Multiple sequence alignment - TraesCS2D01G056200

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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 TraesCS2D01G056200 chr2D 100.000 7265 0 0 1 7265 22462890 22470154 0.000000e+00 13417.0
1 TraesCS2D01G056200 chr2D 92.514 4769 214 59 2067 6764 22432745 22428049 0.000000e+00 6697.0
2 TraesCS2D01G056200 chr2D 87.413 1287 96 36 787 2050 22434165 22432922 0.000000e+00 1419.0
3 TraesCS2D01G056200 chr2D 91.056 928 70 9 3143 4066 30549031 30549949 0.000000e+00 1242.0
4 TraesCS2D01G056200 chr2D 85.492 834 94 14 5 823 22434997 22434176 0.000000e+00 845.0
5 TraesCS2D01G056200 chr2D 83.024 754 83 21 2085 2803 30547934 30548677 6.140000e-180 641.0
6 TraesCS2D01G056200 chr2D 87.984 516 57 3 5238 5751 30550398 30550910 8.060000e-169 604.0
7 TraesCS2D01G056200 chr2D 78.458 882 138 34 3208 4067 30586481 30587332 4.990000e-146 529.0
8 TraesCS2D01G056200 chr2D 85.680 412 54 2 5875 6282 30551009 30551419 5.210000e-116 429.0
9 TraesCS2D01G056200 chr2D 78.475 590 97 22 5249 5833 30587923 30588487 6.930000e-95 359.0
10 TraesCS2D01G056200 chr2D 83.942 274 25 11 2080 2351 22433244 22432988 2.020000e-60 244.0
11 TraesCS2D01G056200 chr2D 82.353 255 32 9 6380 6629 30551473 30551719 7.390000e-50 209.0
12 TraesCS2D01G056200 chr2D 86.508 126 16 1 7105 7230 22386089 22386213 3.530000e-28 137.0
13 TraesCS2D01G056200 chr2D 80.128 156 22 8 4553 4702 30550185 30550337 2.770000e-19 108.0
14 TraesCS2D01G056200 chr2D 94.737 38 1 1 5796 5833 30550911 30550947 2.830000e-04 58.4
15 TraesCS2D01G056200 chr2B 96.291 2103 34 16 3064 5158 39368965 39371031 0.000000e+00 3411.0
16 TraesCS2D01G056200 chr2B 94.613 1615 65 12 5160 6764 39371094 39372696 0.000000e+00 2481.0
17 TraesCS2D01G056200 chr2B 89.172 1533 132 15 1 1511 39207430 39205910 0.000000e+00 1881.0
18 TraesCS2D01G056200 chr2B 87.944 1294 90 31 787 2050 39366571 39367828 0.000000e+00 1465.0
19 TraesCS2D01G056200 chr2B 93.652 961 33 14 2075 3013 39368015 39368969 0.000000e+00 1411.0
20 TraesCS2D01G056200 chr2B 89.374 1007 77 19 3077 4068 50288584 50289575 0.000000e+00 1240.0
21 TraesCS2D01G056200 chr2B 86.504 615 75 4 5139 5751 50290386 50290994 0.000000e+00 669.0
22 TraesCS2D01G056200 chr2B 85.150 633 76 14 206 823 39365930 39366559 3.700000e-177 632.0
23 TraesCS2D01G056200 chr2B 77.727 880 149 34 3208 4067 50347531 50348383 5.060000e-136 496.0
24 TraesCS2D01G056200 chr2B 87.239 431 50 4 2375 2803 50287888 50288315 3.050000e-133 486.0
25 TraesCS2D01G056200 chr2B 87.374 396 49 1 5875 6270 50291093 50291487 3.090000e-123 453.0
26 TraesCS2D01G056200 chr2B 85.816 423 54 3 6 422 39350586 39351008 1.860000e-120 444.0
27 TraesCS2D01G056200 chr2B 82.005 439 67 8 5249 5683 50348986 50349416 5.360000e-96 363.0
28 TraesCS2D01G056200 chr2B 79.496 278 19 14 6955 7202 39375985 39376254 5.830000e-36 163.0
29 TraesCS2D01G056200 chr2B 97.561 41 1 0 835 875 793384529 793384489 3.640000e-08 71.3
30 TraesCS2D01G056200 chr2B 97.368 38 0 1 5796 5833 50290995 50291031 6.080000e-06 63.9
31 TraesCS2D01G056200 chr2A 88.056 2160 126 56 787 2891 24165887 24163805 0.000000e+00 2438.0
32 TraesCS2D01G056200 chr2A 93.991 1581 64 19 4253 5816 24162317 24160751 0.000000e+00 2364.0
33 TraesCS2D01G056200 chr2A 94.996 1139 47 7 3122 4255 24163811 24162678 0.000000e+00 1779.0
34 TraesCS2D01G056200 chr2A 87.437 1186 92 36 2900 4068 32529606 32530751 0.000000e+00 1312.0
35 TraesCS2D01G056200 chr2A 90.338 859 45 16 5921 6754 24160755 24159910 0.000000e+00 1092.0
36 TraesCS2D01G056200 chr2A 80.726 1240 154 36 4554 5751 32530991 32532187 0.000000e+00 887.0
37 TraesCS2D01G056200 chr2A 83.497 715 85 21 2093 2785 32528579 32529282 2.860000e-178 636.0
38 TraesCS2D01G056200 chr2A 77.866 881 145 37 3208 4067 32542999 32543850 1.090000e-137 501.0
39 TraesCS2D01G056200 chr2A 76.222 1064 181 41 5249 6270 32544349 32545382 1.410000e-136 497.0
40 TraesCS2D01G056200 chr2A 84.646 508 56 9 328 823 24166395 24165898 3.050000e-133 486.0
41 TraesCS2D01G056200 chr2A 86.869 396 51 1 5875 6270 32532368 32532762 6.690000e-120 442.0
42 TraesCS2D01G056200 chr2A 84.502 271 38 3 1 268 24166661 24166392 1.550000e-66 265.0
43 TraesCS2D01G056200 chr2A 92.903 155 8 1 7113 7264 24144984 24144830 9.490000e-54 222.0
44 TraesCS2D01G056200 chr2A 90.909 110 10 0 7105 7214 24109845 24109954 1.630000e-31 148.0
45 TraesCS2D01G056200 chr2A 88.421 95 8 2 6797 6890 24159918 24159826 2.140000e-20 111.0
46 TraesCS2D01G056200 chr5B 89.607 356 21 10 3732 4080 123212501 123212155 8.650000e-119 438.0
47 TraesCS2D01G056200 chr5B 89.045 356 23 10 3732 4080 123429819 123429473 1.870000e-115 427.0
48 TraesCS2D01G056200 chr7B 89.826 344 23 8 3730 4068 131086900 131087236 1.450000e-116 431.0
49 TraesCS2D01G056200 chr3B 78.860 544 86 19 4578 5094 35054626 35054085 2.510000e-89 340.0
50 TraesCS2D01G056200 chr3B 78.860 544 86 19 4578 5094 35138626 35138085 2.510000e-89 340.0
51 TraesCS2D01G056200 chr3B 97.222 36 1 0 832 867 425387510 425387475 2.190000e-05 62.1
52 TraesCS2D01G056200 chr4A 77.939 553 89 22 4571 5093 688556043 688556592 1.520000e-81 315.0
53 TraesCS2D01G056200 chr4A 77.758 553 90 22 4571 5093 688539283 688539832 7.080000e-80 309.0
54 TraesCS2D01G056200 chrUn 89.941 169 14 2 7100 7265 353860751 353860583 1.590000e-51 215.0
55 TraesCS2D01G056200 chrUn 89.349 169 15 2 7100 7265 247787246 247787078 7.390000e-50 209.0
56 TraesCS2D01G056200 chrUn 89.855 138 11 2 7100 7234 298695393 298695530 2.690000e-39 174.0
57 TraesCS2D01G056200 chrUn 86.260 131 16 2 7105 7234 16898800 16898929 2.730000e-29 141.0
58 TraesCS2D01G056200 chr4B 83.069 189 28 4 2498 2685 658574251 658574436 1.250000e-37 169.0
59 TraesCS2D01G056200 chr4B 88.000 50 6 0 825 874 649614280 649614231 7.870000e-05 60.2
60 TraesCS2D01G056200 chr3D 95.349 43 0 2 825 867 2133372 2133332 4.700000e-07 67.6


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 TraesCS2D01G056200 chr2D 22462890 22470154 7264 False 13417.000000 13417 100.000000 1 7265 1 chr2D.!!$F2 7264
1 TraesCS2D01G056200 chr2D 22428049 22434997 6948 True 2301.250000 6697 87.340250 5 6764 4 chr2D.!!$R1 6759
2 TraesCS2D01G056200 chr2D 30547934 30551719 3785 False 470.200000 1242 86.423143 2085 6629 7 chr2D.!!$F3 4544
3 TraesCS2D01G056200 chr2D 30586481 30588487 2006 False 444.000000 529 78.466500 3208 5833 2 chr2D.!!$F4 2625
4 TraesCS2D01G056200 chr2B 39205910 39207430 1520 True 1881.000000 1881 89.172000 1 1511 1 chr2B.!!$R1 1510
5 TraesCS2D01G056200 chr2B 39365930 39376254 10324 False 1593.833333 3411 89.524333 206 7202 6 chr2B.!!$F2 6996
6 TraesCS2D01G056200 chr2B 50287888 50291487 3599 False 582.380000 1240 89.571800 2375 6270 5 chr2B.!!$F3 3895
7 TraesCS2D01G056200 chr2B 50347531 50349416 1885 False 429.500000 496 79.866000 3208 5683 2 chr2B.!!$F4 2475
8 TraesCS2D01G056200 chr2A 24159826 24166661 6835 True 1219.285714 2438 89.278571 1 6890 7 chr2A.!!$R2 6889
9 TraesCS2D01G056200 chr2A 32528579 32532762 4183 False 819.250000 1312 84.632250 2093 6270 4 chr2A.!!$F2 4177
10 TraesCS2D01G056200 chr2A 32542999 32545382 2383 False 499.000000 501 77.044000 3208 6270 2 chr2A.!!$F3 3062
11 TraesCS2D01G056200 chr3B 35054085 35054626 541 True 340.000000 340 78.860000 4578 5094 1 chr3B.!!$R1 516
12 TraesCS2D01G056200 chr3B 35138085 35138626 541 True 340.000000 340 78.860000 4578 5094 1 chr3B.!!$R2 516
13 TraesCS2D01G056200 chr4A 688556043 688556592 549 False 315.000000 315 77.939000 4571 5093 1 chr4A.!!$F2 522
14 TraesCS2D01G056200 chr4A 688539283 688539832 549 False 309.000000 309 77.758000 4571 5093 1 chr4A.!!$F1 522

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
956 1047 0.036858 GAGCCGAAAGAAGCCAGAGT 60.037 55.000 0.00 0.0 0.00 3.24 F
981 1072 0.336392 GGAGGGGCAGAAAGGGAAAT 59.664 55.000 0.00 0.0 0.00 2.17 F
1869 2026 0.823769 CCCGAGGACGAGGATGATGA 60.824 60.000 0.00 0.0 42.66 2.92 F
1871 2028 1.067985 CCGAGGACGAGGATGATGATG 60.068 57.143 0.00 0.0 42.66 3.07 F
2594 2970 1.333524 CGCATGATCTTGTTCGGCATC 60.334 52.381 10.05 0.0 0.00 3.91 F
2689 3065 2.253610 ACATACCTCCGACCACTGAAA 58.746 47.619 0.00 0.0 0.00 2.69 F
4068 4773 0.895100 TGTGGCCTGAATTGTCCAGC 60.895 55.000 3.32 0.0 0.00 4.85 F
4435 5515 2.616842 CGGGCCATCGTAAAAGCTAAAT 59.383 45.455 4.39 0.0 0.00 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2198 2533 1.173913 TCATCTTCGTCTTCGAGCCA 58.826 50.000 0.00 0.00 46.81 4.75 R
2203 2538 2.099921 ACCCTCATCATCTTCGTCTTCG 59.900 50.000 0.00 0.00 38.55 3.79 R
2689 3065 2.164624 GACACTGAGAATACGGCAGTCT 59.835 50.000 0.00 0.00 40.63 3.24 R
3774 4469 5.038033 CGAGTAACTTCAGCTTGACTATCC 58.962 45.833 0.00 0.00 0.00 2.59 R
4068 4773 1.442769 ACCACATCTTACAAGCAGCG 58.557 50.000 0.00 0.00 0.00 5.18 R
4951 6131 5.343593 CGGTGTTCAAAATTTAAATAGCGCA 59.656 36.000 11.47 0.00 30.62 6.09 R
6168 7646 2.045536 CCACTTCCCAGCTCCAGC 60.046 66.667 0.00 0.00 42.49 4.85 R
6345 7853 2.482316 CCAACATGGCCATGCTGTATTG 60.482 50.000 39.74 32.63 42.39 1.90 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
43 48 5.429130 AGATGATAAGAAAAAGGGACGGTC 58.571 41.667 0.00 0.00 0.00 4.79
53 58 0.113776 AGGGACGGTCTACACCTTGA 59.886 55.000 8.23 0.00 41.17 3.02
58 63 3.080319 GACGGTCTACACCTTGAGTACT 58.920 50.000 0.00 0.00 41.17 2.73
67 72 7.444487 GTCTACACCTTGAGTACTTGGAAAAAT 59.556 37.037 14.70 0.00 0.00 1.82
92 101 0.543277 TCCTAGCCACTGGATGCAAG 59.457 55.000 0.00 0.00 0.00 4.01
161 171 1.295357 ACGAATGGATCACGCGCAAA 61.295 50.000 5.73 0.00 0.00 3.68
168 178 0.315382 GATCACGCGCAAATCTTCCG 60.315 55.000 5.73 0.00 0.00 4.30
183 193 1.465200 TTCCGTCCACCGACATGTCA 61.465 55.000 24.93 2.54 39.11 3.58
205 215 2.091278 CACTCTATCCACCTACCTCCCA 60.091 54.545 0.00 0.00 0.00 4.37
279 290 6.767524 AACCAGATTTTGACCGCAATAATA 57.232 33.333 0.00 0.00 33.25 0.98
312 325 7.062839 CGCTAGAAATGAGGATCTAGTAAATGC 59.937 40.741 10.51 0.00 44.51 3.56
331 344 1.339929 GCCAAAGGAACATCGGTTTGT 59.660 47.619 0.00 0.00 37.36 2.83
346 362 1.112315 TTTGTGCATCACCCCACACC 61.112 55.000 0.00 0.00 41.26 4.16
357 373 2.906897 CCACACCACGCAGGCTTT 60.907 61.111 0.00 0.00 43.14 3.51
403 421 0.613260 TTGGAGAACCCGAGTCATGG 59.387 55.000 0.00 0.00 37.93 3.66
490 520 6.806668 TTGATACACCACTATCAAGATCCA 57.193 37.500 0.00 0.00 37.93 3.41
492 522 7.379059 TGATACACCACTATCAAGATCCAAT 57.621 36.000 0.00 0.00 31.44 3.16
504 534 3.947612 AGATCCAATGAGAGCCAACAT 57.052 42.857 0.00 0.00 0.00 2.71
510 540 1.496060 ATGAGAGCCAACATACCCGA 58.504 50.000 0.00 0.00 0.00 5.14
513 543 0.537188 AGAGCCAACATACCCGACAG 59.463 55.000 0.00 0.00 0.00 3.51
574 605 2.100989 GTCGTGATGTAGGGAGAGGTT 58.899 52.381 0.00 0.00 0.00 3.50
630 661 4.996758 CACTACCTCATCAATGTTGTCACA 59.003 41.667 0.00 0.00 37.31 3.58
712 749 0.105194 TCCCACTCCTCTTGTCACCA 60.105 55.000 0.00 0.00 0.00 4.17
746 783 4.806339 AGGAGGAAGGGAGGCCGG 62.806 72.222 0.00 0.00 0.00 6.13
954 1045 1.079819 CGAGCCGAAAGAAGCCAGA 60.080 57.895 0.00 0.00 0.00 3.86
956 1047 0.036858 GAGCCGAAAGAAGCCAGAGT 60.037 55.000 0.00 0.00 0.00 3.24
980 1071 1.774300 GGAGGGGCAGAAAGGGAAA 59.226 57.895 0.00 0.00 0.00 3.13
981 1072 0.336392 GGAGGGGCAGAAAGGGAAAT 59.664 55.000 0.00 0.00 0.00 2.17
985 1076 1.686428 GGGGCAGAAAGGGAAATCTCC 60.686 57.143 0.00 0.00 41.59 3.71
986 1077 1.005924 GGGCAGAAAGGGAAATCTCCA 59.994 52.381 0.00 0.00 44.51 3.86
987 1078 2.557452 GGGCAGAAAGGGAAATCTCCAA 60.557 50.000 0.00 0.00 44.51 3.53
988 1079 2.493675 GGCAGAAAGGGAAATCTCCAAC 59.506 50.000 0.00 0.00 44.51 3.77
1024 1115 5.650283 TGGGGATAAATTTCAAGGTCAAGT 58.350 37.500 0.00 0.00 0.00 3.16
1243 1346 1.566703 TCCTCCTGTAGTCTCCTGGAG 59.433 57.143 17.84 17.84 43.76 3.86
1333 1445 1.627550 GCTTCGTTCTTGGTCCGCTC 61.628 60.000 0.00 0.00 0.00 5.03
1443 1556 2.342910 TCTTGGCTACGTTCTTCGAC 57.657 50.000 0.00 0.00 42.86 4.20
1458 1571 5.978934 TCTTCGACTTGGTGTAGTTTTTC 57.021 39.130 0.00 0.00 0.00 2.29
1477 1590 2.583472 CCTTGTTGGGAAGATGGGC 58.417 57.895 0.00 0.00 0.00 5.36
1511 1624 2.099098 CGCGAGCCCTCCAATTAATTTT 59.901 45.455 0.00 0.00 0.00 1.82
1642 1766 3.636153 GGTGACCAGGAAAGCTAGATT 57.364 47.619 0.00 0.00 0.00 2.40
1769 1903 1.919918 TTTGCGCTGGAAAGTGTTTG 58.080 45.000 9.73 0.00 0.00 2.93
1796 1932 3.025978 CAATGCCCTGCCATTTTCTAGA 58.974 45.455 0.00 0.00 33.35 2.43
1854 2011 1.383109 AGGATGATGACTGGCCCGA 60.383 57.895 0.00 0.00 0.00 5.14
1855 2012 1.070445 GGATGATGACTGGCCCGAG 59.930 63.158 0.00 0.00 0.00 4.63
1856 2013 1.070445 GATGATGACTGGCCCGAGG 59.930 63.158 0.00 0.00 0.00 4.63
1857 2014 1.383109 ATGATGACTGGCCCGAGGA 60.383 57.895 0.00 0.00 0.00 3.71
1858 2015 1.690219 ATGATGACTGGCCCGAGGAC 61.690 60.000 0.00 0.00 0.00 3.85
1859 2016 3.432051 GATGACTGGCCCGAGGACG 62.432 68.421 0.00 0.00 29.56 4.79
1860 2017 3.957435 ATGACTGGCCCGAGGACGA 62.957 63.158 0.00 0.00 42.66 4.20
1861 2018 3.827898 GACTGGCCCGAGGACGAG 61.828 72.222 0.00 0.00 42.66 4.18
1864 2021 4.458829 TGGCCCGAGGACGAGGAT 62.459 66.667 0.00 0.00 42.66 3.24
1865 2022 3.917760 GGCCCGAGGACGAGGATG 61.918 72.222 0.00 0.00 42.66 3.51
1866 2023 2.833582 GCCCGAGGACGAGGATGA 60.834 66.667 0.00 0.00 42.66 2.92
1867 2024 2.203771 GCCCGAGGACGAGGATGAT 61.204 63.158 0.00 0.00 42.66 2.45
1868 2025 1.662608 CCCGAGGACGAGGATGATG 59.337 63.158 0.00 0.00 42.66 3.07
1869 2026 0.823769 CCCGAGGACGAGGATGATGA 60.824 60.000 0.00 0.00 42.66 2.92
1870 2027 1.252175 CCGAGGACGAGGATGATGAT 58.748 55.000 0.00 0.00 42.66 2.45
1871 2028 1.067985 CCGAGGACGAGGATGATGATG 60.068 57.143 0.00 0.00 42.66 3.07
1974 2133 6.808008 CAGTTGTTCTGGACACATAGATTT 57.192 37.500 0.00 0.00 38.18 2.17
2012 2175 8.134895 GTCATCACAGTGTTGGATTTTCTTTTA 58.865 33.333 11.05 0.00 0.00 1.52
2046 2209 8.447833 TGATTGTATTCGTTGGAGTTTGAATAC 58.552 33.333 14.03 14.03 46.76 1.89
2050 2213 5.917541 TTCGTTGGAGTTTGAATACAGTC 57.082 39.130 0.00 0.00 0.00 3.51
2051 2214 4.951254 TCGTTGGAGTTTGAATACAGTCA 58.049 39.130 0.00 0.00 0.00 3.41
2053 2216 5.637810 TCGTTGGAGTTTGAATACAGTCATC 59.362 40.000 0.00 0.00 0.00 2.92
2054 2217 5.408299 CGTTGGAGTTTGAATACAGTCATCA 59.592 40.000 0.00 0.00 0.00 3.07
2055 2218 6.603095 GTTGGAGTTTGAATACAGTCATCAC 58.397 40.000 0.00 0.00 0.00 3.06
2056 2219 5.863965 TGGAGTTTGAATACAGTCATCACA 58.136 37.500 0.00 0.00 0.00 3.58
2057 2220 5.934043 TGGAGTTTGAATACAGTCATCACAG 59.066 40.000 0.00 0.00 0.00 3.66
2062 2225 6.544038 TTGAATACAGTCATCACAGTGTTG 57.456 37.500 5.36 5.36 32.03 3.33
2063 2226 5.610398 TGAATACAGTCATCACAGTGTTGT 58.390 37.500 10.76 0.00 38.31 3.32
2073 2397 4.562394 CATCACAGTGTTGTGGTTGTTTTC 59.438 41.667 7.72 0.00 46.38 2.29
2090 2414 4.837860 TGTTTTCCTAATGATGCCTGGTTT 59.162 37.500 0.00 0.00 0.00 3.27
2123 2449 2.479566 TTCCCACTGTTCTCTGCATC 57.520 50.000 0.00 0.00 0.00 3.91
2188 2523 4.219115 TCTAGGATCAAGGACTGGATGAC 58.781 47.826 0.00 0.00 0.00 3.06
2195 2530 3.129109 CAAGGACTGGATGACGATGATG 58.871 50.000 0.00 0.00 0.00 3.07
2198 2533 3.645212 AGGACTGGATGACGATGATGATT 59.355 43.478 0.00 0.00 0.00 2.57
2199 2534 3.744942 GGACTGGATGACGATGATGATTG 59.255 47.826 0.00 0.00 0.00 2.67
2200 2535 3.736720 ACTGGATGACGATGATGATTGG 58.263 45.455 0.00 0.00 0.00 3.16
2201 2536 2.483106 CTGGATGACGATGATGATTGGC 59.517 50.000 0.00 0.00 0.00 4.52
2202 2537 2.105306 TGGATGACGATGATGATTGGCT 59.895 45.455 0.00 0.00 0.00 4.75
2203 2538 2.740981 GGATGACGATGATGATTGGCTC 59.259 50.000 0.00 0.00 0.00 4.70
2296 2641 8.442632 TGCTATTCTTAGTTCAATTCCATGAG 57.557 34.615 0.00 0.00 0.00 2.90
2347 2700 1.998315 CTGAACACAGAGAAGGATGCG 59.002 52.381 0.00 0.00 33.94 4.73
2352 2706 2.103143 AGAGAAGGATGCGTCGCG 59.897 61.111 13.38 0.00 0.00 5.87
2356 2710 4.373116 AAGGATGCGTCGCGGTGT 62.373 61.111 13.38 0.00 0.00 4.16
2372 2739 5.049336 TCGCGGTGTTGAATTGATTTTCTAA 60.049 36.000 6.13 0.00 0.00 2.10
2398 2772 5.769662 TGTTGATTGCATTAGTTGGAGTCTT 59.230 36.000 0.00 0.00 34.15 3.01
2432 2806 9.828852 TGTTTTAGTTGTTTACTACACTTGTTG 57.171 29.630 0.00 0.00 39.05 3.33
2435 2809 9.828852 TTTAGTTGTTTACTACACTTGTTGTTG 57.171 29.630 1.81 0.00 39.05 3.33
2594 2970 1.333524 CGCATGATCTTGTTCGGCATC 60.334 52.381 10.05 0.00 0.00 3.91
2647 3023 5.529581 TTTCTCTGTGGGAAAATTGGAAC 57.470 39.130 0.00 0.00 30.94 3.62
2689 3065 2.253610 ACATACCTCCGACCACTGAAA 58.746 47.619 0.00 0.00 0.00 2.69
2718 3094 3.057526 CGTATTCTCAGTGTCAGTGGTGA 60.058 47.826 7.82 4.37 0.00 4.02
2957 3600 3.274288 TGAGTGTGTGTTACATGCAACA 58.726 40.909 7.43 7.43 42.24 3.33
3542 4235 2.297315 TGCCACTATAGGAGCATTCTCG 59.703 50.000 13.26 0.00 40.26 4.04
3774 4469 4.927425 CAGGAAAATCTTGGACAAATGCAG 59.073 41.667 0.00 0.00 0.00 4.41
4068 4773 0.895100 TGTGGCCTGAATTGTCCAGC 60.895 55.000 3.32 0.00 0.00 4.85
4435 5515 2.616842 CGGGCCATCGTAAAAGCTAAAT 59.383 45.455 4.39 0.00 0.00 1.40
4436 5516 3.303791 CGGGCCATCGTAAAAGCTAAATC 60.304 47.826 4.39 0.00 0.00 2.17
4437 5517 3.883489 GGGCCATCGTAAAAGCTAAATCT 59.117 43.478 4.39 0.00 0.00 2.40
4438 5518 5.061179 GGGCCATCGTAAAAGCTAAATCTA 58.939 41.667 4.39 0.00 0.00 1.98
5230 6557 5.182487 CCACACCATTACAACTGCTGTATA 58.818 41.667 0.00 0.00 40.27 1.47
5234 6561 4.081309 ACCATTACAACTGCTGTATACCGT 60.081 41.667 0.00 0.00 40.27 4.83
5235 6562 5.127519 ACCATTACAACTGCTGTATACCGTA 59.872 40.000 0.00 0.00 40.27 4.02
5236 6563 6.183360 ACCATTACAACTGCTGTATACCGTAT 60.183 38.462 0.00 0.00 40.27 3.06
5689 7038 9.750125 GATTACAAATCATTTATCCCTGGAAAC 57.250 33.333 0.00 0.00 0.00 2.78
5695 7044 6.773976 TCATTTATCCCTGGAAACATGAAC 57.226 37.500 0.00 0.00 41.51 3.18
5696 7045 6.252233 TCATTTATCCCTGGAAACATGAACA 58.748 36.000 0.00 0.00 41.51 3.18
5778 7127 7.591006 TTATGTATCCTTTGTCTTTGTCGTC 57.409 36.000 0.00 0.00 0.00 4.20
5782 7131 6.485313 TGTATCCTTTGTCTTTGTCGTCAAAT 59.515 34.615 8.25 0.00 41.77 2.32
6167 7645 1.421646 CTCAACCTCAACCCCTGAACT 59.578 52.381 0.00 0.00 32.17 3.01
6168 7646 1.142870 TCAACCTCAACCCCTGAACTG 59.857 52.381 0.00 0.00 32.17 3.16
6345 7853 9.066892 TGGCACAATTAAATCTATTGATAGTCC 57.933 33.333 0.00 0.00 36.67 3.85
6364 7872 1.758280 CCAATACAGCATGGCCATGTT 59.242 47.619 39.08 33.82 43.62 2.71
6405 7913 5.466058 GCATCTGATCTCAATCTACTTGTGG 59.534 44.000 0.00 0.00 36.20 4.17
6414 7922 4.067896 CAATCTACTTGTGGAGTTGTGCT 58.932 43.478 0.00 0.00 39.86 4.40
6415 7923 3.838244 TCTACTTGTGGAGTTGTGCTT 57.162 42.857 0.00 0.00 39.86 3.91
6429 7938 5.523369 AGTTGTGCTTTTACTCATTTGAGC 58.477 37.500 7.48 0.00 45.79 4.26
6528 8041 2.821969 ACTGGCATCAGGAAATGTGAAC 59.178 45.455 0.00 0.00 44.99 3.18
6645 8158 5.452078 TGTTTTCCAGCTTCCTTGTATTG 57.548 39.130 0.00 0.00 0.00 1.90
6655 8168 4.381932 GCTTCCTTGTATTGGGGTGAAATG 60.382 45.833 0.00 0.00 0.00 2.32
6656 8169 4.396357 TCCTTGTATTGGGGTGAAATGT 57.604 40.909 0.00 0.00 0.00 2.71
6665 8179 5.975693 TTGGGGTGAAATGTAATCTTGAC 57.024 39.130 0.00 0.00 0.00 3.18
6745 8260 6.840780 AATACCAGTTTCCAAGATTTCTGG 57.159 37.500 7.36 7.36 45.24 3.86
6764 8279 5.080337 TCTGGAGTCAGACTTGTCTAACAT 58.920 41.667 4.05 0.00 44.39 2.71
6765 8280 5.540337 TCTGGAGTCAGACTTGTCTAACATT 59.460 40.000 4.05 0.00 44.39 2.71
6770 8285 7.309255 GGAGTCAGACTTGTCTAACATTCACTA 60.309 40.741 4.05 0.00 0.00 2.74
6773 8288 9.856488 GTCAGACTTGTCTAACATTCACTATTA 57.144 33.333 2.72 0.00 0.00 0.98
6862 8377 2.223572 CGTTTGGCAGCTCAGTCTTTTT 60.224 45.455 0.00 0.00 0.00 1.94
6866 8381 0.038801 GCAGCTCAGTCTTTTTGGGC 60.039 55.000 0.00 0.00 42.42 5.36
6871 8386 3.062042 GCTCAGTCTTTTTGGGCATTTG 58.938 45.455 0.00 0.00 41.70 2.32
6883 8398 8.503458 TTTTTGGGCATTTGAATTATACCATG 57.497 30.769 0.00 0.00 0.00 3.66
6915 8514 4.333690 TCGAGGGCTAGTGGTTATCTATC 58.666 47.826 0.00 0.00 0.00 2.08
6918 8517 6.069556 TCGAGGGCTAGTGGTTATCTATCTAT 60.070 42.308 0.00 0.00 0.00 1.98
6941 11570 4.506255 CCGGCCAATGGAGTCCCC 62.506 72.222 2.05 0.00 0.00 4.81
6942 11571 4.856801 CGGCCAATGGAGTCCCCG 62.857 72.222 2.05 8.11 37.93 5.73
6945 11574 4.506255 CCAATGGAGTCCCCGCCC 62.506 72.222 6.74 0.00 37.93 6.13
6946 11575 4.506255 CAATGGAGTCCCCGCCCC 62.506 72.222 6.74 0.00 37.93 5.80
6991 11620 1.041447 TCCTCCGATTTCTCCGACCC 61.041 60.000 0.00 0.00 0.00 4.46
6998 11627 2.094390 CGATTTCTCCGACCCAACTACA 60.094 50.000 0.00 0.00 0.00 2.74
6999 11628 2.825861 TTTCTCCGACCCAACTACAC 57.174 50.000 0.00 0.00 0.00 2.90
7018 11647 3.833070 ACACCTCCTAGATTCACTCGTTT 59.167 43.478 0.00 0.00 0.00 3.60
7025 11654 1.000145 GATTCACTCGTTTCTCCGGC 59.000 55.000 0.00 0.00 0.00 6.13
7040 11669 2.975799 GGCCGAACACCTCGCAAA 60.976 61.111 0.00 0.00 46.71 3.68
7041 11670 2.251371 GCCGAACACCTCGCAAAC 59.749 61.111 0.00 0.00 46.71 2.93
7042 11671 2.549282 CCGAACACCTCGCAAACG 59.451 61.111 0.00 0.00 46.71 3.60
7053 11682 1.866925 CGCAAACGAAGAGGGTTCC 59.133 57.895 0.00 0.00 43.93 3.62
7054 11683 0.602905 CGCAAACGAAGAGGGTTCCT 60.603 55.000 0.00 0.00 43.93 3.36
7055 11684 0.875059 GCAAACGAAGAGGGTTCCTG 59.125 55.000 0.00 0.00 31.76 3.86
7056 11685 1.523758 CAAACGAAGAGGGTTCCTGG 58.476 55.000 0.00 0.00 31.76 4.45
7057 11686 0.400594 AAACGAAGAGGGTTCCTGGG 59.599 55.000 0.00 0.00 31.76 4.45
7058 11687 0.473117 AACGAAGAGGGTTCCTGGGA 60.473 55.000 0.00 0.00 31.76 4.37
7069 11698 3.406200 CCTGGGACTGGGAGCAGG 61.406 72.222 0.00 0.00 44.20 4.85
7070 11699 3.406200 CTGGGACTGGGAGCAGGG 61.406 72.222 0.00 0.00 0.00 4.45
7090 11719 1.758514 GTGCGAGATGGGAGGAGGA 60.759 63.158 0.00 0.00 0.00 3.71
7091 11720 1.456518 TGCGAGATGGGAGGAGGAG 60.457 63.158 0.00 0.00 0.00 3.69
7092 11721 2.206536 GCGAGATGGGAGGAGGAGG 61.207 68.421 0.00 0.00 0.00 4.30
7093 11722 1.532794 CGAGATGGGAGGAGGAGGG 60.533 68.421 0.00 0.00 0.00 4.30
7095 11724 2.288643 GATGGGAGGAGGAGGGCT 59.711 66.667 0.00 0.00 0.00 5.19
7096 11725 1.841103 GATGGGAGGAGGAGGGCTC 60.841 68.421 0.00 0.00 0.00 4.70
7153 11809 2.802106 GCGTTCCTCCTCCTCTCG 59.198 66.667 0.00 0.00 0.00 4.04
7202 11858 0.028242 CATCGACGTCCTCTTCCTCG 59.972 60.000 10.58 0.00 0.00 4.63
7203 11859 1.716826 ATCGACGTCCTCTTCCTCGC 61.717 60.000 10.58 0.00 0.00 5.03
7204 11860 2.490685 GACGTCCTCTTCCTCGCC 59.509 66.667 3.51 0.00 0.00 5.54
7205 11861 3.398353 GACGTCCTCTTCCTCGCCG 62.398 68.421 3.51 0.00 0.00 6.46
7206 11862 4.856607 CGTCCTCTTCCTCGCCGC 62.857 72.222 0.00 0.00 0.00 6.53
7207 11863 4.516195 GTCCTCTTCCTCGCCGCC 62.516 72.222 0.00 0.00 0.00 6.13
7208 11864 4.761058 TCCTCTTCCTCGCCGCCT 62.761 66.667 0.00 0.00 0.00 5.52
7209 11865 4.214327 CCTCTTCCTCGCCGCCTC 62.214 72.222 0.00 0.00 0.00 4.70
7210 11866 4.560856 CTCTTCCTCGCCGCCTCG 62.561 72.222 0.00 0.00 0.00 4.63
7261 11917 3.431725 GGCGCGTCCCCTGAAAAG 61.432 66.667 8.43 0.00 0.00 2.27
7262 11918 3.431725 GCGCGTCCCCTGAAAAGG 61.432 66.667 8.43 0.00 0.00 3.11
7263 11919 2.345991 CGCGTCCCCTGAAAAGGA 59.654 61.111 0.00 0.00 0.00 3.36
7264 11920 1.741770 CGCGTCCCCTGAAAAGGAG 60.742 63.158 0.00 0.00 31.17 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 7.652507 CCGTCCCTTTTTCTTATCATCTACTAC 59.347 40.741 0.00 0.00 0.00 2.73
19 20 6.383147 AGACCGTCCCTTTTTCTTATCATCTA 59.617 38.462 0.00 0.00 0.00 1.98
43 48 7.745620 ATTTTTCCAAGTACTCAAGGTGTAG 57.254 36.000 0.00 0.00 0.00 2.74
58 63 8.912988 CAGTGGCTAGGATATTAATTTTTCCAA 58.087 33.333 11.95 0.00 0.00 3.53
67 72 4.597075 TGCATCCAGTGGCTAGGATATTAA 59.403 41.667 3.51 0.00 42.61 1.40
75 84 1.376543 CACTTGCATCCAGTGGCTAG 58.623 55.000 3.51 2.00 38.54 3.42
97 107 4.466370 AGGTTTAAGACGATGATCCAGTCA 59.534 41.667 12.68 0.00 42.06 3.41
161 171 0.175760 CATGTCGGTGGACGGAAGAT 59.824 55.000 0.00 0.00 46.49 2.40
168 178 0.033504 AGTGTGACATGTCGGTGGAC 59.966 55.000 20.54 13.00 43.71 4.02
183 193 2.091222 GGGAGGTAGGTGGATAGAGTGT 60.091 54.545 0.00 0.00 0.00 3.55
279 290 4.487714 TCCTCATTTCTAGCGGTGAATT 57.512 40.909 0.00 0.00 0.00 2.17
312 325 2.862140 GCACAAACCGATGTTCCTTTGG 60.862 50.000 0.00 0.00 32.15 3.28
331 344 2.115052 GTGGTGTGGGGTGATGCA 59.885 61.111 0.00 0.00 0.00 3.96
346 362 0.883833 AAGGATTGAAAGCCTGCGTG 59.116 50.000 0.00 0.00 45.74 5.34
357 373 1.351017 GGACTGGTGGTGAAGGATTGA 59.649 52.381 0.00 0.00 0.00 2.57
403 421 1.202143 CCCTTTCAATTTACTCGGCGC 60.202 52.381 0.00 0.00 0.00 6.53
490 520 1.837439 TCGGGTATGTTGGCTCTCATT 59.163 47.619 0.00 0.00 0.00 2.57
492 522 0.535335 GTCGGGTATGTTGGCTCTCA 59.465 55.000 0.00 0.00 0.00 3.27
504 534 1.965643 GGGTATATGTGCTGTCGGGTA 59.034 52.381 0.00 0.00 0.00 3.69
510 540 3.519510 AGTTGTGAGGGTATATGTGCTGT 59.480 43.478 0.00 0.00 0.00 4.40
513 543 5.424757 TGTAAGTTGTGAGGGTATATGTGC 58.575 41.667 0.00 0.00 0.00 4.57
574 605 4.454504 GCCCGTTAGAATGAAGTCTTTTCA 59.545 41.667 0.96 0.00 0.00 2.69
712 749 4.837085 TCCTTCGGAGACCTCGTT 57.163 55.556 0.00 0.00 34.32 3.85
762 799 0.612174 AGCCCGTCACTCAAGCTCTA 60.612 55.000 0.00 0.00 0.00 2.43
956 1047 1.537889 TTTCTGCCCCTCCGAGGAA 60.538 57.895 16.69 0.00 37.67 3.36
980 1071 2.859165 TTCTTTCGCCTGTTGGAGAT 57.141 45.000 0.00 0.00 41.68 2.75
981 1072 2.631160 TTTCTTTCGCCTGTTGGAGA 57.369 45.000 0.00 0.00 40.41 3.71
985 1076 1.067635 CCCCATTTCTTTCGCCTGTTG 60.068 52.381 0.00 0.00 0.00 3.33
986 1077 1.203001 TCCCCATTTCTTTCGCCTGTT 60.203 47.619 0.00 0.00 0.00 3.16
987 1078 0.404040 TCCCCATTTCTTTCGCCTGT 59.596 50.000 0.00 0.00 0.00 4.00
988 1079 1.767759 ATCCCCATTTCTTTCGCCTG 58.232 50.000 0.00 0.00 0.00 4.85
1024 1115 0.177141 GCCCTGTCCGTGCTGTATAA 59.823 55.000 0.00 0.00 0.00 0.98
1243 1346 1.683011 CCATCACCATTCACCCAGGAC 60.683 57.143 0.00 0.00 0.00 3.85
1313 1425 3.011760 GCGGACCAAGAACGAAGCG 62.012 63.158 0.00 0.00 0.00 4.68
1403 1516 5.894807 AGAAAATGATGATTAAACTGCGGG 58.105 37.500 0.00 0.00 0.00 6.13
1443 1556 5.348164 CAACAAGGGAAAAACTACACCAAG 58.652 41.667 0.00 0.00 0.00 3.61
1511 1624 9.667107 CAAAAGAATTCAGGTACTACATAAGGA 57.333 33.333 8.44 0.00 36.02 3.36
1769 1903 1.767759 ATGGCAGGGCATTGTAAGAC 58.232 50.000 2.07 0.00 0.00 3.01
1796 1932 3.054434 TCATCAACATCCGGTCCTTCATT 60.054 43.478 0.00 0.00 0.00 2.57
1854 2011 2.158400 TCCTCATCATCATCCTCGTCCT 60.158 50.000 0.00 0.00 0.00 3.85
1855 2012 2.029470 GTCCTCATCATCATCCTCGTCC 60.029 54.545 0.00 0.00 0.00 4.79
1856 2013 2.351253 CGTCCTCATCATCATCCTCGTC 60.351 54.545 0.00 0.00 0.00 4.20
1857 2014 1.611006 CGTCCTCATCATCATCCTCGT 59.389 52.381 0.00 0.00 0.00 4.18
1858 2015 1.882623 TCGTCCTCATCATCATCCTCG 59.117 52.381 0.00 0.00 0.00 4.63
1859 2016 2.230992 CCTCGTCCTCATCATCATCCTC 59.769 54.545 0.00 0.00 0.00 3.71
1860 2017 2.246469 CCTCGTCCTCATCATCATCCT 58.754 52.381 0.00 0.00 0.00 3.24
1861 2018 1.967066 ACCTCGTCCTCATCATCATCC 59.033 52.381 0.00 0.00 0.00 3.51
1862 2019 2.625314 TCACCTCGTCCTCATCATCATC 59.375 50.000 0.00 0.00 0.00 2.92
1863 2020 2.670939 TCACCTCGTCCTCATCATCAT 58.329 47.619 0.00 0.00 0.00 2.45
1864 2021 2.143876 TCACCTCGTCCTCATCATCA 57.856 50.000 0.00 0.00 0.00 3.07
1865 2022 3.526931 TTTCACCTCGTCCTCATCATC 57.473 47.619 0.00 0.00 0.00 2.92
1866 2023 3.981071 TTTTCACCTCGTCCTCATCAT 57.019 42.857 0.00 0.00 0.00 2.45
1867 2024 3.981071 ATTTTCACCTCGTCCTCATCA 57.019 42.857 0.00 0.00 0.00 3.07
1868 2025 4.455877 ACAAATTTTCACCTCGTCCTCATC 59.544 41.667 0.00 0.00 0.00 2.92
1869 2026 4.216257 CACAAATTTTCACCTCGTCCTCAT 59.784 41.667 0.00 0.00 0.00 2.90
1870 2027 3.563808 CACAAATTTTCACCTCGTCCTCA 59.436 43.478 0.00 0.00 0.00 3.86
1871 2028 3.564225 ACACAAATTTTCACCTCGTCCTC 59.436 43.478 0.00 0.00 0.00 3.71
1962 2121 6.085555 TGACGAGGGATAAATCTATGTGTC 57.914 41.667 0.00 0.00 0.00 3.67
1968 2127 6.016192 GTGATGACTGACGAGGGATAAATCTA 60.016 42.308 0.00 0.00 0.00 1.98
1972 2131 3.767131 TGTGATGACTGACGAGGGATAAA 59.233 43.478 0.00 0.00 0.00 1.40
1974 2133 2.952310 CTGTGATGACTGACGAGGGATA 59.048 50.000 0.00 0.00 0.00 2.59
2012 2175 7.606456 ACTCCAACGAATACAATCAACAAGTAT 59.394 33.333 0.00 0.00 0.00 2.12
2029 2192 4.951254 TGACTGTATTCAAACTCCAACGA 58.049 39.130 0.00 0.00 0.00 3.85
2054 2217 3.161866 AGGAAAACAACCACAACACTGT 58.838 40.909 0.00 0.00 35.63 3.55
2055 2218 3.866883 AGGAAAACAACCACAACACTG 57.133 42.857 0.00 0.00 0.00 3.66
2056 2219 5.654650 TCATTAGGAAAACAACCACAACACT 59.345 36.000 0.00 0.00 0.00 3.55
2057 2220 5.897050 TCATTAGGAAAACAACCACAACAC 58.103 37.500 0.00 0.00 0.00 3.32
2062 2225 4.220602 AGGCATCATTAGGAAAACAACCAC 59.779 41.667 0.00 0.00 0.00 4.16
2063 2226 4.220382 CAGGCATCATTAGGAAAACAACCA 59.780 41.667 0.00 0.00 0.00 3.67
2064 2227 4.381932 CCAGGCATCATTAGGAAAACAACC 60.382 45.833 0.00 0.00 0.00 3.77
2065 2228 4.220602 ACCAGGCATCATTAGGAAAACAAC 59.779 41.667 0.00 0.00 0.00 3.32
2073 2397 4.463891 AGTGAAAAACCAGGCATCATTAGG 59.536 41.667 0.00 0.00 0.00 2.69
2090 2414 3.096092 AGTGGGAAAAAGTGCAGTGAAA 58.904 40.909 0.00 0.00 0.00 2.69
2188 2523 2.474359 GTCTTCGAGCCAATCATCATCG 59.526 50.000 0.00 0.00 34.80 3.84
2195 2530 2.279582 TCTTCGTCTTCGAGCCAATC 57.720 50.000 0.00 0.00 46.81 2.67
2198 2533 1.173913 TCATCTTCGTCTTCGAGCCA 58.826 50.000 0.00 0.00 46.81 4.75
2199 2534 2.123342 CATCATCTTCGTCTTCGAGCC 58.877 52.381 0.00 0.00 46.81 4.70
2200 2535 3.042189 CTCATCATCTTCGTCTTCGAGC 58.958 50.000 0.00 0.00 46.81 5.03
2201 2536 3.549827 CCCTCATCATCTTCGTCTTCGAG 60.550 52.174 0.00 0.00 46.81 4.04
2202 2537 2.359214 CCCTCATCATCTTCGTCTTCGA 59.641 50.000 0.00 0.00 44.66 3.71
2203 2538 2.099921 ACCCTCATCATCTTCGTCTTCG 59.900 50.000 0.00 0.00 38.55 3.79
2296 2641 7.724305 TGGACAAATAACTCAAGTCACTAAC 57.276 36.000 0.00 0.00 0.00 2.34
2299 2644 7.285401 ACAATTGGACAAATAACTCAAGTCACT 59.715 33.333 10.83 0.00 0.00 3.41
2347 2700 2.611974 AATCAATTCAACACCGCGAC 57.388 45.000 8.23 0.00 0.00 5.19
2372 2739 6.435277 AGACTCCAACTAATGCAATCAACAAT 59.565 34.615 0.00 0.00 0.00 2.71
2594 2970 3.414700 GTTGAGCGGCACCGAGTG 61.415 66.667 14.43 0.25 42.83 3.51
2689 3065 2.164624 GACACTGAGAATACGGCAGTCT 59.835 50.000 0.00 0.00 40.63 3.24
2957 3600 9.107177 TGATTGCAGTTTGACAAACATTTTAAT 57.893 25.926 28.07 19.85 43.79 1.40
3096 3763 7.081857 AGGGTAAGTTCCACTGTAATTACAA 57.918 36.000 18.55 1.83 35.50 2.41
3774 4469 5.038033 CGAGTAACTTCAGCTTGACTATCC 58.962 45.833 0.00 0.00 0.00 2.59
4068 4773 1.442769 ACCACATCTTACAAGCAGCG 58.557 50.000 0.00 0.00 0.00 5.18
4951 6131 5.343593 CGGTGTTCAAAATTTAAATAGCGCA 59.656 36.000 11.47 0.00 30.62 6.09
5388 6721 7.394016 TGTAACTTAATGTCATGTCCTGTCAT 58.606 34.615 0.00 0.00 35.50 3.06
5689 7038 5.678583 ACTCTAACCTGATGGATGTTCATG 58.321 41.667 0.00 0.00 37.04 3.07
5695 7044 7.659390 GGATAAGAAACTCTAACCTGATGGATG 59.341 40.741 0.00 0.00 37.04 3.51
5696 7045 7.202139 GGGATAAGAAACTCTAACCTGATGGAT 60.202 40.741 0.00 0.00 37.04 3.41
6167 7645 2.752358 CACTTCCCAGCTCCAGCA 59.248 61.111 0.48 0.00 45.16 4.41
6168 7646 2.045536 CCACTTCCCAGCTCCAGC 60.046 66.667 0.00 0.00 42.49 4.85
6345 7853 2.482316 CCAACATGGCCATGCTGTATTG 60.482 50.000 39.74 32.63 42.39 1.90
6364 7872 6.065374 TCAGATGCCAGTAAACTAAAAACCA 58.935 36.000 0.00 0.00 0.00 3.67
6405 7913 5.626955 GCTCAAATGAGTAAAAGCACAACTC 59.373 40.000 11.77 0.00 43.85 3.01
6552 8065 6.852420 ACAGAAGCAAAGGAGTACAGTATA 57.148 37.500 0.00 0.00 0.00 1.47
6553 8066 5.746990 ACAGAAGCAAAGGAGTACAGTAT 57.253 39.130 0.00 0.00 0.00 2.12
6554 8067 6.852420 ATACAGAAGCAAAGGAGTACAGTA 57.148 37.500 0.00 0.00 0.00 2.74
6555 8068 5.746990 ATACAGAAGCAAAGGAGTACAGT 57.253 39.130 0.00 0.00 0.00 3.55
6645 8158 4.764823 TGTGTCAAGATTACATTTCACCCC 59.235 41.667 0.00 0.00 0.00 4.95
6742 8257 4.855715 TGTTAGACAAGTCTGACTCCAG 57.144 45.455 20.98 7.01 43.89 3.86
6745 8260 6.451393 AGTGAATGTTAGACAAGTCTGACTC 58.549 40.000 20.98 13.85 43.89 3.36
6831 8346 2.652313 TGCCAAACGCAGCCTTAAT 58.348 47.368 0.00 0.00 44.64 1.40
6832 8347 4.165926 TGCCAAACGCAGCCTTAA 57.834 50.000 0.00 0.00 44.64 1.85
6862 8377 5.215069 ACCATGGTATAATTCAAATGCCCA 58.785 37.500 18.10 0.00 0.00 5.36
6892 8491 2.588620 AGATAACCACTAGCCCTCGAG 58.411 52.381 5.13 5.13 0.00 4.04
6895 8494 7.397761 ACAATAGATAGATAACCACTAGCCCTC 59.602 40.741 0.00 0.00 0.00 4.30
6898 8497 6.814146 GCACAATAGATAGATAACCACTAGCC 59.186 42.308 0.00 0.00 0.00 3.93
6899 8498 6.814146 GGCACAATAGATAGATAACCACTAGC 59.186 42.308 0.00 0.00 0.00 3.42
6900 8499 7.324178 GGGCACAATAGATAGATAACCACTAG 58.676 42.308 0.00 0.00 0.00 2.57
6901 8500 6.071560 CGGGCACAATAGATAGATAACCACTA 60.072 42.308 0.00 0.00 0.00 2.74
6903 8502 4.929808 CGGGCACAATAGATAGATAACCAC 59.070 45.833 0.00 0.00 0.00 4.16
6915 8514 1.735360 CATTGGCCGGGCACAATAG 59.265 57.895 32.91 14.68 35.67 1.73
6918 8517 4.292145 TCCATTGGCCGGGCACAA 62.292 61.111 32.91 18.66 0.00 3.33
6971 11600 0.102663 GGTCGGAGAAATCGGAGGAC 59.897 60.000 0.00 0.00 39.69 3.85
6973 11602 1.327690 TGGGTCGGAGAAATCGGAGG 61.328 60.000 0.00 0.00 39.69 4.30
6976 11605 0.249398 AGTTGGGTCGGAGAAATCGG 59.751 55.000 0.00 0.00 39.69 4.18
6977 11606 2.094390 TGTAGTTGGGTCGGAGAAATCG 60.094 50.000 0.00 0.00 39.69 3.34
6991 11620 5.449314 CGAGTGAATCTAGGAGGTGTAGTTG 60.449 48.000 0.00 0.00 0.00 3.16
6998 11627 4.345854 AGAAACGAGTGAATCTAGGAGGT 58.654 43.478 0.00 0.00 0.00 3.85
6999 11628 4.202070 GGAGAAACGAGTGAATCTAGGAGG 60.202 50.000 0.00 0.00 0.00 4.30
7018 11647 3.379445 GAGGTGTTCGGCCGGAGA 61.379 66.667 27.83 13.95 0.00 3.71
7036 11665 0.875059 CAGGAACCCTCTTCGTTTGC 59.125 55.000 0.00 0.00 0.00 3.68
7038 11667 0.400594 CCCAGGAACCCTCTTCGTTT 59.599 55.000 0.00 0.00 0.00 3.60
7039 11668 0.473117 TCCCAGGAACCCTCTTCGTT 60.473 55.000 0.00 0.00 0.00 3.85
7040 11669 1.157751 TCCCAGGAACCCTCTTCGT 59.842 57.895 0.00 0.00 0.00 3.85
7041 11670 0.905337 AGTCCCAGGAACCCTCTTCG 60.905 60.000 0.00 0.00 0.00 3.79
7042 11671 0.615850 CAGTCCCAGGAACCCTCTTC 59.384 60.000 0.00 0.00 0.00 2.87
7044 11673 1.229658 CCAGTCCCAGGAACCCTCT 60.230 63.158 0.00 0.00 0.00 3.69
7047 11676 2.204090 TCCCAGTCCCAGGAACCC 60.204 66.667 0.00 0.00 0.00 4.11
7049 11678 2.190488 CTGCTCCCAGTCCCAGGAAC 62.190 65.000 0.00 0.00 34.31 3.62
7050 11679 1.920325 CTGCTCCCAGTCCCAGGAA 60.920 63.158 0.00 0.00 34.31 3.36
7051 11680 2.284921 CTGCTCCCAGTCCCAGGA 60.285 66.667 0.00 0.00 34.31 3.86
7052 11681 3.406200 CCTGCTCCCAGTCCCAGG 61.406 72.222 0.00 0.00 38.93 4.45
7053 11682 3.406200 CCCTGCTCCCAGTCCCAG 61.406 72.222 0.00 0.00 37.38 4.45
7057 11686 4.767255 CACGCCCTGCTCCCAGTC 62.767 72.222 0.00 0.00 37.38 3.51
7069 11698 4.899239 CCTCCCATCTCGCACGCC 62.899 72.222 0.00 0.00 0.00 5.68
7070 11699 3.781770 CTCCTCCCATCTCGCACGC 62.782 68.421 0.00 0.00 0.00 5.34
7072 11701 1.743321 CTCCTCCTCCCATCTCGCAC 61.743 65.000 0.00 0.00 0.00 5.34
7111 11767 4.493747 CCGACGAAGGAGCCGGAC 62.494 72.222 5.05 0.00 44.29 4.79
7131 11787 3.839432 GGAGGAGGAACGCGAGGG 61.839 72.222 15.93 0.00 0.00 4.30
7190 11846 4.516195 GGCGGCGAGGAAGAGGAC 62.516 72.222 12.98 0.00 0.00 3.85
7244 11900 3.431725 CTTTTCAGGGGACGCGCC 61.432 66.667 5.73 8.77 36.67 6.53
7245 11901 3.431725 CCTTTTCAGGGGACGCGC 61.432 66.667 5.73 0.00 36.36 6.86
7246 11902 1.741770 CTCCTTTTCAGGGGACGCG 60.742 63.158 3.53 3.53 45.08 6.01
7247 11903 4.303257 CTCCTTTTCAGGGGACGC 57.697 61.111 0.00 0.00 45.08 5.19


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

AutoCloner maintained by Alex Coulton.