Multiple sequence alignment - TraesCS1D01G446000

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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 TraesCS1D01G446000 chr1D 100.000 3117 0 0 1 3117 488715143 488718259 0.000000e+00 5757
1 TraesCS1D01G446000 chr1D 86.752 468 47 9 1066 1521 488735075 488735539 9.970000e-140 507
2 TraesCS1D01G446000 chr1D 97.664 214 3 2 1559 1770 481226963 481227176 1.770000e-97 366
3 TraesCS1D01G446000 chr1D 77.879 330 67 6 6 332 97084567 97084241 1.900000e-47 200
4 TraesCS1D01G446000 chrUn 94.796 884 28 5 382 1248 399149462 399148580 0.000000e+00 1362
5 TraesCS1D01G446000 chrUn 94.683 884 29 5 382 1248 438668741 438667859 0.000000e+00 1356
6 TraesCS1D01G446000 chrUn 91.473 645 23 5 2504 3117 362418336 362417693 0.000000e+00 857
7 TraesCS1D01G446000 chrUn 91.318 645 24 6 2504 3117 343981386 343980743 0.000000e+00 852
8 TraesCS1D01G446000 chrUn 87.304 764 46 23 1767 2502 281285612 281284872 0.000000e+00 826
9 TraesCS1D01G446000 chrUn 87.304 764 46 22 1767 2502 343982189 343981449 0.000000e+00 826
10 TraesCS1D01G446000 chrUn 90.402 646 29 8 2504 3117 281284809 281284165 0.000000e+00 819
11 TraesCS1D01G446000 chrUn 92.599 554 38 2 4 554 58510956 58510403 0.000000e+00 793
12 TraesCS1D01G446000 chrUn 91.906 556 42 3 1 554 59596482 59597036 0.000000e+00 774
13 TraesCS1D01G446000 chrUn 92.184 499 30 7 2009 2502 362418893 362418399 0.000000e+00 697
14 TraesCS1D01G446000 chrUn 94.611 334 17 1 1 333 321684828 321685161 1.660000e-142 516
15 TraesCS1D01G446000 chrUn 88.679 424 41 4 1105 1521 281286033 281285610 7.710000e-141 510
16 TraesCS1D01G446000 chrUn 88.679 424 41 4 1105 1521 308140302 308139879 7.710000e-141 510
17 TraesCS1D01G446000 chrUn 88.679 424 41 4 1105 1521 450202267 450201844 7.710000e-141 510
18 TraesCS1D01G446000 chrUn 84.630 527 33 19 1767 2265 450201846 450201340 6.050000e-132 481
19 TraesCS1D01G446000 chrUn 88.542 384 37 4 1145 1521 343982570 343982187 2.830000e-125 459
20 TraesCS1D01G446000 chrUn 98.558 208 3 0 1559 1766 80168059 80168266 4.910000e-98 368
21 TraesCS1D01G446000 chrUn 98.558 208 3 0 1559 1766 90451752 90451545 4.910000e-98 368
22 TraesCS1D01G446000 chrUn 90.045 221 21 1 335 554 311420959 311420739 5.090000e-73 285
23 TraesCS1D01G446000 chrUn 86.070 201 9 9 1767 1967 308139881 308139700 6.820000e-47 198
24 TraesCS1D01G446000 chrUn 94.000 100 4 2 2648 2746 281279520 281279422 1.940000e-32 150
25 TraesCS1D01G446000 chr1A 94.796 884 28 5 382 1248 588221025 588221907 0.000000e+00 1362
26 TraesCS1D01G446000 chr1A 95.658 737 28 2 1767 2502 587981298 587982031 0.000000e+00 1181
27 TraesCS1D01G446000 chr1A 91.512 648 23 9 2501 3117 588188580 588189226 0.000000e+00 863
28 TraesCS1D01G446000 chr1A 91.512 648 23 5 2501 3117 588205410 588206056 0.000000e+00 863
29 TraesCS1D01G446000 chr1A 91.512 648 23 5 2501 3117 588212132 588212778 0.000000e+00 863
30 TraesCS1D01G446000 chr1A 91.358 648 24 5 2501 3117 588181647 588182293 0.000000e+00 857
31 TraesCS1D01G446000 chr1A 91.358 648 24 5 2501 3117 588195297 588195943 0.000000e+00 857
32 TraesCS1D01G446000 chr1A 87.696 764 43 22 1767 2502 588187780 588188520 0.000000e+00 843
33 TraesCS1D01G446000 chr1A 87.696 764 43 22 1767 2502 588211332 588212072 0.000000e+00 843
34 TraesCS1D01G446000 chr1A 87.516 761 44 22 1767 2499 588204610 588205347 0.000000e+00 832
35 TraesCS1D01G446000 chr1A 87.042 764 45 24 1767 2502 588180850 588181587 0.000000e+00 813
36 TraesCS1D01G446000 chr1A 87.042 764 43 23 1767 2502 588194502 588195237 0.000000e+00 811
37 TraesCS1D01G446000 chr1A 93.090 521 26 7 1020 1533 587980796 587981313 0.000000e+00 754
38 TraesCS1D01G446000 chr1A 88.679 424 41 4 1105 1521 588187359 588187782 7.710000e-141 510
39 TraesCS1D01G446000 chr1A 88.679 424 41 4 1105 1521 588194081 588194504 7.710000e-141 510
40 TraesCS1D01G446000 chr1A 88.679 424 41 4 1105 1521 588222313 588222736 7.710000e-141 510
41 TraesCS1D01G446000 chr1A 88.443 424 42 4 1105 1521 588180429 588180852 3.590000e-139 505
42 TraesCS1D01G446000 chr1A 93.252 163 9 2 2774 2935 587982192 587982353 4.020000e-59 239
43 TraesCS1D01G446000 chr5B 92.460 557 41 1 1 556 6870753 6870197 0.000000e+00 795
44 TraesCS1D01G446000 chr5D 87.770 556 67 1 3 557 43389351 43388796 0.000000e+00 649
45 TraesCS1D01G446000 chr5D 98.558 208 3 0 1559 1766 358628856 358628649 4.910000e-98 368
46 TraesCS1D01G446000 chr5D 98.558 208 3 0 1559 1766 488831726 488831933 4.910000e-98 368
47 TraesCS1D01G446000 chr5A 86.965 537 67 3 1 535 33155047 33154512 4.450000e-168 601
48 TraesCS1D01G446000 chr7D 98.571 210 3 0 1559 1768 25716245 25716454 3.800000e-99 372
49 TraesCS1D01G446000 chr7D 76.948 308 66 5 42 347 115246237 115245933 1.490000e-38 171
50 TraesCS1D01G446000 chr4D 98.565 209 3 0 1559 1767 6721559 6721351 1.370000e-98 370
51 TraesCS1D01G446000 chr4D 98.113 212 3 1 1559 1769 487227772 487227983 4.910000e-98 368
52 TraesCS1D01G446000 chr6D 96.804 219 5 2 1559 1777 440503856 440504072 6.350000e-97 364
53 TraesCS1D01G446000 chr3D 91.589 214 17 1 344 556 20563687 20563474 8.450000e-76 294
54 TraesCS1D01G446000 chr6B 76.385 343 77 4 6 346 423184165 423183825 6.870000e-42 182
55 TraesCS1D01G446000 chr2B 74.832 298 69 6 1 295 772427767 772427473 2.520000e-26 130


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 TraesCS1D01G446000 chr1D 488715143 488718259 3116 False 5757.000000 5757 100.000000 1 3117 1 chr1D.!!$F2 3116
1 TraesCS1D01G446000 chrUn 399148580 399149462 882 True 1362.000000 1362 94.796000 382 1248 1 chrUn.!!$R5 866
2 TraesCS1D01G446000 chrUn 438667859 438668741 882 True 1356.000000 1356 94.683000 382 1248 1 chrUn.!!$R6 866
3 TraesCS1D01G446000 chrUn 58510403 58510956 553 True 793.000000 793 92.599000 4 554 1 chrUn.!!$R1 550
4 TraesCS1D01G446000 chrUn 362417693 362418893 1200 True 777.000000 857 91.828500 2009 3117 2 chrUn.!!$R10 1108
5 TraesCS1D01G446000 chrUn 59596482 59597036 554 False 774.000000 774 91.906000 1 554 1 chrUn.!!$F1 553
6 TraesCS1D01G446000 chrUn 281284165 281286033 1868 True 718.333333 826 88.795000 1105 3117 3 chrUn.!!$R7 2012
7 TraesCS1D01G446000 chrUn 343980743 343982570 1827 True 712.333333 852 89.054667 1145 3117 3 chrUn.!!$R9 1972
8 TraesCS1D01G446000 chrUn 450201340 450202267 927 True 495.500000 510 86.654500 1105 2265 2 chrUn.!!$R11 1160
9 TraesCS1D01G446000 chrUn 308139700 308140302 602 True 354.000000 510 87.374500 1105 1967 2 chrUn.!!$R8 862
10 TraesCS1D01G446000 chr1A 588221025 588222736 1711 False 936.000000 1362 91.737500 382 1521 2 chr1A.!!$F7 1139
11 TraesCS1D01G446000 chr1A 588211332 588212778 1446 False 853.000000 863 89.604000 1767 3117 2 chr1A.!!$F6 1350
12 TraesCS1D01G446000 chr1A 588204610 588206056 1446 False 847.500000 863 89.514000 1767 3117 2 chr1A.!!$F5 1350
13 TraesCS1D01G446000 chr1A 588187359 588189226 1867 False 738.666667 863 89.295667 1105 3117 3 chr1A.!!$F3 2012
14 TraesCS1D01G446000 chr1A 588194081 588195943 1862 False 726.000000 857 89.026333 1105 3117 3 chr1A.!!$F4 2012
15 TraesCS1D01G446000 chr1A 588180429 588182293 1864 False 725.000000 857 88.947667 1105 3117 3 chr1A.!!$F2 2012
16 TraesCS1D01G446000 chr1A 587980796 587982353 1557 False 724.666667 1181 94.000000 1020 2935 3 chr1A.!!$F1 1915
17 TraesCS1D01G446000 chr5B 6870197 6870753 556 True 795.000000 795 92.460000 1 556 1 chr5B.!!$R1 555
18 TraesCS1D01G446000 chr5D 43388796 43389351 555 True 649.000000 649 87.770000 3 557 1 chr5D.!!$R1 554
19 TraesCS1D01G446000 chr5A 33154512 33155047 535 True 601.000000 601 86.965000 1 535 1 chr5A.!!$R1 534

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
596 608 0.179156 CCATGCATGACAAGCGTTCC 60.179 55.0 28.31 0.00 33.85 3.62 F
1256 1828 0.455464 TACACTGCCGAATCGACACG 60.455 55.0 3.36 6.17 0.00 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1536 2116 0.028642 ATGGGGGAGTATGGAAGCCT 60.029 55.0 0.00 0.00 0.0 4.58 R
2656 3332 0.394938 TCGTTTGTCTTGCCTGGCTA 59.605 50.0 21.03 11.84 0.0 3.93 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 2.818130 AATTCGTTTGGTGCTGCATT 57.182 40.000 5.27 0.00 0.00 3.56
55 56 1.442520 CGTTTGGTGCTGCATTCGG 60.443 57.895 5.27 0.00 0.00 4.30
70 71 1.827399 TTCGGTCCTGGCTCCAAGTC 61.827 60.000 8.11 0.00 0.00 3.01
138 139 1.263356 CTGTCGGGGTCCTCTAAACA 58.737 55.000 0.00 0.00 0.00 2.83
225 226 1.802880 CGAACATGTCTTCCCGGCTAG 60.803 57.143 0.00 0.00 0.00 3.42
231 232 2.058595 TCTTCCCGGCTAGACCTGC 61.059 63.158 0.00 0.00 35.61 4.85
271 274 2.561858 TGGCATATTTTTGCAGCAGTGA 59.438 40.909 0.00 0.00 44.59 3.41
338 341 2.569853 TCTTCCAAGATTCGGGCTACAA 59.430 45.455 0.00 0.00 0.00 2.41
349 352 2.028385 TCGGGCTACAACTTCCTCTTTC 60.028 50.000 0.00 0.00 0.00 2.62
350 353 2.289444 CGGGCTACAACTTCCTCTTTCA 60.289 50.000 0.00 0.00 0.00 2.69
368 371 2.052690 ACGCGCAGAGTACCAGGAT 61.053 57.895 5.73 0.00 39.99 3.24
390 393 1.485294 TAGCGGGTTGGCTTCCTTGA 61.485 55.000 0.00 0.00 41.39 3.02
535 539 5.117355 GGCTTTATTTATAAAGTCGGGCC 57.883 43.478 18.51 12.56 46.78 5.80
596 608 0.179156 CCATGCATGACAAGCGTTCC 60.179 55.000 28.31 0.00 33.85 3.62
603 615 1.045407 TGACAAGCGTTCCACTAGGT 58.955 50.000 0.00 0.00 35.89 3.08
991 1011 0.532862 ATAGCAAGCCAATCGTCGGG 60.533 55.000 0.00 0.00 0.00 5.14
1000 1020 1.578583 CAATCGTCGGGTGGTATTCC 58.421 55.000 0.00 0.00 0.00 3.01
1231 1803 2.096406 CGATGACAAAGTGCCGCG 59.904 61.111 0.00 0.00 0.00 6.46
1252 1824 1.226575 CGCTACACTGCCGAATCGA 60.227 57.895 3.36 0.00 0.00 3.59
1256 1828 0.455464 TACACTGCCGAATCGACACG 60.455 55.000 3.36 6.17 0.00 4.49
1265 1837 1.525596 GAATCGACACGACTCGACAG 58.474 55.000 5.20 0.00 45.14 3.51
1441 2019 3.121328 CGATATTTGGAGCGATGAACGTC 60.121 47.826 0.00 0.00 44.60 4.34
1521 2101 9.083422 TGTAGATATATAGATTGATGGGCTAGC 57.917 37.037 6.04 6.04 0.00 3.42
1522 2102 9.083422 GTAGATATATAGATTGATGGGCTAGCA 57.917 37.037 18.24 0.00 0.00 3.49
1523 2103 7.961351 AGATATATAGATTGATGGGCTAGCAC 58.039 38.462 18.24 14.86 0.00 4.40
1524 2104 7.788867 AGATATATAGATTGATGGGCTAGCACT 59.211 37.037 19.73 3.29 0.00 4.40
1525 2105 9.083422 GATATATAGATTGATGGGCTAGCACTA 57.917 37.037 19.73 4.96 0.00 2.74
1526 2106 5.674052 ATAGATTGATGGGCTAGCACTAG 57.326 43.478 19.73 0.07 36.29 2.57
1527 2107 3.312890 AGATTGATGGGCTAGCACTAGT 58.687 45.455 19.73 4.00 35.65 2.57
1528 2108 4.483950 AGATTGATGGGCTAGCACTAGTA 58.516 43.478 19.73 0.00 35.65 1.82
1529 2109 4.526262 AGATTGATGGGCTAGCACTAGTAG 59.474 45.833 19.73 0.00 35.65 2.57
1530 2110 3.595190 TGATGGGCTAGCACTAGTAGA 57.405 47.619 19.73 0.00 35.65 2.59
1531 2111 3.910989 TGATGGGCTAGCACTAGTAGAA 58.089 45.455 19.73 0.00 35.65 2.10
1532 2112 4.286707 TGATGGGCTAGCACTAGTAGAAA 58.713 43.478 19.73 0.00 35.65 2.52
1533 2113 4.714802 TGATGGGCTAGCACTAGTAGAAAA 59.285 41.667 19.73 0.00 35.65 2.29
1534 2114 5.188948 TGATGGGCTAGCACTAGTAGAAAAA 59.811 40.000 19.73 0.00 35.65 1.94
1552 2132 2.828661 AAAAGGCTTCCATACTCCCC 57.171 50.000 0.00 0.00 0.00 4.81
1553 2133 0.927029 AAAGGCTTCCATACTCCCCC 59.073 55.000 0.00 0.00 0.00 5.40
1554 2134 0.253630 AAGGCTTCCATACTCCCCCA 60.254 55.000 0.00 0.00 0.00 4.96
1555 2135 0.028642 AGGCTTCCATACTCCCCCAT 60.029 55.000 0.00 0.00 0.00 4.00
1556 2136 0.853530 GGCTTCCATACTCCCCCATT 59.146 55.000 0.00 0.00 0.00 3.16
1557 2137 2.062636 GGCTTCCATACTCCCCCATTA 58.937 52.381 0.00 0.00 0.00 1.90
1558 2138 2.040412 GGCTTCCATACTCCCCCATTAG 59.960 54.545 0.00 0.00 0.00 1.73
1559 2139 2.711547 GCTTCCATACTCCCCCATTAGT 59.288 50.000 0.00 0.00 0.00 2.24
1560 2140 3.244596 GCTTCCATACTCCCCCATTAGTC 60.245 52.174 0.00 0.00 0.00 2.59
1561 2141 2.986050 TCCATACTCCCCCATTAGTCC 58.014 52.381 0.00 0.00 0.00 3.85
1562 2142 2.527057 TCCATACTCCCCCATTAGTCCT 59.473 50.000 0.00 0.00 0.00 3.85
1563 2143 2.907042 CCATACTCCCCCATTAGTCCTC 59.093 54.545 0.00 0.00 0.00 3.71
1564 2144 2.789323 TACTCCCCCATTAGTCCTCC 57.211 55.000 0.00 0.00 0.00 4.30
1565 2145 0.398664 ACTCCCCCATTAGTCCTCCG 60.399 60.000 0.00 0.00 0.00 4.63
1566 2146 1.759459 CTCCCCCATTAGTCCTCCGC 61.759 65.000 0.00 0.00 0.00 5.54
1567 2147 2.819284 CCCCCATTAGTCCTCCGCC 61.819 68.421 0.00 0.00 0.00 6.13
1568 2148 2.819284 CCCCATTAGTCCTCCGCCC 61.819 68.421 0.00 0.00 0.00 6.13
1569 2149 2.819284 CCCATTAGTCCTCCGCCCC 61.819 68.421 0.00 0.00 0.00 5.80
1570 2150 2.421739 CATTAGTCCTCCGCCCCG 59.578 66.667 0.00 0.00 0.00 5.73
1571 2151 2.131709 CATTAGTCCTCCGCCCCGA 61.132 63.158 0.00 0.00 0.00 5.14
1572 2152 2.132352 ATTAGTCCTCCGCCCCGAC 61.132 63.158 0.00 0.00 0.00 4.79
1603 2183 4.636435 CCACGTGGACGGGCCTTT 62.636 66.667 31.31 0.00 42.34 3.11
1604 2184 2.344500 CACGTGGACGGGCCTTTA 59.656 61.111 7.95 0.00 44.95 1.85
1605 2185 1.740296 CACGTGGACGGGCCTTTAG 60.740 63.158 7.95 0.00 44.95 1.85
1606 2186 2.212110 ACGTGGACGGGCCTTTAGT 61.212 57.895 0.84 0.00 44.95 2.24
1607 2187 1.447314 CGTGGACGGGCCTTTAGTC 60.447 63.158 0.84 7.66 37.63 2.59
1609 2189 2.588439 GGACGGGCCTTTAGTCCC 59.412 66.667 21.39 9.76 46.40 4.46
1613 2193 2.588439 GGGCCTTTAGTCCCGGTC 59.412 66.667 0.84 0.00 32.00 4.79
1614 2194 2.295602 GGGCCTTTAGTCCCGGTCA 61.296 63.158 0.84 0.00 32.00 4.02
1615 2195 1.221021 GGCCTTTAGTCCCGGTCAG 59.779 63.158 0.00 0.00 0.00 3.51
1616 2196 1.449778 GCCTTTAGTCCCGGTCAGC 60.450 63.158 0.00 0.00 0.00 4.26
1617 2197 1.221021 CCTTTAGTCCCGGTCAGCC 59.779 63.158 0.00 0.00 0.00 4.85
1618 2198 1.550130 CCTTTAGTCCCGGTCAGCCA 61.550 60.000 0.00 0.00 34.09 4.75
1619 2199 0.541863 CTTTAGTCCCGGTCAGCCAT 59.458 55.000 0.00 0.00 34.09 4.40
1620 2200 1.760613 CTTTAGTCCCGGTCAGCCATA 59.239 52.381 0.00 0.00 34.09 2.74
1621 2201 1.868713 TTAGTCCCGGTCAGCCATAA 58.131 50.000 0.00 0.00 34.09 1.90
1622 2202 1.410004 TAGTCCCGGTCAGCCATAAG 58.590 55.000 0.00 0.00 34.09 1.73
1623 2203 0.325296 AGTCCCGGTCAGCCATAAGA 60.325 55.000 0.00 0.00 34.09 2.10
1624 2204 0.539986 GTCCCGGTCAGCCATAAGAA 59.460 55.000 0.00 0.00 34.09 2.52
1625 2205 1.141053 GTCCCGGTCAGCCATAAGAAT 59.859 52.381 0.00 0.00 34.09 2.40
1626 2206 1.416401 TCCCGGTCAGCCATAAGAATC 59.584 52.381 0.00 0.00 34.09 2.52
1627 2207 1.502231 CCGGTCAGCCATAAGAATCG 58.498 55.000 0.00 0.00 34.09 3.34
1628 2208 1.502231 CGGTCAGCCATAAGAATCGG 58.498 55.000 0.00 0.00 34.09 4.18
1629 2209 1.873903 CGGTCAGCCATAAGAATCGGG 60.874 57.143 0.00 0.00 34.09 5.14
1630 2210 1.416401 GGTCAGCCATAAGAATCGGGA 59.584 52.381 0.00 0.00 34.09 5.14
1631 2211 2.484889 GTCAGCCATAAGAATCGGGAC 58.515 52.381 0.00 0.00 0.00 4.46
1632 2212 2.103263 GTCAGCCATAAGAATCGGGACT 59.897 50.000 0.00 0.00 0.00 3.85
1633 2213 3.321111 GTCAGCCATAAGAATCGGGACTA 59.679 47.826 0.00 0.00 0.00 2.59
1634 2214 3.964688 TCAGCCATAAGAATCGGGACTAA 59.035 43.478 0.00 0.00 0.00 2.24
1635 2215 4.407621 TCAGCCATAAGAATCGGGACTAAA 59.592 41.667 0.00 0.00 0.00 1.85
1636 2216 4.752101 CAGCCATAAGAATCGGGACTAAAG 59.248 45.833 0.00 0.00 0.00 1.85
1637 2217 3.498777 GCCATAAGAATCGGGACTAAAGC 59.501 47.826 0.00 0.00 0.00 3.51
1638 2218 4.065789 CCATAAGAATCGGGACTAAAGCC 58.934 47.826 0.00 0.00 0.00 4.35
1639 2219 4.202367 CCATAAGAATCGGGACTAAAGCCT 60.202 45.833 0.00 0.00 0.00 4.58
1640 2220 5.368989 CATAAGAATCGGGACTAAAGCCTT 58.631 41.667 0.00 0.00 0.00 4.35
1641 2221 4.302559 AAGAATCGGGACTAAAGCCTTT 57.697 40.909 0.00 0.00 0.00 3.11
1642 2222 5.431179 AAGAATCGGGACTAAAGCCTTTA 57.569 39.130 0.00 0.00 0.00 1.85
1643 2223 5.024785 AGAATCGGGACTAAAGCCTTTAG 57.975 43.478 20.10 20.10 46.26 1.85
1652 2232 2.180432 AAAGCCTTTAGTCGTGGTCC 57.820 50.000 0.00 0.00 0.00 4.46
1653 2233 0.037605 AAGCCTTTAGTCGTGGTCCG 60.038 55.000 0.00 0.00 38.13 4.79
1654 2234 1.183676 AGCCTTTAGTCGTGGTCCGT 61.184 55.000 0.00 0.00 37.94 4.69
1655 2235 0.527565 GCCTTTAGTCGTGGTCCGTA 59.472 55.000 0.00 0.00 37.94 4.02
1656 2236 1.067635 GCCTTTAGTCGTGGTCCGTAA 60.068 52.381 0.00 0.00 37.94 3.18
1657 2237 2.872370 CCTTTAGTCGTGGTCCGTAAG 58.128 52.381 0.00 0.00 37.94 2.34
1658 2238 2.489329 CCTTTAGTCGTGGTCCGTAAGA 59.511 50.000 0.00 0.00 43.02 2.10
1659 2239 3.427233 CCTTTAGTCGTGGTCCGTAAGAG 60.427 52.174 0.00 0.00 43.02 2.85
1660 2240 1.742761 TAGTCGTGGTCCGTAAGAGG 58.257 55.000 0.00 0.00 43.02 3.69
1661 2241 1.153881 GTCGTGGTCCGTAAGAGGC 60.154 63.158 0.00 0.00 43.02 4.70
1662 2242 2.202570 CGTGGTCCGTAAGAGGCG 60.203 66.667 0.00 0.00 43.02 5.52
1663 2243 2.508663 GTGGTCCGTAAGAGGCGC 60.509 66.667 0.00 0.00 43.02 6.53
1664 2244 4.124351 TGGTCCGTAAGAGGCGCG 62.124 66.667 0.00 0.00 43.02 6.86
1665 2245 3.818787 GGTCCGTAAGAGGCGCGA 61.819 66.667 12.10 0.00 43.02 5.87
1666 2246 2.578981 GTCCGTAAGAGGCGCGAC 60.579 66.667 12.10 7.34 43.02 5.19
1667 2247 2.749044 TCCGTAAGAGGCGCGACT 60.749 61.111 18.34 18.34 43.02 4.18
1668 2248 1.450134 TCCGTAAGAGGCGCGACTA 60.450 57.895 18.29 0.00 43.02 2.59
1669 2249 1.026182 TCCGTAAGAGGCGCGACTAA 61.026 55.000 18.29 0.00 43.02 2.24
1670 2250 0.179156 CCGTAAGAGGCGCGACTAAA 60.179 55.000 18.29 0.00 43.02 1.85
1671 2251 1.189403 CGTAAGAGGCGCGACTAAAG 58.811 55.000 18.29 1.48 43.02 1.85
1672 2252 1.557651 GTAAGAGGCGCGACTAAAGG 58.442 55.000 18.29 0.00 0.00 3.11
1673 2253 0.458669 TAAGAGGCGCGACTAAAGGG 59.541 55.000 18.29 0.00 0.00 3.95
1674 2254 2.202892 GAGGCGCGACTAAAGGGG 60.203 66.667 18.29 0.00 0.00 4.79
1675 2255 3.735037 GAGGCGCGACTAAAGGGGG 62.735 68.421 18.29 0.00 0.00 5.40
1690 2270 2.510918 GGGGGTCTTTAGTCGCGC 60.511 66.667 0.00 0.00 0.00 6.86
1691 2271 2.263540 GGGGTCTTTAGTCGCGCA 59.736 61.111 8.75 0.00 0.00 6.09
1692 2272 1.153429 GGGGTCTTTAGTCGCGCAT 60.153 57.895 8.75 0.00 0.00 4.73
1693 2273 0.103572 GGGGTCTTTAGTCGCGCATA 59.896 55.000 8.75 0.00 0.00 3.14
1694 2274 1.270147 GGGGTCTTTAGTCGCGCATAT 60.270 52.381 8.75 0.00 0.00 1.78
1695 2275 2.480845 GGGTCTTTAGTCGCGCATATT 58.519 47.619 8.75 0.00 0.00 1.28
1696 2276 2.870411 GGGTCTTTAGTCGCGCATATTT 59.130 45.455 8.75 0.00 0.00 1.40
1697 2277 4.053295 GGGTCTTTAGTCGCGCATATTTA 58.947 43.478 8.75 0.00 0.00 1.40
1698 2278 4.150098 GGGTCTTTAGTCGCGCATATTTAG 59.850 45.833 8.75 0.00 0.00 1.85
1699 2279 4.743644 GGTCTTTAGTCGCGCATATTTAGT 59.256 41.667 8.75 0.00 0.00 2.24
1700 2280 5.107951 GGTCTTTAGTCGCGCATATTTAGTC 60.108 44.000 8.75 0.00 0.00 2.59
1701 2281 4.980434 TCTTTAGTCGCGCATATTTAGTCC 59.020 41.667 8.75 0.00 0.00 3.85
1702 2282 2.150397 AGTCGCGCATATTTAGTCCC 57.850 50.000 8.75 0.00 0.00 4.46
1703 2283 0.782384 GTCGCGCATATTTAGTCCCG 59.218 55.000 8.75 0.00 0.00 5.14
1704 2284 0.319211 TCGCGCATATTTAGTCCCGG 60.319 55.000 8.75 0.00 0.00 5.73
1705 2285 0.599204 CGCGCATATTTAGTCCCGGT 60.599 55.000 8.75 0.00 0.00 5.28
1706 2286 1.589803 GCGCATATTTAGTCCCGGTT 58.410 50.000 0.30 0.00 0.00 4.44
1707 2287 1.263217 GCGCATATTTAGTCCCGGTTG 59.737 52.381 0.30 0.00 0.00 3.77
1708 2288 1.263217 CGCATATTTAGTCCCGGTTGC 59.737 52.381 0.00 0.00 0.00 4.17
1709 2289 2.294074 GCATATTTAGTCCCGGTTGCA 58.706 47.619 0.00 0.00 0.00 4.08
1710 2290 2.032924 GCATATTTAGTCCCGGTTGCAC 59.967 50.000 0.00 0.00 0.00 4.57
1711 2291 3.275143 CATATTTAGTCCCGGTTGCACA 58.725 45.455 0.00 0.00 0.00 4.57
1712 2292 1.821216 ATTTAGTCCCGGTTGCACAG 58.179 50.000 0.00 0.00 0.00 3.66
1713 2293 0.887387 TTTAGTCCCGGTTGCACAGC 60.887 55.000 0.00 0.00 0.00 4.40
1714 2294 2.741486 TTAGTCCCGGTTGCACAGCC 62.741 60.000 0.00 0.00 0.00 4.85
1720 2300 4.643387 GGTTGCACAGCCGGGACT 62.643 66.667 2.18 0.00 0.00 3.85
1721 2301 2.345991 GTTGCACAGCCGGGACTA 59.654 61.111 2.18 0.00 0.00 2.59
1722 2302 1.302192 GTTGCACAGCCGGGACTAA 60.302 57.895 2.18 0.00 0.00 2.24
1723 2303 0.887387 GTTGCACAGCCGGGACTAAA 60.887 55.000 2.18 0.00 0.00 1.85
1724 2304 0.605319 TTGCACAGCCGGGACTAAAG 60.605 55.000 2.18 0.00 0.00 1.85
1725 2305 1.745489 GCACAGCCGGGACTAAAGG 60.745 63.158 2.18 0.00 0.00 3.11
1729 2309 2.669240 GCCGGGACTAAAGGCTGT 59.331 61.111 2.18 0.00 46.83 4.40
1730 2310 1.002502 GCCGGGACTAAAGGCTGTT 60.003 57.895 2.18 0.00 46.83 3.16
1731 2311 1.305930 GCCGGGACTAAAGGCTGTTG 61.306 60.000 2.18 0.00 46.83 3.33
1732 2312 1.305930 CCGGGACTAAAGGCTGTTGC 61.306 60.000 0.00 0.00 38.76 4.17
1733 2313 1.635663 CGGGACTAAAGGCTGTTGCG 61.636 60.000 0.00 0.00 40.82 4.85
1734 2314 0.321298 GGGACTAAAGGCTGTTGCGA 60.321 55.000 0.00 0.00 40.82 5.10
1735 2315 1.519408 GGACTAAAGGCTGTTGCGAA 58.481 50.000 0.00 0.00 40.82 4.70
1736 2316 1.197036 GGACTAAAGGCTGTTGCGAAC 59.803 52.381 0.00 0.00 40.82 3.95
1737 2317 1.197036 GACTAAAGGCTGTTGCGAACC 59.803 52.381 0.00 0.00 40.82 3.62
1738 2318 0.165944 CTAAAGGCTGTTGCGAACCG 59.834 55.000 0.00 0.00 40.82 4.44
1739 2319 1.231958 TAAAGGCTGTTGCGAACCGG 61.232 55.000 0.00 0.00 40.82 5.28
1742 2322 3.723348 GCTGTTGCGAACCGGGAC 61.723 66.667 6.32 0.00 0.00 4.46
1743 2323 2.030562 CTGTTGCGAACCGGGACT 59.969 61.111 6.32 0.00 0.00 3.85
1744 2324 1.290955 CTGTTGCGAACCGGGACTA 59.709 57.895 6.32 0.00 0.00 2.59
1745 2325 0.320073 CTGTTGCGAACCGGGACTAA 60.320 55.000 6.32 0.00 0.00 2.24
1746 2326 0.106335 TGTTGCGAACCGGGACTAAA 59.894 50.000 6.32 0.00 0.00 1.85
1747 2327 0.794473 GTTGCGAACCGGGACTAAAG 59.206 55.000 6.32 0.00 0.00 1.85
1748 2328 0.320946 TTGCGAACCGGGACTAAAGG 60.321 55.000 6.32 0.00 0.00 3.11
1749 2329 1.449070 GCGAACCGGGACTAAAGGG 60.449 63.158 6.32 0.00 0.00 3.95
1750 2330 1.449070 CGAACCGGGACTAAAGGGC 60.449 63.158 6.32 0.00 0.00 5.19
1751 2331 1.896122 CGAACCGGGACTAAAGGGCT 61.896 60.000 6.32 0.00 0.00 5.19
1752 2332 0.327259 GAACCGGGACTAAAGGGCTT 59.673 55.000 6.32 0.00 0.00 4.35
1753 2333 0.775542 AACCGGGACTAAAGGGCTTT 59.224 50.000 6.32 0.00 36.63 3.51
1754 2334 0.775542 ACCGGGACTAAAGGGCTTTT 59.224 50.000 6.32 0.00 34.23 2.27
1755 2335 1.146359 ACCGGGACTAAAGGGCTTTTT 59.854 47.619 6.32 0.00 34.23 1.94
1827 2407 3.667960 GCACAAGCTATTTCGGTGTTGAG 60.668 47.826 0.00 0.00 37.91 3.02
1860 2441 7.469537 TTCCTTTTAGTTGTGGAGTTTTTCA 57.530 32.000 0.00 0.00 0.00 2.69
1932 2513 7.889589 AATAGGCAAAAAGTTATTTCTGTGC 57.110 32.000 0.00 0.00 33.28 4.57
2105 2711 4.710375 TCTTGAACGAATACTCCTAGGCTT 59.290 41.667 2.96 0.00 0.00 4.35
2476 3085 3.726607 ACAAATACGTACGACCAAACCA 58.273 40.909 24.41 0.00 0.00 3.67
2502 3111 6.543831 GTCATTAAAGTAGCACAGATTCCCAT 59.456 38.462 0.00 0.00 0.00 4.00
2530 3200 1.338337 CACACCGCCATTAAACCAACA 59.662 47.619 0.00 0.00 0.00 3.33
2532 3202 0.594110 ACCGCCATTAAACCAACACG 59.406 50.000 0.00 0.00 0.00 4.49
2558 3228 3.023949 ATGCCACAGGAGTCGCCTC 62.024 63.158 0.00 0.00 46.97 4.70
2606 3276 1.914764 TTGGGTAGTGGGTCCCGAC 60.915 63.158 2.65 2.89 46.13 4.79
2622 3298 1.511850 CGACAGTCTTGGTGCAATGA 58.488 50.000 0.00 0.00 0.00 2.57
2626 3302 4.333649 CGACAGTCTTGGTGCAATGATAAT 59.666 41.667 0.00 0.00 0.00 1.28
2628 3304 6.292542 CGACAGTCTTGGTGCAATGATAATAG 60.293 42.308 0.00 0.00 0.00 1.73
2630 3306 7.564793 ACAGTCTTGGTGCAATGATAATAGTA 58.435 34.615 0.00 0.00 0.00 1.82
2697 3373 2.713154 GTCACACGCACCACCAAC 59.287 61.111 0.00 0.00 0.00 3.77
2751 3427 6.265577 CCAAATTTACATAGGCACAAGCTAC 58.734 40.000 0.00 0.00 41.70 3.58
2835 3511 8.158169 TCAATTATACGTACTACCGATGAAGT 57.842 34.615 0.00 0.00 0.00 3.01
2985 3661 5.465724 GTGTTCCCTCACTACTTGTACAAAG 59.534 44.000 10.03 7.71 35.68 2.77
3028 3729 3.914426 ATAGAGGCGGTTCATCAAACT 57.086 42.857 0.00 0.00 38.02 2.66
3101 3804 8.205131 AGACTACGACAATTAAACACAGTTTT 57.795 30.769 0.03 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 2.203788 ACTTGGAGCCAGGACCGA 60.204 61.111 5.58 0.00 0.00 4.69
55 56 2.435059 GCGACTTGGAGCCAGGAC 60.435 66.667 5.58 0.00 0.00 3.85
138 139 2.227194 CAAACGCTACCCAGAAAACCT 58.773 47.619 0.00 0.00 0.00 3.50
153 154 1.509787 CAACAGATCGCCGCAAACG 60.510 57.895 0.00 0.00 39.67 3.60
231 232 6.012658 TGCCAGTTTTAAATAAGCAGTCAG 57.987 37.500 0.00 0.00 0.00 3.51
271 274 3.738281 CGGCGTCCTTAGTCAATGATCTT 60.738 47.826 0.00 0.00 0.00 2.40
338 341 0.946221 CTGCGCGTGAAAGAGGAAGT 60.946 55.000 8.43 0.00 0.00 3.01
349 352 2.284798 ATCCTGGTACTCTGCGCGTG 62.285 60.000 8.43 0.68 0.00 5.34
350 353 0.750546 TATCCTGGTACTCTGCGCGT 60.751 55.000 8.43 0.00 0.00 6.01
368 371 1.209621 AGGAAGCCAACCCGCTAATA 58.790 50.000 0.00 0.00 38.44 0.98
390 393 3.457380 AGGCCATAGAACTCATGACACAT 59.543 43.478 5.01 0.00 0.00 3.21
565 577 1.609072 CATGCATGGCCAGATTGAGAG 59.391 52.381 19.40 0.00 0.00 3.20
596 608 8.873215 AACGATCATGTTAAGATTACCTAGTG 57.127 34.615 0.00 0.00 0.00 2.74
991 1011 8.283291 CGCTTCAAAAATAGATAGGAATACCAC 58.717 37.037 0.00 0.00 38.94 4.16
1000 1020 9.916397 ACGTATTTTCGCTTCAAAAATAGATAG 57.084 29.630 0.00 0.00 38.54 2.08
1231 1803 4.752879 TTCGGCAGTGTAGCGGGC 62.753 66.667 0.00 0.00 35.76 6.13
1252 1824 1.299926 GCAACCTGTCGAGTCGTGT 60.300 57.895 13.12 3.36 0.00 4.49
1256 1828 1.444553 CCGAGCAACCTGTCGAGTC 60.445 63.158 0.00 0.00 38.50 3.36
1278 1856 2.834043 TCCACGTCCACCACACGA 60.834 61.111 0.00 0.00 39.75 4.35
1281 1859 3.936203 GCCTCCACGTCCACCACA 61.936 66.667 0.00 0.00 0.00 4.17
1327 1905 1.442987 GGTTGCCAGCAAAGCACTT 59.557 52.632 6.64 0.00 40.69 3.16
1441 2019 1.202806 AGTCCACCACCTGAACATGTG 60.203 52.381 0.00 3.84 0.00 3.21
1496 2076 9.083422 TGCTAGCCCATCAATCTATATATCTAC 57.917 37.037 13.29 0.00 0.00 2.59
1510 2090 3.595190 TCTACTAGTGCTAGCCCATCA 57.405 47.619 13.29 0.00 36.66 3.07
1532 2112 2.292257 GGGGGAGTATGGAAGCCTTTTT 60.292 50.000 0.00 0.00 0.00 1.94
1533 2113 1.288037 GGGGGAGTATGGAAGCCTTTT 59.712 52.381 0.00 0.00 0.00 2.27
1534 2114 0.927029 GGGGGAGTATGGAAGCCTTT 59.073 55.000 0.00 0.00 0.00 3.11
1535 2115 0.253630 TGGGGGAGTATGGAAGCCTT 60.254 55.000 0.00 0.00 0.00 4.35
1536 2116 0.028642 ATGGGGGAGTATGGAAGCCT 60.029 55.000 0.00 0.00 0.00 4.58
1537 2117 0.853530 AATGGGGGAGTATGGAAGCC 59.146 55.000 0.00 0.00 0.00 4.35
1538 2118 2.711547 ACTAATGGGGGAGTATGGAAGC 59.288 50.000 0.00 0.00 0.00 3.86
1539 2119 3.328050 GGACTAATGGGGGAGTATGGAAG 59.672 52.174 0.00 0.00 0.00 3.46
1540 2120 3.050564 AGGACTAATGGGGGAGTATGGAA 60.051 47.826 0.00 0.00 0.00 3.53
1541 2121 2.527057 AGGACTAATGGGGGAGTATGGA 59.473 50.000 0.00 0.00 0.00 3.41
1542 2122 2.907042 GAGGACTAATGGGGGAGTATGG 59.093 54.545 0.00 0.00 0.00 2.74
1543 2123 2.907042 GGAGGACTAATGGGGGAGTATG 59.093 54.545 0.00 0.00 0.00 2.39
1544 2124 2.492940 CGGAGGACTAATGGGGGAGTAT 60.493 54.545 0.00 0.00 0.00 2.12
1545 2125 1.133262 CGGAGGACTAATGGGGGAGTA 60.133 57.143 0.00 0.00 0.00 2.59
1546 2126 0.398664 CGGAGGACTAATGGGGGAGT 60.399 60.000 0.00 0.00 0.00 3.85
1547 2127 1.759459 GCGGAGGACTAATGGGGGAG 61.759 65.000 0.00 0.00 0.00 4.30
1548 2128 1.764854 GCGGAGGACTAATGGGGGA 60.765 63.158 0.00 0.00 0.00 4.81
1549 2129 2.819284 GGCGGAGGACTAATGGGGG 61.819 68.421 0.00 0.00 0.00 5.40
1550 2130 2.819284 GGGCGGAGGACTAATGGGG 61.819 68.421 0.00 0.00 0.00 4.96
1551 2131 2.819284 GGGGCGGAGGACTAATGGG 61.819 68.421 0.00 0.00 0.00 4.00
1552 2132 2.829592 GGGGCGGAGGACTAATGG 59.170 66.667 0.00 0.00 0.00 3.16
1553 2133 2.131709 TCGGGGCGGAGGACTAATG 61.132 63.158 0.00 0.00 0.00 1.90
1554 2134 2.132352 GTCGGGGCGGAGGACTAAT 61.132 63.158 0.00 0.00 0.00 1.73
1555 2135 2.757099 GTCGGGGCGGAGGACTAA 60.757 66.667 0.00 0.00 0.00 2.24
1586 2166 3.242897 TAAAGGCCCGTCCACGTGG 62.243 63.158 29.26 29.26 37.29 4.94
1587 2167 1.740296 CTAAAGGCCCGTCCACGTG 60.740 63.158 9.08 9.08 37.29 4.49
1588 2168 2.163601 GACTAAAGGCCCGTCCACGT 62.164 60.000 0.00 0.00 37.29 4.49
1589 2169 1.447314 GACTAAAGGCCCGTCCACG 60.447 63.158 0.00 0.00 37.29 4.94
1590 2170 1.078637 GGACTAAAGGCCCGTCCAC 60.079 63.158 20.23 2.00 45.08 4.02
1591 2171 3.395630 GGACTAAAGGCCCGTCCA 58.604 61.111 20.23 0.00 45.08 4.02
1592 2172 2.588439 GGGACTAAAGGCCCGTCC 59.412 66.667 18.06 18.06 45.02 4.79
1596 2176 2.253403 CTGACCGGGACTAAAGGCCC 62.253 65.000 11.29 11.29 41.11 5.80
1597 2177 1.221021 CTGACCGGGACTAAAGGCC 59.779 63.158 6.32 0.00 0.00 5.19
1598 2178 1.449778 GCTGACCGGGACTAAAGGC 60.450 63.158 6.32 0.00 0.00 4.35
1599 2179 1.221021 GGCTGACCGGGACTAAAGG 59.779 63.158 6.32 0.00 0.00 3.11
1600 2180 0.541863 ATGGCTGACCGGGACTAAAG 59.458 55.000 6.32 0.00 39.70 1.85
1601 2181 1.868713 TATGGCTGACCGGGACTAAA 58.131 50.000 6.32 0.00 39.70 1.85
1602 2182 1.760613 CTTATGGCTGACCGGGACTAA 59.239 52.381 6.32 0.00 39.70 2.24
1603 2183 1.063492 TCTTATGGCTGACCGGGACTA 60.063 52.381 6.32 0.00 39.70 2.59
1604 2184 0.325296 TCTTATGGCTGACCGGGACT 60.325 55.000 6.32 0.00 39.70 3.85
1605 2185 0.539986 TTCTTATGGCTGACCGGGAC 59.460 55.000 6.32 0.00 39.70 4.46
1606 2186 1.416401 GATTCTTATGGCTGACCGGGA 59.584 52.381 6.32 0.00 39.70 5.14
1607 2187 1.873903 CGATTCTTATGGCTGACCGGG 60.874 57.143 6.32 0.00 39.70 5.73
1608 2188 1.502231 CGATTCTTATGGCTGACCGG 58.498 55.000 0.00 0.00 39.70 5.28
1609 2189 1.502231 CCGATTCTTATGGCTGACCG 58.498 55.000 0.00 0.00 39.70 4.79
1610 2190 1.416401 TCCCGATTCTTATGGCTGACC 59.584 52.381 0.00 0.00 0.00 4.02
1611 2191 2.103263 AGTCCCGATTCTTATGGCTGAC 59.897 50.000 0.00 0.00 0.00 3.51
1612 2192 2.398588 AGTCCCGATTCTTATGGCTGA 58.601 47.619 0.00 0.00 0.00 4.26
1613 2193 2.918712 AGTCCCGATTCTTATGGCTG 57.081 50.000 0.00 0.00 0.00 4.85
1614 2194 4.743955 GCTTTAGTCCCGATTCTTATGGCT 60.744 45.833 0.00 0.00 0.00 4.75
1615 2195 3.498777 GCTTTAGTCCCGATTCTTATGGC 59.501 47.826 0.00 0.00 0.00 4.40
1616 2196 4.065789 GGCTTTAGTCCCGATTCTTATGG 58.934 47.826 0.00 0.00 0.00 2.74
1617 2197 4.962155 AGGCTTTAGTCCCGATTCTTATG 58.038 43.478 0.00 0.00 0.00 1.90
1618 2198 5.632034 AAGGCTTTAGTCCCGATTCTTAT 57.368 39.130 0.00 0.00 0.00 1.73
1619 2199 5.431179 AAAGGCTTTAGTCCCGATTCTTA 57.569 39.130 11.52 0.00 0.00 2.10
1620 2200 4.302559 AAAGGCTTTAGTCCCGATTCTT 57.697 40.909 11.52 0.00 0.00 2.52
1621 2201 5.024785 CTAAAGGCTTTAGTCCCGATTCT 57.975 43.478 30.21 2.07 38.21 2.40
1631 2211 3.259902 GGACCACGACTAAAGGCTTTAG 58.740 50.000 34.37 34.37 46.26 1.85
1632 2212 3.323751 GGACCACGACTAAAGGCTTTA 57.676 47.619 18.11 18.11 0.00 1.85
1633 2213 2.180432 GGACCACGACTAAAGGCTTT 57.820 50.000 17.76 17.76 0.00 3.51
1634 2214 3.929660 GGACCACGACTAAAGGCTT 57.070 52.632 0.00 0.00 0.00 4.35
1646 2226 2.508663 GCGCCTCTTACGGACCAC 60.509 66.667 0.00 0.00 0.00 4.16
1647 2227 4.124351 CGCGCCTCTTACGGACCA 62.124 66.667 0.00 0.00 0.00 4.02
1648 2228 3.818787 TCGCGCCTCTTACGGACC 61.819 66.667 0.00 0.00 0.00 4.46
1649 2229 1.709147 TAGTCGCGCCTCTTACGGAC 61.709 60.000 0.00 0.00 33.64 4.79
1650 2230 1.026182 TTAGTCGCGCCTCTTACGGA 61.026 55.000 0.00 0.00 0.00 4.69
1651 2231 0.179156 TTTAGTCGCGCCTCTTACGG 60.179 55.000 0.00 0.00 0.00 4.02
1652 2232 1.189403 CTTTAGTCGCGCCTCTTACG 58.811 55.000 0.00 0.00 0.00 3.18
1653 2233 1.557651 CCTTTAGTCGCGCCTCTTAC 58.442 55.000 0.00 0.00 0.00 2.34
1654 2234 0.458669 CCCTTTAGTCGCGCCTCTTA 59.541 55.000 0.00 0.00 0.00 2.10
1655 2235 1.218316 CCCTTTAGTCGCGCCTCTT 59.782 57.895 0.00 0.00 0.00 2.85
1656 2236 2.722201 CCCCTTTAGTCGCGCCTCT 61.722 63.158 0.00 2.63 0.00 3.69
1657 2237 2.202892 CCCCTTTAGTCGCGCCTC 60.203 66.667 0.00 0.00 0.00 4.70
1658 2238 3.782443 CCCCCTTTAGTCGCGCCT 61.782 66.667 0.00 0.00 0.00 5.52
1673 2253 2.510918 GCGCGACTAAAGACCCCC 60.511 66.667 12.10 0.00 0.00 5.40
1674 2254 0.103572 TATGCGCGACTAAAGACCCC 59.896 55.000 12.10 0.00 0.00 4.95
1675 2255 2.150397 ATATGCGCGACTAAAGACCC 57.850 50.000 12.10 0.00 0.00 4.46
1676 2256 4.743644 ACTAAATATGCGCGACTAAAGACC 59.256 41.667 12.10 0.00 0.00 3.85
1677 2257 5.107951 GGACTAAATATGCGCGACTAAAGAC 60.108 44.000 12.10 0.00 0.00 3.01
1678 2258 4.980434 GGACTAAATATGCGCGACTAAAGA 59.020 41.667 12.10 0.00 0.00 2.52
1679 2259 4.150098 GGGACTAAATATGCGCGACTAAAG 59.850 45.833 12.10 0.00 0.00 1.85
1680 2260 4.053295 GGGACTAAATATGCGCGACTAAA 58.947 43.478 12.10 0.00 0.00 1.85
1681 2261 3.645884 GGGACTAAATATGCGCGACTAA 58.354 45.455 12.10 0.00 0.00 2.24
1682 2262 2.351060 CGGGACTAAATATGCGCGACTA 60.351 50.000 12.10 0.00 38.72 2.59
1683 2263 1.602165 CGGGACTAAATATGCGCGACT 60.602 52.381 12.10 0.00 38.72 4.18
1684 2264 0.782384 CGGGACTAAATATGCGCGAC 59.218 55.000 12.10 0.88 38.72 5.19
1685 2265 0.319211 CCGGGACTAAATATGCGCGA 60.319 55.000 12.10 0.00 38.72 5.87
1686 2266 0.599204 ACCGGGACTAAATATGCGCG 60.599 55.000 6.32 0.00 36.61 6.86
1687 2267 1.263217 CAACCGGGACTAAATATGCGC 59.737 52.381 6.32 0.00 0.00 6.09
1688 2268 1.263217 GCAACCGGGACTAAATATGCG 59.737 52.381 6.32 0.00 0.00 4.73
1689 2269 2.032924 GTGCAACCGGGACTAAATATGC 59.967 50.000 6.32 2.60 34.56 3.14
1690 2270 3.275143 TGTGCAACCGGGACTAAATATG 58.725 45.455 6.32 0.00 38.87 1.78
1691 2271 3.541632 CTGTGCAACCGGGACTAAATAT 58.458 45.455 6.32 0.00 38.87 1.28
1692 2272 2.937873 GCTGTGCAACCGGGACTAAATA 60.938 50.000 6.32 0.00 38.87 1.40
1693 2273 1.821216 CTGTGCAACCGGGACTAAAT 58.179 50.000 6.32 0.00 38.87 1.40
1694 2274 0.887387 GCTGTGCAACCGGGACTAAA 60.887 55.000 6.32 0.00 38.87 1.85
1695 2275 1.302192 GCTGTGCAACCGGGACTAA 60.302 57.895 6.32 0.00 38.87 2.24
1696 2276 2.345991 GCTGTGCAACCGGGACTA 59.654 61.111 6.32 0.00 38.87 2.59
1697 2277 4.643387 GGCTGTGCAACCGGGACT 62.643 66.667 6.32 0.00 38.87 3.85
1703 2283 2.741486 TTAGTCCCGGCTGTGCAACC 62.741 60.000 0.00 0.00 34.36 3.77
1704 2284 0.887387 TTTAGTCCCGGCTGTGCAAC 60.887 55.000 0.00 0.00 37.35 4.17
1705 2285 0.605319 CTTTAGTCCCGGCTGTGCAA 60.605 55.000 0.00 0.00 0.00 4.08
1706 2286 1.003839 CTTTAGTCCCGGCTGTGCA 60.004 57.895 0.00 0.00 0.00 4.57
1707 2287 1.745489 CCTTTAGTCCCGGCTGTGC 60.745 63.158 0.00 0.00 0.00 4.57
1708 2288 1.745489 GCCTTTAGTCCCGGCTGTG 60.745 63.158 0.00 0.00 40.62 3.66
1709 2289 2.669240 GCCTTTAGTCCCGGCTGT 59.331 61.111 0.00 0.00 40.62 4.40
1712 2292 1.002502 AACAGCCTTTAGTCCCGGC 60.003 57.895 0.00 0.00 44.09 6.13
1713 2293 1.305930 GCAACAGCCTTTAGTCCCGG 61.306 60.000 0.00 0.00 0.00 5.73
1714 2294 1.635663 CGCAACAGCCTTTAGTCCCG 61.636 60.000 0.00 0.00 0.00 5.14
1715 2295 0.321298 TCGCAACAGCCTTTAGTCCC 60.321 55.000 0.00 0.00 0.00 4.46
1716 2296 1.197036 GTTCGCAACAGCCTTTAGTCC 59.803 52.381 0.00 0.00 0.00 3.85
1717 2297 1.197036 GGTTCGCAACAGCCTTTAGTC 59.803 52.381 2.28 0.00 0.00 2.59
1718 2298 1.235724 GGTTCGCAACAGCCTTTAGT 58.764 50.000 2.28 0.00 0.00 2.24
1719 2299 0.165944 CGGTTCGCAACAGCCTTTAG 59.834 55.000 2.28 0.00 0.00 1.85
1720 2300 1.231958 CCGGTTCGCAACAGCCTTTA 61.232 55.000 0.00 0.00 0.00 1.85
1721 2301 2.551912 CCGGTTCGCAACAGCCTTT 61.552 57.895 0.00 0.00 0.00 3.11
1722 2302 2.978010 CCGGTTCGCAACAGCCTT 60.978 61.111 0.00 0.00 0.00 4.35
1725 2305 2.775032 TAGTCCCGGTTCGCAACAGC 62.775 60.000 0.00 0.00 0.00 4.40
1726 2306 0.320073 TTAGTCCCGGTTCGCAACAG 60.320 55.000 0.00 0.00 0.00 3.16
1727 2307 0.106335 TTTAGTCCCGGTTCGCAACA 59.894 50.000 0.00 0.00 0.00 3.33
1728 2308 0.794473 CTTTAGTCCCGGTTCGCAAC 59.206 55.000 0.00 0.00 0.00 4.17
1729 2309 0.320946 CCTTTAGTCCCGGTTCGCAA 60.321 55.000 0.00 0.00 0.00 4.85
1730 2310 1.294138 CCTTTAGTCCCGGTTCGCA 59.706 57.895 0.00 0.00 0.00 5.10
1731 2311 1.449070 CCCTTTAGTCCCGGTTCGC 60.449 63.158 0.00 0.00 0.00 4.70
1732 2312 1.449070 GCCCTTTAGTCCCGGTTCG 60.449 63.158 0.00 0.00 0.00 3.95
1733 2313 0.327259 AAGCCCTTTAGTCCCGGTTC 59.673 55.000 0.00 0.00 0.00 3.62
1734 2314 0.775542 AAAGCCCTTTAGTCCCGGTT 59.224 50.000 0.00 0.00 0.00 4.44
1735 2315 0.775542 AAAAGCCCTTTAGTCCCGGT 59.224 50.000 0.00 0.00 31.63 5.28
1736 2316 1.919240 AAAAAGCCCTTTAGTCCCGG 58.081 50.000 0.00 0.00 31.63 5.73
1758 2338 8.962884 TGTTACTATAATCGACTACACTGGTA 57.037 34.615 0.00 0.00 0.00 3.25
1759 2339 7.870509 TGTTACTATAATCGACTACACTGGT 57.129 36.000 0.00 0.00 0.00 4.00
1760 2340 9.823098 GTATGTTACTATAATCGACTACACTGG 57.177 37.037 0.00 0.00 0.00 4.00
1827 2407 8.766000 TCCACAACTAAAAGGAAAAGAAAAAC 57.234 30.769 0.00 0.00 0.00 2.43
1896 2477 8.171164 ACTTTTTGCCTATTATTATCTCCAGC 57.829 34.615 0.00 0.00 0.00 4.85
2105 2711 9.553064 AATAAAACTGCAATGTTTAATTGTCCA 57.447 25.926 4.67 0.00 38.98 4.02
2359 2968 8.882415 ATTTTGATGAAATATGACCATCTTGC 57.118 30.769 0.00 0.00 36.20 4.01
2476 3085 6.116126 GGGAATCTGTGCTACTTTAATGACT 58.884 40.000 0.00 0.00 0.00 3.41
2512 3182 1.664588 CGTGTTGGTTTAATGGCGGTG 60.665 52.381 0.00 0.00 0.00 4.94
2513 3183 0.594110 CGTGTTGGTTTAATGGCGGT 59.406 50.000 0.00 0.00 0.00 5.68
2515 3185 0.875728 TCCGTGTTGGTTTAATGGCG 59.124 50.000 0.00 0.00 39.52 5.69
2530 3200 1.077501 CTGTGGCATGGGAATCCGT 60.078 57.895 0.00 0.00 35.24 4.69
2532 3202 0.466922 CTCCTGTGGCATGGGAATCC 60.467 60.000 11.48 0.00 0.00 3.01
2562 3232 5.026121 TCTACTGGATTTGACTCCATCAGT 58.974 41.667 0.00 0.00 44.23 3.41
2606 3276 6.932356 ACTATTATCATTGCACCAAGACTG 57.068 37.500 0.00 0.00 0.00 3.51
2656 3332 0.394938 TCGTTTGTCTTGCCTGGCTA 59.605 50.000 21.03 11.84 0.00 3.93
2697 3373 6.582295 AGAAAAACACGGATCGAAATTGATTG 59.418 34.615 0.00 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.