Multiple sequence alignment - TraesCS7B01G285100

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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 TraesCS7B01G285100 chr7B 100.000 5667 0 0 405 6071 518907032 518912698 0.000000e+00 10466.0
1 TraesCS7B01G285100 chr7B 100.000 300 0 0 6258 6557 518912885 518913184 7.430000e-154 555.0
2 TraesCS7B01G285100 chr7B 94.253 174 8 1 5740 5911 497576613 497576786 1.400000e-66 265.0
3 TraesCS7B01G285100 chr7B 92.655 177 11 1 5740 5914 155387834 155387658 3.030000e-63 254.0
4 TraesCS7B01G285100 chr7B 100.000 45 0 0 1 45 518906628 518906672 4.210000e-12 84.2
5 TraesCS7B01G285100 chr7B 94.340 53 1 1 4002 4052 213466332 213466280 5.450000e-11 80.5
6 TraesCS7B01G285100 chr7B 91.071 56 3 2 4003 4056 741667153 741667098 2.540000e-09 75.0
7 TraesCS7B01G285100 chr7B 89.362 47 5 0 5973 6019 455535582 455535536 7.100000e-05 60.2
8 TraesCS7B01G285100 chr7D 96.814 2731 69 13 2266 4986 490346280 490349002 0.000000e+00 4545.0
9 TraesCS7B01G285100 chr7D 92.545 1878 89 13 405 2252 490344328 490346184 0.000000e+00 2645.0
10 TraesCS7B01G285100 chr7D 94.358 709 26 11 5051 5750 490349092 490349795 0.000000e+00 1075.0
11 TraesCS7B01G285100 chr7D 93.056 288 16 3 6273 6557 490349927 490350213 1.020000e-112 418.0
12 TraesCS7B01G285100 chr7D 88.770 187 20 1 5726 5911 32870167 32870353 1.840000e-55 228.0
13 TraesCS7B01G285100 chr7D 97.692 130 3 0 5910 6039 490349794 490349923 2.380000e-54 224.0
14 TraesCS7B01G285100 chr7D 87.135 171 20 1 5741 5911 271768744 271768576 6.710000e-45 193.0
15 TraesCS7B01G285100 chr7D 94.949 99 4 1 4971 5069 342585476 342585379 3.170000e-33 154.0
16 TraesCS7B01G285100 chr7D 95.833 48 2 0 4008 4055 136810814 136810767 1.960000e-10 78.7
17 TraesCS7B01G285100 chr7D 92.308 52 4 0 4005 4056 99195586 99195637 2.540000e-09 75.0
18 TraesCS7B01G285100 chr7A 91.387 1846 87 27 440 2248 556657943 556659753 0.000000e+00 2462.0
19 TraesCS7B01G285100 chr7A 95.218 941 38 5 4045 4981 556661691 556662628 0.000000e+00 1482.0
20 TraesCS7B01G285100 chr7A 88.955 1168 68 21 2285 3422 556659746 556660882 0.000000e+00 1386.0
21 TraesCS7B01G285100 chr7A 94.556 698 30 3 5061 5750 556662625 556663322 0.000000e+00 1072.0
22 TraesCS7B01G285100 chr7A 89.254 335 25 7 3418 3748 556660916 556661243 6.120000e-110 409.0
23 TraesCS7B01G285100 chr7A 89.161 286 22 5 6273 6557 556663459 556663736 1.350000e-91 348.0
24 TraesCS7B01G285100 chr7A 95.349 129 6 0 5910 6038 556663321 556663449 8.620000e-49 206.0
25 TraesCS7B01G285100 chr7A 91.954 87 5 1 3838 3922 556661255 556661341 3.210000e-23 121.0
26 TraesCS7B01G285100 chr7A 97.778 45 1 0 4008 4052 252187641 252187597 1.960000e-10 78.7
27 TraesCS7B01G285100 chr6D 95.238 168 7 1 5744 5911 90890448 90890282 1.400000e-66 265.0
28 TraesCS7B01G285100 chr6D 96.774 93 3 0 4970 5062 36675388 36675480 8.800000e-34 156.0
29 TraesCS7B01G285100 chr6D 97.619 42 1 0 4008 4049 115051911 115051870 9.120000e-09 73.1
30 TraesCS7B01G285100 chr6D 93.182 44 3 0 4008 4051 56554343 56554386 1.530000e-06 65.8
31 TraesCS7B01G285100 chr6D 90.000 50 3 1 4003 4050 299191300 299191349 5.490000e-06 63.9
32 TraesCS7B01G285100 chr1B 95.732 164 7 0 5748 5911 582929882 582929719 1.400000e-66 265.0
33 TraesCS7B01G285100 chr1B 91.071 56 4 1 4002 4057 115751937 115751991 2.540000e-09 75.0
34 TraesCS7B01G285100 chr5B 95.706 163 7 0 5749 5911 660485148 660485310 5.040000e-66 263.0
35 TraesCS7B01G285100 chr5B 95.181 166 8 0 5749 5914 701551811 701551646 5.040000e-66 263.0
36 TraesCS7B01G285100 chr5B 94.643 168 9 0 5745 5912 243426369 243426536 1.810000e-65 261.0
37 TraesCS7B01G285100 chr5B 97.826 92 1 1 4978 5068 345770208 345770299 2.450000e-34 158.0
38 TraesCS7B01G285100 chr5B 77.778 180 35 3 5735 5911 265434072 265434249 8.990000e-19 106.0
39 TraesCS7B01G285100 chr2B 95.706 163 7 0 5749 5911 664125200 664125038 5.040000e-66 263.0
40 TraesCS7B01G285100 chr3D 94.118 170 10 0 5749 5918 604180845 604180676 6.520000e-65 259.0
41 TraesCS7B01G285100 chr3D 94.949 99 4 1 4969 5066 54783418 54783320 3.170000e-33 154.0
42 TraesCS7B01G285100 chr3D 92.453 53 4 0 4003 4055 357439838 357439786 7.050000e-10 76.8
43 TraesCS7B01G285100 chr3D 92.308 52 2 1 4003 4052 610206618 610206669 9.120000e-09 73.1
44 TraesCS7B01G285100 chr3B 86.034 179 21 3 5734 5911 653510005 653510180 8.680000e-44 189.0
45 TraesCS7B01G285100 chr3B 96.000 50 1 1 4003 4051 776359580 776359629 5.450000e-11 80.5
46 TraesCS7B01G285100 chr5A 85.876 177 17 5 5738 5911 488629113 488629284 1.450000e-41 182.0
47 TraesCS7B01G285100 chr5A 89.796 49 4 1 5976 6024 482620027 482619980 1.970000e-05 62.1
48 TraesCS7B01G285100 chr4A 96.809 94 3 0 4974 5067 708630107 708630014 2.450000e-34 158.0
49 TraesCS7B01G285100 chr2A 97.802 91 2 0 4978 5068 407739182 407739272 2.450000e-34 158.0
50 TraesCS7B01G285100 chrUn 96.809 94 2 1 4976 5069 2693228 2693320 8.800000e-34 156.0
51 TraesCS7B01G285100 chrUn 93.023 43 3 0 4008 4050 287061787 287061829 5.490000e-06 63.9
52 TraesCS7B01G285100 chrUn 95.000 40 2 0 4011 4050 348315147 348315108 5.490000e-06 63.9
53 TraesCS7B01G285100 chrUn 95.000 40 2 0 4011 4050 377707889 377707850 5.490000e-06 63.9
54 TraesCS7B01G285100 chrUn 93.023 43 3 0 4008 4050 382593731 382593773 5.490000e-06 63.9
55 TraesCS7B01G285100 chrUn 93.023 43 3 0 4008 4050 427230657 427230699 5.490000e-06 63.9
56 TraesCS7B01G285100 chrUn 100.000 28 0 0 4023 4050 217847776 217847749 1.200000e-02 52.8
57 TraesCS7B01G285100 chrUn 91.892 37 3 0 4013 4049 259481111 259481147 1.200000e-02 52.8
58 TraesCS7B01G285100 chrUn 100.000 28 0 0 4023 4050 265151708 265151681 1.200000e-02 52.8
59 TraesCS7B01G285100 chr6A 89.655 116 8 4 4978 5090 558041266 558041380 1.910000e-30 145.0
60 TraesCS7B01G285100 chr6A 91.429 105 8 1 4960 5063 7122647 7122751 6.850000e-30 143.0
61 TraesCS7B01G285100 chr2D 96.000 50 2 0 4006 4055 188810560 188810511 1.520000e-11 82.4
62 TraesCS7B01G285100 chr2D 92.453 53 4 0 4003 4055 594457053 594457001 7.050000e-10 76.8
63 TraesCS7B01G285100 chr5D 94.118 51 3 0 4001 4051 422943152 422943202 1.960000e-10 78.7
64 TraesCS7B01G285100 chr5D 100.000 41 0 0 4008 4048 458870300 458870340 7.050000e-10 76.8
65 TraesCS7B01G285100 chr5D 95.556 45 2 0 4007 4051 230018324 230018368 9.120000e-09 73.1
66 TraesCS7B01G285100 chr5D 95.455 44 2 0 4008 4051 381151957 381151914 3.280000e-08 71.3
67 TraesCS7B01G285100 chr4B 91.071 56 3 1 4002 4055 277407942 277407997 2.540000e-09 75.0
68 TraesCS7B01G285100 chr1D 94.000 50 2 1 4001 4050 326479981 326480029 2.540000e-09 75.0
69 TraesCS7B01G285100 chr1D 97.619 42 1 0 4008 4049 356862350 356862309 9.120000e-09 73.1
70 TraesCS7B01G285100 chr1D 90.909 55 2 2 4003 4054 46311284 46311338 3.280000e-08 71.3
71 TraesCS7B01G285100 chr1D 93.750 48 2 1 4008 4054 111518820 111518773 3.280000e-08 71.3
72 TraesCS7B01G285100 chr1D 92.157 51 3 1 4001 4051 251707275 251707226 3.280000e-08 71.3
73 TraesCS7B01G285100 chr1A 94.000 50 2 1 4001 4050 413795991 413795943 2.540000e-09 75.0
74 TraesCS7B01G285100 chr1A 92.157 51 2 1 4003 4051 209362107 209362157 3.280000e-08 71.3
75 TraesCS7B01G285100 chr4D 95.652 46 1 1 4005 4049 391719294 391719339 9.120000e-09 73.1
76 TraesCS7B01G285100 chr4D 95.455 44 2 0 4008 4051 402527965 402528008 3.280000e-08 71.3
77 TraesCS7B01G285100 chr4D 95.349 43 2 0 4008 4050 64347405 64347447 1.180000e-07 69.4
78 TraesCS7B01G285100 chr4D 95.349 43 2 0 4008 4050 245478382 245478424 1.180000e-07 69.4
79 TraesCS7B01G285100 chr4D 95.349 43 2 0 4008 4050 282079988 282079946 1.180000e-07 69.4
80 TraesCS7B01G285100 chr4D 95.238 42 2 0 4009 4050 31718474 31718433 4.240000e-07 67.6
81 TraesCS7B01G285100 chr4D 91.667 48 3 1 4008 4055 23320489 23320443 1.530000e-06 65.8
82 TraesCS7B01G285100 chr4D 90.000 50 4 1 4001 4050 505657727 505657775 5.490000e-06 63.9


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 TraesCS7B01G285100 chr7B 518906628 518913184 6556 False 3701.733333 10466 100.00000 1 6557 3 chr7B.!!$F2 6556
1 TraesCS7B01G285100 chr7D 490344328 490350213 5885 False 1781.400000 4545 94.89300 405 6557 5 chr7D.!!$F3 6152
2 TraesCS7B01G285100 chr7A 556657943 556663736 5793 False 935.750000 2462 91.97925 440 6557 8 chr7A.!!$F1 6117

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
32 33 0.099082 GAGGGAAGTCGAGCTACGTG 59.901 60.000 0.00 0.0 43.13 4.49 F
873 912 0.245266 TGTAGATTTCGCTCGGTGCA 59.755 50.000 2.75 0.0 43.06 4.57 F
1551 1596 1.000283 CAGAGATATGCCTCGGTGGAC 60.000 57.143 0.00 0.0 38.19 4.02 F
2660 2800 3.780850 CTGGTTCTAGGGGGACAAATACT 59.219 47.826 0.00 0.0 0.00 2.12 F
3030 3197 0.106769 ACTGTCATGTGTTGTGGGCA 60.107 50.000 0.00 0.0 0.00 5.36 F
3590 3798 1.406539 CATTGGTTATGCTCAGGTGGC 59.593 52.381 0.00 0.0 0.00 5.01 F
5080 5600 1.156736 ACTATGTTGCACCGCTTGTC 58.843 50.000 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1239 1284 0.249238 CGAGGCTGATCTCCGGAAAG 60.249 60.000 5.23 1.98 0.00 2.62 R
1914 1971 1.965643 ACAGCAAGGCATGTGAATGTT 59.034 42.857 0.00 0.00 0.00 2.71 R
2979 3145 0.179004 ATGCACCAAGAAACGGGACA 60.179 50.000 0.00 0.00 0.00 4.02 R
4561 5052 1.400494 ACACAGCAAACGACCAAGAAC 59.600 47.619 0.00 0.00 0.00 3.01 R
4850 5341 1.302511 CCAGGGAAGGACAACACCG 60.303 63.158 0.00 0.00 34.73 4.94 R
5461 5992 0.325671 AGGAAATCCTCGCTCCTCCA 60.326 55.000 0.00 0.00 44.77 3.86 R
6050 6582 0.173708 CTCGTTCCCTTTCCTCGGAG 59.826 60.000 0.00 0.00 0.00 4.63 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
17 18 2.808315 CCACTGATCGACGGAGGG 59.192 66.667 0.00 0.00 33.04 4.30
18 19 1.753078 CCACTGATCGACGGAGGGA 60.753 63.158 0.00 0.00 33.04 4.20
19 20 1.320344 CCACTGATCGACGGAGGGAA 61.320 60.000 0.00 0.00 33.04 3.97
20 21 0.101399 CACTGATCGACGGAGGGAAG 59.899 60.000 0.00 0.00 0.00 3.46
21 22 0.323542 ACTGATCGACGGAGGGAAGT 60.324 55.000 0.00 0.00 0.00 3.01
22 23 0.382515 CTGATCGACGGAGGGAAGTC 59.617 60.000 0.00 0.00 0.00 3.01
26 27 2.490685 GACGGAGGGAAGTCGAGC 59.509 66.667 0.00 0.00 0.00 5.03
27 28 2.035940 ACGGAGGGAAGTCGAGCT 59.964 61.111 0.00 0.00 0.00 4.09
28 29 0.747283 GACGGAGGGAAGTCGAGCTA 60.747 60.000 0.00 0.00 0.00 3.32
29 30 1.031029 ACGGAGGGAAGTCGAGCTAC 61.031 60.000 0.00 0.00 0.00 3.58
30 31 1.728672 GGAGGGAAGTCGAGCTACG 59.271 63.158 0.00 0.00 44.09 3.51
31 32 1.031029 GGAGGGAAGTCGAGCTACGT 61.031 60.000 0.00 0.00 43.13 3.57
32 33 0.099082 GAGGGAAGTCGAGCTACGTG 59.901 60.000 0.00 0.00 43.13 4.49
33 34 1.516603 GGGAAGTCGAGCTACGTGC 60.517 63.158 0.00 0.00 43.13 5.34
42 43 3.423154 GCTACGTGCTGTGTGCCC 61.423 66.667 0.00 0.00 42.00 5.36
44 45 4.673298 TACGTGCTGTGTGCCCGG 62.673 66.667 0.00 0.00 46.47 5.73
544 562 2.660552 AGCAACGTCCAACGACCG 60.661 61.111 6.48 0.00 46.05 4.79
547 566 2.660552 AACGTCCAACGACCGCAG 60.661 61.111 6.48 0.00 46.05 5.18
620 639 0.608856 TGCACGGCTGGACAATCATT 60.609 50.000 0.00 0.00 0.00 2.57
724 761 4.364860 CGGGTTTTCAAATTTCGAAACCT 58.635 39.130 27.56 0.08 46.39 3.50
730 767 1.201414 CAAATTTCGAAACCTCCCCGG 59.799 52.381 13.81 0.00 39.35 5.73
873 912 0.245266 TGTAGATTTCGCTCGGTGCA 59.755 50.000 2.75 0.00 43.06 4.57
915 954 1.597663 CATTCCCGTTCGTTATCTGGC 59.402 52.381 0.00 0.00 0.00 4.85
918 957 1.881252 CCGTTCGTTATCTGGCCCG 60.881 63.158 0.00 0.00 0.00 6.13
1512 1557 3.747976 GCGGCGGCTGAAAATGGT 61.748 61.111 14.15 0.00 35.83 3.55
1515 1560 2.125952 GCGGCTGAAAATGGTGCC 60.126 61.111 0.00 0.00 41.76 5.01
1551 1596 1.000283 CAGAGATATGCCTCGGTGGAC 60.000 57.143 0.00 0.00 38.19 4.02
1771 1828 9.369904 TGTTATTAATTTCGTACCCAAGTCTAC 57.630 33.333 0.00 0.00 0.00 2.59
1811 1868 3.821748 TGAGATGGAGTATGTAGACGCT 58.178 45.455 0.00 0.00 0.00 5.07
1904 1961 5.640218 ATTTTGTGTTTCTTCGTGCATTG 57.360 34.783 0.00 0.00 0.00 2.82
1982 2039 8.601476 GGTCTTGTTTAAGTCTATTTATGGACG 58.399 37.037 1.29 0.00 42.33 4.79
2029 2086 5.440610 AGGAAGCAGGGAATTGTGTTATAG 58.559 41.667 0.00 0.00 0.00 1.31
2245 2302 8.882415 AATGCCATTGATAGCTTGAAATTAAG 57.118 30.769 0.00 0.00 0.00 1.85
2246 2303 7.408756 TGCCATTGATAGCTTGAAATTAAGT 57.591 32.000 0.00 0.00 0.00 2.24
2247 2304 8.518430 TGCCATTGATAGCTTGAAATTAAGTA 57.482 30.769 0.00 0.00 0.00 2.24
2248 2305 9.135189 TGCCATTGATAGCTTGAAATTAAGTAT 57.865 29.630 0.00 0.00 0.00 2.12
2437 2577 9.465985 GGGATTTGTTTAATTTTCGTCAAAGTA 57.534 29.630 0.00 0.00 0.00 2.24
2462 2602 7.948034 TGTAATCACCCGATTCCTTATTTTT 57.052 32.000 0.00 0.00 41.09 1.94
2660 2800 3.780850 CTGGTTCTAGGGGGACAAATACT 59.219 47.826 0.00 0.00 0.00 2.12
2665 2805 6.771267 GGTTCTAGGGGGACAAATACTAAATG 59.229 42.308 0.00 0.00 0.00 2.32
2819 2959 6.727824 TTTTCTGTGCTGCTAGAAACTATC 57.272 37.500 22.77 0.00 41.23 2.08
2846 2986 4.276926 CACTGATAAGGCCCTTGCTATTTC 59.723 45.833 6.16 0.00 37.74 2.17
2864 3004 7.814107 TGCTATTTCTGGATGTGAAAATTGAAC 59.186 33.333 0.00 0.00 37.05 3.18
2978 3144 4.344359 TTTGGGGGTAGAAAATTTGTGC 57.656 40.909 0.00 0.00 0.00 4.57
2979 3145 3.252554 TGGGGGTAGAAAATTTGTGCT 57.747 42.857 0.00 0.00 0.00 4.40
2980 3146 2.896685 TGGGGGTAGAAAATTTGTGCTG 59.103 45.455 0.00 0.00 0.00 4.41
2981 3147 2.897326 GGGGGTAGAAAATTTGTGCTGT 59.103 45.455 0.00 0.00 0.00 4.40
2982 3148 3.056821 GGGGGTAGAAAATTTGTGCTGTC 60.057 47.826 0.00 0.00 0.00 3.51
2984 3150 3.056821 GGGTAGAAAATTTGTGCTGTCCC 60.057 47.826 0.00 3.99 0.00 4.46
3030 3197 0.106769 ACTGTCATGTGTTGTGGGCA 60.107 50.000 0.00 0.00 0.00 5.36
3079 3247 5.389642 TTCGACATTGAATATCTTCGTGC 57.610 39.130 0.00 0.00 33.86 5.34
3125 3293 7.582667 TCGTTAACTGATGATGAATCTAGGA 57.417 36.000 3.71 0.00 36.15 2.94
3206 3374 9.753674 AGGAGAAGGTTGATTTCACAATATTAA 57.246 29.630 0.00 0.00 32.36 1.40
3583 3791 4.022849 GCCAGGATTACATTGGTTATGCTC 60.023 45.833 0.00 0.00 33.27 4.26
3590 3798 1.406539 CATTGGTTATGCTCAGGTGGC 59.593 52.381 0.00 0.00 0.00 5.01
3650 3859 4.516698 CACTTGGTTGTAGTGCTTTGAGAT 59.483 41.667 0.00 0.00 36.88 2.75
3814 4026 8.128322 ACATGGTATTGGCTTGTTGTTTAATA 57.872 30.769 0.00 0.00 0.00 0.98
3823 4035 9.988815 TTGGCTTGTTGTTTAATATGTAAACAT 57.011 25.926 16.78 0.63 44.00 2.71
3841 4053 9.112725 TGTAAACATGTATGATCTTGATTCCTG 57.887 33.333 0.00 0.00 0.00 3.86
3922 4137 9.923786 AAACTTAACAAAAAGTTGAAACAACAC 57.076 25.926 15.29 0.00 46.40 3.32
4003 4493 9.640963 ATGAACTTTAGTCTAATCTGTGTGTAC 57.359 33.333 0.00 0.00 0.00 2.90
4018 4508 9.682465 ATCTGTGTGTACTACTAGTGATCTAAA 57.318 33.333 5.39 0.00 0.00 1.85
4019 4509 9.511272 TCTGTGTGTACTACTAGTGATCTAAAA 57.489 33.333 5.39 0.00 0.00 1.52
4020 4510 9.776158 CTGTGTGTACTACTAGTGATCTAAAAG 57.224 37.037 5.39 0.00 0.00 2.27
4077 4567 6.877611 AGAGCTGGATTCGAAAAAGTTTAA 57.122 33.333 0.00 0.00 0.00 1.52
4142 4632 6.093771 CACTGAAAGCTCTTATCTTGCTCATT 59.906 38.462 0.00 0.00 37.60 2.57
4144 4634 7.176340 ACTGAAAGCTCTTATCTTGCTCATTTT 59.824 33.333 0.00 0.00 37.60 1.82
4580 5071 1.594518 CGTTCTTGGTCGTTTGCTGTG 60.595 52.381 0.00 0.00 0.00 3.66
4727 5218 8.641498 ATTTCCTGTCAAATGTTGAAGATACT 57.359 30.769 0.00 0.00 42.15 2.12
4823 5314 3.056107 CGGAAACTCATGTAGTCCTTCCA 60.056 47.826 18.59 0.00 42.03 3.53
4850 5341 1.299541 CACCACCTGTTGTGTCAGAC 58.700 55.000 0.00 0.00 43.85 3.51
4930 5421 4.134563 ACCACAATCAAGACACAGGTAAC 58.865 43.478 0.00 0.00 0.00 2.50
4936 5427 3.146066 TCAAGACACAGGTAACAATGGC 58.854 45.455 0.00 0.00 41.41 4.40
4969 5463 8.877864 ACTTGTGGAAATAGTAAATCAATCCA 57.122 30.769 0.00 0.00 33.32 3.41
4971 5465 9.956720 CTTGTGGAAATAGTAAATCAATCCATC 57.043 33.333 0.00 0.00 37.76 3.51
4986 5481 5.907662 TCAATCCATCATTTCTACTCCCTCT 59.092 40.000 0.00 0.00 0.00 3.69
4989 5484 5.777449 TCCATCATTTCTACTCCCTCTGTA 58.223 41.667 0.00 0.00 0.00 2.74
4990 5485 6.202331 TCCATCATTTCTACTCCCTCTGTAA 58.798 40.000 0.00 0.00 0.00 2.41
4991 5486 6.672218 TCCATCATTTCTACTCCCTCTGTAAA 59.328 38.462 0.00 0.00 0.00 2.01
4992 5487 6.763610 CCATCATTTCTACTCCCTCTGTAAAC 59.236 42.308 0.00 0.00 0.00 2.01
4993 5488 7.365117 CCATCATTTCTACTCCCTCTGTAAACT 60.365 40.741 0.00 0.00 0.00 2.66
5004 5499 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
5005 5500 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
5006 5501 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
5007 5502 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
5008 5503 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
5025 5520 9.570488 AAGAGCGTTTAGATTACTAAAGTAGTG 57.430 33.333 0.00 0.00 45.42 2.74
5026 5521 8.954350 AGAGCGTTTAGATTACTAAAGTAGTGA 58.046 33.333 0.00 0.00 45.42 3.41
5028 5523 9.733219 AGCGTTTAGATTACTAAAGTAGTGATC 57.267 33.333 10.62 10.62 46.38 2.92
5080 5600 1.156736 ACTATGTTGCACCGCTTGTC 58.843 50.000 0.00 0.00 0.00 3.18
5117 5640 5.287674 TCATTTTGCACAAGGAAATGGAA 57.712 34.783 16.77 1.16 39.82 3.53
5120 5643 5.809719 TTTTGCACAAGGAAATGGAAAAC 57.190 34.783 0.00 0.00 40.03 2.43
5123 5646 4.219115 TGCACAAGGAAATGGAAAACCTA 58.781 39.130 0.00 0.00 32.06 3.08
5170 5697 4.289672 ACCTTCAGATAACAGTCCATTGGT 59.710 41.667 1.86 0.00 0.00 3.67
5173 5700 6.349611 CCTTCAGATAACAGTCCATTGGTTTG 60.350 42.308 1.86 5.25 0.00 2.93
5180 5707 6.817765 AACAGTCCATTGGTTTGTACTATG 57.182 37.500 12.84 0.00 0.00 2.23
5187 5714 6.210385 TCCATTGGTTTGTACTATGCAAATGT 59.790 34.615 1.86 0.00 38.00 2.71
5249 5780 4.580580 ACAATCTTGTTTCAAGTCCCTGAC 59.419 41.667 8.93 0.00 38.47 3.51
5382 5913 2.025226 TGGACTACTCTCCAGGTTCGAT 60.025 50.000 0.00 0.00 35.23 3.59
5461 5992 2.379005 TGGACGACTATCTGCATCTGT 58.621 47.619 0.00 0.00 0.00 3.41
5708 6239 3.191371 AGCTAACTTTGGCATAGTTGTGC 59.809 43.478 26.80 26.51 44.31 4.57
5728 6259 8.442384 GTTGTGCTTTTTCTTTCAGAAATTGAA 58.558 29.630 0.00 0.00 43.06 2.69
5736 6268 6.391227 TCTTTCAGAAATTGAACACCCTTC 57.609 37.500 0.00 0.00 45.22 3.46
5750 6282 2.681344 CACCCTTCGGCTTGGTTAATAC 59.319 50.000 0.00 0.00 0.00 1.89
5751 6283 2.574824 ACCCTTCGGCTTGGTTAATACT 59.425 45.455 0.00 0.00 0.00 2.12
5752 6284 3.203716 CCCTTCGGCTTGGTTAATACTC 58.796 50.000 0.00 0.00 0.00 2.59
5753 6285 3.203716 CCTTCGGCTTGGTTAATACTCC 58.796 50.000 0.00 0.00 0.00 3.85
5754 6286 2.994186 TCGGCTTGGTTAATACTCCC 57.006 50.000 0.00 0.00 0.00 4.30
5755 6287 2.474112 TCGGCTTGGTTAATACTCCCT 58.526 47.619 0.00 0.00 0.00 4.20
5756 6288 2.433239 TCGGCTTGGTTAATACTCCCTC 59.567 50.000 0.00 0.00 0.00 4.30
5757 6289 2.484947 CGGCTTGGTTAATACTCCCTCC 60.485 54.545 0.00 0.00 0.00 4.30
5758 6290 2.778270 GGCTTGGTTAATACTCCCTCCT 59.222 50.000 0.00 0.00 0.00 3.69
5759 6291 3.202373 GGCTTGGTTAATACTCCCTCCTT 59.798 47.826 0.00 0.00 0.00 3.36
5760 6292 4.325109 GGCTTGGTTAATACTCCCTCCTTT 60.325 45.833 0.00 0.00 0.00 3.11
5761 6293 4.882427 GCTTGGTTAATACTCCCTCCTTTC 59.118 45.833 0.00 0.00 0.00 2.62
5762 6294 5.437946 CTTGGTTAATACTCCCTCCTTTCC 58.562 45.833 0.00 0.00 0.00 3.13
5763 6295 4.706616 TGGTTAATACTCCCTCCTTTCCT 58.293 43.478 0.00 0.00 0.00 3.36
5764 6296 5.857134 TGGTTAATACTCCCTCCTTTCCTA 58.143 41.667 0.00 0.00 0.00 2.94
5765 6297 6.273889 TGGTTAATACTCCCTCCTTTCCTAA 58.726 40.000 0.00 0.00 0.00 2.69
5766 6298 6.736655 TGGTTAATACTCCCTCCTTTCCTAAA 59.263 38.462 0.00 0.00 0.00 1.85
5767 6299 7.407918 TGGTTAATACTCCCTCCTTTCCTAAAT 59.592 37.037 0.00 0.00 0.00 1.40
5768 6300 7.720074 GGTTAATACTCCCTCCTTTCCTAAATG 59.280 40.741 0.00 0.00 0.00 2.32
5769 6301 6.910259 AATACTCCCTCCTTTCCTAAATGT 57.090 37.500 0.00 0.00 0.00 2.71
5770 6302 9.510062 TTAATACTCCCTCCTTTCCTAAATGTA 57.490 33.333 0.00 0.00 0.00 2.29
5771 6303 8.401955 AATACTCCCTCCTTTCCTAAATGTAA 57.598 34.615 0.00 0.00 0.00 2.41
5772 6304 6.314899 ACTCCCTCCTTTCCTAAATGTAAG 57.685 41.667 0.00 0.00 0.00 2.34
5773 6305 5.791141 ACTCCCTCCTTTCCTAAATGTAAGT 59.209 40.000 0.00 0.00 0.00 2.24
5774 6306 6.070136 ACTCCCTCCTTTCCTAAATGTAAGTC 60.070 42.308 0.00 0.00 0.00 3.01
5775 6307 6.030082 TCCCTCCTTTCCTAAATGTAAGTCT 58.970 40.000 0.00 0.00 0.00 3.24
5776 6308 6.504279 TCCCTCCTTTCCTAAATGTAAGTCTT 59.496 38.462 0.00 0.00 0.00 3.01
5777 6309 7.018249 TCCCTCCTTTCCTAAATGTAAGTCTTT 59.982 37.037 0.00 0.00 0.00 2.52
5778 6310 7.121315 CCCTCCTTTCCTAAATGTAAGTCTTTG 59.879 40.741 0.00 0.00 0.00 2.77
5779 6311 7.665974 CCTCCTTTCCTAAATGTAAGTCTTTGT 59.334 37.037 0.00 0.00 0.00 2.83
5780 6312 9.720769 CTCCTTTCCTAAATGTAAGTCTTTGTA 57.279 33.333 0.00 0.00 0.00 2.41
5781 6313 9.720769 TCCTTTCCTAAATGTAAGTCTTTGTAG 57.279 33.333 0.00 0.00 0.00 2.74
5782 6314 9.720769 CCTTTCCTAAATGTAAGTCTTTGTAGA 57.279 33.333 0.00 0.00 0.00 2.59
5790 6322 8.779354 AATGTAAGTCTTTGTAGAGATTCCAC 57.221 34.615 0.00 0.00 0.00 4.02
5791 6323 7.540474 TGTAAGTCTTTGTAGAGATTCCACT 57.460 36.000 0.00 0.00 0.00 4.00
5792 6324 8.645814 TGTAAGTCTTTGTAGAGATTCCACTA 57.354 34.615 0.00 0.00 0.00 2.74
5793 6325 9.256228 TGTAAGTCTTTGTAGAGATTCCACTAT 57.744 33.333 0.00 0.00 0.00 2.12
5852 6384 8.970691 AGTTTAGATTCATTCATTTTGTTCCG 57.029 30.769 0.00 0.00 0.00 4.30
5853 6385 8.576442 AGTTTAGATTCATTCATTTTGTTCCGT 58.424 29.630 0.00 0.00 0.00 4.69
5854 6386 9.834628 GTTTAGATTCATTCATTTTGTTCCGTA 57.165 29.630 0.00 0.00 0.00 4.02
5857 6389 8.055279 AGATTCATTCATTTTGTTCCGTATGT 57.945 30.769 0.00 0.00 0.00 2.29
5858 6390 9.173021 AGATTCATTCATTTTGTTCCGTATGTA 57.827 29.630 0.00 0.00 0.00 2.29
5859 6391 9.438291 GATTCATTCATTTTGTTCCGTATGTAG 57.562 33.333 0.00 0.00 0.00 2.74
5860 6392 7.915293 TCATTCATTTTGTTCCGTATGTAGT 57.085 32.000 0.00 0.00 0.00 2.73
5861 6393 7.970384 TCATTCATTTTGTTCCGTATGTAGTC 58.030 34.615 0.00 0.00 0.00 2.59
5862 6394 6.730960 TTCATTTTGTTCCGTATGTAGTCC 57.269 37.500 0.00 0.00 0.00 3.85
5863 6395 5.795972 TCATTTTGTTCCGTATGTAGTCCA 58.204 37.500 0.00 0.00 0.00 4.02
5864 6396 5.640357 TCATTTTGTTCCGTATGTAGTCCAC 59.360 40.000 0.00 0.00 0.00 4.02
5865 6397 2.925578 TGTTCCGTATGTAGTCCACG 57.074 50.000 0.00 0.00 35.50 4.94
5866 6398 2.161855 TGTTCCGTATGTAGTCCACGT 58.838 47.619 0.00 0.00 33.93 4.49
5867 6399 3.342719 TGTTCCGTATGTAGTCCACGTA 58.657 45.455 0.00 0.00 33.93 3.57
5868 6400 3.374988 TGTTCCGTATGTAGTCCACGTAG 59.625 47.826 0.00 0.00 33.93 3.51
5886 6418 5.952033 ACGTAGTGGAATCTCTACAAAGAC 58.048 41.667 13.06 0.00 42.51 3.01
5887 6419 5.711036 ACGTAGTGGAATCTCTACAAAGACT 59.289 40.000 13.06 0.00 42.51 3.24
5888 6420 6.208994 ACGTAGTGGAATCTCTACAAAGACTT 59.791 38.462 13.06 0.00 42.51 3.01
5889 6421 7.392673 ACGTAGTGGAATCTCTACAAAGACTTA 59.607 37.037 13.06 0.00 42.51 2.24
5890 6422 8.407064 CGTAGTGGAATCTCTACAAAGACTTAT 58.593 37.037 13.06 0.00 38.94 1.73
5904 6436 8.943909 ACAAAGACTTATATTTAGGAACGGAG 57.056 34.615 0.00 0.00 0.00 4.63
5905 6437 7.985752 ACAAAGACTTATATTTAGGAACGGAGG 59.014 37.037 0.00 0.00 0.00 4.30
5906 6438 7.909485 AAGACTTATATTTAGGAACGGAGGA 57.091 36.000 0.00 0.00 0.00 3.71
5907 6439 7.909485 AGACTTATATTTAGGAACGGAGGAA 57.091 36.000 0.00 0.00 0.00 3.36
5908 6440 7.953752 AGACTTATATTTAGGAACGGAGGAAG 58.046 38.462 0.00 0.00 0.00 3.46
5909 6441 7.564292 AGACTTATATTTAGGAACGGAGGAAGT 59.436 37.037 0.00 0.00 0.00 3.01
5910 6442 8.773033 ACTTATATTTAGGAACGGAGGAAGTA 57.227 34.615 0.00 0.00 0.00 2.24
5911 6443 8.858094 ACTTATATTTAGGAACGGAGGAAGTAG 58.142 37.037 0.00 0.00 0.00 2.57
5912 6444 9.075678 CTTATATTTAGGAACGGAGGAAGTAGA 57.924 37.037 0.00 0.00 0.00 2.59
5913 6445 7.909485 ATATTTAGGAACGGAGGAAGTAGAA 57.091 36.000 0.00 0.00 0.00 2.10
5914 6446 5.397142 TTTAGGAACGGAGGAAGTAGAAC 57.603 43.478 0.00 0.00 0.00 3.01
5996 6528 2.422803 GCCTAATGTATGGCTGGAACCA 60.423 50.000 0.00 0.00 45.26 3.67
6038 6570 7.657761 TGGTCAAATTTGTTTACTTGTGTTTGT 59.342 29.630 17.47 0.00 0.00 2.83
6039 6571 9.141400 GGTCAAATTTGTTTACTTGTGTTTGTA 57.859 29.630 17.47 0.00 0.00 2.41
6046 6578 9.915629 TTTGTTTACTTGTGTTTGTATCTTTGT 57.084 25.926 0.00 0.00 0.00 2.83
6047 6579 9.562583 TTGTTTACTTGTGTTTGTATCTTTGTC 57.437 29.630 0.00 0.00 0.00 3.18
6048 6580 8.952278 TGTTTACTTGTGTTTGTATCTTTGTCT 58.048 29.630 0.00 0.00 0.00 3.41
6051 6583 9.826574 TTACTTGTGTTTGTATCTTTGTCTACT 57.173 29.630 0.00 0.00 0.00 2.57
6052 6584 8.366671 ACTTGTGTTTGTATCTTTGTCTACTC 57.633 34.615 0.00 0.00 0.00 2.59
6053 6585 7.441458 ACTTGTGTTTGTATCTTTGTCTACTCC 59.559 37.037 0.00 0.00 0.00 3.85
6054 6586 5.924254 TGTGTTTGTATCTTTGTCTACTCCG 59.076 40.000 0.00 0.00 0.00 4.63
6055 6587 6.154445 GTGTTTGTATCTTTGTCTACTCCGA 58.846 40.000 0.00 0.00 0.00 4.55
6056 6588 6.308282 GTGTTTGTATCTTTGTCTACTCCGAG 59.692 42.308 0.00 0.00 0.00 4.63
6057 6589 5.578005 TTGTATCTTTGTCTACTCCGAGG 57.422 43.478 0.00 0.00 0.00 4.63
6058 6590 4.851843 TGTATCTTTGTCTACTCCGAGGA 58.148 43.478 0.00 0.00 0.00 3.71
6059 6591 5.258841 TGTATCTTTGTCTACTCCGAGGAA 58.741 41.667 0.00 0.00 0.00 3.36
6060 6592 5.713389 TGTATCTTTGTCTACTCCGAGGAAA 59.287 40.000 0.00 0.00 0.00 3.13
6061 6593 4.785511 TCTTTGTCTACTCCGAGGAAAG 57.214 45.455 0.00 0.00 0.00 2.62
6062 6594 3.510360 TCTTTGTCTACTCCGAGGAAAGG 59.490 47.826 0.00 0.00 0.00 3.11
6063 6595 1.848652 TGTCTACTCCGAGGAAAGGG 58.151 55.000 0.00 0.00 0.00 3.95
6064 6596 1.356738 TGTCTACTCCGAGGAAAGGGA 59.643 52.381 0.00 0.00 0.00 4.20
6065 6597 2.225192 TGTCTACTCCGAGGAAAGGGAA 60.225 50.000 0.00 0.00 0.00 3.97
6066 6598 2.166050 GTCTACTCCGAGGAAAGGGAAC 59.834 54.545 0.00 0.00 0.00 3.62
6067 6599 1.134560 CTACTCCGAGGAAAGGGAACG 59.865 57.143 0.00 0.00 0.00 3.95
6068 6600 0.541296 ACTCCGAGGAAAGGGAACGA 60.541 55.000 0.00 0.00 0.00 3.85
6069 6601 0.173708 CTCCGAGGAAAGGGAACGAG 59.826 60.000 0.00 0.00 0.00 4.18
6070 6602 0.251474 TCCGAGGAAAGGGAACGAGA 60.251 55.000 0.00 0.00 0.00 4.04
6314 6846 7.523293 TTACATGTGGAATCAAACATTCACT 57.477 32.000 9.11 0.00 34.81 3.41
6328 6860 4.010349 ACATTCACTTAACCTAGGCTTGC 58.990 43.478 9.30 0.00 0.00 4.01
6359 6891 2.799126 TTAGTGCCTAACCCCATGTG 57.201 50.000 0.00 0.00 0.00 3.21
6387 6919 2.037902 TGCGGTGAAAATCAGTACTGGA 59.962 45.455 22.48 9.94 0.00 3.86
6413 6945 1.177401 GGGAGGAAGTTTCATGCCAC 58.823 55.000 11.43 0.00 46.76 5.01
6419 6951 0.467290 AAGTTTCATGCCACGTGGGT 60.467 50.000 34.58 0.55 39.65 4.51
6505 7038 6.432783 TGGAAGATGAAACATGGAACGTTATT 59.567 34.615 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.320344 TTCCCTCCGTCGATCAGTGG 61.320 60.000 0.00 0.00 0.00 4.00
1 2 0.101399 CTTCCCTCCGTCGATCAGTG 59.899 60.000 0.00 0.00 0.00 3.66
2 3 0.323542 ACTTCCCTCCGTCGATCAGT 60.324 55.000 0.00 0.00 0.00 3.41
3 4 0.382515 GACTTCCCTCCGTCGATCAG 59.617 60.000 0.00 0.00 0.00 2.90
4 5 2.490165 GACTTCCCTCCGTCGATCA 58.510 57.895 0.00 0.00 0.00 2.92
9 10 0.747283 TAGCTCGACTTCCCTCCGTC 60.747 60.000 0.00 0.00 0.00 4.79
10 11 1.031029 GTAGCTCGACTTCCCTCCGT 61.031 60.000 0.00 0.00 0.00 4.69
11 12 1.728672 GTAGCTCGACTTCCCTCCG 59.271 63.158 0.00 0.00 0.00 4.63
12 13 1.031029 ACGTAGCTCGACTTCCCTCC 61.031 60.000 11.64 0.00 42.86 4.30
13 14 0.099082 CACGTAGCTCGACTTCCCTC 59.901 60.000 11.64 0.00 42.86 4.30
14 15 1.935327 GCACGTAGCTCGACTTCCCT 61.935 60.000 11.64 0.00 42.86 4.20
15 16 1.516603 GCACGTAGCTCGACTTCCC 60.517 63.158 11.64 0.00 42.86 3.97
16 17 4.074454 GCACGTAGCTCGACTTCC 57.926 61.111 11.64 0.00 42.86 3.46
409 410 0.103755 TGCAGAGCTCGGCTATTGAG 59.896 55.000 33.55 7.83 39.88 3.02
414 415 4.498520 GCGTGCAGAGCTCGGCTA 62.499 66.667 33.55 20.17 44.09 3.93
563 582 3.573489 GAAACGTTGCGAGCCCACG 62.573 63.158 0.00 13.20 0.00 4.94
564 583 2.251371 GAAACGTTGCGAGCCCAC 59.749 61.111 0.00 0.00 0.00 4.61
565 584 2.975799 GGAAACGTTGCGAGCCCA 60.976 61.111 0.00 0.00 0.00 5.36
566 585 3.733960 GGGAAACGTTGCGAGCCC 61.734 66.667 0.00 4.63 0.00 5.19
567 586 3.733960 GGGGAAACGTTGCGAGCC 61.734 66.667 0.00 0.00 0.00 4.70
568 587 3.733960 GGGGGAAACGTTGCGAGC 61.734 66.667 0.00 0.00 0.00 5.03
592 611 0.457035 CCAGCCGTGCAAGCATTTAT 59.543 50.000 12.15 0.00 0.00 1.40
620 639 1.419762 TGTACTGCTGCAGGAAAGGAA 59.580 47.619 31.00 8.65 35.51 3.36
709 746 2.156098 CGGGGAGGTTTCGAAATTTGA 58.844 47.619 14.69 0.00 0.00 2.69
818 857 2.158519 CCCCTGTTTGGACTTTGGTAGT 60.159 50.000 0.00 0.00 40.71 2.73
824 863 2.394632 GTTTCCCCCTGTTTGGACTTT 58.605 47.619 0.00 0.00 38.35 2.66
831 870 3.243602 CGAAAATTCGTTTCCCCCTGTTT 60.244 43.478 7.37 0.00 45.09 2.83
834 873 2.629639 CGAAAATTCGTTTCCCCCTG 57.370 50.000 7.37 0.00 45.09 4.45
915 954 2.185350 CAGCAGAGCACTACCGGG 59.815 66.667 6.32 0.00 0.00 5.73
918 957 1.807573 GTCGCAGCAGAGCACTACC 60.808 63.158 0.00 0.00 0.00 3.18
968 1007 2.124695 CCAGCGGCTAGGGTTTCC 60.125 66.667 0.26 0.00 0.00 3.13
969 1008 2.124695 CCCAGCGGCTAGGGTTTC 60.125 66.667 22.05 0.00 40.34 2.78
1239 1284 0.249238 CGAGGCTGATCTCCGGAAAG 60.249 60.000 5.23 1.98 0.00 2.62
1269 1314 2.506438 GCCCGGAAGAACTCGTCG 60.506 66.667 0.73 0.00 0.00 5.12
1497 1542 2.125952 GCACCATTTTCAGCCGCC 60.126 61.111 0.00 0.00 0.00 6.13
1741 1798 6.988622 TGGGTACGAAATTAATAACACTGG 57.011 37.500 0.00 0.00 0.00 4.00
1771 1828 8.350722 CCATCTCATTTATTCAATCTGGTCAAG 58.649 37.037 0.00 0.00 0.00 3.02
1788 1845 4.830046 AGCGTCTACATACTCCATCTCATT 59.170 41.667 0.00 0.00 0.00 2.57
1904 1961 5.409214 AGGCATGTGAATGTTAAATGCAAAC 59.591 36.000 8.07 0.00 44.26 2.93
1911 1968 4.039004 ACAGCAAGGCATGTGAATGTTAAA 59.961 37.500 0.00 0.00 0.00 1.52
1914 1971 1.965643 ACAGCAAGGCATGTGAATGTT 59.034 42.857 0.00 0.00 0.00 2.71
1957 2014 9.362539 TCGTCCATAAATAGACTTAAACAAGAC 57.637 33.333 0.00 0.00 0.00 3.01
2012 2069 7.554118 ACATCTGTTCTATAACACAATTCCCTG 59.446 37.037 0.00 0.00 40.69 4.45
2013 2070 7.633789 ACATCTGTTCTATAACACAATTCCCT 58.366 34.615 0.00 0.00 40.69 4.20
2029 2086 4.158384 CAATTGGCAACGTACATCTGTTC 58.842 43.478 0.00 0.00 42.51 3.18
2246 2303 9.273016 GCTCCTGCACTACTTGAAAAATATATA 57.727 33.333 0.00 0.00 39.41 0.86
2247 2304 7.995488 AGCTCCTGCACTACTTGAAAAATATAT 59.005 33.333 0.00 0.00 42.74 0.86
2248 2305 7.338710 AGCTCCTGCACTACTTGAAAAATATA 58.661 34.615 0.00 0.00 42.74 0.86
2249 2306 6.183347 AGCTCCTGCACTACTTGAAAAATAT 58.817 36.000 0.00 0.00 42.74 1.28
2250 2307 5.560724 AGCTCCTGCACTACTTGAAAAATA 58.439 37.500 0.00 0.00 42.74 1.40
2251 2308 4.401925 AGCTCCTGCACTACTTGAAAAAT 58.598 39.130 0.00 0.00 42.74 1.82
2253 2310 3.071602 AGAGCTCCTGCACTACTTGAAAA 59.928 43.478 10.93 0.00 42.74 2.29
2254 2311 2.634940 AGAGCTCCTGCACTACTTGAAA 59.365 45.455 10.93 0.00 42.74 2.69
2255 2312 2.028658 CAGAGCTCCTGCACTACTTGAA 60.029 50.000 10.93 0.00 42.74 2.69
2437 2577 8.533569 AAAAATAAGGAATCGGGTGATTACAT 57.466 30.769 3.28 0.00 46.28 2.29
2462 2602 3.565307 ACAAAGTGCAGGATCAAAAGGA 58.435 40.909 0.00 0.00 0.00 3.36
2660 2800 4.408921 AGACTATGGCCACTGCTACATTTA 59.591 41.667 8.16 0.00 37.74 1.40
2665 2805 2.231215 CAGACTATGGCCACTGCTAC 57.769 55.000 8.16 0.00 37.74 3.58
2702 2842 8.908786 TTGTCAGAGTTTGATTCACTTTAGAT 57.091 30.769 0.00 0.00 38.29 1.98
2777 2917 9.256228 ACAGAAAATACAAGATGAGAGGTACTA 57.744 33.333 0.00 0.00 41.55 1.82
2819 2959 2.579873 CAAGGGCCTTATCAGTGATGG 58.420 52.381 20.44 10.28 0.00 3.51
2846 2986 6.276832 AGATGGTTCAATTTTCACATCCAG 57.723 37.500 0.00 0.00 36.32 3.86
2968 3134 3.132111 AGAAACGGGACAGCACAAATTTT 59.868 39.130 0.00 0.00 0.00 1.82
2975 3141 0.818040 ACCAAGAAACGGGACAGCAC 60.818 55.000 0.00 0.00 0.00 4.40
2976 3142 0.817634 CACCAAGAAACGGGACAGCA 60.818 55.000 0.00 0.00 0.00 4.41
2977 3143 1.949257 CACCAAGAAACGGGACAGC 59.051 57.895 0.00 0.00 0.00 4.40
2978 3144 0.817634 TGCACCAAGAAACGGGACAG 60.818 55.000 0.00 0.00 0.00 3.51
2979 3145 0.179004 ATGCACCAAGAAACGGGACA 60.179 50.000 0.00 0.00 0.00 4.02
2980 3146 1.816074 TATGCACCAAGAAACGGGAC 58.184 50.000 0.00 0.00 0.00 4.46
2981 3147 2.570415 TTATGCACCAAGAAACGGGA 57.430 45.000 0.00 0.00 0.00 5.14
2982 3148 4.156922 TGTTATTATGCACCAAGAAACGGG 59.843 41.667 0.00 0.00 0.00 5.28
2984 3150 7.008266 GTCAATGTTATTATGCACCAAGAAACG 59.992 37.037 0.00 0.00 0.00 3.60
3079 3247 2.681848 AGAATGGCTCTGCGAAAATCAG 59.318 45.455 0.00 0.00 31.12 2.90
3125 3293 7.122353 ACTTCTGCTATGAAAAGAATGAGCATT 59.878 33.333 0.00 0.00 39.08 3.56
3206 3374 7.839680 AAACTCTAGTTGTGGGAATTTGAAT 57.160 32.000 0.00 0.00 38.44 2.57
3427 3635 6.553100 TCCCCTTTCATTGTAACAATCAAACT 59.447 34.615 0.00 0.00 0.00 2.66
3538 3746 4.581824 GCCATCAACCAGTAACATCATCAT 59.418 41.667 0.00 0.00 0.00 2.45
3539 3747 3.947196 GCCATCAACCAGTAACATCATCA 59.053 43.478 0.00 0.00 0.00 3.07
3583 3791 1.619654 TTTCATTGTCCTGCCACCTG 58.380 50.000 0.00 0.00 0.00 4.00
3650 3859 8.475639 GTTGTAACCCTATTCTCTTCAGTCATA 58.524 37.037 0.00 0.00 0.00 2.15
3749 3961 5.184864 TCAAACATGTTTGTTCAGAACCACT 59.815 36.000 37.39 7.41 45.30 4.00
3755 3967 7.624360 AAGTACTCAAACATGTTTGTTCAGA 57.376 32.000 37.39 23.66 45.30 3.27
3782 3994 1.837439 AGCCAATACCATGTCCTTCGA 59.163 47.619 0.00 0.00 0.00 3.71
3814 4026 9.857656 AGGAATCAAGATCATACATGTTTACAT 57.142 29.630 2.30 0.00 36.96 2.29
3823 4035 7.429374 AGACTTCAGGAATCAAGATCATACA 57.571 36.000 0.00 0.00 0.00 2.29
3922 4137 6.643845 CGCATCAATGTCATTAGTTAGTCTG 58.356 40.000 0.00 0.00 0.00 3.51
4018 4508 9.280456 TCCCTCTGTAAAGAAATATAAGACCTT 57.720 33.333 0.00 0.00 0.00 3.50
4019 4509 8.855804 TCCCTCTGTAAAGAAATATAAGACCT 57.144 34.615 0.00 0.00 0.00 3.85
4020 4510 8.706521 ACTCCCTCTGTAAAGAAATATAAGACC 58.293 37.037 0.00 0.00 0.00 3.85
4033 4523 7.180408 AGCTCTAAATTGTACTCCCTCTGTAAA 59.820 37.037 0.00 0.00 0.00 2.01
4077 4567 5.583854 GCATGAGTGATGACTATTCAACAGT 59.416 40.000 0.00 1.01 40.06 3.55
4142 4632 6.649155 TGAATAGCATTACTGTAGGCAGAAA 58.351 36.000 13.60 0.80 45.28 2.52
4144 4634 5.363868 ACTGAATAGCATTACTGTAGGCAGA 59.636 40.000 13.60 4.37 45.28 4.26
4214 4705 7.353414 TGGACAATGTATGGTCAAAGAAAAA 57.647 32.000 2.09 0.00 35.74 1.94
4561 5052 1.400494 ACACAGCAAACGACCAAGAAC 59.600 47.619 0.00 0.00 0.00 3.01
4727 5218 6.324561 TCACCATCAAACGATGAAAAATCA 57.675 33.333 4.03 0.00 42.54 2.57
4823 5314 1.899142 ACAACAGGTGGTGCAACTTTT 59.101 42.857 2.04 0.00 35.82 2.27
4850 5341 1.302511 CCAGGGAAGGACAACACCG 60.303 63.158 0.00 0.00 34.73 4.94
4930 5421 4.331968 TCCACAAGTAGTTTAGGCCATTG 58.668 43.478 5.01 0.00 0.00 2.82
4968 5462 7.560368 AGTTTACAGAGGGAGTAGAAATGATG 58.440 38.462 0.00 0.00 0.00 3.07
4969 5463 7.741554 AGTTTACAGAGGGAGTAGAAATGAT 57.258 36.000 0.00 0.00 0.00 2.45
4999 5494 9.570488 CACTACTTTAGTAATCTAAACGCTCTT 57.430 33.333 0.00 0.00 40.05 2.85
5000 5495 8.954350 TCACTACTTTAGTAATCTAAACGCTCT 58.046 33.333 0.00 0.00 40.05 4.09
5002 5497 9.733219 GATCACTACTTTAGTAATCTAAACGCT 57.267 33.333 0.00 0.00 40.05 5.07
5003 5498 9.733219 AGATCACTACTTTAGTAATCTAAACGC 57.267 33.333 0.00 0.00 40.05 4.84
5042 5537 9.490083 AACATAGTACTCCCTCTGTAAACTAAT 57.510 33.333 0.00 0.00 0.00 1.73
5044 5539 7.147949 GCAACATAGTACTCCCTCTGTAAACTA 60.148 40.741 0.00 0.00 0.00 2.24
5045 5540 6.351117 GCAACATAGTACTCCCTCTGTAAACT 60.351 42.308 0.00 0.00 0.00 2.66
5046 5541 5.811100 GCAACATAGTACTCCCTCTGTAAAC 59.189 44.000 0.00 0.00 0.00 2.01
5048 5543 5.020795 TGCAACATAGTACTCCCTCTGTAA 58.979 41.667 0.00 0.00 0.00 2.41
5049 5544 4.401519 GTGCAACATAGTACTCCCTCTGTA 59.598 45.833 0.00 0.00 36.32 2.74
5052 5572 2.766828 GGTGCAACATAGTACTCCCTCT 59.233 50.000 0.00 0.00 39.98 3.69
5102 5625 3.751479 AGGTTTTCCATTTCCTTGTGC 57.249 42.857 0.00 0.00 43.73 4.57
5143 5670 7.419518 CCAATGGACTGTTATCTGAAGGTCTAT 60.420 40.741 0.00 0.00 0.00 1.98
5146 5673 4.878397 CCAATGGACTGTTATCTGAAGGTC 59.122 45.833 0.00 0.00 0.00 3.85
5156 5683 6.373216 GCATAGTACAAACCAATGGACTGTTA 59.627 38.462 6.16 0.00 44.28 2.41
5161 5688 5.637006 TTGCATAGTACAAACCAATGGAC 57.363 39.130 6.16 0.00 34.14 4.02
5461 5992 0.325671 AGGAAATCCTCGCTCCTCCA 60.326 55.000 0.00 0.00 44.77 3.86
5484 6015 0.919981 GCTTCTGACTCAATCGCTCG 59.080 55.000 0.00 0.00 0.00 5.03
5736 6268 2.484947 GGAGGGAGTATTAACCAAGCCG 60.485 54.545 0.00 0.00 0.00 5.52
5750 6282 6.157123 AGACTTACATTTAGGAAAGGAGGGAG 59.843 42.308 0.00 0.00 0.00 4.30
5751 6283 6.030082 AGACTTACATTTAGGAAAGGAGGGA 58.970 40.000 0.00 0.00 0.00 4.20
5752 6284 6.314899 AGACTTACATTTAGGAAAGGAGGG 57.685 41.667 0.00 0.00 0.00 4.30
5753 6285 7.665974 ACAAAGACTTACATTTAGGAAAGGAGG 59.334 37.037 0.00 0.00 0.00 4.30
5754 6286 8.622948 ACAAAGACTTACATTTAGGAAAGGAG 57.377 34.615 0.00 0.00 0.00 3.69
5755 6287 9.720769 CTACAAAGACTTACATTTAGGAAAGGA 57.279 33.333 0.00 0.00 0.00 3.36
5756 6288 9.720769 TCTACAAAGACTTACATTTAGGAAAGG 57.279 33.333 0.00 0.00 0.00 3.11
5764 6296 9.220767 GTGGAATCTCTACAAAGACTTACATTT 57.779 33.333 0.00 0.00 0.00 2.32
5765 6297 8.598041 AGTGGAATCTCTACAAAGACTTACATT 58.402 33.333 0.00 0.00 29.47 2.71
5766 6298 8.140112 AGTGGAATCTCTACAAAGACTTACAT 57.860 34.615 0.00 0.00 29.47 2.29
5767 6299 7.540474 AGTGGAATCTCTACAAAGACTTACA 57.460 36.000 0.00 0.00 29.47 2.41
5826 6358 9.410556 CGGAACAAAATGAATGAATCTAAACTT 57.589 29.630 0.00 0.00 0.00 2.66
5827 6359 8.576442 ACGGAACAAAATGAATGAATCTAAACT 58.424 29.630 0.00 0.00 0.00 2.66
5828 6360 8.742554 ACGGAACAAAATGAATGAATCTAAAC 57.257 30.769 0.00 0.00 0.00 2.01
5831 6363 9.173021 ACATACGGAACAAAATGAATGAATCTA 57.827 29.630 0.00 0.00 0.00 1.98
5832 6364 8.055279 ACATACGGAACAAAATGAATGAATCT 57.945 30.769 0.00 0.00 0.00 2.40
5833 6365 9.438291 CTACATACGGAACAAAATGAATGAATC 57.562 33.333 0.00 0.00 0.00 2.52
5834 6366 8.956426 ACTACATACGGAACAAAATGAATGAAT 58.044 29.630 0.00 0.00 0.00 2.57
5835 6367 8.330466 ACTACATACGGAACAAAATGAATGAA 57.670 30.769 0.00 0.00 0.00 2.57
5836 6368 7.065324 GGACTACATACGGAACAAAATGAATGA 59.935 37.037 0.00 0.00 0.00 2.57
5837 6369 7.148323 TGGACTACATACGGAACAAAATGAATG 60.148 37.037 0.00 0.00 0.00 2.67
5838 6370 6.882140 TGGACTACATACGGAACAAAATGAAT 59.118 34.615 0.00 0.00 0.00 2.57
5839 6371 6.148150 GTGGACTACATACGGAACAAAATGAA 59.852 38.462 0.00 0.00 0.00 2.57
5840 6372 5.640357 GTGGACTACATACGGAACAAAATGA 59.360 40.000 0.00 0.00 0.00 2.57
5841 6373 5.445407 CGTGGACTACATACGGAACAAAATG 60.445 44.000 0.00 0.00 34.43 2.32
5842 6374 4.628333 CGTGGACTACATACGGAACAAAAT 59.372 41.667 0.00 0.00 34.43 1.82
5843 6375 3.989167 CGTGGACTACATACGGAACAAAA 59.011 43.478 0.00 0.00 34.43 2.44
5844 6376 3.005684 ACGTGGACTACATACGGAACAAA 59.994 43.478 0.00 0.00 41.74 2.83
5845 6377 2.557924 ACGTGGACTACATACGGAACAA 59.442 45.455 0.00 0.00 41.74 2.83
5846 6378 2.161855 ACGTGGACTACATACGGAACA 58.838 47.619 0.00 0.00 41.74 3.18
5847 6379 2.927553 ACGTGGACTACATACGGAAC 57.072 50.000 0.00 0.00 41.74 3.62
5848 6380 3.374988 CACTACGTGGACTACATACGGAA 59.625 47.826 5.70 0.00 41.74 4.30
5849 6381 2.938451 CACTACGTGGACTACATACGGA 59.062 50.000 5.70 0.00 41.74 4.69
5850 6382 3.329743 CACTACGTGGACTACATACGG 57.670 52.381 5.70 0.00 41.74 4.02
5862 6394 5.800941 GTCTTTGTAGAGATTCCACTACGTG 59.199 44.000 0.00 0.00 40.98 4.49
5863 6395 5.711036 AGTCTTTGTAGAGATTCCACTACGT 59.289 40.000 0.00 0.00 40.98 3.57
5864 6396 6.197364 AGTCTTTGTAGAGATTCCACTACG 57.803 41.667 11.38 0.00 40.98 3.51
5879 6411 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
5880 6412 8.202137 TCCTCCGTTCCTAAATATAAGTCTTTG 58.798 37.037 0.00 0.00 0.00 2.77
5881 6413 8.315220 TCCTCCGTTCCTAAATATAAGTCTTT 57.685 34.615 0.00 0.00 0.00 2.52
5882 6414 7.909485 TCCTCCGTTCCTAAATATAAGTCTT 57.091 36.000 0.00 0.00 0.00 3.01
5883 6415 7.564292 ACTTCCTCCGTTCCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
5884 6416 7.724287 ACTTCCTCCGTTCCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
5885 6417 7.672122 ACTTCCTCCGTTCCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
5886 6418 9.075678 TCTACTTCCTCCGTTCCTAAATATAAG 57.924 37.037 0.00 0.00 0.00 1.73
5887 6419 9.425248 TTCTACTTCCTCCGTTCCTAAATATAA 57.575 33.333 0.00 0.00 0.00 0.98
5888 6420 8.854117 GTTCTACTTCCTCCGTTCCTAAATATA 58.146 37.037 0.00 0.00 0.00 0.86
5889 6421 7.201983 GGTTCTACTTCCTCCGTTCCTAAATAT 60.202 40.741 0.00 0.00 0.00 1.28
5890 6422 6.097412 GGTTCTACTTCCTCCGTTCCTAAATA 59.903 42.308 0.00 0.00 0.00 1.40
5891 6423 5.105023 GGTTCTACTTCCTCCGTTCCTAAAT 60.105 44.000 0.00 0.00 0.00 1.40
5892 6424 4.221482 GGTTCTACTTCCTCCGTTCCTAAA 59.779 45.833 0.00 0.00 0.00 1.85
5893 6425 3.766051 GGTTCTACTTCCTCCGTTCCTAA 59.234 47.826 0.00 0.00 0.00 2.69
5894 6426 3.359950 GGTTCTACTTCCTCCGTTCCTA 58.640 50.000 0.00 0.00 0.00 2.94
5895 6427 2.177734 GGTTCTACTTCCTCCGTTCCT 58.822 52.381 0.00 0.00 0.00 3.36
5896 6428 1.206610 GGGTTCTACTTCCTCCGTTCC 59.793 57.143 0.00 0.00 0.00 3.62
5897 6429 2.094130 CAGGGTTCTACTTCCTCCGTTC 60.094 54.545 0.00 0.00 0.00 3.95
5898 6430 1.900486 CAGGGTTCTACTTCCTCCGTT 59.100 52.381 0.00 0.00 0.00 4.44
5899 6431 1.203149 ACAGGGTTCTACTTCCTCCGT 60.203 52.381 0.00 0.00 0.00 4.69
5900 6432 1.477295 GACAGGGTTCTACTTCCTCCG 59.523 57.143 0.00 0.00 0.00 4.63
5901 6433 2.234168 GTGACAGGGTTCTACTTCCTCC 59.766 54.545 0.00 0.00 0.00 4.30
5902 6434 2.897969 TGTGACAGGGTTCTACTTCCTC 59.102 50.000 0.00 0.00 0.00 3.71
5903 6435 2.900546 CTGTGACAGGGTTCTACTTCCT 59.099 50.000 4.28 0.00 0.00 3.36
5904 6436 2.613223 GCTGTGACAGGGTTCTACTTCC 60.613 54.545 15.24 0.00 31.21 3.46
5905 6437 2.300437 AGCTGTGACAGGGTTCTACTTC 59.700 50.000 15.24 0.00 31.21 3.01
5906 6438 2.330216 AGCTGTGACAGGGTTCTACTT 58.670 47.619 15.24 0.00 31.21 2.24
5907 6439 2.016905 AGCTGTGACAGGGTTCTACT 57.983 50.000 15.24 0.00 31.21 2.57
5908 6440 2.841442 AAGCTGTGACAGGGTTCTAC 57.159 50.000 15.24 0.00 31.21 2.59
5909 6441 3.135712 TCAAAAGCTGTGACAGGGTTCTA 59.864 43.478 15.24 0.00 31.21 2.10
5910 6442 2.092429 TCAAAAGCTGTGACAGGGTTCT 60.092 45.455 15.24 0.00 31.21 3.01
5911 6443 2.291741 CTCAAAAGCTGTGACAGGGTTC 59.708 50.000 15.24 0.00 31.21 3.62
5912 6444 2.301346 CTCAAAAGCTGTGACAGGGTT 58.699 47.619 15.24 4.34 31.21 4.11
5913 6445 1.212935 ACTCAAAAGCTGTGACAGGGT 59.787 47.619 15.24 0.00 31.21 4.34
5914 6446 1.605710 CACTCAAAAGCTGTGACAGGG 59.394 52.381 15.24 0.00 33.95 4.45
5996 6528 6.783708 TTTGACCAACTTAGGTGAATGTTT 57.216 33.333 0.00 0.00 43.38 2.83
6038 6570 5.360144 CCTTTCCTCGGAGTAGACAAAGATA 59.640 44.000 4.02 0.00 0.00 1.98
6039 6571 4.160626 CCTTTCCTCGGAGTAGACAAAGAT 59.839 45.833 4.02 0.00 0.00 2.40
6041 6573 3.368531 CCCTTTCCTCGGAGTAGACAAAG 60.369 52.174 4.02 4.49 0.00 2.77
6042 6574 2.565834 CCCTTTCCTCGGAGTAGACAAA 59.434 50.000 4.02 0.00 0.00 2.83
6045 6577 2.140839 TCCCTTTCCTCGGAGTAGAC 57.859 55.000 4.02 0.00 0.00 2.59
6046 6578 2.454538 GTTCCCTTTCCTCGGAGTAGA 58.545 52.381 4.02 0.00 0.00 2.59
6047 6579 1.134560 CGTTCCCTTTCCTCGGAGTAG 59.865 57.143 4.02 0.00 0.00 2.57
6048 6580 1.180029 CGTTCCCTTTCCTCGGAGTA 58.820 55.000 4.02 0.00 0.00 2.59
6049 6581 0.541296 TCGTTCCCTTTCCTCGGAGT 60.541 55.000 4.02 0.00 0.00 3.85
6050 6582 0.173708 CTCGTTCCCTTTCCTCGGAG 59.826 60.000 0.00 0.00 0.00 4.63
6051 6583 0.251474 TCTCGTTCCCTTTCCTCGGA 60.251 55.000 0.00 0.00 0.00 4.55
6052 6584 2.273908 TCTCGTTCCCTTTCCTCGG 58.726 57.895 0.00 0.00 0.00 4.63
6257 6789 0.186386 TTCCCTTTTCCTTTCCCGCA 59.814 50.000 0.00 0.00 0.00 5.69
6258 6790 1.272490 CTTTCCCTTTTCCTTTCCCGC 59.728 52.381 0.00 0.00 0.00 6.13
6259 6791 1.893137 CCTTTCCCTTTTCCTTTCCCG 59.107 52.381 0.00 0.00 0.00 5.14
6260 6792 2.158219 TCCCTTTCCCTTTTCCTTTCCC 60.158 50.000 0.00 0.00 0.00 3.97
6261 6793 3.254093 TCCCTTTCCCTTTTCCTTTCC 57.746 47.619 0.00 0.00 0.00 3.13
6262 6794 4.838423 TCATTCCCTTTCCCTTTTCCTTTC 59.162 41.667 0.00 0.00 0.00 2.62
6263 6795 4.826616 TCATTCCCTTTCCCTTTTCCTTT 58.173 39.130 0.00 0.00 0.00 3.11
6264 6796 4.107961 TCTCATTCCCTTTCCCTTTTCCTT 59.892 41.667 0.00 0.00 0.00 3.36
6265 6797 3.662642 TCTCATTCCCTTTCCCTTTTCCT 59.337 43.478 0.00 0.00 0.00 3.36
6266 6798 4.019858 CTCTCATTCCCTTTCCCTTTTCC 58.980 47.826 0.00 0.00 0.00 3.13
6267 6799 4.667573 ACTCTCATTCCCTTTCCCTTTTC 58.332 43.478 0.00 0.00 0.00 2.29
6268 6800 4.749048 ACTCTCATTCCCTTTCCCTTTT 57.251 40.909 0.00 0.00 0.00 2.27
6269 6801 4.749048 AACTCTCATTCCCTTTCCCTTT 57.251 40.909 0.00 0.00 0.00 3.11
6270 6802 4.749048 AAACTCTCATTCCCTTTCCCTT 57.251 40.909 0.00 0.00 0.00 3.95
6271 6803 4.601857 TGTAAACTCTCATTCCCTTTCCCT 59.398 41.667 0.00 0.00 0.00 4.20
6314 6846 3.071479 CAACTTCGCAAGCCTAGGTTAA 58.929 45.455 11.31 0.00 37.18 2.01
6359 6891 1.606668 TGATTTTCACCGCACTCCAAC 59.393 47.619 0.00 0.00 0.00 3.77
6387 6919 5.308014 GCATGAAACTTCCTCCCAAATTTT 58.692 37.500 0.00 0.00 0.00 1.82
6413 6945 3.305744 CCTTGGTTTTTATTCCACCCACG 60.306 47.826 0.00 0.00 33.12 4.94
6419 6951 6.408662 CCTTTTCCACCTTGGTTTTTATTCCA 60.409 38.462 0.00 0.00 39.03 3.53


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

AutoCloner maintained by Alex Coulton.