Multiple sequence alignment - TraesCS5D01G514000

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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 TraesCS5D01G514000 chr5D 100.000 4740 0 0 3487 8226 537757603 537762342 0.000000e+00 8754.0
1 TraesCS5D01G514000 chr5D 100.000 3127 0 0 1 3127 537754117 537757243 0.000000e+00 5775.0
2 TraesCS5D01G514000 chr4A 94.670 3771 151 22 4488 8226 631960225 631963977 0.000000e+00 5805.0
3 TraesCS5D01G514000 chr4A 90.491 1283 70 25 690 1931 631956743 631958014 0.000000e+00 1646.0
4 TraesCS5D01G514000 chr4A 92.732 1142 50 12 1914 3053 631958032 631959142 0.000000e+00 1618.0
5 TraesCS5D01G514000 chr4A 92.522 896 28 5 3516 4388 631959138 631960017 0.000000e+00 1247.0
6 TraesCS5D01G514000 chr4A 93.529 649 35 3 1 645 631956110 631956755 0.000000e+00 959.0
7 TraesCS5D01G514000 chr4A 85.470 117 12 3 3653 3769 709868724 709868613 5.220000e-22 117.0
8 TraesCS5D01G514000 chr5B 94.085 2130 86 20 6105 8225 678511304 678513402 0.000000e+00 3199.0
9 TraesCS5D01G514000 chr5B 95.730 1616 67 2 4488 6103 678509572 678511185 0.000000e+00 2601.0
10 TraesCS5D01G514000 chr5B 92.590 1201 53 10 1930 3127 678507377 678508544 0.000000e+00 1692.0
11 TraesCS5D01G514000 chr5B 92.354 1007 35 18 3494 4491 678508560 678509533 0.000000e+00 1395.0
12 TraesCS5D01G514000 chr5B 86.002 1043 59 32 633 1658 678506004 678506976 0.000000e+00 1037.0
13 TraesCS5D01G514000 chr5B 91.963 535 33 4 1 535 678494001 678494525 0.000000e+00 741.0
14 TraesCS5D01G514000 chr5B 94.613 297 15 1 1635 1931 678506995 678507290 7.520000e-125 459.0
15 TraesCS5D01G514000 chrUn 89.841 502 31 2 6888 7388 332035095 332034613 1.950000e-175 627.0
16 TraesCS5D01G514000 chrUn 89.641 502 32 2 6888 7388 60686130 60685648 9.070000e-174 621.0
17 TraesCS5D01G514000 chrUn 89.641 502 32 2 6888 7388 60692635 60692153 9.070000e-174 621.0
18 TraesCS5D01G514000 chrUn 89.780 499 31 2 6888 7385 340605678 340606157 9.070000e-174 621.0
19 TraesCS5D01G514000 chrUn 89.641 502 32 2 6888 7388 351584965 351584483 9.070000e-174 621.0
20 TraesCS5D01G514000 chrUn 89.442 502 33 2 6888 7388 60743882 60743400 4.220000e-172 616.0
21 TraesCS5D01G514000 chrUn 89.442 502 33 2 6888 7388 224196083 224195601 4.220000e-172 616.0
22 TraesCS5D01G514000 chrUn 89.834 482 29 2 6905 7385 221985954 221986416 1.180000e-167 601.0
23 TraesCS5D01G514000 chrUn 86.716 271 16 2 6888 7157 375249043 375249294 4.860000e-72 283.0
24 TraesCS5D01G514000 chr4B 89.442 502 33 2 6888 7388 656332646 656332164 4.220000e-172 616.0
25 TraesCS5D01G514000 chr6B 93.204 309 13 7 7919 8226 59405899 59406200 1.630000e-121 448.0
26 TraesCS5D01G514000 chr6B 86.325 117 11 3 3653 3769 530986715 530986826 1.120000e-23 122.0
27 TraesCS5D01G514000 chr1A 92.537 201 12 2 447 645 299726972 299726773 1.350000e-72 285.0
28 TraesCS5D01G514000 chr1A 89.706 204 18 3 445 645 546226648 546226445 2.950000e-64 257.0
29 TraesCS5D01G514000 chr7A 81.234 389 40 14 3697 4058 715758902 715759284 4.860000e-72 283.0
30 TraesCS5D01G514000 chr1B 81.234 389 40 14 3697 4058 633784115 633784497 4.860000e-72 283.0
31 TraesCS5D01G514000 chr1B 85.484 186 23 3 461 645 8857078 8857260 3.030000e-44 191.0
32 TraesCS5D01G514000 chr1D 90.640 203 16 3 446 645 451647421 451647219 4.890000e-67 267.0
33 TraesCS5D01G514000 chr1D 90.196 204 16 3 446 645 451665011 451664808 6.330000e-66 263.0
34 TraesCS5D01G514000 chr3B 83.571 280 34 7 2711 2981 755770546 755770270 1.370000e-62 252.0
35 TraesCS5D01G514000 chr2A 85.047 214 25 5 3653 3866 755384349 755384143 2.330000e-50 211.0
36 TraesCS5D01G514000 chr6D 97.143 35 1 0 569 603 466782165 466782131 8.920000e-05 60.2


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 TraesCS5D01G514000 chr5D 537754117 537762342 8225 False 7264.5 8754 100.000000 1 8226 2 chr5D.!!$F1 8225
1 TraesCS5D01G514000 chr4A 631956110 631963977 7867 False 2255.0 5805 92.788800 1 8226 5 chr4A.!!$F1 8225
2 TraesCS5D01G514000 chr5B 678506004 678513402 7398 False 1730.5 3199 92.562333 633 8225 6 chr5B.!!$F2 7592
3 TraesCS5D01G514000 chr5B 678494001 678494525 524 False 741.0 741 91.963000 1 535 1 chr5B.!!$F1 534

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
732 737 0.042581 TCCCATGTGCTCCCTGTCTA 59.957 55.000 0.00 0.00 0.00 2.59 F
1441 1462 0.112218 TGGTTGGTTCACATGGGAGG 59.888 55.000 0.00 0.00 0.00 4.30 F
2123 2287 1.806542 CTGCTGAACGTTTATGCCAGT 59.193 47.619 0.46 0.00 0.00 4.00 F
2332 2496 0.035458 AGGTCACTTTCTCCTTGCCG 59.965 55.000 0.00 0.00 0.00 5.69 F
2333 2497 0.250338 GGTCACTTTCTCCTTGCCGT 60.250 55.000 0.00 0.00 0.00 5.68 F
3715 3920 0.034756 TGAACAGCATGCCGTACTGT 59.965 50.000 15.66 9.04 46.27 3.55 F
3716 3921 1.273886 TGAACAGCATGCCGTACTGTA 59.726 47.619 15.66 0.00 43.63 2.74 F
5153 5475 0.308684 CCGGATTCATGGCGTCAATG 59.691 55.000 0.00 0.00 0.00 2.82 F
5685 6010 2.151202 TCGAGTGGAAAAGGCATGAAC 58.849 47.619 0.00 0.00 0.00 3.18 F
6727 7176 0.593128 GGTTAACCTGCTGTGCACTG 59.407 55.000 19.41 18.94 33.79 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2102 2266 0.521291 TGGCATAAACGTTCAGCAGC 59.479 50.000 17.51 10.8 0.00 5.25 R
2322 2486 0.809385 CTCGAACTACGGCAAGGAGA 59.191 55.000 0.00 0.0 42.82 3.71 R
2925 3113 0.819666 GGCAGATTTAAGGCCTCCCG 60.820 60.000 5.23 0.0 44.32 5.14 R
3636 3841 3.129638 TCCAGTTTGTTTTCCTTTCGTGG 59.870 43.478 0.00 0.0 0.00 4.94 R
4044 4251 3.489738 CCTTTGGCACTTCAAACTCTGTG 60.490 47.826 0.00 0.0 33.62 3.66 R
4925 5247 0.253044 ATGGACACAGTAGCCGCATT 59.747 50.000 0.00 0.0 0.00 3.56 R
5163 5486 0.465705 ACATGCCAGATACCGGACAG 59.534 55.000 9.46 0.0 0.00 3.51 R
6254 6700 0.807496 GAGGGCTCACTTGAATGCAC 59.193 55.000 0.00 0.0 0.00 4.57 R
6875 7325 1.853963 ATCCAACACTCGGCTACTCT 58.146 50.000 0.00 0.0 0.00 3.24 R
7882 8355 0.984995 ACTGGTACCCTTCCAAGAGC 59.015 55.000 10.07 0.0 34.35 4.09 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
87 88 4.899616 GCACATTGTTTGCTTGAAAATTCG 59.100 37.500 0.00 0.00 37.00 3.34
92 93 8.113675 ACATTGTTTGCTTGAAAATTCGTAAAC 58.886 29.630 0.00 0.00 0.00 2.01
98 99 5.202640 GCTTGAAAATTCGTAAACGTGTCT 58.797 37.500 2.02 0.00 40.80 3.41
183 184 7.374272 TGATGCTTCCAAATACGAATTTTGAA 58.626 30.769 9.80 0.00 35.49 2.69
251 252 9.182933 CTAATACGCCTCTCTCTTGTAAATAAC 57.817 37.037 0.00 0.00 0.00 1.89
327 332 2.815503 TCGTTGATAGACGGTCACTTGA 59.184 45.455 11.27 0.00 42.98 3.02
328 333 3.253921 TCGTTGATAGACGGTCACTTGAA 59.746 43.478 11.27 0.00 42.98 2.69
444 449 7.460082 AGGAACTCCTTTATTGTAGGGAACTTA 59.540 37.037 0.00 0.00 46.09 2.24
488 493 8.871862 GTTTTATTGCTCAAAATGCACATGATA 58.128 29.630 0.00 0.00 40.40 2.15
512 517 4.894705 TGGGATACAAAATGGATCATGTGG 59.105 41.667 5.03 0.00 39.50 4.17
515 520 6.549364 GGGATACAAAATGGATCATGTGGTTA 59.451 38.462 5.03 0.00 39.50 2.85
564 569 4.644234 TCAAGAGAATGTGAAAACTTGGCA 59.356 37.500 0.00 0.00 36.45 4.92
565 570 5.126869 TCAAGAGAATGTGAAAACTTGGCAA 59.873 36.000 0.00 0.00 36.45 4.52
683 688 7.994425 TTGAATTACTTACCACATGTGTCAT 57.006 32.000 23.79 11.74 0.00 3.06
696 701 6.775088 CACATGTGTCATGTGGTTACTATTC 58.225 40.000 25.74 0.00 44.04 1.75
729 734 1.595311 TATTCCCATGTGCTCCCTGT 58.405 50.000 0.00 0.00 0.00 4.00
732 737 0.042581 TCCCATGTGCTCCCTGTCTA 59.957 55.000 0.00 0.00 0.00 2.59
783 789 7.434307 GGCATCATATCAACTCTTTTGATTGTG 59.566 37.037 4.89 5.59 39.59 3.33
821 827 3.532542 GGCCTACGAACAAGAGCTAAAT 58.467 45.455 0.00 0.00 0.00 1.40
835 841 4.102367 AGAGCTAAATTCTTCCAGGCCTAG 59.898 45.833 3.98 0.00 0.00 3.02
883 889 2.885861 CCGTCGTCTTCCTCCTGG 59.114 66.667 0.00 0.00 0.00 4.45
907 918 2.869101 AAAGAGAGAGAGGCCCAAAC 57.131 50.000 0.00 0.00 0.00 2.93
924 935 4.814771 CCCAAACGTCTATTATCCACTTCC 59.185 45.833 0.00 0.00 0.00 3.46
1035 1056 1.552792 CTCTCCTCCAGTGGGTTTCTC 59.447 57.143 9.92 0.00 34.93 2.87
1060 1081 4.148645 GCTCCCGTTTTCGCTCGC 62.149 66.667 0.00 0.00 42.58 5.03
1068 1089 2.903547 TTTTCGCTCGCTTGTGGGC 61.904 57.895 0.00 0.00 0.00 5.36
1260 1281 4.436998 CCTGGTGAGTCGCCGTCC 62.437 72.222 17.76 0.34 36.72 4.79
1289 1310 1.900486 CCCCCTCCCGTATGTTCTATC 59.100 57.143 0.00 0.00 0.00 2.08
1297 1318 2.288640 CCGTATGTTCTATCCCGTTCCC 60.289 54.545 0.00 0.00 0.00 3.97
1306 1327 1.007607 ATCCCGTTCCCCTTGGATTT 58.992 50.000 0.00 0.00 41.40 2.17
1325 1346 3.660111 GGTGGTGCGAGTTGTGCC 61.660 66.667 0.00 0.00 0.00 5.01
1326 1347 2.591715 GTGGTGCGAGTTGTGCCT 60.592 61.111 0.00 0.00 0.00 4.75
1344 1365 2.364632 CCTGTGCAATCGGATTGGTTA 58.635 47.619 27.00 4.71 40.57 2.85
1375 1396 1.452108 CTTCCACTCCGGGGAATGC 60.452 63.158 9.33 0.00 43.16 3.56
1421 1442 2.625823 CGGTTGATTGCGCTTGGGT 61.626 57.895 9.73 0.00 0.00 4.51
1441 1462 0.112218 TGGTTGGTTCACATGGGAGG 59.888 55.000 0.00 0.00 0.00 4.30
1491 1512 2.100252 GCTTGAGCATATGCCAACACAT 59.900 45.455 23.96 3.36 43.38 3.21
1610 1633 9.754382 AAAAATAATGTCTTATAGGCAATGCTG 57.246 29.630 4.82 0.00 31.33 4.41
1611 1634 8.469309 AAATAATGTCTTATAGGCAATGCTGT 57.531 30.769 4.82 0.00 31.33 4.40
1637 1713 4.103785 ACCATGTGCAAGCTCTCCTTATAT 59.896 41.667 0.00 0.00 31.00 0.86
1731 1807 9.227777 ACTCCTTTGTTTATTGTATTGTAGGAC 57.772 33.333 0.00 0.00 0.00 3.85
1789 1865 5.305386 TGCCTCATCTGCTGTATAATACTGT 59.695 40.000 0.00 0.00 0.00 3.55
1888 1964 2.633967 AGCAGAAATTGTTTGCCCATCA 59.366 40.909 5.70 0.00 38.58 3.07
1897 1973 5.496133 TTGTTTGCCCATCAATTTGTTTG 57.504 34.783 0.00 0.00 34.12 2.93
2049 2213 3.771216 AGTTTGATCCATTTCTGTGGCT 58.229 40.909 0.00 0.00 39.19 4.75
2083 2247 6.578919 GCTGTTCATTTCTTGCTTACTGTAAC 59.421 38.462 0.00 0.00 0.00 2.50
2085 2249 8.896320 TGTTCATTTCTTGCTTACTGTAACTA 57.104 30.769 0.00 0.00 0.00 2.24
2091 2255 9.991906 ATTTCTTGCTTACTGTAACTAACACTA 57.008 29.630 0.00 0.00 33.45 2.74
2123 2287 1.806542 CTGCTGAACGTTTATGCCAGT 59.193 47.619 0.46 0.00 0.00 4.00
2171 2335 2.297315 CCTGAAGAAAAAGGAACTGGCC 59.703 50.000 0.00 0.00 40.86 5.36
2183 2347 2.681344 GGAACTGGCCAAAAGGTATACG 59.319 50.000 7.01 0.00 0.00 3.06
2322 2486 6.299805 TCATAGTGCTATTGAGGTCACTTT 57.700 37.500 0.00 0.00 40.01 2.66
2331 2495 1.072331 TGAGGTCACTTTCTCCTTGCC 59.928 52.381 0.00 0.00 0.00 4.52
2332 2496 0.035458 AGGTCACTTTCTCCTTGCCG 59.965 55.000 0.00 0.00 0.00 5.69
2333 2497 0.250338 GGTCACTTTCTCCTTGCCGT 60.250 55.000 0.00 0.00 0.00 5.68
2334 2498 1.001633 GGTCACTTTCTCCTTGCCGTA 59.998 52.381 0.00 0.00 0.00 4.02
2335 2499 2.338500 GTCACTTTCTCCTTGCCGTAG 58.662 52.381 0.00 0.00 0.00 3.51
2336 2500 1.968493 TCACTTTCTCCTTGCCGTAGT 59.032 47.619 0.00 0.00 0.00 2.73
2337 2501 2.367567 TCACTTTCTCCTTGCCGTAGTT 59.632 45.455 0.00 0.00 0.00 2.24
2338 2502 2.737252 CACTTTCTCCTTGCCGTAGTTC 59.263 50.000 0.00 0.00 0.00 3.01
2339 2503 1.993370 CTTTCTCCTTGCCGTAGTTCG 59.007 52.381 0.00 0.00 39.52 3.95
2340 2504 1.250328 TTCTCCTTGCCGTAGTTCGA 58.750 50.000 0.00 0.00 42.86 3.71
2341 2505 0.809385 TCTCCTTGCCGTAGTTCGAG 59.191 55.000 0.00 0.00 42.86 4.04
2342 2506 0.809385 CTCCTTGCCGTAGTTCGAGA 59.191 55.000 0.00 0.00 42.86 4.04
2343 2507 1.201647 CTCCTTGCCGTAGTTCGAGAA 59.798 52.381 0.00 0.00 42.86 2.87
2344 2508 1.822990 TCCTTGCCGTAGTTCGAGAAT 59.177 47.619 0.00 0.00 42.86 2.40
2345 2509 2.159282 TCCTTGCCGTAGTTCGAGAATC 60.159 50.000 0.00 0.00 42.86 2.52
2346 2510 2.159226 CCTTGCCGTAGTTCGAGAATCT 60.159 50.000 0.00 0.00 42.86 2.40
2347 2511 2.846039 TGCCGTAGTTCGAGAATCTC 57.154 50.000 0.00 0.00 42.86 2.75
2348 2512 1.404391 TGCCGTAGTTCGAGAATCTCC 59.596 52.381 4.47 0.00 42.86 3.71
2349 2513 1.404391 GCCGTAGTTCGAGAATCTCCA 59.596 52.381 4.47 0.00 42.86 3.86
2350 2514 2.159282 GCCGTAGTTCGAGAATCTCCAA 60.159 50.000 4.47 0.00 42.86 3.53
2351 2515 3.436496 CCGTAGTTCGAGAATCTCCAAC 58.564 50.000 11.91 11.91 42.86 3.77
2359 2544 2.758130 GAGAATCTCCAACCCTCCTCT 58.242 52.381 0.00 0.00 0.00 3.69
2464 2649 7.494298 TCAGTTGAAAAATTTAGCAAAAGGACC 59.506 33.333 7.08 0.00 0.00 4.46
2600 2786 4.199310 AGCTTTGTCTGCAAACTCAGTAA 58.801 39.130 0.00 0.00 39.43 2.24
2665 2851 7.661040 CACATGATAAGGTCTTTTGTTCCTTT 58.339 34.615 0.00 0.00 41.17 3.11
2708 2894 1.623811 ACAACGATGGCTGTAAGAGGT 59.376 47.619 0.00 0.00 34.07 3.85
2745 2931 4.906060 GGGTGTCCCTATAGTTGAGGTATT 59.094 45.833 0.00 0.00 41.34 1.89
2793 2979 8.375465 GTTGCTTCAAATATTTCTGTACATTGC 58.625 33.333 0.00 0.00 0.00 3.56
2798 2984 8.334263 TCAAATATTTCTGTACATTGCAGTCA 57.666 30.769 0.00 0.00 35.60 3.41
2823 3009 6.876257 ACAGATGAGTTAGTTTCCTCATTGAC 59.124 38.462 3.88 0.00 45.87 3.18
2839 3025 2.132740 TGACGTGCTTTTTCAATGCC 57.867 45.000 0.00 0.00 0.00 4.40
2852 3039 7.468631 GCTTTTTCAATGCCGAGGAGATTAATA 60.469 37.037 0.00 0.00 0.00 0.98
2903 3090 7.074653 AGAAGTAATCACCAGGTTTTCACTA 57.925 36.000 0.00 0.00 0.00 2.74
2904 3091 7.514721 AGAAGTAATCACCAGGTTTTCACTAA 58.485 34.615 0.00 0.00 0.00 2.24
2963 3151 6.169094 TCTGCCTCAAATCTAAGTTCTCTTG 58.831 40.000 0.00 0.00 35.36 3.02
3037 3225 3.012518 CCTAGAAACTGTTCAGGCATGG 58.987 50.000 0.00 0.00 36.09 3.66
3087 3275 1.200948 GCCTTGAGCAATGAACCAGTC 59.799 52.381 0.00 0.00 42.97 3.51
3623 3828 3.438781 GCAATCAACAGATGTTTCCCGTA 59.561 43.478 0.00 0.00 35.83 4.02
3714 3919 1.372582 ATGAACAGCATGCCGTACTG 58.627 50.000 15.66 8.30 42.53 2.74
3715 3920 0.034756 TGAACAGCATGCCGTACTGT 59.965 50.000 15.66 9.04 46.27 3.55
3716 3921 1.273886 TGAACAGCATGCCGTACTGTA 59.726 47.619 15.66 0.00 43.63 2.74
3717 3922 2.289133 TGAACAGCATGCCGTACTGTAA 60.289 45.455 15.66 1.35 43.63 2.41
3769 3974 2.680339 GGCCTTCATGAGCTTTACTGTC 59.320 50.000 6.87 0.00 0.00 3.51
3877 4082 3.317711 CCATAAGGTGCAACAGACAAACA 59.682 43.478 3.64 0.00 39.98 2.83
3923 4130 9.914834 TTTATTACCCAAGTAGCATGACTTAAT 57.085 29.630 0.00 0.00 37.57 1.40
4044 4251 8.850007 ACCTTAGTTTTAAGAAATCTCCTGTC 57.150 34.615 0.00 0.00 38.88 3.51
4084 4291 8.141268 TGCCAAAGGTAAATTCTTCTAGTTTTG 58.859 33.333 0.00 0.00 0.00 2.44
4393 4606 8.685427 CATGGACACAATATACTCAATTCCAAA 58.315 33.333 0.00 0.00 0.00 3.28
4422 4635 2.843701 CAGCAGAACTGTGGAAGAAGT 58.156 47.619 3.77 0.00 41.86 3.01
4423 4636 2.547211 CAGCAGAACTGTGGAAGAAGTG 59.453 50.000 3.77 0.00 41.86 3.16
4424 4637 2.171448 AGCAGAACTGTGGAAGAAGTGT 59.829 45.455 3.77 0.00 0.00 3.55
4426 4639 4.127171 GCAGAACTGTGGAAGAAGTGTAA 58.873 43.478 3.77 0.00 0.00 2.41
4428 4641 5.334414 GCAGAACTGTGGAAGAAGTGTAATG 60.334 44.000 3.77 0.00 0.00 1.90
4430 4643 5.992217 AGAACTGTGGAAGAAGTGTAATGTC 59.008 40.000 0.00 0.00 0.00 3.06
4433 4646 5.070446 ACTGTGGAAGAAGTGTAATGTCTCA 59.930 40.000 0.00 0.00 0.00 3.27
4434 4647 5.541845 TGTGGAAGAAGTGTAATGTCTCAG 58.458 41.667 0.00 0.00 0.00 3.35
4435 4648 4.932200 GTGGAAGAAGTGTAATGTCTCAGG 59.068 45.833 0.00 0.00 0.00 3.86
4436 4649 3.935828 GGAAGAAGTGTAATGTCTCAGGC 59.064 47.826 0.00 0.00 0.00 4.85
4437 4650 4.323104 GGAAGAAGTGTAATGTCTCAGGCT 60.323 45.833 0.00 0.00 0.00 4.58
4438 4651 4.899352 AGAAGTGTAATGTCTCAGGCTT 57.101 40.909 0.00 0.00 0.00 4.35
4439 4652 4.826556 AGAAGTGTAATGTCTCAGGCTTC 58.173 43.478 0.00 0.00 33.43 3.86
4441 4654 4.199432 AGTGTAATGTCTCAGGCTTCAG 57.801 45.455 0.00 0.00 0.00 3.02
4442 4655 3.834813 AGTGTAATGTCTCAGGCTTCAGA 59.165 43.478 0.00 0.00 0.00 3.27
4463 4741 9.611284 TTCAGATTCATAATATATTGTTTGCGC 57.389 29.630 8.28 0.00 0.00 6.09
4469 4747 3.878086 ATATATTGTTTGCGCTCACCG 57.122 42.857 9.73 0.00 40.75 4.94
4479 4757 3.926821 TGCGCTCACCGTATATGATTA 57.073 42.857 9.73 0.00 39.71 1.75
4483 4761 5.699001 TGCGCTCACCGTATATGATTAAAAT 59.301 36.000 9.73 0.00 39.71 1.82
4484 4762 6.015504 GCGCTCACCGTATATGATTAAAATG 58.984 40.000 0.00 0.00 39.71 2.32
4485 4763 6.347402 GCGCTCACCGTATATGATTAAAATGT 60.347 38.462 0.00 0.00 39.71 2.71
4486 4764 7.148705 GCGCTCACCGTATATGATTAAAATGTA 60.149 37.037 0.00 0.00 39.71 2.29
4487 4765 8.869897 CGCTCACCGTATATGATTAAAATGTAT 58.130 33.333 0.00 0.00 0.00 2.29
4488 4766 9.973246 GCTCACCGTATATGATTAAAATGTATG 57.027 33.333 0.00 0.00 0.00 2.39
4489 4767 9.973246 CTCACCGTATATGATTAAAATGTATGC 57.027 33.333 0.00 0.00 0.00 3.14
4560 4881 8.430063 CCATTTTTGAATCTTGACAAATCTTCG 58.570 33.333 0.00 0.00 36.21 3.79
4761 5083 4.782019 TGTTGGCAGCAAAGTATTAAGG 57.218 40.909 0.00 0.00 0.00 2.69
4821 5143 7.730364 TCAAACTCCTCATTGAGAAAACTAC 57.270 36.000 15.36 0.00 36.22 2.73
4823 5145 4.246458 ACTCCTCATTGAGAAAACTACGC 58.754 43.478 15.36 0.00 36.22 4.42
4906 5228 1.885887 TGGGCATGCTAAAACACTGAC 59.114 47.619 18.92 0.00 0.00 3.51
4908 5230 2.493278 GGGCATGCTAAAACACTGACAT 59.507 45.455 18.92 0.00 0.00 3.06
4925 5247 6.429692 CACTGACATACCCTTTCAATGTAACA 59.570 38.462 0.00 0.00 34.09 2.41
4929 5251 6.630071 ACATACCCTTTCAATGTAACAATGC 58.370 36.000 0.00 0.00 32.21 3.56
4933 5255 3.367292 CCTTTCAATGTAACAATGCGGCT 60.367 43.478 0.00 0.00 0.00 5.52
5080 5402 1.599071 CACATGTCATGCCACCGTATC 59.401 52.381 12.91 0.00 0.00 2.24
5125 5447 1.530013 CCCTGCCTTCTGCTGTTTGG 61.530 60.000 0.00 0.00 42.00 3.28
5136 5458 1.595093 GCTGTTTGGATCCAACCCCG 61.595 60.000 27.04 16.53 35.46 5.73
5153 5475 0.308684 CCGGATTCATGGCGTCAATG 59.691 55.000 0.00 0.00 0.00 2.82
5163 5486 2.189499 GCGTCAATGGGGGCTGATC 61.189 63.158 0.00 0.00 0.00 2.92
5212 5535 7.865707 ACTTTTGATGACTAGTTTGTGATGAC 58.134 34.615 0.00 0.00 0.00 3.06
5269 5592 4.709886 AGTGGGCAATTGTTTATTACTCCC 59.290 41.667 7.40 6.20 33.45 4.30
5345 5668 7.984422 ATTTTGACCAGAAATTTGAATTCCC 57.016 32.000 2.27 0.00 0.00 3.97
5386 5709 4.745649 ACTATGTCTAGTTTTGACGAGGC 58.254 43.478 0.00 0.00 34.42 4.70
5409 5734 7.451566 AGGCACTCCAAGTAATCTAAAATGTTT 59.548 33.333 0.00 0.00 33.74 2.83
5499 5824 3.280295 TCGAACCTTGTTTAAGCAACCA 58.720 40.909 0.00 0.00 33.97 3.67
5570 5895 7.798596 AAGAGGTTATGCTTGATAACTCATG 57.201 36.000 0.00 0.00 44.20 3.07
5644 5969 3.853475 CCTTGTGAATTTCCTGGCATTC 58.147 45.455 10.10 10.10 0.00 2.67
5685 6010 2.151202 TCGAGTGGAAAAGGCATGAAC 58.849 47.619 0.00 0.00 0.00 3.18
5702 6027 5.400485 GCATGAACGCATCTTTATTTCATCC 59.600 40.000 0.00 0.00 35.25 3.51
5961 6286 6.799827 AGCTAACCTATCAGGATCTACAGAT 58.200 40.000 0.00 0.00 37.67 2.90
5972 6297 5.833667 CAGGATCTACAGATAAGGTGTGGTA 59.166 44.000 0.00 0.00 34.37 3.25
6254 6700 2.513753 TCCTTGCGGCCCATTATTATG 58.486 47.619 0.00 0.00 0.00 1.90
6287 6735 1.289231 AGCCCTCTGTAGATGGACTCA 59.711 52.381 7.31 0.00 32.39 3.41
6398 6846 4.819105 TGTACCATTAACTGAGGGTGAG 57.181 45.455 0.00 0.00 34.88 3.51
6422 6870 4.906618 AGTTTCGATGGGAGAAGCTAAAA 58.093 39.130 0.00 0.00 37.39 1.52
6434 6882 6.404184 GGGAGAAGCTAAAATTCTTCTTGCTC 60.404 42.308 8.16 0.00 46.32 4.26
6466 6914 4.887655 AGATGTCCTTTTGAAACCGAAACT 59.112 37.500 0.00 0.00 0.00 2.66
6727 7176 0.593128 GGTTAACCTGCTGTGCACTG 59.407 55.000 19.41 18.94 33.79 3.66
6875 7325 6.640518 AGTATTCTTCATTTCTTCTGGCGTA 58.359 36.000 0.00 0.00 0.00 4.42
7520 7970 7.996098 AATACACATATACCCCTTGCATTAC 57.004 36.000 0.00 0.00 0.00 1.89
7573 8023 7.220741 ACACGAGCTATGTTGATCATATAGT 57.779 36.000 20.14 12.05 38.21 2.12
7607 8059 2.357009 GCACGATCTTTTCATGGAGCAT 59.643 45.455 0.00 0.00 0.00 3.79
7608 8060 3.561310 GCACGATCTTTTCATGGAGCATA 59.439 43.478 0.00 0.00 0.00 3.14
7627 8079 4.991687 GCATAGAGGTTGTACATTAGCCTC 59.008 45.833 19.84 19.84 44.37 4.70
7762 8217 4.789807 CCTTGGAAATCCTGATGACATCT 58.210 43.478 16.25 0.00 36.82 2.90
7768 8223 0.543277 TCCTGATGACATCTGTGCCC 59.457 55.000 16.25 0.00 0.00 5.36
7874 8347 3.762247 CAACATTGGCGGCTGGGG 61.762 66.667 11.43 0.00 0.00 4.96
7882 8355 3.365265 GCGGCTGGGGAACAACAG 61.365 66.667 0.00 0.00 37.80 3.16
8024 8497 2.811431 TCATGCCACTTTTGTAGGAACG 59.189 45.455 0.00 0.00 0.00 3.95
8041 8517 2.895424 CGGGGAGGTTCTGGCTTGT 61.895 63.158 0.00 0.00 0.00 3.16
8042 8518 1.303643 GGGGAGGTTCTGGCTTGTG 60.304 63.158 0.00 0.00 0.00 3.33
8043 8519 1.303643 GGGAGGTTCTGGCTTGTGG 60.304 63.158 0.00 0.00 0.00 4.17
8044 8520 1.973812 GGAGGTTCTGGCTTGTGGC 60.974 63.158 0.00 0.00 40.90 5.01
8089 8565 6.801539 TTAGATTTGAACACTAGCCTGTTG 57.198 37.500 3.62 0.00 34.40 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 7.493743 TTTCAAGCAAACAATGTGCATATTT 57.506 28.000 5.87 0.00 44.74 1.40
110 111 5.369404 TCATTGGGACATACTACCATGTGAT 59.631 40.000 0.00 0.00 39.25 3.06
162 163 9.877137 AAAAATTCAAAATTCGTATTTGGAAGC 57.123 25.926 18.50 0.00 43.49 3.86
302 303 4.624015 AGTGACCGTCTATCAACGAAAAA 58.376 39.130 0.00 0.00 45.37 1.94
488 493 5.541101 CCACATGATCCATTTTGTATCCCAT 59.459 40.000 0.00 0.00 0.00 4.00
512 517 3.746492 GTGACATGTCTGGTTGGTCTAAC 59.254 47.826 25.55 7.95 38.60 2.34
515 520 1.072331 GGTGACATGTCTGGTTGGTCT 59.928 52.381 25.55 0.00 0.00 3.85
657 662 8.402798 TGACACATGTGGTAAGTAATTCAAAT 57.597 30.769 28.64 2.45 34.19 2.32
662 667 7.144722 CACATGACACATGTGGTAAGTAATT 57.855 36.000 28.64 5.13 44.04 1.40
675 680 7.568349 AGATGAATAGTAACCACATGACACAT 58.432 34.615 0.00 0.00 0.00 3.21
683 688 5.277250 TCAGGGAGATGAATAGTAACCACA 58.723 41.667 0.00 0.00 0.00 4.17
690 695 8.997734 GGGAATATTATCAGGGAGATGAATAGT 58.002 37.037 0.00 0.00 37.57 2.12
696 701 6.827251 CACATGGGAATATTATCAGGGAGATG 59.173 42.308 0.00 0.00 37.57 2.90
729 734 7.733773 TGGATGTCTTTTATCAGTTCCTAGA 57.266 36.000 0.00 0.00 0.00 2.43
732 737 6.660949 CCTTTGGATGTCTTTTATCAGTTCCT 59.339 38.462 0.00 0.00 0.00 3.36
783 789 2.439519 CCGGCCCATGTACAACCC 60.440 66.667 0.00 0.00 0.00 4.11
821 827 3.769844 CACTCTAACTAGGCCTGGAAGAA 59.230 47.826 24.81 4.56 34.07 2.52
835 841 2.271800 CCATTCGCCTGTCACTCTAAC 58.728 52.381 0.00 0.00 0.00 2.34
907 918 2.029290 CCGGGGAAGTGGATAATAGACG 60.029 54.545 0.00 0.00 0.00 4.18
1060 1081 4.047125 ACATCGGGGGCCCACAAG 62.047 66.667 27.55 15.74 35.37 3.16
1125 1146 1.608283 GCAGCTTCGTCAAACCCTAGT 60.608 52.381 0.00 0.00 0.00 2.57
1297 1318 1.876497 CGCACCACCCAAATCCAAGG 61.876 60.000 0.00 0.00 0.00 3.61
1306 1327 2.203139 CACAACTCGCACCACCCA 60.203 61.111 0.00 0.00 0.00 4.51
1325 1346 2.355756 CCTAACCAATCCGATTGCACAG 59.644 50.000 14.68 10.15 38.92 3.66
1326 1347 2.026729 TCCTAACCAATCCGATTGCACA 60.027 45.455 14.68 2.08 38.92 4.57
1344 1365 2.172293 GAGTGGAAGAATGGCATCTCCT 59.828 50.000 18.59 7.65 35.26 3.69
1405 1426 0.667184 CCAACCCAAGCGCAATCAAC 60.667 55.000 11.47 0.00 0.00 3.18
1421 1442 1.480312 CCTCCCATGTGAACCAACCAA 60.480 52.381 0.00 0.00 0.00 3.67
1441 1462 1.226101 CGTCATGGCACGCACAATC 60.226 57.895 0.00 0.00 31.96 2.67
1464 1485 3.090790 TGGCATATGCTCAAGCTTTTGA 58.909 40.909 26.12 0.00 42.66 2.69
1491 1512 9.567776 TCCTACACAAAATAGACAGATGAAAAA 57.432 29.630 0.00 0.00 0.00 1.94
1589 1612 7.880160 AAACAGCATTGCCTATAAGACATTA 57.120 32.000 4.70 0.00 0.00 1.90
1591 1614 6.263168 GGTAAACAGCATTGCCTATAAGACAT 59.737 38.462 4.70 0.00 32.86 3.06
1592 1615 5.588648 GGTAAACAGCATTGCCTATAAGACA 59.411 40.000 4.70 0.00 32.86 3.41
1593 1616 5.588648 TGGTAAACAGCATTGCCTATAAGAC 59.411 40.000 4.70 0.00 36.19 3.01
1595 1618 6.039717 ACATGGTAAACAGCATTGCCTATAAG 59.960 38.462 4.70 0.00 36.19 1.73
1597 1620 5.299028 CACATGGTAAACAGCATTGCCTATA 59.701 40.000 4.70 0.00 36.19 1.31
1598 1621 4.098349 CACATGGTAAACAGCATTGCCTAT 59.902 41.667 4.70 0.00 36.19 2.57
1599 1622 3.443329 CACATGGTAAACAGCATTGCCTA 59.557 43.478 4.70 0.00 36.19 3.93
1600 1623 2.231964 CACATGGTAAACAGCATTGCCT 59.768 45.455 4.70 0.00 36.19 4.75
1601 1624 2.609350 CACATGGTAAACAGCATTGCC 58.391 47.619 4.70 0.00 35.81 4.52
1602 1625 1.994779 GCACATGGTAAACAGCATTGC 59.005 47.619 0.00 0.00 0.00 3.56
1603 1626 3.300852 TGCACATGGTAAACAGCATTG 57.699 42.857 0.00 0.00 0.00 2.82
1604 1627 3.861886 GCTTGCACATGGTAAACAGCATT 60.862 43.478 0.00 0.00 29.34 3.56
1605 1628 2.353011 GCTTGCACATGGTAAACAGCAT 60.353 45.455 0.00 0.00 29.34 3.79
1606 1629 1.000385 GCTTGCACATGGTAAACAGCA 60.000 47.619 0.00 0.00 0.00 4.41
1608 1631 2.816087 AGAGCTTGCACATGGTAAACAG 59.184 45.455 0.00 0.00 0.00 3.16
1609 1632 2.813754 GAGAGCTTGCACATGGTAAACA 59.186 45.455 0.00 0.00 0.00 2.83
1610 1633 2.162408 GGAGAGCTTGCACATGGTAAAC 59.838 50.000 0.00 0.00 0.00 2.01
1611 1634 2.040278 AGGAGAGCTTGCACATGGTAAA 59.960 45.455 0.00 0.00 0.00 2.01
1637 1713 9.643735 TTACTAATAAGAAACCCCTTTTGTCAA 57.356 29.630 0.00 0.00 0.00 3.18
1675 1751 1.743394 GGGGAATTGTTTACCAGCGAG 59.257 52.381 0.00 0.00 37.61 5.03
1731 1807 1.810959 CCACATGGTTTGGCAAATGG 58.189 50.000 16.74 14.84 0.00 3.16
1789 1865 4.105697 ACCACAACCTAGAGAAATGGGAAA 59.894 41.667 0.00 0.00 0.00 3.13
1846 1922 1.071471 CCTTGTGACTTCACCGGCT 59.929 57.895 0.00 0.00 45.88 5.52
1897 1973 9.499585 CATCATGAGTTCAATAACATTTCAGAC 57.500 33.333 0.09 0.00 38.12 3.51
1915 1991 9.445878 ACCATATGAGCTAATAAACATCATGAG 57.554 33.333 3.65 0.00 32.99 2.90
2049 2213 1.606668 GAAATGAACAGCGACCAACCA 59.393 47.619 0.00 0.00 0.00 3.67
2091 2255 0.771127 TTCAGCAGCTAACCCCTGTT 59.229 50.000 0.00 0.00 38.52 3.16
2102 2266 0.521291 TGGCATAAACGTTCAGCAGC 59.479 50.000 17.51 10.80 0.00 5.25
2123 2287 2.762887 TGGCTCACCATCAAACACAAAA 59.237 40.909 0.00 0.00 42.67 2.44
2149 2313 2.297315 GCCAGTTCCTTTTTCTTCAGGG 59.703 50.000 0.00 0.00 0.00 4.45
2171 2335 5.448632 GGAATGGTTCAGCGTATACCTTTTG 60.449 44.000 0.00 0.00 31.69 2.44
2322 2486 0.809385 CTCGAACTACGGCAAGGAGA 59.191 55.000 0.00 0.00 42.82 3.71
2331 2495 3.436496 GGTTGGAGATTCTCGAACTACG 58.564 50.000 29.04 0.00 44.60 3.51
2332 2496 3.447944 AGGGTTGGAGATTCTCGAACTAC 59.552 47.826 29.04 23.70 44.60 2.73
2333 2497 3.700038 GAGGGTTGGAGATTCTCGAACTA 59.300 47.826 29.04 3.62 44.60 2.24
2334 2498 2.498078 GAGGGTTGGAGATTCTCGAACT 59.502 50.000 29.04 17.51 44.60 3.01
2335 2499 2.418884 GGAGGGTTGGAGATTCTCGAAC 60.419 54.545 25.09 25.09 44.52 3.95
2336 2500 1.831736 GGAGGGTTGGAGATTCTCGAA 59.168 52.381 6.99 6.99 0.00 3.71
2337 2501 1.007238 AGGAGGGTTGGAGATTCTCGA 59.993 52.381 7.57 0.68 0.00 4.04
2338 2502 1.410882 GAGGAGGGTTGGAGATTCTCG 59.589 57.143 7.57 0.00 0.00 4.04
2339 2503 2.758130 AGAGGAGGGTTGGAGATTCTC 58.242 52.381 5.03 5.03 0.00 2.87
2340 2504 2.959421 AGAGGAGGGTTGGAGATTCT 57.041 50.000 0.00 0.00 0.00 2.40
2341 2505 4.471747 ACTAAAGAGGAGGGTTGGAGATTC 59.528 45.833 0.00 0.00 0.00 2.52
2342 2506 4.439860 ACTAAAGAGGAGGGTTGGAGATT 58.560 43.478 0.00 0.00 0.00 2.40
2343 2507 4.034410 GACTAAAGAGGAGGGTTGGAGAT 58.966 47.826 0.00 0.00 0.00 2.75
2344 2508 3.442076 GACTAAAGAGGAGGGTTGGAGA 58.558 50.000 0.00 0.00 0.00 3.71
2345 2509 2.166664 CGACTAAAGAGGAGGGTTGGAG 59.833 54.545 0.00 0.00 0.00 3.86
2346 2510 2.176889 CGACTAAAGAGGAGGGTTGGA 58.823 52.381 0.00 0.00 0.00 3.53
2347 2511 1.900486 ACGACTAAAGAGGAGGGTTGG 59.100 52.381 0.00 0.00 0.00 3.77
2348 2512 2.561419 TGACGACTAAAGAGGAGGGTTG 59.439 50.000 0.00 0.00 0.00 3.77
2349 2513 2.885616 TGACGACTAAAGAGGAGGGTT 58.114 47.619 0.00 0.00 0.00 4.11
2350 2514 2.599408 TGACGACTAAAGAGGAGGGT 57.401 50.000 0.00 0.00 0.00 4.34
2351 2515 2.482142 GCATGACGACTAAAGAGGAGGG 60.482 54.545 0.00 0.00 0.00 4.30
2359 2544 6.649141 ACAAATACAGAAGCATGACGACTAAA 59.351 34.615 0.00 0.00 0.00 1.85
2423 2608 8.413309 TTTTCAACTGAATCTTCATCTCCAAT 57.587 30.769 0.00 0.00 36.46 3.16
2600 2786 6.207417 CCACTTCAGAACATGGTAAAGAATGT 59.793 38.462 6.94 0.00 38.66 2.71
2665 2851 6.376864 TGTGTTCTTTTGTGATCTGGAAAGAA 59.623 34.615 18.28 18.28 42.54 2.52
2708 2894 4.340617 GGGACACCCATCAATCTTAACAA 58.659 43.478 1.54 0.00 44.65 2.83
2761 2947 8.114331 ACAGAAATATTTGAAGCAACTGATGA 57.886 30.769 5.17 0.00 0.00 2.92
2765 2951 9.630098 AATGTACAGAAATATTTGAAGCAACTG 57.370 29.630 5.17 7.26 0.00 3.16
2766 2952 9.630098 CAATGTACAGAAATATTTGAAGCAACT 57.370 29.630 5.17 0.00 0.00 3.16
2783 2969 4.248058 TCATCTGTGACTGCAATGTACAG 58.752 43.478 0.33 11.64 39.95 2.74
2793 2979 5.788450 AGGAAACTAACTCATCTGTGACTG 58.212 41.667 0.00 0.00 40.61 3.51
2823 3009 1.330306 CTCGGCATTGAAAAAGCACG 58.670 50.000 0.00 0.00 43.40 5.34
2839 3025 9.703892 ATTCTGAATGTTCTATTAATCTCCTCG 57.296 33.333 1.31 0.00 0.00 4.63
2852 3039 4.823442 TGTGCACAAGATTCTGAATGTTCT 59.177 37.500 19.28 0.00 0.00 3.01
2869 3056 6.403636 CCTGGTGATTACTTCTTTATGTGCAC 60.404 42.308 10.75 10.75 0.00 4.57
2925 3113 0.819666 GGCAGATTTAAGGCCTCCCG 60.820 60.000 5.23 0.00 44.32 5.14
2963 3151 6.127647 TGAGAAAACATTATCAGCCCACATTC 60.128 38.462 0.00 0.00 0.00 2.67
3054 3242 2.546373 GCTCAAGGCTTCACATTTTGCA 60.546 45.455 0.00 0.00 38.06 4.08
3087 3275 3.922171 AAAGATAGAGACAAGCAGGGG 57.078 47.619 0.00 0.00 0.00 4.79
3486 3674 7.680730 AGAACACCAAACAGATATCTTGTACT 58.319 34.615 1.33 0.00 0.00 2.73
3487 3675 7.819900 AGAGAACACCAAACAGATATCTTGTAC 59.180 37.037 1.33 0.81 0.00 2.90
3488 3676 7.907389 AGAGAACACCAAACAGATATCTTGTA 58.093 34.615 1.33 0.00 0.00 2.41
3489 3677 6.773638 AGAGAACACCAAACAGATATCTTGT 58.226 36.000 1.33 0.86 0.00 3.16
3490 3678 7.678947 AAGAGAACACCAAACAGATATCTTG 57.321 36.000 1.33 0.18 0.00 3.02
3491 3679 9.220767 GTTAAGAGAACACCAAACAGATATCTT 57.779 33.333 1.33 0.00 0.00 2.40
3492 3680 7.824779 GGTTAAGAGAACACCAAACAGATATCT 59.175 37.037 0.00 0.00 0.00 1.98
3623 3828 8.411991 TTTCCTTTCGTGGTATTTCCTAAATT 57.588 30.769 0.00 0.00 37.07 1.82
3636 3841 3.129638 TCCAGTTTGTTTTCCTTTCGTGG 59.870 43.478 0.00 0.00 0.00 4.94
3751 3956 5.807520 ACATACGACAGTAAAGCTCATGAAG 59.192 40.000 0.00 0.00 36.29 3.02
3923 4130 4.218200 CCTGGCACTCACAATGAAATACAA 59.782 41.667 0.00 0.00 0.00 2.41
4044 4251 3.489738 CCTTTGGCACTTCAAACTCTGTG 60.490 47.826 0.00 0.00 33.62 3.66
4420 4633 3.834813 TCTGAAGCCTGAGACATTACACT 59.165 43.478 0.00 0.00 0.00 3.55
4421 4634 4.193826 TCTGAAGCCTGAGACATTACAC 57.806 45.455 0.00 0.00 0.00 2.90
4422 4635 5.046376 TGAATCTGAAGCCTGAGACATTACA 60.046 40.000 0.00 0.00 0.00 2.41
4423 4636 5.423015 TGAATCTGAAGCCTGAGACATTAC 58.577 41.667 0.00 0.00 0.00 1.89
4424 4637 5.682234 TGAATCTGAAGCCTGAGACATTA 57.318 39.130 0.00 0.00 0.00 1.90
4426 4639 4.774660 ATGAATCTGAAGCCTGAGACAT 57.225 40.909 0.00 0.00 0.00 3.06
4437 4650 9.611284 GCGCAAACAATATATTATGAATCTGAA 57.389 29.630 0.30 0.00 0.00 3.02
4438 4651 9.002600 AGCGCAAACAATATATTATGAATCTGA 57.997 29.630 11.47 0.00 0.00 3.27
4439 4652 9.270576 GAGCGCAAACAATATATTATGAATCTG 57.729 33.333 11.47 0.00 0.00 2.90
4441 4654 9.055248 GTGAGCGCAAACAATATATTATGAATC 57.945 33.333 11.47 0.00 0.00 2.52
4442 4655 8.023128 GGTGAGCGCAAACAATATATTATGAAT 58.977 33.333 11.47 0.00 0.00 2.57
4463 4741 9.973246 GCATACATTTTAATCATATACGGTGAG 57.027 33.333 0.00 0.00 0.00 3.51
4479 4757 8.034215 TGCACTATAAGCAAAAGCATACATTTT 58.966 29.630 0.00 0.00 39.39 1.82
4483 4761 5.449041 GCTGCACTATAAGCAAAAGCATACA 60.449 40.000 0.00 0.00 42.17 2.29
4484 4762 4.972440 GCTGCACTATAAGCAAAAGCATAC 59.028 41.667 0.00 0.00 42.17 2.39
4485 4763 4.260743 CGCTGCACTATAAGCAAAAGCATA 60.261 41.667 0.00 0.00 42.17 3.14
4486 4764 3.488047 CGCTGCACTATAAGCAAAAGCAT 60.488 43.478 0.00 0.00 42.17 3.79
4487 4765 2.159531 CGCTGCACTATAAGCAAAAGCA 60.160 45.455 0.00 0.00 42.17 3.91
4488 4766 2.095853 TCGCTGCACTATAAGCAAAAGC 59.904 45.455 0.00 1.67 42.17 3.51
4489 4767 4.340894 TTCGCTGCACTATAAGCAAAAG 57.659 40.909 0.00 0.00 42.17 2.27
4580 4901 8.162746 ACATTAAAATGGTTGTGGATTTTGGAT 58.837 29.630 7.56 0.00 40.70 3.41
4761 5083 2.555757 AGATGGACTGCAAAAAGAGTGC 59.444 45.455 0.00 0.00 42.55 4.40
4821 5143 1.535028 TGTGCCTAGTGTTCAATTGCG 59.465 47.619 0.00 0.00 0.00 4.85
4823 5145 4.771590 ATGTGTGCCTAGTGTTCAATTG 57.228 40.909 0.00 0.00 0.00 2.32
4906 5228 5.743398 CGCATTGTTACATTGAAAGGGTATG 59.257 40.000 10.89 0.00 0.00 2.39
4908 5230 4.156922 CCGCATTGTTACATTGAAAGGGTA 59.843 41.667 10.89 0.00 0.00 3.69
4925 5247 0.253044 ATGGACACAGTAGCCGCATT 59.747 50.000 0.00 0.00 0.00 3.56
4929 5251 2.967362 TGTTAATGGACACAGTAGCCG 58.033 47.619 0.00 0.00 28.96 5.52
4933 5255 7.432148 AGGATGTATGTTAATGGACACAGTA 57.568 36.000 0.00 0.00 31.30 2.74
5080 5402 2.667536 AACAGCAGCACAGGAGCG 60.668 61.111 0.00 0.00 40.15 5.03
5136 5458 0.670162 CCCATTGACGCCATGAATCC 59.330 55.000 0.00 0.00 0.00 3.01
5153 5475 3.866582 CCGGACAGATCAGCCCCC 61.867 72.222 0.00 0.00 0.00 5.40
5163 5486 0.465705 ACATGCCAGATACCGGACAG 59.534 55.000 9.46 0.00 0.00 3.51
5234 5557 3.591196 TTGCCCACTGAAATGTTATGC 57.409 42.857 0.00 0.00 0.00 3.14
5269 5592 6.106673 AGAATTAACTACCACCTTGACATCG 58.893 40.000 0.00 0.00 0.00 3.84
5345 5668 1.537202 GTTGTCTACTGCAAAGCCCAG 59.463 52.381 0.00 0.00 36.41 4.45
5386 5709 8.576442 ACCAAACATTTTAGATTACTTGGAGTG 58.424 33.333 4.60 0.00 36.42 3.51
5409 5734 6.995686 ACATATGAGTGTGTTCAGTAAAACCA 59.004 34.615 10.38 0.00 0.00 3.67
5570 5895 3.754323 TGGAAAAACATGGACCGTATGAC 59.246 43.478 0.00 0.00 0.00 3.06
5644 5969 5.051039 TCGATCAGAACTGAAACTGTTTTCG 60.051 40.000 7.28 9.12 43.71 3.46
5685 6010 3.248363 TGCTCGGATGAAATAAAGATGCG 59.752 43.478 0.00 0.00 32.80 4.73
5702 6027 7.763172 ACAAGAGATTAAATAAGAGTGCTCG 57.237 36.000 0.00 0.00 34.09 5.03
5931 6256 3.845860 TCCTGATAGGTTAGCTACTGGG 58.154 50.000 0.00 0.00 36.53 4.45
5961 6286 2.656432 AGGGGACTAGTACCACACCTTA 59.344 50.000 25.92 0.00 40.61 2.69
6063 6388 9.932207 AGAGAGAGAGATTTATGAAGCATTATG 57.068 33.333 0.00 0.00 0.00 1.90
6071 6396 8.717717 AGAGAGAGAGAGAGAGAGATTTATGAA 58.282 37.037 0.00 0.00 0.00 2.57
6188 6634 3.266510 TGCTCAAACTAATCTGCCGAT 57.733 42.857 0.00 0.00 0.00 4.18
6254 6700 0.807496 GAGGGCTCACTTGAATGCAC 59.193 55.000 0.00 0.00 0.00 4.57
6287 6735 1.095228 CACCTGTTTCACTGTGCCGT 61.095 55.000 2.12 0.00 0.00 5.68
6398 6846 2.979240 AGCTTCTCCCATCGAAACTTC 58.021 47.619 0.00 0.00 0.00 3.01
6422 6870 7.766278 ACATCTTATTACACGAGCAAGAAGAAT 59.234 33.333 6.92 0.00 36.07 2.40
6434 6882 7.749126 GGTTTCAAAAGGACATCTTATTACACG 59.251 37.037 0.00 0.00 34.78 4.49
6466 6914 9.162764 GATAAAAGAGGCTCAACACTTATTACA 57.837 33.333 18.26 0.00 0.00 2.41
6603 7051 6.601741 ACTTTGTGTGGCATTTAATTGTTG 57.398 33.333 0.00 0.00 0.00 3.33
6727 7176 2.361230 GTGTGGGTAAGCCAGGCC 60.361 66.667 8.22 0.00 36.17 5.19
6858 7308 4.537135 ACTCTACGCCAGAAGAAATGAA 57.463 40.909 0.00 0.00 31.12 2.57
6875 7325 1.853963 ATCCAACACTCGGCTACTCT 58.146 50.000 0.00 0.00 0.00 3.24
6912 7362 6.297582 TCAAAACATGCCCAGAAAAATCATT 58.702 32.000 0.00 0.00 0.00 2.57
6913 7363 5.867330 TCAAAACATGCCCAGAAAAATCAT 58.133 33.333 0.00 0.00 0.00 2.45
7063 7513 3.569194 TGTCCTGAAGCACCTAAAACA 57.431 42.857 0.00 0.00 0.00 2.83
7486 7936 6.320164 GGGGTATATGTGTATTTTGTCAGCAA 59.680 38.462 0.00 0.00 0.00 3.91
7487 7937 5.825679 GGGGTATATGTGTATTTTGTCAGCA 59.174 40.000 0.00 0.00 0.00 4.41
7488 7938 6.062095 AGGGGTATATGTGTATTTTGTCAGC 58.938 40.000 0.00 0.00 0.00 4.26
7489 7939 7.468631 GCAAGGGGTATATGTGTATTTTGTCAG 60.469 40.741 0.00 0.00 0.00 3.51
7490 7940 6.320164 GCAAGGGGTATATGTGTATTTTGTCA 59.680 38.462 0.00 0.00 0.00 3.58
7491 7941 6.320164 TGCAAGGGGTATATGTGTATTTTGTC 59.680 38.462 0.00 0.00 0.00 3.18
7493 7943 6.707440 TGCAAGGGGTATATGTGTATTTTG 57.293 37.500 0.00 0.00 0.00 2.44
7500 7950 4.985538 AGGTAATGCAAGGGGTATATGTG 58.014 43.478 0.00 0.00 0.00 3.21
7520 7970 5.238650 ACAAAACATTTACTCCAGTTCGAGG 59.761 40.000 0.00 0.00 33.93 4.63
7551 8001 9.547753 AAAAACTATATGATCAACATAGCTCGT 57.452 29.630 19.99 6.23 43.48 4.18
7573 8023 5.947228 AAGATCGTGCAGAATCTGAAAAA 57.053 34.783 15.38 0.00 32.44 1.94
7607 8059 3.965347 GGGAGGCTAATGTACAACCTCTA 59.035 47.826 24.81 5.27 45.16 2.43
7608 8060 2.772515 GGGAGGCTAATGTACAACCTCT 59.227 50.000 24.81 11.22 45.16 3.69
7627 8079 3.497103 TTCCTGTATCATGAGCATGGG 57.503 47.619 10.31 2.24 39.24 4.00
7762 8217 2.664825 GGCATAACCAAAGGGCACA 58.335 52.632 0.00 0.00 38.86 4.57
7768 8223 9.078452 TGAGCATATCATGTGGCATAACCAAAG 62.078 40.741 0.00 0.00 39.81 2.77
7874 8347 1.882623 CCCTTCCAAGAGCTGTTGTTC 59.117 52.381 20.95 0.00 0.00 3.18
7882 8355 0.984995 ACTGGTACCCTTCCAAGAGC 59.015 55.000 10.07 0.00 34.35 4.09
7884 8357 1.975680 GTGACTGGTACCCTTCCAAGA 59.024 52.381 10.07 0.00 34.35 3.02
7922 8395 4.202182 CCTGGATTTTTGCATACATGAGGG 60.202 45.833 0.00 0.00 0.00 4.30
8024 8497 1.303643 CACAAGCCAGAACCTCCCC 60.304 63.158 0.00 0.00 0.00 4.81
8045 8521 1.748122 GCTCTCATGTGCCCACTGG 60.748 63.158 0.00 0.00 0.00 4.00
8046 8522 1.748122 GGCTCTCATGTGCCCACTG 60.748 63.158 13.44 0.00 44.54 3.66
8047 8523 2.673523 GGCTCTCATGTGCCCACT 59.326 61.111 13.44 0.00 44.54 4.00
8067 8543 5.865085 ACAACAGGCTAGTGTTCAAATCTA 58.135 37.500 0.00 0.00 38.65 1.98
8089 8565 3.740115 TGCCACTTTCCTACAGAAGAAC 58.260 45.455 0.00 0.00 35.40 3.01


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

AutoCloner maintained by Alex Coulton.