Multiple sequence alignment - TraesCS4D01G099800

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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 TraesCS4D01G099800 chr4D 100.000 4937 0 0 1 4937 77024533 77029469 0.000000e+00 9118
1 TraesCS4D01G099800 chr4D 95.453 2793 99 7 1012 3782 76611898 76609112 0.000000e+00 4429
2 TraesCS4D01G099800 chr4D 93.673 980 51 10 1 974 463349680 463348706 0.000000e+00 1456
3 TraesCS4D01G099800 chr4D 82.517 429 55 15 4491 4914 414060202 414060615 4.700000e-95 359
4 TraesCS4D01G099800 chr4D 94.624 93 5 0 3780 3872 76605416 76605324 1.430000e-30 145
5 TraesCS4D01G099800 chr4B 94.416 2883 116 12 1033 3872 109049751 109046871 0.000000e+00 4390
6 TraesCS4D01G099800 chr4B 88.636 132 14 1 3865 3995 39932486 39932355 5.120000e-35 159
7 TraesCS4D01G099800 chr4A 95.257 2319 91 9 1008 3310 511079002 511081317 0.000000e+00 3655
8 TraesCS4D01G099800 chr4A 98.077 208 4 0 3306 3513 511084570 511084777 3.630000e-96 363
9 TraesCS4D01G099800 chr4A 95.495 222 10 0 3507 3728 511131309 511131530 6.080000e-94 355
10 TraesCS4D01G099800 chr4A 91.827 208 11 3 1008 1209 511076685 511076892 8.090000e-73 285
11 TraesCS4D01G099800 chr5D 97.143 980 20 4 1 978 116750001 116749028 0.000000e+00 1648
12 TraesCS4D01G099800 chr6D 94.888 978 44 5 1 975 58443241 58444215 0.000000e+00 1524
13 TraesCS4D01G099800 chr2D 94.324 969 47 7 10 975 398509812 398508849 0.000000e+00 1478
14 TraesCS4D01G099800 chr2D 93.215 339 15 7 4158 4489 532880220 532880557 4.440000e-135 492
15 TraesCS4D01G099800 chr2D 93.215 339 15 7 4158 4489 532922379 532922716 4.440000e-135 492
16 TraesCS4D01G099800 chr2D 85.919 419 47 10 4522 4935 470195409 470194998 2.110000e-118 436
17 TraesCS4D01G099800 chr3D 93.795 983 48 11 1 975 608916448 608917425 0.000000e+00 1465
18 TraesCS4D01G099800 chr3D 93.865 978 48 9 1 976 8823105 8822138 0.000000e+00 1463
19 TraesCS4D01G099800 chr3D 88.571 455 25 11 4490 4937 21600609 21601043 1.220000e-145 527
20 TraesCS4D01G099800 chr3D 88.261 460 15 15 4490 4922 330912040 330911593 9.480000e-142 514
21 TraesCS4D01G099800 chr1D 93.763 978 50 9 1 976 50712841 50713809 0.000000e+00 1458
22 TraesCS4D01G099800 chr1D 88.106 454 33 13 4489 4937 202314415 202314852 2.040000e-143 520
23 TraesCS4D01G099800 chr7B 93.503 985 52 9 1 980 379730399 379729422 0.000000e+00 1454
24 TraesCS4D01G099800 chr7D 93.565 979 53 8 1 976 536432591 536431620 0.000000e+00 1450
25 TraesCS4D01G099800 chr7D 93.987 632 18 7 3876 4489 189345288 189344659 0.000000e+00 939
26 TraesCS4D01G099800 chr7D 87.002 477 23 9 4489 4937 571725667 571725202 7.380000e-138 501
27 TraesCS4D01G099800 chr7D 90.551 127 12 0 3877 4003 19715988 19716114 8.500000e-38 169
28 TraesCS4D01G099800 chrUn 96.552 290 9 1 3867 4156 369131119 369130831 3.460000e-131 479
29 TraesCS4D01G099800 chrUn 96.552 290 9 1 3867 4156 466955492 466955780 3.460000e-131 479
30 TraesCS4D01G099800 chrUn 85.961 406 41 12 4543 4937 97636260 97635860 2.130000e-113 420
31 TraesCS4D01G099800 chr7A 83.259 448 60 10 4484 4922 555646743 555647184 9.960000e-107 398
32 TraesCS4D01G099800 chr7A 87.302 126 14 2 3877 4001 6087070 6087194 5.150000e-30 143
33 TraesCS4D01G099800 chr2B 82.099 486 41 15 4490 4937 95340907 95340430 1.680000e-99 374
34 TraesCS4D01G099800 chr2B 82.127 442 58 14 4492 4923 652821259 652820829 4.700000e-95 359
35 TraesCS4D01G099800 chr3A 77.778 540 67 22 3872 4392 7120593 7121098 2.910000e-72 283
36 TraesCS4D01G099800 chr3A 89.216 204 16 5 4737 4935 171781844 171781642 2.950000e-62 250
37 TraesCS4D01G099800 chr5A 92.437 119 9 0 3877 3995 461665062 461665180 2.360000e-38 171
38 TraesCS4D01G099800 chr5A 90.826 109 8 2 3875 3982 247466637 247466744 1.430000e-30 145


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 TraesCS4D01G099800 chr4D 77024533 77029469 4936 False 9118.000000 9118 100.000000 1 4937 1 chr4D.!!$F1 4936
1 TraesCS4D01G099800 chr4D 76605324 76611898 6574 True 2287.000000 4429 95.038500 1012 3872 2 chr4D.!!$R2 2860
2 TraesCS4D01G099800 chr4D 463348706 463349680 974 True 1456.000000 1456 93.673000 1 974 1 chr4D.!!$R1 973
3 TraesCS4D01G099800 chr4B 109046871 109049751 2880 True 4390.000000 4390 94.416000 1033 3872 1 chr4B.!!$R2 2839
4 TraesCS4D01G099800 chr4A 511076685 511084777 8092 False 1434.333333 3655 95.053667 1008 3513 3 chr4A.!!$F2 2505
5 TraesCS4D01G099800 chr5D 116749028 116750001 973 True 1648.000000 1648 97.143000 1 978 1 chr5D.!!$R1 977
6 TraesCS4D01G099800 chr6D 58443241 58444215 974 False 1524.000000 1524 94.888000 1 975 1 chr6D.!!$F1 974
7 TraesCS4D01G099800 chr2D 398508849 398509812 963 True 1478.000000 1478 94.324000 10 975 1 chr2D.!!$R1 965
8 TraesCS4D01G099800 chr3D 608916448 608917425 977 False 1465.000000 1465 93.795000 1 975 1 chr3D.!!$F2 974
9 TraesCS4D01G099800 chr3D 8822138 8823105 967 True 1463.000000 1463 93.865000 1 976 1 chr3D.!!$R1 975
10 TraesCS4D01G099800 chr1D 50712841 50713809 968 False 1458.000000 1458 93.763000 1 976 1 chr1D.!!$F1 975
11 TraesCS4D01G099800 chr7B 379729422 379730399 977 True 1454.000000 1454 93.503000 1 980 1 chr7B.!!$R1 979
12 TraesCS4D01G099800 chr7D 536431620 536432591 971 True 1450.000000 1450 93.565000 1 976 1 chr7D.!!$R2 975
13 TraesCS4D01G099800 chr7D 189344659 189345288 629 True 939.000000 939 93.987000 3876 4489 1 chr7D.!!$R1 613
14 TraesCS4D01G099800 chr3A 7120593 7121098 505 False 283.000000 283 77.778000 3872 4392 1 chr3A.!!$F1 520

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
848 867 0.546747 AACCGATGAAGTGGGGGAGA 60.547 55.000 0.0 0.0 0.00 3.71 F
1439 3804 1.519455 CTAAGGAGCAAGCGACCGG 60.519 63.158 0.0 0.0 0.00 5.28 F
2454 4819 0.746659 AGTGGTTTGCTTGCACCTTC 59.253 50.000 0.0 0.0 33.76 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1704 4069 1.375140 CTCACACGCATGCAGAGGT 60.375 57.895 19.57 4.10 31.08 3.85 R
2924 5334 1.000283 AGCTTCTCGAGAACAGGTGTG 60.000 52.381 23.74 13.12 0.00 3.82 R
4002 13373 0.039437 GAGCGAGACAGGTGAAACGA 60.039 55.000 0.00 0.00 38.12 3.85 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
20 24 2.283834 TCCCTCTTCCTCACTCTCTCT 58.716 52.381 0.00 0.00 0.00 3.10
23 27 2.654863 CTCTTCCTCACTCTCTCTCCC 58.345 57.143 0.00 0.00 0.00 4.30
27 31 0.926293 CCTCACTCTCTCTCCCCTCT 59.074 60.000 0.00 0.00 0.00 3.69
29 35 0.923358 TCACTCTCTCTCCCCTCTCC 59.077 60.000 0.00 0.00 0.00 3.71
493 510 2.328473 GGCCTCAAGAATCAAAAACGC 58.672 47.619 0.00 0.00 0.00 4.84
848 867 0.546747 AACCGATGAAGTGGGGGAGA 60.547 55.000 0.00 0.00 0.00 3.71
852 871 1.813102 GATGAAGTGGGGGAGAGGAT 58.187 55.000 0.00 0.00 0.00 3.24
1002 1027 8.867112 TTTATTACTCAGTGTTTAGATAGGCG 57.133 34.615 0.00 0.00 0.00 5.52
1003 1028 3.802948 ACTCAGTGTTTAGATAGGCGG 57.197 47.619 0.00 0.00 0.00 6.13
1004 1029 3.097614 ACTCAGTGTTTAGATAGGCGGT 58.902 45.455 0.00 0.00 0.00 5.68
1005 1030 3.514309 ACTCAGTGTTTAGATAGGCGGTT 59.486 43.478 0.00 0.00 0.00 4.44
1006 1031 4.020485 ACTCAGTGTTTAGATAGGCGGTTT 60.020 41.667 0.00 0.00 0.00 3.27
1126 1160 4.280677 CCCAGAAGCATCTAGACCTAAGAG 59.719 50.000 0.00 0.00 33.50 2.85
1437 3802 1.815840 GCCTAAGGAGCAAGCGACC 60.816 63.158 0.00 3.82 0.00 4.79
1439 3804 1.519455 CTAAGGAGCAAGCGACCGG 60.519 63.158 0.00 0.00 0.00 5.28
1884 4249 1.170290 TCGTCTCTCCGCACTTGACA 61.170 55.000 0.00 0.00 0.00 3.58
1893 4258 1.021202 CGCACTTGACAAGGTTGGAA 58.979 50.000 19.16 0.00 0.00 3.53
2280 4645 5.769662 AGATTGTGTGCTTCTCAATGGTTTA 59.230 36.000 11.96 0.00 39.40 2.01
2453 4818 1.134729 CAAGTGGTTTGCTTGCACCTT 60.135 47.619 0.00 0.00 37.18 3.50
2454 4819 0.746659 AGTGGTTTGCTTGCACCTTC 59.253 50.000 0.00 0.00 33.76 3.46
2495 4860 6.918892 TTTCCCGTGACTGTATTCATATTG 57.081 37.500 0.00 0.00 0.00 1.90
2681 5060 4.721776 TCTGATATGGGTTACAAGCCTCTT 59.278 41.667 11.23 0.23 46.54 2.85
2682 5061 5.191722 TCTGATATGGGTTACAAGCCTCTTT 59.808 40.000 11.23 0.00 46.54 2.52
2763 5169 5.014202 TCAGTAGCATCACACCTTGTACTA 58.986 41.667 0.00 0.00 0.00 1.82
2767 5173 5.165961 AGCATCACACCTTGTACTACAAT 57.834 39.130 2.02 0.00 37.48 2.71
2771 5177 7.334421 AGCATCACACCTTGTACTACAATAAAG 59.666 37.037 2.02 0.00 37.48 1.85
2924 5334 2.358898 ACTCATGTGCTTTGTCCAACAC 59.641 45.455 0.00 0.00 0.00 3.32
2976 5386 3.303395 GCTTTGTCAGGTATATGCTTCGC 60.303 47.826 0.00 0.00 0.00 4.70
2995 5405 5.282055 TCGCAAATCTGATAGATGTTCCT 57.718 39.130 0.00 0.00 34.65 3.36
2996 5406 5.052481 TCGCAAATCTGATAGATGTTCCTG 58.948 41.667 0.00 0.00 34.65 3.86
3096 5507 1.473434 GGAAGCTACAATCTGACGGGG 60.473 57.143 0.00 0.00 0.00 5.73
3266 5680 3.057033 GGTTAGTAGGTTCTTGACGCTCA 60.057 47.826 0.00 0.00 0.00 4.26
3775 9448 6.237901 TGCATGTCAGTTTATCTTGTTAGGT 58.762 36.000 0.00 0.00 0.00 3.08
3792 13163 5.993441 TGTTAGGTACTTAACTGTTGGAAGC 59.007 40.000 23.51 0.04 41.75 3.86
3845 13216 5.323382 TGGTGAATGGGATTATGCTATGT 57.677 39.130 0.00 0.00 0.00 2.29
3849 13220 6.040842 GGTGAATGGGATTATGCTATGTTTGT 59.959 38.462 0.00 0.00 0.00 2.83
3976 13347 0.981183 TCCCTACAATGTGAGCCGTT 59.019 50.000 0.00 0.00 0.00 4.44
4002 13373 2.722094 TGGCATCTAACGGCTGAAAAT 58.278 42.857 0.00 0.00 0.00 1.82
4154 13525 7.828508 AATCAACCATAATGACACATATGCT 57.171 32.000 1.58 0.00 0.00 3.79
4174 13545 3.452474 CTTCGCTACCTCTGGATCTTTG 58.548 50.000 0.00 0.00 0.00 2.77
4215 13587 0.251165 TGCCAAGCTTTACTCCCCAC 60.251 55.000 0.00 0.00 0.00 4.61
4293 13673 2.428530 CACATCTCCCGTCTTCTCATCA 59.571 50.000 0.00 0.00 0.00 3.07
4298 13678 0.467384 CCCGTCTTCTCATCAGCCAT 59.533 55.000 0.00 0.00 0.00 4.40
4423 13830 5.798132 TGTGAAGAACATGTGCTAAGATCT 58.202 37.500 6.81 0.00 32.36 2.75
4424 13831 6.935167 TGTGAAGAACATGTGCTAAGATCTA 58.065 36.000 6.81 0.00 32.36 1.98
4425 13832 6.813649 TGTGAAGAACATGTGCTAAGATCTAC 59.186 38.462 6.81 3.42 32.36 2.59
4426 13833 6.813649 GTGAAGAACATGTGCTAAGATCTACA 59.186 38.462 6.81 0.00 0.00 2.74
4427 13834 7.009999 GTGAAGAACATGTGCTAAGATCTACAG 59.990 40.741 6.81 0.00 0.00 2.74
4489 13896 0.889306 AGAAACGGGAGACTTCGAGG 59.111 55.000 6.23 0.00 32.89 4.63
4490 13897 0.108756 GAAACGGGAGACTTCGAGGG 60.109 60.000 0.00 0.00 0.00 4.30
4491 13898 1.542187 AAACGGGAGACTTCGAGGGG 61.542 60.000 0.00 0.00 0.00 4.79
4492 13899 2.044252 CGGGAGACTTCGAGGGGA 60.044 66.667 0.00 0.00 0.00 4.81
4493 13900 2.122167 CGGGAGACTTCGAGGGGAG 61.122 68.421 0.00 0.00 0.00 4.30
4494 13901 2.428085 GGGAGACTTCGAGGGGAGC 61.428 68.421 0.00 0.00 0.00 4.70
4495 13902 1.682684 GGAGACTTCGAGGGGAGCA 60.683 63.158 0.00 0.00 0.00 4.26
4496 13903 1.258445 GGAGACTTCGAGGGGAGCAA 61.258 60.000 0.00 0.00 0.00 3.91
4497 13904 0.108567 GAGACTTCGAGGGGAGCAAC 60.109 60.000 0.00 0.00 0.00 4.17
4498 13905 0.543174 AGACTTCGAGGGGAGCAACT 60.543 55.000 0.00 0.00 0.00 3.16
4499 13906 1.183549 GACTTCGAGGGGAGCAACTA 58.816 55.000 0.00 0.00 0.00 2.24
4500 13907 1.135333 GACTTCGAGGGGAGCAACTAG 59.865 57.143 0.00 0.00 0.00 2.57
4501 13908 1.187087 CTTCGAGGGGAGCAACTAGT 58.813 55.000 0.00 0.00 0.00 2.57
4502 13909 1.550976 CTTCGAGGGGAGCAACTAGTT 59.449 52.381 1.12 1.12 0.00 2.24
4503 13910 2.519771 TCGAGGGGAGCAACTAGTTA 57.480 50.000 8.04 0.00 0.00 2.24
4504 13911 2.811410 TCGAGGGGAGCAACTAGTTAA 58.189 47.619 8.04 0.00 0.00 2.01
4505 13912 2.494870 TCGAGGGGAGCAACTAGTTAAC 59.505 50.000 8.04 3.72 0.00 2.01
4506 13913 2.734492 CGAGGGGAGCAACTAGTTAACG 60.734 54.545 8.04 0.00 0.00 3.18
4507 13914 2.494870 GAGGGGAGCAACTAGTTAACGA 59.505 50.000 8.04 0.00 0.00 3.85
4508 13915 2.496470 AGGGGAGCAACTAGTTAACGAG 59.504 50.000 13.50 13.50 0.00 4.18
4509 13916 2.269172 GGGAGCAACTAGTTAACGAGC 58.731 52.381 14.82 7.28 0.00 5.03
4510 13917 1.918609 GGAGCAACTAGTTAACGAGCG 59.081 52.381 14.82 8.20 0.00 5.03
4511 13918 1.320852 GAGCAACTAGTTAACGAGCGC 59.679 52.381 14.82 16.38 0.00 5.92
4512 13919 1.067776 AGCAACTAGTTAACGAGCGCT 60.068 47.619 20.45 20.45 0.00 5.92
4513 13920 1.320852 GCAACTAGTTAACGAGCGCTC 59.679 52.381 27.64 27.64 0.00 5.03
4514 13921 1.918609 CAACTAGTTAACGAGCGCTCC 59.081 52.381 30.66 16.60 0.00 4.70
4515 13922 1.461559 ACTAGTTAACGAGCGCTCCT 58.538 50.000 30.66 22.52 0.00 3.69
4516 13923 1.817447 ACTAGTTAACGAGCGCTCCTT 59.183 47.619 30.66 26.03 0.00 3.36
4517 13924 2.159407 ACTAGTTAACGAGCGCTCCTTC 60.159 50.000 30.66 14.44 0.00 3.46
4518 13925 0.456312 AGTTAACGAGCGCTCCTTCG 60.456 55.000 30.66 22.24 0.00 3.79
4519 13926 1.153901 TTAACGAGCGCTCCTTCGG 60.154 57.895 30.66 18.71 0.00 4.30
4520 13927 2.552585 TTAACGAGCGCTCCTTCGGG 62.553 60.000 30.66 17.99 0.00 5.14
4530 13937 4.082523 CCTTCGGGAGCCTCGCAA 62.083 66.667 9.61 2.18 37.25 4.85
4531 13938 2.815647 CTTCGGGAGCCTCGCAAC 60.816 66.667 9.61 0.00 0.00 4.17
4532 13939 4.735132 TTCGGGAGCCTCGCAACG 62.735 66.667 9.61 0.36 0.00 4.10
4534 13941 4.514577 CGGGAGCCTCGCAACGAT 62.515 66.667 9.61 0.00 34.61 3.73
4535 13942 2.586357 GGGAGCCTCGCAACGATC 60.586 66.667 3.57 0.00 34.61 3.69
4536 13943 2.184322 GGAGCCTCGCAACGATCA 59.816 61.111 0.00 0.00 34.61 2.92
4537 13944 1.880340 GGAGCCTCGCAACGATCAG 60.880 63.158 0.00 0.00 34.61 2.90
4538 13945 2.510238 AGCCTCGCAACGATCAGC 60.510 61.111 0.00 0.00 34.61 4.26
4544 13951 3.121030 GCAACGATCAGCGCCACT 61.121 61.111 2.29 0.00 46.04 4.00
4545 13952 2.680913 GCAACGATCAGCGCCACTT 61.681 57.895 2.29 0.00 46.04 3.16
4546 13953 1.133253 CAACGATCAGCGCCACTTG 59.867 57.895 2.29 0.00 46.04 3.16
4547 13954 2.034879 AACGATCAGCGCCACTTGG 61.035 57.895 2.29 0.00 46.04 3.61
4558 13965 3.485431 CACTTGGCGCGCTCTCAG 61.485 66.667 32.29 21.96 0.00 3.35
4564 13971 3.934684 GCGCGCTCTCAGCCATTC 61.935 66.667 26.67 0.00 38.18 2.67
4565 13972 3.624300 CGCGCTCTCAGCCATTCG 61.624 66.667 5.56 0.00 38.18 3.34
4566 13973 3.934684 GCGCTCTCAGCCATTCGC 61.935 66.667 0.00 0.00 38.18 4.70
4567 13974 3.267860 CGCTCTCAGCCATTCGCC 61.268 66.667 0.00 0.00 38.18 5.54
4568 13975 2.124983 GCTCTCAGCCATTCGCCA 60.125 61.111 0.00 0.00 38.78 5.69
4569 13976 2.467826 GCTCTCAGCCATTCGCCAC 61.468 63.158 0.00 0.00 38.78 5.01
4570 13977 2.125552 TCTCAGCCATTCGCCACG 60.126 61.111 0.00 0.00 38.78 4.94
4571 13978 2.434884 CTCAGCCATTCGCCACGT 60.435 61.111 0.00 0.00 38.78 4.49
4572 13979 2.741985 TCAGCCATTCGCCACGTG 60.742 61.111 9.08 9.08 38.78 4.49
4573 13980 3.049674 CAGCCATTCGCCACGTGT 61.050 61.111 15.65 0.00 38.78 4.49
4574 13981 2.742372 AGCCATTCGCCACGTGTC 60.742 61.111 15.65 0.00 38.78 3.67
4575 13982 4.147322 GCCATTCGCCACGTGTCG 62.147 66.667 13.61 13.61 0.00 4.35
4576 13983 4.147322 CCATTCGCCACGTGTCGC 62.147 66.667 15.09 10.47 0.00 5.19
4584 13991 4.700365 CACGTGTCGCGCTCTGGA 62.700 66.667 7.58 0.00 46.11 3.86
4585 13992 3.749064 ACGTGTCGCGCTCTGGAT 61.749 61.111 5.56 0.00 46.11 3.41
4586 13993 3.250323 CGTGTCGCGCTCTGGATG 61.250 66.667 5.56 0.00 0.00 3.51
4587 13994 2.125912 GTGTCGCGCTCTGGATGT 60.126 61.111 5.56 0.00 0.00 3.06
4588 13995 1.738099 GTGTCGCGCTCTGGATGTT 60.738 57.895 5.56 0.00 0.00 2.71
4589 13996 1.446099 TGTCGCGCTCTGGATGTTC 60.446 57.895 5.56 0.00 0.00 3.18
4590 13997 2.167861 GTCGCGCTCTGGATGTTCC 61.168 63.158 5.56 0.00 36.96 3.62
4591 13998 2.892425 CGCGCTCTGGATGTTCCC 60.892 66.667 5.56 0.00 35.03 3.97
4592 13999 2.586792 GCGCTCTGGATGTTCCCT 59.413 61.111 0.00 0.00 35.03 4.20
4593 14000 1.522580 GCGCTCTGGATGTTCCCTC 60.523 63.158 0.00 0.00 35.03 4.30
4594 14001 1.144936 CGCTCTGGATGTTCCCTCC 59.855 63.158 0.00 0.00 35.03 4.30
4595 14002 1.617018 CGCTCTGGATGTTCCCTCCA 61.617 60.000 0.00 0.00 40.49 3.86
4602 14009 3.700538 TGGATGTTCCCTCCAGATTTTG 58.299 45.455 0.00 0.00 37.87 2.44
4603 14010 3.075882 TGGATGTTCCCTCCAGATTTTGT 59.924 43.478 0.00 0.00 37.87 2.83
4604 14011 4.089361 GGATGTTCCCTCCAGATTTTGTT 58.911 43.478 0.00 0.00 32.72 2.83
4605 14012 4.528206 GGATGTTCCCTCCAGATTTTGTTT 59.472 41.667 0.00 0.00 32.72 2.83
4606 14013 5.012046 GGATGTTCCCTCCAGATTTTGTTTT 59.988 40.000 0.00 0.00 32.72 2.43
4607 14014 5.948742 TGTTCCCTCCAGATTTTGTTTTT 57.051 34.783 0.00 0.00 0.00 1.94
4629 14036 2.235238 TTTCTATTTTTCCGCACGCG 57.765 45.000 3.53 3.53 39.44 6.01
4630 14037 1.149987 TTCTATTTTTCCGCACGCGT 58.850 45.000 5.58 5.58 37.81 6.01
4631 14038 1.149987 TCTATTTTTCCGCACGCGTT 58.850 45.000 10.22 0.00 37.81 4.84
4632 14039 1.532007 TCTATTTTTCCGCACGCGTTT 59.468 42.857 10.22 0.00 37.81 3.60
4633 14040 2.031857 TCTATTTTTCCGCACGCGTTTT 60.032 40.909 10.22 0.00 37.81 2.43
4634 14041 1.125270 ATTTTTCCGCACGCGTTTTC 58.875 45.000 10.22 0.04 37.81 2.29
4636 14043 2.968330 TTTTCCGCACGCGTTTTCGG 62.968 55.000 28.08 28.08 44.29 4.30
4639 14046 4.659874 CGCACGCGTTTTCGGCTT 62.660 61.111 10.22 0.00 44.29 4.35
4640 14047 2.353030 GCACGCGTTTTCGGCTTT 60.353 55.556 10.22 0.00 44.29 3.51
4641 14048 1.942223 GCACGCGTTTTCGGCTTTT 60.942 52.632 10.22 0.00 44.29 2.27
4642 14049 1.476235 GCACGCGTTTTCGGCTTTTT 61.476 50.000 10.22 0.00 44.29 1.94
4643 14050 1.744374 CACGCGTTTTCGGCTTTTTA 58.256 45.000 10.22 0.00 44.29 1.52
4644 14051 2.110226 CACGCGTTTTCGGCTTTTTAA 58.890 42.857 10.22 0.00 44.29 1.52
4645 14052 2.530700 CACGCGTTTTCGGCTTTTTAAA 59.469 40.909 10.22 0.00 44.29 1.52
4646 14053 2.531103 ACGCGTTTTCGGCTTTTTAAAC 59.469 40.909 5.58 0.00 44.29 2.01
4648 14055 3.739484 CGTTTTCGGCTTTTTAAACGG 57.261 42.857 10.17 0.00 45.26 4.44
4649 14056 3.107407 CGTTTTCGGCTTTTTAAACGGT 58.893 40.909 10.17 0.00 45.26 4.83
4650 14057 3.547068 CGTTTTCGGCTTTTTAAACGGTT 59.453 39.130 10.17 0.00 45.26 4.44
4651 14058 4.316584 CGTTTTCGGCTTTTTAAACGGTTC 60.317 41.667 10.17 0.00 45.26 3.62
4652 14059 4.635833 TTTCGGCTTTTTAAACGGTTCT 57.364 36.364 0.00 0.00 0.00 3.01
4653 14060 4.635833 TTCGGCTTTTTAAACGGTTCTT 57.364 36.364 0.00 0.00 0.00 2.52
4654 14061 4.635833 TCGGCTTTTTAAACGGTTCTTT 57.364 36.364 0.00 0.00 0.00 2.52
4655 14062 4.996344 TCGGCTTTTTAAACGGTTCTTTT 58.004 34.783 0.00 0.00 0.00 2.27
4656 14063 5.036090 TCGGCTTTTTAAACGGTTCTTTTC 58.964 37.500 0.00 0.00 0.00 2.29
4657 14064 4.085974 CGGCTTTTTAAACGGTTCTTTTCG 60.086 41.667 0.00 0.00 0.00 3.46
4658 14065 5.036090 GGCTTTTTAAACGGTTCTTTTCGA 58.964 37.500 0.00 0.00 0.00 3.71
4659 14066 5.052172 GGCTTTTTAAACGGTTCTTTTCGAC 60.052 40.000 0.00 0.00 0.00 4.20
4660 14067 5.330278 GCTTTTTAAACGGTTCTTTTCGACG 60.330 40.000 0.00 0.00 0.00 5.12
4661 14068 4.856115 TTTAAACGGTTCTTTTCGACGT 57.144 36.364 0.00 0.00 39.74 4.34
4664 14071 3.745332 AACGGTTCTTTTCGACGTTTT 57.255 38.095 2.34 0.00 44.21 2.43
4665 14072 3.042311 ACGGTTCTTTTCGACGTTTTG 57.958 42.857 0.00 0.00 33.54 2.44
4666 14073 2.223089 ACGGTTCTTTTCGACGTTTTGG 60.223 45.455 0.00 0.00 33.54 3.28
4667 14074 2.223089 CGGTTCTTTTCGACGTTTTGGT 60.223 45.455 0.00 0.00 0.00 3.67
4668 14075 3.728566 CGGTTCTTTTCGACGTTTTGGTT 60.729 43.478 0.00 0.00 0.00 3.67
4669 14076 4.168014 GGTTCTTTTCGACGTTTTGGTTT 58.832 39.130 0.00 0.00 0.00 3.27
4670 14077 4.622313 GGTTCTTTTCGACGTTTTGGTTTT 59.378 37.500 0.00 0.00 0.00 2.43
4671 14078 5.220080 GGTTCTTTTCGACGTTTTGGTTTTC 60.220 40.000 0.00 0.00 0.00 2.29
4672 14079 4.413969 TCTTTTCGACGTTTTGGTTTTCC 58.586 39.130 0.00 0.00 41.14 3.13
4673 14080 2.847959 TTCGACGTTTTGGTTTTCCC 57.152 45.000 0.00 0.00 39.73 3.97
4674 14081 1.023502 TCGACGTTTTGGTTTTCCCC 58.976 50.000 0.00 0.00 39.73 4.81
4675 14082 0.317186 CGACGTTTTGGTTTTCCCCG 60.317 55.000 0.00 0.00 39.73 5.73
4676 14083 0.031043 GACGTTTTGGTTTTCCCCGG 59.969 55.000 0.00 0.00 39.73 5.73
4677 14084 0.683828 ACGTTTTGGTTTTCCCCGGT 60.684 50.000 0.00 0.00 39.73 5.28
4678 14085 0.031043 CGTTTTGGTTTTCCCCGGTC 59.969 55.000 0.00 0.00 39.73 4.79
4679 14086 1.405872 GTTTTGGTTTTCCCCGGTCT 58.594 50.000 0.00 0.00 39.73 3.85
4680 14087 1.758280 GTTTTGGTTTTCCCCGGTCTT 59.242 47.619 0.00 0.00 39.73 3.01
4681 14088 1.694844 TTTGGTTTTCCCCGGTCTTC 58.305 50.000 0.00 0.00 39.73 2.87
4682 14089 0.178984 TTGGTTTTCCCCGGTCTTCC 60.179 55.000 0.00 0.00 39.73 3.46
4683 14090 1.063654 TGGTTTTCCCCGGTCTTCCT 61.064 55.000 0.00 0.00 39.73 3.36
4684 14091 0.111832 GGTTTTCCCCGGTCTTCCTT 59.888 55.000 0.00 0.00 0.00 3.36
4685 14092 1.352017 GGTTTTCCCCGGTCTTCCTTA 59.648 52.381 0.00 0.00 0.00 2.69
4686 14093 2.617276 GGTTTTCCCCGGTCTTCCTTAG 60.617 54.545 0.00 0.00 0.00 2.18
4687 14094 0.616891 TTTCCCCGGTCTTCCTTAGC 59.383 55.000 0.00 0.00 0.00 3.09
4688 14095 1.610554 TTCCCCGGTCTTCCTTAGCG 61.611 60.000 0.00 0.00 37.58 4.26
4689 14096 2.356780 CCCCGGTCTTCCTTAGCGT 61.357 63.158 0.00 0.00 36.16 5.07
4690 14097 1.595357 CCCGGTCTTCCTTAGCGTT 59.405 57.895 0.00 0.00 36.16 4.84
4691 14098 0.036671 CCCGGTCTTCCTTAGCGTTT 60.037 55.000 0.00 0.00 36.16 3.60
4692 14099 1.356938 CCGGTCTTCCTTAGCGTTTC 58.643 55.000 0.00 0.00 36.16 2.78
4693 14100 0.989890 CGGTCTTCCTTAGCGTTTCG 59.010 55.000 0.00 0.00 33.40 3.46
4694 14101 1.401931 CGGTCTTCCTTAGCGTTTCGA 60.402 52.381 0.00 0.00 33.40 3.71
4695 14102 1.991264 GGTCTTCCTTAGCGTTTCGAC 59.009 52.381 0.00 0.00 0.00 4.20
4696 14103 1.991264 GTCTTCCTTAGCGTTTCGACC 59.009 52.381 0.00 0.00 0.00 4.79
4697 14104 1.614903 TCTTCCTTAGCGTTTCGACCA 59.385 47.619 0.00 0.00 0.00 4.02
4698 14105 2.036217 TCTTCCTTAGCGTTTCGACCAA 59.964 45.455 0.00 0.00 0.00 3.67
4699 14106 2.529780 TCCTTAGCGTTTCGACCAAA 57.470 45.000 0.00 0.00 0.00 3.28
4700 14107 2.836262 TCCTTAGCGTTTCGACCAAAA 58.164 42.857 0.00 0.00 0.00 2.44
4701 14108 3.204526 TCCTTAGCGTTTCGACCAAAAA 58.795 40.909 0.00 0.00 0.00 1.94
4770 14177 7.626144 TTTTTCTTTCGTGAAAAGTCGTTTT 57.374 28.000 11.21 0.00 43.79 2.43
4771 14178 7.626144 TTTTCTTTCGTGAAAAGTCGTTTTT 57.374 28.000 8.69 1.13 44.07 1.94
4788 14195 2.513159 TTTTTCCGCGAGAGTCACG 58.487 52.632 8.23 5.53 0.00 4.35
4790 14197 3.909258 TTTCCGCGAGAGTCACGGC 62.909 63.158 8.23 3.61 46.49 5.68
4849 14256 3.854286 TTTTTCTTTCGCGAGAGTCAC 57.146 42.857 24.05 0.00 43.69 3.67
4850 14257 1.405461 TTTCTTTCGCGAGAGTCACG 58.595 50.000 24.05 5.53 43.69 4.35
4851 14258 0.386858 TTCTTTCGCGAGAGTCACGG 60.387 55.000 24.05 0.86 43.69 4.94
4852 14259 1.081376 CTTTCGCGAGAGTCACGGT 60.081 57.895 17.92 0.00 43.69 4.83
4853 14260 0.663568 CTTTCGCGAGAGTCACGGTT 60.664 55.000 17.92 0.00 43.69 4.44
4854 14261 0.249155 TTTCGCGAGAGTCACGGTTT 60.249 50.000 9.59 0.00 43.69 3.27
4855 14262 0.249155 TTCGCGAGAGTCACGGTTTT 60.249 50.000 9.59 0.00 43.69 2.43
4856 14263 0.592637 TCGCGAGAGTCACGGTTTTA 59.407 50.000 3.71 0.00 34.84 1.52
4857 14264 0.706729 CGCGAGAGTCACGGTTTTAC 59.293 55.000 11.95 0.00 0.00 2.01
4858 14265 1.665161 CGCGAGAGTCACGGTTTTACT 60.665 52.381 11.95 0.00 0.00 2.24
4859 14266 2.401351 GCGAGAGTCACGGTTTTACTT 58.599 47.619 11.95 0.00 0.00 2.24
4860 14267 2.407696 GCGAGAGTCACGGTTTTACTTC 59.592 50.000 11.95 0.00 0.00 3.01
4861 14268 2.985139 CGAGAGTCACGGTTTTACTTCC 59.015 50.000 1.62 0.00 0.00 3.46
4867 14274 3.111536 CGGTTTTACTTCCGCGAGA 57.888 52.632 8.23 0.00 40.28 4.04
4868 14275 0.989890 CGGTTTTACTTCCGCGAGAG 59.010 55.000 8.23 7.50 40.28 3.20
4869 14276 1.356938 GGTTTTACTTCCGCGAGAGG 58.643 55.000 8.23 6.41 0.00 3.69
4870 14277 0.720027 GTTTTACTTCCGCGAGAGGC 59.280 55.000 8.23 0.00 38.69 4.70
4871 14278 0.319083 TTTTACTTCCGCGAGAGGCA 59.681 50.000 8.23 0.00 43.84 4.75
4872 14279 0.389426 TTTACTTCCGCGAGAGGCAC 60.389 55.000 8.23 0.00 43.84 5.01
4873 14280 2.537792 TTACTTCCGCGAGAGGCACG 62.538 60.000 8.23 0.00 43.84 5.34
4887 14294 4.588084 CACGGTTGTGCTTTCGTG 57.412 55.556 0.00 0.00 44.98 4.35
4888 14295 4.524869 ACGGTTGTGCTTTCGTGA 57.475 50.000 0.00 0.00 34.40 4.35
4889 14296 2.307363 ACGGTTGTGCTTTCGTGAG 58.693 52.632 0.00 0.00 34.40 3.51
4890 14297 0.179094 ACGGTTGTGCTTTCGTGAGA 60.179 50.000 0.00 0.00 34.40 3.27
4891 14298 0.508641 CGGTTGTGCTTTCGTGAGAG 59.491 55.000 0.00 0.00 43.69 3.20
4892 14299 1.583054 GGTTGTGCTTTCGTGAGAGT 58.417 50.000 0.00 0.00 43.69 3.24
4893 14300 1.527311 GGTTGTGCTTTCGTGAGAGTC 59.473 52.381 0.00 0.00 43.69 3.36
4894 14301 2.201732 GTTGTGCTTTCGTGAGAGTCA 58.798 47.619 0.00 0.00 43.69 3.41
4895 14302 1.852942 TGTGCTTTCGTGAGAGTCAC 58.147 50.000 0.00 0.00 43.65 3.67
4902 14309 2.430921 GTGAGAGTCACGGCCGTG 60.431 66.667 45.04 45.04 46.64 4.94
4903 14310 4.357947 TGAGAGTCACGGCCGTGC 62.358 66.667 45.55 38.06 45.04 5.34
4916 14323 2.125512 CGTGCCTCTCGGAAAGGG 60.126 66.667 0.00 0.00 34.26 3.95
4917 14324 2.646175 CGTGCCTCTCGGAAAGGGA 61.646 63.158 0.00 0.00 34.26 4.20
4918 14325 1.677552 GTGCCTCTCGGAAAGGGAA 59.322 57.895 0.00 0.00 35.86 3.97
4919 14326 0.036306 GTGCCTCTCGGAAAGGGAAA 59.964 55.000 0.00 0.00 35.86 3.13
4920 14327 0.768622 TGCCTCTCGGAAAGGGAAAA 59.231 50.000 0.00 0.00 34.26 2.29
4921 14328 1.144093 TGCCTCTCGGAAAGGGAAAAA 59.856 47.619 0.00 0.00 34.26 1.94
4922 14329 1.540267 GCCTCTCGGAAAGGGAAAAAC 59.460 52.381 0.00 0.00 34.26 2.43
4923 14330 2.858745 CCTCTCGGAAAGGGAAAAACA 58.141 47.619 0.00 0.00 0.00 2.83
4924 14331 3.219281 CCTCTCGGAAAGGGAAAAACAA 58.781 45.455 0.00 0.00 0.00 2.83
4925 14332 3.634910 CCTCTCGGAAAGGGAAAAACAAA 59.365 43.478 0.00 0.00 0.00 2.83
4926 14333 4.098807 CCTCTCGGAAAGGGAAAAACAAAA 59.901 41.667 0.00 0.00 0.00 2.44
4927 14334 5.001237 TCTCGGAAAGGGAAAAACAAAAC 57.999 39.130 0.00 0.00 0.00 2.43
4928 14335 3.771798 TCGGAAAGGGAAAAACAAAACG 58.228 40.909 0.00 0.00 0.00 3.60
4929 14336 2.283086 CGGAAAGGGAAAAACAAAACGC 59.717 45.455 0.00 0.00 0.00 4.84
4930 14337 2.283086 GGAAAGGGAAAAACAAAACGCG 59.717 45.455 3.53 3.53 0.00 6.01
4931 14338 2.658373 AAGGGAAAAACAAAACGCGT 57.342 40.000 5.58 5.58 0.00 6.01
4932 14339 2.658373 AGGGAAAAACAAAACGCGTT 57.342 40.000 20.79 20.79 0.00 4.84
4933 14340 2.962125 AGGGAAAAACAAAACGCGTTT 58.038 38.095 30.36 30.36 38.19 3.60
4934 14341 3.327626 AGGGAAAAACAAAACGCGTTTT 58.672 36.364 36.93 36.93 45.90 2.43
4935 14342 3.368539 AGGGAAAAACAAAACGCGTTTTC 59.631 39.130 38.94 28.37 43.82 2.29
4936 14343 3.368539 GGGAAAAACAAAACGCGTTTTCT 59.631 39.130 38.94 28.85 43.82 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 24 0.047176 AGAGAGAGAGGGAGAGGGGA 59.953 60.000 0.00 0.00 0.00 4.81
23 27 3.053991 TGTGTTAGAGAGAGAGGGAGAGG 60.054 52.174 0.00 0.00 0.00 3.69
27 31 3.181433 TGTGTGTGTTAGAGAGAGAGGGA 60.181 47.826 0.00 0.00 0.00 4.20
29 35 3.570125 TGTGTGTGTGTTAGAGAGAGAGG 59.430 47.826 0.00 0.00 0.00 3.69
493 510 1.248785 TTCCCTCTCCGTTGTCGAGG 61.249 60.000 0.00 0.00 43.11 4.63
800 818 2.754472 CGTCATCCTCTCACACAACAA 58.246 47.619 0.00 0.00 0.00 2.83
801 819 1.605457 GCGTCATCCTCTCACACAACA 60.605 52.381 0.00 0.00 0.00 3.33
980 1005 5.363005 ACCGCCTATCTAAACACTGAGTAAT 59.637 40.000 0.00 0.00 0.00 1.89
981 1006 4.708421 ACCGCCTATCTAAACACTGAGTAA 59.292 41.667 0.00 0.00 0.00 2.24
982 1007 4.275810 ACCGCCTATCTAAACACTGAGTA 58.724 43.478 0.00 0.00 0.00 2.59
983 1008 3.097614 ACCGCCTATCTAAACACTGAGT 58.902 45.455 0.00 0.00 0.00 3.41
984 1009 3.802948 ACCGCCTATCTAAACACTGAG 57.197 47.619 0.00 0.00 0.00 3.35
985 1010 4.250464 CAAACCGCCTATCTAAACACTGA 58.750 43.478 0.00 0.00 0.00 3.41
986 1011 3.374058 CCAAACCGCCTATCTAAACACTG 59.626 47.826 0.00 0.00 0.00 3.66
987 1012 3.008704 ACCAAACCGCCTATCTAAACACT 59.991 43.478 0.00 0.00 0.00 3.55
988 1013 3.340928 ACCAAACCGCCTATCTAAACAC 58.659 45.455 0.00 0.00 0.00 3.32
989 1014 3.008157 TGACCAAACCGCCTATCTAAACA 59.992 43.478 0.00 0.00 0.00 2.83
990 1015 3.602483 TGACCAAACCGCCTATCTAAAC 58.398 45.455 0.00 0.00 0.00 2.01
991 1016 3.985019 TGACCAAACCGCCTATCTAAA 57.015 42.857 0.00 0.00 0.00 1.85
992 1017 3.985019 TTGACCAAACCGCCTATCTAA 57.015 42.857 0.00 0.00 0.00 2.10
993 1018 3.985019 TTTGACCAAACCGCCTATCTA 57.015 42.857 0.00 0.00 0.00 1.98
994 1019 2.817844 GTTTTGACCAAACCGCCTATCT 59.182 45.455 0.00 0.00 39.22 1.98
995 1020 2.554893 TGTTTTGACCAAACCGCCTATC 59.445 45.455 0.10 0.00 43.87 2.08
996 1021 2.556622 CTGTTTTGACCAAACCGCCTAT 59.443 45.455 0.10 0.00 43.87 2.57
997 1022 1.950909 CTGTTTTGACCAAACCGCCTA 59.049 47.619 0.10 0.00 43.87 3.93
998 1023 0.744281 CTGTTTTGACCAAACCGCCT 59.256 50.000 0.10 0.00 43.87 5.52
999 1024 0.458260 ACTGTTTTGACCAAACCGCC 59.542 50.000 0.10 0.00 43.87 6.13
1000 1025 1.135228 ACACTGTTTTGACCAAACCGC 60.135 47.619 0.10 0.00 43.87 5.68
1001 1026 2.920490 CAACACTGTTTTGACCAAACCG 59.080 45.455 0.42 0.00 43.87 4.44
1002 1027 3.056465 TCCAACACTGTTTTGACCAAACC 60.056 43.478 8.19 0.00 43.87 3.27
1003 1028 4.082463 TCTCCAACACTGTTTTGACCAAAC 60.082 41.667 8.19 0.00 44.64 2.93
1004 1029 4.082845 TCTCCAACACTGTTTTGACCAAA 58.917 39.130 8.19 0.00 0.00 3.28
1005 1030 3.691575 TCTCCAACACTGTTTTGACCAA 58.308 40.909 8.19 0.00 0.00 3.67
1006 1031 3.358111 TCTCCAACACTGTTTTGACCA 57.642 42.857 8.19 0.00 0.00 4.02
1126 1160 3.122971 GGACCGGGCTGCGTAAAC 61.123 66.667 7.57 0.00 0.00 2.01
1704 4069 1.375140 CTCACACGCATGCAGAGGT 60.375 57.895 19.57 4.10 31.08 3.85
1884 4249 1.822371 ACGTTGCAAAGTTCCAACCTT 59.178 42.857 12.50 0.00 38.41 3.50
1893 4258 6.366315 TCATTTAACACTACGTTGCAAAGT 57.634 33.333 21.49 21.49 38.63 2.66
2280 4645 3.265479 ACTCCAAGCTTTTAGCCTCTGAT 59.735 43.478 0.00 0.00 43.77 2.90
2453 4818 9.581289 ACGGGAAATTAAATCCATATAATGTGA 57.419 29.630 11.53 0.00 38.80 3.58
2454 4819 9.624697 CACGGGAAATTAAATCCATATAATGTG 57.375 33.333 11.53 5.63 38.80 3.21
2495 4860 8.717821 TGCAGTTTCAGAAGTAATACAATACAC 58.282 33.333 0.00 0.00 0.00 2.90
2617 4996 8.472007 TTTACCCCCTTGCATAACATATAAAG 57.528 34.615 0.00 0.00 0.00 1.85
2771 5177 7.283127 TGCAAATGGGTAAGAATATCTCAAGAC 59.717 37.037 0.00 0.00 0.00 3.01
2916 5326 1.940613 GAGAACAGGTGTGTGTTGGAC 59.059 52.381 0.00 0.00 40.83 4.02
2924 5334 1.000283 AGCTTCTCGAGAACAGGTGTG 60.000 52.381 23.74 13.12 0.00 3.82
3027 5438 4.339247 GCCTGTATGTGTATGGAGCAAAAT 59.661 41.667 0.00 0.00 0.00 1.82
3096 5507 3.668656 GCTTGTTAGATGAAAACGGTTGC 59.331 43.478 0.00 0.00 0.00 4.17
3106 5517 7.903145 TCAAGTACCTTAAGCTTGTTAGATGA 58.097 34.615 9.86 1.69 40.14 2.92
3266 5680 2.225117 GCAATTGGGGCCTAGATGGTAT 60.225 50.000 7.72 0.00 38.35 2.73
3775 9448 4.591498 TCTCCAGCTTCCAACAGTTAAGTA 59.409 41.667 0.00 0.00 0.00 2.24
3792 13163 3.044986 CAACATGCAACGTTTTCTCCAG 58.955 45.455 0.00 0.00 0.00 3.86
3906 13277 1.520787 CGGACGGCCTACATTCACC 60.521 63.158 5.33 0.00 0.00 4.02
3976 13347 2.423185 CAGCCGTTAGATGCCAAAATCA 59.577 45.455 0.00 0.00 0.00 2.57
4002 13373 0.039437 GAGCGAGACAGGTGAAACGA 60.039 55.000 0.00 0.00 38.12 3.85
4154 13525 2.168521 CCAAAGATCCAGAGGTAGCGAA 59.831 50.000 0.00 0.00 0.00 4.70
4174 13545 1.069227 CAAAGCAAGGTAACGCAGTCC 60.069 52.381 0.00 0.00 45.00 3.85
4267 13641 3.188786 GACGGGAGATGTGCACGC 61.189 66.667 13.13 6.90 0.00 5.34
4298 13678 1.144913 GGCTACCATGGATTTGGCCTA 59.855 52.381 21.47 0.00 40.68 3.93
4418 13825 9.999660 TCTCGTTCTGTATATTACTGTAGATCT 57.000 33.333 0.00 0.00 0.00 2.75
4420 13827 9.999660 TCTCTCGTTCTGTATATTACTGTAGAT 57.000 33.333 0.00 0.00 0.00 1.98
4421 13828 9.258826 GTCTCTCGTTCTGTATATTACTGTAGA 57.741 37.037 0.00 0.00 0.00 2.59
4422 13829 8.215792 CGTCTCTCGTTCTGTATATTACTGTAG 58.784 40.741 0.00 0.00 34.52 2.74
4423 13830 7.922811 TCGTCTCTCGTTCTGTATATTACTGTA 59.077 37.037 0.00 0.00 40.80 2.74
4424 13831 6.760298 TCGTCTCTCGTTCTGTATATTACTGT 59.240 38.462 0.00 0.00 40.80 3.55
4425 13832 7.169476 TCTCGTCTCTCGTTCTGTATATTACTG 59.831 40.741 0.00 0.00 40.80 2.74
4426 13833 7.208777 TCTCGTCTCTCGTTCTGTATATTACT 58.791 38.462 0.00 0.00 40.80 2.24
4427 13834 7.405469 TCTCGTCTCTCGTTCTGTATATTAC 57.595 40.000 0.00 0.00 40.80 1.89
4489 13896 2.269172 GCTCGTTAACTAGTTGCTCCC 58.731 52.381 18.56 0.76 0.00 4.30
4490 13897 1.918609 CGCTCGTTAACTAGTTGCTCC 59.081 52.381 18.56 2.45 0.00 4.70
4491 13898 1.320852 GCGCTCGTTAACTAGTTGCTC 59.679 52.381 18.56 3.86 0.00 4.26
4492 13899 1.067776 AGCGCTCGTTAACTAGTTGCT 60.068 47.619 18.56 17.34 0.00 3.91
4493 13900 1.320852 GAGCGCTCGTTAACTAGTTGC 59.679 52.381 23.61 11.18 0.00 4.17
4494 13901 1.918609 GGAGCGCTCGTTAACTAGTTG 59.081 52.381 29.81 1.62 0.00 3.16
4495 13902 1.817447 AGGAGCGCTCGTTAACTAGTT 59.183 47.619 29.81 13.68 0.00 2.24
4496 13903 1.461559 AGGAGCGCTCGTTAACTAGT 58.538 50.000 29.81 3.95 0.00 2.57
4497 13904 2.452105 GAAGGAGCGCTCGTTAACTAG 58.548 52.381 36.96 3.24 37.75 2.57
4498 13905 1.202110 CGAAGGAGCGCTCGTTAACTA 60.202 52.381 36.96 0.00 37.75 2.24
4499 13906 0.456312 CGAAGGAGCGCTCGTTAACT 60.456 55.000 36.96 23.16 37.75 2.24
4500 13907 1.989163 CGAAGGAGCGCTCGTTAAC 59.011 57.895 36.96 26.47 37.75 2.01
4501 13908 4.470876 CGAAGGAGCGCTCGTTAA 57.529 55.556 36.96 0.00 37.75 2.01
4514 13921 2.815647 GTTGCGAGGCTCCCGAAG 60.816 66.667 9.32 0.00 0.00 3.79
4515 13922 4.735132 CGTTGCGAGGCTCCCGAA 62.735 66.667 9.32 0.00 0.00 4.30
4517 13924 4.514577 ATCGTTGCGAGGCTCCCG 62.515 66.667 9.32 6.56 39.91 5.14
4518 13925 2.586357 GATCGTTGCGAGGCTCCC 60.586 66.667 9.32 0.00 39.91 4.30
4519 13926 1.880340 CTGATCGTTGCGAGGCTCC 60.880 63.158 9.32 2.37 39.91 4.70
4520 13927 2.520904 GCTGATCGTTGCGAGGCTC 61.521 63.158 3.87 3.87 39.91 4.70
4521 13928 2.510238 GCTGATCGTTGCGAGGCT 60.510 61.111 0.00 0.00 39.91 4.58
4527 13934 2.680913 AAGTGGCGCTGATCGTTGC 61.681 57.895 7.64 0.00 41.07 4.17
4528 13935 1.133253 CAAGTGGCGCTGATCGTTG 59.867 57.895 7.64 0.00 41.07 4.10
4529 13936 2.034879 CCAAGTGGCGCTGATCGTT 61.035 57.895 7.64 0.00 41.07 3.85
4530 13937 2.434884 CCAAGTGGCGCTGATCGT 60.435 61.111 7.64 0.00 41.07 3.73
4541 13948 3.485431 CTGAGAGCGCGCCAAGTG 61.485 66.667 30.33 12.20 0.00 3.16
4547 13954 3.934684 GAATGGCTGAGAGCGCGC 61.935 66.667 26.66 26.66 43.62 6.86
4548 13955 3.624300 CGAATGGCTGAGAGCGCG 61.624 66.667 0.00 0.00 43.62 6.86
4549 13956 3.934684 GCGAATGGCTGAGAGCGC 61.935 66.667 0.00 0.00 43.62 5.92
4550 13957 3.267860 GGCGAATGGCTGAGAGCG 61.268 66.667 0.00 0.00 43.62 5.03
4551 13958 2.124983 TGGCGAATGGCTGAGAGC 60.125 61.111 0.00 0.00 42.94 4.09
4552 13959 2.169789 CGTGGCGAATGGCTGAGAG 61.170 63.158 0.00 0.00 42.94 3.20
4553 13960 2.125552 CGTGGCGAATGGCTGAGA 60.126 61.111 0.00 0.00 42.94 3.27
4554 13961 2.434884 ACGTGGCGAATGGCTGAG 60.435 61.111 0.00 0.00 42.94 3.35
4555 13962 2.741985 CACGTGGCGAATGGCTGA 60.742 61.111 7.95 0.00 42.94 4.26
4556 13963 3.027170 GACACGTGGCGAATGGCTG 62.027 63.158 21.57 0.00 42.94 4.85
4557 13964 2.742372 GACACGTGGCGAATGGCT 60.742 61.111 21.57 0.00 42.94 4.75
4567 13974 3.971453 ATCCAGAGCGCGACACGTG 62.971 63.158 15.48 15.48 46.11 4.49
4568 13975 3.749064 ATCCAGAGCGCGACACGT 61.749 61.111 12.10 0.00 46.11 4.49
4570 13977 1.687494 GAACATCCAGAGCGCGACAC 61.687 60.000 12.10 0.00 0.00 3.67
4571 13978 1.446099 GAACATCCAGAGCGCGACA 60.446 57.895 12.10 0.00 0.00 4.35
4572 13979 2.167861 GGAACATCCAGAGCGCGAC 61.168 63.158 12.10 2.22 36.28 5.19
4573 13980 2.184322 GGAACATCCAGAGCGCGA 59.816 61.111 12.10 0.00 36.28 5.87
4574 13981 2.892425 GGGAACATCCAGAGCGCG 60.892 66.667 0.00 0.00 38.64 6.86
4575 13982 1.522580 GAGGGAACATCCAGAGCGC 60.523 63.158 0.00 0.00 38.64 5.92
4576 13983 1.144936 GGAGGGAACATCCAGAGCG 59.855 63.158 0.00 0.00 38.64 5.03
4577 13984 2.300996 TGGAGGGAACATCCAGAGC 58.699 57.895 0.00 0.00 41.96 4.09
4581 13988 3.075882 ACAAAATCTGGAGGGAACATCCA 59.924 43.478 2.47 2.47 44.63 3.41
4582 13989 3.701664 ACAAAATCTGGAGGGAACATCC 58.298 45.455 0.00 0.00 37.35 3.51
4583 13990 5.728637 AAACAAAATCTGGAGGGAACATC 57.271 39.130 0.00 0.00 0.00 3.06
4584 13991 6.499106 AAAAACAAAATCTGGAGGGAACAT 57.501 33.333 0.00 0.00 0.00 2.71
4585 13992 5.948742 AAAAACAAAATCTGGAGGGAACA 57.051 34.783 0.00 0.00 0.00 3.18
4608 14015 2.974536 CGCGTGCGGAAAAATAGAAAAA 59.025 40.909 6.30 0.00 35.56 1.94
4609 14016 2.031857 ACGCGTGCGGAAAAATAGAAAA 60.032 40.909 12.93 0.00 44.69 2.29
4610 14017 1.532007 ACGCGTGCGGAAAAATAGAAA 59.468 42.857 12.93 0.00 44.69 2.52
4611 14018 1.149987 ACGCGTGCGGAAAAATAGAA 58.850 45.000 12.93 0.00 44.69 2.10
4612 14019 1.149987 AACGCGTGCGGAAAAATAGA 58.850 45.000 14.98 0.00 44.69 1.98
4613 14020 1.958417 AAACGCGTGCGGAAAAATAG 58.042 45.000 14.98 0.00 44.69 1.73
4614 14021 2.308811 GAAAACGCGTGCGGAAAAATA 58.691 42.857 14.98 0.00 44.69 1.40
4615 14022 1.125270 GAAAACGCGTGCGGAAAAAT 58.875 45.000 14.98 0.00 44.69 1.82
4616 14023 1.194896 CGAAAACGCGTGCGGAAAAA 61.195 50.000 14.98 0.00 44.69 1.94
4617 14024 1.651730 CGAAAACGCGTGCGGAAAA 60.652 52.632 14.98 0.00 44.69 2.29
4618 14025 2.052941 CGAAAACGCGTGCGGAAA 60.053 55.556 14.98 0.00 44.69 3.13
4619 14026 4.003011 CCGAAAACGCGTGCGGAA 62.003 61.111 31.93 0.00 46.29 4.30
4622 14029 4.659874 AAGCCGAAAACGCGTGCG 62.660 61.111 14.98 17.33 46.03 5.34
4623 14030 1.476235 AAAAAGCCGAAAACGCGTGC 61.476 50.000 14.98 12.13 0.00 5.34
4624 14031 1.744374 TAAAAAGCCGAAAACGCGTG 58.256 45.000 14.98 0.00 0.00 5.34
4625 14032 2.471862 TTAAAAAGCCGAAAACGCGT 57.528 40.000 5.58 5.58 0.00 6.01
4626 14033 2.406245 CGTTTAAAAAGCCGAAAACGCG 60.406 45.455 3.53 3.53 44.94 6.01
4627 14034 3.130797 CGTTTAAAAAGCCGAAAACGC 57.869 42.857 6.30 0.00 44.94 4.84
4629 14036 4.799949 AGAACCGTTTAAAAAGCCGAAAAC 59.200 37.500 0.00 0.00 0.00 2.43
4630 14037 4.996344 AGAACCGTTTAAAAAGCCGAAAA 58.004 34.783 0.00 0.00 0.00 2.29
4631 14038 4.635833 AGAACCGTTTAAAAAGCCGAAA 57.364 36.364 0.00 0.00 0.00 3.46
4632 14039 4.635833 AAGAACCGTTTAAAAAGCCGAA 57.364 36.364 0.00 0.00 0.00 4.30
4633 14040 4.635833 AAAGAACCGTTTAAAAAGCCGA 57.364 36.364 0.00 0.00 0.00 5.54
4634 14041 4.085974 CGAAAAGAACCGTTTAAAAAGCCG 60.086 41.667 0.00 0.00 0.00 5.52
4635 14042 5.036090 TCGAAAAGAACCGTTTAAAAAGCC 58.964 37.500 0.00 0.00 0.00 4.35
4636 14043 5.330278 CGTCGAAAAGAACCGTTTAAAAAGC 60.330 40.000 0.00 0.00 0.00 3.51
4637 14044 5.734035 ACGTCGAAAAGAACCGTTTAAAAAG 59.266 36.000 0.00 0.00 28.88 2.27
4638 14045 5.626211 ACGTCGAAAAGAACCGTTTAAAAA 58.374 33.333 0.00 0.00 28.88 1.94
4639 14046 5.215239 ACGTCGAAAAGAACCGTTTAAAA 57.785 34.783 0.00 0.00 28.88 1.52
4640 14047 4.856115 ACGTCGAAAAGAACCGTTTAAA 57.144 36.364 0.00 0.00 28.88 1.52
4641 14048 4.856115 AACGTCGAAAAGAACCGTTTAA 57.144 36.364 0.00 0.00 38.03 1.52
4642 14049 4.856115 AAACGTCGAAAAGAACCGTTTA 57.144 36.364 15.85 0.00 44.33 2.01
4643 14050 3.745332 AAACGTCGAAAAGAACCGTTT 57.255 38.095 12.79 12.79 42.67 3.60
4644 14051 3.419004 CAAAACGTCGAAAAGAACCGTT 58.581 40.909 0.00 2.34 41.36 4.44
4645 14052 2.223089 CCAAAACGTCGAAAAGAACCGT 60.223 45.455 0.00 0.00 33.76 4.83
4646 14053 2.223089 ACCAAAACGTCGAAAAGAACCG 60.223 45.455 0.00 0.00 0.00 4.44
4647 14054 3.409851 ACCAAAACGTCGAAAAGAACC 57.590 42.857 0.00 0.00 0.00 3.62
4648 14055 5.220080 GGAAAACCAAAACGTCGAAAAGAAC 60.220 40.000 0.00 0.00 0.00 3.01
4649 14056 4.858140 GGAAAACCAAAACGTCGAAAAGAA 59.142 37.500 0.00 0.00 0.00 2.52
4650 14057 4.413969 GGAAAACCAAAACGTCGAAAAGA 58.586 39.130 0.00 0.00 0.00 2.52
4651 14058 3.548668 GGGAAAACCAAAACGTCGAAAAG 59.451 43.478 0.00 0.00 39.85 2.27
4652 14059 3.509740 GGGAAAACCAAAACGTCGAAAA 58.490 40.909 0.00 0.00 39.85 2.29
4653 14060 2.159268 GGGGAAAACCAAAACGTCGAAA 60.159 45.455 0.00 0.00 42.91 3.46
4654 14061 1.404748 GGGGAAAACCAAAACGTCGAA 59.595 47.619 0.00 0.00 42.91 3.71
4655 14062 1.023502 GGGGAAAACCAAAACGTCGA 58.976 50.000 0.00 0.00 42.91 4.20
4656 14063 0.317186 CGGGGAAAACCAAAACGTCG 60.317 55.000 0.00 0.00 42.91 5.12
4657 14064 0.031043 CCGGGGAAAACCAAAACGTC 59.969 55.000 0.00 0.00 42.91 4.34
4658 14065 0.683828 ACCGGGGAAAACCAAAACGT 60.684 50.000 6.32 0.00 42.91 3.99
4659 14066 0.031043 GACCGGGGAAAACCAAAACG 59.969 55.000 6.32 0.00 42.91 3.60
4660 14067 1.405872 AGACCGGGGAAAACCAAAAC 58.594 50.000 6.32 0.00 42.91 2.43
4661 14068 2.033372 GAAGACCGGGGAAAACCAAAA 58.967 47.619 6.32 0.00 42.91 2.44
4662 14069 1.694844 GAAGACCGGGGAAAACCAAA 58.305 50.000 6.32 0.00 42.91 3.28
4663 14070 0.178984 GGAAGACCGGGGAAAACCAA 60.179 55.000 6.32 0.00 42.91 3.67
4664 14071 1.063654 AGGAAGACCGGGGAAAACCA 61.064 55.000 6.32 0.00 42.91 3.67
4665 14072 0.111832 AAGGAAGACCGGGGAAAACC 59.888 55.000 6.32 1.16 41.83 3.27
4666 14073 2.708051 CTAAGGAAGACCGGGGAAAAC 58.292 52.381 6.32 0.00 41.83 2.43
4667 14074 1.003928 GCTAAGGAAGACCGGGGAAAA 59.996 52.381 6.32 0.00 41.83 2.29
4668 14075 0.616891 GCTAAGGAAGACCGGGGAAA 59.383 55.000 6.32 0.00 41.83 3.13
4669 14076 1.610554 CGCTAAGGAAGACCGGGGAA 61.611 60.000 6.32 0.00 41.83 3.97
4670 14077 2.056223 CGCTAAGGAAGACCGGGGA 61.056 63.158 6.32 0.00 41.83 4.81
4671 14078 1.896122 AACGCTAAGGAAGACCGGGG 61.896 60.000 6.32 0.00 41.83 5.73
4672 14079 0.036671 AAACGCTAAGGAAGACCGGG 60.037 55.000 6.32 0.00 41.83 5.73
4673 14080 1.356938 GAAACGCTAAGGAAGACCGG 58.643 55.000 0.00 0.00 41.83 5.28
4674 14081 0.989890 CGAAACGCTAAGGAAGACCG 59.010 55.000 0.00 0.00 41.83 4.79
4675 14082 1.991264 GTCGAAACGCTAAGGAAGACC 59.009 52.381 0.00 0.00 0.00 3.85
4676 14083 1.991264 GGTCGAAACGCTAAGGAAGAC 59.009 52.381 0.00 0.00 0.00 3.01
4677 14084 1.614903 TGGTCGAAACGCTAAGGAAGA 59.385 47.619 0.00 0.00 0.00 2.87
4678 14085 2.074547 TGGTCGAAACGCTAAGGAAG 57.925 50.000 0.00 0.00 0.00 3.46
4679 14086 2.529780 TTGGTCGAAACGCTAAGGAA 57.470 45.000 0.00 0.00 0.00 3.36
4680 14087 2.529780 TTTGGTCGAAACGCTAAGGA 57.470 45.000 0.00 0.00 0.00 3.36
4681 14088 3.612472 TTTTTGGTCGAAACGCTAAGG 57.388 42.857 0.00 0.00 0.00 2.69
4746 14153 7.626144 AAAACGACTTTTCACGAAAGAAAAA 57.374 28.000 13.15 2.57 46.24 1.94
4747 14154 7.626144 AAAAACGACTTTTCACGAAAGAAAA 57.374 28.000 5.60 12.12 46.24 2.29
4770 14177 2.513159 CGTGACTCTCGCGGAAAAA 58.487 52.632 6.13 0.00 45.61 1.94
4771 14178 4.238385 CGTGACTCTCGCGGAAAA 57.762 55.556 6.13 0.00 45.61 2.29
4829 14236 3.854286 GTGACTCTCGCGAAAGAAAAA 57.146 42.857 17.91 0.00 0.00 1.94
4839 14246 2.061740 AGTAAAACCGTGACTCTCGC 57.938 50.000 0.00 0.00 0.00 5.03
4840 14247 2.985139 GGAAGTAAAACCGTGACTCTCG 59.015 50.000 0.00 0.00 0.00 4.04
4841 14248 2.985139 CGGAAGTAAAACCGTGACTCTC 59.015 50.000 0.00 0.00 43.53 3.20
4842 14249 3.022607 CGGAAGTAAAACCGTGACTCT 57.977 47.619 0.00 0.00 43.53 3.24
4850 14257 1.356938 CCTCTCGCGGAAGTAAAACC 58.643 55.000 6.13 0.00 0.00 3.27
4851 14258 0.720027 GCCTCTCGCGGAAGTAAAAC 59.280 55.000 6.13 0.00 0.00 2.43
4852 14259 0.319083 TGCCTCTCGCGGAAGTAAAA 59.681 50.000 6.13 0.00 42.08 1.52
4853 14260 0.389426 GTGCCTCTCGCGGAAGTAAA 60.389 55.000 6.13 0.00 42.08 2.01
4854 14261 1.214589 GTGCCTCTCGCGGAAGTAA 59.785 57.895 6.13 0.00 42.08 2.24
4855 14262 2.882876 GTGCCTCTCGCGGAAGTA 59.117 61.111 6.13 0.00 42.08 2.24
4856 14263 4.421479 CGTGCCTCTCGCGGAAGT 62.421 66.667 6.13 0.00 44.36 3.01
4862 14269 3.414700 CACAACCGTGCCTCTCGC 61.415 66.667 0.00 0.00 36.06 5.03
4870 14277 4.588084 CACGAAAGCACAACCGTG 57.412 55.556 0.00 0.00 46.56 4.94
4871 14278 0.179094 TCTCACGAAAGCACAACCGT 60.179 50.000 0.00 0.00 35.46 4.83
4872 14279 0.508641 CTCTCACGAAAGCACAACCG 59.491 55.000 0.00 0.00 0.00 4.44
4873 14280 1.527311 GACTCTCACGAAAGCACAACC 59.473 52.381 0.00 0.00 0.00 3.77
4874 14281 2.033662 GTGACTCTCACGAAAGCACAAC 60.034 50.000 0.00 0.00 37.67 3.32
4875 14282 2.201732 GTGACTCTCACGAAAGCACAA 58.798 47.619 0.00 0.00 37.67 3.33
4876 14283 1.852942 GTGACTCTCACGAAAGCACA 58.147 50.000 0.00 0.00 37.67 4.57
4904 14311 4.911514 TTTGTTTTTCCCTTTCCGAGAG 57.088 40.909 0.00 0.00 0.00 3.20
4905 14312 4.439016 CGTTTTGTTTTTCCCTTTCCGAGA 60.439 41.667 0.00 0.00 0.00 4.04
4906 14313 3.794564 CGTTTTGTTTTTCCCTTTCCGAG 59.205 43.478 0.00 0.00 0.00 4.63
4907 14314 3.771798 CGTTTTGTTTTTCCCTTTCCGA 58.228 40.909 0.00 0.00 0.00 4.55
4908 14315 2.283086 GCGTTTTGTTTTTCCCTTTCCG 59.717 45.455 0.00 0.00 0.00 4.30
4909 14316 2.283086 CGCGTTTTGTTTTTCCCTTTCC 59.717 45.455 0.00 0.00 0.00 3.13
4910 14317 2.924926 ACGCGTTTTGTTTTTCCCTTTC 59.075 40.909 5.58 0.00 0.00 2.62
4911 14318 2.962125 ACGCGTTTTGTTTTTCCCTTT 58.038 38.095 5.58 0.00 0.00 3.11
4912 14319 2.658373 ACGCGTTTTGTTTTTCCCTT 57.342 40.000 5.58 0.00 0.00 3.95
4913 14320 2.658373 AACGCGTTTTGTTTTTCCCT 57.342 40.000 20.79 0.00 0.00 4.20
4914 14321 3.368539 AGAAAACGCGTTTTGTTTTTCCC 59.631 39.130 44.12 29.39 46.40 3.97
4915 14322 4.571375 AGAAAACGCGTTTTGTTTTTCC 57.429 36.364 44.12 30.00 46.40 3.13


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

AutoCloner maintained by Alex Coulton.