Multiple sequence alignment - TraesCS3D01G322400

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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 TraesCS3D01G322400 chr3D 100.000 3887 0 0 1 3887 435300421 435296535 0.000000e+00 7179.0
1 TraesCS3D01G322400 chr3D 91.304 115 7 3 619 732 336539292 336539180 1.870000e-33 154.0
2 TraesCS3D01G322400 chr3B 94.651 3178 139 9 731 3887 571304367 571301200 0.000000e+00 4898.0
3 TraesCS3D01G322400 chr3B 89.450 218 21 2 426 642 571304594 571304378 1.380000e-69 274.0
4 TraesCS3D01G322400 chr3B 85.878 262 15 5 1 240 571305117 571304856 3.850000e-65 259.0
5 TraesCS3D01G322400 chr3B 95.000 120 2 1 308 427 571304870 571304755 6.630000e-43 185.0
6 TraesCS3D01G322400 chr3B 93.333 105 4 3 629 732 181342616 181342514 6.730000e-33 152.0
7 TraesCS3D01G322400 chr3A 96.976 1488 45 0 1265 2752 574017316 574015829 0.000000e+00 2499.0
8 TraesCS3D01G322400 chr3A 94.691 1149 36 11 2751 3887 574015477 574014342 0.000000e+00 1760.0
9 TraesCS3D01G322400 chr3A 87.747 253 9 5 10 240 574017647 574017395 3.830000e-70 276.0
10 TraesCS3D01G322400 chr3A 90.722 97 1 2 308 404 574017409 574017321 5.270000e-24 122.0
11 TraesCS3D01G322400 chr3A 95.082 61 3 0 3486 3546 66036722 66036782 3.200000e-16 97.1
12 TraesCS3D01G322400 chr2B 96.000 100 2 1 645 742 696361738 696361639 1.120000e-35 161.0
13 TraesCS3D01G322400 chr2B 100.000 86 0 0 647 732 575147073 575146988 4.020000e-35 159.0
14 TraesCS3D01G322400 chr2B 96.739 92 3 0 648 739 709839327 709839418 1.870000e-33 154.0
15 TraesCS3D01G322400 chr2B 95.789 95 2 2 643 737 7641713 7641621 6.730000e-33 152.0
16 TraesCS3D01G322400 chr7B 95.000 100 2 3 642 741 157681766 157681670 1.870000e-33 154.0
17 TraesCS3D01G322400 chr4D 96.739 92 3 0 641 732 489440949 489441040 1.870000e-33 154.0
18 TraesCS3D01G322400 chr2D 90.351 114 6 5 629 741 166544653 166544544 1.130000e-30 145.0
19 TraesCS3D01G322400 chrUn 95.082 61 3 0 3486 3546 45094349 45094289 3.200000e-16 97.1
20 TraesCS3D01G322400 chrUn 95.082 61 3 0 3486 3546 171044636 171044576 3.200000e-16 97.1
21 TraesCS3D01G322400 chrUn 95.082 61 3 0 3486 3546 336782531 336782471 3.200000e-16 97.1
22 TraesCS3D01G322400 chrUn 95.082 61 3 0 3486 3546 405916133 405916073 3.200000e-16 97.1
23 TraesCS3D01G322400 chr6D 95.082 61 3 0 3486 3546 425972972 425972912 3.200000e-16 97.1
24 TraesCS3D01G322400 chr1A 95.082 61 3 0 3486 3546 94759224 94759164 3.200000e-16 97.1
25 TraesCS3D01G322400 chr2A 100.000 32 0 0 3451 3482 764734352 764734321 4.190000e-05 60.2


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 TraesCS3D01G322400 chr3D 435296535 435300421 3886 True 7179.00 7179 100.00000 1 3887 1 chr3D.!!$R2 3886
1 TraesCS3D01G322400 chr3B 571301200 571305117 3917 True 1404.00 4898 91.24475 1 3887 4 chr3B.!!$R2 3886
2 TraesCS3D01G322400 chr3A 574014342 574017647 3305 True 1164.25 2499 92.53400 10 3887 4 chr3A.!!$R1 3877

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
252 275 0.034337 TAGCGAAAAACTGTCGGCCT 59.966 50.0 0.0 0.0 38.93 5.19 F
664 855 0.178970 GCTACTCCCTCCGTCCCATA 60.179 60.0 0.0 0.0 0.00 2.74 F
1842 2034 0.388649 CTCGCCGTGCTTGTCTAGTT 60.389 55.0 0.0 0.0 0.00 2.24 F
1873 2065 0.537143 TCAGGCAACAGAAACGGCAT 60.537 50.0 0.0 0.0 41.41 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1351 1543 0.181114 AACAACACAGGAGCTGCTGA 59.819 50.000 37.98 0.0 34.37 4.26 R
2595 2787 1.234615 ACCAAACCGGCATGTTCTCG 61.235 55.000 0.00 0.0 39.03 4.04 R
2689 2881 0.671472 TTCCACTGCTCAGACATGCG 60.671 55.000 3.60 0.0 0.00 4.73 R
3833 4399 1.142667 TGGGCGATCTTTATGGATGCA 59.857 47.619 0.00 0.0 0.00 3.96 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
67 68 2.438434 CTTCGCCGGCCTGGATTT 60.438 61.111 23.46 0.00 42.00 2.17
75 76 1.392131 GGCCTGGATTTCCCCCTTT 59.608 57.895 0.00 0.00 34.29 3.11
95 118 5.778241 CCTTTTATTCCCCTTTACCTGTTGT 59.222 40.000 0.00 0.00 0.00 3.32
96 119 6.949463 CCTTTTATTCCCCTTTACCTGTTGTA 59.051 38.462 0.00 0.00 0.00 2.41
113 136 3.505464 TGTAGCGGAAAGAGTAAGAGC 57.495 47.619 0.00 0.00 0.00 4.09
201 224 1.964891 CGCTATGCTCCATGGCCTG 60.965 63.158 6.96 0.00 43.76 4.85
240 263 2.037251 GGATAGATGTGCCCTAGCGAAA 59.963 50.000 0.00 0.00 44.31 3.46
241 264 3.494398 GGATAGATGTGCCCTAGCGAAAA 60.494 47.826 0.00 0.00 44.31 2.29
242 265 2.489938 AGATGTGCCCTAGCGAAAAA 57.510 45.000 0.00 0.00 44.31 1.94
243 266 2.084546 AGATGTGCCCTAGCGAAAAAC 58.915 47.619 0.00 0.00 44.31 2.43
244 267 2.084546 GATGTGCCCTAGCGAAAAACT 58.915 47.619 0.00 0.00 44.31 2.66
245 268 1.234821 TGTGCCCTAGCGAAAAACTG 58.765 50.000 0.00 0.00 44.31 3.16
246 269 1.235724 GTGCCCTAGCGAAAAACTGT 58.764 50.000 0.00 0.00 44.31 3.55
247 270 1.197036 GTGCCCTAGCGAAAAACTGTC 59.803 52.381 0.00 0.00 44.31 3.51
248 271 0.442699 GCCCTAGCGAAAAACTGTCG 59.557 55.000 0.00 0.00 41.46 4.35
249 272 1.076332 CCCTAGCGAAAAACTGTCGG 58.924 55.000 0.00 0.00 38.93 4.79
250 273 0.442699 CCTAGCGAAAAACTGTCGGC 59.557 55.000 0.00 0.00 38.93 5.54
251 274 0.442699 CTAGCGAAAAACTGTCGGCC 59.557 55.000 0.00 0.00 38.93 6.13
252 275 0.034337 TAGCGAAAAACTGTCGGCCT 59.966 50.000 0.00 0.00 38.93 5.19
253 276 1.082104 GCGAAAAACTGTCGGCCTG 60.082 57.895 0.00 0.00 38.93 4.85
254 277 1.574428 CGAAAAACTGTCGGCCTGG 59.426 57.895 0.00 0.00 34.85 4.45
255 278 1.852067 CGAAAAACTGTCGGCCTGGG 61.852 60.000 0.00 0.00 34.85 4.45
256 279 2.142357 GAAAAACTGTCGGCCTGGGC 62.142 60.000 10.75 10.75 41.06 5.36
257 280 2.640581 AAAAACTGTCGGCCTGGGCT 62.641 55.000 18.81 0.00 41.60 5.19
272 295 2.951458 GCTGTGTGCCCCGTTTAC 59.049 61.111 0.00 0.00 35.15 2.01
273 296 1.894756 GCTGTGTGCCCCGTTTACA 60.895 57.895 0.00 0.00 35.15 2.41
274 297 1.448922 GCTGTGTGCCCCGTTTACAA 61.449 55.000 0.00 0.00 35.15 2.41
275 298 1.243902 CTGTGTGCCCCGTTTACAAT 58.756 50.000 0.00 0.00 0.00 2.71
276 299 2.428491 CTGTGTGCCCCGTTTACAATA 58.572 47.619 0.00 0.00 0.00 1.90
277 300 2.814919 CTGTGTGCCCCGTTTACAATAA 59.185 45.455 0.00 0.00 0.00 1.40
278 301 3.220110 TGTGTGCCCCGTTTACAATAAA 58.780 40.909 0.00 0.00 0.00 1.40
279 302 3.635373 TGTGTGCCCCGTTTACAATAAAA 59.365 39.130 0.00 0.00 0.00 1.52
280 303 4.098960 TGTGTGCCCCGTTTACAATAAAAA 59.901 37.500 0.00 0.00 0.00 1.94
281 304 5.221461 TGTGTGCCCCGTTTACAATAAAAAT 60.221 36.000 0.00 0.00 0.00 1.82
282 305 5.119434 GTGTGCCCCGTTTACAATAAAAATG 59.881 40.000 0.00 0.00 0.00 2.32
283 306 4.627900 GTGCCCCGTTTACAATAAAAATGG 59.372 41.667 0.00 0.00 40.99 3.16
289 312 7.354025 CCGTTTACAATAAAAATGGGGAAAC 57.646 36.000 0.00 0.00 38.71 2.78
366 389 5.130292 TGCTCTTTAGTAAGCAAGTACGT 57.870 39.130 0.00 0.00 45.09 3.57
367 390 6.258230 TGCTCTTTAGTAAGCAAGTACGTA 57.742 37.500 0.00 0.00 45.09 3.57
368 391 6.320171 TGCTCTTTAGTAAGCAAGTACGTAG 58.680 40.000 0.00 0.00 45.09 3.51
411 434 4.726876 GCAATTAGCAAGTTAGTACACCGC 60.727 45.833 0.00 0.00 44.79 5.68
440 625 9.793259 ACTTTCACATCTAGTTTTCTTATTCCA 57.207 29.630 0.00 0.00 0.00 3.53
518 703 4.685169 TTTGATTCATTTCGCCTGAGAC 57.315 40.909 0.00 0.00 0.00 3.36
521 706 4.433615 TGATTCATTTCGCCTGAGACTAC 58.566 43.478 0.00 0.00 0.00 2.73
535 720 6.630413 GCCTGAGACTACACCTGATTAATCAA 60.630 42.308 18.47 3.37 36.18 2.57
536 721 7.504403 CCTGAGACTACACCTGATTAATCAAT 58.496 38.462 18.47 7.70 36.18 2.57
539 724 8.539544 TGAGACTACACCTGATTAATCAATTCA 58.460 33.333 18.47 7.17 36.18 2.57
540 725 9.553064 GAGACTACACCTGATTAATCAATTCAT 57.447 33.333 18.47 6.82 36.18 2.57
562 747 4.778143 CCAAGTTAGCGGCGCCCT 62.778 66.667 30.40 21.00 0.00 5.19
563 748 2.185867 CAAGTTAGCGGCGCCCTA 59.814 61.111 30.40 19.89 0.00 3.53
590 775 8.700051 TGTCAAATTAATTCCTGGAAAACTTCA 58.300 29.630 14.03 0.00 0.00 3.02
619 804 3.773418 TTTGATCTTACCGAACCACCA 57.227 42.857 0.00 0.00 0.00 4.17
627 812 5.058490 TCTTACCGAACCACCAAAGTAAAG 58.942 41.667 0.00 0.00 0.00 1.85
628 813 2.578786 ACCGAACCACCAAAGTAAAGG 58.421 47.619 0.00 0.00 0.00 3.11
629 814 1.268625 CCGAACCACCAAAGTAAAGGC 59.731 52.381 0.00 0.00 0.00 4.35
657 848 1.339610 CAGAGAATGCTACTCCCTCCG 59.660 57.143 0.00 0.00 35.27 4.63
658 849 1.063567 AGAGAATGCTACTCCCTCCGT 60.064 52.381 0.00 0.00 35.27 4.69
659 850 1.338655 GAGAATGCTACTCCCTCCGTC 59.661 57.143 0.00 0.00 0.00 4.79
660 851 0.389757 GAATGCTACTCCCTCCGTCC 59.610 60.000 0.00 0.00 0.00 4.79
661 852 1.049289 AATGCTACTCCCTCCGTCCC 61.049 60.000 0.00 0.00 0.00 4.46
662 853 2.043248 GCTACTCCCTCCGTCCCA 60.043 66.667 0.00 0.00 0.00 4.37
663 854 1.457831 GCTACTCCCTCCGTCCCAT 60.458 63.158 0.00 0.00 0.00 4.00
664 855 0.178970 GCTACTCCCTCCGTCCCATA 60.179 60.000 0.00 0.00 0.00 2.74
665 856 1.756690 GCTACTCCCTCCGTCCCATAA 60.757 57.143 0.00 0.00 0.00 1.90
666 857 2.890814 CTACTCCCTCCGTCCCATAAT 58.109 52.381 0.00 0.00 0.00 1.28
667 858 3.816842 GCTACTCCCTCCGTCCCATAATA 60.817 52.174 0.00 0.00 0.00 0.98
668 859 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
669 860 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
670 861 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
671 862 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
672 863 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
673 864 5.657446 TCCCTCCGTCCCATAATATAAGAA 58.343 41.667 0.00 0.00 0.00 2.52
674 865 5.482878 TCCCTCCGTCCCATAATATAAGAAC 59.517 44.000 0.00 0.00 0.00 3.01
675 866 5.408356 CCTCCGTCCCATAATATAAGAACG 58.592 45.833 0.00 0.00 0.00 3.95
676 867 5.047519 CCTCCGTCCCATAATATAAGAACGT 60.048 44.000 0.00 0.00 0.00 3.99
677 868 6.409524 TCCGTCCCATAATATAAGAACGTT 57.590 37.500 0.00 0.00 0.00 3.99
678 869 6.819284 TCCGTCCCATAATATAAGAACGTTT 58.181 36.000 0.46 0.00 0.00 3.60
679 870 7.274447 TCCGTCCCATAATATAAGAACGTTTT 58.726 34.615 0.46 0.00 0.00 2.43
680 871 7.769970 TCCGTCCCATAATATAAGAACGTTTTT 59.230 33.333 9.22 9.22 0.00 1.94
681 872 7.853929 CCGTCCCATAATATAAGAACGTTTTTG 59.146 37.037 13.87 0.00 0.00 2.44
682 873 8.605746 CGTCCCATAATATAAGAACGTTTTTGA 58.394 33.333 13.87 2.81 0.00 2.69
683 874 9.712359 GTCCCATAATATAAGAACGTTTTTGAC 57.288 33.333 13.87 5.89 0.00 3.18
684 875 9.451002 TCCCATAATATAAGAACGTTTTTGACA 57.549 29.630 13.87 0.01 0.00 3.58
685 876 9.498307 CCCATAATATAAGAACGTTTTTGACAC 57.502 33.333 13.87 0.00 0.00 3.67
692 883 8.876275 ATAAGAACGTTTTTGACACTAGTGTA 57.124 30.769 27.98 11.50 45.05 2.90
693 884 6.823678 AGAACGTTTTTGACACTAGTGTAG 57.176 37.500 27.98 14.79 45.05 2.74
694 885 6.335777 AGAACGTTTTTGACACTAGTGTAGT 58.664 36.000 27.98 15.35 45.05 2.73
707 898 6.579491 ACTAGTGTAGTGTCAAAAACGTTC 57.421 37.500 0.00 0.00 37.69 3.95
708 899 6.335777 ACTAGTGTAGTGTCAAAAACGTTCT 58.664 36.000 0.00 0.00 37.69 3.01
709 900 6.815142 ACTAGTGTAGTGTCAAAAACGTTCTT 59.185 34.615 0.00 0.00 37.69 2.52
710 901 7.975616 ACTAGTGTAGTGTCAAAAACGTTCTTA 59.024 33.333 0.00 0.00 37.69 2.10
711 902 7.781548 AGTGTAGTGTCAAAAACGTTCTTAT 57.218 32.000 0.00 0.00 0.00 1.73
712 903 8.876275 AGTGTAGTGTCAAAAACGTTCTTATA 57.124 30.769 0.00 0.00 0.00 0.98
713 904 9.485206 AGTGTAGTGTCAAAAACGTTCTTATAT 57.515 29.630 0.00 0.00 0.00 0.86
719 910 9.498307 GTGTCAAAAACGTTCTTATATTATGGG 57.502 33.333 0.00 0.00 0.00 4.00
720 911 9.451002 TGTCAAAAACGTTCTTATATTATGGGA 57.549 29.630 0.00 0.00 0.00 4.37
723 914 9.677567 CAAAAACGTTCTTATATTATGGGATGG 57.322 33.333 0.00 0.00 0.00 3.51
724 915 9.635404 AAAAACGTTCTTATATTATGGGATGGA 57.365 29.630 0.00 0.00 0.00 3.41
725 916 8.848474 AAACGTTCTTATATTATGGGATGGAG 57.152 34.615 0.00 0.00 0.00 3.86
726 917 6.947464 ACGTTCTTATATTATGGGATGGAGG 58.053 40.000 0.00 0.00 0.00 4.30
727 918 6.070194 ACGTTCTTATATTATGGGATGGAGGG 60.070 42.308 0.00 0.00 0.00 4.30
728 919 6.156256 CGTTCTTATATTATGGGATGGAGGGA 59.844 42.308 0.00 0.00 0.00 4.20
729 920 7.569240 GTTCTTATATTATGGGATGGAGGGAG 58.431 42.308 0.00 0.00 0.00 4.30
730 921 6.826727 TCTTATATTATGGGATGGAGGGAGT 58.173 40.000 0.00 0.00 0.00 3.85
731 922 7.961940 TCTTATATTATGGGATGGAGGGAGTA 58.038 38.462 0.00 0.00 0.00 2.59
736 927 4.717328 ATGGGATGGAGGGAGTATGATA 57.283 45.455 0.00 0.00 0.00 2.15
746 937 5.105146 GGAGGGAGTATGATATACAAGCTGG 60.105 48.000 0.00 0.00 0.00 4.85
747 938 4.223923 AGGGAGTATGATATACAAGCTGGC 59.776 45.833 0.00 0.00 0.00 4.85
748 939 4.223923 GGGAGTATGATATACAAGCTGGCT 59.776 45.833 0.00 0.00 0.00 4.75
766 957 3.751175 TGGCTACAATGCACTTGTCTTAC 59.249 43.478 14.94 7.75 44.99 2.34
778 969 4.441415 CACTTGTCTTACGAACAGAGTGTC 59.559 45.833 0.00 0.00 34.59 3.67
800 991 7.755373 GTGTCAGTATAATTTTCTCCTTTTGCC 59.245 37.037 0.00 0.00 0.00 4.52
805 996 4.783764 AATTTTCTCCTTTTGCCCTACG 57.216 40.909 0.00 0.00 0.00 3.51
811 1002 2.626266 CTCCTTTTGCCCTACGGTTTTT 59.374 45.455 0.00 0.00 0.00 1.94
835 1026 5.772825 TTTCTTTTCATGAAGTGACAGGG 57.227 39.130 8.41 0.00 36.32 4.45
862 1053 5.580297 GCTGTCATTTGGTTTCAAAGAAACA 59.420 36.000 20.30 7.50 44.87 2.83
871 1062 5.237779 TGGTTTCAAAGAAACACCGTAGATC 59.762 40.000 20.30 4.57 32.04 2.75
874 1065 6.721571 TTCAAAGAAACACCGTAGATCATC 57.278 37.500 0.00 0.00 0.00 2.92
875 1066 4.862574 TCAAAGAAACACCGTAGATCATCG 59.137 41.667 0.00 0.00 0.00 3.84
881 1072 2.265904 CCGTAGATCATCGGCCGGA 61.266 63.158 27.83 16.64 40.28 5.14
894 1085 1.282875 GCCGGAGAACACAGTTTGC 59.717 57.895 5.05 0.00 0.00 3.68
951 1142 1.065851 TCTGTGCGTGTCTGTCGTTAA 59.934 47.619 0.00 0.00 0.00 2.01
980 1171 8.594881 TTATGTCTGTTTCTCTTCAGAGTTTC 57.405 34.615 3.73 0.00 42.60 2.78
982 1173 6.045318 TGTCTGTTTCTCTTCAGAGTTTCAG 58.955 40.000 3.73 9.89 42.60 3.02
991 1182 6.703607 TCTCTTCAGAGTTTCAGTTCATTGAC 59.296 38.462 3.73 0.00 42.60 3.18
992 1183 5.760253 TCTTCAGAGTTTCAGTTCATTGACC 59.240 40.000 0.00 0.00 0.00 4.02
1016 1208 4.813296 AAAAGATGTCACACGAAAGGAC 57.187 40.909 0.00 0.00 0.00 3.85
1017 1209 3.753294 AAGATGTCACACGAAAGGACT 57.247 42.857 0.00 0.00 32.84 3.85
1044 1236 2.505405 GAAGTTGTGTCCCCCTTTCTC 58.495 52.381 0.00 0.00 0.00 2.87
1063 1255 3.618594 TCTCATGCAGTTATCGAAAGCAC 59.381 43.478 0.00 0.00 38.12 4.40
1086 1278 3.997021 GAGTTCATTCGTTGACACTGGAT 59.003 43.478 9.02 0.00 32.84 3.41
1155 1347 1.344438 AGAGAAGCACGTGACATGGAA 59.656 47.619 22.23 0.00 0.00 3.53
1206 1398 7.890127 TGGGAAAGTGAGATTATCAATGACTTT 59.110 33.333 0.00 0.00 40.43 2.66
1215 1407 9.784531 GAGATTATCAATGACTTTGGAGGAATA 57.215 33.333 0.00 0.00 35.92 1.75
1284 1476 9.713740 CAATTTGTACATTCTAAGCTTCAGATC 57.286 33.333 0.00 0.00 0.00 2.75
1318 1510 3.202829 TGTCCAACTTAAAAGACCGCT 57.797 42.857 0.00 0.00 0.00 5.52
1351 1543 5.246981 TCTCCATGTTCCTTTGATCAAGT 57.753 39.130 8.41 0.00 0.00 3.16
1364 1556 0.982704 ATCAAGTCAGCAGCTCCTGT 59.017 50.000 4.16 0.00 33.43 4.00
1389 1581 8.064222 GTGTTGTTATCATCATCTTTACCATCG 58.936 37.037 0.00 0.00 0.00 3.84
1500 1692 6.648310 TGCAGCTCAGCTATTATAATCTTGAC 59.352 38.462 0.00 1.46 36.40 3.18
1534 1726 3.425892 GCTGTGCTTGTTATGCTTCTCTG 60.426 47.826 0.00 0.00 0.00 3.35
1569 1761 3.508845 TCCATTATTAGCAAGAGGGCC 57.491 47.619 0.00 0.00 0.00 5.80
1682 1874 4.276058 TCACTGCAGAGATGATTGAACA 57.724 40.909 23.35 0.00 0.00 3.18
1689 1881 4.551603 GCAGAGATGATTGAACATGTACGC 60.552 45.833 0.00 0.00 0.00 4.42
1842 2034 0.388649 CTCGCCGTGCTTGTCTAGTT 60.389 55.000 0.00 0.00 0.00 2.24
1873 2065 0.537143 TCAGGCAACAGAAACGGCAT 60.537 50.000 0.00 0.00 41.41 4.40
2163 2355 6.041865 TCTCAAATCTCAGGATCTTGGATCTC 59.958 42.308 4.83 0.00 0.00 2.75
2529 2721 2.031769 TGAACAAGATTCAGCAGCAACG 60.032 45.455 0.00 0.00 0.00 4.10
2565 2757 3.056832 GTTATCCCTTCCTCCCCATCTT 58.943 50.000 0.00 0.00 0.00 2.40
2595 2787 3.273080 CTTGCGTTGCTTCCCTGGC 62.273 63.158 0.00 0.00 0.00 4.85
2604 2796 1.372087 GCTTCCCTGGCGAGAACATG 61.372 60.000 0.00 0.00 0.00 3.21
2638 2830 1.751924 GTCCGAGTAGGCTGTTGAGAT 59.248 52.381 0.00 0.00 40.77 2.75
2643 2835 3.117046 GAGTAGGCTGTTGAGATTACGC 58.883 50.000 0.00 0.00 0.00 4.42
2689 2881 0.110010 GCGCACTTTTGGAGAGAAGC 60.110 55.000 0.30 0.00 0.00 3.86
2697 2889 0.610174 TTGGAGAGAAGCGCATGTCT 59.390 50.000 12.45 12.45 0.00 3.41
2865 3410 3.096852 TGGAGTGTGGATGAACTACGAT 58.903 45.455 0.00 0.00 32.52 3.73
2888 3433 2.763448 CCCAGGAAACCAGAGAGTAGAG 59.237 54.545 0.00 0.00 0.00 2.43
2902 3447 5.046304 AGAGAGTAGAGCAAAGCACCAAATA 60.046 40.000 0.00 0.00 0.00 1.40
3165 3726 4.402829 TCCATTTTCACTGATTTCCCGAA 58.597 39.130 0.00 0.00 0.00 4.30
3210 3771 0.250252 TGTGAGCGCATTGTCAGGAA 60.250 50.000 11.47 0.00 0.00 3.36
3219 3780 3.181513 CGCATTGTCAGGAAAGAGTGATG 60.182 47.826 0.00 0.00 0.00 3.07
3220 3781 3.755378 GCATTGTCAGGAAAGAGTGATGT 59.245 43.478 0.00 0.00 0.00 3.06
3397 3958 9.814899 TGTATGTTTGTCTTGAATTTTTGTCAT 57.185 25.926 0.00 0.00 0.00 3.06
3516 4077 4.467438 ACTTATTTTGCAGGGAGAAATGGG 59.533 41.667 4.00 0.52 0.00 4.00
3518 4079 2.220653 TTTGCAGGGAGAAATGGGAG 57.779 50.000 0.00 0.00 0.00 4.30
3524 4085 1.450531 GGGAGAAATGGGAGCATGCG 61.451 60.000 13.01 0.00 0.00 4.73
3581 4142 9.754382 GAATTTATGCCATAACTTTCATGTGAT 57.246 29.630 11.63 0.00 0.00 3.06
3790 4356 6.148645 GTCTGAAGAATTTCCTCTTTCAGGTC 59.851 42.308 18.53 12.15 43.95 3.85
3812 4378 3.914966 CGTTAATAGCTGCGAGATCGATT 59.085 43.478 6.39 0.00 43.02 3.34
3827 4393 3.973206 TCGATTGGCTGTCTTTCCTTA 57.027 42.857 0.00 0.00 0.00 2.69
3833 4399 4.640771 TGGCTGTCTTTCCTTATTCAGT 57.359 40.909 0.00 0.00 0.00 3.41
3875 4441 2.347322 GCTCTCTCTGTCGGCCAGT 61.347 63.158 2.24 0.00 42.19 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 3.272818 GGTAAAGGGGAATAAAAGGGGGA 59.727 47.826 0.00 0.00 0.00 4.81
75 76 5.503002 GCTACAACAGGTAAAGGGGAATAA 58.497 41.667 0.00 0.00 0.00 1.40
95 118 2.688958 GGAGCTCTTACTCTTTCCGCTA 59.311 50.000 14.64 0.00 36.87 4.26
96 119 1.478916 GGAGCTCTTACTCTTTCCGCT 59.521 52.381 14.64 0.00 36.87 5.52
113 136 5.814705 AGAAATTTGAACTCTAGATGCGGAG 59.185 40.000 0.00 0.00 35.86 4.63
145 168 2.561478 AGGCAACCGTGAAACAGTAT 57.439 45.000 0.00 0.00 35.74 2.12
147 170 1.140252 ACTAGGCAACCGTGAAACAGT 59.860 47.619 0.00 0.00 35.74 3.55
201 224 3.907894 TCCAGTTCGTAAAAACATGCC 57.092 42.857 0.00 0.00 0.00 4.40
240 263 3.570212 AGCCCAGGCCGACAGTTT 61.570 61.111 4.70 0.00 43.17 2.66
241 264 4.335647 CAGCCCAGGCCGACAGTT 62.336 66.667 4.70 0.00 43.17 3.16
255 278 1.448922 TTGTAAACGGGGCACACAGC 61.449 55.000 0.00 0.00 44.65 4.40
256 279 1.243902 ATTGTAAACGGGGCACACAG 58.756 50.000 0.00 0.00 0.00 3.66
257 280 2.563261 TATTGTAAACGGGGCACACA 57.437 45.000 0.00 0.00 0.00 3.72
258 281 3.919223 TTTATTGTAAACGGGGCACAC 57.081 42.857 0.00 0.00 0.00 3.82
259 282 4.931661 TTTTTATTGTAAACGGGGCACA 57.068 36.364 0.00 0.00 0.00 4.57
260 283 4.627900 CCATTTTTATTGTAAACGGGGCAC 59.372 41.667 0.00 0.00 0.00 5.01
261 284 4.322801 CCCATTTTTATTGTAAACGGGGCA 60.323 41.667 0.00 0.00 31.02 5.36
262 285 4.185394 CCCATTTTTATTGTAAACGGGGC 58.815 43.478 0.00 0.00 31.02 5.80
263 286 4.466726 TCCCCATTTTTATTGTAAACGGGG 59.533 41.667 11.31 11.31 44.47 5.73
264 287 5.662674 TCCCCATTTTTATTGTAAACGGG 57.337 39.130 0.00 0.00 32.99 5.28
265 288 6.369340 GGTTTCCCCATTTTTATTGTAAACGG 59.631 38.462 0.00 0.00 0.00 4.44
266 289 6.929606 TGGTTTCCCCATTTTTATTGTAAACG 59.070 34.615 0.00 0.00 38.72 3.60
278 301 7.802340 TTTTGATCAAAAGTGGTTTCCCCATTT 60.802 33.333 26.01 0.00 44.46 2.32
279 302 6.353429 TTTTGATCAAAAGTGGTTTCCCCATT 60.353 34.615 26.01 0.00 39.24 3.16
280 303 5.131809 TTTTGATCAAAAGTGGTTTCCCCAT 59.868 36.000 26.01 0.00 39.24 4.00
281 304 3.320610 TGATCAAAAGTGGTTTCCCCA 57.679 42.857 0.00 0.00 42.51 4.96
282 305 4.681074 TTTGATCAAAAGTGGTTTCCCC 57.319 40.909 18.45 0.00 0.00 4.81
303 326 2.427095 GGATTCGCTAGGGCACATTTTT 59.573 45.455 1.02 0.00 38.60 1.94
304 327 2.024414 GGATTCGCTAGGGCACATTTT 58.976 47.619 1.02 0.00 38.60 1.82
305 328 1.680338 GGATTCGCTAGGGCACATTT 58.320 50.000 1.02 0.00 38.60 2.32
306 329 0.532862 CGGATTCGCTAGGGCACATT 60.533 55.000 1.02 0.00 38.60 2.71
307 330 1.069765 CGGATTCGCTAGGGCACAT 59.930 57.895 1.02 0.00 38.60 3.21
308 331 2.499205 CGGATTCGCTAGGGCACA 59.501 61.111 1.02 0.00 38.60 4.57
309 332 2.280186 CCGGATTCGCTAGGGCAC 60.280 66.667 0.00 0.00 38.60 5.01
310 333 2.306255 GAACCGGATTCGCTAGGGCA 62.306 60.000 9.46 0.00 38.60 5.36
311 334 1.594564 GAACCGGATTCGCTAGGGC 60.595 63.158 9.46 0.00 34.56 5.19
312 335 0.249489 CTGAACCGGATTCGCTAGGG 60.249 60.000 9.46 0.00 40.56 3.53
313 336 0.460311 ACTGAACCGGATTCGCTAGG 59.540 55.000 9.46 1.16 40.56 3.02
314 337 1.134367 TCACTGAACCGGATTCGCTAG 59.866 52.381 9.46 4.90 40.56 3.42
315 338 1.179152 TCACTGAACCGGATTCGCTA 58.821 50.000 9.46 0.00 40.56 4.26
316 339 0.537188 ATCACTGAACCGGATTCGCT 59.463 50.000 9.46 0.00 40.56 4.93
317 340 0.652592 CATCACTGAACCGGATTCGC 59.347 55.000 9.46 0.00 40.56 4.70
318 341 1.290203 CCATCACTGAACCGGATTCG 58.710 55.000 9.46 7.61 40.56 3.34
319 342 1.017387 GCCATCACTGAACCGGATTC 58.983 55.000 9.46 9.24 37.88 2.52
320 343 0.327924 TGCCATCACTGAACCGGATT 59.672 50.000 9.46 0.00 0.00 3.01
321 344 0.548031 ATGCCATCACTGAACCGGAT 59.452 50.000 9.46 0.00 0.00 4.18
365 388 9.677567 TTGCAATTCAGAAGAAAAACATACTAC 57.322 29.630 0.00 0.00 37.29 2.73
367 390 9.768662 AATTGCAATTCAGAAGAAAAACATACT 57.231 25.926 18.99 0.00 37.29 2.12
408 431 4.749245 AACTAGATGTGAAAGTTTGCGG 57.251 40.909 0.00 0.00 29.25 5.69
458 643 5.922053 TCGGATCTTCAAATCAGATGTGAT 58.078 37.500 3.95 0.00 46.01 3.06
467 652 2.282820 GTGTCGCTCGGATCTTCAAATC 59.717 50.000 0.00 0.00 0.00 2.17
479 664 1.577328 AAATGCCCAAGTGTCGCTCG 61.577 55.000 0.00 0.00 0.00 5.03
521 706 8.252417 TGGTTCAATGAATTGATTAATCAGGTG 58.748 33.333 17.28 10.61 45.30 4.00
535 720 3.119495 GCCGCTAACTTGGTTCAATGAAT 60.119 43.478 0.00 0.00 0.00 2.57
536 721 2.227865 GCCGCTAACTTGGTTCAATGAA 59.772 45.455 0.00 0.00 0.00 2.57
539 724 0.802494 CGCCGCTAACTTGGTTCAAT 59.198 50.000 0.00 0.00 0.00 2.57
540 725 1.847890 GCGCCGCTAACTTGGTTCAA 61.848 55.000 0.00 0.00 0.00 2.69
563 748 9.710900 GAAGTTTTCCAGGAATTAATTTGACAT 57.289 29.630 1.58 0.00 0.00 3.06
601 786 3.071892 ACTTTGGTGGTTCGGTAAGATCA 59.928 43.478 0.00 0.00 0.00 2.92
603 788 3.782656 ACTTTGGTGGTTCGGTAAGAT 57.217 42.857 0.00 0.00 0.00 2.40
611 796 2.288213 GCTGCCTTTACTTTGGTGGTTC 60.288 50.000 0.00 0.00 0.00 3.62
614 799 1.270550 CTGCTGCCTTTACTTTGGTGG 59.729 52.381 0.00 0.00 0.00 4.61
619 804 2.157738 CTGCTCTGCTGCCTTTACTTT 58.842 47.619 0.00 0.00 0.00 2.66
627 812 2.395651 CATTCTCTGCTCTGCTGCC 58.604 57.895 0.00 0.00 0.00 4.85
649 840 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
650 841 5.279562 TCTTATATTATGGGACGGAGGGA 57.720 43.478 0.00 0.00 0.00 4.20
651 842 5.623824 CGTTCTTATATTATGGGACGGAGGG 60.624 48.000 0.00 0.00 0.00 4.30
652 843 5.047519 ACGTTCTTATATTATGGGACGGAGG 60.048 44.000 13.18 0.00 0.00 4.30
653 844 6.022163 ACGTTCTTATATTATGGGACGGAG 57.978 41.667 13.18 0.00 0.00 4.63
654 845 6.409524 AACGTTCTTATATTATGGGACGGA 57.590 37.500 0.00 0.00 0.00 4.69
655 846 7.486802 AAAACGTTCTTATATTATGGGACGG 57.513 36.000 0.00 1.76 0.00 4.79
656 847 8.605746 TCAAAAACGTTCTTATATTATGGGACG 58.394 33.333 0.00 9.33 0.00 4.79
657 848 9.712359 GTCAAAAACGTTCTTATATTATGGGAC 57.288 33.333 0.00 0.00 0.00 4.46
658 849 9.451002 TGTCAAAAACGTTCTTATATTATGGGA 57.549 29.630 0.00 0.00 0.00 4.37
659 850 9.498307 GTGTCAAAAACGTTCTTATATTATGGG 57.502 33.333 0.00 0.00 0.00 4.00
665 856 9.485206 ACACTAGTGTCAAAAACGTTCTTATAT 57.515 29.630 22.95 0.00 40.24 0.86
666 857 8.876275 ACACTAGTGTCAAAAACGTTCTTATA 57.124 30.769 22.95 0.00 40.24 0.98
667 858 7.781548 ACACTAGTGTCAAAAACGTTCTTAT 57.218 32.000 22.95 0.00 40.24 1.73
668 859 7.975616 ACTACACTAGTGTCAAAAACGTTCTTA 59.024 33.333 31.11 8.36 43.74 2.10
669 860 6.815142 ACTACACTAGTGTCAAAAACGTTCTT 59.185 34.615 31.11 4.99 43.74 2.52
670 861 6.335777 ACTACACTAGTGTCAAAAACGTTCT 58.664 36.000 31.11 5.44 43.74 3.01
671 862 6.579491 ACTACACTAGTGTCAAAAACGTTC 57.421 37.500 31.11 0.00 43.74 3.95
684 875 6.335777 AGAACGTTTTTGACACTACACTAGT 58.664 36.000 0.46 0.00 40.28 2.57
685 876 6.823678 AGAACGTTTTTGACACTACACTAG 57.176 37.500 0.46 0.00 0.00 2.57
686 877 8.876275 ATAAGAACGTTTTTGACACTACACTA 57.124 30.769 13.87 0.00 0.00 2.74
687 878 7.781548 ATAAGAACGTTTTTGACACTACACT 57.218 32.000 13.87 0.00 0.00 3.55
693 884 9.498307 CCCATAATATAAGAACGTTTTTGACAC 57.502 33.333 13.87 0.00 0.00 3.67
694 885 9.451002 TCCCATAATATAAGAACGTTTTTGACA 57.549 29.630 13.87 0.01 0.00 3.58
697 888 9.677567 CCATCCCATAATATAAGAACGTTTTTG 57.322 33.333 13.87 0.00 0.00 2.44
698 889 9.635404 TCCATCCCATAATATAAGAACGTTTTT 57.365 29.630 9.22 9.22 0.00 1.94
699 890 9.284968 CTCCATCCCATAATATAAGAACGTTTT 57.715 33.333 0.46 0.00 0.00 2.43
700 891 7.883311 CCTCCATCCCATAATATAAGAACGTTT 59.117 37.037 0.46 0.00 0.00 3.60
701 892 7.394816 CCTCCATCCCATAATATAAGAACGTT 58.605 38.462 0.00 0.00 0.00 3.99
702 893 6.070194 CCCTCCATCCCATAATATAAGAACGT 60.070 42.308 0.00 0.00 0.00 3.99
703 894 6.156256 TCCCTCCATCCCATAATATAAGAACG 59.844 42.308 0.00 0.00 0.00 3.95
704 895 7.182930 ACTCCCTCCATCCCATAATATAAGAAC 59.817 40.741 0.00 0.00 0.00 3.01
705 896 7.263901 ACTCCCTCCATCCCATAATATAAGAA 58.736 38.462 0.00 0.00 0.00 2.52
706 897 6.826727 ACTCCCTCCATCCCATAATATAAGA 58.173 40.000 0.00 0.00 0.00 2.10
707 898 8.654997 CATACTCCCTCCATCCCATAATATAAG 58.345 40.741 0.00 0.00 0.00 1.73
708 899 8.359118 TCATACTCCCTCCATCCCATAATATAA 58.641 37.037 0.00 0.00 0.00 0.98
709 900 7.904322 TCATACTCCCTCCATCCCATAATATA 58.096 38.462 0.00 0.00 0.00 0.86
710 901 6.766795 TCATACTCCCTCCATCCCATAATAT 58.233 40.000 0.00 0.00 0.00 1.28
711 902 6.178995 TCATACTCCCTCCATCCCATAATA 57.821 41.667 0.00 0.00 0.00 0.98
712 903 5.041695 TCATACTCCCTCCATCCCATAAT 57.958 43.478 0.00 0.00 0.00 1.28
713 904 4.502036 TCATACTCCCTCCATCCCATAA 57.498 45.455 0.00 0.00 0.00 1.90
714 905 4.717328 ATCATACTCCCTCCATCCCATA 57.283 45.455 0.00 0.00 0.00 2.74
715 906 3.592221 ATCATACTCCCTCCATCCCAT 57.408 47.619 0.00 0.00 0.00 4.00
716 907 4.717328 ATATCATACTCCCTCCATCCCA 57.283 45.455 0.00 0.00 0.00 4.37
717 908 5.529289 TGTATATCATACTCCCTCCATCCC 58.471 45.833 0.00 0.00 0.00 3.85
718 909 6.407525 GCTTGTATATCATACTCCCTCCATCC 60.408 46.154 0.00 0.00 0.00 3.51
719 910 6.382570 AGCTTGTATATCATACTCCCTCCATC 59.617 42.308 0.00 0.00 0.00 3.51
720 911 6.155910 CAGCTTGTATATCATACTCCCTCCAT 59.844 42.308 0.00 0.00 0.00 3.41
721 912 5.481824 CAGCTTGTATATCATACTCCCTCCA 59.518 44.000 0.00 0.00 0.00 3.86
722 913 5.105146 CCAGCTTGTATATCATACTCCCTCC 60.105 48.000 0.00 0.00 0.00 4.30
723 914 5.625656 GCCAGCTTGTATATCATACTCCCTC 60.626 48.000 0.00 0.00 0.00 4.30
724 915 4.223923 GCCAGCTTGTATATCATACTCCCT 59.776 45.833 0.00 0.00 0.00 4.20
725 916 4.223923 AGCCAGCTTGTATATCATACTCCC 59.776 45.833 0.00 0.00 0.00 4.30
726 917 5.413309 AGCCAGCTTGTATATCATACTCC 57.587 43.478 0.00 0.00 0.00 3.85
727 918 6.925211 TGTAGCCAGCTTGTATATCATACTC 58.075 40.000 0.00 0.00 0.00 2.59
728 919 6.918067 TGTAGCCAGCTTGTATATCATACT 57.082 37.500 0.00 0.00 0.00 2.12
729 920 7.413438 GCATTGTAGCCAGCTTGTATATCATAC 60.413 40.741 0.00 0.00 0.00 2.39
730 921 6.595326 GCATTGTAGCCAGCTTGTATATCATA 59.405 38.462 0.00 0.00 0.00 2.15
731 922 5.413833 GCATTGTAGCCAGCTTGTATATCAT 59.586 40.000 0.00 0.00 0.00 2.45
736 927 2.684881 GTGCATTGTAGCCAGCTTGTAT 59.315 45.455 0.00 0.00 0.00 2.29
766 957 8.467402 AGAAAATTATACTGACACTCTGTTCG 57.533 34.615 0.00 0.00 31.00 3.95
778 969 7.410120 AGGGCAAAAGGAGAAAATTATACTG 57.590 36.000 0.00 0.00 0.00 2.74
811 1002 6.406849 CCCCTGTCACTTCATGAAAAGAAAAA 60.407 38.462 9.88 0.19 39.72 1.94
814 1005 4.141274 TCCCCTGTCACTTCATGAAAAGAA 60.141 41.667 9.88 1.84 39.72 2.52
815 1006 3.394274 TCCCCTGTCACTTCATGAAAAGA 59.606 43.478 9.88 7.44 39.72 2.52
816 1007 3.754965 TCCCCTGTCACTTCATGAAAAG 58.245 45.455 9.88 5.09 39.72 2.27
819 1010 1.003580 GCTCCCCTGTCACTTCATGAA 59.996 52.381 8.12 8.12 39.72 2.57
820 1011 0.615331 GCTCCCCTGTCACTTCATGA 59.385 55.000 0.00 0.00 33.79 3.07
821 1012 0.617413 AGCTCCCCTGTCACTTCATG 59.383 55.000 0.00 0.00 0.00 3.07
822 1013 0.617413 CAGCTCCCCTGTCACTTCAT 59.383 55.000 0.00 0.00 36.79 2.57
823 1014 2.061220 CAGCTCCCCTGTCACTTCA 58.939 57.895 0.00 0.00 36.79 3.02
835 1026 4.037923 TCTTTGAAACCAAATGACAGCTCC 59.962 41.667 0.00 0.00 33.55 4.70
871 1062 1.811266 CTGTGTTCTCCGGCCGATG 60.811 63.158 30.73 18.96 0.00 3.84
874 1065 1.597027 AAACTGTGTTCTCCGGCCG 60.597 57.895 21.04 21.04 0.00 6.13
875 1066 1.949257 CAAACTGTGTTCTCCGGCC 59.051 57.895 0.00 0.00 0.00 6.13
932 1123 1.483316 TTAACGACAGACACGCACAG 58.517 50.000 0.00 0.00 0.00 3.66
951 1142 8.592809 ACTCTGAAGAGAAACAGACATAAGAAT 58.407 33.333 14.20 0.00 44.74 2.40
998 1190 3.753294 AAGTCCTTTCGTGTGACATCT 57.247 42.857 0.00 0.00 0.00 2.90
1008 1200 3.127425 ACTTCCTCCAAAGTCCTTTCG 57.873 47.619 0.00 0.00 34.37 3.46
1016 1208 2.230660 GGGACACAACTTCCTCCAAAG 58.769 52.381 0.00 0.00 33.17 2.77
1017 1209 1.133606 GGGGACACAACTTCCTCCAAA 60.134 52.381 0.00 0.00 33.17 3.28
1044 1236 2.348362 TCGTGCTTTCGATAACTGCATG 59.652 45.455 0.00 0.00 40.69 4.06
1063 1255 2.155732 CCAGTGTCAACGAATGAACTCG 59.844 50.000 0.00 0.00 40.50 4.18
1086 1278 4.955335 TCTCTGAAGGTAAACTATCCCCA 58.045 43.478 0.00 0.00 0.00 4.96
1155 1347 3.097614 AGACACCCGCTTTAGTACATCT 58.902 45.455 0.00 0.00 0.00 2.90
1206 1398 1.131638 AATGCCGAGCTATTCCTCCA 58.868 50.000 0.00 0.00 0.00 3.86
1215 1407 2.988010 TGTCATCTAAATGCCGAGCT 57.012 45.000 0.00 0.00 32.58 4.09
1250 1442 3.194116 AGAATGTACAAATTGCTGCTGGG 59.806 43.478 0.00 0.00 0.00 4.45
1284 1476 3.312421 AGTTGGACATTTCAGTGTTCACG 59.688 43.478 0.00 0.00 37.33 4.35
1318 1510 5.644188 AGGAACATGGAGAGGAAATTTCAA 58.356 37.500 19.49 0.00 0.00 2.69
1351 1543 0.181114 AACAACACAGGAGCTGCTGA 59.819 50.000 37.98 0.00 34.37 4.26
1364 1556 7.984617 TCGATGGTAAAGATGATGATAACAACA 59.015 33.333 0.00 0.00 33.64 3.33
1534 1726 9.914131 GCTAATAATGGAATTTTCTGGGAATAC 57.086 33.333 0.00 0.00 37.87 1.89
1682 1874 4.497300 ACAGTTACGTTTATGGCGTACAT 58.503 39.130 0.00 0.67 43.28 2.29
1689 1881 6.128742 GGTTCACACTACAGTTACGTTTATGG 60.129 42.308 0.00 0.00 0.00 2.74
1842 2034 4.019411 TCTGTTGCCTGAATATGTTCTCCA 60.019 41.667 3.72 0.00 35.33 3.86
1873 2065 4.286808 TGGATTGGACTGATTTCTGAGTGA 59.713 41.667 0.00 0.00 0.00 3.41
2163 2355 4.264253 TCTCAAGGTTATGACAAGCATGG 58.736 43.478 0.00 0.00 37.87 3.66
2458 2650 2.819019 CCCATGTAATTGTCAGCACACA 59.181 45.455 0.00 0.00 29.76 3.72
2529 2721 6.144078 AGGGATAACGAATTTAACAATGCC 57.856 37.500 0.00 0.00 0.00 4.40
2595 2787 1.234615 ACCAAACCGGCATGTTCTCG 61.235 55.000 0.00 0.00 39.03 4.04
2604 2796 2.613506 CGGACTCAACCAAACCGGC 61.614 63.158 0.00 0.00 39.92 6.13
2638 2830 1.890489 TGTGAAGTAGAGCCTGCGTAA 59.110 47.619 0.00 0.00 0.00 3.18
2643 2835 1.480137 CCTCCTGTGAAGTAGAGCCTG 59.520 57.143 0.00 0.00 0.00 4.85
2689 2881 0.671472 TTCCACTGCTCAGACATGCG 60.671 55.000 3.60 0.00 0.00 4.73
2697 2889 3.708403 ATCTCAATGTTCCACTGCTCA 57.292 42.857 0.00 0.00 0.00 4.26
2865 3410 2.715763 ACTCTCTGGTTTCCTGGGTA 57.284 50.000 0.00 0.00 0.00 3.69
2888 3433 4.620982 ACTCACTTTATTTGGTGCTTTGC 58.379 39.130 0.00 0.00 33.91 3.68
2943 3492 4.478206 TTTTGTTTCAACATTGAGGGCA 57.522 36.364 0.00 0.00 38.95 5.36
3165 3726 7.729116 TGAAAAAGCCTGAAAAGAAGAATGAT 58.271 30.769 0.00 0.00 0.00 2.45
3210 3771 8.579850 TTGCTTTCCATTAATACATCACTCTT 57.420 30.769 0.00 0.00 0.00 2.85
3219 3780 9.294030 CTGATCAAACTTGCTTTCCATTAATAC 57.706 33.333 0.00 0.00 0.00 1.89
3220 3781 9.241919 TCTGATCAAACTTGCTTTCCATTAATA 57.758 29.630 0.00 0.00 0.00 0.98
3516 4077 3.090952 AGAAGATCTACACGCATGCTC 57.909 47.619 17.13 4.33 0.00 4.26
3518 4079 3.452474 AGAAGAAGATCTACACGCATGC 58.548 45.455 7.91 7.91 0.00 4.06
3524 4085 4.081972 TGGCTGTGAGAAGAAGATCTACAC 60.082 45.833 0.00 1.44 32.69 2.90
3608 4169 7.174253 GTCATGGACCAAAAAGACACTACATAA 59.826 37.037 0.00 0.00 0.00 1.90
3648 4209 4.095036 GCTTGAGTAGTGGAAATGTAAGGC 59.905 45.833 0.00 0.00 0.00 4.35
3650 4211 8.547967 TTAAGCTTGAGTAGTGGAAATGTAAG 57.452 34.615 9.86 0.00 0.00 2.34
3790 4356 2.917363 TCGATCTCGCAGCTATTAACG 58.083 47.619 0.00 0.00 39.60 3.18
3812 4378 4.326826 CACTGAATAAGGAAAGACAGCCA 58.673 43.478 0.00 0.00 0.00 4.75
3827 4393 4.214971 GCGATCTTTATGGATGCACTGAAT 59.785 41.667 0.00 0.00 0.00 2.57
3833 4399 1.142667 TGGGCGATCTTTATGGATGCA 59.857 47.619 0.00 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.