Multiple sequence alignment - TraesCS3A01G341000

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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 TraesCS3A01G341000 chr3A 100.000 5555 0 0 1 5555 588436196 588441750 0.000000e+00 10259.0
1 TraesCS3A01G341000 chr3A 93.893 524 30 2 2576 3098 588627725 588628247 0.000000e+00 789.0
2 TraesCS3A01G341000 chr3A 86.931 681 66 12 3103 3782 588630510 588631168 0.000000e+00 743.0
3 TraesCS3A01G341000 chr3D 90.685 3886 163 78 247 4062 446487988 446491744 0.000000e+00 4987.0
4 TraesCS3A01G341000 chr3D 91.060 1208 87 9 2576 3782 446760393 446761580 0.000000e+00 1613.0
5 TraesCS3A01G341000 chr3D 95.358 797 31 3 4088 4881 446491838 446492631 0.000000e+00 1262.0
6 TraesCS3A01G341000 chr3D 90.759 303 8 6 5035 5317 446493331 446493633 2.430000e-103 387.0
7 TraesCS3A01G341000 chr3D 91.593 226 12 2 1 221 446487770 446487993 6.990000e-79 305.0
8 TraesCS3A01G341000 chr3D 95.690 116 5 0 5365 5480 446493644 446493759 2.640000e-43 187.0
9 TraesCS3A01G341000 chr3D 97.531 81 2 0 4867 4947 446492643 446492723 7.500000e-29 139.0
10 TraesCS3A01G341000 chr3D 100.000 40 0 0 5003 5042 446492790 446492829 2.150000e-09 75.0
11 TraesCS3A01G341000 chr3B 94.729 2068 63 14 2034 4058 585830400 585832464 0.000000e+00 3173.0
12 TraesCS3A01G341000 chr3B 86.562 2106 119 68 1 2035 585828352 585830364 0.000000e+00 2170.0
13 TraesCS3A01G341000 chr3B 95.950 716 27 2 4088 4801 585832560 585833275 0.000000e+00 1160.0
14 TraesCS3A01G341000 chr3B 88.440 545 45 9 4088 4629 586049408 586049937 4.690000e-180 641.0
15 TraesCS3A01G341000 chr3B 92.019 426 29 5 2328 2751 585848176 585848598 1.330000e-165 593.0
16 TraesCS3A01G341000 chr3B 91.866 209 16 1 2034 2242 585843222 585843429 1.960000e-74 291.0
17 TraesCS3A01G341000 chr3B 87.079 178 9 4 3894 4057 586049135 586049312 7.350000e-44 189.0
18 TraesCS3A01G341000 chr3B 93.421 76 5 0 5480 5555 618740430 618740505 4.550000e-21 113.0
19 TraesCS3A01G341000 chr3B 93.243 74 5 0 5480 5553 813523830 813523903 5.880000e-20 110.0
20 TraesCS3A01G341000 chr3B 97.368 38 1 0 5008 5045 585833274 585833311 1.290000e-06 65.8
21 TraesCS3A01G341000 chr3B 100.000 28 0 0 4060 4087 585832492 585832519 1.000000e-02 52.8
22 TraesCS3A01G341000 chr2A 97.368 76 2 0 5480 5555 641223137 641223062 4.520000e-26 130.0
23 TraesCS3A01G341000 chr1B 96.104 77 3 0 5479 5555 677699650 677699726 5.840000e-25 126.0
24 TraesCS3A01G341000 chr5A 94.737 76 4 0 5480 5555 74556959 74557034 9.780000e-23 119.0
25 TraesCS3A01G341000 chr5A 94.737 76 3 1 5480 5555 369504775 369504701 3.520000e-22 117.0
26 TraesCS3A01G341000 chr1A 94.667 75 4 0 5479 5553 474160547 474160621 3.520000e-22 117.0
27 TraesCS3A01G341000 chrUn 94.444 72 4 0 5483 5554 23548572 23548643 1.640000e-20 111.0
28 TraesCS3A01G341000 chr5B 93.243 74 5 0 5480 5553 474440047 474439974 5.880000e-20 110.0


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 TraesCS3A01G341000 chr3A 588436196 588441750 5554 False 10259.000000 10259 100.000000 1 5555 1 chr3A.!!$F1 5554
1 TraesCS3A01G341000 chr3A 588627725 588631168 3443 False 766.000000 789 90.412000 2576 3782 2 chr3A.!!$F2 1206
2 TraesCS3A01G341000 chr3D 446760393 446761580 1187 False 1613.000000 1613 91.060000 2576 3782 1 chr3D.!!$F1 1206
3 TraesCS3A01G341000 chr3D 446487770 446493759 5989 False 1048.857143 4987 94.516571 1 5480 7 chr3D.!!$F2 5479
4 TraesCS3A01G341000 chr3B 585828352 585833311 4959 False 1324.320000 3173 94.921800 1 5045 5 chr3B.!!$F5 5044
5 TraesCS3A01G341000 chr3B 586049135 586049937 802 False 415.000000 641 87.759500 3894 4629 2 chr3B.!!$F6 735

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
736 819 0.039165 CGATCAATCGCCGGATCTGA 60.039 55.000 5.05 1.39 43.84 3.27 F
975 1081 0.039256 CCTGATTTTGTGTGCGGTGG 60.039 55.000 0.00 0.00 0.00 4.61 F
2268 2440 1.201954 CATTGTGATGAACGCCAGACG 60.202 52.381 0.00 0.00 40.97 4.18 F
3866 6325 1.079073 CATCCTTGGTTTGCCCCCT 59.921 57.895 0.00 0.00 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1728 1863 0.170561 ACTGCTCGGTACTAACAGCG 59.829 55.0 0.00 0.0 40.65 5.18 R
2443 2621 0.644331 CACGAAGCTGAGCAAGATCG 59.356 55.0 7.39 13.2 40.56 3.69 R
4054 6526 0.257328 TCACTGAAACTGTGCCCCAA 59.743 50.0 0.00 0.0 34.16 4.12 R
4998 7572 0.037232 GGTTAGTGCACGGAGCTCTT 60.037 55.0 14.64 0.0 44.16 2.85 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
74 80 3.782443 CCGGTTCTCCTTCCCCCG 61.782 72.222 0.00 0.00 38.39 5.73
75 81 3.001406 CGGTTCTCCTTCCCCCGT 61.001 66.667 0.00 0.00 34.10 5.28
165 171 2.554462 TCGATTTTGAAAACGGCATCCA 59.446 40.909 10.85 0.00 35.30 3.41
168 174 4.143347 CGATTTTGAAAACGGCATCCAAAG 60.143 41.667 0.00 0.00 31.64 2.77
219 231 4.794439 CGCCGTCACGCCTGATGA 62.794 66.667 6.50 0.00 35.65 2.92
220 232 2.887568 GCCGTCACGCCTGATGAG 60.888 66.667 6.50 0.00 35.65 2.90
221 233 2.573869 CCGTCACGCCTGATGAGT 59.426 61.111 6.50 0.00 35.65 3.41
222 234 1.079819 CCGTCACGCCTGATGAGTT 60.080 57.895 6.50 0.00 35.65 3.01
223 235 0.670546 CCGTCACGCCTGATGAGTTT 60.671 55.000 6.50 0.00 35.65 2.66
224 236 1.148310 CGTCACGCCTGATGAGTTTT 58.852 50.000 0.00 0.00 35.65 2.43
225 237 1.126846 CGTCACGCCTGATGAGTTTTC 59.873 52.381 0.00 0.00 35.65 2.29
226 238 2.143122 GTCACGCCTGATGAGTTTTCA 58.857 47.619 0.00 0.00 37.81 2.69
227 239 2.548057 GTCACGCCTGATGAGTTTTCAA 59.452 45.455 0.00 0.00 36.78 2.69
228 240 3.003275 GTCACGCCTGATGAGTTTTCAAA 59.997 43.478 0.00 0.00 36.78 2.69
229 241 3.629855 TCACGCCTGATGAGTTTTCAAAA 59.370 39.130 0.00 0.00 36.78 2.44
230 242 4.278170 TCACGCCTGATGAGTTTTCAAAAT 59.722 37.500 0.00 0.00 36.78 1.82
231 243 4.618489 CACGCCTGATGAGTTTTCAAAATC 59.382 41.667 0.00 0.00 36.78 2.17
232 244 4.278170 ACGCCTGATGAGTTTTCAAAATCA 59.722 37.500 5.00 5.00 45.47 2.57
233 245 5.221224 ACGCCTGATGAGTTTTCAAAATCAA 60.221 36.000 6.52 0.00 44.71 2.57
234 246 5.691305 CGCCTGATGAGTTTTCAAAATCAAA 59.309 36.000 6.52 0.00 44.71 2.69
235 247 6.200665 CGCCTGATGAGTTTTCAAAATCAAAA 59.799 34.615 6.52 0.00 44.71 2.44
236 248 7.568134 CGCCTGATGAGTTTTCAAAATCAAAAG 60.568 37.037 6.52 7.12 44.71 2.27
237 249 7.225341 GCCTGATGAGTTTTCAAAATCAAAAGT 59.775 33.333 6.52 0.00 44.71 2.66
238 250 9.748708 CCTGATGAGTTTTCAAAATCAAAAGTA 57.251 29.630 6.52 0.00 44.71 2.24
268 299 2.887568 GGCCTGCGATCTGACGTG 60.888 66.667 0.00 0.00 35.59 4.49
276 307 1.380403 CGATCTGACGTGGAGAGCCT 61.380 60.000 0.00 0.00 34.31 4.58
356 402 3.001939 CGTCCAATATAAAACTGGCGGAC 59.998 47.826 0.00 0.00 38.63 4.79
357 403 3.001939 GTCCAATATAAAACTGGCGGACG 59.998 47.826 0.00 0.00 33.03 4.79
358 404 2.289547 CCAATATAAAACTGGCGGACGG 59.710 50.000 0.00 0.00 0.00 4.79
359 405 3.199677 CAATATAAAACTGGCGGACGGA 58.800 45.455 0.00 0.00 0.00 4.69
360 406 3.764237 ATATAAAACTGGCGGACGGAT 57.236 42.857 0.00 0.00 0.00 4.18
361 407 1.949465 ATAAAACTGGCGGACGGATC 58.051 50.000 0.00 0.00 0.00 3.36
362 408 0.899720 TAAAACTGGCGGACGGATCT 59.100 50.000 0.00 0.00 0.00 2.75
363 409 0.391263 AAAACTGGCGGACGGATCTC 60.391 55.000 0.00 0.00 0.00 2.75
364 410 2.558554 AAACTGGCGGACGGATCTCG 62.559 60.000 0.00 0.00 45.88 4.04
394 440 0.583438 CGCATCTACCAAATCAGGCG 59.417 55.000 0.00 0.00 37.17 5.52
399 476 3.526931 TCTACCAAATCAGGCGAAGAG 57.473 47.619 0.00 0.00 0.00 2.85
406 483 1.949847 ATCAGGCGAAGAGACCGGTG 61.950 60.000 14.63 0.00 0.00 4.94
410 487 1.733399 GCGAAGAGACCGGTGACAC 60.733 63.158 14.63 0.00 0.00 3.67
412 489 1.524863 CGAAGAGACCGGTGACACCT 61.525 60.000 22.14 0.62 35.66 4.00
414 491 1.186267 AAGAGACCGGTGACACCTCC 61.186 60.000 22.14 10.73 35.66 4.30
601 683 1.807142 CCGCTCTCCCAAAAGTTCTTC 59.193 52.381 0.00 0.00 0.00 2.87
602 684 2.551071 CCGCTCTCCCAAAAGTTCTTCT 60.551 50.000 0.00 0.00 0.00 2.85
603 685 3.142174 CGCTCTCCCAAAAGTTCTTCTT 58.858 45.455 0.00 0.00 38.10 2.52
702 785 1.535088 GTAAGCTCGCCGAAATTTGC 58.465 50.000 0.00 0.00 0.00 3.68
704 787 1.244019 AAGCTCGCCGAAATTTGCCT 61.244 50.000 0.00 0.00 0.00 4.75
706 789 0.388520 GCTCGCCGAAATTTGCCTTT 60.389 50.000 0.00 0.00 0.00 3.11
708 791 2.669950 GCTCGCCGAAATTTGCCTTTTA 60.670 45.455 0.00 0.00 0.00 1.52
736 819 0.039165 CGATCAATCGCCGGATCTGA 60.039 55.000 5.05 1.39 43.84 3.27
738 821 0.752658 ATCAATCGCCGGATCTGACA 59.247 50.000 5.05 0.00 30.81 3.58
740 823 1.227380 AATCGCCGGATCTGACAGC 60.227 57.895 5.05 0.00 30.81 4.40
748 831 1.524482 GATCTGACAGCCCAGGTCC 59.476 63.158 0.00 0.00 38.13 4.46
789 872 9.574458 GAATTTTAGAGGAAGAAAAATACAGCC 57.426 33.333 0.00 0.00 32.98 4.85
864 948 3.617669 CGCTTTAATTCGTGCTAATGGG 58.382 45.455 0.00 0.00 0.00 4.00
919 1004 3.545426 GGTGATTTAGCGCGGTTAATGAC 60.545 47.826 24.92 24.63 0.00 3.06
965 1071 1.664016 GCTGCACGTGACCTGATTTTG 60.664 52.381 22.23 0.00 0.00 2.44
966 1072 1.603802 CTGCACGTGACCTGATTTTGT 59.396 47.619 22.23 0.00 0.00 2.83
967 1073 1.333308 TGCACGTGACCTGATTTTGTG 59.667 47.619 22.23 0.00 0.00 3.33
968 1074 1.333619 GCACGTGACCTGATTTTGTGT 59.666 47.619 22.23 0.00 0.00 3.72
969 1075 2.854424 GCACGTGACCTGATTTTGTGTG 60.854 50.000 22.23 0.00 0.00 3.82
970 1076 1.333619 ACGTGACCTGATTTTGTGTGC 59.666 47.619 0.00 0.00 0.00 4.57
971 1077 1.660052 CGTGACCTGATTTTGTGTGCG 60.660 52.381 0.00 0.00 0.00 5.34
972 1078 0.950836 TGACCTGATTTTGTGTGCGG 59.049 50.000 0.00 0.00 0.00 5.69
973 1079 0.951558 GACCTGATTTTGTGTGCGGT 59.048 50.000 0.00 0.00 0.00 5.68
974 1080 0.667993 ACCTGATTTTGTGTGCGGTG 59.332 50.000 0.00 0.00 0.00 4.94
975 1081 0.039256 CCTGATTTTGTGTGCGGTGG 60.039 55.000 0.00 0.00 0.00 4.61
1198 1316 3.544684 CCAGCTGCACATATTACCTTCA 58.455 45.455 8.66 0.00 0.00 3.02
1202 1320 6.226052 CAGCTGCACATATTACCTTCATCTA 58.774 40.000 0.00 0.00 0.00 1.98
1250 1371 5.637006 TCCTTTTGTCGGATTTAATGTGG 57.363 39.130 0.00 0.00 0.00 4.17
1268 1389 5.801531 TGTGGTTAAGTCACATACTCACT 57.198 39.130 7.30 0.00 39.83 3.41
1269 1390 5.779922 TGTGGTTAAGTCACATACTCACTC 58.220 41.667 7.30 0.00 39.83 3.51
1270 1391 5.169295 GTGGTTAAGTCACATACTCACTCC 58.831 45.833 4.53 0.00 37.50 3.85
1271 1392 4.222145 TGGTTAAGTCACATACTCACTCCC 59.778 45.833 0.00 0.00 37.50 4.30
1352 1473 3.420893 TGATGTGAATGTTGGACCCTTC 58.579 45.455 0.00 0.00 0.00 3.46
1388 1509 4.811024 AGTGTCAATATGGTGCAATCGTAG 59.189 41.667 0.00 0.00 0.00 3.51
1417 1551 4.092120 CACACTGTAATTCTCGAGTCTCG 58.908 47.826 16.33 16.33 42.10 4.04
1480 1614 2.992124 TCCAACCTGAACTTGTTCGA 57.008 45.000 8.68 0.00 0.00 3.71
1536 1670 3.374988 CCGCATAACTTTGCTTGAGATGA 59.625 43.478 0.00 0.00 40.54 2.92
1557 1691 7.713073 AGATGAGCAATTACTAAGCTTAACTCC 59.287 37.037 7.74 0.00 39.02 3.85
1705 1840 4.846779 TGCTCAAGGGTATGTGTTTTTC 57.153 40.909 0.00 0.00 0.00 2.29
1727 1862 8.533569 TTTCCCCCTTTGAAATATGTATTCTC 57.466 34.615 0.00 0.00 0.00 2.87
1728 1863 6.610830 TCCCCCTTTGAAATATGTATTCTCC 58.389 40.000 0.00 0.00 0.00 3.71
1743 1878 1.376543 TCTCCGCTGTTAGTACCGAG 58.623 55.000 0.00 0.00 0.00 4.63
1781 1916 8.812147 TTGTTACAAGTTCTGATACAGTAGTG 57.188 34.615 0.00 0.00 32.61 2.74
1786 1921 8.958119 ACAAGTTCTGATACAGTAGTGAAAAA 57.042 30.769 4.09 0.00 32.61 1.94
1789 1924 7.963532 AGTTCTGATACAGTAGTGAAAAAGGA 58.036 34.615 4.09 0.00 32.61 3.36
1802 1937 4.035675 GTGAAAAAGGACACCTGACTTCAG 59.964 45.833 0.00 0.00 43.40 3.02
1849 1984 3.060895 GGTCTTCTAGTTTTGCATCGTCG 59.939 47.826 0.00 0.00 0.00 5.12
1855 1990 5.404096 TCTAGTTTTGCATCGTCGTCAATA 58.596 37.500 0.00 0.00 0.00 1.90
1856 1991 6.040247 TCTAGTTTTGCATCGTCGTCAATAT 58.960 36.000 0.00 0.00 0.00 1.28
1858 1993 5.323900 AGTTTTGCATCGTCGTCAATATTG 58.676 37.500 9.29 9.29 0.00 1.90
1861 1996 4.937696 TGCATCGTCGTCAATATTGTTT 57.062 36.364 14.97 0.00 0.00 2.83
1939 2074 8.256611 AGTTATGTTACATAGTTTGCTGTCTG 57.743 34.615 5.17 0.00 0.00 3.51
2241 2413 1.421646 AGACCAAGTGCAGGTTAGCTT 59.578 47.619 0.00 0.00 40.09 3.74
2268 2440 1.201954 CATTGTGATGAACGCCAGACG 60.202 52.381 0.00 0.00 40.97 4.18
2443 2621 5.694910 TGGTTTCGTAGAGACAATTGAGAAC 59.305 40.000 13.59 2.19 44.06 3.01
2628 2809 8.698973 TTTTCCTGGTGAAATTAAGTCATGTA 57.301 30.769 0.00 0.00 42.38 2.29
2779 2960 3.298619 CAATGATCAGTATTTGCCCCCA 58.701 45.455 0.09 0.00 0.00 4.96
3178 5617 2.526432 AGTTAGTCATGACTCGGGTGT 58.474 47.619 31.09 9.15 42.54 4.16
3250 5690 4.164843 ACAAATGTGGGTCAAGTACTGT 57.835 40.909 0.00 0.00 0.00 3.55
3347 5805 7.394016 AGGAAAGTGATTTCTTTGGTTTGTTT 58.606 30.769 1.20 0.00 37.70 2.83
3401 5859 2.092323 GGGGCAAAGCTTAACTACAGG 58.908 52.381 0.00 0.00 0.00 4.00
3403 5861 2.554564 GGGCAAAGCTTAACTACAGGGT 60.555 50.000 0.00 0.00 0.00 4.34
3405 5863 2.747989 GCAAAGCTTAACTACAGGGTCC 59.252 50.000 0.00 0.00 0.00 4.46
3469 5928 4.156008 GTCCATTCAGCGTTTATTGACCTT 59.844 41.667 0.00 0.00 0.00 3.50
3474 5933 6.417191 TTCAGCGTTTATTGACCTTATGAC 57.583 37.500 0.00 0.00 0.00 3.06
3562 6021 5.297029 AGGTCTAAAGTTTGTTCTGTGCTTC 59.703 40.000 0.00 0.00 0.00 3.86
3569 6028 5.650543 AGTTTGTTCTGTGCTTCGAAATTT 58.349 33.333 0.00 0.00 0.00 1.82
3601 6060 8.969121 TGTTTCTGCACATTTGTATTTATGAG 57.031 30.769 0.00 0.00 0.00 2.90
3634 6093 6.603237 TTTGTTCATAACAGTGAGACAGTG 57.397 37.500 0.00 0.00 43.27 3.66
3843 6302 5.784578 AGGAATTTGGAAAGGTGTAACAC 57.215 39.130 0.00 0.00 39.98 3.32
3845 6304 3.636282 ATTTGGAAAGGTGTAACACGC 57.364 42.857 0.00 0.00 39.98 5.34
3866 6325 1.079073 CATCCTTGGTTTGCCCCCT 59.921 57.895 0.00 0.00 0.00 4.79
3883 6342 7.118496 TGCCCCCTTAAATTTACATAACATG 57.882 36.000 0.00 0.00 0.00 3.21
4058 6530 8.930846 ATCTATATCCTGAAAGTTGAATTGGG 57.069 34.615 0.00 0.00 0.00 4.12
4379 6920 1.733402 TTGGTTTTGACCTGCCTGCG 61.733 55.000 0.00 0.00 0.00 5.18
4620 7165 3.706600 TGTCGCTATAGTTTTGGGGTT 57.293 42.857 0.84 0.00 0.00 4.11
4684 7232 0.368227 CACGCTTGCTCGAACTCATC 59.632 55.000 0.00 0.00 0.00 2.92
4685 7233 0.038251 ACGCTTGCTCGAACTCATCA 60.038 50.000 0.00 0.00 0.00 3.07
4686 7234 1.284657 CGCTTGCTCGAACTCATCAT 58.715 50.000 0.00 0.00 0.00 2.45
4746 7294 8.528643 GTTAGCTCTATTTTGTAATTTGGGGTT 58.471 33.333 0.00 0.00 0.00 4.11
4831 7379 0.899720 TCTTCAGGTAAACGCCCGAT 59.100 50.000 0.00 0.00 0.00 4.18
4842 7390 3.491581 CGCCCGATAATAGCGTTCT 57.508 52.632 0.00 0.00 44.65 3.01
4903 7477 0.404040 AGCAATGAAGGAAACGGGGA 59.596 50.000 0.00 0.00 0.00 4.81
4947 7521 2.059541 GTAAGCCGTGACTCACAGAAC 58.940 52.381 9.84 0.00 33.40 3.01
4948 7522 0.753262 AAGCCGTGACTCACAGAACT 59.247 50.000 9.84 0.00 33.40 3.01
4950 7524 0.946221 GCCGTGACTCACAGAACTGG 60.946 60.000 9.84 2.57 33.40 4.00
4952 7526 1.491670 CGTGACTCACAGAACTGGTG 58.508 55.000 9.84 3.17 37.60 4.17
4953 7527 1.067060 CGTGACTCACAGAACTGGTGA 59.933 52.381 9.84 6.79 42.62 4.02
4957 7531 2.452116 TCACAGAACTGGTGAGGGG 58.548 57.895 6.76 0.00 40.16 4.79
4960 7534 1.062488 ACAGAACTGGTGAGGGGCTT 61.062 55.000 6.76 0.00 34.19 4.35
4961 7535 0.607489 CAGAACTGGTGAGGGGCTTG 60.607 60.000 0.00 0.00 0.00 4.01
4962 7536 1.303643 GAACTGGTGAGGGGCTTGG 60.304 63.158 0.00 0.00 0.00 3.61
4964 7538 2.069165 AACTGGTGAGGGGCTTGGAC 62.069 60.000 0.00 0.00 0.00 4.02
4965 7539 3.612247 CTGGTGAGGGGCTTGGACG 62.612 68.421 0.00 0.00 0.00 4.79
4967 7541 4.329545 GTGAGGGGCTTGGACGCA 62.330 66.667 0.00 0.00 0.00 5.24
4968 7542 4.329545 TGAGGGGCTTGGACGCAC 62.330 66.667 0.00 0.00 0.00 5.34
4972 7546 3.365265 GGGCTTGGACGCACCTTG 61.365 66.667 1.15 0.00 39.86 3.61
4973 7547 4.043200 GGCTTGGACGCACCTTGC 62.043 66.667 1.15 5.09 40.69 4.01
4974 7548 3.286751 GCTTGGACGCACCTTGCA 61.287 61.111 0.00 0.00 45.36 4.08
4975 7549 2.629656 GCTTGGACGCACCTTGCAT 61.630 57.895 0.00 0.00 45.36 3.96
4976 7550 1.210931 CTTGGACGCACCTTGCATG 59.789 57.895 0.00 0.00 45.36 4.06
4990 7564 0.961019 TGCATGCCAAACTCCAACTC 59.039 50.000 16.68 0.00 0.00 3.01
4991 7565 0.244721 GCATGCCAAACTCCAACTCC 59.755 55.000 6.36 0.00 0.00 3.85
4992 7566 0.890683 CATGCCAAACTCCAACTCCC 59.109 55.000 0.00 0.00 0.00 4.30
4993 7567 0.779997 ATGCCAAACTCCAACTCCCT 59.220 50.000 0.00 0.00 0.00 4.20
4994 7568 0.555769 TGCCAAACTCCAACTCCCTT 59.444 50.000 0.00 0.00 0.00 3.95
4995 7569 1.063266 TGCCAAACTCCAACTCCCTTT 60.063 47.619 0.00 0.00 0.00 3.11
4997 7571 1.963515 CCAAACTCCAACTCCCTTTGG 59.036 52.381 0.00 0.00 46.64 3.28
5062 8156 1.762858 TTGGGTCGAGTGGTGTGGA 60.763 57.895 0.00 0.00 0.00 4.02
5107 8203 0.250081 TGGTGTTACATGCGTGCTCA 60.250 50.000 5.64 0.00 0.00 4.26
5110 8206 1.731709 GTGTTACATGCGTGCTCATCA 59.268 47.619 5.64 0.00 0.00 3.07
5148 8244 3.577649 TGAGAAGCTAAACCTCGTCTG 57.422 47.619 0.00 0.00 0.00 3.51
5155 8251 2.662156 GCTAAACCTCGTCTGTCTTTCG 59.338 50.000 0.00 0.00 0.00 3.46
5156 8252 3.611057 GCTAAACCTCGTCTGTCTTTCGA 60.611 47.826 0.00 0.00 0.00 3.71
5159 8255 2.160205 ACCTCGTCTGTCTTTCGATCA 58.840 47.619 0.00 0.00 33.26 2.92
5231 8345 8.040727 ACAAAGCAAAAACACTCTTTTATCCTT 58.959 29.630 0.00 0.00 0.00 3.36
5317 8431 1.205655 CTGGCCATGACGAAGAGAAGA 59.794 52.381 5.51 0.00 0.00 2.87
5318 8432 1.623311 TGGCCATGACGAAGAGAAGAA 59.377 47.619 0.00 0.00 0.00 2.52
5319 8433 2.237143 TGGCCATGACGAAGAGAAGAAT 59.763 45.455 0.00 0.00 0.00 2.40
5320 8434 2.611292 GGCCATGACGAAGAGAAGAATG 59.389 50.000 0.00 0.00 0.00 2.67
5322 8436 3.063180 GCCATGACGAAGAGAAGAATGTG 59.937 47.826 0.00 0.00 0.00 3.21
5324 8438 2.328473 TGACGAAGAGAAGAATGTGCG 58.672 47.619 0.00 0.00 0.00 5.34
5325 8439 1.656095 GACGAAGAGAAGAATGTGCGG 59.344 52.381 0.00 0.00 0.00 5.69
5327 8441 1.404181 CGAAGAGAAGAATGTGCGGGA 60.404 52.381 0.00 0.00 0.00 5.14
5328 8442 2.275318 GAAGAGAAGAATGTGCGGGAG 58.725 52.381 0.00 0.00 0.00 4.30
5329 8443 0.539051 AGAGAAGAATGTGCGGGAGG 59.461 55.000 0.00 0.00 0.00 4.30
5330 8444 0.462759 GAGAAGAATGTGCGGGAGGG 60.463 60.000 0.00 0.00 0.00 4.30
5331 8445 1.201429 AGAAGAATGTGCGGGAGGGT 61.201 55.000 0.00 0.00 0.00 4.34
5332 8446 0.744771 GAAGAATGTGCGGGAGGGTC 60.745 60.000 0.00 0.00 0.00 4.46
5333 8447 2.511600 GAATGTGCGGGAGGGTCG 60.512 66.667 0.00 0.00 0.00 4.79
5334 8448 3.310860 GAATGTGCGGGAGGGTCGT 62.311 63.158 0.00 0.00 0.00 4.34
5335 8449 3.605749 AATGTGCGGGAGGGTCGTG 62.606 63.158 0.00 0.00 0.00 4.35
5338 8452 4.682334 TGCGGGAGGGTCGTGGTA 62.682 66.667 0.00 0.00 0.00 3.25
5339 8453 3.834799 GCGGGAGGGTCGTGGTAG 61.835 72.222 0.00 0.00 0.00 3.18
5340 8454 2.044650 CGGGAGGGTCGTGGTAGA 60.045 66.667 0.00 0.00 0.00 2.59
5341 8455 2.413142 CGGGAGGGTCGTGGTAGAC 61.413 68.421 0.00 0.00 40.25 2.59
5342 8456 1.304713 GGGAGGGTCGTGGTAGACA 60.305 63.158 0.00 0.00 42.62 3.41
5343 8457 1.602327 GGGAGGGTCGTGGTAGACAC 61.602 65.000 0.00 0.00 44.51 3.67
5359 8473 4.590487 ACATAGGTGACAACGGCG 57.410 55.556 4.80 4.80 0.00 6.46
5360 8474 1.079405 ACATAGGTGACAACGGCGG 60.079 57.895 13.24 0.00 0.00 6.13
5361 8475 1.079405 CATAGGTGACAACGGCGGT 60.079 57.895 13.24 0.00 0.00 5.68
5362 8476 1.079405 ATAGGTGACAACGGCGGTG 60.079 57.895 25.44 25.44 0.00 4.94
5363 8477 1.823169 ATAGGTGACAACGGCGGTGT 61.823 55.000 33.01 33.01 0.00 4.16
5396 8510 1.412710 ACAGAGGAAGCAACAGTTCGA 59.587 47.619 0.00 0.00 0.00 3.71
5457 8571 4.572389 GCATGTCTTCGACCATGAATTAGT 59.428 41.667 18.25 0.00 0.00 2.24
5458 8572 5.065218 GCATGTCTTCGACCATGAATTAGTT 59.935 40.000 18.25 0.00 0.00 2.24
5459 8573 6.709643 CATGTCTTCGACCATGAATTAGTTC 58.290 40.000 11.58 0.00 34.85 3.01
5480 8594 0.802494 CAACAACACGCCCATAGTCC 59.198 55.000 0.00 0.00 0.00 3.85
5481 8595 0.322187 AACAACACGCCCATAGTCCC 60.322 55.000 0.00 0.00 0.00 4.46
5482 8596 1.198759 ACAACACGCCCATAGTCCCT 61.199 55.000 0.00 0.00 0.00 4.20
5483 8597 0.828022 CAACACGCCCATAGTCCCTA 59.172 55.000 0.00 0.00 0.00 3.53
5484 8598 1.208535 CAACACGCCCATAGTCCCTAA 59.791 52.381 0.00 0.00 0.00 2.69
5485 8599 1.802553 ACACGCCCATAGTCCCTAAT 58.197 50.000 0.00 0.00 0.00 1.73
5486 8600 2.966915 ACACGCCCATAGTCCCTAATA 58.033 47.619 0.00 0.00 0.00 0.98
5487 8601 3.311091 ACACGCCCATAGTCCCTAATAA 58.689 45.455 0.00 0.00 0.00 1.40
5488 8602 3.908103 ACACGCCCATAGTCCCTAATAAT 59.092 43.478 0.00 0.00 0.00 1.28
5489 8603 5.088730 ACACGCCCATAGTCCCTAATAATA 58.911 41.667 0.00 0.00 0.00 0.98
5490 8604 5.544948 ACACGCCCATAGTCCCTAATAATAA 59.455 40.000 0.00 0.00 0.00 1.40
5491 8605 6.043474 ACACGCCCATAGTCCCTAATAATAAA 59.957 38.462 0.00 0.00 0.00 1.40
5492 8606 6.594159 CACGCCCATAGTCCCTAATAATAAAG 59.406 42.308 0.00 0.00 0.00 1.85
5493 8607 5.585047 CGCCCATAGTCCCTAATAATAAAGC 59.415 44.000 0.00 0.00 0.00 3.51
5494 8608 6.481643 GCCCATAGTCCCTAATAATAAAGCA 58.518 40.000 0.00 0.00 0.00 3.91
5495 8609 7.119387 GCCCATAGTCCCTAATAATAAAGCAT 58.881 38.462 0.00 0.00 0.00 3.79
5496 8610 7.283354 GCCCATAGTCCCTAATAATAAAGCATC 59.717 40.741 0.00 0.00 0.00 3.91
5497 8611 8.552296 CCCATAGTCCCTAATAATAAAGCATCT 58.448 37.037 0.00 0.00 0.00 2.90
5515 8629 5.835911 CATCTATTGCTTCTGATGGTACG 57.164 43.478 0.00 0.00 34.40 3.67
5516 8630 3.717707 TCTATTGCTTCTGATGGTACGC 58.282 45.455 0.00 0.00 0.00 4.42
5517 8631 1.668419 ATTGCTTCTGATGGTACGCC 58.332 50.000 0.00 0.00 0.00 5.68
5529 8643 2.294074 TGGTACGCCATCTAATTTGCC 58.706 47.619 0.00 0.00 40.46 4.52
5530 8644 1.607148 GGTACGCCATCTAATTTGCCC 59.393 52.381 0.00 0.00 34.09 5.36
5531 8645 1.607148 GTACGCCATCTAATTTGCCCC 59.393 52.381 0.00 0.00 0.00 5.80
5532 8646 0.258774 ACGCCATCTAATTTGCCCCT 59.741 50.000 0.00 0.00 0.00 4.79
5533 8647 1.493022 ACGCCATCTAATTTGCCCCTA 59.507 47.619 0.00 0.00 0.00 3.53
5534 8648 2.092103 ACGCCATCTAATTTGCCCCTAA 60.092 45.455 0.00 0.00 0.00 2.69
5535 8649 2.955660 CGCCATCTAATTTGCCCCTAAA 59.044 45.455 0.00 0.00 0.00 1.85
5536 8650 3.004734 CGCCATCTAATTTGCCCCTAAAG 59.995 47.826 0.00 0.00 0.00 1.85
5537 8651 3.960755 GCCATCTAATTTGCCCCTAAAGT 59.039 43.478 0.00 0.00 0.00 2.66
5538 8652 4.405680 GCCATCTAATTTGCCCCTAAAGTT 59.594 41.667 0.00 0.00 0.00 2.66
5539 8653 5.682212 GCCATCTAATTTGCCCCTAAAGTTG 60.682 44.000 0.00 0.00 0.00 3.16
5540 8654 5.351458 CATCTAATTTGCCCCTAAAGTTGC 58.649 41.667 0.00 0.00 0.00 4.17
5541 8655 4.672899 TCTAATTTGCCCCTAAAGTTGCT 58.327 39.130 0.00 0.00 0.00 3.91
5542 8656 5.822204 TCTAATTTGCCCCTAAAGTTGCTA 58.178 37.500 0.00 0.00 0.00 3.49
5543 8657 6.249951 TCTAATTTGCCCCTAAAGTTGCTAA 58.750 36.000 0.00 0.00 0.00 3.09
5544 8658 5.816955 AATTTGCCCCTAAAGTTGCTAAA 57.183 34.783 0.00 0.00 0.00 1.85
5545 8659 6.373005 AATTTGCCCCTAAAGTTGCTAAAT 57.627 33.333 0.00 0.00 0.00 1.40
5546 8660 7.489239 AATTTGCCCCTAAAGTTGCTAAATA 57.511 32.000 0.00 0.00 0.00 1.40
5547 8661 7.675161 ATTTGCCCCTAAAGTTGCTAAATAT 57.325 32.000 0.00 0.00 0.00 1.28
5548 8662 7.489239 TTTGCCCCTAAAGTTGCTAAATATT 57.511 32.000 0.00 0.00 0.00 1.28
5549 8663 8.596781 TTTGCCCCTAAAGTTGCTAAATATTA 57.403 30.769 0.00 0.00 0.00 0.98
5550 8664 7.576861 TGCCCCTAAAGTTGCTAAATATTAC 57.423 36.000 0.00 0.00 0.00 1.89
5551 8665 6.548251 TGCCCCTAAAGTTGCTAAATATTACC 59.452 38.462 0.00 0.00 0.00 2.85
5552 8666 6.015688 GCCCCTAAAGTTGCTAAATATTACCC 60.016 42.308 0.00 0.00 0.00 3.69
5553 8667 7.064229 CCCCTAAAGTTGCTAAATATTACCCA 58.936 38.462 0.00 0.00 0.00 4.51
5554 8668 7.013942 CCCCTAAAGTTGCTAAATATTACCCAC 59.986 40.741 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 116 7.328249 TGCTATTTTAAAATGTTTCTCCGCAAG 59.672 33.333 21.19 8.61 0.00 4.01
165 171 4.192317 GCCGTGAGTTGGATATTCTCTTT 58.808 43.478 0.00 0.00 0.00 2.52
168 174 2.103263 AGGCCGTGAGTTGGATATTCTC 59.897 50.000 0.00 0.00 0.00 2.87
227 239 8.961634 GCCTCCTCTTTCTATTACTTTTGATTT 58.038 33.333 0.00 0.00 0.00 2.17
228 240 7.558081 GGCCTCCTCTTTCTATTACTTTTGATT 59.442 37.037 0.00 0.00 0.00 2.57
229 241 7.057264 GGCCTCCTCTTTCTATTACTTTTGAT 58.943 38.462 0.00 0.00 0.00 2.57
230 242 6.215636 AGGCCTCCTCTTTCTATTACTTTTGA 59.784 38.462 0.00 0.00 0.00 2.69
231 243 6.317391 CAGGCCTCCTCTTTCTATTACTTTTG 59.683 42.308 0.00 0.00 0.00 2.44
232 244 6.418946 CAGGCCTCCTCTTTCTATTACTTTT 58.581 40.000 0.00 0.00 0.00 2.27
233 245 5.630304 GCAGGCCTCCTCTTTCTATTACTTT 60.630 44.000 0.00 0.00 0.00 2.66
234 246 4.141597 GCAGGCCTCCTCTTTCTATTACTT 60.142 45.833 0.00 0.00 0.00 2.24
235 247 3.389656 GCAGGCCTCCTCTTTCTATTACT 59.610 47.826 0.00 0.00 0.00 2.24
236 248 3.734463 GCAGGCCTCCTCTTTCTATTAC 58.266 50.000 0.00 0.00 0.00 1.89
237 249 2.365617 CGCAGGCCTCCTCTTTCTATTA 59.634 50.000 0.00 0.00 0.00 0.98
238 250 1.139853 CGCAGGCCTCCTCTTTCTATT 59.860 52.381 0.00 0.00 0.00 1.73
239 251 0.755686 CGCAGGCCTCCTCTTTCTAT 59.244 55.000 0.00 0.00 0.00 1.98
240 252 0.324368 TCGCAGGCCTCCTCTTTCTA 60.324 55.000 0.00 0.00 0.00 2.10
241 253 0.980231 ATCGCAGGCCTCCTCTTTCT 60.980 55.000 0.00 0.00 0.00 2.52
242 254 0.531753 GATCGCAGGCCTCCTCTTTC 60.532 60.000 0.00 0.00 0.00 2.62
243 255 0.980231 AGATCGCAGGCCTCCTCTTT 60.980 55.000 0.00 0.00 0.00 2.52
244 256 1.382420 AGATCGCAGGCCTCCTCTT 60.382 57.895 0.00 0.00 0.00 2.85
245 257 2.132996 CAGATCGCAGGCCTCCTCT 61.133 63.158 0.00 0.00 0.00 3.69
246 258 2.130426 TCAGATCGCAGGCCTCCTC 61.130 63.158 0.00 0.00 0.00 3.71
247 259 2.042537 TCAGATCGCAGGCCTCCT 60.043 61.111 0.00 0.00 0.00 3.69
268 299 0.107116 TCACGAGTCCTAGGCTCTCC 60.107 60.000 22.71 10.28 0.00 3.71
276 307 2.359107 ACGCCGTCACGAGTCCTA 60.359 61.111 0.00 0.00 36.70 2.94
370 416 0.304705 GATTTGGTAGATGCGGTGCG 59.695 55.000 0.00 0.00 0.00 5.34
371 417 1.331756 CTGATTTGGTAGATGCGGTGC 59.668 52.381 0.00 0.00 0.00 5.01
372 418 1.942657 CCTGATTTGGTAGATGCGGTG 59.057 52.381 0.00 0.00 0.00 4.94
373 419 1.747206 GCCTGATTTGGTAGATGCGGT 60.747 52.381 0.00 0.00 0.00 5.68
374 420 0.947244 GCCTGATTTGGTAGATGCGG 59.053 55.000 0.00 0.00 0.00 5.69
375 421 0.583438 CGCCTGATTTGGTAGATGCG 59.417 55.000 0.00 0.00 34.52 4.73
376 422 1.953559 TCGCCTGATTTGGTAGATGC 58.046 50.000 0.00 0.00 0.00 3.91
394 440 0.244178 GAGGTGTCACCGGTCTCTTC 59.756 60.000 16.44 2.98 44.90 2.87
399 476 1.878656 CTGAGGAGGTGTCACCGGTC 61.879 65.000 16.44 13.92 44.90 4.79
406 483 2.574399 GACGGCTGAGGAGGTGTC 59.426 66.667 0.00 0.00 0.00 3.67
410 487 2.835431 ATCGGACGGCTGAGGAGG 60.835 66.667 5.73 0.00 31.75 4.30
412 489 3.147595 CCATCGGACGGCTGAGGA 61.148 66.667 14.67 0.00 33.09 3.71
601 683 0.591236 CGTGTGGTTTGCGGAACAAG 60.591 55.000 0.00 0.00 40.06 3.16
602 684 1.025113 TCGTGTGGTTTGCGGAACAA 61.025 50.000 0.00 0.00 40.13 2.83
603 685 1.025113 TTCGTGTGGTTTGCGGAACA 61.025 50.000 0.00 0.00 40.13 3.18
629 712 1.683385 GGCTGTTCTCACCTTTGCTTT 59.317 47.619 0.00 0.00 0.00 3.51
630 713 1.322442 GGCTGTTCTCACCTTTGCTT 58.678 50.000 0.00 0.00 0.00 3.91
646 729 2.919839 TCGAGATCGAGAGGGGCT 59.080 61.111 0.00 0.00 44.22 5.19
702 785 5.006746 CGATTGATCGGAGGAAACTAAAAGG 59.993 44.000 5.51 0.00 45.93 3.11
729 812 1.524482 GACCTGGGCTGTCAGATCC 59.476 63.158 3.32 4.91 36.93 3.36
736 819 1.771255 GATGAATAGGACCTGGGCTGT 59.229 52.381 3.53 0.00 0.00 4.40
738 821 1.051812 CGATGAATAGGACCTGGGCT 58.948 55.000 3.53 0.00 0.00 5.19
740 823 3.580458 AGATTCGATGAATAGGACCTGGG 59.420 47.826 3.53 0.00 31.89 4.45
773 856 5.154222 CGACAAAGGCTGTATTTTTCTTCC 58.846 41.667 0.00 0.00 38.84 3.46
788 871 7.012044 CCCCTATAACTAATCAAACGACAAAGG 59.988 40.741 0.00 0.00 0.00 3.11
789 872 7.012044 CCCCCTATAACTAATCAAACGACAAAG 59.988 40.741 0.00 0.00 0.00 2.77
937 1043 1.737735 TCACGTGCAGCGAATCCAG 60.738 57.895 11.67 0.00 44.77 3.86
965 1071 1.588667 CAAGCAAACCACCGCACAC 60.589 57.895 0.00 0.00 0.00 3.82
966 1072 1.106351 ATCAAGCAAACCACCGCACA 61.106 50.000 0.00 0.00 0.00 4.57
967 1073 0.031994 AATCAAGCAAACCACCGCAC 59.968 50.000 0.00 0.00 0.00 5.34
968 1074 0.031857 CAATCAAGCAAACCACCGCA 59.968 50.000 0.00 0.00 0.00 5.69
969 1075 0.313672 TCAATCAAGCAAACCACCGC 59.686 50.000 0.00 0.00 0.00 5.68
970 1076 3.302365 AATCAATCAAGCAAACCACCG 57.698 42.857 0.00 0.00 0.00 4.94
971 1077 4.319694 GCAAAATCAATCAAGCAAACCACC 60.320 41.667 0.00 0.00 0.00 4.61
972 1078 4.272991 TGCAAAATCAATCAAGCAAACCAC 59.727 37.500 0.00 0.00 0.00 4.16
973 1079 4.449131 TGCAAAATCAATCAAGCAAACCA 58.551 34.783 0.00 0.00 0.00 3.67
974 1080 4.083696 CCTGCAAAATCAATCAAGCAAACC 60.084 41.667 0.00 0.00 0.00 3.27
975 1081 4.751098 TCCTGCAAAATCAATCAAGCAAAC 59.249 37.500 0.00 0.00 0.00 2.93
1178 1284 5.061853 AGATGAAGGTAATATGTGCAGCTG 58.938 41.667 10.11 10.11 0.00 4.24
1202 1320 7.273712 TGCATGCAACCATAATCACATTAAAT 58.726 30.769 20.30 0.00 0.00 1.40
1223 1344 5.913137 TTAAATCCGACAAAAGGATGCAT 57.087 34.783 0.00 0.00 46.99 3.96
1250 1371 4.421948 CGGGAGTGAGTATGTGACTTAAC 58.578 47.826 0.00 0.00 39.06 2.01
1265 1386 2.159099 TGCTTAATCTACAGCGGGAGTG 60.159 50.000 0.00 0.00 39.04 3.51
1266 1387 2.108168 TGCTTAATCTACAGCGGGAGT 58.892 47.619 0.00 0.00 39.04 3.85
1267 1388 2.890808 TGCTTAATCTACAGCGGGAG 57.109 50.000 0.00 0.00 39.04 4.30
1268 1389 2.037251 GGATGCTTAATCTACAGCGGGA 59.963 50.000 0.00 0.00 39.04 5.14
1269 1390 2.037772 AGGATGCTTAATCTACAGCGGG 59.962 50.000 0.00 0.00 39.04 6.13
1270 1391 3.062763 CAGGATGCTTAATCTACAGCGG 58.937 50.000 0.00 0.00 39.04 5.52
1271 1392 3.982475 TCAGGATGCTTAATCTACAGCG 58.018 45.455 0.00 0.00 39.04 5.18
1367 1488 3.559655 GCTACGATTGCACCATATTGACA 59.440 43.478 0.00 0.00 0.00 3.58
1376 1497 0.931005 GCACTAGCTACGATTGCACC 59.069 55.000 0.00 0.00 37.91 5.01
1388 1509 3.304559 CGAGAATTACAGTGTGCACTAGC 59.695 47.826 19.41 8.39 40.20 3.42
1536 1670 5.731591 ACGGAGTTAAGCTTAGTAATTGCT 58.268 37.500 6.24 0.56 37.78 3.91
1557 1691 1.275291 TCTCAGGAGCACCCTAAAACG 59.725 52.381 0.00 0.00 45.60 3.60
1705 1840 5.473504 CGGAGAATACATATTTCAAAGGGGG 59.526 44.000 0.00 0.00 0.00 5.40
1727 1862 0.525668 CTGCTCGGTACTAACAGCGG 60.526 60.000 0.00 0.00 39.77 5.52
1728 1863 0.170561 ACTGCTCGGTACTAACAGCG 59.829 55.000 0.00 0.00 40.65 5.18
1781 1916 3.003793 GCTGAAGTCAGGTGTCCTTTTTC 59.996 47.826 10.25 0.00 43.94 2.29
1849 1984 8.391106 CCTAGCAGAGTTACAAACAATATTGAC 58.609 37.037 22.16 8.37 34.38 3.18
1855 1990 5.705905 GGTTCCTAGCAGAGTTACAAACAAT 59.294 40.000 0.00 0.00 0.00 2.71
1856 1991 5.061179 GGTTCCTAGCAGAGTTACAAACAA 58.939 41.667 0.00 0.00 0.00 2.83
1858 1993 4.638304 TGGTTCCTAGCAGAGTTACAAAC 58.362 43.478 0.00 0.00 0.00 2.93
1861 1996 3.838317 ACATGGTTCCTAGCAGAGTTACA 59.162 43.478 0.00 0.00 34.83 2.41
1914 2049 8.094548 TCAGACAGCAAACTATGTAACATAACT 58.905 33.333 0.00 0.00 0.00 2.24
1994 2129 9.669353 GCATACAAGTGAAACAGAATATAATGG 57.331 33.333 0.00 0.00 41.43 3.16
2241 2413 3.065233 GGCGTTCATCACAATGATTGCTA 59.935 43.478 4.84 0.00 41.49 3.49
2443 2621 0.644331 CACGAAGCTGAGCAAGATCG 59.356 55.000 7.39 13.20 40.56 3.69
2628 2809 5.580691 CAGTCATTCTGCAATGCATCAAAAT 59.419 36.000 8.91 4.06 39.56 1.82
2636 2817 2.089980 ACTCCAGTCATTCTGCAATGC 58.910 47.619 0.00 0.00 42.38 3.56
2779 2960 5.587844 GCCACTCTCATCAACTATCACAAAT 59.412 40.000 0.00 0.00 0.00 2.32
2890 3071 9.624697 TCAAATTTATCAAAATCAGGAAACTCG 57.375 29.630 0.00 0.00 34.16 4.18
3205 5645 4.689612 TCAATGGGAGTATGCTAACCTC 57.310 45.455 5.77 0.00 0.00 3.85
3324 5782 9.967245 GTAAAACAAACCAAAGAAATCACTTTC 57.033 29.630 0.00 0.00 40.95 2.62
3373 5831 0.398381 AAGCTTTGCCCCCAGACAAA 60.398 50.000 0.00 0.00 34.73 2.83
3447 5906 3.950397 AGGTCAATAAACGCTGAATGGA 58.050 40.909 0.00 0.00 0.00 3.41
3469 5928 8.597167 CACAATTATGAGAATAGGGGAGTCATA 58.403 37.037 0.00 0.00 0.00 2.15
3562 6021 7.471721 TGTGCAGAAACATAGGATAAATTTCG 58.528 34.615 0.00 0.00 35.10 3.46
3569 6028 8.978874 ATACAAATGTGCAGAAACATAGGATA 57.021 30.769 0.00 0.00 39.89 2.59
3634 6093 3.665745 AATGTGACATGGCCAAACTTC 57.334 42.857 10.96 4.25 0.00 3.01
3843 6302 1.154225 GCAAACCAAGGATGTCGCG 60.154 57.895 0.00 0.00 0.00 5.87
3845 6304 1.595093 GGGGCAAACCAAGGATGTCG 61.595 60.000 0.00 0.00 42.91 4.35
3883 6342 6.780706 AATACGCACCTACAAGCATATAAC 57.219 37.500 0.00 0.00 0.00 1.89
3954 6413 1.066908 GCCTTGCAAGCAACAACTGTA 59.933 47.619 21.43 0.00 0.00 2.74
3978 6437 1.998315 CTCACCTTGACAGCTTCATCG 59.002 52.381 0.00 0.00 32.84 3.84
4032 6504 9.007901 CCCAATTCAACTTTCAGGATATAGATC 57.992 37.037 0.00 0.00 0.00 2.75
4054 6526 0.257328 TCACTGAAACTGTGCCCCAA 59.743 50.000 0.00 0.00 34.16 4.12
4058 6530 3.715628 ATTTGTCACTGAAACTGTGCC 57.284 42.857 0.00 0.00 34.16 5.01
4563 7107 0.961019 TTTGGCTTCAAAGAGCGCAT 59.039 45.000 11.47 0.00 43.62 4.73
4572 7116 3.554752 GGCTACAGCAATTTTGGCTTCAA 60.555 43.478 3.24 0.00 44.36 2.69
4620 7165 2.093021 TGATGCGATCATTCCTTGACCA 60.093 45.455 0.00 0.00 37.11 4.02
4684 7232 5.473162 TCCACCTTTCTCAATGTTACACATG 59.527 40.000 0.00 0.00 37.97 3.21
4685 7233 5.630121 TCCACCTTTCTCAATGTTACACAT 58.370 37.500 0.00 0.00 41.31 3.21
4686 7234 5.042463 TCCACCTTTCTCAATGTTACACA 57.958 39.130 0.00 0.00 0.00 3.72
4746 7294 2.030262 GCAAACCCGCATGGCAAA 59.970 55.556 0.00 0.00 37.83 3.68
4842 7390 2.311463 CTCAAGGGAGAGCGAGGATAA 58.689 52.381 0.00 0.00 44.26 1.75
4903 7477 4.677673 AGCAGTCTGGCTTTGAAATTTT 57.322 36.364 1.14 0.00 42.71 1.82
4940 7514 1.302832 GCCCCTCACCAGTTCTGTG 60.303 63.158 0.00 0.00 35.01 3.66
4947 7521 2.352805 GTCCAAGCCCCTCACCAG 59.647 66.667 0.00 0.00 0.00 4.00
4948 7522 3.636231 CGTCCAAGCCCCTCACCA 61.636 66.667 0.00 0.00 0.00 4.17
4950 7524 4.329545 TGCGTCCAAGCCCCTCAC 62.330 66.667 0.00 0.00 36.02 3.51
4955 7529 3.365265 CAAGGTGCGTCCAAGCCC 61.365 66.667 0.75 0.00 39.02 5.19
4956 7530 4.043200 GCAAGGTGCGTCCAAGCC 62.043 66.667 0.75 0.00 39.02 4.35
4965 7539 0.668401 GAGTTTGGCATGCAAGGTGC 60.668 55.000 21.36 2.03 45.29 5.01
4966 7540 0.037975 GGAGTTTGGCATGCAAGGTG 60.038 55.000 21.36 0.00 0.00 4.00
4967 7541 0.469705 TGGAGTTTGGCATGCAAGGT 60.470 50.000 21.36 0.00 0.00 3.50
4968 7542 0.680618 TTGGAGTTTGGCATGCAAGG 59.319 50.000 21.36 0.00 0.00 3.61
4970 7544 1.340889 GAGTTGGAGTTTGGCATGCAA 59.659 47.619 21.36 4.92 0.00 4.08
4971 7545 0.961019 GAGTTGGAGTTTGGCATGCA 59.039 50.000 21.36 2.54 0.00 3.96
4972 7546 0.244721 GGAGTTGGAGTTTGGCATGC 59.755 55.000 9.90 9.90 0.00 4.06
4973 7547 0.890683 GGGAGTTGGAGTTTGGCATG 59.109 55.000 0.00 0.00 0.00 4.06
4974 7548 0.779997 AGGGAGTTGGAGTTTGGCAT 59.220 50.000 0.00 0.00 0.00 4.40
4975 7549 0.555769 AAGGGAGTTGGAGTTTGGCA 59.444 50.000 0.00 0.00 0.00 4.92
4976 7550 1.341209 CAAAGGGAGTTGGAGTTTGGC 59.659 52.381 0.00 0.00 0.00 4.52
4997 7571 1.351153 GTTAGTGCACGGAGCTCTTC 58.649 55.000 14.64 0.00 44.16 2.87
4998 7572 0.037232 GGTTAGTGCACGGAGCTCTT 60.037 55.000 14.64 0.00 44.16 2.85
5000 7574 1.448013 GGGTTAGTGCACGGAGCTC 60.448 63.158 12.01 4.71 45.94 4.09
5001 7575 2.663196 GGGTTAGTGCACGGAGCT 59.337 61.111 12.01 0.00 45.94 4.09
5062 8156 1.203174 ACTTTTGGCCCCAACAGCTAT 60.203 47.619 11.98 0.00 37.27 2.97
5107 8203 8.908786 TCTCATTATTTCCTTATTTCGCTGAT 57.091 30.769 0.00 0.00 0.00 2.90
5110 8206 7.500559 AGCTTCTCATTATTTCCTTATTTCGCT 59.499 33.333 0.00 0.00 0.00 4.93
5141 8237 4.021191 TGATGATCGAAAGACAGACGAG 57.979 45.455 0.00 0.00 46.97 4.18
5159 8255 1.301244 GCGATGGCCGATCACTGAT 60.301 57.895 13.41 0.00 41.76 2.90
5231 8345 2.358957 CATGACAGGCGAAGGAATTCA 58.641 47.619 7.93 0.00 0.00 2.57
5303 8417 2.926200 CGCACATTCTTCTCTTCGTCAT 59.074 45.455 0.00 0.00 0.00 3.06
5317 8431 3.319198 ACGACCCTCCCGCACATT 61.319 61.111 0.00 0.00 0.00 2.71
5318 8432 4.082523 CACGACCCTCCCGCACAT 62.083 66.667 0.00 0.00 0.00 3.21
5322 8436 3.834799 CTACCACGACCCTCCCGC 61.835 72.222 0.00 0.00 0.00 6.13
5324 8438 1.304713 TGTCTACCACGACCCTCCC 60.305 63.158 0.00 0.00 32.97 4.30
5325 8439 1.888736 GTGTCTACCACGACCCTCC 59.111 63.158 0.00 0.00 33.61 4.30
5333 8447 4.243270 GTTGTCACCTATGTGTCTACCAC 58.757 47.826 0.00 0.00 43.26 4.16
5334 8448 3.057104 CGTTGTCACCTATGTGTCTACCA 60.057 47.826 0.00 0.00 43.26 3.25
5335 8449 3.508762 CGTTGTCACCTATGTGTCTACC 58.491 50.000 0.00 0.00 43.26 3.18
5336 8450 3.508762 CCGTTGTCACCTATGTGTCTAC 58.491 50.000 0.00 0.02 43.26 2.59
5337 8451 2.094390 GCCGTTGTCACCTATGTGTCTA 60.094 50.000 0.00 0.00 43.26 2.59
5338 8452 1.337823 GCCGTTGTCACCTATGTGTCT 60.338 52.381 0.00 0.00 43.26 3.41
5339 8453 1.076332 GCCGTTGTCACCTATGTGTC 58.924 55.000 0.00 0.00 43.26 3.67
5340 8454 0.669318 CGCCGTTGTCACCTATGTGT 60.669 55.000 0.00 0.00 43.26 3.72
5341 8455 1.358725 CCGCCGTTGTCACCTATGTG 61.359 60.000 0.00 0.00 44.18 3.21
5342 8456 1.079405 CCGCCGTTGTCACCTATGT 60.079 57.895 0.00 0.00 0.00 2.29
5343 8457 1.079405 ACCGCCGTTGTCACCTATG 60.079 57.895 0.00 0.00 0.00 2.23
5344 8458 1.079405 CACCGCCGTTGTCACCTAT 60.079 57.895 0.00 0.00 0.00 2.57
5345 8459 2.340809 CACCGCCGTTGTCACCTA 59.659 61.111 0.00 0.00 0.00 3.08
5346 8460 3.857038 ACACCGCCGTTGTCACCT 61.857 61.111 0.00 0.00 0.00 4.00
5347 8461 3.645975 CACACCGCCGTTGTCACC 61.646 66.667 0.00 0.00 0.00 4.02
5348 8462 2.893404 ACACACCGCCGTTGTCAC 60.893 61.111 0.00 0.00 0.00 3.67
5349 8463 2.892914 CACACACCGCCGTTGTCA 60.893 61.111 0.00 0.00 0.00 3.58
5350 8464 2.893404 ACACACACCGCCGTTGTC 60.893 61.111 0.00 0.00 0.00 3.18
5351 8465 3.199190 CACACACACCGCCGTTGT 61.199 61.111 0.00 0.00 0.00 3.32
5352 8466 3.947841 CCACACACACCGCCGTTG 61.948 66.667 0.00 0.00 0.00 4.10
5356 8470 4.927782 TCAGCCACACACACCGCC 62.928 66.667 0.00 0.00 0.00 6.13
5357 8471 3.649986 GTCAGCCACACACACCGC 61.650 66.667 0.00 0.00 0.00 5.68
5358 8472 1.817520 TTGTCAGCCACACACACCG 60.818 57.895 0.00 0.00 33.41 4.94
5359 8473 1.029408 TGTTGTCAGCCACACACACC 61.029 55.000 0.00 0.00 33.41 4.16
5360 8474 0.378257 CTGTTGTCAGCCACACACAC 59.622 55.000 0.00 0.00 33.41 3.82
5361 8475 0.251634 TCTGTTGTCAGCCACACACA 59.748 50.000 0.00 0.00 41.10 3.72
5362 8476 0.940126 CTCTGTTGTCAGCCACACAC 59.060 55.000 0.00 0.00 41.10 3.82
5363 8477 0.179048 CCTCTGTTGTCAGCCACACA 60.179 55.000 0.00 0.00 41.10 3.72
5370 8484 2.547211 CTGTTGCTTCCTCTGTTGTCAG 59.453 50.000 0.00 0.00 42.54 3.51
5396 8510 1.277557 GTCTTCCTGATGAGCACTGGT 59.722 52.381 0.00 0.00 0.00 4.00
5457 8571 2.224426 ACTATGGGCGTGTTGTTGAGAA 60.224 45.455 0.00 0.00 0.00 2.87
5458 8572 1.346395 ACTATGGGCGTGTTGTTGAGA 59.654 47.619 0.00 0.00 0.00 3.27
5459 8573 1.732259 GACTATGGGCGTGTTGTTGAG 59.268 52.381 0.00 0.00 0.00 3.02
5493 8607 4.151335 GCGTACCATCAGAAGCAATAGATG 59.849 45.833 0.00 0.00 38.03 2.90
5494 8608 4.310769 GCGTACCATCAGAAGCAATAGAT 58.689 43.478 0.00 0.00 0.00 1.98
5495 8609 3.492656 GGCGTACCATCAGAAGCAATAGA 60.493 47.826 0.00 0.00 35.26 1.98
5496 8610 2.802816 GGCGTACCATCAGAAGCAATAG 59.197 50.000 0.00 0.00 35.26 1.73
5497 8611 2.169561 TGGCGTACCATCAGAAGCAATA 59.830 45.455 0.00 0.00 42.67 1.90
5498 8612 1.065491 TGGCGTACCATCAGAAGCAAT 60.065 47.619 0.00 0.00 42.67 3.56
5499 8613 0.323302 TGGCGTACCATCAGAAGCAA 59.677 50.000 0.00 0.00 42.67 3.91
5500 8614 1.979262 TGGCGTACCATCAGAAGCA 59.021 52.632 0.00 0.00 42.67 3.91
5501 8615 4.932789 TGGCGTACCATCAGAAGC 57.067 55.556 0.00 0.00 42.67 3.86
5510 8624 1.607148 GGGCAAATTAGATGGCGTACC 59.393 52.381 0.00 0.00 43.72 3.34
5511 8625 1.607148 GGGGCAAATTAGATGGCGTAC 59.393 52.381 0.00 0.00 43.72 3.67
5512 8626 1.493022 AGGGGCAAATTAGATGGCGTA 59.507 47.619 0.00 0.00 43.72 4.42
5513 8627 0.258774 AGGGGCAAATTAGATGGCGT 59.741 50.000 0.00 0.00 43.72 5.68
5514 8628 2.270352 TAGGGGCAAATTAGATGGCG 57.730 50.000 0.00 0.00 43.72 5.69
5515 8629 3.960755 ACTTTAGGGGCAAATTAGATGGC 59.039 43.478 0.00 0.00 42.20 4.40
5516 8630 5.682212 GCAACTTTAGGGGCAAATTAGATGG 60.682 44.000 0.00 0.00 0.00 3.51
5517 8631 5.127682 AGCAACTTTAGGGGCAAATTAGATG 59.872 40.000 0.00 0.00 0.00 2.90
5518 8632 5.272402 AGCAACTTTAGGGGCAAATTAGAT 58.728 37.500 0.00 0.00 0.00 1.98
5519 8633 4.672899 AGCAACTTTAGGGGCAAATTAGA 58.327 39.130 0.00 0.00 0.00 2.10
5520 8634 6.524101 TTAGCAACTTTAGGGGCAAATTAG 57.476 37.500 0.00 0.00 0.00 1.73
5521 8635 6.919775 TTTAGCAACTTTAGGGGCAAATTA 57.080 33.333 0.00 0.00 0.00 1.40
5522 8636 5.816955 TTTAGCAACTTTAGGGGCAAATT 57.183 34.783 0.00 0.00 0.00 1.82
5523 8637 7.675161 ATATTTAGCAACTTTAGGGGCAAAT 57.325 32.000 0.00 0.00 0.00 2.32
5524 8638 7.489239 AATATTTAGCAACTTTAGGGGCAAA 57.511 32.000 0.00 0.00 0.00 3.68
5525 8639 7.068962 GGTAATATTTAGCAACTTTAGGGGCAA 59.931 37.037 0.00 0.00 0.00 4.52
5526 8640 6.548251 GGTAATATTTAGCAACTTTAGGGGCA 59.452 38.462 0.00 0.00 0.00 5.36
5527 8641 6.015688 GGGTAATATTTAGCAACTTTAGGGGC 60.016 42.308 0.00 0.00 0.00 5.80
5528 8642 7.013942 GTGGGTAATATTTAGCAACTTTAGGGG 59.986 40.741 0.00 0.00 0.00 4.79
5529 8643 7.937649 GTGGGTAATATTTAGCAACTTTAGGG 58.062 38.462 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.