTCC 60.093 50.000 0.00 0.00 0.00 3.46
5491 5823 3.258971 AGCACCTGTCTAAGCATCTTC 57.741 47.619 0.00 0.00 0.00 2.87
5556 5888 3.639094 TGGAATGTTCGGTTGGATGTTTT 59.361 39.130 0.00 0.00 0.00 2.43
5569 5904 4.593956 ACTCAGGAAGGAATGGAATGTTC 58.406 43.478 0.00 0.00 0.00 3.18
5589 5924 6.681729 TCCATCTTGGAGTAAGTGTTAACT 57.318 37.500 7.22 0.00 42.67 2.24
5604 5939 4.024218 GCTGCTAACTGCTAATCCATCTTG 60.024 45.833 0.00 0.00 43.37 3.02
5644 6237 7.750229 ACATGCTAAATTCGTATCCATCATT 57.250 32.000 0.00 0.00 0.00 2.57
5682 6275 5.513233 ACACTTTGGCATCCTTTCATAGAT 58.487 37.500 0.00 0.00 0.00 1.98
5683 6276 4.922206 ACACTTTGGCATCCTTTCATAGA 58.078 39.130 0.00 0.00 0.00 1.98
5688 6281 3.552890 GGTTGACACTTTGGCATCCTTTC 60.553 47.826 2.33 0.00 41.11 2.62
5693 6286 0.951558 ACGGTTGACACTTTGGCATC 59.048 50.000 0.00 0.00 33.90 3.91
5782 6375 1.065491 AGTGCCTGTGATAATTGCCGA 60.065 47.619 0.00 0.00 0.00 5.54
5837 6435 3.696518 TAGCCTCACCCAGCCGGAT 62.697 63.158 5.05 0.00 34.64 4.18
5840 6438 2.125106 GTTAGCCTCACCCAGCCG 60.125 66.667 0.00 0.00 0.00 5.52
5844 6442 0.685097 GACAGTGTTAGCCTCACCCA 59.315 55.000 0.00 0.00 36.58 4.51
5936 6534 7.955918 TGCTTATCAAGATGCAAGAGATACTA 58.044 34.615 0.00 0.00 32.12 1.82
5937 6535 6.824553 TGCTTATCAAGATGCAAGAGATACT 58.175 36.000 0.00 0.00 32.12 2.12
5938 6536 7.488187 TTGCTTATCAAGATGCAAGAGATAC 57.512 36.000 0.00 0.00 39.98 2.24


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

AutoCloner maintained by Alex Coulton.