Multiple sequence alignment - TraesCS2A01G182400

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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 TraesCS2A01G182400 chr2A 100.000 4856 0 0 1 4856 141880928 141885783 0.000000e+00 8968.0
1 TraesCS2A01G182400 chr2A 82.929 1277 213 2 1415 2686 21209379 21208103 0.000000e+00 1146.0
2 TraesCS2A01G182400 chr2A 78.768 1785 314 32 1478 3236 21240752 21239007 0.000000e+00 1136.0
3 TraesCS2A01G182400 chr2A 86.686 676 75 10 2567 3238 21233310 21232646 0.000000e+00 736.0
4 TraesCS2A01G182400 chr2A 100.000 349 0 0 5099 5447 141886026 141886374 0.000000e+00 645.0
5 TraesCS2A01G182400 chr2A 80.597 603 104 9 2673 3273 21208083 21207492 2.310000e-123 453.0
6 TraesCS2A01G182400 chr2A 85.532 235 34 0 2287 2521 21233550 21233316 4.210000e-61 246.0
7 TraesCS2A01G182400 chr2D 92.925 4820 246 42 65 4835 134291826 134296599 0.000000e+00 6924.0
8 TraesCS2A01G182400 chr2D 84.489 2134 292 22 1149 3266 20611424 20609314 0.000000e+00 2071.0
9 TraesCS2A01G182400 chr2D 83.408 2019 317 6 1220 3238 20619601 20617601 0.000000e+00 1857.0
10 TraesCS2A01G182400 chr2D 80.161 993 168 16 2282 3266 20636999 20636028 0.000000e+00 715.0
11 TraesCS2A01G182400 chr2D 81.885 817 128 8 2423 3238 20654671 20653874 0.000000e+00 671.0
12 TraesCS2A01G182400 chr2D 83.969 524 84 0 1220 1743 20657722 20657199 2.260000e-138 503.0
13 TraesCS2A01G182400 chr2D 82.486 354 26 16 5099 5417 134296655 134297007 1.490000e-70 278.0
14 TraesCS2A01G182400 chr2D 85.135 74 10 1 4669 4741 144997935 144998008 2.100000e-09 75.0
15 TraesCS2A01G182400 chr2B 93.159 4137 207 33 520 4590 190194796 190198922 0.000000e+00 6002.0
16 TraesCS2A01G182400 chr2B 86.962 744 91 3 1525 2267 33771831 33771093 0.000000e+00 832.0
17 TraesCS2A01G182400 chr2B 87.528 441 27 14 60 488 190194055 190194479 8.200000e-133 484.0
18 TraesCS2A01G182400 chrUn 82.340 1410 241 7 1155 2557 373122184 373123592 0.000000e+00 1218.0
19 TraesCS2A01G182400 chr3D 88.571 70 7 1 4669 4737 11271271 11271340 3.500000e-12 84.2
20 TraesCS2A01G182400 chr3D 95.000 40 2 0 3573 3612 341495006 341495045 4.550000e-06 63.9
21 TraesCS2A01G182400 chr1B 83.951 81 12 1 4672 4751 20044115 20044195 5.850000e-10 76.8
22 TraesCS2A01G182400 chr1B 82.500 80 10 2 3568 3645 603092216 603092139 3.520000e-07 67.6
23 TraesCS2A01G182400 chr1B 81.333 75 10 2 3573 3645 603147907 603147835 2.120000e-04 58.4
24 TraesCS2A01G182400 chr1D 82.500 80 10 2 3568 3645 443428056 443427979 3.520000e-07 67.6
25 TraesCS2A01G182400 chr1A 82.278 79 12 2 3568 3645 539426727 539426650 3.520000e-07 67.6
26 TraesCS2A01G182400 chr3A 82.667 75 9 2 3573 3645 461840113 461840041 4.550000e-06 63.9
27 TraesCS2A01G182400 chr3B 97.059 34 1 0 3573 3606 440230441 440230474 2.120000e-04 58.4


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 TraesCS2A01G182400 chr2A 141880928 141886374 5446 False 4806.5 8968 100.0000 1 5447 2 chr2A.!!$F1 5446
1 TraesCS2A01G182400 chr2A 21239007 21240752 1745 True 1136.0 1136 78.7680 1478 3236 1 chr2A.!!$R1 1758
2 TraesCS2A01G182400 chr2A 21207492 21209379 1887 True 799.5 1146 81.7630 1415 3273 2 chr2A.!!$R2 1858
3 TraesCS2A01G182400 chr2A 21232646 21233550 904 True 491.0 736 86.1090 2287 3238 2 chr2A.!!$R3 951
4 TraesCS2A01G182400 chr2D 134291826 134297007 5181 False 3601.0 6924 87.7055 65 5417 2 chr2D.!!$F2 5352
5 TraesCS2A01G182400 chr2D 20609314 20611424 2110 True 2071.0 2071 84.4890 1149 3266 1 chr2D.!!$R1 2117
6 TraesCS2A01G182400 chr2D 20617601 20619601 2000 True 1857.0 1857 83.4080 1220 3238 1 chr2D.!!$R2 2018
7 TraesCS2A01G182400 chr2D 20636028 20636999 971 True 715.0 715 80.1610 2282 3266 1 chr2D.!!$R3 984
8 TraesCS2A01G182400 chr2D 20653874 20657722 3848 True 587.0 671 82.9270 1220 3238 2 chr2D.!!$R4 2018
9 TraesCS2A01G182400 chr2B 190194055 190198922 4867 False 3243.0 6002 90.3435 60 4590 2 chr2B.!!$F1 4530
10 TraesCS2A01G182400 chr2B 33771093 33771831 738 True 832.0 832 86.9620 1525 2267 1 chr2B.!!$R1 742
11 TraesCS2A01G182400 chrUn 373122184 373123592 1408 False 1218.0 1218 82.3400 1155 2557 1 chrUn.!!$F1 1402

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
906 1251 0.103755 CGAGCATAGCAGAGAAGCCA 59.896 55.0 0.00 0.0 34.23 4.75 F
1169 1544 0.398318 GCTCTTGAAGGTGAGGTGGT 59.602 55.0 0.00 0.0 0.00 4.16 F
2082 2498 0.459489 TGAGCACCAACAAGTTTGGC 59.541 50.0 2.85 0.0 43.23 4.52 F
2667 5178 0.107165 GCTATCCCCCGTTCAGCTTT 60.107 55.0 0.00 0.0 0.00 3.51 F
3273 5832 0.109781 GCAGCGTACCAACAACCATG 60.110 55.0 0.00 0.0 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2082 2498 0.932585 AAATTTGTTGCACGTCGCCG 60.933 50.000 7.38 0.00 41.33 6.46 R
2406 2822 0.954449 GCATCAGCCATAGCAGCGAT 60.954 55.000 0.00 0.00 43.56 4.58 R
3208 5767 1.227734 CTTCCGGTCGTGGTGGTTT 60.228 57.895 0.00 0.00 0.00 3.27 R
4276 6844 1.337703 CAGCTCGAGAAGATCCCAGAG 59.662 57.143 18.75 0.00 0.00 3.35 R
4777 7349 0.035439 AAGTGATTGACGCGGGGAAT 60.035 50.000 12.47 5.02 0.00 3.01 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
18 19 3.812577 GTTTGAAAGGGCGGATTGG 57.187 52.632 0.00 0.00 0.00 3.16
19 20 0.966179 GTTTGAAAGGGCGGATTGGT 59.034 50.000 0.00 0.00 0.00 3.67
20 21 2.164338 GTTTGAAAGGGCGGATTGGTA 58.836 47.619 0.00 0.00 0.00 3.25
21 22 2.559231 GTTTGAAAGGGCGGATTGGTAA 59.441 45.455 0.00 0.00 0.00 2.85
22 23 2.122783 TGAAAGGGCGGATTGGTAAG 57.877 50.000 0.00 0.00 0.00 2.34
23 24 1.631388 TGAAAGGGCGGATTGGTAAGA 59.369 47.619 0.00 0.00 0.00 2.10
24 25 2.014857 GAAAGGGCGGATTGGTAAGAC 58.985 52.381 0.00 0.00 0.00 3.01
25 26 0.107848 AAGGGCGGATTGGTAAGACG 60.108 55.000 0.00 0.00 0.00 4.18
26 27 1.219935 GGGCGGATTGGTAAGACGT 59.780 57.895 0.00 0.00 0.00 4.34
27 28 1.087771 GGGCGGATTGGTAAGACGTG 61.088 60.000 0.00 0.00 0.00 4.49
28 29 0.390735 GGCGGATTGGTAAGACGTGT 60.391 55.000 0.00 0.00 0.00 4.49
29 30 0.997196 GCGGATTGGTAAGACGTGTC 59.003 55.000 0.00 0.00 0.00 3.67
30 31 1.403780 GCGGATTGGTAAGACGTGTCT 60.404 52.381 0.00 0.00 42.75 3.41
31 32 2.259618 CGGATTGGTAAGACGTGTCTG 58.740 52.381 2.78 0.00 40.36 3.51
32 33 2.352421 CGGATTGGTAAGACGTGTCTGT 60.352 50.000 2.78 0.00 40.36 3.41
33 34 2.993899 GGATTGGTAAGACGTGTCTGTG 59.006 50.000 2.78 0.00 40.36 3.66
34 35 2.519377 TTGGTAAGACGTGTCTGTGG 57.481 50.000 2.78 0.00 40.36 4.17
35 36 0.677288 TGGTAAGACGTGTCTGTGGG 59.323 55.000 2.78 0.00 40.36 4.61
36 37 0.677842 GGTAAGACGTGTCTGTGGGT 59.322 55.000 2.78 0.00 40.36 4.51
37 38 1.604693 GGTAAGACGTGTCTGTGGGTG 60.605 57.143 2.78 0.00 40.36 4.61
38 39 1.068127 GTAAGACGTGTCTGTGGGTGT 59.932 52.381 2.78 0.00 40.36 4.16
39 40 0.539986 AAGACGTGTCTGTGGGTGTT 59.460 50.000 2.78 0.00 40.36 3.32
40 41 0.539986 AGACGTGTCTGTGGGTGTTT 59.460 50.000 0.86 0.00 38.75 2.83
41 42 0.655733 GACGTGTCTGTGGGTGTTTG 59.344 55.000 0.00 0.00 0.00 2.93
42 43 0.250793 ACGTGTCTGTGGGTGTTTGA 59.749 50.000 0.00 0.00 0.00 2.69
43 44 0.937304 CGTGTCTGTGGGTGTTTGAG 59.063 55.000 0.00 0.00 0.00 3.02
44 45 1.308998 GTGTCTGTGGGTGTTTGAGG 58.691 55.000 0.00 0.00 0.00 3.86
45 46 0.182537 TGTCTGTGGGTGTTTGAGGG 59.817 55.000 0.00 0.00 0.00 4.30
46 47 0.472471 GTCTGTGGGTGTTTGAGGGA 59.528 55.000 0.00 0.00 0.00 4.20
47 48 0.472471 TCTGTGGGTGTTTGAGGGAC 59.528 55.000 0.00 0.00 0.00 4.46
48 49 0.537371 CTGTGGGTGTTTGAGGGACC 60.537 60.000 0.00 0.00 0.00 4.46
49 50 1.599797 GTGGGTGTTTGAGGGACCG 60.600 63.158 0.00 0.00 0.00 4.79
50 51 1.766864 TGGGTGTTTGAGGGACCGA 60.767 57.895 0.00 0.00 0.00 4.69
51 52 1.346479 TGGGTGTTTGAGGGACCGAA 61.346 55.000 0.00 0.00 0.00 4.30
52 53 0.887836 GGGTGTTTGAGGGACCGAAC 60.888 60.000 0.00 0.00 0.00 3.95
53 54 1.226030 GGTGTTTGAGGGACCGAACG 61.226 60.000 0.00 0.00 0.00 3.95
54 55 1.070105 TGTTTGAGGGACCGAACGG 59.930 57.895 11.83 11.83 42.03 4.44
55 56 2.031465 TTTGAGGGACCGAACGGC 59.969 61.111 13.32 6.19 39.32 5.68
56 57 2.513259 TTTGAGGGACCGAACGGCT 61.513 57.895 13.32 2.44 39.32 5.52
57 58 2.725203 TTTGAGGGACCGAACGGCTG 62.725 60.000 13.32 0.00 39.32 4.85
58 59 3.692406 GAGGGACCGAACGGCTGT 61.692 66.667 13.32 0.00 39.32 4.40
59 60 3.236003 GAGGGACCGAACGGCTGTT 62.236 63.158 11.62 11.62 42.23 3.16
60 61 3.047877 GGGACCGAACGGCTGTTG 61.048 66.667 17.49 4.78 38.78 3.33
61 62 3.723348 GGACCGAACGGCTGTTGC 61.723 66.667 17.49 6.71 38.78 4.17
62 63 2.665185 GACCGAACGGCTGTTGCT 60.665 61.111 17.49 0.00 38.78 3.91
63 64 2.665185 ACCGAACGGCTGTTGCTC 60.665 61.111 17.49 0.00 38.78 4.26
100 106 2.473816 GTAGAGCGCATCATTACTGCA 58.526 47.619 11.47 0.00 39.64 4.41
131 137 0.880278 GGAAGCTTCACGTCTGCACA 60.880 55.000 27.02 0.00 0.00 4.57
206 215 1.073199 CGGCCCCATCATAACTCCC 59.927 63.158 0.00 0.00 0.00 4.30
234 243 4.337060 GACCCAAACCGTTGCCGC 62.337 66.667 0.00 0.00 33.01 6.53
239 248 3.292159 AAACCGTTGCCGCCCTTC 61.292 61.111 0.00 0.00 0.00 3.46
307 318 6.823689 CCAAGCCAAAACATCATAGTACTACT 59.176 38.462 4.31 0.00 0.00 2.57
338 349 7.964604 TTTTCTTTCAGGGAAAAACGAAAAA 57.035 28.000 11.59 4.56 38.97 1.94
339 350 6.954616 TTCTTTCAGGGAAAAACGAAAAAC 57.045 33.333 0.00 0.00 30.84 2.43
340 351 5.096849 TCTTTCAGGGAAAAACGAAAAACG 58.903 37.500 0.00 0.00 38.30 3.60
364 377 8.790718 ACGTTACTAGTAGTTGATCAAGAGAAA 58.209 33.333 8.80 0.00 0.00 2.52
365 378 9.279904 CGTTACTAGTAGTTGATCAAGAGAAAG 57.720 37.037 8.80 6.91 0.00 2.62
474 489 2.447443 TGGTAGCTTGAGATGTCGTCT 58.553 47.619 0.00 0.00 40.81 4.18
510 794 1.754226 AGTCTTGCTCGATCCCTTCTC 59.246 52.381 0.00 0.00 0.00 2.87
548 848 2.476051 CGACATTGCTGACGTGCC 59.524 61.111 0.00 0.00 36.12 5.01
569 869 7.594758 CGTGCCTTCTCTCAAATTTAAAAATCA 59.405 33.333 0.00 0.00 0.00 2.57
570 870 9.428097 GTGCCTTCTCTCAAATTTAAAAATCAT 57.572 29.630 0.00 0.00 0.00 2.45
572 872 8.801913 GCCTTCTCTCAAATTTAAAAATCATCG 58.198 33.333 0.00 0.00 0.00 3.84
618 918 0.856982 TTGGAGGGAAAGCAAGGGAA 59.143 50.000 0.00 0.00 0.00 3.97
619 919 1.084018 TGGAGGGAAAGCAAGGGAAT 58.916 50.000 0.00 0.00 0.00 3.01
620 920 1.432807 TGGAGGGAAAGCAAGGGAATT 59.567 47.619 0.00 0.00 0.00 2.17
621 921 2.103373 GGAGGGAAAGCAAGGGAATTC 58.897 52.381 0.00 0.00 0.00 2.17
624 939 0.817654 GGAAAGCAAGGGAATTCGGG 59.182 55.000 0.00 0.00 0.00 5.14
640 961 1.441311 GGGCACAACCAAACCAGTG 59.559 57.895 0.00 0.00 42.05 3.66
641 962 1.040339 GGGCACAACCAAACCAGTGA 61.040 55.000 0.00 0.00 42.05 3.41
731 1052 2.084546 GGGAATTCAAAGGTCCAGACG 58.915 52.381 7.93 0.00 32.70 4.18
866 1196 1.515954 GGCCTCGTCTTCGGATTGA 59.484 57.895 0.00 0.00 37.69 2.57
872 1212 1.521681 GTCTTCGGATTGAGGGGCG 60.522 63.158 0.00 0.00 0.00 6.13
901 1241 1.439228 GCACCGAGCATAGCAGAGA 59.561 57.895 0.00 0.00 44.79 3.10
906 1251 0.103755 CGAGCATAGCAGAGAAGCCA 59.896 55.000 0.00 0.00 34.23 4.75
920 1265 2.107204 AGAAGCCAAGCCAAGAAGAAGA 59.893 45.455 0.00 0.00 0.00 2.87
925 1270 4.018960 AGCCAAGCCAAGAAGAAGAATAGA 60.019 41.667 0.00 0.00 0.00 1.98
982 1336 7.158021 GTCTAGGATTCGATTCTTCCATGATT 58.842 38.462 7.21 0.00 31.65 2.57
983 1337 8.307483 GTCTAGGATTCGATTCTTCCATGATTA 58.693 37.037 7.21 0.00 31.65 1.75
984 1338 9.040259 TCTAGGATTCGATTCTTCCATGATTAT 57.960 33.333 7.21 0.00 31.65 1.28
1032 1386 2.581354 CTCCGGTTCCTCTGCCTG 59.419 66.667 0.00 0.00 0.00 4.85
1051 1405 1.810532 CTCCTCCTCGCAGGTACAC 59.189 63.158 0.00 0.00 36.53 2.90
1100 1471 3.863086 TCTCTTCTTCTCTTCTTGGGGT 58.137 45.455 0.00 0.00 0.00 4.95
1104 1475 1.699634 TCTTCTCTTCTTGGGGTGTGG 59.300 52.381 0.00 0.00 0.00 4.17
1150 1521 3.877508 GTCTAATTTGAGGGGGTCGATTG 59.122 47.826 0.00 0.00 0.00 2.67
1166 1541 2.613977 CGATTGCTCTTGAAGGTGAGGT 60.614 50.000 0.00 0.00 0.00 3.85
1169 1544 0.398318 GCTCTTGAAGGTGAGGTGGT 59.602 55.000 0.00 0.00 0.00 4.16
1176 1551 0.773644 AAGGTGAGGTGGTGCTGATT 59.226 50.000 0.00 0.00 0.00 2.57
1354 1749 4.154613 CGTCTCTGAACCTGACGC 57.845 61.111 4.58 0.00 45.00 5.19
1497 1896 2.348998 CTCCTGCGCCTCAACCTT 59.651 61.111 4.18 0.00 0.00 3.50
1676 2075 1.376683 GCAACATCACCGGCCTGTA 60.377 57.895 0.00 0.00 0.00 2.74
1820 2231 3.655481 GTGGAGCACGTTTCCTGG 58.345 61.111 15.00 0.00 35.67 4.45
1998 2414 2.699954 GAGACGCTGATTCTTGGGAAA 58.300 47.619 0.00 0.00 34.90 3.13
2046 2462 2.125912 CTGACGAACTGCGGGAGG 60.126 66.667 0.51 0.00 46.49 4.30
2082 2498 0.459489 TGAGCACCAACAAGTTTGGC 59.541 50.000 2.85 0.00 43.23 4.52
2112 2528 3.308323 TGCAACAAATTTTCGGCAACTTC 59.692 39.130 5.25 0.00 0.00 3.01
2157 2573 2.365941 TCATCACAACAACTACACCGGA 59.634 45.455 9.46 0.00 0.00 5.14
2248 2664 1.682684 GGCGAACTCCCTCCAGAGA 60.683 63.158 0.00 0.00 37.33 3.10
2373 2789 1.979469 CTGTCTAACAACACGCTCTCG 59.021 52.381 0.00 0.00 42.43 4.04
2589 5089 0.672401 TCGCCAAGAACCGGAATGAC 60.672 55.000 9.46 0.00 0.00 3.06
2643 5145 0.255890 CCATGAAACGGTGGATCCCT 59.744 55.000 9.90 0.00 37.72 4.20
2667 5178 0.107165 GCTATCCCCCGTTCAGCTTT 60.107 55.000 0.00 0.00 0.00 3.51
2757 5301 1.000843 GTCCCAATTTGCACCAACTCC 59.999 52.381 0.00 0.00 0.00 3.85
2812 5368 1.072159 GTGCAGCTGTCAGGGAACT 59.928 57.895 16.64 0.00 46.44 3.01
3147 5706 1.079127 CCAGTTCGGCACCTTCGAT 60.079 57.895 0.00 0.00 36.49 3.59
3189 5748 2.159212 CCCGCTCATTTCATTGCATCAA 60.159 45.455 0.00 0.00 0.00 2.57
3208 5767 2.656069 GGTGGAGCTGCCGGTAAGA 61.656 63.158 1.90 0.00 40.66 2.10
3273 5832 0.109781 GCAGCGTACCAACAACCATG 60.110 55.000 0.00 0.00 0.00 3.66
3302 5864 1.404315 GCTTTTCTCCCTCGTCATCGT 60.404 52.381 0.00 0.00 38.33 3.73
3535 6103 0.172803 GTTCACCTACCGCGACATCT 59.827 55.000 8.23 0.00 0.00 2.90
3540 6108 1.141881 CTACCGCGACATCTTGGCT 59.858 57.895 8.23 0.00 0.00 4.75
3807 6375 1.595466 AGATACTGGTCTACGAGCGG 58.405 55.000 0.00 0.70 41.57 5.52
3848 6416 3.558411 GCTGATCTGCGACACGGC 61.558 66.667 8.95 0.00 0.00 5.68
3849 6417 3.250323 CTGATCTGCGACACGGCG 61.250 66.667 4.80 4.80 35.06 6.46
4284 6852 4.101448 GGCACGGTGCTCTGGGAT 62.101 66.667 29.92 0.00 44.28 3.85
4287 6855 1.599047 CACGGTGCTCTGGGATCTT 59.401 57.895 0.00 0.00 0.00 2.40
4394 6962 3.792047 CGACGTGGGCTGTGCATG 61.792 66.667 0.00 0.00 0.00 4.06
4508 7077 4.911514 AAATGCGGTTGTTTAGTTCAGT 57.088 36.364 0.00 0.00 0.00 3.41
4513 7082 2.946990 CGGTTGTTTAGTTCAGTTGGGT 59.053 45.455 0.00 0.00 0.00 4.51
4518 7087 3.623960 TGTTTAGTTCAGTTGGGTGTTCG 59.376 43.478 0.00 0.00 0.00 3.95
4531 7100 4.247258 TGGGTGTTCGTTCATGTATGTAC 58.753 43.478 0.00 0.00 0.00 2.90
4536 7105 6.023435 GTGTTCGTTCATGTATGTACGTAGA 58.977 40.000 18.80 9.21 46.84 2.59
4608 7178 9.384682 GTGAAAAACCAATGAAAAATAAGCATG 57.615 29.630 0.00 0.00 0.00 4.06
4609 7179 8.074972 TGAAAAACCAATGAAAAATAAGCATGC 58.925 29.630 10.51 10.51 0.00 4.06
4610 7180 7.748691 AAAACCAATGAAAAATAAGCATGCT 57.251 28.000 16.30 16.30 0.00 3.79
4611 7181 8.845413 AAAACCAATGAAAAATAAGCATGCTA 57.155 26.923 23.00 9.95 0.00 3.49
4612 7182 7.832503 AACCAATGAAAAATAAGCATGCTAC 57.167 32.000 23.00 7.31 0.00 3.58
4613 7183 6.340522 ACCAATGAAAAATAAGCATGCTACC 58.659 36.000 23.00 5.84 0.00 3.18
4614 7184 6.070881 ACCAATGAAAAATAAGCATGCTACCA 60.071 34.615 23.00 9.92 0.00 3.25
4615 7185 6.256321 CCAATGAAAAATAAGCATGCTACCAC 59.744 38.462 23.00 9.55 0.00 4.16
4616 7186 5.973899 TGAAAAATAAGCATGCTACCACA 57.026 34.783 23.00 11.96 0.00 4.17
4617 7187 6.338214 TGAAAAATAAGCATGCTACCACAA 57.662 33.333 23.00 2.94 0.00 3.33
4623 7193 4.989279 AAGCATGCTACCACAAAATAGG 57.011 40.909 23.00 0.00 0.00 2.57
4624 7194 3.290710 AGCATGCTACCACAAAATAGGG 58.709 45.455 21.21 0.00 0.00 3.53
4651 7221 6.127619 GGCCCCTAAAATATGCTATTAGCTTG 60.128 42.308 16.29 0.00 42.97 4.01
4662 7232 4.864806 TGCTATTAGCTTGCTATATCACGC 59.135 41.667 16.29 0.00 42.97 5.34
4664 7234 6.127730 TGCTATTAGCTTGCTATATCACGCTA 60.128 38.462 16.29 9.89 42.97 4.26
4665 7235 6.416455 GCTATTAGCTTGCTATATCACGCTAG 59.584 42.308 12.70 6.84 42.26 3.42
4666 7236 5.707242 TTAGCTTGCTATATCACGCTAGT 57.293 39.130 12.70 0.00 42.26 2.57
4702 7273 8.443160 ACGAGACATTGTACACTGATTTATTTG 58.557 33.333 19.02 5.17 0.00 2.32
4707 7279 5.895636 TGTACACTGATTTATTTGGCAGG 57.104 39.130 0.00 0.00 32.82 4.85
4712 7284 5.421693 ACACTGATTTATTTGGCAGGCATTA 59.578 36.000 0.00 0.00 32.82 1.90
4713 7285 6.070881 ACACTGATTTATTTGGCAGGCATTAA 60.071 34.615 0.00 0.00 32.82 1.40
4715 7287 6.987992 ACTGATTTATTTGGCAGGCATTAATG 59.012 34.615 11.27 11.27 32.82 1.90
4717 7289 7.563020 TGATTTATTTGGCAGGCATTAATGAA 58.437 30.769 19.73 2.94 0.00 2.57
4721 7293 4.613925 TTGGCAGGCATTAATGAAAACA 57.386 36.364 19.73 7.73 0.00 2.83
4723 7295 3.323115 TGGCAGGCATTAATGAAAACACA 59.677 39.130 19.73 7.25 0.00 3.72
4729 7301 7.973388 GCAGGCATTAATGAAAACACAATAGTA 59.027 33.333 19.73 0.00 0.00 1.82
4742 7314 8.833231 AAACACAATAGTATGCTATTAGCGAT 57.167 30.769 14.73 8.13 46.26 4.58
4745 7317 8.740906 ACACAATAGTATGCTATTAGCGATACT 58.259 33.333 26.16 26.16 46.26 2.12
4751 7323 8.678593 AGTATGCTATTAGCGATACTATAGCA 57.321 34.615 22.45 22.45 46.26 3.49
4752 7324 9.290988 AGTATGCTATTAGCGATACTATAGCAT 57.709 33.333 28.85 28.85 46.26 3.79
4753 7325 9.335891 GTATGCTATTAGCGATACTATAGCATG 57.664 37.037 31.32 3.73 45.63 4.06
4754 7326 6.209361 TGCTATTAGCGATACTATAGCATGC 58.791 40.000 18.45 10.51 46.26 4.06
4756 7328 7.228706 TGCTATTAGCGATACTATAGCATGCTA 59.771 37.037 28.72 28.72 46.26 3.49
4757 7329 8.240682 GCTATTAGCGATACTATAGCATGCTAT 58.759 37.037 35.68 35.68 41.58 2.97
4758 7330 9.767684 CTATTAGCGATACTATAGCATGCTATC 57.232 37.037 37.09 25.48 39.65 2.08
4810 7382 5.358160 GTCAATCACTTATGCTTTAGGCCTT 59.642 40.000 12.58 0.00 40.92 4.35
4811 7383 5.357878 TCAATCACTTATGCTTTAGGCCTTG 59.642 40.000 12.58 2.69 40.92 3.61
4822 7394 4.703897 CTTTAGGCCTTGATATCCAACGA 58.296 43.478 12.58 0.00 0.00 3.85
4825 7397 2.705658 AGGCCTTGATATCCAACGATCA 59.294 45.455 0.00 0.00 0.00 2.92
4826 7398 3.070018 GGCCTTGATATCCAACGATCAG 58.930 50.000 0.00 0.00 33.73 2.90
4828 7400 4.380531 GCCTTGATATCCAACGATCAGAA 58.619 43.478 0.00 0.00 33.73 3.02
4829 7401 4.450419 GCCTTGATATCCAACGATCAGAAG 59.550 45.833 0.00 0.00 33.73 2.85
4830 7402 4.450419 CCTTGATATCCAACGATCAGAAGC 59.550 45.833 0.00 0.00 33.73 3.86
4831 7403 3.642705 TGATATCCAACGATCAGAAGCG 58.357 45.455 0.00 0.00 40.92 4.68
4838 7410 1.417592 CGATCAGAAGCGTGTGTGC 59.582 57.895 0.00 0.00 0.00 4.57
4839 7411 1.790387 GATCAGAAGCGTGTGTGCC 59.210 57.895 0.00 0.00 34.65 5.01
4840 7412 1.959899 GATCAGAAGCGTGTGTGCCG 61.960 60.000 0.00 0.00 34.65 5.69
4841 7413 2.715532 ATCAGAAGCGTGTGTGCCGT 62.716 55.000 0.00 0.00 34.65 5.68
4842 7414 2.661866 AGAAGCGTGTGTGCCGTC 60.662 61.111 0.00 0.00 34.65 4.79
4843 7415 2.964925 GAAGCGTGTGTGCCGTCA 60.965 61.111 0.00 0.00 34.65 4.35
4845 7417 1.841663 GAAGCGTGTGTGCCGTCATT 61.842 55.000 0.00 0.00 34.65 2.57
4846 7418 2.116736 AAGCGTGTGTGCCGTCATTG 62.117 55.000 0.00 0.00 34.65 2.82
5121 7693 1.407656 TTCTTCCTGCTCCACACGGT 61.408 55.000 0.00 0.00 0.00 4.83
5183 7764 4.742201 TTGTCGCTGCCTCGCCTC 62.742 66.667 0.00 0.00 0.00 4.70
5201 7782 0.908910 TCCACCCGCAGATGTATTGT 59.091 50.000 0.00 0.00 0.00 2.71
5238 7819 1.077787 CTTAAGCCCCGCACCATCA 60.078 57.895 0.00 0.00 0.00 3.07
5249 7830 2.030007 CCGCACCATCAATGAACAACTT 60.030 45.455 0.00 0.00 0.00 2.66
5251 7832 3.236816 GCACCATCAATGAACAACTTCG 58.763 45.455 0.00 0.00 0.00 3.79
5252 7833 3.825308 CACCATCAATGAACAACTTCGG 58.175 45.455 0.00 0.00 0.00 4.30
5253 7834 3.253188 CACCATCAATGAACAACTTCGGT 59.747 43.478 0.00 0.00 0.00 4.69
5256 7837 4.156556 CCATCAATGAACAACTTCGGTGAT 59.843 41.667 0.00 0.00 34.85 3.06
5269 7850 3.732938 GTGATCCCCTGCACCTCT 58.267 61.111 0.00 0.00 0.00 3.69
5304 7911 3.654806 AGATAATATGGCTGTGGCTTCCT 59.345 43.478 0.00 0.00 38.73 3.36
5318 7925 7.255277 GCTGTGGCTTCCTTTAAAATAGATAGG 60.255 40.741 0.00 0.00 35.22 2.57
5340 7947 1.671379 GTTGGTTCTCCGGTGAGGC 60.671 63.158 6.29 4.22 39.23 4.70
5358 7965 3.532155 GCGGCCTCTCCATCTCGT 61.532 66.667 0.00 0.00 34.01 4.18
5417 8024 3.476552 TGACGCAAGAAGAAAATCCAGT 58.523 40.909 0.00 0.00 43.62 4.00
5418 8025 3.250762 TGACGCAAGAAGAAAATCCAGTG 59.749 43.478 0.00 0.00 43.62 3.66
5419 8026 3.214328 ACGCAAGAAGAAAATCCAGTGT 58.786 40.909 0.00 0.00 43.62 3.55
5420 8027 3.003689 ACGCAAGAAGAAAATCCAGTGTG 59.996 43.478 0.00 0.00 43.62 3.82
5421 8028 3.250762 CGCAAGAAGAAAATCCAGTGTGA 59.749 43.478 0.00 0.00 43.02 3.58
5422 8029 4.612259 CGCAAGAAGAAAATCCAGTGTGAG 60.612 45.833 0.00 0.00 43.02 3.51
5423 8030 4.516698 GCAAGAAGAAAATCCAGTGTGAGA 59.483 41.667 0.00 0.00 0.00 3.27
5424 8031 5.561725 GCAAGAAGAAAATCCAGTGTGAGAC 60.562 44.000 0.00 0.00 0.00 3.36
5425 8032 5.296151 AGAAGAAAATCCAGTGTGAGACA 57.704 39.130 0.00 0.00 0.00 3.41
5426 8033 5.684704 AGAAGAAAATCCAGTGTGAGACAA 58.315 37.500 0.00 0.00 0.00 3.18
5427 8034 6.302269 AGAAGAAAATCCAGTGTGAGACAAT 58.698 36.000 0.00 0.00 0.00 2.71
5428 8035 7.453393 AGAAGAAAATCCAGTGTGAGACAATA 58.547 34.615 0.00 0.00 0.00 1.90
5429 8036 7.605691 AGAAGAAAATCCAGTGTGAGACAATAG 59.394 37.037 0.00 0.00 0.00 1.73
5430 8037 7.009179 AGAAAATCCAGTGTGAGACAATAGA 57.991 36.000 0.00 0.00 0.00 1.98
5431 8038 7.628234 AGAAAATCCAGTGTGAGACAATAGAT 58.372 34.615 0.00 0.00 0.00 1.98
5432 8039 8.105829 AGAAAATCCAGTGTGAGACAATAGATT 58.894 33.333 0.00 0.00 0.00 2.40
5433 8040 8.641498 AAAATCCAGTGTGAGACAATAGATTT 57.359 30.769 5.22 5.22 35.47 2.17
5434 8041 7.621428 AATCCAGTGTGAGACAATAGATTTG 57.379 36.000 0.00 0.00 0.00 2.32
5435 8042 5.491070 TCCAGTGTGAGACAATAGATTTGG 58.509 41.667 0.00 0.00 0.00 3.28
5436 8043 4.637534 CCAGTGTGAGACAATAGATTTGGG 59.362 45.833 0.00 0.00 0.00 4.12
5437 8044 4.637534 CAGTGTGAGACAATAGATTTGGGG 59.362 45.833 0.00 0.00 0.00 4.96
5438 8045 3.947834 GTGTGAGACAATAGATTTGGGGG 59.052 47.826 0.00 0.00 0.00 5.40
5439 8046 3.849574 TGTGAGACAATAGATTTGGGGGA 59.150 43.478 0.00 0.00 0.00 4.81
5440 8047 4.290985 TGTGAGACAATAGATTTGGGGGAA 59.709 41.667 0.00 0.00 0.00 3.97
5441 8048 5.044179 TGTGAGACAATAGATTTGGGGGAAT 60.044 40.000 0.00 0.00 0.00 3.01
5442 8049 5.532779 GTGAGACAATAGATTTGGGGGAATC 59.467 44.000 0.00 0.00 36.50 2.52
5443 8050 4.718961 AGACAATAGATTTGGGGGAATCG 58.281 43.478 0.00 0.00 40.22 3.34
5444 8051 3.821033 GACAATAGATTTGGGGGAATCGG 59.179 47.826 0.00 0.00 40.22 4.18
5445 8052 2.558359 CAATAGATTTGGGGGAATCGGC 59.442 50.000 0.00 0.00 40.22 5.54
5446 8053 1.518367 TAGATTTGGGGGAATCGGCT 58.482 50.000 0.00 0.00 40.22 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.966179 ACCAATCCGCCCTTTCAAAC 59.034 50.000 0.00 0.00 0.00 2.93
2 3 2.040545 TCTTACCAATCCGCCCTTTCAA 59.959 45.455 0.00 0.00 0.00 2.69
4 5 2.014857 GTCTTACCAATCCGCCCTTTC 58.985 52.381 0.00 0.00 0.00 2.62
5 6 1.677820 CGTCTTACCAATCCGCCCTTT 60.678 52.381 0.00 0.00 0.00 3.11
6 7 0.107848 CGTCTTACCAATCCGCCCTT 60.108 55.000 0.00 0.00 0.00 3.95
7 8 1.262640 ACGTCTTACCAATCCGCCCT 61.263 55.000 0.00 0.00 0.00 5.19
8 9 1.087771 CACGTCTTACCAATCCGCCC 61.088 60.000 0.00 0.00 0.00 6.13
9 10 0.390735 ACACGTCTTACCAATCCGCC 60.391 55.000 0.00 0.00 0.00 6.13
10 11 0.997196 GACACGTCTTACCAATCCGC 59.003 55.000 0.00 0.00 0.00 5.54
11 12 2.259618 CAGACACGTCTTACCAATCCG 58.740 52.381 0.00 0.00 37.98 4.18
12 13 2.993899 CACAGACACGTCTTACCAATCC 59.006 50.000 0.00 0.00 37.98 3.01
13 14 2.993899 CCACAGACACGTCTTACCAATC 59.006 50.000 0.00 0.00 37.98 2.67
14 15 2.289444 CCCACAGACACGTCTTACCAAT 60.289 50.000 0.00 0.00 37.98 3.16
15 16 1.069513 CCCACAGACACGTCTTACCAA 59.930 52.381 0.00 0.00 37.98 3.67
16 17 0.677288 CCCACAGACACGTCTTACCA 59.323 55.000 0.00 0.00 37.98 3.25
17 18 0.677842 ACCCACAGACACGTCTTACC 59.322 55.000 0.00 0.00 37.98 2.85
18 19 1.068127 ACACCCACAGACACGTCTTAC 59.932 52.381 0.00 0.00 37.98 2.34
19 20 1.405872 ACACCCACAGACACGTCTTA 58.594 50.000 0.00 0.00 37.98 2.10
20 21 0.539986 AACACCCACAGACACGTCTT 59.460 50.000 0.00 0.00 37.98 3.01
21 22 0.539986 AAACACCCACAGACACGTCT 59.460 50.000 0.00 0.00 41.37 4.18
22 23 0.655733 CAAACACCCACAGACACGTC 59.344 55.000 0.00 0.00 0.00 4.34
23 24 0.250793 TCAAACACCCACAGACACGT 59.749 50.000 0.00 0.00 0.00 4.49
24 25 0.937304 CTCAAACACCCACAGACACG 59.063 55.000 0.00 0.00 0.00 4.49
25 26 1.308998 CCTCAAACACCCACAGACAC 58.691 55.000 0.00 0.00 0.00 3.67
26 27 0.182537 CCCTCAAACACCCACAGACA 59.817 55.000 0.00 0.00 0.00 3.41
27 28 0.472471 TCCCTCAAACACCCACAGAC 59.528 55.000 0.00 0.00 0.00 3.51
28 29 0.472471 GTCCCTCAAACACCCACAGA 59.528 55.000 0.00 0.00 0.00 3.41
29 30 0.537371 GGTCCCTCAAACACCCACAG 60.537 60.000 0.00 0.00 0.00 3.66
30 31 1.534697 GGTCCCTCAAACACCCACA 59.465 57.895 0.00 0.00 0.00 4.17
31 32 1.599797 CGGTCCCTCAAACACCCAC 60.600 63.158 0.00 0.00 0.00 4.61
32 33 1.346479 TTCGGTCCCTCAAACACCCA 61.346 55.000 0.00 0.00 0.00 4.51
33 34 0.887836 GTTCGGTCCCTCAAACACCC 60.888 60.000 0.00 0.00 0.00 4.61
34 35 1.226030 CGTTCGGTCCCTCAAACACC 61.226 60.000 0.00 0.00 0.00 4.16
35 36 1.226030 CCGTTCGGTCCCTCAAACAC 61.226 60.000 2.82 0.00 0.00 3.32
36 37 1.070105 CCGTTCGGTCCCTCAAACA 59.930 57.895 2.82 0.00 0.00 2.83
37 38 2.322830 GCCGTTCGGTCCCTCAAAC 61.323 63.158 12.81 0.00 0.00 2.93
38 39 2.031465 GCCGTTCGGTCCCTCAAA 59.969 61.111 12.81 0.00 0.00 2.69
39 40 2.920912 AGCCGTTCGGTCCCTCAA 60.921 61.111 12.81 0.00 0.00 3.02
40 41 3.691342 CAGCCGTTCGGTCCCTCA 61.691 66.667 12.81 0.00 0.00 3.86
41 42 3.236003 AACAGCCGTTCGGTCCCTC 62.236 63.158 12.81 0.00 0.00 4.30
42 43 3.239253 AACAGCCGTTCGGTCCCT 61.239 61.111 12.81 0.00 0.00 4.20
43 44 3.047877 CAACAGCCGTTCGGTCCC 61.048 66.667 12.81 0.00 31.13 4.46
44 45 3.723348 GCAACAGCCGTTCGGTCC 61.723 66.667 12.81 0.00 31.13 4.46
45 46 2.665185 AGCAACAGCCGTTCGGTC 60.665 61.111 12.81 5.49 31.13 4.79
46 47 2.660258 AAGAGCAACAGCCGTTCGGT 62.660 55.000 12.81 0.00 31.13 4.69
47 48 0.669318 TAAGAGCAACAGCCGTTCGG 60.669 55.000 6.90 6.90 31.13 4.30
48 49 1.136336 GTTAAGAGCAACAGCCGTTCG 60.136 52.381 0.00 0.00 31.13 3.95
49 50 2.143925 AGTTAAGAGCAACAGCCGTTC 58.856 47.619 0.00 0.00 31.13 3.95
50 51 2.143925 GAGTTAAGAGCAACAGCCGTT 58.856 47.619 0.00 0.00 35.01 4.44
51 52 1.344763 AGAGTTAAGAGCAACAGCCGT 59.655 47.619 0.00 0.00 0.00 5.68
52 53 2.086054 AGAGTTAAGAGCAACAGCCG 57.914 50.000 0.00 0.00 0.00 5.52
53 54 3.187432 GTGAAGAGTTAAGAGCAACAGCC 59.813 47.826 0.00 0.00 0.00 4.85
54 55 3.809832 TGTGAAGAGTTAAGAGCAACAGC 59.190 43.478 0.00 0.00 0.00 4.40
55 56 4.084849 CGTGTGAAGAGTTAAGAGCAACAG 60.085 45.833 0.00 0.00 0.00 3.16
56 57 3.802139 CGTGTGAAGAGTTAAGAGCAACA 59.198 43.478 0.00 0.00 0.00 3.33
57 58 3.363084 GCGTGTGAAGAGTTAAGAGCAAC 60.363 47.826 0.00 0.00 0.00 4.17
58 59 2.800544 GCGTGTGAAGAGTTAAGAGCAA 59.199 45.455 0.00 0.00 0.00 3.91
59 60 2.404215 GCGTGTGAAGAGTTAAGAGCA 58.596 47.619 0.00 0.00 0.00 4.26
60 61 1.387084 CGCGTGTGAAGAGTTAAGAGC 59.613 52.381 0.00 0.00 0.00 4.09
61 62 2.662700 ACGCGTGTGAAGAGTTAAGAG 58.337 47.619 12.93 0.00 0.00 2.85
62 63 2.787601 ACGCGTGTGAAGAGTTAAGA 57.212 45.000 12.93 0.00 0.00 2.10
63 64 3.818387 TCTACGCGTGTGAAGAGTTAAG 58.182 45.455 24.59 6.45 0.00 1.85
100 106 4.972591 GCTTCCAAAGCGCACAAT 57.027 50.000 11.47 0.00 45.74 2.71
108 114 1.069636 GCAGACGTGAAGCTTCCAAAG 60.070 52.381 23.42 13.68 0.00 2.77
190 199 1.600916 GCGGGAGTTATGATGGGGC 60.601 63.158 0.00 0.00 0.00 5.80
193 202 1.961277 GCCGCGGGAGTTATGATGG 60.961 63.158 29.38 0.00 0.00 3.51
234 243 1.228124 TTGTTGACAGGCGGAAGGG 60.228 57.895 0.00 0.00 0.00 3.95
239 248 4.025401 GCCGTTGTTGACAGGCGG 62.025 66.667 18.41 18.41 43.76 6.13
307 318 7.483580 TTTTTCCCTGAAAGAAAAACTGGTA 57.516 32.000 7.19 0.00 44.25 3.25
332 343 8.219436 TGATCAACTACTAGTAACGTTTTTCG 57.781 34.615 5.91 0.00 46.00 3.46
338 349 7.918536 TCTCTTGATCAACTACTAGTAACGT 57.081 36.000 3.38 0.00 0.00 3.99
339 350 9.279904 CTTTCTCTTGATCAACTACTAGTAACG 57.720 37.037 3.38 0.00 0.00 3.18
340 351 9.575783 CCTTTCTCTTGATCAACTACTAGTAAC 57.424 37.037 3.38 0.00 0.00 2.50
341 352 9.529823 TCCTTTCTCTTGATCAACTACTAGTAA 57.470 33.333 3.38 0.00 0.00 2.24
342 353 9.529823 TTCCTTTCTCTTGATCAACTACTAGTA 57.470 33.333 3.38 1.89 0.00 1.82
343 354 8.423906 TTCCTTTCTCTTGATCAACTACTAGT 57.576 34.615 3.38 0.00 0.00 2.57
344 355 9.145865 GTTTCCTTTCTCTTGATCAACTACTAG 57.854 37.037 3.38 0.00 0.00 2.57
352 365 6.207417 GGATGTTGTTTCCTTTCTCTTGATCA 59.793 38.462 0.00 0.00 0.00 2.92
364 377 2.293399 GCTTCGTTGGATGTTGTTTCCT 59.707 45.455 0.00 0.00 34.17 3.36
365 378 2.293399 AGCTTCGTTGGATGTTGTTTCC 59.707 45.455 0.00 0.00 0.00 3.13
416 429 5.242615 CGACATCTCAAGATCCTTGATCCTA 59.757 44.000 9.51 0.00 39.66 2.94
418 431 4.202202 ACGACATCTCAAGATCCTTGATCC 60.202 45.833 9.51 0.00 39.66 3.36
421 434 3.763897 TGACGACATCTCAAGATCCTTGA 59.236 43.478 8.83 8.83 31.21 3.02
488 503 1.205893 GAAGGGATCGAGCAAGACTGT 59.794 52.381 1.84 0.00 0.00 3.55
489 504 1.480137 AGAAGGGATCGAGCAAGACTG 59.520 52.381 1.84 0.00 0.00 3.51
490 505 1.754226 GAGAAGGGATCGAGCAAGACT 59.246 52.381 1.84 0.00 0.00 3.24
491 506 1.535015 CGAGAAGGGATCGAGCAAGAC 60.535 57.143 1.84 0.00 42.76 3.01
492 507 0.741326 CGAGAAGGGATCGAGCAAGA 59.259 55.000 1.84 0.00 42.76 3.02
493 508 0.457851 ACGAGAAGGGATCGAGCAAG 59.542 55.000 1.84 0.00 42.76 4.01
494 509 0.895530 AACGAGAAGGGATCGAGCAA 59.104 50.000 1.84 0.00 42.76 3.91
496 511 0.741915 AGAACGAGAAGGGATCGAGC 59.258 55.000 1.94 0.00 42.76 5.03
497 512 1.003331 CGAGAACGAGAAGGGATCGAG 60.003 57.143 1.94 0.00 42.76 4.04
498 513 1.015109 CGAGAACGAGAAGGGATCGA 58.985 55.000 1.94 0.00 42.76 3.59
510 794 3.181774 CGGGAATAAATACTGCGAGAACG 59.818 47.826 0.00 0.00 42.93 3.95
569 869 6.904498 TGATTTGTCACCGTTTTTAATCGAT 58.096 32.000 0.00 0.00 0.00 3.59
570 870 6.301687 TGATTTGTCACCGTTTTTAATCGA 57.698 33.333 0.00 0.00 0.00 3.59
572 872 6.128929 GCCTTGATTTGTCACCGTTTTTAATC 60.129 38.462 0.00 0.00 0.00 1.75
573 873 5.694458 GCCTTGATTTGTCACCGTTTTTAAT 59.306 36.000 0.00 0.00 0.00 1.40
584 884 2.517959 CTCCAAGGCCTTGATTTGTCA 58.482 47.619 41.10 17.14 42.93 3.58
618 918 0.757188 TGGTTTGGTTGTGCCCGAAT 60.757 50.000 0.00 0.00 36.04 3.34
619 919 1.379977 TGGTTTGGTTGTGCCCGAA 60.380 52.632 0.00 0.00 36.04 4.30
620 920 1.826054 CTGGTTTGGTTGTGCCCGA 60.826 57.895 0.00 0.00 36.04 5.14
621 921 2.124693 ACTGGTTTGGTTGTGCCCG 61.125 57.895 0.00 0.00 36.04 6.13
624 939 1.334869 CTCTCACTGGTTTGGTTGTGC 59.665 52.381 0.00 0.00 0.00 4.57
754 1077 2.243221 GTGGGTGGAGGGACTAGTAGTA 59.757 54.545 1.88 0.00 41.55 1.82
755 1078 1.006878 GTGGGTGGAGGGACTAGTAGT 59.993 57.143 1.37 1.37 41.55 2.73
756 1079 1.006758 TGTGGGTGGAGGGACTAGTAG 59.993 57.143 0.00 0.00 41.55 2.57
872 1212 4.742201 TCGGTGCTCGCTTGGCTC 62.742 66.667 0.00 0.00 39.05 4.70
883 1223 0.179100 TTCTCTGCTATGCTCGGTGC 60.179 55.000 0.00 0.00 43.25 5.01
893 1233 0.692476 TTGGCTTGGCTTCTCTGCTA 59.308 50.000 0.00 0.00 0.00 3.49
901 1241 2.664402 TCTTCTTCTTGGCTTGGCTT 57.336 45.000 0.00 0.00 0.00 4.35
906 1251 4.508662 CGGTCTATTCTTCTTCTTGGCTT 58.491 43.478 0.00 0.00 0.00 4.35
982 1336 0.698886 ATGGCCTGCCCTCCTGAATA 60.699 55.000 3.32 0.00 34.56 1.75
983 1337 2.011044 ATGGCCTGCCCTCCTGAAT 61.011 57.895 3.32 0.00 34.56 2.57
984 1338 2.614969 ATGGCCTGCCCTCCTGAA 60.615 61.111 3.32 0.00 34.56 3.02
1032 1386 2.052690 TGTACCTGCGAGGAGGAGC 61.053 63.158 17.59 9.42 37.67 4.70
1100 1471 2.334946 GCGCAATTCAGCTCCCACA 61.335 57.895 0.30 0.00 0.00 4.17
1104 1475 2.099062 CACGCGCAATTCAGCTCC 59.901 61.111 5.73 0.00 0.00 4.70
1150 1521 0.398318 ACCACCTCACCTTCAAGAGC 59.602 55.000 0.00 0.00 0.00 4.09
1410 1805 0.036671 TGTCAGAGAGGTCGAGCGTA 60.037 55.000 9.28 0.00 0.00 4.42
1411 1806 0.889638 TTGTCAGAGAGGTCGAGCGT 60.890 55.000 9.28 0.00 0.00 5.07
1497 1896 0.036164 CGGTGATGAGGTTGTGGGAA 59.964 55.000 0.00 0.00 0.00 3.97
1743 2142 1.166531 CCCTGAATTTCGCGATCCCC 61.167 60.000 10.88 0.42 0.00 4.81
1746 2145 3.312421 TGAATTCCCTGAATTTCGCGATC 59.688 43.478 10.88 5.25 41.56 3.69
1820 2231 4.341783 ACTGGAGCCTGCAGCCAC 62.342 66.667 13.67 0.00 45.47 5.01
1998 2414 4.868734 GGTATCTTCCGATCGAACTTGTTT 59.131 41.667 18.66 0.00 0.00 2.83
2046 2462 2.161211 GCTCATGTCCAAGAACTGAAGC 59.839 50.000 0.00 0.00 0.00 3.86
2082 2498 0.932585 AAATTTGTTGCACGTCGCCG 60.933 50.000 7.38 0.00 41.33 6.46
2097 2513 2.604614 GCTCGTGAAGTTGCCGAAAATT 60.605 45.455 0.00 0.00 0.00 1.82
2112 2528 3.181526 GCACAAGATACTTCAAGCTCGTG 60.182 47.826 0.00 3.05 0.00 4.35
2248 2664 1.153086 GGCTCTTCATGTCGGCCAT 60.153 57.895 2.24 0.00 42.08 4.40
2406 2822 0.954449 GCATCAGCCATAGCAGCGAT 60.954 55.000 0.00 0.00 43.56 4.58
2412 2828 3.251974 GCGAGCATCAGCCATAGC 58.748 61.111 0.00 0.00 43.56 2.97
2643 5145 2.762459 AACGGGGGATAGCTCGCA 60.762 61.111 0.00 0.00 36.10 5.10
2769 5325 1.752833 GGAGACCGTGTTGGACCTT 59.247 57.895 0.00 0.00 42.00 3.50
2812 5368 2.396590 GGTATCTCACCGGAAAGCAA 57.603 50.000 9.46 0.00 37.63 3.91
3075 5634 4.463209 GGTTGTATGACACGTTGAACATG 58.537 43.478 0.00 0.00 0.00 3.21
3147 5706 2.650116 GCCGAGGAAGGACTGCTCA 61.650 63.158 0.00 0.00 42.49 4.26
3189 5748 2.606519 TTACCGGCAGCTCCACCT 60.607 61.111 0.00 0.00 34.01 4.00
3208 5767 1.227734 CTTCCGGTCGTGGTGGTTT 60.228 57.895 0.00 0.00 0.00 3.27
3273 5832 1.527433 GGGAGAAAAGCAGCCACACC 61.527 60.000 0.00 0.00 0.00 4.16
3302 5864 4.812476 CGGTGCCGGCGATGAAGA 62.812 66.667 23.90 0.00 35.56 2.87
3322 5884 2.456119 GGCTGGTGATCGCGAACAG 61.456 63.158 20.05 20.92 0.00 3.16
3382 5944 3.084579 GTGCTCGCACGAGAATGG 58.915 61.111 23.33 0.00 44.53 3.16
4276 6844 1.337703 CAGCTCGAGAAGATCCCAGAG 59.662 57.143 18.75 0.00 0.00 3.35
4284 6852 1.519246 CATGCCCAGCTCGAGAAGA 59.481 57.895 18.75 0.00 0.00 2.87
4287 6855 4.519437 CGCATGCCCAGCTCGAGA 62.519 66.667 18.75 0.00 0.00 4.04
4326 6894 4.783621 GGCATGTCTGGCCGCTCA 62.784 66.667 0.00 0.00 42.39 4.26
4335 6903 2.680352 AGGACGACCGGCATGTCT 60.680 61.111 17.57 1.95 41.83 3.41
4400 6968 1.604879 TCGCTGTGTCCTGAGCTCT 60.605 57.895 16.19 0.00 32.70 4.09
4508 7077 3.745799 ACATACATGAACGAACACCCAA 58.254 40.909 0.00 0.00 0.00 4.12
4513 7082 6.180771 TCTACGTACATACATGAACGAACA 57.819 37.500 0.00 0.00 0.00 3.18
4518 7087 8.456904 TCTTTGTTCTACGTACATACATGAAC 57.543 34.615 0.00 12.26 33.76 3.18
4531 7100 8.283291 ACTTTGCTTCTTTATCTTTGTTCTACG 58.717 33.333 0.00 0.00 0.00 3.51
4536 7105 8.882736 CCAAAACTTTGCTTCTTTATCTTTGTT 58.117 29.630 0.00 0.00 36.86 2.83
4601 7171 4.887071 CCCTATTTTGTGGTAGCATGCTTA 59.113 41.667 28.02 10.26 0.00 3.09
4602 7172 3.701040 CCCTATTTTGTGGTAGCATGCTT 59.299 43.478 28.02 10.27 0.00 3.91
4603 7173 3.290710 CCCTATTTTGTGGTAGCATGCT 58.709 45.455 25.99 25.99 0.00 3.79
4604 7174 3.023832 ACCCTATTTTGTGGTAGCATGC 58.976 45.455 10.51 10.51 0.00 4.06
4605 7175 3.381272 CCACCCTATTTTGTGGTAGCATG 59.619 47.826 0.00 0.00 45.61 4.06
4606 7176 3.631250 CCACCCTATTTTGTGGTAGCAT 58.369 45.455 0.00 0.00 45.61 3.79
4607 7177 3.080300 CCACCCTATTTTGTGGTAGCA 57.920 47.619 0.00 0.00 45.61 3.49
4623 7193 2.381752 AGCATATTTTAGGGGCCACC 57.618 50.000 0.00 0.57 40.67 4.61
4624 7194 5.125578 GCTAATAGCATATTTTAGGGGCCAC 59.874 44.000 4.39 0.00 41.89 5.01
4635 7205 9.254133 CGTGATATAGCAAGCTAATAGCATATT 57.746 33.333 15.28 0.00 45.56 1.28
4651 7221 8.636843 GTTAATAACACACTAGCGTGATATAGC 58.363 37.037 17.55 6.03 43.97 2.97
4659 7229 5.091431 GTCTCGTTAATAACACACTAGCGT 58.909 41.667 3.91 0.00 0.00 5.07
4660 7230 5.090757 TGTCTCGTTAATAACACACTAGCG 58.909 41.667 3.91 0.00 0.00 4.26
4662 7232 8.462143 ACAATGTCTCGTTAATAACACACTAG 57.538 34.615 3.91 0.00 0.00 2.57
4664 7234 7.868922 TGTACAATGTCTCGTTAATAACACACT 59.131 33.333 3.91 0.00 0.00 3.55
4665 7235 7.948363 GTGTACAATGTCTCGTTAATAACACAC 59.052 37.037 0.00 2.84 34.12 3.82
4666 7236 7.868922 AGTGTACAATGTCTCGTTAATAACACA 59.131 33.333 0.00 1.03 35.87 3.72
4670 7241 9.647797 AATCAGTGTACAATGTCTCGTTAATAA 57.352 29.630 21.56 0.00 0.00 1.40
4672 7243 8.547967 AAATCAGTGTACAATGTCTCGTTAAT 57.452 30.769 21.56 3.88 0.00 1.40
4702 7273 3.924144 TGTGTTTTCATTAATGCCTGCC 58.076 40.909 10.76 0.00 0.00 4.85
4707 7279 9.520204 AGCATACTATTGTGTTTTCATTAATGC 57.480 29.630 10.76 0.00 0.00 3.56
4715 7287 8.761497 TCGCTAATAGCATACTATTGTGTTTTC 58.239 33.333 13.15 0.00 46.36 2.29
4717 7289 8.833231 ATCGCTAATAGCATACTATTGTGTTT 57.167 30.769 13.15 0.00 46.36 2.83
4729 7301 6.865726 GCATGCTATAGTATCGCTAATAGCAT 59.134 38.462 18.27 18.27 45.36 3.79
4731 7303 6.442952 AGCATGCTATAGTATCGCTAATAGC 58.557 40.000 21.21 1.41 37.34 2.97
4777 7349 0.035439 AAGTGATTGACGCGGGGAAT 60.035 50.000 12.47 5.02 0.00 3.01
4779 7351 0.828022 ATAAGTGATTGACGCGGGGA 59.172 50.000 12.47 0.00 0.00 4.81
4781 7353 0.304705 GCATAAGTGATTGACGCGGG 59.695 55.000 12.47 0.00 0.00 6.13
4782 7354 1.290203 AGCATAAGTGATTGACGCGG 58.710 50.000 12.47 0.00 0.00 6.46
4783 7355 3.389687 AAAGCATAAGTGATTGACGCG 57.610 42.857 3.53 3.53 33.54 6.01
4784 7356 4.786609 GCCTAAAGCATAAGTGATTGACGC 60.787 45.833 0.00 0.00 42.97 5.19
4785 7357 4.260784 GGCCTAAAGCATAAGTGATTGACG 60.261 45.833 0.00 0.00 46.50 4.35
4786 7358 4.884164 AGGCCTAAAGCATAAGTGATTGAC 59.116 41.667 1.29 0.00 46.50 3.18
4788 7360 5.357878 TCAAGGCCTAAAGCATAAGTGATTG 59.642 40.000 5.16 0.00 46.50 2.67
4789 7361 5.509498 TCAAGGCCTAAAGCATAAGTGATT 58.491 37.500 5.16 0.00 46.50 2.57
4790 7362 5.116084 TCAAGGCCTAAAGCATAAGTGAT 57.884 39.130 5.16 0.00 46.50 3.06
4810 7382 3.068165 ACGCTTCTGATCGTTGGATATCA 59.932 43.478 4.83 0.00 35.09 2.15
4811 7383 3.426859 CACGCTTCTGATCGTTGGATATC 59.573 47.826 0.00 0.00 36.73 1.63
4822 7394 2.029288 CGGCACACACGCTTCTGAT 61.029 57.895 0.00 0.00 0.00 2.90
4825 7397 2.661866 GACGGCACACACGCTTCT 60.662 61.111 0.00 0.00 34.00 2.85
4826 7398 1.841663 AATGACGGCACACACGCTTC 61.842 55.000 0.00 0.00 34.00 3.86
4828 7400 2.280797 AATGACGGCACACACGCT 60.281 55.556 0.00 0.00 34.00 5.07
4829 7401 2.127270 CAATGACGGCACACACGC 60.127 61.111 0.00 0.00 34.00 5.34
4830 7402 2.127270 GCAATGACGGCACACACG 60.127 61.111 0.00 0.00 37.36 4.49
4831 7403 2.255252 GGCAATGACGGCACACAC 59.745 61.111 0.00 0.00 0.00 3.82
4832 7404 2.983030 GGGCAATGACGGCACACA 60.983 61.111 0.00 0.00 33.96 3.72
4833 7405 3.747976 GGGGCAATGACGGCACAC 61.748 66.667 0.00 0.00 36.03 3.82
4838 7410 4.506255 GGGAGGGGGCAATGACGG 62.506 72.222 0.00 0.00 0.00 4.79
5140 7712 2.034687 CACAAGGGGTGGAGGCAG 59.965 66.667 0.00 0.00 44.04 4.85
5179 7751 2.044806 ATACATCTGCGGGTGGAGGC 62.045 60.000 11.30 0.00 33.73 4.70
5183 7764 1.670811 GAACAATACATCTGCGGGTGG 59.329 52.381 11.30 0.00 0.00 4.61
5184 7765 1.327460 CGAACAATACATCTGCGGGTG 59.673 52.381 3.61 3.61 0.00 4.61
5193 7774 1.822186 GGGGCGGCGAACAATACAT 60.822 57.895 12.98 0.00 0.00 2.29
5238 7819 3.081804 GGGATCACCGAAGTTGTTCATT 58.918 45.455 0.00 0.00 36.97 2.57
5249 7830 3.399181 GGTGCAGGGGATCACCGA 61.399 66.667 8.77 0.00 42.67 4.69
5252 7833 1.267574 TGAGAGGTGCAGGGGATCAC 61.268 60.000 0.00 0.00 0.00 3.06
5253 7834 1.080907 TGAGAGGTGCAGGGGATCA 59.919 57.895 0.00 0.00 0.00 2.92
5256 7837 2.607750 GGTGAGAGGTGCAGGGGA 60.608 66.667 0.00 0.00 0.00 4.81
5290 7871 2.373335 TTTAAAGGAAGCCACAGCCA 57.627 45.000 0.00 0.00 41.25 4.75
5293 7874 7.229506 CCCTATCTATTTTAAAGGAAGCCACAG 59.770 40.741 0.00 0.00 0.00 3.66
5304 7911 8.395605 AGAACCAACCACCCTATCTATTTTAAA 58.604 33.333 0.00 0.00 0.00 1.52
5318 7925 1.599797 CACCGGAGAACCAACCACC 60.600 63.158 9.46 0.00 35.59 4.61
5340 7947 4.637489 CGAGATGGAGAGGCCGCG 62.637 72.222 0.00 0.00 40.66 6.46
5349 7956 4.193334 CCGAGCGCACGAGATGGA 62.193 66.667 28.63 0.00 35.09 3.41
5400 8007 4.516698 TCTCACACTGGATTTTCTTCTTGC 59.483 41.667 0.00 0.00 0.00 4.01
5417 8024 3.849574 TCCCCCAAATCTATTGTCTCACA 59.150 43.478 0.00 0.00 0.00 3.58
5418 8025 4.503714 TCCCCCAAATCTATTGTCTCAC 57.496 45.455 0.00 0.00 0.00 3.51
5419 8026 5.687441 CGATTCCCCCAAATCTATTGTCTCA 60.687 44.000 0.00 0.00 34.19 3.27
5420 8027 4.757149 CGATTCCCCCAAATCTATTGTCTC 59.243 45.833 0.00 0.00 34.19 3.36
5421 8028 4.446311 CCGATTCCCCCAAATCTATTGTCT 60.446 45.833 0.00 0.00 34.19 3.41
5422 8029 3.821033 CCGATTCCCCCAAATCTATTGTC 59.179 47.826 0.00 0.00 34.19 3.18
5423 8030 3.832527 CCGATTCCCCCAAATCTATTGT 58.167 45.455 0.00 0.00 34.19 2.71
5424 8031 2.558359 GCCGATTCCCCCAAATCTATTG 59.442 50.000 0.00 0.00 34.19 1.90
5425 8032 2.447047 AGCCGATTCCCCCAAATCTATT 59.553 45.455 0.00 0.00 34.19 1.73
5426 8033 2.065799 AGCCGATTCCCCCAAATCTAT 58.934 47.619 0.00 0.00 34.19 1.98
5427 8034 1.518367 AGCCGATTCCCCCAAATCTA 58.482 50.000 0.00 0.00 34.19 1.98
5428 8035 2.321720 AGCCGATTCCCCCAAATCT 58.678 52.632 0.00 0.00 34.19 2.40


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

AutoCloner maintained by Alex Coulton.