Multiple sequence alignment - TraesCS2D01G121700

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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 TraesCS2D01G121700 chr2D 100.000 3638 0 0 1 3638 70822823 70819186 0.000000e+00 6719.0
1 TraesCS2D01G121700 chr2D 82.773 238 30 8 2568 2803 71205356 71205584 6.160000e-48 202.0
2 TraesCS2D01G121700 chr2D 84.264 197 24 6 2568 2761 71385403 71385595 6.200000e-43 185.0
3 TraesCS2D01G121700 chr2D 83.756 197 25 6 2568 2761 71259247 71259439 2.890000e-41 180.0
4 TraesCS2D01G121700 chr2D 81.116 233 22 8 2926 3158 71207578 71207788 2.250000e-37 167.0
5 TraesCS2D01G121700 chr2D 86.923 130 17 0 3029 3158 71263320 71263449 2.930000e-31 147.0
6 TraesCS2D01G121700 chr2D 87.903 124 13 2 3035 3158 71389333 71389454 1.050000e-30 145.0
7 TraesCS2D01G121700 chr2D 83.871 124 14 3 985 1108 543516958 543517075 2.970000e-21 113.0
8 TraesCS2D01G121700 chr2B 93.176 2462 124 20 1186 3638 107118493 107116067 0.000000e+00 3576.0
9 TraesCS2D01G121700 chr2B 82.700 237 30 7 2559 2793 107500216 107500443 2.220000e-47 200.0
10 TraesCS2D01G121700 chr2B 81.513 238 35 6 2568 2803 107526417 107526647 1.720000e-43 187.0
11 TraesCS2D01G121700 chr2B 76.834 259 37 11 2898 3156 107500487 107500722 1.370000e-24 124.0
12 TraesCS2D01G121700 chr2B 81.416 113 15 3 999 1111 676758871 676758765 1.800000e-13 87.9
13 TraesCS2D01G121700 chr2A 93.645 1432 58 19 1052 2475 70184130 70182724 0.000000e+00 2109.0
14 TraesCS2D01G121700 chr2A 90.976 820 30 15 2565 3379 70182725 70181945 0.000000e+00 1064.0
15 TraesCS2D01G121700 chr2A 86.322 987 89 25 1 968 70185185 70184226 0.000000e+00 1033.0
16 TraesCS2D01G121700 chr2A 79.136 810 137 19 1826 2619 70187231 70188024 6.920000e-147 531.0
17 TraesCS2D01G121700 chr2A 79.139 302 37 12 2859 3158 70188266 70188543 6.200000e-43 185.0
18 TraesCS2D01G121700 chr2A 80.000 245 30 10 2559 2793 70188011 70188246 2.910000e-36 163.0
19 TraesCS2D01G121700 chr2A 80.357 224 35 5 1183 1405 70186672 70186887 1.050000e-35 161.0
20 TraesCS2D01G121700 chr4A 83.824 204 28 4 2 205 11192634 11192832 4.800000e-44 189.0
21 TraesCS2D01G121700 chr4A 84.314 102 16 0 3390 3491 710754868 710754767 2.310000e-17 100.0
22 TraesCS2D01G121700 chr6B 91.071 112 10 0 151 262 580305534 580305423 6.290000e-33 152.0
23 TraesCS2D01G121700 chr6B 78.659 164 26 6 3378 3534 78296165 78296004 2.310000e-17 100.0
24 TraesCS2D01G121700 chr6B 78.750 160 27 7 3387 3540 156256557 156256399 2.310000e-17 100.0
25 TraesCS2D01G121700 chr6B 83.784 111 9 8 1013 1120 661928360 661928464 2.990000e-16 97.1
26 TraesCS2D01G121700 chr7A 82.609 138 15 6 972 1108 200634943 200634814 2.970000e-21 113.0
27 TraesCS2D01G121700 chr7A 78.571 154 27 5 3387 3534 567516058 567515905 2.990000e-16 97.1
28 TraesCS2D01G121700 chr1B 80.795 151 21 4 3391 3534 622978776 622978627 1.070000e-20 111.0
29 TraesCS2D01G121700 chr5D 84.545 110 11 2 999 1108 104561823 104561926 1.790000e-18 104.0
30 TraesCS2D01G121700 chr5D 84.536 97 15 0 3387 3483 559971650 559971746 2.990000e-16 97.1
31 TraesCS2D01G121700 chr4B 75.210 238 46 9 3387 3618 507514052 507514282 2.310000e-17 100.0
32 TraesCS2D01G121700 chr3B 82.883 111 13 4 999 1109 62022216 62022320 1.080000e-15 95.3
33 TraesCS2D01G121700 chr3B 84.848 99 9 2 1010 1108 675253604 675253696 1.080000e-15 95.3
34 TraesCS2D01G121700 chr3B 79.562 137 22 5 3404 3534 11238093 11238229 3.870000e-15 93.5
35 TraesCS2D01G121700 chr3B 82.727 110 13 3 999 1108 780154545 780154648 3.870000e-15 93.5


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 TraesCS2D01G121700 chr2D 70819186 70822823 3637 True 6719 6719 100.000000 1 3638 1 chr2D.!!$R1 3637
1 TraesCS2D01G121700 chr2B 107116067 107118493 2426 True 3576 3576 93.176000 1186 3638 1 chr2B.!!$R1 2452
2 TraesCS2D01G121700 chr2A 70181945 70185185 3240 True 1402 2109 90.314333 1 3379 3 chr2A.!!$R1 3378
3 TraesCS2D01G121700 chr2A 70186672 70188543 1871 False 260 531 79.658000 1183 3158 4 chr2A.!!$F1 1975

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
992 1008 0.313987 GAAGTTCCCAAAACCGCTGG 59.686 55.0 0.0 0.0 0.0 4.85 F
2474 2579 0.036732 TGATCGGGCAGCTTTGACTT 59.963 50.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2530 2635 0.034896 ATTGGCGATACCCCACGATC 59.965 55.0 0.0 0.0 37.83 3.69 R
3585 3837 0.820891 AGTGCTGGCTGTGGTGAAAG 60.821 55.0 0.0 0.0 0.00 2.62 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
27 28 4.277921 GCAAATGAGATGGAGGAAGGAATC 59.722 45.833 0.00 0.00 0.00 2.52
28 29 5.692928 CAAATGAGATGGAGGAAGGAATCT 58.307 41.667 0.00 0.00 32.10 2.40
48 49 0.892755 AACTCGTGACCGCCAGATTA 59.107 50.000 0.00 0.00 0.00 1.75
53 54 1.583054 GTGACCGCCAGATTATCCAC 58.417 55.000 0.00 0.00 0.00 4.02
56 57 0.389391 ACCGCCAGATTATCCACGAG 59.611 55.000 0.00 0.00 0.00 4.18
59 60 1.067060 CGCCAGATTATCCACGAGTGA 59.933 52.381 4.59 0.00 0.00 3.41
61 62 3.062763 GCCAGATTATCCACGAGTGATG 58.937 50.000 4.59 0.00 0.00 3.07
74 75 2.542618 CGAGTGATGCTAGCCACTACAG 60.543 54.545 21.89 14.37 43.02 2.74
75 76 1.759445 AGTGATGCTAGCCACTACAGG 59.241 52.381 20.89 0.00 41.38 4.00
90 91 1.843368 ACAGGCAACGGCTACTACTA 58.157 50.000 0.00 0.00 46.39 1.82
95 96 4.019174 AGGCAACGGCTACTACTAACTTA 58.981 43.478 0.00 0.00 46.39 2.24
98 99 5.461407 GGCAACGGCTACTACTAACTTATTC 59.539 44.000 0.00 0.00 40.87 1.75
100 101 6.417339 GCAACGGCTACTACTAACTTATTCTC 59.583 42.308 0.00 0.00 36.96 2.87
106 107 6.520447 GCTACTACTAACTTATTCTCGCATCG 59.480 42.308 0.00 0.00 0.00 3.84
113 114 4.651994 ACTTATTCTCGCATCGCAAAAAG 58.348 39.130 0.00 0.00 0.00 2.27
168 177 1.402613 GCACCTTGTTTGTTGTACCGT 59.597 47.619 0.00 0.00 0.00 4.83
172 181 5.122711 GCACCTTGTTTGTTGTACCGTATAT 59.877 40.000 0.00 0.00 0.00 0.86
213 222 9.535170 TGAAAATATTACAGGAAACCCATACAA 57.465 29.630 0.00 0.00 0.00 2.41
281 290 4.891168 ACATCTTTCGTAAAACCCCAAAGT 59.109 37.500 0.00 0.00 0.00 2.66
282 291 5.361571 ACATCTTTCGTAAAACCCCAAAGTT 59.638 36.000 0.00 0.00 0.00 2.66
283 292 5.918426 TCTTTCGTAAAACCCCAAAGTTT 57.082 34.783 0.00 0.00 41.67 2.66
317 326 6.398918 TCCCAAACATTTTGTCGAAAAAGAA 58.601 32.000 0.20 0.00 34.72 2.52
627 642 8.757164 AAACTTTTCTGAAATTTTCGAACACT 57.243 26.923 3.31 0.00 0.00 3.55
629 644 8.394667 ACTTTTCTGAAATTTTCGAACACTTC 57.605 30.769 3.31 0.00 0.00 3.01
632 647 7.969387 TTCTGAAATTTTCGAACACTTCTTG 57.031 32.000 7.00 1.34 0.00 3.02
642 657 4.151689 TCGAACACTTCTTGGAAATAAGCG 59.848 41.667 0.00 0.00 33.75 4.68
646 661 4.819630 ACACTTCTTGGAAATAAGCGAACA 59.180 37.500 0.00 0.00 33.75 3.18
648 663 6.183360 ACACTTCTTGGAAATAAGCGAACAAA 60.183 34.615 0.00 0.00 33.75 2.83
662 677 9.959749 ATAAGCGAACAAATTTTGAAGTTCTAA 57.040 25.926 15.81 0.00 38.50 2.10
663 678 8.696410 AAGCGAACAAATTTTGAAGTTCTAAA 57.304 26.923 15.81 13.59 38.50 1.85
664 679 8.340230 AGCGAACAAATTTTGAAGTTCTAAAG 57.660 30.769 15.81 7.13 38.50 1.85
751 767 4.283978 TGGAACAAATGTTGGAGAATGCAT 59.716 37.500 3.05 0.00 38.56 3.96
853 869 8.923609 AGAAAAGAAAAAGAGAAGCAGAAAAG 57.076 30.769 0.00 0.00 0.00 2.27
854 870 8.743714 AGAAAAGAAAAAGAGAAGCAGAAAAGA 58.256 29.630 0.00 0.00 0.00 2.52
855 871 9.358872 GAAAAGAAAAAGAGAAGCAGAAAAGAA 57.641 29.630 0.00 0.00 0.00 2.52
856 872 8.923609 AAAGAAAAAGAGAAGCAGAAAAGAAG 57.076 30.769 0.00 0.00 0.00 2.85
857 873 6.502652 AGAAAAAGAGAAGCAGAAAAGAAGC 58.497 36.000 0.00 0.00 0.00 3.86
858 874 5.841957 AAAAGAGAAGCAGAAAAGAAGCA 57.158 34.783 0.00 0.00 0.00 3.91
859 875 4.827304 AAGAGAAGCAGAAAAGAAGCAC 57.173 40.909 0.00 0.00 0.00 4.40
860 876 3.813443 AGAGAAGCAGAAAAGAAGCACA 58.187 40.909 0.00 0.00 0.00 4.57
863 879 5.126061 AGAGAAGCAGAAAAGAAGCACAAAA 59.874 36.000 0.00 0.00 0.00 2.44
864 880 5.723295 AGAAGCAGAAAAGAAGCACAAAAA 58.277 33.333 0.00 0.00 0.00 1.94
906 922 5.518487 GCGAGAAACAGAAACCAAATGAAAA 59.482 36.000 0.00 0.00 0.00 2.29
907 923 6.507929 GCGAGAAACAGAAACCAAATGAAAAC 60.508 38.462 0.00 0.00 0.00 2.43
908 924 6.019881 CGAGAAACAGAAACCAAATGAAAACC 60.020 38.462 0.00 0.00 0.00 3.27
909 925 6.706295 AGAAACAGAAACCAAATGAAAACCA 58.294 32.000 0.00 0.00 0.00 3.67
910 926 6.818142 AGAAACAGAAACCAAATGAAAACCAG 59.182 34.615 0.00 0.00 0.00 4.00
911 927 5.930837 ACAGAAACCAAATGAAAACCAGA 57.069 34.783 0.00 0.00 0.00 3.86
912 928 6.293004 ACAGAAACCAAATGAAAACCAGAA 57.707 33.333 0.00 0.00 0.00 3.02
913 929 6.706295 ACAGAAACCAAATGAAAACCAGAAA 58.294 32.000 0.00 0.00 0.00 2.52
914 930 7.164803 ACAGAAACCAAATGAAAACCAGAAAA 58.835 30.769 0.00 0.00 0.00 2.29
989 1005 2.223745 TGTAGAAGTTCCCAAAACCGC 58.776 47.619 0.00 0.00 0.00 5.68
990 1006 2.158726 TGTAGAAGTTCCCAAAACCGCT 60.159 45.455 0.00 0.00 0.00 5.52
992 1008 0.313987 GAAGTTCCCAAAACCGCTGG 59.686 55.000 0.00 0.00 0.00 4.85
993 1009 1.744320 AAGTTCCCAAAACCGCTGGC 61.744 55.000 0.00 0.00 32.10 4.85
994 1010 2.915137 TTCCCAAAACCGCTGGCC 60.915 61.111 0.00 0.00 32.10 5.36
998 1014 4.404654 CAAAACCGCTGGCCGCTC 62.405 66.667 15.78 0.00 36.13 5.03
999 1015 4.643387 AAAACCGCTGGCCGCTCT 62.643 61.111 15.78 0.28 36.13 4.09
1010 1076 0.521735 GGCCGCTCTGTTTAAAGGTG 59.478 55.000 0.00 0.00 0.00 4.00
1043 1109 4.212913 ATGTCTCGGCGCTCGCAT 62.213 61.111 16.36 5.77 44.11 4.73
1044 1110 4.854784 TGTCTCGGCGCTCGCATC 62.855 66.667 16.36 3.82 44.11 3.91
1047 1113 4.880537 CTCGGCGCTCGCATCCTT 62.881 66.667 16.36 0.00 44.11 3.36
1048 1114 4.451150 TCGGCGCTCGCATCCTTT 62.451 61.111 16.36 0.00 44.11 3.11
1049 1115 4.228097 CGGCGCTCGCATCCTTTG 62.228 66.667 16.36 0.00 44.11 2.77
1057 1123 3.291611 GCATCCTTTGCCCCTGTG 58.708 61.111 0.00 0.00 46.15 3.66
1058 1124 3.010413 GCATCCTTTGCCCCTGTGC 62.010 63.158 0.00 0.00 46.15 4.57
1059 1125 2.361610 ATCCTTTGCCCCTGTGCG 60.362 61.111 0.00 0.00 0.00 5.34
1060 1126 2.905996 ATCCTTTGCCCCTGTGCGA 61.906 57.895 0.00 0.00 0.00 5.10
1061 1127 2.424842 ATCCTTTGCCCCTGTGCGAA 62.425 55.000 0.00 0.00 33.63 4.70
1062 1128 1.978617 CCTTTGCCCCTGTGCGAAT 60.979 57.895 0.00 0.00 34.23 3.34
1105 1171 1.087771 CGAGCGGCGAATAGGGTTTT 61.088 55.000 12.98 0.00 44.57 2.43
1107 1173 0.746923 AGCGGCGAATAGGGTTTTCC 60.747 55.000 12.98 0.00 39.75 3.13
1144 1210 1.450025 CTCCCGCTAAACCCAACTTC 58.550 55.000 0.00 0.00 0.00 3.01
1153 1219 3.655615 AAACCCAACTTCACACTACCA 57.344 42.857 0.00 0.00 0.00 3.25
1158 1224 1.531149 CAACTTCACACTACCAAGGCG 59.469 52.381 0.00 0.00 0.00 5.52
1162 1228 3.246112 ACACTACCAAGGCGCCCA 61.246 61.111 26.15 2.06 0.00 5.36
1170 1236 0.679640 CCAAGGCGCCCACATCTAAA 60.680 55.000 26.15 0.00 0.00 1.85
1196 1263 1.361993 CTCTGCTACCTGCGCCTAG 59.638 63.158 4.18 1.93 46.63 3.02
1290 1358 1.153549 GGACGCGCTCATCTTCCTT 60.154 57.895 5.73 0.00 0.00 3.36
1369 1437 3.522731 CTCTGGGCGAGGTCGAGG 61.523 72.222 2.94 0.00 43.02 4.63
1370 1438 4.361971 TCTGGGCGAGGTCGAGGT 62.362 66.667 2.94 0.00 43.02 3.85
1371 1439 3.827898 CTGGGCGAGGTCGAGGTC 61.828 72.222 2.94 0.00 43.02 3.85
1537 1606 4.326504 AATGTTCCTCTGTGCCTTTTTG 57.673 40.909 0.00 0.00 0.00 2.44
1565 1653 2.697431 CGATTTGCTTCAAACCGGAA 57.303 45.000 9.46 0.00 36.79 4.30
1567 1655 3.376540 CGATTTGCTTCAAACCGGAAAA 58.623 40.909 9.46 0.00 36.79 2.29
1568 1656 3.987220 CGATTTGCTTCAAACCGGAAAAT 59.013 39.130 9.46 0.86 36.79 1.82
1667 1755 9.955208 TTAAGATCCATCATTTTCATGAATTCG 57.045 29.630 9.40 0.64 42.93 3.34
1686 1774 4.782019 TCGAAACTGGCATTTGCTTTAT 57.218 36.364 2.12 0.00 41.70 1.40
1689 1777 6.682746 TCGAAACTGGCATTTGCTTTATTTA 58.317 32.000 2.12 0.00 41.70 1.40
1726 1818 6.255596 TCCGTCTAGCTTAAGTGCATATAG 57.744 41.667 4.02 0.00 34.99 1.31
1802 1894 3.498661 GGATATCAAAGAGCCCCCGAAAT 60.499 47.826 4.83 0.00 0.00 2.17
1818 1910 3.403038 CGAAATCTCTTCACCAGGTTGT 58.597 45.455 0.00 0.00 0.00 3.32
1822 1914 1.211703 TCTCTTCACCAGGTTGTGCAA 59.788 47.619 0.00 0.00 36.17 4.08
1906 1998 3.140325 AGTCATGACGATTTGGTGGTT 57.860 42.857 19.85 0.00 36.20 3.67
1925 2017 2.136298 TGGTCTGTTGCCTGTGAAAA 57.864 45.000 0.00 0.00 0.00 2.29
1929 2021 4.072131 GGTCTGTTGCCTGTGAAAAGATA 58.928 43.478 0.00 0.00 0.00 1.98
1972 2064 1.128200 TATTGAGGGATGTGGGGTCG 58.872 55.000 0.00 0.00 0.00 4.79
2061 2162 7.101652 TGAAGTAGAGAGTTATGTGGATGTC 57.898 40.000 0.00 0.00 0.00 3.06
2079 2180 7.432013 TGGATGTCCTGTTGAGGTATATACCC 61.432 46.154 25.43 17.76 41.17 3.69
2120 2221 6.014584 TCTCCTATTGGCGTCACATTATATGT 60.015 38.462 0.00 0.00 46.22 2.29
2175 2277 6.203723 GGTGAATATCCTGATAACTTGTGAGC 59.796 42.308 0.00 0.00 0.00 4.26
2280 2382 3.317430 GGTACATCCCAGTTAGACCTACG 59.683 52.174 0.00 0.00 0.00 3.51
2472 2577 1.953559 TATGATCGGGCAGCTTTGAC 58.046 50.000 0.00 0.00 0.00 3.18
2473 2578 0.254178 ATGATCGGGCAGCTTTGACT 59.746 50.000 0.00 0.00 0.00 3.41
2474 2579 0.036732 TGATCGGGCAGCTTTGACTT 59.963 50.000 0.00 0.00 0.00 3.01
2475 2580 1.168714 GATCGGGCAGCTTTGACTTT 58.831 50.000 0.00 0.00 0.00 2.66
2476 2581 0.883833 ATCGGGCAGCTTTGACTTTG 59.116 50.000 0.00 0.00 0.00 2.77
2477 2582 0.179032 TCGGGCAGCTTTGACTTTGA 60.179 50.000 0.00 0.00 0.00 2.69
2478 2583 0.667993 CGGGCAGCTTTGACTTTGAA 59.332 50.000 0.00 0.00 0.00 2.69
2479 2584 1.270550 CGGGCAGCTTTGACTTTGAAT 59.729 47.619 0.00 0.00 0.00 2.57
2486 2591 6.091305 GGCAGCTTTGACTTTGAATTTTATCC 59.909 38.462 0.00 0.00 0.00 2.59
2487 2592 6.646240 GCAGCTTTGACTTTGAATTTTATCCA 59.354 34.615 0.00 0.00 0.00 3.41
2488 2593 7.359514 GCAGCTTTGACTTTGAATTTTATCCAC 60.360 37.037 0.00 0.00 0.00 4.02
2490 2595 6.089417 GCTTTGACTTTGAATTTTATCCACCG 59.911 38.462 0.00 0.00 0.00 4.94
2499 2604 3.512219 TTTTATCCACCGAAACCCACT 57.488 42.857 0.00 0.00 0.00 4.00
2501 2606 4.637387 TTTATCCACCGAAACCCACTAA 57.363 40.909 0.00 0.00 0.00 2.24
2502 2607 2.781681 ATCCACCGAAACCCACTAAG 57.218 50.000 0.00 0.00 0.00 2.18
2503 2608 1.426751 TCCACCGAAACCCACTAAGT 58.573 50.000 0.00 0.00 0.00 2.24
2504 2609 1.071071 TCCACCGAAACCCACTAAGTG 59.929 52.381 0.00 0.00 0.00 3.16
2513 2618 4.625800 CACTAAGTGGCAGGCCTC 57.374 61.111 0.00 8.11 36.94 4.70
2514 2619 1.679311 CACTAAGTGGCAGGCCTCA 59.321 57.895 0.00 0.00 36.94 3.86
2515 2620 0.036732 CACTAAGTGGCAGGCCTCAA 59.963 55.000 0.00 0.04 36.94 3.02
2516 2621 0.771127 ACTAAGTGGCAGGCCTCAAA 59.229 50.000 0.00 0.00 36.94 2.69
2517 2622 1.355720 ACTAAGTGGCAGGCCTCAAAT 59.644 47.619 0.00 0.00 36.94 2.32
2518 2623 2.225117 ACTAAGTGGCAGGCCTCAAATT 60.225 45.455 0.00 0.00 36.94 1.82
2519 2624 1.720781 AAGTGGCAGGCCTCAAATTT 58.279 45.000 0.00 0.00 36.94 1.82
2520 2625 1.260544 AGTGGCAGGCCTCAAATTTC 58.739 50.000 0.00 0.00 36.94 2.17
2521 2626 0.968405 GTGGCAGGCCTCAAATTTCA 59.032 50.000 0.00 0.00 36.94 2.69
2522 2627 1.344114 GTGGCAGGCCTCAAATTTCAA 59.656 47.619 0.00 0.00 36.94 2.69
2523 2628 2.045524 TGGCAGGCCTCAAATTTCAAA 58.954 42.857 0.00 0.00 36.94 2.69
2524 2629 2.037511 TGGCAGGCCTCAAATTTCAAAG 59.962 45.455 0.00 0.00 36.94 2.77
2525 2630 2.613725 GGCAGGCCTCAAATTTCAAAGG 60.614 50.000 0.00 6.47 0.00 3.11
2526 2631 2.613725 GCAGGCCTCAAATTTCAAAGGG 60.614 50.000 0.00 0.00 0.00 3.95
2527 2632 2.634453 CAGGCCTCAAATTTCAAAGGGT 59.366 45.455 0.00 0.00 0.00 4.34
2528 2633 3.071457 CAGGCCTCAAATTTCAAAGGGTT 59.929 43.478 0.00 0.00 0.00 4.11
2529 2634 3.071457 AGGCCTCAAATTTCAAAGGGTTG 59.929 43.478 0.00 0.00 35.95 3.77
2530 2635 3.402110 GCCTCAAATTTCAAAGGGTTGG 58.598 45.455 11.07 0.00 35.29 3.77
2531 2636 3.070878 GCCTCAAATTTCAAAGGGTTGGA 59.929 43.478 11.07 0.00 35.29 3.53
2532 2637 4.263025 GCCTCAAATTTCAAAGGGTTGGAT 60.263 41.667 11.07 0.00 35.29 3.41
2533 2638 5.482006 CCTCAAATTTCAAAGGGTTGGATC 58.518 41.667 0.00 0.00 35.29 3.36
2534 2639 5.132897 TCAAATTTCAAAGGGTTGGATCG 57.867 39.130 0.00 0.00 35.29 3.69
2535 2640 4.586841 TCAAATTTCAAAGGGTTGGATCGT 59.413 37.500 0.00 0.00 35.29 3.73
2536 2641 4.519540 AATTTCAAAGGGTTGGATCGTG 57.480 40.909 0.00 0.00 35.29 4.35
2537 2642 1.904287 TTCAAAGGGTTGGATCGTGG 58.096 50.000 0.00 0.00 35.29 4.94
2538 2643 0.037590 TCAAAGGGTTGGATCGTGGG 59.962 55.000 0.00 0.00 35.29 4.61
2539 2644 0.965363 CAAAGGGTTGGATCGTGGGG 60.965 60.000 0.00 0.00 0.00 4.96
2540 2645 1.432023 AAAGGGTTGGATCGTGGGGT 61.432 55.000 0.00 0.00 0.00 4.95
2541 2646 0.548197 AAGGGTTGGATCGTGGGGTA 60.548 55.000 0.00 0.00 0.00 3.69
2542 2647 0.327191 AGGGTTGGATCGTGGGGTAT 60.327 55.000 0.00 0.00 0.00 2.73
2543 2648 0.108019 GGGTTGGATCGTGGGGTATC 59.892 60.000 0.00 0.00 0.00 2.24
2544 2649 0.249741 GGTTGGATCGTGGGGTATCG 60.250 60.000 0.00 0.00 0.00 2.92
2545 2650 0.878961 GTTGGATCGTGGGGTATCGC 60.879 60.000 0.00 0.00 0.00 4.58
2546 2651 2.035237 TTGGATCGTGGGGTATCGCC 62.035 60.000 0.00 0.00 36.97 5.54
2547 2652 2.504274 GGATCGTGGGGTATCGCCA 61.504 63.158 1.46 1.46 44.19 5.69
2556 2661 4.927978 TGGGGTATCGCCAATTTAATTG 57.072 40.909 10.46 10.46 43.44 2.32
2557 2662 3.068873 TGGGGTATCGCCAATTTAATTGC 59.931 43.478 11.82 7.01 43.44 3.56
2558 2663 3.068873 GGGGTATCGCCAATTTAATTGCA 59.931 43.478 11.82 0.00 38.92 4.08
2559 2664 4.262420 GGGGTATCGCCAATTTAATTGCAT 60.262 41.667 11.82 6.28 38.92 3.96
2560 2665 5.296748 GGGTATCGCCAATTTAATTGCATT 58.703 37.500 11.82 0.33 38.92 3.56
2561 2666 6.451393 GGGTATCGCCAATTTAATTGCATTA 58.549 36.000 11.82 0.00 38.92 1.90
2562 2667 7.096551 GGGTATCGCCAATTTAATTGCATTAT 58.903 34.615 11.82 5.53 38.92 1.28
2563 2668 7.275560 GGGTATCGCCAATTTAATTGCATTATC 59.724 37.037 11.82 2.26 38.92 1.75
2579 2768 9.616634 ATTGCATTATCTTGTTATTTATCTGCG 57.383 29.630 0.00 0.00 0.00 5.18
2990 3237 5.711976 ACTGTTGGGGAGTCAATTCAATAAG 59.288 40.000 0.00 0.00 0.00 1.73
2991 3238 5.886609 TGTTGGGGAGTCAATTCAATAAGA 58.113 37.500 0.00 0.00 0.00 2.10
2992 3239 5.710099 TGTTGGGGAGTCAATTCAATAAGAC 59.290 40.000 0.00 0.00 0.00 3.01
2993 3240 5.779241 TGGGGAGTCAATTCAATAAGACT 57.221 39.130 5.35 5.35 43.50 3.24
2995 3242 6.889198 TGGGGAGTCAATTCAATAAGACTAG 58.111 40.000 5.61 0.00 41.10 2.57
3093 3342 1.547372 GCCATGCTTTGTTCTGTCCAT 59.453 47.619 0.00 0.00 0.00 3.41
3118 3367 5.639082 CAGTCTTCACAGTGTAATGCATGTA 59.361 40.000 0.00 0.00 0.00 2.29
3227 3476 1.959985 TGCAACCCGATTCAAACACAT 59.040 42.857 0.00 0.00 0.00 3.21
3238 3487 4.517952 TTCAAACACATGGCACCATAAG 57.482 40.909 0.89 0.60 34.91 1.73
3239 3488 3.495331 TCAAACACATGGCACCATAAGT 58.505 40.909 0.89 1.24 34.91 2.24
3240 3489 3.505680 TCAAACACATGGCACCATAAGTC 59.494 43.478 0.89 0.00 34.91 3.01
3241 3490 2.128771 ACACATGGCACCATAAGTCC 57.871 50.000 0.89 0.00 34.91 3.85
3242 3491 1.354031 ACACATGGCACCATAAGTCCA 59.646 47.619 0.89 0.00 34.91 4.02
3243 3492 2.025037 ACACATGGCACCATAAGTCCAT 60.025 45.455 0.89 0.00 37.05 3.41
3244 3493 3.201930 ACACATGGCACCATAAGTCCATA 59.798 43.478 0.89 0.00 35.73 2.74
3245 3494 4.206375 CACATGGCACCATAAGTCCATAA 58.794 43.478 0.89 0.00 35.73 1.90
3251 3500 4.261801 GCACCATAAGTCCATAACACACT 58.738 43.478 0.00 0.00 0.00 3.55
3308 3557 4.954970 AGCAGCAACACCACCCCG 62.955 66.667 0.00 0.00 0.00 5.73
3318 3567 1.152183 ACCACCCCGTACAACTCCT 60.152 57.895 0.00 0.00 0.00 3.69
3336 3585 2.846206 TCCTAGCAAACATCAGGTGGAT 59.154 45.455 0.00 0.00 36.39 3.41
3373 3622 2.468915 GAGTTACTAGGGCCCTCAACT 58.531 52.381 31.78 31.78 0.00 3.16
3399 3648 1.372582 GACAATGAGATGAAGCCGCA 58.627 50.000 0.00 0.00 0.00 5.69
3402 3651 1.089920 AATGAGATGAAGCCGCACAC 58.910 50.000 0.00 0.00 0.00 3.82
3405 3654 0.807667 GAGATGAAGCCGCACACGAT 60.808 55.000 0.00 0.00 43.93 3.73
3406 3655 1.086067 AGATGAAGCCGCACACGATG 61.086 55.000 0.00 0.00 43.93 3.84
3426 3675 2.048222 CCGTGAGCTTCAAGGCGA 60.048 61.111 5.51 0.00 39.05 5.54
3428 3677 1.664649 CGTGAGCTTCAAGGCGACA 60.665 57.895 0.00 0.00 37.29 4.35
3429 3678 1.862806 GTGAGCTTCAAGGCGACAC 59.137 57.895 0.00 0.00 37.29 3.67
3456 3705 1.412710 GAAGGTCATGATACCGGAGCA 59.587 52.381 9.46 0.30 44.77 4.26
3490 3739 2.118403 TCCAAGGATCAGGGTATCCC 57.882 55.000 0.00 0.00 45.74 3.85
3508 3757 0.747255 CCTCGGATCCAGACAACGAT 59.253 55.000 13.41 0.00 32.75 3.73
3540 3792 1.067776 ACGCCTTCAAGAAGAGTACGG 60.068 52.381 11.25 0.00 40.79 4.02
3551 3803 1.731969 GAGTACGGCGCTGAAACGT 60.732 57.895 25.98 18.53 43.88 3.99
3552 3804 1.280206 GAGTACGGCGCTGAAACGTT 61.280 55.000 25.98 5.62 41.53 3.99
3561 3813 3.536498 CTGAAACGTTGCCACCGCC 62.536 63.158 0.00 0.00 0.00 6.13
3592 3844 0.250338 AGTCAGAACGGGCTTTCACC 60.250 55.000 0.00 0.00 0.00 4.02
3593 3845 0.534203 GTCAGAACGGGCTTTCACCA 60.534 55.000 0.00 0.00 0.00 4.17
3609 3861 2.111669 CACAGCCAGCACTCACCA 59.888 61.111 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 5.692928 AGATTCCTTCCTCCATCTCATTTG 58.307 41.667 0.00 0.00 0.00 2.32
27 28 0.456221 ATCTGGCGGTCACGAGTTAG 59.544 55.000 0.00 0.00 44.60 2.34
28 29 0.892755 AATCTGGCGGTCACGAGTTA 59.107 50.000 0.00 0.00 44.60 2.24
48 49 0.390860 GGCTAGCATCACTCGTGGAT 59.609 55.000 18.24 0.00 0.00 3.41
53 54 1.405463 TGTAGTGGCTAGCATCACTCG 59.595 52.381 24.35 0.00 42.51 4.18
56 57 2.231215 CCTGTAGTGGCTAGCATCAC 57.769 55.000 18.24 15.93 0.00 3.06
74 75 2.955477 AGTTAGTAGTAGCCGTTGCC 57.045 50.000 0.00 0.00 38.69 4.52
75 76 6.271566 AGAATAAGTTAGTAGTAGCCGTTGC 58.728 40.000 0.00 0.00 37.95 4.17
78 79 5.277731 GCGAGAATAAGTTAGTAGTAGCCGT 60.278 44.000 0.00 0.00 0.00 5.68
80 81 6.069684 TGCGAGAATAAGTTAGTAGTAGCC 57.930 41.667 0.00 0.00 0.00 3.93
90 91 4.678509 TTTTGCGATGCGAGAATAAGTT 57.321 36.364 0.00 0.00 0.00 2.66
95 96 3.559238 AACTTTTTGCGATGCGAGAAT 57.441 38.095 0.00 0.00 0.00 2.40
98 99 4.463209 TCTTAAACTTTTTGCGATGCGAG 58.537 39.130 0.00 0.00 0.00 5.03
100 101 4.675114 ACTTCTTAAACTTTTTGCGATGCG 59.325 37.500 0.00 0.00 0.00 4.73
133 134 8.768955 CAAACAAGGTGCTACTATGAATAGATC 58.231 37.037 4.34 0.00 34.50 2.75
134 135 8.267894 ACAAACAAGGTGCTACTATGAATAGAT 58.732 33.333 4.34 0.00 34.50 1.98
135 136 7.620880 ACAAACAAGGTGCTACTATGAATAGA 58.379 34.615 4.34 0.00 34.50 1.98
136 137 7.849804 ACAAACAAGGTGCTACTATGAATAG 57.150 36.000 0.00 0.00 36.46 1.73
137 138 7.663905 ACAACAAACAAGGTGCTACTATGAATA 59.336 33.333 0.00 0.00 0.00 1.75
198 207 8.748412 TCTTCATAAAATTGTATGGGTTTCCTG 58.252 33.333 14.44 0.00 33.11 3.86
199 208 8.893563 TCTTCATAAAATTGTATGGGTTTCCT 57.106 30.769 14.44 0.00 33.11 3.36
213 222 8.879227 TGTTCCCATTTCCTTTCTTCATAAAAT 58.121 29.630 0.00 0.00 0.00 1.82
253 262 8.632906 TTGGGGTTTTACGAAAGATGTATTAA 57.367 30.769 0.00 0.00 0.00 1.40
297 306 9.634163 ACTTAGTTCTTTTTCGACAAAATGTTT 57.366 25.926 0.00 0.00 31.39 2.83
373 382 7.652507 GTGTACGGGGAATTTTAAAAATGTTCA 59.347 33.333 4.44 0.21 0.00 3.18
616 631 6.915843 GCTTATTTCCAAGAAGTGTTCGAAAA 59.084 34.615 0.00 0.00 34.02 2.29
619 634 4.151689 CGCTTATTTCCAAGAAGTGTTCGA 59.848 41.667 0.00 0.00 34.02 3.71
627 642 8.547069 CAAAATTTGTTCGCTTATTTCCAAGAA 58.453 29.630 0.00 0.00 0.00 2.52
629 644 8.071122 TCAAAATTTGTTCGCTTATTTCCAAG 57.929 30.769 5.56 0.00 0.00 3.61
632 647 8.072238 ACTTCAAAATTTGTTCGCTTATTTCC 57.928 30.769 5.56 0.00 0.00 3.13
821 837 9.710900 TGCTTCTCTTTTTCTTTTCTTTTCTTT 57.289 25.926 0.00 0.00 0.00 2.52
822 838 9.363763 CTGCTTCTCTTTTTCTTTTCTTTTCTT 57.636 29.630 0.00 0.00 0.00 2.52
823 839 8.743714 TCTGCTTCTCTTTTTCTTTTCTTTTCT 58.256 29.630 0.00 0.00 0.00 2.52
839 855 3.813443 TGTGCTTCTTTTCTGCTTCTCT 58.187 40.909 0.00 0.00 0.00 3.10
881 897 3.882888 TCATTTGGTTTCTGTTTCTCGCT 59.117 39.130 0.00 0.00 0.00 4.93
882 898 4.223320 TCATTTGGTTTCTGTTTCTCGC 57.777 40.909 0.00 0.00 0.00 5.03
883 899 6.019881 GGTTTTCATTTGGTTTCTGTTTCTCG 60.020 38.462 0.00 0.00 0.00 4.04
892 908 7.094592 TGGTTTTTCTGGTTTTCATTTGGTTTC 60.095 33.333 0.00 0.00 0.00 2.78
906 922 6.353404 TGTTTCTTTTCTGGTTTTTCTGGT 57.647 33.333 0.00 0.00 0.00 4.00
907 923 6.648725 TGTTGTTTCTTTTCTGGTTTTTCTGG 59.351 34.615 0.00 0.00 0.00 3.86
908 924 7.170658 TGTGTTGTTTCTTTTCTGGTTTTTCTG 59.829 33.333 0.00 0.00 0.00 3.02
909 925 7.170828 GTGTGTTGTTTCTTTTCTGGTTTTTCT 59.829 33.333 0.00 0.00 0.00 2.52
910 926 7.287950 GTGTGTTGTTTCTTTTCTGGTTTTTC 58.712 34.615 0.00 0.00 0.00 2.29
911 927 6.074034 CGTGTGTTGTTTCTTTTCTGGTTTTT 60.074 34.615 0.00 0.00 0.00 1.94
912 928 5.404066 CGTGTGTTGTTTCTTTTCTGGTTTT 59.596 36.000 0.00 0.00 0.00 2.43
913 929 4.920927 CGTGTGTTGTTTCTTTTCTGGTTT 59.079 37.500 0.00 0.00 0.00 3.27
914 930 4.216687 TCGTGTGTTGTTTCTTTTCTGGTT 59.783 37.500 0.00 0.00 0.00 3.67
956 972 6.874664 GGGAACTTCTACAAACCTTCTAGAAG 59.125 42.308 23.31 23.31 44.83 2.85
961 977 5.382664 TTGGGAACTTCTACAAACCTTCT 57.617 39.130 0.00 0.00 0.00 2.85
966 982 4.603985 CGGTTTTGGGAACTTCTACAAAC 58.396 43.478 9.99 6.66 33.08 2.93
967 983 3.067040 GCGGTTTTGGGAACTTCTACAAA 59.933 43.478 7.60 7.60 0.00 2.83
968 984 2.619646 GCGGTTTTGGGAACTTCTACAA 59.380 45.455 0.00 0.00 0.00 2.41
969 985 2.158726 AGCGGTTTTGGGAACTTCTACA 60.159 45.455 0.00 0.00 0.00 2.74
970 986 2.225727 CAGCGGTTTTGGGAACTTCTAC 59.774 50.000 0.00 0.00 0.00 2.59
971 987 2.500229 CAGCGGTTTTGGGAACTTCTA 58.500 47.619 0.00 0.00 0.00 2.10
972 988 1.318576 CAGCGGTTTTGGGAACTTCT 58.681 50.000 0.00 0.00 0.00 2.85
973 989 0.313987 CCAGCGGTTTTGGGAACTTC 59.686 55.000 0.00 0.00 31.87 3.01
974 990 1.744320 GCCAGCGGTTTTGGGAACTT 61.744 55.000 0.00 0.00 36.19 2.66
975 991 2.200337 GCCAGCGGTTTTGGGAACT 61.200 57.895 0.00 0.00 36.19 3.01
989 1005 0.804989 CCTTTAAACAGAGCGGCCAG 59.195 55.000 2.24 0.00 0.00 4.85
990 1006 0.109723 ACCTTTAAACAGAGCGGCCA 59.890 50.000 2.24 0.00 0.00 5.36
992 1008 0.521735 CCACCTTTAAACAGAGCGGC 59.478 55.000 0.00 0.00 0.00 6.53
993 1009 2.178912 TCCACCTTTAAACAGAGCGG 57.821 50.000 0.00 0.00 0.00 5.52
994 1010 3.058914 CACTTCCACCTTTAAACAGAGCG 60.059 47.826 0.00 0.00 0.00 5.03
995 1011 3.253432 CCACTTCCACCTTTAAACAGAGC 59.747 47.826 0.00 0.00 0.00 4.09
996 1012 3.821033 CCCACTTCCACCTTTAAACAGAG 59.179 47.826 0.00 0.00 0.00 3.35
997 1013 3.827722 CCCACTTCCACCTTTAAACAGA 58.172 45.455 0.00 0.00 0.00 3.41
998 1014 2.296190 GCCCACTTCCACCTTTAAACAG 59.704 50.000 0.00 0.00 0.00 3.16
999 1015 2.312390 GCCCACTTCCACCTTTAAACA 58.688 47.619 0.00 0.00 0.00 2.83
1000 1016 1.616865 GGCCCACTTCCACCTTTAAAC 59.383 52.381 0.00 0.00 0.00 2.01
1026 1092 4.212913 ATGCGAGCGCCGAGACAT 62.213 61.111 20.06 11.70 41.76 3.06
1027 1093 4.854784 GATGCGAGCGCCGAGACA 62.855 66.667 20.06 10.12 41.76 3.41
1030 1096 4.880537 AAGGATGCGAGCGCCGAG 62.881 66.667 20.06 6.25 41.76 4.63
1031 1097 4.451150 AAAGGATGCGAGCGCCGA 62.451 61.111 20.06 7.46 41.76 5.54
1032 1098 4.228097 CAAAGGATGCGAGCGCCG 62.228 66.667 12.70 9.10 41.09 6.46
1033 1099 4.543084 GCAAAGGATGCGAGCGCC 62.543 66.667 12.70 3.37 46.87 6.53
1041 1107 2.703798 CGCACAGGGGCAAAGGATG 61.704 63.158 0.00 0.00 0.00 3.51
1042 1108 2.361610 CGCACAGGGGCAAAGGAT 60.362 61.111 0.00 0.00 0.00 3.24
1043 1109 2.424842 ATTCGCACAGGGGCAAAGGA 62.425 55.000 0.00 0.00 0.00 3.36
1044 1110 1.937546 GATTCGCACAGGGGCAAAGG 61.938 60.000 0.00 0.00 0.00 3.11
1045 1111 1.508088 GATTCGCACAGGGGCAAAG 59.492 57.895 0.00 0.00 0.00 2.77
1046 1112 1.976474 GGATTCGCACAGGGGCAAA 60.976 57.895 0.00 0.00 0.00 3.68
1047 1113 2.361104 GGATTCGCACAGGGGCAA 60.361 61.111 0.00 0.00 0.00 4.52
1048 1114 4.424711 GGGATTCGCACAGGGGCA 62.425 66.667 0.00 0.00 0.00 5.36
1050 1116 4.856801 CGGGGATTCGCACAGGGG 62.857 72.222 2.94 0.00 0.00 4.79
1051 1117 4.096003 ACGGGGATTCGCACAGGG 62.096 66.667 2.94 0.00 0.00 4.45
1052 1118 2.511600 GACGGGGATTCGCACAGG 60.512 66.667 2.94 0.00 0.00 4.00
1053 1119 2.511600 GGACGGGGATTCGCACAG 60.512 66.667 2.94 0.00 0.00 3.66
1054 1120 4.090588 GGGACGGGGATTCGCACA 62.091 66.667 2.94 0.00 0.00 4.57
1055 1121 4.090588 TGGGACGGGGATTCGCAC 62.091 66.667 2.94 0.00 31.47 5.34
1056 1122 4.090588 GTGGGACGGGGATTCGCA 62.091 66.667 2.94 0.00 33.84 5.10
1057 1123 2.886730 ATTGTGGGACGGGGATTCGC 62.887 60.000 0.00 0.00 0.00 4.70
1058 1124 0.393808 AATTGTGGGACGGGGATTCG 60.394 55.000 0.00 0.00 0.00 3.34
1059 1125 1.389555 GAATTGTGGGACGGGGATTC 58.610 55.000 0.00 0.00 0.00 2.52
1060 1126 0.393808 CGAATTGTGGGACGGGGATT 60.394 55.000 0.00 0.00 0.00 3.01
1061 1127 1.223487 CGAATTGTGGGACGGGGAT 59.777 57.895 0.00 0.00 0.00 3.85
1062 1128 2.666207 CGAATTGTGGGACGGGGA 59.334 61.111 0.00 0.00 0.00 4.81
1101 1167 2.353958 GAGGGGGACGGGGAAAAC 59.646 66.667 0.00 0.00 0.00 2.43
1144 1210 2.746277 GGGCGCCTTGGTAGTGTG 60.746 66.667 28.56 0.00 0.00 3.82
1153 1219 1.917872 TTTTTAGATGTGGGCGCCTT 58.082 45.000 28.56 9.05 0.00 4.35
1170 1236 2.808543 CGCAGGTAGCAGAGTTCTTTTT 59.191 45.455 0.00 0.00 46.13 1.94
1184 1251 2.039951 AACCCCTAGGCGCAGGTA 59.960 61.111 10.83 0.00 36.11 3.08
1537 1606 4.685169 TTGAAGCAAATCGGATCTGTTC 57.315 40.909 0.42 0.00 0.00 3.18
1604 1692 6.648879 ATTGGCAACTTATATAAACCGCAT 57.351 33.333 0.00 0.32 37.61 4.73
1605 1693 6.458232 AATTGGCAACTTATATAAACCGCA 57.542 33.333 0.00 0.00 37.61 5.69
1614 1702 8.830915 TTCTTATTGGGAATTGGCAACTTATA 57.169 30.769 0.00 0.00 37.61 0.98
1726 1818 3.870633 AAGGTCAGAACGAGGTCATAC 57.129 47.619 0.00 0.00 0.00 2.39
1802 1894 0.836606 TGCACAACCTGGTGAAGAGA 59.163 50.000 0.00 0.00 41.32 3.10
1906 1998 2.023673 CTTTTCACAGGCAACAGACCA 58.976 47.619 0.00 0.00 41.41 4.02
1925 2017 4.651503 ACGAACATGTTCCCTCTGATATCT 59.348 41.667 28.40 0.00 36.27 1.98
1929 2021 3.007940 TGAACGAACATGTTCCCTCTGAT 59.992 43.478 28.40 11.93 46.04 2.90
1972 2064 3.869473 TACTGCGCCGACACCCAAC 62.869 63.158 4.18 0.00 0.00 3.77
2061 2162 3.008049 GGCAGGGTATATACCTCAACAGG 59.992 52.174 27.24 12.48 45.72 4.00
2079 2180 1.206849 GGAGAACAGAGAAGAGGGCAG 59.793 57.143 0.00 0.00 0.00 4.85
2127 2228 8.038944 CACCAAACTAGAAACAGTAGGCTTATA 58.961 37.037 0.00 0.00 30.69 0.98
2175 2277 5.603170 ATGATAGGGGCACAAATGAAAAG 57.397 39.130 0.00 0.00 0.00 2.27
2280 2382 4.655762 AGCCAAGAAACCAAACTTTCTC 57.344 40.909 0.00 0.00 39.18 2.87
2472 2577 5.867174 GGGTTTCGGTGGATAAAATTCAAAG 59.133 40.000 0.00 0.00 0.00 2.77
2473 2578 5.304614 TGGGTTTCGGTGGATAAAATTCAAA 59.695 36.000 0.00 0.00 0.00 2.69
2474 2579 4.833380 TGGGTTTCGGTGGATAAAATTCAA 59.167 37.500 0.00 0.00 0.00 2.69
2475 2580 4.218852 GTGGGTTTCGGTGGATAAAATTCA 59.781 41.667 0.00 0.00 0.00 2.57
2476 2581 4.461431 AGTGGGTTTCGGTGGATAAAATTC 59.539 41.667 0.00 0.00 0.00 2.17
2477 2582 4.412843 AGTGGGTTTCGGTGGATAAAATT 58.587 39.130 0.00 0.00 0.00 1.82
2478 2583 4.042271 AGTGGGTTTCGGTGGATAAAAT 57.958 40.909 0.00 0.00 0.00 1.82
2479 2584 3.512219 AGTGGGTTTCGGTGGATAAAA 57.488 42.857 0.00 0.00 0.00 1.52
2499 2604 2.603075 AATTTGAGGCCTGCCACTTA 57.397 45.000 12.00 0.00 38.92 2.24
2501 2606 1.260544 GAAATTTGAGGCCTGCCACT 58.739 50.000 12.00 0.00 38.92 4.00
2502 2607 0.968405 TGAAATTTGAGGCCTGCCAC 59.032 50.000 12.00 4.63 38.92 5.01
2503 2608 1.714541 TTGAAATTTGAGGCCTGCCA 58.285 45.000 12.00 0.00 38.92 4.92
2504 2609 2.613725 CCTTTGAAATTTGAGGCCTGCC 60.614 50.000 12.00 0.00 0.00 4.85
2505 2610 2.613725 CCCTTTGAAATTTGAGGCCTGC 60.614 50.000 12.00 1.89 0.00 4.85
2508 2613 3.402110 CAACCCTTTGAAATTTGAGGCC 58.598 45.455 0.00 0.00 34.24 5.19
2509 2614 3.070878 TCCAACCCTTTGAAATTTGAGGC 59.929 43.478 0.00 0.00 34.24 4.70
2510 2615 4.953940 TCCAACCCTTTGAAATTTGAGG 57.046 40.909 0.00 0.10 34.24 3.86
2511 2616 5.163513 CGATCCAACCCTTTGAAATTTGAG 58.836 41.667 0.00 0.00 34.24 3.02
2512 2617 4.586841 ACGATCCAACCCTTTGAAATTTGA 59.413 37.500 0.00 0.00 34.24 2.69
2513 2618 4.685628 CACGATCCAACCCTTTGAAATTTG 59.314 41.667 0.00 0.00 34.24 2.32
2514 2619 4.262420 CCACGATCCAACCCTTTGAAATTT 60.262 41.667 0.00 0.00 34.24 1.82
2515 2620 3.258123 CCACGATCCAACCCTTTGAAATT 59.742 43.478 0.00 0.00 34.24 1.82
2516 2621 2.825532 CCACGATCCAACCCTTTGAAAT 59.174 45.455 0.00 0.00 34.24 2.17
2517 2622 2.235016 CCACGATCCAACCCTTTGAAA 58.765 47.619 0.00 0.00 34.24 2.69
2518 2623 1.546773 CCCACGATCCAACCCTTTGAA 60.547 52.381 0.00 0.00 34.24 2.69
2519 2624 0.037590 CCCACGATCCAACCCTTTGA 59.962 55.000 0.00 0.00 34.24 2.69
2520 2625 0.965363 CCCCACGATCCAACCCTTTG 60.965 60.000 0.00 0.00 0.00 2.77
2521 2626 1.382629 CCCCACGATCCAACCCTTT 59.617 57.895 0.00 0.00 0.00 3.11
2522 2627 0.548197 TACCCCACGATCCAACCCTT 60.548 55.000 0.00 0.00 0.00 3.95
2523 2628 0.327191 ATACCCCACGATCCAACCCT 60.327 55.000 0.00 0.00 0.00 4.34
2524 2629 0.108019 GATACCCCACGATCCAACCC 59.892 60.000 0.00 0.00 0.00 4.11
2525 2630 0.249741 CGATACCCCACGATCCAACC 60.250 60.000 0.00 0.00 0.00 3.77
2526 2631 0.878961 GCGATACCCCACGATCCAAC 60.879 60.000 0.00 0.00 0.00 3.77
2527 2632 1.444250 GCGATACCCCACGATCCAA 59.556 57.895 0.00 0.00 0.00 3.53
2528 2633 2.504274 GGCGATACCCCACGATCCA 61.504 63.158 0.00 0.00 0.00 3.41
2529 2634 2.035237 TTGGCGATACCCCACGATCC 62.035 60.000 0.00 0.00 37.83 3.36
2530 2635 0.034896 ATTGGCGATACCCCACGATC 59.965 55.000 0.00 0.00 37.83 3.69
2531 2636 0.472471 AATTGGCGATACCCCACGAT 59.528 50.000 0.00 0.00 37.83 3.73
2532 2637 0.253610 AAATTGGCGATACCCCACGA 59.746 50.000 0.00 0.00 37.83 4.35
2533 2638 1.956297 TAAATTGGCGATACCCCACG 58.044 50.000 0.00 0.00 37.83 4.94
2534 2639 4.616953 CAATTAAATTGGCGATACCCCAC 58.383 43.478 0.00 0.00 37.83 4.61
2535 2640 3.068873 GCAATTAAATTGGCGATACCCCA 59.931 43.478 0.00 0.00 40.57 4.96
2536 2641 3.068873 TGCAATTAAATTGGCGATACCCC 59.931 43.478 0.00 0.00 40.57 4.95
2537 2642 4.314740 TGCAATTAAATTGGCGATACCC 57.685 40.909 0.00 0.00 40.57 3.69
2538 2643 8.028938 AGATAATGCAATTAAATTGGCGATACC 58.971 33.333 0.00 0.00 42.96 2.73
2539 2644 8.970691 AGATAATGCAATTAAATTGGCGATAC 57.029 30.769 0.00 0.00 42.96 2.24
2540 2645 9.409312 CAAGATAATGCAATTAAATTGGCGATA 57.591 29.630 0.00 0.00 42.96 2.92
2541 2646 7.927629 ACAAGATAATGCAATTAAATTGGCGAT 59.072 29.630 0.00 0.00 42.96 4.58
2542 2647 7.264221 ACAAGATAATGCAATTAAATTGGCGA 58.736 30.769 0.00 0.00 42.96 5.54
2543 2648 7.467557 ACAAGATAATGCAATTAAATTGGCG 57.532 32.000 0.00 0.00 42.96 5.69
2553 2658 9.616634 CGCAGATAAATAACAAGATAATGCAAT 57.383 29.630 0.00 0.00 0.00 3.56
2554 2659 8.620416 ACGCAGATAAATAACAAGATAATGCAA 58.380 29.630 0.00 0.00 0.00 4.08
2555 2660 8.153479 ACGCAGATAAATAACAAGATAATGCA 57.847 30.769 0.00 0.00 0.00 3.96
2556 2661 9.450807 AAACGCAGATAAATAACAAGATAATGC 57.549 29.630 0.00 0.00 0.00 3.56
2561 2666 9.691362 AAAACAAACGCAGATAAATAACAAGAT 57.309 25.926 0.00 0.00 0.00 2.40
2562 2667 9.176181 GAAAACAAACGCAGATAAATAACAAGA 57.824 29.630 0.00 0.00 0.00 3.02
2563 2668 9.180678 AGAAAACAAACGCAGATAAATAACAAG 57.819 29.630 0.00 0.00 0.00 3.16
2698 2940 5.789521 TGCAAGTATATATTAGCTGCGGAA 58.210 37.500 0.00 0.00 0.00 4.30
2990 3237 0.375106 GTGGCATTTCAGCGCTAGTC 59.625 55.000 10.99 0.00 34.64 2.59
2991 3238 0.036010 AGTGGCATTTCAGCGCTAGT 60.036 50.000 10.99 0.00 34.64 2.57
2992 3239 1.063174 GAAGTGGCATTTCAGCGCTAG 59.937 52.381 10.99 4.86 34.64 3.42
2993 3240 1.086696 GAAGTGGCATTTCAGCGCTA 58.913 50.000 10.99 0.00 34.64 4.26
2995 3242 0.171903 ATGAAGTGGCATTTCAGCGC 59.828 50.000 26.07 0.00 37.91 5.92
3093 3342 4.335400 TGCATTACACTGTGAAGACTGA 57.665 40.909 15.86 0.00 0.00 3.41
3125 3374 6.821616 ACTATCTTGAGATCATGAACCCTT 57.178 37.500 0.00 0.00 36.05 3.95
3146 3395 5.506708 AGCCTTTTTCGGTATATGGAAACT 58.493 37.500 1.86 0.00 32.30 2.66
3198 3447 0.255604 ATCGGGTTGCATGATGGTCA 59.744 50.000 0.00 0.00 0.00 4.02
3227 3476 3.009584 TGTGTTATGGACTTATGGTGCCA 59.990 43.478 0.00 0.00 35.29 4.92
3238 3487 2.806244 GGTGTGTGAGTGTGTTATGGAC 59.194 50.000 0.00 0.00 0.00 4.02
3239 3488 2.224426 GGGTGTGTGAGTGTGTTATGGA 60.224 50.000 0.00 0.00 0.00 3.41
3240 3489 2.151202 GGGTGTGTGAGTGTGTTATGG 58.849 52.381 0.00 0.00 0.00 2.74
3241 3490 2.844946 TGGGTGTGTGAGTGTGTTATG 58.155 47.619 0.00 0.00 0.00 1.90
3242 3491 3.476552 CTTGGGTGTGTGAGTGTGTTAT 58.523 45.455 0.00 0.00 0.00 1.89
3243 3492 2.420827 CCTTGGGTGTGTGAGTGTGTTA 60.421 50.000 0.00 0.00 0.00 2.41
3244 3493 1.681780 CCTTGGGTGTGTGAGTGTGTT 60.682 52.381 0.00 0.00 0.00 3.32
3245 3494 0.107214 CCTTGGGTGTGTGAGTGTGT 60.107 55.000 0.00 0.00 0.00 3.72
3251 3500 4.263572 CCGGCCTTGGGTGTGTGA 62.264 66.667 0.00 0.00 0.00 3.58
3287 3536 2.333938 GTGGTGTTGCTGCTGCTG 59.666 61.111 17.00 0.77 40.48 4.41
3288 3537 2.908940 GGTGGTGTTGCTGCTGCT 60.909 61.111 17.00 0.00 40.48 4.24
3289 3538 3.982241 GGGTGGTGTTGCTGCTGC 61.982 66.667 8.89 8.89 40.20 5.25
3290 3539 3.297620 GGGGTGGTGTTGCTGCTG 61.298 66.667 0.00 0.00 0.00 4.41
3291 3540 4.954970 CGGGGTGGTGTTGCTGCT 62.955 66.667 0.00 0.00 0.00 4.24
3292 3541 3.835790 TACGGGGTGGTGTTGCTGC 62.836 63.158 0.00 0.00 0.00 5.25
3308 3557 4.631813 CCTGATGTTTGCTAGGAGTTGTAC 59.368 45.833 0.00 0.00 31.91 2.90
3318 3567 6.486657 GCTTATTATCCACCTGATGTTTGCTA 59.513 38.462 0.00 0.00 34.76 3.49
3373 3622 3.433274 GCTTCATCTCATTGTCGTTCACA 59.567 43.478 0.00 0.00 0.00 3.58
3406 3655 1.869690 GCCTTGAAGCTCACGGTTC 59.130 57.895 9.37 0.00 45.47 3.62
3429 3678 3.005897 CGGTATCATGACCTTCCTGTAGG 59.994 52.174 0.00 0.00 41.31 3.18
3432 3681 1.762957 CCGGTATCATGACCTTCCTGT 59.237 52.381 0.00 0.00 37.34 4.00
3490 3739 2.159240 TCAATCGTTGTCTGGATCCGAG 60.159 50.000 7.39 6.08 0.00 4.63
3508 3757 4.595538 AGGCGTCGTTGCGGTCAA 62.596 61.111 0.00 0.00 35.06 3.18
3540 3792 2.725815 GTGGCAACGTTTCAGCGC 60.726 61.111 0.00 0.00 42.51 5.92
3585 3837 0.820891 AGTGCTGGCTGTGGTGAAAG 60.821 55.000 0.00 0.00 0.00 2.62
3592 3844 2.111669 TGGTGAGTGCTGGCTGTG 59.888 61.111 0.00 0.00 0.00 3.66
3593 3845 2.111878 GTGGTGAGTGCTGGCTGT 59.888 61.111 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.