Multiple sequence alignment - TraesCS4B01G279000

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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 TraesCS4B01G279000 chr4B 100.000 4373 0 0 1 4373 562354875 562359247 0.000000e+00 8076
1 TraesCS4B01G279000 chr4A 96.111 2777 80 5 928 3684 17261841 17259073 0.000000e+00 4505
2 TraesCS4B01G279000 chr4A 87.431 541 31 16 3744 4270 17259077 17258560 4.870000e-164 588
3 TraesCS4B01G279000 chr4A 75.726 758 95 53 1 738 17262550 17261862 9.190000e-77 298
4 TraesCS4B01G279000 chr4A 96.639 119 4 0 790 908 631238730 631238612 9.590000e-47 198
5 TraesCS4B01G279000 chr4A 91.406 128 9 2 781 907 739864910 739864784 1.620000e-39 174
6 TraesCS4B01G279000 chr4A 89.630 135 12 2 786 918 618561560 618561426 2.090000e-38 171
7 TraesCS4B01G279000 chr4A 96.117 103 2 2 4269 4370 17258502 17258401 2.710000e-37 167
8 TraesCS4B01G279000 chr4D 95.277 2795 97 8 905 3684 449731655 449734429 0.000000e+00 4397
9 TraesCS4B01G279000 chr4D 93.571 560 23 9 3824 4373 449734463 449735019 0.000000e+00 822
10 TraesCS4B01G279000 chr4D 89.873 474 28 9 320 781 449731187 449731652 3.770000e-165 592
11 TraesCS4B01G279000 chr4D 79.656 349 21 17 9 333 449730840 449731162 5.730000e-49 206
12 TraesCS4B01G279000 chr7D 96.850 127 4 0 780 906 247324134 247324260 3.430000e-51 213
13 TraesCS4B01G279000 chr7D 97.521 121 3 0 786 906 628410928 628411048 1.590000e-49 207
14 TraesCS4B01G279000 chr7D 97.436 117 3 0 790 906 182605350 182605466 2.670000e-47 200
15 TraesCS4B01G279000 chr1D 95.798 119 5 0 790 908 209564264 209564146 4.460000e-45 193
16 TraesCS4B01G279000 chr6B 94.309 123 5 2 785 907 365553 365673 2.080000e-43 187
17 TraesCS4B01G279000 chr5B 92.969 128 9 0 787 914 38365243 38365116 2.080000e-43 187


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 TraesCS4B01G279000 chr4B 562354875 562359247 4372 False 8076.00 8076 100.00000 1 4373 1 chr4B.!!$F1 4372
1 TraesCS4B01G279000 chr4A 17258401 17262550 4149 True 1389.50 4505 88.84625 1 4370 4 chr4A.!!$R4 4369
2 TraesCS4B01G279000 chr4D 449730840 449735019 4179 False 1504.25 4397 89.59425 9 4373 4 chr4D.!!$F1 4364

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
808 891 0.032813 TACTCCCTCCGTCCCGAATT 60.033 55.0 0.0 0.0 0.00 2.17 F
811 894 0.032813 TCCCTCCGTCCCGAATTACT 60.033 55.0 0.0 0.0 0.00 2.24 F
817 900 0.643820 CGTCCCGAATTACTTGTCGC 59.356 55.0 0.0 0.0 35.93 5.19 F
1449 1538 0.871722 TGGCGTGCAACAGTTACATC 59.128 50.0 0.0 0.0 35.74 3.06 F
2658 2747 0.469705 ACCTCTTGCATTGTGCCCAA 60.470 50.0 0.0 0.0 44.23 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2018 2107 0.036732 TTGGCTCTCGGTCAGCAATT 59.963 50.000 4.00 0.0 38.77 2.32 R
2425 2514 0.682852 TCAACGAAGGACCGGACAAT 59.317 50.000 9.46 0.0 0.00 2.71 R
2649 2738 3.215568 CCGCACTGTTGGGCACAA 61.216 61.111 0.00 0.0 33.87 3.33 R
3141 3230 0.753262 ACAGAAGGTTGACGAGCTGT 59.247 50.000 0.00 0.0 35.94 4.40 R
3816 3922 0.324923 ACCACTACCGTATCCCAGCA 60.325 55.000 0.00 0.0 0.00 4.41 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
26 27 0.533032 GAGCTATAGACGGATGGCCC 59.467 60.000 3.21 0.00 34.02 5.80
27 28 0.115349 AGCTATAGACGGATGGCCCT 59.885 55.000 3.21 0.00 34.02 5.19
28 29 1.358103 AGCTATAGACGGATGGCCCTA 59.642 52.381 3.21 0.00 34.02 3.53
29 30 2.023888 AGCTATAGACGGATGGCCCTAT 60.024 50.000 3.21 0.82 34.02 2.57
30 31 2.766828 GCTATAGACGGATGGCCCTATT 59.233 50.000 3.21 0.00 0.00 1.73
60 61 0.663153 GCCACGCACACTTTCTTTCT 59.337 50.000 0.00 0.00 0.00 2.52
61 62 1.065551 GCCACGCACACTTTCTTTCTT 59.934 47.619 0.00 0.00 0.00 2.52
62 63 2.479560 GCCACGCACACTTTCTTTCTTT 60.480 45.455 0.00 0.00 0.00 2.52
63 64 3.363178 CCACGCACACTTTCTTTCTTTC 58.637 45.455 0.00 0.00 0.00 2.62
64 65 3.065371 CCACGCACACTTTCTTTCTTTCT 59.935 43.478 0.00 0.00 0.00 2.52
65 66 4.438744 CCACGCACACTTTCTTTCTTTCTT 60.439 41.667 0.00 0.00 0.00 2.52
66 67 5.095490 CACGCACACTTTCTTTCTTTCTTT 58.905 37.500 0.00 0.00 0.00 2.52
67 68 5.228012 CACGCACACTTTCTTTCTTTCTTTC 59.772 40.000 0.00 0.00 0.00 2.62
68 69 4.735338 CGCACACTTTCTTTCTTTCTTTCC 59.265 41.667 0.00 0.00 0.00 3.13
69 70 5.043903 GCACACTTTCTTTCTTTCTTTCCC 58.956 41.667 0.00 0.00 0.00 3.97
70 71 5.273944 CACACTTTCTTTCTTTCTTTCCCG 58.726 41.667 0.00 0.00 0.00 5.14
71 72 5.065988 CACACTTTCTTTCTTTCTTTCCCGA 59.934 40.000 0.00 0.00 0.00 5.14
72 73 5.297029 ACACTTTCTTTCTTTCTTTCCCGAG 59.703 40.000 0.00 0.00 0.00 4.63
83 84 4.742649 TCCCGAGCGAGGCTGTCT 62.743 66.667 0.00 0.00 39.88 3.41
194 195 4.587189 CGCCGATCCCGTCCCTTC 62.587 72.222 0.00 0.00 0.00 3.46
196 197 3.912907 CCGATCCCGTCCCTTCCG 61.913 72.222 0.00 0.00 0.00 4.30
197 198 3.912907 CGATCCCGTCCCTTCCGG 61.913 72.222 0.00 0.00 45.07 5.14
198 199 4.237207 GATCCCGTCCCTTCCGGC 62.237 72.222 0.00 0.00 44.13 6.13
228 229 2.202987 CATCCCGCCTCAGTGAGC 60.203 66.667 15.10 9.29 0.00 4.26
234 235 1.817099 CGCCTCAGTGAGCATTCCC 60.817 63.158 15.10 0.00 0.00 3.97
250 262 3.847042 TTCCCTCCCTTCTCTTCTACA 57.153 47.619 0.00 0.00 0.00 2.74
259 271 4.024725 CCCTTCTCTTCTACATACGTCTCG 60.025 50.000 0.00 0.00 0.00 4.04
260 272 4.809958 CCTTCTCTTCTACATACGTCTCGA 59.190 45.833 0.00 0.00 0.00 4.04
262 274 4.752146 TCTCTTCTACATACGTCTCGACA 58.248 43.478 0.00 0.00 0.00 4.35
263 275 5.173664 TCTCTTCTACATACGTCTCGACAA 58.826 41.667 0.00 0.00 0.00 3.18
264 276 5.816258 TCTCTTCTACATACGTCTCGACAAT 59.184 40.000 0.00 0.00 0.00 2.71
265 277 5.807344 TCTTCTACATACGTCTCGACAATG 58.193 41.667 0.00 7.47 33.23 2.82
266 278 3.948851 TCTACATACGTCTCGACAATGC 58.051 45.455 0.00 0.00 31.32 3.56
267 279 2.647529 ACATACGTCTCGACAATGCA 57.352 45.000 0.00 0.00 31.32 3.96
270 282 0.455464 TACGTCTCGACAATGCACGG 60.455 55.000 0.00 0.00 34.75 4.94
271 283 1.443702 CGTCTCGACAATGCACGGA 60.444 57.895 0.00 0.00 0.00 4.69
272 284 1.674611 CGTCTCGACAATGCACGGAC 61.675 60.000 0.00 0.00 0.00 4.79
273 285 1.443702 TCTCGACAATGCACGGACG 60.444 57.895 0.00 0.00 0.00 4.79
291 315 2.187946 CTGCCCCATCGGTCTGTC 59.812 66.667 0.00 0.00 0.00 3.51
295 319 1.381872 CCCCATCGGTCTGTCCTCT 60.382 63.158 0.00 0.00 0.00 3.69
298 322 1.395826 CCATCGGTCTGTCCTCTCCC 61.396 65.000 0.00 0.00 0.00 4.30
312 337 4.467084 TCCCCGCGTGGATTGAGC 62.467 66.667 18.79 0.00 37.49 4.26
432 498 3.529734 AGGAGAGATGTAGACAAGGGAGA 59.470 47.826 0.00 0.00 0.00 3.71
443 509 4.664267 AGGGAGAGGCCACCTGCA 62.664 66.667 16.21 0.00 43.89 4.41
444 510 3.415087 GGGAGAGGCCACCTGCAT 61.415 66.667 16.21 0.00 43.89 3.96
445 511 2.124403 GGAGAGGCCACCTGCATG 60.124 66.667 5.01 0.00 43.89 4.06
446 512 2.827642 GAGAGGCCACCTGCATGC 60.828 66.667 11.82 11.82 43.89 4.06
512 578 4.033009 TCCAATGGAGATTACTCTCTGCA 58.967 43.478 9.69 2.04 45.89 4.41
522 588 6.561614 AGATTACTCTCTGCAATGCAATTTG 58.438 36.000 9.92 3.01 38.41 2.32
602 671 2.094545 AGCAATTTGGTTGAGCGATTCC 60.095 45.455 0.00 0.00 40.37 3.01
603 672 2.879826 CAATTTGGTTGAGCGATTCCC 58.120 47.619 0.00 0.00 40.37 3.97
604 673 1.474330 ATTTGGTTGAGCGATTCCCC 58.526 50.000 0.00 0.00 0.00 4.81
605 674 0.404040 TTTGGTTGAGCGATTCCCCT 59.596 50.000 0.00 0.00 0.00 4.79
606 675 1.281419 TTGGTTGAGCGATTCCCCTA 58.719 50.000 0.00 0.00 0.00 3.53
607 676 0.830648 TGGTTGAGCGATTCCCCTAG 59.169 55.000 0.00 0.00 0.00 3.02
608 677 0.533085 GGTTGAGCGATTCCCCTAGC 60.533 60.000 0.00 0.00 0.00 3.42
613 682 0.252197 AGCGATTCCCCTAGCGTTTT 59.748 50.000 0.00 0.00 34.34 2.43
661 740 3.375299 CACGGAATGATCCTTGTTCTTCC 59.625 47.826 0.00 0.00 44.17 3.46
735 818 0.939106 GCCGCGTCAATTTGCTTTGT 60.939 50.000 4.92 0.00 0.00 2.83
743 826 4.566360 CGTCAATTTGCTTTGTTTTGACCT 59.434 37.500 8.12 0.00 41.84 3.85
772 855 2.597455 ACTGCCTTACAAACTGCCAAT 58.403 42.857 0.00 0.00 0.00 3.16
774 857 3.506067 ACTGCCTTACAAACTGCCAATAC 59.494 43.478 0.00 0.00 0.00 1.89
781 864 7.521585 GCCTTACAAACTGCCAATACCATATAC 60.522 40.741 0.00 0.00 0.00 1.47
782 865 7.719633 CCTTACAAACTGCCAATACCATATACT 59.280 37.037 0.00 0.00 0.00 2.12
783 866 8.671384 TTACAAACTGCCAATACCATATACTC 57.329 34.615 0.00 0.00 0.00 2.59
784 867 6.062095 ACAAACTGCCAATACCATATACTCC 58.938 40.000 0.00 0.00 0.00 3.85
785 868 6.126478 ACAAACTGCCAATACCATATACTCCT 60.126 38.462 0.00 0.00 0.00 3.69
786 869 7.071950 ACAAACTGCCAATACCATATACTCCTA 59.928 37.037 0.00 0.00 0.00 2.94
787 870 7.814693 AACTGCCAATACCATATACTCCTAT 57.185 36.000 0.00 0.00 0.00 2.57
788 871 8.911018 AACTGCCAATACCATATACTCCTATA 57.089 34.615 0.00 0.00 0.00 1.31
789 872 9.507381 AACTGCCAATACCATATACTCCTATAT 57.493 33.333 0.00 0.00 0.00 0.86
798 881 8.059565 ACCATATACTCCTATATACTCCCTCC 57.940 42.308 0.00 0.00 0.00 4.30
799 882 7.169591 CCATATACTCCTATATACTCCCTCCG 58.830 46.154 0.00 0.00 0.00 4.63
800 883 7.202204 CCATATACTCCTATATACTCCCTCCGT 60.202 44.444 0.00 0.00 0.00 4.69
801 884 4.573021 ACTCCTATATACTCCCTCCGTC 57.427 50.000 0.00 0.00 0.00 4.79
802 885 3.266513 ACTCCTATATACTCCCTCCGTCC 59.733 52.174 0.00 0.00 0.00 4.79
803 886 2.579860 TCCTATATACTCCCTCCGTCCC 59.420 54.545 0.00 0.00 0.00 4.46
804 887 2.641305 CTATATACTCCCTCCGTCCCG 58.359 57.143 0.00 0.00 0.00 5.14
805 888 1.070604 ATATACTCCCTCCGTCCCGA 58.929 55.000 0.00 0.00 0.00 5.14
806 889 0.846015 TATACTCCCTCCGTCCCGAA 59.154 55.000 0.00 0.00 0.00 4.30
807 890 0.187851 ATACTCCCTCCGTCCCGAAT 59.812 55.000 0.00 0.00 0.00 3.34
808 891 0.032813 TACTCCCTCCGTCCCGAATT 60.033 55.000 0.00 0.00 0.00 2.17
809 892 0.032813 ACTCCCTCCGTCCCGAATTA 60.033 55.000 0.00 0.00 0.00 1.40
810 893 0.388294 CTCCCTCCGTCCCGAATTAC 59.612 60.000 0.00 0.00 0.00 1.89
811 894 0.032813 TCCCTCCGTCCCGAATTACT 60.033 55.000 0.00 0.00 0.00 2.24
812 895 0.828677 CCCTCCGTCCCGAATTACTT 59.171 55.000 0.00 0.00 0.00 2.24
813 896 1.472728 CCCTCCGTCCCGAATTACTTG 60.473 57.143 0.00 0.00 0.00 3.16
814 897 1.206371 CCTCCGTCCCGAATTACTTGT 59.794 52.381 0.00 0.00 0.00 3.16
815 898 2.537401 CTCCGTCCCGAATTACTTGTC 58.463 52.381 0.00 0.00 0.00 3.18
816 899 1.135315 TCCGTCCCGAATTACTTGTCG 60.135 52.381 0.00 0.00 37.01 4.35
817 900 0.643820 CGTCCCGAATTACTTGTCGC 59.356 55.000 0.00 0.00 35.93 5.19
818 901 1.717194 GTCCCGAATTACTTGTCGCA 58.283 50.000 0.00 0.00 35.93 5.10
819 902 1.392510 GTCCCGAATTACTTGTCGCAC 59.607 52.381 0.00 0.00 35.93 5.34
820 903 1.001068 TCCCGAATTACTTGTCGCACA 59.999 47.619 0.00 0.00 35.93 4.57
821 904 1.801771 CCCGAATTACTTGTCGCACAA 59.198 47.619 2.49 2.49 36.54 3.33
822 905 2.224549 CCCGAATTACTTGTCGCACAAA 59.775 45.455 3.84 0.00 37.69 2.83
823 906 3.119990 CCCGAATTACTTGTCGCACAAAT 60.120 43.478 3.84 0.00 37.69 2.32
824 907 3.845775 CCGAATTACTTGTCGCACAAATG 59.154 43.478 3.84 0.00 37.69 2.32
825 908 3.845775 CGAATTACTTGTCGCACAAATGG 59.154 43.478 3.84 0.00 37.69 3.16
826 909 4.377943 CGAATTACTTGTCGCACAAATGGA 60.378 41.667 3.84 0.00 37.69 3.41
827 910 5.640732 GAATTACTTGTCGCACAAATGGAT 58.359 37.500 3.84 0.00 37.69 3.41
828 911 6.456315 CGAATTACTTGTCGCACAAATGGATA 60.456 38.462 3.84 0.00 37.69 2.59
829 912 6.751514 ATTACTTGTCGCACAAATGGATAA 57.248 33.333 3.84 0.00 37.69 1.75
830 913 6.561737 TTACTTGTCGCACAAATGGATAAA 57.438 33.333 3.84 0.00 37.69 1.40
831 914 5.446143 ACTTGTCGCACAAATGGATAAAA 57.554 34.783 3.84 0.00 37.69 1.52
832 915 5.460646 ACTTGTCGCACAAATGGATAAAAG 58.539 37.500 3.84 0.00 37.69 2.27
833 916 5.009610 ACTTGTCGCACAAATGGATAAAAGT 59.990 36.000 3.84 0.00 37.69 2.66
834 917 5.041951 TGTCGCACAAATGGATAAAAGTC 57.958 39.130 0.00 0.00 0.00 3.01
835 918 4.088648 GTCGCACAAATGGATAAAAGTCG 58.911 43.478 0.00 0.00 0.00 4.18
836 919 3.997681 TCGCACAAATGGATAAAAGTCGA 59.002 39.130 0.00 0.00 0.00 4.20
837 920 4.634004 TCGCACAAATGGATAAAAGTCGAT 59.366 37.500 0.00 0.00 0.00 3.59
838 921 4.730042 CGCACAAATGGATAAAAGTCGATG 59.270 41.667 0.00 0.00 0.00 3.84
839 922 5.640732 GCACAAATGGATAAAAGTCGATGT 58.359 37.500 0.00 0.00 0.00 3.06
840 923 6.456315 CGCACAAATGGATAAAAGTCGATGTA 60.456 38.462 0.00 0.00 0.00 2.29
841 924 7.417612 GCACAAATGGATAAAAGTCGATGTAT 58.582 34.615 0.00 0.00 0.00 2.29
842 925 7.587757 GCACAAATGGATAAAAGTCGATGTATC 59.412 37.037 0.00 0.00 0.00 2.24
843 926 8.830580 CACAAATGGATAAAAGTCGATGTATCT 58.169 33.333 0.00 0.00 0.00 1.98
846 929 9.712305 AAATGGATAAAAGTCGATGTATCTAGG 57.288 33.333 0.00 0.00 0.00 3.02
847 930 8.651589 ATGGATAAAAGTCGATGTATCTAGGA 57.348 34.615 0.00 0.00 0.00 2.94
848 931 7.883217 TGGATAAAAGTCGATGTATCTAGGAC 58.117 38.462 0.00 0.00 0.00 3.85
849 932 7.724506 TGGATAAAAGTCGATGTATCTAGGACT 59.275 37.037 0.00 0.00 39.50 3.85
850 933 9.228949 GGATAAAAGTCGATGTATCTAGGACTA 57.771 37.037 0.00 0.00 36.99 2.59
879 962 6.332735 TGTCTAGATACATCCATTTCTCCG 57.667 41.667 0.00 0.00 0.00 4.63
880 963 6.068670 TGTCTAGATACATCCATTTCTCCGA 58.931 40.000 0.00 0.00 0.00 4.55
881 964 6.016192 TGTCTAGATACATCCATTTCTCCGAC 60.016 42.308 0.00 0.00 0.00 4.79
882 965 6.016192 GTCTAGATACATCCATTTCTCCGACA 60.016 42.308 0.00 0.00 0.00 4.35
883 966 5.614324 AGATACATCCATTTCTCCGACAA 57.386 39.130 0.00 0.00 0.00 3.18
884 967 5.605534 AGATACATCCATTTCTCCGACAAG 58.394 41.667 0.00 0.00 0.00 3.16
885 968 3.703001 ACATCCATTTCTCCGACAAGT 57.297 42.857 0.00 0.00 0.00 3.16
886 969 4.819105 ACATCCATTTCTCCGACAAGTA 57.181 40.909 0.00 0.00 0.00 2.24
887 970 5.359194 ACATCCATTTCTCCGACAAGTAT 57.641 39.130 0.00 0.00 0.00 2.12
888 971 5.745227 ACATCCATTTCTCCGACAAGTATT 58.255 37.500 0.00 0.00 0.00 1.89
889 972 6.180472 ACATCCATTTCTCCGACAAGTATTT 58.820 36.000 0.00 0.00 0.00 1.40
890 973 6.659242 ACATCCATTTCTCCGACAAGTATTTT 59.341 34.615 0.00 0.00 0.00 1.82
891 974 6.737254 TCCATTTCTCCGACAAGTATTTTC 57.263 37.500 0.00 0.00 0.00 2.29
892 975 5.350365 TCCATTTCTCCGACAAGTATTTTCG 59.650 40.000 0.00 0.00 0.00 3.46
898 981 2.598589 CGACAAGTATTTTCGGACGGA 58.401 47.619 0.00 0.00 0.00 4.69
899 982 2.597305 CGACAAGTATTTTCGGACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
900 983 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
901 984 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
902 985 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
903 986 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
916 999 3.006644 ACGGAGGGAGTACTTCTTTGTTC 59.993 47.826 0.01 0.00 0.00 3.18
923 1006 6.557633 AGGGAGTACTTCTTTGTTCCTTCTAA 59.442 38.462 0.01 0.00 0.00 2.10
924 1007 6.649973 GGGAGTACTTCTTTGTTCCTTCTAAC 59.350 42.308 0.01 0.00 0.00 2.34
925 1008 6.649973 GGAGTACTTCTTTGTTCCTTCTAACC 59.350 42.308 0.00 0.00 0.00 2.85
926 1009 6.221659 AGTACTTCTTTGTTCCTTCTAACCG 58.778 40.000 0.00 0.00 0.00 4.44
970 1056 1.398390 CTCCCATAACTGCGCTGAAAC 59.602 52.381 21.92 0.00 0.00 2.78
1025 1114 2.301296 CTGACCAGCCAAAGAAGAGAGA 59.699 50.000 0.00 0.00 0.00 3.10
1026 1115 2.301296 TGACCAGCCAAAGAAGAGAGAG 59.699 50.000 0.00 0.00 0.00 3.20
1056 1145 3.148279 GGCGATGGAGGTCTCGGT 61.148 66.667 0.00 0.00 35.48 4.69
1092 1181 3.065610 TTCATTGCAAACGGCGAGGAC 62.066 52.381 16.62 0.15 45.82 3.85
1131 1220 1.960612 CGGGTTTGATTCCGGCAAA 59.039 52.632 0.00 0.00 42.32 3.68
1257 1346 3.049674 CTGCGCGGTGTGATGGTT 61.050 61.111 8.83 0.00 0.00 3.67
1350 1439 5.235305 TGTTGAAGCTTGACAAACTTCTC 57.765 39.130 24.50 18.92 40.36 2.87
1377 1466 6.479660 AGTTGTATTCGGTCAAGAAAAACGTA 59.520 34.615 0.00 0.00 33.43 3.57
1411 1500 4.026886 TGACGATATTGAAGATTTGCGTCG 60.027 41.667 0.00 0.00 46.78 5.12
1449 1538 0.871722 TGGCGTGCAACAGTTACATC 59.128 50.000 0.00 0.00 35.74 3.06
1530 1619 5.510179 CCTGCAAAACATTCCTGTGAAGATT 60.510 40.000 0.00 0.00 35.22 2.40
1543 1632 9.581289 TTCCTGTGAAGATTATTAAAAAGGTGA 57.419 29.630 0.00 0.00 0.00 4.02
1653 1742 1.817099 CAAGCAGATCGGGCAGGTC 60.817 63.158 13.69 0.00 0.00 3.85
1724 1813 1.521616 GGCAGAGAGAGGCTGAAGG 59.478 63.158 0.00 0.00 35.39 3.46
1842 1931 1.004610 CGAACGCATCACATCCATGTC 60.005 52.381 0.00 0.00 39.39 3.06
1843 1932 2.283298 GAACGCATCACATCCATGTCT 58.717 47.619 0.00 0.00 39.39 3.41
2002 2091 4.539509 TTTATTGTTGAACAACGCGTCT 57.460 36.364 14.44 0.00 41.40 4.18
2018 2107 2.394708 CGTCTTTCGAACTGCAGAGAA 58.605 47.619 23.35 18.65 42.86 2.87
2083 2172 4.294232 CGTTGCGAAGATGACATCTCTAT 58.706 43.478 18.21 3.06 39.08 1.98
2166 2255 2.935201 CACTCTTATGGCTGCAGTTCTC 59.065 50.000 16.64 3.69 0.00 2.87
2200 2289 1.885887 ACCAAACCACACCATTGATCG 59.114 47.619 0.00 0.00 0.00 3.69
2271 2360 1.742768 CCGGAGGCAGGTAGATGAC 59.257 63.158 0.00 0.00 46.14 3.06
2425 2514 1.939934 CTGTTCCAGAAGTTTGTCGCA 59.060 47.619 0.00 0.00 32.44 5.10
2649 2738 4.511527 CTTGTGATCTGTACCTCTTGCAT 58.488 43.478 0.00 0.00 0.00 3.96
2658 2747 0.469705 ACCTCTTGCATTGTGCCCAA 60.470 50.000 0.00 0.00 44.23 4.12
2781 2870 4.914177 AAACATGGCCAATTCCAAGATT 57.086 36.364 10.96 0.00 39.96 2.40
2952 3041 1.053835 TTGTCTCTGGTGCAGTGGGA 61.054 55.000 0.00 0.00 32.61 4.37
2976 3065 3.253677 ACATCTCGGACTCGATAATGACC 59.746 47.826 14.01 0.00 45.04 4.02
3096 3185 4.101448 ATCACCGGGCTGGCAGAC 62.101 66.667 20.86 17.26 43.94 3.51
3141 3230 6.070596 TCAGAGATTGCTTGGTTGAGATAAGA 60.071 38.462 0.00 0.00 0.00 2.10
3306 3395 1.362355 CCTTTCCAACCGCAACACC 59.638 57.895 0.00 0.00 0.00 4.16
3404 3505 1.277273 TCAATCCTGCTCAGTGTCCAG 59.723 52.381 6.01 6.01 0.00 3.86
3423 3524 8.730680 GTGTCCAGCTTCTGAATTTTATTTCTA 58.269 33.333 0.00 0.00 32.44 2.10
3478 3582 2.543238 CGTCTATTTGTCCGTCTAGGCC 60.543 54.545 0.00 0.00 40.77 5.19
3489 3593 1.393539 CGTCTAGGCCATGTTTTGACG 59.606 52.381 5.01 8.57 39.43 4.35
3514 3618 7.318141 GGTTTATCAGTTACAGTGCAGTAGTA 58.682 38.462 0.00 0.00 0.00 1.82
3532 3636 8.398665 GCAGTAGTACCCTCAAATAATTTTCAG 58.601 37.037 0.00 0.00 0.00 3.02
3538 3642 9.419297 GTACCCTCAAATAATTTTCAGTTTTCC 57.581 33.333 0.00 0.00 0.00 3.13
3539 3643 8.028652 ACCCTCAAATAATTTTCAGTTTTCCA 57.971 30.769 0.00 0.00 0.00 3.53
3544 3648 9.844257 TCAAATAATTTTCAGTTTTCCATGGTT 57.156 25.926 12.58 0.00 0.00 3.67
3636 3740 7.119605 CAGAGTTTTGAGATTCTCTGTCTTG 57.880 40.000 14.54 2.14 44.82 3.02
3674 3780 5.705905 AGGACATAGTTTGAAGCCTGTTAAC 59.294 40.000 0.00 0.00 0.00 2.01
3680 3786 1.234615 TGAAGCCTGTTAACTGCGCC 61.235 55.000 4.18 7.53 0.00 6.53
3681 3787 1.923227 GAAGCCTGTTAACTGCGCCC 61.923 60.000 4.18 4.36 0.00 6.13
3682 3788 2.359975 GCCTGTTAACTGCGCCCT 60.360 61.111 4.18 0.00 0.00 5.19
3683 3789 2.690778 GCCTGTTAACTGCGCCCTG 61.691 63.158 4.18 0.00 0.00 4.45
3684 3790 2.690778 CCTGTTAACTGCGCCCTGC 61.691 63.158 4.18 0.00 46.70 4.85
3685 3791 1.672356 CTGTTAACTGCGCCCTGCT 60.672 57.895 4.18 0.00 46.63 4.24
3686 3792 1.915614 CTGTTAACTGCGCCCTGCTG 61.916 60.000 4.18 0.00 46.63 4.41
3687 3793 3.055719 TTAACTGCGCCCTGCTGC 61.056 61.111 4.18 0.00 45.63 5.25
3697 3803 3.506096 CCTGCTGCCATGTGCGAG 61.506 66.667 0.00 0.00 45.60 5.03
3698 3804 2.745100 CTGCTGCCATGTGCGAGT 60.745 61.111 0.00 0.00 45.60 4.18
3699 3805 1.448365 CTGCTGCCATGTGCGAGTA 60.448 57.895 0.00 0.00 45.60 2.59
3700 3806 0.812811 CTGCTGCCATGTGCGAGTAT 60.813 55.000 0.00 0.00 45.60 2.12
3701 3807 0.463620 TGCTGCCATGTGCGAGTATA 59.536 50.000 0.00 0.00 45.60 1.47
3702 3808 1.134551 TGCTGCCATGTGCGAGTATAA 60.135 47.619 0.00 0.00 45.60 0.98
3703 3809 1.261619 GCTGCCATGTGCGAGTATAAC 59.738 52.381 0.00 0.00 45.60 1.89
3704 3810 2.549926 CTGCCATGTGCGAGTATAACA 58.450 47.619 0.00 0.00 45.60 2.41
3705 3811 3.133691 CTGCCATGTGCGAGTATAACAT 58.866 45.455 0.00 0.00 45.60 2.71
3706 3812 2.871633 TGCCATGTGCGAGTATAACATG 59.128 45.455 7.81 7.81 46.92 3.21
3707 3813 2.872245 GCCATGTGCGAGTATAACATGT 59.128 45.455 12.51 0.00 46.28 3.21
3708 3814 3.312421 GCCATGTGCGAGTATAACATGTT 59.688 43.478 16.68 16.68 46.28 2.71
3709 3815 4.201910 GCCATGTGCGAGTATAACATGTTT 60.202 41.667 17.78 7.40 46.28 2.83
3710 3816 5.007234 GCCATGTGCGAGTATAACATGTTTA 59.993 40.000 17.78 6.41 46.28 2.01
3711 3817 6.293407 GCCATGTGCGAGTATAACATGTTTAT 60.293 38.462 17.78 10.48 46.28 1.40
3712 3818 7.095397 GCCATGTGCGAGTATAACATGTTTATA 60.095 37.037 17.78 9.54 46.28 0.98
3713 3819 8.935844 CCATGTGCGAGTATAACATGTTTATAT 58.064 33.333 17.78 6.99 46.28 0.86
3716 3822 9.968870 TGTGCGAGTATAACATGTTTATATACA 57.031 29.630 22.83 13.93 35.78 2.29
3739 3845 4.622701 AAAAGCGACTTATTCATGAGCC 57.377 40.909 0.00 0.00 0.00 4.70
3740 3846 2.988010 AGCGACTTATTCATGAGCCA 57.012 45.000 0.00 0.00 0.00 4.75
3741 3847 2.555199 AGCGACTTATTCATGAGCCAC 58.445 47.619 0.00 0.00 0.00 5.01
3742 3848 1.599542 GCGACTTATTCATGAGCCACC 59.400 52.381 0.00 0.00 0.00 4.61
3743 3849 2.213499 CGACTTATTCATGAGCCACCC 58.787 52.381 0.00 0.00 0.00 4.61
3765 3871 4.432712 CCCTGTTCCACAAACAAAAGAAG 58.567 43.478 0.00 0.00 46.95 2.85
3808 3914 7.698506 AAACCGATAGTATAGCATACTAGCA 57.301 36.000 20.98 6.25 36.53 3.49
3809 3915 7.883391 AACCGATAGTATAGCATACTAGCAT 57.117 36.000 20.98 11.99 36.53 3.79
3810 3916 7.265647 ACCGATAGTATAGCATACTAGCATG 57.734 40.000 20.98 16.24 36.53 4.06
3898 4004 2.079925 GAGACAAGCACATGGAACTCC 58.920 52.381 0.00 0.00 0.00 3.85
3899 4005 1.701847 AGACAAGCACATGGAACTCCT 59.298 47.619 0.00 0.00 36.82 3.69
3900 4006 1.808945 GACAAGCACATGGAACTCCTG 59.191 52.381 0.00 0.00 36.82 3.86
3944 4054 5.335583 GCAATTGGCAAGGTTAAAAATTCCC 60.336 40.000 7.72 0.00 43.97 3.97
3977 4087 2.675423 GTGGGGCCCCGTCTTTTC 60.675 66.667 36.00 15.23 39.42 2.29
4117 4227 2.526304 TTTGAGACGTCAACCTGGAG 57.474 50.000 19.50 0.00 42.60 3.86
4133 4243 1.487976 TGGAGGACTGAATCTCATGCC 59.512 52.381 0.00 0.00 0.00 4.40
4157 4267 2.881074 AGCGTAATGTACAGCTCTGTG 58.119 47.619 12.43 0.00 44.63 3.66
4187 4297 2.433838 CCAGCAGCACCGAGTCAG 60.434 66.667 0.00 0.00 0.00 3.51
4214 4324 1.084289 AGTACGATTCCTTTTGCGCC 58.916 50.000 4.18 0.00 0.00 6.53
4215 4325 0.247537 GTACGATTCCTTTTGCGCCG 60.248 55.000 4.18 0.00 0.00 6.46
4216 4326 1.363145 TACGATTCCTTTTGCGCCGG 61.363 55.000 4.18 0.00 0.00 6.13
4217 4327 2.395360 CGATTCCTTTTGCGCCGGA 61.395 57.895 5.05 2.42 0.00 5.14
4218 4328 1.429423 GATTCCTTTTGCGCCGGAG 59.571 57.895 5.05 1.55 0.00 4.63
4221 4331 0.952010 TTCCTTTTGCGCCGGAGTAC 60.952 55.000 5.05 0.00 0.00 2.73
4291 4471 6.007076 TGTAATTGATTAGCAGGTCAACCAA 58.993 36.000 1.33 0.00 37.19 3.67
4325 4505 1.021390 CACGGCATGTGGAGGACTTC 61.021 60.000 0.00 0.00 45.21 3.01
4367 4548 1.003839 TGCGGTTGATCAGGTCCAC 60.004 57.895 12.04 1.21 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 2.927014 GCGTGGCCGGAGAATAGAATAG 60.927 54.545 5.05 0.00 33.68 1.73
27 28 1.000506 GCGTGGCCGGAGAATAGAATA 59.999 52.381 5.05 0.00 33.68 1.75
28 29 0.249911 GCGTGGCCGGAGAATAGAAT 60.250 55.000 5.05 0.00 33.68 2.40
29 30 1.143183 GCGTGGCCGGAGAATAGAA 59.857 57.895 5.05 0.00 33.68 2.10
30 31 2.055633 TGCGTGGCCGGAGAATAGA 61.056 57.895 5.05 0.00 33.68 1.98
60 61 1.375523 GCCTCGCTCGGGAAAGAAA 60.376 57.895 0.00 0.00 0.00 2.52
61 62 2.264794 GCCTCGCTCGGGAAAGAA 59.735 61.111 0.00 0.00 0.00 2.52
62 63 2.680352 AGCCTCGCTCGGGAAAGA 60.680 61.111 0.00 0.00 30.62 2.52
63 64 2.510238 CAGCCTCGCTCGGGAAAG 60.510 66.667 0.00 0.00 36.40 2.62
64 65 3.296709 GACAGCCTCGCTCGGGAAA 62.297 63.158 0.00 0.00 36.40 3.13
65 66 3.760035 GACAGCCTCGCTCGGGAA 61.760 66.667 0.00 0.00 36.40 3.97
66 67 4.742649 AGACAGCCTCGCTCGGGA 62.743 66.667 0.00 0.00 36.40 5.14
67 68 4.504916 CAGACAGCCTCGCTCGGG 62.505 72.222 0.00 0.00 36.40 5.14
68 69 4.504916 CCAGACAGCCTCGCTCGG 62.505 72.222 0.00 0.00 36.40 4.63
132 133 0.250513 AATGGAACCTCTGGCGAGTC 59.749 55.000 0.00 0.00 35.43 3.36
204 205 4.008933 GAGGCGGGATGGGATCGG 62.009 72.222 0.00 0.00 0.00 4.18
210 211 2.503061 CTCACTGAGGCGGGATGG 59.497 66.667 0.00 0.00 0.00 3.51
228 229 4.033709 TGTAGAAGAGAAGGGAGGGAATG 58.966 47.826 0.00 0.00 0.00 2.67
234 235 5.127491 AGACGTATGTAGAAGAGAAGGGAG 58.873 45.833 0.00 0.00 0.00 4.30
250 262 1.545759 CGTGCATTGTCGAGACGTAT 58.454 50.000 0.00 0.00 0.00 3.06
259 271 2.476051 CAGCGTCCGTGCATTGTC 59.524 61.111 0.00 0.00 37.31 3.18
260 272 3.726517 GCAGCGTCCGTGCATTGT 61.727 61.111 0.00 0.00 40.86 2.71
291 315 3.470888 AATCCACGCGGGGAGAGG 61.471 66.667 36.16 14.36 41.08 3.69
295 319 4.467084 GCTCAATCCACGCGGGGA 62.467 66.667 35.71 35.71 42.21 4.81
443 509 3.133691 CTGCACAATACATAGACCGCAT 58.866 45.455 0.00 0.00 0.00 4.73
444 510 2.093711 ACTGCACAATACATAGACCGCA 60.094 45.455 0.00 0.00 0.00 5.69
445 511 2.285220 CACTGCACAATACATAGACCGC 59.715 50.000 0.00 0.00 0.00 5.68
446 512 3.521560 ACACTGCACAATACATAGACCG 58.478 45.455 0.00 0.00 0.00 4.79
522 588 2.202570 CAAATCGCTGCAGCAGGC 60.203 61.111 36.03 12.71 42.21 4.85
616 685 7.993681 CGTGATTGACGTATCCAAAAAGGAAAA 60.994 37.037 0.00 0.00 46.25 2.29
618 687 5.106869 CGTGATTGACGTATCCAAAAAGGAA 60.107 40.000 0.00 0.00 46.25 3.36
619 688 4.390603 CGTGATTGACGTATCCAAAAAGGA 59.609 41.667 0.00 0.00 46.78 3.36
620 689 4.647964 CGTGATTGACGTATCCAAAAAGG 58.352 43.478 0.00 0.00 43.50 3.11
627 696 4.307432 ATCATTCCGTGATTGACGTATCC 58.693 43.478 0.00 0.00 45.25 2.59
709 792 0.732571 AAATTGACGCGGCGATTCAT 59.267 45.000 27.28 10.66 0.00 2.57
772 855 9.180282 GGAGGGAGTATATAGGAGTATATGGTA 57.820 40.741 0.00 0.00 34.29 3.25
774 857 7.169591 CGGAGGGAGTATATAGGAGTATATGG 58.830 46.154 0.00 0.00 34.29 2.74
781 864 3.371810 GGGACGGAGGGAGTATATAGGAG 60.372 56.522 0.00 0.00 0.00 3.69
782 865 2.579860 GGGACGGAGGGAGTATATAGGA 59.420 54.545 0.00 0.00 0.00 2.94
783 866 3.015675 GGGACGGAGGGAGTATATAGG 57.984 57.143 0.00 0.00 0.00 2.57
799 882 1.392510 GTGCGACAAGTAATTCGGGAC 59.607 52.381 0.00 0.00 35.73 4.46
800 883 1.001068 TGTGCGACAAGTAATTCGGGA 59.999 47.619 0.00 0.00 35.73 5.14
801 884 1.434555 TGTGCGACAAGTAATTCGGG 58.565 50.000 0.00 0.00 35.73 5.14
802 885 3.529634 TTTGTGCGACAAGTAATTCGG 57.470 42.857 0.00 0.00 39.53 4.30
803 886 3.845775 CCATTTGTGCGACAAGTAATTCG 59.154 43.478 0.00 0.00 39.53 3.34
804 887 5.041951 TCCATTTGTGCGACAAGTAATTC 57.958 39.130 0.00 0.00 39.53 2.17
805 888 5.643379 ATCCATTTGTGCGACAAGTAATT 57.357 34.783 0.00 0.00 39.53 1.40
806 889 6.751514 TTATCCATTTGTGCGACAAGTAAT 57.248 33.333 0.00 0.00 39.53 1.89
807 890 6.561737 TTTATCCATTTGTGCGACAAGTAA 57.438 33.333 0.00 0.00 39.53 2.24
808 891 6.205853 ACTTTTATCCATTTGTGCGACAAGTA 59.794 34.615 0.00 0.00 39.53 2.24
809 892 5.009610 ACTTTTATCCATTTGTGCGACAAGT 59.990 36.000 0.00 0.00 39.53 3.16
810 893 5.460646 ACTTTTATCCATTTGTGCGACAAG 58.539 37.500 0.00 0.00 39.53 3.16
811 894 5.446143 ACTTTTATCCATTTGTGCGACAA 57.554 34.783 0.00 0.00 36.11 3.18
812 895 4.377943 CGACTTTTATCCATTTGTGCGACA 60.378 41.667 0.00 0.00 0.00 4.35
813 896 4.088648 CGACTTTTATCCATTTGTGCGAC 58.911 43.478 0.00 0.00 0.00 5.19
814 897 3.997681 TCGACTTTTATCCATTTGTGCGA 59.002 39.130 0.00 0.00 0.00 5.10
815 898 4.335082 TCGACTTTTATCCATTTGTGCG 57.665 40.909 0.00 0.00 0.00 5.34
816 899 5.640732 ACATCGACTTTTATCCATTTGTGC 58.359 37.500 0.00 0.00 0.00 4.57
817 900 8.830580 AGATACATCGACTTTTATCCATTTGTG 58.169 33.333 0.00 0.00 0.00 3.33
818 901 8.964476 AGATACATCGACTTTTATCCATTTGT 57.036 30.769 0.00 0.00 0.00 2.83
820 903 9.712305 CCTAGATACATCGACTTTTATCCATTT 57.288 33.333 0.00 0.00 0.00 2.32
821 904 9.090103 TCCTAGATACATCGACTTTTATCCATT 57.910 33.333 0.00 0.00 0.00 3.16
822 905 8.524487 GTCCTAGATACATCGACTTTTATCCAT 58.476 37.037 0.00 0.00 0.00 3.41
823 906 7.724506 AGTCCTAGATACATCGACTTTTATCCA 59.275 37.037 0.00 0.00 29.59 3.41
824 907 8.113173 AGTCCTAGATACATCGACTTTTATCC 57.887 38.462 0.00 0.00 29.59 2.59
853 936 8.690884 CGGAGAAATGGATGTATCTAGACATAT 58.309 37.037 0.00 0.00 40.18 1.78
854 937 7.888546 TCGGAGAAATGGATGTATCTAGACATA 59.111 37.037 0.00 0.00 40.18 2.29
855 938 6.721668 TCGGAGAAATGGATGTATCTAGACAT 59.278 38.462 0.00 0.00 42.82 3.06
856 939 6.016192 GTCGGAGAAATGGATGTATCTAGACA 60.016 42.308 0.00 0.00 39.69 3.41
857 940 6.016192 TGTCGGAGAAATGGATGTATCTAGAC 60.016 42.308 0.00 0.00 39.69 2.59
858 941 6.068670 TGTCGGAGAAATGGATGTATCTAGA 58.931 40.000 0.00 0.00 39.69 2.43
859 942 6.332735 TGTCGGAGAAATGGATGTATCTAG 57.667 41.667 0.00 0.00 39.69 2.43
860 943 6.323996 ACTTGTCGGAGAAATGGATGTATCTA 59.676 38.462 0.00 0.00 39.69 1.98
861 944 5.129485 ACTTGTCGGAGAAATGGATGTATCT 59.871 40.000 0.00 0.00 39.69 1.98
862 945 5.360591 ACTTGTCGGAGAAATGGATGTATC 58.639 41.667 0.00 0.00 39.69 2.24
863 946 5.359194 ACTTGTCGGAGAAATGGATGTAT 57.641 39.130 0.00 0.00 39.69 2.29
864 947 4.819105 ACTTGTCGGAGAAATGGATGTA 57.181 40.909 0.00 0.00 39.69 2.29
865 948 3.703001 ACTTGTCGGAGAAATGGATGT 57.297 42.857 0.00 0.00 39.69 3.06
866 949 6.683974 AAATACTTGTCGGAGAAATGGATG 57.316 37.500 0.00 0.00 39.69 3.51
867 950 6.037172 CGAAAATACTTGTCGGAGAAATGGAT 59.963 38.462 0.00 0.00 39.69 3.41
868 951 5.350365 CGAAAATACTTGTCGGAGAAATGGA 59.650 40.000 0.00 0.00 39.69 3.41
869 952 5.560148 CGAAAATACTTGTCGGAGAAATGG 58.440 41.667 0.00 0.00 39.69 3.16
878 961 2.597305 CTCCGTCCGAAAATACTTGTCG 59.403 50.000 0.00 0.00 34.58 4.35
879 962 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
880 963 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
881 964 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
882 965 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
883 966 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
884 967 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
885 968 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
886 969 1.479730 GTACTCCCTCCGTCCGAAAAT 59.520 52.381 0.00 0.00 0.00 1.82
887 970 0.890683 GTACTCCCTCCGTCCGAAAA 59.109 55.000 0.00 0.00 0.00 2.29
888 971 0.038744 AGTACTCCCTCCGTCCGAAA 59.961 55.000 0.00 0.00 0.00 3.46
889 972 0.038744 AAGTACTCCCTCCGTCCGAA 59.961 55.000 0.00 0.00 0.00 4.30
890 973 0.393537 GAAGTACTCCCTCCGTCCGA 60.394 60.000 0.00 0.00 0.00 4.55
891 974 0.394080 AGAAGTACTCCCTCCGTCCG 60.394 60.000 0.00 0.00 0.00 4.79
892 975 1.849977 AAGAAGTACTCCCTCCGTCC 58.150 55.000 0.00 0.00 0.00 4.79
893 976 2.561858 ACAAAGAAGTACTCCCTCCGTC 59.438 50.000 0.00 0.00 0.00 4.79
894 977 2.606378 ACAAAGAAGTACTCCCTCCGT 58.394 47.619 0.00 0.00 0.00 4.69
895 978 3.586892 GAACAAAGAAGTACTCCCTCCG 58.413 50.000 0.00 0.00 0.00 4.63
896 979 3.583526 AGGAACAAAGAAGTACTCCCTCC 59.416 47.826 0.00 0.00 0.00 4.30
897 980 4.893829 AGGAACAAAGAAGTACTCCCTC 57.106 45.455 0.00 0.00 0.00 4.30
898 981 4.908481 AGAAGGAACAAAGAAGTACTCCCT 59.092 41.667 0.00 0.00 0.00 4.20
899 982 5.230323 AGAAGGAACAAAGAAGTACTCCC 57.770 43.478 0.00 0.00 0.00 4.30
900 983 6.649973 GGTTAGAAGGAACAAAGAAGTACTCC 59.350 42.308 0.00 0.00 0.00 3.85
901 984 6.365518 CGGTTAGAAGGAACAAAGAAGTACTC 59.634 42.308 0.00 0.00 0.00 2.59
902 985 6.183360 ACGGTTAGAAGGAACAAAGAAGTACT 60.183 38.462 0.00 0.00 0.00 2.73
903 986 5.987953 ACGGTTAGAAGGAACAAAGAAGTAC 59.012 40.000 0.00 0.00 0.00 2.73
916 999 3.136009 AGTTTGGGAACGGTTAGAAGG 57.864 47.619 0.00 0.00 40.75 3.46
923 1006 3.236896 TCTCTAGAAGTTTGGGAACGGT 58.763 45.455 0.00 0.00 40.75 4.83
924 1007 3.955650 TCTCTAGAAGTTTGGGAACGG 57.044 47.619 0.00 0.00 40.75 4.44
925 1008 3.619038 GCATCTCTAGAAGTTTGGGAACG 59.381 47.826 0.00 0.00 40.75 3.95
926 1009 4.579869 TGCATCTCTAGAAGTTTGGGAAC 58.420 43.478 0.00 0.00 35.97 3.62
970 1056 7.426929 AACTGTAAAAAGAGCAGATGTACAG 57.573 36.000 0.33 6.42 41.61 2.74
1025 1114 4.498520 CGCCGCTGTCCACGATCT 62.499 66.667 0.00 0.00 0.00 2.75
1026 1115 3.774959 ATCGCCGCTGTCCACGATC 62.775 63.158 0.00 0.00 41.06 3.69
1092 1181 2.822637 CCGGATCATGGGACCCAGG 61.823 68.421 19.53 19.53 36.75 4.45
1240 1329 3.049674 AACCATCACACCGCGCAG 61.050 61.111 8.75 0.00 0.00 5.18
1257 1346 0.972471 TCTTGAGCTCCTCGGCATCA 60.972 55.000 12.15 0.00 32.35 3.07
1350 1439 5.585500 TTTTCTTGACCGAATACAACTCG 57.415 39.130 0.00 0.00 36.06 4.18
1377 1466 2.301296 CAATATCGTCATGGCCTCTCCT 59.699 50.000 3.32 0.00 35.26 3.69
1411 1500 2.684881 CCATGCACAGGGTAATGACTTC 59.315 50.000 0.00 0.00 0.00 3.01
1449 1538 1.936547 GGATGGAACTTAGCTTCTGCG 59.063 52.381 0.00 0.00 45.42 5.18
1530 1619 7.695055 TCTGTCTCCCAATCACCTTTTTAATA 58.305 34.615 0.00 0.00 0.00 0.98
1543 1632 3.724478 TCAGTGGTATCTGTCTCCCAAT 58.276 45.455 0.00 0.00 36.85 3.16
1653 1742 2.853731 AAGAGGCGTGACTTATCGAG 57.146 50.000 0.00 0.00 0.00 4.04
1735 1824 1.065636 CATGTGCTGATCTGGTCCAGT 60.066 52.381 18.65 6.24 32.61 4.00
1842 1931 1.403814 TCTCTCCAATACCGAGGCAG 58.596 55.000 0.00 0.00 0.00 4.85
1843 1932 1.757118 CTTCTCTCCAATACCGAGGCA 59.243 52.381 0.00 0.00 0.00 4.75
2002 2091 3.565482 AGCAATTTCTCTGCAGTTCGAAA 59.435 39.130 21.50 21.50 42.48 3.46
2018 2107 0.036732 TTGGCTCTCGGTCAGCAATT 59.963 50.000 4.00 0.00 38.77 2.32
2083 2172 1.878102 GCGAGAAAACTGGCTCTCCAA 60.878 52.381 0.00 0.00 42.91 3.53
2200 2289 4.747605 GTCCCTGCTTCTCGAAAGAATATC 59.252 45.833 10.34 0.00 40.68 1.63
2218 2307 1.420138 CAGTTGGTGGTACTTGTCCCT 59.580 52.381 0.00 0.00 0.00 4.20
2271 2360 6.092396 GCTCATATGAGTCATTAGCAAGGATG 59.908 42.308 28.92 13.00 43.85 3.51
2425 2514 0.682852 TCAACGAAGGACCGGACAAT 59.317 50.000 9.46 0.00 0.00 2.71
2649 2738 3.215568 CCGCACTGTTGGGCACAA 61.216 61.111 0.00 0.00 33.87 3.33
2658 2747 3.925630 CTTGGGGATGCCGCACTGT 62.926 63.158 0.00 0.00 46.01 3.55
2781 2870 5.357878 GTCCAAGAGCACCATAAAATCATCA 59.642 40.000 0.00 0.00 0.00 3.07
3096 3185 1.616159 ACGTTGTTTCCTTCCCCATG 58.384 50.000 0.00 0.00 0.00 3.66
3141 3230 0.753262 ACAGAAGGTTGACGAGCTGT 59.247 50.000 0.00 0.00 35.94 4.40
3404 3505 8.144478 GGGGGAATAGAAATAAAATTCAGAAGC 58.856 37.037 0.00 0.00 0.00 3.86
3478 3582 7.356540 TGTAACTGATAAACCGTCAAAACATG 58.643 34.615 0.00 0.00 0.00 3.21
3489 3593 6.164176 ACTACTGCACTGTAACTGATAAACC 58.836 40.000 0.00 0.00 0.00 3.27
3514 3618 8.028652 TGGAAAACTGAAAATTATTTGAGGGT 57.971 30.769 0.00 0.00 34.48 4.34
3532 3636 6.754193 TCACAGGATTTTAACCATGGAAAAC 58.246 36.000 21.47 7.41 0.00 2.43
3538 3642 7.448161 TGCCTATATCACAGGATTTTAACCATG 59.552 37.037 0.00 0.00 34.91 3.66
3539 3643 7.448469 GTGCCTATATCACAGGATTTTAACCAT 59.552 37.037 0.00 0.00 34.91 3.55
3544 3648 6.894682 TGTGTGCCTATATCACAGGATTTTA 58.105 36.000 7.87 0.00 44.11 1.52
3636 3740 8.564574 CAAACTATGTCCTCTGAGAGATACTAC 58.435 40.741 11.82 1.95 0.00 2.73
3680 3786 2.857575 TACTCGCACATGGCAGCAGG 62.858 60.000 0.00 0.00 45.17 4.85
3681 3787 0.812811 ATACTCGCACATGGCAGCAG 60.813 55.000 0.00 2.05 45.17 4.24
3682 3788 0.463620 TATACTCGCACATGGCAGCA 59.536 50.000 0.00 0.00 45.17 4.41
3683 3789 1.261619 GTTATACTCGCACATGGCAGC 59.738 52.381 0.00 0.00 45.17 5.25
3684 3790 2.549926 TGTTATACTCGCACATGGCAG 58.450 47.619 0.00 1.62 45.17 4.85
3685 3791 2.682155 TGTTATACTCGCACATGGCA 57.318 45.000 0.00 0.00 45.17 4.92
3686 3792 3.526385 CATGTTATACTCGCACATGGC 57.474 47.619 0.00 0.00 42.74 4.40
3690 3796 9.968870 TGTATATAAACATGTTATACTCGCACA 57.031 29.630 21.89 12.86 32.50 4.57
3717 3823 4.458989 TGGCTCATGAATAAGTCGCTTTTT 59.541 37.500 0.00 0.00 0.00 1.94
3718 3824 4.009675 TGGCTCATGAATAAGTCGCTTTT 58.990 39.130 0.00 0.00 0.00 2.27
3719 3825 3.375299 GTGGCTCATGAATAAGTCGCTTT 59.625 43.478 0.00 0.00 0.00 3.51
3720 3826 2.939103 GTGGCTCATGAATAAGTCGCTT 59.061 45.455 0.00 0.00 0.00 4.68
3721 3827 2.555199 GTGGCTCATGAATAAGTCGCT 58.445 47.619 0.00 0.00 0.00 4.93
3722 3828 1.599542 GGTGGCTCATGAATAAGTCGC 59.400 52.381 0.00 0.00 0.00 5.19
3723 3829 2.213499 GGGTGGCTCATGAATAAGTCG 58.787 52.381 0.00 0.00 0.00 4.18
3724 3830 2.576615 GGGGTGGCTCATGAATAAGTC 58.423 52.381 0.00 0.00 0.00 3.01
3725 3831 1.215423 GGGGGTGGCTCATGAATAAGT 59.785 52.381 0.00 0.00 0.00 2.24
3726 3832 1.496429 AGGGGGTGGCTCATGAATAAG 59.504 52.381 0.00 0.00 0.00 1.73
3727 3833 1.215173 CAGGGGGTGGCTCATGAATAA 59.785 52.381 0.00 0.00 0.00 1.40
3728 3834 0.846015 CAGGGGGTGGCTCATGAATA 59.154 55.000 0.00 0.00 0.00 1.75
3729 3835 1.217057 ACAGGGGGTGGCTCATGAAT 61.217 55.000 0.00 0.00 0.00 2.57
3730 3836 1.434513 AACAGGGGGTGGCTCATGAA 61.435 55.000 0.00 0.00 0.00 2.57
3731 3837 1.852157 AACAGGGGGTGGCTCATGA 60.852 57.895 0.00 0.00 0.00 3.07
3732 3838 1.379044 GAACAGGGGGTGGCTCATG 60.379 63.158 0.00 0.00 0.00 3.07
3733 3839 2.616458 GGAACAGGGGGTGGCTCAT 61.616 63.158 0.00 0.00 0.00 2.90
3734 3840 3.256960 GGAACAGGGGGTGGCTCA 61.257 66.667 0.00 0.00 0.00 4.26
3735 3841 3.256960 TGGAACAGGGGGTGGCTC 61.257 66.667 0.00 0.00 0.00 4.70
3736 3842 3.580319 GTGGAACAGGGGGTGGCT 61.580 66.667 0.00 0.00 41.80 4.75
3737 3843 3.897122 TGTGGAACAGGGGGTGGC 61.897 66.667 0.00 0.00 45.67 5.01
3765 3871 8.491605 TCGGTTTTAACAAACGAAACAATATC 57.508 30.769 7.69 0.00 43.01 1.63
3775 3881 7.897920 TGCTATACTATCGGTTTTAACAAACG 58.102 34.615 2.63 2.63 43.01 3.60
3810 3916 2.185004 ACCGTATCCCAGCAATATGC 57.815 50.000 0.00 0.00 45.46 3.14
3811 3917 4.245660 CACTACCGTATCCCAGCAATATG 58.754 47.826 0.00 0.00 0.00 1.78
3812 3918 3.260884 CCACTACCGTATCCCAGCAATAT 59.739 47.826 0.00 0.00 0.00 1.28
3813 3919 2.631062 CCACTACCGTATCCCAGCAATA 59.369 50.000 0.00 0.00 0.00 1.90
3814 3920 1.416401 CCACTACCGTATCCCAGCAAT 59.584 52.381 0.00 0.00 0.00 3.56
3815 3921 0.828022 CCACTACCGTATCCCAGCAA 59.172 55.000 0.00 0.00 0.00 3.91
3816 3922 0.324923 ACCACTACCGTATCCCAGCA 60.325 55.000 0.00 0.00 0.00 4.41
3817 3923 0.828677 AACCACTACCGTATCCCAGC 59.171 55.000 0.00 0.00 0.00 4.85
3818 3924 2.104967 TGAACCACTACCGTATCCCAG 58.895 52.381 0.00 0.00 0.00 4.45
3819 3925 2.234414 GTTGAACCACTACCGTATCCCA 59.766 50.000 0.00 0.00 0.00 4.37
3820 3926 2.419159 GGTTGAACCACTACCGTATCCC 60.419 54.545 9.98 0.00 38.42 3.85
3821 3927 2.498885 AGGTTGAACCACTACCGTATCC 59.501 50.000 17.83 0.00 46.16 2.59
3822 3928 3.518590 CAGGTTGAACCACTACCGTATC 58.481 50.000 17.83 0.00 46.16 2.24
3933 4043 7.648039 ATGGTATAAGCACGGGAATTTTTAA 57.352 32.000 0.00 0.00 0.00 1.52
3944 4054 1.864711 CCCACGAATGGTATAAGCACG 59.135 52.381 0.00 0.00 45.66 5.34
3977 4087 3.251479 TGTTCCATGTCTTCATCTCCG 57.749 47.619 0.00 0.00 31.15 4.63
4117 4227 2.706339 ACAGGCATGAGATTCAGTCC 57.294 50.000 4.84 0.00 0.00 3.85
4133 4243 4.038361 CAGAGCTGTACATTACGCTACAG 58.962 47.826 7.27 4.60 41.91 2.74
4145 4255 2.416162 GCCTAGACACACAGAGCTGTAC 60.416 54.545 2.36 0.00 42.83 2.90
4181 4291 5.573669 GGAATCGTACTTTCAGAACTGACTC 59.426 44.000 3.88 0.00 39.66 3.36
4187 4297 5.851703 GCAAAAGGAATCGTACTTTCAGAAC 59.148 40.000 7.47 0.00 35.99 3.01
4214 4324 3.987547 TCCGATCTACAGTAGTACTCCG 58.012 50.000 0.00 5.49 0.00 4.63
4215 4325 5.008514 GGTTTCCGATCTACAGTAGTACTCC 59.991 48.000 0.00 0.00 0.00 3.85
4216 4326 5.587844 TGGTTTCCGATCTACAGTAGTACTC 59.412 44.000 0.00 3.20 0.00 2.59
4217 4327 5.503927 TGGTTTCCGATCTACAGTAGTACT 58.496 41.667 7.50 0.00 0.00 2.73
4218 4328 5.587844 TCTGGTTTCCGATCTACAGTAGTAC 59.412 44.000 7.50 0.00 0.00 2.73
4221 4331 5.578005 TTCTGGTTTCCGATCTACAGTAG 57.422 43.478 0.47 0.47 0.00 2.57
4291 4471 3.420893 TGCCGTGGAATTCTTTCTGAAT 58.579 40.909 5.23 0.00 46.49 2.57
4325 4505 3.181506 GCCTAACTGAGAAAATGGAAGCG 60.182 47.826 0.00 0.00 0.00 4.68


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

AutoCloner maintained by Alex Coulton.