Multiple sequence alignment - TraesCS4A01G114100

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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 TraesCS4A01G114100 chr4A 100.000 3670 0 0 1 3670 138416877 138420546 0.000000e+00 6778.0
1 TraesCS4A01G114100 chr4A 92.593 81 6 0 1377 1457 708627154 708627074 2.320000e-22 117.0
2 TraesCS4A01G114100 chr4B 90.850 1847 126 22 599 2441 412779595 412777788 0.000000e+00 2435.0
3 TraesCS4A01G114100 chr4B 96.465 396 9 4 2510 2904 412777761 412777370 0.000000e+00 649.0
4 TraesCS4A01G114100 chr4B 79.087 679 65 35 2888 3514 412777237 412776584 2.660000e-106 396.0
5 TraesCS4A01G114100 chr4B 86.919 344 33 5 80 419 412790124 412789789 3.460000e-100 375.0
6 TraesCS4A01G114100 chr4B 94.915 59 2 1 3608 3665 412776397 412776339 1.400000e-14 91.6
7 TraesCS4A01G114100 chr4D 91.830 1224 56 17 1726 2947 334963120 334961939 0.000000e+00 1666.0
8 TraesCS4A01G114100 chr4D 93.048 1122 60 10 617 1728 334964314 334963201 0.000000e+00 1624.0
9 TraesCS4A01G114100 chr4D 87.544 570 55 14 1 565 334965329 334964771 0.000000e+00 645.0
10 TraesCS4A01G114100 chr4D 82.895 304 38 8 3355 3650 334961373 334961076 1.010000e-65 261.0
11 TraesCS4A01G114100 chr1B 85.271 258 24 7 1907 2162 250524094 250523849 1.690000e-63 254.0
12 TraesCS4A01G114100 chr1B 84.884 258 24 6 1907 2162 369821714 369821958 2.830000e-61 246.0
13 TraesCS4A01G114100 chr1B 87.234 188 24 0 2116 2303 201776449 201776636 7.980000e-52 215.0
14 TraesCS4A01G114100 chr1B 97.222 36 1 0 1405 1440 668914093 668914058 1.100000e-05 62.1
15 TraesCS4A01G114100 chr3B 85.271 258 23 6 1907 2162 253406969 253406725 6.080000e-63 252.0
16 TraesCS4A01G114100 chr7A 84.884 258 24 6 1907 2162 278385397 278385153 2.830000e-61 246.0
17 TraesCS4A01G114100 chr7A 84.109 258 26 6 1907 2162 713946505 713946749 6.130000e-58 235.0
18 TraesCS4A01G114100 chr1A 85.259 251 22 6 1914 2162 5838917 5838680 1.020000e-60 244.0
19 TraesCS4A01G114100 chr1A 86.243 189 26 0 2115 2303 163382763 163382575 4.800000e-49 206.0
20 TraesCS4A01G114100 chr7B 84.496 258 25 6 1907 2162 235730883 235730639 1.320000e-59 241.0
21 TraesCS4A01G114100 chr7B 100.000 29 0 0 2721 2749 547967795 547967767 2.000000e-03 54.7
22 TraesCS4A01G114100 chr1D 86.702 188 25 0 2116 2303 134683420 134683607 3.710000e-50 209.0
23 TraesCS4A01G114100 chr1D 78.125 320 51 14 1193 1502 134682442 134682752 6.260000e-43 185.0
24 TraesCS4A01G114100 chr5A 78.305 295 48 8 997 1278 238691762 238692053 3.770000e-40 176.0
25 TraesCS4A01G114100 chr5A 87.500 104 13 0 976 1079 610215788 610215891 1.790000e-23 121.0


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 TraesCS4A01G114100 chr4A 138416877 138420546 3669 False 6778.0 6778 100.00000 1 3670 1 chr4A.!!$F1 3669
1 TraesCS4A01G114100 chr4B 412776339 412779595 3256 True 892.9 2435 90.32925 599 3665 4 chr4B.!!$R2 3066
2 TraesCS4A01G114100 chr4D 334961076 334965329 4253 True 1049.0 1666 88.82925 1 3650 4 chr4D.!!$R1 3649

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
149 150 0.457166 CATCTGGTTCCGACGCGTTA 60.457 55.0 15.53 0.00 0.00 3.18 F
154 155 0.664166 GGTTCCGACGCGTTAGTTGA 60.664 55.0 15.53 2.92 0.00 3.18 F
1294 1735 0.246635 AGTCGCCGTTTGCTACATCT 59.753 50.0 0.00 0.00 38.09 2.90 F
1366 1807 0.801067 GTTCTGATACGGTCGCGCTT 60.801 55.0 5.56 0.00 0.00 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1218 1659 0.036388 TCTTAAGCTCCTGGTTGCCG 60.036 55.0 0.00 0.0 35.36 5.69 R
1362 1803 0.038892 ATCTGGCTGCAAACAAAGCG 60.039 50.0 0.50 0.0 40.46 4.68 R
2561 3087 0.040958 CAGTGTTGTTGCGCTCCTTC 60.041 55.0 9.73 0.0 0.00 3.46 R
3304 4082 0.397564 TAGTCAAAACCCCACGTCCC 59.602 55.0 0.00 0.0 0.00 4.46 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 9.097257 GGGGTGATAACAATGAACATTTTATTG 57.903 33.333 0.00 2.75 37.71 1.90
53 54 3.272285 TCCTCCAGAGTTTCCTCTCCATA 59.728 47.826 0.00 0.00 45.08 2.74
55 56 4.100808 CCTCCAGAGTTTCCTCTCCATAAG 59.899 50.000 0.00 0.00 45.08 1.73
68 69 8.657387 TCCTCTCCATAAGGAATCTACAATAG 57.343 38.462 0.00 0.00 45.19 1.73
70 71 9.094578 CCTCTCCATAAGGAATCTACAATAGAA 57.905 37.037 0.00 0.00 45.19 2.10
71 72 9.921637 CTCTCCATAAGGAATCTACAATAGAAC 57.078 37.037 0.00 0.00 45.19 3.01
99 100 2.040178 ACCTCCTCACGACAAAGTTCT 58.960 47.619 0.00 0.00 0.00 3.01
127 128 3.417101 TCTAAAAGAAATGAGCCGGCAA 58.583 40.909 31.54 17.66 0.00 4.52
128 129 2.730550 AAAAGAAATGAGCCGGCAAG 57.269 45.000 31.54 0.00 0.00 4.01
149 150 0.457166 CATCTGGTTCCGACGCGTTA 60.457 55.000 15.53 0.00 0.00 3.18
154 155 0.664166 GGTTCCGACGCGTTAGTTGA 60.664 55.000 15.53 2.92 0.00 3.18
164 165 3.863424 ACGCGTTAGTTGAGAACATATGG 59.137 43.478 5.58 0.00 0.00 2.74
182 183 1.202794 TGGAACAGAGCATGCTTGACA 60.203 47.619 23.61 17.71 0.00 3.58
184 185 2.097142 GGAACAGAGCATGCTTGACATC 59.903 50.000 23.61 15.78 36.64 3.06
185 186 2.484742 ACAGAGCATGCTTGACATCA 57.515 45.000 23.61 0.00 36.64 3.07
207 209 5.303333 TCAAGTTCAGTATAGACACCACACA 59.697 40.000 0.00 0.00 0.00 3.72
208 210 5.801531 AGTTCAGTATAGACACCACACAA 57.198 39.130 0.00 0.00 0.00 3.33
209 211 6.169557 AGTTCAGTATAGACACCACACAAA 57.830 37.500 0.00 0.00 0.00 2.83
210 212 6.223852 AGTTCAGTATAGACACCACACAAAG 58.776 40.000 0.00 0.00 0.00 2.77
211 213 4.566004 TCAGTATAGACACCACACAAAGC 58.434 43.478 0.00 0.00 0.00 3.51
212 214 4.283467 TCAGTATAGACACCACACAAAGCT 59.717 41.667 0.00 0.00 0.00 3.74
234 236 6.706746 GCTAAAGCTTAGTTTATCTCGGTTG 58.293 40.000 0.00 0.00 38.21 3.77
237 239 9.530633 CTAAAGCTTAGTTTATCTCGGTTGTAT 57.469 33.333 0.00 0.00 0.00 2.29
266 268 1.677217 GGCACATGTGAGAGAACCTCC 60.677 57.143 29.80 13.28 41.25 4.30
268 270 2.676463 GCACATGTGAGAGAACCTCCTC 60.676 54.545 29.80 2.76 41.25 3.71
288 290 8.001292 CCTCCTCAATTCCAATAGTTCCTTTAT 58.999 37.037 0.00 0.00 0.00 1.40
337 340 3.099905 TGTAGTCATAGGTGCAAGCTCT 58.900 45.455 0.00 0.00 44.61 4.09
340 343 2.568956 AGTCATAGGTGCAAGCTCTTGA 59.431 45.455 13.33 0.00 44.61 3.02
347 350 1.674962 GTGCAAGCTCTTGATGATCCC 59.325 52.381 13.33 0.00 42.93 3.85
356 359 4.626287 GCTCTTGATGATCCCCACTAAACA 60.626 45.833 0.00 0.00 0.00 2.83
363 366 2.507407 TCCCCACTAAACAAGCCATC 57.493 50.000 0.00 0.00 0.00 3.51
398 401 6.488715 AGCCTATCAATTTGGTTCTTCTTCT 58.511 36.000 0.00 0.00 0.00 2.85
400 403 7.452813 AGCCTATCAATTTGGTTCTTCTTCTTT 59.547 33.333 0.00 0.00 0.00 2.52
407 410 4.258702 TGGTTCTTCTTCTTTCGAGAGG 57.741 45.455 2.75 0.00 0.00 3.69
440 443 3.081804 CGAAGGCTTTATTGTTGTCCCT 58.918 45.455 0.00 0.00 0.00 4.20
443 446 5.508994 CGAAGGCTTTATTGTTGTCCCTTTT 60.509 40.000 0.00 0.00 31.81 2.27
444 447 5.887214 AGGCTTTATTGTTGTCCCTTTTT 57.113 34.783 0.00 0.00 0.00 1.94
458 461 2.093235 CCCTTTTTGCCAACCACTGAAA 60.093 45.455 0.00 0.00 0.00 2.69
460 463 3.373748 CCTTTTTGCCAACCACTGAAAAC 59.626 43.478 0.00 0.00 0.00 2.43
471 474 2.097466 CCACTGAAAACGAGCAAGTTGT 59.903 45.455 4.48 0.00 34.14 3.32
474 477 3.190535 ACTGAAAACGAGCAAGTTGTTGT 59.809 39.130 4.48 0.00 35.92 3.32
475 478 3.497118 TGAAAACGAGCAAGTTGTTGTG 58.503 40.909 4.48 0.00 35.92 3.33
508 512 6.917217 TTAGGCAAACCACATTTTCTTTTG 57.083 33.333 0.00 0.00 39.06 2.44
509 513 5.096443 AGGCAAACCACATTTTCTTTTGA 57.904 34.783 0.00 0.00 39.06 2.69
517 521 5.971895 CACATTTTCTTTTGAAGGTGTGG 57.028 39.130 13.07 0.00 43.68 4.17
551 555 2.810439 TTTTTGGAGCGGTGGATTTG 57.190 45.000 0.00 0.00 0.00 2.32
552 556 1.698506 TTTTGGAGCGGTGGATTTGT 58.301 45.000 0.00 0.00 0.00 2.83
556 560 1.339610 TGGAGCGGTGGATTTGTTTTG 59.660 47.619 0.00 0.00 0.00 2.44
557 561 1.339929 GGAGCGGTGGATTTGTTTTGT 59.660 47.619 0.00 0.00 0.00 2.83
558 562 2.223947 GGAGCGGTGGATTTGTTTTGTT 60.224 45.455 0.00 0.00 0.00 2.83
559 563 3.453424 GAGCGGTGGATTTGTTTTGTTT 58.547 40.909 0.00 0.00 0.00 2.83
560 564 3.194062 AGCGGTGGATTTGTTTTGTTTG 58.806 40.909 0.00 0.00 0.00 2.93
562 566 3.245048 GCGGTGGATTTGTTTTGTTTGAG 59.755 43.478 0.00 0.00 0.00 3.02
563 567 4.677584 CGGTGGATTTGTTTTGTTTGAGA 58.322 39.130 0.00 0.00 0.00 3.27
564 568 5.105752 CGGTGGATTTGTTTTGTTTGAGAA 58.894 37.500 0.00 0.00 0.00 2.87
565 569 5.578727 CGGTGGATTTGTTTTGTTTGAGAAA 59.421 36.000 0.00 0.00 0.00 2.52
566 570 6.454981 CGGTGGATTTGTTTTGTTTGAGAAAC 60.455 38.462 0.00 0.00 41.73 2.78
578 582 6.707440 TGTTTGAGAAACAGATAAAAGCCA 57.293 33.333 0.00 0.00 45.79 4.75
579 583 6.503524 TGTTTGAGAAACAGATAAAAGCCAC 58.496 36.000 0.00 0.00 45.79 5.01
580 584 6.096141 TGTTTGAGAAACAGATAAAAGCCACA 59.904 34.615 0.00 0.00 45.79 4.17
581 585 6.899393 TTGAGAAACAGATAAAAGCCACAT 57.101 33.333 0.00 0.00 0.00 3.21
582 586 7.994425 TTGAGAAACAGATAAAAGCCACATA 57.006 32.000 0.00 0.00 0.00 2.29
583 587 7.377766 TGAGAAACAGATAAAAGCCACATAC 57.622 36.000 0.00 0.00 0.00 2.39
584 588 7.168219 TGAGAAACAGATAAAAGCCACATACT 58.832 34.615 0.00 0.00 0.00 2.12
585 589 7.665559 TGAGAAACAGATAAAAGCCACATACTT 59.334 33.333 0.00 0.00 0.00 2.24
586 590 8.409358 AGAAACAGATAAAAGCCACATACTTT 57.591 30.769 0.00 0.00 38.98 2.66
587 591 8.860088 AGAAACAGATAAAAGCCACATACTTTT 58.140 29.630 6.70 6.70 46.30 2.27
588 592 9.476202 GAAACAGATAAAAGCCACATACTTTTT 57.524 29.630 6.78 0.00 43.08 1.94
653 1084 2.880443 TCTTCATTGAAAAGCCAGCCT 58.120 42.857 0.01 0.00 0.00 4.58
705 1144 1.869767 CGCTCATTTAAGCTGGGCTAG 59.130 52.381 9.49 0.00 38.25 3.42
709 1148 1.952296 CATTTAAGCTGGGCTAGGCTG 59.048 52.381 16.80 10.49 38.25 4.85
713 1152 0.761802 AAGCTGGGCTAGGCTGATAC 59.238 55.000 16.80 0.00 38.25 2.24
719 1158 1.211949 GGGCTAGGCTGATACACCAAA 59.788 52.381 16.80 0.00 0.00 3.28
720 1159 2.565841 GGCTAGGCTGATACACCAAAG 58.434 52.381 9.46 0.00 0.00 2.77
721 1160 2.092914 GGCTAGGCTGATACACCAAAGT 60.093 50.000 9.46 0.00 0.00 2.66
722 1161 3.134081 GGCTAGGCTGATACACCAAAGTA 59.866 47.826 9.46 0.00 0.00 2.24
723 1162 4.383770 GGCTAGGCTGATACACCAAAGTAA 60.384 45.833 9.46 0.00 0.00 2.24
866 1307 1.077068 CTGCTCCCTCGTCTCCTCT 60.077 63.158 0.00 0.00 0.00 3.69
948 1389 2.316867 CGTTGCTGATCCGTGTGCA 61.317 57.895 0.00 0.00 0.00 4.57
1108 1549 4.824515 CGTCCCTCCTCTCCGGCT 62.825 72.222 0.00 0.00 0.00 5.52
1109 1550 2.364448 GTCCCTCCTCTCCGGCTT 60.364 66.667 0.00 0.00 0.00 4.35
1110 1551 2.042843 TCCCTCCTCTCCGGCTTC 60.043 66.667 0.00 0.00 0.00 3.86
1111 1552 2.042435 CCCTCCTCTCCGGCTTCT 60.042 66.667 0.00 0.00 0.00 2.85
1115 1556 1.677217 CCTCCTCTCCGGCTTCTTTTG 60.677 57.143 0.00 0.00 0.00 2.44
1131 1572 5.109500 TCTTTTGGCCATTCCTTTGTTTT 57.891 34.783 6.09 0.00 35.26 2.43
1218 1659 2.554462 GGCTTTCTTTGACCTGGAGAAC 59.446 50.000 0.00 0.00 0.00 3.01
1233 1674 1.600916 GAACGGCAACCAGGAGCTT 60.601 57.895 0.00 0.00 0.00 3.74
1285 1726 1.196808 CTGCAATGTAAGTCGCCGTTT 59.803 47.619 0.00 0.00 0.00 3.60
1294 1735 0.246635 AGTCGCCGTTTGCTACATCT 59.753 50.000 0.00 0.00 38.09 2.90
1295 1736 1.475280 AGTCGCCGTTTGCTACATCTA 59.525 47.619 0.00 0.00 38.09 1.98
1314 1755 7.079048 ACATCTAAGACCCTCCTGATCTATTT 58.921 38.462 0.00 0.00 0.00 1.40
1350 1791 1.735559 GGTAGTGGTGGACGCGTTC 60.736 63.158 15.53 13.50 33.90 3.95
1357 1798 1.138047 GGTGGACGCGTTCTGATACG 61.138 60.000 20.15 7.64 44.09 3.06
1362 1803 2.565394 CGCGTTCTGATACGGTCGC 61.565 63.158 0.00 0.00 41.65 5.19
1366 1807 0.801067 GTTCTGATACGGTCGCGCTT 60.801 55.000 5.56 0.00 0.00 4.68
1394 1835 0.819582 GCCAGATGGATGTTGTTGGG 59.180 55.000 2.18 0.00 37.39 4.12
1424 1865 1.377072 CGTGGTGATCCATGTGCCA 60.377 57.895 0.00 0.00 46.20 4.92
1548 1989 4.151798 GTTGTGCTTCGCTTTATCAGTTC 58.848 43.478 0.00 0.00 0.00 3.01
1557 1998 6.032956 TCGCTTTATCAGTTCCTGTCTAAA 57.967 37.500 0.00 0.00 32.61 1.85
1634 2075 7.440556 CAGTAGCAGTGCTGAACAATTAGATAT 59.559 37.037 27.97 0.00 40.10 1.63
1710 2151 6.211986 AGGATGTGAATGTCAAAATTCATGGT 59.788 34.615 3.18 0.00 45.66 3.55
1714 2155 6.099341 GTGAATGTCAAAATTCATGGTACCC 58.901 40.000 10.07 0.00 45.66 3.69
1745 2269 9.603298 GCATAATACATGACAACATCATTAGTG 57.397 33.333 0.00 0.00 46.54 2.74
1775 2301 7.145932 AGTTGGTTAAGACAAATGTATCAGC 57.854 36.000 0.00 0.00 0.00 4.26
1776 2302 6.942576 AGTTGGTTAAGACAAATGTATCAGCT 59.057 34.615 0.00 0.00 0.00 4.24
2040 2566 4.456535 TGTTGTTTAGCTGCAGGAGTTTA 58.543 39.130 17.12 0.00 0.00 2.01
2041 2567 4.884744 TGTTGTTTAGCTGCAGGAGTTTAA 59.115 37.500 17.12 0.00 0.00 1.52
2042 2568 5.358442 TGTTGTTTAGCTGCAGGAGTTTAAA 59.642 36.000 17.12 0.00 0.00 1.52
2043 2569 5.432885 TGTTTAGCTGCAGGAGTTTAAAC 57.567 39.130 17.12 10.47 36.00 2.01
2044 2570 4.884744 TGTTTAGCTGCAGGAGTTTAAACA 59.115 37.500 20.06 20.04 39.23 2.83
2045 2571 5.534654 TGTTTAGCTGCAGGAGTTTAAACAT 59.465 36.000 20.06 5.65 38.06 2.71
2233 2759 5.370584 TCATGATGGTATCTTGGAGGATGTT 59.629 40.000 0.00 0.00 35.73 2.71
2269 2795 2.358737 GTGGGGAAGCGTGTCAGG 60.359 66.667 0.00 0.00 0.00 3.86
2306 2832 2.237392 GCCAAGGTCATCAAGGTAGTCT 59.763 50.000 0.00 0.00 0.00 3.24
2307 2833 3.307762 GCCAAGGTCATCAAGGTAGTCTT 60.308 47.826 0.00 0.00 35.79 3.01
2310 2836 5.182001 CCAAGGTCATCAAGGTAGTCTTTTG 59.818 44.000 0.00 0.00 32.41 2.44
2318 2844 8.621286 TCATCAAGGTAGTCTTTTGAACTTTTC 58.379 33.333 0.00 0.00 34.80 2.29
2349 2875 7.806409 TTGATCATCATGTAAATACCCTGTG 57.194 36.000 0.00 0.00 0.00 3.66
2382 2908 7.122501 TGAAACATGCATATACTCATTTGGTGT 59.877 33.333 0.00 0.00 0.00 4.16
2391 2917 2.620115 ACTCATTTGGTGTCTGCAGTTG 59.380 45.455 14.67 0.72 0.00 3.16
2393 2919 3.814625 TCATTTGGTGTCTGCAGTTGTA 58.185 40.909 14.67 0.00 0.00 2.41
2396 2922 2.238942 TGGTGTCTGCAGTTGTAGTG 57.761 50.000 14.67 0.00 0.00 2.74
2431 2957 8.673711 GGTACTGTTTGATATGATGCTTGTTTA 58.326 33.333 0.00 0.00 0.00 2.01
2452 2978 8.988934 TGTTTAGCAACTTCTTACATTAGTCTG 58.011 33.333 0.00 0.00 33.58 3.51
2459 2985 3.861840 TCTTACATTAGTCTGGCAGCAC 58.138 45.455 10.34 9.19 0.00 4.40
2487 3013 3.566261 GCACTCTGCTTGCGCTTA 58.434 55.556 9.73 0.00 40.96 3.09
2488 3014 1.423056 GCACTCTGCTTGCGCTTAG 59.577 57.895 9.73 7.40 40.96 2.18
2489 3015 2.574813 GCACTCTGCTTGCGCTTAGC 62.575 60.000 22.67 22.67 43.07 3.09
2535 3061 7.798596 ATTCTAGTGCTGATGTTATTCTTGG 57.201 36.000 0.00 0.00 0.00 3.61
2561 3087 3.447586 TCTTTCAGATCTACTTGGACCCG 59.552 47.826 0.00 0.00 0.00 5.28
2582 3108 0.882042 AGGAGCGCAACAACACTGAG 60.882 55.000 11.47 0.00 0.00 3.35
2663 3189 3.305720 TGAGTACCCTGTGACTGAAACT 58.694 45.455 0.00 0.00 0.00 2.66
2869 3396 7.679638 GCATTTAAATTATGAACCTCTGCTCGT 60.680 37.037 0.00 0.00 0.00 4.18
2970 3677 5.006261 CGAATCGTTTGCCTGTTATGTCATA 59.994 40.000 0.00 0.00 0.00 2.15
2983 3690 7.148188 CCTGTTATGTCATATGTTTGTGCTCTT 60.148 37.037 1.90 0.00 0.00 2.85
3020 3727 9.744468 AGTGTTTTGATGTTTAACTTACAATCC 57.256 29.630 0.00 0.00 0.00 3.01
3023 3732 9.620660 GTTTTGATGTTTAACTTACAATCCGAT 57.379 29.630 0.00 0.00 0.00 4.18
3026 3735 8.554835 TGATGTTTAACTTACAATCCGATCAA 57.445 30.769 0.00 0.00 0.00 2.57
3027 3736 8.447833 TGATGTTTAACTTACAATCCGATCAAC 58.552 33.333 0.00 0.00 0.00 3.18
3031 3740 8.447833 GTTTAACTTACAATCCGATCAACATGA 58.552 33.333 0.00 0.00 0.00 3.07
3034 3743 6.115446 ACTTACAATCCGATCAACATGATGT 58.885 36.000 0.00 0.00 37.20 3.06
3036 3745 7.768582 ACTTACAATCCGATCAACATGATGTAA 59.231 33.333 0.00 0.77 37.20 2.41
3091 3800 3.055240 ACATGCCCACCAAAATTGTATGG 60.055 43.478 0.00 6.68 42.60 2.74
3184 3917 2.998279 GCATCCTTGCTGTGTGGGC 61.998 63.158 0.00 0.00 45.77 5.36
3186 3919 1.153524 ATCCTTGCTGTGTGGGCAA 59.846 52.632 0.00 0.00 45.70 4.52
3187 3920 0.251922 ATCCTTGCTGTGTGGGCAAT 60.252 50.000 1.64 0.00 46.46 3.56
3188 3921 1.180456 TCCTTGCTGTGTGGGCAATG 61.180 55.000 1.64 0.17 46.46 2.82
3192 3935 2.967397 CTGTGTGGGCAATGCTGG 59.033 61.111 4.82 0.00 0.00 4.85
3196 3939 1.604308 TGTGGGCAATGCTGGAGTG 60.604 57.895 4.82 0.00 0.00 3.51
3214 3957 4.666253 GGAGGGGCTGCAGCAACA 62.666 66.667 37.63 0.00 44.36 3.33
3220 3967 4.099170 GCTGCAGCAACAGAGGCG 62.099 66.667 33.36 0.00 40.25 5.52
3234 3981 1.103803 GAGGCGGTCAGTGATAGTCA 58.896 55.000 0.00 0.00 0.00 3.41
3248 3995 1.248785 TAGTCAGGGACAGCGTGGAC 61.249 60.000 0.00 0.00 34.60 4.02
3257 4004 2.048222 AGCGTGGACGATGTGTGG 60.048 61.111 2.73 0.00 43.02 4.17
3258 4005 2.357034 GCGTGGACGATGTGTGGT 60.357 61.111 2.73 0.00 43.02 4.16
3259 4006 1.959226 GCGTGGACGATGTGTGGTT 60.959 57.895 2.73 0.00 43.02 3.67
3263 4038 2.332654 GGACGATGTGTGGTTGCCC 61.333 63.158 0.00 0.00 0.00 5.36
3300 4078 1.456518 TGCCGAGATGGAGAGGAGG 60.457 63.158 0.00 0.00 42.00 4.30
3301 4079 2.206536 GCCGAGATGGAGAGGAGGG 61.207 68.421 0.00 0.00 42.00 4.30
3303 4081 2.206536 CGAGATGGAGAGGAGGGCC 61.207 68.421 0.00 0.00 0.00 5.80
3304 4082 2.123077 AGATGGAGAGGAGGGCCG 60.123 66.667 0.00 0.00 39.96 6.13
3322 4100 1.149854 GGGACGTGGGGTTTTGACT 59.850 57.895 0.00 0.00 0.00 3.41
3325 4103 2.553685 GGGACGTGGGGTTTTGACTAAT 60.554 50.000 0.00 0.00 0.00 1.73
3333 4111 4.142038 GGGGTTTTGACTAATGTGACACT 58.858 43.478 7.20 0.00 0.00 3.55
3341 4119 4.346709 TGACTAATGTGACACTGGAAAGGA 59.653 41.667 7.20 0.00 0.00 3.36
3402 4300 1.312815 GAGTGCTTCTTGTTGGCAGT 58.687 50.000 0.00 0.00 41.54 4.40
3407 4305 1.153066 TTCTTGTTGGCAGTGGCGA 60.153 52.632 12.58 7.47 42.47 5.54
3422 4320 4.659874 CGACGGTGCGTTTGGTGC 62.660 66.667 0.00 0.00 41.37 5.01
3423 4321 4.322385 GACGGTGCGTTTGGTGCC 62.322 66.667 0.00 0.00 41.37 5.01
3426 4324 4.622456 GGTGCGTTTGGTGCCGTG 62.622 66.667 0.00 0.00 0.00 4.94
3427 4325 3.883180 GTGCGTTTGGTGCCGTGT 61.883 61.111 0.00 0.00 0.00 4.49
3428 4326 3.882013 TGCGTTTGGTGCCGTGTG 61.882 61.111 0.00 0.00 0.00 3.82
3443 4341 3.807538 GTGCATGCACGAGGGCTG 61.808 66.667 33.20 0.00 37.19 4.85
3444 4342 4.334118 TGCATGCACGAGGGCTGT 62.334 61.111 18.46 0.00 34.04 4.40
3445 4343 3.058160 GCATGCACGAGGGCTGTT 61.058 61.111 14.21 0.00 34.04 3.16
3446 4344 2.629656 GCATGCACGAGGGCTGTTT 61.630 57.895 14.21 0.00 34.04 2.83
3447 4345 1.210931 CATGCACGAGGGCTGTTTG 59.789 57.895 0.00 0.00 34.04 2.93
3448 4346 1.973281 ATGCACGAGGGCTGTTTGG 60.973 57.895 0.00 0.00 34.04 3.28
3449 4347 2.594592 GCACGAGGGCTGTTTGGT 60.595 61.111 0.00 0.00 0.00 3.67
3455 4353 3.216292 GGGCTGTTTGGTGCGTGT 61.216 61.111 0.00 0.00 0.00 4.49
3535 4457 6.037500 CGAAGGATATCTTGATCTGCAACAAA 59.962 38.462 2.05 0.00 35.50 2.83
3568 4490 1.375013 CATGCCTTGCAACAAGGGC 60.375 57.895 23.93 18.05 43.62 5.19
3571 4493 4.362476 CCTTGCAACAAGGGCGGC 62.362 66.667 16.97 0.00 33.79 6.53
3584 4506 2.355718 GCGGCGTTGCAAACCAAT 60.356 55.556 17.44 0.00 46.28 3.16
3585 4507 2.656807 GCGGCGTTGCAAACCAATG 61.657 57.895 17.44 5.09 46.28 2.82
3586 4508 1.299773 CGGCGTTGCAAACCAATGT 60.300 52.632 17.44 0.00 46.28 2.71
3587 4509 0.039978 CGGCGTTGCAAACCAATGTA 60.040 50.000 17.44 0.00 46.28 2.29
3588 4510 1.402194 CGGCGTTGCAAACCAATGTAT 60.402 47.619 17.44 0.00 46.28 2.29
3589 4511 1.991965 GGCGTTGCAAACCAATGTATG 59.008 47.619 13.58 0.00 46.28 2.39
3603 4531 0.250793 TGTATGGGGTTGCTACGTGG 59.749 55.000 0.00 0.00 0.00 4.94
3608 4536 3.124921 GGTTGCTACGTGGCGCAT 61.125 61.111 19.46 0.00 35.85 4.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 9.274206 GGTAATTGGAGTTCTATTGTAGATTCC 57.726 37.037 9.42 9.42 38.45 3.01
62 63 6.443849 TGAGGAGGTAATTGGAGTTCTATTGT 59.556 38.462 0.00 0.00 0.00 2.71
68 69 3.194968 TCGTGAGGAGGTAATTGGAGTTC 59.805 47.826 0.00 0.00 0.00 3.01
70 71 2.496470 GTCGTGAGGAGGTAATTGGAGT 59.504 50.000 0.00 0.00 0.00 3.85
71 72 2.496070 TGTCGTGAGGAGGTAATTGGAG 59.504 50.000 0.00 0.00 0.00 3.86
76 77 4.283722 AGAACTTTGTCGTGAGGAGGTAAT 59.716 41.667 0.00 0.00 0.00 1.89
99 100 7.090173 CCGGCTCATTTCTTTTAGAAAAATGA 58.910 34.615 6.01 8.84 46.08 2.57
127 128 2.579201 CGTCGGAACCAGATGGCT 59.421 61.111 0.00 0.00 39.32 4.75
128 129 3.195698 GCGTCGGAACCAGATGGC 61.196 66.667 0.00 0.00 39.32 4.40
137 138 0.592637 TCTCAACTAACGCGTCGGAA 59.407 50.000 14.44 0.00 0.00 4.30
149 150 5.181748 GCTCTGTTCCATATGTTCTCAACT 58.818 41.667 1.24 0.00 0.00 3.16
154 155 3.881688 GCATGCTCTGTTCCATATGTTCT 59.118 43.478 11.37 0.00 0.00 3.01
164 165 2.745821 TGATGTCAAGCATGCTCTGTTC 59.254 45.455 22.93 14.51 38.06 3.18
182 183 6.014584 TGTGTGGTGTCTATACTGAACTTGAT 60.015 38.462 0.00 0.00 0.00 2.57
184 185 5.538118 TGTGTGGTGTCTATACTGAACTTG 58.462 41.667 0.00 0.00 0.00 3.16
185 186 5.801531 TGTGTGGTGTCTATACTGAACTT 57.198 39.130 0.00 0.00 0.00 2.66
210 212 6.313164 ACAACCGAGATAAACTAAGCTTTAGC 59.687 38.462 3.20 0.00 42.49 3.09
211 213 7.829378 ACAACCGAGATAAACTAAGCTTTAG 57.171 36.000 3.20 2.77 0.00 1.85
212 214 9.525409 GATACAACCGAGATAAACTAAGCTTTA 57.475 33.333 3.20 0.00 0.00 1.85
324 327 3.432749 GGATCATCAAGAGCTTGCACCTA 60.433 47.826 5.37 0.00 40.24 3.08
327 330 1.674962 GGGATCATCAAGAGCTTGCAC 59.325 52.381 5.37 0.00 40.24 4.57
329 332 1.316651 GGGGATCATCAAGAGCTTGC 58.683 55.000 5.37 0.00 40.24 4.01
337 340 4.016444 GCTTGTTTAGTGGGGATCATCAA 58.984 43.478 0.00 0.00 0.00 2.57
340 343 2.311542 TGGCTTGTTTAGTGGGGATCAT 59.688 45.455 0.00 0.00 0.00 2.45
347 350 1.094785 CCGGATGGCTTGTTTAGTGG 58.905 55.000 0.00 0.00 0.00 4.00
398 401 1.056660 AAGAAGGCCACCTCTCGAAA 58.943 50.000 5.01 0.00 30.89 3.46
400 403 1.183549 GTAAGAAGGCCACCTCTCGA 58.816 55.000 5.01 0.00 30.89 4.04
425 428 5.363939 TGGCAAAAAGGGACAACAATAAAG 58.636 37.500 0.00 0.00 0.00 1.85
440 443 2.996621 CGTTTTCAGTGGTTGGCAAAAA 59.003 40.909 0.00 0.00 0.00 1.94
443 446 1.403679 CTCGTTTTCAGTGGTTGGCAA 59.596 47.619 0.00 0.00 0.00 4.52
444 447 1.021202 CTCGTTTTCAGTGGTTGGCA 58.979 50.000 0.00 0.00 0.00 4.92
458 461 2.356135 AGTCACAACAACTTGCTCGTT 58.644 42.857 0.00 0.00 0.00 3.85
460 463 2.609459 AGAAGTCACAACAACTTGCTCG 59.391 45.455 0.00 0.00 37.10 5.03
556 560 6.503524 TGTGGCTTTTATCTGTTTCTCAAAC 58.496 36.000 0.00 0.00 41.73 2.93
557 561 6.707440 TGTGGCTTTTATCTGTTTCTCAAA 57.293 33.333 0.00 0.00 0.00 2.69
558 562 6.899393 ATGTGGCTTTTATCTGTTTCTCAA 57.101 33.333 0.00 0.00 0.00 3.02
559 563 7.168219 AGTATGTGGCTTTTATCTGTTTCTCA 58.832 34.615 0.00 0.00 0.00 3.27
560 564 7.617041 AGTATGTGGCTTTTATCTGTTTCTC 57.383 36.000 0.00 0.00 0.00 2.87
562 566 9.476202 AAAAAGTATGTGGCTTTTATCTGTTTC 57.524 29.630 3.87 0.00 38.51 2.78
585 589 7.546250 TGTGGCTTTTATTATCCCTCAAAAA 57.454 32.000 0.00 0.00 0.00 1.94
586 590 7.732222 ATGTGGCTTTTATTATCCCTCAAAA 57.268 32.000 0.00 0.00 0.00 2.44
587 591 8.691797 GTTATGTGGCTTTTATTATCCCTCAAA 58.308 33.333 0.00 0.00 0.00 2.69
588 592 7.836685 TGTTATGTGGCTTTTATTATCCCTCAA 59.163 33.333 0.00 0.00 0.00 3.02
589 593 7.284489 GTGTTATGTGGCTTTTATTATCCCTCA 59.716 37.037 0.00 0.00 0.00 3.86
590 594 7.284489 TGTGTTATGTGGCTTTTATTATCCCTC 59.716 37.037 0.00 0.00 0.00 4.30
591 595 7.122715 TGTGTTATGTGGCTTTTATTATCCCT 58.877 34.615 0.00 0.00 0.00 4.20
592 596 7.341445 TGTGTTATGTGGCTTTTATTATCCC 57.659 36.000 0.00 0.00 0.00 3.85
593 597 9.463443 GAATGTGTTATGTGGCTTTTATTATCC 57.537 33.333 0.00 0.00 0.00 2.59
653 1084 1.717038 TTCCGGGGTTGCCCTTGTTA 61.717 55.000 0.00 0.00 44.66 2.41
670 1107 0.305009 GAGCGCGGCCTTTTATCTTC 59.695 55.000 8.83 0.00 0.00 2.87
675 1112 1.740297 TAAATGAGCGCGGCCTTTTA 58.260 45.000 8.83 7.92 0.00 1.52
676 1113 0.885196 TTAAATGAGCGCGGCCTTTT 59.115 45.000 8.83 8.85 0.00 2.27
677 1114 0.451783 CTTAAATGAGCGCGGCCTTT 59.548 50.000 8.83 6.77 0.00 3.11
705 1144 4.672409 GCATTTACTTTGGTGTATCAGCC 58.328 43.478 0.00 0.00 0.00 4.85
709 1148 3.488553 GGCCGCATTTACTTTGGTGTATC 60.489 47.826 0.00 0.00 0.00 2.24
713 1152 0.108851 GGGCCGCATTTACTTTGGTG 60.109 55.000 0.00 0.00 0.00 4.17
770 1211 2.806818 GCGCTCTTATAAAACCCTAGCC 59.193 50.000 0.00 0.00 0.00 3.93
866 1307 1.540267 GGAGATAAGATACCTGCGCGA 59.460 52.381 12.10 0.00 0.00 5.87
948 1389 0.693049 AAGGGTTGGATTCGCAGAGT 59.307 50.000 0.00 0.00 38.43 3.24
1085 1526 4.824515 AGAGGAGGGACGCGGGAG 62.825 72.222 12.47 0.00 0.00 4.30
1108 1549 4.769345 AACAAAGGAATGGCCAAAAGAA 57.231 36.364 10.96 0.00 40.02 2.52
1109 1550 4.769345 AAACAAAGGAATGGCCAAAAGA 57.231 36.364 10.96 0.00 40.02 2.52
1110 1551 4.275689 GGAAAACAAAGGAATGGCCAAAAG 59.724 41.667 10.96 0.00 40.02 2.27
1111 1552 4.203226 GGAAAACAAAGGAATGGCCAAAA 58.797 39.130 10.96 0.00 40.02 2.44
1115 1556 1.003118 GGGGAAAACAAAGGAATGGCC 59.997 52.381 0.00 0.00 0.00 5.36
1131 1572 3.755628 CGAAGAGCGGTTCGGGGA 61.756 66.667 13.77 0.00 44.53 4.81
1218 1659 0.036388 TCTTAAGCTCCTGGTTGCCG 60.036 55.000 0.00 0.00 35.36 5.69
1233 1674 1.183549 GGTCCTTGAGGTCGCTCTTA 58.816 55.000 0.00 0.00 36.34 2.10
1285 1726 3.052869 TCAGGAGGGTCTTAGATGTAGCA 60.053 47.826 0.00 0.00 0.00 3.49
1294 1735 5.302059 CGACAAATAGATCAGGAGGGTCTTA 59.698 44.000 0.00 0.00 0.00 2.10
1295 1736 4.100189 CGACAAATAGATCAGGAGGGTCTT 59.900 45.833 0.00 0.00 0.00 3.01
1314 1755 1.340211 ACCAAATAAATCGGCCCGACA 60.340 47.619 8.62 0.00 39.18 4.35
1350 1791 1.076533 ACAAAGCGCGACCGTATCAG 61.077 55.000 12.10 0.00 36.67 2.90
1357 1798 2.010817 CTGCAAACAAAGCGCGACC 61.011 57.895 12.10 0.00 33.85 4.79
1362 1803 0.038892 ATCTGGCTGCAAACAAAGCG 60.039 50.000 0.50 0.00 40.46 4.68
1366 1807 1.546923 CATCCATCTGGCTGCAAACAA 59.453 47.619 0.50 0.00 34.44 2.83
1394 1835 1.966451 CACCACGGCCTTCCTGTTC 60.966 63.158 0.00 0.00 0.00 3.18
1424 1865 2.511600 GGCTTGCGCAGACGGTAT 60.512 61.111 11.31 0.00 40.57 2.73
1478 1919 1.710013 TGCCGCTAAACTTCTTCTCG 58.290 50.000 0.00 0.00 0.00 4.04
1548 1989 5.607119 ACTTAAACATGCGTTTAGACAGG 57.393 39.130 0.00 0.00 45.78 4.00
1557 1998 3.562141 TGTGTAGCAACTTAAACATGCGT 59.438 39.130 0.00 0.00 44.60 5.24
1634 2075 5.142061 TCAGTCGGCTTCTTACAATAACA 57.858 39.130 0.00 0.00 0.00 2.41
1642 2083 6.824553 TCTAGTATACTCAGTCGGCTTCTTA 58.175 40.000 9.12 0.00 0.00 2.10
1643 2084 5.682659 TCTAGTATACTCAGTCGGCTTCTT 58.317 41.667 9.12 0.00 0.00 2.52
1676 2117 7.959658 TTGACATTCACATCCTAAAATGGAT 57.040 32.000 0.00 0.00 46.91 3.41
1682 2123 9.642327 CATGAATTTTGACATTCACATCCTAAA 57.358 29.630 0.00 0.00 44.19 1.85
1710 2151 4.904853 TGTCATGTATTATGCTCTGGGGTA 59.095 41.667 0.00 0.00 0.00 3.69
1714 2155 6.484308 TGATGTTGTCATGTATTATGCTCTGG 59.516 38.462 0.00 0.00 34.06 3.86
1775 2301 3.888424 TCATGGATGCCACCTTGAG 57.112 52.632 9.61 0.00 38.55 3.02
1776 2302 0.394762 GCTCATGGATGCCACCTTGA 60.395 55.000 12.01 12.01 40.26 3.02
1796 2322 3.132824 AGGGAAAAACTTGAGGCAAACAG 59.867 43.478 0.00 0.00 0.00 3.16
1802 2328 2.039418 ACCAAGGGAAAAACTTGAGGC 58.961 47.619 6.74 0.00 46.27 4.70
2040 2566 8.141268 ACATCATTTCGGAGTTTAAACATGTTT 58.859 29.630 25.99 25.99 36.63 2.83
2041 2567 7.657336 ACATCATTTCGGAGTTTAAACATGTT 58.343 30.769 20.06 4.92 0.00 2.71
2042 2568 7.214467 ACATCATTTCGGAGTTTAAACATGT 57.786 32.000 20.06 13.49 0.00 3.21
2043 2569 7.807433 TCAACATCATTTCGGAGTTTAAACATG 59.193 33.333 20.06 13.01 0.00 3.21
2044 2570 7.881142 TCAACATCATTTCGGAGTTTAAACAT 58.119 30.769 20.06 5.65 0.00 2.71
2045 2571 7.265647 TCAACATCATTTCGGAGTTTAAACA 57.734 32.000 20.06 0.00 0.00 2.83
2086 2612 8.143193 ACAAGTGAAGCACATTTATCAAATTCA 58.857 29.630 0.00 0.00 36.74 2.57
2087 2613 8.524870 ACAAGTGAAGCACATTTATCAAATTC 57.475 30.769 0.00 0.00 36.74 2.17
2093 2619 6.371548 TCCTGTACAAGTGAAGCACATTTATC 59.628 38.462 0.00 0.00 36.74 1.75
2146 2672 1.672356 CTTCTTGGGTGGCCTCACG 60.672 63.158 3.32 0.00 44.50 4.35
2233 2759 1.977854 ACAATCTCAGCTGGGTACACA 59.022 47.619 14.66 0.00 0.00 3.72
2269 2795 0.606944 TGGCACCATCCAAACGGTAC 60.607 55.000 0.00 0.00 32.98 3.34
2336 2862 7.227910 TGTTTCAACTTCTCACAGGGTATTTAC 59.772 37.037 0.00 0.00 0.00 2.01
2349 2875 8.201554 TGAGTATATGCATGTTTCAACTTCTC 57.798 34.615 10.16 3.75 0.00 2.87
2391 2917 4.516365 ACAGTACCAGTTGTAGCACTAC 57.484 45.455 0.70 0.70 36.63 2.73
2393 2919 4.127171 CAAACAGTACCAGTTGTAGCACT 58.873 43.478 2.44 0.00 0.00 4.40
2396 2922 6.816640 TCATATCAAACAGTACCAGTTGTAGC 59.183 38.462 2.44 0.00 0.00 3.58
2431 2957 4.938226 GCCAGACTAATGTAAGAAGTTGCT 59.062 41.667 0.00 0.00 0.00 3.91
2436 2962 4.331168 GTGCTGCCAGACTAATGTAAGAAG 59.669 45.833 0.00 0.00 0.00 2.85
2437 2963 4.253685 GTGCTGCCAGACTAATGTAAGAA 58.746 43.478 0.00 0.00 0.00 2.52
2438 2964 3.369471 GGTGCTGCCAGACTAATGTAAGA 60.369 47.826 0.00 0.00 37.17 2.10
2439 2965 2.939103 GGTGCTGCCAGACTAATGTAAG 59.061 50.000 0.00 0.00 37.17 2.34
2440 2966 2.571653 AGGTGCTGCCAGACTAATGTAA 59.428 45.455 0.00 0.00 40.61 2.41
2441 2967 2.187958 AGGTGCTGCCAGACTAATGTA 58.812 47.619 0.00 0.00 40.61 2.29
2442 2968 0.987294 AGGTGCTGCCAGACTAATGT 59.013 50.000 0.00 0.00 40.61 2.71
2443 2969 1.741706 CAAGGTGCTGCCAGACTAATG 59.258 52.381 0.00 0.00 40.61 1.90
2444 2970 1.952367 GCAAGGTGCTGCCAGACTAAT 60.952 52.381 0.00 0.00 40.96 1.73
2447 2973 2.282040 GCAAGGTGCTGCCAGACT 60.282 61.111 0.00 0.00 40.96 3.24
2488 3014 0.599558 TTGCCAATCAAGCAGAGTGC 59.400 50.000 1.65 0.00 45.46 4.40
2489 3015 2.631418 CTTGCCAATCAAGCAGAGTG 57.369 50.000 0.33 0.33 44.85 3.51
2497 3023 4.618927 GCACTAGAATTGCTTGCCAATCAA 60.619 41.667 0.00 0.00 43.22 2.57
2561 3087 0.040958 CAGTGTTGTTGCGCTCCTTC 60.041 55.000 9.73 0.00 0.00 3.46
2582 3108 2.829120 AGAGAAGGTCTCCAGCTTGTAC 59.171 50.000 1.62 0.00 44.42 2.90
2663 3189 0.627451 AAGGCATGGATCTTCAGGCA 59.373 50.000 10.12 0.00 45.03 4.75
2869 3396 7.036996 TGACAATCAAGTGCAACAAGATAAA 57.963 32.000 0.00 0.00 41.43 1.40
2951 3645 5.484173 ACATATGACATAACAGGCAAACG 57.516 39.130 10.38 0.00 0.00 3.60
2970 3677 5.736951 ACTAGAGAGAAGAGCACAAACAT 57.263 39.130 0.00 0.00 0.00 2.71
3019 3726 9.513727 CTAGAGATATTACATCATGTTGATCGG 57.486 37.037 10.74 0.00 34.28 4.18
3020 3727 9.018716 GCTAGAGATATTACATCATGTTGATCG 57.981 37.037 10.74 0.00 34.28 3.69
3049 3758 9.918630 GGCATGTCTTATATTAATCAAAGCAAT 57.081 29.630 0.00 0.00 0.00 3.56
3050 3759 8.359642 GGGCATGTCTTATATTAATCAAAGCAA 58.640 33.333 0.00 0.00 0.00 3.91
3051 3760 7.505248 TGGGCATGTCTTATATTAATCAAAGCA 59.495 33.333 0.00 1.28 0.00 3.91
3066 3775 2.705127 ACAATTTTGGTGGGCATGTCTT 59.295 40.909 0.00 0.00 0.00 3.01
3067 3776 2.328319 ACAATTTTGGTGGGCATGTCT 58.672 42.857 0.00 0.00 0.00 3.41
3071 3780 2.504996 CCCATACAATTTTGGTGGGCAT 59.495 45.455 17.59 0.00 45.09 4.40
3091 3800 3.216800 TGCTGCAACATCTCCATTATCC 58.783 45.455 0.00 0.00 0.00 2.59
3092 3801 3.304525 GCTGCTGCAACATCTCCATTATC 60.305 47.826 11.11 0.00 39.41 1.75
3093 3802 2.621998 GCTGCTGCAACATCTCCATTAT 59.378 45.455 11.11 0.00 39.41 1.28
3184 3917 1.077212 CCCTCCCACTCCAGCATTG 60.077 63.158 0.00 0.00 0.00 2.82
3186 3919 2.693864 CCCCTCCCACTCCAGCAT 60.694 66.667 0.00 0.00 0.00 3.79
3192 3935 4.106925 CTGCAGCCCCTCCCACTC 62.107 72.222 0.00 0.00 0.00 3.51
3212 3955 1.107114 CTATCACTGACCGCCTCTGT 58.893 55.000 0.00 0.00 0.00 3.41
3214 3957 1.341089 TGACTATCACTGACCGCCTCT 60.341 52.381 0.00 0.00 0.00 3.69
3220 3967 2.428890 CTGTCCCTGACTATCACTGACC 59.571 54.545 0.00 0.00 33.15 4.02
3234 3981 2.680352 ATCGTCCACGCTGTCCCT 60.680 61.111 0.00 0.00 39.60 4.20
3282 4057 1.456518 CCTCCTCTCCATCTCGGCA 60.457 63.158 0.00 0.00 33.14 5.69
3283 4058 2.206536 CCCTCCTCTCCATCTCGGC 61.207 68.421 0.00 0.00 33.14 5.54
3301 4079 4.960866 AAAACCCCACGTCCCGGC 62.961 66.667 0.00 0.00 0.00 6.13
3303 4081 2.111460 TCAAAACCCCACGTCCCG 59.889 61.111 0.00 0.00 0.00 5.14
3304 4082 0.397564 TAGTCAAAACCCCACGTCCC 59.602 55.000 0.00 0.00 0.00 4.46
3307 4085 2.882137 CACATTAGTCAAAACCCCACGT 59.118 45.455 0.00 0.00 0.00 4.49
3308 4086 3.058501 GTCACATTAGTCAAAACCCCACG 60.059 47.826 0.00 0.00 0.00 4.94
3309 4087 3.886505 TGTCACATTAGTCAAAACCCCAC 59.113 43.478 0.00 0.00 0.00 4.61
3310 4088 3.886505 GTGTCACATTAGTCAAAACCCCA 59.113 43.478 0.00 0.00 0.00 4.96
3311 4089 4.023193 CAGTGTCACATTAGTCAAAACCCC 60.023 45.833 5.62 0.00 0.00 4.95
3314 4092 6.371809 TTCCAGTGTCACATTAGTCAAAAC 57.628 37.500 5.62 0.00 0.00 2.43
3322 4100 5.513094 CCTCTTCCTTTCCAGTGTCACATTA 60.513 44.000 5.62 0.00 0.00 1.90
3325 4103 2.104792 CCTCTTCCTTTCCAGTGTCACA 59.895 50.000 5.62 0.00 0.00 3.58
3333 4111 1.767692 GCCACCCTCTTCCTTTCCA 59.232 57.895 0.00 0.00 0.00 3.53
3341 4119 4.003788 CACCGTCGCCACCCTCTT 62.004 66.667 0.00 0.00 0.00 2.85
3386 4284 1.737355 GCCACTGCCAACAAGAAGCA 61.737 55.000 0.00 0.00 34.79 3.91
3424 4322 4.107051 GCCCTCGTGCATGCACAC 62.107 66.667 40.95 24.51 46.47 3.82
3425 4323 4.334118 AGCCCTCGTGCATGCACA 62.334 61.111 40.95 28.94 46.47 4.57
3426 4324 3.807538 CAGCCCTCGTGCATGCAC 61.808 66.667 35.76 35.76 43.01 4.57
3427 4325 3.848301 AACAGCCCTCGTGCATGCA 62.848 57.895 18.46 18.46 0.00 3.96
3428 4326 2.629656 AAACAGCCCTCGTGCATGC 61.630 57.895 11.82 11.82 0.00 4.06
3429 4327 1.210931 CAAACAGCCCTCGTGCATG 59.789 57.895 0.00 0.00 0.00 4.06
3430 4328 1.973281 CCAAACAGCCCTCGTGCAT 60.973 57.895 0.00 0.00 0.00 3.96
3431 4329 2.594303 CCAAACAGCCCTCGTGCA 60.594 61.111 0.00 0.00 0.00 4.57
3432 4330 2.594592 ACCAAACAGCCCTCGTGC 60.595 61.111 0.00 0.00 0.00 5.34
3433 4331 2.908073 GCACCAAACAGCCCTCGTG 61.908 63.158 0.00 0.00 0.00 4.35
3434 4332 2.594592 GCACCAAACAGCCCTCGT 60.595 61.111 0.00 0.00 0.00 4.18
3435 4333 3.726517 CGCACCAAACAGCCCTCG 61.727 66.667 0.00 0.00 0.00 4.63
3436 4334 2.594592 ACGCACCAAACAGCCCTC 60.595 61.111 0.00 0.00 0.00 4.30
3437 4335 2.906897 CACGCACCAAACAGCCCT 60.907 61.111 0.00 0.00 0.00 5.19
3438 4336 3.216292 ACACGCACCAAACAGCCC 61.216 61.111 0.00 0.00 0.00 5.19
3439 4337 2.026014 CACACGCACCAAACAGCC 59.974 61.111 0.00 0.00 0.00 4.85
3440 4338 2.655044 GCACACGCACCAAACAGC 60.655 61.111 0.00 0.00 38.36 4.40
3441 4339 2.797330 TGCACACGCACCAAACAG 59.203 55.556 0.00 0.00 45.36 3.16
3455 4353 4.334118 ACAGCCCTCGTGCATGCA 62.334 61.111 18.46 18.46 0.00 3.96
3489 4387 0.683504 GTCTTCTACCTCCGGCCTCA 60.684 60.000 0.00 0.00 0.00 3.86
3514 4435 5.221126 GGGTTTGTTGCAGATCAAGATATCC 60.221 44.000 0.00 0.00 34.91 2.59
3545 4467 1.171549 TTGTTGCAAGGCATGAGCGA 61.172 50.000 0.00 0.00 43.41 4.93
3551 4473 2.934570 CGCCCTTGTTGCAAGGCAT 61.935 57.895 22.79 0.00 46.08 4.40
3552 4474 3.604667 CGCCCTTGTTGCAAGGCA 61.605 61.111 22.79 6.92 46.08 4.75
3568 4490 0.039978 TACATTGGTTTGCAACGCCG 60.040 50.000 0.00 0.00 0.00 6.46
3571 4493 2.605030 CCCATACATTGGTTTGCAACG 58.395 47.619 0.00 0.00 44.83 4.10
3584 4506 0.250793 CCACGTAGCAACCCCATACA 59.749 55.000 0.00 0.00 0.00 2.29
3585 4507 1.093496 GCCACGTAGCAACCCCATAC 61.093 60.000 0.00 0.00 0.00 2.39
3586 4508 1.222387 GCCACGTAGCAACCCCATA 59.778 57.895 0.00 0.00 0.00 2.74
3587 4509 2.045340 GCCACGTAGCAACCCCAT 60.045 61.111 0.00 0.00 0.00 4.00
3588 4510 4.690719 CGCCACGTAGCAACCCCA 62.691 66.667 6.80 0.00 0.00 4.96
3603 4531 2.279659 CGGTCAAATTTTGATCATGCGC 59.720 45.455 19.58 0.00 40.87 6.09
3608 4536 4.085733 ACCATCCGGTCAAATTTTGATCA 58.914 39.130 19.58 4.43 44.71 2.92


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

AutoCloner maintained by Alex Coulton.