Multiple sequence alignment - TraesCS1A01G125000

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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 TraesCS1A01G125000 chr1A 100.000 5555 0 0 1 5555 148266325 148271879 0.000000e+00 10259.0
1 TraesCS1A01G125000 chr1A 94.737 228 7 4 3870 4094 516048068 516047843 3.180000e-92 350.0
2 TraesCS1A01G125000 chr1A 80.000 85 13 4 37 121 14127792 14127712 6.010000e-05 60.2
3 TraesCS1A01G125000 chr1A 100.000 29 0 0 5334 5362 148271622 148271650 3.000000e-03 54.7
4 TraesCS1A01G125000 chr1A 100.000 29 0 0 5298 5326 148271658 148271686 3.000000e-03 54.7
5 TraesCS1A01G125000 chr1D 95.661 2351 60 19 2 2327 142153135 142150802 0.000000e+00 3738.0
6 TraesCS1A01G125000 chr1D 97.294 1552 40 2 2325 3875 142150772 142149222 0.000000e+00 2632.0
7 TraesCS1A01G125000 chr1D 96.144 1141 37 5 4092 5229 142149233 142148097 0.000000e+00 1857.0
8 TraesCS1A01G125000 chr1D 88.175 981 82 20 1494 2452 468030352 468031320 0.000000e+00 1138.0
9 TraesCS1A01G125000 chr1D 95.633 229 8 2 5327 5555 142148058 142147832 3.160000e-97 366.0
10 TraesCS1A01G125000 chr1B 95.460 2357 71 15 2 2327 191000959 191003310 0.000000e+00 3727.0
11 TraesCS1A01G125000 chr1B 95.900 1561 40 10 2325 3875 191003340 191004886 0.000000e+00 2507.0
12 TraesCS1A01G125000 chr1B 95.795 1094 30 6 4094 5174 191004877 191005967 0.000000e+00 1751.0
13 TraesCS1A01G125000 chr1B 91.504 565 40 5 1765 2327 590412998 590412440 0.000000e+00 771.0
14 TraesCS1A01G125000 chr1B 93.886 229 13 1 5327 5555 191011925 191012152 1.480000e-90 344.0
15 TraesCS1A01G125000 chr7B 88.876 836 69 11 1494 2327 210630008 210629195 0.000000e+00 1007.0
16 TraesCS1A01G125000 chr7B 95.067 223 8 2 3872 4094 742117958 742118177 1.150000e-91 348.0
17 TraesCS1A01G125000 chr5A 91.815 562 38 5 1765 2324 473425986 473426541 0.000000e+00 776.0
18 TraesCS1A01G125000 chr5A 97.696 217 3 2 3878 4094 454669667 454669881 6.800000e-99 372.0
19 TraesCS1A01G125000 chr5B 88.264 622 52 15 1709 2327 407322374 407321771 0.000000e+00 725.0
20 TraesCS1A01G125000 chr5B 86.624 157 19 1 1494 1650 407322542 407322388 7.400000e-39 172.0
21 TraesCS1A01G125000 chr4A 88.103 622 53 15 1709 2327 638241367 638240764 0.000000e+00 719.0
22 TraesCS1A01G125000 chr4A 87.261 157 18 1 1494 1650 638241535 638241381 1.590000e-40 178.0
23 TraesCS1A01G125000 chr5D 87.759 580 48 9 1750 2327 69675402 69675960 0.000000e+00 656.0
24 TraesCS1A01G125000 chr2A 87.759 580 48 8 1750 2327 448555055 448554497 0.000000e+00 656.0
25 TraesCS1A01G125000 chr2A 97.696 217 2 3 3878 4094 232273856 232273643 2.440000e-98 370.0
26 TraesCS1A01G125000 chr2A 96.759 216 6 1 3879 4094 197552507 197552293 5.290000e-95 359.0
27 TraesCS1A01G125000 chrUn 92.619 420 27 3 1796 2213 477073136 477072719 7.960000e-168 601.0
28 TraesCS1A01G125000 chr7A 97.222 216 3 3 3880 4094 623446242 623446029 4.090000e-96 363.0
29 TraesCS1A01G125000 chr4B 97.630 211 5 0 3884 4094 357931834 357931624 4.090000e-96 363.0
30 TraesCS1A01G125000 chr2B 95.455 220 8 2 3876 4094 154123062 154123280 3.180000e-92 350.0
31 TraesCS1A01G125000 chr6A 95.833 216 7 2 3880 4094 69369259 69369045 1.150000e-91 348.0
32 TraesCS1A01G125000 chr6A 85.714 98 14 0 5170 5267 38556350 38556253 2.740000e-18 104.0
33 TraesCS1A01G125000 chr3D 75.879 199 35 10 37 226 120100793 120100987 7.660000e-14 89.8
34 TraesCS1A01G125000 chr3B 81.319 91 12 5 5194 5283 221752977 221753063 9.990000e-08 69.4


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 TraesCS1A01G125000 chr1A 148266325 148271879 5554 False 3456.133333 10259 100.000000 1 5555 3 chr1A.!!$F1 5554
1 TraesCS1A01G125000 chr1D 142147832 142153135 5303 True 2148.250000 3738 96.183000 2 5555 4 chr1D.!!$R1 5553
2 TraesCS1A01G125000 chr1D 468030352 468031320 968 False 1138.000000 1138 88.175000 1494 2452 1 chr1D.!!$F1 958
3 TraesCS1A01G125000 chr1B 191000959 191005967 5008 False 2661.666667 3727 95.718333 2 5174 3 chr1B.!!$F2 5172
4 TraesCS1A01G125000 chr1B 590412440 590412998 558 True 771.000000 771 91.504000 1765 2327 1 chr1B.!!$R1 562
5 TraesCS1A01G125000 chr7B 210629195 210630008 813 True 1007.000000 1007 88.876000 1494 2327 1 chr7B.!!$R1 833
6 TraesCS1A01G125000 chr5A 473425986 473426541 555 False 776.000000 776 91.815000 1765 2324 1 chr5A.!!$F2 559
7 TraesCS1A01G125000 chr5B 407321771 407322542 771 True 448.500000 725 87.444000 1494 2327 2 chr5B.!!$R1 833
8 TraesCS1A01G125000 chr4A 638240764 638241535 771 True 448.500000 719 87.682000 1494 2327 2 chr4A.!!$R1 833
9 TraesCS1A01G125000 chr5D 69675402 69675960 558 False 656.000000 656 87.759000 1750 2327 1 chr5D.!!$F1 577
10 TraesCS1A01G125000 chr2A 448554497 448555055 558 True 656.000000 656 87.759000 1750 2327 1 chr2A.!!$R3 577

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
925 938 1.005394 CAAGCCAAGCCAAGCCAAG 60.005 57.895 0.00 0.00 0.00 3.61 F
1100 1114 0.465097 GGATCTGTGCTGGGATGGTG 60.465 60.000 0.00 0.00 0.00 4.17 F
2681 2767 0.995024 AGCTGGCCAGGTGTTAAGAT 59.005 50.000 35.74 2.37 37.82 2.40 F
4058 4154 0.255890 ACAACCGGCTGGCATAAGAT 59.744 50.000 12.89 0.00 39.70 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2611 2697 0.179076 TAGCACAGACCATGATGCCG 60.179 55.00 0.00 0.0 36.92 5.69 R
2774 2860 5.831702 AAGCAAGAATTCAGCAATCTAGG 57.168 39.13 20.49 0.0 0.00 3.02 R
4418 4514 0.168788 CCCATAAGCACAACAGCACG 59.831 55.00 0.00 0.0 36.85 5.34 R
5310 5419 0.179161 GTCTGTCACAGGATCGGACG 60.179 60.00 4.57 0.0 34.32 4.79 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
33 34 9.617523 CCAAAAATAAGGAGGCATTAAAATGAT 57.382 29.630 6.87 0.00 38.70 2.45
76 77 4.247258 TGCCAATGCACTTGAATTTGATC 58.753 39.130 9.56 0.00 44.23 2.92
148 149 7.334671 TGCAAACAAGAATGATACGGTGTTATA 59.665 33.333 0.00 0.00 0.00 0.98
166 168 2.983907 TACCCGTGTGACAAGTTTCA 57.016 45.000 0.00 0.00 0.00 2.69
182 184 7.257722 ACAAGTTTCACGAATGAATGAGTTTT 58.742 30.769 0.00 0.00 44.36 2.43
402 405 1.901833 GTTGCAATGGGACCCAAGATT 59.098 47.619 19.58 4.38 36.95 2.40
435 438 5.766150 TTCCGGGCATTAAAATGACATAG 57.234 39.130 10.58 1.75 46.48 2.23
436 439 4.787551 TCCGGGCATTAAAATGACATAGT 58.212 39.130 10.58 0.00 46.48 2.12
437 440 5.931294 TCCGGGCATTAAAATGACATAGTA 58.069 37.500 10.58 0.00 46.48 1.82
491 494 1.035139 ATGCGCCATCAATTTCTCCC 58.965 50.000 4.18 0.00 0.00 4.30
557 560 9.612620 ATTTTCACAAATTTCTCTGACGAATAC 57.387 29.630 0.00 0.00 0.00 1.89
562 565 3.777465 TTTCTCTGACGAATACCCTCG 57.223 47.619 0.00 0.00 44.50 4.63
583 586 8.936864 CCCTCGTATATTATCAGTTCATTTTCC 58.063 37.037 0.00 0.00 0.00 3.13
637 642 5.652994 TTTAGCGGCATTGTTATCCTTTT 57.347 34.783 1.45 0.00 0.00 2.27
728 733 3.073274 GGTACTCCCAGCAATTTGACT 57.927 47.619 0.00 0.00 0.00 3.41
922 935 4.383861 GCCAAGCCAAGCCAAGCC 62.384 66.667 0.00 0.00 0.00 4.35
923 936 2.918802 CCAAGCCAAGCCAAGCCA 60.919 61.111 0.00 0.00 0.00 4.75
924 937 2.509651 CCAAGCCAAGCCAAGCCAA 61.510 57.895 0.00 0.00 0.00 4.52
925 938 1.005394 CAAGCCAAGCCAAGCCAAG 60.005 57.895 0.00 0.00 0.00 3.61
926 939 2.875804 AAGCCAAGCCAAGCCAAGC 61.876 57.895 0.00 0.00 0.00 4.01
1100 1114 0.465097 GGATCTGTGCTGGGATGGTG 60.465 60.000 0.00 0.00 0.00 4.17
1291 1306 2.749441 GCCCAAGCAGGTGAGCTC 60.749 66.667 6.82 6.82 45.89 4.09
1309 1324 2.280183 GCTCAGCGTCTCTTATGTTTCG 59.720 50.000 0.00 0.00 0.00 3.46
1362 1377 2.107204 AGTTCTTGCCTTGGTGAGATGT 59.893 45.455 0.00 0.00 0.00 3.06
1363 1378 2.189594 TCTTGCCTTGGTGAGATGTG 57.810 50.000 0.00 0.00 0.00 3.21
1368 1383 1.446907 CCTTGGTGAGATGTGTCTGC 58.553 55.000 0.00 0.00 33.97 4.26
1455 1493 8.684520 TGGTTAGATTTTTCTTCGTTTACCAAA 58.315 29.630 0.00 0.00 0.00 3.28
1456 1494 9.687210 GGTTAGATTTTTCTTCGTTTACCAAAT 57.313 29.630 0.00 0.00 0.00 2.32
1606 1647 2.128771 ATATGCCTGTGTGGTGTTCC 57.871 50.000 0.00 0.00 38.35 3.62
1699 1740 6.096846 TCTGTTACTATGAGCAACAGCTGATA 59.903 38.462 23.35 5.53 45.60 2.15
2387 2473 4.035558 GTGAACACTGAACAGATTTGCTCA 59.964 41.667 8.87 1.71 0.00 4.26
2408 2494 6.571150 GCTCAGTTTTCATGTATGGCTTTTCT 60.571 38.462 0.00 0.00 0.00 2.52
2439 2525 1.419762 TGAACTTGCCTCCACTTGCTA 59.580 47.619 0.00 0.00 0.00 3.49
2440 2526 2.040278 TGAACTTGCCTCCACTTGCTAT 59.960 45.455 0.00 0.00 0.00 2.97
2559 2645 4.862574 TGATACGTACACACTGCTTCAATC 59.137 41.667 0.00 0.00 0.00 2.67
2641 2727 7.988737 TCATGGTCTGTGCTATTTTGATTTAG 58.011 34.615 0.00 0.00 0.00 1.85
2681 2767 0.995024 AGCTGGCCAGGTGTTAAGAT 59.005 50.000 35.74 2.37 37.82 2.40
2730 2816 8.598041 ACCTTACAGTTTGACTTCTTCAGATAT 58.402 33.333 0.00 0.00 34.94 1.63
2774 2860 5.844004 TCTCTGTATTCCGCTTATTCCTTC 58.156 41.667 0.00 0.00 0.00 3.46
2856 2942 2.099141 ACATTGGATGTCCGACACTG 57.901 50.000 2.57 0.06 39.92 3.66
2862 2948 4.545208 TGGATGTCCGACACTGAATTTA 57.455 40.909 2.57 0.00 39.43 1.40
2934 3020 5.312120 ACTTACCTGCTAATCCGATATCG 57.688 43.478 18.31 18.31 39.44 2.92
2945 3031 7.064064 GCTAATCCGATATCGTTTTTCTTGTC 58.936 38.462 22.81 0.13 37.74 3.18
3126 3212 6.392354 AGTTCCTTCGTTTCGTTCACATATA 58.608 36.000 0.00 0.00 0.00 0.86
3133 3219 7.010697 TCGTTTCGTTCACATATATTGCAAT 57.989 32.000 17.56 17.56 0.00 3.56
3164 3250 7.106239 AGGTTCCAACTAAGATGTCAATACTG 58.894 38.462 0.00 0.00 0.00 2.74
3231 3317 2.669670 CGAGAGTGCAGTCGATCAACTT 60.670 50.000 15.76 0.00 38.50 2.66
3389 3475 6.757947 CGAATTATACGGAGTTTAGGTTTCCA 59.242 38.462 0.00 0.00 37.78 3.53
3441 3527 5.769484 AGGCTTGCAATCTCATTCTAATG 57.231 39.130 0.00 0.00 37.75 1.90
3502 3588 8.029782 TGTGGCTCACTGTTATTAATATAGGT 57.970 34.615 0.00 0.00 35.11 3.08
3582 3668 2.033801 ACTGATTGCACTTTGCTGTGAC 59.966 45.455 8.75 2.47 45.31 3.67
3703 3789 0.944386 TTCACGTTGCTTGCTCTTCC 59.056 50.000 0.00 0.00 0.00 3.46
3716 3802 1.269257 GCTCTTCCAGGTGTTTGTTGC 60.269 52.381 0.00 0.00 0.00 4.17
3742 3828 5.396213 GCAAGTAGGAGAGGAACAGATGAAT 60.396 44.000 0.00 0.00 0.00 2.57
3869 3965 9.244292 TGTCAAACTAGATTGATCAGTACTAGT 57.756 33.333 17.27 21.66 43.31 2.57
3870 3966 9.724839 GTCAAACTAGATTGATCAGTACTAGTC 57.275 37.037 24.66 15.58 41.51 2.59
3871 3967 9.688091 TCAAACTAGATTGATCAGTACTAGTCT 57.312 33.333 24.66 16.18 41.51 3.24
3874 3970 9.914834 AACTAGATTGATCAGTACTAGTCTTCT 57.085 33.333 24.66 14.57 41.51 2.85
3875 3971 9.914834 ACTAGATTGATCAGTACTAGTCTTCTT 57.085 33.333 21.66 8.16 39.25 2.52
3917 4013 4.247380 CTCCCCGGCCTCTGCATC 62.247 72.222 0.00 0.00 40.13 3.91
3919 4015 4.559063 CCCCGGCCTCTGCATCAG 62.559 72.222 0.00 0.00 40.13 2.90
3920 4016 3.473647 CCCGGCCTCTGCATCAGA 61.474 66.667 0.00 0.00 38.25 3.27
3933 4029 1.066136 CATCAGAGCGATGCATACGG 58.934 55.000 16.56 4.54 44.95 4.02
3934 4030 0.668706 ATCAGAGCGATGCATACGGC 60.669 55.000 16.56 12.82 45.13 5.68
3935 4031 2.029666 AGAGCGATGCATACGGCC 59.970 61.111 16.56 0.00 43.89 6.13
3936 4032 2.280119 GAGCGATGCATACGGCCA 60.280 61.111 16.56 0.00 43.89 5.36
3937 4033 2.588877 AGCGATGCATACGGCCAC 60.589 61.111 16.56 4.18 43.89 5.01
3938 4034 2.894879 GCGATGCATACGGCCACA 60.895 61.111 16.56 0.00 43.89 4.17
3939 4035 2.468670 GCGATGCATACGGCCACAA 61.469 57.895 16.56 0.00 43.89 3.33
3940 4036 1.785041 GCGATGCATACGGCCACAAT 61.785 55.000 16.56 0.00 43.89 2.71
3941 4037 0.662619 CGATGCATACGGCCACAATT 59.337 50.000 2.24 0.00 43.89 2.32
3942 4038 1.870402 CGATGCATACGGCCACAATTA 59.130 47.619 2.24 0.00 43.89 1.40
3943 4039 2.483877 CGATGCATACGGCCACAATTAT 59.516 45.455 2.24 0.00 43.89 1.28
3944 4040 3.682377 CGATGCATACGGCCACAATTATA 59.318 43.478 2.24 0.00 43.89 0.98
3945 4041 4.153296 CGATGCATACGGCCACAATTATAA 59.847 41.667 2.24 0.00 43.89 0.98
3946 4042 5.334491 CGATGCATACGGCCACAATTATAAA 60.334 40.000 2.24 0.00 43.89 1.40
3947 4043 6.588719 ATGCATACGGCCACAATTATAAAT 57.411 33.333 2.24 0.00 43.89 1.40
3948 4044 7.413548 CGATGCATACGGCCACAATTATAAATA 60.414 37.037 2.24 0.00 43.89 1.40
3949 4045 7.511959 TGCATACGGCCACAATTATAAATAA 57.488 32.000 2.24 0.00 43.89 1.40
3950 4046 7.941919 TGCATACGGCCACAATTATAAATAAA 58.058 30.769 2.24 0.00 43.89 1.40
3951 4047 8.580720 TGCATACGGCCACAATTATAAATAAAT 58.419 29.630 2.24 0.00 43.89 1.40
3974 4070 5.500645 AAAGTAGTTCAACAAGGTCTTGC 57.499 39.130 10.31 0.00 44.03 4.01
3975 4071 4.150897 AGTAGTTCAACAAGGTCTTGCA 57.849 40.909 10.31 0.00 44.03 4.08
3976 4072 4.523083 AGTAGTTCAACAAGGTCTTGCAA 58.477 39.130 10.31 0.00 44.03 4.08
3977 4073 5.133221 AGTAGTTCAACAAGGTCTTGCAAT 58.867 37.500 10.31 0.00 44.03 3.56
3978 4074 4.574599 AGTTCAACAAGGTCTTGCAATC 57.425 40.909 10.31 0.00 44.03 2.67
3979 4075 4.210331 AGTTCAACAAGGTCTTGCAATCT 58.790 39.130 10.31 0.00 44.03 2.40
3980 4076 4.037208 AGTTCAACAAGGTCTTGCAATCTG 59.963 41.667 10.31 0.00 44.03 2.90
3981 4077 2.294233 TCAACAAGGTCTTGCAATCTGC 59.706 45.455 10.31 0.00 44.03 4.26
3982 4078 2.283145 ACAAGGTCTTGCAATCTGCT 57.717 45.000 10.31 0.00 45.31 4.24
3983 4079 1.884579 ACAAGGTCTTGCAATCTGCTG 59.115 47.619 10.31 0.00 45.31 4.41
3984 4080 0.886563 AAGGTCTTGCAATCTGCTGC 59.113 50.000 0.00 0.00 45.31 5.25
4005 4101 2.656947 AAAAAGTAGGCTGGCTCACA 57.343 45.000 7.13 0.00 0.00 3.58
4006 4102 2.656947 AAAAGTAGGCTGGCTCACAA 57.343 45.000 7.13 0.00 0.00 3.33
4007 4103 2.656947 AAAGTAGGCTGGCTCACAAA 57.343 45.000 7.13 0.00 0.00 2.83
4008 4104 2.191128 AAGTAGGCTGGCTCACAAAG 57.809 50.000 7.13 0.00 0.00 2.77
4009 4105 1.352083 AGTAGGCTGGCTCACAAAGA 58.648 50.000 7.13 0.00 0.00 2.52
4025 4121 8.687824 CTCACAAAGAGCTAGAAAAACAAAAA 57.312 30.769 0.00 0.00 37.59 1.94
4045 4141 2.028925 GCCCAAAAGCCACAACCG 59.971 61.111 0.00 0.00 0.00 4.44
4046 4142 2.733945 CCCAAAAGCCACAACCGG 59.266 61.111 0.00 0.00 0.00 5.28
4054 4150 2.045438 CCACAACCGGCTGGCATA 60.045 61.111 12.89 0.00 39.70 3.14
4055 4151 1.677300 CCACAACCGGCTGGCATAA 60.677 57.895 12.89 0.00 39.70 1.90
4056 4152 1.656818 CCACAACCGGCTGGCATAAG 61.657 60.000 12.89 0.00 39.70 1.73
4057 4153 0.676466 CACAACCGGCTGGCATAAGA 60.676 55.000 12.89 0.00 39.70 2.10
4058 4154 0.255890 ACAACCGGCTGGCATAAGAT 59.744 50.000 12.89 0.00 39.70 2.40
4059 4155 1.488812 ACAACCGGCTGGCATAAGATA 59.511 47.619 12.89 0.00 39.70 1.98
4060 4156 2.146342 CAACCGGCTGGCATAAGATAG 58.854 52.381 12.89 0.00 39.70 2.08
4061 4157 1.717032 ACCGGCTGGCATAAGATAGA 58.283 50.000 12.89 0.00 39.70 1.98
4062 4158 2.260822 ACCGGCTGGCATAAGATAGAT 58.739 47.619 12.89 0.00 39.70 1.98
4063 4159 3.441101 ACCGGCTGGCATAAGATAGATA 58.559 45.455 12.89 0.00 39.70 1.98
4064 4160 3.449018 ACCGGCTGGCATAAGATAGATAG 59.551 47.826 12.89 0.00 39.70 2.08
4065 4161 3.701542 CCGGCTGGCATAAGATAGATAGA 59.298 47.826 0.00 0.00 0.00 1.98
4066 4162 4.343526 CCGGCTGGCATAAGATAGATAGAT 59.656 45.833 0.00 0.00 0.00 1.98
4067 4163 5.536538 CCGGCTGGCATAAGATAGATAGATA 59.463 44.000 0.00 0.00 0.00 1.98
4068 4164 6.294453 CCGGCTGGCATAAGATAGATAGATAG 60.294 46.154 0.00 0.00 0.00 2.08
4069 4165 6.294453 CGGCTGGCATAAGATAGATAGATAGG 60.294 46.154 1.08 0.00 0.00 2.57
4070 4166 6.553100 GGCTGGCATAAGATAGATAGATAGGT 59.447 42.308 0.00 0.00 0.00 3.08
4071 4167 7.726291 GGCTGGCATAAGATAGATAGATAGGTA 59.274 40.741 0.00 0.00 0.00 3.08
4072 4168 9.137459 GCTGGCATAAGATAGATAGATAGGTAA 57.863 37.037 0.00 0.00 0.00 2.85
4083 4179 9.924010 ATAGATAGATAGGTAAACTAATCGCCT 57.076 33.333 0.00 0.00 34.79 5.52
4085 4181 9.924010 AGATAGATAGGTAAACTAATCGCCTAT 57.076 33.333 0.00 0.00 43.06 2.57
4088 4184 7.407393 GATAGGTAAACTAATCGCCTATCCT 57.593 40.000 14.62 0.00 46.08 3.24
4089 4185 8.517062 GATAGGTAAACTAATCGCCTATCCTA 57.483 38.462 14.62 0.00 46.08 2.94
4090 4186 9.134055 GATAGGTAAACTAATCGCCTATCCTAT 57.866 37.037 14.62 0.00 46.08 2.57
4091 4187 7.793948 AGGTAAACTAATCGCCTATCCTATT 57.206 36.000 0.00 0.00 0.00 1.73
4092 4188 8.890410 AGGTAAACTAATCGCCTATCCTATTA 57.110 34.615 0.00 0.00 0.00 0.98
4093 4189 8.747471 AGGTAAACTAATCGCCTATCCTATTAC 58.253 37.037 0.00 0.00 0.00 1.89
4094 4190 8.747471 GGTAAACTAATCGCCTATCCTATTACT 58.253 37.037 0.00 0.00 0.00 2.24
4135 4231 6.437477 TCATAATCATAGTTATGAGGACCGCT 59.563 38.462 7.78 0.00 45.01 5.52
4212 4308 6.682863 GTCTTGTAACATGTTTTGCTATAGCG 59.317 38.462 17.78 6.15 45.83 4.26
4245 4341 2.284190 TCACGCATTTGAATATCCGCA 58.716 42.857 0.00 0.00 0.00 5.69
4287 4383 4.514441 CGCATCCTTTCTTTGATGAGCTAT 59.486 41.667 3.80 0.00 40.64 2.97
4418 4514 5.982516 TGACAAAAATGTATGCAACCTGTTC 59.017 36.000 0.00 0.00 0.00 3.18
4444 4540 2.025981 TGTTGTGCTTATGGGATCTGCT 60.026 45.455 0.00 0.00 0.00 4.24
4736 4836 0.043183 TCATCTGCCAGGGAAGGAGA 59.957 55.000 0.00 0.00 0.00 3.71
4954 5056 1.276138 CCACTGCCTGTCATGTAGTCA 59.724 52.381 0.00 0.00 0.00 3.41
4961 5063 3.257393 CCTGTCATGTAGTCAAGCTGTC 58.743 50.000 0.00 0.00 0.00 3.51
5004 5113 3.710044 CGTCGTGAGATGGCATGG 58.290 61.111 3.81 0.00 45.19 3.66
5016 5125 0.040058 TGGCATGGCTGAACTGGAAT 59.960 50.000 21.08 0.00 0.00 3.01
5101 5210 8.799367 CAATATAATCCAATGCTGATTCCAGAA 58.201 33.333 0.00 0.00 43.02 3.02
5106 5215 3.922240 CCAATGCTGATTCCAGAAAAACG 59.078 43.478 0.00 0.00 43.02 3.60
5185 5294 7.736893 AGTGAACTGATACAATAATACTCCCC 58.263 38.462 0.00 0.00 0.00 4.81
5187 5296 8.211629 GTGAACTGATACAATAATACTCCCCTT 58.788 37.037 0.00 0.00 0.00 3.95
5188 5297 8.210946 TGAACTGATACAATAATACTCCCCTTG 58.789 37.037 0.00 0.00 0.00 3.61
5192 5301 8.331931 TGATACAATAATACTCCCCTTGTCTT 57.668 34.615 0.00 0.00 32.66 3.01
5225 5334 8.962679 ACTGTCTCAATTTTGTACCAACTTTAA 58.037 29.630 0.00 0.00 0.00 1.52
5261 5370 9.760077 ATACTACGGTTAAGACATCTATTTTGG 57.240 33.333 0.00 0.00 0.00 3.28
5267 5376 7.203218 GGTTAAGACATCTATTTTGGAATGGC 58.797 38.462 0.00 0.00 0.00 4.40
5268 5377 7.147915 GGTTAAGACATCTATTTTGGAATGGCA 60.148 37.037 0.00 0.00 0.00 4.92
5272 5381 4.336433 ACATCTATTTTGGAATGGCACGAG 59.664 41.667 0.00 0.00 0.00 4.18
5282 5391 5.979993 TGGAATGGCACGAGTAGTAAATAA 58.020 37.500 0.00 0.00 0.00 1.40
5302 5411 8.697507 AAATAATGGTTGAATAGATGGAGTCC 57.302 34.615 0.73 0.73 0.00 3.85
5303 5412 4.713792 ATGGTTGAATAGATGGAGTCCC 57.286 45.455 6.74 0.00 0.00 4.46
5305 5414 3.199946 TGGTTGAATAGATGGAGTCCCAC 59.800 47.826 6.74 0.29 46.98 4.61
5306 5415 3.458189 GTTGAATAGATGGAGTCCCACG 58.542 50.000 6.74 0.00 46.98 4.94
5307 5416 3.026707 TGAATAGATGGAGTCCCACGA 57.973 47.619 6.74 0.00 46.98 4.35
5308 5417 2.959030 TGAATAGATGGAGTCCCACGAG 59.041 50.000 6.74 0.00 46.98 4.18
5309 5418 1.333177 ATAGATGGAGTCCCACGAGC 58.667 55.000 6.74 0.00 46.98 5.03
5310 5419 0.755698 TAGATGGAGTCCCACGAGCC 60.756 60.000 6.74 0.00 46.98 4.70
5311 5420 3.432051 GATGGAGTCCCACGAGCCG 62.432 68.421 6.74 0.00 46.98 5.52
5312 5421 4.988716 TGGAGTCCCACGAGCCGT 62.989 66.667 6.74 0.00 42.36 5.68
5313 5422 4.131088 GGAGTCCCACGAGCCGTC 62.131 72.222 0.00 0.00 38.32 4.79
5314 5423 4.131088 GAGTCCCACGAGCCGTCC 62.131 72.222 0.00 0.00 38.32 4.79
5318 5427 4.570663 CCCACGAGCCGTCCGATC 62.571 72.222 0.00 0.00 38.32 3.69
5319 5428 4.570663 CCACGAGCCGTCCGATCC 62.571 72.222 0.00 0.00 38.32 3.36
5320 5429 3.518998 CACGAGCCGTCCGATCCT 61.519 66.667 0.00 0.00 38.32 3.24
5321 5430 3.518998 ACGAGCCGTCCGATCCTG 61.519 66.667 0.00 0.00 33.69 3.86
5322 5431 3.518998 CGAGCCGTCCGATCCTGT 61.519 66.667 0.00 0.00 0.00 4.00
5323 5432 2.105128 GAGCCGTCCGATCCTGTG 59.895 66.667 0.00 0.00 0.00 3.66
5324 5433 2.362503 AGCCGTCCGATCCTGTGA 60.363 61.111 0.00 0.00 0.00 3.58
5325 5434 2.202756 GCCGTCCGATCCTGTGAC 60.203 66.667 0.00 0.00 0.00 3.67
5326 5435 3.001902 GCCGTCCGATCCTGTGACA 62.002 63.158 0.00 0.00 0.00 3.58
5327 5436 1.139734 CCGTCCGATCCTGTGACAG 59.860 63.158 5.42 5.42 0.00 3.51
5447 5556 1.979308 TGACAATACCTCCCCGTGAAA 59.021 47.619 0.00 0.00 0.00 2.69
5465 5574 4.331717 GTGAAAGACGAACTTGTCCTCAAA 59.668 41.667 0.00 0.00 39.77 2.69
5466 5575 5.007724 GTGAAAGACGAACTTGTCCTCAAAT 59.992 40.000 0.00 0.00 39.77 2.32
5476 5585 5.256474 ACTTGTCCTCAAATAGTTGATGGG 58.744 41.667 6.00 5.51 42.85 4.00
5493 5602 2.586357 GCGATCGAACCAGCCTCC 60.586 66.667 21.57 0.00 0.00 4.30
5496 5605 0.962489 CGATCGAACCAGCCTCCTAT 59.038 55.000 10.26 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.872585 TGCCTCCTTATTTTTGGATCAAAT 57.127 33.333 0.00 0.00 33.19 2.32
33 34 1.218047 CGAGACCCAAAGATCCGCA 59.782 57.895 0.00 0.00 0.00 5.69
148 149 1.375551 GTGAAACTTGTCACACGGGT 58.624 50.000 0.00 0.00 46.00 5.28
235 237 5.535030 GGACTCCTTGACATAAACAAAAGGT 59.465 40.000 0.00 0.00 38.81 3.50
379 382 0.831288 TTGGGTCCCATTGCAACCTG 60.831 55.000 12.68 0.00 31.53 4.00
380 383 0.542702 CTTGGGTCCCATTGCAACCT 60.543 55.000 12.68 0.00 31.53 3.50
402 405 4.447138 AATGCCCGGAAATACCTAATGA 57.553 40.909 0.73 0.00 36.31 2.57
442 445 8.585881 TGTCATATAGGAGAACCTTATTAGTGC 58.414 37.037 0.00 0.00 45.36 4.40
461 464 3.414269 TGATGGCGCATTCATGTCATAT 58.586 40.909 10.83 0.00 0.00 1.78
491 494 9.622004 CTGTACAAATATACTAGGGTATTCGTG 57.378 37.037 0.00 0.00 39.19 4.35
557 560 8.936864 GGAAAATGAACTGATAATATACGAGGG 58.063 37.037 0.00 0.00 0.00 4.30
562 565 8.094798 TGCCGGAAAATGAACTGATAATATAC 57.905 34.615 5.05 0.00 0.00 1.47
569 572 3.071874 TCTGCCGGAAAATGAACTGAT 57.928 42.857 5.05 0.00 0.00 2.90
679 684 6.206829 GGCATCAGGTTGGGTTTTATATAGTC 59.793 42.308 0.00 0.00 0.00 2.59
728 733 1.153208 GACTAGACGAGCCTCGGGA 60.153 63.158 19.61 1.85 45.59 5.14
922 935 0.979665 TGGTCCTCTTCTCTGGCTTG 59.020 55.000 0.00 0.00 0.00 4.01
923 936 1.274712 CTGGTCCTCTTCTCTGGCTT 58.725 55.000 0.00 0.00 0.00 4.35
924 937 0.617249 CCTGGTCCTCTTCTCTGGCT 60.617 60.000 0.00 0.00 0.00 4.75
925 938 1.904032 CCTGGTCCTCTTCTCTGGC 59.096 63.158 0.00 0.00 0.00 4.85
926 939 1.904032 GCCTGGTCCTCTTCTCTGG 59.096 63.158 0.00 0.00 0.00 3.86
1100 1114 0.248866 CCAAGAAACACACGGCCAAC 60.249 55.000 2.24 0.00 0.00 3.77
1291 1306 2.703190 GCGAAACATAAGAGACGCTG 57.297 50.000 0.00 0.00 42.19 5.18
1309 1324 0.250467 TCAGGCCAAGAGACACAAGC 60.250 55.000 5.01 0.00 0.00 4.01
1368 1383 4.405116 AAAGAGAATAGCTGCAGGAGAG 57.595 45.455 17.12 0.00 0.00 3.20
1401 1439 7.741027 ATCCACACAGCTATATTTCAATGAG 57.259 36.000 0.00 0.00 0.00 2.90
1606 1647 2.081462 GTCCCGAAAACCCACAGTATG 58.919 52.381 0.00 0.00 46.00 2.39
1699 1740 3.133365 AACTGGGCGCCAAAGAGGT 62.133 57.895 30.85 13.88 40.61 3.85
1899 1945 4.083862 GCCACTGTCTCCCCGGTC 62.084 72.222 0.00 0.00 0.00 4.79
2233 2284 1.609239 CCCCTGAATAGCTGCCACA 59.391 57.895 0.00 0.00 0.00 4.17
2387 2473 5.928264 GCAAGAAAAGCCATACATGAAAACT 59.072 36.000 0.00 0.00 0.00 2.66
2408 2494 4.370917 GAGGCAAGTTCAAAATCAAGCAA 58.629 39.130 0.00 0.00 0.00 3.91
2559 2645 2.346803 CCTACACGACAGGACAAATGG 58.653 52.381 0.00 0.00 34.91 3.16
2611 2697 0.179076 TAGCACAGACCATGATGCCG 60.179 55.000 0.00 0.00 36.92 5.69
2641 2727 7.224949 CCAGCTATAAGCCTAAAACAGTAAGAC 59.775 40.741 0.00 0.00 43.77 3.01
2767 2853 6.909076 AGAATTCAGCAATCTAGGAAGGAAT 58.091 36.000 8.44 0.00 0.00 3.01
2774 2860 5.831702 AAGCAAGAATTCAGCAATCTAGG 57.168 39.130 20.49 0.00 0.00 3.02
2878 2964 8.251383 AGTACTATGCAGGTTGATATTGTAGT 57.749 34.615 0.00 0.00 0.00 2.73
3126 3212 4.018050 AGTTGGAACCTAGGAGATTGCAAT 60.018 41.667 17.98 12.83 31.56 3.56
3133 3219 5.590818 ACATCTTAGTTGGAACCTAGGAGA 58.409 41.667 17.98 4.51 0.00 3.71
3210 3296 1.135546 AGTTGATCGACTGCACTCTCG 60.136 52.381 15.14 0.00 0.00 4.04
3231 3317 6.544928 TTGCAGACCTTGATTATCTCTACA 57.455 37.500 0.00 0.00 0.00 2.74
3389 3475 3.950395 GCCAAGGATGAGCTTTTATCTGT 59.050 43.478 0.00 0.00 0.00 3.41
3441 3527 7.879070 ACAGCAAATGTGATATATGATTGGAC 58.121 34.615 0.00 0.00 41.91 4.02
3501 3587 5.317733 AGCAGATCTTATATACGGCTGAC 57.682 43.478 0.00 5.81 33.27 3.51
3688 3774 0.886490 ACCTGGAAGAGCAAGCAACG 60.886 55.000 0.00 0.00 34.07 4.10
3703 3789 0.871163 CTTGCCGCAACAAACACCTG 60.871 55.000 0.38 0.00 0.00 4.00
3716 3802 0.895530 TGTTCCTCTCCTACTTGCCG 59.104 55.000 0.00 0.00 0.00 5.69
3788 3874 7.882179 AGTTACCAACAATCAATAAGGACAAC 58.118 34.615 0.00 0.00 0.00 3.32
3840 3936 9.209175 AGTACTGATCAATCTAGTTTGACAAAC 57.791 33.333 21.09 21.09 38.37 2.93
3900 3996 4.247380 GATGCAGAGGCCGGGGAG 62.247 72.222 2.18 0.00 40.13 4.30
3902 3998 4.559063 CTGATGCAGAGGCCGGGG 62.559 72.222 2.18 0.00 40.13 5.73
3903 3999 3.473647 TCTGATGCAGAGGCCGGG 61.474 66.667 2.18 0.00 35.39 5.73
3915 4011 0.668706 GCCGTATGCATCGCTCTGAT 60.669 55.000 0.19 0.00 40.77 2.90
3916 4012 1.300156 GCCGTATGCATCGCTCTGA 60.300 57.895 0.19 0.00 40.77 3.27
3917 4013 2.313172 GGCCGTATGCATCGCTCTG 61.313 63.158 0.19 0.00 43.89 3.35
3918 4014 2.029666 GGCCGTATGCATCGCTCT 59.970 61.111 0.19 0.00 43.89 4.09
3919 4015 2.280119 TGGCCGTATGCATCGCTC 60.280 61.111 0.19 2.96 43.89 5.03
3920 4016 2.588877 GTGGCCGTATGCATCGCT 60.589 61.111 0.19 0.00 43.89 4.93
3921 4017 1.785041 ATTGTGGCCGTATGCATCGC 61.785 55.000 0.19 3.34 43.89 4.58
3922 4018 0.662619 AATTGTGGCCGTATGCATCG 59.337 50.000 0.19 7.03 43.89 3.84
3923 4019 5.621197 TTATAATTGTGGCCGTATGCATC 57.379 39.130 0.19 0.00 43.89 3.91
3924 4020 6.588719 ATTTATAATTGTGGCCGTATGCAT 57.411 33.333 3.79 3.79 43.89 3.96
3925 4021 7.511959 TTATTTATAATTGTGGCCGTATGCA 57.488 32.000 0.00 0.00 43.89 3.96
3926 4022 8.980143 ATTTATTTATAATTGTGGCCGTATGC 57.020 30.769 0.00 0.00 40.16 3.14
3948 4044 8.135529 GCAAGACCTTGTTGAACTACTTTATTT 58.864 33.333 10.96 0.00 42.31 1.40
3949 4045 7.284489 TGCAAGACCTTGTTGAACTACTTTATT 59.716 33.333 10.96 0.00 42.31 1.40
3950 4046 6.770785 TGCAAGACCTTGTTGAACTACTTTAT 59.229 34.615 10.96 0.00 42.31 1.40
3951 4047 6.116806 TGCAAGACCTTGTTGAACTACTTTA 58.883 36.000 10.96 0.00 42.31 1.85
3952 4048 4.947388 TGCAAGACCTTGTTGAACTACTTT 59.053 37.500 10.96 0.00 42.31 2.66
3953 4049 4.523083 TGCAAGACCTTGTTGAACTACTT 58.477 39.130 10.96 0.00 42.31 2.24
3954 4050 4.150897 TGCAAGACCTTGTTGAACTACT 57.849 40.909 10.96 0.00 42.31 2.57
3955 4051 4.893424 TTGCAAGACCTTGTTGAACTAC 57.107 40.909 10.96 0.00 42.31 2.73
3956 4052 5.239306 CAGATTGCAAGACCTTGTTGAACTA 59.761 40.000 4.94 0.00 42.31 2.24
3957 4053 4.037208 CAGATTGCAAGACCTTGTTGAACT 59.963 41.667 4.94 3.32 42.31 3.01
3958 4054 4.293415 CAGATTGCAAGACCTTGTTGAAC 58.707 43.478 4.94 0.00 42.31 3.18
3959 4055 3.243501 GCAGATTGCAAGACCTTGTTGAA 60.244 43.478 4.94 3.42 44.26 2.69
3960 4056 2.294233 GCAGATTGCAAGACCTTGTTGA 59.706 45.455 4.94 0.00 44.26 3.18
3961 4057 2.669364 GCAGATTGCAAGACCTTGTTG 58.331 47.619 4.94 0.00 44.26 3.33
3986 4082 2.656947 TGTGAGCCAGCCTACTTTTT 57.343 45.000 0.00 0.00 0.00 1.94
3987 4083 2.656947 TTGTGAGCCAGCCTACTTTT 57.343 45.000 0.00 0.00 0.00 2.27
3988 4084 2.106511 TCTTTGTGAGCCAGCCTACTTT 59.893 45.455 0.00 0.00 0.00 2.66
3989 4085 1.699634 TCTTTGTGAGCCAGCCTACTT 59.300 47.619 0.00 0.00 0.00 2.24
3990 4086 1.277557 CTCTTTGTGAGCCAGCCTACT 59.722 52.381 0.00 0.00 35.84 2.57
3991 4087 1.731720 CTCTTTGTGAGCCAGCCTAC 58.268 55.000 0.00 0.00 35.84 3.18
4000 4096 8.687824 TTTTTGTTTTTCTAGCTCTTTGTGAG 57.312 30.769 0.00 0.00 45.33 3.51
4028 4124 2.028925 CGGTTGTGGCTTTTGGGC 59.971 61.111 0.00 0.00 41.27 5.36
4029 4125 2.733945 CCGGTTGTGGCTTTTGGG 59.266 61.111 0.00 0.00 0.00 4.12
4037 4133 1.656818 CTTATGCCAGCCGGTTGTGG 61.657 60.000 17.69 15.43 36.85 4.17
4038 4134 0.676466 TCTTATGCCAGCCGGTTGTG 60.676 55.000 17.69 9.73 33.28 3.33
4039 4135 0.255890 ATCTTATGCCAGCCGGTTGT 59.744 50.000 17.69 1.06 33.28 3.32
4040 4136 2.146342 CTATCTTATGCCAGCCGGTTG 58.854 52.381 11.98 11.98 33.28 3.77
4041 4137 2.047061 TCTATCTTATGCCAGCCGGTT 58.953 47.619 1.90 0.00 33.28 4.44
4042 4138 1.717032 TCTATCTTATGCCAGCCGGT 58.283 50.000 1.90 0.00 33.28 5.28
4043 4139 3.701542 TCTATCTATCTTATGCCAGCCGG 59.298 47.826 0.00 0.00 0.00 6.13
4044 4140 4.991153 TCTATCTATCTTATGCCAGCCG 57.009 45.455 0.00 0.00 0.00 5.52
4045 4141 6.553100 ACCTATCTATCTATCTTATGCCAGCC 59.447 42.308 0.00 0.00 0.00 4.85
4046 4142 7.595819 ACCTATCTATCTATCTTATGCCAGC 57.404 40.000 0.00 0.00 0.00 4.85
4057 4153 9.924010 AGGCGATTAGTTTACCTATCTATCTAT 57.076 33.333 0.00 0.00 0.00 1.98
4059 4155 9.924010 ATAGGCGATTAGTTTACCTATCTATCT 57.076 33.333 0.00 0.00 39.01 1.98
4065 4161 9.490083 AATAGGATAGGCGATTAGTTTACCTAT 57.510 33.333 0.00 0.00 44.49 2.57
4066 4162 8.890410 AATAGGATAGGCGATTAGTTTACCTA 57.110 34.615 0.00 0.00 37.40 3.08
4067 4163 7.793948 AATAGGATAGGCGATTAGTTTACCT 57.206 36.000 0.00 0.00 34.42 3.08
4068 4164 8.747471 AGTAATAGGATAGGCGATTAGTTTACC 58.253 37.037 0.00 0.00 0.00 2.85
4071 4167 9.531158 ACTAGTAATAGGATAGGCGATTAGTTT 57.469 33.333 1.80 0.00 0.00 2.66
4072 4168 9.176460 GACTAGTAATAGGATAGGCGATTAGTT 57.824 37.037 0.00 0.00 0.00 2.24
4073 4169 8.550585 AGACTAGTAATAGGATAGGCGATTAGT 58.449 37.037 0.00 0.00 29.43 2.24
4074 4170 8.967664 AGACTAGTAATAGGATAGGCGATTAG 57.032 38.462 0.00 0.00 29.43 1.73
4075 4171 9.393512 GAAGACTAGTAATAGGATAGGCGATTA 57.606 37.037 0.00 0.00 29.43 1.75
4076 4172 8.110908 AGAAGACTAGTAATAGGATAGGCGATT 58.889 37.037 0.00 0.00 29.43 3.34
4077 4173 7.635648 AGAAGACTAGTAATAGGATAGGCGAT 58.364 38.462 0.00 0.00 29.43 4.58
4078 4174 7.018487 AGAAGACTAGTAATAGGATAGGCGA 57.982 40.000 0.00 0.00 29.43 5.54
4079 4175 8.832521 CATAGAAGACTAGTAATAGGATAGGCG 58.167 40.741 0.00 0.00 29.43 5.52
4080 4176 9.908747 TCATAGAAGACTAGTAATAGGATAGGC 57.091 37.037 0.00 0.00 31.78 3.93
4084 4180 9.989296 ATGCTCATAGAAGACTAGTAATAGGAT 57.011 33.333 0.00 0.00 31.78 3.24
4085 4181 9.456147 GATGCTCATAGAAGACTAGTAATAGGA 57.544 37.037 0.00 0.00 31.78 2.94
4086 4182 9.237187 TGATGCTCATAGAAGACTAGTAATAGG 57.763 37.037 0.00 0.00 31.78 2.57
4092 4188 9.306777 TGATTATGATGCTCATAGAAGACTAGT 57.693 33.333 0.00 0.00 40.13 2.57
4107 4203 7.223582 CGGTCCTCATAACTATGATTATGATGC 59.776 40.741 11.71 7.08 45.84 3.91
4135 4231 5.952347 AGCATCGATCTATGGTACTGGATTA 59.048 40.000 9.95 0.00 35.88 1.75
4190 4286 6.147985 TCACGCTATAGCAAAACATGTTACAA 59.852 34.615 23.99 0.00 42.21 2.41
4212 4308 5.049474 TCAAATGCGTGAATATAGCCATCAC 60.049 40.000 0.00 0.00 39.98 3.06
4224 4320 2.680339 TGCGGATATTCAAATGCGTGAA 59.320 40.909 0.42 0.42 42.03 3.18
4418 4514 0.168788 CCCATAAGCACAACAGCACG 59.831 55.000 0.00 0.00 36.85 5.34
4456 4556 2.558554 GAAGCATTGGCCAGCTGCAG 62.559 60.000 31.98 10.11 43.89 4.41
4736 4836 0.178953 ATGCTGTTTCCCTGGCAAGT 60.179 50.000 0.00 0.00 38.21 3.16
4835 4935 6.482308 ACAAAATAGTTGACAACTTACGAGCT 59.518 34.615 25.10 2.08 42.81 4.09
4954 5056 4.729868 ACCCAACAGAAAATAGACAGCTT 58.270 39.130 0.00 0.00 0.00 3.74
4961 5063 4.693566 TCGCAACTACCCAACAGAAAATAG 59.306 41.667 0.00 0.00 0.00 1.73
5004 5113 2.678336 CGAACCCTAATTCCAGTTCAGC 59.322 50.000 12.29 0.00 38.80 4.26
5016 5125 1.108776 CTCGATCCCACGAACCCTAA 58.891 55.000 0.00 0.00 41.67 2.69
5080 5189 7.322664 GTTTTTCTGGAATCAGCATTGGATTA 58.677 34.615 0.00 0.00 40.69 1.75
5101 5210 2.565391 CAATTTAAGCCTCCCCCGTTTT 59.435 45.455 0.00 0.00 0.00 2.43
5235 5344 9.760077 CCAAAATAGATGTCTTAACCGTAGTAT 57.240 33.333 0.00 0.00 0.00 2.12
5236 5345 8.970020 TCCAAAATAGATGTCTTAACCGTAGTA 58.030 33.333 0.00 0.00 0.00 1.82
5237 5346 7.844009 TCCAAAATAGATGTCTTAACCGTAGT 58.156 34.615 0.00 0.00 0.00 2.73
5238 5347 8.712285 TTCCAAAATAGATGTCTTAACCGTAG 57.288 34.615 0.00 0.00 0.00 3.51
5239 5348 9.104965 CATTCCAAAATAGATGTCTTAACCGTA 57.895 33.333 0.00 0.00 0.00 4.02
5240 5349 7.067008 CCATTCCAAAATAGATGTCTTAACCGT 59.933 37.037 0.00 0.00 0.00 4.83
5241 5350 7.417612 CCATTCCAAAATAGATGTCTTAACCG 58.582 38.462 0.00 0.00 0.00 4.44
5242 5351 7.147915 TGCCATTCCAAAATAGATGTCTTAACC 60.148 37.037 0.00 0.00 0.00 2.85
5243 5352 7.702348 GTGCCATTCCAAAATAGATGTCTTAAC 59.298 37.037 0.00 0.00 0.00 2.01
5244 5353 7.415095 CGTGCCATTCCAAAATAGATGTCTTAA 60.415 37.037 0.00 0.00 0.00 1.85
5245 5354 6.038161 CGTGCCATTCCAAAATAGATGTCTTA 59.962 38.462 0.00 0.00 0.00 2.10
5246 5355 5.163622 CGTGCCATTCCAAAATAGATGTCTT 60.164 40.000 0.00 0.00 0.00 3.01
5247 5356 4.336433 CGTGCCATTCCAAAATAGATGTCT 59.664 41.667 0.00 0.00 0.00 3.41
5248 5357 4.335315 TCGTGCCATTCCAAAATAGATGTC 59.665 41.667 0.00 0.00 0.00 3.06
5249 5358 4.269183 TCGTGCCATTCCAAAATAGATGT 58.731 39.130 0.00 0.00 0.00 3.06
5250 5359 4.336433 ACTCGTGCCATTCCAAAATAGATG 59.664 41.667 0.00 0.00 0.00 2.90
5251 5360 4.526970 ACTCGTGCCATTCCAAAATAGAT 58.473 39.130 0.00 0.00 0.00 1.98
5252 5361 3.950397 ACTCGTGCCATTCCAAAATAGA 58.050 40.909 0.00 0.00 0.00 1.98
5253 5362 4.876107 ACTACTCGTGCCATTCCAAAATAG 59.124 41.667 0.00 0.00 0.00 1.73
5261 5370 6.482308 ACCATTATTTACTACTCGTGCCATTC 59.518 38.462 0.00 0.00 0.00 2.67
5282 5391 4.047166 TGGGACTCCATCTATTCAACCAT 58.953 43.478 0.00 0.00 38.32 3.55
5294 5403 3.461773 CGGCTCGTGGGACTCCAT 61.462 66.667 0.00 0.00 46.09 3.41
5295 5404 4.988716 ACGGCTCGTGGGACTCCA 62.989 66.667 0.00 0.00 39.18 3.86
5296 5405 4.131088 GACGGCTCGTGGGACTCC 62.131 72.222 4.94 0.00 41.37 3.85
5297 5406 4.131088 GGACGGCTCGTGGGACTC 62.131 72.222 4.94 0.00 41.37 3.36
5301 5410 4.570663 GATCGGACGGCTCGTGGG 62.571 72.222 4.94 0.00 41.37 4.61
5302 5411 4.570663 GGATCGGACGGCTCGTGG 62.571 72.222 4.94 0.00 41.37 4.94
5303 5412 3.518998 AGGATCGGACGGCTCGTG 61.519 66.667 4.94 0.00 41.37 4.35
5304 5413 3.518998 CAGGATCGGACGGCTCGT 61.519 66.667 0.00 0.00 45.10 4.18
5305 5414 3.518998 ACAGGATCGGACGGCTCG 61.519 66.667 0.00 0.00 0.00 5.03
5306 5415 2.105128 CACAGGATCGGACGGCTC 59.895 66.667 0.00 0.00 0.00 4.70
5307 5416 2.362503 TCACAGGATCGGACGGCT 60.363 61.111 0.00 0.00 0.00 5.52
5308 5417 2.202756 GTCACAGGATCGGACGGC 60.203 66.667 0.00 0.00 0.00 5.68
5309 5418 1.139734 CTGTCACAGGATCGGACGG 59.860 63.158 0.00 0.00 34.32 4.79
5310 5419 0.179161 GTCTGTCACAGGATCGGACG 60.179 60.000 4.57 0.00 34.32 4.79
5311 5420 0.179161 CGTCTGTCACAGGATCGGAC 60.179 60.000 4.57 0.00 31.51 4.79
5312 5421 1.313091 CCGTCTGTCACAGGATCGGA 61.313 60.000 23.01 0.00 40.09 4.55
5313 5422 1.139734 CCGTCTGTCACAGGATCGG 59.860 63.158 17.54 17.54 35.78 4.18
5314 5423 1.517257 GCCGTCTGTCACAGGATCG 60.517 63.158 4.57 7.85 31.51 3.69
5315 5424 1.517257 CGCCGTCTGTCACAGGATC 60.517 63.158 4.57 0.00 31.51 3.36
5316 5425 1.938657 CTCGCCGTCTGTCACAGGAT 61.939 60.000 4.57 0.00 31.51 3.24
5317 5426 2.596338 TCGCCGTCTGTCACAGGA 60.596 61.111 4.57 0.00 31.51 3.86
5318 5427 2.126307 CTCGCCGTCTGTCACAGG 60.126 66.667 4.57 0.00 31.51 4.00
5319 5428 1.442857 GACTCGCCGTCTGTCACAG 60.443 63.158 0.00 0.00 39.61 3.66
5320 5429 2.643272 GACTCGCCGTCTGTCACA 59.357 61.111 3.69 0.00 39.61 3.58
5321 5430 2.126424 GGACTCGCCGTCTGTCAC 60.126 66.667 9.01 0.00 42.44 3.67
5322 5431 3.371063 GGGACTCGCCGTCTGTCA 61.371 66.667 9.01 0.00 42.44 3.58
5323 5432 3.371063 TGGGACTCGCCGTCTGTC 61.371 66.667 4.98 0.00 42.44 3.51
5324 5433 3.681835 GTGGGACTCGCCGTCTGT 61.682 66.667 4.98 0.00 42.44 3.41
5325 5434 4.778415 CGTGGGACTCGCCGTCTG 62.778 72.222 4.98 0.00 42.44 3.51
5327 5436 4.477975 CTCGTGGGACTCGCCGTC 62.478 72.222 0.00 0.00 45.51 4.79
5341 5450 3.518998 ACAGGATCGGACGGCTCG 61.519 66.667 0.00 0.00 0.00 5.03
5410 5519 2.084546 GTCAGGCCGAAACTGCTTTAT 58.915 47.619 0.00 0.00 35.94 1.40
5412 5521 0.465460 TGTCAGGCCGAAACTGCTTT 60.465 50.000 0.00 0.00 35.94 3.51
5447 5556 5.470047 ACTATTTGAGGACAAGTTCGTCT 57.530 39.130 5.73 0.00 39.48 4.18
5465 5574 2.548067 GGTTCGATCGCCCATCAACTAT 60.548 50.000 11.09 0.00 0.00 2.12
5466 5575 1.202486 GGTTCGATCGCCCATCAACTA 60.202 52.381 11.09 0.00 0.00 2.24
5476 5585 1.735376 TAGGAGGCTGGTTCGATCGC 61.735 60.000 11.09 0.00 0.00 4.58
5491 5600 4.261994 GCCTTGTTCAAGCAAACAATAGGA 60.262 41.667 15.84 0.00 45.37 2.94
5493 5602 3.989817 GGCCTTGTTCAAGCAAACAATAG 59.010 43.478 11.06 8.11 45.37 1.73
5496 5605 1.470632 CGGCCTTGTTCAAGCAAACAA 60.471 47.619 0.00 10.42 44.59 2.83


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

AutoCloner maintained by Alex Coulton.