Multiple sequence alignment - TraesCS4D01G081200

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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 TraesCS4D01G081200 chr4D 100.000 8814 0 0 1 8814 55060402 55051589 0.000000e+00 16277
1 TraesCS4D01G081200 chr4D 84.163 783 86 21 1994 2775 55057335 55056590 0.000000e+00 725
2 TraesCS4D01G081200 chr4D 84.163 783 86 21 3068 3813 55058409 55057628 0.000000e+00 725
3 TraesCS4D01G081200 chr4D 85.855 509 54 8 3068 3561 36665776 36665271 7.840000e-145 525
4 TraesCS4D01G081200 chr4D 81.736 553 73 17 1978 2528 36665792 36665266 3.780000e-118 436
5 TraesCS4D01G081200 chr4D 86.972 284 16 8 3813 4092 36665267 36665001 5.170000e-77 300
6 TraesCS4D01G081200 chr4D 92.357 157 8 4 2774 2928 55056677 55056523 4.140000e-53 220
7 TraesCS4D01G081200 chr4D 92.357 157 8 4 3726 3880 55057629 55057475 4.140000e-53 220
8 TraesCS4D01G081200 chr4D 82.400 125 15 3 1780 1904 55057474 55057357 1.570000e-17 102
9 TraesCS4D01G081200 chr4D 82.400 125 15 3 2929 3046 55058623 55058499 1.570000e-17 102
10 TraesCS4D01G081200 chr4B 95.064 5733 169 44 3165 8814 82014097 82008396 0.000000e+00 8914
11 TraesCS4D01G081200 chr4B 91.209 2457 124 41 729 3168 82016636 82014255 0.000000e+00 3256
12 TraesCS4D01G081200 chr4B 85.306 769 81 16 3068 3805 82015422 82014655 0.000000e+00 765
13 TraesCS4D01G081200 chr4B 85.197 635 65 15 2102 2735 82014092 82013486 7.510000e-175 625
14 TraesCS4D01G081200 chr4B 83.200 125 14 4 1780 1904 82014495 82014378 3.360000e-19 108
15 TraesCS4D01G081200 chr4A 93.746 4749 177 43 2074 6741 542027280 542031989 0.000000e+00 7014
16 TraesCS4D01G081200 chr4A 96.236 2099 56 10 6738 8814 542032069 542034166 0.000000e+00 3417
17 TraesCS4D01G081200 chr4A 90.634 1324 67 24 727 2029 542025983 542027270 0.000000e+00 1705
18 TraesCS4D01G081200 chr4A 91.940 732 39 11 1 729 488247548 488248262 0.000000e+00 1007
19 TraesCS4D01G081200 chr4A 84.527 782 82 21 1992 2772 542028265 542029008 0.000000e+00 737
20 TraesCS4D01G081200 chr4A 86.330 673 65 17 3163 3810 542027301 542027971 0.000000e+00 708
21 TraesCS4D01G081200 chr4A 94.904 157 5 3 2774 2928 542028924 542029079 8.840000e-60 243
22 TraesCS4D01G081200 chr4A 82.400 125 15 3 1780 1904 542028127 542028244 1.570000e-17 102
23 TraesCS4D01G081200 chr4A 93.939 66 3 1 2961 3025 542026738 542026803 2.030000e-16 99
24 TraesCS4D01G081200 chr2A 89.390 1197 97 17 2369 3560 347687850 347686679 0.000000e+00 1480
25 TraesCS4D01G081200 chr2A 89.300 1028 65 17 4509 5520 347686053 347685055 0.000000e+00 1247
26 TraesCS4D01G081200 chr2A 90.494 547 37 5 3801 4339 347686667 347686128 0.000000e+00 708
27 TraesCS4D01G081200 chr2A 85.156 384 45 7 3425 3799 347687840 347687460 4.990000e-102 383
28 TraesCS4D01G081200 chr2A 80.150 534 69 24 1995 2527 347687171 347686674 1.810000e-96 364
29 TraesCS4D01G081200 chr2A 84.091 176 14 4 5518 5692 347682500 347682338 3.290000e-34 158
30 TraesCS4D01G081200 chr2A 83.523 176 15 4 5518 5692 347683698 347683536 1.530000e-32 152
31 TraesCS4D01G081200 chr2A 97.015 67 1 1 2782 2848 347687525 347687460 2.600000e-20 111
32 TraesCS4D01G081200 chr5D 94.003 717 36 6 17 732 415245194 415244484 0.000000e+00 1079
33 TraesCS4D01G081200 chr5D 79.618 471 96 0 8333 8803 159658036 159657566 1.100000e-88 339
34 TraesCS4D01G081200 chr2D 93.204 721 46 3 12 731 72687769 72687051 0.000000e+00 1057
35 TraesCS4D01G081200 chr2D 92.798 722 44 8 14 731 12769533 12770250 0.000000e+00 1038
36 TraesCS4D01G081200 chr7D 92.798 722 44 6 14 731 605537025 605537742 0.000000e+00 1038
37 TraesCS4D01G081200 chr7D 91.855 663 50 3 2369 3031 157533371 157532713 0.000000e+00 922
38 TraesCS4D01G081200 chr7D 88.745 773 35 16 4934 5688 157532698 157531960 0.000000e+00 898
39 TraesCS4D01G081200 chr7D 85.714 399 47 7 3424 3813 157533362 157532965 6.370000e-111 412
40 TraesCS4D01G081200 chr1D 92.213 732 54 3 1 731 450063618 450062889 0.000000e+00 1033
41 TraesCS4D01G081200 chr7B 89.467 845 40 14 4503 5334 693647895 693648703 0.000000e+00 1022
42 TraesCS4D01G081200 chr7B 91.541 331 16 6 4016 4339 693647500 693647825 6.280000e-121 446
43 TraesCS4D01G081200 chr3D 92.127 724 51 6 10 731 32435030 32435749 0.000000e+00 1016
44 TraesCS4D01G081200 chr3D 86.275 510 50 11 3068 3561 388750043 388750548 3.620000e-148 536
45 TraesCS4D01G081200 chr3D 87.279 283 19 10 3813 4092 388750552 388750820 3.090000e-79 307
46 TraesCS4D01G081200 chr3B 91.540 721 56 5 10 729 738128173 738127457 0.000000e+00 989
47 TraesCS4D01G081200 chr3B 86.111 72 7 3 661 731 687752578 687752647 3.410000e-09 75
48 TraesCS4D01G081200 chr5A 90.959 730 57 7 1 729 16630204 16629483 0.000000e+00 974
49 TraesCS4D01G081200 chr5A 79.839 496 98 2 8306 8800 245952932 245953426 2.340000e-95 361
50 TraesCS4D01G081200 chr1A 85.265 509 56 10 3068 3561 4381023 4381527 2.840000e-139 507
51 TraesCS4D01G081200 chr1A 85.098 510 54 14 3068 3561 293639894 293640397 1.320000e-137 501
52 TraesCS4D01G081200 chr1A 81.159 552 77 18 1978 2528 4381007 4381532 1.370000e-112 418
53 TraesCS4D01G081200 chr1A 81.125 551 78 15 1978 2528 293639878 293640402 1.370000e-112 418
54 TraesCS4D01G081200 chr1A 87.676 284 16 6 3813 4092 4381531 4381799 6.640000e-81 313
55 TraesCS4D01G081200 chr1A 85.563 284 20 7 3813 4092 293640401 293640667 2.420000e-70 278
56 TraesCS4D01G081200 chr5B 79.596 495 101 0 8306 8800 176214627 176215121 1.090000e-93 355
57 TraesCS4D01G081200 chr1B 86.449 214 28 1 2560 2773 107513633 107513421 5.320000e-57 233
58 TraesCS4D01G081200 chr1B 85.446 213 30 1 3598 3810 107513633 107513422 4.140000e-53 220


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 TraesCS4D01G081200 chr4D 55051589 55060402 8813 True 2624.428571 16277 88.262857 1 8814 7 chr4D.!!$R2 8813
1 TraesCS4D01G081200 chr4D 36665001 36665792 791 True 420.333333 525 84.854333 1978 4092 3 chr4D.!!$R1 2114
2 TraesCS4D01G081200 chr4B 82008396 82016636 8240 True 2733.600000 8914 87.995200 729 8814 5 chr4B.!!$R1 8085
3 TraesCS4D01G081200 chr4A 542025983 542031989 6006 False 2939.333333 7014 92.773000 727 6741 3 chr4A.!!$F2 6014
4 TraesCS4D01G081200 chr4A 542027301 542034166 6865 False 1041.400000 3417 88.879400 1780 8814 5 chr4A.!!$F3 7034
5 TraesCS4D01G081200 chr4A 488247548 488248262 714 False 1007.000000 1007 91.940000 1 729 1 chr4A.!!$F1 728
6 TraesCS4D01G081200 chr2A 347682338 347687850 5512 True 575.375000 1480 87.389875 1995 5692 8 chr2A.!!$R1 3697
7 TraesCS4D01G081200 chr5D 415244484 415245194 710 True 1079.000000 1079 94.003000 17 732 1 chr5D.!!$R2 715
8 TraesCS4D01G081200 chr2D 72687051 72687769 718 True 1057.000000 1057 93.204000 12 731 1 chr2D.!!$R1 719
9 TraesCS4D01G081200 chr2D 12769533 12770250 717 False 1038.000000 1038 92.798000 14 731 1 chr2D.!!$F1 717
10 TraesCS4D01G081200 chr7D 605537025 605537742 717 False 1038.000000 1038 92.798000 14 731 1 chr7D.!!$F1 717
11 TraesCS4D01G081200 chr7D 157531960 157533371 1411 True 744.000000 922 88.771333 2369 5688 3 chr7D.!!$R1 3319
12 TraesCS4D01G081200 chr1D 450062889 450063618 729 True 1033.000000 1033 92.213000 1 731 1 chr1D.!!$R1 730
13 TraesCS4D01G081200 chr7B 693647500 693648703 1203 False 734.000000 1022 90.504000 4016 5334 2 chr7B.!!$F1 1318
14 TraesCS4D01G081200 chr3D 32435030 32435749 719 False 1016.000000 1016 92.127000 10 731 1 chr3D.!!$F1 721
15 TraesCS4D01G081200 chr3D 388750043 388750820 777 False 421.500000 536 86.777000 3068 4092 2 chr3D.!!$F2 1024
16 TraesCS4D01G081200 chr3B 738127457 738128173 716 True 989.000000 989 91.540000 10 729 1 chr3B.!!$R1 719
17 TraesCS4D01G081200 chr5A 16629483 16630204 721 True 974.000000 974 90.959000 1 729 1 chr5A.!!$R1 728
18 TraesCS4D01G081200 chr1A 4381007 4381799 792 False 412.666667 507 84.700000 1978 4092 3 chr1A.!!$F1 2114
19 TraesCS4D01G081200 chr1A 293639878 293640667 789 False 399.000000 501 83.928667 1978 4092 3 chr1A.!!$F2 2114

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
747 756 0.466543 TAACCAGTTGACACGGCAGT 59.533 50.000 0.00 0.00 0.00 4.40 F
938 961 1.000396 GCAGCCCTGTTCCTCCAAT 60.000 57.895 0.00 0.00 0.00 3.16 F
2235 2272 0.817634 TGAACCGGGTGCTTGAAGTG 60.818 55.000 6.32 0.00 0.00 3.16 F
2244 2281 2.147150 GTGCTTGAAGTGAAGGAGGAC 58.853 52.381 0.00 0.00 0.00 3.85 F
2265 2302 3.108376 CCTTCCTAAGAAGCAGGTACCT 58.892 50.000 9.21 9.21 46.97 3.08 F
3883 4435 2.158385 TGTGCAGTAATCCCCCTTTTGT 60.158 45.455 0.00 0.00 0.00 2.83 F
5286 5923 1.868713 TGGATTGCAGATTGGCCATT 58.131 45.000 6.09 1.72 0.00 3.16 F
6163 9388 0.768221 AGAGGGGCACTGTGGAAGAA 60.768 55.000 10.21 0.00 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2204 2241 0.960861 CCGGTTCAGCCTTTTCCTCC 60.961 60.000 0.00 0.0 34.25 4.30 R
2266 2303 1.927895 ATAGTTAGTCAGCACGCAGC 58.072 50.000 0.00 0.0 46.19 5.25 R
3420 3628 0.320073 TAACCGAACACTCAAGCCCG 60.320 55.000 0.00 0.0 0.00 6.13 R
3422 3630 1.130561 GCATAACCGAACACTCAAGCC 59.869 52.381 0.00 0.0 0.00 4.35 R
3983 4536 2.677914 TCTCCAACCTGACTGAAGACA 58.322 47.619 0.00 0.0 0.00 3.41 R
5685 8890 0.868406 CCGTGGAAACTGAACTGAGC 59.132 55.000 0.00 0.0 0.00 4.26 R
6840 10160 0.250727 GTCTAAAGCAGGGCCACACA 60.251 55.000 6.18 0.0 0.00 3.72 R
7938 11278 0.957395 AGTTCTCCAATGGCACTGCG 60.957 55.000 0.00 0.0 0.00 5.18 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
400 406 1.673337 ATCGACCTCACCGACGACA 60.673 57.895 0.00 0.00 38.97 4.35
546 553 6.347888 CGTTTGACCGGTCACTTTATGTTTAT 60.348 38.462 36.40 0.00 39.66 1.40
604 612 2.676471 GGCACATTTGGGTCGGCT 60.676 61.111 0.00 0.00 0.00 5.52
743 752 1.270094 TGCTCTAACCAGTTGACACGG 60.270 52.381 0.00 0.00 0.00 4.94
747 756 0.466543 TAACCAGTTGACACGGCAGT 59.533 50.000 0.00 0.00 0.00 4.40
757 766 2.573869 ACGGCAGTGATCCACTCG 59.426 61.111 0.00 2.15 43.43 4.18
758 767 2.202797 CGGCAGTGATCCACTCGG 60.203 66.667 0.00 0.00 43.43 4.63
775 791 1.362355 GGAGGCCAACAAACAACCG 59.638 57.895 5.01 0.00 0.00 4.44
936 959 2.530151 AGCAGCCCTGTTCCTCCA 60.530 61.111 0.00 0.00 0.00 3.86
937 960 2.156098 AGCAGCCCTGTTCCTCCAA 61.156 57.895 0.00 0.00 0.00 3.53
938 961 1.000396 GCAGCCCTGTTCCTCCAAT 60.000 57.895 0.00 0.00 0.00 3.16
939 962 1.034292 GCAGCCCTGTTCCTCCAATC 61.034 60.000 0.00 0.00 0.00 2.67
1062 1091 1.826024 GATCTCCGCCATGTCCAGT 59.174 57.895 0.00 0.00 0.00 4.00
1176 1205 3.221771 TGTGCTTGTGTATTTCCTTGCT 58.778 40.909 0.00 0.00 0.00 3.91
1205 1234 8.972458 TTTGCTGCTAGTATTATGGAAATACA 57.028 30.769 0.00 0.00 35.99 2.29
1207 1236 9.573166 TTGCTGCTAGTATTATGGAAATACATT 57.427 29.630 0.00 0.00 35.99 2.71
1230 1259 9.788960 CATTTAGTTGGTTATTTCTCTTAAGCC 57.211 33.333 0.00 0.00 0.00 4.35
1231 1260 9.755122 ATTTAGTTGGTTATTTCTCTTAAGCCT 57.245 29.630 0.00 0.00 0.00 4.58
1232 1261 8.561738 TTAGTTGGTTATTTCTCTTAAGCCTG 57.438 34.615 0.00 0.00 0.00 4.85
1233 1262 6.543735 AGTTGGTTATTTCTCTTAAGCCTGT 58.456 36.000 0.00 0.00 0.00 4.00
1234 1263 6.431234 AGTTGGTTATTTCTCTTAAGCCTGTG 59.569 38.462 0.00 0.00 0.00 3.66
1235 1264 5.253330 TGGTTATTTCTCTTAAGCCTGTGG 58.747 41.667 0.00 0.00 0.00 4.17
1236 1265 5.013704 TGGTTATTTCTCTTAAGCCTGTGGA 59.986 40.000 0.00 0.00 0.00 4.02
1237 1266 5.586643 GGTTATTTCTCTTAAGCCTGTGGAG 59.413 44.000 0.00 0.00 0.00 3.86
1238 1267 3.703001 TTTCTCTTAAGCCTGTGGAGG 57.297 47.619 0.00 0.00 43.19 4.30
1239 1268 2.623418 TCTCTTAAGCCTGTGGAGGA 57.377 50.000 0.00 0.00 42.93 3.71
1240 1269 2.902608 TCTCTTAAGCCTGTGGAGGAA 58.097 47.619 0.00 0.00 42.93 3.36
1241 1270 2.834549 TCTCTTAAGCCTGTGGAGGAAG 59.165 50.000 0.00 0.00 42.93 3.46
1250 1279 3.610911 CCTGTGGAGGAAGTGGTTATTC 58.389 50.000 0.00 0.00 42.93 1.75
1298 1327 4.926162 ACCCCACCCGCCCAAAAC 62.926 66.667 0.00 0.00 0.00 2.43
1299 1328 4.924187 CCCCACCCGCCCAAAACA 62.924 66.667 0.00 0.00 0.00 2.83
1331 1360 6.418101 TCTTATCAATAAAAGCTCAGTGGCT 58.582 36.000 0.75 0.75 45.30 4.75
1367 1396 7.953158 TTTCACTTGACAAATTGTGTGAAAA 57.047 28.000 26.59 16.88 42.49 2.29
1439 1472 8.413229 ACTTTTAGTAATCATGTGCTTGTTTGT 58.587 29.630 0.00 0.00 0.00 2.83
1440 1473 9.248291 CTTTTAGTAATCATGTGCTTGTTTGTT 57.752 29.630 0.00 0.00 0.00 2.83
1441 1474 8.572828 TTTAGTAATCATGTGCTTGTTTGTTG 57.427 30.769 0.00 0.00 0.00 3.33
1442 1475 6.389830 AGTAATCATGTGCTTGTTTGTTGA 57.610 33.333 0.00 0.00 0.00 3.18
1443 1476 6.804677 AGTAATCATGTGCTTGTTTGTTGAA 58.195 32.000 0.00 0.00 0.00 2.69
1507 1540 5.718649 TTGCGTAGATGAGTTATTTCTGC 57.281 39.130 0.00 0.00 0.00 4.26
1633 1669 3.694566 AGTCGCAAAGTTTCAGTCCTTTT 59.305 39.130 0.00 0.00 0.00 2.27
1637 1673 4.440112 CGCAAAGTTTCAGTCCTTTTTCCT 60.440 41.667 0.00 0.00 0.00 3.36
1645 1681 1.494721 AGTCCTTTTTCCTCTGGCACA 59.505 47.619 0.00 0.00 0.00 4.57
1646 1682 1.609072 GTCCTTTTTCCTCTGGCACAC 59.391 52.381 0.00 0.00 0.00 3.82
1778 1814 3.059461 CCATGTGCTTGTTTGTTGAATGC 60.059 43.478 0.00 0.00 0.00 3.56
1796 1832 7.862512 TGAATGCAAGGAAAACAATTTTTCT 57.137 28.000 9.17 0.00 46.80 2.52
1837 1873 5.375417 TTTCTGTATGTTCATGTTGCCTG 57.625 39.130 0.00 0.00 0.00 4.85
1860 1896 6.449698 TGAAGGCTGAAGCTTTAATTTCAAG 58.550 36.000 0.00 0.00 40.57 3.02
1925 1961 3.149436 TGCAAGAAGTTTGCTTGTCAC 57.851 42.857 12.45 0.00 45.13 3.67
1934 1970 8.261492 AGAAGTTTGCTTGTCACTTATATCTG 57.739 34.615 0.00 0.00 34.61 2.90
2012 2048 4.997395 ACTACGCATCAATTCACTTCAACT 59.003 37.500 0.00 0.00 0.00 3.16
2204 2241 5.391310 CCAAGTCTGAAATGAATTCCGTCAG 60.391 44.000 17.70 17.70 37.22 3.51
2235 2272 0.817634 TGAACCGGGTGCTTGAAGTG 60.818 55.000 6.32 0.00 0.00 3.16
2244 2281 2.147150 GTGCTTGAAGTGAAGGAGGAC 58.853 52.381 0.00 0.00 0.00 3.85
2263 2300 3.118702 GGACCTTCCTAAGAAGCAGGTAC 60.119 52.174 0.00 0.00 46.97 3.34
2265 2302 3.108376 CCTTCCTAAGAAGCAGGTACCT 58.892 50.000 9.21 9.21 46.97 3.08
2266 2303 3.118592 CCTTCCTAAGAAGCAGGTACCTG 60.119 52.174 33.74 33.74 46.97 4.00
2511 2548 3.932545 TTTTGGTCCAATTCATGTCCG 57.067 42.857 4.80 0.00 0.00 4.79
2612 2650 3.334272 AAACGTCAGTAACTGCAAAGC 57.666 42.857 0.00 0.00 0.00 3.51
2682 2720 7.393234 TCGATGTTTCCTCTAAATGGTTTGATT 59.607 33.333 0.00 0.00 0.00 2.57
2744 2782 5.332732 CCATGTGCTTATATTTTGCATTGCG 60.333 40.000 3.84 0.00 39.00 4.85
2887 2925 6.646653 TGTTGCATGTTTGTGTTTGTTTCTTA 59.353 30.769 0.00 0.00 0.00 2.10
2982 3020 9.283768 TCACTTATTTCTGTATGTTCATGTTGT 57.716 29.630 0.00 0.00 0.00 3.32
3196 3399 3.125316 GTCTAAAGAACGATTGGTGCCTG 59.875 47.826 0.00 0.00 0.00 4.85
3406 3614 7.120432 GCATCACTAATTCTTCTTCCTGACTTT 59.880 37.037 0.00 0.00 0.00 2.66
3420 3628 8.349983 TCTTCCTGACTTTGTTTAAATTACTGC 58.650 33.333 0.00 0.00 0.00 4.40
3422 3630 5.856455 CCTGACTTTGTTTAAATTACTGCGG 59.144 40.000 0.00 0.00 0.00 5.69
3446 3654 3.394674 TGAGTGTTCGGTTATGCTGAA 57.605 42.857 0.00 0.00 39.97 3.02
3561 3778 3.208747 TCAGGTCCCACTGAAGAAAAC 57.791 47.619 0.00 0.00 44.03 2.43
3630 3847 3.736252 CGATATGTAAAGACCGAGGCAAG 59.264 47.826 0.00 0.00 0.00 4.01
3883 4435 2.158385 TGTGCAGTAATCCCCCTTTTGT 60.158 45.455 0.00 0.00 0.00 2.83
3940 4492 3.991773 GCACGTGTCATTTTACTGTAGGA 59.008 43.478 18.38 0.00 0.00 2.94
3983 4536 6.603599 GTCCTATGAAAAGCTTACCCTTTCAT 59.396 38.462 21.09 21.09 34.12 2.57
4354 4942 5.295540 CCTGAGTATGCTTTCCTTTTAGCTC 59.704 44.000 0.00 0.00 38.22 4.09
4429 5017 5.942826 AGATTTGGCTGAAGACCTTTAGAAG 59.057 40.000 5.83 0.00 0.00 2.85
4474 5062 1.905215 TGGCCCATGTTACCAAAATGG 59.095 47.619 0.00 1.64 45.02 3.16
4587 5199 4.766373 TGCATCATTTTGTCCATGTAGTGT 59.234 37.500 0.00 0.00 0.00 3.55
4616 5228 8.650490 ACATTCTTTTGTGGGATCAATTTAACT 58.350 29.630 0.00 0.00 0.00 2.24
4663 5275 3.760151 CCTTTTGATTCCTGCAGACATCA 59.240 43.478 17.39 18.25 0.00 3.07
4723 5337 8.553459 TTCTTTCAACTTAGGCTCTTGAATAG 57.447 34.615 12.91 12.53 34.65 1.73
4760 5374 7.854557 TTTCCTGACTTCAGATCATTACATG 57.145 36.000 7.87 0.00 46.59 3.21
5082 5710 8.739972 AGTTGTTCAGATTCAAAGTGTAGTTTT 58.260 29.630 0.00 0.00 0.00 2.43
5088 5716 7.915397 TCAGATTCAAAGTGTAGTTTTCAAAGC 59.085 33.333 0.00 0.00 0.00 3.51
5255 5892 3.441572 AGAAAATGCAGTCTGTACATGGC 59.558 43.478 0.00 0.00 0.00 4.40
5286 5923 1.868713 TGGATTGCAGATTGGCCATT 58.131 45.000 6.09 1.72 0.00 3.16
5373 6016 7.330208 AGTTTTGCACATTGATCTGCTATTTTC 59.670 33.333 6.27 0.00 34.29 2.29
5559 7563 5.276461 AGATGAAGTTACGCATGGTATGA 57.724 39.130 0.00 0.00 0.00 2.15
5685 8890 1.059369 CGCTCGGCAGTTCAAATCG 59.941 57.895 0.00 0.00 0.00 3.34
5846 9051 2.676839 CTGTGAATGCTGAAGCTGGTAG 59.323 50.000 3.61 0.00 42.66 3.18
5885 9090 5.655488 TGAAAATTGTTCAAATGTGACGGT 58.345 33.333 0.00 0.00 31.90 4.83
6013 9218 7.010091 CCCTGTTTTGACAATTGTTAGAAACAC 59.990 37.037 26.65 17.30 41.97 3.32
6014 9219 7.543868 CCTGTTTTGACAATTGTTAGAAACACA 59.456 33.333 26.65 19.52 41.97 3.72
6085 9310 5.192927 TGCTCATCCCTTGTTGGTATAAAG 58.807 41.667 0.00 0.00 0.00 1.85
6143 9368 7.750229 ATAAATGTGCTATACTGTTGGATGG 57.250 36.000 0.00 0.00 0.00 3.51
6152 9377 1.541118 TGTTGGATGGAGAGGGGCA 60.541 57.895 0.00 0.00 0.00 5.36
6163 9388 0.768221 AGAGGGGCACTGTGGAAGAA 60.768 55.000 10.21 0.00 0.00 2.52
6444 9679 9.281371 CATGACTACATATTCCACTGAATTGAT 57.719 33.333 0.00 0.00 41.44 2.57
6522 9759 7.040548 ACTGTACTTAGTAGCGTTTCTCTTTCT 60.041 37.037 0.00 0.00 0.00 2.52
6523 9760 7.655490 TGTACTTAGTAGCGTTTCTCTTTCTT 58.345 34.615 0.00 0.00 0.00 2.52
6528 9765 5.952033 AGTAGCGTTTCTCTTTCTTACGAT 58.048 37.500 0.00 0.00 34.36 3.73
6529 9766 7.081526 AGTAGCGTTTCTCTTTCTTACGATA 57.918 36.000 0.00 0.00 34.36 2.92
6530 9767 7.705214 AGTAGCGTTTCTCTTTCTTACGATAT 58.295 34.615 0.00 0.00 35.87 1.63
6531 9768 8.189460 AGTAGCGTTTCTCTTTCTTACGATATT 58.811 33.333 0.00 0.00 35.87 1.28
6533 9770 8.922058 AGCGTTTCTCTTTCTTACGATATTTA 57.078 30.769 0.00 0.00 34.36 1.40
6534 9771 8.805688 AGCGTTTCTCTTTCTTACGATATTTAC 58.194 33.333 0.00 0.00 34.36 2.01
6535 9772 8.589629 GCGTTTCTCTTTCTTACGATATTTACA 58.410 33.333 0.00 0.00 34.36 2.41
6680 9917 1.691976 GTAAGTTGCCAGGGCCTTTTT 59.308 47.619 1.32 0.27 41.09 1.94
6731 9968 6.206048 ACCTTCCTGATTTAGTTTAAACGGTG 59.794 38.462 12.54 4.54 0.00 4.94
6772 10092 9.453572 AGTATCTGAAGCTATGAACATGAAAAA 57.546 29.630 0.00 0.00 0.00 1.94
6840 10160 6.136857 TGCCAATAGATAACAGACTAGACCT 58.863 40.000 0.00 0.00 0.00 3.85
6843 10163 7.429633 CCAATAGATAACAGACTAGACCTGTG 58.570 42.308 18.29 1.87 43.42 3.66
6845 10165 5.906113 AGATAACAGACTAGACCTGTGTG 57.094 43.478 18.29 0.07 43.42 3.82
6846 10166 4.707448 AGATAACAGACTAGACCTGTGTGG 59.293 45.833 18.29 0.00 43.42 4.17
6869 10189 4.083271 GCCCTGCTTTAGACTTTGTTACTG 60.083 45.833 0.00 0.00 0.00 2.74
6874 10194 6.578944 TGCTTTAGACTTTGTTACTGTCTCA 58.421 36.000 8.76 0.00 40.86 3.27
6968 10288 1.804151 GTCATCTTTGCACCGCTTACA 59.196 47.619 0.00 0.00 0.00 2.41
7568 10900 8.950007 TTTCTTTCCTATTTCCAAGTAACCAT 57.050 30.769 0.00 0.00 0.00 3.55
7581 10913 6.655003 TCCAAGTAACCATAAGCTCTTCTTTG 59.345 38.462 0.00 0.00 36.25 2.77
7648 10985 7.201732 CGTAATTCCCAGAAATGCTTGTCTTAT 60.202 37.037 0.00 0.00 0.00 1.73
7655 10992 6.320171 CAGAAATGCTTGTCTTATGTTGGAG 58.680 40.000 0.00 0.00 0.00 3.86
7923 11263 6.524101 TCTTTTGGTTGGCCTATATTGTTC 57.476 37.500 3.32 0.00 35.27 3.18
7938 11278 2.981859 TGTTCGGATAGCCTCCTTTC 57.018 50.000 0.00 0.00 42.47 2.62
8021 11365 5.564651 CGACCCTGTCAAGTTGCAATATTTT 60.565 40.000 0.59 0.00 32.09 1.82
8023 11367 5.170748 CCCTGTCAAGTTGCAATATTTTCC 58.829 41.667 0.59 0.00 0.00 3.13
8047 11391 4.153475 GTGATCGAAGGAAAATCGTCCAAA 59.847 41.667 0.00 0.00 40.48 3.28
8136 11482 6.653273 TCTCTCTTTCATTCATTGCTTACG 57.347 37.500 0.00 0.00 0.00 3.18
8146 11492 6.966632 TCATTCATTGCTTACGAAAATGCTAC 59.033 34.615 0.00 0.00 32.50 3.58
8151 11498 4.006989 TGCTTACGAAAATGCTACCATGT 58.993 39.130 0.00 0.00 0.00 3.21
8279 11632 4.329545 GTGGCTGGTCCTTCGGCA 62.330 66.667 0.00 0.00 40.61 5.69
8380 11733 2.815211 GCGAGCATCTTGTCCGCA 60.815 61.111 0.00 0.00 44.55 5.69
8659 12012 0.036010 CGTCCACCAGGCTCTTGATT 60.036 55.000 0.00 0.00 33.74 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 4.170062 CTTACGCGTCGGCTCCGA 62.170 66.667 18.63 6.95 46.87 4.55
218 220 2.741985 CGTTGGAGCATGGCGTCA 60.742 61.111 0.00 0.00 0.00 4.35
400 406 3.036084 CTTGCCGTCGACGTTGCT 61.036 61.111 33.49 0.00 37.74 3.91
566 573 8.235226 TGTGCCGTCGTGAAAAATAATAATAAA 58.765 29.630 0.00 0.00 0.00 1.40
604 612 2.690653 CTTGACCGCCCAACAGGGAA 62.691 60.000 4.37 0.00 46.20 3.97
685 694 2.602694 CCAAACGGACGCGTGTTTTATT 60.603 45.455 20.70 0.50 36.22 1.40
687 696 0.304098 CCAAACGGACGCGTGTTTTA 59.696 50.000 20.70 0.00 36.22 1.52
743 752 1.142748 CCTCCGAGTGGATCACTGC 59.857 63.158 5.20 0.00 45.44 4.40
747 756 1.612146 TTGGCCTCCGAGTGGATCA 60.612 57.895 3.32 0.00 45.33 2.92
749 758 1.488705 TTGTTGGCCTCCGAGTGGAT 61.489 55.000 3.32 0.00 45.33 3.41
757 766 1.362355 CGGTTGTTTGTTGGCCTCC 59.638 57.895 3.32 0.00 0.00 4.30
758 767 1.104577 TCCGGTTGTTTGTTGGCCTC 61.105 55.000 3.32 0.00 0.00 4.70
775 791 1.657794 GCGTCGCCTCTCGTAATCC 60.658 63.158 5.75 0.00 39.67 3.01
936 959 1.635051 GAGGGAGGGAGGGAGGATT 59.365 63.158 0.00 0.00 0.00 3.01
937 960 2.416923 GGAGGGAGGGAGGGAGGAT 61.417 68.421 0.00 0.00 0.00 3.24
938 961 3.036959 GGAGGGAGGGAGGGAGGA 61.037 72.222 0.00 0.00 0.00 3.71
939 962 4.179599 GGGAGGGAGGGAGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
989 1012 3.951769 AAGGGCATGGGCAGCTGAC 62.952 63.158 20.43 16.66 43.71 3.51
990 1013 3.650298 GAAGGGCATGGGCAGCTGA 62.650 63.158 20.43 0.00 43.71 4.26
995 1018 4.424711 GACGGAAGGGCATGGGCA 62.425 66.667 0.00 0.00 43.71 5.36
1139 1168 7.816995 ACACAAGCACAGAACTGAATTTAAAAA 59.183 29.630 8.87 0.00 0.00 1.94
1176 1205 6.186420 TCCATAATACTAGCAGCAAATGGA 57.814 37.500 0.00 7.61 39.36 3.41
1205 1234 9.755122 AGGCTTAAGAGAAATAACCAACTAAAT 57.245 29.630 6.67 0.00 0.00 1.40
1207 1236 8.161425 ACAGGCTTAAGAGAAATAACCAACTAA 58.839 33.333 6.67 0.00 0.00 2.24
1210 1239 6.349363 CCACAGGCTTAAGAGAAATAACCAAC 60.349 42.308 6.67 0.00 0.00 3.77
1211 1240 5.710099 CCACAGGCTTAAGAGAAATAACCAA 59.290 40.000 6.67 0.00 0.00 3.67
1213 1242 5.497474 TCCACAGGCTTAAGAGAAATAACC 58.503 41.667 6.67 0.00 0.00 2.85
1214 1243 5.586643 CCTCCACAGGCTTAAGAGAAATAAC 59.413 44.000 6.67 0.00 30.98 1.89
1215 1244 5.487488 TCCTCCACAGGCTTAAGAGAAATAA 59.513 40.000 6.67 0.00 40.12 1.40
1216 1245 5.030147 TCCTCCACAGGCTTAAGAGAAATA 58.970 41.667 6.67 0.00 40.12 1.40
1217 1246 3.846588 TCCTCCACAGGCTTAAGAGAAAT 59.153 43.478 6.67 0.00 40.12 2.17
1218 1247 3.248024 TCCTCCACAGGCTTAAGAGAAA 58.752 45.455 6.67 0.00 40.12 2.52
1219 1248 2.902608 TCCTCCACAGGCTTAAGAGAA 58.097 47.619 6.67 0.00 40.12 2.87
1220 1249 2.623418 TCCTCCACAGGCTTAAGAGA 57.377 50.000 6.67 0.00 40.12 3.10
1221 1250 2.569404 ACTTCCTCCACAGGCTTAAGAG 59.431 50.000 6.67 0.00 40.12 2.85
1222 1251 2.303022 CACTTCCTCCACAGGCTTAAGA 59.697 50.000 6.67 0.00 40.12 2.10
1223 1252 2.616510 CCACTTCCTCCACAGGCTTAAG 60.617 54.545 0.00 0.00 40.12 1.85
1224 1253 1.351017 CCACTTCCTCCACAGGCTTAA 59.649 52.381 0.00 0.00 40.12 1.85
1225 1254 0.984230 CCACTTCCTCCACAGGCTTA 59.016 55.000 0.00 0.00 40.12 3.09
1226 1255 1.062488 ACCACTTCCTCCACAGGCTT 61.062 55.000 0.00 0.00 40.12 4.35
1227 1256 1.062488 AACCACTTCCTCCACAGGCT 61.062 55.000 0.00 0.00 40.12 4.58
1228 1257 0.690762 TAACCACTTCCTCCACAGGC 59.309 55.000 0.00 0.00 40.12 4.85
1229 1258 3.610911 GAATAACCACTTCCTCCACAGG 58.389 50.000 0.00 0.00 42.01 4.00
1230 1259 3.610911 GGAATAACCACTTCCTCCACAG 58.389 50.000 0.00 0.00 39.30 3.66
1231 1260 3.713826 GGAATAACCACTTCCTCCACA 57.286 47.619 0.00 0.00 39.30 4.17
1237 1266 5.185828 AGCATTTCAAGGAATAACCACTTCC 59.814 40.000 0.00 0.00 42.13 3.46
1238 1267 6.272822 AGCATTTCAAGGAATAACCACTTC 57.727 37.500 0.00 0.00 42.04 3.01
1239 1268 6.948309 ACTAGCATTTCAAGGAATAACCACTT 59.052 34.615 0.00 0.00 42.04 3.16
1240 1269 6.485171 ACTAGCATTTCAAGGAATAACCACT 58.515 36.000 0.00 0.00 42.04 4.00
1241 1270 6.759497 ACTAGCATTTCAAGGAATAACCAC 57.241 37.500 0.00 0.00 42.04 4.16
1250 1279 7.606456 TCCAACTTTAGTACTAGCATTTCAAGG 59.394 37.037 2.23 0.00 0.00 3.61
1315 1344 3.439857 TTCCAGCCACTGAGCTTTTAT 57.560 42.857 0.00 0.00 42.61 1.40
1331 1360 6.462552 TGTCAAGTGAAATGAACAATTCCA 57.537 33.333 0.00 0.00 0.00 3.53
1367 1396 4.348863 AATCTTCAAGAGAGCACACTGT 57.651 40.909 0.00 0.00 37.93 3.55
1469 1502 4.946784 ACGCAATGTCTTCCTTACATTC 57.053 40.909 0.00 0.00 43.84 2.67
1507 1540 4.261578 AGGTTCAGGCAACATGAAAATG 57.738 40.909 0.00 0.00 38.34 2.32
1633 1669 2.091885 AGAAAAAGGTGTGCCAGAGGAA 60.092 45.455 0.00 0.00 37.19 3.36
1637 1673 1.214175 TCCAGAAAAAGGTGTGCCAGA 59.786 47.619 0.00 0.00 37.19 3.86
1645 1681 6.478512 TTTGTAGCATTTCCAGAAAAAGGT 57.521 33.333 0.00 2.13 33.56 3.50
1646 1682 7.209475 TCTTTTGTAGCATTTCCAGAAAAAGG 58.791 34.615 0.00 0.00 35.25 3.11
1756 1792 3.059461 GCATTCAACAAACAAGCACATGG 60.059 43.478 0.00 0.00 0.00 3.66
1818 1854 4.142534 CCTTCAGGCAACATGAACATACAG 60.143 45.833 0.00 0.00 41.41 2.74
1837 1873 5.866092 CCTTGAAATTAAAGCTTCAGCCTTC 59.134 40.000 0.00 0.57 43.38 3.46
1860 1896 5.406649 TCAATTTTGGATCGTGTTTATGCC 58.593 37.500 0.00 0.00 0.00 4.40
1934 1970 7.141363 TGAGCTTTTCTTCTTGTCAATTAAGC 58.859 34.615 0.00 0.00 36.60 3.09
2012 2048 4.597004 AGAATGGGAAGTAGTGAGTCGTA 58.403 43.478 0.00 0.00 0.00 3.43
2204 2241 0.960861 CCGGTTCAGCCTTTTCCTCC 60.961 60.000 0.00 0.00 34.25 4.30
2244 2281 3.108376 AGGTACCTGCTTCTTAGGAAGG 58.892 50.000 15.42 3.33 46.49 3.46
2266 2303 1.927895 ATAGTTAGTCAGCACGCAGC 58.072 50.000 0.00 0.00 46.19 5.25
2267 2304 6.129431 CGTTATTATAGTTAGTCAGCACGCAG 60.129 42.308 0.00 0.00 0.00 5.18
2268 2305 5.684184 CGTTATTATAGTTAGTCAGCACGCA 59.316 40.000 0.00 0.00 0.00 5.24
2269 2306 5.684626 ACGTTATTATAGTTAGTCAGCACGC 59.315 40.000 0.00 0.00 0.00 5.34
2270 2307 7.675270 AACGTTATTATAGTTAGTCAGCACG 57.325 36.000 0.00 0.00 0.00 5.34
2327 2364 6.936900 TGAGAAGTCCAGAAAGAAATCGAAAT 59.063 34.615 0.00 0.00 0.00 2.17
2511 2548 9.455847 GCATATGTGGAAATATTTTCTTCAGTC 57.544 33.333 7.98 0.00 0.00 3.51
2612 2650 5.995282 TCTTATTTAATGATGCTGGTACCCG 59.005 40.000 10.07 3.73 0.00 5.28
2628 2666 9.802039 AATTACCTGGTGAACTGTTCTTATTTA 57.198 29.630 20.18 3.83 0.00 1.40
2695 2733 7.066284 GGTACATGTAGAGCAATTGATTGACTT 59.934 37.037 10.34 0.84 40.14 3.01
2696 2734 6.540189 GGTACATGTAGAGCAATTGATTGACT 59.460 38.462 10.34 0.00 40.14 3.41
2744 2782 9.310716 ACTTTTAGCATTCGTAATAGTCCTTAC 57.689 33.333 0.00 0.00 0.00 2.34
3059 3097 4.481930 AGTGAATCGATGCGAAACAAAA 57.518 36.364 0.00 0.00 39.99 2.44
3063 3101 3.663908 CTGAAGTGAATCGATGCGAAAC 58.336 45.455 0.00 0.00 39.99 2.78
3064 3102 2.094258 GCTGAAGTGAATCGATGCGAAA 59.906 45.455 0.00 0.00 39.99 3.46
3168 3209 6.491394 CACCAATCGTTCTTTAGACAAAACA 58.509 36.000 0.00 0.00 0.00 2.83
3182 3384 1.238439 CTGAACAGGCACCAATCGTT 58.762 50.000 0.00 0.00 0.00 3.85
3184 3386 2.174334 CCTGAACAGGCACCAATCG 58.826 57.895 7.95 0.00 42.44 3.34
3196 3399 5.007724 CACTTCACTTCCTTTACACCTGAAC 59.992 44.000 0.00 0.00 0.00 3.18
3374 3581 8.049117 AGGAAGAAGAATTAGTGATGCATAACA 58.951 33.333 16.79 0.00 0.00 2.41
3406 3614 3.821600 TCAAGCCCGCAGTAATTTAAACA 59.178 39.130 0.00 0.00 0.00 2.83
3420 3628 0.320073 TAACCGAACACTCAAGCCCG 60.320 55.000 0.00 0.00 0.00 6.13
3422 3630 1.130561 GCATAACCGAACACTCAAGCC 59.869 52.381 0.00 0.00 0.00 4.35
3446 3654 5.964958 AAGTGCAGCTGTACAATTACATT 57.035 34.783 32.33 15.87 37.58 2.71
3561 3778 5.342433 CACCAACCTGCATATGTGTAAATG 58.658 41.667 4.29 0.00 0.00 2.32
3630 3847 6.879400 ACCCTCTTTGTAGATACTGATGTTC 58.121 40.000 0.00 0.00 0.00 3.18
3883 4435 6.663093 ACAAGATTAACCATATGCAGGAAACA 59.337 34.615 0.00 0.00 0.00 2.83
3940 4492 8.058847 TCATAGGACATAAGGGCAAAATTTACT 58.941 33.333 0.00 0.00 0.00 2.24
3983 4536 2.677914 TCTCCAACCTGACTGAAGACA 58.322 47.619 0.00 0.00 0.00 3.41
4120 4675 5.664457 AGAATAACAGCGACATCATCTCAA 58.336 37.500 0.00 0.00 0.00 3.02
4275 4863 2.307392 TGGTGCATTCTAGTAAAGGGCA 59.693 45.455 0.00 0.00 0.00 5.36
4354 4942 7.330900 AGGAAATGAGATTGCTTATTCACAG 57.669 36.000 0.00 0.00 29.94 3.66
4429 5017 9.994432 CATCTGGAACACTAGAAATGAATTTAC 57.006 33.333 0.00 0.00 0.00 2.01
4474 5062 7.290857 TGCGTCTGTCTATTTTAAAGATCAC 57.709 36.000 0.00 0.00 0.00 3.06
4616 5228 6.524734 CCAGAATGTAGGAGCAACATGTATA 58.475 40.000 0.00 0.00 37.62 1.47
4663 5275 7.209475 CGTGAAAAATTAGGCATCCCAATAAT 58.791 34.615 0.00 0.00 0.00 1.28
4723 5337 2.742589 GTCAGGAAAAGTGGACCGAATC 59.257 50.000 0.00 0.00 0.00 2.52
4760 5374 2.443887 TTCAAGTGGTACTGGTACGC 57.556 50.000 5.04 1.66 36.94 4.42
5082 5710 6.245408 ACTGTTCATAGTAAATGGGCTTTGA 58.755 36.000 0.00 0.00 0.00 2.69
5088 5716 7.442364 CCTCATGTACTGTTCATAGTAAATGGG 59.558 40.741 13.35 10.95 44.06 4.00
5255 5892 3.887110 TCTGCAATCCATTAGCCATGAAG 59.113 43.478 0.00 0.00 34.31 3.02
5286 5923 3.969466 TGGATCAATAGGCCCAAATCA 57.031 42.857 0.00 0.00 0.00 2.57
5673 8878 2.224079 TGAACTGAGCGATTTGAACTGC 59.776 45.455 0.00 0.00 0.00 4.40
5685 8890 0.868406 CCGTGGAAACTGAACTGAGC 59.132 55.000 0.00 0.00 0.00 4.26
5846 9051 7.092716 ACAATTTTCAGCAGAACATGGATTAC 58.907 34.615 0.00 0.00 32.39 1.89
5885 9090 6.934083 TGCTGTTGAACATCTATGTAAGAACA 59.066 34.615 0.00 5.48 40.80 3.18
6013 9218 7.928908 TTTCTGCTAATTGCTAACAAACTTG 57.071 32.000 0.00 0.00 43.37 3.16
6014 9219 8.197439 AGTTTTCTGCTAATTGCTAACAAACTT 58.803 29.630 0.00 0.00 43.37 2.66
6022 9227 5.874810 ACGATCAGTTTTCTGCTAATTGCTA 59.125 36.000 0.00 0.00 46.59 3.49
6040 9245 5.561919 GCAAACCAGACAAACAATACGATCA 60.562 40.000 0.00 0.00 0.00 2.92
6041 9246 4.851558 GCAAACCAGACAAACAATACGATC 59.148 41.667 0.00 0.00 0.00 3.69
6085 9310 7.094634 CCATAATGGTTAGATCCATGCAAGTAC 60.095 40.741 0.00 0.00 46.14 2.73
6143 9368 1.194781 TCTTCCACAGTGCCCCTCTC 61.195 60.000 0.00 0.00 0.00 3.20
6152 9377 2.490903 GCATGCTCAATTCTTCCACAGT 59.509 45.455 11.37 0.00 0.00 3.55
6163 9388 2.751259 CACAGGTGTAAGCATGCTCAAT 59.249 45.455 22.93 8.31 36.26 2.57
6321 9555 7.775397 AAAAATCAATTCAGTGGACAAACAG 57.225 32.000 0.00 0.00 0.00 3.16
6444 9679 9.950680 GAGTGACTTTTTCATGACAAGATTAAA 57.049 29.630 17.23 2.29 36.32 1.52
6529 9766 9.396022 CAGTCCAAAATAGGTAGTCATGTAAAT 57.604 33.333 0.00 0.00 0.00 1.40
6530 9767 8.598916 TCAGTCCAAAATAGGTAGTCATGTAAA 58.401 33.333 0.00 0.00 0.00 2.01
6531 9768 8.141298 TCAGTCCAAAATAGGTAGTCATGTAA 57.859 34.615 0.00 0.00 0.00 2.41
6533 9770 6.620877 TCAGTCCAAAATAGGTAGTCATGT 57.379 37.500 0.00 0.00 0.00 3.21
6534 9771 8.400947 CAATTCAGTCCAAAATAGGTAGTCATG 58.599 37.037 0.00 0.00 0.00 3.07
6535 9772 8.109634 ACAATTCAGTCCAAAATAGGTAGTCAT 58.890 33.333 0.00 0.00 0.00 3.06
6538 9775 9.975218 ATAACAATTCAGTCCAAAATAGGTAGT 57.025 29.630 0.00 0.00 0.00 2.73
6540 9777 9.967451 TGATAACAATTCAGTCCAAAATAGGTA 57.033 29.630 0.00 0.00 0.00 3.08
6541 9778 8.877864 TGATAACAATTCAGTCCAAAATAGGT 57.122 30.769 0.00 0.00 0.00 3.08
6542 9779 7.917505 GCTGATAACAATTCAGTCCAAAATAGG 59.082 37.037 2.97 0.00 42.12 2.57
6543 9780 8.680903 AGCTGATAACAATTCAGTCCAAAATAG 58.319 33.333 2.97 0.00 42.12 1.73
6680 9917 9.693739 TGCCATTACTTTTGATCCTAATTAAGA 57.306 29.630 0.00 0.00 0.00 2.10
6840 10160 0.250727 GTCTAAAGCAGGGCCACACA 60.251 55.000 6.18 0.00 0.00 3.72
6843 10163 1.541588 CAAAGTCTAAAGCAGGGCCAC 59.458 52.381 6.18 0.00 0.00 5.01
6845 10165 1.911057 ACAAAGTCTAAAGCAGGGCC 58.089 50.000 0.00 0.00 0.00 5.80
6846 10166 4.072839 AGTAACAAAGTCTAAAGCAGGGC 58.927 43.478 0.00 0.00 0.00 5.19
6869 10189 4.989279 ATTGCAATTACCCACATGAGAC 57.011 40.909 5.99 0.00 0.00 3.36
6977 10297 9.737427 CAGTACTGTATAAATAGTTGACCTCAG 57.263 37.037 15.06 0.00 0.00 3.35
7568 10900 3.888930 CCCACCAAACAAAGAAGAGCTTA 59.111 43.478 0.00 0.00 35.24 3.09
7581 10913 1.002624 TGCTCGATCCCCACCAAAC 60.003 57.895 0.00 0.00 0.00 2.93
7648 10985 4.401022 ACATGAGATTTTCAGCTCCAACA 58.599 39.130 0.00 0.00 39.68 3.33
7655 10992 4.943705 TCCAACCTACATGAGATTTTCAGC 59.056 41.667 0.00 0.00 39.68 4.26
7938 11278 0.957395 AGTTCTCCAATGGCACTGCG 60.957 55.000 0.00 0.00 0.00 5.18
7989 11329 5.050091 GCAACTTGACAGGGTCGATAATATG 60.050 44.000 0.00 0.00 34.95 1.78
8021 11365 2.094390 ACGATTTTCCTTCGATCACGGA 60.094 45.455 0.00 0.00 39.81 4.69
8023 11367 2.281762 GGACGATTTTCCTTCGATCACG 59.718 50.000 0.00 0.00 39.81 4.35
8047 11391 7.761249 GCAAGCAATACAAGACAAGGATTAAAT 59.239 33.333 0.00 0.00 0.00 1.40
8098 11444 4.447138 AGAGAGATCTCCTGATTACCGT 57.553 45.455 19.30 0.00 43.88 4.83
8100 11446 6.723298 TGAAAGAGAGATCTCCTGATTACC 57.277 41.667 19.30 2.61 43.88 2.85
8151 11498 6.602803 TGCATAGTTAAATTTCAGATGCCAGA 59.397 34.615 17.60 4.44 37.90 3.86
8165 11512 6.096282 GGGGATTAAGCAGTTGCATAGTTAAA 59.904 38.462 6.90 0.00 45.16 1.52
8225 11578 7.123697 TGCCTAGCTAGTACAGTTTAATCAAGA 59.876 37.037 19.31 0.00 0.00 3.02
8380 11733 1.375268 GCTGCTCGAGGACAAGCTT 60.375 57.895 15.58 0.00 39.31 3.74
8659 12012 4.801624 CGCAGCAGCTACGGCAGA 62.802 66.667 7.19 0.00 41.70 4.26


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

AutoCloner maintained by Alex Coulton.