Multiple sequence alignment - TraesCS2D01G493100

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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 TraesCS2D01G493100 chr2D 100.000 4409 0 0 787 5195 590674881 590679289 0.000000e+00 8142.0
1 TraesCS2D01G493100 chr2D 100.000 564 0 0 5487 6050 590679581 590680144 0.000000e+00 1042.0
2 TraesCS2D01G493100 chr2D 100.000 502 0 0 1 502 590674095 590674596 0.000000e+00 928.0
3 TraesCS2D01G493100 chr2D 90.545 550 46 5 5503 6050 180537861 180538406 0.000000e+00 723.0
4 TraesCS2D01G493100 chr2D 90.164 549 53 1 5503 6050 196860963 196861511 0.000000e+00 713.0
5 TraesCS2D01G493100 chr2B 94.413 2273 89 19 2944 5195 715925511 715927766 0.000000e+00 3459.0
6 TraesCS2D01G493100 chr2B 93.737 1852 65 21 883 2719 715923085 715924900 0.000000e+00 2730.0
7 TraesCS2D01G493100 chr2B 89.306 346 21 8 160 502 715922267 715922599 2.610000e-113 420.0
8 TraesCS2D01G493100 chr2B 93.137 204 8 2 2745 2946 715924993 715925192 1.650000e-75 294.0
9 TraesCS2D01G493100 chr2B 95.283 106 5 0 1171 1276 23656782 23656677 1.040000e-37 169.0
10 TraesCS2D01G493100 chr2B 100.000 44 0 0 1595 1638 715923832 715923875 1.400000e-11 82.4
11 TraesCS2D01G493100 chr2B 97.059 34 1 0 811 844 715922659 715922692 2.360000e-04 58.4
12 TraesCS2D01G493100 chr2A 93.894 2047 92 17 3173 5195 725345794 725347831 0.000000e+00 3057.0
13 TraesCS2D01G493100 chr2A 94.244 1303 50 14 1420 2716 725343880 725345163 0.000000e+00 1967.0
14 TraesCS2D01G493100 chr2A 93.356 587 21 12 811 1385 725343301 725343881 0.000000e+00 852.0
15 TraesCS2D01G493100 chr2A 92.871 533 16 5 2579 3109 725345160 725345672 0.000000e+00 754.0
16 TraesCS2D01G493100 chr2A 86.851 289 15 8 221 502 725342972 725343244 9.850000e-78 302.0
17 TraesCS2D01G493100 chr5D 92.153 548 40 3 5503 6049 486145156 486145701 0.000000e+00 771.0
18 TraesCS2D01G493100 chr5D 91.058 548 49 0 5503 6050 449254144 449253597 0.000000e+00 741.0
19 TraesCS2D01G493100 chr5D 90.545 550 49 3 5503 6050 519335153 519334605 0.000000e+00 725.0
20 TraesCS2D01G493100 chr5D 90.364 550 48 5 5503 6050 370298096 370298642 0.000000e+00 717.0
21 TraesCS2D01G493100 chr5D 98.113 106 2 0 1171 1276 54191000 54190895 1.040000e-42 185.0
22 TraesCS2D01G493100 chr5D 95.455 44 1 1 48 90 208137438 208137481 1.090000e-07 69.4
23 TraesCS2D01G493100 chr7D 91.289 551 45 3 5503 6050 136239942 136240492 0.000000e+00 749.0
24 TraesCS2D01G493100 chr7D 90.744 551 48 3 5503 6050 630617025 630617575 0.000000e+00 732.0
25 TraesCS2D01G493100 chr3D 90.182 550 51 3 5503 6050 598879663 598879115 0.000000e+00 713.0
26 TraesCS2D01G493100 chr3B 89.427 227 24 0 1041 1267 45148856 45148630 2.760000e-73 287.0
27 TraesCS2D01G493100 chr6B 87.826 230 25 1 1041 1267 632002244 632002015 3.590000e-67 267.0
28 TraesCS2D01G493100 chr5A 90.608 181 16 1 1096 1276 709452332 709452153 7.840000e-59 239.0
29 TraesCS2D01G493100 chr1B 95.283 106 5 0 1171 1276 102154827 102154932 1.040000e-37 169.0
30 TraesCS2D01G493100 chr5B 94.340 106 6 0 1171 1276 674913697 674913802 4.850000e-36 163.0
31 TraesCS2D01G493100 chr7B 86.667 75 6 2 1083 1156 634555346 634555275 5.030000e-11 80.5


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 TraesCS2D01G493100 chr2D 590674095 590680144 6049 False 3370.666667 8142 100.000000 1 6050 3 chr2D.!!$F3 6049
1 TraesCS2D01G493100 chr2D 180537861 180538406 545 False 723.000000 723 90.545000 5503 6050 1 chr2D.!!$F1 547
2 TraesCS2D01G493100 chr2D 196860963 196861511 548 False 713.000000 713 90.164000 5503 6050 1 chr2D.!!$F2 547
3 TraesCS2D01G493100 chr2B 715922267 715927766 5499 False 1173.966667 3459 94.608667 160 5195 6 chr2B.!!$F1 5035
4 TraesCS2D01G493100 chr2A 725342972 725347831 4859 False 1386.400000 3057 92.243200 221 5195 5 chr2A.!!$F1 4974
5 TraesCS2D01G493100 chr5D 486145156 486145701 545 False 771.000000 771 92.153000 5503 6049 1 chr5D.!!$F3 546
6 TraesCS2D01G493100 chr5D 449253597 449254144 547 True 741.000000 741 91.058000 5503 6050 1 chr5D.!!$R2 547
7 TraesCS2D01G493100 chr5D 519334605 519335153 548 True 725.000000 725 90.545000 5503 6050 1 chr5D.!!$R3 547
8 TraesCS2D01G493100 chr5D 370298096 370298642 546 False 717.000000 717 90.364000 5503 6050 1 chr5D.!!$F2 547
9 TraesCS2D01G493100 chr7D 136239942 136240492 550 False 749.000000 749 91.289000 5503 6050 1 chr7D.!!$F1 547
10 TraesCS2D01G493100 chr7D 630617025 630617575 550 False 732.000000 732 90.744000 5503 6050 1 chr7D.!!$F2 547
11 TraesCS2D01G493100 chr3D 598879115 598879663 548 True 713.000000 713 90.182000 5503 6050 1 chr3D.!!$R1 547

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
845 854 0.030369 CTATATATCCCGGGCGACGC 59.970 60.000 18.49 12.43 42.52 5.19 F
1114 1484 1.077644 CGACGAGGAGGAGGAGGAA 60.078 63.158 0.00 0.00 0.00 3.36 F
1763 2150 0.174162 GTCCATCAACCAAGCCATGC 59.826 55.000 0.00 0.00 0.00 4.06 F
1765 2152 0.174845 CCATCAACCAAGCCATGCAG 59.825 55.000 0.00 0.00 0.00 4.41 F
1766 2153 0.459585 CATCAACCAAGCCATGCAGC 60.460 55.000 0.00 0.00 0.00 5.25 F
1767 2154 0.901114 ATCAACCAAGCCATGCAGCA 60.901 50.000 0.00 0.00 34.23 4.41 F
3165 4099 1.065600 CAACTGTTGTGCCAACGGG 59.934 57.895 22.71 15.33 37.18 5.28 F
4847 5844 0.736636 CATACAGCTGTGGCATGGTG 59.263 55.000 29.57 16.97 41.70 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1666 2053 0.031178 CACCAACAGGAAGCAGCAAC 59.969 55.000 0.00 0.00 0.00 4.17 R
2734 3345 0.106419 AAAAGGGAGCCACGTTTCCA 60.106 50.000 11.42 0.00 35.09 3.53 R
3720 4714 0.320421 TGGCAAAGACGTCAGCTACC 60.320 55.000 19.50 12.48 0.00 3.18 R
3877 4871 6.749923 ATGTGAAGTTCTAATCAAAGCTCC 57.250 37.500 4.17 0.00 0.00 4.70 R
3939 4933 5.927819 AGAGCCACAAAATCATTCCAAAAA 58.072 33.333 0.00 0.00 0.00 1.94 R
4267 5261 8.311109 TCTCTCATATACACTTGCACTGTTAAA 58.689 33.333 1.61 0.00 0.00 1.52 R
4876 5878 0.309922 TTCCACACGACGAGACACTC 59.690 55.000 0.00 0.00 0.00 3.51 R
5735 6760 1.336887 CCTCTGCTCTTTTTCCGACGA 60.337 52.381 0.00 0.00 0.00 4.20 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
28 29 3.325293 ACTGGACTAGTGACATTGCAG 57.675 47.619 0.00 0.00 38.49 4.41
29 30 2.899900 ACTGGACTAGTGACATTGCAGA 59.100 45.455 0.00 0.00 38.49 4.26
30 31 3.324846 ACTGGACTAGTGACATTGCAGAA 59.675 43.478 0.00 0.00 38.49 3.02
31 32 3.664107 TGGACTAGTGACATTGCAGAAC 58.336 45.455 0.00 0.00 0.00 3.01
32 33 3.003480 GGACTAGTGACATTGCAGAACC 58.997 50.000 0.00 0.00 0.00 3.62
33 34 3.003480 GACTAGTGACATTGCAGAACCC 58.997 50.000 0.00 0.00 0.00 4.11
34 35 2.371841 ACTAGTGACATTGCAGAACCCA 59.628 45.455 0.00 0.00 0.00 4.51
35 36 1.609208 AGTGACATTGCAGAACCCAC 58.391 50.000 0.00 0.00 0.00 4.61
36 37 0.598065 GTGACATTGCAGAACCCACC 59.402 55.000 0.00 0.00 0.00 4.61
37 38 0.478072 TGACATTGCAGAACCCACCT 59.522 50.000 0.00 0.00 0.00 4.00
38 39 0.883833 GACATTGCAGAACCCACCTG 59.116 55.000 0.00 0.00 34.88 4.00
39 40 0.185901 ACATTGCAGAACCCACCTGT 59.814 50.000 0.00 0.00 34.29 4.00
40 41 1.423541 ACATTGCAGAACCCACCTGTA 59.576 47.619 0.00 0.00 34.29 2.74
41 42 2.158534 ACATTGCAGAACCCACCTGTAA 60.159 45.455 0.00 0.00 39.76 2.41
42 43 1.975660 TTGCAGAACCCACCTGTAAC 58.024 50.000 0.00 0.00 32.67 2.50
43 44 0.250124 TGCAGAACCCACCTGTAACG 60.250 55.000 0.00 0.00 34.29 3.18
44 45 0.250166 GCAGAACCCACCTGTAACGT 60.250 55.000 0.00 0.00 34.29 3.99
45 46 1.812708 GCAGAACCCACCTGTAACGTT 60.813 52.381 5.88 5.88 34.29 3.99
46 47 2.140717 CAGAACCCACCTGTAACGTTC 58.859 52.381 2.82 0.00 34.40 3.95
47 48 2.044758 AGAACCCACCTGTAACGTTCT 58.955 47.619 2.82 0.00 38.60 3.01
48 49 3.006110 CAGAACCCACCTGTAACGTTCTA 59.994 47.826 2.82 0.00 40.80 2.10
49 50 3.006217 AGAACCCACCTGTAACGTTCTAC 59.994 47.826 2.82 0.00 40.92 2.59
50 51 2.601905 ACCCACCTGTAACGTTCTACT 58.398 47.619 2.82 0.00 0.00 2.57
51 52 2.967887 ACCCACCTGTAACGTTCTACTT 59.032 45.455 2.82 0.00 0.00 2.24
52 53 3.006217 ACCCACCTGTAACGTTCTACTTC 59.994 47.826 2.82 0.00 0.00 3.01
53 54 3.582780 CCACCTGTAACGTTCTACTTCC 58.417 50.000 2.82 0.00 0.00 3.46
54 55 3.257624 CCACCTGTAACGTTCTACTTCCT 59.742 47.826 2.82 0.00 0.00 3.36
55 56 4.262335 CCACCTGTAACGTTCTACTTCCTT 60.262 45.833 2.82 0.00 0.00 3.36
56 57 4.922103 CACCTGTAACGTTCTACTTCCTTC 59.078 45.833 2.82 0.00 0.00 3.46
57 58 4.164294 CCTGTAACGTTCTACTTCCTTCG 58.836 47.826 2.82 0.00 0.00 3.79
58 59 4.320788 CCTGTAACGTTCTACTTCCTTCGT 60.321 45.833 2.82 0.00 0.00 3.85
59 60 5.106555 CCTGTAACGTTCTACTTCCTTCGTA 60.107 44.000 2.82 0.00 0.00 3.43
60 61 6.312399 TGTAACGTTCTACTTCCTTCGTAA 57.688 37.500 2.82 0.00 0.00 3.18
61 62 6.142817 TGTAACGTTCTACTTCCTTCGTAAC 58.857 40.000 2.82 0.00 0.00 2.50
62 63 5.444663 AACGTTCTACTTCCTTCGTAACT 57.555 39.130 0.00 0.00 0.00 2.24
63 64 5.444663 ACGTTCTACTTCCTTCGTAACTT 57.555 39.130 0.00 0.00 0.00 2.66
64 65 6.560253 ACGTTCTACTTCCTTCGTAACTTA 57.440 37.500 0.00 0.00 0.00 2.24
65 66 6.970484 ACGTTCTACTTCCTTCGTAACTTAA 58.030 36.000 0.00 0.00 0.00 1.85
66 67 7.597386 ACGTTCTACTTCCTTCGTAACTTAAT 58.403 34.615 0.00 0.00 0.00 1.40
67 68 8.730680 ACGTTCTACTTCCTTCGTAACTTAATA 58.269 33.333 0.00 0.00 0.00 0.98
68 69 9.727627 CGTTCTACTTCCTTCGTAACTTAATAT 57.272 33.333 0.00 0.00 0.00 1.28
74 75 9.727627 ACTTCCTTCGTAACTTAATATAAGACG 57.272 33.333 4.24 4.96 0.00 4.18
75 76 9.727627 CTTCCTTCGTAACTTAATATAAGACGT 57.272 33.333 4.24 0.00 0.00 4.34
106 107 9.796120 TTTACACTGTTTTGGACTCTAAAAATG 57.204 29.630 2.15 4.70 0.00 2.32
107 108 7.404671 ACACTGTTTTGGACTCTAAAAATGT 57.595 32.000 2.15 5.21 0.00 2.71
108 109 7.836842 ACACTGTTTTGGACTCTAAAAATGTT 58.163 30.769 2.15 0.00 0.00 2.71
109 110 8.962679 ACACTGTTTTGGACTCTAAAAATGTTA 58.037 29.630 2.15 0.00 0.00 2.41
110 111 9.965824 CACTGTTTTGGACTCTAAAAATGTTAT 57.034 29.630 2.15 0.00 0.00 1.89
167 168 5.188327 AGCTTACAAAGGAAAGAAAGTGC 57.812 39.130 0.00 0.00 0.00 4.40
169 170 4.038042 GCTTACAAAGGAAAGAAAGTGCCT 59.962 41.667 0.00 0.00 0.00 4.75
183 184 6.247727 GAAAGTGCCTTTCTAAGAGGAAAG 57.752 41.667 16.08 9.25 44.33 2.62
203 204 0.673644 AAAACAGATCACGGCGGAGG 60.674 55.000 13.24 0.00 0.00 4.30
429 437 1.898574 CACAGTGCTTCACCCACCC 60.899 63.158 0.00 0.00 34.49 4.61
844 853 0.666913 CCTATATATCCCGGGCGACG 59.333 60.000 18.49 0.00 43.80 5.12
845 854 0.030369 CTATATATCCCGGGCGACGC 59.970 60.000 18.49 12.43 42.52 5.19
895 1254 2.901975 GGGGGAAAATCCAAGGCTC 58.098 57.895 0.00 0.00 38.64 4.70
938 1299 4.760047 ACACGGCACATCTCGGGC 62.760 66.667 0.00 0.00 0.00 6.13
1114 1484 1.077644 CGACGAGGAGGAGGAGGAA 60.078 63.158 0.00 0.00 0.00 3.36
1279 1658 2.504519 GGCACCCGAGGTATGGTC 59.495 66.667 0.00 0.00 32.11 4.02
1280 1659 2.106332 GCACCCGAGGTATGGTCG 59.894 66.667 0.00 0.00 32.11 4.79
1404 1783 2.048222 CGCGCTCTCTGGAAACCA 60.048 61.111 5.56 0.00 0.00 3.67
1418 1797 3.390967 TGGAAACCACAGAGTCATTCAGA 59.609 43.478 0.00 0.00 0.00 3.27
1485 1864 2.154074 AGAGCGAGGGGTTTGGGTT 61.154 57.895 0.00 0.00 0.00 4.11
1565 1944 6.127814 GCCTGAGGTTTAATTTAAGGTGGTAC 60.128 42.308 0.00 0.00 0.00 3.34
1646 2033 5.757320 AGTGATCATTGCTGCTATAGTGTTC 59.243 40.000 0.00 0.00 0.00 3.18
1647 2034 5.049818 GTGATCATTGCTGCTATAGTGTTCC 60.050 44.000 0.00 0.00 0.00 3.62
1648 2035 4.760530 TCATTGCTGCTATAGTGTTCCT 57.239 40.909 0.00 0.00 0.00 3.36
1649 2036 4.697514 TCATTGCTGCTATAGTGTTCCTC 58.302 43.478 0.00 0.00 0.00 3.71
1650 2037 2.871182 TGCTGCTATAGTGTTCCTCG 57.129 50.000 0.00 0.00 0.00 4.63
1651 2038 1.409064 TGCTGCTATAGTGTTCCTCGG 59.591 52.381 0.00 0.00 0.00 4.63
1652 2039 1.870167 GCTGCTATAGTGTTCCTCGGC 60.870 57.143 0.84 0.00 0.00 5.54
1653 2040 1.683917 CTGCTATAGTGTTCCTCGGCT 59.316 52.381 0.84 0.00 0.00 5.52
1666 2053 0.309302 CTCGGCTGGTAGAGTGATCG 59.691 60.000 0.00 0.00 0.00 3.69
1676 2063 1.719600 AGAGTGATCGTTGCTGCTTC 58.280 50.000 0.00 0.00 0.00 3.86
1687 2074 1.529244 GCTGCTTCCTGTTGGTGGT 60.529 57.895 0.00 0.00 34.23 4.16
1697 2084 1.000060 CTGTTGGTGGTCCATGCTTTG 60.000 52.381 0.00 0.00 43.91 2.77
1713 2100 6.375377 CATGCTTTGAAAATTTGGTGATTGG 58.625 36.000 0.00 0.00 0.00 3.16
1750 2137 2.236146 TGATGTGGGTGTAGTGTCCATC 59.764 50.000 0.00 0.00 32.71 3.51
1757 2144 3.074412 GGTGTAGTGTCCATCAACCAAG 58.926 50.000 0.00 0.00 0.00 3.61
1763 2150 0.174162 GTCCATCAACCAAGCCATGC 59.826 55.000 0.00 0.00 0.00 4.06
1764 2151 0.251698 TCCATCAACCAAGCCATGCA 60.252 50.000 0.00 0.00 0.00 3.96
1765 2152 0.174845 CCATCAACCAAGCCATGCAG 59.825 55.000 0.00 0.00 0.00 4.41
1766 2153 0.459585 CATCAACCAAGCCATGCAGC 60.460 55.000 0.00 0.00 0.00 5.25
1767 2154 0.901114 ATCAACCAAGCCATGCAGCA 60.901 50.000 0.00 0.00 34.23 4.41
1768 2155 1.080093 CAACCAAGCCATGCAGCAG 60.080 57.895 0.00 0.00 34.23 4.24
1769 2156 2.939261 AACCAAGCCATGCAGCAGC 61.939 57.895 0.00 0.00 42.57 5.25
1838 2225 3.310774 CGCAATATCTCTTGGAAGTGTGG 59.689 47.826 0.00 0.00 0.00 4.17
1846 2233 3.138304 TCTTGGAAGTGTGGATTTGACG 58.862 45.455 0.00 0.00 0.00 4.35
1982 2370 6.687958 CAGTTAACCGTTATTGTTGTCGTTTT 59.312 34.615 0.88 0.00 0.00 2.43
2021 2409 1.511850 CTTGATGGTCAACACGCAGA 58.488 50.000 0.00 0.00 32.21 4.26
2237 2627 6.906157 ATGATTATCAACTTAGGCCAATGG 57.094 37.500 5.01 0.00 0.00 3.16
2724 3335 8.549338 TCAAACGTGGTTCATACATATGTTTA 57.451 30.769 14.77 0.00 33.81 2.01
2726 3337 9.781834 CAAACGTGGTTCATACATATGTTTAAT 57.218 29.630 14.77 0.00 33.81 1.40
2727 3338 9.997482 AAACGTGGTTCATACATATGTTTAATC 57.003 29.630 14.77 7.18 33.81 1.75
2728 3339 8.958119 ACGTGGTTCATACATATGTTTAATCT 57.042 30.769 14.77 0.00 35.26 2.40
2729 3340 9.042008 ACGTGGTTCATACATATGTTTAATCTC 57.958 33.333 14.77 6.70 35.26 2.75
2730 3341 8.495949 CGTGGTTCATACATATGTTTAATCTCC 58.504 37.037 14.77 8.96 35.26 3.71
2731 3342 9.337396 GTGGTTCATACATATGTTTAATCTCCA 57.663 33.333 14.77 11.21 35.26 3.86
2736 3347 9.506018 TCATACATATGTTTAATCTCCATGTGG 57.494 33.333 14.77 0.00 33.55 4.17
2737 3348 9.506018 CATACATATGTTTAATCTCCATGTGGA 57.494 33.333 14.77 1.17 43.08 4.02
2739 3350 8.821686 ACATATGTTTAATCTCCATGTGGAAA 57.178 30.769 1.41 0.00 44.91 3.13
2740 3351 8.686334 ACATATGTTTAATCTCCATGTGGAAAC 58.314 33.333 1.41 5.12 44.91 2.78
2741 3352 5.621197 TGTTTAATCTCCATGTGGAAACG 57.379 39.130 2.97 0.00 44.91 3.60
2742 3353 5.067273 TGTTTAATCTCCATGTGGAAACGT 58.933 37.500 2.97 0.00 44.91 3.99
2743 3354 5.049060 TGTTTAATCTCCATGTGGAAACGTG 60.049 40.000 2.97 0.00 44.91 4.49
2783 3394 7.516198 AATTTAGCAGTTCATGAGTCTTTGT 57.484 32.000 0.00 0.00 0.00 2.83
2922 3535 3.068024 TGCCAGTGGAGAAATGACAAAAC 59.932 43.478 15.20 0.00 0.00 2.43
3003 3937 4.262635 CGACCCTGTTGGCTATAGATGAAT 60.263 45.833 3.21 0.00 37.83 2.57
3004 3938 4.978099 ACCCTGTTGGCTATAGATGAATG 58.022 43.478 3.21 0.00 37.83 2.67
3104 4038 1.338769 ACCGAACTGAACCACCTATGC 60.339 52.381 0.00 0.00 0.00 3.14
3165 4099 1.065600 CAACTGTTGTGCCAACGGG 59.934 57.895 22.71 15.33 37.18 5.28
3331 4323 2.746359 GAGGATGGGCTGGGATCG 59.254 66.667 0.00 0.00 0.00 3.69
3720 4714 2.627699 TGGGTTAAGCAAGCTTTCAAGG 59.372 45.455 13.06 0.00 37.47 3.61
3877 4871 7.509797 GGAGAACTTTAAATGCAAAAATTCGG 58.490 34.615 0.00 0.00 0.00 4.30
3939 4933 1.722034 TTGAGGGTGAGAACAGCTCT 58.278 50.000 0.00 0.00 44.27 4.09
4267 5261 6.209192 TGATGTGAAGCTGAATGGTTTTACAT 59.791 34.615 0.00 0.00 41.87 2.29
4324 5318 3.957591 ATGCTACTGATCATCGAGCAT 57.042 42.857 23.41 23.41 46.11 3.79
4488 5482 1.898574 CGGGTGCAAGCTTCAGGTT 60.899 57.895 0.00 0.00 35.98 3.50
4539 5533 3.326747 AGCAGTTTATTCCGTCTCACAC 58.673 45.455 0.00 0.00 0.00 3.82
4560 5554 1.464608 CGTGGAGCCATAGTTGTTGTG 59.535 52.381 0.00 0.00 0.00 3.33
4566 5560 1.202348 GCCATAGTTGTTGTGGAAGCC 59.798 52.381 0.00 0.00 40.33 4.35
4620 5614 5.000012 AGAAAATCAGGAGTAGTACAGCG 58.000 43.478 2.52 0.00 0.00 5.18
4623 5617 1.366679 TCAGGAGTAGTACAGCGACG 58.633 55.000 2.52 0.00 0.00 5.12
4682 5676 3.119352 GCCAAGGCATCCTTTTTACAGAG 60.119 47.826 6.14 0.00 41.69 3.35
4721 5715 6.264067 GCTAATCAGGAAGTATGAATGGCTTT 59.736 38.462 0.00 0.00 32.93 3.51
4722 5716 6.705863 AATCAGGAAGTATGAATGGCTTTC 57.294 37.500 6.20 6.20 34.72 2.62
4752 5746 9.368674 CATATACTGATAGAATCTCAGCCAAAG 57.631 37.037 0.12 0.00 43.18 2.77
4759 5753 5.033589 AGAATCTCAGCCAAAGGATACAG 57.966 43.478 0.00 0.00 41.41 2.74
4770 5764 6.069963 AGCCAAAGGATACAGTGAGTCTAATT 60.070 38.462 0.00 0.00 41.41 1.40
4782 5776 3.830178 TGAGTCTAATTCCCAGTCGTCAA 59.170 43.478 0.00 0.00 0.00 3.18
4797 5791 1.251251 GTCAATTCAGCAAGGCAGGT 58.749 50.000 0.00 0.00 0.00 4.00
4826 5823 5.164080 CGACGACTCTTATGGTTTGAAGTTC 60.164 44.000 0.00 0.00 0.00 3.01
4831 5828 7.759886 CGACTCTTATGGTTTGAAGTTCTCATA 59.240 37.037 4.17 4.95 32.78 2.15
4837 5834 4.756642 TGGTTTGAAGTTCTCATACAGCTG 59.243 41.667 13.48 13.48 37.64 4.24
4847 5844 0.736636 CATACAGCTGTGGCATGGTG 59.263 55.000 29.57 16.97 41.70 4.17
4848 5845 1.033746 ATACAGCTGTGGCATGGTGC 61.034 55.000 29.57 8.63 44.08 5.01
4863 5865 2.255406 TGGTGCCATTTTACCATTGCT 58.745 42.857 0.00 0.00 41.80 3.91
4876 5878 3.958147 ATTGCTGGTGGGAGCGACG 62.958 63.158 0.00 0.00 42.32 5.12
4879 5881 3.374402 CTGGTGGGAGCGACGAGT 61.374 66.667 0.00 0.00 0.00 4.18
4880 5882 3.633094 CTGGTGGGAGCGACGAGTG 62.633 68.421 0.00 0.00 0.00 3.51
4881 5883 3.681835 GGTGGGAGCGACGAGTGT 61.682 66.667 0.00 0.00 0.00 3.55
4915 5917 5.471116 TGGAATGTTGTGTCTGAAGAAGATG 59.529 40.000 0.00 0.00 37.23 2.90
4934 5936 4.278419 AGATGTAACCAGAAGCACCAAAAC 59.722 41.667 0.00 0.00 0.00 2.43
4935 5937 3.626930 TGTAACCAGAAGCACCAAAACT 58.373 40.909 0.00 0.00 0.00 2.66
4936 5938 4.020543 TGTAACCAGAAGCACCAAAACTT 58.979 39.130 0.00 0.00 0.00 2.66
4966 5968 3.048337 TCTCCCGTGTTGTACCATTTC 57.952 47.619 0.00 0.00 0.00 2.17
4970 5974 2.888414 CCCGTGTTGTACCATTTCCTTT 59.112 45.455 0.00 0.00 0.00 3.11
4973 5977 5.009811 CCCGTGTTGTACCATTTCCTTTAAA 59.990 40.000 0.00 0.00 0.00 1.52
4974 5978 5.916320 CCGTGTTGTACCATTTCCTTTAAAC 59.084 40.000 0.00 0.00 0.00 2.01
4976 5980 5.916320 GTGTTGTACCATTTCCTTTAAACGG 59.084 40.000 0.00 0.00 36.47 4.44
4981 5985 5.385509 ACCATTTCCTTTAAACGGATGTG 57.614 39.130 7.08 8.45 33.97 3.21
5028 6032 2.472909 GGCTGTGCCGAGCAATACC 61.473 63.158 6.41 0.00 41.47 2.73
5040 6044 5.614013 GCCGAGCAATACCGTATAAATGTTC 60.614 44.000 0.00 0.00 0.00 3.18
5047 6051 7.797123 GCAATACCGTATAAATGTTCTAAGTGC 59.203 37.037 0.00 0.00 0.00 4.40
5052 6056 7.148474 ACCGTATAAATGTTCTAAGTGCTTGTG 60.148 37.037 0.00 0.00 0.00 3.33
5054 6058 8.865978 CGTATAAATGTTCTAAGTGCTTGTGTA 58.134 33.333 0.00 0.00 0.00 2.90
5055 6059 9.968743 GTATAAATGTTCTAAGTGCTTGTGTAC 57.031 33.333 0.00 0.00 0.00 2.90
5057 6061 9.938280 ATAAATGTTCTAAGTGCTTGTGTACTA 57.062 29.630 0.00 0.00 38.17 1.82
5058 6062 7.891183 AATGTTCTAAGTGCTTGTGTACTAG 57.109 36.000 0.00 0.00 38.17 2.57
5102 6114 2.709125 TTCTGTTCGTCCTGCGTGGG 62.709 60.000 0.00 0.00 42.13 4.61
5116 6128 2.282180 TGGGGGCTGTTCGCTTTC 60.282 61.111 0.00 0.00 39.13 2.62
5149 6171 2.174363 GGTACCCAAGCGTAGTGTTT 57.826 50.000 0.00 0.00 0.00 2.83
5177 6199 4.441634 GGAAGTCTACATCCATAGCGTTGT 60.442 45.833 0.00 0.00 34.11 3.32
5185 6207 5.352284 ACATCCATAGCGTTGTTCTCTTAG 58.648 41.667 0.00 0.00 0.00 2.18
5186 6208 5.127194 ACATCCATAGCGTTGTTCTCTTAGA 59.873 40.000 0.00 0.00 0.00 2.10
5187 6209 5.250235 TCCATAGCGTTGTTCTCTTAGAG 57.750 43.478 2.23 2.23 0.00 2.43
5188 6210 3.799420 CCATAGCGTTGTTCTCTTAGAGC 59.201 47.826 4.03 0.00 0.00 4.09
5189 6211 4.424626 CATAGCGTTGTTCTCTTAGAGCA 58.575 43.478 4.03 0.00 33.54 4.26
5190 6212 3.601443 AGCGTTGTTCTCTTAGAGCAT 57.399 42.857 4.03 0.00 35.39 3.79
5191 6213 3.516615 AGCGTTGTTCTCTTAGAGCATC 58.483 45.455 4.03 0.00 35.39 3.91
5517 6539 2.571757 TCGACGCCGAAATCTGCT 59.428 55.556 0.00 0.00 42.51 4.24
5636 6661 1.497991 CGTCAGGCGAAAAGTCAAGA 58.502 50.000 0.00 0.00 44.77 3.02
5640 6665 3.429207 GTCAGGCGAAAAGTCAAGACTAC 59.571 47.826 2.72 0.00 41.58 2.73
5664 6689 3.090532 GATTCGCCTCCCACCCCT 61.091 66.667 0.00 0.00 0.00 4.79
5694 6719 2.505982 CGCCAACCGGATGATCCT 59.494 61.111 14.18 0.00 33.30 3.24
5734 6759 0.839946 ACCGCTAGATTGCCCATTCT 59.160 50.000 0.00 0.00 0.00 2.40
5735 6760 1.212935 ACCGCTAGATTGCCCATTCTT 59.787 47.619 0.00 0.00 0.00 2.52
5738 6763 2.565841 GCTAGATTGCCCATTCTTCGT 58.434 47.619 0.00 0.00 0.00 3.85
5762 6787 2.262423 AAAAGAGCAGAGGTTTCGCT 57.738 45.000 0.00 0.00 36.42 4.93
5898 6925 2.225791 CTCGGCAATGGACTCGGACA 62.226 60.000 0.00 0.00 0.00 4.02
6016 7043 0.039256 GCGAGCAATGAAAAGCCACA 60.039 50.000 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.899900 TCTGCAATGTCACTAGTCCAGT 59.100 45.455 0.00 0.00 38.32 4.00
9 10 3.599730 TCTGCAATGTCACTAGTCCAG 57.400 47.619 0.00 0.00 0.00 3.86
10 11 3.557054 GGTTCTGCAATGTCACTAGTCCA 60.557 47.826 0.00 0.00 0.00 4.02
11 12 3.003480 GGTTCTGCAATGTCACTAGTCC 58.997 50.000 0.00 0.00 0.00 3.85
12 13 3.003480 GGGTTCTGCAATGTCACTAGTC 58.997 50.000 0.00 0.00 0.00 2.59
13 14 2.371841 TGGGTTCTGCAATGTCACTAGT 59.628 45.455 0.00 0.00 0.00 2.57
14 15 2.744202 GTGGGTTCTGCAATGTCACTAG 59.256 50.000 0.00 0.00 0.00 2.57
15 16 2.552155 GGTGGGTTCTGCAATGTCACTA 60.552 50.000 0.00 0.00 0.00 2.74
16 17 1.609208 GTGGGTTCTGCAATGTCACT 58.391 50.000 0.00 0.00 0.00 3.41
17 18 0.598065 GGTGGGTTCTGCAATGTCAC 59.402 55.000 0.00 0.00 0.00 3.67
18 19 0.478072 AGGTGGGTTCTGCAATGTCA 59.522 50.000 0.00 0.00 0.00 3.58
19 20 0.883833 CAGGTGGGTTCTGCAATGTC 59.116 55.000 0.00 0.00 0.00 3.06
20 21 0.185901 ACAGGTGGGTTCTGCAATGT 59.814 50.000 0.00 0.00 35.78 2.71
21 22 2.198827 TACAGGTGGGTTCTGCAATG 57.801 50.000 0.00 0.00 35.78 2.82
22 23 2.514803 GTTACAGGTGGGTTCTGCAAT 58.485 47.619 0.00 0.00 35.78 3.56
23 24 1.812324 CGTTACAGGTGGGTTCTGCAA 60.812 52.381 0.00 0.00 35.78 4.08
24 25 0.250124 CGTTACAGGTGGGTTCTGCA 60.250 55.000 0.00 0.00 35.78 4.41
25 26 0.250166 ACGTTACAGGTGGGTTCTGC 60.250 55.000 0.00 0.00 35.78 4.26
26 27 2.140717 GAACGTTACAGGTGGGTTCTG 58.859 52.381 0.00 0.00 35.36 3.02
27 28 2.044758 AGAACGTTACAGGTGGGTTCT 58.955 47.619 0.00 0.00 41.65 3.01
28 29 2.538512 AGAACGTTACAGGTGGGTTC 57.461 50.000 0.00 0.00 37.77 3.62
29 30 2.967887 AGTAGAACGTTACAGGTGGGTT 59.032 45.455 0.00 0.00 0.00 4.11
30 31 2.601905 AGTAGAACGTTACAGGTGGGT 58.398 47.619 0.00 0.00 0.00 4.51
31 32 3.582780 GAAGTAGAACGTTACAGGTGGG 58.417 50.000 0.00 0.00 0.00 4.61
32 33 3.257624 AGGAAGTAGAACGTTACAGGTGG 59.742 47.826 0.00 0.00 0.00 4.61
33 34 4.516365 AGGAAGTAGAACGTTACAGGTG 57.484 45.455 0.00 0.00 0.00 4.00
34 35 4.320788 CGAAGGAAGTAGAACGTTACAGGT 60.321 45.833 0.00 0.00 0.00 4.00
35 36 4.164294 CGAAGGAAGTAGAACGTTACAGG 58.836 47.826 0.00 0.00 0.00 4.00
36 37 4.791974 ACGAAGGAAGTAGAACGTTACAG 58.208 43.478 0.00 0.00 0.00 2.74
37 38 4.836125 ACGAAGGAAGTAGAACGTTACA 57.164 40.909 0.00 0.00 0.00 2.41
38 39 6.374578 AGTTACGAAGGAAGTAGAACGTTAC 58.625 40.000 0.00 0.00 34.93 2.50
39 40 6.560253 AGTTACGAAGGAAGTAGAACGTTA 57.440 37.500 0.00 0.00 35.66 3.18
40 41 5.444663 AGTTACGAAGGAAGTAGAACGTT 57.555 39.130 0.00 0.00 35.66 3.99
41 42 5.444663 AAGTTACGAAGGAAGTAGAACGT 57.555 39.130 0.00 0.00 37.68 3.99
42 43 9.727627 ATATTAAGTTACGAAGGAAGTAGAACG 57.272 33.333 0.00 0.00 0.00 3.95
48 49 9.727627 CGTCTTATATTAAGTTACGAAGGAAGT 57.272 33.333 0.00 0.00 0.00 3.01
49 50 9.727627 ACGTCTTATATTAAGTTACGAAGGAAG 57.272 33.333 12.57 0.00 33.40 3.46
80 81 9.796120 CATTTTTAGAGTCCAAAACAGTGTAAA 57.204 29.630 0.00 0.00 0.00 2.01
81 82 8.962679 ACATTTTTAGAGTCCAAAACAGTGTAA 58.037 29.630 0.00 0.00 0.00 2.41
82 83 8.514330 ACATTTTTAGAGTCCAAAACAGTGTA 57.486 30.769 0.00 0.00 0.00 2.90
83 84 7.404671 ACATTTTTAGAGTCCAAAACAGTGT 57.595 32.000 0.00 0.00 0.00 3.55
84 85 9.965824 ATAACATTTTTAGAGTCCAAAACAGTG 57.034 29.630 0.00 0.00 0.00 3.66
140 141 9.750125 CACTTTCTTTCCTTTGTAAGCTTTTAT 57.250 29.630 3.20 0.00 0.00 1.40
141 142 7.704899 GCACTTTCTTTCCTTTGTAAGCTTTTA 59.295 33.333 3.20 0.00 0.00 1.52
142 143 6.535150 GCACTTTCTTTCCTTTGTAAGCTTTT 59.465 34.615 3.20 0.00 0.00 2.27
143 144 6.042777 GCACTTTCTTTCCTTTGTAAGCTTT 58.957 36.000 3.20 0.00 0.00 3.51
144 145 5.451937 GGCACTTTCTTTCCTTTGTAAGCTT 60.452 40.000 3.48 3.48 0.00 3.74
145 146 4.038042 GGCACTTTCTTTCCTTTGTAAGCT 59.962 41.667 0.00 0.00 0.00 3.74
146 147 4.038042 AGGCACTTTCTTTCCTTTGTAAGC 59.962 41.667 0.00 0.00 27.25 3.09
147 148 5.774498 AGGCACTTTCTTTCCTTTGTAAG 57.226 39.130 0.00 0.00 27.25 2.34
169 170 9.057089 GTGATCTGTTTTCTTTCCTCTTAGAAA 57.943 33.333 0.00 0.00 38.30 2.52
183 184 0.721718 CTCCGCCGTGATCTGTTTTC 59.278 55.000 0.00 0.00 0.00 2.29
184 185 0.673644 CCTCCGCCGTGATCTGTTTT 60.674 55.000 0.00 0.00 0.00 2.43
185 186 1.079127 CCTCCGCCGTGATCTGTTT 60.079 57.895 0.00 0.00 0.00 2.83
186 187 2.579201 CCTCCGCCGTGATCTGTT 59.421 61.111 0.00 0.00 0.00 3.16
187 188 4.148825 GCCTCCGCCGTGATCTGT 62.149 66.667 0.00 0.00 0.00 3.41
188 189 3.781770 GAGCCTCCGCCGTGATCTG 62.782 68.421 0.00 0.00 34.57 2.90
189 190 3.532155 GAGCCTCCGCCGTGATCT 61.532 66.667 0.00 0.00 34.57 2.75
190 191 4.593864 GGAGCCTCCGCCGTGATC 62.594 72.222 0.00 0.00 34.57 2.92
203 204 0.526954 CGTGTATACGTGTGGGGAGC 60.527 60.000 3.56 0.00 44.99 4.70
204 205 3.635433 CGTGTATACGTGTGGGGAG 57.365 57.895 3.56 0.00 44.99 4.30
344 351 2.434359 CCGAGGGAAGAACGGTGC 60.434 66.667 0.00 0.00 41.47 5.01
420 428 4.865228 TGGGTTGGGGGTGGGTGA 62.865 66.667 0.00 0.00 0.00 4.02
793 802 3.403057 CACGCAGTTGACGACGGG 61.403 66.667 0.00 0.00 41.61 5.28
794 803 3.403057 CCACGCAGTTGACGACGG 61.403 66.667 0.00 0.00 41.61 4.79
795 804 4.059459 GCCACGCAGTTGACGACG 62.059 66.667 0.00 0.00 41.61 5.12
796 805 4.059459 CGCCACGCAGTTGACGAC 62.059 66.667 0.00 0.00 41.61 4.34
853 864 0.674895 CCTCTCCTTTTCGCCCACAG 60.675 60.000 0.00 0.00 0.00 3.66
957 1318 3.077556 CGTGGAGAGTGGAGGGGG 61.078 72.222 0.00 0.00 0.00 5.40
1388 1767 1.294659 CTGTGGTTTCCAGAGAGCGC 61.295 60.000 0.00 0.00 46.28 5.92
1394 1773 3.390967 TGAATGACTCTGTGGTTTCCAGA 59.609 43.478 0.00 0.00 37.40 3.86
1400 1779 2.369860 TGCTCTGAATGACTCTGTGGTT 59.630 45.455 0.00 0.00 0.00 3.67
1404 1783 1.973515 TGGTGCTCTGAATGACTCTGT 59.026 47.619 0.00 0.00 0.00 3.41
1412 1791 0.108424 GTCGCTCTGGTGCTCTGAAT 60.108 55.000 0.00 0.00 0.00 2.57
1496 1875 4.024048 CGAAATGGAATATTCGGGGAACAG 60.024 45.833 9.32 0.00 43.41 3.16
1539 1918 4.159693 CCACCTTAAATTAAACCTCAGGCC 59.840 45.833 0.00 0.00 0.00 5.19
1565 1944 3.119531 TGAACAAACCACTCACAGCAAAG 60.120 43.478 0.00 0.00 0.00 2.77
1646 2033 0.671251 GATCACTCTACCAGCCGAGG 59.329 60.000 0.00 0.00 0.00 4.63
1647 2034 0.309302 CGATCACTCTACCAGCCGAG 59.691 60.000 0.00 0.00 0.00 4.63
1648 2035 0.393944 ACGATCACTCTACCAGCCGA 60.394 55.000 0.00 0.00 0.00 5.54
1649 2036 0.456221 AACGATCACTCTACCAGCCG 59.544 55.000 0.00 0.00 0.00 5.52
1650 2037 1.927895 CAACGATCACTCTACCAGCC 58.072 55.000 0.00 0.00 0.00 4.85
1651 2038 1.134965 AGCAACGATCACTCTACCAGC 60.135 52.381 0.00 0.00 0.00 4.85
1652 2039 2.534298 CAGCAACGATCACTCTACCAG 58.466 52.381 0.00 0.00 0.00 4.00
1653 2040 1.404181 GCAGCAACGATCACTCTACCA 60.404 52.381 0.00 0.00 0.00 3.25
1666 2053 0.031178 CACCAACAGGAAGCAGCAAC 59.969 55.000 0.00 0.00 0.00 4.17
1687 2074 5.287674 TCACCAAATTTTCAAAGCATGGA 57.712 34.783 0.00 0.00 0.00 3.41
1750 2137 1.080093 CTGCTGCATGGCTTGGTTG 60.080 57.895 1.31 0.00 0.00 3.77
1763 2150 2.746671 CAGTCCTGCTGGCTGCTG 60.747 66.667 17.45 16.04 41.42 4.41
1838 2225 6.669485 AAGTCGCAATTAAAACGTCAAATC 57.331 33.333 0.00 0.00 0.00 2.17
1846 2233 6.927933 ATACTGCAAAGTCGCAATTAAAAC 57.072 33.333 0.00 0.00 42.45 2.43
1868 2255 9.396022 CAACTTCACCACCTTTTATAGTCATAT 57.604 33.333 0.00 0.00 0.00 1.78
1884 2271 2.115427 TCCACTGAGACAACTTCACCA 58.885 47.619 0.00 0.00 0.00 4.17
1982 2370 5.419788 TCAAGGACTAAGCGGTATCTTAACA 59.580 40.000 0.00 0.00 0.00 2.41
2021 2409 6.357579 TCTTAATTCCACAAATGCCATGTT 57.642 33.333 0.00 0.00 0.00 2.71
2552 2945 5.363101 GACAATCCAGCAGACAATATCTCA 58.637 41.667 0.00 0.00 34.41 3.27
2724 3335 2.436417 CCACGTTTCCACATGGAGATT 58.564 47.619 0.00 0.00 46.36 2.40
2726 3337 0.605319 GCCACGTTTCCACATGGAGA 60.605 55.000 0.00 0.00 46.36 3.71
2727 3338 0.606401 AGCCACGTTTCCACATGGAG 60.606 55.000 0.00 0.00 46.36 3.86
2728 3339 0.605319 GAGCCACGTTTCCACATGGA 60.605 55.000 0.00 0.00 43.73 3.41
2729 3340 1.586154 GGAGCCACGTTTCCACATGG 61.586 60.000 0.00 0.00 33.55 3.66
2730 3341 1.586154 GGGAGCCACGTTTCCACATG 61.586 60.000 11.42 0.00 35.09 3.21
2731 3342 1.303317 GGGAGCCACGTTTCCACAT 60.303 57.895 11.42 0.00 35.09 3.21
2732 3343 1.990160 AAGGGAGCCACGTTTCCACA 61.990 55.000 11.42 0.00 35.09 4.17
2733 3344 0.822121 AAAGGGAGCCACGTTTCCAC 60.822 55.000 11.42 3.13 35.09 4.02
2734 3345 0.106419 AAAAGGGAGCCACGTTTCCA 60.106 50.000 11.42 0.00 35.09 3.53
2735 3346 1.000607 GAAAAAGGGAGCCACGTTTCC 60.001 52.381 2.59 2.59 0.00 3.13
2736 3347 1.679153 TGAAAAAGGGAGCCACGTTTC 59.321 47.619 0.00 0.00 0.00 2.78
2737 3348 1.770294 TGAAAAAGGGAGCCACGTTT 58.230 45.000 0.00 0.00 0.00 3.60
2738 3349 1.770294 TTGAAAAAGGGAGCCACGTT 58.230 45.000 0.00 0.00 0.00 3.99
2739 3350 1.995376 ATTGAAAAAGGGAGCCACGT 58.005 45.000 0.00 0.00 0.00 4.49
2740 3351 4.718940 ATTATTGAAAAAGGGAGCCACG 57.281 40.909 0.00 0.00 0.00 4.94
2741 3352 6.535150 GCTAAATTATTGAAAAAGGGAGCCAC 59.465 38.462 0.00 0.00 0.00 5.01
2742 3353 6.212388 TGCTAAATTATTGAAAAAGGGAGCCA 59.788 34.615 0.00 0.00 0.00 4.75
2743 3354 6.639563 TGCTAAATTATTGAAAAAGGGAGCC 58.360 36.000 0.00 0.00 0.00 4.70
2922 3535 8.932791 AGATTACCAAACACTCGTTAACTAATG 58.067 33.333 3.71 0.00 33.99 1.90
3056 3990 4.925068 ACAAGCACACAATCTTGAAAGTC 58.075 39.130 8.72 0.00 41.50 3.01
3388 4380 6.103330 ACGAAAAGCAACAACCTTAAACATT 58.897 32.000 0.00 0.00 0.00 2.71
3631 4625 2.622942 TGAACGGAAGCAAGCAAGATTT 59.377 40.909 0.00 0.00 0.00 2.17
3633 4627 1.808945 CTGAACGGAAGCAAGCAAGAT 59.191 47.619 0.00 0.00 0.00 2.40
3642 4636 3.056952 CATTGTATGCTGAACGGAAGC 57.943 47.619 0.00 0.00 41.22 3.86
3720 4714 0.320421 TGGCAAAGACGTCAGCTACC 60.320 55.000 19.50 12.48 0.00 3.18
3877 4871 6.749923 ATGTGAAGTTCTAATCAAAGCTCC 57.250 37.500 4.17 0.00 0.00 4.70
3939 4933 5.927819 AGAGCCACAAAATCATTCCAAAAA 58.072 33.333 0.00 0.00 0.00 1.94
4267 5261 8.311109 TCTCTCATATACACTTGCACTGTTAAA 58.689 33.333 1.61 0.00 0.00 1.52
4324 5318 3.057315 GGCAAATGCAGCTCAGAACTAAA 60.057 43.478 7.80 0.00 44.36 1.85
4488 5482 3.903714 TCTGTCTTGTCATCCTTTCCTGA 59.096 43.478 0.00 0.00 0.00 3.86
4539 5533 1.086696 CAACAACTATGGCTCCACGG 58.913 55.000 0.00 0.00 0.00 4.94
4560 5554 0.895100 TGCAGATGTGGTTGGCTTCC 60.895 55.000 0.00 0.00 0.00 3.46
4566 5560 5.278315 CCTTGATATCATGCAGATGTGGTTG 60.278 44.000 6.17 0.00 37.57 3.77
4572 5566 3.009805 TCCCCCTTGATATCATGCAGATG 59.990 47.826 6.17 0.00 37.57 2.90
4620 5614 1.606668 TGACCCAAAACTGCAATCGTC 59.393 47.619 0.00 0.00 0.00 4.20
4623 5617 3.733443 AACTGACCCAAAACTGCAATC 57.267 42.857 0.00 0.00 0.00 2.67
4682 5676 6.929625 TCCTGATTAGCAGTATCTAAGATGC 58.070 40.000 0.00 0.00 43.33 3.91
4714 5708 8.298729 TCTATCAGTATATGATCGAAAGCCAT 57.701 34.615 0.00 0.00 46.01 4.40
4721 5715 8.835439 GCTGAGATTCTATCAGTATATGATCGA 58.165 37.037 5.00 0.00 46.01 3.59
4722 5716 8.075574 GGCTGAGATTCTATCAGTATATGATCG 58.924 40.741 5.00 0.00 46.01 3.69
4752 5746 5.364157 ACTGGGAATTAGACTCACTGTATCC 59.636 44.000 0.00 0.00 0.00 2.59
4759 5753 3.192844 TGACGACTGGGAATTAGACTCAC 59.807 47.826 0.00 0.00 0.00 3.51
4770 5764 0.684535 TGCTGAATTGACGACTGGGA 59.315 50.000 0.00 0.00 0.00 4.37
4782 5776 2.119801 CAGTACCTGCCTTGCTGAAT 57.880 50.000 0.00 0.00 0.00 2.57
4797 5791 2.362736 ACCATAAGAGTCGTCGCAGTA 58.637 47.619 0.00 0.00 0.00 2.74
4810 5804 7.335422 AGCTGTATGAGAACTTCAAACCATAAG 59.665 37.037 0.00 0.00 39.77 1.73
4826 5823 1.306148 CCATGCCACAGCTGTATGAG 58.694 55.000 23.68 11.45 40.80 2.90
4831 5828 2.987547 GCACCATGCCACAGCTGT 60.988 61.111 15.25 15.25 37.42 4.40
4847 5844 2.620242 CACCAGCAATGGTAAAATGGC 58.380 47.619 0.00 0.00 40.85 4.40
4848 5845 2.093553 CCCACCAGCAATGGTAAAATGG 60.094 50.000 0.00 0.00 40.85 3.16
4850 5847 3.099141 CTCCCACCAGCAATGGTAAAAT 58.901 45.455 0.00 0.00 40.85 1.82
4851 5848 2.524306 CTCCCACCAGCAATGGTAAAA 58.476 47.619 0.00 0.00 40.85 1.52
4855 5852 2.036256 GCTCCCACCAGCAATGGT 59.964 61.111 0.00 0.00 44.23 3.55
4863 5865 3.680786 CACTCGTCGCTCCCACCA 61.681 66.667 0.00 0.00 0.00 4.17
4876 5878 0.309922 TTCCACACGACGAGACACTC 59.690 55.000 0.00 0.00 0.00 3.51
4879 5881 0.671796 ACATTCCACACGACGAGACA 59.328 50.000 0.00 0.00 0.00 3.41
4880 5882 1.455786 CAACATTCCACACGACGAGAC 59.544 52.381 0.00 0.00 0.00 3.36
4881 5883 1.067974 ACAACATTCCACACGACGAGA 59.932 47.619 0.00 0.00 0.00 4.04
4889 5891 4.149511 TCTTCAGACACAACATTCCACA 57.850 40.909 0.00 0.00 0.00 4.17
4915 5917 4.649088 AAGTTTTGGTGCTTCTGGTTAC 57.351 40.909 0.00 0.00 0.00 2.50
4934 5936 3.473625 ACACGGGAGAACCAAAACTAAG 58.526 45.455 0.00 0.00 40.22 2.18
4935 5937 3.564053 ACACGGGAGAACCAAAACTAA 57.436 42.857 0.00 0.00 40.22 2.24
4936 5938 3.207778 CAACACGGGAGAACCAAAACTA 58.792 45.455 0.00 0.00 40.22 2.24
4966 5968 7.120726 AGGATAACTTTCACATCCGTTTAAAGG 59.879 37.037 0.81 0.81 42.60 3.11
4970 5974 6.759827 GCTAGGATAACTTTCACATCCGTTTA 59.240 38.462 0.00 0.00 42.60 2.01
4973 5977 4.694339 GCTAGGATAACTTTCACATCCGT 58.306 43.478 0.00 0.00 42.60 4.69
4974 5978 3.736252 CGCTAGGATAACTTTCACATCCG 59.264 47.826 0.00 0.00 42.60 4.18
4976 5980 5.581085 ACAACGCTAGGATAACTTTCACATC 59.419 40.000 0.00 0.00 0.00 3.06
4981 5985 5.519206 CACCTACAACGCTAGGATAACTTTC 59.481 44.000 3.87 0.00 37.35 2.62
5028 6032 7.739295 ACACAAGCACTTAGAACATTTATACG 58.261 34.615 0.00 0.00 0.00 3.06
5040 6044 5.950883 TGCTACTAGTACACAAGCACTTAG 58.049 41.667 12.26 0.00 38.22 2.18
5047 6051 7.435068 ACCAAAATTGCTACTAGTACACAAG 57.565 36.000 15.31 3.24 0.00 3.16
5054 6058 8.052748 TGGAATGATACCAAAATTGCTACTAGT 58.947 33.333 0.00 0.00 34.25 2.57
5055 6059 8.450578 TGGAATGATACCAAAATTGCTACTAG 57.549 34.615 0.00 0.00 34.25 2.57
5057 6061 6.183360 GCTGGAATGATACCAAAATTGCTACT 60.183 38.462 0.00 0.00 36.95 2.57
5058 6062 5.979517 GCTGGAATGATACCAAAATTGCTAC 59.020 40.000 0.00 0.00 36.95 3.58
5116 6128 1.029947 GGTACCCTGCATCAAACCGG 61.030 60.000 0.00 0.00 0.00 5.28
5149 6171 3.627395 ATGGATGTAGACTTCCGCAAA 57.373 42.857 9.37 0.00 41.58 3.68
5487 6509 2.629763 GTCGACTGCGGCGTTTTT 59.370 55.556 8.70 0.00 38.28 1.94
5495 6517 3.126722 GATTTCGGCGTCGACTGCG 62.127 63.158 13.73 16.59 45.92 5.18
5496 6518 1.805945 AGATTTCGGCGTCGACTGC 60.806 57.895 13.73 19.52 45.92 4.40
5497 6519 1.991430 CAGATTTCGGCGTCGACTG 59.009 57.895 13.73 13.33 45.92 3.51
5498 6520 1.805945 GCAGATTTCGGCGTCGACT 60.806 57.895 13.73 2.63 45.92 4.18
5499 6521 1.805945 AGCAGATTTCGGCGTCGAC 60.806 57.895 13.73 5.18 45.92 4.20
5500 6522 1.805539 CAGCAGATTTCGGCGTCGA 60.806 57.895 8.66 8.66 44.44 4.20
5501 6523 2.697425 CAGCAGATTTCGGCGTCG 59.303 61.111 1.15 1.15 41.91 5.12
5589 6614 2.213499 CCAGACGTGCTTTTCTCTTGT 58.787 47.619 0.00 0.00 0.00 3.16
5636 6661 1.757699 GAGGCGAATCTGGAAGGTAGT 59.242 52.381 0.00 0.00 0.00 2.73
5640 6665 1.147153 GGGAGGCGAATCTGGAAGG 59.853 63.158 0.00 0.00 0.00 3.46
5734 6759 2.404215 CTCTGCTCTTTTTCCGACGAA 58.596 47.619 0.00 0.00 0.00 3.85
5735 6760 1.336887 CCTCTGCTCTTTTTCCGACGA 60.337 52.381 0.00 0.00 0.00 4.20
5738 6763 2.930826 AACCTCTGCTCTTTTTCCGA 57.069 45.000 0.00 0.00 0.00 4.55
5762 6787 2.436109 GGTGGAAAGGCTGCCTCA 59.564 61.111 23.61 13.26 30.89 3.86


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

AutoCloner maintained by Alex Coulton.