Multiple sequence alignment - TraesCS1B01G191200

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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 TraesCS1B01G191200 chr1B 100.000 5270 0 0 1 5270 342113335 342118604 0.000000e+00 9732.0
1 TraesCS1B01G191200 chr1B 90.122 2136 134 37 2558 4643 58323032 58325140 0.000000e+00 2704.0
2 TraesCS1B01G191200 chr1B 86.364 638 59 16 1938 2558 58322342 58322968 0.000000e+00 671.0
3 TraesCS1B01G191200 chr1B 84.570 512 29 28 765 1264 58321554 58322027 3.720000e-126 462.0
4 TraesCS1B01G191200 chr1B 82.394 142 8 6 1374 1508 58322026 58322157 2.010000e-19 108.0
5 TraesCS1B01G191200 chr1B 90.278 72 4 3 1937 2007 342115131 342115200 2.020000e-14 91.6
6 TraesCS1B01G191200 chr1B 90.278 72 4 3 1797 1866 342115271 342115341 2.020000e-14 91.6
7 TraesCS1B01G191200 chr1D 92.995 3412 167 46 1866 5241 236804840 236808215 0.000000e+00 4911.0
8 TraesCS1B01G191200 chr1D 87.777 2389 151 61 2558 4874 38550944 38553263 0.000000e+00 2663.0
9 TraesCS1B01G191200 chr1D 89.708 1370 59 34 179 1506 236802438 236803767 0.000000e+00 1674.0
10 TraesCS1B01G191200 chr1D 88.180 643 55 12 1937 2558 38550235 38550877 0.000000e+00 747.0
11 TraesCS1B01G191200 chr1D 84.167 480 26 27 784 1252 38549534 38549974 2.270000e-113 420.0
12 TraesCS1B01G191200 chr1D 84.701 268 16 8 1600 1851 38550036 38550294 1.470000e-60 244.0
13 TraesCS1B01G191200 chr1D 89.947 189 16 3 3 189 236797318 236797505 1.900000e-59 241.0
14 TraesCS1B01G191200 chr1D 88.430 121 9 3 1489 1606 240128148 240128266 1.980000e-29 141.0
15 TraesCS1B01G191200 chr1A 95.563 2975 93 18 1626 4592 308815518 308812575 0.000000e+00 4726.0
16 TraesCS1B01G191200 chr1A 89.375 2033 135 33 2558 4550 37479833 37481824 0.000000e+00 2483.0
17 TraesCS1B01G191200 chr1A 88.054 971 46 26 1 922 308817133 308816184 0.000000e+00 1086.0
18 TraesCS1B01G191200 chr1A 88.873 719 43 16 4570 5270 308812563 308811864 0.000000e+00 850.0
19 TraesCS1B01G191200 chr1A 87.013 616 37 20 907 1505 308816167 308815578 0.000000e+00 654.0
20 TraesCS1B01G191200 chr1A 84.418 507 38 17 765 1262 37478337 37478811 1.340000e-125 460.0
21 TraesCS1B01G191200 chr1A 83.333 354 24 18 331 679 37478010 37478333 1.440000e-75 294.0
22 TraesCS1B01G191200 chr1A 95.876 97 4 0 1505 1601 375114044 375114140 1.960000e-34 158.0
23 TraesCS1B01G191200 chr1A 95.161 62 2 1 1413 1474 37478860 37478920 4.340000e-16 97.1
24 TraesCS1B01G191200 chr7A 87.567 1126 140 0 3132 4257 80853315 80852190 0.000000e+00 1304.0
25 TraesCS1B01G191200 chr7A 86.139 303 38 4 2733 3035 80853680 80853382 1.830000e-84 324.0
26 TraesCS1B01G191200 chr7B 86.767 1126 149 0 3132 4257 23441772 23440647 0.000000e+00 1254.0
27 TraesCS1B01G191200 chr7B 84.158 303 44 4 2733 3035 23442137 23441839 1.860000e-74 291.0
28 TraesCS1B01G191200 chr7B 95.789 95 4 0 1508 1602 316391958 316391864 2.540000e-33 154.0
29 TraesCS1B01G191200 chr7D 86.590 1126 151 0 3132 4257 76732902 76731777 0.000000e+00 1243.0
30 TraesCS1B01G191200 chr7D 84.488 303 43 4 2733 3035 76733267 76732969 3.990000e-76 296.0
31 TraesCS1B01G191200 chr5B 96.842 95 3 0 1505 1599 143296588 143296494 5.460000e-35 159.0
32 TraesCS1B01G191200 chr5B 95.876 97 4 0 1505 1601 97516696 97516600 1.960000e-34 158.0
33 TraesCS1B01G191200 chr2D 95.000 100 5 0 1505 1604 468096942 468096843 1.960000e-34 158.0
34 TraesCS1B01G191200 chr2D 92.453 106 7 1 1498 1602 522707117 522707222 3.290000e-32 150.0
35 TraesCS1B01G191200 chr4B 93.333 105 7 0 1497 1601 260123233 260123337 7.070000e-34 156.0
36 TraesCS1B01G191200 chr3D 90.909 110 10 0 1495 1604 19269824 19269715 1.180000e-31 148.0


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 TraesCS1B01G191200 chr1B 342113335 342118604 5269 False 3305.066667 9732 93.518667 1 5270 3 chr1B.!!$F2 5269
1 TraesCS1B01G191200 chr1B 58321554 58325140 3586 False 986.250000 2704 85.862500 765 4643 4 chr1B.!!$F1 3878
2 TraesCS1B01G191200 chr1D 236802438 236808215 5777 False 3292.500000 4911 91.351500 179 5241 2 chr1D.!!$F4 5062
3 TraesCS1B01G191200 chr1D 38549534 38553263 3729 False 1018.500000 2663 86.206250 784 4874 4 chr1D.!!$F3 4090
4 TraesCS1B01G191200 chr1A 308811864 308817133 5269 True 1829.000000 4726 89.875750 1 5270 4 chr1A.!!$R1 5269
5 TraesCS1B01G191200 chr1A 37478010 37481824 3814 False 833.525000 2483 88.071750 331 4550 4 chr1A.!!$F2 4219
6 TraesCS1B01G191200 chr7A 80852190 80853680 1490 True 814.000000 1304 86.853000 2733 4257 2 chr7A.!!$R1 1524
7 TraesCS1B01G191200 chr7B 23440647 23442137 1490 True 772.500000 1254 85.462500 2733 4257 2 chr7B.!!$R2 1524
8 TraesCS1B01G191200 chr7D 76731777 76733267 1490 True 769.500000 1243 85.539000 2733 4257 2 chr7D.!!$R1 1524

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
236 242 0.027979 CACACACCACAAACGAGCAG 59.972 55.000 0.00 0.0 0.00 4.24 F
238 244 0.813610 CACACCACAAACGAGCAGGA 60.814 55.000 0.00 0.0 0.00 3.86 F
751 809 1.153628 CTTAACCTCCGGTCCGCAG 60.154 63.158 5.50 0.0 33.12 5.18 F
1764 2979 0.241213 TCTTGGAGACACGCTCTTCG 59.759 55.000 0.00 0.0 43.43 3.79 F
1943 3219 1.207488 AGGGCTTGGCATGTACAGGA 61.207 55.000 12.53 0.0 0.00 3.86 F
3119 4523 1.456331 GCCCTAATGCCCATGCTGT 60.456 57.895 0.00 0.0 38.71 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1587 1854 0.173708 CACAGCTACTCCCTCCGTTC 59.826 60.000 0.00 0.00 0.00 3.95 R
1590 1857 0.173708 GAACACAGCTACTCCCTCCG 59.826 60.000 0.00 0.00 0.00 4.63 R
1923 3199 0.546122 CCTGTACATGCCAAGCCCTA 59.454 55.000 0.00 0.00 0.00 3.53 R
3053 4455 3.542969 ACCAAAAAGGGATAAGCAGGT 57.457 42.857 0.00 0.00 43.89 4.00 R
3915 5326 1.228657 AAGCCTCGAACCGTTTCAGC 61.229 55.000 0.00 0.00 0.00 4.26 R
4274 5686 0.038159 CAGACGGACAAGTGTCTCCC 60.038 60.000 11.07 1.46 43.33 4.30 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
60 61 1.614413 GGTTAGGGGATCTGCTAGACG 59.386 57.143 0.00 0.00 0.00 4.18
72 73 3.156401 CTAGACGAGCAGCGATGAC 57.844 57.895 4.02 0.00 44.57 3.06
143 149 2.037772 AGGATCTGTCACAGACGCTTTT 59.962 45.455 10.48 0.00 43.63 2.27
148 154 3.006430 TCTGTCACAGACGCTTTTATGGA 59.994 43.478 2.36 0.00 35.39 3.41
167 173 1.551883 GACTCCCATTGGCTGCAATTT 59.448 47.619 0.50 0.00 0.00 1.82
168 174 1.276989 ACTCCCATTGGCTGCAATTTG 59.723 47.619 0.50 0.00 0.00 2.32
190 196 0.602638 TCGTGACAACAGCATGGTCC 60.603 55.000 0.00 0.00 43.62 4.46
230 236 4.601019 CTCTCAATTCACACACCACAAAC 58.399 43.478 0.00 0.00 0.00 2.93
231 237 3.064682 TCTCAATTCACACACCACAAACG 59.935 43.478 0.00 0.00 0.00 3.60
232 238 3.010420 TCAATTCACACACCACAAACGA 58.990 40.909 0.00 0.00 0.00 3.85
233 239 3.064682 TCAATTCACACACCACAAACGAG 59.935 43.478 0.00 0.00 0.00 4.18
234 240 0.730265 TTCACACACCACAAACGAGC 59.270 50.000 0.00 0.00 0.00 5.03
235 241 0.391793 TCACACACCACAAACGAGCA 60.392 50.000 0.00 0.00 0.00 4.26
236 242 0.027979 CACACACCACAAACGAGCAG 59.972 55.000 0.00 0.00 0.00 4.24
238 244 0.813610 CACACCACAAACGAGCAGGA 60.814 55.000 0.00 0.00 0.00 3.86
444 464 3.081409 ACCCCGTCAGGAATCCGG 61.081 66.667 0.00 0.00 41.02 5.14
521 548 3.430862 GCGTCAAAGGATGCGGCA 61.431 61.111 4.58 4.58 45.37 5.69
522 549 2.787249 CGTCAAAGGATGCGGCAG 59.213 61.111 9.25 0.00 0.00 4.85
523 550 2.486966 GTCAAAGGATGCGGCAGC 59.513 61.111 10.24 10.24 45.41 5.25
658 716 2.975799 CCCACACCGAACCCAACG 60.976 66.667 0.00 0.00 0.00 4.10
679 737 1.737249 GCGCGCGCATTAGAAAATTA 58.263 45.000 46.11 0.00 41.49 1.40
681 739 2.298300 CGCGCGCATTAGAAAATTAGG 58.702 47.619 32.61 5.06 0.00 2.69
682 740 2.044135 GCGCGCATTAGAAAATTAGGC 58.956 47.619 29.10 0.00 0.00 3.93
683 741 2.650608 CGCGCATTAGAAAATTAGGCC 58.349 47.619 8.75 0.00 0.00 5.19
684 742 2.290641 CGCGCATTAGAAAATTAGGCCT 59.709 45.455 11.78 11.78 0.00 5.19
685 743 3.607078 CGCGCATTAGAAAATTAGGCCTC 60.607 47.826 9.68 0.00 0.00 4.70
686 744 3.607078 GCGCATTAGAAAATTAGGCCTCG 60.607 47.826 9.68 2.23 0.00 4.63
687 745 3.607078 CGCATTAGAAAATTAGGCCTCGC 60.607 47.826 9.68 0.00 0.00 5.03
700 758 3.827898 CTCGCCCGACCCACTCTC 61.828 72.222 0.00 0.00 0.00 3.20
701 759 4.671590 TCGCCCGACCCACTCTCA 62.672 66.667 0.00 0.00 0.00 3.27
702 760 4.436998 CGCCCGACCCACTCTCAC 62.437 72.222 0.00 0.00 0.00 3.51
703 761 2.997897 GCCCGACCCACTCTCACT 60.998 66.667 0.00 0.00 0.00 3.41
704 762 2.973899 CCCGACCCACTCTCACTG 59.026 66.667 0.00 0.00 0.00 3.66
705 763 2.262915 CCGACCCACTCTCACTGC 59.737 66.667 0.00 0.00 0.00 4.40
706 764 2.262915 CGACCCACTCTCACTGCC 59.737 66.667 0.00 0.00 0.00 4.85
707 765 2.665603 GACCCACTCTCACTGCCC 59.334 66.667 0.00 0.00 0.00 5.36
708 766 3.302347 GACCCACTCTCACTGCCCG 62.302 68.421 0.00 0.00 0.00 6.13
709 767 4.767255 CCCACTCTCACTGCCCGC 62.767 72.222 0.00 0.00 0.00 6.13
746 804 3.317109 CCCCCTTAACCTCCGGTC 58.683 66.667 0.00 0.00 33.12 4.79
747 805 2.372890 CCCCCTTAACCTCCGGTCC 61.373 68.421 0.00 0.00 33.12 4.46
748 806 2.728435 CCCCTTAACCTCCGGTCCG 61.728 68.421 3.60 3.60 33.12 4.79
749 807 2.186125 CCTTAACCTCCGGTCCGC 59.814 66.667 5.50 0.00 33.12 5.54
750 808 2.652095 CCTTAACCTCCGGTCCGCA 61.652 63.158 5.50 0.00 33.12 5.69
751 809 1.153628 CTTAACCTCCGGTCCGCAG 60.154 63.158 5.50 0.00 33.12 5.18
752 810 3.305177 TTAACCTCCGGTCCGCAGC 62.305 63.158 5.50 0.00 33.12 5.25
804 970 3.157252 GCGGCTCATCCTCCCTCA 61.157 66.667 0.00 0.00 0.00 3.86
922 1130 9.458727 CCGGTTTTGTACCTATCTATCTATCTA 57.541 37.037 0.00 0.00 45.40 1.98
1215 1438 2.159254 GCTCGAGCAGTTCAAGATCTCT 60.159 50.000 31.91 0.00 41.59 3.10
1281 1507 2.508436 GCTTCCTCTAGCCCTGCC 59.492 66.667 0.00 0.00 35.06 4.85
1325 1559 1.448893 GGTGGTGCGCGAATTAGGA 60.449 57.895 12.10 0.00 0.00 2.94
1333 1567 2.362397 TGCGCGAATTAGGAGATCTCTT 59.638 45.455 21.81 17.25 0.00 2.85
1336 1570 3.183373 CGCGAATTAGGAGATCTCTTTGC 59.817 47.826 21.81 19.78 0.00 3.68
1337 1571 3.496507 GCGAATTAGGAGATCTCTTTGCC 59.503 47.826 21.81 5.99 0.00 4.52
1340 1574 3.802948 TTAGGAGATCTCTTTGCCGTC 57.197 47.619 21.81 3.12 0.00 4.79
1405 1665 5.000591 GGAGAGTTGGAGAAGAGAAAAAGG 58.999 45.833 0.00 0.00 0.00 3.11
1511 1778 8.783660 TGATCTGTCATTACTAATTACTCCCT 57.216 34.615 0.00 0.00 0.00 4.20
1512 1779 8.861086 TGATCTGTCATTACTAATTACTCCCTC 58.139 37.037 0.00 0.00 0.00 4.30
1513 1780 7.598759 TCTGTCATTACTAATTACTCCCTCC 57.401 40.000 0.00 0.00 0.00 4.30
1514 1781 6.264744 TCTGTCATTACTAATTACTCCCTCCG 59.735 42.308 0.00 0.00 0.00 4.63
1515 1782 5.895534 TGTCATTACTAATTACTCCCTCCGT 59.104 40.000 0.00 0.00 0.00 4.69
1516 1783 6.381994 TGTCATTACTAATTACTCCCTCCGTT 59.618 38.462 0.00 0.00 0.00 4.44
1517 1784 6.922407 GTCATTACTAATTACTCCCTCCGTTC 59.078 42.308 0.00 0.00 0.00 3.95
1518 1785 5.859205 TTACTAATTACTCCCTCCGTTCC 57.141 43.478 0.00 0.00 0.00 3.62
1519 1786 3.716431 ACTAATTACTCCCTCCGTTCCA 58.284 45.455 0.00 0.00 0.00 3.53
1520 1787 4.098894 ACTAATTACTCCCTCCGTTCCAA 58.901 43.478 0.00 0.00 0.00 3.53
1521 1788 4.533311 ACTAATTACTCCCTCCGTTCCAAA 59.467 41.667 0.00 0.00 0.00 3.28
1522 1789 4.376225 AATTACTCCCTCCGTTCCAAAA 57.624 40.909 0.00 0.00 0.00 2.44
1523 1790 4.586306 ATTACTCCCTCCGTTCCAAAAT 57.414 40.909 0.00 0.00 0.00 1.82
1524 1791 5.703730 ATTACTCCCTCCGTTCCAAAATA 57.296 39.130 0.00 0.00 0.00 1.40
1525 1792 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
1526 1793 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
1527 1794 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
1528 1795 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
1529 1796 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
1530 1797 4.412199 TCCCTCCGTTCCAAAATAGATGAT 59.588 41.667 0.00 0.00 0.00 2.45
1531 1798 5.104109 TCCCTCCGTTCCAAAATAGATGATT 60.104 40.000 0.00 0.00 0.00 2.57
1532 1799 5.239525 CCCTCCGTTCCAAAATAGATGATTC 59.760 44.000 0.00 0.00 0.00 2.52
1533 1800 5.822519 CCTCCGTTCCAAAATAGATGATTCA 59.177 40.000 0.00 0.00 0.00 2.57
1534 1801 6.318648 CCTCCGTTCCAAAATAGATGATTCAA 59.681 38.462 0.00 0.00 0.00 2.69
1535 1802 7.083875 TCCGTTCCAAAATAGATGATTCAAC 57.916 36.000 0.00 0.00 0.00 3.18
1536 1803 6.884295 TCCGTTCCAAAATAGATGATTCAACT 59.116 34.615 1.83 1.83 0.00 3.16
1537 1804 7.393234 TCCGTTCCAAAATAGATGATTCAACTT 59.607 33.333 1.47 0.00 0.00 2.66
1538 1805 8.028938 CCGTTCCAAAATAGATGATTCAACTTT 58.971 33.333 1.47 0.00 0.00 2.66
1580 1847 8.706322 AAAGTTAATACAAAGTTGGGTCATCT 57.294 30.769 0.00 0.00 0.00 2.90
1581 1848 9.802039 AAAGTTAATACAAAGTTGGGTCATCTA 57.198 29.630 0.00 0.00 0.00 1.98
1582 1849 9.975218 AAGTTAATACAAAGTTGGGTCATCTAT 57.025 29.630 0.00 0.00 0.00 1.98
1583 1850 9.975218 AGTTAATACAAAGTTGGGTCATCTATT 57.025 29.630 0.00 0.00 0.00 1.73
1587 1854 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
1588 1855 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
1589 1856 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
1590 1857 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
1591 1858 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
1592 1859 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
1593 1860 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
1594 1861 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
1595 1862 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
1596 1863 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
1597 1864 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
1598 1865 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
1602 1869 0.611714 TTTGGAACGGAGGGAGTAGC 59.388 55.000 0.00 0.00 0.00 3.58
1662 1963 7.979786 AGGAGACAATTGGACTTAGAGATTA 57.020 36.000 10.83 0.00 0.00 1.75
1694 2906 6.164176 TCTTGAGGAAAACCTCGATTAGTTC 58.836 40.000 10.95 0.00 39.49 3.01
1737 2950 2.614829 AGGTTCGCAAGTTGTAGTGT 57.385 45.000 4.48 0.00 39.48 3.55
1759 2974 1.261480 ACTGATCTTGGAGACACGCT 58.739 50.000 0.00 0.00 42.67 5.07
1764 2979 0.241213 TCTTGGAGACACGCTCTTCG 59.759 55.000 0.00 0.00 43.43 3.79
1853 3129 3.447229 GCAGCCTAAATAAAGGAGCCAAA 59.553 43.478 0.00 0.00 39.15 3.28
1885 3161 6.956299 AATTTAGCACTACGTATGTTCGTT 57.044 33.333 0.00 0.00 43.80 3.85
1932 3208 8.519799 TTTCTTATTTCAATAGTAGGGCTTGG 57.480 34.615 0.00 0.00 0.00 3.61
1943 3219 1.207488 AGGGCTTGGCATGTACAGGA 61.207 55.000 12.53 0.00 0.00 3.86
2131 3419 8.495148 GTTCATGTTCTCTTTGTTGTTTTGTTT 58.505 29.630 0.00 0.00 0.00 2.83
2146 3437 9.194271 GTTGTTTTGTTTTGTAACCTGAGTTTA 57.806 29.630 0.00 0.00 37.42 2.01
2150 3441 5.184711 TGTTTTGTAACCTGAGTTTACCGT 58.815 37.500 0.00 0.00 37.42 4.83
2391 3697 2.426522 CTGTGTAGCTTGGCTTTGCTA 58.573 47.619 0.00 0.00 40.44 3.49
2472 3783 7.870509 TTAAGCAGTAGTTTATCCTACTCGA 57.129 36.000 0.00 0.00 44.49 4.04
2473 3784 6.963083 AAGCAGTAGTTTATCCTACTCGAT 57.037 37.500 0.00 0.00 44.49 3.59
2474 3785 6.320494 AGCAGTAGTTTATCCTACTCGATG 57.680 41.667 0.00 0.00 44.49 3.84
2476 3787 6.717540 AGCAGTAGTTTATCCTACTCGATGAT 59.282 38.462 0.00 0.00 44.49 2.45
2478 3789 7.868415 GCAGTAGTTTATCCTACTCGATGATTT 59.132 37.037 0.00 0.00 44.49 2.17
2479 3790 9.186323 CAGTAGTTTATCCTACTCGATGATTTG 57.814 37.037 0.00 0.00 44.49 2.32
2480 3791 9.132923 AGTAGTTTATCCTACTCGATGATTTGA 57.867 33.333 0.00 0.00 43.17 2.69
2487 3803 8.970859 ATCCTACTCGATGATTTGATTTTTCT 57.029 30.769 0.00 0.00 0.00 2.52
2629 4012 5.116882 AGCTGTGTAACGAACTTCTTTTCT 58.883 37.500 0.00 0.00 42.39 2.52
2638 4021 9.647679 GTAACGAACTTCTTTTCTTCCTTTAAG 57.352 33.333 0.00 0.00 36.45 1.85
3010 4412 5.552178 GACTGGATGTCAAAGGTAAGAGTT 58.448 41.667 0.00 0.00 44.73 3.01
3011 4413 6.681729 ACTGGATGTCAAAGGTAAGAGTTA 57.318 37.500 0.00 0.00 0.00 2.24
3053 4455 2.642311 TGCCCTGTCCATACTCTTTTGA 59.358 45.455 0.00 0.00 0.00 2.69
3081 4483 5.741673 GCTTATCCCTTTTTGGTTGCTCAAA 60.742 40.000 0.00 0.00 35.15 2.69
3103 4507 5.954296 ATGTGCAGTATATCAATGAAGCC 57.046 39.130 0.00 0.00 0.00 4.35
3119 4523 1.456331 GCCCTAATGCCCATGCTGT 60.456 57.895 0.00 0.00 38.71 4.40
3207 4618 2.669569 AGTGATGCCACACGCCAC 60.670 61.111 0.00 0.00 45.54 5.01
3915 5326 4.381932 GCCCAAACAATCATTACCCAAGAG 60.382 45.833 0.00 0.00 0.00 2.85
4005 5416 1.406065 CCGACAGGATCAGGGCATCT 61.406 60.000 0.00 0.00 41.02 2.90
4089 5500 3.386237 GAGGAGCTGAGCACGGGT 61.386 66.667 7.39 0.00 35.70 5.28
4170 5581 2.030562 ACCCTGGACGAAACGCTG 59.969 61.111 0.00 0.00 0.00 5.18
4274 5686 0.035458 AAGACCCAAAGCTGAGACCG 59.965 55.000 0.00 0.00 0.00 4.79
4306 5718 8.618677 CACTTGTCCGTCTGTATATCTACTTAA 58.381 37.037 0.00 0.00 0.00 1.85
4433 5867 1.895798 TGTGTTGTAGAGAGGAGCAGG 59.104 52.381 0.00 0.00 0.00 4.85
4545 5989 8.928270 ACTGTACTCTATTGGACGAAATAAAG 57.072 34.615 0.00 0.00 0.00 1.85
4608 6093 2.686915 ACTTGCATTAGCTCCTGCATTC 59.313 45.455 20.13 0.00 46.87 2.67
4648 6134 2.979240 AGATTTCCGAACTCTGAAGGC 58.021 47.619 0.41 0.00 0.00 4.35
4653 6139 1.080501 CGAACTCTGAAGGCGCTCA 60.081 57.895 7.64 2.69 0.00 4.26
4656 6142 0.394565 AACTCTGAAGGCGCTCAGTT 59.605 50.000 21.80 11.15 42.93 3.16
4657 6143 0.320247 ACTCTGAAGGCGCTCAGTTG 60.320 55.000 21.80 18.05 42.93 3.16
4658 6144 1.633852 CTCTGAAGGCGCTCAGTTGC 61.634 60.000 21.80 0.00 42.93 4.17
4659 6145 1.670406 CTGAAGGCGCTCAGTTGCT 60.670 57.895 16.35 0.00 38.43 3.91
4661 6147 0.034756 TGAAGGCGCTCAGTTGCTTA 59.965 50.000 7.64 0.00 0.00 3.09
4662 6148 1.339055 TGAAGGCGCTCAGTTGCTTAT 60.339 47.619 7.64 0.00 0.00 1.73
4663 6149 2.093711 TGAAGGCGCTCAGTTGCTTATA 60.094 45.455 7.64 0.00 0.00 0.98
4669 6157 3.786635 CGCTCAGTTGCTTATAGGTTCT 58.213 45.455 0.00 0.00 0.00 3.01
4697 6185 6.426646 ACTCCTTTCTTCAGTGTTATCTGT 57.573 37.500 0.00 0.00 36.85 3.41
4698 6186 6.459923 ACTCCTTTCTTCAGTGTTATCTGTC 58.540 40.000 0.00 0.00 36.85 3.51
4699 6187 6.268847 ACTCCTTTCTTCAGTGTTATCTGTCT 59.731 38.462 0.00 0.00 36.85 3.41
4700 6188 6.459066 TCCTTTCTTCAGTGTTATCTGTCTG 58.541 40.000 0.00 0.00 36.85 3.51
4710 6209 5.419471 AGTGTTATCTGTCTGTTCTCCCTAC 59.581 44.000 0.00 0.00 0.00 3.18
4720 6219 1.002773 GTTCTCCCTACGAGGCCAAAA 59.997 52.381 5.01 0.00 39.30 2.44
4749 6248 3.674997 ACACATCAATAACCAGTTCGCT 58.325 40.909 0.00 0.00 0.00 4.93
4767 6266 5.309323 TCGCTGATTATCTTTTTGTTGGG 57.691 39.130 0.00 0.00 0.00 4.12
4789 6309 3.068590 GCCAATACATTGCTGCCTAACAT 59.931 43.478 0.00 0.00 36.48 2.71
4798 6318 2.298729 TGCTGCCTAACATTTTTGGTCC 59.701 45.455 0.00 0.00 30.79 4.46
4875 6405 1.447140 GTGCGGCGACCAAGACATA 60.447 57.895 12.98 0.00 0.00 2.29
4917 6447 3.698382 GCGAGGTGCATCTCTTCG 58.302 61.111 24.11 13.64 45.45 3.79
5014 6547 2.430465 GAAGCCAGTTCATCTGCTGAA 58.570 47.619 0.00 0.00 42.38 3.02
5017 6550 1.747709 CCAGTTCATCTGCTGAAGGG 58.252 55.000 0.00 0.00 44.44 3.95
5018 6551 1.093159 CAGTTCATCTGCTGAAGGGC 58.907 55.000 0.00 0.00 44.44 5.19
5019 6552 0.694771 AGTTCATCTGCTGAAGGGCA 59.305 50.000 0.00 0.00 44.44 5.36
5020 6553 0.807496 GTTCATCTGCTGAAGGGCAC 59.193 55.000 0.00 0.00 44.44 5.01
5033 6566 2.356667 GGCACCCCCTCTCCTTTG 59.643 66.667 0.00 0.00 0.00 2.77
5067 6600 0.973496 GTCTCCCTCTCCCTGTCCAC 60.973 65.000 0.00 0.00 0.00 4.02
5068 6601 1.687493 CTCCCTCTCCCTGTCCACC 60.687 68.421 0.00 0.00 0.00 4.61
5069 6602 2.689034 CCCTCTCCCTGTCCACCC 60.689 72.222 0.00 0.00 0.00 4.61
5135 6668 2.542907 GGTGTGGCGTCAAGTGTGG 61.543 63.158 0.00 0.00 0.00 4.17
5140 6673 1.069090 GGCGTCAAGTGTGGAGACA 59.931 57.895 0.00 0.00 38.70 3.41
5159 6696 4.156190 AGACACTATCTAACCTGTCACACG 59.844 45.833 0.00 0.00 35.15 4.49
5167 6704 1.359117 CCTGTCACACGTCACGAGT 59.641 57.895 2.91 0.00 0.00 4.18
5241 6778 0.031414 GGAGTTAGGTAGGGGCTGGA 60.031 60.000 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 5.968167 TCTAGCAGATCCCCTAACCTAAAAA 59.032 40.000 0.00 0.00 0.00 1.94
35 36 5.365895 GTCTAGCAGATCCCCTAACCTAAAA 59.634 44.000 0.00 0.00 0.00 1.52
43 44 2.570415 CTCGTCTAGCAGATCCCCTA 57.430 55.000 0.00 0.00 0.00 3.53
104 107 9.890915 ACAGATCCTCTATCCTAAAAGTCTTAT 57.109 33.333 0.00 0.00 34.90 1.73
130 136 3.585862 GAGTCCATAAAAGCGTCTGTGA 58.414 45.455 0.00 0.00 0.00 3.58
133 139 2.280628 GGGAGTCCATAAAAGCGTCTG 58.719 52.381 12.30 0.00 0.00 3.51
148 154 1.276989 CAAATTGCAGCCAATGGGAGT 59.723 47.619 0.00 0.00 40.69 3.85
167 173 0.936600 CATGCTGTTGTCACGACACA 59.063 50.000 0.00 0.00 41.67 3.72
168 174 0.235665 CCATGCTGTTGTCACGACAC 59.764 55.000 0.00 0.00 41.67 3.67
230 236 1.025113 TGTCGTCTACCTCCTGCTCG 61.025 60.000 0.00 0.00 0.00 5.03
231 237 0.452585 GTGTCGTCTACCTCCTGCTC 59.547 60.000 0.00 0.00 0.00 4.26
232 238 0.251209 TGTGTCGTCTACCTCCTGCT 60.251 55.000 0.00 0.00 0.00 4.24
233 239 0.171455 CTGTGTCGTCTACCTCCTGC 59.829 60.000 0.00 0.00 0.00 4.85
234 240 0.171455 GCTGTGTCGTCTACCTCCTG 59.829 60.000 0.00 0.00 0.00 3.86
235 241 0.966370 GGCTGTGTCGTCTACCTCCT 60.966 60.000 0.00 0.00 0.00 3.69
236 242 1.511768 GGCTGTGTCGTCTACCTCC 59.488 63.158 0.00 0.00 0.00 4.30
238 244 2.991076 GCGGCTGTGTCGTCTACCT 61.991 63.158 0.00 0.00 31.29 3.08
293 300 1.523711 CCTGTGCGGCATATTCGGT 60.524 57.895 5.72 0.00 0.00 4.69
481 508 2.203056 CGGATTGCTGGCGATGGA 60.203 61.111 0.00 0.00 0.00 3.41
482 509 3.957535 GCGGATTGCTGGCGATGG 61.958 66.667 0.00 0.00 41.73 3.51
483 510 3.957535 GGCGGATTGCTGGCGATG 61.958 66.667 0.00 0.00 45.43 3.84
520 547 0.888619 TATCCGCTCCCTTATCGCTG 59.111 55.000 0.00 0.00 0.00 5.18
521 548 1.178276 CTATCCGCTCCCTTATCGCT 58.822 55.000 0.00 0.00 0.00 4.93
522 549 0.889306 ACTATCCGCTCCCTTATCGC 59.111 55.000 0.00 0.00 0.00 4.58
523 550 1.402984 GCACTATCCGCTCCCTTATCG 60.403 57.143 0.00 0.00 0.00 2.92
524 551 1.066787 GGCACTATCCGCTCCCTTATC 60.067 57.143 0.00 0.00 0.00 1.75
525 552 0.977395 GGCACTATCCGCTCCCTTAT 59.023 55.000 0.00 0.00 0.00 1.73
526 553 1.461091 CGGCACTATCCGCTCCCTTA 61.461 60.000 0.00 0.00 43.18 2.69
527 554 2.797278 CGGCACTATCCGCTCCCTT 61.797 63.158 0.00 0.00 43.18 3.95
683 741 3.827898 GAGAGTGGGTCGGGCGAG 61.828 72.222 0.00 0.00 0.00 5.03
684 742 4.671590 TGAGAGTGGGTCGGGCGA 62.672 66.667 0.00 0.00 0.00 5.54
685 743 4.436998 GTGAGAGTGGGTCGGGCG 62.437 72.222 0.00 0.00 0.00 6.13
686 744 2.997897 AGTGAGAGTGGGTCGGGC 60.998 66.667 0.00 0.00 0.00 6.13
687 745 2.973899 CAGTGAGAGTGGGTCGGG 59.026 66.667 0.00 0.00 0.00 5.14
688 746 2.262915 GCAGTGAGAGTGGGTCGG 59.737 66.667 0.00 0.00 0.00 4.79
689 747 2.262915 GGCAGTGAGAGTGGGTCG 59.737 66.667 0.00 0.00 0.00 4.79
690 748 2.665603 GGGCAGTGAGAGTGGGTC 59.334 66.667 0.00 0.00 0.00 4.46
691 749 3.314331 CGGGCAGTGAGAGTGGGT 61.314 66.667 0.00 0.00 0.00 4.51
692 750 4.767255 GCGGGCAGTGAGAGTGGG 62.767 72.222 0.00 0.00 0.00 4.61
749 807 3.635268 GAAGGGGTCCTGGCAGCTG 62.635 68.421 10.11 10.11 32.13 4.24
750 808 3.334054 GAAGGGGTCCTGGCAGCT 61.334 66.667 9.56 0.00 32.13 4.24
751 809 2.828480 GAAGAAGGGGTCCTGGCAGC 62.828 65.000 9.56 0.00 32.13 5.25
752 810 1.301293 GAAGAAGGGGTCCTGGCAG 59.699 63.158 7.75 7.75 32.13 4.85
753 811 2.231380 GGAAGAAGGGGTCCTGGCA 61.231 63.158 0.00 0.00 32.13 4.92
754 812 1.916206 GAGGAAGAAGGGGTCCTGGC 61.916 65.000 0.00 0.00 44.57 4.85
755 813 1.617947 CGAGGAAGAAGGGGTCCTGG 61.618 65.000 0.00 0.00 44.57 4.45
756 814 1.901085 CGAGGAAGAAGGGGTCCTG 59.099 63.158 0.00 0.00 44.57 3.86
758 816 2.245438 CTGCGAGGAAGAAGGGGTCC 62.245 65.000 0.00 0.00 0.00 4.46
759 817 1.219393 CTGCGAGGAAGAAGGGGTC 59.781 63.158 0.00 0.00 0.00 4.46
760 818 1.229209 TCTGCGAGGAAGAAGGGGT 60.229 57.895 0.00 0.00 0.00 4.95
761 819 1.219393 GTCTGCGAGGAAGAAGGGG 59.781 63.158 0.00 0.00 0.00 4.79
762 820 1.153745 CGTCTGCGAGGAAGAAGGG 60.154 63.158 0.00 0.00 41.33 3.95
763 821 1.807573 GCGTCTGCGAGGAAGAAGG 60.808 63.158 0.00 0.00 41.33 3.46
922 1130 3.131396 CGAACCGTACGTAGGTATAGGT 58.869 50.000 15.21 15.51 41.95 3.08
923 1131 3.059597 CACGAACCGTACGTAGGTATAGG 60.060 52.174 15.21 14.55 41.95 2.57
924 1132 3.059597 CCACGAACCGTACGTAGGTATAG 60.060 52.174 15.21 11.17 41.95 1.31
926 1134 1.670811 CCACGAACCGTACGTAGGTAT 59.329 52.381 15.21 2.54 41.95 2.73
1281 1507 4.518970 ACTAAACCTGCACAACCTTACATG 59.481 41.667 0.00 0.00 0.00 3.21
1325 1559 4.504132 GCGACGGCAAAGAGATCT 57.496 55.556 0.00 0.00 39.62 2.75
1336 1570 0.450482 CAAAACTTACGCTGCGACGG 60.450 55.000 30.47 18.31 37.37 4.79
1337 1571 0.450482 CCAAAACTTACGCTGCGACG 60.450 55.000 30.47 17.39 39.50 5.12
1340 1574 0.996727 GCACCAAAACTTACGCTGCG 60.997 55.000 21.91 21.91 0.00 5.18
1347 1591 1.904287 ATCGGCAGCACCAAAACTTA 58.096 45.000 0.00 0.00 39.03 2.24
1405 1665 1.162698 GCAAGTTCCCCTACGTTTCC 58.837 55.000 0.00 0.00 0.00 3.13
1507 1774 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
1508 1775 4.150897 TCATCTATTTTGGAACGGAGGG 57.849 45.455 0.00 0.00 0.00 4.30
1509 1776 5.822519 TGAATCATCTATTTTGGAACGGAGG 59.177 40.000 0.00 0.00 0.00 4.30
1510 1777 6.925610 TGAATCATCTATTTTGGAACGGAG 57.074 37.500 0.00 0.00 0.00 4.63
1511 1778 6.884295 AGTTGAATCATCTATTTTGGAACGGA 59.116 34.615 0.00 0.00 0.00 4.69
1512 1779 7.088589 AGTTGAATCATCTATTTTGGAACGG 57.911 36.000 0.00 0.00 0.00 4.44
1513 1780 8.970691 AAAGTTGAATCATCTATTTTGGAACG 57.029 30.769 0.00 0.00 0.00 3.95
1554 1821 9.802039 AGATGACCCAACTTTGTATTAACTTTA 57.198 29.630 0.00 0.00 0.00 1.85
1555 1822 8.706322 AGATGACCCAACTTTGTATTAACTTT 57.294 30.769 0.00 0.00 0.00 2.66
1556 1823 9.975218 ATAGATGACCCAACTTTGTATTAACTT 57.025 29.630 0.00 0.00 0.00 2.66
1557 1824 9.975218 AATAGATGACCCAACTTTGTATTAACT 57.025 29.630 0.00 0.00 0.00 2.24
1561 1828 8.531146 CCAAAATAGATGACCCAACTTTGTATT 58.469 33.333 0.00 0.00 0.00 1.89
1562 1829 7.893302 TCCAAAATAGATGACCCAACTTTGTAT 59.107 33.333 0.00 0.00 0.00 2.29
1563 1830 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
1564 1831 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
1565 1832 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
1566 1833 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
1567 1834 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
1568 1835 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
1569 1836 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
1570 1837 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
1571 1838 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
1572 1839 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
1573 1840 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
1574 1841 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
1575 1842 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
1576 1843 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
1577 1844 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
1578 1845 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
1579 1846 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
1580 1847 3.118519 GCTACTCCCTCCGTTCCAAAATA 60.119 47.826 0.00 0.00 0.00 1.40
1581 1848 2.355818 GCTACTCCCTCCGTTCCAAAAT 60.356 50.000 0.00 0.00 0.00 1.82
1582 1849 1.002773 GCTACTCCCTCCGTTCCAAAA 59.997 52.381 0.00 0.00 0.00 2.44
1583 1850 0.611714 GCTACTCCCTCCGTTCCAAA 59.388 55.000 0.00 0.00 0.00 3.28
1584 1851 0.252103 AGCTACTCCCTCCGTTCCAA 60.252 55.000 0.00 0.00 0.00 3.53
1585 1852 0.970937 CAGCTACTCCCTCCGTTCCA 60.971 60.000 0.00 0.00 0.00 3.53
1586 1853 0.971447 ACAGCTACTCCCTCCGTTCC 60.971 60.000 0.00 0.00 0.00 3.62
1587 1854 0.173708 CACAGCTACTCCCTCCGTTC 59.826 60.000 0.00 0.00 0.00 3.95
1588 1855 0.542232 ACACAGCTACTCCCTCCGTT 60.542 55.000 0.00 0.00 0.00 4.44
1589 1856 0.542232 AACACAGCTACTCCCTCCGT 60.542 55.000 0.00 0.00 0.00 4.69
1590 1857 0.173708 GAACACAGCTACTCCCTCCG 59.826 60.000 0.00 0.00 0.00 4.63
1591 1858 1.066787 GTGAACACAGCTACTCCCTCC 60.067 57.143 0.00 0.00 0.00 4.30
1592 1859 1.618837 TGTGAACACAGCTACTCCCTC 59.381 52.381 3.39 0.00 36.21 4.30
1593 1860 1.717032 TGTGAACACAGCTACTCCCT 58.283 50.000 3.39 0.00 36.21 4.20
1639 1940 8.207545 ACATAATCTCTAAGTCCAATTGTCTCC 58.792 37.037 4.43 0.00 0.00 3.71
1694 2906 2.097202 CGACACTCGTGCAGAAAAAGAG 60.097 50.000 0.00 0.00 34.72 2.85
1737 2950 3.258372 AGCGTGTCTCCAAGATCAGTTAA 59.742 43.478 0.00 0.00 0.00 2.01
1759 2974 1.824852 TGGTCTGCTAATCTGCGAAGA 59.175 47.619 0.00 0.00 35.36 2.87
1764 2979 3.249559 GTGCTAATGGTCTGCTAATCTGC 59.750 47.826 0.00 0.00 0.00 4.26
1853 3129 3.619929 CGTAGTGCTAAATTTTAGCCGGT 59.380 43.478 29.19 19.26 39.69 5.28
1866 3142 3.191162 ACCAACGAACATACGTAGTGCTA 59.809 43.478 0.08 0.00 45.83 3.49
1885 3161 9.621629 AGAAATATAACGGTTTATTCATCACCA 57.378 29.630 0.00 0.00 0.00 4.17
1914 3190 3.730215 TGCCAAGCCCTACTATTGAAA 57.270 42.857 0.00 0.00 0.00 2.69
1915 3191 3.053693 ACATGCCAAGCCCTACTATTGAA 60.054 43.478 0.00 0.00 0.00 2.69
1916 3192 2.509548 ACATGCCAAGCCCTACTATTGA 59.490 45.455 0.00 0.00 0.00 2.57
1917 3193 2.936202 ACATGCCAAGCCCTACTATTG 58.064 47.619 0.00 0.00 0.00 1.90
1918 3194 3.458118 TGTACATGCCAAGCCCTACTATT 59.542 43.478 0.00 0.00 0.00 1.73
1919 3195 3.045634 TGTACATGCCAAGCCCTACTAT 58.954 45.455 0.00 0.00 0.00 2.12
1920 3196 2.434336 CTGTACATGCCAAGCCCTACTA 59.566 50.000 0.00 0.00 0.00 1.82
1921 3197 1.210478 CTGTACATGCCAAGCCCTACT 59.790 52.381 0.00 0.00 0.00 2.57
1922 3198 1.668419 CTGTACATGCCAAGCCCTAC 58.332 55.000 0.00 0.00 0.00 3.18
1923 3199 0.546122 CCTGTACATGCCAAGCCCTA 59.454 55.000 0.00 0.00 0.00 3.53
1930 3206 2.304470 TGTTAAGCTCCTGTACATGCCA 59.696 45.455 0.00 0.00 0.00 4.92
1932 3208 5.371115 TTTTGTTAAGCTCCTGTACATGC 57.629 39.130 0.00 1.62 0.00 4.06
1963 3239 6.717540 TCCTTTATTTAGGCTGCAAACACTAA 59.282 34.615 0.50 0.00 35.15 2.24
1969 3245 4.085733 TGCTCCTTTATTTAGGCTGCAAA 58.914 39.130 0.50 0.00 39.61 3.68
1970 3246 3.696045 TGCTCCTTTATTTAGGCTGCAA 58.304 40.909 0.50 0.00 39.61 4.08
2131 3419 3.560896 GCAACGGTAAACTCAGGTTACAA 59.439 43.478 14.70 0.00 34.90 2.41
2146 3437 5.560183 CGAATCTTGAAGTTTTAGCAACGGT 60.560 40.000 0.00 0.00 0.00 4.83
2391 3697 2.092321 ACAGGCTATCGGACTACTGTCT 60.092 50.000 0.00 0.00 42.54 3.41
2472 3783 8.985805 GCACAAAGAAGAGAAAAATCAAATCAT 58.014 29.630 0.00 0.00 0.00 2.45
2473 3784 8.199449 AGCACAAAGAAGAGAAAAATCAAATCA 58.801 29.630 0.00 0.00 0.00 2.57
2474 3785 8.585189 AGCACAAAGAAGAGAAAAATCAAATC 57.415 30.769 0.00 0.00 0.00 2.17
2476 3787 7.201548 GCAAGCACAAAGAAGAGAAAAATCAAA 60.202 33.333 0.00 0.00 0.00 2.69
2478 3789 5.750067 GCAAGCACAAAGAAGAGAAAAATCA 59.250 36.000 0.00 0.00 0.00 2.57
2479 3790 5.981915 AGCAAGCACAAAGAAGAGAAAAATC 59.018 36.000 0.00 0.00 0.00 2.17
2480 3791 5.751990 CAGCAAGCACAAAGAAGAGAAAAAT 59.248 36.000 0.00 0.00 0.00 1.82
2485 3801 2.615447 CACAGCAAGCACAAAGAAGAGA 59.385 45.455 0.00 0.00 0.00 3.10
2486 3802 2.287427 CCACAGCAAGCACAAAGAAGAG 60.287 50.000 0.00 0.00 0.00 2.85
2487 3803 1.677576 CCACAGCAAGCACAAAGAAGA 59.322 47.619 0.00 0.00 0.00 2.87
2638 4021 6.093633 ACGTTTTCTTAGTAATGATGCCTTCC 59.906 38.462 0.00 0.00 0.00 3.46
2651 4047 7.081976 GCAAATCACCATAACGTTTTCTTAGT 58.918 34.615 5.91 0.00 0.00 2.24
2753 4155 7.404980 ACTCTTTTCCTTCATATACCCTGGTAA 59.595 37.037 0.00 0.00 33.99 2.85
2764 4166 5.050490 GCGATGCTACTCTTTTCCTTCATA 58.950 41.667 0.00 0.00 0.00 2.15
3010 4412 7.495279 GGGCAAACAAGCATTTGATCAAATATA 59.505 33.333 28.61 6.68 41.28 0.86
3011 4413 6.316890 GGGCAAACAAGCATTTGATCAAATAT 59.683 34.615 28.61 19.15 41.28 1.28
3053 4455 3.542969 ACCAAAAAGGGATAAGCAGGT 57.457 42.857 0.00 0.00 43.89 4.00
3081 4483 4.763793 GGGCTTCATTGATATACTGCACAT 59.236 41.667 0.00 0.00 0.00 3.21
3103 4507 3.615224 AAAAACAGCATGGGCATTAGG 57.385 42.857 0.00 0.00 43.62 2.69
3915 5326 1.228657 AAGCCTCGAACCGTTTCAGC 61.229 55.000 0.00 0.00 0.00 4.26
4005 5416 1.588597 CAGGCACTTCTCGAGCTCA 59.411 57.895 15.40 0.00 34.60 4.26
4089 5500 4.381612 CCGTGAAGGAGCTTGTTCACTATA 60.382 45.833 26.81 2.65 46.92 1.31
4170 5581 2.045926 AGGGCGTGCATGTTCTCC 60.046 61.111 7.93 4.89 0.00 3.71
4274 5686 0.038159 CAGACGGACAAGTGTCTCCC 60.038 60.000 11.07 1.46 43.33 4.30
4306 5718 1.202580 GCGACATTCTGGGAGCAGTAT 60.203 52.381 0.00 0.00 0.00 2.12
4433 5867 2.802247 GTTTTGGAGCAAACATGCTTCC 59.198 45.455 6.65 8.88 46.36 3.46
4545 5989 9.950496 ATCCATTAACACACTGATATATTCCTC 57.050 33.333 0.00 0.00 0.00 3.71
4648 6134 3.553511 CAGAACCTATAAGCAACTGAGCG 59.446 47.826 0.00 0.00 40.15 5.03
4653 6139 4.463186 AGTCGACAGAACCTATAAGCAACT 59.537 41.667 19.50 0.00 0.00 3.16
4656 6142 3.380637 GGAGTCGACAGAACCTATAAGCA 59.619 47.826 19.50 0.00 0.00 3.91
4657 6143 3.633065 AGGAGTCGACAGAACCTATAAGC 59.367 47.826 19.50 0.00 34.99 3.09
4658 6144 5.838531 AAGGAGTCGACAGAACCTATAAG 57.161 43.478 19.50 0.00 35.44 1.73
4659 6145 5.950549 AGAAAGGAGTCGACAGAACCTATAA 59.049 40.000 19.50 0.00 35.44 0.98
4661 6147 4.345854 AGAAAGGAGTCGACAGAACCTAT 58.654 43.478 19.50 7.67 35.44 2.57
4662 6148 3.764218 AGAAAGGAGTCGACAGAACCTA 58.236 45.455 19.50 0.00 35.44 3.08
4663 6149 2.599677 AGAAAGGAGTCGACAGAACCT 58.400 47.619 19.50 16.51 37.14 3.50
4669 6157 2.693591 ACACTGAAGAAAGGAGTCGACA 59.306 45.455 19.50 0.00 0.00 4.35
4697 6185 0.683504 GGCCTCGTAGGGAGAACAGA 60.684 60.000 0.00 0.00 46.23 3.41
4698 6186 0.970937 TGGCCTCGTAGGGAGAACAG 60.971 60.000 3.32 0.00 46.23 3.16
4699 6187 0.543410 TTGGCCTCGTAGGGAGAACA 60.543 55.000 3.32 0.00 46.23 3.18
4700 6188 0.611714 TTTGGCCTCGTAGGGAGAAC 59.388 55.000 3.32 0.00 46.23 3.01
4710 6209 0.109132 GTCCAGCAATTTTGGCCTCG 60.109 55.000 3.32 0.00 35.62 4.63
4749 6248 5.815233 TTGGCCCAACAAAAAGATAATCA 57.185 34.783 0.00 0.00 0.00 2.57
4767 6266 2.426738 TGTTAGGCAGCAATGTATTGGC 59.573 45.455 6.72 2.75 38.21 4.52
4798 6318 4.341366 AACCTTGCCAAATTCCAAGAAG 57.659 40.909 12.44 0.00 40.59 2.85
4875 6405 7.040617 GCTCATCAATCATCACAAGATACCAAT 60.041 37.037 0.00 0.00 31.88 3.16
4917 6447 1.136147 CAGCAGCAATCGTCCAAGC 59.864 57.895 0.00 0.00 0.00 4.01
5014 6547 3.523681 AAAGGAGAGGGGGTGCCCT 62.524 63.158 7.26 0.00 44.66 5.19
5017 6550 2.356667 CCAAAGGAGAGGGGGTGC 59.643 66.667 0.00 0.00 0.00 5.01
5018 6551 1.685820 GACCAAAGGAGAGGGGGTG 59.314 63.158 0.00 0.00 30.55 4.61
5019 6552 1.541620 GGACCAAAGGAGAGGGGGT 60.542 63.158 0.00 0.00 33.78 4.95
5020 6553 2.309504 GGGACCAAAGGAGAGGGGG 61.310 68.421 0.00 0.00 0.00 5.40
5135 6668 5.642686 GTGTGACAGGTTAGATAGTGTCTC 58.357 45.833 0.00 0.57 40.06 3.36
5140 6673 4.077108 TGACGTGTGACAGGTTAGATAGT 58.923 43.478 12.50 0.00 32.46 2.12
5141 6674 4.413087 GTGACGTGTGACAGGTTAGATAG 58.587 47.826 12.50 0.00 32.46 2.08
5142 6675 3.120095 CGTGACGTGTGACAGGTTAGATA 60.120 47.826 12.50 0.00 32.46 1.98
5144 6677 1.002142 CGTGACGTGTGACAGGTTAGA 60.002 52.381 12.50 0.00 32.46 2.10
5145 6678 1.002142 TCGTGACGTGTGACAGGTTAG 60.002 52.381 12.50 7.26 32.46 2.34
5159 6696 1.134965 CCTCCCTGAATCACTCGTGAC 60.135 57.143 1.26 0.00 43.11 3.67
5167 6704 2.042464 CCGATCTTCCTCCCTGAATCA 58.958 52.381 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.