Multiple sequence alignment - TraesCS7D01G015100

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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 TraesCS7D01G015100 chr7D 100.000 3413 0 0 1 3413 6490044 6493456 0.000000e+00 6303.0
1 TraesCS7D01G015100 chr7D 81.731 1560 210 44 835 2380 6582113 6583611 0.000000e+00 1232.0
2 TraesCS7D01G015100 chr7D 83.013 677 62 19 2480 3143 6583686 6584322 6.390000e-157 564.0
3 TraesCS7D01G015100 chr7D 80.802 698 58 38 800 1483 6465252 6464617 8.570000e-131 477.0
4 TraesCS7D01G015100 chr7D 78.481 553 90 19 2479 3025 6584697 6585226 5.460000e-88 335.0
5 TraesCS7D01G015100 chr7D 82.913 357 45 9 20 363 6567004 6567357 1.190000e-79 307.0
6 TraesCS7D01G015100 chr7D 92.982 57 3 1 3167 3223 19284595 19284540 7.850000e-12 82.4
7 TraesCS7D01G015100 chr7A 90.647 2673 164 46 498 3143 7628359 7630972 0.000000e+00 3472.0
8 TraesCS7D01G015100 chr7A 82.395 1403 193 33 999 2387 7634193 7635555 0.000000e+00 1173.0
9 TraesCS7D01G015100 chr7A 82.317 1131 174 15 1263 2387 7669614 7670724 0.000000e+00 957.0
10 TraesCS7D01G015100 chr7A 86.726 678 63 20 2479 3143 7670794 7671457 0.000000e+00 728.0
11 TraesCS7D01G015100 chr7A 88.911 514 48 7 2 507 7627595 7628107 2.890000e-175 625.0
12 TraesCS7D01G015100 chr7A 83.161 677 59 19 2480 3143 7635625 7636259 4.940000e-158 568.0
13 TraesCS7D01G015100 chr7A 94.819 193 10 0 3221 3413 7631135 7631327 5.540000e-78 302.0
14 TraesCS7D01G015100 chr7A 77.046 562 90 27 2479 3025 7636634 7637171 1.550000e-73 287.0
15 TraesCS7D01G015100 chr7A 80.000 230 27 7 940 1163 7669286 7669502 5.900000e-33 152.0
16 TraesCS7D01G015100 chr7A 91.525 59 5 0 3164 3222 337920479 337920421 7.850000e-12 82.4
17 TraesCS7D01G015100 chr7A 87.500 64 8 0 1306 1369 673126700 673126763 1.310000e-09 75.0
18 TraesCS7D01G015100 chr4A 90.860 2046 119 25 727 2740 733672430 733670421 0.000000e+00 2680.0
19 TraesCS7D01G015100 chr4A 82.789 1592 199 39 809 2382 733741209 733742743 0.000000e+00 1352.0
20 TraesCS7D01G015100 chr4A 92.203 885 54 6 1632 2504 733761469 733762350 0.000000e+00 1238.0
21 TraesCS7D01G015100 chr4A 80.991 1473 216 39 940 2387 733640383 733638950 0.000000e+00 1110.0
22 TraesCS7D01G015100 chr4A 89.964 827 56 12 819 1635 733759877 733760686 0.000000e+00 1042.0
23 TraesCS7D01G015100 chr4A 85.420 679 74 15 2479 3146 733638881 733638217 0.000000e+00 682.0
24 TraesCS7D01G015100 chr4A 90.101 495 32 10 2558 3046 733762369 733762852 8.040000e-176 627.0
25 TraesCS7D01G015100 chr4A 91.185 329 18 7 2821 3146 733670376 733670056 1.450000e-118 436.0
26 TraesCS7D01G015100 chr4A 85.143 175 24 1 557 729 666202253 666202079 9.730000e-41 178.0
27 TraesCS7D01G015100 chr4A 84.530 181 26 1 551 729 703764766 703764946 9.730000e-41 178.0
28 TraesCS7D01G015100 chr4A 80.176 227 36 5 512 731 521058454 521058678 9.800000e-36 161.0
29 TraesCS7D01G015100 chr4A 95.238 63 2 1 3351 3413 733669840 733669779 7.790000e-17 99.0
30 TraesCS7D01G015100 chr4A 84.091 88 13 1 1 87 733673748 733673661 2.180000e-12 84.2
31 TraesCS7D01G015100 chr4A 84.091 88 13 1 1 87 733674413 733674326 2.180000e-12 84.2
32 TraesCS7D01G015100 chr4A 82.759 87 15 0 1 87 733673084 733672998 1.020000e-10 78.7
33 TraesCS7D01G015100 chr6D 86.705 173 23 0 557 729 444880600 444880428 3.480000e-45 193.0
34 TraesCS7D01G015100 chr6D 91.379 58 5 0 3165 3222 20134865 20134808 2.820000e-11 80.5
35 TraesCS7D01G015100 chr3A 85.549 173 23 1 557 727 630764156 630763984 2.710000e-41 180.0
36 TraesCS7D01G015100 chr3A 84.831 178 25 1 548 723 142902964 142903141 9.730000e-41 178.0
37 TraesCS7D01G015100 chr7B 84.831 178 25 1 554 729 640272230 640272407 9.730000e-41 178.0
38 TraesCS7D01G015100 chr1B 85.143 175 24 1 557 729 601378761 601378587 9.730000e-41 178.0
39 TraesCS7D01G015100 chr1B 85.143 175 24 1 557 729 673633913 673633739 9.730000e-41 178.0
40 TraesCS7D01G015100 chr5B 93.103 58 4 0 3166 3223 7227272 7227329 6.070000e-13 86.1
41 TraesCS7D01G015100 chr5B 91.379 58 5 0 3166 3223 7351331 7351388 2.820000e-11 80.5
42 TraesCS7D01G015100 chr1D 93.103 58 4 0 3165 3222 293591231 293591174 6.070000e-13 86.1
43 TraesCS7D01G015100 chr1D 91.667 60 5 0 3165 3224 420068334 420068275 2.180000e-12 84.2
44 TraesCS7D01G015100 chr1D 91.525 59 5 0 3165 3223 430320447 430320505 7.850000e-12 82.4
45 TraesCS7D01G015100 chr2D 92.857 56 4 0 3164 3219 473094384 473094439 7.850000e-12 82.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G015100 chr7D 6490044 6493456 3412 False 6303.000000 6303 100.000000 1 3413 1 chr7D.!!$F1 3412
1 TraesCS7D01G015100 chr7D 6582113 6585226 3113 False 710.333333 1232 81.075000 835 3143 3 chr7D.!!$F3 2308
2 TraesCS7D01G015100 chr7D 6464617 6465252 635 True 477.000000 477 80.802000 800 1483 1 chr7D.!!$R1 683
3 TraesCS7D01G015100 chr7A 7627595 7637171 9576 False 1071.166667 3472 86.163167 2 3413 6 chr7A.!!$F2 3411
4 TraesCS7D01G015100 chr7A 7669286 7671457 2171 False 612.333333 957 83.014333 940 3143 3 chr7A.!!$F3 2203
5 TraesCS7D01G015100 chr4A 733741209 733742743 1534 False 1352.000000 1352 82.789000 809 2382 1 chr4A.!!$F3 1573
6 TraesCS7D01G015100 chr4A 733759877 733762852 2975 False 969.000000 1238 90.756000 819 3046 3 chr4A.!!$F4 2227
7 TraesCS7D01G015100 chr4A 733638217 733640383 2166 True 896.000000 1110 83.205500 940 3146 2 chr4A.!!$R2 2206
8 TraesCS7D01G015100 chr4A 733669779 733674413 4634 True 577.016667 2680 88.037333 1 3413 6 chr4A.!!$R3 3412

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
64 66 0.036388 GTTGCTCGAGGACATCCCAA 60.036 55.0 15.58 4.93 37.41 4.12 F
173 815 0.178955 TCTCGTTGGGTGGTAGGACA 60.179 55.0 0.00 0.00 0.00 4.02 F
457 1764 0.324943 TTCAGAAAAGAGGAGGCGGG 59.675 55.0 0.00 0.00 0.00 6.13 F
1253 2930 0.322008 CAGAGGAACCAGAGGCAACC 60.322 60.0 0.00 0.00 37.17 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1226 2903 1.273606 TCTGGTTCCTCTGCTTCTTCG 59.726 52.381 0.00 0.0 0.0 3.79 R
1229 2906 1.274712 CCTCTGGTTCCTCTGCTTCT 58.725 55.000 0.00 0.0 0.0 2.85 R
2181 4666 0.670854 GGCGGCGATAATCCTCTTCC 60.671 60.000 12.98 0.0 0.0 3.46 R
3157 11017 0.178990 GTTGTTGTTCTGCCTCCCCT 60.179 55.000 0.00 0.0 0.0 4.79 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
47 49 2.531942 GTGGGGTCCTCCAGGGTT 60.532 66.667 0.00 0.00 37.50 4.11
59 61 1.599047 CAGGGTTGCTCGAGGACAT 59.401 57.895 15.58 0.00 0.00 3.06
64 66 0.036388 GTTGCTCGAGGACATCCCAA 60.036 55.000 15.58 4.93 37.41 4.12
75 77 2.496470 GGACATCCCAAGAGTTAGACGT 59.504 50.000 0.00 0.00 34.14 4.34
92 94 3.478857 ACGTGAGTACCAAATGGACAA 57.521 42.857 6.42 0.00 46.88 3.18
104 106 4.094146 CCAAATGGACAACAAACAAACACC 59.906 41.667 0.00 0.00 37.39 4.16
105 107 4.543590 AATGGACAACAAACAAACACCA 57.456 36.364 0.00 0.00 0.00 4.17
106 108 4.543590 ATGGACAACAAACAAACACCAA 57.456 36.364 0.00 0.00 0.00 3.67
120 762 9.691362 AAACAAACACCAATGAATTACTCATAC 57.309 29.630 0.00 0.00 44.43 2.39
146 788 0.947244 CTTTTCTTGCAGGTCAGCGT 59.053 50.000 0.00 0.00 37.31 5.07
150 792 0.894835 TCTTGCAGGTCAGCGTCATA 59.105 50.000 0.00 0.00 37.31 2.15
171 813 1.255667 GCTCTCGTTGGGTGGTAGGA 61.256 60.000 0.00 0.00 0.00 2.94
173 815 0.178955 TCTCGTTGGGTGGTAGGACA 60.179 55.000 0.00 0.00 0.00 4.02
222 1529 7.118680 GTGTATCAATAGTCCGAACCAAAAAGA 59.881 37.037 0.00 0.00 0.00 2.52
248 1555 2.006888 CAATATCGACGCCAAGTGGTT 58.993 47.619 0.00 0.00 37.57 3.67
279 1586 3.856521 GCATAACAACATTAATGTGCGCA 59.143 39.130 21.46 5.66 41.61 6.09
291 1598 7.330454 ACATTAATGTGCGCAATTAAAACATCA 59.670 29.630 26.45 14.28 40.03 3.07
373 1680 8.363390 TGTTATGCAAAAGTTATGGTGAAATCA 58.637 29.630 0.00 0.00 0.00 2.57
412 1719 7.747155 TCCACCGTTGATTTATTGTTAAAGA 57.253 32.000 0.00 0.00 31.07 2.52
416 1723 8.372521 CACCGTTGATTTATTGTTAAAGATTGC 58.627 33.333 0.00 0.00 31.07 3.56
457 1764 0.324943 TTCAGAAAAGAGGAGGCGGG 59.675 55.000 0.00 0.00 0.00 6.13
458 1765 0.836400 TCAGAAAAGAGGAGGCGGGT 60.836 55.000 0.00 0.00 0.00 5.28
460 1767 1.486726 CAGAAAAGAGGAGGCGGGTAT 59.513 52.381 0.00 0.00 0.00 2.73
493 1802 1.976045 GACCAAGCGTGTTAATTTGCG 59.024 47.619 0.00 0.00 0.00 4.85
507 1816 1.803334 TTTGCGTGCAGGTAAGGTAG 58.197 50.000 9.79 0.00 0.00 3.18
549 2117 0.733150 TCCAGACGTAGACGCTCATG 59.267 55.000 1.14 0.00 44.43 3.07
567 2139 1.996292 TGCGTGCTTACACTCATCTC 58.004 50.000 0.00 0.00 45.10 2.75
582 2154 4.218635 ACTCATCTCTATGAACACACACGT 59.781 41.667 0.00 0.00 41.57 4.49
593 2165 2.522185 ACACACACGTACATCCTACCT 58.478 47.619 0.00 0.00 0.00 3.08
594 2166 2.895404 ACACACACGTACATCCTACCTT 59.105 45.455 0.00 0.00 0.00 3.50
604 2177 4.423625 ACATCCTACCTTTATGAGCACC 57.576 45.455 0.00 0.00 0.00 5.01
607 2180 3.995636 TCCTACCTTTATGAGCACCTCT 58.004 45.455 0.00 0.00 0.00 3.69
634 2210 2.620115 ACTGAGCCGGCATATCATTTTG 59.380 45.455 31.54 13.72 0.00 2.44
639 2215 4.910195 AGCCGGCATATCATTTTGAGATA 58.090 39.130 31.54 0.00 32.93 1.98
640 2216 5.316167 AGCCGGCATATCATTTTGAGATAA 58.684 37.500 31.54 0.00 32.22 1.75
655 2231 7.827819 TTTGAGATAAACGAAGTCACCATAG 57.172 36.000 0.00 0.00 45.00 2.23
656 2232 6.525578 TGAGATAAACGAAGTCACCATAGT 57.474 37.500 0.00 0.00 45.00 2.12
658 2234 5.579718 AGATAAACGAAGTCACCATAGTCG 58.420 41.667 0.00 0.00 45.00 4.18
659 2235 3.655276 AAACGAAGTCACCATAGTCGT 57.345 42.857 0.00 0.00 45.00 4.34
666 2242 3.196463 AGTCACCATAGTCGTCTCGTAG 58.804 50.000 0.00 0.00 0.00 3.51
669 2245 2.934553 CACCATAGTCGTCTCGTAGTCA 59.065 50.000 0.00 0.00 0.00 3.41
694 2270 3.310246 GAGACGTCTCTTTCCACTGAAC 58.690 50.000 33.28 7.27 39.81 3.18
695 2271 2.052157 GACGTCTCTTTCCACTGAACG 58.948 52.381 8.70 0.00 0.00 3.95
696 2272 0.784778 CGTCTCTTTCCACTGAACGC 59.215 55.000 0.00 0.00 0.00 4.84
701 2277 2.143122 TCTTTCCACTGAACGCACATC 58.857 47.619 0.00 0.00 0.00 3.06
703 2279 1.565156 TTCCACTGAACGCACATCGC 61.565 55.000 0.00 0.00 43.23 4.58
706 2282 0.642291 CACTGAACGCACATCGCTAG 59.358 55.000 0.00 0.00 43.23 3.42
714 2290 1.789464 CGCACATCGCTAGAAATCCTC 59.211 52.381 0.00 0.00 39.08 3.71
759 2373 6.156256 CCGTCCTCCTAATTATCCCATCATAA 59.844 42.308 0.00 0.00 0.00 1.90
953 2577 2.509561 GGCGAGCTCCGGAACTTC 60.510 66.667 9.15 4.30 39.04 3.01
1135 2763 1.110442 AGCTTCTCAGGTCTGATCCG 58.890 55.000 0.75 0.00 39.13 4.18
1183 2844 1.025041 GGTCAATGGAAGGGAATCGC 58.975 55.000 0.00 0.00 0.00 4.58
1205 2866 4.506095 GCCCGGGAGCCTAATTAATCTTTA 60.506 45.833 29.31 0.00 0.00 1.85
1226 2903 3.498927 TTCGGTCCGTTCATAGAAGAC 57.501 47.619 11.88 0.00 0.00 3.01
1227 2904 1.399440 TCGGTCCGTTCATAGAAGACG 59.601 52.381 11.88 0.00 0.00 4.18
1228 2905 1.399440 CGGTCCGTTCATAGAAGACGA 59.601 52.381 2.08 0.00 0.00 4.20
1229 2906 2.159476 CGGTCCGTTCATAGAAGACGAA 60.159 50.000 2.08 0.00 0.00 3.85
1238 2915 5.242069 TCATAGAAGACGAAGAAGCAGAG 57.758 43.478 0.00 0.00 0.00 3.35
1239 2916 4.097135 TCATAGAAGACGAAGAAGCAGAGG 59.903 45.833 0.00 0.00 0.00 3.69
1240 2917 2.520069 AGAAGACGAAGAAGCAGAGGA 58.480 47.619 0.00 0.00 0.00 3.71
1241 2918 2.894126 AGAAGACGAAGAAGCAGAGGAA 59.106 45.455 0.00 0.00 0.00 3.36
1242 2919 2.734276 AGACGAAGAAGCAGAGGAAC 57.266 50.000 0.00 0.00 0.00 3.62
1243 2920 1.273886 AGACGAAGAAGCAGAGGAACC 59.726 52.381 0.00 0.00 0.00 3.62
1244 2921 1.000955 GACGAAGAAGCAGAGGAACCA 59.999 52.381 0.00 0.00 0.00 3.67
1245 2922 1.001406 ACGAAGAAGCAGAGGAACCAG 59.999 52.381 0.00 0.00 0.00 4.00
1246 2923 1.273606 CGAAGAAGCAGAGGAACCAGA 59.726 52.381 0.00 0.00 0.00 3.86
1247 2924 2.673610 CGAAGAAGCAGAGGAACCAGAG 60.674 54.545 0.00 0.00 0.00 3.35
1248 2925 1.274712 AGAAGCAGAGGAACCAGAGG 58.725 55.000 0.00 0.00 0.00 3.69
1249 2926 0.392327 GAAGCAGAGGAACCAGAGGC 60.392 60.000 0.00 0.00 0.00 4.70
1250 2927 1.130054 AAGCAGAGGAACCAGAGGCA 61.130 55.000 0.00 0.00 0.00 4.75
1251 2928 1.130054 AGCAGAGGAACCAGAGGCAA 61.130 55.000 0.00 0.00 0.00 4.52
1252 2929 0.957888 GCAGAGGAACCAGAGGCAAC 60.958 60.000 0.00 0.00 0.00 4.17
1253 2930 0.322008 CAGAGGAACCAGAGGCAACC 60.322 60.000 0.00 0.00 37.17 3.77
1254 2931 1.376037 GAGGAACCAGAGGCAACCG 60.376 63.158 0.00 0.00 37.17 4.44
1255 2932 3.056328 GGAACCAGAGGCAACCGC 61.056 66.667 0.00 0.00 37.44 5.68
1695 4167 0.389948 ACGACGAAGACCCTGAATGC 60.390 55.000 0.00 0.00 0.00 3.56
1754 4226 3.110178 CCCGTCTCGTTTCGTGGC 61.110 66.667 0.00 0.00 0.00 5.01
1800 4272 1.368493 CGTCGTGGCGGTATACTCG 60.368 63.158 2.25 6.14 0.00 4.18
1806 4278 0.535780 TGGCGGTATACTCGTCGGAT 60.536 55.000 11.81 0.00 34.67 4.18
1824 4296 1.760613 GATACCGGACAATGGACTCCA 59.239 52.381 9.46 0.00 38.19 3.86
1882 4357 2.511600 CGGAATGTGCCGTCCTCC 60.512 66.667 0.00 0.00 46.07 4.30
1883 4358 2.990479 GGAATGTGCCGTCCTCCT 59.010 61.111 0.00 0.00 0.00 3.69
1884 4359 1.153349 GGAATGTGCCGTCCTCCTC 60.153 63.158 0.00 0.00 0.00 3.71
1975 4451 1.906574 AGGTTTGTCGGGAGATTGCTA 59.093 47.619 0.00 0.00 43.27 3.49
2053 4532 3.209410 GGACTCCTTCATGCTTGGTATG 58.791 50.000 0.00 0.00 0.00 2.39
2102 4581 3.129287 GTGTGGGTGCTCAAGGATTATTG 59.871 47.826 0.00 0.00 0.00 1.90
2110 4589 4.877823 TGCTCAAGGATTATTGTGCTACTG 59.122 41.667 12.82 0.00 45.39 2.74
2111 4590 5.118990 GCTCAAGGATTATTGTGCTACTGA 58.881 41.667 6.32 0.00 43.12 3.41
2112 4591 5.762218 GCTCAAGGATTATTGTGCTACTGAT 59.238 40.000 6.32 0.00 43.12 2.90
2127 4606 4.159506 GCTACTGATGAAGAAGAGTGGACT 59.840 45.833 0.00 0.00 0.00 3.85
2146 4625 2.751259 ACTCTAAAGCATACCGTCGACA 59.249 45.455 17.16 0.00 0.00 4.35
2224 4709 1.145571 GGATGGGGCCCATAAGTACA 58.854 55.000 37.41 11.03 45.26 2.90
2295 4780 4.960469 TGGAAGGAGGTAAATCTGTCGTAT 59.040 41.667 0.00 0.00 0.00 3.06
2382 4868 1.337118 TTCCCTGCTTTGCGGATTTT 58.663 45.000 0.00 0.00 37.02 1.82
2466 4968 6.405176 GCCTCCTAGCATTCCAAATTATATGC 60.405 42.308 0.00 0.00 42.76 3.14
2550 5063 0.880278 CCGATCCAGTGGGTAATGCG 60.880 60.000 9.92 1.32 34.93 4.73
2658 5176 2.092211 GTCGGCTGAATGTGAGTTTACG 59.908 50.000 0.00 0.00 0.00 3.18
2675 5193 9.146984 TGAGTTTACGTTATCCATGTTTAGAAG 57.853 33.333 0.00 0.00 0.00 2.85
2760 5287 4.201657 TGTCCATCTATGCTGAACATTGG 58.798 43.478 0.00 0.00 40.38 3.16
2768 5295 1.237285 GCTGAACATTGGTGACGCCT 61.237 55.000 6.60 0.00 38.35 5.52
2774 5301 1.336755 ACATTGGTGACGCCTTGTTTC 59.663 47.619 6.60 0.00 38.35 2.78
2811 5338 0.953471 TTTGCGGATGGTTGGTCTCG 60.953 55.000 0.00 0.00 0.00 4.04
2874 5412 8.902806 GTGTCATTTATGAAACCAATATGGAGA 58.097 33.333 2.85 0.00 38.76 3.71
2972 5514 2.615912 GGGGAGAGAGCAAAATGATTCG 59.384 50.000 0.00 0.00 0.00 3.34
2998 5540 4.799428 CCGTAGCTAAAACTAAGCACTCTC 59.201 45.833 0.00 0.00 42.62 3.20
3025 5567 3.040147 TGCTGTTTGTCACTAGCTACC 57.960 47.619 0.00 0.00 37.10 3.18
3049 5591 9.143155 ACCAGTGTGTTTCTAATTAATTTCCTT 57.857 29.630 5.91 0.00 0.00 3.36
3134 10992 4.283467 TGACCATACTGTTGAACTGCTAGT 59.717 41.667 1.92 0.00 0.00 2.57
3143 11003 4.332543 TGTTGAACTGCTAGTGTTGTCAAG 59.667 41.667 7.75 0.00 26.17 3.02
3146 11006 0.792640 CTGCTAGTGTTGTCAAGCCG 59.207 55.000 0.00 0.00 33.99 5.52
3147 11007 1.227999 TGCTAGTGTTGTCAAGCCGC 61.228 55.000 0.00 0.00 33.99 6.53
3148 11008 1.227999 GCTAGTGTTGTCAAGCCGCA 61.228 55.000 0.00 0.00 0.00 5.69
3149 11009 1.225855 CTAGTGTTGTCAAGCCGCAA 58.774 50.000 0.00 0.00 0.00 4.85
3150 11010 1.601903 CTAGTGTTGTCAAGCCGCAAA 59.398 47.619 0.00 0.00 0.00 3.68
3153 11013 1.028130 TGTTGTCAAGCCGCAAATGA 58.972 45.000 0.00 0.00 0.00 2.57
3156 11016 2.634982 TGTCAAGCCGCAAATGATTC 57.365 45.000 0.00 0.00 0.00 2.52
3157 11017 1.885233 TGTCAAGCCGCAAATGATTCA 59.115 42.857 0.00 0.00 0.00 2.57
3159 11019 1.473677 TCAAGCCGCAAATGATTCAGG 59.526 47.619 0.00 0.00 0.00 3.86
3160 11020 0.819582 AAGCCGCAAATGATTCAGGG 59.180 50.000 0.00 0.00 0.00 4.45
3162 11022 1.037030 GCCGCAAATGATTCAGGGGA 61.037 55.000 14.83 0.00 36.29 4.81
3163 11023 1.027357 CCGCAAATGATTCAGGGGAG 58.973 55.000 7.59 0.00 36.29 4.30
3164 11024 1.027357 CGCAAATGATTCAGGGGAGG 58.973 55.000 0.00 0.00 0.00 4.30
3166 11026 1.961435 GCAAATGATTCAGGGGAGGCA 60.961 52.381 0.00 0.00 0.00 4.75
3167 11027 2.029623 CAAATGATTCAGGGGAGGCAG 58.970 52.381 0.00 0.00 0.00 4.85
3168 11028 1.600058 AATGATTCAGGGGAGGCAGA 58.400 50.000 0.00 0.00 0.00 4.26
3170 11030 0.620556 TGATTCAGGGGAGGCAGAAC 59.379 55.000 0.00 0.00 0.00 3.01
3172 11032 1.004745 GATTCAGGGGAGGCAGAACAA 59.995 52.381 0.00 0.00 0.00 2.83
3173 11033 0.110486 TTCAGGGGAGGCAGAACAAC 59.890 55.000 0.00 0.00 0.00 3.32
3174 11034 1.059584 TCAGGGGAGGCAGAACAACA 61.060 55.000 0.00 0.00 0.00 3.33
3175 11035 0.178992 CAGGGGAGGCAGAACAACAA 60.179 55.000 0.00 0.00 0.00 2.83
3176 11036 0.178990 AGGGGAGGCAGAACAACAAC 60.179 55.000 0.00 0.00 0.00 3.32
3177 11037 1.179174 GGGGAGGCAGAACAACAACC 61.179 60.000 0.00 0.00 0.00 3.77
3178 11038 1.515521 GGGAGGCAGAACAACAACCG 61.516 60.000 0.00 0.00 0.00 4.44
3179 11039 1.282875 GAGGCAGAACAACAACCGC 59.717 57.895 0.00 0.00 0.00 5.68
3180 11040 2.130073 GAGGCAGAACAACAACCGCC 62.130 60.000 0.00 0.00 39.90 6.13
3181 11041 2.051345 GCAGAACAACAACCGCCG 60.051 61.111 0.00 0.00 0.00 6.46
3182 11042 2.051345 CAGAACAACAACCGCCGC 60.051 61.111 0.00 0.00 0.00 6.53
3183 11043 3.284449 AGAACAACAACCGCCGCC 61.284 61.111 0.00 0.00 0.00 6.13
3184 11044 4.676586 GAACAACAACCGCCGCCG 62.677 66.667 0.00 0.00 0.00 6.46
3187 11047 4.459331 CAACAACCGCCGCCGATG 62.459 66.667 0.00 0.00 36.29 3.84
3188 11048 4.690719 AACAACCGCCGCCGATGA 62.691 61.111 0.00 0.00 36.29 2.92
3190 11050 3.864686 CAACCGCCGCCGATGAAG 61.865 66.667 0.00 0.00 36.29 3.02
3191 11051 4.077184 AACCGCCGCCGATGAAGA 62.077 61.111 0.00 0.00 36.29 2.87
3192 11052 4.514577 ACCGCCGCCGATGAAGAG 62.515 66.667 0.00 0.00 36.29 2.85
3197 11057 1.658717 CCGCCGATGAAGAGTAGCG 60.659 63.158 0.00 0.00 42.99 4.26
3201 11061 2.386249 GCCGATGAAGAGTAGCGTAAG 58.614 52.381 0.00 0.00 43.44 2.34
3202 11062 2.223525 GCCGATGAAGAGTAGCGTAAGT 60.224 50.000 0.00 0.00 41.68 2.24
3203 11063 3.619729 CCGATGAAGAGTAGCGTAAGTC 58.380 50.000 0.00 0.00 41.68 3.01
3204 11064 3.281601 CGATGAAGAGTAGCGTAAGTCG 58.718 50.000 0.00 0.00 43.12 4.18
3206 11066 2.703416 TGAAGAGTAGCGTAAGTCGGA 58.297 47.619 0.00 0.00 40.26 4.55
3207 11067 3.076621 TGAAGAGTAGCGTAAGTCGGAA 58.923 45.455 0.00 0.00 40.26 4.30
3208 11068 3.126514 TGAAGAGTAGCGTAAGTCGGAAG 59.873 47.826 0.00 0.00 40.26 3.46
3209 11069 2.015587 AGAGTAGCGTAAGTCGGAAGG 58.984 52.381 0.00 0.00 40.26 3.46
3210 11070 2.012673 GAGTAGCGTAAGTCGGAAGGA 58.987 52.381 0.00 0.00 40.26 3.36
3217 11413 2.793933 CGTAAGTCGGAAGGATCGAACC 60.794 54.545 2.97 2.97 38.42 3.62
3218 11414 1.558233 AAGTCGGAAGGATCGAACCT 58.442 50.000 8.70 8.70 42.69 3.50
3219 11415 1.104630 AGTCGGAAGGATCGAACCTC 58.895 55.000 15.38 8.45 39.62 3.85
3227 11423 2.257207 AGGATCGAACCTCAAACCTCA 58.743 47.619 8.70 0.00 34.98 3.86
3236 11432 2.887152 ACCTCAAACCTCAATGTTCAGC 59.113 45.455 0.00 0.00 0.00 4.26
3278 11474 7.393234 TCAATAAAAACATCTTCAGGTAGGGTG 59.607 37.037 0.00 0.00 0.00 4.61
3279 11475 2.789409 AACATCTTCAGGTAGGGTGC 57.211 50.000 0.00 0.00 0.00 5.01
3280 11476 0.912486 ACATCTTCAGGTAGGGTGCC 59.088 55.000 0.00 0.00 0.00 5.01
3281 11477 1.207791 CATCTTCAGGTAGGGTGCCT 58.792 55.000 0.00 0.00 37.71 4.75
3282 11478 2.292918 ACATCTTCAGGTAGGGTGCCTA 60.293 50.000 0.00 0.00 34.61 3.93
3283 11479 2.634639 TCTTCAGGTAGGGTGCCTAA 57.365 50.000 0.00 0.00 37.91 2.69
3284 11480 2.467880 TCTTCAGGTAGGGTGCCTAAG 58.532 52.381 0.00 0.00 37.91 2.18
3285 11481 2.188817 CTTCAGGTAGGGTGCCTAAGT 58.811 52.381 0.00 0.00 37.91 2.24
3286 11482 2.337359 TCAGGTAGGGTGCCTAAGTT 57.663 50.000 0.00 0.00 37.91 2.66
3287 11483 3.478175 TCAGGTAGGGTGCCTAAGTTA 57.522 47.619 0.00 0.00 37.91 2.24
3288 11484 3.102204 TCAGGTAGGGTGCCTAAGTTAC 58.898 50.000 0.00 0.00 37.91 2.50
3289 11485 3.105283 CAGGTAGGGTGCCTAAGTTACT 58.895 50.000 0.00 0.00 37.91 2.24
3290 11486 3.105283 AGGTAGGGTGCCTAAGTTACTG 58.895 50.000 0.00 0.00 37.91 2.74
3291 11487 3.102204 GGTAGGGTGCCTAAGTTACTGA 58.898 50.000 0.00 0.00 37.91 3.41
3292 11488 3.516700 GGTAGGGTGCCTAAGTTACTGAA 59.483 47.826 0.00 0.00 37.91 3.02
3293 11489 3.697619 AGGGTGCCTAAGTTACTGAAC 57.302 47.619 0.00 0.00 31.07 3.18
3294 11490 2.028385 AGGGTGCCTAAGTTACTGAACG 60.028 50.000 0.00 0.00 34.45 3.95
3295 11491 2.028748 GGGTGCCTAAGTTACTGAACGA 60.029 50.000 0.00 0.00 40.76 3.85
3296 11492 3.555586 GGGTGCCTAAGTTACTGAACGAA 60.556 47.826 0.00 0.00 40.76 3.85
3297 11493 4.060205 GGTGCCTAAGTTACTGAACGAAA 58.940 43.478 0.00 0.00 40.76 3.46
3298 11494 4.151867 GGTGCCTAAGTTACTGAACGAAAG 59.848 45.833 0.00 0.00 40.76 2.62
3299 11495 3.744426 TGCCTAAGTTACTGAACGAAAGC 59.256 43.478 0.00 0.00 40.76 3.51
3300 11496 3.124806 GCCTAAGTTACTGAACGAAAGCC 59.875 47.826 0.00 0.00 40.76 4.35
3301 11497 4.312443 CCTAAGTTACTGAACGAAAGCCA 58.688 43.478 0.00 0.00 40.76 4.75
3302 11498 4.151867 CCTAAGTTACTGAACGAAAGCCAC 59.848 45.833 0.00 0.00 40.76 5.01
3303 11499 3.188159 AGTTACTGAACGAAAGCCACA 57.812 42.857 0.00 0.00 40.76 4.17
3304 11500 3.740115 AGTTACTGAACGAAAGCCACAT 58.260 40.909 0.00 0.00 40.76 3.21
3305 11501 4.890088 AGTTACTGAACGAAAGCCACATA 58.110 39.130 0.00 0.00 40.76 2.29
3306 11502 4.929808 AGTTACTGAACGAAAGCCACATAG 59.070 41.667 0.00 0.00 40.76 2.23
3307 11503 3.678056 ACTGAACGAAAGCCACATAGA 57.322 42.857 0.00 0.00 0.00 1.98
3308 11504 4.002906 ACTGAACGAAAGCCACATAGAA 57.997 40.909 0.00 0.00 0.00 2.10
3309 11505 3.997021 ACTGAACGAAAGCCACATAGAAG 59.003 43.478 0.00 0.00 0.00 2.85
3310 11506 3.334691 TGAACGAAAGCCACATAGAAGG 58.665 45.455 0.00 0.00 0.00 3.46
3311 11507 3.007506 TGAACGAAAGCCACATAGAAGGA 59.992 43.478 0.00 0.00 0.00 3.36
3312 11508 3.695830 ACGAAAGCCACATAGAAGGAA 57.304 42.857 0.00 0.00 0.00 3.36
3313 11509 3.335579 ACGAAAGCCACATAGAAGGAAC 58.664 45.455 0.00 0.00 0.00 3.62
3314 11510 3.244422 ACGAAAGCCACATAGAAGGAACA 60.244 43.478 0.00 0.00 0.00 3.18
3315 11511 3.941483 CGAAAGCCACATAGAAGGAACAT 59.059 43.478 0.00 0.00 0.00 2.71
3316 11512 4.396166 CGAAAGCCACATAGAAGGAACATT 59.604 41.667 0.00 0.00 0.00 2.71
3317 11513 5.644644 GAAAGCCACATAGAAGGAACATTG 58.355 41.667 0.00 0.00 0.00 2.82
3318 11514 4.574674 AGCCACATAGAAGGAACATTGA 57.425 40.909 0.00 0.00 0.00 2.57
3319 11515 4.922206 AGCCACATAGAAGGAACATTGAA 58.078 39.130 0.00 0.00 0.00 2.69
3320 11516 4.946157 AGCCACATAGAAGGAACATTGAAG 59.054 41.667 0.00 0.00 0.00 3.02
3321 11517 4.943705 GCCACATAGAAGGAACATTGAAGA 59.056 41.667 0.00 0.00 0.00 2.87
3322 11518 5.415701 GCCACATAGAAGGAACATTGAAGAA 59.584 40.000 0.00 0.00 0.00 2.52
3323 11519 6.071952 GCCACATAGAAGGAACATTGAAGAAA 60.072 38.462 0.00 0.00 0.00 2.52
3324 11520 7.523709 GCCACATAGAAGGAACATTGAAGAAAA 60.524 37.037 0.00 0.00 0.00 2.29
3325 11521 8.359642 CCACATAGAAGGAACATTGAAGAAAAA 58.640 33.333 0.00 0.00 0.00 1.94
3326 11522 9.403110 CACATAGAAGGAACATTGAAGAAAAAG 57.597 33.333 0.00 0.00 0.00 2.27
3327 11523 9.354673 ACATAGAAGGAACATTGAAGAAAAAGA 57.645 29.630 0.00 0.00 0.00 2.52
3330 11526 7.720442 AGAAGGAACATTGAAGAAAAAGAAGG 58.280 34.615 0.00 0.00 0.00 3.46
3331 11527 6.410942 AGGAACATTGAAGAAAAAGAAGGG 57.589 37.500 0.00 0.00 0.00 3.95
3332 11528 5.305386 AGGAACATTGAAGAAAAAGAAGGGG 59.695 40.000 0.00 0.00 0.00 4.79
3333 11529 4.607293 ACATTGAAGAAAAAGAAGGGGC 57.393 40.909 0.00 0.00 0.00 5.80
3342 11538 5.368145 AGAAAAAGAAGGGGCAATTCAAAC 58.632 37.500 4.10 0.00 0.00 2.93
3353 11549 2.339418 CAATTCAAACGGCACATGCAT 58.661 42.857 6.15 0.00 44.36 3.96
3354 11550 2.282701 ATTCAAACGGCACATGCATC 57.717 45.000 6.15 0.00 44.36 3.91
3355 11551 0.957362 TTCAAACGGCACATGCATCA 59.043 45.000 6.15 0.00 44.36 3.07
3356 11552 1.175654 TCAAACGGCACATGCATCAT 58.824 45.000 6.15 0.00 44.36 2.45
3357 11553 1.135344 TCAAACGGCACATGCATCATG 60.135 47.619 6.15 0.00 46.18 3.07
3358 11554 0.458889 AAACGGCACATGCATCATGC 60.459 50.000 19.84 19.84 44.80 4.06
3400 11596 4.041567 TGGTGTCATGGTCCATATGGTATC 59.958 45.833 21.28 12.49 36.34 2.24
3401 11597 4.287067 GGTGTCATGGTCCATATGGTATCT 59.713 45.833 21.28 3.02 36.34 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 6.414732 CACCACCTACCCATATTATACCATG 58.585 44.000 0.00 0.00 0.00 3.66
6 7 5.491078 CCACCACCTACCCATATTATACCAT 59.509 44.000 0.00 0.00 0.00 3.55
11 12 3.655777 CCACCACCACCTACCCATATTAT 59.344 47.826 0.00 0.00 0.00 1.28
16 18 1.928567 CCCACCACCACCTACCCAT 60.929 63.158 0.00 0.00 0.00 4.00
47 49 0.614697 TCTTGGGATGTCCTCGAGCA 60.615 55.000 6.99 0.23 36.20 4.26
59 61 2.872732 ACTCACGTCTAACTCTTGGGA 58.127 47.619 0.00 0.00 0.00 4.37
64 66 5.336531 CCATTTGGTACTCACGTCTAACTCT 60.337 44.000 0.00 0.00 0.00 3.24
75 77 4.950475 TGTTTGTTGTCCATTTGGTACTCA 59.050 37.500 0.00 0.00 36.34 3.41
80 82 4.693095 GTGTTTGTTTGTTGTCCATTTGGT 59.307 37.500 0.00 0.00 36.34 3.67
90 92 8.195617 AGTAATTCATTGGTGTTTGTTTGTTG 57.804 30.769 0.00 0.00 0.00 3.33
92 94 7.551585 TGAGTAATTCATTGGTGTTTGTTTGT 58.448 30.769 0.00 0.00 0.00 2.83
104 106 5.755375 AGCGACCTGTATGAGTAATTCATTG 59.245 40.000 0.00 0.00 44.14 2.82
105 107 5.918608 AGCGACCTGTATGAGTAATTCATT 58.081 37.500 0.00 0.00 44.14 2.57
120 762 0.239347 CCTGCAAGAAAAGCGACCTG 59.761 55.000 0.00 0.00 34.07 4.00
146 788 1.138859 CCACCCAACGAGAGCATATGA 59.861 52.381 6.97 0.00 0.00 2.15
150 792 0.537188 CTACCACCCAACGAGAGCAT 59.463 55.000 0.00 0.00 0.00 3.79
171 813 0.195096 TAGGGGAAGAGTGGGGTTGT 59.805 55.000 0.00 0.00 0.00 3.32
173 815 0.496841 AGTAGGGGAAGAGTGGGGTT 59.503 55.000 0.00 0.00 0.00 4.11
222 1529 1.046472 TGGCGTCGATATTGGAGGGT 61.046 55.000 0.00 0.00 0.00 4.34
248 1555 7.069702 ACATTAATGTTGTTATGCATCATGGGA 59.930 33.333 15.47 0.00 37.90 4.37
279 1586 9.191995 GAATCGAAGTTGGTTGATGTTTTAATT 57.808 29.630 0.00 0.00 0.00 1.40
359 1666 5.006941 GCATGCCAAATGATTTCACCATAAC 59.993 40.000 6.36 0.00 0.00 1.89
412 1719 5.750352 AAATTTCTTGGTCCATCTGCAAT 57.250 34.783 0.00 0.00 0.00 3.56
416 1723 7.885297 TGAAACTAAATTTCTTGGTCCATCTG 58.115 34.615 0.00 0.00 46.05 2.90
476 1785 1.122323 GCACGCAAATTAACACGCTTG 59.878 47.619 0.00 0.00 0.00 4.01
522 2090 2.915463 CGTCTACGTCTGGATTGTGTTC 59.085 50.000 0.00 0.00 34.11 3.18
531 2099 0.867753 GCATGAGCGTCTACGTCTGG 60.868 60.000 0.00 0.00 42.22 3.86
555 2127 7.090808 GTGTGTGTTCATAGAGATGAGTGTAA 58.909 38.462 0.00 0.00 43.03 2.41
567 2139 4.744570 AGGATGTACGTGTGTGTTCATAG 58.255 43.478 0.00 0.00 0.00 2.23
582 2154 5.216622 AGGTGCTCATAAAGGTAGGATGTA 58.783 41.667 0.00 0.00 0.00 2.29
593 2165 4.159321 CAGTCTCTCAGAGGTGCTCATAAA 59.841 45.833 0.57 0.00 32.06 1.40
594 2166 3.698539 CAGTCTCTCAGAGGTGCTCATAA 59.301 47.826 0.57 0.00 32.06 1.90
604 2177 2.003658 GCCGGCTCAGTCTCTCAGAG 62.004 65.000 22.15 0.00 33.62 3.35
607 2180 0.395724 TATGCCGGCTCAGTCTCTCA 60.396 55.000 29.70 2.45 0.00 3.27
634 2210 5.681982 CGACTATGGTGACTTCGTTTATCTC 59.318 44.000 0.00 0.00 0.00 2.75
639 2215 3.255149 AGACGACTATGGTGACTTCGTTT 59.745 43.478 0.00 0.00 42.69 3.60
640 2216 2.818432 AGACGACTATGGTGACTTCGTT 59.182 45.455 0.00 0.00 42.69 3.85
655 2231 2.735663 TCTCTGTTGACTACGAGACGAC 59.264 50.000 0.00 0.00 34.10 4.34
656 2232 2.735663 GTCTCTGTTGACTACGAGACGA 59.264 50.000 18.03 5.91 42.11 4.20
658 2234 2.479656 ACGTCTCTGTTGACTACGAGAC 59.520 50.000 20.51 20.51 44.59 3.36
659 2235 2.735663 GACGTCTCTGTTGACTACGAGA 59.264 50.000 8.70 7.21 37.04 4.04
695 2271 2.826428 TGAGGATTTCTAGCGATGTGC 58.174 47.619 0.00 0.00 46.98 4.57
696 2272 5.998454 ATTTGAGGATTTCTAGCGATGTG 57.002 39.130 0.00 0.00 0.00 3.21
701 2277 7.308229 CCTGGATTTATTTGAGGATTTCTAGCG 60.308 40.741 0.00 0.00 0.00 4.26
703 2279 9.804977 ATCCTGGATTTATTTGAGGATTTCTAG 57.195 33.333 2.57 0.00 40.02 2.43
714 2290 6.149474 GGACGGTGATATCCTGGATTTATTTG 59.851 42.308 15.55 4.49 31.75 2.32
731 2307 3.236896 GGGATAATTAGGAGGACGGTGA 58.763 50.000 0.00 0.00 0.00 4.02
759 2373 2.159142 CCTACCTTATCGCGAACCAACT 60.159 50.000 15.24 0.00 0.00 3.16
815 2430 7.201591 CGAGATAACCGTCCGTATGTATATCTT 60.202 40.741 0.00 0.00 31.07 2.40
1135 2763 7.826744 AGAAAGATTGATTGGAAGAAGAGGTAC 59.173 37.037 0.00 0.00 0.00 3.34
1183 2844 3.790089 AAGATTAATTAGGCTCCCGGG 57.210 47.619 16.85 16.85 0.00 5.73
1205 2866 3.488721 CGTCTTCTATGAACGGACCGAAT 60.489 47.826 23.38 13.23 0.00 3.34
1226 2903 1.273606 TCTGGTTCCTCTGCTTCTTCG 59.726 52.381 0.00 0.00 0.00 3.79
1227 2904 2.354604 CCTCTGGTTCCTCTGCTTCTTC 60.355 54.545 0.00 0.00 0.00 2.87
1228 2905 1.627834 CCTCTGGTTCCTCTGCTTCTT 59.372 52.381 0.00 0.00 0.00 2.52
1229 2906 1.274712 CCTCTGGTTCCTCTGCTTCT 58.725 55.000 0.00 0.00 0.00 2.85
1238 2915 3.056328 GCGGTTGCCTCTGGTTCC 61.056 66.667 0.00 0.00 33.98 3.62
1428 3108 2.481276 GGCCAAGTTGTTGTGGAAGAAC 60.481 50.000 0.00 0.00 41.08 3.01
1695 4167 3.553922 GGAAGGGATACATCAGCTCGAAG 60.554 52.174 0.00 0.00 39.74 3.79
1754 4226 3.814268 CCATGAGGGGCGCAAACG 61.814 66.667 10.83 0.00 44.07 3.60
1806 4278 1.553248 CTTGGAGTCCATTGTCCGGTA 59.447 52.381 14.00 0.00 35.37 4.02
1824 4296 3.249189 TCTTCCCACCCGCTGCTT 61.249 61.111 0.00 0.00 0.00 3.91
1858 4330 2.706636 CGGCACATTCCGGATTGAT 58.293 52.632 28.38 7.33 45.38 2.57
1882 4357 4.507756 CAGAAAATGCATCATGCCATTGAG 59.492 41.667 7.30 0.00 44.23 3.02
1883 4358 4.438148 CAGAAAATGCATCATGCCATTGA 58.562 39.130 7.30 0.00 44.23 2.57
1884 4359 4.794248 CAGAAAATGCATCATGCCATTG 57.206 40.909 7.30 0.00 44.23 2.82
1975 4451 2.905085 CTCCTAGCATGTCATCTGGGAT 59.095 50.000 13.78 0.00 38.91 3.85
2053 4532 3.072184 AGCTGGTAATCATGAGGATCCAC 59.928 47.826 15.82 8.65 34.28 4.02
2102 4581 4.081972 TCCACTCTTCTTCATCAGTAGCAC 60.082 45.833 0.00 0.00 0.00 4.40
2127 4606 3.243301 GGATGTCGACGGTATGCTTTAGA 60.243 47.826 11.62 0.00 0.00 2.10
2146 4625 3.391665 CTCCAAAGAGCCGCGGGAT 62.392 63.158 29.38 6.09 32.13 3.85
2181 4666 0.670854 GGCGGCGATAATCCTCTTCC 60.671 60.000 12.98 0.00 0.00 3.46
2224 4709 3.257873 TCCGGATGAATTGCAAACACATT 59.742 39.130 1.71 0.00 0.00 2.71
2295 4780 1.561076 ACTTGCCTGCTGTCCATATCA 59.439 47.619 0.00 0.00 0.00 2.15
2382 4868 2.360483 TGATTTTTGCAAAGGTCGAGCA 59.640 40.909 18.15 4.60 36.32 4.26
2466 4968 1.466167 CCACAAAACATCTGGAGAGCG 59.534 52.381 0.00 0.00 0.00 5.03
2550 5063 6.149474 ACCAAGTCATTCATACAACTAAGCAC 59.851 38.462 0.00 0.00 0.00 4.40
2760 5287 1.194772 GCTACAGAAACAAGGCGTCAC 59.805 52.381 0.00 0.00 0.00 3.67
2774 5301 5.082059 CGCAAAATTCTGTTACTGCTACAG 58.918 41.667 0.00 0.00 43.41 2.74
2811 5338 6.219473 ACACTCTGTATATGCAGCATAGAAC 58.781 40.000 19.83 18.76 36.49 3.01
2889 5427 7.321908 TGGTAAGATGCATACGTACTGTTTAA 58.678 34.615 0.00 0.00 0.00 1.52
2890 5428 6.865411 TGGTAAGATGCATACGTACTGTTTA 58.135 36.000 0.00 0.00 0.00 2.01
2891 5429 5.726397 TGGTAAGATGCATACGTACTGTTT 58.274 37.500 0.00 0.00 0.00 2.83
2893 5431 4.643334 TCTGGTAAGATGCATACGTACTGT 59.357 41.667 0.00 0.00 0.00 3.55
2894 5432 5.183014 TCTGGTAAGATGCATACGTACTG 57.817 43.478 0.00 0.00 0.00 2.74
2895 5433 7.704578 ATATCTGGTAAGATGCATACGTACT 57.295 36.000 0.00 0.00 43.27 2.73
2896 5434 8.675504 ACTATATCTGGTAAGATGCATACGTAC 58.324 37.037 0.00 6.45 43.27 3.67
2897 5435 8.674607 CACTATATCTGGTAAGATGCATACGTA 58.325 37.037 0.00 0.00 43.27 3.57
2898 5436 7.393515 TCACTATATCTGGTAAGATGCATACGT 59.606 37.037 0.00 0.00 43.27 3.57
2899 5437 7.762382 TCACTATATCTGGTAAGATGCATACG 58.238 38.462 0.00 0.00 43.27 3.06
2972 5514 1.938577 GCTTAGTTTTAGCTACGGGCC 59.061 52.381 0.00 0.00 43.05 5.80
2998 5540 5.237344 AGCTAGTGACAAACAGCAAACTTAG 59.763 40.000 6.88 0.00 36.18 2.18
3049 5591 3.003480 CCCGCAAAAACAGGTTCAAAAA 58.997 40.909 0.00 0.00 0.00 1.94
3054 5596 0.966179 ATCCCCGCAAAAACAGGTTC 59.034 50.000 0.00 0.00 0.00 3.62
3055 5597 1.069978 CAATCCCCGCAAAAACAGGTT 59.930 47.619 0.00 0.00 0.00 3.50
3057 5599 0.965439 TCAATCCCCGCAAAAACAGG 59.035 50.000 0.00 0.00 0.00 4.00
3059 5601 2.035632 AGTTCAATCCCCGCAAAAACA 58.964 42.857 0.00 0.00 0.00 2.83
3060 5602 2.812358 AGTTCAATCCCCGCAAAAAC 57.188 45.000 0.00 0.00 0.00 2.43
3134 10992 1.028130 TCATTTGCGGCTTGACAACA 58.972 45.000 0.00 0.00 0.00 3.33
3143 11003 1.037030 TCCCCTGAATCATTTGCGGC 61.037 55.000 0.00 0.00 0.00 6.53
3146 11006 0.749049 GCCTCCCCTGAATCATTTGC 59.251 55.000 0.00 0.00 0.00 3.68
3147 11007 2.029623 CTGCCTCCCCTGAATCATTTG 58.970 52.381 0.00 0.00 0.00 2.32
3148 11008 1.925255 TCTGCCTCCCCTGAATCATTT 59.075 47.619 0.00 0.00 0.00 2.32
3149 11009 1.600058 TCTGCCTCCCCTGAATCATT 58.400 50.000 0.00 0.00 0.00 2.57
3150 11010 1.213926 GTTCTGCCTCCCCTGAATCAT 59.786 52.381 0.00 0.00 0.00 2.45
3153 11013 1.075601 TTGTTCTGCCTCCCCTGAAT 58.924 50.000 0.00 0.00 0.00 2.57
3156 11016 0.178992 TTGTTGTTCTGCCTCCCCTG 60.179 55.000 0.00 0.00 0.00 4.45
3157 11017 0.178990 GTTGTTGTTCTGCCTCCCCT 60.179 55.000 0.00 0.00 0.00 4.79
3159 11019 1.515521 CGGTTGTTGTTCTGCCTCCC 61.516 60.000 0.00 0.00 0.00 4.30
3160 11020 1.949257 CGGTTGTTGTTCTGCCTCC 59.051 57.895 0.00 0.00 0.00 4.30
3162 11022 3.432186 GCGGTTGTTGTTCTGCCT 58.568 55.556 0.00 0.00 0.00 4.75
3163 11023 2.335011 GGCGGTTGTTGTTCTGCC 59.665 61.111 0.00 0.00 46.60 4.85
3164 11024 2.051345 CGGCGGTTGTTGTTCTGC 60.051 61.111 0.00 0.00 35.47 4.26
3166 11026 3.284449 GGCGGCGGTTGTTGTTCT 61.284 61.111 9.78 0.00 0.00 3.01
3167 11027 4.676586 CGGCGGCGGTTGTTGTTC 62.677 66.667 25.36 0.00 0.00 3.18
3170 11030 4.459331 CATCGGCGGCGGTTGTTG 62.459 66.667 31.73 16.47 0.00 3.33
3172 11032 4.690719 TTCATCGGCGGCGGTTGT 62.691 61.111 31.73 12.34 0.00 3.32
3173 11033 3.864686 CTTCATCGGCGGCGGTTG 61.865 66.667 31.73 26.46 0.00 3.77
3174 11034 4.077184 TCTTCATCGGCGGCGGTT 62.077 61.111 31.73 16.58 0.00 4.44
3175 11035 4.514577 CTCTTCATCGGCGGCGGT 62.515 66.667 31.73 23.77 0.00 5.68
3176 11036 3.133767 TACTCTTCATCGGCGGCGG 62.134 63.158 31.73 16.54 0.00 6.13
3177 11037 1.658717 CTACTCTTCATCGGCGGCG 60.659 63.158 27.15 27.15 0.00 6.46
3178 11038 1.951631 GCTACTCTTCATCGGCGGC 60.952 63.158 7.21 0.00 0.00 6.53
3179 11039 1.658717 CGCTACTCTTCATCGGCGG 60.659 63.158 7.21 0.00 39.12 6.13
3180 11040 0.306840 TACGCTACTCTTCATCGGCG 59.693 55.000 0.00 0.00 46.47 6.46
3181 11041 2.223525 ACTTACGCTACTCTTCATCGGC 60.224 50.000 0.00 0.00 0.00 5.54
3182 11042 3.619729 GACTTACGCTACTCTTCATCGG 58.380 50.000 0.00 0.00 0.00 4.18
3183 11043 3.281601 CGACTTACGCTACTCTTCATCG 58.718 50.000 0.00 0.00 34.51 3.84
3184 11044 3.311871 TCCGACTTACGCTACTCTTCATC 59.688 47.826 0.00 0.00 41.07 2.92
3186 11046 2.703416 TCCGACTTACGCTACTCTTCA 58.297 47.619 0.00 0.00 41.07 3.02
3187 11047 3.487209 CCTTCCGACTTACGCTACTCTTC 60.487 52.174 0.00 0.00 41.07 2.87
3188 11048 2.422832 CCTTCCGACTTACGCTACTCTT 59.577 50.000 0.00 0.00 41.07 2.85
3190 11050 2.012673 TCCTTCCGACTTACGCTACTC 58.987 52.381 0.00 0.00 41.07 2.59
3191 11051 2.119801 TCCTTCCGACTTACGCTACT 57.880 50.000 0.00 0.00 41.07 2.57
3192 11052 2.601741 CGATCCTTCCGACTTACGCTAC 60.602 54.545 0.00 0.00 41.07 3.58
3197 11057 2.426381 AGGTTCGATCCTTCCGACTTAC 59.574 50.000 9.33 0.00 35.61 2.34
3201 11061 0.815734 TGAGGTTCGATCCTTCCGAC 59.184 55.000 16.11 4.12 38.02 4.79
3202 11062 1.552578 TTGAGGTTCGATCCTTCCGA 58.447 50.000 16.11 2.16 38.02 4.55
3203 11063 2.000447 GTTTGAGGTTCGATCCTTCCG 59.000 52.381 16.11 0.00 38.02 4.30
3204 11064 2.027100 AGGTTTGAGGTTCGATCCTTCC 60.027 50.000 16.11 14.77 38.02 3.46
3206 11066 2.637872 TGAGGTTTGAGGTTCGATCCTT 59.362 45.455 16.11 0.00 38.02 3.36
3207 11067 2.257207 TGAGGTTTGAGGTTCGATCCT 58.743 47.619 14.99 14.99 40.97 3.24
3208 11068 2.762535 TGAGGTTTGAGGTTCGATCC 57.237 50.000 4.21 4.21 0.00 3.36
3209 11069 4.003648 ACATTGAGGTTTGAGGTTCGATC 58.996 43.478 0.00 0.00 0.00 3.69
3210 11070 4.021102 ACATTGAGGTTTGAGGTTCGAT 57.979 40.909 0.00 0.00 0.00 3.59
3217 11413 2.095567 CCGCTGAACATTGAGGTTTGAG 60.096 50.000 0.00 0.00 0.00 3.02
3218 11414 1.879380 CCGCTGAACATTGAGGTTTGA 59.121 47.619 0.00 0.00 0.00 2.69
3219 11415 1.666888 GCCGCTGAACATTGAGGTTTG 60.667 52.381 0.00 0.00 0.00 2.93
3227 11423 2.048444 ATGATGAGCCGCTGAACATT 57.952 45.000 0.00 0.00 0.00 2.71
3236 11432 9.546909 GTTTTTATTGATACATATGATGAGCCG 57.453 33.333 10.38 0.00 0.00 5.52
3265 11461 2.188817 ACTTAGGCACCCTACCTGAAG 58.811 52.381 0.00 0.00 35.63 3.02
3278 11474 3.124806 GGCTTTCGTTCAGTAACTTAGGC 59.875 47.826 0.00 0.00 33.15 3.93
3279 11475 4.151867 GTGGCTTTCGTTCAGTAACTTAGG 59.848 45.833 0.00 0.00 33.15 2.69
3280 11476 4.748102 TGTGGCTTTCGTTCAGTAACTTAG 59.252 41.667 0.00 0.00 33.15 2.18
3281 11477 4.695396 TGTGGCTTTCGTTCAGTAACTTA 58.305 39.130 0.00 0.00 33.15 2.24
3282 11478 3.537580 TGTGGCTTTCGTTCAGTAACTT 58.462 40.909 0.00 0.00 33.15 2.66
3283 11479 3.188159 TGTGGCTTTCGTTCAGTAACT 57.812 42.857 0.00 0.00 33.15 2.24
3284 11480 4.927425 TCTATGTGGCTTTCGTTCAGTAAC 59.073 41.667 0.00 0.00 0.00 2.50
3285 11481 5.142061 TCTATGTGGCTTTCGTTCAGTAA 57.858 39.130 0.00 0.00 0.00 2.24
3286 11482 4.794278 TCTATGTGGCTTTCGTTCAGTA 57.206 40.909 0.00 0.00 0.00 2.74
3287 11483 3.678056 TCTATGTGGCTTTCGTTCAGT 57.322 42.857 0.00 0.00 0.00 3.41
3288 11484 3.372206 CCTTCTATGTGGCTTTCGTTCAG 59.628 47.826 0.00 0.00 0.00 3.02
3289 11485 3.007506 TCCTTCTATGTGGCTTTCGTTCA 59.992 43.478 0.00 0.00 0.00 3.18
3290 11486 3.596214 TCCTTCTATGTGGCTTTCGTTC 58.404 45.455 0.00 0.00 0.00 3.95
3291 11487 3.695830 TCCTTCTATGTGGCTTTCGTT 57.304 42.857 0.00 0.00 0.00 3.85
3292 11488 3.244422 TGTTCCTTCTATGTGGCTTTCGT 60.244 43.478 0.00 0.00 0.00 3.85
3293 11489 3.334691 TGTTCCTTCTATGTGGCTTTCG 58.665 45.455 0.00 0.00 0.00 3.46
3294 11490 5.415701 TCAATGTTCCTTCTATGTGGCTTTC 59.584 40.000 0.00 0.00 0.00 2.62
3295 11491 5.324409 TCAATGTTCCTTCTATGTGGCTTT 58.676 37.500 0.00 0.00 0.00 3.51
3296 11492 4.922206 TCAATGTTCCTTCTATGTGGCTT 58.078 39.130 0.00 0.00 0.00 4.35
3297 11493 4.574674 TCAATGTTCCTTCTATGTGGCT 57.425 40.909 0.00 0.00 0.00 4.75
3298 11494 4.943705 TCTTCAATGTTCCTTCTATGTGGC 59.056 41.667 0.00 0.00 0.00 5.01
3299 11495 7.452880 TTTCTTCAATGTTCCTTCTATGTGG 57.547 36.000 0.00 0.00 0.00 4.17
3300 11496 9.403110 CTTTTTCTTCAATGTTCCTTCTATGTG 57.597 33.333 0.00 0.00 0.00 3.21
3301 11497 9.354673 TCTTTTTCTTCAATGTTCCTTCTATGT 57.645 29.630 0.00 0.00 0.00 2.29
3304 11500 8.850156 CCTTCTTTTTCTTCAATGTTCCTTCTA 58.150 33.333 0.00 0.00 0.00 2.10
3305 11501 7.201947 CCCTTCTTTTTCTTCAATGTTCCTTCT 60.202 37.037 0.00 0.00 0.00 2.85
3306 11502 6.925718 CCCTTCTTTTTCTTCAATGTTCCTTC 59.074 38.462 0.00 0.00 0.00 3.46
3307 11503 6.183361 CCCCTTCTTTTTCTTCAATGTTCCTT 60.183 38.462 0.00 0.00 0.00 3.36
3308 11504 5.305386 CCCCTTCTTTTTCTTCAATGTTCCT 59.695 40.000 0.00 0.00 0.00 3.36
3309 11505 5.541845 CCCCTTCTTTTTCTTCAATGTTCC 58.458 41.667 0.00 0.00 0.00 3.62
3310 11506 4.991056 GCCCCTTCTTTTTCTTCAATGTTC 59.009 41.667 0.00 0.00 0.00 3.18
3311 11507 4.408596 TGCCCCTTCTTTTTCTTCAATGTT 59.591 37.500 0.00 0.00 0.00 2.71
3312 11508 3.966665 TGCCCCTTCTTTTTCTTCAATGT 59.033 39.130 0.00 0.00 0.00 2.71
3313 11509 4.605640 TGCCCCTTCTTTTTCTTCAATG 57.394 40.909 0.00 0.00 0.00 2.82
3314 11510 5.830799 ATTGCCCCTTCTTTTTCTTCAAT 57.169 34.783 0.00 0.00 0.00 2.57
3315 11511 5.130145 TGAATTGCCCCTTCTTTTTCTTCAA 59.870 36.000 0.00 0.00 0.00 2.69
3316 11512 4.653341 TGAATTGCCCCTTCTTTTTCTTCA 59.347 37.500 0.00 0.00 0.00 3.02
3317 11513 5.213891 TGAATTGCCCCTTCTTTTTCTTC 57.786 39.130 0.00 0.00 0.00 2.87
3318 11514 5.628797 TTGAATTGCCCCTTCTTTTTCTT 57.371 34.783 0.00 0.00 0.00 2.52
3319 11515 5.368145 GTTTGAATTGCCCCTTCTTTTTCT 58.632 37.500 0.00 0.00 0.00 2.52
3320 11516 4.211164 CGTTTGAATTGCCCCTTCTTTTTC 59.789 41.667 0.00 0.00 0.00 2.29
3321 11517 4.126437 CGTTTGAATTGCCCCTTCTTTTT 58.874 39.130 0.00 0.00 0.00 1.94
3322 11518 3.494223 CCGTTTGAATTGCCCCTTCTTTT 60.494 43.478 0.00 0.00 0.00 2.27
3323 11519 2.037121 CCGTTTGAATTGCCCCTTCTTT 59.963 45.455 0.00 0.00 0.00 2.52
3324 11520 1.618343 CCGTTTGAATTGCCCCTTCTT 59.382 47.619 0.00 0.00 0.00 2.52
3325 11521 1.256812 CCGTTTGAATTGCCCCTTCT 58.743 50.000 0.00 0.00 0.00 2.85
3326 11522 0.389817 GCCGTTTGAATTGCCCCTTC 60.390 55.000 0.00 0.00 0.00 3.46
3327 11523 1.118356 TGCCGTTTGAATTGCCCCTT 61.118 50.000 0.00 0.00 0.00 3.95
3328 11524 1.532794 TGCCGTTTGAATTGCCCCT 60.533 52.632 0.00 0.00 0.00 4.79
3329 11525 1.374125 GTGCCGTTTGAATTGCCCC 60.374 57.895 0.00 0.00 0.00 5.80
3330 11526 0.037419 ATGTGCCGTTTGAATTGCCC 60.037 50.000 0.00 0.00 0.00 5.36
3331 11527 1.070038 CATGTGCCGTTTGAATTGCC 58.930 50.000 0.00 0.00 0.00 4.52
3332 11528 0.439600 GCATGTGCCGTTTGAATTGC 59.560 50.000 0.00 0.00 34.31 3.56
3333 11529 1.780806 TGCATGTGCCGTTTGAATTG 58.219 45.000 2.07 0.00 41.18 2.32
3357 11553 5.530171 CACCATATATATCCCAGCATTCTGC 59.470 44.000 0.00 0.00 45.46 4.26
3358 11554 6.656902 ACACCATATATATCCCAGCATTCTG 58.343 40.000 0.00 0.00 40.02 3.02
3359 11555 6.444816 TGACACCATATATATCCCAGCATTCT 59.555 38.462 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.