Multiple sequence alignment - TraesCS5D01G561200

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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 TraesCS5D01G561200 chr5D 100.000 4953 0 0 1 4953 561894926 561899878 0.000000e+00 9147.0
1 TraesCS5D01G561200 chr5D 86.958 3067 328 35 949 3962 556541134 556538087 0.000000e+00 3382.0
2 TraesCS5D01G561200 chr5D 90.443 2595 184 32 1426 3961 561923650 561926239 0.000000e+00 3360.0
3 TraesCS5D01G561200 chr5D 92.498 2146 144 10 2576 4711 561643497 561641359 0.000000e+00 3055.0
4 TraesCS5D01G561200 chr5D 88.720 1977 188 18 1444 3385 552860752 552858776 0.000000e+00 2383.0
5 TraesCS5D01G561200 chr5D 91.118 957 56 17 3971 4920 561926315 561927249 0.000000e+00 1269.0
6 TraesCS5D01G561200 chr5D 83.761 351 41 7 976 1317 552861309 552860966 8.000000e-83 318.0
7 TraesCS5D01G561200 chr5D 87.500 288 18 4 1030 1317 551878547 551878816 2.880000e-82 316.0
8 TraesCS5D01G561200 chr5D 83.824 340 41 8 977 1315 561645345 561645019 1.340000e-80 311.0
9 TraesCS5D01G561200 chr5B 88.933 4012 351 35 965 4953 711930368 711934309 0.000000e+00 4863.0
10 TraesCS5D01G561200 chr5B 90.791 2530 219 9 1444 3961 711962260 711964787 0.000000e+00 3369.0
11 TraesCS5D01G561200 chr5B 90.734 1662 149 5 2217 3875 711736526 711738185 0.000000e+00 2211.0
12 TraesCS5D01G561200 chr5B 91.752 1370 108 3 2353 3718 711334774 711333406 0.000000e+00 1899.0
13 TraesCS5D01G561200 chr5B 87.118 1048 106 9 3877 4920 711738222 711739244 0.000000e+00 1160.0
14 TraesCS5D01G561200 chr5B 87.227 963 103 9 3971 4925 711333109 711332159 0.000000e+00 1079.0
15 TraesCS5D01G561200 chr5B 86.010 965 99 14 3971 4920 711350892 711349949 0.000000e+00 1002.0
16 TraesCS5D01G561200 chr5B 87.101 690 75 4 4238 4920 711406810 711406128 0.000000e+00 769.0
17 TraesCS5D01G561200 chr5B 87.324 639 79 2 3479 4117 711968299 711968935 0.000000e+00 730.0
18 TraesCS5D01G561200 chr5B 89.013 537 40 4 782 1317 712206532 712207050 0.000000e+00 647.0
19 TraesCS5D01G561200 chr5B 90.634 331 22 1 987 1317 711354091 711353770 9.850000e-117 431.0
20 TraesCS5D01G561200 chr5B 88.571 315 27 6 1000 1314 711414156 711413851 1.680000e-99 374.0
21 TraesCS5D01G561200 chr5B 86.293 321 40 4 999 1317 711961665 711961983 3.670000e-91 346.0
22 TraesCS5D01G561200 chr5B 84.861 251 34 4 365 613 712206168 712206416 2.960000e-62 250.0
23 TraesCS5D01G561200 chr5B 88.462 104 11 1 653 756 712206432 712206534 1.870000e-24 124.0
24 TraesCS5D01G561200 chr5B 97.222 36 1 0 580 615 542991356 542991391 1.490000e-05 62.1
25 TraesCS5D01G561200 chr5B 90.000 50 1 3 582 627 687805646 687805597 1.490000e-05 62.1
26 TraesCS5D01G561200 chr7B 88.637 3397 323 30 1566 4920 1305185 1308560 0.000000e+00 4076.0
27 TraesCS5D01G561200 chr7B 96.179 2486 71 9 71 2548 891942 889473 0.000000e+00 4043.0
28 TraesCS5D01G561200 chr7B 88.663 2558 239 24 1444 3960 1348513 1351060 0.000000e+00 3070.0
29 TraesCS5D01G561200 chr7B 87.975 948 101 7 3971 4916 1351137 1352073 0.000000e+00 1107.0
30 TraesCS5D01G561200 chr7B 86.709 948 105 8 3971 4915 883486 882557 0.000000e+00 1033.0
31 TraesCS5D01G561200 chr7B 86.709 948 105 8 3971 4915 887957 887028 0.000000e+00 1033.0
32 TraesCS5D01G561200 chr7B 83.673 980 115 16 3971 4920 1034448 1033484 0.000000e+00 881.0
33 TraesCS5D01G561200 chr7B 86.786 560 57 9 4403 4953 1101507 1100956 4.240000e-170 608.0
34 TraesCS5D01G561200 chr7B 83.178 321 42 6 999 1317 1103514 1103204 2.920000e-72 283.0
35 TraesCS5D01G561200 chr7B 92.683 41 1 2 582 620 704318544 704318504 1.930000e-04 58.4
36 TraesCS5D01G561200 chr4B 89.121 2537 253 16 1444 3961 656879439 656881971 0.000000e+00 3134.0
37 TraesCS5D01G561200 chr4B 92.941 85 6 0 446 530 116483345 116483429 1.870000e-24 124.0
38 TraesCS5D01G561200 chr4B 89.130 46 3 2 582 625 371968222 371968267 6.930000e-04 56.5
39 TraesCS5D01G561200 chr4D 89.082 2537 254 13 1444 3961 509854585 509852053 0.000000e+00 3129.0
40 TraesCS5D01G561200 chr5A 88.654 2415 234 28 1568 3964 698691992 698689600 0.000000e+00 2905.0
41 TraesCS5D01G561200 chr5A 89.706 68 5 2 295 360 538996794 538996861 8.830000e-13 86.1
42 TraesCS5D01G561200 chr1B 85.269 706 75 13 920 1624 594144359 594145036 0.000000e+00 701.0
43 TraesCS5D01G561200 chr1B 90.244 41 2 2 582 620 520879751 520879711 9.000000e-03 52.8
44 TraesCS5D01G561200 chr1A 85.142 599 49 18 1057 1654 535065705 535066264 1.200000e-160 577.0
45 TraesCS5D01G561200 chr1A 81.928 166 28 2 991 1155 549490661 549490825 6.690000e-29 139.0
46 TraesCS5D01G561200 chr1A 92.500 40 2 1 582 620 432251075 432251114 6.930000e-04 56.5
47 TraesCS5D01G561200 chr2D 83.221 149 21 4 218 362 50226874 50226726 3.110000e-27 134.0
48 TraesCS5D01G561200 chr2D 85.185 108 12 3 436 541 167566672 167566567 1.890000e-19 108.0
49 TraesCS5D01G561200 chr6B 91.765 85 7 0 446 530 453266625 453266709 8.710000e-23 119.0
50 TraesCS5D01G561200 chr6B 92.188 64 3 2 301 363 617281101 617281039 6.830000e-14 89.8
51 TraesCS5D01G561200 chr3D 87.755 98 12 0 433 530 108210734 108210831 1.130000e-21 115.0
52 TraesCS5D01G561200 chr3B 87.255 102 11 2 439 540 327059386 327059287 1.130000e-21 115.0
53 TraesCS5D01G561200 chr3B 82.258 124 20 2 243 364 2338418 2338541 6.780000e-19 106.0
54 TraesCS5D01G561200 chr3B 78.882 161 21 7 218 377 782993717 782993569 4.080000e-16 97.1
55 TraesCS5D01G561200 chr3B 85.393 89 12 1 275 362 816250816 816250728 1.900000e-14 91.6
56 TraesCS5D01G561200 chr3B 91.045 67 4 2 302 366 733334060 733333994 6.830000e-14 89.8
57 TraesCS5D01G561200 chr3A 86.111 108 12 3 439 543 467651287 467651394 4.050000e-21 113.0
58 TraesCS5D01G561200 chr3A 86.275 51 5 2 582 632 644678399 644678447 2.000000e-03 54.7
59 TraesCS5D01G561200 chr4A 85.981 107 9 6 439 542 665186504 665186401 5.240000e-20 110.0
60 TraesCS5D01G561200 chr6A 85.000 100 13 2 266 363 21514447 21514348 3.150000e-17 100.0
61 TraesCS5D01G561200 chr6A 89.362 47 2 3 583 627 549230399 549230354 6.930000e-04 56.5


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 TraesCS5D01G561200 chr5D 561894926 561899878 4952 False 9147.000000 9147 100.000000 1 4953 1 chr5D.!!$F2 4952
1 TraesCS5D01G561200 chr5D 556538087 556541134 3047 True 3382.000000 3382 86.958000 949 3962 1 chr5D.!!$R1 3013
2 TraesCS5D01G561200 chr5D 561923650 561927249 3599 False 2314.500000 3360 90.780500 1426 4920 2 chr5D.!!$F3 3494
3 TraesCS5D01G561200 chr5D 561641359 561645345 3986 True 1683.000000 3055 88.161000 977 4711 2 chr5D.!!$R3 3734
4 TraesCS5D01G561200 chr5D 552858776 552861309 2533 True 1350.500000 2383 86.240500 976 3385 2 chr5D.!!$R2 2409
5 TraesCS5D01G561200 chr5B 711930368 711934309 3941 False 4863.000000 4863 88.933000 965 4953 1 chr5B.!!$F2 3988
6 TraesCS5D01G561200 chr5B 711736526 711739244 2718 False 1685.500000 2211 88.926000 2217 4920 2 chr5B.!!$F3 2703
7 TraesCS5D01G561200 chr5B 711332159 711334774 2615 True 1489.000000 1899 89.489500 2353 4925 2 chr5B.!!$R4 2572
8 TraesCS5D01G561200 chr5B 711961665 711968935 7270 False 1481.666667 3369 88.136000 999 4117 3 chr5B.!!$F4 3118
9 TraesCS5D01G561200 chr5B 711406128 711406810 682 True 769.000000 769 87.101000 4238 4920 1 chr5B.!!$R2 682
10 TraesCS5D01G561200 chr5B 711349949 711354091 4142 True 716.500000 1002 88.322000 987 4920 2 chr5B.!!$R5 3933
11 TraesCS5D01G561200 chr5B 712206168 712207050 882 False 340.333333 647 87.445333 365 1317 3 chr5B.!!$F5 952
12 TraesCS5D01G561200 chr7B 1305185 1308560 3375 False 4076.000000 4076 88.637000 1566 4920 1 chr7B.!!$F1 3354
13 TraesCS5D01G561200 chr7B 1348513 1352073 3560 False 2088.500000 3070 88.319000 1444 4916 2 chr7B.!!$F2 3472
14 TraesCS5D01G561200 chr7B 882557 891942 9385 True 2036.333333 4043 89.865667 71 4915 3 chr7B.!!$R3 4844
15 TraesCS5D01G561200 chr7B 1033484 1034448 964 True 881.000000 881 83.673000 3971 4920 1 chr7B.!!$R1 949
16 TraesCS5D01G561200 chr7B 1100956 1103514 2558 True 445.500000 608 84.982000 999 4953 2 chr7B.!!$R4 3954
17 TraesCS5D01G561200 chr4B 656879439 656881971 2532 False 3134.000000 3134 89.121000 1444 3961 1 chr4B.!!$F3 2517
18 TraesCS5D01G561200 chr4D 509852053 509854585 2532 True 3129.000000 3129 89.082000 1444 3961 1 chr4D.!!$R1 2517
19 TraesCS5D01G561200 chr5A 698689600 698691992 2392 True 2905.000000 2905 88.654000 1568 3964 1 chr5A.!!$R1 2396
20 TraesCS5D01G561200 chr1B 594144359 594145036 677 False 701.000000 701 85.269000 920 1624 1 chr1B.!!$F1 704
21 TraesCS5D01G561200 chr1A 535065705 535066264 559 False 577.000000 577 85.142000 1057 1654 1 chr1A.!!$F2 597

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
27 28 0.041833 AGCTGCCACCTAGAGGAGAA 59.958 55.000 1.60 0.0 38.94 2.87 F
30 31 0.325671 TGCCACCTAGAGGAGAAGGG 60.326 60.000 1.60 0.0 37.18 3.95 F
35 36 0.325671 CCTAGAGGAGAAGGGGCACA 60.326 60.000 0.00 0.0 37.39 4.57 F
42 43 0.393537 GAGAAGGGGCACACCATCTG 60.394 60.000 0.50 0.0 42.91 2.90 F
821 824 0.464013 TTCCACCGGCGTCAAAAGAA 60.464 50.000 6.01 0.0 0.00 2.52 F
1050 1067 1.071471 CCTCGGCAAGGTGTTCACT 59.929 57.895 2.98 0.0 40.67 3.41 F
2637 3051 1.881973 TCTGCACAAGAATGCCTCAAC 59.118 47.619 0.00 0.0 45.50 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1237 1257 2.420890 CAGCAGATCCTCCGCCTC 59.579 66.667 0.00 0.00 0.00 4.70 R
1719 2058 7.227314 GTCCTTGCATCATTATACAGATGTTGA 59.773 37.037 12.66 0.00 42.72 3.18 R
2334 2712 8.571461 TCTTTAAAGATGGCATGATATCATCC 57.429 34.615 15.49 17.93 38.33 3.51 R
2610 3024 3.047796 GCATTCTTGTGCAGAAACACTG 58.952 45.455 0.00 0.00 45.06 3.66 R
2950 3394 3.689347 TCATTTCCCTGTCAATGTGAGG 58.311 45.455 0.00 0.00 32.96 3.86 R
3292 3739 3.951680 TCCTTCAGGTTCCTTTTCAACAC 59.048 43.478 0.00 0.00 36.34 3.32 R
3969 4422 0.165944 GGAACAAACCGTCGCATCTG 59.834 55.000 0.00 0.00 0.00 2.90 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
18 19 3.890527 CCTGAAATAGCTGCCACCT 57.109 52.632 0.00 0.00 0.00 4.00
20 21 2.843701 CCTGAAATAGCTGCCACCTAG 58.156 52.381 0.00 0.00 0.00 3.02
21 22 2.435805 CCTGAAATAGCTGCCACCTAGA 59.564 50.000 0.00 0.00 0.00 2.43
22 23 3.494048 CCTGAAATAGCTGCCACCTAGAG 60.494 52.174 0.00 0.00 0.00 2.43
23 24 2.435805 TGAAATAGCTGCCACCTAGAGG 59.564 50.000 0.00 0.00 42.17 3.69
24 25 2.478872 AATAGCTGCCACCTAGAGGA 57.521 50.000 1.60 0.00 38.94 3.71
25 26 2.008242 ATAGCTGCCACCTAGAGGAG 57.992 55.000 1.60 0.00 38.94 3.69
26 27 0.927029 TAGCTGCCACCTAGAGGAGA 59.073 55.000 1.60 0.00 38.94 3.71
27 28 0.041833 AGCTGCCACCTAGAGGAGAA 59.958 55.000 1.60 0.00 38.94 2.87
28 29 0.463620 GCTGCCACCTAGAGGAGAAG 59.536 60.000 1.60 0.00 38.94 2.85
29 30 1.118838 CTGCCACCTAGAGGAGAAGG 58.881 60.000 1.60 0.14 38.94 3.46
30 31 0.325671 TGCCACCTAGAGGAGAAGGG 60.326 60.000 1.60 0.00 37.18 3.95
31 32 1.051556 GCCACCTAGAGGAGAAGGGG 61.052 65.000 1.60 0.00 37.18 4.79
32 33 1.051556 CCACCTAGAGGAGAAGGGGC 61.052 65.000 1.60 0.00 34.72 5.80
33 34 0.325671 CACCTAGAGGAGAAGGGGCA 60.326 60.000 1.60 0.00 37.18 5.36
34 35 0.325765 ACCTAGAGGAGAAGGGGCAC 60.326 60.000 1.60 0.00 37.18 5.01
35 36 0.325671 CCTAGAGGAGAAGGGGCACA 60.326 60.000 0.00 0.00 37.39 4.57
36 37 0.827368 CTAGAGGAGAAGGGGCACAC 59.173 60.000 0.00 0.00 0.00 3.82
37 38 0.617820 TAGAGGAGAAGGGGCACACC 60.618 60.000 0.00 0.00 39.11 4.16
38 39 2.121963 AGGAGAAGGGGCACACCA 60.122 61.111 0.00 0.00 42.91 4.17
39 40 1.542375 AGGAGAAGGGGCACACCAT 60.542 57.895 0.00 0.00 42.91 3.55
40 41 1.077429 GGAGAAGGGGCACACCATC 60.077 63.158 0.00 0.00 42.91 3.51
41 42 1.566298 GGAGAAGGGGCACACCATCT 61.566 60.000 0.00 0.00 42.91 2.90
42 43 0.393537 GAGAAGGGGCACACCATCTG 60.394 60.000 0.50 0.00 42.91 2.90
43 44 2.036256 AAGGGGCACACCATCTGC 59.964 61.111 0.00 0.00 42.91 4.26
44 45 2.769652 GAAGGGGCACACCATCTGCA 62.770 60.000 0.00 0.00 42.91 4.41
45 46 2.283101 GGGGCACACCATCTGCAA 60.283 61.111 0.00 0.00 42.91 4.08
46 47 2.639327 GGGGCACACCATCTGCAAC 61.639 63.158 0.00 0.00 42.91 4.17
47 48 1.604593 GGGCACACCATCTGCAACT 60.605 57.895 0.00 0.00 39.85 3.16
48 49 1.582968 GGCACACCATCTGCAACTG 59.417 57.895 0.00 0.00 36.27 3.16
49 50 1.080974 GCACACCATCTGCAACTGC 60.081 57.895 0.00 0.00 42.50 4.40
50 51 1.582968 CACACCATCTGCAACTGCC 59.417 57.895 0.00 0.00 41.18 4.85
51 52 1.604593 ACACCATCTGCAACTGCCC 60.605 57.895 0.00 0.00 41.18 5.36
52 53 1.604308 CACCATCTGCAACTGCCCA 60.604 57.895 0.00 0.00 41.18 5.36
53 54 1.604593 ACCATCTGCAACTGCCCAC 60.605 57.895 0.00 0.00 41.18 4.61
54 55 1.604308 CCATCTGCAACTGCCCACA 60.604 57.895 0.00 0.00 41.18 4.17
55 56 1.582968 CATCTGCAACTGCCCACAC 59.417 57.895 0.00 0.00 41.18 3.82
56 57 1.968017 ATCTGCAACTGCCCACACG 60.968 57.895 0.00 0.00 41.18 4.49
57 58 4.332637 CTGCAACTGCCCACACGC 62.333 66.667 0.00 0.00 41.18 5.34
61 62 4.514585 AACTGCCCACACGCCCAA 62.515 61.111 0.00 0.00 0.00 4.12
62 63 4.954970 ACTGCCCACACGCCCAAG 62.955 66.667 0.00 0.00 0.00 3.61
178 179 3.584406 TTTCCATACAAATGCAACCCG 57.416 42.857 0.00 0.00 0.00 5.28
280 281 3.312697 GGGGCACGAGAATGATTTACTTC 59.687 47.826 0.00 0.00 0.00 3.01
325 326 2.563050 TAGCTGCACTGTAGCGCCTG 62.563 60.000 12.80 0.00 45.61 4.85
451 452 6.513180 TCTAAATCATGTACTCATTCCGTCC 58.487 40.000 0.00 0.00 31.15 4.79
569 571 5.319140 TGTTTCGGATTGTATCTCGAGAA 57.681 39.130 20.91 2.56 34.91 2.87
579 581 4.546570 TGTATCTCGAGAAGTGTGTGTTG 58.453 43.478 20.91 0.00 0.00 3.33
622 624 8.258850 TCTTATATTATGAAACGGGGAGTCTT 57.741 34.615 0.00 0.00 0.00 3.01
746 749 5.496556 TGTATCCATAGGTTGGTCAAACAG 58.503 41.667 1.40 0.00 46.52 3.16
759 762 3.057526 GGTCAAACAGCTCAAACCATACC 60.058 47.826 0.00 0.00 0.00 2.73
762 765 4.037446 TCAAACAGCTCAAACCATACCAAC 59.963 41.667 0.00 0.00 0.00 3.77
769 772 3.300388 TCAAACCATACCAACCAAGCAA 58.700 40.909 0.00 0.00 0.00 3.91
770 773 3.320541 TCAAACCATACCAACCAAGCAAG 59.679 43.478 0.00 0.00 0.00 4.01
771 774 1.256812 ACCATACCAACCAAGCAAGC 58.743 50.000 0.00 0.00 0.00 4.01
772 775 1.255882 CCATACCAACCAAGCAAGCA 58.744 50.000 0.00 0.00 0.00 3.91
773 776 1.617850 CCATACCAACCAAGCAAGCAA 59.382 47.619 0.00 0.00 0.00 3.91
774 777 2.353011 CCATACCAACCAAGCAAGCAAG 60.353 50.000 0.00 0.00 0.00 4.01
775 778 0.673437 TACCAACCAAGCAAGCAAGC 59.327 50.000 0.00 0.00 0.00 4.01
776 779 1.329171 ACCAACCAAGCAAGCAAGCA 61.329 50.000 3.19 0.00 36.85 3.91
817 820 2.975799 GCTTCCACCGGCGTCAAA 60.976 61.111 6.01 0.00 0.00 2.69
818 821 2.548295 GCTTCCACCGGCGTCAAAA 61.548 57.895 6.01 0.00 0.00 2.44
819 822 1.574428 CTTCCACCGGCGTCAAAAG 59.426 57.895 6.01 0.41 0.00 2.27
820 823 0.882927 CTTCCACCGGCGTCAAAAGA 60.883 55.000 6.01 0.00 0.00 2.52
821 824 0.464013 TTCCACCGGCGTCAAAAGAA 60.464 50.000 6.01 0.00 0.00 2.52
1050 1067 1.071471 CCTCGGCAAGGTGTTCACT 59.929 57.895 2.98 0.00 40.67 3.41
1092 1109 2.809601 GCGTACGTGGACAGCCTG 60.810 66.667 17.90 0.00 34.31 4.85
1164 1181 3.594775 CTGCTGCACAACGCCCAA 61.595 61.111 0.00 0.00 41.33 4.12
1719 2058 5.221441 GGGTATTGGAAAGACAACTTTTGCT 60.221 40.000 0.00 0.00 44.97 3.91
2309 2684 4.151883 TGGAATGGAGTTCTTGAAAAGGG 58.848 43.478 0.00 0.00 46.24 3.95
2433 2811 4.141390 GGCCTTTTCCCTGAAGATCATAGA 60.141 45.833 0.00 0.00 0.00 1.98
2436 2814 6.206438 GCCTTTTCCCTGAAGATCATAGATTC 59.794 42.308 0.00 0.00 0.00 2.52
2610 3024 9.770503 CATGATTTAATGCATGAGCTATCTAAC 57.229 33.333 0.00 0.00 43.43 2.34
2637 3051 1.881973 TCTGCACAAGAATGCCTCAAC 59.118 47.619 0.00 0.00 45.50 3.18
2658 3072 7.168219 TCAACATAAGTGGCTTAGATTTCAGT 58.832 34.615 0.00 0.00 29.02 3.41
2682 3096 2.663188 GCCATCCCGCGATCTGTC 60.663 66.667 8.23 0.00 0.00 3.51
2700 3114 6.961360 TCTGTCCGACACTTATCTATCAAT 57.039 37.500 0.00 0.00 0.00 2.57
2701 3115 6.739112 TCTGTCCGACACTTATCTATCAATG 58.261 40.000 0.00 0.00 0.00 2.82
2741 3155 7.385752 TGATGCAAATTTTGAGGAAGAAATGTC 59.614 33.333 13.26 0.00 0.00 3.06
2773 3190 6.767456 AGGGAGAAGATAGACATTGCTAATG 58.233 40.000 7.16 7.16 44.48 1.90
2826 3270 4.553330 AGAAGAAAGAACCGCCAAGATA 57.447 40.909 0.00 0.00 0.00 1.98
2900 3344 4.276926 GGTGAAGTCTGCACAATCTTTTCT 59.723 41.667 13.22 0.00 37.99 2.52
2906 3350 6.421485 AGTCTGCACAATCTTTTCTGGATAT 58.579 36.000 0.00 0.00 0.00 1.63
2950 3394 6.371825 CCTCCAGTACCTCAAAATTAGTTCAC 59.628 42.308 0.00 0.00 0.00 3.18
3714 4167 6.348050 CCTTTCCAAGTCTTGAAGAAATCGAG 60.348 42.308 14.42 4.62 40.48 4.04
3718 4171 4.264460 AGTCTTGAAGAAATCGAGTGCT 57.736 40.909 0.00 0.00 40.10 4.40
3784 4237 1.869342 GCACCAATTTGCGCAGTCTTT 60.869 47.619 11.31 0.00 31.51 2.52
3786 4239 3.836949 CACCAATTTGCGCAGTCTTTAT 58.163 40.909 11.31 0.00 0.00 1.40
3791 4244 5.177327 CCAATTTGCGCAGTCTTTATGTTTT 59.823 36.000 11.31 0.00 0.00 2.43
3794 4247 3.637432 TGCGCAGTCTTTATGTTTTTGG 58.363 40.909 5.66 0.00 0.00 3.28
3795 4248 2.986479 GCGCAGTCTTTATGTTTTTGGG 59.014 45.455 0.30 0.00 0.00 4.12
3817 4270 1.565390 CCCCAAGATGTCTCTGCCCA 61.565 60.000 0.00 0.00 0.00 5.36
3851 4304 2.224621 CCTCCACACTGACAGATTTGGT 60.225 50.000 10.08 0.00 0.00 3.67
3852 4305 3.480470 CTCCACACTGACAGATTTGGTT 58.520 45.455 10.08 0.00 0.00 3.67
3856 4309 4.353737 CACACTGACAGATTTGGTTGTTG 58.646 43.478 10.08 0.00 0.00 3.33
3857 4310 3.381272 ACACTGACAGATTTGGTTGTTGG 59.619 43.478 10.08 0.00 0.00 3.77
3858 4311 3.631686 CACTGACAGATTTGGTTGTTGGA 59.368 43.478 10.08 0.00 0.00 3.53
3860 4313 4.895297 ACTGACAGATTTGGTTGTTGGAAT 59.105 37.500 10.08 0.00 0.00 3.01
3862 4315 6.207417 ACTGACAGATTTGGTTGTTGGAATAG 59.793 38.462 10.08 0.00 0.00 1.73
3874 4327 6.127897 GGTTGTTGGAATAGGTGATTCAGAAG 60.128 42.308 0.17 0.00 45.15 2.85
3880 4333 2.206576 AGGTGATTCAGAAGGGTTGC 57.793 50.000 0.00 0.00 0.00 4.17
3909 4362 7.595819 TGATGGAAAGAAATTGGTTGTTAGT 57.404 32.000 0.00 0.00 0.00 2.24
3911 4364 6.155475 TGGAAAGAAATTGGTTGTTAGTGG 57.845 37.500 0.00 0.00 0.00 4.00
3989 4508 0.953960 AGATGCGACGGTTTGTTCCC 60.954 55.000 0.00 0.00 0.00 3.97
3991 4510 1.234615 ATGCGACGGTTTGTTCCCTG 61.235 55.000 0.00 0.00 0.00 4.45
3996 4515 2.779506 GACGGTTTGTTCCCTGAAGAT 58.220 47.619 0.00 0.00 0.00 2.40
3997 4516 3.146847 GACGGTTTGTTCCCTGAAGATT 58.853 45.455 0.00 0.00 0.00 2.40
4009 4528 3.094572 CCTGAAGATTTGGATGGCAGTT 58.905 45.455 0.00 0.00 0.00 3.16
4019 4538 1.200020 GGATGGCAGTTTTGTCTTCCG 59.800 52.381 0.00 0.00 41.58 4.30
4031 4550 6.596497 AGTTTTGTCTTCCGTTCAGTTAAGAA 59.404 34.615 0.00 0.00 30.24 2.52
4037 4556 6.089685 GTCTTCCGTTCAGTTAAGAATCTCAC 59.910 42.308 0.00 0.00 30.24 3.51
4042 4561 7.544566 TCCGTTCAGTTAAGAATCTCACATTAC 59.455 37.037 0.00 0.00 0.00 1.89
4052 4571 8.809159 AAGAATCTCACATTACATGTATCTCG 57.191 34.615 6.36 0.00 42.70 4.04
4057 4576 8.446599 TCTCACATTACATGTATCTCGTCTTA 57.553 34.615 6.36 0.00 42.70 2.10
4059 4578 7.423199 TCACATTACATGTATCTCGTCTTACC 58.577 38.462 6.36 0.00 42.70 2.85
4060 4579 7.067737 TCACATTACATGTATCTCGTCTTACCA 59.932 37.037 6.36 0.00 42.70 3.25
4061 4580 7.379797 CACATTACATGTATCTCGTCTTACCAG 59.620 40.741 6.36 0.00 42.70 4.00
4077 4596 1.674441 ACCAGCAGCAAATCATCATCG 59.326 47.619 0.00 0.00 0.00 3.84
4107 4626 4.338400 GTGTTAAACTGTTTCCCAGCTCTT 59.662 41.667 9.38 0.00 45.68 2.85
4117 4636 0.595095 CCCAGCTCTTTCTGTGTTGC 59.405 55.000 0.00 0.00 32.32 4.17
4118 4637 1.311859 CCAGCTCTTTCTGTGTTGCA 58.688 50.000 0.00 0.00 32.32 4.08
4119 4638 1.002033 CCAGCTCTTTCTGTGTTGCAC 60.002 52.381 0.00 0.00 32.32 4.57
4124 4643 3.748048 GCTCTTTCTGTGTTGCACATAGA 59.252 43.478 10.22 10.22 43.19 1.98
4126 4645 5.447010 GCTCTTTCTGTGTTGCACATAGATC 60.447 44.000 13.49 0.00 44.06 2.75
4127 4646 5.550290 TCTTTCTGTGTTGCACATAGATCA 58.450 37.500 13.49 6.17 44.06 2.92
4130 4649 4.248058 TCTGTGTTGCACATAGATCACTG 58.752 43.478 10.22 0.00 43.71 3.66
4135 4654 3.531934 TGCACATAGATCACTGTGAGG 57.468 47.619 24.00 5.79 44.35 3.86
4136 4655 3.099141 TGCACATAGATCACTGTGAGGA 58.901 45.455 24.00 4.25 44.35 3.71
4137 4656 3.131755 TGCACATAGATCACTGTGAGGAG 59.868 47.826 24.00 6.77 44.35 3.69
4138 4657 3.492309 GCACATAGATCACTGTGAGGAGG 60.492 52.174 24.00 7.86 44.35 4.30
4559 13661 1.619827 AGCAGATATGCTCTCAGAGGC 59.380 52.381 9.54 0.73 42.12 4.70
4632 13752 8.010697 TCTAGATTGGAGGTACTTATCATGGAA 58.989 37.037 0.00 0.00 41.55 3.53
4774 13897 2.039624 TCCTCACCTCCCTCCAGC 59.960 66.667 0.00 0.00 0.00 4.85
4775 13898 3.465403 CCTCACCTCCCTCCAGCG 61.465 72.222 0.00 0.00 0.00 5.18
4916 14040 1.355066 CTCCCGCTTTCGCTGAGAAC 61.355 60.000 0.00 0.00 38.83 3.01
4922 14046 0.436531 CTTTCGCTGAGAACACTCGC 59.563 55.000 0.00 0.00 38.83 5.03
4923 14047 0.249280 TTTCGCTGAGAACACTCGCA 60.249 50.000 0.00 0.00 38.83 5.10
4928 14052 1.340657 CTGAGAACACTCGCAGTCGC 61.341 60.000 0.00 0.00 42.66 5.19
4929 14053 2.049063 AGAACACTCGCAGTCGCC 60.049 61.111 0.00 0.00 35.26 5.54
4930 14054 2.049063 GAACACTCGCAGTCGCCT 60.049 61.111 0.00 0.00 35.26 5.52
4931 14055 2.049063 AACACTCGCAGTCGCCTC 60.049 61.111 0.00 0.00 35.26 4.70
4945 14078 0.678395 CGCCTCCAGCACTGAGATAT 59.322 55.000 0.00 0.00 44.04 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.700897 TCCTCTAGGTGGCAGCTATTTC 59.299 50.000 25.09 0.00 36.34 2.17
5 6 2.091055 TCTCCTCTAGGTGGCAGCTATT 60.091 50.000 25.09 4.49 36.34 1.73
6 7 1.501170 TCTCCTCTAGGTGGCAGCTAT 59.499 52.381 25.09 5.25 36.34 2.97
9 10 0.463620 CTTCTCCTCTAGGTGGCAGC 59.536 60.000 9.02 9.02 36.34 5.25
11 12 0.325671 CCCTTCTCCTCTAGGTGGCA 60.326 60.000 0.00 0.00 36.34 4.92
12 13 1.051556 CCCCTTCTCCTCTAGGTGGC 61.052 65.000 0.00 0.00 36.34 5.01
13 14 1.051556 GCCCCTTCTCCTCTAGGTGG 61.052 65.000 0.00 0.00 36.34 4.61
14 15 0.325671 TGCCCCTTCTCCTCTAGGTG 60.326 60.000 0.00 0.00 36.34 4.00
15 16 0.325765 GTGCCCCTTCTCCTCTAGGT 60.326 60.000 0.00 0.00 36.34 3.08
16 17 0.325671 TGTGCCCCTTCTCCTCTAGG 60.326 60.000 0.00 0.00 0.00 3.02
17 18 0.827368 GTGTGCCCCTTCTCCTCTAG 59.173 60.000 0.00 0.00 0.00 2.43
18 19 0.617820 GGTGTGCCCCTTCTCCTCTA 60.618 60.000 0.00 0.00 0.00 2.43
19 20 1.920835 GGTGTGCCCCTTCTCCTCT 60.921 63.158 0.00 0.00 0.00 3.69
20 21 1.566298 ATGGTGTGCCCCTTCTCCTC 61.566 60.000 0.00 0.00 0.00 3.71
21 22 1.542375 ATGGTGTGCCCCTTCTCCT 60.542 57.895 0.00 0.00 0.00 3.69
22 23 1.077429 GATGGTGTGCCCCTTCTCC 60.077 63.158 0.00 0.00 0.00 3.71
23 24 0.393537 CAGATGGTGTGCCCCTTCTC 60.394 60.000 0.00 0.00 37.00 2.87
24 25 1.687612 CAGATGGTGTGCCCCTTCT 59.312 57.895 0.00 0.00 39.02 2.85
25 26 2.048603 GCAGATGGTGTGCCCCTTC 61.049 63.158 0.00 0.00 34.67 3.46
26 27 2.036256 GCAGATGGTGTGCCCCTT 59.964 61.111 0.00 0.00 34.67 3.95
27 28 2.844195 TTGCAGATGGTGTGCCCCT 61.844 57.895 0.00 0.00 40.43 4.79
28 29 2.283101 TTGCAGATGGTGTGCCCC 60.283 61.111 0.00 0.00 40.43 5.80
29 30 1.604593 AGTTGCAGATGGTGTGCCC 60.605 57.895 0.00 0.00 40.43 5.36
30 31 1.582968 CAGTTGCAGATGGTGTGCC 59.417 57.895 0.00 0.00 40.43 5.01
31 32 1.080974 GCAGTTGCAGATGGTGTGC 60.081 57.895 0.00 0.00 41.59 4.57
32 33 1.582968 GGCAGTTGCAGATGGTGTG 59.417 57.895 6.43 0.00 44.36 3.82
33 34 1.604593 GGGCAGTTGCAGATGGTGT 60.605 57.895 6.43 0.00 44.36 4.16
34 35 1.604308 TGGGCAGTTGCAGATGGTG 60.604 57.895 6.43 0.00 44.36 4.17
35 36 1.604593 GTGGGCAGTTGCAGATGGT 60.605 57.895 6.43 0.00 44.36 3.55
36 37 1.604308 TGTGGGCAGTTGCAGATGG 60.604 57.895 6.43 0.00 44.36 3.51
37 38 1.582968 GTGTGGGCAGTTGCAGATG 59.417 57.895 6.43 0.00 44.36 2.90
38 39 1.968017 CGTGTGGGCAGTTGCAGAT 60.968 57.895 6.43 0.00 44.36 2.90
39 40 2.591429 CGTGTGGGCAGTTGCAGA 60.591 61.111 6.43 0.00 44.36 4.26
40 41 4.332637 GCGTGTGGGCAGTTGCAG 62.333 66.667 6.43 0.00 44.36 4.41
44 45 4.514585 TTGGGCGTGTGGGCAGTT 62.515 61.111 0.00 0.00 44.56 3.16
45 46 4.954970 CTTGGGCGTGTGGGCAGT 62.955 66.667 0.00 0.00 44.56 4.40
56 57 3.129913 GATGCCATCACGCTTGGGC 62.130 63.158 0.00 3.87 46.58 5.36
57 58 1.033746 AAGATGCCATCACGCTTGGG 61.034 55.000 7.56 0.00 34.66 4.12
58 59 0.379669 GAAGATGCCATCACGCTTGG 59.620 55.000 7.56 0.00 37.31 3.61
59 60 0.379669 GGAAGATGCCATCACGCTTG 59.620 55.000 7.56 0.00 0.00 4.01
60 61 0.035152 TGGAAGATGCCATCACGCTT 60.035 50.000 7.56 0.00 31.66 4.68
61 62 0.182061 ATGGAAGATGCCATCACGCT 59.818 50.000 7.56 0.00 45.36 5.07
62 63 0.309922 CATGGAAGATGCCATCACGC 59.690 55.000 7.56 0.00 45.36 5.34
63 64 1.332686 CACATGGAAGATGCCATCACG 59.667 52.381 7.56 0.00 45.36 4.35
64 65 2.372264 ACACATGGAAGATGCCATCAC 58.628 47.619 7.56 0.56 45.36 3.06
65 66 2.812836 ACACATGGAAGATGCCATCA 57.187 45.000 7.56 0.00 45.36 3.07
66 67 4.460948 AAAACACATGGAAGATGCCATC 57.539 40.909 0.00 0.00 45.36 3.51
68 69 4.096231 CGATAAAACACATGGAAGATGCCA 59.904 41.667 0.00 0.00 43.23 4.92
69 70 4.498009 CCGATAAAACACATGGAAGATGCC 60.498 45.833 0.00 0.00 0.00 4.40
108 109 6.518516 TTTTAGGGAGAGTGGAAGGTTTTA 57.481 37.500 0.00 0.00 0.00 1.52
152 153 6.349197 GGGTTGCATTTGTATGGAAATTTTGG 60.349 38.462 0.00 0.00 42.66 3.28
171 172 2.034053 TCTCAACATTTTCACGGGTTGC 59.966 45.455 0.00 0.00 40.20 4.17
264 265 5.498700 CGGTCAACGAAGTAAATCATTCTCG 60.499 44.000 0.00 0.00 45.00 4.04
268 269 3.181524 CGCGGTCAACGAAGTAAATCATT 60.182 43.478 0.00 0.00 45.00 2.57
444 445 4.888239 TGAAACACTTATTTTGGGACGGAA 59.112 37.500 0.00 0.00 0.00 4.30
501 502 6.128795 CCGTCTCAAAATAAGTGTCTCAACTC 60.129 42.308 0.00 0.00 0.00 3.01
648 650 5.631096 GCTGAAAGGTTTCTTTACAGAATGC 59.369 40.000 15.50 0.00 42.72 3.56
746 749 2.352715 GCTTGGTTGGTATGGTTTGAGC 60.353 50.000 0.00 0.00 0.00 4.26
759 762 1.796459 GATTGCTTGCTTGCTTGGTTG 59.204 47.619 3.47 0.00 0.00 3.77
762 765 0.390735 GGGATTGCTTGCTTGCTTGG 60.391 55.000 3.47 0.00 0.00 3.61
769 772 1.607467 GGTGTGGGGATTGCTTGCT 60.607 57.895 0.00 0.00 0.00 3.91
770 773 2.973082 GGTGTGGGGATTGCTTGC 59.027 61.111 0.00 0.00 0.00 4.01
771 774 2.993471 GCGGTGTGGGGATTGCTTG 61.993 63.158 0.00 0.00 0.00 4.01
772 775 1.847798 TAGCGGTGTGGGGATTGCTT 61.848 55.000 0.00 0.00 34.08 3.91
773 776 2.257409 CTAGCGGTGTGGGGATTGCT 62.257 60.000 0.00 0.00 36.51 3.91
774 777 1.819632 CTAGCGGTGTGGGGATTGC 60.820 63.158 0.00 0.00 0.00 3.56
775 778 0.179073 CTCTAGCGGTGTGGGGATTG 60.179 60.000 0.00 0.00 0.00 2.67
776 779 1.972660 GCTCTAGCGGTGTGGGGATT 61.973 60.000 0.00 0.00 0.00 3.01
817 820 4.562552 CGGGGCAATAATTGGTGTTTTCTT 60.563 41.667 0.00 0.00 0.00 2.52
818 821 3.056179 CGGGGCAATAATTGGTGTTTTCT 60.056 43.478 0.00 0.00 0.00 2.52
819 822 3.258228 CGGGGCAATAATTGGTGTTTTC 58.742 45.455 0.00 0.00 0.00 2.29
820 823 2.027653 CCGGGGCAATAATTGGTGTTTT 60.028 45.455 0.00 0.00 0.00 2.43
821 824 1.552792 CCGGGGCAATAATTGGTGTTT 59.447 47.619 0.00 0.00 0.00 2.83
875 878 4.063967 CCACCGCACAGCCGTAGA 62.064 66.667 0.00 0.00 0.00 2.59
1092 1109 2.435059 GAGTTGTGGCCGAGCTCC 60.435 66.667 8.47 0.00 0.00 4.70
1237 1257 2.420890 CAGCAGATCCTCCGCCTC 59.579 66.667 0.00 0.00 0.00 4.70
1719 2058 7.227314 GTCCTTGCATCATTATACAGATGTTGA 59.773 37.037 12.66 0.00 42.72 3.18
2334 2712 8.571461 TCTTTAAAGATGGCATGATATCATCC 57.429 34.615 15.49 17.93 38.33 3.51
2610 3024 3.047796 GCATTCTTGTGCAGAAACACTG 58.952 45.455 0.00 0.00 45.06 3.66
2637 3051 5.587844 AGCACTGAAATCTAAGCCACTTATG 59.412 40.000 0.00 0.00 0.00 1.90
2675 3089 6.561737 TGATAGATAAGTGTCGGACAGATC 57.438 41.667 11.83 13.88 0.00 2.75
2682 3096 8.568794 TCTTCTACATTGATAGATAAGTGTCGG 58.431 37.037 0.00 0.00 31.25 4.79
2700 3114 8.969260 AATTTGCATCATATCTGTCTTCTACA 57.031 30.769 0.00 0.00 36.42 2.74
2746 3160 6.814954 AGCAATGTCTATCTTCTCCCTTAA 57.185 37.500 0.00 0.00 0.00 1.85
2773 3190 5.938322 TCTAAAAATCATCAAAGTCCGCAC 58.062 37.500 0.00 0.00 0.00 5.34
2809 3253 5.560966 TTCAATATCTTGGCGGTTCTTTC 57.439 39.130 0.00 0.00 32.95 2.62
2810 3254 5.710099 TCTTTCAATATCTTGGCGGTTCTTT 59.290 36.000 0.00 0.00 32.95 2.52
2811 3255 5.253330 TCTTTCAATATCTTGGCGGTTCTT 58.747 37.500 0.00 0.00 32.95 2.52
2816 3260 4.999950 AGCTATCTTTCAATATCTTGGCGG 59.000 41.667 0.00 0.00 32.95 6.13
2906 3350 5.894393 TGGAGGTGGATAAGTTTTGAAAACA 59.106 36.000 21.34 3.59 0.00 2.83
2950 3394 3.689347 TCATTTCCCTGTCAATGTGAGG 58.311 45.455 0.00 0.00 32.96 3.86
3292 3739 3.951680 TCCTTCAGGTTCCTTTTCAACAC 59.048 43.478 0.00 0.00 36.34 3.32
3794 4247 0.393537 CAGAGACATCTTGGGGCACC 60.394 60.000 0.00 0.00 40.89 5.01
3795 4248 1.028868 GCAGAGACATCTTGGGGCAC 61.029 60.000 0.00 0.00 31.64 5.01
3817 4270 1.847506 TGGAGGTGTGAGGCATGGT 60.848 57.895 0.00 0.00 0.00 3.55
3851 4304 5.945784 CCTTCTGAATCACCTATTCCAACAA 59.054 40.000 0.00 0.00 42.97 2.83
3852 4305 5.500234 CCTTCTGAATCACCTATTCCAACA 58.500 41.667 0.00 0.00 42.97 3.33
3856 4309 4.779993 ACCCTTCTGAATCACCTATTCC 57.220 45.455 0.00 0.00 42.97 3.01
3857 4310 4.336713 GCAACCCTTCTGAATCACCTATTC 59.663 45.833 0.00 0.00 43.77 1.75
3858 4311 4.273318 GCAACCCTTCTGAATCACCTATT 58.727 43.478 0.00 0.00 0.00 1.73
3860 4313 2.354704 CGCAACCCTTCTGAATCACCTA 60.355 50.000 0.00 0.00 0.00 3.08
3862 4315 0.804989 CGCAACCCTTCTGAATCACC 59.195 55.000 0.00 0.00 0.00 4.02
3874 4327 3.013921 TCTTTCCATCATAACGCAACCC 58.986 45.455 0.00 0.00 0.00 4.11
3880 4333 7.090173 ACAACCAATTTCTTTCCATCATAACG 58.910 34.615 0.00 0.00 0.00 3.18
3909 4362 1.677300 CAAAGCACCGCCATACCCA 60.677 57.895 0.00 0.00 0.00 4.51
3911 4364 3.063743 GCCAAAGCACCGCCATACC 62.064 63.158 0.00 0.00 39.53 2.73
3960 4413 1.061131 CCGTCGCATCTGTTGACAATC 59.939 52.381 0.00 0.00 32.91 2.67
3961 4414 1.078709 CCGTCGCATCTGTTGACAAT 58.921 50.000 0.00 0.00 32.91 2.71
3962 4415 0.249699 ACCGTCGCATCTGTTGACAA 60.250 50.000 0.00 0.00 32.91 3.18
3964 4417 0.865769 AAACCGTCGCATCTGTTGAC 59.134 50.000 0.00 0.00 0.00 3.18
3966 4419 0.586319 ACAAACCGTCGCATCTGTTG 59.414 50.000 0.00 0.00 0.00 3.33
3967 4420 1.263217 GAACAAACCGTCGCATCTGTT 59.737 47.619 0.00 0.00 0.00 3.16
3968 4421 0.865769 GAACAAACCGTCGCATCTGT 59.134 50.000 0.00 0.00 0.00 3.41
3969 4422 0.165944 GGAACAAACCGTCGCATCTG 59.834 55.000 0.00 0.00 0.00 2.90
3989 4508 4.796038 AAACTGCCATCCAAATCTTCAG 57.204 40.909 0.00 0.00 0.00 3.02
3991 4510 4.886579 ACAAAACTGCCATCCAAATCTTC 58.113 39.130 0.00 0.00 0.00 2.87
3996 4515 3.069443 GGAAGACAAAACTGCCATCCAAA 59.931 43.478 0.00 0.00 35.72 3.28
3997 4516 2.627699 GGAAGACAAAACTGCCATCCAA 59.372 45.455 0.00 0.00 35.72 3.53
4009 4528 6.990349 AGATTCTTAACTGAACGGAAGACAAA 59.010 34.615 0.00 0.00 0.00 2.83
4019 4538 9.979270 CATGTAATGTGAGATTCTTAACTGAAC 57.021 33.333 0.00 0.00 40.20 3.18
4042 4561 4.294232 CTGCTGGTAAGACGAGATACATG 58.706 47.826 0.00 0.00 0.00 3.21
4052 4571 3.691118 TGATGATTTGCTGCTGGTAAGAC 59.309 43.478 0.00 0.00 0.00 3.01
4057 4576 1.674441 CGATGATGATTTGCTGCTGGT 59.326 47.619 0.00 0.00 0.00 4.00
4059 4578 2.353579 TGACGATGATGATTTGCTGCTG 59.646 45.455 0.00 0.00 0.00 4.41
4060 4579 2.635714 TGACGATGATGATTTGCTGCT 58.364 42.857 0.00 0.00 0.00 4.24
4061 4580 3.409851 TTGACGATGATGATTTGCTGC 57.590 42.857 0.00 0.00 0.00 5.25
4077 4596 6.391537 TGGGAAACAGTTTAACACTTTTGAC 58.608 36.000 0.00 0.00 30.92 3.18
4117 4636 3.956848 TCCTCCTCACAGTGATCTATGTG 59.043 47.826 19.04 19.04 46.52 3.21
4118 4637 4.256983 TCCTCCTCACAGTGATCTATGT 57.743 45.455 2.97 0.00 0.00 2.29
4119 4638 5.070180 ACATTCCTCCTCACAGTGATCTATG 59.930 44.000 2.97 5.44 0.00 2.23
4124 4643 2.909006 ACACATTCCTCCTCACAGTGAT 59.091 45.455 2.97 0.00 0.00 3.06
4126 4645 2.847327 ACACATTCCTCCTCACAGTG 57.153 50.000 0.00 0.00 0.00 3.66
4127 4646 4.836825 CATTACACATTCCTCCTCACAGT 58.163 43.478 0.00 0.00 0.00 3.55
4130 4649 3.609853 TGCATTACACATTCCTCCTCAC 58.390 45.455 0.00 0.00 0.00 3.51
4135 4654 3.378427 GGGAACTGCATTACACATTCCTC 59.622 47.826 0.00 0.00 36.62 3.71
4136 4655 3.245229 TGGGAACTGCATTACACATTCCT 60.245 43.478 0.00 0.00 36.62 3.36
4137 4656 3.088532 TGGGAACTGCATTACACATTCC 58.911 45.455 0.00 0.00 35.81 3.01
4138 4657 4.398988 TGATGGGAACTGCATTACACATTC 59.601 41.667 0.00 0.00 0.00 2.67
4559 13661 2.105984 CTCTGAGAGTGAGAGGCCG 58.894 63.158 0.16 0.00 34.42 6.13
4632 13752 2.867624 ACAAGCAATCCACACATGTCT 58.132 42.857 0.00 0.00 0.00 3.41
4774 13897 4.260620 CCCGCATTTGGAAAATACTAGACG 60.261 45.833 0.00 0.00 0.00 4.18
4775 13898 4.036380 CCCCGCATTTGGAAAATACTAGAC 59.964 45.833 0.00 0.00 0.00 2.59
4903 14027 0.436531 GCGAGTGTTCTCAGCGAAAG 59.563 55.000 0.00 0.00 40.44 2.62
4922 14046 2.433838 CAGTGCTGGAGGCGACTG 60.434 66.667 0.00 0.00 44.43 3.51
4924 14048 1.954362 ATCTCAGTGCTGGAGGCGAC 61.954 60.000 0.00 0.00 45.43 5.19
4926 14050 0.678395 ATATCTCAGTGCTGGAGGCG 59.322 55.000 0.00 0.00 45.43 5.52
4928 14052 3.149981 TCGTATATCTCAGTGCTGGAGG 58.850 50.000 0.00 0.00 33.18 4.30
4929 14053 3.365868 GCTCGTATATCTCAGTGCTGGAG 60.366 52.174 0.00 0.00 0.00 3.86
4930 14054 2.554462 GCTCGTATATCTCAGTGCTGGA 59.446 50.000 0.00 0.00 0.00 3.86
4931 14055 2.294512 TGCTCGTATATCTCAGTGCTGG 59.705 50.000 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.