Multiple sequence alignment - TraesCS7A01G529900

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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 TraesCS7A01G529900 chr7A 100.000 6954 0 0 1 6954 709410966 709404013 0.000000e+00 12842.0
1 TraesCS7A01G529900 chr7A 81.048 496 47 18 706 1183 709541966 709541500 1.110000e-92 351.0
2 TraesCS7A01G529900 chr7A 86.411 287 28 9 419 699 709542473 709542192 3.150000e-78 303.0
3 TraesCS7A01G529900 chr7A 90.196 153 6 2 6290 6433 709394106 709393954 2.560000e-44 191.0
4 TraesCS7A01G529900 chr7A 86.364 132 12 2 113 244 709544903 709544778 9.410000e-29 139.0
5 TraesCS7A01G529900 chr7B 92.985 5916 291 65 349 6196 709614189 709608330 0.000000e+00 8512.0
6 TraesCS7A01G529900 chr7B 94.407 447 25 0 6508 6954 709982583 709983029 0.000000e+00 688.0
7 TraesCS7A01G529900 chr7B 96.414 251 8 1 88 338 709616470 709616221 5.020000e-111 412.0
8 TraesCS7A01G529900 chr7B 80.645 496 48 22 706 1183 709744232 709743767 2.400000e-89 340.0
9 TraesCS7A01G529900 chr7B 90.698 215 17 2 485 699 709744669 709744458 4.110000e-72 283.0
10 TraesCS7A01G529900 chr7B 89.583 192 9 4 6290 6470 710004296 710004487 4.190000e-57 233.0
11 TraesCS7A01G529900 chr7B 88.571 175 11 3 6290 6455 709982194 709982368 3.290000e-48 204.0
12 TraesCS7A01G529900 chr7B 95.604 91 4 0 1 91 709616673 709616583 5.620000e-31 147.0
13 TraesCS7A01G529900 chr7B 92.424 66 5 0 215 280 709950404 709950339 2.060000e-15 95.3
14 TraesCS7A01G529900 chr7D 91.681 5866 311 86 479 6291 616510946 616505205 0.000000e+00 7965.0
15 TraesCS7A01G529900 chr7D 91.806 659 44 4 6306 6954 606811768 606811110 0.000000e+00 909.0
16 TraesCS7A01G529900 chr7D 88.506 174 10 4 6306 6469 606809111 606808938 1.180000e-47 202.0
17 TraesCS7A01G529900 chr7D 90.517 116 6 3 479 593 616521225 616521114 1.560000e-31 148.0
18 TraesCS7A01G529900 chr3B 91.765 680 41 3 6290 6954 820770581 820769902 0.000000e+00 931.0
19 TraesCS7A01G529900 chr3B 87.817 197 14 3 6290 6476 820765599 820765403 9.080000e-54 222.0
20 TraesCS7A01G529900 chr2B 90.694 677 49 5 6290 6954 175497501 175498175 0.000000e+00 889.0
21 TraesCS7A01G529900 chr6B 88.000 675 62 8 6294 6952 125639301 125638630 0.000000e+00 780.0
22 TraesCS7A01G529900 chr6B 83.604 677 91 15 6290 6954 716696454 716695786 9.910000e-173 617.0
23 TraesCS7A01G529900 chr2D 84.094 679 88 14 6290 6954 109019674 109020346 7.610000e-179 638.0
24 TraesCS7A01G529900 chr2D 86.413 184 13 6 6290 6463 453740276 453740457 2.560000e-44 191.0
25 TraesCS7A01G529900 chr2D 93.407 91 6 0 1 91 186655296 186655386 1.220000e-27 135.0
26 TraesCS7A01G529900 chr2D 86.813 91 12 0 1 91 154829480 154829570 1.230000e-17 102.0
27 TraesCS7A01G529900 chr6D 87.569 547 65 3 6409 6954 448466892 448466348 1.270000e-176 630.0
28 TraesCS7A01G529900 chr5B 83.655 673 90 14 6290 6954 37805161 37804501 3.560000e-172 616.0
29 TraesCS7A01G529900 chr2A 87.198 414 36 9 6306 6708 161358563 161358156 8.220000e-124 455.0
30 TraesCS7A01G529900 chr4D 89.011 91 10 0 1 91 439883186 439883276 5.700000e-21 113.0


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 TraesCS7A01G529900 chr7A 709404013 709410966 6953 True 12842.000000 12842 100.000000 1 6954 1 chr7A.!!$R2 6953
1 TraesCS7A01G529900 chr7A 709541500 709544903 3403 True 264.333333 351 84.607667 113 1183 3 chr7A.!!$R3 1070
2 TraesCS7A01G529900 chr7B 709608330 709616673 8343 True 3023.666667 8512 95.001000 1 6196 3 chr7B.!!$R2 6195
3 TraesCS7A01G529900 chr7B 709982194 709983029 835 False 446.000000 688 91.489000 6290 6954 2 chr7B.!!$F2 664
4 TraesCS7A01G529900 chr7B 709743767 709744669 902 True 311.500000 340 85.671500 485 1183 2 chr7B.!!$R3 698
5 TraesCS7A01G529900 chr7D 616505205 616510946 5741 True 7965.000000 7965 91.681000 479 6291 1 chr7D.!!$R1 5812
6 TraesCS7A01G529900 chr7D 606808938 606811768 2830 True 555.500000 909 90.156000 6306 6954 2 chr7D.!!$R3 648
7 TraesCS7A01G529900 chr3B 820769902 820770581 679 True 931.000000 931 91.765000 6290 6954 1 chr3B.!!$R2 664
8 TraesCS7A01G529900 chr2B 175497501 175498175 674 False 889.000000 889 90.694000 6290 6954 1 chr2B.!!$F1 664
9 TraesCS7A01G529900 chr6B 125638630 125639301 671 True 780.000000 780 88.000000 6294 6952 1 chr6B.!!$R1 658
10 TraesCS7A01G529900 chr6B 716695786 716696454 668 True 617.000000 617 83.604000 6290 6954 1 chr6B.!!$R2 664
11 TraesCS7A01G529900 chr2D 109019674 109020346 672 False 638.000000 638 84.094000 6290 6954 1 chr2D.!!$F1 664
12 TraesCS7A01G529900 chr6D 448466348 448466892 544 True 630.000000 630 87.569000 6409 6954 1 chr6D.!!$R1 545
13 TraesCS7A01G529900 chr5B 37804501 37805161 660 True 616.000000 616 83.655000 6290 6954 1 chr5B.!!$R1 664

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
67 68 0.037605 GTCCACCGTACCCAGACAAG 60.038 60.000 0.00 0.00 0.0 3.16 F
673 4450 0.107703 GACAGATCCCGCACCAATCA 60.108 55.000 0.00 0.00 0.0 2.57 F
1210 5233 0.526524 GCAGCGCGAGTAGATTCTGT 60.527 55.000 12.10 0.00 0.0 3.41 F
2071 6106 1.000955 GAGAAGTTCGAGTTCCAGGCA 59.999 52.381 6.09 0.00 0.0 4.75 F
3508 7576 0.730834 GTTGTGTTGTGTGCGTGCAA 60.731 50.000 0.00 0.00 0.0 4.08 F
4630 8706 1.531423 AGTCAGATGGCAAGCTTGTG 58.469 50.000 26.55 16.62 0.0 3.33 F
5348 9448 0.039074 AGTCGTTCAAGGAGCTGACG 60.039 55.000 0.00 0.00 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1785 5819 0.107508 TCTTAGCTGCAGGCACATCC 60.108 55.000 17.12 0.0 44.79 3.51 R
2059 6094 1.079543 CACCTCTGCCTGGAACTCG 60.080 63.158 0.00 0.0 0.00 4.18 R
2954 6997 1.212935 GCCTTGGACTCCCACACATAT 59.787 52.381 0.00 0.0 43.41 1.78 R
3662 7730 0.035056 CAGTAACCTCCTTGGGGCTG 60.035 60.000 0.00 0.0 41.11 4.85 R
5103 9203 0.961753 GCCAAGCCTAGCACAAAGTT 59.038 50.000 0.00 0.0 0.00 2.66 R
5797 9900 1.009900 CGACCGGTAGATGCTCGAC 60.010 63.158 7.34 0.0 0.00 4.20 R
6505 10656 1.264749 ATGAGTTCCGTGCCAGCCTA 61.265 55.000 0.00 0.0 0.00 3.93 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
28 29 1.275666 ACGGATGAGGGTGATGACAA 58.724 50.000 0.00 0.00 0.00 3.18
67 68 0.037605 GTCCACCGTACCCAGACAAG 60.038 60.000 0.00 0.00 0.00 3.16
142 259 2.745968 AGGAAAAAGGAAACTGCACCA 58.254 42.857 0.00 0.00 42.68 4.17
181 298 2.064014 GGCCGTACAAAGTGTCACTAC 58.936 52.381 5.77 0.00 0.00 2.73
340 504 4.180057 CACTGCATCCTCTGAAACTACTC 58.820 47.826 0.00 0.00 0.00 2.59
342 506 3.173151 TGCATCCTCTGAAACTACTCCA 58.827 45.455 0.00 0.00 0.00 3.86
344 508 4.225942 TGCATCCTCTGAAACTACTCCAAT 59.774 41.667 0.00 0.00 0.00 3.16
346 510 5.755861 GCATCCTCTGAAACTACTCCAATAC 59.244 44.000 0.00 0.00 0.00 1.89
381 3468 5.693104 GTCAGTATCACTGGACGTGTTTTTA 59.307 40.000 0.00 0.00 45.94 1.52
469 4237 3.373565 CCAGCCCGAAAACCCAGC 61.374 66.667 0.00 0.00 0.00 4.85
525 4302 2.218066 AACACCCCGTTGACTGACT 58.782 52.632 0.00 0.00 36.12 3.41
526 4303 0.179056 AACACCCCGTTGACTGACTG 60.179 55.000 0.00 0.00 36.12 3.51
527 4304 1.046472 ACACCCCGTTGACTGACTGA 61.046 55.000 0.00 0.00 0.00 3.41
528 4305 0.600255 CACCCCGTTGACTGACTGAC 60.600 60.000 0.00 0.00 0.00 3.51
673 4450 0.107703 GACAGATCCCGCACCAATCA 60.108 55.000 0.00 0.00 0.00 2.57
680 4457 2.034066 CGCACCAATCACACCCCT 59.966 61.111 0.00 0.00 0.00 4.79
681 4458 1.298340 CGCACCAATCACACCCCTA 59.702 57.895 0.00 0.00 0.00 3.53
702 4480 1.157870 ACGTGTCAAACCCTTCAGCG 61.158 55.000 0.00 0.00 0.00 5.18
704 4482 2.250939 TGTCAAACCCTTCAGCGCG 61.251 57.895 0.00 0.00 0.00 6.86
798 4794 4.609018 CCCCGCGCCATCCACTAG 62.609 72.222 0.00 0.00 0.00 2.57
1179 5202 0.528684 GGTGGTAGCTCGTGATCTGC 60.529 60.000 0.00 0.00 0.00 4.26
1207 5230 0.937231 GAGGCAGCGCGAGTAGATTC 60.937 60.000 12.10 0.00 0.00 2.52
1208 5231 1.066587 GGCAGCGCGAGTAGATTCT 59.933 57.895 12.10 0.00 0.00 2.40
1210 5233 0.526524 GCAGCGCGAGTAGATTCTGT 60.527 55.000 12.10 0.00 0.00 3.41
1368 5400 2.093075 TCGTGTAGAGGCTAGTGCTACT 60.093 50.000 11.12 0.00 39.59 2.57
1428 5460 3.049206 GCTGTAGATCTCGCATCTGAAC 58.951 50.000 0.00 0.00 0.00 3.18
1486 5518 1.210204 ATCTGATGTGGTGGCAGGGT 61.210 55.000 0.00 0.00 0.00 4.34
1523 5555 2.159841 CGTGTTCGACATTACTGGCTTG 60.160 50.000 0.00 0.00 39.71 4.01
1527 5559 2.076100 TCGACATTACTGGCTTGCTTG 58.924 47.619 0.00 0.00 0.00 4.01
1651 5684 5.940192 TGCACCAATCTAGTGTTTACTTG 57.060 39.130 0.00 0.00 38.36 3.16
1698 5731 3.751518 TGATCTAGCGCTCTACCATACA 58.248 45.455 16.34 1.91 0.00 2.29
1699 5732 3.753797 TGATCTAGCGCTCTACCATACAG 59.246 47.826 16.34 1.55 0.00 2.74
1705 5738 2.030981 GCGCTCTACCATACAGTACTCC 60.031 54.545 0.00 0.00 0.00 3.85
1708 5741 4.451774 CGCTCTACCATACAGTACTCCTAC 59.548 50.000 0.00 0.00 0.00 3.18
1731 5765 7.964604 ACTGAATTCAAACTCTTGTACCTAC 57.035 36.000 9.88 0.00 33.94 3.18
1732 5766 7.736893 ACTGAATTCAAACTCTTGTACCTACT 58.263 34.615 9.88 0.00 33.94 2.57
1733 5767 8.867097 ACTGAATTCAAACTCTTGTACCTACTA 58.133 33.333 9.88 0.00 33.94 1.82
1734 5768 9.877178 CTGAATTCAAACTCTTGTACCTACTAT 57.123 33.333 9.88 0.00 33.94 2.12
1738 5772 6.864342 TCAAACTCTTGTACCTACTATCTGC 58.136 40.000 0.00 0.00 33.94 4.26
1739 5773 6.663953 TCAAACTCTTGTACCTACTATCTGCT 59.336 38.462 0.00 0.00 33.94 4.24
1740 5774 6.458232 AACTCTTGTACCTACTATCTGCTG 57.542 41.667 0.00 0.00 0.00 4.41
1741 5775 5.511363 ACTCTTGTACCTACTATCTGCTGT 58.489 41.667 0.00 0.00 0.00 4.40
1742 5776 6.660800 ACTCTTGTACCTACTATCTGCTGTA 58.339 40.000 0.00 0.00 0.00 2.74
1743 5777 7.117397 ACTCTTGTACCTACTATCTGCTGTAA 58.883 38.462 0.00 0.00 0.00 2.41
1744 5778 7.780745 ACTCTTGTACCTACTATCTGCTGTAAT 59.219 37.037 0.00 0.00 0.00 1.89
1745 5779 8.167605 TCTTGTACCTACTATCTGCTGTAATC 57.832 38.462 0.00 0.00 0.00 1.75
1753 5787 6.791867 ACTATCTGCTGTAATCTACACCAA 57.208 37.500 0.00 0.00 34.46 3.67
1758 5792 6.941857 TCTGCTGTAATCTACACCAATACAA 58.058 36.000 0.00 0.00 34.46 2.41
1769 5803 5.734855 ACACCAATACAACATATTCGAGC 57.265 39.130 0.00 0.00 0.00 5.03
1785 5819 1.998315 CGAGCTGTTTGTCTGATCCTG 59.002 52.381 0.00 0.00 0.00 3.86
1930 5965 1.153745 GTCCAGAGGTGCGCACTAG 60.154 63.158 36.84 23.42 0.00 2.57
1932 5967 1.153745 CCAGAGGTGCGCACTAGTC 60.154 63.158 36.84 28.66 0.00 2.59
1938 5973 1.517832 GTGCGCACTAGTCCCTGAT 59.482 57.895 32.55 0.00 0.00 2.90
1940 5975 1.299468 GCGCACTAGTCCCTGATCG 60.299 63.158 0.30 0.00 0.00 3.69
1945 5980 1.102222 ACTAGTCCCTGATCGACGCC 61.102 60.000 0.00 0.00 35.33 5.68
1946 5981 1.077285 TAGTCCCTGATCGACGCCA 60.077 57.895 0.00 0.00 35.33 5.69
1955 5990 1.436983 GATCGACGCCAATGGTTCCC 61.437 60.000 0.00 0.00 0.00 3.97
1970 6005 2.825532 GGTTCCCATTACATGCTGTTGT 59.174 45.455 0.00 0.00 0.00 3.32
1986 6021 5.869344 TGCTGTTGTCATTCTGTACTGATAC 59.131 40.000 3.03 3.92 0.00 2.24
2059 6094 1.273886 AGGAACTCGGCTGAGAAGTTC 59.726 52.381 29.29 20.94 45.57 3.01
2071 6106 1.000955 GAGAAGTTCGAGTTCCAGGCA 59.999 52.381 6.09 0.00 0.00 4.75
2686 6725 7.476667 TGAAATGTGCCCGTAAATAACATTAG 58.523 34.615 0.00 0.00 39.80 1.73
2841 6880 7.587629 CACAATGATGACAAACAGTAAGACAT 58.412 34.615 0.00 0.00 0.00 3.06
2842 6881 7.747799 CACAATGATGACAAACAGTAAGACATC 59.252 37.037 0.00 0.00 34.98 3.06
2843 6882 7.445096 ACAATGATGACAAACAGTAAGACATCA 59.555 33.333 16.68 16.68 43.74 3.07
2845 6884 7.800155 TGATGACAAACAGTAAGACATCAAA 57.200 32.000 13.86 0.00 39.29 2.69
2848 6887 7.015226 TGACAAACAGTAAGACATCAAACAG 57.985 36.000 0.00 0.00 0.00 3.16
2854 6893 2.664402 AAGACATCAAACAGTGCCCT 57.336 45.000 0.00 0.00 0.00 5.19
2857 6896 1.956477 GACATCAAACAGTGCCCTTGT 59.044 47.619 0.00 0.00 0.00 3.16
2858 6897 1.682854 ACATCAAACAGTGCCCTTGTG 59.317 47.619 0.00 0.00 0.00 3.33
2862 6901 3.357203 TCAAACAGTGCCCTTGTGTTTA 58.643 40.909 0.00 0.00 41.37 2.01
2863 6902 3.764434 TCAAACAGTGCCCTTGTGTTTAA 59.236 39.130 0.00 0.00 41.37 1.52
2866 6905 2.687935 ACAGTGCCCTTGTGTTTAACAG 59.312 45.455 0.00 0.00 40.74 3.16
2868 6907 2.949644 AGTGCCCTTGTGTTTAACAGAC 59.050 45.455 0.00 0.00 40.74 3.51
2871 6910 3.211045 GCCCTTGTGTTTAACAGACTGA 58.789 45.455 10.08 0.00 40.74 3.41
2877 6920 5.284861 TGTGTTTAACAGACTGAGCCTTA 57.715 39.130 10.08 0.00 33.78 2.69
2879 6922 5.700832 TGTGTTTAACAGACTGAGCCTTATG 59.299 40.000 10.08 0.00 33.78 1.90
2895 6938 6.228273 GCCTTATGCTTTTGGTTCTTTTTC 57.772 37.500 0.00 0.00 36.87 2.29
2902 6945 4.271049 GCTTTTGGTTCTTTTTCTGCCTTC 59.729 41.667 0.00 0.00 0.00 3.46
2911 6954 3.719268 TTTTCTGCCTTCCTCTATGCA 57.281 42.857 0.00 0.00 0.00 3.96
2923 6966 7.381323 CCTTCCTCTATGCAATTTTCTTGTTT 58.619 34.615 0.00 0.00 0.00 2.83
2938 6981 4.671377 TCTTGTTTCTGTTGTGACATTGC 58.329 39.130 0.00 0.00 34.72 3.56
2954 6997 4.229639 ACATTGCATCCCTCTCTGATAGA 58.770 43.478 0.00 0.00 0.00 1.98
2972 7015 5.305386 TGATAGATATGTGTGGGAGTCCAAG 59.695 44.000 12.30 0.00 46.04 3.61
2996 7039 4.435253 GCTGATGGATCATTCGCTATTTCG 60.435 45.833 0.00 0.00 36.02 3.46
3011 7054 4.691216 GCTATTTCGGAGGATACATGGAAC 59.309 45.833 0.00 0.00 41.41 3.62
3105 7148 4.453819 GCAAGCTGAAGGTATCACCATATC 59.546 45.833 0.00 0.00 41.95 1.63
3107 7150 5.220710 AGCTGAAGGTATCACCATATCAC 57.779 43.478 0.00 0.00 41.95 3.06
3116 7159 6.101734 AGGTATCACCATATCACCATGTCTTT 59.898 38.462 0.00 0.00 41.95 2.52
3117 7160 6.772716 GGTATCACCATATCACCATGTCTTTT 59.227 38.462 0.00 0.00 38.42 2.27
3143 7186 9.724839 TTTGTTGTTAGTGCAGTTTATACTTTC 57.275 29.630 0.00 0.00 30.26 2.62
3144 7187 8.439993 TGTTGTTAGTGCAGTTTATACTTTCA 57.560 30.769 0.00 0.00 30.26 2.69
3145 7188 9.062524 TGTTGTTAGTGCAGTTTATACTTTCAT 57.937 29.630 0.00 0.00 30.26 2.57
3146 7189 9.893305 GTTGTTAGTGCAGTTTATACTTTCATT 57.107 29.630 0.00 0.00 30.26 2.57
3179 7222 9.609346 TTATTGCTGTATTTCTACTTAAGACCC 57.391 33.333 10.09 0.00 32.51 4.46
3180 7223 6.614694 TGCTGTATTTCTACTTAAGACCCA 57.385 37.500 10.09 0.00 32.51 4.51
3181 7224 6.640518 TGCTGTATTTCTACTTAAGACCCAG 58.359 40.000 10.09 4.76 32.51 4.45
3182 7225 6.212791 TGCTGTATTTCTACTTAAGACCCAGT 59.787 38.462 10.09 0.00 32.51 4.00
3183 7226 7.104290 GCTGTATTTCTACTTAAGACCCAGTT 58.896 38.462 10.09 0.00 32.51 3.16
3184 7227 7.064728 GCTGTATTTCTACTTAAGACCCAGTTG 59.935 40.741 10.09 0.00 32.51 3.16
3185 7228 8.197592 TGTATTTCTACTTAAGACCCAGTTGA 57.802 34.615 10.09 0.00 32.51 3.18
3186 7229 8.822805 TGTATTTCTACTTAAGACCCAGTTGAT 58.177 33.333 10.09 0.00 32.51 2.57
3187 7230 9.315525 GTATTTCTACTTAAGACCCAGTTGATC 57.684 37.037 10.09 0.00 32.51 2.92
3188 7231 7.554959 TTTCTACTTAAGACCCAGTTGATCT 57.445 36.000 10.09 0.00 32.51 2.75
3189 7232 6.531503 TCTACTTAAGACCCAGTTGATCTG 57.468 41.667 10.09 0.00 43.27 2.90
3190 7233 6.253758 TCTACTTAAGACCCAGTTGATCTGA 58.746 40.000 10.09 0.00 46.27 3.27
3191 7234 5.825593 ACTTAAGACCCAGTTGATCTGAA 57.174 39.130 10.09 0.00 46.27 3.02
3192 7235 6.380079 ACTTAAGACCCAGTTGATCTGAAT 57.620 37.500 10.09 0.00 46.27 2.57
3193 7236 6.784031 ACTTAAGACCCAGTTGATCTGAATT 58.216 36.000 10.09 0.00 46.27 2.17
3194 7237 7.234355 ACTTAAGACCCAGTTGATCTGAATTT 58.766 34.615 10.09 0.00 46.27 1.82
3195 7238 7.725844 ACTTAAGACCCAGTTGATCTGAATTTT 59.274 33.333 10.09 0.00 46.27 1.82
3196 7239 9.231297 CTTAAGACCCAGTTGATCTGAATTTTA 57.769 33.333 0.00 0.00 46.27 1.52
3197 7240 7.454260 AAGACCCAGTTGATCTGAATTTTAC 57.546 36.000 0.00 0.00 46.27 2.01
3198 7241 5.946377 AGACCCAGTTGATCTGAATTTTACC 59.054 40.000 0.00 0.00 46.27 2.85
3199 7242 5.892348 ACCCAGTTGATCTGAATTTTACCT 58.108 37.500 0.00 0.00 46.27 3.08
3200 7243 5.711976 ACCCAGTTGATCTGAATTTTACCTG 59.288 40.000 0.00 0.00 46.27 4.00
3201 7244 5.945784 CCCAGTTGATCTGAATTTTACCTGA 59.054 40.000 0.00 0.00 46.27 3.86
3202 7245 6.434028 CCCAGTTGATCTGAATTTTACCTGAA 59.566 38.462 0.00 0.00 46.27 3.02
3203 7246 7.362401 CCCAGTTGATCTGAATTTTACCTGAAG 60.362 40.741 0.00 0.00 46.27 3.02
3204 7247 7.362401 CCAGTTGATCTGAATTTTACCTGAAGG 60.362 40.741 0.00 0.00 46.27 3.46
3224 7292 5.622346 AGGTCTCATCAATAGGTCTTTCC 57.378 43.478 0.00 0.00 0.00 3.13
3232 7300 4.513442 TCAATAGGTCTTTCCGTCCAATG 58.487 43.478 0.00 0.00 41.99 2.82
3234 7302 2.474410 AGGTCTTTCCGTCCAATGTC 57.526 50.000 0.00 0.00 41.99 3.06
3272 7340 9.828039 CATTATATGACAGTACATATCTGCCAT 57.172 33.333 0.00 0.00 41.67 4.40
3293 7361 6.890558 CCATTTTGAGGCACTTTTTATGTTG 58.109 36.000 0.00 0.00 41.55 3.33
3294 7362 6.482973 CCATTTTGAGGCACTTTTTATGTTGT 59.517 34.615 0.00 0.00 41.55 3.32
3295 7363 7.655328 CCATTTTGAGGCACTTTTTATGTTGTA 59.345 33.333 0.00 0.00 41.55 2.41
3296 7364 8.702438 CATTTTGAGGCACTTTTTATGTTGTAG 58.298 33.333 0.00 0.00 41.55 2.74
3297 7365 6.952773 TTGAGGCACTTTTTATGTTGTAGT 57.047 33.333 0.00 0.00 41.55 2.73
3298 7366 6.952773 TGAGGCACTTTTTATGTTGTAGTT 57.047 33.333 0.00 0.00 41.55 2.24
3299 7367 7.341445 TGAGGCACTTTTTATGTTGTAGTTT 57.659 32.000 0.00 0.00 41.55 2.66
3304 7372 9.303537 GGCACTTTTTATGTTGTAGTTTGTTTA 57.696 29.630 0.00 0.00 0.00 2.01
3321 7389 9.206870 AGTTTGTTTAATTGATATGGTTGCTTG 57.793 29.630 0.00 0.00 0.00 4.01
3371 7439 3.944015 CTGAGTTCATCAACTTCCCCATC 59.056 47.826 0.00 0.00 43.37 3.51
3417 7485 1.241165 TGTTGAAGTGCCAGCTGATG 58.759 50.000 17.39 0.00 0.00 3.07
3418 7486 1.202794 TGTTGAAGTGCCAGCTGATGA 60.203 47.619 17.39 0.00 0.00 2.92
3419 7487 1.467734 GTTGAAGTGCCAGCTGATGAG 59.532 52.381 17.39 0.00 0.00 2.90
3455 7523 7.875554 AGTGAAGAAGAGGAATCAAGTAAGTTC 59.124 37.037 0.00 0.00 0.00 3.01
3457 7525 7.875041 TGAAGAAGAGGAATCAAGTAAGTTCTG 59.125 37.037 0.00 0.00 0.00 3.02
3459 7527 5.489792 AGAGGAATCAAGTAAGTTCTGCA 57.510 39.130 0.00 0.00 0.00 4.41
3476 7544 6.435277 AGTTCTGCACTCAATGTTATCCATTT 59.565 34.615 0.00 0.00 41.93 2.32
3508 7576 0.730834 GTTGTGTTGTGTGCGTGCAA 60.731 50.000 0.00 0.00 0.00 4.08
3522 7590 2.168384 CGTGCAATCACTAACGCATTG 58.832 47.619 0.00 0.00 40.99 2.82
3547 7615 6.037610 GTCCATTATTTTGTAGCCACAGAGAG 59.962 42.308 0.00 0.00 35.67 3.20
3716 7784 4.515567 GCAAAGTTTTACCACTCACTAGCT 59.484 41.667 0.00 0.00 0.00 3.32
3728 7796 5.828859 CCACTCACTAGCTAAGGTACATACT 59.171 44.000 0.00 0.00 0.00 2.12
3973 8041 6.116806 TGCTAACAAGTCAAACCTCAAGTTA 58.883 36.000 0.00 0.00 37.88 2.24
4021 8089 6.585416 TGATGAATTCGATGATCTTCTTCCA 58.415 36.000 6.99 0.00 0.00 3.53
4067 8135 6.986817 GGTACTGCATATTGACTTGTACAGAT 59.013 38.462 0.00 0.00 32.89 2.90
4108 8177 5.181245 GCTCCACTTGCACAGATTAACTTAA 59.819 40.000 0.00 0.00 0.00 1.85
4109 8178 6.554334 TCCACTTGCACAGATTAACTTAAC 57.446 37.500 0.00 0.00 0.00 2.01
4110 8179 6.296026 TCCACTTGCACAGATTAACTTAACT 58.704 36.000 0.00 0.00 0.00 2.24
4111 8180 7.446769 TCCACTTGCACAGATTAACTTAACTA 58.553 34.615 0.00 0.00 0.00 2.24
4322 8391 5.175388 GGTAACTATGGTTTCTGGGAAGT 57.825 43.478 0.00 0.00 36.92 3.01
4325 8394 6.150641 GGTAACTATGGTTTCTGGGAAGTTTC 59.849 42.308 0.00 0.00 36.92 2.78
4337 8406 2.687935 GGGAAGTTTCAAGTCACTTGCA 59.312 45.455 13.15 0.00 41.72 4.08
4528 8597 4.560128 TCTGAGATTTGAGAGGTTTGTCG 58.440 43.478 0.00 0.00 0.00 4.35
4550 8619 5.523552 TCGTGCATTCTGTATTCCAGTATTG 59.476 40.000 0.00 0.00 42.19 1.90
4571 8640 7.700322 ATTGTTCATGCTGTAGTTCTATACG 57.300 36.000 0.00 0.00 0.00 3.06
4590 8659 1.731700 CTGGGGCGCAGAATTGATG 59.268 57.895 25.76 0.00 0.00 3.07
4624 8700 2.486982 CAGTTCCAAGTCAGATGGCAAG 59.513 50.000 0.00 0.00 37.88 4.01
4630 8706 1.531423 AGTCAGATGGCAAGCTTGTG 58.469 50.000 26.55 16.62 0.00 3.33
4855 8931 1.722011 ATTTGTCCCGCTTACTCACG 58.278 50.000 0.00 0.00 0.00 4.35
4871 8947 4.844267 ACTCACGTATGCACTTTTGAAAC 58.156 39.130 0.00 0.00 0.00 2.78
4969 9059 6.963322 ACAGCATTTTAGGAGATTTAGGACT 58.037 36.000 0.00 0.00 0.00 3.85
5102 9202 0.178950 TCAGAGTGTCAGGAGCTGGT 60.179 55.000 0.00 0.00 31.51 4.00
5103 9203 1.075536 TCAGAGTGTCAGGAGCTGGTA 59.924 52.381 0.00 0.00 31.51 3.25
5128 9228 0.890683 GTGCTAGGCTTGGCATTTGT 59.109 50.000 10.68 0.00 43.05 2.83
5150 9250 9.742144 TTTGTAGCAGGTTTAAATGGTAATCTA 57.258 29.630 3.04 0.00 31.74 1.98
5180 9280 6.765403 AGCTTGTGAAGTAACATAGTAACCA 58.235 36.000 0.00 0.00 0.00 3.67
5348 9448 0.039074 AGTCGTTCAAGGAGCTGACG 60.039 55.000 0.00 0.00 0.00 4.35
5426 9526 3.297620 CTGCACAACACCCCCTGC 61.298 66.667 0.00 0.00 0.00 4.85
5529 9629 4.868900 CGTACATGCGCGGCAAGC 62.869 66.667 8.83 0.00 43.62 4.01
5597 9697 2.526873 AAGGTCGCCCAGGACAGT 60.527 61.111 0.00 0.00 38.70 3.55
5600 9700 2.048127 GTCGCCCAGGACAGTGAC 60.048 66.667 0.00 0.00 36.91 3.67
5624 9727 5.278364 CGTAAGTACAGCCTTCCCTGTATAG 60.278 48.000 5.45 0.00 46.53 1.31
5626 9729 1.879575 ACAGCCTTCCCTGTATAGCA 58.120 50.000 0.00 0.00 43.86 3.49
5645 9748 3.229552 GCACGATTTTTGCTCTCTGAAC 58.770 45.455 0.00 0.00 37.00 3.18
5782 9885 2.355115 GGGTTCAACCTGCCGGAT 59.645 61.111 5.05 0.00 38.64 4.18
5797 9900 1.369091 CGGATCCCAAGGACTTTGCG 61.369 60.000 6.06 0.00 32.98 4.85
5845 9948 2.765807 CTGGACCTGAGCCCCGAT 60.766 66.667 0.00 0.00 0.00 4.18
5890 9996 2.444895 GAGGAGCCCGAGGTGGAT 60.445 66.667 0.00 0.00 42.00 3.41
5891 9997 2.765807 AGGAGCCCGAGGTGGATG 60.766 66.667 0.00 0.00 42.00 3.51
5892 9998 2.764128 GGAGCCCGAGGTGGATGA 60.764 66.667 0.00 0.00 42.00 2.92
5961 10067 1.678269 GACGAGCTGTAGTTGCTGCG 61.678 60.000 0.00 0.00 41.30 5.18
5995 10104 4.123506 GCCCATTTAGCTCTCAGTAGAAC 58.876 47.826 0.00 0.00 0.00 3.01
6088 10204 4.870221 ACGAGGTTTTTGTCAGTGTAAC 57.130 40.909 0.00 0.00 0.00 2.50
6094 10210 5.292589 AGGTTTTTGTCAGTGTAACGTACTG 59.707 40.000 10.15 10.15 45.86 2.74
6095 10211 5.063817 GGTTTTTGTCAGTGTAACGTACTGT 59.936 40.000 14.84 0.00 45.86 3.55
6096 10212 6.255453 GGTTTTTGTCAGTGTAACGTACTGTA 59.745 38.462 14.84 5.15 45.86 2.74
6097 10213 6.810888 TTTTGTCAGTGTAACGTACTGTAC 57.189 37.500 14.84 7.90 45.86 2.90
6098 10214 4.488126 TGTCAGTGTAACGTACTGTACC 57.512 45.455 14.84 6.87 45.86 3.34
6099 10215 4.136796 TGTCAGTGTAACGTACTGTACCT 58.863 43.478 14.84 2.85 45.86 3.08
6100 10216 5.304778 TGTCAGTGTAACGTACTGTACCTA 58.695 41.667 14.84 1.94 45.86 3.08
6101 10217 5.409520 TGTCAGTGTAACGTACTGTACCTAG 59.590 44.000 14.84 1.54 45.86 3.02
6103 10219 5.997746 TCAGTGTAACGTACTGTACCTAGTT 59.002 40.000 14.84 12.17 45.86 2.24
6106 10223 7.113965 CAGTGTAACGTACTGTACCTAGTTTTG 59.886 40.741 12.08 0.00 45.86 2.44
6111 10228 7.848223 ACGTACTGTACCTAGTTTTGTTTTT 57.152 32.000 12.08 0.00 32.19 1.94
6168 10285 1.578206 GCCTGGTTTCAGTCCGAAGC 61.578 60.000 0.00 0.00 39.31 3.86
6201 10326 3.525268 ACTTGCTGTTTTGGTTTCCTG 57.475 42.857 0.00 0.00 0.00 3.86
6202 10327 2.204237 CTTGCTGTTTTGGTTTCCTGC 58.796 47.619 0.00 0.00 0.00 4.85
6223 10348 3.552684 GCCAGTGGTGTACGTAGTTACAA 60.553 47.826 11.74 0.00 37.78 2.41
6256 10381 2.174360 GGGTTACGAAGGTAGTCTGGT 58.826 52.381 0.00 0.00 0.00 4.00
6257 10382 2.094338 GGGTTACGAAGGTAGTCTGGTG 60.094 54.545 0.00 0.00 0.00 4.17
6262 10387 2.165167 CGAAGGTAGTCTGGTGGTACA 58.835 52.381 0.00 0.00 0.00 2.90
6271 10396 5.211174 AGTCTGGTGGTACAGAGTTTTAC 57.789 43.478 0.00 0.00 46.25 2.01
6273 10398 3.968649 TCTGGTGGTACAGAGTTTTACCA 59.031 43.478 0.00 0.00 44.52 3.25
6286 10411 6.016555 AGAGTTTTACCAATGCAGGGTTATT 58.983 36.000 17.04 2.36 39.85 1.40
6423 10561 8.186985 TGGATCCTATAATCTAGGAATGGACTT 58.813 37.037 14.23 0.00 45.83 3.01
6437 10575 5.048713 GGAATGGACTTGGTTTACAGAACTG 60.049 44.000 0.00 0.00 0.00 3.16
6469 10620 7.261325 ACAATGCACAAGTACATGTTTAACAA 58.739 30.769 2.30 0.00 0.00 2.83
6540 10843 5.220777 GGAACTCATGAAAAACTTGTGACGA 60.221 40.000 0.00 0.00 0.00 4.20
6605 10908 0.251354 ATGCAGAACACGAGCCTCAT 59.749 50.000 0.00 0.00 0.00 2.90
6622 10925 1.827344 TCATCCAGAGCAACACGATCT 59.173 47.619 0.00 0.00 42.52 2.75
6623 10926 2.234661 TCATCCAGAGCAACACGATCTT 59.765 45.455 0.00 0.00 38.68 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.066215 TGTTGTCATCACCCTCATCCG 60.066 52.381 0.00 0.00 0.00 4.18
12 13 6.949352 AATTATGTTGTCATCACCCTCATC 57.051 37.500 0.00 0.00 35.70 2.92
28 29 7.203910 GTGGACATCTCTCGACTTAATTATGT 58.796 38.462 3.79 3.79 0.00 2.29
67 68 2.433604 TCTGTCAGATCATCCAAGGCTC 59.566 50.000 0.00 0.00 0.00 4.70
142 259 3.243602 GGCCGGTTTACATTTTCAACACT 60.244 43.478 1.90 0.00 0.00 3.55
221 338 0.746063 CAAGAACCAACAAGCAGCCA 59.254 50.000 0.00 0.00 0.00 4.75
340 504 3.378742 ACTGACAGAGAGCTACGTATTGG 59.621 47.826 10.08 0.00 0.00 3.16
342 506 6.017770 GTGATACTGACAGAGAGCTACGTATT 60.018 42.308 10.08 0.00 0.00 1.89
344 508 4.809958 GTGATACTGACAGAGAGCTACGTA 59.190 45.833 10.08 0.00 0.00 3.57
346 510 3.874543 AGTGATACTGACAGAGAGCTACG 59.125 47.826 10.08 0.00 0.00 3.51
381 3468 9.035890 TCCAGTCATATACGATCCTCAAATAAT 57.964 33.333 0.00 0.00 0.00 1.28
399 3910 1.356124 AGCACAACTCCTCCAGTCAT 58.644 50.000 0.00 0.00 32.30 3.06
401 3912 1.346068 AGAAGCACAACTCCTCCAGTC 59.654 52.381 0.00 0.00 32.30 3.51
469 4237 3.635331 TCGGACGTCAGAGTTAAAGTTG 58.365 45.455 18.91 0.00 0.00 3.16
525 4302 3.506743 TTTGGGCTGGCCTGGTCA 61.507 61.111 21.72 0.00 36.10 4.02
526 4303 2.991540 GTTTGGGCTGGCCTGGTC 60.992 66.667 21.72 1.86 36.10 4.02
527 4304 4.974721 CGTTTGGGCTGGCCTGGT 62.975 66.667 21.72 0.00 36.10 4.00
546 4323 2.757099 CCAAGGGCTGTGATGGGC 60.757 66.667 0.00 0.00 0.00 5.36
657 4434 0.392998 GTGTGATTGGTGCGGGATCT 60.393 55.000 0.00 0.00 0.00 2.75
658 4435 1.376609 GGTGTGATTGGTGCGGGATC 61.377 60.000 0.00 0.00 0.00 3.36
680 4457 2.828877 CTGAAGGGTTTGACACGTGTA 58.171 47.619 23.44 3.61 0.00 2.90
681 4458 1.663695 CTGAAGGGTTTGACACGTGT 58.336 50.000 23.64 23.64 0.00 4.49
1128 5151 2.039624 ACCCGCAGAGATCACCCT 59.960 61.111 0.00 0.00 0.00 4.34
1208 5231 2.023404 TGATAAGCTACCTCCTGGGACA 60.023 50.000 0.00 0.00 38.76 4.02
1210 5233 2.247635 ACTGATAAGCTACCTCCTGGGA 59.752 50.000 0.00 0.00 38.76 4.37
1335 5367 2.587956 TCTACACGAACGGATCAAACG 58.412 47.619 0.00 0.00 37.36 3.60
1368 5400 2.507452 CATCAGAGATGGCGCCCA 59.493 61.111 26.77 12.96 38.19 5.36
1428 5460 2.729479 ATCGGGACAGAGCCAGCAG 61.729 63.158 0.00 0.00 0.00 4.24
1496 5528 1.654105 GTAATGTCGAACACGGAGCAG 59.346 52.381 0.00 0.00 0.00 4.24
1499 5531 2.259618 CCAGTAATGTCGAACACGGAG 58.740 52.381 0.00 0.00 0.00 4.63
1523 5555 3.125316 CACAACGGATCTAAGAACCAAGC 59.875 47.826 0.00 0.00 0.00 4.01
1527 5559 3.604875 TCCACAACGGATCTAAGAACC 57.395 47.619 0.00 0.00 39.64 3.62
1651 5684 0.462759 AGCAGCACTAGATTTCCGCC 60.463 55.000 0.00 0.00 0.00 6.13
1674 5707 2.656002 TGGTAGAGCGCTAGATCAGTT 58.344 47.619 11.50 0.00 34.73 3.16
1698 5731 7.784470 AGAGTTTGAATTCAGTAGGAGTACT 57.216 36.000 8.41 0.00 40.38 2.73
1699 5732 7.873505 ACAAGAGTTTGAATTCAGTAGGAGTAC 59.126 37.037 8.41 0.00 37.73 2.73
1705 5738 9.141400 GTAGGTACAAGAGTTTGAATTCAGTAG 57.859 37.037 8.41 0.00 37.73 2.57
1708 5741 9.877178 ATAGTAGGTACAAGAGTTTGAATTCAG 57.123 33.333 8.41 0.00 37.73 3.02
1720 5754 7.999545 AGATTACAGCAGATAGTAGGTACAAGA 59.000 37.037 0.00 0.00 0.00 3.02
1742 5776 9.261180 CTCGAATATGTTGTATTGGTGTAGATT 57.739 33.333 0.00 0.00 0.00 2.40
1743 5777 7.385205 GCTCGAATATGTTGTATTGGTGTAGAT 59.615 37.037 0.00 0.00 0.00 1.98
1744 5778 6.700081 GCTCGAATATGTTGTATTGGTGTAGA 59.300 38.462 0.00 0.00 0.00 2.59
1745 5779 6.701841 AGCTCGAATATGTTGTATTGGTGTAG 59.298 38.462 0.00 0.00 0.00 2.74
1753 5787 6.818644 AGACAAACAGCTCGAATATGTTGTAT 59.181 34.615 9.52 2.39 37.24 2.29
1758 5792 4.820897 TCAGACAAACAGCTCGAATATGT 58.179 39.130 0.00 0.00 0.00 2.29
1769 5803 3.688185 CACATCCAGGATCAGACAAACAG 59.312 47.826 0.00 0.00 0.00 3.16
1785 5819 0.107508 TCTTAGCTGCAGGCACATCC 60.108 55.000 17.12 0.00 44.79 3.51
1845 5880 3.173965 CTCCTCTACCTTGGGAAAGTCA 58.826 50.000 0.00 0.00 0.00 3.41
1930 5965 1.144057 ATTGGCGTCGATCAGGGAC 59.856 57.895 0.00 0.00 0.00 4.46
1932 5967 1.889105 CCATTGGCGTCGATCAGGG 60.889 63.158 0.00 0.00 0.00 4.45
1965 6000 6.353404 TGGTATCAGTACAGAATGACAACA 57.647 37.500 0.00 0.00 39.69 3.33
1970 6005 7.423844 AAGTCATGGTATCAGTACAGAATGA 57.576 36.000 0.00 0.00 39.69 2.57
1986 6021 3.495193 CTTCGCACATCAAAAGTCATGG 58.505 45.455 0.00 0.00 0.00 3.66
2059 6094 1.079543 CACCTCTGCCTGGAACTCG 60.080 63.158 0.00 0.00 0.00 4.18
2071 6106 1.270414 CCATGAGCCTGGACACCTCT 61.270 60.000 0.00 0.00 38.69 3.69
2491 6530 6.518200 GCAATGGTTCCAAGGTTCTTAATCAA 60.518 38.462 0.00 0.00 0.00 2.57
2841 6880 1.846007 AACACAAGGGCACTGTTTGA 58.154 45.000 0.00 0.00 0.00 2.69
2842 6881 2.671130 AAACACAAGGGCACTGTTTG 57.329 45.000 4.17 0.00 36.87 2.93
2843 6882 3.511934 TGTTAAACACAAGGGCACTGTTT 59.488 39.130 9.46 9.46 40.40 2.83
2845 6884 2.687935 CTGTTAAACACAAGGGCACTGT 59.312 45.455 0.00 0.00 33.87 3.55
2848 6887 2.949644 AGTCTGTTAAACACAAGGGCAC 59.050 45.455 0.00 0.00 33.87 5.01
2854 6893 4.150897 AGGCTCAGTCTGTTAAACACAA 57.849 40.909 0.00 0.00 33.87 3.33
2857 6896 4.695455 GCATAAGGCTCAGTCTGTTAAACA 59.305 41.667 0.00 0.00 40.25 2.83
2858 6897 5.223225 GCATAAGGCTCAGTCTGTTAAAC 57.777 43.478 0.00 0.00 40.25 2.01
2877 6920 4.129380 GGCAGAAAAAGAACCAAAAGCAT 58.871 39.130 0.00 0.00 0.00 3.79
2879 6922 3.797039 AGGCAGAAAAAGAACCAAAAGC 58.203 40.909 0.00 0.00 0.00 3.51
2890 6933 4.032960 TGCATAGAGGAAGGCAGAAAAA 57.967 40.909 0.00 0.00 0.00 1.94
2893 6936 3.939740 ATTGCATAGAGGAAGGCAGAA 57.060 42.857 0.00 0.00 37.59 3.02
2894 6937 3.939740 AATTGCATAGAGGAAGGCAGA 57.060 42.857 0.00 0.00 37.59 4.26
2895 6938 4.643784 AGAAAATTGCATAGAGGAAGGCAG 59.356 41.667 0.00 0.00 37.59 4.85
2902 6945 7.373493 ACAGAAACAAGAAAATTGCATAGAGG 58.627 34.615 0.00 0.00 0.00 3.69
2911 6954 8.658609 CAATGTCACAACAGAAACAAGAAAATT 58.341 29.630 0.00 0.00 39.20 1.82
2923 6966 2.161855 GGGATGCAATGTCACAACAGA 58.838 47.619 0.00 0.00 39.20 3.41
2938 6981 6.127394 CCACACATATCTATCAGAGAGGGATG 60.127 46.154 0.00 0.00 37.70 3.51
2954 6997 1.212935 GCCTTGGACTCCCACACATAT 59.787 52.381 0.00 0.00 43.41 1.78
2972 7015 2.462456 TAGCGAATGATCCATCAGCC 57.538 50.000 0.00 0.00 40.64 4.85
2996 7039 2.484947 GGGTTCGTTCCATGTATCCTCC 60.485 54.545 0.00 0.00 0.00 4.30
3117 7160 9.724839 GAAAGTATAAACTGCACTAACAACAAA 57.275 29.630 0.00 0.00 35.62 2.83
3155 7198 7.630082 TGGGTCTTAAGTAGAAATACAGCAAT 58.370 34.615 1.63 0.00 33.81 3.56
3174 7217 5.946377 GGTAAAATTCAGATCAACTGGGTCT 59.054 40.000 0.00 0.00 45.76 3.85
3175 7218 5.946377 AGGTAAAATTCAGATCAACTGGGTC 59.054 40.000 0.00 0.00 45.76 4.46
3176 7219 5.711976 CAGGTAAAATTCAGATCAACTGGGT 59.288 40.000 0.00 0.00 45.76 4.51
3179 7222 7.533426 CCTTCAGGTAAAATTCAGATCAACTG 58.467 38.462 0.00 0.00 46.97 3.16
3180 7223 7.693969 CCTTCAGGTAAAATTCAGATCAACT 57.306 36.000 0.00 0.00 0.00 3.16
3197 7240 4.653341 AGACCTATTGATGAGACCTTCAGG 59.347 45.833 0.00 0.00 39.68 3.86
3198 7241 5.867903 AGACCTATTGATGAGACCTTCAG 57.132 43.478 0.00 0.00 39.68 3.02
3199 7242 6.352222 GGAAAGACCTATTGATGAGACCTTCA 60.352 42.308 0.00 0.00 36.53 3.02
3200 7243 6.052360 GGAAAGACCTATTGATGAGACCTTC 58.948 44.000 0.00 0.00 35.41 3.46
3201 7244 5.395768 CGGAAAGACCTATTGATGAGACCTT 60.396 44.000 0.00 0.00 36.31 3.50
3202 7245 4.100189 CGGAAAGACCTATTGATGAGACCT 59.900 45.833 0.00 0.00 36.31 3.85
3203 7246 4.141914 ACGGAAAGACCTATTGATGAGACC 60.142 45.833 0.00 0.00 36.31 3.85
3204 7247 5.012328 ACGGAAAGACCTATTGATGAGAC 57.988 43.478 0.00 0.00 36.31 3.36
3205 7248 4.099573 GGACGGAAAGACCTATTGATGAGA 59.900 45.833 0.00 0.00 36.31 3.27
3206 7249 4.141937 TGGACGGAAAGACCTATTGATGAG 60.142 45.833 0.00 0.00 35.66 2.90
3207 7250 3.772572 TGGACGGAAAGACCTATTGATGA 59.227 43.478 0.00 0.00 35.66 2.92
3208 7251 4.137116 TGGACGGAAAGACCTATTGATG 57.863 45.455 0.00 0.00 35.66 3.07
3212 7280 4.225267 AGACATTGGACGGAAAGACCTATT 59.775 41.667 0.00 0.00 35.66 1.73
3224 7292 5.996219 TGTTTCAAATACAGACATTGGACG 58.004 37.500 0.00 0.00 0.00 4.79
3272 7340 7.777095 ACTACAACATAAAAAGTGCCTCAAAA 58.223 30.769 0.00 0.00 0.00 2.44
3293 7361 9.855021 AGCAACCATATCAATTAAACAAACTAC 57.145 29.630 0.00 0.00 0.00 2.73
3295 7363 9.206870 CAAGCAACCATATCAATTAAACAAACT 57.793 29.630 0.00 0.00 0.00 2.66
3296 7364 8.987890 ACAAGCAACCATATCAATTAAACAAAC 58.012 29.630 0.00 0.00 0.00 2.93
3297 7365 9.553064 AACAAGCAACCATATCAATTAAACAAA 57.447 25.926 0.00 0.00 0.00 2.83
3298 7366 9.553064 AAACAAGCAACCATATCAATTAAACAA 57.447 25.926 0.00 0.00 0.00 2.83
3299 7367 9.553064 AAAACAAGCAACCATATCAATTAAACA 57.447 25.926 0.00 0.00 0.00 2.83
3304 7372 6.767456 TGGAAAACAAGCAACCATATCAATT 58.233 32.000 0.00 0.00 0.00 2.32
3305 7373 6.357579 TGGAAAACAAGCAACCATATCAAT 57.642 33.333 0.00 0.00 0.00 2.57
3308 7376 4.462483 TCCTGGAAAACAAGCAACCATATC 59.538 41.667 0.00 0.00 0.00 1.63
3312 7380 1.754226 GTCCTGGAAAACAAGCAACCA 59.246 47.619 0.00 0.00 0.00 3.67
3326 7394 5.246429 AGAGTACTTCTTTACCAAGTCCTGG 59.754 44.000 0.00 0.00 41.80 4.45
3338 7406 7.731054 AGTTGATGAACTCAGAGTACTTCTTT 58.269 34.615 2.64 0.00 38.01 2.52
3371 7439 1.202879 TCCTTGGTTGCCCACAAGTAG 60.203 52.381 9.54 0.00 41.67 2.57
3395 7463 1.202794 TCAGCTGGCACTTCAACATCA 60.203 47.619 15.13 0.00 0.00 3.07
3417 7485 5.413309 TCTTCTTCACTTGATTCCTCCTC 57.587 43.478 0.00 0.00 0.00 3.71
3418 7486 4.224818 CCTCTTCTTCACTTGATTCCTCCT 59.775 45.833 0.00 0.00 0.00 3.69
3419 7487 4.223923 TCCTCTTCTTCACTTGATTCCTCC 59.776 45.833 0.00 0.00 0.00 4.30
3476 7544 5.126869 ACACAACACAACATGATCCAGAAAA 59.873 36.000 0.00 0.00 0.00 2.29
3482 7550 2.664916 GCACACAACACAACATGATCC 58.335 47.619 0.00 0.00 0.00 3.36
3489 7557 0.730834 TTGCACGCACACAACACAAC 60.731 50.000 0.00 0.00 0.00 3.32
3494 7562 2.494550 GTGATTGCACGCACACAAC 58.505 52.632 12.02 0.00 34.94 3.32
3508 7576 6.942532 AATAATGGACAATGCGTTAGTGAT 57.057 33.333 0.00 0.00 0.00 3.06
3522 7590 5.880332 TCTCTGTGGCTACAAAATAATGGAC 59.120 40.000 3.88 0.00 36.14 4.02
3547 7615 3.426615 TCTGTCTCTTCTTCCTCTGTCC 58.573 50.000 0.00 0.00 0.00 4.02
3605 7673 6.049955 TCCCATTCAGTAGTAGTTTCCTTG 57.950 41.667 0.00 0.00 0.00 3.61
3611 7679 5.026790 AGAAGCTCCCATTCAGTAGTAGTT 58.973 41.667 0.00 0.00 0.00 2.24
3614 7682 4.610333 TCAGAAGCTCCCATTCAGTAGTA 58.390 43.478 0.00 0.00 0.00 1.82
3662 7730 0.035056 CAGTAACCTCCTTGGGGCTG 60.035 60.000 0.00 0.00 41.11 4.85
3664 7732 0.696501 TTCAGTAACCTCCTTGGGGC 59.303 55.000 0.00 0.00 41.11 5.80
3741 7809 9.372189 AGCTTGGCATTTTCTCCTATAAATTAT 57.628 29.630 0.00 0.00 0.00 1.28
3973 8041 8.772250 TCAGAGATGAAAACCCTTCTAACATAT 58.228 33.333 0.00 0.00 0.00 1.78
4021 8089 5.140454 ACCATCAAAAAGCTGAGGTACTTT 58.860 37.500 0.00 0.00 41.55 2.66
4074 8143 1.068055 GCAAGTGGAGCATCACAAAGG 60.068 52.381 11.17 0.73 39.93 3.11
4110 8179 9.249053 CCCTAGAGAGAGAAATAGCATGTTATA 57.751 37.037 2.17 0.00 0.00 0.98
4111 8180 7.732593 ACCCTAGAGAGAGAAATAGCATGTTAT 59.267 37.037 0.00 0.00 0.00 1.89
4308 8377 3.951680 GACTTGAAACTTCCCAGAAACCA 59.048 43.478 0.00 0.00 0.00 3.67
4325 8394 7.962373 TCGTCATAAATTATTGCAAGTGACTTG 59.038 33.333 20.42 20.42 43.57 3.16
4550 8619 5.174035 CAGCGTATAGAACTACAGCATGAAC 59.826 44.000 0.00 0.00 39.69 3.18
4571 8640 2.123428 ATCAATTCTGCGCCCCAGC 61.123 57.895 4.18 0.00 41.50 4.85
4579 8648 6.476380 TGAAACAGACAAAACATCAATTCTGC 59.524 34.615 0.00 0.00 34.98 4.26
4590 8659 5.709966 ACTTGGAACTGAAACAGACAAAAC 58.290 37.500 5.76 0.00 35.18 2.43
4624 8700 2.191128 ACTCATCAAGGGACACAAGC 57.809 50.000 0.00 0.00 0.00 4.01
4899 8975 7.120579 TGTGATCTTCAGTAAAAACTGTGTTGT 59.879 33.333 5.51 0.00 38.75 3.32
4900 8976 7.471721 TGTGATCTTCAGTAAAAACTGTGTTG 58.528 34.615 5.51 0.00 38.75 3.33
4901 8977 7.624360 TGTGATCTTCAGTAAAAACTGTGTT 57.376 32.000 5.51 0.00 38.75 3.32
4902 8978 7.120579 TGTTGTGATCTTCAGTAAAAACTGTGT 59.879 33.333 5.51 0.00 38.75 3.72
4969 9059 3.625313 TGTGCGTTCAACTCAGAATTTGA 59.375 39.130 0.00 0.00 0.00 2.69
5072 9172 1.302033 CACTCTGACAGGGGTGTGC 60.302 63.158 7.39 0.00 0.00 4.57
5102 9202 2.159382 GCCAAGCCTAGCACAAAGTTA 58.841 47.619 0.00 0.00 0.00 2.24
5103 9203 0.961753 GCCAAGCCTAGCACAAAGTT 59.038 50.000 0.00 0.00 0.00 2.66
5180 9280 7.398024 AGTAGATAACCTGCAAGAAGAAATGT 58.602 34.615 0.00 0.00 34.07 2.71
5348 9448 1.002011 GGCCTTCTTCCACCAGTCC 60.002 63.158 0.00 0.00 0.00 3.85
5529 9629 1.522569 GGTTGATCTCCAGGACCCG 59.477 63.158 0.00 0.00 0.00 5.28
5597 9697 1.547372 GGGAAGGCTGTACTTACGTCA 59.453 52.381 0.00 0.00 31.83 4.35
5600 9700 1.549170 ACAGGGAAGGCTGTACTTACG 59.451 52.381 0.00 0.00 31.83 3.18
5608 9708 1.539065 CGTGCTATACAGGGAAGGCTG 60.539 57.143 0.00 0.00 0.00 4.85
5624 9727 3.229552 GTTCAGAGAGCAAAAATCGTGC 58.770 45.455 0.00 0.00 42.55 5.34
5626 9729 2.096218 GCGTTCAGAGAGCAAAAATCGT 60.096 45.455 0.00 0.00 0.00 3.73
5797 9900 1.009900 CGACCGGTAGATGCTCGAC 60.010 63.158 7.34 0.00 0.00 4.20
5890 9996 1.544825 CCTTGCCCGACTCCTTCTCA 61.545 60.000 0.00 0.00 0.00 3.27
5891 9997 1.219393 CCTTGCCCGACTCCTTCTC 59.781 63.158 0.00 0.00 0.00 2.87
5892 9998 2.960688 GCCTTGCCCGACTCCTTCT 61.961 63.158 0.00 0.00 0.00 2.85
5961 10067 2.044123 AAATGGGCGATGAGAAGACC 57.956 50.000 0.00 0.00 0.00 3.85
5995 10104 3.192001 CCATCACATTTCCAGTCCAACAG 59.808 47.826 0.00 0.00 0.00 3.16
6061 10177 4.062991 ACTGACAAAAACCTCGTATCACC 58.937 43.478 0.00 0.00 0.00 4.02
6135 10252 5.046448 TGAAACCAGGCATGCTAATTTGAAT 60.046 36.000 18.92 0.00 0.00 2.57
6168 10285 2.747446 ACAGCAAGTATACAAAAGGGCG 59.253 45.455 5.50 0.00 0.00 6.13
6201 10326 2.030007 TGTAACTACGTACACCACTGGC 60.030 50.000 0.00 0.00 0.00 4.85
6202 10327 3.921119 TGTAACTACGTACACCACTGG 57.079 47.619 0.00 0.00 0.00 4.00
6223 10348 6.666113 ACCTTCGTAACCCCATTATTCATTTT 59.334 34.615 0.00 0.00 0.00 1.82
6256 10381 4.720046 TGCATTGGTAAAACTCTGTACCA 58.280 39.130 0.00 0.00 46.35 3.25
6257 10382 4.156008 CCTGCATTGGTAAAACTCTGTACC 59.844 45.833 0.00 0.00 40.28 3.34
6262 10387 3.525800 ACCCTGCATTGGTAAAACTCT 57.474 42.857 6.28 0.00 33.26 3.24
6271 10396 3.222603 GTCCCTAATAACCCTGCATTGG 58.777 50.000 1.00 1.00 0.00 3.16
6273 10398 3.785887 TCTGTCCCTAATAACCCTGCATT 59.214 43.478 0.00 0.00 0.00 3.56
6423 10561 5.417811 TGTAACGTTCAGTTCTGTAAACCA 58.582 37.500 2.82 0.00 43.06 3.67
6437 10575 5.085636 TGTACTTGTGCATTGTAACGTTC 57.914 39.130 2.82 0.00 0.00 3.95
6505 10656 1.264749 ATGAGTTCCGTGCCAGCCTA 61.265 55.000 0.00 0.00 0.00 3.93
6540 10843 6.183360 TGCTGATTTGTTCACCAAAGGTTTAT 60.183 34.615 0.00 0.00 45.79 1.40
6605 10908 1.338105 CCAAGATCGTGTTGCTCTGGA 60.338 52.381 7.88 0.00 0.00 3.86
6622 10925 5.152623 AGATTGATCTTCACTTCGTCCAA 57.847 39.130 0.00 0.00 31.97 3.53
6623 10926 4.220602 TGAGATTGATCTTCACTTCGTCCA 59.779 41.667 0.00 0.00 37.25 4.02
6741 11044 3.405831 CAACTCTTGCATGACCTCAAGA 58.594 45.455 11.48 11.48 44.33 3.02


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

AutoCloner maintained by Alex Coulton.