Multiple sequence alignment - TraesCS6B01G249500

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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 TraesCS6B01G249500 chr6B 100.000 5813 0 0 1 5813 447883846 447889658 0.000000e+00 10735.0
1 TraesCS6B01G249500 chr6A 94.768 3345 100 29 2426 5714 438587741 438584416 0.000000e+00 5138.0
2 TraesCS6B01G249500 chr6A 96.129 1421 45 4 849 2260 438589187 438587768 0.000000e+00 2311.0
3 TraesCS6B01G249500 chr6D 95.947 2813 75 12 2698 5480 287020201 287023004 0.000000e+00 4527.0
4 TraesCS6B01G249500 chr6D 94.888 1565 58 10 775 2319 287017166 287018728 0.000000e+00 2427.0
5 TraesCS6B01G249500 chr6D 83.622 635 79 10 1 615 287015812 287016441 1.820000e-159 573.0
6 TraesCS6B01G249500 chr6D 97.778 270 6 0 2426 2695 287018725 287018994 3.170000e-127 466.0
7 TraesCS6B01G249500 chr6D 83.659 410 53 11 372 776 287016710 287017110 1.980000e-99 374.0
8 TraesCS6B01G249500 chr6D 87.085 271 16 6 5562 5813 287023149 287023419 7.370000e-74 289.0
9 TraesCS6B01G249500 chr6D 91.411 163 13 1 3834 3996 351233596 351233435 7.580000e-54 222.0
10 TraesCS6B01G249500 chr3A 86.722 241 20 10 2087 2319 38273341 38273105 2.080000e-64 257.0
11 TraesCS6B01G249500 chr3A 90.000 170 15 2 3831 4000 726768965 726769132 9.810000e-53 219.0
12 TraesCS6B01G249500 chr3A 85.000 220 26 4 1806 2019 38273567 38273349 3.530000e-52 217.0
13 TraesCS6B01G249500 chr3A 84.343 198 24 4 1803 2000 195454968 195455158 2.770000e-43 187.0
14 TraesCS6B01G249500 chr3A 73.418 316 63 15 311 617 532854687 532854384 1.330000e-16 99.0
15 TraesCS6B01G249500 chr5B 88.073 218 20 2 2087 2298 622970808 622971025 2.690000e-63 254.0
16 TraesCS6B01G249500 chr5B 88.073 218 20 2 2087 2298 633310351 633310134 2.690000e-63 254.0
17 TraesCS6B01G249500 chr5B 82.143 224 31 6 1802 2019 622970580 622970800 3.580000e-42 183.0
18 TraesCS6B01G249500 chr5B 85.475 179 23 3 1822 2000 633310559 633310384 3.580000e-42 183.0
19 TraesCS6B01G249500 chr5B 79.512 205 40 2 477 679 224325388 224325184 1.690000e-30 145.0
20 TraesCS6B01G249500 chr2A 87.727 220 19 4 2087 2300 393114419 393114636 3.480000e-62 250.0
21 TraesCS6B01G249500 chr5D 87.615 218 21 2 2087 2298 501344593 501344810 1.250000e-61 248.0
22 TraesCS6B01G249500 chr5D 91.566 166 13 1 3831 3996 461072599 461072763 1.630000e-55 228.0
23 TraesCS6B01G249500 chr5D 83.258 221 25 9 1802 2013 501344358 501344575 5.940000e-45 193.0
24 TraesCS6B01G249500 chr5D 89.655 116 9 2 2316 2428 499408598 499408713 1.690000e-30 145.0
25 TraesCS6B01G249500 chr5D 87.037 108 13 1 1803 1910 307087712 307087818 2.850000e-23 121.0
26 TraesCS6B01G249500 chr7A 85.774 239 23 8 2087 2319 498941351 498941118 5.820000e-60 243.0
27 TraesCS6B01G249500 chr7A 88.268 179 20 1 1822 2000 648145222 648145045 4.560000e-51 213.0
28 TraesCS6B01G249500 chr7A 85.784 204 21 7 1803 2000 192661232 192661433 5.900000e-50 209.0
29 TraesCS6B01G249500 chr7B 85.477 241 24 8 2087 2319 612313369 612313132 2.090000e-59 241.0
30 TraesCS6B01G249500 chr7B 87.709 179 21 1 1822 2000 612313579 612313402 2.120000e-49 207.0
31 TraesCS6B01G249500 chr7B 90.244 123 6 5 2317 2438 594954419 594954302 7.800000e-34 156.0
32 TraesCS6B01G249500 chr4A 91.617 167 13 1 3832 3998 150653311 150653476 4.530000e-56 230.0
33 TraesCS6B01G249500 chr7D 91.124 169 14 1 3830 3998 566026740 566026573 1.630000e-55 228.0
34 TraesCS6B01G249500 chr7D 81.026 195 35 2 1806 1999 431982213 431982020 2.810000e-33 154.0
35 TraesCS6B01G249500 chr7D 89.256 121 11 2 2316 2435 390929782 390929901 3.630000e-32 150.0
36 TraesCS6B01G249500 chr1B 91.463 164 12 2 3833 3996 314565538 314565699 2.110000e-54 224.0
37 TraesCS6B01G249500 chr1B 88.281 128 9 5 2310 2436 1735174 1735296 1.310000e-31 148.0
38 TraesCS6B01G249500 chr1B 90.351 114 6 2 2316 2428 483293919 483294028 1.690000e-30 145.0
39 TraesCS6B01G249500 chr3B 85.455 220 25 4 1806 2019 490891204 490890986 7.580000e-54 222.0
40 TraesCS6B01G249500 chr3B 88.525 122 4 5 2314 2428 10116362 10116480 7.850000e-29 139.0
41 TraesCS6B01G249500 chr3B 88.496 113 5 6 2317 2428 772893013 772892908 4.730000e-26 130.0
42 TraesCS6B01G249500 chr3B 75.824 273 52 7 371 631 544549283 544549553 6.120000e-25 126.0
43 TraesCS6B01G249500 chr4B 90.361 166 15 1 3832 3997 28724141 28724305 3.530000e-52 217.0
44 TraesCS6B01G249500 chr4B 87.288 118 10 3 2316 2428 545016604 545016487 4.730000e-26 130.0
45 TraesCS6B01G249500 chr5A 90.385 156 15 0 1806 1961 390369095 390368940 7.640000e-49 206.0
46 TraesCS6B01G249500 chr5A 84.434 212 24 6 1814 2019 626027067 626026859 3.550000e-47 200.0
47 TraesCS6B01G249500 chr5A 75.185 270 34 13 317 569 272950526 272950273 4.790000e-16 97.1
48 TraesCS6B01G249500 chr3D 87.500 168 18 3 1835 2000 264698751 264698585 2.140000e-44 191.0
49 TraesCS6B01G249500 chr3D 88.525 122 6 4 2309 2428 590847121 590847236 2.180000e-29 141.0
50 TraesCS6B01G249500 chr3D 73.333 360 74 15 311 660 418227907 418228254 4.760000e-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 TraesCS6B01G249500 chr6B 447883846 447889658 5812 False 10735.000000 10735 100.0000 1 5813 1 chr6B.!!$F1 5812
1 TraesCS6B01G249500 chr6A 438584416 438589187 4771 True 3724.500000 5138 95.4485 849 5714 2 chr6A.!!$R1 4865
2 TraesCS6B01G249500 chr6D 287015812 287023419 7607 False 1442.666667 4527 90.4965 1 5813 6 chr6D.!!$F1 5812

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
527 805 1.107945 TGCCATGCCACATCAATGAG 58.892 50.000 0.0 0.0 0.00 2.90 F
1499 2106 1.003580 TGCTTGGAAGGTGGTCATCTC 59.996 52.381 0.0 0.0 0.00 2.75 F
2085 2699 0.037882 TTTCTGCTCCTGCTCGTGAG 60.038 55.000 0.0 0.0 40.48 3.51 F
2848 4668 0.623723 TGGGTAGGGCATTTCCTGAC 59.376 55.000 0.0 0.0 37.75 3.51 F
4090 5913 1.112113 GCCACCTCCTATCGTGAAGA 58.888 55.000 0.0 0.0 31.36 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1772 2379 0.244721 GGAAGCCATTGTGAAGCCAC 59.755 55.000 0.00 0.00 43.46 5.01 R
2771 4591 1.209261 TCTGGTTCATGGCATCGCTAA 59.791 47.619 0.00 0.00 0.00 3.09 R
3351 5174 2.228582 CTGAGTATGCTAGCGCTCTCAT 59.771 50.000 24.77 20.49 37.88 2.90 R
4550 6394 0.727970 CTGACAGAGCAGCAGATTGC 59.272 55.000 0.00 0.00 45.46 3.56 R
4960 6805 0.178992 TTTCAGGGGGTGCAAGTCAG 60.179 55.000 0.00 0.00 0.00 3.51 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
63 64 1.202486 TCGGCGTGGGTGAGATAAATC 60.202 52.381 6.85 0.00 0.00 2.17
69 70 4.073293 GTGGGTGAGATAAATCCACGAT 57.927 45.455 0.00 0.00 38.50 3.73
73 74 3.466836 GTGAGATAAATCCACGATGGCA 58.533 45.455 0.00 0.00 37.47 4.92
93 94 2.221055 CACAACGTCGAAGAAGGGAAAG 59.779 50.000 5.05 0.00 41.22 2.62
152 153 7.387265 TGGGTATGGATATAAGTGTGTCAAT 57.613 36.000 0.00 0.00 0.00 2.57
153 154 8.499288 TGGGTATGGATATAAGTGTGTCAATA 57.501 34.615 0.00 0.00 0.00 1.90
166 167 4.216257 GTGTGTCAATACTGCTGGTTTGAT 59.784 41.667 11.64 0.00 32.31 2.57
184 185 7.893302 TGGTTTGATTAAGGACCTCAATATTGT 59.107 33.333 14.97 0.00 33.33 2.71
190 191 4.574674 AGGACCTCAATATTGTGCTGAA 57.425 40.909 14.97 0.00 28.95 3.02
200 201 6.094464 TCAATATTGTGCTGAAGTTCCATCAG 59.906 38.462 14.97 0.00 45.65 2.90
201 202 3.490439 TTGTGCTGAAGTTCCATCAGA 57.510 42.857 7.67 0.00 45.74 3.27
204 205 3.260740 GTGCTGAAGTTCCATCAGAGAG 58.739 50.000 7.67 0.00 45.74 3.20
211 212 2.192263 GTTCCATCAGAGAGGTCCCTT 58.808 52.381 0.00 0.00 0.00 3.95
212 213 1.871418 TCCATCAGAGAGGTCCCTTG 58.129 55.000 0.00 0.00 0.00 3.61
214 215 2.191400 CCATCAGAGAGGTCCCTTGAA 58.809 52.381 0.00 0.00 0.00 2.69
224 225 4.469945 AGAGGTCCCTTGAACGAATTATCA 59.530 41.667 0.00 0.00 31.67 2.15
228 229 5.008712 GGTCCCTTGAACGAATTATCATTCC 59.991 44.000 0.00 0.00 36.18 3.01
233 234 6.073765 CCTTGAACGAATTATCATTCCCTACG 60.074 42.308 0.00 0.00 36.18 3.51
235 236 6.213677 TGAACGAATTATCATTCCCTACGAG 58.786 40.000 0.00 0.00 36.18 4.18
245 246 2.820728 TCCCTACGAGAGGTCATTCA 57.179 50.000 7.25 0.00 45.03 2.57
252 253 1.656095 CGAGAGGTCATTCAAGCGAAC 59.344 52.381 0.00 0.00 32.81 3.95
267 268 1.861542 CGAACGCTGCCATTTGGGAA 61.862 55.000 0.00 0.00 40.01 3.97
281 282 5.928264 CCATTTGGGAATGTTCTCTCAAAAC 59.072 40.000 2.97 0.00 40.85 2.43
288 289 5.067805 GGAATGTTCTCTCAAAACACCACTT 59.932 40.000 0.00 0.00 39.29 3.16
289 290 6.405842 GGAATGTTCTCTCAAAACACCACTTT 60.406 38.462 0.00 0.00 39.29 2.66
290 291 5.309323 TGTTCTCTCAAAACACCACTTTG 57.691 39.130 0.00 0.00 35.51 2.77
323 324 6.552859 TCGAGAATTGTCATGCTAAAACAA 57.447 33.333 3.24 0.00 37.32 2.83
326 327 7.386573 TCGAGAATTGTCATGCTAAAACAACTA 59.613 33.333 3.24 0.00 35.87 2.24
333 334 8.909708 TGTCATGCTAAAACAACTATATTTGC 57.090 30.769 2.90 0.00 0.00 3.68
405 682 1.608055 TTGTCATGTTGCACCAGAGG 58.392 50.000 0.00 0.00 0.00 3.69
416 693 2.025981 TGCACCAGAGGAATTGCTATGT 60.026 45.455 18.59 5.98 35.91 2.29
432 709 6.768029 TGCTATGTGTTTTCAAGAATTTGC 57.232 33.333 0.00 0.00 34.21 3.68
499 777 1.134367 CAGGATTTGACATGCTGGCAG 59.866 52.381 10.94 10.94 36.33 4.85
501 779 1.820519 GGATTTGACATGCTGGCAGAA 59.179 47.619 20.86 8.68 36.33 3.02
524 802 3.637911 AAATTGCCATGCCACATCAAT 57.362 38.095 0.00 0.00 0.00 2.57
526 804 1.558233 TTGCCATGCCACATCAATGA 58.442 45.000 0.00 0.00 0.00 2.57
527 805 1.107945 TGCCATGCCACATCAATGAG 58.892 50.000 0.00 0.00 0.00 2.90
530 808 2.480759 GCCATGCCACATCAATGAGAAC 60.481 50.000 0.00 0.00 0.00 3.01
532 810 3.181490 CCATGCCACATCAATGAGAACTG 60.181 47.826 0.00 0.00 0.00 3.16
549 827 6.127647 TGAGAACTGATGAAAATTGCCATACC 60.128 38.462 0.00 0.00 0.00 2.73
553 831 6.400568 ACTGATGAAAATTGCCATACCAAAG 58.599 36.000 0.00 0.00 0.00 2.77
556 834 6.873076 TGATGAAAATTGCCATACCAAAGAAC 59.127 34.615 0.00 0.00 0.00 3.01
557 835 6.166984 TGAAAATTGCCATACCAAAGAACA 57.833 33.333 0.00 0.00 0.00 3.18
558 836 6.586344 TGAAAATTGCCATACCAAAGAACAA 58.414 32.000 0.00 0.00 0.00 2.83
564 842 6.857777 TGCCATACCAAAGAACAAAATTTG 57.142 33.333 3.89 3.89 36.40 2.32
593 871 3.890756 TGGATGTGTTTGCTCAGATTGTT 59.109 39.130 0.00 0.00 0.00 2.83
597 875 6.127925 GGATGTGTTTGCTCAGATTGTTATCA 60.128 38.462 0.00 0.00 32.95 2.15
598 876 6.822667 TGTGTTTGCTCAGATTGTTATCAT 57.177 33.333 0.00 0.00 32.95 2.45
599 877 7.920160 TGTGTTTGCTCAGATTGTTATCATA 57.080 32.000 0.00 0.00 32.95 2.15
610 888 7.438160 TCAGATTGTTATCATAAGCGAATCGTT 59.562 33.333 4.07 0.00 32.95 3.85
615 893 9.644993 TTGTTATCATAAGCGAATCGTTTAATG 57.355 29.630 15.24 13.22 36.31 1.90
617 895 9.646336 GTTATCATAAGCGAATCGTTTAATGTT 57.354 29.630 15.24 11.14 36.31 2.71
626 904 3.774282 TCGTTTAATGTTGTCGGTTCG 57.226 42.857 0.00 0.00 0.00 3.95
629 907 4.382457 TCGTTTAATGTTGTCGGTTCGTAG 59.618 41.667 0.00 0.00 0.00 3.51
630 908 4.148696 CGTTTAATGTTGTCGGTTCGTAGT 59.851 41.667 0.00 0.00 0.00 2.73
631 909 5.602516 GTTTAATGTTGTCGGTTCGTAGTC 58.397 41.667 0.00 0.00 0.00 2.59
632 910 2.358939 ATGTTGTCGGTTCGTAGTCC 57.641 50.000 0.00 0.00 0.00 3.85
677 1212 4.333649 CGAACAGTGATTGCCATATGTCTT 59.666 41.667 0.00 0.00 30.35 3.01
679 1214 4.592942 ACAGTGATTGCCATATGTCTTGT 58.407 39.130 0.00 0.22 0.00 3.16
680 1215 5.744171 ACAGTGATTGCCATATGTCTTGTA 58.256 37.500 0.00 0.00 0.00 2.41
681 1216 5.586243 ACAGTGATTGCCATATGTCTTGTAC 59.414 40.000 0.00 0.00 0.00 2.90
682 1217 5.585844 CAGTGATTGCCATATGTCTTGTACA 59.414 40.000 1.24 0.00 43.86 2.90
683 1218 5.586243 AGTGATTGCCATATGTCTTGTACAC 59.414 40.000 0.00 3.84 42.09 2.90
684 1219 4.570369 TGATTGCCATATGTCTTGTACACG 59.430 41.667 0.00 0.00 42.09 4.49
685 1220 3.603158 TGCCATATGTCTTGTACACGT 57.397 42.857 0.00 0.00 42.09 4.49
686 1221 3.932822 TGCCATATGTCTTGTACACGTT 58.067 40.909 0.00 0.00 42.09 3.99
689 1224 5.239744 TGCCATATGTCTTGTACACGTTTTT 59.760 36.000 0.00 0.00 42.09 1.94
714 1249 8.918961 TTTAGAACACACGAAAATTGAACATT 57.081 26.923 0.00 0.00 0.00 2.71
715 1250 8.555166 TTAGAACACACGAAAATTGAACATTC 57.445 30.769 0.00 0.00 0.00 2.67
716 1251 6.795399 AGAACACACGAAAATTGAACATTCT 58.205 32.000 0.00 0.00 0.00 2.40
719 1254 5.977129 ACACACGAAAATTGAACATTCTTCC 59.023 36.000 0.00 0.00 0.00 3.46
720 1255 6.183360 ACACACGAAAATTGAACATTCTTCCT 60.183 34.615 0.00 0.00 0.00 3.36
721 1256 6.360681 CACACGAAAATTGAACATTCTTCCTC 59.639 38.462 0.00 0.00 0.00 3.71
722 1257 6.039270 ACACGAAAATTGAACATTCTTCCTCA 59.961 34.615 0.00 0.00 0.00 3.86
723 1258 6.917477 CACGAAAATTGAACATTCTTCCTCAA 59.083 34.615 0.00 0.00 32.67 3.02
750 1286 3.735514 GCCCTCTGAACTAACGTCAGATC 60.736 52.174 4.56 0.00 39.42 2.75
762 1298 4.921470 ACGTCAGATCGTTAACATTTGG 57.079 40.909 6.39 0.00 41.37 3.28
791 1384 8.383175 TGATTAATATAGATCCGAGGCCTTTTT 58.617 33.333 6.77 0.00 0.00 1.94
845 1448 8.339714 TGAAAATTTAGTCTTTCATCGTTCGTT 58.660 29.630 0.00 0.00 36.79 3.85
859 1462 4.545610 TCGTTCGTTATTTACACTCGGTT 58.454 39.130 0.00 0.00 0.00 4.44
1467 2074 6.762661 AGAAATTGAGGTTCAAATGTGGTTTG 59.237 34.615 0.00 0.00 46.86 2.93
1499 2106 1.003580 TGCTTGGAAGGTGGTCATCTC 59.996 52.381 0.00 0.00 0.00 2.75
1545 2152 1.269883 CGGTGGTAGTGTGCTGTTGTA 60.270 52.381 0.00 0.00 0.00 2.41
1866 2474 1.364171 CTGCTATTCGGACCCCTCG 59.636 63.158 0.00 0.00 0.00 4.63
1898 2506 7.303634 AGAACGTGTTATTCGAGCAATTAAT 57.696 32.000 0.00 0.00 0.00 1.40
1935 2543 4.853924 ATTTGTCTGACAAGCCGATTTT 57.146 36.364 21.13 0.88 39.53 1.82
1940 2548 5.000591 TGTCTGACAAGCCGATTTTATCAA 58.999 37.500 8.27 0.00 0.00 2.57
1945 2553 5.106712 TGACAAGCCGATTTTATCAACTGTC 60.107 40.000 0.00 0.00 0.00 3.51
1956 2564 1.522668 TCAACTGTCAGGCCGAATTG 58.477 50.000 4.53 4.45 0.00 2.32
1958 2566 1.608590 CAACTGTCAGGCCGAATTGTT 59.391 47.619 4.53 0.00 0.00 2.83
1980 2588 1.544246 GTCGGGCCAATTAACTGCTTT 59.456 47.619 4.39 0.00 0.00 3.51
1985 2593 3.524541 GGCCAATTAACTGCTTTCCATG 58.475 45.455 0.00 0.00 0.00 3.66
2005 2613 0.953003 TTTTAGCCCAAAACCGTCCG 59.047 50.000 0.00 0.00 31.05 4.79
2030 2644 3.189287 CCTACTTTTCACAGCCACACATC 59.811 47.826 0.00 0.00 0.00 3.06
2050 2664 2.783288 GGTAGGTCGCTCCCTTCCG 61.783 68.421 0.00 0.00 33.06 4.30
2076 2690 3.070018 CGTTTGATCTGTTTCTGCTCCT 58.930 45.455 0.00 0.00 0.00 3.69
2085 2699 0.037882 TTTCTGCTCCTGCTCGTGAG 60.038 55.000 0.00 0.00 40.48 3.51
2124 2738 0.656259 CGGCTGCAACATCATCAGAG 59.344 55.000 0.50 0.00 0.00 3.35
2171 2785 6.481644 GCTATGTAGCCTAGGATTGCATATTC 59.518 42.308 14.75 9.58 43.39 1.75
2172 2786 4.820897 TGTAGCCTAGGATTGCATATTCG 58.179 43.478 14.75 0.00 0.00 3.34
2183 2797 2.267426 TGCATATTCGGACACTTCGTG 58.733 47.619 0.00 0.00 39.75 4.35
2199 2813 4.635765 ACTTCGTGCATTACATGTTGCTAT 59.364 37.500 20.22 1.29 39.60 2.97
2204 2818 6.589907 TCGTGCATTACATGTTGCTATATAGG 59.410 38.462 20.22 8.11 39.60 2.57
2281 2895 5.902613 TTCAGTCAAATGGATGATTCACC 57.097 39.130 0.00 0.00 0.00 4.02
2326 2940 3.510360 CCAGTAATATGGTACTCCCTCCG 59.490 52.174 0.00 0.00 35.47 4.63
2327 2941 4.150359 CAGTAATATGGTACTCCCTCCGT 58.850 47.826 0.00 0.00 31.78 4.69
2328 2942 5.319453 CAGTAATATGGTACTCCCTCCGTA 58.681 45.833 0.00 0.00 31.78 4.02
2329 2943 5.771666 CAGTAATATGGTACTCCCTCCGTAA 59.228 44.000 0.00 0.00 31.78 3.18
2330 2944 6.266103 CAGTAATATGGTACTCCCTCCGTAAA 59.734 42.308 0.00 0.00 31.78 2.01
2331 2945 5.541953 AATATGGTACTCCCTCCGTAAAC 57.458 43.478 0.00 0.00 0.00 2.01
2332 2946 2.610438 TGGTACTCCCTCCGTAAACT 57.390 50.000 0.00 0.00 0.00 2.66
2333 2947 3.737559 TGGTACTCCCTCCGTAAACTA 57.262 47.619 0.00 0.00 0.00 2.24
2334 2948 4.046286 TGGTACTCCCTCCGTAAACTAA 57.954 45.455 0.00 0.00 0.00 2.24
2335 2949 4.613437 TGGTACTCCCTCCGTAAACTAAT 58.387 43.478 0.00 0.00 0.00 1.73
2336 2950 5.765510 TGGTACTCCCTCCGTAAACTAATA 58.234 41.667 0.00 0.00 0.00 0.98
2337 2951 6.376248 TGGTACTCCCTCCGTAAACTAATAT 58.624 40.000 0.00 0.00 0.00 1.28
2338 2952 7.526041 TGGTACTCCCTCCGTAAACTAATATA 58.474 38.462 0.00 0.00 0.00 0.86
2339 2953 8.004215 TGGTACTCCCTCCGTAAACTAATATAA 58.996 37.037 0.00 0.00 0.00 0.98
2340 2954 8.860088 GGTACTCCCTCCGTAAACTAATATAAA 58.140 37.037 0.00 0.00 0.00 1.40
2343 2957 7.930325 ACTCCCTCCGTAAACTAATATAAAAGC 59.070 37.037 0.00 0.00 0.00 3.51
2344 2958 6.925165 TCCCTCCGTAAACTAATATAAAAGCG 59.075 38.462 0.00 0.00 0.00 4.68
2345 2959 6.703165 CCCTCCGTAAACTAATATAAAAGCGT 59.297 38.462 0.00 0.00 0.00 5.07
2346 2960 7.225341 CCCTCCGTAAACTAATATAAAAGCGTT 59.775 37.037 0.00 0.00 0.00 4.84
2347 2961 8.606602 CCTCCGTAAACTAATATAAAAGCGTTT 58.393 33.333 2.53 2.53 0.00 3.60
2422 3036 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
2423 3037 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
2424 3038 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
2425 3039 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
2426 3040 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
2438 3052 2.165845 CAGAGGGAGTAACAGTTACCGG 59.834 54.545 18.27 0.00 36.81 5.28
2673 3289 2.851263 TGGTAAGATCGCAAACTGGT 57.149 45.000 0.00 0.00 0.00 4.00
2690 3306 2.226330 TGGTGTGAGTACATGGTTTGC 58.774 47.619 0.00 0.00 39.39 3.68
2771 4591 5.562298 AAGTAATGGTAGGAACTGTGTGT 57.438 39.130 0.00 0.00 41.52 3.72
2780 4600 1.128692 GGAACTGTGTGTTAGCGATGC 59.871 52.381 0.00 0.00 39.30 3.91
2790 4610 1.331756 GTTAGCGATGCCATGAACCAG 59.668 52.381 0.00 0.00 0.00 4.00
2848 4668 0.623723 TGGGTAGGGCATTTCCTGAC 59.376 55.000 0.00 0.00 37.75 3.51
2871 4691 6.668323 ACGTTTTGACCTTATATATGCATGC 58.332 36.000 11.82 11.82 0.00 4.06
3351 5174 3.694043 TTGCCACTTACTGCAGTGATA 57.306 42.857 29.57 13.15 46.29 2.15
3392 5215 4.579340 TCAGAAACCTACCACGCTATCTAG 59.421 45.833 0.00 0.00 0.00 2.43
3408 5231 7.148255 ACGCTATCTAGAAATCAACAATTTGCA 60.148 33.333 0.00 0.00 37.70 4.08
3435 5258 3.386768 TCTAGACACTGTTGGTTGCTC 57.613 47.619 0.00 0.00 0.00 4.26
3896 5719 4.832590 ATACAGACTACATACGGAGCAC 57.167 45.455 0.00 0.00 0.00 4.40
3898 5721 2.163815 ACAGACTACATACGGAGCACAC 59.836 50.000 0.00 0.00 0.00 3.82
4090 5913 1.112113 GCCACCTCCTATCGTGAAGA 58.888 55.000 0.00 0.00 31.36 2.87
4169 6010 4.122776 GCATATAGCTGCACTACACAGTT 58.877 43.478 1.02 0.00 41.87 3.16
4639 6483 5.441500 TGACTCGGATTCTAAGAGAGATGT 58.558 41.667 9.92 0.00 36.03 3.06
4689 6533 3.566351 ACCTTTTCTTTCCCTCCACTTG 58.434 45.455 0.00 0.00 0.00 3.16
4791 6636 6.890979 TCTGATGATGAAGATGACGACTAT 57.109 37.500 0.00 0.00 0.00 2.12
4829 6674 2.747446 GCTGAACCCGAGAAGCAAATTA 59.253 45.455 0.00 0.00 35.69 1.40
4929 6774 5.212532 TCACATTTTGCCTGCATTTTAGT 57.787 34.783 0.00 0.00 0.00 2.24
4945 6790 8.236586 TGCATTTTAGTATCAGTTCATCAACAC 58.763 33.333 0.00 0.00 34.60 3.32
5009 6854 6.555812 CATGTGTATGCTGCTGATTAAGAT 57.444 37.500 0.00 0.00 0.00 2.40
5155 7005 6.785076 TGACCTGATATTTAAGGAAACACCA 58.215 36.000 6.97 0.00 42.04 4.17
5156 7006 7.235079 TGACCTGATATTTAAGGAAACACCAA 58.765 34.615 6.97 0.00 42.04 3.67
5265 7119 1.149101 AGCCTGTTTTCTTCTCCCCA 58.851 50.000 0.00 0.00 0.00 4.96
5388 7244 1.008309 GCCGCGACCATCTCTCTAC 60.008 63.158 8.23 0.00 0.00 2.59
5411 7267 2.359975 CCCAACCTCCTGTTCGGC 60.360 66.667 0.00 0.00 34.00 5.54
5413 7269 2.429930 CAACCTCCTGTTCGGCCA 59.570 61.111 2.24 0.00 34.00 5.36
5460 7316 2.037367 TAGCCTCCGCCTCACAGT 59.963 61.111 0.00 0.00 34.57 3.55
5494 7381 3.434319 GTGCCATGGCCGACACTG 61.434 66.667 33.44 0.00 41.09 3.66
5507 7394 3.030308 CACTGCGCTCGTCACGTT 61.030 61.111 9.73 0.00 0.00 3.99
5510 7397 2.583868 TGCGCTCGTCACGTTGTT 60.584 55.556 9.73 0.00 0.00 2.83
5525 7412 2.748465 CGTTGTTCCCTCCTTTGTCCTT 60.748 50.000 0.00 0.00 0.00 3.36
5530 7417 1.600636 CCTCCTTTGTCCTTGCGCA 60.601 57.895 5.66 5.66 0.00 6.09
5566 7485 4.072131 ACTGGCGCTAGATTCTTTTTCAA 58.928 39.130 28.72 0.00 0.00 2.69
5588 7510 4.813027 AGCACCTGATATTTTGCAAGTTG 58.187 39.130 0.00 0.00 37.44 3.16
5596 7518 6.747125 TGATATTTTGCAAGTTGTGTGATGT 58.253 32.000 4.48 0.00 0.00 3.06
5624 7546 5.183140 ACCTGGGTATTGAATGTTTTTCTCG 59.817 40.000 0.00 0.00 0.00 4.04
5660 7583 5.635120 AGAAAAGAAGGATGCCTGTAAGTT 58.365 37.500 0.00 0.00 32.13 2.66
5666 7589 4.222124 AGGATGCCTGTAAGTTTCGAAT 57.778 40.909 0.00 0.00 29.57 3.34
5685 7608 2.869101 TGTTCGGGATTTGTCCATGA 57.131 45.000 0.00 0.00 0.00 3.07
5714 7637 9.790389 AATCGAACGTTATTTATGGCAATTTAA 57.210 25.926 0.00 0.00 0.00 1.52
5715 7638 8.829514 TCGAACGTTATTTATGGCAATTTAAG 57.170 30.769 0.00 0.00 0.00 1.85
5743 7681 4.307032 AGTTGGTAAGCATGACAATCCT 57.693 40.909 0.00 0.00 0.00 3.24
5754 7692 4.082571 GCATGACAATCCTGCTTAGTTTGT 60.083 41.667 0.00 0.00 35.54 2.83
5763 7701 4.081420 TCCTGCTTAGTTTGTTTTTGCCAA 60.081 37.500 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 3.536956 TCGTGGATTTATCTCACCCAC 57.463 47.619 0.00 0.00 42.72 4.61
55 56 3.558931 TGTGCCATCGTGGATTTATCT 57.441 42.857 8.04 0.00 40.96 1.98
63 64 2.860293 GACGTTGTGCCATCGTGG 59.140 61.111 13.58 0.25 39.40 4.94
67 68 1.126846 CTTCTTCGACGTTGTGCCATC 59.873 52.381 1.96 0.00 0.00 3.51
69 70 0.878523 CCTTCTTCGACGTTGTGCCA 60.879 55.000 1.96 0.00 0.00 4.92
73 74 2.480845 CTTTCCCTTCTTCGACGTTGT 58.519 47.619 1.96 0.00 0.00 3.32
107 108 5.694458 CCCATTTGTTTTTCTTTCCCGTAAG 59.306 40.000 0.00 0.00 0.00 2.34
108 109 5.128991 ACCCATTTGTTTTTCTTTCCCGTAA 59.871 36.000 0.00 0.00 0.00 3.18
111 112 4.066646 ACCCATTTGTTTTTCTTTCCCG 57.933 40.909 0.00 0.00 0.00 5.14
113 114 6.764379 TCCATACCCATTTGTTTTTCTTTCC 58.236 36.000 0.00 0.00 0.00 3.13
126 127 7.387265 TGACACACTTATATCCATACCCATT 57.613 36.000 0.00 0.00 0.00 3.16
152 153 4.288626 AGGTCCTTAATCAAACCAGCAGTA 59.711 41.667 0.00 0.00 34.09 2.74
153 154 3.074538 AGGTCCTTAATCAAACCAGCAGT 59.925 43.478 0.00 0.00 34.09 4.40
166 167 6.061022 TCAGCACAATATTGAGGTCCTTAA 57.939 37.500 22.16 0.00 0.00 1.85
184 185 2.235650 CCTCTCTGATGGAACTTCAGCA 59.764 50.000 7.14 0.00 40.35 4.41
190 191 1.364328 AGGGACCTCTCTGATGGAACT 59.636 52.381 4.22 0.00 0.00 3.01
200 201 3.336138 AATTCGTTCAAGGGACCTCTC 57.664 47.619 0.00 0.00 0.00 3.20
201 202 4.469945 TGATAATTCGTTCAAGGGACCTCT 59.530 41.667 0.00 0.00 0.00 3.69
204 205 5.008712 GGAATGATAATTCGTTCAAGGGACC 59.991 44.000 9.44 0.00 45.77 4.46
211 212 6.040054 TCTCGTAGGGAATGATAATTCGTTCA 59.960 38.462 9.44 0.00 45.77 3.18
212 213 6.444633 TCTCGTAGGGAATGATAATTCGTTC 58.555 40.000 0.00 0.32 44.05 3.95
214 215 5.047943 CCTCTCGTAGGGAATGATAATTCGT 60.048 44.000 0.00 0.00 42.32 3.85
233 234 1.656095 CGTTCGCTTGAATGACCTCTC 59.344 52.381 0.00 0.00 40.40 3.20
235 236 0.095417 GCGTTCGCTTGAATGACCTC 59.905 55.000 9.99 0.00 40.40 3.85
245 246 1.081242 CAAATGGCAGCGTTCGCTT 60.081 52.632 17.05 0.00 39.76 4.68
252 253 0.247185 AACATTCCCAAATGGCAGCG 59.753 50.000 0.00 0.00 45.48 5.18
255 256 3.091545 GAGAGAACATTCCCAAATGGCA 58.908 45.455 0.00 0.00 45.48 4.92
267 268 5.652014 TCAAAGTGGTGTTTTGAGAGAACAT 59.348 36.000 0.00 0.00 39.05 2.71
281 282 1.261619 GAGCGTTCACTCAAAGTGGTG 59.738 52.381 7.21 0.00 45.94 4.17
288 289 2.724977 ATTCTCGAGCGTTCACTCAA 57.275 45.000 7.81 0.00 36.42 3.02
289 290 2.288213 ACAATTCTCGAGCGTTCACTCA 60.288 45.455 7.81 0.00 36.42 3.41
290 291 2.329379 ACAATTCTCGAGCGTTCACTC 58.671 47.619 7.81 0.00 0.00 3.51
293 294 2.432206 TGACAATTCTCGAGCGTTCA 57.568 45.000 7.81 2.89 0.00 3.18
297 298 1.284657 AGCATGACAATTCTCGAGCG 58.715 50.000 7.81 0.00 0.00 5.03
329 330 9.531942 CAAATCTTTATACAATAGCATGGCAAA 57.468 29.630 0.00 0.00 0.00 3.68
330 331 8.143193 CCAAATCTTTATACAATAGCATGGCAA 58.857 33.333 0.00 0.00 0.00 4.52
331 332 7.660112 CCAAATCTTTATACAATAGCATGGCA 58.340 34.615 0.00 0.00 0.00 4.92
332 333 6.587608 GCCAAATCTTTATACAATAGCATGGC 59.412 38.462 0.00 0.00 40.08 4.40
333 334 7.660112 TGCCAAATCTTTATACAATAGCATGG 58.340 34.615 0.00 0.00 0.00 3.66
371 372 8.124199 GCAACATGACAAATTTCTGACAATTTT 58.876 29.630 0.00 2.74 34.70 1.82
372 373 7.280428 TGCAACATGACAAATTTCTGACAATTT 59.720 29.630 0.00 5.36 36.90 1.82
373 374 6.762187 TGCAACATGACAAATTTCTGACAATT 59.238 30.769 0.00 0.00 0.00 2.32
394 671 2.877097 TAGCAATTCCTCTGGTGCAA 57.123 45.000 0.00 0.00 39.50 4.08
405 682 9.801714 CAAATTCTTGAAAACACATAGCAATTC 57.198 29.630 0.00 0.00 34.14 2.17
416 693 5.179742 GCATCATGGCAAATTCTTGAAAACA 59.820 36.000 0.00 0.00 34.14 2.83
432 709 4.270084 GCAATTCTTCATGTTGCATCATGG 59.730 41.667 28.78 18.12 45.57 3.66
483 761 2.799017 TCTTCTGCCAGCATGTCAAAT 58.201 42.857 0.00 0.00 0.00 2.32
499 777 3.042871 TGTGGCATGGCAATTTTCTTC 57.957 42.857 25.11 9.38 0.00 2.87
501 779 2.568062 TGATGTGGCATGGCAATTTTCT 59.432 40.909 25.11 4.92 0.00 2.52
524 802 5.988310 ATGGCAATTTTCATCAGTTCTCA 57.012 34.783 0.00 0.00 0.00 3.27
526 804 5.716228 TGGTATGGCAATTTTCATCAGTTCT 59.284 36.000 0.00 0.00 0.00 3.01
527 805 5.964758 TGGTATGGCAATTTTCATCAGTTC 58.035 37.500 0.00 0.00 0.00 3.01
530 808 6.632909 TCTTTGGTATGGCAATTTTCATCAG 58.367 36.000 0.00 0.00 0.00 2.90
532 810 6.873076 TGTTCTTTGGTATGGCAATTTTCATC 59.127 34.615 0.00 0.00 0.00 2.92
553 831 8.397148 ACACATCCAAAATGACAAATTTTGTTC 58.603 29.630 15.54 9.66 45.52 3.18
556 834 9.011407 CAAACACATCCAAAATGACAAATTTTG 57.989 29.630 13.92 13.92 44.32 2.44
557 835 7.701501 GCAAACACATCCAAAATGACAAATTTT 59.298 29.630 0.00 0.00 0.00 1.82
558 836 7.067251 AGCAAACACATCCAAAATGACAAATTT 59.933 29.630 0.00 0.00 0.00 1.82
564 842 4.619973 TGAGCAAACACATCCAAAATGAC 58.380 39.130 0.00 0.00 0.00 3.06
571 849 3.489355 ACAATCTGAGCAAACACATCCA 58.511 40.909 0.00 0.00 0.00 3.41
593 871 8.822855 ACAACATTAAACGATTCGCTTATGATA 58.177 29.630 5.86 0.00 0.00 2.15
597 875 6.182634 CGACAACATTAAACGATTCGCTTAT 58.817 36.000 5.86 0.00 0.00 1.73
598 876 5.444877 CCGACAACATTAAACGATTCGCTTA 60.445 40.000 5.86 1.57 0.00 3.09
599 877 4.391358 CGACAACATTAAACGATTCGCTT 58.609 39.130 5.86 2.67 0.00 4.68
610 888 4.236935 GGACTACGAACCGACAACATTAA 58.763 43.478 0.00 0.00 0.00 1.40
626 904 1.823610 ACACCCTTCTAAGCGGACTAC 59.176 52.381 4.78 0.00 0.00 2.73
629 907 0.320697 ACACACCCTTCTAAGCGGAC 59.679 55.000 4.78 0.00 0.00 4.79
630 908 0.320374 CACACACCCTTCTAAGCGGA 59.680 55.000 4.78 0.00 0.00 5.54
631 909 0.320374 TCACACACCCTTCTAAGCGG 59.680 55.000 0.00 0.00 0.00 5.52
632 910 1.272490 TCTCACACACCCTTCTAAGCG 59.728 52.381 0.00 0.00 0.00 4.68
689 1224 8.918961 AATGTTCAATTTTCGTGTGTTCTAAA 57.081 26.923 0.00 0.00 0.00 1.85
690 1225 8.402472 AGAATGTTCAATTTTCGTGTGTTCTAA 58.598 29.630 0.00 0.00 0.00 2.10
692 1227 6.795399 AGAATGTTCAATTTTCGTGTGTTCT 58.205 32.000 0.00 0.00 0.00 3.01
693 1228 7.305993 GGAAGAATGTTCAATTTTCGTGTGTTC 60.306 37.037 0.00 0.00 0.00 3.18
694 1229 6.475402 GGAAGAATGTTCAATTTTCGTGTGTT 59.525 34.615 0.00 0.00 0.00 3.32
695 1230 5.977129 GGAAGAATGTTCAATTTTCGTGTGT 59.023 36.000 0.00 0.00 0.00 3.72
696 1231 6.208644 AGGAAGAATGTTCAATTTTCGTGTG 58.791 36.000 0.00 0.00 0.00 3.82
723 1258 3.813724 GACGTTAGTTCAGAGGGCTTTTT 59.186 43.478 0.00 0.00 0.00 1.94
728 1263 1.544691 TCTGACGTTAGTTCAGAGGGC 59.455 52.381 7.27 0.00 35.81 5.19
729 1264 3.487711 CGATCTGACGTTAGTTCAGAGGG 60.488 52.174 16.01 5.08 42.76 4.30
743 1279 7.072177 TCAATCCAAATGTTAACGATCTGAC 57.928 36.000 0.26 0.00 0.00 3.51
762 1298 7.731054 AGGCCTCGGATCTATATTAATCAATC 58.269 38.462 0.00 0.00 0.00 2.67
791 1384 8.312669 TCCCACTATTTTCCTTTTTCTTCAAA 57.687 30.769 0.00 0.00 0.00 2.69
792 1385 7.906199 TCCCACTATTTTCCTTTTTCTTCAA 57.094 32.000 0.00 0.00 0.00 2.69
794 1387 8.246871 CAGATCCCACTATTTTCCTTTTTCTTC 58.753 37.037 0.00 0.00 0.00 2.87
795 1388 7.950124 TCAGATCCCACTATTTTCCTTTTTCTT 59.050 33.333 0.00 0.00 0.00 2.52
796 1389 7.470192 TCAGATCCCACTATTTTCCTTTTTCT 58.530 34.615 0.00 0.00 0.00 2.52
797 1390 7.703058 TCAGATCCCACTATTTTCCTTTTTC 57.297 36.000 0.00 0.00 0.00 2.29
799 1392 8.491045 TTTTCAGATCCCACTATTTTCCTTTT 57.509 30.769 0.00 0.00 0.00 2.27
814 1417 8.669243 ACGATGAAAGACTAAATTTTCAGATCC 58.331 33.333 0.00 0.00 43.97 3.36
829 1432 7.727017 AGTGTAAATAACGAACGATGAAAGAC 58.273 34.615 0.14 0.00 0.00 3.01
842 1445 5.333046 ACAACAACCGAGTGTAAATAACG 57.667 39.130 0.00 0.00 0.00 3.18
845 1448 6.762187 TCAGAAACAACAACCGAGTGTAAATA 59.238 34.615 0.00 0.00 0.00 1.40
847 1450 4.936411 TCAGAAACAACAACCGAGTGTAAA 59.064 37.500 0.00 0.00 0.00 2.01
859 1462 2.424234 CCCCTTTCCCTCAGAAACAACA 60.424 50.000 0.00 0.00 39.60 3.33
1282 1887 1.605753 GGGTCTTGGTGTTCTTGTCC 58.394 55.000 0.00 0.00 0.00 4.02
1467 2074 4.340381 ACCTTCCAAGCATCTAATTGCATC 59.660 41.667 0.00 0.00 45.23 3.91
1499 2106 9.162793 GAATTAAGTCAATGCATAATCAGAACG 57.837 33.333 0.00 0.00 0.00 3.95
1772 2379 0.244721 GGAAGCCATTGTGAAGCCAC 59.755 55.000 0.00 0.00 43.46 5.01
1866 2474 0.921347 ATAACACGTTCTCGCATCGC 59.079 50.000 0.00 0.00 41.18 4.58
1935 2543 3.270027 CAATTCGGCCTGACAGTTGATA 58.730 45.455 0.00 0.00 0.00 2.15
1940 2548 1.238439 CAACAATTCGGCCTGACAGT 58.762 50.000 0.00 0.00 0.00 3.55
1945 2553 1.501741 CGACCAACAATTCGGCCTG 59.498 57.895 0.00 0.00 0.00 4.85
2002 2610 1.001633 GCTGTGAAAAGTAGGGACGGA 59.998 52.381 0.00 0.00 0.00 4.69
2005 2613 2.152016 GTGGCTGTGAAAAGTAGGGAC 58.848 52.381 0.00 0.00 0.00 4.46
2050 2664 3.609409 GCAGAAACAGATCAAACGGGAAC 60.609 47.826 0.00 0.00 0.00 3.62
2076 2690 0.392461 GCCATAAACCCTCACGAGCA 60.392 55.000 0.00 0.00 0.00 4.26
2085 2699 2.587522 GATCTGGAAGGCCATAAACCC 58.412 52.381 5.01 0.00 44.91 4.11
2124 2738 4.260334 GCAACAAGGAAAAGTGTTTGATGC 60.260 41.667 3.26 3.26 40.41 3.91
2204 2818 8.340757 ACTAGGGCCATATCTATATATCCTAGC 58.659 40.741 6.18 1.37 38.21 3.42
2265 2879 7.086376 GGATTAATCGGTGAATCATCCATTTG 58.914 38.462 8.07 0.00 34.36 2.32
2273 2887 5.600898 TGAGTAGGGATTAATCGGTGAATCA 59.399 40.000 8.07 6.80 34.36 2.57
2279 2893 2.633481 GGCTGAGTAGGGATTAATCGGT 59.367 50.000 9.32 1.80 35.62 4.69
2281 2895 3.574396 TGAGGCTGAGTAGGGATTAATCG 59.426 47.826 9.32 0.00 0.00 3.34
2319 2933 6.925165 CGCTTTTATATTAGTTTACGGAGGGA 59.075 38.462 0.00 0.00 0.00 4.20
2320 2934 6.703165 ACGCTTTTATATTAGTTTACGGAGGG 59.297 38.462 0.00 0.00 0.00 4.30
2321 2935 7.704789 ACGCTTTTATATTAGTTTACGGAGG 57.295 36.000 0.00 0.00 0.00 4.30
2396 3010 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
2397 3011 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
2398 3012 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
2399 3013 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
2400 3014 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
2406 3020 9.490083 ACTGTTACTCCCTCTGTAAACTAATAT 57.510 33.333 0.00 0.00 32.58 1.28
2407 3021 8.890410 ACTGTTACTCCCTCTGTAAACTAATA 57.110 34.615 0.00 0.00 32.58 0.98
2408 3022 7.793948 ACTGTTACTCCCTCTGTAAACTAAT 57.206 36.000 0.00 0.00 32.58 1.73
2409 3023 7.607615 AACTGTTACTCCCTCTGTAAACTAA 57.392 36.000 0.00 0.00 32.58 2.24
2410 3024 7.177392 GGTAACTGTTACTCCCTCTGTAAACTA 59.823 40.741 25.04 0.00 36.39 2.24
2411 3025 6.014755 GGTAACTGTTACTCCCTCTGTAAACT 60.015 42.308 25.04 0.00 36.39 2.66
2412 3026 6.162079 GGTAACTGTTACTCCCTCTGTAAAC 58.838 44.000 25.04 5.19 36.39 2.01
2413 3027 5.047802 CGGTAACTGTTACTCCCTCTGTAAA 60.048 44.000 25.04 0.00 36.39 2.01
2414 3028 4.460382 CGGTAACTGTTACTCCCTCTGTAA 59.540 45.833 25.04 0.00 36.39 2.41
2415 3029 4.012374 CGGTAACTGTTACTCCCTCTGTA 58.988 47.826 25.04 0.00 36.39 2.74
2416 3030 2.824341 CGGTAACTGTTACTCCCTCTGT 59.176 50.000 25.04 0.00 36.39 3.41
2417 3031 2.165845 CCGGTAACTGTTACTCCCTCTG 59.834 54.545 25.04 7.75 36.39 3.35
2418 3032 2.225217 ACCGGTAACTGTTACTCCCTCT 60.225 50.000 25.04 4.90 36.39 3.69
2419 3033 2.174360 ACCGGTAACTGTTACTCCCTC 58.826 52.381 25.04 10.96 36.39 4.30
2420 3034 2.315720 ACCGGTAACTGTTACTCCCT 57.684 50.000 25.04 7.49 36.39 4.20
2421 3035 3.068732 GGATACCGGTAACTGTTACTCCC 59.931 52.174 25.04 11.83 36.39 4.30
2422 3036 3.956848 AGGATACCGGTAACTGTTACTCC 59.043 47.826 25.04 22.33 34.93 3.85
2423 3037 4.641989 TCAGGATACCGGTAACTGTTACTC 59.358 45.833 31.88 19.10 34.93 2.59
2424 3038 4.603131 TCAGGATACCGGTAACTGTTACT 58.397 43.478 31.88 17.05 34.93 2.24
2425 3039 4.989279 TCAGGATACCGGTAACTGTTAC 57.011 45.455 31.88 19.81 34.93 2.50
2426 3040 4.771577 TGTTCAGGATACCGGTAACTGTTA 59.228 41.667 31.88 23.64 34.93 2.41
2427 3041 3.579586 TGTTCAGGATACCGGTAACTGTT 59.420 43.478 31.88 14.95 34.93 3.16
2428 3042 3.167485 TGTTCAGGATACCGGTAACTGT 58.833 45.455 31.88 15.27 37.88 3.55
2438 3052 9.155975 GATACATATGACCAATGTTCAGGATAC 57.844 37.037 10.38 0.00 38.49 2.24
2673 3289 3.769739 AGAGCAAACCATGTACTCACA 57.230 42.857 0.00 0.00 39.52 3.58
2690 3306 6.183360 GCAACAGTTAGATCAGCCTTTAAGAG 60.183 42.308 0.00 0.00 0.00 2.85
2771 4591 1.209261 TCTGGTTCATGGCATCGCTAA 59.791 47.619 0.00 0.00 0.00 3.09
2780 4600 3.956199 ACAAGGCATATTCTGGTTCATGG 59.044 43.478 0.00 0.00 0.00 3.66
2790 4610 6.959639 TTTATCCCAGAACAAGGCATATTC 57.040 37.500 0.00 0.00 0.00 1.75
2848 4668 6.667370 TGCATGCATATATAAGGTCAAAACG 58.333 36.000 18.46 0.00 0.00 3.60
2900 4722 7.710475 TCAAATATATCGATGCAGACAAGAACA 59.290 33.333 8.54 0.00 0.00 3.18
3351 5174 2.228582 CTGAGTATGCTAGCGCTCTCAT 59.771 50.000 24.77 20.49 37.88 2.90
3408 5231 3.008375 ACCAACAGTGTCTAGATGCACAT 59.992 43.478 14.08 1.66 38.02 3.21
3418 5241 2.717639 AAGAGCAACCAACAGTGTCT 57.282 45.000 0.00 0.00 0.00 3.41
3514 5337 7.439655 CCTCTTCGTTAGATTCATTAAGGAAGG 59.560 40.741 19.10 13.15 44.76 3.46
3980 5803 4.579869 TGGCAAATACTCTCTCTGTTTCC 58.420 43.478 0.00 0.00 0.00 3.13
4090 5913 3.307339 GGGCTCTGTCAGAAGAAGTCAAT 60.307 47.826 3.67 0.00 0.00 2.57
4196 6037 2.897823 ACTGGACTCCCTCCCATTAT 57.102 50.000 0.00 0.00 38.49 1.28
4550 6394 0.727970 CTGACAGAGCAGCAGATTGC 59.272 55.000 0.00 0.00 45.46 3.56
4639 6483 7.847096 TGATGTAAGTACAGGCTCTTGATTAA 58.153 34.615 0.00 0.00 39.92 1.40
4791 6636 2.457778 GCGCCGGCGTTTCTTATCA 61.458 57.895 45.02 0.00 42.09 2.15
4829 6674 4.804868 TTGTGCATTTGAATATGGCAGT 57.195 36.364 0.00 0.00 0.00 4.40
4929 6774 4.640364 TGCACTGTGTTGATGAACTGATA 58.360 39.130 9.86 0.00 32.79 2.15
4960 6805 0.178992 TTTCAGGGGGTGCAAGTCAG 60.179 55.000 0.00 0.00 0.00 3.51
5182 7036 6.849502 ACGTCTCAGATTTTCGACTTACATA 58.150 36.000 0.00 0.00 0.00 2.29
5183 7037 5.710984 ACGTCTCAGATTTTCGACTTACAT 58.289 37.500 0.00 0.00 0.00 2.29
5184 7038 5.117355 ACGTCTCAGATTTTCGACTTACA 57.883 39.130 0.00 0.00 0.00 2.41
5265 7119 2.221169 TCAAGCGCTGATCTGTTTGTT 58.779 42.857 12.58 0.00 0.00 2.83
5388 7244 2.716217 GAACAGGAGGTTGGGAGAATG 58.284 52.381 0.00 0.00 40.63 2.67
5411 7267 4.275508 AGGTGTGGGCACTGCTGG 62.276 66.667 0.00 0.00 44.65 4.85
5413 7269 1.705002 TAACAGGTGTGGGCACTGCT 61.705 55.000 0.00 0.00 44.65 4.24
5491 7378 3.030308 CAACGTGACGAGCGCAGT 61.030 61.111 13.70 9.64 0.00 4.40
5494 7381 2.167918 GAACAACGTGACGAGCGC 59.832 61.111 13.70 0.00 0.00 5.92
5500 7387 1.602377 CAAAGGAGGGAACAACGTGAC 59.398 52.381 0.00 0.00 0.00 3.67
5507 7394 1.478654 GCAAGGACAAAGGAGGGAACA 60.479 52.381 0.00 0.00 0.00 3.18
5510 7397 1.374947 CGCAAGGACAAAGGAGGGA 59.625 57.895 0.00 0.00 0.00 4.20
5530 7417 1.267806 CGCCAGTCACTTTTCTGCATT 59.732 47.619 0.00 0.00 0.00 3.56
5566 7485 4.281688 ACAACTTGCAAAATATCAGGTGCT 59.718 37.500 0.00 0.00 37.87 4.40
5588 7510 0.687354 ACCCAGGTCTCACATCACAC 59.313 55.000 0.00 0.00 0.00 3.82
5596 7518 4.927267 AACATTCAATACCCAGGTCTCA 57.073 40.909 0.00 0.00 0.00 3.27
5635 7557 6.963322 ACTTACAGGCATCCTTCTTTTCTAT 58.037 36.000 0.00 0.00 0.00 1.98
5641 7564 4.003648 CGAAACTTACAGGCATCCTTCTT 58.996 43.478 0.00 0.00 0.00 2.52
5666 7589 2.224646 TGTCATGGACAAATCCCGAACA 60.225 45.455 0.00 0.00 45.59 3.18
5685 7608 6.184580 TGCCATAAATAACGTTCGATTTGT 57.815 33.333 15.93 8.92 0.00 2.83
5714 7637 6.296026 TGTCATGCTTACCAACTAAACTTCT 58.704 36.000 0.00 0.00 0.00 2.85
5715 7638 6.554334 TGTCATGCTTACCAACTAAACTTC 57.446 37.500 0.00 0.00 0.00 3.01
5743 7681 5.078411 TCTTGGCAAAAACAAACTAAGCA 57.922 34.783 0.00 0.00 0.00 3.91
5747 7685 6.597280 AGCAATTTCTTGGCAAAAACAAACTA 59.403 30.769 0.00 0.00 32.72 2.24
5754 7692 3.212685 CCCAGCAATTTCTTGGCAAAAA 58.787 40.909 0.00 5.78 32.72 1.94
5763 7701 2.560105 GTTGAGAAGCCCAGCAATTTCT 59.440 45.455 0.00 0.00 32.87 2.52


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

AutoCloner maintained by Alex Coulton.