Multiple sequence alignment - TraesCS5D01G424400

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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 TraesCS5D01G424400 chr5D 100.000 5236 0 0 1 5236 483712787 483707552 0.000000e+00 9670
1 TraesCS5D01G424400 chr5A 95.513 2095 49 25 2294 4374 605225915 605223852 0.000000e+00 3306
2 TraesCS5D01G424400 chr5A 91.790 1620 88 27 2 1598 605228321 605226724 0.000000e+00 2213
3 TraesCS5D01G424400 chr5A 88.571 735 49 17 1600 2301 605226685 605225953 0.000000e+00 859
4 TraesCS5D01G424400 chr5A 83.915 889 86 32 4369 5236 605223039 605222187 0.000000e+00 797
5 TraesCS5D01G424400 chr5B 91.475 2041 109 34 2292 4310 594915377 594913380 0.000000e+00 2745
6 TraesCS5D01G424400 chr5B 92.698 1616 84 14 1 1598 594917815 594916216 0.000000e+00 2300
7 TraesCS5D01G424400 chr5B 89.598 423 35 7 1600 2015 594916177 594915757 3.590000e-146 529
8 TraesCS5D01G424400 chr5B 83.768 345 26 13 1987 2301 594915756 594915412 3.060000e-77 300
9 TraesCS5D01G424400 chr5B 85.714 280 30 7 4958 5236 594912687 594912417 2.390000e-73 287
10 TraesCS5D01G424400 chr5B 96.970 66 2 0 4309 4374 594913337 594913272 1.540000e-20 111
11 TraesCS5D01G424400 chr4D 82.373 295 44 6 4666 4956 399222068 399221778 3.130000e-62 250
12 TraesCS5D01G424400 chr6D 82.156 269 42 5 4676 4940 3599533 3599799 5.280000e-55 226
13 TraesCS5D01G424400 chr3A 86.598 194 25 1 4761 4954 567569076 567569268 4.110000e-51 213
14 TraesCS5D01G424400 chrUn 80.913 241 42 4 4671 4910 40740814 40740577 2.490000e-43 187
15 TraesCS5D01G424400 chrUn 81.466 232 39 4 4671 4901 40747091 40747319 2.490000e-43 187
16 TraesCS5D01G424400 chrUn 80.913 241 42 4 4671 4910 303400368 303400131 2.490000e-43 187
17 TraesCS5D01G424400 chr7D 79.487 273 49 7 4668 4938 554414445 554414178 2.490000e-43 187
18 TraesCS5D01G424400 chr6A 80.159 252 47 3 4663 4913 28893068 28893317 8.950000e-43 185
19 TraesCS5D01G424400 chr7B 79.771 262 43 6 4705 4959 134627877 134628135 1.160000e-41 182


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 TraesCS5D01G424400 chr5D 483707552 483712787 5235 True 9670.000000 9670 100.000000 1 5236 1 chr5D.!!$R1 5235
1 TraesCS5D01G424400 chr5A 605222187 605228321 6134 True 1793.750000 3306 89.947250 2 5236 4 chr5A.!!$R1 5234
2 TraesCS5D01G424400 chr5B 594912417 594917815 5398 True 1045.333333 2745 90.037167 1 5236 6 chr5B.!!$R1 5235

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
636 637 0.597637 GGACGTACATGCCGATGAGG 60.598 60.000 11.82 0.00 44.97 3.86 F
949 958 1.068588 TGGACTTGAACTCTCACGTGG 59.931 52.381 17.00 6.71 34.39 4.94 F
1464 1485 0.108804 TCCTAGAGCAACGCCTTTCG 60.109 55.000 0.00 0.00 45.38 3.46 F
1937 2008 0.036294 AAAGGAGAGGTAGCGGTTGC 60.036 55.000 0.00 0.00 43.24 4.17 F
2754 2942 0.610687 AGGAAGGAGCAGAAAGGTCG 59.389 55.000 0.00 0.00 45.66 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1445 1466 0.108804 CGAAAGGCGTTGCTCTAGGA 60.109 55.000 0.0 0.0 34.64 2.94 R
1914 1985 0.179097 CCGCTACCTCTCCTTTGCTC 60.179 60.000 0.0 0.0 0.00 4.26 R
2282 2422 2.130395 GAAGTGCAAGCAAAAGAAGGC 58.870 47.619 0.0 0.0 0.00 4.35 R
3905 4096 3.118261 TCGAGCTGAATAAAGCCTGGAAT 60.118 43.478 0.0 0.0 44.68 3.01 R
4710 5812 0.194080 TAGGGGTAGGTTGGGTGTGT 59.806 55.000 0.0 0.0 0.00 3.72 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
44 45 2.840066 CGGCGACCTCTGGCTCTAG 61.840 68.421 0.00 0.00 0.00 2.43
81 82 2.203337 GTGTGGAGCTGCAACCCA 60.203 61.111 10.44 0.24 0.00 4.51
95 96 1.071385 CAACCCAGAGAGCAAGTCAGT 59.929 52.381 0.00 0.00 0.00 3.41
636 637 0.597637 GGACGTACATGCCGATGAGG 60.598 60.000 11.82 0.00 44.97 3.86
926 935 3.243401 GGAAACGAGGCAGAAAATTGTGT 60.243 43.478 0.00 0.00 0.00 3.72
936 945 5.634859 GGCAGAAAATTGTGTTATGGACTTG 59.365 40.000 0.00 0.00 0.00 3.16
949 958 1.068588 TGGACTTGAACTCTCACGTGG 59.931 52.381 17.00 6.71 34.39 4.94
969 978 2.528743 GCTCACGTGCCATCCATCG 61.529 63.158 11.67 0.00 0.00 3.84
988 997 4.986875 TCGTTCTATCGTTCTATCTCGG 57.013 45.455 0.00 0.00 0.00 4.63
1336 1357 1.136085 CAACGCCATTGTAAGTCACCG 60.136 52.381 0.00 0.00 33.20 4.94
1347 1368 1.800805 AAGTCACCGATTGAGCACAG 58.199 50.000 0.00 0.00 33.71 3.66
1359 1380 3.050275 GCACAGACAGAACCCGCC 61.050 66.667 0.00 0.00 0.00 6.13
1391 1412 1.523758 AAAATGCTCCTGTCCGTGAC 58.476 50.000 0.00 0.00 0.00 3.67
1409 1430 2.568696 ACAAGGATGTCATCTCGTCG 57.431 50.000 12.54 0.00 33.41 5.12
1442 1463 2.419057 CCGGGGGCAATGAATTCTC 58.581 57.895 7.05 0.00 0.00 2.87
1443 1464 1.447317 CCGGGGGCAATGAATTCTCG 61.447 60.000 7.05 0.00 0.00 4.04
1444 1465 1.735973 GGGGGCAATGAATTCTCGC 59.264 57.895 7.05 6.41 0.00 5.03
1445 1466 0.753111 GGGGGCAATGAATTCTCGCT 60.753 55.000 7.05 0.00 0.00 4.93
1447 1468 0.665298 GGGCAATGAATTCTCGCTCC 59.335 55.000 7.05 6.56 0.00 4.70
1448 1469 1.673168 GGCAATGAATTCTCGCTCCT 58.327 50.000 7.05 0.00 0.00 3.69
1449 1470 2.485479 GGGCAATGAATTCTCGCTCCTA 60.485 50.000 7.05 0.00 0.00 2.94
1450 1471 2.805099 GGCAATGAATTCTCGCTCCTAG 59.195 50.000 7.05 0.00 0.00 3.02
1451 1472 3.493350 GGCAATGAATTCTCGCTCCTAGA 60.493 47.826 7.05 0.00 0.00 2.43
1452 1473 3.740321 GCAATGAATTCTCGCTCCTAGAG 59.260 47.826 7.05 0.00 37.09 2.43
1464 1485 0.108804 TCCTAGAGCAACGCCTTTCG 60.109 55.000 0.00 0.00 45.38 3.46
1468 1489 2.380084 AGAGCAACGCCTTTCGATTA 57.620 45.000 0.00 0.00 41.67 1.75
1479 1500 2.673368 CCTTTCGATTAGTGCACTGGTC 59.327 50.000 29.57 22.92 0.00 4.02
1480 1501 3.325870 CTTTCGATTAGTGCACTGGTCA 58.674 45.455 29.57 6.24 0.00 4.02
1484 1505 3.056179 TCGATTAGTGCACTGGTCATTCA 60.056 43.478 29.57 3.27 0.00 2.57
1487 1508 1.242076 AGTGCACTGGTCATTCAAGC 58.758 50.000 20.97 0.00 0.00 4.01
1529 1558 2.733026 GGCAATGTCACTGCATTTGAAC 59.267 45.455 8.74 0.00 41.78 3.18
1554 1583 1.062587 CGATGTTTTGCCGCTTAGAGG 59.937 52.381 0.00 0.00 0.00 3.69
1557 1586 1.202710 TGTTTTGCCGCTTAGAGGTGA 60.203 47.619 3.59 0.00 0.00 4.02
1559 1588 3.267483 GTTTTGCCGCTTAGAGGTGATA 58.733 45.455 3.59 0.00 0.00 2.15
1560 1589 2.596904 TTGCCGCTTAGAGGTGATAC 57.403 50.000 3.59 0.00 0.00 2.24
1561 1590 1.776662 TGCCGCTTAGAGGTGATACT 58.223 50.000 3.59 0.00 0.00 2.12
1565 1594 2.688446 CCGCTTAGAGGTGATACTGTCA 59.312 50.000 0.00 0.00 0.00 3.58
1587 1616 9.921637 TGTCAAAAGGTTGAAATGGTTAATATC 57.078 29.630 0.00 0.00 45.29 1.63
1663 1730 5.357878 TGCTTCATGGAATGGTTTCTATGTC 59.642 40.000 10.55 4.48 45.83 3.06
1668 1735 2.540101 GGAATGGTTTCTATGTCTCGCG 59.460 50.000 0.00 0.00 32.16 5.87
1671 1738 3.520290 TGGTTTCTATGTCTCGCGATT 57.480 42.857 10.36 0.00 0.00 3.34
1672 1739 3.857052 TGGTTTCTATGTCTCGCGATTT 58.143 40.909 10.36 0.00 0.00 2.17
1703 1774 5.233902 GCAATTGGCATGTATTTATCGCAAA 59.766 36.000 7.72 0.00 43.97 3.68
1797 1868 1.689273 TGCACCATAAACCCAAACACC 59.311 47.619 0.00 0.00 0.00 4.16
1839 1910 3.175240 CGCTTGGACGTGCTCTCG 61.175 66.667 8.99 4.88 0.00 4.04
1872 1943 4.052229 AAGCAGACGGTCCCGACG 62.052 66.667 13.54 4.45 42.83 5.12
1914 1985 2.815647 GGCCTCGTCAAAGGAGCG 60.816 66.667 0.00 0.00 38.87 5.03
1930 2001 0.820871 AGCGAGCAAAGGAGAGGTAG 59.179 55.000 0.00 0.00 0.00 3.18
1937 2008 0.036294 AAAGGAGAGGTAGCGGTTGC 60.036 55.000 0.00 0.00 43.24 4.17
1952 2024 2.726681 CGGTTGCCTTCGTTTTATTCCG 60.727 50.000 0.00 0.00 0.00 4.30
1955 2027 1.735571 TGCCTTCGTTTTATTCCGAGC 59.264 47.619 0.00 0.00 34.16 5.03
1985 2057 6.303970 CACAGAACATGTCGATGATTGTTTTC 59.696 38.462 0.00 0.00 41.41 2.29
2085 2187 6.550108 GTGAAGTGGATTCTATACTCCAGGTA 59.450 42.308 0.00 0.00 42.10 3.08
2100 2202 3.882888 TCCAGGTAAGTTTGCTGACTTTG 59.117 43.478 9.91 4.12 40.24 2.77
2101 2203 3.632145 CCAGGTAAGTTTGCTGACTTTGT 59.368 43.478 9.91 0.00 40.24 2.83
2102 2204 4.819630 CCAGGTAAGTTTGCTGACTTTGTA 59.180 41.667 9.91 0.00 40.24 2.41
2104 2206 5.527582 CAGGTAAGTTTGCTGACTTTGTAGT 59.472 40.000 9.91 0.00 40.24 2.73
2105 2207 6.704493 CAGGTAAGTTTGCTGACTTTGTAGTA 59.296 38.462 9.91 0.00 40.24 1.82
2131 2233 5.927281 ATATTTGTGCTCTCAGGCATTTT 57.073 34.783 0.00 0.00 44.34 1.82
2135 2237 2.555325 TGTGCTCTCAGGCATTTTTCAG 59.445 45.455 0.00 0.00 44.34 3.02
2169 2306 3.441222 CCATGTTTCTCAACTGCTGCATA 59.559 43.478 1.31 0.00 33.58 3.14
2241 2378 7.510675 TTCTCCAATAGATGTTCCTTTACCT 57.489 36.000 0.00 0.00 33.05 3.08
2242 2379 7.510675 TCTCCAATAGATGTTCCTTTACCTT 57.489 36.000 0.00 0.00 0.00 3.50
2243 2380 7.565680 TCTCCAATAGATGTTCCTTTACCTTC 58.434 38.462 0.00 0.00 0.00 3.46
2244 2381 7.182026 TCTCCAATAGATGTTCCTTTACCTTCA 59.818 37.037 0.00 0.00 0.00 3.02
2245 2382 7.338710 TCCAATAGATGTTCCTTTACCTTCAG 58.661 38.462 0.00 0.00 0.00 3.02
2246 2383 7.037586 TCCAATAGATGTTCCTTTACCTTCAGT 60.038 37.037 0.00 0.00 0.00 3.41
2247 2384 7.611855 CCAATAGATGTTCCTTTACCTTCAGTT 59.388 37.037 0.00 0.00 0.00 3.16
2248 2385 8.669243 CAATAGATGTTCCTTTACCTTCAGTTC 58.331 37.037 0.00 0.00 0.00 3.01
2249 2386 6.187727 AGATGTTCCTTTACCTTCAGTTCA 57.812 37.500 0.00 0.00 0.00 3.18
2251 2388 4.134563 TGTTCCTTTACCTTCAGTTCAGC 58.865 43.478 0.00 0.00 0.00 4.26
2252 2389 3.040147 TCCTTTACCTTCAGTTCAGCG 57.960 47.619 0.00 0.00 0.00 5.18
2260 2400 2.548067 CCTTCAGTTCAGCGGTTGTACT 60.548 50.000 0.00 0.00 37.85 2.73
2266 2406 4.451096 CAGTTCAGCGGTTGTACTATGTTT 59.549 41.667 3.99 0.00 35.50 2.83
2275 2415 5.410132 CGGTTGTACTATGTTTGAACATCCA 59.590 40.000 12.28 4.15 46.10 3.41
2282 2422 9.507280 GTACTATGTTTGAACATCCAATGATTG 57.493 33.333 12.28 0.00 46.10 2.67
2285 2425 4.283978 TGTTTGAACATCCAATGATTGCCT 59.716 37.500 0.00 0.00 33.17 4.75
2287 2427 4.724074 TGAACATCCAATGATTGCCTTC 57.276 40.909 0.00 0.00 0.00 3.46
2292 2432 5.484715 ACATCCAATGATTGCCTTCTTTTG 58.515 37.500 0.00 0.00 0.00 2.44
2295 2435 4.040706 TCCAATGATTGCCTTCTTTTGCTT 59.959 37.500 0.00 0.00 0.00 3.91
2301 2441 1.481772 TGCCTTCTTTTGCTTGCACTT 59.518 42.857 0.00 0.00 0.00 3.16
2302 2442 2.130395 GCCTTCTTTTGCTTGCACTTC 58.870 47.619 0.00 0.00 0.00 3.01
2303 2443 2.747436 CCTTCTTTTGCTTGCACTTCC 58.253 47.619 0.00 0.00 0.00 3.46
2337 2520 6.959639 ACATAATAGGCTATTGGTTGTTGG 57.040 37.500 26.16 10.80 0.00 3.77
2350 2533 3.141272 TGGTTGTTGGGGTTCTAAGGATT 59.859 43.478 0.00 0.00 0.00 3.01
2351 2534 3.509967 GGTTGTTGGGGTTCTAAGGATTG 59.490 47.826 0.00 0.00 0.00 2.67
2528 2711 5.573337 ATGAAAAGTTCTGCTATCCTTGC 57.427 39.130 0.00 0.00 0.00 4.01
2529 2712 4.655963 TGAAAAGTTCTGCTATCCTTGCT 58.344 39.130 0.00 0.00 0.00 3.91
2531 2714 6.237901 TGAAAAGTTCTGCTATCCTTGCTTA 58.762 36.000 0.00 0.00 0.00 3.09
2532 2715 6.372659 TGAAAAGTTCTGCTATCCTTGCTTAG 59.627 38.462 0.00 0.00 0.00 2.18
2533 2716 5.428184 AAGTTCTGCTATCCTTGCTTAGT 57.572 39.130 0.00 0.00 0.00 2.24
2534 2717 6.546428 AAGTTCTGCTATCCTTGCTTAGTA 57.454 37.500 0.00 0.00 0.00 1.82
2535 2718 6.155475 AGTTCTGCTATCCTTGCTTAGTAG 57.845 41.667 0.00 0.00 31.67 2.57
2586 2772 8.918202 TGTTCATATCTTAACCAAGACAGTTT 57.082 30.769 0.00 0.00 43.50 2.66
2588 2774 9.612620 GTTCATATCTTAACCAAGACAGTTTTG 57.387 33.333 0.00 0.00 43.50 2.44
2589 2775 8.918202 TCATATCTTAACCAAGACAGTTTTGT 57.082 30.769 3.29 0.00 43.50 2.83
2663 2849 8.762481 AAACTAAGGATCCACAAGTAAAAGTT 57.238 30.769 15.82 6.66 0.00 2.66
2673 2859 9.636789 ATCCACAAGTAAAAGTTAAGGTAAGTT 57.363 29.630 0.00 0.00 32.93 2.66
2729 2917 7.201522 GGTTTTGTTCTTGATTCCAGTTTTCAC 60.202 37.037 0.00 0.00 0.00 3.18
2745 2933 2.604912 TCACTACTCAGGAAGGAGCA 57.395 50.000 0.00 0.00 39.94 4.26
2754 2942 0.610687 AGGAAGGAGCAGAAAGGTCG 59.389 55.000 0.00 0.00 45.66 4.79
2757 2945 2.436824 GGAGCAGAAAGGTCGGGC 60.437 66.667 0.00 0.00 45.66 6.13
3190 3379 2.124122 GGCAACTTGGTAAAAGCAACG 58.876 47.619 0.00 0.00 31.65 4.10
3254 3443 3.260740 CAGGTGAATCTCTTCTGCTGTC 58.739 50.000 0.00 0.00 32.29 3.51
3276 3465 5.523916 GTCAAGACACTTTGTTCTTCAGCTA 59.476 40.000 0.00 0.00 0.00 3.32
3353 3544 6.438741 TGGACCATTATTGCAGGTTTTATTCA 59.561 34.615 0.00 0.00 35.36 2.57
3618 3809 9.439500 GTACTGTACCATTATTTTCTGGTGTTA 57.561 33.333 6.70 0.00 45.28 2.41
3905 4096 5.068329 TGTGACAACAATACCATGCAAGAAA 59.932 36.000 0.00 0.00 31.82 2.52
3922 4113 5.809051 GCAAGAAATTCCAGGCTTTATTCAG 59.191 40.000 0.00 0.00 0.00 3.02
3993 4184 5.279106 CCATCAGATTTTGTCTTTGAGGCAA 60.279 40.000 0.00 0.00 38.17 4.52
4050 4241 8.624367 TTCGGAGGAAAATACAGTCATTTTTA 57.376 30.769 0.00 0.00 38.04 1.52
4273 4479 6.617782 ATTATGTGATCCCAGGAGTCTATG 57.382 41.667 0.00 0.00 0.00 2.23
4435 5516 8.090831 CGATAATCCAATCTACTCCTCATGAAA 58.909 37.037 0.00 0.00 0.00 2.69
4447 5528 7.839680 ACTCCTCATGAAAAGTAAATTTGGT 57.160 32.000 7.67 0.00 0.00 3.67
4530 5612 3.388308 TGCAAATTTCCGTGGTCATTTG 58.612 40.909 15.40 15.40 38.91 2.32
4565 5650 0.605083 AGCACACTCGAGCATCTTCA 59.395 50.000 13.61 0.00 0.00 3.02
4646 5736 4.524714 TCATTCCGGAGCAATTTAAAACCA 59.475 37.500 3.34 0.00 0.00 3.67
4649 5739 4.082845 TCCGGAGCAATTTAAAACCATCA 58.917 39.130 0.00 0.00 0.00 3.07
4650 5740 4.524714 TCCGGAGCAATTTAAAACCATCAA 59.475 37.500 0.00 0.00 0.00 2.57
4653 5743 7.038659 CCGGAGCAATTTAAAACCATCAATAA 58.961 34.615 0.00 0.00 0.00 1.40
4683 5785 4.212143 ACACAGATGCTCACATACACAT 57.788 40.909 0.00 0.00 36.35 3.21
4699 5801 2.504175 ACACATACATACACTCACCCCC 59.496 50.000 0.00 0.00 0.00 5.40
4700 5802 2.771943 CACATACATACACTCACCCCCT 59.228 50.000 0.00 0.00 0.00 4.79
4702 5804 4.407621 CACATACATACACTCACCCCCTAA 59.592 45.833 0.00 0.00 0.00 2.69
4710 5812 0.250553 CTCACCCCCTAAAACGCACA 60.251 55.000 0.00 0.00 0.00 4.57
4712 5814 0.820074 CACCCCCTAAAACGCACACA 60.820 55.000 0.00 0.00 0.00 3.72
4714 5816 0.820074 CCCCCTAAAACGCACACACA 60.820 55.000 0.00 0.00 0.00 3.72
4715 5817 0.309612 CCCCTAAAACGCACACACAC 59.690 55.000 0.00 0.00 0.00 3.82
4718 5820 1.018148 CTAAAACGCACACACACCCA 58.982 50.000 0.00 0.00 0.00 4.51
4719 5821 1.402259 CTAAAACGCACACACACCCAA 59.598 47.619 0.00 0.00 0.00 4.12
4720 5822 0.109039 AAAACGCACACACACCCAAC 60.109 50.000 0.00 0.00 0.00 3.77
4721 5823 1.939769 AAACGCACACACACCCAACC 61.940 55.000 0.00 0.00 0.00 3.77
4723 5825 1.227704 CGCACACACACCCAACCTA 60.228 57.895 0.00 0.00 0.00 3.08
4724 5826 1.503818 CGCACACACACCCAACCTAC 61.504 60.000 0.00 0.00 0.00 3.18
4725 5827 1.170290 GCACACACACCCAACCTACC 61.170 60.000 0.00 0.00 0.00 3.18
4726 5828 0.536460 CACACACACCCAACCTACCC 60.536 60.000 0.00 0.00 0.00 3.69
4727 5829 1.074248 CACACACCCAACCTACCCC 59.926 63.158 0.00 0.00 0.00 4.95
4729 5831 0.194080 ACACACCCAACCTACCCCTA 59.806 55.000 0.00 0.00 0.00 3.53
4730 5832 1.203518 ACACACCCAACCTACCCCTAT 60.204 52.381 0.00 0.00 0.00 2.57
4731 5833 1.211949 CACACCCAACCTACCCCTATG 59.788 57.143 0.00 0.00 0.00 2.23
4732 5834 0.843984 CACCCAACCTACCCCTATGG 59.156 60.000 0.00 0.00 41.37 2.74
4750 5852 1.146263 GGCACCTTCGGGATACTGG 59.854 63.158 0.00 0.00 45.79 4.00
4751 5853 1.146263 GCACCTTCGGGATACTGGG 59.854 63.158 0.00 0.00 45.79 4.45
4758 5860 4.564110 GGGATACTGGGCCGGCAC 62.564 72.222 30.85 28.40 0.00 5.01
4761 5863 2.045340 ATACTGGGCCGGCACAAC 60.045 61.111 34.54 17.48 0.00 3.32
4768 5870 0.963355 GGGCCGGCACAACATCTTAA 60.963 55.000 30.85 0.00 0.00 1.85
4771 5873 2.017049 GCCGGCACAACATCTTAAGAT 58.983 47.619 24.80 12.37 34.56 2.40
4772 5874 2.423538 GCCGGCACAACATCTTAAGATT 59.576 45.455 24.80 0.10 31.21 2.40
4773 5875 3.731867 GCCGGCACAACATCTTAAGATTG 60.732 47.826 24.80 14.93 31.21 2.67
4774 5876 3.181497 CCGGCACAACATCTTAAGATTGG 60.181 47.826 15.49 8.12 31.21 3.16
4789 5891 3.544772 TGGCGAAGTCACCACAGA 58.455 55.556 0.00 0.00 36.97 3.41
4797 5899 2.022129 GTCACCACAGACGCCTTCG 61.022 63.158 0.00 0.00 42.43 3.79
4816 5918 5.334260 CCTTCGTAGTCGATAGGAATGTCTC 60.334 48.000 10.74 0.00 45.65 3.36
4820 5922 6.027535 CGTAGTCGATAGGAATGTCTCCTCT 61.028 48.000 0.00 0.00 45.13 3.69
4836 5938 4.092771 TCCTCTCACTAAACGAACATCG 57.907 45.455 0.00 0.00 46.93 3.84
4839 5941 1.320555 CTCACTAAACGAACATCGCCG 59.679 52.381 0.00 0.00 45.12 6.46
4858 5960 5.028375 CGCCGAAAAGTCTGAAATAAATCC 58.972 41.667 0.00 0.00 0.00 3.01
4859 5961 5.391523 CGCCGAAAAGTCTGAAATAAATCCA 60.392 40.000 0.00 0.00 0.00 3.41
4861 5963 6.555315 CCGAAAAGTCTGAAATAAATCCAGG 58.445 40.000 0.00 0.00 0.00 4.45
4868 5970 8.884124 AGTCTGAAATAAATCCAGGAAAATGA 57.116 30.769 0.00 0.00 0.00 2.57
4869 5971 8.964772 AGTCTGAAATAAATCCAGGAAAATGAG 58.035 33.333 0.00 0.00 0.00 2.90
4872 5974 7.775120 TGAAATAAATCCAGGAAAATGAGAGC 58.225 34.615 0.00 0.00 0.00 4.09
4873 5975 7.396907 TGAAATAAATCCAGGAAAATGAGAGCA 59.603 33.333 0.00 0.00 0.00 4.26
4874 5976 7.909485 AATAAATCCAGGAAAATGAGAGCAT 57.091 32.000 0.00 0.00 35.92 3.79
4875 5977 5.848833 AAATCCAGGAAAATGAGAGCATC 57.151 39.130 0.00 0.00 32.35 3.91
4876 5978 4.515028 ATCCAGGAAAATGAGAGCATCA 57.485 40.909 0.00 0.00 43.70 3.07
4877 5979 3.882444 TCCAGGAAAATGAGAGCATCAG 58.118 45.455 0.00 0.00 42.53 2.90
4878 5980 3.265221 TCCAGGAAAATGAGAGCATCAGT 59.735 43.478 0.00 0.00 42.53 3.41
4879 5981 3.377485 CCAGGAAAATGAGAGCATCAGTG 59.623 47.826 0.00 0.00 42.53 3.66
4880 5982 4.008330 CAGGAAAATGAGAGCATCAGTGT 58.992 43.478 0.00 0.00 42.53 3.55
4881 5983 4.094590 CAGGAAAATGAGAGCATCAGTGTC 59.905 45.833 1.99 1.99 42.53 3.67
4882 5984 4.005650 GGAAAATGAGAGCATCAGTGTCA 58.994 43.478 10.53 0.00 41.21 3.58
4886 5988 3.309961 TGAGAGCATCAGTGTCAAGTC 57.690 47.619 0.00 0.00 37.82 3.01
4890 5992 4.339748 AGAGCATCAGTGTCAAGTCTAGA 58.660 43.478 0.00 0.00 37.82 2.43
4924 6026 0.476771 GGGTTGGTTCCACCTCAAGA 59.523 55.000 9.18 0.00 39.58 3.02
4928 6030 3.020984 GTTGGTTCCACCTCAAGAAACA 58.979 45.455 0.00 0.00 39.58 2.83
4943 6045 9.667107 CCTCAAGAAACATAACCATCTTAGTTA 57.333 33.333 0.00 0.00 34.38 2.24
4949 6051 6.808321 ACATAACCATCTTAGTTAGGCTCA 57.192 37.500 0.00 0.00 35.46 4.26
4954 6056 4.142138 ACCATCTTAGTTAGGCTCAGTTCG 60.142 45.833 0.00 0.00 0.00 3.95
4955 6057 4.142138 CCATCTTAGTTAGGCTCAGTTCGT 60.142 45.833 0.00 0.00 0.00 3.85
4960 6062 4.868314 AGTTAGGCTCAGTTCGTAAACT 57.132 40.909 0.00 0.00 46.80 2.66
5034 6136 9.793252 ATTATGATTAAGTTGTTTGATCAGCAC 57.207 29.630 0.00 0.00 42.77 4.40
5098 6201 5.126061 GCCACCAACAATAGTTTGATCATCT 59.874 40.000 0.00 1.04 35.28 2.90
5154 6257 1.626686 CCAAAGCCCACCACAACATA 58.373 50.000 0.00 0.00 0.00 2.29
5159 6262 1.133637 AGCCCACCACAACATACACAA 60.134 47.619 0.00 0.00 0.00 3.33
5178 6281 4.636206 CACAAAACCCTCCTCATAAGTAGC 59.364 45.833 0.00 0.00 0.00 3.58
5183 6287 3.385111 ACCCTCCTCATAAGTAGCGAAAG 59.615 47.826 0.00 0.00 0.00 2.62
5216 6320 1.271926 TGACGAGTGATCACCCTCTCA 60.272 52.381 22.21 14.17 0.00 3.27
5224 6328 3.129638 GTGATCACCCTCTCAGTGTAGTC 59.870 52.174 15.31 0.00 36.58 2.59
5227 6331 1.469308 CACCCTCTCAGTGTAGTCGAC 59.531 57.143 7.70 7.70 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 1.819632 CTGGCGGTGAAGTATGGGC 60.820 63.158 0.00 0.00 0.00 5.36
81 82 1.173043 CGGAGACTGACTTGCTCTCT 58.827 55.000 0.00 0.00 32.50 3.10
615 616 0.384309 TCATCGGCATGTACGTCCTC 59.616 55.000 10.83 0.00 0.00 3.71
898 899 0.836400 TCTGCCTCGTTTCCCTCCTT 60.836 55.000 0.00 0.00 0.00 3.36
926 935 4.556233 CACGTGAGAGTTCAAGTCCATAA 58.444 43.478 10.90 0.00 42.88 1.90
936 945 2.049063 AGCGCCACGTGAGAGTTC 60.049 61.111 19.30 0.00 0.00 3.01
969 978 3.502979 AGCCCGAGATAGAACGATAGAAC 59.497 47.826 0.00 0.00 41.38 3.01
988 997 2.760385 AGGCACGAGGGACTAGCC 60.760 66.667 0.00 0.00 46.82 3.93
1336 1357 2.079925 GGGTTCTGTCTGTGCTCAATC 58.920 52.381 0.00 0.00 0.00 2.67
1347 1368 3.423154 CAAGCGGCGGGTTCTGTC 61.423 66.667 9.78 0.00 0.00 3.51
1359 1380 6.146021 ACAGGAGCATTTTTAATTTTCAAGCG 59.854 34.615 0.00 0.00 0.00 4.68
1391 1412 2.356069 TCTCGACGAGATGACATCCTTG 59.644 50.000 23.27 4.90 33.35 3.61
1409 1430 2.548295 CCGGCTACCTCGAGCTCTC 61.548 68.421 12.85 0.00 42.43 3.20
1444 1465 1.646189 GAAAGGCGTTGCTCTAGGAG 58.354 55.000 0.00 0.00 0.00 3.69
1445 1466 0.108804 CGAAAGGCGTTGCTCTAGGA 60.109 55.000 0.00 0.00 34.64 2.94
1447 1468 1.927895 ATCGAAAGGCGTTGCTCTAG 58.072 50.000 0.00 0.00 41.80 2.43
1448 1469 2.380084 AATCGAAAGGCGTTGCTCTA 57.620 45.000 0.00 0.00 41.80 2.43
1449 1470 2.271800 CTAATCGAAAGGCGTTGCTCT 58.728 47.619 0.00 0.00 41.80 4.09
1450 1471 2.000447 ACTAATCGAAAGGCGTTGCTC 59.000 47.619 0.00 0.00 41.80 4.26
1451 1472 1.732259 CACTAATCGAAAGGCGTTGCT 59.268 47.619 0.00 0.00 41.80 3.91
1452 1473 1.790481 GCACTAATCGAAAGGCGTTGC 60.790 52.381 0.00 0.00 41.80 4.17
1453 1474 1.463056 TGCACTAATCGAAAGGCGTTG 59.537 47.619 0.00 0.00 41.80 4.10
1454 1475 1.463444 GTGCACTAATCGAAAGGCGTT 59.537 47.619 10.32 0.00 41.80 4.84
1455 1476 1.076332 GTGCACTAATCGAAAGGCGT 58.924 50.000 10.32 0.00 41.80 5.68
1456 1477 1.061131 CAGTGCACTAATCGAAAGGCG 59.939 52.381 21.20 0.00 42.69 5.52
1457 1478 1.398390 CCAGTGCACTAATCGAAAGGC 59.602 52.381 21.20 0.00 0.00 4.35
1458 1479 2.673368 GACCAGTGCACTAATCGAAAGG 59.327 50.000 21.20 16.14 0.00 3.11
1459 1480 3.325870 TGACCAGTGCACTAATCGAAAG 58.674 45.455 21.20 4.15 0.00 2.62
1460 1481 3.394674 TGACCAGTGCACTAATCGAAA 57.605 42.857 21.20 1.66 0.00 3.46
1464 1485 4.437930 GCTTGAATGACCAGTGCACTAATC 60.438 45.833 21.20 19.46 0.00 1.75
1468 1489 1.242076 GCTTGAATGACCAGTGCACT 58.758 50.000 15.25 15.25 0.00 4.40
1479 1500 3.360533 GCACGATTCATCTGCTTGAATG 58.639 45.455 12.70 8.85 44.35 2.67
1480 1501 2.031314 CGCACGATTCATCTGCTTGAAT 59.969 45.455 9.03 9.03 46.39 2.57
1484 1505 0.723414 CACGCACGATTCATCTGCTT 59.277 50.000 0.00 0.00 32.51 3.91
1487 1508 1.854743 CCTACACGCACGATTCATCTG 59.145 52.381 0.00 0.00 0.00 2.90
1495 1516 2.949909 ATTGCCCCTACACGCACGA 61.950 57.895 0.00 0.00 33.97 4.35
1529 1558 0.238289 AGCGGCAAAACATCGAACAG 59.762 50.000 1.45 0.00 0.00 3.16
1554 1583 6.863126 CCATTTCAACCTTTTGACAGTATCAC 59.137 38.462 0.00 0.00 41.64 3.06
1557 1586 6.976934 ACCATTTCAACCTTTTGACAGTAT 57.023 33.333 0.00 0.00 41.64 2.12
1559 1588 5.675684 AACCATTTCAACCTTTTGACAGT 57.324 34.783 0.00 0.00 41.64 3.55
1560 1589 9.927668 ATATTAACCATTTCAACCTTTTGACAG 57.072 29.630 0.00 0.00 41.64 3.51
1561 1590 9.921637 GATATTAACCATTTCAACCTTTTGACA 57.078 29.630 0.00 0.00 41.64 3.58
1592 1621 1.299541 CAGTGAGCGTGAACCAAGTT 58.700 50.000 0.00 0.00 0.00 2.66
1594 1623 1.571460 GCAGTGAGCGTGAACCAAG 59.429 57.895 0.00 0.00 0.00 3.61
1595 1624 3.731136 GCAGTGAGCGTGAACCAA 58.269 55.556 0.00 0.00 0.00 3.67
1638 1705 5.716228 ACATAGAAACCATTCCATGAAGCAA 59.284 36.000 0.00 0.00 36.98 3.91
1663 1730 4.934144 GCGTCTCAAAATCGCGAG 57.066 55.556 16.66 0.00 40.51 5.03
1668 1735 2.945278 TGCCAATTGCGTCTCAAAATC 58.055 42.857 0.00 0.00 45.60 2.17
1671 1738 1.612950 ACATGCCAATTGCGTCTCAAA 59.387 42.857 0.00 0.00 45.60 2.69
1672 1739 1.246649 ACATGCCAATTGCGTCTCAA 58.753 45.000 0.00 0.00 45.60 3.02
1678 1745 3.361644 GCGATAAATACATGCCAATTGCG 59.638 43.478 0.00 0.00 45.60 4.85
1703 1774 6.616947 TGAGAAACGAACTCACATTTTGTTT 58.383 32.000 0.00 0.99 41.35 2.83
1797 1868 2.960129 GGAATAGCCACGACGCCG 60.960 66.667 0.00 0.00 42.50 6.46
1839 1910 3.815401 TCTGCTTGGACTTGCTTAACTTC 59.185 43.478 0.00 0.00 0.00 3.01
1872 1943 1.795768 TGTCGACAAGCTCAATGGAC 58.204 50.000 17.62 0.00 0.00 4.02
1914 1985 0.179097 CCGCTACCTCTCCTTTGCTC 60.179 60.000 0.00 0.00 0.00 4.26
1930 2001 2.247637 GAATAAAACGAAGGCAACCGC 58.752 47.619 0.00 0.00 37.44 5.68
1937 2008 1.267383 GCGCTCGGAATAAAACGAAGG 60.267 52.381 0.00 0.00 38.79 3.46
1952 2024 1.134075 CATGTTCTGTGCTGCGCTC 59.866 57.895 14.92 0.28 0.00 5.03
1955 2027 1.131218 CGACATGTTCTGTGCTGCG 59.869 57.895 0.00 0.00 38.54 5.18
2100 2202 9.522804 GCCTGAGAGCACAAATATATATACTAC 57.477 37.037 0.00 0.00 0.00 2.73
2101 2203 9.255029 TGCCTGAGAGCACAAATATATATACTA 57.745 33.333 0.00 0.00 38.00 1.82
2102 2204 8.138928 TGCCTGAGAGCACAAATATATATACT 57.861 34.615 0.00 0.00 38.00 2.12
2131 2233 2.025981 ACATGGGAATGCAGCTACTGAA 60.026 45.455 0.00 0.00 32.44 3.02
2135 2237 3.019564 AGAAACATGGGAATGCAGCTAC 58.980 45.455 0.00 0.00 0.00 3.58
2183 2320 7.765695 TTCAAACTCTGCAAAATAAGAGGAT 57.234 32.000 4.83 0.00 43.54 3.24
2239 2376 1.798813 GTACAACCGCTGAACTGAAGG 59.201 52.381 0.00 0.00 0.00 3.46
2241 2378 2.902705 AGTACAACCGCTGAACTGAA 57.097 45.000 0.00 0.00 0.00 3.02
2242 2379 3.257375 ACATAGTACAACCGCTGAACTGA 59.743 43.478 0.00 0.00 0.00 3.41
2243 2380 3.585862 ACATAGTACAACCGCTGAACTG 58.414 45.455 0.00 0.00 0.00 3.16
2244 2381 3.955650 ACATAGTACAACCGCTGAACT 57.044 42.857 0.00 0.00 0.00 3.01
2245 2382 4.449743 TCAAACATAGTACAACCGCTGAAC 59.550 41.667 0.00 0.00 0.00 3.18
2246 2383 4.633175 TCAAACATAGTACAACCGCTGAA 58.367 39.130 0.00 0.00 0.00 3.02
2247 2384 4.260139 TCAAACATAGTACAACCGCTGA 57.740 40.909 0.00 0.00 0.00 4.26
2248 2385 4.212425 TGTTCAAACATAGTACAACCGCTG 59.788 41.667 0.00 0.00 33.17 5.18
2249 2386 4.382291 TGTTCAAACATAGTACAACCGCT 58.618 39.130 0.00 0.00 33.17 5.52
2266 2406 4.346730 AGAAGGCAATCATTGGATGTTCA 58.653 39.130 0.00 0.00 32.92 3.18
2275 2415 3.749609 GCAAGCAAAAGAAGGCAATCATT 59.250 39.130 0.00 0.00 0.00 2.57
2282 2422 2.130395 GAAGTGCAAGCAAAAGAAGGC 58.870 47.619 0.00 0.00 0.00 4.35
2285 2425 3.441496 CTGGAAGTGCAAGCAAAAGAA 57.559 42.857 0.00 0.00 0.00 2.52
2301 2441 7.775053 AGCCTATTATGTTTTTCAAACTGGA 57.225 32.000 1.33 0.00 0.00 3.86
2337 2520 4.876679 GTGCTAAGTCAATCCTTAGAACCC 59.123 45.833 11.16 0.00 43.50 4.11
2350 2533 6.061441 TGAAGAAAAGATTGGTGCTAAGTCA 58.939 36.000 0.00 0.00 0.00 3.41
2351 2534 6.560253 TGAAGAAAAGATTGGTGCTAAGTC 57.440 37.500 0.00 0.00 0.00 3.01
2509 2692 6.241645 ACTAAGCAAGGATAGCAGAACTTTT 58.758 36.000 0.00 0.00 0.00 2.27
2510 2693 5.810095 ACTAAGCAAGGATAGCAGAACTTT 58.190 37.500 0.00 0.00 0.00 2.66
2511 2694 5.428184 ACTAAGCAAGGATAGCAGAACTT 57.572 39.130 0.00 0.00 0.00 2.66
2512 2695 6.155475 CTACTAAGCAAGGATAGCAGAACT 57.845 41.667 0.00 0.00 0.00 3.01
2596 2782 5.660417 TCCAATCTCTTCTCTATCTGCAGTT 59.340 40.000 14.67 8.22 0.00 3.16
2684 2872 9.975218 ACAAAACCTATCAAATAATGGTAGAGT 57.025 29.630 0.00 0.00 44.25 3.24
2729 2917 3.118811 CCTTTCTGCTCCTTCCTGAGTAG 60.119 52.174 0.00 0.00 43.85 2.57
2745 2933 3.782656 TTTTCTAAGCCCGACCTTTCT 57.217 42.857 0.00 0.00 0.00 2.52
3190 3379 8.859236 AAGTTCTTAGTCCCAAAAGGTTATAC 57.141 34.615 0.00 0.00 36.75 1.47
3254 3443 4.889832 AGCTGAAGAACAAAGTGTCTTG 57.110 40.909 0.00 0.00 0.00 3.02
3353 3544 9.507329 AATACAGTAACAGAATTGTGAGAATGT 57.493 29.630 9.96 13.11 37.67 2.71
3618 3809 9.751542 TGTGACCGTTGTGAAATTATTAAAATT 57.248 25.926 0.00 0.00 0.00 1.82
3756 3947 5.471456 CCTTGTGTGCTTCATCTCTAAAACT 59.529 40.000 0.00 0.00 0.00 2.66
3905 4096 3.118261 TCGAGCTGAATAAAGCCTGGAAT 60.118 43.478 0.00 0.00 44.68 3.01
3922 4113 4.802039 TGTAAGTCCGTATGAAATTCGAGC 59.198 41.667 0.00 0.00 39.64 5.03
3993 4184 3.407698 TGCCGAGTACATGAACAATTGT 58.592 40.909 4.92 4.92 0.00 2.71
4050 4241 8.743085 AAGTATCTGCAGATGTTACATGAAAT 57.257 30.769 34.48 11.47 36.05 2.17
4054 4245 8.501580 CCATTAAGTATCTGCAGATGTTACATG 58.498 37.037 34.48 27.52 36.05 3.21
4187 4382 1.351683 AGTCGGACACTCTCCTACTGT 59.648 52.381 11.27 0.00 42.33 3.55
4188 4383 2.116827 AGTCGGACACTCTCCTACTG 57.883 55.000 11.27 0.00 42.33 2.74
4189 4384 1.951424 GCAGTCGGACACTCTCCTACT 60.951 57.143 11.27 0.00 44.30 2.57
4239 4434 8.816894 CCTGGGATCACATAATACTATAACTGT 58.183 37.037 0.00 0.00 0.00 3.55
4273 4479 7.055667 TCAGATGTTGGAGTATATTGGAGTC 57.944 40.000 0.00 0.00 0.00 3.36
4404 5485 6.402222 AGGAGTAGATTGGATTATCGATTGC 58.598 40.000 1.71 0.00 0.00 3.56
4465 5546 6.628844 GCATCCTTGGTGCTAAAAATTCAGAT 60.629 38.462 0.00 0.00 39.45 2.90
4530 5612 6.259550 AGTGTGCTATGGAAAATTTCAGAC 57.740 37.500 8.09 0.00 0.00 3.51
4627 5717 4.082845 TGATGGTTTTAAATTGCTCCGGA 58.917 39.130 2.93 2.93 0.00 5.14
4628 5718 4.448537 TGATGGTTTTAAATTGCTCCGG 57.551 40.909 0.00 0.00 0.00 5.14
4660 5750 5.146010 TGTGTATGTGAGCATCTGTGTTA 57.854 39.130 0.00 0.00 36.58 2.41
4662 5752 3.683365 TGTGTATGTGAGCATCTGTGT 57.317 42.857 0.00 0.00 36.58 3.72
4663 5753 5.111293 TGTATGTGTATGTGAGCATCTGTG 58.889 41.667 0.00 0.00 36.58 3.66
4664 5754 5.343307 TGTATGTGTATGTGAGCATCTGT 57.657 39.130 0.00 0.00 36.58 3.41
4665 5755 6.925165 TGTATGTATGTGTATGTGAGCATCTG 59.075 38.462 0.00 0.00 36.58 2.90
4666 5756 6.925718 GTGTATGTATGTGTATGTGAGCATCT 59.074 38.462 0.00 0.00 36.58 2.90
4667 5757 6.925718 AGTGTATGTATGTGTATGTGAGCATC 59.074 38.462 0.00 0.00 36.58 3.91
4669 5759 6.127479 TGAGTGTATGTATGTGTATGTGAGCA 60.127 38.462 0.00 0.00 0.00 4.26
4670 5760 6.199154 GTGAGTGTATGTATGTGTATGTGAGC 59.801 42.308 0.00 0.00 0.00 4.26
4671 5761 6.697455 GGTGAGTGTATGTATGTGTATGTGAG 59.303 42.308 0.00 0.00 0.00 3.51
4672 5762 6.406512 GGGTGAGTGTATGTATGTGTATGTGA 60.407 42.308 0.00 0.00 0.00 3.58
4673 5763 5.753438 GGGTGAGTGTATGTATGTGTATGTG 59.247 44.000 0.00 0.00 0.00 3.21
4674 5764 5.163343 GGGGTGAGTGTATGTATGTGTATGT 60.163 44.000 0.00 0.00 0.00 2.29
4675 5765 5.297547 GGGGTGAGTGTATGTATGTGTATG 58.702 45.833 0.00 0.00 0.00 2.39
4676 5766 4.347000 GGGGGTGAGTGTATGTATGTGTAT 59.653 45.833 0.00 0.00 0.00 2.29
4677 5767 3.707611 GGGGGTGAGTGTATGTATGTGTA 59.292 47.826 0.00 0.00 0.00 2.90
4683 5785 4.081531 CGTTTTAGGGGGTGAGTGTATGTA 60.082 45.833 0.00 0.00 0.00 2.29
4699 5801 1.018148 TGGGTGTGTGTGCGTTTTAG 58.982 50.000 0.00 0.00 0.00 1.85
4700 5802 1.132643 GTTGGGTGTGTGTGCGTTTTA 59.867 47.619 0.00 0.00 0.00 1.52
4702 5804 1.509004 GTTGGGTGTGTGTGCGTTT 59.491 52.632 0.00 0.00 0.00 3.60
4710 5812 0.194080 TAGGGGTAGGTTGGGTGTGT 59.806 55.000 0.00 0.00 0.00 3.72
4712 5814 1.591768 CATAGGGGTAGGTTGGGTGT 58.408 55.000 0.00 0.00 0.00 4.16
4714 5816 3.352505 CCATAGGGGTAGGTTGGGT 57.647 57.895 0.00 0.00 0.00 4.51
4737 5839 2.421739 CGGCCCAGTATCCCGAAG 59.578 66.667 0.00 0.00 44.55 3.79
4738 5840 3.158648 CCGGCCCAGTATCCCGAA 61.159 66.667 0.00 0.00 44.55 4.30
4750 5852 0.451783 CTTAAGATGTTGTGCCGGCC 59.548 55.000 26.77 16.24 0.00 6.13
4751 5853 1.448985 TCTTAAGATGTTGTGCCGGC 58.551 50.000 22.73 22.73 0.00 6.13
4758 5860 5.122239 TGACTTCGCCAATCTTAAGATGTTG 59.878 40.000 18.61 14.09 34.49 3.33
4761 5863 4.034510 GGTGACTTCGCCAATCTTAAGATG 59.965 45.833 18.61 12.11 45.55 2.90
4773 5875 2.022129 CGTCTGTGGTGACTTCGCC 61.022 63.158 1.56 1.56 46.40 5.54
4774 5876 2.658707 GCGTCTGTGGTGACTTCGC 61.659 63.158 0.00 0.00 35.00 4.70
4816 5918 2.599082 GCGATGTTCGTTTAGTGAGAGG 59.401 50.000 0.00 0.00 42.81 3.69
4820 5922 1.068402 TCGGCGATGTTCGTTTAGTGA 60.068 47.619 4.99 0.00 42.81 3.41
4823 5925 3.120786 ACTTTTCGGCGATGTTCGTTTAG 60.121 43.478 11.76 0.71 42.81 1.85
4825 5927 1.600485 ACTTTTCGGCGATGTTCGTTT 59.400 42.857 11.76 0.00 42.81 3.60
4836 5938 5.949735 TGGATTTATTTCAGACTTTTCGGC 58.050 37.500 0.00 0.00 0.00 5.54
4839 5941 9.981114 TTTTCCTGGATTTATTTCAGACTTTTC 57.019 29.630 0.00 0.00 0.00 2.29
4858 5960 4.008330 ACACTGATGCTCTCATTTTCCTG 58.992 43.478 0.00 0.00 32.10 3.86
4859 5961 4.260170 GACACTGATGCTCTCATTTTCCT 58.740 43.478 0.00 0.00 32.10 3.36
4861 5963 5.180868 ACTTGACACTGATGCTCTCATTTTC 59.819 40.000 0.00 0.00 32.10 2.29
4868 5970 4.339748 TCTAGACTTGACACTGATGCTCT 58.660 43.478 0.00 0.00 0.00 4.09
4869 5971 4.710423 TCTAGACTTGACACTGATGCTC 57.290 45.455 0.00 0.00 0.00 4.26
4886 5988 3.059352 CCACCAGGGTTCAAGTTCTAG 57.941 52.381 0.00 0.00 0.00 2.43
4900 6002 4.174305 GTGGAACCAACCCACCAG 57.826 61.111 0.00 0.00 46.30 4.00
4912 6014 5.055265 TGGTTATGTTTCTTGAGGTGGAA 57.945 39.130 0.00 0.00 0.00 3.53
4917 6019 8.567285 AACTAAGATGGTTATGTTTCTTGAGG 57.433 34.615 0.00 0.00 31.29 3.86
4919 6021 9.667107 CCTAACTAAGATGGTTATGTTTCTTGA 57.333 33.333 0.00 0.00 31.29 3.02
4924 6026 7.630082 TGAGCCTAACTAAGATGGTTATGTTT 58.370 34.615 0.00 0.00 0.00 2.83
4928 6030 7.439108 AACTGAGCCTAACTAAGATGGTTAT 57.561 36.000 0.00 0.00 30.25 1.89
4943 6045 4.463186 AGTGATAGTTTACGAACTGAGCCT 59.537 41.667 2.25 0.00 45.46 4.58
5031 6133 2.793278 AAAAACCTGATGTTCCGTGC 57.207 45.000 0.00 0.00 35.67 5.34
5074 6176 4.782019 TGATCAAACTATTGTTGGTGGC 57.218 40.909 0.00 0.00 37.79 5.01
5154 6257 4.724279 ACTTATGAGGAGGGTTTTGTGT 57.276 40.909 0.00 0.00 0.00 3.72
5159 6262 3.371965 TCGCTACTTATGAGGAGGGTTT 58.628 45.455 12.79 0.00 44.87 3.27
5178 6281 5.769367 TCGTCATTATCACCCTATCTTTCG 58.231 41.667 0.00 0.00 0.00 3.46
5183 6287 5.707242 TCACTCGTCATTATCACCCTATC 57.293 43.478 0.00 0.00 0.00 2.08


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

AutoCloner maintained by Alex Coulton.