Multiple sequence alignment - TraesCS5D01G012900

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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 TraesCS5D01G012900 chr5D 100.000 5609 0 0 1 5609 7009523 7003915 0.000000e+00 10358.0
1 TraesCS5D01G012900 chr5D 92.709 919 23 11 1 880 365119391 365118478 0.000000e+00 1286.0
2 TraesCS5D01G012900 chr5D 94.737 589 12 3 1 574 82082037 82082621 0.000000e+00 898.0
3 TraesCS5D01G012900 chr5D 90.541 148 8 3 5316 5463 549240432 549240291 2.060000e-44 191.0
4 TraesCS5D01G012900 chr5D 93.182 88 6 0 3024 3111 535136261 535136174 4.560000e-26 130.0
5 TraesCS5D01G012900 chr5A 89.621 2534 141 56 3068 5576 2872165 2869729 0.000000e+00 3110.0
6 TraesCS5D01G012900 chr5A 85.085 1703 150 61 889 2559 2874464 2872834 0.000000e+00 1642.0
7 TraesCS5D01G012900 chr5A 93.771 594 25 6 1 593 184707350 184706768 0.000000e+00 881.0
8 TraesCS5D01G012900 chr5A 97.733 397 9 0 2647 3043 2872558 2872162 0.000000e+00 684.0
9 TraesCS5D01G012900 chr5A 87.033 509 26 5 411 880 77080752 77080245 6.390000e-149 538.0
10 TraesCS5D01G012900 chr5A 89.091 55 5 1 3571 3625 623210619 623210672 3.630000e-07 67.6
11 TraesCS5D01G012900 chrUn 93.905 1132 64 4 1769 2897 65433214 65434343 0.000000e+00 1703.0
12 TraesCS5D01G012900 chrUn 90.495 1252 70 28 3686 4903 65435450 65436686 0.000000e+00 1607.0
13 TraesCS5D01G012900 chrUn 92.698 808 37 7 2899 3685 65434483 65435289 0.000000e+00 1146.0
14 TraesCS5D01G012900 chrUn 88.746 702 46 17 889 1579 65432508 65433187 0.000000e+00 828.0
15 TraesCS5D01G012900 chrUn 80.556 396 27 25 5217 5591 65436942 65437308 5.570000e-65 259.0
16 TraesCS5D01G012900 chrUn 89.189 148 9 5 5316 5463 28596674 28596814 1.610000e-40 178.0
17 TraesCS5D01G012900 chrUn 88.421 95 5 1 3025 3113 65434701 65434607 5.940000e-20 110.0
18 TraesCS5D01G012900 chrUn 100.000 38 0 0 2941 2978 65434448 65434485 2.800000e-08 71.3
19 TraesCS5D01G012900 chr1D 93.246 918 19 7 1 880 189394833 189395745 0.000000e+00 1312.0
20 TraesCS5D01G012900 chr1D 92.283 920 25 10 1 880 471281951 471282864 0.000000e+00 1264.0
21 TraesCS5D01G012900 chr1D 86.614 508 28 6 411 880 18338937 18339442 4.980000e-145 525.0
22 TraesCS5D01G012900 chr2D 92.927 919 20 8 1 880 16905445 16906357 0.000000e+00 1295.0
23 TraesCS5D01G012900 chr2D 92.159 931 26 11 1 893 142522349 142521428 0.000000e+00 1271.0
24 TraesCS5D01G012900 chr2D 90.959 918 26 13 1 880 393212387 393211489 0.000000e+00 1182.0
25 TraesCS5D01G012900 chr2D 90.541 148 8 3 5316 5463 336916890 336917031 2.060000e-44 191.0
26 TraesCS5D01G012900 chr2D 89.865 148 7 5 5316 5463 193917379 193917240 3.450000e-42 183.0
27 TraesCS5D01G012900 chr3D 92.810 918 21 7 1 880 8303652 8302742 0.000000e+00 1288.0
28 TraesCS5D01G012900 chr3D 94.907 589 11 3 1 574 73871213 73871797 0.000000e+00 904.0
29 TraesCS5D01G012900 chr3D 89.300 486 34 4 411 880 411637908 411637425 1.350000e-165 593.0
30 TraesCS5D01G012900 chr3D 89.189 148 10 3 5316 5463 510785276 510785135 4.460000e-41 180.0
31 TraesCS5D01G012900 chr6D 92.532 924 20 8 1 880 31860111 31861029 0.000000e+00 1279.0
32 TraesCS5D01G012900 chr6D 92.151 930 27 9 1 892 427235769 427234848 0.000000e+00 1271.0
33 TraesCS5D01G012900 chr6D 92.283 920 22 14 1 880 413390152 413391062 0.000000e+00 1260.0
34 TraesCS5D01G012900 chr4D 91.626 824 23 9 1 785 484448744 484449560 0.000000e+00 1098.0
35 TraesCS5D01G012900 chr7D 94.567 589 11 4 1 574 37280942 37281524 0.000000e+00 891.0
36 TraesCS5D01G012900 chr7D 94.268 314 14 3 576 888 536396686 536396996 1.410000e-130 477.0
37 TraesCS5D01G012900 chr7D 85.714 203 14 3 411 598 550273034 550273236 3.430000e-47 200.0
38 TraesCS5D01G012900 chr7D 89.189 148 10 3 5316 5463 47173239 47173380 4.460000e-41 180.0
39 TraesCS5D01G012900 chr7D 88.514 148 11 3 5316 5463 461078983 461079124 2.080000e-39 174.0
40 TraesCS5D01G012900 chr7D 92.063 63 4 1 1886 1948 8965914 8965853 2.780000e-13 87.9
41 TraesCS5D01G012900 chr1A 90.349 487 28 6 411 880 331313240 331313724 6.170000e-174 621.0
42 TraesCS5D01G012900 chr6A 87.841 477 39 9 411 870 371241357 371241831 4.940000e-150 542.0
43 TraesCS5D01G012900 chr3B 85.517 290 27 9 4451 4734 801589180 801589460 7.110000e-74 289.0
44 TraesCS5D01G012900 chr3B 80.000 320 37 13 4967 5265 801589470 801589783 1.580000e-50 211.0
45 TraesCS5D01G012900 chr3B 89.726 146 9 3 5318 5463 165341285 165341146 1.240000e-41 182.0
46 TraesCS5D01G012900 chr3B 90.566 53 3 2 3585 3636 549443964 549444015 1.010000e-07 69.4
47 TraesCS5D01G012900 chr2B 85.393 89 10 1 3023 3111 215214354 215214269 7.740000e-14 89.8
48 TraesCS5D01G012900 chr2B 87.931 58 4 2 3562 3616 708703726 708703669 1.300000e-06 65.8
49 TraesCS5D01G012900 chr3A 92.063 63 4 1 1886 1948 382369845 382369784 2.780000e-13 87.9
50 TraesCS5D01G012900 chr3A 97.727 44 1 0 3582 3625 671258123 671258080 6.030000e-10 76.8
51 TraesCS5D01G012900 chr7B 84.706 85 13 0 3027 3111 46886110 46886026 1.000000e-12 86.1
52 TraesCS5D01G012900 chr7B 84.615 91 9 4 3021 3111 432500675 432500590 1.000000e-12 86.1
53 TraesCS5D01G012900 chr7A 83.133 83 14 0 3028 3110 96169247 96169165 6.030000e-10 76.8
54 TraesCS5D01G012900 chr6B 95.349 43 2 0 3579 3621 553269403 553269445 1.010000e-07 69.4
55 TraesCS5D01G012900 chr5B 95.349 43 2 0 3579 3621 507803799 507803841 1.010000e-07 69.4
56 TraesCS5D01G012900 chr4A 93.478 46 3 0 3584 3629 692072012 692072057 1.010000e-07 69.4


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 TraesCS5D01G012900 chr5D 7003915 7009523 5608 True 10358.000000 10358 100.000000 1 5609 1 chr5D.!!$R1 5608
1 TraesCS5D01G012900 chr5D 365118478 365119391 913 True 1286.000000 1286 92.709000 1 880 1 chr5D.!!$R2 879
2 TraesCS5D01G012900 chr5D 82082037 82082621 584 False 898.000000 898 94.737000 1 574 1 chr5D.!!$F1 573
3 TraesCS5D01G012900 chr5A 2869729 2874464 4735 True 1812.000000 3110 90.813000 889 5576 3 chr5A.!!$R3 4687
4 TraesCS5D01G012900 chr5A 184706768 184707350 582 True 881.000000 881 93.771000 1 593 1 chr5A.!!$R2 592
5 TraesCS5D01G012900 chr5A 77080245 77080752 507 True 538.000000 538 87.033000 411 880 1 chr5A.!!$R1 469
6 TraesCS5D01G012900 chrUn 65432508 65437308 4800 False 935.716667 1703 91.066667 889 5591 6 chrUn.!!$F2 4702
7 TraesCS5D01G012900 chr1D 189394833 189395745 912 False 1312.000000 1312 93.246000 1 880 1 chr1D.!!$F2 879
8 TraesCS5D01G012900 chr1D 471281951 471282864 913 False 1264.000000 1264 92.283000 1 880 1 chr1D.!!$F3 879
9 TraesCS5D01G012900 chr1D 18338937 18339442 505 False 525.000000 525 86.614000 411 880 1 chr1D.!!$F1 469
10 TraesCS5D01G012900 chr2D 16905445 16906357 912 False 1295.000000 1295 92.927000 1 880 1 chr2D.!!$F1 879
11 TraesCS5D01G012900 chr2D 142521428 142522349 921 True 1271.000000 1271 92.159000 1 893 1 chr2D.!!$R1 892
12 TraesCS5D01G012900 chr2D 393211489 393212387 898 True 1182.000000 1182 90.959000 1 880 1 chr2D.!!$R3 879
13 TraesCS5D01G012900 chr3D 8302742 8303652 910 True 1288.000000 1288 92.810000 1 880 1 chr3D.!!$R1 879
14 TraesCS5D01G012900 chr3D 73871213 73871797 584 False 904.000000 904 94.907000 1 574 1 chr3D.!!$F1 573
15 TraesCS5D01G012900 chr6D 31860111 31861029 918 False 1279.000000 1279 92.532000 1 880 1 chr6D.!!$F1 879
16 TraesCS5D01G012900 chr6D 427234848 427235769 921 True 1271.000000 1271 92.151000 1 892 1 chr6D.!!$R1 891
17 TraesCS5D01G012900 chr6D 413390152 413391062 910 False 1260.000000 1260 92.283000 1 880 1 chr6D.!!$F2 879
18 TraesCS5D01G012900 chr4D 484448744 484449560 816 False 1098.000000 1098 91.626000 1 785 1 chr4D.!!$F1 784
19 TraesCS5D01G012900 chr7D 37280942 37281524 582 False 891.000000 891 94.567000 1 574 1 chr7D.!!$F1 573
20 TraesCS5D01G012900 chr3B 801589180 801589783 603 False 250.000000 289 82.758500 4451 5265 2 chr3B.!!$F2 814

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
991 1221 0.322456 CCAGCCTTCCACCGAATTCA 60.322 55.0 6.22 0.0 0.00 2.57 F
2140 2390 0.033504 TTGACTCTGCTGTCCGTTCC 59.966 55.0 0.00 0.0 36.21 3.62 F
2644 2901 0.041576 GTTTCGTTCACAAGGGTCGC 60.042 55.0 0.00 0.0 0.00 5.19 F
2706 3150 1.568504 ATTAACTCAGGTGAGCCGGA 58.431 50.0 5.05 0.0 45.79 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2574 2830 0.376852 TTTTGCGTGCAGTGAGTCAC 59.623 50.000 15.78 15.78 34.1 3.67 R
3087 3675 1.553248 TCCCTCCGTTCCACAATACAG 59.447 52.381 0.00 0.00 0.0 2.74 R
4366 5143 1.256812 CCTGAAAATTGAACCCGCCT 58.743 50.000 0.00 0.00 0.0 5.52 R
4694 5480 3.131400 GGACTAGCAGCTAAGCTACACTT 59.869 47.826 3.09 0.00 44.5 3.16 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
65 66 4.643387 GGCGGTGTCACCTGGCTT 62.643 66.667 23.58 0.00 35.66 4.35
200 212 6.642733 ATATATCGATGGAGGGGTGATTTT 57.357 37.500 8.54 0.00 0.00 1.82
724 881 7.611855 AGTGAAGAGAAAAATAAACCGATGGAT 59.388 33.333 0.00 0.00 0.00 3.41
886 1113 7.737869 TCGTCATTAGGAGTAGAGAGATTAGT 58.262 38.462 0.00 0.00 0.00 2.24
887 1114 7.658167 TCGTCATTAGGAGTAGAGAGATTAGTG 59.342 40.741 0.00 0.00 0.00 2.74
932 1159 1.230635 CGGCCCACACTATAGCATGC 61.231 60.000 10.51 10.51 0.00 4.06
962 1190 3.028094 TGGGTCTACACTATCCAGTCC 57.972 52.381 0.00 0.00 30.46 3.85
963 1191 2.313643 TGGGTCTACACTATCCAGTCCA 59.686 50.000 0.00 0.00 30.46 4.02
964 1192 2.694109 GGGTCTACACTATCCAGTCCAC 59.306 54.545 0.00 0.00 30.46 4.02
966 1194 3.627747 GGTCTACACTATCCAGTCCACCT 60.628 52.174 0.00 0.00 30.46 4.00
970 1200 1.556911 CACTATCCAGTCCACCTTGCT 59.443 52.381 0.00 0.00 30.46 3.91
991 1221 0.322456 CCAGCCTTCCACCGAATTCA 60.322 55.000 6.22 0.00 0.00 2.57
1083 1314 3.626680 CTTCGTCTTGCGCGGGAGA 62.627 63.158 8.83 3.06 41.07 3.71
1200 1431 2.443016 CGCCCCTAGCTCCTGACT 60.443 66.667 0.00 0.00 40.39 3.41
1287 1521 0.870307 CGTCGATAAGGGCCAAGACG 60.870 60.000 18.86 18.86 43.79 4.18
1348 1582 4.506802 GGAAGTTCTTGTCCAAGGTACCAT 60.507 45.833 15.94 0.00 38.88 3.55
1349 1583 4.021102 AGTTCTTGTCCAAGGTACCATG 57.979 45.455 15.94 12.93 38.88 3.66
1351 1585 1.004277 TCTTGTCCAAGGTACCATGCC 59.996 52.381 15.94 6.39 38.88 4.40
1352 1586 0.774276 TTGTCCAAGGTACCATGCCA 59.226 50.000 15.94 9.00 0.00 4.92
1381 1616 6.567050 CAATGTCTTATTTCCATTGGACTGG 58.433 40.000 4.45 0.00 40.95 4.00
1393 1628 2.579410 TGGACTGGAAAAAGGCTACC 57.421 50.000 0.00 0.00 0.00 3.18
1416 1651 5.357257 CGCTATGGTGTTCCTTAAGTATGT 58.643 41.667 0.97 0.00 34.23 2.29
1417 1652 6.461927 CCGCTATGGTGTTCCTTAAGTATGTA 60.462 42.308 0.97 0.00 34.23 2.29
1418 1653 7.152645 CGCTATGGTGTTCCTTAAGTATGTAT 58.847 38.462 0.97 0.00 34.23 2.29
1419 1654 7.116376 CGCTATGGTGTTCCTTAAGTATGTATG 59.884 40.741 0.97 0.00 34.23 2.39
1425 1660 9.174166 GGTGTTCCTTAAGTATGTATGAATTGT 57.826 33.333 0.97 0.00 0.00 2.71
1526 1762 1.008875 CGCGCACTTTGCAGACTCTA 61.009 55.000 8.75 0.00 45.36 2.43
1579 1819 5.376854 AGTGCTGTGGATTTGTAATTGTC 57.623 39.130 0.00 0.00 0.00 3.18
1580 1820 4.218417 AGTGCTGTGGATTTGTAATTGTCC 59.782 41.667 0.00 0.00 0.00 4.02
1581 1821 4.022416 GTGCTGTGGATTTGTAATTGTCCA 60.022 41.667 0.00 0.00 38.37 4.02
1582 1822 4.586421 TGCTGTGGATTTGTAATTGTCCAA 59.414 37.500 0.00 0.00 42.01 3.53
1583 1823 5.163513 GCTGTGGATTTGTAATTGTCCAAG 58.836 41.667 0.00 0.00 42.01 3.61
1584 1824 5.713025 CTGTGGATTTGTAATTGTCCAAGG 58.287 41.667 0.00 0.00 42.01 3.61
1585 1825 5.144100 TGTGGATTTGTAATTGTCCAAGGT 58.856 37.500 0.00 0.00 42.01 3.50
1588 1828 5.712917 TGGATTTGTAATTGTCCAAGGTACC 59.287 40.000 2.73 2.73 37.78 3.34
1589 1829 5.712917 GGATTTGTAATTGTCCAAGGTACCA 59.287 40.000 15.94 0.00 0.00 3.25
1590 1830 6.379988 GGATTTGTAATTGTCCAAGGTACCAT 59.620 38.462 15.94 0.00 0.00 3.55
1591 1831 6.582677 TTTGTAATTGTCCAAGGTACCATG 57.417 37.500 15.94 12.93 0.00 3.66
1592 1832 4.013728 TGTAATTGTCCAAGGTACCATGC 58.986 43.478 15.94 1.05 0.00 4.06
1596 1836 1.357420 TGTCCAAGGTACCATGCCAAT 59.643 47.619 15.94 0.00 0.00 3.16
1598 1838 1.357420 TCCAAGGTACCATGCCAATGT 59.643 47.619 15.94 0.00 31.27 2.71
1604 1844 2.294233 GGTACCATGCCAATGTATGCAG 59.706 50.000 7.15 0.00 41.46 4.41
1605 1845 0.748450 ACCATGCCAATGTATGCAGC 59.252 50.000 0.00 0.00 41.46 5.25
1606 1846 1.037493 CCATGCCAATGTATGCAGCT 58.963 50.000 0.00 0.00 41.46 4.24
1607 1847 1.269569 CCATGCCAATGTATGCAGCTG 60.270 52.381 10.11 10.11 41.46 4.24
1608 1848 1.407618 CATGCCAATGTATGCAGCTGT 59.592 47.619 16.64 0.00 41.46 4.40
1609 1849 1.097232 TGCCAATGTATGCAGCTGTC 58.903 50.000 16.64 8.39 32.77 3.51
1610 1850 1.340308 TGCCAATGTATGCAGCTGTCT 60.340 47.619 16.64 5.47 32.77 3.41
1611 1851 1.065102 GCCAATGTATGCAGCTGTCTG 59.935 52.381 16.64 2.62 43.16 3.51
1612 1852 2.362736 CCAATGTATGCAGCTGTCTGT 58.637 47.619 16.64 1.62 42.29 3.41
1613 1853 2.096980 CCAATGTATGCAGCTGTCTGTG 59.903 50.000 16.64 4.90 42.29 3.66
1628 1875 3.181455 TGTCTGTGTTCTAGCCATTGTGT 60.181 43.478 0.00 0.00 0.00 3.72
1642 1889 3.378112 CCATTGTGTTGTGTCAGTCAGTT 59.622 43.478 0.00 0.00 0.00 3.16
1652 1899 2.872245 TGTCAGTCAGTTAGTTTGCTGC 59.128 45.455 0.00 0.00 33.09 5.25
1660 1907 2.558359 AGTTAGTTTGCTGCCCATTCAC 59.442 45.455 0.00 0.00 0.00 3.18
1661 1908 2.558359 GTTAGTTTGCTGCCCATTCACT 59.442 45.455 0.00 0.00 0.00 3.41
1663 1910 0.037975 GTTTGCTGCCCATTCACTGG 60.038 55.000 0.00 0.00 45.51 4.00
1699 1946 2.702898 CAATGTGTGCACCATTTCGA 57.297 45.000 22.94 0.00 0.00 3.71
1701 1948 3.173599 CAATGTGTGCACCATTTCGATC 58.826 45.455 22.94 3.22 0.00 3.69
1702 1949 1.889545 TGTGTGCACCATTTCGATCA 58.110 45.000 15.69 0.00 0.00 2.92
1704 1951 0.804364 TGTGCACCATTTCGATCAGC 59.196 50.000 15.69 0.00 0.00 4.26
1705 1952 0.804364 GTGCACCATTTCGATCAGCA 59.196 50.000 5.22 0.00 0.00 4.41
1709 1956 1.811965 CACCATTTCGATCAGCAACCA 59.188 47.619 0.00 0.00 0.00 3.67
1715 1962 6.098679 CCATTTCGATCAGCAACCATAAAAA 58.901 36.000 0.00 0.00 0.00 1.94
1759 2006 7.462109 TTTTTCAGTCAATTGTTACATGTGC 57.538 32.000 9.11 1.72 0.00 4.57
1761 2008 5.611796 TCAGTCAATTGTTACATGTGCTC 57.388 39.130 9.11 0.00 0.00 4.26
1763 2010 5.764686 TCAGTCAATTGTTACATGTGCTCTT 59.235 36.000 9.11 0.00 0.00 2.85
1792 2039 9.793252 AGCTTGTGATTGTCATTTATCAAATAC 57.207 29.630 0.00 0.00 32.94 1.89
2016 2265 7.566760 TGTCTACTGTTTTGATTGTCATGTT 57.433 32.000 0.00 0.00 0.00 2.71
2136 2386 1.929836 GCTATTTGACTCTGCTGTCCG 59.070 52.381 0.00 0.00 36.21 4.79
2140 2390 0.033504 TTGACTCTGCTGTCCGTTCC 59.966 55.000 0.00 0.00 36.21 3.62
2163 2413 4.526970 GTTATCATCCACACACCCTTCAT 58.473 43.478 0.00 0.00 0.00 2.57
2165 2415 1.984424 TCATCCACACACCCTTCATCA 59.016 47.619 0.00 0.00 0.00 3.07
2299 2549 8.653338 GTTGAGAAGCGTACTATTGATTTTGTA 58.347 33.333 0.00 0.00 0.00 2.41
2326 2576 9.140286 GATTACATCAGCGCTAATTATGTCTTA 57.860 33.333 22.39 13.72 33.15 2.10
2355 2605 2.101700 GCAGCAGCCAACAGGTATC 58.898 57.895 0.00 0.00 33.58 2.24
2398 2648 8.130469 GCTTACTCTACTAGACACCATAAACTC 58.870 40.741 0.00 0.00 0.00 3.01
2411 2661 7.924541 ACACCATAAACTCTTTCCCTTACATA 58.075 34.615 0.00 0.00 0.00 2.29
2482 2738 2.210144 TATTCCACCTGTGCCCAGCC 62.210 60.000 0.00 0.00 37.38 4.85
2493 2749 1.678101 GTGCCCAGCCTATTCACATTC 59.322 52.381 0.00 0.00 0.00 2.67
2540 2796 2.453521 TCTATCCGGGGTATTGATCCG 58.546 52.381 0.00 0.00 43.05 4.18
2573 2829 5.868043 TGCAAATCTCATACTCACAAGTG 57.132 39.130 0.00 0.00 36.92 3.16
2574 2830 4.696877 TGCAAATCTCATACTCACAAGTGG 59.303 41.667 0.00 0.00 36.92 4.00
2586 2842 0.541392 ACAAGTGGTGACTCACTGCA 59.459 50.000 9.08 0.00 46.17 4.41
2587 2843 0.940126 CAAGTGGTGACTCACTGCAC 59.060 55.000 9.08 9.28 46.17 4.57
2588 2844 0.530650 AAGTGGTGACTCACTGCACG 60.531 55.000 9.08 0.00 46.17 5.34
2620 2877 0.322906 CCCTCCTTTTCTCCTGCCAC 60.323 60.000 0.00 0.00 0.00 5.01
2639 2896 2.220133 CACGTAGGTTTCGTTCACAAGG 59.780 50.000 0.00 0.00 39.55 3.61
2643 2900 0.584876 GGTTTCGTTCACAAGGGTCG 59.415 55.000 0.00 0.00 0.00 4.79
2644 2901 0.041576 GTTTCGTTCACAAGGGTCGC 60.042 55.000 0.00 0.00 0.00 5.19
2706 3150 1.568504 ATTAACTCAGGTGAGCCGGA 58.431 50.000 5.05 0.00 45.79 5.14
2940 3522 7.272978 GGAACATAGCTGGATCTAGTGTTTTA 58.727 38.462 12.72 0.00 0.00 1.52
3051 3633 3.254060 CTCTGTCCCACAATACAAGACG 58.746 50.000 0.00 0.00 0.00 4.18
3067 3649 5.164954 ACAAGACGTTTTTGCAAGCTAAAA 58.835 33.333 9.67 9.67 0.00 1.52
3069 3651 4.739195 AGACGTTTTTGCAAGCTAAAACA 58.261 34.783 29.55 7.24 45.11 2.83
3087 3675 3.282831 ACATAGCTTGCAAAAACGTCC 57.717 42.857 0.00 0.00 0.00 4.79
3435 4034 6.716628 AGATGGACATTGCTTTCTGTTTCTTA 59.283 34.615 0.00 0.00 0.00 2.10
3465 4064 5.602978 CCTCCCTTATTAGGCTTTCTGAGTA 59.397 44.000 0.00 0.00 40.50 2.59
3466 4065 6.099845 CCTCCCTTATTAGGCTTTCTGAGTAA 59.900 42.308 0.00 0.00 40.50 2.24
3608 4211 4.941263 CCATTTCTCCGACAAGTATTTCCA 59.059 41.667 0.00 0.00 0.00 3.53
3612 4215 3.830178 TCTCCGACAAGTATTTCCAGACA 59.170 43.478 0.00 0.00 0.00 3.41
3714 4479 9.113838 CATTATGGTGAAGCTGTACTAAGATTT 57.886 33.333 0.00 0.00 0.00 2.17
4283 5059 1.674221 GCAGGAGAGGTAACAGCACAG 60.674 57.143 0.00 0.00 41.41 3.66
4351 5128 7.042335 GTGTGATCTTGCTGTAGGTACTTAAT 58.958 38.462 0.00 0.00 41.75 1.40
4366 5143 0.967662 TTAATGTCGACGGGGTCACA 59.032 50.000 11.62 0.00 32.00 3.58
4390 5167 3.504520 GCGGGTTCAATTTTCAGGTAAGA 59.495 43.478 0.00 0.00 0.00 2.10
4404 5181 9.488762 TTTTCAGGTAAGAAGTAGATATCTCCA 57.511 33.333 8.95 0.00 0.00 3.86
4406 5183 7.583625 TCAGGTAAGAAGTAGATATCTCCACA 58.416 38.462 8.95 0.00 0.00 4.17
4407 5184 7.721842 TCAGGTAAGAAGTAGATATCTCCACAG 59.278 40.741 8.95 0.00 0.00 3.66
4409 5186 5.446143 AAGAAGTAGATATCTCCACAGCG 57.554 43.478 8.95 0.00 0.00 5.18
4410 5187 3.823873 AGAAGTAGATATCTCCACAGCGG 59.176 47.826 8.95 0.00 0.00 5.52
4411 5188 3.510531 AGTAGATATCTCCACAGCGGA 57.489 47.619 8.95 0.00 43.61 5.54
4412 5189 4.040936 AGTAGATATCTCCACAGCGGAT 57.959 45.455 8.95 0.00 45.19 4.18
4413 5190 4.411927 AGTAGATATCTCCACAGCGGATT 58.588 43.478 8.95 0.00 45.19 3.01
4414 5191 5.571285 AGTAGATATCTCCACAGCGGATTA 58.429 41.667 8.95 0.00 45.19 1.75
4415 5192 5.650266 AGTAGATATCTCCACAGCGGATTAG 59.350 44.000 8.95 0.00 45.19 1.73
4416 5193 4.411927 AGATATCTCCACAGCGGATTAGT 58.588 43.478 0.00 0.00 45.19 2.24
4417 5194 5.571285 AGATATCTCCACAGCGGATTAGTA 58.429 41.667 0.00 0.00 45.19 1.82
4419 5196 6.493802 AGATATCTCCACAGCGGATTAGTAAA 59.506 38.462 0.00 0.00 45.19 2.01
4420 5197 4.811969 TCTCCACAGCGGATTAGTAAAA 57.188 40.909 0.00 0.00 45.19 1.52
4421 5198 5.155278 TCTCCACAGCGGATTAGTAAAAA 57.845 39.130 0.00 0.00 45.19 1.94
4422 5199 4.933400 TCTCCACAGCGGATTAGTAAAAAC 59.067 41.667 0.00 0.00 45.19 2.43
4423 5200 4.901868 TCCACAGCGGATTAGTAAAAACT 58.098 39.130 0.00 0.00 39.64 2.66
4425 5202 5.180492 TCCACAGCGGATTAGTAAAAACTTG 59.820 40.000 0.00 0.00 39.64 3.16
4426 5203 5.390613 CACAGCGGATTAGTAAAAACTTGG 58.609 41.667 0.00 0.00 0.00 3.61
4427 5204 5.180492 CACAGCGGATTAGTAAAAACTTGGA 59.820 40.000 0.00 0.00 0.00 3.53
4428 5205 5.411669 ACAGCGGATTAGTAAAAACTTGGAG 59.588 40.000 0.00 0.00 0.00 3.86
4429 5206 5.642063 CAGCGGATTAGTAAAAACTTGGAGA 59.358 40.000 0.00 0.00 0.00 3.71
4430 5207 6.316390 CAGCGGATTAGTAAAAACTTGGAGAT 59.684 38.462 0.00 0.00 0.00 2.75
4431 5208 6.316390 AGCGGATTAGTAAAAACTTGGAGATG 59.684 38.462 0.00 0.00 0.00 2.90
4432 5209 6.487103 CGGATTAGTAAAAACTTGGAGATGC 58.513 40.000 0.00 0.00 0.00 3.91
4433 5210 6.316390 CGGATTAGTAAAAACTTGGAGATGCT 59.684 38.462 0.00 0.00 0.00 3.79
4434 5211 7.148239 CGGATTAGTAAAAACTTGGAGATGCTT 60.148 37.037 0.00 0.00 0.00 3.91
4435 5212 8.184848 GGATTAGTAAAAACTTGGAGATGCTTC 58.815 37.037 0.00 0.00 0.00 3.86
4436 5213 5.966742 AGTAAAAACTTGGAGATGCTTCC 57.033 39.130 0.00 0.00 37.77 3.46
4437 5214 5.385198 AGTAAAAACTTGGAGATGCTTCCA 58.615 37.500 1.71 1.71 45.34 3.53
4438 5215 6.012745 AGTAAAAACTTGGAGATGCTTCCAT 58.987 36.000 6.10 0.00 46.22 3.41
4439 5216 5.813513 AAAAACTTGGAGATGCTTCCATT 57.186 34.783 6.10 0.00 46.22 3.16
4440 5217 6.916360 AAAAACTTGGAGATGCTTCCATTA 57.084 33.333 6.10 0.00 46.22 1.90
4444 5221 7.486407 AACTTGGAGATGCTTCCATTAAAAT 57.514 32.000 6.10 0.00 46.22 1.82
4445 5226 7.486407 ACTTGGAGATGCTTCCATTAAAATT 57.514 32.000 6.10 0.00 46.22 1.82
4641 5423 4.782691 TGAAATCATGACAAGGAGGGTAGA 59.217 41.667 0.00 0.00 0.00 2.59
4680 5462 5.061179 GGTTCTTACTGGCTGACAAACTTA 58.939 41.667 0.00 0.00 0.00 2.24
4681 5463 5.705905 GGTTCTTACTGGCTGACAAACTTAT 59.294 40.000 0.00 0.00 0.00 1.73
4694 5480 9.730420 GCTGACAAACTTATAAAAACTTCTGAA 57.270 29.630 0.00 0.00 0.00 3.02
4731 5541 4.098044 TGCTAGTCCACAGTATTGTAGCTC 59.902 45.833 10.33 0.00 35.75 4.09
4782 5593 3.646491 TCGACTAACTGTATCGTCGTG 57.354 47.619 18.90 1.76 46.55 4.35
4789 5600 4.494350 AACTGTATCGTCGTGTTGTAGT 57.506 40.909 0.00 0.00 0.00 2.73
4843 5654 4.211164 TGAGCAACTTGTGAATCGTTGTAG 59.789 41.667 0.00 0.00 39.98 2.74
4856 5667 4.530710 TCGTTGTAGACTTGGCAGTAAT 57.469 40.909 0.00 0.00 31.22 1.89
4868 5679 7.714377 AGACTTGGCAGTAATAATCAGAAGATG 59.286 37.037 0.00 0.00 30.97 2.90
4903 5714 4.170292 CATTCACTGCTTTTCCTGAAGG 57.830 45.455 0.00 0.00 0.00 3.46
4904 5715 3.297134 TTCACTGCTTTTCCTGAAGGT 57.703 42.857 0.00 0.00 36.34 3.50
4905 5716 3.297134 TCACTGCTTTTCCTGAAGGTT 57.703 42.857 0.00 0.00 36.34 3.50
4906 5717 2.951642 TCACTGCTTTTCCTGAAGGTTG 59.048 45.455 0.00 0.00 36.34 3.77
4907 5718 2.035066 CACTGCTTTTCCTGAAGGTTGG 59.965 50.000 0.00 0.00 36.34 3.77
4908 5719 1.615392 CTGCTTTTCCTGAAGGTTGGG 59.385 52.381 0.00 0.00 36.34 4.12
4909 5720 0.318441 GCTTTTCCTGAAGGTTGGGC 59.682 55.000 0.00 0.00 36.34 5.36
4910 5721 2.001076 CTTTTCCTGAAGGTTGGGCT 57.999 50.000 0.00 0.00 36.34 5.19
4911 5722 1.615392 CTTTTCCTGAAGGTTGGGCTG 59.385 52.381 0.00 0.00 36.34 4.85
4912 5723 0.178964 TTTCCTGAAGGTTGGGCTGG 60.179 55.000 0.00 0.00 36.34 4.85
4913 5724 1.065410 TTCCTGAAGGTTGGGCTGGA 61.065 55.000 0.00 0.00 36.34 3.86
4914 5725 1.065410 TCCTGAAGGTTGGGCTGGAA 61.065 55.000 0.00 0.00 36.34 3.53
4915 5726 0.040204 CCTGAAGGTTGGGCTGGAAT 59.960 55.000 0.00 0.00 0.00 3.01
4916 5727 1.550869 CCTGAAGGTTGGGCTGGAATT 60.551 52.381 0.00 0.00 0.00 2.17
4917 5728 2.250924 CTGAAGGTTGGGCTGGAATTT 58.749 47.619 0.00 0.00 0.00 1.82
4918 5729 3.430453 CTGAAGGTTGGGCTGGAATTTA 58.570 45.455 0.00 0.00 0.00 1.40
4919 5730 3.161866 TGAAGGTTGGGCTGGAATTTAC 58.838 45.455 0.00 0.00 0.00 2.01
4934 5745 6.065374 TGGAATTTACAGCTAAAACACCTGA 58.935 36.000 13.79 0.70 0.00 3.86
4936 5747 7.029563 GGAATTTACAGCTAAAACACCTGATG 58.970 38.462 0.00 0.00 0.00 3.07
4953 5764 5.301551 ACCTGATGTGCTGAAACATAAAACA 59.698 36.000 0.00 0.00 40.87 2.83
4954 5765 6.183360 ACCTGATGTGCTGAAACATAAAACAA 60.183 34.615 0.00 0.00 40.87 2.83
4960 5771 7.914465 TGTGCTGAAACATAAAACAAAATTCC 58.086 30.769 0.00 0.00 0.00 3.01
4996 5807 9.798994 ATTTAGAATGCAACAAATCAATCTCTC 57.201 29.630 0.00 0.00 0.00 3.20
5013 5855 5.551305 TCTCTCAATGTTCCTTCTCACAA 57.449 39.130 0.00 0.00 0.00 3.33
5015 5857 5.760253 TCTCTCAATGTTCCTTCTCACAAAC 59.240 40.000 0.00 0.00 0.00 2.93
5021 5863 8.352201 TCAATGTTCCTTCTCACAAACAAATAG 58.648 33.333 0.00 0.00 35.46 1.73
5023 5865 7.873719 TGTTCCTTCTCACAAACAAATAGAA 57.126 32.000 0.00 0.00 0.00 2.10
5024 5866 7.930217 TGTTCCTTCTCACAAACAAATAGAAG 58.070 34.615 0.00 0.00 41.73 2.85
5031 5873 9.965824 TTCTCACAAACAAATAGAAGGAAATTC 57.034 29.630 0.00 0.00 38.28 2.17
5033 5875 9.617975 CTCACAAACAAATAGAAGGAAATTCTC 57.382 33.333 0.00 0.00 45.50 2.87
5035 5877 9.918630 CACAAACAAATAGAAGGAAATTCTCAT 57.081 29.630 0.00 0.00 45.50 2.90
5083 5943 6.889722 TGATTTTAGTCCCTAAATGTTCCCAG 59.110 38.462 0.00 0.00 36.10 4.45
5084 5944 6.457159 TTTTAGTCCCTAAATGTTCCCAGA 57.543 37.500 0.00 0.00 36.10 3.86
5085 5945 6.652205 TTTAGTCCCTAAATGTTCCCAGAT 57.348 37.500 0.00 0.00 31.94 2.90
5086 5946 7.758820 TTTAGTCCCTAAATGTTCCCAGATA 57.241 36.000 0.00 0.00 31.94 1.98
5087 5947 7.758820 TTAGTCCCTAAATGTTCCCAGATAA 57.241 36.000 0.00 0.00 0.00 1.75
5088 5948 6.652205 AGTCCCTAAATGTTCCCAGATAAA 57.348 37.500 0.00 0.00 0.00 1.40
5089 5949 7.226059 AGTCCCTAAATGTTCCCAGATAAAT 57.774 36.000 0.00 0.00 0.00 1.40
5090 5950 8.344939 AGTCCCTAAATGTTCCCAGATAAATA 57.655 34.615 0.00 0.00 0.00 1.40
5091 5951 8.787818 AGTCCCTAAATGTTCCCAGATAAATAA 58.212 33.333 0.00 0.00 0.00 1.40
5092 5952 9.067986 GTCCCTAAATGTTCCCAGATAAATAAG 57.932 37.037 0.00 0.00 0.00 1.73
5093 5953 8.787818 TCCCTAAATGTTCCCAGATAAATAAGT 58.212 33.333 0.00 0.00 0.00 2.24
5094 5954 9.421399 CCCTAAATGTTCCCAGATAAATAAGTT 57.579 33.333 0.00 0.00 0.00 2.66
5100 5960 7.162761 TGTTCCCAGATAAATAAGTTTCGACA 58.837 34.615 0.00 0.00 0.00 4.35
5109 5969 1.779569 AAGTTTCGACACGCTACAGG 58.220 50.000 0.00 0.00 0.00 4.00
5151 6024 5.964958 ATTACACACAACCAAGATTCAGG 57.035 39.130 0.00 0.00 0.00 3.86
5164 6037 5.453903 CCAAGATTCAGGAAGGTACATCGAT 60.454 44.000 0.00 0.00 0.00 3.59
5178 6053 7.654568 AGGTACATCGATTAATTGTATCGTCA 58.345 34.615 18.36 6.64 43.91 4.35
5190 6065 7.734924 AATTGTATCGTCACATCATAGCAAT 57.265 32.000 0.00 0.00 0.00 3.56
5216 6091 2.378038 TGCTGTGAAGCAAAAGTTCCT 58.622 42.857 0.00 0.00 42.40 3.36
5277 6154 1.820519 TCAGAAGACCAATGCATTGCC 59.179 47.619 30.15 22.98 36.48 4.52
5300 6177 2.305635 TCCAGAAGGCTAGATTGCAACA 59.694 45.455 0.00 0.00 33.74 3.33
5301 6178 3.084039 CCAGAAGGCTAGATTGCAACAA 58.916 45.455 0.00 0.00 34.04 2.83
5302 6179 3.698040 CCAGAAGGCTAGATTGCAACAAT 59.302 43.478 0.00 0.00 34.04 2.71
5303 6180 4.439700 CCAGAAGGCTAGATTGCAACAATG 60.440 45.833 0.00 0.00 34.04 2.82
5328 6223 8.886719 TGCAATGTCTAAATGTCTAATTCAGAG 58.113 33.333 0.00 0.00 32.51 3.35
5404 6299 7.060421 AGTTTGGAAAGATAAGAACTCAACCA 58.940 34.615 0.00 0.00 0.00 3.67
5406 6301 7.452880 TTGGAAAGATAAGAACTCAACCATG 57.547 36.000 0.00 0.00 0.00 3.66
5413 6308 7.324178 AGATAAGAACTCAACCATGACTACAC 58.676 38.462 0.00 0.00 0.00 2.90
5471 6366 3.265221 AGAACAGATGCTTCCTTCATCCA 59.735 43.478 9.17 0.00 40.79 3.41
5482 6377 5.416952 GCTTCCTTCATCCAAAAGAGAATGA 59.583 40.000 0.00 0.00 0.00 2.57
5593 6488 3.130160 CGGAAGCAGAAGCAGGCC 61.130 66.667 0.00 0.00 45.49 5.19
5594 6489 2.753446 GGAAGCAGAAGCAGGCCC 60.753 66.667 0.00 0.00 45.49 5.80
5595 6490 2.354343 GAAGCAGAAGCAGGCCCT 59.646 61.111 0.00 0.00 45.49 5.19
5596 6491 1.604378 GAAGCAGAAGCAGGCCCTA 59.396 57.895 0.00 0.00 45.49 3.53
5597 6492 0.035056 GAAGCAGAAGCAGGCCCTAA 60.035 55.000 0.00 0.00 45.49 2.69
5598 6493 0.627986 AAGCAGAAGCAGGCCCTAAT 59.372 50.000 0.00 0.00 45.49 1.73
5599 6494 0.627986 AGCAGAAGCAGGCCCTAATT 59.372 50.000 0.00 0.00 45.49 1.40
5600 6495 1.846439 AGCAGAAGCAGGCCCTAATTA 59.154 47.619 0.00 0.00 45.49 1.40
5601 6496 2.242196 AGCAGAAGCAGGCCCTAATTAA 59.758 45.455 0.00 0.00 45.49 1.40
5602 6497 2.620585 GCAGAAGCAGGCCCTAATTAAG 59.379 50.000 0.00 0.00 41.58 1.85
5603 6498 3.685550 GCAGAAGCAGGCCCTAATTAAGA 60.686 47.826 0.00 0.00 41.58 2.10
5604 6499 4.526970 CAGAAGCAGGCCCTAATTAAGAA 58.473 43.478 0.00 0.00 0.00 2.52
5605 6500 4.336713 CAGAAGCAGGCCCTAATTAAGAAC 59.663 45.833 0.00 0.00 0.00 3.01
5606 6501 4.228438 AGAAGCAGGCCCTAATTAAGAACT 59.772 41.667 0.00 0.00 0.00 3.01
5607 6502 5.428783 AGAAGCAGGCCCTAATTAAGAACTA 59.571 40.000 0.00 0.00 0.00 2.24
5608 6503 5.710409 AGCAGGCCCTAATTAAGAACTAA 57.290 39.130 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 1.072489 TCGCATAAACACCTCCACCAA 59.928 47.619 0.00 0.00 0.00 3.67
179 191 4.599241 AGAAAATCACCCCTCCATCGATAT 59.401 41.667 0.00 0.00 0.00 1.63
180 192 3.973973 AGAAAATCACCCCTCCATCGATA 59.026 43.478 0.00 0.00 0.00 2.92
181 193 2.780010 AGAAAATCACCCCTCCATCGAT 59.220 45.455 0.00 0.00 0.00 3.59
182 194 2.196595 AGAAAATCACCCCTCCATCGA 58.803 47.619 0.00 0.00 0.00 3.59
200 212 9.581289 TTTTCTATGTTTTCCACCTATTGAAGA 57.419 29.630 0.00 0.00 0.00 2.87
279 291 3.385755 ACCCCATTTGCATAGAAATCAGC 59.614 43.478 0.00 0.00 0.00 4.26
596 753 9.710900 ATTCCTTTTATTGGTTCAATTTGTCTC 57.289 29.630 0.00 0.00 35.54 3.36
769 928 2.358015 CCTGGTCCGCGGTTTATTTTA 58.642 47.619 27.15 0.00 0.00 1.52
880 1107 3.067320 GCTGGAGCCCAAATTCACTAATC 59.933 47.826 0.00 0.00 30.80 1.75
906 1133 0.544697 ATAGTGTGGGCCGGGTTTAG 59.455 55.000 2.18 0.00 0.00 1.85
948 1176 2.500098 GCAAGGTGGACTGGATAGTGTA 59.500 50.000 0.00 0.00 37.25 2.90
970 1200 0.404040 AATTCGGTGGAAGGCTGGAA 59.596 50.000 0.00 0.00 35.19 3.53
1200 1431 1.078918 CTCCTGCATGGCGAACAGA 60.079 57.895 4.04 0.00 33.10 3.41
1287 1521 3.650950 TTGAGGTGGGGAGCCAGC 61.651 66.667 0.00 0.00 38.33 4.85
1348 1582 4.382901 GGAAATAAGACATTGGCATTGGCA 60.383 41.667 16.87 9.11 43.71 4.92
1349 1583 4.122046 GGAAATAAGACATTGGCATTGGC 58.878 43.478 13.39 10.51 40.13 4.52
1351 1585 7.241663 CAATGGAAATAAGACATTGGCATTG 57.758 36.000 7.78 7.78 44.63 2.82
1393 1628 5.357257 ACATACTTAAGGAACACCATAGCG 58.643 41.667 7.53 0.00 0.00 4.26
1416 1651 5.069383 CAGCCATCCATTCCAACAATTCATA 59.931 40.000 0.00 0.00 0.00 2.15
1417 1652 4.035112 AGCCATCCATTCCAACAATTCAT 58.965 39.130 0.00 0.00 0.00 2.57
1418 1653 3.196039 CAGCCATCCATTCCAACAATTCA 59.804 43.478 0.00 0.00 0.00 2.57
1419 1654 3.788937 CAGCCATCCATTCCAACAATTC 58.211 45.455 0.00 0.00 0.00 2.17
1425 1660 0.685131 CCTGCAGCCATCCATTCCAA 60.685 55.000 8.66 0.00 0.00 3.53
1579 1819 1.851304 ACATTGGCATGGTACCTTGG 58.149 50.000 24.78 12.84 34.27 3.61
1580 1820 3.243501 GCATACATTGGCATGGTACCTTG 60.244 47.826 20.77 20.77 34.27 3.61
1581 1821 2.958355 GCATACATTGGCATGGTACCTT 59.042 45.455 14.36 3.50 34.27 3.50
1582 1822 2.091939 TGCATACATTGGCATGGTACCT 60.092 45.455 14.36 0.00 34.58 3.08
1583 1823 2.294233 CTGCATACATTGGCATGGTACC 59.706 50.000 4.43 4.43 39.65 3.34
1584 1824 2.287788 GCTGCATACATTGGCATGGTAC 60.288 50.000 0.00 0.00 39.65 3.34
1585 1825 1.955778 GCTGCATACATTGGCATGGTA 59.044 47.619 0.00 0.00 39.65 3.25
1588 1828 1.407618 ACAGCTGCATACATTGGCATG 59.592 47.619 15.27 0.00 39.65 4.06
1589 1829 1.679680 GACAGCTGCATACATTGGCAT 59.320 47.619 15.27 0.00 39.65 4.40
1590 1830 1.097232 GACAGCTGCATACATTGGCA 58.903 50.000 15.27 0.00 38.52 4.92
1591 1831 1.065102 CAGACAGCTGCATACATTGGC 59.935 52.381 15.27 0.00 34.95 4.52
1592 1832 2.096980 CACAGACAGCTGCATACATTGG 59.903 50.000 15.27 0.00 46.26 3.16
1596 1836 2.037641 AGAACACAGACAGCTGCATACA 59.962 45.455 15.27 0.00 46.26 2.29
1598 1838 3.677148 GCTAGAACACAGACAGCTGCATA 60.677 47.826 15.27 0.00 46.26 3.14
1604 1844 2.393271 ATGGCTAGAACACAGACAGC 57.607 50.000 0.00 0.00 33.61 4.40
1605 1845 3.434641 CACAATGGCTAGAACACAGACAG 59.565 47.826 0.00 0.00 33.61 3.51
1606 1846 3.181455 ACACAATGGCTAGAACACAGACA 60.181 43.478 0.00 0.00 34.93 3.41
1607 1847 3.403038 ACACAATGGCTAGAACACAGAC 58.597 45.455 0.00 0.00 0.00 3.51
1608 1848 3.769739 ACACAATGGCTAGAACACAGA 57.230 42.857 0.00 0.00 0.00 3.41
1609 1849 3.565482 ACAACACAATGGCTAGAACACAG 59.435 43.478 0.00 0.00 0.00 3.66
1610 1850 3.314913 CACAACACAATGGCTAGAACACA 59.685 43.478 0.00 0.00 0.00 3.72
1611 1851 3.315191 ACACAACACAATGGCTAGAACAC 59.685 43.478 0.00 0.00 0.00 3.32
1612 1852 3.550820 ACACAACACAATGGCTAGAACA 58.449 40.909 0.00 0.00 0.00 3.18
1613 1853 3.563808 TGACACAACACAATGGCTAGAAC 59.436 43.478 0.00 0.00 0.00 3.01
1628 1875 4.332543 CAGCAAACTAACTGACTGACACAA 59.667 41.667 0.00 0.00 35.90 3.33
1642 1889 2.161855 CAGTGAATGGGCAGCAAACTA 58.838 47.619 0.00 0.00 0.00 2.24
1660 1907 1.676746 CCACCATCTCATTCAGCCAG 58.323 55.000 0.00 0.00 0.00 4.85
1661 1908 0.394762 GCCACCATCTCATTCAGCCA 60.395 55.000 0.00 0.00 0.00 4.75
1663 1910 1.466856 TTGCCACCATCTCATTCAGC 58.533 50.000 0.00 0.00 0.00 4.26
1670 1917 0.171903 GCACACATTGCCACCATCTC 59.828 55.000 0.00 0.00 46.63 2.75
1689 1936 1.811965 TGGTTGCTGATCGAAATGGTG 59.188 47.619 0.00 0.00 0.00 4.17
1724 1971 9.787435 ACAATTGACTGAAAAATAGTAGTGGTA 57.213 29.630 13.59 0.00 0.00 3.25
1725 1972 8.691661 ACAATTGACTGAAAAATAGTAGTGGT 57.308 30.769 13.59 0.00 0.00 4.16
1733 1980 9.190858 GCACATGTAACAATTGACTGAAAAATA 57.809 29.630 13.59 0.00 0.00 1.40
1734 1981 7.927629 AGCACATGTAACAATTGACTGAAAAAT 59.072 29.630 13.59 0.00 0.00 1.82
1735 1982 7.264221 AGCACATGTAACAATTGACTGAAAAA 58.736 30.769 13.59 0.00 0.00 1.94
1736 1983 6.804677 AGCACATGTAACAATTGACTGAAAA 58.195 32.000 13.59 0.00 0.00 2.29
1737 1984 6.262944 AGAGCACATGTAACAATTGACTGAAA 59.737 34.615 13.59 0.00 0.00 2.69
1738 1985 5.764686 AGAGCACATGTAACAATTGACTGAA 59.235 36.000 13.59 0.00 0.00 3.02
1739 1986 5.308014 AGAGCACATGTAACAATTGACTGA 58.692 37.500 13.59 0.00 0.00 3.41
1740 1987 5.618056 AGAGCACATGTAACAATTGACTG 57.382 39.130 13.59 4.45 0.00 3.51
1741 1988 6.639632 AAAGAGCACATGTAACAATTGACT 57.360 33.333 13.59 1.05 0.00 3.41
1742 1989 8.440021 CTTAAAGAGCACATGTAACAATTGAC 57.560 34.615 13.59 0.92 0.00 3.18
1761 2008 9.844790 TGATAAATGACAATCACAAGCTTAAAG 57.155 29.630 0.00 0.00 0.00 1.85
1792 2039 5.104776 TCACCAGTCCCTGAGAATTGAATAG 60.105 44.000 0.00 0.00 32.44 1.73
1798 2045 2.907892 TCTCACCAGTCCCTGAGAATT 58.092 47.619 0.00 0.00 39.97 2.17
1814 2061 5.795079 TGTACCCCCTAGGATAATTTCTCA 58.205 41.667 11.48 0.00 39.89 3.27
1931 2178 4.698201 TCCTGAAGTAAATGTGGTGTGA 57.302 40.909 0.00 0.00 0.00 3.58
1990 2238 8.846943 ACATGACAATCAAAACAGTAGACATA 57.153 30.769 0.00 0.00 0.00 2.29
1991 2240 7.750229 ACATGACAATCAAAACAGTAGACAT 57.250 32.000 0.00 0.00 0.00 3.06
2136 2386 2.676342 GGTGTGTGGATGATAACGGAAC 59.324 50.000 0.00 0.00 0.00 3.62
2140 2390 2.691409 AGGGTGTGTGGATGATAACG 57.309 50.000 0.00 0.00 0.00 3.18
2299 2549 7.382110 AGACATAATTAGCGCTGATGTAATCT 58.618 34.615 22.90 15.46 45.81 2.40
2310 2560 5.659048 AGCAACTAAGACATAATTAGCGC 57.341 39.130 0.00 0.00 34.25 5.92
2347 2597 7.556844 CACCTATTTAGTGTTCAGATACCTGT 58.443 38.462 0.00 0.00 41.16 4.00
2355 2605 7.324178 AGAGTAAGCACCTATTTAGTGTTCAG 58.676 38.462 0.00 0.00 37.56 3.02
2411 2661 3.728385 AGCCCTGCAAGTAAGAGAAAT 57.272 42.857 0.00 0.00 0.00 2.17
2482 2738 8.523523 TTGTCTGCAATTTTGAATGTGAATAG 57.476 30.769 0.00 0.00 0.00 1.73
2493 2749 2.722629 CAGTCGCTTGTCTGCAATTTTG 59.277 45.455 0.00 0.00 33.65 2.44
2523 2779 2.301009 GTTACGGATCAATACCCCGGAT 59.699 50.000 0.73 0.00 46.83 4.18
2573 2829 1.436195 TTTGCGTGCAGTGAGTCACC 61.436 55.000 19.71 6.13 34.49 4.02
2574 2830 0.376852 TTTTGCGTGCAGTGAGTCAC 59.623 50.000 15.78 15.78 34.10 3.67
2576 2832 2.046313 CATTTTTGCGTGCAGTGAGTC 58.954 47.619 0.00 0.00 0.00 3.36
2577 2833 1.675483 TCATTTTTGCGTGCAGTGAGT 59.325 42.857 0.00 0.00 0.00 3.41
2578 2834 2.404265 TCATTTTTGCGTGCAGTGAG 57.596 45.000 0.00 0.00 0.00 3.51
2579 2835 3.307674 GAATCATTTTTGCGTGCAGTGA 58.692 40.909 0.00 0.00 0.00 3.41
2580 2836 2.409378 GGAATCATTTTTGCGTGCAGTG 59.591 45.455 0.00 0.00 0.00 3.66
2581 2837 2.610232 GGGAATCATTTTTGCGTGCAGT 60.610 45.455 0.00 0.00 0.00 4.40
2582 2838 1.994779 GGGAATCATTTTTGCGTGCAG 59.005 47.619 0.00 0.00 0.00 4.41
2583 2839 1.337635 GGGGAATCATTTTTGCGTGCA 60.338 47.619 0.00 0.00 0.00 4.57
2584 2840 1.066929 AGGGGAATCATTTTTGCGTGC 60.067 47.619 0.00 0.00 0.00 5.34
2586 2842 1.824852 GGAGGGGAATCATTTTTGCGT 59.175 47.619 0.00 0.00 0.00 5.24
2587 2843 2.102578 AGGAGGGGAATCATTTTTGCG 58.897 47.619 0.00 0.00 0.00 4.85
2588 2844 4.558226 AAAGGAGGGGAATCATTTTTGC 57.442 40.909 0.00 0.00 29.43 3.68
2620 2877 1.796459 CCCTTGTGAACGAAACCTACG 59.204 52.381 0.00 0.00 0.00 3.51
2639 2896 0.730494 GCATCAGTTTTGCTGCGACC 60.730 55.000 0.00 0.00 44.66 4.79
2940 3522 5.235616 CACAAAATGCACAAGCTGAAGAAAT 59.764 36.000 0.00 0.00 42.74 2.17
3067 3649 2.884639 AGGACGTTTTTGCAAGCTATGT 59.115 40.909 0.00 0.68 0.00 2.29
3069 3651 2.884639 ACAGGACGTTTTTGCAAGCTAT 59.115 40.909 0.00 0.00 0.00 2.97
3087 3675 1.553248 TCCCTCCGTTCCACAATACAG 59.447 52.381 0.00 0.00 0.00 2.74
3608 4211 4.593206 TCATACAAAACACTCCCTCTGTCT 59.407 41.667 0.00 0.00 0.00 3.41
3612 4215 5.568620 AAGTCATACAAAACACTCCCTCT 57.431 39.130 0.00 0.00 0.00 3.69
4189 4965 8.859090 TCTTTACAACAGATGAACAATTTGGAT 58.141 29.630 0.78 0.00 0.00 3.41
4195 4971 8.338259 GCGATATCTTTACAACAGATGAACAAT 58.662 33.333 0.34 0.00 32.94 2.71
4283 5059 1.269257 GGGTTGCAAGTTCAAGACAGC 60.269 52.381 0.00 0.00 33.68 4.40
4351 5128 3.299977 CCTGTGACCCCGTCGACA 61.300 66.667 17.16 0.00 34.95 4.35
4366 5143 1.256812 CCTGAAAATTGAACCCGCCT 58.743 50.000 0.00 0.00 0.00 5.52
4390 5167 3.833732 TCCGCTGTGGAGATATCTACTT 58.166 45.455 16.10 0.00 43.74 2.24
4402 5179 5.390613 CAAGTTTTTACTAATCCGCTGTGG 58.609 41.667 0.00 0.00 40.09 4.17
4404 5181 5.310451 TCCAAGTTTTTACTAATCCGCTGT 58.690 37.500 0.00 0.00 0.00 4.40
4406 5183 5.801380 TCTCCAAGTTTTTACTAATCCGCT 58.199 37.500 0.00 0.00 0.00 5.52
4407 5184 6.487103 CATCTCCAAGTTTTTACTAATCCGC 58.513 40.000 0.00 0.00 0.00 5.54
4409 5186 7.631717 AGCATCTCCAAGTTTTTACTAATCC 57.368 36.000 0.00 0.00 0.00 3.01
4410 5187 8.184848 GGAAGCATCTCCAAGTTTTTACTAATC 58.815 37.037 0.00 0.00 35.36 1.75
4411 5188 7.669722 TGGAAGCATCTCCAAGTTTTTACTAAT 59.330 33.333 0.03 0.00 42.69 1.73
4412 5189 7.001674 TGGAAGCATCTCCAAGTTTTTACTAA 58.998 34.615 0.03 0.00 42.69 2.24
4413 5190 6.539173 TGGAAGCATCTCCAAGTTTTTACTA 58.461 36.000 0.03 0.00 42.69 1.82
4414 5191 5.385198 TGGAAGCATCTCCAAGTTTTTACT 58.615 37.500 0.03 0.00 42.69 2.24
4415 5192 5.705609 TGGAAGCATCTCCAAGTTTTTAC 57.294 39.130 0.03 0.00 42.69 2.01
4423 5200 8.596293 AAAGAATTTTAATGGAAGCATCTCCAA 58.404 29.630 6.32 0.00 41.93 3.53
4560 5341 4.321082 GCTTGCTCTTCTTTGAGAATGCTT 60.321 41.667 13.14 0.00 38.80 3.91
4657 5439 3.477530 AGTTTGTCAGCCAGTAAGAACC 58.522 45.455 0.00 0.00 0.00 3.62
4681 5463 8.557029 GCTAAGCTACACTTTCAGAAGTTTTTA 58.443 33.333 0.00 0.00 43.48 1.52
4694 5480 3.131400 GGACTAGCAGCTAAGCTACACTT 59.869 47.826 3.09 0.00 44.50 3.16
4731 5541 7.769272 TCTTGGTTATCTTTGCTTGTTTTTG 57.231 32.000 0.00 0.00 0.00 2.44
4789 5600 5.129634 TCTTACTCCACAGCAAAATTGTCA 58.870 37.500 0.00 0.00 0.00 3.58
4837 5648 7.764443 TCTGATTATTACTGCCAAGTCTACAAC 59.236 37.037 0.00 0.00 37.88 3.32
4843 5654 7.712639 TCATCTTCTGATTATTACTGCCAAGTC 59.287 37.037 0.00 0.00 37.88 3.01
4856 5667 6.938596 CACTGGGCATATTCATCTTCTGATTA 59.061 38.462 0.00 0.00 32.72 1.75
4888 5699 1.615392 CCCAACCTTCAGGAAAAGCAG 59.385 52.381 0.00 0.00 38.94 4.24
4901 5712 2.807676 CTGTAAATTCCAGCCCAACCT 58.192 47.619 0.00 0.00 0.00 3.50
4909 5720 6.575162 AGGTGTTTTAGCTGTAAATTCCAG 57.425 37.500 0.00 1.65 35.38 3.86
4934 5745 8.558700 GGAATTTTGTTTTATGTTTCAGCACAT 58.441 29.630 0.00 0.00 40.61 3.21
4936 5747 7.011857 TGGGAATTTTGTTTTATGTTTCAGCAC 59.988 33.333 0.00 0.00 0.00 4.40
4938 5749 7.489574 TGGGAATTTTGTTTTATGTTTCAGC 57.510 32.000 0.00 0.00 0.00 4.26
4954 5765 9.822185 GCATTCTAAATTAGACAATGGGAATTT 57.178 29.630 13.51 7.03 35.99 1.82
4960 5771 8.984891 TTGTTGCATTCTAAATTAGACAATGG 57.015 30.769 13.51 1.13 33.84 3.16
4992 5803 5.528690 TGTTTGTGAGAAGGAACATTGAGAG 59.471 40.000 0.00 0.00 0.00 3.20
4996 5807 8.352201 TCTATTTGTTTGTGAGAAGGAACATTG 58.648 33.333 0.00 0.00 32.64 2.82
5063 5905 7.758820 TTATCTGGGAACATTTAGGGACTAA 57.241 36.000 0.00 0.00 44.93 2.24
5064 5906 7.758820 TTTATCTGGGAACATTTAGGGACTA 57.241 36.000 0.00 0.00 39.36 2.59
5083 5943 7.213252 TGTAGCGTGTCGAAACTTATTTATC 57.787 36.000 3.82 0.00 0.00 1.75
5084 5944 6.255020 CCTGTAGCGTGTCGAAACTTATTTAT 59.745 38.462 3.82 0.00 0.00 1.40
5085 5945 5.574055 CCTGTAGCGTGTCGAAACTTATTTA 59.426 40.000 3.82 0.00 0.00 1.40
5086 5946 4.387862 CCTGTAGCGTGTCGAAACTTATTT 59.612 41.667 3.82 0.00 0.00 1.40
5087 5947 3.924686 CCTGTAGCGTGTCGAAACTTATT 59.075 43.478 3.82 0.00 0.00 1.40
5088 5948 3.508762 CCTGTAGCGTGTCGAAACTTAT 58.491 45.455 3.82 0.00 0.00 1.73
5089 5949 2.923605 GCCTGTAGCGTGTCGAAACTTA 60.924 50.000 3.82 0.00 0.00 2.24
5090 5950 1.779569 CCTGTAGCGTGTCGAAACTT 58.220 50.000 3.82 0.00 0.00 2.66
5091 5951 0.666577 GCCTGTAGCGTGTCGAAACT 60.667 55.000 3.82 0.00 0.00 2.66
5092 5952 1.779683 GCCTGTAGCGTGTCGAAAC 59.220 57.895 0.00 0.00 0.00 2.78
5093 5953 4.255126 GCCTGTAGCGTGTCGAAA 57.745 55.556 0.00 0.00 0.00 3.46
5109 5969 8.583765 GTGTAATTTCATCTTTTATGGTTTCGC 58.416 33.333 0.00 0.00 0.00 4.70
5116 5976 9.689976 TGGTTGTGTGTAATTTCATCTTTTATG 57.310 29.630 0.00 0.00 0.00 1.90
5121 5981 7.581213 TCTTGGTTGTGTGTAATTTCATCTT 57.419 32.000 0.00 0.00 0.00 2.40
5164 6037 8.655651 TTGCTATGATGTGACGATACAATTAA 57.344 30.769 0.00 0.00 33.69 1.40
5209 6084 3.117888 TCAGAAGTTTGCTCCAGGAACTT 60.118 43.478 4.18 4.18 43.95 2.66
5210 6085 2.439507 TCAGAAGTTTGCTCCAGGAACT 59.560 45.455 0.00 0.00 43.88 3.01
5216 6091 4.321452 GCATCAATTCAGAAGTTTGCTCCA 60.321 41.667 7.67 0.00 0.00 3.86
5251 6126 4.508461 TGCATTGGTCTTCTGATTGTTG 57.492 40.909 0.00 0.00 0.00 3.33
5277 6154 3.272574 TGCAATCTAGCCTTCTGGAAG 57.727 47.619 3.57 3.57 33.39 3.46
5296 6173 8.969121 TTAGACATTTAGACATTGCATTGTTG 57.031 30.769 14.95 11.17 0.00 3.33
5301 6178 9.399797 TCTGAATTAGACATTTAGACATTGCAT 57.600 29.630 0.00 0.00 0.00 3.96
5302 6179 8.791327 TCTGAATTAGACATTTAGACATTGCA 57.209 30.769 0.00 0.00 0.00 4.08
5303 6180 8.887717 ACTCTGAATTAGACATTTAGACATTGC 58.112 33.333 0.00 0.00 0.00 3.56
5305 6182 8.887717 GCACTCTGAATTAGACATTTAGACATT 58.112 33.333 0.00 0.00 0.00 2.71
5306 6183 8.043113 TGCACTCTGAATTAGACATTTAGACAT 58.957 33.333 0.00 0.00 0.00 3.06
5308 6185 7.834068 TGCACTCTGAATTAGACATTTAGAC 57.166 36.000 0.00 0.00 0.00 2.59
5309 6186 7.877612 TGTTGCACTCTGAATTAGACATTTAGA 59.122 33.333 0.00 0.00 0.00 2.10
5310 6187 8.032952 TGTTGCACTCTGAATTAGACATTTAG 57.967 34.615 0.00 0.00 0.00 1.85
5311 6188 7.977789 TGTTGCACTCTGAATTAGACATTTA 57.022 32.000 0.00 0.00 0.00 1.40
5312 6189 6.882610 TGTTGCACTCTGAATTAGACATTT 57.117 33.333 0.00 0.00 0.00 2.32
5376 6271 9.490379 GTTGAGTTCTTATCTTTCCAAACTCTA 57.510 33.333 12.61 4.42 41.83 2.43
5377 6272 7.445707 GGTTGAGTTCTTATCTTTCCAAACTCT 59.554 37.037 12.61 0.00 41.83 3.24
5378 6273 7.228706 TGGTTGAGTTCTTATCTTTCCAAACTC 59.771 37.037 6.19 6.19 41.72 3.01
5389 6284 7.324178 AGTGTAGTCATGGTTGAGTTCTTATC 58.676 38.462 0.00 0.00 36.84 1.75
5404 6299 5.176958 GCGTGTGTTAAGAAAGTGTAGTCAT 59.823 40.000 0.00 0.00 0.00 3.06
5406 6301 4.505191 TGCGTGTGTTAAGAAAGTGTAGTC 59.495 41.667 0.00 0.00 0.00 2.59
5413 6308 1.260561 AGCGTGCGTGTGTTAAGAAAG 59.739 47.619 0.00 0.00 0.00 2.62
5471 6366 6.409524 TTTGTGGAGCAATCATTCTCTTTT 57.590 33.333 0.00 0.00 36.89 2.27
5482 6377 1.069049 GGTGCAGTTTTGTGGAGCAAT 59.931 47.619 0.00 0.00 36.39 3.56
5549 6444 5.591472 TCTGCTTCTGCTAGGTTACGTTATA 59.409 40.000 0.00 0.00 40.48 0.98
5577 6472 1.915078 TAGGGCCTGCTTCTGCTTCC 61.915 60.000 18.53 0.00 40.48 3.46


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

AutoCloner maintained by Alex Coulton.