Multiple sequence alignment - TraesCS4B01G039300

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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 TraesCS4B01G039300 chr4B 100.000 5382 0 0 1 5382 28073756 28068375 0.000000e+00 9939.0
1 TraesCS4B01G039300 chr4B 91.770 887 61 9 4425 5300 27977312 27976427 0.000000e+00 1223.0
2 TraesCS4B01G039300 chr4B 85.222 697 67 18 4378 5058 28041314 28040638 0.000000e+00 684.0
3 TraesCS4B01G039300 chr4B 88.358 335 30 4 5049 5382 27978939 27978613 1.410000e-105 394.0
4 TraesCS4B01G039300 chr4B 92.760 221 11 2 4215 4433 27977942 27977725 1.130000e-81 315.0
5 TraesCS4B01G039300 chr4B 96.491 171 5 1 674 843 395819387 395819217 1.140000e-71 281.0
6 TraesCS4B01G039300 chr4B 85.366 82 10 1 5024 5103 27941260 27941179 3.450000e-12 84.2
7 TraesCS4B01G039300 chr4B 93.750 48 3 0 5335 5382 27940942 27940895 7.480000e-09 73.1
8 TraesCS4B01G039300 chr4B 100.000 30 0 0 4376 4405 27978473 27978502 7.530000e-04 56.5
9 TraesCS4B01G039300 chr4D 93.951 2860 148 16 842 3686 16235202 16232353 0.000000e+00 4300.0
10 TraesCS4B01G039300 chr4D 93.168 805 37 7 4078 4881 16231946 16231159 0.000000e+00 1166.0
11 TraesCS4B01G039300 chr4D 91.260 492 39 3 4893 5382 16228890 16228401 0.000000e+00 667.0
12 TraesCS4B01G039300 chr4D 86.039 616 45 21 51 633 16235857 16235250 1.650000e-174 623.0
13 TraesCS4B01G039300 chr4D 96.429 280 10 0 3698 3977 16232261 16231982 3.800000e-126 462.0
14 TraesCS4B01G039300 chr4D 93.478 46 3 0 4012 4057 44749400 44749355 9.670000e-08 69.4
15 TraesCS4B01G039300 chr4A 94.033 2430 112 19 842 3268 584272736 584275135 0.000000e+00 3653.0
16 TraesCS4B01G039300 chr4A 91.132 1714 101 27 3698 5382 584275560 584277251 0.000000e+00 2276.0
17 TraesCS4B01G039300 chr4A 85.286 700 54 20 1 682 584272070 584272738 0.000000e+00 676.0
18 TraesCS4B01G039300 chr4A 87.267 322 35 4 3371 3686 584275148 584275469 3.960000e-96 363.0
19 TraesCS4B01G039300 chr4A 79.798 495 73 16 4904 5382 584339919 584340402 8.640000e-88 335.0
20 TraesCS4B01G039300 chr5B 83.426 899 145 4 1013 1909 2562565 2561669 0.000000e+00 832.0
21 TraesCS4B01G039300 chr3B 80.735 898 171 2 1013 1909 720834042 720833146 0.000000e+00 699.0
22 TraesCS4B01G039300 chr3B 95.954 173 4 3 676 848 768309021 768308852 1.480000e-70 278.0
23 TraesCS4B01G039300 chr5D 79.512 737 130 17 2234 2959 2669658 2668932 6.220000e-139 505.0
24 TraesCS4B01G039300 chr5A 78.912 735 141 13 2234 2959 2112173 2112902 2.250000e-133 486.0
25 TraesCS4B01G039300 chr7B 99.390 164 1 0 680 843 710105048 710104885 1.130000e-76 298.0
26 TraesCS4B01G039300 chr7B 99.390 164 1 0 680 843 710116657 710116494 1.130000e-76 298.0
27 TraesCS4B01G039300 chr7B 99.390 164 1 0 680 843 710127757 710127594 1.130000e-76 298.0
28 TraesCS4B01G039300 chr7B 97.093 172 3 2 680 850 483770770 483770600 6.820000e-74 289.0
29 TraesCS4B01G039300 chr7B 95.954 173 6 1 672 843 64695631 64695459 4.100000e-71 279.0
30 TraesCS4B01G039300 chr2B 97.006 167 5 0 677 843 180617957 180618123 1.140000e-71 281.0
31 TraesCS4B01G039300 chr7D 89.767 215 12 9 655 864 193241785 193241994 3.200000e-67 267.0


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 TraesCS4B01G039300 chr4B 28068375 28073756 5381 True 9939.0 9939 100.000000 1 5382 1 chr4B.!!$R2 5381
1 TraesCS4B01G039300 chr4B 28040638 28041314 676 True 684.0 684 85.222000 4378 5058 1 chr4B.!!$R1 680
2 TraesCS4B01G039300 chr4B 27976427 27978939 2512 True 644.0 1223 90.962667 4215 5382 3 chr4B.!!$R5 1167
3 TraesCS4B01G039300 chr4D 16228401 16235857 7456 True 1443.6 4300 92.169400 51 5382 5 chr4D.!!$R2 5331
4 TraesCS4B01G039300 chr4A 584272070 584277251 5181 False 1742.0 3653 89.429500 1 5382 4 chr4A.!!$F2 5381
5 TraesCS4B01G039300 chr5B 2561669 2562565 896 True 832.0 832 83.426000 1013 1909 1 chr5B.!!$R1 896
6 TraesCS4B01G039300 chr3B 720833146 720834042 896 True 699.0 699 80.735000 1013 1909 1 chr3B.!!$R1 896
7 TraesCS4B01G039300 chr5D 2668932 2669658 726 True 505.0 505 79.512000 2234 2959 1 chr5D.!!$R1 725
8 TraesCS4B01G039300 chr5A 2112173 2112902 729 False 486.0 486 78.912000 2234 2959 1 chr5A.!!$F1 725

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
291 315 0.179020 TGCTGTGGTCAAGGGTTGAG 60.179 55.0 0.00 0.00 41.01 3.02 F
957 1002 0.523072 TTCTGCATTTGCTCTTCCGC 59.477 50.0 3.94 0.00 42.66 5.54 F
1333 1378 0.035152 TGTGCACATCATCCCTGACC 60.035 55.0 17.42 0.00 33.22 4.02 F
2343 2397 0.812014 TAGCTCGACGAGAGGCTGAG 60.812 60.0 28.43 0.24 46.91 3.35 F
3289 3354 0.549950 ACCATGAGGGCCATCTTCTG 59.450 55.0 19.75 12.79 42.05 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1317 1362 1.099879 GCAGGTCAGGGATGATGTGC 61.100 60.000 0.00 0.0 0.0 4.57 R
2913 2976 1.669779 GTCATCACTTGCAGCTGGATC 59.330 52.381 17.12 0.0 0.0 3.36 R
3275 3340 0.322816 TGCAACAGAAGATGGCCCTC 60.323 55.000 0.00 0.0 0.0 4.30 R
3395 3460 0.469144 GGGTTGGTTTGGGCTTCTCA 60.469 55.000 0.00 0.0 0.0 3.27 R
4408 4563 0.249073 CGACTCCCTACTTGATGCCG 60.249 60.000 0.00 0.0 0.0 5.69 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
42 46 3.732849 CTTCACTGCCCCTCCCCC 61.733 72.222 0.00 0.00 0.00 5.40
85 89 3.859414 GCGCATCTGGCTCCCTCT 61.859 66.667 0.30 0.00 41.67 3.69
86 90 2.420890 CGCATCTGGCTCCCTCTC 59.579 66.667 0.00 0.00 41.67 3.20
287 311 1.529244 GCTTGCTGTGGTCAAGGGT 60.529 57.895 5.10 0.00 40.79 4.34
289 313 0.670162 CTTGCTGTGGTCAAGGGTTG 59.330 55.000 0.00 0.00 37.77 3.77
291 315 0.179020 TGCTGTGGTCAAGGGTTGAG 60.179 55.000 0.00 0.00 41.01 3.02
292 316 0.890996 GCTGTGGTCAAGGGTTGAGG 60.891 60.000 0.00 0.00 41.01 3.86
293 317 0.890996 CTGTGGTCAAGGGTTGAGGC 60.891 60.000 0.00 0.00 41.01 4.70
310 334 1.821332 GCGGAGGGGCTGATTCTTG 60.821 63.158 0.00 0.00 0.00 3.02
343 367 2.442272 GGAGGCGTCCCTGCTAGA 60.442 66.667 14.75 0.00 45.41 2.43
345 369 2.443016 AGGCGTCCCTGCTAGAGG 60.443 66.667 0.00 0.00 40.94 3.69
350 374 4.777854 TCCCTGCTAGAGGCGGCA 62.778 66.667 13.08 0.00 45.46 5.69
451 491 2.046217 GTCGAGTGGGGAAAGGGC 60.046 66.667 0.00 0.00 0.00 5.19
455 495 1.460699 GAGTGGGGAAAGGGCAAGT 59.539 57.895 0.00 0.00 0.00 3.16
494 535 3.093278 CTGAAATGCGACGGGAGC 58.907 61.111 0.00 0.00 0.00 4.70
511 552 2.159462 GGAGCGCTGAAATTCAGGAAAG 60.159 50.000 18.48 0.15 44.43 2.62
513 554 2.485814 AGCGCTGAAATTCAGGAAAGAC 59.514 45.455 22.73 5.68 44.43 3.01
606 648 1.476085 TGCCTCTTGTTGTGTGTTTGG 59.524 47.619 0.00 0.00 0.00 3.28
634 676 7.032580 GCTCTACTCCTATGCTATATGTGTTG 58.967 42.308 0.00 0.00 0.00 3.33
635 677 7.309499 GCTCTACTCCTATGCTATATGTGTTGT 60.309 40.741 0.00 0.00 0.00 3.32
637 679 6.485830 ACTCCTATGCTATATGTGTTGTGT 57.514 37.500 0.00 0.00 0.00 3.72
639 681 6.986817 ACTCCTATGCTATATGTGTTGTGTTC 59.013 38.462 0.00 0.00 0.00 3.18
641 683 6.761242 TCCTATGCTATATGTGTTGTGTTCAC 59.239 38.462 0.00 0.00 36.48 3.18
644 686 5.066593 TGCTATATGTGTTGTGTTCACCAA 58.933 37.500 0.37 0.00 35.25 3.67
645 687 5.049060 TGCTATATGTGTTGTGTTCACCAAC 60.049 40.000 0.37 0.00 41.97 3.77
646 688 5.181245 GCTATATGTGTTGTGTTCACCAACT 59.819 40.000 14.19 3.75 42.09 3.16
647 689 6.293955 GCTATATGTGTTGTGTTCACCAACTT 60.294 38.462 14.19 6.60 42.09 2.66
648 690 3.840890 TGTGTTGTGTTCACCAACTTC 57.159 42.857 14.19 10.22 42.09 3.01
649 691 2.490115 TGTGTTGTGTTCACCAACTTCC 59.510 45.455 14.19 7.37 42.09 3.46
653 695 2.639065 TGTGTTCACCAACTTCCAGTC 58.361 47.619 0.37 0.00 33.17 3.51
654 696 1.947456 GTGTTCACCAACTTCCAGTCC 59.053 52.381 0.00 0.00 33.17 3.85
655 697 1.843851 TGTTCACCAACTTCCAGTCCT 59.156 47.619 0.00 0.00 33.17 3.85
656 698 3.042682 TGTTCACCAACTTCCAGTCCTA 58.957 45.455 0.00 0.00 33.17 2.94
692 737 9.768662 TTTATGTTATTATTACTCCCTCCGTTC 57.231 33.333 0.00 0.00 0.00 3.95
693 738 6.165700 TGTTATTATTACTCCCTCCGTTCC 57.834 41.667 0.00 0.00 0.00 3.62
694 739 5.901276 TGTTATTATTACTCCCTCCGTTCCT 59.099 40.000 0.00 0.00 0.00 3.36
696 741 7.564660 TGTTATTATTACTCCCTCCGTTCCTAA 59.435 37.037 0.00 0.00 0.00 2.69
697 742 8.424133 GTTATTATTACTCCCTCCGTTCCTAAA 58.576 37.037 0.00 0.00 0.00 1.85
698 743 7.628501 ATTATTACTCCCTCCGTTCCTAAAT 57.371 36.000 0.00 0.00 0.00 1.40
699 744 8.731591 ATTATTACTCCCTCCGTTCCTAAATA 57.268 34.615 0.00 0.00 0.00 1.40
700 745 8.731591 TTATTACTCCCTCCGTTCCTAAATAT 57.268 34.615 0.00 0.00 0.00 1.28
701 746 7.628501 ATTACTCCCTCCGTTCCTAAATATT 57.371 36.000 0.00 0.00 0.00 1.28
703 748 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
704 749 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
705 750 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
707 752 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
708 753 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
709 754 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
710 755 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
712 757 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
713 758 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
738 783 9.350357 GAGATTTTAACAAGTGACTACATACGA 57.650 33.333 0.00 0.00 0.00 3.43
739 784 9.701098 AGATTTTAACAAGTGACTACATACGAA 57.299 29.630 0.00 0.00 0.00 3.85
740 785 9.953825 GATTTTAACAAGTGACTACATACGAAG 57.046 33.333 0.00 0.00 0.00 3.79
761 806 9.436957 ACGAAGTAAAATGAGTGAATCTACATT 57.563 29.630 0.00 0.00 41.94 2.71
785 830 8.642908 TTCTAAAATGTGTCTACATACATCCG 57.357 34.615 0.00 0.00 46.54 4.18
786 831 7.778083 TCTAAAATGTGTCTACATACATCCGT 58.222 34.615 0.00 0.00 46.54 4.69
788 833 9.692749 CTAAAATGTGTCTACATACATCCGTAT 57.307 33.333 0.00 0.00 46.54 3.06
792 837 9.639601 AATGTGTCTACATACATCCGTATATTG 57.360 33.333 0.00 0.00 46.54 1.90
795 840 9.770503 GTGTCTACATACATCCGTATATTGTAG 57.229 37.037 0.00 0.00 38.71 2.74
796 841 9.511272 TGTCTACATACATCCGTATATTGTAGT 57.489 33.333 0.00 0.00 38.60 2.73
797 842 9.985318 GTCTACATACATCCGTATATTGTAGTC 57.015 37.037 0.00 0.00 38.60 2.59
798 843 9.170734 TCTACATACATCCGTATATTGTAGTCC 57.829 37.037 0.00 0.00 38.60 3.85
803 848 7.962964 ACATCCGTATATTGTAGTCCATTTG 57.037 36.000 0.00 0.00 0.00 2.32
805 850 8.208224 ACATCCGTATATTGTAGTCCATTTGAA 58.792 33.333 0.00 0.00 0.00 2.69
806 851 9.219603 CATCCGTATATTGTAGTCCATTTGAAT 57.780 33.333 0.00 0.00 0.00 2.57
807 852 8.601845 TCCGTATATTGTAGTCCATTTGAATG 57.398 34.615 0.00 0.00 36.17 2.67
809 854 8.495949 CCGTATATTGTAGTCCATTTGAATGTC 58.504 37.037 3.30 0.00 34.60 3.06
810 855 9.261180 CGTATATTGTAGTCCATTTGAATGTCT 57.739 33.333 3.30 4.19 34.60 3.41
815 860 9.739276 ATTGTAGTCCATTTGAATGTCTAGAAA 57.261 29.630 0.00 0.00 33.18 2.52
816 861 8.777865 TGTAGTCCATTTGAATGTCTAGAAAG 57.222 34.615 0.00 0.00 34.60 2.62
834 879 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
836 881 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
837 882 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
838 883 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
839 884 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
840 885 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
845 890 3.393426 TTAGGAACGGAGGGAGTACAT 57.607 47.619 0.00 0.00 0.00 2.29
935 980 2.910319 AGTGGGTTGAGCATGGTAACTA 59.090 45.455 0.00 0.00 37.61 2.24
949 994 6.237915 GCATGGTAACTAATTTCTGCATTTGC 60.238 38.462 0.00 0.00 38.68 3.68
957 1002 0.523072 TTCTGCATTTGCTCTTCCGC 59.477 50.000 3.94 0.00 42.66 5.54
982 1027 2.975410 ATGTTGTGACAACTGATGCG 57.025 45.000 26.50 0.00 39.66 4.73
1164 1209 1.823295 CCCGTACAGATGGGTCCTG 59.177 63.158 0.00 0.00 45.96 3.86
1239 1284 0.655733 GGACTTTCACCACACACACG 59.344 55.000 0.00 0.00 0.00 4.49
1266 1311 1.819632 GGCCATGGTCATGACGGTC 60.820 63.158 19.33 12.89 41.20 4.79
1317 1362 0.453282 CGACGGCTTTGATGCTTGTG 60.453 55.000 0.00 0.00 0.00 3.33
1332 1377 1.741706 CTTGTGCACATCATCCCTGAC 59.258 52.381 22.39 0.00 33.22 3.51
1333 1378 0.035152 TGTGCACATCATCCCTGACC 60.035 55.000 17.42 0.00 33.22 4.02
1362 1407 1.531578 GTCAAAACGAGGGAGCTGTTC 59.468 52.381 0.00 0.00 0.00 3.18
1515 1560 2.551270 ACCATTGTGGAGCTAGGAAGA 58.449 47.619 2.45 0.00 40.96 2.87
1945 1992 2.143122 TCTCGAACACAATGCCACTTC 58.857 47.619 0.00 0.00 0.00 3.01
1963 2010 6.014925 GCCACTTCTTTTCCCTTGGTTATTTA 60.015 38.462 0.00 0.00 0.00 1.40
2000 2047 7.252612 TCATAGGAGTGAATGGTGTTTAAGA 57.747 36.000 0.00 0.00 0.00 2.10
2007 2054 7.346751 AGTGAATGGTGTTTAAGATGTTGTT 57.653 32.000 0.00 0.00 0.00 2.83
2014 2061 6.638873 TGGTGTTTAAGATGTTGTTAAATGCG 59.361 34.615 0.00 0.00 33.19 4.73
2040 2089 4.463515 CATGTGATGCTTTGACCGATAG 57.536 45.455 0.00 0.00 0.00 2.08
2058 2107 4.201970 CGATAGAGACTCTTCAACTGGGAC 60.202 50.000 10.96 0.00 39.76 4.46
2068 2117 6.207417 ACTCTTCAACTGGGACATGTTTTATG 59.793 38.462 0.00 0.00 38.20 1.90
2081 2130 9.769093 GGACATGTTTTATGTATTCACAACTAC 57.231 33.333 0.00 0.00 38.42 2.73
2091 2140 7.956420 TGTATTCACAACTACGAATTGTTCT 57.044 32.000 0.00 0.00 38.22 3.01
2093 2142 9.478768 TGTATTCACAACTACGAATTGTTCTAA 57.521 29.630 0.00 0.00 38.22 2.10
2162 2216 4.571919 TGAAACCGAACGATACCAAGATT 58.428 39.130 0.00 0.00 0.00 2.40
2163 2217 5.722263 TGAAACCGAACGATACCAAGATTA 58.278 37.500 0.00 0.00 0.00 1.75
2170 2224 9.017509 ACCGAACGATACCAAGATTAATAGATA 57.982 33.333 0.00 0.00 0.00 1.98
2171 2225 9.504710 CCGAACGATACCAAGATTAATAGATAG 57.495 37.037 0.00 0.00 0.00 2.08
2181 2235 9.930693 CCAAGATTAATAGATAGGGTCTAACAC 57.069 37.037 0.00 0.00 42.51 3.32
2343 2397 0.812014 TAGCTCGACGAGAGGCTGAG 60.812 60.000 28.43 0.24 46.91 3.35
2611 2665 2.603173 GCTGTTTTCAAAGAGGTCGCAG 60.603 50.000 0.00 0.00 30.60 5.18
2662 2721 6.042638 AGTCTGTATGCATACTTCACTTGT 57.957 37.500 31.35 11.30 34.41 3.16
2669 2728 6.882610 ATGCATACTTCACTTGTCTGAAAA 57.117 33.333 0.00 0.00 29.66 2.29
2702 2765 5.250200 GTGTTACAGGTGATGGGTTTCATA 58.750 41.667 0.00 0.00 35.97 2.15
2913 2976 3.003480 GAGTTCAGAACCCCAGATTTCG 58.997 50.000 9.85 0.00 0.00 3.46
3106 3169 5.692115 TGGAGATACCTTTGCTCAACATA 57.308 39.130 0.00 0.00 39.86 2.29
3156 3220 6.534634 ACCATTACTTATCACTATTGGGCTC 58.465 40.000 0.00 0.00 0.00 4.70
3196 3260 1.813513 AATCTCGGCTGGACTGTTTG 58.186 50.000 0.00 0.00 0.00 2.93
3287 3352 3.620966 GCTATACCATGAGGGCCATCTTC 60.621 52.174 19.75 3.91 42.05 2.87
3289 3354 0.549950 ACCATGAGGGCCATCTTCTG 59.450 55.000 19.75 12.79 42.05 3.02
3296 3361 0.743097 GGGCCATCTTCTGTTGCATC 59.257 55.000 4.39 0.00 0.00 3.91
3300 3365 3.428589 GGCCATCTTCTGTTGCATCTTTC 60.429 47.826 0.00 0.00 0.00 2.62
3301 3366 3.442977 GCCATCTTCTGTTGCATCTTTCT 59.557 43.478 0.00 0.00 0.00 2.52
3316 3381 5.401674 GCATCTTTCTTGCAAAAACAGAGAG 59.598 40.000 0.00 0.00 39.90 3.20
3321 3386 4.423732 TCTTGCAAAAACAGAGAGCAAAC 58.576 39.130 0.00 0.00 43.63 2.93
3322 3387 3.865011 TGCAAAAACAGAGAGCAAACA 57.135 38.095 0.00 0.00 31.42 2.83
3329 3394 2.042464 ACAGAGAGCAAACAGAGACCA 58.958 47.619 0.00 0.00 0.00 4.02
3344 3409 4.272018 CAGAGACCAAGATTGAATTAGCCG 59.728 45.833 0.00 0.00 0.00 5.52
3350 3415 6.156519 ACCAAGATTGAATTAGCCGAAAAAC 58.843 36.000 0.00 0.00 0.00 2.43
3351 3416 5.576774 CCAAGATTGAATTAGCCGAAAAACC 59.423 40.000 0.00 0.00 0.00 3.27
3357 3422 4.279671 TGAATTAGCCGAAAAACCACACAT 59.720 37.500 0.00 0.00 0.00 3.21
3361 3426 2.627699 AGCCGAAAAACCACACATCATT 59.372 40.909 0.00 0.00 0.00 2.57
3362 3427 3.823873 AGCCGAAAAACCACACATCATTA 59.176 39.130 0.00 0.00 0.00 1.90
3395 3460 4.080695 ACATGAAGCAGTGGTACATGAGAT 60.081 41.667 0.00 0.00 44.52 2.75
3401 3466 4.118410 GCAGTGGTACATGAGATGAGAAG 58.882 47.826 0.00 0.00 44.52 2.85
3419 3484 1.906333 GCCCAAACCAACCCATCGT 60.906 57.895 0.00 0.00 0.00 3.73
3435 3500 3.873361 CCATCGTGTTCTCAACTATGCAT 59.127 43.478 3.79 3.79 0.00 3.96
3482 3548 8.571336 ACAAAAACTTCCATCAGATTCAGTTAG 58.429 33.333 0.80 0.00 0.00 2.34
3483 3549 7.693969 AAAACTTCCATCAGATTCAGTTAGG 57.306 36.000 0.80 0.00 0.00 2.69
3504 3570 9.003658 GTTAGGAGAACATTTCATCAGAAAAGA 57.996 33.333 0.00 0.00 46.06 2.52
3505 3571 9.573166 TTAGGAGAACATTTCATCAGAAAAGAA 57.427 29.630 0.00 0.00 46.06 2.52
3511 3577 7.144722 ACATTTCATCAGAAAAGAACGCATA 57.855 32.000 0.00 0.00 46.06 3.14
3524 3590 4.926244 AGAACGCATACTGACATGACTAG 58.074 43.478 0.00 0.00 0.00 2.57
3527 3593 4.673441 ACGCATACTGACATGACTAGAAC 58.327 43.478 0.00 0.00 0.00 3.01
3528 3594 4.399618 ACGCATACTGACATGACTAGAACT 59.600 41.667 0.00 0.00 0.00 3.01
3529 3595 4.973051 CGCATACTGACATGACTAGAACTC 59.027 45.833 0.00 0.00 0.00 3.01
3530 3596 5.220951 CGCATACTGACATGACTAGAACTCT 60.221 44.000 0.00 0.00 0.00 3.24
3544 3611 4.891992 AGAACTCTGGTTTAGCTGCTAA 57.108 40.909 17.67 17.67 35.58 3.09
3550 3617 2.151202 TGGTTTAGCTGCTAACAGTGC 58.849 47.619 20.95 9.35 46.30 4.40
3562 3629 3.181450 GCTAACAGTGCTCCTGGGAATAT 60.181 47.826 8.50 0.00 46.06 1.28
3563 3630 4.687219 GCTAACAGTGCTCCTGGGAATATT 60.687 45.833 8.50 0.00 46.06 1.28
3630 3701 3.940209 TGCCACAGAAACATGGATTTC 57.060 42.857 0.00 0.00 38.34 2.17
3631 3702 3.229293 TGCCACAGAAACATGGATTTCA 58.771 40.909 10.43 0.00 40.43 2.69
3638 3709 6.860023 CACAGAAACATGGATTTCAAGAGAAC 59.140 38.462 10.43 0.00 40.43 3.01
3645 3716 5.047566 TGGATTTCAAGAGAACTGGTTGA 57.952 39.130 0.00 0.00 32.39 3.18
3655 3726 6.966534 AGAGAACTGGTTGATCAAAAACAT 57.033 33.333 10.35 0.00 0.00 2.71
3659 3730 9.132521 GAGAACTGGTTGATCAAAAACATTATG 57.867 33.333 10.35 1.41 0.00 1.90
3679 3750 9.277565 CATTATGTAACTGTAAAACTGATGTGC 57.722 33.333 0.00 0.00 0.00 4.57
3686 3757 6.615088 ACTGTAAAACTGATGTGCAATCATC 58.385 36.000 9.74 9.74 42.95 2.92
3702 3853 8.895845 GTGCAATCATCATTTAATTACTTAGCG 58.104 33.333 0.00 0.00 0.00 4.26
3771 3922 1.876156 GATACAGGCTGTGGCATTAGC 59.124 52.381 29.65 15.70 40.87 3.09
3827 3978 1.623811 TCAAACTCAGCCTGGAGGTAC 59.376 52.381 0.00 0.00 39.27 3.34
3913 4064 4.205587 TCGATCTCCTTACTTGTAGACCC 58.794 47.826 0.00 0.00 0.00 4.46
4250 4403 0.169672 CGTATCCGACAACACCGACT 59.830 55.000 0.00 0.00 35.63 4.18
4407 4562 1.298563 TAAACTATCGACGGCGCCG 60.299 57.895 44.88 44.88 46.03 6.46
4437 5013 3.807553 AGTAGGGAGTCGTAGCTAGTTC 58.192 50.000 0.00 0.00 0.00 3.01
4466 5042 4.080299 CCCCTCTAATTTTGTGCCTAGTCT 60.080 45.833 0.00 0.00 0.00 3.24
4542 5118 1.616159 TTGCAGTTAAGTTCCTGGGC 58.384 50.000 0.00 0.00 0.00 5.36
4567 5143 1.283793 CCAACTTGCTGCGTTCAGG 59.716 57.895 0.00 0.00 40.65 3.86
4599 5175 4.677514 CGGTCAGCCAATTTGCATATTTCA 60.678 41.667 4.12 0.00 34.09 2.69
4603 5179 6.369615 GTCAGCCAATTTGCATATTTCAAGTT 59.630 34.615 4.12 0.00 0.00 2.66
4608 5184 4.644044 TTTGCATATTTCAAGTTTGCGC 57.356 36.364 0.00 0.00 36.11 6.09
4625 5201 0.108804 CGCGAGCCCGGTTATATCAT 60.109 55.000 0.00 0.00 36.06 2.45
4644 5226 3.498777 TCATATCGAAGCTACTCTCCGTG 59.501 47.826 0.00 0.00 0.00 4.94
4645 5227 1.025812 ATCGAAGCTACTCTCCGTGG 58.974 55.000 0.00 0.00 0.00 4.94
4646 5228 0.035725 TCGAAGCTACTCTCCGTGGA 60.036 55.000 0.00 0.00 0.00 4.02
4647 5229 0.809385 CGAAGCTACTCTCCGTGGAA 59.191 55.000 0.00 0.00 0.00 3.53
4648 5230 1.201647 CGAAGCTACTCTCCGTGGAAA 59.798 52.381 0.00 0.00 0.00 3.13
4649 5231 2.159226 CGAAGCTACTCTCCGTGGAAAT 60.159 50.000 0.00 0.00 0.00 2.17
4682 5264 6.415702 TGTGTAAAAGTTTCGACGAATTCTG 58.584 36.000 11.71 0.00 0.00 3.02
4865 5457 4.657814 AATAGGTGGGCTCTTTTCTGAA 57.342 40.909 0.00 0.00 0.00 3.02
4884 7722 6.715280 TCTGAAAAAGATAGGAACATGCTCT 58.285 36.000 0.00 0.00 0.00 4.09
4930 7796 6.308524 TCACTACAAATACACAAACCGATACG 59.691 38.462 0.00 0.00 0.00 3.06
4941 7807 2.494445 CGATACGCTGTGGCTCCA 59.506 61.111 0.00 0.00 36.09 3.86
4945 7811 2.610479 CGATACGCTGTGGCTCCATATT 60.610 50.000 0.00 0.00 36.09 1.28
4982 7877 5.551760 CCATCAACTGGTAATGTGAAGAC 57.448 43.478 0.00 0.00 40.49 3.01
5064 7963 5.565259 GTGAATGTAATCTTTGCACGTCAAG 59.435 40.000 0.00 0.00 35.84 3.02
5344 8256 4.269363 GGCATTGAAGCATAAGATTTGTGC 59.731 41.667 2.78 2.78 46.60 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 89 1.396594 GAAGGAAGGGAGGGAGGGA 59.603 63.158 0.00 0.00 0.00 4.20
86 90 1.694525 GGAAGGAAGGGAGGGAGGG 60.695 68.421 0.00 0.00 0.00 4.30
289 313 3.468326 GAATCAGCCCCTCCGCCTC 62.468 68.421 0.00 0.00 0.00 4.70
291 315 3.049080 AAGAATCAGCCCCTCCGCC 62.049 63.158 0.00 0.00 0.00 6.13
292 316 1.821332 CAAGAATCAGCCCCTCCGC 60.821 63.158 0.00 0.00 0.00 5.54
293 317 1.153086 CCAAGAATCAGCCCCTCCG 60.153 63.158 0.00 0.00 0.00 4.63
301 325 1.755783 GCCTGCCCCCAAGAATCAG 60.756 63.158 0.00 0.00 0.00 2.90
332 356 4.228567 GCCGCCTCTAGCAGGGAC 62.229 72.222 9.44 0.00 43.70 4.46
374 398 0.526524 AAGCGATCGGAGCGAAGAAG 60.527 55.000 20.91 0.00 39.99 2.85
451 491 2.791158 GCGTGTCACTTGAAACCACTTG 60.791 50.000 0.65 0.00 0.00 3.16
455 495 1.433053 CCGCGTGTCACTTGAAACCA 61.433 55.000 4.92 0.00 0.00 3.67
494 535 4.453819 AGAAGTCTTTCCTGAATTTCAGCG 59.546 41.667 19.04 12.93 42.98 5.18
511 552 4.269844 GGCATCTCTGAATTTCGAGAAGTC 59.730 45.833 18.20 14.13 39.49 3.01
513 554 4.186926 TGGCATCTCTGAATTTCGAGAAG 58.813 43.478 18.20 15.96 39.49 2.85
606 648 1.535833 TAGCATAGGAGTAGAGCGCC 58.464 55.000 2.29 0.00 37.31 6.53
679 724 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
680 725 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
681 726 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
682 727 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
684 729 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
685 730 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
686 731 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
687 732 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
712 757 9.350357 TCGTATGTAGTCACTTGTTAAAATCTC 57.650 33.333 0.00 0.00 0.00 2.75
713 758 9.701098 TTCGTATGTAGTCACTTGTTAAAATCT 57.299 29.630 0.00 0.00 0.00 2.40
714 759 9.953825 CTTCGTATGTAGTCACTTGTTAAAATC 57.046 33.333 0.00 0.00 0.00 2.17
715 760 9.485206 ACTTCGTATGTAGTCACTTGTTAAAAT 57.515 29.630 0.00 0.00 0.00 1.82
716 761 8.876275 ACTTCGTATGTAGTCACTTGTTAAAA 57.124 30.769 0.00 0.00 0.00 1.52
717 762 9.964303 TTACTTCGTATGTAGTCACTTGTTAAA 57.036 29.630 0.00 0.00 0.00 1.52
718 763 9.964303 TTTACTTCGTATGTAGTCACTTGTTAA 57.036 29.630 0.00 0.00 0.00 2.01
720 765 8.876275 TTTTACTTCGTATGTAGTCACTTGTT 57.124 30.769 0.00 0.00 0.00 2.83
721 766 8.922676 CATTTTACTTCGTATGTAGTCACTTGT 58.077 33.333 0.00 0.00 0.00 3.16
722 767 9.135843 TCATTTTACTTCGTATGTAGTCACTTG 57.864 33.333 0.00 0.00 0.00 3.16
723 768 9.355215 CTCATTTTACTTCGTATGTAGTCACTT 57.645 33.333 0.00 0.00 0.00 3.16
725 770 8.584600 CACTCATTTTACTTCGTATGTAGTCAC 58.415 37.037 0.00 0.00 0.00 3.67
726 771 8.517056 TCACTCATTTTACTTCGTATGTAGTCA 58.483 33.333 0.00 0.00 0.00 3.41
727 772 8.906636 TCACTCATTTTACTTCGTATGTAGTC 57.093 34.615 0.00 0.00 0.00 2.59
728 773 9.871238 ATTCACTCATTTTACTTCGTATGTAGT 57.129 29.630 0.00 0.00 0.00 2.73
735 780 9.436957 AATGTAGATTCACTCATTTTACTTCGT 57.563 29.630 0.00 0.00 0.00 3.85
759 804 9.261180 CGGATGTATGTAGACACATTTTAGAAT 57.739 33.333 0.00 0.00 42.98 2.40
761 806 7.778083 ACGGATGTATGTAGACACATTTTAGA 58.222 34.615 0.00 0.00 42.98 2.10
766 811 9.639601 CAATATACGGATGTATGTAGACACATT 57.360 33.333 0.00 0.00 42.98 2.71
768 813 8.173542 ACAATATACGGATGTATGTAGACACA 57.826 34.615 0.00 0.00 41.37 3.72
769 814 9.770503 CTACAATATACGGATGTATGTAGACAC 57.229 37.037 17.69 0.00 40.69 3.67
770 815 9.511272 ACTACAATATACGGATGTATGTAGACA 57.489 33.333 24.44 0.00 40.69 3.41
772 817 9.170734 GGACTACAATATACGGATGTATGTAGA 57.829 37.037 24.44 2.20 40.69 2.59
773 818 8.953313 TGGACTACAATATACGGATGTATGTAG 58.047 37.037 19.56 19.56 42.27 2.74
774 819 8.866970 TGGACTACAATATACGGATGTATGTA 57.133 34.615 0.00 0.00 41.37 2.29
776 821 9.653287 AAATGGACTACAATATACGGATGTATG 57.347 33.333 0.00 0.00 41.37 2.39
778 823 8.862085 TCAAATGGACTACAATATACGGATGTA 58.138 33.333 0.00 0.00 34.45 2.29
779 824 7.732025 TCAAATGGACTACAATATACGGATGT 58.268 34.615 0.00 0.00 0.00 3.06
780 825 8.601845 TTCAAATGGACTACAATATACGGATG 57.398 34.615 0.00 0.00 0.00 3.51
781 826 9.219603 CATTCAAATGGACTACAATATACGGAT 57.780 33.333 0.00 0.00 32.78 4.18
783 828 8.378172 ACATTCAAATGGACTACAATATACGG 57.622 34.615 7.58 0.00 40.70 4.02
789 834 9.739276 TTTCTAGACATTCAAATGGACTACAAT 57.261 29.630 7.58 0.00 40.70 2.71
809 854 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
810 855 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
811 856 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
812 857 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
813 858 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
814 859 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
815 860 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
816 861 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
820 865 5.901276 TGTACTCCCTCCGTTCCTAAATATT 59.099 40.000 0.00 0.00 0.00 1.28
821 866 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
822 867 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
823 868 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
824 869 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
825 870 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
826 871 4.524802 TTATGTACTCCCTCCGTTCCTA 57.475 45.455 0.00 0.00 0.00 2.94
827 872 3.393426 TTATGTACTCCCTCCGTTCCT 57.607 47.619 0.00 0.00 0.00 3.36
828 873 4.502777 GGAATTATGTACTCCCTCCGTTCC 60.503 50.000 0.00 0.00 0.00 3.62
829 874 4.344390 AGGAATTATGTACTCCCTCCGTTC 59.656 45.833 0.00 0.00 0.00 3.95
831 876 3.641906 CAGGAATTATGTACTCCCTCCGT 59.358 47.826 0.00 0.00 0.00 4.69
832 877 3.641906 ACAGGAATTATGTACTCCCTCCG 59.358 47.826 0.00 0.00 0.00 4.63
833 878 5.632034 AACAGGAATTATGTACTCCCTCC 57.368 43.478 0.00 0.00 0.00 4.30
834 879 7.362802 AGTAACAGGAATTATGTACTCCCTC 57.637 40.000 0.00 0.00 0.00 4.30
836 881 9.895138 TTAAAGTAACAGGAATTATGTACTCCC 57.105 33.333 0.00 0.00 0.00 4.30
867 912 8.946085 CAACAACACTACAACAGGTTCATATAT 58.054 33.333 0.00 0.00 0.00 0.86
880 925 4.196193 CTGGAACTCCAACAACACTACAA 58.804 43.478 0.00 0.00 46.97 2.41
884 929 1.064758 TGCTGGAACTCCAACAACACT 60.065 47.619 0.00 0.00 46.97 3.55
935 980 3.841643 CGGAAGAGCAAATGCAGAAATT 58.158 40.909 8.28 0.00 45.16 1.82
957 1002 3.213506 TCAGTTGTCACAACATTCCCTG 58.786 45.455 22.66 10.79 34.73 4.45
1038 1083 0.108424 ACTTGATGAGCAGCTCGTCC 60.108 55.000 32.87 19.71 43.59 4.79
1164 1209 1.909700 TGAAGGCACCAAACTGGATC 58.090 50.000 0.00 0.00 40.96 3.36
1200 1245 2.618045 CCACAGGTTTATGAGGTGGGTC 60.618 54.545 0.00 0.00 44.06 4.46
1239 1284 1.745489 GACCATGGCCACGGTCTTC 60.745 63.158 37.63 17.50 46.83 2.87
1266 1311 4.084888 GCCGTCGAAACCTTGGCG 62.085 66.667 0.00 0.00 35.77 5.69
1317 1362 1.099879 GCAGGTCAGGGATGATGTGC 61.100 60.000 0.00 0.00 0.00 4.57
1332 1377 1.528586 CTCGTTTTGACACTCAGCAGG 59.471 52.381 0.00 0.00 0.00 4.85
1333 1378 1.528586 CCTCGTTTTGACACTCAGCAG 59.471 52.381 0.00 0.00 0.00 4.24
1362 1407 3.743899 GCTCCTCAGCCTTATTCTTCAGG 60.744 52.174 0.00 0.00 40.14 3.86
1515 1560 1.421646 CACTCTTCCAGACCCAAGGTT 59.578 52.381 0.00 0.00 35.25 3.50
1974 2021 7.606456 TCTTAAACACCATTCACTCCTATGAAC 59.394 37.037 0.00 0.00 41.29 3.18
1977 2024 7.554118 ACATCTTAAACACCATTCACTCCTATG 59.446 37.037 0.00 0.00 0.00 2.23
1978 2025 7.633789 ACATCTTAAACACCATTCACTCCTAT 58.366 34.615 0.00 0.00 0.00 2.57
1983 2030 6.959639 ACAACATCTTAAACACCATTCACT 57.040 33.333 0.00 0.00 0.00 3.41
2028 2075 5.568685 TGAAGAGTCTCTATCGGTCAAAG 57.431 43.478 1.88 0.00 0.00 2.77
2031 2078 4.396478 CAGTTGAAGAGTCTCTATCGGTCA 59.604 45.833 1.88 0.00 0.00 4.02
2036 2085 4.707448 TGTCCCAGTTGAAGAGTCTCTATC 59.293 45.833 1.88 4.22 0.00 2.08
2039 2088 2.964209 TGTCCCAGTTGAAGAGTCTCT 58.036 47.619 0.00 0.00 0.00 3.10
2040 2089 3.007398 ACATGTCCCAGTTGAAGAGTCTC 59.993 47.826 0.00 0.00 0.00 3.36
2147 2201 9.804758 CCCTATCTATTAATCTTGGTATCGTTC 57.195 37.037 0.00 0.00 0.00 3.95
2150 2204 9.191479 AGACCCTATCTATTAATCTTGGTATCG 57.809 37.037 0.00 0.00 35.15 2.92
2163 2217 9.830186 ATGTATCAGTGTTAGACCCTATCTATT 57.170 33.333 0.00 0.00 39.75 1.73
2170 2224 7.914427 TGATAATGTATCAGTGTTAGACCCT 57.086 36.000 0.00 0.00 40.09 4.34
2289 2343 8.107591 CAACATTTTGCTCCATTAGTAAATCG 57.892 34.615 0.00 0.00 39.21 3.34
2343 2397 2.969238 CGAGCACGGATGGCCATC 60.969 66.667 33.90 33.90 37.11 3.51
2653 2712 7.253750 CCAACGAAAATTTTCAGACAAGTGAAG 60.254 37.037 26.20 10.85 37.72 3.02
2662 2721 6.853720 TGTAACACCAACGAAAATTTTCAGA 58.146 32.000 26.20 3.82 37.01 3.27
2669 2728 4.200874 TCACCTGTAACACCAACGAAAAT 58.799 39.130 0.00 0.00 0.00 1.82
2702 2765 4.592942 TCTTGATAGCTGCAATTGGTCTT 58.407 39.130 7.72 0.00 0.00 3.01
2913 2976 1.669779 GTCATCACTTGCAGCTGGATC 59.330 52.381 17.12 0.00 0.00 3.36
3106 3169 7.994911 TCAGAAGTGGCTAATTTCATACATCAT 59.005 33.333 0.00 0.00 0.00 2.45
3156 3220 2.202987 GATGTGCCTCGAGCCCAG 60.203 66.667 6.99 0.00 42.71 4.45
3174 3238 0.976641 ACAGTCCAGCCGAGATTTCA 59.023 50.000 0.00 0.00 0.00 2.69
3196 3260 4.214332 GGACAACTTGAAGATGACTTGACC 59.786 45.833 9.53 4.18 36.39 4.02
3275 3340 0.322816 TGCAACAGAAGATGGCCCTC 60.323 55.000 0.00 0.00 0.00 4.30
3296 3361 4.675510 TGCTCTCTGTTTTTGCAAGAAAG 58.324 39.130 3.66 5.07 0.00 2.62
3300 3365 4.175516 TGTTTGCTCTCTGTTTTTGCAAG 58.824 39.130 0.00 0.00 43.13 4.01
3301 3366 4.082300 TCTGTTTGCTCTCTGTTTTTGCAA 60.082 37.500 0.00 0.00 41.10 4.08
3307 3372 3.118261 TGGTCTCTGTTTGCTCTCTGTTT 60.118 43.478 0.00 0.00 0.00 2.83
3312 3377 3.393089 TCTTGGTCTCTGTTTGCTCTC 57.607 47.619 0.00 0.00 0.00 3.20
3316 3381 4.836125 TTCAATCTTGGTCTCTGTTTGC 57.164 40.909 0.00 0.00 0.00 3.68
3321 3386 4.272018 CGGCTAATTCAATCTTGGTCTCTG 59.728 45.833 0.00 0.00 0.00 3.35
3322 3387 4.162320 TCGGCTAATTCAATCTTGGTCTCT 59.838 41.667 0.00 0.00 0.00 3.10
3329 3394 6.156519 GTGGTTTTTCGGCTAATTCAATCTT 58.843 36.000 0.00 0.00 0.00 2.40
3344 3409 9.868277 TCCATTTATAATGATGTGTGGTTTTTC 57.132 29.630 1.11 0.00 0.00 2.29
3350 3415 9.251792 CATGTTTCCATTTATAATGATGTGTGG 57.748 33.333 1.11 0.00 0.00 4.17
3357 3422 8.970020 ACTGCTTCATGTTTCCATTTATAATGA 58.030 29.630 1.11 0.00 0.00 2.57
3361 3426 6.663093 ACCACTGCTTCATGTTTCCATTTATA 59.337 34.615 0.00 0.00 0.00 0.98
3362 3427 5.481473 ACCACTGCTTCATGTTTCCATTTAT 59.519 36.000 0.00 0.00 0.00 1.40
3395 3460 0.469144 GGGTTGGTTTGGGCTTCTCA 60.469 55.000 0.00 0.00 0.00 3.27
3401 3466 1.906333 ACGATGGGTTGGTTTGGGC 60.906 57.895 0.00 0.00 0.00 5.36
3419 3484 2.931969 CGCTCATGCATAGTTGAGAACA 59.068 45.455 17.26 0.00 41.53 3.18
3471 3537 8.324306 TGATGAAATGTTCTCCTAACTGAATCT 58.676 33.333 0.00 0.00 0.00 2.40
3482 3548 6.798959 CGTTCTTTTCTGATGAAATGTTCTCC 59.201 38.462 0.00 0.00 41.24 3.71
3483 3549 6.304208 GCGTTCTTTTCTGATGAAATGTTCTC 59.696 38.462 0.00 0.00 41.24 2.87
3504 3570 4.983671 TCTAGTCATGTCAGTATGCGTT 57.016 40.909 0.00 0.00 34.76 4.84
3505 3571 4.399618 AGTTCTAGTCATGTCAGTATGCGT 59.600 41.667 0.00 0.00 34.76 5.24
3511 3577 4.411927 ACCAGAGTTCTAGTCATGTCAGT 58.588 43.478 0.00 0.00 0.00 3.41
3524 3590 4.315803 TGTTAGCAGCTAAACCAGAGTTC 58.684 43.478 16.74 1.89 34.19 3.01
3527 3593 3.681897 CACTGTTAGCAGCTAAACCAGAG 59.318 47.826 27.64 20.28 46.30 3.35
3528 3594 3.664107 CACTGTTAGCAGCTAAACCAGA 58.336 45.455 27.64 4.61 46.30 3.86
3529 3595 2.160417 GCACTGTTAGCAGCTAAACCAG 59.840 50.000 22.56 22.56 46.30 4.00
3530 3596 2.151202 GCACTGTTAGCAGCTAAACCA 58.849 47.619 16.74 10.42 46.30 3.67
3544 3611 4.040755 AGTAATATTCCCAGGAGCACTGT 58.959 43.478 7.53 0.00 46.06 3.55
3593 3661 4.637091 TGTGGCATGTTCATGATCTGTAAG 59.363 41.667 15.74 0.00 0.00 2.34
3630 3701 6.563422 TGTTTTTGATCAACCAGTTCTCTTG 58.437 36.000 7.89 0.00 0.00 3.02
3631 3702 6.773976 TGTTTTTGATCAACCAGTTCTCTT 57.226 33.333 7.89 0.00 0.00 2.85
3638 3709 9.912634 AGTTACATAATGTTTTTGATCAACCAG 57.087 29.630 7.89 0.00 0.00 4.00
3655 3726 8.384607 TGCACATCAGTTTTACAGTTACATAA 57.615 30.769 0.00 0.00 0.00 1.90
3659 3730 7.359595 TGATTGCACATCAGTTTTACAGTTAC 58.640 34.615 7.27 0.00 0.00 2.50
3686 3757 9.450807 CCAGGAAAATCGCTAAGTAATTAAATG 57.549 33.333 0.00 0.00 0.00 2.32
3687 3758 9.185680 ACCAGGAAAATCGCTAAGTAATTAAAT 57.814 29.630 0.00 0.00 0.00 1.40
3688 3759 8.570068 ACCAGGAAAATCGCTAAGTAATTAAA 57.430 30.769 0.00 0.00 0.00 1.52
3689 3760 8.570068 AACCAGGAAAATCGCTAAGTAATTAA 57.430 30.769 0.00 0.00 0.00 1.40
3691 3762 8.747538 ATAACCAGGAAAATCGCTAAGTAATT 57.252 30.769 0.00 0.00 0.00 1.40
3692 3763 8.747538 AATAACCAGGAAAATCGCTAAGTAAT 57.252 30.769 0.00 0.00 0.00 1.89
3693 3764 9.669887 TTAATAACCAGGAAAATCGCTAAGTAA 57.330 29.630 0.00 0.00 0.00 2.24
3695 3766 8.570068 TTTAATAACCAGGAAAATCGCTAAGT 57.430 30.769 0.00 0.00 0.00 2.24
3702 3853 7.122799 ACAGAGGCTTTAATAACCAGGAAAATC 59.877 37.037 0.00 0.00 0.00 2.17
3738 3889 3.117738 AGCCTGTATCCTTTAGCTGCAAT 60.118 43.478 1.02 0.00 0.00 3.56
3771 3922 1.356124 CATGGGGTAGATCCTGAGGG 58.644 60.000 0.00 0.00 36.25 4.30
3827 3978 2.170607 CCACTACCACTGTATCCTTGGG 59.829 54.545 0.00 0.00 34.41 4.12
3913 4064 7.223582 CCAAGCACAATAACATACACTCTAGAG 59.776 40.741 18.49 18.49 0.00 2.43
4028 4181 5.240183 TCCCTCCGTAACTCAATATAAGACG 59.760 44.000 0.00 0.00 0.00 4.18
4046 4199 9.823647 CATGACACAAATATATATACTCCCTCC 57.176 37.037 0.00 0.00 0.00 4.30
4065 4218 3.009143 AGTTAAGAACCCCTCCATGACAC 59.991 47.826 0.00 0.00 0.00 3.67
4210 4363 0.926155 CGAGCCTGATGATGAACGTG 59.074 55.000 0.00 0.00 0.00 4.49
4407 4562 0.530870 GACTCCCTACTTGATGCCGC 60.531 60.000 0.00 0.00 0.00 6.53
4408 4563 0.249073 CGACTCCCTACTTGATGCCG 60.249 60.000 0.00 0.00 0.00 5.69
4409 4564 0.824759 ACGACTCCCTACTTGATGCC 59.175 55.000 0.00 0.00 0.00 4.40
4466 5042 5.132502 ACAATATATGCCAGCTACAGCAAA 58.867 37.500 9.06 0.18 43.36 3.68
4504 5080 3.428589 GCAATCTGAAGTCCCATTTGCTC 60.429 47.826 0.00 0.00 34.74 4.26
4567 5143 0.815213 TTGGCTGACCGCATATGCTC 60.815 55.000 24.56 16.64 41.67 4.26
4603 5179 2.372040 ATATAACCGGGCTCGCGCAA 62.372 55.000 8.75 0.00 38.10 4.85
4608 5184 3.314357 TCGATATGATATAACCGGGCTCG 59.686 47.826 6.32 0.00 0.00 5.03
4644 5226 6.521162 ACTTTTACACATGGTTTCCATTTCC 58.479 36.000 0.00 0.00 42.23 3.13
4645 5227 8.432110 AAACTTTTACACATGGTTTCCATTTC 57.568 30.769 0.00 0.00 42.23 2.17
4646 5228 7.223777 CGAAACTTTTACACATGGTTTCCATTT 59.776 33.333 12.76 0.00 42.23 2.32
4647 5229 6.699642 CGAAACTTTTACACATGGTTTCCATT 59.300 34.615 12.76 0.00 42.23 3.16
4648 5230 6.039941 TCGAAACTTTTACACATGGTTTCCAT 59.960 34.615 12.76 0.00 46.37 3.41
4649 5231 5.357314 TCGAAACTTTTACACATGGTTTCCA 59.643 36.000 12.76 1.99 41.18 3.53
4682 5264 7.762588 ATCACCTCCACTGTATACATACTAC 57.237 40.000 5.91 0.00 34.41 2.73
4785 5373 7.913674 ACTTCTGTTTCTGGAACAAGATATC 57.086 36.000 2.68 0.00 46.99 1.63
4865 5457 7.630082 GCATTTCAGAGCATGTTCCTATCTTTT 60.630 37.037 5.87 0.00 0.00 2.27
4872 5464 2.097825 GGCATTTCAGAGCATGTTCCT 58.902 47.619 5.87 0.00 0.00 3.36
4884 7722 4.541250 AGGATATTCCTTGGGCATTTCA 57.459 40.909 0.00 0.00 46.91 2.69
4930 7796 2.099756 GGAAACAATATGGAGCCACAGC 59.900 50.000 0.00 0.00 40.32 4.40
4945 7811 4.709397 AGTTGATGGTCTTGTTTGGAAACA 59.291 37.500 0.70 0.70 46.35 2.83
4982 7877 3.435566 TCTAACTTCGTCGCAGCTTATG 58.564 45.455 0.00 0.00 0.00 1.90
5033 7932 6.747280 GTGCAAAGATTACATTCACCATGTAC 59.253 38.462 0.00 0.00 46.30 2.90
5263 8167 4.572389 GGTGTGCATAAGTACCATCTTCAG 59.428 45.833 0.00 0.00 33.42 3.02
5344 8256 6.208988 TGTTTACATCTGCTCCTAGTACTG 57.791 41.667 5.39 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.