Multiple sequence alignment - TraesCS3D01G001000

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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 TraesCS3D01G001000 chr3D 100.000 2573 0 0 1 2573 639906 642478 0.000000e+00 4752
1 TraesCS3D01G001000 chr3D 88.166 1707 177 10 881 2571 846695 844998 0.000000e+00 2010
2 TraesCS3D01G001000 chr3D 78.351 194 40 2 1094 1286 13427763 13427571 9.670000e-25 124
3 TraesCS3D01G001000 chr3A 88.346 1699 183 11 887 2573 8837585 8839280 0.000000e+00 2026
4 TraesCS3D01G001000 chr3A 91.761 352 29 0 2216 2567 8785946 8786297 8.270000e-135 490
5 TraesCS3D01G001000 chr3A 85.680 419 33 8 35 453 8836385 8836776 1.420000e-112 416
6 TraesCS3D01G001000 chr3A 77.835 194 41 2 1094 1286 23641245 23641437 4.500000e-23 119
7 TraesCS3D01G001000 chr4A 86.949 1701 206 7 887 2573 725162550 725164248 0.000000e+00 1897
8 TraesCS3D01G001000 chr3B 88.417 941 109 0 1631 2571 5983938 5982998 0.000000e+00 1134
9 TraesCS3D01G001000 chr3B 77.041 196 38 6 1094 1286 19397007 19396816 3.500000e-19 106
10 TraesCS3D01G001000 chr1B 76.904 407 85 7 998 1398 9693116 9692713 3.330000e-54 222
11 TraesCS3D01G001000 chr1B 76.786 280 58 5 1137 1411 9611637 9611360 1.590000e-32 150


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 TraesCS3D01G001000 chr3D 639906 642478 2572 False 4752 4752 100.000 1 2573 1 chr3D.!!$F1 2572
1 TraesCS3D01G001000 chr3D 844998 846695 1697 True 2010 2010 88.166 881 2571 1 chr3D.!!$R1 1690
2 TraesCS3D01G001000 chr3A 8836385 8839280 2895 False 1221 2026 87.013 35 2573 2 chr3A.!!$F3 2538
3 TraesCS3D01G001000 chr4A 725162550 725164248 1698 False 1897 1897 86.949 887 2573 1 chr4A.!!$F1 1686
4 TraesCS3D01G001000 chr3B 5982998 5983938 940 True 1134 1134 88.417 1631 2571 1 chr3B.!!$R1 940

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
404 405 0.321671 TCTAGCCAGTGCCACTTCAC 59.678 55.0 0.0 0.0 38.69 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1744 2168 0.031994 GCGTTGGTGGCATCAACTTT 59.968 50.0 33.57 0.0 41.47 2.66 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 21 1.859080 GCTACGAATTAGTCCAAGCCG 59.141 52.381 0.00 0.00 0.00 5.52
21 22 2.737679 GCTACGAATTAGTCCAAGCCGT 60.738 50.000 0.00 0.00 34.12 5.68
22 23 3.489738 GCTACGAATTAGTCCAAGCCGTA 60.490 47.826 0.00 0.00 32.60 4.02
23 24 3.814005 ACGAATTAGTCCAAGCCGTAT 57.186 42.857 0.00 0.00 0.00 3.06
24 25 4.133013 ACGAATTAGTCCAAGCCGTATT 57.867 40.909 0.00 0.00 0.00 1.89
25 26 4.510571 ACGAATTAGTCCAAGCCGTATTT 58.489 39.130 0.00 0.00 0.00 1.40
26 27 5.663456 ACGAATTAGTCCAAGCCGTATTTA 58.337 37.500 0.00 0.00 0.00 1.40
27 28 6.285990 ACGAATTAGTCCAAGCCGTATTTAT 58.714 36.000 0.00 0.00 0.00 1.40
28 29 6.423001 ACGAATTAGTCCAAGCCGTATTTATC 59.577 38.462 0.00 0.00 0.00 1.75
29 30 6.645415 CGAATTAGTCCAAGCCGTATTTATCT 59.355 38.462 0.00 0.00 0.00 1.98
30 31 7.170998 CGAATTAGTCCAAGCCGTATTTATCTT 59.829 37.037 0.00 0.00 0.00 2.40
31 32 7.730364 ATTAGTCCAAGCCGTATTTATCTTG 57.270 36.000 0.00 0.00 36.57 3.02
32 33 5.353394 AGTCCAAGCCGTATTTATCTTGA 57.647 39.130 0.00 0.00 38.45 3.02
33 34 5.360591 AGTCCAAGCCGTATTTATCTTGAG 58.639 41.667 0.00 0.00 38.45 3.02
43 44 5.523552 CGTATTTATCTTGAGCACATCCACA 59.476 40.000 0.00 0.00 0.00 4.17
50 51 0.376152 GAGCACATCCACAGCAATCG 59.624 55.000 0.00 0.00 0.00 3.34
51 52 1.028330 AGCACATCCACAGCAATCGG 61.028 55.000 0.00 0.00 0.00 4.18
56 57 1.399440 CATCCACAGCAATCGGTTCTG 59.601 52.381 6.39 6.39 0.00 3.02
62 63 2.749621 ACAGCAATCGGTTCTGAATTCC 59.250 45.455 12.78 0.00 0.00 3.01
63 64 2.098117 CAGCAATCGGTTCTGAATTCCC 59.902 50.000 2.27 0.00 0.00 3.97
94 95 6.320164 GGACATATATGTTGGCCAAAAGTACA 59.680 38.462 22.47 15.30 42.29 2.90
107 108 8.710239 TGGCCAAAAGTACATATATACTTGAGA 58.290 33.333 0.61 0.00 43.17 3.27
113 114 8.887264 AAGTACATATATACTTGAGAGGAGGG 57.113 38.462 5.60 0.00 42.53 4.30
117 118 0.760945 ATACTTGAGAGGAGGGCGGG 60.761 60.000 0.00 0.00 0.00 6.13
184 185 6.173339 TCTTGAGATTCACAGGGTGATAAAC 58.827 40.000 0.00 0.00 42.40 2.01
192 193 5.914033 TCACAGGGTGATAAACTAGTATGC 58.086 41.667 0.00 0.00 37.67 3.14
200 201 8.531982 GGGTGATAAACTAGTATGCTATCATCA 58.468 37.037 19.12 9.06 33.57 3.07
203 204 9.533831 TGATAAACTAGTATGCTATCATCAGGA 57.466 33.333 0.00 0.00 34.22 3.86
208 209 5.495926 AGTATGCTATCATCAGGAAAGGG 57.504 43.478 0.00 0.00 34.22 3.95
219 220 7.406620 TCATCAGGAAAGGGGATATGTATTT 57.593 36.000 0.00 0.00 0.00 1.40
239 240 3.023939 TCTCAGCCTTGATCAGAGCTA 57.976 47.619 18.09 4.15 33.33 3.32
240 241 3.574749 TCTCAGCCTTGATCAGAGCTAT 58.425 45.455 18.09 0.00 33.33 2.97
241 242 4.734266 TCTCAGCCTTGATCAGAGCTATA 58.266 43.478 18.09 10.56 33.33 1.31
242 243 5.331906 TCTCAGCCTTGATCAGAGCTATAT 58.668 41.667 18.09 0.00 33.33 0.86
258 259 5.769367 AGCTATATATCTTTTGACGCGTGA 58.231 37.500 20.70 4.74 0.00 4.35
283 284 9.282247 GAATCTGACAATAATACTTTGTGCTTG 57.718 33.333 0.00 0.00 37.43 4.01
291 292 2.314323 ACTTTGTGCTTGCAAAAGGG 57.686 45.000 21.69 12.95 37.82 3.95
296 297 0.678950 GTGCTTGCAAAAGGGCCTAA 59.321 50.000 6.41 0.00 0.00 2.69
302 303 4.322725 GCTTGCAAAAGGGCCTAATTAACT 60.323 41.667 6.41 0.00 0.00 2.24
304 305 6.573485 GCTTGCAAAAGGGCCTAATTAACTAA 60.573 38.462 6.41 0.00 0.00 2.24
349 350 1.299648 CATCGGGGCAGGAACTTCA 59.700 57.895 0.00 0.00 34.60 3.02
350 351 0.322456 CATCGGGGCAGGAACTTCAA 60.322 55.000 0.00 0.00 34.60 2.69
353 354 1.631388 TCGGGGCAGGAACTTCAATTA 59.369 47.619 0.00 0.00 34.60 1.40
354 355 2.017049 CGGGGCAGGAACTTCAATTAG 58.983 52.381 0.00 0.00 34.60 1.73
355 356 1.751351 GGGGCAGGAACTTCAATTAGC 59.249 52.381 0.00 0.00 34.60 3.09
356 357 2.621668 GGGGCAGGAACTTCAATTAGCT 60.622 50.000 0.00 0.00 34.60 3.32
357 358 2.424956 GGGCAGGAACTTCAATTAGCTG 59.575 50.000 0.00 0.00 34.60 4.24
358 359 3.347216 GGCAGGAACTTCAATTAGCTGA 58.653 45.455 0.00 0.00 34.60 4.26
359 360 3.950395 GGCAGGAACTTCAATTAGCTGAT 59.050 43.478 0.00 0.00 34.60 2.90
360 361 4.201990 GGCAGGAACTTCAATTAGCTGATG 60.202 45.833 0.00 0.00 34.60 3.07
361 362 4.637534 GCAGGAACTTCAATTAGCTGATGA 59.362 41.667 0.00 0.00 34.60 2.92
362 363 5.124457 GCAGGAACTTCAATTAGCTGATGAA 59.876 40.000 0.00 3.47 34.60 2.57
363 364 6.549952 CAGGAACTTCAATTAGCTGATGAAC 58.450 40.000 0.00 0.00 34.60 3.18
364 365 6.149973 CAGGAACTTCAATTAGCTGATGAACA 59.850 38.462 0.00 0.00 34.60 3.18
365 366 6.716628 AGGAACTTCAATTAGCTGATGAACAA 59.283 34.615 0.00 0.00 27.25 2.83
366 367 7.395489 AGGAACTTCAATTAGCTGATGAACAAT 59.605 33.333 0.00 0.00 27.25 2.71
367 368 8.677300 GGAACTTCAATTAGCTGATGAACAATA 58.323 33.333 0.00 0.00 0.00 1.90
372 373 9.720667 TTCAATTAGCTGATGAACAATATTTCG 57.279 29.630 0.00 0.00 0.00 3.46
373 374 8.892723 TCAATTAGCTGATGAACAATATTTCGT 58.107 29.630 0.00 0.00 0.00 3.85
374 375 9.507280 CAATTAGCTGATGAACAATATTTCGTT 57.493 29.630 0.00 0.00 0.00 3.85
393 394 5.601662 TCGTTTAGATCCAAATCTAGCCAG 58.398 41.667 0.00 0.00 43.64 4.85
404 405 0.321671 TCTAGCCAGTGCCACTTCAC 59.678 55.000 0.00 0.00 38.69 3.18
415 416 5.048504 CAGTGCCACTTCACAAACTATTCAT 60.049 40.000 0.00 0.00 39.35 2.57
417 418 6.714810 AGTGCCACTTCACAAACTATTCATTA 59.285 34.615 0.00 0.00 39.35 1.90
421 422 8.391106 GCCACTTCACAAACTATTCATTAGTAG 58.609 37.037 0.00 0.00 40.37 2.57
425 426 9.979270 CTTCACAAACTATTCATTAGTAGCAAG 57.021 33.333 0.00 0.00 40.37 4.01
446 447 6.204882 GCAAGGAGTAAAAAGAGTAAGCAAGA 59.795 38.462 0.00 0.00 0.00 3.02
448 449 7.913674 AGGAGTAAAAAGAGTAAGCAAGATG 57.086 36.000 0.00 0.00 0.00 2.90
453 454 8.778358 AGTAAAAAGAGTAAGCAAGATGAACAG 58.222 33.333 0.00 0.00 0.00 3.16
454 455 7.807977 AAAAAGAGTAAGCAAGATGAACAGA 57.192 32.000 0.00 0.00 0.00 3.41
455 456 7.432350 AAAAGAGTAAGCAAGATGAACAGAG 57.568 36.000 0.00 0.00 0.00 3.35
461 617 3.924144 AGCAAGATGAACAGAGTCTCAC 58.076 45.455 1.94 0.00 0.00 3.51
501 801 3.202818 TGTTTAGGTGGATGATGGCTCAT 59.797 43.478 0.02 0.02 44.93 2.90
503 803 1.514983 AGGTGGATGATGGCTCATGA 58.485 50.000 0.00 0.00 42.27 3.07
505 805 1.142465 GGTGGATGATGGCTCATGAGT 59.858 52.381 23.38 4.19 42.27 3.41
508 808 2.367894 TGGATGATGGCTCATGAGTCTC 59.632 50.000 26.71 20.39 42.27 3.36
509 809 2.367894 GGATGATGGCTCATGAGTCTCA 59.632 50.000 26.71 24.49 42.27 3.27
510 810 2.975732 TGATGGCTCATGAGTCTCAC 57.024 50.000 26.71 17.49 33.37 3.51
512 812 0.835941 ATGGCTCATGAGTCTCACCC 59.164 55.000 26.71 16.65 33.37 4.61
513 813 1.267574 TGGCTCATGAGTCTCACCCC 61.268 60.000 26.71 15.98 33.37 4.95
516 816 1.211457 GCTCATGAGTCTCACCCCAAT 59.789 52.381 23.38 0.00 0.00 3.16
517 817 2.435805 GCTCATGAGTCTCACCCCAATA 59.564 50.000 23.38 0.00 0.00 1.90
535 867 5.392380 CCCAATAGTCATGTGCAGTTTCTTC 60.392 44.000 0.00 0.00 0.00 2.87
539 871 3.562973 AGTCATGTGCAGTTTCTTCACTG 59.437 43.478 0.00 0.00 46.15 3.66
544 876 2.615912 GTGCAGTTTCTTCACTGAAGCT 59.384 45.455 13.24 3.26 46.29 3.74
552 884 6.429385 AGTTTCTTCACTGAAGCTTTGGATAG 59.571 38.462 13.24 0.00 39.29 2.08
564 896 7.613022 TGAAGCTTTGGATAGAAATTGAGATGT 59.387 33.333 0.00 0.00 0.00 3.06
599 931 6.480763 TCTACAGGCAAGGATTTCAATGTAA 58.519 36.000 0.00 0.00 0.00 2.41
625 957 6.363577 TGATGAAACTTTCAGTTCTGTCAC 57.636 37.500 9.97 0.00 43.98 3.67
626 958 5.879777 TGATGAAACTTTCAGTTCTGTCACA 59.120 36.000 9.97 0.00 43.98 3.58
627 959 5.801350 TGAAACTTTCAGTTCTGTCACAG 57.199 39.130 0.00 0.00 37.47 3.66
628 960 4.635765 TGAAACTTTCAGTTCTGTCACAGG 59.364 41.667 4.57 0.00 37.47 4.00
632 964 4.396166 ACTTTCAGTTCTGTCACAGGTTTG 59.604 41.667 4.57 1.12 31.51 2.93
635 967 2.017049 AGTTCTGTCACAGGTTTGCAC 58.983 47.619 4.57 0.00 31.51 4.57
636 968 2.017049 GTTCTGTCACAGGTTTGCACT 58.983 47.619 4.57 0.00 31.51 4.40
637 969 2.418368 TCTGTCACAGGTTTGCACTT 57.582 45.000 4.57 0.00 31.51 3.16
638 970 2.016318 TCTGTCACAGGTTTGCACTTG 58.984 47.619 4.57 0.00 36.07 3.16
639 971 1.745087 CTGTCACAGGTTTGCACTTGT 59.255 47.619 0.00 0.00 43.80 3.16
643 975 1.544724 ACAGGTTTGCACTTGTGTGT 58.455 45.000 2.61 0.00 41.51 3.72
644 976 1.202114 ACAGGTTTGCACTTGTGTGTG 59.798 47.619 2.61 0.00 41.51 3.82
646 978 1.202114 AGGTTTGCACTTGTGTGTGTG 59.798 47.619 2.61 0.00 45.44 3.82
648 980 1.984990 GTTTGCACTTGTGTGTGTGTG 59.015 47.619 2.61 0.00 45.44 3.82
658 990 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
659 991 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
661 993 2.480802 GTGTGTGTGTGTGTGTGTGTTA 59.519 45.455 0.00 0.00 0.00 2.41
669 1001 5.239744 TGTGTGTGTGTGTGTTAGTTTCTTT 59.760 36.000 0.00 0.00 0.00 2.52
671 1003 4.557301 GTGTGTGTGTGTTAGTTTCTTTGC 59.443 41.667 0.00 0.00 0.00 3.68
674 1006 5.963586 GTGTGTGTGTTAGTTTCTTTGCTAC 59.036 40.000 0.00 0.00 0.00 3.58
676 1008 5.963586 GTGTGTGTTAGTTTCTTTGCTACAC 59.036 40.000 0.00 0.00 0.00 2.90
680 1012 6.320164 TGTGTTAGTTTCTTTGCTACACCATT 59.680 34.615 0.00 0.00 0.00 3.16
681 1013 7.499563 TGTGTTAGTTTCTTTGCTACACCATTA 59.500 33.333 0.00 0.00 0.00 1.90
683 1015 9.073475 TGTTAGTTTCTTTGCTACACCATTATT 57.927 29.630 0.00 0.00 0.00 1.40
747 1079 9.225682 ACTAATAAAAATGAGAGGATAGGGACA 57.774 33.333 0.00 0.00 0.00 4.02
748 1080 9.717942 CTAATAAAAATGAGAGGATAGGGACAG 57.282 37.037 0.00 0.00 0.00 3.51
764 1096 1.827789 CAGTGGTGGTGGTGGTTGG 60.828 63.158 0.00 0.00 0.00 3.77
791 1123 3.069586 AGACGAATGTGTCCAGAAAGTCA 59.930 43.478 0.00 0.00 39.77 3.41
804 1136 2.443255 AGAAAGTCATCAGTTGGTGGGT 59.557 45.455 0.00 0.00 0.00 4.51
806 1138 1.434188 AGTCATCAGTTGGTGGGTCA 58.566 50.000 0.00 0.00 0.00 4.02
807 1139 1.988107 AGTCATCAGTTGGTGGGTCAT 59.012 47.619 0.00 0.00 0.00 3.06
808 1140 2.086869 GTCATCAGTTGGTGGGTCATG 58.913 52.381 0.00 0.00 0.00 3.07
815 1147 0.398696 TTGGTGGGTCATGCGTACTT 59.601 50.000 0.00 0.00 0.00 2.24
828 1223 4.466567 TGCGTACTTGCATATACAATGC 57.533 40.909 3.05 3.05 40.62 3.56
842 1237 2.387757 ACAATGCCAACTTGGTTGAGT 58.612 42.857 14.98 5.57 45.28 3.41
843 1238 2.101249 ACAATGCCAACTTGGTTGAGTG 59.899 45.455 14.98 9.25 45.28 3.51
845 1240 1.008538 GCCAACTTGGTTGAGTGCG 60.009 57.895 9.63 0.00 45.28 5.34
846 1241 1.008538 CCAACTTGGTTGAGTGCGC 60.009 57.895 0.00 0.00 45.28 6.09
853 1248 1.725641 TGGTTGAGTGCGCTGATTAG 58.274 50.000 3.44 0.00 0.00 1.73
854 1249 1.275010 TGGTTGAGTGCGCTGATTAGA 59.725 47.619 3.44 0.00 0.00 2.10
855 1250 2.093500 TGGTTGAGTGCGCTGATTAGAT 60.093 45.455 3.44 0.00 0.00 1.98
856 1251 2.939103 GGTTGAGTGCGCTGATTAGATT 59.061 45.455 3.44 0.00 0.00 2.40
857 1252 3.001736 GGTTGAGTGCGCTGATTAGATTC 59.998 47.826 3.44 0.00 0.00 2.52
858 1253 2.826428 TGAGTGCGCTGATTAGATTCC 58.174 47.619 3.44 0.00 0.00 3.01
859 1254 2.432146 TGAGTGCGCTGATTAGATTCCT 59.568 45.455 3.44 0.00 0.00 3.36
860 1255 2.799412 GAGTGCGCTGATTAGATTCCTG 59.201 50.000 3.44 0.00 0.00 3.86
861 1256 2.169352 AGTGCGCTGATTAGATTCCTGT 59.831 45.455 9.73 0.00 0.00 4.00
862 1257 2.286294 GTGCGCTGATTAGATTCCTGTG 59.714 50.000 9.73 0.00 0.00 3.66
863 1258 2.168313 TGCGCTGATTAGATTCCTGTGA 59.832 45.455 9.73 0.00 0.00 3.58
864 1259 2.799412 GCGCTGATTAGATTCCTGTGAG 59.201 50.000 0.00 0.00 0.00 3.51
865 1260 3.491619 GCGCTGATTAGATTCCTGTGAGA 60.492 47.826 0.00 0.00 0.00 3.27
866 1261 4.047822 CGCTGATTAGATTCCTGTGAGAC 58.952 47.826 0.00 0.00 0.00 3.36
867 1262 4.376146 GCTGATTAGATTCCTGTGAGACC 58.624 47.826 0.00 0.00 0.00 3.85
868 1263 4.141846 GCTGATTAGATTCCTGTGAGACCA 60.142 45.833 0.00 0.00 0.00 4.02
869 1264 5.599732 CTGATTAGATTCCTGTGAGACCAG 58.400 45.833 0.00 0.00 0.00 4.00
870 1265 5.272402 TGATTAGATTCCTGTGAGACCAGA 58.728 41.667 0.00 0.00 34.23 3.86
871 1266 5.127845 TGATTAGATTCCTGTGAGACCAGAC 59.872 44.000 0.00 0.00 34.23 3.51
872 1267 2.894731 AGATTCCTGTGAGACCAGACA 58.105 47.619 0.00 0.00 34.23 3.41
873 1268 2.830923 AGATTCCTGTGAGACCAGACAG 59.169 50.000 0.00 0.00 39.51 3.51
885 1296 1.697982 ACCAGACAGTAACTTGGTCCC 59.302 52.381 0.00 0.00 31.99 4.46
914 1325 5.473504 ACTTTTCATCACATGACCACCTAAC 59.526 40.000 0.00 0.00 39.39 2.34
915 1326 4.632327 TTCATCACATGACCACCTAACA 57.368 40.909 0.00 0.00 39.39 2.41
916 1327 3.937814 TCATCACATGACCACCTAACAC 58.062 45.455 0.00 0.00 33.59 3.32
917 1328 3.582647 TCATCACATGACCACCTAACACT 59.417 43.478 0.00 0.00 33.59 3.55
918 1329 3.678056 TCACATGACCACCTAACACTC 57.322 47.619 0.00 0.00 0.00 3.51
968 1392 2.287188 CGCATACACCAGATCCATTTGC 60.287 50.000 0.00 0.00 0.00 3.68
1073 1497 1.518903 AAAGAGGCAGCAACCTTCGC 61.519 55.000 0.00 0.00 41.32 4.70
1075 1499 1.079127 GAGGCAGCAACCTTCGCTA 60.079 57.895 0.00 0.00 41.32 4.26
1077 1501 2.740714 GGCAGCAACCTTCGCTACG 61.741 63.158 0.00 0.00 37.72 3.51
1081 1505 0.388649 AGCAACCTTCGCTACGTCAG 60.389 55.000 0.00 0.00 38.15 3.51
1089 1513 0.380733 TCGCTACGTCAGTGCTATGG 59.619 55.000 0.00 0.00 34.56 2.74
1110 1534 0.700564 AGGAAGCATCTGCCCTCAAA 59.299 50.000 0.00 0.00 43.38 2.69
1170 1594 1.898472 GAGAGCATGCAGGCCTATCTA 59.102 52.381 21.42 0.00 0.00 1.98
1219 1643 2.915659 AGACCACCGGCGTCTTCA 60.916 61.111 17.01 0.00 37.28 3.02
1239 1663 2.978156 TCAACAAGATCAGGGGCTTT 57.022 45.000 0.00 0.00 0.00 3.51
1310 1734 1.217057 AGGCATGGGGGATTCACTGT 61.217 55.000 0.00 0.00 0.00 3.55
1323 1747 5.707298 GGGATTCACTGTGAAGATGAAGAAA 59.293 40.000 25.40 1.96 40.05 2.52
1332 1756 5.299279 TGTGAAGATGAAGAAAAGGGTCAAC 59.701 40.000 0.00 0.00 0.00 3.18
1362 1786 2.616330 ATGGCGCCGTTTGACACTG 61.616 57.895 23.90 0.00 0.00 3.66
1446 1870 1.936631 AGAGGGATTGAGAGAGAGGGT 59.063 52.381 0.00 0.00 0.00 4.34
1494 1918 4.259356 CTGACCATTCTCTGAATCTTGCA 58.741 43.478 0.00 0.00 0.00 4.08
1524 1948 3.269381 AGGATCTTGTGGGCATTAAGGAA 59.731 43.478 0.00 0.00 0.00 3.36
1570 1994 1.715931 TGGTGGGTGATTTGGAGGAAT 59.284 47.619 0.00 0.00 0.00 3.01
1706 2130 5.730550 TGTATCAAGTAGCTACCAAGTTGG 58.269 41.667 20.76 20.76 45.02 3.77
1734 2158 3.745975 TGTTAAAACAGATCGCCAGTGAG 59.254 43.478 0.00 0.00 34.30 3.51
1743 2167 4.102113 GCCAGTGAGTTGGGCATT 57.898 55.556 0.00 0.00 46.92 3.56
1744 2168 3.264574 GCCAGTGAGTTGGGCATTA 57.735 52.632 0.00 0.00 46.92 1.90
1745 2169 1.544724 GCCAGTGAGTTGGGCATTAA 58.455 50.000 0.00 0.00 46.92 1.40
1747 2171 2.094545 GCCAGTGAGTTGGGCATTAAAG 60.095 50.000 0.00 0.00 46.92 1.85
1751 2175 4.278170 CAGTGAGTTGGGCATTAAAGTTGA 59.722 41.667 0.00 0.00 0.00 3.18
1754 2178 4.176271 GAGTTGGGCATTAAAGTTGATGC 58.824 43.478 11.28 11.28 45.99 3.91
1795 2219 3.452627 CCTGGTTGAGGTAATCTGTAGCT 59.547 47.826 0.00 0.00 37.02 3.32
1800 2224 6.611642 TGGTTGAGGTAATCTGTAGCTATCTT 59.388 38.462 0.00 0.00 0.00 2.40
1816 2240 9.771534 GTAGCTATCTTCAAGGTTCAGAATATT 57.228 33.333 0.00 0.00 0.00 1.28
1896 2320 0.603569 CTACAGAAGGCACTGGTCGT 59.396 55.000 14.24 0.00 40.86 4.34
1933 2357 4.851639 AGAATTCAGGAGGTAGCATTGT 57.148 40.909 8.44 0.00 0.00 2.71
2041 2465 0.399091 TGGGGACAAAACATGCCCAA 60.399 50.000 1.22 0.00 43.34 4.12
2050 2474 4.407296 ACAAAACATGCCCAAAGGAACTAA 59.593 37.500 0.00 0.00 38.49 2.24
2138 2562 1.816835 CTTGTTGTCATGCAGGCATCT 59.183 47.619 3.30 0.00 33.90 2.90
2202 2626 7.658261 AGTCGCAGCTTAGTAATAATGTGATA 58.342 34.615 3.85 0.00 30.78 2.15
2236 2660 3.698029 TTGTTCTGAAAGTCAGCTTGC 57.302 42.857 0.17 0.00 43.95 4.01
2250 2674 1.856265 GCTTGCAGGACCTTCCAACG 61.856 60.000 0.00 0.00 39.61 4.10
2353 2777 4.036734 GGATCGCAGCTGGATTCATTAAAA 59.963 41.667 17.12 0.00 0.00 1.52
2376 2800 5.766150 AAACATCGAACAGAACATTGGAA 57.234 34.783 0.00 0.00 0.00 3.53
2496 2920 3.006940 TGACATTATCCGTGTTCTTGCC 58.993 45.455 0.00 0.00 0.00 4.52
2526 2950 5.911378 AATCAGAAGAGGAATCCTTTTGC 57.089 39.130 10.01 2.44 31.76 3.68
2550 2974 5.336451 CCAAGTTTACAATGGCTTAAGACCC 60.336 44.000 5.69 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.859080 CGGCTTGGACTAATTCGTAGC 59.141 52.381 0.00 0.00 32.45 3.58
1 2 3.160777 ACGGCTTGGACTAATTCGTAG 57.839 47.619 0.00 0.00 35.75 3.51
2 3 4.924305 ATACGGCTTGGACTAATTCGTA 57.076 40.909 8.24 8.24 35.30 3.43
3 4 3.814005 ATACGGCTTGGACTAATTCGT 57.186 42.857 0.00 0.00 33.54 3.85
4 5 6.645415 AGATAAATACGGCTTGGACTAATTCG 59.355 38.462 0.00 0.00 0.00 3.34
5 6 7.964604 AGATAAATACGGCTTGGACTAATTC 57.035 36.000 0.00 0.00 0.00 2.17
6 7 7.990886 TCAAGATAAATACGGCTTGGACTAATT 59.009 33.333 0.00 0.00 38.53 1.40
7 8 7.506114 TCAAGATAAATACGGCTTGGACTAAT 58.494 34.615 0.00 0.00 38.53 1.73
8 9 6.880484 TCAAGATAAATACGGCTTGGACTAA 58.120 36.000 0.00 0.00 38.53 2.24
9 10 6.474140 TCAAGATAAATACGGCTTGGACTA 57.526 37.500 0.00 0.00 38.53 2.59
10 11 5.353394 TCAAGATAAATACGGCTTGGACT 57.647 39.130 0.00 0.00 38.53 3.85
11 12 4.024809 GCTCAAGATAAATACGGCTTGGAC 60.025 45.833 0.00 0.00 38.53 4.02
12 13 4.127171 GCTCAAGATAAATACGGCTTGGA 58.873 43.478 0.00 0.00 38.53 3.53
13 14 3.876914 TGCTCAAGATAAATACGGCTTGG 59.123 43.478 0.00 0.00 38.53 3.61
14 15 4.332543 TGTGCTCAAGATAAATACGGCTTG 59.667 41.667 0.00 0.00 39.17 4.01
15 16 4.513442 TGTGCTCAAGATAAATACGGCTT 58.487 39.130 0.00 0.00 0.00 4.35
16 17 4.137116 TGTGCTCAAGATAAATACGGCT 57.863 40.909 0.00 0.00 0.00 5.52
17 18 4.083802 GGATGTGCTCAAGATAAATACGGC 60.084 45.833 0.00 0.00 0.00 5.68
18 19 5.050091 GTGGATGTGCTCAAGATAAATACGG 60.050 44.000 0.00 0.00 0.00 4.02
19 20 5.523552 TGTGGATGTGCTCAAGATAAATACG 59.476 40.000 0.00 0.00 0.00 3.06
20 21 6.512415 GCTGTGGATGTGCTCAAGATAAATAC 60.512 42.308 0.00 0.00 0.00 1.89
21 22 5.528690 GCTGTGGATGTGCTCAAGATAAATA 59.471 40.000 0.00 0.00 0.00 1.40
22 23 4.337555 GCTGTGGATGTGCTCAAGATAAAT 59.662 41.667 0.00 0.00 0.00 1.40
23 24 3.691118 GCTGTGGATGTGCTCAAGATAAA 59.309 43.478 0.00 0.00 0.00 1.40
24 25 3.273434 GCTGTGGATGTGCTCAAGATAA 58.727 45.455 0.00 0.00 0.00 1.75
25 26 2.236893 TGCTGTGGATGTGCTCAAGATA 59.763 45.455 0.00 0.00 0.00 1.98
26 27 1.003928 TGCTGTGGATGTGCTCAAGAT 59.996 47.619 0.00 0.00 0.00 2.40
27 28 0.397564 TGCTGTGGATGTGCTCAAGA 59.602 50.000 0.00 0.00 0.00 3.02
28 29 1.241165 TTGCTGTGGATGTGCTCAAG 58.759 50.000 0.00 0.00 0.00 3.02
29 30 1.814394 GATTGCTGTGGATGTGCTCAA 59.186 47.619 0.00 0.00 0.00 3.02
30 31 1.456296 GATTGCTGTGGATGTGCTCA 58.544 50.000 0.00 0.00 0.00 4.26
31 32 0.376152 CGATTGCTGTGGATGTGCTC 59.624 55.000 0.00 0.00 0.00 4.26
32 33 1.028330 CCGATTGCTGTGGATGTGCT 61.028 55.000 0.00 0.00 0.00 4.40
33 34 1.308069 ACCGATTGCTGTGGATGTGC 61.308 55.000 0.00 0.00 0.00 4.57
43 44 2.369394 GGGAATTCAGAACCGATTGCT 58.631 47.619 7.93 0.00 0.00 3.91
50 51 2.102578 CCATGTGGGGAATTCAGAACC 58.897 52.381 7.93 4.44 0.00 3.62
51 52 2.755103 GTCCATGTGGGGAATTCAGAAC 59.245 50.000 7.93 2.46 39.05 3.01
56 57 6.248433 ACATATATGTCCATGTGGGGAATTC 58.752 40.000 12.75 0.00 39.05 2.17
62 63 3.507233 GCCAACATATATGTCCATGTGGG 59.493 47.826 24.88 12.43 45.55 4.61
63 64 3.507233 GGCCAACATATATGTCCATGTGG 59.493 47.826 21.70 21.70 40.80 4.17
94 95 4.282496 CCGCCCTCCTCTCAAGTATATAT 58.718 47.826 0.00 0.00 0.00 0.86
117 118 4.207019 GCAAATTAATTAGCATGTCGGTGC 59.793 41.667 0.01 0.04 45.38 5.01
121 122 7.847078 CCAAAATGCAAATTAATTAGCATGTCG 59.153 33.333 9.84 0.00 46.10 4.35
123 124 8.452534 CACCAAAATGCAAATTAATTAGCATGT 58.547 29.630 9.84 3.21 46.10 3.21
184 185 6.351711 CCCCTTTCCTGATGATAGCATACTAG 60.352 46.154 0.00 0.00 34.11 2.57
192 193 6.633325 ACATATCCCCTTTCCTGATGATAG 57.367 41.667 0.00 0.00 0.00 2.08
200 201 6.466470 GCTGAGAAATACATATCCCCTTTCCT 60.466 42.308 0.00 0.00 0.00 3.36
203 204 5.373854 AGGCTGAGAAATACATATCCCCTTT 59.626 40.000 0.00 0.00 0.00 3.11
208 209 7.164122 TGATCAAGGCTGAGAAATACATATCC 58.836 38.462 0.00 0.00 34.23 2.59
219 220 1.863325 AGCTCTGATCAAGGCTGAGA 58.137 50.000 17.70 0.66 34.23 3.27
239 240 6.923508 TCAGATTCACGCGTCAAAAGATATAT 59.076 34.615 9.86 0.00 0.00 0.86
240 241 6.198403 GTCAGATTCACGCGTCAAAAGATATA 59.802 38.462 9.86 0.00 0.00 0.86
241 242 5.005779 GTCAGATTCACGCGTCAAAAGATAT 59.994 40.000 9.86 0.01 0.00 1.63
242 243 4.326278 GTCAGATTCACGCGTCAAAAGATA 59.674 41.667 9.86 0.00 0.00 1.98
258 259 7.756722 GCAAGCACAAAGTATTATTGTCAGATT 59.243 33.333 0.00 0.00 38.90 2.40
283 284 5.681437 GCCTTAGTTAATTAGGCCCTTTTGC 60.681 44.000 0.00 0.00 46.94 3.68
311 312 2.101415 TGGTCATGATCCGTTAGCTCAG 59.899 50.000 2.86 0.00 0.00 3.35
318 319 0.106708 CCCGATGGTCATGATCCGTT 59.893 55.000 2.86 0.00 0.00 4.44
353 354 8.492673 TCTAAACGAAATATTGTTCATCAGCT 57.507 30.769 0.00 0.00 31.71 4.24
354 355 9.374960 GATCTAAACGAAATATTGTTCATCAGC 57.625 33.333 0.00 0.00 31.71 4.26
355 356 9.869844 GGATCTAAACGAAATATTGTTCATCAG 57.130 33.333 0.00 0.00 31.71 2.90
356 357 9.389755 TGGATCTAAACGAAATATTGTTCATCA 57.610 29.630 0.00 0.00 31.71 3.07
365 366 9.220767 GGCTAGATTTGGATCTAAACGAAATAT 57.779 33.333 6.37 0.00 42.71 1.28
366 367 8.208224 TGGCTAGATTTGGATCTAAACGAAATA 58.792 33.333 6.37 0.00 42.71 1.40
367 368 7.054124 TGGCTAGATTTGGATCTAAACGAAAT 58.946 34.615 6.37 0.00 42.71 2.17
368 369 6.411376 TGGCTAGATTTGGATCTAAACGAAA 58.589 36.000 6.37 0.00 42.71 3.46
369 370 5.984725 TGGCTAGATTTGGATCTAAACGAA 58.015 37.500 6.37 0.00 42.71 3.85
370 371 5.128827 ACTGGCTAGATTTGGATCTAAACGA 59.871 40.000 6.37 0.00 42.71 3.85
371 372 5.235186 CACTGGCTAGATTTGGATCTAAACG 59.765 44.000 6.37 0.00 42.71 3.60
372 373 5.008118 GCACTGGCTAGATTTGGATCTAAAC 59.992 44.000 6.37 1.77 42.71 2.01
373 374 5.126067 GCACTGGCTAGATTTGGATCTAAA 58.874 41.667 3.17 6.71 42.71 1.85
374 375 4.444876 GGCACTGGCTAGATTTGGATCTAA 60.445 45.833 3.17 0.00 42.71 2.10
375 376 3.071602 GGCACTGGCTAGATTTGGATCTA 59.928 47.826 3.17 0.00 41.55 1.98
393 394 4.829064 TGAATAGTTTGTGAAGTGGCAC 57.171 40.909 10.29 10.29 39.22 5.01
404 405 8.723942 ACTCCTTGCTACTAATGAATAGTTTG 57.276 34.615 0.00 0.00 42.31 2.93
415 416 9.924650 CTTACTCTTTTTACTCCTTGCTACTAA 57.075 33.333 0.00 0.00 0.00 2.24
417 418 6.874664 GCTTACTCTTTTTACTCCTTGCTACT 59.125 38.462 0.00 0.00 0.00 2.57
421 422 5.941948 TGCTTACTCTTTTTACTCCTTGC 57.058 39.130 0.00 0.00 0.00 4.01
425 426 7.907214 TCATCTTGCTTACTCTTTTTACTCC 57.093 36.000 0.00 0.00 0.00 3.85
446 447 2.030027 TGGGGTGAGACTCTGTTCAT 57.970 50.000 3.68 0.00 0.00 2.57
448 449 3.118592 CCTATTGGGGTGAGACTCTGTTC 60.119 52.174 3.68 0.00 0.00 3.18
453 454 3.108376 AGAACCTATTGGGGTGAGACTC 58.892 50.000 0.00 0.00 39.85 3.36
454 455 3.108376 GAGAACCTATTGGGGTGAGACT 58.892 50.000 0.00 0.00 39.85 3.24
455 456 2.838202 TGAGAACCTATTGGGGTGAGAC 59.162 50.000 0.00 0.00 39.85 3.36
461 617 1.916181 ACAGGTGAGAACCTATTGGGG 59.084 52.381 0.00 0.00 38.22 4.96
479 776 2.575735 TGAGCCATCATCCACCTAAACA 59.424 45.455 0.00 0.00 0.00 2.83
481 778 3.459227 TCATGAGCCATCATCCACCTAAA 59.541 43.478 0.00 0.00 44.58 1.85
482 779 3.047857 TCATGAGCCATCATCCACCTAA 58.952 45.455 0.00 0.00 44.58 2.69
484 781 1.420514 CTCATGAGCCATCATCCACCT 59.579 52.381 10.38 0.00 44.58 4.00
485 782 1.142465 ACTCATGAGCCATCATCCACC 59.858 52.381 22.83 0.00 44.58 4.61
487 787 2.367894 GAGACTCATGAGCCATCATCCA 59.632 50.000 22.83 0.00 44.58 3.41
491 791 1.483827 GGTGAGACTCATGAGCCATCA 59.516 52.381 22.83 19.31 40.50 3.07
501 801 3.184382 TGACTATTGGGGTGAGACTCA 57.816 47.619 0.00 0.00 0.00 3.41
503 803 3.198635 CACATGACTATTGGGGTGAGACT 59.801 47.826 0.00 0.00 0.00 3.24
505 805 2.092968 GCACATGACTATTGGGGTGAGA 60.093 50.000 0.00 0.00 0.00 3.27
508 808 2.019249 CTGCACATGACTATTGGGGTG 58.981 52.381 0.00 0.00 0.00 4.61
509 809 1.635487 ACTGCACATGACTATTGGGGT 59.365 47.619 0.00 0.00 0.00 4.95
510 810 2.425143 ACTGCACATGACTATTGGGG 57.575 50.000 0.00 0.00 0.00 4.96
512 812 5.181811 TGAAGAAACTGCACATGACTATTGG 59.818 40.000 0.00 0.00 0.00 3.16
513 813 6.072838 AGTGAAGAAACTGCACATGACTATTG 60.073 38.462 11.71 0.00 42.23 1.90
516 816 4.751600 CAGTGAAGAAACTGCACATGACTA 59.248 41.667 11.71 0.00 42.23 2.59
517 817 3.562973 CAGTGAAGAAACTGCACATGACT 59.437 43.478 11.71 0.00 42.23 3.41
535 867 7.120285 TCTCAATTTCTATCCAAAGCTTCAGTG 59.880 37.037 0.00 0.00 0.00 3.66
539 871 7.994194 ACATCTCAATTTCTATCCAAAGCTTC 58.006 34.615 0.00 0.00 0.00 3.86
564 896 6.957631 TCCTTGCCTGTAGATTCATCTTTTA 58.042 36.000 0.00 0.00 38.32 1.52
575 907 4.922206 ACATTGAAATCCTTGCCTGTAGA 58.078 39.130 0.00 0.00 0.00 2.59
579 911 7.098477 TCAAATTACATTGAAATCCTTGCCTG 58.902 34.615 0.00 0.00 36.42 4.85
610 942 4.731773 GCAAACCTGTGACAGAACTGAAAG 60.732 45.833 15.33 0.00 34.52 2.62
619 951 1.745087 ACAAGTGCAAACCTGTGACAG 59.255 47.619 5.42 5.42 0.00 3.51
635 967 1.535028 ACACACACACACACACACAAG 59.465 47.619 0.00 0.00 0.00 3.16
636 968 1.265365 CACACACACACACACACACAA 59.735 47.619 0.00 0.00 0.00 3.33
637 969 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
638 970 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
639 971 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
640 972 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
641 973 1.598882 AACACACACACACACACACA 58.401 45.000 0.00 0.00 0.00 3.72
642 974 2.739913 ACTAACACACACACACACACAC 59.260 45.455 0.00 0.00 0.00 3.82
643 975 3.046968 ACTAACACACACACACACACA 57.953 42.857 0.00 0.00 0.00 3.72
644 976 4.153475 AGAAACTAACACACACACACACAC 59.847 41.667 0.00 0.00 0.00 3.82
646 978 4.939509 AGAAACTAACACACACACACAC 57.060 40.909 0.00 0.00 0.00 3.82
648 980 4.557301 GCAAAGAAACTAACACACACACAC 59.443 41.667 0.00 0.00 0.00 3.82
721 1053 9.225682 TGTCCCTATCCTCTCATTTTTATTAGT 57.774 33.333 0.00 0.00 0.00 2.24
722 1054 9.717942 CTGTCCCTATCCTCTCATTTTTATTAG 57.282 37.037 0.00 0.00 0.00 1.73
723 1055 9.225682 ACTGTCCCTATCCTCTCATTTTTATTA 57.774 33.333 0.00 0.00 0.00 0.98
732 1064 1.646447 ACCACTGTCCCTATCCTCTCA 59.354 52.381 0.00 0.00 0.00 3.27
747 1079 2.600731 CCAACCACCACCACCACT 59.399 61.111 0.00 0.00 0.00 4.00
748 1080 2.520741 CCCAACCACCACCACCAC 60.521 66.667 0.00 0.00 0.00 4.16
764 1096 1.221021 GGACACATTCGTCTCCCCC 59.779 63.158 0.00 0.00 36.12 5.40
771 1103 3.469008 TGACTTTCTGGACACATTCGT 57.531 42.857 0.00 0.00 0.00 3.85
772 1104 3.996363 TGATGACTTTCTGGACACATTCG 59.004 43.478 0.00 0.00 0.00 3.34
774 1106 4.978099 ACTGATGACTTTCTGGACACATT 58.022 39.130 0.00 0.00 0.00 2.71
777 1109 3.499918 CCAACTGATGACTTTCTGGACAC 59.500 47.826 0.00 0.00 0.00 3.67
780 1112 3.496692 CCACCAACTGATGACTTTCTGGA 60.497 47.826 0.00 0.00 0.00 3.86
791 1123 0.677731 CGCATGACCCACCAACTGAT 60.678 55.000 0.00 0.00 0.00 2.90
807 1139 3.249799 GGCATTGTATATGCAAGTACGCA 59.750 43.478 11.95 0.00 46.21 5.24
808 1140 3.249799 TGGCATTGTATATGCAAGTACGC 59.750 43.478 11.95 10.72 46.21 4.42
815 1147 4.022603 ACCAAGTTGGCATTGTATATGCA 58.977 39.130 22.25 0.00 46.21 3.96
823 1218 2.746269 CACTCAACCAAGTTGGCATTG 58.254 47.619 22.25 18.52 42.67 2.82
828 1223 1.008538 GCGCACTCAACCAAGTTGG 60.009 57.895 20.76 20.76 42.99 3.77
842 1237 2.168313 TCACAGGAATCTAATCAGCGCA 59.832 45.455 11.47 0.00 0.00 6.09
843 1238 2.799412 CTCACAGGAATCTAATCAGCGC 59.201 50.000 0.00 0.00 0.00 5.92
845 1240 4.141846 TGGTCTCACAGGAATCTAATCAGC 60.142 45.833 0.00 0.00 0.00 4.26
846 1241 5.362143 TCTGGTCTCACAGGAATCTAATCAG 59.638 44.000 0.00 0.00 38.98 2.90
853 1248 2.564947 ACTGTCTGGTCTCACAGGAATC 59.435 50.000 4.22 0.00 43.78 2.52
854 1249 2.614259 ACTGTCTGGTCTCACAGGAAT 58.386 47.619 4.22 0.00 43.78 3.01
855 1250 2.088104 ACTGTCTGGTCTCACAGGAA 57.912 50.000 4.22 0.00 43.78 3.36
856 1251 2.891580 GTTACTGTCTGGTCTCACAGGA 59.108 50.000 4.22 0.00 43.78 3.86
857 1252 2.894126 AGTTACTGTCTGGTCTCACAGG 59.106 50.000 4.22 0.00 43.78 4.00
858 1253 4.302455 CAAGTTACTGTCTGGTCTCACAG 58.698 47.826 0.00 0.00 44.83 3.66
859 1254 3.069586 CCAAGTTACTGTCTGGTCTCACA 59.930 47.826 0.00 0.00 0.00 3.58
860 1255 3.069729 ACCAAGTTACTGTCTGGTCTCAC 59.930 47.826 1.66 0.00 0.00 3.51
861 1256 3.305720 ACCAAGTTACTGTCTGGTCTCA 58.694 45.455 1.66 0.00 0.00 3.27
862 1257 3.306156 GGACCAAGTTACTGTCTGGTCTC 60.306 52.174 25.00 15.88 43.67 3.36
863 1258 2.633481 GGACCAAGTTACTGTCTGGTCT 59.367 50.000 25.00 0.77 43.67 3.85
864 1259 2.289506 GGGACCAAGTTACTGTCTGGTC 60.290 54.545 20.59 20.59 43.51 4.02
865 1260 1.697982 GGGACCAAGTTACTGTCTGGT 59.302 52.381 6.90 6.90 0.00 4.00
866 1261 1.337823 CGGGACCAAGTTACTGTCTGG 60.338 57.143 0.41 0.41 0.00 3.86
867 1262 1.616865 TCGGGACCAAGTTACTGTCTG 59.383 52.381 0.00 0.00 0.00 3.51
868 1263 1.893801 CTCGGGACCAAGTTACTGTCT 59.106 52.381 0.00 0.00 0.00 3.41
869 1264 1.067071 CCTCGGGACCAAGTTACTGTC 60.067 57.143 0.00 0.00 0.00 3.51
870 1265 0.974383 CCTCGGGACCAAGTTACTGT 59.026 55.000 0.00 0.00 0.00 3.55
871 1266 1.067071 GTCCTCGGGACCAAGTTACTG 60.067 57.143 10.92 0.00 46.19 2.74
872 1267 1.264295 GTCCTCGGGACCAAGTTACT 58.736 55.000 10.92 0.00 46.19 2.24
873 1268 3.828657 GTCCTCGGGACCAAGTTAC 57.171 57.895 10.92 0.00 46.19 2.50
885 1296 3.372206 GGTCATGTGATGAAAAGTCCTCG 59.628 47.826 0.00 0.00 41.69 4.63
891 1302 5.473162 TGTTAGGTGGTCATGTGATGAAAAG 59.527 40.000 0.00 0.00 41.69 2.27
914 1325 1.876156 GTTGCCCTGTTCTTCAGAGTG 59.124 52.381 0.00 0.00 46.27 3.51
915 1326 1.202818 GGTTGCCCTGTTCTTCAGAGT 60.203 52.381 0.00 0.00 46.27 3.24
916 1327 1.528129 GGTTGCCCTGTTCTTCAGAG 58.472 55.000 0.00 0.00 46.27 3.35
917 1328 0.110486 GGGTTGCCCTGTTCTTCAGA 59.890 55.000 0.00 0.00 46.27 3.27
918 1329 0.178992 TGGGTTGCCCTGTTCTTCAG 60.179 55.000 5.73 0.00 45.70 3.02
1048 1472 1.821136 GGTTGCTGCCTCTTTTGCTAT 59.179 47.619 0.00 0.00 0.00 2.97
1073 1497 2.688446 TCCTTCCATAGCACTGACGTAG 59.312 50.000 0.00 0.00 0.00 3.51
1075 1499 1.557099 TCCTTCCATAGCACTGACGT 58.443 50.000 0.00 0.00 0.00 4.34
1077 1501 2.284190 GCTTCCTTCCATAGCACTGAC 58.716 52.381 0.00 0.00 35.05 3.51
1081 1505 2.877168 CAGATGCTTCCTTCCATAGCAC 59.123 50.000 0.00 0.00 46.55 4.40
1089 1513 0.254178 TGAGGGCAGATGCTTCCTTC 59.746 55.000 4.59 0.00 41.70 3.46
1110 1534 1.770294 GGATCTCACCGAAGAGACCT 58.230 55.000 8.62 0.00 46.58 3.85
1213 1637 3.944015 CCCCTGATCTTGTTGATGAAGAC 59.056 47.826 0.00 0.00 35.14 3.01
1219 1643 3.094572 CAAAGCCCCTGATCTTGTTGAT 58.905 45.455 0.00 0.00 38.27 2.57
1260 1684 3.614150 GCTTGTAGGTGAACTCATCGACA 60.614 47.826 2.21 2.21 40.08 4.35
1292 1716 1.039233 CACAGTGAATCCCCCATGCC 61.039 60.000 0.00 0.00 0.00 4.40
1310 1734 4.827284 GGTTGACCCTTTTCTTCATCTTCA 59.173 41.667 0.00 0.00 0.00 3.02
1323 1747 1.823250 GCCTTGATGTGGTTGACCCTT 60.823 52.381 0.00 0.00 34.29 3.95
1332 1756 2.802792 CGCCATGCCTTGATGTGG 59.197 61.111 0.00 0.00 34.84 4.17
1362 1786 2.551938 GCCCTTGATATCCTGGAGCTTC 60.552 54.545 1.52 0.00 0.00 3.86
1446 1870 7.522073 GCAGATTTTGACTGAACATTGTTCCTA 60.522 37.037 23.22 7.99 37.54 2.94
1494 1918 1.918957 CCCACAAGATCCTCTTCCCTT 59.081 52.381 0.00 0.00 33.78 3.95
1524 1948 2.035066 GTGCATCAGCTTGTCCTTGTTT 59.965 45.455 0.00 0.00 42.74 2.83
1706 2130 4.451096 TGGCGATCTGTTTTAACAAGTCTC 59.549 41.667 0.00 0.00 38.66 3.36
1743 2167 1.268352 GCGTTGGTGGCATCAACTTTA 59.732 47.619 33.57 3.41 41.47 1.85
1744 2168 0.031994 GCGTTGGTGGCATCAACTTT 59.968 50.000 33.57 0.00 41.47 2.66
1745 2169 1.106351 TGCGTTGGTGGCATCAACTT 61.106 50.000 33.57 0.00 41.47 2.66
1747 2171 0.249238 TTTGCGTTGGTGGCATCAAC 60.249 50.000 29.29 29.29 40.62 3.18
1751 2175 1.363443 CTGTTTGCGTTGGTGGCAT 59.637 52.632 0.00 0.00 40.62 4.40
1754 2178 0.248866 GTTCCTGTTTGCGTTGGTGG 60.249 55.000 0.00 0.00 0.00 4.61
1789 2213 6.605471 TTCTGAACCTTGAAGATAGCTACA 57.395 37.500 0.00 0.00 0.00 2.74
1790 2214 9.771534 AATATTCTGAACCTTGAAGATAGCTAC 57.228 33.333 0.00 0.00 0.00 3.58
1793 2217 9.113838 TGAAATATTCTGAACCTTGAAGATAGC 57.886 33.333 0.00 0.00 0.00 2.97
1816 2240 5.357878 GCCAAACATCATCCAGAACTATGAA 59.642 40.000 0.00 0.00 35.82 2.57
1885 2309 0.951558 ATGACAAAACGACCAGTGCC 59.048 50.000 0.00 0.00 0.00 5.01
1896 2320 6.430925 CCTGAATTCTAGTGGTGATGACAAAA 59.569 38.462 7.05 0.00 0.00 2.44
1946 2370 9.703892 CTAATGGTTCCAATTTGATTGTACAAA 57.296 29.630 13.23 0.00 42.58 2.83
1947 2371 9.083422 TCTAATGGTTCCAATTTGATTGTACAA 57.917 29.630 11.41 11.41 38.59 2.41
2026 2450 3.130633 GTTCCTTTGGGCATGTTTTGTC 58.869 45.455 0.00 0.00 0.00 3.18
2041 2465 6.976934 TTGAGCCAAATCTTTTAGTTCCTT 57.023 33.333 0.00 0.00 0.00 3.36
2050 2474 6.827762 TCCAAAAACATTTGAGCCAAATCTTT 59.172 30.769 9.39 8.38 41.40 2.52
2071 2495 2.513753 CAAGCCACCACACTTATCCAA 58.486 47.619 0.00 0.00 0.00 3.53
2138 2562 9.802039 ATAAACTTTCCCATTGACAGTAAGTTA 57.198 29.630 0.00 0.00 32.83 2.24
2202 2626 9.436957 ACTTTCAGAACAATATTAACATCGAGT 57.563 29.630 0.00 0.00 0.00 4.18
2236 2660 0.905357 AGATCCGTTGGAAGGTCCTG 59.095 55.000 0.00 0.00 37.46 3.86
2250 2674 5.860716 GTGCAGAAAACAATTCTTCAGATCC 59.139 40.000 0.00 0.00 0.00 3.36
2314 2738 2.519013 GATCCAATGCCTGATTACCCC 58.481 52.381 0.00 0.00 0.00 4.95
2353 2777 5.766150 TCCAATGTTCTGTTCGATGTTTT 57.234 34.783 0.00 0.00 0.00 2.43
2359 2783 4.511454 CACTTCTTCCAATGTTCTGTTCGA 59.489 41.667 0.00 0.00 0.00 3.71
2360 2784 4.319766 CCACTTCTTCCAATGTTCTGTTCG 60.320 45.833 0.00 0.00 0.00 3.95
2366 2790 3.149196 TCTGCCACTTCTTCCAATGTTC 58.851 45.455 0.00 0.00 0.00 3.18
2376 2800 1.268283 GGTAGCCCTCTGCCACTTCT 61.268 60.000 0.00 0.00 43.62 2.85
2430 2854 1.336440 CCACACAAATTCCGCTTGACA 59.664 47.619 0.00 0.00 0.00 3.58
2434 2858 1.665442 GGCCACACAAATTCCGCTT 59.335 52.632 0.00 0.00 0.00 4.68
2496 2920 4.392921 TTCCTCTTCTGATTTAGCGAGG 57.607 45.455 0.00 0.00 41.42 4.63
2526 2950 5.336451 GGGTCTTAAGCCATTGTAAACTTGG 60.336 44.000 15.09 0.00 42.92 3.61
2547 2971 0.754472 TGTTCTCGGTCGAAAAGGGT 59.246 50.000 0.00 0.00 0.00 4.34
2550 2974 0.161024 GCGTGTTCTCGGTCGAAAAG 59.839 55.000 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.