Multiple sequence alignment - TraesCS2A01G433500

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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 TraesCS2A01G433500 chr2A 100.000 4369 0 0 1 4369 686699695 686704063 0.000000e+00 8069.0
1 TraesCS2A01G433500 chr2A 91.667 408 32 1 3918 4325 686777079 686777484 8.200000e-157 564.0
2 TraesCS2A01G433500 chr2A 82.927 246 27 9 181 423 686691453 686691686 1.590000e-49 207.0
3 TraesCS2A01G433500 chr2A 97.436 117 3 0 65 181 686691299 686691415 2.660000e-47 200.0
4 TraesCS2A01G433500 chr2A 86.111 180 23 2 4131 4309 686798040 686797862 4.460000e-45 193.0
5 TraesCS2A01G433500 chr2A 96.875 32 0 1 413 444 433418394 433418364 8.000000e-03 52.8
6 TraesCS2A01G433500 chr2D 90.449 2094 111 53 2326 4369 543844902 543846956 0.000000e+00 2676.0
7 TraesCS2A01G433500 chr2D 89.911 1576 99 27 594 2130 543843162 543844716 0.000000e+00 1975.0
8 TraesCS2A01G433500 chr2D 92.293 519 25 4 478 982 543839349 543839866 0.000000e+00 723.0
9 TraesCS2A01G433500 chr2D 92.195 410 31 1 3915 4324 544170441 544170849 2.930000e-161 579.0
10 TraesCS2A01G433500 chr2D 81.383 376 40 15 627 982 543835338 543835703 3.330000e-71 279.0
11 TraesCS2A01G433500 chr2D 94.326 141 8 0 41 181 543839028 543839168 2.650000e-52 217.0
12 TraesCS2A01G433500 chr2D 93.525 139 9 0 43 181 543834692 543834830 1.590000e-49 207.0
13 TraesCS2A01G433500 chr2D 85.475 179 26 0 4131 4309 544260356 544260178 2.070000e-43 187.0
14 TraesCS2A01G433500 chr2D 81.944 216 23 10 182 393 543834869 543835072 7.510000e-38 169.0
15 TraesCS2A01G433500 chr2B 87.925 1557 98 43 654 2155 649475413 649476934 0.000000e+00 1751.0
16 TraesCS2A01G433500 chr2B 87.417 1208 87 37 2310 3497 649477050 649478212 0.000000e+00 1328.0
17 TraesCS2A01G433500 chr2B 91.451 889 38 22 3497 4369 649479045 649479911 0.000000e+00 1186.0
18 TraesCS2A01G433500 chr2B 94.656 131 7 0 43 173 649464593 649464723 2.060000e-48 204.0
19 TraesCS2A01G433500 chr2B 81.633 196 13 9 424 618 649474811 649474984 1.640000e-29 141.0
20 TraesCS2A01G433500 chr2B 93.182 44 3 0 1 44 649464522 649464565 1.010000e-06 65.8
21 TraesCS2A01G433500 chr2B 95.000 40 2 0 5 44 649474167 649474206 3.650000e-06 63.9
22 TraesCS2A01G433500 chr6D 83.200 250 41 1 4069 4318 426984739 426984491 1.220000e-55 228.0
23 TraesCS2A01G433500 chr6B 82.609 253 42 2 4067 4318 642724956 642724705 5.690000e-54 222.0
24 TraesCS2A01G433500 chr6B 97.297 37 1 0 455 491 72383600 72383564 3.650000e-06 63.9
25 TraesCS2A01G433500 chr6A 82.400 250 43 1 4069 4318 571683849 571683601 2.650000e-52 217.0
26 TraesCS2A01G433500 chr7A 83.422 187 26 4 1586 1769 620750056 620749872 7.510000e-38 169.0
27 TraesCS2A01G433500 chr7A 82.967 182 27 2 1594 1773 619633660 619633481 1.260000e-35 161.0
28 TraesCS2A01G433500 chr7A 83.240 179 26 2 1594 1770 619907538 619907714 1.260000e-35 161.0
29 TraesCS2A01G433500 chr7A 81.771 192 29 5 1594 1781 619576284 619576095 5.850000e-34 156.0
30 TraesCS2A01G433500 chr7A 92.857 42 3 0 454 495 124792665 124792624 1.310000e-05 62.1
31 TraesCS2A01G433500 chr7A 96.875 32 0 1 413 444 378967431 378967461 8.000000e-03 52.8
32 TraesCS2A01G433500 chr7D 83.607 183 24 5 1594 1773 538332924 538332745 2.700000e-37 167.0
33 TraesCS2A01G433500 chr7D 82.474 194 29 4 1586 1776 539134170 539133979 9.720000e-37 165.0
34 TraesCS2A01G433500 chr7D 81.771 192 29 5 1594 1781 538140456 538140267 5.850000e-34 156.0
35 TraesCS2A01G433500 chr7D 97.297 37 1 0 454 490 119894009 119894045 3.650000e-06 63.9
36 TraesCS2A01G433500 chr5D 86.301 73 4 1 424 490 546857356 546857284 1.690000e-09 75.0
37 TraesCS2A01G433500 chr1D 85.333 75 8 2 421 493 291839575 291839502 1.690000e-09 75.0
38 TraesCS2A01G433500 chr1B 89.796 49 5 0 447 495 597156853 597156805 3.650000e-06 63.9
39 TraesCS2A01G433500 chr1A 95.000 40 2 0 454 493 330769278 330769239 3.650000e-06 63.9
40 TraesCS2A01G433500 chr4D 82.432 74 9 2 421 493 75264150 75264080 1.310000e-05 62.1
41 TraesCS2A01G433500 chr3A 87.273 55 4 1 437 491 117319712 117319661 4.720000e-05 60.2
42 TraesCS2A01G433500 chr5A 96.875 32 0 1 413 444 502661478 502661448 8.000000e-03 52.8
43 TraesCS2A01G433500 chr4A 96.875 32 0 1 413 444 419965203 419965233 8.000000e-03 52.8
44 TraesCS2A01G433500 chr4A 96.875 32 0 1 413 444 428567635 428567605 8.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G433500 chr2A 686699695 686704063 4368 False 8069.000000 8069 100.000000 1 4369 1 chr2A.!!$F1 4368
1 TraesCS2A01G433500 chr2D 543834692 543846956 12264 False 892.285714 2676 89.118714 41 4369 7 chr2D.!!$F2 4328
2 TraesCS2A01G433500 chr2B 649474167 649479911 5744 False 893.980000 1751 88.685200 5 4369 5 chr2B.!!$F2 4364

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
32 33 0.172578 CTGGATTGCGACGTACTCCA 59.827 55.0 20.66 20.66 34.88 3.86 F
1029 9360 0.179000 AGTTCCATCCATCTCGTGCC 59.821 55.0 0.00 0.00 0.00 5.01 F
2053 10393 0.179004 TTGCCGGCCCGAAATATCAT 60.179 50.0 26.77 0.00 0.00 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1502 9840 0.179029 ACACAGGCCCAATATACGCC 60.179 55.0 0.0 0.0 43.35 5.68 R
2271 10651 0.034896 GGAGGAGGCTCGTTGTTTCA 59.965 55.0 11.5 0.0 0.00 2.69 R
3899 13183 0.158928 GTGAGCAGTTTTCGTCGTCG 59.841 55.0 0.0 0.0 38.55 5.12 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
32 33 0.172578 CTGGATTGCGACGTACTCCA 59.827 55.000 20.66 20.66 34.88 3.86
38 39 1.424403 TGCGACGTACTCCACATTTG 58.576 50.000 0.00 0.00 0.00 2.32
44 45 4.127171 GACGTACTCCACATTTGGCATAT 58.873 43.478 0.00 0.00 43.56 1.78
45 46 3.876914 ACGTACTCCACATTTGGCATATG 59.123 43.478 15.16 15.16 43.56 1.78
66 128 4.585879 TGTGCCTCTTTATTCTTACACCC 58.414 43.478 0.00 0.00 0.00 4.61
68 130 3.053917 TGCCTCTTTATTCTTACACCCCC 60.054 47.826 0.00 0.00 0.00 5.40
195 296 1.069636 CAAGTCGCAGAGGTGAAAAGC 60.070 52.381 0.00 0.00 36.95 3.51
228 332 2.297880 TGGAGAACCTCGTCGAAAATCA 59.702 45.455 0.00 0.00 37.04 2.57
229 333 3.056107 TGGAGAACCTCGTCGAAAATCAT 60.056 43.478 0.00 0.00 37.04 2.45
234 338 7.062371 GGAGAACCTCGTCGAAAATCATATATG 59.938 40.741 6.36 6.36 0.00 1.78
244 348 8.511321 GTCGAAAATCATATATGTGGCCAATAA 58.489 33.333 7.24 0.00 0.00 1.40
276 380 7.792374 TTTTCTCTAGAATATGTGCATCCAC 57.208 36.000 0.00 0.00 36.88 4.02
286 390 3.979101 TGTGCATCCACACATCTCTAA 57.021 42.857 0.00 0.00 46.51 2.10
317 423 8.489559 CACGGTAAATATAAACGCATTAGCTAA 58.510 33.333 8.99 8.99 39.10 3.09
407 513 5.358442 ACAGTTTGGCGCCAACATATTATAA 59.642 36.000 40.36 20.52 35.46 0.98
410 516 4.839668 TGGCGCCAACATATTATAAACC 57.160 40.909 30.74 0.00 0.00 3.27
490 4802 7.427989 AACGTCTTATATTTTGGTAGGGAGA 57.572 36.000 0.00 0.00 0.00 3.71
491 4803 7.613551 ACGTCTTATATTTTGGTAGGGAGAT 57.386 36.000 0.00 0.00 0.00 2.75
492 4804 8.716674 ACGTCTTATATTTTGGTAGGGAGATA 57.283 34.615 0.00 0.00 0.00 1.98
525 4837 0.322322 ACGTCCAATACTCGCCCAAA 59.678 50.000 0.00 0.00 0.00 3.28
526 4838 1.006832 CGTCCAATACTCGCCCAAAG 58.993 55.000 0.00 0.00 0.00 2.77
564 4876 5.651387 TCAAGACTCTGTCTATGTTCCAG 57.349 43.478 0.34 0.00 42.59 3.86
686 8983 3.493129 CGTGATGTCGGAAACTTCTCAAA 59.507 43.478 0.00 0.00 34.08 2.69
712 9009 2.705658 TCCTGCCCTATCCTTACATGTG 59.294 50.000 9.11 0.00 0.00 3.21
713 9010 2.439507 CCTGCCCTATCCTTACATGTGT 59.560 50.000 9.11 0.00 0.00 3.72
730 9041 0.180642 TGTGGTTTAACAGCGACCCA 59.819 50.000 0.00 0.00 32.39 4.51
747 9061 2.884639 ACCCATGTAATTAAGCATCCGC 59.115 45.455 0.00 0.00 38.99 5.54
748 9062 2.228822 CCCATGTAATTAAGCATCCGCC 59.771 50.000 0.00 0.00 39.83 6.13
749 9063 2.884012 CCATGTAATTAAGCATCCGCCA 59.116 45.455 0.00 0.00 39.83 5.69
760 9074 2.172717 AGCATCCGCCAGTTAACCTAAT 59.827 45.455 0.88 0.00 39.83 1.73
761 9075 3.389983 AGCATCCGCCAGTTAACCTAATA 59.610 43.478 0.88 0.00 39.83 0.98
762 9076 4.131596 GCATCCGCCAGTTAACCTAATAA 58.868 43.478 0.88 0.00 0.00 1.40
763 9077 4.760204 GCATCCGCCAGTTAACCTAATAAT 59.240 41.667 0.88 0.00 0.00 1.28
764 9078 5.935789 GCATCCGCCAGTTAACCTAATAATA 59.064 40.000 0.88 0.00 0.00 0.98
765 9079 6.092259 GCATCCGCCAGTTAACCTAATAATAG 59.908 42.308 0.88 0.00 0.00 1.73
766 9080 6.736110 TCCGCCAGTTAACCTAATAATAGT 57.264 37.500 0.88 0.00 0.00 2.12
767 9081 7.838079 TCCGCCAGTTAACCTAATAATAGTA 57.162 36.000 0.88 0.00 0.00 1.82
902 9231 3.670377 GCGCCAACCCAACCAGAC 61.670 66.667 0.00 0.00 0.00 3.51
916 9245 1.070134 ACCAGACTTGTGCACGTATGT 59.930 47.619 13.13 7.90 0.00 2.29
951 9280 1.128724 GACTCGTCAGTCGACATGCG 61.129 60.000 19.50 17.35 44.01 4.73
952 9281 1.154207 CTCGTCAGTCGACATGCGT 60.154 57.895 19.50 0.00 44.01 5.24
973 9302 2.652530 TGGCGTACCCAACTCGAC 59.347 61.111 1.01 0.00 41.82 4.20
980 9309 3.691342 CCCAACTCGACGGCCTGA 61.691 66.667 0.00 0.00 0.00 3.86
993 9322 1.593006 CGGCCTGAACACTATAAAGCG 59.407 52.381 0.00 0.00 0.00 4.68
1029 9360 0.179000 AGTTCCATCCATCTCGTGCC 59.821 55.000 0.00 0.00 0.00 5.01
1046 9377 3.487376 CGTGCCAACATACATAGCCAAAG 60.487 47.826 0.00 0.00 0.00 2.77
1047 9378 2.426738 TGCCAACATACATAGCCAAAGC 59.573 45.455 0.00 0.00 40.32 3.51
1056 9393 1.061131 CATAGCCAAAGCACTCGAACG 59.939 52.381 0.00 0.00 43.56 3.95
1128 9465 1.731613 CGTCGTCGCCTGCTGTTTA 60.732 57.895 0.00 0.00 0.00 2.01
1242 9579 4.609247 GAGATCGTCGACGGCGGG 62.609 72.222 35.05 9.62 40.29 6.13
1344 9681 1.880340 GGAGATGAAGCTCGTGCCG 60.880 63.158 5.73 0.00 40.80 5.69
1416 9753 3.848272 ACCACCAATACTTTTCATGCG 57.152 42.857 0.00 0.00 0.00 4.73
1435 9773 2.095466 GCGACTTCTCTCCCAGATATCG 60.095 54.545 0.00 0.00 39.91 2.92
1462 9800 1.080637 TGCGTTGAATGCATGCACC 60.081 52.632 25.37 18.22 34.76 5.01
1516 9854 0.671472 GTACGGGCGTATATTGGGCC 60.671 60.000 0.00 0.00 46.14 5.80
1527 9865 4.438200 CGTATATTGGGCCTGTGTTTTGAC 60.438 45.833 4.53 0.00 0.00 3.18
1538 9876 1.854126 GTGTTTTGACTGTGCATGCAC 59.146 47.619 38.00 38.00 46.33 4.57
1548 9886 1.541475 GTGCATGCACGATGATGTTG 58.459 50.000 33.20 0.00 37.19 3.33
1549 9887 1.130938 GTGCATGCACGATGATGTTGA 59.869 47.619 33.20 0.00 37.19 3.18
1550 9888 2.018515 TGCATGCACGATGATGTTGAT 58.981 42.857 18.46 0.00 33.31 2.57
1551 9889 2.223386 TGCATGCACGATGATGTTGATG 60.223 45.455 18.46 0.00 33.31 3.07
1552 9890 2.032426 GCATGCACGATGATGTTGATGA 59.968 45.455 14.21 0.00 33.31 2.92
1668 10006 2.935955 CAGACCAACGTGTTCGCC 59.064 61.111 0.00 0.00 41.18 5.54
1704 10042 2.496817 GAGCAGCGGTCCTACCTG 59.503 66.667 0.00 0.00 35.66 4.00
1797 10135 2.746277 GACGTGTCCCCCATGCAC 60.746 66.667 0.00 0.00 33.01 4.57
1814 10152 5.458015 CATGCACGCATCTAATCATTCATT 58.542 37.500 0.44 0.00 33.90 2.57
1815 10153 5.099484 TGCACGCATCTAATCATTCATTC 57.901 39.130 0.00 0.00 0.00 2.67
1816 10154 4.575645 TGCACGCATCTAATCATTCATTCA 59.424 37.500 0.00 0.00 0.00 2.57
1817 10155 5.239963 TGCACGCATCTAATCATTCATTCAT 59.760 36.000 0.00 0.00 0.00 2.57
1818 10156 6.147581 GCACGCATCTAATCATTCATTCATT 58.852 36.000 0.00 0.00 0.00 2.57
1925 10263 3.751621 CTGAAAATTAAGCAGGCGTGAG 58.248 45.455 11.29 0.00 0.00 3.51
1938 10276 1.432251 CGTGAGCCCGACGATAAGT 59.568 57.895 0.00 0.00 39.21 2.24
1954 10292 5.575606 ACGATAAGTACATGAAGACCAAACG 59.424 40.000 0.00 0.00 0.00 3.60
1967 10305 1.156736 CCAAACGCGAGAGGACAAAT 58.843 50.000 15.93 0.00 0.00 2.32
1968 10306 1.135972 CCAAACGCGAGAGGACAAATG 60.136 52.381 15.93 0.00 0.00 2.32
2004 10343 1.591158 GACTCTTTCAACGCGTGTTCA 59.409 47.619 14.98 0.00 35.72 3.18
2027 10367 5.676744 CACGCATGAAAATATGACCGTTTAG 59.323 40.000 0.00 0.00 28.79 1.85
2053 10393 0.179004 TTGCCGGCCCGAAATATCAT 60.179 50.000 26.77 0.00 0.00 2.45
2059 10399 3.429822 CCGGCCCGAAATATCATATACGT 60.430 47.826 3.71 0.00 0.00 3.57
2068 10408 7.042725 CCGAAATATCATATACGTATGGGCTTG 60.043 40.741 18.37 7.86 38.57 4.01
2071 10411 1.393539 CATATACGTATGGGCTTGCGC 59.606 52.381 18.37 0.00 35.16 6.09
2085 10425 1.416813 TTGCGCGCACCAAGTTTTTG 61.417 50.000 36.72 0.00 0.00 2.44
2130 10483 2.835764 AGGCCCGTTTACTCACAAGATA 59.164 45.455 0.00 0.00 0.00 1.98
2131 10484 3.454812 AGGCCCGTTTACTCACAAGATAT 59.545 43.478 0.00 0.00 0.00 1.63
2243 10608 3.982576 TTCTTTTCTTTGCGAACCTCC 57.017 42.857 0.00 0.00 0.00 4.30
2244 10609 3.208747 TCTTTTCTTTGCGAACCTCCT 57.791 42.857 0.00 0.00 0.00 3.69
2246 10611 1.892209 TTTCTTTGCGAACCTCCTCC 58.108 50.000 0.00 0.00 0.00 4.30
2251 10631 2.172483 TTGCGAACCTCCTCCTCTGC 62.172 60.000 0.00 0.00 0.00 4.26
2259 10639 0.325110 CTCCTCCTCTGCCCTCTCAA 60.325 60.000 0.00 0.00 0.00 3.02
2263 10643 2.421248 CCTCCTCTGCCCTCTCAAATTC 60.421 54.545 0.00 0.00 0.00 2.17
2264 10644 2.238144 CTCCTCTGCCCTCTCAAATTCA 59.762 50.000 0.00 0.00 0.00 2.57
2270 10650 6.029346 TCTGCCCTCTCAAATTCATTTTTC 57.971 37.500 0.00 0.00 0.00 2.29
2271 10651 5.776716 TCTGCCCTCTCAAATTCATTTTTCT 59.223 36.000 0.00 0.00 0.00 2.52
2272 10652 5.786311 TGCCCTCTCAAATTCATTTTTCTG 58.214 37.500 0.00 0.00 0.00 3.02
2276 10656 7.095481 GCCCTCTCAAATTCATTTTTCTGAAAC 60.095 37.037 1.58 0.00 38.55 2.78
2278 10658 9.316730 CCTCTCAAATTCATTTTTCTGAAACAA 57.683 29.630 1.58 1.86 38.55 2.83
2280 10660 8.806634 TCTCAAATTCATTTTTCTGAAACAACG 58.193 29.630 1.58 0.00 38.55 4.10
2282 10662 8.806634 TCAAATTCATTTTTCTGAAACAACGAG 58.193 29.630 1.58 0.00 38.55 4.18
2284 10664 4.606961 TCATTTTTCTGAAACAACGAGCC 58.393 39.130 1.58 0.00 0.00 4.70
2285 10665 4.338118 TCATTTTTCTGAAACAACGAGCCT 59.662 37.500 1.58 0.00 0.00 4.58
2287 10667 1.878953 TTCTGAAACAACGAGCCTCC 58.121 50.000 0.00 0.00 0.00 4.30
2290 10670 0.034896 TGAAACAACGAGCCTCCTCC 59.965 55.000 0.00 0.00 34.49 4.30
2291 10671 0.321996 GAAACAACGAGCCTCCTCCT 59.678 55.000 0.00 0.00 34.49 3.69
2292 10672 0.321996 AAACAACGAGCCTCCTCCTC 59.678 55.000 0.00 0.00 34.49 3.71
2293 10673 0.543174 AACAACGAGCCTCCTCCTCT 60.543 55.000 0.00 0.00 34.49 3.69
2294 10674 1.254284 ACAACGAGCCTCCTCCTCTG 61.254 60.000 0.00 0.00 34.49 3.35
2295 10675 1.077625 AACGAGCCTCCTCCTCTGT 59.922 57.895 0.00 0.00 34.49 3.41
2296 10676 0.968393 AACGAGCCTCCTCCTCTGTC 60.968 60.000 0.00 0.00 34.49 3.51
2298 10678 1.309688 GAGCCTCCTCCTCTGTCCT 59.690 63.158 0.00 0.00 31.68 3.85
2299 10679 0.755327 GAGCCTCCTCCTCTGTCCTC 60.755 65.000 0.00 0.00 31.68 3.71
2300 10680 1.221213 AGCCTCCTCCTCTGTCCTCT 61.221 60.000 0.00 0.00 0.00 3.69
2301 10681 0.755327 GCCTCCTCCTCTGTCCTCTC 60.755 65.000 0.00 0.00 0.00 3.20
2302 10682 0.465460 CCTCCTCCTCTGTCCTCTCG 60.465 65.000 0.00 0.00 0.00 4.04
2303 10683 0.544223 CTCCTCCTCTGTCCTCTCGA 59.456 60.000 0.00 0.00 0.00 4.04
2304 10684 0.992695 TCCTCCTCTGTCCTCTCGAA 59.007 55.000 0.00 0.00 0.00 3.71
2305 10685 1.354705 TCCTCCTCTGTCCTCTCGAAA 59.645 52.381 0.00 0.00 0.00 3.46
2306 10686 2.171840 CCTCCTCTGTCCTCTCGAAAA 58.828 52.381 0.00 0.00 0.00 2.29
2307 10687 2.563179 CCTCCTCTGTCCTCTCGAAAAA 59.437 50.000 0.00 0.00 0.00 1.94
2308 10688 3.367910 CCTCCTCTGTCCTCTCGAAAAAG 60.368 52.174 0.00 0.00 0.00 2.27
2320 10700 5.520288 CCTCTCGAAAAAGATAAAGCGATGA 59.480 40.000 0.00 0.00 0.00 2.92
2324 10704 7.904977 TCTCGAAAAAGATAAAGCGATGATTTG 59.095 33.333 0.00 0.00 0.00 2.32
2361 10741 2.487762 TGCAAAAATGGAAGGCGACTAG 59.512 45.455 0.00 0.00 42.68 2.57
2368 10748 4.755266 ATGGAAGGCGACTAGTATGTTT 57.245 40.909 0.00 0.00 42.68 2.83
2374 10754 4.171754 AGGCGACTAGTATGTTTCGTTTC 58.828 43.478 0.00 0.00 40.61 2.78
2384 10764 2.206750 TGTTTCGTTTCGGTCAGAAGG 58.793 47.619 0.00 0.00 40.40 3.46
2386 10766 3.181477 TGTTTCGTTTCGGTCAGAAGGTA 60.181 43.478 0.00 0.00 40.40 3.08
2387 10767 3.293311 TTCGTTTCGGTCAGAAGGTAG 57.707 47.619 0.00 0.00 40.40 3.18
2390 10770 2.415625 CGTTTCGGTCAGAAGGTAGGAG 60.416 54.545 0.00 0.00 40.40 3.69
2397 10777 3.117813 GGTCAGAAGGTAGGAGAGCTAGA 60.118 52.174 0.00 0.00 33.71 2.43
2398 10778 4.134563 GTCAGAAGGTAGGAGAGCTAGAG 58.865 52.174 0.00 0.00 33.71 2.43
2399 10779 2.884639 CAGAAGGTAGGAGAGCTAGAGC 59.115 54.545 0.00 0.00 42.49 4.09
2400 10780 2.512056 AGAAGGTAGGAGAGCTAGAGCA 59.488 50.000 4.01 0.00 45.16 4.26
2401 10781 2.358322 AGGTAGGAGAGCTAGAGCAC 57.642 55.000 4.01 0.00 45.16 4.40
2408 10788 2.032426 GGAGAGCTAGAGCACGTAAGAC 59.968 54.545 4.01 0.00 45.16 3.01
2413 10793 3.506455 AGCTAGAGCACGTAAGACTCAAA 59.494 43.478 4.01 0.00 45.16 2.69
2415 10795 4.684703 GCTAGAGCACGTAAGACTCAAAAA 59.315 41.667 0.00 0.00 43.31 1.94
2470 10851 1.264288 CTTTCACTGTCGGTTTGGAGC 59.736 52.381 0.00 0.00 0.00 4.70
2471 10852 0.534203 TTCACTGTCGGTTTGGAGCC 60.534 55.000 0.00 0.00 0.00 4.70
2478 10859 4.303257 GGTTTGGAGCCGAGGAAG 57.697 61.111 0.00 0.00 0.00 3.46
2479 10860 1.377333 GGTTTGGAGCCGAGGAAGG 60.377 63.158 0.00 0.00 0.00 3.46
2480 10861 1.375326 GTTTGGAGCCGAGGAAGGT 59.625 57.895 0.00 0.00 0.00 3.50
2481 10862 0.611714 GTTTGGAGCCGAGGAAGGTA 59.388 55.000 0.00 0.00 0.00 3.08
2482 10863 0.902531 TTTGGAGCCGAGGAAGGTAG 59.097 55.000 0.00 0.00 0.00 3.18
2483 10864 0.040646 TTGGAGCCGAGGAAGGTAGA 59.959 55.000 0.00 0.00 0.00 2.59
2484 10865 0.040646 TGGAGCCGAGGAAGGTAGAA 59.959 55.000 0.00 0.00 0.00 2.10
2485 10866 1.192428 GGAGCCGAGGAAGGTAGAAA 58.808 55.000 0.00 0.00 0.00 2.52
2486 10867 1.553704 GGAGCCGAGGAAGGTAGAAAA 59.446 52.381 0.00 0.00 0.00 2.29
2487 10868 2.418884 GGAGCCGAGGAAGGTAGAAAAG 60.419 54.545 0.00 0.00 0.00 2.27
2505 10886 5.415701 AGAAAAGACTTGAACAGCAACTTGA 59.584 36.000 0.00 0.00 31.96 3.02
2511 10892 4.757149 ACTTGAACAGCAACTTGATACTCC 59.243 41.667 0.00 0.00 31.96 3.85
2519 10900 1.794714 ACTTGATACTCCGGCCATCT 58.205 50.000 2.24 0.00 0.00 2.90
2521 10902 1.414181 CTTGATACTCCGGCCATCTGT 59.586 52.381 2.24 0.00 0.00 3.41
2541 10945 8.910666 CATCTGTGAGACGATATCATTCTAAAC 58.089 37.037 3.12 6.61 0.00 2.01
2543 10947 6.513180 TGTGAGACGATATCATTCTAAACCC 58.487 40.000 3.12 0.00 0.00 4.11
2544 10948 6.323996 TGTGAGACGATATCATTCTAAACCCT 59.676 38.462 3.12 0.00 0.00 4.34
2548 10952 6.015027 ACGATATCATTCTAAACCCTCTCG 57.985 41.667 3.12 0.00 0.00 4.04
2596 11000 2.289002 GGCATATTTGGAAGCACGAGAG 59.711 50.000 0.00 0.00 0.00 3.20
2611 11015 2.177594 GAGAGCACCACCTGTCCCAG 62.178 65.000 0.00 0.00 0.00 4.45
2637 11041 3.549574 CTGCTCTTTCAAACGAAGAAGC 58.450 45.455 0.00 0.00 33.10 3.86
2677 11081 3.807538 CACATGAGGTGCCTGCGC 61.808 66.667 0.00 0.00 41.36 6.09
2739 11143 5.802451 AGCTAATGATGCGATAATCGTACTG 59.198 40.000 0.00 0.00 42.81 2.74
2821 11225 8.249638 TGAATCAAAATCTCGGCAAATTCAATA 58.750 29.630 0.00 0.00 31.11 1.90
2822 11226 8.638685 AATCAAAATCTCGGCAAATTCAATAG 57.361 30.769 0.00 0.00 0.00 1.73
2823 11227 6.035843 TCAAAATCTCGGCAAATTCAATAGC 58.964 36.000 0.00 0.00 0.00 2.97
2867 11274 0.913924 TGCATCCAGGCATCTTCTCA 59.086 50.000 0.00 0.00 39.25 3.27
2868 11275 1.493446 TGCATCCAGGCATCTTCTCAT 59.507 47.619 0.00 0.00 39.25 2.90
2869 11276 2.152830 GCATCCAGGCATCTTCTCATC 58.847 52.381 0.00 0.00 0.00 2.92
2870 11277 2.486727 GCATCCAGGCATCTTCTCATCA 60.487 50.000 0.00 0.00 0.00 3.07
2880 11287 3.309961 TCTTCTCATCACTGCACTGAC 57.690 47.619 0.00 0.00 0.00 3.51
2914 11321 1.269673 CGGATCTCCTGCATCTGTCTG 60.270 57.143 0.00 0.00 0.00 3.51
2918 11325 2.250924 TCTCCTGCATCTGTCTGACAA 58.749 47.619 12.16 3.79 0.00 3.18
2920 11327 3.262660 TCTCCTGCATCTGTCTGACAATT 59.737 43.478 12.16 0.00 0.00 2.32
2922 11329 3.754850 TCCTGCATCTGTCTGACAATTTG 59.245 43.478 12.16 10.23 0.00 2.32
2926 11333 5.522456 TGCATCTGTCTGACAATTTGTTTC 58.478 37.500 12.16 0.00 0.00 2.78
2927 11334 4.919754 GCATCTGTCTGACAATTTGTTTCC 59.080 41.667 12.16 0.00 0.00 3.13
2930 11337 4.272504 TCTGTCTGACAATTTGTTTCCGTC 59.727 41.667 12.16 0.00 0.00 4.79
3138 11550 2.123982 CCTACGGGACCTACGCCT 60.124 66.667 0.00 0.00 34.00 5.52
3359 11777 2.364842 ATGGACCAGCTCGCCTCT 60.365 61.111 0.00 0.00 0.00 3.69
3374 11792 1.363744 CCTCTGCCGTCTGATTGTTC 58.636 55.000 0.00 0.00 0.00 3.18
3484 11914 1.813178 CTGCTAGGTCGTCTCACTCAA 59.187 52.381 0.00 0.00 0.00 3.02
3548 12816 1.950909 AGGAGTTTCTCTAGCGGATCG 59.049 52.381 0.00 0.00 0.00 3.69
3552 12820 3.543665 AGTTTCTCTAGCGGATCGTAGT 58.456 45.455 0.00 0.00 0.00 2.73
3664 12936 1.205655 CTCGACATCTTGAGCCTGGAA 59.794 52.381 0.00 0.00 0.00 3.53
3737 13015 0.196118 AAGTGGAGGAAAGGGGAGGA 59.804 55.000 0.00 0.00 0.00 3.71
3740 13018 1.612739 GGAGGAAAGGGGAGGACGT 60.613 63.158 0.00 0.00 0.00 4.34
3748 13028 0.685660 AGGGGAGGACGTTCAGAAAC 59.314 55.000 0.00 0.00 0.00 2.78
3804 13084 5.573282 CGTACCTGTTTCTTCAGATGTACAG 59.427 44.000 0.33 0.00 35.19 2.74
3844 13128 8.579006 ACGATACTATATCGAACCCAAACAATA 58.421 33.333 21.58 0.00 43.59 1.90
3845 13129 9.582431 CGATACTATATCGAACCCAAACAATAT 57.418 33.333 11.87 0.00 43.59 1.28
3849 13133 9.793259 ACTATATCGAACCCAAACAATATGAAT 57.207 29.630 0.00 0.00 0.00 2.57
3863 13147 1.463674 ATGAATTGTCGCTCAACCCC 58.536 50.000 0.00 0.00 38.97 4.95
3893 13177 3.408851 GCCAAACCCGACGACGAC 61.409 66.667 9.28 0.00 42.66 4.34
3894 13178 3.101428 CCAAACCCGACGACGACG 61.101 66.667 12.66 12.66 42.66 5.12
3896 13180 2.050985 AAACCCGACGACGACGAC 60.051 61.111 20.63 7.02 42.66 4.34
3912 13196 2.775847 GACGACGACGACGAAAACT 58.224 52.632 25.15 3.08 42.66 2.66
3913 13197 0.424920 GACGACGACGACGAAAACTG 59.575 55.000 25.15 0.00 42.66 3.16
3998 13282 1.062294 GTCGGTGCAGTAGTCGTAGAG 59.938 57.143 0.00 0.00 36.95 2.43
4013 13297 2.579873 GTAGAGGACGTAGCCCATGTA 58.420 52.381 0.00 0.00 0.00 2.29
4286 13570 0.101040 TCCTCGTTGTTGTCGAACGT 59.899 50.000 6.49 0.00 45.09 3.99
4323 13607 0.321564 CCACCTCGATCCTGCACAAA 60.322 55.000 0.00 0.00 0.00 2.83
4338 13622 2.298300 CACAAATTCAGTTCACGTCGC 58.702 47.619 0.00 0.00 0.00 5.19
4342 13626 1.702886 ATTCAGTTCACGTCGCTCTG 58.297 50.000 0.00 0.00 0.00 3.35
4354 13638 3.242518 CGTCGCTCTGTATGTTCAGAAA 58.757 45.455 0.00 0.00 42.73 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.551071 GCAATCCAGATGGGGCTACTAC 60.551 54.545 0.00 0.00 37.22 2.73
1 2 1.699634 GCAATCCAGATGGGGCTACTA 59.300 52.381 0.00 0.00 37.22 1.82
2 3 0.475906 GCAATCCAGATGGGGCTACT 59.524 55.000 0.00 0.00 37.22 2.57
44 45 4.566907 GGGGTGTAAGAATAAAGAGGCACA 60.567 45.833 0.00 0.00 0.00 4.57
45 46 3.945921 GGGGTGTAAGAATAAAGAGGCAC 59.054 47.826 0.00 0.00 0.00 5.01
66 128 5.868043 AAACGTAATAACTCGGAAAAGGG 57.132 39.130 0.00 0.00 0.00 3.95
68 130 7.851963 TCACAAAAACGTAATAACTCGGAAAAG 59.148 33.333 0.00 0.00 0.00 2.27
166 228 2.344950 CTCTGCGACTTGCTTTGATCT 58.655 47.619 0.00 0.00 46.63 2.75
195 296 1.602377 GGTTCTCCAAACCAACGACTG 59.398 52.381 2.12 0.00 40.03 3.51
234 338 7.550712 AGAGAAAATCTTCAATTATTGGCCAC 58.449 34.615 3.88 0.00 32.99 5.01
268 372 4.096833 GCAAATTAGAGATGTGTGGATGCA 59.903 41.667 0.00 0.00 0.00 3.96
276 380 5.794687 TTACCGTGCAAATTAGAGATGTG 57.205 39.130 0.00 0.00 0.00 3.21
286 390 5.881447 TGCGTTTATATTTACCGTGCAAAT 58.119 33.333 0.00 0.00 0.00 2.32
306 410 9.549509 TTTACTAAAAACACATTAGCTAATGCG 57.450 29.630 35.65 30.69 45.24 4.73
341 447 8.292448 ACTGTTTCTTGACATATGTGATGAAAC 58.708 33.333 34.47 34.47 46.22 2.78
391 497 5.432885 AGTGGTTTATAATATGTTGGCGC 57.567 39.130 0.00 0.00 0.00 6.53
407 513 4.219288 CGGAGGTAGTACTTTGTAGTGGTT 59.781 45.833 0.00 0.00 35.78 3.67
410 516 5.163713 GGTACGGAGGTAGTACTTTGTAGTG 60.164 48.000 0.00 0.00 42.81 2.74
453 4765 9.691362 AAATATAAGACGTTTTTGCAGTTCAAT 57.309 25.926 0.00 0.00 34.12 2.57
456 4768 8.424731 CCAAAATATAAGACGTTTTTGCAGTTC 58.575 33.333 13.03 0.00 37.60 3.01
459 4771 7.867445 ACCAAAATATAAGACGTTTTTGCAG 57.133 32.000 13.03 5.81 37.60 4.41
490 4802 5.717078 TGGACGTCTAACTTTGACAGTAT 57.283 39.130 16.46 0.00 32.94 2.12
491 4803 5.518848 TTGGACGTCTAACTTTGACAGTA 57.481 39.130 16.46 0.00 32.94 2.74
492 4804 4.395959 TTGGACGTCTAACTTTGACAGT 57.604 40.909 16.46 3.40 37.30 3.55
525 4837 6.821388 AGTCTTGAACGCCTGATTATTATCT 58.179 36.000 0.00 0.00 0.00 1.98
526 4838 6.926272 AGAGTCTTGAACGCCTGATTATTATC 59.074 38.462 0.00 0.00 0.00 1.75
673 8970 4.068599 CAGGAGGACTTTGAGAAGTTTCC 58.931 47.826 12.23 12.23 45.88 3.13
686 8983 0.644937 AAGGATAGGGCAGGAGGACT 59.355 55.000 0.00 0.00 0.00 3.85
712 9009 1.199097 CATGGGTCGCTGTTAAACCAC 59.801 52.381 0.00 0.00 34.62 4.16
713 9010 1.202830 ACATGGGTCGCTGTTAAACCA 60.203 47.619 0.00 0.00 34.62 3.67
730 9041 3.820557 ACTGGCGGATGCTTAATTACAT 58.179 40.909 0.00 0.00 42.25 2.29
760 9074 8.655970 GCATGCGATGTAATCATTGTACTATTA 58.344 33.333 0.00 0.00 45.97 0.98
761 9075 7.173047 TGCATGCGATGTAATCATTGTACTATT 59.827 33.333 14.09 0.00 45.97 1.73
762 9076 6.650390 TGCATGCGATGTAATCATTGTACTAT 59.350 34.615 14.09 0.00 45.97 2.12
763 9077 5.988561 TGCATGCGATGTAATCATTGTACTA 59.011 36.000 14.09 0.00 45.97 1.82
764 9078 4.815846 TGCATGCGATGTAATCATTGTACT 59.184 37.500 14.09 0.00 45.97 2.73
765 9079 4.905866 GTGCATGCGATGTAATCATTGTAC 59.094 41.667 14.09 0.00 45.97 2.90
766 9080 4.318689 CGTGCATGCGATGTAATCATTGTA 60.319 41.667 14.09 0.00 45.97 2.41
767 9081 3.546616 CGTGCATGCGATGTAATCATTGT 60.547 43.478 14.09 0.00 45.97 2.71
800 9114 1.799258 AAGTCGTTACGTGGCCGTCT 61.799 55.000 4.24 0.00 46.28 4.18
803 9117 1.632422 ATTAAGTCGTTACGTGGCCG 58.368 50.000 4.24 0.00 40.83 6.13
804 9118 2.094734 CCAATTAAGTCGTTACGTGGCC 59.905 50.000 4.24 0.00 0.00 5.36
813 9127 2.936498 CCATTCGAGCCAATTAAGTCGT 59.064 45.455 0.00 0.00 34.07 4.34
916 9245 2.598589 GAGTCACGCATGGTAACGTAA 58.401 47.619 0.00 0.00 41.32 3.18
970 9299 2.572191 TTATAGTGTTCAGGCCGTCG 57.428 50.000 0.00 0.00 0.00 5.12
973 9302 1.593006 CGCTTTATAGTGTTCAGGCCG 59.407 52.381 0.00 0.00 0.00 6.13
980 9309 2.483014 TGTGCCCGCTTTATAGTGTT 57.517 45.000 0.00 0.00 0.00 3.32
993 9322 3.332493 CTGTGCGAGCATTGTGCCC 62.332 63.158 0.00 0.00 46.52 5.36
1029 9360 4.494690 CGAGTGCTTTGGCTATGTATGTTG 60.495 45.833 0.00 0.00 39.59 3.33
1046 9377 1.818850 TTCTATACGCGTTCGAGTGC 58.181 50.000 20.78 1.19 39.41 4.40
1047 9378 3.605056 TGTTTTCTATACGCGTTCGAGTG 59.395 43.478 20.78 2.40 39.41 3.51
1056 9393 4.206609 GGACTCGACATGTTTTCTATACGC 59.793 45.833 0.00 0.00 0.00 4.42
1107 9444 2.507102 CAGCAGGCGACGACGATT 60.507 61.111 12.29 0.00 42.66 3.34
1416 9753 3.504520 GGACGATATCTGGGAGAGAAGTC 59.495 52.174 0.34 0.00 33.12 3.01
1435 9773 1.595489 GCATTCAACGCATGATCGGAC 60.595 52.381 0.00 0.00 38.03 4.79
1462 9800 8.090214 ACATCAAATTGGAAGGAAAGTATGTTG 58.910 33.333 0.00 0.00 0.00 3.33
1502 9840 0.179029 ACACAGGCCCAATATACGCC 60.179 55.000 0.00 0.00 43.35 5.68
1516 9854 2.121786 GCATGCACAGTCAAAACACAG 58.878 47.619 14.21 0.00 0.00 3.66
1527 9865 0.730840 ACATCATCGTGCATGCACAG 59.269 50.000 40.95 33.12 46.47 3.66
1538 9876 2.548480 AGCTGCATCATCAACATCATCG 59.452 45.455 1.02 0.00 0.00 3.84
1548 9886 1.963172 TGGATGTCAGCTGCATCATC 58.037 50.000 32.80 28.72 43.17 2.92
1549 9887 2.298610 CTTGGATGTCAGCTGCATCAT 58.701 47.619 32.80 24.99 43.17 2.45
1550 9888 1.680860 CCTTGGATGTCAGCTGCATCA 60.681 52.381 32.80 23.14 43.17 3.07
1551 9889 1.022735 CCTTGGATGTCAGCTGCATC 58.977 55.000 28.42 28.42 41.30 3.91
1552 9890 0.622136 TCCTTGGATGTCAGCTGCAT 59.378 50.000 19.30 19.30 0.00 3.96
1704 10042 1.080705 CTCTGTCGGGTCGAACCAC 60.081 63.158 21.79 16.79 41.02 4.16
1797 10135 8.902735 CAAGAAATGAATGAATGATTAGATGCG 58.097 33.333 0.00 0.00 0.00 4.73
1925 10263 2.787601 TCATGTACTTATCGTCGGGC 57.212 50.000 0.00 0.00 0.00 6.13
1938 10276 2.029739 TCTCGCGTTTGGTCTTCATGTA 60.030 45.455 5.77 0.00 0.00 2.29
1967 10305 0.531974 GTCGTCTCCAGGCACAAACA 60.532 55.000 0.00 0.00 0.00 2.83
1968 10306 0.249911 AGTCGTCTCCAGGCACAAAC 60.250 55.000 0.00 0.00 0.00 2.93
1975 10313 2.678324 GTTGAAAGAGTCGTCTCCAGG 58.322 52.381 6.04 0.00 41.26 4.45
2004 10343 4.695217 AAACGGTCATATTTTCATGCGT 57.305 36.364 0.00 0.00 0.00 5.24
2044 10384 7.516785 CGCAAGCCCATACGTATATGATATTTC 60.517 40.741 7.96 0.00 40.75 2.17
2068 10408 2.584967 CCAAAAACTTGGTGCGCGC 61.585 57.895 27.26 27.26 37.32 6.86
2071 10411 1.594021 GGCCCAAAAACTTGGTGCG 60.594 57.895 0.00 0.00 40.46 5.34
2080 10420 4.966247 GGGAGGAAGGCCCAAAAA 57.034 55.556 0.00 0.00 45.31 1.94
2085 10425 2.548547 AAACCAGGGAGGAAGGCCC 61.549 63.158 0.00 0.00 46.40 5.80
2086 10426 1.304464 CAAACCAGGGAGGAAGGCC 60.304 63.158 0.00 0.00 41.22 5.19
2087 10427 0.609406 GACAAACCAGGGAGGAAGGC 60.609 60.000 0.00 0.00 41.22 4.35
2093 10446 0.253327 GCCTAGGACAAACCAGGGAG 59.747 60.000 14.75 0.00 42.04 4.30
2224 10589 3.139077 GAGGAGGTTCGCAAAGAAAAGA 58.861 45.455 0.00 0.00 41.10 2.52
2229 10594 0.608640 GAGGAGGAGGTTCGCAAAGA 59.391 55.000 0.00 0.00 0.00 2.52
2231 10596 0.321671 CAGAGGAGGAGGTTCGCAAA 59.678 55.000 0.00 0.00 0.00 3.68
2232 10597 1.975327 CAGAGGAGGAGGTTCGCAA 59.025 57.895 0.00 0.00 0.00 4.85
2233 10598 2.650116 GCAGAGGAGGAGGTTCGCA 61.650 63.158 0.00 0.00 0.00 5.10
2234 10599 2.185608 GCAGAGGAGGAGGTTCGC 59.814 66.667 0.00 0.00 0.00 4.70
2237 10602 1.306568 GAGGGCAGAGGAGGAGGTT 60.307 63.158 0.00 0.00 0.00 3.50
2238 10603 2.236959 GAGAGGGCAGAGGAGGAGGT 62.237 65.000 0.00 0.00 0.00 3.85
2240 10605 0.325110 TTGAGAGGGCAGAGGAGGAG 60.325 60.000 0.00 0.00 0.00 3.69
2241 10606 0.117140 TTTGAGAGGGCAGAGGAGGA 59.883 55.000 0.00 0.00 0.00 3.71
2242 10607 1.211456 ATTTGAGAGGGCAGAGGAGG 58.789 55.000 0.00 0.00 0.00 4.30
2243 10608 2.238144 TGAATTTGAGAGGGCAGAGGAG 59.762 50.000 0.00 0.00 0.00 3.69
2244 10609 2.269023 TGAATTTGAGAGGGCAGAGGA 58.731 47.619 0.00 0.00 0.00 3.71
2246 10611 5.656213 AAAATGAATTTGAGAGGGCAGAG 57.344 39.130 0.00 0.00 0.00 3.35
2251 10631 7.927629 TGTTTCAGAAAAATGAATTTGAGAGGG 59.072 33.333 0.00 0.00 38.90 4.30
2259 10639 6.200854 GGCTCGTTGTTTCAGAAAAATGAATT 59.799 34.615 0.00 0.00 38.90 2.17
2263 10643 4.610945 AGGCTCGTTGTTTCAGAAAAATG 58.389 39.130 0.00 1.32 0.00 2.32
2264 10644 4.261614 GGAGGCTCGTTGTTTCAGAAAAAT 60.262 41.667 8.69 0.00 0.00 1.82
2270 10650 1.433534 GAGGAGGCTCGTTGTTTCAG 58.566 55.000 11.50 0.00 0.00 3.02
2271 10651 0.034896 GGAGGAGGCTCGTTGTTTCA 59.965 55.000 11.50 0.00 0.00 2.69
2272 10652 0.321996 AGGAGGAGGCTCGTTGTTTC 59.678 55.000 11.50 0.00 0.00 2.78
2276 10656 1.254284 ACAGAGGAGGAGGCTCGTTG 61.254 60.000 11.50 8.01 0.00 4.10
2278 10658 1.379309 GACAGAGGAGGAGGCTCGT 60.379 63.158 9.87 9.87 0.00 4.18
2279 10659 2.124693 GGACAGAGGAGGAGGCTCG 61.125 68.421 8.69 0.00 0.00 5.03
2280 10660 0.755327 GAGGACAGAGGAGGAGGCTC 60.755 65.000 5.78 5.78 0.00 4.70
2282 10662 0.755327 GAGAGGACAGAGGAGGAGGC 60.755 65.000 0.00 0.00 0.00 4.70
2284 10664 0.544223 TCGAGAGGACAGAGGAGGAG 59.456 60.000 0.00 0.00 0.00 3.69
2285 10665 0.992695 TTCGAGAGGACAGAGGAGGA 59.007 55.000 0.00 0.00 0.00 3.71
2287 10667 3.508012 TCTTTTTCGAGAGGACAGAGGAG 59.492 47.826 0.00 0.00 0.00 3.69
2290 10670 6.035542 GCTTTATCTTTTTCGAGAGGACAGAG 59.964 42.308 0.00 0.00 0.00 3.35
2291 10671 5.869888 GCTTTATCTTTTTCGAGAGGACAGA 59.130 40.000 0.00 0.00 0.00 3.41
2292 10672 5.220303 CGCTTTATCTTTTTCGAGAGGACAG 60.220 44.000 0.00 0.00 0.00 3.51
2293 10673 4.625742 CGCTTTATCTTTTTCGAGAGGACA 59.374 41.667 0.00 0.00 0.00 4.02
2294 10674 4.863131 TCGCTTTATCTTTTTCGAGAGGAC 59.137 41.667 0.00 0.00 0.00 3.85
2295 10675 5.068234 TCGCTTTATCTTTTTCGAGAGGA 57.932 39.130 0.00 0.00 0.00 3.71
2296 10676 5.520288 TCATCGCTTTATCTTTTTCGAGAGG 59.480 40.000 0.00 0.00 0.00 3.69
2298 10678 7.539712 AATCATCGCTTTATCTTTTTCGAGA 57.460 32.000 0.00 0.00 0.00 4.04
2299 10679 7.693951 ACAAATCATCGCTTTATCTTTTTCGAG 59.306 33.333 0.00 0.00 0.00 4.04
2300 10680 7.526608 ACAAATCATCGCTTTATCTTTTTCGA 58.473 30.769 0.00 0.00 0.00 3.71
2301 10681 7.693951 AGACAAATCATCGCTTTATCTTTTTCG 59.306 33.333 0.00 0.00 0.00 3.46
2302 10682 8.902040 AGACAAATCATCGCTTTATCTTTTTC 57.098 30.769 0.00 0.00 0.00 2.29
2303 10683 8.514594 TGAGACAAATCATCGCTTTATCTTTTT 58.485 29.630 0.00 0.00 0.00 1.94
2304 10684 8.044060 TGAGACAAATCATCGCTTTATCTTTT 57.956 30.769 0.00 0.00 0.00 2.27
2305 10685 7.615582 TGAGACAAATCATCGCTTTATCTTT 57.384 32.000 0.00 0.00 0.00 2.52
2306 10686 7.615582 TTGAGACAAATCATCGCTTTATCTT 57.384 32.000 0.00 0.00 0.00 2.40
2307 10687 7.615582 TTTGAGACAAATCATCGCTTTATCT 57.384 32.000 0.00 0.00 0.00 1.98
2308 10688 9.935682 TTATTTGAGACAAATCATCGCTTTATC 57.064 29.630 12.02 0.00 0.00 1.75
2341 10721 2.488153 ACTAGTCGCCTTCCATTTTTGC 59.512 45.455 0.00 0.00 0.00 3.68
2353 10733 3.001365 CGAAACGAAACATACTAGTCGCC 60.001 47.826 0.00 0.00 36.99 5.54
2361 10741 4.143179 CCTTCTGACCGAAACGAAACATAC 60.143 45.833 0.00 0.00 0.00 2.39
2368 10748 1.542915 CCTACCTTCTGACCGAAACGA 59.457 52.381 0.00 0.00 0.00 3.85
2374 10754 0.741915 GCTCTCCTACCTTCTGACCG 59.258 60.000 0.00 0.00 0.00 4.79
2384 10764 1.670791 ACGTGCTCTAGCTCTCCTAC 58.329 55.000 3.26 0.00 42.66 3.18
2386 10766 2.092861 TCTTACGTGCTCTAGCTCTCCT 60.093 50.000 0.00 0.00 42.66 3.69
2387 10767 2.032426 GTCTTACGTGCTCTAGCTCTCC 59.968 54.545 0.00 0.00 42.66 3.71
2390 10770 2.678836 TGAGTCTTACGTGCTCTAGCTC 59.321 50.000 0.00 0.00 42.66 4.09
2413 10793 8.669946 ATGGTTGTTTAATTTGGACGAATTTT 57.330 26.923 3.07 0.00 31.96 1.82
2415 10795 8.669946 AAATGGTTGTTTAATTTGGACGAATT 57.330 26.923 0.00 3.27 33.95 2.17
2416 10796 8.669946 AAAATGGTTGTTTAATTTGGACGAAT 57.330 26.923 0.00 0.00 0.00 3.34
2453 10834 1.070786 GGCTCCAAACCGACAGTGA 59.929 57.895 0.00 0.00 0.00 3.41
2470 10851 4.021368 TCAAGTCTTTTCTACCTTCCTCGG 60.021 45.833 0.00 0.00 0.00 4.63
2471 10852 5.135508 TCAAGTCTTTTCTACCTTCCTCG 57.864 43.478 0.00 0.00 0.00 4.63
2473 10854 6.248569 TGTTCAAGTCTTTTCTACCTTCCT 57.751 37.500 0.00 0.00 0.00 3.36
2475 10856 5.527582 TGCTGTTCAAGTCTTTTCTACCTTC 59.472 40.000 0.00 0.00 0.00 3.46
2476 10857 5.437060 TGCTGTTCAAGTCTTTTCTACCTT 58.563 37.500 0.00 0.00 0.00 3.50
2477 10858 5.036117 TGCTGTTCAAGTCTTTTCTACCT 57.964 39.130 0.00 0.00 0.00 3.08
2478 10859 5.297029 AGTTGCTGTTCAAGTCTTTTCTACC 59.703 40.000 0.00 0.00 33.14 3.18
2479 10860 6.364945 AGTTGCTGTTCAAGTCTTTTCTAC 57.635 37.500 0.00 0.00 33.14 2.59
2480 10861 6.597672 TCAAGTTGCTGTTCAAGTCTTTTCTA 59.402 34.615 0.00 0.00 37.35 2.10
2481 10862 5.415701 TCAAGTTGCTGTTCAAGTCTTTTCT 59.584 36.000 0.00 0.00 37.35 2.52
2482 10863 5.640732 TCAAGTTGCTGTTCAAGTCTTTTC 58.359 37.500 0.00 0.00 37.35 2.29
2483 10864 5.643379 TCAAGTTGCTGTTCAAGTCTTTT 57.357 34.783 0.00 0.00 37.35 2.27
2484 10865 5.841957 ATCAAGTTGCTGTTCAAGTCTTT 57.158 34.783 0.00 0.00 37.35 2.52
2485 10866 6.058183 AGTATCAAGTTGCTGTTCAAGTCTT 58.942 36.000 0.00 0.00 37.35 3.01
2486 10867 5.615289 AGTATCAAGTTGCTGTTCAAGTCT 58.385 37.500 0.00 0.00 37.35 3.24
2487 10868 5.106908 GGAGTATCAAGTTGCTGTTCAAGTC 60.107 44.000 0.00 0.00 37.35 3.01
2505 10886 1.043816 CTCACAGATGGCCGGAGTAT 58.956 55.000 5.05 0.00 0.00 2.12
2511 10892 0.668535 TATCGTCTCACAGATGGCCG 59.331 55.000 0.00 0.00 32.20 6.13
2519 10900 6.323996 AGGGTTTAGAATGATATCGTCTCACA 59.676 38.462 11.04 0.00 0.00 3.58
2521 10902 6.778069 AGAGGGTTTAGAATGATATCGTCTCA 59.222 38.462 11.04 0.25 0.00 3.27
2543 10947 7.670717 GCTAAATTAAGCCCTCTTTCCGAGAG 61.671 46.154 0.00 0.00 41.09 3.20
2544 10948 4.569719 AAATTAAGCCCTCTTTCCGAGA 57.430 40.909 0.00 0.00 42.62 4.04
2611 11015 0.386478 CGTTTGAAAGAGCAGCTGGC 60.386 55.000 17.12 7.98 45.30 4.85
2625 11029 1.321743 CCTCGATCGCTTCTTCGTTTG 59.678 52.381 11.09 0.00 36.74 2.93
2637 11041 1.135489 TCCTCACGTTTTCCTCGATCG 60.135 52.381 9.36 9.36 0.00 3.69
2677 11081 2.143122 AGTTGACGTGCATGTTACCTG 58.857 47.619 13.92 0.00 0.00 4.00
2739 11143 0.739813 AGCATTTGACTCCGCGTACC 60.740 55.000 4.92 0.00 0.00 3.34
2789 11193 3.549625 GCCGAGATTTTGATTCAGATGCC 60.550 47.826 0.00 0.00 0.00 4.40
2821 11225 2.203538 CAACTGGCCTTGGGTGCT 60.204 61.111 3.32 0.00 0.00 4.40
2822 11226 3.305516 CCAACTGGCCTTGGGTGC 61.306 66.667 14.69 0.00 37.62 5.01
2863 11270 0.244721 CGGTCAGTGCAGTGATGAGA 59.755 55.000 26.31 1.34 0.00 3.27
2864 11271 0.244721 TCGGTCAGTGCAGTGATGAG 59.755 55.000 26.31 19.20 0.00 2.90
2867 11274 2.479566 AATTCGGTCAGTGCAGTGAT 57.520 45.000 26.31 8.12 0.00 3.06
2868 11275 3.394674 TTAATTCGGTCAGTGCAGTGA 57.605 42.857 20.39 20.39 0.00 3.41
2869 11276 3.728864 GCATTAATTCGGTCAGTGCAGTG 60.729 47.826 15.76 15.76 0.00 3.66
2870 11277 2.420022 GCATTAATTCGGTCAGTGCAGT 59.580 45.455 0.00 0.00 0.00 4.40
2914 11321 2.908626 GCATCGACGGAAACAAATTGTC 59.091 45.455 0.00 0.00 0.00 3.18
2918 11325 2.416547 CAGAGCATCGACGGAAACAAAT 59.583 45.455 0.00 0.00 42.67 2.32
2920 11327 1.270094 ACAGAGCATCGACGGAAACAA 60.270 47.619 0.00 0.00 42.67 2.83
2922 11329 1.429463 AACAGAGCATCGACGGAAAC 58.571 50.000 0.00 0.00 42.67 2.78
2926 11333 0.721718 GGAAAACAGAGCATCGACGG 59.278 55.000 0.00 0.00 42.67 4.79
2927 11334 1.428448 TGGAAAACAGAGCATCGACG 58.572 50.000 0.00 0.00 42.67 5.12
3280 11692 3.706698 CAGTAGTCCATCACCATGTACG 58.293 50.000 0.00 0.00 0.00 3.67
3359 11777 4.277239 CCGAACAATCAGACGGCA 57.723 55.556 0.00 0.00 38.98 5.69
3374 11792 1.727511 TAGTATGGCCGACGGAACCG 61.728 60.000 20.50 11.83 46.03 4.44
3417 11839 1.067565 ACCGTACGTCTGTCTCGTCTA 60.068 52.381 15.21 0.00 41.72 2.59
3422 11844 2.049228 CAAACACCGTACGTCTGTCTC 58.951 52.381 15.21 0.00 0.00 3.36
3484 11914 1.400846 CTACGCCTACACGTCACATCT 59.599 52.381 0.00 0.00 44.43 2.90
3521 12784 3.695060 CGCTAGAGAAACTCCTGGTTAGA 59.305 47.826 0.00 0.00 37.12 2.10
3522 12785 3.181485 CCGCTAGAGAAACTCCTGGTTAG 60.181 52.174 0.00 0.00 37.12 2.34
3527 12795 2.287308 CGATCCGCTAGAGAAACTCCTG 60.287 54.545 0.00 0.00 0.00 3.86
3552 12820 5.862846 CAGGTTTCTGCAGGAATCATCCTTA 60.863 44.000 20.31 0.00 42.89 2.69
3664 12936 2.071778 TTTGGCCAGTTTGCTCTTCT 57.928 45.000 5.11 0.00 0.00 2.85
3737 13015 4.204012 TCTTTCATTGGGTTTCTGAACGT 58.796 39.130 0.00 0.00 36.61 3.99
3740 13018 6.975196 TGATTCTTTCATTGGGTTTCTGAA 57.025 33.333 0.00 0.00 0.00 3.02
3748 13028 2.159198 CGGGCTTGATTCTTTCATTGGG 60.159 50.000 0.00 0.00 33.34 4.12
3844 13128 1.463674 GGGGTTGAGCGACAATTCAT 58.536 50.000 3.08 0.00 40.76 2.57
3845 13129 0.608035 GGGGGTTGAGCGACAATTCA 60.608 55.000 3.08 0.00 40.76 2.57
3846 13130 0.322546 AGGGGGTTGAGCGACAATTC 60.323 55.000 3.08 0.47 40.76 2.17
3847 13131 0.322546 GAGGGGGTTGAGCGACAATT 60.323 55.000 3.08 0.00 40.76 2.32
3848 13132 1.299976 GAGGGGGTTGAGCGACAAT 59.700 57.895 3.08 0.00 40.76 2.71
3849 13133 2.747686 GAGGGGGTTGAGCGACAA 59.252 61.111 0.00 0.00 36.02 3.18
3850 13134 3.691342 CGAGGGGGTTGAGCGACA 61.691 66.667 0.00 0.00 0.00 4.35
3893 13177 0.988825 AGTTTTCGTCGTCGTCGTCG 60.989 55.000 14.18 14.18 46.06 5.12
3894 13178 0.424920 CAGTTTTCGTCGTCGTCGTC 59.575 55.000 11.41 0.00 38.33 4.20
3896 13180 1.125266 GCAGTTTTCGTCGTCGTCG 59.875 57.895 5.50 5.50 38.33 5.12
3897 13181 0.430110 GAGCAGTTTTCGTCGTCGTC 59.570 55.000 1.33 0.00 38.33 4.20
3898 13182 0.248743 TGAGCAGTTTTCGTCGTCGT 60.249 50.000 1.33 0.00 38.33 4.34
3899 13183 0.158928 GTGAGCAGTTTTCGTCGTCG 59.841 55.000 0.00 0.00 38.55 5.12
3900 13184 0.158928 CGTGAGCAGTTTTCGTCGTC 59.841 55.000 0.00 0.00 0.00 4.20
3901 13185 1.213094 CCGTGAGCAGTTTTCGTCGT 61.213 55.000 0.00 0.00 0.00 4.34
3902 13186 1.487231 CCGTGAGCAGTTTTCGTCG 59.513 57.895 0.00 0.00 0.00 5.12
3903 13187 1.860078 CCCGTGAGCAGTTTTCGTC 59.140 57.895 0.00 0.00 0.00 4.20
3904 13188 2.251642 GCCCGTGAGCAGTTTTCGT 61.252 57.895 0.00 0.00 0.00 3.85
3905 13189 2.556287 GCCCGTGAGCAGTTTTCG 59.444 61.111 0.00 0.00 0.00 3.46
3906 13190 2.556287 CGCCCGTGAGCAGTTTTC 59.444 61.111 0.00 0.00 0.00 2.29
3907 13191 2.978010 CCGCCCGTGAGCAGTTTT 60.978 61.111 0.00 0.00 0.00 2.43
3976 13260 0.800631 TACGACTACTGCACCGACAG 59.199 55.000 0.00 0.00 43.59 3.51
3998 13282 1.299926 CGCTACATGGGCTACGTCC 60.300 63.158 0.00 0.00 0.00 4.79
4323 13607 1.000163 ACAGAGCGACGTGAACTGAAT 60.000 47.619 15.19 0.00 33.53 2.57
4338 13622 5.655488 ACCGATCTTTCTGAACATACAGAG 58.345 41.667 0.00 0.00 45.63 3.35
4342 13626 4.738740 CCGTACCGATCTTTCTGAACATAC 59.261 45.833 0.00 0.00 0.00 2.39


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

AutoCloner maintained by Alex Coulton.