Multiple sequence alignment - TraesCS3D01G043600

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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 TraesCS3D01G043600 chr3D 100.000 8220 0 0 1 8220 16625100 16616881 0.000000e+00 15180.0
1 TraesCS3D01G043600 chr3D 87.021 809 79 10 1 792 593274 594073 0.000000e+00 889.0
2 TraesCS3D01G043600 chr3D 84.259 108 14 1 7791 7895 14344689 14344582 1.460000e-17 102.0
3 TraesCS3D01G043600 chr3D 81.731 104 16 3 7791 7893 372634253 372634354 5.290000e-12 84.2
4 TraesCS3D01G043600 chr3A 97.885 4492 78 9 2545 7030 19999792 20004272 0.000000e+00 7753.0
5 TraesCS3D01G043600 chr3A 88.594 1131 73 23 7011 8120 20004285 20005380 0.000000e+00 1323.0
6 TraesCS3D01G043600 chr3A 91.826 783 27 14 1783 2550 19998919 19999679 0.000000e+00 1057.0
7 TraesCS3D01G043600 chr3A 90.660 803 55 12 1 792 19991878 19992671 0.000000e+00 1050.0
8 TraesCS3D01G043600 chr3A 88.587 736 22 16 933 1622 19998201 19998920 0.000000e+00 837.0
9 TraesCS3D01G043600 chr3A 94.737 38 0 1 2884 2921 724528086 724528051 3.200000e-04 58.4
10 TraesCS3D01G043600 chr3B 95.987 4784 131 28 2545 7308 24012108 24007366 0.000000e+00 7714.0
11 TraesCS3D01G043600 chr3B 90.318 1508 61 31 1078 2550 24013678 24012221 0.000000e+00 1897.0
12 TraesCS3D01G043600 chr3B 87.947 755 48 12 291 1019 24014627 24013890 0.000000e+00 850.0
13 TraesCS3D01G043600 chr3B 94.828 232 11 1 7590 7821 24007332 24007102 2.180000e-95 361.0
14 TraesCS3D01G043600 chr3B 85.981 107 13 1 7791 7895 7133997 7134103 6.740000e-21 113.0
15 TraesCS3D01G043600 chr3B 100.000 55 0 0 1 55 24014677 24014623 1.460000e-17 102.0
16 TraesCS3D01G043600 chr3B 86.585 82 7 2 7321 7402 609305077 609305000 4.090000e-13 87.9
17 TraesCS3D01G043600 chr3B 97.561 41 1 0 7546 7586 24007362 24007322 4.120000e-08 71.3
18 TraesCS3D01G043600 chr4A 90.958 2798 202 30 2920 5697 583150852 583153618 0.000000e+00 3718.0
19 TraesCS3D01G043600 chr4A 91.067 862 59 14 5694 6550 583153672 583154520 0.000000e+00 1149.0
20 TraesCS3D01G043600 chr4A 84.789 664 84 12 6554 7213 583154561 583155211 0.000000e+00 651.0
21 TraesCS3D01G043600 chr4A 83.333 636 52 25 1036 1648 583150203 583150807 9.390000e-149 538.0
22 TraesCS3D01G043600 chr4A 93.617 47 3 0 5916 5962 616236950 616236904 4.120000e-08 71.3
23 TraesCS3D01G043600 chr4B 90.472 2477 153 38 3264 5697 29662589 29665025 0.000000e+00 3190.0
24 TraesCS3D01G043600 chr4B 90.270 1110 75 11 3405 4506 29713984 29712900 0.000000e+00 1421.0
25 TraesCS3D01G043600 chr4B 90.090 1110 70 20 4600 5681 29712902 29711805 0.000000e+00 1404.0
26 TraesCS3D01G043600 chr4B 90.300 866 62 15 5695 6550 29665081 29665934 0.000000e+00 1114.0
27 TraesCS3D01G043600 chr4B 90.207 868 65 11 5695 6549 29711560 29710700 0.000000e+00 1114.0
28 TraesCS3D01G043600 chr4B 84.969 805 82 21 1 789 479035656 479036437 0.000000e+00 780.0
29 TraesCS3D01G043600 chr4B 88.136 531 50 5 2920 3444 29714507 29713984 3.260000e-173 619.0
30 TraesCS3D01G043600 chr4B 83.511 564 63 18 6554 7111 29710658 29710119 4.430000e-137 499.0
31 TraesCS3D01G043600 chr4B 85.882 425 48 7 6554 6970 29665975 29666395 7.570000e-120 442.0
32 TraesCS3D01G043600 chr4B 83.594 512 39 27 1155 1652 29715029 29714549 9.790000e-119 438.0
33 TraesCS3D01G043600 chr4B 82.562 281 21 8 4079 4356 29662132 29662387 1.070000e-53 222.0
34 TraesCS3D01G043600 chr4B 90.476 126 9 1 3143 3265 29662382 29662507 6.600000e-36 163.0
35 TraesCS3D01G043600 chr4B 89.610 77 6 2 7790 7865 16680442 16680517 6.790000e-16 97.1
36 TraesCS3D01G043600 chr4B 82.243 107 17 2 7790 7895 10799913 10799808 3.160000e-14 91.6
37 TraesCS3D01G043600 chr4D 89.025 1713 118 26 2918 4614 17864124 17862466 0.000000e+00 2058.0
38 TraesCS3D01G043600 chr4D 88.513 1567 136 30 5694 7232 17861252 17859702 0.000000e+00 1857.0
39 TraesCS3D01G043600 chr4D 92.237 1095 66 13 4610 5697 17862388 17861306 0.000000e+00 1533.0
40 TraesCS3D01G043600 chr4D 85.586 333 17 10 1321 1652 17864467 17864165 3.700000e-83 320.0
41 TraesCS3D01G043600 chr4D 83.117 231 21 10 1036 1249 17865156 17864927 2.340000e-45 195.0
42 TraesCS3D01G043600 chr2D 87.593 806 73 13 1 792 49361421 49360629 0.000000e+00 909.0
43 TraesCS3D01G043600 chr2D 88.555 533 44 8 2918 3440 408774267 408774792 1.510000e-176 630.0
44 TraesCS3D01G043600 chr7D 85.697 818 78 16 1 792 46372438 46373242 0.000000e+00 826.0
45 TraesCS3D01G043600 chr7D 84.578 817 90 19 1 792 46269547 46268742 0.000000e+00 778.0
46 TraesCS3D01G043600 chr7D 86.996 223 18 5 581 792 46164073 46163851 2.960000e-59 241.0
47 TraesCS3D01G043600 chr7D 89.362 47 5 0 865 911 46154326 46154280 8.910000e-05 60.2
48 TraesCS3D01G043600 chr7D 87.755 49 2 4 865 911 46270398 46270444 4.000000e-03 54.7
49 TraesCS3D01G043600 chr5D 85.452 818 80 21 1 792 400002926 400002122 0.000000e+00 815.0
50 TraesCS3D01G043600 chr5D 87.342 79 6 3 7318 7396 439334479 439334405 4.090000e-13 87.9
51 TraesCS3D01G043600 chr1B 84.625 813 91 19 1 792 189866768 189867567 0.000000e+00 778.0
52 TraesCS3D01G043600 chr1B 87.371 388 33 6 6855 7240 637358533 637358160 1.640000e-116 431.0
53 TraesCS3D01G043600 chr1B 88.479 217 17 2 6628 6844 637367223 637367015 1.060000e-63 255.0
54 TraesCS3D01G043600 chr1B 87.821 156 12 3 7368 7516 637358087 637357932 8.480000e-40 176.0
55 TraesCS3D01G043600 chr1B 93.617 47 3 0 865 911 189870635 189870681 4.120000e-08 71.3
56 TraesCS3D01G043600 chr1B 87.234 47 6 0 865 911 189865913 189865867 4.000000e-03 54.7
57 TraesCS3D01G043600 chr1B 100.000 29 0 0 6835 6863 637359164 637359136 4.000000e-03 54.7
58 TraesCS3D01G043600 chr2A 87.430 533 50 7 2918 3440 606699181 606698656 1.530000e-166 597.0
59 TraesCS3D01G043600 chr2A 82.700 237 31 8 1798 2029 758656212 758656443 1.400000e-47 202.0
60 TraesCS3D01G043600 chr1D 79.965 564 55 26 6982 7516 462295802 462295268 6.060000e-96 363.0
61 TraesCS3D01G043600 chr1D 91.525 236 20 0 6628 6863 462296690 462296455 7.960000e-85 326.0
62 TraesCS3D01G043600 chr1D 84.906 106 13 3 7791 7895 234715125 234715022 4.060000e-18 104.0
63 TraesCS3D01G043600 chr1D 87.209 86 9 1 5916 5999 298570222 298570137 6.790000e-16 97.1
64 TraesCS3D01G043600 chr5B 88.112 143 15 2 2786 2927 158820056 158819915 1.420000e-37 169.0
65 TraesCS3D01G043600 chr5B 83.212 137 15 6 2788 2916 452028162 452028298 1.450000e-22 119.0
66 TraesCS3D01G043600 chr5B 83.088 136 14 6 2789 2921 706376251 706376380 1.870000e-21 115.0
67 TraesCS3D01G043600 chr5A 85.616 146 15 4 2785 2927 663923089 663923231 1.850000e-31 148.0
68 TraesCS3D01G043600 chr7B 89.320 103 8 3 2792 2894 415231616 415231715 8.660000e-25 126.0
69 TraesCS3D01G043600 chr7B 82.857 105 9 8 7290 7393 724809038 724808942 1.470000e-12 86.1
70 TraesCS3D01G043600 chr7B 86.076 79 7 2 7318 7396 296356897 296356823 1.900000e-11 82.4
71 TraesCS3D01G043600 chr7B 81.250 96 14 1 7307 7402 245070347 245070438 3.180000e-09 75.0
72 TraesCS3D01G043600 chr7A 89.320 103 8 3 2792 2894 45821245 45821344 8.660000e-25 126.0
73 TraesCS3D01G043600 chr7A 86.486 111 14 1 2784 2894 283079483 283079592 4.030000e-23 121.0
74 TraesCS3D01G043600 chr7A 86.667 60 4 2 2873 2928 80084696 80084755 6.890000e-06 63.9
75 TraesCS3D01G043600 chr7A 90.698 43 3 1 2885 2927 560587751 560587710 1.000000e-03 56.5
76 TraesCS3D01G043600 chr1A 89.535 86 7 1 5916 5999 372239154 372239069 3.140000e-19 108.0
77 TraesCS3D01G043600 chr1A 81.443 97 14 1 7306 7402 64714430 64714338 8.850000e-10 76.8
78 TraesCS3D01G043600 chr6B 81.553 103 19 0 7791 7893 58909417 58909519 1.470000e-12 86.1
79 TraesCS3D01G043600 chr6B 86.250 80 6 2 7317 7396 62403522 62403448 1.900000e-11 82.4
80 TraesCS3D01G043600 chr6A 85.057 87 8 2 7307 7393 34179549 34179630 5.290000e-12 84.2
81 TraesCS3D01G043600 chr2B 80.000 105 20 1 7791 7895 94283563 94283666 8.850000e-10 76.8


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 TraesCS3D01G043600 chr3D 16616881 16625100 8219 True 15180.000000 15180 100.000000 1 8220 1 chr3D.!!$R2 8219
1 TraesCS3D01G043600 chr3D 593274 594073 799 False 889.000000 889 87.021000 1 792 1 chr3D.!!$F1 791
2 TraesCS3D01G043600 chr3A 19998201 20005380 7179 False 2742.500000 7753 91.723000 933 8120 4 chr3A.!!$F2 7187
3 TraesCS3D01G043600 chr3A 19991878 19992671 793 False 1050.000000 1050 90.660000 1 792 1 chr3A.!!$F1 791
4 TraesCS3D01G043600 chr3B 24007102 24014677 7575 True 1832.550000 7714 94.440167 1 7821 6 chr3B.!!$R2 7820
5 TraesCS3D01G043600 chr4A 583150203 583155211 5008 False 1514.000000 3718 87.536750 1036 7213 4 chr4A.!!$F1 6177
6 TraesCS3D01G043600 chr4B 29662132 29666395 4263 False 1026.200000 3190 87.938400 3143 6970 5 chr4B.!!$F3 3827
7 TraesCS3D01G043600 chr4B 29710119 29715029 4910 True 915.833333 1421 87.634667 1155 7111 6 chr4B.!!$R2 5956
8 TraesCS3D01G043600 chr4B 479035656 479036437 781 False 780.000000 780 84.969000 1 789 1 chr4B.!!$F2 788
9 TraesCS3D01G043600 chr4D 17859702 17865156 5454 True 1192.600000 2058 87.695600 1036 7232 5 chr4D.!!$R1 6196
10 TraesCS3D01G043600 chr2D 49360629 49361421 792 True 909.000000 909 87.593000 1 792 1 chr2D.!!$R1 791
11 TraesCS3D01G043600 chr2D 408774267 408774792 525 False 630.000000 630 88.555000 2918 3440 1 chr2D.!!$F1 522
12 TraesCS3D01G043600 chr7D 46372438 46373242 804 False 826.000000 826 85.697000 1 792 1 chr7D.!!$F2 791
13 TraesCS3D01G043600 chr7D 46268742 46269547 805 True 778.000000 778 84.578000 1 792 1 chr7D.!!$R3 791
14 TraesCS3D01G043600 chr5D 400002122 400002926 804 True 815.000000 815 85.452000 1 792 1 chr5D.!!$R1 791
15 TraesCS3D01G043600 chr1B 189866768 189870681 3913 False 424.650000 778 89.121000 1 911 2 chr1B.!!$F1 910
16 TraesCS3D01G043600 chr1B 637357932 637359164 1232 True 220.566667 431 91.730667 6835 7516 3 chr1B.!!$R3 681
17 TraesCS3D01G043600 chr2A 606698656 606699181 525 True 597.000000 597 87.430000 2918 3440 1 chr2A.!!$R1 522
18 TraesCS3D01G043600 chr1D 462295268 462296690 1422 True 344.500000 363 85.745000 6628 7516 2 chr1D.!!$R3 888

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
205 215 1.144716 GCAGATGCGGAGATGTCCA 59.855 57.895 9.94 0.0 44.18 4.02 F
1710 2357 0.536687 CCATGCTTGCGATGGGAGAT 60.537 55.000 12.83 0.0 37.33 2.75 F
1830 2477 0.109597 CACCGGAAGAGCATTTGCAC 60.110 55.000 9.46 0.0 45.16 4.57 F
2440 3108 0.741221 GACGCATCCTCGCCTTCTTT 60.741 55.000 0.00 0.0 0.00 2.52 F
2531 3202 1.132588 GCGTATGCCTCTGAATCGTC 58.867 55.000 0.00 0.0 33.98 4.20 F
3378 4833 3.065371 CGCTGGAGTAAATTTGGTGGATC 59.935 47.826 0.00 0.0 0.00 3.36 F
4276 5966 0.820871 TTTCGTTGCTTTGCCTTGGT 59.179 45.000 0.00 0.0 0.00 3.67 F
4578 7260 6.698008 TCTGCATTGTACCATCCATAAAAG 57.302 37.500 0.00 0.0 0.00 2.27 F
6245 9770 4.717991 TGTTTATTGTGCGTTGCAGATAC 58.282 39.130 0.00 0.0 40.08 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1713 2360 0.105862 TCCGGACGGGAGGTGATATT 60.106 55.000 11.27 0.00 40.94 1.28 R
3094 3898 1.005340 GCTTCAATGGTCAGAGCTCG 58.995 55.000 8.37 3.55 0.00 5.03 R
3711 5228 8.339714 TCAAGTAAAACACTAATTCAAGAACGG 58.660 33.333 0.00 0.00 36.04 4.44 R
4042 5566 2.890311 CCACCCACTGTAATTCAAAGCA 59.110 45.455 0.00 0.00 0.00 3.91 R
4276 5966 4.528206 TCATGCAGAAGACAAGTAGGAGAA 59.472 41.667 0.00 0.00 0.00 2.87 R
4578 7260 8.110860 TCTCAGATCCAATTACCAAAAAGTTC 57.889 34.615 0.00 0.00 0.00 3.01 R
5981 9503 3.153919 AGAGCAATGTTTTTAAGGCGGA 58.846 40.909 0.00 0.00 0.00 5.54 R
6365 9890 1.647346 CATGGGATGCAAATGTGTGC 58.353 50.000 0.00 0.00 45.15 4.57 R
8007 12279 0.740868 CAACATGAGGGCACGATCGT 60.741 55.000 16.60 16.60 0.00 3.73 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
75 77 3.028130 TCGGCATGAGTACCTGTAATGA 58.972 45.455 0.00 0.00 0.00 2.57
185 195 7.601130 AGAAAAAGTGTACATATCTACAACGCA 59.399 33.333 0.00 0.00 0.00 5.24
205 215 1.144716 GCAGATGCGGAGATGTCCA 59.855 57.895 9.94 0.00 44.18 4.02
425 437 5.069516 AGTTTCTTGTTGATGGCAGTGAAAT 59.930 36.000 0.00 0.00 0.00 2.17
440 452 6.437928 GCAGTGAAATTGACTACAACATTGA 58.562 36.000 0.00 0.00 38.90 2.57
446 458 8.514594 TGAAATTGACTACAACATTGATCTTCC 58.485 33.333 0.00 0.00 38.90 3.46
518 530 5.919755 TGACAAATCTGTGTAGTGTACCAA 58.080 37.500 0.00 0.00 35.30 3.67
537 549 3.341823 CAACCCTCTCAGGTGAATTCTG 58.658 50.000 7.05 0.00 40.05 3.02
554 566 4.412796 TTCTGGGCATTGAGAGTGATAG 57.587 45.455 0.00 0.00 0.00 2.08
557 575 4.225942 TCTGGGCATTGAGAGTGATAGTTT 59.774 41.667 0.00 0.00 0.00 2.66
651 677 8.402798 TGAATTAAGTGATGCCAACTCTTTTA 57.597 30.769 0.00 0.00 0.00 1.52
698 726 5.063944 CCGTTTGATGAATTCTCTACACCTG 59.936 44.000 7.05 0.00 0.00 4.00
792 827 7.681903 TGTTCAAGTTTTTCTTCTCTTCGTAC 58.318 34.615 0.00 0.00 33.63 3.67
851 886 5.701224 ACAAAGGTCTTTTCCAAGGATGTA 58.299 37.500 0.00 0.00 0.00 2.29
854 889 6.650427 AAGGTCTTTTCCAAGGATGTAAAC 57.350 37.500 0.00 0.00 0.00 2.01
859 894 2.459060 TCCAAGGATGTAAACGCGAA 57.541 45.000 15.93 0.00 0.00 4.70
920 971 3.584848 AGTGGCTCAAAACATCTCCTACT 59.415 43.478 0.00 0.00 0.00 2.57
928 979 4.489306 AAACATCTCCTACTAAGCCCAC 57.511 45.455 0.00 0.00 0.00 4.61
1200 1435 0.612229 TCGAGGAGGTACAGTCGACT 59.388 55.000 13.58 13.58 36.56 4.18
1276 1520 1.643310 AACTCTCCTGCTGCTTCTCT 58.357 50.000 0.00 0.00 0.00 3.10
1622 2253 7.795482 TTTACTGCTACTGTTACATGTTTGT 57.205 32.000 2.30 0.84 39.98 2.83
1623 2254 7.795482 TTACTGCTACTGTTACATGTTTGTT 57.205 32.000 2.30 0.00 37.28 2.83
1624 2255 6.693315 ACTGCTACTGTTACATGTTTGTTT 57.307 33.333 2.30 0.00 37.28 2.83
1625 2256 6.494842 ACTGCTACTGTTACATGTTTGTTTG 58.505 36.000 2.30 0.00 37.28 2.93
1703 2350 3.255725 CAAAAATGTCCATGCTTGCGAT 58.744 40.909 0.00 0.00 0.00 4.58
1707 2354 1.451927 GTCCATGCTTGCGATGGGA 60.452 57.895 17.42 7.06 40.84 4.37
1708 2355 1.153107 TCCATGCTTGCGATGGGAG 60.153 57.895 17.42 1.56 40.84 4.30
1709 2356 1.153107 CCATGCTTGCGATGGGAGA 60.153 57.895 12.83 0.00 37.33 3.71
1710 2357 0.536687 CCATGCTTGCGATGGGAGAT 60.537 55.000 12.83 0.00 37.33 2.75
1711 2358 1.271001 CCATGCTTGCGATGGGAGATA 60.271 52.381 12.83 0.00 37.33 1.98
1712 2359 2.497138 CATGCTTGCGATGGGAGATAA 58.503 47.619 0.00 0.00 0.00 1.75
1713 2360 2.708216 TGCTTGCGATGGGAGATAAA 57.292 45.000 0.00 0.00 0.00 1.40
1714 2361 2.997980 TGCTTGCGATGGGAGATAAAA 58.002 42.857 0.00 0.00 0.00 1.52
1715 2362 3.554934 TGCTTGCGATGGGAGATAAAAT 58.445 40.909 0.00 0.00 0.00 1.82
1716 2363 4.713553 TGCTTGCGATGGGAGATAAAATA 58.286 39.130 0.00 0.00 0.00 1.40
1717 2364 5.316167 TGCTTGCGATGGGAGATAAAATAT 58.684 37.500 0.00 0.00 0.00 1.28
1727 2374 4.286291 GGGAGATAAAATATCACCTCCCGT 59.714 45.833 9.23 0.00 46.97 5.28
1781 2428 5.414360 TCTCAACAGCTAGCTAGTGAAATG 58.586 41.667 18.86 12.33 0.00 2.32
1784 2431 3.866651 ACAGCTAGCTAGTGAAATGTGG 58.133 45.455 18.86 2.64 0.00 4.17
1829 2476 1.243342 CCACCGGAAGAGCATTTGCA 61.243 55.000 9.46 0.00 45.16 4.08
1830 2477 0.109597 CACCGGAAGAGCATTTGCAC 60.110 55.000 9.46 0.00 45.16 4.57
1831 2478 1.244019 ACCGGAAGAGCATTTGCACC 61.244 55.000 9.46 2.33 45.16 5.01
1832 2479 1.135315 CGGAAGAGCATTTGCACCG 59.865 57.895 5.20 9.96 45.16 4.94
1833 2480 1.298157 CGGAAGAGCATTTGCACCGA 61.298 55.000 18.18 0.00 45.16 4.69
1834 2481 1.098050 GGAAGAGCATTTGCACCGAT 58.902 50.000 5.20 0.00 45.16 4.18
1835 2482 1.202222 GGAAGAGCATTTGCACCGATG 60.202 52.381 5.20 0.00 45.16 3.84
1844 2491 2.747460 GCACCGATGCCTTGCTGA 60.747 61.111 0.00 0.00 46.97 4.26
1845 2492 2.334946 GCACCGATGCCTTGCTGAA 61.335 57.895 0.00 0.00 46.97 3.02
1846 2493 1.865788 GCACCGATGCCTTGCTGAAA 61.866 55.000 0.00 0.00 46.97 2.69
1847 2494 0.813184 CACCGATGCCTTGCTGAAAT 59.187 50.000 0.00 0.00 0.00 2.17
1848 2495 0.813184 ACCGATGCCTTGCTGAAATG 59.187 50.000 0.00 0.00 0.00 2.32
1865 2512 6.535274 TGAAATGATGCATTGACTATCTCG 57.465 37.500 0.00 0.00 34.04 4.04
1873 2520 3.553511 GCATTGACTATCTCGAACCTGTG 59.446 47.826 0.00 0.00 0.00 3.66
1924 2571 8.579850 AAGGAACATTGCATTATAAAGACTCA 57.420 30.769 0.00 0.00 0.00 3.41
1925 2572 7.989826 AGGAACATTGCATTATAAAGACTCAC 58.010 34.615 0.00 0.00 0.00 3.51
1926 2573 6.907212 GGAACATTGCATTATAAAGACTCACG 59.093 38.462 0.00 0.00 0.00 4.35
2029 2685 7.537306 GCCCATACTTACGCATATAAAATTGTG 59.463 37.037 0.00 0.00 0.00 3.33
2116 2772 3.482436 GGGGTGTGACATGTTCAAACTA 58.518 45.455 0.00 0.00 41.75 2.24
2272 2928 3.118223 CCTCCCTGTATCTCTTCCCAAAC 60.118 52.174 0.00 0.00 0.00 2.93
2320 2985 5.582550 TGTTGCACATGTACGAATTGAAAA 58.417 33.333 0.00 0.00 0.00 2.29
2346 3011 4.691216 GGTCTGATTTTGTACACTCTGGTC 59.309 45.833 0.00 0.00 0.00 4.02
2440 3108 0.741221 GACGCATCCTCGCCTTCTTT 60.741 55.000 0.00 0.00 0.00 2.52
2531 3202 1.132588 GCGTATGCCTCTGAATCGTC 58.867 55.000 0.00 0.00 33.98 4.20
2825 3621 9.331282 CCTCGGATAGTAAAAATTCTCAGAAAT 57.669 33.333 0.00 0.00 0.00 2.17
3075 3877 7.990886 AGGTCTCATCTAGTTCTAGTAAGACAG 59.009 40.741 22.93 10.05 33.88 3.51
3094 3898 4.893608 ACAGGCAACCAAATTAATTCACC 58.106 39.130 0.10 0.00 37.17 4.02
3165 3970 5.880332 GGATGTTGCTAGAGTGGTTGAATTA 59.120 40.000 0.00 0.00 0.00 1.40
3246 4055 8.138712 GTGTTACCATTTGTCTTGGTCATTAAA 58.861 33.333 0.00 0.00 44.15 1.52
3378 4833 3.065371 CGCTGGAGTAAATTTGGTGGATC 59.935 47.826 0.00 0.00 0.00 3.36
3379 4834 3.065371 GCTGGAGTAAATTTGGTGGATCG 59.935 47.826 0.00 0.00 0.00 3.69
4042 5566 9.816354 AGACTGTTAAGTTGCATTTGTATTTTT 57.184 25.926 0.00 0.00 36.52 1.94
4077 5601 3.198635 AGTGGGTGGATTGTGTATCTCAG 59.801 47.826 0.00 0.00 33.53 3.35
4155 5685 6.879458 AGTATTTACTCATGGAAACTCACACC 59.121 38.462 0.00 0.00 0.00 4.16
4276 5966 0.820871 TTTCGTTGCTTTGCCTTGGT 59.179 45.000 0.00 0.00 0.00 3.67
4578 7260 6.698008 TCTGCATTGTACCATCCATAAAAG 57.302 37.500 0.00 0.00 0.00 2.27
6245 9770 4.717991 TGTTTATTGTGCGTTGCAGATAC 58.282 39.130 0.00 0.00 40.08 2.24
6365 9890 6.434596 TCTTGTTGTTGTTTCGGATTATGTG 58.565 36.000 0.00 0.00 0.00 3.21
6579 10148 8.887264 TTGTTGGTTCTAATGGGTTGTAATAT 57.113 30.769 0.00 0.00 0.00 1.28
6759 10328 2.244486 TCCTCTGTCAGGCTGATCTT 57.756 50.000 21.84 0.00 43.08 2.40
6814 10383 2.833943 TCCTCTGCTCAGTTGCTTCATA 59.166 45.455 0.00 0.00 0.00 2.15
7017 11209 5.353678 CAGAGGACAATTTGATTCTGGTCTC 59.646 44.000 2.79 0.00 0.00 3.36
7191 11424 8.655935 AACTGGAATTTCTTGGATTATGTCTT 57.344 30.769 0.00 0.00 0.00 3.01
7204 11437 5.873164 GGATTATGTCTTGTGTTAAGACCGT 59.127 40.000 14.98 8.12 44.47 4.83
7213 11446 5.518848 TGTGTTAAGACCGTCTCAACTTA 57.481 39.130 14.44 2.60 0.00 2.24
7240 11475 1.300853 GCCATTGCACGTTGCCTTT 60.301 52.632 7.38 0.00 44.23 3.11
7241 11476 1.559149 GCCATTGCACGTTGCCTTTG 61.559 55.000 7.38 3.42 44.23 2.77
7242 11477 0.031857 CCATTGCACGTTGCCTTTGA 59.968 50.000 7.38 0.00 44.23 2.69
7243 11478 1.411394 CATTGCACGTTGCCTTTGAG 58.589 50.000 7.38 0.00 44.23 3.02
7246 11481 1.282875 GCACGTTGCCTTTGAGACC 59.717 57.895 0.00 0.00 37.42 3.85
7247 11482 1.569493 CACGTTGCCTTTGAGACCG 59.431 57.895 0.00 0.00 0.00 4.79
7248 11483 0.878523 CACGTTGCCTTTGAGACCGA 60.879 55.000 0.00 0.00 0.00 4.69
7249 11484 0.878961 ACGTTGCCTTTGAGACCGAC 60.879 55.000 0.00 0.00 0.00 4.79
7250 11485 0.600255 CGTTGCCTTTGAGACCGACT 60.600 55.000 0.00 0.00 0.00 4.18
7261 11496 3.093717 GAGACCGACTCAACTTGTTGA 57.906 47.619 14.42 14.42 44.36 3.18
7270 11505 4.761235 CTCAACTTGTTGAGCATGTCAT 57.239 40.909 24.52 0.00 41.51 3.06
7271 11506 5.117355 CTCAACTTGTTGAGCATGTCATT 57.883 39.130 24.52 0.00 41.51 2.57
7272 11507 4.862350 TCAACTTGTTGAGCATGTCATTG 58.138 39.130 11.62 0.00 34.84 2.82
7273 11508 3.293311 ACTTGTTGAGCATGTCATTGC 57.707 42.857 0.00 0.00 43.09 3.56
7310 11547 4.637091 AGTTTGCCTTGTGTAACGTTACTT 59.363 37.500 32.10 1.05 42.39 2.24
7314 11551 3.185797 GCCTTGTGTAACGTTACTTCCTG 59.814 47.826 32.10 20.77 42.39 3.86
7403 11640 9.479549 AGTGTCAATTAATATGAATTGGAGGTT 57.520 29.630 20.88 5.58 43.87 3.50
7519 11780 5.744171 TCACAGGCTTCATTTATTAGCTCA 58.256 37.500 0.00 0.00 35.30 4.26
7587 11848 2.706339 TTGGTTTGCAGCCAATTTGT 57.294 40.000 17.46 0.00 40.69 2.83
7588 11849 1.950828 TGGTTTGCAGCCAATTTGTG 58.049 45.000 9.30 0.00 32.29 3.33
7637 11898 0.385390 AAAGCTGGAAGTTGCCAACG 59.615 50.000 1.20 0.00 37.52 4.10
7638 11899 0.465460 AAGCTGGAAGTTGCCAACGA 60.465 50.000 1.20 0.00 37.52 3.85
7789 12055 9.259832 AGCAAATTCTTTATAATGGAAGAACCT 57.740 29.630 1.11 0.00 42.67 3.50
7795 12061 9.886132 TTCTTTATAATGGAAGAACCTGAGTAC 57.114 33.333 0.00 0.00 37.06 2.73
7810 12076 2.550606 TGAGTACATTGCGGAAAACCAC 59.449 45.455 0.00 0.00 0.00 4.16
7887 12158 1.411977 CCACCACCATTTTGCTGACAA 59.588 47.619 0.00 0.00 0.00 3.18
7893 12164 3.560481 CACCATTTTGCTGACAATTTGCA 59.440 39.130 0.00 0.00 35.21 4.08
7897 12168 5.387279 CATTTTGCTGACAATTTGCAATCC 58.613 37.500 0.00 0.00 44.55 3.01
7900 12171 2.253603 GCTGACAATTTGCAATCCGTC 58.746 47.619 0.00 7.78 0.00 4.79
7905 12176 5.639757 TGACAATTTGCAATCCGTCAATAG 58.360 37.500 17.87 0.00 30.88 1.73
7912 12183 2.671396 GCAATCCGTCAATAGACACGTT 59.329 45.455 0.00 0.00 45.23 3.99
7913 12184 3.861113 GCAATCCGTCAATAGACACGTTA 59.139 43.478 0.00 0.00 45.23 3.18
7922 12193 4.098960 TCAATAGACACGTTAGATGGGACC 59.901 45.833 0.00 0.00 0.00 4.46
7926 12197 0.462047 CACGTTAGATGGGACCTGCC 60.462 60.000 0.00 0.00 0.00 4.85
7968 12240 7.619161 GCAACAAAACTTACACTGTTTGACTTG 60.619 37.037 2.25 0.00 37.64 3.16
7996 12268 3.850098 CTGCACACAGGACCCACCC 62.850 68.421 0.00 0.00 40.48 4.61
8007 12279 3.479203 CCCACCCGCCAGCATCTA 61.479 66.667 0.00 0.00 0.00 1.98
8008 12280 2.203070 CCACCCGCCAGCATCTAC 60.203 66.667 0.00 0.00 0.00 2.59
8013 12285 1.730902 CCGCCAGCATCTACGATCG 60.731 63.158 14.88 14.88 0.00 3.69
8018 12290 0.941463 CAGCATCTACGATCGTGCCC 60.941 60.000 30.23 13.40 38.31 5.36
8020 12292 0.664767 GCATCTACGATCGTGCCCTC 60.665 60.000 30.23 12.64 0.00 4.30
8022 12294 1.270826 CATCTACGATCGTGCCCTCAT 59.729 52.381 30.23 9.80 0.00 2.90
8025 12297 0.821517 TACGATCGTGCCCTCATGTT 59.178 50.000 30.23 1.10 0.00 2.71
8040 12312 2.827322 TCATGTTGGAATTGGCTTGAGG 59.173 45.455 0.00 0.00 0.00 3.86
8059 12331 3.782244 CGTGCGTGCTGAGAAGGC 61.782 66.667 0.00 0.00 0.00 4.35
8078 12350 2.516930 GTGGCCATCACCATCGGG 60.517 66.667 9.72 0.00 43.01 5.14
8079 12351 4.504596 TGGCCATCACCATCGGGC 62.505 66.667 0.00 0.00 45.67 6.13
8082 12354 2.271821 CCATCACCATCGGGCACA 59.728 61.111 0.00 0.00 37.90 4.57
8083 12355 1.378382 CCATCACCATCGGGCACAA 60.378 57.895 0.00 0.00 37.90 3.33
8085 12357 0.677731 CATCACCATCGGGCACAACT 60.678 55.000 0.00 0.00 37.90 3.16
8086 12358 0.038166 ATCACCATCGGGCACAACTT 59.962 50.000 0.00 0.00 37.90 2.66
8099 12371 2.413371 GCACAACTTGGCGAATCTTCTC 60.413 50.000 0.00 0.00 0.00 2.87
8120 12392 2.257409 ATCAGGCAAACGCTCCCGAT 62.257 55.000 0.00 0.00 38.29 4.18
8121 12393 2.436646 AGGCAAACGCTCCCGATG 60.437 61.111 0.00 0.00 38.29 3.84
8122 12394 2.435938 GGCAAACGCTCCCGATGA 60.436 61.111 0.00 0.00 38.29 2.92
8123 12395 2.750888 GGCAAACGCTCCCGATGAC 61.751 63.158 0.00 0.00 38.29 3.06
8124 12396 3.081133 CAAACGCTCCCGATGACG 58.919 61.111 0.00 0.00 38.29 4.35
8125 12397 1.445410 CAAACGCTCCCGATGACGA 60.445 57.895 0.00 0.00 42.66 4.20
8126 12398 0.806102 CAAACGCTCCCGATGACGAT 60.806 55.000 0.00 0.00 42.66 3.73
8127 12399 0.108329 AAACGCTCCCGATGACGATT 60.108 50.000 0.00 0.00 42.66 3.34
8128 12400 0.742505 AACGCTCCCGATGACGATTA 59.257 50.000 0.00 0.00 42.66 1.75
8129 12401 0.959553 ACGCTCCCGATGACGATTAT 59.040 50.000 0.00 0.00 42.66 1.28
8130 12402 1.068472 ACGCTCCCGATGACGATTATC 60.068 52.381 0.00 0.00 42.66 1.75
8131 12403 1.068541 CGCTCCCGATGACGATTATCA 60.069 52.381 0.00 0.00 42.66 2.15
8132 12404 2.416027 CGCTCCCGATGACGATTATCAT 60.416 50.000 0.00 0.00 42.15 2.45
8144 12416 8.668510 ATGACGATTATCATCCATATTTAGGC 57.331 34.615 0.00 0.00 33.99 3.93
8145 12417 7.047891 TGACGATTATCATCCATATTTAGGCC 58.952 38.462 0.00 0.00 0.00 5.19
8146 12418 6.357367 ACGATTATCATCCATATTTAGGCCC 58.643 40.000 0.00 0.00 0.00 5.80
8147 12419 6.069673 ACGATTATCATCCATATTTAGGCCCA 60.070 38.462 0.00 0.00 0.00 5.36
8148 12420 7.000472 CGATTATCATCCATATTTAGGCCCAT 59.000 38.462 0.00 0.00 0.00 4.00
8149 12421 7.503566 CGATTATCATCCATATTTAGGCCCATT 59.496 37.037 0.00 0.00 0.00 3.16
8150 12422 9.205513 GATTATCATCCATATTTAGGCCCATTT 57.794 33.333 0.00 0.00 0.00 2.32
8151 12423 8.593945 TTATCATCCATATTTAGGCCCATTTC 57.406 34.615 0.00 0.00 0.00 2.17
8152 12424 6.218195 TCATCCATATTTAGGCCCATTTCT 57.782 37.500 0.00 0.00 0.00 2.52
8153 12425 6.623329 TCATCCATATTTAGGCCCATTTCTT 58.377 36.000 0.00 0.00 0.00 2.52
8154 12426 6.494491 TCATCCATATTTAGGCCCATTTCTTG 59.506 38.462 0.00 0.00 0.00 3.02
8155 12427 4.588528 TCCATATTTAGGCCCATTTCTTGC 59.411 41.667 0.00 0.00 0.00 4.01
8156 12428 4.344679 CCATATTTAGGCCCATTTCTTGCA 59.655 41.667 0.00 0.00 0.00 4.08
8157 12429 5.510179 CCATATTTAGGCCCATTTCTTGCAG 60.510 44.000 0.00 0.00 0.00 4.41
8158 12430 2.897271 TTAGGCCCATTTCTTGCAGA 57.103 45.000 0.00 0.00 0.00 4.26
8159 12431 2.897271 TAGGCCCATTTCTTGCAGAA 57.103 45.000 0.00 0.00 31.28 3.02
8160 12432 2.014010 AGGCCCATTTCTTGCAGAAA 57.986 45.000 0.00 11.88 46.89 2.52
8161 12433 1.620323 AGGCCCATTTCTTGCAGAAAC 59.380 47.619 0.00 2.59 45.83 2.78
8162 12434 1.669795 GGCCCATTTCTTGCAGAAACG 60.670 52.381 11.78 5.85 45.83 3.60
8163 12435 1.701704 CCCATTTCTTGCAGAAACGC 58.298 50.000 11.78 0.00 45.83 4.84
8164 12436 1.000385 CCCATTTCTTGCAGAAACGCA 60.000 47.619 11.78 0.00 45.83 5.24
8165 12437 2.353011 CCCATTTCTTGCAGAAACGCAT 60.353 45.455 11.78 0.00 45.83 4.73
8166 12438 3.319755 CCATTTCTTGCAGAAACGCATT 58.680 40.909 11.78 0.00 45.83 3.56
8167 12439 4.484236 CCATTTCTTGCAGAAACGCATTA 58.516 39.130 11.78 0.00 45.83 1.90
8168 12440 4.922692 CCATTTCTTGCAGAAACGCATTAA 59.077 37.500 11.78 0.00 45.83 1.40
8169 12441 5.404968 CCATTTCTTGCAGAAACGCATTAAA 59.595 36.000 11.78 0.00 45.83 1.52
8170 12442 5.881637 TTTCTTGCAGAAACGCATTAAAC 57.118 34.783 7.09 0.00 42.62 2.01
8171 12443 4.560136 TCTTGCAGAAACGCATTAAACA 57.440 36.364 0.00 0.00 42.62 2.83
8172 12444 4.536065 TCTTGCAGAAACGCATTAAACAG 58.464 39.130 0.00 0.00 42.62 3.16
8173 12445 4.274705 TCTTGCAGAAACGCATTAAACAGA 59.725 37.500 0.00 0.00 42.62 3.41
8174 12446 4.145876 TGCAGAAACGCATTAAACAGAG 57.854 40.909 0.00 0.00 36.86 3.35
8175 12447 3.058293 TGCAGAAACGCATTAAACAGAGG 60.058 43.478 0.00 0.00 36.86 3.69
8176 12448 3.188460 GCAGAAACGCATTAAACAGAGGA 59.812 43.478 0.00 0.00 0.00 3.71
8177 12449 4.142600 GCAGAAACGCATTAAACAGAGGAT 60.143 41.667 0.00 0.00 0.00 3.24
8178 12450 5.619981 GCAGAAACGCATTAAACAGAGGATT 60.620 40.000 0.00 0.00 0.00 3.01
8179 12451 6.381801 CAGAAACGCATTAAACAGAGGATTT 58.618 36.000 0.00 0.00 0.00 2.17
8180 12452 7.526608 CAGAAACGCATTAAACAGAGGATTTA 58.473 34.615 0.00 0.00 0.00 1.40
8181 12453 7.693951 CAGAAACGCATTAAACAGAGGATTTAG 59.306 37.037 0.00 0.00 0.00 1.85
8182 12454 7.606456 AGAAACGCATTAAACAGAGGATTTAGA 59.394 33.333 0.00 0.00 0.00 2.10
8183 12455 7.865706 AACGCATTAAACAGAGGATTTAGAT 57.134 32.000 0.00 0.00 0.00 1.98
8184 12456 7.865706 ACGCATTAAACAGAGGATTTAGATT 57.134 32.000 0.00 0.00 0.00 2.40
8185 12457 8.281212 ACGCATTAAACAGAGGATTTAGATTT 57.719 30.769 0.00 0.00 0.00 2.17
8186 12458 8.739972 ACGCATTAAACAGAGGATTTAGATTTT 58.260 29.630 0.00 0.00 0.00 1.82
8187 12459 9.573133 CGCATTAAACAGAGGATTTAGATTTTT 57.427 29.630 0.00 0.00 0.00 1.94
8211 12483 8.984891 TTTTTGCATTCATTAGTCATTAGTGG 57.015 30.769 0.00 0.00 0.00 4.00
8212 12484 5.756195 TGCATTCATTAGTCATTAGTGGC 57.244 39.130 0.00 0.00 0.00 5.01
8213 12485 5.192176 TGCATTCATTAGTCATTAGTGGCA 58.808 37.500 0.00 0.00 30.45 4.92
8214 12486 5.297527 TGCATTCATTAGTCATTAGTGGCAG 59.702 40.000 0.00 0.00 30.45 4.85
8215 12487 5.297776 GCATTCATTAGTCATTAGTGGCAGT 59.702 40.000 0.00 0.00 30.45 4.40
8216 12488 6.483307 GCATTCATTAGTCATTAGTGGCAGTA 59.517 38.462 0.00 0.00 30.45 2.74
8217 12489 7.173907 GCATTCATTAGTCATTAGTGGCAGTAT 59.826 37.037 2.28 0.00 30.45 2.12
8218 12490 8.715998 CATTCATTAGTCATTAGTGGCAGTATC 58.284 37.037 2.28 0.00 30.45 2.24
8219 12491 7.360113 TCATTAGTCATTAGTGGCAGTATCA 57.640 36.000 2.28 0.00 30.45 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 77 9.078753 CGTTTTTACCACAACAAACTATCTTTT 57.921 29.630 0.00 0.00 0.00 2.27
168 170 4.982295 TCTGCATGCGTTGTAGATATGTAC 59.018 41.667 14.09 3.09 41.50 2.90
185 195 0.250209 GGACATCTCCGCATCTGCAT 60.250 55.000 2.72 0.00 42.21 3.96
364 376 3.223435 TCTCTTATCTGCTTCCCTACGG 58.777 50.000 0.00 0.00 0.00 4.02
365 377 4.261825 CCTTCTCTTATCTGCTTCCCTACG 60.262 50.000 0.00 0.00 0.00 3.51
425 437 7.815840 TTTGGAAGATCAATGTTGTAGTCAA 57.184 32.000 0.00 0.00 0.00 3.18
440 452 5.355350 CGCTAGTTTTCTCCATTTGGAAGAT 59.645 40.000 0.18 0.00 44.91 2.40
446 458 2.487762 TGGCGCTAGTTTTCTCCATTTG 59.512 45.455 7.64 0.00 0.00 2.32
518 530 1.912043 CCAGAATTCACCTGAGAGGGT 59.088 52.381 8.44 0.00 40.58 4.34
537 549 5.904362 AAAAACTATCACTCTCAATGCCC 57.096 39.130 0.00 0.00 0.00 5.36
560 578 8.579850 ACATATTGTCATAAAGAGGCAAGAAA 57.420 30.769 0.00 0.00 0.00 2.52
561 579 8.213518 GACATATTGTCATAAAGAGGCAAGAA 57.786 34.615 2.85 0.00 46.22 2.52
562 580 7.792374 GACATATTGTCATAAAGAGGCAAGA 57.208 36.000 2.85 0.00 46.22 3.02
619 639 4.016444 GGCATCACTTAATTCAAGGGTCA 58.984 43.478 0.00 0.00 38.90 4.02
621 641 4.046286 TGGCATCACTTAATTCAAGGGT 57.954 40.909 0.00 0.00 38.90 4.34
651 677 5.184671 GGAAGCAAAGTGGAATTCATCTCTT 59.815 40.000 7.93 4.91 0.00 2.85
698 726 7.319646 TCTAGAGAAAAGCATTGTCTCTTCTC 58.680 38.462 15.54 10.98 44.51 2.87
792 827 9.388506 ACTTGAACATCCAGAGATTACAAATAG 57.611 33.333 0.00 0.00 0.00 1.73
851 886 1.463444 GCTCAGGTACAATTCGCGTTT 59.537 47.619 5.77 0.00 0.00 3.60
854 889 0.460284 AGGCTCAGGTACAATTCGCG 60.460 55.000 0.00 0.00 0.00 5.87
859 894 4.589374 GGTACAGATAGGCTCAGGTACAAT 59.411 45.833 15.72 0.00 38.04 2.71
920 971 0.320858 TTGCGTTCGATGTGGGCTTA 60.321 50.000 0.00 0.00 0.00 3.09
928 979 1.272781 GGAGAGACTTGCGTTCGATG 58.727 55.000 0.00 0.00 0.00 3.84
1063 1131 2.103143 CGGCGCAGAGTAGACTGG 59.897 66.667 10.83 0.00 38.22 4.00
1200 1435 1.686566 CGATGCGCTGCTTCTTCGAA 61.687 55.000 9.73 0.00 31.76 3.71
1295 1544 2.095415 GGAAAATTCGGGGAAACACTCG 60.095 50.000 0.00 0.00 0.00 4.18
1622 2253 3.131933 ACAAGTTGTACATTGCAGCCAAA 59.868 39.130 6.75 0.00 34.05 3.28
1623 2254 2.692557 ACAAGTTGTACATTGCAGCCAA 59.307 40.909 6.75 0.00 35.01 4.52
1624 2255 2.305928 ACAAGTTGTACATTGCAGCCA 58.694 42.857 6.75 0.00 0.00 4.75
1625 2256 3.369546 AACAAGTTGTACATTGCAGCC 57.630 42.857 9.37 0.00 0.00 4.85
1707 2354 4.021368 CGGACGGGAGGTGATATTTTATCT 60.021 45.833 0.00 0.00 0.00 1.98
1708 2355 4.243270 CGGACGGGAGGTGATATTTTATC 58.757 47.826 0.00 0.00 0.00 1.75
1709 2356 3.007614 CCGGACGGGAGGTGATATTTTAT 59.992 47.826 0.00 0.00 38.47 1.40
1710 2357 2.366266 CCGGACGGGAGGTGATATTTTA 59.634 50.000 0.00 0.00 38.47 1.52
1711 2358 1.140252 CCGGACGGGAGGTGATATTTT 59.860 52.381 0.00 0.00 38.47 1.82
1712 2359 0.756903 CCGGACGGGAGGTGATATTT 59.243 55.000 0.00 0.00 38.47 1.40
1713 2360 0.105862 TCCGGACGGGAGGTGATATT 60.106 55.000 11.27 0.00 40.94 1.28
1714 2361 1.540166 TCCGGACGGGAGGTGATAT 59.460 57.895 11.27 0.00 40.94 1.63
1715 2362 3.009275 TCCGGACGGGAGGTGATA 58.991 61.111 11.27 0.00 40.94 2.15
1727 2374 1.225983 CTCTCTGGCTCTCTCCGGA 59.774 63.158 2.93 2.93 39.12 5.14
1784 2431 3.140814 GCTTTCGGATGGGGGCAC 61.141 66.667 0.00 0.00 0.00 5.01
1829 2476 0.813184 CATTTCAGCAAGGCATCGGT 59.187 50.000 0.00 0.00 0.00 4.69
1830 2477 1.097232 TCATTTCAGCAAGGCATCGG 58.903 50.000 0.00 0.00 0.00 4.18
1831 2478 2.727777 CATCATTTCAGCAAGGCATCG 58.272 47.619 0.00 0.00 0.00 3.84
1832 2479 2.159156 TGCATCATTTCAGCAAGGCATC 60.159 45.455 0.00 0.00 34.97 3.91
1833 2480 1.828595 TGCATCATTTCAGCAAGGCAT 59.171 42.857 0.00 0.00 34.97 4.40
1834 2481 1.258676 TGCATCATTTCAGCAAGGCA 58.741 45.000 0.00 0.00 34.97 4.75
1835 2482 2.596904 ATGCATCATTTCAGCAAGGC 57.403 45.000 0.00 0.00 42.15 4.35
1836 2483 3.863424 GTCAATGCATCATTTCAGCAAGG 59.137 43.478 0.00 0.00 42.15 3.61
1837 2484 4.744570 AGTCAATGCATCATTTCAGCAAG 58.255 39.130 0.00 0.00 42.15 4.01
1838 2485 4.794278 AGTCAATGCATCATTTCAGCAA 57.206 36.364 0.00 0.00 42.15 3.91
1839 2486 5.826208 AGATAGTCAATGCATCATTTCAGCA 59.174 36.000 0.00 0.00 43.14 4.41
1840 2487 6.315091 AGATAGTCAATGCATCATTTCAGC 57.685 37.500 0.00 0.00 31.05 4.26
1841 2488 6.423001 TCGAGATAGTCAATGCATCATTTCAG 59.577 38.462 0.00 0.00 31.05 3.02
1842 2489 6.282930 TCGAGATAGTCAATGCATCATTTCA 58.717 36.000 0.00 0.00 31.05 2.69
1843 2490 6.775939 TCGAGATAGTCAATGCATCATTTC 57.224 37.500 0.00 0.00 31.05 2.17
1844 2491 6.017605 GGTTCGAGATAGTCAATGCATCATTT 60.018 38.462 0.00 0.00 31.05 2.32
1845 2492 5.468072 GGTTCGAGATAGTCAATGCATCATT 59.532 40.000 0.00 0.00 34.04 2.57
1846 2493 4.993584 GGTTCGAGATAGTCAATGCATCAT 59.006 41.667 0.00 0.00 0.00 2.45
1847 2494 4.100035 AGGTTCGAGATAGTCAATGCATCA 59.900 41.667 0.00 0.00 0.00 3.07
1848 2495 4.447054 CAGGTTCGAGATAGTCAATGCATC 59.553 45.833 0.00 0.00 0.00 3.91
1865 2512 3.569701 TGAGATTTTCTTGGCACAGGTTC 59.430 43.478 0.00 0.00 42.39 3.62
1873 2520 3.243839 TGCAGGTTTGAGATTTTCTTGGC 60.244 43.478 0.00 0.00 0.00 4.52
1904 2551 7.609760 TTCGTGAGTCTTTATAATGCAATGT 57.390 32.000 0.00 0.00 0.00 2.71
1924 2571 2.571212 TGTGCAGGTTTGAGATTTCGT 58.429 42.857 0.00 0.00 0.00 3.85
1925 2572 3.624326 TTGTGCAGGTTTGAGATTTCG 57.376 42.857 0.00 0.00 0.00 3.46
1926 2573 5.125100 TGATTGTGCAGGTTTGAGATTTC 57.875 39.130 0.00 0.00 0.00 2.17
2043 2699 9.996554 TGAAGTCAGTGATAACAGAAGAATAAA 57.003 29.630 0.00 0.00 0.00 1.40
2068 2724 5.185668 TGTGTTGGTGATTGATTTCAGTG 57.814 39.130 0.00 0.00 0.00 3.66
2116 2772 2.512896 AGCTTCATGATTGTGAGGGGAT 59.487 45.455 0.00 0.00 0.00 3.85
2180 2836 2.007608 GGCATTCGTCCAAGGAAGTAC 58.992 52.381 2.06 0.00 0.00 2.73
2272 2928 0.887933 AAGTGCTTTTGGTATGGCGG 59.112 50.000 0.00 0.00 0.00 6.13
2320 2985 5.300752 CAGAGTGTACAAAATCAGACCTGT 58.699 41.667 0.00 0.00 0.00 4.00
2346 3011 2.887568 GCACGTCGCTCCCTGATG 60.888 66.667 0.00 0.00 37.77 3.07
2400 3068 1.898154 CGGGAGACGGGAAGACAAT 59.102 57.895 0.00 0.00 39.42 2.71
2531 3202 2.814919 ACACGTCTCACTCCTGAACTAG 59.185 50.000 0.00 0.00 0.00 2.57
2579 3370 5.249420 CCAAAGGGAAACAAACAGGAAAAA 58.751 37.500 0.00 0.00 35.59 1.94
2580 3371 4.837972 CCAAAGGGAAACAAACAGGAAAA 58.162 39.130 0.00 0.00 35.59 2.29
2615 3406 3.925090 GGACGGCCCCTCATACGG 61.925 72.222 0.00 0.00 0.00 4.02
2617 3408 4.603946 GCGGACGGCCCCTCATAC 62.604 72.222 0.00 0.00 34.80 2.39
3005 3803 3.196254 TCATCATACAGCTGCTCTTCACA 59.804 43.478 15.27 0.00 0.00 3.58
3075 3877 4.173256 CTCGGTGAATTAATTTGGTTGCC 58.827 43.478 1.43 0.00 0.00 4.52
3094 3898 1.005340 GCTTCAATGGTCAGAGCTCG 58.995 55.000 8.37 3.55 0.00 5.03
3711 5228 8.339714 TCAAGTAAAACACTAATTCAAGAACGG 58.660 33.333 0.00 0.00 36.04 4.44
4042 5566 2.890311 CCACCCACTGTAATTCAAAGCA 59.110 45.455 0.00 0.00 0.00 3.91
4077 5601 7.761409 TGCATAAAGACAATATTCTGAACACC 58.239 34.615 0.00 0.00 0.00 4.16
4155 5685 9.678941 CAATGAACAAGAGAAATATGATCATGG 57.321 33.333 18.72 0.00 36.89 3.66
4276 5966 4.528206 TCATGCAGAAGACAAGTAGGAGAA 59.472 41.667 0.00 0.00 0.00 2.87
4578 7260 8.110860 TCTCAGATCCAATTACCAAAAAGTTC 57.889 34.615 0.00 0.00 0.00 3.01
5981 9503 3.153919 AGAGCAATGTTTTTAAGGCGGA 58.846 40.909 0.00 0.00 0.00 5.54
6365 9890 1.647346 CATGGGATGCAAATGTGTGC 58.353 50.000 0.00 0.00 45.15 4.57
6377 9902 4.282703 GCATTTCTAATCTTGGCATGGGAT 59.717 41.667 0.00 0.00 0.00 3.85
6579 10148 7.549615 CATGTCTGCAAAGAGATTCAAGATA 57.450 36.000 0.00 0.00 0.00 1.98
6759 10328 6.018262 CCAAATACAGAACACGAACTTCTTCA 60.018 38.462 0.00 0.00 0.00 3.02
6814 10383 2.040278 TGATGTAACTTCCCTGCTGCTT 59.960 45.455 0.00 0.00 0.00 3.91
7017 11209 4.005650 TCTAATCAGCAAACAGAAGCCAG 58.994 43.478 0.00 0.00 0.00 4.85
7191 11424 4.395959 AAGTTGAGACGGTCTTAACACA 57.604 40.909 33.49 17.19 43.08 3.72
7241 11476 3.093717 TCAACAAGTTGAGTCGGTCTC 57.906 47.619 10.54 0.00 43.90 3.36
7250 11485 4.793678 GCAATGACATGCTCAACAAGTTGA 60.794 41.667 10.54 14.29 45.75 3.18
7252 11487 3.645884 GCAATGACATGCTCAACAAGTT 58.354 40.909 0.00 0.00 43.06 2.66
7253 11488 3.293311 GCAATGACATGCTCAACAAGT 57.707 42.857 0.00 0.00 43.06 3.16
7262 11497 1.458064 GCACAACAAGCAATGACATGC 59.542 47.619 0.00 0.00 46.78 4.06
7263 11498 2.729360 CAGCACAACAAGCAATGACATG 59.271 45.455 0.00 0.00 0.00 3.21
7264 11499 2.363038 ACAGCACAACAAGCAATGACAT 59.637 40.909 0.00 0.00 0.00 3.06
7265 11500 1.750206 ACAGCACAACAAGCAATGACA 59.250 42.857 0.00 0.00 0.00 3.58
7267 11502 3.631686 ACTTACAGCACAACAAGCAATGA 59.368 39.130 0.00 0.00 0.00 2.57
7268 11503 3.968649 ACTTACAGCACAACAAGCAATG 58.031 40.909 0.00 0.00 0.00 2.82
7269 11504 4.654091 AACTTACAGCACAACAAGCAAT 57.346 36.364 0.00 0.00 0.00 3.56
7270 11505 4.172505 CAAACTTACAGCACAACAAGCAA 58.827 39.130 0.00 0.00 0.00 3.91
7271 11506 3.768406 CAAACTTACAGCACAACAAGCA 58.232 40.909 0.00 0.00 0.00 3.91
7272 11507 2.535574 GCAAACTTACAGCACAACAAGC 59.464 45.455 0.00 0.00 0.00 4.01
7273 11508 3.115554 GGCAAACTTACAGCACAACAAG 58.884 45.455 0.00 0.00 0.00 3.16
7274 11509 2.757868 AGGCAAACTTACAGCACAACAA 59.242 40.909 0.00 0.00 0.00 2.83
7310 11547 9.070179 CAACATCAATTAATATGGATCACAGGA 57.930 33.333 0.00 0.00 0.00 3.86
7435 11691 9.903682 CTCTTATAATGGCAGTGGATTTTTATG 57.096 33.333 0.00 0.00 0.00 1.90
7519 11780 9.338622 GCCTACATGTGGTAATTATTCTAACTT 57.661 33.333 9.11 0.00 0.00 2.66
7548 11809 6.312529 ACCAATCAGCCTCATTATCAATCAT 58.687 36.000 0.00 0.00 0.00 2.45
7586 11847 1.005867 CCAACAACTGGCATGCCAC 60.006 57.895 35.59 11.48 41.89 5.01
7587 11848 3.457484 CCAACAACTGGCATGCCA 58.543 55.556 36.26 36.26 45.02 4.92
7595 11856 3.319755 CAAATAGGCTTGCCAACAACTG 58.680 45.455 14.54 0.00 0.00 3.16
7596 11857 2.289010 GCAAATAGGCTTGCCAACAACT 60.289 45.455 14.54 0.00 44.88 3.16
7597 11858 2.068519 GCAAATAGGCTTGCCAACAAC 58.931 47.619 14.54 0.00 44.88 3.32
7598 11859 2.453983 GCAAATAGGCTTGCCAACAA 57.546 45.000 14.54 0.00 44.88 2.83
7637 11898 2.758497 GCAGCCAAACATGCCAATC 58.242 52.632 0.00 0.00 36.41 2.67
7681 11942 1.468127 CAAGCATGTTGACACCGCATA 59.532 47.619 9.27 0.00 31.97 3.14
7779 12045 3.674997 GCAATGTACTCAGGTTCTTCCA 58.325 45.455 0.00 0.00 39.02 3.53
7789 12055 2.852449 TGGTTTTCCGCAATGTACTCA 58.148 42.857 0.00 0.00 44.36 3.41
7850 12116 3.244215 TGGTGGACTTTTGCAACAACAAA 60.244 39.130 0.00 0.00 37.93 2.83
7852 12118 1.895798 TGGTGGACTTTTGCAACAACA 59.104 42.857 0.00 0.00 37.93 3.33
7853 12119 2.267426 GTGGTGGACTTTTGCAACAAC 58.733 47.619 0.00 0.00 43.28 3.32
7856 12122 0.820871 TGGTGGTGGACTTTTGCAAC 59.179 50.000 0.00 0.00 0.00 4.17
7865 12136 1.000274 GTCAGCAAAATGGTGGTGGAC 60.000 52.381 9.40 0.00 45.21 4.02
7887 12158 4.201812 CGTGTCTATTGACGGATTGCAAAT 60.202 41.667 1.71 0.00 45.70 2.32
7893 12164 5.571784 TCTAACGTGTCTATTGACGGATT 57.428 39.130 2.86 0.07 45.70 3.01
7897 12168 4.042398 CCCATCTAACGTGTCTATTGACG 58.958 47.826 2.86 0.00 45.70 4.35
7900 12171 4.099573 AGGTCCCATCTAACGTGTCTATTG 59.900 45.833 0.00 0.00 0.00 1.90
7905 12176 1.739371 GCAGGTCCCATCTAACGTGTC 60.739 57.143 0.00 0.00 34.59 3.67
7912 12183 3.161450 GCCGGCAGGTCCCATCTA 61.161 66.667 24.80 0.00 40.50 1.98
7922 12193 2.411701 CATCAGCATTGCCGGCAG 59.588 61.111 30.75 20.54 0.00 4.85
7926 12197 2.103538 GCCACATCAGCATTGCCG 59.896 61.111 4.70 0.00 0.00 5.69
7968 12240 1.135972 CCTGTGTGCAGCATAACGTTC 60.136 52.381 2.82 0.00 41.26 3.95
7996 12268 1.008424 ACGATCGTAGATGCTGGCG 60.008 57.895 21.32 0.00 45.12 5.69
7998 12270 0.941463 GGCACGATCGTAGATGCTGG 60.941 60.000 22.26 7.02 45.12 4.85
8007 12279 0.740868 CAACATGAGGGCACGATCGT 60.741 55.000 16.60 16.60 0.00 3.73
8008 12280 1.431488 CCAACATGAGGGCACGATCG 61.431 60.000 14.88 14.88 0.00 3.69
8013 12285 1.205417 CCAATTCCAACATGAGGGCAC 59.795 52.381 0.00 0.00 0.00 5.01
8018 12290 3.119245 CCTCAAGCCAATTCCAACATGAG 60.119 47.826 0.00 0.00 34.33 2.90
8020 12292 2.093869 CCCTCAAGCCAATTCCAACATG 60.094 50.000 0.00 0.00 0.00 3.21
8022 12294 1.631405 CCCTCAAGCCAATTCCAACA 58.369 50.000 0.00 0.00 0.00 3.33
8025 12297 1.678635 CGCCCTCAAGCCAATTCCA 60.679 57.895 0.00 0.00 0.00 3.53
8040 12312 3.782244 CTTCTCAGCACGCACGCC 61.782 66.667 0.00 0.00 0.00 5.68
8068 12340 0.888736 CAAGTTGTGCCCGATGGTGA 60.889 55.000 0.00 0.00 0.00 4.02
8071 12343 2.993471 GCCAAGTTGTGCCCGATGG 61.993 63.158 1.45 0.00 0.00 3.51
8073 12345 3.055719 CGCCAAGTTGTGCCCGAT 61.056 61.111 1.45 0.00 0.00 4.18
8074 12346 3.758973 TTCGCCAAGTTGTGCCCGA 62.759 57.895 1.45 2.03 0.00 5.14
8076 12348 1.212751 GATTCGCCAAGTTGTGCCC 59.787 57.895 1.45 0.00 0.00 5.36
8078 12350 1.537202 AGAAGATTCGCCAAGTTGTGC 59.463 47.619 1.45 4.33 0.00 4.57
8079 12351 2.160417 GGAGAAGATTCGCCAAGTTGTG 59.840 50.000 10.10 0.00 45.20 3.33
8080 12352 2.427506 GGAGAAGATTCGCCAAGTTGT 58.572 47.619 10.10 0.00 45.20 3.32
8099 12371 2.409870 GGGAGCGTTTGCCTGATGG 61.410 63.158 0.00 0.00 44.31 3.51
8120 12392 7.047891 GGCCTAAATATGGATGATAATCGTCA 58.952 38.462 0.00 0.00 34.15 4.35
8121 12393 6.483640 GGGCCTAAATATGGATGATAATCGTC 59.516 42.308 0.84 0.00 0.00 4.20
8122 12394 6.069673 TGGGCCTAAATATGGATGATAATCGT 60.070 38.462 4.53 0.00 0.00 3.73
8123 12395 6.356556 TGGGCCTAAATATGGATGATAATCG 58.643 40.000 4.53 0.00 0.00 3.34
8124 12396 8.773033 AATGGGCCTAAATATGGATGATAATC 57.227 34.615 4.53 0.00 0.00 1.75
8125 12397 9.205513 GAAATGGGCCTAAATATGGATGATAAT 57.794 33.333 4.53 0.00 0.00 1.28
8126 12398 8.401105 AGAAATGGGCCTAAATATGGATGATAA 58.599 33.333 4.53 0.00 0.00 1.75
8127 12399 7.943076 AGAAATGGGCCTAAATATGGATGATA 58.057 34.615 4.53 0.00 0.00 2.15
8128 12400 6.808357 AGAAATGGGCCTAAATATGGATGAT 58.192 36.000 4.53 0.00 0.00 2.45
8129 12401 6.218195 AGAAATGGGCCTAAATATGGATGA 57.782 37.500 4.53 0.00 0.00 2.92
8130 12402 6.694447 CAAGAAATGGGCCTAAATATGGATG 58.306 40.000 4.53 0.00 0.00 3.51
8131 12403 5.246883 GCAAGAAATGGGCCTAAATATGGAT 59.753 40.000 4.53 0.00 0.00 3.41
8132 12404 4.588528 GCAAGAAATGGGCCTAAATATGGA 59.411 41.667 4.53 0.00 0.00 3.41
8133 12405 4.344679 TGCAAGAAATGGGCCTAAATATGG 59.655 41.667 4.53 0.00 0.00 2.74
8134 12406 5.302568 TCTGCAAGAAATGGGCCTAAATATG 59.697 40.000 4.53 0.00 42.31 1.78
8135 12407 5.457686 TCTGCAAGAAATGGGCCTAAATAT 58.542 37.500 4.53 0.00 42.31 1.28
8136 12408 4.865905 TCTGCAAGAAATGGGCCTAAATA 58.134 39.130 4.53 0.00 42.31 1.40
8137 12409 3.711863 TCTGCAAGAAATGGGCCTAAAT 58.288 40.909 4.53 0.00 42.31 1.40
8138 12410 3.168035 TCTGCAAGAAATGGGCCTAAA 57.832 42.857 4.53 0.00 42.31 1.85
8139 12411 2.897271 TCTGCAAGAAATGGGCCTAA 57.103 45.000 4.53 0.00 42.31 2.69
8154 12426 3.188460 TCCTCTGTTTAATGCGTTTCTGC 59.812 43.478 0.00 0.00 0.00 4.26
8155 12427 5.551760 ATCCTCTGTTTAATGCGTTTCTG 57.448 39.130 0.00 0.00 0.00 3.02
8156 12428 6.575162 AAATCCTCTGTTTAATGCGTTTCT 57.425 33.333 0.00 0.00 0.00 2.52
8157 12429 7.748847 TCTAAATCCTCTGTTTAATGCGTTTC 58.251 34.615 0.00 0.00 0.00 2.78
8158 12430 7.681939 TCTAAATCCTCTGTTTAATGCGTTT 57.318 32.000 0.00 0.00 0.00 3.60
8159 12431 7.865706 ATCTAAATCCTCTGTTTAATGCGTT 57.134 32.000 0.00 0.00 0.00 4.84
8160 12432 7.865706 AATCTAAATCCTCTGTTTAATGCGT 57.134 32.000 0.00 0.00 0.00 5.24
8161 12433 9.573133 AAAAATCTAAATCCTCTGTTTAATGCG 57.427 29.630 0.00 0.00 0.00 4.73
8186 12458 7.545265 GCCACTAATGACTAATGAATGCAAAAA 59.455 33.333 0.00 0.00 0.00 1.94
8187 12459 7.035004 GCCACTAATGACTAATGAATGCAAAA 58.965 34.615 0.00 0.00 0.00 2.44
8188 12460 6.152492 TGCCACTAATGACTAATGAATGCAAA 59.848 34.615 0.00 0.00 0.00 3.68
8189 12461 5.651576 TGCCACTAATGACTAATGAATGCAA 59.348 36.000 0.00 0.00 0.00 4.08
8190 12462 5.192176 TGCCACTAATGACTAATGAATGCA 58.808 37.500 0.00 0.00 0.00 3.96
8191 12463 5.297776 ACTGCCACTAATGACTAATGAATGC 59.702 40.000 0.00 0.00 0.00 3.56
8192 12464 6.932356 ACTGCCACTAATGACTAATGAATG 57.068 37.500 0.00 0.00 0.00 2.67
8193 12465 8.432013 TGATACTGCCACTAATGACTAATGAAT 58.568 33.333 0.00 0.00 0.00 2.57
8194 12466 7.791029 TGATACTGCCACTAATGACTAATGAA 58.209 34.615 0.00 0.00 0.00 2.57
8195 12467 7.360113 TGATACTGCCACTAATGACTAATGA 57.640 36.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.