Multiple sequence alignment - TraesCS6B01G083900

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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 TraesCS6B01G083900 chr6B 100.000 2567 0 0 1 2567 60861456 60858890 0.000000e+00 4741
1 TraesCS6B01G083900 chr6B 91.647 419 32 1 6 421 61225681 61226099 6.160000e-161 577
2 TraesCS6B01G083900 chr6A 87.500 1440 118 36 1 1402 33540375 33538960 0.000000e+00 1605
3 TraesCS6B01G083900 chr6A 90.353 425 31 7 1 421 33585480 33585898 1.340000e-152 549
4 TraesCS6B01G083900 chr6A 78.172 733 112 25 926 1624 575446856 575447574 8.490000e-115 424
5 TraesCS6B01G083900 chr5D 81.766 1393 154 58 628 1956 114916238 114917594 0.000000e+00 1074
6 TraesCS6B01G083900 chr5D 78.534 382 63 12 809 1187 124540826 124540461 1.540000e-57 233
7 TraesCS6B01G083900 chr3B 81.484 1388 175 36 628 1964 562783760 562785116 0.000000e+00 1064
8 TraesCS6B01G083900 chr3B 81.132 1325 180 43 698 1966 761690556 761689246 0.000000e+00 998
9 TraesCS6B01G083900 chr3B 83.107 515 66 12 628 1127 761703919 761703411 1.400000e-122 449
10 TraesCS6B01G083900 chr3B 82.921 445 55 2 1 424 765002433 765001989 5.180000e-102 381
11 TraesCS6B01G083900 chr3B 86.885 244 24 5 1997 2235 562785176 562785416 1.510000e-67 267
12 TraesCS6B01G083900 chr3B 86.224 196 21 3 2026 2215 761689159 761688964 9.310000e-50 207
13 TraesCS6B01G083900 chr6D 91.772 632 43 5 1 627 29001009 29001636 0.000000e+00 870
14 TraesCS6B01G083900 chr6D 91.211 421 31 3 1 421 28940414 28940000 3.710000e-158 568
15 TraesCS6B01G083900 chr6D 79.576 661 106 17 985 1624 82906639 82907291 1.810000e-121 446
16 TraesCS6B01G083900 chr6D 77.353 733 118 25 926 1624 464533014 464532296 8.610000e-105 390
17 TraesCS6B01G083900 chr2B 77.096 847 136 37 809 1624 692145061 692145880 1.090000e-118 436
18 TraesCS6B01G083900 chr2D 84.821 448 44 9 628 1051 39206589 39207036 1.820000e-116 429
19 TraesCS6B01G083900 chr2D 78.095 735 111 26 926 1624 645194961 645195681 1.100000e-113 420
20 TraesCS6B01G083900 chr2D 83.333 468 38 12 2105 2567 39207037 39207469 1.850000e-106 396
21 TraesCS6B01G083900 chrUn 77.506 778 123 26 880 1624 33192937 33193695 1.100000e-113 420
22 TraesCS6B01G083900 chr1D 78.035 733 113 28 926 1624 490433038 490433756 3.950000e-113 418
23 TraesCS6B01G083900 chr3D 84.282 439 51 3 1 421 574919261 574919699 1.840000e-111 412
24 TraesCS6B01G083900 chr7B 75.952 840 154 28 809 1625 716374290 716373476 3.100000e-104 388
25 TraesCS6B01G083900 chr3A 85.926 270 38 0 155 424 710699254 710698985 3.230000e-74 289


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 TraesCS6B01G083900 chr6B 60858890 60861456 2566 True 4741.0 4741 100.0000 1 2567 1 chr6B.!!$R1 2566
1 TraesCS6B01G083900 chr6A 33538960 33540375 1415 True 1605.0 1605 87.5000 1 1402 1 chr6A.!!$R1 1401
2 TraesCS6B01G083900 chr6A 575446856 575447574 718 False 424.0 424 78.1720 926 1624 1 chr6A.!!$F2 698
3 TraesCS6B01G083900 chr5D 114916238 114917594 1356 False 1074.0 1074 81.7660 628 1956 1 chr5D.!!$F1 1328
4 TraesCS6B01G083900 chr3B 562783760 562785416 1656 False 665.5 1064 84.1845 628 2235 2 chr3B.!!$F1 1607
5 TraesCS6B01G083900 chr3B 761688964 761690556 1592 True 602.5 998 83.6780 698 2215 2 chr3B.!!$R3 1517
6 TraesCS6B01G083900 chr3B 761703411 761703919 508 True 449.0 449 83.1070 628 1127 1 chr3B.!!$R1 499
7 TraesCS6B01G083900 chr6D 29001009 29001636 627 False 870.0 870 91.7720 1 627 1 chr6D.!!$F1 626
8 TraesCS6B01G083900 chr6D 82906639 82907291 652 False 446.0 446 79.5760 985 1624 1 chr6D.!!$F2 639
9 TraesCS6B01G083900 chr6D 464532296 464533014 718 True 390.0 390 77.3530 926 1624 1 chr6D.!!$R2 698
10 TraesCS6B01G083900 chr2B 692145061 692145880 819 False 436.0 436 77.0960 809 1624 1 chr2B.!!$F1 815
11 TraesCS6B01G083900 chr2D 645194961 645195681 720 False 420.0 420 78.0950 926 1624 1 chr2D.!!$F1 698
12 TraesCS6B01G083900 chr2D 39206589 39207469 880 False 412.5 429 84.0770 628 2567 2 chr2D.!!$F2 1939
13 TraesCS6B01G083900 chrUn 33192937 33193695 758 False 420.0 420 77.5060 880 1624 1 chrUn.!!$F1 744
14 TraesCS6B01G083900 chr1D 490433038 490433756 718 False 418.0 418 78.0350 926 1624 1 chr1D.!!$F1 698
15 TraesCS6B01G083900 chr7B 716373476 716374290 814 True 388.0 388 75.9520 809 1625 1 chr7B.!!$R1 816

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
321 325 0.963962 GAGGGTCGTGGTCAACTACA 59.036 55.0 0.0 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1957 2157 0.387565 AACACGGGTGCACCATTTTC 59.612 50.0 35.78 17.87 40.22 2.29 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
26 27 3.737172 GCCGAGCACCGCATGTTT 61.737 61.111 0.00 0.00 36.84 2.83
236 240 1.153765 CATCGACGCAGAGCTGGAA 60.154 57.895 0.00 0.00 0.00 3.53
257 261 2.431942 GGCGTGGTGTACCTGACG 60.432 66.667 8.94 8.94 38.14 4.35
306 310 2.202932 CGCCGGTGATGAAGAGGG 60.203 66.667 10.20 0.00 0.00 4.30
321 325 0.963962 GAGGGTCGTGGTCAACTACA 59.036 55.000 0.00 0.00 0.00 2.74
380 384 3.439540 GCGCTCGCCATTCCCAAA 61.440 61.111 0.00 0.00 34.56 3.28
394 398 1.065636 TCCCAAAGATCAGCTGCTCAG 60.066 52.381 19.13 8.64 0.00 3.35
488 505 5.581605 TCTTTTGCAGAACTTGTTGATGAC 58.418 37.500 0.00 0.00 0.00 3.06
505 525 6.327177 TGATGACGACGACTTATTTTTAGC 57.673 37.500 0.00 0.00 0.00 3.09
506 526 5.865013 TGATGACGACGACTTATTTTTAGCA 59.135 36.000 0.00 0.00 0.00 3.49
543 563 5.239306 CAGTGTAAACCTCTGAATTCTGCAA 59.761 40.000 7.05 0.00 0.00 4.08
569 593 1.679680 GGATGATCCTGTGCACCAATG 59.320 52.381 15.69 1.80 32.53 2.82
641 665 2.270434 AGGAAGGGTGAATAGCTCCA 57.730 50.000 0.00 0.00 31.65 3.86
734 767 6.546034 GGCAACAATAGTTCCTATGTAACCAT 59.454 38.462 0.00 0.00 35.28 3.55
738 771 8.562949 ACAATAGTTCCTATGTAACCATACCT 57.437 34.615 0.00 0.00 32.29 3.08
807 846 4.767255 CCACCTCACCTCAGCGCC 62.767 72.222 2.29 0.00 0.00 6.53
1015 1067 2.548057 CGAGAGATGTCTAGCTCCAGTC 59.452 54.545 0.00 0.00 40.18 3.51
1055 1107 2.584608 GCGGTATGGTCCAGTGCT 59.415 61.111 0.00 0.00 0.00 4.40
1172 1263 2.031012 CGAGAGCAGGCCACAACA 59.969 61.111 5.01 0.00 0.00 3.33
1187 1278 1.710809 ACAACAGGGGCAGGTTAGATT 59.289 47.619 0.00 0.00 0.00 2.40
1200 1291 6.166982 GCAGGTTAGATTTGAGTACTCTGTT 58.833 40.000 23.01 7.94 0.00 3.16
1242 1333 7.107639 TCTCCCGATTTCTTTCTTTTGTTTT 57.892 32.000 0.00 0.00 0.00 2.43
1291 1411 1.574428 CGCCGTTTTCAGGTTCTGG 59.426 57.895 0.00 0.00 31.51 3.86
1477 1609 6.108687 GGGGAATTGAAGAAAATAAGCAAGG 58.891 40.000 0.00 0.00 0.00 3.61
1492 1624 1.471684 GCAAGGAACTGAAGCAGATGG 59.528 52.381 0.82 0.00 40.86 3.51
1544 1677 5.417580 TGGTTGGAGGATTTTATTGCTGTAC 59.582 40.000 0.00 0.00 0.00 2.90
1577 1710 6.391537 TGGGTTTCTTTTAGTTGTTGTTCAC 58.608 36.000 0.00 0.00 0.00 3.18
1653 1809 4.379339 TTTTCAGTTACAGTTTGGGCAC 57.621 40.909 0.00 0.00 0.00 5.01
1680 1837 3.560882 CCCTAGATCATTTGCATCCCCTC 60.561 52.174 0.00 0.00 0.00 4.30
1699 1856 5.454187 CCCCTCATGAATAAAATGCAGCAAT 60.454 40.000 0.00 0.00 0.00 3.56
1708 1865 0.390209 AATGCAGCAATTCGCCCAAC 60.390 50.000 0.00 0.00 44.04 3.77
1727 1884 4.511527 CAACTATGTCTCCTCTGTTGCAT 58.488 43.478 0.00 0.00 0.00 3.96
1765 1954 3.580458 AGTTAACAGAGAGTGCAGGACAT 59.420 43.478 8.61 0.00 0.00 3.06
1774 1963 2.497675 GAGTGCAGGACATAGTTCAGGA 59.502 50.000 0.00 0.00 0.00 3.86
1779 1968 5.183904 GTGCAGGACATAGTTCAGGAAAAAT 59.816 40.000 0.00 0.00 0.00 1.82
1783 1972 8.470002 GCAGGACATAGTTCAGGAAAAATAAAT 58.530 33.333 0.00 0.00 0.00 1.40
1802 1991 9.528489 AAATAAATAGATATTGGGTTATGGCGT 57.472 29.630 0.00 0.00 0.00 5.68
1803 1992 6.817765 AAATAGATATTGGGTTATGGCGTG 57.182 37.500 0.00 0.00 0.00 5.34
1804 1993 3.140325 AGATATTGGGTTATGGCGTGG 57.860 47.619 0.00 0.00 0.00 4.94
1805 1994 1.539827 GATATTGGGTTATGGCGTGGC 59.460 52.381 0.00 0.00 0.00 5.01
1806 1995 0.548989 TATTGGGTTATGGCGTGGCT 59.451 50.000 0.00 0.00 0.00 4.75
1807 1996 0.324275 ATTGGGTTATGGCGTGGCTT 60.324 50.000 0.00 0.00 0.00 4.35
1808 1997 0.540830 TTGGGTTATGGCGTGGCTTT 60.541 50.000 0.00 0.00 0.00 3.51
1809 1998 1.247419 TGGGTTATGGCGTGGCTTTG 61.247 55.000 0.00 0.00 0.00 2.77
1810 1999 0.963355 GGGTTATGGCGTGGCTTTGA 60.963 55.000 0.00 0.00 0.00 2.69
1811 2000 0.170339 GGTTATGGCGTGGCTTTGAC 59.830 55.000 0.00 0.00 0.00 3.18
1812 2001 0.878416 GTTATGGCGTGGCTTTGACA 59.122 50.000 0.00 0.00 0.00 3.58
1813 2002 1.268352 GTTATGGCGTGGCTTTGACAA 59.732 47.619 0.00 0.00 0.00 3.18
1814 2003 1.832883 TATGGCGTGGCTTTGACAAT 58.167 45.000 0.00 0.00 0.00 2.71
1815 2004 1.832883 ATGGCGTGGCTTTGACAATA 58.167 45.000 0.00 0.00 0.00 1.90
1816 2005 1.610363 TGGCGTGGCTTTGACAATAA 58.390 45.000 0.00 0.00 0.00 1.40
1817 2006 1.957177 TGGCGTGGCTTTGACAATAAA 59.043 42.857 0.00 0.00 0.00 1.40
1818 2007 2.362397 TGGCGTGGCTTTGACAATAAAA 59.638 40.909 0.00 0.00 0.00 1.52
1819 2008 3.006323 TGGCGTGGCTTTGACAATAAAAT 59.994 39.130 0.00 0.00 0.00 1.82
1865 2054 2.143876 ACAAGCCCACCCATCATTAC 57.856 50.000 0.00 0.00 0.00 1.89
1866 2055 1.640670 ACAAGCCCACCCATCATTACT 59.359 47.619 0.00 0.00 0.00 2.24
1876 2065 5.185454 CACCCATCATTACTTAGCACAAGA 58.815 41.667 5.20 0.00 0.00 3.02
1877 2066 5.824624 CACCCATCATTACTTAGCACAAGAT 59.175 40.000 5.20 0.00 0.00 2.40
1879 2068 5.471456 CCCATCATTACTTAGCACAAGATCC 59.529 44.000 5.20 0.00 0.00 3.36
1881 2070 5.692115 TCATTACTTAGCACAAGATCCCA 57.308 39.130 5.20 0.00 0.00 4.37
1882 2071 6.061022 TCATTACTTAGCACAAGATCCCAA 57.939 37.500 5.20 0.00 0.00 4.12
1883 2072 6.662755 TCATTACTTAGCACAAGATCCCAAT 58.337 36.000 5.20 0.00 0.00 3.16
1884 2073 6.767902 TCATTACTTAGCACAAGATCCCAATC 59.232 38.462 5.20 0.00 0.00 2.67
1885 2074 4.851639 ACTTAGCACAAGATCCCAATCT 57.148 40.909 5.20 0.00 44.37 2.40
1887 2076 5.675538 ACTTAGCACAAGATCCCAATCTAC 58.324 41.667 5.20 0.00 41.54 2.59
1888 2077 5.189736 ACTTAGCACAAGATCCCAATCTACA 59.810 40.000 5.20 0.00 41.54 2.74
1889 2078 4.148128 AGCACAAGATCCCAATCTACAG 57.852 45.455 0.00 0.00 41.54 2.74
1890 2079 2.615912 GCACAAGATCCCAATCTACAGC 59.384 50.000 0.00 0.00 41.54 4.40
1891 2080 3.877559 CACAAGATCCCAATCTACAGCA 58.122 45.455 0.00 0.00 41.54 4.41
1893 2082 4.275196 CACAAGATCCCAATCTACAGCATG 59.725 45.833 0.00 0.00 41.54 4.06
1957 2157 1.228124 TGCACCCGTGGAGAAAAGG 60.228 57.895 0.00 0.00 0.00 3.11
1975 2199 1.460273 GGAAAATGGTGCACCCGTGT 61.460 55.000 32.62 15.81 35.15 4.49
1976 2200 0.387565 GAAAATGGTGCACCCGTGTT 59.612 50.000 32.62 21.64 31.83 3.32
1977 2201 0.827368 AAAATGGTGCACCCGTGTTT 59.173 45.000 32.62 22.63 35.15 2.83
1978 2202 0.387565 AAATGGTGCACCCGTGTTTC 59.612 50.000 32.62 5.95 35.15 2.78
1979 2203 1.460273 AATGGTGCACCCGTGTTTCC 61.460 55.000 32.62 5.24 35.15 3.13
1980 2204 3.656045 GGTGCACCCGTGTTTCCG 61.656 66.667 26.31 0.00 0.00 4.30
1981 2205 2.898343 GTGCACCCGTGTTTCCGT 60.898 61.111 5.22 0.00 0.00 4.69
1982 2206 2.897846 TGCACCCGTGTTTCCGTG 60.898 61.111 0.00 0.00 0.00 4.94
1983 2207 4.322385 GCACCCGTGTTTCCGTGC 62.322 66.667 0.00 0.00 44.17 5.34
1984 2208 2.897846 CACCCGTGTTTCCGTGCA 60.898 61.111 0.00 0.00 0.00 4.57
1985 2209 2.898343 ACCCGTGTTTCCGTGCAC 60.898 61.111 6.82 6.82 0.00 4.57
1987 2211 2.897846 CCGTGTTTCCGTGCACCA 60.898 61.111 12.15 0.00 32.40 4.17
1988 2212 2.258013 CCGTGTTTCCGTGCACCAT 61.258 57.895 12.15 0.00 32.40 3.55
1989 2213 1.652012 CGTGTTTCCGTGCACCATT 59.348 52.632 12.15 0.00 32.40 3.16
1990 2214 0.660005 CGTGTTTCCGTGCACCATTG 60.660 55.000 12.15 0.00 32.40 2.82
1991 2215 0.383949 GTGTTTCCGTGCACCATTGT 59.616 50.000 12.15 0.00 0.00 2.71
1992 2216 1.604755 GTGTTTCCGTGCACCATTGTA 59.395 47.619 12.15 0.00 0.00 2.41
1994 2218 1.604755 GTTTCCGTGCACCATTGTACA 59.395 47.619 12.15 0.00 38.19 2.90
2006 2255 6.989759 TGCACCATTGTACATACCATAAGTAG 59.010 38.462 0.00 0.00 33.42 2.57
2007 2256 6.990349 GCACCATTGTACATACCATAAGTAGT 59.010 38.462 0.00 0.00 33.42 2.73
2008 2257 7.497909 GCACCATTGTACATACCATAAGTAGTT 59.502 37.037 0.00 0.00 33.42 2.24
2015 2264 9.439500 TGTACATACCATAAGTAGTTTGTTTCC 57.561 33.333 0.00 0.00 33.42 3.13
2016 2265 7.605410 ACATACCATAAGTAGTTTGTTTCCG 57.395 36.000 0.00 0.00 33.42 4.30
2141 2394 3.536956 AGATCCATTTTTGCATGGCTG 57.463 42.857 0.00 0.00 43.31 4.85
2174 2427 6.076653 ATGTATTTACATGATGGCATTCCCA 58.923 36.000 0.00 0.00 45.72 4.37
2175 2428 6.015180 ATGTATTTACATGATGGCATTCCCAC 60.015 38.462 0.00 0.00 45.06 4.61
2218 2471 6.192044 TCATAACTTGGAAATAAAGGTCCCC 58.808 40.000 0.00 0.00 32.48 4.81
2219 2472 4.759793 AACTTGGAAATAAAGGTCCCCT 57.240 40.909 0.00 0.00 33.87 4.79
2220 2473 4.317530 ACTTGGAAATAAAGGTCCCCTC 57.682 45.455 0.00 0.00 30.89 4.30
2221 2474 3.660669 ACTTGGAAATAAAGGTCCCCTCA 59.339 43.478 0.00 0.00 30.89 3.86
2255 2508 6.603940 TTTTTCTAGCACAAGGGCATTATT 57.396 33.333 0.00 0.00 35.83 1.40
2256 2509 7.710676 TTTTTCTAGCACAAGGGCATTATTA 57.289 32.000 0.00 0.00 35.83 0.98
2257 2510 6.693315 TTTCTAGCACAAGGGCATTATTAC 57.307 37.500 0.00 0.00 35.83 1.89
2258 2511 5.630415 TCTAGCACAAGGGCATTATTACT 57.370 39.130 0.00 0.00 35.83 2.24
2259 2512 6.001449 TCTAGCACAAGGGCATTATTACTT 57.999 37.500 0.00 0.00 35.83 2.24
2260 2513 6.055588 TCTAGCACAAGGGCATTATTACTTC 58.944 40.000 0.00 0.00 35.83 3.01
2261 2514 4.860022 AGCACAAGGGCATTATTACTTCT 58.140 39.130 0.00 0.00 35.83 2.85
2262 2515 5.264395 AGCACAAGGGCATTATTACTTCTT 58.736 37.500 0.00 0.00 35.83 2.52
2263 2516 5.358160 AGCACAAGGGCATTATTACTTCTTC 59.642 40.000 0.00 0.00 35.83 2.87
2264 2517 5.125417 GCACAAGGGCATTATTACTTCTTCA 59.875 40.000 0.00 0.00 0.00 3.02
2265 2518 6.350110 GCACAAGGGCATTATTACTTCTTCAA 60.350 38.462 0.00 0.00 0.00 2.69
2266 2519 7.601856 CACAAGGGCATTATTACTTCTTCAAA 58.398 34.615 0.00 0.00 0.00 2.69
2267 2520 7.542130 CACAAGGGCATTATTACTTCTTCAAAC 59.458 37.037 0.00 0.00 0.00 2.93
2268 2521 7.232534 ACAAGGGCATTATTACTTCTTCAAACA 59.767 33.333 0.00 0.00 0.00 2.83
2269 2522 7.775053 AGGGCATTATTACTTCTTCAAACAA 57.225 32.000 0.00 0.00 0.00 2.83
2270 2523 7.830739 AGGGCATTATTACTTCTTCAAACAAG 58.169 34.615 0.00 0.00 0.00 3.16
2271 2524 7.451566 AGGGCATTATTACTTCTTCAAACAAGT 59.548 33.333 0.00 0.00 36.75 3.16
2272 2525 8.736244 GGGCATTATTACTTCTTCAAACAAGTA 58.264 33.333 0.00 0.00 34.60 2.24
2273 2526 9.556030 GGCATTATTACTTCTTCAAACAAGTAC 57.444 33.333 0.00 0.00 35.32 2.73
2283 2536 8.561738 TTCTTCAAACAAGTACAAGAAGAAGT 57.438 30.769 10.36 0.00 43.28 3.01
2284 2537 8.561738 TCTTCAAACAAGTACAAGAAGAAGTT 57.438 30.769 0.00 0.00 38.67 2.66
2285 2538 8.665685 TCTTCAAACAAGTACAAGAAGAAGTTC 58.334 33.333 0.00 0.00 38.67 3.01
2286 2539 7.915293 TCAAACAAGTACAAGAAGAAGTTCA 57.085 32.000 5.50 0.00 34.82 3.18
2287 2540 8.330466 TCAAACAAGTACAAGAAGAAGTTCAA 57.670 30.769 5.50 0.00 34.82 2.69
2288 2541 8.788806 TCAAACAAGTACAAGAAGAAGTTCAAA 58.211 29.630 5.50 0.00 34.82 2.69
2289 2542 9.405587 CAAACAAGTACAAGAAGAAGTTCAAAA 57.594 29.630 5.50 0.00 34.82 2.44
2307 2560 9.567848 AGTTCAAAATATAGTGTATTTTTGCGG 57.432 29.630 13.23 4.92 35.61 5.69
2308 2561 8.803799 GTTCAAAATATAGTGTATTTTTGCGGG 58.196 33.333 13.23 4.63 35.61 6.13
2309 2562 7.484975 TCAAAATATAGTGTATTTTTGCGGGG 58.515 34.615 13.23 4.06 35.61 5.73
2310 2563 7.122948 TCAAAATATAGTGTATTTTTGCGGGGT 59.877 33.333 13.23 0.00 35.61 4.95
2311 2564 8.407064 CAAAATATAGTGTATTTTTGCGGGGTA 58.593 33.333 13.23 0.00 35.61 3.69
2312 2565 8.522542 AAATATAGTGTATTTTTGCGGGGTAA 57.477 30.769 0.00 0.00 0.00 2.85
2313 2566 8.522542 AATATAGTGTATTTTTGCGGGGTAAA 57.477 30.769 0.00 0.00 0.00 2.01
2314 2567 8.700439 ATATAGTGTATTTTTGCGGGGTAAAT 57.300 30.769 0.00 0.00 0.00 1.40
2315 2568 9.796180 ATATAGTGTATTTTTGCGGGGTAAATA 57.204 29.630 0.00 0.00 0.00 1.40
2316 2569 8.700439 ATAGTGTATTTTTGCGGGGTAAATAT 57.300 30.769 0.00 0.00 0.00 1.28
2317 2570 9.796180 ATAGTGTATTTTTGCGGGGTAAATATA 57.204 29.630 0.00 0.00 0.00 0.86
2318 2571 8.161699 AGTGTATTTTTGCGGGGTAAATATAG 57.838 34.615 0.00 0.00 0.00 1.31
2319 2572 7.776500 AGTGTATTTTTGCGGGGTAAATATAGT 59.224 33.333 0.00 0.00 0.00 2.12
2320 2573 8.407832 GTGTATTTTTGCGGGGTAAATATAGTT 58.592 33.333 0.00 0.00 0.00 2.24
2321 2574 8.968969 TGTATTTTTGCGGGGTAAATATAGTTT 58.031 29.630 0.00 0.00 0.00 2.66
2344 2597 9.887406 GTTTATTTATTTTCACTTCCTCGAACA 57.113 29.630 0.00 0.00 0.00 3.18
2347 2600 7.795482 TTTATTTTCACTTCCTCGAACAAGA 57.205 32.000 9.47 0.00 0.00 3.02
2348 2601 7.795482 TTATTTTCACTTCCTCGAACAAGAA 57.205 32.000 9.47 0.00 0.00 2.52
2349 2602 5.479716 TTTTCACTTCCTCGAACAAGAAC 57.520 39.130 9.47 0.00 0.00 3.01
2350 2603 3.812156 TCACTTCCTCGAACAAGAACA 57.188 42.857 9.47 0.00 0.00 3.18
2351 2604 4.131649 TCACTTCCTCGAACAAGAACAA 57.868 40.909 9.47 0.00 0.00 2.83
2352 2605 4.119862 TCACTTCCTCGAACAAGAACAAG 58.880 43.478 9.47 0.00 0.00 3.16
2353 2606 3.871594 CACTTCCTCGAACAAGAACAAGT 59.128 43.478 9.47 0.00 0.00 3.16
2354 2607 4.332819 CACTTCCTCGAACAAGAACAAGTT 59.667 41.667 9.47 0.00 0.00 2.66
2355 2608 4.571176 ACTTCCTCGAACAAGAACAAGTTC 59.429 41.667 9.47 4.82 40.45 3.01
2356 2609 4.131649 TCCTCGAACAAGAACAAGTTCA 57.868 40.909 14.69 0.00 43.20 3.18
2357 2610 4.509616 TCCTCGAACAAGAACAAGTTCAA 58.490 39.130 14.69 0.00 43.20 2.69
2358 2611 4.938832 TCCTCGAACAAGAACAAGTTCAAA 59.061 37.500 14.69 0.00 43.20 2.69
2359 2612 5.588648 TCCTCGAACAAGAACAAGTTCAAAT 59.411 36.000 14.69 0.00 43.20 2.32
2360 2613 6.764085 TCCTCGAACAAGAACAAGTTCAAATA 59.236 34.615 14.69 0.00 43.20 1.40
2361 2614 7.444183 TCCTCGAACAAGAACAAGTTCAAATAT 59.556 33.333 14.69 0.00 43.20 1.28
2362 2615 8.717821 CCTCGAACAAGAACAAGTTCAAATATA 58.282 33.333 14.69 0.00 43.20 0.86
2363 2616 9.746711 CTCGAACAAGAACAAGTTCAAATATAG 57.253 33.333 14.69 1.53 43.20 1.31
2364 2617 9.268268 TCGAACAAGAACAAGTTCAAATATAGT 57.732 29.630 14.69 0.91 43.20 2.12
2365 2618 9.318041 CGAACAAGAACAAGTTCAAATATAGTG 57.682 33.333 14.69 3.22 43.20 2.74
2397 2650 8.740123 TTTTCAGTTGAAATACAGTGGTAAGA 57.260 30.769 8.02 0.00 42.83 2.10
2398 2651 8.740123 TTTCAGTTGAAATACAGTGGTAAGAA 57.260 30.769 3.28 0.00 38.94 2.52
2399 2652 7.962964 TCAGTTGAAATACAGTGGTAAGAAG 57.037 36.000 0.00 0.00 32.19 2.85
2400 2653 7.732025 TCAGTTGAAATACAGTGGTAAGAAGA 58.268 34.615 0.00 0.00 32.19 2.87
2401 2654 8.208224 TCAGTTGAAATACAGTGGTAAGAAGAA 58.792 33.333 0.00 0.00 32.19 2.52
2402 2655 8.499162 CAGTTGAAATACAGTGGTAAGAAGAAG 58.501 37.037 0.00 0.00 32.19 2.85
2403 2656 8.211629 AGTTGAAATACAGTGGTAAGAAGAAGT 58.788 33.333 0.00 0.00 32.19 3.01
2404 2657 9.485206 GTTGAAATACAGTGGTAAGAAGAAGTA 57.515 33.333 0.00 0.00 32.19 2.24
2405 2658 9.706691 TTGAAATACAGTGGTAAGAAGAAGTAG 57.293 33.333 0.00 0.00 32.19 2.57
2406 2659 9.085645 TGAAATACAGTGGTAAGAAGAAGTAGA 57.914 33.333 0.00 0.00 32.19 2.59
2407 2660 9.924650 GAAATACAGTGGTAAGAAGAAGTAGAA 57.075 33.333 0.00 0.00 32.19 2.10
2447 2700 9.908152 ACTTTTACAACTATATTGGCAAAGAAC 57.092 29.630 3.01 0.00 31.99 3.01
2448 2701 9.906660 CTTTTACAACTATATTGGCAAAGAACA 57.093 29.630 3.01 0.00 30.46 3.18
2453 2706 9.777297 ACAACTATATTGGCAAAGAACAAATTT 57.223 25.926 3.01 0.00 0.00 1.82
2462 2715 8.954950 TGGCAAAGAACAAATTTATGAAAAGA 57.045 26.923 0.00 0.00 0.00 2.52
2489 2742 5.950758 ACCACAAATAATAGCACGAACAA 57.049 34.783 0.00 0.00 0.00 2.83
2522 2783 9.224267 AGATATGGTAGCACAAATAATAGCAAG 57.776 33.333 0.00 0.00 0.00 4.01
2523 2784 9.219603 GATATGGTAGCACAAATAATAGCAAGA 57.780 33.333 0.00 0.00 0.00 3.02
2524 2785 7.880160 ATGGTAGCACAAATAATAGCAAGAA 57.120 32.000 0.00 0.00 0.00 2.52
2525 2786 7.083875 TGGTAGCACAAATAATAGCAAGAAC 57.916 36.000 0.00 0.00 0.00 3.01
2526 2787 6.657117 TGGTAGCACAAATAATAGCAAGAACA 59.343 34.615 0.00 0.00 0.00 3.18
2527 2788 7.339212 TGGTAGCACAAATAATAGCAAGAACAT 59.661 33.333 0.00 0.00 0.00 2.71
2528 2789 8.190784 GGTAGCACAAATAATAGCAAGAACATT 58.809 33.333 0.00 0.00 0.00 2.71
2553 2814 9.976255 TTAATATAGTTGCACGAACATAACAAC 57.024 29.630 0.00 0.00 40.65 3.32
2555 2816 4.624336 AGTTGCACGAACATAACAACAA 57.376 36.364 6.91 0.00 42.32 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
242 246 2.260434 CCCGTCAGGTACACCACG 59.740 66.667 0.38 2.89 38.89 4.94
291 295 1.141881 CGACCCTCTTCATCACCGG 59.858 63.158 0.00 0.00 0.00 5.28
294 298 0.608640 ACCACGACCCTCTTCATCAC 59.391 55.000 0.00 0.00 0.00 3.06
306 310 4.164294 GTGTAGATGTAGTTGACCACGAC 58.836 47.826 0.00 0.00 0.00 4.34
380 384 1.674764 CGACCCTGAGCAGCTGATCT 61.675 60.000 30.29 13.46 0.00 2.75
394 398 1.453762 CTCGTAGGTGATCCCGACCC 61.454 65.000 7.54 0.00 35.55 4.46
433 437 3.454371 AGACACTAGAAACGCACAAGT 57.546 42.857 0.00 0.00 0.00 3.16
438 442 2.404215 GAGCAAGACACTAGAAACGCA 58.596 47.619 0.00 0.00 0.00 5.24
488 505 6.248420 CCATTTGTGCTAAAAATAAGTCGTCG 59.752 38.462 0.00 0.00 0.00 5.12
505 525 6.071952 AGGTTTACACTGCTAATCCATTTGTG 60.072 38.462 0.00 0.00 0.00 3.33
506 526 6.010219 AGGTTTACACTGCTAATCCATTTGT 58.990 36.000 0.00 0.00 0.00 2.83
543 563 1.453235 CACAGGATCATCCGGGCAT 59.547 57.895 8.86 0.00 42.75 4.40
579 603 4.344968 AGCTTGTAGGCAATCCAAAGTTTT 59.655 37.500 0.00 0.00 33.65 2.43
580 604 3.897505 AGCTTGTAGGCAATCCAAAGTTT 59.102 39.130 0.00 0.00 33.65 2.66
599 623 3.354948 TTAGATCATGCCACAACAGCT 57.645 42.857 0.00 0.00 0.00 4.24
641 665 2.976589 TCATGTCAATGATGTCGCACT 58.023 42.857 0.00 0.00 37.91 4.40
728 761 9.218440 CGTTTTAGGTTAAAGAAGGTATGGTTA 57.782 33.333 0.00 0.00 0.00 2.85
729 762 7.308770 GCGTTTTAGGTTAAAGAAGGTATGGTT 60.309 37.037 0.00 0.00 0.00 3.67
734 767 6.991531 TCTTGCGTTTTAGGTTAAAGAAGGTA 59.008 34.615 0.00 0.00 0.00 3.08
738 771 6.539464 TGTCTCTTGCGTTTTAGGTTAAAGAA 59.461 34.615 0.00 0.00 0.00 2.52
794 830 4.504916 CTCCGGCGCTGAGGTGAG 62.505 72.222 20.25 11.89 0.00 3.51
807 846 1.338674 TGTGGATTAGTTGTGGCTCCG 60.339 52.381 0.00 0.00 0.00 4.63
1015 1067 2.389449 ATGATGGGTGGGAGGCTGG 61.389 63.158 0.00 0.00 0.00 4.85
1055 1107 2.046023 CGGGGCATCTTGTCAGCA 60.046 61.111 0.00 0.00 0.00 4.41
1092 1175 3.259876 TCACATAGGTAAACCGCTTCAGT 59.740 43.478 0.00 0.00 42.08 3.41
1172 1263 2.279173 ACTCAAATCTAACCTGCCCCT 58.721 47.619 0.00 0.00 0.00 4.79
1187 1278 4.820897 CATACAGCCAACAGAGTACTCAA 58.179 43.478 24.44 0.00 0.00 3.02
1242 1333 7.181361 TGAACCCTAGATTCCAAATTCAATGA 58.819 34.615 0.00 0.00 0.00 2.57
1322 1442 5.045942 TCCAATTGTAGCCTCTCAATGTACA 60.046 40.000 4.43 0.00 34.98 2.90
1477 1609 2.370281 TCGACCATCTGCTTCAGTTC 57.630 50.000 0.00 0.00 32.61 3.01
1492 1624 1.069022 TGCTTGCTGCTTCAAATCGAC 60.069 47.619 0.00 0.00 43.37 4.20
1577 1710 4.452455 ACTCAAACAATTTCTAGCGACTGG 59.548 41.667 0.00 0.00 0.00 4.00
1653 1809 2.589720 TGCAAATGATCTAGGGCATGG 58.410 47.619 0.00 0.00 0.00 3.66
1660 1816 4.362470 TGAGGGGATGCAAATGATCTAG 57.638 45.455 0.00 0.00 0.00 2.43
1661 1817 4.351704 TCATGAGGGGATGCAAATGATCTA 59.648 41.667 0.00 0.00 0.00 1.98
1662 1818 3.139584 TCATGAGGGGATGCAAATGATCT 59.860 43.478 0.00 0.00 0.00 2.75
1680 1837 5.428770 GCGAATTGCTGCATTTTATTCATG 58.571 37.500 19.20 9.19 41.73 3.07
1699 1856 1.480954 GAGGAGACATAGTTGGGCGAA 59.519 52.381 0.00 0.00 0.00 4.70
1708 1865 5.911752 AGTTATGCAACAGAGGAGACATAG 58.088 41.667 0.00 0.00 37.10 2.23
1742 1931 4.149598 TGTCCTGCACTCTCTGTTAACTA 58.850 43.478 7.22 0.00 0.00 2.24
1779 1968 6.882140 CCACGCCATAACCCAATATCTATTTA 59.118 38.462 0.00 0.00 0.00 1.40
1783 1972 3.558321 GCCACGCCATAACCCAATATCTA 60.558 47.826 0.00 0.00 0.00 1.98
1784 1973 2.814097 GCCACGCCATAACCCAATATCT 60.814 50.000 0.00 0.00 0.00 1.98
1795 1984 1.832883 ATTGTCAAAGCCACGCCATA 58.167 45.000 0.00 0.00 0.00 2.74
1796 1985 1.832883 TATTGTCAAAGCCACGCCAT 58.167 45.000 0.00 0.00 0.00 4.40
1797 1986 1.610363 TTATTGTCAAAGCCACGCCA 58.390 45.000 0.00 0.00 0.00 5.69
1798 1987 2.715737 TTTATTGTCAAAGCCACGCC 57.284 45.000 0.00 0.00 0.00 5.68
1799 1988 5.220209 GCTAATTTTATTGTCAAAGCCACGC 60.220 40.000 0.00 0.00 0.00 5.34
1800 1989 6.092748 AGCTAATTTTATTGTCAAAGCCACG 58.907 36.000 0.00 0.00 0.00 4.94
1801 1990 7.090173 TGAGCTAATTTTATTGTCAAAGCCAC 58.910 34.615 0.00 0.00 0.00 5.01
1802 1991 7.225784 TGAGCTAATTTTATTGTCAAAGCCA 57.774 32.000 0.00 0.00 0.00 4.75
1803 1992 7.814587 ACTTGAGCTAATTTTATTGTCAAAGCC 59.185 33.333 0.00 0.00 0.00 4.35
1804 1993 8.748380 ACTTGAGCTAATTTTATTGTCAAAGC 57.252 30.769 0.00 0.00 0.00 3.51
1808 1997 9.515226 ACCTTACTTGAGCTAATTTTATTGTCA 57.485 29.630 0.00 0.00 0.00 3.58
1809 1998 9.989869 GACCTTACTTGAGCTAATTTTATTGTC 57.010 33.333 0.00 0.00 0.00 3.18
1810 1999 8.957466 GGACCTTACTTGAGCTAATTTTATTGT 58.043 33.333 0.00 0.00 0.00 2.71
1811 2000 8.956426 TGGACCTTACTTGAGCTAATTTTATTG 58.044 33.333 0.00 0.00 0.00 1.90
1812 2001 9.528489 TTGGACCTTACTTGAGCTAATTTTATT 57.472 29.630 0.00 0.00 0.00 1.40
1813 2002 9.528489 TTTGGACCTTACTTGAGCTAATTTTAT 57.472 29.630 0.00 0.00 0.00 1.40
1814 2003 8.927675 TTTGGACCTTACTTGAGCTAATTTTA 57.072 30.769 0.00 0.00 0.00 1.52
1815 2004 7.724061 TCTTTGGACCTTACTTGAGCTAATTTT 59.276 33.333 0.00 0.00 0.00 1.82
1816 2005 7.231467 TCTTTGGACCTTACTTGAGCTAATTT 58.769 34.615 0.00 0.00 0.00 1.82
1817 2006 6.779860 TCTTTGGACCTTACTTGAGCTAATT 58.220 36.000 0.00 0.00 0.00 1.40
1818 2007 6.213600 TCTCTTTGGACCTTACTTGAGCTAAT 59.786 38.462 0.00 0.00 0.00 1.73
1819 2008 5.542635 TCTCTTTGGACCTTACTTGAGCTAA 59.457 40.000 0.00 0.00 0.00 3.09
1865 2054 5.674525 TGTAGATTGGGATCTTGTGCTAAG 58.325 41.667 0.00 0.00 42.55 2.18
1866 2055 5.674525 CTGTAGATTGGGATCTTGTGCTAA 58.325 41.667 0.00 0.00 42.55 3.09
1876 2065 3.181447 CCTCACATGCTGTAGATTGGGAT 60.181 47.826 0.00 0.00 0.00 3.85
1877 2066 2.171237 CCTCACATGCTGTAGATTGGGA 59.829 50.000 0.00 0.00 0.00 4.37
1879 2068 2.941064 CACCTCACATGCTGTAGATTGG 59.059 50.000 0.00 0.00 0.00 3.16
1881 2070 2.092753 CCCACCTCACATGCTGTAGATT 60.093 50.000 0.00 0.00 0.00 2.40
1882 2071 1.487976 CCCACCTCACATGCTGTAGAT 59.512 52.381 0.00 0.00 0.00 1.98
1883 2072 0.904649 CCCACCTCACATGCTGTAGA 59.095 55.000 0.00 0.00 0.00 2.59
1884 2073 0.615331 ACCCACCTCACATGCTGTAG 59.385 55.000 0.00 0.00 0.00 2.74
1885 2074 1.064003 AACCCACCTCACATGCTGTA 58.936 50.000 0.00 0.00 0.00 2.74
1887 2076 1.870055 GCAACCCACCTCACATGCTG 61.870 60.000 0.00 0.00 0.00 4.41
1888 2077 1.604593 GCAACCCACCTCACATGCT 60.605 57.895 0.00 0.00 0.00 3.79
1889 2078 1.181098 AAGCAACCCACCTCACATGC 61.181 55.000 0.00 0.00 0.00 4.06
1890 2079 0.883833 GAAGCAACCCACCTCACATG 59.116 55.000 0.00 0.00 0.00 3.21
1891 2080 0.478072 TGAAGCAACCCACCTCACAT 59.522 50.000 0.00 0.00 0.00 3.21
1893 2082 1.172812 GGTGAAGCAACCCACCTCAC 61.173 60.000 0.00 0.00 46.94 3.51
1957 2157 0.387565 AACACGGGTGCACCATTTTC 59.612 50.000 35.78 17.87 40.22 2.29
1975 2199 1.968704 TGTACAATGGTGCACGGAAA 58.031 45.000 11.45 0.00 34.53 3.13
1976 2200 2.192664 ATGTACAATGGTGCACGGAA 57.807 45.000 11.45 0.00 42.53 4.30
1977 2201 2.623535 GTATGTACAATGGTGCACGGA 58.376 47.619 11.45 0.00 42.53 4.69
1978 2202 1.668751 GGTATGTACAATGGTGCACGG 59.331 52.381 11.45 2.79 42.53 4.94
1979 2203 2.351455 TGGTATGTACAATGGTGCACG 58.649 47.619 11.45 0.00 42.53 5.34
1980 2204 5.588648 ACTTATGGTATGTACAATGGTGCAC 59.411 40.000 8.80 8.80 42.53 4.57
1981 2205 5.750524 ACTTATGGTATGTACAATGGTGCA 58.249 37.500 0.00 0.00 43.88 4.57
1982 2206 6.990349 ACTACTTATGGTATGTACAATGGTGC 59.010 38.462 0.00 0.00 0.00 5.01
1983 2207 8.958119 AACTACTTATGGTATGTACAATGGTG 57.042 34.615 0.00 0.00 0.00 4.17
1984 2208 9.391006 CAAACTACTTATGGTATGTACAATGGT 57.609 33.333 0.00 0.00 0.00 3.55
1985 2209 9.391006 ACAAACTACTTATGGTATGTACAATGG 57.609 33.333 0.00 0.00 0.00 3.16
1989 2213 9.439500 GGAAACAAACTACTTATGGTATGTACA 57.561 33.333 0.00 0.00 0.00 2.90
1990 2214 8.598075 CGGAAACAAACTACTTATGGTATGTAC 58.402 37.037 0.00 0.00 0.00 2.90
1991 2215 7.765360 CCGGAAACAAACTACTTATGGTATGTA 59.235 37.037 0.00 0.00 0.00 2.29
1992 2216 6.596497 CCGGAAACAAACTACTTATGGTATGT 59.404 38.462 0.00 0.00 0.00 2.29
1994 2218 6.949715 TCCGGAAACAAACTACTTATGGTAT 58.050 36.000 0.00 0.00 0.00 2.73
2028 2277 4.219944 TGCACGGTAGAGTTTATGTTCTCT 59.780 41.667 0.00 0.00 42.62 3.10
2097 2346 8.654997 TCTATCTATCCTCCAGAAAAAGAATGG 58.345 37.037 0.00 0.00 35.30 3.16
2106 2355 8.748179 AAAATGGATCTATCTATCCTCCAGAA 57.252 34.615 4.63 0.00 44.98 3.02
2107 2356 8.600668 CAAAAATGGATCTATCTATCCTCCAGA 58.399 37.037 4.63 0.00 44.98 3.86
2108 2357 7.336427 GCAAAAATGGATCTATCTATCCTCCAG 59.664 40.741 4.63 0.00 44.98 3.86
2141 2394 7.752239 GCCATCATGTAAATACATAGTTCATGC 59.248 37.037 5.78 0.96 44.57 4.06
2235 2488 6.001449 AGTAATAATGCCCTTGTGCTAGAA 57.999 37.500 0.00 0.00 0.00 2.10
2236 2489 5.630415 AGTAATAATGCCCTTGTGCTAGA 57.370 39.130 0.00 0.00 0.00 2.43
2237 2490 6.058183 AGAAGTAATAATGCCCTTGTGCTAG 58.942 40.000 0.00 0.00 0.00 3.42
2238 2491 6.001449 AGAAGTAATAATGCCCTTGTGCTA 57.999 37.500 0.00 0.00 0.00 3.49
2239 2492 4.860022 AGAAGTAATAATGCCCTTGTGCT 58.140 39.130 0.00 0.00 0.00 4.40
2240 2493 5.125417 TGAAGAAGTAATAATGCCCTTGTGC 59.875 40.000 0.00 0.00 0.00 4.57
2241 2494 6.757897 TGAAGAAGTAATAATGCCCTTGTG 57.242 37.500 0.00 0.00 0.00 3.33
2242 2495 7.232534 TGTTTGAAGAAGTAATAATGCCCTTGT 59.767 33.333 0.00 0.00 0.00 3.16
2243 2496 7.601856 TGTTTGAAGAAGTAATAATGCCCTTG 58.398 34.615 0.00 0.00 0.00 3.61
2244 2497 7.775053 TGTTTGAAGAAGTAATAATGCCCTT 57.225 32.000 0.00 0.00 0.00 3.95
2245 2498 7.451566 ACTTGTTTGAAGAAGTAATAATGCCCT 59.548 33.333 4.64 0.00 40.28 5.19
2246 2499 7.602753 ACTTGTTTGAAGAAGTAATAATGCCC 58.397 34.615 4.64 0.00 40.28 5.36
2247 2500 9.556030 GTACTTGTTTGAAGAAGTAATAATGCC 57.444 33.333 13.11 0.00 43.55 4.40
2254 2507 9.661563 TCTTCTTGTACTTGTTTGAAGAAGTAA 57.338 29.630 20.35 7.64 43.55 2.24
2255 2508 9.661563 TTCTTCTTGTACTTGTTTGAAGAAGTA 57.338 29.630 20.35 13.29 45.14 2.24
2256 2509 8.561738 TTCTTCTTGTACTTGTTTGAAGAAGT 57.438 30.769 20.35 10.54 45.14 3.01
2258 2511 8.561738 ACTTCTTCTTGTACTTGTTTGAAGAA 57.438 30.769 13.09 13.09 43.63 2.52
2259 2512 8.561738 AACTTCTTCTTGTACTTGTTTGAAGA 57.438 30.769 15.98 0.00 38.34 2.87
2260 2513 8.450964 TGAACTTCTTCTTGTACTTGTTTGAAG 58.549 33.333 0.00 0.00 35.78 3.02
2261 2514 8.330466 TGAACTTCTTCTTGTACTTGTTTGAA 57.670 30.769 0.00 0.00 0.00 2.69
2262 2515 7.915293 TGAACTTCTTCTTGTACTTGTTTGA 57.085 32.000 0.00 0.00 0.00 2.69
2263 2516 8.964420 TTTGAACTTCTTCTTGTACTTGTTTG 57.036 30.769 0.00 0.00 0.00 2.93
2281 2534 9.567848 CCGCAAAAATACACTATATTTTGAACT 57.432 29.630 12.49 0.00 42.48 3.01
2282 2535 8.803799 CCCGCAAAAATACACTATATTTTGAAC 58.196 33.333 12.49 1.99 42.48 3.18
2283 2536 7.976734 CCCCGCAAAAATACACTATATTTTGAA 59.023 33.333 12.49 0.00 42.48 2.69
2284 2537 7.122948 ACCCCGCAAAAATACACTATATTTTGA 59.877 33.333 12.49 0.00 42.48 2.69
2285 2538 7.262048 ACCCCGCAAAAATACACTATATTTTG 58.738 34.615 5.62 5.67 42.66 2.44
2286 2539 7.412853 ACCCCGCAAAAATACACTATATTTT 57.587 32.000 0.00 0.00 38.37 1.82
2287 2540 8.522542 TTACCCCGCAAAAATACACTATATTT 57.477 30.769 0.00 0.00 0.00 1.40
2288 2541 8.522542 TTTACCCCGCAAAAATACACTATATT 57.477 30.769 0.00 0.00 0.00 1.28
2289 2542 8.700439 ATTTACCCCGCAAAAATACACTATAT 57.300 30.769 0.00 0.00 0.00 0.86
2290 2543 9.796180 ATATTTACCCCGCAAAAATACACTATA 57.204 29.630 0.00 0.00 30.24 1.31
2291 2544 8.700439 ATATTTACCCCGCAAAAATACACTAT 57.300 30.769 0.00 0.00 30.24 2.12
2292 2545 9.275398 CTATATTTACCCCGCAAAAATACACTA 57.725 33.333 0.00 0.00 30.24 2.74
2293 2546 7.776500 ACTATATTTACCCCGCAAAAATACACT 59.224 33.333 0.00 0.00 30.24 3.55
2294 2547 7.933396 ACTATATTTACCCCGCAAAAATACAC 58.067 34.615 0.00 0.00 30.24 2.90
2295 2548 8.522542 AACTATATTTACCCCGCAAAAATACA 57.477 30.769 0.00 0.00 30.24 2.29
2318 2571 9.887406 TGTTCGAGGAAGTGAAAATAAATAAAC 57.113 29.630 0.00 0.00 0.00 2.01
2321 2574 9.496873 TCTTGTTCGAGGAAGTGAAAATAAATA 57.503 29.630 5.65 0.00 0.00 1.40
2322 2575 8.391075 TCTTGTTCGAGGAAGTGAAAATAAAT 57.609 30.769 5.65 0.00 0.00 1.40
2323 2576 7.795482 TCTTGTTCGAGGAAGTGAAAATAAA 57.205 32.000 5.65 0.00 0.00 1.40
2324 2577 7.281324 TGTTCTTGTTCGAGGAAGTGAAAATAA 59.719 33.333 5.65 0.00 0.00 1.40
2325 2578 6.764085 TGTTCTTGTTCGAGGAAGTGAAAATA 59.236 34.615 5.65 0.00 0.00 1.40
2326 2579 5.588648 TGTTCTTGTTCGAGGAAGTGAAAAT 59.411 36.000 5.65 0.00 0.00 1.82
2327 2580 4.938832 TGTTCTTGTTCGAGGAAGTGAAAA 59.061 37.500 5.65 0.00 0.00 2.29
2328 2581 4.509616 TGTTCTTGTTCGAGGAAGTGAAA 58.490 39.130 5.65 0.00 0.00 2.69
2329 2582 4.131649 TGTTCTTGTTCGAGGAAGTGAA 57.868 40.909 5.65 0.00 0.00 3.18
2330 2583 3.812156 TGTTCTTGTTCGAGGAAGTGA 57.188 42.857 5.65 0.00 0.00 3.41
2331 2584 3.871594 ACTTGTTCTTGTTCGAGGAAGTG 59.128 43.478 5.65 0.00 0.00 3.16
2332 2585 4.138487 ACTTGTTCTTGTTCGAGGAAGT 57.862 40.909 5.65 0.00 0.00 3.01
2333 2586 4.570772 TGAACTTGTTCTTGTTCGAGGAAG 59.429 41.667 13.65 0.19 43.73 3.46
2334 2587 4.509616 TGAACTTGTTCTTGTTCGAGGAA 58.490 39.130 13.65 0.00 43.73 3.36
2335 2588 4.131649 TGAACTTGTTCTTGTTCGAGGA 57.868 40.909 13.65 0.00 43.73 3.71
2336 2589 4.875544 TTGAACTTGTTCTTGTTCGAGG 57.124 40.909 13.65 0.00 43.73 4.63
2337 2590 9.746711 CTATATTTGAACTTGTTCTTGTTCGAG 57.253 33.333 13.65 1.84 43.73 4.04
2338 2591 9.268268 ACTATATTTGAACTTGTTCTTGTTCGA 57.732 29.630 13.65 0.00 43.73 3.71
2339 2592 9.318041 CACTATATTTGAACTTGTTCTTGTTCG 57.682 33.333 13.65 1.95 43.73 3.95
2371 2624 9.349713 TCTTACCACTGTATTTCAACTGAAAAT 57.650 29.630 8.84 1.85 45.81 1.82
2372 2625 8.740123 TCTTACCACTGTATTTCAACTGAAAA 57.260 30.769 8.84 0.00 45.81 2.29
2373 2626 8.740123 TTCTTACCACTGTATTTCAACTGAAA 57.260 30.769 7.31 7.31 46.60 2.69
2374 2627 8.208224 TCTTCTTACCACTGTATTTCAACTGAA 58.792 33.333 0.00 0.00 0.00 3.02
2375 2628 7.732025 TCTTCTTACCACTGTATTTCAACTGA 58.268 34.615 0.00 0.00 0.00 3.41
2376 2629 7.962964 TCTTCTTACCACTGTATTTCAACTG 57.037 36.000 0.00 0.00 0.00 3.16
2377 2630 8.211629 ACTTCTTCTTACCACTGTATTTCAACT 58.788 33.333 0.00 0.00 0.00 3.16
2378 2631 8.379457 ACTTCTTCTTACCACTGTATTTCAAC 57.621 34.615 0.00 0.00 0.00 3.18
2379 2632 9.706691 CTACTTCTTCTTACCACTGTATTTCAA 57.293 33.333 0.00 0.00 0.00 2.69
2380 2633 9.085645 TCTACTTCTTCTTACCACTGTATTTCA 57.914 33.333 0.00 0.00 0.00 2.69
2381 2634 9.924650 TTCTACTTCTTCTTACCACTGTATTTC 57.075 33.333 0.00 0.00 0.00 2.17
2421 2674 9.908152 GTTCTTTGCCAATATAGTTGTAAAAGT 57.092 29.630 9.94 0.00 0.00 2.66
2422 2675 9.906660 TGTTCTTTGCCAATATAGTTGTAAAAG 57.093 29.630 0.00 0.00 0.00 2.27
2438 2691 8.011673 GCTCTTTTCATAAATTTGTTCTTTGCC 58.988 33.333 0.00 0.00 0.00 4.52
2446 2699 8.584157 TGTGGTATGCTCTTTTCATAAATTTGT 58.416 29.630 0.00 0.00 0.00 2.83
2447 2700 8.984891 TGTGGTATGCTCTTTTCATAAATTTG 57.015 30.769 0.00 0.00 0.00 2.32
2448 2701 9.995003 TTTGTGGTATGCTCTTTTCATAAATTT 57.005 25.926 0.00 0.00 0.00 1.82
2455 2708 8.405531 GCTATTATTTGTGGTATGCTCTTTTCA 58.594 33.333 0.00 0.00 0.00 2.69
2456 2709 8.405531 TGCTATTATTTGTGGTATGCTCTTTTC 58.594 33.333 0.00 0.00 0.00 2.29
2457 2710 8.190784 GTGCTATTATTTGTGGTATGCTCTTTT 58.809 33.333 0.00 0.00 0.00 2.27
2458 2711 7.467267 CGTGCTATTATTTGTGGTATGCTCTTT 60.467 37.037 0.00 0.00 0.00 2.52
2459 2712 6.017934 CGTGCTATTATTTGTGGTATGCTCTT 60.018 38.462 0.00 0.00 0.00 2.85
2460 2713 5.466728 CGTGCTATTATTTGTGGTATGCTCT 59.533 40.000 0.00 0.00 0.00 4.09
2461 2714 5.465390 TCGTGCTATTATTTGTGGTATGCTC 59.535 40.000 0.00 0.00 0.00 4.26
2462 2715 5.364778 TCGTGCTATTATTTGTGGTATGCT 58.635 37.500 0.00 0.00 0.00 3.79
2497 2750 9.219603 TCTTGCTATTATTTGTGCTACCATATC 57.780 33.333 0.00 0.00 0.00 1.63
2502 2755 7.083875 TGTTCTTGCTATTATTTGTGCTACC 57.916 36.000 0.00 0.00 0.00 3.18
2516 2777 8.547894 CGTGCAACTATATTAATGTTCTTGCTA 58.452 33.333 18.77 9.27 35.02 3.49
2517 2778 7.279981 TCGTGCAACTATATTAATGTTCTTGCT 59.720 33.333 18.77 0.00 35.02 3.91
2518 2779 7.406553 TCGTGCAACTATATTAATGTTCTTGC 58.593 34.615 14.53 14.53 34.63 4.01
2519 2780 9.210426 GTTCGTGCAACTATATTAATGTTCTTG 57.790 33.333 0.00 0.00 31.75 3.02
2520 2781 8.941977 TGTTCGTGCAACTATATTAATGTTCTT 58.058 29.630 0.00 0.00 35.79 2.52
2521 2782 8.487313 TGTTCGTGCAACTATATTAATGTTCT 57.513 30.769 0.00 0.00 35.79 3.01
2527 2788 9.976255 GTTGTTATGTTCGTGCAACTATATTAA 57.024 29.630 0.00 0.00 37.17 1.40
2528 2789 9.152595 TGTTGTTATGTTCGTGCAACTATATTA 57.847 29.630 0.00 0.00 39.81 0.98


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

AutoCloner maintained by Alex Coulton.