Multiple sequence alignment - TraesCS2A01G567000

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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 TraesCS2A01G567000 chr2A 100.000 6073 0 0 1 6073 765995628 766001700 0.000000e+00 11215.0
1 TraesCS2A01G567000 chr2A 80.519 231 30 9 765 986 182858942 182858718 4.870000e-36 163.0
2 TraesCS2A01G567000 chr2A 100.000 35 0 0 3609 3643 765999185 765999219 1.410000e-06 65.8
3 TraesCS2A01G567000 chr2A 100.000 35 0 0 3558 3592 765999236 765999270 1.410000e-06 65.8
4 TraesCS2A01G567000 chr2D 90.678 1963 126 25 3535 5457 163280103 163278158 0.000000e+00 2558.0
5 TraesCS2A01G567000 chr2D 92.851 1077 70 7 1474 2546 163311748 163310675 0.000000e+00 1555.0
6 TraesCS2A01G567000 chr2D 89.329 909 91 3 2619 3526 163288478 163287575 0.000000e+00 1136.0
7 TraesCS2A01G567000 chr2D 91.636 550 20 2 1 524 88578378 88577829 0.000000e+00 737.0
8 TraesCS2A01G567000 chr2D 86.478 673 68 10 527 1186 6464937 6465599 0.000000e+00 717.0
9 TraesCS2A01G567000 chr2D 83.254 633 59 19 1662 2267 6466409 6467021 6.930000e-149 538.0
10 TraesCS2A01G567000 chr2D 90.494 263 23 2 1185 1447 6465632 6465892 4.510000e-91 346.0
11 TraesCS2A01G567000 chr2D 82.063 223 25 9 773 986 565531029 565530813 6.260000e-40 176.0
12 TraesCS2A01G567000 chr2D 96.203 79 3 0 2543 2621 163296555 163296477 4.940000e-26 130.0
13 TraesCS2A01G567000 chr2D 97.333 75 2 0 1399 1473 163312074 163312000 1.780000e-25 128.0
14 TraesCS2A01G567000 chr1D 86.988 2221 168 56 3380 5564 427901377 427899242 0.000000e+00 2388.0
15 TraesCS2A01G567000 chr1D 89.247 372 15 4 1 347 392698655 392699026 5.590000e-120 442.0
16 TraesCS2A01G567000 chr1D 89.498 219 19 4 527 744 427902060 427901845 2.160000e-69 274.0
17 TraesCS2A01G567000 chr1D 92.857 42 3 0 2893 2934 74910455 74910414 1.830000e-05 62.1
18 TraesCS2A01G567000 chr1A 86.404 2236 182 57 3367 5564 584950874 584953025 0.000000e+00 2333.0
19 TraesCS2A01G567000 chr1A 88.889 216 21 3 527 741 584950212 584950425 4.670000e-66 263.0
20 TraesCS2A01G567000 chr1A 79.808 208 27 11 788 986 450978453 450978252 2.950000e-28 137.0
21 TraesCS2A01G567000 chr7A 87.962 2002 176 28 3324 5298 690522418 690520455 0.000000e+00 2302.0
22 TraesCS2A01G567000 chr7A 89.594 567 31 10 1 540 735731347 735731912 0.000000e+00 695.0
23 TraesCS2A01G567000 chr7A 81.739 230 29 10 765 986 499852516 499852740 4.840000e-41 180.0
24 TraesCS2A01G567000 chr7A 81.818 231 27 9 765 986 499900875 499901099 4.840000e-41 180.0
25 TraesCS2A01G567000 chr7A 83.962 106 14 1 5806 5908 670180872 670180977 1.390000e-16 99.0
26 TraesCS2A01G567000 chr5B 84.612 2281 240 60 3317 5561 708042047 708044252 0.000000e+00 2165.0
27 TraesCS2A01G567000 chr5B 87.939 1252 114 16 3317 4563 186847556 186848775 0.000000e+00 1441.0
28 TraesCS2A01G567000 chr5B 88.634 915 66 11 4400 5298 186848767 186849659 0.000000e+00 1079.0
29 TraesCS2A01G567000 chr5B 87.654 324 15 7 1 299 73548074 73547751 2.690000e-93 353.0
30 TraesCS2A01G567000 chr5B 87.037 324 17 10 1 299 102943418 102943741 5.830000e-90 342.0
31 TraesCS2A01G567000 chr5B 94.977 219 9 2 1 218 267833205 267832988 5.830000e-90 342.0
32 TraesCS2A01G567000 chr5B 85.514 214 28 3 313 523 547827081 547827294 2.850000e-53 220.0
33 TraesCS2A01G567000 chr5B 79.646 226 32 7 765 982 166676462 166676681 3.790000e-32 150.0
34 TraesCS2A01G567000 chr5B 76.163 172 34 7 2893 3059 405742721 405742890 3.900000e-12 84.2
35 TraesCS2A01G567000 chr5B 91.525 59 5 0 5500 5558 186850077 186850135 1.400000e-11 82.4
36 TraesCS2A01G567000 chr5B 82.927 82 7 6 2225 2303 578793974 578793897 3.930000e-07 67.6
37 TraesCS2A01G567000 chr7B 89.247 1674 132 15 3642 5298 394816328 394817970 0.000000e+00 2050.0
38 TraesCS2A01G567000 chr7B 79.795 975 121 42 4632 5559 399244762 399245707 1.850000e-179 640.0
39 TraesCS2A01G567000 chr7B 85.811 296 33 7 3317 3608 394815436 394815726 7.650000e-79 305.0
40 TraesCS2A01G567000 chr3B 87.802 1738 140 21 3642 5352 173553256 173554948 0.000000e+00 1969.0
41 TraesCS2A01G567000 chr3B 90.000 430 19 9 5561 5966 174984137 174983708 8.960000e-148 534.0
42 TraesCS2A01G567000 chr3B 85.219 548 50 17 1 519 829294734 829294189 8.960000e-148 534.0
43 TraesCS2A01G567000 chr3B 87.346 324 16 10 1 299 480458142 480458465 1.250000e-91 348.0
44 TraesCS2A01G567000 chr2B 89.120 1250 101 10 3644 4890 795016728 795015511 0.000000e+00 1522.0
45 TraesCS2A01G567000 chr2B 87.309 1245 120 17 3317 4556 74180822 74179611 0.000000e+00 1389.0
46 TraesCS2A01G567000 chr2B 89.410 916 72 8 4399 5298 74179615 74178709 0.000000e+00 1131.0
47 TraesCS2A01G567000 chr2B 89.767 430 19 8 5561 5966 628949891 628949463 1.500000e-145 527.0
48 TraesCS2A01G567000 chr2B 80.227 440 22 20 5561 5961 726688271 726687858 2.790000e-68 270.0
49 TraesCS2A01G567000 chr2B 79.532 171 31 4 2893 3059 597543811 597543981 1.070000e-22 119.0
50 TraesCS2A01G567000 chr2B 89.474 76 8 0 5489 5564 74178357 74178282 5.010000e-16 97.1
51 TraesCS2A01G567000 chr6D 80.586 989 162 17 2225 3200 122376249 122375278 0.000000e+00 736.0
52 TraesCS2A01G567000 chr3D 91.176 544 20 16 1 518 110263803 110263262 0.000000e+00 713.0
53 TraesCS2A01G567000 chr3A 85.438 673 75 10 527 1186 359069039 359068377 0.000000e+00 678.0
54 TraesCS2A01G567000 chr3A 83.412 633 58 19 1662 2267 359067570 359066958 1.490000e-150 544.0
55 TraesCS2A01G567000 chr3A 87.197 289 26 5 1185 1473 359068344 359068067 9.820000e-83 318.0
56 TraesCS2A01G567000 chr3A 81.633 98 18 0 2310 2407 359066953 359066856 1.400000e-11 82.4
57 TraesCS2A01G567000 chr5D 87.956 548 24 12 1 521 200804343 200803811 5.200000e-170 608.0
58 TraesCS2A01G567000 chr5D 88.542 192 20 2 328 518 58537290 58537480 1.320000e-56 231.0
59 TraesCS2A01G567000 chr5D 94.000 50 3 0 2893 2942 27253690 27253739 6.530000e-10 76.8
60 TraesCS2A01G567000 chr6A 91.647 431 11 10 5561 5966 307899130 307899560 1.900000e-159 573.0
61 TraesCS2A01G567000 chr6A 81.053 190 32 4 3012 3200 149920018 149920204 1.360000e-31 148.0
62 TraesCS2A01G567000 chr4A 89.977 429 19 9 5562 5966 706194444 706194872 3.220000e-147 532.0
63 TraesCS2A01G567000 chr4A 94.340 53 3 0 5966 6018 706196647 706196699 1.400000e-11 82.4
64 TraesCS2A01G567000 chr7D 89.583 192 18 2 328 518 567973519 567973709 6.080000e-60 243.0
65 TraesCS2A01G567000 chr7D 82.716 81 7 5 2225 2303 612726636 612726711 1.410000e-06 65.8
66 TraesCS2A01G567000 chr4D 87.940 199 23 1 328 525 479955253 479955451 3.660000e-57 233.0
67 TraesCS2A01G567000 chr5A 85.648 216 30 1 304 518 295072122 295072337 6.120000e-55 226.0
68 TraesCS2A01G567000 chr6B 80.000 190 34 4 3012 3200 214057439 214057253 2.950000e-28 137.0
69 TraesCS2A01G567000 chr6B 82.927 82 14 0 2894 2975 49729866 49729785 2.350000e-09 75.0
70 TraesCS2A01G567000 chr6B 82.927 82 9 5 2893 2971 712186674 712186753 1.090000e-07 69.4
71 TraesCS2A01G567000 chr1B 78.182 110 19 5 2894 3000 598924617 598924510 1.410000e-06 65.8


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 TraesCS2A01G567000 chr2A 765995628 766001700 6072 False 3782.200000 11215 100.0000 1 6073 3 chr2A.!!$F1 6072
1 TraesCS2A01G567000 chr2D 163278158 163280103 1945 True 2558.000000 2558 90.6780 3535 5457 1 chr2D.!!$R2 1922
2 TraesCS2A01G567000 chr2D 163287575 163288478 903 True 1136.000000 1136 89.3290 2619 3526 1 chr2D.!!$R3 907
3 TraesCS2A01G567000 chr2D 163310675 163312074 1399 True 841.500000 1555 95.0920 1399 2546 2 chr2D.!!$R6 1147
4 TraesCS2A01G567000 chr2D 88577829 88578378 549 True 737.000000 737 91.6360 1 524 1 chr2D.!!$R1 523
5 TraesCS2A01G567000 chr2D 6464937 6467021 2084 False 533.666667 717 86.7420 527 2267 3 chr2D.!!$F1 1740
6 TraesCS2A01G567000 chr1D 427899242 427902060 2818 True 1331.000000 2388 88.2430 527 5564 2 chr1D.!!$R2 5037
7 TraesCS2A01G567000 chr1A 584950212 584953025 2813 False 1298.000000 2333 87.6465 527 5564 2 chr1A.!!$F1 5037
8 TraesCS2A01G567000 chr7A 690520455 690522418 1963 True 2302.000000 2302 87.9620 3324 5298 1 chr7A.!!$R1 1974
9 TraesCS2A01G567000 chr7A 735731347 735731912 565 False 695.000000 695 89.5940 1 540 1 chr7A.!!$F4 539
10 TraesCS2A01G567000 chr5B 708042047 708044252 2205 False 2165.000000 2165 84.6120 3317 5561 1 chr5B.!!$F5 2244
11 TraesCS2A01G567000 chr5B 186847556 186850135 2579 False 867.466667 1441 89.3660 3317 5558 3 chr5B.!!$F6 2241
12 TraesCS2A01G567000 chr7B 394815436 394817970 2534 False 1177.500000 2050 87.5290 3317 5298 2 chr7B.!!$F2 1981
13 TraesCS2A01G567000 chr7B 399244762 399245707 945 False 640.000000 640 79.7950 4632 5559 1 chr7B.!!$F1 927
14 TraesCS2A01G567000 chr3B 173553256 173554948 1692 False 1969.000000 1969 87.8020 3642 5352 1 chr3B.!!$F1 1710
15 TraesCS2A01G567000 chr3B 829294189 829294734 545 True 534.000000 534 85.2190 1 519 1 chr3B.!!$R2 518
16 TraesCS2A01G567000 chr2B 795015511 795016728 1217 True 1522.000000 1522 89.1200 3644 4890 1 chr2B.!!$R3 1246
17 TraesCS2A01G567000 chr2B 74178282 74180822 2540 True 872.366667 1389 88.7310 3317 5564 3 chr2B.!!$R4 2247
18 TraesCS2A01G567000 chr6D 122375278 122376249 971 True 736.000000 736 80.5860 2225 3200 1 chr6D.!!$R1 975
19 TraesCS2A01G567000 chr3D 110263262 110263803 541 True 713.000000 713 91.1760 1 518 1 chr3D.!!$R1 517
20 TraesCS2A01G567000 chr3A 359066856 359069039 2183 True 405.600000 678 84.4200 527 2407 4 chr3A.!!$R1 1880
21 TraesCS2A01G567000 chr5D 200803811 200804343 532 True 608.000000 608 87.9560 1 521 1 chr5D.!!$R1 520
22 TraesCS2A01G567000 chr4A 706194444 706196699 2255 False 307.200000 532 92.1585 5562 6018 2 chr4A.!!$F1 456

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
803 845 0.464036 TCAGCAGTATAACGCCCTGG 59.536 55.0 0.00 0.00 0.00 4.45 F
1037 1091 0.250467 ATGTCACTTTGGTGCGCTCT 60.250 50.0 9.73 0.00 42.72 4.09 F
2794 3236 0.245539 GCACAAGCTTGGATGCACAT 59.754 50.0 27.90 6.64 38.00 3.21 F
3172 3619 0.176680 CAGATCTGGTGCCGTTAGCT 59.823 55.0 15.38 0.00 44.23 3.32 F
3313 3760 0.178944 TCCAGGGTTCTCCTTCGTCA 60.179 55.0 0.00 0.00 45.47 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2775 3217 0.245539 ATGTGCATCCAAGCTTGTGC 59.754 50.000 26.78 26.78 38.05 4.57 R
2957 3404 0.181350 ATTTCCTGGAGATGTCGGCC 59.819 55.000 0.00 0.00 0.00 6.13 R
4204 5234 0.951558 CCACAGGCACACTACCAAAC 59.048 55.000 0.00 0.00 0.00 2.93 R
4925 6178 1.380650 TTTAATGCCCCCGCCTTCC 60.381 57.895 0.00 0.00 0.00 3.46 R
5074 6377 2.875933 TCACGGACTTCAAAATCCACAC 59.124 45.455 0.00 0.00 34.35 3.82 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
119 120 3.963687 TAGTGGCGTCGCTCGGAGA 62.964 63.158 18.11 0.00 40.26 3.71
511 545 9.816787 AACTTTATTCAGGGTAGTAAAATGGAA 57.183 29.630 0.00 0.00 0.00 3.53
562 596 6.604735 TCTCTAACAGAAAGTTTGTTGCTC 57.395 37.500 0.00 0.00 41.64 4.26
564 598 6.258727 TCTCTAACAGAAAGTTTGTTGCTCTG 59.741 38.462 0.00 0.00 41.64 3.35
566 600 5.643379 AACAGAAAGTTTGTTGCTCTGAA 57.357 34.783 6.93 0.00 37.03 3.02
585 619 7.391148 TCTGAAAAATGCTAATGGTACCTTC 57.609 36.000 14.36 4.93 0.00 3.46
641 676 3.832490 GGGGCTTCCTTTAATGTTCTGTT 59.168 43.478 0.00 0.00 0.00 3.16
668 709 8.287350 ACCTCCTTTCTATAGTTACAGTATCCA 58.713 37.037 0.00 0.00 0.00 3.41
706 747 6.464895 AACAAATGAAACATGGTAATTGCG 57.535 33.333 0.00 0.00 0.00 4.85
709 750 3.463533 TGAAACATGGTAATTGCGTCG 57.536 42.857 0.00 0.00 0.00 5.12
712 753 4.155099 TGAAACATGGTAATTGCGTCGATT 59.845 37.500 0.00 0.00 0.00 3.34
729 770 5.561919 CGTCGATTGAAAATTTGGTCCTTCA 60.562 40.000 0.00 0.00 0.00 3.02
734 775 7.274250 CGATTGAAAATTTGGTCCTTCAGATTC 59.726 37.037 0.00 0.00 0.00 2.52
735 776 6.975196 TGAAAATTTGGTCCTTCAGATTCA 57.025 33.333 0.00 0.00 0.00 2.57
736 777 6.985117 TGAAAATTTGGTCCTTCAGATTCAG 58.015 36.000 0.00 0.00 0.00 3.02
803 845 0.464036 TCAGCAGTATAACGCCCTGG 59.536 55.000 0.00 0.00 0.00 4.45
807 850 1.134491 GCAGTATAACGCCCTGGTCTT 60.134 52.381 0.00 0.00 0.00 3.01
810 853 4.369182 CAGTATAACGCCCTGGTCTTAAG 58.631 47.826 0.00 0.00 0.00 1.85
824 867 6.254281 TGGTCTTAAGTCTTTATTTGCTGC 57.746 37.500 1.63 0.00 0.00 5.25
828 871 7.814587 GGTCTTAAGTCTTTATTTGCTGCAAAT 59.185 33.333 34.60 34.60 44.74 2.32
869 912 9.284594 CGTGTTTATATGTTCCAAAATTGTAGG 57.715 33.333 0.00 0.00 0.00 3.18
870 913 9.083080 GTGTTTATATGTTCCAAAATTGTAGGC 57.917 33.333 0.00 0.00 0.00 3.93
910 953 5.368816 TGATGAGGATCTTCTGATGGATGTT 59.631 40.000 6.38 0.00 39.76 2.71
965 1019 8.951243 GCATCTTCCTTTCTTTAGTAACTCAAT 58.049 33.333 0.00 0.00 0.00 2.57
990 1044 2.568509 CCAATGGGCAACTCAATTTCCT 59.431 45.455 0.00 0.00 0.00 3.36
992 1046 4.381932 CCAATGGGCAACTCAATTTCCTAC 60.382 45.833 0.00 0.00 0.00 3.18
999 1053 3.695830 ACTCAATTTCCTACGGCTTGA 57.304 42.857 0.00 0.00 0.00 3.02
1025 1079 4.760047 GGGTCGCGCCATGTCACT 62.760 66.667 18.87 0.00 39.65 3.41
1027 1081 2.325082 GGTCGCGCCATGTCACTTT 61.325 57.895 13.61 0.00 37.17 2.66
1032 1086 1.081242 CGCCATGTCACTTTGGTGC 60.081 57.895 0.00 0.00 42.72 5.01
1037 1091 0.250467 ATGTCACTTTGGTGCGCTCT 60.250 50.000 9.73 0.00 42.72 4.09
1040 1094 1.597854 CACTTTGGTGCGCTCTGGA 60.598 57.895 9.73 0.00 36.61 3.86
1048 1102 2.340328 TGCGCTCTGGAGACGCTAA 61.340 57.895 25.92 13.65 46.30 3.09
1050 1104 1.803943 CGCTCTGGAGACGCTAAGT 59.196 57.895 1.35 0.00 0.00 2.24
1081 1135 2.125350 CTCGGCTGCAGAGGGTTC 60.125 66.667 20.43 0.00 32.38 3.62
1092 1146 0.896940 AGAGGGTTCGTTCGGCAGTA 60.897 55.000 0.00 0.00 0.00 2.74
1103 1157 4.294523 GGCAGTAATGTGGCGTGA 57.705 55.556 0.00 0.00 32.71 4.35
1105 1159 1.094785 GGCAGTAATGTGGCGTGATT 58.905 50.000 0.00 0.00 32.71 2.57
1108 1162 1.094785 AGTAATGTGGCGTGATTGGC 58.905 50.000 0.00 0.00 0.00 4.52
1148 1202 2.738480 GGTGACACCGTGGCTACA 59.262 61.111 9.33 0.00 0.00 2.74
1159 1213 1.270094 CGTGGCTACAACAGAGGACAA 60.270 52.381 0.00 0.00 0.00 3.18
1161 1215 2.047061 TGGCTACAACAGAGGACAACT 58.953 47.619 0.00 0.00 0.00 3.16
1162 1216 2.438021 TGGCTACAACAGAGGACAACTT 59.562 45.455 0.00 0.00 0.00 2.66
1165 1219 3.304057 GCTACAACAGAGGACAACTTTGC 60.304 47.826 0.00 0.00 34.79 3.68
1166 1220 3.004752 ACAACAGAGGACAACTTTGCT 57.995 42.857 0.00 0.00 34.79 3.91
1217 1305 0.811616 GTTACTGGCCTCTGCATCGG 60.812 60.000 3.32 0.00 40.13 4.18
1219 1307 4.172512 CTGGCCTCTGCATCGGCT 62.173 66.667 21.40 0.00 45.57 5.52
1221 1309 4.479993 GGCCTCTGCATCGGCTGT 62.480 66.667 21.40 0.00 45.57 4.40
1227 1315 2.743538 TGCATCGGCTGTGTGCTC 60.744 61.111 20.62 0.00 42.39 4.26
1275 1363 4.512914 GGGCATGGCTGGGTCCTC 62.513 72.222 19.78 0.00 0.00 3.71
1277 1365 3.785859 GCATGGCTGGGTCCTCGA 61.786 66.667 0.00 0.00 0.00 4.04
1279 1367 2.284625 ATGGCTGGGTCCTCGACA 60.285 61.111 0.00 0.00 33.68 4.35
1283 1371 2.105128 CTGGGTCCTCGACATCGC 59.895 66.667 0.00 0.00 39.60 4.58
1284 1372 3.432051 CTGGGTCCTCGACATCGCC 62.432 68.421 0.00 0.00 39.60 5.54
1288 1376 1.009900 GTCCTCGACATCGCCTACG 60.010 63.158 0.00 0.00 39.60 3.51
1296 1384 0.458543 ACATCGCCTACGTGAGCTTG 60.459 55.000 0.00 4.30 41.18 4.01
1343 1431 6.798482 TGGTTTGATCTCAATGCAACATATC 58.202 36.000 0.00 0.00 35.55 1.63
1349 1437 8.102800 TGATCTCAATGCAACATATCAATACC 57.897 34.615 0.00 0.00 0.00 2.73
1350 1438 6.882610 TCTCAATGCAACATATCAATACCC 57.117 37.500 0.00 0.00 0.00 3.69
1357 1445 5.356751 TGCAACATATCAATACCCAGTGTTC 59.643 40.000 0.00 0.00 0.00 3.18
1377 1465 5.355071 TGTTCCTTATTCTGCACATGATCAC 59.645 40.000 0.00 0.00 0.00 3.06
1391 1479 7.122501 TGCACATGATCACAGTAATTGGTATTT 59.877 33.333 0.00 0.00 0.00 1.40
1417 1505 3.007614 GTGCCACTTTGTCTAGAAGGGTA 59.992 47.826 0.00 0.00 0.00 3.69
1485 1825 5.296151 TGATGGATTAGGAGGACATTCAC 57.704 43.478 0.00 0.00 0.00 3.18
1515 1855 1.078918 CCATCTGCGAACAGGCTCA 60.079 57.895 0.00 0.00 44.59 4.26
1718 2126 2.483877 TCGCAGATGACAAATCAACCAC 59.516 45.455 0.00 0.00 38.69 4.16
1753 2161 6.668541 ACCTTTGTAATTCTCATCATGTCG 57.331 37.500 0.00 0.00 0.00 4.35
1757 2165 4.122046 TGTAATTCTCATCATGTCGCAGG 58.878 43.478 0.00 0.00 0.00 4.85
1761 2169 4.406648 TTCTCATCATGTCGCAGGTAAT 57.593 40.909 0.00 0.00 0.00 1.89
1836 2247 9.154632 TGCTAATAAAATGGGAGTCAGAGTATA 57.845 33.333 0.00 0.00 0.00 1.47
1966 2377 4.237724 TCTCAACATAAGCAGAACACGAG 58.762 43.478 0.00 0.00 0.00 4.18
1970 2381 2.480419 ACATAAGCAGAACACGAGCAAC 59.520 45.455 0.00 0.00 0.00 4.17
2041 2452 5.470437 GGAAACAGAAACGGAGAATTCTCTT 59.530 40.000 29.64 18.93 42.48 2.85
2047 2458 7.813627 ACAGAAACGGAGAATTCTCTTTAGTAC 59.186 37.037 29.64 20.13 42.48 2.73
2121 2532 7.452630 TTTAATTGTTAACACCGCAAAGTTC 57.547 32.000 8.07 0.00 0.00 3.01
2165 2601 8.501580 CAGTACATGTTGATCATTGCTAATAGG 58.498 37.037 2.30 0.00 34.09 2.57
2176 2612 9.323985 GATCATTGCTAATAGGATGAATAGGTC 57.676 37.037 0.00 0.00 0.00 3.85
2189 2625 7.121759 AGGATGAATAGGTCTGTTCATTGTTTG 59.878 37.037 19.08 0.00 46.60 2.93
2306 2744 8.810652 TTGAATTAACAAAGCCATTAACTGAC 57.189 30.769 0.00 0.00 0.00 3.51
2353 2791 8.920665 CAACATAACACAAGAACAACAGAAAAA 58.079 29.630 0.00 0.00 0.00 1.94
2392 2831 6.310467 TGCACTTGAAAGTAGATTACTAAGCG 59.690 38.462 0.00 0.00 38.26 4.68
2457 2899 1.956297 AGACATCGAGGTCCTCTACG 58.044 55.000 25.28 4.72 38.59 3.51
2495 2937 1.144936 AGAAGCATGCCGGCTCTAC 59.855 57.895 29.70 14.46 45.07 2.59
2497 2939 0.744414 GAAGCATGCCGGCTCTACAA 60.744 55.000 29.70 6.08 45.07 2.41
2520 2962 1.667724 GGAATGAAGATGCACCGTCAG 59.332 52.381 2.37 0.00 0.00 3.51
2521 2963 2.350522 GAATGAAGATGCACCGTCAGT 58.649 47.619 2.37 0.00 0.00 3.41
2644 3086 2.443416 TCCGTCGGAAGATCAGAAAGA 58.557 47.619 12.68 0.00 45.19 2.52
2671 3113 0.820891 GAACATGGATGGATGCCGCT 60.821 55.000 0.00 0.00 0.00 5.52
2681 3123 3.704231 GATGCCGCTGGGTGGTCAT 62.704 63.158 0.00 6.71 35.34 3.06
2775 3217 0.602905 AGAACACGGCGGAGGAAAAG 60.603 55.000 13.24 0.00 0.00 2.27
2794 3236 0.245539 GCACAAGCTTGGATGCACAT 59.754 50.000 27.90 6.64 38.00 3.21
2798 3240 0.251922 AAGCTTGGATGCACATGGGT 60.252 50.000 0.00 0.00 34.99 4.51
2812 3254 0.538977 ATGGGTATGCCATCTGCTGC 60.539 55.000 1.04 0.00 42.00 5.25
2815 3257 0.465097 GGTATGCCATCTGCTGCTGT 60.465 55.000 0.00 0.00 42.00 4.40
2817 3259 0.542805 TATGCCATCTGCTGCTGTCA 59.457 50.000 0.00 0.00 42.00 3.58
2831 3273 1.742831 GCTGTCACTGAACACAAACCA 59.257 47.619 0.00 0.00 0.00 3.67
2971 3418 2.303549 GACCTGGCCGACATCTCCAG 62.304 65.000 0.00 9.04 45.24 3.86
3020 3467 2.885644 CATCGTGGCCGGTCGAAG 60.886 66.667 18.32 12.06 39.45 3.79
3132 3579 1.072505 GGGAAGGAAGCACACCGAA 59.927 57.895 0.00 0.00 0.00 4.30
3151 3598 0.827925 ACAGGGAAGACGAGCAGTGA 60.828 55.000 0.00 0.00 0.00 3.41
3172 3619 0.176680 CAGATCTGGTGCCGTTAGCT 59.823 55.000 15.38 0.00 44.23 3.32
3173 3620 1.409064 CAGATCTGGTGCCGTTAGCTA 59.591 52.381 15.38 0.00 44.23 3.32
3215 3662 1.152963 CAAGGCCCCTAATCCACCG 60.153 63.158 0.00 0.00 0.00 4.94
3216 3663 2.383601 AAGGCCCCTAATCCACCGG 61.384 63.158 0.00 0.00 0.00 5.28
3232 3679 2.264794 GGTGGTCCGTCTGCGAAT 59.735 61.111 0.00 0.00 41.33 3.34
3248 3695 1.927174 CGAATCGACCAGACCATCAAC 59.073 52.381 0.00 0.00 0.00 3.18
3249 3696 2.280628 GAATCGACCAGACCATCAACC 58.719 52.381 0.00 0.00 0.00 3.77
3250 3697 1.275666 ATCGACCAGACCATCAACCA 58.724 50.000 0.00 0.00 0.00 3.67
3251 3698 0.320374 TCGACCAGACCATCAACCAC 59.680 55.000 0.00 0.00 0.00 4.16
3313 3760 0.178944 TCCAGGGTTCTCCTTCGTCA 60.179 55.000 0.00 0.00 45.47 4.35
3359 3806 4.447342 CAATCCCCGGCTGCCCTT 62.447 66.667 14.12 0.00 0.00 3.95
3407 3858 2.291043 GGCGGTGAGGAGGGAAAGA 61.291 63.158 0.00 0.00 0.00 2.52
3510 3967 7.878644 ACTGAACCTTATCTTGTTCCTTAGTTC 59.121 37.037 0.00 0.00 40.06 3.01
3528 3985 9.590451 CCTTAGTTCATTTAGACCGTTTGTATA 57.410 33.333 0.00 0.00 0.00 1.47
3531 3988 8.658499 AGTTCATTTAGACCGTTTGTATATCC 57.342 34.615 0.00 0.00 0.00 2.59
3616 4646 9.319143 AGTAGAACATTTACTATGCAGATGAAC 57.681 33.333 0.00 0.00 29.85 3.18
3619 4649 9.890629 AGAACATTTACTATGCAGATGAACTAA 57.109 29.630 0.00 0.00 0.00 2.24
3632 4662 9.905713 TGCAGATGAACTAATAAAGGAATACTT 57.094 29.630 0.00 0.00 42.52 2.24
3704 4734 2.008752 TTGCTTGAATCGCTCGATCA 57.991 45.000 5.17 3.34 33.08 2.92
3723 4753 9.778993 CTCGATCATTCAATCTATTTGTTGTTT 57.221 29.630 0.00 0.00 36.65 2.83
3793 4823 0.627451 AAAGATGGCCCTGCTCATCA 59.373 50.000 0.00 0.00 38.08 3.07
3866 4896 2.362369 CCGTGCACCTCTCCCTGAT 61.362 63.158 12.15 0.00 0.00 2.90
3932 4962 5.847111 ACGCAGGTTCAGTTATCTACATA 57.153 39.130 0.00 0.00 0.00 2.29
3935 4965 6.183360 ACGCAGGTTCAGTTATCTACATACAT 60.183 38.462 0.00 0.00 0.00 2.29
3938 4968 9.712305 GCAGGTTCAGTTATCTACATACATAAT 57.288 33.333 0.00 0.00 0.00 1.28
4014 5044 1.285667 TCACATTGGCCACATCATCCT 59.714 47.619 3.88 0.00 0.00 3.24
4142 5172 4.382685 GGTGGAGCTAAACTATACAGCACA 60.383 45.833 0.00 0.00 37.78 4.57
4158 5188 4.984161 ACAGCACAATACACAAATTCTTGC 59.016 37.500 0.00 0.00 35.84 4.01
4204 5234 3.742385 ACATTTCCCTGGTTTGCATTTG 58.258 40.909 0.00 0.00 0.00 2.32
4226 5256 1.064003 TGGTAGTGTGCCTGTGGAAT 58.936 50.000 0.00 0.00 0.00 3.01
4317 5347 6.198650 TCTGTGCAGACCATCAAATAAATG 57.801 37.500 0.00 0.00 31.41 2.32
4318 5348 4.746729 TGTGCAGACCATCAAATAAATGC 58.253 39.130 0.00 0.00 0.00 3.56
4319 5349 4.220163 TGTGCAGACCATCAAATAAATGCA 59.780 37.500 0.00 0.00 39.89 3.96
4517 5572 2.744202 CTGTTGTCCAGTTGATGCTACC 59.256 50.000 0.00 0.00 36.37 3.18
4570 5780 9.379791 TCTGCATGATATCTGCTTAAATATGAG 57.620 33.333 20.51 11.04 40.34 2.90
4664 5874 5.062528 GGACTCAAATTTTTGGATTGGCAA 58.937 37.500 0.68 0.68 38.66 4.52
4760 5975 3.699038 CAGGTGGAGGTTCTGTTTTCAAA 59.301 43.478 0.00 0.00 0.00 2.69
4925 6178 3.065655 CTCTTCAGAGTTGGAGCACTTG 58.934 50.000 0.00 0.00 37.40 3.16
5074 6377 8.716619 TTTACCGATTTGACGAAATGTTAAAG 57.283 30.769 0.00 0.00 39.14 1.85
5082 6385 6.627395 TGACGAAATGTTAAAGTGTGGATT 57.373 33.333 0.00 0.00 0.00 3.01
5127 6431 9.826574 AGTTTGTGTTTGAGTCAAGTACTATTA 57.173 29.630 17.26 0.00 39.07 0.98
5149 6453 4.090761 TGTGGATGGATCTTCTTATGCC 57.909 45.455 0.00 0.00 0.00 4.40
5262 6569 9.871238 ATCGAGTTTTGTACTAATCTTATGTGT 57.129 29.630 2.80 0.00 37.17 3.72
5388 6714 8.677148 ACAGTAGTTAATGAATGTCAACACTT 57.323 30.769 0.00 0.00 0.00 3.16
5404 6932 0.688087 ACTTAGCGAGGAAGAGGGGG 60.688 60.000 0.00 0.00 0.00 5.40
5405 6933 0.688087 CTTAGCGAGGAAGAGGGGGT 60.688 60.000 0.00 0.00 0.00 4.95
5406 6934 0.632835 TTAGCGAGGAAGAGGGGGTA 59.367 55.000 0.00 0.00 0.00 3.69
5449 7001 3.312890 AGAGAGAGAGAGAGAGAGAGGG 58.687 54.545 0.00 0.00 0.00 4.30
5450 7002 3.051803 AGAGAGAGAGAGAGAGAGAGGGA 60.052 52.174 0.00 0.00 0.00 4.20
5451 7003 3.312890 AGAGAGAGAGAGAGAGAGGGAG 58.687 54.545 0.00 0.00 0.00 4.30
5452 7004 3.051803 AGAGAGAGAGAGAGAGAGGGAGA 60.052 52.174 0.00 0.00 0.00 3.71
5453 7005 3.312890 AGAGAGAGAGAGAGAGGGAGAG 58.687 54.545 0.00 0.00 0.00 3.20
5454 7006 3.051803 AGAGAGAGAGAGAGAGGGAGAGA 60.052 52.174 0.00 0.00 0.00 3.10
5455 7007 3.312890 AGAGAGAGAGAGAGGGAGAGAG 58.687 54.545 0.00 0.00 0.00 3.20
5456 7008 3.051803 AGAGAGAGAGAGAGGGAGAGAGA 60.052 52.174 0.00 0.00 0.00 3.10
5457 7009 3.312890 AGAGAGAGAGAGGGAGAGAGAG 58.687 54.545 0.00 0.00 0.00 3.20
5458 7010 3.051803 AGAGAGAGAGAGGGAGAGAGAGA 60.052 52.174 0.00 0.00 0.00 3.10
5459 7011 3.711704 GAGAGAGAGAGGGAGAGAGAGAA 59.288 52.174 0.00 0.00 0.00 2.87
5460 7012 4.111577 AGAGAGAGAGGGAGAGAGAGAAA 58.888 47.826 0.00 0.00 0.00 2.52
5461 7013 4.164988 AGAGAGAGAGGGAGAGAGAGAAAG 59.835 50.000 0.00 0.00 0.00 2.62
5462 7014 4.111577 AGAGAGAGGGAGAGAGAGAAAGA 58.888 47.826 0.00 0.00 0.00 2.52
5463 7015 4.164988 AGAGAGAGGGAGAGAGAGAAAGAG 59.835 50.000 0.00 0.00 0.00 2.85
5464 7016 3.852578 AGAGAGGGAGAGAGAGAAAGAGT 59.147 47.826 0.00 0.00 0.00 3.24
5467 7019 4.044065 AGAGGGAGAGAGAGAAAGAGTGAA 59.956 45.833 0.00 0.00 0.00 3.18
5585 7138 6.260050 TGGCGTTAGATGATTGTAAGGATTTC 59.740 38.462 0.00 0.00 0.00 2.17
5587 7140 7.201696 GGCGTTAGATGATTGTAAGGATTTCAA 60.202 37.037 0.00 0.00 39.66 2.69
5595 7148 8.463930 TGATTGTAAGGATTTCAAGTGACTTT 57.536 30.769 0.00 0.00 38.74 2.66
5660 7213 9.555727 ACACACATGTACTCTTGTACTAAAAAT 57.444 29.630 0.00 0.00 46.70 1.82
5689 7242 6.818644 ACAATCTAAAAGTATGCACGTCAGAT 59.181 34.615 0.00 0.00 0.00 2.90
5718 7271 1.443828 GCACCTAGCTAGACAGGGC 59.556 63.158 22.70 14.21 41.15 5.19
5775 7328 2.182825 GAATCGAGATGTACGCACGTT 58.817 47.619 0.00 0.00 0.00 3.99
5778 7355 1.131693 TCGAGATGTACGCACGTTGAT 59.868 47.619 0.00 0.00 0.00 2.57
5782 7359 2.923655 AGATGTACGCACGTTGATGAAG 59.076 45.455 0.00 0.00 0.00 3.02
5785 7362 2.063266 GTACGCACGTTGATGAAGGAA 58.937 47.619 0.00 0.00 0.00 3.36
5790 7367 3.185594 CGCACGTTGATGAAGGAAAACTA 59.814 43.478 0.00 0.00 0.00 2.24
5906 7483 3.130160 CGCCTTCTTCAGCAGCCC 61.130 66.667 0.00 0.00 0.00 5.19
5926 7503 1.079543 GCTCTGCTCTTGCCGAAGA 60.080 57.895 0.00 0.00 38.71 2.87
5931 7508 0.391661 TGCTCTTGCCGAAGATGGAC 60.392 55.000 0.00 0.00 37.58 4.02
5946 7523 1.374758 GGACTGCCTGGAGACGTTG 60.375 63.158 0.00 0.00 0.00 4.10
6007 9359 6.303054 TGTAGGATATGAGTGAGAAGGAGAG 58.697 44.000 0.00 0.00 0.00 3.20
6018 9370 2.360801 GAGAAGGAGAGGGATTCTGTCG 59.639 54.545 0.00 0.00 36.71 4.35
6019 9371 2.104170 GAAGGAGAGGGATTCTGTCGT 58.896 52.381 0.00 0.00 36.71 4.34
6020 9372 2.239681 AGGAGAGGGATTCTGTCGTT 57.760 50.000 0.00 0.00 36.71 3.85
6021 9373 1.827969 AGGAGAGGGATTCTGTCGTTG 59.172 52.381 0.00 0.00 36.71 4.10
6022 9374 1.550976 GGAGAGGGATTCTGTCGTTGT 59.449 52.381 0.00 0.00 36.71 3.32
6023 9375 2.028020 GGAGAGGGATTCTGTCGTTGTT 60.028 50.000 0.00 0.00 36.71 2.83
6024 9376 3.254892 GAGAGGGATTCTGTCGTTGTTC 58.745 50.000 0.00 0.00 35.87 3.18
6025 9377 2.632996 AGAGGGATTCTGTCGTTGTTCA 59.367 45.455 0.00 0.00 33.93 3.18
6026 9378 3.071023 AGAGGGATTCTGTCGTTGTTCAA 59.929 43.478 0.00 0.00 33.93 2.69
6027 9379 3.813166 GAGGGATTCTGTCGTTGTTCAAA 59.187 43.478 0.00 0.00 0.00 2.69
6028 9380 4.204012 AGGGATTCTGTCGTTGTTCAAAA 58.796 39.130 0.00 0.00 0.00 2.44
6029 9381 4.642885 AGGGATTCTGTCGTTGTTCAAAAA 59.357 37.500 0.00 0.00 0.00 1.94
6049 9401 3.982576 AAAAATCCACTGACACGGTTC 57.017 42.857 0.00 0.00 0.00 3.62
6050 9402 1.892209 AAATCCACTGACACGGTTCC 58.108 50.000 0.00 0.00 0.00 3.62
6051 9403 0.320421 AATCCACTGACACGGTTCCG 60.320 55.000 9.81 9.81 0.00 4.30
6052 9404 2.167398 ATCCACTGACACGGTTCCGG 62.167 60.000 15.66 0.00 0.00 5.14
6053 9405 2.357034 CACTGACACGGTTCCGGG 60.357 66.667 12.16 12.16 38.99 5.73
6054 9406 3.622826 ACTGACACGGTTCCGGGG 61.623 66.667 17.81 10.46 37.14 5.73
6070 9422 4.416738 GGCTGCCACCTCCCACTC 62.417 72.222 15.17 0.00 0.00 3.51
6071 9423 4.416738 GCTGCCACCTCCCACTCC 62.417 72.222 0.00 0.00 0.00 3.85
6072 9424 3.721706 CTGCCACCTCCCACTCCC 61.722 72.222 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.735857 GCCGTCGCCGTTAACAGT 60.736 61.111 6.39 0.00 0.00 3.55
101 102 3.506096 CTCCGAGCGACGCCACTA 61.506 66.667 17.79 0.00 41.07 2.74
119 120 1.429148 GATTTGCTCCGTTCGGCGAT 61.429 55.000 11.76 0.00 44.77 4.58
126 127 2.388232 GCCGTCGATTTGCTCCGTT 61.388 57.895 0.00 0.00 0.00 4.44
306 332 1.039785 ACGGCTGAGATAGAGCTGCA 61.040 55.000 0.00 0.00 45.30 4.41
336 368 4.752594 TGACCTAGGTGGGGCCCC 62.753 72.222 36.14 36.14 41.11 5.80
555 589 5.010922 ACCATTAGCATTTTTCAGAGCAACA 59.989 36.000 0.00 0.00 0.00 3.33
556 590 5.473039 ACCATTAGCATTTTTCAGAGCAAC 58.527 37.500 0.00 0.00 0.00 4.17
562 596 7.094205 ACAGAAGGTACCATTAGCATTTTTCAG 60.094 37.037 15.94 4.55 0.00 3.02
564 598 7.158099 ACAGAAGGTACCATTAGCATTTTTC 57.842 36.000 15.94 4.92 0.00 2.29
566 600 6.493458 ACAACAGAAGGTACCATTAGCATTTT 59.507 34.615 15.94 0.00 0.00 1.82
585 619 9.817365 CAAGACTTTAGAATGTATCAACAACAG 57.183 33.333 0.00 0.00 39.58 3.16
641 676 9.804977 GGATACTGTAACTATAGAAAGGAGGTA 57.195 37.037 6.78 1.82 0.00 3.08
676 717 6.343226 ACCATGTTTCATTTGTTTGTTTCG 57.657 33.333 0.00 0.00 0.00 3.46
693 734 3.266636 TCAATCGACGCAATTACCATGT 58.733 40.909 0.00 0.00 0.00 3.21
706 747 5.768317 TGAAGGACCAAATTTTCAATCGAC 58.232 37.500 0.00 0.00 0.00 4.20
709 750 8.090214 TGAATCTGAAGGACCAAATTTTCAATC 58.910 33.333 0.00 0.00 0.00 2.67
712 753 6.015180 CCTGAATCTGAAGGACCAAATTTTCA 60.015 38.462 0.00 0.00 35.40 2.69
734 775 6.317893 GTTGTCCAACTAAATATGGGTACCTG 59.682 42.308 12.72 0.00 43.43 4.00
735 776 6.420638 GTTGTCCAACTAAATATGGGTACCT 58.579 40.000 12.72 0.00 43.43 3.08
736 777 6.688637 GTTGTCCAACTAAATATGGGTACC 57.311 41.667 2.17 2.17 43.37 3.34
766 808 6.715347 TGCTGATAAGCAGTATAGAGTGAA 57.285 37.500 0.00 0.00 46.62 3.18
786 828 0.464452 GACCAGGGCGTTATACTGCT 59.536 55.000 0.00 0.00 0.00 4.24
803 845 8.748380 ATTTGCAGCAAATAAAGACTTAAGAC 57.252 30.769 28.50 2.62 41.50 3.01
807 850 8.303156 TGCTAATTTGCAGCAAATAAAGACTTA 58.697 29.630 30.07 19.79 45.71 2.24
810 853 6.949578 TGCTAATTTGCAGCAAATAAAGAC 57.050 33.333 30.07 23.83 45.71 3.01
824 867 7.851822 AACACGACATTAAAGTGCTAATTTG 57.148 32.000 0.00 0.00 39.31 2.32
869 912 4.933330 TCATCACTGAAGTAGTATTCCGC 58.067 43.478 0.00 0.00 37.60 5.54
870 913 5.299531 TCCTCATCACTGAAGTAGTATTCCG 59.700 44.000 0.00 0.00 37.60 4.30
932 986 5.628797 AAAGAAAGGAAGATGCCCAAAAA 57.371 34.783 0.00 0.00 0.00 1.94
965 1019 4.703379 AATTGAGTTGCCCATTGGAAAA 57.297 36.364 3.62 0.00 27.89 2.29
972 1026 3.016736 CGTAGGAAATTGAGTTGCCCAT 58.983 45.455 0.00 0.00 35.93 4.00
990 1044 1.153449 CCTCCGCATTCAAGCCGTA 60.153 57.895 0.00 0.00 0.00 4.02
992 1046 3.204827 CCCTCCGCATTCAAGCCG 61.205 66.667 0.00 0.00 0.00 5.52
1025 1079 1.301716 GTCTCCAGAGCGCACCAAA 60.302 57.895 11.47 0.00 0.00 3.28
1027 1081 4.056125 CGTCTCCAGAGCGCACCA 62.056 66.667 11.47 0.00 0.00 4.17
1032 1086 0.248296 GACTTAGCGTCTCCAGAGCG 60.248 60.000 7.00 7.00 39.61 5.03
1037 1091 1.275291 CCCTTTGACTTAGCGTCTCCA 59.725 52.381 0.00 0.00 43.25 3.86
1040 1094 1.002087 CCACCCTTTGACTTAGCGTCT 59.998 52.381 0.00 0.00 43.25 4.18
1048 1102 3.553095 GAGCCGCCACCCTTTGACT 62.553 63.158 0.00 0.00 0.00 3.41
1050 1104 4.697756 CGAGCCGCCACCCTTTGA 62.698 66.667 0.00 0.00 0.00 2.69
1072 1126 1.738099 CTGCCGAACGAACCCTCTG 60.738 63.158 0.00 0.00 0.00 3.35
1081 1135 1.423845 GCCACATTACTGCCGAACG 59.576 57.895 0.00 0.00 0.00 3.95
1092 1146 3.287445 GGCCAATCACGCCACATT 58.713 55.556 0.00 0.00 46.27 2.71
1100 1154 2.894919 GCACATGGGGCCAATCAC 59.105 61.111 4.39 0.00 0.00 3.06
1120 1174 1.071471 GTGTCACCCTCCACCACAG 59.929 63.158 0.00 0.00 0.00 3.66
1148 1202 1.678101 GCAGCAAAGTTGTCCTCTGTT 59.322 47.619 0.00 0.00 0.00 3.16
1159 1213 0.390124 CAACCCATGTGCAGCAAAGT 59.610 50.000 0.00 0.00 0.00 2.66
1161 1215 1.747145 CCAACCCATGTGCAGCAAA 59.253 52.632 0.00 0.00 0.00 3.68
1162 1216 2.208619 CCCAACCCATGTGCAGCAA 61.209 57.895 0.00 0.00 0.00 3.91
1165 1219 3.384532 GGCCCAACCCATGTGCAG 61.385 66.667 0.00 0.00 33.59 4.41
1166 1220 4.230566 TGGCCCAACCCATGTGCA 62.231 61.111 0.00 0.00 33.59 4.57
1195 1283 0.916358 ATGCAGAGGCCAGTAACCCT 60.916 55.000 5.01 0.00 40.13 4.34
1217 1305 2.433318 GGAGGACGAGCACACAGC 60.433 66.667 0.00 0.00 46.19 4.40
1237 1325 3.046087 CCTGACTGTGCAGCCACG 61.046 66.667 0.00 0.00 45.04 4.94
1275 1363 1.939785 GCTCACGTAGGCGATGTCG 60.940 63.158 0.00 0.00 42.00 4.35
1277 1365 0.458543 CAAGCTCACGTAGGCGATGT 60.459 55.000 6.33 0.00 42.00 3.06
1279 1367 0.179134 GACAAGCTCACGTAGGCGAT 60.179 55.000 6.33 0.00 42.00 4.58
1283 1371 0.888619 TCTGGACAAGCTCACGTAGG 59.111 55.000 0.00 0.00 0.00 3.18
1284 1372 2.600731 CTTCTGGACAAGCTCACGTAG 58.399 52.381 0.00 0.00 0.00 3.51
1288 1376 0.398318 ACCCTTCTGGACAAGCTCAC 59.602 55.000 0.00 0.00 38.00 3.51
1296 1384 3.369576 GGATGACACTTACCCTTCTGGAC 60.370 52.174 0.00 0.00 38.00 4.02
1343 1431 5.066505 GCAGAATAAGGAACACTGGGTATTG 59.933 44.000 0.00 0.00 0.00 1.90
1349 1437 3.411446 TGTGCAGAATAAGGAACACTGG 58.589 45.455 0.00 0.00 0.00 4.00
1350 1438 4.696877 TCATGTGCAGAATAAGGAACACTG 59.303 41.667 0.00 0.00 0.00 3.66
1357 1445 4.880120 ACTGTGATCATGTGCAGAATAAGG 59.120 41.667 15.75 0.00 33.57 2.69
1377 1465 5.777802 TGGCACACAAAATACCAATTACTG 58.222 37.500 0.00 0.00 0.00 2.74
1417 1505 7.961326 ACTCCAGCAAAATCCTAAATGTATT 57.039 32.000 0.00 0.00 0.00 1.89
1515 1855 6.112058 ACCACATGCAAATTTGTTAAGTTGT 58.888 32.000 19.03 11.45 40.47 3.32
1657 1999 7.094377 TGCTAACATCCCAACTTAGTGAATTTC 60.094 37.037 0.00 0.00 0.00 2.17
1705 2113 5.347342 TGTTTGTCATGTGGTTGATTTGTC 58.653 37.500 0.00 0.00 0.00 3.18
1757 2165 7.849804 AATGTCTTGTCAGGTACATGATTAC 57.150 36.000 14.07 9.86 42.36 1.89
1761 2169 8.100164 TGATAAAATGTCTTGTCAGGTACATGA 58.900 33.333 6.03 6.03 39.30 3.07
1966 2377 0.533308 TAACCCGGTGTCACAGTTGC 60.533 55.000 5.12 0.00 0.00 4.17
1970 2381 2.773487 TCAATTAACCCGGTGTCACAG 58.227 47.619 5.12 0.00 0.00 3.66
2047 2458 9.117183 GGTAGGTGGGTAGTTAATCAATTTAAG 57.883 37.037 0.00 0.00 30.46 1.85
2060 2471 5.409712 AGAACTTAAAGGTAGGTGGGTAGT 58.590 41.667 0.00 0.00 0.00 2.73
2121 2532 9.373750 CATGTACTGATTGCTAACAATTATTCG 57.626 33.333 0.00 0.00 46.59 3.34
2165 2601 8.044060 TCAAACAATGAACAGACCTATTCATC 57.956 34.615 4.25 0.00 43.21 2.92
2306 2744 1.165907 ATGTTGCGGCCGTATCATGG 61.166 55.000 30.87 2.37 0.00 3.66
2353 2791 9.236006 ACTTTCAAGTGCATCTATATGTTTCTT 57.764 29.630 0.00 0.00 37.98 2.52
2392 2831 1.261619 CTTCCTGCGTGAAGTGTTGAC 59.738 52.381 6.83 0.00 37.54 3.18
2457 2899 2.540101 CTGTGTTCCTTGTTCAGTCGTC 59.460 50.000 0.00 0.00 0.00 4.20
2495 2937 2.159338 CGGTGCATCTTCATTCCCTTTG 60.159 50.000 0.00 0.00 0.00 2.77
2497 2939 1.004745 ACGGTGCATCTTCATTCCCTT 59.995 47.619 0.00 0.00 0.00 3.95
2520 2962 2.029110 AGTGTTTGGTTATGGCATGCAC 60.029 45.455 21.36 8.78 0.00 4.57
2521 2963 2.246469 AGTGTTTGGTTATGGCATGCA 58.754 42.857 21.36 6.13 0.00 3.96
2602 3044 2.268920 GTGCCTTGCGATCCAGGA 59.731 61.111 0.00 0.00 0.00 3.86
2644 3086 0.855598 CCATCCATGTTCCTGGGGAT 59.144 55.000 0.00 0.00 40.71 3.85
2671 3113 1.488812 CCCGATCTAAATGACCACCCA 59.511 52.381 0.00 0.00 0.00 4.51
2681 3123 2.531771 TGTGTCCTGACCCGATCTAAA 58.468 47.619 0.00 0.00 0.00 1.85
2755 3197 0.680618 TTTTCCTCCGCCGTGTTCTA 59.319 50.000 0.00 0.00 0.00 2.10
2775 3217 0.245539 ATGTGCATCCAAGCTTGTGC 59.754 50.000 26.78 26.78 38.05 4.57
2798 3240 0.542805 TGACAGCAGCAGATGGCATA 59.457 50.000 0.00 0.00 45.95 3.14
2812 3254 3.793129 GCATGGTTTGTGTTCAGTGACAG 60.793 47.826 0.00 0.00 0.00 3.51
2815 3257 2.618241 GAGCATGGTTTGTGTTCAGTGA 59.382 45.455 0.00 0.00 0.00 3.41
2817 3259 2.358898 GTGAGCATGGTTTGTGTTCAGT 59.641 45.455 0.00 0.00 37.46 3.41
2831 3273 3.233507 AGATTTTTGTGGTGGTGAGCAT 58.766 40.909 0.00 0.00 30.75 3.79
2929 3376 2.043227 CACTACCTCTTCCCATCTCCC 58.957 57.143 0.00 0.00 0.00 4.30
2930 3377 1.414550 GCACTACCTCTTCCCATCTCC 59.585 57.143 0.00 0.00 0.00 3.71
2957 3404 0.181350 ATTTCCTGGAGATGTCGGCC 59.819 55.000 0.00 0.00 0.00 6.13
2958 3405 2.910688 TATTTCCTGGAGATGTCGGC 57.089 50.000 9.84 0.00 0.00 5.54
2971 3418 1.743394 CGAGGGCACTGGTTTATTTCC 59.257 52.381 0.00 0.00 0.00 3.13
3020 3467 0.849417 AGGAGAAATCCCTGGATGGC 59.151 55.000 0.00 0.00 34.70 4.40
3092 3539 2.268920 GATCTTGGCCACGCTGGA 59.731 61.111 3.88 0.00 40.96 3.86
3132 3579 0.827925 TCACTGCTCGTCTTCCCTGT 60.828 55.000 0.00 0.00 0.00 4.00
3215 3662 1.810030 GATTCGCAGACGGACCACC 60.810 63.158 0.00 0.00 40.63 4.61
3216 3663 2.158959 CGATTCGCAGACGGACCAC 61.159 63.158 0.00 0.00 40.63 4.16
3221 3668 1.874019 CTGGTCGATTCGCAGACGG 60.874 63.158 7.64 0.00 40.63 4.79
3222 3669 1.134530 GTCTGGTCGATTCGCAGACG 61.135 60.000 22.32 4.29 38.20 4.18
3224 3671 1.248101 TGGTCTGGTCGATTCGCAGA 61.248 55.000 10.97 10.97 0.00 4.26
3232 3679 0.320374 GTGGTTGATGGTCTGGTCGA 59.680 55.000 0.00 0.00 0.00 4.20
3248 3695 2.635443 GGTGGGAATTGCGTGGTGG 61.635 63.158 0.00 0.00 0.00 4.61
3249 3696 2.961768 GGTGGGAATTGCGTGGTG 59.038 61.111 0.00 0.00 0.00 4.17
3250 3697 2.671619 CGGTGGGAATTGCGTGGT 60.672 61.111 0.00 0.00 0.00 4.16
3251 3698 4.114997 GCGGTGGGAATTGCGTGG 62.115 66.667 0.00 0.00 0.00 4.94
3285 3732 3.023735 AACCCTGGATCTGGGGCC 61.024 66.667 22.23 0.00 45.34 5.80
3313 3760 2.033757 CTTGTGCTGCTCCTGCCT 59.966 61.111 0.00 0.00 38.71 4.75
3434 3885 4.918360 ACACAGCCCCCTCCCACA 62.918 66.667 0.00 0.00 0.00 4.17
3630 4660 6.910536 AAAGTGAGATGCTATTTACGGAAG 57.089 37.500 0.00 0.00 0.00 3.46
3631 4661 8.958119 AATAAAGTGAGATGCTATTTACGGAA 57.042 30.769 0.00 0.00 0.00 4.30
3670 4700 3.760151 TCAAGCAAAGATTCAGACATGGG 59.240 43.478 0.00 0.00 0.00 4.00
3674 4704 4.378770 GCGATTCAAGCAAAGATTCAGACA 60.379 41.667 0.00 0.00 34.19 3.41
3793 4823 4.687215 TCGCCGCTGCTTGAGCTT 62.687 61.111 4.44 0.00 46.64 3.74
3866 4896 1.985473 AACACCAAGCTGCATTGAGA 58.015 45.000 1.02 0.00 31.55 3.27
4102 5132 7.406104 AGCTCCACCAAAATCTAAATACTCTT 58.594 34.615 0.00 0.00 0.00 2.85
4142 5172 6.956299 GCAATCAGCAAGAATTTGTGTATT 57.044 33.333 0.00 0.00 44.79 1.89
4158 5188 8.788813 GTCGACATTTTAAAATACTGCAATCAG 58.211 33.333 11.55 0.38 45.71 2.90
4192 5222 4.081420 ACACTACCAAACAAATGCAAACCA 60.081 37.500 0.00 0.00 0.00 3.67
4204 5234 0.951558 CCACAGGCACACTACCAAAC 59.048 55.000 0.00 0.00 0.00 2.93
4226 5256 7.924412 ACTCGTAATACTCAAGTTCTCACAAAA 59.076 33.333 0.00 0.00 0.00 2.44
4310 5340 8.984891 TTTCATTCTCGACATTTGCATTTATT 57.015 26.923 0.00 0.00 0.00 1.40
4311 5341 8.984891 TTTTCATTCTCGACATTTGCATTTAT 57.015 26.923 0.00 0.00 0.00 1.40
4314 5344 7.385752 ACAATTTTCATTCTCGACATTTGCATT 59.614 29.630 0.00 0.00 0.00 3.56
4315 5345 6.869913 ACAATTTTCATTCTCGACATTTGCAT 59.130 30.769 0.00 0.00 0.00 3.96
4317 5347 6.695292 ACAATTTTCATTCTCGACATTTGC 57.305 33.333 0.00 0.00 0.00 3.68
4570 5780 5.066634 TGTCGAGATACTGACTTCCTCATTC 59.933 44.000 0.00 0.00 36.10 2.67
4854 6071 4.670765 AGCTCTTCCATCTTGTTCCAATT 58.329 39.130 0.00 0.00 0.00 2.32
4925 6178 1.380650 TTTAATGCCCCCGCCTTCC 60.381 57.895 0.00 0.00 0.00 3.46
5046 6346 6.062434 ACATTTCGTCAAATCGGTAAAACA 57.938 33.333 0.00 0.00 28.97 2.83
5047 6347 6.979701 AACATTTCGTCAAATCGGTAAAAC 57.020 33.333 0.00 0.00 28.97 2.43
5074 6377 2.875933 TCACGGACTTCAAAATCCACAC 59.124 45.455 0.00 0.00 34.35 3.82
5082 6385 6.932400 ACAAACTACATATCACGGACTTCAAA 59.068 34.615 0.00 0.00 0.00 2.69
5127 6431 4.660168 GGCATAAGAAGATCCATCCACAT 58.340 43.478 0.00 0.00 0.00 3.21
5149 6453 4.497006 GCATTCTCCATTTCAAGATGGTCG 60.497 45.833 4.02 0.00 45.53 4.79
5268 6575 8.598916 TGGAACCTCTAAGTAACAACAATGATA 58.401 33.333 0.00 0.00 0.00 2.15
5370 6696 6.092122 CCTCGCTAAGTGTTGACATTCATTAA 59.908 38.462 0.00 0.00 0.00 1.40
5371 6697 5.580691 CCTCGCTAAGTGTTGACATTCATTA 59.419 40.000 0.00 0.00 0.00 1.90
5388 6714 0.185416 CTACCCCCTCTTCCTCGCTA 59.815 60.000 0.00 0.00 0.00 4.26
5404 6932 3.116300 CTCTCACACACACACACACTAC 58.884 50.000 0.00 0.00 0.00 2.73
5405 6933 3.020984 TCTCTCACACACACACACACTA 58.979 45.455 0.00 0.00 0.00 2.74
5406 6934 1.824852 TCTCTCACACACACACACACT 59.175 47.619 0.00 0.00 0.00 3.55
5449 7001 6.817765 TCTCTTTCACTCTTTCTCTCTCTC 57.182 41.667 0.00 0.00 0.00 3.20
5450 7002 6.153340 CCATCTCTTTCACTCTTTCTCTCTCT 59.847 42.308 0.00 0.00 0.00 3.10
5451 7003 6.152661 TCCATCTCTTTCACTCTTTCTCTCTC 59.847 42.308 0.00 0.00 0.00 3.20
5452 7004 6.015918 TCCATCTCTTTCACTCTTTCTCTCT 58.984 40.000 0.00 0.00 0.00 3.10
5453 7005 6.279513 TCCATCTCTTTCACTCTTTCTCTC 57.720 41.667 0.00 0.00 0.00 3.20
5454 7006 5.187576 CCTCCATCTCTTTCACTCTTTCTCT 59.812 44.000 0.00 0.00 0.00 3.10
5455 7007 5.418676 CCTCCATCTCTTTCACTCTTTCTC 58.581 45.833 0.00 0.00 0.00 2.87
5456 7008 4.224818 CCCTCCATCTCTTTCACTCTTTCT 59.775 45.833 0.00 0.00 0.00 2.52
5457 7009 4.019771 ACCCTCCATCTCTTTCACTCTTTC 60.020 45.833 0.00 0.00 0.00 2.62
5458 7010 3.913163 ACCCTCCATCTCTTTCACTCTTT 59.087 43.478 0.00 0.00 0.00 2.52
5459 7011 3.262915 CACCCTCCATCTCTTTCACTCTT 59.737 47.826 0.00 0.00 0.00 2.85
5460 7012 2.836981 CACCCTCCATCTCTTTCACTCT 59.163 50.000 0.00 0.00 0.00 3.24
5461 7013 2.834549 TCACCCTCCATCTCTTTCACTC 59.165 50.000 0.00 0.00 0.00 3.51
5462 7014 2.907892 TCACCCTCCATCTCTTTCACT 58.092 47.619 0.00 0.00 0.00 3.41
5463 7015 3.922171 ATCACCCTCCATCTCTTTCAC 57.078 47.619 0.00 0.00 0.00 3.18
5464 7016 4.883759 TCTATCACCCTCCATCTCTTTCA 58.116 43.478 0.00 0.00 0.00 2.69
5467 7019 6.046643 ACTCTATCTATCACCCTCCATCTCTT 59.953 42.308 0.00 0.00 0.00 2.85
5534 7087 7.601130 ACGGGCCTTTTAATTTATTTTCTTGAC 59.399 33.333 0.84 0.00 0.00 3.18
5564 7117 9.994432 CACTTGAAATCCTTACAATCATCTAAC 57.006 33.333 0.00 0.00 0.00 2.34
5587 7140 7.549488 CCGGAAGATGAACTTATTAAAGTCACT 59.451 37.037 0.00 0.00 45.37 3.41
5595 7148 9.273016 GATTCATTCCGGAAGATGAACTTATTA 57.727 33.333 27.39 10.73 39.13 0.98
5660 7213 7.815549 TGACGTGCATACTTTTAGATTGTTCTA 59.184 33.333 0.00 0.00 33.17 2.10
5670 7223 4.109766 CGGATCTGACGTGCATACTTTTA 58.890 43.478 0.00 0.00 0.00 1.52
5679 7232 1.875813 CTCTGCGGATCTGACGTGC 60.876 63.158 5.48 0.00 0.00 5.34
5689 7242 4.392166 TAGGTGCCCCTCTGCGGA 62.392 66.667 0.00 0.00 41.45 5.54
5744 7297 0.179084 TCTCGATTCATCCCGGTTGC 60.179 55.000 0.00 0.00 0.00 4.17
5775 7328 6.377996 CCATGTCCAATAGTTTTCCTTCATCA 59.622 38.462 0.00 0.00 0.00 3.07
5778 7355 5.476599 CACCATGTCCAATAGTTTTCCTTCA 59.523 40.000 0.00 0.00 0.00 3.02
5782 7359 4.340617 TCCACCATGTCCAATAGTTTTCC 58.659 43.478 0.00 0.00 0.00 3.13
5785 7362 3.309121 CCCTCCACCATGTCCAATAGTTT 60.309 47.826 0.00 0.00 0.00 2.66
5790 7367 2.010067 CCCCTCCACCATGTCCAAT 58.990 57.895 0.00 0.00 0.00 3.16
5839 7416 0.807667 CTTGGCGTCCTCATCTTCGG 60.808 60.000 0.00 0.00 0.00 4.30
5885 7462 2.359107 TGCTGAAGAAGGCGCAGG 60.359 61.111 10.83 0.00 0.00 4.85
5922 7499 1.134551 GTCTCCAGGCAGTCCATCTTC 60.135 57.143 0.00 0.00 33.74 2.87
5926 7503 1.194781 AACGTCTCCAGGCAGTCCAT 61.195 55.000 0.00 0.00 33.74 3.41
5931 7508 1.230635 CCAACAACGTCTCCAGGCAG 61.231 60.000 0.00 0.00 0.00 4.85
5996 9348 3.370104 GACAGAATCCCTCTCCTTCTCA 58.630 50.000 0.00 0.00 29.07 3.27
6001 9353 1.827969 CAACGACAGAATCCCTCTCCT 59.172 52.381 0.00 0.00 29.07 3.69
6007 9359 4.561735 TTTTGAACAACGACAGAATCCC 57.438 40.909 0.00 0.00 0.00 3.85
6029 9381 2.621526 GGAACCGTGTCAGTGGATTTTT 59.378 45.455 0.00 0.00 0.00 1.94
6030 9382 2.227194 GGAACCGTGTCAGTGGATTTT 58.773 47.619 0.00 0.00 0.00 1.82
6031 9383 1.876416 CGGAACCGTGTCAGTGGATTT 60.876 52.381 4.99 0.00 34.35 2.17
6032 9384 0.320421 CGGAACCGTGTCAGTGGATT 60.320 55.000 4.99 0.00 34.35 3.01
6033 9385 1.292223 CGGAACCGTGTCAGTGGAT 59.708 57.895 4.99 0.00 34.35 3.41
6034 9386 2.732016 CGGAACCGTGTCAGTGGA 59.268 61.111 4.99 0.00 34.35 4.02
6035 9387 2.357034 CCGGAACCGTGTCAGTGG 60.357 66.667 12.23 0.00 37.81 4.00
6036 9388 2.357034 CCCGGAACCGTGTCAGTG 60.357 66.667 0.73 0.00 37.81 3.66
6037 9389 3.622826 CCCCGGAACCGTGTCAGT 61.623 66.667 0.73 0.00 37.81 3.41
6053 9405 4.416738 GAGTGGGAGGTGGCAGCC 62.417 72.222 13.95 3.66 0.00 4.85
6054 9406 4.416738 GGAGTGGGAGGTGGCAGC 62.417 72.222 9.02 9.02 0.00 5.25
6055 9407 3.721706 GGGAGTGGGAGGTGGCAG 61.722 72.222 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.