Multiple sequence alignment - TraesCS5A01G138000

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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 TraesCS5A01G138000 chr5A 100.000 5040 0 0 1 5040 310426620 310421581 0.000000e+00 9308
1 TraesCS5A01G138000 chr5A 96.700 3000 89 7 2040 5037 199302248 199305239 0.000000e+00 4983
2 TraesCS5A01G138000 chr5A 94.052 1429 49 8 282 1696 199298078 199299484 0.000000e+00 2135
3 TraesCS5A01G138000 chr5A 96.300 1054 32 4 3987 5040 243490001 243488955 0.000000e+00 1724
4 TraesCS5A01G138000 chr5A 96.190 105 3 1 1947 2050 199301972 199302076 2.410000e-38 171
5 TraesCS5A01G138000 chr4A 96.076 4179 134 14 880 5039 33793436 33789269 0.000000e+00 6782
6 TraesCS5A01G138000 chr4A 96.974 793 23 1 3781 4573 110334739 110333948 0.000000e+00 1330
7 TraesCS5A01G138000 chr4A 94.020 602 36 0 283 884 33797030 33796429 0.000000e+00 913
8 TraesCS5A01G138000 chr4A 95.608 296 11 2 4746 5040 110333949 110333655 1.640000e-129 473
9 TraesCS5A01G138000 chr4A 92.958 284 20 0 3 286 160306563 160306280 1.010000e-111 414
10 TraesCS5A01G138000 chr3D 96.797 2872 59 12 756 3605 306831549 306828689 0.000000e+00 4763
11 TraesCS5A01G138000 chr3D 94.410 161 8 1 1643 1802 568191316 568191156 3.900000e-61 246
12 TraesCS5A01G138000 chr2A 97.471 2610 53 8 1947 4549 475926070 475928673 0.000000e+00 4442
13 TraesCS5A01G138000 chr2A 86.870 1409 114 20 283 1642 113094706 113096092 0.000000e+00 1511
14 TraesCS5A01G138000 chr2A 93.886 736 36 3 283 1009 475920975 475921710 0.000000e+00 1101
15 TraesCS5A01G138000 chr2A 96.828 599 11 2 1099 1696 475922063 475922654 0.000000e+00 994
16 TraesCS5A01G138000 chr2A 93.080 289 17 1 1 286 574497716 574497428 2.170000e-113 420
17 TraesCS5A01G138000 chr2A 94.231 208 11 1 4834 5040 355400013 355400220 2.930000e-82 316
18 TraesCS5A01G138000 chr4B 93.234 2675 134 17 282 2938 279025675 279023030 0.000000e+00 3893
19 TraesCS5A01G138000 chr4B 94.482 1468 58 6 2334 3784 372845005 372843544 0.000000e+00 2241
20 TraesCS5A01G138000 chr4B 92.035 339 19 5 3785 4116 534070784 534071121 2.120000e-128 470
21 TraesCS5A01G138000 chr4B 94.426 305 10 1 3781 4078 372843447 372843143 3.550000e-126 462
22 TraesCS5A01G138000 chr2B 93.246 2058 118 14 283 2322 303247487 303245433 0.000000e+00 3011
23 TraesCS5A01G138000 chr1D 97.607 1755 39 3 2031 3784 104594886 104596638 0.000000e+00 3005
24 TraesCS5A01G138000 chr1D 97.362 796 19 2 3778 4573 104596732 104597525 0.000000e+00 1352
25 TraesCS5A01G138000 chr1D 95.623 297 11 2 4746 5040 104597524 104597820 4.570000e-130 475
26 TraesCS5A01G138000 chr3B 96.248 1546 49 7 2241 3784 279966287 279967825 0.000000e+00 2525
27 TraesCS5A01G138000 chr3B 93.434 792 29 9 3783 4573 279967924 279968693 0.000000e+00 1153
28 TraesCS5A01G138000 chr3B 93.919 296 16 2 4746 5040 279968692 279968986 3.580000e-121 446
29 TraesCS5A01G138000 chr3B 84.143 391 54 8 1643 2030 293695691 293695306 6.160000e-99 372
30 TraesCS5A01G138000 chr1A 95.400 1413 57 3 2375 3784 93771432 93770025 0.000000e+00 2242
31 TraesCS5A01G138000 chr1A 94.315 387 22 0 3781 4167 93769928 93769542 1.210000e-165 593
32 TraesCS5A01G138000 chr6B 93.993 1465 71 11 2329 3784 649167930 649166474 0.000000e+00 2202
33 TraesCS5A01G138000 chr6B 94.426 305 10 1 3781 4078 649166377 649166073 3.550000e-126 462
34 TraesCS5A01G138000 chr5B 96.302 1298 41 4 2031 3324 328771466 328772760 0.000000e+00 2124
35 TraesCS5A01G138000 chr5B 95.712 793 31 2 3781 4573 328773298 328774087 0.000000e+00 1273
36 TraesCS5A01G138000 chr5B 95.608 296 11 2 4746 5040 328774086 328774380 1.640000e-129 473
37 TraesCS5A01G138000 chr7B 89.366 1420 94 21 283 1645 474554243 474552824 0.000000e+00 1733
38 TraesCS5A01G138000 chr7B 95.299 702 30 2 4134 4833 256090002 256090702 0.000000e+00 1110
39 TraesCS5A01G138000 chr6A 88.235 1411 113 18 283 1645 179188362 179186957 0.000000e+00 1637
40 TraesCS5A01G138000 chr5D 94.124 987 35 9 4076 5040 487306791 487305806 0.000000e+00 1480
41 TraesCS5A01G138000 chr5D 93.310 284 19 0 3 286 171568999 171568716 2.170000e-113 420
42 TraesCS5A01G138000 chr5D 92.958 284 20 0 3 286 289574649 289574932 1.010000e-111 414
43 TraesCS5A01G138000 chr5D 94.712 208 10 1 4834 5040 104693878 104693671 6.290000e-84 322
44 TraesCS5A01G138000 chr7A 93.127 742 35 8 283 1015 308449041 308449775 0.000000e+00 1074
45 TraesCS5A01G138000 chr7A 93.080 289 17 1 1 286 158492853 158492565 2.170000e-113 420
46 TraesCS5A01G138000 chr4D 93.641 629 14 6 1040 1642 126517683 126518311 0.000000e+00 917
47 TraesCS5A01G138000 chr4D 92.683 287 18 1 3 286 214417362 214417648 1.310000e-110 411
48 TraesCS5A01G138000 chr6D 93.175 630 21 3 1035 1642 259463088 259462459 0.000000e+00 905
49 TraesCS5A01G138000 chr6D 92.575 633 25 3 1035 1645 259465510 259464878 0.000000e+00 889
50 TraesCS5A01G138000 chr6D 89.755 654 65 2 279 931 259466151 259465499 0.000000e+00 835
51 TraesCS5A01G138000 chr6D 90.575 626 55 4 308 931 259463700 259463077 0.000000e+00 826
52 TraesCS5A01G138000 chr2D 93.080 289 17 1 1 286 261060412 261060700 2.170000e-113 420
53 TraesCS5A01G138000 chr2D 93.031 287 17 1 3 286 590457816 590458102 2.810000e-112 416
54 TraesCS5A01G138000 chr7D 92.734 289 18 1 1 286 476822286 476821998 1.010000e-111 414
55 TraesCS5A01G138000 chr7D 84.833 389 56 3 1643 2030 38913597 38913211 6.120000e-104 388


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 TraesCS5A01G138000 chr5A 310421581 310426620 5039 True 9308.000000 9308 100.000000 1 5040 1 chr5A.!!$R2 5039
1 TraesCS5A01G138000 chr5A 199298078 199305239 7161 False 2429.666667 4983 95.647333 282 5037 3 chr5A.!!$F1 4755
2 TraesCS5A01G138000 chr5A 243488955 243490001 1046 True 1724.000000 1724 96.300000 3987 5040 1 chr5A.!!$R1 1053
3 TraesCS5A01G138000 chr4A 33789269 33797030 7761 True 3847.500000 6782 95.048000 283 5039 2 chr4A.!!$R2 4756
4 TraesCS5A01G138000 chr4A 110333655 110334739 1084 True 901.500000 1330 96.291000 3781 5040 2 chr4A.!!$R3 1259
5 TraesCS5A01G138000 chr3D 306828689 306831549 2860 True 4763.000000 4763 96.797000 756 3605 1 chr3D.!!$R1 2849
6 TraesCS5A01G138000 chr2A 475920975 475928673 7698 False 2179.000000 4442 96.061667 283 4549 3 chr2A.!!$F3 4266
7 TraesCS5A01G138000 chr2A 113094706 113096092 1386 False 1511.000000 1511 86.870000 283 1642 1 chr2A.!!$F1 1359
8 TraesCS5A01G138000 chr4B 279023030 279025675 2645 True 3893.000000 3893 93.234000 282 2938 1 chr4B.!!$R1 2656
9 TraesCS5A01G138000 chr4B 372843143 372845005 1862 True 1351.500000 2241 94.454000 2334 4078 2 chr4B.!!$R2 1744
10 TraesCS5A01G138000 chr2B 303245433 303247487 2054 True 3011.000000 3011 93.246000 283 2322 1 chr2B.!!$R1 2039
11 TraesCS5A01G138000 chr1D 104594886 104597820 2934 False 1610.666667 3005 96.864000 2031 5040 3 chr1D.!!$F1 3009
12 TraesCS5A01G138000 chr3B 279966287 279968986 2699 False 1374.666667 2525 94.533667 2241 5040 3 chr3B.!!$F1 2799
13 TraesCS5A01G138000 chr1A 93769542 93771432 1890 True 1417.500000 2242 94.857500 2375 4167 2 chr1A.!!$R1 1792
14 TraesCS5A01G138000 chr6B 649166073 649167930 1857 True 1332.000000 2202 94.209500 2329 4078 2 chr6B.!!$R1 1749
15 TraesCS5A01G138000 chr5B 328771466 328774380 2914 False 1290.000000 2124 95.874000 2031 5040 3 chr5B.!!$F1 3009
16 TraesCS5A01G138000 chr7B 474552824 474554243 1419 True 1733.000000 1733 89.366000 283 1645 1 chr7B.!!$R1 1362
17 TraesCS5A01G138000 chr7B 256090002 256090702 700 False 1110.000000 1110 95.299000 4134 4833 1 chr7B.!!$F1 699
18 TraesCS5A01G138000 chr6A 179186957 179188362 1405 True 1637.000000 1637 88.235000 283 1645 1 chr6A.!!$R1 1362
19 TraesCS5A01G138000 chr5D 487305806 487306791 985 True 1480.000000 1480 94.124000 4076 5040 1 chr5D.!!$R3 964
20 TraesCS5A01G138000 chr7A 308449041 308449775 734 False 1074.000000 1074 93.127000 283 1015 1 chr7A.!!$F1 732
21 TraesCS5A01G138000 chr4D 126517683 126518311 628 False 917.000000 917 93.641000 1040 1642 1 chr4D.!!$F1 602
22 TraesCS5A01G138000 chr6D 259462459 259466151 3692 True 863.750000 905 91.520000 279 1645 4 chr6D.!!$R1 1366

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
814 3238 0.098376 GTAGGTCGTCTTCGCGATGT 59.902 55.0 19.92 4.14 43.07 3.06 F
1676 7392 1.548357 GCTCACCTGAAGCTCCCTCA 61.548 60.0 0.00 0.00 0.00 3.86 F
1976 10861 0.037326 TGGTCTCGCAATGACAGGTC 60.037 55.0 0.00 0.00 36.26 3.85 F
3703 12844 0.476338 TCCTGTTAGCCCAAGTGCAA 59.524 50.0 0.00 0.00 0.00 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1821 9589 1.144093 TCACCCAACGAAATCCAACCT 59.856 47.619 0.0 0.0 0.00 3.50 R
2786 11877 4.099573 ACATGGACAGTAGCACCTACATAC 59.900 45.833 0.0 0.0 39.22 2.39 R
3894 13136 5.239306 CACTCTCAAAAGGCACATTCAGTAA 59.761 40.000 0.0 0.0 0.00 2.24 R
4541 13802 2.522836 TAGGCGACACCGTAAAAACA 57.477 45.000 0.0 0.0 46.52 2.83 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
19 20 2.270275 CGAGAGACTAAGTGCCACTG 57.730 55.000 0.00 0.00 0.00 3.66
20 21 1.135257 CGAGAGACTAAGTGCCACTGG 60.135 57.143 0.00 0.00 0.00 4.00
21 22 2.171840 GAGAGACTAAGTGCCACTGGA 58.828 52.381 0.00 0.00 0.00 3.86
22 23 1.896465 AGAGACTAAGTGCCACTGGAC 59.104 52.381 0.00 0.00 0.00 4.02
23 24 1.618837 GAGACTAAGTGCCACTGGACA 59.381 52.381 0.00 0.00 0.00 4.02
24 25 2.234908 GAGACTAAGTGCCACTGGACAT 59.765 50.000 0.00 0.00 0.00 3.06
25 26 2.234908 AGACTAAGTGCCACTGGACATC 59.765 50.000 0.00 0.00 0.00 3.06
26 27 2.234908 GACTAAGTGCCACTGGACATCT 59.765 50.000 0.00 0.00 0.00 2.90
27 28 2.639839 ACTAAGTGCCACTGGACATCTT 59.360 45.455 0.00 6.08 0.00 2.40
28 29 2.191128 AAGTGCCACTGGACATCTTC 57.809 50.000 0.00 0.00 0.00 2.87
29 30 1.059098 AGTGCCACTGGACATCTTCA 58.941 50.000 0.00 0.00 0.00 3.02
30 31 1.421268 AGTGCCACTGGACATCTTCAA 59.579 47.619 0.00 0.00 0.00 2.69
31 32 1.537202 GTGCCACTGGACATCTTCAAC 59.463 52.381 0.00 0.00 0.00 3.18
32 33 1.421268 TGCCACTGGACATCTTCAACT 59.579 47.619 0.00 0.00 0.00 3.16
33 34 2.158623 TGCCACTGGACATCTTCAACTT 60.159 45.455 0.00 0.00 0.00 2.66
34 35 2.485814 GCCACTGGACATCTTCAACTTC 59.514 50.000 0.00 0.00 0.00 3.01
35 36 3.743521 CCACTGGACATCTTCAACTTCA 58.256 45.455 0.00 0.00 0.00 3.02
36 37 3.499918 CCACTGGACATCTTCAACTTCAC 59.500 47.826 0.00 0.00 0.00 3.18
37 38 3.185188 CACTGGACATCTTCAACTTCACG 59.815 47.826 0.00 0.00 0.00 4.35
38 39 3.181465 ACTGGACATCTTCAACTTCACGT 60.181 43.478 0.00 0.00 0.00 4.49
39 40 3.130633 TGGACATCTTCAACTTCACGTG 58.869 45.455 9.94 9.94 0.00 4.49
40 41 3.181470 TGGACATCTTCAACTTCACGTGA 60.181 43.478 15.76 15.76 0.00 4.35
41 42 3.184581 GGACATCTTCAACTTCACGTGAC 59.815 47.826 19.90 1.27 0.00 3.67
42 43 4.051922 GACATCTTCAACTTCACGTGACT 58.948 43.478 19.90 3.04 0.00 3.41
43 44 4.442706 ACATCTTCAACTTCACGTGACTT 58.557 39.130 19.90 9.83 0.00 3.01
44 45 4.876107 ACATCTTCAACTTCACGTGACTTT 59.124 37.500 19.90 11.40 0.00 2.66
45 46 4.857871 TCTTCAACTTCACGTGACTTTG 57.142 40.909 19.90 22.23 0.00 2.77
46 47 4.250464 TCTTCAACTTCACGTGACTTTGT 58.750 39.130 26.23 17.49 0.00 2.83
47 48 5.412640 TCTTCAACTTCACGTGACTTTGTA 58.587 37.500 26.23 20.05 0.00 2.41
48 49 6.046593 TCTTCAACTTCACGTGACTTTGTAT 58.953 36.000 26.23 7.48 0.00 2.29
49 50 6.537301 TCTTCAACTTCACGTGACTTTGTATT 59.463 34.615 26.23 10.55 0.00 1.89
50 51 6.043327 TCAACTTCACGTGACTTTGTATTG 57.957 37.500 26.23 18.54 0.00 1.90
51 52 5.813157 TCAACTTCACGTGACTTTGTATTGA 59.187 36.000 26.23 19.90 0.00 2.57
52 53 5.652744 ACTTCACGTGACTTTGTATTGAC 57.347 39.130 19.90 0.00 0.00 3.18
53 54 5.113383 ACTTCACGTGACTTTGTATTGACA 58.887 37.500 19.90 0.00 0.00 3.58
54 55 5.006358 ACTTCACGTGACTTTGTATTGACAC 59.994 40.000 19.90 0.00 34.48 3.67
55 56 4.434520 TCACGTGACTTTGTATTGACACA 58.565 39.130 15.76 0.00 34.48 3.72
56 57 4.870991 TCACGTGACTTTGTATTGACACAA 59.129 37.500 15.76 0.00 36.65 3.33
57 58 5.525745 TCACGTGACTTTGTATTGACACAAT 59.474 36.000 15.76 0.00 38.18 2.71
58 59 5.845953 CACGTGACTTTGTATTGACACAATC 59.154 40.000 10.90 0.00 38.18 2.67
59 60 5.525745 ACGTGACTTTGTATTGACACAATCA 59.474 36.000 0.00 0.00 38.18 2.57
60 61 6.073369 CGTGACTTTGTATTGACACAATCAG 58.927 40.000 0.00 0.00 38.99 2.90
61 62 6.292865 CGTGACTTTGTATTGACACAATCAGT 60.293 38.462 0.00 0.00 38.99 3.41
62 63 7.095816 CGTGACTTTGTATTGACACAATCAGTA 60.096 37.037 0.00 0.00 38.99 2.74
63 64 8.009974 GTGACTTTGTATTGACACAATCAGTAC 58.990 37.037 0.00 3.40 45.99 2.73
69 70 7.005062 GTATTGACACAATCAGTACATGGAC 57.995 40.000 0.00 0.00 45.42 4.02
70 71 4.615588 TGACACAATCAGTACATGGACA 57.384 40.909 11.55 0.00 31.91 4.02
71 72 4.314961 TGACACAATCAGTACATGGACAC 58.685 43.478 11.55 0.00 31.91 3.67
72 73 4.202305 TGACACAATCAGTACATGGACACA 60.202 41.667 11.55 0.00 31.91 3.72
73 74 4.318332 ACACAATCAGTACATGGACACAG 58.682 43.478 11.55 0.00 0.00 3.66
74 75 3.686241 CACAATCAGTACATGGACACAGG 59.314 47.826 11.55 0.00 0.00 4.00
75 76 3.582647 ACAATCAGTACATGGACACAGGA 59.417 43.478 11.55 2.53 31.68 3.86
76 77 4.225942 ACAATCAGTACATGGACACAGGAT 59.774 41.667 11.55 4.88 31.68 3.24
77 78 3.893326 TCAGTACATGGACACAGGATG 57.107 47.619 11.55 0.00 46.00 3.51
95 96 4.836125 GATGTAATCCGCATCACCAATT 57.164 40.909 0.00 0.00 41.56 2.32
96 97 4.787598 GATGTAATCCGCATCACCAATTC 58.212 43.478 0.00 0.00 41.56 2.17
97 98 3.884895 TGTAATCCGCATCACCAATTCT 58.115 40.909 0.00 0.00 0.00 2.40
98 99 3.876914 TGTAATCCGCATCACCAATTCTC 59.123 43.478 0.00 0.00 0.00 2.87
99 100 1.972872 ATCCGCATCACCAATTCTCC 58.027 50.000 0.00 0.00 0.00 3.71
100 101 0.911769 TCCGCATCACCAATTCTCCT 59.088 50.000 0.00 0.00 0.00 3.69
101 102 1.134401 TCCGCATCACCAATTCTCCTC 60.134 52.381 0.00 0.00 0.00 3.71
102 103 1.134280 CCGCATCACCAATTCTCCTCT 60.134 52.381 0.00 0.00 0.00 3.69
103 104 2.636830 CGCATCACCAATTCTCCTCTT 58.363 47.619 0.00 0.00 0.00 2.85
104 105 3.012518 CGCATCACCAATTCTCCTCTTT 58.987 45.455 0.00 0.00 0.00 2.52
105 106 3.181503 CGCATCACCAATTCTCCTCTTTG 60.182 47.826 0.00 0.00 0.00 2.77
106 107 3.760684 GCATCACCAATTCTCCTCTTTGT 59.239 43.478 0.00 0.00 0.00 2.83
107 108 4.943705 GCATCACCAATTCTCCTCTTTGTA 59.056 41.667 0.00 0.00 0.00 2.41
108 109 5.163713 GCATCACCAATTCTCCTCTTTGTAC 60.164 44.000 0.00 0.00 0.00 2.90
109 110 5.825593 TCACCAATTCTCCTCTTTGTACT 57.174 39.130 0.00 0.00 0.00 2.73
110 111 6.187727 TCACCAATTCTCCTCTTTGTACTT 57.812 37.500 0.00 0.00 0.00 2.24
111 112 6.601332 TCACCAATTCTCCTCTTTGTACTTT 58.399 36.000 0.00 0.00 0.00 2.66
112 113 6.710744 TCACCAATTCTCCTCTTTGTACTTTC 59.289 38.462 0.00 0.00 0.00 2.62
113 114 6.486657 CACCAATTCTCCTCTTTGTACTTTCA 59.513 38.462 0.00 0.00 0.00 2.69
114 115 6.712547 ACCAATTCTCCTCTTTGTACTTTCAG 59.287 38.462 0.00 0.00 0.00 3.02
115 116 6.348868 CCAATTCTCCTCTTTGTACTTTCAGC 60.349 42.308 0.00 0.00 0.00 4.26
116 117 4.273148 TCTCCTCTTTGTACTTTCAGCC 57.727 45.455 0.00 0.00 0.00 4.85
117 118 3.646162 TCTCCTCTTTGTACTTTCAGCCA 59.354 43.478 0.00 0.00 0.00 4.75
118 119 4.102524 TCTCCTCTTTGTACTTTCAGCCAA 59.897 41.667 0.00 0.00 0.00 4.52
119 120 4.787551 TCCTCTTTGTACTTTCAGCCAAA 58.212 39.130 0.00 0.00 0.00 3.28
120 121 5.385198 TCCTCTTTGTACTTTCAGCCAAAT 58.615 37.500 0.00 0.00 0.00 2.32
121 122 5.833131 TCCTCTTTGTACTTTCAGCCAAATT 59.167 36.000 0.00 0.00 0.00 1.82
122 123 6.016276 TCCTCTTTGTACTTTCAGCCAAATTC 60.016 38.462 0.00 0.00 0.00 2.17
123 124 6.239008 CCTCTTTGTACTTTCAGCCAAATTCA 60.239 38.462 0.00 0.00 0.00 2.57
124 125 7.288810 TCTTTGTACTTTCAGCCAAATTCAT 57.711 32.000 0.00 0.00 0.00 2.57
125 126 7.147312 TCTTTGTACTTTCAGCCAAATTCATG 58.853 34.615 0.00 0.00 0.00 3.07
126 127 6.647334 TTGTACTTTCAGCCAAATTCATGA 57.353 33.333 0.00 0.00 0.00 3.07
127 128 6.647334 TGTACTTTCAGCCAAATTCATGAA 57.353 33.333 11.26 11.26 0.00 2.57
128 129 6.446318 TGTACTTTCAGCCAAATTCATGAAC 58.554 36.000 11.07 0.00 31.72 3.18
129 130 5.796424 ACTTTCAGCCAAATTCATGAACT 57.204 34.783 11.07 0.00 31.72 3.01
130 131 5.776744 ACTTTCAGCCAAATTCATGAACTC 58.223 37.500 11.07 0.00 31.72 3.01
131 132 5.537674 ACTTTCAGCCAAATTCATGAACTCT 59.462 36.000 11.07 0.91 31.72 3.24
132 133 5.381174 TTCAGCCAAATTCATGAACTCTG 57.619 39.130 11.07 12.71 0.00 3.35
133 134 4.401022 TCAGCCAAATTCATGAACTCTGT 58.599 39.130 11.07 0.00 0.00 3.41
134 135 4.456911 TCAGCCAAATTCATGAACTCTGTC 59.543 41.667 11.07 0.00 0.00 3.51
135 136 4.216902 CAGCCAAATTCATGAACTCTGTCA 59.783 41.667 11.07 0.00 0.00 3.58
136 137 5.014858 AGCCAAATTCATGAACTCTGTCAT 58.985 37.500 11.07 0.00 38.84 3.06
142 143 2.708051 CATGAACTCTGTCATGCCACT 58.292 47.619 2.48 0.00 46.14 4.00
143 144 2.174363 TGAACTCTGTCATGCCACTG 57.826 50.000 0.00 0.00 0.00 3.66
144 145 1.693606 TGAACTCTGTCATGCCACTGA 59.306 47.619 0.00 0.00 0.00 3.41
145 146 2.303890 TGAACTCTGTCATGCCACTGAT 59.696 45.455 0.00 0.00 0.00 2.90
146 147 3.515104 TGAACTCTGTCATGCCACTGATA 59.485 43.478 0.00 0.00 0.00 2.15
147 148 4.020307 TGAACTCTGTCATGCCACTGATAA 60.020 41.667 0.00 0.00 0.00 1.75
148 149 4.558226 ACTCTGTCATGCCACTGATAAA 57.442 40.909 0.00 0.00 0.00 1.40
149 150 4.910195 ACTCTGTCATGCCACTGATAAAA 58.090 39.130 0.00 0.00 0.00 1.52
150 151 5.503927 ACTCTGTCATGCCACTGATAAAAT 58.496 37.500 0.00 0.00 0.00 1.82
151 152 5.587844 ACTCTGTCATGCCACTGATAAAATC 59.412 40.000 0.00 0.00 0.00 2.17
152 153 5.748402 TCTGTCATGCCACTGATAAAATCT 58.252 37.500 0.00 0.00 0.00 2.40
153 154 5.587443 TCTGTCATGCCACTGATAAAATCTG 59.413 40.000 0.00 0.00 0.00 2.90
154 155 4.096833 TGTCATGCCACTGATAAAATCTGC 59.903 41.667 0.00 0.00 0.00 4.26
155 156 3.313249 TCATGCCACTGATAAAATCTGCG 59.687 43.478 0.00 0.00 0.00 5.18
156 157 2.016318 TGCCACTGATAAAATCTGCGG 58.984 47.619 0.00 0.00 34.64 5.69
157 158 2.017049 GCCACTGATAAAATCTGCGGT 58.983 47.619 0.00 0.00 34.21 5.68
158 159 2.423538 GCCACTGATAAAATCTGCGGTT 59.576 45.455 0.00 0.00 34.21 4.44
159 160 3.487544 GCCACTGATAAAATCTGCGGTTC 60.488 47.826 0.00 0.00 34.21 3.62
160 161 3.941483 CCACTGATAAAATCTGCGGTTCT 59.059 43.478 0.00 0.00 0.00 3.01
161 162 4.034510 CCACTGATAAAATCTGCGGTTCTC 59.965 45.833 0.00 0.00 0.00 2.87
162 163 4.034510 CACTGATAAAATCTGCGGTTCTCC 59.965 45.833 0.00 0.00 0.00 3.71
163 164 4.191544 CTGATAAAATCTGCGGTTCTCCA 58.808 43.478 0.00 0.00 0.00 3.86
164 165 4.584874 TGATAAAATCTGCGGTTCTCCAA 58.415 39.130 0.00 0.00 0.00 3.53
165 166 5.192927 TGATAAAATCTGCGGTTCTCCAAT 58.807 37.500 0.00 0.00 0.00 3.16
166 167 5.652014 TGATAAAATCTGCGGTTCTCCAATT 59.348 36.000 0.00 0.00 0.00 2.32
167 168 4.440839 AAAATCTGCGGTTCTCCAATTC 57.559 40.909 0.00 0.00 0.00 2.17
168 169 3.356529 AATCTGCGGTTCTCCAATTCT 57.643 42.857 0.00 0.00 0.00 2.40
169 170 2.859165 TCTGCGGTTCTCCAATTCTT 57.141 45.000 0.00 0.00 0.00 2.52
170 171 2.699954 TCTGCGGTTCTCCAATTCTTC 58.300 47.619 0.00 0.00 0.00 2.87
171 172 2.038426 TCTGCGGTTCTCCAATTCTTCA 59.962 45.455 0.00 0.00 0.00 3.02
172 173 3.012518 CTGCGGTTCTCCAATTCTTCAT 58.987 45.455 0.00 0.00 0.00 2.57
173 174 3.009723 TGCGGTTCTCCAATTCTTCATC 58.990 45.455 0.00 0.00 0.00 2.92
174 175 2.356069 GCGGTTCTCCAATTCTTCATCC 59.644 50.000 0.00 0.00 0.00 3.51
175 176 3.609853 CGGTTCTCCAATTCTTCATCCA 58.390 45.455 0.00 0.00 0.00 3.41
176 177 4.202441 CGGTTCTCCAATTCTTCATCCAT 58.798 43.478 0.00 0.00 0.00 3.41
177 178 4.641989 CGGTTCTCCAATTCTTCATCCATT 59.358 41.667 0.00 0.00 0.00 3.16
178 179 5.449588 CGGTTCTCCAATTCTTCATCCATTG 60.450 44.000 0.00 0.00 0.00 2.82
179 180 5.653769 GGTTCTCCAATTCTTCATCCATTGA 59.346 40.000 0.00 0.00 30.66 2.57
180 181 6.183360 GGTTCTCCAATTCTTCATCCATTGAG 60.183 42.308 0.00 0.00 35.27 3.02
181 182 6.317663 TCTCCAATTCTTCATCCATTGAGA 57.682 37.500 0.00 0.00 35.27 3.27
182 183 6.907961 TCTCCAATTCTTCATCCATTGAGAT 58.092 36.000 0.00 0.00 35.27 2.75
183 184 7.351952 TCTCCAATTCTTCATCCATTGAGATT 58.648 34.615 0.00 0.00 35.27 2.40
184 185 7.284716 TCTCCAATTCTTCATCCATTGAGATTG 59.715 37.037 0.00 0.00 35.27 2.67
185 186 6.893554 TCCAATTCTTCATCCATTGAGATTGT 59.106 34.615 0.00 0.00 35.27 2.71
186 187 7.398047 TCCAATTCTTCATCCATTGAGATTGTT 59.602 33.333 0.00 0.00 35.27 2.83
187 188 7.705325 CCAATTCTTCATCCATTGAGATTGTTC 59.295 37.037 0.00 0.00 35.27 3.18
188 189 6.764308 TTCTTCATCCATTGAGATTGTTCC 57.236 37.500 0.00 0.00 35.27 3.62
189 190 5.818887 TCTTCATCCATTGAGATTGTTCCA 58.181 37.500 0.00 0.00 35.27 3.53
190 191 6.429151 TCTTCATCCATTGAGATTGTTCCAT 58.571 36.000 0.00 0.00 35.27 3.41
191 192 6.544931 TCTTCATCCATTGAGATTGTTCCATC 59.455 38.462 0.00 0.00 35.27 3.51
192 193 6.009908 TCATCCATTGAGATTGTTCCATCT 57.990 37.500 0.00 0.00 0.00 2.90
193 194 5.826208 TCATCCATTGAGATTGTTCCATCTG 59.174 40.000 0.00 0.00 0.00 2.90
194 195 3.949754 TCCATTGAGATTGTTCCATCTGC 59.050 43.478 0.00 0.00 0.00 4.26
195 196 3.697542 CCATTGAGATTGTTCCATCTGCA 59.302 43.478 0.00 0.00 0.00 4.41
196 197 4.439700 CCATTGAGATTGTTCCATCTGCAC 60.440 45.833 0.00 0.00 0.00 4.57
197 198 2.715046 TGAGATTGTTCCATCTGCACC 58.285 47.619 0.00 0.00 0.00 5.01
198 199 2.040145 TGAGATTGTTCCATCTGCACCA 59.960 45.455 0.00 0.00 0.00 4.17
199 200 2.421424 GAGATTGTTCCATCTGCACCAC 59.579 50.000 0.00 0.00 0.00 4.16
200 201 2.161855 GATTGTTCCATCTGCACCACA 58.838 47.619 0.00 0.00 0.00 4.17
201 202 1.317613 TTGTTCCATCTGCACCACAC 58.682 50.000 0.00 0.00 0.00 3.82
202 203 0.884259 TGTTCCATCTGCACCACACG 60.884 55.000 0.00 0.00 0.00 4.49
203 204 0.602638 GTTCCATCTGCACCACACGA 60.603 55.000 0.00 0.00 0.00 4.35
204 205 0.320683 TTCCATCTGCACCACACGAG 60.321 55.000 0.00 0.00 0.00 4.18
205 206 1.004560 CCATCTGCACCACACGAGT 60.005 57.895 0.00 0.00 0.00 4.18
206 207 1.293963 CCATCTGCACCACACGAGTG 61.294 60.000 5.96 5.96 45.47 3.51
241 242 9.535878 AAAAACAACAACATTAATACACGGATT 57.464 25.926 0.00 0.00 0.00 3.01
252 253 9.458374 CATTAATACACGGATTAATTGTTTCCC 57.542 33.333 4.76 0.00 39.09 3.97
253 254 8.577048 TTAATACACGGATTAATTGTTTCCCA 57.423 30.769 0.00 0.00 0.00 4.37
254 255 7.469537 AATACACGGATTAATTGTTTCCCAA 57.530 32.000 0.00 0.00 37.49 4.12
255 256 5.793030 ACACGGATTAATTGTTTCCCAAA 57.207 34.783 0.00 0.00 36.44 3.28
256 257 5.778862 ACACGGATTAATTGTTTCCCAAAG 58.221 37.500 0.00 0.00 36.44 2.77
257 258 5.536916 ACACGGATTAATTGTTTCCCAAAGA 59.463 36.000 0.00 0.00 36.44 2.52
258 259 6.210584 ACACGGATTAATTGTTTCCCAAAGAT 59.789 34.615 0.00 0.00 36.44 2.40
259 260 6.531240 CACGGATTAATTGTTTCCCAAAGATG 59.469 38.462 0.00 0.00 36.44 2.90
260 261 5.519927 CGGATTAATTGTTTCCCAAAGATGC 59.480 40.000 0.00 0.00 36.44 3.91
261 262 6.405538 GGATTAATTGTTTCCCAAAGATGCA 58.594 36.000 0.00 0.00 36.44 3.96
262 263 7.049754 GGATTAATTGTTTCCCAAAGATGCAT 58.950 34.615 0.00 0.00 36.44 3.96
263 264 7.011669 GGATTAATTGTTTCCCAAAGATGCATG 59.988 37.037 2.46 0.00 36.44 4.06
264 265 2.747396 TGTTTCCCAAAGATGCATGC 57.253 45.000 11.82 11.82 0.00 4.06
265 266 1.969208 TGTTTCCCAAAGATGCATGCA 59.031 42.857 25.04 25.04 0.00 3.96
266 267 2.568062 TGTTTCCCAAAGATGCATGCAT 59.432 40.909 32.66 32.66 39.69 3.96
267 268 3.768215 TGTTTCCCAAAGATGCATGCATA 59.232 39.130 32.27 13.00 36.70 3.14
268 269 4.222366 TGTTTCCCAAAGATGCATGCATAA 59.778 37.500 32.27 18.19 36.70 1.90
269 270 5.177326 GTTTCCCAAAGATGCATGCATAAA 58.823 37.500 32.27 22.55 36.70 1.40
270 271 5.617528 TTCCCAAAGATGCATGCATAAAT 57.382 34.783 32.27 18.51 36.70 1.40
271 272 5.204409 TCCCAAAGATGCATGCATAAATC 57.796 39.130 32.27 20.87 36.70 2.17
272 273 4.650131 TCCCAAAGATGCATGCATAAATCA 59.350 37.500 32.27 11.09 36.70 2.57
273 274 4.748102 CCCAAAGATGCATGCATAAATCAC 59.252 41.667 32.27 18.63 36.70 3.06
274 275 5.353111 CCAAAGATGCATGCATAAATCACA 58.647 37.500 32.27 1.53 36.70 3.58
275 276 5.813157 CCAAAGATGCATGCATAAATCACAA 59.187 36.000 32.27 0.68 36.70 3.33
276 277 6.019075 CCAAAGATGCATGCATAAATCACAAG 60.019 38.462 32.27 14.63 36.70 3.16
277 278 5.196341 AGATGCATGCATAAATCACAAGG 57.804 39.130 32.27 0.00 36.70 3.61
316 317 9.553064 CTATAATGAAGCTATCAAACTCACCTT 57.447 33.333 0.00 0.00 42.54 3.50
367 369 1.470979 GCCGTTCGATCTGCCTTTCTA 60.471 52.381 0.00 0.00 0.00 2.10
376 378 2.106332 GCCTTTCTAGCGCGCCTA 59.894 61.111 30.33 17.98 0.00 3.93
647 649 2.737180 CCTCGATCCCCACCATCG 59.263 66.667 0.00 0.00 43.77 3.84
811 3235 2.780643 CGTAGGTCGTCTTCGCGA 59.219 61.111 3.71 3.71 38.68 5.87
814 3238 0.098376 GTAGGTCGTCTTCGCGATGT 59.902 55.000 19.92 4.14 43.07 3.06
820 3244 2.434185 TCTTCGCGATGTGGGTGC 60.434 61.111 19.92 0.00 0.00 5.01
958 6380 4.056125 CTCGCTCACCTGTCGGCA 62.056 66.667 0.00 0.00 0.00 5.69
1341 7051 5.821470 AGAATCAGTTGATGCTATTGACCAG 59.179 40.000 0.56 0.00 38.65 4.00
1429 7143 6.869913 CAGCCATTGTTGTTAGATTGATGTTT 59.130 34.615 0.00 0.00 0.00 2.83
1523 7237 7.079475 TGTTGCATAATGATATTGATTCTGCG 58.921 34.615 11.14 0.00 36.30 5.18
1676 7392 1.548357 GCTCACCTGAAGCTCCCTCA 61.548 60.000 0.00 0.00 0.00 3.86
1715 7431 3.513912 ACCCATTCGATCTACACAAGTCA 59.486 43.478 0.00 0.00 0.00 3.41
1754 7700 3.930848 CCGGACGTTAGATTTTTACTGCT 59.069 43.478 0.00 0.00 0.00 4.24
1758 7704 7.360269 CCGGACGTTAGATTTTTACTGCTTTTA 60.360 37.037 0.00 0.00 0.00 1.52
1848 10423 0.534203 TTTCGTTGGGTGAGCCTGTC 60.534 55.000 1.06 0.00 34.45 3.51
1873 10448 2.799502 CGTCGCACGTCATGTCGT 60.800 61.111 12.25 12.25 45.10 4.34
1882 10457 0.179197 CGTCATGTCGTACGCTGACT 60.179 55.000 27.26 6.79 37.26 3.41
1893 10477 2.658593 GCTGACTGCGTCGTGTGT 60.659 61.111 0.00 0.00 34.95 3.72
1976 10861 0.037326 TGGTCTCGCAATGACAGGTC 60.037 55.000 0.00 0.00 36.26 3.85
2369 11440 5.482163 TCTGTGATTGTACTCAATGGTGA 57.518 39.130 0.00 0.00 43.33 4.02
2556 11627 6.238869 CCTCTGATTCAATGTCTGACGATCTA 60.239 42.308 2.98 0.00 32.21 1.98
2612 11683 2.930950 TGGTGAAGAAGAACAAGGTGG 58.069 47.619 0.00 0.00 0.00 4.61
3238 12336 5.341617 GTTTTGTTGGTCAAATCCGTTACA 58.658 37.500 0.00 0.00 44.15 2.41
3250 12348 6.315144 TCAAATCCGTTACATGTATGTCCTTG 59.685 38.462 6.36 7.00 41.97 3.61
3338 12436 9.807649 TCGTACTAAAGTAATCTAAAATGGTCC 57.192 33.333 0.00 0.00 31.52 4.46
3703 12844 0.476338 TCCTGTTAGCCCAAGTGCAA 59.524 50.000 0.00 0.00 0.00 4.08
3860 13102 6.903883 ATGCAACTACTTATTCAGGTTACG 57.096 37.500 0.00 0.00 0.00 3.18
4190 13443 2.549064 TCTGTCGATAATGCCCATGG 57.451 50.000 4.14 4.14 0.00 3.66
4541 13802 8.927675 TTATTGTGTCACCTATGTTTACCTTT 57.072 30.769 0.00 0.00 0.00 3.11
4542 13803 6.627395 TTGTGTCACCTATGTTTACCTTTG 57.373 37.500 0.00 0.00 0.00 2.77
4971 14257 4.703379 ATTGTGCAATTTCCCTTTTCCA 57.297 36.364 0.00 0.00 0.00 3.53
4973 14259 3.802866 TGTGCAATTTCCCTTTTCCAAC 58.197 40.909 0.00 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.135257 CCAGTGGCACTTAGTCTCTCG 60.135 57.143 19.43 2.95 0.00 4.04
1 2 2.094442 GTCCAGTGGCACTTAGTCTCTC 60.094 54.545 19.43 0.00 0.00 3.20
2 3 1.896465 GTCCAGTGGCACTTAGTCTCT 59.104 52.381 19.43 0.00 0.00 3.10
4 5 1.717032 TGTCCAGTGGCACTTAGTCT 58.283 50.000 19.43 0.00 0.00 3.24
5 6 2.234908 AGATGTCCAGTGGCACTTAGTC 59.765 50.000 19.43 10.74 0.00 2.59
7 8 3.265791 GAAGATGTCCAGTGGCACTTAG 58.734 50.000 19.43 12.79 0.00 2.18
8 9 2.637382 TGAAGATGTCCAGTGGCACTTA 59.363 45.455 19.43 6.36 0.00 2.24
9 10 1.421268 TGAAGATGTCCAGTGGCACTT 59.579 47.619 19.43 2.22 0.00 3.16
10 11 1.059098 TGAAGATGTCCAGTGGCACT 58.941 50.000 15.88 15.88 0.00 4.40
11 12 1.537202 GTTGAAGATGTCCAGTGGCAC 59.463 52.381 10.29 10.29 0.00 5.01
12 13 1.421268 AGTTGAAGATGTCCAGTGGCA 59.579 47.619 3.51 6.52 0.00 4.92
13 14 2.191128 AGTTGAAGATGTCCAGTGGC 57.809 50.000 3.51 0.00 0.00 5.01
14 15 3.499918 GTGAAGTTGAAGATGTCCAGTGG 59.500 47.826 1.40 1.40 0.00 4.00
15 16 3.185188 CGTGAAGTTGAAGATGTCCAGTG 59.815 47.826 0.00 0.00 0.00 3.66
16 17 3.181465 ACGTGAAGTTGAAGATGTCCAGT 60.181 43.478 0.00 0.00 0.00 4.00
17 18 3.185188 CACGTGAAGTTGAAGATGTCCAG 59.815 47.826 10.90 0.00 0.00 3.86
18 19 3.130633 CACGTGAAGTTGAAGATGTCCA 58.869 45.455 10.90 0.00 0.00 4.02
19 20 3.184581 GTCACGTGAAGTTGAAGATGTCC 59.815 47.826 21.95 0.00 0.00 4.02
20 21 4.051922 AGTCACGTGAAGTTGAAGATGTC 58.948 43.478 21.95 2.64 0.00 3.06
21 22 4.060038 AGTCACGTGAAGTTGAAGATGT 57.940 40.909 21.95 0.00 0.00 3.06
22 23 5.200454 CAAAGTCACGTGAAGTTGAAGATG 58.800 41.667 26.81 13.36 0.00 2.90
23 24 4.876107 ACAAAGTCACGTGAAGTTGAAGAT 59.124 37.500 32.89 17.64 0.00 2.40
24 25 4.250464 ACAAAGTCACGTGAAGTTGAAGA 58.750 39.130 32.89 6.59 0.00 2.87
25 26 4.600012 ACAAAGTCACGTGAAGTTGAAG 57.400 40.909 32.89 20.06 0.00 3.02
26 27 6.314152 TCAATACAAAGTCACGTGAAGTTGAA 59.686 34.615 32.89 16.61 0.00 2.69
27 28 5.813157 TCAATACAAAGTCACGTGAAGTTGA 59.187 36.000 32.89 23.87 0.00 3.18
28 29 5.901884 GTCAATACAAAGTCACGTGAAGTTG 59.098 40.000 28.08 28.08 0.00 3.16
29 30 5.583061 TGTCAATACAAAGTCACGTGAAGTT 59.417 36.000 21.95 14.07 30.91 2.66
30 31 5.006358 GTGTCAATACAAAGTCACGTGAAGT 59.994 40.000 21.95 17.84 37.36 3.01
31 32 5.006261 TGTGTCAATACAAAGTCACGTGAAG 59.994 40.000 21.95 12.92 37.36 3.02
32 33 4.870991 TGTGTCAATACAAAGTCACGTGAA 59.129 37.500 21.95 3.40 37.36 3.18
33 34 4.434520 TGTGTCAATACAAAGTCACGTGA 58.565 39.130 15.76 15.76 37.36 4.35
34 35 4.787381 TGTGTCAATACAAAGTCACGTG 57.213 40.909 9.94 9.94 37.36 4.49
35 36 5.525745 TGATTGTGTCAATACAAAGTCACGT 59.474 36.000 0.00 0.00 43.13 4.49
36 37 5.984627 TGATTGTGTCAATACAAAGTCACG 58.015 37.500 0.00 0.00 43.13 4.35
37 38 6.959361 ACTGATTGTGTCAATACAAAGTCAC 58.041 36.000 0.00 0.00 43.13 3.67
38 39 7.713073 TGTACTGATTGTGTCAATACAAAGTCA 59.287 33.333 0.00 0.00 44.07 3.41
39 40 8.083462 TGTACTGATTGTGTCAATACAAAGTC 57.917 34.615 0.00 0.00 44.07 3.01
45 46 6.593770 TGTCCATGTACTGATTGTGTCAATAC 59.406 38.462 0.00 0.00 39.40 1.89
46 47 6.593770 GTGTCCATGTACTGATTGTGTCAATA 59.406 38.462 0.00 0.00 36.14 1.90
47 48 5.412594 GTGTCCATGTACTGATTGTGTCAAT 59.587 40.000 0.00 0.00 36.14 2.57
48 49 4.754618 GTGTCCATGTACTGATTGTGTCAA 59.245 41.667 0.00 0.00 36.14 3.18
49 50 4.202305 TGTGTCCATGTACTGATTGTGTCA 60.202 41.667 0.00 0.00 35.05 3.58
50 51 4.314961 TGTGTCCATGTACTGATTGTGTC 58.685 43.478 0.00 0.00 0.00 3.67
51 52 4.318332 CTGTGTCCATGTACTGATTGTGT 58.682 43.478 0.00 0.00 0.00 3.72
52 53 3.686241 CCTGTGTCCATGTACTGATTGTG 59.314 47.826 0.00 0.00 0.00 3.33
53 54 3.582647 TCCTGTGTCCATGTACTGATTGT 59.417 43.478 0.00 0.00 0.00 2.71
54 55 4.206477 TCCTGTGTCCATGTACTGATTG 57.794 45.455 0.00 0.00 0.00 2.67
55 56 4.225942 ACATCCTGTGTCCATGTACTGATT 59.774 41.667 0.00 0.00 35.77 2.57
56 57 3.776969 ACATCCTGTGTCCATGTACTGAT 59.223 43.478 0.00 0.00 35.77 2.90
57 58 3.173151 ACATCCTGTGTCCATGTACTGA 58.827 45.455 0.00 0.00 35.77 3.41
58 59 3.616956 ACATCCTGTGTCCATGTACTG 57.383 47.619 0.00 0.00 35.77 2.74
59 60 5.163301 GGATTACATCCTGTGTCCATGTACT 60.163 44.000 0.00 0.00 46.19 2.73
60 61 5.057149 GGATTACATCCTGTGTCCATGTAC 58.943 45.833 0.00 0.00 46.19 2.90
61 62 5.290493 GGATTACATCCTGTGTCCATGTA 57.710 43.478 0.00 0.00 46.19 2.29
62 63 4.156455 GGATTACATCCTGTGTCCATGT 57.844 45.455 0.00 0.00 46.19 3.21
73 74 2.254546 TGGTGATGCGGATTACATCC 57.745 50.000 13.63 0.00 42.68 3.51
74 75 4.516698 AGAATTGGTGATGCGGATTACATC 59.483 41.667 13.63 3.80 43.46 3.06
75 76 4.464008 AGAATTGGTGATGCGGATTACAT 58.536 39.130 13.63 0.00 0.00 2.29
76 77 3.876914 GAGAATTGGTGATGCGGATTACA 59.123 43.478 13.63 0.00 0.00 2.41
77 78 3.251004 GGAGAATTGGTGATGCGGATTAC 59.749 47.826 3.05 3.05 0.00 1.89
78 79 3.136443 AGGAGAATTGGTGATGCGGATTA 59.864 43.478 0.00 0.00 0.00 1.75
79 80 2.092212 AGGAGAATTGGTGATGCGGATT 60.092 45.455 0.00 0.00 0.00 3.01
80 81 1.492176 AGGAGAATTGGTGATGCGGAT 59.508 47.619 0.00 0.00 0.00 4.18
81 82 0.911769 AGGAGAATTGGTGATGCGGA 59.088 50.000 0.00 0.00 0.00 5.54
82 83 1.134280 AGAGGAGAATTGGTGATGCGG 60.134 52.381 0.00 0.00 0.00 5.69
83 84 2.322355 AGAGGAGAATTGGTGATGCG 57.678 50.000 0.00 0.00 0.00 4.73
84 85 3.760684 ACAAAGAGGAGAATTGGTGATGC 59.239 43.478 0.00 0.00 0.00 3.91
85 86 6.176183 AGTACAAAGAGGAGAATTGGTGATG 58.824 40.000 0.00 0.00 0.00 3.07
86 87 6.380079 AGTACAAAGAGGAGAATTGGTGAT 57.620 37.500 0.00 0.00 0.00 3.06
87 88 5.825593 AGTACAAAGAGGAGAATTGGTGA 57.174 39.130 0.00 0.00 0.00 4.02
88 89 6.486657 TGAAAGTACAAAGAGGAGAATTGGTG 59.513 38.462 0.00 0.00 0.00 4.17
89 90 6.601332 TGAAAGTACAAAGAGGAGAATTGGT 58.399 36.000 0.00 0.00 0.00 3.67
90 91 6.348868 GCTGAAAGTACAAAGAGGAGAATTGG 60.349 42.308 0.00 0.00 35.30 3.16
91 92 6.348868 GGCTGAAAGTACAAAGAGGAGAATTG 60.349 42.308 0.00 0.00 35.30 2.32
92 93 5.707764 GGCTGAAAGTACAAAGAGGAGAATT 59.292 40.000 0.00 0.00 35.30 2.17
93 94 5.221925 TGGCTGAAAGTACAAAGAGGAGAAT 60.222 40.000 0.00 0.00 35.30 2.40
94 95 4.102524 TGGCTGAAAGTACAAAGAGGAGAA 59.897 41.667 0.00 0.00 35.30 2.87
95 96 3.646162 TGGCTGAAAGTACAAAGAGGAGA 59.354 43.478 0.00 0.00 35.30 3.71
96 97 4.008074 TGGCTGAAAGTACAAAGAGGAG 57.992 45.455 0.00 0.00 35.30 3.69
97 98 4.431416 TTGGCTGAAAGTACAAAGAGGA 57.569 40.909 0.00 0.00 35.30 3.71
98 99 5.712152 ATTTGGCTGAAAGTACAAAGAGG 57.288 39.130 0.00 0.00 42.75 3.69
99 100 6.738114 TGAATTTGGCTGAAAGTACAAAGAG 58.262 36.000 0.00 0.00 42.75 2.85
100 101 6.707440 TGAATTTGGCTGAAAGTACAAAGA 57.293 33.333 0.00 0.00 42.75 2.52
101 102 7.147312 TCATGAATTTGGCTGAAAGTACAAAG 58.853 34.615 0.00 0.00 42.75 2.77
102 103 7.048629 TCATGAATTTGGCTGAAAGTACAAA 57.951 32.000 0.00 0.00 43.30 2.83
103 104 6.647334 TCATGAATTTGGCTGAAAGTACAA 57.353 33.333 0.00 0.00 35.30 2.41
104 105 6.265196 AGTTCATGAATTTGGCTGAAAGTACA 59.735 34.615 12.12 0.00 35.30 2.90
105 106 6.681777 AGTTCATGAATTTGGCTGAAAGTAC 58.318 36.000 12.12 0.00 35.30 2.73
106 107 6.716628 AGAGTTCATGAATTTGGCTGAAAGTA 59.283 34.615 12.12 0.00 35.30 2.24
107 108 5.537674 AGAGTTCATGAATTTGGCTGAAAGT 59.462 36.000 12.12 0.00 35.30 2.66
108 109 5.862323 CAGAGTTCATGAATTTGGCTGAAAG 59.138 40.000 12.12 0.00 30.06 2.62
109 110 5.302568 ACAGAGTTCATGAATTTGGCTGAAA 59.697 36.000 18.87 0.00 30.06 2.69
110 111 4.828939 ACAGAGTTCATGAATTTGGCTGAA 59.171 37.500 18.87 0.00 0.00 3.02
111 112 4.401022 ACAGAGTTCATGAATTTGGCTGA 58.599 39.130 18.87 0.00 0.00 4.26
112 113 4.216902 TGACAGAGTTCATGAATTTGGCTG 59.783 41.667 12.12 12.90 0.00 4.85
113 114 4.401022 TGACAGAGTTCATGAATTTGGCT 58.599 39.130 12.12 3.15 0.00 4.75
114 115 4.771590 TGACAGAGTTCATGAATTTGGC 57.228 40.909 12.12 12.64 0.00 4.52
123 124 2.303890 TCAGTGGCATGACAGAGTTCAT 59.696 45.455 0.00 0.00 36.62 2.57
124 125 1.693606 TCAGTGGCATGACAGAGTTCA 59.306 47.619 0.00 0.00 0.00 3.18
125 126 2.462456 TCAGTGGCATGACAGAGTTC 57.538 50.000 0.00 0.00 0.00 3.01
126 127 4.558226 TTATCAGTGGCATGACAGAGTT 57.442 40.909 0.00 0.00 30.46 3.01
127 128 4.558226 TTTATCAGTGGCATGACAGAGT 57.442 40.909 0.00 0.00 30.46 3.24
128 129 5.821470 AGATTTTATCAGTGGCATGACAGAG 59.179 40.000 0.00 0.00 30.46 3.35
129 130 5.587443 CAGATTTTATCAGTGGCATGACAGA 59.413 40.000 0.00 0.00 30.46 3.41
130 131 5.732528 GCAGATTTTATCAGTGGCATGACAG 60.733 44.000 0.00 0.00 30.46 3.51
131 132 4.096833 GCAGATTTTATCAGTGGCATGACA 59.903 41.667 0.00 0.00 30.46 3.58
132 133 4.604976 GCAGATTTTATCAGTGGCATGAC 58.395 43.478 0.00 0.00 30.46 3.06
133 134 3.313249 CGCAGATTTTATCAGTGGCATGA 59.687 43.478 0.00 0.00 0.00 3.07
134 135 3.549423 CCGCAGATTTTATCAGTGGCATG 60.549 47.826 0.00 0.00 39.16 4.06
135 136 2.620115 CCGCAGATTTTATCAGTGGCAT 59.380 45.455 0.00 0.00 39.16 4.40
136 137 2.016318 CCGCAGATTTTATCAGTGGCA 58.984 47.619 0.00 0.00 39.16 4.92
137 138 2.017049 ACCGCAGATTTTATCAGTGGC 58.983 47.619 10.45 0.00 46.66 5.01
139 140 4.034510 GGAGAACCGCAGATTTTATCAGTG 59.965 45.833 0.00 0.00 0.00 3.66
140 141 4.192317 GGAGAACCGCAGATTTTATCAGT 58.808 43.478 0.00 0.00 0.00 3.41
141 142 4.191544 TGGAGAACCGCAGATTTTATCAG 58.808 43.478 0.00 0.00 39.42 2.90
142 143 4.214986 TGGAGAACCGCAGATTTTATCA 57.785 40.909 0.00 0.00 39.42 2.15
143 144 5.757850 ATTGGAGAACCGCAGATTTTATC 57.242 39.130 0.00 0.00 39.42 1.75
144 145 5.888161 AGAATTGGAGAACCGCAGATTTTAT 59.112 36.000 0.00 0.00 39.42 1.40
145 146 5.253330 AGAATTGGAGAACCGCAGATTTTA 58.747 37.500 0.00 0.00 39.42 1.52
146 147 4.082125 AGAATTGGAGAACCGCAGATTTT 58.918 39.130 0.00 0.00 39.42 1.82
147 148 3.690460 AGAATTGGAGAACCGCAGATTT 58.310 40.909 0.00 0.00 39.42 2.17
148 149 3.356529 AGAATTGGAGAACCGCAGATT 57.643 42.857 0.00 0.00 39.42 2.40
149 150 3.274288 GAAGAATTGGAGAACCGCAGAT 58.726 45.455 0.00 0.00 39.42 2.90
150 151 2.038426 TGAAGAATTGGAGAACCGCAGA 59.962 45.455 0.00 0.00 39.42 4.26
151 152 2.426522 TGAAGAATTGGAGAACCGCAG 58.573 47.619 0.00 0.00 39.42 5.18
152 153 2.559698 TGAAGAATTGGAGAACCGCA 57.440 45.000 0.00 0.00 39.42 5.69
153 154 2.356069 GGATGAAGAATTGGAGAACCGC 59.644 50.000 0.00 0.00 39.42 5.68
154 155 3.609853 TGGATGAAGAATTGGAGAACCG 58.390 45.455 0.00 0.00 39.42 4.44
155 156 5.653769 TCAATGGATGAAGAATTGGAGAACC 59.346 40.000 0.00 0.00 34.30 3.62
156 157 6.600822 TCTCAATGGATGAAGAATTGGAGAAC 59.399 38.462 0.00 0.00 37.67 3.01
157 158 6.724351 TCTCAATGGATGAAGAATTGGAGAA 58.276 36.000 0.00 0.00 37.67 2.87
158 159 6.317663 TCTCAATGGATGAAGAATTGGAGA 57.682 37.500 0.00 0.00 37.67 3.71
159 160 7.068348 ACAATCTCAATGGATGAAGAATTGGAG 59.932 37.037 0.00 0.00 37.11 3.86
160 161 6.893554 ACAATCTCAATGGATGAAGAATTGGA 59.106 34.615 0.00 0.00 37.11 3.53
161 162 7.108841 ACAATCTCAATGGATGAAGAATTGG 57.891 36.000 0.00 0.00 37.11 3.16
162 163 7.705325 GGAACAATCTCAATGGATGAAGAATTG 59.295 37.037 0.00 0.00 37.67 2.32
163 164 7.398047 TGGAACAATCTCAATGGATGAAGAATT 59.602 33.333 0.00 0.00 33.59 2.17
164 165 6.893554 TGGAACAATCTCAATGGATGAAGAAT 59.106 34.615 0.00 0.00 33.59 2.40
165 166 6.247676 TGGAACAATCTCAATGGATGAAGAA 58.752 36.000 0.00 0.00 33.59 2.52
166 167 5.818887 TGGAACAATCTCAATGGATGAAGA 58.181 37.500 0.00 0.00 33.59 2.87
184 185 0.602638 TCGTGTGGTGCAGATGGAAC 60.603 55.000 0.00 0.00 0.00 3.62
185 186 0.320683 CTCGTGTGGTGCAGATGGAA 60.321 55.000 0.00 0.00 0.00 3.53
186 187 1.293179 CTCGTGTGGTGCAGATGGA 59.707 57.895 0.00 0.00 0.00 3.41
187 188 1.004560 ACTCGTGTGGTGCAGATGG 60.005 57.895 0.00 0.00 0.00 3.51
188 189 2.156542 CACTCGTGTGGTGCAGATG 58.843 57.895 9.74 0.00 40.33 2.90
189 190 4.681421 CACTCGTGTGGTGCAGAT 57.319 55.556 9.74 0.00 40.33 2.90
215 216 9.535878 AATCCGTGTATTAATGTTGTTGTTTTT 57.464 25.926 0.00 0.00 0.00 1.94
226 227 9.458374 GGGAAACAATTAATCCGTGTATTAATG 57.542 33.333 0.00 6.08 39.82 1.90
227 228 9.191479 TGGGAAACAATTAATCCGTGTATTAAT 57.809 29.630 0.00 0.00 41.57 1.40
228 229 8.577048 TGGGAAACAATTAATCCGTGTATTAA 57.423 30.769 0.00 0.00 36.15 1.40
229 230 8.577048 TTGGGAAACAATTAATCCGTGTATTA 57.423 30.769 0.00 0.00 33.18 0.98
230 231 7.469537 TTGGGAAACAATTAATCCGTGTATT 57.530 32.000 0.00 0.00 33.18 1.89
231 232 7.394923 TCTTTGGGAAACAATTAATCCGTGTAT 59.605 33.333 0.00 0.00 39.21 2.29
232 233 6.715718 TCTTTGGGAAACAATTAATCCGTGTA 59.284 34.615 0.00 0.00 39.21 2.90
233 234 5.536916 TCTTTGGGAAACAATTAATCCGTGT 59.463 36.000 0.00 0.00 39.21 4.49
234 235 6.019779 TCTTTGGGAAACAATTAATCCGTG 57.980 37.500 0.00 0.00 39.21 4.94
235 236 6.630071 CATCTTTGGGAAACAATTAATCCGT 58.370 36.000 0.00 0.00 39.21 4.69
236 237 5.519927 GCATCTTTGGGAAACAATTAATCCG 59.480 40.000 0.00 0.00 39.21 4.18
237 238 6.405538 TGCATCTTTGGGAAACAATTAATCC 58.594 36.000 0.00 0.00 39.21 3.01
238 239 7.466320 GCATGCATCTTTGGGAAACAATTAATC 60.466 37.037 14.21 0.00 39.21 1.75
239 240 6.316890 GCATGCATCTTTGGGAAACAATTAAT 59.683 34.615 14.21 0.00 39.21 1.40
240 241 5.642919 GCATGCATCTTTGGGAAACAATTAA 59.357 36.000 14.21 0.00 39.21 1.40
241 242 5.177326 GCATGCATCTTTGGGAAACAATTA 58.823 37.500 14.21 0.00 39.21 1.40
242 243 4.004982 GCATGCATCTTTGGGAAACAATT 58.995 39.130 14.21 0.00 39.21 2.32
243 244 3.008157 TGCATGCATCTTTGGGAAACAAT 59.992 39.130 18.46 0.00 39.21 2.71
244 245 2.367894 TGCATGCATCTTTGGGAAACAA 59.632 40.909 18.46 0.00 37.28 2.83
245 246 1.969208 TGCATGCATCTTTGGGAAACA 59.031 42.857 18.46 0.00 0.00 2.83
246 247 2.747396 TGCATGCATCTTTGGGAAAC 57.253 45.000 18.46 0.00 0.00 2.78
247 248 5.417754 TTTATGCATGCATCTTTGGGAAA 57.582 34.783 35.35 23.89 37.82 3.13
248 249 5.128991 TGATTTATGCATGCATCTTTGGGAA 59.871 36.000 35.35 19.66 37.82 3.97
249 250 4.650131 TGATTTATGCATGCATCTTTGGGA 59.350 37.500 35.35 14.61 37.82 4.37
250 251 4.748102 GTGATTTATGCATGCATCTTTGGG 59.252 41.667 35.35 0.00 37.82 4.12
251 252 5.353111 TGTGATTTATGCATGCATCTTTGG 58.647 37.500 35.35 0.00 37.82 3.28
252 253 6.019075 CCTTGTGATTTATGCATGCATCTTTG 60.019 38.462 35.35 16.07 37.82 2.77
253 254 6.046593 CCTTGTGATTTATGCATGCATCTTT 58.953 36.000 35.35 20.68 37.82 2.52
254 255 5.128171 ACCTTGTGATTTATGCATGCATCTT 59.872 36.000 35.35 21.04 37.82 2.40
255 256 4.647853 ACCTTGTGATTTATGCATGCATCT 59.352 37.500 35.35 21.24 37.82 2.90
256 257 4.940463 ACCTTGTGATTTATGCATGCATC 58.060 39.130 35.35 22.66 37.82 3.91
257 258 5.347620 AACCTTGTGATTTATGCATGCAT 57.652 34.783 33.92 33.92 40.19 3.96
258 259 4.804868 AACCTTGTGATTTATGCATGCA 57.195 36.364 25.04 25.04 0.00 3.96
259 260 7.775397 ATAAAACCTTGTGATTTATGCATGC 57.225 32.000 11.82 11.82 30.29 4.06
316 317 0.250234 CAATCGAGGGAGCCTTGTGA 59.750 55.000 0.00 0.00 36.45 3.58
329 330 1.509463 CCGACGAACCTCCAATCGA 59.491 57.895 0.00 0.00 41.43 3.59
367 369 3.204827 CAATGGCTTAGGCGCGCT 61.205 61.111 32.29 19.12 39.81 5.92
376 378 2.097825 GCTGTGAAGATCCAATGGCTT 58.902 47.619 0.00 0.00 0.00 4.35
458 460 3.977244 CCAGCCAACCAACGTGCC 61.977 66.667 0.00 0.00 0.00 5.01
647 649 4.828925 GGCTGCTGGCGAGGAGAC 62.829 72.222 21.20 14.94 40.04 3.36
811 3235 1.526887 CCTACATCCGCACCCACAT 59.473 57.895 0.00 0.00 0.00 3.21
814 3238 3.087253 CCCCTACATCCGCACCCA 61.087 66.667 0.00 0.00 0.00 4.51
820 3244 1.329256 CTACACCTCCCCTACATCCG 58.671 60.000 0.00 0.00 0.00 4.18
894 6316 0.387565 GGATCGCTCACCTTCTCCTC 59.612 60.000 0.00 0.00 0.00 3.71
1070 6537 1.138661 GATGAGCTCCTGGTTCCTCTG 59.861 57.143 12.15 0.00 0.00 3.35
1341 7051 5.179555 AGGAACTGTAACAAAAATCGCTCTC 59.820 40.000 0.00 0.00 37.18 3.20
1429 7143 5.782893 CCAAACAAAGTGGTAATCAAGGA 57.217 39.130 0.00 0.00 0.00 3.36
1676 7392 6.017109 CGAATGGGTAGAATCGAATGGAAATT 60.017 38.462 0.00 0.00 37.48 1.82
1715 7431 2.358003 GCAGAGCAGCGTTGACCT 60.358 61.111 2.38 0.00 0.00 3.85
1754 7700 7.574217 GCCACGAAAGAACATCAGGTAATAAAA 60.574 37.037 0.00 0.00 0.00 1.52
1758 7704 3.689649 GCCACGAAAGAACATCAGGTAAT 59.310 43.478 0.00 0.00 0.00 1.89
1816 9584 1.396996 CAACGAAATCCAACCTAGCCG 59.603 52.381 0.00 0.00 0.00 5.52
1821 9589 1.144093 TCACCCAACGAAATCCAACCT 59.856 47.619 0.00 0.00 0.00 3.50
1882 10457 2.952264 CACGACACACACGACGCA 60.952 61.111 0.00 0.00 34.70 5.24
1893 10477 2.184020 CTCCATGGCTTCCCACGACA 62.184 60.000 6.96 0.00 45.77 4.35
2369 11440 2.104967 CAATGTCCATGGACCTGCAAT 58.895 47.619 36.27 22.50 43.97 3.56
2579 11650 6.533730 TCTTCTTCACCAAATTCTTCTGCTA 58.466 36.000 0.00 0.00 0.00 3.49
2786 11877 4.099573 ACATGGACAGTAGCACCTACATAC 59.900 45.833 0.00 0.00 39.22 2.39
2907 12005 8.947055 AAGTGCTTTGAAACATAGAATTTTGT 57.053 26.923 0.00 0.00 0.00 2.83
3314 12412 9.807649 TCGGACCATTTTAGATTACTTTAGTAC 57.192 33.333 0.00 0.00 0.00 2.73
3325 12423 8.483758 ACTACAACTATTCGGACCATTTTAGAT 58.516 33.333 0.00 0.00 0.00 1.98
3476 12617 7.123247 GGTACCAGTTAACTCCTATTGTGTCTA 59.877 40.741 7.15 0.00 0.00 2.59
3773 12915 5.306419 TCCATTGCTCTCTGATGTTATAGCT 59.694 40.000 0.00 0.00 0.00 3.32
3894 13136 5.239306 CACTCTCAAAAGGCACATTCAGTAA 59.761 40.000 0.00 0.00 0.00 2.24
4190 13443 9.826574 TGGTCAAACATACACTAAGAATATACC 57.173 33.333 0.00 0.00 0.00 2.73
4450 13711 8.455903 TGATGAATAAAGCTATCCCTCAAAAG 57.544 34.615 0.00 0.00 0.00 2.27
4541 13802 2.522836 TAGGCGACACCGTAAAAACA 57.477 45.000 0.00 0.00 46.52 2.83
4542 13803 2.738314 ACATAGGCGACACCGTAAAAAC 59.262 45.455 0.00 0.00 46.52 2.43
4953 14238 3.559655 GTGTTGGAAAAGGGAAATTGCAC 59.440 43.478 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.