Multiple sequence alignment - TraesCS1B01G373800

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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 TraesCS1B01G373800 chr1B 100.000 8250 0 0 1 8250 604318291 604310042 0.000000e+00 15235.0
1 TraesCS1B01G373800 chr1B 99.386 1792 9 2 1643 3434 24997497 24995708 0.000000e+00 3247.0
2 TraesCS1B01G373800 chr1B 87.360 1788 213 9 1645 3431 151453689 151455464 0.000000e+00 2037.0
3 TraesCS1B01G373800 chr1A 94.529 3802 148 26 3798 7582 539968021 539964263 0.000000e+00 5814.0
4 TraesCS1B01G373800 chr1A 83.566 1789 276 13 1648 3434 554989576 554991348 0.000000e+00 1659.0
5 TraesCS1B01G373800 chr1A 93.162 585 28 4 7666 8250 539963096 539962524 0.000000e+00 848.0
6 TraesCS1B01G373800 chr1A 77.356 1369 296 13 2073 3434 324860679 324859318 0.000000e+00 798.0
7 TraesCS1B01G373800 chr1A 87.414 723 47 19 891 1603 539969083 539968395 0.000000e+00 791.0
8 TraesCS1B01G373800 chr1A 92.537 335 17 4 3436 3768 539968348 539968020 2.690000e-129 473.0
9 TraesCS1B01G373800 chr1A 83.857 477 41 17 69 525 539970283 539969823 9.900000e-114 422.0
10 TraesCS1B01G373800 chr1A 94.000 50 2 1 1 50 539970449 539970401 3.190000e-09 75.0
11 TraesCS1B01G373800 chr1D 93.545 3594 163 29 3436 6995 444339105 444335547 0.000000e+00 5288.0
12 TraesCS1B01G373800 chr1D 78.056 1800 354 33 1648 3434 427861771 427863542 0.000000e+00 1098.0
13 TraesCS1B01G373800 chr1D 87.615 872 60 23 753 1603 444339995 444339151 0.000000e+00 968.0
14 TraesCS1B01G373800 chr1D 94.258 627 33 3 7021 7645 444335551 444334926 0.000000e+00 955.0
15 TraesCS1B01G373800 chr1D 94.188 585 25 4 7666 8250 444333836 444333261 0.000000e+00 883.0
16 TraesCS1B01G373800 chr1D 85.662 544 38 13 1 511 444340986 444340450 3.390000e-148 536.0
17 TraesCS1B01G373800 chr7A 99.497 1789 7 2 1646 3434 20643615 20645401 0.000000e+00 3253.0
18 TraesCS1B01G373800 chr4B 99.273 1789 12 1 1646 3434 618565503 618567290 0.000000e+00 3230.0
19 TraesCS1B01G373800 chr3B 82.928 1810 262 27 1648 3434 658485078 658483293 0.000000e+00 1587.0
20 TraesCS1B01G373800 chr5A 81.410 1802 299 30 1645 3434 436190982 436189205 0.000000e+00 1439.0
21 TraesCS1B01G373800 chr3A 80.791 1796 302 31 1649 3431 415958929 415960694 0.000000e+00 1365.0
22 TraesCS1B01G373800 chr7B 77.346 1801 360 38 1647 3434 644546402 644548167 0.000000e+00 1022.0
23 TraesCS1B01G373800 chr2D 77.146 1794 367 35 1650 3434 590023562 590021803 0.000000e+00 1002.0
24 TraesCS1B01G373800 chr2D 97.500 40 1 0 5090 5129 133768810 133768849 1.490000e-07 69.4
25 TraesCS1B01G373800 chr6B 76.855 1806 359 47 1647 3434 679295929 679297693 0.000000e+00 965.0
26 TraesCS1B01G373800 chr6B 76.383 1681 332 49 1646 3317 674559114 674560738 0.000000e+00 845.0
27 TraesCS1B01G373800 chr7D 85.063 395 29 9 146 525 632031141 632031520 7.820000e-100 375.0
28 TraesCS1B01G373800 chr5B 78.102 274 39 16 1646 1917 694223970 694223716 3.990000e-33 154.0
29 TraesCS1B01G373800 chr5B 95.652 46 1 1 5085 5129 682702849 682702804 1.150000e-08 73.1
30 TraesCS1B01G373800 chrUn 97.059 68 1 1 1645 1712 30082695 30082629 6.770000e-21 113.0
31 TraesCS1B01G373800 chr2A 85.294 102 2 5 5036 5134 102688124 102688033 8.820000e-15 93.5
32 TraesCS1B01G373800 chr2B 95.745 47 2 0 5085 5131 556680348 556680302 8.880000e-10 76.8
33 TraesCS1B01G373800 chr6D 81.818 99 9 6 5034 5132 417896972 417896883 3.190000e-09 75.0
34 TraesCS1B01G373800 chr6D 93.878 49 1 2 5032 5078 166762400 166762448 1.150000e-08 73.1
35 TraesCS1B01G373800 chr5D 82.474 97 4 6 5034 5128 50780521 50780436 1.150000e-08 73.1
36 TraesCS1B01G373800 chr5D 83.333 90 3 5 5040 5128 528622477 528622555 1.150000e-08 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 TraesCS1B01G373800 chr1B 604310042 604318291 8249 True 15235.000000 15235 100.0000 1 8250 1 chr1B.!!$R2 8249
1 TraesCS1B01G373800 chr1B 24995708 24997497 1789 True 3247.000000 3247 99.3860 1643 3434 1 chr1B.!!$R1 1791
2 TraesCS1B01G373800 chr1B 151453689 151455464 1775 False 2037.000000 2037 87.3600 1645 3431 1 chr1B.!!$F1 1786
3 TraesCS1B01G373800 chr1A 554989576 554991348 1772 False 1659.000000 1659 83.5660 1648 3434 1 chr1A.!!$F1 1786
4 TraesCS1B01G373800 chr1A 539962524 539970449 7925 True 1403.833333 5814 90.9165 1 8250 6 chr1A.!!$R2 8249
5 TraesCS1B01G373800 chr1A 324859318 324860679 1361 True 798.000000 798 77.3560 2073 3434 1 chr1A.!!$R1 1361
6 TraesCS1B01G373800 chr1D 444333261 444340986 7725 True 1726.000000 5288 91.0536 1 8250 5 chr1D.!!$R1 8249
7 TraesCS1B01G373800 chr1D 427861771 427863542 1771 False 1098.000000 1098 78.0560 1648 3434 1 chr1D.!!$F1 1786
8 TraesCS1B01G373800 chr7A 20643615 20645401 1786 False 3253.000000 3253 99.4970 1646 3434 1 chr7A.!!$F1 1788
9 TraesCS1B01G373800 chr4B 618565503 618567290 1787 False 3230.000000 3230 99.2730 1646 3434 1 chr4B.!!$F1 1788
10 TraesCS1B01G373800 chr3B 658483293 658485078 1785 True 1587.000000 1587 82.9280 1648 3434 1 chr3B.!!$R1 1786
11 TraesCS1B01G373800 chr5A 436189205 436190982 1777 True 1439.000000 1439 81.4100 1645 3434 1 chr5A.!!$R1 1789
12 TraesCS1B01G373800 chr3A 415958929 415960694 1765 False 1365.000000 1365 80.7910 1649 3431 1 chr3A.!!$F1 1782
13 TraesCS1B01G373800 chr7B 644546402 644548167 1765 False 1022.000000 1022 77.3460 1647 3434 1 chr7B.!!$F1 1787
14 TraesCS1B01G373800 chr2D 590021803 590023562 1759 True 1002.000000 1002 77.1460 1650 3434 1 chr2D.!!$R1 1784
15 TraesCS1B01G373800 chr6B 679295929 679297693 1764 False 965.000000 965 76.8550 1647 3434 1 chr6B.!!$F2 1787
16 TraesCS1B01G373800 chr6B 674559114 674560738 1624 False 845.000000 845 76.3830 1646 3317 1 chr6B.!!$F1 1671

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
906 1457 0.179004 AGTCAATTGCCCCACGAACA 60.179 50.000 0.00 0.00 0.00 3.18 F
1472 2036 0.253044 TGCTTCGATCCCTTTGGAGG 59.747 55.000 0.00 0.00 46.08 4.30 F
1557 2131 0.313043 CAATGGATGATTGGCGAGCC 59.687 55.000 7.26 7.26 38.27 4.70 F
1560 2134 0.464373 TGGATGATTGGCGAGCCTTC 60.464 55.000 15.75 12.20 36.94 3.46 F
1629 2212 0.670854 GAGCGTCCCCAGTTCAGTTC 60.671 60.000 0.00 0.00 0.00 3.01 F
1634 2217 0.971386 TCCCCAGTTCAGTTCCGTAC 59.029 55.000 0.00 0.00 0.00 3.67 F
3642 4269 1.002430 TCGTCTCAAAGCCTGCTTGAT 59.998 47.619 4.95 0.00 36.26 2.57 F
3914 4558 0.040603 GTGCAGAGAAGTGCTGTTGC 60.041 55.000 0.00 0.00 44.32 4.17 F
4379 5030 0.527600 CGCGCTGCCTTACATACTGA 60.528 55.000 5.56 0.00 0.00 3.41 F
4649 5302 0.814010 ACGCCTGGTTTCTGTCACAC 60.814 55.000 0.00 0.00 0.00 3.82 F
5560 6226 1.207089 TCTTAGTGAGGCCGACAATGG 59.793 52.381 14.18 8.33 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1941 2534 4.141482 ACTGGTAGTTGCTTCTCTGGAAAA 60.141 41.667 0.00 0.0 0.00 2.29 R
3547 4172 4.994852 TCTCCTGGTTAAAAATGTCGAGTG 59.005 41.667 0.00 0.0 0.00 3.51 R
3590 4216 3.004106 GCATCAGGAATTTGGAATCCTCG 59.996 47.826 0.00 0.0 44.26 4.63 R
3642 4269 2.373335 TGCTAACCCTTTTGGCTCAA 57.627 45.000 0.00 0.0 37.83 3.02 R
3673 4307 0.820871 AAAGGCGGTGTTCAAAAGCA 59.179 45.000 0.00 0.0 0.00 3.91 R
3771 4405 8.407313 TCCCCTTTCTAAAAGATTTAGATCCT 57.593 34.615 12.02 0.0 31.78 3.24 R
5173 5832 0.034896 AAGCTAAGGTGTGACACGGG 59.965 55.000 9.90 1.0 34.83 5.28 R
5560 6226 2.356227 GGATGAAGTTCCCCCTCACTTC 60.356 54.545 0.00 5.3 46.26 3.01 R
6324 6990 4.202398 GCTGACTGATATTGATCCCTGGAA 60.202 45.833 0.00 0.0 0.00 3.53 R
6528 7194 2.666619 GCAAAGATTCAGGCGACACAAG 60.667 50.000 0.00 0.0 0.00 3.16 R
7362 8028 0.182299 GCCAGCCCTATCTGCTTCTT 59.818 55.000 0.00 0.0 36.81 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
50 56 3.182572 GTCAGCGCAACAGCATAGTATAC 59.817 47.826 11.47 0.00 40.15 1.47
107 213 3.583086 CCGGTTAGTCATCCCCTGAATAT 59.417 47.826 0.00 0.00 34.62 1.28
124 230 7.379529 CCCTGAATATGAAAATAAACATGCGTC 59.620 37.037 0.00 0.00 0.00 5.19
154 260 1.672881 CTTCCTGCACGATTTCATCCC 59.327 52.381 0.00 0.00 0.00 3.85
164 270 2.031683 CGATTTCATCCCGTACCAAAGC 59.968 50.000 0.00 0.00 0.00 3.51
167 273 1.202099 TCATCCCGTACCAAAGCCCA 61.202 55.000 0.00 0.00 0.00 5.36
188 297 6.268566 CCCAGGTACACGTAGTAGTATTTTC 58.731 44.000 0.00 0.00 41.61 2.29
206 315 9.667107 AGTATTTTCCTTCGAGTTTAATCATCA 57.333 29.630 0.00 0.00 0.00 3.07
207 316 9.922305 GTATTTTCCTTCGAGTTTAATCATCAG 57.078 33.333 0.00 0.00 0.00 2.90
209 318 5.677319 TCCTTCGAGTTTAATCATCAGGT 57.323 39.130 0.00 0.00 0.00 4.00
210 319 6.049955 TCCTTCGAGTTTAATCATCAGGTT 57.950 37.500 0.00 0.00 0.00 3.50
213 322 5.414789 TCGAGTTTAATCATCAGGTTGGA 57.585 39.130 0.00 0.00 0.00 3.53
214 323 5.419542 TCGAGTTTAATCATCAGGTTGGAG 58.580 41.667 0.00 0.00 0.00 3.86
215 324 4.572389 CGAGTTTAATCATCAGGTTGGAGG 59.428 45.833 0.00 0.00 0.00 4.30
216 325 4.860022 AGTTTAATCATCAGGTTGGAGGG 58.140 43.478 0.00 0.00 0.00 4.30
217 326 4.540099 AGTTTAATCATCAGGTTGGAGGGA 59.460 41.667 0.00 0.00 0.00 4.20
218 327 5.194537 AGTTTAATCATCAGGTTGGAGGGAT 59.805 40.000 0.00 0.00 0.00 3.85
266 375 8.048534 TCATTGAGGATCTCTTTGTGATTTTC 57.951 34.615 0.00 0.00 34.92 2.29
272 381 8.940397 AGGATCTCTTTGTGATTTTCCTTTTA 57.060 30.769 0.00 0.00 28.78 1.52
273 382 9.539194 AGGATCTCTTTGTGATTTTCCTTTTAT 57.461 29.630 0.00 0.00 28.78 1.40
291 400 8.531146 TCCTTTTATTGGAACTCATTGGAAATC 58.469 33.333 0.00 0.00 0.00 2.17
329 438 1.607467 GGGCCAAATCCAGCACACT 60.607 57.895 4.39 0.00 30.81 3.55
370 479 5.727434 TGCTTAGGCAGTTAGGTTAGTTAC 58.273 41.667 0.00 0.00 44.28 2.50
423 564 7.973388 CCAGTTTTCTGTCAATTGTTCTGTTTA 59.027 33.333 5.13 0.00 45.68 2.01
435 577 7.617041 ATTGTTCTGTTTAGCTAACCAGATC 57.383 36.000 27.97 26.05 35.81 2.75
437 579 5.932303 TGTTCTGTTTAGCTAACCAGATCAC 59.068 40.000 27.65 24.16 35.81 3.06
441 584 5.479306 TGTTTAGCTAACCAGATCACTGTC 58.521 41.667 5.45 0.00 42.05 3.51
451 597 3.497118 CAGATCACTGTCTCACGACTTC 58.503 50.000 0.00 0.00 40.86 3.01
519 665 3.155093 AGTTCAGCAACTGCAAAACTG 57.845 42.857 16.33 2.26 41.64 3.16
520 666 2.754552 AGTTCAGCAACTGCAAAACTGA 59.245 40.909 16.33 4.72 41.64 3.41
521 667 3.111098 GTTCAGCAACTGCAAAACTGAG 58.889 45.455 4.22 0.00 45.16 3.35
528 882 2.378038 ACTGCAAAACTGAGCCTTTCA 58.622 42.857 0.00 0.00 0.00 2.69
537 891 4.899352 ACTGAGCCTTTCATGTACTCTT 57.101 40.909 0.00 0.00 34.68 2.85
567 921 1.570347 AATTACGCCGCGTTTCTGCA 61.570 50.000 25.47 0.92 41.54 4.41
636 992 4.037923 ACAGAAATACCCAGCAACAAAGTG 59.962 41.667 0.00 0.00 0.00 3.16
637 993 4.037923 CAGAAATACCCAGCAACAAAGTGT 59.962 41.667 0.00 0.00 0.00 3.55
638 994 4.649218 AGAAATACCCAGCAACAAAGTGTT 59.351 37.500 0.00 0.00 42.08 3.32
706 1092 6.416750 GGAAAAATACTCAAAACCAGTTCGTG 59.583 38.462 0.00 0.00 0.00 4.35
783 1235 2.110578 AGGAGCAAGGCAAAACAGTTT 58.889 42.857 0.00 0.00 0.00 2.66
796 1248 5.681543 GCAAAACAGTTTAAGAAAGAGACGG 59.318 40.000 0.00 0.00 0.00 4.79
854 1306 3.817647 GCTGTCTTAACCATCCATCCATC 59.182 47.826 0.00 0.00 0.00 3.51
855 1307 4.392940 CTGTCTTAACCATCCATCCATCC 58.607 47.826 0.00 0.00 0.00 3.51
856 1308 3.785325 TGTCTTAACCATCCATCCATCCA 59.215 43.478 0.00 0.00 0.00 3.41
857 1309 4.416513 TGTCTTAACCATCCATCCATCCAT 59.583 41.667 0.00 0.00 0.00 3.41
858 1310 5.006386 GTCTTAACCATCCATCCATCCATC 58.994 45.833 0.00 0.00 0.00 3.51
859 1311 2.986534 AACCATCCATCCATCCATCC 57.013 50.000 0.00 0.00 0.00 3.51
860 1312 0.694771 ACCATCCATCCATCCATCCG 59.305 55.000 0.00 0.00 0.00 4.18
861 1313 0.694771 CCATCCATCCATCCATCCGT 59.305 55.000 0.00 0.00 0.00 4.69
906 1457 0.179004 AGTCAATTGCCCCACGAACA 60.179 50.000 0.00 0.00 0.00 3.18
967 1518 3.622060 AAACCCAGATGACCCCGCG 62.622 63.158 0.00 0.00 0.00 6.46
984 1535 2.081212 CGGACAAGTCACGACGAGC 61.081 63.158 0.00 0.00 36.20 5.03
985 1536 1.733399 GGACAAGTCACGACGAGCC 60.733 63.158 0.00 0.00 36.20 4.70
987 1538 2.805353 CAAGTCACGACGAGCCCG 60.805 66.667 0.00 0.00 42.50 6.13
988 1539 4.719369 AAGTCACGACGAGCCCGC 62.719 66.667 0.00 0.00 39.95 6.13
1044 1598 2.113139 CCGTTGCTCCCACCTTGT 59.887 61.111 0.00 0.00 0.00 3.16
1053 1607 2.938756 GCTCCCACCTTGTCAAGATGAG 60.939 54.545 14.42 13.18 0.00 2.90
1059 1613 2.575279 ACCTTGTCAAGATGAGCAGGAT 59.425 45.455 14.42 0.00 0.00 3.24
1060 1614 3.776969 ACCTTGTCAAGATGAGCAGGATA 59.223 43.478 14.42 0.00 0.00 2.59
1061 1615 4.225942 ACCTTGTCAAGATGAGCAGGATAA 59.774 41.667 14.42 0.00 0.00 1.75
1065 1619 4.100653 TGTCAAGATGAGCAGGATAAGGAG 59.899 45.833 0.00 0.00 0.00 3.69
1071 1625 0.687757 AGCAGGATAAGGAGGACGCA 60.688 55.000 0.00 0.00 0.00 5.24
1073 1627 0.390860 CAGGATAAGGAGGACGCAGG 59.609 60.000 0.00 0.00 0.00 4.85
1152 1706 3.378427 GCTTGGGAATTACTAGCTTGTGG 59.622 47.826 11.27 0.00 0.00 4.17
1169 1723 5.163581 GCTTGTGGTAGATTGCTGATGAAAT 60.164 40.000 0.00 0.00 0.00 2.17
1170 1724 6.441093 TTGTGGTAGATTGCTGATGAAATC 57.559 37.500 0.00 0.00 45.83 2.17
1348 1902 3.612371 GACTTCAGCGCCGACGAGT 62.612 63.158 2.29 0.00 43.93 4.18
1349 1903 2.430921 CTTCAGCGCCGACGAGTT 60.431 61.111 2.29 0.00 43.93 3.01
1407 1967 2.190578 CAAGGTCCGCCCATCTCC 59.809 66.667 0.00 0.00 34.66 3.71
1415 1976 1.361993 CGCCCATCTCCTCTCTTCG 59.638 63.158 0.00 0.00 0.00 3.79
1423 1987 1.285078 TCTCCTCTCTTCGGTGATCCA 59.715 52.381 0.00 0.00 0.00 3.41
1464 2028 2.279784 CCGCTCTGCTTCGATCCC 60.280 66.667 0.00 0.00 0.00 3.85
1465 2029 2.790791 CCGCTCTGCTTCGATCCCT 61.791 63.158 0.00 0.00 0.00 4.20
1467 2031 0.460987 CGCTCTGCTTCGATCCCTTT 60.461 55.000 0.00 0.00 0.00 3.11
1472 2036 0.253044 TGCTTCGATCCCTTTGGAGG 59.747 55.000 0.00 0.00 46.08 4.30
1503 2077 2.813754 TGTGCTTACAGAAATGCAGACC 59.186 45.455 0.00 0.00 36.03 3.85
1519 2093 2.030007 CAGACCACCACATTGCGAATTT 60.030 45.455 0.00 0.00 0.00 1.82
1553 2127 1.335810 CCTCACAATGGATGATTGGCG 59.664 52.381 0.00 0.00 45.20 5.69
1557 2131 0.313043 CAATGGATGATTGGCGAGCC 59.687 55.000 7.26 7.26 38.27 4.70
1560 2134 0.464373 TGGATGATTGGCGAGCCTTC 60.464 55.000 15.75 12.20 36.94 3.46
1603 2177 2.343843 CGCTTTCTCGTCTGAGTTCATG 59.656 50.000 0.00 0.00 43.09 3.07
1604 2178 3.579709 GCTTTCTCGTCTGAGTTCATGA 58.420 45.455 0.00 0.00 43.09 3.07
1629 2212 0.670854 GAGCGTCCCCAGTTCAGTTC 60.671 60.000 0.00 0.00 0.00 3.01
1634 2217 0.971386 TCCCCAGTTCAGTTCCGTAC 59.029 55.000 0.00 0.00 0.00 3.67
1640 2223 2.165030 CAGTTCAGTTCCGTACGGGTAT 59.835 50.000 32.80 16.41 37.00 2.73
1641 2224 2.827921 AGTTCAGTTCCGTACGGGTATT 59.172 45.455 32.80 15.80 37.00 1.89
1683 2267 3.365472 GCTCACACCCCTTTCCATTAAT 58.635 45.455 0.00 0.00 0.00 1.40
3434 4059 8.860088 AGCTTTTTAATCAGTTTACCATCAAGT 58.140 29.630 0.00 0.00 0.00 3.16
3573 4198 6.544564 ACTCGACATTTTTAACCAGGAGAAAA 59.455 34.615 0.00 0.00 0.00 2.29
3590 4216 4.127907 AGAAAAGTTTGGTCGAGGAGTTC 58.872 43.478 0.00 0.00 0.00 3.01
3642 4269 1.002430 TCGTCTCAAAGCCTGCTTGAT 59.998 47.619 4.95 0.00 36.26 2.57
3643 4270 1.808945 CGTCTCAAAGCCTGCTTGATT 59.191 47.619 4.95 0.00 36.26 2.57
3644 4271 2.413765 CGTCTCAAAGCCTGCTTGATTG 60.414 50.000 4.95 0.52 36.26 2.67
3645 4272 2.816087 GTCTCAAAGCCTGCTTGATTGA 59.184 45.455 4.95 5.01 36.26 2.57
3661 4295 2.373335 TTGAGCCAAAAGGGTTAGCA 57.627 45.000 0.00 0.00 39.65 3.49
3705 4339 4.404691 CCTTTTCGAGGCTGCCTT 57.595 55.556 24.26 6.49 39.09 4.35
3762 4396 4.126437 GGCTGTTAATTTGTTTTGTGCCT 58.874 39.130 0.00 0.00 34.42 4.75
3766 4400 6.256757 GCTGTTAATTTGTTTTGTGCCTTGTA 59.743 34.615 0.00 0.00 0.00 2.41
3767 4401 7.201565 GCTGTTAATTTGTTTTGTGCCTTGTAA 60.202 33.333 0.00 0.00 0.00 2.41
3768 4402 8.190888 TGTTAATTTGTTTTGTGCCTTGTAAG 57.809 30.769 0.00 0.00 0.00 2.34
3769 4403 8.035394 TGTTAATTTGTTTTGTGCCTTGTAAGA 58.965 29.630 0.00 0.00 0.00 2.10
3770 4404 8.539674 GTTAATTTGTTTTGTGCCTTGTAAGAG 58.460 33.333 0.00 0.00 0.00 2.85
3771 4405 5.906113 TTTGTTTTGTGCCTTGTAAGAGA 57.094 34.783 0.00 0.00 0.00 3.10
3772 4406 5.499139 TTGTTTTGTGCCTTGTAAGAGAG 57.501 39.130 0.00 0.00 0.00 3.20
3773 4407 3.882888 TGTTTTGTGCCTTGTAAGAGAGG 59.117 43.478 0.00 0.00 36.09 3.69
3774 4408 4.134563 GTTTTGTGCCTTGTAAGAGAGGA 58.865 43.478 0.00 0.00 34.91 3.71
3776 4410 3.895232 TGTGCCTTGTAAGAGAGGATC 57.105 47.619 0.00 0.00 34.91 3.36
3795 4429 8.684386 GAGGATCTAAATCTTTTAGAAAGGGG 57.316 38.462 12.31 0.00 34.99 4.79
3876 4520 3.731216 CGATGATCATACGTGTTCTGACC 59.269 47.826 8.54 0.00 0.00 4.02
3879 4523 0.885879 TCATACGTGTTCTGACCGCT 59.114 50.000 0.00 0.00 0.00 5.52
3885 4529 2.066262 CGTGTTCTGACCGCTATGTTT 58.934 47.619 0.00 0.00 0.00 2.83
3887 4531 1.804151 TGTTCTGACCGCTATGTTTGC 59.196 47.619 0.00 0.00 0.00 3.68
3893 4537 1.599542 GACCGCTATGTTTGCTCCATC 59.400 52.381 0.00 0.00 0.00 3.51
3911 4555 0.755079 TCTGTGCAGAGAAGTGCTGT 59.245 50.000 11.79 0.00 44.32 4.40
3914 4558 0.040603 GTGCAGAGAAGTGCTGTTGC 60.041 55.000 0.00 0.00 44.32 4.17
3931 4575 1.846007 TGCTGGGAACACAAACTGTT 58.154 45.000 0.00 0.00 46.44 3.16
3941 4585 5.505173 AACACAAACTGTTTGATGAGGAG 57.495 39.130 33.05 17.44 40.45 3.69
3990 4634 6.035542 GGGCACGATTGGTAATTTAATTGTTG 59.964 38.462 0.00 0.00 30.42 3.33
4040 4684 2.559998 AAACAGTTGTTGGCAGTTCG 57.440 45.000 0.00 0.00 38.44 3.95
4104 4751 3.490348 ACCTTATATCCATGCCAGCAAC 58.510 45.455 0.00 0.00 0.00 4.17
4120 4767 4.503910 CAGCAACTAGGCATTGTGTAGTA 58.496 43.478 0.00 0.00 35.83 1.82
4166 4813 6.121776 TGGATAGTGCTTTTCCACTTTCTA 57.878 37.500 10.85 4.46 43.19 2.10
4172 4819 7.150783 AGTGCTTTTCCACTTTCTATGAATC 57.849 36.000 0.00 0.00 43.19 2.52
4236 4887 4.876107 CGGTCTGACTTTACATAAAGCCAT 59.124 41.667 7.85 0.00 44.92 4.40
4237 4888 5.354234 CGGTCTGACTTTACATAAAGCCATT 59.646 40.000 7.85 0.00 44.92 3.16
4239 4890 7.574967 CGGTCTGACTTTACATAAAGCCATTTT 60.575 37.037 7.85 0.00 44.92 1.82
4341 4992 6.644136 GTTTTGTTACATTAAACGACCGTC 57.356 37.500 0.00 0.00 31.76 4.79
4379 5030 0.527600 CGCGCTGCCTTACATACTGA 60.528 55.000 5.56 0.00 0.00 3.41
4389 5040 5.105675 TGCCTTACATACTGACACGAACATA 60.106 40.000 0.00 0.00 0.00 2.29
4400 5051 5.060506 TGACACGAACATATGTTTGACCTT 58.939 37.500 33.17 18.03 40.94 3.50
4503 5154 1.800586 TGCAATTCAGAGACACTTCGC 59.199 47.619 0.00 0.00 0.00 4.70
4592 5245 5.860941 TGGCCTTTTTGACAGTATTTTCA 57.139 34.783 3.32 0.00 0.00 2.69
4627 5280 7.013750 TGTGTGGTTACTGAAATAAAATGCTCA 59.986 33.333 0.00 0.00 0.00 4.26
4649 5302 0.814010 ACGCCTGGTTTCTGTCACAC 60.814 55.000 0.00 0.00 0.00 3.82
4905 5558 5.455392 ACTTTCAATTGCACGAATCTTCAG 58.545 37.500 0.00 0.00 0.00 3.02
5135 5793 5.209659 AGTTACGGAGGGAGTATCTGAAAT 58.790 41.667 0.00 0.00 33.73 2.17
5144 5802 7.255625 GGAGGGAGTATCTGAAATTTATTTGGC 60.256 40.741 0.00 0.00 33.73 4.52
5173 5832 6.374333 TGGCTGGTATCTAATCAGTTTTTCAC 59.626 38.462 0.00 0.00 0.00 3.18
5194 5853 2.334838 CCGTGTCACACCTTAGCTTAC 58.665 52.381 1.24 0.00 0.00 2.34
5407 6073 3.871463 GCTGAAGATGACCATCCAGTTGT 60.871 47.826 13.75 0.00 38.58 3.32
5411 6077 5.719563 TGAAGATGACCATCCAGTTGTAGTA 59.280 40.000 6.40 0.00 38.58 1.82
5560 6226 1.207089 TCTTAGTGAGGCCGACAATGG 59.793 52.381 14.18 8.33 0.00 3.16
5965 6631 9.331466 AGATAATCTGGACCATGATGTTAGTAT 57.669 33.333 0.00 0.00 0.00 2.12
5987 6653 9.053840 AGTATCGATAATAGAGTCGTTGAAAGA 57.946 33.333 6.72 0.00 38.85 2.52
6218 6884 6.591062 TCATGCCTAAGTTTTCATTTCATTGC 59.409 34.615 0.00 0.00 0.00 3.56
6262 6928 8.618702 ATCAGTTCTTATTAGATTCAGCATGG 57.381 34.615 0.00 0.00 36.16 3.66
6288 6954 9.632807 GATACACTTGTTGGATACTATCTGATC 57.367 37.037 0.00 0.00 37.61 2.92
6324 6990 5.845103 TGATGACATTTGTTTCTGCAATGT 58.155 33.333 0.00 0.00 0.00 2.71
6528 7194 2.415512 GACCATGAGTAAGTCGGCAAAC 59.584 50.000 0.00 0.00 0.00 2.93
6687 7353 7.009179 AGAACACATGAACTTATCTCCAGAA 57.991 36.000 0.00 0.00 0.00 3.02
6895 7561 6.554334 TTTAATTCAGATAAGTATGCGGGC 57.446 37.500 0.00 0.00 0.00 6.13
6991 7657 8.390354 TGTTTCGCACATTTAATCTGATAAGAG 58.610 33.333 0.00 0.00 0.00 2.85
7060 7726 2.194271 GCATACTTCTGTAGGTGCGAC 58.806 52.381 0.00 0.00 33.48 5.19
7075 7741 2.284417 GTGCGACCGGATTCTTTCATAC 59.716 50.000 9.46 0.00 0.00 2.39
7199 7865 3.004106 CCACAGAAAGTTTCAGAAGGCTG 59.996 47.826 17.65 7.64 43.67 4.85
7225 7891 5.808042 CATTCACCAATGTAGAGGTTGAG 57.192 43.478 0.00 0.00 35.52 3.02
7272 7938 5.913137 AACACTTGTTGAATGAAGAACCA 57.087 34.783 0.00 0.00 36.80 3.67
7292 7958 3.055602 CCATGGACTGTGAGAGAACATGA 60.056 47.826 5.56 0.00 39.54 3.07
7362 8028 8.918202 ATTTCAGACAAGTTACCAGAATGTAA 57.082 30.769 0.00 0.00 0.00 2.41
7377 8043 5.238214 CAGAATGTAAAGAAGCAGATAGGGC 59.762 44.000 0.00 0.00 0.00 5.19
7582 8280 9.516314 GTACTGTTCTTGCTTCTTTTTAATGTT 57.484 29.630 0.00 0.00 0.00 2.71
7609 8307 9.904198 TGATGATGATTAACCACTCAAGATAAA 57.096 29.630 0.00 0.00 0.00 1.40
7640 8338 6.899114 AGCTGCTAAGTACAAACATGTAAAC 58.101 36.000 0.00 0.00 0.00 2.01
7645 8343 9.856488 TGCTAAGTACAAACATGTAAACAAAAA 57.144 25.926 0.00 0.00 0.00 1.94
7676 9462 5.184711 ACACTTGAAAATGTTGCCAACAAT 58.815 33.333 15.17 2.79 45.86 2.71
7710 9496 3.099438 CGAGAGCAAGCATGGCAG 58.901 61.111 0.00 0.00 37.68 4.85
7738 9524 3.276857 CATGGAGACTTGGTTGAGATGG 58.723 50.000 0.00 0.00 32.13 3.51
7824 9610 0.983467 TGGACACCATGAGCAGCTTA 59.017 50.000 0.00 0.00 0.00 3.09
7830 9616 3.091633 ACCATGAGCAGCTTAAATGGT 57.908 42.857 23.32 23.32 44.80 3.55
7833 9619 1.737838 TGAGCAGCTTAAATGGTCCG 58.262 50.000 13.88 0.00 43.00 4.79
8078 9864 1.826340 TAGCGTCCAAGGCAGAAGCA 61.826 55.000 11.28 0.00 44.61 3.91
8084 9870 1.302033 CAAGGCAGAAGCACTCCGT 60.302 57.895 0.00 0.00 44.61 4.69
8114 9900 4.430388 TGGAGGGTCCAGGTTGTT 57.570 55.556 0.00 0.00 42.67 2.83
8117 9903 1.074951 GAGGGTCCAGGTTGTTGGG 59.925 63.158 0.00 0.00 38.81 4.12
8119 9905 2.117423 GGTCCAGGTTGTTGGGGG 59.883 66.667 0.00 0.00 38.81 5.40
8184 9970 4.025401 GTGGTGGGCGTGAAAGCG 62.025 66.667 0.00 0.00 38.18 4.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 5.123820 TGCGCTGACTATTAGCTTGAATTTT 59.876 36.000 9.73 0.00 39.00 1.82
13 14 4.635765 TGCGCTGACTATTAGCTTGAATTT 59.364 37.500 9.73 0.00 39.00 1.82
17 18 2.930040 GTTGCGCTGACTATTAGCTTGA 59.070 45.455 9.73 0.00 39.00 3.02
50 56 5.010516 TGGTTGAGGGTCATTTTTGTGTATG 59.989 40.000 0.00 0.00 0.00 2.39
107 213 2.500888 CGCGACGCATGTTTATTTTCA 58.499 42.857 21.35 0.00 0.00 2.69
154 260 3.148340 GTACCTGGGCTTTGGTACG 57.852 57.895 14.60 0.00 45.89 3.67
164 270 5.841957 AAATACTACTACGTGTACCTGGG 57.158 43.478 0.00 0.00 0.00 4.45
167 273 7.414540 CGAAGGAAAATACTACTACGTGTACCT 60.415 40.741 0.00 0.00 0.00 3.08
174 280 9.559958 TTAAACTCGAAGGAAAATACTACTACG 57.440 33.333 0.00 0.00 0.00 3.51
188 297 5.065218 CCAACCTGATGATTAAACTCGAAGG 59.935 44.000 0.00 0.00 0.00 3.46
205 314 3.733709 GGCATATCCCTCCAACCTG 57.266 57.895 0.00 0.00 0.00 4.00
215 324 0.321653 GACATGTCCCGGGCATATCC 60.322 60.000 24.22 14.86 0.00 2.59
216 325 0.670546 CGACATGTCCCGGGCATATC 60.671 60.000 24.22 22.05 0.00 1.63
217 326 1.371183 CGACATGTCCCGGGCATAT 59.629 57.895 24.22 16.94 0.00 1.78
218 327 2.818841 CGACATGTCCCGGGCATA 59.181 61.111 24.22 11.15 0.00 3.14
266 375 8.313292 TGATTTCCAATGAGTTCCAATAAAAGG 58.687 33.333 0.00 0.00 0.00 3.11
272 381 6.268387 AGTTGTGATTTCCAATGAGTTCCAAT 59.732 34.615 0.00 0.00 0.00 3.16
273 382 5.598005 AGTTGTGATTTCCAATGAGTTCCAA 59.402 36.000 0.00 0.00 0.00 3.53
291 400 5.104374 GCCCAATCATGTGAATTAGTTGTG 58.896 41.667 0.00 0.00 0.00 3.33
329 438 7.210174 CCTAAGCACATTATTCTACAGCAGTA 58.790 38.462 0.00 0.00 0.00 2.74
364 473 2.167693 CCACCTCAATCAGCCGTAACTA 59.832 50.000 0.00 0.00 0.00 2.24
370 479 2.620251 TAATCCACCTCAATCAGCCG 57.380 50.000 0.00 0.00 0.00 5.52
423 564 3.194542 GTGAGACAGTGATCTGGTTAGCT 59.805 47.826 0.00 0.00 45.14 3.32
441 584 9.450807 AATTTGTTATGAAAAAGAAGTCGTGAG 57.549 29.630 0.00 0.00 0.00 3.51
485 631 6.536582 AGTTGCTGAACTGTAGTGCAATATAG 59.463 38.462 15.26 15.26 43.87 1.31
490 636 2.917933 AGTTGCTGAACTGTAGTGCAA 58.082 42.857 9.19 9.19 41.12 4.08
501 647 2.480073 GCTCAGTTTTGCAGTTGCTGAA 60.480 45.455 5.62 0.00 42.66 3.02
516 662 4.899352 AAGAGTACATGAAAGGCTCAGT 57.101 40.909 0.00 0.00 37.52 3.41
517 663 6.566197 AAAAAGAGTACATGAAAGGCTCAG 57.434 37.500 0.00 0.00 37.52 3.35
613 967 4.037923 CACTTTGTTGCTGGGTATTTCTGT 59.962 41.667 0.00 0.00 0.00 3.41
622 976 3.965780 GGAACACTTTGTTGCTGGG 57.034 52.632 3.54 0.00 43.96 4.45
636 992 4.022068 TGTGCATTTCATTCAGGAAGGAAC 60.022 41.667 8.46 0.00 40.25 3.62
637 993 4.151121 TGTGCATTTCATTCAGGAAGGAA 58.849 39.130 5.13 5.13 39.03 3.36
638 994 3.765381 TGTGCATTTCATTCAGGAAGGA 58.235 40.909 0.00 0.00 0.00 3.36
682 1068 6.416750 CCACGAACTGGTTTTGAGTATTTTTC 59.583 38.462 0.00 0.00 34.90 2.29
683 1069 6.095720 TCCACGAACTGGTTTTGAGTATTTTT 59.904 34.615 0.00 0.00 41.52 1.94
744 1160 6.437477 TGCTCCTAACCGTATCATCATTATCT 59.563 38.462 0.00 0.00 0.00 1.98
745 1161 6.631016 TGCTCCTAACCGTATCATCATTATC 58.369 40.000 0.00 0.00 0.00 1.75
746 1162 6.605471 TGCTCCTAACCGTATCATCATTAT 57.395 37.500 0.00 0.00 0.00 1.28
748 1164 4.955811 TGCTCCTAACCGTATCATCATT 57.044 40.909 0.00 0.00 0.00 2.57
751 1203 3.654414 CCTTGCTCCTAACCGTATCATC 58.346 50.000 0.00 0.00 0.00 2.92
783 1235 1.217244 GCCCGCCGTCTCTTTCTTA 59.783 57.895 0.00 0.00 0.00 2.10
854 1306 2.658593 GCGATGACGGACGGATGG 60.659 66.667 0.00 0.00 40.15 3.51
855 1307 2.658593 GGCGATGACGGACGGATG 60.659 66.667 0.00 0.00 40.15 3.51
856 1308 4.266070 CGGCGATGACGGACGGAT 62.266 66.667 0.00 0.00 40.15 4.18
967 1518 1.733399 GGCTCGTCGTGACTTGTCC 60.733 63.158 0.00 0.00 0.00 4.02
987 1538 2.126346 GCCATTGCCGTTCTGTGC 60.126 61.111 0.00 0.00 0.00 4.57
988 1539 2.176546 CGCCATTGCCGTTCTGTG 59.823 61.111 0.00 0.00 0.00 3.66
989 1540 2.281484 ACGCCATTGCCGTTCTGT 60.281 55.556 0.00 0.00 34.96 3.41
991 1542 2.746277 GGACGCCATTGCCGTTCT 60.746 61.111 0.00 0.00 39.30 3.01
993 1544 2.746277 GAGGACGCCATTGCCGTT 60.746 61.111 0.00 0.00 39.30 4.44
1037 1591 2.082231 CCTGCTCATCTTGACAAGGTG 58.918 52.381 20.49 20.49 41.07 4.00
1044 1598 3.645212 CCTCCTTATCCTGCTCATCTTGA 59.355 47.826 0.00 0.00 0.00 3.02
1053 1607 0.249657 CTGCGTCCTCCTTATCCTGC 60.250 60.000 0.00 0.00 0.00 4.85
1059 1613 2.978824 GCACCTGCGTCCTCCTTA 59.021 61.111 0.00 0.00 0.00 2.69
1097 1651 3.077556 CCAGTACCTGCTCCCGCT 61.078 66.667 0.00 0.00 36.97 5.52
1152 1706 4.024556 CCACCGATTTCATCAGCAATCTAC 60.025 45.833 0.00 0.00 0.00 2.59
1407 1967 2.224161 GGGAATGGATCACCGAAGAGAG 60.224 54.545 0.00 0.00 39.42 3.20
1423 1987 1.758122 GCGCAGGAAATGGGGGAAT 60.758 57.895 0.30 0.00 42.01 3.01
1478 2042 5.748152 GTCTGCATTTCTGTAAGCACAAAAA 59.252 36.000 0.00 0.00 33.22 1.94
1479 2043 5.280945 GTCTGCATTTCTGTAAGCACAAAA 58.719 37.500 0.00 0.00 33.22 2.44
1480 2044 4.261572 GGTCTGCATTTCTGTAAGCACAAA 60.262 41.667 0.00 0.00 33.22 2.83
1481 2045 3.253188 GGTCTGCATTTCTGTAAGCACAA 59.747 43.478 0.00 0.00 33.22 3.33
1482 2046 2.813754 GGTCTGCATTTCTGTAAGCACA 59.186 45.455 0.00 0.00 32.87 4.57
1484 2048 2.813754 GTGGTCTGCATTTCTGTAAGCA 59.186 45.455 0.00 0.00 35.43 3.91
1485 2049 2.162408 GGTGGTCTGCATTTCTGTAAGC 59.838 50.000 0.00 0.00 0.00 3.09
1486 2050 3.189287 GTGGTGGTCTGCATTTCTGTAAG 59.811 47.826 0.00 0.00 0.00 2.34
1488 2052 2.105649 TGTGGTGGTCTGCATTTCTGTA 59.894 45.455 0.00 0.00 0.00 2.74
1489 2053 1.133823 TGTGGTGGTCTGCATTTCTGT 60.134 47.619 0.00 0.00 0.00 3.41
1490 2054 1.608055 TGTGGTGGTCTGCATTTCTG 58.392 50.000 0.00 0.00 0.00 3.02
1491 2055 2.559668 CAATGTGGTGGTCTGCATTTCT 59.440 45.455 0.00 0.00 30.17 2.52
1492 2056 2.927871 GCAATGTGGTGGTCTGCATTTC 60.928 50.000 0.00 0.00 33.19 2.17
1493 2057 1.001181 GCAATGTGGTGGTCTGCATTT 59.999 47.619 0.00 0.00 33.19 2.32
1494 2058 0.604578 GCAATGTGGTGGTCTGCATT 59.395 50.000 0.00 0.00 33.19 3.56
1495 2059 1.588824 CGCAATGTGGTGGTCTGCAT 61.589 55.000 0.00 0.00 33.19 3.96
1503 2077 1.780806 TGCAAATTCGCAATGTGGTG 58.219 45.000 0.00 0.00 39.45 4.17
1519 2093 2.202878 GAGGCTATCGGCGTTGCA 60.203 61.111 6.85 0.00 42.94 4.08
1527 2101 3.391506 TCATCCATTGTGAGGCTATCG 57.608 47.619 0.00 0.00 0.00 2.92
1557 2131 4.796038 AATGAACAATTGAGCTGGGAAG 57.204 40.909 13.59 0.00 0.00 3.46
1603 2177 0.179000 ACTGGGGACGCTCATGAATC 59.821 55.000 0.00 0.00 0.00 2.52
1604 2178 0.620556 AACTGGGGACGCTCATGAAT 59.379 50.000 0.00 0.00 0.00 2.57
1615 2198 0.971386 GTACGGAACTGAACTGGGGA 59.029 55.000 0.00 0.00 0.00 4.81
1617 2200 0.389426 CCGTACGGAACTGAACTGGG 60.389 60.000 30.64 0.00 37.50 4.45
1654 2237 4.265056 GGGTGTGAGCCCGGTTGT 62.265 66.667 0.00 0.00 39.17 3.32
1683 2267 6.925718 TGATGTATTTCCGTTGATTGCAAAAA 59.074 30.769 1.71 0.00 35.42 1.94
1941 2534 4.141482 ACTGGTAGTTGCTTCTCTGGAAAA 60.141 41.667 0.00 0.00 0.00 2.29
3547 4172 4.994852 TCTCCTGGTTAAAAATGTCGAGTG 59.005 41.667 0.00 0.00 0.00 3.51
3590 4216 3.004106 GCATCAGGAATTTGGAATCCTCG 59.996 47.826 0.00 0.00 44.26 4.63
3642 4269 2.373335 TGCTAACCCTTTTGGCTCAA 57.627 45.000 0.00 0.00 37.83 3.02
3643 4270 2.373335 TTGCTAACCCTTTTGGCTCA 57.627 45.000 0.00 0.00 37.83 4.26
3644 4271 3.744238 TTTTGCTAACCCTTTTGGCTC 57.256 42.857 0.00 0.00 37.83 4.70
3645 4272 3.454447 ACTTTTTGCTAACCCTTTTGGCT 59.546 39.130 0.00 0.00 37.83 4.75
3661 4295 4.759183 TGTTCAAAAGCAGCCAAACTTTTT 59.241 33.333 0.00 0.00 42.00 1.94
3673 4307 0.820871 AAAGGCGGTGTTCAAAAGCA 59.179 45.000 0.00 0.00 0.00 3.91
3768 4402 9.554395 CCCTTTCTAAAAGATTTAGATCCTCTC 57.446 37.037 12.02 0.00 31.78 3.20
3769 4403 8.498575 CCCCTTTCTAAAAGATTTAGATCCTCT 58.501 37.037 12.02 0.00 31.78 3.69
3770 4404 8.495260 TCCCCTTTCTAAAAGATTTAGATCCTC 58.505 37.037 12.02 0.00 31.78 3.71
3771 4405 8.407313 TCCCCTTTCTAAAAGATTTAGATCCT 57.593 34.615 12.02 0.00 31.78 3.24
3772 4406 9.475620 TTTCCCCTTTCTAAAAGATTTAGATCC 57.524 33.333 12.02 0.00 31.78 3.36
3777 4411 9.608718 TGGATTTTCCCCTTTCTAAAAGATTTA 57.391 29.630 1.06 0.00 35.03 1.40
3778 4412 8.504811 TGGATTTTCCCCTTTCTAAAAGATTT 57.495 30.769 1.06 0.00 35.03 2.17
3779 4413 8.542926 CATGGATTTTCCCCTTTCTAAAAGATT 58.457 33.333 1.06 0.00 35.03 2.40
3780 4414 7.126268 CCATGGATTTTCCCCTTTCTAAAAGAT 59.874 37.037 5.56 0.00 35.03 2.40
3781 4415 6.440328 CCATGGATTTTCCCCTTTCTAAAAGA 59.560 38.462 5.56 0.00 35.03 2.52
3782 4416 6.643388 CCATGGATTTTCCCCTTTCTAAAAG 58.357 40.000 5.56 0.00 35.03 2.27
3783 4417 5.045942 GCCATGGATTTTCCCCTTTCTAAAA 60.046 40.000 18.40 0.00 35.03 1.52
3785 4419 4.030216 GCCATGGATTTTCCCCTTTCTAA 58.970 43.478 18.40 0.00 35.03 2.10
3786 4420 3.642141 GCCATGGATTTTCCCCTTTCTA 58.358 45.455 18.40 0.00 35.03 2.10
3787 4421 2.470990 GCCATGGATTTTCCCCTTTCT 58.529 47.619 18.40 0.00 35.03 2.52
3788 4422 1.136891 CGCCATGGATTTTCCCCTTTC 59.863 52.381 18.40 0.00 35.03 2.62
3789 4423 1.194218 CGCCATGGATTTTCCCCTTT 58.806 50.000 18.40 0.00 35.03 3.11
3791 4425 1.758122 GCGCCATGGATTTTCCCCT 60.758 57.895 18.40 0.00 35.03 4.79
3793 4427 0.536724 AAAGCGCCATGGATTTTCCC 59.463 50.000 18.40 0.00 35.03 3.97
3795 4429 4.622740 GCATATAAAGCGCCATGGATTTTC 59.377 41.667 18.40 0.00 0.00 2.29
3830 4470 7.330454 TCGATATCAATCTGCAGATTTAAGCTC 59.670 37.037 34.17 24.32 42.41 4.09
3876 4520 2.031314 CACAGATGGAGCAAACATAGCG 59.969 50.000 0.00 0.00 37.01 4.26
3879 4523 3.011818 CTGCACAGATGGAGCAAACATA 58.988 45.455 0.00 0.00 37.48 2.29
3885 4529 0.978907 TTCTCTGCACAGATGGAGCA 59.021 50.000 0.00 2.90 43.70 4.26
3887 4531 2.619147 CACTTCTCTGCACAGATGGAG 58.381 52.381 9.21 2.91 45.32 3.86
3893 4537 1.263484 CAACAGCACTTCTCTGCACAG 59.737 52.381 0.00 0.00 39.86 3.66
3911 4555 1.846007 ACAGTTTGTGTTCCCAGCAA 58.154 45.000 0.00 0.00 34.94 3.91
3931 4575 1.959985 GCGATCTCCTCTCCTCATCAA 59.040 52.381 0.00 0.00 0.00 2.57
3941 4585 0.526524 CAAGTCCACGCGATCTCCTC 60.527 60.000 15.93 0.00 0.00 3.71
3990 4634 6.566197 ACATTCTTCTCCAACAAATGAGAC 57.434 37.500 0.00 0.00 32.86 3.36
4085 4729 4.940046 CCTAGTTGCTGGCATGGATATAAG 59.060 45.833 0.00 0.00 0.00 1.73
4104 4751 8.942338 TTTTATCACTACTACACAATGCCTAG 57.058 34.615 0.00 0.00 0.00 3.02
4197 4848 5.869888 GTCAGACCGTCTGTTCTTTATCATT 59.130 40.000 24.56 0.00 44.58 2.57
4211 4862 4.329256 GGCTTTATGTAAAGTCAGACCGTC 59.671 45.833 11.20 0.00 44.87 4.79
4268 4919 0.407139 AAAGGCATCCAGGTGCTTCT 59.593 50.000 2.42 0.00 44.45 2.85
4341 4992 1.393539 CGTCAACGAATGGCTTACCAG 59.606 52.381 0.00 0.00 46.36 4.00
4379 5030 4.215399 CCAAGGTCAAACATATGTTCGTGT 59.785 41.667 21.02 3.10 37.25 4.49
4389 5040 5.358922 CAATTGTCAACCAAGGTCAAACAT 58.641 37.500 0.00 0.00 36.25 2.71
4400 5051 6.152492 TCAGCATATAAAGCAATTGTCAACCA 59.848 34.615 7.40 0.00 0.00 3.67
4475 5126 5.827797 AGTGTCTCTGAATTGCACCTTTTAA 59.172 36.000 0.00 0.00 0.00 1.52
4503 5154 2.159639 AGCGACATCGATATACTGAGCG 60.160 50.000 5.26 0.00 43.02 5.03
4567 5220 7.278875 TGAAAATACTGTCAAAAAGGCCAAAT 58.721 30.769 5.01 0.00 0.00 2.32
4627 5280 2.224426 TGTGACAGAAACCAGGCGTATT 60.224 45.455 0.00 0.00 0.00 1.89
5135 5793 6.372931 AGATACCAGCCAATAGCCAAATAAA 58.627 36.000 0.00 0.00 45.47 1.40
5144 5802 8.682936 AAAACTGATTAGATACCAGCCAATAG 57.317 34.615 0.00 0.00 0.00 1.73
5148 5806 6.374333 GTGAAAAACTGATTAGATACCAGCCA 59.626 38.462 0.00 0.00 0.00 4.75
5173 5832 0.034896 AAGCTAAGGTGTGACACGGG 59.965 55.000 9.90 1.00 34.83 5.28
5194 5853 8.246180 ACAACAAATCACATCTTAGCCAAATAG 58.754 33.333 0.00 0.00 0.00 1.73
5407 6073 7.533289 TCACGAATGATATGTTCCCATACTA 57.467 36.000 0.00 0.00 36.40 1.82
5411 6077 6.122277 AGTTTCACGAATGATATGTTCCCAT 58.878 36.000 0.00 0.00 33.85 4.00
5560 6226 2.356227 GGATGAAGTTCCCCCTCACTTC 60.356 54.545 0.00 5.30 46.26 3.01
5948 6614 9.737427 CTATTATCGATACTAACATCATGGTCC 57.263 37.037 4.16 0.00 0.00 4.46
5965 6631 8.975410 TTTTCTTTCAACGACTCTATTATCGA 57.025 30.769 0.00 0.00 40.86 3.59
6002 6668 5.398176 TTTGCTTGCTTATTATCCGTACG 57.602 39.130 8.69 8.69 0.00 3.67
6218 6884 4.711399 TGATATGAGATGACAAGGCAAGG 58.289 43.478 0.00 0.00 0.00 3.61
6262 6928 9.632807 GATCAGATAGTATCCAACAAGTGTATC 57.367 37.037 6.53 0.44 0.00 2.24
6288 6954 9.850628 AACAAATGTCATCAGATGATTTTGTAG 57.149 29.630 32.34 20.05 46.25 2.74
6324 6990 4.202398 GCTGACTGATATTGATCCCTGGAA 60.202 45.833 0.00 0.00 0.00 3.53
6528 7194 2.666619 GCAAAGATTCAGGCGACACAAG 60.667 50.000 0.00 0.00 0.00 3.16
6687 7353 7.552050 TGTCAAACAATAAATCCCATTCCTT 57.448 32.000 0.00 0.00 0.00 3.36
6793 7459 1.177401 GCCCTTTCATCAGTTCCCAC 58.823 55.000 0.00 0.00 0.00 4.61
6895 7561 0.317854 TCGCAGATATTGGCTCGTCG 60.318 55.000 0.00 0.00 0.00 5.12
6910 7576 0.610174 ATGCAGGTCTTCTTCTCGCA 59.390 50.000 0.00 0.00 0.00 5.10
6939 7605 2.225467 GCAGGAGCTTAATTAGGCAGG 58.775 52.381 20.30 8.43 37.91 4.85
6991 7657 2.295349 CCCAAACATGAGCTATGATGGC 59.705 50.000 0.00 0.00 41.61 4.40
7075 7741 1.315257 CCAACCTGATGCCCTTTCCG 61.315 60.000 0.00 0.00 0.00 4.30
7222 7888 6.138967 TCTCTCCAATAACAGATGATCCTCA 58.861 40.000 0.62 0.00 0.00 3.86
7225 7891 7.002250 TCATCTCTCCAATAACAGATGATCC 57.998 40.000 6.41 0.00 44.05 3.36
7251 7917 5.221303 CCATGGTTCTTCATTCAACAAGTGT 60.221 40.000 2.57 0.00 0.00 3.55
7272 7938 4.285517 ACTTCATGTTCTCTCACAGTCCAT 59.714 41.667 0.00 0.00 0.00 3.41
7292 7958 2.168521 TGCGCCTATGAGCTAAGAACTT 59.831 45.455 4.18 0.00 38.24 2.66
7362 8028 0.182299 GCCAGCCCTATCTGCTTCTT 59.818 55.000 0.00 0.00 36.81 2.52
7377 8043 3.562973 CCTAGTATGCATCAAACTGCCAG 59.437 47.826 0.19 0.00 41.58 4.85
7491 8157 8.502387 GCAGATCCTGTTAGATATGAACAATTC 58.498 37.037 0.60 0.00 37.62 2.17
7560 8227 8.994429 TCAAACATTAAAAAGAAGCAAGAACA 57.006 26.923 0.00 0.00 0.00 3.18
7582 8280 9.904198 TTATCTTGAGTGGTTAATCATCATCAA 57.096 29.630 11.29 11.29 30.10 2.57
7649 8347 5.590530 TGGCAACATTTTCAAGTGTACTT 57.409 34.783 0.00 0.00 46.17 2.24
7676 9462 2.721167 CGCAGTAGCCCTAGCACCA 61.721 63.158 0.00 0.00 43.56 4.17
7710 9496 1.956477 ACCAAGTCTCCATGTGCAAAC 59.044 47.619 0.00 0.00 0.00 2.93
7721 9507 2.479566 TGCCATCTCAACCAAGTCTC 57.520 50.000 0.00 0.00 0.00 3.36
7724 9510 1.742761 CGATGCCATCTCAACCAAGT 58.257 50.000 2.75 0.00 0.00 3.16
7820 9606 1.379527 CCACTCCGGACCATTTAAGC 58.620 55.000 0.00 0.00 36.56 3.09
7824 9610 1.002134 CTGCCACTCCGGACCATTT 60.002 57.895 0.00 0.00 36.56 2.32
8097 9883 1.715019 CCAACAACCTGGACCCTCCA 61.715 60.000 0.00 0.00 45.98 3.86
8117 9903 2.572284 CGAGGTCGTCTTCACCCC 59.428 66.667 0.00 0.00 33.96 4.95


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

AutoCloner maintained by Alex Coulton.