Multiple sequence alignment - TraesCS3D01G247400

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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 TraesCS3D01G247400 chr3D 100.000 5041 0 0 1 5041 346638708 346643748 0.000000e+00 9310.0
1 TraesCS3D01G247400 chr3A 96.655 2661 77 4 825 3475 457088854 457086196 0.000000e+00 4410.0
2 TraesCS3D01G247400 chr3A 96.557 610 9 5 4440 5041 457085183 457084578 0.000000e+00 1000.0
3 TraesCS3D01G247400 chr3A 93.606 563 16 7 3863 4422 457085715 457085170 0.000000e+00 822.0
4 TraesCS3D01G247400 chr3A 98.214 224 3 1 3633 3855 457086195 457085972 1.700000e-104 390.0
5 TraesCS3D01G247400 chr3A 92.655 177 12 1 3470 3645 671642739 671642915 2.330000e-63 254.0
6 TraesCS3D01G247400 chr3A 85.377 212 23 6 4094 4305 550416958 550417161 3.950000e-51 213.0
7 TraesCS3D01G247400 chr3A 93.506 77 4 1 753 829 457094614 457094539 4.120000e-21 113.0
8 TraesCS3D01G247400 chr3B 93.564 2626 140 19 826 3430 446168720 446171337 0.000000e+00 3886.0
9 TraesCS3D01G247400 chr3B 96.073 382 12 2 4661 5041 446172525 446172904 1.990000e-173 619.0
10 TraesCS3D01G247400 chr3B 82.237 304 32 11 4096 4398 157245935 157245653 5.040000e-60 243.0
11 TraesCS3D01G247400 chr3B 90.805 174 12 3 3670 3839 446171458 446171631 3.930000e-56 230.0
12 TraesCS3D01G247400 chr3B 93.506 77 5 0 753 829 446144621 446144697 1.150000e-21 115.0
13 TraesCS3D01G247400 chr5A 90.160 752 60 10 1 738 136632427 136633178 0.000000e+00 966.0
14 TraesCS3D01G247400 chr5A 82.517 286 36 9 4116 4397 644359601 644359876 6.520000e-59 239.0
15 TraesCS3D01G247400 chr5A 89.474 57 5 1 682 738 616440301 616440356 2.520000e-08 71.3
16 TraesCS3D01G247400 chr5B 90.308 650 49 10 1 637 12345346 12345994 0.000000e+00 839.0
17 TraesCS3D01G247400 chr5B 88.926 298 27 5 449 742 36993572 36993277 3.710000e-96 363.0
18 TraesCS3D01G247400 chr5B 87.458 295 31 5 449 738 425385805 425385512 8.090000e-88 335.0
19 TraesCS3D01G247400 chr5B 87.805 287 31 3 449 731 507642549 507642263 2.910000e-87 333.0
20 TraesCS3D01G247400 chr5B 94.186 172 10 0 3470 3641 575812973 575812802 3.870000e-66 263.0
21 TraesCS3D01G247400 chr5B 80.412 291 45 10 4116 4400 649730527 649730811 1.420000e-50 211.0
22 TraesCS3D01G247400 chr2D 83.837 761 95 23 1 743 566725696 566724946 0.000000e+00 699.0
23 TraesCS3D01G247400 chr2D 85.760 625 71 13 2 613 626612591 626613210 0.000000e+00 645.0
24 TraesCS3D01G247400 chr2D 89.456 294 25 4 451 738 614807656 614807363 2.870000e-97 366.0
25 TraesCS3D01G247400 chr2D 92.697 178 13 0 3461 3638 135284802 135284979 1.800000e-64 257.0
26 TraesCS3D01G247400 chr2D 85.377 212 25 6 1 206 446879136 446879347 1.100000e-51 215.0
27 TraesCS3D01G247400 chr2D 80.788 203 34 5 4094 4293 614646701 614646901 2.430000e-33 154.0
28 TraesCS3D01G247400 chr2B 84.839 620 80 13 1 608 174366794 174367411 3.340000e-171 612.0
29 TraesCS3D01G247400 chr2B 94.186 172 10 0 3470 3641 719520673 719520502 3.870000e-66 263.0
30 TraesCS3D01G247400 chr2B 79.553 313 51 12 4094 4398 26559424 26559117 1.420000e-50 211.0
31 TraesCS3D01G247400 chr1B 81.081 740 113 21 21 738 130781020 130781754 2.630000e-157 566.0
32 TraesCS3D01G247400 chr1B 80.526 760 117 24 4 738 131120850 131121603 5.700000e-154 555.0
33 TraesCS3D01G247400 chr1B 80.108 553 85 21 206 738 131371474 131372021 6.120000e-104 388.0
34 TraesCS3D01G247400 chr4D 83.628 623 64 14 1 612 49845662 49845067 7.380000e-153 551.0
35 TraesCS3D01G247400 chr6A 88.814 295 27 5 449 738 77156454 77156161 1.730000e-94 357.0
36 TraesCS3D01G247400 chr7B 83.662 355 51 5 1 348 138783244 138782890 1.350000e-85 327.0
37 TraesCS3D01G247400 chr7B 86.254 291 35 4 451 738 558265902 558265614 1.360000e-80 311.0
38 TraesCS3D01G247400 chr6B 86.084 309 34 6 438 738 661914960 661915267 1.750000e-84 324.0
39 TraesCS3D01G247400 chr6B 93.220 177 12 0 3468 3644 211161649 211161473 1.390000e-65 261.0
40 TraesCS3D01G247400 chr6B 77.558 303 51 12 4102 4396 438097990 438098283 3.120000e-37 167.0
41 TraesCS3D01G247400 chr4A 94.706 170 9 0 3470 3639 362067907 362068076 1.080000e-66 265.0
42 TraesCS3D01G247400 chr7D 94.706 170 8 1 3473 3642 192936185 192936017 3.870000e-66 263.0
43 TraesCS3D01G247400 chr1D 94.186 172 10 0 3470 3641 178466474 178466303 3.870000e-66 263.0
44 TraesCS3D01G247400 chr4B 92.737 179 11 2 3460 3638 168553373 168553549 1.800000e-64 257.0
45 TraesCS3D01G247400 chr6D 79.697 330 53 10 4094 4416 30131298 30130976 5.080000e-55 226.0
46 TraesCS3D01G247400 chr2A 76.792 293 46 20 4094 4376 564615786 564615506 1.460000e-30 145.0
47 TraesCS3D01G247400 chr1A 76.703 279 53 10 4094 4369 492270531 492270262 1.460000e-30 145.0


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 TraesCS3D01G247400 chr3D 346638708 346643748 5040 False 9310.000000 9310 100.000000 1 5041 1 chr3D.!!$F1 5040
1 TraesCS3D01G247400 chr3A 457084578 457088854 4276 True 1655.500000 4410 96.258000 825 5041 4 chr3A.!!$R2 4216
2 TraesCS3D01G247400 chr3B 446168720 446172904 4184 False 1578.333333 3886 93.480667 826 5041 3 chr3B.!!$F2 4215
3 TraesCS3D01G247400 chr5A 136632427 136633178 751 False 966.000000 966 90.160000 1 738 1 chr5A.!!$F1 737
4 TraesCS3D01G247400 chr5B 12345346 12345994 648 False 839.000000 839 90.308000 1 637 1 chr5B.!!$F1 636
5 TraesCS3D01G247400 chr2D 566724946 566725696 750 True 699.000000 699 83.837000 1 743 1 chr2D.!!$R1 742
6 TraesCS3D01G247400 chr2D 626612591 626613210 619 False 645.000000 645 85.760000 2 613 1 chr2D.!!$F4 611
7 TraesCS3D01G247400 chr2B 174366794 174367411 617 False 612.000000 612 84.839000 1 608 1 chr2B.!!$F1 607
8 TraesCS3D01G247400 chr1B 130781020 130781754 734 False 566.000000 566 81.081000 21 738 1 chr1B.!!$F1 717
9 TraesCS3D01G247400 chr1B 131120850 131121603 753 False 555.000000 555 80.526000 4 738 1 chr1B.!!$F2 734
10 TraesCS3D01G247400 chr1B 131371474 131372021 547 False 388.000000 388 80.108000 206 738 1 chr1B.!!$F3 532
11 TraesCS3D01G247400 chr4D 49845067 49845662 595 True 551.000000 551 83.628000 1 612 1 chr4D.!!$R1 611

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
811 842 0.033503 TACTCTGCACGGATCCCTGA 60.034 55.000 14.25 5.58 0.00 3.86 F
813 844 0.249784 CTCTGCACGGATCCCTGATG 60.250 60.000 14.25 5.41 0.00 3.07 F
1495 1535 0.320421 GTCTGCCGTCAGTGCCTTTA 60.320 55.000 0.00 0.00 41.10 1.85 F
1898 1938 0.321298 CGGGAGTTTGACCGGATGTT 60.321 55.000 9.46 0.00 46.08 2.71 F
2163 2203 1.295101 CATGTACACCAGGTGCGGA 59.705 57.895 20.48 3.37 36.98 5.54 F
3367 3425 3.744660 AGCAGTTCTCCAAGTAACCTTG 58.255 45.455 0.00 0.00 46.33 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2163 2203 1.002134 CCGGGCTCTTCCAACATGT 60.002 57.895 0.0 0.0 36.21 3.21 R
2826 2866 1.531365 CAAGAGCAACCCCAAGCCA 60.531 57.895 0.0 0.0 0.00 4.75 R
3183 3238 1.036707 AGAGAAGCGATAGGACTGCC 58.963 55.000 0.0 0.0 0.00 4.85 R
3466 3524 4.635473 AGGAATGGAGGGAGTAGATGAAA 58.365 43.478 0.0 0.0 0.00 2.69 R
3623 3681 4.876679 GCTGTTAATTACTCCCTCTGTTCC 59.123 45.833 0.0 0.0 0.00 3.62 R
4412 5035 0.598942 GCGGGAAACGTTTGGCAAAT 60.599 50.000 20.1 0.0 46.52 2.32 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
36 40 3.187842 TCTGCATCGCATATGAATTGCTC 59.812 43.478 18.75 0.00 38.13 4.26
39 43 3.187842 GCATCGCATATGAATTGCTCTGA 59.812 43.478 6.97 0.00 37.96 3.27
200 206 1.335182 CACTCTCATCGGCATAGTCGT 59.665 52.381 0.00 0.00 30.45 4.34
224 231 7.148639 CGTACATGTGCTTTTGTAATACTGACT 60.149 37.037 9.11 0.00 30.59 3.41
279 286 2.282040 GCAGTTGGCCAGAGCACT 60.282 61.111 17.92 11.07 42.56 4.40
349 359 4.314121 GGTGCCATTAGTGAAAATTGCAA 58.686 39.130 0.00 0.00 38.69 4.08
407 417 1.516386 CTAGTTGCGCACCGACGAT 60.516 57.895 11.12 0.00 32.77 3.73
410 420 1.058284 GTTGCGCACCGACGATTAC 59.942 57.895 11.12 0.00 34.06 1.89
417 430 1.330521 GCACCGACGATTACATTGCAT 59.669 47.619 0.00 0.00 0.00 3.96
545 560 2.365820 TTCGACACGCGGTTTAAAAC 57.634 45.000 12.47 0.00 41.33 2.43
551 566 4.608890 CGACACGCGGTTTAAAACTTATGT 60.609 41.667 12.47 0.00 36.03 2.29
635 658 7.778470 TTTGGGTGTTTACATGATTGTTTTC 57.222 32.000 0.00 0.00 37.28 2.29
636 659 6.723298 TGGGTGTTTACATGATTGTTTTCT 57.277 33.333 0.00 0.00 37.28 2.52
745 776 3.839432 GGCCGCTCGCTAGACCTT 61.839 66.667 0.00 0.00 37.74 3.50
746 777 2.184579 GCCGCTCGCTAGACCTTT 59.815 61.111 0.00 0.00 0.00 3.11
747 778 1.448013 GCCGCTCGCTAGACCTTTT 60.448 57.895 0.00 0.00 0.00 2.27
748 779 1.019805 GCCGCTCGCTAGACCTTTTT 61.020 55.000 0.00 0.00 0.00 1.94
773 804 7.672983 TTTTCAGGTAAACACTGATGATCTC 57.327 36.000 0.00 0.00 43.82 2.75
774 805 6.611613 TTCAGGTAAACACTGATGATCTCT 57.388 37.500 0.00 0.00 43.82 3.10
775 806 6.611613 TCAGGTAAACACTGATGATCTCTT 57.388 37.500 0.00 0.00 39.87 2.85
776 807 7.009179 TCAGGTAAACACTGATGATCTCTTT 57.991 36.000 0.00 0.00 39.87 2.52
777 808 7.099764 TCAGGTAAACACTGATGATCTCTTTC 58.900 38.462 0.00 0.00 39.87 2.62
778 809 6.314896 CAGGTAAACACTGATGATCTCTTTCC 59.685 42.308 0.00 0.00 38.20 3.13
779 810 5.586643 GGTAAACACTGATGATCTCTTTCCC 59.413 44.000 0.00 0.00 0.00 3.97
780 811 5.511386 AAACACTGATGATCTCTTTCCCT 57.489 39.130 0.00 0.00 0.00 4.20
781 812 5.511386 AACACTGATGATCTCTTTCCCTT 57.489 39.130 0.00 0.00 0.00 3.95
782 813 5.511386 ACACTGATGATCTCTTTCCCTTT 57.489 39.130 0.00 0.00 0.00 3.11
783 814 5.251764 ACACTGATGATCTCTTTCCCTTTG 58.748 41.667 0.00 0.00 0.00 2.77
784 815 5.222007 ACACTGATGATCTCTTTCCCTTTGT 60.222 40.000 0.00 0.00 0.00 2.83
785 816 5.123502 CACTGATGATCTCTTTCCCTTTGTG 59.876 44.000 0.00 0.00 0.00 3.33
786 817 5.222007 ACTGATGATCTCTTTCCCTTTGTGT 60.222 40.000 0.00 0.00 0.00 3.72
787 818 5.005740 TGATGATCTCTTTCCCTTTGTGTG 58.994 41.667 0.00 0.00 0.00 3.82
788 819 4.437682 TGATCTCTTTCCCTTTGTGTGT 57.562 40.909 0.00 0.00 0.00 3.72
789 820 4.389374 TGATCTCTTTCCCTTTGTGTGTC 58.611 43.478 0.00 0.00 0.00 3.67
790 821 2.833794 TCTCTTTCCCTTTGTGTGTCG 58.166 47.619 0.00 0.00 0.00 4.35
791 822 1.264288 CTCTTTCCCTTTGTGTGTCGC 59.736 52.381 0.00 0.00 0.00 5.19
792 823 1.134220 TCTTTCCCTTTGTGTGTCGCT 60.134 47.619 0.00 0.00 0.00 4.93
793 824 2.103432 TCTTTCCCTTTGTGTGTCGCTA 59.897 45.455 0.00 0.00 0.00 4.26
794 825 1.873698 TTCCCTTTGTGTGTCGCTAC 58.126 50.000 0.00 0.00 0.00 3.58
795 826 1.045407 TCCCTTTGTGTGTCGCTACT 58.955 50.000 0.00 0.00 0.00 2.57
796 827 1.000506 TCCCTTTGTGTGTCGCTACTC 59.999 52.381 0.00 0.00 0.00 2.59
797 828 1.000955 CCCTTTGTGTGTCGCTACTCT 59.999 52.381 0.00 0.00 0.00 3.24
798 829 2.061773 CCTTTGTGTGTCGCTACTCTG 58.938 52.381 0.00 0.00 0.00 3.35
799 830 1.457303 CTTTGTGTGTCGCTACTCTGC 59.543 52.381 0.00 0.00 0.00 4.26
800 831 0.387565 TTGTGTGTCGCTACTCTGCA 59.612 50.000 0.00 0.00 0.00 4.41
801 832 0.318699 TGTGTGTCGCTACTCTGCAC 60.319 55.000 0.00 0.00 0.00 4.57
802 833 1.081442 TGTGTCGCTACTCTGCACG 60.081 57.895 0.00 0.00 33.23 5.34
803 834 1.801913 GTGTCGCTACTCTGCACGG 60.802 63.158 0.00 0.00 0.00 4.94
804 835 1.969589 TGTCGCTACTCTGCACGGA 60.970 57.895 0.00 0.00 0.00 4.69
805 836 1.313091 TGTCGCTACTCTGCACGGAT 61.313 55.000 0.00 0.00 0.00 4.18
806 837 0.592754 GTCGCTACTCTGCACGGATC 60.593 60.000 0.00 0.00 0.00 3.36
807 838 1.299468 CGCTACTCTGCACGGATCC 60.299 63.158 0.00 0.00 0.00 3.36
808 839 1.068250 GCTACTCTGCACGGATCCC 59.932 63.158 6.06 0.00 0.00 3.85
809 840 1.395826 GCTACTCTGCACGGATCCCT 61.396 60.000 6.06 0.00 0.00 4.20
810 841 0.387202 CTACTCTGCACGGATCCCTG 59.613 60.000 6.06 6.25 0.00 4.45
811 842 0.033503 TACTCTGCACGGATCCCTGA 60.034 55.000 14.25 5.58 0.00 3.86
812 843 0.689080 ACTCTGCACGGATCCCTGAT 60.689 55.000 14.25 0.00 0.00 2.90
813 844 0.249784 CTCTGCACGGATCCCTGATG 60.250 60.000 14.25 5.41 0.00 3.07
814 845 0.687427 TCTGCACGGATCCCTGATGA 60.687 55.000 14.25 8.10 0.00 2.92
815 846 0.249784 CTGCACGGATCCCTGATGAG 60.250 60.000 14.25 3.41 0.00 2.90
816 847 1.070445 GCACGGATCCCTGATGAGG 59.930 63.158 14.25 0.00 39.42 3.86
817 848 1.402896 GCACGGATCCCTGATGAGGA 61.403 60.000 14.25 0.00 42.93 3.71
818 849 0.678395 CACGGATCCCTGATGAGGAG 59.322 60.000 6.06 0.00 42.93 3.69
819 850 0.558220 ACGGATCCCTGATGAGGAGA 59.442 55.000 6.06 0.00 42.93 3.71
820 851 1.255882 CGGATCCCTGATGAGGAGAG 58.744 60.000 6.06 0.00 42.93 3.20
821 852 1.202989 CGGATCCCTGATGAGGAGAGA 60.203 57.143 6.06 0.00 42.93 3.10
822 853 2.247358 GGATCCCTGATGAGGAGAGAC 58.753 57.143 0.00 0.00 42.93 3.36
823 854 2.425538 GGATCCCTGATGAGGAGAGACA 60.426 54.545 0.00 0.00 42.93 3.41
903 934 1.895051 CATTCGCGAACCCAAATCAC 58.105 50.000 26.00 0.00 0.00 3.06
947 978 4.639824 GTCGCCGTGACTACAACA 57.360 55.556 4.77 0.00 44.58 3.33
977 1008 4.697828 TGCGCTTCCATATAACTGAACAAA 59.302 37.500 9.73 0.00 0.00 2.83
1249 1289 2.621371 CTTTCTCTCCGCGCTCTCCC 62.621 65.000 5.56 0.00 0.00 4.30
1374 1414 4.015406 ACCGCATCGTCCTGCCAA 62.015 61.111 2.67 0.00 39.00 4.52
1377 1417 2.045926 GCATCGTCCTGCCAAGGT 60.046 61.111 0.00 0.00 44.82 3.50
1407 1447 1.817099 CTCCCATGCTCTTGTCCGC 60.817 63.158 0.00 0.00 0.00 5.54
1434 1474 2.879756 GCTTGGGGATGTCTTTGTGCTA 60.880 50.000 0.00 0.00 0.00 3.49
1490 1530 2.433318 GGAGTCTGCCGTCAGTGC 60.433 66.667 0.00 0.00 41.10 4.40
1495 1535 0.320421 GTCTGCCGTCAGTGCCTTTA 60.320 55.000 0.00 0.00 41.10 1.85
1506 1546 0.733150 GTGCCTTTAACGAGATGCCC 59.267 55.000 0.00 0.00 0.00 5.36
1518 1558 0.982852 AGATGCCCGTCAAGGATCCA 60.983 55.000 15.82 0.00 45.00 3.41
1567 1607 6.115446 GGATATTCAAAGTCTGGTGATGTGA 58.885 40.000 0.00 0.00 0.00 3.58
1584 1624 2.019984 GTGAATAAGGCCAGGAAGCTG 58.980 52.381 5.01 0.00 0.00 4.24
1807 1847 0.395862 TCTGATCGGTGAGGAGGACC 60.396 60.000 0.42 0.00 0.00 4.46
1898 1938 0.321298 CGGGAGTTTGACCGGATGTT 60.321 55.000 9.46 0.00 46.08 2.71
2040 2080 3.492102 ACACTTGTTGGTGTGCTATCT 57.508 42.857 0.00 0.00 46.93 1.98
2163 2203 1.295101 CATGTACACCAGGTGCGGA 59.705 57.895 20.48 3.37 36.98 5.54
2826 2866 4.611943 CTGAGATTTATGACGTCGTCCAT 58.388 43.478 22.05 16.59 0.00 3.41
3183 3238 9.241919 AGTTGGAGTGAGTATATGATCTCATAG 57.758 37.037 6.12 0.00 41.58 2.23
3367 3425 3.744660 AGCAGTTCTCCAAGTAACCTTG 58.255 45.455 0.00 0.00 46.33 3.61
3466 3524 4.973168 TGTAGAAAGCAATGACCTCTGTT 58.027 39.130 0.00 0.00 0.00 3.16
3475 3533 5.645497 AGCAATGACCTCTGTTTTCATCTAC 59.355 40.000 0.00 0.00 0.00 2.59
3476 3534 5.645497 GCAATGACCTCTGTTTTCATCTACT 59.355 40.000 0.00 0.00 0.00 2.57
3477 3535 6.183360 GCAATGACCTCTGTTTTCATCTACTC 60.183 42.308 0.00 0.00 0.00 2.59
3478 3536 5.407407 TGACCTCTGTTTTCATCTACTCC 57.593 43.478 0.00 0.00 0.00 3.85
3479 3537 4.223032 TGACCTCTGTTTTCATCTACTCCC 59.777 45.833 0.00 0.00 0.00 4.30
3480 3538 4.430441 ACCTCTGTTTTCATCTACTCCCT 58.570 43.478 0.00 0.00 0.00 4.20
3481 3539 4.468153 ACCTCTGTTTTCATCTACTCCCTC 59.532 45.833 0.00 0.00 0.00 4.30
3482 3540 4.141824 CCTCTGTTTTCATCTACTCCCTCC 60.142 50.000 0.00 0.00 0.00 4.30
3483 3541 4.425772 TCTGTTTTCATCTACTCCCTCCA 58.574 43.478 0.00 0.00 0.00 3.86
3484 3542 5.032846 TCTGTTTTCATCTACTCCCTCCAT 58.967 41.667 0.00 0.00 0.00 3.41
3485 3543 5.488919 TCTGTTTTCATCTACTCCCTCCATT 59.511 40.000 0.00 0.00 0.00 3.16
3486 3544 5.745227 TGTTTTCATCTACTCCCTCCATTC 58.255 41.667 0.00 0.00 0.00 2.67
3487 3545 5.126779 GTTTTCATCTACTCCCTCCATTCC 58.873 45.833 0.00 0.00 0.00 3.01
3488 3546 4.286813 TTCATCTACTCCCTCCATTCCT 57.713 45.455 0.00 0.00 0.00 3.36
3489 3547 5.418692 TTCATCTACTCCCTCCATTCCTA 57.581 43.478 0.00 0.00 0.00 2.94
3490 3548 5.418692 TCATCTACTCCCTCCATTCCTAA 57.581 43.478 0.00 0.00 0.00 2.69
3491 3549 5.788430 TCATCTACTCCCTCCATTCCTAAA 58.212 41.667 0.00 0.00 0.00 1.85
3492 3550 6.393897 TCATCTACTCCCTCCATTCCTAAAT 58.606 40.000 0.00 0.00 0.00 1.40
3493 3551 7.544650 TCATCTACTCCCTCCATTCCTAAATA 58.455 38.462 0.00 0.00 0.00 1.40
3494 3552 8.186985 TCATCTACTCCCTCCATTCCTAAATAT 58.813 37.037 0.00 0.00 0.00 1.28
3495 3553 8.830741 CATCTACTCCCTCCATTCCTAAATATT 58.169 37.037 0.00 0.00 0.00 1.28
3496 3554 8.814448 TCTACTCCCTCCATTCCTAAATATTT 57.186 34.615 5.89 5.89 0.00 1.40
3497 3555 8.660435 TCTACTCCCTCCATTCCTAAATATTTG 58.340 37.037 11.05 1.40 0.00 2.32
3498 3556 7.226059 ACTCCCTCCATTCCTAAATATTTGT 57.774 36.000 11.05 0.00 0.00 2.83
3499 3557 7.290813 ACTCCCTCCATTCCTAAATATTTGTC 58.709 38.462 11.05 0.00 0.00 3.18
3500 3558 7.129504 ACTCCCTCCATTCCTAAATATTTGTCT 59.870 37.037 11.05 0.00 0.00 3.41
3501 3559 7.882755 TCCCTCCATTCCTAAATATTTGTCTT 58.117 34.615 11.05 0.00 0.00 3.01
3502 3560 8.343787 TCCCTCCATTCCTAAATATTTGTCTTT 58.656 33.333 11.05 0.00 0.00 2.52
3503 3561 8.633561 CCCTCCATTCCTAAATATTTGTCTTTC 58.366 37.037 11.05 0.00 0.00 2.62
3504 3562 9.413734 CCTCCATTCCTAAATATTTGTCTTTCT 57.586 33.333 11.05 0.00 0.00 2.52
3520 3578 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
3521 3579 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
3522 3580 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
3523 3581 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
3524 3582 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
3525 3583 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
3526 3584 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
3527 3585 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
3528 3586 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
3531 3589 9.376075 AGAGATTTCAACAAGTGACTACATATG 57.624 33.333 0.00 0.00 35.39 1.78
3532 3590 8.498054 AGATTTCAACAAGTGACTACATATGG 57.502 34.615 7.80 0.00 35.39 2.74
3533 3591 8.321353 AGATTTCAACAAGTGACTACATATGGA 58.679 33.333 7.80 0.00 35.39 3.41
3534 3592 7.905604 TTTCAACAAGTGACTACATATGGAG 57.094 36.000 13.77 13.77 35.39 3.86
3535 3593 5.419542 TCAACAAGTGACTACATATGGAGC 58.580 41.667 15.30 8.47 0.00 4.70
3536 3594 5.046663 TCAACAAGTGACTACATATGGAGCA 60.047 40.000 15.30 10.95 0.00 4.26
3537 3595 5.420725 ACAAGTGACTACATATGGAGCAA 57.579 39.130 15.30 0.16 0.00 3.91
3538 3596 5.804639 ACAAGTGACTACATATGGAGCAAA 58.195 37.500 15.30 0.00 0.00 3.68
3539 3597 6.237901 ACAAGTGACTACATATGGAGCAAAA 58.762 36.000 15.30 0.00 0.00 2.44
3540 3598 6.886459 ACAAGTGACTACATATGGAGCAAAAT 59.114 34.615 15.30 0.00 0.00 1.82
3541 3599 6.932356 AGTGACTACATATGGAGCAAAATG 57.068 37.500 15.30 0.00 0.00 2.32
3542 3600 6.653020 AGTGACTACATATGGAGCAAAATGA 58.347 36.000 15.30 0.00 0.00 2.57
3543 3601 6.765036 AGTGACTACATATGGAGCAAAATGAG 59.235 38.462 15.30 0.00 0.00 2.90
3544 3602 6.540189 GTGACTACATATGGAGCAAAATGAGT 59.460 38.462 15.30 0.00 0.00 3.41
3545 3603 6.539826 TGACTACATATGGAGCAAAATGAGTG 59.460 38.462 15.30 0.00 0.00 3.51
3546 3604 6.653020 ACTACATATGGAGCAAAATGAGTGA 58.347 36.000 15.30 0.00 0.00 3.41
3547 3605 7.112122 ACTACATATGGAGCAAAATGAGTGAA 58.888 34.615 15.30 0.00 0.00 3.18
3548 3606 7.776969 ACTACATATGGAGCAAAATGAGTGAAT 59.223 33.333 15.30 0.00 0.00 2.57
3549 3607 7.035840 ACATATGGAGCAAAATGAGTGAATC 57.964 36.000 7.80 0.00 0.00 2.52
3550 3608 6.832384 ACATATGGAGCAAAATGAGTGAATCT 59.168 34.615 7.80 0.00 0.00 2.40
3551 3609 7.994911 ACATATGGAGCAAAATGAGTGAATCTA 59.005 33.333 7.80 0.00 0.00 1.98
3552 3610 6.690194 ATGGAGCAAAATGAGTGAATCTAC 57.310 37.500 0.00 0.00 0.00 2.59
3553 3611 5.559770 TGGAGCAAAATGAGTGAATCTACA 58.440 37.500 0.00 0.00 0.00 2.74
3554 3612 5.412594 TGGAGCAAAATGAGTGAATCTACAC 59.587 40.000 0.00 0.00 40.60 2.90
3593 3651 9.788889 CTATATACATCCGTATATGGTAGTCCA 57.211 37.037 10.85 3.57 46.31 4.02
3610 3668 9.589461 TGGTAGTCCATTTGAAACCTATAAAAA 57.411 29.630 0.00 0.00 39.03 1.94
3614 3672 9.588096 AGTCCATTTGAAACCTATAAAAAGACT 57.412 29.630 0.00 0.00 31.00 3.24
3823 3961 3.265737 TCCTGGATCGGAATTTGGAGAAA 59.734 43.478 0.00 0.00 0.00 2.52
4201 4822 5.067936 TCCAAAAGTGGTATTTTCGAAAGCA 59.932 36.000 10.98 3.32 46.11 3.91
4282 4905 4.405116 TTTTGCAGGCACTCAAAAGATT 57.595 36.364 0.00 0.00 39.02 2.40
4289 4912 4.741676 CAGGCACTCAAAAGATTTGTCAAC 59.258 41.667 3.06 0.00 34.60 3.18
4295 4918 4.109050 TCAAAAGATTTGTCAACGTTGGC 58.891 39.130 25.54 25.54 0.00 4.52
4296 4919 2.793278 AAGATTTGTCAACGTTGGCC 57.207 45.000 28.59 18.83 30.03 5.36
4297 4920 1.686355 AGATTTGTCAACGTTGGCCA 58.314 45.000 28.59 21.01 30.03 5.36
4298 4921 1.336755 AGATTTGTCAACGTTGGCCAC 59.663 47.619 28.59 19.10 30.03 5.01
4299 4922 1.066303 GATTTGTCAACGTTGGCCACA 59.934 47.619 28.59 21.36 30.03 4.17
4300 4923 0.888619 TTTGTCAACGTTGGCCACAA 59.111 45.000 28.59 25.27 30.03 3.33
4301 4924 0.888619 TTGTCAACGTTGGCCACAAA 59.111 45.000 28.59 14.25 38.54 2.83
4362 4985 7.922505 TTTTTGGATTTTACTGTTCATCACG 57.077 32.000 0.00 0.00 0.00 4.35
4363 4986 6.869315 TTTGGATTTTACTGTTCATCACGA 57.131 33.333 0.00 0.00 0.00 4.35
4364 4987 6.480524 TTGGATTTTACTGTTCATCACGAG 57.519 37.500 0.00 0.00 0.00 4.18
4365 4988 4.391830 TGGATTTTACTGTTCATCACGAGC 59.608 41.667 0.00 0.00 0.00 5.03
4366 4989 4.631813 GGATTTTACTGTTCATCACGAGCT 59.368 41.667 0.00 0.00 0.00 4.09
4367 4990 5.220491 GGATTTTACTGTTCATCACGAGCTC 60.220 44.000 2.73 2.73 0.00 4.09
4368 4991 3.934457 TTACTGTTCATCACGAGCTCA 57.066 42.857 15.40 0.00 0.00 4.26
4369 4992 2.820059 ACTGTTCATCACGAGCTCAA 57.180 45.000 15.40 0.00 0.00 3.02
4370 4993 3.325293 ACTGTTCATCACGAGCTCAAT 57.675 42.857 15.40 0.72 0.00 2.57
4410 5033 0.958822 ACTTTCGGTTCATGGGCAAC 59.041 50.000 0.00 0.00 0.00 4.17
4411 5034 1.247567 CTTTCGGTTCATGGGCAACT 58.752 50.000 0.00 0.00 0.00 3.16
4412 5035 2.224670 ACTTTCGGTTCATGGGCAACTA 60.225 45.455 0.00 0.00 0.00 2.24
4413 5036 2.799126 TTCGGTTCATGGGCAACTAT 57.201 45.000 0.00 0.00 39.02 2.12
4414 5037 2.799126 TCGGTTCATGGGCAACTATT 57.201 45.000 0.00 0.00 34.29 1.73
4415 5038 3.080300 TCGGTTCATGGGCAACTATTT 57.920 42.857 0.00 0.00 34.29 1.40
4416 5039 2.752354 TCGGTTCATGGGCAACTATTTG 59.248 45.455 0.00 0.00 34.29 2.32
4428 5051 4.965042 CAACTATTTGCCAAACGTTTCC 57.035 40.909 11.37 5.92 0.00 3.13
4429 5052 3.653539 ACTATTTGCCAAACGTTTCCC 57.346 42.857 11.37 5.55 0.00 3.97
4430 5053 2.030628 ACTATTTGCCAAACGTTTCCCG 60.031 45.455 11.37 2.74 44.03 5.14
4431 5054 0.598942 ATTTGCCAAACGTTTCCCGC 60.599 50.000 11.37 13.23 41.42 6.13
4432 5055 1.945354 TTTGCCAAACGTTTCCCGCA 61.945 50.000 18.18 18.18 41.42 5.69
4433 5056 1.945354 TTGCCAAACGTTTCCCGCAA 61.945 50.000 24.74 24.74 41.42 4.85
4434 5057 1.227002 GCCAAACGTTTCCCGCAAA 60.227 52.632 11.37 0.00 41.42 3.68
4435 5058 0.806492 GCCAAACGTTTCCCGCAAAA 60.806 50.000 11.37 0.00 41.42 2.44
4436 5059 1.641577 CCAAACGTTTCCCGCAAAAA 58.358 45.000 11.37 0.00 41.42 1.94
4513 5136 0.591170 CCACCCTTTTAGCACGTGTG 59.409 55.000 18.38 3.68 0.00 3.82
4681 5341 2.287608 CGAGTGTTGGCCTTCCTTTTTC 60.288 50.000 3.32 0.00 0.00 2.29
4759 5419 6.696441 TGTTTTTGGTAACCGTAGATTTGT 57.304 33.333 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
200 206 7.333423 GGAGTCAGTATTACAAAAGCACATGTA 59.667 37.037 0.00 0.00 0.00 2.29
274 281 4.341783 GTCTGCTGCCCCAGTGCT 62.342 66.667 0.00 0.00 33.43 4.40
279 286 1.074775 AATTTCGTCTGCTGCCCCA 59.925 52.632 0.00 0.00 0.00 4.96
325 332 3.055891 GCAATTTTCACTAATGGCACCCT 60.056 43.478 0.00 0.00 35.06 4.34
349 359 7.232534 TGCAACCTTTTTCTATAAATGTGGACT 59.767 33.333 0.00 0.00 0.00 3.85
397 407 0.724549 TGCAATGTAATCGTCGGTGC 59.275 50.000 0.00 0.00 0.00 5.01
407 417 4.323417 AGTCTCCGTTTGATGCAATGTAA 58.677 39.130 0.00 0.00 0.00 2.41
410 420 4.393062 ACTTAGTCTCCGTTTGATGCAATG 59.607 41.667 0.00 0.00 0.00 2.82
417 430 3.128349 GTGCAACTTAGTCTCCGTTTGA 58.872 45.455 0.00 0.00 0.00 2.69
566 581 9.934190 GTGTGAATGCATTTAATTTGAGTTTTT 57.066 25.926 14.33 0.00 0.00 1.94
697 728 3.850173 ACAGGAAGCTTTGGTCCCTAATA 59.150 43.478 0.00 0.00 34.13 0.98
711 742 1.006220 CCGGCCAAAAACAGGAAGC 60.006 57.895 2.24 0.00 0.00 3.86
748 779 7.939039 AGAGATCATCAGTGTTTACCTGAAAAA 59.061 33.333 0.00 0.00 0.00 1.94
749 780 7.453393 AGAGATCATCAGTGTTTACCTGAAAA 58.547 34.615 0.00 0.00 0.00 2.29
750 781 7.009179 AGAGATCATCAGTGTTTACCTGAAA 57.991 36.000 0.00 0.00 0.00 2.69
751 782 6.611613 AGAGATCATCAGTGTTTACCTGAA 57.388 37.500 0.00 0.00 0.00 3.02
752 783 6.611613 AAGAGATCATCAGTGTTTACCTGA 57.388 37.500 0.00 0.00 0.00 3.86
753 784 6.314896 GGAAAGAGATCATCAGTGTTTACCTG 59.685 42.308 0.00 0.00 0.00 4.00
754 785 6.410540 GGAAAGAGATCATCAGTGTTTACCT 58.589 40.000 0.00 0.00 0.00 3.08
755 786 5.586643 GGGAAAGAGATCATCAGTGTTTACC 59.413 44.000 0.00 0.00 0.00 2.85
756 787 6.410540 AGGGAAAGAGATCATCAGTGTTTAC 58.589 40.000 0.00 0.00 0.00 2.01
757 788 6.627087 AGGGAAAGAGATCATCAGTGTTTA 57.373 37.500 0.00 0.00 0.00 2.01
758 789 5.511386 AGGGAAAGAGATCATCAGTGTTT 57.489 39.130 0.00 0.00 0.00 2.83
759 790 5.511386 AAGGGAAAGAGATCATCAGTGTT 57.489 39.130 0.00 0.00 0.00 3.32
760 791 5.222007 ACAAAGGGAAAGAGATCATCAGTGT 60.222 40.000 0.00 0.00 0.00 3.55
761 792 5.123502 CACAAAGGGAAAGAGATCATCAGTG 59.876 44.000 0.00 0.00 0.00 3.66
762 793 5.222007 ACACAAAGGGAAAGAGATCATCAGT 60.222 40.000 0.00 0.00 0.00 3.41
763 794 5.123502 CACACAAAGGGAAAGAGATCATCAG 59.876 44.000 0.00 0.00 0.00 2.90
764 795 5.005740 CACACAAAGGGAAAGAGATCATCA 58.994 41.667 0.00 0.00 0.00 3.07
765 796 5.006386 ACACACAAAGGGAAAGAGATCATC 58.994 41.667 0.00 0.00 0.00 2.92
766 797 4.990526 ACACACAAAGGGAAAGAGATCAT 58.009 39.130 0.00 0.00 0.00 2.45
767 798 4.389374 GACACACAAAGGGAAAGAGATCA 58.611 43.478 0.00 0.00 0.00 2.92
768 799 3.433615 CGACACACAAAGGGAAAGAGATC 59.566 47.826 0.00 0.00 0.00 2.75
769 800 3.403038 CGACACACAAAGGGAAAGAGAT 58.597 45.455 0.00 0.00 0.00 2.75
770 801 2.833794 CGACACACAAAGGGAAAGAGA 58.166 47.619 0.00 0.00 0.00 3.10
771 802 1.264288 GCGACACACAAAGGGAAAGAG 59.736 52.381 0.00 0.00 0.00 2.85
772 803 1.134220 AGCGACACACAAAGGGAAAGA 60.134 47.619 0.00 0.00 0.00 2.52
773 804 1.308998 AGCGACACACAAAGGGAAAG 58.691 50.000 0.00 0.00 0.00 2.62
774 805 2.158871 AGTAGCGACACACAAAGGGAAA 60.159 45.455 0.00 0.00 0.00 3.13
775 806 1.414919 AGTAGCGACACACAAAGGGAA 59.585 47.619 0.00 0.00 0.00 3.97
776 807 1.000506 GAGTAGCGACACACAAAGGGA 59.999 52.381 0.00 0.00 0.00 4.20
777 808 1.000955 AGAGTAGCGACACACAAAGGG 59.999 52.381 0.00 0.00 0.00 3.95
778 809 2.061773 CAGAGTAGCGACACACAAAGG 58.938 52.381 0.00 0.00 0.00 3.11
779 810 1.457303 GCAGAGTAGCGACACACAAAG 59.543 52.381 0.00 0.00 0.00 2.77
780 811 1.202475 TGCAGAGTAGCGACACACAAA 60.202 47.619 0.00 0.00 37.31 2.83
781 812 0.387565 TGCAGAGTAGCGACACACAA 59.612 50.000 0.00 0.00 37.31 3.33
782 813 0.318699 GTGCAGAGTAGCGACACACA 60.319 55.000 0.00 0.00 37.31 3.72
783 814 1.337817 CGTGCAGAGTAGCGACACAC 61.338 60.000 0.00 1.53 37.31 3.82
784 815 1.081442 CGTGCAGAGTAGCGACACA 60.081 57.895 0.00 0.00 37.31 3.72
785 816 1.801913 CCGTGCAGAGTAGCGACAC 60.802 63.158 0.00 0.00 37.31 3.67
786 817 1.313091 ATCCGTGCAGAGTAGCGACA 61.313 55.000 0.00 0.00 37.31 4.35
787 818 0.592754 GATCCGTGCAGAGTAGCGAC 60.593 60.000 0.00 0.00 37.31 5.19
788 819 1.725557 GGATCCGTGCAGAGTAGCGA 61.726 60.000 0.00 0.00 37.31 4.93
789 820 1.299468 GGATCCGTGCAGAGTAGCG 60.299 63.158 0.00 0.00 37.31 4.26
790 821 1.068250 GGGATCCGTGCAGAGTAGC 59.932 63.158 5.45 0.00 0.00 3.58
791 822 0.387202 CAGGGATCCGTGCAGAGTAG 59.613 60.000 20.81 0.00 0.00 2.57
792 823 0.033503 TCAGGGATCCGTGCAGAGTA 60.034 55.000 26.35 8.21 0.00 2.59
793 824 0.689080 ATCAGGGATCCGTGCAGAGT 60.689 55.000 26.35 9.26 0.00 3.24
794 825 0.249784 CATCAGGGATCCGTGCAGAG 60.250 60.000 26.35 13.34 0.00 3.35
795 826 0.687427 TCATCAGGGATCCGTGCAGA 60.687 55.000 26.35 22.01 0.00 4.26
796 827 0.249784 CTCATCAGGGATCCGTGCAG 60.250 60.000 26.35 20.38 0.00 4.41
797 828 1.689243 CCTCATCAGGGATCCGTGCA 61.689 60.000 26.35 16.69 35.89 4.57
798 829 1.070445 CCTCATCAGGGATCCGTGC 59.930 63.158 26.35 3.94 35.89 5.34
799 830 0.678395 CTCCTCATCAGGGATCCGTG 59.322 60.000 25.45 25.45 40.80 4.94
800 831 0.558220 TCTCCTCATCAGGGATCCGT 59.442 55.000 5.45 2.61 40.80 4.69
801 832 1.202989 TCTCTCCTCATCAGGGATCCG 60.203 57.143 5.45 0.00 40.80 4.18
802 833 2.247358 GTCTCTCCTCATCAGGGATCC 58.753 57.143 1.92 1.92 40.80 3.36
803 834 2.627699 GTGTCTCTCCTCATCAGGGATC 59.372 54.545 0.00 0.00 40.80 3.36
804 835 2.676748 GTGTCTCTCCTCATCAGGGAT 58.323 52.381 0.00 0.00 40.80 3.85
805 836 1.342474 GGTGTCTCTCCTCATCAGGGA 60.342 57.143 0.00 0.00 40.80 4.20
806 837 1.118838 GGTGTCTCTCCTCATCAGGG 58.881 60.000 0.00 0.00 40.80 4.45
807 838 2.157640 AGGTGTCTCTCCTCATCAGG 57.842 55.000 0.00 0.00 42.01 3.86
808 839 2.622942 GCTAGGTGTCTCTCCTCATCAG 59.377 54.545 0.00 0.00 36.60 2.90
809 840 2.024941 TGCTAGGTGTCTCTCCTCATCA 60.025 50.000 0.00 0.00 36.60 3.07
810 841 2.622942 CTGCTAGGTGTCTCTCCTCATC 59.377 54.545 0.00 0.00 36.60 2.92
811 842 2.024464 ACTGCTAGGTGTCTCTCCTCAT 60.024 50.000 0.00 0.00 36.60 2.90
812 843 1.356059 ACTGCTAGGTGTCTCTCCTCA 59.644 52.381 0.00 0.00 36.60 3.86
813 844 2.021457 GACTGCTAGGTGTCTCTCCTC 58.979 57.143 0.00 0.00 36.60 3.71
814 845 1.638589 AGACTGCTAGGTGTCTCTCCT 59.361 52.381 0.00 0.00 39.04 3.69
815 846 2.137810 AGACTGCTAGGTGTCTCTCC 57.862 55.000 0.00 0.00 39.04 3.71
816 847 2.616842 GCTAGACTGCTAGGTGTCTCTC 59.383 54.545 0.00 0.00 43.54 3.20
817 848 2.025793 TGCTAGACTGCTAGGTGTCTCT 60.026 50.000 0.00 0.00 43.54 3.10
818 849 2.357637 CTGCTAGACTGCTAGGTGTCTC 59.642 54.545 0.00 0.00 43.54 3.36
819 850 2.374184 CTGCTAGACTGCTAGGTGTCT 58.626 52.381 0.00 0.00 43.54 3.41
820 851 1.202359 GCTGCTAGACTGCTAGGTGTC 60.202 57.143 0.00 0.00 43.54 3.67
821 852 0.820871 GCTGCTAGACTGCTAGGTGT 59.179 55.000 0.00 0.00 43.54 4.16
822 853 0.820226 TGCTGCTAGACTGCTAGGTG 59.180 55.000 0.00 0.00 43.54 4.00
823 854 1.205893 GTTGCTGCTAGACTGCTAGGT 59.794 52.381 0.00 0.00 43.54 3.08
885 916 1.468520 CAGTGATTTGGGTTCGCGAAT 59.531 47.619 26.23 7.56 0.00 3.34
937 968 1.602920 CGCAGAGTGCTGTTGTAGTCA 60.603 52.381 0.00 0.00 44.17 3.41
977 1008 1.349067 AAGGTGAGGCTCGGTTAACT 58.651 50.000 10.42 0.00 0.00 2.24
1026 1057 3.296836 TTTGACGGCTCGACGGGA 61.297 61.111 0.00 0.00 38.39 5.14
1073 1113 2.186903 GCTCGGCGGGAGATTTGA 59.813 61.111 12.93 0.00 46.23 2.69
1101 1141 4.431131 CGGGCCTCCATTGCTGGT 62.431 66.667 0.84 0.00 43.61 4.00
1122 1162 3.991536 GAGCGGTCGGGTCTTGAGC 62.992 68.421 0.00 0.00 40.05 4.26
1337 1377 2.497628 GCGCGCACGACTTGAAAG 60.498 61.111 29.10 0.00 43.93 2.62
1374 1414 2.294078 GGAGTGCACCTGCCTACCT 61.294 63.158 14.63 0.00 41.18 3.08
1407 1447 4.431131 ACATCCCCAAGCAGCCCG 62.431 66.667 0.00 0.00 0.00 6.13
1434 1474 4.521146 CATAGAAATCCACCAGAGCTGTT 58.479 43.478 0.00 0.00 0.00 3.16
1490 1530 1.287425 GACGGGCATCTCGTTAAAGG 58.713 55.000 0.00 0.00 41.22 3.11
1495 1535 1.079127 CCTTGACGGGCATCTCGTT 60.079 57.895 0.00 0.00 41.22 3.85
1506 1546 2.882927 TCGGTATTGGATCCTTGACG 57.117 50.000 14.23 11.18 0.00 4.35
1518 1558 6.036735 CGGTGATCAAACAGTTTATCGGTATT 59.963 38.462 0.00 0.00 0.00 1.89
1567 1607 2.827921 CAAACAGCTTCCTGGCCTTATT 59.172 45.455 3.32 0.00 43.53 1.40
1584 1624 0.036388 TCCTCTCCATGCCGTCAAAC 60.036 55.000 0.00 0.00 0.00 2.93
1593 1633 0.678395 CGGATGTCCTCCTCTCCATG 59.322 60.000 0.00 0.00 42.47 3.66
1807 1847 1.391485 GTGCACTATCACGTTCTGCAG 59.609 52.381 10.32 7.63 38.49 4.41
1898 1938 1.216444 GCCACGACATCTCTCTGCA 59.784 57.895 0.00 0.00 0.00 4.41
2163 2203 1.002134 CCGGGCTCTTCCAACATGT 60.002 57.895 0.00 0.00 36.21 3.21
2826 2866 1.531365 CAAGAGCAACCCCAAGCCA 60.531 57.895 0.00 0.00 0.00 4.75
2927 2969 6.040278 TCAATGTAATGCTTTGTGTTCCTTCA 59.960 34.615 0.00 0.00 34.83 3.02
2946 2988 1.660560 GCAGCTCGCCCAATCAATGT 61.661 55.000 0.00 0.00 32.94 2.71
3183 3238 1.036707 AGAGAAGCGATAGGACTGCC 58.963 55.000 0.00 0.00 0.00 4.85
3244 3299 8.677300 GGCAAAATGTCTGAAAGTCTATATTCA 58.323 33.333 0.00 0.00 34.57 2.57
3296 3354 5.693961 TCAATTGCCCAAATGCTATCTAGA 58.306 37.500 0.00 0.00 0.00 2.43
3298 3356 7.725397 ACTTATCAATTGCCCAAATGCTATCTA 59.275 33.333 0.00 0.00 0.00 1.98
3367 3425 5.175673 GTGCTTCCTAAAGTGCAAATTTGTC 59.824 40.000 19.03 11.87 33.75 3.18
3415 3473 7.761249 GCATATTTGTCAAGGTTATTGCTTTCT 59.239 33.333 0.00 0.00 0.00 2.52
3466 3524 4.635473 AGGAATGGAGGGAGTAGATGAAA 58.365 43.478 0.00 0.00 0.00 2.69
3475 3533 7.521669 AGACAAATATTTAGGAATGGAGGGAG 58.478 38.462 0.00 0.00 0.00 4.30
3476 3534 7.465900 AGACAAATATTTAGGAATGGAGGGA 57.534 36.000 0.00 0.00 0.00 4.20
3477 3535 8.539117 AAAGACAAATATTTAGGAATGGAGGG 57.461 34.615 0.00 0.00 0.00 4.30
3478 3536 9.413734 AGAAAGACAAATATTTAGGAATGGAGG 57.586 33.333 0.00 0.00 0.00 4.30
3494 3552 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
3495 3553 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
3496 3554 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
3497 3555 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
3498 3556 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
3499 3557 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
3500 3558 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
3501 3559 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
3502 3560 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
3503 3561 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
3505 3563 9.376075 CATATGTAGTCACTTGTTGAAATCTCT 57.624 33.333 0.00 0.00 35.39 3.10
3506 3564 8.607459 CCATATGTAGTCACTTGTTGAAATCTC 58.393 37.037 1.24 0.00 35.39 2.75
3507 3565 8.321353 TCCATATGTAGTCACTTGTTGAAATCT 58.679 33.333 1.24 0.00 35.39 2.40
3508 3566 8.492673 TCCATATGTAGTCACTTGTTGAAATC 57.507 34.615 1.24 0.00 35.39 2.17
3509 3567 7.066284 GCTCCATATGTAGTCACTTGTTGAAAT 59.934 37.037 1.24 0.00 35.39 2.17
3510 3568 6.371548 GCTCCATATGTAGTCACTTGTTGAAA 59.628 38.462 1.24 0.00 35.39 2.69
3511 3569 5.874810 GCTCCATATGTAGTCACTTGTTGAA 59.125 40.000 1.24 0.00 35.39 2.69
3512 3570 5.046663 TGCTCCATATGTAGTCACTTGTTGA 60.047 40.000 1.24 0.00 0.00 3.18
3513 3571 5.178061 TGCTCCATATGTAGTCACTTGTTG 58.822 41.667 1.24 0.00 0.00 3.33
3514 3572 5.420725 TGCTCCATATGTAGTCACTTGTT 57.579 39.130 1.24 0.00 0.00 2.83
3515 3573 5.420725 TTGCTCCATATGTAGTCACTTGT 57.579 39.130 1.24 0.00 0.00 3.16
3516 3574 6.741992 TTTTGCTCCATATGTAGTCACTTG 57.258 37.500 1.24 0.00 0.00 3.16
3517 3575 7.112122 TCATTTTGCTCCATATGTAGTCACTT 58.888 34.615 1.24 0.00 0.00 3.16
3518 3576 6.653020 TCATTTTGCTCCATATGTAGTCACT 58.347 36.000 1.24 0.00 0.00 3.41
3519 3577 6.540189 ACTCATTTTGCTCCATATGTAGTCAC 59.460 38.462 1.24 0.00 0.00 3.67
3520 3578 6.539826 CACTCATTTTGCTCCATATGTAGTCA 59.460 38.462 1.24 0.00 0.00 3.41
3521 3579 6.763135 TCACTCATTTTGCTCCATATGTAGTC 59.237 38.462 1.24 0.00 0.00 2.59
3522 3580 6.653020 TCACTCATTTTGCTCCATATGTAGT 58.347 36.000 1.24 0.00 0.00 2.73
3523 3581 7.558161 TTCACTCATTTTGCTCCATATGTAG 57.442 36.000 1.24 0.00 0.00 2.74
3524 3582 7.994911 AGATTCACTCATTTTGCTCCATATGTA 59.005 33.333 1.24 0.00 0.00 2.29
3525 3583 6.832384 AGATTCACTCATTTTGCTCCATATGT 59.168 34.615 1.24 0.00 0.00 2.29
3526 3584 7.273320 AGATTCACTCATTTTGCTCCATATG 57.727 36.000 0.00 0.00 0.00 1.78
3527 3585 7.994911 TGTAGATTCACTCATTTTGCTCCATAT 59.005 33.333 0.00 0.00 0.00 1.78
3528 3586 7.280876 GTGTAGATTCACTCATTTTGCTCCATA 59.719 37.037 0.00 0.00 35.68 2.74
3529 3587 6.094603 GTGTAGATTCACTCATTTTGCTCCAT 59.905 38.462 0.00 0.00 35.68 3.41
3530 3588 5.412594 GTGTAGATTCACTCATTTTGCTCCA 59.587 40.000 0.00 0.00 35.68 3.86
3531 3589 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
3532 3590 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
3588 3646 9.588096 AGTCTTTTTATAGGTTTCAAATGGACT 57.412 29.630 0.00 0.00 0.00 3.85
3607 3665 9.907229 CCCTCTGTTCCTTAATATAAGTCTTTT 57.093 33.333 0.00 0.00 0.00 2.27
3608 3666 9.280456 TCCCTCTGTTCCTTAATATAAGTCTTT 57.720 33.333 0.00 0.00 0.00 2.52
3609 3667 8.855804 TCCCTCTGTTCCTTAATATAAGTCTT 57.144 34.615 0.00 0.00 0.00 3.01
3610 3668 8.068733 ACTCCCTCTGTTCCTTAATATAAGTCT 58.931 37.037 0.00 0.00 0.00 3.24
3611 3669 8.252624 ACTCCCTCTGTTCCTTAATATAAGTC 57.747 38.462 0.00 0.00 0.00 3.01
3612 3670 9.725206 TTACTCCCTCTGTTCCTTAATATAAGT 57.275 33.333 0.00 0.00 0.00 2.24
3618 3676 8.832735 TGTTAATTACTCCCTCTGTTCCTTAAT 58.167 33.333 0.00 0.00 0.00 1.40
3619 3677 8.209802 TGTTAATTACTCCCTCTGTTCCTTAA 57.790 34.615 0.00 0.00 0.00 1.85
3620 3678 7.580882 GCTGTTAATTACTCCCTCTGTTCCTTA 60.581 40.741 0.00 0.00 0.00 2.69
3621 3679 6.697641 TGTTAATTACTCCCTCTGTTCCTT 57.302 37.500 0.00 0.00 0.00 3.36
3622 3680 5.338463 GCTGTTAATTACTCCCTCTGTTCCT 60.338 44.000 0.00 0.00 0.00 3.36
3623 3681 4.876679 GCTGTTAATTACTCCCTCTGTTCC 59.123 45.833 0.00 0.00 0.00 3.62
3624 3682 5.488341 TGCTGTTAATTACTCCCTCTGTTC 58.512 41.667 0.00 0.00 0.00 3.18
3625 3683 5.499004 TGCTGTTAATTACTCCCTCTGTT 57.501 39.130 0.00 0.00 0.00 3.16
3626 3684 5.700402 ATGCTGTTAATTACTCCCTCTGT 57.300 39.130 0.00 0.00 0.00 3.41
3627 3685 7.173907 CCAATATGCTGTTAATTACTCCCTCTG 59.826 40.741 0.00 0.00 0.00 3.35
3628 3686 7.072454 TCCAATATGCTGTTAATTACTCCCTCT 59.928 37.037 0.00 0.00 0.00 3.69
3629 3687 7.173390 GTCCAATATGCTGTTAATTACTCCCTC 59.827 40.741 0.00 0.00 0.00 4.30
3630 3688 6.998673 GTCCAATATGCTGTTAATTACTCCCT 59.001 38.462 0.00 0.00 0.00 4.20
3631 3689 6.770785 TGTCCAATATGCTGTTAATTACTCCC 59.229 38.462 0.00 0.00 0.00 4.30
3823 3961 7.392494 TCTAACGAAGAAGATGTACATGTCT 57.608 36.000 14.43 12.51 0.00 3.41
3855 3993 8.853077 TCATATGAATCTTGACTTTGAACACT 57.147 30.769 1.98 0.00 0.00 3.55
4230 4853 3.501828 TGAAATGACATTTGTGGGAGTCG 59.498 43.478 18.00 0.00 33.83 4.18
4282 4905 0.888619 TTTGTGGCCAACGTTGACAA 59.111 45.000 29.35 25.50 0.00 3.18
4344 4967 5.348724 TGAGCTCGTGATGAACAGTAAAATC 59.651 40.000 9.64 0.00 0.00 2.17
4365 4988 3.156511 TCTACTCGCAAGCTCATTGAG 57.843 47.619 9.40 9.40 41.83 3.02
4366 4989 3.193479 TCTTCTACTCGCAAGCTCATTGA 59.807 43.478 0.00 0.00 41.83 2.57
4367 4990 3.515630 TCTTCTACTCGCAAGCTCATTG 58.484 45.455 0.00 0.00 42.20 2.82
4368 4991 3.876274 TCTTCTACTCGCAAGCTCATT 57.124 42.857 0.00 0.00 37.18 2.57
4369 4992 3.382865 TCATCTTCTACTCGCAAGCTCAT 59.617 43.478 0.00 0.00 37.18 2.90
4370 4993 2.755103 TCATCTTCTACTCGCAAGCTCA 59.245 45.455 0.00 0.00 37.18 4.26
4410 5033 2.591133 CGGGAAACGTTTGGCAAATAG 58.409 47.619 20.10 15.21 37.93 1.73
4411 5034 1.336056 GCGGGAAACGTTTGGCAAATA 60.336 47.619 20.10 0.00 46.52 1.40
4412 5035 0.598942 GCGGGAAACGTTTGGCAAAT 60.599 50.000 20.10 0.00 46.52 2.32
4413 5036 1.227002 GCGGGAAACGTTTGGCAAA 60.227 52.632 20.10 8.93 46.52 3.68
4414 5037 1.945354 TTGCGGGAAACGTTTGGCAA 61.945 50.000 26.66 26.66 46.52 4.52
4415 5038 1.945354 TTTGCGGGAAACGTTTGGCA 61.945 50.000 20.10 20.39 46.52 4.92
4416 5039 0.806492 TTTTGCGGGAAACGTTTGGC 60.806 50.000 20.10 18.11 46.52 4.52
4417 5040 1.641577 TTTTTGCGGGAAACGTTTGG 58.358 45.000 20.10 8.53 46.52 3.28
4437 5060 8.769891 CGGAAAGTAAATTTGGCAAATAGTTTT 58.230 29.630 24.58 20.02 0.00 2.43
4438 5061 7.386573 CCGGAAAGTAAATTTGGCAAATAGTTT 59.613 33.333 24.58 22.18 0.00 2.66
4439 5062 6.871492 CCGGAAAGTAAATTTGGCAAATAGTT 59.129 34.615 24.58 18.07 0.00 2.24
4440 5063 6.014925 ACCGGAAAGTAAATTTGGCAAATAGT 60.015 34.615 24.58 17.60 0.00 2.12
4513 5136 6.272822 ACAGAAAGGTATTTTGAATGGAGC 57.727 37.500 0.00 0.00 0.00 4.70
4655 5308 0.822121 GAAGGCCAACACTCGGGTTT 60.822 55.000 5.01 0.00 0.00 3.27
4711 5371 6.664428 AAATAGGCAAGTTCTAGGCAAAAA 57.336 33.333 0.00 0.00 0.00 1.94
4712 5372 6.664428 AAAATAGGCAAGTTCTAGGCAAAA 57.336 33.333 0.00 0.00 0.00 2.44
4759 5419 3.073062 GGAATTGGGCTGCTTATAGGAGA 59.927 47.826 0.00 0.00 35.49 3.71


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

AutoCloner maintained by Alex Coulton.