Multiple sequence alignment - TraesCS6A01G147000

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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 TraesCS6A01G147000 chr6A 100.000 6021 0 0 1 6021 126910893 126916913 0.000000e+00 11119.0
1 TraesCS6A01G147000 chr6D 95.583 2694 96 6 2581 5272 104766403 104769075 0.000000e+00 4294.0
2 TraesCS6A01G147000 chr6D 96.788 716 19 4 1515 2228 104764892 104765605 0.000000e+00 1192.0
3 TraesCS6A01G147000 chr6D 96.983 696 21 0 5326 6021 104783114 104783809 0.000000e+00 1170.0
4 TraesCS6A01G147000 chr6D 98.056 360 7 0 2223 2582 104765988 104766347 1.420000e-175 627.0
5 TraesCS6A01G147000 chr6B 94.036 2733 123 21 3315 6021 191198132 191200850 0.000000e+00 4108.0
6 TraesCS6A01G147000 chr6B 96.218 1190 29 5 2128 3317 191196836 191198009 0.000000e+00 1934.0
7 TraesCS6A01G147000 chr6B 94.788 825 29 4 926 1745 191195968 191196783 0.000000e+00 1273.0
8 TraesCS6A01G147000 chr6B 100.000 54 0 0 2205 2258 191196786 191196839 3.840000e-17 100.0
9 TraesCS6A01G147000 chr4B 79.904 831 147 15 1 824 327051154 327051971 5.200000e-165 592.0
10 TraesCS6A01G147000 chr7B 100.000 32 0 0 3668 3699 145695599 145695568 6.520000e-05 60.2
11 TraesCS6A01G147000 chr5B 100.000 28 0 0 3668 3695 56692873 56692846 1.100000e-02 52.8
12 TraesCS6A01G147000 chr2B 100.000 28 0 0 831 858 11010895 11010922 1.100000e-02 52.8


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 TraesCS6A01G147000 chr6A 126910893 126916913 6020 False 11119.000000 11119 100.0000 1 6021 1 chr6A.!!$F1 6020
1 TraesCS6A01G147000 chr6D 104764892 104769075 4183 False 2037.666667 4294 96.8090 1515 5272 3 chr6D.!!$F2 3757
2 TraesCS6A01G147000 chr6D 104783114 104783809 695 False 1170.000000 1170 96.9830 5326 6021 1 chr6D.!!$F1 695
3 TraesCS6A01G147000 chr6B 191195968 191200850 4882 False 1853.750000 4108 96.2605 926 6021 4 chr6B.!!$F1 5095
4 TraesCS6A01G147000 chr4B 327051154 327051971 817 False 592.000000 592 79.9040 1 824 1 chr4B.!!$F1 823

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
166 167 0.034896 GACAACGGAGGAAGAGGCAA 59.965 55.000 0.00 0.00 0.00 4.52 F
639 643 0.250124 ACGCAACGGAACATCCAGAA 60.250 50.000 0.00 0.00 35.91 3.02 F
869 874 0.318699 TCTCGCTGTGTTGAACCTCG 60.319 55.000 0.00 0.00 0.00 4.63 F
911 916 0.534203 TCAACAGACCGGAAGTTGCC 60.534 55.000 23.70 1.70 41.67 4.52 F
1029 1039 0.685785 ATCTTCTCTCCTCCAGCGCA 60.686 55.000 11.47 0.00 0.00 6.09 F
1639 1649 0.997932 GCTCAGAGTTGATGCTGTCG 59.002 55.000 0.00 0.00 33.90 4.35 F
2068 2078 1.137697 ATCATCTGATGCAGAGGCCA 58.862 50.000 12.78 0.00 44.08 5.36 F
2090 2100 2.027100 GGGCTATATCCTCCTTTTCGGG 60.027 54.545 0.00 0.00 0.00 5.14 F
2588 3044 2.694628 TGCAAATTGATGGATGCCTACC 59.305 45.455 0.00 0.00 38.00 3.18 F
4381 4963 0.391661 TGGAGATTTGCAGGTCGAGC 60.392 55.000 6.48 6.48 0.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1613 1623 0.107800 ATCAACTCTGAGCAGCGCAT 60.108 50.000 11.47 0.00 34.23 4.73 R
1639 1649 1.084370 CAGCAACAGCGGTAGTAGGC 61.084 60.000 0.00 0.00 0.00 3.93 R
2709 3165 1.609208 ATCGGCCATGGCAAATAGTC 58.391 50.000 36.56 17.19 44.11 2.59 R
2909 3365 4.503296 GGATAGTGCAGGTGTAAGGTATGG 60.503 50.000 0.00 0.00 0.00 2.74 R
2986 3442 5.221661 GGTTATACCCAGGGATAAGACACTG 60.222 48.000 14.54 0.00 40.57 3.66 R
3021 3477 5.507985 GCTTAACCAGTTTGCTTCAACAGAT 60.508 40.000 0.00 0.00 0.00 2.90 R
3775 4357 2.299582 CCAAAACAGACATGCCAATGGA 59.700 45.455 2.05 0.00 38.19 3.41 R
4095 4677 1.888512 TCTGGATTGAACCTTTGCTGC 59.111 47.619 0.00 0.00 0.00 5.25 R
4426 5008 0.171903 GGACACCATCAGCATTGCAC 59.828 55.000 11.91 0.00 0.00 4.57 R
5428 6043 0.530744 CCGACGAAGGAGATTGGTGA 59.469 55.000 0.00 0.00 28.85 4.02 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
23 24 1.227205 GTGCCTCTCCAGCTCATCG 60.227 63.158 0.00 0.00 0.00 3.84
34 35 3.741435 GCTCATCGAGCGACTGCGA 62.741 63.158 0.00 0.00 45.85 5.10
50 51 4.824166 GAGCGCCGCACAATGCAG 62.824 66.667 13.36 0.00 45.36 4.41
58 59 3.044059 GCACAATGCAGACCTCCGC 62.044 63.158 0.00 0.00 44.26 5.54
59 60 2.045926 ACAATGCAGACCTCCGCC 60.046 61.111 0.00 0.00 0.00 6.13
64 65 4.162690 GCAGACCTCCGCCGGATT 62.163 66.667 6.16 0.00 0.00 3.01
68 69 1.521681 GACCTCCGCCGGATTGAAG 60.522 63.158 6.16 0.00 0.00 3.02
70 71 2.584608 CTCCGCCGGATTGAAGGT 59.415 61.111 6.16 0.00 0.00 3.50
74 75 2.452813 CGCCGGATTGAAGGTCGTG 61.453 63.158 5.05 0.00 0.00 4.35
107 108 2.362632 AGCCTAGTCGCCGGAAGT 60.363 61.111 5.05 0.00 0.00 3.01
110 111 1.888018 CCTAGTCGCCGGAAGTGAA 59.112 57.895 5.05 0.00 36.56 3.18
116 117 2.747855 GCCGGAAGTGAAGGCCAG 60.748 66.667 5.05 0.00 44.80 4.85
158 159 3.998672 GGCGGTGACAACGGAGGA 61.999 66.667 15.86 0.00 0.00 3.71
161 162 1.663739 CGGTGACAACGGAGGAAGA 59.336 57.895 4.57 0.00 0.00 2.87
162 163 0.388649 CGGTGACAACGGAGGAAGAG 60.389 60.000 4.57 0.00 0.00 2.85
164 165 0.670854 GTGACAACGGAGGAAGAGGC 60.671 60.000 0.00 0.00 0.00 4.70
165 166 1.118965 TGACAACGGAGGAAGAGGCA 61.119 55.000 0.00 0.00 0.00 4.75
166 167 0.034896 GACAACGGAGGAAGAGGCAA 59.965 55.000 0.00 0.00 0.00 4.52
167 168 0.472471 ACAACGGAGGAAGAGGCAAA 59.528 50.000 0.00 0.00 0.00 3.68
173 177 2.360475 GGAAGAGGCAAAGGCGCT 60.360 61.111 7.64 0.00 42.47 5.92
177 181 2.811542 AAGAGGCAAAGGCGCTCCTC 62.812 60.000 7.64 14.96 43.40 3.71
183 187 2.289532 AAAGGCGCTCCTCTGCTCT 61.290 57.895 7.64 0.00 43.40 4.09
184 188 1.835927 AAAGGCGCTCCTCTGCTCTT 61.836 55.000 7.64 0.00 43.40 2.85
191 195 1.566211 CTCCTCTGCTCTTCCCAGAA 58.434 55.000 0.00 0.00 38.73 3.02
194 198 1.627834 CCTCTGCTCTTCCCAGAACTT 59.372 52.381 0.00 0.00 38.73 2.66
204 208 2.037136 CCAGAACTTGCTCTGCCCG 61.037 63.158 0.00 0.00 41.36 6.13
230 234 4.148825 GCCGAGCCACTCACCGAT 62.149 66.667 0.00 0.00 0.00 4.18
233 237 1.663379 CCGAGCCACTCACCGATACA 61.663 60.000 0.00 0.00 0.00 2.29
234 238 0.525668 CGAGCCACTCACCGATACAC 60.526 60.000 0.00 0.00 0.00 2.90
236 240 1.153429 GCCACTCACCGATACACCC 60.153 63.158 0.00 0.00 0.00 4.61
269 273 1.136774 CGAGATCTTGGCGACGACA 59.863 57.895 0.00 0.00 0.00 4.35
287 291 2.276743 CGACGACGAAGCTCCTCG 60.277 66.667 0.00 6.27 44.50 4.63
314 318 2.887360 GGGTTACGAGGCTGCGTA 59.113 61.111 12.86 12.86 43.61 4.42
317 321 0.388907 GGTTACGAGGCTGCGTACAA 60.389 55.000 15.41 5.17 45.32 2.41
320 324 2.531927 TACGAGGCTGCGTACAACCG 62.532 60.000 12.86 0.00 43.61 4.44
335 339 4.864334 CCGCCAGACCCATGCCTC 62.864 72.222 0.00 0.00 0.00 4.70
340 344 1.153489 CAGACCCATGCCTCGACAG 60.153 63.158 0.00 0.00 0.00 3.51
357 361 3.573491 GCCCGCACCGAATACAGC 61.573 66.667 0.00 0.00 0.00 4.40
374 378 2.751436 CCGATGGGGTTGGTGCAG 60.751 66.667 0.00 0.00 0.00 4.41
380 384 2.034221 GGGTTGGTGCAGTCCCTC 59.966 66.667 7.82 0.00 37.18 4.30
382 386 2.358737 GTTGGTGCAGTCCCTCCG 60.359 66.667 0.00 0.00 0.00 4.63
383 387 2.525629 TTGGTGCAGTCCCTCCGA 60.526 61.111 0.00 0.00 0.00 4.55
389 393 1.376037 GCAGTCCCTCCGAAAGTGG 60.376 63.158 0.00 0.00 0.00 4.00
395 399 0.905357 CCCTCCGAAAGTGGTCATCT 59.095 55.000 0.00 0.00 0.00 2.90
401 405 4.456535 TCCGAAAGTGGTCATCTTTGAAA 58.543 39.130 0.00 0.00 35.62 2.69
480 484 4.660938 GGCGGCTTGGTGGGTTCT 62.661 66.667 0.00 0.00 0.00 3.01
484 488 1.303643 GGCTTGGTGGGTTCTGAGG 60.304 63.158 0.00 0.00 0.00 3.86
495 499 3.719121 TCTGAGGCCCAGAGAAGC 58.281 61.111 17.12 0.00 46.38 3.86
519 523 2.418910 CGCCTCCACCGAGATCTGT 61.419 63.158 0.00 0.00 38.52 3.41
521 525 1.730487 CCTCCACCGAGATCTGTCG 59.270 63.158 0.00 0.00 38.52 4.35
531 535 1.753463 GATCTGTCGGGAGGGACGT 60.753 63.158 0.00 0.00 39.83 4.34
639 643 0.250124 ACGCAACGGAACATCCAGAA 60.250 50.000 0.00 0.00 35.91 3.02
645 649 1.275291 ACGGAACATCCAGAACACGAT 59.725 47.619 0.00 0.00 35.91 3.73
648 652 2.673368 GGAACATCCAGAACACGATGAC 59.327 50.000 4.17 0.00 38.53 3.06
653 657 3.469008 TCCAGAACACGATGACAAACT 57.531 42.857 0.00 0.00 0.00 2.66
657 661 4.152402 CCAGAACACGATGACAAACTAAGG 59.848 45.833 0.00 0.00 0.00 2.69
660 664 2.224426 ACACGATGACAAACTAAGGCCA 60.224 45.455 5.01 0.00 0.00 5.36
663 667 2.932614 CGATGACAAACTAAGGCCAGAG 59.067 50.000 5.01 3.48 0.00 3.35
666 670 2.703536 TGACAAACTAAGGCCAGAGACA 59.296 45.455 5.01 0.00 0.00 3.41
668 672 3.477530 ACAAACTAAGGCCAGAGACAAC 58.522 45.455 5.01 0.00 0.00 3.32
669 673 3.136626 ACAAACTAAGGCCAGAGACAACT 59.863 43.478 5.01 0.00 0.00 3.16
732 736 3.479203 TGGTCAGCCATAGCCGGG 61.479 66.667 2.18 0.00 40.46 5.73
733 737 4.256180 GGTCAGCCATAGCCGGGG 62.256 72.222 2.18 0.00 41.25 5.73
736 740 3.946201 CAGCCATAGCCGGGGAGG 61.946 72.222 2.18 0.00 41.25 4.30
740 744 2.201490 CATAGCCGGGGAGGAGGA 59.799 66.667 2.18 0.00 45.00 3.71
742 746 2.091924 ATAGCCGGGGAGGAGGAGA 61.092 63.158 2.18 0.00 45.00 3.71
752 756 3.003763 GGAGGAGAAGGTGGCCGT 61.004 66.667 0.00 0.00 0.00 5.68
756 760 2.432628 GAGAAGGTGGCCGTCACG 60.433 66.667 0.00 0.00 46.96 4.35
776 781 4.379143 CGAGTGACACGCGACGGA 62.379 66.667 24.93 0.00 44.09 4.69
779 784 3.179265 GTGACACGCGACGGATGG 61.179 66.667 15.93 0.00 0.00 3.51
790 795 4.175337 CGGATGGGCGGTGGACAT 62.175 66.667 0.00 0.00 0.00 3.06
798 803 4.386951 CGGTGGACATCGGTGCCA 62.387 66.667 7.62 7.62 33.90 4.92
826 831 4.796495 CGGCGAAAAGGGGAGGGG 62.796 72.222 0.00 0.00 0.00 4.79
827 832 3.335729 GGCGAAAAGGGGAGGGGA 61.336 66.667 0.00 0.00 0.00 4.81
828 833 2.761160 GCGAAAAGGGGAGGGGAA 59.239 61.111 0.00 0.00 0.00 3.97
829 834 1.378646 GCGAAAAGGGGAGGGGAAG 60.379 63.158 0.00 0.00 0.00 3.46
830 835 1.303282 CGAAAAGGGGAGGGGAAGG 59.697 63.158 0.00 0.00 0.00 3.46
831 836 1.000486 GAAAAGGGGAGGGGAAGGC 60.000 63.158 0.00 0.00 0.00 4.35
832 837 1.468202 AAAAGGGGAGGGGAAGGCT 60.468 57.895 0.00 0.00 0.00 4.58
833 838 1.510431 AAAAGGGGAGGGGAAGGCTC 61.510 60.000 0.00 0.00 0.00 4.70
834 839 2.438666 AAAGGGGAGGGGAAGGCTCT 62.439 60.000 0.00 0.00 0.00 4.09
835 840 2.286502 GGGGAGGGGAAGGCTCTT 60.287 66.667 0.00 0.00 0.00 2.85
836 841 2.684499 GGGGAGGGGAAGGCTCTTG 61.684 68.421 0.00 0.00 0.00 3.02
837 842 2.273776 GGAGGGGAAGGCTCTTGC 59.726 66.667 0.00 0.00 38.76 4.01
838 843 2.304831 GGAGGGGAAGGCTCTTGCT 61.305 63.158 6.45 0.00 39.59 3.91
839 844 1.223211 GAGGGGAAGGCTCTTGCTC 59.777 63.158 6.45 3.02 39.59 4.26
840 845 1.229788 AGGGGAAGGCTCTTGCTCT 60.230 57.895 3.52 3.52 39.59 4.09
841 846 1.223211 GGGGAAGGCTCTTGCTCTC 59.777 63.158 6.45 0.00 39.59 3.20
842 847 1.153469 GGGAAGGCTCTTGCTCTCG 60.153 63.158 6.45 0.00 39.59 4.04
843 848 1.813337 GGAAGGCTCTTGCTCTCGC 60.813 63.158 0.00 0.00 39.59 5.03
844 849 1.217779 GAAGGCTCTTGCTCTCGCT 59.782 57.895 0.00 0.00 39.59 4.93
845 850 0.805711 GAAGGCTCTTGCTCTCGCTC 60.806 60.000 0.00 0.00 39.59 5.03
846 851 1.257055 AAGGCTCTTGCTCTCGCTCT 61.257 55.000 0.00 0.00 39.59 4.09
847 852 1.226945 GGCTCTTGCTCTCGCTCTC 60.227 63.158 0.00 0.00 39.59 3.20
848 853 1.586042 GCTCTTGCTCTCGCTCTCG 60.586 63.158 0.00 0.00 36.97 4.04
849 854 1.586042 CTCTTGCTCTCGCTCTCGC 60.586 63.158 0.00 0.00 36.97 5.03
850 855 1.992233 CTCTTGCTCTCGCTCTCGCT 61.992 60.000 0.00 0.00 36.97 4.93
851 856 1.586042 CTTGCTCTCGCTCTCGCTC 60.586 63.158 0.00 0.00 36.97 5.03
852 857 1.992233 CTTGCTCTCGCTCTCGCTCT 61.992 60.000 0.00 0.00 36.97 4.09
853 858 1.987704 TTGCTCTCGCTCTCGCTCTC 61.988 60.000 0.00 0.00 36.97 3.20
854 859 2.625906 CTCTCGCTCTCGCTCTCG 59.374 66.667 0.00 0.00 35.26 4.04
855 860 3.506312 CTCTCGCTCTCGCTCTCGC 62.506 68.421 0.00 0.00 35.26 5.03
856 861 3.572539 CTCGCTCTCGCTCTCGCT 61.573 66.667 0.00 0.00 35.26 4.93
857 862 3.788586 CTCGCTCTCGCTCTCGCTG 62.789 68.421 0.00 0.00 35.26 5.18
858 863 4.172772 CGCTCTCGCTCTCGCTGT 62.173 66.667 0.00 0.00 35.26 4.40
859 864 2.579249 GCTCTCGCTCTCGCTGTG 60.579 66.667 0.00 0.00 35.26 3.66
860 865 2.874019 CTCTCGCTCTCGCTGTGT 59.126 61.111 0.00 0.00 35.26 3.72
861 866 1.211449 CTCTCGCTCTCGCTGTGTT 59.789 57.895 0.00 0.00 35.26 3.32
862 867 1.069924 CTCTCGCTCTCGCTGTGTTG 61.070 60.000 0.00 0.00 35.26 3.33
863 868 1.081175 CTCGCTCTCGCTGTGTTGA 60.081 57.895 0.00 0.00 35.26 3.18
864 869 0.664466 CTCGCTCTCGCTGTGTTGAA 60.664 55.000 0.00 0.00 35.26 2.69
865 870 0.939577 TCGCTCTCGCTGTGTTGAAC 60.940 55.000 0.00 0.00 35.26 3.18
866 871 1.862806 GCTCTCGCTGTGTTGAACC 59.137 57.895 0.00 0.00 0.00 3.62
867 872 0.601311 GCTCTCGCTGTGTTGAACCT 60.601 55.000 0.00 0.00 0.00 3.50
868 873 1.423395 CTCTCGCTGTGTTGAACCTC 58.577 55.000 0.00 0.00 0.00 3.85
869 874 0.318699 TCTCGCTGTGTTGAACCTCG 60.319 55.000 0.00 0.00 0.00 4.63
870 875 1.891060 CTCGCTGTGTTGAACCTCGC 61.891 60.000 0.00 0.00 0.00 5.03
871 876 2.946762 GCTGTGTTGAACCTCGCC 59.053 61.111 0.00 0.00 0.00 5.54
872 877 2.617274 GCTGTGTTGAACCTCGCCC 61.617 63.158 0.00 0.00 0.00 6.13
873 878 1.966451 CTGTGTTGAACCTCGCCCC 60.966 63.158 0.00 0.00 0.00 5.80
874 879 3.047877 GTGTTGAACCTCGCCCCG 61.048 66.667 0.00 0.00 0.00 5.73
887 892 4.636435 CCCCGCGGTTGTCAAGGT 62.636 66.667 26.12 0.00 0.00 3.50
888 893 2.593436 CCCGCGGTTGTCAAGGTT 60.593 61.111 26.12 0.00 0.00 3.50
889 894 2.613506 CCCGCGGTTGTCAAGGTTC 61.614 63.158 26.12 0.00 0.00 3.62
890 895 1.890041 CCGCGGTTGTCAAGGTTCA 60.890 57.895 19.50 0.00 0.00 3.18
891 896 1.234615 CCGCGGTTGTCAAGGTTCAT 61.235 55.000 19.50 0.00 0.00 2.57
892 897 0.591170 CGCGGTTGTCAAGGTTCATT 59.409 50.000 0.00 0.00 0.00 2.57
893 898 1.399727 CGCGGTTGTCAAGGTTCATTC 60.400 52.381 0.00 0.00 0.00 2.67
894 899 1.606668 GCGGTTGTCAAGGTTCATTCA 59.393 47.619 0.00 0.00 0.00 2.57
895 900 2.034053 GCGGTTGTCAAGGTTCATTCAA 59.966 45.455 0.00 0.00 0.00 2.69
896 901 3.628017 CGGTTGTCAAGGTTCATTCAAC 58.372 45.455 0.00 0.00 35.79 3.18
897 902 3.066064 CGGTTGTCAAGGTTCATTCAACA 59.934 43.478 0.00 0.00 37.48 3.33
898 903 4.610945 GGTTGTCAAGGTTCATTCAACAG 58.389 43.478 0.00 0.00 37.48 3.16
899 904 4.338118 GGTTGTCAAGGTTCATTCAACAGA 59.662 41.667 0.00 0.00 37.48 3.41
900 905 5.273944 GTTGTCAAGGTTCATTCAACAGAC 58.726 41.667 0.00 0.00 36.61 3.51
901 906 3.882888 TGTCAAGGTTCATTCAACAGACC 59.117 43.478 0.00 0.00 36.61 3.85
902 907 3.058914 GTCAAGGTTCATTCAACAGACCG 60.059 47.826 0.00 0.00 36.61 4.79
903 908 2.185004 AGGTTCATTCAACAGACCGG 57.815 50.000 0.00 0.00 36.61 5.28
904 909 1.697432 AGGTTCATTCAACAGACCGGA 59.303 47.619 9.46 0.00 36.61 5.14
905 910 2.105821 AGGTTCATTCAACAGACCGGAA 59.894 45.455 9.46 0.00 36.61 4.30
906 911 2.484264 GGTTCATTCAACAGACCGGAAG 59.516 50.000 9.46 0.00 36.61 3.46
907 912 3.139077 GTTCATTCAACAGACCGGAAGT 58.861 45.455 9.46 0.00 34.76 3.01
908 913 3.485463 TCATTCAACAGACCGGAAGTT 57.515 42.857 9.46 6.80 0.00 2.66
909 914 3.138304 TCATTCAACAGACCGGAAGTTG 58.862 45.455 23.01 23.01 42.90 3.16
910 915 1.305201 TTCAACAGACCGGAAGTTGC 58.695 50.000 23.70 3.29 41.67 4.17
911 916 0.534203 TCAACAGACCGGAAGTTGCC 60.534 55.000 23.70 1.70 41.67 4.52
912 917 1.228154 AACAGACCGGAAGTTGCCC 60.228 57.895 9.46 0.00 0.00 5.36
913 918 1.705997 AACAGACCGGAAGTTGCCCT 61.706 55.000 9.46 0.00 0.00 5.19
914 919 1.376037 CAGACCGGAAGTTGCCCTC 60.376 63.158 9.46 0.00 0.00 4.30
915 920 2.046217 GACCGGAAGTTGCCCTCC 60.046 66.667 9.46 0.00 0.00 4.30
916 921 3.952628 GACCGGAAGTTGCCCTCCG 62.953 68.421 9.46 3.53 44.50 4.63
928 933 4.888325 CCTCCGCCCCATCCTCCT 62.888 72.222 0.00 0.00 0.00 3.69
952 960 2.975732 TGTGCAAATCAAAGCCAACA 57.024 40.000 0.00 0.00 0.00 3.33
957 965 3.384146 TGCAAATCAAAGCCAACAAGAGA 59.616 39.130 0.00 0.00 0.00 3.10
971 979 4.142609 ACAAGAGACTGTTTGCTTCTCA 57.857 40.909 0.00 0.00 38.63 3.27
1029 1039 0.685785 ATCTTCTCTCCTCCAGCGCA 60.686 55.000 11.47 0.00 0.00 6.09
1094 1104 1.188871 CCCGCCCTCTTCTATCTCCC 61.189 65.000 0.00 0.00 0.00 4.30
1192 1202 3.792047 CCGCATGTGCTCACGGTG 61.792 66.667 0.56 0.56 40.77 4.94
1345 1355 2.636830 CTGCCCGATTTCTTCACTCAT 58.363 47.619 0.00 0.00 0.00 2.90
1597 1607 5.212532 AGTGCTAGCTATTGGAAGATCTG 57.787 43.478 17.23 0.00 0.00 2.90
1613 1623 6.874134 GGAAGATCTGTTTAGTGCTCTGTTTA 59.126 38.462 0.00 0.00 0.00 2.01
1639 1649 0.997932 GCTCAGAGTTGATGCTGTCG 59.002 55.000 0.00 0.00 33.90 4.35
1868 1878 4.884458 TCATGCAAGTTTTGTTGTACGA 57.116 36.364 0.00 0.00 0.00 3.43
1932 1942 2.438975 ATGCTGCCCCGATGTGTG 60.439 61.111 0.00 0.00 0.00 3.82
1952 1962 1.704641 TCCTATGTGGATGACCTCGG 58.295 55.000 0.00 0.00 40.56 4.63
1953 1963 1.216930 TCCTATGTGGATGACCTCGGA 59.783 52.381 0.00 0.00 40.56 4.55
2068 2078 1.137697 ATCATCTGATGCAGAGGCCA 58.862 50.000 12.78 0.00 44.08 5.36
2089 2099 2.907042 AGGGCTATATCCTCCTTTTCGG 59.093 50.000 0.00 0.00 0.00 4.30
2090 2100 2.027100 GGGCTATATCCTCCTTTTCGGG 60.027 54.545 0.00 0.00 0.00 5.14
2091 2101 2.027100 GGCTATATCCTCCTTTTCGGGG 60.027 54.545 0.00 0.00 0.00 5.73
2588 3044 2.694628 TGCAAATTGATGGATGCCTACC 59.305 45.455 0.00 0.00 38.00 3.18
2891 3347 6.836577 TTTATTTCTTTGTTTTGAAGCGGG 57.163 33.333 0.00 0.00 0.00 6.13
2909 3365 3.933332 GCGGGTCATACCTTATCTATTGC 59.067 47.826 0.00 0.00 38.64 3.56
2948 3404 6.149129 CACTATCCTGTGCTTGTACTGATA 57.851 41.667 0.00 1.31 0.00 2.15
2950 3406 6.644181 CACTATCCTGTGCTTGTACTGATATG 59.356 42.308 0.00 0.00 0.00 1.78
2986 3442 8.456471 GTTAACTTACATGGGTAAAAGTCATCC 58.544 37.037 0.00 0.00 38.92 3.51
3007 3463 4.171243 TCCAGTGTCTTATCCCTGGGTATA 59.829 45.833 13.56 6.70 43.77 1.47
3021 3477 8.072409 TCCCTGGGTATAACCTTCTAAGTATA 57.928 38.462 13.56 0.00 38.64 1.47
3673 4255 8.682710 TCTGTTCCATATTAATTGGCACTAAAC 58.317 33.333 15.02 11.93 32.43 2.01
3677 4259 7.122715 TCCATATTAATTGGCACTAAACCAGT 58.877 34.615 10.23 0.00 38.73 4.00
3775 4357 7.896811 TCATCTGTAGACTGTTAAGTGTTGAT 58.103 34.615 0.00 0.00 36.52 2.57
4095 4677 5.639506 GTGTCCTCCATACAATATTGGATCG 59.360 44.000 19.37 9.53 41.09 3.69
4167 4749 0.608130 GGATGAACAAAAGGTGGGGC 59.392 55.000 0.00 0.00 0.00 5.80
4334 4916 5.409826 AGAGAAAAGGACATTGAATCACGAC 59.590 40.000 0.00 0.00 0.00 4.34
4366 4948 1.945354 CTGCCAAGGCTTGCATGGAG 61.945 60.000 21.77 14.37 42.51 3.86
4381 4963 0.391661 TGGAGATTTGCAGGTCGAGC 60.392 55.000 6.48 6.48 0.00 5.03
4423 5005 1.479323 GACCGTGTAGACATTGCCCTA 59.521 52.381 0.00 0.00 0.00 3.53
4426 5008 1.571919 GTGTAGACATTGCCCTAGCG 58.428 55.000 0.00 0.00 44.31 4.26
4453 5035 1.887956 GCTGATGGTGTCCATGTTGGT 60.888 52.381 5.98 0.00 45.26 3.67
4492 5074 3.715015 GAGGTTCGGGAGCTCCTT 58.285 61.111 31.36 10.89 45.14 3.36
4519 5101 3.677700 CGGGTAAAATCATCGGTGTCTCA 60.678 47.826 0.00 0.00 0.00 3.27
4534 5116 1.001764 CTCATGCAAGACCCCTGCA 60.002 57.895 0.00 0.00 43.04 4.41
4669 5251 0.601046 GCTTGGCTTCAAAGTTGCCC 60.601 55.000 0.00 0.00 45.56 5.36
4675 5257 0.310854 CTTCAAAGTTGCCCGTGGTC 59.689 55.000 0.00 0.00 0.00 4.02
4725 5307 1.697432 AGGTTCGGTGATGGAACTTGA 59.303 47.619 4.86 0.00 42.58 3.02
4727 5309 2.550208 GGTTCGGTGATGGAACTTGACT 60.550 50.000 4.86 0.00 42.58 3.41
4774 5356 1.059835 GTCTCTGCTTTGTTCGATCGC 59.940 52.381 11.09 0.00 0.00 4.58
4817 5399 4.450053 GAGAAACCTCAGATCCATCTTGG 58.550 47.826 0.00 4.58 39.43 3.61
4845 5427 1.017387 CGTTGCTTGGCTTAGATCCC 58.983 55.000 0.00 0.00 0.00 3.85
4873 5455 6.319911 AGCTAGCTTTCACTTCTCTTGTTTTT 59.680 34.615 12.68 0.00 0.00 1.94
4937 5519 8.782339 AATCCATCTGAAAAATTGGAAATCAC 57.218 30.769 1.38 0.00 41.36 3.06
4968 5551 0.455464 GCGGTGGTACGAAATTTGCC 60.455 55.000 0.00 0.00 35.47 4.52
4983 5566 2.799126 TTGCCTCCACGGTTTGATAT 57.201 45.000 0.00 0.00 34.25 1.63
5115 5698 5.486775 TCTCCATGACATCTTCCTCTCTTTT 59.513 40.000 0.00 0.00 0.00 2.27
5116 5699 6.013032 TCTCCATGACATCTTCCTCTCTTTTT 60.013 38.462 0.00 0.00 0.00 1.94
5167 5750 7.831691 TTTGACCAACATCTCTAAATTTCCA 57.168 32.000 0.00 0.00 0.00 3.53
5170 5753 5.640147 ACCAACATCTCTAAATTTCCACCA 58.360 37.500 0.00 0.00 0.00 4.17
5175 5758 9.740239 CAACATCTCTAAATTTCCACCAATATG 57.260 33.333 0.00 0.00 0.00 1.78
5190 5773 5.754890 CACCAATATGAACGATCTGATGACA 59.245 40.000 0.00 0.00 0.00 3.58
5254 5842 9.651718 GACTAATTTTGTTTCTGAAGTGTACTG 57.348 33.333 0.00 0.00 0.00 2.74
5284 5872 2.346766 AGTAAATGGCCGATGATGCA 57.653 45.000 0.00 0.00 0.00 3.96
5285 5873 2.224606 AGTAAATGGCCGATGATGCAG 58.775 47.619 0.00 0.00 0.00 4.41
5286 5874 0.953727 TAAATGGCCGATGATGCAGC 59.046 50.000 0.00 0.00 0.00 5.25
5287 5875 0.754217 AAATGGCCGATGATGCAGCT 60.754 50.000 2.53 0.00 0.00 4.24
5288 5876 1.452953 AATGGCCGATGATGCAGCTG 61.453 55.000 10.11 10.11 0.00 4.24
5289 5877 3.285215 GGCCGATGATGCAGCTGG 61.285 66.667 17.12 3.67 0.00 4.85
5307 5895 2.554032 CTGGAGCTGGTTGTTAAGTTGG 59.446 50.000 0.00 0.00 0.00 3.77
5362 5976 3.350219 AAGTTCTGGTATCGCCACATT 57.650 42.857 0.00 0.00 43.61 2.71
5423 6038 1.906333 ATTTGACAACACCCCCGCC 60.906 57.895 0.00 0.00 0.00 6.13
5428 6043 4.676951 CAACACCCCCGCCACCAT 62.677 66.667 0.00 0.00 0.00 3.55
5589 6204 3.793144 GCGTTCTTGGCAGAGGCG 61.793 66.667 0.00 0.00 42.47 5.52
5940 6555 2.997897 ACCGAGGACCAGCTGGAC 60.998 66.667 39.19 31.70 38.94 4.02
5941 6556 2.997315 CCGAGGACCAGCTGGACA 60.997 66.667 39.19 0.00 38.94 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.227205 CGATGAGCTGGAGAGGCAC 60.227 63.158 0.00 0.00 0.00 5.01
6 7 1.380380 TCGATGAGCTGGAGAGGCA 60.380 57.895 0.00 0.00 0.00 4.75
50 51 1.521681 CTTCAATCCGGCGGAGGTC 60.522 63.158 33.82 0.00 34.05 3.85
58 59 0.739813 GGACACGACCTTCAATCCGG 60.740 60.000 0.00 0.00 0.00 5.14
59 60 0.037697 TGGACACGACCTTCAATCCG 60.038 55.000 0.00 0.00 0.00 4.18
62 63 0.320421 CGGTGGACACGACCTTCAAT 60.320 55.000 0.00 0.00 0.00 2.57
64 65 2.732016 CGGTGGACACGACCTTCA 59.268 61.111 0.00 0.00 0.00 3.02
95 96 2.657237 CCTTCACTTCCGGCGACT 59.343 61.111 9.30 0.00 0.00 4.18
148 149 0.472471 TTTGCCTCTTCCTCCGTTGT 59.528 50.000 0.00 0.00 0.00 3.32
149 150 1.160137 CTTTGCCTCTTCCTCCGTTG 58.840 55.000 0.00 0.00 0.00 4.10
150 151 0.036875 CCTTTGCCTCTTCCTCCGTT 59.963 55.000 0.00 0.00 0.00 4.44
151 152 1.679898 CCTTTGCCTCTTCCTCCGT 59.320 57.895 0.00 0.00 0.00 4.69
152 153 1.746991 GCCTTTGCCTCTTCCTCCG 60.747 63.158 0.00 0.00 0.00 4.63
155 156 2.360475 GCGCCTTTGCCTCTTCCT 60.360 61.111 0.00 0.00 0.00 3.36
158 159 2.360475 GGAGCGCCTTTGCCTCTT 60.360 61.111 2.29 0.00 36.00 2.85
173 177 1.203237 AGTTCTGGGAAGAGCAGAGGA 60.203 52.381 0.00 0.00 0.00 3.71
176 180 1.271054 GCAAGTTCTGGGAAGAGCAGA 60.271 52.381 0.00 0.00 0.00 4.26
177 181 1.163554 GCAAGTTCTGGGAAGAGCAG 58.836 55.000 0.00 0.00 0.00 4.24
183 187 0.250901 GGCAGAGCAAGTTCTGGGAA 60.251 55.000 14.41 0.00 43.80 3.97
184 188 1.376466 GGCAGAGCAAGTTCTGGGA 59.624 57.895 14.41 0.00 43.80 4.37
191 195 4.711949 CAGCCGGGCAGAGCAAGT 62.712 66.667 23.09 0.00 0.00 3.16
218 222 1.153429 GGGTGTATCGGTGAGTGGC 60.153 63.158 0.00 0.00 0.00 5.01
245 249 4.918201 GCCAAGATCTCGGGCCGG 62.918 72.222 27.98 17.02 41.90 6.13
247 251 3.849951 TCGCCAAGATCTCGGGCC 61.850 66.667 24.84 12.54 44.90 5.80
250 254 1.586564 GTCGTCGCCAAGATCTCGG 60.587 63.158 0.00 0.00 0.00 4.63
254 258 1.154093 TCGTGTCGTCGCCAAGATC 60.154 57.895 0.00 0.00 0.00 2.75
269 273 2.868920 GAGGAGCTTCGTCGTCGT 59.131 61.111 1.33 0.00 38.33 4.34
296 300 3.055080 TACGCAGCCTCGTAACCCG 62.055 63.158 5.71 0.00 41.33 5.28
302 306 2.048503 GGTTGTACGCAGCCTCGT 60.049 61.111 6.13 6.13 41.96 4.18
313 317 1.298340 CATGGGTCTGGCGGTTGTA 59.702 57.895 0.00 0.00 0.00 2.41
314 318 2.034066 CATGGGTCTGGCGGTTGT 59.966 61.111 0.00 0.00 0.00 3.32
320 324 3.785859 TCGAGGCATGGGTCTGGC 61.786 66.667 0.00 0.00 41.74 4.85
323 327 3.023949 GCTGTCGAGGCATGGGTCT 62.024 63.158 5.56 0.00 0.00 3.85
335 339 3.709880 TATTCGGTGCGGGCTGTCG 62.710 63.158 0.00 0.00 0.00 4.35
340 344 3.573491 GCTGTATTCGGTGCGGGC 61.573 66.667 0.00 0.00 0.00 6.13
347 351 1.301716 CCCCATCGGCTGTATTCGG 60.302 63.158 0.00 0.00 0.00 4.30
350 354 0.106719 CCAACCCCATCGGCTGTATT 60.107 55.000 0.00 0.00 33.26 1.89
357 361 2.751436 CTGCACCAACCCCATCGG 60.751 66.667 0.00 0.00 37.81 4.18
374 378 0.613777 ATGACCACTTTCGGAGGGAC 59.386 55.000 0.00 0.00 0.00 4.46
380 384 4.036262 TGTTTCAAAGATGACCACTTTCGG 59.964 41.667 0.00 0.00 35.74 4.30
382 386 4.978580 GCTGTTTCAAAGATGACCACTTTC 59.021 41.667 0.00 0.00 35.74 2.62
383 387 4.498009 CGCTGTTTCAAAGATGACCACTTT 60.498 41.667 0.00 0.00 37.96 2.66
389 393 3.814945 CTTCCGCTGTTTCAAAGATGAC 58.185 45.455 0.00 0.00 34.61 3.06
395 399 1.098869 TGTGCTTCCGCTGTTTCAAA 58.901 45.000 0.00 0.00 36.97 2.69
401 405 1.675641 GGGATTGTGCTTCCGCTGT 60.676 57.895 0.00 0.00 36.97 4.40
416 420 4.137615 TCGCCGGAGATGGAGGGA 62.138 66.667 5.05 0.00 0.00 4.20
464 468 3.365265 CAGAACCCACCAAGCCGC 61.365 66.667 0.00 0.00 0.00 6.53
467 471 1.973812 GCCTCAGAACCCACCAAGC 60.974 63.158 0.00 0.00 0.00 4.01
470 474 3.256960 GGGCCTCAGAACCCACCA 61.257 66.667 0.84 0.00 46.22 4.17
480 484 3.393970 CCGCTTCTCTGGGCCTCA 61.394 66.667 4.53 0.00 0.00 3.86
500 504 2.043852 AGATCTCGGTGGAGGCGT 60.044 61.111 0.00 0.00 40.85 5.68
534 538 4.864334 GAGGCGCCATGGGTCCAG 62.864 72.222 31.54 0.00 0.00 3.86
620 624 0.250124 TTCTGGATGTTCCGTTGCGT 60.250 50.000 0.00 0.00 40.17 5.24
623 627 1.194547 CGTGTTCTGGATGTTCCGTTG 59.805 52.381 0.00 0.00 40.17 4.10
624 628 1.069513 TCGTGTTCTGGATGTTCCGTT 59.930 47.619 0.00 0.00 40.17 4.44
625 629 0.677288 TCGTGTTCTGGATGTTCCGT 59.323 50.000 0.00 0.00 40.17 4.69
627 631 2.673368 GTCATCGTGTTCTGGATGTTCC 59.327 50.000 1.48 0.00 40.64 3.62
631 635 3.748048 AGTTTGTCATCGTGTTCTGGATG 59.252 43.478 0.00 0.00 41.05 3.51
633 637 3.469008 AGTTTGTCATCGTGTTCTGGA 57.531 42.857 0.00 0.00 0.00 3.86
639 643 2.224426 TGGCCTTAGTTTGTCATCGTGT 60.224 45.455 3.32 0.00 0.00 4.49
645 649 2.703536 TGTCTCTGGCCTTAGTTTGTCA 59.296 45.455 3.32 0.00 0.00 3.58
648 652 3.499918 CAGTTGTCTCTGGCCTTAGTTTG 59.500 47.826 3.32 0.00 0.00 2.93
660 664 2.932234 CGACCGCCCAGTTGTCTCT 61.932 63.158 0.00 0.00 0.00 3.10
720 724 4.172232 TCCTCCCCGGCTATGGCT 62.172 66.667 0.00 0.00 38.73 4.75
726 730 3.684628 TTCTCCTCCTCCCCGGCT 61.685 66.667 0.00 0.00 0.00 5.52
727 731 3.157949 CTTCTCCTCCTCCCCGGC 61.158 72.222 0.00 0.00 0.00 6.13
730 734 1.690985 CCACCTTCTCCTCCTCCCC 60.691 68.421 0.00 0.00 0.00 4.81
731 735 2.371259 GCCACCTTCTCCTCCTCCC 61.371 68.421 0.00 0.00 0.00 4.30
732 736 2.371259 GGCCACCTTCTCCTCCTCC 61.371 68.421 0.00 0.00 0.00 4.30
733 737 2.726351 CGGCCACCTTCTCCTCCTC 61.726 68.421 2.24 0.00 0.00 3.71
736 740 2.283529 TGACGGCCACCTTCTCCTC 61.284 63.158 2.24 0.00 0.00 3.71
740 744 4.003788 CCGTGACGGCCACCTTCT 62.004 66.667 12.53 0.00 42.76 2.85
752 756 4.337060 CGTGTCACTCGGCCGTGA 62.337 66.667 32.11 23.16 41.33 4.35
776 781 4.175337 CCGATGTCCACCGCCCAT 62.175 66.667 0.00 0.00 0.00 4.00
781 786 4.386951 TGGCACCGATGTCCACCG 62.387 66.667 0.00 0.00 30.11 4.94
789 794 2.573869 CGTCACTCTGGCACCGAT 59.426 61.111 0.00 0.00 0.00 4.18
790 795 4.357947 GCGTCACTCTGGCACCGA 62.358 66.667 0.00 0.00 0.00 4.69
814 819 1.468202 AGCCTTCCCCTCCCCTTTT 60.468 57.895 0.00 0.00 0.00 2.27
815 820 1.931180 GAGCCTTCCCCTCCCCTTT 60.931 63.158 0.00 0.00 0.00 3.11
817 822 2.898813 AAGAGCCTTCCCCTCCCCT 61.899 63.158 0.00 0.00 0.00 4.79
824 829 1.153469 CGAGAGCAAGAGCCTTCCC 60.153 63.158 0.00 0.00 43.56 3.97
825 830 4.511636 CGAGAGCAAGAGCCTTCC 57.488 61.111 0.00 0.00 43.56 3.46
849 854 1.423395 GAGGTTCAACACAGCGAGAG 58.577 55.000 0.00 0.00 0.00 3.20
850 855 0.318699 CGAGGTTCAACACAGCGAGA 60.319 55.000 0.00 0.00 0.00 4.04
851 856 1.891060 GCGAGGTTCAACACAGCGAG 61.891 60.000 0.00 0.00 0.00 5.03
852 857 1.954146 GCGAGGTTCAACACAGCGA 60.954 57.895 0.00 0.00 0.00 4.93
853 858 2.551270 GCGAGGTTCAACACAGCG 59.449 61.111 0.00 0.00 0.00 5.18
854 859 2.617274 GGGCGAGGTTCAACACAGC 61.617 63.158 0.00 0.00 0.00 4.40
855 860 1.966451 GGGGCGAGGTTCAACACAG 60.966 63.158 0.00 0.00 0.00 3.66
856 861 2.112297 GGGGCGAGGTTCAACACA 59.888 61.111 0.00 0.00 0.00 3.72
857 862 3.047877 CGGGGCGAGGTTCAACAC 61.048 66.667 0.00 0.00 0.00 3.32
870 875 4.636435 ACCTTGACAACCGCGGGG 62.636 66.667 31.76 23.38 40.11 5.73
871 876 2.593436 AACCTTGACAACCGCGGG 60.593 61.111 31.76 15.62 0.00 6.13
872 877 1.234615 ATGAACCTTGACAACCGCGG 61.235 55.000 26.86 26.86 0.00 6.46
873 878 0.591170 AATGAACCTTGACAACCGCG 59.409 50.000 0.00 0.00 0.00 6.46
874 879 1.606668 TGAATGAACCTTGACAACCGC 59.393 47.619 0.00 0.00 0.00 5.68
875 880 3.066064 TGTTGAATGAACCTTGACAACCG 59.934 43.478 0.00 0.00 37.42 4.44
876 881 4.338118 TCTGTTGAATGAACCTTGACAACC 59.662 41.667 0.00 0.00 37.42 3.77
877 882 5.273944 GTCTGTTGAATGAACCTTGACAAC 58.726 41.667 0.00 0.00 38.29 3.32
878 883 4.338118 GGTCTGTTGAATGAACCTTGACAA 59.662 41.667 0.00 0.00 33.54 3.18
879 884 3.882888 GGTCTGTTGAATGAACCTTGACA 59.117 43.478 0.00 0.00 33.54 3.58
880 885 3.058914 CGGTCTGTTGAATGAACCTTGAC 60.059 47.826 0.00 0.00 33.07 3.18
881 886 3.138304 CGGTCTGTTGAATGAACCTTGA 58.862 45.455 0.00 0.00 33.07 3.02
882 887 2.226437 CCGGTCTGTTGAATGAACCTTG 59.774 50.000 0.00 0.00 33.07 3.61
883 888 2.105821 TCCGGTCTGTTGAATGAACCTT 59.894 45.455 0.00 0.00 33.07 3.50
884 889 1.697432 TCCGGTCTGTTGAATGAACCT 59.303 47.619 0.00 0.00 33.07 3.50
885 890 2.178912 TCCGGTCTGTTGAATGAACC 57.821 50.000 0.00 0.00 33.07 3.62
886 891 3.139077 ACTTCCGGTCTGTTGAATGAAC 58.861 45.455 0.00 0.00 34.84 3.18
887 892 3.485463 ACTTCCGGTCTGTTGAATGAA 57.515 42.857 0.00 0.00 0.00 2.57
888 893 3.138304 CAACTTCCGGTCTGTTGAATGA 58.862 45.455 22.58 0.00 42.35 2.57
889 894 2.350772 GCAACTTCCGGTCTGTTGAATG 60.351 50.000 27.49 12.24 42.35 2.67
890 895 1.880027 GCAACTTCCGGTCTGTTGAAT 59.120 47.619 27.49 2.24 42.35 2.57
891 896 1.305201 GCAACTTCCGGTCTGTTGAA 58.695 50.000 27.49 5.47 42.35 2.69
892 897 0.534203 GGCAACTTCCGGTCTGTTGA 60.534 55.000 27.49 0.00 42.35 3.18
893 898 1.515521 GGGCAACTTCCGGTCTGTTG 61.516 60.000 22.64 22.64 42.55 3.33
894 899 1.228154 GGGCAACTTCCGGTCTGTT 60.228 57.895 0.00 2.33 0.00 3.16
895 900 2.113243 GAGGGCAACTTCCGGTCTGT 62.113 60.000 0.00 0.00 36.51 3.41
896 901 1.376037 GAGGGCAACTTCCGGTCTG 60.376 63.158 0.00 0.00 36.51 3.51
897 902 3.069778 GAGGGCAACTTCCGGTCT 58.930 61.111 0.00 0.00 36.51 3.85
911 916 2.965226 TTAGGAGGATGGGGCGGAGG 62.965 65.000 0.00 0.00 0.00 4.30
912 917 1.054406 TTTAGGAGGATGGGGCGGAG 61.054 60.000 0.00 0.00 0.00 4.63
913 918 0.401395 ATTTAGGAGGATGGGGCGGA 60.401 55.000 0.00 0.00 0.00 5.54
914 919 0.478507 AATTTAGGAGGATGGGGCGG 59.521 55.000 0.00 0.00 0.00 6.13
915 920 1.133792 ACAATTTAGGAGGATGGGGCG 60.134 52.381 0.00 0.00 0.00 6.13
916 921 2.310538 CACAATTTAGGAGGATGGGGC 58.689 52.381 0.00 0.00 0.00 5.80
917 922 2.310538 GCACAATTTAGGAGGATGGGG 58.689 52.381 0.00 0.00 0.00 4.96
918 923 3.017048 TGCACAATTTAGGAGGATGGG 57.983 47.619 0.00 0.00 0.00 4.00
919 924 5.127519 TGATTTGCACAATTTAGGAGGATGG 59.872 40.000 0.00 0.00 0.00 3.51
920 925 6.211587 TGATTTGCACAATTTAGGAGGATG 57.788 37.500 0.00 0.00 0.00 3.51
921 926 6.855763 TTGATTTGCACAATTTAGGAGGAT 57.144 33.333 0.00 0.00 0.00 3.24
922 927 6.662865 TTTGATTTGCACAATTTAGGAGGA 57.337 33.333 0.00 0.00 0.00 3.71
923 928 5.349543 GCTTTGATTTGCACAATTTAGGAGG 59.650 40.000 0.00 0.00 0.00 4.30
924 929 5.349543 GGCTTTGATTTGCACAATTTAGGAG 59.650 40.000 0.00 0.00 0.00 3.69
928 933 5.819379 TGTTGGCTTTGATTTGCACAATTTA 59.181 32.000 0.00 0.00 0.00 1.40
952 960 6.515272 TTTTTGAGAAGCAAACAGTCTCTT 57.485 33.333 0.00 0.00 45.64 2.85
1094 1104 2.911143 CCGTGGGGATGAGAAGGG 59.089 66.667 0.00 0.00 34.06 3.95
1345 1355 4.532834 ACAGCAAGTGAAAAAGGAACCTA 58.467 39.130 0.00 0.00 0.00 3.08
1597 1607 3.125316 AGCGCATAAACAGAGCACTAAAC 59.875 43.478 11.47 0.00 34.04 2.01
1613 1623 0.107800 ATCAACTCTGAGCAGCGCAT 60.108 50.000 11.47 0.00 34.23 4.73
1639 1649 1.084370 CAGCAACAGCGGTAGTAGGC 61.084 60.000 0.00 0.00 0.00 3.93
1868 1878 5.574188 AGAGTTGAGGCCAATCAAATAAGT 58.426 37.500 5.01 0.00 40.72 2.24
1879 1889 2.441750 ACAAAACCTAGAGTTGAGGCCA 59.558 45.455 5.01 0.00 39.19 5.36
1977 1987 2.369860 ACTGAGGCTGATCAAAGTGACA 59.630 45.455 0.00 0.00 0.00 3.58
2068 2078 2.907042 CCGAAAAGGAGGATATAGCCCT 59.093 50.000 2.64 0.00 45.00 5.19
2459 2858 4.164988 ACCACTAAAGCTGCCTTCAGATAT 59.835 41.667 0.00 0.00 42.95 1.63
2588 3044 8.114290 CACATAGTACAAAACAAGTATTAGCCG 58.886 37.037 0.00 0.00 0.00 5.52
2709 3165 1.609208 ATCGGCCATGGCAAATAGTC 58.391 50.000 36.56 17.19 44.11 2.59
2891 3347 7.852263 AGGTATGGCAATAGATAAGGTATGAC 58.148 38.462 0.00 0.00 0.00 3.06
2909 3365 4.503296 GGATAGTGCAGGTGTAAGGTATGG 60.503 50.000 0.00 0.00 0.00 2.74
2948 3404 6.127647 CCATGTAAGTTAACAACTGGATGCAT 60.128 38.462 8.61 0.00 41.91 3.96
2950 3406 5.393027 CCCATGTAAGTTAACAACTGGATGC 60.393 44.000 19.50 0.00 41.91 3.91
2986 3442 5.221661 GGTTATACCCAGGGATAAGACACTG 60.222 48.000 14.54 0.00 40.57 3.66
3007 3463 8.540388 TGCTTCAACAGATATACTTAGAAGGTT 58.460 33.333 0.00 0.00 33.07 3.50
3021 3477 5.507985 GCTTAACCAGTTTGCTTCAACAGAT 60.508 40.000 0.00 0.00 0.00 2.90
3467 4048 6.293955 GCATACTTGAACCTTTTGCTAACTCA 60.294 38.462 0.00 0.00 0.00 3.41
3673 4255 6.230472 TCCGATCCATATTAATTGTCACTGG 58.770 40.000 0.00 0.00 0.00 4.00
3677 4259 7.773224 ACAAACTCCGATCCATATTAATTGTCA 59.227 33.333 0.00 0.00 0.00 3.58
3775 4357 2.299582 CCAAAACAGACATGCCAATGGA 59.700 45.455 2.05 0.00 38.19 3.41
4095 4677 1.888512 TCTGGATTGAACCTTTGCTGC 59.111 47.619 0.00 0.00 0.00 5.25
4167 4749 4.129380 TCACGGCATCTTCTATTGAATGG 58.871 43.478 0.00 0.00 0.00 3.16
4293 4875 6.385649 TTTCTCTGAACATTACCAAACACC 57.614 37.500 0.00 0.00 0.00 4.16
4334 4916 2.747855 GGCAGCCTCCAAGAACGG 60.748 66.667 3.29 0.00 0.00 4.44
4366 4948 1.424493 CTCCGCTCGACCTGCAAATC 61.424 60.000 0.00 0.00 0.00 2.17
4423 5005 1.676635 ACCATCAGCATTGCACGCT 60.677 52.632 11.91 3.95 41.47 5.07
4426 5008 0.171903 GGACACCATCAGCATTGCAC 59.828 55.000 11.91 0.00 0.00 4.57
4453 5035 1.731709 CGTGCCGAAATGTCTGATTGA 59.268 47.619 0.00 0.00 0.00 2.57
4492 5074 1.134340 CCGATGATTTTACCCGGTCCA 60.134 52.381 0.00 0.00 35.83 4.02
4519 5101 0.896940 CTTGTGCAGGGGTCTTGCAT 60.897 55.000 7.89 0.00 40.84 3.96
4669 5251 3.430862 CCACCAATGGCGACCACG 61.431 66.667 0.00 0.00 39.82 4.94
4725 5307 2.447047 ACACCTTTGAGATTGGGGAAGT 59.553 45.455 0.00 0.00 0.00 3.01
4727 5309 2.552155 CGACACCTTTGAGATTGGGGAA 60.552 50.000 0.00 0.00 0.00 3.97
4774 5356 0.097150 TCTCAGACGAGACGCATTCG 59.903 55.000 0.00 2.75 43.55 3.34
4817 5399 2.425773 CAAGCAACGCACACTCGC 60.426 61.111 0.00 0.00 0.00 5.03
4845 5427 4.454728 AGAGAAGTGAAAGCTAGCTCTG 57.545 45.455 19.65 0.00 32.67 3.35
4873 5455 6.388619 AGTAAAAGCTTATCCTCCCTTGAA 57.611 37.500 0.00 0.00 0.00 2.69
4937 5519 0.742990 ACCACCGCACCATGTAATCG 60.743 55.000 0.00 0.00 0.00 3.34
4968 5551 3.873910 ACTTCCATATCAAACCGTGGAG 58.126 45.455 0.00 0.00 41.41 3.86
4983 5566 6.073276 CGGAATTTCGCATTCATATACTTCCA 60.073 38.462 0.00 0.00 0.00 3.53
5162 5745 5.739959 TCAGATCGTTCATATTGGTGGAAA 58.260 37.500 0.00 0.00 0.00 3.13
5167 5750 5.917462 TGTCATCAGATCGTTCATATTGGT 58.083 37.500 0.00 0.00 0.00 3.67
5190 5773 2.328319 GCCTCTCCAGAGATGGATTCT 58.672 52.381 5.08 0.00 44.74 2.40
5193 5776 1.767681 GTTGCCTCTCCAGAGATGGAT 59.232 52.381 5.08 0.00 44.74 3.41
5201 5784 1.163554 GCTTCAAGTTGCCTCTCCAG 58.836 55.000 0.00 0.00 0.00 3.86
5211 5794 2.590821 AGTCTGGCAATGCTTCAAGTT 58.409 42.857 4.82 0.00 0.00 2.66
5254 5842 3.619038 CGGCCATTTACTTTGAGAGAGAC 59.381 47.826 2.24 0.00 0.00 3.36
5285 5873 1.897560 ACTTAACAACCAGCTCCAGC 58.102 50.000 0.00 0.00 42.49 4.85
5286 5874 2.554032 CCAACTTAACAACCAGCTCCAG 59.446 50.000 0.00 0.00 0.00 3.86
5287 5875 2.582052 CCAACTTAACAACCAGCTCCA 58.418 47.619 0.00 0.00 0.00 3.86
5288 5876 1.269723 GCCAACTTAACAACCAGCTCC 59.730 52.381 0.00 0.00 0.00 4.70
5289 5877 1.953686 TGCCAACTTAACAACCAGCTC 59.046 47.619 0.00 0.00 0.00 4.09
5298 5886 3.748021 GCACGTCTGCCAACTTAAC 57.252 52.632 0.00 0.00 37.45 2.01
5307 5895 3.372554 GAGTAGGGGGCACGTCTGC 62.373 68.421 0.00 0.00 43.41 4.26
5362 5976 3.006752 CCTACTCCATTGCAAAAGCCAAA 59.993 43.478 1.71 0.00 0.00 3.28
5423 6038 2.283298 CGAAGGAGATTGGTGATGGTG 58.717 52.381 0.00 0.00 0.00 4.17
5428 6043 0.530744 CCGACGAAGGAGATTGGTGA 59.469 55.000 0.00 0.00 28.85 4.02
5558 6173 3.226429 AACGCCTGCAGCTTCTCGA 62.226 57.895 8.66 0.00 40.39 4.04
5589 6204 4.388499 TCGTTCTTGGCCGCCTCC 62.388 66.667 11.61 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.