Multiple sequence alignment - TraesCS2D01G503400

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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 TraesCS2D01G503400 chr2D 100.000 4667 0 0 1 4667 598281783 598277117 0.000000e+00 8619
1 TraesCS2D01G503400 chr2D 86.804 1849 196 28 2366 4185 642056322 642058151 0.000000e+00 2019
2 TraesCS2D01G503400 chr2D 86.750 1849 197 20 2366 4185 598300727 598302556 0.000000e+00 2013
3 TraesCS2D01G503400 chr2D 79.861 2438 369 71 1 2352 642053847 642056248 0.000000e+00 1670
4 TraesCS2D01G503400 chr2D 79.779 2171 347 58 1 2102 598293786 598295933 0.000000e+00 1493
5 TraesCS2D01G503400 chr2D 92.936 991 37 18 1981 2957 642153664 642152693 0.000000e+00 1411
6 TraesCS2D01G503400 chr2D 93.709 922 39 4 3365 4279 642136236 642135327 0.000000e+00 1363
7 TraesCS2D01G503400 chr2D 80.739 1272 202 30 2896 4145 598303794 598305044 0.000000e+00 952
8 TraesCS2D01G503400 chr2D 80.150 1330 216 35 2839 4145 642059337 642060641 0.000000e+00 950
9 TraesCS2D01G503400 chr2D 82.676 964 135 28 2846 3796 642037162 642036218 0.000000e+00 826
10 TraesCS2D01G503400 chr2D 82.435 928 138 16 3207 4116 642198790 642199710 0.000000e+00 787
11 TraesCS2D01G503400 chr2D 80.745 940 140 18 3207 4132 597960626 597959714 0.000000e+00 695
12 TraesCS2D01G503400 chr2D 94.602 389 19 1 2949 3337 642136618 642136232 6.680000e-168 601
13 TraesCS2D01G503400 chr2D 89.706 408 26 2 4260 4667 642134175 642133784 1.500000e-139 507
14 TraesCS2D01G503400 chr2D 82.353 289 41 9 2916 3200 597961440 597961158 4.670000e-60 243
15 TraesCS2D01G503400 chr2D 88.083 193 23 0 4127 4319 642061023 642061215 3.630000e-56 230
16 TraesCS2D01G503400 chr2D 83.843 229 17 11 2132 2352 598300437 598300653 2.850000e-47 200
17 TraesCS2D01G503400 chr2D 88.679 159 18 0 4161 4319 598305228 598305386 1.330000e-45 195
18 TraesCS2D01G503400 chr2D 84.076 157 20 5 2446 2601 642198007 642198159 3.760000e-31 147
19 TraesCS2D01G503400 chr2D 81.967 122 21 1 2465 2586 642037349 642037229 8.260000e-18 102
20 TraesCS2D01G503400 chr2A 86.037 1991 225 23 2703 4663 766969889 766971856 0.000000e+00 2087
21 TraesCS2D01G503400 chr2A 86.342 1457 177 14 1 1443 766966974 766968422 0.000000e+00 1568
22 TraesCS2D01G503400 chr2A 80.379 1845 295 40 1 1788 767001968 767003802 0.000000e+00 1339
23 TraesCS2D01G503400 chr2A 78.767 1719 298 41 80 1751 769956291 769957989 0.000000e+00 1090
24 TraesCS2D01G503400 chr2A 80.694 1326 206 33 2843 4145 767005540 767006838 0.000000e+00 985
25 TraesCS2D01G503400 chr2A 77.755 1488 277 34 255 1705 769654156 769655626 0.000000e+00 865
26 TraesCS2D01G503400 chr2A 79.932 877 133 26 1502 2350 766968442 766969303 5.170000e-169 604
27 TraesCS2D01G503400 chr2A 87.906 339 37 4 2376 2713 766969462 766969797 3.380000e-106 396
28 TraesCS2D01G503400 chr2A 89.119 193 21 0 4127 4319 767006998 767007190 1.680000e-59 241
29 TraesCS2D01G503400 chr2A 84.076 157 20 5 2446 2601 766899333 766899485 3.760000e-31 147
30 TraesCS2D01G503400 chr2B 81.867 932 142 19 3207 4119 799618765 799617842 0.000000e+00 760
31 TraesCS2D01G503400 chr2B 84.428 411 58 4 245 654 790890572 790890167 2.620000e-107 399
32 TraesCS2D01G503400 chr2B 83.766 154 20 5 2449 2601 799619506 799619357 1.750000e-29 141


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 TraesCS2D01G503400 chr2D 598277117 598281783 4666 True 8619.000000 8619 100.000000 1 4667 1 chr2D.!!$R1 4666
1 TraesCS2D01G503400 chr2D 598293786 598295933 2147 False 1493.000000 1493 79.779000 1 2102 1 chr2D.!!$F1 2101
2 TraesCS2D01G503400 chr2D 642152693 642153664 971 True 1411.000000 1411 92.936000 1981 2957 1 chr2D.!!$R2 976
3 TraesCS2D01G503400 chr2D 642053847 642061215 7368 False 1217.250000 2019 83.724500 1 4319 4 chr2D.!!$F3 4318
4 TraesCS2D01G503400 chr2D 598300437 598305386 4949 False 840.000000 2013 85.002750 2132 4319 4 chr2D.!!$F2 2187
5 TraesCS2D01G503400 chr2D 642133784 642136618 2834 True 823.666667 1363 92.672333 2949 4667 3 chr2D.!!$R5 1718
6 TraesCS2D01G503400 chr2D 597959714 597961440 1726 True 469.000000 695 81.549000 2916 4132 2 chr2D.!!$R3 1216
7 TraesCS2D01G503400 chr2D 642198007 642199710 1703 False 467.000000 787 83.255500 2446 4116 2 chr2D.!!$F4 1670
8 TraesCS2D01G503400 chr2D 642036218 642037349 1131 True 464.000000 826 82.321500 2465 3796 2 chr2D.!!$R4 1331
9 TraesCS2D01G503400 chr2A 766966974 766971856 4882 False 1163.750000 2087 85.054250 1 4663 4 chr2A.!!$F4 4662
10 TraesCS2D01G503400 chr2A 769956291 769957989 1698 False 1090.000000 1090 78.767000 80 1751 1 chr2A.!!$F3 1671
11 TraesCS2D01G503400 chr2A 769654156 769655626 1470 False 865.000000 865 77.755000 255 1705 1 chr2A.!!$F2 1450
12 TraesCS2D01G503400 chr2A 767001968 767007190 5222 False 855.000000 1339 83.397333 1 4319 3 chr2A.!!$F5 4318
13 TraesCS2D01G503400 chr2B 799617842 799619506 1664 True 450.500000 760 82.816500 2449 4119 2 chr2B.!!$R2 1670

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
262 273 0.033503 TATGAGCACAGGGAGGACGA 60.034 55.0 0.00 0.0 0.00 4.20 F
588 605 0.318784 GCGAGAACGTCTCCACTGTT 60.319 55.0 8.73 0.0 40.34 3.16 F
1726 1797 0.321671 ACATCCCAACAGACCAGTCG 59.678 55.0 0.00 0.0 34.09 4.18 F
2020 2787 1.159098 TTACCACGACCCGTTTGCAC 61.159 55.0 0.00 0.0 38.32 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1310 1375 0.528466 CGAGTGATGGATCCACGGTG 60.528 60.0 18.99 0.0 39.38 4.94 R
1829 1910 0.583438 CGTGGACAGTTGAGTTGCTG 59.417 55.0 0.00 0.0 38.58 4.41 R
2894 4267 0.388649 GTCGCACACACCCTACTCAG 60.389 60.0 0.00 0.0 0.00 3.35 R
3960 8149 0.106708 GCCTTCTGTGCGGATCCATA 59.893 55.0 13.41 0.0 0.00 2.74 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
35 36 4.157607 CAAAGGAGTTGGTGGCGT 57.842 55.556 0.00 0.00 33.18 5.68
36 37 1.949257 CAAAGGAGTTGGTGGCGTC 59.051 57.895 0.00 0.00 33.18 5.19
46 47 2.305127 GGTGGCGTCGTGTACACAC 61.305 63.158 24.98 19.14 43.15 3.82
50 51 1.002250 GGCGTCGTGTACACACTGAG 61.002 60.000 24.98 12.07 44.34 3.35
51 52 1.002250 GCGTCGTGTACACACTGAGG 61.002 60.000 24.98 18.75 44.34 3.86
54 55 1.733041 CGTGTACACACTGAGGCCG 60.733 63.158 24.98 4.63 44.34 6.13
57 58 1.446272 GTACACACTGAGGCCGCTC 60.446 63.158 8.34 0.00 0.00 5.03
58 59 2.646175 TACACACTGAGGCCGCTCC 61.646 63.158 8.34 0.00 0.00 4.70
59 60 4.007644 CACACTGAGGCCGCTCCA 62.008 66.667 8.34 0.00 37.29 3.86
69 70 2.046892 CCGCTCCACCCTGTCAAG 60.047 66.667 0.00 0.00 0.00 3.02
70 71 2.046892 CGCTCCACCCTGTCAAGG 60.047 66.667 0.00 0.00 44.06 3.61
73 74 2.847234 TCCACCCTGTCAAGGCGT 60.847 61.111 0.00 0.00 42.96 5.68
75 76 0.907704 TCCACCCTGTCAAGGCGTAT 60.908 55.000 0.00 0.00 42.96 3.06
88 89 1.404391 AGGCGTATGAGTTACTCCGTG 59.596 52.381 10.10 0.00 40.09 4.94
98 99 0.605319 TTACTCCGTGCCAAAGCTGG 60.605 55.000 0.00 0.00 46.65 4.85
99 100 2.463589 TACTCCGTGCCAAAGCTGGG 62.464 60.000 0.27 0.27 43.74 4.45
114 115 2.936202 GCTGGGGCTGAAAGATATGAA 58.064 47.619 0.00 0.00 34.07 2.57
115 116 2.620585 GCTGGGGCTGAAAGATATGAAC 59.379 50.000 0.00 0.00 34.07 3.18
116 117 3.889815 CTGGGGCTGAAAGATATGAACA 58.110 45.455 0.00 0.00 34.07 3.18
118 119 4.464008 TGGGGCTGAAAGATATGAACATC 58.536 43.478 0.00 0.00 34.07 3.06
125 126 7.977853 GGCTGAAAGATATGAACATCAATTTGT 59.022 33.333 0.00 0.00 34.07 2.83
126 127 9.017669 GCTGAAAGATATGAACATCAATTTGTC 57.982 33.333 0.00 0.00 34.07 3.18
133 134 4.558178 TGAACATCAATTTGTCATGGTGC 58.442 39.130 0.00 0.00 30.67 5.01
143 144 5.389859 TTTGTCATGGTGCCAGATAAAAG 57.610 39.130 0.00 0.00 0.00 2.27
144 145 4.299586 TGTCATGGTGCCAGATAAAAGA 57.700 40.909 0.00 0.00 0.00 2.52
145 146 4.661222 TGTCATGGTGCCAGATAAAAGAA 58.339 39.130 0.00 0.00 0.00 2.52
149 150 5.716228 TCATGGTGCCAGATAAAAGAATGTT 59.284 36.000 0.00 0.00 0.00 2.71
150 151 5.389859 TGGTGCCAGATAAAAGAATGTTG 57.610 39.130 0.00 0.00 0.00 3.33
151 152 4.176271 GGTGCCAGATAAAAGAATGTTGC 58.824 43.478 0.00 0.00 0.00 4.17
152 153 4.082026 GGTGCCAGATAAAAGAATGTTGCT 60.082 41.667 0.00 0.00 0.00 3.91
182 183 1.063792 TGGTGTGCCAATAGCCATCAT 60.064 47.619 0.00 0.00 42.83 2.45
195 196 8.708378 CCAATAGCCATCATTATGATAGGTAGA 58.292 37.037 15.19 0.00 33.45 2.59
196 197 9.761504 CAATAGCCATCATTATGATAGGTAGAG 57.238 37.037 15.19 8.44 33.45 2.43
199 200 6.728164 AGCCATCATTATGATAGGTAGAGTGT 59.272 38.462 7.44 0.00 34.28 3.55
203 204 9.770097 CATCATTATGATAGGTAGAGTGTTTGT 57.230 33.333 7.44 0.00 34.28 2.83
204 205 9.988815 ATCATTATGATAGGTAGAGTGTTTGTC 57.011 33.333 5.83 0.00 34.88 3.18
206 207 9.254133 CATTATGATAGGTAGAGTGTTTGTCAG 57.746 37.037 0.00 0.00 0.00 3.51
214 215 7.227156 AGGTAGAGTGTTTGTCAGAAATCAAT 58.773 34.615 0.00 0.00 0.00 2.57
215 216 7.721399 AGGTAGAGTGTTTGTCAGAAATCAATT 59.279 33.333 0.00 0.00 0.00 2.32
223 224 4.996793 TGTCAGAAATCAATTCAAGGGGA 58.003 39.130 0.00 0.00 40.72 4.81
227 228 1.767759 AATCAATTCAAGGGGAGGCG 58.232 50.000 0.00 0.00 0.00 5.52
228 229 0.106519 ATCAATTCAAGGGGAGGCGG 60.107 55.000 0.00 0.00 0.00 6.13
229 230 2.043953 AATTCAAGGGGAGGCGGC 60.044 61.111 0.00 0.00 0.00 6.53
239 240 4.814294 GAGGCGGCGGTGTGTAGG 62.814 72.222 9.78 0.00 0.00 3.18
253 264 2.233676 TGTGTAGGGTGTATGAGCACAG 59.766 50.000 0.00 0.00 40.89 3.66
262 273 0.033503 TATGAGCACAGGGAGGACGA 60.034 55.000 0.00 0.00 0.00 4.20
274 285 3.703127 GGACGAGGGCTTTCCGGT 61.703 66.667 0.00 0.00 41.52 5.28
302 313 5.763876 AGGAAGGTGTTGTCTTATAGCTT 57.236 39.130 0.00 0.00 33.99 3.74
351 362 5.428253 CAATGCTTTCTGTACCTAAGCCTA 58.572 41.667 16.35 4.58 42.70 3.93
435 446 5.480073 CCTTGTTCCTGATGGGTTATTTGAA 59.520 40.000 0.00 0.00 36.25 2.69
463 474 4.361420 GGAGACCTATTTCAACGAGCTAC 58.639 47.826 0.00 0.00 0.00 3.58
553 564 3.189080 CGTTTTGATGCTTGACCTCATCA 59.811 43.478 1.25 1.25 44.99 3.07
555 566 3.986996 TTGATGCTTGACCTCATCAGA 57.013 42.857 5.27 0.00 46.49 3.27
556 567 3.257469 TGATGCTTGACCTCATCAGAC 57.743 47.619 1.25 0.00 42.72 3.51
576 587 0.601311 ACCTGTCAAGCAGCGAGAAC 60.601 55.000 0.00 0.00 43.71 3.01
577 594 1.621301 CCTGTCAAGCAGCGAGAACG 61.621 60.000 0.00 0.00 43.71 3.95
588 605 0.318784 GCGAGAACGTCTCCACTGTT 60.319 55.000 8.73 0.00 40.34 3.16
589 606 1.068748 GCGAGAACGTCTCCACTGTTA 60.069 52.381 8.73 0.00 40.34 2.41
595 612 2.453521 ACGTCTCCACTGTTATAGGCA 58.546 47.619 0.00 0.00 0.00 4.75
598 615 4.647853 ACGTCTCCACTGTTATAGGCATAA 59.352 41.667 0.00 0.00 0.00 1.90
600 617 6.183360 ACGTCTCCACTGTTATAGGCATAAAT 60.183 38.462 0.00 0.00 0.00 1.40
601 618 6.366332 CGTCTCCACTGTTATAGGCATAAATC 59.634 42.308 0.00 0.00 0.00 2.17
628 648 0.394352 GAGCACATCCCAAACCGGAT 60.394 55.000 9.46 0.00 43.79 4.18
690 737 1.615424 TAGCCTGGAAGTGGGGGAC 60.615 63.158 0.00 0.00 0.00 4.46
732 791 1.518572 CGGTAGTAGCTTGCCACCG 60.519 63.158 11.86 11.86 45.25 4.94
804 863 3.616956 TCCGTCAGAGATTGCAATCTT 57.383 42.857 35.91 24.36 45.39 2.40
805 864 3.942829 TCCGTCAGAGATTGCAATCTTT 58.057 40.909 35.91 29.61 45.39 2.52
814 873 4.267536 AGATTGCAATCTTTAGCAGCTCA 58.732 39.130 31.78 0.00 42.96 4.26
831 890 2.228343 GCTCAGCAGATTGAAAGTGCTT 59.772 45.455 2.24 0.00 45.31 3.91
892 951 1.401905 CAAGCAAAATAGGACGCCTCC 59.598 52.381 1.46 0.00 34.61 4.30
931 990 4.451150 TGACGGCGACTGGCATCC 62.451 66.667 16.62 0.00 46.16 3.51
990 1049 2.515757 TGTCTGCGTGCTGGCAAA 60.516 55.556 3.44 0.00 43.39 3.68
1013 1072 2.427753 GAGGATGATGGGTCGGGC 59.572 66.667 0.00 0.00 0.00 6.13
1014 1073 3.521529 GAGGATGATGGGTCGGGCG 62.522 68.421 0.00 0.00 0.00 6.13
1119 1178 2.438975 ATGCGGGTGCTGGTGATG 60.439 61.111 0.00 0.00 43.34 3.07
1167 1226 2.617532 GCAGAAGAAGCTGGTGGAATCT 60.618 50.000 0.00 0.00 36.41 2.40
1225 1284 1.072331 GGTTCAGCACAGAGGGAAAGA 59.928 52.381 0.00 0.00 0.00 2.52
1306 1371 2.927056 GGGCCATCCTACCCAAGG 59.073 66.667 4.39 0.00 46.22 3.61
1422 1487 3.069980 GATGCCGTCACTCCGCTCT 62.070 63.158 0.00 0.00 0.00 4.09
1452 1517 2.774234 CCACATGGAGGAGGACAAGTAT 59.226 50.000 0.00 0.00 37.39 2.12
1455 1520 1.112113 TGGAGGAGGACAAGTATCGC 58.888 55.000 0.00 0.00 0.00 4.58
1494 1559 2.036733 CAGGGACGAGTTCAAGGTGTTA 59.963 50.000 0.00 0.00 0.00 2.41
1497 1562 3.576648 GGACGAGTTCAAGGTGTTAGAG 58.423 50.000 0.00 0.00 0.00 2.43
1533 1601 1.179174 TAGAGCTGGTATGCGGCGAT 61.179 55.000 12.98 3.86 38.13 4.58
1555 1623 1.063166 GCGCTGCCACTAATTCAGC 59.937 57.895 0.00 6.10 46.98 4.26
1567 1635 2.299326 AATTCAGCAGCTGGAGGTTT 57.701 45.000 22.62 2.11 31.51 3.27
1577 1645 1.001020 TGGAGGTTTGCGGCATCAT 60.001 52.632 2.28 0.00 0.00 2.45
1582 1653 1.455383 GGTTTGCGGCATCATAGGGG 61.455 60.000 2.28 0.00 0.00 4.79
1583 1654 0.751643 GTTTGCGGCATCATAGGGGT 60.752 55.000 2.28 0.00 0.00 4.95
1598 1669 4.643387 GGTGGACGTTGGCCTGCT 62.643 66.667 3.32 0.00 0.00 4.24
1622 1693 1.480954 GAACATGCCCCTACTCGAGAA 59.519 52.381 21.68 0.00 0.00 2.87
1685 1756 2.817396 GCGTGAGGCAGAGGAAGC 60.817 66.667 0.00 0.00 42.87 3.86
1689 1760 2.511145 GAGGCAGAGGAAGCGCTG 60.511 66.667 12.58 0.00 35.28 5.18
1690 1761 4.093291 AGGCAGAGGAAGCGCTGG 62.093 66.667 12.58 0.00 32.83 4.85
1692 1763 4.087892 GCAGAGGAAGCGCTGGGA 62.088 66.667 12.58 0.00 32.83 4.37
1705 1776 4.329545 TGGGACAGGCGAGCCAAC 62.330 66.667 17.18 6.76 38.92 3.77
1706 1777 4.329545 GGGACAGGCGAGCCAACA 62.330 66.667 17.18 0.00 38.92 3.33
1710 1781 1.228245 ACAGGCGAGCCAACAACAT 60.228 52.632 17.18 0.00 38.92 2.71
1719 1790 1.133513 AGCCAACAACATCCCAACAGA 60.134 47.619 0.00 0.00 0.00 3.41
1726 1797 0.321671 ACATCCCAACAGACCAGTCG 59.678 55.000 0.00 0.00 34.09 4.18
1753 1827 4.673441 CATAAAGAGATGGAACGACGAGT 58.327 43.478 0.00 0.00 0.00 4.18
1779 1853 7.872113 ATGTTCCTCTTCATTTCAGGTAATC 57.128 36.000 0.00 0.00 0.00 1.75
1783 1857 7.687941 TCCTCTTCATTTCAGGTAATCAAAC 57.312 36.000 0.00 0.00 0.00 2.93
1787 1861 9.748708 CTCTTCATTTCAGGTAATCAAACAAAA 57.251 29.630 0.00 0.00 0.00 2.44
1865 1947 7.606456 ACTGTCCACGTTCAGTTGATTAATTAT 59.394 33.333 10.68 0.00 41.33 1.28
1868 1950 9.916397 GTCCACGTTCAGTTGATTAATTATTAG 57.084 33.333 0.00 0.00 0.00 1.73
1869 1951 8.609176 TCCACGTTCAGTTGATTAATTATTAGC 58.391 33.333 0.00 0.00 0.00 3.09
1907 1997 7.106439 ACCTAGCTATCATCTGCATACATAC 57.894 40.000 0.00 0.00 0.00 2.39
1920 2677 3.002656 GCATACATACTTGCGCTGATTGT 59.997 43.478 9.73 8.76 0.00 2.71
1935 2696 4.355437 CTGATTGTTTTTAACCACGCACA 58.645 39.130 0.00 0.00 0.00 4.57
1940 2701 2.039818 TTTTAACCACGCACACAGGA 57.960 45.000 0.00 0.00 0.00 3.86
1942 2703 2.039818 TTAACCACGCACACAGGAAA 57.960 45.000 0.00 0.00 0.00 3.13
1948 2709 2.551270 GCACACAGGAAACGAGCG 59.449 61.111 0.00 0.00 0.00 5.03
1949 2710 2.244651 GCACACAGGAAACGAGCGT 61.245 57.895 0.00 0.00 0.00 5.07
1950 2711 1.772063 GCACACAGGAAACGAGCGTT 61.772 55.000 1.93 1.93 40.45 4.84
1963 2724 3.909430 ACGAGCGTTAGTGATTCTGAAA 58.091 40.909 0.00 0.00 0.00 2.69
1964 2725 3.921021 ACGAGCGTTAGTGATTCTGAAAG 59.079 43.478 0.00 0.00 0.00 2.62
1969 2730 5.758296 AGCGTTAGTGATTCTGAAAGTGAAA 59.242 36.000 0.00 0.00 33.76 2.69
1971 2732 6.074005 CGTTAGTGATTCTGAAAGTGAAAGC 58.926 40.000 0.00 0.00 33.76 3.51
2020 2787 1.159098 TTACCACGACCCGTTTGCAC 61.159 55.000 0.00 0.00 38.32 4.57
2021 2788 4.007940 CCACGACCCGTTTGCACG 62.008 66.667 0.00 0.00 46.71 5.34
2028 2795 2.334653 CCGTTTGCACGCCATGTT 59.665 55.556 0.00 0.00 45.72 2.71
2035 2802 2.703798 GCACGCCATGTTGAGCCAT 61.704 57.895 0.00 0.00 0.00 4.40
2102 2869 5.114780 CACCATCTCTAGTGTTTGATCCAG 58.885 45.833 0.00 0.00 0.00 3.86
2108 2883 2.457366 AGTGTTTGATCCAGACGTCC 57.543 50.000 13.01 0.00 0.00 4.79
2125 2900 5.082251 ACGTCCTTATCTTAACTTGTCCC 57.918 43.478 0.00 0.00 0.00 4.46
2300 3085 1.485066 GGCTACCTAGCTTGCAGGTTA 59.515 52.381 11.89 0.00 44.18 2.85
2357 3152 1.545651 GGCTGTTACTTCACCCAAGCT 60.546 52.381 0.00 0.00 35.17 3.74
2713 3768 6.671614 TTTTGTTGTTACAGTAGGACACAG 57.328 37.500 0.00 0.00 35.28 3.66
2884 4257 5.759763 TGATCGATGTTGTATGCTGCTAATT 59.240 36.000 0.54 0.00 0.00 1.40
2885 4258 6.928492 TGATCGATGTTGTATGCTGCTAATTA 59.072 34.615 0.54 0.00 0.00 1.40
2888 4261 8.825667 TCGATGTTGTATGCTGCTAATTAATA 57.174 30.769 0.00 0.00 0.00 0.98
2889 4262 8.708742 TCGATGTTGTATGCTGCTAATTAATAC 58.291 33.333 0.00 0.00 0.00 1.89
2890 4263 8.495148 CGATGTTGTATGCTGCTAATTAATACA 58.505 33.333 0.00 2.75 33.17 2.29
2893 4266 8.783093 TGTTGTATGCTGCTAATTAATACATCC 58.217 33.333 0.00 1.18 34.60 3.51
2894 4267 7.921786 TGTATGCTGCTAATTAATACATCCC 57.078 36.000 0.00 0.00 30.75 3.85
2911 4296 1.079819 CCTGAGTAGGGTGTGTGCG 60.080 63.158 0.00 0.00 40.63 5.34
3099 4484 3.802866 TGAAGGAACCATTGTTTTTGGC 58.197 40.909 0.00 0.00 37.81 4.52
3178 4563 1.112113 TCTGTCCGGTAATGAGGCTC 58.888 55.000 7.79 7.79 0.00 4.70
3179 4564 1.115467 CTGTCCGGTAATGAGGCTCT 58.885 55.000 16.72 0.00 0.00 4.09
3260 7430 9.163899 CATCTATATCTGGATTCCAATGACAAG 57.836 37.037 6.88 1.24 30.80 3.16
3335 7505 6.490721 TCACGTTACAAAATTATCAAAGGGGT 59.509 34.615 0.00 0.00 0.00 4.95
3345 7515 1.408969 TCAAAGGGGTTTGTGAAGGC 58.591 50.000 0.00 0.00 33.82 4.35
3480 7651 2.015736 AGTGCTATGGCGAAGAACAG 57.984 50.000 0.00 0.00 42.25 3.16
3540 7718 8.062065 AGTAATTGCTTCCCGAAAATGAAATA 57.938 30.769 0.00 0.00 0.00 1.40
3582 7762 6.017440 TGCTCTTCGTAATATTTATGTTGCCC 60.017 38.462 0.00 0.00 0.00 5.36
3629 7809 9.025041 CCAGAATACTTATTTGGAAGAAAGGTT 57.975 33.333 0.00 0.00 31.43 3.50
3666 7846 7.327975 TGACATTTATAGTCTGGGTGTTGTAG 58.672 38.462 0.00 0.00 36.94 2.74
3681 7861 7.504238 TGGGTGTTGTAGTGACAAAGATAATTT 59.496 33.333 0.00 0.00 46.99 1.82
3906 8095 1.067565 TGGAGTTCTGCGCAACTAGAG 60.068 52.381 14.46 0.00 36.71 2.43
3956 8145 0.447011 GAGATTGCACTGAGCTGCAC 59.553 55.000 8.77 0.00 46.90 4.57
3957 8146 0.250597 AGATTGCACTGAGCTGCACA 60.251 50.000 8.77 0.00 46.90 4.57
3960 8149 0.250597 TTGCACTGAGCTGCACAGAT 60.251 50.000 29.31 13.53 46.90 2.90
3967 8156 3.244146 ACTGAGCTGCACAGATATGGATC 60.244 47.826 29.31 2.37 38.55 3.36
3968 8157 2.038164 TGAGCTGCACAGATATGGATCC 59.962 50.000 4.20 4.20 31.81 3.36
3971 8160 0.758123 TGCACAGATATGGATCCGCA 59.242 50.000 7.39 4.87 32.66 5.69
3997 8186 7.071196 ACAGAAGGCCAAGTATAGTGAATATCA 59.929 37.037 5.01 0.00 0.00 2.15
3999 8188 8.664079 AGAAGGCCAAGTATAGTGAATATCATT 58.336 33.333 5.01 0.00 0.00 2.57
4012 8201 8.797350 AGTGAATATCATTGATGAACTGAACA 57.203 30.769 9.46 0.00 40.69 3.18
4037 8226 9.533253 CAAGACTGAAAAATGTATTGAAAAGGT 57.467 29.630 0.00 0.00 37.52 3.50
4065 8254 4.590850 TCATGAACTAGATCCATCACCG 57.409 45.455 0.00 0.00 0.00 4.94
4066 8255 3.960755 TCATGAACTAGATCCATCACCGT 59.039 43.478 0.00 0.00 0.00 4.83
4069 8258 3.130516 TGAACTAGATCCATCACCGTCAC 59.869 47.826 0.00 0.00 0.00 3.67
4085 8274 2.354510 CGTCACTTGCTTCCACTTCAAA 59.645 45.455 0.00 0.00 0.00 2.69
4165 11291 0.609957 TGCCTCCTTCTCCGACGTTA 60.610 55.000 0.00 0.00 0.00 3.18
4200 11326 5.351189 CCGTGATGACATTGACATAACTTCA 59.649 40.000 12.73 1.51 29.56 3.02
4221 11350 3.019564 AGAAGCCAAAGATCAATTCCCG 58.980 45.455 0.00 0.00 0.00 5.14
4236 11365 0.034477 TCCCGGAGAATTCCAAAGCC 60.034 55.000 0.73 0.00 44.26 4.35
4283 12582 6.433716 TGCCATCACAATCAACTTATTCTTGA 59.566 34.615 0.00 0.00 32.24 3.02
4361 12660 0.178992 CAAAGGTGGCAGGTGAAGGA 60.179 55.000 0.00 0.00 0.00 3.36
4393 12699 6.106673 ACCTACCAGTCGAATCATTTGTAAG 58.893 40.000 0.00 0.00 0.00 2.34
4394 12700 4.946784 ACCAGTCGAATCATTTGTAAGC 57.053 40.909 0.00 0.00 0.00 3.09
4413 12719 1.725931 GCGTTCAAGAGATGTTTGGCG 60.726 52.381 0.00 0.00 0.00 5.69
4429 12753 4.829064 TTGGCGATATCAACTAAATGGC 57.171 40.909 3.12 0.00 0.00 4.40
4430 12754 4.085357 TGGCGATATCAACTAAATGGCT 57.915 40.909 3.12 0.00 0.00 4.75
4431 12755 4.460263 TGGCGATATCAACTAAATGGCTT 58.540 39.130 3.12 0.00 0.00 4.35
4432 12756 4.275689 TGGCGATATCAACTAAATGGCTTG 59.724 41.667 3.12 0.00 0.00 4.01
4433 12757 4.320494 GGCGATATCAACTAAATGGCTTGG 60.320 45.833 3.12 0.00 0.00 3.61
4434 12758 4.787598 CGATATCAACTAAATGGCTTGGC 58.212 43.478 3.12 0.00 0.00 4.52
4435 12759 4.516698 CGATATCAACTAAATGGCTTGGCT 59.483 41.667 3.12 0.00 0.00 4.75
4436 12760 5.334414 CGATATCAACTAAATGGCTTGGCTC 60.334 44.000 3.12 0.00 0.00 4.70
4437 12761 3.153369 TCAACTAAATGGCTTGGCTCA 57.847 42.857 0.00 0.00 0.00 4.26
4438 12762 3.084039 TCAACTAAATGGCTTGGCTCAG 58.916 45.455 0.00 0.00 0.00 3.35
4439 12763 3.084039 CAACTAAATGGCTTGGCTCAGA 58.916 45.455 0.00 0.00 0.00 3.27
4440 12764 3.439857 ACTAAATGGCTTGGCTCAGAA 57.560 42.857 0.00 0.00 0.00 3.02
4441 12765 3.350833 ACTAAATGGCTTGGCTCAGAAG 58.649 45.455 0.00 0.00 0.00 2.85
4442 12766 1.553706 AAATGGCTTGGCTCAGAAGG 58.446 50.000 0.00 0.00 0.00 3.46
4443 12767 0.324091 AATGGCTTGGCTCAGAAGGG 60.324 55.000 0.00 0.00 0.00 3.95
4557 12881 0.318762 GTCTGTCCACACTGGTCTCC 59.681 60.000 0.00 0.00 39.03 3.71
4661 12985 4.813235 GCCACGCCATTGCCCCTA 62.813 66.667 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 4.329545 TTGACAGGGTGGAGCGGC 62.330 66.667 0.00 0.00 0.00 6.53
54 55 2.360475 GCCTTGACAGGGTGGAGC 60.360 66.667 5.38 0.00 41.21 4.70
57 58 0.744414 CATACGCCTTGACAGGGTGG 60.744 60.000 20.09 8.40 41.21 4.61
58 59 0.249120 TCATACGCCTTGACAGGGTG 59.751 55.000 15.14 15.14 41.21 4.61
59 60 0.537188 CTCATACGCCTTGACAGGGT 59.463 55.000 5.38 0.00 41.21 4.34
70 71 1.197910 GCACGGAGTAACTCATACGC 58.802 55.000 0.00 0.00 41.61 4.42
73 74 3.857052 CTTTGGCACGGAGTAACTCATA 58.143 45.455 0.00 0.00 41.61 2.15
75 76 1.876416 GCTTTGGCACGGAGTAACTCA 60.876 52.381 0.00 0.00 41.61 3.41
98 99 6.645790 ATTGATGTTCATATCTTTCAGCCC 57.354 37.500 0.00 0.00 0.00 5.19
99 100 7.977853 ACAAATTGATGTTCATATCTTTCAGCC 59.022 33.333 0.00 0.00 0.00 4.85
108 109 6.982141 GCACCATGACAAATTGATGTTCATAT 59.018 34.615 0.00 0.00 32.57 1.78
109 110 6.331845 GCACCATGACAAATTGATGTTCATA 58.668 36.000 0.00 0.00 32.57 2.15
114 115 2.898612 TGGCACCATGACAAATTGATGT 59.101 40.909 0.00 0.00 28.38 3.06
115 116 3.193903 TCTGGCACCATGACAAATTGATG 59.806 43.478 0.00 0.00 33.21 3.07
116 117 3.433343 TCTGGCACCATGACAAATTGAT 58.567 40.909 0.00 0.00 33.21 2.57
118 119 3.880047 ATCTGGCACCATGACAAATTG 57.120 42.857 0.00 0.00 33.21 2.32
125 126 5.263599 ACATTCTTTTATCTGGCACCATGA 58.736 37.500 0.00 0.00 0.00 3.07
126 127 5.587388 ACATTCTTTTATCTGGCACCATG 57.413 39.130 0.00 0.00 0.00 3.66
128 129 4.321899 GCAACATTCTTTTATCTGGCACCA 60.322 41.667 0.00 0.00 0.00 4.17
129 130 4.082026 AGCAACATTCTTTTATCTGGCACC 60.082 41.667 0.00 0.00 0.00 5.01
133 134 9.643693 ACATTTAAGCAACATTCTTTTATCTGG 57.356 29.630 0.00 0.00 0.00 3.86
143 144 4.685628 CACCACCACATTTAAGCAACATTC 59.314 41.667 0.00 0.00 0.00 2.67
144 145 4.100808 ACACCACCACATTTAAGCAACATT 59.899 37.500 0.00 0.00 0.00 2.71
145 146 3.640967 ACACCACCACATTTAAGCAACAT 59.359 39.130 0.00 0.00 0.00 2.71
149 150 1.339610 GCACACCACCACATTTAAGCA 59.660 47.619 0.00 0.00 0.00 3.91
150 151 1.336795 GGCACACCACCACATTTAAGC 60.337 52.381 0.00 0.00 35.26 3.09
151 152 1.959985 TGGCACACCACCACATTTAAG 59.040 47.619 0.00 0.00 42.67 1.85
152 153 2.073252 TGGCACACCACCACATTTAA 57.927 45.000 0.00 0.00 42.67 1.52
177 178 9.770097 ACAAACACTCTACCTATCATAATGATG 57.230 33.333 0.00 0.00 37.70 3.07
182 183 8.589701 TCTGACAAACACTCTACCTATCATAA 57.410 34.615 0.00 0.00 0.00 1.90
195 196 7.205297 CCTTGAATTGATTTCTGACAAACACT 58.795 34.615 0.00 0.00 35.23 3.55
196 197 6.421801 CCCTTGAATTGATTTCTGACAAACAC 59.578 38.462 0.00 0.00 35.23 3.32
199 200 5.837979 TCCCCTTGAATTGATTTCTGACAAA 59.162 36.000 0.00 0.00 35.23 2.83
203 204 4.603131 CCTCCCCTTGAATTGATTTCTGA 58.397 43.478 0.00 0.00 35.23 3.27
204 205 3.131755 GCCTCCCCTTGAATTGATTTCTG 59.868 47.826 0.00 0.00 35.23 3.02
206 207 2.099756 CGCCTCCCCTTGAATTGATTTC 59.900 50.000 0.00 0.00 34.72 2.17
227 228 0.461339 CATACACCCTACACACCGCC 60.461 60.000 0.00 0.00 0.00 6.13
228 229 0.533491 TCATACACCCTACACACCGC 59.467 55.000 0.00 0.00 0.00 5.68
229 230 1.470979 GCTCATACACCCTACACACCG 60.471 57.143 0.00 0.00 0.00 4.94
232 233 2.233676 CTGTGCTCATACACCCTACACA 59.766 50.000 0.00 0.00 39.93 3.72
233 234 2.418746 CCTGTGCTCATACACCCTACAC 60.419 54.545 0.00 0.00 39.93 2.90
234 235 1.831106 CCTGTGCTCATACACCCTACA 59.169 52.381 0.00 0.00 39.93 2.74
235 236 1.139058 CCCTGTGCTCATACACCCTAC 59.861 57.143 0.00 0.00 39.93 3.18
236 237 1.007842 TCCCTGTGCTCATACACCCTA 59.992 52.381 0.00 0.00 39.93 3.53
237 238 0.252696 TCCCTGTGCTCATACACCCT 60.253 55.000 0.00 0.00 39.93 4.34
239 240 0.179000 CCTCCCTGTGCTCATACACC 59.821 60.000 0.00 0.00 39.93 4.16
240 241 1.134670 GTCCTCCCTGTGCTCATACAC 60.135 57.143 0.00 0.00 41.10 2.90
242 243 0.103208 CGTCCTCCCTGTGCTCATAC 59.897 60.000 0.00 0.00 0.00 2.39
253 264 2.585153 GAAAGCCCTCGTCCTCCC 59.415 66.667 0.00 0.00 0.00 4.30
262 273 1.489230 CCTTATGTACCGGAAAGCCCT 59.511 52.381 9.46 0.00 0.00 5.19
274 285 8.202137 GCTATAAGACAACACCTTCCTTATGTA 58.798 37.037 0.00 0.00 33.59 2.29
328 339 4.265073 AGGCTTAGGTACAGAAAGCATTG 58.735 43.478 20.71 0.00 45.86 2.82
435 446 3.307480 CGTTGAAATAGGTCTCCCCAGTT 60.307 47.826 0.00 0.00 34.66 3.16
463 474 4.322574 CCACTGGATCATGCACCTATCTAG 60.323 50.000 13.36 13.36 35.16 2.43
500 511 2.520458 CACCTTGGCTGGGGTCAA 59.480 61.111 2.53 0.00 35.60 3.18
532 543 4.771590 TGATGAGGTCAAGCATCAAAAC 57.228 40.909 0.00 0.00 45.55 2.43
576 587 3.735237 ATGCCTATAACAGTGGAGACG 57.265 47.619 0.00 0.00 0.00 4.18
577 594 7.217200 TGATTTATGCCTATAACAGTGGAGAC 58.783 38.462 0.00 0.00 0.00 3.36
588 605 5.337894 GCTCTCCTGCTGATTTATGCCTATA 60.338 44.000 0.00 0.00 0.00 1.31
589 606 4.565236 GCTCTCCTGCTGATTTATGCCTAT 60.565 45.833 0.00 0.00 0.00 2.57
595 612 3.920231 TGTGCTCTCCTGCTGATTTAT 57.080 42.857 0.00 0.00 0.00 1.40
598 615 1.134159 GGATGTGCTCTCCTGCTGATT 60.134 52.381 0.00 0.00 0.00 2.57
600 617 1.620739 GGGATGTGCTCTCCTGCTGA 61.621 60.000 0.00 0.00 33.05 4.26
601 618 1.153208 GGGATGTGCTCTCCTGCTG 60.153 63.158 4.87 0.00 33.05 4.41
628 648 5.310331 TGTGGATGGCTAATCTATGAATGGA 59.690 40.000 0.93 0.00 35.43 3.41
700 747 1.006220 TACCGGCGCATGCATAGAG 60.006 57.895 19.57 1.33 45.35 2.43
732 791 1.642037 GCCGTTTAAACCTCCGGAGC 61.642 60.000 26.87 9.42 43.01 4.70
766 825 3.197766 ACGGATAAATCACAGCTCTCCAA 59.802 43.478 0.00 0.00 0.00 3.53
804 863 3.339253 TTCAATCTGCTGAGCTGCTAA 57.661 42.857 5.83 0.00 0.00 3.09
805 864 3.268330 CTTTCAATCTGCTGAGCTGCTA 58.732 45.455 5.83 0.00 0.00 3.49
814 873 8.970859 ATATACTTAAGCACTTTCAATCTGCT 57.029 30.769 1.29 0.00 43.21 4.24
831 890 3.203263 TGCCCACAAGCCCAATATACTTA 59.797 43.478 0.00 0.00 0.00 2.24
876 935 1.017387 GCTGGAGGCGTCCTATTTTG 58.983 55.000 24.96 9.96 44.30 2.44
892 951 2.222213 CGTCGAGTATCTGTAGGAGCTG 59.778 54.545 0.00 0.00 0.00 4.24
931 990 2.811317 GAACGGTGGCAGCTCTCG 60.811 66.667 15.48 1.25 0.00 4.04
975 1034 2.979676 CCTTTGCCAGCACGCAGA 60.980 61.111 0.00 0.00 40.53 4.26
990 1049 1.690219 GACCCATCATCCTCGTGCCT 61.690 60.000 0.00 0.00 0.00 4.75
1014 1073 4.021925 AGGCACGTCAGCTTCCCC 62.022 66.667 0.00 0.00 34.17 4.81
1119 1178 1.557443 CGTCCACCTCGTCAAAGTGC 61.557 60.000 0.00 0.00 0.00 4.40
1125 1184 2.675423 CCCTCGTCCACCTCGTCA 60.675 66.667 0.00 0.00 0.00 4.35
1167 1226 1.980765 AGCTTGTTCAGATGGACCAGA 59.019 47.619 0.00 0.00 0.00 3.86
1225 1284 2.270205 CCAGCTGTTGAGGCGGAT 59.730 61.111 13.81 0.00 34.52 4.18
1234 1293 1.525995 CGTTGTCACCCCAGCTGTT 60.526 57.895 13.81 0.00 0.00 3.16
1244 1309 2.258726 GGGAAGGGCACGTTGTCAC 61.259 63.158 0.00 0.00 36.18 3.67
1245 1310 2.112297 GGGAAGGGCACGTTGTCA 59.888 61.111 0.00 0.00 36.18 3.58
1306 1371 0.824109 TGATGGATCCACGGTGTCTC 59.176 55.000 18.99 9.54 0.00 3.36
1310 1375 0.528466 CGAGTGATGGATCCACGGTG 60.528 60.000 18.99 0.00 39.38 4.94
1475 1540 2.298163 TCTAACACCTTGAACTCGTCCC 59.702 50.000 0.00 0.00 0.00 4.46
1477 1542 3.982058 CACTCTAACACCTTGAACTCGTC 59.018 47.826 0.00 0.00 0.00 4.20
1497 1562 2.744202 CTCTATGTTGGTGTTGAGGCAC 59.256 50.000 0.00 0.00 38.56 5.01
1546 1614 2.706339 ACCTCCAGCTGCTGAATTAG 57.294 50.000 30.10 19.25 32.44 1.73
1548 1616 1.891150 CAAACCTCCAGCTGCTGAATT 59.109 47.619 30.10 14.93 32.44 2.17
1555 1623 3.741476 GCCGCAAACCTCCAGCTG 61.741 66.667 6.78 6.78 0.00 4.24
1567 1635 2.510411 CACCCCTATGATGCCGCA 59.490 61.111 0.00 0.00 0.00 5.69
1577 1645 3.324108 GGCCAACGTCCACCCCTA 61.324 66.667 0.00 0.00 0.00 3.53
1582 1653 3.357079 CAGCAGGCCAACGTCCAC 61.357 66.667 5.01 0.00 0.00 4.02
1583 1654 4.641645 CCAGCAGGCCAACGTCCA 62.642 66.667 5.01 0.00 0.00 4.02
1611 1682 1.115467 ATGTGGCCTTCTCGAGTAGG 58.885 55.000 28.51 28.51 35.90 3.18
1622 1693 1.305802 TCGAGGTGGTATGTGGCCT 60.306 57.895 3.32 0.00 0.00 5.19
1671 1742 2.999648 AGCGCTTCCTCTGCCTCA 61.000 61.111 2.64 0.00 0.00 3.86
1672 1743 2.511145 CAGCGCTTCCTCTGCCTC 60.511 66.667 7.50 0.00 0.00 4.70
1689 1760 3.842925 TTGTTGGCTCGCCTGTCCC 62.843 63.158 9.65 0.00 36.94 4.46
1690 1761 2.281484 TTGTTGGCTCGCCTGTCC 60.281 61.111 9.65 0.00 36.94 4.02
1692 1763 1.228245 ATGTTGTTGGCTCGCCTGT 60.228 52.632 9.65 0.00 36.94 4.00
1705 1776 2.154462 GACTGGTCTGTTGGGATGTTG 58.846 52.381 0.00 0.00 0.00 3.33
1706 1777 1.270839 CGACTGGTCTGTTGGGATGTT 60.271 52.381 0.00 0.00 0.00 2.71
1710 1781 0.757561 TGACGACTGGTCTGTTGGGA 60.758 55.000 0.00 0.00 46.24 4.37
1719 1790 3.162666 TCTCTTTATGGTGACGACTGGT 58.837 45.455 0.00 0.00 0.00 4.00
1726 1797 4.567159 GTCGTTCCATCTCTTTATGGTGAC 59.433 45.833 2.98 6.41 45.67 3.67
1752 1826 8.561738 TTACCTGAAATGAAGAGGAACATAAC 57.438 34.615 0.00 0.00 0.00 1.89
1753 1827 9.396022 GATTACCTGAAATGAAGAGGAACATAA 57.604 33.333 0.00 0.00 0.00 1.90
1811 1885 9.208022 GAGTTGCTGCATGAGTATACATAATTA 57.792 33.333 1.84 0.00 0.00 1.40
1812 1886 7.716560 TGAGTTGCTGCATGAGTATACATAATT 59.283 33.333 1.84 0.00 0.00 1.40
1813 1887 7.219322 TGAGTTGCTGCATGAGTATACATAAT 58.781 34.615 1.84 0.00 0.00 1.28
1814 1888 6.581712 TGAGTTGCTGCATGAGTATACATAA 58.418 36.000 1.84 0.00 0.00 1.90
1817 1891 4.470334 TGAGTTGCTGCATGAGTATACA 57.530 40.909 1.84 0.00 0.00 2.29
1818 1892 4.872691 AGTTGAGTTGCTGCATGAGTATAC 59.127 41.667 1.84 0.00 0.00 1.47
1819 1893 4.872124 CAGTTGAGTTGCTGCATGAGTATA 59.128 41.667 1.84 0.00 0.00 1.47
1820 1894 3.688185 CAGTTGAGTTGCTGCATGAGTAT 59.312 43.478 1.84 0.00 0.00 2.12
1821 1895 3.069289 CAGTTGAGTTGCTGCATGAGTA 58.931 45.455 1.84 0.00 0.00 2.59
1822 1896 1.878088 CAGTTGAGTTGCTGCATGAGT 59.122 47.619 1.84 0.00 0.00 3.41
1823 1897 1.878088 ACAGTTGAGTTGCTGCATGAG 59.122 47.619 1.84 0.00 36.26 2.90
1824 1898 1.875514 GACAGTTGAGTTGCTGCATGA 59.124 47.619 1.84 0.00 36.26 3.07
1825 1899 1.068748 GGACAGTTGAGTTGCTGCATG 60.069 52.381 1.84 0.00 36.26 4.06
1829 1910 0.583438 CGTGGACAGTTGAGTTGCTG 59.417 55.000 0.00 0.00 38.58 4.41
1865 1947 5.221009 GCTAGGTAGCGAAAGAACTAGCTAA 60.221 44.000 10.90 0.00 44.47 3.09
1868 1950 3.373849 GCTAGGTAGCGAAAGAACTAGC 58.626 50.000 3.39 3.39 39.82 3.42
1884 1973 7.345422 AGTATGTATGCAGATGATAGCTAGG 57.655 40.000 0.00 0.00 0.00 3.02
1907 1997 4.047822 TGGTTAAAAACAATCAGCGCAAG 58.952 39.130 11.47 0.72 43.44 4.01
1920 2677 2.366533 TCCTGTGTGCGTGGTTAAAAA 58.633 42.857 0.00 0.00 0.00 1.94
1935 2696 1.338973 TCACTAACGCTCGTTTCCTGT 59.661 47.619 13.03 5.27 39.31 4.00
1940 2701 3.909430 TCAGAATCACTAACGCTCGTTT 58.091 40.909 13.03 0.00 39.31 3.60
1942 2703 3.570926 TTCAGAATCACTAACGCTCGT 57.429 42.857 0.00 0.00 0.00 4.18
1948 2709 6.017109 TGGCTTTCACTTTCAGAATCACTAAC 60.017 38.462 0.00 0.00 0.00 2.34
1949 2710 6.061441 TGGCTTTCACTTTCAGAATCACTAA 58.939 36.000 0.00 0.00 0.00 2.24
1950 2711 5.620206 TGGCTTTCACTTTCAGAATCACTA 58.380 37.500 0.00 0.00 0.00 2.74
1963 2724 2.028930 CGGTAGAGACTTGGCTTTCACT 60.029 50.000 0.00 0.00 0.00 3.41
1964 2725 2.029290 TCGGTAGAGACTTGGCTTTCAC 60.029 50.000 0.00 0.00 0.00 3.18
1969 2730 1.272769 GTTGTCGGTAGAGACTTGGCT 59.727 52.381 0.00 0.00 41.47 4.75
1971 2732 3.254060 CATGTTGTCGGTAGAGACTTGG 58.746 50.000 0.00 0.00 41.47 3.61
2003 2764 2.898343 GTGCAAACGGGTCGTGGT 60.898 61.111 0.00 0.00 39.99 4.16
2020 2787 2.711311 CGATGGCTCAACATGGCG 59.289 61.111 0.00 0.00 0.00 5.69
2021 2788 2.410469 GCGATGGCTCAACATGGC 59.590 61.111 0.00 0.00 43.48 4.40
2023 2790 1.430632 GTGGCGATGGCTCAACATG 59.569 57.895 0.00 0.00 39.81 3.21
2028 2795 3.002583 TGAGGTGGCGATGGCTCA 61.003 61.111 0.00 0.00 39.81 4.26
2035 2802 2.029623 GATACTTACCTGAGGTGGCGA 58.970 52.381 15.83 0.00 36.19 5.54
2102 2869 5.105432 AGGGACAAGTTAAGATAAGGACGTC 60.105 44.000 7.13 7.13 0.00 4.34
2108 2883 6.049955 TGGACAGGGACAAGTTAAGATAAG 57.950 41.667 0.00 0.00 0.00 1.73
2125 2900 6.805713 TGAGTGTGTATACATACATGGACAG 58.194 40.000 27.93 0.00 44.25 3.51
2300 3085 4.039004 GGAGTGAGATGAGATGTAGCACAT 59.961 45.833 0.00 2.02 42.43 3.21
2357 3152 4.227300 ACAATGAACCAATCTAGGTAGCCA 59.773 41.667 0.00 0.00 42.25 4.75
2893 4266 1.079819 CGCACACACCCTACTCAGG 60.080 63.158 0.00 0.00 42.22 3.86
2894 4267 0.388649 GTCGCACACACCCTACTCAG 60.389 60.000 0.00 0.00 0.00 3.35
2909 4294 3.164011 CTTGTCCGTCGTCGTCGC 61.164 66.667 6.36 0.00 36.96 5.19
2910 4295 2.073220 CACTTGTCCGTCGTCGTCG 61.073 63.158 4.87 4.87 38.55 5.12
2911 4296 1.728426 CCACTTGTCCGTCGTCGTC 60.728 63.158 0.71 0.00 35.01 4.20
3099 4484 3.405170 AGTGCTTTGTCTGTTGTTTCG 57.595 42.857 0.00 0.00 0.00 3.46
3156 4541 1.412710 GCCTCATTACCGGACAGATGA 59.587 52.381 9.46 10.73 0.00 2.92
3178 4563 9.197694 GTACATAGTATAATTGAAGTGGAGCAG 57.802 37.037 0.00 0.00 0.00 4.24
3179 4564 8.700973 TGTACATAGTATAATTGAAGTGGAGCA 58.299 33.333 0.00 0.00 0.00 4.26
3430 7600 3.140623 CAAAATCTGCAAGTTTTGGGGG 58.859 45.455 20.40 3.82 39.27 5.40
3480 7651 1.625818 AGGACTTGTGTCATCCTGGTC 59.374 52.381 0.00 0.00 44.61 4.02
3540 7718 9.167311 ACGAAGAGCATTTATTCACTAGAAATT 57.833 29.630 0.00 0.00 37.29 1.82
3558 7736 6.204882 AGGGCAACATAAATATTACGAAGAGC 59.795 38.462 0.00 0.00 39.74 4.09
3582 7762 3.130280 TGGCATGTATCCACTGCATAG 57.870 47.619 0.00 0.00 37.64 2.23
3666 7846 4.706962 AGGCCCTGAAATTATCTTTGTCAC 59.293 41.667 0.00 0.00 0.00 3.67
3746 7929 8.125978 TCTTTTTGTGCAATCAAGGAGATATT 57.874 30.769 0.00 0.00 35.39 1.28
3956 8145 3.324117 CTTCTGTGCGGATCCATATCTG 58.676 50.000 13.41 3.54 40.89 2.90
3957 8146 2.301296 CCTTCTGTGCGGATCCATATCT 59.699 50.000 13.41 0.00 32.29 1.98
3960 8149 0.106708 GCCTTCTGTGCGGATCCATA 59.893 55.000 13.41 0.00 0.00 2.74
3967 8156 0.392998 ATACTTGGCCTTCTGTGCGG 60.393 55.000 3.32 0.00 0.00 5.69
3968 8157 2.205074 CTATACTTGGCCTTCTGTGCG 58.795 52.381 3.32 0.00 0.00 5.34
3971 8160 5.700402 ATTCACTATACTTGGCCTTCTGT 57.300 39.130 3.32 0.00 0.00 3.41
3997 8186 7.572523 TTTCAGTCTTGTTCAGTTCATCAAT 57.427 32.000 0.00 0.00 0.00 2.57
3999 8188 7.389803 TTTTTCAGTCTTGTTCAGTTCATCA 57.610 32.000 0.00 0.00 0.00 3.07
4011 8200 9.533253 ACCTTTTCAATACATTTTTCAGTCTTG 57.467 29.630 0.00 0.00 0.00 3.02
4045 8234 4.202151 TGACGGTGATGGATCTAGTTCATG 60.202 45.833 3.30 0.00 0.00 3.07
4052 8241 2.159099 GCAAGTGACGGTGATGGATCTA 60.159 50.000 0.00 0.00 0.00 1.98
4065 8254 3.695816 GTTTGAAGTGGAAGCAAGTGAC 58.304 45.455 0.00 0.00 0.00 3.67
4066 8255 2.354510 CGTTTGAAGTGGAAGCAAGTGA 59.645 45.455 0.00 0.00 0.00 3.41
4069 8258 3.108144 CAACGTTTGAAGTGGAAGCAAG 58.892 45.455 0.00 0.00 0.00 4.01
4085 8274 1.029408 TGCTGCAGGTTGAACAACGT 61.029 50.000 17.12 8.92 42.02 3.99
4165 11291 2.695147 TGTCATCACGGTCTAGCATCAT 59.305 45.455 0.00 0.00 0.00 2.45
4200 11326 3.019564 CGGGAATTGATCTTTGGCTTCT 58.980 45.455 0.00 0.00 0.00 2.85
4221 11350 1.340114 ACCTCGGCTTTGGAATTCTCC 60.340 52.381 5.23 0.00 42.81 3.71
4236 11365 6.073222 GGCAACAAGGATTATTACATACCTCG 60.073 42.308 0.00 0.00 0.00 4.63
4361 12660 0.256464 CGACTGGTAGGTCCTCCTCT 59.744 60.000 0.00 0.00 43.94 3.69
4393 12699 1.725931 CGCCAAACATCTCTTGAACGC 60.726 52.381 0.00 0.00 0.00 4.84
4394 12700 1.798223 TCGCCAAACATCTCTTGAACG 59.202 47.619 0.00 0.00 0.00 3.95
4413 12719 5.532406 TGAGCCAAGCCATTTAGTTGATATC 59.468 40.000 0.00 0.00 0.00 1.63
4429 12753 1.101331 GCATTCCCTTCTGAGCCAAG 58.899 55.000 0.00 0.00 0.00 3.61
4430 12754 0.700564 AGCATTCCCTTCTGAGCCAA 59.299 50.000 0.00 0.00 0.00 4.52
4431 12755 0.034767 CAGCATTCCCTTCTGAGCCA 60.035 55.000 0.00 0.00 0.00 4.75
4432 12756 1.382692 GCAGCATTCCCTTCTGAGCC 61.383 60.000 0.00 0.00 0.00 4.70
4433 12757 0.679002 TGCAGCATTCCCTTCTGAGC 60.679 55.000 0.00 0.00 0.00 4.26
4434 12758 1.339824 ACTGCAGCATTCCCTTCTGAG 60.340 52.381 15.27 0.00 0.00 3.35
4435 12759 0.694771 ACTGCAGCATTCCCTTCTGA 59.305 50.000 15.27 0.00 0.00 3.27
4436 12760 1.093159 GACTGCAGCATTCCCTTCTG 58.907 55.000 15.27 0.00 0.00 3.02
4437 12761 0.034670 GGACTGCAGCATTCCCTTCT 60.035 55.000 19.10 0.00 28.56 2.85
4438 12762 0.322816 TGGACTGCAGCATTCCCTTC 60.323 55.000 25.08 0.31 33.07 3.46
4439 12763 0.323178 CTGGACTGCAGCATTCCCTT 60.323 55.000 25.08 0.00 33.07 3.95
4440 12764 1.302285 CTGGACTGCAGCATTCCCT 59.698 57.895 25.08 0.00 33.07 4.20
4441 12765 0.610232 AACTGGACTGCAGCATTCCC 60.610 55.000 25.08 13.58 33.07 3.97
4442 12766 0.807496 GAACTGGACTGCAGCATTCC 59.193 55.000 22.22 22.22 34.38 3.01
4443 12767 1.527034 TGAACTGGACTGCAGCATTC 58.473 50.000 15.27 10.86 0.00 2.67
4557 12881 2.030562 GTGTCGTCCACCCACCAG 59.969 66.667 0.00 0.00 38.18 4.00
4575 12899 4.452733 CCGTCTCCCTGCCCGTTC 62.453 72.222 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.