Multiple sequence alignment - TraesCS3B01G155000

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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 TraesCS3B01G155000 chr3B 100.000 5526 0 0 1 5526 147552331 147546806 0.000000e+00 10205.0
1 TraesCS3B01G155000 chr3D 94.426 2673 85 15 2871 5526 96397414 96394789 0.000000e+00 4052.0
2 TraesCS3B01G155000 chr3D 90.720 1487 95 13 93 1552 96400093 96398623 0.000000e+00 1941.0
3 TraesCS3B01G155000 chr3D 91.591 1213 62 19 1608 2811 96398603 96397422 0.000000e+00 1639.0
4 TraesCS3B01G155000 chr3A 87.008 1447 143 30 3493 4922 114427750 114426332 0.000000e+00 1589.0
5 TraesCS3B01G155000 chr3A 92.067 1021 61 11 1796 2811 114429430 114428425 0.000000e+00 1419.0
6 TraesCS3B01G155000 chr3A 88.826 1056 70 17 746 1786 114430571 114429549 0.000000e+00 1253.0
7 TraesCS3B01G155000 chr3A 92.417 633 39 3 2874 3497 114428414 114427782 0.000000e+00 894.0
8 TraesCS3B01G155000 chr3A 93.333 210 14 0 5317 5526 114426212 114426003 1.490000e-80 311.0
9 TraesCS3B01G155000 chr5B 93.165 278 15 1 1211 1488 613107303 613107576 6.670000e-109 405.0
10 TraesCS3B01G155000 chr4B 89.655 58 6 0 35 92 633065614 633065557 2.130000e-09 75.0
11 TraesCS3B01G155000 chr6D 85.135 74 8 2 1 73 412832329 412832258 7.680000e-09 73.1
12 TraesCS3B01G155000 chr2D 84.932 73 9 2 1 72 615146601 615146530 7.680000e-09 73.1


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 TraesCS3B01G155000 chr3B 147546806 147552331 5525 True 10205.0 10205 100.000000 1 5526 1 chr3B.!!$R1 5525
1 TraesCS3B01G155000 chr3D 96394789 96400093 5304 True 2544.0 4052 92.245667 93 5526 3 chr3D.!!$R1 5433
2 TraesCS3B01G155000 chr3A 114426003 114430571 4568 True 1093.2 1589 90.730200 746 5526 5 chr3A.!!$R1 4780

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
486 492 0.037326 GGGCTCATGACTGTCAACGA 60.037 55.000 15.31 12.96 0.00 3.85 F
1392 1426 0.892755 AGTGCAATGCTGTCAATGGG 59.107 50.000 6.82 0.00 0.00 4.00 F
2098 2286 0.318955 GCTGGTTTGATTTGCGCACT 60.319 50.000 11.12 0.00 0.00 4.40 F
2125 2313 0.674581 TGCTCTTGACCATTGAGGCG 60.675 55.000 0.00 0.00 43.14 5.52 F
2869 3062 1.069513 CGTCCTTGGTTACTGGTCACA 59.930 52.381 0.00 0.00 0.00 3.58 F
3940 4179 1.191489 CCCCCGCAAAATCCAAAGGT 61.191 55.000 0.00 0.00 0.00 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1448 1504 0.035458 AACCGCTCACTGCTAAAGCT 59.965 50.000 3.26 0.0 42.66 3.74 R
2849 3042 1.069513 TGTGACCAGTAACCAAGGACG 59.930 52.381 0.00 0.0 0.00 4.79 R
3174 3375 1.276421 GCTAAGGGAGACAGTTGCAGA 59.724 52.381 0.00 0.0 0.00 4.26 R
3925 4164 2.558359 AGAAGGACCTTTGGATTTTGCG 59.442 45.455 8.49 0.0 0.00 4.85 R
4160 4399 2.457080 GGAACTTTCCCTTCTCGCG 58.543 57.895 0.00 0.0 41.62 5.87 R
5182 5467 0.097150 GGTCTTTTCGCGCAGGATTC 59.903 55.000 8.75 0.0 0.00 2.52 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
59 60 8.635765 TTTTGATTTTACTATTCACCTGAGCT 57.364 30.769 0.00 0.00 0.00 4.09
60 61 7.849804 TTGATTTTACTATTCACCTGAGCTC 57.150 36.000 6.82 6.82 0.00 4.09
61 62 6.946340 TGATTTTACTATTCACCTGAGCTCA 58.054 36.000 17.19 17.19 0.00 4.26
62 63 7.568349 TGATTTTACTATTCACCTGAGCTCAT 58.432 34.615 18.63 3.37 0.00 2.90
63 64 8.049117 TGATTTTACTATTCACCTGAGCTCATT 58.951 33.333 18.63 4.31 0.00 2.57
64 65 8.814038 ATTTTACTATTCACCTGAGCTCATTT 57.186 30.769 18.63 3.90 0.00 2.32
65 66 7.615582 TTTACTATTCACCTGAGCTCATTTG 57.384 36.000 18.63 16.74 0.00 2.32
66 67 5.426689 ACTATTCACCTGAGCTCATTTGA 57.573 39.130 18.63 18.77 0.00 2.69
67 68 5.426504 ACTATTCACCTGAGCTCATTTGAG 58.573 41.667 18.63 12.54 44.75 3.02
79 80 4.313277 CTCATTTGAGCTCGGATGTAGA 57.687 45.455 21.51 8.66 35.13 2.59
80 81 4.880759 CTCATTTGAGCTCGGATGTAGAT 58.119 43.478 21.51 0.00 35.13 1.98
81 82 6.018589 CTCATTTGAGCTCGGATGTAGATA 57.981 41.667 21.51 7.68 35.13 1.98
82 83 5.773575 TCATTTGAGCTCGGATGTAGATAC 58.226 41.667 21.51 0.00 0.00 2.24
83 84 5.536538 TCATTTGAGCTCGGATGTAGATACT 59.463 40.000 21.51 0.00 0.00 2.12
84 85 5.854010 TTTGAGCTCGGATGTAGATACTT 57.146 39.130 9.64 0.00 0.00 2.24
85 86 5.440234 TTGAGCTCGGATGTAGATACTTC 57.560 43.478 9.64 0.00 0.00 3.01
86 87 3.498777 TGAGCTCGGATGTAGATACTTCG 59.501 47.826 9.64 0.00 32.83 3.79
87 88 2.226912 AGCTCGGATGTAGATACTTCGC 59.773 50.000 0.00 0.00 32.83 4.70
88 89 2.840673 CTCGGATGTAGATACTTCGCG 58.159 52.381 0.00 0.00 32.83 5.87
89 90 2.216046 TCGGATGTAGATACTTCGCGT 58.784 47.619 5.77 0.00 32.83 6.01
90 91 2.222678 TCGGATGTAGATACTTCGCGTC 59.777 50.000 5.77 0.00 32.83 5.19
91 92 2.664971 CGGATGTAGATACTTCGCGTCC 60.665 54.545 5.77 0.00 35.90 4.79
103 104 1.655654 CGCGTCCGATAGAGCACTG 60.656 63.158 0.00 0.00 36.29 3.66
111 112 4.023107 GTCCGATAGAGCACTGCTATACAA 60.023 45.833 7.54 0.00 39.88 2.41
130 131 9.887406 CTATACAACCGACACTTTTTAAACAAT 57.113 29.630 0.00 0.00 0.00 2.71
173 174 4.749598 CCAGCCATTTTGTACTTTTGTTCC 59.250 41.667 0.00 0.00 0.00 3.62
186 188 5.574188 ACTTTTGTTCCTAAGGCATCTCAT 58.426 37.500 0.00 0.00 0.00 2.90
196 198 0.179702 GGCATCTCATGGTGCAGAGA 59.820 55.000 16.58 5.92 44.27 3.10
205 207 6.417258 TCTCATGGTGCAGAGAAATTATTGA 58.583 36.000 1.13 0.00 37.91 2.57
248 250 5.478407 ACATCGTGTGTACATCAATTCTGA 58.522 37.500 0.00 0.00 39.91 3.27
276 278 2.898729 ATTCGAGGTACATCTGCCTG 57.101 50.000 5.91 0.00 34.81 4.85
314 316 1.065928 CGGCCTGTCCACGTCTATC 59.934 63.158 0.00 0.00 34.01 2.08
331 337 0.526662 ATCGTTGACCTCGTCTCCAC 59.473 55.000 0.00 0.00 33.15 4.02
333 339 1.080705 GTTGACCTCGTCTCCACCG 60.081 63.158 0.00 0.00 33.15 4.94
338 344 1.032657 ACCTCGTCTCCACCGATGAG 61.033 60.000 0.00 0.00 43.48 2.90
341 347 1.265635 CTCGTCTCCACCGATGAGATC 59.734 57.143 4.45 0.00 45.60 2.75
357 363 0.935898 GATCGCGAACTCCTACGAGA 59.064 55.000 15.24 0.00 41.58 4.04
359 365 1.159285 TCGCGAACTCCTACGAGAAA 58.841 50.000 6.20 0.00 38.52 2.52
360 366 1.741706 TCGCGAACTCCTACGAGAAAT 59.258 47.619 6.20 0.00 38.52 2.17
375 381 6.910536 ACGAGAAATAGTATGGCTTGAAAG 57.089 37.500 0.00 0.00 0.00 2.62
382 388 3.600388 AGTATGGCTTGAAAGAAGACGG 58.400 45.455 0.00 0.00 0.00 4.79
384 390 1.227999 TGGCTTGAAAGAAGACGGCG 61.228 55.000 4.80 4.80 0.00 6.46
395 401 2.185103 AAGACGGCGTCTCGTGTCTC 62.185 60.000 39.00 12.21 42.59 3.36
412 418 3.448660 TGTCTCATGTGGGTCAGTCTATG 59.551 47.826 0.00 0.00 0.00 2.23
420 426 1.202313 GGGTCAGTCTATGTCTCGTGC 60.202 57.143 0.00 0.00 0.00 5.34
436 442 1.467713 CGTGCCTTACTCTTCTCGTCC 60.468 57.143 0.00 0.00 0.00 4.79
438 444 0.525882 GCCTTACTCTTCTCGTCCGC 60.526 60.000 0.00 0.00 0.00 5.54
460 466 3.460857 ACCCATATCTTCACTCTTCGC 57.539 47.619 0.00 0.00 0.00 4.70
461 467 2.103263 ACCCATATCTTCACTCTTCGCC 59.897 50.000 0.00 0.00 0.00 5.54
462 468 2.366916 CCCATATCTTCACTCTTCGCCT 59.633 50.000 0.00 0.00 0.00 5.52
463 469 3.553922 CCCATATCTTCACTCTTCGCCTC 60.554 52.174 0.00 0.00 0.00 4.70
464 470 3.320541 CCATATCTTCACTCTTCGCCTCT 59.679 47.826 0.00 0.00 0.00 3.69
465 471 4.202202 CCATATCTTCACTCTTCGCCTCTT 60.202 45.833 0.00 0.00 0.00 2.85
466 472 3.518634 ATCTTCACTCTTCGCCTCTTC 57.481 47.619 0.00 0.00 0.00 2.87
467 473 1.200252 TCTTCACTCTTCGCCTCTTCG 59.800 52.381 0.00 0.00 0.00 3.79
477 483 4.844420 CCTCTTCGGGCTCATGAC 57.156 61.111 0.00 0.00 0.00 3.06
478 484 2.206635 CCTCTTCGGGCTCATGACT 58.793 57.895 0.00 0.00 0.00 3.41
485 491 1.354337 CGGGCTCATGACTGTCAACG 61.354 60.000 15.31 9.25 0.00 4.10
486 492 0.037326 GGGCTCATGACTGTCAACGA 60.037 55.000 15.31 12.96 0.00 3.85
491 497 3.424039 GCTCATGACTGTCAACGAACATG 60.424 47.826 15.31 6.77 37.18 3.21
516 522 6.304882 GGAACAACAAAGACTTAGAATACGC 58.695 40.000 0.00 0.00 0.00 4.42
533 539 7.023575 AGAATACGCATGACAACAAAGATTTC 58.976 34.615 0.00 0.00 0.00 2.17
534 540 4.566545 ACGCATGACAACAAAGATTTCA 57.433 36.364 0.00 0.00 0.00 2.69
535 541 4.539870 ACGCATGACAACAAAGATTTCAG 58.460 39.130 0.00 0.00 0.00 3.02
536 542 3.916172 CGCATGACAACAAAGATTTCAGG 59.084 43.478 0.00 0.00 0.00 3.86
591 613 4.060205 AGTGATTGTGTACCGGTACAAAC 58.940 43.478 41.27 31.20 46.33 2.93
621 643 4.637387 TCCGGTTGGTTTAAATCCTGTA 57.363 40.909 0.00 0.00 36.30 2.74
658 680 7.544566 GGACAAATTCACGAACAGAAGATACTA 59.455 37.037 0.00 0.00 0.00 1.82
660 682 9.268268 ACAAATTCACGAACAGAAGATACTAAA 57.732 29.630 0.00 0.00 0.00 1.85
667 689 9.582431 CACGAACAGAAGATACTAAAAGGATTA 57.418 33.333 0.00 0.00 0.00 1.75
710 732 2.446435 CACCTCGATTCCCACCAAAAT 58.554 47.619 0.00 0.00 0.00 1.82
713 735 3.245264 ACCTCGATTCCCACCAAAATCTT 60.245 43.478 0.00 0.00 31.15 2.40
714 736 3.763897 CCTCGATTCCCACCAAAATCTTT 59.236 43.478 0.00 0.00 31.15 2.52
718 740 4.160252 CGATTCCCACCAAAATCTTTCCAT 59.840 41.667 0.00 0.00 31.15 3.41
848 875 6.681777 CCCCACTTGTCTTTCTGAAATAAAG 58.318 40.000 2.88 9.82 35.66 1.85
878 905 6.489603 AGGATCTCATCTAGACCGTTCATAT 58.510 40.000 0.00 0.00 36.93 1.78
1145 1178 2.767445 CGTCATCCGGCGAGGTACA 61.767 63.158 9.30 0.00 41.99 2.90
1172 1205 2.187992 CTCGCTCTGAGCCTCTGAA 58.812 57.895 22.97 2.34 38.18 3.02
1232 1265 1.839747 TCAACACCCTGTAGCCCGT 60.840 57.895 0.00 0.00 0.00 5.28
1261 1294 1.327690 CCTCACGCTGCCCCTAGTTA 61.328 60.000 0.00 0.00 0.00 2.24
1265 1298 1.598130 CGCTGCCCCTAGTTATGGC 60.598 63.158 0.00 0.00 45.56 4.40
1292 1325 2.561858 GGTTTCTCTCGGTTAGGACACT 59.438 50.000 0.00 0.00 0.00 3.55
1358 1391 2.185350 GCTCGCCTGCTGCTTCTA 59.815 61.111 0.00 0.00 38.05 2.10
1392 1426 0.892755 AGTGCAATGCTGTCAATGGG 59.107 50.000 6.82 0.00 0.00 4.00
1420 1454 1.205064 CTTCGCACTGGCTTTGTCG 59.795 57.895 0.00 0.00 38.10 4.35
1432 1488 1.135575 GCTTTGTCGATGGAGGCTTTG 60.136 52.381 0.00 0.00 0.00 2.77
1433 1489 1.470098 CTTTGTCGATGGAGGCTTTGG 59.530 52.381 0.00 0.00 0.00 3.28
1434 1490 0.960364 TTGTCGATGGAGGCTTTGGC 60.960 55.000 0.00 0.00 37.82 4.52
1435 1491 2.125147 TCGATGGAGGCTTTGGCG 60.125 61.111 0.00 0.00 39.81 5.69
1436 1492 2.436646 CGATGGAGGCTTTGGCGT 60.437 61.111 0.00 0.00 39.81 5.68
1437 1493 2.753966 CGATGGAGGCTTTGGCGTG 61.754 63.158 0.00 0.00 39.81 5.34
1438 1494 2.361610 ATGGAGGCTTTGGCGTGG 60.362 61.111 0.00 0.00 39.81 4.94
1544 1614 2.224597 TGTTCTTGCTTCTCAGGATGCA 60.225 45.455 0.00 0.00 46.25 3.96
1576 1646 2.113860 TGCTGCAGGATTAACTGGAC 57.886 50.000 17.12 0.00 38.90 4.02
1600 1670 6.052840 CACATCTTGTGGATAGCATTGTAC 57.947 41.667 0.00 0.00 44.27 2.90
1601 1671 5.819379 CACATCTTGTGGATAGCATTGTACT 59.181 40.000 0.00 0.00 44.27 2.73
1602 1672 6.986231 CACATCTTGTGGATAGCATTGTACTA 59.014 38.462 0.00 0.00 44.27 1.82
1603 1673 7.658982 CACATCTTGTGGATAGCATTGTACTAT 59.341 37.037 0.00 0.00 44.27 2.12
1760 1836 2.093973 CGCCTCTCACAGAAGTATTGGT 60.094 50.000 0.00 0.00 0.00 3.67
1765 1841 5.336531 CCTCTCACAGAAGTATTGGTAACGT 60.337 44.000 0.00 0.00 42.51 3.99
1786 1862 8.597662 AACGTTTTATGCTCAGTAGAAAGTAA 57.402 30.769 0.00 0.00 0.00 2.24
1787 1863 8.015409 ACGTTTTATGCTCAGTAGAAAGTAAC 57.985 34.615 0.00 0.00 0.00 2.50
1788 1864 7.871463 ACGTTTTATGCTCAGTAGAAAGTAACT 59.129 33.333 0.00 0.00 0.00 2.24
1833 2018 3.687698 ACGCGGCACTAGAATATTTTGTT 59.312 39.130 12.47 0.00 0.00 2.83
1845 2030 9.338622 CTAGAATATTTTGTTAAGGTACTGGGG 57.661 37.037 0.00 0.00 40.86 4.96
1852 2037 2.641321 GTTAAGGTACTGGGGAAGTGGT 59.359 50.000 0.00 0.00 40.86 4.16
1860 2045 1.985895 CTGGGGAAGTGGTAAGTCCTT 59.014 52.381 0.00 0.00 37.07 3.36
1873 2059 5.427157 TGGTAAGTCCTTGTATTATGCTCCA 59.573 40.000 0.00 0.00 37.07 3.86
1901 2087 6.935208 GCCAGTAGGTTATTTCCTTATGTAGG 59.065 42.308 0.00 0.00 40.59 3.18
1902 2088 7.419865 GCCAGTAGGTTATTTCCTTATGTAGGT 60.420 40.741 0.00 0.00 40.31 3.08
1903 2089 8.148999 CCAGTAGGTTATTTCCTTATGTAGGTC 58.851 40.741 0.00 0.00 45.03 3.85
1904 2090 8.925338 CAGTAGGTTATTTCCTTATGTAGGTCT 58.075 37.037 0.00 0.00 45.03 3.85
1922 2108 4.074970 GGTCTTCTTTCCATTTCTGCAGA 58.925 43.478 13.74 13.74 0.00 4.26
1961 2147 7.524717 AGTTGCTAATGGTTATTCAACACTT 57.475 32.000 0.00 0.00 37.02 3.16
1963 2149 7.230510 AGTTGCTAATGGTTATTCAACACTTCA 59.769 33.333 0.00 0.00 37.02 3.02
1986 2172 8.514330 TCAAAACCTTAGGCATATAATTTCGT 57.486 30.769 0.00 0.00 0.00 3.85
2020 2206 1.347707 TCTGATGTTTCTGCCCTTCGT 59.652 47.619 0.00 0.00 0.00 3.85
2021 2207 1.734465 CTGATGTTTCTGCCCTTCGTC 59.266 52.381 0.00 0.00 0.00 4.20
2041 2229 7.962964 TCGTCAATCTCATGTTCTAAACTTT 57.037 32.000 0.00 0.00 0.00 2.66
2098 2286 0.318955 GCTGGTTTGATTTGCGCACT 60.319 50.000 11.12 0.00 0.00 4.40
2125 2313 0.674581 TGCTCTTGACCATTGAGGCG 60.675 55.000 0.00 0.00 43.14 5.52
2236 2424 3.936453 ACGAGCAAACTTCACACACTTTA 59.064 39.130 0.00 0.00 0.00 1.85
2302 2490 8.862325 ATATGTATCGGCTGGAAATGAAATTA 57.138 30.769 0.00 0.00 33.67 1.40
2358 2546 8.413229 CACCCACTTAATATTTGTATTCCCAAG 58.587 37.037 0.00 0.00 0.00 3.61
2378 2567 3.006940 AGTCGAAGTTGTGACTTTTGCA 58.993 40.909 2.27 0.00 45.88 4.08
2387 2576 5.704978 AGTTGTGACTTTTGCATTGGTTTTT 59.295 32.000 0.00 0.00 29.87 1.94
2391 2580 7.548097 TGTGACTTTTGCATTGGTTTTTACTA 58.452 30.769 0.00 0.00 0.00 1.82
2439 2628 3.359033 CAGGGATCTCAATCAAAGCCAA 58.641 45.455 0.00 0.00 33.21 4.52
2532 2721 9.807386 CTTTTAGTCTTTTTATTACGGTGTGAG 57.193 33.333 0.00 0.00 0.00 3.51
2670 2860 3.492102 TGCTGTCAGTTCTAAAGGCTT 57.508 42.857 0.93 0.00 0.00 4.35
2806 2999 8.826765 ACTTAGAACCAAGAAGGATTAGATCAA 58.173 33.333 0.00 0.00 41.22 2.57
2807 3000 9.844257 CTTAGAACCAAGAAGGATTAGATCAAT 57.156 33.333 0.00 0.00 41.22 2.57
2813 3006 9.190317 ACCAAGAAGGATTAGATCAATAAAACC 57.810 33.333 0.00 0.00 41.22 3.27
2834 3027 5.691896 ACCAGTACTTTTTGGTTCTAAGCT 58.308 37.500 0.00 0.00 45.16 3.74
2835 3028 5.531287 ACCAGTACTTTTTGGTTCTAAGCTG 59.469 40.000 0.00 0.00 45.16 4.24
2836 3029 5.531287 CCAGTACTTTTTGGTTCTAAGCTGT 59.469 40.000 0.00 0.00 0.00 4.40
2837 3030 6.708949 CCAGTACTTTTTGGTTCTAAGCTGTA 59.291 38.462 0.00 0.00 0.00 2.74
2838 3031 7.227910 CCAGTACTTTTTGGTTCTAAGCTGTAA 59.772 37.037 0.00 0.00 0.00 2.41
2839 3032 8.784043 CAGTACTTTTTGGTTCTAAGCTGTAAT 58.216 33.333 0.00 0.00 0.00 1.89
2840 3033 9.350951 AGTACTTTTTGGTTCTAAGCTGTAATT 57.649 29.630 0.00 0.00 0.00 1.40
2841 3034 9.394477 GTACTTTTTGGTTCTAAGCTGTAATTG 57.606 33.333 0.00 0.00 0.00 2.32
2842 3035 7.433680 ACTTTTTGGTTCTAAGCTGTAATTGG 58.566 34.615 0.00 0.00 0.00 3.16
2843 3036 6.969993 TTTTGGTTCTAAGCTGTAATTGGT 57.030 33.333 0.00 0.00 0.00 3.67
2844 3037 6.969993 TTTGGTTCTAAGCTGTAATTGGTT 57.030 33.333 0.00 0.00 0.00 3.67
2845 3038 6.569179 TTGGTTCTAAGCTGTAATTGGTTC 57.431 37.500 0.00 0.00 0.00 3.62
2846 3039 5.876357 TGGTTCTAAGCTGTAATTGGTTCT 58.124 37.500 0.00 0.00 0.00 3.01
2847 3040 7.011499 TGGTTCTAAGCTGTAATTGGTTCTA 57.989 36.000 0.00 0.00 0.00 2.10
2848 3041 7.455058 TGGTTCTAAGCTGTAATTGGTTCTAA 58.545 34.615 0.00 0.00 0.00 2.10
2849 3042 7.389607 TGGTTCTAAGCTGTAATTGGTTCTAAC 59.610 37.037 0.00 0.00 0.00 2.34
2850 3043 7.412672 GGTTCTAAGCTGTAATTGGTTCTAACG 60.413 40.741 0.00 0.00 0.00 3.18
2851 3044 6.694447 TCTAAGCTGTAATTGGTTCTAACGT 58.306 36.000 0.00 0.00 0.00 3.99
2852 3045 5.857822 AAGCTGTAATTGGTTCTAACGTC 57.142 39.130 0.00 0.00 0.00 4.34
2853 3046 4.251268 AGCTGTAATTGGTTCTAACGTCC 58.749 43.478 0.00 0.00 0.00 4.79
2854 3047 4.020485 AGCTGTAATTGGTTCTAACGTCCT 60.020 41.667 0.00 0.00 0.00 3.85
2855 3048 4.694037 GCTGTAATTGGTTCTAACGTCCTT 59.306 41.667 0.00 0.00 0.00 3.36
2856 3049 5.390567 GCTGTAATTGGTTCTAACGTCCTTG 60.391 44.000 0.00 0.00 0.00 3.61
2857 3050 4.998672 TGTAATTGGTTCTAACGTCCTTGG 59.001 41.667 0.00 0.00 0.00 3.61
2858 3051 3.782656 ATTGGTTCTAACGTCCTTGGT 57.217 42.857 0.00 0.00 0.00 3.67
2859 3052 3.564053 TTGGTTCTAACGTCCTTGGTT 57.436 42.857 0.00 0.00 0.00 3.67
2860 3053 4.686191 TTGGTTCTAACGTCCTTGGTTA 57.314 40.909 0.00 0.00 0.00 2.85
2861 3054 3.993920 TGGTTCTAACGTCCTTGGTTAC 58.006 45.455 0.00 0.00 0.00 2.50
2862 3055 3.642848 TGGTTCTAACGTCCTTGGTTACT 59.357 43.478 0.00 0.00 0.00 2.24
2863 3056 3.992427 GGTTCTAACGTCCTTGGTTACTG 59.008 47.826 0.00 0.00 0.00 2.74
2864 3057 3.947910 TCTAACGTCCTTGGTTACTGG 57.052 47.619 0.00 0.00 0.00 4.00
2865 3058 3.233507 TCTAACGTCCTTGGTTACTGGT 58.766 45.455 0.00 0.00 0.00 4.00
2866 3059 2.538512 AACGTCCTTGGTTACTGGTC 57.461 50.000 0.00 0.00 0.00 4.02
2867 3060 1.416243 ACGTCCTTGGTTACTGGTCA 58.584 50.000 0.00 0.00 0.00 4.02
2868 3061 1.069668 ACGTCCTTGGTTACTGGTCAC 59.930 52.381 0.00 0.00 0.00 3.67
2869 3062 1.069513 CGTCCTTGGTTACTGGTCACA 59.930 52.381 0.00 0.00 0.00 3.58
3026 3227 7.125507 ACTCTTCCTCTCACAGATTGTCAATAT 59.874 37.037 0.00 0.00 0.00 1.28
3028 3229 5.836347 TCCTCTCACAGATTGTCAATATCG 58.164 41.667 0.00 0.00 0.00 2.92
3063 3264 3.751175 TGTACAAAAGATTGAGGGAAGCG 59.249 43.478 0.00 0.00 38.94 4.68
3100 3301 6.601332 TCCTTATGTGGTCTGGATAAATTCC 58.399 40.000 0.00 0.00 45.69 3.01
3142 3343 5.012613 CAGTGTTTAAGTTTTGTTTTGCGC 58.987 37.500 0.00 0.00 0.00 6.09
3156 3357 5.724328 TGTTTTGCGCATTATTATTCCCAA 58.276 33.333 12.75 0.00 0.00 4.12
3174 3375 4.282195 TCCCAATTTAATGTTTCCGTTGCT 59.718 37.500 0.00 0.00 0.00 3.91
3240 3442 5.124457 CAGTGTACAATTCATTCCTTGGAGG 59.876 44.000 0.00 0.00 36.46 4.30
3477 3681 8.068380 GGGCGAACACTATTTTCTATTGATTAC 58.932 37.037 0.00 0.00 0.00 1.89
3537 3776 4.280174 GCCTTGTCCTGATAATGATGCATT 59.720 41.667 0.00 0.00 37.80 3.56
3594 3833 4.861102 AAGGCATATTAAATGCAGCTCC 57.139 40.909 18.16 6.43 46.21 4.70
3639 3878 8.048534 AGAGTCGCACTAGTTAGTTTACATAA 57.951 34.615 0.00 0.00 33.46 1.90
3644 3883 9.123902 TCGCACTAGTTAGTTTACATAATAGGA 57.876 33.333 0.00 0.00 33.46 2.94
3682 3921 9.283768 TGATTCATTGAAAAGTTGTAAGCTCTA 57.716 29.630 2.68 0.00 0.00 2.43
3720 3959 7.781324 TGCTATTATCAGATGTGGATCAGTA 57.219 36.000 0.00 0.00 0.00 2.74
3766 4005 7.259088 AGGATCACCTGAGTTACAAAATAGT 57.741 36.000 0.00 0.00 45.92 2.12
3925 4164 4.657814 TCTAGAATATGAATTGGCCCCC 57.342 45.455 0.00 0.00 0.00 5.40
3940 4179 1.191489 CCCCCGCAAAATCCAAAGGT 61.191 55.000 0.00 0.00 0.00 3.50
3978 4217 2.749621 GGTCGACCATGAGCTCAAAAAT 59.250 45.455 29.75 6.68 35.64 1.82
4120 4359 8.239038 TCTATGTTCCTTACTTATCTCACTGG 57.761 38.462 0.00 0.00 0.00 4.00
4130 4369 9.307121 CTTACTTATCTCACTGGTTCACTAATG 57.693 37.037 0.00 0.00 0.00 1.90
4160 4399 1.000274 ACAGGGCATTTTCAGCGTTTC 60.000 47.619 0.00 0.00 0.00 2.78
4195 4434 5.061721 AGTTCCTTGTTTCAGGTGGTAAT 57.938 39.130 0.00 0.00 35.15 1.89
4359 4602 2.106684 TGGCACTAACACCACCAATACA 59.893 45.455 0.00 0.00 0.00 2.29
4360 4603 3.245087 TGGCACTAACACCACCAATACAT 60.245 43.478 0.00 0.00 0.00 2.29
4361 4604 4.019231 TGGCACTAACACCACCAATACATA 60.019 41.667 0.00 0.00 0.00 2.29
4362 4605 5.130350 GGCACTAACACCACCAATACATAT 58.870 41.667 0.00 0.00 0.00 1.78
4363 4606 6.126739 TGGCACTAACACCACCAATACATATA 60.127 38.462 0.00 0.00 0.00 0.86
4364 4607 6.426937 GGCACTAACACCACCAATACATATAG 59.573 42.308 0.00 0.00 0.00 1.31
4365 4608 7.214381 GCACTAACACCACCAATACATATAGA 58.786 38.462 0.00 0.00 0.00 1.98
4367 4610 9.778741 CACTAACACCACCAATACATATAGATT 57.221 33.333 0.00 0.00 0.00 2.40
4429 4674 7.647318 GGCATAATACTGACATCTGATCTATCG 59.353 40.741 0.00 0.00 0.00 2.92
4612 4857 1.259840 ATCAGTGCCATGTTTGCCCC 61.260 55.000 0.00 0.00 0.00 5.80
4624 4869 1.827399 TTTGCCCCGACTCCTGTCTC 61.827 60.000 0.00 0.00 40.86 3.36
4636 4881 5.067153 CGACTCCTGTCTCTTCATATGAACT 59.933 44.000 14.23 0.00 40.86 3.01
4682 4927 6.764379 TGGTGAAATGACAGTACATGACTTA 58.236 36.000 0.00 0.00 35.64 2.24
4688 4962 7.482169 AATGACAGTACATGACTTAAGAGGA 57.518 36.000 10.09 0.00 35.64 3.71
4708 4982 5.082425 AGGATCTGCAGAAACCATCTTTTT 58.918 37.500 31.04 15.29 35.73 1.94
4709 4983 5.047519 AGGATCTGCAGAAACCATCTTTTTG 60.048 40.000 31.04 0.00 35.73 2.44
4710 4984 5.279156 GGATCTGCAGAAACCATCTTTTTGT 60.279 40.000 27.40 7.29 35.73 2.83
4751 5027 8.467598 GTGGTACTGAAATCTTGTACTCTGATA 58.532 37.037 12.97 0.00 37.35 2.15
4790 5066 7.665559 AGACATGTATATCTTTGTTGTGTTGGT 59.334 33.333 0.00 0.00 0.00 3.67
4878 5154 8.275632 GGTGAAATGTGCTTAAATCTTTTGTTC 58.724 33.333 0.00 0.00 0.00 3.18
4882 5158 6.707440 TGTGCTTAAATCTTTTGTTCTCCA 57.293 33.333 0.00 0.00 0.00 3.86
4931 5207 2.579410 TCTTACAAAGGCCCAGTTCC 57.421 50.000 0.00 0.00 0.00 3.62
4962 5239 1.871418 TCTGGAGAATCTGGGTCTGG 58.129 55.000 0.00 0.00 33.73 3.86
4983 5260 8.382875 GTCTGGAAAATCAACAAAACAAAAGAG 58.617 33.333 0.00 0.00 0.00 2.85
4989 5266 5.499139 TCAACAAAACAAAAGAGCTCGAT 57.501 34.783 8.37 0.00 0.00 3.59
4997 5274 4.936891 ACAAAAGAGCTCGATTTTGCTTT 58.063 34.783 28.00 14.74 45.81 3.51
5001 5278 3.350833 AGAGCTCGATTTTGCTTTGGAT 58.649 40.909 8.37 0.00 39.91 3.41
5088 5365 3.492102 TTCTGGACAACTCCCTCAAAG 57.508 47.619 0.00 0.00 35.34 2.77
5103 5380 4.278419 CCCTCAAAGGAAAACGTTTCAGAT 59.722 41.667 15.01 0.00 37.67 2.90
5114 5391 7.011202 GGAAAACGTTTCAGATAGGAGAATACC 59.989 40.741 15.01 0.00 0.00 2.73
5154 5439 3.494048 GGATCCTAGTGCAGATTCTGTGG 60.494 52.174 14.90 9.57 33.43 4.17
5161 5446 0.964358 GCAGATTCTGTGGGCAGCTT 60.964 55.000 14.90 0.00 42.29 3.74
5200 5485 1.061276 GAGAATCCTGCGCGAAAAGAC 59.939 52.381 12.10 0.00 0.00 3.01
5202 5487 0.321653 AATCCTGCGCGAAAAGACCT 60.322 50.000 12.10 0.00 0.00 3.85
5212 5497 0.969149 GAAAAGACCTGGGCCAAAGG 59.031 55.000 19.66 19.66 40.93 3.11
5244 5529 4.404507 AACGTTGTGATTGTGATACAGC 57.595 40.909 0.00 0.00 0.00 4.40
5285 5572 6.426980 TTTCTAGCAACAGCTATGAACATG 57.573 37.500 2.99 0.00 39.92 3.21
5402 5701 2.619074 GGAACCTGTTGGAATCCCTCAG 60.619 54.545 11.87 11.87 37.10 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 9.077885 AGCTCAGGTGAATAGTAAAATCAAAAA 57.922 29.630 0.00 0.00 0.00 1.94
34 35 8.635765 AGCTCAGGTGAATAGTAAAATCAAAA 57.364 30.769 0.00 0.00 0.00 2.44
35 36 7.882791 TGAGCTCAGGTGAATAGTAAAATCAAA 59.117 33.333 13.74 0.00 0.00 2.69
36 37 7.394016 TGAGCTCAGGTGAATAGTAAAATCAA 58.606 34.615 13.74 0.00 0.00 2.57
37 38 6.946340 TGAGCTCAGGTGAATAGTAAAATCA 58.054 36.000 13.74 0.00 0.00 2.57
38 39 8.443953 AATGAGCTCAGGTGAATAGTAAAATC 57.556 34.615 22.96 0.00 0.00 2.17
39 40 8.680903 CAAATGAGCTCAGGTGAATAGTAAAAT 58.319 33.333 22.96 0.00 0.00 1.82
40 41 7.882791 TCAAATGAGCTCAGGTGAATAGTAAAA 59.117 33.333 22.96 0.72 0.00 1.52
41 42 7.394016 TCAAATGAGCTCAGGTGAATAGTAAA 58.606 34.615 22.96 1.39 0.00 2.01
42 43 6.946340 TCAAATGAGCTCAGGTGAATAGTAA 58.054 36.000 22.96 2.08 0.00 2.24
43 44 6.544928 TCAAATGAGCTCAGGTGAATAGTA 57.455 37.500 22.96 2.75 0.00 1.82
44 45 5.426504 CTCAAATGAGCTCAGGTGAATAGT 58.573 41.667 24.55 4.53 35.13 2.12
45 46 5.987777 CTCAAATGAGCTCAGGTGAATAG 57.012 43.478 24.55 14.38 35.13 1.73
58 59 4.313277 TCTACATCCGAGCTCAAATGAG 57.687 45.455 24.61 18.13 44.75 2.90
59 60 4.944619 ATCTACATCCGAGCTCAAATGA 57.055 40.909 24.61 12.03 0.00 2.57
60 61 5.777802 AGTATCTACATCCGAGCTCAAATG 58.222 41.667 15.40 17.53 0.00 2.32
61 62 6.412362 AAGTATCTACATCCGAGCTCAAAT 57.588 37.500 15.40 3.09 0.00 2.32
62 63 5.505819 CGAAGTATCTACATCCGAGCTCAAA 60.506 44.000 15.40 0.33 0.00 2.69
63 64 4.023963 CGAAGTATCTACATCCGAGCTCAA 60.024 45.833 15.40 0.75 0.00 3.02
64 65 3.498777 CGAAGTATCTACATCCGAGCTCA 59.501 47.826 15.40 0.00 0.00 4.26
65 66 3.668491 GCGAAGTATCTACATCCGAGCTC 60.668 52.174 2.73 2.73 0.00 4.09
66 67 2.226912 GCGAAGTATCTACATCCGAGCT 59.773 50.000 0.00 0.00 0.00 4.09
67 68 2.586900 GCGAAGTATCTACATCCGAGC 58.413 52.381 0.00 0.00 0.00 5.03
68 69 2.223611 ACGCGAAGTATCTACATCCGAG 59.776 50.000 15.93 0.00 0.00 4.63
69 70 2.216046 ACGCGAAGTATCTACATCCGA 58.784 47.619 15.93 0.00 0.00 4.55
70 71 2.572243 GACGCGAAGTATCTACATCCG 58.428 52.381 15.93 0.00 0.00 4.18
71 72 2.664971 CGGACGCGAAGTATCTACATCC 60.665 54.545 15.93 3.08 0.00 3.51
72 73 2.222678 TCGGACGCGAAGTATCTACATC 59.777 50.000 15.93 0.00 0.00 3.06
73 74 2.216046 TCGGACGCGAAGTATCTACAT 58.784 47.619 15.93 0.00 0.00 2.29
74 75 1.655484 TCGGACGCGAAGTATCTACA 58.345 50.000 15.93 0.00 0.00 2.74
75 76 2.965477 ATCGGACGCGAAGTATCTAC 57.035 50.000 15.93 0.00 0.00 2.59
76 77 3.917988 TCTATCGGACGCGAAGTATCTA 58.082 45.455 15.93 0.00 0.00 1.98
77 78 2.737783 CTCTATCGGACGCGAAGTATCT 59.262 50.000 15.93 0.00 0.00 1.98
78 79 2.725452 GCTCTATCGGACGCGAAGTATC 60.725 54.545 15.93 0.00 0.00 2.24
79 80 1.197264 GCTCTATCGGACGCGAAGTAT 59.803 52.381 15.93 3.38 0.00 2.12
80 81 0.585357 GCTCTATCGGACGCGAAGTA 59.415 55.000 15.93 0.00 0.00 2.24
81 82 1.355916 GCTCTATCGGACGCGAAGT 59.644 57.895 15.93 0.00 0.00 3.01
82 83 0.930742 GTGCTCTATCGGACGCGAAG 60.931 60.000 15.93 3.07 0.00 3.79
83 84 1.063649 GTGCTCTATCGGACGCGAA 59.936 57.895 15.93 0.00 0.00 4.70
84 85 1.818363 AGTGCTCTATCGGACGCGA 60.818 57.895 15.93 0.00 0.00 5.87
85 86 1.655654 CAGTGCTCTATCGGACGCG 60.656 63.158 3.53 3.53 0.00 6.01
86 87 1.946650 GCAGTGCTCTATCGGACGC 60.947 63.158 8.18 0.00 0.00 5.19
87 88 0.945099 TAGCAGTGCTCTATCGGACG 59.055 55.000 23.64 0.00 40.44 4.79
88 89 3.502595 TGTATAGCAGTGCTCTATCGGAC 59.497 47.826 23.64 7.15 40.44 4.79
89 90 3.751518 TGTATAGCAGTGCTCTATCGGA 58.248 45.455 23.64 1.66 40.44 4.55
90 91 4.230657 GTTGTATAGCAGTGCTCTATCGG 58.769 47.826 23.64 0.00 40.44 4.18
91 92 4.230657 GGTTGTATAGCAGTGCTCTATCG 58.769 47.826 23.64 0.00 40.44 2.92
103 104 7.354257 TGTTTAAAAAGTGTCGGTTGTATAGC 58.646 34.615 0.00 0.00 0.00 2.97
111 112 6.639279 GTGCATATTGTTTAAAAAGTGTCGGT 59.361 34.615 0.00 0.00 0.00 4.69
161 162 5.938125 TGAGATGCCTTAGGAACAAAAGTAC 59.062 40.000 0.69 0.00 0.00 2.73
173 174 2.158856 TCTGCACCATGAGATGCCTTAG 60.159 50.000 12.27 5.51 41.33 2.18
186 188 4.701651 CCAGTCAATAATTTCTCTGCACCA 59.298 41.667 0.00 0.00 0.00 4.17
248 250 6.428159 GCAGATGTACCTCGAATATCCATTTT 59.572 38.462 0.00 0.00 0.00 1.82
260 262 1.589993 CGCAGGCAGATGTACCTCG 60.590 63.158 0.00 0.00 32.56 4.63
307 309 1.664659 AGACGAGGTCAACGATAGACG 59.335 52.381 0.00 0.00 40.51 4.18
314 316 1.080705 GGTGGAGACGAGGTCAACG 60.081 63.158 0.00 0.00 34.60 4.10
333 339 2.663334 CGTAGGAGTTCGCGATCTCATC 60.663 54.545 35.39 25.69 32.93 2.92
338 344 0.935898 TCTCGTAGGAGTTCGCGATC 59.064 55.000 10.88 9.88 41.26 3.69
341 347 2.190325 ATTTCTCGTAGGAGTTCGCG 57.810 50.000 11.97 0.00 41.26 5.87
357 363 6.316390 CCGTCTTCTTTCAAGCCATACTATTT 59.684 38.462 0.00 0.00 0.00 1.40
359 365 5.360591 CCGTCTTCTTTCAAGCCATACTAT 58.639 41.667 0.00 0.00 0.00 2.12
360 366 4.755411 CCGTCTTCTTTCAAGCCATACTA 58.245 43.478 0.00 0.00 0.00 1.82
375 381 1.796749 GACACGAGACGCCGTCTTC 60.797 63.158 22.17 11.01 43.53 2.87
382 388 1.073216 CCACATGAGACACGAGACGC 61.073 60.000 0.00 0.00 0.00 5.19
384 390 0.603569 ACCCACATGAGACACGAGAC 59.396 55.000 0.00 0.00 0.00 3.36
395 401 3.489908 CGAGACATAGACTGACCCACATG 60.490 52.174 0.00 0.00 0.00 3.21
412 418 2.476519 CGAGAAGAGTAAGGCACGAGAC 60.477 54.545 0.00 0.00 0.00 3.36
420 426 0.809385 TGCGGACGAGAAGAGTAAGG 59.191 55.000 0.00 0.00 0.00 2.69
436 442 3.185246 AGAGTGAAGATATGGGTTGCG 57.815 47.619 0.00 0.00 0.00 4.85
438 444 3.557595 GCGAAGAGTGAAGATATGGGTTG 59.442 47.826 0.00 0.00 0.00 3.77
460 466 0.179089 CAGTCATGAGCCCGAAGAGG 60.179 60.000 0.00 0.00 40.63 3.69
461 467 0.534412 ACAGTCATGAGCCCGAAGAG 59.466 55.000 0.00 0.00 0.00 2.85
462 468 0.532573 GACAGTCATGAGCCCGAAGA 59.467 55.000 0.00 0.00 0.00 2.87
463 469 0.247460 TGACAGTCATGAGCCCGAAG 59.753 55.000 0.00 0.00 0.00 3.79
464 470 0.684535 TTGACAGTCATGAGCCCGAA 59.315 50.000 3.45 0.00 0.00 4.30
465 471 0.037326 GTTGACAGTCATGAGCCCGA 60.037 55.000 3.45 0.00 0.00 5.14
466 472 1.354337 CGTTGACAGTCATGAGCCCG 61.354 60.000 3.45 0.00 0.00 6.13
467 473 0.037326 TCGTTGACAGTCATGAGCCC 60.037 55.000 3.45 0.00 0.00 5.19
474 480 1.414550 TCCCATGTTCGTTGACAGTCA 59.585 47.619 0.00 0.00 32.19 3.41
477 483 2.217750 TGTTCCCATGTTCGTTGACAG 58.782 47.619 0.00 0.00 32.19 3.51
478 484 2.333688 TGTTCCCATGTTCGTTGACA 57.666 45.000 0.00 0.00 0.00 3.58
485 491 4.918810 AGTCTTTGTTGTTCCCATGTTC 57.081 40.909 0.00 0.00 0.00 3.18
486 492 6.126409 TCTAAGTCTTTGTTGTTCCCATGTT 58.874 36.000 0.00 0.00 0.00 2.71
491 497 6.620089 GCGTATTCTAAGTCTTTGTTGTTCCC 60.620 42.308 0.00 0.00 0.00 3.97
502 508 5.720202 TGTTGTCATGCGTATTCTAAGTCT 58.280 37.500 0.00 0.00 0.00 3.24
511 517 6.252967 TGAAATCTTTGTTGTCATGCGTAT 57.747 33.333 0.00 0.00 0.00 3.06
512 518 5.334802 CCTGAAATCTTTGTTGTCATGCGTA 60.335 40.000 0.00 0.00 0.00 4.42
516 522 4.682860 GCACCTGAAATCTTTGTTGTCATG 59.317 41.667 0.00 0.00 0.00 3.07
558 580 7.118680 CCGGTACACAATCACTACACTTTTAAT 59.881 37.037 0.00 0.00 0.00 1.40
574 596 2.879002 TCGTTTGTACCGGTACACAA 57.121 45.000 40.21 31.58 44.81 3.33
591 613 3.569250 AAACCAACCGGATGATTTTCG 57.431 42.857 14.18 0.00 35.59 3.46
658 680 6.658849 ACTTGCAAGGGTTTTTAATCCTTTT 58.341 32.000 29.18 0.00 38.70 2.27
660 682 5.887214 ACTTGCAAGGGTTTTTAATCCTT 57.113 34.783 29.18 0.93 41.15 3.36
662 684 8.439993 TTTTAACTTGCAAGGGTTTTTAATCC 57.560 30.769 29.18 0.00 0.00 3.01
667 689 6.317642 GTGGATTTTAACTTGCAAGGGTTTTT 59.682 34.615 29.18 16.47 0.00 1.94
710 732 4.429505 TCTCTTGAGGAGGAATGGAAAGA 58.570 43.478 0.00 0.00 42.10 2.52
833 855 5.046591 TCCTCGCTCCTTTATTTCAGAAAGA 60.047 40.000 1.28 0.00 36.22 2.52
848 875 2.747446 GTCTAGATGAGATCCTCGCTCC 59.253 54.545 0.00 0.00 36.29 4.70
972 999 3.774702 GCCGGTGAAGACGCGAAC 61.775 66.667 15.93 6.52 0.00 3.95
1145 1178 0.730265 CTCAGAGCGAGTAGAAGCGT 59.270 55.000 0.00 0.00 36.94 5.07
1246 1279 1.830145 CCATAACTAGGGGCAGCGT 59.170 57.895 0.00 0.00 0.00 5.07
1261 1294 1.760192 GAGAGAAACCATGCTGCCAT 58.240 50.000 0.00 0.00 0.00 4.40
1265 1298 1.813513 AACCGAGAGAAACCATGCTG 58.186 50.000 0.00 0.00 0.00 4.41
1351 1384 0.107752 TGCGGCATCACATAGAAGCA 60.108 50.000 0.00 0.00 42.56 3.91
1356 1389 2.130395 CACTACTGCGGCATCACATAG 58.870 52.381 1.75 3.75 0.00 2.23
1358 1391 1.091771 GCACTACTGCGGCATCACAT 61.092 55.000 1.75 0.00 32.44 3.21
1382 1416 1.382522 CAACCGGATCCCATTGACAG 58.617 55.000 9.46 0.00 0.00 3.51
1385 1419 0.331278 AAGCAACCGGATCCCATTGA 59.669 50.000 21.50 0.00 0.00 2.57
1420 1454 2.409870 CCACGCCAAAGCCTCCATC 61.410 63.158 0.00 0.00 34.57 3.51
1441 1497 3.260740 CTCACTGCTAAAGCTCAAGGAG 58.739 50.000 13.23 13.23 42.66 3.69
1442 1498 2.613977 GCTCACTGCTAAAGCTCAAGGA 60.614 50.000 3.26 0.00 42.66 3.36
1443 1499 1.736681 GCTCACTGCTAAAGCTCAAGG 59.263 52.381 3.26 0.00 42.66 3.61
1444 1500 1.392853 CGCTCACTGCTAAAGCTCAAG 59.607 52.381 3.26 0.00 42.66 3.02
1445 1501 1.432514 CGCTCACTGCTAAAGCTCAA 58.567 50.000 3.26 0.00 42.66 3.02
1446 1502 0.390340 CCGCTCACTGCTAAAGCTCA 60.390 55.000 3.26 0.00 42.66 4.26
1447 1503 0.390472 ACCGCTCACTGCTAAAGCTC 60.390 55.000 3.26 0.00 42.66 4.09
1448 1504 0.035458 AACCGCTCACTGCTAAAGCT 59.965 50.000 3.26 0.00 42.66 3.74
1449 1505 0.166814 CAACCGCTCACTGCTAAAGC 59.833 55.000 0.00 0.00 40.11 3.51
1450 1506 1.728971 CTCAACCGCTCACTGCTAAAG 59.271 52.381 0.00 0.00 40.11 1.85
1451 1507 1.795768 CTCAACCGCTCACTGCTAAA 58.204 50.000 0.00 0.00 40.11 1.85
1452 1508 0.670546 GCTCAACCGCTCACTGCTAA 60.671 55.000 0.00 0.00 40.11 3.09
1453 1509 1.079819 GCTCAACCGCTCACTGCTA 60.080 57.895 0.00 0.00 40.11 3.49
1459 1515 2.778299 ACAAATTAGCTCAACCGCTCA 58.222 42.857 0.00 0.00 41.30 4.26
1597 1667 5.163519 ACAAGGGCATTGCATTCAATAGTAC 60.164 40.000 12.40 0.00 43.15 2.73
1598 1668 4.955450 ACAAGGGCATTGCATTCAATAGTA 59.045 37.500 12.40 0.00 43.15 1.82
1599 1669 3.770933 ACAAGGGCATTGCATTCAATAGT 59.229 39.130 12.40 0.00 43.15 2.12
1600 1670 4.116961 CACAAGGGCATTGCATTCAATAG 58.883 43.478 12.40 0.00 43.15 1.73
1601 1671 3.768215 TCACAAGGGCATTGCATTCAATA 59.232 39.130 12.40 0.00 43.15 1.90
1602 1672 2.568062 TCACAAGGGCATTGCATTCAAT 59.432 40.909 12.40 0.00 43.15 2.57
1603 1673 1.969208 TCACAAGGGCATTGCATTCAA 59.031 42.857 12.40 0.00 43.15 2.69
1760 1836 9.695526 TTACTTTCTACTGAGCATAAAACGTTA 57.304 29.630 0.00 0.00 0.00 3.18
1786 1862 6.660521 TGCCATTTCTCATCTCAATTTACAGT 59.339 34.615 0.00 0.00 0.00 3.55
1787 1863 6.971184 GTGCCATTTCTCATCTCAATTTACAG 59.029 38.462 0.00 0.00 0.00 2.74
1788 1864 6.403527 CGTGCCATTTCTCATCTCAATTTACA 60.404 38.462 0.00 0.00 0.00 2.41
1793 1978 2.357009 GCGTGCCATTTCTCATCTCAAT 59.643 45.455 0.00 0.00 0.00 2.57
1794 1979 1.739466 GCGTGCCATTTCTCATCTCAA 59.261 47.619 0.00 0.00 0.00 3.02
1833 2018 2.727429 ACCACTTCCCCAGTACCTTA 57.273 50.000 0.00 0.00 32.76 2.69
1845 2030 7.048512 AGCATAATACAAGGACTTACCACTTC 58.951 38.462 0.00 0.00 42.04 3.01
1860 2045 2.509548 ACTGGCCTTGGAGCATAATACA 59.490 45.455 3.32 0.00 0.00 2.29
1873 2059 4.948062 AAGGAAATAACCTACTGGCCTT 57.052 40.909 3.32 0.00 39.62 4.35
1901 2087 5.695851 TTCTGCAGAAATGGAAAGAAGAC 57.304 39.130 26.61 0.00 0.00 3.01
1902 2088 6.713762 TTTTCTGCAGAAATGGAAAGAAGA 57.286 33.333 35.66 18.22 42.83 2.87
1903 2089 7.958053 AATTTTCTGCAGAAATGGAAAGAAG 57.042 32.000 35.66 0.00 42.83 2.85
1904 2090 8.420222 TGTAATTTTCTGCAGAAATGGAAAGAA 58.580 29.630 35.66 21.83 42.83 2.52
1961 2147 8.514330 ACGAAATTATATGCCTAAGGTTTTGA 57.486 30.769 0.00 0.00 0.00 2.69
1963 2149 9.623000 AGTACGAAATTATATGCCTAAGGTTTT 57.377 29.630 0.00 0.00 0.00 2.43
1986 2172 9.653287 CAGAAACATCAGAATTACCAAGTAGTA 57.347 33.333 0.00 0.00 0.00 1.82
2047 2235 5.964477 TCCATCCTAAGGTGACAGAATAAGT 59.036 40.000 0.00 0.00 0.00 2.24
2098 2286 5.559770 TCAATGGTCAAGAGCACATCTTTA 58.440 37.500 3.85 0.00 46.49 1.85
2125 2313 7.922811 CAGATGGAAGAAATAGGTTTATTTGCC 59.077 37.037 0.00 0.00 39.10 4.52
2211 2399 1.134521 TGTGTGAAGTTTGCTCGTCCT 60.135 47.619 0.00 0.00 0.00 3.85
2217 2405 6.127758 TGACATTAAAGTGTGTGAAGTTTGCT 60.128 34.615 0.00 0.00 31.16 3.91
2302 2490 5.723672 ACCATACGAATATCGAAGGACAT 57.276 39.130 6.78 0.00 43.74 3.06
2358 2546 3.398954 TGCAAAAGTCACAACTTCGAC 57.601 42.857 0.00 0.00 45.07 4.20
2505 2694 9.545105 TCACACCGTAATAAAAAGACTAAAAGA 57.455 29.630 0.00 0.00 0.00 2.52
2532 2721 7.033791 AGAAAATTCACAATCACAGCATCATC 58.966 34.615 0.00 0.00 0.00 2.92
2743 2933 5.485209 AAACCAGTACTTCTGAACCTAGG 57.515 43.478 7.41 7.41 46.27 3.02
2812 3005 5.531287 ACAGCTTAGAACCAAAAAGTACTGG 59.469 40.000 0.00 0.00 38.77 4.00
2813 3006 6.619801 ACAGCTTAGAACCAAAAAGTACTG 57.380 37.500 0.00 0.00 0.00 2.74
2815 3008 9.394477 CAATTACAGCTTAGAACCAAAAAGTAC 57.606 33.333 0.00 0.00 0.00 2.73
2817 3010 7.069455 ACCAATTACAGCTTAGAACCAAAAAGT 59.931 33.333 0.00 0.00 0.00 2.66
2818 3011 7.433680 ACCAATTACAGCTTAGAACCAAAAAG 58.566 34.615 0.00 0.00 0.00 2.27
2819 3012 7.354751 ACCAATTACAGCTTAGAACCAAAAA 57.645 32.000 0.00 0.00 0.00 1.94
2820 3013 6.969993 ACCAATTACAGCTTAGAACCAAAA 57.030 33.333 0.00 0.00 0.00 2.44
2821 3014 6.775629 AGAACCAATTACAGCTTAGAACCAAA 59.224 34.615 0.00 0.00 0.00 3.28
2822 3015 6.303839 AGAACCAATTACAGCTTAGAACCAA 58.696 36.000 0.00 0.00 0.00 3.67
2823 3016 5.876357 AGAACCAATTACAGCTTAGAACCA 58.124 37.500 0.00 0.00 0.00 3.67
2824 3017 7.412672 CGTTAGAACCAATTACAGCTTAGAACC 60.413 40.741 0.00 0.00 0.00 3.62
2825 3018 7.117379 ACGTTAGAACCAATTACAGCTTAGAAC 59.883 37.037 0.00 0.00 0.00 3.01
2826 3019 7.156673 ACGTTAGAACCAATTACAGCTTAGAA 58.843 34.615 0.00 0.00 0.00 2.10
2827 3020 6.694447 ACGTTAGAACCAATTACAGCTTAGA 58.306 36.000 0.00 0.00 0.00 2.10
2828 3021 6.035758 GGACGTTAGAACCAATTACAGCTTAG 59.964 42.308 0.00 0.00 0.00 2.18
2829 3022 5.870978 GGACGTTAGAACCAATTACAGCTTA 59.129 40.000 0.00 0.00 0.00 3.09
2830 3023 4.694037 GGACGTTAGAACCAATTACAGCTT 59.306 41.667 0.00 0.00 0.00 3.74
2831 3024 4.020485 AGGACGTTAGAACCAATTACAGCT 60.020 41.667 0.00 0.00 0.00 4.24
2832 3025 4.251268 AGGACGTTAGAACCAATTACAGC 58.749 43.478 0.00 0.00 0.00 4.40
2833 3026 5.121768 CCAAGGACGTTAGAACCAATTACAG 59.878 44.000 0.00 0.00 0.00 2.74
2834 3027 4.998672 CCAAGGACGTTAGAACCAATTACA 59.001 41.667 0.00 0.00 0.00 2.41
2835 3028 4.999311 ACCAAGGACGTTAGAACCAATTAC 59.001 41.667 0.00 0.00 0.00 1.89
2836 3029 5.231702 ACCAAGGACGTTAGAACCAATTA 57.768 39.130 0.00 0.00 0.00 1.40
2837 3030 4.094830 ACCAAGGACGTTAGAACCAATT 57.905 40.909 0.00 0.00 0.00 2.32
2838 3031 3.782656 ACCAAGGACGTTAGAACCAAT 57.217 42.857 0.00 0.00 0.00 3.16
2839 3032 3.564053 AACCAAGGACGTTAGAACCAA 57.436 42.857 0.00 0.00 0.00 3.67
2840 3033 3.642848 AGTAACCAAGGACGTTAGAACCA 59.357 43.478 0.00 0.00 0.00 3.67
2841 3034 3.992427 CAGTAACCAAGGACGTTAGAACC 59.008 47.826 0.00 0.00 0.00 3.62
2842 3035 3.992427 CCAGTAACCAAGGACGTTAGAAC 59.008 47.826 0.00 0.00 0.00 3.01
2843 3036 3.642848 ACCAGTAACCAAGGACGTTAGAA 59.357 43.478 0.00 0.00 0.00 2.10
2844 3037 3.233507 ACCAGTAACCAAGGACGTTAGA 58.766 45.455 0.00 0.00 0.00 2.10
2845 3038 3.006110 TGACCAGTAACCAAGGACGTTAG 59.994 47.826 0.00 0.00 0.00 2.34
2846 3039 2.964464 TGACCAGTAACCAAGGACGTTA 59.036 45.455 0.00 0.00 0.00 3.18
2847 3040 1.764134 TGACCAGTAACCAAGGACGTT 59.236 47.619 0.00 0.00 0.00 3.99
2848 3041 1.069668 GTGACCAGTAACCAAGGACGT 59.930 52.381 0.00 0.00 0.00 4.34
2849 3042 1.069513 TGTGACCAGTAACCAAGGACG 59.930 52.381 0.00 0.00 0.00 4.79
2850 3043 2.922740 TGTGACCAGTAACCAAGGAC 57.077 50.000 0.00 0.00 0.00 3.85
2851 3044 2.486548 GCTTGTGACCAGTAACCAAGGA 60.487 50.000 0.00 0.00 34.51 3.36
2852 3045 1.880027 GCTTGTGACCAGTAACCAAGG 59.120 52.381 0.00 0.00 34.51 3.61
2853 3046 2.571212 TGCTTGTGACCAGTAACCAAG 58.429 47.619 0.00 0.00 36.47 3.61
2854 3047 2.719531 TGCTTGTGACCAGTAACCAA 57.280 45.000 0.00 0.00 0.00 3.67
2855 3048 2.171659 TCTTGCTTGTGACCAGTAACCA 59.828 45.455 0.00 0.00 0.00 3.67
2856 3049 2.808543 CTCTTGCTTGTGACCAGTAACC 59.191 50.000 0.00 0.00 0.00 2.85
2857 3050 2.808543 CCTCTTGCTTGTGACCAGTAAC 59.191 50.000 0.00 0.00 0.00 2.50
2858 3051 2.703536 TCCTCTTGCTTGTGACCAGTAA 59.296 45.455 0.00 0.00 0.00 2.24
2859 3052 2.325484 TCCTCTTGCTTGTGACCAGTA 58.675 47.619 0.00 0.00 0.00 2.74
2860 3053 1.131638 TCCTCTTGCTTGTGACCAGT 58.868 50.000 0.00 0.00 0.00 4.00
2861 3054 2.486472 ATCCTCTTGCTTGTGACCAG 57.514 50.000 0.00 0.00 0.00 4.00
2862 3055 2.158623 ACAATCCTCTTGCTTGTGACCA 60.159 45.455 0.00 0.00 32.16 4.02
2863 3056 2.508526 ACAATCCTCTTGCTTGTGACC 58.491 47.619 0.00 0.00 32.16 4.02
2864 3057 3.304928 CCAACAATCCTCTTGCTTGTGAC 60.305 47.826 0.00 0.00 33.60 3.67
2865 3058 2.886523 CCAACAATCCTCTTGCTTGTGA 59.113 45.455 0.00 0.00 33.60 3.58
2866 3059 2.886523 TCCAACAATCCTCTTGCTTGTG 59.113 45.455 0.00 0.00 33.60 3.33
2867 3060 3.228188 TCCAACAATCCTCTTGCTTGT 57.772 42.857 0.00 0.00 34.71 3.16
2868 3061 5.416952 AGTTATCCAACAATCCTCTTGCTTG 59.583 40.000 0.00 0.00 37.10 4.01
2869 3062 5.574188 AGTTATCCAACAATCCTCTTGCTT 58.426 37.500 0.00 0.00 37.10 3.91
3003 3204 6.420306 CGATATTGACAATCTGTGAGAGGAAG 59.580 42.308 3.36 0.00 0.00 3.46
3026 3227 2.556257 TGTACAAGCACTTTTGAGCGA 58.444 42.857 0.00 0.00 40.96 4.93
3028 3229 5.339990 TCTTTTGTACAAGCACTTTTGAGC 58.660 37.500 8.56 0.00 36.25 4.26
3100 3301 9.965824 AAACACTGTTATTTGATGAAAAGGTAG 57.034 29.630 0.00 0.00 0.00 3.18
3156 3357 4.022416 TGCAGAGCAACGGAAACATTAAAT 60.022 37.500 0.00 0.00 34.76 1.40
3174 3375 1.276421 GCTAAGGGAGACAGTTGCAGA 59.724 52.381 0.00 0.00 0.00 4.26
3187 3389 7.223387 GCAAATCTGTTGAAATATTGCTAAGGG 59.777 37.037 0.00 0.00 38.79 3.95
3477 3681 6.742109 TCGGAAATAGAAGAATTAGGTACCG 58.258 40.000 6.18 0.00 36.27 4.02
3537 3776 7.672660 TCATGAGGTTTACTAGGAACTGTTAGA 59.327 37.037 10.03 3.31 41.52 2.10
3594 3833 9.658475 CGACTCTTCTTTCTAATAGACACATAG 57.342 37.037 0.00 0.00 0.00 2.23
3720 3959 6.485313 TCCTGACATTCAACAGAAATACGTTT 59.515 34.615 0.00 0.00 36.38 3.60
3757 3996 7.237209 ACTACCCGAAGAACTACTATTTTGT 57.763 36.000 0.00 0.00 0.00 2.83
3766 4005 3.624777 CCCTGTACTACCCGAAGAACTA 58.375 50.000 0.00 0.00 0.00 2.24
3925 4164 2.558359 AGAAGGACCTTTGGATTTTGCG 59.442 45.455 8.49 0.00 0.00 4.85
3978 4217 3.048600 CTCCCATCCCCAAGATCAGTTA 58.951 50.000 0.00 0.00 30.59 2.24
4130 4369 4.038642 TGAAAATGCCCTGTTAAGTGGTTC 59.961 41.667 0.00 0.00 0.00 3.62
4160 4399 2.457080 GGAACTTTCCCTTCTCGCG 58.543 57.895 0.00 0.00 41.62 5.87
4195 4434 3.261580 CCATACTTTCAGTGATGCGTCA 58.738 45.455 3.97 3.97 0.00 4.35
4368 4611 9.073475 TCAATGGCATAGTAACTAACAAAGTTT 57.927 29.630 0.00 0.00 46.61 2.66
4429 4674 7.380333 GCAGTACACAACCAATTTACCTAAAAC 59.620 37.037 0.00 0.00 0.00 2.43
4431 4676 6.773685 AGCAGTACACAACCAATTTACCTAAA 59.226 34.615 0.00 0.00 0.00 1.85
4432 4677 6.300703 AGCAGTACACAACCAATTTACCTAA 58.699 36.000 0.00 0.00 0.00 2.69
4433 4678 5.871834 AGCAGTACACAACCAATTTACCTA 58.128 37.500 0.00 0.00 0.00 3.08
4612 4857 5.067153 AGTTCATATGAAGAGACAGGAGTCG 59.933 44.000 18.47 0.00 41.18 4.18
4624 4869 4.035324 CAGCTGGCTTGAGTTCATATGAAG 59.965 45.833 18.47 7.63 34.27 3.02
4682 4927 3.522750 AGATGGTTTCTGCAGATCCTCTT 59.477 43.478 27.32 17.55 31.79 2.85
4688 4962 5.796424 ACAAAAAGATGGTTTCTGCAGAT 57.204 34.783 19.04 0.85 33.93 2.90
4708 4982 8.205512 TCAGTACCACATAACTTTTGTCTTACA 58.794 33.333 0.00 0.00 0.00 2.41
4709 4983 8.597662 TCAGTACCACATAACTTTTGTCTTAC 57.402 34.615 0.00 0.00 0.00 2.34
4710 4984 9.616156 TTTCAGTACCACATAACTTTTGTCTTA 57.384 29.630 0.00 0.00 0.00 2.10
4751 5027 7.784073 AGATATACATGTCTATCCTAGCAGCAT 59.216 37.037 21.43 3.80 0.00 3.79
4962 5239 7.009174 TCGAGCTCTTTTGTTTTGTTGATTTTC 59.991 33.333 12.85 0.00 0.00 2.29
4983 5260 5.429957 AGATATCCAAAGCAAAATCGAGC 57.570 39.130 0.00 0.00 0.00 5.03
4989 5266 4.771577 TCTGCCAAGATATCCAAAGCAAAA 59.228 37.500 0.00 0.00 0.00 2.44
4997 5274 4.413189 TCCAGAATTCTGCCAAGATATCCA 59.587 41.667 27.01 0.00 42.47 3.41
5001 5278 5.698741 TTCTCCAGAATTCTGCCAAGATA 57.301 39.130 27.01 15.80 42.47 1.98
5088 5365 6.986904 ATTCTCCTATCTGAAACGTTTTCC 57.013 37.500 15.89 3.77 0.00 3.13
5103 5380 7.778853 GTGATAATCGATAGGGGTATTCTCCTA 59.221 40.741 0.00 0.00 39.64 2.94
5114 5391 6.369629 AGGATCCTAGTGATAATCGATAGGG 58.630 44.000 14.27 0.00 34.89 3.53
5140 5425 4.402851 TGCCCACAGAATCTGCAC 57.597 55.556 10.62 0.00 34.37 4.57
5154 5439 2.440409 TCAAGATTCTGGAAAGCTGCC 58.560 47.619 0.00 0.00 0.00 4.85
5182 5467 0.097150 GGTCTTTTCGCGCAGGATTC 59.903 55.000 8.75 0.00 0.00 2.52
5193 5478 0.969149 CCTTTGGCCCAGGTCTTTTC 59.031 55.000 9.60 0.00 0.00 2.29
5212 5497 0.318614 CACAACGTTTGGGGACATGC 60.319 55.000 0.00 0.00 42.32 4.06
5216 5501 1.679153 ACAATCACAACGTTTGGGGAC 59.321 47.619 0.00 0.00 33.95 4.46
5402 5701 1.139654 TGTGCAGCAGGGAGATCATAC 59.860 52.381 0.00 0.00 0.00 2.39
5412 5711 2.336945 TATCCAAGATGTGCAGCAGG 57.663 50.000 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.